Multiple sequence alignment - TraesCS6B01G427000

Loading Multiple Alignment...

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 TraesCS6B01G427000 chr6B 100.000 3179 0 0 1820 4998 695796748 695793570 0.000000e+00 5871.0
1 TraesCS6B01G427000 chr6B 100.000 1369 0 0 1 1369 695798567 695797199 0.000000e+00 2529.0
2 TraesCS6B01G427000 chr6B 72.489 458 115 11 4497 4949 174573495 174573946 2.430000e-28 137.0
3 TraesCS6B01G427000 chr6D 91.891 2454 125 30 1820 4242 457141333 457138923 0.000000e+00 3362.0
4 TraesCS6B01G427000 chr6D 94.839 872 34 7 502 1369 457142276 457141412 0.000000e+00 1351.0
5 TraesCS6B01G427000 chr6D 85.278 1080 93 33 3946 4998 457130039 457128999 0.000000e+00 1053.0
6 TraesCS6B01G427000 chr6D 93.082 318 17 1 249 566 457142587 457142275 1.270000e-125 460.0
7 TraesCS6B01G427000 chr6D 94.332 247 7 3 1 244 457142929 457142687 6.110000e-99 372.0
8 TraesCS6B01G427000 chr6D 93.617 94 3 2 3783 3875 457133911 457133820 2.430000e-28 137.0
9 TraesCS6B01G427000 chr6D 96.154 78 2 1 3874 3950 457133293 457133216 5.250000e-25 126.0
10 TraesCS6B01G427000 chr6D 100.000 43 0 0 4239 4281 457138811 457138769 4.150000e-11 80.5
11 TraesCS6B01G427000 chr6A 94.449 1351 60 7 3063 4404 604108539 604107195 0.000000e+00 2065.0
12 TraesCS6B01G427000 chr6A 91.485 963 60 13 2105 3054 604109577 604108624 0.000000e+00 1304.0
13 TraesCS6B01G427000 chr6A 95.623 594 19 2 779 1369 604115587 604114998 0.000000e+00 946.0
14 TraesCS6B01G427000 chr6A 89.979 479 30 11 1 469 604116064 604115594 1.990000e-168 603.0
15 TraesCS6B01G427000 chr6A 83.307 623 70 14 4396 4998 604106361 604105753 1.220000e-150 544.0
16 TraesCS6B01G427000 chr6A 81.699 306 19 12 1820 2110 604114919 604114636 2.340000e-53 220.0
17 TraesCS6B01G427000 chr6A 88.525 61 6 1 4908 4967 28345655 28345595 6.940000e-09 73.1
18 TraesCS6B01G427000 chr5A 92.527 1472 57 19 2670 4108 531467391 531468842 0.000000e+00 2060.0
19 TraesCS6B01G427000 chr5A 93.802 597 14 2 773 1369 531465934 531466507 0.000000e+00 876.0
20 TraesCS6B01G427000 chr5A 90.544 423 25 9 1 416 531465521 531465935 3.400000e-151 545.0
21 TraesCS6B01G427000 chr5A 89.535 430 26 10 1820 2232 531466587 531467014 1.230000e-145 527.0
22 TraesCS6B01G427000 chr5A 92.603 365 16 4 2282 2644 531467037 531467392 9.590000e-142 514.0
23 TraesCS6B01G427000 chr5A 90.278 216 14 3 4067 4281 531468843 531469052 4.930000e-70 276.0
24 TraesCS6B01G427000 chr5A 100.000 29 0 0 878 906 531467038 531467010 3.000000e-03 54.7
25 TraesCS6B01G427000 chr5D 87.125 567 49 8 34 600 337531813 337531271 5.500000e-174 621.0
26 TraesCS6B01G427000 chr5B 86.160 513 46 9 108 600 396326779 396326272 9.530000e-147 531.0
27 TraesCS6B01G427000 chr3D 82.935 627 70 17 1 600 94651560 94650944 9.530000e-147 531.0
28 TraesCS6B01G427000 chr2A 82.531 561 79 13 47 588 658994420 658994980 4.530000e-130 475.0
29 TraesCS6B01G427000 chr1B 89.205 352 38 0 249 600 4949308 4949659 1.650000e-119 440.0
30 TraesCS6B01G427000 chrUn 83.369 469 60 12 47 497 269147941 269148409 7.740000e-113 418.0
31 TraesCS6B01G427000 chrUn 83.824 68 11 0 4882 4949 10611183 10611250 1.160000e-06 65.8
32 TraesCS6B01G427000 chr2D 83.369 469 60 12 47 497 514999794 515000262 7.740000e-113 418.0
33 TraesCS6B01G427000 chr2D 83.156 469 61 12 47 497 515013141 515013609 3.600000e-111 412.0
34 TraesCS6B01G427000 chr2B 80.893 560 77 17 55 588 606750679 606751234 1.000000e-111 414.0
35 TraesCS6B01G427000 chr2B 73.478 460 108 14 4497 4949 110858375 110858827 1.440000e-35 161.0
36 TraesCS6B01G427000 chr7B 72.707 458 113 12 4497 4949 742647175 742647625 5.220000e-30 143.0
