Multiple sequence alignment - TraesCS6D01G101700

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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 TraesCS6D01G101700 chr6D 100.000 4164 0 0 1 4164 65096148 65091985 0.000000e+00 7690.0
1 TraesCS6D01G101700 chr6D 85.599 1486 182 21 893 2369 65343522 65342060 0.000000e+00 1530.0
2 TraesCS6D01G101700 chr6D 84.610 1501 174 21 898 2366 65051547 65053022 0.000000e+00 1439.0
3 TraesCS6D01G101700 chr6D 84.767 1418 181 19 968 2369 65361092 65359694 0.000000e+00 1389.0
4 TraesCS6D01G101700 chr6D 76.059 1299 216 58 2491 3731 65359162 65357901 4.640000e-164 588.0
5 TraesCS6D01G101700 chr6D 77.844 1002 171 32 2491 3459 65053538 65054521 1.300000e-159 573.0
6 TraesCS6D01G101700 chr6A 93.623 3246 127 35 828 4031 83644378 83647585 0.000000e+00 4774.0
7 TraesCS6D01G101700 chr6A 85.891 1375 182 10 968 2336 83435033 83436401 0.000000e+00 1454.0
8 TraesCS6D01G101700 chr6A 84.584 1479 201 20 893 2369 83599425 83600878 0.000000e+00 1443.0
9 TraesCS6D01G101700 chr6A 82.515 652 105 6 2485 3133 83600958 83601603 7.810000e-157 564.0
10 TraesCS6D01G101700 chr6A 77.468 1003 172 36 2491 3459 83437094 83438076 6.080000e-153 551.0
11 TraesCS6D01G101700 chr6B 94.870 1462 50 11 831 2280 140097590 140096142 0.000000e+00 2261.0
12 TraesCS6D01G101700 chr6B 94.621 1134 57 4 2491 3622 140094752 140093621 0.000000e+00 1753.0
13 TraesCS6D01G101700 chr6B 86.454 1410 171 14 968 2369 140367294 140365897 0.000000e+00 1528.0
14 TraesCS6D01G101700 chr6B 84.569 1484 184 22 893 2369 140333590 140332145 0.000000e+00 1430.0
15 TraesCS6D01G101700 chr6B 85.025 1409 176 17 968 2366 139883752 139885135 0.000000e+00 1400.0
16 TraesCS6D01G101700 chr6B 77.268 1003 175 34 2491 3459 139885650 139886633 1.320000e-149 540.0
17 TraesCS6D01G101700 chr6B 94.265 279 12 3 3744 4019 140093621 140093344 1.380000e-114 424.0
18 TraesCS6D01G101700 chr4B 88.700 823 85 4 1 819 638821698 638822516 0.000000e+00 998.0
19 TraesCS6D01G101700 chr4B 79.508 732 133 10 99 828 29703155 29703871 4.800000e-139 505.0
20 TraesCS6D01G101700 chr2D 93.722 669 30 3 1 669 405167911 405168567 0.000000e+00 992.0
21 TraesCS6D01G101700 chr2D 96.190 105 3 1 716 819 405168727 405168831 1.990000e-38 171.0
22 TraesCS6D01G101700 chr1B 82.847 822 127 11 2 819 400150411 400149600 0.000000e+00 725.0
23 TraesCS6D01G101700 chrUn 86.420 648 65 15 183 820 73673453 73674087 0.000000e+00 688.0
24 TraesCS6D01G101700 chrUn 76.388 1279 225 50 2491 3720 388715020 388713770 5.910000e-173 617.0
25 TraesCS6D01G101700 chr5B 79.933 897 132 21 967 1856 261676900 261676045 2.130000e-172 616.0
26 TraesCS6D01G101700 chr5B 74.491 933 209 19 2483 3397 261675397 261674476 1.090000e-100 377.0
27 TraesCS6D01G101700 chr7A 94.885 391 19 1 1 391 310627986 310628375 9.900000e-171 610.0
28 TraesCS6D01G101700 chr7A 95.238 63 2 1 712 774 310628379 310628440 9.530000e-17 99.0
29 TraesCS6D01G101700 chr7A 95.000 60 1 2 770 828 310650121 310650179 4.430000e-15 93.5
30 TraesCS6D01G101700 chr2B 81.046 153 29 0 213 365 794615649 794615801 5.650000e-24 122.0


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 TraesCS6D01G101700 chr6D 65091985 65096148 4163 True 7690.000000 7690 100.000000 1 4164 1 chr6D.!!$R1 4163
1 TraesCS6D01G101700 chr6D 65342060 65343522 1462 True 1530.000000 1530 85.599000 893 2369 1 chr6D.!!$R2 1476
