Multiple sequence alignment - TraesCS6A01G282900

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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 TraesCS6A01G282900 chr6A 100.000 4451 0 0 1 4451 514038310 514042760 0.000000e+00 8220.0
1 TraesCS6A01G282900 chr6D 96.184 2385 84 2 1118 3497 372173996 372176378 0.000000e+00 3893.0
2 TraesCS6A01G282900 chr6D 95.815 908 24 6 3552 4451 372176376 372177277 0.000000e+00 1454.0
3 TraesCS6A01G282900 chr6D 89.675 707 46 13 3339 4039 372181127 372181812 0.000000e+00 876.0
4 TraesCS6A01G282900 chr6D 92.293 519 29 3 175 692 372172693 372173201 0.000000e+00 726.0
5 TraesCS6A01G282900 chr6D 90.380 447 27 7 694 1126 372173463 372173907 1.390000e-159 573.0
6 TraesCS6A01G282900 chr6D 84.108 409 43 13 4055 4451 372181977 372182375 4.200000e-100 375.0
7 TraesCS6A01G282900 chr6D 93.678 174 11 0 1 174 372172490 372172663 1.230000e-65 261.0
8 TraesCS6A01G282900 chr1D 86.792 53 6 1 3133 3185 433214044 433213993 1.730000e-04 58.4
9 TraesCS6A01G282900 chr1B 86.792 53 6 1 3133 3185 585074087 585074036 1.730000e-04 58.4
10 TraesCS6A01G282900 chr1A 86.792 53 6 1 3133 3185 531608811 531608760 1.730000e-04 58.4


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 TraesCS6A01G282900 chr6A 514038310 514042760 4450 False 8220.000000 8220 100.000000 1 4451 1 chr6A.!!$F1 4450
1 TraesCS6A01G282900 chr6D 372172490 372182375 9885 False 1165.428571 3893 91.733286 1 4451 7 chr6D.!!$F1 4450

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
191 221 0.179032 TGGTGTCGCCTCAAATGTGT 60.179 50.0 3.62 0.0 38.35 3.72 F
1300 1701 0.321564 CAATTCGGCTGACAGGACCA 60.322 55.0 4.26 0.0 0.00 4.02 F
2856 3257 0.314935 CGCTGGCCATGTTCTTGTTT 59.685 50.0 5.51 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 2576 0.241749 ACTCAAATGCCACACATGCG 59.758 50.0 0.00 0.0 39.60 4.73 R
3150 3551 0.179468 GCACCACCCCGAAGCTATAA 59.821 55.0 0.00 0.0 0.00 0.98 R
3693 4099 0.266152 ATCCAGAGTACAGGAGGGGG 59.734 60.0 7.61 0.0 35.26 5.40 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
83 84 6.438425 AGTTTTCTCATCAATGCTTAACCCAT 59.562 34.615 0.00 0.00 0.00 4.00
97 98 6.435904 TGCTTAACCCATAGCAACATTTTAGT 59.564 34.615 0.00 0.00 43.88 2.24
98 99 7.612244 TGCTTAACCCATAGCAACATTTTAGTA 59.388 33.333 0.00 0.00 43.88 1.82
99 100 8.463607 GCTTAACCCATAGCAACATTTTAGTAA 58.536 33.333 0.00 0.00 37.35 2.24
135 136 7.515957 GAGCATCCAATTATTTCAAACTGTG 57.484 36.000 0.00 0.00 0.00 3.66
142 143 6.146021 CCAATTATTTCAAACTGTGACAAGGC 59.854 38.462 0.00 0.00 35.39 4.35
174 175 0.604578 CAACCAACTGCATTCCCTGG 59.395 55.000 0.00 0.00 0.00 4.45
175 176 0.188342 AACCAACTGCATTCCCTGGT 59.812 50.000 0.00 0.00 42.21 4.00
176 177 0.540365 ACCAACTGCATTCCCTGGTG 60.540 55.000 0.00 0.00 38.95 4.17
177 178 0.540365 CCAACTGCATTCCCTGGTGT 60.540 55.000 0.00 0.00 0.00 4.16
178 179 0.883833 CAACTGCATTCCCTGGTGTC 59.116 55.000 0.00 0.00 0.00 3.67
184 214 1.918293 ATTCCCTGGTGTCGCCTCA 60.918 57.895 3.62 0.00 38.35 3.86
191 221 0.179032 TGGTGTCGCCTCAAATGTGT 60.179 50.000 3.62 0.00 38.35 3.72
198 228 2.091541 CGCCTCAAATGTGTAACCCAT 58.908 47.619 0.00 0.00 34.36 4.00
199 229 2.491693 CGCCTCAAATGTGTAACCCATT 59.508 45.455 0.00 0.00 34.36 3.16
221 251 5.304686 TGATTTGAACCTACACCAAGAGT 57.695 39.130 0.00 0.00 0.00 3.24
236 266 4.939439 ACCAAGAGTAACAAACGTTTGAGT 59.061 37.500 39.63 28.99 40.55 3.41
238 268 5.499047 CAAGAGTAACAAACGTTTGAGTCC 58.501 41.667 39.63 24.91 40.55 3.85
240 270 4.809426 AGAGTAACAAACGTTTGAGTCCAG 59.191 41.667 39.63 17.59 40.55 3.86
254 284 1.062044 AGTCCAGGATAGGGGGAGTTC 60.062 57.143 0.00 0.00 30.15 3.01
352 383 3.388024 TCATACTACCATGGCAAGAGGTC 59.612 47.826 19.03 0.00 36.87 3.85
369 400 2.360350 CGCCACCAACCTCAGCAT 60.360 61.111 0.00 0.00 0.00 3.79
372 403 1.310933 GCCACCAACCTCAGCATCAG 61.311 60.000 0.00 0.00 0.00 2.90
373 404 1.310933 CCACCAACCTCAGCATCAGC 61.311 60.000 0.00 0.00 42.56 4.26
393 424 9.010029 CATCAGCGGGGTATATAAAACTTTTAT 57.990 33.333 10.84 10.84 0.00 1.40
396 427 8.287503 CAGCGGGGTATATAAAACTTTTATCAC 58.712 37.037 9.60 9.18 0.00 3.06
398 429 8.843262 GCGGGGTATATAAAACTTTTATCACTT 58.157 33.333 9.60 0.00 0.00 3.16
444 475 4.158579 GCCATCTTCCCCTAAACTTCTTTG 59.841 45.833 0.00 0.00 0.00 2.77
559 590 8.655935 ATGGATGGAAGAAACTAAAACAGATT 57.344 30.769 0.00 0.00 0.00 2.40
632 663 7.754851 ATTACCGTTCCCCATATAAAATCAC 57.245 36.000 0.00 0.00 0.00 3.06
