Multiple sequence alignment - TraesCS4A01G171600

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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 TraesCS4A01G171600 chr4A 100.000 3908 0 0 1 3908 435440267 435444174 0.000000e+00 7217
1 TraesCS4A01G171600 chr4A 94.009 651 36 3 3260 3908 28743599 28742950 0.000000e+00 983
2 TraesCS4A01G171600 chr4A 89.145 304 31 2 2955 3257 483392483 483392785 1.020000e-100 377
3 TraesCS4A01G171600 chr4A 81.481 297 39 12 3258 3549 428797322 428797607 3.040000e-56 230
4 TraesCS4A01G171600 chr4D 95.876 1164 30 3 1802 2947 131042194 131041031 0.000000e+00 1868
5 TraesCS4A01G171600 chr4D 95.479 1106 41 5 629 1727 131043425 131042322 0.000000e+00 1757
6 TraesCS4A01G171600 chr4D 88.083 386 29 4 2 372 421969621 421970004 3.580000e-120 442
7 TraesCS4A01G171600 chr4D 92.581 310 18 5 2951 3259 313881767 313881462 1.290000e-119 440
8 TraesCS4A01G171600 chr4D 93.023 258 18 0 361 618 421970190 421970447 1.020000e-100 377
9 TraesCS4A01G171600 chrUn 94.510 1184 54 6 629 1806 59602135 59600957 0.000000e+00 1816
10 TraesCS4A01G171600 chrUn 94.047 1159 53 9 1804 2947 59600931 59599774 0.000000e+00 1744
11 TraesCS4A01G171600 chrUn 95.532 940 36 4 629 1562 54266351 54265412 0.000000e+00 1498
12 TraesCS4A01G171600 chrUn 93.524 803 42 5 999 1796 407431463 407430666 0.000000e+00 1186
13 TraesCS4A01G171600 chrUn 96.025 629 21 4 2321 2947 383555397 383554771 0.000000e+00 1020
14 TraesCS4A01G171600 chrUn 93.276 699 32 8 1804 2488 456594315 456595012 0.000000e+00 1016
15 TraesCS4A01G171600 chrUn 94.935 612 25 1 2336 2947 362328950 362329555 0.000000e+00 953
16 TraesCS4A01G171600 chrUn 85.585 881 126 1 1968 2848 29986578 29987457 0.000000e+00 922
17 TraesCS4A01G171600 chrUn 97.269 476 12 1 629 1103 336661376 336661851 0.000000e+00 806
18 TraesCS4A01G171600 chrUn 92.264 530 26 8 1804 2319 407430629 407430101 0.000000e+00 737
19 TraesCS4A01G171600 chrUn 92.264 530 26 8 1804 2319 473572692 473573220 0.000000e+00 737
20 TraesCS4A01G171600 chrUn 93.069 303 20 1 2956 3257 344657596 344657898 3.580000e-120 442
21 TraesCS4A01G171600 chrUn 92.763 304 20 2 2956 3257 24616501 24616804 4.640000e-119 438
22 TraesCS4A01G171600 chrUn 92.763 304 20 2 2956 3257 344621232 344621535 4.640000e-119 438
23 TraesCS4A01G171600 chrUn 88.477 243 23 2 1564 1806 456594052 456594289 4.940000e-74 289
24 TraesCS4A01G171600 chr2A 95.238 651 30 1 3259 3908 710648641 710649291 0.000000e+00 1029
25 TraesCS4A01G171600 chr2A 96.148 623 23 1 1 623 509360720 509360099 0.000000e+00 1016
26 TraesCS4A01G171600 chr1A 94.624 651 33 2 3260 3908 520263731 520264381 0.000000e+00 1007
27 TraesCS4A01G171600 chr1A 87.391 571 49 9 69 625 490521399 490521960 5.510000e-178 634
28 TraesCS4A01G171600 chr1A 89.333 300 31 1 2955 3253 333963178 333963477 3.690000e-100 375
29 TraesCS4A01G171600 chr3A 93.692 650 31 3 3260 3908 663037138 663036498 0.000000e+00 965
30 TraesCS4A01G171600 chr3A 83.442 924 130 18 1936 2854 586792428 586791523 0.000000e+00 837
31 TraesCS4A01G171600 chr3A 78.037 601 98 25 828 1421 586793954 586793381 8.040000e-92 348
32 TraesCS4A01G171600 chr5A 92.890 661 45 2 3250 3908 567005565 567006225 0.000000e+00 959
33 TraesCS4A01G171600 chr5A 94.217 415 23 1 3260 3673 474477234 474476820 1.980000e-177 632
34 TraesCS4A01G171600 chr5A 84.629 566 84 2 1941 2506 706479819 706480381 9.480000e-156 560
35 TraesCS4A01G171600 chr5A 81.882 425 69 6 1032 1453 706475241 706475660 6.210000e-93 351
36 TraesCS4A01G171600 chr5A 91.556 225 8 1 3657 3870 474476806 474476582 2.280000e-77 300
37 TraesCS4A01G171600 chr5A 82.653 294 29 17 3265 3549 519883743 519884023 1.400000e-59 241
38 TraesCS4A01G171600 chr5A 97.674 43 1 0 3866 3908 474454195 474454153 1.510000e-09 75
39 TraesCS4A01G171600 chr2B 93.559 621 32 6 1 618 325831763 325831148 0.000000e+00 918
40 TraesCS4A01G171600 chr2B 92.593 297 18 4 2945 3238 707729727 707730022 1.300000e-114 424
41 TraesCS4A01G171600 chr5B 93.823 599 33 3 1 596 462750434 462751031 0.000000e+00 898
42 TraesCS4A01G171600 chr5B 93.485 307 19 1 2954 3259 611934396 611934702 4.600000e-124 455
43 TraesCS4A01G171600 chr3B 84.336 881 114 19 1980 2854 583825545 583824683 0.000000e+00 841
44 TraesCS4A01G171600 chr3B 77.575 602 96 28 828 1421 583826768 583826198 1.050000e-85 327
45 TraesCS4A01G171600 chr3D 84.888 847 110 14 2011 2854 445105945 445105114 0.000000e+00 839
46 TraesCS4A01G171600 chr3D 96.970 297 9 0 3612 3908 12909767 12909471 2.100000e-137 499
47 TraesCS4A01G171600 chr3D 77.547 579 99 21 847 1421 445108014 445107463 1.750000e-83 320
48 TraesCS4A01G171600 chr3D 94.521 146 8 0 3481 3626 12909955 12909810 3.930000e-55 226
49 TraesCS4A01G171600 chr7A 94.458 415 22 1 3260 3673 566004906 566004492 4.260000e-179 638
50 TraesCS4A01G171600 chr7A 90.850 306 27 1 2954 3259 544145054 544145358 3.630000e-110 409
51 TraesCS4A01G171600 chr7A 94.841 252 13 0 3657 3908 566004478 566004227 1.020000e-105 394
52 TraesCS4A01G171600 chr1D 83.333 636 82 15 3 618 448381947 448381316 2.040000e-157 566
53 TraesCS4A01G171600 chr5D 83.203 637 83 15 3 619 406461054 406461686 2.640000e-156 562
54 TraesCS4A01G171600 chr5D 83.176 636 83 15 3 618 386601215 386600584 9.480000e-156 560
55 TraesCS4A01G171600 chr5D 81.135 599 86 23 2278 2860 111995389 111995976 4.600000e-124 455
