Multiple sequence alignment - TraesCS1A01G045300

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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 TraesCS1A01G045300 chr1A 100.000 5054 0 0 1 5054 26963400 26958347 0.000000e+00 9334
1 TraesCS1A01G045300 chr1A 86.426 1385 118 34 3359 4710 26931905 26930558 0.000000e+00 1452
2 TraesCS1A01G045300 chr1A 84.101 1151 105 37 3586 4705 26195675 26194572 0.000000e+00 1040
3 TraesCS1A01G045300 chr1A 82.671 906 96 31 4171 5049 26936419 26935548 0.000000e+00 747
4 TraesCS1A01G045300 chr1A 87.071 379 25 11 2932 3303 26932281 26931920 1.690000e-109 407
5 TraesCS1A01G045300 chr1A 77.049 305 46 18 3818 4113 26937613 26937324 2.440000e-33 154
6 TraesCS1A01G045300 chr1D 93.296 3371 151 35 2 3356 25733364 25730053 0.000000e+00 4903
7 TraesCS1A01G045300 chr1D 90.186 1345 72 27 3516 4822 25729929 25728607 0.000000e+00 1698
8 TraesCS1A01G045300 chr1D 93.293 492 20 6 4563 5052 25720487 25720007 0.000000e+00 713
9 TraesCS1A01G045300 chr1D 92.713 494 23 6 4563 5054 25723269 25722787 0.000000e+00 701
10 TraesCS1A01G045300 chr1D 92.510 494 24 6 4563 5054 25726049 25725567 0.000000e+00 695
11 TraesCS1A01G045300 chr1D 82.493 754 61 27 4104 4812 25673706 25672979 3.370000e-166 595
12 TraesCS1A01G045300 chr1D 83.091 550 72 12 3358 3894 25676412 25675871 9.840000e-132 481
13 TraesCS1A01G045300 chr1D 87.823 271 10 2 4784 5054 25728594 25728347 3.830000e-76 296
14 TraesCS1A01G045300 chr1D 86.806 144 17 2 4838 4981 25462849 25462708 5.240000e-35 159
15 TraesCS1A01G045300 chr1D 92.683 82 5 1 3346 3427 25730034 25729954 3.200000e-22 117
16 TraesCS1A01G045300 chr1D 89.412 85 9 0 4029 4113 25675772 25675688 1.920000e-19 108
17 TraesCS1A01G045300 chr1B 92.690 3338 176 40 40 3356 41089642 41086352 0.000000e+00 4750
18 TraesCS1A01G045300 chr1B 86.343 1340 126 29 3359 4667 40943616 40942303 0.000000e+00 1408
19 TraesCS1A01G045300 chr1B 91.218 854 42 15 3748 4571 41086061 41085211 0.000000e+00 1131
20 TraesCS1A01G045300 chr1B 80.775 1316 138 63 3727 4979 40962420 40961157 0.000000e+00 922
21 TraesCS1A01G045300 chr1B 89.600 500 33 9 4568 5054 41085088 41084595 7.190000e-173 617
22 TraesCS1A01G045300 chr1B 89.182 379 26 8 2932 3303 40944001 40943631 4.610000e-125 459
23 TraesCS1A01G045300 chr1B 81.538 325 44 9 4729 5049 40941963 40941651 2.340000e-63 254
24 TraesCS1A01G045300 chr1B 86.806 144 17 2 4838 4981 40840057 40839916 5.240000e-35 159
25 TraesCS1A01G045300 chr1B 94.286 70 3 1 3346 3415 41086334 41086266 6.920000e-19 106
26 TraesCS1A01G045300 chr3B 87.764 474 32 13 4105 4577 697145744 697145296 9.630000e-147 531
27 TraesCS1A01G045300 chr3B 85.111 497 58 11 3359 3842 697147445 697146952 1.260000e-135 494
