Multiple sequence alignment - TraesCS7A01G042800

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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 TraesCS7A01G042800 chr7A 100.000 4879 0 0 1 4879 19954864 19959742 0.000000e+00 9010.0
1 TraesCS7A01G042800 chr7A 86.320 731 69 17 4156 4879 603330313 603331019 0.000000e+00 767.0
2 TraesCS7A01G042800 chr7A 83.747 726 87 14 4161 4879 566789586 566788885 0.000000e+00 658.0
3 TraesCS7A01G042800 chr7A 82.292 192 25 2 4256 4440 566909638 566909449 1.820000e-34 158.0
4 TraesCS7A01G042800 chr7A 87.500 136 16 1 3125 3260 172593635 172593769 6.540000e-34 156.0
5 TraesCS7A01G042800 chr7A 93.151 73 3 2 557 629 7805313 7805383 6.680000e-19 106.0
6 TraesCS7A01G042800 chr7D 94.790 2495 100 18 628 3120 19710366 19712832 0.000000e+00 3860.0
7 TraesCS7A01G042800 chr7D 85.553 1066 80 21 3248 4288 19712959 19713975 0.000000e+00 1048.0
8 TraesCS7A01G042800 chr7D 86.320 731 69 17 4156 4879 523055672 523056378 0.000000e+00 767.0
9 TraesCS7A01G042800 chr7D 84.298 726 83 14 4161 4879 500775090 500774389 0.000000e+00 680.0
10 TraesCS7A01G042800 chr7D 84.371 723 82 14 4164 4879 523126813 523127511 0.000000e+00 680.0
11 TraesCS7A01G042800 chr7D 83.310 725 90 16 4162 4879 523132468 523133168 1.480000e-179 640.0
12 TraesCS7A01G042800 chr7D 85.056 629 68 12 4216 4837 113582828 113582219 6.940000e-173 617.0
13 TraesCS7A01G042800 chr7D 86.713 429 38 11 139 552 19709934 19710358 4.450000e-125 459.0
14 TraesCS7A01G042800 chr7D 88.966 145 16 0 3116 3260 596879274 596879418 3.880000e-41 180.0
15 TraesCS7A01G042800 chr7D 88.722 133 13 2 3 134 19709772 19709903 1.410000e-35 161.0
16 TraesCS7A01G042800 chr7D 95.946 74 2 1 557 630 13036222 13036150 8.580000e-23 119.0
17 TraesCS7A01G042800 chrUn 94.148 2512 96 11 627 3121 50756847 50754370 0.000000e+00 3777.0
18 TraesCS7A01G042800 chrUn 85.522 594 37 24 1 554 50757433 50756849 4.240000e-160 575.0
19 TraesCS7A01G042800 chrUn 84.989 453 38 16 3474 3898 50754251 50753801 2.700000e-117 433.0
20 TraesCS7A01G042800 chrUn 97.222 108 3 0 3259 3366 50754374 50754267 3.000000e-42 183.0
21 TraesCS7A01G042800 chrUn 79.793 193 17 13 3915 4091 50753724 50753538 2.390000e-23 121.0
22 TraesCS7A01G042800 chr7B 84.319 727 80 18 4161 4879 528872985 528872285 0.000000e+00 680.0
23 TraesCS7A01G042800 chr7B 84.919 683 75 11 4162 4837 557490261 557490922 0.000000e+00 665.0
24 TraesCS7A01G042800 chr7B 83.965 686 72 15 4161 4829 73175517 73174853 1.490000e-174 623.0
25 TraesCS7A01G042800 chr7B 82.988 723 88 17 4164 4879 557459302 557459996 5.360000e-174 621.0
26 TraesCS7A01G042800 chr3D 82.892 567 79 10 4161 4719 603683683 603683127 1.220000e-135 494.0
27 TraesCS7A01G042800 chr2A 89.189 148 15 1 3117 3264 642916028 642916174 3.000000e-42 183.0
28 TraesCS7A01G042800 chr2B 89.041 146 14 2 3116 3260 161206975 161206831 3.880000e-41 180.0
