Multiple sequence alignment - TraesCS1B01G271700

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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 TraesCS1B01G271700 chr1B 100.000 7057 0 0 1 7057 477387856 477394912 0.000000e+00 13032.0
1 TraesCS1B01G271700 chr1B 86.833 562 62 4 55 607 2922090 2921532 1.010000e-172 617.0
2 TraesCS1B01G271700 chr1B 84.401 609 85 2 8 607 298255310 298254703 2.190000e-164 590.0
3 TraesCS1B01G271700 chr1B 77.977 613 117 10 8 607 583848825 583849432 1.120000e-97 368.0
4 TraesCS1B01G271700 chr1B 78.982 452 70 19 3399 3846 477402807 477403237 1.160000e-72 285.0
5 TraesCS1B01G271700 chr1B 78.163 490 72 19 3970 4455 681455727 681456185 5.390000e-71 279.0
6 TraesCS1B01G271700 chr1B 77.009 448 73 23 4512 4937 477404021 477404460 5.510000e-56 230.0
7 TraesCS1B01G271700 chr1B 77.419 372 56 21 4088 4455 456155204 456154857 5.580000e-46 196.0
8 TraesCS1B01G271700 chr1B 94.231 104 4 2 996 1099 477399763 477399864 2.640000e-34 158.0
9 TraesCS1B01G271700 chr1B 77.536 276 42 15 4679 4937 477416054 477416326 1.590000e-31 148.0
10 TraesCS1B01G271700 chr1B 84.496 129 18 2 3973 4100 456155497 456155370 7.430000e-25 126.0
11 TraesCS1B01G271700 chr1B 89.474 76 8 0 1764 1839 477402240 477402315 5.830000e-16 97.1
12 TraesCS1B01G271700 chr1A 94.761 3741 146 26 2761 6467 455024589 455028313 0.000000e+00 5777.0
13 TraesCS1B01G271700 chr1A 91.378 2134 97 38 607 2703 455022494 455024577 0.000000e+00 2841.0
14 TraesCS1B01G271700 chr1A 95.964 446 15 1 6614 7056 455028313 455028758 0.000000e+00 721.0
15 TraesCS1B01G271700 chr1A 84.337 581 61 21 5143 5708 557971821 557971256 6.230000e-150 542.0
16 TraesCS1B01G271700 chr1A 82.069 435 58 15 5280 5707 520607227 520607648 3.130000e-93 353.0
17 TraesCS1B01G271700 chr1A 76.923 507 104 10 110 605 117871957 117872461 6.970000e-70 276.0
18 TraesCS1B01G271700 chr1A 78.587 453 70 19 3399 3846 455034703 455035133 2.510000e-69 274.0
19 TraesCS1B01G271700 chr1A 76.991 452 70 24 4512 4937 455035911 455036354 1.980000e-55 228.0
20 TraesCS1B01G271700 chr1A 76.882 372 49 17 4085 4455 426235019 426235354 7.280000e-40 176.0
21 TraesCS1B01G271700 chr1A 95.192 104 3 2 996 1099 455031219 455031320 5.660000e-36 163.0
22 TraesCS1B01G271700 chr1A 84.677 124 18 1 3970 4093 426234569 426234691 9.610000e-24 122.0
23 TraesCS1B01G271700 chr1A 89.474 76 8 0 1764 1839 455034135 455034210 5.830000e-16 97.1
24 TraesCS1B01G271700 chr1D 95.441 3312 106 21 637 3918 355164430 355167726 0.000000e+00 5238.0
25 TraesCS1B01G271700 chr1D 95.683 3150 120 11 3916 7057 355167807 355170948 0.000000e+00 5049.0
26 TraesCS1B01G271700 chr1D 78.587 453 70 19 3399 3846 355177874 355178304 2.510000e-69 274.0
27 TraesCS1B01G271700 chr1D 77.655 452 66 25 4512 4937 355179084 355179526 7.070000e-60 243.0
28 TraesCS1B01G271700 chr1D 95.192 104 3 2 996 1099 355174418 355174519 5.660000e-36 163.0
29 TraesCS1B01G271700 chr1D 89.474 76 8 0 1764 1839 355177317 355177392 5.830000e-16 97.1
30 TraesCS1B01G271700 chr6B 92.869 617 35 1 1 608 471679632 471680248 0.000000e+00 887.0
31 TraesCS1B01G271700 chr5B 85.691 615 79 3 1 606 489567474 489568088 2.150000e-179 640.0
32 TraesCS1B01G271700 chr5B 82.483 451 70 1 166 607 620917800 620917350 3.090000e-103 387.0
33 TraesCS1B01G271700 chr5B 92.857 98 7 0 994 1091 47108773 47108870 7.380000e-30 143.0
34 TraesCS1B01G271700 chr5B 82.955 88 15 0 2038 2125 47109701 47109788 5.870000e-11 80.5
35 TraesCS1B01G271700 chr7A 86.596 567 59 10 5143 5708 30406760 30407310 1.680000e-170 610.0
36 TraesCS1B01G271700 chr7A 82.087 575 74 17 5143 5703 133672210 133672769 1.390000e-126 464.0
