Multiple sequence alignment - TraesCS1B01G363100

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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 TraesCS1B01G363100 chr1B 100.000 3197 0 0 1 3197 591452851 591449655 0.000000e+00 5904
1 TraesCS1B01G363100 chr1A 87.718 3037 206 83 70 3038 533734662 533731725 0.000000e+00 3387
2 TraesCS1B01G363100 chr1A 76.471 459 54 30 351 800 30919295 30919708 1.940000e-47 200
3 TraesCS1B01G363100 chr1A 97.436 78 1 1 3104 3180 533731729 533731652 7.200000e-27 132
4 TraesCS1B01G363100 chr1D 90.283 2542 118 50 565 3038 436654696 436652216 0.000000e+00 3206
5 TraesCS1B01G363100 chr1D 80.250 400 35 19 32 407 436655186 436654807 8.800000e-66 261
6 TraesCS1B01G363100 chr1D 96.842 95 2 1 3104 3197 436652220 436652126 1.190000e-34 158
7 TraesCS1B01G363100 chr7D 89.856 1321 113 9 969 2288 496785497 496786797 0.000000e+00 1677
8 TraesCS1B01G363100 chr7B 88.561 1390 130 14 963 2352 524919263 524920623 0.000000e+00 1659
9 TraesCS1B01G363100 chr7B 77.750 1200 189 43 131 1298 194924539 194925692 0.000000e+00 665
10 TraesCS1B01G363100 chr7B 74.709 344 52 22 306 630 524920793 524921120 1.560000e-23 121
11 TraesCS1B01G363100 chr7A 88.456 1386 127 15 969 2351 562215664 562217019 0.000000e+00 1642
12 TraesCS1B01G363100 chr2A 77.527 752 88 47 70 800 643979103 643979794 8.370000e-101 377
13 TraesCS1B01G363100 chr4A 76.862 752 93 46 70 800 119349451 119348760 1.820000e-92 350
14 TraesCS1B01G363100 chr5A 79.355 465 59 23 71 519 555367268 555366825 3.120000e-75 292


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 TraesCS1B01G363100 chr1B 591449655 591452851 3196 True 5904.000000 5904 100.000 1 3197 1 chr1B.!!$R1 3196
1 TraesCS1B01G363100 chr1A 533731652 533734662 3010 True 1759.500000 3387 92.577 70 3180 2 chr1A.!!$R1 3110
2 TraesCS1B01G363100 chr1D 436652126 436655186 3060 True 1208.333333 3206 89.125 32 3197 3 chr1D.!!$R1 3165
3 TraesCS1B01G363100 chr7D 496785497 496786797 1300 False 1677.000000 1677 89.856 969 2288 1 chr7D.!!$F1 1319
4 TraesCS1B01G363100 chr7B 524919263 524921120 1857 False 890.000000 1659 81.635 306 2352 2 chr7B.!!$F2 2046
5 TraesCS1B01G363100 chr7B 194924539 194925692 1153 False 665.000000 665 77.750 131 1298 1 chr7B.!!$F1 1167
6 TraesCS1B01G363100 chr7A 562215664 562217019 1355 False 1642.000000 1642 88.456 969 2351 1 chr7A.!!$F1 1382
7 TraesCS1B01G363100 chr2A 643979103 643979794 691 False 377.000000 377 77.527 70 800 1 chr2A.!!$F1 730
8 TraesCS1B01G363100 chr4A 119348760 119349451 691 True 350.000000 350 76.862 70 800 1 chr4A.!!$R1 730

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
487 545 0.443869 GTACAGCCTGCATCGTGTTG 59.556 55.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 2525 0.322008 AGGCTACAAGAACAGCAGGC 60.322 55.0 0.0 0.0 39.63 4.85 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
212 214 2.898729 TTGAGGTATGAGCAGCTAGC 57.101 50.000 6.62 6.62 46.19 3.42
229 249 4.519350 AGCTAGCTAGGTTGTTTGTTTTCC 59.481 41.667 17.69 0.00 0.00 3.13
230 250 4.277423 GCTAGCTAGGTTGTTTGTTTTCCA 59.723 41.667 22.10 0.00 0.00 3.53
239 259 5.290885 GGTTGTTTGTTTTCCATCTGTTGTC 59.709 40.000 0.00 0.00 0.00 3.18
276 303 4.874533 GGGTACGGAGGGGAGGGG 62.875 77.778 0.00 0.00 0.00 4.79
322 355 1.429463 CGCACTATTTAGATCCGCCC 58.571 55.000 0.00 0.00 0.00 6.13
