Multiple sequence alignment - TraesCS3B01G507000

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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 TraesCS3B01G507000 chr3B 100.000 4250 0 0 1 4250 750787508 750783259 0.000000e+00 7849.0
1 TraesCS3B01G507000 chr3B 99.090 769 6 1 3483 4250 756186037 756186805 0.000000e+00 1380.0
2 TraesCS3B01G507000 chr3B 91.412 687 31 6 3548 4206 824552376 824553062 0.000000e+00 917.0
3 TraesCS3B01G507000 chr3B 94.328 476 19 7 3779 4250 751942726 751942255 0.000000e+00 723.0
4 TraesCS3B01G507000 chr3B 91.158 475 42 0 1914 2388 750785505 750785031 0.000000e+00 645.0
5 TraesCS3B01G507000 chr3B 91.158 475 42 0 2004 2478 750785595 750785121 0.000000e+00 645.0
6 TraesCS3B01G507000 chr3B 95.101 347 15 2 3483 3827 751943139 751942793 2.890000e-151 545.0
7 TraesCS3B01G507000 chr3B 83.784 555 44 16 306 820 685496366 685495818 6.390000e-133 484.0
8 TraesCS3B01G507000 chr3B 89.683 378 39 0 1921 2298 750785408 750785031 2.300000e-132 483.0
9 TraesCS3B01G507000 chr3B 89.683 378 39 0 2101 2478 750785588 750785211 2.300000e-132 483.0
10 TraesCS3B01G507000 chr3B 87.500 288 36 0 2191 2478 750785588 750785301 2.450000e-87 333.0
11 TraesCS3B01G507000 chr3B 75.824 546 103 19 300 820 755118639 755119180 2.540000e-62 250.0
12 TraesCS3B01G507000 chr3B 86.869 198 26 0 2281 2478 750785588 750785391 5.530000e-54 222.0
13 TraesCS3B01G507000 chr3A 94.222 1575 81 2 818 2388 698004378 698002810 0.000000e+00 2396.0
14 TraesCS3B01G507000 chr3A 93.092 1491 83 6 2011 3482 698003277 698001788 0.000000e+00 2165.0
15 TraesCS3B01G507000 chr3A 88.312 385 45 0 1914 2298 698003194 698002810 2.990000e-126 462.0
16 TraesCS3B01G507000 chr3A 88.298 376 44 0 2101 2476 698003277 698002902 6.480000e-123 451.0
17 TraesCS3B01G507000 chr3A 87.847 288 35 0 1921 2208 698003097 698002810 5.260000e-89 339.0
18 TraesCS3B01G507000 chr3A 91.509 106 9 0 1923 2028 698002915 698002810 3.420000e-31 147.0
19 TraesCS3B01G507000 chr3A 96.364 55 2 0 33 87 702964975 702964921 1.630000e-14 91.6
20 TraesCS3B01G507000 chr3D 94.548 1394 57 4 818 2198 563419504 563418117 0.000000e+00 2135.0
21 TraesCS3B01G507000 chr3D 92.548 1315 76 3 2191 3483 563418394 563417080 0.000000e+00 1866.0
22 TraesCS3B01G507000 chr3D 77.130 446 47 25 3859 4250 549055499 549055943 1.550000e-49 207.0
23 TraesCS3B01G507000 chr3D 74.460 556 80 42 309 817 424498497 424497957 2.610000e-42 183.0
24 TraesCS3B01G507000 chr3D 92.453 106 8 0 1918 2023 563418217 563418112 7.360000e-33 152.0
25 TraesCS3B01G507000 chr3D 85.484 62 9 0 2462 2523 563418171 563418110 9.860000e-07 65.8
26 TraesCS3B01G507000 chr7A 93.502 831 39 9 1 817 722574445 722573616 0.000000e+00 1221.0
27 TraesCS3B01G507000 chr7A 78.027 446 41 25 3859 4250 2659557 2659999 1.190000e-55 228.0
