Multiple sequence alignment - TraesCS4A01G427000

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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 TraesCS4A01G427000 chr4A 100.000 4705 0 0 1 4705 698108018 698103314 0.000000e+00 8689.0
1 TraesCS4A01G427000 chr4A 93.021 3410 166 32 549 3912 698889968 698886585 0.000000e+00 4913.0
2 TraesCS4A01G427000 chr4A 83.632 446 54 5 95 521 281701525 281701970 7.330000e-108 401.0
3 TraesCS4A01G427000 chr7A 90.469 2644 148 30 1077 3640 30673861 30676480 0.000000e+00 3391.0
4 TraesCS4A01G427000 chr7A 95.699 279 12 0 3636 3914 30682646 30682924 2.580000e-122 449.0
5 TraesCS4A01G427000 chr7A 95.041 121 6 0 4457 4577 232743917 232743797 1.730000e-44 191.0
6 TraesCS4A01G427000 chr7A 94.828 116 6 0 4456 4571 91928197 91928082 1.040000e-41 182.0
7 TraesCS4A01G427000 chr7A 90.299 134 12 1 4456 4589 679064059 679063927 1.740000e-39 174.0
8 TraesCS4A01G427000 chr7A 74.854 342 75 9 4 340 363604688 363605023 1.360000e-30 145.0
9 TraesCS4A01G427000 chr7A 94.340 53 3 0 1931 1983 727882041 727881989 1.090000e-11 82.4
10 TraesCS4A01G427000 chr7D 92.911 2003 92 9 1744 3713 30285668 30287653 0.000000e+00 2867.0
11 TraesCS4A01G427000 chr7D 90.367 1308 89 17 1230 2504 30284364 30285667 0.000000e+00 1683.0
12 TraesCS4A01G427000 chr7D 80.550 545 80 11 3 526 277000150 276999611 3.410000e-106 396.0
13 TraesCS4A01G427000 chr7D 96.279 215 8 0 3699 3913 30289078 30289292 2.080000e-93 353.0
14 TraesCS4A01G427000 chr7D 78.918 536 91 13 5 519 316202507 316203041 1.250000e-90 344.0
15 TraesCS4A01G427000 chr7D 92.017 238 15 2 959 1194 30284133 30284368 9.760000e-87 331.0
16 TraesCS4A01G427000 chr7D 77.695 538 96 17 6 521 531866896 531866361 1.640000e-79 307.0
17 TraesCS4A01G427000 chr6A 90.386 1217 64 15 2528 3710 226068774 226069971 0.000000e+00 1550.0
18 TraesCS4A01G427000 chr6A 86.486 222 25 3 1196 1413 226067041 226067261 6.080000e-59 239.0
19 TraesCS4A01G427000 chr6A 87.562 201 22 2 1649 1846 226068574 226068774 3.660000e-56 230.0
20 TraesCS4A01G427000 chr6A 83.410 217 23 6 3709 3913 226070271 226070486 6.220000e-44 189.0
21 TraesCS4A01G427000 chr6A 95.652 115 5 0 4457 4571 586802395 586802509 8.040000e-43 185.0
22 TraesCS4A01G427000 chr6A 86.555 119 7 6 960 1072 226066707 226066822 6.390000e-24 122.0
23 TraesCS4A01G427000 chr6D 90.058 1217 68 17 2528 3710 170963623 170964820 0.000000e+00 1528.0
24 TraesCS4A01G427000 chr6D 81.331 541 80 10 1 521 11699427 11698888 2.020000e-113 420.0
25 TraesCS4A01G427000 chr6D 85.915 284 34 4 3938 4221 8674655 8674932 9.900000e-77 298.0
26 TraesCS4A01G427000 chr6D 79.634 383 62 12 3 380 176101778 176101407 1.300000e-65 261.0
27 TraesCS4A01G427000 chr6D 87.838 222 22 3 1196 1413 170961892 170962112 6.040000e-64 255.0
28 TraesCS4A01G427000 chr6D 88.060 201 21 2 1649 1846 170963423 170963623 7.870000e-58 235.0
29 TraesCS4A01G427000 chr6D 91.667 168 13 1 4284 4451 8674933 8675099 1.020000e-56 231.0
30 TraesCS4A01G427000 chr6D 90.000 140 9 1 4566 4705 8675094 8675228 4.840000e-40 176.0
31 TraesCS4A01G427000 chr6D 82.488 217 23 7 3709 3913 170965122 170965335 4.840000e-40 176.0
32 TraesCS4A01G427000 chr6D 88.462 78 5 3 984 1059 170961593 170961668 1.800000e-14 91.6
33 TraesCS4A01G427000 chr6B 89.804 1226 72 14 2528 3719 384964001 384962795 0.000000e+00 1522.0