323 356 1.000955 CGCACTATTTAGATCCGCCCT 59.999 52.381 0.00 0.00 0.00 5.19
324 357 2.417719 GCACTATTTAGATCCGCCCTG 58.582 52.381 0.00 0.00 0.00 4.45
358 398 1.518325 TTGTGTGGCGTCATAGGTTG 58.482 50.000 0.00 0.00 0.00 3.77
365 406 3.377172 GTGGCGTCATAGGTTGCTAATTT 59.623 43.478 0.00 0.00 0.00 1.82
375 416 5.695851 AGGTTGCTAATTTCTGTTGTGAG 57.304 39.130 0.00 0.00 0.00 3.51
376 417 5.376625 AGGTTGCTAATTTCTGTTGTGAGA 58.623 37.500 0.00 0.00 0.00 3.27
377 418 6.006449 AGGTTGCTAATTTCTGTTGTGAGAT 58.994 36.000 0.00 0.00 0.00 2.75
378 419 6.491403 AGGTTGCTAATTTCTGTTGTGAGATT 59.509 34.615 0.00 0.00 0.00 2.40
379 420 6.583806 GGTTGCTAATTTCTGTTGTGAGATTG 59.416 38.462 0.00 0.00 0.00 2.67
487 545 0.443869 GTACAGCCTGCATCGTGTTG 59.556 55.000 0.00 0.00 0.00 3.33
499 557 0.730265 TCGTGTTGAGCAAAAGCGTT 59.270 45.000 0.00 0.00 0.00 4.84
503 561 3.357823 CGTGTTGAGCAAAAGCGTTAATC 59.642 43.478 0.00 0.00 0.00 1.75
521 579 6.588552 GTTAATCGCTGCATTCTGAATAGAG 58.411 40.000 1.98 3.39 33.70 2.43
538 596 9.727627 CTGAATAGAGGATGAAATAACTTTTGC 57.272 33.333 0.00 0.00 0.00 3.68
554 612 4.022849 ACTTTTGCTGATTCTGTAAGGTGC 60.023 41.667 0.00 0.00 0.00 5.01
558 616 2.012673 CTGATTCTGTAAGGTGCTGCC 58.987 52.381 0.00 0.00 37.58 4.85
592 650 7.897864 ACTAGGGAAATTTATCTCCTGATACG 58.102 38.462 10.36 0.00 35.14 3.06
597 655 7.497909 GGGAAATTTATCTCCTGATACGTTTCA 59.502 37.037 8.45 8.45 38.65 2.69
603 661 6.668541 ATCTCCTGATACGTTTCATTTGTG 57.331 37.500 9.19 3.44 0.00 3.33
604 662 5.547465 TCTCCTGATACGTTTCATTTGTGT 58.453 37.500 9.19 0.00 0.00 3.72
605 663 5.408299 TCTCCTGATACGTTTCATTTGTGTG 59.592 40.000 9.19 0.00 0.00 3.82
606 664 4.083537 TCCTGATACGTTTCATTTGTGTGC 60.084 41.667 9.19 0.00 0.00 4.57
607 665 4.320129 CCTGATACGTTTCATTTGTGTGCA 60.320 41.667 9.19 0.00 0.00 4.57
608 666 5.175090 TGATACGTTTCATTTGTGTGCAA 57.825 34.783 4.46 0.00 0.00 4.08
611 669 6.362016 TGATACGTTTCATTTGTGTGCAATTC 59.638 34.615 4.46 0.00 34.18 2.17
612 670 3.485378 ACGTTTCATTTGTGTGCAATTCG 59.515 39.130 0.00 0.00 34.18 3.34
613 671 3.658852 CGTTTCATTTGTGTGCAATTCGC 60.659 43.478 0.00 0.00 42.89 4.70
630 694 3.904800 TCGCACTCTGGGAATAAATGA 57.095 42.857 0.00 0.00 36.34 2.57
644 708 6.640907 GGGAATAAATGACACAAGTGTTTGTC 59.359 38.462 7.35 0.00 45.53 3.18
653 717 7.026562 TGACACAAGTGTTTGTCTGTAATTTG 58.973 34.615 7.35 0.00 45.53 2.32
659 723 6.795399 AGTGTTTGTCTGTAATTTGGAACTG 58.205 36.000 0.00 0.00 0.00 3.16
666 730 8.177119 TGTCTGTAATTTGGAACTGCTATTTT 57.823 30.769 0.00 0.00 0.00 1.82
668 733 9.556030 GTCTGTAATTTGGAACTGCTATTTTAC 57.444 33.333 0.00 0.00 0.00 2.01
670 735 9.559958 CTGTAATTTGGAACTGCTATTTTACTG 57.440 33.333 0.00 0.00 0.00 2.74
719 784 4.202010 ACCGTTGTTTCCTTTGATGTTCAG 60.202 41.667 0.00 0.00 0.00 3.02
721 786 5.207768 CGTTGTTTCCTTTGATGTTCAGAG 58.792 41.667 0.00 0.00 0.00 3.35
724 789 4.580167 TGTTTCCTTTGATGTTCAGAGTGG 59.420 41.667 0.00 0.00 27.52 4.00
729 794 1.279496 TGATGTTCAGAGTGGAGGGG 58.721 55.000 0.00 0.00 0.00 4.79
763 828 3.444742 GCCATCACTTGTTCCATTGATGA 59.555 43.478 11.16 0.00 45.50 2.92
765 830 5.588240 CCATCACTTGTTCCATTGATGATG 58.412 41.667 11.16 0.00 45.50 3.07
766 831 5.358725 CCATCACTTGTTCCATTGATGATGA 59.641 40.000 11.81 0.00 45.50 2.92
767 832 6.040504 CCATCACTTGTTCCATTGATGATGAT 59.959 38.462 11.81 0.00 45.50 2.45
