Multiple sequence alignment - TraesCS2D01G088400

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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 TraesCS2D01G088400 chr2D 100.000 3453 0 0 1 3453 38239988 38236536 0.000000e+00 6377.0
1 TraesCS2D01G088400 chr2D 81.359 2001 318 35 952 2934 38218747 38216784 0.000000e+00 1578.0
2 TraesCS2D01G088400 chr2D 80.010 1996 364 26 1004 2973 38442077 38440091 0.000000e+00 1443.0
3 TraesCS2D01G088400 chr2D 90.476 315 21 6 3139 3453 38253831 38253526 1.150000e-109 407.0
4 TraesCS2D01G088400 chr2A 81.718 2002 322 33 952 2934 43282291 43280315 0.000000e+00 1629.0
5 TraesCS2D01G088400 chr2A 79.940 1999 359 28 1004 2973 43304848 43302863 0.000000e+00 1432.0
6 TraesCS2D01G088400 chr2A 78.846 2028 362 37 994 2974 43299700 43297693 0.000000e+00 1306.0
7 TraesCS2D01G088400 chr2A 78.269 1560 298 28 994 2531 147542955 147541415 0.000000e+00 965.0
8 TraesCS2D01G088400 chr2A 93.534 232 14 1 539 770 43301904 43301674 9.180000e-91 344.0
9 TraesCS2D01G088400 chr2A 84.639 319 24 11 232 547 43302366 43302070 9.370000e-76 294.0
10 TraesCS2D01G088400 chr2A 90.141 213 10 6 820 1026 43301585 43301378 2.040000e-67 267.0
11 TraesCS2D01G088400 chr2A 84.043 94 9 2 1018 1111 43300913 43300826 6.140000e-13 86.1
12 TraesCS2D01G088400 chr2B 84.331 1621 242 9 1440 3055 67204120 67202507 0.000000e+00 1576.0
13 TraesCS2D01G088400 chr2B 80.539 1968 346 28 1030 2974 67081759 67079806 0.000000e+00 1478.0
14 TraesCS2D01G088400 chr2B 88.013 1218 133 9 1093 2298 67217704 67216488 0.000000e+00 1428.0
15 TraesCS2D01G088400 chr2B 92.000 850 61 6 2298 3143 66806118 66805272 0.000000e+00 1186.0
16 TraesCS2D01G088400 chr2B 88.281 896 71 13 1751 2646 66959255 66958394 0.000000e+00 1042.0
17 TraesCS2D01G088400 chr2B 83.495 1030 161 5 1912 2934 66766558 66765531 0.000000e+00 952.0
18 TraesCS2D01G088400 chr2B 76.532 1811 382 30 1100 2887 210932649 210930859 0.000000e+00 950.0
19 TraesCS2D01G088400 chr2B 90.733 723 41 10 3 718 67276074 67275371 0.000000e+00 941.0
20 TraesCS2D01G088400 chr2B 77.196 1662 338 29 985 2625 211187292 211188933 0.000000e+00 931.0
21 TraesCS2D01G088400 chr2B 86.070 603 74 4 1153 1746 66961709 66961108 1.040000e-179 640.0
22 TraesCS2D01G088400 chr2B 90.654 321 22 4 3139 3453 66951920 66951602 1.480000e-113 420.0
23 TraesCS2D01G088400 chr2B 85.574 305 15 9 812 1116 67218077 67217802 3.370000e-75 292.0
24 TraesCS2D01G088400 chr2B 91.813 171 13 1 3283 3453 66804778 66804609 1.600000e-58 237.0
25 TraesCS2D01G088400 chr2B 85.165 182 17 7 3273 3453 67213248 67213076 9.850000e-41 178.0
26 TraesCS2D01G088400 chr2B 96.825 63 2 0 1093 1155 67217767 67217705 4.710000e-19 106.0


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 TraesCS2D01G088400 chr2D 38236536 38239988 3452 True 6377.000000 6377 100.00000 1 3453 1 chr2D.!!$R2 3452
1 TraesCS2D01G088400 chr2D 38216784 38218747 1963 True 1578.000000 1578 81.35900 952 2934 1 chr2D.!!$R1 1982
2 TraesCS2D01G088400 chr2D 38440091 38442077 1986 True 1443.000000 1443 80.01000 1004 2973 1 chr2D.!!$R4 1969
3 TraesCS2D01G088400 chr2A 43280315 43282291 1976 True 1629.000000 1629 81.71800 952 2934 1 chr2A.!!$R1 1982
4 TraesCS2D01G088400 chr2A 147541415 147542955 1540 True 965.000000 965 78.26900 994 2531 1 chr2A.!!$R2 1537
5 TraesCS2D01G088400 chr2A 43297693 43304848 7155 True 621.516667 1432 85.19050 232 2974 6 chr2A.!!$R3 2742
6 TraesCS2D01G088400 chr2B 67202507 67204120 1613 True 1576.000000 1576 84.33100 1440 3055 1 chr2B.!!$R4 1615
7 TraesCS2D01G088400 chr2B 67079806 67081759 1953 True 1478.000000 1478 80.53900 1030 2974 1 chr2B.!!$R3 1944
8 TraesCS2D01G088400 chr2B 66765531 66766558 1027 True 952.000000 952 83.49500 1912 2934 1 chr2B.!!$R1 1022
9 TraesCS2D01G088400 chr2B 210930859 210932649 1790 True 950.000000 950 76.53200 1100 2887 1 chr2B.!!$R6 1787
10 TraesCS2D01G088400 chr2B 67275371 67276074 703 True 941.000000 941 90.73300 3 718 1 chr2B.!!$R5 715
11 TraesCS2D01G088400 chr2B 211187292 211188933 1641 False 931.000000 931 77.19600 985 2625 1 chr2B.!!$F1 1640
12 TraesCS2D01G088400 chr2B 66958394 66961709 3315 True 841.000000 1042 87.17550 1153 2646 2 chr2B.!!$R8 1493