2 TraesCS6D01G101700 chr6D 65051547 65054521 2974 False 1006.000000 1439 81.227000 898 3459 2 chr6D.!!$F1 2561
3 TraesCS6D01G101700 chr6D 65357901 65361092 3191 True 988.500000 1389 80.413000 968 3731 2 chr6D.!!$R3 2763
4 TraesCS6D01G101700 chr6A 83644378 83647585 3207 False 4774.000000 4774 93.623000 828 4031 1 chr6A.!!$F1 3203
5 TraesCS6D01G101700 chr6A 83599425 83601603 2178 False 1003.500000 1443 83.549500 893 3133 2 chr6A.!!$F3 2240
6 TraesCS6D01G101700 chr6A 83435033 83438076 3043 False 1002.500000 1454 81.679500 968 3459 2 chr6A.!!$F2 2491
7 TraesCS6D01G101700 chr6B 140365897 140367294 1397 True 1528.000000 1528 86.454000 968 2369 1 chr6B.!!$R2 1401
8 TraesCS6D01G101700 chr6B 140093344 140097590 4246 True 1479.333333 2261 94.585333 831 4019 3 chr6B.!!$R3 3188
9 TraesCS6D01G101700 chr6B 140332145 140333590 1445 True 1430.000000 1430 84.569000 893 2369 1 chr6B.!!$R1 1476
10 TraesCS6D01G101700 chr6B 139883752 139886633 2881 False 970.000000 1400 81.146500 968 3459 2 chr6B.!!$F1 2491
11 TraesCS6D01G101700 chr4B 638821698 638822516 818 False 998.000000 998 88.700000 1 819 1 chr4B.!!$F2 818
12 TraesCS6D01G101700 chr4B 29703155 29703871 716 False 505.000000 505 79.508000 99 828 1 chr4B.!!$F1 729
13 TraesCS6D01G101700 chr2D 405167911 405168831 920 False 581.500000 992 94.956000 1 819 2 chr2D.!!$F1 818
14 TraesCS6D01G101700 chr1B 400149600 400150411 811 True 725.000000 725 82.847000 2 819 1 chr1B.!!$R1 817
15 TraesCS6D01G101700 chrUn 73673453 73674087 634 False 688.000000 688 86.420000 183 820 1 chrUn.!!$F1 637
16 TraesCS6D01G101700 chrUn 388713770 388715020 1250 True 617.000000 617 76.388000 2491 3720 1 chrUn.!!$R1 1229
17 TraesCS6D01G101700 chr5B 261674476 261676900 2424 True 496.500000 616 77.212000 967 3397 2 chr5B.!!$R1 2430

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
735 852 1.078072 TGAAGTTGCACCACGGTGT 60.078 52.632 17.26 0.0 46.90 4.16 F
1804 2000 0.382515 CGAGGACAGGGAAGTCGATC 59.617 60.000 0.00 0.0 39.42 3.69 F
2445 3918 0.508641 CAAGTTGCGACTCAAGACGG 59.491 55.000 7.17 0.0 34.21 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 3900 0.104304 ACCGTCTTGAGTCGCAACTT 59.896 50.0 0.00 0.00 35.28 2.66 R
2971 5333 0.396417 CTGACATCGGACCTCCCTCT 60.396 60.0 0.00 0.00 0.00 3.69 R
4140 6568 0.034059 CCTGGTCAGTGGTCACAGAC 59.966 60.0 15.34 15.34 44.11 3.51 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
31 32 4.627611 GCATGAGCTTCTCTTAATGCAA 57.372 40.909 0.00 0.00 41.26 4.08
65 66 2.936202 CTGCAACCCCTAATGCTACAT 58.064 47.619 0.00 0.00 42.97 2.29
127 128 2.612212 CAGCGCAGGATATTTTTACCGT 59.388 45.455 11.47 0.00 0.00 4.83
255 256 7.770433 CAGACTCAACACCAGAAATAATATGGA 59.230 37.037 0.00 0.00 37.54 3.41
546 547 2.878429 CTCGTGGACGGACTCCTG 59.122 66.667 0.00 0.00 40.26 3.86
735 852 1.078072 TGAAGTTGCACCACGGTGT 60.078 52.632 17.26 0.00 46.90 4.16
793 911 6.016555 ACAGCCTGTTTTGAAATATAAGGGT 58.983 36.000 0.00 0.00 34.52 4.34
823 942 6.560711 GCGCCTCCTTTTATCTTCAATTTTA 58.439 36.000 0.00 0.00 0.00 1.52
871 997 1.682854 CAAGGCAGACCAAAAAGAGCA 59.317 47.619 0.00 0.00 39.06 4.26
872 998 2.298163 CAAGGCAGACCAAAAAGAGCAT 59.702 45.455 0.00 0.00 39.06 3.79
1081 1238 1.200716 CGCACTTCAACAATCTGGCAT 59.799 47.619 0.00 0.00 0.00 4.40
1804 2000 0.382515 CGAGGACAGGGAAGTCGATC 59.617 60.000 0.00 0.00 39.42 3.69
