Multiple sequence alignment - TraesCS3A01G123000

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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 TraesCS3A01G123000 chr3A 100.000 6611 0 0 1 6611 98847125 98840515 0.000000e+00 12209.0
1 TraesCS3A01G123000 chr3A 100.000 465 0 0 6913 7377 98840213 98839749 0.000000e+00 859.0
2 TraesCS3A01G123000 chr3D 92.546 6413 305 59 64 6407 82760716 82754408 0.000000e+00 9034.0
3 TraesCS3A01G123000 chr3D 91.202 466 25 9 6921 7375 82754200 82753740 2.920000e-173 619.0
4 TraesCS3A01G123000 chr3D 85.859 198 16 5 6921 7111 82795427 82795235 4.510000e-47 200.0
5 TraesCS3A01G123000 chr3B 93.178 5981 290 56 461 6407 129442169 129436273 0.000000e+00 8676.0
6 TraesCS3A01G123000 chr3B 81.830 743 108 20 1 728 129531965 129531235 3.810000e-167 599.0
7 TraesCS3A01G123000 chr3B 90.728 453 27 7 6936 7375 129430315 129429865 2.290000e-164 590.0
8 TraesCS3A01G123000 chr3B 84.459 148 22 1 240 387 129531004 129530858 2.150000e-30 145.0
9 TraesCS3A01G123000 chr3B 74.346 191 40 9 1 187 4204415 4204600 1.030000e-08 73.1
10 TraesCS3A01G123000 chr3B 77.778 126 21 7 65 187 5060519 5060640 3.690000e-08 71.3
11 TraesCS3A01G123000 chr2D 72.787 305 77 6 3199 3500 76548084 76548385 1.690000e-16 99.0
12 TraesCS3A01G123000 chr2B 75.248 202 50 0 3304 3505 117629055 117629256 6.090000e-16 97.1


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 TraesCS3A01G123000 chr3A 98839749 98847125 7376 True 6534.0 12209 100.0000 1 7377 2 chr3A.!!$R1 7376
1 TraesCS3A01G123000 chr3D 82753740 82760716 6976 True 4826.5 9034 91.8740 64 7375 2 chr3D.!!$R2 7311
2 TraesCS3A01G123000 chr3B 129436273 129442169 5896 True 8676.0 8676 93.1780 461 6407 1 chr3B.!!$R2 5946
3 TraesCS3A01G123000 chr3B 129530858 129531965 1107 True 372.0 599 83.1445 1 728 2 chr3B.!!$R3 727

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
546 567 0.036952 AGTGAGAACATGAGTGGCGG 60.037 55.000 0.00 0.00 0.00 6.13 F
1046 1080 0.030773 TCGATCTCCGCCAAATCTCG 59.969 55.000 0.00 0.00 38.37 4.04 F
1100 1135 0.617413 AGAGTTCCTCCATGCCTGTG 59.383 55.000 0.00 0.00 0.00 3.66 F
1472 1507 0.629058 AGGTTTTGTGTGGGTGTCCT 59.371 50.000 0.00 0.00 0.00 3.85 F
2056 2100 0.663269 TGCTGTACTGCTTCGTGTCG 60.663 55.000 23.07 0.00 0.00 4.35 F
2587 2631 1.002011 GGAGGACAAGTTCAGGGCC 60.002 63.158 0.00 0.00 0.00 5.80 F
3900 3981 0.107017 ATCCAACGAAGGAGCCATGG 60.107 55.000 7.63 7.63 41.90 3.66 F
5657 5756 0.188587 TCGATCCTCTGGGCCTGTAT 59.811 55.000 4.53 0.17 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2100 0.818445 TCTCCTGCCGATCGGAGTAC 60.818 60.000 37.64 19.76 45.57 2.73 R
2782 2826 1.070445 CATCCTCATGGGCTCCGAC 59.930 63.158 0.00 0.00 34.39 4.79 R
2818 2862 1.208052 ACCTTGACCTGGATCATGACG 59.792 52.381 0.00 0.00 0.00 4.35 R
3004 3048 2.434884 ATCTTCTGCCCGTGCGTG 60.435 61.111 0.00 0.00 41.78 5.34 R
3887 3968 0.036010 ACTGAACCATGGCTCCTTCG 60.036 55.000 13.04 7.27 0.00 3.79 R
4175 4256 0.678684 TCATCACCGCGTAGACTCCA 60.679 55.000 4.92 0.00 0.00 3.86 R
5786 5885 1.068055 CAATGCCTGTGAAAGACCAGC 60.068 52.381 0.00 0.00 0.00 4.85 R
7217 7322 1.082104 GTAAATAGCATGCGGCCGC 60.082 57.895 42.35 42.35 46.50 6.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.319025 TCCATGTGGACCTGTAGACA 57.681 50.000 0.00 0.00 39.78 3.41
28 29 1.623311 CATGTGGACCTGTAGACACCA 59.377 52.381 0.00 0.00 33.07 4.17
31 32 0.677288 TGGACCTGTAGACACCAACG 59.323 55.000 0.00 0.00 0.00 4.10
33 34 1.549170 GGACCTGTAGACACCAACGAT 59.451 52.381 0.00 0.00 0.00 3.73
43 44 3.130516 AGACACCAACGATCACGATATGT 59.869 43.478 0.00 0.00 42.66 2.29
98 99 4.649674 TCGATAAGGGCATGTAGAAACTCT 59.350 41.667 0.00 0.00 0.00 3.24
107 108 5.351740 GGCATGTAGAAACTCTAAAGACCAC 59.648 44.000 0.00 0.00 29.58 4.16
115 117 6.661805 AGAAACTCTAAAGACCACAAAACCAA 59.338 34.615 0.00 0.00 0.00 3.67
129 131 5.626543 CACAAAACCAATCGAATTCAGACAG 59.373 40.000 6.22 1.19 0.00 3.51
161 164 3.947910 ACTAGAACGACCAAATTCCGA 57.052 42.857 0.00 0.00 0.00 4.55
204 207 1.614317 CCACAATCCCTCCAACTGACC 60.614 57.143 0.00 0.00 0.00 4.02
224 227 3.243267 ACCATAAGCACACCAAACGAAAC 60.243 43.478 0.00 0.00 0.00 2.78
259 262 5.692654 GGAGAGAACATTAATTCCTAGACGC 59.307 44.000 0.00 0.00 0.00 5.19
361 364 2.046314 CGCCAGATCCGGGTTTGT 60.046 61.111 4.30 0.00 0.00 2.83
382 385 4.680237 CGGGCACGCCTCTGTCAA 62.680 66.667 8.20 0.00 36.10 3.18
393 396 1.477558 CCTCTGTCAAAGGTTGCCACT 60.478 52.381 0.00 0.00 0.00 4.00
410 425 4.329545 TGCCAGCCGAAGACCACC 62.330 66.667 0.00 0.00 0.00 4.61
419 434 1.672356 GAAGACCACCGCAGCACAT 60.672 57.895 0.00 0.00 0.00 3.21
420 435 1.639298 GAAGACCACCGCAGCACATC 61.639 60.000 0.00 0.00 0.00 3.06