13 TraesCS2D01G088400 chr2B 66804609 66806118 1509 True 711.500000 1186 91.90650 2298 3453 2 chr2B.!!$R7 1155
14 TraesCS2D01G088400 chr2B 67213076 67218077 5001 True 501.000000 1428 88.89425 812 3453 4 chr2B.!!$R9 2641

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
560 563 0.180406 AACACCAAGTTCAGCTCCGT 59.820 50.0 0.00 0.00 34.74 4.69 F
751 759 0.247695 GAATTTTTCCCTCGAGCGCG 60.248 55.0 6.99 2.41 39.35 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 8955 0.521867 CGTTCATGATGCCTGTTGCG 60.522 55.0 0.0 0.0 45.6 4.85 R
2647 11447 0.034756 CGTCCACATGTCACCTCCAA 59.965 55.0 0.0 0.0 0.0 3.53 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.787994 ACAGAATGGTTGCTCTGAAGG 58.212 47.619 6.10 0.00 43.62 3.46
52 53 3.199891 GGTCACAATACCGCCGCC 61.200 66.667 0.00 0.00 0.00 6.13
65 66 4.545706 CCGCCGCTGCCTATTCCA 62.546 66.667 0.00 0.00 0.00 3.53
66 67 3.272334 CGCCGCTGCCTATTCCAC 61.272 66.667 0.00 0.00 0.00 4.02
67 68 2.902343 GCCGCTGCCTATTCCACC 60.902 66.667 0.00 0.00 0.00 4.61
68 69 2.203209 CCGCTGCCTATTCCACCC 60.203 66.667 0.00 0.00 0.00 4.61
69 70 2.589540 CGCTGCCTATTCCACCCA 59.410 61.111 0.00 0.00 0.00 4.51
70 71 1.149174 CGCTGCCTATTCCACCCAT 59.851 57.895 0.00 0.00 0.00 4.00
71 72 1.168407 CGCTGCCTATTCCACCCATG 61.168 60.000 0.00 0.00 0.00 3.66
72 73 1.458639 GCTGCCTATTCCACCCATGC 61.459 60.000 0.00 0.00 0.00 4.06
75 76 1.458639 GCCTATTCCACCCATGCAGC 61.459 60.000 0.00 0.00 0.00 5.25
128 129 3.932710 GGATTGCATCACGTGAACTTAGA 59.067 43.478 24.13 7.23 0.00 2.10
129 130 4.391830 GGATTGCATCACGTGAACTTAGAA 59.608 41.667 24.13 9.91 0.00 2.10
204 206 1.224069 GCAAGCTGTCAGAAGCACGA 61.224 55.000 3.32 0.00 46.08 4.35
207 209 0.894141 AGCTGTCAGAAGCACGAGAT 59.106 50.000 3.32 0.00 46.08 2.75
208 210 1.274728 AGCTGTCAGAAGCACGAGATT 59.725 47.619 3.32 0.00 46.08 2.40
210 212 2.928301 GCTGTCAGAAGCACGAGATTGA 60.928 50.000 3.32 0.00 43.01 2.57
229 231 6.944862 AGATTGAAAAGATTCAGGCAAGTAGT 59.055 34.615 0.00 0.00 45.82 2.73
293 295 3.135348 CCAATGGAGATGCTACTGGAGAA 59.865 47.826 0.00 0.00 0.00 2.87
314 316 7.254151 GGAGAACTGTTTTACTCGATAATGAGC 60.254 40.741 0.00 0.00 39.68 4.26
322 324 6.465439 TTACTCGATAATGAGCCTGAAGAA 57.535 37.500 0.00 0.00 39.68 2.52
350 352 3.492011 GTCGCCGAGAAACACTAAGAAAA 59.508 43.478 0.00 0.00 0.00 2.29
351 353 3.492011 TCGCCGAGAAACACTAAGAAAAC 59.508 43.478 0.00 0.00 0.00 2.43
352 354 3.246699 CGCCGAGAAACACTAAGAAAACA 59.753 43.478 0.00 0.00 0.00 2.83
353 355 4.524749 GCCGAGAAACACTAAGAAAACAC 58.475 43.478 0.00 0.00 0.00 3.32
384 387 5.821995 CAGAATCCAGAGGAGAAGGAAATTC 59.178 44.000 0.00 0.00 34.05 2.17
399 402 3.803778 GGAAATTCTGGTTGTTTGTGCAG 59.196 43.478 0.00 0.00 0.00 4.41
404 407 0.740149 TGGTTGTTTGTGCAGCAGAG 59.260 50.000 0.00 0.00 0.00 3.35
414 417 0.390866 TGCAGCAGAGCAGCTAAGAC 60.391 55.000 7.84 0.00 44.54 3.01
419 422 4.186926 CAGCAGAGCAGCTAAGACAAATA 58.813 43.478 0.00 0.00 44.54 1.40
430 433 6.096987 CAGCTAAGACAAATACCTCCTCTGTA 59.903 42.308 0.00 0.00 0.00 2.74
434 437 6.287589 AGACAAATACCTCCTCTGTAAGTG 57.712 41.667 0.00 0.00 33.76 3.16
455 458 2.815478 CTACGGCCTGAACATTCTCTC 58.185 52.381 0.00 0.00 0.00 3.20
474 477 5.546499 TCTCTCCCTACAAATGTAACAAGGT 59.454 40.000 0.00 0.00 0.00 3.50
478 481 9.220906 TCTCCCTACAAATGTAACAAGGTATAT 57.779 33.333 0.00 0.00 0.00 0.86
479 482 9.847224 CTCCCTACAAATGTAACAAGGTATATT 57.153 33.333 0.00 0.00 0.00 1.28
511 514 6.075762 TCTGACAGAATTGTGACCATTTTG 57.924 37.500 9.96 0.00 37.76 2.44
546 549 2.132762 CACTCGTCAGGTAACAACACC 58.867 52.381 0.00 0.00 39.02 4.16
557 560 3.003378 GGTAACAACACCAAGTTCAGCTC 59.997 47.826 0.00 0.00 38.74 4.09
559 562 0.588252 CAACACCAAGTTCAGCTCCG 59.412 55.000 0.00 0.00 38.74 4.63
560 563 0.180406 AACACCAAGTTCAGCTCCGT 59.820 50.000 0.00 0.00 34.74 4.69
567 570 0.319641 AGTTCAGCTCCGTTTCCGAC 60.320 55.000 0.00 0.00 35.63 4.79
615 618 9.393249 TGAATTTCTGATTGTTCATCGTAAAAC 57.607 29.630 0.00 0.00 34.08 2.43
623 626 2.004583 TCATCGTAAAACCAGGCTCG 57.995 50.000 0.00 0.00 0.00 5.03
654 657 4.745125 GGATGAACGAGAAAATGATAGCGA 59.255 41.667 0.00 0.00 0.00 4.93
656 659 6.073548 GGATGAACGAGAAAATGATAGCGATT 60.074 38.462 0.00 0.00 0.00 3.34
676 684 7.010552 AGCGATTATTGATACTTTGAGTGACAC 59.989 37.037 0.00 0.00 0.00 3.67
