Multiple sequence alignment - TraesCS1B01G266300

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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 TraesCS1B01G266300 chr1B 100.000 2873 0 0 1 2873 468259486 468256614 0.000000e+00 5306.0
1 TraesCS1B01G266300 chr1A 94.648 1476 52 9 810 2275 447749161 447747703 0.000000e+00 2263.0
2 TraesCS1B01G266300 chr1A 85.613 563 67 9 21 571 447750167 447749607 1.920000e-161 579.0
3 TraesCS1B01G266300 chr1A 89.199 287 23 5 2335 2614 447746987 447746702 4.550000e-93 351.0
4 TraesCS1B01G266300 chr1D 95.873 1381 47 7 806 2182 347301904 347300530 0.000000e+00 2226.0
5 TraesCS1B01G266300 chr1D 80.531 678 114 12 93 754 415528611 415527936 3.300000e-139 505.0
6 TraesCS1B01G266300 chr1D 85.784 408 36 10 2223 2614 347300529 347300128 2.060000e-111 412.0
7 TraesCS1B01G266300 chr1D 94.737 114 6 0 2760 2873 347300130 347300017 8.180000e-41 178.0
8 TraesCS1B01G266300 chr1D 87.671 73 9 0 2633 2705 420947657 420947729 5.100000e-13 86.1
9 TraesCS1B01G266300 chr4D 82.138 739 115 12 1 724 342831031 342830295 4.070000e-173 617.0
10 TraesCS1B01G266300 chr4D 82.192 657 101 13 1 643 491000712 491001366 4.180000e-153 551.0
11 TraesCS1B01G266300 chr3A 81.429 770 121 18 1 754 500998468 500997705 6.810000e-171 610.0
12 TraesCS1B01G266300 chr3A 80.111 719 119 15 1 697 349156073 349156789 5.490000e-142 514.0
13 TraesCS1B01G266300 chr5B 81.150 748 132 8 1 741 17976652 17975907 2.470000e-165 592.0
14 TraesCS1B01G266300 chr5B 87.324 71 9 0 2637 2707 27812327 27812397 6.600000e-12 82.4
15 TraesCS1B01G266300 chr5A 79.216 765 140 16 1 748 659170706 659171468 5.490000e-142 514.0
16 TraesCS1B01G266300 chr4B 79.447 759 124 25 1 736 563828279 563827530 2.550000e-140 508.0
17 TraesCS1B01G266300 chr4B 100.000 28 0 0 2611 2638 466724536 466724563 5.000000e-03 52.8
18 TraesCS1B01G266300 chr3B 84.444 90 14 0 2633 2722 94874392 94874303 3.940000e-14 89.8
19 TraesCS1B01G266300 chr3B 82.979 94 14 2 2634 2726 16209619 16209527 1.830000e-12 84.2
20 TraesCS1B01G266300 chr3B 80.435 92 16 2 2633 2723 27265714 27265804 5.140000e-08 69.4
21 TraesCS1B01G266300 chr5D 82.979 94 16 0 2633 2726 7054512 7054419 5.100000e-13 86.1
22 TraesCS1B01G266300 chr2B 87.838 74 7 2 2633 2705 784931709 784931781 5.100000e-13 86.1
23 TraesCS1B01G266300 chr7A 82.609 92 14 2 2633 2723 89933890 89933800 2.370000e-11 80.5
24 TraesCS1B01G266300 chr2A 84.932 73 11 0 2633 2705 652160631 652160703 1.100000e-09 75.0
25 TraesCS1B01G266300 chr7B 100.000 31 0 0 2610 2640 223705608 223705578 1.110000e-04 58.4


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 TraesCS1B01G266300 chr1B 468256614 468259486 2872 True 5306.000000 5306 100.000000 1 2873 1 chr1B.!!$R1 2872
1 TraesCS1B01G266300 chr1A 447746702 447750167 3465 True 1064.333333 2263 89.820000 21 2614 3 chr1A.!!$R1 2593
2 TraesCS1B01G266300 chr1D 347300017 347301904 1887 True 938.666667 2226 92.131333 806 2873 3 chr1D.!!$R2 2067
3 TraesCS1B01G266300 chr1D 415527936 415528611 675 True 505.000000 505 80.531000 93 754 1 chr1D.!!$R1 661
4 TraesCS1B01G266300 chr4D 342830295 342831031 736 True 617.000000 617 82.138000 1 724 1 chr4D.!!$R1 723
5 TraesCS1B01G266300 chr4D 491000712 491001366 654 False 551.000000 551 82.192000 1 643 1 chr4D.!!$F1 642
6 TraesCS1B01G266300 chr3A 500997705 500998468 763 True 610.000000 610 81.429000 1 754 1 chr3A.!!$R1 753
7 TraesCS1B01G266300 chr3A 349156073 349156789 716 False 514.000000 514 80.111000 1 697 1 chr3A.!!$F1 696
8 TraesCS1B01G266300 chr5B 17975907 17976652 745 True 592.000000 592 81.150000 1 741 1 chr5B.!!$R1 740
9 TraesCS1B01G266300 chr5A 659170706 659171468 762 False 514.000000 514 79.216000 1 748 1 chr5A.!!$F1 747
10 TraesCS1B01G266300 chr4B 563827530 563828279 749 True 508.000000 508 79.447000 1 736 1 chr4B.!!$R1 735

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
580 774 0.037326 GTCTGACAAGTGATCCGGCA 60.037 55.0 2.24 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 3358 0.713883 CGGTTCGGTCGTCAAATCAG 59.286 55.0 0.0 0.0 0.0 2.9 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
40 41 4.462483 GCCAAAGGATAACCATCAAGTCAA 59.538 41.667 0.00 0.00 38.94 3.18
102 105 2.006888 CGGCTACAAAATGTCGTCCAT 58.993 47.619 0.00 0.00 34.36 3.41
185 190 0.453390 GCGCAAAAGAAGAGGATGGG 59.547 55.000 0.30 0.00 0.00 4.00
186 191 0.453390 CGCAAAAGAAGAGGATGGGC 59.547 55.000 0.00 0.00 0.00 5.36