29 TraesCS7A01G042800 chr2B 89.552 134 14 0 3120 3253 341941257 341941124 2.340000e-38 171.0
30 TraesCS7A01G042800 chr2B 89.873 79 4 1 557 635 149844809 149844735 1.120000e-16 99.0
31 TraesCS7A01G042800 chr5A 87.919 149 18 0 3116 3264 568062699 568062551 5.020000e-40 176.0
32 TraesCS7A01G042800 chr5A 83.688 141 14 2 3120 3260 309596826 309596695 1.840000e-24 124.0
33 TraesCS7A01G042800 chr5B 88.983 118 13 0 3118 3235 663632415 663632298 3.940000e-31 147.0
34 TraesCS7A01G042800 chr1B 88.034 117 14 0 3116 3232 447509590 447509706 6.590000e-29 139.0
35 TraesCS7A01G042800 chr1B 94.521 73 3 1 557 629 421421364 421421293 1.440000e-20 111.0
36 TraesCS7A01G042800 chr6B 93.243 74 3 1 556 629 541936725 541936654 1.860000e-19 108.0
37 TraesCS7A01G042800 chr3A 91.781 73 6 0 557 629 101905551 101905479 8.640000e-18 102.0
38 TraesCS7A01G042800 chr3A 89.024 82 6 3 556 636 60870417 60870338 1.120000e-16 99.0
39 TraesCS7A01G042800 chr2D 90.000 80 7 1 550 629 170613464 170613542 8.640000e-18 102.0
40 TraesCS7A01G042800 chr4A 90.123 81 2 5 556 632 59674910 59674988 3.110000e-17 100.0
41 TraesCS7A01G042800 chr3B 90.411 73 7 0 4161 4233 806064503 806064575 4.020000e-16 97.1


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 TraesCS7A01G042800 chr7A 19954864 19959742 4878 False 9010.0 9010 100.0000 1 4879 1 chr7A.!!$F2 4878
1 TraesCS7A01G042800 chr7A 603330313 603331019 706 False 767.0 767 86.3200 4156 4879 1 chr7A.!!$F4 723
2 TraesCS7A01G042800 chr7A 566788885 566789586 701 True 658.0 658 83.7470 4161 4879 1 chr7A.!!$R1 718
3 TraesCS7A01G042800 chr7D 19709772 19713975 4203 False 1382.0 3860 88.9445 3 4288 4 chr7D.!!$F5 4285
4 TraesCS7A01G042800 chr7D 523055672 523056378 706 False 767.0 767 86.3200 4156 4879 1 chr7D.!!$F1 723
5 TraesCS7A01G042800 chr7D 500774389 500775090 701 True 680.0 680 84.2980 4161 4879 1 chr7D.!!$R3 718
6 TraesCS7A01G042800 chr7D 523126813 523127511 698 False 680.0 680 84.3710 4164 4879 1 chr7D.!!$F2 715
7 TraesCS7A01G042800 chr7D 523132468 523133168 700 False 640.0 640 83.3100 4162 4879 1 chr7D.!!$F3 717
8 TraesCS7A01G042800 chr7D 113582219 113582828 609 True 617.0 617 85.0560 4216 4837 1 chr7D.!!$R2 621
9 TraesCS7A01G042800 chrUn 50753538 50757433 3895 True 1017.8 3777 88.3348 1 4091 5 chrUn.!!$R1 4090
10 TraesCS7A01G042800 chr7B 528872285 528872985 700 True 680.0 680 84.3190 4161 4879 1 chr7B.!!$R2 718
11 TraesCS7A01G042800 chr7B 557490261 557490922 661 False 665.0 665 84.9190 4162 4837 1 chr7B.!!$F2 675
12 TraesCS7A01G042800 chr7B 73174853 73175517 664 True 623.0 623 83.9650 4161 4829 1 chr7B.!!$R1 668
13 TraesCS7A01G042800 chr7B 557459302 557459996 694 False 621.0 621 82.9880 4164 4879 1 chr7B.!!$F1 715
14 TraesCS7A01G042800 chr3D 603683127 603683683 556 True 494.0 494 82.8920 4161 4719 1 chr3D.!!$R1 558

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
