Multiple sequence alignment - TraesCS2B01G247700

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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 TraesCS2B01G247700 chr2B 100.000 4587 0 0 1 4587 254289853 254285267 0.000000e+00 8471
1 TraesCS2B01G247700 chr2B 94.838 678 34 1 3911 4587 232353753 232353076 0.000000e+00 1057
2 TraesCS2B01G247700 chr2B 94.340 106 5 1 3810 3914 18200884 18200779 1.320000e-35 161
3 TraesCS2B01G247700 chr2B 94.340 106 5 1 3810 3914 232353927 232353822 1.320000e-35 161
4 TraesCS2B01G247700 chr2D 93.762 1539 42 14 672 2209 196860775 196859290 0.000000e+00 2261
5 TraesCS2B01G247700 chr2D 91.593 678 53 4 3911 4587 114810656 114811330 0.000000e+00 933
6 TraesCS2B01G247700 chr2D 91.617 668 32 12 2683 3346 196858697 196858050 0.000000e+00 902
7 TraesCS2B01G247700 chr2D 96.307 352 11 1 3335 3684 196856601 196856250 1.110000e-160 577
8 TraesCS2B01G247700 chr2D 94.444 270 15 0 2342 2611 196859057 196858788 2.550000e-112 416
9 TraesCS2B01G247700 chr2D 94.815 135 7 0 3658 3792 196856249 196856115 1.290000e-50 211
10 TraesCS2B01G247700 chr2D 92.453 106 7 1 3810 3914 114810483 114810588 2.860000e-32 150
11 TraesCS2B01G247700 chr2D 92.453 106 7 1 3810 3914 584617489 584617594 2.860000e-32 150
12 TraesCS2B01G247700 chr2D 94.048 84 4 1 703 786 196860879 196860797 4.820000e-25 126
13 TraesCS2B01G247700 chr2A 93.986 1297 33 16 940 2224 213114284 213113021 0.000000e+00 1921
14 TraesCS2B01G247700 chr2A 93.097 1101 51 14 2701 3791 213111148 213110063 0.000000e+00 1589
15 TraesCS2B01G247700 chr2A 84.845 970 79 31 8 941 213115251 213114314 0.000000e+00 915
16 TraesCS2B01G247700 chr2A 95.238 315 15 0 2301 2615 213112987 213112673 2.460000e-137 499
17 TraesCS2B01G247700 chr6D 94.395 678 37 1 3911 4587 471804852 471804175 0.000000e+00 1040
18 TraesCS2B01G247700 chr4D 93.979 681 37 3 3911 4587 46424720 46425400 0.000000e+00 1027
19 TraesCS2B01G247700 chr4D 91.298 678 58 1 3911 4587 144817886 144817209 0.000000e+00 924
20 TraesCS2B01G247700 chr4D 94.681 94 5 0 3810 3903 506740180 506740273 3.700000e-31 147
21 TraesCS2B01G247700 chr5B 93.824 680 39 2 3911 4587 599902647 599901968 0.000000e+00 1020
22 TraesCS2B01G247700 chr5B 92.453 106 6 2 3810 3914 599902820 599902716 2.860000e-32 150
23 TraesCS2B01G247700 chr5A 92.330 678 51 1 3911 4587 524125500 524124823 0.000000e+00 963
24 TraesCS2B01G247700 chr5A 77.280 647 133 13 1393 2032 705822896 705823535 7.250000e-98 368
25 TraesCS2B01G247700 chr5A 77.097 310 53 10 1393 1700 536871889 536872182 3.670000e-36 163
26 TraesCS2B01G247700 chr5A 92.453 106 7 1 3810 3914 524125672 524125567 2.860000e-32 150
27 TraesCS2B01G247700 chr3D 91.593 678 56 1 3911 4587 549483226 549483903 0.000000e+00 935
28 TraesCS2B01G247700 chr3D 77.755 490 105 4 1389 1876 593216058 593216545 9.650000e-77 298
29 TraesCS2B01G247700 chr3D 94.118 68 4 0 2779 2846 152542541 152542608 2.260000e-18 104
30 TraesCS2B01G247700 chr5D 91.176 680 55 5 3911 4587 289741739 289742416 0.000000e+00 918
31 TraesCS2B01G247700 chr4B 78.019 646 130 12 1393 2032 665855317 665855956 3.330000e-106 396
32 TraesCS2B01G247700 chr4B 93.396 106 6 1 3810 3914 386481479 386481374 6.140000e-34 156
33 TraesCS2B01G247700 chrUn 77.245 646 135 12 1393 2032 108369416 108368777 7.250000e-98 368
34 TraesCS2B01G247700 chr1A 84.839 310 43 4 1393 1700 13973238 13973545 4.460000e-80 309
35 TraesCS2B01G247700 chr3B 81.553 309 55 2 1393 1700 731484977 731485284 2.120000e-63 254
36 TraesCS2B01G247700 chr3B 81.683 202 35 2 1092 1291 795810069 795809868 2.840000e-37 167
37 TraesCS2B01G247700 chr3A 76.132 486 112 4 1393 1876 724484269 724484752 7.620000e-63 252
38 TraesCS2B01G247700 chr1D 92.453 106 7 1 3810 3914 67110497 67110392 2.860000e-32 150


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 TraesCS2B01G247700 chr2B 254285267 254289853 4586 True 8471.000000 8471 100.0000 1 4587 1 chr2B.!!$R2 4586
1 TraesCS2B01G247700 chr2B 232353076 232353927 851 True 609.000000 1057 94.5890 3810 4587 2 chr2B.!!$R3 777
2 TraesCS2B01G247700 chr2D 196856115 196860879 4764 True 748.833333 2261 94.1655 672 3792 6 chr2D.!!$R1 3120
3 TraesCS2B01G247700 chr2D 114810483 114811330 847 False 541.500000 933 92.0230 3810 4587 2 chr2D.!!$F2 777
4 TraesCS2B01G247700 chr2A 213110063 213115251 5188 True 1231.000000 1921 91.7915 8 3791 4 chr2A.!!$R1 3783
5 TraesCS2B01G247700 chr6D 471804175 471804852 677 True 1040.000000 1040 94.3950 3911 4587 1 chr6D.!!$R1 676
6 TraesCS2B01G247700 chr4D 46424720 46425400 680 False 1027.000000 1027 93.9790 3911 4587 1 chr4D.!!$F1 676
7 TraesCS2B01G247700 chr4D 144817209 144817886 677 True 924.000000 924 91.2980 3911 4587 1 chr4D.!!$R1 676
8 TraesCS2B01G247700 chr5B 599901968 599902820 852 True 585.000000 1020 93.1385 3810 4587 2 chr5B.!!$R1 777
9 TraesCS2B01G247700 chr5A 524124823 524125672 849 True 556.500000 963 92.3915 3810 4587 2 chr5A.!!$R1 777
10 TraesCS2B01G247700 chr5A 705822896 705823535 639 False 368.000000 368 77.2800 1393 2032 1 chr5A.!!$F2 639
11 TraesCS2B01G247700 chr3D 549483226 549483903 677 False 935.000000 935 91.5930 3911 4587 1 chr3D.!!$F2 676
12 TraesCS2B01G247700 chr5D 289741739 289742416 677 False 918.000000 918 91.1760 3911 4587 1 chr5D.!!$F1 676
13 TraesCS2B01G247700 chr4B 665855317 665855956 639 False 396.000000 396 78.0190 1393 2032 1 chr4B.!!$F1 639