28 TraesCS3B01G507000 chr7A 96.364 55 2 0 33 87 21230357 21230303 1.630000e-14 91.6
29 TraesCS3B01G507000 chr7A 80.374 107 13 6 719 821 106755690 106755588 1.640000e-09 75.0
30 TraesCS3B01G507000 chr4B 94.316 475 20 6 3780 4250 95450071 95450542 0.000000e+00 721.0
31 TraesCS3B01G507000 chr4B 94.813 347 16 2 3483 3827 95449658 95450004 1.340000e-149 540.0
32 TraesCS3B01G507000 chr4B 75.046 545 87 32 300 814 648820085 648820610 1.550000e-49 207.0
33 TraesCS3B01G507000 chr4A 94.316 475 20 6 3780 4250 645358330 645358801 0.000000e+00 721.0
34 TraesCS3B01G507000 chr4A 95.389 347 14 2 3483 3827 645357779 645358125 6.210000e-153 551.0
35 TraesCS3B01G507000 chr4A 95.312 64 1 2 3766 3827 645358200 645358263 2.700000e-17 100.0
36 TraesCS3B01G507000 chr4A 95.161 62 1 2 3768 3827 645358133 645358194 3.500000e-16 97.1
37 TraesCS3B01G507000 chr7B 95.165 455 20 2 74 528 588062302 588061850 0.000000e+00 717.0
38 TraesCS3B01G507000 chr7B 96.639 238 8 0 580 817 588060265 588060028 3.080000e-106 396.0
39 TraesCS3B01G507000 chr6B 94.105 475 21 6 3780 4250 716766172 716766643 0.000000e+00 715.0
40 TraesCS3B01G507000 chr6B 94.105 475 21 6 3780 4250 716819663 716820134 0.000000e+00 715.0
41 TraesCS3B01G507000 chr6B 95.389 347 14 2 3483 3827 716765759 716766105 6.210000e-153 551.0
42 TraesCS3B01G507000 chr6B 95.389 347 14 2 3483 3827 716819250 716819596 6.210000e-153 551.0
43 TraesCS3B01G507000 chr6B 86.076 158 22 0 4087 4244 713194376 713194533 2.030000e-38 171.0
44 TraesCS3B01G507000 chr7D 91.239 468 37 4 358 823 64071962 64071497 6.000000e-178 634.0
45 TraesCS3B01G507000 chr7D 84.688 320 25 11 1 298 64072467 64072150 8.930000e-77 298.0
46 TraesCS3B01G507000 chr7D 87.611 113 10 4 89 200 64078427 64078318 1.240000e-25 128.0
47 TraesCS3B01G507000 chr7D 84.146 82 11 2 218 298 64078252 64078172 1.270000e-10 78.7
48 TraesCS3B01G507000 chr2D 92.890 436 27 4 358 791 59474143 59473710 7.760000e-177 630.0
49 TraesCS3B01G507000 chr2D 85.000 320 25 10 1 298 59474649 59474331 1.920000e-78 303.0
50 TraesCS3B01G507000 chr2D 77.578 446 45 25 3859 4250 31475774 31475330 7.150000e-53 219.0
51 TraesCS3B01G507000 chr2D 86.066 122 12 5 89 208 59475376 59475258 4.460000e-25 126.0
52 TraesCS3B01G507000 chr2D 84.146 82 11 2 218 298 59475200 59475120 1.270000e-10 78.7
53 TraesCS3B01G507000 chr5A 90.634 363 31 3 458 818 631999327 631999688 2.970000e-131 479.0
54 TraesCS3B01G507000 chr5A 78.727 550 81 22 300 820 445277967 445277425 6.810000e-88 335.0
55 TraesCS3B01G507000 chr5A 93.388 121 6 2 88 208 631998898 631999016 1.210000e-40 178.0
56 TraesCS3B01G507000 chr2B 76.340 541 86 29 309 817 703720370 703719840 7.050000e-63 252.0