34 TraesCS4A01G427000 chr6B 83.685 521 55 17 2008 2511 495426779 495426272 9.220000e-127 464.0
35 TraesCS4A01G427000 chr6B 83.140 344 46 8 1949 2288 203577211 203576876 2.130000e-78 303.0
36 TraesCS4A01G427000 chr6B 88.060 201 21 2 1649 1846 384964201 384964001 7.870000e-58 235.0
37 TraesCS4A01G427000 chr6B 86.036 222 23 4 1196 1413 384965750 384965533 1.020000e-56 231.0
38 TraesCS4A01G427000 chr6B 83.871 217 22 6 3709 3913 384962501 384962286 1.340000e-45 195.0
39 TraesCS4A01G427000 chr6B 84.553 123 8 5 955 1072 384966084 384965968 1.380000e-20 111.0
40 TraesCS4A01G427000 chr2B 97.730 793 14 1 3913 4705 359066671 359067459 0.000000e+00 1362.0
41 TraesCS4A01G427000 chr2B 80.926 540 74 19 4 520 463464055 463464588 2.640000e-107 399.0
42 TraesCS4A01G427000 chr2B 80.996 542 70 17 4 520 463480022 463480555 2.640000e-107 399.0
43 TraesCS4A01G427000 chr2B 88.889 306 31 1 2216 2518 773173086 773172781 1.600000e-99 374.0
44 TraesCS4A01G427000 chr2B 77.449 541 95 13 3 522 411116700 411117234 9.900000e-77 298.0
45 TraesCS4A01G427000 chr2B 85.971 278 35 1 3916 4193 484593800 484594073 1.280000e-75 294.0
46 TraesCS4A01G427000 chr2B 77.574 544 72 26 3 521 411002375 411002893 2.770000e-72 283.0
47 TraesCS4A01G427000 chr2B 84.528 265 35 4 3910 4173 359069365 359069106 1.680000e-64 257.0
48 TraesCS4A01G427000 chr3B 96.992 798 20 1 3908 4705 447226165 447226958 0.000000e+00 1338.0
49 TraesCS4A01G427000 chr3B 80.055 366 69 4 3 367 472664148 472664510 7.760000e-68 268.0
50 TraesCS4A01G427000 chr1B 97.219 791 18 1 3915 4705 109425065 109425851 0.000000e+00 1336.0
51 TraesCS4A01G427000 chr1B 89.926 675 58 6 1838 2504 632703498 632702826 0.000000e+00 861.0
52 TraesCS4A01G427000 chrUn 100.000 621 0 0 4085 4705 357693348 357693968 0.000000e+00 1147.0
53 TraesCS4A01G427000 chr5B 90.284 669 54 7 1846 2506 250923439 250924104 0.000000e+00 865.0
54 TraesCS4A01G427000 chr5D 90.635 630 52 6 1839 2466 365031235 365031859 0.000000e+00 830.0
55 TraesCS4A01G427000 chr7B 94.249 539 25 4 3913 4451 551497632 551497100 0.000000e+00 819.0
56 TraesCS4A01G427000 chr7B 93.321 539 29 4 3914 4451 121871173 121870641 0.000000e+00 789.0
57 TraesCS4A01G427000 chr7B 83.803 284 32 8 2008 2287 508138885 508139158 1.680000e-64 257.0
58 TraesCS4A01G427000 chr7B 97.600 125 3 0 4581 4705 551497083 551496959 1.030000e-51 215.0
59 TraesCS4A01G427000 chr7B 96.800 125 4 0 4581 4705 121870624 121870500 4.770000e-50 209.0
60 TraesCS4A01G427000 chr1D 85.132 417 41 4 130 526 288080270 288080685 1.580000e-109 407.0
61 TraesCS4A01G427000 chr1D 90.226 133 13 0 2 134 288053126 288053258 1.740000e-39 174.0
62 TraesCS4A01G427000 chr2A 79.667 541 85 15 3 521 380784724 380785261 2.680000e-97 366.0
63 TraesCS4A01G427000 chr2A 82.828 396 63 5 3 395 454816326 454816719 2.690000e-92 350.0
64 TraesCS4A01G427000 chr2A 74.635 548 103 24 3 521 166109397 166108857 4.770000e-50 209.0
65 TraesCS4A01G427000 chr2A 96.460 113 4 0 4458 4570 755622653 755622541 2.240000e-43 187.0
66 TraesCS4A01G427000 chr2D 90.262 267 20 4 3915 4181 593352690 593352950 1.250000e-90 344.0
67 TraesCS4A01G427000 chr2D 92.021 188 14 1 4265 4451 593352952 593353139 3.610000e-66 263.0
68 TraesCS4A01G427000 chr2D 96.429 140 5 0 4566 4705 593353134 593353273 1.020000e-56 231.0
69 TraesCS4A01G427000 chr2D 90.580 138 13 0 4568 4705 317938270 317938407 2.890000e-42 183.0