768 833 6.688637 TCACTTGTTCCATTGATGATGATC 57.311 37.500 0.00 0.00 38.03 2.92
780 849 8.027189 CCATTGATGATGATCGCAAGAAAATAT 58.973 33.333 6.67 0.00 40.23 1.28
815 885 8.843262 ACTTACAATCAACTACCCTTGTTTTAC 58.157 33.333 0.00 0.00 34.02 2.01
835 905 9.959749 GTTTTACTCTCATTACCATTTGTTTCA 57.040 29.630 0.00 0.00 0.00 2.69
846 916 6.976934 ACCATTTGTTTCAAGTGTTCCTAT 57.023 33.333 4.78 0.00 0.00 2.57
848 918 7.882179 ACCATTTGTTTCAAGTGTTCCTATAC 58.118 34.615 4.78 0.00 0.00 1.47
880 950 7.230108 CCATGGATTGTGTAATTAGAATCTGCT 59.770 37.037 5.56 0.00 32.60 4.24
891 961 8.947115 GTAATTAGAATCTGCTTTTACCACTGT 58.053 33.333 0.00 0.00 0.00 3.55
900 970 8.086143 TCTGCTTTTACCACTGTATATTAGGT 57.914 34.615 0.00 0.00 36.40 3.08
932 1003 7.595130 GTGTGGTTCAAATTTCTTAGATGGAAC 59.405 37.037 5.60 5.60 34.26 3.62
1042 1113 1.002430 CTTCAGTTAGTGCTCAGGCCA 59.998 52.381 5.01 0.00 37.74 5.36
1066 1137 1.063266 TGGTTTCAAGGCCAAGGAGTT 60.063 47.619 5.01 0.00 0.00 3.01
1071 1142 2.274542 TCAAGGCCAAGGAGTTATGGA 58.725 47.619 5.01 0.00 39.12 3.41
1073 1144 2.755103 CAAGGCCAAGGAGTTATGGAAC 59.245 50.000 5.01 0.00 39.12 3.62
1086 1157 1.530323 ATGGAACCACAAGTTACGGC 58.470 50.000 0.00 0.00 42.93 5.68
1140 1211 3.459598 TCGAATTGGGATCCTCATTCCTT 59.540 43.478 21.43 8.26 33.53 3.36
1210 1281 1.239968 GGCAAAGTCTGTGGCTCAGG 61.240 60.000 15.86 1.60 43.76 3.86
1215 1286 1.551452 AGTCTGTGGCTCAGGTACTC 58.449 55.000 15.86 3.49 43.76 2.59
1404 1475 0.623723 TCATGGACTTTACTGGCCCC 59.376 55.000 0.00 0.00 0.00 5.80
1764 1835 1.474077 GTTGGTGGTCATGCTGGAATC 59.526 52.381 0.00 0.00 0.00 2.52
1803 1874 2.237392 GTCCAAGACTAGGCCATCTGTT 59.763 50.000 5.01 0.00 0.00 3.16
1854 1925 2.599082 GACAAAGAGGATACAGAACGCG 59.401 50.000 3.53 3.53 41.41 6.01
1900 1971 1.680522 CGGTGCTGGATCTGCTACCT 61.681 60.000 19.07 0.00 32.32 3.08
2162 2233 1.673033 CGAGAAGGGCATCGAGTTTGT 60.673 52.381 0.00 0.00 41.40 2.83
2207 2278 3.326747 CGTCTGTTTGAGGTAAAGGAGG 58.673 50.000 0.00 0.00 0.00 4.30
2209 2280 4.570930 GTCTGTTTGAGGTAAAGGAGGAG 58.429 47.826 0.00 0.00 0.00 3.69
2210 2281 4.040584 GTCTGTTTGAGGTAAAGGAGGAGT 59.959 45.833 0.00 0.00 0.00 3.85
2211 2282 4.658901 TCTGTTTGAGGTAAAGGAGGAGTT 59.341 41.667 0.00 0.00 0.00 3.01
2215 2286 6.769341 TGTTTGAGGTAAAGGAGGAGTTTAAC 59.231 38.462 0.00 0.00 0.00 2.01
2216 2287 6.758806 TTGAGGTAAAGGAGGAGTTTAACT 57.241 37.500 0.00 0.00 39.59 2.24
2301 2376 3.054434 TGTTGACATCATGTAGGAAGGGG 60.054 47.826 0.00 0.00 0.00 4.79
2302 2377 2.126882 TGACATCATGTAGGAAGGGGG 58.873 52.381 0.00 0.00 0.00 5.40
2349 2426 2.681344 GTCAGTTGTTGGTCGGTTTCTT 59.319 45.455 0.00 0.00 0.00 2.52
2350 2427 3.872771 GTCAGTTGTTGGTCGGTTTCTTA 59.127 43.478 0.00 0.00 0.00 2.10
2394 2497 6.155475 TGTTCTGGGGTCTTATTTTGTTTG 57.845 37.500 0.00 0.00 0.00 2.93
2395 2498 5.894393 TGTTCTGGGGTCTTATTTTGTTTGA 59.106 36.000 0.00 0.00 0.00 2.69
2396 2499 6.183360 TGTTCTGGGGTCTTATTTTGTTTGAC 60.183 38.462 0.00 0.00 0.00 3.18
2407 2525 7.794810 TCTTATTTTGTTTGACGACACATTACG 59.205 33.333 0.00 0.00 0.00 3.18
2425 2543 1.639298 CGCCTGCTGTTCTTGTAGCC 61.639 60.000 0.00 0.00 39.15 3.93
2510 2629 6.154706 ACCTCTTATGTGGGAACTTGTACTAG 59.845 42.308 2.56 2.56 0.00 2.57
2523 2642 6.912951 ACTTGTACTAGTATGTTGTGGTCT 57.087 37.500 8.27 0.00 0.00 3.85
2619 2750 1.529226 TGATTGGCGATTCCGTTGTT 58.471 45.000 0.00 0.00 37.80 2.83