14 TraesCS2B01G247700 chrUn 108368777 108369416 639 True 368.000000 368 77.2450 1393 2032 1 chrUn.!!$R1 639

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
856 889 0.036732 TGTCACTTCACCAGCCATCC 59.963 55.0 0.00 0.0 0.00 3.51 F
938 971 0.179043 TAGTGAAGCGCCAACCACAA 60.179 50.0 2.29 0.0 32.35 3.33 F
2615 2852 0.465705 CCCGTGCTATCAGGTGATGT 59.534 55.0 2.56 0.0 36.05 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2137 0.385473 CGACGGACAAAACCATGTGC 60.385 55.0 0.00 0.0 38.18 4.57 R
2629 2866 0.527817 AGTTAGATACCGCAGCGCAC 60.528 55.0 11.47 0.0 0.00 5.34 R
4147 7444 0.674895 AGCAGCTGATCGGGTTGTTC 60.675 55.0 20.43 0.0 0.00 3.18 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
95 116 8.774546 TTGGAAAATATGCACCCATAGATTTA 57.225 30.769 0.00 0.00 37.36 1.40
136 157 6.262193 TCGAAATTCCATGTTACCTTTTCC 57.738 37.500 0.00 0.00 0.00 3.13
199 220 6.495181 AGTTCACTTCTCCTCAAGATCAACTA 59.505 38.462 0.00 0.00 32.82 2.24
205 226 2.427453 TCCTCAAGATCAACTAGCGGAC 59.573 50.000 0.00 0.00 0.00 4.79
211 232 6.914259 TCAAGATCAACTAGCGGACATATAG 58.086 40.000 0.00 0.00 0.00 1.31
219 240 1.374252 CGGACATATAGCCGCCACC 60.374 63.158 2.89 0.00 41.17 4.61
231 252 2.897350 GCCACCAGCTATGCCGTC 60.897 66.667 0.00 0.00 38.99 4.79
232 253 2.903357 CCACCAGCTATGCCGTCT 59.097 61.111 0.00 0.00 0.00 4.18
255 276 7.167468 GTCTTTTGTTCGTCTAAAATGCAATGT 59.833 33.333 0.00 0.00 0.00 2.71
257 278 4.707563 TGTTCGTCTAAAATGCAATGTCG 58.292 39.130 0.00 0.00 0.00 4.35
293 314 3.559242 GTGCTTGAGATCTTGGAGTATGC 59.441 47.826 0.00 0.00 0.00 3.14
316 337 5.316987 CAGAAAGATAGACTTGGGGTTGTT 58.683 41.667 0.00 0.00 38.98 2.83
326 347 0.250513 TGGGGTTGTTTGGTTTGTGC 59.749 50.000 0.00 0.00 0.00 4.57
328 349 0.808060 GGGTTGTTTGGTTTGTGCCG 60.808 55.000 0.00 0.00 0.00 5.69
343 364 2.823829 GCCGATGTTAGCCTTGCCG 61.824 63.158 0.00 0.00 0.00 5.69
347 368 1.806247 CGATGTTAGCCTTGCCGATCA 60.806 52.381 0.00 0.00 0.00 2.92
381 402 1.329913 AATTGGCGCTGGATTTCCCC 61.330 55.000 7.64 0.00 34.29 4.81
390 411 3.131478 GATTTCCCCACCCACGCG 61.131 66.667 3.53 3.53 0.00 6.01
421 442 2.687935 AGTTGGTTGCGAATTGAACTGT 59.312 40.909 0.00 0.00 0.00 3.55
426 447 3.682858 GGTTGCGAATTGAACTGTAGCTA 59.317 43.478 0.00 0.00 0.00 3.32
427 448 4.332819 GGTTGCGAATTGAACTGTAGCTAT 59.667 41.667 0.00 0.00 0.00 2.97
429 450 5.011090 TGCGAATTGAACTGTAGCTATCT 57.989 39.130 0.00 0.00 0.00 1.98
468 491 6.700352 CCAATTATTTGGTCACCACTCAAAT 58.300 36.000 0.00 0.00 46.27 2.32
476 499 2.293399 GTCACCACTCAAATGAACACCC 59.707 50.000 0.00 0.00 0.00 4.61
477 500 2.092158 TCACCACTCAAATGAACACCCA 60.092 45.455 0.00 0.00 0.00 4.51
479 502 2.174639 ACCACTCAAATGAACACCCAGA 59.825 45.455 0.00 0.00 0.00 3.86
480 503 2.554032 CCACTCAAATGAACACCCAGAC 59.446 50.000 0.00 0.00 0.00 3.51
481 504 3.213506 CACTCAAATGAACACCCAGACA 58.786 45.455 0.00 0.00 0.00 3.41
482 505 3.251729 CACTCAAATGAACACCCAGACAG 59.748 47.826 0.00 0.00 0.00 3.51
483 506 2.227388 CTCAAATGAACACCCAGACAGC 59.773 50.000 0.00 0.00 0.00 4.40
484 507 1.270550 CAAATGAACACCCAGACAGCC 59.729 52.381 0.00 0.00 0.00 4.85
485 508 0.478072 AATGAACACCCAGACAGCCA 59.522 50.000 0.00 0.00 0.00 4.75
486 509 0.037303 ATGAACACCCAGACAGCCAG 59.963 55.000 0.00 0.00 0.00 4.85
487 510 1.053835 TGAACACCCAGACAGCCAGA 61.054 55.000 0.00 0.00 0.00 3.86
488 511 0.603975 GAACACCCAGACAGCCAGAC 60.604 60.000 0.00 0.00 0.00 3.51
489 512 1.056700 AACACCCAGACAGCCAGACT 61.057 55.000 0.00 0.00 0.00 3.24
494 517 1.294780 CAGACAGCCAGACTGGGTC 59.705 63.158 23.36 20.45 46.99 4.46
512 535 9.458546 GACTGGGTCAACATCCAATATTTTGGG 62.459 44.444 14.11 2.92 41.40 4.12
520 543 0.104671 CAATATTTTGGGGCAGGGCG 59.895 55.000 0.00 0.00 0.00 6.13
531 554 4.463879 CAGGGCGTCTCAGGGCAG 62.464 72.222 0.00 0.00 0.00 4.85
533 556 4.767255 GGGCGTCTCAGGGCAGTG 62.767 72.222 0.00 0.00 0.00 3.66
534 557 3.695606 GGCGTCTCAGGGCAGTGA 61.696 66.667 0.00 0.00 0.00 3.41
535 558 2.343758 GCGTCTCAGGGCAGTGAA 59.656 61.111 0.00 0.00 0.00 3.18
536 559 2.029844 GCGTCTCAGGGCAGTGAAC 61.030 63.158 0.00 0.00 0.00 3.18
537 560 1.374758 CGTCTCAGGGCAGTGAACC 60.375 63.158 0.00 0.00 0.00 3.62
538 561 1.821061 CGTCTCAGGGCAGTGAACCT 61.821 60.000 0.00 0.00 37.66 3.50
554 577 4.451096 GTGAACCTCGAATAGCAAGTTGAA 59.549 41.667 7.16 0.00 0.00 2.69
568 591 4.688063 CAAGTTGAAACGTACGTGAGATG 58.312 43.478 23.57 10.95 0.00 2.90
578 601 5.998553 ACGTACGTGAGATGTATAGGATTG 58.001 41.667 22.14 0.00 0.00 2.67
582 605 7.482113 CGTACGTGAGATGTATAGGATTGAATC 59.518 40.741 7.22 0.00 0.00 2.52
600 623 6.811253 TGAATCGCCTAACAAACTTGTAAT 57.189 33.333 0.00 0.00 41.31 1.89
611 634 9.341899 CTAACAAACTTGTAATAACCTTGCATC 57.658 33.333 0.00 0.00 41.31 3.91
615 638 6.455360 ACTTGTAATAACCTTGCATCCATG 57.545 37.500 0.00 0.00 0.00 3.66
616 639 5.951747 ACTTGTAATAACCTTGCATCCATGT 59.048 36.000 0.00 0.00 0.00 3.21
617 640 6.437162 ACTTGTAATAACCTTGCATCCATGTT 59.563 34.615 0.00 0.00 0.00 2.71
618 641 6.449635 TGTAATAACCTTGCATCCATGTTC 57.550 37.500 0.00 0.00 0.00 3.18
619 642 5.948758 TGTAATAACCTTGCATCCATGTTCA 59.051 36.000 0.00 0.00 0.00 3.18
620 643 5.999205 AATAACCTTGCATCCATGTTCAA 57.001 34.783 0.00 0.00 0.00 2.69
622 645 7.658525 AATAACCTTGCATCCATGTTCAATA 57.341 32.000 0.00 0.00 0.00 1.90
623 646 7.844493 ATAACCTTGCATCCATGTTCAATAT 57.156 32.000 0.00 0.00 0.00 1.28
626 649 8.938801 AACCTTGCATCCATGTTCAATATATA 57.061 30.769 0.00 0.00 0.00 0.86