37 TraesCS6B01G427000 chr3A 86.567 67 7 2 4898 4962 427785602 427785668 6.940000e-09 73.1
38 TraesCS6B01G427000 chr3A 89.286 56 3 3 4903 4956 102236852 102236906 3.230000e-07 67.6
39 TraesCS6B01G427000 chr3A 88.000 50 6 0 4900 4949 21280534 21280583 5.400000e-05 60.2


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 TraesCS6B01G427000 chr6B 695793570 695798567 4997 True 4200.000000 5871 100.000000 1 4998 2 chr6B.!!$R1 4997
1 TraesCS6B01G427000 chr6D 457138769 457142929 4160 True 1125.100000 3362 94.828800 1 4281 5 chr6D.!!$R2 4280
2 TraesCS6B01G427000 chr6D 457128999 457133911 4912 True 438.666667 1053 91.683000 3783 4998 3 chr6D.!!$R1 1215
3 TraesCS6B01G427000 chr6A 604105753 604109577 3824 True 1304.333333 2065 89.747000 2105 4998 3 chr6A.!!$R2 2893
4 TraesCS6B01G427000 chr6A 604114636 604116064 1428 True 589.666667 946 89.100333 1 2110 3 chr6A.!!$R3 2109
5 TraesCS6B01G427000 chr5A 531465521 531469052 3531 False 799.666667 2060 91.548167 1 4281 6 chr5A.!!$F1 4280
6 TraesCS6B01G427000 chr5D 337531271 337531813 542 True 621.000000 621 87.125000 34 600 1 chr5D.!!$R1 566
7 TraesCS6B01G427000 chr5B 396326272 396326779 507 True 531.000000 531 86.160000 108 600 1 chr5B.!!$R1 492
8 TraesCS6B01G427000 chr3D 94650944 94651560 616 True 531.000000 531 82.935000 1 600 1 chr3D.!!$R1 599
9 TraesCS6B01G427000 chr2A 658994420 658994980 560 False 475.000000 475 82.531000 47 588 1 chr2A.!!$F1 541
10 TraesCS6B01G427000 chr2B 606750679 606751234 555 False 414.000000 414 80.893000 55 588 1 chr2B.!!$F2 533

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
867 1065 1.066645 ACGTAATCCCGTTGGAGAACC 60.067 52.381 0.0 0.0 46.08 3.62 F
2038 2255 1.000060 GTACCACTACCACGCAGTTGA 60.000 52.381 0.0 0.0 41.61 3.18 F
2508 2739 0.463204 CATCAGCCCTCGTGATCAGT 59.537 55.000 0.0 0.0 32.06 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2436 0.109179 GCGGATTTGCAACAGCATGA 60.109 50.0 0.00 0.0 38.23 3.07 R
3708 4054 0.606604 TGTCCTGAACTCCGGCTTAC 59.393 55.0 0.00 0.0 0.00 2.34 R
4429 9501 0.473694 TTCAGAGAGTGGGCCTTCCA 60.474 55.0 4.53 0.0 44.79 3.53 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
28 32 4.020573 TGTTGGAGTAATGGACCAGTACAG 60.021 45.833 28.58 0.00 37.38 2.74
29 33 4.055710 TGGAGTAATGGACCAGTACAGA 57.944 45.455 28.58 12.65 37.38 3.41
30 34 4.620723 TGGAGTAATGGACCAGTACAGAT 58.379 43.478 28.58 12.47 37.38 2.90
31 35 4.405680 TGGAGTAATGGACCAGTACAGATG 59.594 45.833 28.58 0.00 37.38 2.90
83 87 6.255215 TCAGATTTCGTTTGTTCACTGAAAC 58.745 36.000 0.00 0.00 32.02 2.78
275 399 1.374758 AAGGCCGTCGAGAAGCAAG 60.375 57.895 0.00 0.00 0.00 4.01
329 453 8.867097 TGTAGAACCTAATGATTCTATGGTACC 58.133 37.037 4.43 4.43 39.11 3.34
368 492 4.021280 TGTTGCTTTCATTGGTATGCACAT 60.021 37.500 0.00 0.00 0.00 3.21
515 649 8.466086 AGAAACTGAAGATTTTGAAACAACAC 57.534 30.769 0.00 0.00 0.00 3.32
534 668 3.060614 ATGGGTCCTTCGGCCATGG 62.061 63.158 7.63 7.63 27.16 3.66
538 672 3.407967 TCCTTCGGCCATGGGTCC 61.408 66.667 15.13 6.06 0.00 4.46
562 759 6.102663 CACTACAACAATCTCTCGATCCTTT 58.897 40.000 0.00 0.00 0.00 3.11
590 787 6.998074 TGGCAAAATCTGAATAATATCCTCGT 59.002 34.615 0.00 0.00 0.00 4.18
600 797 5.730296 ATAATATCCTCGTGAAGACCAGG 57.270 43.478 0.00 0.00 0.00 4.45
606 803 1.376037 CGTGAAGACCAGGAAGCCC 60.376 63.158 0.00 0.00 32.66 5.19
607 804 1.376037 GTGAAGACCAGGAAGCCCG 60.376 63.158 0.00 0.00 37.58 6.13
665 862 1.955778 CATGAGAACCACACTGCCAAA 59.044 47.619 0.00 0.00 0.00 3.28
676 873 1.283613 CACTGCCAAATACCCAGGGTA 59.716 52.381 21.53 21.53 42.80 3.69
715 912 2.969990 GGAGACGACTAAAAACTCCCC 58.030 52.381 0.00 0.00 40.58 4.81