212 217 0.461961 CGGAAGAGGGCGAAGAAGAT 59.538 55.000 0.00 0.00 0.00 2.40
227 232 6.857964 GCGAAGAAGATGTTGAAAATTGAGAA 59.142 34.615 0.00 0.00 0.00 2.87
270 275 4.558538 GCAAGAGGCGTTGATCAAATAT 57.441 40.909 10.35 0.00 0.00 1.28
356 362 1.673168 GATGCAGGGGATGTGAAGAC 58.327 55.000 0.00 0.00 0.00 3.01
363 369 3.054434 CAGGGGATGTGAAGACCATGTTA 60.054 47.826 0.00 0.00 30.71 2.41
388 394 3.146847 GACGAAACCCTTTTGGATGAGT 58.853 45.455 0.00 0.00 44.07 3.41
407 416 2.821969 AGTATGCAAAGAAGTGGCTTGG 59.178 45.455 0.00 0.00 0.00 3.61
423 435 5.250774 GTGGCTTGGGGATAATAAGGAGATA 59.749 44.000 0.00 0.00 0.00 1.98
564 584 2.672996 GCGGCATTGGTGGTGTCT 60.673 61.111 0.00 0.00 0.00 3.41
580 774 0.037326 GTCTGACAAGTGATCCGGCA 60.037 55.000 2.24 0.00 0.00 5.69
585 779 0.957395 ACAAGTGATCCGGCAAGCAG 60.957 55.000 0.00 0.00 0.00 4.24
621 819 7.800155 TGCTCGGACATGAATATAATTTTGA 57.200 32.000 0.00 0.00 0.00 2.69
665 879 9.912634 ACTATGATTGTTTCATTTGTTTCGAAT 57.087 25.926 0.00 0.00 42.62 3.34
699 913 8.827177 ACGGATAATTTGTATCGTATGATTGT 57.173 30.769 2.02 0.00 35.99 2.71
706 920 7.440541 TTTGTATCGTATGATTGTCGTGTAC 57.559 36.000 2.02 0.00 35.99 2.90
736 951 5.290158 GCATGAATTTGAAGATCGCATTTGT 59.710 36.000 0.00 0.00 0.00 2.83
748 963 7.750229 AGATCGCATTTGTGGTATATGAATT 57.250 32.000 0.00 0.00 0.00 2.17
751 966 7.094508 TCGCATTTGTGGTATATGAATTTGT 57.905 32.000 0.00 0.00 0.00 2.83
754 969 6.479660 GCATTTGTGGTATATGAATTTGTGGG 59.520 38.462 0.00 0.00 0.00 4.61
759 974 8.458573 TGTGGTATATGAATTTGTGGGAATAC 57.541 34.615 0.00 0.00 0.00 1.89
764 979 3.616219 TGAATTTGTGGGAATACGAGGG 58.384 45.455 0.00 0.00 0.00 4.30
765 980 2.729028 ATTTGTGGGAATACGAGGGG 57.271 50.000 0.00 0.00 0.00 4.79
766 981 1.364269 TTTGTGGGAATACGAGGGGT 58.636 50.000 0.00 0.00 0.00 4.95
767 982 0.616371 TTGTGGGAATACGAGGGGTG 59.384 55.000 0.00 0.00 0.00 4.61
768 983 0.252330 TGTGGGAATACGAGGGGTGA 60.252 55.000 0.00 0.00 0.00 4.02
770 985 1.335132 TGGGAATACGAGGGGTGAGC 61.335 60.000 0.00 0.00 0.00 4.26
771 986 1.067582 GGAATACGAGGGGTGAGCG 59.932 63.158 0.00 0.00 0.00 5.03
772 987 1.067582 GAATACGAGGGGTGAGCGG 59.932 63.158 0.00 0.00 0.00 5.52
773 988 1.673808 GAATACGAGGGGTGAGCGGT 61.674 60.000 0.00 0.00 0.00 5.68
774 989 1.262640 AATACGAGGGGTGAGCGGTT 61.263 55.000 0.00 0.00 0.00 4.44
776 991 1.315257 TACGAGGGGTGAGCGGTTAC 61.315 60.000 0.13 0.13 0.00 2.50
777 992 2.348888 CGAGGGGTGAGCGGTTACT 61.349 63.158 9.50 0.00 0.00 2.24
778 993 1.218316 GAGGGGTGAGCGGTTACTG 59.782 63.158 9.50 0.00 0.00 2.74
779 994 1.535687 AGGGGTGAGCGGTTACTGT 60.536 57.895 9.50 0.00 0.00 3.55
780 995 1.079336 GGGGTGAGCGGTTACTGTC 60.079 63.158 9.50 0.37 0.00 3.51
781 996 1.079336 GGGTGAGCGGTTACTGTCC 60.079 63.158 9.50 0.00 0.00 4.02
782 997 1.669440 GGTGAGCGGTTACTGTCCA 59.331 57.895 9.50 0.00 0.00 4.02
783 998 0.669625 GGTGAGCGGTTACTGTCCAC 60.670 60.000 9.50 0.77 0.00 4.02
786 1001 1.139256 TGAGCGGTTACTGTCCACAAA 59.861 47.619 0.00 0.00 0.00 2.83
787 1002 1.529865 GAGCGGTTACTGTCCACAAAC 59.470 52.381 0.00 0.00 0.00 2.93
788 1003 0.233848 GCGGTTACTGTCCACAAACG 59.766 55.000 0.00 0.00 0.00 3.60
789 1004 0.233848 CGGTTACTGTCCACAAACGC 59.766 55.000 0.00 0.00 0.00 4.84
793 1008 2.400269 TACTGTCCACAAACGCCCCC 62.400 60.000 0.00 0.00 0.00 5.40
794 1009 3.491598 CTGTCCACAAACGCCCCCT 62.492 63.158 0.00 0.00 0.00 4.79
795 1010 2.983592 GTCCACAAACGCCCCCTG 60.984 66.667 0.00 0.00 0.00 4.45
796 1011 3.172106 TCCACAAACGCCCCCTGA 61.172 61.111 0.00 0.00 0.00 3.86
797 1012 2.983592 CCACAAACGCCCCCTGAC 60.984 66.667 0.00 0.00 0.00 3.51
798 1013 2.203280 CACAAACGCCCCCTGACA 60.203 61.111 0.00 0.00 0.00 3.58
799 1014 1.826054 CACAAACGCCCCCTGACAA 60.826 57.895 0.00 0.00 0.00 3.18
800 1015 1.528309 ACAAACGCCCCCTGACAAG 60.528 57.895 0.00 0.00 0.00 3.16
801 1016 1.528309 CAAACGCCCCCTGACAAGT 60.528 57.895 0.00 0.00 0.00 3.16
802 1017 1.228154 AAACGCCCCCTGACAAGTC 60.228 57.895 0.00 0.00 0.00 3.01
803 1018 2.692273 AAACGCCCCCTGACAAGTCC 62.692 60.000 0.00 0.00 0.00 3.85
804 1019 3.322466 CGCCCCCTGACAAGTCCT 61.322 66.667 0.00 0.00 0.00 3.85
822 1066 3.107601 TCCTCTCAGGATCCACGATTTT 58.892 45.455 15.82 0.00 40.06 1.82
832 1076 1.202758 TCCACGATTTTGACTGTGCCT 60.203 47.619 0.00 0.00 0.00 4.75
834 1078 2.416547 CCACGATTTTGACTGTGCCTAG 59.583 50.000 0.00 0.00 0.00 3.02
837 1081 3.258372 ACGATTTTGACTGTGCCTAGAGA 59.742 43.478 0.00 0.00 0.00 3.10
