Multiple sequence alignment - TraesCS1B01G351800

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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 TraesCS1B01G351800 chr1B 100.000 6824 0 0 1 6824 582551851 582545028 0.000000e+00 12602.0
1 TraesCS1B01G351800 chr1B 98.325 597 10 0 1 597 137570085 137570681 0.000000e+00 1048.0
2 TraesCS1B01G351800 chr1B 96.078 204 8 0 2095 2298 582549552 582549349 3.940000e-87 333.0
3 TraesCS1B01G351800 chr1B 96.078 204 8 0 2300 2503 582549757 582549554 3.940000e-87 333.0
4 TraesCS1B01G351800 chr1B 95.283 106 5 0 5435 5540 582546381 582546276 1.180000e-37 169.0
5 TraesCS1B01G351800 chr1B 95.283 106 5 0 5471 5576 582546417 582546312 1.180000e-37 169.0
6 TraesCS1B01G351800 chr1B 95.652 69 3 0 5436 5504 582546344 582546276 2.010000e-20 111.0
7 TraesCS1B01G351800 chr1B 84.211 95 13 2 6731 6824 480656715 480656622 2.620000e-14 91.6
8 TraesCS1B01G351800 chr1B 83.908 87 12 1 6064 6148 582545641 582545555 1.580000e-11 82.4
9 TraesCS1B01G351800 chr1B 83.908 87 12 1 6211 6297 582545788 582545704 1.580000e-11 82.4
10 TraesCS1B01G351800 chr1D 95.547 4559 151 13 2300 6824 431431657 431427117 0.000000e+00 7247.0
11 TraesCS1B01G351800 chr1D 92.075 1716 77 28 614 2299 431433148 431431462 0.000000e+00 2361.0
12 TraesCS1B01G351800 chr1D 96.226 106 4 0 5471 5576 431428525 431428420 2.530000e-39 174.0
13 TraesCS1B01G351800 chr1D 93.636 110 7 0 5435 5544 431428489 431428380 1.520000e-36 165.0
14 TraesCS1B01G351800 chr1D 98.551 69 1 0 5508 5576 431428524 431428456 9.290000e-24 122.0
15 TraesCS1B01G351800 chr1D 92.537 67 5 0 5436 5502 431428452 431428386 5.630000e-16 97.1
16 TraesCS1B01G351800 chr1D 84.211 95 13 2 6731 6824 357215056 357214963 2.620000e-14 91.6
17 TraesCS1B01G351800 chr1D 85.057 87 11 1 6064 6148 431427735 431427649 3.390000e-13 87.9
18 TraesCS1B01G351800 chr1D 85.057 87 11 1 6211 6297 431427882 431427798 3.390000e-13 87.9
19 TraesCS1B01G351800 chr1A 95.985 4085 139 11 2758 6824 529669521 529665444 0.000000e+00 6612.0
20 TraesCS1B01G351800 chr1A 91.818 1650 73 31 691 2299 529671446 529669818 0.000000e+00 2242.0
21 TraesCS1B01G351800 chr1A 99.502 602 2 1 1 601 547924000 547924601 0.000000e+00 1094.0
22 TraesCS1B01G351800 chr1A 98.495 598 9 0 1 598 565280443 565281040 0.000000e+00 1055.0
23 TraesCS1B01G351800 chr1A 92.902 479 27 4 2300 2771 529670022 529669544 0.000000e+00 689.0
24 TraesCS1B01G351800 chr1A 98.113 106 2 0 5471 5576 529666843 529666738 1.170000e-42 185.0
25 TraesCS1B01G351800 chr1A 96.364 110 4 0 5435 5544 529666807 529666698 1.510000e-41 182.0
26 TraesCS1B01G351800 chr1A 98.551 69 1 0 5508 5576 529666842 529666774 9.290000e-24 122.0
27 TraesCS1B01G351800 chr1A 94.286 70 4 0 5435 5504 529666771 529666702 2.600000e-19 108.0
28 TraesCS1B01G351800 chr1A 81.982 111 18 2 6715 6824 458396976 458396867 7.290000e-15 93.5
29 TraesCS1B01G351800 chr1A 84.091 88 12 1 6211 6298 529666201 529666116 4.390000e-12 84.2
30 TraesCS1B01G351800 chr7A 99.503 604 3 0 1 604 657728369 657727766 0.000000e+00 1099.0
31 TraesCS1B01G351800 chr7A 99.331 598 4 0 1 598 45933342 45932745 0.000000e+00 1083.0
32 TraesCS1B01G351800 chr5A 98.495 598 9 0 1 598 445433755 445434352 0.000000e+00 1055.0