57 TraesCS3B01G507000 chr1A 89.726 146 9 3 3861 4001 10967720 10967864 9.390000e-42 182.0
58 TraesCS3B01G507000 chr1D 96.226 53 2 0 33 85 360469996 360470048 2.110000e-13 87.9
59 TraesCS3B01G507000 chr2A 82.353 102 15 3 95 196 44062103 44062005 7.570000e-13 86.1


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 TraesCS3B01G507000 chr3B 750783259 750787508 4249 True 1522.857143 7849 90.864429 1 4250 7 chr3B.!!$R2 4249
1 TraesCS3B01G507000 chr3B 756186037 756186805 768 False 1380.000000 1380 99.090000 3483 4250 1 chr3B.!!$F2 767
2 TraesCS3B01G507000 chr3B 824552376 824553062 686 False 917.000000 917 91.412000 3548 4206 1 chr3B.!!$F3 658
3 TraesCS3B01G507000 chr3B 751942255 751943139 884 True 634.000000 723 94.714500 3483 4250 2 chr3B.!!$R3 767
4 TraesCS3B01G507000 chr3B 685495818 685496366 548 True 484.000000 484 83.784000 306 820 1 chr3B.!!$R1 514
5 TraesCS3B01G507000 chr3B 755118639 755119180 541 False 250.000000 250 75.824000 300 820 1 chr3B.!!$F1 520
6 TraesCS3B01G507000 chr3A 698001788 698004378 2590 True 993.333333 2396 90.546667 818 3482 6 chr3A.!!$R2 2664
7 TraesCS3B01G507000 chr3D 563417080 563419504 2424 True 1054.700000 2135 91.258250 818 3483 4 chr3D.!!$R2 2665
8 TraesCS3B01G507000 chr7A 722573616 722574445 829 True 1221.000000 1221 93.502000 1 817 1 chr7A.!!$R3 816
9 TraesCS3B01G507000 chr4B 95449658 95450542 884 False 630.500000 721 94.564500 3483 4250 2 chr4B.!!$F2 767
10 TraesCS3B01G507000 chr4B 648820085 648820610 525 False 207.000000 207 75.046000 300 814 1 chr4B.!!$F1 514
11 TraesCS3B01G507000 chr4A 645357779 645358801 1022 False 367.275000 721 95.044500 3483 4250 4 chr4A.!!$F1 767
12 TraesCS3B01G507000 chr7B 588060028 588062302 2274 True 556.500000 717 95.902000 74 817 2 chr7B.!!$R1 743
13 TraesCS3B01G507000 chr6B 716765759 716766643 884 False 633.000000 715 94.747000 3483 4250 2 chr6B.!!$F2 767
14 TraesCS3B01G507000 chr6B 716819250 716820134 884 False 633.000000 715 94.747000 3483 4250 2 chr6B.!!$F3 767
15 TraesCS3B01G507000 chr7D 64071497 64072467 970 True 466.000000 634 87.963500 1 823 2 chr7D.!!$R1 822
16 TraesCS3B01G507000 chr2D 59473710 59475376 1666 True 284.425000 630 87.025500 1 791 4 chr2D.!!$R2 790
17 TraesCS3B01G507000 chr5A 445277425 445277967 542 True 335.000000 335 78.727000 300 820 1 chr5A.!!$R1 520
18 TraesCS3B01G507000 chr5A 631998898 631999688 790 False 328.500000 479 92.011000 88 818 2 chr5A.!!$F1 730
19 TraesCS3B01G507000 chr2B 703719840 703720370 530 True 252.000000 252 76.340000 309 817 1 chr2B.!!$R1 508

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
883 3471 1.170442 ACGGTTCCCCTAATTTTGCG 58.830 50.0 0.00 0.0 0.00 4.85 F
1283 3875 0.677414 GTCGTCGGGGAGAAGAGAGT 60.677 60.0 0.00 0.0 38.01 3.24 F
2049 4650 0.183014 TTAACGTTGCCACCTTCCCA 59.817 50.0 11.99 0.0 0.00 4.37 F