37 TraesCS1B01G271700 chr5D 83.184 446 48 17 5280 5707 22837482 22837046 3.990000e-102 383.0
38 TraesCS1B01G271700 chr5D 86.589 343 37 6 5143 5484 505897600 505897934 3.110000e-98 370.0
39 TraesCS1B01G271700 chr5D 93.878 98 6 0 994 1091 46040055 46040152 1.590000e-31 148.0
40 TraesCS1B01G271700 chr5D 81.915 94 17 0 2032 2125 46040847 46040940 5.870000e-11 80.5
41 TraesCS1B01G271700 chr4B 83.879 397 45 7 3973 4359 97561292 97560905 1.870000e-95 361.0
42 TraesCS1B01G271700 chr4B 81.674 442 56 17 5280 5707 588067958 588067528 1.880000e-90 344.0
43 TraesCS1B01G271700 chr4B 76.861 618 117 14 8 607 584545941 584546550 6.830000e-85 326.0
44 TraesCS1B01G271700 chr4B 78.980 490 55 23 3970 4455 527743975 527744420 2.490000e-74 291.0
45 TraesCS1B01G271700 chr4B 78.234 487 58 23 3973 4455 438148208 438147766 1.170000e-67 268.0
46 TraesCS1B01G271700 chr4B 78.249 377 44 19 4081 4455 69295607 69295267 2.580000e-49 207.0
47 TraesCS1B01G271700 chr4B 92.857 70 4 1 5139 5208 588068043 588067975 4.500000e-17 100.0
48 TraesCS1B01G271700 chr2A 85.797 345 39 6 5143 5484 752418616 752418279 2.420000e-94 357.0
49 TraesCS1B01G271700 chr2A 84.483 348 40 5 3973 4319 14945613 14945279 1.470000e-86 331.0
50 TraesCS1B01G271700 chr2A 76.803 513 105 8 107 607 41061836 41062346 6.970000e-70 276.0
51 TraesCS1B01G271700 chr2A 82.474 194 29 3 3973 4165 14939099 14938910 1.570000e-36 165.0
52 TraesCS1B01G271700 chr2A 85.714 133 18 1 4323 4455 14938813 14938682 9.550000e-29 139.0
53 TraesCS1B01G271700 chrUn 77.124 612 127 4 7 607 143851321 143850712 6.780000e-90 342.0
54 TraesCS1B01G271700 chr3B 77.543 521 105 6 97 607 737582847 737583365 3.200000e-78 303.0
55 TraesCS1B01G271700 chr7B 81.522 368 54 6 3987 4351 716486127 716485771 2.490000e-74 291.0
56 TraesCS1B01G271700 chr7B 75.203 617 143 2 1 608 619618786 619618171 4.170000e-72 283.0
57 TraesCS1B01G271700 chr6D 78.645 487 64 22 3973 4455 472098473 472098023 3.220000e-73 287.0
58 TraesCS1B01G271700 chr6D 74.533 428 95 8 191 607 6739510 6739086 2.620000e-39 174.0
59 TraesCS1B01G271700 chr6D 74.186 430 96 9 191 608 456372524 456372098 1.570000e-36 165.0
60 TraesCS1B01G271700 chr7D 93.960 149 9 0 6466 6614 102303010 102303158 7.120000e-55 226.0
61 TraesCS1B01G271700 chr3D 91.892 148 12 0 6467 6614 390069058 390068911 2.580000e-49 207.0
62 TraesCS1B01G271700 chr4A 89.189 148 13 1 6467 6614 3445459 3445603 1.560000e-41 182.0
63 TraesCS1B01G271700 chr6A 90.517 116 11 0 493 608 602998137 602998022 3.410000e-33 154.0
64 TraesCS1B01G271700 chr5A 92.857 98 7 0 994 1091 37055876 37055973 7.380000e-30 143.0
65 TraesCS1B01G271700 chr5A 81.915 94 17 0 2032 2125 37056629 37056722 5.870000e-11 80.5
66 TraesCS1B01G271700 chr2D 93.939 66 4 0 5143 5208 638314207 638314272 4.500000e-17 100.0


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 TraesCS1B01G271700 chr1B 477387856 477394912 7056 False 13032.000000 13032 100.000000 1 7057 1 chr1B.!!$F1 7056
1 TraesCS1B01G271700 chr1B 2921532 2922090 558 True 617.000000 617 86.833000 55 607 1 chr1B.!!$R1 552
2 TraesCS1B01G271700 chr1B 298254703 298255310 607 True 590.000000 590 84.401000 8 607 1 chr1B.!!$R2 599
3 TraesCS1B01G271700 chr1B 583848825 583849432 607 False 368.000000 368 77.977000 8 607 1 chr1B.!!$F3 599
4 TraesCS1B01G271700 chr1A 455022494 455036354 13860 False 1443.014286 5777 88.906714 607 7056 7 chr1A.!!$F4 6449
5 TraesCS1B01G271700 chr1A 557971256 557971821 565 True 542.000000 542 84.337000 5143 5708 1 chr1A.!!$R1 565