905 1151 3.264897 CCCATAGACGCGCTGCAC 61.265 66.667 5.73 0.00 0.00 4.57
935 1181 8.076178 CCTCCAAAACTTTCAAGTGTGTATAAG 58.924 37.037 0.00 0.00 39.66 1.73
980 1226 1.675483 CCATCTCACTCCACTCTCTCG 59.325 57.143 0.00 0.00 0.00 4.04
1071 1317 3.157252 GCCGCCCTCCTCTCATCA 61.157 66.667 0.00 0.00 0.00 3.07
1365 1611 0.817654 CCATGTGCGACTCCTACTCA 59.182 55.000 0.00 0.00 0.00 3.41
1984 2239 0.460284 AGATTCGTGTGGATGGCGAC 60.460 55.000 0.00 0.00 34.21 5.19
2017 2273 0.876777 CCGCGTGCCGAATAATGGTA 60.877 55.000 4.92 0.00 40.02 3.25
2018 2274 0.506932 CGCGTGCCGAATAATGGTAG 59.493 55.000 0.00 0.00 40.02 3.18
2019 2275 1.578583 GCGTGCCGAATAATGGTAGT 58.421 50.000 0.00 0.00 0.00 2.73
2020 2276 2.746269 GCGTGCCGAATAATGGTAGTA 58.254 47.619 0.00 0.00 0.00 1.82
2199 2456 0.096454 GTATCGTCGTTTTGCAGCCC 59.904 55.000 0.00 0.00 0.00 5.19
2201 2458 1.169661 ATCGTCGTTTTGCAGCCCAA 61.170 50.000 0.00 0.00 0.00 4.12
2221 2478 3.599730 ATTGCTGCTTTTTAGGCTTCC 57.400 42.857 0.00 0.00 0.00 3.46
2258 2515 1.466360 GCCTCGAACAACATGCATCAC 60.466 52.381 0.00 0.00 0.00 3.06
2279 2566 6.174049 TCACGGATGTGTGGATTATTGTAAA 58.826 36.000 0.00 0.00 46.49 2.01
2280 2567 6.315144 TCACGGATGTGTGGATTATTGTAAAG 59.685 38.462 0.00 0.00 46.49 1.85
2281 2568 6.315144 CACGGATGTGTGGATTATTGTAAAGA 59.685 38.462 0.00 0.00 41.34 2.52
2282 2569 7.012327 CACGGATGTGTGGATTATTGTAAAGAT 59.988 37.037 0.00 0.00 41.34 2.40
2283 2570 7.226720 ACGGATGTGTGGATTATTGTAAAGATC 59.773 37.037 0.00 0.00 0.00 2.75
2284 2571 7.569408 CGGATGTGTGGATTATTGTAAAGATCG 60.569 40.741 0.00 0.00 0.00 3.69
2285 2572 7.226720 GGATGTGTGGATTATTGTAAAGATCGT 59.773 37.037 0.00 0.00 0.00 3.73
2286 2573 9.256477 GATGTGTGGATTATTGTAAAGATCGTA 57.744 33.333 0.00 0.00 0.00 3.43
2305 3206 4.656041 CGTAGTAGTACGCTTACTTTGCT 58.344 43.478 16.63 7.42 45.22 3.91
2364 3282 0.329596 ATCCAGAAGACAACCCTGGC 59.670 55.000 0.00 0.00 45.29 4.85
2370 3288 1.541588 GAAGACAACCCTGGCATTGAC 59.458 52.381 13.88 8.88 30.13 3.18
2371 3289 0.478072 AGACAACCCTGGCATTGACA 59.522 50.000 13.88 0.00 30.13 3.58
2372 3290 1.133513 AGACAACCCTGGCATTGACAA 60.134 47.619 13.88 0.00 30.13 3.18
2373 3291 1.686052 GACAACCCTGGCATTGACAAA 59.314 47.619 13.88 0.00 0.00 2.83
2374 3292 2.299867 GACAACCCTGGCATTGACAAAT 59.700 45.455 13.88 0.00 0.00 2.32
2375 3293 2.037511 ACAACCCTGGCATTGACAAATG 59.962 45.455 13.88 0.00 45.13 2.32
2377 3295 1.269012 CCCTGGCATTGACAAATGGT 58.731 50.000 0.00 0.00 42.98 3.55
2380 3298 1.619827 CTGGCATTGACAAATGGTGGT 59.380 47.619 0.00 0.00 42.98 4.16
2381 3299 2.824936 CTGGCATTGACAAATGGTGGTA 59.175 45.455 0.00 0.00 42.98 3.25
2385 3303 3.758554 GCATTGACAAATGGTGGTAGTCT 59.241 43.478 0.00 0.00 42.98 3.24
2396 3320 4.980573 TGGTGGTAGTCTTGCTGTAAAAT 58.019 39.130 0.00 0.00 0.00 1.82
2434 3358 3.872771 TCGACGGGTTATATTTTTCAGCC 59.127 43.478 0.00 0.00 0.00 4.85
2503 3427 4.496183 CGAACACGCAGTAAGTCTAAGATC 59.504 45.833 0.00 0.00 41.61 2.75
2514 3438 4.839668 AGTCTAAGATCGCACCTGATAC 57.160 45.455 0.00 0.00 0.00 2.24
2524 3448 0.183492 CACCTGATACCCCACCATGG 59.817 60.000 11.19 11.19 37.25 3.66
2571 3495 4.209911 CGAAGGTGGATGCGCATATATATG 59.790 45.833 25.40 17.01 36.78 1.78
2611 3537 4.380973 CGATCTGCTACAATATCATCGGGT 60.381 45.833 0.00 0.00 0.00 5.28
2614 3540 6.025749 TCTGCTACAATATCATCGGGTTAG 57.974 41.667 0.00 0.00 0.00 2.34
2615 3541 5.047306 TCTGCTACAATATCATCGGGTTAGG 60.047 44.000 0.00 0.00 0.00 2.69
2616 3542 3.933332 GCTACAATATCATCGGGTTAGGC 59.067 47.826 0.00 0.00 0.00 3.93
2617 3543 3.418684 ACAATATCATCGGGTTAGGCC 57.581 47.619 0.00 0.00 0.00 5.19
2618 3544 2.708861 ACAATATCATCGGGTTAGGCCA 59.291 45.455 5.01 0.00 39.65 5.36
2619 3545 3.137544 ACAATATCATCGGGTTAGGCCAA 59.862 43.478 5.01 0.00 39.65 4.52
2620 3546 2.922740 TATCATCGGGTTAGGCCAAC 57.077 50.000 5.01 7.55 39.65 3.77
2621 3547 1.213296 ATCATCGGGTTAGGCCAACT 58.787 50.000 5.01 0.00 39.65 3.16
2622 3548 0.539986 TCATCGGGTTAGGCCAACTC 59.460 55.000 5.01 6.69 39.65 3.01
2623 3549 0.463833 CATCGGGTTAGGCCAACTCC 60.464 60.000 5.01 9.87 39.65 3.85
2624 3550 0.912487 ATCGGGTTAGGCCAACTCCA 60.912 55.000 5.01 0.00 39.65 3.86
2625 3551 1.376812 CGGGTTAGGCCAACTCCAC 60.377 63.158 5.01 0.00 39.65 4.02
2626 3552 1.001269 GGGTTAGGCCAACTCCACC 60.001 63.158 5.01 0.61 39.65 4.61
2627 3553 1.376812 GGTTAGGCCAACTCCACCG 60.377 63.158 5.01 0.00 37.30 4.94
2628 3554 2.038837 GTTAGGCCAACTCCACCGC 61.039 63.158 5.01 0.00 34.06 5.68