28 TraesCS1A01G045300 chr3B 90.395 177 12 3 3913 4088 697146917 697146745 1.420000e-55 228
29 TraesCS1A01G045300 chr3B 89.147 129 8 4 3134 3262 697147615 697147493 6.770000e-34 156


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 TraesCS1A01G045300 chr1A 26958347 26963400 5053 True 9334.000000 9334 100.000000 1 5054 1 chr1A.!!$R2 5053
1 TraesCS1A01G045300 chr1A 26194572 26195675 1103 True 1040.000000 1040 84.101000 3586 4705 1 chr1A.!!$R1 1119
2 TraesCS1A01G045300 chr1A 26930558 26937613 7055 True 690.000000 1452 83.304250 2932 5049 4 chr1A.!!$R3 2117
3 TraesCS1A01G045300 chr1D 25720007 25733364 13357 True 1303.285714 4903 91.786286 2 5054 7 chr1D.!!$R3 5052
4 TraesCS1A01G045300 chr1D 25672979 25676412 3433 True 394.666667 595 84.998667 3358 4812 3 chr1D.!!$R2 1454
5 TraesCS1A01G045300 chr1B 41084595 41089642 5047 True 1651.000000 4750 91.948500 40 5054 4 chr1B.!!$R4 5014
6 TraesCS1A01G045300 chr1B 40961157 40962420 1263 True 922.000000 922 80.775000 3727 4979 1 chr1B.!!$R2 1252
7 TraesCS1A01G045300 chr1B 40941651 40944001 2350 True 707.000000 1408 85.687667 2932 5049 3 chr1B.!!$R3 2117
8 TraesCS1A01G045300 chr3B 697145296 697147615 2319 True 352.250000 531 88.104250 3134 4577 4 chr3B.!!$R1 1443

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
917 946 0.187606 GGTTCTTGGTTCTTGGGGGT 59.812 55.0 0.00 0.0 0.00 4.95 F
2125 2158 0.605319 CGCCTTTTCCAGTGCACCTA 60.605 55.0 14.63 0.0 0.00 3.08 F
3219 5628 1.083489 TTAAGGTGCGTGCATACTGC 58.917 50.0 0.00 0.0 45.29 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2713 2746 0.689055 AGTGATGGCAGCTTCAGACA 59.311 50.0 3.69 0.0 0.0 3.41 R
3490 5928 0.620556 TCACAAAGGATGAGGGGCTC 59.379 55.0 0.00 0.0 0.0 4.70 R
4804 10349 0.608640 GTCGTCTCCAACCTCCACAT 59.391 55.0 0.00 0.0 0.0 3.21 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
26 27 8.388103 AGTAAAACAGTTGCGATATTACATGAC 58.612 33.333 0.00 0.00 0.00 3.06
36 37 6.183360 TGCGATATTACATGACAAATGGCTTT 60.183 34.615 0.00 0.00 0.00 3.51
75 76 4.461198 AGGTCTTTGATCGTTGAACCTTT 58.539 39.130 1.91 0.00 0.00 3.11
76 77 4.275936 AGGTCTTTGATCGTTGAACCTTTG 59.724 41.667 1.91 0.00 0.00 2.77
79 80 3.347958 TTGATCGTTGAACCTTTGTGC 57.652 42.857 0.00 0.00 0.00 4.57
80 81 2.293170 TGATCGTTGAACCTTTGTGCA 58.707 42.857 0.00 0.00 0.00 4.57
88 89 3.443037 TGAACCTTTGTGCACATTTTCG 58.557 40.909 22.39 9.18 0.00 3.46
91 92 1.537776 CCTTTGTGCACATTTTCGGCA 60.538 47.619 22.39 0.00 34.70 5.69
95 96 2.190170 TGCACATTTTCGGCACCGT 61.190 52.632 9.23 0.00 40.74 4.83
119 120 3.365969 CCTTCCTTTCATAACGTGGCAAC 60.366 47.826 0.00 0.00 0.00 4.17
148 150 1.874872 TCGTTGGTTTTCATCCGGTTC 59.125 47.619 0.00 0.00 0.00 3.62
163 167 1.294459 GTTCCCGACTACACACCCC 59.706 63.158 0.00 0.00 0.00 4.95