427 442 2.260154 CCGCAGCACATCCACACAA 61.260 57.895 0.00 0.00 0.00 3.33
436 457 1.074889 ACATCCACACAACCCCTAACC 59.925 52.381 0.00 0.00 0.00 2.85
437 458 1.354368 CATCCACACAACCCCTAACCT 59.646 52.381 0.00 0.00 0.00 3.50
533 554 1.299562 GACGTGGCGAGAGAGTGAGA 61.300 60.000 0.00 0.00 0.00 3.27
545 566 1.067283 AGAGTGAGAACATGAGTGGCG 60.067 52.381 0.00 0.00 0.00 5.69
546 567 0.036952 AGTGAGAACATGAGTGGCGG 60.037 55.000 0.00 0.00 0.00 6.13
547 568 1.375908 TGAGAACATGAGTGGCGGC 60.376 57.895 0.00 0.00 0.00 6.53
548 569 1.078848 GAGAACATGAGTGGCGGCT 60.079 57.895 11.43 0.00 0.00 5.52
549 570 0.175760 GAGAACATGAGTGGCGGCTA 59.824 55.000 11.43 0.00 0.00 3.93
601 622 2.124903 TCTCTCACACGAAGCGTTTTC 58.875 47.619 0.00 0.00 38.32 2.29
619 640 0.179015 TCCCGTTTGCTTACTGCCAA 60.179 50.000 0.00 0.00 42.00 4.52
630 651 1.267121 TACTGCCAACCACTCCTCTC 58.733 55.000 0.00 0.00 0.00 3.20
633 654 1.072965 CTGCCAACCACTCCTCTCTTT 59.927 52.381 0.00 0.00 0.00 2.52
634 655 1.494721 TGCCAACCACTCCTCTCTTTT 59.505 47.619 0.00 0.00 0.00 2.27
637 658 2.417719 CAACCACTCCTCTCTTTTCCG 58.582 52.381 0.00 0.00 0.00 4.30
639 660 2.541466 ACCACTCCTCTCTTTTCCGAT 58.459 47.619 0.00 0.00 0.00 4.18
640 661 2.234908 ACCACTCCTCTCTTTTCCGATG 59.765 50.000 0.00 0.00 0.00 3.84
641 662 2.275318 CACTCCTCTCTTTTCCGATGC 58.725 52.381 0.00 0.00 0.00 3.91
711 735 1.194772 CTTTCCTTTCCGTCGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
715 739 1.535462 CCTTTCCGTCGCTTGTCATTT 59.465 47.619 0.00 0.00 0.00 2.32
718 742 1.144969 TCCGTCGCTTGTCATTTGTC 58.855 50.000 0.00 0.00 0.00 3.18
784 812 2.117137 CCTTCGTCCACAATATCGTCG 58.883 52.381 0.00 0.00 0.00 5.12
793 821 4.702081 ATATCGTCGCGGCCGCTC 62.702 66.667 43.60 33.46 39.32 5.03
798 826 4.789075 GTCGCGGCCGCTCACTTA 62.789 66.667 43.60 21.15 39.32 2.24
814 844 2.093447 CACTTACCAGTGGAGTGGATCC 60.093 54.545 18.40 4.20 46.10 3.36
855 885 2.125713 CACGGCGCCACTGACATA 60.126 61.111 28.98 0.00 0.00 2.29
856 886 2.167219 CACGGCGCCACTGACATAG 61.167 63.158 28.98 9.11 0.00 2.23
857 887 2.184322 CGGCGCCACTGACATAGT 59.816 61.111 28.98 0.00 41.36 2.12
910 940 1.920325 CTCCACCTCCTCCCTGCAA 60.920 63.158 0.00 0.00 0.00 4.08
957 987 9.710900 ATCATTTTTATCTTTGTTTGGTTCCTC 57.289 29.630 0.00 0.00 0.00 3.71
960 990 6.945938 TTTATCTTTGTTTGGTTCCTCGAA 57.054 33.333 0.00 0.00 0.00 3.71
974 1004 1.535015 CCTCGAATCCTCGTGAAGCTC 60.535 57.143 0.00 0.00 45.62 4.09
998 1028 0.248907 TTATTCTCGAGGAAGCGGCG 60.249 55.000 13.56 0.51 37.36 6.46
1007 1037 3.929948 GAAGCGGCGAATGGAGCG 61.930 66.667 12.98 0.00 35.00 5.03
1023 1053 1.805945 GCGAGGTAGTCAACGCCAG 60.806 63.158 0.00 0.00 44.27 4.85
1046 1080 0.030773 TCGATCTCCGCCAAATCTCG 59.969 55.000 0.00 0.00 38.37 4.04
1048 1082 1.224722 GATCTCCGCCAAATCTCGCC 61.225 60.000 0.00 0.00 0.00 5.54
1056 1090 1.876156 GCCAAATCTCGCCTCCATTAG 59.124 52.381 0.00 0.00 0.00 1.73
1059 1094 3.947834 CCAAATCTCGCCTCCATTAGTTT 59.052 43.478 0.00 0.00 0.00 2.66
1100 1135 0.617413 AGAGTTCCTCCATGCCTGTG 59.383 55.000 0.00 0.00 0.00 3.66
1129 1164 2.151202 CAGTTTACGATGGTTGCAGGT 58.849 47.619 0.00 0.00 0.00 4.00
1131 1166 3.370978 CAGTTTACGATGGTTGCAGGTAG 59.629 47.826 0.00 0.00 0.00 3.18
1132 1167 3.007614 AGTTTACGATGGTTGCAGGTAGT 59.992 43.478 0.00 0.00 0.00 2.73
1133 1168 4.221262 AGTTTACGATGGTTGCAGGTAGTA 59.779 41.667 0.00 0.00 0.00 1.82
1136 1171 2.268298 CGATGGTTGCAGGTAGTACAC 58.732 52.381 2.06 0.00 0.00 2.90
1193 1228 1.327303 CCAAGGAGGAGGAGATCTCG 58.673 60.000 16.46 0.00 43.34 4.04
1221 1256 1.823250 GCTGGGTTCCCTGTGTTTCAT 60.823 52.381 14.56 0.00 0.00 2.57
1222 1257 2.162681 CTGGGTTCCCTGTGTTTCATC 58.837 52.381 9.43 0.00 0.00 2.92
1223 1258 1.496857 TGGGTTCCCTGTGTTTCATCA 59.503 47.619 9.43 0.00 0.00 3.07
1230 1265 1.808945 CCTGTGTTTCATCAGCCAGAC 59.191 52.381 0.00 0.00 0.00 3.51
1263 1298 4.380023 CGATCTCGTGAACCTTCTTCTCTT 60.380 45.833 0.00 0.00 34.11 2.85
1264 1299 4.244425 TCTCGTGAACCTTCTTCTCTTG 57.756 45.455 0.00 0.00 0.00 3.02
1268 1303 1.270839 TGAACCTTCTTCTCTTGGCCG 60.271 52.381 0.00 0.00 0.00 6.13
1283 1318 1.008309 GCCGTCTATGTCTCGAGCC 60.008 63.158 7.81 0.00 0.00 4.70
1317 1352 0.768221 TGCAAGAGGGAGTTCAGGGT 60.768 55.000 0.00 0.00 0.00 4.34
1327 1362 3.691342 TTCAGGGTCGTCAGGGCG 61.691 66.667 0.00 0.00 0.00 6.13
1328 1363 4.671590 TCAGGGTCGTCAGGGCGA 62.672 66.667 0.00 0.00 38.68 5.54
1330 1365 4.361971 AGGGTCGTCAGGGCGAGA 62.362 66.667 0.00 0.00 41.85 4.04
1333 1368 2.766400 GGTCGTCAGGGCGAGAGAG 61.766 68.421 0.00 0.00 41.85 3.20
1456 1491 1.543802 CTGCTCTTCTTCGTGAGAGGT 59.456 52.381 2.93 0.00 43.69 3.85
1472 1507 0.629058 AGGTTTTGTGTGGGTGTCCT 59.371 50.000 0.00 0.00 0.00 3.85
