Multiple sequence alignment - TraesCS3D01G038800

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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 TraesCS3D01G038800 chr3D 100.000 4675 0 0 1 4675 14417525 14412851 0.000000e+00 8634.0
1 TraesCS3D01G038800 chr3D 90.242 1568 123 14 917 2456 14407227 14405662 0.000000e+00 2021.0
2 TraesCS3D01G038800 chr3D 77.829 1290 212 43 1442 2697 9105585 9106834 0.000000e+00 730.0
3 TraesCS3D01G038800 chr3D 83.553 152 19 1 3385 3530 14393693 14393542 2.270000e-28 137.0
4 TraesCS3D01G038800 chr3D 80.702 171 17 11 2906 3070 9107974 9108134 8.220000e-23 119.0
5 TraesCS3D01G038800 chr3B 91.261 3330 226 30 1370 4675 21387423 21384135 0.000000e+00 4477.0
6 TraesCS3D01G038800 chr3B 84.803 1066 110 25 1411 2456 21346698 21345665 0.000000e+00 1024.0
7 TraesCS3D01G038800 chr3B 91.213 717 53 9 1 712 21388851 21388140 0.000000e+00 966.0
8 TraesCS3D01G038800 chr3B 89.875 642 48 5 816 1455 21388012 21387386 0.000000e+00 809.0
9 TraesCS3D01G038800 chr3B 90.942 552 38 6 829 1376 21347228 21346685 0.000000e+00 732.0
10 TraesCS3D01G038800 chr3B 78.745 1068 159 43 1517 2554 11232096 11233125 0.000000e+00 652.0
11 TraesCS3D01G038800 chr3B 81.967 793 100 20 2774 3530 21334666 21333881 2.370000e-177 632.0
12 TraesCS3D01G038800 chr3B 76.127 1198 221 41 1517 2689 11187193 11186036 6.790000e-158 568.0
13 TraesCS3D01G038800 chr3B 86.301 365 44 4 994 1358 11231516 11231874 4.390000e-105 392.0
14 TraesCS3D01G038800 chr3B 88.814 295 32 1 335 628 21347693 21347399 1.240000e-95 361.0
15 TraesCS3D01G038800 chr3B 97.500 40 1 0 2657 2696 11233169 11233208 8.390000e-08 69.4
16 TraesCS3D01G038800 chr3A 89.406 2105 176 23 826 2906 22247463 22249544 0.000000e+00 2608.0
17 TraesCS3D01G038800 chr3A 84.512 1414 151 40 2909 4290 22249609 22250986 0.000000e+00 1336.0
18 TraesCS3D01G038800 chr3A 87.871 371 43 2 324 693 22243683 22244052 7.180000e-118 435.0
19 TraesCS3D01G038800 chr3A 85.366 369 49 4 994 1361 11882914 11882550 1.230000e-100 377.0
20 TraesCS3D01G038800 chr3A 87.248 149 14 3 4395 4542 22251145 22251289 1.040000e-36 165.0
21 TraesCS3D01G038800 chr3A 91.667 84 5 1 242 325 698339410 698339329 1.060000e-21 115.0
22 TraesCS3D01G038800 chr3A 82.759 116 17 3 691 806 22246899 22247011 2.980000e-17 100.0
23 TraesCS3D01G038800 chr7B 76.450 1707 269 73 1049 2700 594763622 594765250 0.000000e+00 802.0
24 TraesCS3D01G038800 chr7B 92.771 83 4 2 242 324 484271025 484270945 8.220000e-23 119.0
25 TraesCS3D01G038800 chr7A 77.427 1205 198 43 1517 2697 635553078 635554232 0.000000e+00 651.0
26 TraesCS3D01G038800 chr7A 87.097 310 40 0 1049 1358 635552571 635552880 7.440000e-93 351.0
27 TraesCS3D01G038800 chr7A 82.587 402 59 7 3091 3490 635554398 635554790 1.250000e-90 344.0
28 TraesCS3D01G038800 chr7A 81.181 271 36 12 3705 3960 635555416 635555686 2.210000e-48 204.0
29 TraesCS3D01G038800 chr7A 76.418 335 42 23 2702 3003 635554848 635555178 3.770000e-31 147.0
30 TraesCS3D01G038800 chr7A 93.902 82 4 1 243 324 84043937 84044017 6.350000e-24 122.0
