Multiple sequence alignment - TraesCS2B01G411700

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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 TraesCS2B01G411700 chr2B 100.000 5723 0 0 1 5723 585896621 585890899 0.000000e+00 10569.0
1 TraesCS2B01G411700 chr2B 95.909 220 9 0 4694 4913 768578014 768578233 1.960000e-94 357.0
2 TraesCS2B01G411700 chr2B 92.994 157 7 4 2425 2579 133949976 133949822 5.770000e-55 226.0
3 TraesCS2B01G411700 chr2B 85.057 87 9 4 4896 4980 625260758 625260842 1.020000e-12 86.1
4 TraesCS2B01G411700 chr2A 91.674 3615 177 26 699 4297 643444336 643440830 0.000000e+00 4894.0
5 TraesCS2B01G411700 chr2A 94.327 899 34 7 4294 5186 643440750 643439863 0.000000e+00 1362.0
6 TraesCS2B01G411700 chr2A 85.484 620 52 17 1 593 643471720 643471112 3.790000e-171 612.0
7 TraesCS2B01G411700 chr2A 87.156 545 51 9 5185 5721 643439737 643439204 8.200000e-168 601.0
8 TraesCS2B01G411700 chr2D 92.802 3001 147 24 2577 5539 498770776 498767807 0.000000e+00 4281.0
9 TraesCS2B01G411700 chr2D 94.598 1740 62 19 699 2423 498772531 498770809 0.000000e+00 2663.0
10 TraesCS2B01G411700 chr2D 89.763 674 27 15 39 680 498778082 498777419 0.000000e+00 824.0
11 TraesCS2B01G411700 chr2D 92.308 156 11 1 2428 2583 179130242 179130088 2.680000e-53 220.0
12 TraesCS2B01G411700 chr5A 89.708 787 45 9 1635 2409 591602517 591603279 0.000000e+00 972.0
13 TraesCS2B01G411700 chr5A 89.602 779 45 9 1643 2409 296660149 296660903 0.000000e+00 957.0
14 TraesCS2B01G411700 chr5A 74.552 279 53 15 1439 1703 653717133 653716859 7.840000e-19 106.0
15 TraesCS2B01G411700 chr5A 93.750 64 4 0 1564 1627 482945865 482945928 4.720000e-16 97.1
16 TraesCS2B01G411700 chr7A 95.909 220 9 0 4694 4913 660478701 660478920 1.960000e-94 357.0
17 TraesCS2B01G411700 chr7A 86.620 284 20 3 4063 4343 16021562 16021830 1.210000e-76 298.0
18 TraesCS2B01G411700 chr7A 86.620 284 20 3 4063 4343 660478917 660479185 1.210000e-76 298.0
19 TraesCS2B01G411700 chr5B 95.909 220 9 0 4694 4913 608634452 608634671 1.960000e-94 357.0
20 TraesCS2B01G411700 chr5B 86.620 284 20 3 4063 4343 608634668 608634936 1.210000e-76 298.0
21 TraesCS2B01G411700 chr5B 93.506 154 10 0 2426 2579 446430700 446430547 4.460000e-56 230.0
22 TraesCS2B01G411700 chr5B 91.875 160 13 0 2420 2579 314297471 314297312 2.080000e-54 224.0
23 TraesCS2B01G411700 chr5B 75.986 279 49 14 1439 1703 662036915 662036641 1.670000e-25 128.0
24 TraesCS2B01G411700 chr4A 95.909 220 9 0 4694 4913 718030823 718031042 1.960000e-94 357.0
25 TraesCS2B01G411700 chr4A 85.915 284 22 3 4063 4343 718031039 718031307 2.610000e-73 287.0
26 TraesCS2B01G411700 chr4A 89.474 171 15 3 2409 2579 321329068 321329235 4.490000e-51 213.0
27 TraesCS2B01G411700 chr4A 95.312 64 3 0 1564 1627 536323212 536323275 1.010000e-17 102.0
28 TraesCS2B01G411700 chr5D 95.872 218 9 0 4694 4911 533542567 533542784 2.540000e-93 353.0
29 TraesCS2B01G411700 chr5D 86.833 281 19 3 4066 4343 412253279 412253014 1.210000e-76 298.0
30 TraesCS2B01G411700 chr5D 76.071 280 47 17 1439 1703 526572118 526571844 1.670000e-25 128.0
31 TraesCS2B01G411700 chr1D 95.455 220 10 0 4694 4913 111702086 111701867 9.120000e-93 351.0
32 TraesCS2B01G411700 chr1D 95.455 220 10 0 4694 4913 111710485 111710704 9.120000e-93 351.0
33 TraesCS2B01G411700 chr1D 86.833 281 19 3 4066 4343 111701867 111701602 1.210000e-76 298.0
34 TraesCS2B01G411700 chr1D 86.620 284 20 3 4063 4343 111710701 111710969 1.210000e-76 298.0
35 TraesCS2B01G411700 chr4D 92.045 176 11 2 2407 2579 145579488 145579663 1.590000e-60 244.0
36 TraesCS2B01G411700 chr6D 92.500 160 12 0 2420 2579 348087597 348087756 4.460000e-56 230.0
37 TraesCS2B01G411700 chr3D 93.421 152 10 0 2428 2579 481710201 481710352 5.770000e-55 226.0
38 TraesCS2B01G411700 chr3D 97.059 34 1 0 1572 1605 230766786 230766753 2.230000e-04 58.4
39 TraesCS2B01G411700 chr7D 75.887 282 34 20 4705 4975 134466003 134466261 4.690000e-21 113.0
40 TraesCS2B01G411700 chr3A 95.312 64 3 0 1564 1627 56077025 56077088 1.010000e-17 102.0
41 TraesCS2B01G411700 chr3B 86.905 84 9 2 1597 1679 228690629 228690547 6.110000e-15 93.5
42 TraesCS2B01G411700 chr1B 74.886 219 45 9 1478 1692 533324618 533324406 2.200000e-14 91.6


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 TraesCS2B01G411700 chr2B 585890899 585896621 5722 True 10569.000000 10569 100.000000 1 5723 1 chr2B.!!$R2 5722
1 TraesCS2B01G411700 chr2A 643439204 643444336 5132 True 2285.666667 4894 91.052333 699 5721 3 chr2A.!!$R2 5022
2 TraesCS2B01G411700 chr2A 643471112 643471720 608 True 612.000000 612 85.484000 1 593 1 chr2A.!!$R1 592
3 TraesCS2B01G411700 chr2D 498767807 498772531 4724 True 3472.000000 4281 93.700000 699 5539 2 chr2D.!!$R3 4840
4 TraesCS2B01G411700 chr2D 498777419 498778082 663 True 824.000000 824 89.763000 39 680 1 chr2D.!!$R2 641
5 TraesCS2B01G411700 chr5A 591602517 591603279 762 False 972.000000 972 89.708000 1635 2409 1 chr5A.!!$F3 774