6 TraesCS1B01G271700 chr1A 117871957 117872461 504 False 276.000000 276 76.923000 110 605 1 chr1A.!!$F1 495
7 TraesCS1B01G271700 chr1D 355164430 355179526 15096 False 1844.016667 5238 88.672000 637 7057 6 chr1D.!!$F1 6420
8 TraesCS1B01G271700 chr6B 471679632 471680248 616 False 887.000000 887 92.869000 1 608 1 chr6B.!!$F1 607
9 TraesCS1B01G271700 chr5B 489567474 489568088 614 False 640.000000 640 85.691000 1 606 1 chr5B.!!$F1 605
10 TraesCS1B01G271700 chr7A 30406760 30407310 550 False 610.000000 610 86.596000 5143 5708 1 chr7A.!!$F1 565
11 TraesCS1B01G271700 chr7A 133672210 133672769 559 False 464.000000 464 82.087000 5143 5703 1 chr7A.!!$F2 560
12 TraesCS1B01G271700 chr4B 584545941 584546550 609 False 326.000000 326 76.861000 8 607 1 chr4B.!!$F2 599
13 TraesCS1B01G271700 chr4B 588067528 588068043 515 True 222.000000 344 87.265500 5139 5707 2 chr4B.!!$R4 568
14 TraesCS1B01G271700 chr2A 41061836 41062346 510 False 276.000000 276 76.803000 107 607 1 chr2A.!!$F1 500
15 TraesCS1B01G271700 chrUn 143850712 143851321 609 True 342.000000 342 77.124000 7 607 1 chrUn.!!$R1 600
16 TraesCS1B01G271700 chr3B 737582847 737583365 518 False 303.000000 303 77.543000 97 607 1 chr3B.!!$F1 510
17 TraesCS1B01G271700 chr7B 619618171 619618786 615 True 283.000000 283 75.203000 1 608 1 chr7B.!!$R1 607

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
419 420 0.386113 GCACCACTAGGGAGATCGTC 59.614 60.000 0.00 0.00 41.15 4.20 F
1117 1160 1.152694 TCCCCCGTACCGATCGATT 60.153 57.895 18.66 5.49 0.00 3.34 F
1528 1571 0.107703 TCCATGCTTGTAAGGCGAGG 60.108 55.000 0.00 0.00 0.00 4.63 F
2139 2195 0.251341 AAGGTGTGACATGCCCCTTC 60.251 55.000 0.00 0.00 29.62 3.46 F
2560 2624 0.763652 CCTGGATCTGGTGAGGATGG 59.236 60.000 0.00 0.00 0.00 3.51 F
3544 3610 0.254747 TTAGCTTACCCGCATGCCTT 59.745 50.000 13.15 0.00 0.00 4.35 F
4289 4442 0.392193 CGCTTGCTCTTCACAGGGAT 60.392 55.000 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1333 0.532115 AAAACAATCGCCCATCTGCC 59.468 50.000 0.00 0.0 0.00 4.85 R
2516 2580 0.403271 AATGTCTCAAGGCTGCAGGT 59.597 50.000 17.12 0.0 0.00 4.00 R
2884 2949 1.035139 AGATTTGCGGATCAATGGGC 58.965 50.000 0.00 0.0 34.12 5.36 R
3540 3606 4.006319 GCCATCCATACAAGATAGAAGGC 58.994 47.826 0.00 0.0 0.00 4.35 R
4171 4324 1.537202 CTTGCAGTGCAGGAAGTAACC 59.463 52.381 21.88 0.0 40.61 2.85 R
5450 5611 1.001633 GGCTTTAGTTCGGACTGTGGA 59.998 52.381 6.62 0.0 36.60 4.02 R
6154 6388 0.175073 CCTGGAACCCTACGCAGTAC 59.825 60.000 0.00 0.0 45.11 2.73 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
24 25 6.493116 AGTCCGTTATCTACATACAACTTCG 58.507 40.000 0.00 0.00 0.00 3.79
45 46 4.219070 TCGTCTTAAAGTTCATTCGGGAGA 59.781 41.667 0.00 0.00 0.00 3.71
120 121 1.302907 ACAGCCAAGATGGATCCCTT 58.697 50.000 9.90 3.11 40.96 3.95
155 156 1.927710 GCAAAAGTACGAGTCGACGGT 60.928 52.381 21.50 17.29 37.61 4.83
156 157 1.974680 CAAAAGTACGAGTCGACGGTC 59.025 52.381 21.50 6.65 37.61 4.79
189 190 5.952347 AGAGATGGTAATTTTGGTTCCTTCC 59.048 40.000 0.00 0.00 0.00 3.46
248 249 4.446051 GGCGCTTCAGTTATCAAGATCTAC 59.554 45.833 7.64 0.00 0.00 2.59
262 263 2.105134 AGATCTACGGAGTGACGGATCT 59.895 50.000 0.00 0.00 45.73 2.75
293 294 0.884704 AAGCTTTGGCGTGTCGTGAT 60.885 50.000 0.00 0.00 44.37 3.06
320 321 0.984230 CCCTTGCTACTGACCTGGAA 59.016 55.000 0.00 0.00 0.00 3.53
419 420 0.386113 GCACCACTAGGGAGATCGTC 59.614 60.000 0.00 0.00 41.15 4.20
507 517 2.192664 TAGCCATGCTTTCGGTTTGA 57.807 45.000 0.00 0.00 40.44 2.69
553 564 7.470841 GCTGTTAAACCCTCCAAACATTTCTTA 60.471 37.037 0.00 0.00 31.88 2.10
620 631 2.632643 AAAAACGGGCGTTACCTCC 58.367 52.632 0.00 0.00 37.35 4.30