206 210 4.730949 AATTCCAAATACCTCGAGTCGA 57.269 40.909 15.64 15.64 0.00 4.20
217 221 4.796231 GAGTCGACACCGCGCCAT 62.796 66.667 19.50 0.00 35.37 4.40
226 230 0.732571 CACCGCGCCATCACTTAATT 59.267 50.000 0.00 0.00 0.00 1.40
228 232 1.816224 ACCGCGCCATCACTTAATTTT 59.184 42.857 0.00 0.00 0.00 1.82
229 233 2.184448 CCGCGCCATCACTTAATTTTG 58.816 47.619 0.00 0.00 0.00 2.44
254 259 1.358152 TTCCACCGTCCTTTCATCCT 58.642 50.000 0.00 0.00 0.00 3.24
267 272 2.806945 TCATCCTGATTTCCGGCTTT 57.193 45.000 0.00 0.00 0.00 3.51
335 343 1.032794 GCCCTTTCATCCCGATTTCC 58.967 55.000 0.00 0.00 0.00 3.13
363 371 3.022406 ACGCCTTCCTCTTCTAATACGT 58.978 45.455 0.00 0.00 0.00 3.57
364 372 3.066481 ACGCCTTCCTCTTCTAATACGTC 59.934 47.826 0.00 0.00 0.00 4.34
367 375 3.631227 CCTTCCTCTTCTAATACGTCGGT 59.369 47.826 0.00 0.00 0.00 4.69
370 378 4.769688 TCCTCTTCTAATACGTCGGTACA 58.230 43.478 0.00 0.00 0.00 2.90
378 386 9.454585 CTTCTAATACGTCGGTACATAATTTCA 57.545 33.333 0.00 0.00 0.00 2.69
381 389 9.622004 CTAATACGTCGGTACATAATTTCATCT 57.378 33.333 0.00 0.00 0.00 2.90
386 394 6.899771 CGTCGGTACATAATTTCATCTGTTTG 59.100 38.462 0.00 0.00 0.00 2.93
389 397 7.065324 TCGGTACATAATTTCATCTGTTTGGAC 59.935 37.037 0.00 0.00 0.00 4.02
391 399 6.194796 ACATAATTTCATCTGTTTGGACCG 57.805 37.500 0.00 0.00 0.00 4.79
392 400 3.575965 AATTTCATCTGTTTGGACCGC 57.424 42.857 0.00 0.00 0.00 5.68
393 401 1.243902 TTTCATCTGTTTGGACCGCC 58.756 50.000 0.00 0.00 0.00 6.13
394 402 0.608035 TTCATCTGTTTGGACCGCCC 60.608 55.000 0.00 0.00 0.00 6.13
395 403 1.002134 CATCTGTTTGGACCGCCCT 60.002 57.895 0.00 0.00 35.38 5.19
396 404 0.609131 CATCTGTTTGGACCGCCCTT 60.609 55.000 0.00 0.00 35.38 3.95
397 405 0.322546 ATCTGTTTGGACCGCCCTTC 60.323 55.000 0.00 0.00 35.38 3.46
398 406 1.971695 CTGTTTGGACCGCCCTTCC 60.972 63.158 0.00 0.00 35.38 3.46
399 407 2.114411 GTTTGGACCGCCCTTCCA 59.886 61.111 0.00 0.00 41.64 3.53
400 408 1.304134 GTTTGGACCGCCCTTCCAT 60.304 57.895 0.00 0.00 42.88 3.41
486 494 1.170442 CAAATTAGCCGTTCCCCGTT 58.830 50.000 0.00 0.00 33.66 4.44
531 540 3.901222 ACCTAACATTTTGTCCAAAGGGG 59.099 43.478 0.00 0.00 38.37 4.79
777 806 1.583986 CGATCTCCCGATCTGCTCC 59.416 63.158 0.00 0.00 43.14 4.70
778 807 0.893270 CGATCTCCCGATCTGCTCCT 60.893 60.000 0.00 0.00 43.14 3.69
779 808 0.602562 GATCTCCCGATCTGCTCCTG 59.397 60.000 0.00 0.00 42.25 3.86
780 809 1.470996 ATCTCCCGATCTGCTCCTGC 61.471 60.000 0.00 0.00 40.20 4.85
781 810 3.157252 TCCCGATCTGCTCCTGCC 61.157 66.667 0.00 0.00 38.71 4.85
782 811 4.247380 CCCGATCTGCTCCTGCCC 62.247 72.222 0.00 0.00 38.71 5.36
785 814 4.925861 GATCTGCTCCTGCCCGCC 62.926 72.222 0.00 0.00 38.71 6.13
875 904 1.696832 GGATCAGGTGCGCGTTTCTC 61.697 60.000 8.43 0.00 0.00 2.87
893 922 3.567397 TCTCCGGATTTGTTTGGGAAAA 58.433 40.909 3.57 0.00 0.00 2.29
