Multiple sequence alignment - TraesCS4A01G081200

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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 TraesCS4A01G081200 chr4A 100.000 5184 0 0 1 5184 84371422 84366239 0.000000e+00 9574.0
1 TraesCS4A01G081200 chr4D 93.816 3784 166 31 660 4436 380155817 380159539 0.000000e+00 5629.0
2 TraesCS4A01G081200 chr4D 91.223 319 27 1 38 355 380146519 380146837 2.870000e-117 433.0
3 TraesCS4A01G081200 chr4D 95.000 80 4 0 519 598 380146838 380146917 5.450000e-25 126.0
4 TraesCS4A01G081200 chr4D 100.000 32 0 0 630 661 380155798 380155767 5.610000e-05 60.2
5 TraesCS4A01G081200 chr4B 91.210 2298 111 41 2152 4438 467109359 467111576 0.000000e+00 3040.0
6 TraesCS4A01G081200 chr4B 91.889 826 52 7 1220 2044 467108489 467109300 0.000000e+00 1140.0
7 TraesCS4A01G081200 chr4B 90.976 543 21 10 712 1234 467107939 467108473 0.000000e+00 706.0
8 TraesCS4A01G081200 chr4B 90.294 340 27 6 19 355 467105617 467105953 1.710000e-119 440.0
9 TraesCS4A01G081200 chr4B 95.000 80 4 0 519 598 467105954 467106033 5.450000e-25 126.0
10 TraesCS4A01G081200 chr2D 88.815 751 82 2 4435 5184 601402136 601402885 0.000000e+00 920.0
11 TraesCS4A01G081200 chr2D 87.550 747 86 7 4440 5184 76629798 76629057 0.000000e+00 857.0
12 TraesCS4A01G081200 chr2D 86.037 752 101 4 4435 5184 645051845 645052594 0.000000e+00 804.0
13 TraesCS4A01G081200 chr2D 86.152 751 94 6 4438 5184 121365555 121364811 0.000000e+00 802.0
14 TraesCS4A01G081200 chr1D 87.968 748 83 3 4438 5184 346375266 346376007 0.000000e+00 876.0
15 TraesCS4A01G081200 chr1D 92.857 168 12 0 354 521 206955704 206955537 1.440000e-60 244.0
16 TraesCS4A01G081200 chr1D 90.960 177 15 1 347 522 420065416 420065240 2.410000e-58 237.0
17 TraesCS4A01G081200 chr6D 87.049 749 85 6 4439 5184 462397163 462396424 0.000000e+00 835.0
18 TraesCS4A01G081200 chr6D 93.373 166 11 0 357 522 352878326 352878491 4.010000e-61 246.0
19 TraesCS4A01G081200 chr5D 86.702 752 97 3 4435 5184 116455667 116456417 0.000000e+00 832.0
20 TraesCS4A01G081200 chr5D 91.573 178 13 2 346 521 25039967 25040144 1.440000e-60 244.0
21 TraesCS4A01G081200 chr2A 86.303 752 97 5 4435 5184 18191728 18192475 0.000000e+00 813.0
22 TraesCS4A01G081200 chr7A 85.714 756 100 7 4430 5184 472628294 472629042 0.000000e+00 791.0
23 TraesCS4A01G081200 chr7A 93.452 168 11 0 354 521 667231035 667231202 3.100000e-62 250.0
24 TraesCS4A01G081200 chr7A 92.899 169 12 0 353 521 115807519 115807687 4.010000e-61 246.0
25 TraesCS4A01G081200 chr6B 93.976 166 10 0 356 521 534823577 534823742 8.620000e-63 252.0
26 TraesCS4A01G081200 chr5A 92.398 171 13 0 352 522 290391692 290391862 1.440000e-60 244.0
27 TraesCS4A01G081200 chr3A 90.857 175 14 2 348 522 733260577 733260749 3.120000e-57 233.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G081200 chr4A 84366239 84371422 5183 True 9574.0 9574 100.0000 1 5184 1 chr4A.!!$R1 5183
1 TraesCS4A01G081200 chr4D 380155817 380159539 3722 False 5629.0 5629 93.8160 660 4436 1 chr4D.!!$F1 3776
2 TraesCS4A01G081200 chr4B 467105617 467111576 5959 False 1090.4 3040 91.8738 19 4438 5 chr4B.!!$F1 4419
3 TraesCS4A01G081200 chr2D 601402136 601402885 749 False 920.0 920 88.8150 4435 5184 1 chr2D.!!$F1 749
4 TraesCS4A01G081200 chr2D 76629057 76629798 741 True 857.0 857 87.5500 4440 5184 1 chr2D.!!$R1 744
5 TraesCS4A01G081200 chr2D 645051845 645052594 749 False 804.0 804 86.0370 4435 5184 1 chr2D.!!$F2 749
6 TraesCS4A01G081200 chr2D 121364811 121365555 744 True 802.0 802 86.1520 4438 5184 1 chr2D.!!$R2 746
7 TraesCS4A01G081200 chr1D 346375266 346376007 741 False 876.0 876 87.9680 4438 5184 1 chr1D.!!$F1 746
8 TraesCS4A01G081200 chr6D 462396424 462397163 739 True 835.0 835 87.0490 4439 5184 1 chr6D.!!$R1 745
9 TraesCS4A01G081200 chr5D 116455667 116456417 750 False 832.0 832 86.7020 4435 5184 1 chr5D.!!$F2 749
10 TraesCS4A01G081200 chr2A 18191728 18192475 747 False 813.0 813 86.3030 4435 5184 1 chr2A.!!$F1 749
11 TraesCS4A01G081200 chr7A 472628294 472629042 748 False 791.0 791 85.7140 4430 5184 1 chr7A.!!$F2 754

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
613 615 0.034896 AACATTTCGACCACGCTCCT 59.965 50.000 0.00 0.0 39.58 3.69 F
1747 3623 0.368227 GTGAGCGCATTCGAGTTCAG 59.632 55.000 11.47 0.0 38.10 3.02 F
2106 3982 1.065709 GCCCTCCCATTCGTTTAGACA 60.066 52.381 0.00 0.0 0.00 3.41 F
3097 4975 0.251077 CTCCCCTTCTTGCTGCTTGT 60.251 55.000 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 4299 0.394352 GACCCGAATGCCTGGACAAT 60.394 55.0 0.00 0.0 0.00 2.71 R
2573 4450 0.475044 AAGGTAGGCCCGTTTTGTCA 59.525 50.0 0.00 0.0 38.74 3.58 R
3743 5623 0.844503 CGGTCGCTATGAAACGTAGC 59.155 55.0 11.50 11.5 40.83 3.58 R
4657 6554 0.526954 GCACATGCTGCATACAAGCC 60.527 55.0 15.78 0.0 46.29 4.35 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