716 913 2.301009 GGAGACGACTAAAAACTCCCCA 59.699 50.000 0.00 0.00 40.58 4.96
717 914 3.586892 GAGACGACTAAAAACTCCCCAG 58.413 50.000 0.00 0.00 0.00 4.45
718 915 2.074576 GACGACTAAAAACTCCCCAGC 58.925 52.381 0.00 0.00 0.00 4.85
757 955 1.135024 CAACAGCAACTGCAAACCTGT 60.135 47.619 4.22 3.86 45.16 4.00
758 956 1.185315 ACAGCAACTGCAAACCTGTT 58.815 45.000 4.22 0.00 45.16 3.16
759 957 1.550072 ACAGCAACTGCAAACCTGTTT 59.450 42.857 4.22 0.00 45.16 2.83
866 1064 2.094338 AGACGTAATCCCGTTGGAGAAC 60.094 50.000 0.00 0.00 46.08 3.01
867 1065 1.066645 ACGTAATCCCGTTGGAGAACC 60.067 52.381 0.00 0.00 46.08 3.62
1179 1380 2.388232 GGTGTTCGACATGGACGGC 61.388 63.158 12.97 8.22 0.00 5.68
1887 2093 1.722034 GAGGCAGATCAGGTGGGATA 58.278 55.000 0.00 0.00 0.00 2.59
1888 2094 2.050144 GAGGCAGATCAGGTGGGATAA 58.950 52.381 0.00 0.00 0.00 1.75
1895 2101 5.256474 CAGATCAGGTGGGATAAGTTTGTT 58.744 41.667 0.00 0.00 0.00 2.83
1897 2103 4.993705 TCAGGTGGGATAAGTTTGTTCT 57.006 40.909 0.00 0.00 0.00 3.01
1898 2104 4.651778 TCAGGTGGGATAAGTTTGTTCTG 58.348 43.478 0.00 0.00 0.00 3.02
1906 2112 8.739972 GTGGGATAAGTTTGTTCTGAAATGTAT 58.260 33.333 0.00 0.00 0.00 2.29
1922 2128 7.416817 TGAAATGTATCTCAATTTGCATACGG 58.583 34.615 0.00 0.00 0.00 4.02
2038 2255 1.000060 GTACCACTACCACGCAGTTGA 60.000 52.381 0.00 0.00 41.61 3.18
2090 2307 5.125417 GGGCTTTGCTGTATGAATAGTGAAA 59.875 40.000 0.00 0.00 0.00 2.69
2107 2324 4.093998 AGTGAAATGTCTGTCGATTGATGC 59.906 41.667 0.00 0.00 0.00 3.91
2145 2363 6.659824 TCAGGAAGTTAGAGAGGTTGTTTTT 58.340 36.000 0.00 0.00 0.00 1.94
2146 2364 6.766467 TCAGGAAGTTAGAGAGGTTGTTTTTC 59.234 38.462 0.00 0.00 0.00 2.29
2147 2365 6.542370 CAGGAAGTTAGAGAGGTTGTTTTTCA 59.458 38.462 0.00 0.00 0.00 2.69
2196 2421 5.751028 GCTATATAGATTGGATGGCTCGAAC 59.249 44.000 14.16 0.00 0.00 3.95
2204 2429 3.531538 TGGATGGCTCGAACTTTGATAC 58.468 45.455 0.00 0.00 0.00 2.24
2211 2436 3.120649 GCTCGAACTTTGATACGCAAACT 60.121 43.478 0.00 0.00 41.37 2.66
2218 2443 3.745332 TTGATACGCAAACTCATGCTG 57.255 42.857 0.00 0.00 44.21 4.41
2264 2490 3.799035 CAGTTATCTGTTCGCACAACAC 58.201 45.455 0.00 0.00 36.97 3.32
2274 2500 3.226346 TCGCACAACACTATACCTCAC 57.774 47.619 0.00 0.00 0.00 3.51
2285 2511 7.407393 ACACTATACCTCACTTAGAAACCTC 57.593 40.000 0.00 0.00 0.00 3.85
2331 2558 5.173774 TGCTCTGTCAACTTTTTGATGAC 57.826 39.130 0.00 0.00 43.72 3.06
2495 2726 6.818644 TCAACTGACTTCTTAATACCATCAGC 59.181 38.462 0.00 0.00 36.41 4.26
2508 2739 0.463204 CATCAGCCCTCGTGATCAGT 59.537 55.000 0.00 0.00 32.06 3.41
2544 2775 4.202245 CAGCAGGTGCCTTACTAGTTTA 57.798 45.455 0.00 0.00 43.38 2.01
2552 2783 9.005777 CAGGTGCCTTACTAGTTTATTGTTTAA 57.994 33.333 0.00 0.00 0.00 1.52
2580 2813 0.655733 AACAGACACGGTTGCTTTCG 59.344 50.000 0.00 0.00 0.00 3.46
2583 2816 0.935196 AGACACGGTTGCTTTCGTTC 59.065 50.000 0.00 0.00 37.53 3.95
2584 2817 0.653636 GACACGGTTGCTTTCGTTCA 59.346 50.000 0.00 0.00 37.53 3.18
2585 2818 1.263217 GACACGGTTGCTTTCGTTCAT 59.737 47.619 0.00 0.00 37.53 2.57
2586 2819 2.477375 GACACGGTTGCTTTCGTTCATA 59.523 45.455 0.00 0.00 37.53 2.15
2587 2820 3.071479 ACACGGTTGCTTTCGTTCATAT 58.929 40.909 0.00 0.00 37.53 1.78
2588 2821 4.247258 ACACGGTTGCTTTCGTTCATATA 58.753 39.130 0.00 0.00 37.53 0.86
2713 2953 4.541973 TGAGTTCATGTGTAGCATCTGT 57.458 40.909 0.00 0.00 35.19 3.41
2749 2989 4.423625 AATCTGCCAGACTAATGGTACC 57.576 45.455 4.43 4.43 42.75 3.34
2840 3080 6.509418 TTTGTTACTGATTCCTACCATTGC 57.491 37.500 0.00 0.00 0.00 3.56
2858 3098 2.116238 TGCTATTACACAGGAGGGGTC 58.884 52.381 0.00 0.00 0.00 4.46
2963 3204 8.308931 TGTTCATCTCGTGGTTATACTTTTAGT 58.691 33.333 0.00 0.00 0.00 2.24