2629 3555 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
2632 3558 4.752879 GCCAACTCCACCGCGCTA 62.753 66.667 5.56 0.00 0.00 4.26
2633 3559 2.813908 CCAACTCCACCGCGCTAC 60.814 66.667 5.56 0.00 0.00 3.58
2634 3560 2.813908 CAACTCCACCGCGCTACC 60.814 66.667 5.56 0.00 0.00 3.18
2635 3561 4.078516 AACTCCACCGCGCTACCC 62.079 66.667 5.56 0.00 0.00 3.69
2639 3565 4.708386 CCACCGCGCTACCCCAAA 62.708 66.667 5.56 0.00 0.00 3.28
2640 3566 2.670251 CACCGCGCTACCCCAAAA 60.670 61.111 5.56 0.00 0.00 2.44
2641 3567 2.113562 ACCGCGCTACCCCAAAAA 59.886 55.556 5.56 0.00 0.00 1.94
2642 3568 2.263021 ACCGCGCTACCCCAAAAAC 61.263 57.895 5.56 0.00 0.00 2.43
2643 3569 2.174835 CGCGCTACCCCAAAAACG 59.825 61.111 5.56 0.00 0.00 3.60
2644 3570 2.319096 CGCGCTACCCCAAAAACGA 61.319 57.895 5.56 0.00 0.00 3.85
2645 3571 1.208358 GCGCTACCCCAAAAACGAC 59.792 57.895 0.00 0.00 0.00 4.34
2646 3572 1.508808 GCGCTACCCCAAAAACGACA 61.509 55.000 0.00 0.00 0.00 4.35
2647 3573 0.236449 CGCTACCCCAAAAACGACAC 59.764 55.000 0.00 0.00 0.00 3.67
2648 3574 1.310904 GCTACCCCAAAAACGACACA 58.689 50.000 0.00 0.00 0.00 3.72
2649 3575 1.677052 GCTACCCCAAAAACGACACAA 59.323 47.619 0.00 0.00 0.00 3.33
2650 3576 2.099427 GCTACCCCAAAAACGACACAAA 59.901 45.455 0.00 0.00 0.00 2.83
2651 3577 3.243602 GCTACCCCAAAAACGACACAAAT 60.244 43.478 0.00 0.00 0.00 2.32
2652 3578 3.897141 ACCCCAAAAACGACACAAATT 57.103 38.095 0.00 0.00 0.00 1.82
2653 3579 4.209307 ACCCCAAAAACGACACAAATTT 57.791 36.364 0.00 0.00 0.00 1.82
2654 3580 3.935828 ACCCCAAAAACGACACAAATTTG 59.064 39.130 16.67 16.67 0.00 2.32
2655 3581 3.311048 CCCCAAAAACGACACAAATTTGG 59.689 43.478 21.74 12.94 46.05 3.28
2656 3582 3.242576 CCCAAAAACGACACAAATTTGGC 60.243 43.478 21.74 9.92 45.45 4.52
2657 3583 3.242576 CCAAAAACGACACAAATTTGGCC 60.243 43.478 21.74 0.00 42.31 5.36
2658 3584 2.232756 AAACGACACAAATTTGGCCC 57.767 45.000 21.74 9.04 0.00 5.80
2659 3585 1.408969 AACGACACAAATTTGGCCCT 58.591 45.000 21.74 0.00 0.00 5.19
2660 3586 0.673437 ACGACACAAATTTGGCCCTG 59.327 50.000 21.74 13.02 0.00 4.45
2661 3587 0.038343 CGACACAAATTTGGCCCTGG 60.038 55.000 21.74 6.85 0.00 4.45
2662 3588 1.337118 GACACAAATTTGGCCCTGGA 58.663 50.000 21.74 0.00 0.00 3.86
2663 3589 1.691434 GACACAAATTTGGCCCTGGAA 59.309 47.619 21.74 0.00 0.00 3.53
2664 3590 2.302733 GACACAAATTTGGCCCTGGAAT 59.697 45.455 21.74 0.00 0.00 3.01
2665 3591 2.038820 ACACAAATTTGGCCCTGGAATG 59.961 45.455 21.74 10.02 0.00 2.67
2666 3592 1.629861 ACAAATTTGGCCCTGGAATGG 59.370 47.619 21.74 0.00 0.00 3.16
2675 3601 2.309136 CCCTGGAATGGGTCAAAAGT 57.691 50.000 0.00 0.00 42.25 2.66
2676 3602 1.895131 CCCTGGAATGGGTCAAAAGTG 59.105 52.381 0.00 0.00 42.25 3.16
2677 3603 1.895131 CCTGGAATGGGTCAAAAGTGG 59.105 52.381 0.00 0.00 0.00 4.00
2678 3604 2.490718 CCTGGAATGGGTCAAAAGTGGA 60.491 50.000 0.00 0.00 0.00 4.02
2679 3605 2.558359 CTGGAATGGGTCAAAAGTGGAC 59.442 50.000 0.00 0.00 34.52 4.02
2680 3606 2.091610 TGGAATGGGTCAAAAGTGGACA 60.092 45.455 0.00 0.00 37.00 4.02
2681 3607 2.296190 GGAATGGGTCAAAAGTGGACAC 59.704 50.000 0.00 0.00 39.15 3.67
2683 3609 2.516227 TGGGTCAAAAGTGGACACAA 57.484 45.000 5.14 0.00 45.13 3.33
2684 3610 2.808919 TGGGTCAAAAGTGGACACAAA 58.191 42.857 5.14 0.00 45.13 2.83
2685 3611 3.165875 TGGGTCAAAAGTGGACACAAAA 58.834 40.909 5.14 0.00 45.13 2.44
2686 3612 3.056465 TGGGTCAAAAGTGGACACAAAAC 60.056 43.478 5.14 0.00 45.13 2.43
2687 3613 3.175929 GGTCAAAAGTGGACACAAAACG 58.824 45.455 5.14 0.00 37.00 3.60
2688 3614 3.175929 GTCAAAAGTGGACACAAAACGG 58.824 45.455 5.14 0.00 35.36 4.44
2689 3615 3.082548 TCAAAAGTGGACACAAAACGGA 58.917 40.909 5.14 0.00 0.00 4.69
2690 3616 3.697045 TCAAAAGTGGACACAAAACGGAT 59.303 39.130 5.14 0.00 0.00 4.18
2691 3617 4.882427 TCAAAAGTGGACACAAAACGGATA 59.118 37.500 5.14 0.00 0.00 2.59
2692 3618 5.357314 TCAAAAGTGGACACAAAACGGATAA 59.643 36.000 5.14 0.00 0.00 1.75
2693 3619 5.838531 AAAGTGGACACAAAACGGATAAA 57.161 34.783 5.14 0.00 0.00 1.40
2694 3620 5.838531 AAGTGGACACAAAACGGATAAAA 57.161 34.783 5.14 0.00 0.00 1.52
2695 3621 5.432885 AGTGGACACAAAACGGATAAAAG 57.567 39.130 5.14 0.00 0.00 2.27
2696 3622 4.885325 AGTGGACACAAAACGGATAAAAGT 59.115 37.500 5.14 0.00 0.00 2.66
2697 3623 5.008316 AGTGGACACAAAACGGATAAAAGTC 59.992 40.000 5.14 0.00 0.00 3.01
2698 3624 4.276431 TGGACACAAAACGGATAAAAGTCC 59.724 41.667 0.00 0.00 42.44 3.85