31 TraesCS3D01G038800 chr7D 76.355 609 119 16 1517 2117 550213764 550214355 2.110000e-78 303.0
32 TraesCS3D01G038800 chr7D 78.170 481 66 21 2231 2697 550233085 550233540 2.140000e-68 270.0
33 TraesCS3D01G038800 chr6A 83.588 262 41 2 1084 1344 106895341 106895081 1.300000e-60 244.0
34 TraesCS3D01G038800 chr6A 92.683 82 4 1 243 324 615495189 615495268 2.960000e-22 117.0
35 TraesCS3D01G038800 chr6A 91.667 84 5 1 243 326 23493152 23493071 1.060000e-21 115.0
36 TraesCS3D01G038800 chr1B 76.866 402 74 13 426 823 387379162 387379548 4.740000e-50 209.0
37 TraesCS3D01G038800 chr5D 92.683 82 4 1 243 324 526752502 526752581 2.960000e-22 117.0
38 TraesCS3D01G038800 chr4B 91.765 85 5 1 240 324 183523393 183523311 2.960000e-22 117.0
39 TraesCS3D01G038800 chr6B 90.909 88 5 2 243 330 126907832 126907748 1.060000e-21 115.0


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 TraesCS3D01G038800 chr3D 14412851 14417525 4674 True 8634.000000 8634 100.000000 1 4675 1 chr3D.!!$R3 4674
1 TraesCS3D01G038800 chr3D 14405662 14407227 1565 True 2021.000000 2021 90.242000 917 2456 1 chr3D.!!$R2 1539
2 TraesCS3D01G038800 chr3D 9105585 9108134 2549 False 424.500000 730 79.265500 1442 3070 2 chr3D.!!$F1 1628
3 TraesCS3D01G038800 chr3B 21384135 21388851 4716 True 2084.000000 4477 90.783000 1 4675 3 chr3B.!!$R4 4674
4 TraesCS3D01G038800 chr3B 21345665 21347693 2028 True 705.666667 1024 88.186333 335 2456 3 chr3B.!!$R3 2121
5 TraesCS3D01G038800 chr3B 21333881 21334666 785 True 632.000000 632 81.967000 2774 3530 1 chr3B.!!$R2 756
6 TraesCS3D01G038800 chr3B 11186036 11187193 1157 True 568.000000 568 76.127000 1517 2689 1 chr3B.!!$R1 1172
7 TraesCS3D01G038800 chr3B 11231516 11233208 1692 False 371.133333 652 87.515333 994 2696 3 chr3B.!!$F1 1702
8 TraesCS3D01G038800 chr3A 22243683 22251289 7606 False 928.800000 2608 86.359200 324 4542 5 chr3A.!!$F1 4218
9 TraesCS3D01G038800 chr7B 594763622 594765250 1628 False 802.000000 802 76.450000 1049 2700 1 chr7B.!!$F1 1651
10 TraesCS3D01G038800 chr7A 635552571 635555686 3115 False 339.400000 651 80.942000 1049 3960 5 chr7A.!!$F2 2911
11 TraesCS3D01G038800 chr7D 550213764 550214355 591 False 303.000000 303 76.355000 1517 2117 1 chr7D.!!$F1 600

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
737 3590 0.394899 GGTTGAATGAGCCCCCTGAG 60.395 60.0 0.0 0.0 0.0 3.35 F
1997 5561 0.036858 GGAAGGCTCTGTGTGGTCTC 60.037 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 5632 0.179100 ACCTCTCGATGCCATTGTCG 60.179 55.000 0.00 0.0 39.11 4.35 R
3925 8572 1.606668 GTTCGGACAGGACATTGCAAA 59.393 47.619 1.71 0.0 0.00 3.68 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
96 99 1.208052 CACCACACTCGAGATTGGGAT 59.792 52.381 28.83 14.56 33.00 3.85
184 187 8.964476 TTTCTATATGGGAAATGAGACTTGTC 57.036 34.615 0.00 0.00 0.00 3.18
187 190 3.319137 TGGGAAATGAGACTTGTCGAG 57.681 47.619 0.00 0.00 0.00 4.04
212 215 3.243168 TGCTCTTGTACGTCGTTAAGTGT 60.243 43.478 1.78 0.00 0.00 3.55
234 237 4.696899 TGTAGAGACACGGTAATGACTG 57.303 45.455 0.00 0.00 38.01 3.51
355 358 3.342377 TGTTCATAATCACCTCCGCAA 57.658 42.857 0.00 0.00 0.00 4.85