705 713 3.083349 ACGCTAGCATGGGAGGCA 61.083 61.111 16.45 0.00 0.00 4.75
718 726 3.096092 TGGGAGGCACCAATAATTTGAC 58.904 45.455 2.69 0.00 41.20 3.18
719 727 2.099098 GGGAGGCACCAATAATTTGACG 59.901 50.000 2.69 0.00 41.20 4.35
720 728 3.013921 GGAGGCACCAATAATTTGACGA 58.986 45.455 0.00 0.00 38.79 4.20
721 729 3.632145 GGAGGCACCAATAATTTGACGAT 59.368 43.478 0.00 0.00 38.79 3.73
722 730 4.261197 GGAGGCACCAATAATTTGACGATC 60.261 45.833 0.00 0.00 38.79 3.69
723 731 4.526970 AGGCACCAATAATTTGACGATCT 58.473 39.130 0.00 0.00 34.60 2.75
724 732 5.680619 AGGCACCAATAATTTGACGATCTA 58.319 37.500 0.00 0.00 34.60 1.98
725 733 6.119536 AGGCACCAATAATTTGACGATCTAA 58.880 36.000 0.00 0.00 34.60 2.10
726 734 6.772716 AGGCACCAATAATTTGACGATCTAAT 59.227 34.615 0.00 0.00 34.60 1.73
727 735 6.857964 GGCACCAATAATTTGACGATCTAATG 59.142 38.462 0.00 0.00 34.60 1.90
728 736 7.255104 GGCACCAATAATTTGACGATCTAATGA 60.255 37.037 0.00 0.00 34.60 2.57
729 737 7.587757 GCACCAATAATTTGACGATCTAATGAC 59.412 37.037 0.00 0.00 34.60 3.06
730 738 8.070171 CACCAATAATTTGACGATCTAATGACC 58.930 37.037 0.00 0.00 34.60 4.02
731 739 7.773224 ACCAATAATTTGACGATCTAATGACCA 59.227 33.333 0.00 0.00 34.60 4.02
732 740 8.285394 CCAATAATTTGACGATCTAATGACCAG 58.715 37.037 0.00 0.00 34.60 4.00
733 741 9.045223 CAATAATTTGACGATCTAATGACCAGA 57.955 33.333 0.00 0.00 34.60 3.86
734 742 9.613428 AATAATTTGACGATCTAATGACCAGAA 57.387 29.630 0.00 0.00 0.00 3.02
735 743 9.784531 ATAATTTGACGATCTAATGACCAGAAT 57.215 29.630 0.00 0.00 0.00 2.40
736 744 8.511604 AATTTGACGATCTAATGACCAGAATT 57.488 30.769 0.00 0.00 0.00 2.17
737 745 7.921786 TTTGACGATCTAATGACCAGAATTT 57.078 32.000 0.00 0.00 0.00 1.82
738 746 7.921786 TTGACGATCTAATGACCAGAATTTT 57.078 32.000 0.00 0.00 0.00 1.82
739 747 7.921786 TGACGATCTAATGACCAGAATTTTT 57.078 32.000 0.00 0.00 0.00 1.94
740 748 7.974675 TGACGATCTAATGACCAGAATTTTTC 58.025 34.615 0.00 0.00 0.00 2.29
741 749 7.065803 TGACGATCTAATGACCAGAATTTTTCC 59.934 37.037 0.00 0.00 0.00 3.13
742 750 6.318900 ACGATCTAATGACCAGAATTTTTCCC 59.681 38.462 0.00 0.00 0.00 3.97
743 751 6.543831 CGATCTAATGACCAGAATTTTTCCCT 59.456 38.462 0.00 0.00 0.00 4.20
744 752 7.254932 CGATCTAATGACCAGAATTTTTCCCTC 60.255 40.741 0.00 0.00 0.00 4.30
745 753 5.880332 TCTAATGACCAGAATTTTTCCCTCG 59.120 40.000 0.00 0.00 0.00 4.63
746 754 3.780804 TGACCAGAATTTTTCCCTCGA 57.219 42.857 0.00 0.00 0.00 4.04
747 755 3.674997 TGACCAGAATTTTTCCCTCGAG 58.325 45.455 5.13 5.13 0.00 4.04
748 756 2.420372 GACCAGAATTTTTCCCTCGAGC 59.580 50.000 6.99 0.00 0.00 5.03
749 757 1.398390 CCAGAATTTTTCCCTCGAGCG 59.602 52.381 6.99 0.00 0.00 5.03
750 758 1.087501 AGAATTTTTCCCTCGAGCGC 58.912 50.000 6.99 0.00 0.00 5.92
751 759 0.247695 GAATTTTTCCCTCGAGCGCG 60.248 55.000 6.99 2.41 39.35 6.86
752 760 1.644786 AATTTTTCCCTCGAGCGCGG 61.645 55.000 10.69 3.05 38.28 6.46
753 761 2.798148 ATTTTTCCCTCGAGCGCGGT 62.798 55.000 12.23 12.23 38.28 5.68
754 762 3.927163 TTTTCCCTCGAGCGCGGTC 62.927 63.158 27.52 27.52 38.28 4.79
757 765 4.933064 CCCTCGAGCGCGGTCATC 62.933 72.222 34.30 12.14 38.28 2.92
758 766 4.193334 CCTCGAGCGCGGTCATCA 62.193 66.667 34.30 18.28 38.28 3.07
759 767 2.951745 CTCGAGCGCGGTCATCAC 60.952 66.667 34.30 11.37 38.28 3.06
760 768 3.683587 CTCGAGCGCGGTCATCACA 62.684 63.158 34.30 13.60 38.28 3.58
761 769 2.809174 CGAGCGCGGTCATCACAA 60.809 61.111 34.30 0.00 0.00 3.33
762 770 2.379634 CGAGCGCGGTCATCACAAA 61.380 57.895 34.30 0.00 0.00 2.83
763 771 1.421485 GAGCGCGGTCATCACAAAG 59.579 57.895 31.60 0.00 0.00 2.77
764 772 1.291877 GAGCGCGGTCATCACAAAGT 61.292 55.000 31.60 0.00 0.00 2.66
765 773 1.154413 GCGCGGTCATCACAAAGTG 60.154 57.895 8.83 0.00 34.45 3.16
766 774 1.497278 CGCGGTCATCACAAAGTGG 59.503 57.895 0.00 0.00 33.87 4.00
767 775 1.227999 CGCGGTCATCACAAAGTGGT 61.228 55.000 0.00 0.00 33.87 4.16
768 776 0.517316 GCGGTCATCACAAAGTGGTC 59.483 55.000 0.00 0.00 33.87 4.02
769 777 1.877637 CGGTCATCACAAAGTGGTCA 58.122 50.000 0.00 0.00 33.87 4.02
770 778 1.800586 CGGTCATCACAAAGTGGTCAG 59.199 52.381 0.00 0.00 33.87 3.51
771 779 2.547855 CGGTCATCACAAAGTGGTCAGA 60.548 50.000 0.00 0.00 33.87 3.27
772 780 2.808543 GGTCATCACAAAGTGGTCAGAC 59.191 50.000 0.00 0.00 33.87 3.51
