Multiple sequence alignment - TraesCS5A01G363500

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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 TraesCS5A01G363500 chr5A 100.000 5818 0 0 1 5818 564084775 564078958 0.000000e+00 10744
1 TraesCS5A01G363500 chr5D 96.280 2339 80 7 3484 5818 446406987 446404652 0.000000e+00 3831
2 TraesCS5A01G363500 chr5D 92.992 1584 53 20 1940 3474 446408716 446407142 0.000000e+00 2257
3 TraesCS5A01G363500 chr5D 89.135 1583 100 31 473 2024 446410216 446408675 0.000000e+00 1905
4 TraesCS5A01G363500 chr5D 89.474 95 9 1 1 95 446410808 446410715 1.020000e-22 119
5 TraesCS5A01G363500 chr5B 94.800 2346 87 10 3484 5818 544335994 544333673 0.000000e+00 3624
6 TraesCS5A01G363500 chr5B 91.653 1869 102 19 837 2677 544339142 544337300 0.000000e+00 2538
7 TraesCS5A01G363500 chr5B 96.765 742 22 1 2672 3411 544337029 544336288 0.000000e+00 1236
8 TraesCS5A01G363500 chr5B 79.087 263 26 20 1 237 544340035 544339776 2.810000e-33 154
9 TraesCS5A01G363500 chr5B 100.000 68 0 0 3412 3479 544336248 544336181 6.120000e-25 126


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 TraesCS5A01G363500 chr5A 564078958 564084775 5817 True 10744.0 10744 100.00000 1 5818 1 chr5A.!!$R1 5817
1 TraesCS5A01G363500 chr5D 446404652 446410808 6156 True 2028.0 3831 91.97025 1 5818 4 chr5D.!!$R1 5817
2 TraesCS5A01G363500 chr5B 544333673 544340035 6362 True 1535.6 3624 92.46100 1 5818 5 chr5B.!!$R1 5817

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
527 723 0.043053 CATATTCTGACGCGGCGTTG 60.043 55.0 29.98 23.36 41.37 4.10 F
1700 1949 0.174389 GCACTAGCACTCTAGCAGCA 59.826 55.0 0.00 0.00 44.83 4.41 F
2556 2876 0.604243 TAAAACCGGTGCGTGATGCT 60.604 50.0 8.52 0.00 46.63 3.79 F
3250 3854 0.470341 CTGAGCTTTACCCTAGGGCC 59.530 60.0 28.88 11.00 39.32 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2356 0.947180 GCAGCGACACCCGACTTTAA 60.947 55.0 0.00 0.0 41.76 1.52 R
2589 2909 0.040351 CAGGAGTCTCAGACCCTGGA 59.960 60.0 24.58 0.0 42.14 3.86 R
4060 4888 0.467384 CTTGACCCCAGATGCTCGAT 59.533 55.0 0.00 0.0 0.00 3.59 R
5132 5968 0.171231 CTCGTTGATCACCTCTCGCA 59.829 55.0 0.00 0.0 0.00 5.10 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
56 57 1.136057 GCGCACGGGAAAGTAAAAGAG 60.136 52.381 0.30 0.00 0.00 2.85
78 79 6.778069 AGAGGGAAAAAGGTTAAAGAAAGAGG 59.222 38.462 0.00 0.00 0.00 3.69
80 81 5.510861 GGGAAAAAGGTTAAAGAAAGAGGGC 60.511 44.000 0.00 0.00 0.00 5.19
81 82 5.069914 GGAAAAAGGTTAAAGAAAGAGGGCA 59.930 40.000 0.00 0.00 0.00 5.36
82 83 5.531122 AAAAGGTTAAAGAAAGAGGGCAC 57.469 39.130 0.00 0.00 0.00 5.01
84 85 1.810755 GGTTAAAGAAAGAGGGCACGG 59.189 52.381 0.00 0.00 0.00 4.94
85 86 1.199327 GTTAAAGAAAGAGGGCACGGC 59.801 52.381 0.00 0.00 0.00 5.68
86 87 0.398696 TAAAGAAAGAGGGCACGGCA 59.601 50.000 0.00 0.00 0.00 5.69
87 88 1.172812 AAAGAAAGAGGGCACGGCAC 61.173 55.000 0.00 0.00 0.00 5.01
126 142 3.339093 GGCCTGGCCTGGTTACCT 61.339 66.667 30.42 0.00 46.69 3.08
127 143 1.999002 GGCCTGGCCTGGTTACCTA 60.999 63.158 30.42 0.00 46.69 3.08
128 144 1.223763 GCCTGGCCTGGTTACCTAC 59.776 63.158 27.68 7.43 0.00 3.18
148 172 2.161609 ACCGCAGTTCGAATTCAAATCC 59.838 45.455 0.00 0.00 41.67 3.01
150 174 2.477863 CGCAGTTCGAATTCAAATCCCC 60.478 50.000 0.00 0.00 41.67 4.81
154 178 1.378531 TCGAATTCAAATCCCCGCTG 58.621 50.000 6.22 0.00 0.00 5.18
155 179 0.248621 CGAATTCAAATCCCCGCTGC 60.249 55.000 6.22 0.00 0.00 5.25
158 182 1.669999 ATTCAAATCCCCGCTGCTGC 61.670 55.000 5.34 5.34 0.00 5.25
168 192 3.745803 GCTGCTGCTGGTGGAAGC 61.746 66.667 8.53 0.00 46.72 3.86
174 205 2.747855 GCTGGTGGAAGCGGAAGG 60.748 66.667 0.00 0.00 45.47 3.46
177 208 1.535444 TGGTGGAAGCGGAAGGAGA 60.535 57.895 0.00 0.00 36.92 3.71
178 209 1.125093 TGGTGGAAGCGGAAGGAGAA 61.125 55.000 0.00 0.00 36.92 2.87
214 256 1.908340 CTTCTCTCCCCAGGCACAGG 61.908 65.000 0.00 0.00 33.40 4.00
271 349 2.982130 CTGTAAGTGCCGCTCCCT 59.018 61.111 0.00 0.00 0.00 4.20
273 351 0.741221 CTGTAAGTGCCGCTCCCTTC 60.741 60.000 0.00 0.00 0.00 3.46
