Multiple sequence alignment - TraesCS3D01G278100

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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 TraesCS3D01G278100 chr3D 100.000 6186 0 0 1 6186 385428675 385422490 0.000000e+00 11424.0
1 TraesCS3D01G278100 chr3D 81.008 258 37 4 5927 6184 137000289 137000044 1.760000e-45 195.0
2 TraesCS3D01G278100 chr3D 81.008 258 36 4 5927 6181 609897342 609897589 6.330000e-45 193.0
3 TraesCS3D01G278100 chr3A 94.962 1866 65 10 3468 5328 507467530 507465689 0.000000e+00 2898.0
4 TraesCS3D01G278100 chr3A 90.952 2111 103 41 658 2734 507469573 507467517 0.000000e+00 2760.0
5 TraesCS3D01G278100 chr3A 96.724 519 14 3 2952 3470 714422124 714422639 0.000000e+00 861.0
6 TraesCS3D01G278100 chr3A 85.902 532 51 13 10 517 507470233 507469702 4.220000e-151 545.0
7 TraesCS3D01G278100 chr3B 89.957 1872 98 42 665 2491 501391584 501389758 0.000000e+00 2333.0
8 TraesCS3D01G278100 chr3B 93.202 1265 61 15 3642 4897 501389346 501388098 0.000000e+00 1836.0
9 TraesCS3D01G278100 chr3B 90.635 598 32 11 5351 5931 49406335 49406925 0.000000e+00 773.0
10 TraesCS3D01G278100 chr3B 87.825 616 49 12 1 592 501392313 501391700 0.000000e+00 699.0
11 TraesCS3D01G278100 chr3B 90.974 421 33 5 5721 6138 49406865 49407283 4.190000e-156 562.0
12 TraesCS3D01G278100 chr3B 93.243 370 19 5 4905 5269 501388033 501387665 1.960000e-149 540.0
13 TraesCS3D01G278100 chr3B 84.536 97 13 2 5644 5740 734134259 734134353 1.840000e-15 95.3
14 TraesCS3D01G278100 chr6D 98.487 859 12 1 5329 6186 451547917 451548775 0.000000e+00 1513.0
15 TraesCS3D01G278100 chr2D 97.669 858 19 1 5330 6186 220980626 220979769 0.000000e+00 1472.0
16 TraesCS3D01G278100 chr2D 73.537 820 113 62 2735 3470 58683643 58684442 3.760000e-52 217.0
17 TraesCS3D01G278100 chr7D 95.882 850 20 3 5338 6186 126993354 126992519 0.000000e+00 1362.0
18 TraesCS3D01G278100 chr7D 97.139 699 18 2 2772 3470 203173913 203173217 0.000000e+00 1179.0
19 TraesCS3D01G278100 chr7D 89.677 155 12 2 5927 6079 608107601 608107449 1.760000e-45 195.0
20 TraesCS3D01G278100 chr7D 90.411 146 12 1 2734 2877 112053892 112054037 2.280000e-44 191.0
21 TraesCS3D01G278100 chr7A 97.422 737 15 3 2735 3470 74647810 74648543 0.000000e+00 1253.0
22 TraesCS3D01G278100 chr7A 90.827 774 30 15 2735 3470 671784340 671783570 0.000000e+00 998.0
23 TraesCS3D01G278100 chr7A 79.699 399 49 14 2960 3337 89948566 89948179 6.150000e-65 259.0
24 TraesCS3D01G278100 chr6B 88.166 769 48 19 2735 3469 22075986 22076745 0.000000e+00 876.0
25 TraesCS3D01G278100 chr6B 87.760 768 52 19 2735 3469 22001990 22002748 0.000000e+00 859.0
26 TraesCS3D01G278100 chr6B 86.780 764 53 22 2737 3469 655311726 655310980 0.000000e+00 808.0
27 TraesCS3D01G278100 chr6B 96.325 381 13 1 2734 3113 636132649 636133029 5.260000e-175 625.0
28 TraesCS3D01G278100 chr1B 87.875 767 53 19 2735 3469 636820536 636821294 0.000000e+00 865.0
29 TraesCS3D01G278100 chr5A 88.446 727 46 10 2740 3430 670343835 670344559 0.000000e+00 843.0
30 TraesCS3D01G278100 chr5A 85.934 782 71 8 2734 3476 622527026 622526245 0.000000e+00 798.0
31 TraesCS3D01G278100 chr5A 90.588 85 6 1 5997 6079 31652176 31652260 1.820000e-20 111.0
32 TraesCS3D01G278100 chr5A 90.588 85 6 1 5997 6079 31678394 31678478 1.820000e-20 111.0
33 TraesCS3D01G278100 chr5A 90.476 84 6 1 5997 6078 31612608 31612691 6.560000e-20 110.0
34 TraesCS3D01G278100 chrUn 82.061 262 41 4 5927 6184 22819777 22820036 1.040000e-52 219.0


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 TraesCS3D01G278100 chr3D 385422490 385428675 6185 True 11424.000000 11424 100.000000 1 6186 1 chr3D.!!$R2 6185
1 TraesCS3D01G278100 chr3A 507465689 507470233 4544 True 2067.666667 2898 90.605333 10 5328 3 chr3A.!!$R1 5318
2 TraesCS3D01G278100 chr3A 714422124 714422639 515 False 861.000000 861 96.724000 2952 3470 1 chr3A.!!$F1 518
3 TraesCS3D01G278100 chr3B 501387665 501392313 4648 True 1352.000000 2333 91.056750 1 5269 4 chr3B.!!$R1 5268
4 TraesCS3D01G278100 chr3B 49406335 49407283 948 False 667.500000 773 90.804500 5351 6138 2 chr3B.!!$F2 787
5 TraesCS3D01G278100 chr6D 451547917 451548775 858 False 1513.000000 1513 98.487000 5329 6186 1 chr6D.!!$F1 857
6 TraesCS3D01G278100 chr2D 220979769 220980626 857 True 1472.000000 1472 97.669000 5330 6186 1 chr2D.!!$R1 856
7 TraesCS3D01G278100 chr2D 58683643 58684442 799 False 217.000000 217 73.537000 2735 3470 1 chr2D.!!$F1 735