713 767 0.036577 AGTCAGCTGTCCTGTCATGC 60.037 55.000 14.67 0.00 42.38 4.06 F
715 769 1.002990 CAGCTGTCCTGTCATGCCA 60.003 57.895 5.25 0.00 36.79 4.92 F
2606 2674 1.335496 GGCCTAGAGAGCTCGTTACAG 59.665 57.143 8.37 2.71 34.09 2.74 F
3471 3605 0.178924 AGAACTTGGGCTGGGCAAAT 60.179 50.000 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 2654 1.335496 CTGTAACGAGCTCTCTAGGCC 59.665 57.143 12.85 0.0 0.00 5.19 R
2628 2696 3.074390 AGACCAATGTCCTTGATGGTTGA 59.926 43.478 0.00 0.0 45.85 3.18 R
3654 3823 0.036858 GAAGCTTTCTCCGCCTGAGT 60.037 55.000 0.00 0.0 42.12 3.41 R
4315 4588 1.444553 GAAGGACGTCTGCGACAGG 60.445 63.158 16.46 0.0 42.00 4.00 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
25 26 3.643792 CTGATCTATCCCTTTCCCTCGTT 59.356 47.826 0.00 0.00 0.00 3.85
26 27 3.388024 TGATCTATCCCTTTCCCTCGTTG 59.612 47.826 0.00 0.00 0.00 4.10
27 28 2.829023 TCTATCCCTTTCCCTCGTTGT 58.171 47.619 0.00 0.00 0.00 3.32
28 29 2.500098 TCTATCCCTTTCCCTCGTTGTG 59.500 50.000 0.00 0.00 0.00 3.33
29 30 1.358152 ATCCCTTTCCCTCGTTGTGA 58.642 50.000 0.00 0.00 0.00 3.58
31 32 1.702957 TCCCTTTCCCTCGTTGTGATT 59.297 47.619 0.00 0.00 0.00 2.57
32 33 1.812571 CCCTTTCCCTCGTTGTGATTG 59.187 52.381 0.00 0.00 0.00 2.67
33 34 1.812571 CCTTTCCCTCGTTGTGATTGG 59.187 52.381 0.00 0.00 0.00 3.16
99 104 2.632512 TGTGAATTTTTCCCCCTTCAGC 59.367 45.455 0.00 0.00 0.00 4.26
101 106 2.158173 TGAATTTTTCCCCCTTCAGCCT 60.158 45.455 0.00 0.00 0.00 4.58
134 140 2.037772 ACTCTAGTTTCCACCTGCAGTG 59.962 50.000 13.81 10.81 46.83 3.66
160 197 3.003689 GTGCTTGTATCTGTGTGCTGTTT 59.996 43.478 0.00 0.00 0.00 2.83
163 200 4.776743 CTTGTATCTGTGTGCTGTTTGTC 58.223 43.478 0.00 0.00 0.00 3.18
168 205 2.677836 TCTGTGTGCTGTTTGTCTGTTC 59.322 45.455 0.00 0.00 0.00 3.18
246 286 1.032014 ATATTGGATTGCACGGCACC 58.968 50.000 0.00 0.00 38.71 5.01
269 309 4.083003 CCTGTCCTCGATCTAGTGATTAGC 60.083 50.000 0.00 0.00 32.19 3.09
280 326 3.567478 AGTGATTAGCTCAATCCCACC 57.433 47.619 0.00 0.00 42.17 4.61
285 331 0.325296 TAGCTCAATCCCACCGACCT 60.325 55.000 0.00 0.00 0.00 3.85
333 379 2.363680 CCATCTAGATCTGCACTCCGTT 59.636 50.000 5.18 0.00 0.00 4.44
375 421 8.260818 CCATAATACATATTGCTAGCTACCTGT 58.739 37.037 17.23 16.41 0.00 4.00
542 596 1.526575 CGGGCCTGTGTCTGCAAAAT 61.527 55.000 2.29 0.00 0.00 1.82
546 600 2.028748 GGCCTGTGTCTGCAAAATTGAT 60.029 45.455 0.00 0.00 0.00 2.57
554 608 9.630098 CTGTGTCTGCAAAATTGATACTATTTT 57.370 29.630 0.00 0.00 36.03 1.82
555 609 9.624697 TGTGTCTGCAAAATTGATACTATTTTC 57.375 29.630 0.00 0.00 34.01 2.29
562 616 9.952188 GCAAAATTGATACTATTTTCTACTCCC 57.048 33.333 0.00 0.00 34.01 4.30
566 620 8.798975 ATTGATACTATTTTCTACTCCCTCCA 57.201 34.615 0.00 0.00 0.00 3.86
567 621 8.798975 TTGATACTATTTTCTACTCCCTCCAT 57.201 34.615 0.00 0.00 0.00 3.41
568 622 8.423906 TGATACTATTTTCTACTCCCTCCATC 57.576 38.462 0.00 0.00 0.00 3.51
