Multiple sequence alignment - TraesCS5B01G263800

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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 TraesCS5B01G263800 chr5B 100.000 3747 0 0 1 3747 448224849 448221103 0.000000e+00 6920.0
1 TraesCS5B01G263800 chr5B 100.000 1396 0 0 3998 5393 448220852 448219457 0.000000e+00 2579.0
2 TraesCS5B01G263800 chr5B 92.779 734 45 3 35 767 643308951 643308225 0.000000e+00 1055.0
3 TraesCS5B01G263800 chr5B 83.175 315 32 19 458 763 506798665 506798967 8.900000e-68 268.0
4 TraesCS5B01G263800 chr5B 100.000 35 0 0 1 35 643308952 643308918 1.250000e-06 65.8
5 TraesCS5B01G263800 chr5B 90.698 43 4 0 106 148 643308946 643308904 2.100000e-04 58.4
6 TraesCS5B01G263800 chr5D 97.580 1694 36 4 2055 3747 375379602 375377913 0.000000e+00 2896.0
7 TraesCS5B01G263800 chr5D 91.530 1405 70 24 3998 5393 375377854 375376490 0.000000e+00 1890.0
8 TraesCS5B01G263800 chr5D 95.144 659 25 4 902 1559 375387465 375386813 0.000000e+00 1033.0
9 TraesCS5B01G263800 chr5D 87.448 478 47 12 1580 2050 375386825 375386354 6.150000e-149 538.0
10 TraesCS5B01G263800 chr5D 89.831 59 6 0 763 821 375388048 375387990 5.790000e-10 76.8
11 TraesCS5B01G263800 chr5A 91.176 1360 73 27 3998 5344 476683277 476681952 0.000000e+00 1803.0
12 TraesCS5B01G263800 chr5A 97.690 736 14 2 2821 3556 476684611 476683879 0.000000e+00 1262.0
13 TraesCS5B01G263800 chr5A 97.806 638 14 0 2055 2692 476685272 476684635 0.000000e+00 1101.0
14 TraesCS5B01G263800 chr5A 90.196 663 46 12 904 1559 476687450 476686800 0.000000e+00 846.0
15 TraesCS5B01G263800 chr5A 90.299 268 18 6 1724 1983 476686331 476686064 1.440000e-90 344.0
16 TraesCS5B01G263800 chr5A 94.819 193 9 1 3556 3747 476683504 476683312 3.160000e-77 300.0
17 TraesCS5B01G263800 chr5A 89.831 118 9 2 1590 1706 476686521 476686406 1.210000e-31 148.0
18 TraesCS5B01G263800 chr5A 92.308 65 5 0 838 902 476687573 476687509 5.750000e-15 93.5
19 TraesCS5B01G263800 chr1D 84.540 511 57 20 215 717 250203798 250204294 2.260000e-133 486.0
20 TraesCS5B01G263800 chr3D 79.915 468 60 31 215 656 517880977 517881436 4.060000e-81 313.0
21 TraesCS5B01G263800 chr6D 90.123 243 19 3 206 443 408208644 408208886 1.460000e-80 311.0
22 TraesCS5B01G263800 chr6D 87.931 58 6 1 1 57 408208596 408208653 3.490000e-07 67.6
23 TraesCS5B01G263800 chr4A 81.047 401 56 18 375 763 625127951 625127559 8.780000e-78 302.0
24 TraesCS5B01G263800 chr6B 84.345 313 35 13 459 764 690014014 690013709 1.470000e-75 294.0
25 TraesCS5B01G263800 chr6B 84.536 291 37 7 487 772 45834833 45835120 1.140000e-71 281.0
26 TraesCS5B01G263800 chr6B 83.819 309 37 11 461 763 288139804 288140105 1.140000e-71 281.0
27 TraesCS5B01G263800 chr6B 83.175 315 35 16 459 763 717082192 717082498 6.880000e-69 272.0
28 TraesCS5B01G263800 chr1B 85.512 283 32 8 486 763 434763774 434763496 2.460000e-73 287.0
29 TraesCS5B01G263800 chr3A 88.816 152 15 2 215 366 65791494 65791345 9.220000e-43 185.0


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 TraesCS5B01G263800 chr5B 448219457 448224849 5392 True 4749.500000 6920 100.000000 1 5393 2 chr5B.!!$R1 5392
1 TraesCS5B01G263800 chr5B 643308225 643308952 727 True 393.066667 1055 94.492333 1 767 3 chr5B.!!$R2 766
2 TraesCS5B01G263800 chr5D 375376490 375379602 3112 True 2393.000000 2896 94.555000 2055 5393 2 chr5D.!!$R1 3338
3 TraesCS5B01G263800 chr5D 375386354 375388048 1694 True 549.266667 1033 90.807667 763 2050 3 chr5D.!!$R2 1287
4 TraesCS5B01G263800 chr5A 476681952 476687573 5621 True 737.187500 1803 93.015625 838 5344 8 chr5A.!!$R1 4506

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
84 85 0.102120 GTGGAGACGATGAGGAGCAG 59.898 60.0 0.00 0.0 0.00 4.24 F
694 695 0.178767 CAGATCCGATCAAGCCACCA 59.821 55.0 11.01 0.0 0.00 4.17 F
702 703 0.179000 ATCAAGCCACCAGATCCGAC 59.821 55.0 0.00 0.0 0.00 4.79 F
1704 2469 0.035056 GCATCAGGCCAGTTACAGGT 60.035 55.0 5.01 0.0 36.11 4.00 F
1867 2694 0.599060 TCGTCACCTGAATGTGCGTA 59.401 50.0 0.00 0.0 37.20 4.42 F
3720 5678 0.526211 GTGTGCGGGGGATCTTTTTC 59.474 55.0 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 2098 0.392060 TGCACCTATGACAGCAGCAG 60.392 55.000 0.00 0.0 31.43 4.24 R
1583 2100 0.392193 AGTGCACCTATGACAGCAGC 60.392 55.000 14.63 0.0 37.72 5.25 R
1950 2781 1.735571 GCAAATACTGGTGGTGGTACG 59.264 52.381 0.00 0.0 0.00 3.67 R
3619 5577 0.262580 CCATCCATCACCAACCCCAT 59.737 55.000 0.00 0.0 0.00 4.00 R
4003 5962 4.822036 TTGTTTGACCGTTACATTGGAG 57.178 40.909 0.00 0.0 0.00 3.86 R
4932 6904 0.973632 ACGTCTACAAGCACCCATGA 59.026 50.000 0.00 0.0 0.00 3.07 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
72 73 4.477975 CGAGGCGACGGTGGAGAC 62.478 72.222 0.00 0.00 0.00 3.36
73 74 4.477975 GAGGCGACGGTGGAGACG 62.478 72.222 0.00 0.00 37.36 4.18
75 76 3.823330 GGCGACGGTGGAGACGAT 61.823 66.667 0.00 0.00 34.93 3.73
76 77 2.579787 GCGACGGTGGAGACGATG 60.580 66.667 0.00 0.00 34.93 3.84
77 78 3.047718 GCGACGGTGGAGACGATGA 62.048 63.158 0.00 0.00 34.93 2.92
