Multiple sequence alignment - TraesCS1A01G088900

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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 TraesCS1A01G088900 chr1A 100.000 5740 0 0 1 5740 77102902 77108641 0.000000e+00 10600.0
1 TraesCS1A01G088900 chr1A 89.595 519 25 9 5241 5740 583126172 583125664 2.920000e-177 632.0
2 TraesCS1A01G088900 chr1A 84.163 221 30 4 4977 5193 559461041 559460822 5.830000e-50 209.0
3 TraesCS1A01G088900 chr1B 94.035 3705 171 20 847 4520 119883253 119886938 0.000000e+00 5572.0
4 TraesCS1A01G088900 chr1B 94.256 679 32 5 4519 5193 119886969 119887644 0.000000e+00 1031.0
5 TraesCS1A01G088900 chr1B 81.608 821 134 12 47 860 119881033 119881843 0.000000e+00 664.0
6 TraesCS1A01G088900 chr1B 95.122 41 0 2 1 39 119803443 119803483 4.800000e-06 63.9
7 TraesCS1A01G088900 chr1D 95.163 3163 116 19 1382 4520 76498835 76501984 0.000000e+00 4959.0
8 TraesCS1A01G088900 chr1D 94.551 679 30 4 4519 5193 76502016 76502691 0.000000e+00 1042.0
9 TraesCS1A01G088900 chr1D 95.785 522 14 4 881 1400 76498303 76498818 0.000000e+00 835.0
10 TraesCS1A01G088900 chr1D 84.688 640 89 6 1 633 76497243 76497880 1.050000e-176 630.0
11 TraesCS1A01G088900 chr1D 83.857 223 28 5 4977 5193 52847671 52847451 7.540000e-49 206.0
12 TraesCS1A01G088900 chr6A 94.685 508 19 3 5240 5740 390649894 390650400 0.000000e+00 782.0
13 TraesCS1A01G088900 chr6A 92.500 520 22 5 5237 5740 453910157 453909639 0.000000e+00 728.0
14 TraesCS1A01G088900 chr6A 91.506 518 28 5 5239 5740 401211067 401210550 0.000000e+00 699.0
15 TraesCS1A01G088900 chr6A 91.634 514 25 7 5242 5740 86402666 86403176 0.000000e+00 695.0
16 TraesCS1A01G088900 chr7A 94.291 508 18 6 5240 5740 538169455 538169958 0.000000e+00 767.0
17 TraesCS1A01G088900 chr7A 92.816 515 20 5 5242 5740 543441753 543441240 0.000000e+00 730.0
18 TraesCS1A01G088900 chr7A 92.636 516 22 4 5241 5740 632189967 632189452 0.000000e+00 728.0
19 TraesCS1A01G088900 chr7A 92.412 514 23 4 5242 5740 573610016 573609504 0.000000e+00 719.0
20 TraesCS1A01G088900 chr3A 92.650 517 19 7 5241 5740 311448305 311448819 0.000000e+00 726.0
21 TraesCS1A01G088900 chr3A 92.233 515 25 7 5239 5740 714770688 714771200 0.000000e+00 715.0
22 TraesCS1A01G088900 chr3A 91.137 519 27 9 5238 5740 131574731 131575246 0.000000e+00 686.0
23 TraesCS1A01G088900 chr2A 92.039 515 25 5 5241 5740 636058787 636058274 0.000000e+00 710.0
24 TraesCS1A01G088900 chr2A 91.396 523 25 7 5237 5740 81078237 81078758 0.000000e+00 699.0
25 TraesCS1A01G088900 chr5B 84.475 219 28 4 4979 5193 247883565 247883781 1.620000e-50 211.0
26 TraesCS1A01G088900 chr5B 84.475 219 29 3 4979 5193 248057326 248057543 1.620000e-50 211.0
27 TraesCS1A01G088900 chr6D 84.163 221 29 4 4977 5193 458773207 458773425 5.830000e-50 209.0
28 TraesCS1A01G088900 chr5D 83.258 221 32 3 4977 5193 78584925 78584706 1.260000e-46 198.0
29 TraesCS1A01G088900 chr4B 83.258 221 32 4 4977 5193 176158607 176158826 1.260000e-46 198.0


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 TraesCS1A01G088900 chr1A 77102902 77108641 5739 False 10600.000000 10600 100.000000 1 5740 1 chr1A.!!$F1 5739
1 TraesCS1A01G088900 chr1A 583125664 583126172 508 True 632.000000 632 89.595000 5241 5740 1 chr1A.!!$R2 499
2 TraesCS1A01G088900 chr1B 119881033 119887644 6611 False 2422.333333 5572 89.966333 47 5193 3 chr1B.!!$F2 5146
3 TraesCS1A01G088900 chr1D 76497243 76502691 5448 False 1866.500000 4959 92.546750 1 5193 4 chr1D.!!$F1 5192
4 TraesCS1A01G088900 chr6A 390649894 390650400 506 False 782.000000 782 94.685000 5240 5740 1 chr6A.!!$F2 500
5 TraesCS1A01G088900 chr6A 453909639 453910157 518 True 728.000000 728 92.500000 5237 5740 1 chr6A.!!$R2 503
6 TraesCS1A01G088900 chr6A 401210550 401211067 517 True 699.000000 699 91.506000 5239 5740 1 chr6A.!!$R1 501
7 TraesCS1A01G088900 chr6A 86402666 86403176 510 False 695.000000 695 91.634000 5242 5740 1 chr6A.!!$F1 498
8 TraesCS1A01G088900 chr7A 538169455 538169958 503 False 767.000000 767 94.291000 5240 5740 1 chr7A.!!$F1 500
9 TraesCS1A01G088900 chr7A 543441240 543441753 513 True 730.000000 730 92.816000 5242 5740 1 chr7A.!!$R1 498
10 TraesCS1A01G088900 chr7A 632189452 632189967 515 True 728.000000 728 92.636000 5241 5740 1 chr7A.!!$R3 499
11 TraesCS1A01G088900 chr7A 573609504 573610016 512 True 719.000000 719 92.412000 5242 5740 1 chr7A.!!$R2 498