569 623 7.455008 TGATACTATTTTCTACTCCCTCCATCC 59.545 40.741 0.00 0.00 0.00 3.51
570 624 4.908481 ACTATTTTCTACTCCCTCCATCCC 59.092 45.833 0.00 0.00 0.00 3.85
571 625 2.961536 TTTCTACTCCCTCCATCCCA 57.038 50.000 0.00 0.00 0.00 4.37
572 626 3.438131 TTTCTACTCCCTCCATCCCAT 57.562 47.619 0.00 0.00 0.00 4.00
573 627 4.569676 TTTCTACTCCCTCCATCCCATA 57.430 45.455 0.00 0.00 0.00 2.74
574 628 4.569676 TTCTACTCCCTCCATCCCATAA 57.430 45.455 0.00 0.00 0.00 1.90
575 629 4.785173 TCTACTCCCTCCATCCCATAAT 57.215 45.455 0.00 0.00 0.00 1.28
576 630 5.896530 TCTACTCCCTCCATCCCATAATA 57.103 43.478 0.00 0.00 0.00 0.98
577 631 6.438111 TCTACTCCCTCCATCCCATAATAT 57.562 41.667 0.00 0.00 0.00 1.28
578 632 7.554597 TCTACTCCCTCCATCCCATAATATA 57.445 40.000 0.00 0.00 0.00 0.86
579 633 7.961940 TCTACTCCCTCCATCCCATAATATAA 58.038 38.462 0.00 0.00 0.00 0.98
580 634 8.068110 TCTACTCCCTCCATCCCATAATATAAG 58.932 40.741 0.00 0.00 0.00 1.73
581 635 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
582 636 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
583 637 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
584 638 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
585 639 5.129485 CCTCCATCCCATAATATAAGAGCGT 59.871 44.000 0.00 0.00 0.00 5.07
586 640 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
587 641 7.016153 TCCATCCCATAATATAAGAGCGTTT 57.984 36.000 0.00 0.00 0.00 3.60
588 642 7.458397 TCCATCCCATAATATAAGAGCGTTTT 58.542 34.615 0.00 0.00 0.00 2.43
589 643 7.942341 TCCATCCCATAATATAAGAGCGTTTTT 59.058 33.333 0.00 0.00 0.00 1.94
611 665 8.712285 TTTTTACACTAGTGCGCTCTAATATT 57.288 30.769 22.90 7.49 0.00 1.28
612 666 9.806203 TTTTTACACTAGTGCGCTCTAATATTA 57.194 29.630 22.90 6.65 0.00 0.98
613 667 9.976511 TTTTACACTAGTGCGCTCTAATATTAT 57.023 29.630 22.90 0.52 0.00 1.28
614 668 8.965986 TTACACTAGTGCGCTCTAATATTATG 57.034 34.615 22.90 12.43 0.00 1.90
615 669 6.390721 ACACTAGTGCGCTCTAATATTATGG 58.609 40.000 22.90 8.25 0.00 2.74
616 670 5.807520 CACTAGTGCGCTCTAATATTATGGG 59.192 44.000 18.83 7.63 0.00 4.00
617 671 5.715279 ACTAGTGCGCTCTAATATTATGGGA 59.285 40.000 18.83 0.00 0.00 4.37
618 672 4.822026 AGTGCGCTCTAATATTATGGGAC 58.178 43.478 10.83 0.00 0.00 4.46
619 673 3.612860 GTGCGCTCTAATATTATGGGACG 59.387 47.826 9.73 7.54 0.00 4.79
620 674 3.187700 GCGCTCTAATATTATGGGACGG 58.812 50.000 0.00 0.00 0.00 4.79
621 675 3.119245 GCGCTCTAATATTATGGGACGGA 60.119 47.826 0.00 0.00 0.00 4.69
622 676 4.673441 CGCTCTAATATTATGGGACGGAG 58.327 47.826 0.00 0.00 0.00 4.63
623 677 4.440250 CGCTCTAATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
624 678 4.141914 GCTCTAATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
625 679 5.269991 CTCTAATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
626 680 5.269991 TCTAATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
627 681 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