8 TraesCS3D01G278100 chr7D 126992519 126993354 835 True 1362.000000 1362 95.882000 5338 6186 1 chr7D.!!$R1 848
9 TraesCS3D01G278100 chr7D 203173217 203173913 696 True 1179.000000 1179 97.139000 2772 3470 1 chr7D.!!$R2 698
10 TraesCS3D01G278100 chr7A 74647810 74648543 733 False 1253.000000 1253 97.422000 2735 3470 1 chr7A.!!$F1 735
11 TraesCS3D01G278100 chr7A 671783570 671784340 770 True 998.000000 998 90.827000 2735 3470 1 chr7A.!!$R2 735
12 TraesCS3D01G278100 chr6B 22075986 22076745 759 False 876.000000 876 88.166000 2735 3469 1 chr6B.!!$F2 734
13 TraesCS3D01G278100 chr6B 22001990 22002748 758 False 859.000000 859 87.760000 2735 3469 1 chr6B.!!$F1 734
14 TraesCS3D01G278100 chr6B 655310980 655311726 746 True 808.000000 808 86.780000 2737 3469 1 chr6B.!!$R1 732
15 TraesCS3D01G278100 chr1B 636820536 636821294 758 False 865.000000 865 87.875000 2735 3469 1 chr1B.!!$F1 734
16 TraesCS3D01G278100 chr5A 670343835 670344559 724 False 843.000000 843 88.446000 2740 3430 1 chr5A.!!$F4 690
17 TraesCS3D01G278100 chr5A 622526245 622527026 781 True 798.000000 798 85.934000 2734 3476 1 chr5A.!!$R1 742

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
499 524 0.178970 GCCTGATTCATGGCTGGGAT 60.179 55.000 15.64 0.00 45.26 3.85 F
1632 1743 0.037975 TTTAGAACCGTGGCGACTCC 60.038 55.000 0.00 0.00 0.00 3.85 F
2549 2751 0.320073 TTTCCTTGTCGCTGTACCCG 60.320 55.000 0.00 0.00 0.00 5.28 F
3900 4223 2.989909 TGGTGATAGGACAATGCAGTG 58.010 47.619 13.51 13.51 0.00 3.66 F
4551 4880 0.321122 AAAGCAGAAGCAGGACTCCG 60.321 55.000 0.00 0.00 45.49 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1893 0.163788 CACTAAAACGAGCCACAGCG 59.836 55.000 0.00 0.0 46.67 5.18 R
3559 3880 3.493176 GCTGCACTCCAAAAATGAAGGTT 60.493 43.478 0.00 0.0 0.00 3.50 R
3974 4297 0.322997 TGGCCAACCCGTAGAAATGG 60.323 55.000 0.61 0.0 35.87 3.16 R
4707 5038 1.153168 GCAGCCACGTGGGTATGAT 60.153 57.895 36.72 6.3 45.47 2.45 R
5661 6071 1.243342 ACATCACATGGTGGTTGCCG 61.243 55.000 0.00 0.0 33.87 5.69 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
101 102 0.181114 TGTGAGGCAGCAGACTTTGT 59.819 50.000 0.00 0.00 28.39 2.83
107 108 4.006319 GAGGCAGCAGACTTTGTTATTCT 58.994 43.478 0.00 0.00 28.39 2.40
132 133 2.417933 GCACACTGAGGATGTTGATCAC 59.582 50.000 0.00 0.00 0.00 3.06
137 138 1.550072 TGAGGATGTTGATCACGCTGA 59.450 47.619 0.00 0.00 0.00 4.26
165 175 0.823356 AACATGGTGCACAGGTGGTC 60.823 55.000 20.43 0.00 44.50 4.02
183 193 1.933853 GTCGAACCTATGTCCACATGC 59.066 52.381 2.26 0.00 37.15 4.06
210 220 3.724508 AACAATGGTTTCGATGTTGCA 57.275 38.095 0.00 0.00 34.88 4.08
261 274 2.840038 ACTGGAAGGTGATGATGTAGCA 59.160 45.455 0.00 0.00 39.30 3.49
276 289 0.666274 TAGCAACGGCAGAACACGAG 60.666 55.000 0.00 0.00 44.61 4.18
298 311 1.866925 GCGGAGGAGGAAAACAACG 59.133 57.895 0.00 0.00 0.00 4.10
303 316 1.895231 GGAGGAAAACAACGGCGGT 60.895 57.895 13.24 0.00 0.00 5.68
316 329 2.667199 GCGGTTGTAACGGTGCCT 60.667 61.111 4.59 0.00 0.00 4.75
328 341 1.754745 GGTGCCTCTTCCTCACACA 59.245 57.895 0.00 0.00 32.89 3.72
342 355 3.620374 CCTCACACACATAGTTCATCTGC 59.380 47.826 0.00 0.00 0.00 4.26
346 359 2.862536 CACACATAGTTCATCTGCCTCG 59.137 50.000 0.00 0.00 0.00 4.63
354 367 1.039785 TCATCTGCCTCGGAGTCAGG 61.040 60.000 15.33 1.58 0.00 3.86
379 400 2.357009 GACATGATGCGATTCCAGCTTT 59.643 45.455 0.00 0.00 35.28 3.51
380 401 2.098607 ACATGATGCGATTCCAGCTTTG 59.901 45.455 0.00 0.00 35.28 2.77
382 403 1.469703 TGATGCGATTCCAGCTTTGTG 59.530 47.619 0.00 0.00 35.28 3.33
383 404 1.470098 GATGCGATTCCAGCTTTGTGT 59.530 47.619 0.00 0.00 35.28 3.72
386 411 1.400242 GCGATTCCAGCTTTGTGTCAC 60.400 52.381 0.00 0.00 0.00 3.67
391 416 5.503031 CGATTCCAGCTTTGTGTCACATATC 60.503 44.000 6.48 0.00 0.00 1.63
397 422 4.130118 GCTTTGTGTCACATATCTAGGGG 58.870 47.826 6.48 0.00 0.00 4.79
408 433 8.305317 GTCACATATCTAGGGGTTAGATTGTAC 58.695 40.741 2.37 0.00 44.92 2.90
422 447 3.758554 AGATTGTACTTGATGCCGCTTTT 59.241 39.130 0.00 0.00 0.00 2.27
441 466 2.539003 CGGAGTTTGCCGTGATTGA 58.461 52.632 0.00 0.00 46.07 2.57
482 507 2.939460 ATTCGGTTTGTTATGCAGCC 57.061 45.000 0.00 0.00 0.00 4.85
489 514 3.193267 GGTTTGTTATGCAGCCTGATTCA 59.807 43.478 0.00 0.00 0.00 2.57
491 516 4.642445 TTGTTATGCAGCCTGATTCATG 57.358 40.909 0.00 0.00 0.00 3.07
499 524 0.178970 GCCTGATTCATGGCTGGGAT 60.179 55.000 15.64 0.00 45.26 3.85
509 534 4.401022 TCATGGCTGGGATAAATAGCTTG 58.599 43.478 0.00 0.00 37.58 4.01
523 548 6.780457 AAATAGCTTGTTGATGTTGGCTAT 57.220 33.333 0.00 0.00 42.41 2.97