78 79 1.062685 CGACGGTGGAGACGATGAG 59.937 63.158 0.00 0.00 34.93 2.90
79 80 1.433879 GACGGTGGAGACGATGAGG 59.566 63.158 0.00 0.00 34.93 3.86
80 81 1.001269 ACGGTGGAGACGATGAGGA 60.001 57.895 0.00 0.00 34.93 3.71
81 82 1.032657 ACGGTGGAGACGATGAGGAG 61.033 60.000 0.00 0.00 34.93 3.69
82 83 1.439644 GGTGGAGACGATGAGGAGC 59.560 63.158 0.00 0.00 0.00 4.70
83 84 1.323271 GGTGGAGACGATGAGGAGCA 61.323 60.000 0.00 0.00 0.00 4.26
84 85 0.102120 GTGGAGACGATGAGGAGCAG 59.898 60.000 0.00 0.00 0.00 4.24
85 86 0.323816 TGGAGACGATGAGGAGCAGT 60.324 55.000 0.00 0.00 0.00 4.40
86 87 0.102120 GGAGACGATGAGGAGCAGTG 59.898 60.000 0.00 0.00 0.00 3.66
87 88 0.527385 GAGACGATGAGGAGCAGTGC 60.527 60.000 7.13 7.13 0.00 4.40
88 89 1.520342 GACGATGAGGAGCAGTGCC 60.520 63.158 12.58 3.03 0.00 5.01
89 90 2.584418 CGATGAGGAGCAGTGCCG 60.584 66.667 12.58 2.01 0.00 5.69
90 91 2.895680 GATGAGGAGCAGTGCCGA 59.104 61.111 12.58 0.00 0.00 5.54
91 92 1.227205 GATGAGGAGCAGTGCCGAG 60.227 63.158 12.58 0.00 0.00 4.63
92 93 2.641439 GATGAGGAGCAGTGCCGAGG 62.641 65.000 12.58 0.00 0.00 4.63
93 94 4.828925 GAGGAGCAGTGCCGAGGC 62.829 72.222 12.58 7.26 42.35 4.70
138 139 3.574445 CGAGGCGACGACGGAGAT 61.574 66.667 9.67 0.00 40.15 2.75
148 149 2.356382 GACGACGGAGATGATGAGAAGT 59.644 50.000 0.00 0.00 0.00 3.01
256 257 4.612536 GTGCCGCGTGCCATATGC 62.613 66.667 15.40 5.06 40.16 3.14
281 282 4.408821 TTTGCCTCGCCTCGCCAT 62.409 61.111 0.00 0.00 0.00 4.40
295 296 1.341156 CGCCATTCCTCCTTCCCTCT 61.341 60.000 0.00 0.00 0.00 3.69
392 393 1.820481 GAGAGGAGGAGGACGACGG 60.820 68.421 0.00 0.00 0.00 4.79
540 541 4.697026 GCCCCCTTTTATATCCCCATGAAA 60.697 45.833 0.00 0.00 0.00 2.69
602 603 3.656045 GGTGGCACGAAACGGGTG 61.656 66.667 12.17 0.00 38.42 4.61
603 604 2.589442 GTGGCACGAAACGGGTGA 60.589 61.111 0.00 0.00 37.60 4.02
604 605 2.181521 GTGGCACGAAACGGGTGAA 61.182 57.895 0.00 0.00 37.60 3.18
605 606 1.451567 TGGCACGAAACGGGTGAAA 60.452 52.632 0.00 0.00 37.60 2.69
606 607 1.009335 GGCACGAAACGGGTGAAAC 60.009 57.895 0.00 0.00 37.60 2.78
607 608 1.441732 GGCACGAAACGGGTGAAACT 61.442 55.000 0.00 0.00 37.60 2.66
608 609 0.316689 GCACGAAACGGGTGAAACTG 60.317 55.000 0.00 0.00 37.60 3.16
609 610 1.011333 CACGAAACGGGTGAAACTGT 58.989 50.000 0.00 0.00 37.60 3.55
610 611 1.399089 CACGAAACGGGTGAAACTGTT 59.601 47.619 0.00 0.00 37.60 3.16
611 612 1.667212 ACGAAACGGGTGAAACTGTTC 59.333 47.619 0.00 0.00 35.08 3.18
612 613 1.666700 CGAAACGGGTGAAACTGTTCA 59.333 47.619 0.00 0.00 41.57 3.18
613 614 2.289547 CGAAACGGGTGAAACTGTTCAT 59.710 45.455 0.00 0.00 45.38 2.57
614 615 3.242936 CGAAACGGGTGAAACTGTTCATT 60.243 43.478 0.00 0.00 45.38 2.57
615 616 3.708563 AACGGGTGAAACTGTTCATTG 57.291 42.857 0.00 0.00 45.38 2.82
616 617 1.336755 ACGGGTGAAACTGTTCATTGC 59.663 47.619 0.00 0.00 45.38 3.56
617 618 1.336440 CGGGTGAAACTGTTCATTGCA 59.664 47.619 0.00 0.00 45.38 4.08
618 619 2.223688 CGGGTGAAACTGTTCATTGCAA 60.224 45.455 0.00 0.00 45.38 4.08
619 620 3.123050 GGGTGAAACTGTTCATTGCAAC 58.877 45.455 0.00 0.00 45.38 4.17
620 621 3.430098 GGGTGAAACTGTTCATTGCAACA 60.430 43.478 0.00 0.00 45.38 3.33
630 631 7.524294 CTGTTCATTGCAACAGTAACTTTTT 57.476 32.000 0.00 0.00 45.66 1.94
649 650 3.899052 TTTTTATCCGATGGACGAGGT 57.101 42.857 0.00 0.00 45.77 3.85
650 651 3.447918 TTTTATCCGATGGACGAGGTC 57.552 47.619 0.00 0.00 45.77 3.85
651 652 2.061509 TTATCCGATGGACGAGGTCA 57.938 50.000 0.00 0.00 45.77 4.02
652 653 2.287977 TATCCGATGGACGAGGTCAT 57.712 50.000 0.00 0.00 45.77 3.06
653 654 1.414158 ATCCGATGGACGAGGTCATT 58.586 50.000 0.00 0.00 45.77 2.57
654 655 0.744874 TCCGATGGACGAGGTCATTC 59.255 55.000 0.00 0.00 45.77 2.67
655 656 0.249489 CCGATGGACGAGGTCATTCC 60.249 60.000 0.00 0.00 45.77 3.01
656 657 0.459899 CGATGGACGAGGTCATTCCA 59.540 55.000 0.00 0.00 45.77 3.53
657 658 1.536922 CGATGGACGAGGTCATTCCAG 60.537 57.143 0.00 0.00 42.72 3.86
658 659 0.833287 ATGGACGAGGTCATTCCAGG 59.167 55.000 0.00 0.00 42.72 4.45
659 660 1.264749 TGGACGAGGTCATTCCAGGG 61.265 60.000 0.00 0.00 34.35 4.45
660 661 1.153349 GACGAGGTCATTCCAGGGC 60.153 63.158 0.00 0.00 39.02 5.19
661 662 1.613630 ACGAGGTCATTCCAGGGCT 60.614 57.895 0.00 0.00 39.02 5.19
662 663 1.144936 CGAGGTCATTCCAGGGCTC 59.855 63.158 0.00 0.00 39.02 4.70
663 664 1.144936 GAGGTCATTCCAGGGCTCG 59.855 63.158 0.00 0.00 39.02 5.03
664 665 1.306141 AGGTCATTCCAGGGCTCGA 60.306 57.895 0.00 0.00 39.02 4.04
665 666 0.692419 AGGTCATTCCAGGGCTCGAT 60.692 55.000 0.00 0.00 39.02 3.59
666 667 0.250081 GGTCATTCCAGGGCTCGATC 60.250 60.000 0.00 0.00 35.97 3.69
667 668 0.250081 GTCATTCCAGGGCTCGATCC 60.250 60.000 0.00 0.00 0.00 3.36
668 669 1.301244 CATTCCAGGGCTCGATCCG 60.301 63.158 0.00 0.00 0.00 4.18
669 670 1.457643 ATTCCAGGGCTCGATCCGA 60.458 57.895 0.00 0.00 0.00 4.55
670 671 1.749334 ATTCCAGGGCTCGATCCGAC 61.749 60.000 0.00 0.00 0.00 4.79
671 672 4.271816 CCAGGGCTCGATCCGACG 62.272 72.222 0.00 0.00 0.00 5.12
672 673 4.271816 CAGGGCTCGATCCGACGG 62.272 72.222 7.84 7.84 0.00 4.79