2253 2533 0.692476 ATACTGGCTGTCAAGGTGCA 59.308 50.000 0.00 0.00 0.00 4.57
2297 3770 1.480137 AGATGCTGCACACTCTACTCC 59.520 52.381 3.57 0.00 0.00 3.85
2370 3843 8.944029 GTCATATTGATATCTGTTCATCCCTTG 58.056 37.037 3.98 0.00 0.00 3.61
2375 3848 7.616528 TGATATCTGTTCATCCCTTGTATCA 57.383 36.000 3.98 0.00 0.00 2.15
2376 3849 7.445121 TGATATCTGTTCATCCCTTGTATCAC 58.555 38.462 3.98 0.00 0.00 3.06
2378 3851 5.344743 TCTGTTCATCCCTTGTATCACTC 57.655 43.478 0.00 0.00 0.00 3.51
2379 3852 4.162320 TCTGTTCATCCCTTGTATCACTCC 59.838 45.833 0.00 0.00 0.00 3.85
2381 3854 4.080919 TGTTCATCCCTTGTATCACTCCAG 60.081 45.833 0.00 0.00 0.00 3.86
2384 3857 4.649674 TCATCCCTTGTATCACTCCAGTAC 59.350 45.833 0.00 0.00 0.00 2.73
2386 3859 5.461516 TCCCTTGTATCACTCCAGTACTA 57.538 43.478 0.00 0.00 0.00 1.82
2387 3860 5.198965 TCCCTTGTATCACTCCAGTACTAC 58.801 45.833 0.00 0.00 0.00 2.73
2388 3861 5.044328 TCCCTTGTATCACTCCAGTACTACT 60.044 44.000 0.00 0.00 0.00 2.57
2389 3862 5.657302 CCCTTGTATCACTCCAGTACTACTT 59.343 44.000 0.00 0.00 0.00 2.24
2394 3867 8.503458 TGTATCACTCCAGTACTACTTAGTTC 57.497 38.462 0.00 0.00 37.73 3.01
2395 3868 8.105197 TGTATCACTCCAGTACTACTTAGTTCA 58.895 37.037 0.00 0.00 37.73 3.18
2396 3869 9.122779 GTATCACTCCAGTACTACTTAGTTCAT 57.877 37.037 0.00 0.00 37.73 2.57
2397 3870 7.627298 TCACTCCAGTACTACTTAGTTCATC 57.373 40.000 0.00 0.00 37.73 2.92
2398 3871 6.602406 TCACTCCAGTACTACTTAGTTCATCC 59.398 42.308 0.00 0.00 37.73 3.51
2399 3872 5.892686 ACTCCAGTACTACTTAGTTCATCCC 59.107 44.000 0.00 0.00 37.73 3.85
2400 3873 6.088541 TCCAGTACTACTTAGTTCATCCCT 57.911 41.667 0.00 0.00 37.73 4.20
2401 3874 6.500336 TCCAGTACTACTTAGTTCATCCCTT 58.500 40.000 0.00 0.00 37.73 3.95
2402 3875 7.645942 TCCAGTACTACTTAGTTCATCCCTTA 58.354 38.462 0.00 0.00 37.73 2.69
2403 3876 8.287350 TCCAGTACTACTTAGTTCATCCCTTAT 58.713 37.037 0.00 0.00 37.73 1.73
2404 3877 9.584008 CCAGTACTACTTAGTTCATCCCTTATA 57.416 37.037 0.00 0.00 37.73 0.98
2411 3884 8.152023 ACTTAGTTCATCCCTTATATCATCCC 57.848 38.462 0.00 0.00 0.00 3.85
2412 3885 7.739444 ACTTAGTTCATCCCTTATATCATCCCA 59.261 37.037 0.00 0.00 0.00 4.37
2413 3886 8.700145 TTAGTTCATCCCTTATATCATCCCAT 57.300 34.615 0.00 0.00 0.00 4.00
2414 3887 7.594849 AGTTCATCCCTTATATCATCCCATT 57.405 36.000 0.00 0.00 0.00 3.16
2415 3888 8.700145 AGTTCATCCCTTATATCATCCCATTA 57.300 34.615 0.00 0.00 0.00 1.90
2416 3889 8.776119 AGTTCATCCCTTATATCATCCCATTAG 58.224 37.037 0.00 0.00 0.00 1.73
2417 3890 8.552296 GTTCATCCCTTATATCATCCCATTAGT 58.448 37.037 0.00 0.00 0.00 2.24
2418 3891 8.700145 TCATCCCTTATATCATCCCATTAGTT 57.300 34.615 0.00 0.00 0.00 2.24
2419 3892 9.797732 TCATCCCTTATATCATCCCATTAGTTA 57.202 33.333 0.00 0.00 0.00 2.24
2445 3918 0.508641 CAAGTTGCGACTCAAGACGG 59.491 55.000 7.17 0.00 34.21 4.79
2488 4833 7.602644 CAGCTTATTCCAGTACTAGTTGTTCAA 59.397 37.037 0.00 0.00 0.00 2.69
2648 5010 1.123861 TGCTGACTTCTGGCAGTCCT 61.124 55.000 15.27 0.00 42.39 3.85
2793 5155 2.421775 TGAGCGTTGTTTGTGTTGACAT 59.578 40.909 0.00 0.00 30.13 3.06
2873 5235 2.166459 TCATCTGGTGGAAGAAGTAGCG 59.834 50.000 0.00 0.00 0.00 4.26
2970 5332 4.759782 AGTAGCAGTGATGATGTGGTAAC 58.240 43.478 0.00 0.00 0.00 2.50
3006 5368 0.038166 TCAGGTTCCATTGGTGAGGC 59.962 55.000 1.86 0.00 0.00 4.70
3277 5673 6.491062 TCATCATTTTGTGGTGAACTGAGAAT 59.509 34.615 0.00 0.00 44.80 2.40