396 399 3.679980 AGACAACATTGATTTCGGTCTCG 59.320 43.478 0.00 0.00 37.82 4.04
410 413 3.119245 TCGGTCTCGATAAAAACTCCCTG 60.119 47.826 0.00 0.00 40.88 4.45
423 426 2.122768 ACTCCCTGCTCATCCCTTAAG 58.877 52.381 0.00 0.00 0.00 1.85
451 454 5.598769 CAGCTGATGTGATCACAATAGAGA 58.401 41.667 31.08 12.84 45.41 3.10
457 460 5.835113 TGTGATCACAATAGAGACGATGA 57.165 39.130 26.02 0.00 38.56 2.92
520 523 1.325355 CCGGGTAGAAGCGGAATCTA 58.675 55.000 0.00 0.00 0.00 1.98
621 625 3.505680 TGGATGTTTCTTCGTTGATTGGG 59.494 43.478 0.00 0.00 0.00 4.12
628 632 1.732259 CTTCGTTGATTGGGAAGGTCG 59.268 52.381 0.00 0.00 34.85 4.79
629 633 0.682852 TCGTTGATTGGGAAGGTCGT 59.317 50.000 0.00 0.00 0.00 4.34
631 635 1.606994 CGTTGATTGGGAAGGTCGTCA 60.607 52.381 0.00 0.00 0.00 4.35
647 651 7.033530 AGGTCGTCATTAAACATTGTTTTCA 57.966 32.000 19.15 7.98 0.00 2.69
651 655 7.855904 GTCGTCATTAAACATTGTTTTCAGTCT 59.144 33.333 19.15 0.00 0.00 3.24
652 656 8.402472 TCGTCATTAAACATTGTTTTCAGTCTT 58.598 29.630 19.15 0.00 0.00 3.01
688 692 6.148270 CACATGTGCTAGCAAAAATTTCTG 57.852 37.500 21.29 10.69 0.00 3.02
737 3590 0.394899 GGTTGAATGAGCCCCCTGAG 60.395 60.000 0.00 0.00 0.00 3.35
742 3595 0.912486 AATGAGCCCCCTGAGTGTAC 59.088 55.000 0.00 0.00 0.00 2.90
746 3599 0.905337 AGCCCCCTGAGTGTACTGTC 60.905 60.000 0.00 0.00 0.00 3.51
750 3603 1.546476 CCCCTGAGTGTACTGTCAGTC 59.454 57.143 9.26 2.26 38.88 3.51
762 3615 2.831333 CTGTCAGTCAGCTTGTGAACT 58.169 47.619 0.00 0.00 36.74 3.01
764 3617 3.717707 TGTCAGTCAGCTTGTGAACTAC 58.282 45.455 0.00 0.00 36.74 2.73
765 3618 3.384789 TGTCAGTCAGCTTGTGAACTACT 59.615 43.478 0.00 0.00 36.74 2.57
767 3620 3.005897 TCAGTCAGCTTGTGAACTACTCC 59.994 47.826 0.00 0.00 36.74 3.85
768 3621 3.006323 CAGTCAGCTTGTGAACTACTCCT 59.994 47.826 0.00 0.00 36.74 3.69
769 3622 4.218635 CAGTCAGCTTGTGAACTACTCCTA 59.781 45.833 0.00 0.00 36.74 2.94
770 3623 5.020132 AGTCAGCTTGTGAACTACTCCTAT 58.980 41.667 0.00 0.00 36.74 2.57
771 3624 5.105554 AGTCAGCTTGTGAACTACTCCTATG 60.106 44.000 0.00 0.00 36.74 2.23
774 3627 5.020132 AGCTTGTGAACTACTCCTATGTCT 58.980 41.667 0.00 0.00 0.00 3.41
781 3634 7.990886 TGTGAACTACTCCTATGTCTTTGTTTT 59.009 33.333 0.00 0.00 0.00 2.43
782 3635 8.283291 GTGAACTACTCCTATGTCTTTGTTTTG 58.717 37.037 0.00 0.00 0.00 2.44
807 3660 8.786898 TGTCTTAATAAAGCTATTCATGATGGC 58.213 33.333 0.00 1.46 42.13 4.40
808 3661 8.239998 GTCTTAATAAAGCTATTCATGATGGCC 58.760 37.037 0.00 0.00 42.75 5.36
810 3663 8.710749 TTAATAAAGCTATTCATGATGGCCTT 57.289 30.769 3.32 0.00 42.75 4.35
811 3664 7.607615 AATAAAGCTATTCATGATGGCCTTT 57.392 32.000 3.32 6.69 42.75 3.11
814 3667 4.801164 AGCTATTCATGATGGCCTTTTCT 58.199 39.130 3.32 0.00 42.75 2.52
815 3668 5.945310 AGCTATTCATGATGGCCTTTTCTA 58.055 37.500 3.32 0.00 42.75 2.10
816 3669 6.002704 AGCTATTCATGATGGCCTTTTCTAG 58.997 40.000 3.32 0.00 42.75 2.43
817 3670 6.000219 GCTATTCATGATGGCCTTTTCTAGA 59.000 40.000 3.32 0.00 36.32 2.43
818 3671 6.488006 GCTATTCATGATGGCCTTTTCTAGAA 59.512 38.462 3.32 0.00 36.32 2.10
849 4200 6.092670 ACATTGGTTTCAGTCAGATAATGTCG 59.907 38.462 0.00 0.00 33.65 4.35
907 4261 1.215382 GCCTGGTGCCCGATTTTTC 59.785 57.895 0.00 0.00 0.00 2.29