2050 4651 0.250553 TAACGTTGCCACCTTCCCAG 60.251 55.0 11.99 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 4533 0.107643 TGGCAACATCAACCTCGTCA 59.892 50.000 0.00 0.0 46.17 4.35 R
3161 5777 0.030908 GACGGTCAGCTTATCCTCCG 59.969 60.000 2.62 0.0 42.94 4.63 R
3197 5813 0.882927 TGGTTCTTGTTCTTCGCCGG 60.883 55.000 0.00 0.0 0.00 6.13 R
3470 6100 1.071471 AGGCTGACAGGGAAACACG 59.929 57.895 4.26 0.0 0.00 4.49 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
66 796 7.303998 GTCCATGTATCTACGTCCTGTAATAC 58.696 42.308 0.00 0.00 32.99 1.89
72 802 3.873361 TCTACGTCCTGTAATACCAGTCG 59.127 47.826 0.00 0.00 35.53 4.18
92 830 8.181573 CCAGTCGTGCTGTTGTAAAATATTTAT 58.818 33.333 0.01 0.00 43.55 1.40
334 1137 4.536295 TCCCCAGGTTTCTTTCTTCTTT 57.464 40.909 0.00 0.00 0.00 2.52
465 1463 1.372087 GCCAGCAAGAATCGTCTGGG 61.372 60.000 15.96 1.15 44.66 4.45
656 3195 3.521126 TCTCTGGGCTAAAGAAAGAGCAT 59.479 43.478 0.00 0.00 40.64 3.79
883 3471 1.170442 ACGGTTCCCCTAATTTTGCG 58.830 50.000 0.00 0.00 0.00 4.85
927 3515 5.867174 GCATGCAGTATATATACAACACGGA 59.133 40.000 22.00 8.63 35.74 4.69
1280 3872 0.966370 AAGGTCGTCGGGGAGAAGAG 60.966 60.000 0.00 0.00 38.01 2.85
1283 3875 0.677414 GTCGTCGGGGAGAAGAGAGT 60.677 60.000 0.00 0.00 38.01 3.24
1386 3978 1.153628 CGGGCCGAAGAAAGACGAT 60.154 57.895 24.41 0.00 0.00 3.73
1676 4277 2.340809 CGTGGGCGTAGTCACCAA 59.659 61.111 0.00 0.00 35.77 3.67
1726 4327 0.822532 TCCGGCGATAGAGAAGGACC 60.823 60.000 9.30 0.00 39.76 4.46
1731 4332 2.230266 GGCGATAGAGAAGGACCAGATC 59.770 54.545 0.00 0.00 39.76 2.75
1873 4474 3.385111 GGAGGACGAACTTGTATCCATCT 59.615 47.826 0.00 0.00 33.33 2.90
2042 4643 1.154197 GAGGAGGTTAACGTTGCCAC 58.846 55.000 20.71 15.82 0.00 5.01
2043 4644 0.250597 AGGAGGTTAACGTTGCCACC 60.251 55.000 22.85 22.85 33.96 4.61
2044 4645 0.250597 GGAGGTTAACGTTGCCACCT 60.251 55.000 22.00 22.00 42.66 4.00
2045 4646 1.601166 GAGGTTAACGTTGCCACCTT 58.399 50.000 22.46 11.50 39.90 3.50
2046 4647 1.534163 GAGGTTAACGTTGCCACCTTC 59.466 52.381 22.46 14.85 39.90 3.46
2047 4648 0.594602 GGTTAACGTTGCCACCTTCC 59.405 55.000 11.99 0.00 0.00 3.46
2048 4649 0.594602 GTTAACGTTGCCACCTTCCC 59.405 55.000 11.99 0.00 0.00 3.97
2049 4650 0.183014 TTAACGTTGCCACCTTCCCA 59.817 50.000 11.99 0.00 0.00 4.37
2050 4651 0.250553 TAACGTTGCCACCTTCCCAG 60.251 55.000 11.99 0.00 0.00 4.45
2051 4652 3.365265 CGTTGCCACCTTCCCAGC 61.365 66.667 0.00 0.00 0.00 4.85
2052 4653 2.116125 GTTGCCACCTTCCCAGCT 59.884 61.111 0.00 0.00 0.00 4.24
2053 4654 1.531602 GTTGCCACCTTCCCAGCTT 60.532 57.895 0.00 0.00 0.00 3.74
2054 4655 1.228552 TTGCCACCTTCCCAGCTTC 60.229 57.895 0.00 0.00 0.00 3.86
2055 4656 1.719063 TTGCCACCTTCCCAGCTTCT 61.719 55.000 0.00 0.00 0.00 2.85
2056 4657 1.377856 GCCACCTTCCCAGCTTCTC 60.378 63.158 0.00 0.00 0.00 2.87