6 TraesCS2B01G411700 chr5A 296660149 296660903 754 False 957.000000 957 89.602000 1643 2409 1 chr5A.!!$F1 766

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
656 716 0.253020 ACCCGGGTTTATGGACCTCT 60.253 55.000 24.16 0.0 39.71 3.69 F
1238 1309 0.257328 TCCACCAAACTGTCCTTGCA 59.743 50.000 0.00 0.0 0.00 4.08 F
2068 2145 0.833287 TATCTGCTGTCCTGGCCTTC 59.167 55.000 3.32 0.0 0.00 3.46 F
2069 2146 0.913451 ATCTGCTGTCCTGGCCTTCT 60.913 55.000 3.32 0.0 0.00 2.85 F
2077 2154 1.488393 GTCCTGGCCTTCTTATGCTCT 59.512 52.381 3.32 0.0 0.00 4.09 F
3130 3243 2.270352 TTGGACAGTTACTTGCCTGG 57.730 50.000 0.00 0.0 32.90 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1986 0.179129 GATCCCACATTGCGGCAAAG 60.179 55.000 20.48 17.87 0.00 2.77 R
3120 3233 0.254747 ATTAAGCGGCCAGGCAAGTA 59.745 50.000 15.19 0.00 34.64 2.24 R
3712 3830 0.184933 ACTACAACTTGCAGGGCCAA 59.815 50.000 6.18 0.00 0.00 4.52 R
3868 3986 2.754002 AGTTCAAGACGGTCCTAGTAGC 59.246 50.000 4.14 0.00 0.00 3.58 R
3942 4060 6.176975 TGCGATCGTAATCTGTTTGAATTT 57.823 33.333 17.81 0.00 0.00 1.82 R
4974 5185 0.115152 TCAAGCCTCTGGAGTCTGGA 59.885 55.000 0.00 0.00 0.00 3.86 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
28 29 5.407407 TGACCATCTTCTAGAAACACTCC 57.593 43.478 6.63 0.00 0.00 3.85
35 36 6.042638 TCTTCTAGAAACACTCCCATCTTG 57.957 41.667 6.63 0.00 0.00 3.02
96 97 4.038763 CCTACATAACCGGATCTTGCTACA 59.961 45.833 9.46 0.00 0.00 2.74
301 343 2.043980 CACCCGCCCGCTGTAAATT 61.044 57.895 0.00 0.00 0.00 1.82
303 345 2.478033 CCCGCCCGCTGTAAATTCC 61.478 63.158 0.00 0.00 0.00 3.01
307 349 1.068194 CGCCCGCTGTAAATTCCAAAA 60.068 47.619 0.00 0.00 0.00 2.44
308 350 2.333926 GCCCGCTGTAAATTCCAAAAC 58.666 47.619 0.00 0.00 0.00 2.43
309 351 2.929161 GCCCGCTGTAAATTCCAAAACC 60.929 50.000 0.00 0.00 0.00 3.27
310 352 2.560981 CCCGCTGTAAATTCCAAAACCT 59.439 45.455 0.00 0.00 0.00 3.50
311 353 3.006430 CCCGCTGTAAATTCCAAAACCTT 59.994 43.478 0.00 0.00 0.00 3.50
312 354 3.987220 CCGCTGTAAATTCCAAAACCTTG 59.013 43.478 0.00 0.00 0.00 3.61
313 355 4.261825 CCGCTGTAAATTCCAAAACCTTGA 60.262 41.667 0.00 0.00 34.14 3.02
314 356 4.917415 CGCTGTAAATTCCAAAACCTTGAG 59.083 41.667 0.00 0.00 34.14 3.02
315 357 5.507315 CGCTGTAAATTCCAAAACCTTGAGT 60.507 40.000 0.00 0.00 34.14 3.41
316 358 6.293735 CGCTGTAAATTCCAAAACCTTGAGTA 60.294 38.462 0.00 0.00 34.14 2.59
355 397 0.618968 AGAATCCAGAGCCCGTTCCT 60.619 55.000 0.00 0.00 0.00 3.36
594 654 1.352156 GACGGCTTGTCGACCATCAC 61.352 60.000 14.12 0.00 37.96 3.06
595 655 1.374125 CGGCTTGTCGACCATCACA 60.374 57.895 14.12 0.00 0.00 3.58
596 656 0.948623 CGGCTTGTCGACCATCACAA 60.949 55.000 14.12 0.00 0.00 3.33
597 657 0.517316 GGCTTGTCGACCATCACAAC 59.483 55.000 14.12 0.00 0.00 3.32
598 658 1.512926 GCTTGTCGACCATCACAACT 58.487 50.000 14.12 0.00 0.00 3.16
599 659 1.195448 GCTTGTCGACCATCACAACTG 59.805 52.381 14.12 0.00 0.00 3.16
600 660 2.483876 CTTGTCGACCATCACAACTGT 58.516 47.619 14.12 0.00 0.00 3.55
601 661 2.613026 TGTCGACCATCACAACTGTT 57.387 45.000 14.12 0.00 0.00 3.16
602 662 2.912771 TGTCGACCATCACAACTGTTT 58.087 42.857 14.12 0.00 0.00 2.83
603 663 3.275143 TGTCGACCATCACAACTGTTTT 58.725 40.909 14.12 0.00 0.00 2.43
604 664 4.443621 TGTCGACCATCACAACTGTTTTA 58.556 39.130 14.12 0.00 0.00 1.52
605 665 4.876679 TGTCGACCATCACAACTGTTTTAA 59.123 37.500 14.12 0.00 0.00 1.52
606 666 5.007234 TGTCGACCATCACAACTGTTTTAAG 59.993 40.000 14.12 0.00 0.00 1.85
607 667 4.024387 TCGACCATCACAACTGTTTTAAGC 60.024 41.667 0.00 0.00 0.00 3.09
608 668 4.260990 CGACCATCACAACTGTTTTAAGCA 60.261 41.667 0.00 0.00 0.00 3.91
609 669 5.562696 CGACCATCACAACTGTTTTAAGCAT 60.563 40.000 0.00 0.00 0.00 3.79
610 670 5.772521 ACCATCACAACTGTTTTAAGCATC 58.227 37.500 0.00 0.00 0.00 3.91
611 671 5.301551 ACCATCACAACTGTTTTAAGCATCA 59.698 36.000 0.00 0.00 0.00 3.07
612 672 6.015180 ACCATCACAACTGTTTTAAGCATCAT 60.015 34.615 0.00 0.00 0.00 2.45
613 673 6.529125 CCATCACAACTGTTTTAAGCATCATC 59.471 38.462 0.00 0.00 0.00 2.92
614 674 6.631971 TCACAACTGTTTTAAGCATCATCA 57.368 33.333 0.00 0.00 0.00 3.07
615 675 6.671190 TCACAACTGTTTTAAGCATCATCAG 58.329 36.000 0.00 0.00 0.00 2.90
616 676 5.344128 CACAACTGTTTTAAGCATCATCAGC 59.656 40.000 0.00 0.00 0.00 4.26
617 677 5.009911 ACAACTGTTTTAAGCATCATCAGCA 59.990 36.000 0.00 0.00 0.00 4.41
618 678 5.306532 ACTGTTTTAAGCATCATCAGCAG 57.693 39.130 0.00 0.00 0.00 4.24
619 679 4.157289 ACTGTTTTAAGCATCATCAGCAGG 59.843 41.667 0.00 0.00 0.00 4.85
620 680 4.334552 TGTTTTAAGCATCATCAGCAGGA 58.665 39.130 0.00 0.00 0.00 3.86
621 681 4.156556 TGTTTTAAGCATCATCAGCAGGAC 59.843 41.667 0.00 0.00 0.00 3.85
622 682 3.920231 TTAAGCATCATCAGCAGGACT 57.080 42.857 0.00 0.00 0.00 3.85
634 694 3.928005 AGCAGGACTGATCATCAACAT 57.072 42.857 3.00 0.00 0.00 2.71
635 695 3.806380 AGCAGGACTGATCATCAACATC 58.194 45.455 3.00 0.00 0.00 3.06
636 696 3.199289 AGCAGGACTGATCATCAACATCA 59.801 43.478 3.00 0.00 0.00 3.07
637 697 3.943381 GCAGGACTGATCATCAACATCAA 59.057 43.478 3.00 0.00 29.74 2.57
638 698 4.201891 GCAGGACTGATCATCAACATCAAC 60.202 45.833 3.00 0.00 29.74 3.18