32 33 1.380302 GGGGTGTGAAGGCTGACAT 59.620 57.895 3.19 0.00 0.00 3.06
34 35 1.004277 GGGGTGTGAAGGCTGACATAA 59.996 52.381 3.19 0.00 0.00 1.90
36 37 2.684881 GGGTGTGAAGGCTGACATAATG 59.315 50.000 3.19 0.00 0.00 1.90
46 47 4.825634 AGGCTGACATAATGAATGACCATG 59.174 41.667 0.00 0.00 39.07 3.66
52 53 4.586001 ACATAATGAATGACCATGGCTTCC 59.414 41.667 13.04 0.00 39.07 3.46
64 65 3.672066 GGCTTCCAAGGCCTTAACT 57.328 52.632 20.00 0.00 45.57 2.24
67 68 2.238898 GGCTTCCAAGGCCTTAACTAGA 59.761 50.000 20.00 7.44 45.57 2.43
93 94 1.705186 CTCACCCTCCTCCCAAAGAAA 59.295 52.381 0.00 0.00 0.00 2.52
96 97 2.642807 CACCCTCCTCCCAAAGAAACTA 59.357 50.000 0.00 0.00 0.00 2.24
171 172 2.362889 CCAGCGGCCAAATCCCTT 60.363 61.111 2.24 0.00 0.00 3.95
189 190 2.019984 CTTGCTACAAAGGGAGGCATC 58.980 52.381 0.00 0.00 32.87 3.91
193 194 1.207089 CTACAAAGGGAGGCATCGTGA 59.793 52.381 0.00 0.00 0.00 4.35
209 210 1.667724 CGTGATTGGGATCTCTTGTGC 59.332 52.381 0.00 0.00 33.28 4.57
214 215 2.189594 TGGGATCTCTTGTGCAGTTG 57.810 50.000 0.00 0.00 0.00 3.16
251 252 4.873259 TCATCAAAAAGCATTGCATCCATG 59.127 37.500 11.91 5.39 0.00 3.66
254 255 4.020928 TCAAAAAGCATTGCATCCATGACT 60.021 37.500 11.91 0.00 0.00 3.41
270 271 3.979101 TGACTACTTCATGATGGTGCA 57.021 42.857 12.76 3.37 0.00 4.57
272 273 4.002982 TGACTACTTCATGATGGTGCAAC 58.997 43.478 12.76 0.00 0.00 4.17
278 279 5.195185 ACTTCATGATGGTGCAACATATCA 58.805 37.500 19.28 14.32 43.05 2.15
286 287 5.685520 TGGTGCAACATATCAGGTAGTTA 57.314 39.130 0.00 0.00 39.98 2.24
300 301 4.268644 CAGGTAGTTACATTCACATGCTCG 59.731 45.833 0.00 0.00 33.05 5.03
324 325 3.273434 GAGCCACATGTGATGCTTAAGA 58.727 45.455 27.46 0.00 33.41 2.10
326 327 3.054875 AGCCACATGTGATGCTTAAGAGA 60.055 43.478 27.46 0.00 0.00 3.10
333 334 5.784750 TGTGATGCTTAAGAGAAACATCG 57.215 39.130 6.67 0.00 39.96 3.84
344 345 2.744202 GAGAAACATCGTGCATGTCCTT 59.256 45.455 5.68 0.00 45.77 3.36
355 357 4.629634 CGTGCATGTCCTTACTTTGTGATA 59.370 41.667 0.00 0.00 0.00 2.15
356 358 5.294306 CGTGCATGTCCTTACTTTGTGATAT 59.706 40.000 0.00 0.00 0.00 1.63
357 359 6.478673 CGTGCATGTCCTTACTTTGTGATATA 59.521 38.462 0.00 0.00 0.00 0.86
358 360 7.516785 CGTGCATGTCCTTACTTTGTGATATAC 60.517 40.741 0.00 0.00 0.00 1.47
359 361 7.495934 GTGCATGTCCTTACTTTGTGATATACT 59.504 37.037 0.00 0.00 0.00 2.12
360 362 7.710907 TGCATGTCCTTACTTTGTGATATACTC 59.289 37.037 0.00 0.00 0.00 2.59
361 363 7.171678 GCATGTCCTTACTTTGTGATATACTCC 59.828 40.741 0.00 0.00 0.00 3.85
362 364 7.973048 TGTCCTTACTTTGTGATATACTCCT 57.027 36.000 0.00 0.00 0.00 3.69
363 365 8.375493 TGTCCTTACTTTGTGATATACTCCTT 57.625 34.615 0.00 0.00 0.00 3.36
364 366 8.475639 TGTCCTTACTTTGTGATATACTCCTTC 58.524 37.037 0.00 0.00 0.00 3.46
365 367 7.927092 GTCCTTACTTTGTGATATACTCCTTCC 59.073 40.741 0.00 0.00 0.00 3.46
366 368 6.924060 CCTTACTTTGTGATATACTCCTTCCG 59.076 42.308 0.00 0.00 0.00 4.30
367 369 5.934402 ACTTTGTGATATACTCCTTCCGT 57.066 39.130 0.00 0.00 0.00 4.69
368 370 6.295719 ACTTTGTGATATACTCCTTCCGTT 57.704 37.500 0.00 0.00 0.00 4.44
369 371 6.708285 ACTTTGTGATATACTCCTTCCGTTT 58.292 36.000 0.00 0.00 0.00 3.60
370 372 6.817140 ACTTTGTGATATACTCCTTCCGTTTC 59.183 38.462 0.00 0.00 0.00 2.78
371 373 6.540438 TTGTGATATACTCCTTCCGTTTCT 57.460 37.500 0.00 0.00 0.00 2.52
372 374 7.649533 TTGTGATATACTCCTTCCGTTTCTA 57.350 36.000 0.00 0.00 0.00 2.10
373 375 7.649533 TGTGATATACTCCTTCCGTTTCTAA 57.350 36.000 0.00 0.00 0.00 2.10
374 376 8.070034 TGTGATATACTCCTTCCGTTTCTAAA 57.930 34.615 0.00 0.00 0.00 1.85
375 377 8.701895 TGTGATATACTCCTTCCGTTTCTAAAT 58.298 33.333 0.00 0.00 0.00 1.40
381 383 9.901172 ATACTCCTTCCGTTTCTAAATATTTGT 57.099 29.630 11.05 0.00 0.00 2.83
383 385 9.901172 ACTCCTTCCGTTTCTAAATATTTGTAT 57.099 29.630 11.05 0.00 0.00 2.29
405 407 9.527157 TGTATTTCTAGGGATTTCAACAAATGA 57.473 29.630 0.00 0.00 31.94 2.57
406 408 9.788960 GTATTTCTAGGGATTTCAACAAATGAC 57.211 33.333 0.00 0.00 37.92 3.06
407 409 8.655935 ATTTCTAGGGATTTCAACAAATGACT 57.344 30.769 0.00 0.00 37.92 3.41
408 410 9.753674 ATTTCTAGGGATTTCAACAAATGACTA 57.246 29.630 0.00 0.00 37.92 2.59
409 411 8.561738 TTCTAGGGATTTCAACAAATGACTAC 57.438 34.615 0.00 0.00 37.92 2.73
410 412 7.685481 TCTAGGGATTTCAACAAATGACTACA 58.315 34.615 0.00 0.00 37.92 2.74
411 413 8.328758 TCTAGGGATTTCAACAAATGACTACAT 58.671 33.333 0.00 0.00 37.92 2.29
412 414 9.613428 CTAGGGATTTCAACAAATGACTACATA 57.387 33.333 0.00 0.00 37.92 2.29
413 415 8.281212 AGGGATTTCAACAAATGACTACATAC 57.719 34.615 0.00 0.00 37.92 2.39
414 416 7.888021 AGGGATTTCAACAAATGACTACATACA 59.112 33.333 0.00 0.00 37.92 2.29
415 417 8.519526 GGGATTTCAACAAATGACTACATACAA 58.480 33.333 0.00 0.00 37.92 2.41
416 418 9.906660 GGATTTCAACAAATGACTACATACAAA 57.093 29.630 0.00 0.00 37.92 2.83
428 430 9.897744 ATGACTACATACAAAACAAAATGAGTG 57.102 29.630 0.00 0.00 34.71 3.51
429 431 9.114952 TGACTACATACAAAACAAAATGAGTGA 57.885 29.630 0.00 0.00 0.00 3.41