674 697 1.724582 GCACGGAGCAACACCAAACT 61.725 55.000 0.00 0.00 44.79 2.66
692 715 3.277142 ACTAATTTGACCGGGATCCAC 57.723 47.619 15.23 1.85 0.00 4.02
722 745 5.561993 GTGTAACTTCTGTGTTTTAACGCA 58.438 37.500 8.41 8.41 46.17 5.24
758 782 2.253452 CAAGCTGCAGAACGCCAC 59.747 61.111 20.43 0.00 41.33 5.01
762 786 2.661537 CTGCAGAACGCCACGACA 60.662 61.111 8.42 0.00 41.33 4.35
771 795 0.661020 ACGCCACGACAAAAGGAAAG 59.339 50.000 0.00 0.00 0.00 2.62
815 844 5.981315 CAGTACAAACTTCTCGTGTTTCCTA 59.019 40.000 0.00 0.00 35.71 2.94
849 882 2.107366 TGAGACAGTGTCACTTCACCA 58.893 47.619 24.73 8.00 38.91 4.17
856 889 0.036732 TGTCACTTCACCAGCCATCC 59.963 55.000 0.00 0.00 0.00 3.51
873 906 1.133363 TCCCGTCCTCACCTTTTTCA 58.867 50.000 0.00 0.00 0.00 2.69
900 933 2.723124 TTTTTGCGGGAAGATCTTGC 57.277 45.000 17.98 17.98 0.00 4.01
901 934 0.887933 TTTTGCGGGAAGATCTTGCC 59.112 50.000 30.61 30.61 46.10 4.52
902 935 0.965363 TTTGCGGGAAGATCTTGCCC 60.965 55.000 32.93 27.52 46.75 5.36
903 936 1.852157 TTGCGGGAAGATCTTGCCCT 61.852 55.000 32.93 1.65 46.75 5.19
938 971 0.179043 TAGTGAAGCGCCAACCACAA 60.179 50.000 2.29 0.00 32.35 3.33
942 1006 2.127232 AAGCGCCAACCACAAGCTT 61.127 52.632 2.29 0.00 42.51 3.74
955 1019 5.193679 ACCACAAGCTTCTTCAGTAAAACT 58.806 37.500 0.00 0.00 0.00 2.66
958 1022 4.511826 ACAAGCTTCTTCAGTAAAACTCCG 59.488 41.667 0.00 0.00 0.00 4.63
1301 1377 2.376109 CTCCACTCCACCGTATGTACT 58.624 52.381 0.00 0.00 0.00 2.73
1370 1446 3.172575 CTACGTGCACGACTGCCG 61.173 66.667 42.94 17.65 43.51 5.69
1504 1580 4.457496 ACGGTGCTCCTCATGGCG 62.457 66.667 2.85 0.00 0.00 5.69
2061 2137 5.883503 AGTAGTAAGTGAGAAGGAACGAG 57.116 43.478 0.00 0.00 0.00 4.18
2063 2139 2.891580 AGTAAGTGAGAAGGAACGAGCA 59.108 45.455 0.00 0.00 0.00 4.26
2064 2140 2.156343 AAGTGAGAAGGAACGAGCAC 57.844 50.000 0.00 0.00 0.00 4.40
2067 2143 1.728971 GTGAGAAGGAACGAGCACATG 59.271 52.381 0.00 0.00 0.00 3.21
2096 2172 2.285602 CCGTCGAGTCTTTTGTGTGTTG 60.286 50.000 0.00 0.00 0.00 3.33
2236 2384 4.292186 ACTGTGGTTGTCAGCATAATCT 57.708 40.909 0.00 0.00 36.50 2.40
2239 2387 4.910195 TGTGGTTGTCAGCATAATCTTCT 58.090 39.130 0.00 0.00 31.62 2.85
2240 2388 5.316167 TGTGGTTGTCAGCATAATCTTCTT 58.684 37.500 0.00 0.00 31.62 2.52
2241 2389 5.769662 TGTGGTTGTCAGCATAATCTTCTTT 59.230 36.000 0.00 0.00 31.62 2.52
2244 2392 8.296713 GTGGTTGTCAGCATAATCTTCTTTTTA 58.703 33.333 0.00 0.00 31.62 1.52
2245 2393 8.514594 TGGTTGTCAGCATAATCTTCTTTTTAG 58.485 33.333 0.00 0.00 0.00 1.85
2246 2394 7.486232 GGTTGTCAGCATAATCTTCTTTTTAGC 59.514 37.037 0.00 0.00 0.00 3.09
2252 2400 8.457261 CAGCATAATCTTCTTTTTAGCTCAACT 58.543 33.333 0.00 0.00 0.00 3.16
2263 2500 8.375506 TCTTTTTAGCTCAACTATTCTCCAGAA 58.624 33.333 0.00 0.00 38.56 3.02
2270 2507 6.202570 GCTCAACTATTCTCCAGAATTAGCAG 59.797 42.308 7.12 1.92 41.64 4.24
2279 2516 5.824624 TCTCCAGAATTAGCAGCCTAAAATG 59.175 40.000 0.00 0.00 37.12 2.32
2291 2528 2.170166 CCTAAAATGCTGGCCTTGTCA 58.830 47.619 3.32 0.00 0.00 3.58
2424 2661 4.070552 AGGTCTGCCGCGTTCTCC 62.071 66.667 4.92 0.65 40.50 3.71
2464 2701 2.104928 CCGCGCTCATAGCAGTCA 59.895 61.111 5.56 0.00 42.58 3.41
2476 2713 2.813179 GCAGTCATAGCCGGCGTTG 61.813 63.158 23.20 22.14 0.00 4.10
2487 2724 2.027625 CGGCGTTGTGGTCTTCCTC 61.028 63.158 0.00 0.00 34.23 3.71
2520 2757 1.751351 CTCAGCTACATCTTCACCGGA 59.249 52.381 9.46 0.00 0.00 5.14
2615 2852 0.465705 CCCGTGCTATCAGGTGATGT 59.534 55.000 2.56 0.00 36.05 3.06
2616 2853 1.539065 CCCGTGCTATCAGGTGATGTC 60.539 57.143 2.56 0.00 36.05 3.06
2617 2854 1.136891 CCGTGCTATCAGGTGATGTCA 59.863 52.381 2.56 0.00 36.05 3.58
2618 2855 2.224137 CCGTGCTATCAGGTGATGTCAT 60.224 50.000 2.56 0.00 36.05 3.06
2619 2856 3.005791 CCGTGCTATCAGGTGATGTCATA 59.994 47.826 2.56 0.00 36.05 2.15
2620 2857 4.501400 CCGTGCTATCAGGTGATGTCATAA 60.501 45.833 2.56 0.00 36.05 1.90
2621 2858 5.233225 CGTGCTATCAGGTGATGTCATAAT 58.767 41.667 2.56 0.00 36.05 1.28
2622 2859 5.698089 CGTGCTATCAGGTGATGTCATAATT 59.302 40.000 2.56 0.00 36.05 1.40
2623 2860 6.128715 CGTGCTATCAGGTGATGTCATAATTC 60.129 42.308 2.56 0.00 36.05 2.17
2624 2861 6.707608 GTGCTATCAGGTGATGTCATAATTCA 59.292 38.462 2.56 0.00 36.05 2.57
2625 2862 6.932960 TGCTATCAGGTGATGTCATAATTCAG 59.067 38.462 2.56 0.00 36.05 3.02
2626 2863 6.128336 GCTATCAGGTGATGTCATAATTCAGC 60.128 42.308 2.56 0.00 37.97 4.26
2627 2864 4.454678 TCAGGTGATGTCATAATTCAGCC 58.545 43.478 0.81 0.00 38.35 4.85
2628 2865 3.567164 CAGGTGATGTCATAATTCAGCCC 59.433 47.826 0.81 0.00 38.35 5.19
2629 2866 2.549754 GGTGATGTCATAATTCAGCCCG 59.450 50.000 0.00 0.00 33.02 6.13
2630 2867 3.206150 GTGATGTCATAATTCAGCCCGT 58.794 45.455 0.00 0.00 0.00 5.28
2631 2868 3.002656 GTGATGTCATAATTCAGCCCGTG 59.997 47.826 0.00 0.00 0.00 4.94
2632 2869 1.378531 TGTCATAATTCAGCCCGTGC 58.621 50.000 0.00 0.00 37.95 5.34
2633 2870 0.304705 GTCATAATTCAGCCCGTGCG 59.695 55.000 0.00 0.00 44.33 5.34
2634 2871 1.009675 CATAATTCAGCCCGTGCGC 60.010 57.895 0.00 0.00 44.33 6.09
2635 2872 1.153168 ATAATTCAGCCCGTGCGCT 60.153 52.632 9.73 0.00 44.33 5.92
2644 2881 4.873129 CCGTGCGCTGCGGTATCT 62.873 66.667 27.32 0.00 43.84 1.98
2645 2882 2.025584 CGTGCGCTGCGGTATCTA 59.974 61.111 24.61 0.00 0.00 1.98
2646 2883 1.587876 CGTGCGCTGCGGTATCTAA 60.588 57.895 24.61 0.00 0.00 2.10
2647 2884 1.808234 CGTGCGCTGCGGTATCTAAC 61.808 60.000 24.61 4.60 0.00 2.34
2648 2885 0.527817 GTGCGCTGCGGTATCTAACT 60.528 55.000 24.61 0.00 0.00 2.24