897 926 5.301555 TCCGGATTTGTTTGGGAAAATTTC 58.698 37.500 0.00 0.00 0.00 2.17
900 929 5.060506 GGATTTGTTTGGGAAAATTTCGGT 58.939 37.500 0.00 0.00 0.00 4.69
901 930 5.529430 GGATTTGTTTGGGAAAATTTCGGTT 59.471 36.000 0.00 0.00 0.00 4.44
902 931 6.293190 GGATTTGTTTGGGAAAATTTCGGTTC 60.293 38.462 0.00 0.00 0.00 3.62
903 932 5.346181 TTGTTTGGGAAAATTTCGGTTCT 57.654 34.783 0.00 0.00 0.00 3.01
917 946 0.187606 GGTTCTTGGTTCTTGGGGGT 59.812 55.000 0.00 0.00 0.00 4.95
920 949 1.228862 CTTGGTTCTTGGGGGTGGG 60.229 63.158 0.00 0.00 0.00 4.61
1413 1446 2.572284 GCCGAGCACGTCTACCTT 59.428 61.111 2.18 0.00 37.88 3.50
1620 1653 3.386237 GACGTGAGGGAGCAGGCT 61.386 66.667 0.00 0.00 0.00 4.58
1719 1752 1.807165 GCAGAGCTTCGATGACGCA 60.807 57.895 1.89 0.00 39.58 5.24
1737 1770 1.615392 GCATTCCAGTTTGTGAAGGCT 59.385 47.619 0.00 0.00 43.00 4.58
1854 1887 1.138859 CTCAGGATGTATCGGTTGGCA 59.861 52.381 0.00 0.00 37.40 4.92
1866 1899 2.449518 TTGGCACCTCACTCCCCA 60.450 61.111 0.00 0.00 0.00 4.96
1869 1902 1.271840 TGGCACCTCACTCCCCATAC 61.272 60.000 0.00 0.00 0.00 2.39
2125 2158 0.605319 CGCCTTTTCCAGTGCACCTA 60.605 55.000 14.63 0.00 0.00 3.08
2467 2500 2.027653 CCTTTCCTTTCTCCGAGCTCTT 60.028 50.000 12.85 0.00 0.00 2.85
2640 2673 3.804325 AGTCATCTAATGCGGAACATTCG 59.196 43.478 0.00 0.00 46.28 3.34
2703 2736 7.230510 GTCTCATCTATAGCAGAAAGAAGAGGA 59.769 40.741 0.00 0.00 36.32 3.71
2713 2746 5.651576 GCAGAAAGAAGAGGAGGATTTTCAT 59.348 40.000 0.00 0.00 0.00 2.57
2724 2757 4.096081 GGAGGATTTTCATGTCTGAAGCTG 59.904 45.833 0.00 0.00 42.19 4.24
2801 2834 2.035632 AGAGGAAGCCACGGATAAGAG 58.964 52.381 0.00 0.00 0.00 2.85
3120 5529 5.834204 GGTAGGAGGTGAATATGAGTGTAGT 59.166 44.000 0.00 0.00 0.00 2.73
3132 5541 9.431887 GAATATGAGTGTAGTAAAGGTGTTGAA 57.568 33.333 0.00 0.00 0.00 2.69
3215 5624 1.276705 TCCTGTTAAGGTGCGTGCATA 59.723 47.619 0.00 0.00 44.82 3.14
3216 5625 1.396996 CCTGTTAAGGTGCGTGCATAC 59.603 52.381 0.00 0.00 38.96 2.39
3217 5626 2.346803 CTGTTAAGGTGCGTGCATACT 58.653 47.619 0.00 0.00 0.00 2.12
3218 5627 2.073056 TGTTAAGGTGCGTGCATACTG 58.927 47.619 0.00 0.00 0.00 2.74
3219 5628 1.083489 TTAAGGTGCGTGCATACTGC 58.917 50.000 0.00 0.00 45.29 4.40
3264 5674 5.001232 TGTATTCTGGTCTGCTTGTTAACC 58.999 41.667 2.48 0.00 0.00 2.85
3306 5716 9.289303 CCACTTGATATTTGTAAATTGTGTAGC 57.711 33.333 0.00 0.00 0.00 3.58
3315 5725 8.492673 TTTGTAAATTGTGTAGCAGATAGAGG 57.507 34.615 0.00 0.00 0.00 3.69
3321 5731 5.112129 TGTGTAGCAGATAGAGGACTACA 57.888 43.478 0.00 0.00 40.52 2.74
3324 5734 6.607600 TGTGTAGCAGATAGAGGACTACATTT 59.392 38.462 4.66 0.00 43.50 2.32
3327 5737 9.197306 TGTAGCAGATAGAGGACTACATTTTTA 57.803 33.333 0.00 0.00 38.54 1.52
3328 5738 9.685828 GTAGCAGATAGAGGACTACATTTTTAG 57.314 37.037 0.00 0.00 34.65 1.85