430 432 9.944663 GACTACATACAAAACAAAATGAGTGAA 57.055 29.630 0.00 0.00 0.00 3.18
437 439 8.856490 ACAAAACAAAATGAGTGAATCTACAC 57.144 30.769 0.00 0.00 40.60 2.90
481 483 7.778083 ACATTCGTATGTAGTAGTCCATTTGA 58.222 34.615 5.81 0.00 43.12 2.69
482 484 8.255206 ACATTCGTATGTAGTAGTCCATTTGAA 58.745 33.333 5.81 0.00 43.12 2.69
483 485 9.093970 CATTCGTATGTAGTAGTCCATTTGAAA 57.906 33.333 0.00 0.00 0.00 2.69
484 486 9.832445 ATTCGTATGTAGTAGTCCATTTGAAAT 57.168 29.630 0.00 0.00 0.00 2.17
485 487 8.867112 TCGTATGTAGTAGTCCATTTGAAATC 57.133 34.615 0.00 0.00 0.00 2.17
486 488 8.692710 TCGTATGTAGTAGTCCATTTGAAATCT 58.307 33.333 0.00 0.00 0.00 2.40
487 489 8.969267 CGTATGTAGTAGTCCATTTGAAATCTC 58.031 37.037 0.00 0.00 0.00 2.75
540 542 5.009631 AGTAGCACCAAAAGCAATGTATGA 58.990 37.500 0.00 0.00 0.00 2.15
584 586 2.166459 GACAACCTCATGATCTCCACGA 59.834 50.000 0.00 0.00 0.00 4.35
592 594 0.109272 TGATCTCCACGACGCAAGAC 60.109 55.000 0.00 0.00 43.62 3.01
598 600 0.586319 CCACGACGCAAGACAAACAT 59.414 50.000 0.00 0.00 43.62 2.71
599 601 1.002900 CCACGACGCAAGACAAACATT 60.003 47.619 0.00 0.00 43.62 2.71
600 602 2.540769 CCACGACGCAAGACAAACATTT 60.541 45.455 0.00 0.00 43.62 2.32
601 603 2.713976 CACGACGCAAGACAAACATTTC 59.286 45.455 0.00 0.00 43.62 2.17
602 604 1.962547 CGACGCAAGACAAACATTTCG 59.037 47.619 0.00 0.00 43.62 3.46
603 605 2.348125 CGACGCAAGACAAACATTTCGA 60.348 45.455 0.00 0.00 43.62 3.71
604 606 2.964768 GACGCAAGACAAACATTTCGAC 59.035 45.455 0.00 0.00 43.62 4.20
605 607 2.286772 ACGCAAGACAAACATTTCGACC 60.287 45.455 0.00 0.00 43.62 4.79
606 608 2.286713 CGCAAGACAAACATTTCGACCA 60.287 45.455 0.00 0.00 43.02 4.02
607 609 3.042887 GCAAGACAAACATTTCGACCAC 58.957 45.455 0.00 0.00 0.00 4.16
608 610 3.288242 CAAGACAAACATTTCGACCACG 58.712 45.455 0.00 0.00 41.26 4.94
609 611 1.263217 AGACAAACATTTCGACCACGC 59.737 47.619 0.00 0.00 39.58 5.34
610 612 1.263217 GACAAACATTTCGACCACGCT 59.737 47.619 0.00 0.00 39.58 5.07
612 614 0.872388 AAACATTTCGACCACGCTCC 59.128 50.000 0.00 0.00 39.58 4.70
613 615 0.034896 AACATTTCGACCACGCTCCT 59.965 50.000 0.00 0.00 39.58 3.69
614 616 0.034896 ACATTTCGACCACGCTCCTT 59.965 50.000 0.00 0.00 39.58 3.36
615 617 1.156736 CATTTCGACCACGCTCCTTT 58.843 50.000 0.00 0.00 39.58 3.11
616 618 1.535462 CATTTCGACCACGCTCCTTTT 59.465 47.619 0.00 0.00 39.58 2.27
617 619 1.670791 TTTCGACCACGCTCCTTTTT 58.329 45.000 0.00 0.00 39.58 1.94
668 2488 1.510480 GCGTATCCAAGCCCATCTGC 61.510 60.000 0.00 0.00 0.00 4.26
697 2517 2.052782 ATTGGGCCCATTTCGTAGTC 57.947 50.000 29.23 0.00 0.00 2.59
748 2570 3.594603 AGGAATGTCGTTACCTCACAG 57.405 47.619 0.00 0.00 0.00 3.66
785 2607 2.583593 GCTCGTCCATCACTCGGC 60.584 66.667 0.00 0.00 0.00 5.54
786 2608 3.069980 GCTCGTCCATCACTCGGCT 62.070 63.158 0.00 0.00 0.00 5.52
787 2609 1.064946 CTCGTCCATCACTCGGCTC 59.935 63.158 0.00 0.00 0.00 4.70
788 2610 2.278206 CGTCCATCACTCGGCTCG 60.278 66.667 0.00 0.00 0.00 5.03
789 2611 2.105128 GTCCATCACTCGGCTCGG 59.895 66.667 0.00 0.00 0.00 4.63
885 2707 0.999406 CTCCACCAATCGCACGTTAG 59.001 55.000 0.00 0.00 0.00 2.34
919 2757 2.573340 GCCCCCAAATTCACAGCG 59.427 61.111 0.00 0.00 0.00 5.18
964 2802 2.621526 ACACACGAAGAAAACAATCCCC 59.378 45.455 0.00 0.00 0.00 4.81
1024 2862 1.587547 GTTCTTCTCGGGGATCATGC 58.412 55.000 0.00 0.00 0.00 4.06
1026 2864 1.500474 TCTTCTCGGGGATCATGCTT 58.500 50.000 0.00 0.00 0.00 3.91
1131 2969 2.423446 CCTGCCCGGATGCTCTAC 59.577 66.667 0.73 0.00 33.16 2.59
1170 3012 0.502275 CGATGTTTGGTTTGCGTTGC 59.498 50.000 0.00 0.00 0.00 4.17
1187 3029 0.461693 TGCGCCATTGTCGATGATCA 60.462 50.000 4.18 0.00 38.03 2.92
1221 3063 7.381323 TCGACTCGTAGATATATGTTCAGGTA 58.619 38.462 0.00 0.00 33.89 3.08
1243 3115 0.461961 AGCCTGAGTTGATCCGCTAC 59.538 55.000 0.00 0.00 32.33 3.58
1257 3129 1.576356 CGCTACAAGGATTCAGGCTC 58.424 55.000 0.00 0.00 0.00 4.70
1315 3188 1.441016 CTGAAAGCGGTTTCTGCGC 60.441 57.895 32.74 13.78 42.39 6.09
1388 3261 0.583438 CAATGCGCCGGAGTAGATTG 59.417 55.000 5.05 8.91 0.00 2.67
1635 3511 5.003804 CCAGGTGAAATGCTACTTACTGTT 58.996 41.667 0.00 0.00 0.00 3.16
1636 3512 5.106555 CCAGGTGAAATGCTACTTACTGTTG 60.107 44.000 0.00 0.00 0.00 3.33
1637 3513 5.470098 CAGGTGAAATGCTACTTACTGTTGT 59.530 40.000 0.00 0.00 0.00 3.32
1644 3520 9.199982 GAAATGCTACTTACTGTTGTGTTACTA 57.800 33.333 0.00 0.00 0.00 1.82
1647 3523 7.094631 TGCTACTTACTGTTGTGTTACTATGG 58.905 38.462 0.00 0.00 0.00 2.74
1747 3623 0.368227 GTGAGCGCATTCGAGTTCAG 59.632 55.000 11.47 0.00 38.10 3.02
2044 3920 4.278419 GCCTTTTGTTGAAGAGGTACACAT 59.722 41.667 0.00 0.00 0.00 3.21
2074 3950 4.036852 CCTCCTGTGTTCTTCCAGTTTTTC 59.963 45.833 0.00 0.00 0.00 2.29
2078 3954 3.625764 TGTGTTCTTCCAGTTTTTCTCGG 59.374 43.478 0.00 0.00 0.00 4.63
2087 3963 1.303317 TTTTTCTCGGCAGGAGGGC 60.303 57.895 4.42 0.00 43.34 5.19
2106 3982 1.065709 GCCCTCCCATTCGTTTAGACA 60.066 52.381 0.00 0.00 0.00 3.41