2649 2886 1.026584 TGCGCTGCGGTATCTAACTA 58.973 50.000 24.61 0.00 0.00 2.24
2650 2887 1.611977 TGCGCTGCGGTATCTAACTAT 59.388 47.619 24.61 0.00 0.00 2.12
2651 2888 2.251893 GCGCTGCGGTATCTAACTATC 58.748 52.381 24.61 0.00 0.00 2.08
2652 2889 2.095161 GCGCTGCGGTATCTAACTATCT 60.095 50.000 24.61 0.00 0.00 1.98
2653 2890 3.749404 CGCTGCGGTATCTAACTATCTC 58.251 50.000 15.40 0.00 0.00 2.75
2654 2891 3.437395 CGCTGCGGTATCTAACTATCTCT 59.563 47.826 15.40 0.00 0.00 3.10
2655 2892 4.670478 CGCTGCGGTATCTAACTATCTCTG 60.670 50.000 15.40 0.00 0.00 3.35
2656 2893 4.380023 GCTGCGGTATCTAACTATCTCTGG 60.380 50.000 0.00 0.00 0.00 3.86
2657 2894 4.726583 TGCGGTATCTAACTATCTCTGGT 58.273 43.478 0.00 0.00 0.00 4.00
2658 2895 5.138276 TGCGGTATCTAACTATCTCTGGTT 58.862 41.667 0.00 0.00 0.00 3.67
2659 2896 6.301486 TGCGGTATCTAACTATCTCTGGTTA 58.699 40.000 0.00 0.00 0.00 2.85
2660 2897 6.774170 TGCGGTATCTAACTATCTCTGGTTAA 59.226 38.462 0.00 0.00 29.19 2.01
2661 2898 7.450634 TGCGGTATCTAACTATCTCTGGTTAAT 59.549 37.037 0.00 0.00 29.19 1.40
2662 2899 7.969508 GCGGTATCTAACTATCTCTGGTTAATC 59.030 40.741 0.00 0.00 29.19 1.75
2663 2900 9.011095 CGGTATCTAACTATCTCTGGTTAATCA 57.989 37.037 0.00 0.00 29.19 2.57
2668 2905 9.434275 TCTAACTATCTCTGGTTAATCAATGGA 57.566 33.333 0.00 0.00 29.19 3.41
2669 2906 9.703892 CTAACTATCTCTGGTTAATCAATGGAG 57.296 37.037 0.00 0.00 29.19 3.86
2670 2907 7.921041 ACTATCTCTGGTTAATCAATGGAGA 57.079 36.000 8.21 8.21 33.77 3.71
2671 2908 7.731054 ACTATCTCTGGTTAATCAATGGAGAC 58.269 38.462 8.00 0.00 32.39 3.36
2672 2909 5.011090 TCTCTGGTTAATCAATGGAGACG 57.989 43.478 2.81 0.00 0.00 4.18
2673 2910 3.531538 TCTGGTTAATCAATGGAGACGC 58.468 45.455 0.00 0.00 0.00 5.19
2674 2911 2.614057 CTGGTTAATCAATGGAGACGCC 59.386 50.000 0.00 0.00 37.10 5.68
2675 2912 1.947456 GGTTAATCAATGGAGACGCCC 59.053 52.381 0.00 0.00 34.97 6.13
2676 2913 2.639065 GTTAATCAATGGAGACGCCCA 58.361 47.619 0.00 0.00 41.05 5.36
2678 2915 1.972872 AATCAATGGAGACGCCCATC 58.027 50.000 5.24 0.00 45.69 3.51
2679 2916 1.135094 ATCAATGGAGACGCCCATCT 58.865 50.000 5.24 0.00 45.69 2.90
2680 2917 1.788229 TCAATGGAGACGCCCATCTA 58.212 50.000 5.24 0.00 45.69 1.98
2681 2918 1.688735 TCAATGGAGACGCCCATCTAG 59.311 52.381 5.24 0.00 45.69 2.43
2682 2919 1.414181 CAATGGAGACGCCCATCTAGT 59.586 52.381 5.24 0.00 45.69 2.57
2683 2920 2.628178 CAATGGAGACGCCCATCTAGTA 59.372 50.000 5.24 0.00 45.69 1.82
2684 2921 2.447408 TGGAGACGCCCATCTAGTAA 57.553 50.000 0.00 0.00 34.97 2.24
2685 2922 2.307768 TGGAGACGCCCATCTAGTAAG 58.692 52.381 0.00 0.00 34.97 2.34
2693 4407 3.665190 GCCCATCTAGTAAGGGAATTCG 58.335 50.000 17.35 0.00 45.80 3.34
2725 4439 2.032924 GTCTTGACCGGTGTCCTTTTTG 59.967 50.000 14.63 0.00 41.01 2.44
2814 4528 3.173668 TGCTATTACTTCATCGGCGTT 57.826 42.857 6.85 0.00 0.00 4.84
2864 4590 6.415573 AGTTTGACTATGGAATCAAGGTACC 58.584 40.000 2.73 2.73 36.26 3.34
2865 4591 4.665833 TGACTATGGAATCAAGGTACCG 57.334 45.455 6.18 0.00 0.00 4.02
2866 4592 4.028131 TGACTATGGAATCAAGGTACCGT 58.972 43.478 6.18 0.00 0.00 4.83
2867 4593 4.468510 TGACTATGGAATCAAGGTACCGTT 59.531 41.667 6.18 0.27 0.00 4.44
2868 4594 5.657745 TGACTATGGAATCAAGGTACCGTTA 59.342 40.000 6.18 0.00 0.00 3.18
2869 4595 5.910614 ACTATGGAATCAAGGTACCGTTAC 58.089 41.667 6.18 2.15 0.00 2.50
2872 4598 3.196254 TGGAATCAAGGTACCGTTACTCC 59.804 47.826 6.18 11.73 0.00 3.85
2881 4607 1.192428 ACCGTTACTCCCAAGCTAGG 58.808 55.000 0.00 0.00 0.00 3.02
2910 4636 3.611530 GCTTTCAAAGCGCTTATTCACCA 60.612 43.478 25.33 3.17 45.74 4.17
2911 4637 4.545610 CTTTCAAAGCGCTTATTCACCAA 58.454 39.130 25.33 8.62 0.00 3.67
2912 4638 4.576216 TTCAAAGCGCTTATTCACCAAA 57.424 36.364 25.33 6.25 0.00 3.28
2913 4639 4.159377 TCAAAGCGCTTATTCACCAAAG 57.841 40.909 25.33 3.72 0.00 2.77
2914 4640 3.818210 TCAAAGCGCTTATTCACCAAAGA 59.182 39.130 25.33 5.96 0.00 2.52
2952 4678 5.349543 TCATCATTCATGTTGAGTTGACTCG 59.650 40.000 6.66 0.00 38.51 4.18
2957 4683 3.317993 TCATGTTGAGTTGACTCGTCAGA 59.682 43.478 6.66 5.55 45.72 3.27
3061 4787 0.394762 GAGGCATGATTGGAGGCACA 60.395 55.000 0.00 0.00 0.00 4.57
3137 4866 3.181453 GGAGGTAGGAGCAAACCTTATCC 60.181 52.174 2.69 5.11 46.22 2.59
3138 4867 3.712218 GAGGTAGGAGCAAACCTTATCCT 59.288 47.826 2.69 8.26 46.22 3.24
3236 4965 4.690748 GCTAAGCCGCATCTAAATCATGTA 59.309 41.667 0.00 0.00 0.00 2.29
3266 4995 8.190122 ACTCATTATTTTAGCGCAATCATTTCA 58.810 29.630 11.47 0.00 0.00 2.69
3298 5027 3.310501 CGCATGCTTTGTATGATCACTCA 59.689 43.478 17.13 0.00 35.41 3.41
3310 5039 4.897509 TGATCACTCAGGTTGTCTCATT 57.102 40.909 0.00 0.00 0.00 2.57
3327 5056 8.924511 TGTCTCATTTGTCCTCTCTTAATTTT 57.075 30.769 0.00 0.00 0.00 1.82
3330 5059 6.924111 TCATTTGTCCTCTCTTAATTTTGCC 58.076 36.000 0.00 0.00 0.00 4.52
3332 5061 7.888021 TCATTTGTCCTCTCTTAATTTTGCCTA 59.112 33.333 0.00 0.00 0.00 3.93
3354 6544 9.665264 GCCTATAAAACTAATAGTGCATTTCAC 57.335 33.333 0.00 0.00 45.98 3.18
3469 6661 4.310769 CTGTTTCAGTTGTCCTCTCGAAT 58.689 43.478 0.00 0.00 0.00 3.34
3473 6665 3.575630 TCAGTTGTCCTCTCGAATTTCG 58.424 45.455 12.54 12.54 42.10 3.46
3508 6700 3.347958 TGCGAATTTTGTGTCTGAACC 57.652 42.857 0.00 0.00 0.00 3.62
3609 6801 2.095372 GCCCGGAGAAGATTAACGTTTG 59.905 50.000 5.91 0.00 0.00 2.93
3656 6848 4.698201 TCCACTCACCAACTTATGTTCA 57.302 40.909 0.00 0.00 33.52 3.18
3770 6991 0.250234 TGGTGCTCCTTCAGGATTCG 59.750 55.000 6.34 0.00 44.46 3.34
3780 7001 3.058432 CCTTCAGGATTCGCATGCTATTG 60.058 47.826 17.13 5.70 37.39 1.90