56 TraesCS4A01G171600 chr7D 82.962 628 86 15 6 618 15133356 15133977 7.380000e-152 547


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 TraesCS4A01G171600 chr4A 435440267 435444174 3907 False 7217.0 7217 100.0000 1 3908 1 chr4A.!!$F2 3907
1 TraesCS4A01G171600 chr4A 28742950 28743599 649 True 983.0 983 94.0090 3260 3908 1 chr4A.!!$R1 648
2 TraesCS4A01G171600 chr4D 131041031 131043425 2394 True 1812.5 1868 95.6775 629 2947 2 chr4D.!!$R2 2318
3 TraesCS4A01G171600 chr4D 421969621 421970447 826 False 409.5 442 90.5530 2 618 2 chr4D.!!$F1 616
4 TraesCS4A01G171600 chrUn 59599774 59602135 2361 True 1780.0 1816 94.2785 629 2947 2 chrUn.!!$R3 2318
5 TraesCS4A01G171600 chrUn 54265412 54266351 939 True 1498.0 1498 95.5320 629 1562 1 chrUn.!!$R1 933
6 TraesCS4A01G171600 chrUn 383554771 383555397 626 True 1020.0 1020 96.0250 2321 2947 1 chrUn.!!$R2 626
7 TraesCS4A01G171600 chrUn 407430101 407431463 1362 True 961.5 1186 92.8940 999 2319 2 chrUn.!!$R4 1320
8 TraesCS4A01G171600 chrUn 362328950 362329555 605 False 953.0 953 94.9350 2336 2947 1 chrUn.!!$F6 611
9 TraesCS4A01G171600 chrUn 29986578 29987457 879 False 922.0 922 85.5850 1968 2848 1 chrUn.!!$F2 880
10 TraesCS4A01G171600 chrUn 473572692 473573220 528 False 737.0 737 92.2640 1804 2319 1 chrUn.!!$F7 515
11 TraesCS4A01G171600 chrUn 456594052 456595012 960 False 652.5 1016 90.8765 1564 2488 2 chrUn.!!$F8 924
12 TraesCS4A01G171600 chr2A 710648641 710649291 650 False 1029.0 1029 95.2380 3259 3908 1 chr2A.!!$F1 649
13 TraesCS4A01G171600 chr2A 509360099 509360720 621 True 1016.0 1016 96.1480 1 623 1 chr2A.!!$R1 622
14 TraesCS4A01G171600 chr1A 520263731 520264381 650 False 1007.0 1007 94.6240 3260 3908 1 chr1A.!!$F3 648
15 TraesCS4A01G171600 chr1A 490521399 490521960 561 False 634.0 634 87.3910 69 625 1 chr1A.!!$F2 556
16 TraesCS4A01G171600 chr3A 663036498 663037138 640 True 965.0 965 93.6920 3260 3908 1 chr3A.!!$R1 648
17 TraesCS4A01G171600 chr3A 586791523 586793954 2431 True 592.5 837 80.7395 828 2854 2 chr3A.!!$R2 2026
18 TraesCS4A01G171600 chr5A 567005565 567006225 660 False 959.0 959 92.8900 3250 3908 1 chr5A.!!$F2 658
19 TraesCS4A01G171600 chr5A 706479819 706480381 562 False 560.0 560 84.6290 1941 2506 1 chr5A.!!$F4 565
20 TraesCS4A01G171600 chr5A 474476582 474477234 652 True 466.0 632 92.8865 3260 3870 2 chr5A.!!$R2 610
21 TraesCS4A01G171600 chr2B 325831148 325831763 615 True 918.0 918 93.5590 1 618 1 chr2B.!!$R1 617
22 TraesCS4A01G171600 chr5B 462750434 462751031 597 False 898.0 898 93.8230 1 596 1 chr5B.!!$F1 595
23 TraesCS4A01G171600 chr3B 583824683 583826768 2085 True 584.0 841 80.9555 828 2854 2 chr3B.!!$R1 2026
24 TraesCS4A01G171600 chr3D 445105114 445108014 2900 True 579.5 839 81.2175 847 2854 2 chr3D.!!$R2 2007
25 TraesCS4A01G171600 chr7A 566004227 566004906 679 True 516.0 638 94.6495 3260 3908 2 chr7A.!!$R1 648
26 TraesCS4A01G171600 chr1D 448381316 448381947 631 True 566.0 566 83.3330 3 618 1 chr1D.!!$R1 615
27 TraesCS4A01G171600 chr5D 406461054 406461686 632 False 562.0 562 83.2030 3 619 1 chr5D.!!$F2 616
28 TraesCS4A01G171600 chr5D 386600584 386601215 631 True 560.0 560 83.1760 3 618 1 chr5D.!!$R1 615
29 TraesCS4A01G171600 chr5D 111995389 111995976 587 False 455.0 455 81.1350 2278 2860 1 chr5D.!!$F1 582
30 TraesCS4A01G171600 chr7D 15133356 15133977 621 False 547.0 547 82.9620 6 618 1 chr7D.!!$F1 612

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
585 812 0.028902 GACACTTTGTTGTGACCGGC 59.971 55.0 0.0 0.0 40.12 6.13 F
1322 1556 0.106149 GAAGACGAGGTGGTGTTGGT 59.894 55.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 3291 0.033504 TTGTGAGCGGTGAGAGGTTC 59.966 55.0 0.0 0.0 0.0 3.62 R
3029 4743 0.307760 GGTTGTCAAACAGCTCACGG 59.692 55.0 0.0 0.0 38.1 4.94 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
67 68 1.271652 TGTAAAAGCGGCAGGGATCAA 60.272 47.619 1.45 0.00 0.00 2.57
113 118 4.367039 TCGAAATTGAAAAGGGGAGACT 57.633 40.909 0.00 0.00 0.00 3.24
555 782 6.948309 ACCTGGTTTTCTACTAAATTGAGCAT 59.052 34.615 0.00 0.00 0.00 3.79
556 783 7.451566 ACCTGGTTTTCTACTAAATTGAGCATT 59.548 33.333 0.00 0.00 0.00 3.56
557 784 8.956426 CCTGGTTTTCTACTAAATTGAGCATTA 58.044 33.333 0.00 0.00 0.00 1.90
558 785 9.774742 CTGGTTTTCTACTAAATTGAGCATTAC 57.225 33.333 0.00 0.00 0.00 1.89
559 786 8.736244 TGGTTTTCTACTAAATTGAGCATTACC 58.264 33.333 0.00 0.00 0.00 2.85
560 787 8.957466 GGTTTTCTACTAAATTGAGCATTACCT 58.043 33.333 0.00 0.00 0.00 3.08
561 788 9.774742 GTTTTCTACTAAATTGAGCATTACCTG 57.225 33.333 0.00 0.00 0.00 4.00
562 789 9.515226 TTTTCTACTAAATTGAGCATTACCTGT 57.485 29.630 0.00 0.00 0.00 4.00
563 790 9.515226 TTTCTACTAAATTGAGCATTACCTGTT 57.485 29.630 0.00 0.00 0.00 3.16
564 791 9.515226 TTCTACTAAATTGAGCATTACCTGTTT 57.485 29.630 0.00 0.00 0.00 2.83
565 792 8.946085 TCTACTAAATTGAGCATTACCTGTTTG 58.054 33.333 0.00 0.00 0.00 2.93
566 793 6.924111 ACTAAATTGAGCATTACCTGTTTGG 58.076 36.000 0.00 0.00 42.93 3.28
567 794 6.719370 ACTAAATTGAGCATTACCTGTTTGGA 59.281 34.615 0.00 0.00 39.71 3.53
568 795 5.391312 AATTGAGCATTACCTGTTTGGAC 57.609 39.130 0.00 0.00 39.71 4.02
569 796 3.500448 TGAGCATTACCTGTTTGGACA 57.500 42.857 0.00 0.00 39.71 4.02
570 797 3.146066 TGAGCATTACCTGTTTGGACAC 58.854 45.455 0.00 0.00 39.71 3.67
571 798 3.181445 TGAGCATTACCTGTTTGGACACT 60.181 43.478 0.00 0.00 39.71 3.55
572 799 3.821033 GAGCATTACCTGTTTGGACACTT 59.179 43.478 0.00 0.00 39.71 3.16