2057 4658 1.301293 CCACCTTCCCAGCTTCTCC 59.699 63.158 0.00 0.00 0.00 3.71
2058 4659 1.078848 CACCTTCCCAGCTTCTCCG 60.079 63.158 0.00 0.00 0.00 4.63
2059 4660 2.294078 ACCTTCCCAGCTTCTCCGG 61.294 63.158 0.00 0.00 0.00 5.14
2060 4661 2.294078 CCTTCCCAGCTTCTCCGGT 61.294 63.158 0.00 0.00 0.00 5.28
2061 4662 1.078848 CTTCCCAGCTTCTCCGGTG 60.079 63.158 0.00 0.00 0.00 4.94
2064 4665 4.785453 CCAGCTTCTCCGGTGGCC 62.785 72.222 0.00 0.00 44.54 5.36
2065 4666 4.020617 CAGCTTCTCCGGTGGCCA 62.021 66.667 0.00 0.00 0.00 5.36
2066 4667 3.249189 AGCTTCTCCGGTGGCCAA 61.249 61.111 7.24 0.00 0.00 4.52
2067 4668 2.747855 GCTTCTCCGGTGGCCAAG 60.748 66.667 7.24 4.38 0.00 3.61
2068 4669 2.045926 CTTCTCCGGTGGCCAAGG 60.046 66.667 19.66 19.66 0.00 3.61
2069 4670 2.528127 TTCTCCGGTGGCCAAGGA 60.528 61.111 24.77 24.77 0.00 3.36
2071 4672 4.785453 CTCCGGTGGCCAAGGAGC 62.785 72.222 32.98 12.85 44.09 4.70
2075 4676 3.650950 GGTGGCCAAGGAGCAGGA 61.651 66.667 7.24 0.00 0.00 3.86
2076 4677 2.436109 GTGGCCAAGGAGCAGGAA 59.564 61.111 7.24 0.00 0.00 3.36
2077 4678 1.228552 GTGGCCAAGGAGCAGGAAA 60.229 57.895 7.24 0.00 0.00 3.13
2078 4679 1.228552 TGGCCAAGGAGCAGGAAAC 60.229 57.895 0.61 0.00 0.00 2.78
2079 4680 1.979155 GGCCAAGGAGCAGGAAACC 60.979 63.158 0.00 0.00 0.00 3.27
2080 4681 2.335712 GCCAAGGAGCAGGAAACCG 61.336 63.158 0.00 0.00 0.00 4.44
2081 4682 1.374947 CCAAGGAGCAGGAAACCGA 59.625 57.895 0.00 0.00 0.00 4.69
2082 4683 0.250727 CCAAGGAGCAGGAAACCGAA 60.251 55.000 0.00 0.00 0.00 4.30
2083 4684 1.604604 CAAGGAGCAGGAAACCGAAA 58.395 50.000 0.00 0.00 0.00 3.46
2084 4685 1.266989 CAAGGAGCAGGAAACCGAAAC 59.733 52.381 0.00 0.00 0.00 2.78
2085 4686 0.765510 AGGAGCAGGAAACCGAAACT 59.234 50.000 0.00 0.00 0.00 2.66
2086 4687 0.875059 GGAGCAGGAAACCGAAACTG 59.125 55.000 0.00 0.00 0.00 3.16
2089 4690 1.574428 CAGGAAACCGAAACTGCCG 59.426 57.895 0.00 0.00 0.00 5.69
2090 4691 2.254350 GGAAACCGAAACTGCCGC 59.746 61.111 0.00 0.00 0.00 6.53
2091 4692 2.254350 GAAACCGAAACTGCCGCC 59.746 61.111 0.00 0.00 0.00 6.13
2092 4693 3.263503 GAAACCGAAACTGCCGCCC 62.264 63.158 0.00 0.00 0.00 6.13
2093 4694 3.785122 AAACCGAAACTGCCGCCCT 62.785 57.895 0.00 0.00 0.00 5.19
2094 4695 4.699522 ACCGAAACTGCCGCCCTC 62.700 66.667 0.00 0.00 0.00 4.30
2097 4698 3.423154 GAAACTGCCGCCCTCGTG 61.423 66.667 0.00 0.00 0.00 4.35
2104 4705 4.899239 CCGCCCTCGTGGATGCTC 62.899 72.222 4.76 0.00 42.83 4.26
2105 4706 4.899239 CGCCCTCGTGGATGCTCC 62.899 72.222 4.76 0.00 36.96 4.70
2106 4707 4.899239 GCCCTCGTGGATGCTCCG 62.899 72.222 4.76 0.00 40.17 4.63
2107 4708 4.227134 CCCTCGTGGATGCTCCGG 62.227 72.222 4.76 0.00 40.17 5.14
2108 4709 4.899239 CCTCGTGGATGCTCCGGC 62.899 72.222 0.00 0.00 40.17 6.13
2109 4710 4.899239 CTCGTGGATGCTCCGGCC 62.899 72.222 0.00 0.00 40.17 6.13
