Multiple sequence alignment - TraesCS6A01G396700

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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 TraesCS6A01G396700 chr6A 100.000 4595 0 0 1 4595 608681729 608677135 0.000000e+00 8486.0
1 TraesCS6A01G396700 chr6A 97.084 2023 35 6 1588 3589 608793497 608791478 0.000000e+00 3387.0
2 TraesCS6A01G396700 chr6A 86.005 1672 208 19 1685 3351 554834433 554832783 0.000000e+00 1768.0
3 TraesCS6A01G396700 chr6A 84.386 1774 234 24 1685 3438 135224403 135226153 0.000000e+00 1701.0
4 TraesCS6A01G396700 chr6A 83.507 1825 240 35 1706 3495 613092215 613090417 0.000000e+00 1646.0
5 TraesCS6A01G396700 chr6A 84.233 1668 227 26 1698 3340 574222153 574220497 0.000000e+00 1591.0
6 TraesCS6A01G396700 chr6A 99.307 722 5 0 1 722 608688363 608687642 0.000000e+00 1306.0
7 TraesCS6A01G396700 chr6A 98.753 722 7 2 1 722 35607078 35607797 0.000000e+00 1282.0
8 TraesCS6A01G396700 chr6A 98.338 722 10 2 1 722 610486681 610485962 0.000000e+00 1266.0
9 TraesCS6A01G396700 chr6A 98.199 722 11 2 1 722 35600246 35600965 0.000000e+00 1260.0
10 TraesCS6A01G396700 chr6A 98.677 378 5 0 965 1342 608793874 608793497 0.000000e+00 671.0
11 TraesCS6A01G396700 chr6A 89.373 367 31 5 4114 4474 608790836 608790472 5.420000e-124 455.0
12 TraesCS6A01G396700 chr6A 89.884 346 15 6 3792 4117 608791284 608790939 1.180000e-115 427.0
13 TraesCS6A01G396700 chr6A 92.500 120 6 2 3669 3787 608791465 608791348 7.910000e-38 169.0
14 TraesCS6A01G396700 chr6D 95.048 2403 86 12 1111 3488 461820760 461818366 0.000000e+00 3747.0
15 TraesCS6A01G396700 chr6D 91.268 2027 148 13 1590 3601 462026581 462024569 0.000000e+00 2736.0
16 TraesCS6A01G396700 chr6D 83.998 1881 230 41 1685 3538 110868540 110870376 0.000000e+00 1740.0
17 TraesCS6A01G396700 chr6D 78.082 949 142 38 2687 3600 466524960 466525877 1.450000e-149 540.0
18 TraesCS6A01G396700 chr6D 88.649 370 24 14 4114 4479 461816831 461816476 7.060000e-118 435.0
19 TraesCS6A01G396700 chr6D 83.544 316 16 13 3507 3787 461818189 461817875 3.530000e-66 263.0
20 TraesCS6A01G396700 chr6D 92.903 155 11 0 3961 4115 462024176 462024022 4.630000e-55 226.0
21 TraesCS6A01G396700 chr6D 88.966 145 15 1 3970 4113 461817558 461817414 1.310000e-40 178.0
22 TraesCS6A01G396700 chr6B 88.848 2170 165 34 1413 3537 704155930 704153793 0.000000e+00 2595.0
23 TraesCS6A01G396700 chr6B 85.408 1912 228 27 1685 3586 615087849 615085979 0.000000e+00 1938.0
24 TraesCS6A01G396700 chr6B 84.166 1882 228 35 1685 3538 199741455 199743294 0.000000e+00 1760.0
25 TraesCS6A01G396700 chr6B 84.279 1851 239 34 1679 3495 711739402 711737570 0.000000e+00 1759.0
26 TraesCS6A01G396700 chr6B 90.535 243 20 3 4234 4474 704151159 704150918 7.420000e-83 318.0
27 TraesCS6A01G396700 chr6B 89.189 148 14 2 3970 4116 704153429 704153283 2.820000e-42 183.0
28 TraesCS6A01G396700 chr6B 90.476 126 11 1 3662 3787 1183126 1183002 1.020000e-36 165.0
29 TraesCS6A01G396700 chr6B 82.482 137 21 3 1111 1245 708254308 708254443 2.900000e-22 117.0
30 TraesCS6A01G396700 chr3B 83.833 1602 226 17 1693 3269 197791860 197790267 0.000000e+00 1493.0
31 TraesCS6A01G396700 chr3B 91.566 166 14 0 3950 4115 785215961 785216126 3.580000e-56 230.0
32 TraesCS6A01G396700 chr3B 91.270 126 10 1 3662 3787 785215597 785215721 2.200000e-38 171.0
33 TraesCS6A01G396700 chrUn 99.307 722 5 0 1 722 372715931 372715210 0.000000e+00 1306.0
34 TraesCS6A01G396700 chr2A 98.753 722 7 2 1 722 760993278 760993997 0.000000e+00 1282.0
35 TraesCS6A01G396700 chr2A 98.338 722 10 2 1 722 761000143 761000862 0.000000e+00 1266.0
36 TraesCS6A01G396700 chr2A 98.199 722 11 2 1 722 767044504 767045223 0.000000e+00 1260.0
37 TraesCS6A01G396700 chr2A 98.072 726 9 5 1 725 780397957 780397236 0.000000e+00 1258.0
38 TraesCS6A01G396700 chr4B 93.750 176 11 0 937 1112 261074032 261073857 9.800000e-67 265.0
39 TraesCS6A01G396700 chr4B 93.567 171 11 0 942 1112 260904056 260903886 5.900000e-64 255.0
40 TraesCS6A01G396700 chr4B 90.341 176 17 0 937 1112 260747044 260746869 9.940000e-57 231.0
41 TraesCS6A01G396700 chr4B 90.476 126 9 2 3662 3787 215239962 215240084 3.680000e-36 163.0
42 TraesCS6A01G396700 chr5B 80.663 362 35 15 3785 4115 517432217 517432574 9.870000e-62 248.0