283 361 2.381941 GCTCCCTTCCTGCCTCCAT 61.382 63.158 0.00 0.00 0.00 3.41
288 366 0.693767 CCTTCCTGCCTCCATCCTCT 60.694 60.000 0.00 0.00 0.00 3.69
290 368 1.045350 TTCCTGCCTCCATCCTCTCG 61.045 60.000 0.00 0.00 0.00 4.04
291 369 2.420890 CTGCCTCCATCCTCTCGC 59.579 66.667 0.00 0.00 0.00 5.03
299 377 4.531426 ATCCTCTCGCCGCCCTCT 62.531 66.667 0.00 0.00 0.00 3.69
326 482 1.200760 TGCCAGCCAAGCTAAGAGGA 61.201 55.000 0.00 0.00 36.40 3.71
328 484 2.016096 GCCAGCCAAGCTAAGAGGAAG 61.016 57.143 0.00 0.00 36.40 3.46
329 485 1.280421 CCAGCCAAGCTAAGAGGAAGT 59.720 52.381 0.00 0.00 36.40 3.01
340 527 1.848652 AGAGGAAGTTCGAATCCGGA 58.151 50.000 6.61 6.61 40.78 5.14
368 555 4.801624 TGCGCCGTGCTCTAGCTG 62.802 66.667 4.18 0.00 46.63 4.24
371 558 2.584694 GCCGTGCTCTAGCTGCTC 60.585 66.667 4.91 0.00 42.66 4.26
378 565 3.788616 CTCTAGCTGCTCCCTGCGC 62.789 68.421 4.91 0.00 46.63 6.09
395 587 2.103934 CTTCTGCTCCGAGGCGAG 59.896 66.667 0.00 0.00 34.52 5.03
404 596 3.075005 CGAGGCGAGGGAGGGAAA 61.075 66.667 0.00 0.00 0.00 3.13
410 602 1.064979 GGCGAGGGAGGGAAAATAACA 60.065 52.381 0.00 0.00 0.00 2.41
413 605 3.270877 CGAGGGAGGGAAAATAACACTG 58.729 50.000 0.00 0.00 0.00 3.66
437 629 2.809174 CGCGGCGTCATCTTGTCA 60.809 61.111 15.36 0.00 0.00 3.58
438 630 2.167219 CGCGGCGTCATCTTGTCAT 61.167 57.895 15.36 0.00 0.00 3.06
439 631 1.638467 GCGGCGTCATCTTGTCATC 59.362 57.895 9.37 0.00 0.00 2.92
441 633 1.645034 CGGCGTCATCTTGTCATCTT 58.355 50.000 0.00 0.00 0.00 2.40
442 634 1.590238 CGGCGTCATCTTGTCATCTTC 59.410 52.381 0.00 0.00 0.00 2.87
443 635 1.590238 GGCGTCATCTTGTCATCTTCG 59.410 52.381 0.00 0.00 0.00 3.79
444 636 1.590238 GCGTCATCTTGTCATCTTCGG 59.410 52.381 0.00 0.00 0.00 4.30
445 637 2.196749 CGTCATCTTGTCATCTTCGGG 58.803 52.381 0.00 0.00 0.00 5.14
446 638 2.555199 GTCATCTTGTCATCTTCGGGG 58.445 52.381 0.00 0.00 0.00 5.73
447 639 2.093447 GTCATCTTGTCATCTTCGGGGT 60.093 50.000 0.00 0.00 0.00 4.95
448 640 3.132289 GTCATCTTGTCATCTTCGGGGTA 59.868 47.826 0.00 0.00 0.00 3.69
449 641 3.384789 TCATCTTGTCATCTTCGGGGTAG 59.615 47.826 0.00 0.00 0.00 3.18
450 642 2.816411 TCTTGTCATCTTCGGGGTAGT 58.184 47.619 0.00 0.00 0.00 2.73
451 643 2.758979 TCTTGTCATCTTCGGGGTAGTC 59.241 50.000 0.00 0.00 0.00 2.59
452 644 2.526888 TGTCATCTTCGGGGTAGTCT 57.473 50.000 0.00 0.00 0.00 3.24
453 645 3.657398 TGTCATCTTCGGGGTAGTCTA 57.343 47.619 0.00 0.00 0.00 2.59
454 646 3.552875 TGTCATCTTCGGGGTAGTCTAG 58.447 50.000 0.00 0.00 0.00 2.43
455 647 3.053842 TGTCATCTTCGGGGTAGTCTAGT 60.054 47.826 0.00 0.00 0.00 2.57
456 648 4.164796 TGTCATCTTCGGGGTAGTCTAGTA 59.835 45.833 0.00 0.00 0.00 1.82
457 649 4.514816 GTCATCTTCGGGGTAGTCTAGTAC 59.485 50.000 0.00 0.00 0.00 2.73
458 650 4.411540 TCATCTTCGGGGTAGTCTAGTACT 59.588 45.833 0.00 0.00 42.62 2.73
459 651 4.148128 TCTTCGGGGTAGTCTAGTACTG 57.852 50.000 5.39 0.00 39.39 2.74
460 652 3.118112 TCTTCGGGGTAGTCTAGTACTGG 60.118 52.174 5.39 1.87 39.39 4.00
461 653 1.492176 TCGGGGTAGTCTAGTACTGGG 59.508 57.143 5.39 0.00 39.39 4.45
462 654 1.478288 CGGGGTAGTCTAGTACTGGGG 60.478 61.905 5.39 0.00 39.39 4.96
463 655 1.133231 GGGGTAGTCTAGTACTGGGGG 60.133 61.905 5.39 0.00 39.39 5.40
510 706 3.788766 GCCGCGCGTTCAGTTCAT 61.789 61.111 29.95 0.00 0.00 2.57
516 712 2.595188 CGCGCGTTCAGTTCATATTCTG 60.595 50.000 24.19 0.00 0.00 3.02
517 713 2.603110 GCGCGTTCAGTTCATATTCTGA 59.397 45.455 8.43 0.00 38.66 3.27
518 714 3.542291 GCGCGTTCAGTTCATATTCTGAC 60.542 47.826 8.43 0.00 39.87 3.51
519 715 3.301197 CGCGTTCAGTTCATATTCTGACG 60.301 47.826 0.00 0.00 39.87 4.35
520 716 3.542291 GCGTTCAGTTCATATTCTGACGC 60.542 47.826 19.51 19.51 44.35 5.19
522 718 2.809446 TCAGTTCATATTCTGACGCGG 58.191 47.619 12.47 0.00 36.04 6.46
523 719 1.258982 CAGTTCATATTCTGACGCGGC 59.741 52.381 12.47 8.67 32.17 6.53
524 720 0.229753 GTTCATATTCTGACGCGGCG 59.770 55.000 22.36 22.36 32.17 6.46
526 722 0.179121 TCATATTCTGACGCGGCGTT 60.179 50.000 29.98 15.58 41.37 4.84
527 723 0.043053 CATATTCTGACGCGGCGTTG 60.043 55.000 29.98 23.36 41.37 4.10
528 724 1.762222 ATATTCTGACGCGGCGTTGC 61.762 55.000 29.98 17.94 41.37 4.17