70 TraesCS4A01G427000 chr5A 81.148 244 37 4 284 519 323625061 323624819 2.240000e-43 187.0
71 TraesCS4A01G427000 chr4B 88.189 127 15 0 397 523 390414498 390414372 8.150000e-33 152.0
72 TraesCS4A01G427000 chr3A 90.698 43 1 2 1922 1961 678188215 678188257 2.000000e-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 TraesCS4A01G427000 chr4A 698103314 698108018 4704 True 8689.000000 8689 100.0000 1 4705 1 chr4A.!!$R1 4704
1 TraesCS4A01G427000 chr4A 698886585 698889968 3383 True 4913.000000 4913 93.0210 549 3912 1 chr4A.!!$R2 3363
2 TraesCS4A01G427000 chr7A 30673861 30676480 2619 False 3391.000000 3391 90.4690 1077 3640 1 chr7A.!!$F1 2563
3 TraesCS4A01G427000 chr7D 30284133 30289292 5159 False 1308.500000 2867 92.8935 959 3913 4 chr7D.!!$F2 2954
4 TraesCS4A01G427000 chr7D 276999611 277000150 539 True 396.000000 396 80.5500 3 526 1 chr7D.!!$R1 523
5 TraesCS4A01G427000 chr7D 316202507 316203041 534 False 344.000000 344 78.9180 5 519 1 chr7D.!!$F1 514
6 TraesCS4A01G427000 chr7D 531866361 531866896 535 True 307.000000 307 77.6950 6 521 1 chr7D.!!$R2 515
7 TraesCS4A01G427000 chr6A 226066707 226070486 3779 False 466.000000 1550 86.8798 960 3913 5 chr6A.!!$F2 2953
8 TraesCS4A01G427000 chr6D 170961593 170965335 3742 False 457.120000 1528 87.3812 984 3913 5 chr6D.!!$F2 2929
9 TraesCS4A01G427000 chr6D 11698888 11699427 539 True 420.000000 420 81.3310 1 521 1 chr6D.!!$R1 520
10 TraesCS4A01G427000 chr6D 8674655 8675228 573 False 235.000000 298 89.1940 3938 4705 3 chr6D.!!$F1 767
11 TraesCS4A01G427000 chr6B 495426272 495426779 507 True 464.000000 464 83.6850 2008 2511 1 chr6B.!!$R2 503
12 TraesCS4A01G427000 chr6B 384962286 384966084 3798 True 458.800000 1522 86.4648 955 3913 5 chr6B.!!$R3 2958
13 TraesCS4A01G427000 chr2B 359066671 359067459 788 False 1362.000000 1362 97.7300 3913 4705 1 chr2B.!!$F1 792
14 TraesCS4A01G427000 chr2B 463464055 463464588 533 False 399.000000 399 80.9260 4 520 1 chr2B.!!$F4 516
15 TraesCS4A01G427000 chr2B 463480022 463480555 533 False 399.000000 399 80.9960 4 520 1 chr2B.!!$F5 516
16 TraesCS4A01G427000 chr2B 411116700 411117234 534 False 298.000000 298 77.4490 3 522 1 chr2B.!!$F3 519
17 TraesCS4A01G427000 chr2B 411002375 411002893 518 False 283.000000 283 77.5740 3 521 1 chr2B.!!$F2 518
18 TraesCS4A01G427000 chr3B 447226165 447226958 793 False 1338.000000 1338 96.9920 3908 4705 1 chr3B.!!$F1 797
19 TraesCS4A01G427000 chr1B 109425065 109425851 786 False 1336.000000 1336 97.2190 3915 4705 1 chr1B.!!$F1 790
20 TraesCS4A01G427000 chr1B 632702826 632703498 672 True 861.000000 861 89.9260 1838 2504 1 chr1B.!!$R1 666
21 TraesCS4A01G427000 chrUn 357693348 357693968 620 False 1147.000000 1147 100.0000 4085 4705 1 chrUn.!!$F1 620
22 TraesCS4A01G427000 chr5B 250923439 250924104 665 False 865.000000 865 90.2840 1846 2506 1 chr5B.!!$F1 660
23 TraesCS4A01G427000 chr5D 365031235 365031859 624 False 830.000000 830 90.6350 1839 2466 1 chr5D.!!$F1 627
24 TraesCS4A01G427000 chr7B 551496959 551497632 673 True 517.000000 819 95.9245 3913 4705 2 chr7B.!!$R2 792
25 TraesCS4A01G427000 chr7B 121870500 121871173 673 True 499.000000 789 95.0605 3914 4705 2 chr7B.!!$R1 791
26 TraesCS4A01G427000 chr2A 380784724 380785261 537 False 366.000000 366 79.6670 3 521 1 chr2A.!!$F1 518
27 TraesCS4A01G427000 chr2A 166108857 166109397 540 True 209.000000 209 74.6350 3 521 1 chr2A.!!$R1 518