12 TraesCS1A01G088900 chr3A 311448305 311448819 514 False 726.000000 726 92.650000 5241 5740 1 chr3A.!!$F2 499
13 TraesCS1A01G088900 chr3A 714770688 714771200 512 False 715.000000 715 92.233000 5239 5740 1 chr3A.!!$F3 501
14 TraesCS1A01G088900 chr3A 131574731 131575246 515 False 686.000000 686 91.137000 5238 5740 1 chr3A.!!$F1 502
15 TraesCS1A01G088900 chr2A 636058274 636058787 513 True 710.000000 710 92.039000 5241 5740 1 chr2A.!!$R1 499
16 TraesCS1A01G088900 chr2A 81078237 81078758 521 False 699.000000 699 91.396000 5237 5740 1 chr2A.!!$F1 503

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
654 799 0.035439 GTGGAGAGGCCGAAATTGGA 60.035 55.000 0.00 0.00 40.66 3.53 F
860 1007 0.099968 TCGATAAGTTGGAGTCGGCG 59.900 55.000 0.00 0.00 35.01 6.46 F
915 2518 0.803380 AATACTAACGCCGTGACCGC 60.803 55.000 0.00 0.00 0.00 5.68 F
2079 3731 1.068333 CGACACAAAAGCTGGGGATTG 60.068 52.381 0.00 0.00 29.87 2.67 F
2432 4084 1.466856 ATGCTGCAACGTTGGATGAT 58.533 45.000 28.33 17.11 0.00 2.45 F
4166 5838 0.181587 TGAAAAAGCACTCCCGTCCA 59.818 50.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 3121 0.456221 TTCTAGCAGTAGCACTCGGC 59.544 55.000 0.00 0.0 45.49 5.54 R
2041 3693 1.073125 TCGCCAACTCCTTCAATCCAA 59.927 47.619 0.00 0.0 0.00 3.53 R
2432 4084 1.217689 CCCCATGGCTAATTCCCTTCA 59.782 52.381 6.09 0.0 0.00 3.02 R
3968 5640 0.899720 TTACCTGCACTTCTACCCCG 59.100 55.000 0.00 0.0 0.00 5.73 R
4344 6018 1.802960 GTGTGGCAGTTCTGATGAGTG 59.197 52.381 3.84 0.0 0.00 3.51 R
5196 6914 0.323542 TCCCCAACCAAACACGTTGT 60.324 50.000 0.00 0.0 39.16 3.32 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
41 42 2.970639 TTCCAGACGAGGAAGCCG 59.029 61.111 4.98 0.00 42.56 5.52
120 121 6.491383 AGAGGGCGGTATCTTATATAAGACA 58.509 40.000 24.17 12.90 44.30 3.41
124 125 5.421374 GGCGGTATCTTATATAAGACAGGGT 59.579 44.000 24.17 12.62 44.30 4.34
186 188 1.608801 CCGTACTTTGTACACCCCCAC 60.609 57.143 0.00 0.00 0.00 4.61
193 195 0.251121 TGTACACCCCCACTGCAATG 60.251 55.000 0.00 0.00 0.00 2.82
206 208 0.510790 TGCAATGTACAACACGAGCG 59.489 50.000 0.00 0.00 0.00 5.03
254 256 4.079212 AGGGCATAAACATGGATAAGTGGT 60.079 41.667 0.00 0.00 0.00 4.16
257 259 5.127031 GGCATAAACATGGATAAGTGGTTGT 59.873 40.000 0.00 0.00 0.00 3.32
260 262 5.467035 AAACATGGATAAGTGGTTGTTGG 57.533 39.130 0.00 0.00 0.00 3.77
274 276 0.250467 TGTTGGCTGCTCCTCTCAAC 60.250 55.000 0.00 4.99 38.41 3.18
279 281 0.036022 GCTGCTCCTCTCAACCAGTT 59.964 55.000 0.00 0.00 0.00 3.16
282 284 1.202806 TGCTCCTCTCAACCAGTTTGG 60.203 52.381 0.00 0.00 45.02 3.28
323 325 3.508793 TCGGAGTGACGAATTCTTACCTT 59.491 43.478 3.52 0.00 40.34 3.50
332 334 6.129053 ACGAATTCTTACCTTACTAGACGG 57.871 41.667 3.52 0.00 0.00 4.79
333 335 5.649831 ACGAATTCTTACCTTACTAGACGGT 59.350 40.000 3.52 2.10 34.86 4.83
336 338 7.468357 CGAATTCTTACCTTACTAGACGGTGAT 60.468 40.741 3.52 0.00 32.36 3.06
344 346 1.663379 CTAGACGGTGATGGGCGTGA 61.663 60.000 0.00 0.00 0.00 4.35
358 360 1.587933 GCGTGAAGGAGTCTCGACCT 61.588 60.000 2.32 0.00 44.19 3.85
359 362 0.169230 CGTGAAGGAGTCTCGACCTG 59.831 60.000 0.00 0.00 44.19 4.00
364 367 0.605589 AGGAGTCTCGACCTGCAAAG 59.394 55.000 0.00 0.00 34.99 2.77
384 387 1.827789 GCTGAACACCTTGTGGGCA 60.828 57.895 0.00 0.00 37.94 5.36
394 397 0.321564 CTTGTGGGCAACGATGGAGA 60.322 55.000 0.00 0.00 37.60 3.71
410 413 2.733593 GACGGGTGTGCACGAGTC 60.734 66.667 13.13 14.09 45.97 3.36
447 454 2.676121 TTGGCCCGTTCATGCAGG 60.676 61.111 0.00 0.00 0.00 4.85
457 464 1.002430 GTTCATGCAGGAGGTCTGTCA 59.998 52.381 0.00 0.00 45.08 3.58
483 490 2.125326 CATCCTCCGGCGGTGACTA 61.125 63.158 27.97 13.75 0.00 2.59
506 514 3.031736 GAGGTAGAGGTGGTATGCTGAA 58.968 50.000 0.00 0.00 0.00 3.02
530 538 3.387947 CGGCGACCCTGGGTAAGT 61.388 66.667 20.61 0.00 35.25 2.24
547 555 5.420104 GGGTAAGTAGGCTTTGTAGTACTCA 59.580 44.000 0.00 0.00 36.22 3.41
554 562 3.057736 GGCTTTGTAGTACTCAGACGACA 60.058 47.826 0.00 0.00 33.76 4.35
555 563 3.913163 GCTTTGTAGTACTCAGACGACAC 59.087 47.826 0.00 0.00 35.10 3.67
559 567 1.888215 AGTACTCAGACGACACCGAA 58.112 50.000 0.00 0.00 39.50 4.30
562 570 2.589798 ACTCAGACGACACCGAAAAA 57.410 45.000 0.00 0.00 39.50 1.94
603 611 3.799755 GGCGTTGGTGGATGCGAC 61.800 66.667 0.00 0.00 32.29 5.19
625 770 2.652095 GGTGGTCCGGTCGATGGAA 61.652 63.158 10.56 0.00 37.23 3.53
638 783 4.776322 TGGAAGCGGCGATGGTGG 62.776 66.667 12.98 0.00 0.00 4.61