573 800 4.215109 AGCATTACCTGTTTGGACACTTT 58.785 39.130 0.00 0.00 39.71 2.66
574 801 4.037923 AGCATTACCTGTTTGGACACTTTG 59.962 41.667 0.00 0.00 39.71 2.77
575 802 4.202111 GCATTACCTGTTTGGACACTTTGT 60.202 41.667 0.00 0.00 39.71 2.83
576 803 5.681179 GCATTACCTGTTTGGACACTTTGTT 60.681 40.000 0.00 0.00 39.71 2.83
577 804 3.866883 ACCTGTTTGGACACTTTGTTG 57.133 42.857 0.00 0.00 39.71 3.33
578 805 3.161866 ACCTGTTTGGACACTTTGTTGT 58.838 40.909 0.00 0.00 39.71 3.32
579 806 3.056891 ACCTGTTTGGACACTTTGTTGTG 60.057 43.478 0.00 0.00 40.36 3.33
580 807 3.192422 CCTGTTTGGACACTTTGTTGTGA 59.808 43.478 1.47 0.00 40.82 3.58
581 808 4.165779 CTGTTTGGACACTTTGTTGTGAC 58.834 43.478 1.47 0.00 40.12 3.67
584 811 0.661020 GGACACTTTGTTGTGACCGG 59.339 55.000 0.00 0.00 41.24 5.28
585 812 0.028902 GACACTTTGTTGTGACCGGC 59.971 55.000 0.00 0.00 40.12 6.13
586 813 0.678366 ACACTTTGTTGTGACCGGCA 60.678 50.000 0.00 0.00 40.12 5.69
611 838 3.870606 GCTAAGGCGCGTTTCTGA 58.129 55.556 21.55 1.46 0.00 3.27
612 839 2.384203 GCTAAGGCGCGTTTCTGAT 58.616 52.632 21.55 0.00 0.00 2.90
613 840 0.301987 GCTAAGGCGCGTTTCTGATC 59.698 55.000 21.55 0.00 0.00 2.92
614 841 1.927895 CTAAGGCGCGTTTCTGATCT 58.072 50.000 21.55 0.00 0.00 2.75
615 842 2.798499 GCTAAGGCGCGTTTCTGATCTA 60.798 50.000 21.55 0.00 0.00 1.98
616 843 1.927895 AAGGCGCGTTTCTGATCTAG 58.072 50.000 10.00 0.00 0.00 2.43
617 844 0.818296 AGGCGCGTTTCTGATCTAGT 59.182 50.000 8.43 0.00 0.00 2.57
618 845 2.022195 AGGCGCGTTTCTGATCTAGTA 58.978 47.619 8.43 0.00 0.00 1.82
619 846 2.623889 AGGCGCGTTTCTGATCTAGTAT 59.376 45.455 8.43 0.00 0.00 2.12
620 847 3.819337 AGGCGCGTTTCTGATCTAGTATA 59.181 43.478 8.43 0.00 0.00 1.47
621 848 4.459685 AGGCGCGTTTCTGATCTAGTATAT 59.540 41.667 8.43 0.00 0.00 0.86
622 849 5.646793 AGGCGCGTTTCTGATCTAGTATATA 59.353 40.000 8.43 0.00 0.00 0.86
623 850 5.738225 GGCGCGTTTCTGATCTAGTATATAC 59.262 44.000 8.43 4.60 0.00 1.47
624 851 6.403418 GGCGCGTTTCTGATCTAGTATATACT 60.403 42.308 19.07 19.07 40.24 2.12
625 852 6.466413 GCGCGTTTCTGATCTAGTATATACTG 59.534 42.308 23.09 13.78 37.10 2.74
626 853 7.519843 CGCGTTTCTGATCTAGTATATACTGT 58.480 38.462 23.09 10.50 37.10 3.55
627 854 8.654215 CGCGTTTCTGATCTAGTATATACTGTA 58.346 37.037 23.09 12.35 37.10 2.74
759 986 2.502492 CGATCTCCAGCCGGGTCAT 61.502 63.158 1.27 0.00 38.11 3.06
781 1008 0.392863 CCACCGCCATGACTGAATCA 60.393 55.000 0.00 0.00 43.13 2.57
1009 1243 1.102809 CATCTTAAGCATGGGCCGCA 61.103 55.000 6.19 0.00 42.56 5.69
1040 1274 1.377725 CAGTGAGGGTGATGGCCAC 60.378 63.158 8.16 2.36 44.95 5.01
1190 1424 3.559657 GAGTGTGCGTGACGAGGCT 62.560 63.158 10.10 0.00 33.93 4.58
1298 1532 2.547826 GTTCTACACCGGTCTAATGGC 58.452 52.381 2.59 0.00 0.00 4.40
1322 1556 0.106149 GAAGACGAGGTGGTGTTGGT 59.894 55.000 0.00 0.00 0.00 3.67
1566 2372 6.038825 TGTGTGTCTGTTAATTACACCCAAAG 59.961 38.462 12.57 0.00 42.22 2.77
1642 2975 7.809331 GCACATTTCATCTGTCAAATAAGTTGA 59.191 33.333 0.00 0.00 44.20 3.18
1659 3081 2.330440 TGATGCCGTGCTTATCATGT 57.670 45.000 0.00 0.00 0.00 3.21
1665 3087 2.157668 GCCGTGCTTATCATGTAATCCG 59.842 50.000 0.00 0.00 0.00 4.18
1703 3125 6.434028 ACATGCTTTTCTACCTTTTGCTCATA 59.566 34.615 0.00 0.00 0.00 2.15
1711 3133 4.701956 ACCTTTTGCTCATAATCGGTTG 57.298 40.909 0.00 0.00 0.00 3.77
1714 3136 4.438744 CCTTTTGCTCATAATCGGTTGGTC 60.439 45.833 0.00 0.00 0.00 4.02
1727 3149 9.978044 ATAATCGGTTGGTCTCTTACTAAATAC 57.022 33.333 0.00 0.00 29.38 1.89
1729 3151 7.093322 TCGGTTGGTCTCTTACTAAATACTC 57.907 40.000 0.00 0.00 29.38 2.59
1730 3152 6.888632 TCGGTTGGTCTCTTACTAAATACTCT 59.111 38.462 0.00 0.00 29.38 3.24
1767 3213 6.132791 TCTCCGTCTCATAATGTAAGACAC 57.867 41.667 0.00 0.00 39.49 3.67
1826 3303 3.045601 ACTTTGATGAACCTCTCACCG 57.954 47.619 0.00 0.00 36.69 4.94
1836 3313 1.081892 CCTCTCACCGCTCACAATTG 58.918 55.000 3.24 3.24 0.00 2.32
1851 3328 3.649073 ACAATTGTGATGAACGAGTCGA 58.351 40.909 21.50 0.00 0.00 4.20
1942 3471 5.479306 ACACATACTACATGAGTTGTGACC 58.521 41.667 25.09 0.00 43.03 4.02
2115 3804 0.606130 TGCTCGCCATGTTCATGTGT 60.606 50.000 11.13 0.00 0.00 3.72
2498 4201 4.813526 CCTCGTCGTCGTCTGCCG 62.814 72.222 1.33 0.00 38.33 5.69
2538 4241 2.660802 CCGTACCTGCTCCGGTTT 59.339 61.111 0.00 0.00 38.49 3.27
2748 4455 4.865761 GTGCCGAGCGCCGACATA 62.866 66.667 17.96 1.08 41.76 2.29
2947 4661 6.166982 ACAGCTGTCTATTTTCTCCTTACAC 58.833 40.000 15.25 0.00 0.00 2.90
2948 4662 6.166279 CAGCTGTCTATTTTCTCCTTACACA 58.834 40.000 5.25 0.00 0.00 3.72
2949 4663 6.312426 CAGCTGTCTATTTTCTCCTTACACAG 59.688 42.308 5.25 0.00 33.38 3.66
2950 4664 6.014156 AGCTGTCTATTTTCTCCTTACACAGT 60.014 38.462 0.00 0.00 32.91 3.55
2951 4665 6.651225 GCTGTCTATTTTCTCCTTACACAGTT 59.349 38.462 0.00 0.00 32.91 3.16
2952 4666 7.817962 GCTGTCTATTTTCTCCTTACACAGTTA 59.182 37.037 0.00 0.00 32.91 2.24
2953 4667 9.360093 CTGTCTATTTTCTCCTTACACAGTTAG 57.640 37.037 0.00 0.00 0.00 2.34
2954 4668 7.817962 TGTCTATTTTCTCCTTACACAGTTAGC 59.182 37.037 0.00 0.00 0.00 3.09
2955 4669 7.278203 GTCTATTTTCTCCTTACACAGTTAGCC 59.722 40.741 0.00 0.00 0.00 3.93
2956 4670 3.975168 TTCTCCTTACACAGTTAGCCC 57.025 47.619 0.00 0.00 0.00 5.19
2957 4671 2.185387 TCTCCTTACACAGTTAGCCCC 58.815 52.381 0.00 0.00 0.00 5.80
2958 4672 0.899720 TCCTTACACAGTTAGCCCCG 59.100 55.000 0.00 0.00 0.00 5.73
2959 4673 0.611714 CCTTACACAGTTAGCCCCGT 59.388 55.000 0.00 0.00 0.00 5.28
2960 4674 1.002773 CCTTACACAGTTAGCCCCGTT 59.997 52.381 0.00 0.00 0.00 4.44