1094 1133 2.348998 CGGCCTCAAGGTGAAGCT 59.651 61.111 0.00 0.00 34.40 3.74
1117 1160 1.152694 TCCCCCGTACCGATCGATT 60.153 57.895 18.66 5.49 0.00 3.34
1264 1307 2.513897 GGGCGATGGTACTGGTGC 60.514 66.667 0.00 0.00 0.00 5.01
1290 1333 2.029666 GATCCGGACCTGATGCCG 59.970 66.667 6.12 0.00 46.80 5.69
1323 1366 3.910490 TTTTGGCTGCCACACCGC 61.910 61.111 23.30 0.00 30.78 5.68
1366 1409 2.225727 GGAACTGTTGCGAAACTTAGGG 59.774 50.000 8.00 0.00 0.00 3.53
1450 1493 3.071479 TGAATCGGAAGGTAAACTGCAC 58.929 45.455 0.00 0.00 0.00 4.57
1526 1569 1.209261 TGATCCATGCTTGTAAGGCGA 59.791 47.619 0.00 0.00 0.00 5.54
1527 1570 1.869767 GATCCATGCTTGTAAGGCGAG 59.130 52.381 0.00 0.00 0.00 5.03
1528 1571 0.107703 TCCATGCTTGTAAGGCGAGG 60.108 55.000 0.00 0.00 0.00 4.63
1544 1588 2.432444 CGAGGGGTATGAGTTTGCAAA 58.568 47.619 8.05 8.05 0.00 3.68
1665 1709 7.867921 TGGTGTATTAATTGGGTGAGATACTT 58.132 34.615 0.00 0.00 0.00 2.24
1749 1793 8.673711 TGGTGATATTGCTAAATGTGTTCTAAC 58.326 33.333 0.00 0.00 0.00 2.34
1750 1794 8.893727 GGTGATATTGCTAAATGTGTTCTAACT 58.106 33.333 0.00 0.00 0.00 2.24
1755 1799 7.692908 TTGCTAAATGTGTTCTAACTTTTGC 57.307 32.000 0.00 1.27 31.89 3.68
1855 1911 5.337089 GGCAAGCAGCTATATGTCTCTATCA 60.337 44.000 0.00 0.00 44.79 2.15
1963 2019 5.405269 ACAAAAGTCACTCAGTTTGTTTTGC 59.595 36.000 12.32 0.00 40.37 3.68
2033 2089 9.131791 ACCTCTTTAATGTTTGTCTATGTTGTT 57.868 29.630 0.00 0.00 0.00 2.83
2139 2195 0.251341 AAGGTGTGACATGCCCCTTC 60.251 55.000 0.00 0.00 29.62 3.46
2274 2330 8.637986 TGATTTAGCAATAAGGAAAACAGTTGT 58.362 29.630 0.00 0.00 0.00 3.32
2275 2331 9.129209 GATTTAGCAATAAGGAAAACAGTTGTC 57.871 33.333 0.00 0.00 0.00 3.18
2363 2419 4.738252 TCGGTTCGAAATAGATGACAATCG 59.262 41.667 0.00 0.00 33.47 3.34
2465 2529 4.889112 CCAGCTGCCATCCGCCAT 62.889 66.667 8.66 0.00 36.24 4.40
2559 2623 1.504912 ACCTGGATCTGGTGAGGATG 58.495 55.000 0.00 0.00 34.44 3.51
2560 2624 0.763652 CCTGGATCTGGTGAGGATGG 59.236 60.000 0.00 0.00 0.00 3.51
2561 2625 1.693726 CCTGGATCTGGTGAGGATGGA 60.694 57.143 0.00 0.00 0.00 3.41
2592 2656 7.067129 GGTTGGAGACTTTCTTTAACCATATCC 59.933 40.741 13.47 0.00 39.97 2.59
2609 2673 8.337118 ACCATATCCTCTTTTAGATGGAAAGA 57.663 34.615 5.74 0.00 39.95 2.52
2618 2682 3.100862 GATGGAAAGACGGCGCTGC 62.101 63.158 18.15 9.47 0.00 5.25
2621 2685 1.521681 GGAAAGACGGCGCTGCTAT 60.522 57.895 18.15 0.00 0.00 2.97
2671 2735 7.095270 ACGGTACTATGTTTCTTTAGAAGGTG 58.905 38.462 0.00 0.00 35.21 4.00
2884 2949 3.112580 CCAACGTTTTGTAAGTGGCAAG 58.887 45.455 0.00 0.00 0.00 4.01
2898 2963 2.417257 GCAAGCCCATTGATCCGCA 61.417 57.895 0.00 0.00 41.83 5.69
3426 3492 2.294233 CCAGTTTATGATGGCGAATGGG 59.706 50.000 0.00 0.00 0.00 4.00
3540 3606 1.378531 TGCTTTAGCTTACCCGCATG 58.621 50.000 0.00 0.00 42.66 4.06
3544 3610 0.254747 TTAGCTTACCCGCATGCCTT 59.745 50.000 13.15 0.00 0.00 4.35
3837 3904 8.105829 ACAAGGATGACAACTAGAGAATTGATT 58.894 33.333 0.00 0.00 0.00 2.57
3961 4113 8.347035 GTGGCTGAAATGTACAAAAACTAGTTA 58.653 33.333 8.92 0.00 0.00 2.24
3971 4123 5.067954 ACAAAAACTAGTTATGTCCGCCTT 58.932 37.500 17.00 0.51 0.00 4.35
4038 4190 7.701539 TCTTCTGCATTGCCTTTATTCTTAA 57.298 32.000 6.12 0.00 0.00 1.85
4145 4298 6.760298 CAGTATCATGTACTGATCTGCACTTT 59.240 38.462 21.31 0.00 45.69 2.66
4171 4324 7.640209 TCCATTAAAAGTGGAAGGATATCCCTG 60.640 40.741 18.56 0.00 42.56 4.45
4244 4397 2.480419 CAGGAAACACGGATTGAGTGAC 59.520 50.000 3.20 0.00 41.83 3.67
4289 4442 0.392193 CGCTTGCTCTTCACAGGGAT 60.392 55.000 0.00 0.00 0.00 3.85
4319 4472 1.063174 CTAAGCGAGCCAGCAATTGAC 59.937 52.381 10.34 0.30 40.15 3.18
4341 4494 9.997482 TTGACACTGTTAAAAGAATGAAAGTAC 57.003 29.630 0.00 0.00 0.00 2.73