3294 5691 2.363680 AGAATGTAGACTGAGCCCATCG 59.636 50.000 0.00 0.00 0.00 3.84
3345 5750 6.993079 TGTTGCACTCTTGAGTTCTCTATTA 58.007 36.000 0.00 0.00 0.00 0.98
3397 5803 1.406539 CACCCTGGCTGCATATTGTTC 59.593 52.381 0.50 0.00 0.00 3.18
3590 6011 6.399639 AACCATACAAATGAGGTCGTTTTT 57.600 33.333 0.00 0.00 34.84 1.94
3624 6045 2.654863 AGCTATGGTGGGAAAAATCCG 58.345 47.619 0.00 0.00 0.00 4.18
3661 6082 0.033228 TTTGGAATTTGTGGCTGCCG 59.967 50.000 14.98 0.00 0.00 5.69
3783 6207 4.964593 ACATTTTAAGGTACCACGAGTGT 58.035 39.130 15.94 8.68 0.00 3.55
3917 6341 3.192422 CGAGTGGGAAATGCCAATTGTTA 59.808 43.478 4.43 0.00 38.95 2.41
3918 6342 4.321601 CGAGTGGGAAATGCCAATTGTTAA 60.322 41.667 4.43 0.00 38.95 2.01
3968 6393 2.998316 GCTACTTGCCCAGATTCTCT 57.002 50.000 0.00 0.00 35.15 3.10
4012 6440 2.159282 GCAACATAGCTGAGCTGCATTT 60.159 45.455 18.79 1.85 40.10 2.32
4031 6459 0.380378 TGCCAACGTGAAAAGACAGC 59.620 50.000 0.00 0.00 0.00 4.40
4032 6460 0.317854 GCCAACGTGAAAAGACAGCC 60.318 55.000 0.00 0.00 0.00 4.85
4033 6461 0.041312 CCAACGTGAAAAGACAGCCG 60.041 55.000 0.00 0.00 0.00 5.52
4034 6462 0.934496 CAACGTGAAAAGACAGCCGA 59.066 50.000 0.00 0.00 0.00 5.54
4035 6463 1.070577 CAACGTGAAAAGACAGCCGAG 60.071 52.381 0.00 0.00 0.00 4.63
4036 6464 0.600255 ACGTGAAAAGACAGCCGAGG 60.600 55.000 0.00 0.00 0.00 4.63
4037 6465 1.869690 GTGAAAAGACAGCCGAGGC 59.130 57.895 5.89 5.89 42.33 4.70
4048 6476 4.735132 CCGAGGCGAGCGTTGGAA 62.735 66.667 16.73 0.00 37.51 3.53
4049 6477 3.479269 CGAGGCGAGCGTTGGAAC 61.479 66.667 0.00 0.00 0.00 3.62
4050 6478 2.048127 GAGGCGAGCGTTGGAACT 60.048 61.111 0.00 0.00 0.00 3.01
4051 6479 1.214589 GAGGCGAGCGTTGGAACTA 59.785 57.895 0.00 0.00 0.00 2.24
4052 6480 0.389426 GAGGCGAGCGTTGGAACTAA 60.389 55.000 0.00 0.00 0.00 2.24
4053 6481 0.389948 AGGCGAGCGTTGGAACTAAG 60.390 55.000 0.00 0.00 0.00 2.18
4054 6482 0.669625 GGCGAGCGTTGGAACTAAGT 60.670 55.000 0.00 0.00 0.00 2.24
4055 6483 1.145803 GCGAGCGTTGGAACTAAGTT 58.854 50.000 0.00 0.00 0.00 2.66
4056 6484 1.529865 GCGAGCGTTGGAACTAAGTTT 59.470 47.619 0.00 0.00 0.00 2.66
4057 6485 2.411160 GCGAGCGTTGGAACTAAGTTTC 60.411 50.000 0.00 0.00 0.00 2.78
4058 6486 2.157085 CGAGCGTTGGAACTAAGTTTCC 59.843 50.000 0.00 0.00 44.86 3.13
4066 6494 4.224715 GGAACTAAGTTTCCAGTGTTGC 57.775 45.455 0.00 0.00 44.14 4.17
4067 6495 3.303791 GGAACTAAGTTTCCAGTGTTGCG 60.304 47.826 0.00 0.00 44.14 4.85
4068 6496 1.602377 ACTAAGTTTCCAGTGTTGCGC 59.398 47.619 0.00 0.00 0.00 6.09
4069 6497 0.948678 TAAGTTTCCAGTGTTGCGCC 59.051 50.000 4.18 0.00 0.00 6.53
4070 6498 1.734388 AAGTTTCCAGTGTTGCGCCC 61.734 55.000 4.18 0.00 0.00 6.13
4071 6499 2.124109 TTTCCAGTGTTGCGCCCA 60.124 55.556 4.18 0.00 0.00 5.36
4072 6500 2.192861 TTTCCAGTGTTGCGCCCAG 61.193 57.895 4.18 0.00 0.00 4.45
4073 6501 2.902423 TTTCCAGTGTTGCGCCCAGT 62.902 55.000 4.18 1.09 0.00 4.00
4074 6502 3.357079 CCAGTGTTGCGCCCAGTC 61.357 66.667 4.18 0.00 0.00 3.51
4075 6503 2.591429 CAGTGTTGCGCCCAGTCA 60.591 61.111 4.18 0.00 0.00 3.41
4076 6504 2.591715 AGTGTTGCGCCCAGTCAC 60.592 61.111 4.18 7.16 0.00 3.67
4077 6505 3.660111 GTGTTGCGCCCAGTCACC 61.660 66.667 4.18 0.00 0.00 4.02
4079 6507 4.980805 GTTGCGCCCAGTCACCGA 62.981 66.667 4.18 0.00 0.00 4.69
4080 6508 4.980805 TTGCGCCCAGTCACCGAC 62.981 66.667 4.18 0.00 0.00 4.79
4085 6513 3.625897 CCCAGTCACCGACAGCCA 61.626 66.667 0.00 0.00 34.60 4.75