2127 4728 4.699522 GCCGAGGAGGTTGGCGTT 62.700 66.667 0.00 0.00 46.43 4.84
2169 4770 1.979155 GGCCAAGGAGCAGGAAACC 60.979 63.158 0.00 0.00 0.00 3.27
2187 4788 3.423154 GAAACTGCCGCCCTCGTG 61.423 66.667 0.00 0.00 0.00 4.35
2253 4854 0.671781 CTTCGGTGACCAAGGAGCAG 60.672 60.000 1.11 0.00 0.00 4.24
2255 4856 2.583441 CGGTGACCAAGGAGCAGGA 61.583 63.158 1.11 0.00 0.00 3.86
2445 5046 1.884235 AGGAGCAGGAAAGTGAAACG 58.116 50.000 0.00 0.00 45.86 3.60
2464 5065 2.589540 CCGCCTTGGTGGATGCTA 59.410 61.111 13.67 0.00 38.35 3.49
2555 5156 3.231736 AACCACCGTCGAGGCTGT 61.232 61.111 0.00 0.00 46.52 4.40
2828 5429 2.753966 CCGCAGTCGAAGCCAATGG 61.754 63.158 0.00 0.00 38.10 3.16
2840 5441 1.599047 CCAATGGTGAGACCGAGCT 59.401 57.895 0.00 0.00 42.58 4.09
2846 5447 3.014304 TGGTGAGACCGAGCTAACTAT 57.986 47.619 0.00 0.00 42.58 2.12
2848 5449 2.950309 GGTGAGACCGAGCTAACTATGA 59.050 50.000 0.00 0.00 0.00 2.15
2853 5454 1.413077 ACCGAGCTAACTATGAAGGCC 59.587 52.381 0.00 0.00 0.00 5.19
2880 5481 1.079438 GGAGGAGGAGGTGGTCACT 59.921 63.158 0.93 0.00 0.00 3.41
2891 5492 2.276116 TGGTCACTGTCGAGGAGGC 61.276 63.158 0.00 0.00 0.00 4.70
2901 5502 2.893398 GAGGAGGCCGATGTCGTT 59.107 61.111 0.00 0.00 37.74 3.85
2908 5509 2.673114 GCCGATGTCGTTCCGCAAA 61.673 57.895 1.44 0.00 37.74 3.68
3003 5608 8.303876 GGTAGGTTCAATTTCTTCATTTGCTAA 58.696 33.333 0.00 0.00 0.00 3.09
3005 5610 7.725251 AGGTTCAATTTCTTCATTTGCTAACA 58.275 30.769 0.00 0.00 0.00 2.41
3147 5763 2.709475 GAGGCCGCAATAAGCACG 59.291 61.111 0.00 0.00 46.13 5.34
3161 5777 2.041115 GCACGGAGGAAAAGGGAGC 61.041 63.158 0.00 0.00 0.00 4.70
3197 5813 1.468395 CGTCGAGGAAGAGAAGAAGGC 60.468 57.143 0.00 0.00 0.00 4.35
3470 6100 2.825532 ACCATCACATGCTTTTGGGTAC 59.174 45.455 8.79 0.00 0.00 3.34
3724 6355 3.328050 AGTTAGCTGCAGTTTAGGTCCTT 59.672 43.478 16.64 0.00 0.00 3.36
3736 6367 5.778750 AGTTTAGGTCCTTGTTAGCTACAGA 59.221 40.000 0.00 0.00 38.19 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 830 9.602568 AATGCTAAAATTGCACATTCATCATAA 57.397 25.926 0.00 0.00 43.59 1.90
298 1049 1.177401 GGGGATCAAACTGGTTCTGC 58.823 55.000 0.00 0.00 0.00 4.26
334 1137 2.495270 TGTCAGCAGGAAAAGCAAAACA 59.505 40.909 0.00 0.00 0.00 2.83
656 3195 8.730680 GCCTCAGAACATTATGTTTCTTTCTTA 58.269 33.333 12.13 0.00 41.28 2.10
669 3228 6.299141 ACAGAAAGAAAGCCTCAGAACATTA 58.701 36.000 0.00 0.00 0.00 1.90
954 3542 0.035439 AACGCCGGAGATGGATTTGT 60.035 50.000 13.83 0.00 0.00 2.83
1252 3844 4.754667 GACGACCTTGGCCCCGAC 62.755 72.222 0.00 0.00 0.00 4.79
1280 3872 2.270527 GCTTGCTCTCCCCCACTC 59.729 66.667 0.00 0.00 0.00 3.51
1283 3875 3.333219 CCTGCTTGCTCTCCCCCA 61.333 66.667 0.00 0.00 0.00 4.96
1329 3921 4.426313 CCCTTCCCCTTGGCGTCC 62.426 72.222 0.00 0.00 0.00 4.79