2686 2817 0.108756 GACGGCTGGAAGAGTACCAC 60.109 60.000 0.00 0.00 34.07 4.16
2695 2826 5.360144 GCTGGAAGAGTACCACTGAGTATTA 59.640 44.000 0.00 0.00 34.07 0.98
2700 2831 6.716934 AGAGTACCACTGAGTATTATGGTG 57.283 41.667 5.02 0.00 45.14 4.17
2707 2838 6.095440 ACCACTGAGTATTATGGTGCAATTTC 59.905 38.462 0.00 0.00 43.88 2.17
2793 3004 1.813477 GCTGCCTAGATGAAGCCCTTC 60.813 57.143 1.12 1.12 39.91 3.46
2794 3005 1.767681 CTGCCTAGATGAAGCCCTTCT 59.232 52.381 9.23 0.00 40.14 2.85
2795 3006 2.172293 CTGCCTAGATGAAGCCCTTCTT 59.828 50.000 9.23 3.21 40.14 2.52
2837 3089 6.258507 TGTGATTGTCTTGTTCATCCATATCG 59.741 38.462 0.00 0.00 0.00 2.92
2853 3109 4.318760 CCATATCGCGAGGTAATTGTTGTG 60.319 45.833 16.66 2.52 0.00 3.33
2939 3195 3.279434 ACCGATTTAGATTGGGTCAAGC 58.721 45.455 4.59 0.00 40.65 4.01
2940 3196 3.278574 CCGATTTAGATTGGGTCAAGCA 58.721 45.455 0.00 0.00 33.70 3.91
3043 3313 3.940480 TCCAGAGGGGAGGGCACA 61.940 66.667 0.00 0.00 42.15 4.57
3044 3314 3.406200 CCAGAGGGGAGGGCACAG 61.406 72.222 0.00 0.00 40.01 3.66
3045 3315 2.608988 CAGAGGGGAGGGCACAGT 60.609 66.667 0.00 0.00 0.00 3.55
3046 3316 2.284995 AGAGGGGAGGGCACAGTC 60.285 66.667 0.00 0.00 0.00 3.51
3047 3317 2.284995 GAGGGGAGGGCACAGTCT 60.285 66.667 0.00 0.00 0.00 3.24
3048 3318 2.608988 AGGGGAGGGCACAGTCTG 60.609 66.667 0.00 0.00 0.00 3.51
3049 3319 3.721706 GGGGAGGGCACAGTCTGG 61.722 72.222 4.53 0.00 0.00 3.86
3050 3320 3.721706 GGGAGGGCACAGTCTGGG 61.722 72.222 4.53 0.02 0.00 4.45
3051 3321 3.721706 GGAGGGCACAGTCTGGGG 61.722 72.222 3.79 0.00 0.00 4.96
3052 3322 2.607750 GAGGGCACAGTCTGGGGA 60.608 66.667 3.79 0.00 0.00 4.81
3053 3323 2.608988 AGGGCACAGTCTGGGGAG 60.609 66.667 3.79 0.00 0.00 4.30
3054 3324 3.721706 GGGCACAGTCTGGGGAGG 61.722 72.222 3.79 0.00 0.00 4.30
3055 3325 3.721706 GGCACAGTCTGGGGAGGG 61.722 72.222 3.79 0.00 0.00 4.30
3056 3326 2.930562 GCACAGTCTGGGGAGGGT 60.931 66.667 3.79 0.00 0.00 4.34
3057 3327 2.529744 GCACAGTCTGGGGAGGGTT 61.530 63.158 3.79 0.00 0.00 4.11
3058 3328 2.069165 GCACAGTCTGGGGAGGGTTT 62.069 60.000 3.79 0.00 0.00 3.27
3059 3329 0.250901 CACAGTCTGGGGAGGGTTTG 60.251 60.000 4.53 0.00 0.00 2.93
3060 3330 1.380302 CAGTCTGGGGAGGGTTTGG 59.620 63.158 0.00 0.00 0.00 3.28
3061 3331 1.852626 AGTCTGGGGAGGGTTTGGG 60.853 63.158 0.00 0.00 0.00 4.12
3062 3332 3.264845 TCTGGGGAGGGTTTGGGC 61.265 66.667 0.00 0.00 0.00 5.36
3063 3333 4.382541 CTGGGGAGGGTTTGGGCC 62.383 72.222 0.00 0.00 0.00 5.80
3065 3335 4.696805 GGGGAGGGTTTGGGCCAC 62.697 72.222 5.23 0.00 0.00 5.01
3066 3336 4.696805 GGGAGGGTTTGGGCCACC 62.697 72.222 5.23 4.84 37.24 4.61
3068 3338 4.280019 GAGGGTTTGGGCCACCGT 62.280 66.667 5.23 6.96 40.75 4.83
3069 3339 3.802852 GAGGGTTTGGGCCACCGTT 62.803 63.158 5.23 0.00 40.75 4.44
3070 3340 3.611674 GGGTTTGGGCCACCGTTG 61.612 66.667 5.23 0.00 40.75 4.10
3072 3342 3.611674 GTTTGGGCCACCGTTGGG 61.612 66.667 5.23 0.00 44.15 4.12
3073 3343 3.822035 TTTGGGCCACCGTTGGGA 61.822 61.111 5.23 0.00 44.15 4.37
3074 3344 3.801068 TTTGGGCCACCGTTGGGAG 62.801 63.158 5.23 0.00 44.15 4.30
3077 3347 3.961414 GGCCACCGTTGGGAGGAA 61.961 66.667 0.00 0.00 46.20 3.36
3078 3348 2.359975 GCCACCGTTGGGAGGAAG 60.360 66.667 0.00 0.00 46.20 3.46
3079 3349 2.351276 CCACCGTTGGGAGGAAGG 59.649 66.667 0.00 0.00 46.20 3.46
3080 3350 2.221299 CCACCGTTGGGAGGAAGGA 61.221 63.158 0.00 0.00 46.20 3.36