525 550 7.880160 AATAGCTTGTTGATGTTGGCTATAA 57.120 32.000 0.00 0.00 40.59 0.98
526 551 5.824904 AGCTTGTTGATGTTGGCTATAAG 57.175 39.130 0.00 0.00 0.00 1.73
566 591 1.394618 TGTTTAGCCGTGCAGGTTTT 58.605 45.000 5.57 0.00 43.70 2.43
572 597 0.318360 GCCGTGCAGGTTTTGTTACC 60.318 55.000 5.57 0.00 43.70 2.85
576 601 1.406180 GTGCAGGTTTTGTTACCGGTT 59.594 47.619 15.04 0.00 43.21 4.44
582 607 5.463286 CAGGTTTTGTTACCGGTTTAATCC 58.537 41.667 15.04 10.52 43.21 3.01
592 617 2.357952 CCGGTTTAATCCTTTAGCTGGC 59.642 50.000 0.00 0.00 0.00 4.85
594 619 3.632145 CGGTTTAATCCTTTAGCTGGCAT 59.368 43.478 0.00 0.00 0.00 4.40
595 620 4.819630 CGGTTTAATCCTTTAGCTGGCATA 59.180 41.667 0.00 0.00 0.00 3.14
596 621 5.473504 CGGTTTAATCCTTTAGCTGGCATAT 59.526 40.000 0.00 0.00 0.00 1.78
597 622 6.348540 CGGTTTAATCCTTTAGCTGGCATATC 60.349 42.308 0.00 0.00 0.00 1.63
598 623 6.717084 GGTTTAATCCTTTAGCTGGCATATCT 59.283 38.462 0.00 0.00 0.00 1.98
601 626 5.839517 ATCCTTTAGCTGGCATATCTCTT 57.160 39.130 0.00 0.00 0.00 2.85
602 627 5.636903 TCCTTTAGCTGGCATATCTCTTT 57.363 39.130 0.00 0.00 0.00 2.52
603 628 5.371526 TCCTTTAGCTGGCATATCTCTTTG 58.628 41.667 0.00 0.00 0.00 2.77
605 630 4.428294 TTAGCTGGCATATCTCTTTGCT 57.572 40.909 0.00 0.00 38.88 3.91
606 631 5.551305 TTAGCTGGCATATCTCTTTGCTA 57.449 39.130 0.00 0.00 38.88 3.49
607 632 4.428294 AGCTGGCATATCTCTTTGCTAA 57.572 40.909 0.00 0.00 38.88 3.09
609 634 3.879295 GCTGGCATATCTCTTTGCTAACA 59.121 43.478 0.00 0.00 38.88 2.41
610 635 4.336433 GCTGGCATATCTCTTTGCTAACAA 59.664 41.667 0.00 0.00 38.88 2.83
611 636 5.163622 GCTGGCATATCTCTTTGCTAACAAA 60.164 40.000 0.00 0.00 43.45 2.83
612 637 6.460676 GCTGGCATATCTCTTTGCTAACAAAT 60.461 38.462 0.00 0.00 44.54 2.32
613 638 6.798482 TGGCATATCTCTTTGCTAACAAATG 58.202 36.000 0.00 0.00 44.54 2.32
614 639 6.377996 TGGCATATCTCTTTGCTAACAAATGT 59.622 34.615 0.00 0.00 44.54 2.71
615 640 6.914757 GGCATATCTCTTTGCTAACAAATGTC 59.085 38.462 0.00 0.00 44.54 3.06
617 642 7.854916 GCATATCTCTTTGCTAACAAATGTCTC 59.145 37.037 0.00 0.00 44.54 3.36
619 644 7.750229 ATCTCTTTGCTAACAAATGTCTCAA 57.250 32.000 0.00 0.00 44.54 3.02
620 645 7.194607 TCTCTTTGCTAACAAATGTCTCAAG 57.805 36.000 0.00 0.00 44.54 3.02
622 647 6.959361 TCTTTGCTAACAAATGTCTCAAGTC 58.041 36.000 0.00 0.00 44.54 3.01
623 648 6.767902 TCTTTGCTAACAAATGTCTCAAGTCT 59.232 34.615 0.00 0.00 44.54 3.24
625 650 5.610398 TGCTAACAAATGTCTCAAGTCTGA 58.390 37.500 0.00 0.00 0.00 3.27
626 651 6.233434 TGCTAACAAATGTCTCAAGTCTGAT 58.767 36.000 0.00 0.00 0.00 2.90
627 652 6.712095 TGCTAACAAATGTCTCAAGTCTGATT 59.288 34.615 0.00 0.00 0.00 2.57
628 653 7.095060 TGCTAACAAATGTCTCAAGTCTGATTC 60.095 37.037 0.00 0.00 0.00 2.52
630 655 9.645059 CTAACAAATGTCTCAAGTCTGATTCTA 57.355 33.333 0.00 0.00 0.00 2.10
631 656 7.897575 ACAAATGTCTCAAGTCTGATTCTAC 57.102 36.000 0.00 0.00 0.00 2.59
632 657 7.675062 ACAAATGTCTCAAGTCTGATTCTACT 58.325 34.615 0.00 0.00 0.00 2.57
633 658 7.601886 ACAAATGTCTCAAGTCTGATTCTACTG 59.398 37.037 0.00 0.00 0.00 2.74
634 659 5.651387 TGTCTCAAGTCTGATTCTACTGG 57.349 43.478 0.00 0.00 0.00 4.00
637 676 6.151312 TGTCTCAAGTCTGATTCTACTGGTAC 59.849 42.308 0.00 0.00 0.00 3.34
640 679 8.275758 TCTCAAGTCTGATTCTACTGGTACTAT 58.724 37.037 0.00 0.00 0.00 2.12
646 685 9.733219 GTCTGATTCTACTGGTACTATTTACAC 57.267 37.037 0.00 0.00 0.00 2.90
651 690 4.119442 ACTGGTACTATTTACACAGGCG 57.881 45.455 0.00 0.00 0.00 5.52
663 702 2.086869 ACACAGGCGAAATTGGAGATG 58.913 47.619 0.00 0.00 0.00 2.90
670 709 2.415893 GCGAAATTGGAGATGGGTGTTG 60.416 50.000 0.00 0.00 0.00 3.33
671 710 2.819608 CGAAATTGGAGATGGGTGTTGT 59.180 45.455 0.00 0.00 0.00 3.32
672 711 4.006989 CGAAATTGGAGATGGGTGTTGTA 58.993 43.478 0.00 0.00 0.00 2.41
696 767 2.169832 ACACCTTCCACGTCTGAATG 57.830 50.000 0.00 0.00 0.00 2.67
770 851 6.670027 AGATGTCTAGGAGTAGAAAATGTGGT 59.330 38.462 0.00 0.00 37.02 4.16
798 879 1.024579 AGTTGGGCTTTCATACCGCG 61.025 55.000 0.00 0.00 0.00 6.46
849 932 1.203523 GAGTCAGAGTCCAGTGCGATT 59.796 52.381 0.00 0.00 0.00 3.34
864 947 0.943673 CGATTGCCACACAGACACAA 59.056 50.000 0.00 0.00 0.00 3.33
1062 1155 4.589908 AGATGTAAGGCCCTACTTTTGTG 58.410 43.478 12.73 0.00 32.02 3.33
1065 1158 4.538738 TGTAAGGCCCTACTTTTGTGTTT 58.461 39.130 12.73 0.00 32.02 2.83
1067 1160 5.422650 TGTAAGGCCCTACTTTTGTGTTTTT 59.577 36.000 12.73 0.00 32.02 1.94
1068 1161 4.665833 AGGCCCTACTTTTGTGTTTTTC 57.334 40.909 0.00 0.00 0.00 2.29