3792 7013 3.944015 GCATGCTATTGTGAACTCTCCTT 59.056 43.478 11.37 0.00 0.00 3.36
3793 7014 4.034975 GCATGCTATTGTGAACTCTCCTTC 59.965 45.833 11.37 0.00 0.00 3.46
3794 7015 4.890158 TGCTATTGTGAACTCTCCTTCA 57.110 40.909 0.00 0.00 0.00 3.02
3795 7016 4.825422 TGCTATTGTGAACTCTCCTTCAG 58.175 43.478 0.00 0.00 30.63 3.02
3796 7017 4.187694 GCTATTGTGAACTCTCCTTCAGG 58.812 47.826 0.00 0.00 30.63 3.86
3797 7018 4.081420 GCTATTGTGAACTCTCCTTCAGGA 60.081 45.833 0.00 0.00 43.08 3.86
3798 7019 5.396213 GCTATTGTGAACTCTCCTTCAGGAT 60.396 44.000 0.00 0.00 44.46 3.24
3799 7020 4.982241 TTGTGAACTCTCCTTCAGGATT 57.018 40.909 0.00 0.00 44.46 3.01
3800 7021 4.543590 TGTGAACTCTCCTTCAGGATTC 57.456 45.455 0.00 0.00 44.46 2.52
3801 7022 3.903714 TGTGAACTCTCCTTCAGGATTCA 59.096 43.478 6.35 6.35 44.46 2.57
3802 7023 4.249661 GTGAACTCTCCTTCAGGATTCAC 58.750 47.826 18.55 18.55 46.02 3.18
3803 7024 3.903714 TGAACTCTCCTTCAGGATTCACA 59.096 43.478 6.35 0.00 44.46 3.58
3804 7025 3.971245 ACTCTCCTTCAGGATTCACAC 57.029 47.619 0.00 0.00 44.46 3.82
3805 7026 2.232452 ACTCTCCTTCAGGATTCACACG 59.768 50.000 0.00 0.00 44.46 4.49
3806 7027 1.066858 TCTCCTTCAGGATTCACACGC 60.067 52.381 0.00 0.00 44.46 5.34
3807 7028 0.976641 TCCTTCAGGATTCACACGCT 59.023 50.000 0.00 0.00 39.78 5.07
3808 7029 2.166459 CTCCTTCAGGATTCACACGCTA 59.834 50.000 0.00 0.00 44.46 4.26
3831 7052 7.926555 GCTATTCTCAGTAAGTGGCTGTATAAA 59.073 37.037 0.00 0.00 35.60 1.40
3887 7108 5.526846 AGATTCTCCGTAGTAAGTACCTTCG 59.473 44.000 0.00 0.00 0.00 3.79
3903 7124 2.357637 CCTTCGCTCCAAAACTTTGTCA 59.642 45.455 1.76 0.00 36.45 3.58
3904 7125 3.181491 CCTTCGCTCCAAAACTTTGTCAA 60.181 43.478 1.76 0.00 36.45 3.18
3954 7248 2.040278 CACCACAAGATTCTGGGAGGAA 59.960 50.000 8.37 0.00 0.00 3.36
4147 7444 3.008330 CTGATGGAGGTTCAGCTTTCTG 58.992 50.000 0.00 0.00 41.67 3.02
4166 7463 0.674895 GAACAACCCGATCAGCTGCT 60.675 55.000 9.47 0.00 0.00 4.24
4174 7471 0.530211 CGATCAGCTGCTCTGGAAGG 60.530 60.000 15.15 0.00 43.06 3.46
4193 7490 5.339861 GGAAGGTTACTAGGACTGGAGAGTA 60.340 48.000 0.00 0.00 30.16 2.59
4357 7654 1.065600 GCAAAGCGCAACTGGACAA 59.934 52.632 11.47 0.00 41.79 3.18
4383 7681 6.056428 CCTACAAGGTGTAGTTTTTGTGAC 57.944 41.667 13.01 0.00 46.68 3.67
4577 7879 2.224744 TGCTTTATTGTGGGCAGTCTGA 60.225 45.455 3.32 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 126 8.798402 AGGTAACATGGAATTTCGAAAATTGTA 58.202 29.630 15.66 1.38 41.41 2.41
114 135 5.092781 CGGAAAAGGTAACATGGAATTTCG 58.907 41.667 0.00 0.00 41.41 3.46
160 181 7.064728 GGAGAAGTGAACTGCGAGTTATATTTT 59.935 37.037 2.17 0.00 38.80 1.82
164 185 4.705507 AGGAGAAGTGAACTGCGAGTTATA 59.294 41.667 2.17 0.00 38.80 0.98
166 187 2.891580 AGGAGAAGTGAACTGCGAGTTA 59.108 45.455 2.17 0.00 38.80 2.24
205 226 1.208052 ATAGCTGGTGGCGGCTATATG 59.792 52.381 11.43 0.00 46.06 1.78
214 235 2.876368 AAGACGGCATAGCTGGTGGC 62.876 60.000 14.87 14.87 39.57 5.01
215 236 0.392998 AAAGACGGCATAGCTGGTGG 60.393 55.000 0.00 0.00 39.57 4.61
216 237 1.131126 CAAAAGACGGCATAGCTGGTG 59.869 52.381 0.00 0.00 39.57 4.17
219 240 2.474526 CGAACAAAAGACGGCATAGCTG 60.475 50.000 0.00 0.00 41.29 4.24
231 252 7.393551 ACATTGCATTTTAGACGAACAAAAG 57.606 32.000 0.00 0.00 0.00 2.27
232 253 6.141527 CGACATTGCATTTTAGACGAACAAAA 59.858 34.615 0.00 0.00 0.00 2.44
255 276 1.305219 GCACTACTGCCAAATGCCGA 61.305 55.000 0.00 0.00 40.16 5.54
257 278 0.890683 AAGCACTACTGCCAAATGCC 59.109 50.000 0.00 0.00 45.53 4.40
261 282 2.928801 TCTCAAGCACTACTGCCAAA 57.071 45.000 0.00 0.00 45.53 3.28
267 288 4.093011 ACTCCAAGATCTCAAGCACTACT 58.907 43.478 0.00 0.00 0.00 2.57
276 297 5.423290 TCTTTCTGCATACTCCAAGATCTCA 59.577 40.000 0.00 0.00 0.00 3.27
293 314 4.911390 ACAACCCCAAGTCTATCTTTCTG 58.089 43.478 0.00 0.00 33.63 3.02
316 337 1.268352 GCTAACATCGGCACAAACCAA 59.732 47.619 0.00 0.00 0.00 3.67
326 347 0.532862 ATCGGCAAGGCTAACATCGG 60.533 55.000 0.00 0.00 0.00 4.18
328 349 1.953559 TGATCGGCAAGGCTAACATC 58.046 50.000 0.00 0.00 0.00 3.06
343 364 4.612264 ATTATTTGGCAAGCCCATGATC 57.388 40.909 8.89 0.00 44.89 2.92
347 368 3.564053 CCAATTATTTGGCAAGCCCAT 57.436 42.857 8.89 3.46 45.71 4.00
356 377 5.269805 GGAAATCCAGCGCCAATTATTTGG 61.270 45.833 2.29 11.34 44.60 3.28
357 378 3.803778 GGAAATCCAGCGCCAATTATTTG 59.196 43.478 2.29 0.00 35.64 2.32
381 402 3.456431 TTTTTCGCACGCGTGGGTG 62.456 57.895 42.40 25.87 43.11 4.61
406 427 5.419542 AGATAGCTACAGTTCAATTCGCAA 58.580 37.500 0.00 0.00 0.00 4.85
458 481 2.174639 TCTGGGTGTTCATTTGAGTGGT 59.825 45.455 0.00 0.00 0.00 4.16
462 485 2.227388 GCTGTCTGGGTGTTCATTTGAG 59.773 50.000 0.00 0.00 0.00 3.02
463 486 2.229792 GCTGTCTGGGTGTTCATTTGA 58.770 47.619 0.00 0.00 0.00 2.69
468 491 1.053835 TCTGGCTGTCTGGGTGTTCA 61.054 55.000 0.00 0.00 0.00 3.18
476 499 1.294780 GACCCAGTCTGGCTGTCTG 59.705 63.158 13.99 10.73 43.55 3.51
477 500 0.764369 TTGACCCAGTCTGGCTGTCT 60.764 55.000 21.84 0.00 43.55 3.41
479 502 1.344953 TGTTGACCCAGTCTGGCTGT 61.345 55.000 13.99 6.93 43.55 4.40
480 503 0.037303 ATGTTGACCCAGTCTGGCTG 59.963 55.000 13.99 1.37 44.63 4.85
481 504 0.326264 GATGTTGACCCAGTCTGGCT 59.674 55.000 13.99 0.00 35.79 4.75
482 505 0.678048 GGATGTTGACCCAGTCTGGC 60.678 60.000 13.99 1.25 35.79 4.85
483 506 0.692476 TGGATGTTGACCCAGTCTGG 59.308 55.000 12.40 12.40 37.25 3.86
484 507 2.566833 TTGGATGTTGACCCAGTCTG 57.433 50.000 0.00 0.00 33.43 3.51
485 508 5.456921 AATATTGGATGTTGACCCAGTCT 57.543 39.130 0.00 0.00 33.43 3.24