650 795 0.181350 GATGGTGGAGAGGCCGAAAT 59.819 55.000 0.00 0.00 40.66 2.17
654 799 0.035439 GTGGAGAGGCCGAAATTGGA 60.035 55.000 0.00 0.00 40.66 3.53
659 805 1.133976 AGAGGCCGAAATTGGATGAGG 60.134 52.381 0.00 0.00 0.00 3.86
661 807 0.395724 GGCCGAAATTGGATGAGGGT 60.396 55.000 0.00 0.00 0.00 4.34
670 816 0.970937 TGGATGAGGGTGACGAGGAC 60.971 60.000 0.00 0.00 0.00 3.85
671 817 0.970937 GGATGAGGGTGACGAGGACA 60.971 60.000 0.00 0.00 0.00 4.02
691 838 0.474184 ACAAGGTCAGGTGTGGAAGG 59.526 55.000 0.00 0.00 0.00 3.46
700 847 0.996583 GGTGTGGAAGGGGGTAATGA 59.003 55.000 0.00 0.00 0.00 2.57
718 865 3.737032 TGACCGTTGTGTCACAGATAA 57.263 42.857 5.67 0.00 40.22 1.75
729 876 0.471617 CACAGATAAGCCAGGGGAGG 59.528 60.000 0.00 0.00 0.00 4.30
736 883 0.772124 AAGCCAGGGGAGGACAAAGA 60.772 55.000 0.00 0.00 0.00 2.52
737 884 0.772124 AGCCAGGGGAGGACAAAGAA 60.772 55.000 0.00 0.00 0.00 2.52
740 887 1.272147 CCAGGGGAGGACAAAGAAAGG 60.272 57.143 0.00 0.00 0.00 3.11
742 889 2.108250 CAGGGGAGGACAAAGAAAGGAA 59.892 50.000 0.00 0.00 0.00 3.36
744 891 2.108425 GGGGAGGACAAAGAAAGGAAGT 59.892 50.000 0.00 0.00 0.00 3.01
759 906 1.627550 GAAGTCGTGGGCTTTCGCTC 61.628 60.000 0.00 0.00 37.07 5.03
761 908 3.676605 TCGTGGGCTTTCGCTCGA 61.677 61.111 3.15 3.15 44.73 4.04
766 913 2.517450 GGGCTTTCGCTCGATGTCG 61.517 63.158 0.00 0.00 41.45 4.35
779 926 4.976224 TCGATGTCGATGAGTTCCTTTA 57.024 40.909 0.21 0.00 44.22 1.85
780 927 5.515797 TCGATGTCGATGAGTTCCTTTAT 57.484 39.130 0.21 0.00 44.22 1.40
781 928 6.628919 TCGATGTCGATGAGTTCCTTTATA 57.371 37.500 0.21 0.00 44.22 0.98
785 932 5.769367 TGTCGATGAGTTCCTTTATATCGG 58.231 41.667 0.00 0.00 38.26 4.18
788 935 2.750948 TGAGTTCCTTTATATCGGCGC 58.249 47.619 0.00 0.00 0.00 6.53
794 941 2.553602 TCCTTTATATCGGCGCGTTAGA 59.446 45.455 8.43 5.28 0.00 2.10
795 942 2.660236 CCTTTATATCGGCGCGTTAGAC 59.340 50.000 8.43 0.00 0.00 2.59
796 943 3.302555 CTTTATATCGGCGCGTTAGACA 58.697 45.455 8.43 0.00 0.00 3.41
797 944 2.606717 TATATCGGCGCGTTAGACAG 57.393 50.000 8.43 0.00 0.00 3.51
799 946 1.298602 TATCGGCGCGTTAGACAGTA 58.701 50.000 8.43 0.00 0.00 2.74
800 947 0.666913 ATCGGCGCGTTAGACAGTAT 59.333 50.000 8.43 0.00 0.00 2.12
802 949 1.135315 TCGGCGCGTTAGACAGTATTT 60.135 47.619 8.43 0.00 0.00 1.40
804 951 2.093152 CGGCGCGTTAGACAGTATTTTT 59.907 45.455 8.43 0.00 0.00 1.94
832 979 6.310224 GCTACGCAAATTTAAATGGACACAAT 59.690 34.615 0.39 0.00 0.00 2.71
835 982 8.594881 ACGCAAATTTAAATGGACACAATAAA 57.405 26.923 0.39 0.00 0.00 1.40
856 1003 3.821421 ATGGGTCGATAAGTTGGAGTC 57.179 47.619 0.00 0.00 0.00 3.36
860 1007 0.099968 TCGATAAGTTGGAGTCGGCG 59.900 55.000 0.00 0.00 35.01 6.46
861 1008 0.870307 CGATAAGTTGGAGTCGGCGG 60.870 60.000 7.21 0.00 0.00 6.13
902 2505 7.961283 CGTCAAAATATCTCGATCGGAATACTA 59.039 37.037 16.41 1.74 0.00 1.82
914 2517 1.194495 GAATACTAACGCCGTGACCG 58.806 55.000 0.00 0.00 0.00 4.79
915 2518 0.803380 AATACTAACGCCGTGACCGC 60.803 55.000 0.00 0.00 0.00 5.68
916 2519 1.660560 ATACTAACGCCGTGACCGCT 61.661 55.000 0.00 0.00 0.00 5.52
917 2520 1.865788 TACTAACGCCGTGACCGCTT 61.866 55.000 0.00 0.00 0.00 4.68
918 2521 2.025418 CTAACGCCGTGACCGCTTT 61.025 57.895 0.00 0.00 0.00 3.51
989 2598 2.100631 CCAAATCGCGCGACCTCTT 61.101 57.895 37.37 22.92 0.00 2.85
1120 2729 5.590259 CAGTAACCGATTGATCCCAATTTCT 59.410 40.000 0.00 0.00 42.66 2.52
1146 2755 3.507233 TGGTAGTACGATCGGTTCTGTTT 59.493 43.478 20.98 0.00 0.00 2.83
1155 2764 3.553828 TCGGTTCTGTTTCTTGACCTT 57.446 42.857 0.00 0.00 0.00 3.50
1158 2767 4.703093 TCGGTTCTGTTTCTTGACCTTTTT 59.297 37.500 0.00 0.00 0.00 1.94
1160 2769 5.109210 GGTTCTGTTTCTTGACCTTTTTGG 58.891 41.667 0.00 0.00 42.93 3.28
1395 3006 6.447162 TGCTCCTGTGATATTTACATCTACG 58.553 40.000 0.00 0.00 0.00 3.51
1429 3075 1.203758 GGTTGTTGAAAATAGGCCCCG 59.796 52.381 0.00 0.00 0.00 5.73
1441 3087 2.288025 GGCCCCGGTCTCTGTGTTA 61.288 63.158 0.00 0.00 0.00 2.41
1450 3096 5.337330 CCCGGTCTCTGTGTTAAGAACTTAT 60.337 44.000 0.00 0.00 0.00 1.73
1451 3097 6.127535 CCCGGTCTCTGTGTTAAGAACTTATA 60.128 42.308 0.00 0.00 0.00 0.98
1501 3147 5.255710 AGTGCTACTGCTAGAACATGTAG 57.744 43.478 0.00 0.00 40.48 2.74
1547 3193 4.289672 TCTCTAAAAGGGATGCTGGAAAGT 59.710 41.667 0.00 0.00 0.00 2.66
1595 3241 6.325849 TGAACGTATGTTGATGTGTATTCG 57.674 37.500 4.71 0.00 38.78 3.34
1597 3243 4.430007 ACGTATGTTGATGTGTATTCGCT 58.570 39.130 0.00 0.00 0.00 4.93