1069 1162 3.067601 AGGCCCTACTTTTGTGTTTTTCG 59.932 43.478 0.00 0.00 0.00 3.46
1070 1163 3.181484 GGCCCTACTTTTGTGTTTTTCGT 60.181 43.478 0.00 0.00 0.00 3.85
1071 1164 4.426416 GCCCTACTTTTGTGTTTTTCGTT 58.574 39.130 0.00 0.00 0.00 3.85
1072 1165 4.865925 GCCCTACTTTTGTGTTTTTCGTTT 59.134 37.500 0.00 0.00 0.00 3.60
1073 1166 5.349270 GCCCTACTTTTGTGTTTTTCGTTTT 59.651 36.000 0.00 0.00 0.00 2.43
1074 1167 6.671164 GCCCTACTTTTGTGTTTTTCGTTTTG 60.671 38.462 0.00 0.00 0.00 2.44
1075 1168 6.586844 CCCTACTTTTGTGTTTTTCGTTTTGA 59.413 34.615 0.00 0.00 0.00 2.69
1098 1191 0.040958 GATTTGATGATCGTGCCCGC 60.041 55.000 0.00 0.00 0.00 6.13
1120 1216 1.954382 GCTCTTTTCTTTTCCCCGTGT 59.046 47.619 0.00 0.00 0.00 4.49
1141 1237 4.933064 CTGACCTCGGGCGCGATC 62.933 72.222 26.78 21.32 0.00 3.69
1159 1256 2.668212 CCCCGTTGCGCAGAAAGA 60.668 61.111 11.31 0.00 0.00 2.52
1256 1361 0.322997 TGTGTAATTTGGCCTCGGGG 60.323 55.000 3.32 0.00 0.00 5.73
1280 1385 5.831103 AGGAAGAAATGTCCATGGTGTATT 58.169 37.500 12.58 8.20 37.65 1.89
1285 1390 5.774690 AGAAATGTCCATGGTGTATTTGTGT 59.225 36.000 20.35 8.59 0.00 3.72
1296 1401 6.565234 TGGTGTATTTGTGTTGTTTTACCAG 58.435 36.000 0.00 0.00 31.48 4.00
1299 1404 6.198216 GTGTATTTGTGTTGTTTTACCAGCTG 59.802 38.462 6.78 6.78 0.00 4.24
1489 1599 4.744137 TGAGTTTTTGCACATTTTGATCGG 59.256 37.500 0.00 0.00 0.00 4.18
1504 1614 4.838486 CGGGTCGTCGCTCTGCTC 62.838 72.222 0.00 0.00 0.00 4.26
1505 1615 3.444805 GGGTCGTCGCTCTGCTCT 61.445 66.667 0.00 0.00 0.00 4.09
1506 1616 2.202544 GGTCGTCGCTCTGCTCTG 60.203 66.667 0.00 0.00 0.00 3.35
1507 1617 2.878520 GTCGTCGCTCTGCTCTGC 60.879 66.667 0.00 0.00 0.00 4.26
1508 1618 3.058773 TCGTCGCTCTGCTCTGCT 61.059 61.111 0.00 0.00 0.00 4.24
1526 1636 1.660560 CTTTCAGCGGGGAATGCCAG 61.661 60.000 0.00 0.00 35.15 4.85
1530 1640 0.604780 CAGCGGGGAATGCCAGATAG 60.605 60.000 0.00 0.00 35.15 2.08
1542 1652 2.840038 TGCCAGATAGTCATGAAGGTGT 59.160 45.455 0.00 0.00 0.00 4.16
1606 1716 4.038042 CCTGTATAAGGTGATGAGCTCGAA 59.962 45.833 9.64 0.00 41.74 3.71
1607 1717 5.279206 CCTGTATAAGGTGATGAGCTCGAAT 60.279 44.000 9.64 0.00 41.74 3.34
1615 1726 4.096984 GGTGATGAGCTCGAATTGGAATTT 59.903 41.667 9.64 0.00 0.00 1.82
1616 1727 5.296780 GGTGATGAGCTCGAATTGGAATTTA 59.703 40.000 9.64 0.00 0.00 1.40
1617 1728 6.425504 GTGATGAGCTCGAATTGGAATTTAG 58.574 40.000 9.64 0.00 0.00 1.85
1618 1729 6.258727 GTGATGAGCTCGAATTGGAATTTAGA 59.741 38.462 9.64 0.00 0.00 2.10
1619 1730 6.823182 TGATGAGCTCGAATTGGAATTTAGAA 59.177 34.615 9.64 0.00 0.00 2.10
1620 1731 6.422776 TGAGCTCGAATTGGAATTTAGAAC 57.577 37.500 9.64 0.00 0.00 3.01
1621 1732 5.354234 TGAGCTCGAATTGGAATTTAGAACC 59.646 40.000 9.64 0.00 0.00 3.62
1622 1733 4.332819 AGCTCGAATTGGAATTTAGAACCG 59.667 41.667 0.00 0.00 0.00 4.44
1623 1734 4.094442 GCTCGAATTGGAATTTAGAACCGT 59.906 41.667 0.00 0.00 0.00 4.83
1624 1735 5.539582 TCGAATTGGAATTTAGAACCGTG 57.460 39.130 0.00 0.00 0.00 4.94
1625 1736 4.393680 TCGAATTGGAATTTAGAACCGTGG 59.606 41.667 0.00 0.00 0.00 4.94
1626 1737 4.421058 GAATTGGAATTTAGAACCGTGGC 58.579 43.478 0.00 0.00 0.00 5.01
1627 1738 1.444836 TGGAATTTAGAACCGTGGCG 58.555 50.000 0.00 0.00 0.00 5.69
1628 1739 1.002201 TGGAATTTAGAACCGTGGCGA 59.998 47.619 0.00 0.00 0.00 5.54
1629 1740 1.395954 GGAATTTAGAACCGTGGCGAC 59.604 52.381 0.00 0.00 0.00 5.19
1630 1741 2.344025 GAATTTAGAACCGTGGCGACT 58.656 47.619 0.00 0.00 0.00 4.18
1631 1742 2.005971 ATTTAGAACCGTGGCGACTC 57.994 50.000 0.00 0.00 0.00 3.36
1632 1743 0.037975 TTTAGAACCGTGGCGACTCC 60.038 55.000 0.00 0.00 0.00 3.85
1633 1744 1.180456 TTAGAACCGTGGCGACTCCA 61.180 55.000 0.00 0.00 44.18 3.86
1659 1770 2.762535 TCCGTTCTGGATTGTTCCTC 57.237 50.000 0.00 0.00 43.74 3.71
1719 1830 1.484240 GTGGCTGAGTATCTTCTGGCT 59.516 52.381 7.68 0.00 40.62 4.75
1724 1835 3.745458 GCTGAGTATCTTCTGGCTAATGC 59.255 47.826 0.00 0.00 34.92 3.56
1782 1893 0.378257 CACAGATTGCGGTATGTGCC 59.622 55.000 3.46 0.00 34.94 5.01
1804 1915 2.157085 GCTGTGGCTCGTTTTAGTGTAC 59.843 50.000 0.00 0.00 35.22 2.90
1806 1917 3.125316 TGTGGCTCGTTTTAGTGTACAC 58.875 45.455 18.56 18.56 0.00 2.90
1807 1918 3.181473 TGTGGCTCGTTTTAGTGTACACT 60.181 43.478 30.13 30.13 45.02 3.55
1808 1919 3.805971 GTGGCTCGTTTTAGTGTACACTT 59.194 43.478 32.15 16.83 42.54 3.16
1809 1920 4.053295 TGGCTCGTTTTAGTGTACACTTC 58.947 43.478 32.15 18.41 42.54 3.01
1931 2049 1.171549 TCAATGTGCGCAAGAAGGCA 61.172 50.000 14.00 4.80 43.02 4.75
2031 2149 1.985447 CTGCATTGCATTCGCCGTCT 61.985 55.000 12.53 0.00 38.13 4.18