2961 4675 2.551504 CCTTACACAGTTAGCCCCGTTT 60.552 50.000 0.00 0.00 0.00 3.60
2962 4676 2.172851 TACACAGTTAGCCCCGTTTG 57.827 50.000 0.00 0.00 0.00 2.93
2963 4677 0.470766 ACACAGTTAGCCCCGTTTGA 59.529 50.000 0.00 0.00 0.00 2.69
2964 4678 1.073284 ACACAGTTAGCCCCGTTTGAT 59.927 47.619 0.00 0.00 0.00 2.57
2965 4679 2.303600 ACACAGTTAGCCCCGTTTGATA 59.696 45.455 0.00 0.00 0.00 2.15
2966 4680 2.936498 CACAGTTAGCCCCGTTTGATAG 59.064 50.000 0.00 0.00 0.00 2.08
2967 4681 1.940613 CAGTTAGCCCCGTTTGATAGC 59.059 52.381 0.00 0.00 0.00 2.97
2968 4682 1.838077 AGTTAGCCCCGTTTGATAGCT 59.162 47.619 0.00 0.00 37.58 3.32
2969 4683 2.158943 AGTTAGCCCCGTTTGATAGCTC 60.159 50.000 0.00 0.00 35.03 4.09
2970 4684 0.387929 TAGCCCCGTTTGATAGCTCG 59.612 55.000 0.00 0.00 35.03 5.03
2971 4685 1.887707 GCCCCGTTTGATAGCTCGG 60.888 63.158 2.41 2.41 42.22 4.63
2972 4686 1.520666 CCCCGTTTGATAGCTCGGT 59.479 57.895 8.30 0.00 41.17 4.69
2973 4687 0.107848 CCCCGTTTGATAGCTCGGTT 60.108 55.000 8.30 0.00 41.17 4.44
2974 4688 1.677820 CCCCGTTTGATAGCTCGGTTT 60.678 52.381 8.30 0.00 41.17 3.27
2975 4689 2.081462 CCCGTTTGATAGCTCGGTTTT 58.919 47.619 8.30 0.00 41.17 2.43
2976 4690 2.486592 CCCGTTTGATAGCTCGGTTTTT 59.513 45.455 8.30 0.00 41.17 1.94
3002 4716 9.448438 TTCAAAGTATTATGACAATACTGCAGT 57.552 29.630 25.12 25.12 41.24 4.40
3003 4717 9.448438 TCAAAGTATTATGACAATACTGCAGTT 57.552 29.630 27.06 6.57 41.24 3.16
3010 4724 9.979578 ATTATGACAATACTGCAGTTTTTCAAA 57.020 25.926 27.06 20.09 0.00 2.69
3011 4725 9.809096 TTATGACAATACTGCAGTTTTTCAAAA 57.191 25.926 27.06 16.25 0.00 2.44
3012 4726 8.891671 ATGACAATACTGCAGTTTTTCAAAAT 57.108 26.923 27.06 6.67 0.00 1.82
3013 4727 9.979578 ATGACAATACTGCAGTTTTTCAAAATA 57.020 25.926 27.06 2.37 0.00 1.40
3014 4728 9.243637 TGACAATACTGCAGTTTTTCAAAATAC 57.756 29.630 27.06 8.19 0.00 1.89
3015 4729 8.587952 ACAATACTGCAGTTTTTCAAAATACC 57.412 30.769 27.06 0.00 0.00 2.73
3016 4730 8.200792 ACAATACTGCAGTTTTTCAAAATACCA 58.799 29.630 27.06 1.00 0.00 3.25
3017 4731 9.206870 CAATACTGCAGTTTTTCAAAATACCAT 57.793 29.630 27.06 3.75 0.00 3.55
3018 4732 8.761575 ATACTGCAGTTTTTCAAAATACCATG 57.238 30.769 27.06 0.00 0.00 3.66
3019 4733 5.990996 ACTGCAGTTTTTCAAAATACCATGG 59.009 36.000 15.25 11.19 0.00 3.66
3020 4734 5.923204 TGCAGTTTTTCAAAATACCATGGT 58.077 33.333 23.55 23.55 0.00 3.55
3021 4735 6.352516 TGCAGTTTTTCAAAATACCATGGTT 58.647 32.000 25.38 8.28 0.00 3.67
3022 4736 6.825721 TGCAGTTTTTCAAAATACCATGGTTT 59.174 30.769 25.38 13.21 0.00 3.27
3023 4737 7.987458 TGCAGTTTTTCAAAATACCATGGTTTA 59.013 29.630 25.38 6.19 0.00 2.01
3024 4738 8.831550 GCAGTTTTTCAAAATACCATGGTTTAA 58.168 29.630 25.38 5.28 0.00 1.52
3031 4745 9.640963 TTCAAAATACCATGGTTTAATTTACCG 57.359 29.630 25.38 13.97 38.55 4.02
3032 4746 8.804204 TCAAAATACCATGGTTTAATTTACCGT 58.196 29.630 25.38 5.30 38.55 4.83
3038 4752 5.560966 ATGGTTTAATTTACCGTGAGCTG 57.439 39.130 0.00 0.00 38.55 4.24
3039 4753 4.391155 TGGTTTAATTTACCGTGAGCTGT 58.609 39.130 0.00 0.00 38.55 4.40
3040 4754 4.822896 TGGTTTAATTTACCGTGAGCTGTT 59.177 37.500 0.00 0.00 38.55 3.16
3041 4755 5.299782 TGGTTTAATTTACCGTGAGCTGTTT 59.700 36.000 0.00 0.00 38.55 2.83
3042 4756 5.627780 GGTTTAATTTACCGTGAGCTGTTTG 59.372 40.000 0.00 0.00 0.00 2.93
3043 4757 6.432107 GTTTAATTTACCGTGAGCTGTTTGA 58.568 36.000 0.00 0.00 0.00 2.69
3044 4758 4.483476 AATTTACCGTGAGCTGTTTGAC 57.517 40.909 0.00 0.00 0.00 3.18
3045 4759 2.605837 TTACCGTGAGCTGTTTGACA 57.394 45.000 0.00 0.00 0.00 3.58
3046 4760 2.605837 TACCGTGAGCTGTTTGACAA 57.394 45.000 0.00 0.00 0.00 3.18
3047 4761 1.014352 ACCGTGAGCTGTTTGACAAC 58.986 50.000 0.00 0.00 0.00 3.32
3048 4762 0.307760 CCGTGAGCTGTTTGACAACC 59.692 55.000 0.00 0.00 31.02 3.77
3049 4763 1.013596 CGTGAGCTGTTTGACAACCA 58.986 50.000 0.00 0.00 31.02 3.67
3050 4764 1.268032 CGTGAGCTGTTTGACAACCAC 60.268 52.381 0.00 0.00 31.02 4.16
3051 4765 1.742831 GTGAGCTGTTTGACAACCACA 59.257 47.619 0.00 0.00 31.02 4.17
3052 4766 2.163412 GTGAGCTGTTTGACAACCACAA 59.837 45.455 0.00 0.00 31.02 3.33
3053 4767 2.822561 TGAGCTGTTTGACAACCACAAA 59.177 40.909 0.00 0.00 35.34 2.83
3054 4768 3.256879 TGAGCTGTTTGACAACCACAAAA 59.743 39.130 0.00 0.00 38.63 2.44
3055 4769 4.241681 GAGCTGTTTGACAACCACAAAAA 58.758 39.130 0.00 0.00 38.63 1.94
3090 4804 5.873179 ATACTGTGGTATTGTCAAAACCG 57.127 39.130 0.00 0.00 35.32 4.44
3091 4805 3.547746 ACTGTGGTATTGTCAAAACCGT 58.452 40.909 0.00 0.00 35.98 4.83
3092 4806 3.314080 ACTGTGGTATTGTCAAAACCGTG 59.686 43.478 0.00 0.00 35.98 4.94
3093 4807 2.619177 TGTGGTATTGTCAAAACCGTGG 59.381 45.455 0.00 0.00 35.98 4.94
3094 4808 2.619646 GTGGTATTGTCAAAACCGTGGT 59.380 45.455 0.00 0.00 35.98 4.16
3095 4809 3.814283 GTGGTATTGTCAAAACCGTGGTA 59.186 43.478 0.00 0.00 35.98 3.25
3096 4810 4.456566 GTGGTATTGTCAAAACCGTGGTAT 59.543 41.667 0.00 0.00 35.98 2.73
3097 4811 5.048573 GTGGTATTGTCAAAACCGTGGTATT 60.049 40.000 0.00 0.00 35.98 1.89
3098 4812 5.535406 TGGTATTGTCAAAACCGTGGTATTT 59.465 36.000 0.00 0.00 35.98 1.40
3099 4813 6.088173 GGTATTGTCAAAACCGTGGTATTTC 58.912 40.000 0.00 0.00 0.00 2.17
3100 4814 4.571372 TTGTCAAAACCGTGGTATTTCC 57.429 40.909 0.00 0.00 0.00 3.13
3101 4815 3.822940 TGTCAAAACCGTGGTATTTCCT 58.177 40.909 0.00 0.00 37.07 3.36
3102 4816 4.208746 TGTCAAAACCGTGGTATTTCCTT 58.791 39.130 0.00 0.00 37.07 3.36
3103 4817 4.645588 TGTCAAAACCGTGGTATTTCCTTT 59.354 37.500 0.00 0.00 37.07 3.11