33 TraesCS1B01G351800 chr3A 98.157 597 11 0 1 597 688956371 688956967 0.000000e+00 1042.0
34 TraesCS1B01G351800 chr3A 86.310 168 17 4 6659 6823 502165823 502165987 1.960000e-40 178.0
35 TraesCS1B01G351800 chr3A 85.366 82 10 2 6743 6823 56592001 56591921 4.390000e-12 84.2
36 TraesCS1B01G351800 chr7B 97.822 597 10 1 2 598 744749146 744749739 0.000000e+00 1027.0
37 TraesCS1B01G351800 chr6B 97.651 596 14 0 1 596 249446826 249447421 0.000000e+00 1024.0
38 TraesCS1B01G351800 chr5B 84.917 842 100 19 4642 5469 106148870 106149698 0.000000e+00 826.0
39 TraesCS1B01G351800 chr5B 81.662 349 49 11 5545 5882 106149664 106150008 6.740000e-70 276.0
40 TraesCS1B01G351800 chr2D 95.331 514 20 2 3647 4158 99684745 99685256 0.000000e+00 813.0
41 TraesCS1B01G351800 chr3D 95.168 476 23 0 3647 4122 560196302 560195827 0.000000e+00 752.0
42 TraesCS1B01G351800 chr3D 86.310 168 17 4 6659 6823 378032711 378032875 1.960000e-40 178.0
43 TraesCS1B01G351800 chr3D 96.341 82 3 0 4077 4158 560195824 560195743 1.190000e-27 135.0
44 TraesCS1B01G351800 chr3B 85.119 168 19 4 6659 6823 492611184 492611348 4.230000e-37 167.0


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 TraesCS1B01G351800 chr1B 582545028 582551851 6823 True 12602.000000 12602 100.00000 1 6824 1 chr1B.!!$R2 6823
1 TraesCS1B01G351800 chr1B 137570085 137570681 596 False 1048.000000 1048 98.32500 1 597 1 chr1B.!!$F1 596
2 TraesCS1B01G351800 chr1D 431427117 431431657 4540 True 7247.000000 7247 95.54700 2300 6824 1 chr1D.!!$R2 4524
3 TraesCS1B01G351800 chr1D 431427649 431433148 5499 True 442.128571 2361 91.87700 614 6297 7 chr1D.!!$R3 5683
4 TraesCS1B01G351800 chr1A 529665444 529671446 6002 True 1278.025000 6612 94.01375 691 6824 8 chr1A.!!$R2 6133
5 TraesCS1B01G351800 chr1A 547924000 547924601 601 False 1094.000000 1094 99.50200 1 601 1 chr1A.!!$F1 600
6 TraesCS1B01G351800 chr1A 565280443 565281040 597 False 1055.000000 1055 98.49500 1 598 1 chr1A.!!$F2 597
7 TraesCS1B01G351800 chr7A 657727766 657728369 603 True 1099.000000 1099 99.50300 1 604 1 chr7A.!!$R2 603
8 TraesCS1B01G351800 chr7A 45932745 45933342 597 True 1083.000000 1083 99.33100 1 598 1 chr7A.!!$R1 597
9 TraesCS1B01G351800 chr5A 445433755 445434352 597 False 1055.000000 1055 98.49500 1 598 1 chr5A.!!$F1 597
10 TraesCS1B01G351800 chr3A 688956371 688956967 596 False 1042.000000 1042 98.15700 1 597 1 chr3A.!!$F2 596
11 TraesCS1B01G351800 chr7B 744749146 744749739 593 False 1027.000000 1027 97.82200 2 598 1 chr7B.!!$F1 596
12 TraesCS1B01G351800 chr6B 249446826 249447421 595 False 1024.000000 1024 97.65100 1 596 1 chr6B.!!$F1 595
13 TraesCS1B01G351800 chr5B 106148870 106150008 1138 False 551.000000 826 83.28950 4642 5882 2 chr5B.!!$F1 1240
14 TraesCS1B01G351800 chr2D 99684745 99685256 511 False 813.000000 813 95.33100 3647 4158 1 chr2D.!!$F1 511
15 TraesCS1B01G351800 chr3D 560195743 560196302 559 True 443.500000 752 95.75450 3647 4158 2 chr3D.!!$R1 511

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
836 855 0.929734 TAGGCCTCTACTCACCCCCT 60.930 60.0 9.68 0.00 0.00 4.79 F
1553 1604 0.248498 CCAAGCTCGCATCTGCATTG 60.248 55.0 2.72 2.04 42.21 2.82 F