691 745 3.368427 CCATACATGTCCGAGTTGTCTGT 60.368 47.826 0.00 0.00 0.00 3.41
713 767 0.036577 AGTCAGCTGTCCTGTCATGC 60.037 55.000 14.67 0.00 42.38 4.06
715 769 1.002990 CAGCTGTCCTGTCATGCCA 60.003 57.895 5.25 0.00 36.79 4.92
790 844 4.737855 AAGTAGTCACAGTGTCACAACT 57.262 40.909 5.62 5.78 0.00 3.16
799 853 3.712733 ACAGTGTCACAACTAAGGGGTAA 59.287 43.478 5.62 0.00 0.00 2.85
803 857 5.826208 AGTGTCACAACTAAGGGGTAAAAAG 59.174 40.000 5.62 0.00 0.00 2.27
873 927 2.928334 CTCATCTGGTTCCCTTCCATG 58.072 52.381 0.00 0.00 34.26 3.66
985 1042 2.577700 TGCGGTTTTCATGTGTAGGTT 58.422 42.857 0.00 0.00 0.00 3.50
1104 1161 4.827284 ACCAACATGGAAAGTCTTACAAGG 59.173 41.667 2.85 0.00 40.96 3.61
1315 1372 8.759481 AGAGTTAGATGACATGATCAGTTCTA 57.241 34.615 0.00 2.66 41.91 2.10
1368 1425 5.422214 AGGTTTATGACGAAGAATCTGGT 57.578 39.130 0.00 0.00 0.00 4.00
1489 1546 1.879380 CCATTGAGTTTTCCAGCGACA 59.121 47.619 0.00 0.00 0.00 4.35
1574 1642 1.547372 ACAGGAATTGCTGAACATGGC 59.453 47.619 30.84 0.00 0.00 4.40
1593 1661 2.318578 GCGTGTGTGAAAATGGTCATG 58.681 47.619 0.00 0.00 0.00 3.07
1755 1823 3.064820 GCTTCGTCTCCAAACACAAGAAA 59.935 43.478 0.00 0.00 0.00 2.52
1835 1903 1.691434 GCTTCTGAGATACTCCTGGGG 59.309 57.143 0.00 0.00 0.00 4.96
2120 2188 8.474025 TCTAATTCACAGTTGTTGTTGGAAAAT 58.526 29.630 0.00 0.00 38.16 1.82
2127 2195 7.167968 CACAGTTGTTGTTGGAAAATGTATCAG 59.832 37.037 0.00 0.00 38.16 2.90
2234 2302 3.324846 TCCTAAGAGCTGAAAACAGAGCA 59.675 43.478 0.00 0.00 37.70 4.26
2331 2399 1.632018 CCAGGGTTCGGATAAGGCCA 61.632 60.000 5.01 0.00 0.00 5.36
2519 2587 4.427312 CCCTAAATGCTGAATCAAAGTGC 58.573 43.478 0.00 0.00 0.00 4.40
2586 2654 3.567576 TTCTGAGAGCTCGAGTTGAAG 57.432 47.619 15.13 5.30 0.00 3.02
2606 2674 1.335496 GGCCTAGAGAGCTCGTTACAG 59.665 57.143 8.37 2.71 34.09 2.74
2628 2696 5.882557 CAGGAAGCTAACCATGTGAAAGTAT 59.117 40.000 11.59 0.00 0.00 2.12
2666 2734 8.779354 ACATTGGTCTCAGAACTAAAGTTATC 57.221 34.615 0.00 0.00 38.56 1.75
2753 2825 8.743714 TGATTGCATACACACCATTAATGTTTA 58.256 29.630 14.25 0.00 0.00 2.01
2836 2910 3.009723 CGTGGTGGTTGCAGATTTCTAT 58.990 45.455 0.00 0.00 0.00 1.98
2869 2943 6.638610 AGAAGAACAGGATATTGACTCACAG 58.361 40.000 0.00 0.00 0.00 3.66
2904 2978 7.959066 AACTAGTGTTAAGGATGGCACAAAGC 61.959 42.308 0.00 0.00 36.76 3.51
2990 3064 5.766670 AGTTTCAGATTCTTCATCAGCACAA 59.233 36.000 0.00 0.00 33.75 3.33
3087 3161 4.898320 TGCATATAATGAGGTGCTACAGG 58.102 43.478 0.00 0.00 38.37 4.00
3088 3162 4.592778 TGCATATAATGAGGTGCTACAGGA 59.407 41.667 0.00 0.00 38.37 3.86
3111 3185 3.764972 GACATACTCCAGCCCCTATAGAC 59.235 52.174 0.00 0.00 0.00 2.59
3120 3194 3.440872 CAGCCCCTATAGACGCTACTAAG 59.559 52.174 11.73 0.00 0.00 2.18
3122 3196 2.754002 CCCCTATAGACGCTACTAAGGC 59.246 54.545 0.00 0.00 0.00 4.35
3124 3198 2.419324 CCTATAGACGCTACTAAGGCCG 59.581 54.545 0.00 0.00 0.00 6.13