773 781 3.466836 GTCATCACAAAGTGGTCAGACA 58.533 45.455 2.17 0.00 33.87 3.41
774 782 4.067896 GTCATCACAAAGTGGTCAGACAT 58.932 43.478 2.17 0.00 33.87 3.06
775 783 4.067192 TCATCACAAAGTGGTCAGACATG 58.933 43.478 2.17 0.00 33.87 3.21
776 784 3.558931 TCACAAAGTGGTCAGACATGT 57.441 42.857 0.00 0.00 33.87 3.21
777 785 3.466836 TCACAAAGTGGTCAGACATGTC 58.533 45.455 18.47 18.47 33.87 3.06
778 786 3.118445 TCACAAAGTGGTCAGACATGTCA 60.118 43.478 27.02 5.13 33.87 3.58
779 787 3.817084 CACAAAGTGGTCAGACATGTCAT 59.183 43.478 27.02 10.02 0.00 3.06
780 788 3.817084 ACAAAGTGGTCAGACATGTCATG 59.183 43.478 27.02 20.27 0.00 3.07
781 789 8.809792 TCACAAAGTGGTCAGACATGTCATGT 62.810 42.308 27.02 18.45 39.12 3.21
782 790 4.890158 AAGTGGTCAGACATGTCATGTA 57.110 40.909 27.02 6.96 45.03 2.29
783 791 4.193826 AGTGGTCAGACATGTCATGTAC 57.806 45.455 27.02 17.28 45.03 2.90
784 792 2.923655 GTGGTCAGACATGTCATGTACG 59.076 50.000 27.02 12.23 45.03 3.67
785 793 1.927174 GGTCAGACATGTCATGTACGC 59.073 52.381 27.02 6.73 45.03 4.42
786 794 1.583856 GTCAGACATGTCATGTACGCG 59.416 52.381 27.02 3.53 45.03 6.01
787 795 1.201414 TCAGACATGTCATGTACGCGT 59.799 47.619 27.02 19.17 45.03 6.01
788 796 1.992667 CAGACATGTCATGTACGCGTT 59.007 47.619 27.02 0.00 45.03 4.84
789 797 3.119779 TCAGACATGTCATGTACGCGTTA 60.120 43.478 27.02 7.89 45.03 3.18
790 798 3.610677 CAGACATGTCATGTACGCGTTAA 59.389 43.478 27.02 6.53 45.03 2.01
791 799 4.090786 CAGACATGTCATGTACGCGTTAAA 59.909 41.667 27.02 3.40 45.03 1.52
792 800 4.090930 AGACATGTCATGTACGCGTTAAAC 59.909 41.667 27.02 10.95 45.03 2.01
793 801 3.181538 ACATGTCATGTACGCGTTAAACG 60.182 43.478 20.78 2.69 42.78 3.60
805 813 2.333926 CGTTAAACGCACTCATCTCCA 58.666 47.619 0.00 0.00 33.65 3.86
806 814 2.092211 CGTTAAACGCACTCATCTCCAC 59.908 50.000 0.00 0.00 33.65 4.02
807 815 3.064207 GTTAAACGCACTCATCTCCACA 58.936 45.455 0.00 0.00 0.00 4.17
808 816 2.254546 AAACGCACTCATCTCCACAA 57.745 45.000 0.00 0.00 0.00 3.33
809 817 1.800805 AACGCACTCATCTCCACAAG 58.199 50.000 0.00 0.00 0.00 3.16
810 818 0.681733 ACGCACTCATCTCCACAAGT 59.318 50.000 0.00 0.00 0.00 3.16
878 886 2.831333 ACTTCACACTGCAGTCTCAAG 58.169 47.619 18.64 19.33 0.00 3.02
894 902 4.867608 GTCTCAAGACTTCATAAGACAGCC 59.132 45.833 2.86 0.00 41.65 4.85
895 903 3.849911 TCAAGACTTCATAAGACAGCCG 58.150 45.455 0.00 0.00 0.00 5.52
896 904 3.509967 TCAAGACTTCATAAGACAGCCGA 59.490 43.478 0.00 0.00 0.00 5.54
897 905 3.791973 AGACTTCATAAGACAGCCGAG 57.208 47.619 0.00 0.00 0.00 4.63
898 906 2.159170 AGACTTCATAAGACAGCCGAGC 60.159 50.000 0.00 0.00 0.00 5.03
899 907 1.550524 ACTTCATAAGACAGCCGAGCA 59.449 47.619 0.00 0.00 0.00 4.26
901 909 1.474330 TCATAAGACAGCCGAGCAGA 58.526 50.000 0.00 0.00 0.00 4.26
903 911 1.406898 CATAAGACAGCCGAGCAGAGA 59.593 52.381 0.00 0.00 0.00 3.10
904 912 1.098869 TAAGACAGCCGAGCAGAGAG 58.901 55.000 0.00 0.00 0.00 3.20
905 913 2.202730 GACAGCCGAGCAGAGAGC 60.203 66.667 0.00 0.00 46.19 4.09
919 927 2.307934 GAGAGCACAATCTCTGGACC 57.692 55.000 0.00 0.00 43.05 4.46
920 928 1.830477 GAGAGCACAATCTCTGGACCT 59.170 52.381 0.00 0.00 43.05 3.85
921 929 1.830477 AGAGCACAATCTCTGGACCTC 59.170 52.381 0.00 0.00 41.57 3.85
922 930 1.552337 GAGCACAATCTCTGGACCTCA 59.448 52.381 0.00 0.00 0.00 3.86
923 931 2.170187 GAGCACAATCTCTGGACCTCAT 59.830 50.000 0.00 0.00 0.00 2.90
924 932 2.170187 AGCACAATCTCTGGACCTCATC 59.830 50.000 0.00 0.00 0.00 2.92
1164 1311 3.164011 GCGGTCGTCACGTCGAAG 61.164 66.667 17.02 0.00 41.47 3.79
1174 1321 4.194720 CGTCGAAGGGCCTCCTCG 62.195 72.222 19.25 19.25 44.07 4.63
1200 1350 1.515954 CGACGGTACCAGCCAGATT 59.484 57.895 13.54 0.00 0.00 2.40
1238 1388 2.344203 CGTCTCCTCTGCCGTTCCT 61.344 63.158 0.00 0.00 0.00 3.36
1290 1449 3.006644 GGTCCTTCTCCACTACTTTCGTT 59.993 47.826 0.00 0.00 0.00 3.85
1471 1640 2.930682 GAGCTTGACACGATCCTTAACC 59.069 50.000 0.00 0.00 0.00 2.85
1542 1711 2.158959 GGTGTCGCTCGATTCCACG 61.159 63.158 0.00 0.00 0.00 4.94
1604 1780 1.270358 CCTAAGCCTGATAAGCCGGAC 60.270 57.143 5.05 0.00 0.00 4.79
1706 1892 0.918310 AAGAAGCCCCTCCTGCAGAT 60.918 55.000 17.39 0.00 0.00 2.90
1761 8955 1.278238 CGTATGTTGGCTTCTCGTCC 58.722 55.000 0.00 0.00 0.00 4.79
1836 9033 1.961180 ATGGACTAGCACCGGCACTC 61.961 60.000 0.00 0.00 44.61 3.51