2051 2113 0.038251 TCGCTTTCGTCATGCAGACT 60.038 50.0 12.45 0.00 45.32 3.24 F
2217 2288 0.548989 TAGGTGCTTGTGGTGGTTGT 59.451 50.0 0.00 0.00 0.00 3.32 F
3352 3468 0.375106 GCGCAATACAGAAGAGCCAC 59.625 55.0 0.30 0.00 0.00 5.01 F
3605 3721 0.467290 TTCCGTTTGCAAGAAGGCCT 60.467 50.0 0.00 0.00 0.00 5.19 F
4957 5130 0.550914 TGCAGAAACAAGACCAGGGT 59.449 50.0 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1697 0.106719 TTCTCCCATGGCCGGAAATC 60.107 55.0 5.05 0.0 0.00 2.17 R
2952 3068 0.931005 GCTTCCTCTTTCGTATGGCG 59.069 55.0 0.00 0.0 43.01 5.69 R
3352 3468 1.028330 ATCCGCTGATGCACCAACTG 61.028 55.0 0.00 0.0 39.64 3.16 R
3495 3611 1.344065 TGCCGTTGTCCCTCTTAGAA 58.656 50.0 0.00 0.0 0.00 2.10 R
5145 5318 0.320247 CAGTAGATCCATGAGGCCGC 60.320 60.0 0.00 0.0 33.74 6.53 R
5455 5632 0.798776 CCACCATTGAGACGAACTGC 59.201 55.0 0.00 0.0 0.00 4.40 R
6493 6711 2.028658 TCAGTTCACAGTGCCTCAGATC 60.029 50.0 0.00 0.0 0.00 2.75 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
40 41 3.489229 GGACTCAACAAGTGCTGGAAAAC 60.489 47.826 0.00 0.00 42.69 2.43
633 634 4.081030 CAAGCAGCAGCACCGACG 62.081 66.667 3.17 0.00 45.49 5.12
646 647 0.961019 ACCGACGGCAAACAGTAGTA 59.039 50.000 15.39 0.00 0.00 1.82
647 648 1.068055 ACCGACGGCAAACAGTAGTAG 60.068 52.381 15.39 0.00 0.00 2.57
648 649 1.068055 CCGACGGCAAACAGTAGTAGT 60.068 52.381 0.00 0.00 0.00 2.73
649 650 2.162208 CCGACGGCAAACAGTAGTAGTA 59.838 50.000 0.00 0.00 0.00 1.82
654 655 3.259902 GGCAAACAGTAGTAGTAGCACC 58.740 50.000 0.00 0.00 0.00 5.01
745 756 3.627218 GTAATCACGGAGCGCGCC 61.627 66.667 30.33 21.46 0.00 6.53
836 855 0.929734 TAGGCCTCTACTCACCCCCT 60.930 60.000 9.68 0.00 0.00 4.79
837 856 1.762858 GGCCTCTACTCACCCCCTC 60.763 68.421 0.00 0.00 0.00 4.30
905 934 4.803426 GCGGTCGCTCCACTCCAG 62.803 72.222 8.20 0.00 38.26 3.86
906 935 4.803426 CGGTCGCTCCACTCCAGC 62.803 72.222 0.00 0.00 35.57 4.85
913 942 2.039624 TCCACTCCAGCCCTCTCC 59.960 66.667 0.00 0.00 0.00 3.71
914 943 2.040278 CCACTCCAGCCCTCTCCT 59.960 66.667 0.00 0.00 0.00 3.69
920 949 1.305633 CCAGCCCTCTCCTCTCACA 60.306 63.158 0.00 0.00 0.00 3.58
924 953 1.194781 GCCCTCTCCTCTCACAACCA 61.195 60.000 0.00 0.00 0.00 3.67
1057 1096 1.721664 CTTCTCGATCCGGTACCGCA 61.722 60.000 29.15 16.23 38.24 5.69
1472 1511 2.911926 GCTCAGGCCAAGAAGGGGT 61.912 63.158 5.01 0.00 38.09 4.95
1503 1542 4.740822 GGCCCCGGCTGACATTGT 62.741 66.667 5.55 0.00 41.60 2.71
1530 1575 3.120792 GGAAAAAGGTGCGGTTTTTCTC 58.879 45.455 20.86 12.68 46.35 2.87
1533 1584 0.826256 AAGGTGCGGTTTTTCTCCCC 60.826 55.000 0.00 0.00 0.00 4.81
1553 1604 0.248498 CCAAGCTCGCATCTGCATTG 60.248 55.000 2.72 2.04 42.21 2.82
1563 1614 3.267483 GCATCTGCATTGCTTGGATTTT 58.733 40.909 10.49 0.00 41.59 1.82
1583 1634 3.724508 TGATTGGAATGCGTTTGTTGT 57.275 38.095 0.00 0.00 0.00 3.32
1682 1733 1.811359 AGAAGTGATCTTGCAAGCAGC 59.189 47.619 21.99 13.42 45.96 5.25
1708 1759 1.227943 GGATCCAGCGCAATGGCTA 60.228 57.895 11.47 0.00 42.53 3.93
1712 1763 3.945434 CAGCGCAATGGCTAGCCG 61.945 66.667 28.28 16.79 42.53 5.52
1825 1880 1.219213 TCCCCTCTCTTCTCCAGATCC 59.781 57.143 0.00 0.00 0.00 3.36
1830 1885 3.494749 CCTCTCTTCTCCAGATCCATTGC 60.495 52.174 0.00 0.00 0.00 3.56
1971 2033 1.003355 TTAGCAGCACTGGTGGCTC 60.003 57.895 12.42 0.00 40.23 4.70