3007 3248 8.194769 TGCCCATGTATATTACTGTGATATACG 58.805 37.037 25.17 17.12 42.11 3.06
3008 3249 7.169308 GCCCATGTATATTACTGTGATATACGC 59.831 40.741 25.17 20.75 42.11 4.42
3009 3250 8.194769 CCCATGTATATTACTGTGATATACGCA 58.805 37.037 25.17 15.99 42.11 5.24
3010 3251 9.020813 CCATGTATATTACTGTGATATACGCAC 57.979 37.037 25.17 13.45 42.11 5.34
3011 3252 9.567848 CATGTATATTACTGTGATATACGCACA 57.432 33.333 25.17 17.05 42.11 4.57
3016 3257 9.705290 ATATTACTGTGATATACGCACATTCAA 57.295 29.630 9.85 6.13 44.42 2.69
3019 3265 3.874543 TGTGATATACGCACATTCAACCC 59.125 43.478 6.24 0.00 41.00 4.11
3061 3390 7.041372 TGGTAATGTTCTGCAACTAGTTTCTTC 60.041 37.037 5.07 0.00 33.17 2.87
3062 3391 7.173390 GGTAATGTTCTGCAACTAGTTTCTTCT 59.827 37.037 5.07 0.00 33.17 2.85
3063 3392 7.573968 AATGTTCTGCAACTAGTTTCTTCTT 57.426 32.000 5.07 0.00 33.17 2.52
3064 3393 7.573968 ATGTTCTGCAACTAGTTTCTTCTTT 57.426 32.000 5.07 0.00 33.17 2.52
3065 3394 7.016361 TGTTCTGCAACTAGTTTCTTCTTTC 57.984 36.000 5.07 0.00 33.17 2.62
3066 3395 6.823689 TGTTCTGCAACTAGTTTCTTCTTTCT 59.176 34.615 5.07 0.00 33.17 2.52
3067 3396 7.336931 TGTTCTGCAACTAGTTTCTTCTTTCTT 59.663 33.333 5.07 0.00 33.17 2.52
3068 3397 7.251704 TCTGCAACTAGTTTCTTCTTTCTTG 57.748 36.000 5.07 0.00 0.00 3.02
3069 3398 5.821204 TGCAACTAGTTTCTTCTTTCTTGC 58.179 37.500 5.07 3.07 0.00 4.01
3070 3399 4.906437 GCAACTAGTTTCTTCTTTCTTGCG 59.094 41.667 5.07 0.00 0.00 4.85
3111 3440 4.726317 TCATGTTGATCTCCCCAATCCTTA 59.274 41.667 0.00 0.00 0.00 2.69
3120 3449 4.139786 CTCCCCAATCCTTATGTCATGTG 58.860 47.826 0.00 0.00 0.00 3.21
3314 3649 5.847304 TCTTCAATATGCTAATCTCGCACT 58.153 37.500 0.00 0.00 40.65 4.40
3315 3650 6.981722 TCTTCAATATGCTAATCTCGCACTA 58.018 36.000 0.00 0.00 40.65 2.74
3316 3651 7.606349 TCTTCAATATGCTAATCTCGCACTAT 58.394 34.615 0.00 0.00 40.65 2.12
3325 3661 9.712305 ATGCTAATCTCGCACTATTAAACTTAT 57.288 29.630 0.00 0.00 40.65 1.73
3368 3704 0.908910 TAAGCAGAGAATTCCGCCCA 59.091 50.000 0.65 0.00 0.00 5.36
3505 3841 8.043113 TCCCATTATGTAGCTTAGCATATGAAG 58.957 37.037 6.97 3.29 0.00 3.02
3513 3849 6.198237 AGCTTAGCATATGAAGGATTCCTT 57.802 37.500 17.98 17.98 46.93 3.36
3521 3857 7.284034 AGCATATGAAGGATTCCTTTACAGTTG 59.716 37.037 18.89 14.06 46.93 3.16
3575 3916 9.384764 GGCATACTATCAGGATTCCTAAATTAC 57.615 37.037 4.51 0.00 29.64 1.89
3708 4054 6.132791 TGCTCCTTGATTCTACTACTTACG 57.867 41.667 0.00 0.00 0.00 3.18
3743 4101 6.135290 TCAGGACAGTTTTTGTGAATCTTG 57.865 37.500 0.00 0.00 41.05 3.02
3781 4139 2.993220 TGTGCGTGTGTACTGATTCATC 59.007 45.455 0.00 0.00 0.00 2.92
3870 4228 0.179156 GACGAAACAGGGCGATACGA 60.179 55.000 0.00 0.00 0.00 3.43
3887 4773 1.024579 CGACCCCCACGATTCTTTGG 61.025 60.000 0.00 0.00 0.00 3.28
4028 8096 6.567050 ACGTCGTACACCTTGAATGTAATAT 58.433 36.000 0.00 0.00 34.41 1.28
4029 8097 7.037438 ACGTCGTACACCTTGAATGTAATATT 58.963 34.615 0.00 0.00 34.41 1.28
4030 8098 7.546667 ACGTCGTACACCTTGAATGTAATATTT 59.453 33.333 0.00 0.00 34.41 1.40
4087 8195 5.010012 CCATACCCTCCAAAAATATGACTGC 59.990 44.000 0.00 0.00 0.00 4.40
4088 8196 4.322057 ACCCTCCAAAAATATGACTGCT 57.678 40.909 0.00 0.00 0.00 4.24
4089 8197 5.450818 ACCCTCCAAAAATATGACTGCTA 57.549 39.130 0.00 0.00 0.00 3.49
4098 8206 8.616076 CCAAAAATATGACTGCTACTAGAAAGG 58.384 37.037 0.00 0.00 0.00 3.11
4108 8216 7.875971 ACTGCTACTAGAAAGGAATTTGTTTG 58.124 34.615 0.00 0.00 0.00 2.93
4138 8247 0.239082 CGTGATGCAGCTTCAAGCAA 59.761 50.000 13.10 0.00 45.56 3.91
4139 8248 1.135489 CGTGATGCAGCTTCAAGCAAT 60.135 47.619 13.10 1.76 45.56 3.56
4150 8259 4.093998 AGCTTCAAGCAATGTGTCGATTAG 59.906 41.667 13.10 0.00 45.56 1.73