2110 3986 4.521256 CCCTCCCATTCGTTTAGACAAAAA 59.479 41.667 0.00 0.00 0.00 1.94
2171 4047 4.199310 TGAGCCCATGAACTACTTATTGC 58.801 43.478 0.00 0.00 0.00 3.56
2192 4068 3.851105 GCTCTGTTGTTGTTGACATCTGC 60.851 47.826 0.00 0.00 38.26 4.26
2196 4072 4.702831 TGTTGTTGTTGACATCTGCTCTA 58.297 39.130 0.00 0.00 38.26 2.43
2208 4084 6.042638 ACATCTGCTCTAATGTACAGTTGT 57.957 37.500 0.00 0.00 37.93 3.32
2290 4166 2.927580 CGACCGGTGGGGATATCCG 61.928 68.421 14.63 0.87 43.30 4.18
2347 4223 3.864540 GCCACCTAAAATTGAAGGTTGCC 60.865 47.826 18.13 6.70 44.69 4.52
2405 4281 9.047947 AGTGGTAGATAATCTTGTTCTAAAGGT 57.952 33.333 0.00 0.00 0.00 3.50
2423 4299 8.981659 TCTAAAGGTTTCTGATGAGTGATGATA 58.018 33.333 0.00 0.00 0.00 2.15
2493 4369 2.434702 GGATATCGACTTCAAGTGGGGT 59.565 50.000 0.00 0.00 0.00 4.95
2561 4437 1.402968 CCCGATTCAGGTCTGCAAATG 59.597 52.381 0.00 0.00 0.00 2.32
2601 4478 4.036941 ACGGGCCTACCTTAAATTTTCA 57.963 40.909 0.84 0.00 36.97 2.69
2603 4480 3.181490 CGGGCCTACCTTAAATTTTCAGC 60.181 47.826 0.84 0.00 36.97 4.26
2606 4483 4.462834 GGCCTACCTTAAATTTTCAGCAGT 59.537 41.667 0.00 0.00 0.00 4.40
2645 4522 8.485976 TTTAAACCTTGTGAAATTTGACCTTG 57.514 30.769 5.29 0.00 0.00 3.61
2652 4529 6.214191 TGTGAAATTTGACCTTGCAAGTTA 57.786 33.333 24.35 7.96 29.18 2.24
2660 4537 3.249799 TGACCTTGCAAGTTATGTTCGTG 59.750 43.478 24.35 7.95 0.00 4.35
2661 4538 3.211045 ACCTTGCAAGTTATGTTCGTGT 58.789 40.909 24.35 8.58 0.00 4.49
2662 4539 3.003275 ACCTTGCAAGTTATGTTCGTGTG 59.997 43.478 24.35 7.26 0.00 3.82
2667 4544 7.011016 CCTTGCAAGTTATGTTCGTGTGATATA 59.989 37.037 24.35 0.00 0.00 0.86
2670 4547 9.705290 TGCAAGTTATGTTCGTGTGATATATAT 57.295 29.630 0.00 0.00 0.00 0.86
2734 4612 9.184523 CTACAAATGGTAGTAAATCAATTCCCA 57.815 33.333 0.00 0.00 43.73 4.37
2735 4613 8.608185 ACAAATGGTAGTAAATCAATTCCCAT 57.392 30.769 0.00 0.00 33.01 4.00
2736 4614 9.707957 ACAAATGGTAGTAAATCAATTCCCATA 57.292 29.630 0.00 0.00 31.46 2.74
2750 4628 8.737168 TCAATTCCCATATATATGCTTACTGC 57.263 34.615 16.08 0.00 43.25 4.40
2751 4629 8.551440 TCAATTCCCATATATATGCTTACTGCT 58.449 33.333 16.08 0.00 43.37 4.24
2752 4630 9.182214 CAATTCCCATATATATGCTTACTGCTT 57.818 33.333 16.08 0.73 43.37 3.91
2753 4631 8.743085 ATTCCCATATATATGCTTACTGCTTG 57.257 34.615 16.08 0.38 43.37 4.01
2754 4632 7.257790 TCCCATATATATGCTTACTGCTTGT 57.742 36.000 16.08 0.00 43.37 3.16
2755 4633 8.374184 TCCCATATATATGCTTACTGCTTGTA 57.626 34.615 16.08 0.00 43.37 2.41
2834 4712 3.225940 TGACGAGATACCATGCATCTCT 58.774 45.455 22.87 14.87 44.14 3.10
2905 4783 3.951663 ACCACTCTAAATTTTCTCCCGG 58.048 45.455 0.00 0.00 0.00 5.73
3081 4959 0.673956 GTCCCGAGTTTGCTTCCTCC 60.674 60.000 0.00 0.00 0.00 4.30
3097 4975 0.251077 CTCCCCTTCTTGCTGCTTGT 60.251 55.000 0.00 0.00 0.00 3.16
3102 4980 4.079787 TCCCCTTCTTGCTGCTTGTATTAT 60.080 41.667 0.00 0.00 0.00 1.28
3103 4981 4.276926 CCCCTTCTTGCTGCTTGTATTATC 59.723 45.833 0.00 0.00 0.00 1.75
3122 5000 2.092323 TCTCTGTGTCGACGGATGATT 58.908 47.619 11.62 0.00 36.85 2.57
3225 5105 2.981977 TTCCACTGGGCGTTGACGTC 62.982 60.000 9.11 9.11 44.28 4.34
3473 5353 0.458025 GGGTCATCGACGACAACCTC 60.458 60.000 22.73 13.37 37.66 3.85
3602 5482 1.817099 CATCGTCAAGCTGCCCCTC 60.817 63.158 0.00 0.00 0.00 4.30
3743 5623 1.216710 GCCTTCTCCTCGACCTGTG 59.783 63.158 0.00 0.00 0.00 3.66
3753 5633 0.669619 TCGACCTGTGCTACGTTTCA 59.330 50.000 0.00 0.00 0.00 2.69
3754 5634 1.271379 TCGACCTGTGCTACGTTTCAT 59.729 47.619 0.00 0.00 0.00 2.57
3760 5640 2.256174 TGTGCTACGTTTCATAGCGAC 58.744 47.619 0.00 0.00 46.73 5.19
3765 5645 0.179145 ACGTTTCATAGCGACCGAGG 60.179 55.000 0.00 0.00 0.00 4.63
4193 6073 1.000717 TCGACGAGTGACTGATGCAAA 60.001 47.619 0.00 0.00 0.00 3.68
4194 6074 1.125021 CGACGAGTGACTGATGCAAAC 59.875 52.381 0.00 0.00 0.00 2.93
4195 6075 2.408050 GACGAGTGACTGATGCAAACT 58.592 47.619 0.00 0.00 0.00 2.66
4196 6076 2.138320 ACGAGTGACTGATGCAAACTG 58.862 47.619 0.00 0.00 0.00 3.16
4199 6079 3.133691 GAGTGACTGATGCAAACTGTGA 58.866 45.455 10.41 1.65 0.00 3.58
4202 6082 3.750130 GTGACTGATGCAAACTGTGAGAT 59.250 43.478 10.41 0.00 0.00 2.75
4386 6277 5.107298 GCATCTGCCGTATTTGAGTATCTTC 60.107 44.000 0.00 0.00 32.61 2.87
4387 6278 4.607955 TCTGCCGTATTTGAGTATCTTCG 58.392 43.478 0.00 0.00 34.92 3.79
4391 6282 5.462068 TGCCGTATTTGAGTATCTTCGATTG 59.538 40.000 0.00 0.00 34.92 2.67
4418 6309 5.698104 TCTGCATCTGGTATGAAATGGAAT 58.302 37.500 0.00 0.00 0.00 3.01
4429 6320 7.147863 TGGTATGAAATGGAATCAAATCTGGTG 60.148 37.037 0.00 0.00 0.00 4.17
4430 6321 6.862469 ATGAAATGGAATCAAATCTGGTGT 57.138 33.333 0.00 0.00 0.00 4.16
4452 6343 0.470766 TCTAGGGCGTGTTTGGTTGT 59.529 50.000 0.00 0.00 0.00 3.32
4456 6347 1.381165 GGGCGTGTTTGGTTGTCTGT 61.381 55.000 0.00 0.00 0.00 3.41
4481 6373 1.822613 CCTAGCCTAGTCCGCGTGA 60.823 63.158 4.92 0.00 0.00 4.35
4492 6384 0.671796 TCCGCGTGAGAAGAAAGTGA 59.328 50.000 4.92 0.00 0.00 3.41