28 TraesCS4A01G427000 chr2D 593352690 593353273 583 False 279.333333 344 92.9040 3915 4705 3 chr2D.!!$F2 790

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
845 876 0.034863 GTGGAGAGGTCGAGAGGACT 60.035 60.000 0.00 0.00 45.35 3.85 F
874 905 1.374568 GGGGTTTGGGCCATGTTTG 59.625 57.895 7.26 0.00 0.00 2.93 F
957 988 1.809619 CTACGGGTGCATGGTCGTG 60.810 63.158 13.87 4.19 37.10 4.35 F
1637 2500 1.860641 TCTTCTGGGAGGCGAATACA 58.139 50.000 0.00 0.00 0.00 2.29 F
2737 4825 2.355108 GCCTGTTCTTGATCTAGTGGCA 60.355 50.000 18.80 10.60 37.91 4.92 F
3097 5224 1.279271 GCCTCAGTTTAAGAGAGCCCA 59.721 52.381 0.00 0.00 35.09 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 3711 1.132640 GCGTTGCTGACCATTCGAC 59.867 57.895 0.00 0.00 0.00 4.20 R
2737 4825 3.387962 TGTTCCTCCAGCTATTGATCCT 58.612 45.455 0.00 0.00 0.00 3.24 R
2824 4912 6.109156 TCTGCAGTTAAGGATACAAGAACA 57.891 37.500 14.67 0.00 41.41 3.18 R
3052 5173 0.523519 GCACCTTTAACCTGCAGCTC 59.476 55.000 8.66 0.00 0.00 4.09 R
3641 5771 0.106519 ACAGTTGCTTCCAGCCTTGT 60.107 50.000 0.00 0.00 41.51 3.16 R
4050 7631 0.595588 CAACATGGCGCCAGTTGTAA 59.404 50.000 37.07 19.35 38.20 2.41 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
50 51 1.535462 CGGTGTTTAGCAACTTCAGGG 59.465 52.381 0.00 0.00 33.58 4.45
72 73 3.297736 CCCTCTCGGTGAAGGTAATAGT 58.702 50.000 0.00 0.00 0.00 2.12
82 83 5.359292 GGTGAAGGTAATAGTCCTACGTCTT 59.641 44.000 0.00 0.00 34.56 3.01
135 140 7.499232 GGGTATGATTACAGTGATTGCTTAACT 59.501 37.037 0.00 0.00 0.00 2.24
137 142 9.319143 GTATGATTACAGTGATTGCTTAACTCT 57.681 33.333 0.00 0.00 0.00 3.24
144 149 6.047870 CAGTGATTGCTTAACTCTAGCTCAT 58.952 40.000 0.00 0.00 39.38 2.90
146 151 5.236047 GTGATTGCTTAACTCTAGCTCATGG 59.764 44.000 0.00 0.00 39.38 3.66
156 161 0.339859 TAGCTCATGGGGAGGAGTGT 59.660 55.000 0.00 0.00 44.22 3.55
178 183 4.021544 GTGGCTTATATAGAGTGCTCTGCT 60.022 45.833 11.63 2.40 40.71 4.24
179 184 5.184096 GTGGCTTATATAGAGTGCTCTGCTA 59.816 44.000 11.63 4.37 40.71 3.49
180 185 5.184096 TGGCTTATATAGAGTGCTCTGCTAC 59.816 44.000 11.63 0.00 40.71 3.58
249 255 2.407361 CAGTTACAGGTGTAAAGCGTCG 59.593 50.000 4.14 0.00 41.58 5.12
289 295 6.864360 AGTTAACGGTAGCTATGACTCTAG 57.136 41.667 0.00 0.00 0.00 2.43
296 302 7.052873 ACGGTAGCTATGACTCTAGTTTAAGA 58.947 38.462 0.00 0.00 0.00 2.10
307 313 8.750298 TGACTCTAGTTTAAGAATGACTTAGGG 58.250 37.037 0.00 0.00 41.33 3.53
312 318 6.482524 AGTTTAAGAATGACTTAGGGTTCCC 58.517 40.000 0.00 0.00 41.33 3.97
342 348 1.228154 GCTCCCACGTTGTCCCTTT 60.228 57.895 0.00 0.00 0.00 3.11
360 367 4.094476 CCTTTACCTCCCTTGTCTGAGTA 58.906 47.826 0.00 0.00 0.00 2.59
373 380 3.007940 TGTCTGAGTAATGGTGGTCTTGG 59.992 47.826 0.00 0.00 0.00 3.61
386 398 0.389166 GTCTTGGCGACTGAGGAGTG 60.389 60.000 0.00 0.00 39.61 3.51
387 399 1.079543 CTTGGCGACTGAGGAGTGG 60.080 63.158 0.00 0.00 30.16 4.00
388 400 1.821061 CTTGGCGACTGAGGAGTGGT 61.821 60.000 0.00 0.00 30.83 4.16
389 401 1.816863 TTGGCGACTGAGGAGTGGTC 61.817 60.000 0.00 0.00 33.38 4.02
395 426 2.599281 TGAGGAGTGGTCGCCGAA 60.599 61.111 0.00 0.00 38.56 4.30
529 560 2.030027 TGACCTCATCACCACCTTCT 57.970 50.000 0.00 0.00 29.99 2.85
530 561 2.338809 TGACCTCATCACCACCTTCTT 58.661 47.619 0.00 0.00 29.99 2.52
531 562 2.711009 TGACCTCATCACCACCTTCTTT 59.289 45.455 0.00 0.00 29.99 2.52
532 563 3.907474 TGACCTCATCACCACCTTCTTTA 59.093 43.478 0.00 0.00 29.99 1.85
533 564 4.254492 GACCTCATCACCACCTTCTTTAC 58.746 47.826 0.00 0.00 0.00 2.01