4458 4612 7.171337 CCCTTGTTTATTTGTTCTTTGGTGATG 59.829 37.037 0.00 0.00 0.00 3.07
4511 4665 3.853475 AGCATAATGAAACTTTGCTGCC 58.147 40.909 0.00 0.00 41.79 4.85
4810 4964 5.718724 TTATGCCATTGTGTGTGAATTCA 57.281 34.783 3.38 3.38 0.00 2.57
4820 4974 5.837437 TGTGTGTGAATTCATTTACCCAAC 58.163 37.500 12.12 6.87 0.00 3.77
4821 4975 5.596361 TGTGTGTGAATTCATTTACCCAACT 59.404 36.000 12.12 0.00 0.00 3.16
5098 5253 7.327975 TGCATACTGTTTTGCTACATACTAGT 58.672 34.615 14.03 0.00 39.60 2.57
5283 5439 4.555262 CTCACTTTCTGTCTCAGTTCTCC 58.445 47.826 0.00 0.00 32.61 3.71
5432 5592 2.728690 TCATTGCATTTGTGTCTGCC 57.271 45.000 0.00 0.00 37.59 4.85
5438 5598 0.453282 CATTTGTGTCTGCCGAAGCG 60.453 55.000 0.00 0.00 44.31 4.68
5510 5671 7.214467 TGGTCCAGTAGATGAATTGTTTTTC 57.786 36.000 0.00 0.00 0.00 2.29
5795 6025 5.124936 GGTGGGCGATTATTAGTTTCTGTTT 59.875 40.000 0.00 0.00 0.00 2.83
5812 6042 6.938698 TCTGTTTATGTGGGGTAAACTCTA 57.061 37.500 9.36 0.00 40.78 2.43
5838 6068 3.433306 TCACAATTTGTTCCCGAGGAT 57.567 42.857 0.00 0.00 0.00 3.24
5854 6084 5.180117 CCCGAGGATTGCTGTCTATATTTTG 59.820 44.000 0.00 0.00 0.00 2.44
5937 6167 5.244626 AGCTCTTGTATCAGCAATTTTGGTT 59.755 36.000 0.00 0.00 38.18 3.67
5943 6173 7.156876 TGTATCAGCAATTTTGGTTCCTAAG 57.843 36.000 0.00 0.00 36.65 2.18
5945 6175 5.964958 TCAGCAATTTTGGTTCCTAAGAG 57.035 39.130 0.00 0.00 36.65 2.85
5991 6221 4.938226 AGCTGTTTTGGTATAACTCTCTGC 59.062 41.667 0.00 0.00 0.00 4.26
6067 6300 6.681865 GCAGAAGAGTACTAGATCTCAAACCC 60.682 46.154 0.00 0.00 33.63 4.11
6085 6318 3.565307 ACCCAGCATTTTCTTCAAGACA 58.435 40.909 0.00 0.00 0.00 3.41
6086 6319 4.154942 ACCCAGCATTTTCTTCAAGACAT 58.845 39.130 0.00 0.00 0.00 3.06
6087 6320 5.324409 ACCCAGCATTTTCTTCAAGACATA 58.676 37.500 0.00 0.00 0.00 2.29
6088 6321 5.183904 ACCCAGCATTTTCTTCAAGACATAC 59.816 40.000 0.00 0.00 0.00 2.39
6089 6322 5.416952 CCCAGCATTTTCTTCAAGACATACT 59.583 40.000 0.00 0.00 0.00 2.12
6091 6324 7.025963 CCAGCATTTTCTTCAAGACATACTTC 58.974 38.462 0.00 0.00 36.61 3.01
6092 6325 7.025963 CAGCATTTTCTTCAAGACATACTTCC 58.974 38.462 0.00 0.00 36.61 3.46
6093 6326 6.944862 AGCATTTTCTTCAAGACATACTTCCT 59.055 34.615 0.00 0.00 36.61 3.36
6094 6327 7.025963 GCATTTTCTTCAAGACATACTTCCTG 58.974 38.462 0.00 0.00 36.61 3.86
6096 6329 6.433847 TTTCTTCAAGACATACTTCCTGGA 57.566 37.500 0.00 0.00 36.61 3.86
6097 6330 5.667539 TCTTCAAGACATACTTCCTGGAG 57.332 43.478 0.00 0.00 36.61 3.86
6098 6331 4.467795 TCTTCAAGACATACTTCCTGGAGG 59.532 45.833 3.99 3.99 36.61 4.30
6099 6332 4.061131 TCAAGACATACTTCCTGGAGGA 57.939 45.455 13.32 0.00 43.73 3.71
6100 6333 3.769844 TCAAGACATACTTCCTGGAGGAC 59.230 47.826 13.32 0.00 45.39 3.85
6126 6360 0.902531 CACCACCGGAATCCTACTGT 59.097 55.000 9.46 0.00 0.00 3.55
6127 6361 0.902531 ACCACCGGAATCCTACTGTG 59.097 55.000 9.46 0.00 0.00 3.66
6128 6362 0.902531 CCACCGGAATCCTACTGTGT 59.097 55.000 9.46 0.00 0.00 3.72
6154 6388 2.023771 ACGTGTGACATCAGCTGCG 61.024 57.895 9.47 6.70 0.00 5.18
6169 6403 4.083746 GCGTACTGCGTAGGGTTC 57.916 61.111 5.26 0.00 43.66 3.62
6227 6479 1.856629 ATCTTTGGAATGGTGCTGGG 58.143 50.000 0.00 0.00 0.00 4.45
6302 6554 7.936496 TCATAAAGATGGCTTTGACATGTTA 57.064 32.000 0.00 0.00 43.84 2.41
6363 6615 4.006989 TGGTGTCTTGGATGTATTTTCCG 58.993 43.478 0.00 0.00 35.94 4.30
6366 6618 5.048294 GGTGTCTTGGATGTATTTTCCGTTT 60.048 40.000 0.00 0.00 35.94 3.60
6375 6627 5.520022 TGTATTTTCCGTTTCGAGTAAGC 57.480 39.130 0.00 0.00 0.00 3.09
6379 6631 2.631418 TCCGTTTCGAGTAAGCTCAG 57.369 50.000 0.00 0.00 41.71 3.35
6394 6646 4.749245 AGCTCAGTGTGGTTTATTTTCG 57.251 40.909 0.00 0.00 0.00 3.46