670 701 2.530460 ATCAGCCAACCATGCCTTTA 57.470 45.000 0.00 0.00 0.00 1.85
677 708 3.565902 GCCAACCATGCCTTTAGATCTAC 59.434 47.826 0.67 0.00 0.00 2.59
721 1012 9.720769 TTTAAGTAGAACCAAGATAAAGACCTG 57.279 33.333 0.00 0.00 0.00 4.00
724 1015 5.167303 AGAACCAAGATAAAGACCTGACC 57.833 43.478 0.00 0.00 0.00 4.02
725 1016 4.597507 AGAACCAAGATAAAGACCTGACCA 59.402 41.667 0.00 0.00 0.00 4.02
738 1029 4.223923 AGACCTGACCATCCTGAACTTAAG 59.776 45.833 0.00 0.00 0.00 1.85
744 1035 5.167303 ACCATCCTGAACTTAAGAAGTCC 57.833 43.478 10.09 0.00 41.91 3.85
778 1069 1.811266 CTGCCGGATTGGTCGAGTG 60.811 63.158 5.05 0.00 41.21 3.51
815 1106 9.498176 CTATGATGGAGATGTGTGAAATCAATA 57.502 33.333 0.00 0.00 0.00 1.90
817 1108 7.988737 TGATGGAGATGTGTGAAATCAATAAC 58.011 34.615 0.00 0.00 0.00 1.89
835 1133 3.161557 ACAGAGGTTGTGGAGGGC 58.838 61.111 0.00 0.00 38.99 5.19
843 1141 2.582636 AGGTTGTGGAGGGCAGAAATAT 59.417 45.455 0.00 0.00 0.00 1.28
845 1143 4.229582 AGGTTGTGGAGGGCAGAAATATTA 59.770 41.667 0.00 0.00 0.00 0.98
874 1173 5.490139 ACAATCGTCCAAATGATCATGTC 57.510 39.130 9.46 0.00 30.55 3.06
879 1178 3.426025 CGTCCAAATGATCATGTCGCAAA 60.426 43.478 9.46 0.00 0.00 3.68
890 1189 0.533085 TGTCGCAAATCGGTCCAACA 60.533 50.000 0.00 0.00 39.05 3.33
899 1198 3.821421 ATCGGTCCAACAGATTAGGTC 57.179 47.619 0.00 0.00 28.66 3.85
907 1206 7.227156 GGTCCAACAGATTAGGTCATGATTAT 58.773 38.462 0.00 0.00 0.00 1.28
974 1273 7.928908 TTAACACTTTGAATGCAACTTGATC 57.071 32.000 0.00 0.00 32.79 2.92
1032 1331 8.030692 GTGATTTATCTCCTCTCTCATCATCAG 58.969 40.741 0.00 0.00 0.00 2.90
1090 1395 5.775686 CAGCTTCATTTTGGATCTTGAACA 58.224 37.500 0.00 0.00 0.00 3.18
1093 1398 6.209986 AGCTTCATTTTGGATCTTGAACATCA 59.790 34.615 0.00 0.00 0.00 3.07
1098 1403 8.030692 TCATTTTGGATCTTGAACATCACATTC 58.969 33.333 0.00 0.00 0.00 2.67
1105 1410 6.957920 TCTTGAACATCACATTCCTTTTGA 57.042 33.333 0.00 0.00 0.00 2.69
1114 1419 6.131972 TCACATTCCTTTTGATCTCTTCCT 57.868 37.500 0.00 0.00 0.00 3.36
1136 1537 3.595190 TGTAGCTCCCACTATAGCAGA 57.405 47.619 0.00 0.00 41.32 4.26
1148 1549 1.026718 ATAGCAGAAGTTGGCCGTGC 61.027 55.000 0.00 0.00 0.00 5.34
1195 1596 2.825836 CCGTGAAGCATGCCTCCC 60.826 66.667 15.66 0.46 0.00 4.30
1215 1616 2.544694 CCATGTCATAGAGTCGCCTGAC 60.545 54.545 12.90 12.90 45.86 3.51
1227 1628 2.266055 CCTGACGGCACCTTCTCC 59.734 66.667 0.00 0.00 0.00 3.71
1284 1685 2.355108 CCTGTCGATCTGGTTCACCAAT 60.355 50.000 0.00 0.00 46.97 3.16
1300 1701 0.321564 CAATTCGGCTGACAGGACCA 60.322 55.000 4.26 0.00 0.00 4.02
1365 1766 1.490490 TCCAAGGTCAAGCTGAACACT 59.510 47.619 0.00 0.00 36.30 3.55
1521 1922 0.537143 TGTGGCAAAGCTTCGACCAT 60.537 50.000 15.65 0.00 31.99 3.55
1570 1971 2.186826 GTGACGGCCACTGCAAAGT 61.187 57.895 2.24 0.00 42.44 2.66
1593 1994 7.628234 AGTTGGTATCAAAAGATCTCTCACAT 58.372 34.615 0.00 0.00 34.28 3.21
1596 1997 5.994668 GGTATCAAAAGATCTCTCACATCCC 59.005 44.000 0.00 0.00 0.00 3.85
1615 2016 8.204160 CACATCCCTCAAGTTACTATACATTGA 58.796 37.037 0.00 0.00 0.00 2.57
1624 2025 7.966157 AGTTACTATACATTGAGTTTCGACG 57.034 36.000 0.00 0.00 0.00 5.12
1647 2048 1.840181 GATATGTCTTGTCGCTCGCA 58.160 50.000 0.00 0.00 0.00 5.10
1693 2094 1.078989 ACTACTGGCCTAACCCTGACT 59.921 52.381 3.32 0.00 37.83 3.41
1782 2183 4.085357 TCAGTTTGTGGCTACTGACAAT 57.915 40.909 0.64 0.00 44.20 2.71
1839 2240 4.017808 TCAAGAGGAGGCTAACACTAGAC 58.982 47.826 0.00 0.00 32.65 2.59
1842 2243 4.784177 AGAGGAGGCTAACACTAGACTAC 58.216 47.826 0.00 0.00 44.17 2.73
1879 2280 4.592179 GCTTTACAGCCTCGATGAATTTC 58.408 43.478 0.00 0.00 40.61 2.17
1893 2294 3.531538 TGAATTTCATCGGAGCTGGTAC 58.468 45.455 0.00 0.00 0.00 3.34
1995 2396 1.910772 ACGCTGCTCTTGTCCTCCT 60.911 57.895 0.00 0.00 0.00 3.69
2019 2420 3.369892 GCTATGTGGTCAGTGATCCAAGT 60.370 47.826 13.80 9.36 35.38 3.16
2133 2534 3.108881 CGATCTGAACTACACCATGTCG 58.891 50.000 0.00 0.00 0.00 4.35
2175 2576 0.610232 AGATGTGCTTGGGGAGTTGC 60.610 55.000 0.00 0.00 0.00 4.17
2190 2591 0.945265 GTTGCGCATGTGTGGCATTT 60.945 50.000 12.75 0.00 35.19 2.32
2202 2603 4.400884 TGTGTGGCATTTGAGTACAAAACT 59.599 37.500 0.00 0.00 46.77 2.66
2205 2606 6.312672 GTGTGGCATTTGAGTACAAAACTTTT 59.687 34.615 0.00 0.00 46.77 2.27
2329 2730 1.132588 GCACACGTCTGACTCTGTTC 58.867 55.000 6.21 0.00 0.00 3.18
2331 2732 2.799917 GCACACGTCTGACTCTGTTCTT 60.800 50.000 6.21 0.00 0.00 2.52
2340 2741 3.603532 TGACTCTGTTCTTCATCATGGC 58.396 45.455 0.00 0.00 0.00 4.40