1713 3360 3.509967 GGGTTACCATTTTGAACCTCAGG 59.490 47.826 2.98 0.00 41.99 3.86
1756 3403 3.495434 ACCCGTAAGTTGAAATGGTCA 57.505 42.857 0.00 0.00 0.00 4.02
1760 3407 5.183228 CCCGTAAGTTGAAATGGTCAGTAT 58.817 41.667 0.00 0.00 37.61 2.12
1896 3548 6.542852 CGGTTATGTAAACAAACATGGAGAG 58.457 40.000 0.00 0.00 40.29 3.20
1897 3549 6.370442 CGGTTATGTAAACAAACATGGAGAGA 59.630 38.462 0.00 0.00 40.29 3.10
1898 3550 7.413000 CGGTTATGTAAACAAACATGGAGAGAG 60.413 40.741 0.00 0.00 40.29 3.20
2015 3667 6.803320 CAGCATGTTCGTTCAGTAATTTCAAT 59.197 34.615 0.00 0.00 0.00 2.57
2079 3731 1.068333 CGACACAAAAGCTGGGGATTG 60.068 52.381 0.00 0.00 29.87 2.67
2185 3837 4.893608 TCTTTGACAAAGATGACGATCCA 58.106 39.130 23.67 1.10 42.31 3.41
2203 3855 3.866379 ATTTGCACCAGAGCGGGCA 62.866 57.895 0.00 0.00 40.22 5.36
2235 3887 7.466804 TCCTGTAAGTCTTATCAATTTTGGGT 58.533 34.615 0.00 0.00 0.00 4.51
2254 3906 3.058914 GGGTGCAGTATTTCGATATGTGC 60.059 47.826 14.19 14.19 0.00 4.57
2340 3992 5.552178 AGCTTCATCCGGGAGTATAAAATC 58.448 41.667 0.00 0.00 0.00 2.17
2432 4084 1.466856 ATGCTGCAACGTTGGATGAT 58.533 45.000 28.33 17.11 0.00 2.45
2534 4186 5.713025 TCTGTGCATTAGGCTTTTCATTTC 58.287 37.500 0.00 0.00 45.15 2.17
2619 4274 7.648177 AATTATGGGTATGAGTATTCCAGGT 57.352 36.000 0.00 0.00 0.00 4.00
2678 4333 5.829924 AGTGGATCTTTGTGTCAGTCAAAAT 59.170 36.000 0.00 0.00 34.96 1.82
2701 4356 4.145876 TCTGTGATTGTCAACATTTCGC 57.854 40.909 0.00 0.00 0.00 4.70
2712 4367 3.120338 TCAACATTTCGCCGTTCAAGATC 60.120 43.478 0.00 0.00 0.00 2.75
2714 4369 2.416547 ACATTTCGCCGTTCAAGATCTG 59.583 45.455 0.00 0.00 0.00 2.90
2848 4518 4.118410 CAGAACATGCATAGAGAGGTGTC 58.882 47.826 0.00 0.00 0.00 3.67
3125 4795 9.693739 ATATTTGTGGTTGATGGTGTTTCTATA 57.306 29.630 0.00 0.00 0.00 1.31
3126 4796 8.593945 ATTTGTGGTTGATGGTGTTTCTATAT 57.406 30.769 0.00 0.00 0.00 0.86
3423 5094 7.917505 AGAATTATTGCCTTTTTATTCTCAGCG 59.082 33.333 0.00 0.00 28.98 5.18
3425 5096 4.846779 TTGCCTTTTTATTCTCAGCGTT 57.153 36.364 0.00 0.00 0.00 4.84
3501 5172 4.283363 ACTGTCAGCATCAGAGTGATTT 57.717 40.909 0.00 0.00 34.28 2.17
3930 5602 6.403333 TTTTCGTACAAGTCATACTCATGC 57.597 37.500 0.00 0.00 31.73 4.06
3949 5621 2.622942 TGCAAGTGAAGACCCATTTGAC 59.377 45.455 0.00 0.00 36.31 3.18
3953 5625 5.009610 GCAAGTGAAGACCCATTTGACTTAA 59.990 40.000 0.00 0.00 36.31 1.85
3958 5630 8.704668 AGTGAAGACCCATTTGACTTAATTTTT 58.295 29.630 0.00 0.00 0.00 1.94
3959 5631 9.974980 GTGAAGACCCATTTGACTTAATTTTTA 57.025 29.630 0.00 0.00 0.00 1.52
3960 5632 9.974980 TGAAGACCCATTTGACTTAATTTTTAC 57.025 29.630 0.00 0.00 0.00 2.01
4090 5762 6.966021 TCGTTCAATCTTTACCTTTTTCCTG 58.034 36.000 0.00 0.00 0.00 3.86
4150 5822 7.296628 ACAAACTGCCTTAATTTATGGTGAA 57.703 32.000 9.41 0.00 0.00 3.18
4166 5838 0.181587 TGAAAAAGCACTCCCGTCCA 59.818 50.000 0.00 0.00 0.00 4.02
4185 5857 5.163814 CGTCCAGCTTTTACGTAGTACTAGT 60.164 44.000 1.87 0.00 45.76 2.57
4186 5858 6.036083 CGTCCAGCTTTTACGTAGTACTAGTA 59.964 42.308 1.87 0.00 45.76 1.82
4188 5860 7.278868 GTCCAGCTTTTACGTAGTACTAGTAGA 59.721 40.741 1.87 1.49 45.76 2.59
4190 5862 7.254727 CCAGCTTTTACGTAGTACTAGTAGAGG 60.255 44.444 1.87 3.13 45.76 3.69
4191 5863 7.279758 CAGCTTTTACGTAGTACTAGTAGAGGT 59.720 40.741 1.87 8.75 45.76 3.85
4192 5864 7.826744 AGCTTTTACGTAGTACTAGTAGAGGTT 59.173 37.037 1.87 0.64 45.76 3.50
4193 5865 8.454894 GCTTTTACGTAGTACTAGTAGAGGTTT 58.545 37.037 1.87 0.00 45.76 3.27
4243 5915 7.060383 CCACACATATTTATGGGGCAATAAA 57.940 36.000 4.92 6.96 41.37 1.40
4287 5961 5.993441 ACAAATTGGAATCTTTTGGCAGAAG 59.007 36.000 11.32 11.32 35.23 2.85
4292 5966 4.895297 TGGAATCTTTTGGCAGAAGAAGTT 59.105 37.500 22.34 14.02 36.77 2.66
4311 5985 6.495526 AGAAGTTTCAGGTCTCTAGTTAAGCT 59.504 38.462 0.00 0.00 0.00 3.74
4344 6018 1.581934 GAAAACTTGGTTGGGCAAGC 58.418 50.000 0.00 0.00 39.12 4.01
4375 6049 1.064758 ACTGCCACACTGAAGGTTTGA 60.065 47.619 0.00 0.00 0.00 2.69
4529 6247 6.758254 TCATAGTGTCAAGACTGAATGTGAA 58.242 36.000 1.53 0.00 31.88 3.18
4727 6445 4.142227 GCCCTTCTACTTCGTGTATCAGAA 60.142 45.833 0.00 0.00 0.00 3.02
4746 6464 7.592885 TCAGAAAACTTACTGTAGTGGTAGT 57.407 36.000 0.00 0.00 35.84 2.73
4792 6510 9.979578 ATTGTAAATAAAGCTGTGTGATCAAAA 57.020 25.926 0.00 0.00 0.00 2.44
4823 6541 6.096705 GCTCCAGAGTAGCATATATCACTCAT 59.903 42.308 15.81 4.44 39.90 2.90
4901 6619 7.529854 CGTATACGATATGTACTGTCTGAACAC 59.470 40.741 20.58 0.00 43.02 3.32