2708 3634 4.601621 GGATAAAAGTCCGTTTGCTCTC 57.398 45.455 0.00 0.00 0.00 3.20
2709 3635 3.062234 GGATAAAAGTCCGTTTGCTCTCG 59.938 47.826 0.00 0.00 0.00 4.04
2710 3636 1.949465 AAAAGTCCGTTTGCTCTCGT 58.051 45.000 0.00 0.00 0.00 4.18
2711 3637 1.217882 AAAGTCCGTTTGCTCTCGTG 58.782 50.000 0.00 0.00 0.00 4.35
2712 3638 0.104304 AAGTCCGTTTGCTCTCGTGT 59.896 50.000 0.00 0.00 0.00 4.49
2713 3639 0.956633 AGTCCGTTTGCTCTCGTGTA 59.043 50.000 0.00 0.00 0.00 2.90
2714 3640 1.544691 AGTCCGTTTGCTCTCGTGTAT 59.455 47.619 0.00 0.00 0.00 2.29
2715 3641 2.029290 AGTCCGTTTGCTCTCGTGTATT 60.029 45.455 0.00 0.00 0.00 1.89
2716 3642 2.092211 GTCCGTTTGCTCTCGTGTATTG 59.908 50.000 0.00 0.00 0.00 1.90
2717 3643 1.393539 CCGTTTGCTCTCGTGTATTGG 59.606 52.381 0.00 0.00 0.00 3.16
2718 3644 1.393539 CGTTTGCTCTCGTGTATTGGG 59.606 52.381 0.00 0.00 0.00 4.12
2719 3645 1.130561 GTTTGCTCTCGTGTATTGGGC 59.869 52.381 0.00 0.00 0.00 5.36
2720 3646 0.392461 TTGCTCTCGTGTATTGGGCC 60.392 55.000 0.00 0.00 0.00 5.80
2721 3647 1.883084 GCTCTCGTGTATTGGGCCG 60.883 63.158 0.00 0.00 0.00 6.13
2722 3648 1.883084 CTCTCGTGTATTGGGCCGC 60.883 63.158 0.00 0.00 0.00 6.53
2723 3649 3.261951 CTCGTGTATTGGGCCGCG 61.262 66.667 0.00 0.00 36.00 6.46
2738 3664 4.570663 GCGCGCGGACAGGATAGT 62.571 66.667 33.06 0.00 0.00 2.12
2739 3665 2.655364 CGCGCGGACAGGATAGTG 60.655 66.667 24.84 0.00 0.00 2.74
2740 3666 2.962253 GCGCGGACAGGATAGTGC 60.962 66.667 8.83 0.00 0.00 4.40
2741 3667 2.279517 CGCGGACAGGATAGTGCC 60.280 66.667 0.00 0.00 0.00 5.01
2742 3668 2.279517 GCGGACAGGATAGTGCCG 60.280 66.667 0.00 0.00 38.99 5.69
2743 3669 2.279517 CGGACAGGATAGTGCCGC 60.280 66.667 0.00 0.00 32.84 6.53
2744 3670 2.279517 GGACAGGATAGTGCCGCG 60.280 66.667 0.00 0.00 0.00 6.46
2745 3671 2.962253 GACAGGATAGTGCCGCGC 60.962 66.667 0.00 0.00 0.00 6.86
2746 3672 4.873129 ACAGGATAGTGCCGCGCG 62.873 66.667 25.67 25.67 0.00 6.86
2766 3692 2.618045 CGGTGGAGTTGGCCTTATTCTT 60.618 50.000 3.32 0.00 0.00 2.52
2796 3722 1.298859 GCCATGTCGAACTGTCCACC 61.299 60.000 0.00 0.00 0.00 4.61
2813 3739 1.945394 CACCTCATCATGTAGCAAGGC 59.055 52.381 0.00 0.00 0.00 4.35
2841 3767 0.109597 GGGCATGTCGAAACAGCAAG 60.110 55.000 4.45 0.00 39.20 4.01
2854 3780 4.704833 GCAAGCAGGGCAGACGGA 62.705 66.667 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.613437 ACTTGATGGTTATCCTTTGGCAT 58.387 39.130 0.00 0.00 32.09 4.40
40 41 3.542604 ACCTTCTCCCACTTATTTCCCT 58.457 45.455 0.00 0.00 0.00 4.20
80 81 1.076332 GACGACATTTTGTAGCCGCT 58.924 50.000 0.00 0.00 0.00 5.52
102 105 1.384525 CCGAAAAATGCCCGTCCATA 58.615 50.000 0.00 0.00 0.00 2.74
185 190 3.787001 CCCTCTTCCGGTCCCAGC 61.787 72.222 0.00 0.00 0.00 4.85
186 191 3.787001 GCCCTCTTCCGGTCCCAG 61.787 72.222 0.00 0.00 0.00 4.45
212 217 7.095060 CGATCTTCTCCTTCTCAATTTTCAACA 60.095 37.037 0.00 0.00 0.00 3.33
227 232 3.374042 TCTCCAACTCGATCTTCTCCT 57.626 47.619 0.00 0.00 0.00 3.69
259 264 6.258727 GCCTTCTCGAGTTCATATTTGATCAA 59.741 38.462 13.13 3.38 0.00 2.57
270 275 1.000955 GTCTTGGCCTTCTCGAGTTCA 59.999 52.381 13.13 2.41 0.00 3.18
344 350 3.941483 CACTAACATGGTCTTCACATCCC 59.059 47.826 0.00 0.00 0.00 3.85
356 362 2.081462 GGGTTTCGTCCACTAACATGG 58.919 52.381 0.00 0.00 41.57 3.66
363 369 1.213430 TCCAAAAGGGTTTCGTCCACT 59.787 47.619 0.00 0.00 38.11 4.00
388 394 2.170166 CCCAAGCCACTTCTTTGCATA 58.830 47.619 0.00 0.00 0.00 3.14
407 416 5.805994 CGCTCGTTTATCTCCTTATTATCCC 59.194 44.000 0.00 0.00 0.00 3.85
423 435 2.358267 CTCATACTCCCTACGCTCGTTT 59.642 50.000 0.00 0.00 0.00 3.60
496 512 0.179037 GCATGCATCCAGACTGCCTA 60.179 55.000 14.21 0.00 38.89 3.93
522 539 0.178998 CCAAGGCCATGCTAGCATCT 60.179 55.000 27.34 18.27 33.90 2.90
560 580 0.037326 GCCGGATCACTTGTCAGACA 60.037 55.000 5.05 0.00 0.00 3.41
564 584 0.955428 GCTTGCCGGATCACTTGTCA 60.955 55.000 5.05 0.00 0.00 3.58
580 774 1.452651 CATGACGGATGGCCTGCTT 60.453 57.895 3.32 0.00 0.00 3.91
585 779 2.969238 CGAGCATGACGGATGGCC 60.969 66.667 0.00 0.00 31.99 5.36
674 888 8.827177 ACAATCATACGATACAAATTATCCGT 57.173 30.769 0.00 0.00 0.00 4.69
679 893 8.637281 ACACGACAATCATACGATACAAATTA 57.363 30.769 0.00 0.00 0.00 1.40
706 920 5.331309 GCGATCTTCAAATTCATGCAATTCG 60.331 40.000 0.00 0.00 33.16 3.34
717 931 5.138125 ACCACAAATGCGATCTTCAAATT 57.862 34.783 0.00 0.00 0.00 1.82
736 951 7.510407 TCGTATTCCCACAAATTCATATACCA 58.490 34.615 0.00 0.00 0.00 3.25
748 963 0.616371 CACCCCTCGTATTCCCACAA 59.384 55.000 0.00 0.00 0.00 3.33