676 677 4.492160 GCTCGATCCGACGGCACA 62.492 66.667 9.66 0.00 32.76 4.57
677 678 2.278206 CTCGATCCGACGGCACAG 60.278 66.667 9.66 0.39 0.00 3.66
678 679 2.748647 TCGATCCGACGGCACAGA 60.749 61.111 9.66 3.01 0.00 3.41
679 680 2.064723 CTCGATCCGACGGCACAGAT 62.065 60.000 9.66 0.00 0.00 2.90
680 681 1.658717 CGATCCGACGGCACAGATC 60.659 63.158 9.66 5.72 33.34 2.75
681 682 1.300233 GATCCGACGGCACAGATCC 60.300 63.158 9.66 0.00 30.97 3.36
689 690 2.315246 GGCACAGATCCGATCAAGC 58.685 57.895 11.01 10.33 0.00 4.01
690 691 1.162800 GGCACAGATCCGATCAAGCC 61.163 60.000 17.55 17.55 36.24 4.35
691 692 0.462581 GCACAGATCCGATCAAGCCA 60.463 55.000 11.01 0.00 0.00 4.75
692 693 1.293924 CACAGATCCGATCAAGCCAC 58.706 55.000 11.01 0.00 0.00 5.01
693 694 0.179000 ACAGATCCGATCAAGCCACC 59.821 55.000 11.01 0.00 0.00 4.61
694 695 0.178767 CAGATCCGATCAAGCCACCA 59.821 55.000 11.01 0.00 0.00 4.17
695 696 0.467384 AGATCCGATCAAGCCACCAG 59.533 55.000 11.01 0.00 0.00 4.00
696 697 0.465705 GATCCGATCAAGCCACCAGA 59.534 55.000 3.33 0.00 0.00 3.86
697 698 1.071385 GATCCGATCAAGCCACCAGAT 59.929 52.381 3.33 0.00 0.00 2.90
698 699 0.465705 TCCGATCAAGCCACCAGATC 59.534 55.000 0.00 0.00 35.86 2.75
699 700 0.533755 CCGATCAAGCCACCAGATCC 60.534 60.000 0.00 0.00 35.82 3.36
700 701 0.877649 CGATCAAGCCACCAGATCCG 60.878 60.000 0.00 0.00 35.82 4.18
701 702 0.465705 GATCAAGCCACCAGATCCGA 59.534 55.000 0.00 0.00 33.70 4.55
702 703 0.179000 ATCAAGCCACCAGATCCGAC 59.821 55.000 0.00 0.00 0.00 4.79
703 704 1.811266 CAAGCCACCAGATCCGACG 60.811 63.158 0.00 0.00 0.00 5.12
704 705 3.019003 AAGCCACCAGATCCGACGG 62.019 63.158 7.84 7.84 0.00 4.79
706 707 4.530857 CCACCAGATCCGACGGCC 62.531 72.222 9.66 3.31 0.00 6.13
707 708 3.770040 CACCAGATCCGACGGCCA 61.770 66.667 9.66 0.00 0.00 5.36
708 709 3.461773 ACCAGATCCGACGGCCAG 61.462 66.667 9.66 0.00 0.00 4.85
709 710 4.227134 CCAGATCCGACGGCCAGG 62.227 72.222 9.66 6.10 0.00 4.45
710 711 3.147595 CAGATCCGACGGCCAGGA 61.148 66.667 9.66 13.18 41.30 3.86
711 712 2.363795 AGATCCGACGGCCAGGAA 60.364 61.111 9.66 0.00 40.32 3.36
712 713 1.762460 AGATCCGACGGCCAGGAAT 60.762 57.895 9.66 0.00 40.32 3.01
713 714 1.595382 GATCCGACGGCCAGGAATG 60.595 63.158 9.66 0.00 40.32 2.67
714 715 3.757248 ATCCGACGGCCAGGAATGC 62.757 63.158 9.66 0.00 40.32 3.56
748 749 2.501128 CGTGAGGATGACCGGCAT 59.499 61.111 0.00 6.16 41.83 4.40
758 759 4.273148 GATGACCGGCATCCTTATTACT 57.727 45.455 21.35 0.00 46.23 2.24
759 760 3.746045 TGACCGGCATCCTTATTACTC 57.254 47.619 0.00 0.00 0.00 2.59
760 761 2.035449 TGACCGGCATCCTTATTACTCG 59.965 50.000 0.00 0.00 0.00 4.18
761 762 2.295349 GACCGGCATCCTTATTACTCGA 59.705 50.000 0.00 0.00 0.00 4.04
853 1275 3.813724 GAGTAAGTGGTGTCCCTTGAAAC 59.186 47.826 0.00 0.00 0.00 2.78
1167 1682 3.257561 CGATGGTTCGCCTCGCTG 61.258 66.667 0.00 0.00 38.75 5.18
1205 1720 4.003788 CTGACGCCTCCCCGTTGT 62.004 66.667 0.00 0.00 42.24 3.32
1266 1781 3.444642 CGTCAGTACGCGTGTTCC 58.555 61.111 24.59 6.98 43.12 3.62
1368 1884 0.828022 TAAGAATCCGTGTGCCCGAT 59.172 50.000 0.00 0.00 0.00 4.18
1413 1929 2.208431 CTTTGGCATCGGATGAGACTC 58.792 52.381 21.69 3.25 0.00 3.36
1538 2055 6.069905 TGCATACTCTTTACTGATTTACCCCA 60.070 38.462 0.00 0.00 0.00 4.96
1542 2059 6.712276 ACTCTTTACTGATTTACCCCAAGAG 58.288 40.000 0.00 0.00 41.13 2.85
1543 2060 5.497474 TCTTTACTGATTTACCCCAAGAGC 58.503 41.667 0.00 0.00 0.00 4.09
1556 2073 2.763448 CCCAAGAGCTACTCTACTGCTT 59.237 50.000 0.00 0.00 40.28 3.91
1559 2076 4.399618 CCAAGAGCTACTCTACTGCTTGTA 59.600 45.833 0.00 0.00 40.28 2.41
1561 2078 3.949113 AGAGCTACTCTACTGCTTGTACC 59.051 47.826 0.00 0.00 39.28 3.34
1562 2079 2.683867 AGCTACTCTACTGCTTGTACCG 59.316 50.000 0.00 0.00 32.61 4.02
1565 2082 0.460311 CTCTACTGCTTGTACCGGGG 59.540 60.000 6.32 0.00 0.00 5.73
1566 2083 0.251922 TCTACTGCTTGTACCGGGGT 60.252 55.000 6.32 0.00 0.00 4.95
1568 2085 1.002773 CTACTGCTTGTACCGGGGTTT 59.997 52.381 6.32 0.00 0.00 3.27
1570 2087 1.228306 TGCTTGTACCGGGGTTTGG 60.228 57.895 6.32 0.00 0.00 3.28
1571 2088 1.073548 GCTTGTACCGGGGTTTGGA 59.926 57.895 6.32 0.00 0.00 3.53
1576 2093 2.516906 TGTACCGGGGTTTGGATTTTC 58.483 47.619 6.32 0.00 0.00 2.29
1577 2094 2.108601 TGTACCGGGGTTTGGATTTTCT 59.891 45.455 6.32 0.00 0.00 2.52
1578 2095 1.919240 ACCGGGGTTTGGATTTTCTC 58.081 50.000 6.32 0.00 0.00 2.87
1581 2098 2.092323 CGGGGTTTGGATTTTCTCCTC 58.908 52.381 0.00 0.00 45.21 3.71
1583 2100 3.092301 GGGGTTTGGATTTTCTCCTCTG 58.908 50.000 0.00 0.00 45.21 3.35
1585 2102 3.425659 GGTTTGGATTTTCTCCTCTGCT 58.574 45.455 0.00 0.00 45.21 4.24
1586 2103 3.192212 GGTTTGGATTTTCTCCTCTGCTG 59.808 47.826 0.00 0.00 45.21 4.41
1587 2104 2.119801 TGGATTTTCTCCTCTGCTGC 57.880 50.000 0.00 0.00 45.21 5.25
1588 2105 1.632409 TGGATTTTCTCCTCTGCTGCT 59.368 47.619 0.00 0.00 45.21 4.24
1592 2357 1.051008 TTTCTCCTCTGCTGCTGTCA 58.949 50.000 0.00 0.00 0.00 3.58
1640 2405 9.408069 GCTGTATAGGTGTATCATAGTGTAAAC 57.592 37.037 0.00 0.00 0.00 2.01
1669 2434 6.989169 ACCAGCAATTAATAAGCTCTACAGAG 59.011 38.462 11.25 1.68 44.75 3.35