4963 6681 6.116126 ACTATAGTTTCTGAAATCTGCCCAC 58.884 40.000 6.06 0.00 0.00 4.61
5055 6773 0.746659 AGTGGCAGTGCAAACCTTTC 59.253 50.000 18.61 0.00 0.00 2.62
5057 6775 1.069049 GTGGCAGTGCAAACCTTTCAT 59.931 47.619 18.61 0.00 0.00 2.57
5158 6876 3.806949 TGACTGCTTCCCTTGGTTATT 57.193 42.857 0.00 0.00 0.00 1.40
5193 6911 0.102120 TTTTTCAGCCCTTGTGCACG 59.898 50.000 13.13 0.00 0.00 5.34
5194 6912 1.034838 TTTTCAGCCCTTGTGCACGT 61.035 50.000 13.13 0.00 0.00 4.49
5195 6913 1.034838 TTTCAGCCCTTGTGCACGTT 61.035 50.000 13.13 0.00 0.00 3.99
5196 6914 0.179043 TTCAGCCCTTGTGCACGTTA 60.179 50.000 13.13 0.00 0.00 3.18
5197 6915 0.882927 TCAGCCCTTGTGCACGTTAC 60.883 55.000 13.13 0.24 0.00 2.50
5198 6916 1.147376 AGCCCTTGTGCACGTTACA 59.853 52.632 13.13 0.00 0.00 2.41
5199 6917 0.464735 AGCCCTTGTGCACGTTACAA 60.465 50.000 13.13 12.89 36.66 2.41
5200 6918 0.317519 GCCCTTGTGCACGTTACAAC 60.318 55.000 13.13 0.00 34.58 3.32
5212 6930 2.442424 CGTTACAACGTGTTTGGTTGG 58.558 47.619 6.34 0.00 46.89 3.77
5213 6931 2.791849 CGTTACAACGTGTTTGGTTGGG 60.792 50.000 6.34 0.00 46.89 4.12
5214 6932 1.390565 TACAACGTGTTTGGTTGGGG 58.609 50.000 9.20 0.00 46.89 4.96
5215 6933 0.323542 ACAACGTGTTTGGTTGGGGA 60.324 50.000 9.20 0.00 46.89 4.81
5216 6934 1.036707 CAACGTGTTTGGTTGGGGAT 58.963 50.000 0.00 0.00 40.75 3.85
5217 6935 2.231529 CAACGTGTTTGGTTGGGGATA 58.768 47.619 0.00 0.00 40.75 2.59
5218 6936 2.623889 CAACGTGTTTGGTTGGGGATAA 59.376 45.455 0.00 0.00 40.75 1.75
5219 6937 3.163616 ACGTGTTTGGTTGGGGATAAT 57.836 42.857 0.00 0.00 0.00 1.28
5220 6938 3.502356 ACGTGTTTGGTTGGGGATAATT 58.498 40.909 0.00 0.00 0.00 1.40
5221 6939 4.664392 ACGTGTTTGGTTGGGGATAATTA 58.336 39.130 0.00 0.00 0.00 1.40
5222 6940 4.703093 ACGTGTTTGGTTGGGGATAATTAG 59.297 41.667 0.00 0.00 0.00 1.73
5223 6941 4.944930 CGTGTTTGGTTGGGGATAATTAGA 59.055 41.667 0.00 0.00 0.00 2.10
5224 6942 5.065988 CGTGTTTGGTTGGGGATAATTAGAG 59.934 44.000 0.00 0.00 0.00 2.43
5225 6943 4.953579 TGTTTGGTTGGGGATAATTAGAGC 59.046 41.667 0.00 0.00 0.00 4.09
5226 6944 3.876309 TGGTTGGGGATAATTAGAGCC 57.124 47.619 0.00 0.00 0.00 4.70
5227 6945 3.127250 TGGTTGGGGATAATTAGAGCCA 58.873 45.455 0.00 0.00 0.00 4.75
5228 6946 3.138283 TGGTTGGGGATAATTAGAGCCAG 59.862 47.826 0.00 0.00 0.00 4.85
5229 6947 3.498661 GGTTGGGGATAATTAGAGCCAGG 60.499 52.174 0.00 0.00 0.00 4.45
5230 6948 2.348472 TGGGGATAATTAGAGCCAGGG 58.652 52.381 0.00 0.00 0.00 4.45
5231 6949 2.089638 TGGGGATAATTAGAGCCAGGGA 60.090 50.000 0.00 0.00 0.00 4.20
5232 6950 2.986728 GGGGATAATTAGAGCCAGGGAA 59.013 50.000 0.00 0.00 0.00 3.97
5233 6951 3.593780 GGGGATAATTAGAGCCAGGGAAT 59.406 47.826 0.00 0.00 0.00 3.01
5234 6952 4.568592 GGGGATAATTAGAGCCAGGGAATG 60.569 50.000 0.00 0.00 0.00 2.67
5250 6968 3.054065 GGGAATGGGAATGAGAGAAGTGT 60.054 47.826 0.00 0.00 0.00 3.55
5275 6993 2.310779 ACACCTCTCAACTCTAGCCA 57.689 50.000 0.00 0.00 0.00 4.75
5294 7016 9.824216 TCTAGCCATAGTCTAATATACAACCTT 57.176 33.333 0.00 0.00 0.00 3.50
5339 7061 6.545666 TCTGCAATCTTCAACTCTTAAAACCA 59.454 34.615 0.00 0.00 0.00 3.67
5372 7094 1.305381 CTCCTCTCCCCTTGACCGT 60.305 63.158 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.576615 ACAACAAAGCCTCCAGTCTTC 58.423 47.619 0.00 0.00 0.00 2.87
8 9 1.064017 TGGAACAACAAAGCCTCCAGT 60.064 47.619 0.00 0.00 32.42 4.00
11 12 1.609072 GTCTGGAACAACAAAGCCTCC 59.391 52.381 0.00 0.00 38.70 4.30
41 42 2.169330 AGGTGAGTCCTTTACCGTCTC 58.831 52.381 0.00 0.00 45.67 3.36
98 99 5.657302 CCTGTCTTATATAAGATACCGCCCT 59.343 44.000 24.42 0.00 43.49 5.19
120 121 3.053095 TCCCTATCGACTAGTTTGACCCT 60.053 47.826 0.00 0.00 0.00 4.34
124 125 5.258841 TGTTCTCCCTATCGACTAGTTTGA 58.741 41.667 0.00 0.00 0.00 2.69
167 168 1.345415 AGTGGGGGTGTACAAAGTACG 59.655 52.381 0.00 0.00 0.00 3.67
186 188 1.462378 CGCTCGTGTTGTACATTGCAG 60.462 52.381 0.00 0.00 0.00 4.41
193 195 2.190981 CTATTCCCGCTCGTGTTGTAC 58.809 52.381 0.00 0.00 0.00 2.90
206 208 7.571025 TCCTTATGAGGTAAAACACTATTCCC 58.429 38.462 3.04 0.00 43.97 3.97
236 238 6.350949 GCCAACAACCACTTATCCATGTTTAT 60.351 38.462 0.00 0.00 0.00 1.40
254 256 0.473755 TTGAGAGGAGCAGCCAACAA 59.526 50.000 0.00 0.00 40.02 2.83
257 259 1.376466 GGTTGAGAGGAGCAGCCAA 59.624 57.895 0.00 0.00 40.02 4.52
260 262 0.036022 AACTGGTTGAGAGGAGCAGC 59.964 55.000 3.49 0.00 44.29 5.25
274 276 1.303643 GGAGGAGCCACCAAACTGG 60.304 63.158 0.00 0.00 45.02 4.00