534 565 3.650942 ACCTCATCACCACCTTCTTTACA 59.349 43.478 0.00 0.00 0.00 2.41
535 566 4.256920 CCTCATCACCACCTTCTTTACAG 58.743 47.826 0.00 0.00 0.00 2.74
536 567 3.674997 TCATCACCACCTTCTTTACAGC 58.325 45.455 0.00 0.00 0.00 4.40
537 568 3.072330 TCATCACCACCTTCTTTACAGCA 59.928 43.478 0.00 0.00 0.00 4.41
538 569 2.846193 TCACCACCTTCTTTACAGCAC 58.154 47.619 0.00 0.00 0.00 4.40
539 570 2.171659 TCACCACCTTCTTTACAGCACA 59.828 45.455 0.00 0.00 0.00 4.57
540 571 2.948979 CACCACCTTCTTTACAGCACAA 59.051 45.455 0.00 0.00 0.00 3.33
541 572 2.949644 ACCACCTTCTTTACAGCACAAC 59.050 45.455 0.00 0.00 0.00 3.32
542 573 2.032030 CCACCTTCTTTACAGCACAACG 60.032 50.000 0.00 0.00 0.00 4.10
543 574 2.869801 CACCTTCTTTACAGCACAACGA 59.130 45.455 0.00 0.00 0.00 3.85
544 575 3.498397 CACCTTCTTTACAGCACAACGAT 59.502 43.478 0.00 0.00 0.00 3.73
545 576 4.688879 CACCTTCTTTACAGCACAACGATA 59.311 41.667 0.00 0.00 0.00 2.92
546 577 4.929808 ACCTTCTTTACAGCACAACGATAG 59.070 41.667 0.00 0.00 46.19 2.08
594 625 1.305213 GCCTCATTGGGGAAGGCAA 60.305 57.895 6.80 0.00 44.42 4.52
595 626 0.688749 GCCTCATTGGGGAAGGCAAT 60.689 55.000 6.80 0.00 44.42 3.56
597 628 0.462789 CTCATTGGGGAAGGCAATGC 59.537 55.000 0.00 0.00 36.55 3.56
598 629 0.252148 TCATTGGGGAAGGCAATGCA 60.252 50.000 7.79 0.00 36.55 3.96
599 630 0.834612 CATTGGGGAAGGCAATGCAT 59.165 50.000 7.79 0.00 30.94 3.96
600 631 2.040939 CATTGGGGAAGGCAATGCATA 58.959 47.619 7.79 0.00 30.94 3.14
601 632 1.779221 TTGGGGAAGGCAATGCATAG 58.221 50.000 7.79 0.00 0.00 2.23
602 633 0.630673 TGGGGAAGGCAATGCATAGT 59.369 50.000 7.79 0.00 0.00 2.12
603 634 1.035139 GGGGAAGGCAATGCATAGTG 58.965 55.000 7.79 0.00 0.00 2.74
604 635 0.386838 GGGAAGGCAATGCATAGTGC 59.613 55.000 13.87 13.87 46.53 4.40
646 677 1.289160 ATAGCTTCAGACCCTTGCCA 58.711 50.000 0.00 0.00 0.00 4.92
694 725 2.757917 AGCTCCTCCTCGTCTGGC 60.758 66.667 0.00 0.00 0.00 4.85
695 726 3.071206 GCTCCTCCTCGTCTGGCA 61.071 66.667 0.00 0.00 0.00 4.92
715 746 1.296755 CGGACGAGTTCGAGGAGTCA 61.297 60.000 8.72 0.00 43.02 3.41
718 749 1.226156 CGAGTTCGAGGAGTCAGCG 60.226 63.158 0.00 0.00 43.02 5.18
719 750 1.137825 GAGTTCGAGGAGTCAGCGG 59.862 63.158 4.38 0.00 0.00 5.52
738 769 0.817229 GCCAGCTTAGCCCAGTCATC 60.817 60.000 0.00 0.00 0.00 2.92
739 770 0.543277 CCAGCTTAGCCCAGTCATCA 59.457 55.000 0.00 0.00 0.00 3.07
740 771 1.065199 CCAGCTTAGCCCAGTCATCAA 60.065 52.381 0.00 0.00 0.00 2.57
749 780 2.885554 GCCCAGTCATCAAATTGGAGGT 60.886 50.000 0.00 0.00 32.34 3.85
795 826 0.397816 CGGAGAGGGTGGGAGAGATT 60.398 60.000 0.00 0.00 0.00 2.40
816 847 2.321719 GGGGAGAGGAAGGTATGAGAC 58.678 57.143 0.00 0.00 0.00 3.36
845 876 0.034863 GTGGAGAGGTCGAGAGGACT 60.035 60.000 0.00 0.00 45.35 3.85
869 900 2.029892 TTGAGTGGGGTTTGGGCCAT 62.030 55.000 7.26 0.00 0.00 4.40
874 905 1.374568 GGGGTTTGGGCCATGTTTG 59.625 57.895 7.26 0.00 0.00 2.93
952 983 4.467084 ACGGCTACGGGTGCATGG 62.467 66.667 0.00 0.00 46.48 3.66
955 986 2.890474 GCTACGGGTGCATGGTCG 60.890 66.667 0.00 0.00 0.00 4.79
957 988 1.809619 CTACGGGTGCATGGTCGTG 60.810 63.158 13.87 4.19 37.10 4.35
1101 1213 2.487775 ACAGCTTACATATGGGTCCCA 58.512 47.619 14.64 14.64 38.19 4.37
1131 1243 4.602696 CCCTACGTACGGAGCGCG 62.603 72.222 22.52 8.60 0.00 6.86
1186 1319 1.955778 TCCTGCACTTCCACACAATTG 59.044 47.619 3.24 3.24 0.00 2.32
1198 1331 3.736100 CAATTGGTGCGCGCCTCA 61.736 61.111 37.39 25.52 0.00 3.86