4178 8287 4.209538 CATCAGGCACCAAGGAATTATGA 58.790 43.478 0.00 0.00 0.00 2.15
4189 8298 6.210584 ACCAAGGAATTATGACCGTGAAATTT 59.789 34.615 0.00 0.00 37.74 1.82
4299 8525 8.218338 AGATGATTGTGATTGTGTAGATTTCC 57.782 34.615 0.00 0.00 0.00 3.13
4330 8556 2.095415 CAGGTACGCCTTTAAACCTTGC 60.095 50.000 0.00 0.00 44.18 4.01
4333 8559 1.443702 CGCCTTTAAACCTTGCCGC 60.444 57.895 0.00 0.00 0.00 6.53
4335 8561 1.811645 GCCTTTAAACCTTGCCGCCA 61.812 55.000 0.00 0.00 0.00 5.69
4352 8578 2.855963 CGCCAGCTGATAAGCATTTTTG 59.144 45.455 17.39 0.00 37.25 2.44
4424 9496 1.679032 CCTCCTTCGATTTCCCCACAC 60.679 57.143 0.00 0.00 0.00 3.82
4429 9501 1.302993 CGATTTCCCCACACCCGTT 60.303 57.895 0.00 0.00 0.00 4.44
4440 9512 4.280019 ACCCGTTGGAAGGCCCAC 62.280 66.667 0.00 0.00 46.62 4.61
4464 9541 4.020751 TCTCTGAAAGTGACTCATTCTGGG 60.021 45.833 4.72 2.07 30.39 4.45
4478 9555 6.894103 ACTCATTCTGGGCTTCAAGAATATTT 59.106 34.615 0.00 0.00 30.80 1.40
4479 9556 7.398332 ACTCATTCTGGGCTTCAAGAATATTTT 59.602 33.333 0.00 0.00 30.80 1.82
4542 9632 9.512588 AGACTTATCAACATTGATTCTTTGTCT 57.487 29.630 12.16 13.71 45.13 3.41
4561 9651 4.159693 TGTCTAGTCGCATCACAATACCTT 59.840 41.667 0.00 0.00 0.00 3.50
4586 9676 6.721668 TCTCAATAGATCCTTGATCCGTACAT 59.278 38.462 8.35 0.00 39.66 2.29
4589 9679 7.179160 TCAATAGATCCTTGATCCGTACATCAT 59.821 37.037 4.61 0.00 39.66 2.45
4605 9695 3.254166 ACATCATTGACACTGGTTGCTTC 59.746 43.478 0.00 0.00 0.00 3.86
4635 9725 2.880890 AGAGACTGTCATTGGCAAACAC 59.119 45.455 10.88 4.41 0.00 3.32
4698 9788 1.208052 CCGGACTCCATCAACATGAGT 59.792 52.381 0.00 0.00 30.57 3.41
4725 9815 2.094675 GCAAGCATGAAAGCCCTTCTA 58.905 47.619 0.00 0.00 34.86 2.10
4727 9817 3.350833 CAAGCATGAAAGCCCTTCTACT 58.649 45.455 0.00 0.00 34.86 2.57
4736 9826 4.479786 AAGCCCTTCTACTGCTAGAAAG 57.520 45.455 0.00 0.00 38.32 2.62
4737 9827 3.714144 AGCCCTTCTACTGCTAGAAAGA 58.286 45.455 0.00 0.00 38.32 2.52
4749 9839 6.779860 ACTGCTAGAAAGAAAAAGGTATGGA 58.220 36.000 0.00 0.00 0.00 3.41
4767 9857 2.206223 GGAGAAATAGGGTCCCCTTGT 58.794 52.381 10.83 0.00 45.70 3.16
4777 9867 3.322466 CCCCTTGTCGCACTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
4810 9901 0.247185 GCATCCAAACCACCACCATG 59.753 55.000 0.00 0.00 0.00 3.66
4822 9914 0.523072 CCACCATGAAAAGCACCGAG 59.477 55.000 0.00 0.00 0.00 4.63
4823 9915 1.522668 CACCATGAAAAGCACCGAGA 58.477 50.000 0.00 0.00 0.00 4.04
4832 9924 5.120399 TGAAAAGCACCGAGAAAGAAACTA 58.880 37.500 0.00 0.00 0.00 2.24
4840 9932 5.522460 CACCGAGAAAGAAACTAAAGACACA 59.478 40.000 0.00 0.00 0.00 3.72
4843 9935 6.411652 CGAGAAAGAAACTAAAGACACACAC 58.588 40.000 0.00 0.00 0.00 3.82
4844 9936 6.509677 CGAGAAAGAAACTAAAGACACACACC 60.510 42.308 0.00 0.00 0.00 4.16
4845 9937 6.415573 AGAAAGAAACTAAAGACACACACCT 58.584 36.000 0.00 0.00 0.00 4.00
4851 9943 7.990886 AGAAACTAAAGACACACACCTCATAAA 59.009 33.333 0.00 0.00 0.00 1.40
4859 9951 5.120399 ACACACACCTCATAAAAGTTTCGA 58.880 37.500 0.00 0.00 0.00 3.71
4876 9968 2.905075 TCGATGAAACATGGGCTAGTG 58.095 47.619 0.00 0.00 0.00 2.74
4877 9969 1.942657 CGATGAAACATGGGCTAGTGG 59.057 52.381 0.00 0.00 0.00 4.00
4879 9971 0.698238 TGAAACATGGGCTAGTGGCT 59.302 50.000 0.00 0.00 41.46 4.75
4880 9972 1.075374 TGAAACATGGGCTAGTGGCTT 59.925 47.619 0.00 0.00 41.46 4.35
4935 10027 6.270695 TCATTCCAGTCTATCATATGCCTTCA 59.729 38.462 0.00 0.00 0.00 3.02
4950 10042 3.887110 TGCCTTCATCATATCCAGCTTTG 59.113 43.478 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 32 7.377398 TGTTGGCCAATATTTATACATGCATC 58.623 34.615 23.66 2.47 0.00 3.91
29 33 7.300556 TGTTGGCCAATATTTATACATGCAT 57.699 32.000 23.66 0.00 0.00 3.96