639 699 4.334759 CAGGACTGATCATCAACATCAACC 59.665 45.833 0.00 0.00 29.74 3.77
640 700 3.629398 GGACTGATCATCAACATCAACCC 59.371 47.826 0.00 0.00 29.74 4.11
641 701 3.273434 ACTGATCATCAACATCAACCCG 58.727 45.455 0.00 0.00 29.74 5.28
642 702 2.615447 CTGATCATCAACATCAACCCGG 59.385 50.000 0.00 0.00 29.74 5.73
643 703 1.949525 GATCATCAACATCAACCCGGG 59.050 52.381 22.25 22.25 0.00 5.73
644 704 0.695924 TCATCAACATCAACCCGGGT 59.304 50.000 24.16 24.16 0.00 5.28
645 705 1.074727 TCATCAACATCAACCCGGGTT 59.925 47.619 33.74 33.74 39.13 4.11
646 706 1.892474 CATCAACATCAACCCGGGTTT 59.108 47.619 36.59 20.96 36.00 3.27
647 707 2.953284 TCAACATCAACCCGGGTTTA 57.047 45.000 36.59 29.22 36.00 2.01
648 708 3.443145 TCAACATCAACCCGGGTTTAT 57.557 42.857 36.59 30.13 36.00 1.40
649 709 3.085533 TCAACATCAACCCGGGTTTATG 58.914 45.455 40.44 40.44 42.27 1.90
650 710 2.137810 ACATCAACCCGGGTTTATGG 57.862 50.000 42.44 31.06 41.42 2.74
651 711 1.636519 ACATCAACCCGGGTTTATGGA 59.363 47.619 42.44 33.70 41.42 3.41
652 712 2.021457 CATCAACCCGGGTTTATGGAC 58.979 52.381 37.33 0.00 36.57 4.02
653 713 0.328926 TCAACCCGGGTTTATGGACC 59.671 55.000 36.59 0.00 36.00 4.46
654 714 0.330267 CAACCCGGGTTTATGGACCT 59.670 55.000 36.59 9.87 39.71 3.85
655 715 0.622136 AACCCGGGTTTATGGACCTC 59.378 55.000 33.74 0.00 39.71 3.85
656 716 0.253020 ACCCGGGTTTATGGACCTCT 60.253 55.000 24.16 0.00 39.71 3.69
657 717 0.468648 CCCGGGTTTATGGACCTCTC 59.531 60.000 14.18 0.00 39.71 3.20
658 718 1.200519 CCGGGTTTATGGACCTCTCA 58.799 55.000 0.00 0.00 39.71 3.27
659 719 1.557832 CCGGGTTTATGGACCTCTCAA 59.442 52.381 0.00 0.00 39.71 3.02
660 720 2.172717 CCGGGTTTATGGACCTCTCAAT 59.827 50.000 0.00 0.00 39.71 2.57
661 721 3.206150 CGGGTTTATGGACCTCTCAATG 58.794 50.000 0.00 0.00 39.71 2.82
662 722 3.118408 CGGGTTTATGGACCTCTCAATGA 60.118 47.826 0.00 0.00 39.71 2.57
663 723 4.625324 CGGGTTTATGGACCTCTCAATGAA 60.625 45.833 0.00 0.00 39.71 2.57
664 724 4.884164 GGGTTTATGGACCTCTCAATGAAG 59.116 45.833 0.00 0.00 39.71 3.02
665 725 5.339200 GGGTTTATGGACCTCTCAATGAAGA 60.339 44.000 0.00 0.00 39.71 2.87
666 726 6.360618 GGTTTATGGACCTCTCAATGAAGAT 58.639 40.000 0.00 0.00 36.73 2.40
667 727 7.420214 GGGTTTATGGACCTCTCAATGAAGATA 60.420 40.741 0.00 0.00 39.71 1.98
668 728 7.993183 GGTTTATGGACCTCTCAATGAAGATAA 59.007 37.037 0.00 0.00 36.73 1.75
669 729 9.050601 GTTTATGGACCTCTCAATGAAGATAAG 57.949 37.037 0.00 0.00 0.00 1.73
670 730 8.553085 TTATGGACCTCTCAATGAAGATAAGA 57.447 34.615 0.00 0.00 0.00 2.10
671 731 6.477053 TGGACCTCTCAATGAAGATAAGAG 57.523 41.667 0.00 0.00 34.55 2.85
672 732 5.960811 TGGACCTCTCAATGAAGATAAGAGT 59.039 40.000 0.00 0.00 33.23 3.24
673 733 7.126061 TGGACCTCTCAATGAAGATAAGAGTA 58.874 38.462 0.00 0.00 33.23 2.59
674 734 7.786943 TGGACCTCTCAATGAAGATAAGAGTAT 59.213 37.037 0.00 0.00 33.23 2.12
675 735 8.087750 GGACCTCTCAATGAAGATAAGAGTATG 58.912 40.741 0.00 0.00 33.23 2.39
676 736 8.546083 ACCTCTCAATGAAGATAAGAGTATGT 57.454 34.615 0.00 0.00 33.23 2.29
677 737 8.986991 ACCTCTCAATGAAGATAAGAGTATGTT 58.013 33.333 0.00 0.00 33.23 2.71
741 801 1.871772 CGGTGCAGCAGGAAAGAAG 59.128 57.895 17.33 0.00 0.00 2.85
752 813 5.868801 CAGCAGGAAAGAAGACAAAACAAAA 59.131 36.000 0.00 0.00 0.00 2.44
775 836 1.794512 CAAATGCACTTTTTCCGGGG 58.205 50.000 0.00 0.00 0.00 5.73
816 878 2.645838 AAGCTGGAGCACTCAAGAAA 57.354 45.000 6.22 0.00 45.16 2.52
817 879 2.645838 AGCTGGAGCACTCAAGAAAA 57.354 45.000 6.22 0.00 45.16 2.29
818 880 2.936202 AGCTGGAGCACTCAAGAAAAA 58.064 42.857 6.22 0.00 45.16 1.94
912 976 0.753262 AGACAGAACACCGAAGCACT 59.247 50.000 0.00 0.00 0.00 4.40
918 982 0.463654 AACACCGAAGCACTGAAGCA 60.464 50.000 0.00 0.00 36.85 3.91
966 1030 2.612471 CCCTGCTTCACTTCACTGAGAG 60.612 54.545 0.00 0.00 0.00 3.20
968 1032 1.345741 TGCTTCACTTCACTGAGAGGG 59.654 52.381 0.00 0.00 0.00 4.30
969 1033 1.943507 GCTTCACTTCACTGAGAGGGC 60.944 57.143 0.00 0.00 0.00 5.19
970 1034 0.318441 TTCACTTCACTGAGAGGGCG 59.682 55.000 0.00 0.00 0.00 6.13
1159 1226 2.508439 ACGCCATCGGTAAGCACG 60.508 61.111 0.00 0.00 40.69 5.34
1229 1300 3.317993 CCAAGAAACGAATCCACCAAACT 59.682 43.478 0.00 0.00 0.00 2.66
1238 1309 0.257328 TCCACCAAACTGTCCTTGCA 59.743 50.000 0.00 0.00 0.00 4.08
1241 1312 1.750778 CACCAAACTGTCCTTGCACTT 59.249 47.619 0.00 0.00 0.00 3.16
1259 1330 4.794655 GCACTTTTACCAAAATTCCTCGCA 60.795 41.667 0.00 0.00 0.00 5.10
1323 1399 2.253513 CGCCAACGGAATTTCCACT 58.746 52.632 15.58 0.00 35.91 4.00
1368 1444 1.617322 TCTCTGCTCGTACCACAGTT 58.383 50.000 4.82 0.00 33.12 3.16
1434 1511 3.096092 TCTGTGCTTTCTTTTTGTGGGT 58.904 40.909 0.00 0.00 0.00 4.51
1736 1813 1.451028 GATTGCGCTCTGGAAGGCT 60.451 57.895 9.73 0.00 0.00 4.58
1836 1913 2.384828 TGTTCGGCTAGATCTAAGGCA 58.615 47.619 18.80 8.74 0.00 4.75
1847 1924 6.375736 GCTAGATCTAAGGCAAAAGTTTCCTT 59.624 38.462 12.01 12.01 42.40 3.36
1909 1986 2.479219 GCCAAGCTAGAGATTGCTTTGC 60.479 50.000 7.75 7.75 45.91 3.68
1931 2008 2.901840 CCGCAATGTGGGATCCCG 60.902 66.667 26.03 12.18 39.42 5.14
1974 2051 2.356135 CGTTGGTGAGGAAAGTATGGG 58.644 52.381 0.00 0.00 0.00 4.00