3104 4818 4.979815 GTCAAAACCGTGGTATTTCCTTTG 59.020 41.667 5.62 5.62 37.07 2.77
3105 4819 3.653539 AAACCGTGGTATTTCCTTTGC 57.346 42.857 0.00 0.00 37.07 3.68
3106 4820 2.279935 ACCGTGGTATTTCCTTTGCA 57.720 45.000 0.00 0.00 37.07 4.08
3107 4821 2.802719 ACCGTGGTATTTCCTTTGCAT 58.197 42.857 0.00 0.00 37.07 3.96
3108 4822 3.161866 ACCGTGGTATTTCCTTTGCATT 58.838 40.909 0.00 0.00 37.07 3.56
3109 4823 4.337145 ACCGTGGTATTTCCTTTGCATTA 58.663 39.130 0.00 0.00 37.07 1.90
3110 4824 4.767928 ACCGTGGTATTTCCTTTGCATTAA 59.232 37.500 0.00 0.00 37.07 1.40
3111 4825 5.244178 ACCGTGGTATTTCCTTTGCATTAAA 59.756 36.000 0.00 0.00 37.07 1.52
3112 4826 6.159988 CCGTGGTATTTCCTTTGCATTAAAA 58.840 36.000 0.00 0.00 37.07 1.52
3113 4827 6.647067 CCGTGGTATTTCCTTTGCATTAAAAA 59.353 34.615 0.00 0.00 37.07 1.94
3130 4844 3.973472 AAAAAGAACCCTGGACCTCTT 57.027 42.857 0.00 0.00 0.00 2.85
3131 4845 3.973472 AAAAGAACCCTGGACCTCTTT 57.027 42.857 0.00 3.68 39.27 2.52
3132 4846 3.973472 AAAGAACCCTGGACCTCTTTT 57.027 42.857 0.00 0.00 35.15 2.27
3133 4847 3.973472 AAGAACCCTGGACCTCTTTTT 57.027 42.857 0.00 0.00 0.00 1.94
3176 4890 4.385244 AAACAAGACTGTTCGTTATCGC 57.615 40.909 0.00 0.00 45.25 4.58
3177 4891 2.334838 ACAAGACTGTTCGTTATCGCC 58.665 47.619 0.00 0.00 36.96 5.54
3178 4892 2.029290 ACAAGACTGTTCGTTATCGCCT 60.029 45.455 0.00 0.00 36.96 5.52
3179 4893 2.993899 CAAGACTGTTCGTTATCGCCTT 59.006 45.455 0.00 0.00 36.96 4.35
3180 4894 2.877335 AGACTGTTCGTTATCGCCTTC 58.123 47.619 0.00 0.00 36.96 3.46
3181 4895 1.925185 GACTGTTCGTTATCGCCTTCC 59.075 52.381 0.00 0.00 36.96 3.46
3182 4896 1.549170 ACTGTTCGTTATCGCCTTCCT 59.451 47.619 0.00 0.00 36.96 3.36
3183 4897 2.194271 CTGTTCGTTATCGCCTTCCTC 58.806 52.381 0.00 0.00 36.96 3.71
3184 4898 1.197910 GTTCGTTATCGCCTTCCTCG 58.802 55.000 0.00 0.00 36.96 4.63
3185 4899 0.526954 TTCGTTATCGCCTTCCTCGC 60.527 55.000 0.00 0.00 36.96 5.03
3186 4900 1.065928 CGTTATCGCCTTCCTCGCT 59.934 57.895 0.00 0.00 0.00 4.93
3187 4901 0.935366 CGTTATCGCCTTCCTCGCTC 60.935 60.000 0.00 0.00 0.00 5.03
3188 4902 0.597898 GTTATCGCCTTCCTCGCTCC 60.598 60.000 0.00 0.00 0.00 4.70
3189 4903 1.745320 TTATCGCCTTCCTCGCTCCC 61.745 60.000 0.00 0.00 0.00 4.30
3190 4904 2.921853 TATCGCCTTCCTCGCTCCCA 62.922 60.000 0.00 0.00 0.00 4.37
3191 4905 4.082523 CGCCTTCCTCGCTCCCAA 62.083 66.667 0.00 0.00 0.00 4.12
3192 4906 2.124942 GCCTTCCTCGCTCCCAAG 60.125 66.667 0.00 0.00 0.00 3.61
3193 4907 2.124942 CCTTCCTCGCTCCCAAGC 60.125 66.667 0.00 0.00 45.56 4.01
3194 4908 2.124942 CTTCCTCGCTCCCAAGCC 60.125 66.667 0.00 0.00 46.34 4.35
3195 4909 2.927856 TTCCTCGCTCCCAAGCCA 60.928 61.111 0.00 0.00 46.34 4.75
3196 4910 2.262774 CTTCCTCGCTCCCAAGCCAT 62.263 60.000 0.00 0.00 46.34 4.40
3197 4911 2.203126 CCTCGCTCCCAAGCCATC 60.203 66.667 0.00 0.00 46.34 3.51
3198 4912 2.586245 CTCGCTCCCAAGCCATCA 59.414 61.111 0.00 0.00 46.34 3.07
3199 4913 1.817099 CTCGCTCCCAAGCCATCAC 60.817 63.158 0.00 0.00 46.34 3.06
3200 4914 2.046023 CGCTCCCAAGCCATCACA 60.046 61.111 0.00 0.00 46.34 3.58
3201 4915 2.110967 CGCTCCCAAGCCATCACAG 61.111 63.158 0.00 0.00 46.34 3.66
3202 4916 2.413142 GCTCCCAAGCCATCACAGC 61.413 63.158 0.00 0.00 43.10 4.40
3203 4917 1.751927 CTCCCAAGCCATCACAGCC 60.752 63.158 0.00 0.00 0.00 4.85
3204 4918 3.136123 CCCAAGCCATCACAGCCG 61.136 66.667 0.00 0.00 0.00 5.52
3205 4919 3.818787 CCAAGCCATCACAGCCGC 61.819 66.667 0.00 0.00 0.00 6.53
3206 4920 3.818787 CAAGCCATCACAGCCGCC 61.819 66.667 0.00 0.00 0.00 6.13
3210 4924 4.100084 CCATCACAGCCGCCCTGA 62.100 66.667 8.11 0.00 44.64 3.86
3211 4925 2.046023 CATCACAGCCGCCCTGAA 60.046 61.111 8.11 0.00 44.64 3.02
3212 4926 2.110967 CATCACAGCCGCCCTGAAG 61.111 63.158 8.11 1.66 44.64 3.02
3213 4927 2.293318 ATCACAGCCGCCCTGAAGA 61.293 57.895 8.11 6.15 44.64 2.87
3214 4928 1.630126 ATCACAGCCGCCCTGAAGAT 61.630 55.000 8.11 7.79 44.64 2.40
3215 4929 1.817099 CACAGCCGCCCTGAAGATC 60.817 63.158 8.11 0.00 44.64 2.75
3216 4930 2.587194 CAGCCGCCCTGAAGATCG 60.587 66.667 0.00 0.00 44.64 3.69
3217 4931 4.537433 AGCCGCCCTGAAGATCGC 62.537 66.667 0.00 0.00 0.00 4.58
3222 4936 4.918201 CCCTGAAGATCGCCGGCC 62.918 72.222 23.46 7.02 0.00 6.13
3223 4937 4.161295 CCTGAAGATCGCCGGCCA 62.161 66.667 23.46 9.24 0.00 5.36
3224 4938 2.109799 CTGAAGATCGCCGGCCAT 59.890 61.111 23.46 15.35 0.00 4.40
3225 4939 2.203056 TGAAGATCGCCGGCCATG 60.203 61.111 23.46 7.26 0.00 3.66
3226 4940 2.974698 GAAGATCGCCGGCCATGG 60.975 66.667 23.46 7.63 0.00 3.66
3227 4941 4.569180 AAGATCGCCGGCCATGGG 62.569 66.667 23.46 6.36 0.00 4.00
3243 4957 0.401738 TGGGACAAGCCAAGAGAAGG 59.598 55.000 0.00 0.00 38.95 3.46
3318 5032 6.564328 GTTTCCTCATTTGACACTGAAAACT 58.436 36.000 0.00 0.00 0.00 2.66
3490 5206 1.006688 AGTATCGCGCACACACACA 60.007 52.632 8.75 0.00 0.00 3.72
3592 5308 2.990066 AGTGGCTTGACTACATAGGC 57.010 50.000 0.00 0.00 33.79 3.93
3755 5540 2.363680 CGTGATCTCCTACATGCCTCTT 59.636 50.000 0.00 0.00 0.00 2.85
3803 5599 2.917933 CAGCGTATTCCCATCCTTTGA 58.082 47.619 0.00 0.00 0.00 2.69
3858 5654 1.153289 GCCGTGAGATGTGAGGCAT 60.153 57.895 0.00 0.00 46.48 4.40
3860 5656 0.812811 CCGTGAGATGTGAGGCATGG 60.813 60.000 0.00 0.00 38.06 3.66
3899 5695 4.314440 GCCGCTGAGTGACCACCA 62.314 66.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 118 0.244721 CTGATGGACAGTGAGCGACA 59.755 55.000 0.00 0.00 41.30 4.35
555 782 4.767928 ACAACAAAGTGTCCAAACAGGTAA 59.232 37.500 0.00 0.00 35.64 2.85