2355 2756 2.756691 GGCCATGCCTGTGATGCA 60.757 61.111 0.00 0.00 46.69 3.96
2376 2777 1.134521 TCAAACAAGCAGACCGTGAGT 60.135 47.619 0.00 0.00 0.00 3.41
2406 2807 1.374947 CACCAATGACGGACAGGGT 59.625 57.895 1.84 1.84 39.58 4.34
2407 2808 0.955428 CACCAATGACGGACAGGGTG 60.955 60.000 15.45 15.45 44.92 4.61
2441 2842 2.159085 ACTACTATTGGTTCCTCGCTGC 60.159 50.000 0.00 0.00 0.00 5.25
2499 2900 3.213506 CTGGTGGTTCATGTCAAGACAA 58.786 45.455 7.02 0.00 45.41 3.18
2574 2975 4.952262 GGACCATTTCCGTAGTTTTACC 57.048 45.455 0.00 0.00 33.46 2.85
2781 3182 2.273449 CTGGTGAGGGTGATGGGC 59.727 66.667 0.00 0.00 0.00 5.36
2787 3188 0.980754 TGAGGGTGATGGGCGTATGT 60.981 55.000 0.00 0.00 0.00 2.29
2798 3199 2.078226 GCGTATGTTCAGAGCGCAA 58.922 52.632 11.47 0.00 46.23 4.85
2805 3206 1.014044 GTTCAGAGCGCAATCACCGA 61.014 55.000 11.47 0.00 0.00 4.69
2856 3257 0.314935 CGCTGGCCATGTTCTTGTTT 59.685 50.000 5.51 0.00 0.00 2.83
2859 3260 1.688197 CTGGCCATGTTCTTGTTTGGT 59.312 47.619 5.51 0.00 0.00 3.67
2894 3295 1.093972 CAATGGCATCAGCGGTACAA 58.906 50.000 0.00 0.00 43.41 2.41
2967 3368 3.144506 GGATTGGATCATTCACTGCGAT 58.855 45.455 0.00 0.00 0.00 4.58
3057 3458 3.400928 CTGCAGAGAGGCCAGGCT 61.401 66.667 8.42 1.67 0.00 4.58
3090 3491 0.834612 TGTCCAAGGTTCGTGGAACT 59.165 50.000 8.25 0.00 46.66 3.01
3150 3551 5.304357 CCCCTTAACTGAAAAAGTGGATGTT 59.696 40.000 0.00 0.00 39.81 2.71
3158 3559 8.409358 ACTGAAAAAGTGGATGTTTATAGCTT 57.591 30.769 0.00 0.00 37.88 3.74
3213 3614 1.864725 GAGTATCCGAGCGGGCTACC 61.865 65.000 9.29 3.22 34.94 3.18
3255 3656 1.372307 TGCACTGCAGCAGCTAGAA 59.628 52.632 26.04 4.42 40.11 2.10
3264 3665 2.686915 GCAGCAGCTAGAATGGACAATT 59.313 45.455 0.00 0.00 37.91 2.32
3265 3666 3.488721 GCAGCAGCTAGAATGGACAATTG 60.489 47.826 3.24 3.24 37.91 2.32
3300 3701 1.478510 AGTGACGACCTGACATGGATC 59.521 52.381 0.00 0.00 0.00 3.36
3376 3777 1.976132 GATGCTGGAGGTGGCTGCTA 61.976 60.000 0.00 0.00 0.00 3.49
3393 3794 2.093288 TGCTATGTGCTTGGAGAAGGAG 60.093 50.000 0.00 0.00 43.37 3.69
3454 3855 7.723172 AGAAGTTCCTCTCATTTGACTGAATTT 59.277 33.333 0.00 0.00 0.00 1.82
3458 3859 5.474532 TCCTCTCATTTGACTGAATTTGGTG 59.525 40.000 0.00 0.00 0.00 4.17
3474 3880 1.748493 TGGTGACTTGTGTTGCCTTTC 59.252 47.619 0.00 0.00 0.00 2.62
3480 3886 4.142403 TGACTTGTGTTGCCTTTCTTCTTG 60.142 41.667 0.00 0.00 0.00 3.02
3481 3887 3.131046 ACTTGTGTTGCCTTTCTTCTTGG 59.869 43.478 0.00 0.00 0.00 3.61
3482 3888 2.733956 TGTGTTGCCTTTCTTCTTGGT 58.266 42.857 0.00 0.00 0.00 3.67
3494 3900 4.431416 TCTTCTTGGTTTACCTTGCTGA 57.569 40.909 0.00 0.00 36.82 4.26
3495 3901 4.787551 TCTTCTTGGTTTACCTTGCTGAA 58.212 39.130 0.00 0.00 36.82 3.02
3496 3902 5.385198 TCTTCTTGGTTTACCTTGCTGAAT 58.615 37.500 0.00 0.00 36.82 2.57
3497 3903 5.833131 TCTTCTTGGTTTACCTTGCTGAATT 59.167 36.000 0.00 0.00 36.82 2.17
3498 3904 5.705609 TCTTGGTTTACCTTGCTGAATTC 57.294 39.130 0.00 0.00 36.82 2.17
3499 3905 5.385198 TCTTGGTTTACCTTGCTGAATTCT 58.615 37.500 7.05 0.00 36.82 2.40
3500 3906 5.473504 TCTTGGTTTACCTTGCTGAATTCTC 59.526 40.000 7.05 0.00 36.82 2.87
3501 3907 4.079253 TGGTTTACCTTGCTGAATTCTCC 58.921 43.478 7.05 0.00 36.82 3.71
3502 3908 4.202567 TGGTTTACCTTGCTGAATTCTCCT 60.203 41.667 7.05 0.00 36.82 3.69
3503 3909 4.767409 GGTTTACCTTGCTGAATTCTCCTT 59.233 41.667 7.05 0.00 0.00 3.36
3504 3910 5.243954 GGTTTACCTTGCTGAATTCTCCTTT 59.756 40.000 7.05 0.00 0.00 3.11
3505 3911 6.382608 GTTTACCTTGCTGAATTCTCCTTTC 58.617 40.000 7.05 0.00 0.00 2.62
3506 3912 3.425659 ACCTTGCTGAATTCTCCTTTCC 58.574 45.455 7.05 0.00 0.00 3.13
3507 3913 3.075134 ACCTTGCTGAATTCTCCTTTCCT 59.925 43.478 7.05 0.00 0.00 3.36
3508 3914 4.289672 ACCTTGCTGAATTCTCCTTTCCTA 59.710 41.667 7.05 0.00 0.00 2.94
3509 3915 5.044550 ACCTTGCTGAATTCTCCTTTCCTAT 60.045 40.000 7.05 0.00 0.00 2.57
3510 3916 5.890419 CCTTGCTGAATTCTCCTTTCCTATT 59.110 40.000 7.05 0.00 0.00 1.73
3511 3917 6.183360 CCTTGCTGAATTCTCCTTTCCTATTG 60.183 42.308 7.05 0.00 0.00 1.90
3512 3918 5.819991 TGCTGAATTCTCCTTTCCTATTGT 58.180 37.500 7.05 0.00 0.00 2.71
3513 3919 5.649395 TGCTGAATTCTCCTTTCCTATTGTG 59.351 40.000 7.05 0.00 0.00 3.33
3514 3920 5.649831 GCTGAATTCTCCTTTCCTATTGTGT 59.350 40.000 7.05 0.00 0.00 3.72
3515 3921 6.404074 GCTGAATTCTCCTTTCCTATTGTGTG 60.404 42.308 7.05 0.00 0.00 3.82
3516 3922 5.945784 TGAATTCTCCTTTCCTATTGTGTGG 59.054 40.000 7.05 0.00 0.00 4.17
3517 3923 4.993705 TTCTCCTTTCCTATTGTGTGGT 57.006 40.909 0.00 0.00 0.00 4.16