1702 2467 1.089920 GTGCATCAGGCCAGTTACAG 58.910 55.000 5.01 0.00 43.89 2.74
1704 2469 0.035056 GCATCAGGCCAGTTACAGGT 60.035 55.000 5.01 0.00 36.11 4.00
1705 2470 1.742761 CATCAGGCCAGTTACAGGTG 58.257 55.000 5.01 0.00 0.00 4.00
1706 2471 0.035056 ATCAGGCCAGTTACAGGTGC 60.035 55.000 5.01 0.00 0.00 5.01
1707 2472 1.073025 CAGGCCAGTTACAGGTGCA 59.927 57.895 5.01 0.00 0.00 4.57
1710 2475 0.811281 GGCCAGTTACAGGTGCATTC 59.189 55.000 0.00 0.00 0.00 2.67
1711 2476 1.614317 GGCCAGTTACAGGTGCATTCT 60.614 52.381 0.00 0.00 0.00 2.40
1712 2477 2.355716 GGCCAGTTACAGGTGCATTCTA 60.356 50.000 0.00 0.00 0.00 2.10
1713 2478 2.678336 GCCAGTTACAGGTGCATTCTAC 59.322 50.000 0.00 0.00 0.00 2.59
1714 2479 3.619979 GCCAGTTACAGGTGCATTCTACT 60.620 47.826 0.00 0.00 0.00 2.57
1717 2482 5.423015 CAGTTACAGGTGCATTCTACTGAT 58.577 41.667 12.35 2.83 35.06 2.90
1718 2483 5.521735 CAGTTACAGGTGCATTCTACTGATC 59.478 44.000 12.35 0.00 35.06 2.92
1719 2484 5.187772 AGTTACAGGTGCATTCTACTGATCA 59.812 40.000 10.76 0.00 35.08 2.92
1721 2486 3.771479 ACAGGTGCATTCTACTGATCAGA 59.229 43.478 29.27 11.66 35.08 3.27
1733 2556 3.600388 ACTGATCAGAAAAGCTAACCGG 58.400 45.455 29.27 0.00 0.00 5.28
1745 2568 5.622770 AAGCTAACCGGTCTTACAAAATG 57.377 39.130 8.04 0.00 0.00 2.32
1750 2573 6.238130 GCTAACCGGTCTTACAAAATGAGATC 60.238 42.308 8.04 0.00 0.00 2.75
1764 2587 7.551974 ACAAAATGAGATCGAATCTGTTCATCT 59.448 33.333 0.00 0.00 40.38 2.90
1795 2618 4.708726 ATAGTTGCTGAAGATTTGGTGC 57.291 40.909 0.00 0.00 0.00 5.01
1796 2619 2.309613 AGTTGCTGAAGATTTGGTGCA 58.690 42.857 0.00 0.00 0.00 4.57
1798 2621 2.991190 GTTGCTGAAGATTTGGTGCATG 59.009 45.455 0.00 0.00 0.00 4.06
1808 2634 7.984050 TGAAGATTTGGTGCATGTTTCTTTTTA 59.016 29.630 0.00 0.00 0.00 1.52
1850 2677 3.656651 TGCTTTGCTGATTAATCGTCG 57.343 42.857 10.80 3.37 0.00 5.12
1864 2691 0.666274 TCGTCGTCACCTGAATGTGC 60.666 55.000 0.00 0.00 36.17 4.57
1865 2692 1.781555 GTCGTCACCTGAATGTGCG 59.218 57.895 0.00 0.00 37.22 5.34
1866 2693 0.944311 GTCGTCACCTGAATGTGCGT 60.944 55.000 0.00 0.00 37.20 5.24
1867 2694 0.599060 TCGTCACCTGAATGTGCGTA 59.401 50.000 0.00 0.00 37.20 4.42
1869 2696 1.126113 CGTCACCTGAATGTGCGTAAC 59.874 52.381 0.00 0.00 36.17 2.50
1870 2697 2.413837 GTCACCTGAATGTGCGTAACT 58.586 47.619 0.00 0.00 36.17 2.24
1872 2699 3.991773 GTCACCTGAATGTGCGTAACTTA 59.008 43.478 0.00 0.00 36.17 2.24
1873 2700 3.991773 TCACCTGAATGTGCGTAACTTAC 59.008 43.478 0.00 0.00 36.17 2.34
1994 2825 7.490079 TGCATTTTATCAAGCTTAGCATTTCTG 59.510 33.333 7.07 0.00 0.00 3.02
1997 2828 9.798994 ATTTTATCAAGCTTAGCATTTCTGAAG 57.201 29.630 7.07 0.00 0.00 3.02
2011 2842 2.610433 TCTGAAGTCATGATGCGACAC 58.390 47.619 0.00 0.00 35.77 3.67
2050 2881 1.931172 GCATTTGCACTGCCAATCATC 59.069 47.619 8.89 0.00 41.59 2.92
2051 2882 2.675603 GCATTTGCACTGCCAATCATCA 60.676 45.455 8.89 0.00 41.59 3.07
2052 2883 3.186909 CATTTGCACTGCCAATCATCAG 58.813 45.455 0.00 0.00 36.45 2.90
2102 3685 8.037758 AGAGACATGTTTTACTGGACTTATCAG 58.962 37.037 0.00 0.00 38.16 2.90
2139 3722 4.870363 TGAGGTTTGAGCAAATGTTTAGC 58.130 39.130 0.00 0.00 32.36 3.09
2269 3852 4.159244 TGAAATTCCTACATAACCCCCG 57.841 45.455 0.00 0.00 0.00 5.73
2324 3907 7.696872 GTCCTTTTCGGCATTTTCTTCTAATAC 59.303 37.037 0.00 0.00 0.00 1.89
2415 3998 4.871933 ACATTGGCCTAAAGAAACCTTG 57.128 40.909 3.32 0.00 0.00 3.61
2421 4004 4.462483 TGGCCTAAAGAAACCTTGCATTAG 59.538 41.667 3.32 0.00 0.00 1.73
2773 4356 2.294979 GTTCCAAAAGGAGACCGTGTT 58.705 47.619 0.00 0.00 0.00 3.32
2869 4452 9.661563 TGAAAAGTGACCGTACTTCAAATATAT 57.338 29.630 0.00 0.00 39.86 0.86
3004 4587 2.041620 TGAGGGAATGAAAGTTGGAGGG 59.958 50.000 0.00 0.00 0.00 4.30
3029 4612 6.456988 GCAGGTGAGTAATTTCTATGGTTTCG 60.457 42.308 0.00 0.00 0.00 3.46
3178 4761 8.038944 TCAGTCAACCCTTACAAATGATAGTAC 58.961 37.037 0.00 0.00 0.00 2.73
3720 5678 0.526211 GTGTGCGGGGGATCTTTTTC 59.474 55.000 0.00 0.00 0.00 2.29
4060 6019 7.122650 ACTTTTGTGCCACATTAGTGCTTATAT 59.877 33.333 10.47 0.00 44.53 0.86
4094 6053 7.857456 TCCCTGCTATAATCTTGTCAACTTTA 58.143 34.615 0.00 0.00 0.00 1.85
4298 6259 4.887071 TCCATTTGGGTATGTGCAGTTATC 59.113 41.667 0.00 0.00 38.11 1.75
4302 6263 4.835284 TGGGTATGTGCAGTTATCAGAA 57.165 40.909 0.00 0.00 0.00 3.02
4311 6272 7.337480 TGTGCAGTTATCAGAAAATATGCAT 57.663 32.000 3.79 3.79 43.50 3.96
4433 6395 8.510243 TGCAGACAATGATGTATATTTGAACT 57.490 30.769 0.00 0.00 40.74 3.01
4464 6426 1.777878 TGTTACTGCAAGAAAGGGGGA 59.222 47.619 0.00 0.00 37.43 4.81
4489 6451 6.305272 AGATGTATCAGATTTCAGTGGTGT 57.695 37.500 0.00 0.00 0.00 4.16
4491 6453 6.596888 AGATGTATCAGATTTCAGTGGTGTTG 59.403 38.462 0.00 0.00 0.00 3.33
4535 6497 9.683069 CCATAATGTAATATTTGACTTTGGAGC 57.317 33.333 0.00 0.00 0.00 4.70
4673 6641 4.202245 TCGCTCACTTGTATAGCCTTTT 57.798 40.909 0.00 0.00 32.50 2.27
4682 6650 5.412904 ACTTGTATAGCCTTTTCAGCTTCAC 59.587 40.000 0.00 0.00 41.83 3.18
4693 6661 4.890158 TTCAGCTTCACCATCTAGTTCA 57.110 40.909 0.00 0.00 0.00 3.18
4695 6663 3.834813 TCAGCTTCACCATCTAGTTCAGT 59.165 43.478 0.00 0.00 0.00 3.41