751 966 1.335132 GCTCACCCCTCGTATTCCCA 61.335 60.000 0.00 0.00 0.00 4.37
754 969 1.067582 CCGCTCACCCCTCGTATTC 59.932 63.158 0.00 0.00 0.00 1.75
759 974 2.183555 GTAACCGCTCACCCCTCG 59.816 66.667 0.00 0.00 0.00 4.63
764 979 0.669625 GTGGACAGTAACCGCTCACC 60.670 60.000 0.00 0.00 35.35 4.02
765 980 0.032952 TGTGGACAGTAACCGCTCAC 59.967 55.000 0.00 0.00 38.55 3.51
766 981 0.753867 TTGTGGACAGTAACCGCTCA 59.246 50.000 0.00 0.00 38.55 4.26
767 982 1.529865 GTTTGTGGACAGTAACCGCTC 59.470 52.381 0.00 0.00 38.55 5.03
768 983 1.589803 GTTTGTGGACAGTAACCGCT 58.410 50.000 0.00 0.00 38.55 5.52
770 985 0.233848 GCGTTTGTGGACAGTAACCG 59.766 55.000 0.00 0.00 0.00 4.44
771 986 0.589708 GGCGTTTGTGGACAGTAACC 59.410 55.000 0.00 0.00 0.00 2.85
772 987 0.589708 GGGCGTTTGTGGACAGTAAC 59.410 55.000 0.00 0.00 0.00 2.50
773 988 0.535553 GGGGCGTTTGTGGACAGTAA 60.536 55.000 0.00 0.00 0.00 2.24
774 989 1.071814 GGGGCGTTTGTGGACAGTA 59.928 57.895 0.00 0.00 0.00 2.74
776 991 2.983592 GGGGGCGTTTGTGGACAG 60.984 66.667 0.00 0.00 0.00 3.51
777 992 3.494254 AGGGGGCGTTTGTGGACA 61.494 61.111 0.00 0.00 0.00 4.02
778 993 2.983592 CAGGGGGCGTTTGTGGAC 60.984 66.667 0.00 0.00 0.00 4.02
779 994 3.172106 TCAGGGGGCGTTTGTGGA 61.172 61.111 0.00 0.00 0.00 4.02
780 995 2.983592 GTCAGGGGGCGTTTGTGG 60.984 66.667 0.00 0.00 0.00 4.17
781 996 1.795170 CTTGTCAGGGGGCGTTTGTG 61.795 60.000 0.00 0.00 0.00 3.33
782 997 1.528309 CTTGTCAGGGGGCGTTTGT 60.528 57.895 0.00 0.00 0.00 2.83
783 998 1.515521 GACTTGTCAGGGGGCGTTTG 61.516 60.000 0.00 0.00 0.00 2.93
786 1001 3.637273 GGACTTGTCAGGGGGCGT 61.637 66.667 3.08 0.00 0.00 5.68
787 1002 3.316573 GAGGACTTGTCAGGGGGCG 62.317 68.421 3.08 0.00 0.00 6.13
788 1003 1.904990 GAGAGGACTTGTCAGGGGGC 61.905 65.000 3.08 0.00 0.00 5.80
789 1004 0.545309 TGAGAGGACTTGTCAGGGGG 60.545 60.000 3.08 0.00 0.00 5.40
802 1017 3.118629 TCAAAATCGTGGATCCTGAGAGG 60.119 47.826 14.23 0.00 36.46 3.69
803 1018 3.868077 GTCAAAATCGTGGATCCTGAGAG 59.132 47.826 14.23 0.00 0.00 3.20
804 1019 3.515502 AGTCAAAATCGTGGATCCTGAGA 59.484 43.478 14.23 9.89 0.00 3.27
822 1066 1.895798 CCAGTTCTCTAGGCACAGTCA 59.104 52.381 0.00 0.00 0.00 3.41
832 1076 4.278669 GCCTTACATCGATCCAGTTCTCTA 59.721 45.833 0.00 0.00 0.00 2.43
834 1078 3.385577 GCCTTACATCGATCCAGTTCTC 58.614 50.000 0.00 0.00 0.00 2.87
837 1081 1.837439 TGGCCTTACATCGATCCAGTT 59.163 47.619 3.32 0.00 0.00 3.16
905 1151 2.695147 ACTTGAAAGTTTTGGAGGGCAG 59.305 45.455 0.00 0.00 35.21 4.85
935 1181 4.082190 GGGAAATCTCTTTTTGTAGGGCAC 60.082 45.833 0.00 0.00 0.00 5.01
980 1226 3.577313 GGATCGCGGGCAGCTTTC 61.577 66.667 6.13 4.20 45.59 2.62
1026 1272 0.760572 TTTCGGACGAGGAAAGGGTT 59.239 50.000 0.00 0.00 0.00 4.11
1245 1491 0.812811 GCAGCATGAGGAATGAGCGA 60.813 55.000 0.00 0.00 39.69 4.93
1252 1498 2.586245 CGGGAGCAGCATGAGGAA 59.414 61.111 0.00 0.00 39.69 3.36
1931 2179 1.458777 AACTGGAGACCGGGACACA 60.459 57.895 6.32 0.00 33.40 3.72
2199 2456 3.681417 GGAAGCCTAAAAAGCAGCAATTG 59.319 43.478 0.00 0.00 0.00 2.32
2201 2458 3.056322 CAGGAAGCCTAAAAAGCAGCAAT 60.056 43.478 0.00 0.00 29.64 3.56
2221 2478 1.430632 GCGCCAACATCATCACCAG 59.569 57.895 0.00 0.00 0.00 4.00
2258 2515 6.918892 TCTTTACAATAATCCACACATCCG 57.081 37.500 0.00 0.00 0.00 4.18
2279 2566 6.713520 CAAAGTAAGCGTACTACTACGATCT 58.286 40.000 12.87 0.00 44.06 2.75
2280 2567 5.394904 GCAAAGTAAGCGTACTACTACGATC 59.605 44.000 12.87 0.00 44.06 3.69
2281 2568 5.065731 AGCAAAGTAAGCGTACTACTACGAT 59.934 40.000 12.87 0.00 46.74 3.73
2284 2571 4.797349 CCAGCAAAGTAAGCGTACTACTAC 59.203 45.833 12.87 3.77 39.79 2.73
2285 2572 4.701651 TCCAGCAAAGTAAGCGTACTACTA 59.298 41.667 12.87 0.00 39.79 1.82
2286 2573 3.508793 TCCAGCAAAGTAAGCGTACTACT 59.491 43.478 12.87 8.17 39.79 2.57
2295 2582 5.560953 GCAACAGTTACTCCAGCAAAGTAAG 60.561 44.000 6.01 0.54 39.28 2.34
2305 3206 4.469586 TCCATATCAGCAACAGTTACTCCA 59.530 41.667 0.00 0.00 0.00 3.86
2348 3266 1.542915 CAATGCCAGGGTTGTCTTCTG 59.457 52.381 0.00 0.00 0.00 3.02
2351 3269 1.133513 TGTCAATGCCAGGGTTGTCTT 60.134 47.619 0.00 0.00 0.00 3.01
2364 3282 5.702865 CAAGACTACCACCATTTGTCAATG 58.297 41.667 0.00 0.00 39.79 2.82
2370 3288 3.149196 ACAGCAAGACTACCACCATTTG 58.851 45.455 0.00 0.00 0.00 2.32
2371 3289 3.508845 ACAGCAAGACTACCACCATTT 57.491 42.857 0.00 0.00 0.00 2.32
2372 3290 4.634012 TTACAGCAAGACTACCACCATT 57.366 40.909 0.00 0.00 0.00 3.16