4501 6393 4.750098 GTGAGAAGAAAGTGATCCGTTTGA 59.250 41.667 0.00 0.00 0.00 2.69
4505 6397 5.997746 AGAAGAAAGTGATCCGTTTGATTGA 59.002 36.000 0.00 0.00 32.41 2.57
4507 6399 4.455877 AGAAAGTGATCCGTTTGATTGACC 59.544 41.667 0.00 0.00 32.41 4.02
4516 6409 2.662637 CGTTTGATTGACCGCGTTACTA 59.337 45.455 4.92 0.00 0.00 1.82
4547 6442 3.119849 GCATGACACGAACCTTAAAGCAT 60.120 43.478 0.00 0.00 0.00 3.79
4566 6461 1.204786 TACTTGGGCCTGGCTTGCTA 61.205 55.000 19.68 0.00 0.00 3.49
4567 6462 1.076485 CTTGGGCCTGGCTTGCTAT 60.076 57.895 19.68 0.00 0.00 2.97
4573 6468 1.379527 GCCTGGCTTGCTATAAACGT 58.620 50.000 12.43 0.00 0.00 3.99
4601 6496 0.108615 GCAGTTTCTAGCGAGCCAGA 60.109 55.000 0.00 0.00 0.00 3.86
4608 6503 1.133945 TCTAGCGAGCCAGACTGAGAT 60.134 52.381 3.32 0.00 0.00 2.75
4622 6517 6.071503 CCAGACTGAGATGAGTGCATATGATA 60.072 42.308 6.97 0.00 34.11 2.15
4624 6519 6.947158 AGACTGAGATGAGTGCATATGATAGA 59.053 38.462 6.97 0.00 34.11 1.98
4655 6552 3.172339 CAAGGAGAGATGGGAGGGATAG 58.828 54.545 0.00 0.00 0.00 2.08
4657 6554 1.273552 GGAGAGATGGGAGGGATAGGG 60.274 61.905 0.00 0.00 0.00 3.53
4661 6558 0.476611 GATGGGAGGGATAGGGGCTT 60.477 60.000 0.00 0.00 0.00 4.35
4733 6630 7.181125 TCTCTCTAATTTTGTTCTTCCTAGCCT 59.819 37.037 0.00 0.00 0.00 4.58
4739 6636 2.902608 TGTTCTTCCTAGCCTCTTCCA 58.097 47.619 0.00 0.00 0.00 3.53
4779 6676 4.135306 TCGATTCGAGGTAAGCTCTACAT 58.865 43.478 4.29 0.00 0.00 2.29
4781 6678 4.261238 CGATTCGAGGTAAGCTCTACATGT 60.261 45.833 2.69 2.69 0.00 3.21
4792 6689 7.227512 GGTAAGCTCTACATGTAAAAGATGCAT 59.772 37.037 15.70 0.00 34.33 3.96
4827 6724 0.461870 CCATTCAGGCGATCGGTTCA 60.462 55.000 18.30 0.00 0.00 3.18
4839 6736 3.855379 CGATCGGTTCATAGTTTCGTTGA 59.145 43.478 7.38 0.00 0.00 3.18
4842 6739 3.061322 CGGTTCATAGTTTCGTTGACCA 58.939 45.455 0.00 0.00 0.00 4.02
4854 6751 7.858583 AGTTTCGTTGACCATAAGTTCTTAAC 58.141 34.615 0.00 0.00 0.00 2.01
4874 6771 3.358118 ACTTTGTCTTCCCGGTTTGAAA 58.642 40.909 0.00 0.00 0.00 2.69
4882 6779 6.168389 GTCTTCCCGGTTTGAAACTATTCTA 58.832 40.000 8.09 0.00 36.48 2.10
4940 6837 8.695284 CGATCGTTTAAAATTTCATTTGACCAA 58.305 29.630 7.03 0.00 31.77 3.67
5021 6918 6.214191 TCGTAGCTTCATCTCTCTTTGAAT 57.786 37.500 0.00 0.00 31.83 2.57
5065 6962 1.102154 CATGTCGAGCTCCTCTGTCT 58.898 55.000 8.47 0.00 0.00 3.41
5067 6964 0.884514 TGTCGAGCTCCTCTGTCTTG 59.115 55.000 8.47 0.00 0.00 3.02
5072 6969 1.001860 GAGCTCCTCTGTCTTGTGCTT 59.998 52.381 0.87 0.00 0.00 3.91
5079 6976 2.233431 CTCTGTCTTGTGCTTAGAGCCT 59.767 50.000 0.00 0.00 41.51 4.58
5094 6991 1.763545 GAGCCTTCCTATTCGTCCCTT 59.236 52.381 0.00 0.00 0.00 3.95
5166 7063 3.759828 GTCGTTTCCGGTGTCGCG 61.760 66.667 0.00 0.00 34.56 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.034221 GTCAGCCTTCACACCCCC 59.966 66.667 0.00 0.00 0.00 5.40
14 15 0.618458 TATGTCAGCCTTCACACCCC 59.382 55.000 0.00 0.00 0.00 4.95
15 16 2.489938 TTATGTCAGCCTTCACACCC 57.510 50.000 0.00 0.00 0.00 4.61
16 17 3.609853 TCATTATGTCAGCCTTCACACC 58.390 45.455 0.00 0.00 0.00 4.16
17 18 5.355071 TCATTCATTATGTCAGCCTTCACAC 59.645 40.000 0.00 0.00 35.64 3.82
23 24 4.508551 TGGTCATTCATTATGTCAGCCT 57.491 40.909 0.00 0.00 35.64 4.58
25 26 4.558095 GCCATGGTCATTCATTATGTCAGC 60.558 45.833 14.67 0.00 35.64 4.26
26 27 4.825634 AGCCATGGTCATTCATTATGTCAG 59.174 41.667 14.67 0.00 35.64 3.51
27 28 4.795469 AGCCATGGTCATTCATTATGTCA 58.205 39.130 14.67 0.00 35.64 3.58
28 29 5.278660 GGAAGCCATGGTCATTCATTATGTC 60.279 44.000 14.67 0.00 35.64 3.06
32 33 4.248174 TGGAAGCCATGGTCATTCATTA 57.752 40.909 14.67 3.99 0.00 1.90
34 35 2.832643 TGGAAGCCATGGTCATTCAT 57.167 45.000 14.67 0.00 0.00 2.57
36 37 1.753073 CCTTGGAAGCCATGGTCATTC 59.247 52.381 14.67 14.60 41.98 2.67
52 53 2.541556 GAGCGTCTAGTTAAGGCCTTG 58.458 52.381 28.77 10.97 0.00 3.61
64 65 1.076923 GGAGGGTGAGGAGCGTCTA 60.077 63.158 0.00 0.00 35.33 2.59
67 68 2.363147 GAGGAGGGTGAGGAGCGT 60.363 66.667 0.00 0.00 0.00 5.07
93 94 4.225942 TCAATCTTGGAGGCAACATCTAGT 59.774 41.667 0.00 0.00 41.41 2.57
96 97 3.009916 AGTCAATCTTGGAGGCAACATCT 59.990 43.478 0.00 0.00 41.41 2.90
171 172 0.107703 CGATGCCTCCCTTTGTAGCA 60.108 55.000 0.00 0.00 37.94 3.49
184 185 1.071385 AGAGATCCCAATCACGATGCC 59.929 52.381 0.00 0.00 34.07 4.40
189 190 1.667724 GCACAAGAGATCCCAATCACG 59.332 52.381 0.00 0.00 34.07 4.35
193 194 3.087031 CAACTGCACAAGAGATCCCAAT 58.913 45.455 0.00 0.00 0.00 3.16
209 210 3.979948 TGAATGTGCATTGGTTCAACTG 58.020 40.909 1.77 0.00 0.00 3.16
214 215 6.542574 TTTTTGATGAATGTGCATTGGTTC 57.457 33.333 1.77 0.00 0.00 3.62
251 252 4.002982 TGTTGCACCATCATGAAGTAGTC 58.997 43.478 0.00 0.00 0.00 2.59
254 255 6.355747 TGATATGTTGCACCATCATGAAGTA 58.644 36.000 0.00 0.00 0.00 2.24
270 271 9.330063 CATGTGAATGTAACTACCTGATATGTT 57.670 33.333 0.00 0.00 0.00 2.71
272 273 7.658982 AGCATGTGAATGTAACTACCTGATATG 59.341 37.037 0.00 0.00 0.00 1.78
278 279 4.159693 TCGAGCATGTGAATGTAACTACCT 59.840 41.667 0.00 0.00 0.00 3.08