43 TraesCS6A01G396700 chr5B 91.270 126 10 1 3662 3787 517432037 517432161 2.200000e-38 171.0
44 TraesCS6A01G396700 chr7A 80.278 360 37 15 3785 4113 287666167 287666523 1.650000e-59 241.0
45 TraesCS6A01G396700 chr7A 90.476 126 9 2 3662 3787 287665989 287666111 3.680000e-36 163.0
46 TraesCS6A01G396700 chr5A 92.063 126 9 1 3662 3787 450326931 450327055 4.720000e-40 176.0
47 TraesCS6A01G396700 chr7D 85.926 135 14 5 1111 1244 618502100 618501970 6.200000e-29 139.0
48 TraesCS6A01G396700 chr2B 83.077 130 14 7 1111 1237 184113339 184113463 1.350000e-20 111.0
49 TraesCS6A01G396700 chr3D 81.119 143 21 3 1111 1248 382318948 382319089 4.860000e-20 110.0
50 TraesCS6A01G396700 chr7B 80.576 139 23 3 1111 1246 710982922 710983059 2.260000e-18 104.0
51 TraesCS6A01G396700 chr7B 80.986 142 16 7 1111 1246 632942666 632942530 8.130000e-18 102.0
52 TraesCS6A01G396700 chr7B 79.562 137 25 2 1111 1245 380355264 380355129 1.360000e-15 95.3


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 TraesCS6A01G396700 chr6A 608677135 608681729 4594 True 8486.00 8486 100.00000 1 4595 1 chr6A.!!$R3 4594
1 TraesCS6A01G396700 chr6A 554832783 554834433 1650 True 1768.00 1768 86.00500 1685 3351 1 chr6A.!!$R1 1666
2 TraesCS6A01G396700 chr6A 135224403 135226153 1750 False 1701.00 1701 84.38600 1685 3438 1 chr6A.!!$F3 1753
3 TraesCS6A01G396700 chr6A 613090417 613092215 1798 True 1646.00 1646 83.50700 1706 3495 1 chr6A.!!$R6 1789
4 TraesCS6A01G396700 chr6A 574220497 574222153 1656 True 1591.00 1591 84.23300 1698 3340 1 chr6A.!!$R2 1642
5 TraesCS6A01G396700 chr6A 608687642 608688363 721 True 1306.00 1306 99.30700 1 722 1 chr6A.!!$R4 721
6 TraesCS6A01G396700 chr6A 35607078 35607797 719 False 1282.00 1282 98.75300 1 722 1 chr6A.!!$F2 721
7 TraesCS6A01G396700 chr6A 610485962 610486681 719 True 1266.00 1266 98.33800 1 722 1 chr6A.!!$R5 721
8 TraesCS6A01G396700 chr6A 35600246 35600965 719 False 1260.00 1260 98.19900 1 722 1 chr6A.!!$F1 721
9 TraesCS6A01G396700 chr6A 608790472 608793874 3402 True 1021.80 3387 93.50360 965 4474 5 chr6A.!!$R7 3509
10 TraesCS6A01G396700 chr6D 110868540 110870376 1836 False 1740.00 1740 83.99800 1685 3538 1 chr6D.!!$F1 1853
11 TraesCS6A01G396700 chr6D 462024022 462026581 2559 True 1481.00 2736 92.08550 1590 4115 2 chr6D.!!$R2 2525
12 TraesCS6A01G396700 chr6D 461816476 461820760 4284 True 1155.75 3747 89.05175 1111 4479 4 chr6D.!!$R1 3368
13 TraesCS6A01G396700 chr6D 466524960 466525877 917 False 540.00 540 78.08200 2687 3600 1 chr6D.!!$F2 913
14 TraesCS6A01G396700 chr6B 615085979 615087849 1870 True 1938.00 1938 85.40800 1685 3586 1 chr6B.!!$R2 1901
15 TraesCS6A01G396700 chr6B 199741455 199743294 1839 False 1760.00 1760 84.16600 1685 3538 1 chr6B.!!$F1 1853
16 TraesCS6A01G396700 chr6B 711737570 711739402 1832 True 1759.00 1759 84.27900 1679 3495 1 chr6B.!!$R3 1816
17 TraesCS6A01G396700 chr6B 704150918 704155930 5012 True 1032.00 2595 89.52400 1413 4474 3 chr6B.!!$R4 3061
18 TraesCS6A01G396700 chr3B 197790267 197791860 1593 True 1493.00 1493 83.83300 1693 3269 1 chr3B.!!$R1 1576
19 TraesCS6A01G396700 chr3B 785215597 785216126 529 False 200.50 230 91.41800 3662 4115 2 chr3B.!!$F1 453
20 TraesCS6A01G396700 chrUn 372715210 372715931 721 True 1306.00 1306 99.30700 1 722 1 chrUn.!!$R1 721
21 TraesCS6A01G396700 chr2A 760993278 760993997 719 False 1282.00 1282 98.75300 1 722 1 chr2A.!!$F1 721
22 TraesCS6A01G396700 chr2A 761000143 761000862 719 False 1266.00 1266 98.33800 1 722 1 chr2A.!!$F2 721
23 TraesCS6A01G396700 chr2A 767044504 767045223 719 False 1260.00 1260 98.19900 1 722 1 chr2A.!!$F3 721
24 TraesCS6A01G396700 chr2A 780397236 780397957 721 True 1258.00 1258 98.07200 1 725 1 chr2A.!!$R1 724
25 TraesCS6A01G396700 chr5B 517432037 517432574 537 False 209.50 248 85.96650 3662 4115 2 chr5B.!!$F1 453
26 TraesCS6A01G396700 chr7A 287665989 287666523 534 False 202.00 241 85.37700 3662 4113 2 chr7A.!!$F1 451

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
781 784 0.178984 TGCCTATACGATGGACCGGA 60.179 55.0 9.46 0.0 0.00 5.14 F
1342 1345 0.251121 TGATGGCGAACATGGTGGTT 60.251 50.0 0.00 0.0 40.72 3.67 F
1402 1405 1.529226 TACAACATCACCCGCCAAAG 58.471 50.0 0.00 0.0 0.00 2.77 F