1480 1515 1.301479 GTGGGTGTCCTTGTCGGTC 60.301 63.158 0.00 0.00 0.00 4.79
1612 1647 2.751166 ATCTGGGAGTTCTTGACGTG 57.249 50.000 0.00 0.00 0.00 4.49
1613 1648 1.699730 TCTGGGAGTTCTTGACGTGA 58.300 50.000 0.00 0.00 0.00 4.35
1892 1936 2.442188 GCGTGCCGTAAGTTCCTCG 61.442 63.158 0.00 0.00 0.00 4.63
1913 1957 3.432051 GAGTGGCATCGACGGAGGG 62.432 68.421 0.00 0.00 0.00 4.30
2056 2100 0.663269 TGCTGTACTGCTTCGTGTCG 60.663 55.000 23.07 0.00 0.00 4.35
2340 2384 2.045926 GTACTGGCTGCACCTGGG 60.046 66.667 0.50 0.00 41.59 4.45
2587 2631 1.002011 GGAGGACAAGTTCAGGGCC 60.002 63.158 0.00 0.00 0.00 5.80
2761 2805 3.343421 GGCGTGGTGTTCACCGTC 61.343 66.667 15.82 10.89 43.23 4.79
2812 2856 3.746949 GAGGATGCTGCCCGAGGTG 62.747 68.421 0.00 0.00 0.00 4.00
2818 2862 2.187946 CTGCCCGAGGTGATGTCC 59.812 66.667 0.00 0.00 0.00 4.02
2866 2910 1.521681 CCGCATCGGGAAGTTCCTC 60.522 63.158 21.25 10.60 44.15 3.71
3004 3048 1.453155 AAGACATCAACATCACCGCC 58.547 50.000 0.00 0.00 0.00 6.13
3007 3051 1.298157 ACATCAACATCACCGCCACG 61.298 55.000 0.00 0.00 0.00 4.94
3009 3053 3.353029 CAACATCACCGCCACGCA 61.353 61.111 0.00 0.00 0.00 5.24
3110 3154 2.099263 AGAATGTCCGGATCAGTACGTG 59.901 50.000 7.81 0.00 0.00 4.49
3112 3156 1.245376 TGTCCGGATCAGTACGTGCA 61.245 55.000 7.81 0.00 0.00 4.57
3296 3368 1.829096 GGAGTACGAGAGGGCCCTC 60.829 68.421 40.50 40.50 43.03 4.30
3424 3496 2.509336 CGCAAGGGCCGTCTACAG 60.509 66.667 0.00 0.00 36.38 2.74
3505 3577 2.040278 CCACCCTCTTCAATGTCAGGAA 59.960 50.000 0.00 0.00 0.00 3.36
3536 3614 2.892852 CCTTCTCAAACCTCATTGCCAA 59.107 45.455 0.00 0.00 0.00 4.52
3537 3615 3.512724 CCTTCTCAAACCTCATTGCCAAT 59.487 43.478 0.00 0.00 0.00 3.16
3538 3616 4.491676 CTTCTCAAACCTCATTGCCAATG 58.508 43.478 11.24 11.24 40.28 2.82
3539 3617 2.231964 TCTCAAACCTCATTGCCAATGC 59.768 45.455 12.62 0.00 38.77 3.56
3540 3618 1.275856 TCAAACCTCATTGCCAATGCC 59.724 47.619 12.62 0.00 38.77 4.40
3541 3619 1.002201 CAAACCTCATTGCCAATGCCA 59.998 47.619 12.62 0.00 38.77 4.92
3631 3712 2.732597 CGAGGACAAGACGGTCATTCTC 60.733 54.545 11.27 7.91 39.59 2.87
3747 3828 3.674528 CTGTCTGACAGTCACCATCTT 57.325 47.619 25.87 0.00 41.19 2.40
3750 3831 3.134623 TGTCTGACAGTCACCATCTTGTT 59.865 43.478 6.36 0.00 0.00 2.83
3751 3832 3.743396 GTCTGACAGTCACCATCTTGTTC 59.257 47.826 0.00 0.00 0.00 3.18
3752 3833 3.387699 TCTGACAGTCACCATCTTGTTCA 59.612 43.478 0.00 0.00 0.00 3.18
3866 3947 2.680841 TCACCAGGACTCAAAAACAACG 59.319 45.455 0.00 0.00 0.00 4.10
3887 3968 2.945668 GCTGGACTCCAATGTATCCAAC 59.054 50.000 0.00 0.00 40.69 3.77
3900 3981 0.107017 ATCCAACGAAGGAGCCATGG 60.107 55.000 7.63 7.63 41.90 3.66
3919 4000 1.880027 GGTTCAGTACCAACAGCCAAG 59.120 52.381 7.43 0.00 46.92 3.61
4051 4132 2.333389 GACTACGTGTCAGTGTCCAG 57.667 55.000 0.00 0.00 44.73 3.86
4067 4148 2.285743 AGGGGCTGGTTCCTCCTC 60.286 66.667 0.00 0.00 37.07 3.71
4175 4256 1.154016 CAGCGTCAGGATCGTCGTT 60.154 57.895 0.00 0.00 0.00 3.85
4220 4301 1.589716 CCAGCTGCCTGTTTGCCTAC 61.590 60.000 8.66 0.00 37.38 3.18
4238 4319 2.328099 CGTGAGGAGCCTTGTTGCC 61.328 63.158 0.00 0.00 0.00 4.52
4241 4322 3.909086 GAGGAGCCTTGTTGCCGCT 62.909 63.158 0.00 0.00 34.97 5.52
4292 4373 3.519510 TCTTCTCCGGTTTCATGGATTCT 59.480 43.478 0.00 0.00 32.83 2.40
4365 4446 3.029483 TGACCCGGGTATGTGTACATA 57.971 47.619 30.38 0.00 37.76 2.29
4384 4470 9.672086 TGTACATATTAACACAACTTTTTCAGC 57.328 29.630 0.00 0.00 0.00 4.26
4392 4478 5.591099 ACACAACTTTTTCAGCCATACTTG 58.409 37.500 0.00 0.00 0.00 3.16
4432 4518 4.825546 CAGATTTGCAGTCTGAGTTTGT 57.174 40.909 20.54 0.00 44.57 2.83
4445 4531 3.958704 TGAGTTTGTGCACCGTTAATTG 58.041 40.909 15.69 0.00 0.00 2.32
4592 4678 1.282875 GCAAGTCGTTCTGGTTGCC 59.717 57.895 0.00 0.00 39.52 4.52
4595 4681 1.157870 AAGTCGTTCTGGTTGCCGTG 61.158 55.000 0.00 0.00 0.00 4.94
4604 4690 2.668212 GTTGCCGTGCCTGCTGTA 60.668 61.111 0.00 0.00 0.00 2.74
4610 4696 0.960364 CCGTGCCTGCTGTAATTGGT 60.960 55.000 0.00 0.00 0.00 3.67
4633 4719 3.319137 TCTGTACATTCAGGTGAGCAC 57.681 47.619 0.00 0.00 36.25 4.40
4672 4762 3.345508 TCATCTTCTTGTGCAGCAGAT 57.654 42.857 0.00 0.00 0.00 2.90
4776 4866 1.227556 GGCGCCCGTGATGAACTAT 60.228 57.895 18.11 0.00 0.00 2.12
4821 4911 0.679640 TCACCATAAGGGCCTTTGCG 60.680 55.000 26.29 13.84 42.05 4.85
4872 4962 0.599466 AGCTCATCGACATGGATGCG 60.599 55.000 6.99 3.16 42.78 4.73
5003 5093 0.615331 GGATCAGTTGCTCCAGGTGA 59.385 55.000 0.00 0.00 30.98 4.02
5028 5118 5.957771 ATTATTCAGGGCTGAGTACTTCA 57.042 39.130 0.00 0.00 41.13 3.02
5029 5119 5.957771 TTATTCAGGGCTGAGTACTTCAT 57.042 39.130 0.00 0.00 41.13 2.57
5053 5148 3.788333 ATGTGCAGAAATATGGTGTGC 57.212 42.857 0.00 2.70 34.62 4.57