486 509 6.332630 CAAAATATTGGATGTTGACCCAGTC 58.667 40.000 0.00 0.00 33.43 3.51
487 510 6.284891 CAAAATATTGGATGTTGACCCAGT 57.715 37.500 0.00 0.00 33.43 4.00
514 537 4.463879 CTGCCCTGAGACGCCCTG 62.464 72.222 0.00 0.00 0.00 4.45
516 539 4.767255 CACTGCCCTGAGACGCCC 62.767 72.222 0.00 0.00 0.00 6.13
517 540 3.240134 TTCACTGCCCTGAGACGCC 62.240 63.158 0.00 0.00 0.00 5.68
518 541 2.029844 GTTCACTGCCCTGAGACGC 61.030 63.158 0.00 0.00 0.00 5.19
519 542 1.374758 GGTTCACTGCCCTGAGACG 60.375 63.158 0.00 0.00 0.00 4.18
520 543 0.036858 GAGGTTCACTGCCCTGAGAC 60.037 60.000 0.00 0.00 0.00 3.36
531 554 3.994392 TCAACTTGCTATTCGAGGTTCAC 59.006 43.478 0.00 0.00 0.00 3.18
532 555 4.265904 TCAACTTGCTATTCGAGGTTCA 57.734 40.909 0.00 0.00 0.00 3.18
533 556 5.383130 GTTTCAACTTGCTATTCGAGGTTC 58.617 41.667 0.00 0.00 0.00 3.62
534 557 4.084013 CGTTTCAACTTGCTATTCGAGGTT 60.084 41.667 0.00 0.00 0.00 3.50
535 558 3.432252 CGTTTCAACTTGCTATTCGAGGT 59.568 43.478 0.00 0.00 0.00 3.85
536 559 3.432252 ACGTTTCAACTTGCTATTCGAGG 59.568 43.478 0.00 0.00 0.00 4.63
537 560 4.647291 ACGTTTCAACTTGCTATTCGAG 57.353 40.909 0.00 0.00 0.00 4.04
538 561 4.088923 CGTACGTTTCAACTTGCTATTCGA 59.911 41.667 7.22 0.00 0.00 3.71
554 577 6.261603 TCAATCCTATACATCTCACGTACGTT 59.738 38.462 20.23 5.64 0.00 3.99
568 591 7.441458 AGTTTGTTAGGCGATTCAATCCTATAC 59.559 37.037 0.00 0.00 32.96 1.47
578 601 7.695201 GGTTATTACAAGTTTGTTAGGCGATTC 59.305 37.037 2.46 0.00 42.35 2.52
582 605 6.490566 AGGTTATTACAAGTTTGTTAGGCG 57.509 37.500 2.46 0.00 42.35 5.52
600 623 8.938801 ATATATTGAACATGGATGCAAGGTTA 57.061 30.769 7.45 0.00 0.00 2.85
616 639 9.672673 GGCAGCTTCTCCTTTATATATATTGAA 57.327 33.333 0.00 0.00 0.00 2.69
617 640 7.981789 CGGCAGCTTCTCCTTTATATATATTGA 59.018 37.037 0.00 0.00 0.00 2.57
618 641 7.225538 CCGGCAGCTTCTCCTTTATATATATTG 59.774 40.741 0.00 0.00 0.00 1.90
619 642 7.092846 ACCGGCAGCTTCTCCTTTATATATATT 60.093 37.037 0.00 0.00 0.00 1.28
620 643 6.384305 ACCGGCAGCTTCTCCTTTATATATAT 59.616 38.462 0.00 0.00 0.00 0.86
622 645 4.532521 ACCGGCAGCTTCTCCTTTATATAT 59.467 41.667 0.00 0.00 0.00 0.86
623 646 3.901844 ACCGGCAGCTTCTCCTTTATATA 59.098 43.478 0.00 0.00 0.00 0.86
626 649 0.912486 ACCGGCAGCTTCTCCTTTAT 59.088 50.000 0.00 0.00 0.00 1.40
674 697 2.201830 AGGTGGATCCCGGTCAAATTA 58.798 47.619 9.90 0.00 36.75 1.40
692 715 6.920569 AAACACAGAAGTTACACTGTAAGG 57.079 37.500 12.80 6.14 44.07 2.69
713 736 5.219633 GGAGAAAAGAAGCATGCGTTAAAA 58.780 37.500 13.01 0.00 0.00 1.52
722 745 1.428912 TGTGGGGGAGAAAAGAAGCAT 59.571 47.619 0.00 0.00 0.00 3.79
758 782 3.789224 CGTTTTGTCCTTTCCTTTTGTCG 59.211 43.478 0.00 0.00 0.00 4.35
762 786 4.703093 TGACTCGTTTTGTCCTTTCCTTTT 59.297 37.500 0.00 0.00 33.83 2.27
771 795 3.395639 TGGTGTATGACTCGTTTTGTCC 58.604 45.455 0.00 0.00 33.83 4.02
815 844 0.171455 GTCTCACTGCGATCGGAACT 59.829 55.000 18.30 0.00 0.00 3.01
849 882 3.083997 GGTGAGGACGGGATGGCT 61.084 66.667 0.00 0.00 0.00 4.75
856 889 4.037446 TGAAAATGAAAAAGGTGAGGACGG 59.963 41.667 0.00 0.00 0.00 4.79
900 933 1.584724 ACATGTTAGGTGAGGGAGGG 58.415 55.000 0.00 0.00 0.00 4.30
901 934 3.133003 CACTACATGTTAGGTGAGGGAGG 59.867 52.174 2.30 0.00 32.12 4.30
902 935 4.023980 TCACTACATGTTAGGTGAGGGAG 58.976 47.826 18.46 4.67 34.38 4.30
903 936 4.055710 TCACTACATGTTAGGTGAGGGA 57.944 45.455 18.46 8.04 34.38 4.20
938 971 4.602340 TCGGAGTTTTACTGAAGAAGCT 57.398 40.909 0.00 0.00 0.00 3.74
942 1006 7.442656 AGATCTTTTCGGAGTTTTACTGAAGA 58.557 34.615 0.00 0.00 34.73 2.87
1301 1377 2.665649 ACGGATGCGTAGAAATGACA 57.334 45.000 11.73 0.00 0.00 3.58
1321 1397 4.781959 GCGCCCACGTACGTAGCA 62.782 66.667 30.31 0.00 42.83 3.49
1388 1464 2.437180 CATCCCGAGCTGCAGCAA 60.437 61.111 38.24 19.02 45.16 3.91
1444 1520 0.100682 GCATCTCGTACTTCTCGGCA 59.899 55.000 0.00 0.00 0.00 5.69
1483 1559 1.517257 CATGAGGAGCACCGTCGAC 60.517 63.158 5.18 5.18 41.83 4.20
2040 2116 4.082895 TGCTCGTTCCTTCTCACTTACTAC 60.083 45.833 0.00 0.00 0.00 2.73
2041 2117 4.077108 TGCTCGTTCCTTCTCACTTACTA 58.923 43.478 0.00 0.00 0.00 1.82
2042 2118 2.891580 TGCTCGTTCCTTCTCACTTACT 59.108 45.455 0.00 0.00 0.00 2.24
2044 2120 2.626266 TGTGCTCGTTCCTTCTCACTTA 59.374 45.455 0.00 0.00 0.00 2.24
2045 2121 1.412710 TGTGCTCGTTCCTTCTCACTT 59.587 47.619 0.00 0.00 0.00 3.16
2046 2122 1.040646 TGTGCTCGTTCCTTCTCACT 58.959 50.000 0.00 0.00 0.00 3.41
2047 2123 1.728971 CATGTGCTCGTTCCTTCTCAC 59.271 52.381 0.00 0.00 0.00 3.51
2048 2124 1.338105 CCATGTGCTCGTTCCTTCTCA 60.338 52.381 0.00 0.00 0.00 3.27
2049 2125 1.338200 ACCATGTGCTCGTTCCTTCTC 60.338 52.381 0.00 0.00 0.00 2.87
2050 2126 0.687354 ACCATGTGCTCGTTCCTTCT 59.313 50.000 0.00 0.00 0.00 2.85
2051 2127 1.523758 AACCATGTGCTCGTTCCTTC 58.476 50.000 0.00 0.00 0.00 3.46
2052 2128 1.981256 AAACCATGTGCTCGTTCCTT 58.019 45.000 0.00 0.00 0.00 3.36
2053 2129 1.608590 CAAAACCATGTGCTCGTTCCT 59.391 47.619 0.00 0.00 0.00 3.36
2054 2130 1.336755 ACAAAACCATGTGCTCGTTCC 59.663 47.619 0.00 0.00 30.82 3.62
2061 2137 0.385473 CGACGGACAAAACCATGTGC 60.385 55.000 0.00 0.00 38.18 4.57
2063 2139 1.202604 ACTCGACGGACAAAACCATGT 60.203 47.619 0.00 0.00 35.90 3.21
2064 2140 1.459592 GACTCGACGGACAAAACCATG 59.540 52.381 0.00 0.00 0.00 3.66
2067 2143 1.861971 AAGACTCGACGGACAAAACC 58.138 50.000 0.00 0.00 0.00 3.27
2096 2172 2.540101 GGTCACACGATCATCGAATTCC 59.460 50.000 15.60 5.74 43.74 3.01