3081 3351 1.562672 CCACCGTTGGGAGGAAGGAT 61.563 60.000 0.00 0.00 46.20 3.24
3082 3352 0.392998 CACCGTTGGGAGGAAGGATG 60.393 60.000 0.00 0.00 36.97 3.51
3083 3353 0.840722 ACCGTTGGGAGGAAGGATGT 60.841 55.000 0.00 0.00 36.97 3.06
3084 3354 0.107654 CCGTTGGGAGGAAGGATGTC 60.108 60.000 0.00 0.00 34.06 3.06
3085 3355 0.613260 CGTTGGGAGGAAGGATGTCA 59.387 55.000 0.00 0.00 0.00 3.58
3086 3356 1.210478 CGTTGGGAGGAAGGATGTCAT 59.790 52.381 0.00 0.00 0.00 3.06
3087 3357 2.356125 CGTTGGGAGGAAGGATGTCATT 60.356 50.000 0.00 0.00 0.00 2.57
3088 3358 3.019564 GTTGGGAGGAAGGATGTCATTG 58.980 50.000 0.00 0.00 0.00 2.82
3089 3359 1.064463 TGGGAGGAAGGATGTCATTGC 60.064 52.381 0.00 0.00 0.00 3.56
3090 3360 1.064463 GGGAGGAAGGATGTCATTGCA 60.064 52.381 2.03 0.00 30.35 4.08
3091 3361 2.295885 GGAGGAAGGATGTCATTGCAG 58.704 52.381 2.03 0.00 30.35 4.41
3092 3362 2.356535 GGAGGAAGGATGTCATTGCAGT 60.357 50.000 2.03 0.00 30.35 4.40
3093 3363 3.350833 GAGGAAGGATGTCATTGCAGTT 58.649 45.455 2.03 0.00 30.35 3.16
3094 3364 3.087031 AGGAAGGATGTCATTGCAGTTG 58.913 45.455 2.03 0.00 30.35 3.16
3095 3365 2.416431 GGAAGGATGTCATTGCAGTTGC 60.416 50.000 0.00 0.00 42.50 4.17
3096 3366 2.211250 AGGATGTCATTGCAGTTGCT 57.789 45.000 5.62 0.00 42.66 3.91
3097 3367 1.816835 AGGATGTCATTGCAGTTGCTG 59.183 47.619 5.62 0.00 42.66 4.41
3106 3376 2.435586 CAGTTGCTGCTCGAGGGG 60.436 66.667 15.58 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.106925 GAGGCAGGTGGGCAGAGG 62.107 72.222 0.00 0.00 46.44 3.69
21 22 4.106925 GGAGGCAGGTGGGCAGAG 62.107 72.222 0.00 0.00 46.44 3.35
124 125 0.104855 TAGCAGCGGGATGTGATGTC 59.895 55.000 0.00 0.00 0.00 3.06
125 126 0.761187 ATAGCAGCGGGATGTGATGT 59.239 50.000 0.00 0.00 0.00 3.06
126 127 1.001746 AGATAGCAGCGGGATGTGATG 59.998 52.381 0.00 0.00 0.00 3.07
127 128 1.274728 GAGATAGCAGCGGGATGTGAT 59.725 52.381 0.00 0.00 0.00 3.06
128 129 0.676184 GAGATAGCAGCGGGATGTGA 59.324 55.000 0.00 0.00 0.00 3.58
129 130 0.320247 GGAGATAGCAGCGGGATGTG 60.320 60.000 0.00 0.00 0.00 3.21
136 137 2.423446 GGGGTGGAGATAGCAGCG 59.577 66.667 0.00 0.00 0.00 5.18
164 165 1.535202 GACCCAACCCAATGGCCAA 60.535 57.895 10.96 0.00 39.26 4.52
212 214 6.391227 ACAGATGGAAAACAAACAACCTAG 57.609 37.500 0.00 0.00 0.00 3.02
214 216 5.046663 ACAACAGATGGAAAACAAACAACCT 60.047 36.000 0.00 0.00 0.00 3.50
223 225 7.148918 CGATTGATTTGACAACAGATGGAAAAC 60.149 37.037 0.00 0.00 32.50 2.43
229 249 6.197276 GGATCGATTGATTTGACAACAGATG 58.803 40.000 0.00 0.00 34.09 2.90
230 250 5.297776 GGGATCGATTGATTTGACAACAGAT 59.702 40.000 0.00 0.00 34.09 2.90
239 259 2.620115 CCTGGTGGGATCGATTGATTTG 59.380 50.000 0.00 0.00 34.09 2.32
264 285 4.416601 AAGGTCCCCTCCCCTCCG 62.417 72.222 0.00 0.00 30.89 4.63
276 303 0.958876 ACCCGGAAATTGCGAAGGTC 60.959 55.000 8.81 0.00 30.86 3.85
358 398 6.500684 TCCAATCTCACAACAGAAATTAGC 57.499 37.500 0.00 0.00 0.00 3.09
365 406 3.603532 GCTCATCCAATCTCACAACAGA 58.396 45.455 0.00 0.00 0.00 3.41
379 420 1.466856 TCTTGCACAATGGCTCATCC 58.533 50.000 0.00 0.00 34.04 3.51
465 522 0.528466 CACGATGCAGGCTGTACGAT 60.528 55.000 26.17 11.84 0.00 3.73
499 557 5.011023 TCCTCTATTCAGAATGCAGCGATTA 59.989 40.000 5.85 0.00 34.76 1.75
503 561 3.103447 TCCTCTATTCAGAATGCAGCG 57.897 47.619 5.85 0.00 34.76 5.18
521 579 8.031277 ACAGAATCAGCAAAAGTTATTTCATCC 58.969 33.333 0.00 0.00 0.00 3.51