5067 5162 1.230324 GTGTGCCACTCAAGTCTTCC 58.770 55.000 0.00 0.00 0.00 3.46
5128 5223 2.191128 ATGCCTTGACGCTTTCTTCT 57.809 45.000 0.00 0.00 0.00 2.85
5207 5302 5.702670 GTGGAGAGAATCAAACAGTTCATGA 59.297 40.000 0.00 0.00 37.82 3.07
5218 5313 7.397221 TCAAACAGTTCATGAATCTACCATCT 58.603 34.615 12.12 0.00 0.00 2.90
5314 5409 8.426881 AGAACTTGAGAGTAAGAAACTGAAAC 57.573 34.615 0.00 0.00 39.07 2.78
5343 5438 3.341823 ACAACCAGCTCATTCATCTGAC 58.658 45.455 0.00 0.00 0.00 3.51
5344 5439 3.244665 ACAACCAGCTCATTCATCTGACA 60.245 43.478 0.00 0.00 0.00 3.58
5349 5444 5.129980 ACCAGCTCATTCATCTGACATTCTA 59.870 40.000 0.00 0.00 0.00 2.10
5628 5727 1.923227 GCTTTTCAGGGGCAGCGTAC 61.923 60.000 0.00 0.00 0.00 3.67
5651 5750 1.519455 CAACGTCGATCCTCTGGGC 60.519 63.158 0.00 0.00 0.00 5.36
5657 5756 0.188587 TCGATCCTCTGGGCCTGTAT 59.811 55.000 4.53 0.17 0.00 2.29
5683 5782 4.860866 AGATCAGGATATCTGGGAGGTCTA 59.139 45.833 2.05 0.00 43.53 2.59
5684 5783 4.666412 TCAGGATATCTGGGAGGTCTAG 57.334 50.000 2.05 0.00 43.53 2.43
5691 5790 1.207791 CTGGGAGGTCTAGCCACAAT 58.792 55.000 6.07 0.00 40.61 2.71
5767 5866 2.102252 TCTTTGTTGGGGACACATTTGC 59.898 45.455 0.00 0.00 42.67 3.68
5786 5885 1.537776 GCTGATCCTGATCCTGACACG 60.538 57.143 4.76 0.00 37.02 4.49
5796 5895 0.033504 TCCTGACACGCTGGTCTTTC 59.966 55.000 6.25 0.00 38.61 2.62
5803 5902 1.597854 CGCTGGTCTTTCACAGGCA 60.598 57.895 0.00 0.00 35.30 4.75
5830 5929 1.871080 AGTGCCAGTTGAAGAAGACG 58.129 50.000 0.00 0.00 0.00 4.18
5888 5987 8.253810 CAGGTGAGACAATGATCTTTAGTTCTA 58.746 37.037 0.00 0.00 0.00 2.10
5890 5989 9.436957 GGTGAGACAATGATCTTTAGTTCTAAA 57.563 33.333 5.16 5.16 0.00 1.85
6079 6178 2.762234 GTCGATCGACTCGGCCACT 61.762 63.158 34.97 0.00 46.29 4.00
6198 6297 4.141779 GGTCATGGTTCTTTCCTACGGTAT 60.142 45.833 0.00 0.00 0.00 2.73
6243 6342 7.937394 GCTACTAAAATTATGCCGGGGATATAT 59.063 37.037 9.20 3.73 0.00 0.86
6331 6431 2.611292 GCTGATGGAAAATGAGGACTCG 59.389 50.000 0.00 0.00 0.00 4.18
6350 6450 4.082679 ACTCGTCATTCTTTAAGCTCGTCT 60.083 41.667 0.00 0.00 0.00 4.18
6378 6478 7.416438 CGAGTACTGGTCCAACTATAAGTGAAT 60.416 40.741 0.00 0.00 0.00 2.57
6387 6487 6.431543 TCCAACTATAAGTGAATGCGGAAAAA 59.568 34.615 0.00 0.00 0.00 1.94
6407 6507 7.330700 GGAAAAATCAATAATTTTGTCGGCTGA 59.669 33.333 0.00 0.00 44.88 4.26
6408 6508 8.776376 AAAAATCAATAATTTTGTCGGCTGAT 57.224 26.923 0.00 0.00 44.88 2.90
6409 6509 7.992180 AAATCAATAATTTTGTCGGCTGATC 57.008 32.000 0.00 0.00 33.69 2.92
6410 6510 5.499139 TCAATAATTTTGTCGGCTGATCC 57.501 39.130 0.00 0.00 0.00 3.36
6411 6511 8.154889 AAATCAATAATTTTGTCGGCTGATCCG 61.155 37.037 0.00 0.00 46.22 4.18
6421 6521 2.981400 GGCTGATCCGTTTCGAAAAA 57.019 45.000 13.10 1.64 0.00 1.94
6451 6551 0.245539 GTCGGCTGTAGGCTACAACA 59.754 55.000 26.12 8.57 38.38 3.33
6456 6556 2.028020 GGCTGTAGGCTACAACACTTCT 60.028 50.000 26.12 0.00 38.38 2.85
6457 6557 3.557264 GGCTGTAGGCTACAACACTTCTT 60.557 47.826 26.12 0.00 38.38 2.52
6458 6558 3.680458 GCTGTAGGCTACAACACTTCTTC 59.320 47.826 26.12 5.59 38.38 2.87
6460 6560 4.883083 TGTAGGCTACAACACTTCTTCTG 58.117 43.478 24.39 0.00 35.38 3.02
6462 6562 1.807142 GGCTACAACACTTCTTCTGCC 59.193 52.381 0.00 0.00 0.00 4.85
6477 6577 6.219417 TCTTCTGCCAAGTGAAAATTTTGA 57.781 33.333 8.47 0.00 0.00 2.69
6481 6581 6.405538 TCTGCCAAGTGAAAATTTTGAAACT 58.594 32.000 8.47 6.44 0.00 2.66
6495 6595 8.686397 AATTTTGAAACTGAAAATTGTTTGGC 57.314 26.923 0.00 0.00 40.08 4.52
6498 6598 4.328440 TGAAACTGAAAATTGTTTGGCACG 59.672 37.500 0.00 0.00 36.64 5.34
6505 6605 4.701956 AAATTGTTTGGCACGAGATAGG 57.298 40.909 0.00 0.00 0.00 2.57
6511 6611 0.105709 TGGCACGAGATAGGGATGGA 60.106 55.000 0.00 0.00 0.00 3.41
6525 6625 3.645212 AGGGATGGAGATGTATGACACAG 59.355 47.826 0.00 0.00 41.51 3.66
6527 6627 4.141620 GGGATGGAGATGTATGACACAGTT 60.142 45.833 0.00 0.00 41.51 3.16
6599 6699 3.144657 TGCCTTCATCGGATTATGCAT 57.855 42.857 3.79 3.79 0.00 3.96
6949 7049 5.300969 TGTTTCTGCATTTGACATCTAGC 57.699 39.130 0.00 0.00 0.00 3.42
6950 7050 4.142838 TGTTTCTGCATTTGACATCTAGCG 60.143 41.667 0.00 0.00 0.00 4.26
6964 7064 6.985188 ACATCTAGCGTGTCATAATTTGTT 57.015 33.333 0.00 0.00 0.00 2.83
6985 7085 8.684386 TTGTTATAATGAACTGTTGAACTGGA 57.316 30.769 7.13 0.00 0.00 3.86
6991 7091 4.713553 TGAACTGTTGAACTGGATTGCTA 58.286 39.130 7.13 0.00 0.00 3.49
7031 7131 4.096190 ACCTTGCCTATCATCTCAATGG 57.904 45.455 0.00 0.00 33.42 3.16
7032 7132 3.181436 ACCTTGCCTATCATCTCAATGGG 60.181 47.826 0.00 0.00 33.42 4.00
7033 7133 2.574006 TGCCTATCATCTCAATGGGC 57.426 50.000 3.78 3.78 37.90 5.36
7034 7134 2.060275 TGCCTATCATCTCAATGGGCT 58.940 47.619 11.10 0.00 38.11 5.19
7056 7156 2.045926 CCCTCCTTGCCACCTTCG 60.046 66.667 0.00 0.00 0.00 3.79