1334 3926 3.728373 CCGTCCCCTTCCCCTTGG 61.728 72.222 0.00 0.00 0.00 3.61
1395 3987 0.810031 CGGCGACAACCTCCTTATGG 60.810 60.000 0.00 0.00 0.00 2.74
1396 3988 0.174845 TCGGCGACAACCTCCTTATG 59.825 55.000 4.99 0.00 0.00 1.90
1398 3990 0.458669 GATCGGCGACAACCTCCTTA 59.541 55.000 13.76 0.00 0.00 2.69
1571 4163 3.760035 ACGCCGCCTCGTCTTCAT 61.760 61.111 0.00 0.00 38.44 2.57
1593 4185 1.472878 TCCTCGATGTCCTTCTCGTTG 59.527 52.381 0.00 0.00 36.33 4.10
1657 4249 3.376078 GGTGACTACGCCCACGGA 61.376 66.667 0.00 0.00 46.04 4.69
1754 4355 2.826777 ATCCTCGTTGGCCTTGGCTG 62.827 60.000 11.71 0.16 35.26 4.85
1755 4356 2.606587 ATCCTCGTTGGCCTTGGCT 61.607 57.895 11.71 0.00 35.26 4.75
1756 4357 2.044946 ATCCTCGTTGGCCTTGGC 60.045 61.111 3.32 2.49 35.26 4.52
1757 4358 2.409870 GCATCCTCGTTGGCCTTGG 61.410 63.158 3.32 0.00 35.26 3.61
1758 4359 2.409870 GGCATCCTCGTTGGCCTTG 61.410 63.158 3.32 0.00 43.09 3.61
1759 4360 2.044946 GGCATCCTCGTTGGCCTT 60.045 61.111 3.32 0.00 43.09 4.35
1760 4361 4.473520 CGGCATCCTCGTTGGCCT 62.474 66.667 3.32 0.00 44.23 5.19
1873 4474 4.717629 CGCCAACGGAGCAGACGA 62.718 66.667 0.00 0.00 34.97 4.20
1932 4533 0.107643 TGGCAACATCAACCTCGTCA 59.892 50.000 0.00 0.00 46.17 4.35
2042 4643 2.586792 CCGGAGAAGCTGGGAAGG 59.413 66.667 0.00 0.00 39.56 3.46
2048 4649 3.551496 TTGGCCACCGGAGAAGCTG 62.551 63.158 9.46 0.00 0.00 4.24
2049 4650 3.249189 TTGGCCACCGGAGAAGCT 61.249 61.111 9.46 0.00 0.00 3.74
2050 4651 2.747855 CTTGGCCACCGGAGAAGC 60.748 66.667 9.46 4.65 0.00 3.86
2051 4652 2.045926 CCTTGGCCACCGGAGAAG 60.046 66.667 9.46 0.00 0.00 2.85
2052 4653 2.528127 TCCTTGGCCACCGGAGAA 60.528 61.111 17.07 0.00 0.00 2.87
2053 4654 3.003173 CTCCTTGGCCACCGGAGA 61.003 66.667 32.77 14.55 45.67 3.71
2054 4655 4.785453 GCTCCTTGGCCACCGGAG 62.785 72.222 32.27 32.27 45.59 4.63
2058 4659 2.713531 TTTCCTGCTCCTTGGCCACC 62.714 60.000 3.88 0.00 0.00 4.61
2059 4660 1.228552 TTTCCTGCTCCTTGGCCAC 60.229 57.895 3.88 0.00 0.00 5.01
2060 4661 1.228552 GTTTCCTGCTCCTTGGCCA 60.229 57.895 0.00 0.00 0.00 5.36
2061 4662 1.979155 GGTTTCCTGCTCCTTGGCC 60.979 63.158 0.00 0.00 0.00 5.36
2062 4663 2.335712 CGGTTTCCTGCTCCTTGGC 61.336 63.158 0.00 0.00 0.00 4.52
2063 4664 0.250727 TTCGGTTTCCTGCTCCTTGG 60.251 55.000 0.00 0.00 0.00 3.61
2064 4665 1.266989 GTTTCGGTTTCCTGCTCCTTG 59.733 52.381 0.00 0.00 0.00 3.61
2065 4666 1.143073 AGTTTCGGTTTCCTGCTCCTT 59.857 47.619 0.00 0.00 0.00 3.36
2066 4667 0.765510 AGTTTCGGTTTCCTGCTCCT 59.234 50.000 0.00 0.00 0.00 3.69
2067 4668 0.875059 CAGTTTCGGTTTCCTGCTCC 59.125 55.000 0.00 0.00 0.00 4.70
2068 4669 0.238553 GCAGTTTCGGTTTCCTGCTC 59.761 55.000 0.00 0.00 45.25 4.26
2069 4670 2.331265 GCAGTTTCGGTTTCCTGCT 58.669 52.632 0.00 0.00 45.25 4.24
2070 4671 4.944249 GCAGTTTCGGTTTCCTGC 57.056 55.556 0.00 0.00 42.94 4.85