1350 1511 3.595758 GGTGTTGCCAAGTGCGCT 61.596 61.111 9.73 0.00 45.60 5.92
1413 1574 4.221703 CGTATTGCCAATCCTCTATCTCCT 59.778 45.833 0.00 0.00 0.00 3.69
1417 1578 2.566724 GCCAATCCTCTATCTCCTCCAG 59.433 54.545 0.00 0.00 0.00 3.86
1418 1579 3.172339 CCAATCCTCTATCTCCTCCAGG 58.828 54.545 0.00 0.00 0.00 4.45
1419 1580 2.566724 CAATCCTCTATCTCCTCCAGGC 59.433 54.545 0.00 0.00 34.44 4.85
1425 1609 2.514160 TCTATCTCCTCCAGGCACTACA 59.486 50.000 0.00 0.00 36.02 2.74
1437 1621 2.763448 AGGCACTACATTCTCAGAGGAC 59.237 50.000 0.00 0.00 36.02 3.85
1439 1623 2.803451 CACTACATTCTCAGAGGACGC 58.197 52.381 0.00 0.00 0.00 5.19
1584 2446 9.823098 TCAATTGTTGAAATGAAAAACTTTGTG 57.177 25.926 5.13 0.00 36.59 3.33
1637 2500 1.860641 TCTTCTGGGAGGCGAATACA 58.139 50.000 0.00 0.00 0.00 2.29
1715 3004 6.732896 TGGTTATTGTTTAACCCACATGTT 57.267 33.333 11.05 0.00 44.74 2.71
1716 3005 6.750148 TGGTTATTGTTTAACCCACATGTTC 58.250 36.000 11.05 0.00 44.74 3.18
1717 3006 6.323996 TGGTTATTGTTTAACCCACATGTTCA 59.676 34.615 11.05 0.00 44.74 3.18
1718 3007 7.147724 TGGTTATTGTTTAACCCACATGTTCAA 60.148 33.333 11.05 0.00 44.74 2.69
1799 3091 3.770263 TCGTTTCGGACAATCTATCGT 57.230 42.857 0.00 0.00 0.00 3.73
2399 3711 7.333921 GCAGAATCTGATGTAATGGATAGGAAG 59.666 40.741 15.38 0.00 32.44 3.46
2737 4825 2.355108 GCCTGTTCTTGATCTAGTGGCA 60.355 50.000 18.80 10.60 37.91 4.92
2824 4912 7.521669 AGATGGCTTATCAGGTTAGCTATTTT 58.478 34.615 0.00 0.00 36.42 1.82
3052 5173 9.926751 CAACTCAGCACTAACTGATTAATAATG 57.073 33.333 0.00 0.00 45.34 1.90
3077 5198 1.537202 GCAGGTTAAAGGTGCAGTGAG 59.463 52.381 0.00 0.00 37.16 3.51
3097 5224 1.279271 GCCTCAGTTTAAGAGAGCCCA 59.721 52.381 0.00 0.00 35.09 5.36
3269 5399 9.474920 TTCTTTGTTGTTATTGCCAAGATTTAG 57.525 29.630 0.00 0.00 0.00 1.85
3641 5771 5.500234 AGCCTTGCTATGATAGTGAAACAA 58.500 37.500 0.92 0.00 36.59 2.83
3647 5777 5.123820 TGCTATGATAGTGAAACAACAAGGC 59.876 40.000 0.92 0.00 41.43 4.35
3703 5833 8.446273 CAACTATTTGAAGGTGAGACACTTATG 58.554 37.037 0.00 0.00 36.19 1.90
3736 7305 8.542497 TTAGTAGTCGTTAAAATGACATGCTT 57.458 30.769 15.48 0.00 45.24 3.91
4047 7628 2.819608 GTCCACAGCCAATCAAAAGCTA 59.180 45.455 0.00 0.00 34.38 3.32
4048 7629 3.084039 TCCACAGCCAATCAAAAGCTAG 58.916 45.455 0.00 0.00 34.38 3.42
4049 7630 2.416431 CCACAGCCAATCAAAAGCTAGC 60.416 50.000 6.62 6.62 34.38 3.42
4050 7631 2.490903 CACAGCCAATCAAAAGCTAGCT 59.509 45.455 12.68 12.68 34.38 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.272490 CTCAAGGCACAAGACGTAGGA 59.728 52.381 0.00 0.00 0.00 2.94
135 140 0.937441 ACTCCTCCCCATGAGCTAGA 59.063 55.000 0.00 0.00 39.98 2.43
137 142 0.339859 ACACTCCTCCCCATGAGCTA 59.660 55.000 0.00 0.00 39.98 3.32
144 149 0.253160 ATAAGCCACACTCCTCCCCA 60.253 55.000 0.00 0.00 0.00 4.96
146 151 4.417437 TCTATATAAGCCACACTCCTCCC 58.583 47.826 0.00 0.00 0.00 4.30
156 161 4.155709 AGCAGAGCACTCTATATAAGCCA 58.844 43.478 0.00 0.00 37.98 4.75
178 183 0.398522 ACATGGGAGCGATGGAGGTA 60.399 55.000 0.00 0.00 0.00 3.08
179 184 1.690219 GACATGGGAGCGATGGAGGT 61.690 60.000 0.00 0.00 0.00 3.85
180 185 1.070445 GACATGGGAGCGATGGAGG 59.930 63.158 0.00 0.00 0.00 4.30
268 274 7.636150 AAACTAGAGTCATAGCTACCGTTAA 57.364 36.000 0.00 0.00 0.00 2.01
307 313 3.039134 CTGCAACGGTTGGGGAAC 58.961 61.111 21.37 5.83 0.00 3.62
312 318 3.365265 GGGAGCTGCAACGGTTGG 61.365 66.667 21.37 7.76 0.00 3.77