986 4346 1.003118 CGAAACCCTCATTCCACCTGA 59.997 52.381 0.00 0.00 0.00 3.86
1253 4616 0.182537 CTCACCACCCAAGACACCAA 59.817 55.000 0.00 0.00 0.00 3.67
1413 4914 0.544697 AAGATAACGGGGATGGCGTT 59.455 50.000 0.00 0.00 0.00 4.84
1427 4928 2.664436 GCGTTTCCGTTCCTGTCCG 61.664 63.158 0.00 0.00 36.15 4.79
1508 5056 3.390671 ATCCCATCCCCGACCTCGT 62.391 63.158 0.00 0.00 37.74 4.18
1510 5058 3.075005 CCATCCCCGACCTCGTGT 61.075 66.667 0.00 0.00 37.74 4.49
1511 5059 2.184322 CATCCCCGACCTCGTGTG 59.816 66.667 0.00 0.00 37.74 3.82
1512 5060 3.075005 ATCCCCGACCTCGTGTGG 61.075 66.667 0.00 0.00 37.74 4.17
1513 5061 3.899545 ATCCCCGACCTCGTGTGGT 62.900 63.158 0.00 0.00 44.10 4.16
1524 5072 2.093711 CCTCGTGTGGTCATGGTCAATA 60.094 50.000 0.00 0.00 0.00 1.90
1642 5199 2.608988 CTCCCCACCAGGAGCACT 60.609 66.667 0.00 0.00 46.76 4.40
1643 5200 2.964310 CTCCCCACCAGGAGCACTG 61.964 68.421 0.00 1.75 46.76 3.66
1644 5201 4.729918 CCCCACCAGGAGCACTGC 62.730 72.222 0.00 0.00 46.14 4.40
1645 5202 3.957586 CCCACCAGGAGCACTGCA 61.958 66.667 3.30 0.00 46.14 4.41
1646 5203 2.113774 CCACCAGGAGCACTGCAA 59.886 61.111 3.30 0.00 46.14 4.08
1647 5204 1.970114 CCACCAGGAGCACTGCAAG 60.970 63.158 3.30 0.00 46.14 4.01
1720 5280 1.874345 CTCCTTGCCGTACCGTGTCT 61.874 60.000 0.00 0.00 0.00 3.41
1825 5386 1.380785 ATCGACGGGTTCTGGCCTA 60.381 57.895 3.32 0.00 0.00 3.93
1842 5403 2.158813 GCCTAGCAATGGTAAGCTGGTA 60.159 50.000 5.86 0.00 41.97 3.25
1874 5438 5.577100 CATCTATTGGACCATTGGGATGAT 58.423 41.667 18.83 0.00 38.05 2.45
1953 5517 0.609681 ACAGGAGAGGGAGTGACGTC 60.610 60.000 9.11 9.11 0.00 4.34
1997 5561 0.036858 GGAAGGCTCTGTGTGGTCTC 60.037 60.000 0.00 0.00 0.00 3.36
2028 5596 2.767960 GGGGCCATTGACATTTGAATCT 59.232 45.455 4.39 0.00 0.00 2.40
2029 5597 3.960102 GGGGCCATTGACATTTGAATCTA 59.040 43.478 4.39 0.00 0.00 1.98
2030 5598 4.038402 GGGGCCATTGACATTTGAATCTAG 59.962 45.833 4.39 0.00 0.00 2.43
2035 5603 6.501781 CCATTGACATTTGAATCTAGGCTTC 58.498 40.000 0.00 0.00 0.00 3.86
2086 5660 1.293924 CATCGAGAGGTGGATGTTGC 58.706 55.000 0.00 0.00 38.98 4.17
2103 5677 0.107410 TGCACAAGTCACTCCCGTTT 60.107 50.000 0.00 0.00 0.00 3.60
2122 5696 1.883678 TCAGGAGATGGCTGGAATCA 58.116 50.000 0.00 0.00 0.00 2.57
2131 5705 1.557371 TGGCTGGAATCATTCGGTGTA 59.443 47.619 0.00 0.00 0.00 2.90
2135 5709 3.743396 GCTGGAATCATTCGGTGTAGATC 59.257 47.826 0.00 0.00 0.00 2.75
2212 5786 7.421530 TTTGTGTACTTCTCTGCTTATTGTC 57.578 36.000 0.00 0.00 0.00 3.18
2218 5792 2.176045 TCTCTGCTTATTGTCGGGTGA 58.824 47.619 0.00 0.00 0.00 4.02
2240 5814 1.493950 CCGCATCAGCATTCGACTCC 61.494 60.000 0.00 0.00 42.27 3.85
2351 5925 2.433436 GCCTCGTTCTTTGGTTGGTAT 58.567 47.619 0.00 0.00 0.00 2.73
2352 5926 3.602483 GCCTCGTTCTTTGGTTGGTATA 58.398 45.455 0.00 0.00 0.00 1.47
2411 6007 4.251103 TGACTAGGAGGATCACTAAGCA 57.749 45.455 0.00 0.00 36.25 3.91
2465 6075 6.601613 TCTTGCCATGGTAATTCGATTTACTT 59.398 34.615 22.61 12.42 33.49 2.24
2469 6079 7.936847 TGCCATGGTAATTCGATTTACTTATCT 59.063 33.333 22.61 7.15 33.49 1.98
2470 6080 8.230486 GCCATGGTAATTCGATTTACTTATCTG 58.770 37.037 22.61 14.85 33.49 2.90