6399 6651 3.662186 CAGTGTGGTTTATTTTCGTTCGC 59.338 43.478 0.00 0.00 0.00 4.70
6453 6705 6.771188 AATGTTACGTGAGAAACAGAGAAG 57.229 37.500 7.60 0.00 38.87 2.85
6466 6718 2.509964 ACAGAGAAGGTGGGTTTGAAGT 59.490 45.455 0.00 0.00 0.00 3.01
6492 6744 4.643387 AAAGCGGCGCCCTGAACT 62.643 61.111 30.40 4.66 0.00 3.01
6520 6772 5.521010 CCGCTCCGTATACAAAATGAGTAAA 59.479 40.000 3.32 0.00 0.00 2.01
6590 6842 4.269183 TGATTGATTTTGCGGGACTATGT 58.731 39.130 0.00 0.00 0.00 2.29
6629 6882 6.071391 GCATCCCTATTTGAACCAAAGAAAGA 60.071 38.462 0.00 0.00 36.76 2.52
6672 6925 8.886719 TGTTTGATTTATTTGCAACAATTGTCA 58.113 25.926 12.39 3.52 0.00 3.58
6809 7065 4.405116 AATGTGTGTTTCCTTGCAATGT 57.595 36.364 0.00 0.00 0.00 2.71
6813 7069 3.735746 GTGTGTTTCCTTGCAATGTAAGC 59.264 43.478 5.53 0.00 0.00 3.09
6822 7078 4.379394 CCTTGCAATGTAAGCGTGTTGTAT 60.379 41.667 5.53 0.00 33.85 2.29
6825 7081 5.524284 TGCAATGTAAGCGTGTTGTATTTT 58.476 33.333 0.00 0.00 33.85 1.82
6829 7085 5.600908 TGTAAGCGTGTTGTATTTTCTCC 57.399 39.130 0.00 0.00 0.00 3.71
6883 7139 5.950544 AGGGAGTATATGTTTGCTGTGTA 57.049 39.130 0.00 0.00 0.00 2.90
6884 7140 6.308015 AGGGAGTATATGTTTGCTGTGTAA 57.692 37.500 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.232414 CGATCTCCCGAATGAACTTTAAGAC 59.768 44.000 0.00 0.00 0.00 3.01
45 46 0.976641 TTCAGGTTGCACTCCTCGAT 59.023 50.000 6.65 0.00 32.37 3.59
120 121 2.779755 TTTGCTATTCCTTCAGGCGA 57.220 45.000 0.00 0.00 34.44 5.54
155 156 5.677319 AATTACCATCTCTCGAAACAGGA 57.323 39.130 0.00 0.00 0.00 3.86
156 157 6.403636 CCAAAATTACCATCTCTCGAAACAGG 60.404 42.308 0.00 0.00 0.00 4.00
248 249 2.105128 GCCAGATCCGTCACTCCG 59.895 66.667 0.00 0.00 0.00 4.63
262 263 1.372582 CAAAGCTTCTAGCATCGCCA 58.627 50.000 0.00 0.00 45.56 5.69
320 321 1.732732 GCTACGAGAATGTGTGCGAGT 60.733 52.381 0.00 0.00 0.00 4.18
419 420 0.519175 CAAAGCTCGCCGATGTTTCG 60.519 55.000 0.00 0.00 45.08 3.46
507 517 1.832167 ACACATGGCGCCCAAAGTT 60.832 52.632 26.77 0.00 36.95 2.66
553 564 9.986157 ATTGCTCAATAATGTTCATAGGGATAT 57.014 29.630 0.00 0.00 0.00 1.63
625 636 2.738139 CGAGCACATGACGGCACA 60.738 61.111 0.00 0.00 0.00 4.57
704 724 7.906199 TTGAGATTGGGGTTTTTCTTTTAGA 57.094 32.000 0.00 0.00 0.00 2.10
706 726 9.594936 TCTATTGAGATTGGGGTTTTTCTTTTA 57.405 29.630 0.00 0.00 0.00 1.52
707 727 8.491045 TCTATTGAGATTGGGGTTTTTCTTTT 57.509 30.769 0.00 0.00 0.00 2.27
714 734 6.551227 GCCTTTATCTATTGAGATTGGGGTTT 59.449 38.462 0.00 0.00 39.56 3.27
717 737 5.885465 AGCCTTTATCTATTGAGATTGGGG 58.115 41.667 0.00 0.00 39.56 4.96
718 738 5.942826 GGAGCCTTTATCTATTGAGATTGGG 59.057 44.000 0.00 0.00 39.56 4.12
719 739 5.942826 GGGAGCCTTTATCTATTGAGATTGG 59.057 44.000 0.00 0.00 39.56 3.16
720 740 5.641209 CGGGAGCCTTTATCTATTGAGATTG 59.359 44.000 0.00 0.00 39.56 2.67
1105 1148 1.935933 AGGCACAAATCGATCGGTAC 58.064 50.000 16.41 0.00 0.00 3.34
1117 1160 1.529713 GGAACGGGGAAAGGCACAA 60.530 57.895 0.00 0.00 0.00 3.33
1290 1333 0.532115 AAAACAATCGCCCATCTGCC 59.468 50.000 0.00 0.00 0.00 4.85
1323 1366 1.669115 CACCAACAGCAGAGGGACG 60.669 63.158 0.00 0.00 0.00 4.79
1366 1409 2.047560 CCCCAAGTCGAACGACCC 60.048 66.667 20.97 0.68 45.59 4.46
1526 1569 2.171003 GCTTTGCAAACTCATACCCCT 58.829 47.619 8.05 0.00 0.00 4.79
1527 1570 2.094545 CAGCTTTGCAAACTCATACCCC 60.095 50.000 8.05 0.00 0.00 4.95
1528 1571 2.094545 CCAGCTTTGCAAACTCATACCC 60.095 50.000 8.05 0.00 0.00 3.69
1544 1588 2.194388 CTGACTGATGTGCCCCAGCT 62.194 60.000 0.00 0.00 40.80 4.24
1613 1657 4.870636 AGATCATGCTTCCAAAATGGGTA 58.129 39.130 0.00 0.00 38.32 3.69
1855 1911 8.747538 AGTTGTGATCTTAACTTAAACCACTT 57.252 30.769 8.70 0.00 33.59 3.16