2046 2164 0.436150 CGTCTGACTTGTCGTGCATG 59.564 55.000 6.21 0.00 0.00 4.06
2052 2170 3.253230 TGACTTGTCGTGCATGATGTAG 58.747 45.455 12.67 11.77 0.00 2.74
2057 2175 4.647424 TGTCGTGCATGATGTAGACATA 57.353 40.909 12.67 0.00 36.57 2.29
2141 2263 1.678970 GGGGGTGTCATCAACTGGC 60.679 63.158 0.00 0.00 0.00 4.85
2244 2366 2.031465 GGGAAACCGCCTCGTTCA 59.969 61.111 0.00 0.00 43.64 3.18
2245 2367 1.598685 GGGAAACCGCCTCGTTCAA 60.599 57.895 0.00 0.00 43.64 2.69
2246 2368 1.574702 GGGAAACCGCCTCGTTCAAG 61.575 60.000 0.00 0.00 43.64 3.02
2247 2369 1.574702 GGAAACCGCCTCGTTCAAGG 61.575 60.000 0.00 0.00 39.62 3.61
2248 2370 0.601841 GAAACCGCCTCGTTCAAGGA 60.602 55.000 0.00 0.00 38.87 3.36
2277 2408 0.532862 ACACACTGGGAGCAAGAACG 60.533 55.000 0.00 0.00 0.00 3.95
2373 2507 2.353109 GCAAAAGGAGGCTCCAAATCAC 60.353 50.000 33.86 15.39 39.61 3.06
2511 2713 8.778059 TCCTTACCATCTCTAATGTTTGGTTAT 58.222 33.333 0.00 0.00 40.92 1.89
2549 2751 0.320073 TTTCCTTGTCGCTGTACCCG 60.320 55.000 0.00 0.00 0.00 5.28
2704 2906 5.105473 AGTGCCGTCAGCTATTTCTTACTTA 60.105 40.000 0.00 0.00 44.23 2.24
2707 2909 5.006455 GCCGTCAGCTATTTCTTACTTAACC 59.994 44.000 0.00 0.00 38.99 2.85
2732 2934 6.074302 CGTATCAAACATACTCACCATAGCAC 60.074 42.308 0.00 0.00 0.00 4.40
2810 3018 3.634504 TCAATTATGAGCACATGGGCTT 58.365 40.909 26.20 12.14 45.99 4.35
2843 3053 8.035448 TCCCCTAATAAAGATTCTTTCTCTCC 57.965 38.462 14.75 0.00 31.78 3.71
3403 3724 5.763698 AGAATGAATACATGGCATGAGTGAG 59.236 40.000 32.74 6.59 36.79 3.51
3470 3791 4.943705 TGCATGGTAGAATCACTTTTCTCC 59.056 41.667 0.00 0.00 37.20 3.71
3473 3794 5.779241 TGGTAGAATCACTTTTCTCCCAT 57.221 39.130 0.00 0.00 36.96 4.00
3476 3797 5.760743 GGTAGAATCACTTTTCTCCCATAGC 59.239 44.000 0.00 0.00 37.20 2.97
3477 3798 5.441718 AGAATCACTTTTCTCCCATAGCA 57.558 39.130 0.00 0.00 29.99 3.49
3774 4095 8.769891 GTTTGTTTTCTTGACCTTCTTCAAAAA 58.230 29.630 0.00 0.00 35.07 1.94
3810 4131 8.072567 CCTAGCAATATCTTTGTAGCACAAATC 58.927 37.037 12.68 1.59 45.79 2.17
3816 4137 8.895932 ATATCTTTGTAGCACAAATCGTTTTC 57.104 30.769 12.68 0.00 45.79 2.29
3842 4163 7.752239 CCATCTCTTACAGTTGTTTGCAATAAG 59.248 37.037 0.00 3.67 36.92 1.73
3900 4223 2.989909 TGGTGATAGGACAATGCAGTG 58.010 47.619 13.51 13.51 0.00 3.66
3920 4243 7.228108 TGCAGTGATTCTGAAGATTCATAATCC 59.772 37.037 21.41 15.73 44.01 3.01
4119 4442 3.144657 TGGAGTTCTCAGTACGTGGTA 57.855 47.619 0.00 0.00 0.00 3.25
4316 4645 2.103432 TGACACAGCTTTCGACCCTTTA 59.897 45.455 0.00 0.00 0.00 1.85
4466 4795 3.502123 TCGGAGGAGTTGAATTTTGGT 57.498 42.857 0.00 0.00 0.00 3.67
4551 4880 0.321122 AAAGCAGAAGCAGGACTCCG 60.321 55.000 0.00 0.00 45.49 4.63
4665 4994 5.433526 TGAATTTAGCTGCCCGTAAGTATT 58.566 37.500 0.00 0.00 0.00 1.89
4666 4995 5.526111 TGAATTTAGCTGCCCGTAAGTATTC 59.474 40.000 0.00 0.00 0.00 1.75
4667 4996 4.748277 TTTAGCTGCCCGTAAGTATTCT 57.252 40.909 0.00 0.00 0.00 2.40
4739 5071 1.758592 GCTGCCCATACCCCGAATA 59.241 57.895 0.00 0.00 0.00 1.75
4740 5072 0.328258 GCTGCCCATACCCCGAATAT 59.672 55.000 0.00 0.00 0.00 1.28
4744 5076 3.895041 CTGCCCATACCCCGAATATTTTT 59.105 43.478 0.00 0.00 0.00 1.94
4857 5189 2.938838 TCCAGTTACCCACAAACCTTG 58.061 47.619 0.00 0.00 0.00 3.61
4944 5335 8.985315 AGATATTATTCCTGCATTTCTTGACA 57.015 30.769 0.00 0.00 0.00 3.58
5305 5700 4.202020 TGAGTAGATGTATCGCAGAACACC 60.202 45.833 0.00 0.00 43.58 4.16
5486 5884 2.202676 GCGAGGAGAGGAACAGCG 60.203 66.667 0.00 0.00 0.00 5.18
5551 5961 1.966354 AGCCTATGATCTCACGCATCA 59.034 47.619 0.00 0.00 34.74 3.07
5697 6107 1.172175 TGTGTTGCAGCAGTGAACAA 58.828 45.000 2.40 0.00 31.62 2.83
5954 6516 7.278646 TGCTTCATTACAACTCTATTGTAGCAG 59.721 37.037 9.13 2.94 35.40 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.863424 TGAGTCACAGTTTTCGTTCACTC 59.137 43.478 0.00 0.00 0.00 3.51
69 70 1.612726 GCCTCACAGTTCTCAATGGCT 60.613 52.381 0.00 0.00 36.52 4.75
101 102 5.187772 ACATCCTCAGTGTGCTGTAGAATAA 59.812 40.000 0.00 0.00 43.05 1.40
107 108 2.632512 TCAACATCCTCAGTGTGCTGTA 59.367 45.455 0.00 0.00 43.05 2.74
132 133 1.202065 CCATGTTCCATTTCGTCAGCG 60.202 52.381 0.00 0.00 39.92 5.18
137 138 1.269448 GTGCACCATGTTCCATTTCGT 59.731 47.619 5.22 0.00 0.00 3.85
165 175 0.930310 CGCATGTGGACATAGGTTCG 59.070 55.000 0.00 0.00 34.26 3.95
171 181 3.006940 GTTTTCCTCGCATGTGGACATA 58.993 45.455 6.39 0.00 37.49 2.29
183 193 3.889196 TCGAAACCATTGTTTTCCTCG 57.111 42.857 1.62 0.00 44.57 4.63
261 274 1.300697 GTCCTCGTGTTCTGCCGTT 60.301 57.895 0.00 0.00 0.00 4.44