536 594 2.703416 CAGCACCTTACAGAATCAGCA 58.297 47.619 0.00 0.00 0.00 4.41
538 596 2.012673 GGCAGCACCTTACAGAATCAG 58.987 52.381 0.00 0.00 34.51 2.90
558 616 9.213799 GAGATAAATTTCCCTAGTTAGCATCAG 57.786 37.037 0.00 0.00 0.00 2.90
590 648 3.485378 CGAATTGCACACAAATGAAACGT 59.515 39.130 0.00 0.00 39.77 3.99
591 649 3.658852 GCGAATTGCACACAAATGAAACG 60.659 43.478 0.00 0.00 45.45 3.60
592 650 3.786712 GCGAATTGCACACAAATGAAAC 58.213 40.909 0.00 0.00 45.45 2.78
605 663 1.098050 ATTCCCAGAGTGCGAATTGC 58.902 50.000 0.00 0.00 46.70 3.56
606 664 4.963276 TTTATTCCCAGAGTGCGAATTG 57.037 40.909 0.00 0.00 0.00 2.32
607 665 5.066505 GTCATTTATTCCCAGAGTGCGAATT 59.933 40.000 0.00 0.00 0.00 2.17
608 666 4.576463 GTCATTTATTCCCAGAGTGCGAAT 59.424 41.667 0.00 0.00 0.00 3.34
611 669 3.063997 GTGTCATTTATTCCCAGAGTGCG 59.936 47.826 0.00 0.00 0.00 5.34
612 670 4.009675 TGTGTCATTTATTCCCAGAGTGC 58.990 43.478 0.00 0.00 0.00 4.40
613 671 5.707298 ACTTGTGTCATTTATTCCCAGAGTG 59.293 40.000 0.00 0.00 0.00 3.51
614 672 5.707298 CACTTGTGTCATTTATTCCCAGAGT 59.293 40.000 0.00 0.00 0.00 3.24
615 673 5.707298 ACACTTGTGTCATTTATTCCCAGAG 59.293 40.000 0.00 0.00 0.00 3.35
618 682 6.097554 ACAAACACTTGTGTCATTTATTCCCA 59.902 34.615 6.88 0.00 44.28 4.37
630 694 6.151985 TCCAAATTACAGACAAACACTTGTGT 59.848 34.615 0.00 0.00 45.98 3.72
644 708 9.559958 CAGTAAAATAGCAGTTCCAAATTACAG 57.440 33.333 0.00 0.00 0.00 2.74
687 752 7.444299 TCAAAGGAAACAACGGTAGTACTAAT 58.556 34.615 3.61 0.00 0.00 1.73
688 753 6.815089 TCAAAGGAAACAACGGTAGTACTAA 58.185 36.000 3.61 0.00 0.00 2.24
689 754 6.403866 TCAAAGGAAACAACGGTAGTACTA 57.596 37.500 0.00 0.00 0.00 1.82
690 755 5.280654 TCAAAGGAAACAACGGTAGTACT 57.719 39.130 0.00 0.00 0.00 2.73
691 756 5.467735 ACATCAAAGGAAACAACGGTAGTAC 59.532 40.000 0.00 0.00 0.00 2.73
692 757 5.613329 ACATCAAAGGAAACAACGGTAGTA 58.387 37.500 0.00 0.00 0.00 1.82
693 758 4.457466 ACATCAAAGGAAACAACGGTAGT 58.543 39.130 0.00 0.00 0.00 2.73
729 794 4.220602 ACAAGTGATGGCAAACTATTTCCC 59.779 41.667 6.63 0.00 0.00 3.97
763 828 9.764363 TTAGACTACATATTTTCTTGCGATCAT 57.236 29.630 0.00 0.00 0.00 2.45
765 830 9.250624 AGTTAGACTACATATTTTCTTGCGATC 57.749 33.333 0.00 0.00 0.00 3.69
766 831 9.601217 AAGTTAGACTACATATTTTCTTGCGAT 57.399 29.630 0.00 0.00 0.00 4.58
767 832 8.997621 AAGTTAGACTACATATTTTCTTGCGA 57.002 30.769 0.00 0.00 0.00 5.10
780 849 8.526147 GGGTAGTTGATTGTAAGTTAGACTACA 58.474 37.037 11.11 0.00 39.74 2.74
781 850 8.747471 AGGGTAGTTGATTGTAAGTTAGACTAC 58.253 37.037 0.00 0.00 38.17 2.73
786 855 8.617290 AACAAGGGTAGTTGATTGTAAGTTAG 57.383 34.615 0.00 0.00 34.92 2.34
801 870 7.391620 TGGTAATGAGAGTAAAACAAGGGTAG 58.608 38.462 0.00 0.00 0.00 3.18
815 885 7.651808 ACACTTGAAACAAATGGTAATGAGAG 58.348 34.615 0.00 0.00 0.00 3.20
835 905 5.602978 CCATGGAGTAGGTATAGGAACACTT 59.397 44.000 5.56 0.00 0.00 3.16
846 916 7.446106 AATTACACAATCCATGGAGTAGGTA 57.554 36.000 21.33 18.52 0.00 3.08
848 918 7.735917 TCTAATTACACAATCCATGGAGTAGG 58.264 38.462 21.33 14.81 0.00 3.18
932 1003 7.495606 TGGTAACATGCAGAGTCTAATTACATG 59.504 37.037 13.45 13.45 46.17 3.21
933 1004 7.564793 TGGTAACATGCAGAGTCTAATTACAT 58.435 34.615 0.00 0.00 46.17 2.29
1042 1113 1.762370 CCTTGGCCTTGAAACCAAAGT 59.238 47.619 3.32 0.00 45.03 2.66
1066 1137 2.702261 GCCGTAACTTGTGGTTCCATA 58.298 47.619 0.00 0.00 39.17 2.74