2024 2080 6.577103 TCTTCCAGAGCTATCAACAACATAG 58.423 40.000 0.00 0.00 0.00 2.23
2033 2089 4.161189 CCTGAACTTCTTCCAGAGCTATCA 59.839 45.833 0.00 0.00 0.00 2.15
2036 2092 2.834549 CCCTGAACTTCTTCCAGAGCTA 59.165 50.000 0.00 0.00 0.00 3.32
2139 2195 8.843262 TGCATACAGAAAGATGGATTTAATCAG 58.157 33.333 7.29 0.00 0.00 2.90
2363 2419 2.773993 TCGGACACCAAATCCTTACC 57.226 50.000 0.00 0.00 33.70 2.85
2407 2471 9.578576 TCCCATCTTCTAATTTATCTTGATTGG 57.421 33.333 0.00 0.00 0.00 3.16
2465 2529 7.093068 TGTCACTGCTCCTAAGAATGGTATTAA 60.093 37.037 0.00 0.00 0.00 1.40
2516 2580 0.403271 AATGTCTCAAGGCTGCAGGT 59.597 50.000 17.12 0.00 0.00 4.00
2559 2623 1.279558 GAAAGTCTCCAACCCTCCTCC 59.720 57.143 0.00 0.00 0.00 4.30
2560 2624 2.261729 AGAAAGTCTCCAACCCTCCTC 58.738 52.381 0.00 0.00 0.00 3.71
2561 2625 2.424684 AGAAAGTCTCCAACCCTCCT 57.575 50.000 0.00 0.00 0.00 3.69
2592 2656 3.307242 CGCCGTCTTTCCATCTAAAAGAG 59.693 47.826 0.00 0.00 41.94 2.85
2733 2798 4.763793 AGAAGGAGAAAACATGACACATGG 59.236 41.667 14.70 0.00 0.00 3.66
2868 2933 1.410882 TGGGCTTGCCACTTACAAAAC 59.589 47.619 14.04 0.00 0.00 2.43
2872 2937 1.202989 TCAATGGGCTTGCCACTTACA 60.203 47.619 14.04 2.10 34.66 2.41
2884 2949 1.035139 AGATTTGCGGATCAATGGGC 58.965 50.000 0.00 0.00 34.12 5.36
2898 2963 7.309805 GCTTTTAGAACCATGGTTACCAGATTT 60.310 37.037 29.89 4.68 36.75 2.17
3024 3089 4.252971 TGACAGTTTGACACCTACTAGC 57.747 45.455 0.00 0.00 0.00 3.42
3127 3192 5.652994 ATACAAAGGAGCCGCATTAAAAA 57.347 34.783 0.00 0.00 0.00 1.94
3426 3492 5.118817 GTGAATGAGAGTACGAACCAAAGTC 59.881 44.000 0.00 0.00 0.00 3.01
3465 3531 7.148120 CCATCAACAGCTTTGAAAGACAGATAT 60.148 37.037 9.48 0.00 31.55 1.63
3540 3606 4.006319 GCCATCCATACAAGATAGAAGGC 58.994 47.826 0.00 0.00 0.00 4.35
3544 3610 4.234550 AGGTGCCATCCATACAAGATAGA 58.765 43.478 0.00 0.00 0.00 1.98
3837 3904 6.447162 CCATAACAGATGAGATACTTACGCA 58.553 40.000 0.00 0.00 0.00 5.24
3961 4113 4.497291 TTCCTAACAATAAGGCGGACAT 57.503 40.909 0.00 0.00 33.84 3.06
3971 4123 9.461312 ACAAGCATGTATTCTTTCCTAACAATA 57.539 29.630 0.00 0.00 38.24 1.90
4145 4298 6.392842 AGGGATATCCTTCCACTTTTAATGGA 59.607 38.462 21.18 0.00 45.47 3.41
4171 4324 1.537202 CTTGCAGTGCAGGAAGTAACC 59.463 52.381 21.88 0.00 40.61 2.85
4244 4397 7.466455 GCATGGCCAATGAAATCTATAGTATCG 60.466 40.741 10.96 0.00 38.72 2.92
4319 4472 6.577427 GGCGTACTTTCATTCTTTTAACAGTG 59.423 38.462 0.00 0.00 0.00 3.66
4368 4522 9.593565 AGAAACCTTCCATCTTCTTAAGAAAAT 57.406 29.630 18.25 8.74 41.63 1.82
4384 4538 3.634910 TGTTAACAAGCCAGAAACCTTCC 59.365 43.478 5.64 0.00 0.00 3.46
4511 4665 3.318839 ACTCAGAATAGAGCTAGCAGCAG 59.681 47.826 18.83 2.82 45.56 4.24
4810 4964 4.524328 CCTGCAAAAGAGAGTTGGGTAAAT 59.476 41.667 0.00 0.00 0.00 1.40
4820 4974 5.835257 TCAAATTCAACCTGCAAAAGAGAG 58.165 37.500 0.00 0.00 0.00 3.20
4821 4975 5.850557 TCAAATTCAACCTGCAAAAGAGA 57.149 34.783 0.00 0.00 0.00 3.10
5098 5253 5.421056 ACAGAGTAAACGTCATGGGAGAATA 59.579 40.000 0.00 0.00 0.00 1.75
5432 5592 2.034685 TGGATTATCAGTCTCCGCTTCG 59.965 50.000 0.00 0.00 31.36 3.79
5450 5611 1.001633 GGCTTTAGTTCGGACTGTGGA 59.998 52.381 6.62 0.00 36.60 4.02
5510 5671 8.246871 ACTGGTTCATATCTGTCATACATATCG 58.753 37.037 0.00 0.00 0.00 2.92
5641 5867 2.575805 ACTCTGCAAAGAGGGAAAGG 57.424 50.000 7.77 0.00 40.08 3.11
5687 5917 8.709386 ACATATTAAGAACATCTGTCACAGTC 57.291 34.615 4.28 0.00 32.61 3.51
5795 6025 8.044908 GTGAATTCTTAGAGTTTACCCCACATA 58.955 37.037 7.05 0.00 0.00 2.29
5812 6042 5.278957 CCTCGGGAACAAATTGTGAATTCTT 60.279 40.000 7.05 0.00 0.00 2.52
5838 6068 8.935844 CACTAGTGAACAAAATATAGACAGCAA 58.064 33.333 18.45 0.00 0.00 3.91