3356 5766 4.798882 AGGTCCTAGTCTTAGATGACTGG 58.201 47.826 7.34 4.52 45.70 4.00
3423 5861 7.918643 CAAACTTTTGGCAAGTGACAATATTT 58.081 30.769 0.00 0.00 43.55 1.40
3428 5866 9.260002 CTTTTGGCAAGTGACAATATTTAGTTT 57.740 29.630 0.00 0.00 43.55 2.66
3438 5876 8.340443 GTGACAATATTTAGTTTAATCCCGGTC 58.660 37.037 0.00 0.00 0.00 4.79
3458 5896 6.649557 CCGGTCTATAGGAATCCAACATTTAC 59.350 42.308 0.61 0.00 0.00 2.01
3490 5928 6.541278 TCATTGCTCATTGTTCTCCTATCTTG 59.459 38.462 0.00 0.00 0.00 3.02
3495 5939 3.914426 TTGTTCTCCTATCTTGAGCCC 57.086 47.619 0.00 0.00 0.00 5.19
3498 5942 2.367241 GTTCTCCTATCTTGAGCCCCTC 59.633 54.545 0.00 0.00 0.00 4.30
3527 5971 9.888878 CCTTTGTGATTATTGATAGTAGCATTG 57.111 33.333 0.00 0.00 0.00 2.82
3559 6004 5.777526 AATTTGGGAAAACAGGCCATATT 57.222 34.783 5.01 0.00 0.00 1.28
3564 6009 6.478512 TGGGAAAACAGGCCATATTTTATC 57.521 37.500 5.01 5.14 0.00 1.75
3596 6041 7.354751 TGTGTAGTATGATTGTACATAGGCA 57.645 36.000 0.00 0.00 34.11 4.75
3696 6142 2.505407 ACCCTTGGTAACCGGTAATACC 59.495 50.000 23.40 23.40 41.62 2.73
3725 6171 5.512942 TCCACCACCTTATTGATCTTTGA 57.487 39.130 0.00 0.00 0.00 2.69
3783 6235 8.027189 AGTCAAACTGTTTTTCCTTTAAGACAC 58.973 33.333 2.41 0.00 0.00 3.67
3794 6246 3.124636 CCTTTAAGACACGTACACCATGC 59.875 47.826 0.00 0.00 0.00 4.06
3800 6252 3.056107 AGACACGTACACCATGCTAATGT 60.056 43.478 0.00 0.00 31.27 2.71
3808 6260 6.348132 CGTACACCATGCTAATGTCTTTTTGA 60.348 38.462 0.00 0.00 31.27 2.69
3824 6276 8.450964 TGTCTTTTTGAAGCTATCTTTTATCGG 58.549 33.333 0.00 0.00 31.48 4.18
3897 6350 9.113838 GATCACAAACTTCACAACCTCATATAT 57.886 33.333 0.00 0.00 0.00 0.86
3905 6358 9.988815 ACTTCACAACCTCATATATGAATAGAC 57.011 33.333 16.08 0.00 36.18 2.59
3950 6410 3.921021 CGTCAGTTTACTTCTGTAGCTGG 59.079 47.826 0.00 0.00 35.83 4.85
4394 9502 1.606601 CCATAGGCCGGGAGATCGA 60.607 63.158 2.18 0.00 0.00 3.59
4437 9546 6.065976 TGAAAATCATGTACATCTCAGGGT 57.934 37.500 5.07 0.00 0.00 4.34
4523 9642 1.723870 GGCTATTTGCTGTCCTGCG 59.276 57.895 0.00 0.00 42.39 5.18
4547 9666 6.355638 GCATGTCGTATTAGCAATGTACTTC 58.644 40.000 0.00 0.00 0.00 3.01
4593 9847 5.957771 TGCTATCTCATACAAAGTTCCCT 57.042 39.130 0.00 0.00 0.00 4.20
4651 9905 4.241590 TGTCCTTGTCAAATTCATGCAC 57.758 40.909 0.00 0.00 0.00 4.57
4667 9921 2.733956 TGCACCCAATATTCCAAGGAC 58.266 47.619 0.00 0.00 0.00 3.85
4668 9922 2.042297 TGCACCCAATATTCCAAGGACA 59.958 45.455 0.00 0.00 0.00 4.02
4669 9923 2.427095 GCACCCAATATTCCAAGGACAC 59.573 50.000 0.00 0.00 0.00 3.67
4672 9926 5.505780 CACCCAATATTCCAAGGACACTTA 58.494 41.667 0.00 0.00 34.49 2.24
4678 9932 3.788227 TTCCAAGGACACTTAGCACAT 57.212 42.857 0.00 0.00 34.49 3.21
4711 9965 5.210715 GCTGATCCTTTCAATTGCTATTCG 58.789 41.667 0.00 0.00 32.78 3.34
4713 9967 5.192927 TGATCCTTTCAATTGCTATTCGGT 58.807 37.500 0.00 0.00 0.00 4.69