3518 3924 4.993705 TCTCCTTTCCTATTGTGTGGTT 57.006 40.909 0.00 0.00 0.00 3.67
3519 3925 4.651778 TCTCCTTTCCTATTGTGTGGTTG 58.348 43.478 0.00 0.00 0.00 3.77
3520 3926 3.758554 CTCCTTTCCTATTGTGTGGTTGG 59.241 47.826 0.00 0.00 0.00 3.77
3521 3927 2.825532 CCTTTCCTATTGTGTGGTTGGG 59.174 50.000 0.00 0.00 0.00 4.12
3522 3928 3.496331 CTTTCCTATTGTGTGGTTGGGT 58.504 45.455 0.00 0.00 0.00 4.51
3523 3929 4.507691 CCTTTCCTATTGTGTGGTTGGGTA 60.508 45.833 0.00 0.00 0.00 3.69
3524 3930 4.938575 TTCCTATTGTGTGGTTGGGTAT 57.061 40.909 0.00 0.00 0.00 2.73
3525 3931 4.229304 TCCTATTGTGTGGTTGGGTATG 57.771 45.455 0.00 0.00 0.00 2.39
3526 3932 3.589735 TCCTATTGTGTGGTTGGGTATGT 59.410 43.478 0.00 0.00 0.00 2.29
3527 3933 4.043561 TCCTATTGTGTGGTTGGGTATGTT 59.956 41.667 0.00 0.00 0.00 2.71
3528 3934 4.770010 CCTATTGTGTGGTTGGGTATGTTT 59.230 41.667 0.00 0.00 0.00 2.83
3529 3935 4.864704 ATTGTGTGGTTGGGTATGTTTC 57.135 40.909 0.00 0.00 0.00 2.78
3530 3936 3.298686 TGTGTGGTTGGGTATGTTTCA 57.701 42.857 0.00 0.00 0.00 2.69
3531 3937 2.952978 TGTGTGGTTGGGTATGTTTCAC 59.047 45.455 0.00 0.00 0.00 3.18
3532 3938 3.219281 GTGTGGTTGGGTATGTTTCACT 58.781 45.455 0.00 0.00 0.00 3.41
3533 3939 3.634910 GTGTGGTTGGGTATGTTTCACTT 59.365 43.478 0.00 0.00 0.00 3.16
3534 3940 3.886505 TGTGGTTGGGTATGTTTCACTTC 59.113 43.478 0.00 0.00 0.00 3.01
3535 3941 3.886505 GTGGTTGGGTATGTTTCACTTCA 59.113 43.478 0.00 0.00 0.00 3.02
3536 3942 4.522789 GTGGTTGGGTATGTTTCACTTCAT 59.477 41.667 0.00 0.00 0.00 2.57
3537 3943 5.010617 GTGGTTGGGTATGTTTCACTTCATT 59.989 40.000 0.00 0.00 0.00 2.57
3538 3944 5.010516 TGGTTGGGTATGTTTCACTTCATTG 59.989 40.000 0.00 0.00 0.00 2.82
3539 3945 5.010617 GGTTGGGTATGTTTCACTTCATTGT 59.989 40.000 0.00 0.00 0.00 2.71
3540 3946 6.462347 GGTTGGGTATGTTTCACTTCATTGTT 60.462 38.462 0.00 0.00 0.00 2.83
3541 3947 6.083098 TGGGTATGTTTCACTTCATTGTTG 57.917 37.500 0.00 0.00 0.00 3.33
3542 3948 5.596361 TGGGTATGTTTCACTTCATTGTTGT 59.404 36.000 0.00 0.00 0.00 3.32
3543 3949 5.920273 GGGTATGTTTCACTTCATTGTTGTG 59.080 40.000 5.77 5.77 0.00 3.33
3544 3950 5.920273 GGTATGTTTCACTTCATTGTTGTGG 59.080 40.000 10.23 0.00 33.04 4.17
3545 3951 5.850557 ATGTTTCACTTCATTGTTGTGGA 57.149 34.783 10.23 1.90 33.04 4.02
3546 3952 5.651387 TGTTTCACTTCATTGTTGTGGAA 57.349 34.783 10.23 6.66 33.04 3.53
3547 3953 6.030548 TGTTTCACTTCATTGTTGTGGAAA 57.969 33.333 6.94 0.00 31.88 3.13
3548 3954 5.866633 TGTTTCACTTCATTGTTGTGGAAAC 59.133 36.000 0.00 0.00 31.88 2.78
3549 3955 5.651387 TTCACTTCATTGTTGTGGAAACA 57.349 34.783 10.23 0.00 38.70 2.83
3550 3956 5.850557 TCACTTCATTGTTGTGGAAACAT 57.149 34.783 10.23 0.00 46.14 2.71
3554 3960 8.420222 TCACTTCATTGTTGTGGAAACATAATT 58.580 29.630 10.23 0.00 43.63 1.40
3561 3967 9.643693 ATTGTTGTGGAAACATAATTTCATCTC 57.356 29.630 2.14 0.00 43.63 2.75
3577 3983 5.692115 TCATCTCTGTATGTGCCCTTAAA 57.308 39.130 0.00 0.00 0.00 1.52
3578 3984 6.061022 TCATCTCTGTATGTGCCCTTAAAA 57.939 37.500 0.00 0.00 0.00 1.52
3579 3985 5.880332 TCATCTCTGTATGTGCCCTTAAAAC 59.120 40.000 0.00 0.00 0.00 2.43
3601 4007 5.482908 ACATCTCTTTGGTGTAGCAACTAG 58.517 41.667 0.00 0.00 0.00 2.57
3602 4008 5.012148 ACATCTCTTTGGTGTAGCAACTAGT 59.988 40.000 0.00 0.00 0.00 2.57
3603 4009 6.210784 ACATCTCTTTGGTGTAGCAACTAGTA 59.789 38.462 0.00 0.00 0.00 1.82
3640 4046 0.107361 ATATGTGCTGCTGCTGCTGA 60.107 50.000 27.67 16.57 40.01 4.26
3651 4057 3.556775 TGCTGCTGCTGAAAATTTTGTTC 59.443 39.130 17.00 0.00 40.48 3.18
3656 4062 4.025480 GCTGCTGAAAATTTTGTTCTGTGG 60.025 41.667 8.47 0.00 0.00 4.17
3658 4064 4.081198 TGCTGAAAATTTTGTTCTGTGGGT 60.081 37.500 8.47 0.00 0.00 4.51
3663 4069 3.884037 ATTTTGTTCTGTGGGTCTCCT 57.116 42.857 0.00 0.00 0.00 3.69
3709 4121 0.909610 TTGCCCCCTCCTGTACTCTG 60.910 60.000 0.00 0.00 0.00 3.35
3715 4127 2.359781 CCCCTCCTGTACTCTGGATCTT 60.360 54.545 0.00 0.00 40.11 2.40
3741 4153 3.780294 TGTGTGGTCTGCCTATTATCCTT 59.220 43.478 0.00 0.00 35.27 3.36
3746 4158 6.998074 TGTGGTCTGCCTATTATCCTTAAATG 59.002 38.462 0.00 0.00 35.27 2.32
3750 4162 7.604545 GGTCTGCCTATTATCCTTAAATGTCTC 59.395 40.741 0.00 0.00 0.00 3.36
3769 4181 3.188460 TCTCGCTTTGCATTGAAACCTAC 59.812 43.478 0.00 0.00 0.00 3.18
3783 4195 8.971321 CATTGAAACCTACAGTTCAATTTCTTG 58.029 33.333 8.51 0.00 37.88 3.02
3784 4196 7.639113 TGAAACCTACAGTTCAATTTCTTGT 57.361 32.000 0.00 0.00 37.88 3.16
3832 4244 2.550423 CCATGAGATAGCTTGCCTGAGG 60.550 54.545 0.00 0.00 0.00 3.86