286 287 2.306341 CTCCTCGAGCATGTGAATGT 57.694 50.000 6.99 0.00 0.00 2.71
300 301 0.107312 AGCATCACATGTGGCTCCTC 60.107 55.000 25.16 9.16 28.71 3.71
307 308 6.245115 TGTTTCTCTTAAGCATCACATGTG 57.755 37.500 20.18 20.18 0.00 3.21
311 312 5.120674 CACGATGTTTCTCTTAAGCATCACA 59.879 40.000 15.76 9.22 36.64 3.58
324 325 2.479566 AGGACATGCACGATGTTTCT 57.520 45.000 0.00 0.00 45.90 2.52
326 327 3.674997 AGTAAGGACATGCACGATGTTT 58.325 40.909 0.00 0.00 45.90 2.83
333 334 6.683974 ATATCACAAAGTAAGGACATGCAC 57.316 37.500 0.00 0.00 0.00 4.57
340 341 7.201884 CGGAAGGAGTATATCACAAAGTAAGGA 60.202 40.741 0.00 0.00 0.00 3.36
344 345 7.414222 AACGGAAGGAGTATATCACAAAGTA 57.586 36.000 0.00 0.00 0.00 2.24
355 357 9.901172 ACAAATATTTAGAAACGGAAGGAGTAT 57.099 29.630 0.00 0.00 0.00 2.12
357 359 9.901172 ATACAAATATTTAGAAACGGAAGGAGT 57.099 29.630 0.00 0.00 0.00 3.85
379 381 9.527157 TCATTTGTTGAAATCCCTAGAAATACA 57.473 29.630 0.00 0.00 28.65 2.29
380 382 9.788960 GTCATTTGTTGAAATCCCTAGAAATAC 57.211 33.333 0.00 0.00 35.70 1.89
381 383 9.753674 AGTCATTTGTTGAAATCCCTAGAAATA 57.246 29.630 0.00 0.00 35.70 1.40
382 384 8.655935 AGTCATTTGTTGAAATCCCTAGAAAT 57.344 30.769 0.00 0.00 35.70 2.17
383 385 9.010029 GTAGTCATTTGTTGAAATCCCTAGAAA 57.990 33.333 0.00 0.00 35.70 2.52
384 386 8.160765 TGTAGTCATTTGTTGAAATCCCTAGAA 58.839 33.333 0.00 0.00 35.70 2.10
385 387 7.685481 TGTAGTCATTTGTTGAAATCCCTAGA 58.315 34.615 0.00 0.00 35.70 2.43
386 388 7.921786 TGTAGTCATTTGTTGAAATCCCTAG 57.078 36.000 0.00 0.00 35.70 3.02
387 389 9.391006 GTATGTAGTCATTTGTTGAAATCCCTA 57.609 33.333 0.00 0.00 35.70 3.53
388 390 7.888021 TGTATGTAGTCATTTGTTGAAATCCCT 59.112 33.333 0.00 0.00 35.70 4.20
389 391 8.050778 TGTATGTAGTCATTTGTTGAAATCCC 57.949 34.615 0.00 0.00 35.70 3.85
390 392 9.906660 TTTGTATGTAGTCATTTGTTGAAATCC 57.093 29.630 0.00 0.00 35.70 3.01
402 404 9.897744 CACTCATTTTGTTTTGTATGTAGTCAT 57.102 29.630 0.00 0.00 38.00 3.06
403 405 9.114952 TCACTCATTTTGTTTTGTATGTAGTCA 57.885 29.630 0.00 0.00 0.00 3.41
404 406 9.944663 TTCACTCATTTTGTTTTGTATGTAGTC 57.055 29.630 0.00 0.00 0.00 2.59
411 413 9.944663 GTGTAGATTCACTCATTTTGTTTTGTA 57.055 29.630 0.00 0.00 35.68 2.41
412 414 8.686334 AGTGTAGATTCACTCATTTTGTTTTGT 58.314 29.630 0.00 0.00 44.07 2.83
454 456 9.692749 CAAATGGACTACTACATACGAATGTAT 57.307 33.333 0.00 0.00 45.33 2.29
455 457 8.905850 TCAAATGGACTACTACATACGAATGTA 58.094 33.333 0.00 0.00 44.66 2.29
457 459 8.642908 TTCAAATGGACTACTACATACGAATG 57.357 34.615 0.00 0.00 39.17 2.67
458 460 9.832445 ATTTCAAATGGACTACTACATACGAAT 57.168 29.630 0.00 0.00 0.00 3.34
459 461 9.309516 GATTTCAAATGGACTACTACATACGAA 57.690 33.333 0.00 0.00 0.00 3.85
460 462 8.692710 AGATTTCAAATGGACTACTACATACGA 58.307 33.333 0.00 0.00 0.00 3.43
461 463 8.873215 AGATTTCAAATGGACTACTACATACG 57.127 34.615 0.00 0.00 0.00 3.06
493 495 9.997172 ACTCCCTCCATTTCTAAATATTTTTCT 57.003 29.630 5.91 0.00 0.00 2.52
496 498 9.355916 GCTACTCCCTCCATTTCTAAATATTTT 57.644 33.333 5.91 0.00 0.00 1.82
497 499 8.502738 TGCTACTCCCTCCATTTCTAAATATTT 58.497 33.333 5.89 5.89 0.00 1.40
498 500 7.939588 GTGCTACTCCCTCCATTTCTAAATATT 59.060 37.037 0.00 0.00 0.00 1.28
499 501 7.454225 GTGCTACTCCCTCCATTTCTAAATAT 58.546 38.462 0.00 0.00 0.00 1.28
500 502 6.183361 GGTGCTACTCCCTCCATTTCTAAATA 60.183 42.308 0.00 0.00 0.00 1.40
501 503 5.398012 GGTGCTACTCCCTCCATTTCTAAAT 60.398 44.000 0.00 0.00 0.00 1.40
502 504 4.080526 GGTGCTACTCCCTCCATTTCTAAA 60.081 45.833 0.00 0.00 0.00 1.85
503 505 3.454812 GGTGCTACTCCCTCCATTTCTAA 59.545 47.826 0.00 0.00 0.00 2.10
504 506 3.039011 GGTGCTACTCCCTCCATTTCTA 58.961 50.000 0.00 0.00 0.00 2.10
505 507 1.840635 GGTGCTACTCCCTCCATTTCT 59.159 52.381 0.00 0.00 0.00 2.52
506 508 1.559682 TGGTGCTACTCCCTCCATTTC 59.440 52.381 0.00 0.00 0.00 2.17
507 509 1.668826 TGGTGCTACTCCCTCCATTT 58.331 50.000 0.00 0.00 0.00 2.32
508 510 1.668826 TTGGTGCTACTCCCTCCATT 58.331 50.000 0.00 0.00 0.00 3.16
509 511 1.668826 TTTGGTGCTACTCCCTCCAT 58.331 50.000 0.00 0.00 0.00 3.41
510 512 1.351017 CTTTTGGTGCTACTCCCTCCA 59.649 52.381 0.00 0.00 0.00 3.86
511 513 1.950954 GCTTTTGGTGCTACTCCCTCC 60.951 57.143 0.00 0.00 0.00 4.30
512 514 1.271379 TGCTTTTGGTGCTACTCCCTC 60.271 52.381 0.00 0.00 0.00 4.30
513 515 0.771127 TGCTTTTGGTGCTACTCCCT 59.229 50.000 0.00 0.00 0.00 4.20
514 516 1.616159 TTGCTTTTGGTGCTACTCCC 58.384 50.000 0.00 0.00 0.00 4.30
515 517 2.558359 ACATTGCTTTTGGTGCTACTCC 59.442 45.455 0.00 0.00 0.00 3.85
516 518 3.923017 ACATTGCTTTTGGTGCTACTC 57.077 42.857 0.00 0.00 0.00 2.59
517 519 5.009631 TCATACATTGCTTTTGGTGCTACT 58.990 37.500 0.00 0.00 0.00 2.57
540 542 0.320771 GATGGTGGTCGTCAGCTTGT 60.321 55.000 10.73 0.39 43.76 3.16
578 580 0.460459 TGTTTGTCTTGCGTCGTGGA 60.460 50.000 0.00 0.00 0.00 4.02
584 586 2.286772 GGTCGAAATGTTTGTCTTGCGT 60.287 45.455 0.00 0.00 0.00 5.24