4086 6514 2.357517 CCAGTCACCGACAGCCAC 60.358 66.667 0.00 0.00 34.60 5.01
4087 6515 2.737180 CAGTCACCGACAGCCACT 59.263 61.111 0.00 0.00 34.60 4.00
4088 6516 1.665916 CAGTCACCGACAGCCACTG 60.666 63.158 0.00 0.00 34.60 3.66
4089 6517 2.357517 GTCACCGACAGCCACTGG 60.358 66.667 0.00 0.00 35.51 4.00
4090 6518 2.842462 TCACCGACAGCCACTGGT 60.842 61.111 0.00 0.00 35.51 4.00
4091 6519 2.666190 CACCGACAGCCACTGGTG 60.666 66.667 0.00 1.93 45.17 4.17
4105 6533 1.379916 TGGTGGTGCCATCTTCAGG 59.620 57.895 2.93 0.00 43.61 3.86
4114 6542 1.495878 CCATCTTCAGGCTCGATTCG 58.504 55.000 0.00 0.00 0.00 3.34
4115 6543 0.857935 CATCTTCAGGCTCGATTCGC 59.142 55.000 0.00 0.00 0.00 4.70
4116 6544 0.749649 ATCTTCAGGCTCGATTCGCT 59.250 50.000 0.00 0.00 0.00 4.93
4117 6545 0.179127 TCTTCAGGCTCGATTCGCTG 60.179 55.000 0.00 3.64 0.00 5.18
4118 6546 0.459237 CTTCAGGCTCGATTCGCTGT 60.459 55.000 0.00 0.00 0.00 4.40
4119 6547 0.458543 TTCAGGCTCGATTCGCTGTC 60.459 55.000 0.00 0.00 0.00 3.51
4120 6548 1.880340 CAGGCTCGATTCGCTGTCC 60.880 63.158 0.00 0.00 0.00 4.02
4121 6549 2.586357 GGCTCGATTCGCTGTCCC 60.586 66.667 0.00 0.00 0.00 4.46
4122 6550 2.586357 GCTCGATTCGCTGTCCCC 60.586 66.667 0.00 0.00 0.00 4.81
4123 6551 2.278857 CTCGATTCGCTGTCCCCG 60.279 66.667 0.00 0.00 0.00 5.73
4124 6552 4.508128 TCGATTCGCTGTCCCCGC 62.508 66.667 0.00 0.00 0.00 6.13
4141 6569 2.027605 CCGACGGCATATCAGCGT 59.972 61.111 0.00 0.00 34.64 5.07
4142 6570 2.016704 CCGACGGCATATCAGCGTC 61.017 63.158 0.00 0.00 35.90 5.19
4143 6571 1.008424 CGACGGCATATCAGCGTCT 60.008 57.895 0.00 0.00 36.56 4.18
4144 6572 1.271446 CGACGGCATATCAGCGTCTG 61.271 60.000 0.00 1.02 36.56 3.51
4145 6573 0.249073 GACGGCATATCAGCGTCTGT 60.249 55.000 0.00 0.00 36.14 3.41
4146 6574 0.528466 ACGGCATATCAGCGTCTGTG 60.528 55.000 6.72 0.77 34.64 3.66
4147 6575 0.249031 CGGCATATCAGCGTCTGTGA 60.249 55.000 6.72 0.00 34.64 3.58
4148 6576 1.212616 GGCATATCAGCGTCTGTGAC 58.787 55.000 6.72 0.00 34.64 3.67
4149 6577 1.212616 GCATATCAGCGTCTGTGACC 58.787 55.000 6.72 0.00 32.61 4.02
4150 6578 1.471501 GCATATCAGCGTCTGTGACCA 60.472 52.381 6.72 0.00 32.61 4.02
4151 6579 2.196749 CATATCAGCGTCTGTGACCAC 58.803 52.381 6.72 0.00 32.61 4.16
4152 6580 1.545841 TATCAGCGTCTGTGACCACT 58.454 50.000 6.72 0.00 32.61 4.00
4153 6581 0.037882 ATCAGCGTCTGTGACCACTG 60.038 55.000 6.72 1.43 35.74 3.66
4154 6582 1.106944 TCAGCGTCTGTGACCACTGA 61.107 55.000 11.55 11.55 38.81 3.41
4159 6587 2.440946 TCTGTGACCACTGACCAGG 58.559 57.895 5.76 0.00 34.93 4.45
4160 6588 0.398522 TCTGTGACCACTGACCAGGT 60.399 55.000 0.00 0.00 41.83 4.00
4161 6589 0.469917 CTGTGACCACTGACCAGGTT 59.530 55.000 0.00 0.00 38.50 3.50
4162 6590 0.180171 TGTGACCACTGACCAGGTTG 59.820 55.000 0.00 0.00 38.50 3.77
4163 6591 1.148273 TGACCACTGACCAGGTTGC 59.852 57.895 0.00 0.00 38.50 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.374631 GAGTGCGCACATCCTGTCA 60.375 57.895 39.21 0.00 0.00 3.58
127 128 0.898320 CTCCCCGAAAAGAGAGCAGA 59.102 55.000 0.00 0.00 31.43 4.26
151 152 6.462500 CCATACCCAATGATGAAAAACACAA 58.538 36.000 0.00 0.00 37.86 3.33
277 278 1.202794 TCACAATCTGCACTTGGAGCA 60.203 47.619 8.65 0.00 40.19 4.26
368 369 1.360393 AAAGGGGTCAGGAGCAACCA 61.360 55.000 0.56 0.00 42.04 3.67
380 381 0.685458 GATCTGCATGCCAAAGGGGT 60.685 55.000 16.68 0.00 39.65 4.95
467 468 2.019249 GATAGCACATGCAGCAAAGGA 58.981 47.619 12.59 0.00 45.16 3.36