2471 6081 9.489084 CCATGGTAATTCGATTTACTTATCTGA 57.511 33.333 22.61 6.02 33.49 3.27
2524 6143 7.944061 TCTGTTGAGAATTGTCAATCATTTGT 58.056 30.769 19.70 0.00 38.68 2.83
2554 6181 7.654923 TCTTTGAGCATACTAGCAATCATACTG 59.345 37.037 0.00 0.00 36.85 2.74
2576 6203 7.282585 ACTGCTACTCTATGCATATTGGAAAA 58.717 34.615 6.92 0.00 38.59 2.29
2723 6403 5.935206 TGAGTATTTTGTGGCGATCAGTAAA 59.065 36.000 0.00 0.00 0.00 2.01
2726 6406 7.826690 AGTATTTTGTGGCGATCAGTAAAATT 58.173 30.769 13.66 0.00 36.09 1.82
2735 6415 7.429340 GTGGCGATCAGTAAAATTTCTACATTG 59.571 37.037 0.00 0.00 0.00 2.82
2766 6446 7.488322 TGGGAACTAACTTGTTTCTCATTTTG 58.512 34.615 0.00 0.00 0.00 2.44
2770 6450 9.087424 GAACTAACTTGTTTCTCATTTTGCTTT 57.913 29.630 0.00 0.00 0.00 3.51
2786 6466 1.950472 CTTTTGTTAGCAAGGTCGCG 58.050 50.000 0.00 0.00 35.82 5.87
2797 6477 1.986378 CAAGGTCGCGTAAGTTCTCTG 59.014 52.381 5.77 0.00 41.68 3.35
2970 6718 5.805994 GTCCTAGCAATATATCACTAACGCC 59.194 44.000 0.00 0.00 0.00 5.68
2990 6749 4.261238 CGCCCTCTGTACTAGTAGACAATG 60.261 50.000 1.87 0.00 0.00 2.82
3087 6888 1.070134 TGGGCTGTTCGGAGTATATGC 59.930 52.381 0.00 0.00 0.00 3.14
3295 7114 7.972623 ATAGATTTTGAGCTATATCGCGTAC 57.027 36.000 5.77 0.00 34.40 3.67
3341 7160 2.996631 ACCATCTTTGTCATCTCTGGC 58.003 47.619 0.00 0.00 0.00 4.85
3507 8136 4.410228 TGATAGCAACCTAGAGCAATTCCT 59.590 41.667 0.00 0.00 0.00 3.36
3562 8192 4.558226 TTCTCTGATTTAGCAGCCAGAA 57.442 40.909 0.00 0.00 35.52 3.02
3563 8193 3.866651 TCTCTGATTTAGCAGCCAGAAC 58.133 45.455 0.00 0.00 35.52 3.01
3564 8194 2.941720 CTCTGATTTAGCAGCCAGAACC 59.058 50.000 0.00 0.00 35.52 3.62
3565 8195 2.019984 CTGATTTAGCAGCCAGAACCC 58.980 52.381 0.00 0.00 0.00 4.11
3566 8196 1.354031 TGATTTAGCAGCCAGAACCCA 59.646 47.619 0.00 0.00 0.00 4.51
3567 8197 2.019984 GATTTAGCAGCCAGAACCCAG 58.980 52.381 0.00 0.00 0.00 4.45
3568 8198 1.064003 TTTAGCAGCCAGAACCCAGA 58.936 50.000 0.00 0.00 0.00 3.86
3620 8251 6.418057 TTTGCAAAACCATCTAATCCAACT 57.582 33.333 10.02 0.00 0.00 3.16
3682 8314 5.882557 CCAGCTTATCCAGTTAAAGACACAT 59.117 40.000 0.00 0.00 0.00 3.21
3683 8315 6.183360 CCAGCTTATCCAGTTAAAGACACATG 60.183 42.308 0.00 0.00 0.00 3.21
3706 8338 7.664082 TGATTCTCTTCTGTGTTCTTGAATC 57.336 36.000 0.00 0.00 39.04 2.52
3888 8535 6.759827 GCTTCATCAATATGCTGGAATTGTTT 59.240 34.615 0.00 0.00 35.16 2.83
3997 8644 7.094890 GCTAATGTCTGTCAATCTATGGAATGG 60.095 40.741 0.00 0.00 0.00 3.16
4045 8692 7.389330 TCATGTATTGAAACAGTTTCGGTACAT 59.611 33.333 28.99 28.99 44.49 2.29
4061 8708 9.667107 TTTCGGTACATCAATTAGAGAAGAAAT 57.333 29.630 0.00 0.00 0.00 2.17
4062 8709 9.667107 TTCGGTACATCAATTAGAGAAGAAATT 57.333 29.630 0.00 0.00 0.00 1.82
4083 8730 2.535934 TACGAATTTGCCATTGTCGC 57.464 45.000 0.00 0.00 35.15 5.19
4169 8817 8.486383 TGAAACAAAGCGAATGTAAATTTGATG 58.514 29.630 0.00 0.00 35.40 3.07
4180 8828 6.320494 TGTAAATTTGATGTACACACACCC 57.680 37.500 0.00 0.00 37.54 4.61
4246 8894 8.581578 ACAAAAATAAACCTATAGTGGTGTTGG 58.418 33.333 0.00 0.00 40.73 3.77
4269 8920 2.028294 AGACAGATGCTGGACAAGACAG 60.028 50.000 0.00 0.00 35.51 3.51
4299 8950 0.610232 GAGATTGCTGGTGTGGCCTT 60.610 55.000 3.32 0.00 38.35 4.35