1932 9144 1.523938 GGCCTTAGCATCGGTGACC 60.524 63.158 0.00 0.00 42.56 4.02
2160 9378 2.143122 GACATGAAGGTCGCTGTGAAA 58.857 47.619 0.00 0.00 0.00 2.69
2181 9399 5.913137 AAAGGTTGTCACACAATTCAAGA 57.087 34.783 0.00 0.00 40.59 3.02
2249 9467 2.645510 GACACCGGAATATCGCGCG 61.646 63.158 26.76 26.76 0.00 6.86
2483 11281 7.220030 AGTAATGTGCTATTGGATGGTAAGAG 58.780 38.462 0.00 0.00 0.00 2.85
2494 11292 0.539986 TGGTAAGAGGAATGGACGGC 59.460 55.000 0.00 0.00 0.00 5.68
2510 11308 1.436983 CGGCTAGGCGATTTTGGTCC 61.437 60.000 32.94 0.00 0.00 4.46
2543 11341 1.635663 GACCATGAAACCGTCGCTGG 61.636 60.000 0.00 0.00 37.57 4.85
2619 11419 1.104577 GGAAACCAACCGCCTTCACA 61.105 55.000 0.00 0.00 0.00 3.58
2647 11447 1.888512 ACGCATTTGGCATGTTTCTCT 59.111 42.857 0.00 0.00 45.17 3.10
2655 11455 1.815003 GGCATGTTTCTCTTGGAGGTG 59.185 52.381 0.00 0.00 0.00 4.00
2845 11645 1.031571 ATGCACGTACCCATTGCCTG 61.032 55.000 0.00 0.00 35.26 4.85
2927 11727 5.790593 TGATTTATCTCCGGCCTACATAAC 58.209 41.667 0.00 0.00 0.00 1.89
2944 11750 7.287005 CCTACATAACCTACATGAACCTAGTGA 59.713 40.741 0.00 0.00 0.00 3.41
2965 11771 5.983118 GTGAAAAACGAAGGGTTGAATTCAT 59.017 36.000 9.40 0.00 39.30 2.57
2978 11784 6.808212 GGGTTGAATTCATACAACATGAACAG 59.192 38.462 9.40 0.00 45.27 3.16
2979 11785 6.808212 GGTTGAATTCATACAACATGAACAGG 59.192 38.462 9.40 0.00 45.27 4.00
2988 11794 1.331214 ACATGAACAGGCCAGGTTTG 58.669 50.000 5.01 7.91 0.00 2.93
2990 11796 0.542702 ATGAACAGGCCAGGTTTGGG 60.543 55.000 5.01 0.00 45.16 4.12
3021 11827 1.000163 AGCGTTGCCACTATATCCTCG 60.000 52.381 0.00 0.00 0.00 4.63
3080 12411 3.051803 TCATGGGGACTCCTCTTATCAGT 60.052 47.826 0.00 0.00 36.20 3.41
3111 12443 6.830838 CCTCCTTTCATCAAAATTACTAGCCT 59.169 38.462 0.00 0.00 0.00 4.58
3115 12448 9.178758 CCTTTCATCAAAATTACTAGCCTAGTT 57.821 33.333 10.14 0.00 40.14 2.24
3172 12857 8.592529 TCATTTGGAGTCAATAAAATCCATCA 57.407 30.769 0.00 0.00 41.33 3.07
3180 12865 7.785033 AGTCAATAAAATCCATCATTTGTCCC 58.215 34.615 0.00 0.00 34.69 4.46
3185 12870 9.804977 AATAAAATCCATCATTTGTCCCAAAAA 57.195 25.926 0.00 0.00 34.69 1.94
3280 12978 7.175119 ACGCAGTTGCTATTAGTAGATATGAGA 59.825 37.037 2.29 0.00 37.78 3.27
3435 13176 5.972107 AAAGATCCAGACAAAGGATGTTG 57.028 39.130 5.51 0.00 45.65 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.090761 TCAGAGCAACCATTCTGTTTCT 57.909 40.909 1.90 0.00 41.21 2.52
52 53 1.149174 ATGGGTGGAATAGGCAGCG 59.851 57.895 0.00 0.00 0.00 5.18
55 56 0.106569 CTGCATGGGTGGAATAGGCA 60.107 55.000 0.00 0.00 0.00 4.75
59 60 1.152984 CCGCTGCATGGGTGGAATA 60.153 57.895 0.00 0.00 36.54 1.75
60 61 2.440796 CCGCTGCATGGGTGGAAT 60.441 61.111 0.00 0.00 36.54 3.01
67 68 3.506096 CTGACAGCCGCTGCATGG 61.506 66.667 20.56 4.73 41.13 3.66
68 69 2.745100 ACTGACAGCCGCTGCATG 60.745 61.111 20.56 12.12 41.13 4.06
69 70 2.435586 GACTGACAGCCGCTGCAT 60.436 61.111 20.56 1.20 41.13 3.96
70 71 3.459148 TTGACTGACAGCCGCTGCA 62.459 57.895 20.56 16.83 41.13 4.41
71 72 2.666190 TTGACTGACAGCCGCTGC 60.666 61.111 20.56 13.23 34.37 5.25
72 73 2.031516 CCTTGACTGACAGCCGCTG 61.032 63.158 19.08 19.08 37.52 5.18
75 76 0.317160 TGTACCTTGACTGACAGCCG 59.683 55.000 1.25 0.00 0.00 5.52
78 79 4.383118 CCCCTTATGTACCTTGACTGACAG 60.383 50.000 0.00 0.00 0.00 3.51
128 129 4.388485 GGTGATTTTGGTCCAAGCATTTT 58.612 39.130 4.09 0.00 0.00 1.82
129 130 3.554752 CGGTGATTTTGGTCCAAGCATTT 60.555 43.478 4.09 0.00 0.00 2.32
158 159 0.107831 TGTTCTTAGCTGCACGGGTT 59.892 50.000 1.02 0.00 0.00 4.11
159 160 0.107831 TTGTTCTTAGCTGCACGGGT 59.892 50.000 1.02 0.00 0.00 5.28
160 161 0.517316 GTTGTTCTTAGCTGCACGGG 59.483 55.000 1.02 0.00 0.00 5.28
161 162 0.517316 GGTTGTTCTTAGCTGCACGG 59.483 55.000 1.02 0.00 0.00 4.94
204 206 6.944862 ACTACTTGCCTGAATCTTTTCAATCT 59.055 34.615 0.00 0.00 41.22 2.40
207 209 6.061441 TGACTACTTGCCTGAATCTTTTCAA 58.939 36.000 0.00 0.00 41.22 2.69
208 210 5.620206 TGACTACTTGCCTGAATCTTTTCA 58.380 37.500 0.00 0.00 39.54 2.69
210 212 4.457257 GCTGACTACTTGCCTGAATCTTTT 59.543 41.667 0.00 0.00 0.00 2.27
246 248 0.532573 TCAGCGTGAACATCCTCTCC 59.467 55.000 0.00 0.00 0.00 3.71
293 295 5.812642 CAGGCTCATTATCGAGTAAAACAGT 59.187 40.000 0.00 0.00 35.33 3.55