546 547 0.521242 CGCAGCGTTGAACCTTATGC 60.521 55.000 6.65 0.00 0.00 3.14
557 558 0.029035 CGTAGTAGATCCGCAGCGTT 59.971 55.000 15.05 0.00 0.00 4.84
735 852 5.208890 ACATAACATGAGGCTAGTGAGGTA 58.791 41.667 0.00 0.00 0.00 3.08
823 942 9.838975 GAACTTGTGAACCAAAATTTCAAAAAT 57.161 25.926 0.00 0.00 34.78 1.82
871 997 1.536907 TGGGTGGGTGGTGTACGAT 60.537 57.895 0.00 0.00 0.00 3.73
872 998 2.122945 TGGGTGGGTGGTGTACGA 60.123 61.111 0.00 0.00 0.00 3.43
1265 1449 4.498520 CATCGTCCTGCGCCGTCT 62.499 66.667 4.18 0.00 41.07 4.18
1267 1451 4.796231 GTCATCGTCCTGCGCCGT 62.796 66.667 4.18 0.00 41.07 5.68
1362 1546 2.660064 GGAGAGGACCATGGTGCGT 61.660 63.158 28.23 20.53 41.44 5.24
1655 1851 3.853712 CGCAGCTGAGGATATCGC 58.146 61.111 20.43 0.00 0.00 4.58
2064 2323 0.322366 TCACAATGCCGCCAATCTCA 60.322 50.000 0.00 0.00 0.00 3.27
2253 2533 0.171007 CTCCGTGGCATGCGAAAATT 59.829 50.000 12.44 0.00 0.00 1.82
2297 3770 2.005451 CTGAAGGTGAGGAAAGCATCG 58.995 52.381 0.00 0.00 0.00 3.84
2370 3843 8.503458 TGAACTAAGTAGTACTGGAGTGATAC 57.497 38.462 15.47 9.99 34.99 2.24
2374 3847 6.183360 GGGATGAACTAAGTAGTACTGGAGTG 60.183 46.154 15.47 3.80 34.99 3.51
2375 3848 5.892686 GGGATGAACTAAGTAGTACTGGAGT 59.107 44.000 5.39 7.85 34.99 3.85
2376 3849 6.130569 AGGGATGAACTAAGTAGTACTGGAG 58.869 44.000 5.39 7.21 34.99 3.86
2378 3851 6.793505 AAGGGATGAACTAAGTAGTACTGG 57.206 41.667 5.39 2.96 34.99 4.00
2386 3859 7.739444 TGGGATGATATAAGGGATGAACTAAGT 59.261 37.037 0.00 0.00 0.00 2.24
2387 3860 8.150827 TGGGATGATATAAGGGATGAACTAAG 57.849 38.462 0.00 0.00 0.00 2.18
2388 3861 8.700145 ATGGGATGATATAAGGGATGAACTAA 57.300 34.615 0.00 0.00 0.00 2.24
2389 3862 8.700145 AATGGGATGATATAAGGGATGAACTA 57.300 34.615 0.00 0.00 0.00 2.24
2411 3884 4.971830 CGCAACTTGCATCCATAACTAATG 59.028 41.667 14.10 0.00 45.36 1.90
2412 3885 4.881273 TCGCAACTTGCATCCATAACTAAT 59.119 37.500 14.10 0.00 45.36 1.73
2413 3886 4.094294 GTCGCAACTTGCATCCATAACTAA 59.906 41.667 14.10 0.00 45.36 2.24
2414 3887 3.621268 GTCGCAACTTGCATCCATAACTA 59.379 43.478 14.10 0.00 45.36 2.24
2415 3888 2.420022 GTCGCAACTTGCATCCATAACT 59.580 45.455 14.10 0.00 45.36 2.24
2416 3889 2.420022 AGTCGCAACTTGCATCCATAAC 59.580 45.455 14.10 0.84 45.36 1.89
2417 3890 2.677836 GAGTCGCAACTTGCATCCATAA 59.322 45.455 14.10 0.00 45.36 1.90
2418 3891 2.279741 GAGTCGCAACTTGCATCCATA 58.720 47.619 14.10 0.00 45.36 2.74
2419 3892 1.089920 GAGTCGCAACTTGCATCCAT 58.910 50.000 14.10 0.00 45.36 3.41
2420 3893 0.250252 TGAGTCGCAACTTGCATCCA 60.250 50.000 14.10 3.34 45.36 3.41
2421 3894 0.874390 TTGAGTCGCAACTTGCATCC 59.126 50.000 14.10 0.97 45.36 3.51
2422 3895 1.800586 TCTTGAGTCGCAACTTGCATC 59.199 47.619 14.10 8.69 45.36 3.91
2423 3896 1.532868 GTCTTGAGTCGCAACTTGCAT 59.467 47.619 14.10 0.00 45.36 3.96
2427 3900 0.104304 ACCGTCTTGAGTCGCAACTT 59.896 50.000 0.00 0.00 35.28 2.66
2514 4873 7.822658 TGCACCAAATTACAATTAGAAGTACC 58.177 34.615 0.00 0.00 0.00 3.34
2530 4890 5.486735 TCAATCCTCAAATTGCACCAAAT 57.513 34.783 0.00 0.00 36.72 2.32
2648 5010 2.572812 GCAATCGCATGTGCCCAA 59.427 55.556 0.00 0.00 38.36 4.12
2793 5155 5.450453 CTTCCTCTACTCCTACATCCTCAA 58.550 45.833 0.00 0.00 0.00 3.02
2873 5235 3.480470 CCTCCATTACCACATCATCACC 58.520 50.000 0.00 0.00 0.00 4.02
2970 5332 0.684479 TGACATCGGACCTCCCTCTG 60.684 60.000 0.00 0.00 0.00 3.35
2971 5333 0.396417 CTGACATCGGACCTCCCTCT 60.396 60.000 0.00 0.00 0.00 3.69