4020 4432 7.704899 AGTGCAGAAAAACACAAATAAACCTAC 59.295 33.333 0.00 0.00 39.30 3.18
4085 4497 8.958119 ACATTACGACATCATACTGGTTAATT 57.042 30.769 0.00 0.00 0.00 1.40
4301 4715 4.157656 TGGTTTATGGTTATGCTTGCTCAC 59.842 41.667 0.00 0.00 0.00 3.51
4369 4783 8.134895 TCATGCTAAAGACACCTTTTGTTTAAG 58.865 33.333 0.00 0.00 42.26 1.85
4370 4784 6.270064 TGCTAAAGACACCTTTTGTTTAAGC 58.730 36.000 0.00 0.00 42.26 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.301835 AGCATTGCTCCTCTGTATATTGT 57.698 39.130 5.03 0.00 30.62 2.71
40 41 0.179134 CTCCACCGAAGACGATGTCC 60.179 60.000 0.00 0.00 42.66 4.02
83 84 7.233389 TGGGCAAATTACTAAAATGTTGCTA 57.767 32.000 6.19 0.00 40.83 3.49
97 98 3.139957 TGGATGCTCCTATGGGCAAATTA 59.860 43.478 0.00 0.00 41.90 1.40
98 99 2.091166 TGGATGCTCCTATGGGCAAATT 60.091 45.455 0.00 0.00 41.90 1.82
99 100 1.500303 TGGATGCTCCTATGGGCAAAT 59.500 47.619 0.00 0.00 41.90 2.32
135 136 1.085091 CAGAGATGCACTGCCTTGTC 58.915 55.000 0.00 0.00 0.00 3.18
142 143 1.068748 GTTGGTTGCAGAGATGCACTG 60.069 52.381 1.74 0.00 45.32 3.66
162 163 2.401766 GCGACACCAGGGAATGCAG 61.402 63.158 0.00 0.00 0.00 4.41
163 164 2.359850 GCGACACCAGGGAATGCA 60.360 61.111 0.00 0.00 0.00 3.96
174 175 2.095919 GGTTACACATTTGAGGCGACAC 60.096 50.000 0.00 0.00 0.00 3.67
175 176 2.147958 GGTTACACATTTGAGGCGACA 58.852 47.619 0.00 0.00 0.00 4.35
176 177 1.467342 GGGTTACACATTTGAGGCGAC 59.533 52.381 0.00 0.00 0.00 5.19
177 178 1.072489 TGGGTTACACATTTGAGGCGA 59.928 47.619 0.00 0.00 0.00 5.54
178 179 1.529226 TGGGTTACACATTTGAGGCG 58.471 50.000 0.00 0.00 0.00 5.52
184 214 6.934083 GGTTCAAATCAATGGGTTACACATTT 59.066 34.615 10.45 0.00 36.47 2.32
191 221 5.712917 GGTGTAGGTTCAAATCAATGGGTTA 59.287 40.000 0.00 0.00 0.00 2.85
198 228 5.690865 ACTCTTGGTGTAGGTTCAAATCAA 58.309 37.500 0.00 0.00 0.00 2.57
199 229 5.304686 ACTCTTGGTGTAGGTTCAAATCA 57.695 39.130 0.00 0.00 0.00 2.57
221 251 4.139859 TCCTGGACTCAAACGTTTGTTA 57.860 40.909 33.42 18.91 37.31 2.41
236 266 0.105658 CGAACTCCCCCTATCCTGGA 60.106 60.000 0.00 0.00 0.00 3.86
238 268 1.041437 GTCGAACTCCCCCTATCCTG 58.959 60.000 0.00 0.00 0.00 3.86
240 270 1.492764 TTGTCGAACTCCCCCTATCC 58.507 55.000 0.00 0.00 0.00 2.59
319 350 6.611642 GCCATGGTAGTATGATATTCCCTCTA 59.388 42.308 14.67 0.00 0.00 2.43
352 383 2.360350 ATGCTGAGGTTGGTGGCG 60.360 61.111 0.00 0.00 0.00 5.69
369 400 8.212312 TGATAAAAGTTTTATATACCCCGCTGA 58.788 33.333 18.59 0.00 0.00 4.26
372 403 8.387190 AGTGATAAAAGTTTTATATACCCCGC 57.613 34.615 18.59 12.30 0.00 6.13
393 424 7.765819 CACCTGTATGTTCATTGATAGAAGTGA 59.234 37.037 0.00 0.00 0.00 3.41
396 427 7.042187 GCTCACCTGTATGTTCATTGATAGAAG 60.042 40.741 0.00 0.00 0.00 2.85
398 429 6.283694 GCTCACCTGTATGTTCATTGATAGA 58.716 40.000 0.00 0.00 0.00 1.98
399 430 5.468072 GGCTCACCTGTATGTTCATTGATAG 59.532 44.000 0.00 0.00 0.00 2.08
400 431 5.104569 TGGCTCACCTGTATGTTCATTGATA 60.105 40.000 0.00 0.00 36.63 2.15
401 432 4.202441 GGCTCACCTGTATGTTCATTGAT 58.798 43.478 0.00 0.00 0.00 2.57
402 433 3.008923 TGGCTCACCTGTATGTTCATTGA 59.991 43.478 0.00 0.00 36.63 2.57
403 434 3.346315 TGGCTCACCTGTATGTTCATTG 58.654 45.455 0.00 0.00 36.63 2.82
404 435 3.719268 TGGCTCACCTGTATGTTCATT 57.281 42.857 0.00 0.00 36.63 2.57
405 436 3.457380 AGATGGCTCACCTGTATGTTCAT 59.543 43.478 0.00 0.00 36.63 2.57
406 437 2.840038 AGATGGCTCACCTGTATGTTCA 59.160 45.455 0.00 0.00 36.63 3.18
407 438 3.550437 AGATGGCTCACCTGTATGTTC 57.450 47.619 0.00 0.00 36.63 3.18
408 439 3.370953 GGAAGATGGCTCACCTGTATGTT 60.371 47.826 0.00 0.00 36.63 2.71
409 440 2.171448 GGAAGATGGCTCACCTGTATGT 59.829 50.000 0.00 0.00 36.63 2.29
410 441 2.486191 GGGAAGATGGCTCACCTGTATG 60.486 54.545 0.00 0.00 36.63 2.39
411 442 1.771255 GGGAAGATGGCTCACCTGTAT 59.229 52.381 0.00 0.00 36.63 2.29
559 590 2.162319 TGCGCTATCAACAAGTCACA 57.838 45.000 9.73 0.00 0.00 3.58
597 628 3.194116 GGGAACGGTAATATATGGAGCGA 59.806 47.826 20.27 0.00 37.51 4.93
612 643 4.024387 CACGTGATTTTATATGGGGAACGG 60.024 45.833 10.90 0.00 33.09 4.44
632 663 6.018994 GGCTGATAGTATTGGAAAAGTACACG 60.019 42.308 0.00 0.00 0.00 4.49
713 1004 2.982488 AGTTCAGGATGGTCAGGTCTTT 59.018 45.455 0.00 0.00 36.16 2.52
720 1011 5.280011 GGACTTCTTAAGTTCAGGATGGTCA 60.280 44.000 1.63 0.00 43.03 4.02
721 1012 5.179533 GGACTTCTTAAGTTCAGGATGGTC 58.820 45.833 1.63 0.00 43.03 4.02
724 1015 4.518249 GGGGACTTCTTAAGTTCAGGATG 58.482 47.826 1.63 0.00 43.03 3.51