350 352 0.987294 CTGGATTCTGGACAGGGTGT 59.013 55.000 0.00 0.00 0.00 4.16
351 353 1.209019 CTCTGGATTCTGGACAGGGTG 59.791 57.143 0.00 0.00 33.19 4.61
352 354 1.577736 CTCTGGATTCTGGACAGGGT 58.422 55.000 0.00 0.00 33.19 4.34
353 355 0.835941 CCTCTGGATTCTGGACAGGG 59.164 60.000 0.00 0.00 33.19 4.45
384 387 0.740149 TCTGCTGCACAAACAACCAG 59.260 50.000 0.00 0.00 0.00 4.00
399 402 3.311048 GGTATTTGTCTTAGCTGCTCTGC 59.689 47.826 4.91 0.00 0.00 4.26
404 407 4.123506 GAGGAGGTATTTGTCTTAGCTGC 58.876 47.826 0.00 0.00 36.23 5.25
414 417 5.091261 AGCACTTACAGAGGAGGTATTTG 57.909 43.478 0.00 0.00 0.00 2.32
419 422 2.093106 CGTAGCACTTACAGAGGAGGT 58.907 52.381 0.00 0.00 32.27 3.85
430 433 0.324943 ATGTTCAGGCCGTAGCACTT 59.675 50.000 0.00 0.00 42.56 3.16
434 437 1.134670 AGAGAATGTTCAGGCCGTAGC 60.135 52.381 0.00 0.00 38.76 3.58
478 481 8.514594 GTCACAATTCTGTCAGAATAATCCAAA 58.485 33.333 24.95 7.79 43.67 3.28
479 482 7.121168 GGTCACAATTCTGTCAGAATAATCCAA 59.879 37.037 24.95 9.10 43.67 3.53
481 484 6.599244 TGGTCACAATTCTGTCAGAATAATCC 59.401 38.462 24.95 20.79 43.67 3.01
484 487 8.408043 AAATGGTCACAATTCTGTCAGAATAA 57.592 30.769 24.95 10.89 43.67 1.40
511 514 2.980233 GTGTGACCAGCCCTGTGC 60.980 66.667 0.00 0.00 41.71 4.57
559 562 1.595794 TGTTTCGCTCAAGTCGGAAAC 59.404 47.619 8.18 8.18 34.34 2.78
560 563 1.942677 TGTTTCGCTCAAGTCGGAAA 58.057 45.000 0.00 0.00 0.00 3.13
567 570 4.472691 TGACTGATTTGTTTCGCTCAAG 57.527 40.909 0.00 0.00 0.00 3.02
602 605 2.093783 CGAGCCTGGTTTTACGATGAAC 59.906 50.000 0.00 0.00 0.00 3.18
615 618 0.532573 ATCCGTATATGCGAGCCTGG 59.467 55.000 15.21 0.00 0.00 4.45
623 626 5.900339 TTTTCTCGTTCATCCGTATATGC 57.100 39.130 0.00 0.00 0.00 3.14
654 657 7.402054 TGGGTGTCACTCAAAGTATCAATAAT 58.598 34.615 2.07 0.00 0.00 1.28
656 659 6.367374 TGGGTGTCACTCAAAGTATCAATA 57.633 37.500 2.07 0.00 0.00 1.90
676 684 0.386113 GCTAGCGTCTTCTACCTGGG 59.614 60.000 0.00 0.00 0.00 4.45
705 713 7.773224 TGGTCATTAGATCGTCAAATTATTGGT 59.227 33.333 0.00 0.00 37.15 3.67
718 726 6.543831 AGGGAAAAATTCTGGTCATTAGATCG 59.456 38.462 0.00 0.00 0.00 3.69
719 727 7.254932 CGAGGGAAAAATTCTGGTCATTAGATC 60.255 40.741 0.00 0.00 0.00 2.75
720 728 6.543831 CGAGGGAAAAATTCTGGTCATTAGAT 59.456 38.462 0.00 0.00 0.00 1.98
721 729 5.880332 CGAGGGAAAAATTCTGGTCATTAGA 59.120 40.000 0.00 0.00 0.00 2.10
722 730 5.880332 TCGAGGGAAAAATTCTGGTCATTAG 59.120 40.000 0.00 0.00 0.00 1.73
723 731 5.811190 TCGAGGGAAAAATTCTGGTCATTA 58.189 37.500 0.00 0.00 0.00 1.90
724 732 4.662278 TCGAGGGAAAAATTCTGGTCATT 58.338 39.130 0.00 0.00 0.00 2.57
725 733 4.265073 CTCGAGGGAAAAATTCTGGTCAT 58.735 43.478 3.91 0.00 0.00 3.06
726 734 3.674997 CTCGAGGGAAAAATTCTGGTCA 58.325 45.455 3.91 0.00 0.00 4.02
727 735 2.420372 GCTCGAGGGAAAAATTCTGGTC 59.580 50.000 15.58 0.00 0.00 4.02
728 736 2.437413 GCTCGAGGGAAAAATTCTGGT 58.563 47.619 15.58 0.00 0.00 4.00
729 737 1.398390 CGCTCGAGGGAAAAATTCTGG 59.602 52.381 24.08 0.00 0.00 3.86
730 738 1.202076 GCGCTCGAGGGAAAAATTCTG 60.202 52.381 31.36 0.00 0.00 3.02
731 739 1.087501 GCGCTCGAGGGAAAAATTCT 58.912 50.000 31.36 0.00 0.00 2.40
732 740 0.247695 CGCGCTCGAGGGAAAAATTC 60.248 55.000 31.36 11.69 38.10 2.17
733 741 1.644786 CCGCGCTCGAGGGAAAAATT 61.645 55.000 31.36 0.00 38.10 1.82
734 742 2.106683 CCGCGCTCGAGGGAAAAAT 61.107 57.895 31.36 0.00 38.10 1.82
735 743 2.740826 CCGCGCTCGAGGGAAAAA 60.741 61.111 31.36 0.00 38.10 1.94
736 744 3.927163 GACCGCGCTCGAGGGAAAA 62.927 63.158 31.36 0.00 39.47 2.29
737 745 4.430765 GACCGCGCTCGAGGGAAA 62.431 66.667 31.36 0.00 39.47 3.13
740 748 4.933064 GATGACCGCGCTCGAGGG 62.933 72.222 24.07 24.07 39.47 4.30
741 749 4.193334 TGATGACCGCGCTCGAGG 62.193 66.667 15.58 10.41 41.00 4.63
742 750 2.951745 GTGATGACCGCGCTCGAG 60.952 66.667 8.45 8.45 38.10 4.04
743 751 2.757155 TTTGTGATGACCGCGCTCGA 62.757 55.000 5.56 0.00 38.10 4.04
744 752 2.283780 CTTTGTGATGACCGCGCTCG 62.284 60.000 5.56 0.00 0.00 5.03
745 753 1.291877 ACTTTGTGATGACCGCGCTC 61.292 55.000 5.56 0.00 0.00 5.03
746 754 1.301716 ACTTTGTGATGACCGCGCT 60.302 52.632 5.56 0.00 0.00 5.92
747 755 1.154413 CACTTTGTGATGACCGCGC 60.154 57.895 0.00 0.00 35.23 6.86
748 756 1.227999 ACCACTTTGTGATGACCGCG 61.228 55.000 0.00 0.00 35.23 6.46