7080 7180 2.821969 ACTGCCTAATTGTTTGAGCCTG 59.178 45.455 0.00 0.00 0.00 4.85
7082 7182 2.171003 GCCTAATTGTTTGAGCCTGGT 58.829 47.619 0.00 0.00 0.00 4.00
7105 7208 3.879892 GTGCTACCTCCATCTTTCAATCC 59.120 47.826 0.00 0.00 0.00 3.01
7133 7236 7.777910 CCTAACCTACCATGGATATCACAAAAA 59.222 37.037 21.47 0.00 0.00 1.94
7143 7246 5.712446 TGGATATCACAAAAACCGGAAATGA 59.288 36.000 9.46 3.08 0.00 2.57
7189 7293 7.391833 GGTCTTAGTTCTGACATCAAAGGAAAT 59.608 37.037 0.00 0.00 35.11 2.17
7282 7387 5.349061 TCTCTCACATTAGCACATGATGT 57.651 39.130 0.00 0.00 38.59 3.06
7316 7427 6.013206 TGGTTAAAAATGTCTCTAGCACCCTA 60.013 38.462 0.00 0.00 0.00 3.53
7319 7430 5.700402 AAAATGTCTCTAGCACCCTACAT 57.300 39.130 0.00 0.00 0.00 2.29
7322 7433 2.760650 TGTCTCTAGCACCCTACATGTG 59.239 50.000 9.11 0.00 36.79 3.21
7333 7444 2.941064 CCCTACATGTGCACAAGATCAG 59.059 50.000 27.42 18.75 0.00 2.90
7338 7449 4.388485 ACATGTGCACAAGATCAGTTGTA 58.612 39.130 27.42 0.00 38.65 2.41
7364 7475 6.429791 TTTTCGAATGAGACAGTGTTGAAA 57.570 33.333 0.00 0.00 0.00 2.69
7369 7480 3.266510 TGAGACAGTGTTGAAAGCACT 57.733 42.857 0.00 0.00 46.86 4.40
7375 7486 7.042051 TGAGACAGTGTTGAAAGCACTTATAAC 60.042 37.037 0.00 3.88 43.87 1.89
7376 7487 6.204882 AGACAGTGTTGAAAGCACTTATAACC 59.795 38.462 0.00 1.55 43.87 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.623311 TGGTGTCTACAGGTCCACATG 59.377 52.381 0.00 0.00 0.00 3.21
13 14 0.963962 TCGTTGGTGTCTACAGGTCC 59.036 55.000 0.00 0.00 0.00 4.46
56 57 2.486918 GACGTTTTCTTCTCCGGGAAA 58.513 47.619 0.00 0.00 33.07 3.13
58 59 0.038892 CGACGTTTTCTTCTCCGGGA 60.039 55.000 0.00 0.00 0.00 5.14
62 63 3.864003 CCCTTATCGACGTTTTCTTCTCC 59.136 47.826 0.00 0.00 0.00 3.71
98 99 6.642707 ATTCGATTGGTTTTGTGGTCTTTA 57.357 33.333 0.00 0.00 0.00 1.85
107 108 6.000891 TCTGTCTGAATTCGATTGGTTTTG 57.999 37.500 0.04 0.00 0.00 2.44
115 117 4.743057 TGTGGATCTGTCTGAATTCGAT 57.257 40.909 0.04 0.00 0.00 3.59
145 147 3.364664 GGTCTTTCGGAATTTGGTCGTTC 60.365 47.826 0.00 0.00 0.00 3.95
161 164 2.173569 GCCATGTCTCCTATGGGTCTTT 59.826 50.000 6.19 0.00 44.21 2.52
204 207 3.974401 CAGTTTCGTTTGGTGTGCTTATG 59.026 43.478 0.00 0.00 0.00 1.90
224 227 1.688735 TGTTCTCTCCGCATATCCCAG 59.311 52.381 0.00 0.00 0.00 4.45
347 350 1.019278 CGACCACAAACCCGGATCTG 61.019 60.000 0.73 0.00 0.00 2.90
381 384 2.501602 GCTGGCAGTGGCAACCTTT 61.502 57.895 20.97 0.00 43.71 3.11
382 385 2.914097 GCTGGCAGTGGCAACCTT 60.914 61.111 20.97 0.00 43.71 3.50
393 396 4.329545 GGTGGTCTTCGGCTGGCA 62.330 66.667 1.08 0.00 0.00 4.92
410 425 1.081906 GTTGTGTGGATGTGCTGCG 60.082 57.895 0.00 0.00 0.00 5.18
419 434 2.158127 TCTAGGTTAGGGGTTGTGTGGA 60.158 50.000 0.00 0.00 0.00 4.02
420 435 2.262637 TCTAGGTTAGGGGTTGTGTGG 58.737 52.381 0.00 0.00 0.00 4.17
427 442 2.238898 GTTGTGCATCTAGGTTAGGGGT 59.761 50.000 0.00 0.00 0.00 4.95
436 457 1.089920 GTGGGCTGTTGTGCATCTAG 58.910 55.000 0.00 0.00 34.04 2.43
437 458 0.322456 GGTGGGCTGTTGTGCATCTA 60.322 55.000 0.00 0.00 34.04 1.98
459 480 3.319198 TCCTGTTCGTGGAGGGCC 61.319 66.667 0.00 0.00 0.00 5.80
468 489 3.966026 GACGGCGAGGTCCTGTTCG 62.966 68.421 16.62 0.00 39.69 3.95
501 522 4.675029 ACGTCACCGGGGAAAGCG 62.675 66.667 8.74 11.52 38.78 4.68
518 539 1.203287 CATGTTCTCACTCTCTCGCCA 59.797 52.381 0.00 0.00 0.00 5.69
533 554 1.221840 CCTAGCCGCCACTCATGTT 59.778 57.895 0.00 0.00 0.00 2.71
545 566 1.705873 TCTACAAGCCTAGCCTAGCC 58.294 55.000 0.00 0.00 0.00 3.93
546 567 2.094957 CGATCTACAAGCCTAGCCTAGC 60.095 54.545 0.00 0.00 0.00 3.42
547 568 3.150767 ACGATCTACAAGCCTAGCCTAG 58.849 50.000 0.00 0.00 0.00 3.02
548 569 3.147629 GACGATCTACAAGCCTAGCCTA 58.852 50.000 0.00 0.00 0.00 3.93
549 570 1.957877 GACGATCTACAAGCCTAGCCT 59.042 52.381 0.00 0.00 0.00 4.58
601 622 0.039527 GTTGGCAGTAAGCAAACGGG 60.040 55.000 0.00 0.00 46.52 5.28
619 640 2.011122 TCGGAAAAGAGAGGAGTGGT 57.989 50.000 0.00 0.00 0.00 4.16
653 676 2.412089 ACAAACAAGACGCGAGCTATTC 59.588 45.455 15.93 0.00 0.00 1.75
661 684 0.657368 GGCAAGACAAACAAGACGCG 60.657 55.000 3.53 3.53 0.00 6.01
711 735 2.563976 CAGCGACGAACAAGACAAATG 58.436 47.619 0.00 0.00 0.00 2.32
715 739 1.954146 GGCAGCGACGAACAAGACA 60.954 57.895 0.00 0.00 0.00 3.41
718 742 3.036084 ACGGCAGCGACGAACAAG 61.036 61.111 10.68 0.00 35.20 3.16
784 812 4.752879 TGGTAAGTGAGCGGCCGC 62.753 66.667 42.34 42.34 42.33 6.53
810 840 4.864334 CGCTGGCCCCACTGGATC 62.864 72.222 0.00 0.00 35.39 3.36
831 861 3.788766 GTGGCGCCGTGCTAACTG 61.789 66.667 23.90 0.00 45.43 3.16
957 987 3.862291 GCTTGAGCTTCACGAGGATTCG 61.862 54.545 0.00 0.00 44.39 3.34
960 990 3.450028 GCTTGAGCTTCACGAGGAT 57.550 52.632 0.00 0.00 38.21 3.24