1974 2036 2.429058 CAGCACTGGTGGCTCTGT 59.571 61.111 0.00 0.00 40.23 3.41
2006 2068 2.707791 TGAGGATGATGATGGACCTTCC 59.292 50.000 4.99 0.00 36.96 3.46
2051 2113 0.038251 TCGCTTTCGTCATGCAGACT 60.038 50.000 12.45 0.00 45.32 3.24
2153 2215 2.818274 CGTCGCTAGGGTTTGGGC 60.818 66.667 6.70 0.00 0.00 5.36
2216 2287 1.686355 TTAGGTGCTTGTGGTGGTTG 58.314 50.000 0.00 0.00 0.00 3.77
2217 2288 0.548989 TAGGTGCTTGTGGTGGTTGT 59.451 50.000 0.00 0.00 0.00 3.32
2375 2446 4.354893 TTGGGCTTCAATTGCAATCTTT 57.645 36.364 13.38 0.00 0.00 2.52
2412 2483 3.439857 TTGGAGCTCATTAGGTGCTTT 57.560 42.857 17.19 0.00 45.79 3.51
2413 2484 3.439857 TGGAGCTCATTAGGTGCTTTT 57.560 42.857 17.19 0.00 45.79 2.27
2414 2485 3.084039 TGGAGCTCATTAGGTGCTTTTG 58.916 45.455 17.19 0.00 45.79 2.44
2415 2486 2.424956 GGAGCTCATTAGGTGCTTTTGG 59.575 50.000 17.19 0.00 45.79 3.28
2416 2487 3.084786 GAGCTCATTAGGTGCTTTTGGT 58.915 45.455 9.40 0.00 45.79 3.67
2417 2488 2.821969 AGCTCATTAGGTGCTTTTGGTG 59.178 45.455 0.00 0.00 43.47 4.17
2418 2489 2.094545 GCTCATTAGGTGCTTTTGGTGG 60.095 50.000 0.00 0.00 33.29 4.61
2419 2490 3.157087 CTCATTAGGTGCTTTTGGTGGT 58.843 45.455 0.00 0.00 0.00 4.16
2420 2491 3.571590 TCATTAGGTGCTTTTGGTGGTT 58.428 40.909 0.00 0.00 0.00 3.67
2439 2510 3.553917 GGTTGTTTTTATTTGTGCAGCGT 59.446 39.130 0.00 0.00 0.00 5.07
2463 2534 3.003480 GCTGCTCTCGTCCTTGTAATTT 58.997 45.455 0.00 0.00 0.00 1.82
2471 2542 4.076394 TCGTCCTTGTAATTTTCCCCTTG 58.924 43.478 0.00 0.00 0.00 3.61
2482 2553 9.713684 TGTAATTTTCCCCTTGAGATAAATCAT 57.286 29.630 0.00 0.00 0.00 2.45
2483 2554 9.971922 GTAATTTTCCCCTTGAGATAAATCATG 57.028 33.333 0.00 0.00 0.00 3.07
2503 2574 2.359850 TGACATGCCTTCGGGTGC 60.360 61.111 0.00 0.00 37.45 5.01
2542 2615 6.636705 ACAAGCTTGTATTGATGATTTGCAT 58.363 32.000 30.25 0.00 40.16 3.96
2647 2724 5.196695 GTTCTTGCTCCCTTCCTGATAAAT 58.803 41.667 0.00 0.00 0.00 1.40
2650 2727 4.156455 TGCTCCCTTCCTGATAAATCAC 57.844 45.455 0.00 0.00 32.50 3.06
2753 2831 7.957484 GCAGTGTAAAACATGATTAGTGTACAG 59.043 37.037 0.00 0.00 0.00 2.74
2843 2959 9.098355 CTGTATGTGCTATACTGCTTTTCTAAA 57.902 33.333 11.28 0.00 0.00 1.85
2882 2998 5.105187 TCACTTAGAAGGGTGATCTGTCATG 60.105 44.000 0.00 0.00 37.52 3.07
2921 3037 5.342259 AGAAAAATGAAAATGCGAACGCTAC 59.658 36.000 19.32 7.48 42.51 3.58
3064 3180 3.181487 TGGAAGCAAGAAGTCAGTTTTGC 60.181 43.478 0.09 0.09 44.63 3.68
3162 3278 6.698766 GCACATTTCTGAAAAACTCTGATGTT 59.301 34.615 6.95 0.00 32.58 2.71
3352 3468 0.375106 GCGCAATACAGAAGAGCCAC 59.625 55.000 0.30 0.00 0.00 5.01
3495 3611 9.217278 GTGTATCTGAATCATTGCATAGAGATT 57.783 33.333 0.00 0.00 33.70 2.40
3554 3670 2.284921 AGCTGCCCTGCCTAGTCA 60.285 61.111 0.00 0.00 0.00 3.41
3605 3721 0.467290 TTCCGTTTGCAAGAAGGCCT 60.467 50.000 0.00 0.00 0.00 5.19
3623 3739 2.158608 GCCTATGTCTTGGTATTGGGCT 60.159 50.000 0.00 0.00 34.86 5.19
3738 3856 1.470098 CTGTTGCCACATCCTTACAGC 59.530 52.381 0.00 0.00 30.39 4.40
3848 3966 4.810790 ACAGAAGTTCATCCTAGTGTTCG 58.189 43.478 5.50 0.00 0.00 3.95
4060 4180 4.050553 GCTGCTTAAAACACAATGCTTGA 58.949 39.130 0.00 0.00 0.00 3.02
4109 4277 5.215252 TCTCCAACTTTCTTCACACCTAG 57.785 43.478 0.00 0.00 0.00 3.02