2236 2384 8.375506 TCTGGAGAATAGTTGAGCTAAAAAGAA 58.624 33.333 0.00 0.00 32.72 2.52
2239 2387 9.520515 AATTCTGGAGAATAGTTGAGCTAAAAA 57.479 29.630 2.30 0.00 43.41 1.94
2241 2389 9.823647 CTAATTCTGGAGAATAGTTGAGCTAAA 57.176 33.333 2.30 0.00 43.41 1.85
2244 2392 6.126940 TGCTAATTCTGGAGAATAGTTGAGCT 60.127 38.462 2.30 0.00 43.41 4.09
2245 2393 6.051717 TGCTAATTCTGGAGAATAGTTGAGC 58.948 40.000 2.30 7.44 43.41 4.26
2246 2394 6.202570 GCTGCTAATTCTGGAGAATAGTTGAG 59.797 42.308 2.30 0.00 43.41 3.02
2252 2400 6.747414 TTAGGCTGCTAATTCTGGAGAATA 57.253 37.500 0.00 0.00 43.41 1.75
2256 2493 5.506982 GCATTTTAGGCTGCTAATTCTGGAG 60.507 44.000 0.00 0.00 35.49 3.86
2257 2494 4.339247 GCATTTTAGGCTGCTAATTCTGGA 59.661 41.667 0.00 0.00 35.49 3.86
2287 2524 2.835701 GATCCTTGACGCGGCTGACA 62.836 60.000 15.80 0.36 0.00 3.58
2291 2528 2.172483 AACAGATCCTTGACGCGGCT 62.172 55.000 15.80 0.00 0.00 5.52
2293 2530 2.004583 TAAACAGATCCTTGACGCGG 57.995 50.000 12.47 0.00 0.00 6.46
2294 2531 3.243877 CAGATAAACAGATCCTTGACGCG 59.756 47.826 3.53 3.53 0.00 6.01
2295 2532 4.433615 TCAGATAAACAGATCCTTGACGC 58.566 43.478 0.00 0.00 0.00 5.19
2296 2533 7.545362 AATTCAGATAAACAGATCCTTGACG 57.455 36.000 0.00 0.00 0.00 4.35
2330 2567 8.557864 CATCAACATTGATCAACTCTATCCTTC 58.442 37.037 11.07 0.00 45.62 3.46
2334 2571 7.642978 GCAACATCAACATTGATCAACTCTATC 59.357 37.037 11.07 0.00 45.62 2.08
2424 2661 2.890474 GCGGTGACTACCCATGCG 60.890 66.667 0.00 0.00 44.53 4.73
2433 2670 4.760047 GCGGACATGGCGGTGACT 62.760 66.667 8.06 0.00 0.00 3.41
2464 2701 2.125269 GACCACAACGCCGGCTAT 60.125 61.111 26.68 9.97 0.00 2.97
2476 2713 1.194781 TGCCTGAGGAGGAAGACCAC 61.195 60.000 0.65 0.00 42.93 4.16
2487 2724 2.039405 GCTGAGCTTGTGCCTGAGG 61.039 63.158 0.00 0.00 40.80 3.86
2538 2775 2.653448 CAGAGATCTGCGACCGCG 60.653 66.667 0.00 0.00 45.51 6.46
2547 2784 3.616076 CGACAAGCAAAGGACAGAGATCT 60.616 47.826 0.00 0.00 0.00 2.75
2611 2848 2.031682 GCACGGGCTGAATTATGACATC 60.032 50.000 0.00 0.00 36.96 3.06
2615 2852 1.436195 GCGCACGGGCTGAATTATGA 61.436 55.000 8.62 0.00 38.10 2.15
2616 2853 1.009675 GCGCACGGGCTGAATTATG 60.010 57.895 8.62 0.00 38.10 1.90
2617 2854 1.153168 AGCGCACGGGCTGAATTAT 60.153 52.632 11.47 0.00 42.86 1.28
2618 2855 2.267642 AGCGCACGGGCTGAATTA 59.732 55.556 11.47 0.00 42.86 1.40
2628 2865 1.587876 TTAGATACCGCAGCGCACG 60.588 57.895 11.47 13.60 0.00 5.34
2629 2866 0.527817 AGTTAGATACCGCAGCGCAC 60.528 55.000 11.47 0.00 0.00 5.34
2630 2867 1.026584 TAGTTAGATACCGCAGCGCA 58.973 50.000 11.47 0.00 0.00 6.09
2631 2868 2.095161 AGATAGTTAGATACCGCAGCGC 60.095 50.000 10.07 0.00 0.00 5.92
2632 2869 3.437395 AGAGATAGTTAGATACCGCAGCG 59.563 47.826 8.18 8.18 0.00 5.18
2633 2870 4.380023 CCAGAGATAGTTAGATACCGCAGC 60.380 50.000 0.00 0.00 0.00 5.25
2634 2871 4.762765 ACCAGAGATAGTTAGATACCGCAG 59.237 45.833 0.00 0.00 0.00 5.18
2635 2872 4.726583 ACCAGAGATAGTTAGATACCGCA 58.273 43.478 0.00 0.00 0.00 5.69
2636 2873 5.708877 AACCAGAGATAGTTAGATACCGC 57.291 43.478 0.00 0.00 0.00 5.68
2637 2874 9.011095 TGATTAACCAGAGATAGTTAGATACCG 57.989 37.037 0.00 0.00 0.00 4.02
2642 2879 9.434275 TCCATTGATTAACCAGAGATAGTTAGA 57.566 33.333 0.00 0.00 0.00 2.10
2643 2880 9.703892 CTCCATTGATTAACCAGAGATAGTTAG 57.296 37.037 0.00 0.00 0.00 2.34
2644 2881 9.434275 TCTCCATTGATTAACCAGAGATAGTTA 57.566 33.333 0.00 0.00 0.00 2.24
2645 2882 8.207545 GTCTCCATTGATTAACCAGAGATAGTT 58.792 37.037 0.00 0.00 32.05 2.24
2646 2883 7.470702 CGTCTCCATTGATTAACCAGAGATAGT 60.471 40.741 0.00 0.00 32.05 2.12
2647 2884 6.865726 CGTCTCCATTGATTAACCAGAGATAG 59.134 42.308 0.00 0.00 32.05 2.08
2648 2885 6.738731 GCGTCTCCATTGATTAACCAGAGATA 60.739 42.308 0.00 0.00 32.05 1.98
2649 2886 5.605534 CGTCTCCATTGATTAACCAGAGAT 58.394 41.667 0.00 0.00 32.05 2.75
2650 2887 4.680708 GCGTCTCCATTGATTAACCAGAGA 60.681 45.833 0.00 0.00 0.00 3.10
2651 2888 3.557595 GCGTCTCCATTGATTAACCAGAG 59.442 47.826 0.00 0.00 0.00 3.35
2652 2889 3.531538 GCGTCTCCATTGATTAACCAGA 58.468 45.455 0.00 0.00 0.00 3.86
2653 2890 2.614057 GGCGTCTCCATTGATTAACCAG 59.386 50.000 0.00 0.00 34.01 4.00
2654 2891 2.639065 GGCGTCTCCATTGATTAACCA 58.361 47.619 0.00 0.00 34.01 3.67
2655 2892 1.947456 GGGCGTCTCCATTGATTAACC 59.053 52.381 0.00 0.00 36.21 2.85
2656 2893 2.639065 TGGGCGTCTCCATTGATTAAC 58.361 47.619 0.00 0.00 36.21 2.01
2657 2894 3.136443 AGATGGGCGTCTCCATTGATTAA 59.864 43.478 8.13 0.00 46.67 1.40
2658 2895 2.705658 AGATGGGCGTCTCCATTGATTA 59.294 45.455 8.13 0.00 46.67 1.75
2659 2896 1.492176 AGATGGGCGTCTCCATTGATT 59.508 47.619 8.13 0.00 46.67 2.57
2660 2897 1.135094 AGATGGGCGTCTCCATTGAT 58.865 50.000 8.13 0.00 46.67 2.57
2661 2898 1.688735 CTAGATGGGCGTCTCCATTGA 59.311 52.381 8.13 1.03 46.67 2.57
2662 2899 1.414181 ACTAGATGGGCGTCTCCATTG 59.586 52.381 0.00 5.59 46.67 2.82
2663 2900 1.794714 ACTAGATGGGCGTCTCCATT 58.205 50.000 0.00 3.11 46.67 3.16
2665 2902 2.307768 CTTACTAGATGGGCGTCTCCA 58.692 52.381 0.00 0.00 41.60 3.86
2666 2903 1.614413 CCTTACTAGATGGGCGTCTCC 59.386 57.143 0.00 0.00 0.00 3.71
2667 2904 1.614413 CCCTTACTAGATGGGCGTCTC 59.386 57.143 0.00 0.00 35.78 3.36
2668 2905 1.217183 TCCCTTACTAGATGGGCGTCT 59.783 52.381 12.42 0.00 41.55 4.18
2669 2906 1.700955 TCCCTTACTAGATGGGCGTC 58.299 55.000 12.42 0.00 41.55 5.19
2670 2907 2.170012 TTCCCTTACTAGATGGGCGT 57.830 50.000 12.42 0.00 41.55 5.68
2671 2908 3.665190 GAATTCCCTTACTAGATGGGCG 58.335 50.000 12.42 0.00 41.55 6.13