4696 6664 4.284490 TCAGCTTCACCATCTAGTTCAGTT 59.716 41.667 0.00 0.00 0.00 3.16
4697 6665 4.629200 CAGCTTCACCATCTAGTTCAGTTC 59.371 45.833 0.00 0.00 0.00 3.01
4699 6667 5.717178 AGCTTCACCATCTAGTTCAGTTCTA 59.283 40.000 0.00 0.00 0.00 2.10
4788 6758 6.049149 TGCTGGTACTATAGCTGTCAAAATC 58.951 40.000 14.93 0.00 40.52 2.17
4852 6822 2.599848 CGAGCGCCAAATAGGAAATTCG 60.600 50.000 2.29 0.00 41.22 3.34
4904 6874 3.437395 GGCAATACGGAATAACACACACA 59.563 43.478 0.00 0.00 0.00 3.72
4940 6912 5.047802 AGTTTTTGCAGACTAATCATGGGTG 60.048 40.000 0.00 0.00 0.00 4.61
4988 6961 9.877178 AAACTGAAAGGTAGTAGTCATAATCAG 57.123 33.333 0.00 0.00 39.30 2.90
4989 6962 8.824756 ACTGAAAGGTAGTAGTCATAATCAGA 57.175 34.615 0.00 0.00 39.30 3.27
4990 6963 8.908903 ACTGAAAGGTAGTAGTCATAATCAGAG 58.091 37.037 0.00 0.00 39.30 3.35
4991 6964 8.824756 TGAAAGGTAGTAGTCATAATCAGAGT 57.175 34.615 0.00 0.00 0.00 3.24
4992 6965 9.916360 TGAAAGGTAGTAGTCATAATCAGAGTA 57.084 33.333 0.00 0.00 0.00 2.59
4995 6968 9.563748 AAGGTAGTAGTCATAATCAGAGTACTC 57.436 37.037 15.41 15.41 44.76 2.59
4996 6969 8.940982 AGGTAGTAGTCATAATCAGAGTACTCT 58.059 37.037 20.00 20.00 44.76 3.24
4997 6970 9.211485 GGTAGTAGTCATAATCAGAGTACTCTC 57.789 40.741 22.76 8.96 44.76 3.20
4998 6971 9.767228 GTAGTAGTCATAATCAGAGTACTCTCA 57.233 37.037 22.76 11.29 44.76 3.27
5291 7265 2.036387 TGAAGAGGGAAACGTGTGAGA 58.964 47.619 0.00 0.00 0.00 3.27
5344 7318 1.780919 AGGTGCTTAGGGAAGGTGTTT 59.219 47.619 0.00 0.00 32.84 2.83
5354 7328 7.362660 GCTTAGGGAAGGTGTTTGGTAAAATAG 60.363 40.741 0.00 0.00 32.84 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.528684 GCGCTGCTCCTAATCGTCTT 60.529 55.000 0.00 0.00 0.00 3.01
61 62 1.030488 TCCTCATCGTCTCCACCGTC 61.030 60.000 0.00 0.00 0.00 4.79
62 63 1.001269 TCCTCATCGTCTCCACCGT 60.001 57.895 0.00 0.00 0.00 4.83
63 64 1.730487 CTCCTCATCGTCTCCACCG 59.270 63.158 0.00 0.00 0.00 4.94
64 65 1.323271 TGCTCCTCATCGTCTCCACC 61.323 60.000 0.00 0.00 0.00 4.61
65 66 0.102120 CTGCTCCTCATCGTCTCCAC 59.898 60.000 0.00 0.00 0.00 4.02
66 67 0.323816 ACTGCTCCTCATCGTCTCCA 60.324 55.000 0.00 0.00 0.00 3.86
67 68 0.102120 CACTGCTCCTCATCGTCTCC 59.898 60.000 0.00 0.00 0.00 3.71
68 69 0.527385 GCACTGCTCCTCATCGTCTC 60.527 60.000 0.00 0.00 0.00 3.36
69 70 1.515020 GCACTGCTCCTCATCGTCT 59.485 57.895 0.00 0.00 0.00 4.18
70 71 1.520342 GGCACTGCTCCTCATCGTC 60.520 63.158 0.00 0.00 0.00 4.20
71 72 2.581354 GGCACTGCTCCTCATCGT 59.419 61.111 0.00 0.00 0.00 3.73
72 73 2.584418 CGGCACTGCTCCTCATCG 60.584 66.667 0.00 0.00 0.00 3.84
73 74 1.227205 CTCGGCACTGCTCCTCATC 60.227 63.158 0.00 0.00 0.00 2.92
74 75 2.729479 CCTCGGCACTGCTCCTCAT 61.729 63.158 0.00 0.00 0.00 2.90
75 76 3.385384 CCTCGGCACTGCTCCTCA 61.385 66.667 0.00 0.00 0.00 3.86
76 77 4.828925 GCCTCGGCACTGCTCCTC 62.829 72.222 2.41 0.00 41.49 3.71
93 94 3.791928 CTCATCGTCTCCGCCGTCG 62.792 68.421 0.00 0.00 0.00 5.12
94 95 2.024871 CTCATCGTCTCCGCCGTC 59.975 66.667 0.00 0.00 0.00 4.79
131 132 1.066303 GCGACTTCTCATCATCTCCGT 59.934 52.381 0.00 0.00 0.00 4.69
138 139 2.184322 GGCCGCGACTTCTCATCA 59.816 61.111 8.23 0.00 0.00 3.07
276 277 1.147153 GAGGGAAGGAGGAATGGCG 59.853 63.158 0.00 0.00 0.00 5.69
277 278 0.472044 GAGAGGGAAGGAGGAATGGC 59.528 60.000 0.00 0.00 0.00 4.40
278 279 0.755686 CGAGAGGGAAGGAGGAATGG 59.244 60.000 0.00 0.00 0.00 3.16
279 280 1.137872 CACGAGAGGGAAGGAGGAATG 59.862 57.143 0.00 0.00 35.60 2.67
280 281 1.490574 CACGAGAGGGAAGGAGGAAT 58.509 55.000 0.00 0.00 35.60 3.01
281 282 0.614979 CCACGAGAGGGAAGGAGGAA 60.615 60.000 0.00 0.00 35.60 3.36
348 349 1.152139 CCTCCTCCTCCCATCCCTC 60.152 68.421 0.00 0.00 0.00 4.30
417 418 4.408396 TTCCTCCCGCCCCTAGCA 62.408 66.667 0.00 0.00 44.04 3.49
495 496 1.449778 GCCCGTGGAGAAACCTAGC 60.450 63.158 0.00 0.00 39.86 3.42
540 541 2.168313 GGGGGCATTTTCGTCATTTCAT 59.832 45.455 0.00 0.00 0.00 2.57
629 630 3.196039 TGACCTCGTCCATCGGATAAAAA 59.804 43.478 0.00 0.00 40.32 1.94
630 631 2.761767 TGACCTCGTCCATCGGATAAAA 59.238 45.455 0.00 0.00 40.32 1.52
631 632 2.380941 TGACCTCGTCCATCGGATAAA 58.619 47.619 0.00 0.00 40.32 1.40
632 633 2.061509 TGACCTCGTCCATCGGATAA 57.938 50.000 0.00 0.00 40.32 1.75
633 634 2.287977 ATGACCTCGTCCATCGGATA 57.712 50.000 0.00 0.00 40.32 2.59
634 635 1.341531 GAATGACCTCGTCCATCGGAT 59.658 52.381 0.00 0.00 40.32 4.18
635 636 0.744874 GAATGACCTCGTCCATCGGA 59.255 55.000 0.00 0.00 40.32 4.55
636 637 0.249489 GGAATGACCTCGTCCATCGG 60.249 60.000 0.00 0.00 40.32 4.18
637 638 0.459899 TGGAATGACCTCGTCCATCG 59.540 55.000 0.00 0.00 39.86 3.84
638 639 1.202580 CCTGGAATGACCTCGTCCATC 60.203 57.143 0.00 0.00 39.86 3.51
639 640 0.833287 CCTGGAATGACCTCGTCCAT 59.167 55.000 0.00 0.00 39.86 3.41
640 641 1.264749 CCCTGGAATGACCTCGTCCA 61.265 60.000 0.00 0.00 39.86 4.02
641 642 1.522569 CCCTGGAATGACCTCGTCC 59.477 63.158 0.00 0.00 39.86 4.79
642 643 1.153349 GCCCTGGAATGACCTCGTC 60.153 63.158 0.00 0.00 39.86 4.20
643 644 1.613630 AGCCCTGGAATGACCTCGT 60.614 57.895 0.00 0.00 39.86 4.18