4236 4404 2.431782 GCCAACTGCATTCAATATGGGT 59.568 45.455 0.00 0.00 40.77 4.51
4332 4500 1.366319 ACCAGCAAGGGAGTTCAGAT 58.634 50.000 0.04 0.00 43.89 2.90
4344 4512 4.082125 GGAGTTCAGATCAATGTTTGGGT 58.918 43.478 0.00 0.00 0.00 4.51
4349 4517 2.821378 CAGATCAATGTTTGGGTGCTCA 59.179 45.455 0.00 0.00 0.00 4.26
4372 4540 4.801521 TTCCTGGGACATGATGATCAAT 57.198 40.909 0.00 0.00 38.20 2.57
4524 4692 4.170468 AGAAAACTGTGGTCCATGTTCT 57.830 40.909 11.90 2.89 0.00 3.01
4560 4728 1.806542 GCTGAAGATCGTTGCTTTCCA 59.193 47.619 0.00 0.00 0.00 3.53
4584 4752 1.388547 TGTGCACACAAGTTTCTCCC 58.611 50.000 17.42 0.00 38.56 4.30
4592 4760 3.636764 ACACAAGTTTCTCCCCAATTGTC 59.363 43.478 4.43 0.00 0.00 3.18
4698 4870 1.299562 CTGTTCCAGCAGCTGAGCAG 61.300 60.000 24.90 21.39 36.85 4.24
4773 4946 2.949177 ACAAGGTGTCTATGCAACCA 57.051 45.000 7.25 0.00 0.00 3.67
4855 5028 8.165239 AGTTCAGAGTACTGCTAATCATCTAG 57.835 38.462 0.00 0.00 43.17 2.43
4957 5130 0.550914 TGCAGAAACAAGACCAGGGT 59.449 50.000 0.00 0.00 0.00 4.34
5144 5317 4.580167 TCATGTTTTTAGCAGTGAAGCTGT 59.420 37.500 0.00 0.00 46.11 4.40
5145 5318 4.291540 TGTTTTTAGCAGTGAAGCTGTG 57.708 40.909 0.00 0.00 46.11 3.66
5176 5349 1.350351 GATCTACTGCATCCAGGCCAT 59.650 52.381 5.01 0.00 43.53 4.40
5187 5360 0.631212 CCAGGCCATTAGTTCCCCTT 59.369 55.000 5.01 0.00 0.00 3.95
5262 5435 0.610232 GGAGCATGAAACAGGCCACT 60.610 55.000 5.01 0.00 42.45 4.00
5365 5538 7.323420 TGTGTTATTGACATCACCAAACAAAA 58.677 30.769 5.07 0.00 41.10 2.44
5455 5632 2.348998 GGCAGCCCCGAGATATGG 59.651 66.667 0.00 0.00 0.00 2.74
5469 5646 4.626042 GAGATATGGCAGTTCGTCTCAAT 58.374 43.478 0.00 0.00 33.93 2.57
5577 5754 3.027412 AGATATGCCAGTTCGTCTCAGT 58.973 45.455 0.00 0.00 0.00 3.41
5765 5942 2.183300 GCGGTCGGTCATACAGCA 59.817 61.111 0.00 0.00 37.87 4.41
6003 6200 2.808906 AGCCCTTCCCTATTGTTGTC 57.191 50.000 0.00 0.00 0.00 3.18
6158 6362 6.385649 TCTGTTATTTTCCCAACTGTTCAC 57.614 37.500 0.00 0.00 0.00 3.18
6258 6462 0.983467 TTCAGTGCTGCCATAGGTGA 59.017 50.000 0.00 0.00 0.00 4.02
6275 6479 7.147846 CCATAGGTGAAATTTTCTAGCATTGGT 60.148 37.037 10.33 0.00 0.00 3.67
6359 6577 7.592885 AGCTTGTTGCATTCCTATTCATATT 57.407 32.000 0.00 0.00 45.94 1.28
6409 6627 5.536554 ACTAATGAATTCTGTGAACTGCG 57.463 39.130 7.05 0.00 0.00 5.18
6410 6628 3.837213 AATGAATTCTGTGAACTGCGG 57.163 42.857 7.05 0.00 0.00 5.69
6411 6629 2.254546 TGAATTCTGTGAACTGCGGT 57.745 45.000 7.05 0.00 0.00 5.68
6493 6711 1.735571 GTAGTACATGGTTGGTTGCCG 59.264 52.381 0.00 0.00 0.00 5.69
6500 6718 0.321564 TGGTTGGTTGCCGATCTGAG 60.322 55.000 0.00 0.00 0.00 3.35
6542 6763 3.573967 AGGGTACAGTTGCAAAATTCAGG 59.426 43.478 0.00 0.00 0.00 3.86
6582 6803 1.608025 ATGTGTTGGTACACCGCAGAG 60.608 52.381 6.02 0.00 45.89 3.35
6591 6812 1.800805 ACACCGCAGAGTCAGAATTG 58.199 50.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 1.739466 TGATTGCTTCGGCTTGCTTAG 59.261 47.619 0.00 0.00 42.37 2.18
604 605 3.933048 CTGCTTGCCTGGGTCTGGG 62.933 68.421 0.00 0.00 0.00 4.45
605 606 2.360852 CTGCTTGCCTGGGTCTGG 60.361 66.667 0.00 0.00 0.00 3.86
606 607 3.060615 GCTGCTTGCCTGGGTCTG 61.061 66.667 0.00 0.00 35.15 3.51
607 608 3.564345 CTGCTGCTTGCCTGGGTCT 62.564 63.158 0.00 0.00 42.00 3.85