556 783 4.156922 CACAACAAAGTGTCCAAACAGGTA 59.843 41.667 0.00 0.00 35.64 3.08
557 784 3.056891 CACAACAAAGTGTCCAAACAGGT 60.057 43.478 0.00 0.00 35.64 4.00
558 785 3.192422 TCACAACAAAGTGTCCAAACAGG 59.808 43.478 0.00 0.00 40.37 4.00
559 786 4.165779 GTCACAACAAAGTGTCCAAACAG 58.834 43.478 0.00 0.00 40.37 3.16
560 787 3.057174 GGTCACAACAAAGTGTCCAAACA 60.057 43.478 5.68 0.00 43.99 2.83
561 788 3.507786 GGTCACAACAAAGTGTCCAAAC 58.492 45.455 5.68 0.00 43.99 2.93
562 789 2.162608 CGGTCACAACAAAGTGTCCAAA 59.837 45.455 10.13 0.00 44.53 3.28
563 790 1.740585 CGGTCACAACAAAGTGTCCAA 59.259 47.619 10.13 0.00 44.53 3.53
564 791 1.374560 CGGTCACAACAAAGTGTCCA 58.625 50.000 10.13 0.00 44.53 4.02
565 792 0.661020 CCGGTCACAACAAAGTGTCC 59.339 55.000 0.00 0.00 42.06 4.02
566 793 0.028902 GCCGGTCACAACAAAGTGTC 59.971 55.000 1.90 0.00 40.37 3.67
567 794 0.678366 TGCCGGTCACAACAAAGTGT 60.678 50.000 1.90 0.00 40.37 3.55
568 795 0.248458 GTGCCGGTCACAACAAAGTG 60.248 55.000 19.85 0.00 44.98 3.16
569 796 2.103410 GTGCCGGTCACAACAAAGT 58.897 52.632 19.85 0.00 44.98 2.66
594 821 0.301987 GATCAGAAACGCGCCTTAGC 59.698 55.000 5.73 0.00 0.00 3.09
595 822 1.927895 AGATCAGAAACGCGCCTTAG 58.072 50.000 5.73 0.00 0.00 2.18
596 823 2.426024 ACTAGATCAGAAACGCGCCTTA 59.574 45.455 5.73 0.00 0.00 2.69
597 824 1.204941 ACTAGATCAGAAACGCGCCTT 59.795 47.619 5.73 0.00 0.00 4.35
598 825 0.818296 ACTAGATCAGAAACGCGCCT 59.182 50.000 5.73 0.00 0.00 5.52
599 826 2.486951 TACTAGATCAGAAACGCGCC 57.513 50.000 5.73 0.00 0.00 6.53
600 827 6.466413 CAGTATATACTAGATCAGAAACGCGC 59.534 42.308 15.03 0.00 34.13 6.86
601 828 7.519843 ACAGTATATACTAGATCAGAAACGCG 58.480 38.462 15.03 3.53 34.13 6.01
612 839 9.228949 GCACCTAGCTTTACAGTATATACTAGA 57.771 37.037 15.03 3.67 41.15 2.43
613 840 9.011095 TGCACCTAGCTTTACAGTATATACTAG 57.989 37.037 15.03 10.04 45.94 2.57
614 841 8.929260 TGCACCTAGCTTTACAGTATATACTA 57.071 34.615 15.03 0.00 45.94 1.82
615 842 7.524038 GCTGCACCTAGCTTTACAGTATATACT 60.524 40.741 9.71 9.71 45.94 2.12
616 843 6.586844 GCTGCACCTAGCTTTACAGTATATAC 59.413 42.308 4.60 4.60 45.94 1.47
617 844 6.688578 GCTGCACCTAGCTTTACAGTATATA 58.311 40.000 0.00 0.00 45.94 0.86
618 845 5.542779 GCTGCACCTAGCTTTACAGTATAT 58.457 41.667 0.00 0.00 45.94 0.86
619 846 4.945246 GCTGCACCTAGCTTTACAGTATA 58.055 43.478 0.00 0.00 45.94 1.47
620 847 3.798202 GCTGCACCTAGCTTTACAGTAT 58.202 45.455 0.00 0.00 45.94 2.12
621 848 3.247006 GCTGCACCTAGCTTTACAGTA 57.753 47.619 0.00 0.00 45.94 2.74
622 849 2.100605 GCTGCACCTAGCTTTACAGT 57.899 50.000 0.00 0.00 45.94 3.55
702 929 3.077556 GGAAGGAGAGCAGGGCGA 61.078 66.667 0.00 0.00 0.00 5.54
759 986 2.672651 CAGTCATGGCGGTGGCAA 60.673 61.111 0.00 0.00 42.43 4.52
781 1008 2.990479 GAGGAAGGGTGCGGTGAT 59.010 61.111 0.00 0.00 0.00 3.06
972 1206 3.469006 AGATGATTGGGTAGAGGAGGAGA 59.531 47.826 0.00 0.00 0.00 3.71
1009 1243 2.359107 CACTGCCACATCGCTGGT 60.359 61.111 0.00 0.00 33.30 4.00
1190 1424 0.320683 CACCATCACTCTCGGCAACA 60.321 55.000 0.00 0.00 0.00 3.33
1298 1532 0.388649 CACCACCTCGTCTTCTTCCG 60.389 60.000 0.00 0.00 0.00 4.30
1322 1556 3.571828 CGCCATGATCTTCTTCTCCTCTA 59.428 47.826 0.00 0.00 0.00 2.43
1510 1936 6.452242 TGTATGTATAAAGAGTATGGTGCCG 58.548 40.000 0.00 0.00 0.00 5.69
1511 1937 7.878127 ACATGTATGTATAAAGAGTATGGTGCC 59.122 37.037 0.00 0.00 39.68 5.01
1512 1938 8.712363 CACATGTATGTATAAAGAGTATGGTGC 58.288 37.037 0.00 0.00 39.39 5.01
1566 2372 9.604626 CTTCGCATATTTCCATTTAGATTTCTC 57.395 33.333 0.00 0.00 0.00 2.87
1642 2975 3.753272 GGATTACATGATAAGCACGGCAT 59.247 43.478 0.00 0.00 0.00 4.40
1665 3087 2.649331 AGCATGTGTACGTAGGTGAC 57.351 50.000 0.00 0.00 0.00 3.67
1674 3096 5.629435 GCAAAAGGTAGAAAAGCATGTGTAC 59.371 40.000 0.00 0.00 0.00 2.90
1703 3125 8.075761 AGTATTTAGTAAGAGACCAACCGATT 57.924 34.615 0.00 0.00 0.00 3.34
1727 3149 9.887406 GAGACGGAGAAAGATACTTTATTAGAG 57.113 37.037 0.00 0.00 0.00 2.43
1740 3186 7.122204 TGTCTTACATTATGAGACGGAGAAAGA 59.878 37.037 0.00 0.00 44.98 2.52
1743 3189 6.405508 GGTGTCTTACATTATGAGACGGAGAA 60.406 42.308 0.00 0.00 44.98 2.87
1744 3190 5.067413 GGTGTCTTACATTATGAGACGGAGA 59.933 44.000 0.00 0.00 44.98 3.71
1748 3194 7.330946 TCAAAAGGTGTCTTACATTATGAGACG 59.669 37.037 0.00 0.00 44.98 4.18
1751 3197 9.612620 GTTTCAAAAGGTGTCTTACATTATGAG 57.387 33.333 0.00 0.00 30.95 2.90
1799 3246 9.429359 GGTGAGAGGTTCATCAAAGTATATATG 57.571 37.037 0.00 0.00 36.88 1.78
1800 3247 8.307483 CGGTGAGAGGTTCATCAAAGTATATAT 58.693 37.037 0.00 0.00 36.69 0.86
1806 3253 2.872038 GCGGTGAGAGGTTCATCAAAGT 60.872 50.000 0.00 0.00 36.69 2.66
1807 3254 1.734465 GCGGTGAGAGGTTCATCAAAG 59.266 52.381 0.00 0.00 36.69 2.77
1814 3291 0.033504 TTGTGAGCGGTGAGAGGTTC 59.966 55.000 0.00 0.00 0.00 3.62
1836 3313 3.138205 AGACATCGACTCGTTCATCAC 57.862 47.619 0.00 0.00 0.00 3.06
1942 3471 2.503356 ACCCAGAGAGCAGAGTAAATGG 59.497 50.000 0.00 0.00 0.00 3.16
2096 3785 0.606130 ACACATGAACATGGCGAGCA 60.606 50.000 17.25 0.00 42.91 4.26
2748 4455 0.610174 TCTTCTGCACGAGATTGGCT 59.390 50.000 0.00 0.00 0.00 4.75
2860 4567 1.213013 ACGAGCACTTGCCGTCTAG 59.787 57.895 10.66 0.00 41.54 2.43
2938 4652 1.134788 CGGGGCTAACTGTGTAAGGAG 60.135 57.143 0.00 0.00 0.00 3.69
2947 4661 1.940613 GCTATCAAACGGGGCTAACTG 59.059 52.381 0.00 0.00 0.00 3.16
2948 4662 1.838077 AGCTATCAAACGGGGCTAACT 59.162 47.619 0.00 0.00 0.00 2.24
2949 4663 2.210961 GAGCTATCAAACGGGGCTAAC 58.789 52.381 0.00 0.00 33.13 2.34