2659 2720 1.693467 TTGTCAGCGACGTGTATGTC 58.307 50.0 0.00 0.0 34.95 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 2720 2.693762 CCACGACATGGCCAGCAAG 61.694 63.158 13.05 5.49 43.24 4.01 R
3370 3505 3.071602 AGGTTCTCTAAACTGCAGCTTGA 59.928 43.478 15.27 6.99 29.02 3.02 R
3385 3527 6.173339 TCCAAGAATCATACAACAGGTTCTC 58.827 40.000 0.00 0.00 0.00 2.87 R
3601 3955 0.037232 AAGACTAACACAGCGGAGGC 60.037 55.000 0.00 0.00 40.37 4.70 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
632 635 8.846943 ACATCATCTCACAACTAACACATTAA 57.153 30.769 0.00 0.00 0.00 1.40
722 725 3.195825 CGGAGTGACAAACCCTAATCTCT 59.804 47.826 0.00 0.00 0.00 3.10
723 726 4.508662 GGAGTGACAAACCCTAATCTCTG 58.491 47.826 0.00 0.00 0.00 3.35
724 727 4.223032 GGAGTGACAAACCCTAATCTCTGA 59.777 45.833 0.00 0.00 0.00 3.27
725 728 5.104735 GGAGTGACAAACCCTAATCTCTGAT 60.105 44.000 0.00 0.00 0.00 2.90
726 729 6.380079 AGTGACAAACCCTAATCTCTGATT 57.620 37.500 0.00 0.00 0.00 2.57
727 730 7.364762 GGAGTGACAAACCCTAATCTCTGATTA 60.365 40.741 0.00 0.00 0.00 1.75
728 731 8.095452 AGTGACAAACCCTAATCTCTGATTAT 57.905 34.615 1.18 0.00 0.00 1.28
729 732 8.207545 AGTGACAAACCCTAATCTCTGATTATC 58.792 37.037 1.18 0.00 0.00 1.75
730 733 7.987458 GTGACAAACCCTAATCTCTGATTATCA 59.013 37.037 0.00 0.00 0.00 2.15
731 734 7.987458 TGACAAACCCTAATCTCTGATTATCAC 59.013 37.037 0.00 0.00 0.00 3.06
732 735 7.861629 ACAAACCCTAATCTCTGATTATCACA 58.138 34.615 0.00 0.00 0.00 3.58
733 736 8.328758 ACAAACCCTAATCTCTGATTATCACAA 58.671 33.333 0.00 0.00 0.00 3.33
734 737 9.177608 CAAACCCTAATCTCTGATTATCACAAA 57.822 33.333 0.00 0.00 0.00 2.83
735 738 9.753674 AAACCCTAATCTCTGATTATCACAAAA 57.246 29.630 0.00 0.00 0.00 2.44
736 739 9.753674 AACCCTAATCTCTGATTATCACAAAAA 57.246 29.630 0.00 0.00 0.00 1.94
759 762 6.546972 AAATCAGAAGACTTTCGACTTTCC 57.453 37.500 0.00 0.00 38.38 3.13
760 763 4.939052 TCAGAAGACTTTCGACTTTCCT 57.061 40.909 0.00 0.00 38.38 3.36
761 764 4.872664 TCAGAAGACTTTCGACTTTCCTC 58.127 43.478 0.00 0.00 38.38 3.71
762 765 4.585162 TCAGAAGACTTTCGACTTTCCTCT 59.415 41.667 0.00 0.00 38.38 3.69
763 766 4.683781 CAGAAGACTTTCGACTTTCCTCTG 59.316 45.833 0.00 0.00 38.38 3.35
764 767 3.033368 AGACTTTCGACTTTCCTCTGC 57.967 47.619 0.00 0.00 0.00 4.26
765 768 2.070028 GACTTTCGACTTTCCTCTGCC 58.930 52.381 0.00 0.00 0.00 4.85
766 769 1.694696 ACTTTCGACTTTCCTCTGCCT 59.305 47.619 0.00 0.00 0.00 4.75
767 770 2.897969 ACTTTCGACTTTCCTCTGCCTA 59.102 45.455 0.00 0.00 0.00 3.93
768 771 3.515901 ACTTTCGACTTTCCTCTGCCTAT 59.484 43.478 0.00 0.00 0.00 2.57
769 772 4.710375 ACTTTCGACTTTCCTCTGCCTATA 59.290 41.667 0.00 0.00 0.00 1.31
770 773 4.650754 TTCGACTTTCCTCTGCCTATAC 57.349 45.455 0.00 0.00 0.00 1.47
771 774 2.617308 TCGACTTTCCTCTGCCTATACG 59.383 50.000 0.00 0.00 0.00 3.06
772 775 2.617308 CGACTTTCCTCTGCCTATACGA 59.383 50.000 0.00 0.00 0.00 3.43
773 776 3.253677 CGACTTTCCTCTGCCTATACGAT 59.746 47.826 0.00 0.00 0.00 3.73
774 777 4.551388 GACTTTCCTCTGCCTATACGATG 58.449 47.826 0.00 0.00 0.00 3.84
775 778 3.322254 ACTTTCCTCTGCCTATACGATGG 59.678 47.826 0.00 0.00 0.00 3.51
776 779 2.971901 TCCTCTGCCTATACGATGGA 57.028 50.000 0.00 0.00 0.00 3.41
777 780 2.515854 TCCTCTGCCTATACGATGGAC 58.484 52.381 0.00 0.00 0.00 4.02
778 781 1.546476 CCTCTGCCTATACGATGGACC 59.454 57.143 0.00 0.00 0.00 4.46
779 782 1.200252 CTCTGCCTATACGATGGACCG 59.800 57.143 0.00 0.00 0.00 4.79
780 783 0.243907 CTGCCTATACGATGGACCGG 59.756 60.000 0.00 0.00 0.00 5.28
781 784 0.178984 TGCCTATACGATGGACCGGA 60.179 55.000 9.46 0.00 0.00 5.14
782 785 0.526662 GCCTATACGATGGACCGGAG 59.473 60.000 9.46 0.00 0.00 4.63
783 786 1.885359 GCCTATACGATGGACCGGAGA 60.885 57.143 9.46 0.00 0.00 3.71
784 787 2.511659 CCTATACGATGGACCGGAGAA 58.488 52.381 9.46 0.00 0.00 2.87
785 788 2.889045 CCTATACGATGGACCGGAGAAA 59.111 50.000 9.46 0.00 0.00 2.52
786 789 3.057456 CCTATACGATGGACCGGAGAAAG 60.057 52.174 9.46 0.00 0.00 2.62
787 790 2.133281 TACGATGGACCGGAGAAAGA 57.867 50.000 9.46 0.00 0.00 2.52
788 791 1.263356 ACGATGGACCGGAGAAAGAA 58.737 50.000 9.46 0.00 0.00 2.52
789 792 1.621814 ACGATGGACCGGAGAAAGAAA 59.378 47.619 9.46 0.00 0.00 2.52
790 793 2.236395 ACGATGGACCGGAGAAAGAAAT 59.764 45.455 9.46 0.00 0.00 2.17
791 794 2.866762 CGATGGACCGGAGAAAGAAATC 59.133 50.000 9.46 0.00 0.00 2.17