4714 9968 5.652014 TGATCCTTTCAATTGCTATTCGGTT 59.348 36.000 0.00 0.00 0.00 4.44
4715 9969 5.975693 TCCTTTCAATTGCTATTCGGTTT 57.024 34.783 0.00 0.00 0.00 3.27
4748 10287 8.675705 TCTTCAATTTGTTAATGACAGACAGA 57.324 30.769 0.00 0.00 39.94 3.41
4751 10296 4.990543 TTTGTTAATGACAGACAGAGCG 57.009 40.909 0.00 0.00 39.94 5.03
4804 10349 4.571369 TCCGTGTGGTAAAATGGGATAA 57.429 40.909 0.00 0.00 36.30 1.75
4850 13203 1.933247 TTGGGAAAGCAAAGCAAACG 58.067 45.000 0.00 0.00 0.00 3.60
4858 13211 1.539776 GCAAAGCAAACGCTGGTTCG 61.540 55.000 3.34 0.00 45.00 3.95
5052 18976 5.218885 TCCACATGAAACGCAAAACAATAG 58.781 37.500 0.00 0.00 0.00 1.73
5053 18977 4.981674 CCACATGAAACGCAAAACAATAGT 59.018 37.500 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.388103 GTCATGTAATATCGCAACTGTTTTACT 58.612 33.333 10.25 0.00 0.00 2.24
79 80 1.729131 GCACGGTGCCGAAAATGTG 60.729 57.895 22.19 5.03 42.83 3.21
80 81 2.642700 GCACGGTGCCGAAAATGT 59.357 55.556 22.19 0.00 42.83 2.71
91 92 2.433436 GTTATGAAAGGAAGGCACGGT 58.567 47.619 0.00 0.00 0.00 4.83
92 93 1.396996 CGTTATGAAAGGAAGGCACGG 59.603 52.381 0.00 0.00 0.00 4.94
93 94 2.073816 ACGTTATGAAAGGAAGGCACG 58.926 47.619 0.00 0.00 0.00 5.34
95 96 2.432444 CCACGTTATGAAAGGAAGGCA 58.568 47.619 0.00 0.00 0.00 4.75
119 120 6.087555 CGGATGAAAACCAACGAAATTAAGTG 59.912 38.462 0.00 0.00 33.04 3.16
129 130 1.068816 GGAACCGGATGAAAACCAACG 60.069 52.381 9.46 0.00 0.00 4.10
163 167 3.785364 TGTCCCCCAAGAATAAAAAGGG 58.215 45.455 0.00 0.00 39.29 3.95
206 210 0.392461 ATTAAGTGATGGCGCGGTGT 60.392 50.000 8.83 0.00 0.00 4.16
217 221 3.637229 TGGAAACCGGCAAAATTAAGTGA 59.363 39.130 0.00 0.00 0.00 3.41
267 272 2.563179 GCATATTAGGAGAGGAAGGCGA 59.437 50.000 0.00 0.00 0.00 5.54
354 362 9.616634 GATGAAATTATGTACCGACGTATTAGA 57.383 33.333 0.00 0.00 0.00 2.10
363 371 7.065324 GTCCAAACAGATGAAATTATGTACCGA 59.935 37.037 0.00 0.00 0.00 4.69
364 372 7.186804 GTCCAAACAGATGAAATTATGTACCG 58.813 38.462 0.00 0.00 0.00 4.02
367 375 6.183360 GCGGTCCAAACAGATGAAATTATGTA 60.183 38.462 0.00 0.00 0.00 2.29
370 378 4.097892 GGCGGTCCAAACAGATGAAATTAT 59.902 41.667 0.00 0.00 0.00 1.28
378 386 0.322546 GAAGGGCGGTCCAAACAGAT 60.323 55.000 0.00 0.00 38.24 2.90
381 389 2.114411 GGAAGGGCGGTCCAAACA 59.886 61.111 0.00 0.00 38.24 2.83
386 394 4.191015 GGGATGGAAGGGCGGTCC 62.191 72.222 0.00 0.00 35.55 4.46
389 397 2.624674 AAATCGGGATGGAAGGGCGG 62.625 60.000 0.00 0.00 0.00 6.13
391 399 0.823769 GGAAATCGGGATGGAAGGGC 60.824 60.000 0.00 0.00 0.00 5.19
392 400 0.535102 CGGAAATCGGGATGGAAGGG 60.535 60.000 0.00 0.00 34.75 3.95
393 401 3.006672 CGGAAATCGGGATGGAAGG 57.993 57.895 0.00 0.00 34.75 3.46
486 494 1.537814 CCTGCTCTTTGGCAATGGCA 61.538 55.000 19.98 19.98 43.71 4.92