2068 2145 0.833287 TATCTGCTGTCCTGGCCTTC 59.167 55.000 3.32 0.00 0.00 3.46
2069 2146 0.913451 ATCTGCTGTCCTGGCCTTCT 60.913 55.000 3.32 0.00 0.00 2.85
2077 2154 1.488393 GTCCTGGCCTTCTTATGCTCT 59.512 52.381 3.32 0.00 0.00 4.09
2078 2155 2.700897 GTCCTGGCCTTCTTATGCTCTA 59.299 50.000 3.32 0.00 0.00 2.43
2088 2165 6.471146 CCTTCTTATGCTCTATAATGTGGCT 58.529 40.000 0.00 0.00 31.12 4.75
2152 2238 9.988350 CCAAGTGTAAATGTACTAATGTGATTC 57.012 33.333 0.00 0.00 0.00 2.52
2259 2353 8.834212 CGATTTGCGTGATTTGATCAATTATAG 58.166 33.333 9.40 2.94 41.69 1.31
2260 2354 9.669353 GATTTGCGTGATTTGATCAATTATAGT 57.331 29.630 9.40 0.00 41.69 2.12
2346 2440 4.379499 CCGTGGCTCCTTCAGTTTATTTTC 60.379 45.833 0.00 0.00 0.00 2.29
2455 2549 8.767085 TCCGTTTTTATTTACTCCGCATATTAG 58.233 33.333 0.00 0.00 0.00 1.73
2464 2558 5.864418 ACTCCGCATATTAGGTTTGTCTA 57.136 39.130 0.00 0.00 0.00 2.59
2597 2691 4.571375 TTTTATTCCACGATTCACGACG 57.429 40.909 0.00 0.00 45.77 5.12
2624 2718 7.013846 GTCTATGGTTACTAGAGTGCAGAATCT 59.986 40.741 0.00 0.00 0.00 2.40
2635 2729 3.197333 AGTGCAGAATCTGTATGCTGAGT 59.803 43.478 12.29 0.00 40.87 3.41
2639 2733 5.987953 TGCAGAATCTGTATGCTGAGTTATC 59.012 40.000 12.29 0.00 40.87 1.75
2721 2817 5.476945 AGTGATTATCCTGGGTTTTGTTGAC 59.523 40.000 0.00 0.00 0.00 3.18
2737 2833 5.034852 TGTTGACAACTGAGGAATTCTGA 57.965 39.130 18.73 0.00 0.00 3.27
2750 2846 5.444176 AGGAATTCTGAGAAATGTGGATCC 58.556 41.667 4.20 4.20 0.00 3.36
2831 2928 9.459640 CATATTAATGGAGAGTTTGCAAGAATG 57.540 33.333 0.00 0.00 0.00 2.67
3048 3161 6.834168 TGGGATCCTTTAAACAACTTGATC 57.166 37.500 12.58 0.00 0.00 2.92
3067 3180 9.539194 ACTTGATCTATTTTCTTGAGGGAAATT 57.461 29.630 0.00 0.00 35.51 1.82
3130 3243 2.270352 TTGGACAGTTACTTGCCTGG 57.730 50.000 0.00 0.00 32.90 4.45
3134 3247 2.359975 AGTTACTTGCCTGGCCGC 60.360 61.111 17.53 0.00 0.00 6.53
3170 3283 6.099341 AGCTTTACTCTTTTTGTGGTTTGTG 58.901 36.000 0.00 0.00 0.00 3.33
3282 3395 4.393062 TGCTGCTCAGAACATAAAGTTAGC 59.607 41.667 0.00 0.00 41.51 3.09
3320 3436 4.819630 CCACACTTAAAAGGTGTAGCAGAA 59.180 41.667 0.00 0.00 44.75 3.02
3326 3442 9.167311 CACTTAAAAGGTGTAGCAGAAATCTAT 57.833 33.333 0.00 0.00 0.00 1.98
3393 3511 7.816945 ATAAAATGTGCTGTTAATGTGCTTC 57.183 32.000 0.00 0.00 0.00 3.86
3444 3562 4.711399 TCATCAGATGACAATTAGCCTGG 58.289 43.478 9.21 0.00 33.59 4.45
3466 3584 3.293311 GCAATTGGCAGCAATATCGAT 57.707 42.857 7.72 2.16 43.97 3.59
3542 3660 6.651975 ATATAGCTCCTTTACTGTTAGCGT 57.348 37.500 0.00 0.00 38.23 5.07
3844 3962 8.742554 ACAACTTCATTCGATTATTTTTCCAC 57.257 30.769 0.00 0.00 0.00 4.02
3955 4074 9.868277 TTTGTTAGTGTTCAAATTCAAACAGAT 57.132 25.926 5.98 2.44 36.14 2.90
3994 4113 9.085645 TGTAAATTAGTGAAGTTCTACTCCTGA 57.914 33.333 4.17 0.00 0.00 3.86
4026 4145 9.601971 TCAGAATATAAAGTTAAAAACGTGCAC 57.398 29.630 6.82 6.82 36.23 4.57
4028 4147 8.497554 AGAATATAAAGTTAAAAACGTGCACGA 58.502 29.630 42.94 19.98 43.02 4.35
4095 4214 4.579454 TGTGCGTCTAAGTTGTCTAGTT 57.421 40.909 0.00 0.00 0.00 2.24
4140 4259 6.487828 TCTTTGAGATGGTTTCCTGAATGAT 58.512 36.000 0.00 0.00 0.00 2.45
4200 4319 5.884792 GTGATCCTGGAGATTTCATGTTTCT 59.115 40.000 1.52 0.00 34.42 2.52
4212 4331 9.300681 AGATTTCATGTTTCTTAGGACAATTGA 57.699 29.630 13.59 0.00 0.00 2.57
4217 4336 9.904198 TCATGTTTCTTAGGACAATTGATATGA 57.096 29.630 13.59 3.16 0.00 2.15
4219 4338 8.737168 TGTTTCTTAGGACAATTGATATGAGG 57.263 34.615 13.59 0.00 0.00 3.86
4220 4339 7.775093 TGTTTCTTAGGACAATTGATATGAGGG 59.225 37.037 13.59 0.00 0.00 4.30
4221 4340 5.869579 TCTTAGGACAATTGATATGAGGGC 58.130 41.667 13.59 0.00 0.00 5.19
4222 4341 5.369404 TCTTAGGACAATTGATATGAGGGCA 59.631 40.000 13.59 0.00 0.00 5.36
4223 4342 4.736611 AGGACAATTGATATGAGGGCAT 57.263 40.909 13.59 0.00 38.54 4.40
4224 4343 5.070823 AGGACAATTGATATGAGGGCATT 57.929 39.130 13.59 0.00 35.94 3.56
4225 4344 5.461327 AGGACAATTGATATGAGGGCATTT 58.539 37.500 13.59 0.00 35.94 2.32
4226 4345 5.303589 AGGACAATTGATATGAGGGCATTTG 59.696 40.000 13.59 0.00 35.94 2.32
4240 4359 6.838090 TGAGGGCATTTGACATGGAAATATAA 59.162 34.615 0.00 0.00 0.00 0.98
4266 4385 6.181190 TCCTACTATGATCTGGGACTAATCG 58.819 44.000 0.00 0.00 0.00 3.34
4322 4524 2.223203 GCAGGATTCGCATGAGAACAAG 60.223 50.000 14.40 6.26 32.39 3.16
4323 4525 3.005554 CAGGATTCGCATGAGAACAAGT 58.994 45.455 14.40 0.00 32.39 3.16
4324 4526 3.005554 AGGATTCGCATGAGAACAAGTG 58.994 45.455 14.40 0.00 32.39 3.16
4326 4528 3.436704 GGATTCGCATGAGAACAAGTGAA 59.563 43.478 14.40 0.00 44.27 3.18
4343 4548 7.865707 ACAAGTGAAGACAAATAAAGCTACTG 58.134 34.615 0.00 0.00 0.00 2.74
4398 4603 4.225208 GTTCTTTGCTGAGATTGACTTGC 58.775 43.478 0.00 0.00 0.00 4.01
4494 4699 4.910195 TCACAGTCCTAATCAGCAATGTT 58.090 39.130 0.00 0.00 0.00 2.71
4506 4711 2.203480 AATGTTGGTGGCGCTGGT 60.203 55.556 7.64 0.00 0.00 4.00
4512 4717 3.434319 GGTGGCGCTGGTGATGTG 61.434 66.667 7.64 0.00 0.00 3.21
4701 4906 3.320826 GGGAGTTTGGCAAAACATACACT 59.679 43.478 18.82 6.19 46.80 3.55
4789 4995 7.727578 TCATCCTATGAGTTGGTTGTAGTAA 57.272 36.000 0.00 0.00 33.59 2.24