792 795 3.678806 CGATGGACCGGAGAAAGAAATCA 60.679 47.826 9.46 0.00 0.00 2.57
793 796 4.455606 GATGGACCGGAGAAAGAAATCAT 58.544 43.478 9.46 0.00 0.00 2.45
794 797 3.609853 TGGACCGGAGAAAGAAATCATG 58.390 45.455 9.46 0.00 0.00 3.07
795 798 2.945668 GGACCGGAGAAAGAAATCATGG 59.054 50.000 9.46 0.00 0.00 3.66
796 799 2.356069 GACCGGAGAAAGAAATCATGGC 59.644 50.000 9.46 0.00 0.00 4.40
797 800 1.678101 CCGGAGAAAGAAATCATGGCC 59.322 52.381 0.00 0.00 0.00 5.36
798 801 1.678101 CGGAGAAAGAAATCATGGCCC 59.322 52.381 0.00 0.00 0.00 5.80
799 802 2.738743 GGAGAAAGAAATCATGGCCCA 58.261 47.619 0.00 0.00 0.00 5.36
800 803 2.692041 GGAGAAAGAAATCATGGCCCAG 59.308 50.000 0.00 0.00 0.00 4.45
801 804 3.359950 GAGAAAGAAATCATGGCCCAGT 58.640 45.455 0.00 0.00 0.00 4.00
802 805 4.526970 GAGAAAGAAATCATGGCCCAGTA 58.473 43.478 0.00 0.00 0.00 2.74
803 806 4.934356 AGAAAGAAATCATGGCCCAGTAA 58.066 39.130 0.00 0.00 0.00 2.24
804 807 4.706962 AGAAAGAAATCATGGCCCAGTAAC 59.293 41.667 0.00 0.00 0.00 2.50
805 808 3.737559 AGAAATCATGGCCCAGTAACA 57.262 42.857 0.00 0.00 0.00 2.41
806 809 3.356290 AGAAATCATGGCCCAGTAACAC 58.644 45.455 0.00 0.00 0.00 3.32
807 810 3.010584 AGAAATCATGGCCCAGTAACACT 59.989 43.478 0.00 0.00 0.00 3.55
808 811 3.456380 AATCATGGCCCAGTAACACTT 57.544 42.857 0.00 0.00 0.00 3.16
809 812 2.969821 TCATGGCCCAGTAACACTTT 57.030 45.000 0.00 0.00 0.00 2.66
810 813 2.513753 TCATGGCCCAGTAACACTTTG 58.486 47.619 0.00 0.00 0.00 2.77
811 814 2.107378 TCATGGCCCAGTAACACTTTGA 59.893 45.455 0.00 0.00 0.00 2.69
812 815 1.975660 TGGCCCAGTAACACTTTGAC 58.024 50.000 0.00 0.00 0.00 3.18
813 816 1.244816 GGCCCAGTAACACTTTGACC 58.755 55.000 0.00 0.00 0.00 4.02
814 817 1.244816 GCCCAGTAACACTTTGACCC 58.755 55.000 0.00 0.00 0.00 4.46
815 818 1.477923 GCCCAGTAACACTTTGACCCA 60.478 52.381 0.00 0.00 0.00 4.51
816 819 2.817839 GCCCAGTAACACTTTGACCCAT 60.818 50.000 0.00 0.00 0.00 4.00
817 820 3.560453 GCCCAGTAACACTTTGACCCATA 60.560 47.826 0.00 0.00 0.00 2.74
818 821 4.658063 CCCAGTAACACTTTGACCCATAA 58.342 43.478 0.00 0.00 0.00 1.90
819 822 4.457949 CCCAGTAACACTTTGACCCATAAC 59.542 45.833 0.00 0.00 0.00 1.89
820 823 5.067273 CCAGTAACACTTTGACCCATAACA 58.933 41.667 0.00 0.00 0.00 2.41
821 824 5.533154 CCAGTAACACTTTGACCCATAACAA 59.467 40.000 0.00 0.00 0.00 2.83
822 825 6.435428 CAGTAACACTTTGACCCATAACAAC 58.565 40.000 0.00 0.00 0.00 3.32
823 826 4.929819 AACACTTTGACCCATAACAACC 57.070 40.909 0.00 0.00 0.00 3.77
824 827 3.227614 ACACTTTGACCCATAACAACCC 58.772 45.455 0.00 0.00 0.00 4.11
825 828 3.226777 CACTTTGACCCATAACAACCCA 58.773 45.455 0.00 0.00 0.00 4.51
826 829 3.005367 CACTTTGACCCATAACAACCCAC 59.995 47.826 0.00 0.00 0.00 4.61
827 830 1.898902 TTGACCCATAACAACCCACG 58.101 50.000 0.00 0.00 0.00 4.94
828 831 0.606944 TGACCCATAACAACCCACGC 60.607 55.000 0.00 0.00 0.00 5.34
829 832 1.303806 ACCCATAACAACCCACGCC 60.304 57.895 0.00 0.00 0.00 5.68
830 833 2.049767 CCCATAACAACCCACGCCC 61.050 63.158 0.00 0.00 0.00 6.13
831 834 2.049767 CCATAACAACCCACGCCCC 61.050 63.158 0.00 0.00 0.00 5.80
832 835 1.001393 CATAACAACCCACGCCCCT 60.001 57.895 0.00 0.00 0.00 4.79
833 836 1.001393 ATAACAACCCACGCCCCTG 60.001 57.895 0.00 0.00 0.00 4.45
834 837 3.853698 TAACAACCCACGCCCCTGC 62.854 63.158 0.00 0.00 0.00 4.85
931 934 2.445654 CCTCCCAGGAGGCTCCTC 60.446 72.222 33.04 7.97 45.66 3.71
932 935 2.366167 CTCCCAGGAGGCTCCTCA 59.634 66.667 33.04 18.22 45.66 3.86
933 936 1.761667 CTCCCAGGAGGCTCCTCAG 60.762 68.421 33.04 25.18 45.66 3.35
934 937 3.478274 CCCAGGAGGCTCCTCAGC 61.478 72.222 33.04 6.33 45.66 4.26
935 938 2.686470 CCAGGAGGCTCCTCAGCA 60.686 66.667 33.04 0.00 45.66 4.41
936 939 2.583520 CAGGAGGCTCCTCAGCAC 59.416 66.667 33.04 4.72 45.66 4.40
937 940 2.686835 AGGAGGCTCCTCAGCACC 60.687 66.667 30.46 3.01 45.66 5.01
938 941 3.251137 AGGAGGCTCCTCAGCACCT 62.251 63.158 30.46 6.00 45.66 4.00
942 945 3.715097 GCTCCTCAGCACCTGCCT 61.715 66.667 0.00 0.00 46.06 4.75
943 946 2.583520 CTCCTCAGCACCTGCCTC 59.416 66.667 0.00 0.00 43.38 4.70
944 947 1.988956 CTCCTCAGCACCTGCCTCT 60.989 63.158 0.00 0.00 43.38 3.69
945 948 1.958902 CTCCTCAGCACCTGCCTCTC 61.959 65.000 0.00 0.00 43.38 3.20
946 949 2.583520 CTCAGCACCTGCCTCTCC 59.416 66.667 0.00 0.00 43.38 3.71