725 1016 3.197983 CGGGGACTTCTTAAGTTCAGGAT 59.802 47.826 1.63 0.00 43.03 3.24
738 1029 2.545537 CCCTAATAAGCGGGGACTTC 57.454 55.000 0.00 0.00 42.58 3.01
744 1035 1.073199 CAGCCCCCTAATAAGCGGG 59.927 63.158 0.00 0.00 43.00 6.13
786 1077 6.484364 TTTCACACATCTCCATCATAGCTA 57.516 37.500 0.00 0.00 0.00 3.32
787 1078 5.363562 TTTCACACATCTCCATCATAGCT 57.636 39.130 0.00 0.00 0.00 3.32
788 1079 5.761726 TGATTTCACACATCTCCATCATAGC 59.238 40.000 0.00 0.00 0.00 2.97
789 1080 7.797038 TTGATTTCACACATCTCCATCATAG 57.203 36.000 0.00 0.00 0.00 2.23
857 1155 1.665169 TGCGACATGATCATTTGGACG 59.335 47.619 5.16 8.56 0.00 4.79
874 1173 1.086696 ATCTGTTGGACCGATTTGCG 58.913 50.000 0.00 0.00 40.47 4.85
879 1178 3.104512 TGACCTAATCTGTTGGACCGAT 58.895 45.455 0.00 0.00 0.00 4.18
907 1206 9.817809 ATGCGAGTGATTAAGAAGAGTAATTAA 57.182 29.630 0.00 0.00 0.00 1.40
1090 1395 6.729428 AGGAAGAGATCAAAAGGAATGTGAT 58.271 36.000 0.00 0.00 34.71 3.06
1093 1398 6.779539 ACAAAGGAAGAGATCAAAAGGAATGT 59.220 34.615 0.00 0.00 0.00 2.71
1098 1403 5.942826 AGCTACAAAGGAAGAGATCAAAAGG 59.057 40.000 0.00 0.00 0.00 3.11
1105 1410 3.198853 GTGGGAGCTACAAAGGAAGAGAT 59.801 47.826 0.00 0.00 0.00 2.75
1114 1419 4.286707 TCTGCTATAGTGGGAGCTACAAA 58.713 43.478 0.00 0.00 39.54 2.83
1136 1537 1.609841 GGTAGTTAGCACGGCCAACTT 60.610 52.381 10.38 0.00 34.48 2.66
1148 1549 5.091261 AGATCCTTTGTGCAGGTAGTTAG 57.909 43.478 0.00 0.00 35.15 2.34
1195 1596 2.736978 GTCAGGCGACTCTATGACATG 58.263 52.381 3.63 0.00 41.32 3.21
1215 1616 1.675641 CCCAAAGGAGAAGGTGCCG 60.676 63.158 0.00 0.00 33.47 5.69
1254 1655 0.616111 AGATCGACAGGGTGAAGGCT 60.616 55.000 0.00 0.00 0.00 4.58
1284 1685 1.596934 GATGGTCCTGTCAGCCGAA 59.403 57.895 0.00 0.00 0.00 4.30
1339 1740 1.201429 AGCTTGACCTTGGACCCGAT 61.201 55.000 0.00 0.00 0.00 4.18
1365 1766 1.918262 AGGACCATGCTTCTTCCATCA 59.082 47.619 0.00 0.00 0.00 3.07
1473 1874 2.283298 CCACCTTGATCCTTCATCACG 58.717 52.381 0.00 0.00 41.56 4.35
1521 1922 1.002990 TAGCAGAGTGTCGGTCGGA 60.003 57.895 0.00 0.00 0.00 4.55
1570 1971 7.050377 GGATGTGAGAGATCTTTTGATACCAA 58.950 38.462 0.00 0.00 39.67 3.67
1593 1994 7.973048 ACTCAATGTATAGTAACTTGAGGGA 57.027 36.000 13.36 0.00 44.42 4.20
1596 1997 9.569167 TCGAAACTCAATGTATAGTAACTTGAG 57.431 33.333 8.60 8.60 45.21 3.02
1624 2025 2.493713 AGCGACAAGACATATCGGTC 57.506 50.000 0.00 0.00 42.44 4.79
1636 2037 0.249447 CCCTCATATGCGAGCGACAA 60.249 55.000 0.00 0.00 0.00 3.18
1647 2048 1.630878 GAAAGATCCGGCCCCTCATAT 59.369 52.381 0.00 0.00 0.00 1.78
1693 2094 8.941995 ATTCTATAGTTCATCCAGCTACTGTA 57.058 34.615 0.00 0.00 0.00 2.74
1839 2240 4.592485 AAGCCTGAGATTACCATCGTAG 57.408 45.455 0.00 0.00 34.17 3.51
1842 2243 4.693283 TGTAAAGCCTGAGATTACCATCG 58.307 43.478 0.00 0.00 34.17 3.84
1879 2280 1.135083 AGAAACGTACCAGCTCCGATG 60.135 52.381 0.00 0.00 0.00 3.84
1893 2294 1.266989 GAGAAAGCCACCCAAGAAACG 59.733 52.381 0.00 0.00 0.00 3.60
1995 2396 1.486310 GGATCACTGACCACATAGCCA 59.514 52.381 0.00 0.00 0.00 4.75
2175 2576 0.241749 ACTCAAATGCCACACATGCG 59.758 50.000 0.00 0.00 39.60 4.73
2190 2591 5.096849 GCGTTTGGAAAAGTTTTGTACTCA 58.903 37.500 5.36 0.00 35.54 3.41
2202 2603 0.387565 GGAAGCAGGCGTTTGGAAAA 59.612 50.000 0.00 0.00 0.00 2.29
2205 2606 1.302511 GAGGAAGCAGGCGTTTGGA 60.303 57.895 0.00 0.00 0.00 3.53
2316 2717 4.869297 CCATGATGAAGAACAGAGTCAGAC 59.131 45.833 0.00 0.00 0.00 3.51
2346 2747 3.057806 TCTGCTTGTTTGATGCATCACAG 60.058 43.478 28.72 26.82 36.36 3.66
2355 2756 2.146342 CTCACGGTCTGCTTGTTTGAT 58.854 47.619 0.00 0.00 0.00 2.57
2376 2777 3.004171 GTCATTGGTGTGCGTGGTATAA 58.996 45.455 0.00 0.00 0.00 0.98
2385 2786 1.577328 CCTGTCCGTCATTGGTGTGC 61.577 60.000 0.00 0.00 0.00 4.57
2406 2807 4.753516 ATAGTAGTAGTGCCACATTGCA 57.246 40.909 0.00 0.00 39.37 4.08
2407 2808 4.273480 CCAATAGTAGTAGTGCCACATTGC 59.727 45.833 0.00 0.00 0.00 3.56
2441 2842 2.802816 CAGACCTCCACAAGAAAGAACG 59.197 50.000 0.00 0.00 0.00 3.95
2499 2900 0.960861 TCTCTGATCGTGCCGAGTGT 60.961 55.000 3.76 0.00 39.91 3.55
2757 3158 2.335681 TCACCCTCACCAGGTTCATA 57.664 50.000 0.00 0.00 38.30 2.15
2761 3162 1.500783 CCCATCACCCTCACCAGGTT 61.501 60.000 0.00 0.00 38.30 3.50
2781 3182 1.926510 TGATTGCGCTCTGAACATACG 59.073 47.619 9.73 0.00 0.00 3.06
2787 3188 1.014044 GTCGGTGATTGCGCTCTGAA 61.014 55.000 9.73 0.00 0.00 3.02
2805 3206 2.724454 ACATACTCGTAGACCAGCAGT 58.276 47.619 0.00 0.00 0.00 4.40