1071 1142 2.255881 GCCGCCGTAACTTGTGGTT 61.256 57.895 0.00 0.00 41.54 3.67
1073 1144 0.671163 TAAGCCGCCGTAACTTGTGG 60.671 55.000 0.00 0.00 35.21 4.17
1086 1157 1.082117 ACGATGACGCCTTTAAGCCG 61.082 55.000 0.00 0.00 43.96 5.52
1140 1211 2.731691 GAAGAGGTGCGGTCTTGCCA 62.732 60.000 0.12 0.00 34.30 4.92
1210 1281 3.031736 TGTAAGATGCCTCAGGGAGTAC 58.968 50.000 0.00 0.00 33.58 2.73
1215 1286 3.012518 CACTTTGTAAGATGCCTCAGGG 58.987 50.000 0.00 0.00 0.00 4.45
1404 1475 3.611433 GCAGTTGGCTAATTCTGCG 57.389 52.632 9.18 0.00 42.51 5.18
1764 1835 3.007940 TGGACAACAGAGGTAGGATTGTG 59.992 47.826 0.00 0.00 33.76 3.33
1803 1874 2.235402 GGTTTCCTCATCCGTGAAGGTA 59.765 50.000 0.00 0.00 41.99 3.08
1854 1925 2.203938 TCCACCACCTCTGTCCCC 60.204 66.667 0.00 0.00 0.00 4.81
2207 2278 4.154918 TCTTCGTACGGAGGAGTTAAACTC 59.845 45.833 23.14 0.00 44.32 3.01
2209 2280 4.154918 TCTCTTCGTACGGAGGAGTTAAAC 59.845 45.833 23.14 0.00 46.16 2.01
2210 2281 4.326826 TCTCTTCGTACGGAGGAGTTAAA 58.673 43.478 23.14 1.16 46.16 1.52
2211 2282 3.942829 TCTCTTCGTACGGAGGAGTTAA 58.057 45.455 23.14 1.92 46.16 2.01
2216 2287 4.337555 CCTTTATTCTCTTCGTACGGAGGA 59.662 45.833 23.14 15.80 0.00 3.71
2217 2288 4.608951 CCTTTATTCTCTTCGTACGGAGG 58.391 47.826 23.14 13.79 0.00 4.30
2303 2378 1.410850 TAGCTGCTCCAGGGCATACC 61.411 60.000 4.91 0.00 41.63 2.73
2349 2426 8.441311 AACAGGGAGCAATCTAGAATCATATA 57.559 34.615 0.00 0.00 0.00 0.86
2350 2427 6.949117 ACAGGGAGCAATCTAGAATCATAT 57.051 37.500 0.00 0.00 0.00 1.78
2381 2484 7.794810 CGTAATGTGTCGTCAAACAAAATAAGA 59.205 33.333 0.00 0.00 0.00 2.10
2385 2488 4.673311 GCGTAATGTGTCGTCAAACAAAAT 59.327 37.500 0.00 0.00 0.00 1.82
2394 2497 0.736325 AGCAGGCGTAATGTGTCGTC 60.736 55.000 0.00 0.00 0.00 4.20
2395 2498 1.014044 CAGCAGGCGTAATGTGTCGT 61.014 55.000 0.00 0.00 0.00 4.34
2396 2499 1.014044 ACAGCAGGCGTAATGTGTCG 61.014 55.000 0.00 0.00 0.00 4.35
2407 2525 0.322008 AGGCTACAAGAACAGCAGGC 60.322 55.000 0.00 0.00 39.63 4.85
2425 2543 1.260561 CACGGTTTGTCAACTTCGGAG 59.739 52.381 0.00 0.00 32.90 4.63
2470 2589 6.267928 ACATAAGAGGTTCCGAGCAACTATAT 59.732 38.462 0.00 0.00 0.00 0.86
2471 2590 5.597182 ACATAAGAGGTTCCGAGCAACTATA 59.403 40.000 0.00 0.00 0.00 1.31
2531 2650 6.310910 GCCAAGAGCTATAGGAGGAACCTG 62.311 54.167 1.04 0.00 43.70 4.00
2532 2651 4.264922 GCCAAGAGCTATAGGAGGAACCT 61.265 52.174 1.04 0.00 45.08 3.50
2533 2652 2.037902 GCCAAGAGCTATAGGAGGAACC 59.962 54.545 1.04 0.00 38.99 3.62
2534 2653 3.394674 GCCAAGAGCTATAGGAGGAAC 57.605 52.381 1.04 0.00 38.99 3.62
2619 2750 9.863845 TTGTTCACATCGATAATAACAAGACTA 57.136 29.630 19.36 5.68 33.31 2.59
2686 2817 5.751680 CCGAAATTGCACCATAATACTCAG 58.248 41.667 0.00 0.00 0.00 3.35
2695 2826 1.802636 CGAGCCGAAATTGCACCAT 59.197 52.632 0.00 0.00 0.00 3.55
2793 3004 4.406972 TCACATCCCTGGATCTGTAGAAAG 59.593 45.833 0.00 0.00 31.62 2.62
2794 3005 4.361783 TCACATCCCTGGATCTGTAGAAA 58.638 43.478 0.00 0.00 31.62 2.52
2795 3006 3.994317 TCACATCCCTGGATCTGTAGAA 58.006 45.455 0.00 0.00 31.62 2.10
2837 3089 3.991773 TGAGTACACAACAATTACCTCGC 59.008 43.478 0.00 0.00 0.00 5.03
2853 3109 5.659463 AGAGATTCATCTGCTGTTGAGTAC 58.341 41.667 4.78 0.00 37.25 2.73
2940 3196 4.677151 AAAGGCCTCCCTCCCCGT 62.677 66.667 5.23 0.00 41.90 5.28
3038 3308 3.721706 CCCTCCCCAGACTGTGCC 61.722 72.222 0.93 0.00 0.00 5.01
3039 3309 2.069165 AAACCCTCCCCAGACTGTGC 62.069 60.000 0.93 0.00 0.00 4.57