947 950 3.368190 CTCAGCACCTGCCTCTCCG 62.368 68.421 0.00 0.00 43.38 4.63
948 951 3.699894 CAGCACCTGCCTCTCCGT 61.700 66.667 0.00 0.00 43.38 4.69
949 952 3.386237 AGCACCTGCCTCTCCGTC 61.386 66.667 0.00 0.00 43.38 4.79
950 953 4.803426 GCACCTGCCTCTCCGTCG 62.803 72.222 0.00 0.00 34.31 5.12
951 954 4.803426 CACCTGCCTCTCCGTCGC 62.803 72.222 0.00 0.00 0.00 5.19
1070 1073 2.282251 TCCGGCACTCGTCTCAGT 60.282 61.111 0.00 0.00 37.11 3.41
1342 1345 0.251121 TGATGGCGAACATGGTGGTT 60.251 50.000 0.00 0.00 40.72 3.67
1377 1380 5.212745 CTGATCCTCTTTCCTTACCTAGGT 58.787 45.833 20.57 20.57 45.03 3.08
1382 1385 4.326291 CCTCTTTCCTTACCTAGGTCCTCT 60.326 50.000 20.32 0.00 45.03 3.69
1402 1405 1.529226 TACAACATCACCCGCCAAAG 58.471 50.000 0.00 0.00 0.00 2.77
1428 1437 9.174166 GAAAACTACATGGTGGTGAATAATAGT 57.826 33.333 0.00 0.00 0.00 2.12
1470 1479 5.927115 AGAAGTTCAGAACTCGTGGTATTTC 59.073 40.000 16.44 6.96 41.91 2.17
1499 1512 9.992442 TTAGTTTTGGTGGGAATATATAACCAA 57.008 29.630 10.61 10.61 46.43 3.67
2659 2720 1.693467 TTGTCAGCGACGTGTATGTC 58.307 50.000 0.00 0.00 34.95 3.06
2958 3068 6.597562 ACTTTGTGTGACCAGTTAGGAATTA 58.402 36.000 0.00 0.00 41.22 1.40
3195 3311 2.430465 GAAGCAGCTGTGAATCTGGAA 58.570 47.619 16.64 0.00 0.00 3.53
3362 3497 5.803967 GGCAAGTCTTCTCAAAATAATGCTG 59.196 40.000 0.00 0.00 0.00 4.41
3385 3527 2.291465 TGCACTTCAAGCTGCAGTTTAG 59.709 45.455 15.93 12.86 38.49 1.85
3405 3556 8.598041 AGTTTAGAGAACCTGTTGTATGATTCT 58.402 33.333 0.00 0.00 0.00 2.40
3560 3899 8.893219 TCTTATTCATGATAAATGCTCGAACT 57.107 30.769 0.00 0.00 30.07 3.01
3601 3955 0.244450 TTGTACTAAGCGGGACACGG 59.756 55.000 0.00 0.00 44.51 4.94
3626 3980 0.519077 GCTGTGTTAGTCTTGGCTGC 59.481 55.000 0.00 0.00 0.00 5.25
3629 3983 3.664107 CTGTGTTAGTCTTGGCTGCTAA 58.336 45.455 0.00 0.00 0.00 3.09
3634 3988 2.656947 AGTCTTGGCTGCTAAACCAA 57.343 45.000 0.00 0.00 43.59 3.67
3637 3991 2.819608 GTCTTGGCTGCTAAACCAATCA 59.180 45.455 0.00 0.00 44.67 2.57
3724 4101 6.144563 GCTTCAGTTTCAGTGGCTTTTATTTC 59.855 38.462 0.00 0.00 0.00 2.17
3730 4107 9.098355 AGTTTCAGTGGCTTTTATTTCTTTTTC 57.902 29.630 0.00 0.00 0.00 2.29
3731 4108 8.335356 GTTTCAGTGGCTTTTATTTCTTTTTCC 58.665 33.333 0.00 0.00 0.00 3.13
3775 4152 7.226918 GTGGCTTCAGTTTCTTTTACTTCTACT 59.773 37.037 0.00 0.00 0.00 2.57
3790 4226 6.328641 ACTTCTACTGTTGACTAATGTCGT 57.671 37.500 0.00 0.00 45.70 4.34
3833 4269 4.240323 AGGTAGAAGAAGAGGTTTTGGGA 58.760 43.478 0.00 0.00 0.00 4.37
3837 4273 2.978156 AGAAGAGGTTTTGGGATGCA 57.022 45.000 0.00 0.00 0.00 3.96
4037 4606 2.020720 TGAAGTTTCTGAAGCCGCAAA 58.979 42.857 0.32 0.00 0.00 3.68
4090 4660 0.586802 GTTTCGACAGGTTCACAGGC 59.413 55.000 0.00 0.00 0.00 4.85
4117 4687 6.500684 AACTGCTTGTTGAATGATACGAAT 57.499 33.333 0.00 0.00 37.52 3.34
4118 4688 7.609760 AACTGCTTGTTGAATGATACGAATA 57.390 32.000 0.00 0.00 37.52 1.75
4142 5318 2.050144 TCAGAATGATAGGAGCACCCC 58.950 52.381 0.00 0.00 42.56 4.95
4161 5337 3.490890 GCACAAGGCGATCCTGAC 58.509 61.111 0.00 0.00 43.40 3.51
4179 5355 4.433805 CCTGACGTGTAAACATAACTTCGC 60.434 45.833 0.00 0.00 0.00 4.70
4182 5358 4.953269 ACGTGTAAACATAACTTCGCATG 58.047 39.130 0.00 0.00 0.00 4.06
4199 5375 3.367607 GCATGTTTCGTGCTTGTTTGTA 58.632 40.909 6.68 0.00 42.44 2.41
4232 7104 9.034800 ACCACAAGATGACCATTTTTAATATGT 57.965 29.630 0.00 0.00 0.00 2.29
4256 7128 8.865978 TGTACGATGAACATGTTCTAAATACAC 58.134 33.333 32.57 22.00 40.14 2.90
4323 7195 9.039870 TGAACATTTTTAAAACACATGATGGAC 57.960 29.630 14.94 8.11 0.00 4.02
4337 7210 5.066375 ACATGATGGACATTTGGAATACACG 59.934 40.000 0.00 0.00 37.07 4.49
4377 7252 6.646653 ACACGATGAGCATATACGATGAAATT 59.353 34.615 0.00 0.00 0.00 1.82
4475 7350 7.542477 ACACAACGAACATTTTTCAAATACACA 59.458 29.630 0.00 0.00 0.00 3.72
4479 7354 8.641499 ACGAACATTTTTCAAATACACAATGT 57.359 26.923 0.00 0.00 36.61 2.71
4480 7355 8.538856 ACGAACATTTTTCAAATACACAATGTG 58.461 29.630 12.40 12.40 35.53 3.21
4482 7357 9.848172 GAACATTTTTCAAATACACAATGTGTC 57.152 29.630 23.34 0.00 43.92 3.67
4483 7358 8.060020 ACATTTTTCAAATACACAATGTGTCG 57.940 30.769 23.34 10.16 43.92 4.35
4484 7359 6.503616 TTTTTCAAATACACAATGTGTCGC 57.496 33.333 23.34 0.00 43.92 5.19
4485 7360 3.822594 TCAAATACACAATGTGTCGCC 57.177 42.857 23.34 0.00 43.92 5.54