644 645 1.144936 GAGCCCTGGAATGACCTCG 59.855 63.158 0.00 0.00 39.86 4.63
645 646 1.144936 CGAGCCCTGGAATGACCTC 59.855 63.158 0.00 0.00 39.86 3.85
646 647 0.692419 ATCGAGCCCTGGAATGACCT 60.692 55.000 0.00 0.00 39.86 3.85
647 648 0.250081 GATCGAGCCCTGGAATGACC 60.250 60.000 0.00 0.00 39.54 4.02
648 649 0.250081 GGATCGAGCCCTGGAATGAC 60.250 60.000 9.02 0.00 0.00 3.06
649 650 1.748329 CGGATCGAGCCCTGGAATGA 61.748 60.000 15.35 0.00 0.00 2.57
650 651 1.301244 CGGATCGAGCCCTGGAATG 60.301 63.158 15.35 0.00 0.00 2.67
651 652 1.457643 TCGGATCGAGCCCTGGAAT 60.458 57.895 15.35 0.00 0.00 3.01
652 653 2.043349 TCGGATCGAGCCCTGGAA 60.043 61.111 15.35 0.00 0.00 3.53
653 654 2.833582 GTCGGATCGAGCCCTGGA 60.834 66.667 15.35 2.46 36.23 3.86
654 655 4.271816 CGTCGGATCGAGCCCTGG 62.272 72.222 15.35 0.00 36.23 4.45
655 656 4.271816 CCGTCGGATCGAGCCCTG 62.272 72.222 15.35 3.68 36.23 4.45
659 660 4.492160 TGTGCCGTCGGATCGAGC 62.492 66.667 17.49 0.00 36.23 5.03
660 661 2.064723 ATCTGTGCCGTCGGATCGAG 62.065 60.000 17.49 4.58 36.23 4.04
661 662 2.060004 GATCTGTGCCGTCGGATCGA 62.060 60.000 17.49 5.45 39.42 3.59
662 663 1.658717 GATCTGTGCCGTCGGATCG 60.659 63.158 17.49 0.00 39.42 3.69
663 664 1.300233 GGATCTGTGCCGTCGGATC 60.300 63.158 17.49 8.43 44.75 3.36
664 665 2.815308 GGATCTGTGCCGTCGGAT 59.185 61.111 17.49 0.00 36.30 4.18
665 666 3.822192 CGGATCTGTGCCGTCGGA 61.822 66.667 17.49 0.00 43.66 4.55
671 672 1.162800 GGCTTGATCGGATCTGTGCC 61.163 60.000 22.82 22.82 34.55 5.01
672 673 0.462581 TGGCTTGATCGGATCTGTGC 60.463 55.000 18.16 17.02 0.00 4.57
673 674 1.293924 GTGGCTTGATCGGATCTGTG 58.706 55.000 18.16 9.55 0.00 3.66
674 675 0.179000 GGTGGCTTGATCGGATCTGT 59.821 55.000 18.16 0.00 0.00 3.41
675 676 0.178767 TGGTGGCTTGATCGGATCTG 59.821 55.000 18.16 12.02 0.00 2.90
676 677 0.467384 CTGGTGGCTTGATCGGATCT 59.533 55.000 18.16 0.00 0.00 2.75
677 678 0.465705 TCTGGTGGCTTGATCGGATC 59.534 55.000 11.07 11.07 0.00 3.36
678 679 1.071385 GATCTGGTGGCTTGATCGGAT 59.929 52.381 0.00 0.00 0.00 4.18
679 680 0.465705 GATCTGGTGGCTTGATCGGA 59.534 55.000 0.00 0.00 0.00 4.55
680 681 0.533755 GGATCTGGTGGCTTGATCGG 60.534 60.000 0.00 0.00 37.91 4.18
681 682 0.877649 CGGATCTGGTGGCTTGATCG 60.878 60.000 0.00 0.00 37.91 3.69
682 683 0.465705 TCGGATCTGGTGGCTTGATC 59.534 55.000 0.62 0.00 36.72 2.92
683 684 0.179000 GTCGGATCTGGTGGCTTGAT 59.821 55.000 0.62 0.00 0.00 2.57
684 685 1.596934 GTCGGATCTGGTGGCTTGA 59.403 57.895 0.62 0.00 0.00 3.02
685 686 1.811266 CGTCGGATCTGGTGGCTTG 60.811 63.158 0.62 0.00 0.00 4.01
686 687 2.579201 CGTCGGATCTGGTGGCTT 59.421 61.111 0.62 0.00 0.00 4.35
687 688 3.461773 CCGTCGGATCTGGTGGCT 61.462 66.667 4.91 0.00 0.00 4.75
689 690 4.530857 GGCCGTCGGATCTGGTGG 62.531 72.222 17.49 5.20 0.00 4.61
690 691 3.723235 CTGGCCGTCGGATCTGGTG 62.723 68.421 17.49 0.00 0.00 4.17
691 692 3.461773 CTGGCCGTCGGATCTGGT 61.462 66.667 17.49 0.00 0.00 4.00
692 693 4.227134 CCTGGCCGTCGGATCTGG 62.227 72.222 17.49 14.97 0.00 3.86
693 694 2.032860 ATTCCTGGCCGTCGGATCTG 62.033 60.000 17.49 9.91 0.00 2.90
694 695 1.762460 ATTCCTGGCCGTCGGATCT 60.762 57.895 17.49 0.00 0.00 2.75
695 696 1.595382 CATTCCTGGCCGTCGGATC 60.595 63.158 17.49 6.79 0.00 3.36
696 697 2.505982 CATTCCTGGCCGTCGGAT 59.494 61.111 17.49 0.00 0.00 4.18
697 698 4.467084 GCATTCCTGGCCGTCGGA 62.467 66.667 17.49 0.31 0.00 4.55
721 722 2.430610 ATCCTCACGGCTCCTCAGC 61.431 63.158 0.00 0.00 46.06 4.26
722 723 1.039785 TCATCCTCACGGCTCCTCAG 61.040 60.000 0.00 0.00 0.00 3.35
723 724 1.000359 TCATCCTCACGGCTCCTCA 60.000 57.895 0.00 0.00 0.00 3.86
724 725 1.439644 GTCATCCTCACGGCTCCTC 59.560 63.158 0.00 0.00 0.00 3.71
725 726 2.060980 GGTCATCCTCACGGCTCCT 61.061 63.158 0.00 0.00 0.00 3.69
726 727 2.501610 GGTCATCCTCACGGCTCC 59.498 66.667 0.00 0.00 0.00 4.70
727 728 2.105128 CGGTCATCCTCACGGCTC 59.895 66.667 0.00 0.00 0.00 4.70
728 729 3.461773 CCGGTCATCCTCACGGCT 61.462 66.667 0.00 0.00 39.85 5.52
730 731 2.978452 GATGCCGGTCATCCTCACGG 62.978 65.000 21.35 0.00 44.54 4.94
731 732 1.592669 GATGCCGGTCATCCTCACG 60.593 63.158 21.35 0.00 44.54 4.35
732 733 4.445699 GATGCCGGTCATCCTCAC 57.554 61.111 21.35 4.00 44.54 3.51
738 739 3.306088 CGAGTAATAAGGATGCCGGTCAT 60.306 47.826 10.59 10.59 38.32 3.06
739 740 2.035449 CGAGTAATAAGGATGCCGGTCA 59.965 50.000 1.90 1.38 0.00 4.02
740 741 2.295349 TCGAGTAATAAGGATGCCGGTC 59.705 50.000 1.90 0.00 0.00 4.79
741 742 2.313317 TCGAGTAATAAGGATGCCGGT 58.687 47.619 1.90 0.00 0.00 5.28
742 743 3.594603 ATCGAGTAATAAGGATGCCGG 57.405 47.619 0.00 0.00 0.00 6.13
743 744 6.330278 TGAATATCGAGTAATAAGGATGCCG 58.670 40.000 0.00 0.00 0.00 5.69
744 745 8.723942 ATTGAATATCGAGTAATAAGGATGCC 57.276 34.615 0.00 0.00 0.00 4.40
745 746 9.593134 AGATTGAATATCGAGTAATAAGGATGC 57.407 33.333 0.00 0.00 0.00 3.91
761 762 9.935241 ACACTTAATGAGCGATAGATTGAATAT 57.065 29.630 0.00 0.00 39.76 1.28
775 776 4.722194 TCATCGCAAAACACTTAATGAGC 58.278 39.130 0.00 0.00 0.00 4.26
823 824 6.790319 AGGGACACCACTTACTCATTATTTT 58.210 36.000 0.00 0.00 40.13 1.82