542 739 1.336877 CGTTGCTGAGATTCGTTCGA 58.663 50.000 0.00 0.00 0.00 3.71
543 740 1.057847 CGTTGCTGAGATTCGTTCGAC 59.942 52.381 0.00 0.00 0.00 4.20
549 746 2.623889 CTGAGATTCGTTCGACCCCTAT 59.376 50.000 0.00 0.00 0.00 2.57
562 769 0.631212 CCCCTATGGTGGCCTTTTCT 59.369 55.000 3.32 0.00 0.00 2.52
579 786 1.392589 TCTAGGGGTTTAGCCGTACG 58.607 55.000 8.69 8.69 38.44 3.67
580 787 1.106285 CTAGGGGTTTAGCCGTACGT 58.894 55.000 15.21 0.00 38.44 3.57
582 789 0.686789 AGGGGTTTAGCCGTACGTTT 59.313 50.000 15.21 4.23 38.44 3.60
583 790 0.798159 GGGGTTTAGCCGTACGTTTG 59.202 55.000 15.21 0.00 38.44 2.93
584 791 0.798159 GGGTTTAGCCGTACGTTTGG 59.202 55.000 15.21 0.00 38.44 3.28
585 792 0.798159 GGTTTAGCCGTACGTTTGGG 59.202 55.000 15.21 0.00 0.00 4.12
586 793 0.798159 GTTTAGCCGTACGTTTGGGG 59.202 55.000 15.21 0.00 0.00 4.96
587 794 0.321475 TTTAGCCGTACGTTTGGGGG 60.321 55.000 15.21 0.00 0.00 5.40
588 795 1.479368 TTAGCCGTACGTTTGGGGGT 61.479 55.000 15.21 5.73 0.00 4.95
589 796 2.169937 TAGCCGTACGTTTGGGGGTG 62.170 60.000 15.21 0.00 0.00 4.61
590 797 2.358984 CCGTACGTTTGGGGGTGG 60.359 66.667 15.21 0.00 0.00 4.61
591 798 2.358984 CGTACGTTTGGGGGTGGG 60.359 66.667 7.22 0.00 0.00 4.61
594 801 2.831645 TACGTTTGGGGGTGGGGTG 61.832 63.158 0.00 0.00 0.00 4.61
595 802 4.986708 CGTTTGGGGGTGGGGTGG 62.987 72.222 0.00 0.00 0.00 4.61
621 834 4.435436 TCTGCTGCTGGTACGCCG 62.435 66.667 6.69 0.00 37.67 6.46
663 876 4.854924 TGTGCCGGCGATGGATGG 62.855 66.667 23.90 0.00 0.00 3.51
664 877 4.856801 GTGCCGGCGATGGATGGT 62.857 66.667 23.90 0.00 0.00 3.55
665 878 4.108299 TGCCGGCGATGGATGGTT 62.108 61.111 23.90 0.00 0.00 3.67
666 879 3.585990 GCCGGCGATGGATGGTTG 61.586 66.667 12.58 0.00 0.00 3.77
667 880 2.901840 CCGGCGATGGATGGTTGG 60.902 66.667 9.30 0.00 0.00 3.77
668 881 2.189257 CGGCGATGGATGGTTGGA 59.811 61.111 0.00 0.00 0.00 3.53
669 882 1.227943 CGGCGATGGATGGTTGGAT 60.228 57.895 0.00 0.00 0.00 3.41
670 883 1.509644 CGGCGATGGATGGTTGGATG 61.510 60.000 0.00 0.00 0.00 3.51
675 888 2.589720 GATGGATGGTTGGATGATGCA 58.410 47.619 0.00 0.00 0.00 3.96
682 895 1.134753 GGTTGGATGATGCATTTGCGA 59.865 47.619 0.00 0.00 45.83 5.10
698 911 1.001293 TGCGATTTCTGTCAGCTCAGT 59.999 47.619 2.63 0.00 36.85 3.41
712 925 4.023963 TCAGCTCAGTCCGTATCGATTTAG 60.024 45.833 1.71 0.00 0.00 1.85
718 931 6.286758 TCAGTCCGTATCGATTTAGTCTAGT 58.713 40.000 1.71 0.00 0.00 2.57
719 932 7.436933 TCAGTCCGTATCGATTTAGTCTAGTA 58.563 38.462 1.71 0.00 0.00 1.82
729 942 5.050227 CGATTTAGTCTAGTACTCTGTCCGG 60.050 48.000 0.00 0.00 39.80 5.14
738 951 1.376037 CTCTGTCCGGCTGGTTTCC 60.376 63.158 12.43 0.00 36.30 3.13
750 963 2.352127 GCTGGTTTCCATTCAGTTGCTC 60.352 50.000 0.00 0.00 30.82 4.26
756 969 1.425066 TCCATTCAGTTGCTCCCTGTT 59.575 47.619 0.00 0.00 0.00 3.16
757 970 2.158475 TCCATTCAGTTGCTCCCTGTTT 60.158 45.455 0.00 0.00 0.00 2.83
758 971 2.229784 CCATTCAGTTGCTCCCTGTTTC 59.770 50.000 0.00 0.00 0.00 2.78
759 972 2.727123 TTCAGTTGCTCCCTGTTTCA 57.273 45.000 0.00 0.00 0.00 2.69
760 973 2.260844 TCAGTTGCTCCCTGTTTCAG 57.739 50.000 0.00 0.00 0.00 3.02
761 974 1.490490 TCAGTTGCTCCCTGTTTCAGT 59.510 47.619 0.00 0.00 0.00 3.41
762 975 2.092429 TCAGTTGCTCCCTGTTTCAGTT 60.092 45.455 0.00 0.00 0.00 3.16
763 976 2.689983 CAGTTGCTCCCTGTTTCAGTTT 59.310 45.455 0.00 0.00 0.00 2.66
764 977 2.952310 AGTTGCTCCCTGTTTCAGTTTC 59.048 45.455 0.00 0.00 0.00 2.78
765 978 2.687935 GTTGCTCCCTGTTTCAGTTTCA 59.312 45.455 0.00 0.00 0.00 2.69
766 979 2.575532 TGCTCCCTGTTTCAGTTTCAG 58.424 47.619 0.00 0.00 0.00 3.02
767 980 2.092429 TGCTCCCTGTTTCAGTTTCAGT 60.092 45.455 0.00 0.00 0.00 3.41
775 988 6.389906 CCTGTTTCAGTTTCAGTTTCAGTTT 58.610 36.000 0.00 0.00 0.00 2.66
826 1054 4.095036 TGCACGATTTGTTGTCACTTGTTA 59.905 37.500 0.00 0.00 0.00 2.41
864 1108 4.232221 CTGTGCTCGATTTCAAATTGCTT 58.768 39.130 0.00 0.00 0.00 3.91
915 1162 3.943137 TACCACCCCCAGCCCTCAG 62.943 68.421 0.00 0.00 0.00 3.35
1090 1337 0.389817 CCTCAACAAGATCGCCGACA 60.390 55.000 0.00 0.00 0.00 4.35
1122 1369 3.839642 GATCGGCCTCAGCGAGCTC 62.840 68.421 2.73 2.73 41.24 4.09