749 757 0.517316 GACCACTTTGTGATGACCGC 59.483 55.000 0.00 0.00 35.23 5.68
750 758 1.800586 CTGACCACTTTGTGATGACCG 59.199 52.381 0.00 0.00 35.23 4.79
751 759 2.808543 GTCTGACCACTTTGTGATGACC 59.191 50.000 0.00 0.00 35.23 4.02
752 760 3.466836 TGTCTGACCACTTTGTGATGAC 58.533 45.455 5.17 0.00 35.23 3.06
753 761 3.836365 TGTCTGACCACTTTGTGATGA 57.164 42.857 5.17 0.00 35.23 2.92
754 762 3.817084 ACATGTCTGACCACTTTGTGATG 59.183 43.478 5.17 1.78 35.23 3.07
755 763 4.067896 GACATGTCTGACCACTTTGTGAT 58.932 43.478 18.83 0.00 35.23 3.06
756 764 3.118445 TGACATGTCTGACCACTTTGTGA 60.118 43.478 25.55 0.00 35.23 3.58
757 765 3.205338 TGACATGTCTGACCACTTTGTG 58.795 45.455 25.55 0.00 0.00 3.33
758 766 3.558931 TGACATGTCTGACCACTTTGT 57.441 42.857 25.55 1.76 0.00 2.83
759 767 3.817084 ACATGACATGTCTGACCACTTTG 59.183 43.478 25.55 11.41 39.92 2.77
760 768 4.090761 ACATGACATGTCTGACCACTTT 57.909 40.909 25.55 2.78 39.92 2.66
761 769 3.777106 ACATGACATGTCTGACCACTT 57.223 42.857 25.55 3.40 39.92 3.16
762 770 3.367395 CGTACATGACATGTCTGACCACT 60.367 47.826 24.04 8.45 43.67 4.00
763 771 2.923655 CGTACATGACATGTCTGACCAC 59.076 50.000 24.04 14.31 43.67 4.16
764 772 2.673893 GCGTACATGACATGTCTGACCA 60.674 50.000 24.04 7.02 43.67 4.02
765 773 1.927174 GCGTACATGACATGTCTGACC 59.073 52.381 24.04 14.56 43.67 4.02
766 774 1.583856 CGCGTACATGACATGTCTGAC 59.416 52.381 24.04 15.67 43.67 3.51
767 775 1.201414 ACGCGTACATGACATGTCTGA 59.799 47.619 24.04 7.88 43.67 3.27
768 776 1.629013 ACGCGTACATGACATGTCTG 58.371 50.000 24.04 21.27 43.67 3.51
769 777 2.363788 AACGCGTACATGACATGTCT 57.636 45.000 24.04 9.24 43.67 3.41
770 778 4.320491 GTTTAACGCGTACATGACATGTC 58.680 43.478 24.04 19.27 43.67 3.06
771 779 3.181538 CGTTTAACGCGTACATGACATGT 60.182 43.478 23.83 23.83 40.11 3.21
772 780 3.330331 CGTTTAACGCGTACATGACATG 58.670 45.455 14.46 14.02 33.65 3.21
773 781 3.628053 CGTTTAACGCGTACATGACAT 57.372 42.857 14.46 0.00 33.65 3.06
785 793 2.092211 GTGGAGATGAGTGCGTTTAACG 59.908 50.000 13.57 13.57 45.88 3.18
786 794 3.064207 TGTGGAGATGAGTGCGTTTAAC 58.936 45.455 0.00 0.00 0.00 2.01
787 795 3.394674 TGTGGAGATGAGTGCGTTTAA 57.605 42.857 0.00 0.00 0.00 1.52
788 796 3.244078 ACTTGTGGAGATGAGTGCGTTTA 60.244 43.478 0.00 0.00 0.00 2.01
789 797 2.146342 CTTGTGGAGATGAGTGCGTTT 58.854 47.619 0.00 0.00 0.00 3.60
790 798 1.070758 ACTTGTGGAGATGAGTGCGTT 59.929 47.619 0.00 0.00 0.00 4.84
791 799 0.681733 ACTTGTGGAGATGAGTGCGT 59.318 50.000 0.00 0.00 0.00 5.24
792 800 1.073964 CACTTGTGGAGATGAGTGCG 58.926 55.000 0.00 0.00 33.87 5.34
793 801 1.002430 TCCACTTGTGGAGATGAGTGC 59.998 52.381 17.57 0.00 38.48 4.40
794 802 2.693069 GTCCACTTGTGGAGATGAGTG 58.307 52.381 21.36 0.00 38.88 3.51
795 803 1.273606 CGTCCACTTGTGGAGATGAGT 59.726 52.381 21.36 0.00 38.88 3.41
796 804 1.546029 TCGTCCACTTGTGGAGATGAG 59.454 52.381 21.36 11.30 38.88 2.90
797 805 1.272490 GTCGTCCACTTGTGGAGATGA 59.728 52.381 21.36 16.21 38.88 2.92
798 806 1.714794 GTCGTCCACTTGTGGAGATG 58.285 55.000 21.36 14.42 38.88 2.90
799 807 0.243907 CGTCGTCCACTTGTGGAGAT 59.756 55.000 21.36 0.00 38.88 2.75
800 808 0.820482 TCGTCGTCCACTTGTGGAGA 60.820 55.000 21.36 16.92 38.88 3.71
801 809 0.663568 GTCGTCGTCCACTTGTGGAG 60.664 60.000 21.36 15.20 38.88 3.86
802 810 1.105167 AGTCGTCGTCCACTTGTGGA 61.105 55.000 17.57 17.57 35.23 4.02
803 811 0.939577 CAGTCGTCGTCCACTTGTGG 60.940 60.000 13.24 13.24 0.00 4.17
804 812 1.548973 GCAGTCGTCGTCCACTTGTG 61.549 60.000 0.00 0.00 0.00 3.33
805 813 1.299926 GCAGTCGTCGTCCACTTGT 60.300 57.895 0.00 0.00 0.00 3.16
806 814 2.022129 GGCAGTCGTCGTCCACTTG 61.022 63.158 0.00 0.00 0.00 3.16
807 815 2.338984 GGCAGTCGTCGTCCACTT 59.661 61.111 0.00 0.00 0.00 3.16
808 816 4.039357 CGGCAGTCGTCGTCCACT 62.039 66.667 0.00 0.00 34.87 4.00
818 826 1.136984 CGTGAGTAGACCGGCAGTC 59.863 63.158 0.00 0.00 46.71 3.51
878 886 2.197577 GCTCGGCTGTCTTATGAAGTC 58.802 52.381 0.00 0.00 0.00 3.01
891 899 1.897225 ATTGTGCTCTCTGCTCGGCT 61.897 55.000 0.00 0.00 43.37 5.52
892 900 1.427592 GATTGTGCTCTCTGCTCGGC 61.428 60.000 0.00 0.00 43.37 5.54
894 902 1.558741 GAGATTGTGCTCTCTGCTCG 58.441 55.000 0.00 0.00 43.37 5.03
901 909 1.830477 GAGGTCCAGAGATTGTGCTCT 59.170 52.381 0.00 0.00 45.81 4.09
903 911 1.649321 TGAGGTCCAGAGATTGTGCT 58.351 50.000 0.00 0.00 0.00 4.40