3125 3199 0.597072 ATAGACGCTACTAAGGCCGC 59.403 55.000 0.00 0.00 0.00 6.53
3131 3205 1.138247 CTACTAAGGCCGCGTTCGT 59.862 57.895 4.92 4.95 0.00 3.85
3132 3206 0.864797 CTACTAAGGCCGCGTTCGTC 60.865 60.000 4.92 0.00 0.00 4.20
3133 3207 1.585267 TACTAAGGCCGCGTTCGTCA 61.585 55.000 4.92 0.00 0.00 4.35
3134 3208 2.126228 TAAGGCCGCGTTCGTCAG 60.126 61.111 4.92 0.00 0.00 3.51
3135 3209 2.814183 CTAAGGCCGCGTTCGTCAGT 62.814 60.000 4.92 0.00 0.00 3.41
3141 3215 2.504244 GCGTTCGTCAGTCCTCCG 60.504 66.667 0.00 0.00 0.00 4.63
3143 3217 2.504244 GTTCGTCAGTCCTCCGCG 60.504 66.667 0.00 0.00 0.00 6.46
3144 3218 3.744719 TTCGTCAGTCCTCCGCGG 61.745 66.667 22.12 22.12 0.00 6.46
3145 3219 4.710167 TCGTCAGTCCTCCGCGGA 62.710 66.667 29.03 29.03 40.30 5.54
3146 3220 4.180946 CGTCAGTCCTCCGCGGAG 62.181 72.222 41.90 41.90 44.20 4.63
3171 3245 3.490890 CGCAGAGCAGGCCTTAAC 58.509 61.111 0.00 0.00 0.00 2.01
3172 3246 2.109126 CGCAGAGCAGGCCTTAACC 61.109 63.158 0.00 0.00 0.00 2.85
3173 3247 1.002134 GCAGAGCAGGCCTTAACCA 60.002 57.895 0.00 0.00 0.00 3.67
3174 3248 0.609131 GCAGAGCAGGCCTTAACCAA 60.609 55.000 0.00 0.00 0.00 3.67
3175 3249 1.168714 CAGAGCAGGCCTTAACCAAC 58.831 55.000 0.00 0.00 0.00 3.77
3176 3250 1.068121 AGAGCAGGCCTTAACCAACT 58.932 50.000 0.00 0.00 0.00 3.16
3177 3251 1.003696 AGAGCAGGCCTTAACCAACTC 59.996 52.381 0.00 1.52 35.32 3.01
3178 3252 1.003696 GAGCAGGCCTTAACCAACTCT 59.996 52.381 0.00 0.00 33.41 3.24
3179 3253 1.168714 GCAGGCCTTAACCAACTCTG 58.831 55.000 0.00 0.00 0.00 3.35
3180 3254 1.168714 CAGGCCTTAACCAACTCTGC 58.831 55.000 0.00 0.00 0.00 4.26
3181 3255 0.771127 AGGCCTTAACCAACTCTGCA 59.229 50.000 0.00 0.00 0.00 4.41
3182 3256 1.144913 AGGCCTTAACCAACTCTGCAA 59.855 47.619 0.00 0.00 0.00 4.08
3183 3257 1.960689 GGCCTTAACCAACTCTGCAAA 59.039 47.619 0.00 0.00 0.00 3.68
3184 3258 2.562738 GGCCTTAACCAACTCTGCAAAT 59.437 45.455 0.00 0.00 0.00 2.32
3185 3259 3.006859 GGCCTTAACCAACTCTGCAAATT 59.993 43.478 0.00 0.00 0.00 1.82
3186 3260 3.989817 GCCTTAACCAACTCTGCAAATTG 59.010 43.478 0.00 0.00 0.00 2.32
3187 3261 4.501400 GCCTTAACCAACTCTGCAAATTGT 60.501 41.667 0.00 0.00 0.00 2.71
3188 3262 4.984161 CCTTAACCAACTCTGCAAATTGTG 59.016 41.667 0.00 0.00 0.00 3.33
3189 3263 3.457610 AACCAACTCTGCAAATTGTGG 57.542 42.857 0.00 0.00 0.00 4.17
3190 3264 1.069049 ACCAACTCTGCAAATTGTGGC 59.931 47.619 0.00 0.00 0.00 5.01
3191 3265 1.606224 CCAACTCTGCAAATTGTGGCC 60.606 52.381 0.00 0.00 0.00 5.36
3192 3266 1.342174 CAACTCTGCAAATTGTGGCCT 59.658 47.619 3.32 0.00 0.00 5.19
3193 3267 1.708341 ACTCTGCAAATTGTGGCCTT 58.292 45.000 3.32 0.00 0.00 4.35
3194 3268 2.875296 ACTCTGCAAATTGTGGCCTTA 58.125 42.857 3.32 0.00 0.00 2.69
3195 3269 3.230134 ACTCTGCAAATTGTGGCCTTAA 58.770 40.909 3.32 0.00 0.00 1.85
3196 3270 3.834231 ACTCTGCAAATTGTGGCCTTAAT 59.166 39.130 3.32 1.25 0.00 1.40
3197 3271 4.082026 ACTCTGCAAATTGTGGCCTTAATC 60.082 41.667 3.32 0.00 0.00 1.75