2950 4664 1.202486 CGAGCTATCAAACGGGGCTAA 60.202 52.381 0.00 0.00 33.13 3.09
2951 4665 0.387929 CGAGCTATCAAACGGGGCTA 59.612 55.000 0.00 0.00 33.13 3.93
2952 4666 1.144057 CGAGCTATCAAACGGGGCT 59.856 57.895 0.00 0.00 35.86 5.19
2953 4667 1.887707 CCGAGCTATCAAACGGGGC 60.888 63.158 1.46 0.00 41.41 5.80
2954 4668 4.438346 CCGAGCTATCAAACGGGG 57.562 61.111 1.46 0.00 41.41 5.73
2976 4690 9.448438 ACTGCAGTATTGTCATAATACTTTGAA 57.552 29.630 20.16 0.00 40.42 2.69
2977 4691 9.448438 AACTGCAGTATTGTCATAATACTTTGA 57.552 29.630 22.01 0.00 40.42 2.69
2984 4698 9.979578 TTTGAAAAACTGCAGTATTGTCATAAT 57.020 25.926 22.01 0.00 0.00 1.28
2985 4699 9.809096 TTTTGAAAAACTGCAGTATTGTCATAA 57.191 25.926 22.01 20.94 0.00 1.90
2986 4700 9.979578 ATTTTGAAAAACTGCAGTATTGTCATA 57.020 25.926 22.01 17.14 0.00 2.15
2987 4701 8.891671 ATTTTGAAAAACTGCAGTATTGTCAT 57.108 26.923 22.01 9.54 0.00 3.06
2988 4702 9.243637 GTATTTTGAAAAACTGCAGTATTGTCA 57.756 29.630 22.01 21.40 0.00 3.58
2989 4703 8.699749 GGTATTTTGAAAAACTGCAGTATTGTC 58.300 33.333 22.01 19.31 0.00 3.18
2990 4704 8.200792 TGGTATTTTGAAAAACTGCAGTATTGT 58.799 29.630 22.01 11.65 0.00 2.71
2991 4705 8.586570 TGGTATTTTGAAAAACTGCAGTATTG 57.413 30.769 22.01 0.00 0.00 1.90
2992 4706 9.206870 CATGGTATTTTGAAAAACTGCAGTATT 57.793 29.630 22.01 18.16 0.00 1.89
2993 4707 7.818930 CCATGGTATTTTGAAAAACTGCAGTAT 59.181 33.333 22.01 9.71 0.00 2.12
2994 4708 7.151308 CCATGGTATTTTGAAAAACTGCAGTA 58.849 34.615 22.01 0.00 0.00 2.74
2995 4709 5.990996 CCATGGTATTTTGAAAAACTGCAGT 59.009 36.000 15.25 15.25 0.00 4.40
2996 4710 5.990996 ACCATGGTATTTTGAAAAACTGCAG 59.009 36.000 18.10 13.48 0.00 4.41
2997 4711 5.923204 ACCATGGTATTTTGAAAAACTGCA 58.077 33.333 18.10 0.00 0.00 4.41
2998 4712 6.859420 AACCATGGTATTTTGAAAAACTGC 57.141 33.333 20.12 0.00 0.00 4.40
3005 4719 9.640963 CGGTAAATTAAACCATGGTATTTTGAA 57.359 29.630 22.94 7.78 36.78 2.69
3006 4720 8.804204 ACGGTAAATTAAACCATGGTATTTTGA 58.196 29.630 22.94 11.03 36.78 2.69
3007 4721 8.865001 CACGGTAAATTAAACCATGGTATTTTG 58.135 33.333 22.94 16.91 36.78 2.44
3008 4722 8.804204 TCACGGTAAATTAAACCATGGTATTTT 58.196 29.630 22.94 18.59 36.78 1.82
3009 4723 8.350852 TCACGGTAAATTAAACCATGGTATTT 57.649 30.769 20.12 21.28 36.78 1.40
3010 4724 7.415877 GCTCACGGTAAATTAAACCATGGTATT 60.416 37.037 20.12 16.36 36.78 1.89
3011 4725 6.038936 GCTCACGGTAAATTAAACCATGGTAT 59.961 38.462 20.12 5.13 36.78 2.73
3012 4726 5.354792 GCTCACGGTAAATTAAACCATGGTA 59.645 40.000 20.12 2.28 36.78 3.25
3013 4727 4.157105 GCTCACGGTAAATTAAACCATGGT 59.843 41.667 13.00 13.00 36.78 3.55
3014 4728 4.398044 AGCTCACGGTAAATTAAACCATGG 59.602 41.667 11.19 11.19 36.78 3.66
3015 4729 5.106317 ACAGCTCACGGTAAATTAAACCATG 60.106 40.000 9.81 5.43 36.78 3.66
3016 4730 5.007682 ACAGCTCACGGTAAATTAAACCAT 58.992 37.500 9.81 0.00 36.78 3.55
3017 4731 4.391155 ACAGCTCACGGTAAATTAAACCA 58.609 39.130 9.81 0.00 36.78 3.67
3018 4732 5.366829 AACAGCTCACGGTAAATTAAACC 57.633 39.130 0.00 0.65 0.00 3.27
3019 4733 6.358822 GTCAAACAGCTCACGGTAAATTAAAC 59.641 38.462 0.00 0.00 0.00 2.01
3020 4734 6.038382 TGTCAAACAGCTCACGGTAAATTAAA 59.962 34.615 0.00 0.00 0.00 1.52
3021 4735 5.527951 TGTCAAACAGCTCACGGTAAATTAA 59.472 36.000 0.00 0.00 0.00 1.40
3022 4736 5.057819 TGTCAAACAGCTCACGGTAAATTA 58.942 37.500 0.00 0.00 0.00 1.40
3023 4737 3.880490 TGTCAAACAGCTCACGGTAAATT 59.120 39.130 0.00 0.00 0.00 1.82
3024 4738 3.472652 TGTCAAACAGCTCACGGTAAAT 58.527 40.909 0.00 0.00 0.00 1.40
3025 4739 2.907634 TGTCAAACAGCTCACGGTAAA 58.092 42.857 0.00 0.00 0.00 2.01
3026 4740 2.605837 TGTCAAACAGCTCACGGTAA 57.394 45.000 0.00 0.00 0.00 2.85
3027 4741 2.206750 GTTGTCAAACAGCTCACGGTA 58.793 47.619 0.00 0.00 36.24 4.02
3028 4742 1.014352 GTTGTCAAACAGCTCACGGT 58.986 50.000 0.00 0.00 36.24 4.83
3029 4743 0.307760 GGTTGTCAAACAGCTCACGG 59.692 55.000 0.00 0.00 38.10 4.94
3030 4744 1.013596 TGGTTGTCAAACAGCTCACG 58.986 50.000 0.00 0.00 38.10 4.35
3031 4745 1.742831 TGTGGTTGTCAAACAGCTCAC 59.257 47.619 2.78 0.00 38.10 3.51
3032 4746 2.121291 TGTGGTTGTCAAACAGCTCA 57.879 45.000 2.78 0.00 38.10 4.26
3033 4747 3.502191 TTTGTGGTTGTCAAACAGCTC 57.498 42.857 2.78 0.00 38.10 4.09
3034 4748 3.951775 TTTTGTGGTTGTCAAACAGCT 57.048 38.095 2.78 0.00 38.10 4.24
3064 4778 8.455682 CGGTTTTGACAATACCACAGTATAAAT 58.544 33.333 22.61 0.00 38.27 1.40
3065 4779 7.444792 ACGGTTTTGACAATACCACAGTATAAA 59.555 33.333 22.61 0.00 38.27 1.40
3066 4780 6.935771 ACGGTTTTGACAATACCACAGTATAA 59.064 34.615 22.61 0.00 38.27 0.98
3067 4781 6.369340 CACGGTTTTGACAATACCACAGTATA 59.631 38.462 22.61 0.00 38.27 1.47
3068 4782 5.180492 CACGGTTTTGACAATACCACAGTAT 59.820 40.000 22.61 3.38 41.09 2.12
3069 4783 4.512198 CACGGTTTTGACAATACCACAGTA 59.488 41.667 22.61 0.00 32.12 2.74
3070 4784 3.314080 CACGGTTTTGACAATACCACAGT 59.686 43.478 22.61 12.60 32.12 3.55
3071 4785 3.304391 CCACGGTTTTGACAATACCACAG 60.304 47.826 22.61 13.40 32.12 3.66
3072 4786 2.619177 CCACGGTTTTGACAATACCACA 59.381 45.455 22.61 0.00 32.12 4.17
3073 4787 2.619646 ACCACGGTTTTGACAATACCAC 59.380 45.455 22.61 4.30 32.12 4.16
3074 4788 2.933573 ACCACGGTTTTGACAATACCA 58.066 42.857 22.61 0.00 32.12 3.25
3075 4789 5.632244 AATACCACGGTTTTGACAATACC 57.368 39.130 15.62 15.62 0.00 2.73
3076 4790 6.072342 AGGAAATACCACGGTTTTGACAATAC 60.072 38.462 0.00 0.54 42.04 1.89
3077 4791 6.005198 AGGAAATACCACGGTTTTGACAATA 58.995 36.000 0.00 0.00 42.04 1.90