904 912 2.559440 GATGAGGTCCAGAGATTGTGC 58.441 52.381 0.00 0.00 0.00 4.57
905 913 3.191078 GGATGAGGTCCAGAGATTGTG 57.809 52.381 0.00 0.00 46.96 3.33
915 923 5.049129 GATGAAATCGAAATGGATGAGGTCC 60.049 44.000 0.00 0.00 39.79 4.46
916 924 5.995055 GATGAAATCGAAATGGATGAGGTC 58.005 41.667 0.00 0.00 31.13 3.85
926 934 7.211835 GGCTAACGGCTGATGAAATCGAAAT 62.212 44.000 0.00 0.00 41.57 2.17
990 998 0.459078 TGAGAAGCATGGCTCTCTCG 59.541 55.000 17.36 0.00 41.25 4.04
991 999 2.553086 CTTGAGAAGCATGGCTCTCTC 58.447 52.381 16.48 16.48 38.25 3.20
1087 1113 1.673920 GGCGAACTGTTGACCTTCAAA 59.326 47.619 0.00 0.00 38.22 2.69
1088 1114 1.134220 AGGCGAACTGTTGACCTTCAA 60.134 47.619 0.00 0.00 33.32 2.69
1164 1311 4.459089 GTCAGCACGAGGAGGCCC 62.459 72.222 0.00 0.00 0.00 5.80
1174 1321 2.126189 GGTACCGTCGGTCAGCAC 60.126 66.667 22.74 13.47 37.09 4.40
1438 1607 2.048127 AAGCTCCACGGCGAAGAC 60.048 61.111 16.62 4.83 37.29 3.01
1471 1640 1.350193 CTGATGTCGTTGAACTCGGG 58.650 55.000 0.00 0.00 0.00 5.14
1542 1711 2.189499 ATCGTAGTACCCGGCGTCC 61.189 63.158 6.01 0.00 0.00 4.79
1604 1780 3.751246 CCCACACTTGCATGGCCG 61.751 66.667 0.00 0.00 34.37 6.13
1686 1872 1.077858 CTGCAGGAGGGGCTTCTTC 60.078 63.158 5.57 0.00 0.00 2.87
1761 8955 0.521867 CGTTCATGATGCCTGTTGCG 60.522 55.000 0.00 0.00 45.60 4.85
1813 9010 2.044806 GCCGGTGCTAGTCCATCCAT 62.045 60.000 1.90 0.00 33.53 3.41
1836 9033 1.213733 CTGGCAGCATCGAGATGTCG 61.214 60.000 5.80 5.80 42.27 4.35
1932 9144 1.094785 CAATGCCTACCGAAACCAGG 58.905 55.000 0.00 0.00 0.00 4.45
2160 9378 4.704540 TGTCTTGAATTGTGTGACAACCTT 59.295 37.500 0.00 0.00 41.40 3.50
2181 9399 3.767711 GATGAACTCCCTTTTCCCTTGT 58.232 45.455 0.00 0.00 0.00 3.16
2249 9467 1.740025 GTCTGCAGTAGCCCAACAATC 59.260 52.381 14.67 0.00 41.13 2.67
2367 11165 5.009510 CACACCTCTGATGATCTAGTACCTG 59.990 48.000 0.00 0.00 0.00 4.00
2483 11281 2.100879 ATCGCCTAGCCGTCCATTCC 62.101 60.000 0.00 0.00 0.00 3.01
2494 11292 1.017387 GCAGGACCAAAATCGCCTAG 58.983 55.000 0.00 0.00 0.00 3.02
2510 11308 6.072286 GGTTTCATGGTCATATATCCTTGCAG 60.072 42.308 0.00 0.00 0.00 4.41
2543 11341 2.125512 CAGCCACGTGGGTAGCTC 60.126 66.667 36.72 18.51 45.47 4.09
2611 11411 2.821546 TGCGTATACATCTGTGAAGGC 58.178 47.619 3.32 0.00 0.00 4.35
2619 11419 4.136796 ACATGCCAAATGCGTATACATCT 58.863 39.130 3.32 0.00 45.60 2.90
2647 11447 0.034756 CGTCCACATGTCACCTCCAA 59.965 55.000 0.00 0.00 0.00 3.53
2655 11455 0.036765 TTGGCCTACGTCCACATGTC 60.037 55.000 3.32 0.00 32.45 3.06
2845 11645 0.443869 CGCATAATAGGCCGCACATC 59.556 55.000 0.00 0.00 0.00 3.06
2927 11727 5.929992 TCGTTTTTCACTAGGTTCATGTAGG 59.070 40.000 0.00 0.00 0.00 3.18
2944 11750 7.045126 TGTATGAATTCAACCCTTCGTTTTT 57.955 32.000 13.09 0.00 29.93 1.94
2965 11771 1.423541 ACCTGGCCTGTTCATGTTGTA 59.576 47.619 3.32 0.00 0.00 2.41
2988 11794 2.282783 AACGCTCATTTTGGGCCCC 61.283 57.895 22.27 0.85 41.93 5.80
2990 11796 1.737735 GCAACGCTCATTTTGGGCC 60.738 57.895 0.00 0.00 41.93 5.80
2992 11798 0.667184 GTGGCAACGCTCATTTTGGG 60.667 55.000 0.00 0.00 46.04 4.12
3021 11827 1.052287 CGTCTTGCAAAATTGTCGCC 58.948 50.000 0.00 0.00 0.00 5.54
3080 12411 2.673775 TTGATGAAAGGAGGCCACAA 57.326 45.000 5.01 0.00 0.00 3.33
3143 12476 7.039152 TGGATTTTATTGACTCCAAATGAAGCA 60.039 33.333 0.00 0.00 34.91 3.91
3144 12477 7.322664 TGGATTTTATTGACTCCAAATGAAGC 58.677 34.615 0.00 0.00 34.91 3.86
3145 12478 9.525409 GATGGATTTTATTGACTCCAAATGAAG 57.475 33.333 0.00 0.00 40.94 3.02
3185 12870 2.270352 TCCAACGCAACCTTCTCATT 57.730 45.000 0.00 0.00 0.00 2.57
3186 12871 2.489329 CAATCCAACGCAACCTTCTCAT 59.511 45.455 0.00 0.00 0.00 2.90
3187 12872 1.879380 CAATCCAACGCAACCTTCTCA 59.121 47.619 0.00 0.00 0.00 3.27
3191 12876 2.858745 AGTACAATCCAACGCAACCTT 58.141 42.857 0.00 0.00 0.00 3.50
3232 12918 2.287909 CGGAGGAAGATACAGTAGCAGC 60.288 54.545 0.00 0.00 0.00 5.25
3236 12922 2.031857 GCGTCGGAGGAAGATACAGTAG 60.032 54.545 1.18 0.00 0.00 2.57
3242 12928 1.134367 CAACTGCGTCGGAGGAAGATA 59.866 52.381 18.47 0.00 0.00 1.98
3302 13000 8.680001 TCTATCATGGTGATTTTTGATCAAGTG 58.320 33.333 8.41 0.00 38.26 3.16


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

AutoCloner maintained by Alex Coulton.