2071 4672 1.574428 CGGCAGTTTCGGTTTCCTG 59.426 57.895 0.00 0.00 0.00 3.86
2072 4673 2.258726 GCGGCAGTTTCGGTTTCCT 61.259 57.895 0.00 0.00 0.00 3.36
2073 4674 2.254350 GCGGCAGTTTCGGTTTCC 59.746 61.111 0.00 0.00 0.00 3.13
2074 4675 2.254350 GGCGGCAGTTTCGGTTTC 59.746 61.111 3.07 0.00 0.00 2.78
2075 4676 3.292159 GGGCGGCAGTTTCGGTTT 61.292 61.111 12.47 0.00 0.00 3.27
2076 4677 4.265056 AGGGCGGCAGTTTCGGTT 62.265 61.111 12.47 0.00 0.00 4.44
2077 4678 4.699522 GAGGGCGGCAGTTTCGGT 62.700 66.667 12.47 0.00 0.00 4.69
2080 4681 3.423154 CACGAGGGCGGCAGTTTC 61.423 66.667 12.47 1.53 43.17 2.78
2087 4688 4.899239 GAGCATCCACGAGGGCGG 62.899 72.222 0.00 0.00 43.17 6.13
2110 4711 4.699522 AACGCCAACCTCCTCGGC 62.700 66.667 0.00 0.00 42.64 5.54
2111 4712 2.742372 CAACGCCAACCTCCTCGG 60.742 66.667 0.00 0.00 39.35 4.63
2112 4713 3.423154 GCAACGCCAACCTCCTCG 61.423 66.667 0.00 0.00 0.00 4.63
2253 4854 1.285950 GGCGGCAGTTTCACTTTCC 59.714 57.895 3.07 0.00 0.00 3.13
2255 4856 1.152756 AGGGCGGCAGTTTCACTTT 60.153 52.632 12.47 0.00 0.00 2.66
2322 4923 4.680237 TCCTTGCTCACCGGTGCG 62.680 66.667 30.25 25.23 36.33 5.34
2325 4926 3.241530 TGCTCCTTGCTCACCGGT 61.242 61.111 0.00 0.00 43.37 5.28
2332 4933 0.179009 TCACTTTGCTGCTCCTTGCT 60.179 50.000 0.00 0.00 43.37 3.91
2333 4934 0.670162 TTCACTTTGCTGCTCCTTGC 59.330 50.000 0.00 0.00 43.25 4.01
2344 4945 1.035139 AGGGCTGCAGTTTCACTTTG 58.965 50.000 16.64 0.00 0.00 2.77
2463 5064 1.813859 CTCATCCTTGGCGACCGTA 59.186 57.895 0.00 0.00 0.00 4.02
2464 5065 2.579201 CTCATCCTTGGCGACCGT 59.421 61.111 0.00 0.00 0.00 4.83
2664 5265 2.023223 GGCGCTTTCGTCCACGTTA 61.023 57.895 7.64 0.00 40.80 3.18
2740 5341 1.082104 CGTTGTTCAAGGAAGGCGC 60.082 57.895 0.00 0.00 0.00 6.53
2798 5399 3.121030 CTGCGGCCTCTTTGACGG 61.121 66.667 0.00 0.00 0.00 4.79
2828 5429 4.498345 CCTTCATAGTTAGCTCGGTCTCAC 60.498 50.000 0.00 0.00 0.00 3.51
2840 5441 0.179094 CGCCGTGGCCTTCATAGTTA 60.179 55.000 3.32 0.00 37.98 2.24
2880 5481 2.362503 ACATCGGCCTCCTCGACA 60.363 61.111 0.00 0.00 39.55 4.35
2901 5502 2.047274 CTCTCGGCCTTTTGCGGA 60.047 61.111 0.00 0.00 45.89 5.54
3119 5735 2.109126 GCGGCCTCCTTCACATCAC 61.109 63.158 0.00 0.00 0.00 3.06
3147 5763 1.222113 CTCCGCTCCCTTTTCCTCC 59.778 63.158 0.00 0.00 0.00 4.30
3161 5777 0.030908 GACGGTCAGCTTATCCTCCG 59.969 60.000 2.62 0.00 42.94 4.63
3197 5813 0.882927 TGGTTCTTGTTCTTCGCCGG 60.883 55.000 0.00 0.00 0.00 6.13
3380 6010 5.955496 CGCGTGTACATAATTTGTTTCTACC 59.045 40.000 0.00 0.00 39.87 3.18
3470 6100 1.071471 AGGCTGACAGGGAAACACG 59.929 57.895 4.26 0.00 0.00 4.49
3736 6367 8.270030 TCATCCAAGATTCAACAGATGACTAAT 58.730 33.333 0.00 0.00 37.92 1.73
3885 6770 1.348036 ACTAAGTCAAGAGGTGGGCAC 59.652 52.381 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.