342 348 4.030913 CCATTACTCAGACAAGGGAGGTA 58.969 47.826 0.00 0.00 35.45 3.08
360 367 4.397348 GTCGCCAAGACCACCATT 57.603 55.556 0.00 0.00 43.95 3.16
373 380 2.179517 CGACCACTCCTCAGTCGC 59.820 66.667 0.00 0.00 45.72 5.19
387 399 2.202892 GGAGGTCCATTCGGCGAC 60.203 66.667 10.16 0.00 35.64 5.19
388 400 2.363795 AGGAGGTCCATTCGGCGA 60.364 61.111 4.99 4.99 38.89 5.54
389 401 2.202932 CAGGAGGTCCATTCGGCG 60.203 66.667 0.00 0.00 38.89 6.46
526 557 4.688879 CCACTATCGTTGTGCTGTAAAGAA 59.311 41.667 0.00 0.00 34.38 2.52
527 558 4.242475 CCACTATCGTTGTGCTGTAAAGA 58.758 43.478 0.00 0.00 34.38 2.52
528 559 3.994392 ACCACTATCGTTGTGCTGTAAAG 59.006 43.478 0.00 0.00 34.38 1.85
529 560 3.743911 CACCACTATCGTTGTGCTGTAAA 59.256 43.478 0.00 0.00 31.20 2.01
530 561 3.322369 CACCACTATCGTTGTGCTGTAA 58.678 45.455 0.00 0.00 31.20 2.41
531 562 2.954316 CACCACTATCGTTGTGCTGTA 58.046 47.619 0.00 0.00 31.20 2.74
532 563 1.795768 CACCACTATCGTTGTGCTGT 58.204 50.000 0.00 0.00 31.20 4.40
536 567 1.078709 CTGGCACCACTATCGTTGTG 58.921 55.000 0.00 0.00 39.19 3.33
537 568 0.036388 CCTGGCACCACTATCGTTGT 60.036 55.000 0.00 0.00 0.00 3.32
538 569 0.036388 ACCTGGCACCACTATCGTTG 60.036 55.000 0.00 0.00 0.00 4.10
539 570 0.036388 CACCTGGCACCACTATCGTT 60.036 55.000 0.00 0.00 0.00 3.85
540 571 1.596934 CACCTGGCACCACTATCGT 59.403 57.895 0.00 0.00 0.00 3.73
541 572 1.815421 GCACCTGGCACCACTATCG 60.815 63.158 0.00 0.00 43.97 2.92
542 573 4.225497 GCACCTGGCACCACTATC 57.775 61.111 0.00 0.00 43.97 2.08
571 602 0.745845 CTTCCCCAATGAGGCGACAG 60.746 60.000 0.00 0.00 35.39 3.51
592 623 2.328989 CGGCCGCACTATGCATTG 59.671 61.111 14.67 5.32 45.36 2.82
625 656 2.019984 GGCAAGGGTCTGAAGCTATTG 58.980 52.381 0.00 0.00 0.00 1.90
627 658 1.065126 GTGGCAAGGGTCTGAAGCTAT 60.065 52.381 0.00 0.00 0.00 2.97
646 677 2.142357 TTGCTCACAGCGTCGCTAGT 62.142 55.000 21.25 16.91 46.26 2.57
654 685 3.092192 CTCCGCATTGCTCACAGCG 62.092 63.158 7.12 0.00 46.26 5.18
674 705 1.383456 CCAGACGAGGAGGAGCTCAG 61.383 65.000 17.19 1.73 31.08 3.35
694 725 1.134901 CTCCTCGAACTCGTCCGTG 59.865 63.158 0.00 0.00 40.80 4.94
695 726 1.297456 GACTCCTCGAACTCGTCCGT 61.297 60.000 0.00 0.00 40.80 4.69
701 732 1.137825 CCGCTGACTCCTCGAACTC 59.862 63.158 0.00 0.00 0.00 3.01
704 735 3.760035 GGCCGCTGACTCCTCGAA 61.760 66.667 0.00 0.00 0.00 3.71
719 750 0.817229 GATGACTGGGCTAAGCTGGC 60.817 60.000 3.63 3.63 0.00 4.85
738 769 5.410746 CAGATCCGATATCACCTCCAATTTG 59.589 44.000 3.12 0.00 0.00 2.32
739 770 5.555017 CAGATCCGATATCACCTCCAATTT 58.445 41.667 3.12 0.00 0.00 1.82
740 771 4.564406 GCAGATCCGATATCACCTCCAATT 60.564 45.833 3.12 0.00 0.00 2.32
768 799 3.083997 ACCCTCTCCGTCATGGCC 61.084 66.667 0.00 0.00 37.80 5.36
782 813 1.307866 TCCCCAATCTCTCCCACCC 60.308 63.158 0.00 0.00 0.00 4.61
795 826 1.937350 TCTCATACCTTCCTCTCCCCA 59.063 52.381 0.00 0.00 0.00 4.96
816 847 2.055042 CCTCTCCACTCCACTCCCG 61.055 68.421 0.00 0.00 0.00 5.14
827 858 0.253610 GAGTCCTCTCGACCTCTCCA 59.746 60.000 0.00 0.00 43.08 3.86
845 876 0.107831 CCAAACCCCACTCAACTCGA 59.892 55.000 0.00 0.00 0.00 4.04
851 882 2.477893 ATGGCCCAAACCCCACTCA 61.478 57.895 0.00 0.00 33.17 3.41
869 900 1.152943 TAACCAGCCGCCACAAACA 60.153 52.632 0.00 0.00 0.00 2.83
874 905 2.746277 CACCTAACCAGCCGCCAC 60.746 66.667 0.00 0.00 0.00 5.01
879 910 1.338107 AAAAAGCCACCTAACCAGCC 58.662 50.000 0.00 0.00 0.00 4.85
928 959 4.462280 CCCGTAGCCGTCCCAACC 62.462 72.222 0.00 0.00 0.00 3.77