4486 7361 3.407698 TCAAATACACAATGTGTCGCCT 58.592 40.909 23.34 3.49 43.92 5.52
4487 7362 3.435327 TCAAATACACAATGTGTCGCCTC 59.565 43.478 23.34 0.00 43.92 4.70
4488 7363 2.024176 ATACACAATGTGTCGCCTCC 57.976 50.000 23.34 0.00 43.92 4.30
4489 7364 0.036765 TACACAATGTGTCGCCTCCC 60.037 55.000 23.34 0.00 43.92 4.30
4490 7365 2.040544 CACAATGTGTCGCCTCCCC 61.041 63.158 5.00 0.00 0.00 4.81
4491 7366 2.819595 CAATGTGTCGCCTCCCCG 60.820 66.667 0.00 0.00 0.00 5.73
4492 7367 4.778143 AATGTGTCGCCTCCCCGC 62.778 66.667 0.00 0.00 0.00 6.13
4515 7390 4.676951 CCCGGGAGCCAAAAGGCA 62.677 66.667 18.48 0.00 37.35 4.75
4516 7391 3.064324 CCGGGAGCCAAAAGGCAG 61.064 66.667 9.42 0.00 37.35 4.85
4517 7392 3.752339 CGGGAGCCAAAAGGCAGC 61.752 66.667 9.42 0.21 37.35 5.25
4518 7393 3.752339 GGGAGCCAAAAGGCAGCG 61.752 66.667 9.42 0.00 37.35 5.18
4519 7394 4.426112 GGAGCCAAAAGGCAGCGC 62.426 66.667 9.42 0.00 37.35 5.92
4558 7433 4.559063 CTGCCCTCCCCATCGCTG 62.559 72.222 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 178 3.117813 TCCGGGTGAAATCGGGATTTTAT 60.118 43.478 0.00 0.00 45.69 1.40
276 279 1.403814 GAGTCCCGGATGAGATCACA 58.596 55.000 0.73 0.00 0.00 3.58
496 499 4.865925 CGATGACAAAGGGAACAACGTATA 59.134 41.667 0.00 0.00 0.00 1.47
734 737 7.283354 AGGAAAGTCGAAAGTCTTCTGATTTTT 59.717 33.333 8.13 5.02 38.50 1.94
735 738 6.768381 AGGAAAGTCGAAAGTCTTCTGATTTT 59.232 34.615 7.02 7.02 38.50 1.82
736 739 6.292150 AGGAAAGTCGAAAGTCTTCTGATTT 58.708 36.000 0.00 0.00 38.50 2.17
737 740 5.859495 AGGAAAGTCGAAAGTCTTCTGATT 58.141 37.500 0.00 0.00 38.50 2.57
738 741 5.245075 AGAGGAAAGTCGAAAGTCTTCTGAT 59.755 40.000 4.85 0.00 38.50 2.90
739 742 4.585162 AGAGGAAAGTCGAAAGTCTTCTGA 59.415 41.667 4.85 0.00 38.50 3.27
740 743 4.683781 CAGAGGAAAGTCGAAAGTCTTCTG 59.316 45.833 14.23 14.23 38.50 3.02
741 744 4.797933 GCAGAGGAAAGTCGAAAGTCTTCT 60.798 45.833 0.00 0.00 38.50 2.85
742 745 3.430556 GCAGAGGAAAGTCGAAAGTCTTC 59.569 47.826 0.00 0.00 38.50 2.87
743 746 3.394719 GCAGAGGAAAGTCGAAAGTCTT 58.605 45.455 0.00 0.00 41.13 3.01
744 747 2.289133 GGCAGAGGAAAGTCGAAAGTCT 60.289 50.000 0.00 0.00 0.00 3.24
745 748 2.070028 GGCAGAGGAAAGTCGAAAGTC 58.930 52.381 0.00 0.00 0.00 3.01
746 749 1.694696 AGGCAGAGGAAAGTCGAAAGT 59.305 47.619 0.00 0.00 0.00 2.66
747 750 2.464157 AGGCAGAGGAAAGTCGAAAG 57.536 50.000 0.00 0.00 0.00 2.62
748 751 4.439700 CGTATAGGCAGAGGAAAGTCGAAA 60.440 45.833 0.00 0.00 0.00 3.46
749 752 3.066342 CGTATAGGCAGAGGAAAGTCGAA 59.934 47.826 0.00 0.00 0.00 3.71
750 753 2.617308 CGTATAGGCAGAGGAAAGTCGA 59.383 50.000 0.00 0.00 0.00 4.20
751 754 2.617308 TCGTATAGGCAGAGGAAAGTCG 59.383 50.000 0.00 0.00 0.00 4.18
752 755 4.551388 CATCGTATAGGCAGAGGAAAGTC 58.449 47.826 0.00 0.00 0.00 3.01
753 756 3.322254 CCATCGTATAGGCAGAGGAAAGT 59.678 47.826 0.00 0.00 0.00 2.66
754 757 3.574396 TCCATCGTATAGGCAGAGGAAAG 59.426 47.826 0.00 0.00 0.00 2.62
755 758 3.321111 GTCCATCGTATAGGCAGAGGAAA 59.679 47.826 0.00 0.00 0.00 3.13
756 759 2.891580 GTCCATCGTATAGGCAGAGGAA 59.108 50.000 0.00 0.00 0.00 3.36
757 760 2.515854 GTCCATCGTATAGGCAGAGGA 58.484 52.381 0.00 0.00 0.00 3.71
758 761 1.546476 GGTCCATCGTATAGGCAGAGG 59.454 57.143 0.00 0.00 0.00 3.69
759 762 1.200252 CGGTCCATCGTATAGGCAGAG 59.800 57.143 0.00 0.00 0.00 3.35
760 763 1.244816 CGGTCCATCGTATAGGCAGA 58.755 55.000 0.00 0.00 0.00 4.26
761 764 0.243907 CCGGTCCATCGTATAGGCAG 59.756 60.000 0.00 0.00 0.00 4.85
762 765 0.178984 TCCGGTCCATCGTATAGGCA 60.179 55.000 0.00 0.00 0.00 4.75
763 766 0.526662 CTCCGGTCCATCGTATAGGC 59.473 60.000 0.00 0.00 0.00 3.93
764 767 2.195741 TCTCCGGTCCATCGTATAGG 57.804 55.000 0.00 0.00 0.00 2.57
765 768 3.819337 TCTTTCTCCGGTCCATCGTATAG 59.181 47.826 0.00 0.00 0.00 1.31
766 769 3.824133 TCTTTCTCCGGTCCATCGTATA 58.176 45.455 0.00 0.00 0.00 1.47
767 770 2.662866 TCTTTCTCCGGTCCATCGTAT 58.337 47.619 0.00 0.00 0.00 3.06
768 771 2.133281 TCTTTCTCCGGTCCATCGTA 57.867 50.000 0.00 0.00 0.00 3.43
769 772 1.263356 TTCTTTCTCCGGTCCATCGT 58.737 50.000 0.00 0.00 0.00 3.73
770 773 2.380084 TTTCTTTCTCCGGTCCATCG 57.620 50.000 0.00 0.00 0.00 3.84
771 774 3.873910 TGATTTCTTTCTCCGGTCCATC 58.126 45.455 0.00 0.00 0.00 3.51
772 775 4.202441 CATGATTTCTTTCTCCGGTCCAT 58.798 43.478 0.00 0.00 0.00 3.41
773 776 3.609853 CATGATTTCTTTCTCCGGTCCA 58.390 45.455 0.00 0.00 0.00 4.02