3006 5368 1.140161 CCAACTGATGGCGCATTGG 59.860 57.895 10.83 8.95 43.80 3.16
3021 5383 1.927487 ATCATTGCCACTGCTTCCAA 58.073 45.000 0.00 0.00 38.71 3.53
3277 5673 1.393603 CTCGATGGGCTCAGTCTACA 58.606 55.000 0.00 0.00 0.00 2.74
3294 5691 1.279271 TGAAACTAGCTTCCAGGCCTC 59.721 52.381 0.00 0.00 0.00 4.70
3345 5750 5.194942 AGTTCAGAATCCTACTAGTCTCCCT 59.805 44.000 0.00 0.00 0.00 4.20
3397 5803 3.139077 ACAGGCCAAAAGTAAAGACTCG 58.861 45.455 5.01 0.00 33.58 4.18
3486 5895 5.065731 GCAGAGTTATCAACTTAGCAGCAAT 59.934 40.000 0.00 0.00 43.03 3.56
3590 6011 2.945008 CCATAGCTTCCGAATCAGCAAA 59.055 45.455 0.00 0.00 38.61 3.68
3624 6045 2.158561 AACCCAGCCTGAAAATGCGC 62.159 55.000 0.00 0.00 0.00 6.09
3661 6082 7.467131 AATGCAAGCATAGTTTTGGAAAACAAC 60.467 33.333 15.51 3.98 41.92 3.32
3749 6173 8.077991 GGTACCTTAAAATGTTCACCAACTTAC 58.922 37.037 4.06 0.00 33.17 2.34
3783 6207 1.472082 CAAGTGACAGCACCACACAAA 59.528 47.619 0.00 0.00 46.32 2.83
3964 6389 0.829333 GCCTGAATCCTGAGCAGAGA 59.171 55.000 0.00 0.00 0.00 3.10
3968 6393 0.911045 TCCTGCCTGAATCCTGAGCA 60.911 55.000 0.00 0.00 0.00 4.26
4012 6440 0.380378 GCTGTCTTTTCACGTTGGCA 59.620 50.000 0.00 0.00 0.00 4.92
4031 6459 4.735132 TTCCAACGCTCGCCTCGG 62.735 66.667 0.00 0.00 0.00 4.63
4032 6460 2.537792 TAGTTCCAACGCTCGCCTCG 62.538 60.000 0.00 0.00 0.00 4.63
4033 6461 0.389426 TTAGTTCCAACGCTCGCCTC 60.389 55.000 0.00 0.00 0.00 4.70
4034 6462 0.389948 CTTAGTTCCAACGCTCGCCT 60.390 55.000 0.00 0.00 0.00 5.52
4035 6463 0.669625 ACTTAGTTCCAACGCTCGCC 60.670 55.000 0.00 0.00 0.00 5.54
4036 6464 1.145803 AACTTAGTTCCAACGCTCGC 58.854 50.000 0.00 0.00 0.00 5.03
4037 6465 2.157085 GGAAACTTAGTTCCAACGCTCG 59.843 50.000 0.00 0.00 45.57 5.03
4038 6466 3.808116 GGAAACTTAGTTCCAACGCTC 57.192 47.619 0.00 0.00 45.57 5.03
4045 6473 3.303791 CGCAACACTGGAAACTTAGTTCC 60.304 47.826 0.00 2.61 46.32 3.62
4046 6474 3.848554 GCGCAACACTGGAAACTTAGTTC 60.849 47.826 0.30 0.00 0.00 3.01
4047 6475 2.032924 GCGCAACACTGGAAACTTAGTT 59.967 45.455 0.30 0.00 0.00 2.24
4048 6476 1.602377 GCGCAACACTGGAAACTTAGT 59.398 47.619 0.30 0.00 0.00 2.24
4049 6477 1.069227 GGCGCAACACTGGAAACTTAG 60.069 52.381 10.83 0.00 0.00 2.18
4050 6478 0.948678 GGCGCAACACTGGAAACTTA 59.051 50.000 10.83 0.00 0.00 2.24
4051 6479 1.733526 GGCGCAACACTGGAAACTT 59.266 52.632 10.83 0.00 0.00 2.66
4052 6480 2.193536 GGGCGCAACACTGGAAACT 61.194 57.895 10.83 0.00 0.00 2.66
4053 6481 2.335011 GGGCGCAACACTGGAAAC 59.665 61.111 10.83 0.00 0.00 2.78
4054 6482 2.124109 TGGGCGCAACACTGGAAA 60.124 55.556 10.83 0.00 0.00 3.13
4055 6483 2.594303 CTGGGCGCAACACTGGAA 60.594 61.111 10.83 0.00 0.00 3.53
4056 6484 3.825160 GACTGGGCGCAACACTGGA 62.825 63.158 10.83 0.00 0.00 3.86
4057 6485 3.357079 GACTGGGCGCAACACTGG 61.357 66.667 10.83 0.00 0.00 4.00
4058 6486 2.591429 TGACTGGGCGCAACACTG 60.591 61.111 10.83 2.82 0.00 3.66
4059 6487 2.591715 GTGACTGGGCGCAACACT 60.592 61.111 23.45 0.00 0.00 3.55
4060 6488 3.660111 GGTGACTGGGCGCAACAC 61.660 66.667 22.99 22.99 0.00 3.32
4062 6490 4.980805 TCGGTGACTGGGCGCAAC 62.981 66.667 10.83 1.07 0.00 4.17
4063 6491 4.980805 GTCGGTGACTGGGCGCAA 62.981 66.667 10.83 0.00 0.00 4.85
4068 6496 3.625897 TGGCTGTCGGTGACTGGG 61.626 66.667 6.07 0.00 33.20 4.45
4069 6497 2.357517 GTGGCTGTCGGTGACTGG 60.358 66.667 6.07 0.00 33.20 4.00