1158 1405 4.096003 CTCGCCCCGGACATGGTT 62.096 66.667 0.73 0.00 0.00 3.67
1655 1902 6.321181 CCTCTCCTGCTCTCCTATATCAATAC 59.679 46.154 0.00 0.00 0.00 1.89
1699 1948 2.970576 GCACTAGCACTCTAGCAGC 58.029 57.895 0.00 0.00 44.83 5.25
1700 1949 0.174389 GCACTAGCACTCTAGCAGCA 59.826 55.000 0.00 0.00 44.83 4.41
1701 1950 1.919918 CACTAGCACTCTAGCAGCAC 58.080 55.000 0.00 0.00 44.83 4.40
1702 1951 1.476085 CACTAGCACTCTAGCAGCACT 59.524 52.381 0.00 0.00 44.83 4.40
1703 1952 2.685388 CACTAGCACTCTAGCAGCACTA 59.315 50.000 0.00 0.00 44.83 2.74
1704 1953 2.685897 ACTAGCACTCTAGCAGCACTAC 59.314 50.000 0.00 0.00 44.83 2.73
1782 2031 5.481473 TGAGGGCTTTGCTTTTATCATCTTT 59.519 36.000 0.00 0.00 0.00 2.52
1825 2074 5.271598 AGCCATTCTGGTCCATCATTTTTA 58.728 37.500 0.00 0.00 40.46 1.52
1851 2100 5.869888 CAGAACATGGTCTAGGTAGTTGAAC 59.130 44.000 14.23 0.00 0.00 3.18
1891 2140 6.373216 GGCATGCATCATTAATTGCCATAAAT 59.627 34.615 21.36 0.50 46.87 1.40
1936 2190 0.744874 CATGGGAAGGAAGCATGCTG 59.255 55.000 23.48 0.81 0.00 4.41
1951 2205 4.046462 GCATGCTGCATTGTAATAACAGG 58.954 43.478 13.38 0.00 44.26 4.00
1961 2215 6.677920 GCATTGTAATAACAGGGTAGCTGTTG 60.678 42.308 15.48 5.45 43.81 3.33
2037 2334 2.090760 TCAGCAGCTTGTCACACAAAA 58.909 42.857 0.00 0.00 37.69 2.44
2038 2335 2.689471 TCAGCAGCTTGTCACACAAAAT 59.311 40.909 0.00 0.00 37.69 1.82
2039 2336 3.882288 TCAGCAGCTTGTCACACAAAATA 59.118 39.130 0.00 0.00 37.69 1.40
2040 2337 3.976942 CAGCAGCTTGTCACACAAAATAC 59.023 43.478 0.00 0.00 37.69 1.89
2053 2354 5.124457 CACACAAAATACATCTAGCTTGCCT 59.876 40.000 0.00 0.00 0.00 4.75
2055 2356 6.209391 ACACAAAATACATCTAGCTTGCCTTT 59.791 34.615 0.00 0.00 0.00 3.11
2056 2357 7.092716 CACAAAATACATCTAGCTTGCCTTTT 58.907 34.615 0.00 0.00 0.00 2.27
2074 2375 0.947180 TTAAAGTCGGGTGTCGCTGC 60.947 55.000 0.00 0.00 39.05 5.25
2465 2784 7.572539 GCTGTAAATTTGACAAGGTAGGTACAC 60.573 40.741 0.00 0.00 0.00 2.90
2470 2789 4.530710 TGACAAGGTAGGTACACACATC 57.469 45.455 0.00 0.00 0.00 3.06
2527 2847 6.677781 TGCTATAGTAATGTTTGTGCTTCC 57.322 37.500 0.84 0.00 0.00 3.46
2556 2876 0.604243 TAAAACCGGTGCGTGATGCT 60.604 50.000 8.52 0.00 46.63 3.79
2571 2891 4.588899 GTGATGCTATTACCCATGCCATA 58.411 43.478 0.00 0.00 0.00 2.74
2589 2909 4.399303 GCCATACAGTTGTGGAAAGCTATT 59.601 41.667 8.49 0.00 36.04 1.73
2613 2933 1.633774 GGTCTGAGACTCCTGAACCA 58.366 55.000 12.92 0.00 32.47 3.67
2706 3306 5.244626 AGGAAAGCAGATGCAATACTTTGTT 59.755 36.000 7.68 0.00 45.16 2.83
2707 3307 5.928264 GGAAAGCAGATGCAATACTTTGTTT 59.072 36.000 7.68 0.00 45.16 2.83
2998 3602 1.142667 TCAAGTGACTGGCATGTGGAA 59.857 47.619 0.00 0.00 0.00 3.53
3034 3638 3.963374 AGCAGAATACAGTGCCAGATCTA 59.037 43.478 0.00 0.00 40.81 1.98
3036 3640 4.202202 GCAGAATACAGTGCCAGATCTAGT 60.202 45.833 0.00 0.00 33.29 2.57
3240 3844 5.011023 TCACTGAAGATGTCACTGAGCTTTA 59.989 40.000 0.00 0.00 29.04 1.85
3250 3854 0.470341 CTGAGCTTTACCCTAGGGCC 59.530 60.000 28.88 11.00 39.32 5.80
3328 3932 1.134818 ACTTGTTGTCTGAGTGCGACA 60.135 47.619 0.00 0.00 39.45 4.35
3335 3939 2.607635 TGTCTGAGTGCGACAAAAGAAC 59.392 45.455 0.00 0.00 38.36 3.01
3536 4362 3.029320 TCACATGGAAAAATGCTGTGC 57.971 42.857 0.00 0.00 37.66 4.57
3578 4404 6.483974 TGAACAAACCACGTATGTAAAGATGT 59.516 34.615 0.00 0.00 0.00 3.06
3634 4461 5.794726 TGTACTAACTACTGTGGAGCAAA 57.205 39.130 0.00 0.00 0.00 3.68
3643 4470 1.081840 GTGGAGCAAAAGCGCACTC 60.082 57.895 11.47 8.00 0.00 3.51
3848 4676 4.042809 TCTTCACCCAGGCTTTCTAATTCA 59.957 41.667 0.00 0.00 0.00 2.57
3946 4774 3.259374 CACGATCTACCATCTAAGGGCAT 59.741 47.826 0.00 0.00 0.00 4.40
4060 4888 4.993705 ACATTCCAAGTTTAGTGAGGGA 57.006 40.909 0.00 0.00 0.00 4.20
4119 4947 4.801330 TTTACGAGTCCATGTGATCAGT 57.199 40.909 0.00 0.00 0.00 3.41
4272 5100 0.823356 TGGGCCTGTTCTTGACAAGC 60.823 55.000 10.50 0.00 43.53 4.01
4315 5143 7.775053 ATGAACTTTTAAGGGTTATTGCTGA 57.225 32.000 0.00 0.00 0.00 4.26
4327 5155 1.915141 ATTGCTGACCAGTTCCTTGG 58.085 50.000 0.00 0.00 44.09 3.61