276 289 1.740664 GTTTTCCTCCTCCGCGTCC 60.741 63.158 4.92 0.00 0.00 4.79
298 311 3.729698 GGCACCGTTACAACCGCC 61.730 66.667 0.00 0.00 0.00 6.13
303 316 1.001633 GAGGAAGAGGCACCGTTACAA 59.998 52.381 0.00 0.00 0.00 2.41
309 322 1.374758 GTGTGAGGAAGAGGCACCG 60.375 63.158 0.00 0.00 0.00 4.94
316 329 5.481824 AGATGAACTATGTGTGTGAGGAAGA 59.518 40.000 0.00 0.00 0.00 2.87
328 341 2.363680 CTCCGAGGCAGATGAACTATGT 59.636 50.000 0.00 0.00 0.00 2.29
342 355 0.034960 TGTCTCTCCTGACTCCGAGG 60.035 60.000 0.00 0.00 37.79 4.63
346 359 2.224018 GCATCATGTCTCTCCTGACTCC 60.224 54.545 0.00 0.00 37.79 3.85
354 367 3.058450 CTGGAATCGCATCATGTCTCTC 58.942 50.000 0.00 0.00 0.00 3.20
379 400 5.773091 TCTAACCCCTAGATATGTGACACA 58.227 41.667 11.41 11.41 31.28 3.72
380 401 6.919775 ATCTAACCCCTAGATATGTGACAC 57.080 41.667 0.00 0.00 44.22 3.67
382 403 7.304497 ACAATCTAACCCCTAGATATGTGAC 57.696 40.000 0.00 0.00 45.12 3.67
383 404 8.232412 AGTACAATCTAACCCCTAGATATGTGA 58.768 37.037 0.00 0.00 45.12 3.58
386 411 9.090103 TCAAGTACAATCTAACCCCTAGATATG 57.910 37.037 0.00 0.61 45.12 1.78
391 416 5.992217 GCATCAAGTACAATCTAACCCCTAG 59.008 44.000 0.00 0.00 0.00 3.02
397 422 3.871594 AGCGGCATCAAGTACAATCTAAC 59.128 43.478 1.45 0.00 0.00 2.34
403 428 2.095969 CGAAAAGCGGCATCAAGTACAA 60.096 45.455 1.45 0.00 36.03 2.41
441 466 7.148983 CGAATAATGTCAGCAAAAATGAAACGT 60.149 33.333 0.00 0.00 0.00 3.99
482 507 5.125097 GCTATTTATCCCAGCCATGAATCAG 59.875 44.000 0.00 0.00 0.00 2.90
489 514 4.459852 ACAAGCTATTTATCCCAGCCAT 57.540 40.909 0.00 0.00 35.88 4.40
491 516 4.207165 TCAACAAGCTATTTATCCCAGCC 58.793 43.478 0.00 0.00 35.88 4.85
499 524 7.880160 ATAGCCAACATCAACAAGCTATTTA 57.120 32.000 0.00 0.00 39.80 1.40
509 534 7.320443 TGAATCACTTATAGCCAACATCAAC 57.680 36.000 0.00 0.00 0.00 3.18
544 569 1.616159 ACCTGCACGGCTAAACAAAT 58.384 45.000 2.50 0.00 35.61 2.32
545 570 1.394618 AACCTGCACGGCTAAACAAA 58.605 45.000 2.50 0.00 35.61 2.83
548 573 1.066454 ACAAAACCTGCACGGCTAAAC 59.934 47.619 2.50 0.00 35.61 2.01
549 574 1.394618 ACAAAACCTGCACGGCTAAA 58.605 45.000 2.50 0.00 35.61 1.85
554 579 0.040781 CGGTAACAAAACCTGCACGG 60.041 55.000 1.16 1.16 37.39 4.94
566 591 5.644636 CAGCTAAAGGATTAAACCGGTAACA 59.355 40.000 8.00 0.00 34.73 2.41
572 597 3.013921 TGCCAGCTAAAGGATTAAACCG 58.986 45.455 0.00 0.00 34.73 4.44
576 601 7.321717 AGAGATATGCCAGCTAAAGGATTAA 57.678 36.000 0.00 0.00 0.00 1.40
582 607 4.820716 AGCAAAGAGATATGCCAGCTAAAG 59.179 41.667 0.00 0.00 43.57 1.85
592 617 8.886719 TGAGACATTTGTTAGCAAAGAGATATG 58.113 33.333 10.59 5.42 46.30 1.78
594 619 8.846943 TTGAGACATTTGTTAGCAAAGAGATA 57.153 30.769 10.59 0.00 46.30 1.98
595 620 7.446625 ACTTGAGACATTTGTTAGCAAAGAGAT 59.553 33.333 10.59 0.00 46.30 2.75
596 621 6.767902 ACTTGAGACATTTGTTAGCAAAGAGA 59.232 34.615 10.59 0.00 46.30 3.10
597 622 6.963796 ACTTGAGACATTTGTTAGCAAAGAG 58.036 36.000 10.59 8.02 46.30 2.85
598 623 6.767902 AGACTTGAGACATTTGTTAGCAAAGA 59.232 34.615 10.59 0.00 46.30 2.52
601 626 6.054941 TCAGACTTGAGACATTTGTTAGCAA 58.945 36.000 0.00 0.00 0.00 3.91
602 627 5.610398 TCAGACTTGAGACATTTGTTAGCA 58.390 37.500 0.00 0.00 0.00 3.49
603 628 6.734104 ATCAGACTTGAGACATTTGTTAGC 57.266 37.500 0.00 0.00 36.61 3.09
605 630 9.424319 GTAGAATCAGACTTGAGACATTTGTTA 57.576 33.333 0.00 0.00 36.61 2.41
606 631 8.153550 AGTAGAATCAGACTTGAGACATTTGTT 58.846 33.333 0.00 0.00 36.61 2.83
607 632 7.601886 CAGTAGAATCAGACTTGAGACATTTGT 59.398 37.037 0.00 0.00 36.61 2.83
609 634 7.102346 CCAGTAGAATCAGACTTGAGACATTT 58.898 38.462 0.00 0.00 36.61 2.32
610 635 6.212388 ACCAGTAGAATCAGACTTGAGACATT 59.788 38.462 0.00 0.00 36.61 2.71
611 636 5.719085 ACCAGTAGAATCAGACTTGAGACAT 59.281 40.000 0.00 0.00 36.61 3.06
612 637 5.080337 ACCAGTAGAATCAGACTTGAGACA 58.920 41.667 0.00 0.00 36.61 3.41
613 638 5.652994 ACCAGTAGAATCAGACTTGAGAC 57.347 43.478 0.00 0.00 36.61 3.36
614 639 6.486056 AGTACCAGTAGAATCAGACTTGAGA 58.514 40.000 0.00 0.00 36.61 3.27
615 640 6.767524 AGTACCAGTAGAATCAGACTTGAG 57.232 41.667 0.00 0.00 36.61 3.02
619 644 9.696572 TGTAAATAGTACCAGTAGAATCAGACT 57.303 33.333 0.00 0.00 0.00 3.24
620 645 9.733219 GTGTAAATAGTACCAGTAGAATCAGAC 57.267 37.037 0.00 0.00 0.00 3.51
622 647 9.737427 CTGTGTAAATAGTACCAGTAGAATCAG 57.263 37.037 0.00 0.00 0.00 2.90
623 648 8.692710 CCTGTGTAAATAGTACCAGTAGAATCA 58.307 37.037 0.00 0.00 0.00 2.57
625 650 7.498443 GCCTGTGTAAATAGTACCAGTAGAAT 58.502 38.462 0.00 0.00 0.00 2.40