284 286 0.034616 CGAAGGATCATGGAGGAGCC 59.965 60.000 0.00 0.00 43.68 4.70
315 317 4.885907 CCATCACCGTCTAGTAAGGTAAGA 59.114 45.833 6.30 2.78 37.96 2.10
317 319 3.956199 CCCATCACCGTCTAGTAAGGTAA 59.044 47.826 6.30 0.00 37.96 2.85
323 325 0.394762 ACGCCCATCACCGTCTAGTA 60.395 55.000 0.00 0.00 31.00 1.82
332 334 0.741221 GACTCCTTCACGCCCATCAC 60.741 60.000 0.00 0.00 0.00 3.06
333 335 0.904865 AGACTCCTTCACGCCCATCA 60.905 55.000 0.00 0.00 0.00 3.07
336 338 2.636412 CGAGACTCCTTCACGCCCA 61.636 63.158 0.00 0.00 31.33 5.36
344 346 1.001406 CTTTGCAGGTCGAGACTCCTT 59.999 52.381 3.09 0.00 30.91 3.36
358 360 0.396974 AAGGTGTTCAGCCCTTTGCA 60.397 50.000 0.00 0.00 44.83 4.08
359 362 0.032540 CAAGGTGTTCAGCCCTTTGC 59.967 55.000 0.00 0.00 39.04 3.68
364 367 1.903404 CCCACAAGGTGTTCAGCCC 60.903 63.158 0.00 0.00 0.00 5.19
384 387 1.292223 CACACCCGTCTCCATCGTT 59.708 57.895 0.00 0.00 0.00 3.85
394 397 4.640855 CGACTCGTGCACACCCGT 62.641 66.667 18.64 7.33 0.00 5.28
476 483 2.959707 CCACCTCTACCTCATAGTCACC 59.040 54.545 0.00 0.00 32.13 4.02
483 490 2.968574 CAGCATACCACCTCTACCTCAT 59.031 50.000 0.00 0.00 0.00 2.90
528 536 4.395542 CGTCTGAGTACTACAAAGCCTACT 59.604 45.833 0.00 0.00 0.00 2.57
530 538 4.394300 GTCGTCTGAGTACTACAAAGCCTA 59.606 45.833 0.00 0.00 0.00 3.93
566 574 1.338674 CCACTCTTACCGGCATTGTGA 60.339 52.381 0.00 0.00 0.00 3.58
568 576 0.035439 CCCACTCTTACCGGCATTGT 60.035 55.000 0.00 0.00 0.00 2.71
578 586 1.122632 TCCACCAACGCCCACTCTTA 61.123 55.000 0.00 0.00 0.00 2.10
612 620 3.833645 CCGCTTCCATCGACCGGA 61.834 66.667 9.46 1.22 41.34 5.14
615 623 3.792053 ATCGCCGCTTCCATCGACC 62.792 63.158 0.00 0.00 33.59 4.79
625 770 3.842923 CTCTCCACCATCGCCGCT 61.843 66.667 0.00 0.00 0.00 5.52
629 774 4.899239 CGGCCTCTCCACCATCGC 62.899 72.222 0.00 0.00 34.01 4.58
632 777 0.625849 AATTTCGGCCTCTCCACCAT 59.374 50.000 0.00 0.00 34.01 3.55
638 783 2.216898 CTCATCCAATTTCGGCCTCTC 58.783 52.381 0.00 0.00 0.00 3.20
650 795 0.252057 TCCTCGTCACCCTCATCCAA 60.252 55.000 0.00 0.00 0.00 3.53
654 799 0.608640 GTTGTCCTCGTCACCCTCAT 59.391 55.000 0.00 0.00 0.00 2.90
659 805 0.106149 ACCTTGTTGTCCTCGTCACC 59.894 55.000 0.00 0.00 0.00 4.02
661 807 1.068588 CTGACCTTGTTGTCCTCGTCA 59.931 52.381 0.00 0.00 34.25 4.35
670 816 1.949525 CTTCCACACCTGACCTTGTTG 59.050 52.381 0.00 0.00 0.00 3.33
671 817 1.133792 CCTTCCACACCTGACCTTGTT 60.134 52.381 0.00 0.00 0.00 2.83
691 838 1.270947 TGACACAACGGTCATTACCCC 60.271 52.381 0.00 0.00 42.56 4.95
700 847 2.413837 GCTTATCTGTGACACAACGGT 58.586 47.619 10.02 0.00 0.00 4.83
716 863 0.991920 CTTTGTCCTCCCCTGGCTTA 59.008 55.000 0.00 0.00 0.00 3.09
718 865 0.772124 TTCTTTGTCCTCCCCTGGCT 60.772 55.000 0.00 0.00 0.00 4.75
729 876 2.548480 CCCACGACTTCCTTTCTTTGTC 59.452 50.000 0.00 0.00 0.00 3.18
736 883 1.605753 GAAAGCCCACGACTTCCTTT 58.394 50.000 0.00 0.00 0.00 3.11
737 884 0.602905 CGAAAGCCCACGACTTCCTT 60.603 55.000 0.00 0.00 0.00 3.36
759 906 6.249471 CGATATAAAGGAACTCATCGACATCG 59.751 42.308 0.00 0.00 38.49 3.84
761 908 6.390721 CCGATATAAAGGAACTCATCGACAT 58.609 40.000 3.54 0.00 38.49 3.06
766 913 3.368236 GCGCCGATATAAAGGAACTCATC 59.632 47.826 0.00 0.00 38.49 2.92
768 915 2.750948 GCGCCGATATAAAGGAACTCA 58.249 47.619 0.00 0.00 38.49 3.41
773 920 2.553602 TCTAACGCGCCGATATAAAGGA 59.446 45.455 5.73 0.00 0.00 3.36
779 926 0.666913 ACTGTCTAACGCGCCGATAT 59.333 50.000 5.73 0.00 0.00 1.63
780 927 1.298602 TACTGTCTAACGCGCCGATA 58.701 50.000 5.73 0.00 0.00 2.92
781 928 0.666913 ATACTGTCTAACGCGCCGAT 59.333 50.000 5.73 0.00 0.00 4.18
808 955 7.810766 ATTGTGTCCATTTAAATTTGCGTAG 57.189 32.000 0.00 0.00 0.00 3.51
809 956 9.692749 TTTATTGTGTCCATTTAAATTTGCGTA 57.307 25.926 0.00 0.00 0.00 4.42
810 957 8.594881 TTTATTGTGTCCATTTAAATTTGCGT 57.405 26.923 0.00 0.00 0.00 5.24
819 966 6.659668 TCGACCCATTTTATTGTGTCCATTTA 59.340 34.615 0.00 0.00 0.00 1.40
823 970 4.022413 TCGACCCATTTTATTGTGTCCA 57.978 40.909 0.00 0.00 0.00 4.02
832 979 6.057321 ACTCCAACTTATCGACCCATTTTA 57.943 37.500 0.00 0.00 0.00 1.52
835 982 3.430374 CGACTCCAACTTATCGACCCATT 60.430 47.826 0.00 0.00 36.70 3.16
845 992 1.588082 GTCCGCCGACTCCAACTTA 59.412 57.895 0.00 0.00 35.99 2.24
846 993 2.342648 GTCCGCCGACTCCAACTT 59.657 61.111 0.00 0.00 35.99 2.66
860 1007 2.825836 CGATGCAAGCAGGGGTCC 60.826 66.667 0.00 0.00 0.00 4.46
861 1008 2.045926 ACGATGCAAGCAGGGGTC 60.046 61.111 0.00 0.00 0.00 4.46