4882 5093 6.049790 AGGAACGAGCTGATTATTAGGAAAC 58.950 40.000 0.00 0.00 0.00 2.78
4944 5155 8.335532 ACATACTACATGCAGTTGTAATTGTT 57.664 30.769 3.37 0.00 40.79 2.83
4974 5185 9.890629 TGTACTATTTCAAATCTGATAGTTGCT 57.109 29.630 0.00 0.00 32.25 3.91
4976 5187 8.443953 ACTATTTCAAATCTGATAGTTGCTCC 57.556 34.615 0.00 0.00 33.18 4.70
4977 5188 8.049117 ACTATTTCAAATCTGATAGTTGCTCCA 58.951 33.333 0.00 0.00 33.18 3.86
4978 5189 6.748333 TTTCAAATCTGATAGTTGCTCCAG 57.252 37.500 0.00 0.00 33.18 3.86
4979 5190 5.682234 TCAAATCTGATAGTTGCTCCAGA 57.318 39.130 0.00 0.00 39.60 3.86
5004 5215 3.744942 CCAGAGGCTTGATGTATCATTCG 59.255 47.826 0.00 0.00 36.56 3.34
5011 5222 5.455392 GCTTGATGTATCATTCGGAAATGG 58.545 41.667 0.00 0.00 42.19 3.16
5017 5228 5.116180 TGTATCATTCGGAAATGGTCTGAC 58.884 41.667 0.00 0.00 41.58 3.51
5058 5269 8.680001 TTGATGTATCATTCAGAAACATTCTGG 58.320 33.333 17.42 4.84 45.29 3.86
5092 5306 3.885724 TGCTCGTTGTATCATTCAGGA 57.114 42.857 0.00 0.00 0.00 3.86
5172 5386 2.549778 CCCCGCCAACATTGAAACATTT 60.550 45.455 0.00 0.00 0.00 2.32
5246 5589 6.651225 CCAGTAAAACCAAAACCAAACAGAAA 59.349 34.615 0.00 0.00 0.00 2.52
5276 5619 3.849911 TCTTCTACAGATTGCAACGAGG 58.150 45.455 0.00 0.00 0.00 4.63
5283 5626 4.130118 ACAGATTGCAACGAGGGATAATC 58.870 43.478 0.00 0.00 0.00 1.75
5327 5670 4.851558 GCAACAACTCGAATGTTCAATACC 59.148 41.667 12.03 0.00 38.90 2.73
5331 5674 3.518590 ACTCGAATGTTCAATACCGGAC 58.481 45.455 9.46 0.00 0.00 4.79
5349 5692 1.740025 GACCCATTGCAGTTCAGCTAC 59.260 52.381 0.00 0.00 34.99 3.58
5416 5759 6.039270 ACTCAAATGTAAAGTTGCAGCAGTAA 59.961 34.615 2.55 0.00 0.00 2.24
5425 5768 4.192317 AGTTGCAGCAGTAAAGCTATACC 58.808 43.478 2.55 0.00 44.54 2.73
5427 5770 4.214986 TGCAGCAGTAAAGCTATACCAA 57.785 40.909 0.00 0.00 44.54 3.67
5435 5778 6.539103 GCAGTAAAGCTATACCAACTAAAGCT 59.461 38.462 0.00 0.00 45.12 3.74
5501 5844 1.609208 AAACCAGATTCAACGCAGCT 58.391 45.000 0.00 0.00 0.00 4.24
5507 5854 2.995939 CAGATTCAACGCAGCTACTTGA 59.004 45.455 0.00 0.00 0.00 3.02
5532 5879 7.308450 TCAGGATTTCAGGAATAGGTATCTG 57.692 40.000 0.00 0.00 0.00 2.90
5533 5880 5.936956 CAGGATTTCAGGAATAGGTATCTGC 59.063 44.000 0.00 0.00 0.00 4.26
5552 5900 4.278170 TCTGCCGTCTTGATTCACATTTTT 59.722 37.500 0.00 0.00 0.00 1.94
5559 5907 7.362056 CCGTCTTGATTCACATTTTTATGGAGT 60.362 37.037 0.00 0.00 0.00 3.85
5564 5912 8.175925 TGATTCACATTTTTATGGAGTGTTCA 57.824 30.769 0.00 0.00 0.00 3.18
5568 5916 8.862325 TCACATTTTTATGGAGTGTTCATACT 57.138 30.769 0.00 0.00 0.00 2.12
5569 5917 9.295825 TCACATTTTTATGGAGTGTTCATACTT 57.704 29.630 0.00 0.00 0.00 2.24
5570 5918 9.559958 CACATTTTTATGGAGTGTTCATACTTC 57.440 33.333 0.00 0.00 0.00 3.01
5571 5919 9.295825 ACATTTTTATGGAGTGTTCATACTTCA 57.704 29.630 0.00 0.00 40.33 3.02
5586 5934 6.957631 TCATACTTCATACCACTCCAACAAT 58.042 36.000 0.00 0.00 0.00 2.71
5587 5935 8.084985 TCATACTTCATACCACTCCAACAATA 57.915 34.615 0.00 0.00 0.00 1.90
5591 5939 7.175104 ACTTCATACCACTCCAACAATAACAT 58.825 34.615 0.00 0.00 0.00 2.71
5594 5942 7.047891 TCATACCACTCCAACAATAACATCTC 58.952 38.462 0.00 0.00 0.00 2.75
5666 6014 6.593382 CAGTGAAACCAAACCAAATCAAAAGA 59.407 34.615 0.00 0.00 37.80 2.52
5671 6019 5.435291 ACCAAACCAAATCAAAAGAATGCA 58.565 33.333 0.00 0.00 0.00 3.96
5672 6020 6.063404 ACCAAACCAAATCAAAAGAATGCAT 58.937 32.000 0.00 0.00 0.00 3.96
5674 6022 6.428771 CCAAACCAAATCAAAAGAATGCATCT 59.571 34.615 0.00 0.00 41.32 2.90
5683 6031 7.369803 TCAAAAGAATGCATCTCTTCTACAC 57.630 36.000 18.32 0.00 37.42 2.90
5684 6032 6.936335 TCAAAAGAATGCATCTCTTCTACACA 59.064 34.615 18.32 4.43 37.42 3.72
5714 6062 6.106877 CGAGTGGTAAATCGTTCATTCAAT 57.893 37.500 0.00 0.00 34.30 2.57
5718 6066 5.003402 GTGGTAAATCGTTCATTCAATTGCG 59.997 40.000 0.00 0.00 0.00 4.85
5719 6067 5.092781 GGTAAATCGTTCATTCAATTGCGT 58.907 37.500 0.00 0.00 0.00 5.24
5722 6070 5.745653 AATCGTTCATTCAATTGCGTTTC 57.254 34.783 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.511386 AAGATCAAGATGGGAGTGTTTCT 57.489 39.130 0.00 0.00 0.00 2.52
23 24 6.654161 GGAATGATAAGATCAAGATGGGAGTG 59.346 42.308 0.00 0.00 43.50 3.51
28 29 7.120873 GTGGATGGAATGATAAGATCAAGATGG 59.879 40.741 0.00 0.00 43.50 3.51
96 97 2.362242 TTGGCTCTAGTCAACCGCT 58.638 52.632 0.00 0.00 34.31 5.52
123 144 1.327764 GTCGAACCCGAGCAATTGATC 59.672 52.381 13.73 13.73 46.52 2.92
287 329 0.523966 TTTGGAATTTACAGCGGGCG 59.476 50.000 0.00 0.00 0.00 6.13
299 341 5.891551 ACACAAGTACTCAAGGTTTTGGAAT 59.108 36.000 0.00 0.00 34.97 3.01
301 343 4.638421 CACACAAGTACTCAAGGTTTTGGA 59.362 41.667 0.00 0.00 34.97 3.53
303 345 4.351192 GCACACAAGTACTCAAGGTTTTG 58.649 43.478 0.00 0.00 35.57 2.44
307 349 1.202770 GGGCACACAAGTACTCAAGGT 60.203 52.381 0.00 0.00 0.00 3.50
308 350 1.523758 GGGCACACAAGTACTCAAGG 58.476 55.000 0.00 0.00 0.00 3.61
309 351 1.523758 GGGGCACACAAGTACTCAAG 58.476 55.000 0.00 0.00 0.00 3.02
310 352 0.250124 CGGGGCACACAAGTACTCAA 60.250 55.000 0.00 0.00 0.00 3.02
311 353 1.369692 CGGGGCACACAAGTACTCA 59.630 57.895 0.00 0.00 0.00 3.41