5854 6084 5.069781 AGCCAATAGAGGATCACTAGTGAAC 59.930 44.000 28.43 24.73 43.58 3.18
5925 6155 7.233348 TGAAATCTCTTAGGAACCAAAATTGCT 59.767 33.333 0.00 0.00 34.29 3.91
5937 6167 7.523709 GCCACAAAAATGTGAAATCTCTTAGGA 60.524 37.037 10.37 0.00 42.02 2.94
5943 6173 5.531634 TCAGCCACAAAAATGTGAAATCTC 58.468 37.500 10.37 0.00 42.02 2.75
5945 6175 6.601741 TTTCAGCCACAAAAATGTGAAATC 57.398 33.333 10.37 0.00 42.02 2.17
5979 6209 5.921962 TGCAAGAAGAGCAGAGAGTTATA 57.078 39.130 0.00 0.00 37.02 0.98
6067 6300 7.025963 GGAAGTATGTCTTGAAGAAAATGCTG 58.974 38.462 9.42 0.00 36.40 4.41
6091 6324 1.592223 GTGTTCCTCGTCCTCCAGG 59.408 63.158 0.00 0.00 0.00 4.45
6092 6325 1.185618 TGGTGTTCCTCGTCCTCCAG 61.186 60.000 0.00 0.00 34.23 3.86
6093 6326 1.152419 TGGTGTTCCTCGTCCTCCA 60.152 57.895 0.00 0.00 34.23 3.86
6094 6327 1.292541 GTGGTGTTCCTCGTCCTCC 59.707 63.158 0.00 0.00 34.23 4.30
6096 6329 2.571216 CGGTGGTGTTCCTCGTCCT 61.571 63.158 0.00 0.00 34.23 3.85
6097 6330 2.048503 CGGTGGTGTTCCTCGTCC 60.049 66.667 0.00 0.00 34.23 4.79
6098 6331 2.048503 CCGGTGGTGTTCCTCGTC 60.049 66.667 0.00 0.00 32.57 4.20
6099 6332 1.477685 ATTCCGGTGGTGTTCCTCGT 61.478 55.000 0.00 0.00 32.57 4.18
6100 6333 0.739813 GATTCCGGTGGTGTTCCTCG 60.740 60.000 0.00 0.00 34.23 4.63
6137 6371 0.732538 TACGCAGCTGATGTCACACG 60.733 55.000 20.43 11.29 0.00 4.49
6154 6388 0.175073 CCTGGAACCCTACGCAGTAC 59.825 60.000 0.00 0.00 45.11 2.73
6185 6437 8.094548 AGATAATAATTTCGCATAGTGCTGGTA 58.905 33.333 0.10 0.00 42.25 3.25
6187 6439 7.369803 AGATAATAATTTCGCATAGTGCTGG 57.630 36.000 0.10 0.00 42.25 4.85
6212 6464 0.541764 GGAACCCAGCACCATTCCAA 60.542 55.000 5.28 0.00 40.38 3.53
6227 6479 7.605410 TCAATATGGAAGTTAACGAAGGAAC 57.395 36.000 0.00 0.00 0.00 3.62
6280 6532 8.752187 ACATTAACATGTCAAAGCCATCTTTAT 58.248 29.630 0.00 0.00 39.69 1.40
6284 6536 6.594788 AACATTAACATGTCAAAGCCATCT 57.405 33.333 0.00 0.00 43.34 2.90
6294 6546 5.118050 TCGACAAGACGAACATTAACATGTC 59.882 40.000 0.00 0.00 43.34 3.06
6295 6547 4.986034 TCGACAAGACGAACATTAACATGT 59.014 37.500 0.00 0.00 46.34 3.21
6302 6554 6.100004 AGAATACATCGACAAGACGAACATT 58.900 36.000 0.00 0.11 45.16 2.71
6363 6615 2.731976 CCACACTGAGCTTACTCGAAAC 59.268 50.000 0.00 0.00 46.69 2.78
6366 6618 1.617322 ACCACACTGAGCTTACTCGA 58.383 50.000 0.00 0.00 46.69 4.04
6375 6627 5.137403 CGAACGAAAATAAACCACACTGAG 58.863 41.667 0.00 0.00 0.00 3.35
6379 6631 3.880610 AGCGAACGAAAATAAACCACAC 58.119 40.909 0.00 0.00 0.00 3.82
6394 6646 4.398247 CATGCTTACTTTCTTGAGCGAAC 58.602 43.478 0.00 0.00 37.94 3.95
6399 6651 5.448768 CCATCTGCATGCTTACTTTCTTGAG 60.449 44.000 20.33 2.98 0.00 3.02
6453 6705 2.723273 CATCCCTACTTCAAACCCACC 58.277 52.381 0.00 0.00 0.00 4.61
6466 6718 2.513666 CGCCGCTTTGCATCCCTA 60.514 61.111 0.00 0.00 0.00 3.53
6490 6742 0.394762 TGTATACGGAGCGGGACAGT 60.395 55.000 0.00 0.00 0.00 3.55
6492 6744 1.184431 TTTGTATACGGAGCGGGACA 58.816 50.000 0.00 0.00 0.00 4.02
6497 6749 6.255020 ACTTTACTCATTTTGTATACGGAGCG 59.745 38.462 0.00 0.00 0.00 5.03
6520 6772 9.555727 TCTATCAAACAAAAGCTACAACTAACT 57.444 29.630 0.00 0.00 0.00 2.24
6687 6940 7.100458 AGTGCAATATTCCTTGTTACCAATC 57.900 36.000 0.00 0.00 0.00 2.67
6809 7065 4.558178 TCGGAGAAAATACAACACGCTTA 58.442 39.130 0.00 0.00 0.00 3.09
6813 7069 5.520288 AGATCATCGGAGAAAATACAACACG 59.480 40.000 0.00 0.00 43.58 4.49
6822 7078 5.080969 ACCGTTTAGATCATCGGAGAAAA 57.919 39.130 19.12 0.00 44.86 2.29
6825 7081 3.552875 AGACCGTTTAGATCATCGGAGA 58.447 45.455 19.12 0.00 44.86 3.71
6891 7147 2.289320 TGCAGCAACAACAAAAACCAGT 60.289 40.909 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.