3078 4792 4.830600 AGGAAATACCACGGTTTTGACAAT 59.169 37.500 0.00 0.00 42.04 2.71
3079 4793 4.208746 AGGAAATACCACGGTTTTGACAA 58.791 39.130 0.00 0.00 42.04 3.18
3080 4794 3.822940 AGGAAATACCACGGTTTTGACA 58.177 40.909 0.00 0.00 42.04 3.58
3081 4795 4.841443 AAGGAAATACCACGGTTTTGAC 57.159 40.909 0.00 0.00 42.04 3.18
3082 4796 4.500035 GCAAAGGAAATACCACGGTTTTGA 60.500 41.667 11.26 0.00 42.04 2.69
3083 4797 3.738791 GCAAAGGAAATACCACGGTTTTG 59.261 43.478 0.00 0.00 42.04 2.44
3084 4798 3.385111 TGCAAAGGAAATACCACGGTTTT 59.615 39.130 0.00 0.00 42.04 2.43
3085 4799 2.959707 TGCAAAGGAAATACCACGGTTT 59.040 40.909 0.00 0.00 42.04 3.27
3086 4800 2.588620 TGCAAAGGAAATACCACGGTT 58.411 42.857 0.00 0.00 42.04 4.44
3087 4801 2.279935 TGCAAAGGAAATACCACGGT 57.720 45.000 0.00 0.00 42.04 4.83
3088 4802 3.866883 AATGCAAAGGAAATACCACGG 57.133 42.857 0.00 0.00 42.04 4.94
3089 4803 7.644986 TTTTTAATGCAAAGGAAATACCACG 57.355 32.000 0.00 0.00 42.04 4.94
3110 4824 3.973472 AAGAGGTCCAGGGTTCTTTTT 57.027 42.857 0.00 0.00 0.00 1.94
3111 4825 3.973472 AAAGAGGTCCAGGGTTCTTTT 57.027 42.857 7.54 0.00 36.72 2.27
3112 4826 3.973472 AAAAGAGGTCCAGGGTTCTTT 57.027 42.857 7.54 7.54 40.53 2.52
3113 4827 3.973472 AAAAAGAGGTCCAGGGTTCTT 57.027 42.857 0.00 0.00 0.00 2.52
3157 4871 2.029290 AGGCGATAACGAACAGTCTTGT 60.029 45.455 0.00 0.00 42.66 3.16
3158 4872 2.607187 AGGCGATAACGAACAGTCTTG 58.393 47.619 0.00 0.00 42.66 3.02
3159 4873 3.251571 GAAGGCGATAACGAACAGTCTT 58.748 45.455 0.00 0.00 42.66 3.01
3160 4874 2.416972 GGAAGGCGATAACGAACAGTCT 60.417 50.000 0.00 0.00 42.66 3.24
3161 4875 1.925185 GGAAGGCGATAACGAACAGTC 59.075 52.381 0.00 0.00 42.66 3.51
3162 4876 1.549170 AGGAAGGCGATAACGAACAGT 59.451 47.619 0.00 0.00 42.66 3.55
3163 4877 2.194271 GAGGAAGGCGATAACGAACAG 58.806 52.381 0.00 0.00 42.66 3.16
3164 4878 1.468565 CGAGGAAGGCGATAACGAACA 60.469 52.381 0.00 0.00 42.66 3.18
3165 4879 1.197910 CGAGGAAGGCGATAACGAAC 58.802 55.000 0.00 0.00 42.66 3.95
3166 4880 0.526954 GCGAGGAAGGCGATAACGAA 60.527 55.000 0.00 0.00 42.66 3.85
3167 4881 1.065273 GCGAGGAAGGCGATAACGA 59.935 57.895 0.00 0.00 42.66 3.85
3168 4882 0.935366 GAGCGAGGAAGGCGATAACG 60.935 60.000 0.00 0.00 42.93 3.18
3169 4883 0.597898 GGAGCGAGGAAGGCGATAAC 60.598 60.000 0.00 0.00 35.00 1.89
3170 4884 1.740285 GGAGCGAGGAAGGCGATAA 59.260 57.895 0.00 0.00 35.00 1.75
3171 4885 2.201022 GGGAGCGAGGAAGGCGATA 61.201 63.158 0.00 0.00 35.00 2.92
3172 4886 3.541713 GGGAGCGAGGAAGGCGAT 61.542 66.667 0.00 0.00 35.00 4.58
3174 4888 4.082523 TTGGGAGCGAGGAAGGCG 62.083 66.667 0.00 0.00 35.00 5.52
3175 4889 2.124942 CTTGGGAGCGAGGAAGGC 60.125 66.667 0.00 0.00 0.00 4.35
3176 4890 2.124942 GCTTGGGAGCGAGGAAGG 60.125 66.667 0.00 0.00 39.48 3.46
3185 4899 1.751927 GGCTGTGATGGCTTGGGAG 60.752 63.158 0.00 0.00 0.00 4.30
3186 4900 2.356278 GGCTGTGATGGCTTGGGA 59.644 61.111 0.00 0.00 0.00 4.37
3187 4901 3.136123 CGGCTGTGATGGCTTGGG 61.136 66.667 0.00 0.00 0.00 4.12
3188 4902 3.818787 GCGGCTGTGATGGCTTGG 61.819 66.667 0.00 0.00 0.00 3.61
3189 4903 3.818787 GGCGGCTGTGATGGCTTG 61.819 66.667 0.00 0.00 0.00 4.01
3193 4907 3.626996 TTCAGGGCGGCTGTGATGG 62.627 63.158 9.56 0.00 0.00 3.51
3194 4908 2.046023 TTCAGGGCGGCTGTGATG 60.046 61.111 9.56 0.68 0.00 3.07
3195 4909 1.630126 ATCTTCAGGGCGGCTGTGAT 61.630 55.000 9.56 10.31 0.00 3.06
3196 4910 2.244117 GATCTTCAGGGCGGCTGTGA 62.244 60.000 9.56 9.76 0.00 3.58
3197 4911 1.817099 GATCTTCAGGGCGGCTGTG 60.817 63.158 9.56 7.26 0.00 3.66
3198 4912 2.586792 GATCTTCAGGGCGGCTGT 59.413 61.111 9.56 0.00 0.00 4.40
3199 4913 2.587194 CGATCTTCAGGGCGGCTG 60.587 66.667 9.56 5.48 0.00 4.85
3200 4914 4.537433 GCGATCTTCAGGGCGGCT 62.537 66.667 9.56 0.00 0.00 5.52
3205 4919 4.918201 GGCCGGCGATCTTCAGGG 62.918 72.222 22.54 0.00 0.00 4.45
3206 4920 3.466791 ATGGCCGGCGATCTTCAGG 62.467 63.158 22.54 0.00 0.00 3.86
3207 4921 2.109799 ATGGCCGGCGATCTTCAG 59.890 61.111 22.54 0.00 0.00 3.02
3208 4922 2.203056 CATGGCCGGCGATCTTCA 60.203 61.111 22.25 12.40 0.00 3.02
3209 4923 2.974698 CCATGGCCGGCGATCTTC 60.975 66.667 22.25 6.02 0.00 2.87
3210 4924 4.569180 CCCATGGCCGGCGATCTT 62.569 66.667 22.25 0.00 0.00 2.40
3218 4932 4.738998 TGGCTTGTCCCATGGCCG 62.739 66.667 6.09 0.00 46.72 6.13
3219 4933 2.283821 TTGGCTTGTCCCATGGCC 60.284 61.111 6.09 3.56 44.31 5.36
3220 4934 1.304381 TCTTGGCTTGTCCCATGGC 60.304 57.895 6.09 0.00 34.21 4.40
3221 4935 0.329261 TCTCTTGGCTTGTCCCATGG 59.671 55.000 4.14 4.14 34.21 3.66
3222 4936 2.089980 CTTCTCTTGGCTTGTCCCATG 58.910 52.381 0.00 0.00 34.21 3.66
3223 4937 1.005215 CCTTCTCTTGGCTTGTCCCAT 59.995 52.381 0.00 0.00 34.21 4.00
3224 4938 0.401738 CCTTCTCTTGGCTTGTCCCA 59.598 55.000 0.00 0.00 0.00 4.37
3225 4939 0.962855 GCCTTCTCTTGGCTTGTCCC 60.963 60.000 0.00 0.00 46.38 4.46
3226 4940 2.560954 GCCTTCTCTTGGCTTGTCC 58.439 57.895 0.00 0.00 46.38 4.02
3233 4947 9.578439 CTTTTTATTTCTATTGCCTTCTCTTGG 57.422 33.333 0.00 0.00 0.00 3.61
3283 4997 9.587772 TGTCAAATGAGGAAACGAAATTTAAAA 57.412 25.926 0.00 0.00 0.00 1.52
3406 5121 6.096705 CACATATTACATGAGGGGCAAAAAGA 59.903 38.462 0.00 0.00 0.00 2.52
3408 5123 5.395103 GCACATATTACATGAGGGGCAAAAA 60.395 40.000 0.00 0.00 0.00 1.94
3490 5206 1.301637 TGCGTGTATGTGCTGCTGT 60.302 52.632 0.00 0.00 0.00 4.40
3755 5540 1.001887 GGTTGTACCCGGCCATTGA 60.002 57.895 2.24 0.00 30.04 2.57


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

AutoCloner maintained by Alex Coulton.