4827 5656 4.307432 CACCGTGATGTGAAGTACTTCTT 58.693 43.478 30.47 18.17 40.14 2.52
4846 5682 3.907474 TCTTCCTTGTGATGTGACCCTAA 59.093 43.478 0.00 0.00 0.00 2.69
4854 5690 3.684788 GTGATGTGACCCTAATGTGTGTC 59.315 47.826 0.00 0.00 0.00 3.67
4865 5701 2.183478 ATGTGTGTCGAGGCATCAAA 57.817 45.000 0.00 0.00 0.00 2.69
5016 5852 1.949525 CAGAAGAGGTGGTGGTTGTTG 59.050 52.381 0.00 0.00 0.00 3.33
5054 5890 3.248363 TCTTTTCTCGAACACTCGTCGTA 59.752 43.478 0.00 0.00 45.62 3.43
5092 5928 6.926272 GTGTATTAGAAGAAGAATGCCGAGAT 59.074 38.462 0.00 0.00 0.00 2.75
5105 5941 2.789917 GAGATGGCGCTTGCTGTG 59.210 61.111 7.64 0.00 39.13 3.66
5132 5968 2.418368 TGTGTGGTGTTTGCTCTCTT 57.582 45.000 0.00 0.00 0.00 2.85
5226 6063 3.521937 ACTACCTACTTATGCTTGCCCAA 59.478 43.478 0.00 0.00 0.00 4.12
5303 6141 2.721425 AAACACACGGGGAAAGAAGA 57.279 45.000 0.00 0.00 0.00 2.87
5437 6275 3.523564 ACCAGTGTTGCTTACCCTCATAT 59.476 43.478 0.00 0.00 0.00 1.78
5455 6293 9.244292 CCCTCATATGCTGTTCTAGTAAGTATA 57.756 37.037 0.00 0.00 0.00 1.47
5486 6324 0.109342 GGGCATCACCAATCCGAGAT 59.891 55.000 0.00 0.00 42.05 2.75
5499 6337 2.520039 CGAGATGTCGCTGCGCATT 61.520 57.895 24.66 17.23 39.88 3.56
5515 6353 1.519455 ATTGACGCGCTGTAGAGGC 60.519 57.895 5.73 0.00 0.00 4.70
5516 6354 2.907897 ATTGACGCGCTGTAGAGGCC 62.908 60.000 5.73 0.00 0.00 5.19
5568 6406 3.699894 CAGCCGGTGAGCTCCTGT 61.700 66.667 12.15 0.00 42.61 4.00
5577 6415 0.178950 TGAGCTCCTGTGACACCTCT 60.179 55.000 12.15 0.00 0.00 3.69
5584 6422 1.338484 CCTGTGACACCTCTGACATGG 60.338 57.143 2.45 0.00 0.00 3.66
5663 6503 9.745323 GCAGTTTTCAGATTTAATTTTACATGC 57.255 29.630 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 5.510861 GCCCTCTTTCTTTAACCTTTTTCCC 60.511 44.000 0.00 0.00 0.00 3.97
71 72 3.423154 CGTGCCGTGCCCTCTTTC 61.423 66.667 0.00 0.00 0.00 2.62
126 142 3.372822 GGATTTGAATTCGAACTGCGGTA 59.627 43.478 10.38 0.00 41.33 4.02
127 143 2.161609 GGATTTGAATTCGAACTGCGGT 59.838 45.455 10.38 0.00 41.33 5.68
128 144 2.477863 GGGATTTGAATTCGAACTGCGG 60.478 50.000 10.38 0.00 41.33 5.69
129 145 2.477863 GGGGATTTGAATTCGAACTGCG 60.478 50.000 10.38 0.00 42.69 5.18
154 178 4.704833 TCCGCTTCCACCAGCAGC 62.705 66.667 0.00 0.00 40.09 5.25
155 179 2.032528 TTCCGCTTCCACCAGCAG 59.967 61.111 0.00 0.00 40.09 4.24
158 182 1.078848 CTCCTTCCGCTTCCACCAG 60.079 63.158 0.00 0.00 0.00 4.00
163 187 1.222113 CCCTTCTCCTTCCGCTTCC 59.778 63.158 0.00 0.00 0.00 3.46
165 189 2.972819 GCCCCTTCTCCTTCCGCTT 61.973 63.158 0.00 0.00 0.00 4.68
166 190 3.403558 GCCCCTTCTCCTTCCGCT 61.404 66.667 0.00 0.00 0.00 5.52
168 192 4.162690 CGGCCCCTTCTCCTTCCG 62.163 72.222 0.00 0.00 0.00 4.30
174 205 3.930012 CCGATCCGGCCCCTTCTC 61.930 72.222 0.00 0.00 41.17 2.87
245 287 3.545481 CACTTACAGCGCGCTCCG 61.545 66.667 34.28 24.16 40.75 4.63
246 288 3.854459 GCACTTACAGCGCGCTCC 61.854 66.667 34.28 9.63 0.00 4.70
251 293 3.854459 GAGCGGCACTTACAGCGC 61.854 66.667 0.00 0.00 34.34 5.92
252 294 3.188786 GGAGCGGCACTTACAGCG 61.189 66.667 1.45 0.00 34.34 5.18
254 296 0.741221 GAAGGGAGCGGCACTTACAG 60.741 60.000 1.45 0.00 41.32 2.74
256 298 1.449778 GGAAGGGAGCGGCACTTAC 60.450 63.158 1.45 0.43 41.32 2.34
257 299 1.612442 AGGAAGGGAGCGGCACTTA 60.612 57.895 1.45 0.00 41.32 2.24
258 300 2.930562 AGGAAGGGAGCGGCACTT 60.931 61.111 1.45 3.38 44.81 3.16
259 301 3.710722 CAGGAAGGGAGCGGCACT 61.711 66.667 1.45 0.00 0.00 4.40
271 349 1.045350 CGAGAGGATGGAGGCAGGAA 61.045 60.000 0.00 0.00 0.00 3.36
273 351 3.136750 CGAGAGGATGGAGGCAGG 58.863 66.667 0.00 0.00 0.00 4.85
304 382 2.359850 TTAGCTTGGCTGGCACGG 60.360 61.111 2.29 0.98 40.10 4.94
305 383 1.364626 CTCTTAGCTTGGCTGGCACG 61.365 60.000 2.29 2.81 40.10 5.34
306 384 1.028868 CCTCTTAGCTTGGCTGGCAC 61.029 60.000 2.29 0.00 40.10 5.01
308 386 0.035056 TTCCTCTTAGCTTGGCTGGC 60.035 55.000 0.00 0.00 40.10 4.85
309 387 1.280421 ACTTCCTCTTAGCTTGGCTGG 59.720 52.381 0.00 0.00 40.10 4.85
310 388 2.777832 ACTTCCTCTTAGCTTGGCTG 57.222 50.000 0.00 0.00 40.10 4.85
320 476 2.166664 CTCCGGATTCGAACTTCCTCTT 59.833 50.000 3.57 0.00 39.00 2.85