608 609 3.060615 CTGCTGCTTGCCTGGGTC 61.061 66.667 0.00 0.00 42.00 4.46
611 612 4.052229 GTGCTGCTGCTTGCCTGG 62.052 66.667 17.00 0.00 42.00 4.45
612 613 4.052229 GGTGCTGCTGCTTGCCTG 62.052 66.667 17.00 0.00 42.00 4.85
629 630 2.342910 ACTACTACTGTTTGCCGTCG 57.657 50.000 0.00 0.00 0.00 5.12
633 634 3.259902 GGTGCTACTACTACTGTTTGCC 58.740 50.000 0.00 0.00 0.00 4.52
646 647 0.326264 CTTTGCCCTCTGGTGCTACT 59.674 55.000 0.00 0.00 0.00 2.57
647 648 0.678048 CCTTTGCCCTCTGGTGCTAC 60.678 60.000 0.00 0.00 0.00 3.58
648 649 0.840288 TCCTTTGCCCTCTGGTGCTA 60.840 55.000 0.00 0.00 0.00 3.49
649 650 2.156098 TCCTTTGCCCTCTGGTGCT 61.156 57.895 0.00 0.00 0.00 4.40
654 655 1.301677 GCTTCGTCCTTTGCCCTCTG 61.302 60.000 0.00 0.00 0.00 3.35
681 682 5.074804 GGGTATGGGTGTAAAAACAAGAGT 58.925 41.667 0.00 0.00 0.00 3.24
682 683 5.048294 GTGGGTATGGGTGTAAAAACAAGAG 60.048 44.000 0.00 0.00 0.00 2.85
684 695 4.021807 GGTGGGTATGGGTGTAAAAACAAG 60.022 45.833 0.00 0.00 0.00 3.16
688 699 2.792878 CGGTGGGTATGGGTGTAAAAA 58.207 47.619 0.00 0.00 0.00 1.94
693 704 3.723922 GGCGGTGGGTATGGGTGT 61.724 66.667 0.00 0.00 0.00 4.16
824 843 4.208686 GCGCGAGGGGGTGAGTAG 62.209 72.222 12.10 0.00 0.00 2.57
894 923 2.686835 AGAGGGCTGGAGTGGAGC 60.687 66.667 0.00 0.00 35.57 4.70
900 929 1.042559 GTGAGAGGAGAGGGCTGGAG 61.043 65.000 0.00 0.00 0.00 3.86
905 934 1.194781 TGGTTGTGAGAGGAGAGGGC 61.195 60.000 0.00 0.00 0.00 5.19
906 935 0.610687 GTGGTTGTGAGAGGAGAGGG 59.389 60.000 0.00 0.00 0.00 4.30
913 942 2.738521 CGGCGGTGGTTGTGAGAG 60.739 66.667 0.00 0.00 0.00 3.20
914 943 3.220999 CTCGGCGGTGGTTGTGAGA 62.221 63.158 7.21 0.00 0.00 3.27
920 949 4.096003 CCATCCTCGGCGGTGGTT 62.096 66.667 7.21 2.22 32.50 3.67
941 970 4.680237 CTCTGTTCCCGGCGCACA 62.680 66.667 10.83 3.06 0.00 4.57
1057 1096 2.578480 GGAGGAGGGAAAAGGAGTTCAT 59.422 50.000 0.00 0.00 0.00 2.57
1399 1438 2.679287 ACCTTCCTCCCGTCGTCC 60.679 66.667 0.00 0.00 0.00 4.79
1472 1511 1.767692 GGGCCTTGTCCTTCTTGGA 59.232 57.895 0.84 0.00 43.86 3.53
1498 1537 3.052036 CACCTTTTTCCTCGCAACAATG 58.948 45.455 0.00 0.00 0.00 2.82
1503 1542 1.652012 CGCACCTTTTTCCTCGCAA 59.348 52.632 0.00 0.00 0.00 4.85
1533 1584 1.381928 AATGCAGATGCGAGCTTGGG 61.382 55.000 2.37 0.00 45.83 4.12
1553 1604 3.307782 CGCATTCCAATCAAAATCCAAGC 59.692 43.478 0.00 0.00 0.00 4.01
1563 1614 3.067320 TCACAACAAACGCATTCCAATCA 59.933 39.130 0.00 0.00 0.00 2.57
1583 1634 6.252599 ACCAGGCATATAAATCACTTCTCA 57.747 37.500 0.00 0.00 0.00 3.27
1646 1697 0.106719 TTCTCCCATGGCCGGAAATC 60.107 55.000 5.05 0.00 0.00 2.17
1682 1733 1.307355 TGCGCTGGATCCACATTGTG 61.307 55.000 11.44 9.17 0.00 3.33
1684 1735 0.742505 ATTGCGCTGGATCCACATTG 59.257 50.000 11.44 1.77 0.00 2.82
1708 1759 2.746472 GCTCAATACAATCTTCCCGGCT 60.746 50.000 0.00 0.00 0.00 5.52
1712 1763 3.194005 TCCGCTCAATACAATCTTCCC 57.806 47.619 0.00 0.00 0.00 3.97
1808 1863 3.494749 GCAATGGATCTGGAGAAGAGAGG 60.495 52.174 0.00 0.00 38.67 3.69
1825 1880 2.034558 ACGAAAGGACCAAACTGCAATG 59.965 45.455 0.00 0.00 0.00 2.82
1830 1885 0.234884 GCGACGAAAGGACCAAACTG 59.765 55.000 0.00 0.00 0.00 3.16
1971 2033 3.450096 TCATCCTCAACCAGATCTGACAG 59.550 47.826 24.62 12.38 0.00 3.51
1974 2036 4.292643 TCATCATCCTCAACCAGATCTGA 58.707 43.478 24.62 3.11 0.00 3.27