2838 3239 1.606224 CCAAACAAGAACATGGCCAGC 60.606 52.381 13.05 0.00 0.00 4.85
2844 3245 4.805192 CCTTTGTCACCAAACAAGAACATG 59.195 41.667 0.00 0.00 40.08 3.21
2856 3257 1.152777 CAGTGGCCCTTTGTCACCA 60.153 57.895 0.00 0.00 32.29 4.17
2859 3260 0.469705 ATTGCAGTGGCCCTTTGTCA 60.470 50.000 0.00 0.00 40.13 3.58
2949 3350 2.679336 CACATCGCAGTGAATGATCCAA 59.321 45.455 11.60 0.00 42.05 3.53
2967 3368 4.284490 AGAAGTATGTTCTCAGGCTTCACA 59.716 41.667 0.00 0.00 38.96 3.58
3057 3458 0.689412 TGGACATGCTACCGGGATCA 60.689 55.000 6.32 0.00 0.00 2.92
3066 3467 1.338674 CCACGAACCTTGGACATGCTA 60.339 52.381 0.00 0.00 36.02 3.49
3090 3491 1.217942 TCTGGAGCCATGTAGCCTCTA 59.782 52.381 0.00 0.00 0.00 2.43
3105 3506 2.074967 GGTGGACACCCATTCTGGA 58.925 57.895 10.38 0.00 45.68 3.86
3150 3551 0.179468 GCACCACCCCGAAGCTATAA 59.821 55.000 0.00 0.00 0.00 0.98
3180 3581 1.614413 GATACTCGAGACCCCATGACC 59.386 57.143 21.68 0.00 0.00 4.02
3245 3646 4.226427 TCAATTGTCCATTCTAGCTGCT 57.774 40.909 7.57 7.57 0.00 4.24
3255 3656 6.070951 TCCATCTTCTCTTCAATTGTCCAT 57.929 37.500 5.13 0.00 0.00 3.41
3264 3665 4.280929 TCGTCACTTTCCATCTTCTCTTCA 59.719 41.667 0.00 0.00 0.00 3.02
3265 3666 4.623595 GTCGTCACTTTCCATCTTCTCTTC 59.376 45.833 0.00 0.00 0.00 2.87
3300 3701 2.487934 CTAGGATCCACAAAGCCATCG 58.512 52.381 15.82 0.00 0.00 3.84
3376 3777 2.909006 TCTTCTCCTTCTCCAAGCACAT 59.091 45.455 0.00 0.00 0.00 3.21
3393 3794 1.140804 GCTCGGTCTCTGGCTCTTC 59.859 63.158 0.00 0.00 0.00 2.87
3454 3855 1.748493 GAAAGGCAACACAAGTCACCA 59.252 47.619 0.00 0.00 41.41 4.17
3458 3859 4.354587 CAAGAAGAAAGGCAACACAAGTC 58.645 43.478 0.00 0.00 41.41 3.01
3474 3880 5.712152 ATTCAGCAAGGTAAACCAAGAAG 57.288 39.130 1.26 0.00 38.89 2.85
3480 3886 4.336280 AGGAGAATTCAGCAAGGTAAACC 58.664 43.478 8.44 0.00 0.00 3.27
3481 3887 5.966742 AAGGAGAATTCAGCAAGGTAAAC 57.033 39.130 8.44 0.00 0.00 2.01
3482 3888 5.476945 GGAAAGGAGAATTCAGCAAGGTAAA 59.523 40.000 8.44 0.00 0.00 2.01
3494 3900 5.892348 ACCACACAATAGGAAAGGAGAATT 58.108 37.500 0.00 0.00 0.00 2.17
3495 3901 5.520748 ACCACACAATAGGAAAGGAGAAT 57.479 39.130 0.00 0.00 0.00 2.40
3496 3902 4.993705 ACCACACAATAGGAAAGGAGAA 57.006 40.909 0.00 0.00 0.00 2.87
3497 3903 4.506625 CCAACCACACAATAGGAAAGGAGA 60.507 45.833 0.00 0.00 0.00 3.71
3498 3904 3.758554 CCAACCACACAATAGGAAAGGAG 59.241 47.826 0.00 0.00 0.00 3.69
3499 3905 3.499563 CCCAACCACACAATAGGAAAGGA 60.500 47.826 0.00 0.00 0.00 3.36
3500 3906 2.825532 CCCAACCACACAATAGGAAAGG 59.174 50.000 0.00 0.00 0.00 3.11
3501 3907 3.496331 ACCCAACCACACAATAGGAAAG 58.504 45.455 0.00 0.00 0.00 2.62
3502 3908 3.603965 ACCCAACCACACAATAGGAAA 57.396 42.857 0.00 0.00 0.00 3.13
3503 3909 4.043561 ACATACCCAACCACACAATAGGAA 59.956 41.667 0.00 0.00 0.00 3.36
3504 3910 3.589735 ACATACCCAACCACACAATAGGA 59.410 43.478 0.00 0.00 0.00 2.94
3505 3911 3.963129 ACATACCCAACCACACAATAGG 58.037 45.455 0.00 0.00 0.00 2.57
3506 3912 5.475220 TGAAACATACCCAACCACACAATAG 59.525 40.000 0.00 0.00 0.00 1.73
3507 3913 5.241949 GTGAAACATACCCAACCACACAATA 59.758 40.000 0.00 0.00 36.32 1.90
3508 3914 4.038642 GTGAAACATACCCAACCACACAAT 59.961 41.667 0.00 0.00 36.32 2.71
3509 3915 3.381908 GTGAAACATACCCAACCACACAA 59.618 43.478 0.00 0.00 36.32 3.33
3510 3916 2.952978 GTGAAACATACCCAACCACACA 59.047 45.455 0.00 0.00 36.32 3.72
3511 3917 3.219281 AGTGAAACATACCCAACCACAC 58.781 45.455 0.00 0.00 41.43 3.82
3512 3918 3.586470 AGTGAAACATACCCAACCACA 57.414 42.857 0.00 0.00 41.43 4.17
3513 3919 3.886505 TGAAGTGAAACATACCCAACCAC 59.113 43.478 0.00 0.00 41.43 4.16
3514 3920 4.171878 TGAAGTGAAACATACCCAACCA 57.828 40.909 0.00 0.00 41.43 3.67
3515 3921 5.010617 ACAATGAAGTGAAACATACCCAACC 59.989 40.000 0.00 0.00 41.43 3.77
3516 3922 6.084326 ACAATGAAGTGAAACATACCCAAC 57.916 37.500 0.00 0.00 41.43 3.77
3517 3923 6.097554 ACAACAATGAAGTGAAACATACCCAA 59.902 34.615 0.00 0.00 41.43 4.12
3518 3924 5.596361 ACAACAATGAAGTGAAACATACCCA 59.404 36.000 0.00 0.00 41.43 4.51
3519 3925 5.920273 CACAACAATGAAGTGAAACATACCC 59.080 40.000 4.37 0.00 41.43 3.69
3520 3926 5.920273 CCACAACAATGAAGTGAAACATACC 59.080 40.000 10.34 0.00 41.43 2.73
3521 3927 6.734137 TCCACAACAATGAAGTGAAACATAC 58.266 36.000 10.34 0.00 41.43 2.39
3522 3928 6.951062 TCCACAACAATGAAGTGAAACATA 57.049 33.333 10.34 0.00 41.43 2.29
3523 3929 5.850557 TCCACAACAATGAAGTGAAACAT 57.149 34.783 10.34 0.00 41.43 2.71