312 354 2.033194 GCGGGGCACACAAGTACTC 61.033 63.158 0.00 0.00 0.00 2.59
313 355 2.032071 GCGGGGCACACAAGTACT 59.968 61.111 0.00 0.00 0.00 2.73
314 356 3.419759 CGCGGGGCACACAAGTAC 61.420 66.667 0.00 0.00 0.00 2.73
355 397 3.982372 GAGACGCGCCAATCCGACA 62.982 63.158 5.73 0.00 0.00 4.35
594 654 5.463286 TGCTGATGATGCTTAAAACAGTTG 58.537 37.500 0.00 0.00 0.00 3.16
595 655 5.336213 CCTGCTGATGATGCTTAAAACAGTT 60.336 40.000 0.00 0.00 0.00 3.16
596 656 4.157289 CCTGCTGATGATGCTTAAAACAGT 59.843 41.667 0.00 0.00 0.00 3.55
597 657 4.397103 TCCTGCTGATGATGCTTAAAACAG 59.603 41.667 0.00 0.00 0.00 3.16
598 658 4.156556 GTCCTGCTGATGATGCTTAAAACA 59.843 41.667 0.00 0.00 0.00 2.83
599 659 4.397417 AGTCCTGCTGATGATGCTTAAAAC 59.603 41.667 0.00 0.00 0.00 2.43
600 660 4.592942 AGTCCTGCTGATGATGCTTAAAA 58.407 39.130 0.00 0.00 0.00 1.52
601 661 4.226427 AGTCCTGCTGATGATGCTTAAA 57.774 40.909 0.00 0.00 0.00 1.52
602 662 3.920231 AGTCCTGCTGATGATGCTTAA 57.080 42.857 0.00 0.00 0.00 1.85
613 673 2.981898 TGTTGATGATCAGTCCTGCTG 58.018 47.619 0.09 0.00 46.34 4.41
614 674 3.199289 TGATGTTGATGATCAGTCCTGCT 59.801 43.478 0.09 0.00 0.00 4.24
615 675 3.538591 TGATGTTGATGATCAGTCCTGC 58.461 45.455 0.09 0.00 0.00 4.85
616 676 4.334759 GGTTGATGTTGATGATCAGTCCTG 59.665 45.833 0.09 0.00 31.52 3.86
617 677 4.521146 GGTTGATGTTGATGATCAGTCCT 58.479 43.478 0.09 0.00 31.52 3.85
618 678 3.629398 GGGTTGATGTTGATGATCAGTCC 59.371 47.826 0.09 0.00 31.52 3.85
619 679 3.310774 CGGGTTGATGTTGATGATCAGTC 59.689 47.826 0.09 0.00 31.52 3.51
620 680 3.273434 CGGGTTGATGTTGATGATCAGT 58.727 45.455 0.09 0.00 31.52 3.41
621 681 2.615447 CCGGGTTGATGTTGATGATCAG 59.385 50.000 0.09 0.00 31.52 2.90
622 682 2.642427 CCGGGTTGATGTTGATGATCA 58.358 47.619 0.00 0.00 0.00 2.92
623 683 1.949525 CCCGGGTTGATGTTGATGATC 59.050 52.381 14.18 0.00 0.00 2.92
624 684 1.284785 ACCCGGGTTGATGTTGATGAT 59.715 47.619 24.16 0.00 0.00 2.45
625 685 0.695924 ACCCGGGTTGATGTTGATGA 59.304 50.000 24.16 0.00 0.00 2.92
626 686 1.544724 AACCCGGGTTGATGTTGATG 58.455 50.000 37.91 0.21 36.91 3.07
627 687 2.302587 AAACCCGGGTTGATGTTGAT 57.697 45.000 38.87 18.41 38.47 2.57
628 688 2.953284 TAAACCCGGGTTGATGTTGA 57.047 45.000 38.87 15.34 38.47 3.18
629 689 2.165437 CCATAAACCCGGGTTGATGTTG 59.835 50.000 42.63 31.75 42.57 3.33
630 690 2.041891 TCCATAAACCCGGGTTGATGTT 59.958 45.455 42.63 29.86 42.57 2.71
631 691 1.636519 TCCATAAACCCGGGTTGATGT 59.363 47.619 42.63 30.17 42.57 3.06
632 692 2.021457 GTCCATAAACCCGGGTTGATG 58.979 52.381 41.09 41.09 43.33 3.07
633 693 1.064240 GGTCCATAAACCCGGGTTGAT 60.064 52.381 38.87 33.48 38.47 2.57
634 694 0.328926 GGTCCATAAACCCGGGTTGA 59.671 55.000 38.87 32.76 38.47 3.18
635 695 0.330267 AGGTCCATAAACCCGGGTTG 59.670 55.000 38.87 26.80 40.42 3.77
636 696 0.622136 GAGGTCCATAAACCCGGGTT 59.378 55.000 33.74 33.74 40.42 4.11
637 697 0.253020 AGAGGTCCATAAACCCGGGT 60.253 55.000 24.16 24.16 40.42 5.28
638 698 0.468648 GAGAGGTCCATAAACCCGGG 59.531 60.000 22.25 22.25 40.42 5.73
639 699 1.200519 TGAGAGGTCCATAAACCCGG 58.799 55.000 0.00 0.00 40.42 5.73
640 700 3.118408 TCATTGAGAGGTCCATAAACCCG 60.118 47.826 0.00 0.00 40.42 5.28
641 701 4.503714 TCATTGAGAGGTCCATAAACCC 57.496 45.455 0.00 0.00 40.42 4.11
642 702 5.745227 TCTTCATTGAGAGGTCCATAAACC 58.255 41.667 0.00 0.00 39.80 3.27
643 703 8.964476 TTATCTTCATTGAGAGGTCCATAAAC 57.036 34.615 0.00 0.00 0.00 2.01
644 704 8.992349 TCTTATCTTCATTGAGAGGTCCATAAA 58.008 33.333 0.00 0.00 0.00 1.40
645 705 8.553085 TCTTATCTTCATTGAGAGGTCCATAA 57.447 34.615 0.00 0.00 0.00 1.90
646 706 7.786943 ACTCTTATCTTCATTGAGAGGTCCATA 59.213 37.037 0.00 0.00 38.48 2.74
647 707 6.614906 ACTCTTATCTTCATTGAGAGGTCCAT 59.385 38.462 0.00 0.00 38.48 3.41
648 708 5.960811 ACTCTTATCTTCATTGAGAGGTCCA 59.039 40.000 0.00 0.00 38.48 4.02
649 709 6.478512 ACTCTTATCTTCATTGAGAGGTCC 57.521 41.667 0.00 0.00 38.48 4.46
650 710 8.637986 ACATACTCTTATCTTCATTGAGAGGTC 58.362 37.037 0.00 0.00 38.48 3.85
651 711 8.546083 ACATACTCTTATCTTCATTGAGAGGT 57.454 34.615 0.00 0.00 38.48 3.85
691 751 5.022787 TGCCTAGGTGAAATGGCTATTTTT 58.977 37.500 11.31 0.00 45.11 1.94
692 752 4.609301 TGCCTAGGTGAAATGGCTATTTT 58.391 39.130 11.31 0.00 45.11 1.82
693 753 4.249638 TGCCTAGGTGAAATGGCTATTT 57.750 40.909 11.31 7.88 45.11 1.40
694 754 3.951563 TGCCTAGGTGAAATGGCTATT 57.048 42.857 11.31 0.00 45.11 1.73
695 755 3.459598 TCTTGCCTAGGTGAAATGGCTAT 59.540 43.478 11.31 0.00 45.11 2.97
696 756 2.843730 TCTTGCCTAGGTGAAATGGCTA 59.156 45.455 11.31 0.00 45.11 3.93
697 757 1.635487 TCTTGCCTAGGTGAAATGGCT 59.365 47.619 11.31 0.00 45.11 4.75
701 761 3.350833 CAGCTTCTTGCCTAGGTGAAAT 58.649 45.455 11.31 2.56 44.23 2.17
709 769 1.375908 CACCGCAGCTTCTTGCCTA 60.376 57.895 0.00 0.00 44.23 3.93
711 771 4.410743 GCACCGCAGCTTCTTGCC 62.411 66.667 0.00 0.00 44.23 4.52
741 801 5.063817 AGTGCATTTGCTCTTTTGTTTTGTC 59.936 36.000 3.94 0.00 41.50 3.18
752 813 2.288395 CCGGAAAAAGTGCATTTGCTCT 60.288 45.455 0.00 2.64 45.55 4.09
790 852 2.224597 TGAGTGCTCCAGCTTTTGATCA 60.225 45.455 0.00 0.00 42.66 2.92