531 540 2.991540 GGACAAGTTGGGCTGCCC 60.992 66.667 30.97 30.97 45.71 5.36
620 632 3.753070 GAGACGATCGGACGGTGGC 62.753 68.421 20.98 0.00 37.61 5.01
844 873 3.143675 CTGATCCAGGAACACACCG 57.856 57.895 0.00 0.00 34.73 4.94
875 904 4.151512 CGAAATTTTCCCAAACAAATCCGG 59.848 41.667 0.00 0.00 0.00 5.14
893 922 2.890945 CCCAAGAACCAAGAACCGAAAT 59.109 45.455 0.00 0.00 0.00 2.17
897 926 0.893727 CCCCCAAGAACCAAGAACCG 60.894 60.000 0.00 0.00 0.00 4.44
900 929 0.187361 CCACCCCCAAGAACCAAGAA 59.813 55.000 0.00 0.00 0.00 2.52
901 930 1.725169 CCCACCCCCAAGAACCAAGA 61.725 60.000 0.00 0.00 0.00 3.02
902 931 1.228862 CCCACCCCCAAGAACCAAG 60.229 63.158 0.00 0.00 0.00 3.61
903 932 2.784654 CCCCACCCCCAAGAACCAA 61.785 63.158 0.00 0.00 0.00 3.67
920 949 1.503347 ACACCATTATTCCCCATCCCC 59.497 52.381 0.00 0.00 0.00 4.81
1428 1461 2.031919 ATGTCGCGGTTCTTGGCA 59.968 55.556 6.13 0.00 0.00 4.92
1719 1752 1.615392 GCAGCCTTCACAAACTGGAAT 59.385 47.619 0.00 0.00 0.00 3.01
1854 1887 1.001760 AGCGTATGGGGAGTGAGGT 59.998 57.895 0.00 0.00 0.00 3.85
1866 1899 2.035193 CACTAGATGCAGTGGAGCGTAT 59.965 50.000 0.00 0.00 41.88 3.06
1869 1902 2.969157 CACTAGATGCAGTGGAGCG 58.031 57.895 0.00 0.00 41.88 5.03
2125 2158 7.609056 AGCTTCATTTTGCTGTCTGAATTAAT 58.391 30.769 0.00 0.00 38.21 1.40
2467 2500 9.904198 TGAACTAATGGTTGAATCTGATGATAA 57.096 29.630 0.00 0.00 38.41 1.75
2703 2736 3.442977 GCAGCTTCAGACATGAAAATCCT 59.557 43.478 0.00 0.00 44.68 3.24
2713 2746 0.689055 AGTGATGGCAGCTTCAGACA 59.311 50.000 3.69 0.00 0.00 3.41
2801 2834 5.183140 AGCTGTTTCACACCATTGGTATTAC 59.817 40.000 8.31 3.78 32.11 1.89
3083 5492 2.244695 CTCCTACCCATACGCATACCA 58.755 52.381 0.00 0.00 0.00 3.25
3120 5529 7.014711 TGCCAATCAATACTTTCAACACCTTTA 59.985 33.333 0.00 0.00 0.00 1.85
3132 5541 4.813027 CAACTTGCTGCCAATCAATACTT 58.187 39.130 0.00 0.00 0.00 2.24
3264 5674 9.832445 ATATCAAGTGGTACCTAAACATACAAG 57.168 33.333 14.36 0.00 0.00 3.16
3299 5709 5.112129 TGTAGTCCTCTATCTGCTACACA 57.888 43.478 0.00 0.00 37.62 3.72
3314 5724 9.293404 AGGACCTAAAAACTAAAAATGTAGTCC 57.707 33.333 0.00 0.00 33.05 3.85
3327 5737 8.751242 GTCATCTAAGACTAGGACCTAAAAACT 58.249 37.037 2.08 0.00 35.65 2.66
3328 5738 8.751242 AGTCATCTAAGACTAGGACCTAAAAAC 58.249 37.037 2.08 0.00 46.52 2.43
3344 5754 7.492524 TGTCACTAAATAGCCAGTCATCTAAG 58.507 38.462 0.00 0.00 0.00 2.18
3356 5766 4.260375 CCGAGCATGTTGTCACTAAATAGC 60.260 45.833 0.00 0.00 0.00 2.97
3423 5861 7.398332 GGATTCCTATAGACCGGGATTAAACTA 59.602 40.741 6.32 0.00 0.00 2.24
3428 5866 5.279562 TGGATTCCTATAGACCGGGATTA 57.720 43.478 6.32 0.00 0.00 1.75
3432 5870 2.969950 TGTTGGATTCCTATAGACCGGG 59.030 50.000 6.32 0.00 0.00 5.73
3458 5896 6.072618 GGAGAACAATGAGCAATGATCCATAG 60.073 42.308 0.00 0.00 0.00 2.23
3462 5900 4.205587 AGGAGAACAATGAGCAATGATCC 58.794 43.478 0.00 0.00 0.00 3.36