902 2505 2.029369 TAAAGCGGTCACGGCGTT 59.971 55.556 11.19 12.79 41.36 4.84
914 2517 2.824489 GGCGGGGCAGAGTAAAGC 60.824 66.667 0.00 0.00 0.00 3.51
915 2518 0.815615 GATGGCGGGGCAGAGTAAAG 60.816 60.000 0.45 0.00 0.00 1.85
916 2519 1.223487 GATGGCGGGGCAGAGTAAA 59.777 57.895 0.45 0.00 0.00 2.01
917 2520 1.686325 GAGATGGCGGGGCAGAGTAA 61.686 60.000 0.45 0.00 0.00 2.24
918 2521 2.041922 AGATGGCGGGGCAGAGTA 60.042 61.111 0.45 0.00 0.00 2.59
1120 2729 4.753610 CAGAACCGATCGTACTACCAGATA 59.246 45.833 15.09 0.00 0.00 1.98
1146 2755 1.969923 CCATGCCCAAAAAGGTCAAGA 59.030 47.619 0.00 0.00 34.66 3.02
1155 2764 0.251386 TAAGCGGTCCATGCCCAAAA 60.251 50.000 0.00 0.00 0.00 2.44
1158 2767 0.033601 AATTAAGCGGTCCATGCCCA 60.034 50.000 0.00 0.00 0.00 5.36
1160 2769 2.884639 ACATAATTAAGCGGTCCATGCC 59.115 45.455 0.00 0.00 0.00 4.40
1336 2947 7.663905 GGGATAAACAAACAAATTAAAAGGGCT 59.336 33.333 0.00 0.00 0.00 5.19
1395 3006 2.271944 ACAACCACTAACCCTTCAGC 57.728 50.000 0.00 0.00 0.00 4.26
1450 3096 9.787532 GCATTTTCAAACAATAGTAGCATCTTA 57.212 29.630 0.00 0.00 0.00 2.10
1451 3097 7.761249 GGCATTTTCAAACAATAGTAGCATCTT 59.239 33.333 0.00 0.00 0.00 2.40
1475 3121 0.456221 TTCTAGCAGTAGCACTCGGC 59.544 55.000 0.00 0.00 45.49 5.54
1501 3147 2.800746 GCATGTGGCGCGTCAAAC 60.801 61.111 18.26 4.19 0.00 2.93
1547 3193 3.213506 CAAAACCAGAGACATGACACCA 58.786 45.455 0.00 0.00 0.00 4.17
1595 3241 4.002982 TCAGTGATGACCATGTGTAAAGC 58.997 43.478 0.00 0.00 0.00 3.51
1597 3243 5.620206 ACTTCAGTGATGACCATGTGTAAA 58.380 37.500 12.65 0.00 0.00 2.01
1607 3254 2.071688 ACGCAGACTTCAGTGATGAC 57.928 50.000 12.65 6.69 0.00 3.06
1690 3337 7.413141 ACCTGAGGTTCAAAATGGTAACCCA 62.413 44.000 0.00 0.00 43.04 4.51
1771 3418 8.573035 CACCATAAATAACACCACACTAGTTTT 58.427 33.333 0.00 0.00 0.00 2.43
1780 3427 8.288689 AGGAAATACACCATAAATAACACCAC 57.711 34.615 0.00 0.00 0.00 4.16
1855 3507 1.478510 ACCGCCTATGAACTCACTCAG 59.521 52.381 0.00 0.00 0.00 3.35
2041 3693 1.073125 TCGCCAACTCCTTCAATCCAA 59.927 47.619 0.00 0.00 0.00 3.53
2079 3731 2.030274 GTGGTGGTATCAGGCAACAAAC 60.030 50.000 0.00 0.00 41.41 2.93
2185 3837 3.064324 GCCCGCTCTGGTGCAAAT 61.064 61.111 0.00 0.00 34.94 2.32
2235 3887 3.712187 TCGCACATATCGAAATACTGCA 58.288 40.909 0.00 0.00 32.53 4.41
2254 3906 1.446907 AGGAAAATCAGCTGCACTCG 58.553 50.000 9.47 0.00 0.00 4.18
2340 3992 7.095695 ACATATACCGTTTGAATTTCTTGGG 57.904 36.000 0.00 0.00 0.00 4.12
2432 4084 1.217689 CCCCATGGCTAATTCCCTTCA 59.782 52.381 6.09 0.00 0.00 3.02
2534 4186 4.764679 TGGATGACAACAAATTTCTCCG 57.235 40.909 0.00 0.00 0.00 4.63
2615 4270 6.633500 TGGTGTGAAGAATTAAAAGACCTG 57.367 37.500 0.00 0.00 0.00 4.00
2678 4333 5.163764 GGCGAAATGTTGACAATCACAGATA 60.164 40.000 0.00 0.00 0.00 1.98
2701 4356 6.368791 TCAAATTCTGTACAGATCTTGAACGG 59.631 38.462 29.81 15.58 36.39 4.44
2712 4367 9.712359 CATATTGTGACATCAAATTCTGTACAG 57.288 33.333 17.17 17.17 0.00 2.74
3021 4691 9.727627 CATTGATTTGAGGTTCTTAATCTTAGC 57.272 33.333 0.00 0.00 0.00 3.09
3175 4845 8.230472 AGACAAGAATGGATTCATAAATGTCC 57.770 34.615 16.53 5.49 38.47 4.02
3341 5011 6.928348 TCTGTATACAAACCTCCTGAAAGA 57.072 37.500 7.06 0.00 34.07 2.52
3346 5016 6.878923 TCACAAATCTGTATACAAACCTCCTG 59.121 38.462 7.06 1.54 33.22 3.86
3423 5094 8.356533 AATGAAACACATTGTTCAATGAGAAC 57.643 30.769 25.74 16.12 45.99 3.01
3501 5172 6.979465 TGTCATCTGCAATCACATTTGTTAA 58.021 32.000 0.00 0.00 0.00 2.01
3930 5602 6.633500 TTAAGTCAAATGGGTCTTCACTTG 57.367 37.500 0.00 0.00 0.00 3.16
3949 5621 5.711506 ACCCCGTAACCCAGTAAAAATTAAG 59.288 40.000 0.00 0.00 0.00 1.85
3953 5625 3.812611 ACCCCGTAACCCAGTAAAAAT 57.187 42.857 0.00 0.00 0.00 1.82
3958 5630 2.042979 ACTTCTACCCCGTAACCCAGTA 59.957 50.000 0.00 0.00 0.00 2.74
3959 5631 1.203225 ACTTCTACCCCGTAACCCAGT 60.203 52.381 0.00 0.00 0.00 4.00
3960 5632 1.206371 CACTTCTACCCCGTAACCCAG 59.794 57.143 0.00 0.00 0.00 4.45
3961 5633 1.269012 CACTTCTACCCCGTAACCCA 58.731 55.000 0.00 0.00 0.00 4.51
3968 5640 0.899720 TTACCTGCACTTCTACCCCG 59.100 55.000 0.00 0.00 0.00 5.73
4166 5838 7.334858 ACCTCTACTAGTACTACGTAAAAGCT 58.665 38.462 0.00 0.00 0.00 3.74
4243 5915 5.132897 TGTATTTTTCTGAGCGCCATTTT 57.867 34.783 2.29 0.00 0.00 1.82
4287 5961 6.693466 AGCTTAACTAGAGACCTGAAACTTC 58.307 40.000 0.00 0.00 0.00 3.01
4292 5966 6.123651 CCTAGAGCTTAACTAGAGACCTGAA 58.876 44.000 9.05 0.00 39.48 3.02
4311 5985 1.975680 AGTTTTCGCTTGACCCCTAGA 59.024 47.619 0.00 0.00 0.00 2.43