626 651 6.405065 CGCCTGTGTAAATAGTACCAGTAGAA 60.405 42.308 0.00 0.00 0.00 2.10
627 652 5.066893 CGCCTGTGTAAATAGTACCAGTAGA 59.933 44.000 0.00 0.00 0.00 2.59
628 653 5.066893 TCGCCTGTGTAAATAGTACCAGTAG 59.933 44.000 0.00 0.00 0.00 2.57
630 655 3.765511 TCGCCTGTGTAAATAGTACCAGT 59.234 43.478 0.00 0.00 0.00 4.00
631 656 4.380841 TCGCCTGTGTAAATAGTACCAG 57.619 45.455 0.00 0.00 0.00 4.00
632 657 4.804868 TTCGCCTGTGTAAATAGTACCA 57.195 40.909 0.00 0.00 0.00 3.25
633 658 6.457799 CCAATTTCGCCTGTGTAAATAGTACC 60.458 42.308 0.00 0.00 0.00 3.34
634 659 6.314400 TCCAATTTCGCCTGTGTAAATAGTAC 59.686 38.462 0.00 0.00 0.00 2.73
637 676 5.584649 TCTCCAATTTCGCCTGTGTAAATAG 59.415 40.000 0.00 0.00 0.00 1.73
640 679 3.745799 TCTCCAATTTCGCCTGTGTAAA 58.254 40.909 0.00 0.00 0.00 2.01
644 683 1.402968 CCATCTCCAATTTCGCCTGTG 59.597 52.381 0.00 0.00 0.00 3.66
646 685 1.027357 CCCATCTCCAATTTCGCCTG 58.973 55.000 0.00 0.00 0.00 4.85
651 690 5.975693 TTACAACACCCATCTCCAATTTC 57.024 39.130 0.00 0.00 0.00 2.17
670 709 5.232463 TCAGACGTGGAAGGTGTAAATTAC 58.768 41.667 0.00 0.00 33.50 1.89
671 710 5.471556 TCAGACGTGGAAGGTGTAAATTA 57.528 39.130 0.00 0.00 33.50 1.40
672 711 4.345859 TCAGACGTGGAAGGTGTAAATT 57.654 40.909 0.00 0.00 33.50 1.82
696 767 1.005340 CATCTTCGCCTGAAGCTGAC 58.995 55.000 3.45 0.00 46.41 3.51
726 797 5.777732 ACATCTTCGCCTTCTCCTAATCTAT 59.222 40.000 0.00 0.00 0.00 1.98
728 799 3.964031 ACATCTTCGCCTTCTCCTAATCT 59.036 43.478 0.00 0.00 0.00 2.40
729 800 4.038642 AGACATCTTCGCCTTCTCCTAATC 59.961 45.833 0.00 0.00 0.00 1.75
730 801 3.964031 AGACATCTTCGCCTTCTCCTAAT 59.036 43.478 0.00 0.00 0.00 1.73
731 802 3.366396 AGACATCTTCGCCTTCTCCTAA 58.634 45.455 0.00 0.00 0.00 2.69
732 803 3.019799 AGACATCTTCGCCTTCTCCTA 57.980 47.619 0.00 0.00 0.00 2.94
733 804 1.859302 AGACATCTTCGCCTTCTCCT 58.141 50.000 0.00 0.00 0.00 3.69
734 805 2.035321 CCTAGACATCTTCGCCTTCTCC 59.965 54.545 0.00 0.00 0.00 3.71
735 806 2.952978 TCCTAGACATCTTCGCCTTCTC 59.047 50.000 0.00 0.00 0.00 2.87
737 808 2.691011 ACTCCTAGACATCTTCGCCTTC 59.309 50.000 0.00 0.00 0.00 3.46
738 809 2.741145 ACTCCTAGACATCTTCGCCTT 58.259 47.619 0.00 0.00 0.00 4.35
849 932 1.308047 GACATTGTGTCTGTGTGGCA 58.692 50.000 0.00 0.00 43.73 4.92
895 978 0.433492 CGCCGCGGAATAATAACGAG 59.567 55.000 33.48 0.00 0.00 4.18
972 1055 3.056328 GAGACTTGCAACCCCCGC 61.056 66.667 0.00 0.00 0.00 6.13
973 1056 2.359975 GGAGACTTGCAACCCCCG 60.360 66.667 0.00 0.00 0.00 5.73
974 1057 1.303643 CTGGAGACTTGCAACCCCC 60.304 63.158 0.00 0.00 0.00 5.40
1062 1155 9.913451 TCATCAAATCAAATCAAAACGAAAAAC 57.087 25.926 0.00 0.00 0.00 2.43
1065 1158 8.637704 CGATCATCAAATCAAATCAAAACGAAA 58.362 29.630 0.00 0.00 0.00 3.46
1067 1160 7.271008 CACGATCATCAAATCAAATCAAAACGA 59.729 33.333 0.00 0.00 0.00 3.85
1068 1161 7.378047 CACGATCATCAAATCAAATCAAAACG 58.622 34.615 0.00 0.00 0.00 3.60
1069 1162 7.168796 GCACGATCATCAAATCAAATCAAAAC 58.831 34.615 0.00 0.00 0.00 2.43
1070 1163 6.310956 GGCACGATCATCAAATCAAATCAAAA 59.689 34.615 0.00 0.00 0.00 2.44
1071 1164 5.806502 GGCACGATCATCAAATCAAATCAAA 59.193 36.000 0.00 0.00 0.00 2.69
1072 1165 5.342433 GGCACGATCATCAAATCAAATCAA 58.658 37.500 0.00 0.00 0.00 2.57
1073 1166 4.202040 GGGCACGATCATCAAATCAAATCA 60.202 41.667 0.00 0.00 0.00 2.57
1074 1167 4.293415 GGGCACGATCATCAAATCAAATC 58.707 43.478 0.00 0.00 0.00 2.17
1075 1168 3.243168 CGGGCACGATCATCAAATCAAAT 60.243 43.478 0.00 0.00 44.60 2.32
1098 1191 0.521735 CGGGGAAAAGAAAAGAGCGG 59.478 55.000 0.00 0.00 0.00 5.52
1141 1237 3.737172 CTTTCTGCGCAACGGGGG 61.737 66.667 13.05 0.00 0.00 5.40
1159 1256 2.235898 GCACCTTGAGATTGACCTCTCT 59.764 50.000 3.07 0.00 41.87 3.10
1218 1323 2.884012 ACAGGCGAATGAATGAAACACA 59.116 40.909 0.00 0.00 0.00 3.72
1256 1361 3.690460 ACACCATGGACATTTCTTCCTC 58.310 45.455 21.47 0.00 33.84 3.71
1280 1385 2.159170 GGCAGCTGGTAAAACAACACAA 60.159 45.455 17.12 0.00 0.00 3.33
1285 1390 2.356665 TCAGGCAGCTGGTAAAACAA 57.643 45.000 17.12 0.00 0.00 2.83
1296 1401 2.671070 CGGGTACAAAATTTCAGGCAGC 60.671 50.000 0.00 0.00 0.00 5.25
1299 1404 4.036380 CCTATCGGGTACAAAATTTCAGGC 59.964 45.833 0.00 0.00 0.00 4.85
1489 1599 2.202544 CAGAGCAGAGCGACGACC 60.203 66.667 0.00 0.00 0.00 4.79
1507 1617 1.660560 CTGGCATTCCCCGCTGAAAG 61.661 60.000 0.00 0.00 0.00 2.62
1508 1618 1.678635 CTGGCATTCCCCGCTGAAA 60.679 57.895 0.00 0.00 0.00 2.69
1517 1627 4.070716 CCTTCATGACTATCTGGCATTCC 58.929 47.826 0.00 0.00 43.01 3.01