974 1004 2.537625 CGCTTCCTCGAGAATAAGCTTG 59.462 50.000 28.48 18.30 41.67 4.01
984 1014 2.105128 ATTCGCCGCTTCCTCGAG 59.895 61.111 5.13 5.13 33.56 4.04
986 1016 3.264897 CCATTCGCCGCTTCCTCG 61.265 66.667 0.00 0.00 0.00 4.63
987 1017 1.884926 CTCCATTCGCCGCTTCCTC 60.885 63.158 0.00 0.00 0.00 3.71
998 1028 2.541556 GTTGACTACCTCGCTCCATTC 58.458 52.381 0.00 0.00 0.00 2.67
1007 1037 1.448013 GGCTGGCGTTGACTACCTC 60.448 63.158 0.00 0.00 0.00 3.85
1023 1053 2.666596 ATTTGGCGGAGATCGAGGGC 62.667 60.000 0.00 0.00 42.43 5.19
1046 1080 0.733150 GGCACGAAACTAATGGAGGC 59.267 55.000 0.00 0.00 0.00 4.70
1048 1082 3.270027 TCATGGCACGAAACTAATGGAG 58.730 45.455 0.00 0.00 0.00 3.86
1056 1090 3.242870 GGAATGAGATCATGGCACGAAAC 60.243 47.826 0.00 0.00 36.56 2.78
1059 1094 1.202687 GGGAATGAGATCATGGCACGA 60.203 52.381 0.00 0.00 36.56 4.35
1100 1135 6.292381 GCAACCATCGTAAACTGTGAGATATC 60.292 42.308 0.00 0.00 0.00 1.63
1109 1144 2.151202 ACCTGCAACCATCGTAAACTG 58.849 47.619 0.00 0.00 0.00 3.16
1110 1145 2.561478 ACCTGCAACCATCGTAAACT 57.439 45.000 0.00 0.00 0.00 2.66
1117 1152 2.629051 GGTGTACTACCTGCAACCATC 58.371 52.381 7.10 0.00 46.51 3.51
1129 1164 4.751060 CAAGCAAATACTCCGGTGTACTA 58.249 43.478 18.11 0.00 0.00 1.82
1131 1166 2.095372 GCAAGCAAATACTCCGGTGTAC 59.905 50.000 18.11 6.25 0.00 2.90
1132 1167 2.289756 TGCAAGCAAATACTCCGGTGTA 60.290 45.455 18.06 18.06 0.00 2.90
1133 1168 1.165270 GCAAGCAAATACTCCGGTGT 58.835 50.000 14.50 14.50 0.00 4.16
1136 1171 2.016318 TGATGCAAGCAAATACTCCGG 58.984 47.619 0.00 0.00 0.00 5.14
1137 1172 3.313249 TGATGATGCAAGCAAATACTCCG 59.687 43.478 0.00 0.00 33.49 4.63
1139 1174 4.201980 TGCTGATGATGCAAGCAAATACTC 60.202 41.667 7.55 0.00 33.49 2.59
1140 1175 3.697542 TGCTGATGATGCAAGCAAATACT 59.302 39.130 7.55 0.00 33.49 2.12
1141 1176 4.036567 TGCTGATGATGCAAGCAAATAC 57.963 40.909 7.55 0.00 33.49 1.89
1221 1256 1.269257 CGATTAGCATCGTCTGGCTGA 60.269 52.381 0.00 0.00 46.23 4.26
1222 1257 1.135046 CGATTAGCATCGTCTGGCTG 58.865 55.000 0.00 0.00 46.23 4.85
1223 1258 3.577231 CGATTAGCATCGTCTGGCT 57.423 52.632 0.00 0.00 46.23 4.75
1249 1284 1.270893 ACGGCCAAGAGAAGAAGGTTC 60.271 52.381 2.24 0.00 0.00 3.62
1263 1298 1.725557 GCTCGAGACATAGACGGCCA 61.726 60.000 18.75 0.00 0.00 5.36
1264 1299 1.008309 GCTCGAGACATAGACGGCC 60.008 63.158 18.75 0.00 0.00 6.13
1268 1303 1.028905 AGCAGGCTCGAGACATAGAC 58.971 55.000 22.94 4.41 0.00 2.59
1317 1352 3.134792 GCTCTCTCGCCCTGACGA 61.135 66.667 0.00 0.00 40.36 4.20
1327 1362 2.275318 CACGGAAATGGAAGCTCTCTC 58.725 52.381 0.00 0.00 0.00 3.20
1328 1363 1.677217 GCACGGAAATGGAAGCTCTCT 60.677 52.381 0.00 0.00 0.00 3.10
1330 1365 1.021390 CGCACGGAAATGGAAGCTCT 61.021 55.000 0.00 0.00 0.00 4.09
1333 1368 2.202479 GCGCACGGAAATGGAAGC 60.202 61.111 0.30 0.00 0.00 3.86
1448 1483 1.676006 CACCCACACAAAACCTCTCAC 59.324 52.381 0.00 0.00 0.00 3.51
1456 1491 2.096248 GACAAGGACACCCACACAAAA 58.904 47.619 0.00 0.00 33.88 2.44
1472 1507 1.111116 ACGACCAAGGAGACCGACAA 61.111 55.000 0.00 0.00 0.00 3.18
1480 1515 2.572284 GGACGGACGACCAAGGAG 59.428 66.667 8.26 0.00 35.59 3.69
1578 1613 1.442769 CAGATTTCCACCCGTCACAG 58.557 55.000 0.00 0.00 0.00 3.66
1581 1616 0.838554 TCCCAGATTTCCACCCGTCA 60.839 55.000 0.00 0.00 0.00 4.35
1913 1957 1.287425 CTCGTTTTATGCGACTCCCC 58.713 55.000 0.00 0.00 34.47 4.81
2056 2100 0.818445 TCTCCTGCCGATCGGAGTAC 60.818 60.000 37.64 19.76 45.57 2.73
2075 2119 2.300967 TGCCAAGATCCCGCTCCTT 61.301 57.895 0.00 0.00 0.00 3.36
2311 2355 2.183555 CAGTACGGGAACTCGCCC 59.816 66.667 0.00 0.00 45.10 6.13
2340 2384 3.589881 GCACCGGCATGCTCCATC 61.590 66.667 18.92 0.00 42.62 3.51
2686 2730 1.519455 CAAGACCACGGCGGAGATC 60.519 63.158 13.24 0.00 38.63 2.75
2782 2826 1.070445 CATCCTCATGGGCTCCGAC 59.930 63.158 0.00 0.00 34.39 4.79
2812 2856 1.414181 ACCTGGATCATGACGGACATC 59.586 52.381 0.00 0.00 37.07 3.06
2818 2862 1.208052 ACCTTGACCTGGATCATGACG 59.792 52.381 0.00 0.00 0.00 4.35
2923 2967 4.624364 TGGTGCACGTCCAGGCAG 62.624 66.667 11.45 0.00 41.35 4.85
2924 2968 4.927782 GTGGTGCACGTCCAGGCA 62.928 66.667 11.45 0.00 35.49 4.75
2939 2983 3.114616 CCAGCTGAAGACGCCGTG 61.115 66.667 17.39 0.00 0.00 4.94
3004 3048 2.434884 ATCTTCTGCCCGTGCGTG 60.435 61.111 0.00 0.00 41.78 5.34
3007 3051 3.567797 GCGATCTTCTGCCCGTGC 61.568 66.667 0.00 0.00 38.26 5.34
3110 3154 3.187022 GTGCAAGGAAATTGGTTCAATGC 59.813 43.478 0.00 7.83 43.95 3.56
3112 3156 4.686191 TGTGCAAGGAAATTGGTTCAAT 57.314 36.364 0.00 0.00 39.47 2.57
3505 3577 4.488770 AGGTTTGAGAAGGAGAAGAGTCT 58.511 43.478 0.00 0.00 36.55 3.24
3536 3614 0.535335 ACGATCTGTAACCGTGGCAT 59.465 50.000 0.00 0.00 35.02 4.40
3537 3615 0.319083 AACGATCTGTAACCGTGGCA 59.681 50.000 0.00 0.00 36.58 4.92