3524 3930 5.651387 TTCCACAACAATGAAGTGAAACA 57.349 34.783 10.34 0.00 41.43 2.83
3525 3931 5.866633 TGTTTCCACAACAATGAAGTGAAAC 59.133 36.000 17.95 17.95 35.85 2.78
3526 3932 6.030548 TGTTTCCACAACAATGAAGTGAAA 57.969 33.333 10.34 7.11 35.33 2.69
3527 3933 5.651387 TGTTTCCACAACAATGAAGTGAA 57.349 34.783 10.34 2.69 35.33 3.18
3528 3934 5.850557 ATGTTTCCACAACAATGAAGTGA 57.149 34.783 10.34 0.00 36.16 3.41
3529 3935 8.592105 AATTATGTTTCCACAACAATGAAGTG 57.408 30.769 0.00 0.00 36.16 3.16
3530 3936 9.260002 GAAATTATGTTTCCACAACAATGAAGT 57.740 29.630 0.00 0.00 36.16 3.01
3531 3937 9.258826 TGAAATTATGTTTCCACAACAATGAAG 57.741 29.630 0.00 0.00 36.16 3.02
3532 3938 9.775854 ATGAAATTATGTTTCCACAACAATGAA 57.224 25.926 0.00 0.00 36.16 2.57
3533 3939 9.421806 GATGAAATTATGTTTCCACAACAATGA 57.578 29.630 0.00 0.00 36.16 2.57
3534 3940 9.426837 AGATGAAATTATGTTTCCACAACAATG 57.573 29.630 0.00 0.00 36.16 2.82
3535 3941 9.643693 GAGATGAAATTATGTTTCCACAACAAT 57.356 29.630 0.00 0.00 36.16 2.71
3536 3942 8.859090 AGAGATGAAATTATGTTTCCACAACAA 58.141 29.630 0.00 0.00 36.16 2.83
3537 3943 8.298854 CAGAGATGAAATTATGTTTCCACAACA 58.701 33.333 3.79 0.00 36.16 3.33
3538 3944 8.299570 ACAGAGATGAAATTATGTTTCCACAAC 58.700 33.333 3.79 0.00 36.16 3.32
3539 3945 8.408043 ACAGAGATGAAATTATGTTTCCACAA 57.592 30.769 3.79 0.00 36.16 3.33
3540 3946 9.685276 ATACAGAGATGAAATTATGTTTCCACA 57.315 29.630 3.79 0.00 37.31 4.17
3541 3947 9.941664 CATACAGAGATGAAATTATGTTTCCAC 57.058 33.333 3.79 0.00 0.00 4.02
3542 3948 9.685276 ACATACAGAGATGAAATTATGTTTCCA 57.315 29.630 3.79 0.00 28.02 3.53
3543 3949 9.941664 CACATACAGAGATGAAATTATGTTTCC 57.058 33.333 0.00 0.00 29.68 3.13
3544 3950 9.443283 GCACATACAGAGATGAAATTATGTTTC 57.557 33.333 0.00 0.00 29.68 2.78
3545 3951 8.408601 GGCACATACAGAGATGAAATTATGTTT 58.591 33.333 0.00 0.00 29.68 2.83
3546 3952 7.013655 GGGCACATACAGAGATGAAATTATGTT 59.986 37.037 0.00 0.00 29.68 2.71
3547 3953 6.488006 GGGCACATACAGAGATGAAATTATGT 59.512 38.462 0.00 0.00 31.78 2.29
3548 3954 6.713903 AGGGCACATACAGAGATGAAATTATG 59.286 38.462 0.00 0.00 0.00 1.90
3549 3955 6.845908 AGGGCACATACAGAGATGAAATTAT 58.154 36.000 0.00 0.00 0.00 1.28
3550 3956 6.252599 AGGGCACATACAGAGATGAAATTA 57.747 37.500 0.00 0.00 0.00 1.40
3554 3960 5.692115 TTAAGGGCACATACAGAGATGAA 57.308 39.130 0.00 0.00 0.00 2.57
3561 3967 5.882557 AGAGATGTTTTAAGGGCACATACAG 59.117 40.000 0.00 0.00 31.10 2.74
3577 3983 4.718961 AGTTGCTACACCAAAGAGATGTT 58.281 39.130 0.13 0.00 0.00 2.71
3578 3984 4.357918 AGTTGCTACACCAAAGAGATGT 57.642 40.909 0.13 0.00 0.00 3.06
3579 3985 5.482908 ACTAGTTGCTACACCAAAGAGATG 58.517 41.667 0.13 0.00 0.00 2.90
3601 4007 9.277565 CACATATGCTACTCAACAAACAAATAC 57.722 33.333 1.58 0.00 0.00 1.89
3624 4030 1.385756 TTTTCAGCAGCAGCAGCACA 61.386 50.000 12.92 0.00 45.49 4.57
3628 4034 3.128349 ACAAAATTTTCAGCAGCAGCAG 58.872 40.909 3.17 0.00 45.49 4.24
3640 4046 4.962362 AGGAGACCCACAGAACAAAATTTT 59.038 37.500 0.00 0.00 33.88 1.82
3651 4057 2.887151 AAAATGGAGGAGACCCACAG 57.113 50.000 0.00 0.00 36.36 3.66
3656 4062 6.828785 ACATAACACATAAAATGGAGGAGACC 59.171 38.462 0.00 0.00 33.60 3.85
3658 4064 8.739039 CAAACATAACACATAAAATGGAGGAGA 58.261 33.333 0.00 0.00 33.60 3.71
3663 4069 8.933807 CAATGCAAACATAACACATAAAATGGA 58.066 29.630 0.00 0.00 34.62 3.41
3693 4099 0.266152 ATCCAGAGTACAGGAGGGGG 59.734 60.000 7.61 0.00 35.26 5.40
3696 4102 6.098982 ACATAAAAGATCCAGAGTACAGGAGG 59.901 42.308 7.61 0.00 35.26 4.30
3709 4121 3.378427 GGCAGACCACACATAAAAGATCC 59.622 47.826 0.00 0.00 35.26 3.36
3715 4127 6.101150 AGGATAATAGGCAGACCACACATAAA 59.899 38.462 0.00 0.00 39.06 1.40
3741 4153 5.369685 TTCAATGCAAAGCGAGACATTTA 57.630 34.783 0.00 0.00 30.54 1.40
3746 4158 2.030805 AGGTTTCAATGCAAAGCGAGAC 60.031 45.455 0.00 0.00 38.53 3.36
3750 4162 3.236816 CTGTAGGTTTCAATGCAAAGCG 58.763 45.455 0.00 0.00 38.53 4.68
3769 4181 6.824305 AGGTATCCACAAGAAATTGAACTG 57.176 37.500 0.00 0.00 0.00 3.16
3783 4195 3.506067 CCCAAGTTCAACAAGGTATCCAC 59.494 47.826 0.00 0.00 0.00 4.02
3784 4196 3.139397 ACCCAAGTTCAACAAGGTATCCA 59.861 43.478 0.00 0.00 0.00 3.41
4020 4432 7.268199 ACAGATTATTTGTGAGCACCATATG 57.732 36.000 0.00 0.00 0.00 1.78
4160 4572 6.206243 CCAAGTTGTGATCTCTCAAGAACATT 59.794 38.462 1.45 0.00 36.78 2.71
4301 4715 6.992063 AGATATACAACAGGAAAGCAACTG 57.008 37.500 0.00 0.00 40.48 3.16


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

AutoCloner maintained by Alex Coulton.