326 482 0.458025 GTCGCTCCGGATTCGAACTT 60.458 55.000 24.44 0.00 39.00 2.66
328 484 0.866483 GAGTCGCTCCGGATTCGAAC 60.866 60.000 24.44 18.57 39.00 3.95
329 485 1.432251 GAGTCGCTCCGGATTCGAA 59.568 57.895 24.44 0.00 39.00 3.71
350 537 4.803426 AGCTAGAGCACGGCGCAC 62.803 66.667 10.83 0.00 46.13 5.34
378 565 2.103934 CTCGCCTCGGAGCAGAAG 59.896 66.667 0.00 0.00 0.00 2.85
392 584 3.270877 CAGTGTTATTTTCCCTCCCTCG 58.729 50.000 0.00 0.00 0.00 4.63
395 587 3.439129 CGAACAGTGTTATTTTCCCTCCC 59.561 47.826 8.88 0.00 0.00 4.30
419 611 4.210304 GACAAGATGACGCCGCGC 62.210 66.667 13.88 6.47 0.00 6.86
423 615 1.590238 CGAAGATGACAAGATGACGCC 59.410 52.381 0.00 0.00 0.00 5.68
433 625 2.526888 AGACTACCCCGAAGATGACA 57.473 50.000 0.00 0.00 0.00 3.58
437 629 4.446023 CCAGTACTAGACTACCCCGAAGAT 60.446 50.000 0.00 0.00 35.64 2.40
438 630 3.118112 CCAGTACTAGACTACCCCGAAGA 60.118 52.174 0.00 0.00 35.64 2.87
439 631 3.212685 CCAGTACTAGACTACCCCGAAG 58.787 54.545 0.00 0.00 35.64 3.79
441 633 1.492176 CCCAGTACTAGACTACCCCGA 59.508 57.143 0.00 0.00 35.64 5.14
442 634 1.478288 CCCCAGTACTAGACTACCCCG 60.478 61.905 0.00 0.00 35.64 5.73
443 635 1.133231 CCCCCAGTACTAGACTACCCC 60.133 61.905 0.00 0.00 35.64 4.95
444 636 2.378378 CCCCCAGTACTAGACTACCC 57.622 60.000 0.00 0.00 35.64 3.69
460 652 3.140814 GCACAAATCGGAGCCCCC 61.141 66.667 0.00 0.00 0.00 5.40
461 653 3.140814 GGCACAAATCGGAGCCCC 61.141 66.667 0.00 0.00 41.25 5.80
463 655 3.140814 GGGGCACAAATCGGAGCC 61.141 66.667 0.00 0.00 46.28 4.70
464 656 3.508840 CGGGGCACAAATCGGAGC 61.509 66.667 0.00 0.00 0.00 4.70
465 657 0.748005 AATCGGGGCACAAATCGGAG 60.748 55.000 0.00 0.00 0.00 4.63
466 658 0.746563 GAATCGGGGCACAAATCGGA 60.747 55.000 0.00 0.00 0.00 4.55
467 659 1.727467 GAATCGGGGCACAAATCGG 59.273 57.895 0.00 0.00 0.00 4.18
468 660 1.351707 CGAATCGGGGCACAAATCG 59.648 57.895 0.00 0.00 0.00 3.34
469 661 1.064134 GCGAATCGGGGCACAAATC 59.936 57.895 4.35 0.00 0.00 2.17
470 662 2.760159 CGCGAATCGGGGCACAAAT 61.760 57.895 12.03 0.00 36.19 2.32
471 663 3.427425 CGCGAATCGGGGCACAAA 61.427 61.111 12.03 0.00 36.19 2.83
499 695 3.301197 CGCGTCAGAATATGAACTGAACG 60.301 47.826 0.00 0.00 43.29 3.95
504 700 1.571919 GCCGCGTCAGAATATGAACT 58.428 50.000 4.92 0.00 40.43 3.01
510 706 2.449525 GCAACGCCGCGTCAGAATA 61.450 57.895 20.46 0.00 39.99 1.75
517 713 4.742201 ATCTCAGCAACGCCGCGT 62.742 61.111 13.85 13.85 43.97 6.01
518 714 3.425938 GAATCTCAGCAACGCCGCG 62.426 63.158 12.14 12.14 36.85 6.46
519 715 2.401195 GAATCTCAGCAACGCCGC 59.599 61.111 0.00 0.00 0.00 6.53
520 716 1.626654 AACGAATCTCAGCAACGCCG 61.627 55.000 0.00 0.00 0.00 6.46
522 718 0.246912 CGAACGAATCTCAGCAACGC 60.247 55.000 0.00 0.00 0.00 4.84
523 719 1.057847 GTCGAACGAATCTCAGCAACG 59.942 52.381 0.00 0.00 0.00 4.10
524 720 1.390463 GGTCGAACGAATCTCAGCAAC 59.610 52.381 0.00 0.00 0.00 4.17
526 722 0.108804 GGGTCGAACGAATCTCAGCA 60.109 55.000 0.00 0.00 0.00 4.41
527 723 0.806492 GGGGTCGAACGAATCTCAGC 60.806 60.000 0.00 0.00 0.00 4.26
528 724 0.818296 AGGGGTCGAACGAATCTCAG 59.182 55.000 0.00 0.00 0.00 3.35
543 740 0.631212 AGAAAAGGCCACCATAGGGG 59.369 55.000 5.01 0.00 44.81 4.79
549 746 0.774491 ACCCCTAGAAAAGGCCACCA 60.774 55.000 5.01 0.00 45.03 4.17
552 759 2.291346 GCTAAACCCCTAGAAAAGGCCA 60.291 50.000 5.01 0.00 45.03 5.36
555 762 2.026542 ACGGCTAAACCCCTAGAAAAGG 60.027 50.000 0.00 0.00 46.09 3.11
556 763 3.345508 ACGGCTAAACCCCTAGAAAAG 57.654 47.619 0.00 0.00 33.26 2.27
558 765 2.166254 CGTACGGCTAAACCCCTAGAAA 59.834 50.000 7.57 0.00 33.26 2.52
562 769 1.555967 AACGTACGGCTAAACCCCTA 58.444 50.000 21.06 0.00 33.26 3.53
579 786 4.631740 CCCACCCCACCCCCAAAC 62.632 72.222 0.00 0.00 0.00 2.93
600 807 2.097038 CGTACCAGCAGCAGAGCAC 61.097 63.158 0.00 0.00 36.85 4.40
603 810 2.510238 GGCGTACCAGCAGCAGAG 60.510 66.667 0.00 0.00 39.27 3.35
645 858 2.592574 CATCCATCGCCGGCACAT 60.593 61.111 28.98 15.13 0.00 3.21
646 859 4.854924 CCATCCATCGCCGGCACA 62.855 66.667 28.98 13.13 0.00 4.57
647 860 4.856801 ACCATCCATCGCCGGCAC 62.857 66.667 28.98 0.00 0.00 5.01