4300 8951 0.178953 AGATTGCTGGTGTGGCCTTT 60.179 50.000 3.32 0.00 38.35 3.11
4374 9120 1.657804 AGGTGAACCCTTGTCCCTAG 58.342 55.000 0.00 0.00 42.73 3.02
4376 9122 1.982958 GGTGAACCCTTGTCCCTAGAA 59.017 52.381 0.00 0.00 0.00 2.10
4438 9188 6.374333 GGGCTATGTAAACAACTTCTCATTGA 59.626 38.462 0.00 0.00 0.00 2.57
4483 9233 8.610896 TGCATTTTCTTGAAAAACAATAAGGTG 58.389 29.630 11.78 4.83 37.88 4.00
4514 9264 9.464714 GAAAACTAGAACTGGGAATTTCTTTTC 57.535 33.333 0.00 0.00 33.96 2.29
4645 9396 9.598517 AAAAACAAGATGTTGATGTGTTATTGT 57.401 25.926 9.96 0.00 40.14 2.71
4646 9397 8.578308 AAACAAGATGTTGATGTGTTATTGTG 57.422 30.769 9.96 0.00 40.14 3.33
4662 9413 0.681887 TGTGGATTGCTGGCCATCTG 60.682 55.000 5.51 0.00 36.41 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 60 5.179742 GTGGTGATTTGTGTTATGAACCGTA 59.820 40.000 0.00 0.00 0.00 4.02
58 61 4.023536 GTGGTGATTTGTGTTATGAACCGT 60.024 41.667 0.00 0.00 0.00 4.83
59 62 4.023622 TGTGGTGATTTGTGTTATGAACCG 60.024 41.667 0.00 0.00 0.00 4.44
61 64 6.072112 AGTGTGGTGATTTGTGTTATGAAC 57.928 37.500 0.00 0.00 0.00 3.18
63 66 4.450757 CGAGTGTGGTGATTTGTGTTATGA 59.549 41.667 0.00 0.00 0.00 2.15
64 67 4.450757 TCGAGTGTGGTGATTTGTGTTATG 59.549 41.667 0.00 0.00 0.00 1.90
65 68 4.637276 TCGAGTGTGGTGATTTGTGTTAT 58.363 39.130 0.00 0.00 0.00 1.89
66 69 4.055360 CTCGAGTGTGGTGATTTGTGTTA 58.945 43.478 3.62 0.00 0.00 2.41
67 70 2.872245 CTCGAGTGTGGTGATTTGTGTT 59.128 45.455 3.62 0.00 0.00 3.32
109 112 5.675684 AAAACTGTTCCAAAAGGTCATGT 57.324 34.783 0.00 0.00 0.00 3.21
184 187 1.828832 GACGTACAAGAGCATCCTCG 58.171 55.000 0.00 0.00 43.05 4.63
187 190 1.992170 AACGACGTACAAGAGCATCC 58.008 50.000 0.00 0.00 33.66 3.51
212 215 4.617530 GCAGTCATTACCGTGTCTCTACAA 60.618 45.833 0.00 0.00 37.36 2.41
275 278 7.747888 TGTTCGTTGTATTACCATGATTGAAG 58.252 34.615 0.00 0.00 0.00 3.02
355 358 4.110482 GTCTAAACTATCGCGTTGGATGT 58.890 43.478 5.77 0.00 0.00 3.06
396 399 3.885901 GGGATGAGCAGGGAGTTTTTATC 59.114 47.826 0.00 0.00 0.00 1.75
410 413 2.292845 GCTGCATTCTTAAGGGATGAGC 59.707 50.000 18.20 17.68 0.00 4.26
423 426 2.681344 TGTGATCACATCAGCTGCATTC 59.319 45.455 24.56 0.67 40.53 2.67
451 454 1.009078 CCATCGCACATTGTCATCGT 58.991 50.000 0.00 0.00 0.00 3.73
457 460 6.680810 CCAATATAAATCCATCGCACATTGT 58.319 36.000 0.00 0.00 0.00 2.71
520 523 9.264719 GGAGAATTCAACAACAATTTGAGAATT 57.735 29.630 8.44 15.56 44.32 2.17
587 590 2.849880 AACATCCACGCATTATGCAC 57.150 45.000 17.75 0.00 45.36 4.57
621 625 7.646130 TGAAAACAATGTTTAATGACGACCTTC 59.354 33.333 12.11 2.26 0.00 3.46
628 632 9.736023 AGAAGACTGAAAACAATGTTTAATGAC 57.264 29.630 12.11 5.73 0.00 3.06
647 651 5.938125 ACATGTGCCGTTTTATTAGAAGACT 59.062 36.000 0.00 0.00 0.00 3.24
746 3599 3.006323 AGGAGTAGTTCACAAGCTGACTG 59.994 47.826 0.00 0.00 0.00 3.51
750 3603 5.078411 ACATAGGAGTAGTTCACAAGCTG 57.922 43.478 0.00 0.00 0.00 4.24
753 3606 7.155328 ACAAAGACATAGGAGTAGTTCACAAG 58.845 38.462 0.00 0.00 0.00 3.16
781 3634 8.786898 GCCATCATGAATAGCTTTATTAAGACA 58.213 33.333 0.00 0.00 32.92 3.41
782 3635 8.239998 GGCCATCATGAATAGCTTTATTAAGAC 58.760 37.037 0.00 0.00 32.92 3.01