592 594 1.399727 GGAGCGTGGTCGAAATGTTTG 60.400 52.381 0.00 0.00 39.71 2.93
598 600 1.670791 AAAAAGGAGCGTGGTCGAAA 58.329 45.000 0.00 0.00 39.71 3.46
599 601 3.390003 AAAAAGGAGCGTGGTCGAA 57.610 47.368 0.00 0.00 39.71 3.71
616 618 3.058085 GCGTGGTCGAAAATCCCTAAAAA 60.058 43.478 0.00 0.00 39.71 1.94
617 619 2.485038 GCGTGGTCGAAAATCCCTAAAA 59.515 45.455 0.00 0.00 39.71 1.52
619 621 1.276989 AGCGTGGTCGAAAATCCCTAA 59.723 47.619 0.00 0.00 39.71 2.69
620 622 0.899720 AGCGTGGTCGAAAATCCCTA 59.100 50.000 0.00 0.00 39.71 3.53
621 623 0.391263 GAGCGTGGTCGAAAATCCCT 60.391 55.000 0.00 0.00 39.71 4.20
624 626 1.000145 GAGGAGCGTGGTCGAAAATC 59.000 55.000 0.00 0.00 39.71 2.17
626 628 1.005394 GGAGGAGCGTGGTCGAAAA 60.005 57.895 0.00 0.00 39.71 2.29
627 629 1.874345 GAGGAGGAGCGTGGTCGAAA 61.874 60.000 0.00 0.00 39.71 3.46
628 630 2.282958 AGGAGGAGCGTGGTCGAA 60.283 61.111 0.00 0.00 39.71 3.71
651 2468 0.183492 TGGCAGATGGGCTTGGATAC 59.817 55.000 0.00 0.00 43.83 2.24
668 2488 3.211963 GGCCCAATACGCTGCTGG 61.212 66.667 0.00 0.00 0.00 4.85
706 2526 3.622166 AGGTACTACGAAATGGTTGGG 57.378 47.619 0.00 0.00 36.02 4.12
707 2527 5.105228 TCCTAAGGTACTACGAAATGGTTGG 60.105 44.000 0.00 0.00 38.49 3.77
708 2528 5.969423 TCCTAAGGTACTACGAAATGGTTG 58.031 41.667 0.00 0.00 38.49 3.77
748 2570 0.180406 TCCATCGCCTCTAAAAGGGC 59.820 55.000 0.00 0.00 46.32 5.19
789 2611 2.096481 TTTTGACGCGTCGACTTGCC 62.096 55.000 31.88 9.06 0.00 4.52
964 2802 3.274455 CTGGATCGCGATCGGGGAG 62.274 68.421 35.36 25.13 41.34 4.30
1120 2958 3.739810 CAGTGATCAATGTAGAGCATCCG 59.260 47.826 14.89 0.00 36.21 4.18
1121 2959 3.497640 GCAGTGATCAATGTAGAGCATCC 59.502 47.826 22.89 0.87 36.21 3.51
1125 2963 4.573607 TGAATGCAGTGATCAATGTAGAGC 59.426 41.667 22.89 9.91 0.00 4.09
1170 3012 3.614159 AAATGATCATCGACAATGGCG 57.386 42.857 9.06 0.05 35.94 5.69
1187 3029 3.416119 TCTACGAGTCGATGCGAAAAT 57.584 42.857 21.50 0.00 37.72 1.82
1221 3063 1.965754 GCGGATCAACTCAGGCTCCT 61.966 60.000 0.00 0.00 0.00 3.69
1230 3102 3.197766 TGAATCCTTGTAGCGGATCAACT 59.802 43.478 0.00 0.00 40.31 3.16
1243 3115 2.354259 GTCTGTGAGCCTGAATCCTTG 58.646 52.381 0.00 0.00 0.00 3.61
1257 3129 1.795286 GAGCCTGAGAAAACGTCTGTG 59.205 52.381 0.00 0.00 36.41 3.66
1315 3188 2.742372 CAAAGTCGGGGCGTCAGG 60.742 66.667 0.00 0.00 0.00 3.86
1324 3197 4.244862 CCAAATTTCATTCCCAAAGTCGG 58.755 43.478 0.00 0.00 0.00 4.79
1388 3261 1.003696 CTGAAAGGAGTTCCCAGGACC 59.996 57.143 0.00 0.00 35.12 4.46
1635 3511 4.041075 TGTGGAAAGAGCCATAGTAACACA 59.959 41.667 0.00 0.00 40.68 3.72
1636 3512 4.575885 TGTGGAAAGAGCCATAGTAACAC 58.424 43.478 0.00 0.00 40.68 3.32
1637 3513 4.901197 TGTGGAAAGAGCCATAGTAACA 57.099 40.909 0.00 0.00 40.68 2.41
1644 3520 1.683011 CGGGAATGTGGAAAGAGCCAT 60.683 52.381 0.00 0.00 40.68 4.40
1647 3523 2.044123 ATCGGGAATGTGGAAAGAGC 57.956 50.000 0.00 0.00 0.00 4.09
1733 3609 0.994995 CTGGTCTGAACTCGAATGCG 59.005 55.000 0.00 0.00 39.35 4.73
1747 3623 8.964476 TTAGGAATTTGATGACTTATCTGGTC 57.036 34.615 0.00 0.00 36.71 4.02
1939 3815 8.960075 GTTAAAGTACGAAAGCAAGCAAAATAA 58.040 29.630 0.00 0.00 0.00 1.40
2044 3920 6.043938 ACTGGAAGAACACAGGAGGTTAATTA 59.956 38.462 0.00 0.00 39.00 1.40
2087 3963 3.343941 TTGTCTAAACGAATGGGAGGG 57.656 47.619 0.00 0.00 0.00 4.30
2171 4047 3.562973 AGCAGATGTCAACAACAACAGAG 59.437 43.478 0.00 0.00 42.37 3.35
2192 4068 9.659830 GTAACCAAAAACAACTGTACATTAGAG 57.340 33.333 0.00 0.00 0.00 2.43
2196 4072 7.262048 CCTGTAACCAAAAACAACTGTACATT 58.738 34.615 0.00 0.00 0.00 2.71
2208 4084 3.172229 GTTGCTGCCTGTAACCAAAAA 57.828 42.857 0.00 0.00 35.63 1.94
2290 4166 1.797635 GAGTCTGCTGAACTTGAGTGC 59.202 52.381 0.00 0.00 0.00 4.40
2347 4223 3.440173 AGAATTAATGCCACGTTGTCCTG 59.560 43.478 0.00 0.00 0.00 3.86
2405 4281 7.567458 TGGACAATATCATCACTCATCAGAAA 58.433 34.615 0.00 0.00 0.00 2.52
2423 4299 0.394352 GACCCGAATGCCTGGACAAT 60.394 55.000 0.00 0.00 0.00 2.71
2493 4369 1.203137 AGGACGATATTCGGATCCCCA 60.203 52.381 6.06 0.00 45.59 4.96
2567 4443 4.038080 CCCGTTTTGTCAGGCCGC 62.038 66.667 0.00 0.00 0.00 6.53
2573 4450 0.475044 AAGGTAGGCCCGTTTTGTCA 59.525 50.000 0.00 0.00 38.74 3.58
2611 4488 9.829507 AATTTCACAAGGTTTAAATTGTCATGA 57.170 25.926 4.55 0.00 37.54 3.07
2619 4496 9.108284 CAAGGTCAAATTTCACAAGGTTTAAAT 57.892 29.630 0.00 0.00 0.00 1.40
2623 4500 4.875536 GCAAGGTCAAATTTCACAAGGTTT 59.124 37.500 0.00 0.00 0.00 3.27
2629 4506 4.734398 ACTTGCAAGGTCAAATTTCACA 57.266 36.364 29.18 0.00 0.00 3.58
2652 4529 9.056005 ACTTGCAAATATATATCACACGAACAT 57.944 29.630 0.00 0.00 0.00 2.71
2688 4566 4.836125 AGTTCGATTGAAATGCTTGTGT 57.164 36.364 0.00 0.00 35.46 3.72
2725 4603 8.737168 GCAGTAAGCATATATATGGGAATTGA 57.263 34.615 21.50 0.00 44.79 2.57
2741 4619 7.552459 TGAACTGTATATACAAGCAGTAAGCA 58.448 34.615 16.17 7.63 40.79 3.91
2742 4620 8.420374 TTGAACTGTATATACAAGCAGTAAGC 57.580 34.615 16.17 5.61 40.79 3.09