4344 6018 1.802960 GTGTGGCAGTTCTGATGAGTG 59.197 52.381 3.84 0.00 0.00 3.51
4544 6262 3.188460 TCAAACGAAGATAAGCAACTGCC 59.812 43.478 0.00 0.00 43.38 4.85
4727 6445 6.126968 ACACCAACTACCACTACAGTAAGTTT 60.127 38.462 0.00 0.00 0.00 2.66
4746 6464 5.163364 ACAATCCACAATAGCAAAACACCAA 60.163 36.000 0.00 0.00 0.00 3.67
4823 6541 4.455533 GGCAAGAAAGTGTGTCACATATCA 59.544 41.667 9.31 0.00 36.74 2.15
4830 6548 2.418368 AGTGGCAAGAAAGTGTGTCA 57.582 45.000 0.00 0.00 0.00 3.58
4963 6681 0.676782 CTTTGCCCAAGTACCCTCCG 60.677 60.000 0.00 0.00 0.00 4.63
4973 6691 0.614294 CCATTGATGCCTTTGCCCAA 59.386 50.000 0.00 0.00 36.33 4.12
5055 6773 8.776470 AGAATGGAAGCAACAAACAATTAAATG 58.224 29.630 0.00 0.00 0.00 2.32
5057 6775 8.729805 AAGAATGGAAGCAACAAACAATTAAA 57.270 26.923 0.00 0.00 0.00 1.52
5158 6876 5.775686 CTGAAAAAGAGAAACATGGCATGA 58.224 37.500 32.74 5.53 0.00 3.07
5193 6911 2.479901 CCCCAACCAAACACGTTGTAAC 60.480 50.000 0.00 0.00 39.16 2.50
5194 6912 1.749634 CCCCAACCAAACACGTTGTAA 59.250 47.619 0.00 0.00 39.16 2.41
5195 6913 1.064906 TCCCCAACCAAACACGTTGTA 60.065 47.619 0.00 0.00 39.16 2.41
5196 6914 0.323542 TCCCCAACCAAACACGTTGT 60.324 50.000 0.00 0.00 39.16 3.32
5197 6915 1.036707 ATCCCCAACCAAACACGTTG 58.963 50.000 0.00 0.00 40.25 4.10
5198 6916 2.660670 TATCCCCAACCAAACACGTT 57.339 45.000 0.00 0.00 0.00 3.99
5199 6917 2.660670 TTATCCCCAACCAAACACGT 57.339 45.000 0.00 0.00 0.00 4.49
5200 6918 4.944930 TCTAATTATCCCCAACCAAACACG 59.055 41.667 0.00 0.00 0.00 4.49
5201 6919 5.163550 GCTCTAATTATCCCCAACCAAACAC 60.164 44.000 0.00 0.00 0.00 3.32
5202 6920 4.953579 GCTCTAATTATCCCCAACCAAACA 59.046 41.667 0.00 0.00 0.00 2.83
5203 6921 4.341235 GGCTCTAATTATCCCCAACCAAAC 59.659 45.833 0.00 0.00 0.00 2.93
5204 6922 4.017037 TGGCTCTAATTATCCCCAACCAAA 60.017 41.667 0.00 0.00 0.00 3.28
5205 6923 3.529734 TGGCTCTAATTATCCCCAACCAA 59.470 43.478 0.00 0.00 0.00 3.67
5206 6924 3.127250 TGGCTCTAATTATCCCCAACCA 58.873 45.455 0.00 0.00 0.00 3.67
5207 6925 3.498661 CCTGGCTCTAATTATCCCCAACC 60.499 52.174 0.00 0.00 0.00 3.77
5208 6926 3.498661 CCCTGGCTCTAATTATCCCCAAC 60.499 52.174 0.00 0.00 0.00 3.77
5209 6927 2.716424 CCCTGGCTCTAATTATCCCCAA 59.284 50.000 0.00 0.00 0.00 4.12
5210 6928 2.089638 TCCCTGGCTCTAATTATCCCCA 60.090 50.000 0.00 0.00 0.00 4.96
5211 6929 2.632537 TCCCTGGCTCTAATTATCCCC 58.367 52.381 0.00 0.00 0.00 4.81
5212 6930 4.568592 CCATTCCCTGGCTCTAATTATCCC 60.569 50.000 0.00 0.00 38.47 3.85
5213 6931 4.568592 CCCATTCCCTGGCTCTAATTATCC 60.569 50.000 0.00 0.00 44.46 2.59
5214 6932 4.289672 TCCCATTCCCTGGCTCTAATTATC 59.710 45.833 0.00 0.00 44.46 1.75
5215 6933 4.251169 TCCCATTCCCTGGCTCTAATTAT 58.749 43.478 0.00 0.00 44.46 1.28
5216 6934 3.675613 TCCCATTCCCTGGCTCTAATTA 58.324 45.455 0.00 0.00 44.46 1.40
5217 6935 2.502745 TCCCATTCCCTGGCTCTAATT 58.497 47.619 0.00 0.00 44.46 1.40
5218 6936 2.212752 TCCCATTCCCTGGCTCTAAT 57.787 50.000 0.00 0.00 44.46 1.73
5219 6937 1.979809 TTCCCATTCCCTGGCTCTAA 58.020 50.000 0.00 0.00 44.46 2.10
5220 6938 1.776667 CATTCCCATTCCCTGGCTCTA 59.223 52.381 0.00 0.00 44.46 2.43
5221 6939 0.554792 CATTCCCATTCCCTGGCTCT 59.445 55.000 0.00 0.00 44.46 4.09
5222 6940 0.552848 TCATTCCCATTCCCTGGCTC 59.447 55.000 0.00 0.00 44.46 4.70
5223 6941 0.554792 CTCATTCCCATTCCCTGGCT 59.445 55.000 0.00 0.00 44.46 4.75
5224 6942 0.552848 TCTCATTCCCATTCCCTGGC 59.447 55.000 0.00 0.00 44.46 4.85
5225 6943 2.130193 TCTCTCATTCCCATTCCCTGG 58.870 52.381 0.00 0.00 45.51 4.45
5226 6944 3.201708 ACTTCTCTCATTCCCATTCCCTG 59.798 47.826 0.00 0.00 0.00 4.45
5227 6945 3.201708 CACTTCTCTCATTCCCATTCCCT 59.798 47.826 0.00 0.00 0.00 4.20
5228 6946 3.054065 ACACTTCTCTCATTCCCATTCCC 60.054 47.826 0.00 0.00 0.00 3.97
5229 6947 4.227864 ACACTTCTCTCATTCCCATTCC 57.772 45.455 0.00 0.00 0.00 3.01
5232 6950 9.159254 TGTAATATACACTTCTCTCATTCCCAT 57.841 33.333 0.00 0.00 32.89 4.00
5233 6951 8.547481 TGTAATATACACTTCTCTCATTCCCA 57.453 34.615 0.00 0.00 32.89 4.37
5250 6968 7.295340 TGGCTAGAGTTGAGAGGTGTAATATA 58.705 38.462 0.00 0.00 0.00 0.86
5294 7016 5.049680 GCAGATTAGACGGTTTTGAAGTTGA 60.050 40.000 0.00 0.00 0.00 3.18
5339 7061 2.110721 AGAGGAGGGTTGAATTTTGGCT 59.889 45.455 0.00 0.00 0.00 4.75
5372 7094 3.407443 GGTCAGACCCGGTCAAAAA 57.593 52.632 19.95 0.00 34.60 1.94


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

AutoCloner maintained by Alex Coulton.