824 886 3.128589 CACGGGCATATTTTTAGTGCAGT 59.871 43.478 0.00 0.00 40.53 4.40
840 902 1.374560 TTATACATGTGCACACGGGC 58.625 50.000 24.37 0.00 0.00 6.13
912 976 1.372683 GAGGTGGAGCTGTGCTTCA 59.627 57.895 0.00 0.00 42.52 3.02
918 982 1.067295 TGAAATGGAGGTGGAGCTGT 58.933 50.000 0.00 0.00 0.00 4.40
966 1030 3.116531 CTTTTCGTCCGTCCGCCC 61.117 66.667 0.00 0.00 0.00 6.13
968 1032 2.737376 AGCTTTTCGTCCGTCCGC 60.737 61.111 0.00 0.00 0.00 5.54
969 1033 3.011760 GCAGCTTTTCGTCCGTCCG 62.012 63.158 0.00 0.00 0.00 4.79
970 1034 1.228657 AAGCAGCTTTTCGTCCGTCC 61.229 55.000 0.21 0.00 0.00 4.79
1159 1226 1.627550 GAGCGAGGCGAGGTTTGTTC 61.628 60.000 0.00 0.00 0.00 3.18
1191 1258 2.110757 TTGGACTGCTGCCATGACGA 62.111 55.000 0.00 0.00 34.90 4.20
1229 1300 5.606348 ATTTTGGTAAAAGTGCAAGGACA 57.394 34.783 0.00 0.00 33.22 4.02
1238 1309 5.336451 GGATGCGAGGAATTTTGGTAAAAGT 60.336 40.000 0.00 0.00 33.22 2.66
1241 1312 4.082845 TGGATGCGAGGAATTTTGGTAAA 58.917 39.130 0.00 0.00 0.00 2.01
1847 1924 4.520111 CACACAGATTGAATCAGGAAACCA 59.480 41.667 8.03 0.00 0.00 3.67
1909 1986 0.179129 GATCCCACATTGCGGCAAAG 60.179 55.000 20.48 17.87 0.00 2.77
1931 2008 3.721035 ACACTTGCAATTCAGCTTTTCC 58.279 40.909 0.00 0.00 34.99 3.13
1983 2060 4.285790 AGTGGAAGAGGGCCCCCA 62.286 66.667 21.43 16.70 38.92 4.96
2068 2145 6.939163 AGGAAAGCCACATTATAGAGCATAAG 59.061 38.462 0.00 0.00 32.56 1.73
2069 2146 6.841601 AGGAAAGCCACATTATAGAGCATAA 58.158 36.000 0.00 0.00 36.29 1.90
2077 2154 9.742144 TTGTTAGTAAAGGAAAGCCACATTATA 57.258 29.630 0.00 0.00 36.29 0.98
2078 2155 8.644374 TTGTTAGTAAAGGAAAGCCACATTAT 57.356 30.769 0.00 0.00 36.29 1.28
2152 2238 3.502123 TTCCTCCTAACCCAAACACTG 57.498 47.619 0.00 0.00 0.00 3.66
2153 2239 3.750922 GCTTTCCTCCTAACCCAAACACT 60.751 47.826 0.00 0.00 0.00 3.55
2346 2440 1.202927 TCCAACAGAGCCCCAAAGAAG 60.203 52.381 0.00 0.00 0.00 2.85
2518 2612 7.701539 TCCAATGATATATATTTGGTGGTGC 57.298 36.000 19.16 0.00 0.00 5.01
2571 2665 7.849026 CGTCGTGAATCGTGGAATAAAATTTAT 59.151 33.333 0.00 0.00 40.80 1.40
2597 2691 4.888239 TCTGCACTCTAGTAACCATAGACC 59.112 45.833 0.00 0.00 0.00 3.85
2721 2817 6.349115 CCACATTTCTCAGAATTCCTCAGTTG 60.349 42.308 0.65 0.00 0.00 3.16
2737 2833 6.319048 ACTGTCAATAGGATCCACATTTCT 57.681 37.500 15.82 0.00 0.00 2.52
2776 2872 4.471386 ACCAGTCCTTACAGCAGTCAATAT 59.529 41.667 0.00 0.00 0.00 1.28
2820 2916 6.878389 AGAAGTTCCAAAAACATTCTTGCAAA 59.122 30.769 0.00 0.00 0.00 3.68
2831 2928 7.758495 TCAACAACTCTAGAAGTTCCAAAAAC 58.242 34.615 0.00 0.00 45.28 2.43
3116 3229 2.690778 GCGGCCAGGCAAGTAACTG 61.691 63.158 15.19 0.00 34.54 3.16
3120 3233 0.254747 ATTAAGCGGCCAGGCAAGTA 59.745 50.000 15.19 0.00 34.64 2.24
3130 3243 4.820284 AAAGCTAAGATGATTAAGCGGC 57.180 40.909 0.00 0.00 39.94 6.53
3161 3274 7.973944 GGATCTTAAATACCAATCACAAACCAC 59.026 37.037 0.00 0.00 0.00 4.16
3264 3377 6.621596 GCAGGTTGCTAACTTTATGTTCTGAG 60.622 42.308 0.00 0.00 40.96 3.35
3333 3449 9.388506 CATTCATGAAAACATCTAGAAGTACCT 57.611 33.333 13.09 0.00 0.00 3.08
3334 3450 9.383519 TCATTCATGAAAACATCTAGAAGTACC 57.616 33.333 13.09 0.00 33.08 3.34
3336 3452 9.942850 TGTCATTCATGAAAACATCTAGAAGTA 57.057 29.630 13.09 0.00 38.75 2.24
3337 3453 8.853077 TGTCATTCATGAAAACATCTAGAAGT 57.147 30.769 13.09 0.00 38.75 3.01
3371 3488 5.846203 AGAAGCACATTAACAGCACATTTT 58.154 33.333 0.00 0.00 0.00 1.82
3444 3562 1.603678 CGATATTGCTGCCAATTGCCC 60.604 52.381 0.00 0.00 41.68 5.36
3466 3584 3.305516 TCGCAGAGCACAGCAGGA 61.306 61.111 0.00 0.00 0.00 3.86
3542 3660 7.508687 TCTTGGAAATAGTGCTGATTGCTATA 58.491 34.615 0.00 0.00 43.37 1.31
3551 3669 6.808008 TTCTTTCTCTTGGAAATAGTGCTG 57.192 37.500 0.00 0.00 42.25 4.41
3577 3695 6.313905 CAGTGGTTTGTTCTCTACCATACATC 59.686 42.308 0.00 0.00 43.33 3.06
3691 3809 4.766891 CAATTTGATTGTCACCAGGTAGGT 59.233 41.667 0.00 0.00 42.73 3.08
3712 3830 0.184933 ACTACAACTTGCAGGGCCAA 59.815 50.000 6.18 0.00 0.00 4.52
3844 3962 9.643693 AGCACCAATAAATAATGAAGTTTTCTG 57.356 29.630 0.00 0.00 0.00 3.02
3859 3977 3.770933 ACGGTCCTAGTAGCACCAATAAA 59.229 43.478 10.94 0.00 0.00 1.40
3868 3986 2.754002 AGTTCAAGACGGTCCTAGTAGC 59.246 50.000 4.14 0.00 0.00 3.58
3942 4060 6.176975 TGCGATCGTAATCTGTTTGAATTT 57.823 33.333 17.81 0.00 0.00 1.82
3955 4074 7.197703 TCACTAATTTACAGATGCGATCGTAA 58.802 34.615 17.81 6.01 31.51 3.18
4070 4189 6.496571 ACTAGACAACTTAGACGCACATATC 58.503 40.000 0.00 0.00 0.00 1.63
4071 4190 6.452494 ACTAGACAACTTAGACGCACATAT 57.548 37.500 0.00 0.00 0.00 1.78
4095 4214 2.378038 AGCACCTCAACTTTTCAAGCA 58.622 42.857 0.00 0.00 0.00 3.91
4140 4259 6.883756 TGATAGCAGAATGTTGTACAAATCCA 59.116 34.615 10.51 4.79 39.31 3.41
4200 4319 5.645056 TGCCCTCATATCAATTGTCCTAA 57.355 39.130 5.13 0.00 0.00 2.69
4212 4331 4.458256 TCCATGTCAAATGCCCTCATAT 57.542 40.909 0.00 0.00 31.46 1.78
4213 4332 3.949586 TCCATGTCAAATGCCCTCATA 57.050 42.857 0.00 0.00 31.46 2.15
4214 4333 2.832643 TCCATGTCAAATGCCCTCAT 57.167 45.000 0.00 0.00 33.53 2.90
4215 4334 2.601240 TTCCATGTCAAATGCCCTCA 57.399 45.000 0.00 0.00 0.00 3.86