3198 3272 3.831333 TCTGCAAATTGTGGCCTTAATCA 59.169 39.130 3.32 0.00 0.00 2.57
3199 3273 4.282957 TCTGCAAATTGTGGCCTTAATCAA 59.717 37.500 3.32 2.41 0.00 2.57
3200 3274 4.314121 TGCAAATTGTGGCCTTAATCAAC 58.686 39.130 3.32 0.00 0.00 3.18
3201 3275 4.040217 TGCAAATTGTGGCCTTAATCAACT 59.960 37.500 3.32 0.00 0.00 3.16
3202 3276 4.389687 GCAAATTGTGGCCTTAATCAACTG 59.610 41.667 3.32 4.95 0.00 3.16
3203 3277 4.806640 AATTGTGGCCTTAATCAACTGG 57.193 40.909 3.32 0.00 0.00 4.00
3204 3278 3.517296 TTGTGGCCTTAATCAACTGGA 57.483 42.857 3.32 0.00 0.00 3.86
3205 3279 3.737559 TGTGGCCTTAATCAACTGGAT 57.262 42.857 3.32 0.00 38.05 3.41
3255 3389 4.515404 GGAGGGAATCCGAACACG 57.485 61.111 0.00 0.00 38.67 4.49
3387 3521 3.674682 CGTGCAGTTCTCCTCTCCTTTAG 60.675 52.174 0.00 0.00 0.00 1.85
3411 3545 1.884579 CTCATTAGCATCATGGGGTGC 59.115 52.381 9.64 9.64 41.57 5.01
3464 3598 0.959372 CTCTGGCAGAACTTGGGCTG 60.959 60.000 19.29 0.00 35.28 4.85
3468 3602 2.115910 CAGAACTTGGGCTGGGCA 59.884 61.111 0.00 0.00 0.00 5.36
3471 3605 0.178924 AGAACTTGGGCTGGGCAAAT 60.179 50.000 0.00 0.00 0.00 2.32
3472 3606 1.077005 AGAACTTGGGCTGGGCAAATA 59.923 47.619 0.00 0.00 0.00 1.40
3521 3672 5.621197 AGCAAAATATTCGCACTTACACA 57.379 34.783 11.24 0.00 0.00 3.72
3527 3678 2.471607 CGCACTTACACAGCGCTG 59.528 61.111 34.89 34.89 45.14 5.18
3536 3687 0.318107 ACACAGCGCTGACATTTTGC 60.318 50.000 42.03 0.00 0.00 3.68
3582 3735 6.749118 CACACCTTGATCTTATTTTGCTAAGC 59.251 38.462 0.00 0.00 0.00 3.09
3586 3739 7.148171 ACCTTGATCTTATTTTGCTAAGCTGTC 60.148 37.037 0.00 0.00 0.00 3.51
3590 3743 6.441093 TCTTATTTTGCTAAGCTGTCCATG 57.559 37.500 0.00 0.00 0.00 3.66
3619 3785 5.051813 CGCATCGCGTAACAGAGATTGTT 62.052 47.826 5.77 0.00 46.83 2.83
3674 3845 2.057830 TCAGGCGGAGAAAGCTTCA 58.942 52.632 0.00 0.00 34.52 3.02
3686 3857 5.452636 GGAGAAAGCTTCAGACCTTATCGAT 60.453 44.000 2.16 2.16 0.00 3.59
3728 3905 1.231641 CACCGGAGAGGAGGAGGAT 59.768 63.158 9.46 0.00 45.00 3.24
3735 3912 2.427002 GGAGAGGAGGAGGATGATTCCA 60.427 54.545 0.00 0.00 45.30 3.53
3851 4028 2.195411 TGCCACCTGCTGCTTGAA 59.805 55.556 0.00 0.00 42.00 2.69
3979 4221 2.716017 CCGGCCTGAGTGAGACCTC 61.716 68.421 0.00 0.00 0.00 3.85
3986 4228 0.482887 TGAGTGAGACCTCTGGGACA 59.517 55.000 0.00 0.00 36.25 4.02
3993 4235 0.335361 GACCTCTGGGACACCTCCTA 59.665 60.000 0.00 0.00 36.68 2.94
3994 4236 0.041386 ACCTCTGGGACACCTCCTAC 59.959 60.000 0.00 0.00 36.68 3.18
3997 4239 1.006043 CTCTGGGACACCTCCTACTCA 59.994 57.143 0.00 0.00 36.68 3.41
4077 4335 8.472007 TTTGTTAACCTCCTTGTGATTATGTT 57.528 30.769 2.48 0.00 0.00 2.71
4084 4346 5.943416 CCTCCTTGTGATTATGTTTGGTGTA 59.057 40.000 0.00 0.00 0.00 2.90
4109 4371 3.679980 GCAGCAACATTCGAAGAAGAGTA 59.320 43.478 3.35 0.00 45.90 2.59
4110 4372 4.331168 GCAGCAACATTCGAAGAAGAGTAT 59.669 41.667 3.35 0.00 45.90 2.12
4111 4373 5.163814 GCAGCAACATTCGAAGAAGAGTATT 60.164 40.000 3.35 0.00 45.90 1.89