3538 3616 1.435577 AAACGATCTGTAACCGTGGC 58.564 50.000 0.00 0.00 36.58 5.01
3539 3617 3.061322 TGAAAACGATCTGTAACCGTGG 58.939 45.455 0.00 0.00 36.58 4.94
3540 3618 4.435518 CCATGAAAACGATCTGTAACCGTG 60.436 45.833 0.00 0.00 36.58 4.94
3541 3619 3.682858 CCATGAAAACGATCTGTAACCGT 59.317 43.478 0.00 0.00 38.24 4.83
3631 3712 3.423123 GGAACTCAACTTGATGCGTTACG 60.423 47.826 0.00 0.00 28.99 3.18
3751 3832 3.813443 CCCTTCTCCATGACCTAACATG 58.187 50.000 0.00 0.00 44.78 3.21
3752 3833 2.173569 GCCCTTCTCCATGACCTAACAT 59.826 50.000 0.00 0.00 0.00 2.71
3830 3911 1.082496 GTGAGCGTTGACAAGCTGC 60.082 57.895 14.33 7.62 44.69 5.25
3887 3968 0.036010 ACTGAACCATGGCTCCTTCG 60.036 55.000 13.04 7.27 0.00 3.79
3900 3981 1.880027 CCTTGGCTGTTGGTACTGAAC 59.120 52.381 0.00 0.00 0.00 3.18
3983 4064 2.015081 CTCCCTCTCCTCCTCCTGT 58.985 63.158 0.00 0.00 0.00 4.00
4016 4097 4.689345 ACGTAGTCCTTGTATGTTTTCAGC 59.311 41.667 0.00 0.00 29.74 4.26
4051 4132 3.787001 CGAGGAGGAACCAGCCCC 61.787 72.222 0.00 0.00 42.04 5.80
4067 4148 3.690139 ACTGTGTGAGTACTATGAGGACG 59.310 47.826 0.00 0.00 30.86 4.79
4164 4245 2.015587 GTAGACTCCAACGACGATCCT 58.984 52.381 0.00 0.00 0.00 3.24
4175 4256 0.678684 TCATCACCGCGTAGACTCCA 60.679 55.000 4.92 0.00 0.00 3.86
4220 4301 2.328099 GGCAACAAGGCTCCTCACG 61.328 63.158 0.00 0.00 40.24 4.35
4238 4319 2.048222 TTGAGGCCGAAGTGAGCG 60.048 61.111 0.00 0.00 0.00 5.03
4277 4358 3.501828 TGAACACAGAATCCATGAAACCG 59.498 43.478 0.00 0.00 0.00 4.44
4292 4373 1.228831 CATGGGGGCCTTGAACACA 60.229 57.895 0.84 0.00 31.33 3.72
4337 4418 1.276421 CATACCCGGGTCATGATCCTC 59.724 57.143 34.27 0.00 0.00 3.71
4365 4446 7.951591 AGTATGGCTGAAAAAGTTGTGTTAAT 58.048 30.769 0.00 0.00 0.00 1.40
4384 4470 7.063426 CAGTAACATCGGCATATACAAGTATGG 59.937 40.741 3.06 0.00 33.61 2.74
4392 4478 4.556233 TCTGCAGTAACATCGGCATATAC 58.444 43.478 14.67 0.00 37.80 1.47
4592 4678 0.168788 CACCAATTACAGCAGGCACG 59.831 55.000 0.00 0.00 0.00 5.34
4595 4681 2.095059 CAGAACACCAATTACAGCAGGC 60.095 50.000 0.00 0.00 0.00 4.85
4604 4690 5.241506 CACCTGAATGTACAGAACACCAATT 59.758 40.000 0.33 0.00 42.09 2.32
4610 4696 3.070878 TGCTCACCTGAATGTACAGAACA 59.929 43.478 0.33 0.65 43.86 3.18
4633 4719 2.827322 TGAATGCAGGGTTCTTTCATGG 59.173 45.455 0.00 0.00 0.00 3.66
4672 4762 4.216042 CAGTAGCATTGTTCACACATTGGA 59.784 41.667 0.00 0.00 35.60 3.53
4749 4839 3.943691 ACGGGCGCCTTTGTGGTA 61.944 61.111 28.56 0.00 38.35 3.25
4776 4866 1.884464 GAGCATCGATTCAGCGGCA 60.884 57.895 1.45 0.00 0.00 5.69
4821 4911 3.938963 TCTGAATGAACCTATTTGTCGCC 59.061 43.478 0.00 0.00 0.00 5.54
4872 4962 6.437928 TGCATTTGTGTAGAAGAACATTGTC 58.562 36.000 0.00 0.00 0.00 3.18
5003 5093 8.034313 TGAAGTACTCAGCCCTGAATAATATT 57.966 34.615 0.00 0.00 39.39 1.28
5028 5118 7.309377 GGCACACCATATTTCTGCACATTATAT 60.309 37.037 0.00 0.00 35.26 0.86
5029 5119 6.016360 GGCACACCATATTTCTGCACATTATA 60.016 38.462 0.00 0.00 35.26 0.98
5081 5176 2.423373 GGCATAGCCCAAGAAATCCTGA 60.423 50.000 0.00 0.00 44.06 3.86
5128 5223 2.774044 TGTCAAGAACACTTGCGCA 58.226 47.368 5.66 5.66 40.28 6.09
5146 5241 6.531503 TTCTCCAGATTTGAGTAGAATCGT 57.468 37.500 0.00 0.00 38.29 3.73
5207 5302 1.967066 CGGAGGCTCAGATGGTAGATT 59.033 52.381 17.69 0.00 0.00 2.40
5231 5326 2.093075 CAGGCCTTCTGTCACTGATGAT 60.093 50.000 0.00 0.00 37.14 2.45
5233 5328 1.735386 CAGGCCTTCTGTCACTGATG 58.265 55.000 0.00 0.00 38.64 3.07
5314 5409 2.827800 TGAGCTGGTTGTCTCTTGAG 57.172 50.000 0.00 0.00 0.00 3.02
5343 5438 5.571784 ACATGGCATGACACTTTAGAATG 57.428 39.130 32.74 0.00 0.00 2.67
5344 5439 6.594788 AAACATGGCATGACACTTTAGAAT 57.405 33.333 32.74 3.68 0.00 2.40
5349 5444 5.021033 TGAAAAACATGGCATGACACTTT 57.979 34.783 32.74 22.30 0.00 2.66
5359 5454 3.733443 ACTTGACCTGAAAAACATGGC 57.267 42.857 0.00 0.00 0.00 4.40
5628 5727 1.586564 GAGGATCGACGTTGCTCCG 60.587 63.158 17.85 3.72 32.87 4.63
5683 5782 7.716799 TTTCAGAATATGGTAAATTGTGGCT 57.283 32.000 0.00 0.00 30.67 4.75
5684 5783 8.416329 AGATTTCAGAATATGGTAAATTGTGGC 58.584 33.333 0.00 0.00 30.67 5.01
5767 5866 1.537776 GCGTGTCAGGATCAGGATCAG 60.538 57.143 11.12 3.64 39.54 2.90
5786 5885 1.068055 CAATGCCTGTGAAAGACCAGC 60.068 52.381 0.00 0.00 0.00 4.85
5796 5895 2.857592 GCACTTATCCAATGCCTGTG 57.142 50.000 0.00 0.00 33.06 3.66
5803 5902 4.922206 TCTTCAACTGGCACTTATCCAAT 58.078 39.130 0.00 0.00 32.41 3.16
5830 5929 3.971245 AGTTCAGGAAGGACACTGATC 57.029 47.619 0.00 0.00 42.73 2.92
5890 5989 7.976734 GCTTCATTTCATACAGTAGTGAGTACT 59.023 37.037 4.09 0.00 43.31 2.73
5891 5990 7.759886 TGCTTCATTTCATACAGTAGTGAGTAC 59.240 37.037 4.09 0.00 0.00 2.73