30 34 6.721704 TGTTGGCCAATATTTATACATGCA 57.278 33.333 23.66 6.98 0.00 3.96
31 35 7.116662 CACATGTTGGCCAATATTTATACATGC 59.883 37.037 29.73 12.96 43.14 4.06
83 87 0.387239 GTTTAGGTGGCTTGCGCAAG 60.387 55.000 39.20 39.20 41.24 4.01
275 399 5.163513 CCAAGGCATTGATAGTTGTTTCAC 58.836 41.667 13.66 0.00 38.83 3.18
329 453 7.538334 TGAAAGCAACATCAAGATATTTTCACG 59.462 33.333 0.00 0.00 29.93 4.35
368 492 8.831550 GTTGAAAATATGTGTTTAAGCCCAAAA 58.168 29.630 0.00 0.00 0.00 2.44
534 668 3.192844 TCGAGAGATTGTTGTAGTGGACC 59.807 47.826 0.00 0.00 33.31 4.46
562 759 8.945195 AGGATATTATTCAGATTTTGCCATGA 57.055 30.769 0.00 0.00 0.00 3.07
590 787 3.068881 CGGGCTTCCTGGTCTTCA 58.931 61.111 0.00 0.00 0.00 3.02
600 797 1.312815 AATCATGCTTAGCGGGCTTC 58.687 50.000 0.00 0.00 0.00 3.86
606 803 8.499162 AGTTAGCTTATAAAATCATGCTTAGCG 58.501 33.333 0.00 0.00 32.72 4.26
607 804 9.604626 CAGTTAGCTTATAAAATCATGCTTAGC 57.395 33.333 0.00 0.00 32.72 3.09
676 873 1.321474 CCCAGCCGTTGCATTATCAT 58.679 50.000 0.00 0.00 41.13 2.45
866 1064 1.775039 CTGGATTACGCACCGCATGG 61.775 60.000 0.00 0.00 42.84 3.66
867 1065 1.643292 CTGGATTACGCACCGCATG 59.357 57.895 0.00 0.00 0.00 4.06
874 1072 1.069204 GCTCTGATCCTGGATTACGCA 59.931 52.381 11.17 3.19 0.00 5.24
956 1154 3.406361 GTCTGTCTGTGGCGTGCG 61.406 66.667 0.00 0.00 0.00 5.34
957 1155 3.406361 CGTCTGTCTGTGGCGTGC 61.406 66.667 0.00 0.00 0.00 5.34
958 1156 3.406361 GCGTCTGTCTGTGGCGTG 61.406 66.667 0.00 0.00 0.00 5.34
1056 1254 2.684104 CGTGGGAGGAGGAGGAGA 59.316 66.667 0.00 0.00 0.00 3.71
1895 2101 8.337532 CGTATGCAAATTGAGATACATTTCAGA 58.662 33.333 0.00 0.00 0.00 3.27
1897 2103 7.416817 CCGTATGCAAATTGAGATACATTTCA 58.583 34.615 0.00 0.00 0.00 2.69
1898 2104 6.857964 CCCGTATGCAAATTGAGATACATTTC 59.142 38.462 0.00 0.00 0.00 2.17
1906 2112 3.213506 CATCCCCGTATGCAAATTGAGA 58.786 45.455 0.00 0.00 0.00 3.27
1919 2125 1.194781 ACTGAACTGAGCATCCCCGT 61.195 55.000 0.00 0.00 0.00 5.28
1922 2128 2.289945 ACTGAACTGAACTGAGCATCCC 60.290 50.000 0.00 0.00 0.00 3.85
2030 2247 5.143660 TGAATCAACGTTTAATCAACTGCG 58.856 37.500 0.00 0.00 32.53 5.18
2038 2255 6.206395 TCATGGCATGAATCAACGTTTAAT 57.794 33.333 27.03 0.00 36.11 1.40
2090 2307 1.929169 CGTGCATCAATCGACAGACAT 59.071 47.619 0.00 0.00 0.00 3.06
2107 2324 4.315803 ACTTCCTGAAATGTTAGTCCGTG 58.684 43.478 0.00 0.00 0.00 4.94
2145 2363 3.291584 ACGCACTCTTCCTATCATCTGA 58.708 45.455 0.00 0.00 0.00 3.27
2146 2364 3.724508 ACGCACTCTTCCTATCATCTG 57.275 47.619 0.00 0.00 0.00 2.90
2147 2365 3.449018 ACAACGCACTCTTCCTATCATCT 59.551 43.478 0.00 0.00 0.00 2.90
2211 2436 0.109179 GCGGATTTGCAACAGCATGA 60.109 50.000 0.00 0.00 38.23 3.07
2218 2443 2.535934 TGTAATCGCGGATTTGCAAC 57.464 45.000 6.13 1.14 33.95 4.17
2264 2490 7.648039 AGTGAGGTTTCTAAGTGAGGTATAG 57.352 40.000 0.00 0.00 0.00 1.31
2274 2500 8.260818 TGATCATTAGGAAGTGAGGTTTCTAAG 58.739 37.037 0.00 0.00 0.00 2.18
2285 2511 6.137794 AGACGTACTGATCATTAGGAAGTG 57.862 41.667 16.79 0.00 0.00 3.16
2331 2558 5.221048 GGGAATTCCTTGGAATAACACGATG 60.221 44.000 23.63 0.00 35.95 3.84
2487 2718 0.977627 TGATCACGAGGGCTGATGGT 60.978 55.000 0.00 0.00 0.00 3.55
2495 2726 2.166459 TGCTTCTTACTGATCACGAGGG 59.834 50.000 0.00 0.00 0.00 4.30
2508 2739 2.167281 CCTGCTGCTAGAGTGCTTCTTA 59.833 50.000 0.00 0.00 37.36 2.10
2552 2783 6.346096 AGCAACCGTGTCTGTTATATACAAT 58.654 36.000 0.00 0.00 36.02 2.71
2713 2953 9.255304 GTCTGGCAGATTTTTACAATAACAAAA 57.745 29.630 21.84 0.00 0.00 2.44
2749 2989 7.192913 TGCCACTAATAATTGCAGTTATTTCG 58.807 34.615 26.16 20.25 36.15 3.46
2817 3057 6.245408 AGCAATGGTAGGAATCAGTAACAAA 58.755 36.000 0.00 0.00 0.00 2.83