2373 3291 4.634012 TTTACAGCAAGACTACCACCAT 57.366 40.909 0.00 0.00 0.00 3.55
2374 3292 4.425180 TTTTACAGCAAGACTACCACCA 57.575 40.909 0.00 0.00 0.00 4.17
2375 3293 5.585047 CCTATTTTACAGCAAGACTACCACC 59.415 44.000 0.00 0.00 0.00 4.61
2377 3295 6.014070 TCACCTATTTTACAGCAAGACTACCA 60.014 38.462 0.00 0.00 0.00 3.25
2380 3298 7.039293 TCAGTCACCTATTTTACAGCAAGACTA 60.039 37.037 0.00 0.00 32.01 2.59
2381 3299 5.934625 CAGTCACCTATTTTACAGCAAGACT 59.065 40.000 0.00 0.00 33.32 3.24
2385 3303 7.284489 ACTTTTCAGTCACCTATTTTACAGCAA 59.716 33.333 0.00 0.00 0.00 3.91
2396 3320 3.551454 CCGTCGAACTTTTCAGTCACCTA 60.551 47.826 0.00 0.00 30.45 3.08
2434 3358 0.713883 CGGTTCGGTCGTCAAATCAG 59.286 55.000 0.00 0.00 0.00 2.90
2503 3427 1.983119 ATGGTGGGGTATCAGGTGCG 61.983 60.000 0.00 0.00 0.00 5.34
2552 3476 2.549754 GCCATATATATGCGCATCCACC 59.450 50.000 29.11 4.68 33.20 4.61
2571 3495 1.378531 TCGAGCAATTGGTGTATGCC 58.621 50.000 16.18 0.00 40.93 4.40
2611 3537 2.349755 GCGGTGGAGTTGGCCTAA 59.650 61.111 3.32 0.00 0.00 2.69
2615 3541 4.752879 TAGCGCGGTGGAGTTGGC 62.753 66.667 23.02 0.00 0.00 4.52
2616 3542 2.813908 GTAGCGCGGTGGAGTTGG 60.814 66.667 23.02 0.00 0.00 3.77
2617 3543 2.813908 GGTAGCGCGGTGGAGTTG 60.814 66.667 23.02 0.00 0.00 3.16
2618 3544 4.078516 GGGTAGCGCGGTGGAGTT 62.079 66.667 23.02 0.00 0.00 3.01
2622 3548 4.708386 TTTGGGGTAGCGCGGTGG 62.708 66.667 23.02 0.00 0.00 4.61
2623 3549 2.262303 TTTTTGGGGTAGCGCGGTG 61.262 57.895 23.02 0.00 0.00 4.94
2624 3550 2.113562 TTTTTGGGGTAGCGCGGT 59.886 55.556 17.70 17.70 0.00 5.68
2625 3551 2.564458 GTTTTTGGGGTAGCGCGG 59.436 61.111 8.83 0.00 0.00 6.46
2626 3552 2.174835 CGTTTTTGGGGTAGCGCG 59.825 61.111 0.00 0.00 0.00 6.86
2627 3553 1.208358 GTCGTTTTTGGGGTAGCGC 59.792 57.895 0.00 0.00 0.00 5.92
2628 3554 0.236449 GTGTCGTTTTTGGGGTAGCG 59.764 55.000 0.00 0.00 0.00 4.26
2629 3555 1.310904 TGTGTCGTTTTTGGGGTAGC 58.689 50.000 0.00 0.00 0.00 3.58
2630 3556 4.577834 ATTTGTGTCGTTTTTGGGGTAG 57.422 40.909 0.00 0.00 0.00 3.18
2631 3557 5.109903 CAAATTTGTGTCGTTTTTGGGGTA 58.890 37.500 10.15 0.00 0.00 3.69
2632 3558 3.897141 AATTTGTGTCGTTTTTGGGGT 57.103 38.095 0.00 0.00 0.00 4.95
2633 3559 3.311048 CCAAATTTGTGTCGTTTTTGGGG 59.689 43.478 16.73 0.00 41.56 4.96
2634 3560 3.242576 GCCAAATTTGTGTCGTTTTTGGG 60.243 43.478 16.73 0.00 44.10 4.12
2635 3561 3.242576 GGCCAAATTTGTGTCGTTTTTGG 60.243 43.478 16.73 8.08 45.79 3.28
2636 3562 3.242576 GGGCCAAATTTGTGTCGTTTTTG 60.243 43.478 16.73 0.00 0.00 2.44
2637 3563 2.939756 GGGCCAAATTTGTGTCGTTTTT 59.060 40.909 16.73 0.00 0.00 1.94
2638 3564 2.169561 AGGGCCAAATTTGTGTCGTTTT 59.830 40.909 16.73 0.00 0.00 2.43
2639 3565 1.760029 AGGGCCAAATTTGTGTCGTTT 59.240 42.857 16.73 0.00 0.00 3.60
2640 3566 1.068434 CAGGGCCAAATTTGTGTCGTT 59.932 47.619 16.73 0.54 0.00 3.85
2641 3567 0.673437 CAGGGCCAAATTTGTGTCGT 59.327 50.000 16.73 8.65 0.00 4.34
2642 3568 0.038343 CCAGGGCCAAATTTGTGTCG 60.038 55.000 16.73 2.87 0.00 4.35
2643 3569 1.337118 TCCAGGGCCAAATTTGTGTC 58.663 50.000 16.73 9.60 0.00 3.67
2644 3570 1.799933 TTCCAGGGCCAAATTTGTGT 58.200 45.000 16.73 0.00 0.00 3.72
2645 3571 2.616001 CCATTCCAGGGCCAAATTTGTG 60.616 50.000 16.73 8.27 0.00 3.33
2646 3572 1.629861 CCATTCCAGGGCCAAATTTGT 59.370 47.619 16.73 0.00 0.00 2.83
2647 3573 1.065272 CCCATTCCAGGGCCAAATTTG 60.065 52.381 11.40 11.40 43.10 2.32
2648 3574 1.288188 CCCATTCCAGGGCCAAATTT 58.712 50.000 6.18 0.00 43.10 1.82
2649 3575 3.010627 CCCATTCCAGGGCCAAATT 57.989 52.632 6.18 0.00 43.10 1.82
2650 3576 4.813907 CCCATTCCAGGGCCAAAT 57.186 55.556 6.18 0.00 43.10 2.32
2657 3583 1.895131 CCACTTTTGACCCATTCCAGG 59.105 52.381 0.00 0.00 0.00 4.45
2658 3584 2.558359 GTCCACTTTTGACCCATTCCAG 59.442 50.000 0.00 0.00 0.00 3.86
2659 3585 2.091610 TGTCCACTTTTGACCCATTCCA 60.092 45.455 0.00 0.00 31.60 3.53
2660 3586 2.296190 GTGTCCACTTTTGACCCATTCC 59.704 50.000 0.00 0.00 31.60 3.01
2661 3587 2.955660 TGTGTCCACTTTTGACCCATTC 59.044 45.455 0.00 0.00 31.60 2.67
2662 3588 3.025322 TGTGTCCACTTTTGACCCATT 57.975 42.857 0.00 0.00 31.60 3.16
2663 3589 2.746279 TGTGTCCACTTTTGACCCAT 57.254 45.000 0.00 0.00 31.60 4.00
2664 3590 2.516227 TTGTGTCCACTTTTGACCCA 57.484 45.000 0.00 0.00 31.60 4.51
2665 3591 3.517602 GTTTTGTGTCCACTTTTGACCC 58.482 45.455 0.00 0.00 31.60 4.46
2666 3592 3.175929 CGTTTTGTGTCCACTTTTGACC 58.824 45.455 0.00 0.00 31.60 4.02
2667 3593 3.119779 TCCGTTTTGTGTCCACTTTTGAC 60.120 43.478 0.00 0.00 0.00 3.18