774 777 2.945668 CCATGATTTCTTTCTCCGGTCC 59.054 50.000 0.00 0.00 0.00 4.46
775 778 2.356069 GCCATGATTTCTTTCTCCGGTC 59.644 50.000 0.00 0.00 0.00 4.79
776 779 2.369394 GCCATGATTTCTTTCTCCGGT 58.631 47.619 0.00 0.00 0.00 5.28
777 780 1.678101 GGCCATGATTTCTTTCTCCGG 59.322 52.381 0.00 0.00 0.00 5.14
778 781 1.678101 GGGCCATGATTTCTTTCTCCG 59.322 52.381 4.39 0.00 0.00 4.63
779 782 2.692041 CTGGGCCATGATTTCTTTCTCC 59.308 50.000 6.72 0.00 0.00 3.71
780 783 3.359950 ACTGGGCCATGATTTCTTTCTC 58.640 45.455 6.72 0.00 0.00 2.87
781 784 3.463048 ACTGGGCCATGATTTCTTTCT 57.537 42.857 6.72 0.00 0.00 2.52
782 785 4.462483 TGTTACTGGGCCATGATTTCTTTC 59.538 41.667 6.72 0.00 0.00 2.62
783 786 4.220602 GTGTTACTGGGCCATGATTTCTTT 59.779 41.667 6.72 0.00 0.00 2.52
784 787 3.763897 GTGTTACTGGGCCATGATTTCTT 59.236 43.478 6.72 0.00 0.00 2.52
785 788 3.010584 AGTGTTACTGGGCCATGATTTCT 59.989 43.478 6.72 0.00 0.00 2.52
786 789 3.356290 AGTGTTACTGGGCCATGATTTC 58.644 45.455 6.72 0.00 0.00 2.17
787 790 3.456380 AGTGTTACTGGGCCATGATTT 57.544 42.857 6.72 0.00 0.00 2.17
788 791 3.456380 AAGTGTTACTGGGCCATGATT 57.544 42.857 6.72 0.00 0.00 2.57
789 792 3.091545 CAAAGTGTTACTGGGCCATGAT 58.908 45.455 6.72 0.00 0.00 2.45
790 793 2.107378 TCAAAGTGTTACTGGGCCATGA 59.893 45.455 6.72 0.76 0.00 3.07
791 794 2.228822 GTCAAAGTGTTACTGGGCCATG 59.771 50.000 6.72 3.79 0.00 3.66
792 795 2.514803 GTCAAAGTGTTACTGGGCCAT 58.485 47.619 6.72 0.00 0.00 4.40
793 796 1.477923 GGTCAAAGTGTTACTGGGCCA 60.478 52.381 5.85 5.85 30.94 5.36
794 797 1.244816 GGTCAAAGTGTTACTGGGCC 58.755 55.000 0.00 0.00 0.00 5.80
795 798 1.244816 GGGTCAAAGTGTTACTGGGC 58.755 55.000 0.00 0.00 0.00 5.36
796 799 2.649531 TGGGTCAAAGTGTTACTGGG 57.350 50.000 0.00 0.00 0.00 4.45
797 800 5.067273 TGTTATGGGTCAAAGTGTTACTGG 58.933 41.667 0.00 0.00 0.00 4.00
798 801 6.435428 GTTGTTATGGGTCAAAGTGTTACTG 58.565 40.000 0.00 0.00 0.00 2.74
799 802 5.533528 GGTTGTTATGGGTCAAAGTGTTACT 59.466 40.000 0.00 0.00 0.00 2.24
800 803 5.278610 GGGTTGTTATGGGTCAAAGTGTTAC 60.279 44.000 0.00 0.00 0.00 2.50
801 804 4.828387 GGGTTGTTATGGGTCAAAGTGTTA 59.172 41.667 0.00 0.00 0.00 2.41
802 805 3.639561 GGGTTGTTATGGGTCAAAGTGTT 59.360 43.478 0.00 0.00 0.00 3.32
803 806 3.227614 GGGTTGTTATGGGTCAAAGTGT 58.772 45.455 0.00 0.00 0.00 3.55
804 807 3.005367 GTGGGTTGTTATGGGTCAAAGTG 59.995 47.826 0.00 0.00 0.00 3.16
805 808 3.227614 GTGGGTTGTTATGGGTCAAAGT 58.772 45.455 0.00 0.00 0.00 2.66
806 809 2.227865 CGTGGGTTGTTATGGGTCAAAG 59.772 50.000 0.00 0.00 0.00 2.77
807 810 2.231529 CGTGGGTTGTTATGGGTCAAA 58.768 47.619 0.00 0.00 0.00 2.69
808 811 1.898902 CGTGGGTTGTTATGGGTCAA 58.101 50.000 0.00 0.00 0.00 3.18
809 812 0.606944 GCGTGGGTTGTTATGGGTCA 60.607 55.000 0.00 0.00 0.00 4.02
810 813 1.310216 GGCGTGGGTTGTTATGGGTC 61.310 60.000 0.00 0.00 0.00 4.46
811 814 1.303806 GGCGTGGGTTGTTATGGGT 60.304 57.895 0.00 0.00 0.00 4.51
812 815 2.049767 GGGCGTGGGTTGTTATGGG 61.050 63.158 0.00 0.00 0.00 4.00
813 816 2.049767 GGGGCGTGGGTTGTTATGG 61.050 63.158 0.00 0.00 0.00 2.74
814 817 1.001393 AGGGGCGTGGGTTGTTATG 60.001 57.895 0.00 0.00 0.00 1.90
815 818 1.001393 CAGGGGCGTGGGTTGTTAT 60.001 57.895 0.00 0.00 0.00 1.89
816 819 2.432563 CAGGGGCGTGGGTTGTTA 59.567 61.111 0.00 0.00 0.00 2.41
907 910 3.554342 CTCCTGGGAGGATGGGCG 61.554 72.222 8.68 0.00 44.81 6.13
921 924 2.686835 AGGTGCTGAGGAGCCTCC 60.687 66.667 13.69 1.26 45.57 4.30
922 925 2.583520 CAGGTGCTGAGGAGCCTC 59.416 66.667 9.61 9.61 45.57 4.70
923 926 3.715097 GCAGGTGCTGAGGAGCCT 61.715 66.667 0.00 0.00 45.57 4.58
924 927 4.792804 GGCAGGTGCTGAGGAGCC 62.793 72.222 0.00 0.00 45.57 4.70
925 928 3.678951 GAGGCAGGTGCTGAGGAGC 62.679 68.421 1.26 0.00 46.44 4.70
926 929 1.958902 GAGAGGCAGGTGCTGAGGAG 61.959 65.000 1.26 0.00 41.70 3.69
927 930 1.986757 GAGAGGCAGGTGCTGAGGA 60.987 63.158 1.26 0.00 41.70 3.71
928 931 2.583520 GAGAGGCAGGTGCTGAGG 59.416 66.667 1.26 0.00 41.70 3.86
929 932 2.583520 GGAGAGGCAGGTGCTGAG 59.416 66.667 1.26 0.00 41.70 3.35
930 933 3.385384 CGGAGAGGCAGGTGCTGA 61.385 66.667 1.26 0.00 41.70 4.26
931 934 3.655810 GACGGAGAGGCAGGTGCTG 62.656 68.421 1.26 0.00 41.70 4.41
932 935 3.386237 GACGGAGAGGCAGGTGCT 61.386 66.667 1.26 0.00 41.70 4.40