2840 3080 5.839063 TGATTAGACCCCTCCTGTGTAATAG 59.161 44.000 0.00 0.00 33.73 1.73
2858 3098 2.355756 CCTTCACATTGCGGGTGATTAG 59.644 50.000 5.85 2.48 44.11 1.73
2920 3161 6.712095 AGATGAACAGAATGAGTTTAGTGCAA 59.288 34.615 0.00 0.00 39.69 4.08
2963 3204 7.510001 ACATGGGCAAGAAAAATGGATATCATA 59.490 33.333 4.83 0.00 34.44 2.15
2976 3217 7.342581 TCACAGTAATATACATGGGCAAGAAA 58.657 34.615 0.00 0.00 0.00 2.52
3007 3248 2.297033 ACACAGATTGGGTTGAATGTGC 59.703 45.455 3.22 0.00 41.26 4.57
3008 3249 4.589216 AACACAGATTGGGTTGAATGTG 57.411 40.909 0.00 1.83 43.35 3.21
3009 3250 6.916360 ATAAACACAGATTGGGTTGAATGT 57.084 33.333 0.00 0.00 44.40 2.71
3010 3251 8.497554 CAAAATAAACACAGATTGGGTTGAATG 58.502 33.333 0.00 0.00 44.40 2.67
3011 3252 7.661027 CCAAAATAAACACAGATTGGGTTGAAT 59.339 33.333 0.00 0.00 44.40 2.57
3012 3253 6.989169 CCAAAATAAACACAGATTGGGTTGAA 59.011 34.615 0.00 0.00 44.40 2.69
3013 3254 6.098982 ACCAAAATAAACACAGATTGGGTTGA 59.901 34.615 7.22 0.00 44.40 3.18
3016 3257 7.604657 TTACCAAAATAAACACAGATTGGGT 57.395 32.000 7.22 0.00 41.20 4.51
3061 3390 2.033299 TGTTCAGAAAGGCGCAAGAAAG 59.967 45.455 10.83 0.00 43.02 2.62
3062 3391 2.020720 TGTTCAGAAAGGCGCAAGAAA 58.979 42.857 10.83 0.00 43.02 2.52
3063 3392 1.674359 TGTTCAGAAAGGCGCAAGAA 58.326 45.000 10.83 0.27 43.02 2.52
3064 3393 1.896220 ATGTTCAGAAAGGCGCAAGA 58.104 45.000 10.83 0.00 43.02 3.02
3065 3394 2.159517 GGTATGTTCAGAAAGGCGCAAG 60.160 50.000 10.83 0.00 43.44 4.01
3066 3395 1.810151 GGTATGTTCAGAAAGGCGCAA 59.190 47.619 10.83 0.00 0.00 4.85
3067 3396 1.003118 AGGTATGTTCAGAAAGGCGCA 59.997 47.619 10.83 0.00 0.00 6.09
3068 3397 1.739067 AGGTATGTTCAGAAAGGCGC 58.261 50.000 0.00 0.00 0.00 6.53
3069 3398 3.334691 TGAAGGTATGTTCAGAAAGGCG 58.665 45.455 0.00 0.00 32.54 5.52
3070 3399 4.702131 ACATGAAGGTATGTTCAGAAAGGC 59.298 41.667 0.00 0.00 39.78 4.35
3111 3440 2.885135 TCAGCCTTTCCACATGACAT 57.115 45.000 0.00 0.00 0.00 3.06
3120 3449 6.920210 GCTAAATATCAACATTCAGCCTTTCC 59.080 38.462 0.00 0.00 0.00 3.13
3197 3528 4.207165 AGTTGGTTGAGCAGTAACACATT 58.793 39.130 0.00 0.00 0.00 2.71
3315 3650 9.577110 CACAAATGTCATCTGCATAAGTTTAAT 57.423 29.630 0.00 0.00 0.00 1.40
3316 3651 7.541783 GCACAAATGTCATCTGCATAAGTTTAA 59.458 33.333 0.00 0.00 0.00 1.52
3325 3661 1.542472 CAGGCACAAATGTCATCTGCA 59.458 47.619 10.61 0.00 30.46 4.41
3368 3704 3.524826 TGGAGCTGGATCTGGCTTATAT 58.475 45.455 12.61 0.00 39.05 0.86
3505 3841 6.438763 CACAAAGTCAACTGTAAAGGAATCC 58.561 40.000 0.00 0.00 0.00 3.01
3708 4054 0.606604 TGTCCTGAACTCCGGCTTAC 59.393 55.000 0.00 0.00 0.00 2.34
3743 4101 4.148891 CGCACAAGTTATCGGAAAAGTTC 58.851 43.478 0.00 0.00 0.00 3.01
3781 4139 1.413812 AGGTTTTCAAAGGCAAGGCAG 59.586 47.619 0.00 0.00 0.00 4.85
3870 4228 1.304134 GCCAAAGAATCGTGGGGGT 60.304 57.895 7.87 0.00 35.28 4.95
3887 4773 3.604582 AGTCAGGCTTAACATCTTCAGC 58.395 45.455 0.00 0.00 0.00 4.26
3962 8030 1.373497 CGACAGACACTGGAGCCAC 60.373 63.158 0.00 0.00 35.51 5.01
4028 8096 5.918576 CGATACAGCTCGACATATACCAAAA 59.081 40.000 0.00 0.00 41.12 2.44
4029 8097 5.239963 TCGATACAGCTCGACATATACCAAA 59.760 40.000 0.00 0.00 42.38 3.28
4030 8098 4.758165 TCGATACAGCTCGACATATACCAA 59.242 41.667 0.00 0.00 42.38 3.67
4087 8195 7.875971 ACTGCAAACAAATTCCTTTCTAGTAG 58.124 34.615 0.00 0.00 0.00 2.57
4088 8196 7.817418 ACTGCAAACAAATTCCTTTCTAGTA 57.183 32.000 0.00 0.00 0.00 1.82
4089 8197 6.715347 ACTGCAAACAAATTCCTTTCTAGT 57.285 33.333 0.00 0.00 0.00 2.57
4098 8206 3.730715 CGGTCAGAACTGCAAACAAATTC 59.269 43.478 0.00 0.00 0.00 2.17
4108 8216 0.950555 TGCATCACGGTCAGAACTGC 60.951 55.000 0.00 0.00 34.94 4.40