2668 3594 3.082548 TCCGTTTTGTGTCCACTTTTGA 58.917 40.909 0.00 0.00 0.00 2.69
2669 3595 3.495670 TCCGTTTTGTGTCCACTTTTG 57.504 42.857 0.00 0.00 0.00 2.44
2670 3596 5.838531 TTATCCGTTTTGTGTCCACTTTT 57.161 34.783 0.00 0.00 0.00 2.27
2671 3597 5.838531 TTTATCCGTTTTGTGTCCACTTT 57.161 34.783 0.00 0.00 0.00 2.66
2672 3598 5.358725 ACTTTTATCCGTTTTGTGTCCACTT 59.641 36.000 0.00 0.00 0.00 3.16
2673 3599 4.885325 ACTTTTATCCGTTTTGTGTCCACT 59.115 37.500 0.00 0.00 0.00 4.00
2674 3600 5.177725 ACTTTTATCCGTTTTGTGTCCAC 57.822 39.130 0.00 0.00 0.00 4.02
2675 3601 4.276431 GGACTTTTATCCGTTTTGTGTCCA 59.724 41.667 0.00 0.00 40.56 4.02
2676 3602 4.790878 GGACTTTTATCCGTTTTGTGTCC 58.209 43.478 0.00 0.00 35.39 4.02
2687 3613 3.062234 CGAGAGCAAACGGACTTTTATCC 59.938 47.826 0.00 0.00 35.16 2.59
2688 3614 3.678548 ACGAGAGCAAACGGACTTTTATC 59.321 43.478 0.00 0.00 0.00 1.75
2689 3615 3.432252 CACGAGAGCAAACGGACTTTTAT 59.568 43.478 0.00 0.00 0.00 1.40
2690 3616 2.798283 CACGAGAGCAAACGGACTTTTA 59.202 45.455 0.00 0.00 0.00 1.52
2691 3617 1.597663 CACGAGAGCAAACGGACTTTT 59.402 47.619 0.00 0.00 0.00 2.27
2692 3618 1.217882 CACGAGAGCAAACGGACTTT 58.782 50.000 0.00 0.00 0.00 2.66
2693 3619 0.104304 ACACGAGAGCAAACGGACTT 59.896 50.000 0.00 0.00 0.00 3.01
2694 3620 0.956633 TACACGAGAGCAAACGGACT 59.043 50.000 0.00 0.00 0.00 3.85
2695 3621 1.992170 ATACACGAGAGCAAACGGAC 58.008 50.000 0.00 0.00 0.00 4.79
2696 3622 2.333926 CAATACACGAGAGCAAACGGA 58.666 47.619 0.00 0.00 0.00 4.69
2697 3623 1.393539 CCAATACACGAGAGCAAACGG 59.606 52.381 0.00 0.00 0.00 4.44
2698 3624 1.393539 CCCAATACACGAGAGCAAACG 59.606 52.381 0.00 0.00 0.00 3.60
2699 3625 1.130561 GCCCAATACACGAGAGCAAAC 59.869 52.381 0.00 0.00 0.00 2.93
2700 3626 1.448985 GCCCAATACACGAGAGCAAA 58.551 50.000 0.00 0.00 0.00 3.68
2701 3627 0.392461 GGCCCAATACACGAGAGCAA 60.392 55.000 0.00 0.00 0.00 3.91
2702 3628 1.220749 GGCCCAATACACGAGAGCA 59.779 57.895 0.00 0.00 0.00 4.26
2703 3629 1.883084 CGGCCCAATACACGAGAGC 60.883 63.158 0.00 0.00 0.00 4.09
2704 3630 1.883084 GCGGCCCAATACACGAGAG 60.883 63.158 0.00 0.00 0.00 3.20
2705 3631 2.185867 GCGGCCCAATACACGAGA 59.814 61.111 0.00 0.00 0.00 4.04
2706 3632 3.261951 CGCGGCCCAATACACGAG 61.262 66.667 0.00 0.00 0.00 4.18
2721 3647 4.570663 ACTATCCTGTCCGCGCGC 62.571 66.667 27.36 23.91 0.00 6.86
2722 3648 2.655364 CACTATCCTGTCCGCGCG 60.655 66.667 25.67 25.67 0.00 6.86
2723 3649 2.962253 GCACTATCCTGTCCGCGC 60.962 66.667 0.00 0.00 0.00 6.86
2724 3650 2.279517 GGCACTATCCTGTCCGCG 60.280 66.667 0.00 0.00 0.00 6.46
2725 3651 2.279517 CGGCACTATCCTGTCCGC 60.280 66.667 0.00 0.00 33.36 5.54
2726 3652 2.279517 GCGGCACTATCCTGTCCG 60.280 66.667 0.00 0.00 42.68 4.79
2727 3653 2.279517 CGCGGCACTATCCTGTCC 60.280 66.667 0.00 0.00 0.00 4.02
2728 3654 2.962253 GCGCGGCACTATCCTGTC 60.962 66.667 8.83 0.00 0.00 3.51
2729 3655 4.873129 CGCGCGGCACTATCCTGT 62.873 66.667 24.84 0.00 0.00 4.00
2743 3669 2.869503 ATAAGGCCAACTCCACCGCG 62.870 60.000 5.01 0.00 0.00 6.46
2744 3670 0.679960 AATAAGGCCAACTCCACCGC 60.680 55.000 5.01 0.00 0.00 5.68
2745 3671 1.065418 AGAATAAGGCCAACTCCACCG 60.065 52.381 5.01 0.00 0.00 4.94
2746 3672 2.808906 AGAATAAGGCCAACTCCACC 57.191 50.000 5.01 0.00 0.00 4.61
2747 3673 5.099042 TCTAAGAATAAGGCCAACTCCAC 57.901 43.478 5.01 0.00 0.00 4.02
2748 3674 5.428457 TCATCTAAGAATAAGGCCAACTCCA 59.572 40.000 5.01 0.00 0.00 3.86
2749 3675 5.930135 TCATCTAAGAATAAGGCCAACTCC 58.070 41.667 5.01 0.00 0.00 3.85
2750 3676 6.821388 TCTCATCTAAGAATAAGGCCAACTC 58.179 40.000 5.01 0.00 0.00 3.01
2751 3677 6.814954 TCTCATCTAAGAATAAGGCCAACT 57.185 37.500 5.01 0.00 0.00 3.16
2752 3678 6.429385 CCATCTCATCTAAGAATAAGGCCAAC 59.571 42.308 5.01 0.00 0.00 3.77
2753 3679 6.537355 CCATCTCATCTAAGAATAAGGCCAA 58.463 40.000 5.01 0.00 0.00 4.52
2754 3680 5.513788 GCCATCTCATCTAAGAATAAGGCCA 60.514 44.000 5.01 0.00 31.95 5.36
2755 3681 4.940654 GCCATCTCATCTAAGAATAAGGCC 59.059 45.833 0.00 0.00 31.95 5.19
2756 3682 4.940654 GGCCATCTCATCTAAGAATAAGGC 59.059 45.833 0.00 0.00 34.75 4.35
2757 3683 6.119240 TGGCCATCTCATCTAAGAATAAGG 57.881 41.667 0.00 0.00 0.00 2.69
2758 3684 7.166851 ACATGGCCATCTCATCTAAGAATAAG 58.833 38.462 17.61 0.25 0.00 1.73
2766 3692 2.597455 TCGACATGGCCATCTCATCTA 58.403 47.619 17.61 0.57 0.00 1.98
2796 3722 1.224075 CCGCCTTGCTACATGATGAG 58.776 55.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.