797 3650 7.537596 TTTTTCTAGAAAAGGCCATCATGAA 57.462 32.000 25.38 8.23 40.83 2.57
907 4261 3.313524 GGCCCAACAAGCCCAAGG 61.314 66.667 0.00 0.00 45.16 3.61
1524 5072 1.198713 ATCCGTCAAGGCAGTCATCT 58.801 50.000 0.00 0.00 40.77 2.90
1612 5160 3.412408 GGGAGGCAGGGGGAAGAC 61.412 72.222 0.00 0.00 0.00 3.01
1644 5201 3.020026 CTGGCGCTCGCAGTTCTTG 62.020 63.158 16.36 0.00 44.11 3.02
1645 5202 2.154798 TACTGGCGCTCGCAGTTCTT 62.155 55.000 20.38 1.49 44.11 2.52
1646 5203 1.949847 ATACTGGCGCTCGCAGTTCT 61.950 55.000 20.38 8.23 44.11 3.01
1647 5204 1.084370 AATACTGGCGCTCGCAGTTC 61.084 55.000 20.38 0.00 44.11 3.01
1753 5313 3.038280 TGTCCGATGATAAGACCATGGT 58.962 45.455 19.89 19.89 0.00 3.55
1825 5386 3.701040 CCATTTACCAGCTTACCATTGCT 59.299 43.478 0.00 0.00 40.54 3.91
1842 5403 2.961062 GGTCCAATAGATGCAGCCATTT 59.039 45.455 0.00 0.00 0.00 2.32
1953 5517 1.374758 GGTCTCACCAGCCGTCAAG 60.375 63.158 0.00 0.00 38.42 3.02
1997 5561 3.358932 AATGGCCCCTTAGGTGCGG 62.359 63.158 0.00 0.00 38.26 5.69
2028 5596 2.355716 CCGGATCCAAACAAGAAGCCTA 60.356 50.000 13.41 0.00 0.00 3.93
2029 5597 1.614317 CCGGATCCAAACAAGAAGCCT 60.614 52.381 13.41 0.00 0.00 4.58
2030 5598 0.811281 CCGGATCCAAACAAGAAGCC 59.189 55.000 13.41 0.00 0.00 4.35
2035 5603 1.373570 GCTCTCCGGATCCAAACAAG 58.626 55.000 13.41 3.29 0.00 3.16
2057 5625 1.493950 CCTCTCGATGCCATTGTCGC 61.494 60.000 0.00 0.00 37.74 5.19
2058 5632 0.179100 ACCTCTCGATGCCATTGTCG 60.179 55.000 0.00 0.00 39.11 4.35
2068 5642 0.904649 TGCAACATCCACCTCTCGAT 59.095 50.000 0.00 0.00 0.00 3.59
2086 5660 1.867233 CTGAAACGGGAGTGACTTGTG 59.133 52.381 0.00 0.00 46.69 3.33
2103 5677 1.883678 TGATTCCAGCCATCTCCTGA 58.116 50.000 0.00 0.00 32.03 3.86
2112 5686 2.158957 TCTACACCGAATGATTCCAGCC 60.159 50.000 0.00 0.00 0.00 4.85
2122 5696 2.320781 CTCCCTGGATCTACACCGAAT 58.679 52.381 0.00 0.00 0.00 3.34
2135 5709 7.896383 TCAAATTTAACATTATCCTCCCTGG 57.104 36.000 0.00 0.00 37.10 4.45
2212 5786 3.274586 CTGATGCGGCATCACCCG 61.275 66.667 34.98 24.09 44.60 5.28
2229 5803 1.522580 GAGCCAGGGAGTCGAATGC 60.523 63.158 0.00 0.00 0.00 3.56
2240 5814 0.396060 GCAGAAGGATAGGAGCCAGG 59.604 60.000 0.00 0.00 0.00 4.45
2351 5925 4.595781 AGGGATTAGTCACCTTGTTGTGTA 59.404 41.667 0.00 0.00 37.51 2.90
2352 5926 3.394606 AGGGATTAGTCACCTTGTTGTGT 59.605 43.478 0.00 0.00 37.51 3.72
2497 6115 9.419297 CAAATGATTGACAATTCTCAACAGAAT 57.581 29.630 1.39 0.00 43.51 2.40
2528 6147 7.654923 CAGTATGATTGCTAGTATGCTCAAAGA 59.345 37.037 0.00 0.00 39.69 2.52
2554 6181 6.205464 TGCTTTTCCAATATGCATAGAGTAGC 59.795 38.462 12.79 14.56 0.00 3.58
2697 6376 4.943705 ACTGATCGCCACAAAATACTCAAT 59.056 37.500 0.00 0.00 0.00 2.57
2699 6378 3.937814 ACTGATCGCCACAAAATACTCA 58.062 40.909 0.00 0.00 0.00 3.41
2723 6403 8.193953 AGTTCCCATTTGACAATGTAGAAATT 57.806 30.769 0.00 0.00 38.58 1.82
2726 6406 7.942341 AGTTAGTTCCCATTTGACAATGTAGAA 59.058 33.333 0.00 0.00 38.58 2.10
2735 6415 7.039313 AGAAACAAGTTAGTTCCCATTTGAC 57.961 36.000 0.00 0.00 0.00 3.18
2742 6422 6.420903 GCAAAATGAGAAACAAGTTAGTTCCC 59.579 38.462 0.00 0.00 0.00 3.97