663 876 2.565210 TCGCAAATGCATCATCCAAC 57.435 45.000 0.00 0.00 42.21 3.77
664 877 3.804786 AATCGCAAATGCATCATCCAA 57.195 38.095 0.00 0.00 42.21 3.53
665 878 3.382227 AGAAATCGCAAATGCATCATCCA 59.618 39.130 0.00 0.00 42.21 3.41
666 879 3.734231 CAGAAATCGCAAATGCATCATCC 59.266 43.478 0.00 0.00 42.21 3.51
667 880 4.357142 ACAGAAATCGCAAATGCATCATC 58.643 39.130 0.00 0.00 42.21 2.92
668 881 4.142337 TGACAGAAATCGCAAATGCATCAT 60.142 37.500 0.00 0.00 42.21 2.45
669 882 3.190953 TGACAGAAATCGCAAATGCATCA 59.809 39.130 0.00 0.00 42.21 3.07
670 883 3.761657 TGACAGAAATCGCAAATGCATC 58.238 40.909 0.00 0.00 42.21 3.91
675 888 3.076621 TGAGCTGACAGAAATCGCAAAT 58.923 40.909 6.65 0.00 0.00 2.32
682 895 1.620819 ACGGACTGAGCTGACAGAAAT 59.379 47.619 6.65 0.00 40.63 2.17
698 911 7.598118 CAGAGTACTAGACTAAATCGATACGGA 59.402 40.741 0.00 0.00 39.06 4.69
712 925 1.671845 CAGCCGGACAGAGTACTAGAC 59.328 57.143 5.05 0.00 0.00 2.59
718 931 0.606604 GAAACCAGCCGGACAGAGTA 59.393 55.000 5.05 0.00 35.59 2.59
719 932 1.371558 GAAACCAGCCGGACAGAGT 59.628 57.895 5.05 0.00 35.59 3.24
729 942 1.615392 AGCAACTGAATGGAAACCAGC 59.385 47.619 0.00 0.00 36.75 4.85
738 951 2.886523 TGAAACAGGGAGCAACTGAATG 59.113 45.455 8.96 0.00 39.24 2.67
750 963 4.399303 ACTGAAACTGAAACTGAAACAGGG 59.601 41.667 0.00 0.00 35.51 4.45
756 969 6.817765 ACTGAAACTGAAACTGAAACTGAA 57.182 33.333 0.00 0.00 0.00 3.02
757 970 6.817765 AACTGAAACTGAAACTGAAACTGA 57.182 33.333 0.00 0.00 0.00 3.41
758 971 7.083858 TGAAACTGAAACTGAAACTGAAACTG 58.916 34.615 0.00 0.00 0.00 3.16
759 972 7.040409 ACTGAAACTGAAACTGAAACTGAAACT 60.040 33.333 0.00 0.00 0.00 2.66
760 973 7.084486 ACTGAAACTGAAACTGAAACTGAAAC 58.916 34.615 0.00 0.00 0.00 2.78
761 974 7.214467 ACTGAAACTGAAACTGAAACTGAAA 57.786 32.000 0.00 0.00 0.00 2.69
762 975 6.817765 ACTGAAACTGAAACTGAAACTGAA 57.182 33.333 0.00 0.00 0.00 3.02
763 976 6.429692 TCAACTGAAACTGAAACTGAAACTGA 59.570 34.615 0.00 0.00 0.00 3.41
764 977 6.611381 TCAACTGAAACTGAAACTGAAACTG 58.389 36.000 0.00 0.00 0.00 3.16
765 978 6.817765 TCAACTGAAACTGAAACTGAAACT 57.182 33.333 0.00 0.00 0.00 2.66
766 979 8.466086 AAATCAACTGAAACTGAAACTGAAAC 57.534 30.769 0.00 0.00 0.00 2.78
767 980 8.522830 AGAAATCAACTGAAACTGAAACTGAAA 58.477 29.630 0.00 0.00 0.00 2.69
826 1054 5.916883 CGAGCACAGTGAGATTCAAAATTTT 59.083 36.000 4.15 0.00 0.00 1.82
844 1087 4.664891 GCAAAGCAATTTGAAATCGAGCAC 60.665 41.667 0.00 0.00 33.95 4.40
864 1108 0.685131 CCATGGCTTGATCCCTGCAA 60.685 55.000 0.00 0.00 0.00 4.08
912 1159 0.043183 TCATCTTCCCCTGAGGCTGA 59.957 55.000 0.00 0.00 34.51 4.26
915 1162 1.134250 GTCTTCATCTTCCCCTGAGGC 60.134 57.143 0.00 0.00 34.51 4.70
918 1165 2.774234 GGATGTCTTCATCTTCCCCTGA 59.226 50.000 7.89 0.00 46.74 3.86
1063 1310 0.622665 ATCTTGTTGAGGGCCTGGAG 59.377 55.000 12.95 0.95 0.00 3.86
1090 1337 0.397254 CCGATCTGGTAGGTGTCCCT 60.397 60.000 0.00 0.00 45.51 4.20
1158 1405 2.285668 CAGGAGAGGAAGGGGCCA 60.286 66.667 4.39 0.00 0.00 5.36
1497 1744 3.307674 GAAGTAGCTGCTCTCATCGATG 58.692 50.000 19.61 19.61 0.00 3.84
1655 1902 4.806640 AGGGGTTCAATTACAATGCAAG 57.193 40.909 0.00 0.00 0.00 4.01
1703 1952 9.499479 CCAAAATAGAGAGAACATATATGCAGT 57.501 33.333 12.79 0.00 0.00 4.40
1704 1953 8.449397 GCCAAAATAGAGAGAACATATATGCAG 58.551 37.037 12.79 0.00 0.00 4.41
1825 2074 5.958380 TCAACTACCTAGACCATGTTCTGAT 59.042 40.000 2.51 0.00 0.00 2.90
1851 2100 3.181498 TGCATGCCATGACTACAAAATCG 60.181 43.478 16.68 0.00 0.00 3.34
1899 2153 8.418597 TTCCCATGATACTACTACTAATCACC 57.581 38.462 0.00 0.00 31.56 4.02
1902 2156 8.880991 TCCTTCCCATGATACTACTACTAATC 57.119 38.462 0.00 0.00 0.00 1.75
1936 2190 5.424121 CAGCTACCCTGTTATTACAATGC 57.576 43.478 0.00 0.00 36.79 3.56
1951 2205 3.673323 GCAGCCATTAAACAACAGCTACC 60.673 47.826 0.00 0.00 0.00 3.18
2021 2318 6.005583 AGATGTATTTTGTGTGACAAGCTG 57.994 37.500 0.00 0.00 39.53 4.24
2024 2321 7.369803 AGCTAGATGTATTTTGTGTGACAAG 57.630 36.000 0.00 0.00 39.53 3.16
2037 2334 7.011482 CGACTTTAAAAGGCAAGCTAGATGTAT 59.989 37.037 0.00 0.00 35.79 2.29
2038 2335 6.312918 CGACTTTAAAAGGCAAGCTAGATGTA 59.687 38.462 0.00 0.00 35.79 2.29