949 980 2.288457 CGATTAGAGCATCCACGACCAT 60.288 50.000 0.00 0.00 33.66 3.55
952 983 1.772182 CCGATTAGAGCATCCACGAC 58.228 55.000 0.00 0.00 33.66 4.34
955 986 1.802960 CATGCCGATTAGAGCATCCAC 59.197 52.381 0.00 0.00 46.58 4.02
957 988 0.801251 GCATGCCGATTAGAGCATCC 59.199 55.000 6.36 0.00 46.58 3.51
1053 1086 2.162681 AGTTGTTTGGTAGCAGATGGC 58.837 47.619 0.00 0.00 45.30 4.40
1131 1243 2.849880 AGTGAATTGTGTGTGTGTGC 57.150 45.000 0.00 0.00 0.00 4.57
1254 1412 3.457625 CTCCGCTGCCTCCATCAGG 62.458 68.421 0.00 0.00 46.82 3.86
1255 1413 2.108566 CTCCGCTGCCTCCATCAG 59.891 66.667 0.00 0.00 34.79 2.90
1297 1458 2.492090 GATGAGCTCTCGCACGGT 59.508 61.111 16.19 0.00 39.10 4.83
1362 1523 1.590259 GAGGATCTTGACGCGCTCC 60.590 63.158 5.73 3.23 0.00 4.70
1413 1574 2.762887 CTCTGAGAATGTAGTGCCTGGA 59.237 50.000 0.00 0.00 0.00 3.86
1417 1578 2.480416 CGTCCTCTGAGAATGTAGTGCC 60.480 54.545 6.17 0.00 0.00 5.01
1418 1579 2.803451 CGTCCTCTGAGAATGTAGTGC 58.197 52.381 6.17 0.00 0.00 4.40
1419 1580 2.792890 CGCGTCCTCTGAGAATGTAGTG 60.793 54.545 6.17 0.00 0.00 2.74
1425 1609 0.179124 GCTTCGCGTCCTCTGAGAAT 60.179 55.000 5.77 0.00 0.00 2.40
1445 1629 4.867047 CAGCAATCAAGAGTTACTGACGAT 59.133 41.667 0.00 0.00 0.00 3.73
1584 2446 1.006639 ACTCCCAGAGACCTCTTCCTC 59.993 57.143 0.00 0.00 37.98 3.71
1637 2500 5.880332 AGCATAAATGTCAATAACTCGGTGT 59.120 36.000 0.00 0.00 0.00 4.16
1718 3007 9.931210 CTAGTCTGAAACTACGAACAAATTTTT 57.069 29.630 0.00 0.00 39.55 1.94
1732 3024 1.550976 CCGCCCTTCTAGTCTGAAACT 59.449 52.381 0.00 0.00 42.33 2.66
2012 3308 6.211515 CACTATGCAGCCAATATTTTCCTTC 58.788 40.000 0.00 0.00 0.00 3.46
2159 3463 8.632906 AAGACTTCTGATCAACAATTTCTCAT 57.367 30.769 0.00 0.00 0.00 2.90
2349 3659 5.907945 CCATGTGTACTATCTAGACGTTTCG 59.092 44.000 0.00 0.00 0.00 3.46
2399 3711 1.132640 GCGTTGCTGACCATTCGAC 59.867 57.895 0.00 0.00 0.00 4.20
2506 4576 9.562408 ACGTATCCATACCTATATCTACATCTG 57.438 37.037 0.00 0.00 0.00 2.90
2525 4613 7.198390 TGCTAGACTACATTTGTTACGTATCC 58.802 38.462 0.00 0.00 0.00 2.59
2737 4825 3.387962 TGTTCCTCCAGCTATTGATCCT 58.612 45.455 0.00 0.00 0.00 3.24
2824 4912 6.109156 TCTGCAGTTAAGGATACAAGAACA 57.891 37.500 14.67 0.00 41.41 3.18
3018 5139 2.717639 AGTGCTGAGTTGAACAGGTT 57.282 45.000 0.00 0.00 36.09 3.50
3052 5173 0.523519 GCACCTTTAACCTGCAGCTC 59.476 55.000 8.66 0.00 0.00 4.09
3159 5286 3.489391 GCCACGGTATAGGCCTTTT 57.511 52.632 12.58 0.84 45.18 2.27
3526 5656 7.559897 TCAAAATCTTCTTTAGAACAACCAGGT 59.440 33.333 0.00 0.00 36.22 4.00
3528 5658 9.403110 CATCAAAATCTTCTTTAGAACAACCAG 57.597 33.333 0.00 0.00 36.22 4.00
3641 5771 0.106519 ACAGTTGCTTCCAGCCTTGT 60.107 50.000 0.00 0.00 41.51 3.16
3647 5777 2.951642 TCCAGAAAACAGTTGCTTCCAG 59.048 45.455 0.00 0.00 0.00 3.86
3665 5795 9.213777 ACCTTCAAATAGTTGATAGATAGTCCA 57.786 33.333 6.42 0.00 43.29 4.02
3736 7305 5.875224 TGTCTACATTGGTCATCAGGAAAA 58.125 37.500 0.00 0.00 0.00 2.29
3775 7344 2.030363 TGACGACAAATGGGAATTGCAC 60.030 45.455 0.00 0.00 0.00 4.57
4047 7628 1.002134 ATGGCGCCAGTTGTAAGCT 60.002 52.632 35.36 11.90 0.00 3.74
4048 7629 1.137404 CATGGCGCCAGTTGTAAGC 59.863 57.895 35.36 0.00 0.00 3.09
4049 7630 0.881118 AACATGGCGCCAGTTGTAAG 59.119 50.000 35.36 18.74 0.00 2.34
4050 7631 0.595588 CAACATGGCGCCAGTTGTAA 59.404 50.000 37.07 19.35 38.20 2.41


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

AutoCloner maintained by Alex Coulton.