1526 1636 3.375299 GCCACAACACCTTCATGACTATC 59.625 47.826 0.00 0.00 0.00 2.08
1530 1640 1.317613 TGCCACAACACCTTCATGAC 58.682 50.000 0.00 0.00 0.00 3.06
1606 1716 2.422127 CGCCACGGTTCTAAATTCCAAT 59.578 45.455 0.00 0.00 0.00 3.16
1607 1717 1.807742 CGCCACGGTTCTAAATTCCAA 59.192 47.619 0.00 0.00 0.00 3.53
1615 1726 1.604308 TGGAGTCGCCACGGTTCTA 60.604 57.895 0.00 0.00 43.33 2.10
1616 1727 2.915659 TGGAGTCGCCACGGTTCT 60.916 61.111 0.00 0.00 43.33 3.01
1624 1735 4.736896 GACACCGGTGGAGTCGCC 62.737 72.222 36.47 13.42 34.07 5.54
1625 1736 4.736896 GGACACCGGTGGAGTCGC 62.737 72.222 36.47 18.01 42.71 5.19
1626 1737 4.415332 CGGACACCGGTGGAGTCG 62.415 72.222 36.47 27.21 42.71 4.18
1659 1770 3.003689 GTGGAACAAACATCCTGTCAGTG 59.996 47.826 0.00 0.00 44.16 3.66
1719 1830 3.195002 GCGCGCTCAGTGGCATTA 61.195 61.111 26.67 0.00 0.00 1.90
1782 1893 0.163788 CACTAAAACGAGCCACAGCG 59.836 55.000 0.00 0.00 46.67 5.18
1931 2049 3.144506 CACAATGACCAGAACAGCTTCT 58.855 45.455 0.00 0.00 37.19 2.85
2031 2149 2.168326 ACATCATGCACGACAAGTCA 57.832 45.000 0.00 0.00 0.00 3.41
2046 2164 4.781934 AGGCAAGGGTTTATGTCTACATC 58.218 43.478 0.00 0.00 37.76 3.06
2052 2170 2.496070 GGGAAAGGCAAGGGTTTATGTC 59.504 50.000 0.00 0.00 0.00 3.06
2057 2175 0.264657 ACAGGGAAAGGCAAGGGTTT 59.735 50.000 0.00 0.00 0.00 3.27
2105 2227 4.167307 ACCCCCAAGTACCTAAACATATGG 59.833 45.833 7.80 0.00 0.00 2.74
2141 2263 4.673761 GCGCTTGATTTGTATGATGACATG 59.326 41.667 0.00 0.00 37.87 3.21
2243 2365 4.248859 CAGTGTGTCTATCCTTGTCCTTG 58.751 47.826 0.00 0.00 0.00 3.61
2244 2366 3.261897 CCAGTGTGTCTATCCTTGTCCTT 59.738 47.826 0.00 0.00 0.00 3.36
2245 2367 2.834549 CCAGTGTGTCTATCCTTGTCCT 59.165 50.000 0.00 0.00 0.00 3.85
2246 2368 2.093447 CCCAGTGTGTCTATCCTTGTCC 60.093 54.545 0.00 0.00 0.00 4.02
2247 2369 2.832129 TCCCAGTGTGTCTATCCTTGTC 59.168 50.000 0.00 0.00 0.00 3.18
2248 2370 2.834549 CTCCCAGTGTGTCTATCCTTGT 59.165 50.000 0.00 0.00 0.00 3.16
2277 2408 5.296780 TGCTGCTGTAACTTGGCTTATTATC 59.703 40.000 0.00 0.00 0.00 1.75
2373 2507 3.474806 GGCACGTGGATTCGACAG 58.525 61.111 18.88 0.00 34.70 3.51
2399 2533 4.503714 TCCTTTCTGTGAACTTGGAACT 57.496 40.909 0.00 0.00 0.00 3.01
2511 2713 6.891388 AGGAAACCGTGGTAATCATACAATA 58.109 36.000 0.00 0.00 33.45 1.90
2549 2751 9.738832 ACCATGTTAAACAAAGTGTATAACAAC 57.261 29.630 0.00 0.00 31.12 3.32
2704 2906 5.155278 TGGTGAGTATGTTTGATACGGTT 57.845 39.130 0.00 0.00 0.00 4.44
2707 2909 5.983118 TGCTATGGTGAGTATGTTTGATACG 59.017 40.000 0.00 0.00 0.00 3.06
2810 3018 7.321530 AGAATCTTTATTAGGGGATAGGGTGA 58.678 38.462 0.00 0.00 0.00 4.02
3403 3724 3.870633 ACCGTCCATCTTGTTAGAGAC 57.129 47.619 0.00 0.00 32.92 3.36
3476 3797 5.294306 TCTCGGCTAAATAATCAAGCAAGTG 59.706 40.000 0.00 0.00 38.01 3.16
3477 3798 5.294552 GTCTCGGCTAAATAATCAAGCAAGT 59.705 40.000 0.00 0.00 38.01 3.16
3559 3880 3.493176 GCTGCACTCCAAAAATGAAGGTT 60.493 43.478 0.00 0.00 0.00 3.50
3774 4095 8.664079 ACAAAGATATTGCTAGGTCAGGATAAT 58.336 33.333 0.00 0.00 0.00 1.28
3810 4131 5.924475 ACAACTGTAAGAGATGGAAAACG 57.076 39.130 0.00 0.00 37.43 3.60
3816 4137 5.437289 TTGCAAACAACTGTAAGAGATGG 57.563 39.130 0.00 0.00 37.43 3.51
3920 4243 8.993121 CAATTATACAGTCCAATAGCCTACTTG 58.007 37.037 0.00 0.00 0.00 3.16
3974 4297 0.322997 TGGCCAACCCGTAGAAATGG 60.323 55.000 0.61 0.00 35.87 3.16
4033 4356 8.407832 CAAATAGATCAATGTTGTCCTGCAATA 58.592 33.333 0.00 0.00 39.55 1.90
4147 4470 1.973812 GGCTGTGCAGGGGAAGAAC 60.974 63.158 1.11 0.00 0.00 3.01
4160 4483 4.385405 GCAGACGCAGAGGGCTGT 62.385 66.667 0.00 0.00 44.17 4.40
4316 4645 0.984230 TCTTCACCGGAATTCCAGCT 59.016 50.000 24.09 2.54 35.14 4.24
4466 4795 2.735478 CCGTGCGACGTAAAGGCA 60.735 61.111 0.00 0.00 40.58 4.75
4551 4880 1.080569 CTGGTTTTGATGCCGGCAC 60.081 57.895 35.50 25.23 0.00 5.01
4556 4885 0.961019 TCACAGCTGGTTTTGATGCC 59.039 50.000 19.93 0.00 0.00 4.40
4707 5038 1.153168 GCAGCCACGTGGGTATGAT 60.153 57.895 36.72 6.30 45.47 2.45
4744 5076 2.690497 TGATTTTGCAACAGGGACGAAA 59.310 40.909 0.00 0.00 0.00 3.46
4826 5158 4.040095 GTGGGTAACTGGAACTACAAGTCT 59.960 45.833 0.00 0.00 0.00 3.24
5305 5700 6.096036 CCCATCTCTATAACGCAGATTACAG 58.904 44.000 0.00 0.00 0.00 2.74
5551 5961 2.047465 CTGCAAGACAGCCTCGCT 60.047 61.111 0.00 0.00 40.19 4.93
5661 6071 1.243342 ACATCACATGGTGGTTGCCG 61.243 55.000 0.00 0.00 33.87 5.69
5729 6139 2.576832 GCCCTGTTGGTGCTGCAAT 61.577 57.895 2.77 0.00 36.04 3.56


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

AutoCloner maintained by Alex Coulton.