2766 6446 1.686464 GCGACCTTGCTAACAAAAGC 58.314 50.000 0.00 0.00 43.08 3.51
2770 6450 2.063266 CTTACGCGACCTTGCTAACAA 58.937 47.619 15.93 0.00 0.00 2.83
2783 6463 4.171005 TGATAAACCAGAGAACTTACGCG 58.829 43.478 3.53 3.53 0.00 6.01
2784 6464 5.502544 GCATGATAAACCAGAGAACTTACGC 60.503 44.000 0.00 0.00 0.00 4.42
2786 6466 6.371548 TGTGCATGATAAACCAGAGAACTTAC 59.628 38.462 0.00 0.00 0.00 2.34
2928 6674 6.660949 GCTAGGACCAATATGCCTCATAAAAT 59.339 38.462 0.00 0.00 33.28 1.82
3102 6905 1.805943 TGTGACACGATGCAATCAAGG 59.194 47.619 0.22 0.00 45.97 3.61
3323 7142 3.607741 ACTGCCAGAGATGACAAAGATG 58.392 45.455 0.00 0.00 0.00 2.90
3341 7160 5.351465 ACGTGGCAGAGTATTGATTTTACTG 59.649 40.000 0.00 0.00 30.15 2.74
3507 8136 3.114606 TCTCACCCTGCCTGATAAATCA 58.885 45.455 0.00 0.00 35.16 2.57
3562 8192 4.150359 TCGACTTTTACTCTCTTCTGGGT 58.850 43.478 0.00 0.00 0.00 4.51
3563 8193 4.785511 TCGACTTTTACTCTCTTCTGGG 57.214 45.455 0.00 0.00 0.00 4.45
3564 8194 7.659652 AAAATCGACTTTTACTCTCTTCTGG 57.340 36.000 0.00 0.00 35.27 3.86
3620 8251 5.012458 AGAGATATCAATTCGATCAGCCCAA 59.988 40.000 5.32 0.00 35.39 4.12
3682 8314 6.367149 CGATTCAAGAACACAGAAGAGAATCA 59.633 38.462 0.00 0.00 39.80 2.57
3683 8315 6.587990 TCGATTCAAGAACACAGAAGAGAATC 59.412 38.462 0.00 0.00 37.70 2.52
3697 8329 4.389992 GCAGACATCACTTCGATTCAAGAA 59.610 41.667 0.00 0.00 29.21 2.52
3925 8572 1.606668 GTTCGGACAGGACATTGCAAA 59.393 47.619 1.71 0.00 0.00 3.68
3985 8632 6.260936 GTCGTTCAATGTTCCATTCCATAGAT 59.739 38.462 0.00 0.00 0.00 1.98
3997 8644 3.054878 ACGGTGTAGTCGTTCAATGTTC 58.945 45.455 0.00 0.00 37.61 3.18
4061 8708 4.496673 GGCGACAATGGCAAATTCGTATAA 60.497 41.667 14.05 0.00 32.26 0.98
4062 8709 3.002862 GGCGACAATGGCAAATTCGTATA 59.997 43.478 14.05 0.00 32.26 1.47
4065 8712 0.109319 GGCGACAATGGCAAATTCGT 60.109 50.000 14.05 0.00 32.26 3.85
4066 8713 0.109365 TGGCGACAATGGCAAATTCG 60.109 50.000 9.78 9.78 41.96 3.34
4083 8730 1.230635 CGTGTGGCAGGAAAGACTGG 61.231 60.000 0.00 0.00 38.90 4.00
4169 8817 2.228138 TTGTCTTCGGGTGTGTGTAC 57.772 50.000 0.00 0.00 0.00 2.90
4180 8828 7.624706 AGATATTGCTACGTATTTGTCTTCG 57.375 36.000 0.00 0.00 0.00 3.79
4246 8894 1.552337 TCTTGTCCAGCATCTGTCTCC 59.448 52.381 0.00 0.00 0.00 3.71
4269 8920 1.404391 CAGCAATCTCCTGCAATGGAC 59.596 52.381 0.00 0.00 45.18 4.02
4376 9122 8.040727 AGCAAAGAAGTTATTCACCTTGTTTTT 58.959 29.630 0.00 0.00 37.94 1.94
4438 9188 9.933723 AAAATGCAAAAGCTTTGAATAGATAGT 57.066 25.926 13.54 0.00 0.00 2.12
4483 9233 4.635699 TCCCAGTTCTAGTTTTCTTCCC 57.364 45.455 0.00 0.00 0.00 3.97
4558 9308 8.589338 CATCTGTACTAAAACCATAGATAGGCT 58.411 37.037 0.00 0.00 0.00 4.58
4581 9331 8.908786 TGAATAAATCTAACCAGGATCACATC 57.091 34.615 0.00 0.00 0.00 3.06
4623 9374 6.489700 TCCACAATAACACATCAACATCTTGT 59.510 34.615 0.00 0.00 0.00 3.16
4641 9392 1.117150 GATGGCCAGCAATCCACAAT 58.883 50.000 18.08 0.00 34.81 2.71
4645 9396 0.681887 CACAGATGGCCAGCAATCCA 60.682 55.000 25.38 0.00 36.70 3.41
4646 9397 2.012902 GCACAGATGGCCAGCAATCC 62.013 60.000 25.38 4.80 0.00 3.01


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

AutoCloner maintained by Alex Coulton.