2743 4621 9.803315 TCTTGAACTGTATATACAAGCAGTAAG 57.197 33.333 16.17 14.19 40.79 2.34
2746 4624 7.549488 GGTTCTTGAACTGTATATACAAGCAGT 59.451 37.037 16.17 8.13 43.13 4.40
2747 4625 7.766278 AGGTTCTTGAACTGTATATACAAGCAG 59.234 37.037 16.17 7.53 38.13 4.24
2748 4626 7.620880 AGGTTCTTGAACTGTATATACAAGCA 58.379 34.615 16.17 11.27 38.13 3.91
2749 4627 8.494016 AAGGTTCTTGAACTGTATATACAAGC 57.506 34.615 16.17 8.60 38.13 4.01
2750 4628 9.653287 TGAAGGTTCTTGAACTGTATATACAAG 57.347 33.333 16.17 10.40 39.13 3.16
2751 4629 9.653287 CTGAAGGTTCTTGAACTGTATATACAA 57.347 33.333 16.17 0.00 35.50 2.41
2752 4630 8.258007 CCTGAAGGTTCTTGAACTGTATATACA 58.742 37.037 14.75 14.75 34.56 2.29
2753 4631 8.649973 CCTGAAGGTTCTTGAACTGTATATAC 57.350 38.462 12.44 5.89 0.00 1.47
2834 4712 2.551032 CAGAAGAGCAATGACAACAGCA 59.449 45.455 0.00 0.00 0.00 4.41
2905 4783 4.514441 CCAGTGATGCTCAAGGATTCATAC 59.486 45.833 0.00 0.00 0.00 2.39
3081 4959 5.128919 AGATAATACAAGCAGCAAGAAGGG 58.871 41.667 0.00 0.00 0.00 3.95
3097 4975 5.061179 TCATCCGTCGACACAGAGATAATA 58.939 41.667 17.16 0.00 0.00 0.98
3102 4980 1.751437 ATCATCCGTCGACACAGAGA 58.249 50.000 17.16 6.76 0.00 3.10
3103 4981 2.568696 AATCATCCGTCGACACAGAG 57.431 50.000 17.16 0.00 0.00 3.35
3144 5022 4.314440 GCCACGGTGTCCTGCAGA 62.314 66.667 17.39 0.00 0.00 4.26
3225 5105 4.910746 CTGTCAACAGAACCTTATGTCG 57.089 45.455 4.05 0.00 46.59 4.35
3289 5169 2.223377 GGAAACATGTCGTTGTCAGTCC 59.777 50.000 0.00 0.00 38.07 3.85
3473 5353 1.374252 CTCGTTCCACTCCGGGTTG 60.374 63.158 0.00 0.00 34.36 3.77
3743 5623 0.844503 CGGTCGCTATGAAACGTAGC 59.155 55.000 11.50 11.50 40.83 3.58
3765 5645 3.376540 GAATACACAGCTCCATCGAGTC 58.623 50.000 0.00 0.00 38.49 3.36
3794 5674 2.761208 CCTTGGTGTAGAGGTGGTAGAG 59.239 54.545 0.00 0.00 0.00 2.43
4172 6052 0.811281 TGCATCAGTCACTCGTCGAT 59.189 50.000 0.00 0.00 0.00 3.59
4193 6073 4.803098 ACGGTAAAGCTAATCTCACAGT 57.197 40.909 0.00 0.00 0.00 3.55
4194 6074 4.567159 GGAACGGTAAAGCTAATCTCACAG 59.433 45.833 0.00 0.00 0.00 3.66
4195 6075 4.501071 GGAACGGTAAAGCTAATCTCACA 58.499 43.478 0.00 0.00 0.00 3.58
4196 6076 3.869832 GGGAACGGTAAAGCTAATCTCAC 59.130 47.826 0.00 0.00 0.00 3.51
4337 6228 7.329582 CAAACAGTGTCGAAATCAAATCAAAC 58.670 34.615 0.00 0.00 0.00 2.93
4386 6277 6.335777 TCATACCAGATGCAGATATCAATCG 58.664 40.000 5.32 2.83 37.19 3.34
4387 6278 8.557592 TTTCATACCAGATGCAGATATCAATC 57.442 34.615 5.32 5.37 0.00 2.67
4391 6282 7.108194 TCCATTTCATACCAGATGCAGATATC 58.892 38.462 0.00 0.00 0.00 1.63
4418 6309 3.451178 GCCCTAGACTACACCAGATTTGA 59.549 47.826 0.00 0.00 0.00 2.69
4429 6320 1.274447 ACCAAACACGCCCTAGACTAC 59.726 52.381 0.00 0.00 0.00 2.73
4430 6321 1.636148 ACCAAACACGCCCTAGACTA 58.364 50.000 0.00 0.00 0.00 2.59
4473 6364 0.671796 TCACTTTCTTCTCACGCGGA 59.328 50.000 12.47 3.82 0.00 5.54
4481 6373 5.997746 TCAATCAAACGGATCACTTTCTTCT 59.002 36.000 0.00 0.00 34.28 2.85
4492 6384 0.672401 ACGCGGTCAATCAAACGGAT 60.672 50.000 12.47 0.00 38.05 4.18
4530 6423 4.454504 CCAAGTATGCTTTAAGGTTCGTGT 59.545 41.667 0.00 0.00 31.49 4.49
4547 6442 1.204786 TAGCAAGCCAGGCCCAAGTA 61.205 55.000 8.22 0.00 0.00 2.24
4566 6461 3.247006 ACTGCCGATCTGAACGTTTAT 57.753 42.857 0.46 0.00 0.00 1.40
4567 6462 2.736144 ACTGCCGATCTGAACGTTTA 57.264 45.000 0.46 0.00 0.00 2.01
4573 6468 2.735444 CGCTAGAAACTGCCGATCTGAA 60.735 50.000 0.00 0.00 0.00 3.02
4601 6496 6.071447 GGTCTATCATATGCACTCATCTCAGT 60.071 42.308 0.00 0.00 34.22 3.41
4608 6503 5.604565 CAAGTGGTCTATCATATGCACTCA 58.395 41.667 10.58 0.00 0.00 3.41
4622 6517 1.071385 CTCTCCTTGTGCAAGTGGTCT 59.929 52.381 10.56 0.00 36.72 3.85
4624 6519 1.131638 TCTCTCCTTGTGCAAGTGGT 58.868 50.000 10.56 0.00 36.72 4.16
4655 6552 1.039233 ACATGCTGCATACAAGCCCC 61.039 55.000 15.78 0.00 0.00 5.80
4657 6554 0.526954 GCACATGCTGCATACAAGCC 60.527 55.000 15.78 0.00 46.29 4.35
4733 6630 3.659786 CACCGTTGTGTAGATTGGAAGA 58.340 45.455 0.00 0.00 37.72 2.87
4792 6689 1.399714 ATGGAACCGTAGCATCGAGA 58.600 50.000 0.00 0.00 0.00 4.04
4827 6724 9.715121 TTAAGAACTTATGGTCAACGAAACTAT 57.285 29.630 0.00 0.00 0.00 2.12
4854 6751 3.380320 AGTTTCAAACCGGGAAGACAAAG 59.620 43.478 6.32 0.00 0.00 2.77
4863 6760 4.565564 CGTCTAGAATAGTTTCAAACCGGG 59.434 45.833 6.32 0.00 40.38 5.73
4923 6820 5.683681 AGGCTGTTGGTCAAATGAAATTTT 58.316 33.333 0.00 0.00 46.10 1.82
4931 6828 3.941483 CGAGATTAGGCTGTTGGTCAAAT 59.059 43.478 0.00 0.00 0.00 2.32
4940 6837 1.134670 GGAACTGCGAGATTAGGCTGT 60.135 52.381 0.00 0.00 42.11 4.40
5065 6962 4.680708 CGAATAGGAAGGCTCTAAGCACAA 60.681 45.833 0.86 0.00 44.75 3.33
5067 6964 3.181474 ACGAATAGGAAGGCTCTAAGCAC 60.181 47.826 0.86 0.00 44.75 4.40
5072 6969 2.177233 AGGGACGAATAGGAAGGCTCTA 59.823 50.000 0.00 0.00 0.00 2.43
5079 6976 3.515330 GTCGAAAGGGACGAATAGGAA 57.485 47.619 0.00 0.00 41.31 3.36
5104 7001 2.517166 GATCAAGGGGAAGGGCGC 60.517 66.667 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.