2672 2909 3.323979 TCGAATTCCCTTACTAGATGGGC 59.676 47.826 12.42 1.69 41.55 5.36
2673 2910 5.304614 TCTTCGAATTCCCTTACTAGATGGG 59.695 44.000 0.00 4.92 42.90 4.00
2674 2911 6.406692 TCTTCGAATTCCCTTACTAGATGG 57.593 41.667 0.00 0.00 0.00 3.51
2675 2912 7.661968 TGATCTTCGAATTCCCTTACTAGATG 58.338 38.462 0.00 0.00 0.00 2.90
2676 2913 7.841282 TGATCTTCGAATTCCCTTACTAGAT 57.159 36.000 0.00 0.00 0.00 1.98
2677 2914 7.655521 TTGATCTTCGAATTCCCTTACTAGA 57.344 36.000 0.00 0.00 0.00 2.43
2678 2915 8.718102 TTTTGATCTTCGAATTCCCTTACTAG 57.282 34.615 0.00 0.00 0.00 2.57
2679 2916 8.319146 ACTTTTGATCTTCGAATTCCCTTACTA 58.681 33.333 0.00 0.00 0.00 1.82
2680 2917 7.168905 ACTTTTGATCTTCGAATTCCCTTACT 58.831 34.615 0.00 0.00 0.00 2.24
2681 2918 7.334671 AGACTTTTGATCTTCGAATTCCCTTAC 59.665 37.037 0.00 0.00 0.00 2.34
2682 2919 7.394816 AGACTTTTGATCTTCGAATTCCCTTA 58.605 34.615 0.00 0.00 0.00 2.69
2683 2920 6.241645 AGACTTTTGATCTTCGAATTCCCTT 58.758 36.000 0.00 0.00 0.00 3.95
2684 2921 5.810095 AGACTTTTGATCTTCGAATTCCCT 58.190 37.500 0.00 0.00 0.00 4.20
2685 2922 6.149474 TCAAGACTTTTGATCTTCGAATTCCC 59.851 38.462 0.00 0.00 34.08 3.97
2693 4407 4.065789 ACCGGTCAAGACTTTTGATCTTC 58.934 43.478 0.00 0.00 34.08 2.87
2725 4439 2.554032 CAACACCTTCATTGGGTCAGTC 59.446 50.000 0.00 0.00 34.44 3.51
2864 4590 2.873133 CTCCTAGCTTGGGAGTAACG 57.127 55.000 20.71 3.34 43.77 3.18
2872 4598 2.866085 AAGCAGCGCTCCTAGCTTGG 62.866 60.000 26.26 8.03 44.84 3.61
2889 4615 4.159377 TGGTGAATAAGCGCTTTGAAAG 57.841 40.909 30.13 0.00 0.00 2.62
2900 4626 6.690530 TGCCATCTTTTCTTTGGTGAATAAG 58.309 36.000 0.00 0.00 32.90 1.73
2902 4628 6.009589 TCTGCCATCTTTTCTTTGGTGAATA 58.990 36.000 0.00 0.00 32.90 1.75
2910 4636 6.845758 TGATGATTCTGCCATCTTTTCTTT 57.154 33.333 0.00 0.00 40.65 2.52
2911 4637 7.123697 TGAATGATGATTCTGCCATCTTTTCTT 59.876 33.333 6.46 0.00 40.65 2.52
2912 4638 6.605995 TGAATGATGATTCTGCCATCTTTTCT 59.394 34.615 6.46 0.00 40.65 2.52
2913 4639 6.802608 TGAATGATGATTCTGCCATCTTTTC 58.197 36.000 6.46 0.00 40.65 2.29
2914 4640 6.785337 TGAATGATGATTCTGCCATCTTTT 57.215 33.333 6.46 0.00 40.65 2.27
2952 4678 7.426929 AATTTACTGACAGTTGACATCTGAC 57.573 36.000 14.50 13.18 36.81 3.51
2957 4683 7.986085 AAGCTAATTTACTGACAGTTGACAT 57.014 32.000 14.50 0.00 0.00 3.06
3061 4787 8.906867 CACAATAGGATAATTGTTTGGATGAGT 58.093 33.333 0.00 0.00 45.54 3.41
3137 4866 8.425577 AGGAACGTGATAATCTAACAATCAAG 57.574 34.615 0.00 0.00 35.89 3.02
3138 4867 7.222031 CGAGGAACGTGATAATCTAACAATCAA 59.778 37.037 0.00 0.00 37.22 2.57
3236 4965 5.637006 TTGCGCTAAAATAATGAGTTGGT 57.363 34.783 9.73 0.00 0.00 3.67
3266 4995 1.737355 AAAGCATGCGCACACTTGGT 61.737 50.000 23.06 16.08 42.27 3.67
3298 5027 3.906846 AGAGAGGACAAATGAGACAACCT 59.093 43.478 0.00 0.00 0.00 3.50
3310 5039 9.747898 TTTATAGGCAAAATTAAGAGAGGACAA 57.252 29.630 0.00 0.00 0.00 3.18
3327 5056 9.402320 TGAAATGCACTATTAGTTTTATAGGCA 57.598 29.630 0.00 5.54 36.80 4.75
3420 6611 3.387374 ACCTAGATGATGACAGAAGCCAG 59.613 47.826 0.00 0.00 0.00 4.85
3473 6665 9.450807 ACAAAATTCGCAATATACTTTATCAGC 57.549 29.630 0.00 0.00 0.00 4.26
3508 6700 1.894756 CCTCGCCTCCTCGACCTAG 60.895 68.421 0.00 0.00 34.46 3.02
3770 6991 3.539604 AGGAGAGTTCACAATAGCATGC 58.460 45.455 10.51 10.51 0.00 4.06
3792 7013 3.447229 TGAGAATAGCGTGTGAATCCTGA 59.553 43.478 0.00 0.00 0.00 3.86
3793 7014 3.785486 TGAGAATAGCGTGTGAATCCTG 58.215 45.455 0.00 0.00 0.00 3.86
3794 7015 3.449018 ACTGAGAATAGCGTGTGAATCCT 59.551 43.478 0.00 0.00 0.00 3.24
3795 7016 3.786635 ACTGAGAATAGCGTGTGAATCC 58.213 45.455 0.00 0.00 0.00 3.01
3796 7017 6.020281 CACTTACTGAGAATAGCGTGTGAATC 60.020 42.308 0.00 0.00 0.00 2.52
3797 7018 5.807520 CACTTACTGAGAATAGCGTGTGAAT 59.192 40.000 0.00 0.00 0.00 2.57
3798 7019 5.161358 CACTTACTGAGAATAGCGTGTGAA 58.839 41.667 0.00 0.00 0.00 3.18
3799 7020 4.380550 CCACTTACTGAGAATAGCGTGTGA 60.381 45.833 0.00 0.00 0.00 3.58
3800 7021 3.859961 CCACTTACTGAGAATAGCGTGTG 59.140 47.826 0.00 0.00 0.00 3.82
3801 7022 3.676324 GCCACTTACTGAGAATAGCGTGT 60.676 47.826 0.00 0.00 0.00 4.49
3802 7023 2.860735 GCCACTTACTGAGAATAGCGTG 59.139 50.000 0.00 0.00 0.00 5.34
3803 7024 2.761208 AGCCACTTACTGAGAATAGCGT 59.239 45.455 0.00 0.00 0.00 5.07
3804 7025 3.119291 CAGCCACTTACTGAGAATAGCG 58.881 50.000 0.00 0.00 37.32 4.26
3805 7026 4.130286 ACAGCCACTTACTGAGAATAGC 57.870 45.455 0.00 0.00 38.55 2.97
3806 7027 9.988815 ATTTATACAGCCACTTACTGAGAATAG 57.011 33.333 0.00 0.00 38.55 1.73
3831 7052 2.628657 GGCCTCCGTGTCTACAGATAAT 59.371 50.000 0.00 0.00 0.00 1.28
3887 7108 3.865164 CACCTTTGACAAAGTTTTGGAGC 59.135 43.478 23.07 0.00 42.34 4.70
3903 7124 8.466798 CCATTTCCGATTATAAACTTCACCTTT 58.533 33.333 0.00 0.00 0.00 3.11
3904 7125 7.614192 ACCATTTCCGATTATAAACTTCACCTT 59.386 33.333 0.00 0.00 0.00 3.50
3939 7233 3.815757 GCCAAGTTTCCTCCCAGAATCTT 60.816 47.826 0.00 0.00 36.62 2.40
3954 7248 1.203013 GGTGTTTCCCCTAGCCAAGTT 60.203 52.381 0.00 0.00 0.00 2.66
4147 7444 0.674895 AGCAGCTGATCGGGTTGTTC 60.675 55.000 20.43 0.00 0.00 3.18
4166 7463 3.335786 TCCAGTCCTAGTAACCTTCCAGA 59.664 47.826 0.00 0.00 0.00 3.86
4174 7471 8.694581 ATTGTATACTCTCCAGTCCTAGTAAC 57.305 38.462 4.17 0.00 33.62 2.50
4383 7681 3.815401 GGTGTTTGATAGATTCATCCCGG 59.185 47.826 0.00 0.00 33.34 5.73
4507 7808 6.817140 GCTATTTCGGAATCTATCCCGTTAAT 59.183 38.462 0.00 0.00 46.39 1.40


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

AutoCloner maintained by Alex Coulton.