4216 4335 5.796424 ATATTTCCATGTCAAATGCCCTC 57.204 39.130 9.21 0.00 0.00 4.30
4217 4336 7.673641 TTTATATTTCCATGTCAAATGCCCT 57.326 32.000 9.21 0.00 0.00 5.19
4218 4337 7.603784 GGATTTATATTTCCATGTCAAATGCCC 59.396 37.037 9.21 0.00 31.99 5.36
4219 4338 8.370182 AGGATTTATATTTCCATGTCAAATGCC 58.630 33.333 9.21 0.00 34.27 4.40
4240 4359 7.340743 CGATTAGTCCCAGATCATAGTAGGATT 59.659 40.741 0.00 0.00 0.00 3.01
4266 4385 5.126061 ACAAGTAATGAAATGGCCTGACATC 59.874 40.000 3.32 0.00 0.00 3.06
4343 4548 6.431198 TTTTTCCGACAGGTTAATGCTATC 57.569 37.500 0.00 0.00 39.05 2.08
4376 4581 4.023365 AGCAAGTCAATCTCAGCAAAGAAC 60.023 41.667 0.00 0.00 32.11 3.01
4398 4603 5.377358 CACTTGACGCTGTTCATAAGAAAG 58.623 41.667 0.00 0.00 35.08 2.62
4494 4699 3.952508 ACATCACCAGCGCCACCA 61.953 61.111 2.29 0.00 0.00 4.17
4506 4711 5.927281 TGATCTTCACTGATCTCACATCA 57.073 39.130 6.15 0.00 42.30 3.07
4512 4717 6.169094 TGTTCCTTTGATCTTCACTGATCTC 58.831 40.000 6.15 0.00 42.30 2.75
4882 5093 4.701765 AGGCTCTGCACTAAACTGATATG 58.298 43.478 0.00 0.00 0.00 1.78
4973 5184 0.536260 CAAGCCTCTGGAGTCTGGAG 59.464 60.000 6.11 6.11 0.00 3.86
4974 5185 0.115152 TCAAGCCTCTGGAGTCTGGA 59.885 55.000 0.00 0.00 0.00 3.86
4975 5186 1.134461 CATCAAGCCTCTGGAGTCTGG 60.134 57.143 0.00 0.00 0.00 3.86
4976 5187 1.554160 ACATCAAGCCTCTGGAGTCTG 59.446 52.381 0.00 0.00 0.00 3.51
4977 5188 1.949799 ACATCAAGCCTCTGGAGTCT 58.050 50.000 0.00 0.00 0.00 3.24
4978 5189 3.386078 TGATACATCAAGCCTCTGGAGTC 59.614 47.826 0.00 0.00 33.08 3.36
4979 5190 3.378512 TGATACATCAAGCCTCTGGAGT 58.621 45.455 0.00 0.00 33.08 3.85
5004 5215 1.541588 GGCAACTGTCAGACCATTTCC 59.458 52.381 6.91 0.00 0.00 3.13
5011 5222 0.886490 CACTGGGGCAACTGTCAGAC 60.886 60.000 6.91 0.00 34.74 3.51
5017 5228 0.896940 ATCAAGCACTGGGGCAACTG 60.897 55.000 0.00 0.00 35.83 3.16
5058 5269 1.002366 CGAGCATGTGGAGCAACTAC 58.998 55.000 0.00 0.00 0.00 2.73
5213 5556 4.463050 TTTGGTTTTACTGGGGAGTGAT 57.537 40.909 0.00 0.00 0.00 3.06
5246 5589 4.100808 GCAATCTGTAGAAGAGATGGACCT 59.899 45.833 0.00 0.00 38.67 3.85
5283 5626 6.415798 TGCTGAAATGCAATTGAATGAATG 57.584 33.333 10.34 0.00 40.29 2.67
5327 5670 1.926511 GCTGAACTGCAATGGGTCCG 61.927 60.000 0.00 0.00 0.00 4.79
5331 5674 1.098050 GGTAGCTGAACTGCAATGGG 58.902 55.000 0.00 0.00 34.99 4.00
5402 5745 4.636206 GGTATAGCTTTACTGCTGCAACTT 59.364 41.667 13.13 0.00 43.87 2.66
5406 5749 3.904800 TGGTATAGCTTTACTGCTGCA 57.095 42.857 13.13 0.88 43.87 4.41
5407 5750 4.192317 AGTTGGTATAGCTTTACTGCTGC 58.808 43.478 13.13 0.00 43.87 5.25
5473 5816 6.980978 TGCGTTGAATCTGGTTTTGATTTTTA 59.019 30.769 0.00 0.00 34.67 1.52
5496 5839 4.194640 TGAAATCCTGATCAAGTAGCTGC 58.805 43.478 0.00 0.00 0.00 5.25
5501 5844 7.348274 ACCTATTCCTGAAATCCTGATCAAGTA 59.652 37.037 0.00 0.00 0.00 2.24
5507 5854 7.528543 GCAGATACCTATTCCTGAAATCCTGAT 60.529 40.741 0.00 0.00 0.00 2.90
5532 5879 5.516339 CCATAAAAATGTGAATCAAGACGGC 59.484 40.000 0.00 0.00 0.00 5.68
5533 5880 6.851609 TCCATAAAAATGTGAATCAAGACGG 58.148 36.000 0.00 0.00 0.00 4.79
5552 5900 7.344612 AGTGGTATGAAGTATGAACACTCCATA 59.655 37.037 0.00 0.00 33.04 2.74
5559 5907 6.170506 GTTGGAGTGGTATGAAGTATGAACA 58.829 40.000 0.00 0.00 0.00 3.18
5564 5912 8.325787 TGTTATTGTTGGAGTGGTATGAAGTAT 58.674 33.333 0.00 0.00 0.00 2.12
5568 5916 7.402054 AGATGTTATTGTTGGAGTGGTATGAA 58.598 34.615 0.00 0.00 0.00 2.57
5569 5917 6.957631 AGATGTTATTGTTGGAGTGGTATGA 58.042 36.000 0.00 0.00 0.00 2.15
5570 5918 7.011763 CAGAGATGTTATTGTTGGAGTGGTATG 59.988 40.741 0.00 0.00 0.00 2.39
5571 5919 7.050377 CAGAGATGTTATTGTTGGAGTGGTAT 58.950 38.462 0.00 0.00 0.00 2.73
5572 5920 6.406370 CAGAGATGTTATTGTTGGAGTGGTA 58.594 40.000 0.00 0.00 0.00 3.25
5573 5921 5.248640 CAGAGATGTTATTGTTGGAGTGGT 58.751 41.667 0.00 0.00 0.00 4.16
5574 5922 4.095483 GCAGAGATGTTATTGTTGGAGTGG 59.905 45.833 0.00 0.00 0.00 4.00
5586 5934 6.516360 GCAGATCTACAGATGCAGAGATGTTA 60.516 42.308 0.00 0.00 34.37 2.41
5587 5935 5.739647 GCAGATCTACAGATGCAGAGATGTT 60.740 44.000 0.00 0.00 34.37 2.71
5591 5939 3.067883 GTGCAGATCTACAGATGCAGAGA 59.932 47.826 7.57 0.00 35.17 3.10
5594 5942 3.124560 CTGTGCAGATCTACAGATGCAG 58.875 50.000 17.40 8.03 45.46 4.41
5622 5970 5.600898 TCACTGGGGAACGAATCTTGATATA 59.399 40.000 0.00 0.00 0.00 0.86
5624 5972 3.772572 TCACTGGGGAACGAATCTTGATA 59.227 43.478 0.00 0.00 0.00 2.15
5626 5974 1.974957 TCACTGGGGAACGAATCTTGA 59.025 47.619 0.00 0.00 0.00 3.02
5666 6014 4.945543 TGCAATGTGTAGAAGAGATGCATT 59.054 37.500 0.00 0.00 37.61 3.56
5671 6019 4.820897 TCGTTGCAATGTGTAGAAGAGAT 58.179 39.130 17.94 0.00 0.00 2.75
5672 6020 4.237724 CTCGTTGCAATGTGTAGAAGAGA 58.762 43.478 17.94 0.00 0.00 3.10
5674 6022 3.740832 CACTCGTTGCAATGTGTAGAAGA 59.259 43.478 22.18 0.00 0.00 2.87
5683 6031 3.120338 ACGATTTACCACTCGTTGCAATG 60.120 43.478 12.66 12.66 45.15 2.82
5684 6032 3.071479 ACGATTTACCACTCGTTGCAAT 58.929 40.909 0.59 0.00 45.15 3.56


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

AutoCloner maintained by Alex Coulton.