2051 2113 2.033294 TGCCACCACTTGCGCATA 59.967 55.556 12.75 0.83 0.00 3.14
2150 2212 2.234414 TGAAGATTGCAATTGAAGGCCC 59.766 45.455 14.33 0.00 0.00 5.80
2153 2215 5.163794 GGCATTTGAAGATTGCAATTGAAGG 60.164 40.000 14.33 7.29 36.57 3.46
2216 2287 3.603629 GCCAACGCTGCACAAATAAAAAC 60.604 43.478 0.00 0.00 0.00 2.43
2217 2288 2.541762 GCCAACGCTGCACAAATAAAAA 59.458 40.909 0.00 0.00 0.00 1.94
2412 2483 5.245531 TGCACAAATAAAAACAACCACCAA 58.754 33.333 0.00 0.00 0.00 3.67
2413 2484 4.832248 TGCACAAATAAAAACAACCACCA 58.168 34.783 0.00 0.00 0.00 4.17
2414 2485 4.260579 GCTGCACAAATAAAAACAACCACC 60.261 41.667 0.00 0.00 0.00 4.61
2415 2486 4.549871 CGCTGCACAAATAAAAACAACCAC 60.550 41.667 0.00 0.00 0.00 4.16
2416 2487 3.553511 CGCTGCACAAATAAAAACAACCA 59.446 39.130 0.00 0.00 0.00 3.67
2417 2488 3.553917 ACGCTGCACAAATAAAAACAACC 59.446 39.130 0.00 0.00 0.00 3.77
2418 2489 4.770351 ACGCTGCACAAATAAAAACAAC 57.230 36.364 0.00 0.00 0.00 3.32
2419 2490 4.033358 CCAACGCTGCACAAATAAAAACAA 59.967 37.500 0.00 0.00 0.00 2.83
2420 2491 3.553511 CCAACGCTGCACAAATAAAAACA 59.446 39.130 0.00 0.00 0.00 2.83
2439 2510 1.004560 CAAGGACGAGAGCAGCCAA 60.005 57.895 0.00 0.00 0.00 4.52
2463 2534 6.158520 TCAGACATGATTTATCTCAAGGGGAA 59.841 38.462 0.00 0.00 0.00 3.97
2542 2615 6.539173 ACACAATCCACACCTATTCTTTACA 58.461 36.000 0.00 0.00 0.00 2.41
2647 2724 4.574674 ATGAACTTTGGCCATCTAGTGA 57.425 40.909 6.09 2.20 0.00 3.41
2650 2727 5.297776 CCAAGTATGAACTTTGGCCATCTAG 59.702 44.000 6.09 7.43 43.60 2.43
2768 2884 4.455533 GTCACCATGCAACTCAACTCAATA 59.544 41.667 0.00 0.00 0.00 1.90
2769 2885 3.254166 GTCACCATGCAACTCAACTCAAT 59.746 43.478 0.00 0.00 0.00 2.57
2843 2959 6.798427 TCTAAGTGAGATAGCCTTCACATT 57.202 37.500 7.29 2.37 35.73 2.71
2903 3019 2.351726 GAGGTAGCGTTCGCATTTTCAT 59.648 45.455 18.95 0.00 0.00 2.57
2921 3037 9.727627 GAAATAATTGAGAAATGCTAAGTGAGG 57.272 33.333 0.00 0.00 0.00 3.86
2952 3068 0.931005 GCTTCCTCTTTCGTATGGCG 59.069 55.000 0.00 0.00 43.01 5.69
3064 3180 5.815233 TTCTCCATAGCCTTCTGATTAGG 57.185 43.478 0.00 0.00 35.80 2.69
3279 3395 3.455469 GGTTGCTGGGATGCCTGC 61.455 66.667 25.32 25.32 35.65 4.85
3352 3468 1.028330 ATCCGCTGATGCACCAACTG 61.028 55.000 0.00 0.00 39.64 3.16
3495 3611 1.344065 TGCCGTTGTCCCTCTTAGAA 58.656 50.000 0.00 0.00 0.00 2.10
3554 3670 1.959282 CAGACTTTTGAGCAAGCCCTT 59.041 47.619 0.00 0.00 0.00 3.95
3605 3721 4.853468 TGAAGCCCAATACCAAGACATA 57.147 40.909 0.00 0.00 0.00 2.29
3623 3739 5.185454 TCTGACAGTTTTCTTCAGCTTGAA 58.815 37.500 1.59 0.00 36.25 2.69
3738 3856 1.413445 AGAGAAGCAGCATAGCCAGAG 59.587 52.381 0.00 0.00 34.23 3.35
3848 3966 4.097437 TCACCACGTCATTACCAGATCTAC 59.903 45.833 0.00 0.00 0.00 2.59
4109 4277 4.164843 TGGGCATAATCCAAGGAAGTAC 57.835 45.455 0.00 0.00 0.00 2.73
4225 4393 3.689161 CGCTGTCTGAAACCCATATTGAA 59.311 43.478 0.00 0.00 0.00 2.69
4229 4397 2.420129 GGACGCTGTCTGAAACCCATAT 60.420 50.000 8.26 0.00 32.47 1.78
4236 4404 1.301716 GCTGGGACGCTGTCTGAAA 60.302 57.895 8.26 0.00 32.47 2.69
4332 4500 3.006752 GGAATTGAGCACCCAAACATTGA 59.993 43.478 0.00 0.00 0.00 2.57
4344 4512 1.634973 TCATGTCCCAGGAATTGAGCA 59.365 47.619 0.00 0.00 0.00 4.26
4349 4517 4.801521 TGATCATCATGTCCCAGGAATT 57.198 40.909 0.00 0.00 0.00 2.17