3468 5906 6.053632 TCAAGATAGGAGAACAATGAGCAA 57.946 37.500 0.00 0.00 0.00 3.91
3490 5928 0.620556 TCACAAAGGATGAGGGGCTC 59.379 55.000 0.00 0.00 0.00 4.70
3495 5939 8.915057 ACTATCAATAATCACAAAGGATGAGG 57.085 34.615 0.00 0.00 0.00 3.86
3498 5942 9.276590 TGCTACTATCAATAATCACAAAGGATG 57.723 33.333 0.00 0.00 0.00 3.51
3534 5978 5.574970 ATGGCCTGTTTTCCCAAATTAAA 57.425 34.783 3.32 0.00 31.43 1.52
3538 5982 5.777526 AAATATGGCCTGTTTTCCCAAAT 57.222 34.783 3.32 0.00 31.43 2.32
3541 5985 5.365314 GGATAAAATATGGCCTGTTTTCCCA 59.635 40.000 3.32 0.00 31.51 4.37
3581 6026 8.744568 TGTAATGATTTGCCTATGTACAATCA 57.255 30.769 0.00 2.96 0.00 2.57
3596 6041 3.380954 TGCGATGTGCCATGTAATGATTT 59.619 39.130 0.00 0.00 46.28 2.17
3652 6097 6.809196 GGTTGGAATTCAAAATGTACGCATTA 59.191 34.615 7.93 0.00 43.89 1.90
3697 6143 4.216411 TCAATAAGGTGGTGGAACTAGC 57.784 45.455 0.00 0.00 46.91 3.42
3725 6171 4.767578 AGTATCTGGATGACACAGCATT 57.232 40.909 0.00 0.00 35.94 3.56
3783 6235 5.545658 AAAAGACATTAGCATGGTGTACG 57.454 39.130 7.89 0.00 34.27 3.67
3800 6252 8.786826 TCCGATAAAAGATAGCTTCAAAAAGA 57.213 30.769 0.00 0.00 34.14 2.52
3808 6260 9.262358 GTGATTACTTCCGATAAAAGATAGCTT 57.738 33.333 0.00 0.00 35.37 3.74
3824 6276 9.469807 CCAACATCTATGTCTAGTGATTACTTC 57.530 37.037 0.00 0.00 40.80 3.01
3897 6350 6.385759 TCCCTTGCTAACCATAAGTCTATTCA 59.614 38.462 0.00 0.00 0.00 2.57
3905 6358 4.200092 GGACTTCCCTTGCTAACCATAAG 58.800 47.826 0.00 0.00 0.00 1.73
3907 6360 3.926058 GGACTTCCCTTGCTAACCATA 57.074 47.619 0.00 0.00 0.00 2.74
3908 6361 2.808906 GGACTTCCCTTGCTAACCAT 57.191 50.000 0.00 0.00 0.00 3.55
3928 6388 3.921021 CCAGCTACAGAAGTAAACTGACG 59.079 47.826 0.00 0.00 36.95 4.35
4262 9360 2.364970 CCTCCTGCCATTTTGACACAAA 59.635 45.455 0.00 0.00 0.00 2.83
4394 9502 1.426215 AGGGGGTAAAAACGACACCAT 59.574 47.619 0.00 0.00 42.70 3.55
4437 9546 6.823689 GCCAAGAGGATTACAAATCTGTTCTA 59.176 38.462 0.11 0.00 35.24 2.10
4523 9642 5.907197 AGTACATTGCTAATACGACATGC 57.093 39.130 0.00 0.00 0.00 4.06
4593 9847 8.688747 AATTAAATGGCAATTTCTTGGAAACA 57.311 26.923 1.24 0.00 37.23 2.83
4651 9905 4.580580 GCTAAGTGTCCTTGGAATATTGGG 59.419 45.833 0.00 0.00 31.18 4.12
4678 9932 6.647334 TTGAAAGGATCAGCACACAAATTA 57.353 33.333 0.00 0.00 39.77 1.40
4737 10269 3.325293 AATTCACGCTCTGTCTGTCAT 57.675 42.857 0.00 0.00 0.00 3.06
4748 10287 2.869233 AGCACAAACAAATTCACGCT 57.131 40.000 0.00 0.00 0.00 5.07
4751 10296 6.645700 TCTGAAAAGCACAAACAAATTCAC 57.354 33.333 0.00 0.00 0.00 3.18
4804 10349 0.608640 GTCGTCTCCAACCTCCACAT 59.391 55.000 0.00 0.00 0.00 3.21
4850 13203 2.812358 AAAAATGTTCCCGAACCAGC 57.188 45.000 5.17 0.00 40.46 4.85


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

AutoCloner maintained by Alex Coulton.