2039 2336 5.122396 CGACTTTAAAAGGCAAGCTAGATGT 59.878 40.000 0.00 0.00 35.79 3.06
2040 2337 5.447818 CCGACTTTAAAAGGCAAGCTAGATG 60.448 44.000 0.00 0.00 35.79 2.90
2053 2354 1.868498 CAGCGACACCCGACTTTAAAA 59.132 47.619 0.00 0.00 41.76 1.52
2055 2356 0.947180 GCAGCGACACCCGACTTTAA 60.947 55.000 0.00 0.00 41.76 1.52
2056 2357 1.373748 GCAGCGACACCCGACTTTA 60.374 57.895 0.00 0.00 41.76 1.85
2074 2375 2.724977 TACTCGGAGTGAACAAGCAG 57.275 50.000 20.58 0.00 0.00 4.24
2204 2505 7.506114 AGGTCAATCTCAAGTTACAACTTACA 58.494 34.615 7.02 0.00 46.89 2.41
2465 2784 3.849708 CACTGCATCAATTTCACGATGTG 59.150 43.478 0.00 0.00 40.93 3.21
2470 2789 3.541071 TGTCACTGCATCAATTTCACG 57.459 42.857 0.00 0.00 0.00 4.35
2527 2847 3.739300 CGCACCGGTTTTACCTATCATAG 59.261 47.826 2.97 0.00 35.66 2.23
2556 2876 5.129634 CACAACTGTATGGCATGGGTAATA 58.870 41.667 10.98 0.00 0.00 0.98
2571 2891 4.074970 CTGGAATAGCTTTCCACAACTGT 58.925 43.478 19.97 0.00 43.17 3.55
2589 2909 0.040351 CAGGAGTCTCAGACCCTGGA 59.960 60.000 24.58 0.00 42.14 3.86
2595 2915 2.828520 TGATGGTTCAGGAGTCTCAGAC 59.171 50.000 0.00 0.00 0.00 3.51
2794 3398 3.249320 CACTTCTGGCATCATTATGGTCG 59.751 47.826 0.00 0.00 33.38 4.79
2998 3602 7.291182 ACTGTATTCTGCTTAGGGACTGATATT 59.709 37.037 0.00 0.00 41.52 1.28
3034 3638 3.026694 GCTGCCATATCCCTTTTTCACT 58.973 45.455 0.00 0.00 0.00 3.41
3036 3640 3.098774 TGCTGCCATATCCCTTTTTCA 57.901 42.857 0.00 0.00 0.00 2.69
3240 3844 3.028098 TCTCTCGGGCCCTAGGGT 61.028 66.667 28.96 0.00 37.65 4.34
3250 3854 2.034053 GTCTATGCTCTTGGTCTCTCGG 59.966 54.545 0.00 0.00 0.00 4.63
3328 3932 6.829298 GCTTCCTAATAAGGGCTAGTTCTTTT 59.171 38.462 5.32 3.87 43.84 2.27
3335 3939 5.297569 AGTTGCTTCCTAATAAGGGCTAG 57.702 43.478 0.00 0.00 43.84 3.42
3946 4774 3.118038 ACCCTCTTTTACACAAGTGCTCA 60.118 43.478 0.00 0.00 0.00 4.26
3956 4784 7.230747 TCAGAAATTCATGACCCTCTTTTACA 58.769 34.615 0.00 0.00 0.00 2.41
4051 4879 2.234143 CAGATGCTCGATCCCTCACTA 58.766 52.381 0.00 0.00 0.00 2.74
4060 4888 0.467384 CTTGACCCCAGATGCTCGAT 59.533 55.000 0.00 0.00 0.00 3.59
4272 5100 2.368131 TTTGCCGTTTCACGCGACAG 62.368 55.000 15.93 1.66 40.91 3.51
4315 5143 1.341976 ACTTTGTGCCAAGGAACTGGT 60.342 47.619 0.00 0.00 40.86 4.00
4327 5155 3.740832 GGCCAAGTCAAATAACTTTGTGC 59.259 43.478 0.00 0.00 42.02 4.57
4539 5367 2.033141 TGCTTCCTCCAGTGCAGC 59.967 61.111 0.00 0.00 0.00 5.25
4827 5656 3.587061 ACATTAGGGTCACATCACAAGGA 59.413 43.478 0.00 0.00 0.00 3.36
4846 5682 1.806542 GTTTGATGCCTCGACACACAT 59.193 47.619 0.00 0.00 0.00 3.21
4854 5690 2.086869 AGGACATTGTTTGATGCCTCG 58.913 47.619 0.00 0.00 32.01 4.63
4865 5701 1.321474 CACCACTGCAAGGACATTGT 58.679 50.000 11.56 0.00 41.29 2.71
5016 5852 6.140265 CGAGAAAAGAAAACGAAAAAGGCTAC 59.860 38.462 0.00 0.00 0.00 3.58
5054 5890 4.816392 TCTAATACACAATGACACGCACT 58.184 39.130 0.00 0.00 0.00 4.40
5092 5928 3.654201 CTAACACAGCAAGCGCCA 58.346 55.556 2.29 0.00 39.83 5.69
5105 5941 2.798145 GCAAACACCACACAAGGCTAAC 60.798 50.000 0.00 0.00 0.00 2.34
5132 5968 0.171231 CTCGTTGATCACCTCTCGCA 59.829 55.000 0.00 0.00 0.00 5.10
5226 6063 8.225603 TGATACTTCACTGAAAAGAAAGCTTT 57.774 30.769 12.53 12.53 45.95 3.51
5303 6141 4.273480 GTGAACATGTAACTGCACTGAGTT 59.727 41.667 0.00 0.00 39.54 3.01
5455 6293 0.839277 TGATGCCCGTCCATCTGAAT 59.161 50.000 12.08 0.00 41.65 2.57
5499 6337 4.129737 GGCCTCTACAGCGCGTCA 62.130 66.667 8.43 0.00 0.00 4.35
5568 6406 1.679311 GCCCATGTCAGAGGTGTCA 59.321 57.895 0.00 0.00 0.00 3.58
5592 6430 1.961277 GCAGTCTGACCCACGGTTG 60.961 63.158 3.32 0.00 35.25 3.77
5594 6432 2.842462 TGCAGTCTGACCCACGGT 60.842 61.111 3.32 0.00 39.44 4.83
5596 6434 2.047844 CCTGCAGTCTGACCCACG 60.048 66.667 13.81 0.00 0.00 4.94
5598 6436 1.782201 AATGCCTGCAGTCTGACCCA 61.782 55.000 13.81 1.50 0.00 4.51
5701 6541 3.114616 CTGCGTCCAGGTTCAGCG 61.115 66.667 0.00 0.00 35.38 5.18
5723 6563 2.506217 GCTTCGCCGACGTGATCA 60.506 61.111 0.00 0.00 41.18 2.92


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

AutoCloner maintained by Alex Coulton.