4070 6498 1.665916 CAGTGGCTGTCGGTGACTG 60.666 63.158 0.00 0.00 35.18 3.51
4071 6499 2.737180 CAGTGGCTGTCGGTGACT 59.263 61.111 0.00 0.00 33.15 3.41
4072 6500 2.357517 CCAGTGGCTGTCGGTGAC 60.358 66.667 0.00 0.00 0.00 3.67
4073 6501 2.842462 ACCAGTGGCTGTCGGTGA 60.842 61.111 9.78 0.00 0.00 4.02
4074 6502 2.666190 CACCAGTGGCTGTCGGTG 60.666 66.667 9.78 0.00 42.72 4.94
4075 6503 3.941188 CCACCAGTGGCTGTCGGT 61.941 66.667 9.78 0.00 44.73 4.69
4088 6516 4.326255 CCTGAAGATGGCACCACC 57.674 61.111 0.00 0.00 39.84 4.61
4095 6523 1.495878 CGAATCGAGCCTGAAGATGG 58.504 55.000 0.00 0.00 0.00 3.51
4096 6524 0.857935 GCGAATCGAGCCTGAAGATG 59.142 55.000 6.91 0.00 0.00 2.90
4097 6525 0.749649 AGCGAATCGAGCCTGAAGAT 59.250 50.000 6.91 0.00 34.64 2.40
4098 6526 0.179127 CAGCGAATCGAGCCTGAAGA 60.179 55.000 6.91 0.00 34.64 2.87
4099 6527 0.459237 ACAGCGAATCGAGCCTGAAG 60.459 55.000 6.91 0.00 34.64 3.02
4100 6528 0.458543 GACAGCGAATCGAGCCTGAA 60.459 55.000 6.91 0.00 34.64 3.02
4101 6529 1.139734 GACAGCGAATCGAGCCTGA 59.860 57.895 6.91 0.00 34.64 3.86
4102 6530 1.880340 GGACAGCGAATCGAGCCTG 60.880 63.158 6.91 7.03 34.64 4.85
4103 6531 2.496817 GGACAGCGAATCGAGCCT 59.503 61.111 6.91 0.00 34.64 4.58
4104 6532 2.586357 GGGACAGCGAATCGAGCC 60.586 66.667 6.91 0.73 34.64 4.70
4105 6533 2.586357 GGGGACAGCGAATCGAGC 60.586 66.667 6.91 0.00 0.00 5.03
4106 6534 2.278857 CGGGGACAGCGAATCGAG 60.279 66.667 6.91 0.00 0.00 4.04
4107 6535 4.508128 GCGGGGACAGCGAATCGA 62.508 66.667 6.91 0.00 0.00 3.59
4124 6552 2.016704 GACGCTGATATGCCGTCGG 61.017 63.158 6.99 6.99 31.35 4.79
4125 6553 1.008424 AGACGCTGATATGCCGTCG 60.008 57.895 11.42 0.00 39.50 5.12
4126 6554 0.249073 ACAGACGCTGATATGCCGTC 60.249 55.000 12.77 9.96 37.04 4.79
4127 6555 0.528466 CACAGACGCTGATATGCCGT 60.528 55.000 12.77 0.00 35.18 5.68
4128 6556 0.249031 TCACAGACGCTGATATGCCG 60.249 55.000 12.77 0.00 35.18 5.69
4129 6557 1.212616 GTCACAGACGCTGATATGCC 58.787 55.000 12.77 0.00 35.18 4.40
4130 6558 1.212616 GGTCACAGACGCTGATATGC 58.787 55.000 12.77 0.00 35.18 3.14
4131 6559 2.159184 AGTGGTCACAGACGCTGATATG 60.159 50.000 12.77 2.70 35.18 1.78
4132 6560 2.103373 AGTGGTCACAGACGCTGATAT 58.897 47.619 12.77 0.00 35.18 1.63
4133 6561 1.202348 CAGTGGTCACAGACGCTGATA 59.798 52.381 12.77 0.00 37.95 2.15
4134 6562 0.037882 CAGTGGTCACAGACGCTGAT 60.038 55.000 12.77 0.00 37.95 2.90
4135 6563 1.106944 TCAGTGGTCACAGACGCTGA 61.107 55.000 12.77 14.55 40.23 4.26
4136 6564 0.941463 GTCAGTGGTCACAGACGCTG 60.941 60.000 10.11 11.51 37.92 5.18
4137 6565 1.364171 GTCAGTGGTCACAGACGCT 59.636 57.895 10.11 0.00 37.92 5.07
4138 6566 1.664965 GGTCAGTGGTCACAGACGC 60.665 63.158 16.54 8.91 45.27 5.19
4139 6567 0.319040 CTGGTCAGTGGTCACAGACG 60.319 60.000 16.54 4.58 45.27 4.18
4140 6568 0.034059 CCTGGTCAGTGGTCACAGAC 59.966 60.000 15.34 15.34 44.11 3.51
4141 6569 0.398522 ACCTGGTCAGTGGTCACAGA 60.399 55.000 0.00 0.00 29.18 3.41
4142 6570 0.469917 AACCTGGTCAGTGGTCACAG 59.530 55.000 0.00 0.00 35.17 3.66
4143 6571 0.180171 CAACCTGGTCAGTGGTCACA 59.820 55.000 0.00 0.00 35.17 3.58
4144 6572 1.166531 GCAACCTGGTCAGTGGTCAC 61.167 60.000 0.00 0.00 35.17 3.67
4145 6573 1.148273 GCAACCTGGTCAGTGGTCA 59.852 57.895 0.00 0.00 35.17 4.02
4146 6574 4.065110 GCAACCTGGTCAGTGGTC 57.935 61.111 0.00 0.00 35.17 4.02


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

AutoCloner maintained by Alex Coulton.