933 936 4.803426 CGACGGAGAGGCAGGTGC 62.803 72.222 0.00 0.00 41.14 5.01
934 937 4.803426 GCGACGGAGAGGCAGGTG 62.803 72.222 0.00 0.00 0.00 4.00
1070 1073 5.886609 TGGAAAATGGTACCTCAAATCAGA 58.113 37.500 14.36 0.00 0.00 3.27
1314 1317 1.982395 TTCGCCATCACCGGAGAGT 60.982 57.895 9.46 0.00 36.15 3.24
1342 1345 3.135279 AGAGGATCAGGAGGAGGAACTA 58.865 50.000 0.00 0.00 36.25 2.24
1377 1380 1.066430 GCGGGTGATGTTGTAAGAGGA 60.066 52.381 0.00 0.00 0.00 3.71
1382 1385 1.883275 CTTTGGCGGGTGATGTTGTAA 59.117 47.619 0.00 0.00 0.00 2.41
1402 1405 9.174166 ACTATTATTCACCACCATGTAGTTTTC 57.826 33.333 0.00 0.00 0.00 2.29
1428 1437 6.869206 ACTTCTGCTTATGGTTCCTACTTA 57.131 37.500 0.00 0.00 0.00 2.24
1496 1509 6.590068 TCCCCACATAAAAATGCAATATTGG 58.410 36.000 17.02 0.00 0.00 3.16
2659 2720 2.693762 CCACGACATGGCCAGCAAG 61.694 63.158 13.05 5.49 43.24 4.01
3370 3505 3.071602 AGGTTCTCTAAACTGCAGCTTGA 59.928 43.478 15.27 6.99 29.02 3.02
3385 3527 6.173339 TCCAAGAATCATACAACAGGTTCTC 58.827 40.000 0.00 0.00 0.00 2.87
3405 3556 7.458397 AGGTTCACTAGTGACAATTAATCCAA 58.542 34.615 25.13 3.21 39.66 3.53
3459 3610 3.515901 ACACCTTATCCTCCTCAACTCAC 59.484 47.826 0.00 0.00 0.00 3.51
3513 3852 8.924511 AAGAAATATCCACGATATCCATTTGT 57.075 30.769 0.00 0.00 34.57 2.83
3601 3955 0.037232 AAGACTAACACAGCGGAGGC 60.037 55.000 0.00 0.00 40.37 4.70
3626 3980 9.132521 CAAGAAAATACAGCTTGATTGGTTTAG 57.867 33.333 0.00 0.00 41.03 1.85
3629 3983 6.925165 CACAAGAAAATACAGCTTGATTGGTT 59.075 34.615 0.00 0.00 41.03 3.67
3634 3988 6.016024 TGCTTCACAAGAAAATACAGCTTGAT 60.016 34.615 0.00 0.00 41.03 2.57
3637 3991 5.278660 CCTGCTTCACAAGAAAATACAGCTT 60.279 40.000 0.00 0.00 32.35 3.74
3692 4069 3.876914 CCACTGAAACTGAAGCACTTACA 59.123 43.478 0.00 0.00 0.00 2.41
3694 4071 2.878406 GCCACTGAAACTGAAGCACTTA 59.122 45.455 0.00 0.00 0.00 2.24
3724 4101 5.009610 TGAAACTGAATTCCCTCGGAAAAAG 59.990 40.000 2.27 0.00 45.41 2.27
3730 4107 2.744202 CACTGAAACTGAATTCCCTCGG 59.256 50.000 2.27 2.25 0.00 4.63
3731 4108 2.744202 CCACTGAAACTGAATTCCCTCG 59.256 50.000 2.27 0.00 0.00 4.63
3775 4152 5.968848 GCTTTGAAAACGACATTAGTCAACA 59.031 36.000 0.00 0.00 45.23 3.33
3790 4226 5.355910 ACCTCTCGTACTTTTGCTTTGAAAA 59.644 36.000 0.00 0.00 0.00 2.29
3833 4269 1.174712 AGCCGCAGAAGTTTGTGCAT 61.175 50.000 13.42 0.00 46.66 3.96
3837 4273 2.024414 AGAAAAGCCGCAGAAGTTTGT 58.976 42.857 0.00 0.00 0.00 2.83
3879 4315 7.229306 AGTCAATGAAGTTTCTGTAATCTGCAA 59.771 33.333 0.00 0.00 0.00 4.08
3895 4338 2.225019 GGATGGCGCATAGTCAATGAAG 59.775 50.000 10.83 0.00 38.34 3.02
3896 4339 2.158769 AGGATGGCGCATAGTCAATGAA 60.159 45.455 10.83 0.00 38.34 2.57
3897 4340 1.417517 AGGATGGCGCATAGTCAATGA 59.582 47.619 10.83 0.00 38.34 2.57
3898 4341 1.802960 GAGGATGGCGCATAGTCAATG 59.197 52.381 10.83 0.00 38.34 2.82
3900 4343 0.829990 TGAGGATGGCGCATAGTCAA 59.170 50.000 10.83 0.00 38.34 3.18
4037 4606 7.605449 CCACTGATCAATGTTGGAAATAAACT 58.395 34.615 3.12 0.00 0.00 2.66
4090 4660 7.518161 TCGTATCATTCAACAAGCAGTTTAAG 58.482 34.615 0.00 0.00 38.74 1.85
4117 4687 5.163301 GGGTGCTCCTATCATTCTGAAGTTA 60.163 44.000 4.53 0.00 0.00 2.24
4118 4688 4.384647 GGGTGCTCCTATCATTCTGAAGTT 60.385 45.833 4.53 0.00 0.00 2.66
4142 5318 1.078918 TCAGGATCGCCTTGTGCTG 60.079 57.895 0.00 0.00 43.90 4.41
4161 5337 4.953269 ACATGCGAAGTTATGTTTACACG 58.047 39.130 0.00 0.00 34.79 4.49
4179 5355 4.616802 GGATACAAACAAGCACGAAACATG 59.383 41.667 0.00 0.00 0.00 3.21
4199 5375 1.340405 GGTCATCTTGTGGTGCTGGAT 60.340 52.381 0.00 0.00 0.00 3.41
4232 7104 8.035984 TGGTGTATTTAGAACATGTTCATCGTA 58.964 33.333 33.92 20.34 41.84 3.43
4323 7195 5.818136 AATGTCCTCGTGTATTCCAAATG 57.182 39.130 0.00 0.00 0.00 2.32
4328 7201 6.035758 GTCTTACAAATGTCCTCGTGTATTCC 59.964 42.308 0.00 0.00 0.00 3.01
4337 7210 5.168569 TCATCGTGTCTTACAAATGTCCTC 58.831 41.667 0.00 0.00 30.17 3.71
4388 7263 9.681692 CATCTGTACTTCAAAAATGTTCATCAA 57.318 29.630 0.00 0.00 0.00 2.57
4403 7278 9.950680 TGTCTTCAAATTTTTCATCTGTACTTC 57.049 29.630 0.00 0.00 0.00 3.01
4445 7320 8.918961 ATTTGAAAAATGTTCGTTGTGTCTTA 57.081 26.923 0.00 0.00 0.00 2.10
4475 7350 4.778143 GCGGGGAGGCGACACATT 62.778 66.667 0.00 0.00 0.00 2.71
4541 7416 4.559063 CAGCGATGGGGAGGGCAG 62.559 72.222 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.