4372 4540 2.810274 GCATCTCAAGTGACTTCAGCAA 59.190 45.455 0.00 0.00 0.00 3.91
4524 4692 6.605471 TCTTCAGCTCTGATTTGGTTACTA 57.395 37.500 0.00 0.00 39.64 1.82
4560 4728 1.956477 GAAACTTGTGTGCACATCCCT 59.044 47.619 24.69 5.82 41.52 4.20
4584 4752 4.281688 ACCAAACCTTCATGAGACAATTGG 59.718 41.667 19.41 19.41 40.39 3.16
4592 4760 4.157289 CAGGATCAACCAAACCTTCATGAG 59.843 45.833 0.00 0.00 42.04 2.90
4656 4824 7.094634 ACAGAAGAAAAACGTGATGCATATTCT 60.095 33.333 0.00 0.00 0.00 2.40
4698 4870 1.406860 TTTTGCTGAAACCAGGCCCC 61.407 55.000 0.00 0.00 32.40 5.80
4704 4876 5.827797 ACTCTGATTACTTTTGCTGAAACCA 59.172 36.000 0.00 0.00 0.00 3.67
4773 4946 2.234908 GACCTCATTGTACCTGCTCACT 59.765 50.000 0.00 0.00 0.00 3.41
4855 5028 3.050275 GTGCGCAGGACCAGGTTC 61.050 66.667 12.22 0.00 45.47 3.62
4878 5051 4.471338 TGTTGCAACACTAGCGGTACGA 62.471 50.000 27.96 0.41 45.30 3.43
4957 5130 3.560025 GGGAAAAGGCTGAACTGAGATGA 60.560 47.826 0.00 0.00 0.00 2.92
5144 5317 0.760567 AGTAGATCCATGAGGCCGCA 60.761 55.000 12.99 12.99 33.74 5.69
5145 5318 0.320247 CAGTAGATCCATGAGGCCGC 60.320 60.000 0.00 0.00 33.74 6.53
5170 5343 0.927029 GGAAGGGGAACTAATGGCCT 59.073 55.000 3.32 0.00 0.00 5.19
5176 5349 2.301009 GTTCACGAGGAAGGGGAACTAA 59.699 50.000 0.00 0.00 35.82 2.24
5187 5360 2.701951 ACTTTTACCTGGTTCACGAGGA 59.298 45.455 14.42 0.00 43.58 3.71
5262 5435 5.126779 AGACTCGATCTTGATGCTACTACA 58.873 41.667 0.00 0.00 31.62 2.74
5361 5534 4.661993 TCGTACTGCTATGCAAGTTTTG 57.338 40.909 0.00 0.00 38.41 2.44
5365 5538 3.056107 TCCTTTCGTACTGCTATGCAAGT 60.056 43.478 0.00 0.00 38.41 3.16
5455 5632 0.798776 CCACCATTGAGACGAACTGC 59.201 55.000 0.00 0.00 0.00 4.40
5577 5754 4.065088 CTCGAAGAATTGTTTCAGGTCCA 58.935 43.478 0.00 0.00 34.09 4.02
5765 5942 3.464907 CGAGCATCATTCTCCACTTCAT 58.535 45.455 0.00 0.00 33.17 2.57
6003 6200 5.794894 ACCTAAATGGAGGAGCATATTACG 58.205 41.667 0.13 0.00 39.15 3.18
6125 6329 8.414003 GTTGGGAAAATAACAGAACTTCTCTTT 58.586 33.333 0.00 0.00 29.07 2.52
6158 6362 4.461992 ACTAACGACAATGGTTTCAACG 57.538 40.909 0.00 0.00 0.00 4.10
6258 6462 7.790782 TTTCCCTACCAATGCTAGAAAATTT 57.209 32.000 0.00 0.00 0.00 1.82
6297 6501 3.448301 CCACCACTGCCAAAATATCATGT 59.552 43.478 0.00 0.00 0.00 3.21
6302 6506 3.168035 TCACCACCACTGCCAAAATAT 57.832 42.857 0.00 0.00 0.00 1.28
6303 6507 2.666272 TCACCACCACTGCCAAAATA 57.334 45.000 0.00 0.00 0.00 1.40
6371 6589 6.271488 TCATTAGTTTGCTGGGAGAATTTG 57.729 37.500 0.00 0.00 0.00 2.32
6409 6627 4.408182 TTGGCTGAGAAGAATAGCTACC 57.592 45.455 0.00 0.00 37.58 3.18
6410 6628 5.522097 GTCTTTGGCTGAGAAGAATAGCTAC 59.478 44.000 0.00 0.00 37.58 3.58
6411 6629 5.187772 TGTCTTTGGCTGAGAAGAATAGCTA 59.812 40.000 0.00 0.00 37.58 3.32
6460 6678 3.033368 TGTACTACGATTGTGCAGCAA 57.967 42.857 0.00 4.56 41.89 3.91
6493 6711 2.028658 TCAGTTCACAGTGCCTCAGATC 60.029 50.000 0.00 0.00 0.00 2.75
6500 6718 3.321497 CTCTTACTCAGTTCACAGTGCC 58.679 50.000 0.00 0.00 0.00 5.01
6542 6763 2.806288 ACAAGATGATACGTTTGCGC 57.194 45.000 0.00 0.00 42.83 6.09
6582 6803 6.261118 GGTGAAAGATATGCACAATTCTGAC 58.739 40.000 0.00 0.00 34.33 3.51
6591 6812 2.351726 GGTGTCGGTGAAAGATATGCAC 59.648 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.