5892 5991 7.836842 TGCTTCATTTCATACAGTAGTGAGTA 58.163 34.615 4.09 0.00 0.00 2.59
5893 5992 6.701340 TGCTTCATTTCATACAGTAGTGAGT 58.299 36.000 4.09 0.00 0.00 3.41
5895 5994 6.037500 GCATGCTTCATTTCATACAGTAGTGA 59.962 38.462 11.37 0.00 0.00 3.41
5896 5995 6.197276 GCATGCTTCATTTCATACAGTAGTG 58.803 40.000 11.37 0.00 0.00 2.74
5897 5996 5.297776 GGCATGCTTCATTTCATACAGTAGT 59.702 40.000 18.92 0.00 0.00 2.73
6079 6178 2.580815 CTCTGCAGGATGGCGTCA 59.419 61.111 15.13 0.00 35.86 4.35
6198 6297 0.030773 CGCGTAGAGGCAGATGCTTA 59.969 55.000 4.59 0.00 41.70 3.09
6262 6361 5.130350 AGCTTACCTGCAACAAAGAAGTTA 58.870 37.500 5.92 0.00 34.99 2.24
6268 6368 6.595716 ACTCTATAAGCTTACCTGCAACAAAG 59.404 38.462 8.70 0.00 34.99 2.77
6350 6450 2.885135 TAGTTGGACCAGTACTCGGA 57.115 50.000 15.59 0.00 0.00 4.55
6378 6478 6.090088 CCGACAAAATTATTGATTTTTCCGCA 59.910 34.615 7.18 0.00 43.65 5.69
6387 6487 6.076981 GGATCAGCCGACAAAATTATTGAT 57.923 37.500 0.00 0.00 0.00 2.57
6420 6520 5.867174 GCCTACAGCCGACAAAATTATTTTT 59.133 36.000 0.00 0.00 33.36 1.94
6421 6521 5.185056 AGCCTACAGCCGACAAAATTATTTT 59.815 36.000 0.00 0.00 45.47 1.82
6422 6522 4.705023 AGCCTACAGCCGACAAAATTATTT 59.295 37.500 0.00 0.00 45.47 1.40
6451 6551 5.859205 AATTTTCACTTGGCAGAAGAAGT 57.141 34.783 1.93 0.00 32.48 3.01
6456 6556 6.878389 AGTTTCAAAATTTTCACTTGGCAGAA 59.122 30.769 0.00 0.00 0.00 3.02
6457 6557 6.313411 CAGTTTCAAAATTTTCACTTGGCAGA 59.687 34.615 0.00 0.00 0.00 4.26
6458 6558 6.313411 TCAGTTTCAAAATTTTCACTTGGCAG 59.687 34.615 0.00 0.00 0.00 4.85
6460 6560 6.660887 TCAGTTTCAAAATTTTCACTTGGC 57.339 33.333 0.00 0.00 0.00 4.52
6477 6577 4.499183 TCGTGCCAAACAATTTTCAGTTT 58.501 34.783 0.00 0.00 38.40 2.66
6481 6581 4.582701 ATCTCGTGCCAAACAATTTTCA 57.417 36.364 0.00 0.00 0.00 2.69
6495 6595 3.161067 ACATCTCCATCCCTATCTCGTG 58.839 50.000 0.00 0.00 0.00 4.35
6498 6598 5.954752 TGTCATACATCTCCATCCCTATCTC 59.045 44.000 0.00 0.00 0.00 2.75
6505 6605 4.679373 ACTGTGTCATACATCTCCATCC 57.321 45.455 0.00 0.00 38.92 3.51
6511 6611 5.755409 TTGGGTAACTGTGTCATACATCT 57.245 39.130 0.00 0.00 38.92 2.90
6525 6625 6.584185 ACTTCCAACATACATTTGGGTAAC 57.416 37.500 1.39 0.00 43.38 2.50
6527 6627 7.463431 ACTAACTTCCAACATACATTTGGGTA 58.537 34.615 1.39 0.00 43.38 3.69
6578 6678 2.929641 TGCATAATCCGATGAAGGCAA 58.070 42.857 1.90 0.00 0.00 4.52
6924 7024 6.642131 GCTAGATGTCAAATGCAGAAACAAAA 59.358 34.615 0.00 0.00 0.00 2.44
6925 7025 6.151691 GCTAGATGTCAAATGCAGAAACAAA 58.848 36.000 0.00 0.00 0.00 2.83
6926 7026 5.617529 CGCTAGATGTCAAATGCAGAAACAA 60.618 40.000 0.00 0.00 0.00 2.83
6927 7027 4.142838 CGCTAGATGTCAAATGCAGAAACA 60.143 41.667 0.00 0.00 0.00 2.83
6928 7028 4.142816 ACGCTAGATGTCAAATGCAGAAAC 60.143 41.667 0.00 0.00 0.00 2.78
6929 7029 4.002982 ACGCTAGATGTCAAATGCAGAAA 58.997 39.130 0.00 0.00 0.00 2.52
6964 7064 7.611467 AGCAATCCAGTTCAACAGTTCATTATA 59.389 33.333 0.00 0.00 0.00 0.98
6985 7085 3.377172 GGCAACGACATAAAGGTAGCAAT 59.623 43.478 0.00 0.00 0.00 3.56
7031 7131 2.273776 GCAAGGAGGGAAGGAGCC 59.726 66.667 0.00 0.00 0.00 4.70
7032 7132 2.273776 GGCAAGGAGGGAAGGAGC 59.726 66.667 0.00 0.00 0.00 4.70
7033 7133 1.301293 GTGGCAAGGAGGGAAGGAG 59.699 63.158 0.00 0.00 0.00 3.69
7034 7134 2.231380 GGTGGCAAGGAGGGAAGGA 61.231 63.158 0.00 0.00 0.00 3.36
7056 7156 2.164422 GCTCAAACAATTAGGCAGTCCC 59.836 50.000 0.00 0.00 0.00 4.46
7064 7164 3.612479 GCACACCAGGCTCAAACAATTAG 60.612 47.826 0.00 0.00 0.00 1.73
7082 7182 4.517285 GATTGAAAGATGGAGGTAGCACA 58.483 43.478 0.00 0.00 0.00 4.57
7105 7208 5.306937 TGTGATATCCATGGTAGGTTAGGTG 59.693 44.000 12.58 0.00 0.00 4.00
7133 7236 4.379499 GCTCGAGAAAATTTCATTTCCGGT 60.379 41.667 18.75 0.00 39.59 5.28
7143 7246 6.410540 AGACCTCTAATGCTCGAGAAAATTT 58.589 36.000 18.75 0.00 0.00 1.82
7148 7251 5.194432 ACTAAGACCTCTAATGCTCGAGAA 58.806 41.667 18.75 5.90 0.00 2.87
7150 7253 5.298276 AGAACTAAGACCTCTAATGCTCGAG 59.702 44.000 8.45 8.45 0.00 4.04
7217 7322 1.082104 GTAAATAGCATGCGGCCGC 60.082 57.895 42.35 42.35 46.50 6.53
7253 7358 6.732531 TGTGCTAATGTGAGAGATCAAAAG 57.267 37.500 0.00 0.00 0.00 2.27
7282 7387 8.477419 AGAGACATTTTTAACCAAGGAATGAA 57.523 30.769 0.00 0.00 33.24 2.57
7316 7427 3.216800 ACAACTGATCTTGTGCACATGT 58.783 40.909 26.47 19.35 32.95 3.21
7319 7430 2.807967 GCTACAACTGATCTTGTGCACA 59.192 45.455 17.42 17.42 35.87 4.57
7322 7433 4.756084 AAAGCTACAACTGATCTTGTGC 57.244 40.909 9.89 10.59 35.87 4.57
7326 7437 6.650807 TCATTCGAAAAGCTACAACTGATCTT 59.349 34.615 0.00 0.00 0.00 2.40
7333 7444 5.177696 ACTGTCTCATTCGAAAAGCTACAAC 59.822 40.000 0.00 0.00 0.00 3.32
7338 7449 3.733337 ACACTGTCTCATTCGAAAAGCT 58.267 40.909 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.