3040 3310 0.250901 CAAACCCTCCCCAGACTGTG 60.251 60.000 0.93 0.00 0.00 3.66
3041 3311 1.427072 CCAAACCCTCCCCAGACTGT 61.427 60.000 0.93 0.00 0.00 3.55
3042 3312 1.380302 CCAAACCCTCCCCAGACTG 59.620 63.158 0.00 0.00 0.00 3.51
3043 3313 1.852626 CCCAAACCCTCCCCAGACT 60.853 63.158 0.00 0.00 0.00 3.24
3044 3314 2.763902 CCCAAACCCTCCCCAGAC 59.236 66.667 0.00 0.00 0.00 3.51
3045 3315 3.264845 GCCCAAACCCTCCCCAGA 61.265 66.667 0.00 0.00 0.00 3.86
3046 3316 4.382541 GGCCCAAACCCTCCCCAG 62.383 72.222 0.00 0.00 0.00 4.45
3048 3318 4.696805 GTGGCCCAAACCCTCCCC 62.697 72.222 0.00 0.00 0.00 4.81
3049 3319 4.696805 GGTGGCCCAAACCCTCCC 62.697 72.222 0.00 0.00 31.35 4.30
3051 3321 3.802852 AACGGTGGCCCAAACCCTC 62.803 63.158 0.00 0.00 33.88 4.30
3052 3322 3.828023 AACGGTGGCCCAAACCCT 61.828 61.111 0.00 0.00 33.88 4.34
3053 3323 3.611674 CAACGGTGGCCCAAACCC 61.612 66.667 0.00 0.00 33.88 4.11
3054 3324 3.611674 CCAACGGTGGCCCAAACC 61.612 66.667 6.53 0.00 38.35 3.27
3055 3325 3.611674 CCCAACGGTGGCCCAAAC 61.612 66.667 16.13 0.00 44.46 2.93
3056 3326 3.801068 CTCCCAACGGTGGCCCAAA 62.801 63.158 16.13 0.00 44.46 3.28
3057 3327 4.278513 CTCCCAACGGTGGCCCAA 62.279 66.667 16.13 0.00 44.46 4.12
3060 3330 3.920093 CTTCCTCCCAACGGTGGCC 62.920 68.421 16.13 0.00 44.46 5.36
3061 3331 2.359975 CTTCCTCCCAACGGTGGC 60.360 66.667 16.13 0.00 44.46 5.01
3062 3332 1.562672 ATCCTTCCTCCCAACGGTGG 61.563 60.000 14.25 14.25 45.53 4.61
3063 3333 0.392998 CATCCTTCCTCCCAACGGTG 60.393 60.000 0.00 0.00 0.00 4.94
3064 3334 0.840722 ACATCCTTCCTCCCAACGGT 60.841 55.000 0.00 0.00 0.00 4.83
3065 3335 0.107654 GACATCCTTCCTCCCAACGG 60.108 60.000 0.00 0.00 0.00 4.44
3066 3336 0.613260 TGACATCCTTCCTCCCAACG 59.387 55.000 0.00 0.00 0.00 4.10
3067 3337 3.019564 CAATGACATCCTTCCTCCCAAC 58.980 50.000 0.00 0.00 0.00 3.77
3068 3338 2.621407 GCAATGACATCCTTCCTCCCAA 60.621 50.000 0.00 0.00 0.00 4.12
3069 3339 1.064463 GCAATGACATCCTTCCTCCCA 60.064 52.381 0.00 0.00 0.00 4.37
3070 3340 1.064463 TGCAATGACATCCTTCCTCCC 60.064 52.381 0.00 0.00 0.00 4.30
3071 3341 2.295885 CTGCAATGACATCCTTCCTCC 58.704 52.381 0.00 0.00 0.00 4.30
3072 3342 2.996631 ACTGCAATGACATCCTTCCTC 58.003 47.619 0.00 0.00 0.00 3.71
3073 3343 3.087031 CAACTGCAATGACATCCTTCCT 58.913 45.455 0.00 0.00 0.00 3.36
3074 3344 2.416431 GCAACTGCAATGACATCCTTCC 60.416 50.000 3.45 0.00 41.59 3.46
3075 3345 2.490903 AGCAACTGCAATGACATCCTTC 59.509 45.455 4.22 0.00 45.16 3.46
3076 3346 2.230508 CAGCAACTGCAATGACATCCTT 59.769 45.455 4.22 0.00 45.16 3.36
3077 3347 1.816835 CAGCAACTGCAATGACATCCT 59.183 47.619 4.22 0.00 45.16 3.24
3078 3348 2.273370 CAGCAACTGCAATGACATCC 57.727 50.000 4.22 0.00 45.16 3.51
3089 3359 2.435586 CCCCTCGAGCAGCAACTG 60.436 66.667 6.99 0.00 34.12 3.16
3090 3360 4.400961 GCCCCTCGAGCAGCAACT 62.401 66.667 17.19 0.00 0.00 3.16
3091 3361 4.704833 TGCCCCTCGAGCAGCAAC 62.705 66.667 21.10 2.86 34.69 4.17
3092 3362 4.704833 GTGCCCCTCGAGCAGCAA 62.705 66.667 23.88 9.93 41.87 3.91
3104 3374 1.605451 GTAACCAACAGGGGTGCCC 60.605 63.158 0.00 0.00 45.90 5.36
3105 3375 4.090723 GTAACCAACAGGGGTGCC 57.909 61.111 0.00 0.00 41.32 5.01
3106 3376 0.251608 ATGGTAACCAACAGGGGTGC 60.252 55.000 0.00 0.00 41.32 5.01


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

AutoCloner maintained by Alex Coulton.