824 825 6.388619 AGGGACACCACTTACTCATTATTT 57.611 37.500 0.00 0.00 40.13 1.40
825 826 6.012858 TCAAGGGACACCACTTACTCATTATT 60.013 38.462 0.00 0.00 40.13 1.40
828 829 3.650942 TCAAGGGACACCACTTACTCATT 59.349 43.478 0.00 0.00 40.13 2.57
831 832 3.764237 TTCAAGGGACACCACTTACTC 57.236 47.619 0.00 0.00 40.13 2.59
833 834 3.547746 TGTTTCAAGGGACACCACTTAC 58.452 45.455 0.00 0.00 40.13 2.34
853 1275 3.619038 GCTCCTATCCAGTCGAGTTTTTG 59.381 47.826 0.00 0.00 0.00 2.44
1137 1652 3.124921 CATCGCCGGGTGGTTGAC 61.125 66.667 2.18 0.00 37.67 3.18
1205 1720 1.191535 ATCAGGAAATGACCGACGGA 58.808 50.000 23.38 0.00 41.91 4.69
1259 1774 3.427503 GCCATAAAACCATCAGGAACACG 60.428 47.826 0.00 0.00 38.69 4.49
1261 1776 2.752354 CGCCATAAAACCATCAGGAACA 59.248 45.455 0.00 0.00 38.69 3.18
1266 1781 1.534595 GCTGCGCCATAAAACCATCAG 60.535 52.381 4.18 0.00 0.00 2.90
1368 1884 0.464036 ACAACTGAAGCAGGACACGA 59.536 50.000 0.00 0.00 35.51 4.35
1436 1953 1.698506 AACTGCCCAAATCAACCGAA 58.301 45.000 0.00 0.00 0.00 4.30
1538 2055 4.399934 GGTACAAGCAGTAGAGTAGCTCTT 59.600 45.833 3.87 0.00 41.50 2.85
1542 2059 2.223525 CCGGTACAAGCAGTAGAGTAGC 60.224 54.545 0.00 0.00 32.19 3.58
1543 2060 2.358267 CCCGGTACAAGCAGTAGAGTAG 59.642 54.545 0.00 0.00 32.19 2.57
1556 2073 2.108601 AGAAAATCCAAACCCCGGTACA 59.891 45.455 0.00 0.00 0.00 2.90
1559 2076 1.919240 GAGAAAATCCAAACCCCGGT 58.081 50.000 0.00 0.00 0.00 5.28
1570 2087 2.677337 GACAGCAGCAGAGGAGAAAATC 59.323 50.000 0.00 0.00 0.00 2.17
1571 2088 2.039480 TGACAGCAGCAGAGGAGAAAAT 59.961 45.455 0.00 0.00 0.00 1.82
1576 2093 1.068895 CCTATGACAGCAGCAGAGGAG 59.931 57.143 8.02 0.00 45.31 3.69
1577 2094 1.117994 CCTATGACAGCAGCAGAGGA 58.882 55.000 8.02 0.00 45.31 3.71
1578 2095 3.682766 CCTATGACAGCAGCAGAGG 57.317 57.895 0.00 0.00 38.27 3.69
1581 2098 0.392060 TGCACCTATGACAGCAGCAG 60.392 55.000 0.00 0.00 31.43 4.24
1583 2100 0.392193 AGTGCACCTATGACAGCAGC 60.392 55.000 14.63 0.00 37.72 5.25
1585 2102 2.566833 AAAGTGCACCTATGACAGCA 57.433 45.000 14.63 0.00 34.10 4.41
1586 2103 2.352960 GCTAAAGTGCACCTATGACAGC 59.647 50.000 14.63 9.11 0.00 4.40
1587 2104 3.866651 AGCTAAAGTGCACCTATGACAG 58.133 45.455 14.63 2.68 34.99 3.51
1588 2105 3.515502 AGAGCTAAAGTGCACCTATGACA 59.484 43.478 14.63 0.00 34.99 3.58
1592 2357 4.256920 CACAAGAGCTAAAGTGCACCTAT 58.743 43.478 14.63 2.22 34.99 2.57
1640 2405 5.128919 AGAGCTTATTAATTGCTGGTCCAG 58.871 41.667 15.15 15.15 37.16 3.86
1669 2434 3.599343 TGATGCACTGACCATTCTACAC 58.401 45.455 0.00 0.00 0.00 2.90
1702 2467 5.448360 GCTTTTCTGATCAGTAGAATGCACC 60.448 44.000 21.92 1.68 35.74 5.01
1704 2469 5.494724 AGCTTTTCTGATCAGTAGAATGCA 58.505 37.500 27.35 9.70 36.92 3.96
1705 2470 7.405769 GTTAGCTTTTCTGATCAGTAGAATGC 58.594 38.462 21.92 22.78 34.42 3.56
1706 2471 7.254252 CGGTTAGCTTTTCTGATCAGTAGAATG 60.254 40.741 21.92 16.26 34.42 2.67
1707 2472 6.758886 CGGTTAGCTTTTCTGATCAGTAGAAT 59.241 38.462 21.92 11.98 34.42 2.40
1710 2475 4.806247 CCGGTTAGCTTTTCTGATCAGTAG 59.194 45.833 21.92 17.25 0.00 2.57
1711 2476 4.222145 ACCGGTTAGCTTTTCTGATCAGTA 59.778 41.667 21.92 10.43 0.00 2.74
1712 2477 3.008049 ACCGGTTAGCTTTTCTGATCAGT 59.992 43.478 21.92 4.60 0.00 3.41
1713 2478 3.600388 ACCGGTTAGCTTTTCTGATCAG 58.400 45.455 17.07 17.07 0.00 2.90
1714 2479 3.260884 AGACCGGTTAGCTTTTCTGATCA 59.739 43.478 9.42 0.00 0.00 2.92
1717 2482 3.764237 AAGACCGGTTAGCTTTTCTGA 57.236 42.857 9.42 0.00 0.00 3.27
1718 2483 4.312443 TGTAAGACCGGTTAGCTTTTCTG 58.688 43.478 9.42 0.00 0.00 3.02
1719 2484 4.612264 TGTAAGACCGGTTAGCTTTTCT 57.388 40.909 9.42 0.00 0.00 2.52
1721 2486 6.263617 TCATTTTGTAAGACCGGTTAGCTTTT 59.736 34.615 9.42 0.00 0.00 2.27
1733 2556 8.190888 ACAGATTCGATCTCATTTTGTAAGAC 57.809 34.615 0.00 0.00 37.58 3.01
1745 2568 7.864882 TCACATAAGATGAACAGATTCGATCTC 59.135 37.037 0.00 0.00 37.58 2.75
1798 2621 9.285770 CGGCTTATAAGTCCAATAAAAAGAAAC 57.714 33.333 19.47 0.00 0.00 2.78
1808 2634 4.150897 TGCTTCGGCTTATAAGTCCAAT 57.849 40.909 19.47 0.00 42.37 3.16
1839 2665 4.804139 ACATTCAGGTGACGACGATTAATC 59.196 41.667 0.00 5.30 0.00 1.75
1846 2673 1.781555 GCACATTCAGGTGACGACG 59.218 57.895 0.00 0.00 41.32 5.12
1850 2677 2.413837 AGTTACGCACATTCAGGTGAC 58.586 47.619 0.00 0.00 41.32 3.67
1864 2691 4.271533 TGCTCAACACTTTGGTAAGTTACG 59.728 41.667 6.94 0.00 41.85 3.18
1865 2692 5.277828 CCTGCTCAACACTTTGGTAAGTTAC 60.278 44.000 4.32 4.32 41.85 2.50
1866 2693 4.819630 CCTGCTCAACACTTTGGTAAGTTA 59.180 41.667 0.00 0.00 41.85 2.24
1867 2694 3.632145 CCTGCTCAACACTTTGGTAAGTT 59.368 43.478 0.00 0.00 41.85 2.66
1869 2696 3.214328 ACCTGCTCAACACTTTGGTAAG 58.786 45.455 0.00 0.00 37.40 2.34
1870 2697 3.290948 ACCTGCTCAACACTTTGGTAA 57.709 42.857 0.00 0.00 33.06 2.85
1872 2699 2.172717 AGTACCTGCTCAACACTTTGGT 59.827 45.455 0.00 0.00 33.06 3.67
1873 2700 2.851195 AGTACCTGCTCAACACTTTGG 58.149 47.619 0.00 0.00 33.06 3.28
1950 2781 1.735571 GCAAATACTGGTGGTGGTACG 59.264 52.381 0.00 0.00 0.00 3.67
1994 2825 2.995939 TCTTGTGTCGCATCATGACTTC 59.004 45.455 0.00 0.00 37.26 3.01