4138 8247 3.071457 TGATGCATCCCTAATCGACACAT 59.929 43.478 23.67 0.00 0.00 3.21
4139 8248 2.433970 TGATGCATCCCTAATCGACACA 59.566 45.455 23.67 0.00 0.00 3.72
4164 8273 3.992943 TCACGGTCATAATTCCTTGGT 57.007 42.857 0.00 0.00 0.00 3.67
4167 8276 6.099341 GCAAATTTCACGGTCATAATTCCTT 58.901 36.000 0.00 0.00 0.00 3.36
4178 8287 1.686355 TGACAGGCAAATTTCACGGT 58.314 45.000 0.00 0.00 0.00 4.83
4189 8298 5.368145 GTCATTAGGTATTCATGACAGGCA 58.632 41.667 0.00 0.00 44.24 4.75
4222 8332 7.093858 ACTCTACTACTAAATTCCAGTCACCAC 60.094 40.741 0.00 0.00 0.00 4.16
4299 8525 2.813179 GCGTACCTGCGATGCCTTG 61.813 63.158 0.00 0.00 0.00 3.61
4352 8578 1.252904 ACATGTGCAAGGGTGGATGC 61.253 55.000 0.00 0.00 42.86 3.91
4408 9480 1.024579 CGGGTGTGGGGAAATCGAAG 61.025 60.000 0.00 0.00 0.00 3.79
4429 9501 0.473694 TTCAGAGAGTGGGCCTTCCA 60.474 55.000 4.53 0.00 44.79 3.53
4440 9512 5.170021 CCAGAATGAGTCACTTTCAGAGAG 58.830 45.833 8.75 0.00 39.69 3.20
4478 9555 2.244000 GCTGCGAGCCAGTGTAAAA 58.756 52.632 0.00 0.00 43.71 1.52
4479 9556 3.966215 GCTGCGAGCCAGTGTAAA 58.034 55.556 0.00 0.00 43.71 2.01
4495 9572 8.226819 AGTCTTCTATTTATTTTAGCAAGGGC 57.773 34.615 0.00 0.00 41.61 5.19
4516 9606 9.512588 AGACAAAGAATCAATGTTGATAAGTCT 57.487 29.630 8.54 12.73 46.60 3.24
4542 9632 4.401202 TGAGAAGGTATTGTGATGCGACTA 59.599 41.667 0.00 0.00 0.00 2.59
4543 9633 3.195610 TGAGAAGGTATTGTGATGCGACT 59.804 43.478 0.00 0.00 0.00 4.18
4545 9635 3.885724 TGAGAAGGTATTGTGATGCGA 57.114 42.857 0.00 0.00 0.00 5.10
4561 9651 6.068670 TGTACGGATCAAGGATCTATTGAGA 58.931 40.000 15.74 0.00 39.86 3.27
4586 9676 2.929641 TGAAGCAACCAGTGTCAATGA 58.070 42.857 0.89 0.00 0.00 2.57
4589 9679 4.527509 TTTTTGAAGCAACCAGTGTCAA 57.472 36.364 0.00 0.00 0.00 3.18
4626 9716 1.686355 AAATCACCTCGTGTTTGCCA 58.314 45.000 0.00 0.00 34.79 4.92
4635 9725 2.673368 GCACCAGAAGTAAATCACCTCG 59.327 50.000 0.00 0.00 0.00 4.63
4698 9788 3.132925 GGCTTTCATGCTTGCTCAAAAA 58.867 40.909 0.00 0.00 0.00 1.94
4725 9815 6.779860 TCCATACCTTTTTCTTTCTAGCAGT 58.220 36.000 0.00 0.00 0.00 4.40
4727 9817 7.016153 TCTCCATACCTTTTTCTTTCTAGCA 57.984 36.000 0.00 0.00 0.00 3.49
4736 9826 6.546403 GGACCCTATTTCTCCATACCTTTTTC 59.454 42.308 0.00 0.00 0.00 2.29
4737 9827 6.432581 GGACCCTATTTCTCCATACCTTTTT 58.567 40.000 0.00 0.00 0.00 1.94
4767 9857 0.687757 AGGCATCTAAGGGAGTGCGA 60.688 55.000 0.00 0.00 38.43 5.10
4796 9887 2.158986 TGCTTTTCATGGTGGTGGTTTG 60.159 45.455 0.00 0.00 0.00 2.93
4810 9901 4.553756 AGTTTCTTTCTCGGTGCTTTTC 57.446 40.909 0.00 0.00 0.00 2.29
4822 9914 6.315393 TGAGGTGTGTGTCTTTAGTTTCTTTC 59.685 38.462 0.00 0.00 0.00 2.62
4823 9915 6.177610 TGAGGTGTGTGTCTTTAGTTTCTTT 58.822 36.000 0.00 0.00 0.00 2.52
4832 9924 7.404671 AAACTTTTATGAGGTGTGTGTCTTT 57.595 32.000 0.00 0.00 0.00 2.52
4840 9932 7.360361 GTTTCATCGAAACTTTTATGAGGTGT 58.640 34.615 11.42 0.00 45.65 4.16
4859 9951 1.285962 AGCCACTAGCCCATGTTTCAT 59.714 47.619 0.00 0.00 45.47 2.57
4866 9958 4.781934 CTTAAACTAAGCCACTAGCCCAT 58.218 43.478 0.00 0.00 45.47 4.00
4879 9971 9.569122 ACTTGAAGGAAGTTATGCTTAAACTAA 57.431 29.630 0.00 0.00 42.70 2.24
4950 10042 5.410439 TCAAGAGTAACCGGTTTTATGCTTC 59.590 40.000 27.64 12.22 0.00 3.86
4956 10048 3.647590 AGGGTCAAGAGTAACCGGTTTTA 59.352 43.478 27.64 5.17 36.35 1.52
4958 10050 2.052468 AGGGTCAAGAGTAACCGGTTT 58.948 47.619 27.64 8.51 36.35 3.27
4961 10053 2.853235 AAAGGGTCAAGAGTAACCGG 57.147 50.000 0.00 0.00 36.35 5.28
4963 10055 5.847111 AACAAAAAGGGTCAAGAGTAACC 57.153 39.130 0.00 0.00 34.64 2.85
4967 10059 5.993748 TGAAAACAAAAAGGGTCAAGAGT 57.006 34.783 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.