1997 2828 4.346734 AATTCTTGTGTCGCATCATGAC 57.653 40.909 0.00 0.00 36.88 3.06
2011 2842 9.433317 GCAAATGCAAATGATGATAAATTCTTG 57.567 29.630 6.30 0.00 41.59 3.02
2042 2873 6.985645 CCTCTTTTCTCTCTACTGATGATTGG 59.014 42.308 0.00 0.00 0.00 3.16
2050 2881 8.746052 TTATCTCTCCTCTTTTCTCTCTACTG 57.254 38.462 0.00 0.00 0.00 2.74
2051 2882 9.408648 CTTTATCTCTCCTCTTTTCTCTCTACT 57.591 37.037 0.00 0.00 0.00 2.57
2052 2883 9.403583 TCTTTATCTCTCCTCTTTTCTCTCTAC 57.596 37.037 0.00 0.00 0.00 2.59
2102 3685 6.748132 TCAAACCTCATGTTTTCAATTCCTC 58.252 36.000 0.00 0.00 44.80 3.71
2176 3759 3.575805 AGGGTTTGCTTGAAGAATTCCA 58.424 40.909 0.65 0.00 46.93 3.53
2415 3998 5.008712 GGGTTGGAACACTATTAGCTAATGC 59.991 44.000 25.99 7.99 39.29 3.56
2421 4004 4.510340 CGTATGGGTTGGAACACTATTAGC 59.490 45.833 0.00 0.00 39.29 3.09
2737 4320 6.885952 TTTGGAACGATGAAAAGGTGATAA 57.114 33.333 0.00 0.00 0.00 1.75
3004 4587 6.456988 CGAAACCATAGAAATTACTCACCTGC 60.457 42.308 0.00 0.00 0.00 4.85
3068 4651 5.717178 AGCTCTCTACAAAGTCACAGGATTA 59.283 40.000 0.00 0.00 0.00 1.75
3209 4792 9.918630 GGCAACTTAGCATATTTCATAATCATT 57.081 29.630 0.00 0.00 35.83 2.57
3290 4873 5.907391 CGGAACCGAGAAATAATTGTTATGC 59.093 40.000 7.53 0.00 42.83 3.14
3599 5557 6.419791 CCCATATCCCAACAAAGTTACACTA 58.580 40.000 0.00 0.00 0.00 2.74
3619 5577 0.262580 CCATCCATCACCAACCCCAT 59.737 55.000 0.00 0.00 0.00 4.00
4003 5962 4.822036 TTGTTTGACCGTTACATTGGAG 57.178 40.909 0.00 0.00 0.00 3.86
4120 6079 4.142271 CCGGTATTGGAGCAAATTTAGCAA 60.142 41.667 12.88 0.00 0.00 3.91
4121 6080 3.380004 CCGGTATTGGAGCAAATTTAGCA 59.620 43.478 12.88 0.00 0.00 3.49
4122 6081 3.380320 ACCGGTATTGGAGCAAATTTAGC 59.620 43.478 4.49 0.00 0.00 3.09
4123 6082 5.238650 CCTACCGGTATTGGAGCAAATTTAG 59.761 44.000 16.25 0.00 0.00 1.85
4124 6083 5.127491 CCTACCGGTATTGGAGCAAATTTA 58.873 41.667 16.25 0.00 0.00 1.40
4126 6085 3.053917 ACCTACCGGTATTGGAGCAAATT 60.054 43.478 23.11 0.00 43.29 1.82
4127 6086 2.508300 ACCTACCGGTATTGGAGCAAAT 59.492 45.455 23.11 0.57 43.29 2.32
4325 6287 7.012515 TGTTTTTCGTTAGTAATGGCAAGAAGA 59.987 33.333 2.28 0.00 0.00 2.87
4326 6288 7.136119 TGTTTTTCGTTAGTAATGGCAAGAAG 58.864 34.615 2.28 0.00 0.00 2.85
4414 6376 8.407832 TCCAGCAAGTTCAAATATACATCATTG 58.592 33.333 0.00 0.00 0.00 2.82
4433 6395 1.416030 TGCAGTAACACTCTCCAGCAA 59.584 47.619 0.00 0.00 0.00 3.91
4464 6426 8.027524 ACACCACTGAAATCTGATACATCTAT 57.972 34.615 0.00 0.00 0.00 1.98
4489 6451 3.891324 GGTGCACTTATTTACGCAACAA 58.109 40.909 17.98 0.00 41.74 2.83
4491 6453 3.546002 TGGTGCACTTATTTACGCAAC 57.454 42.857 17.98 0.00 42.47 4.17
4673 6641 3.834813 ACTGAACTAGATGGTGAAGCTGA 59.165 43.478 0.00 0.00 0.00 4.26
4682 6650 8.553459 AACAATGTTAGAACTGAACTAGATGG 57.447 34.615 0.00 0.00 0.00 3.51
4788 6758 1.009829 GGATTGCAACTAGACGGCAG 58.990 55.000 0.00 0.00 38.97 4.85
4932 6904 0.973632 ACGTCTACAAGCACCCATGA 59.026 50.000 0.00 0.00 0.00 3.07
4940 6912 1.860676 TGTGGTGAACGTCTACAAGC 58.139 50.000 0.00 0.00 0.00 4.01
4969 6942 9.563748 GAGTACTCTGATTATGACTACTACCTT 57.436 37.037 15.91 0.00 0.00 3.50
4984 6957 8.629158 GTCTTGTGATTATGAGAGTACTCTGAT 58.371 37.037 29.84 27.28 42.99 2.90
4985 6958 7.611855 TGTCTTGTGATTATGAGAGTACTCTGA 59.388 37.037 29.84 22.40 42.99 3.27
4986 6959 7.766283 TGTCTTGTGATTATGAGAGTACTCTG 58.234 38.462 29.84 10.71 42.99 3.35
4987 6960 7.946381 TGTCTTGTGATTATGAGAGTACTCT 57.054 36.000 25.44 25.44 42.99 3.24
4988 6961 9.029243 CATTGTCTTGTGATTATGAGAGTACTC 57.971 37.037 15.41 15.41 42.88 2.59
4989 6962 8.753133 TCATTGTCTTGTGATTATGAGAGTACT 58.247 33.333 0.00 0.00 0.00 2.73
4990 6963 8.932945 TCATTGTCTTGTGATTATGAGAGTAC 57.067 34.615 0.00 0.00 0.00 2.73
4991 6964 7.708322 GCTCATTGTCTTGTGATTATGAGAGTA 59.292 37.037 12.61 0.00 40.94 2.59
4992 6965 6.538021 GCTCATTGTCTTGTGATTATGAGAGT 59.462 38.462 12.61 0.00 40.94 3.24
4993 6966 6.018098 GGCTCATTGTCTTGTGATTATGAGAG 60.018 42.308 12.61 0.00 40.94 3.20
4994 6967 5.819379 GGCTCATTGTCTTGTGATTATGAGA 59.181 40.000 12.61 0.00 40.94 3.27
4995 6968 5.587443 TGGCTCATTGTCTTGTGATTATGAG 59.413 40.000 0.00 0.00 41.14 2.90
4996 6969 5.499313 TGGCTCATTGTCTTGTGATTATGA 58.501 37.500 0.00 0.00 0.00 2.15
4997 6970 5.823209 TGGCTCATTGTCTTGTGATTATG 57.177 39.130 0.00 0.00 0.00 1.90
4998 6971 6.183360 CCATTGGCTCATTGTCTTGTGATTAT 60.183 38.462 0.00 0.00 0.00 1.28
4999 6972 5.125900 CCATTGGCTCATTGTCTTGTGATTA 59.874 40.000 0.00 0.00 0.00 1.75
5000 6973 4.081862 CCATTGGCTCATTGTCTTGTGATT 60.082 41.667 0.00 0.00 0.00 2.57
5061 7034 8.396272 AGCACTATTGTTCTGTTCATTTTACT 57.604 30.769 0.00 0.00 0.00 2.24
5082 7055 4.685169 TGATTCCTTTCGAAATGAGCAC 57.315 40.909 11.70 9.45 33.08 4.40
5291 7265 1.370064 GTGACTTGTGCCCTACGGT 59.630 57.895 0.00 0.00 0.00 4.83
5309 7283 2.158143 AGCACCTATACCTTAGAGGGGG 60.158 54.545 0.00 0.00 40.92 5.40
5344 7318 9.558396 TTAAGAAAAACTCGGTCTATTTTACCA 57.442 29.630 0.00 0.00 36.78 3.25
5354 7328 5.065602 ACTGGTGTTTAAGAAAAACTCGGTC 59.934 40.000 2.67 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.