4112 4374 6.621596 GCAGCAACATTCGAAGAAGAGTATTT 60.622 38.462 3.35 0.00 45.90 1.40
4113 4375 6.958193 CAGCAACATTCGAAGAAGAGTATTTC 59.042 38.462 3.35 0.00 45.90 2.17
4114 4376 6.650807 AGCAACATTCGAAGAAGAGTATTTCA 59.349 34.615 3.35 0.00 45.90 2.69
4115 4377 6.958193 GCAACATTCGAAGAAGAGTATTTCAG 59.042 38.462 3.35 0.00 45.90 3.02
4116 4378 6.654793 ACATTCGAAGAAGAGTATTTCAGC 57.345 37.500 3.35 0.00 45.90 4.26
4117 4379 5.582665 ACATTCGAAGAAGAGTATTTCAGCC 59.417 40.000 3.35 0.00 45.90 4.85
4118 4380 5.407407 TTCGAAGAAGAGTATTTCAGCCT 57.593 39.130 0.00 0.00 45.90 4.58
4119 4381 6.525578 TTCGAAGAAGAGTATTTCAGCCTA 57.474 37.500 0.00 0.00 45.90 3.93
4120 4382 6.525578 TCGAAGAAGAGTATTTCAGCCTAA 57.474 37.500 0.00 0.00 0.00 2.69
4300 4573 3.402681 ATGGCCTCCCTCACCGTG 61.403 66.667 3.32 0.00 0.00 4.94
4362 4642 3.041940 CACACGGCTCCCACGAAC 61.042 66.667 0.00 0.00 34.93 3.95
4407 4687 2.283388 AAGGGCCAGCACACCATG 60.283 61.111 6.18 0.00 0.00 3.66
4625 4909 2.046892 CACCCAGAGGAAGGCGTG 60.047 66.667 0.00 0.00 36.73 5.34
4666 4951 1.371558 AGGAACTCGGTGAACTGCC 59.628 57.895 0.00 0.00 0.00 4.85
4764 5049 3.465403 CCCTCGTCCTCCTGCCAG 61.465 72.222 0.00 0.00 0.00 4.85
4778 5065 2.719376 GCCAGAGGCTTGTGTTTGA 58.281 52.632 0.00 0.00 46.69 2.69
4803 5090 4.838486 GCGGACCTCGACGAGCTG 62.838 72.222 19.55 12.45 42.43 4.24
4804 5091 4.180946 CGGACCTCGACGAGCTGG 62.181 72.222 19.55 9.67 42.43 4.85
4805 5092 4.500116 GGACCTCGACGAGCTGGC 62.500 72.222 19.55 8.85 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.812571 CCAATCACAACGAGGGAAAGG 59.187 52.381 0.00 0.00 29.94 3.11
16 17 2.226330 CAACCAATCACAACGAGGGAA 58.774 47.619 0.00 0.00 29.94 3.97
25 26 2.918345 GCCGCTGCAACCAATCACA 61.918 57.895 0.00 0.00 37.47 3.58
26 27 2.126346 GCCGCTGCAACCAATCAC 60.126 61.111 0.00 0.00 37.47 3.06
27 28 3.372730 GGCCGCTGCAACCAATCA 61.373 61.111 1.55 0.00 40.13 2.57
28 29 4.481112 CGGCCGCTGCAACCAATC 62.481 66.667 14.67 0.00 40.13 2.67
75 80 1.627864 AGGGGGAAAAATTCACACGG 58.372 50.000 0.00 0.00 42.79 4.94
134 140 3.438087 AGCACACAGATACAAGCACAATC 59.562 43.478 0.00 0.00 0.00 2.67
160 197 4.373116 GCCGCTCCCGAACAGACA 62.373 66.667 0.00 0.00 36.29 3.41
246 286 4.083003 GCTAATCACTAGATCGAGGACAGG 60.083 50.000 7.79 0.00 31.90 4.00
269 309 1.141881 CGAGGTCGGTGGGATTGAG 59.858 63.158 0.00 0.00 35.37 3.02
375 421 0.911769 CCCACAGGAATCAGCTACCA 59.088 55.000 0.00 0.00 33.47 3.25
460 509 6.202954 CCTGTCACAAGGTCAAAACTAAGTAG 59.797 42.308 0.00 0.00 32.17 2.57
542 596 8.798975 ATGGAGGGAGTAGAAAATAGTATCAA 57.201 34.615 0.00 0.00 0.00 2.57
546 600 6.082707 GGGATGGAGGGAGTAGAAAATAGTA 58.917 44.000 0.00 0.00 0.00 1.82
554 608 4.785173 ATTATGGGATGGAGGGAGTAGA 57.215 45.455 0.00 0.00 0.00 2.59
555 609 8.068110 TCTTATATTATGGGATGGAGGGAGTAG 58.932 40.741 0.00 0.00 0.00 2.57
560 614 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
561 615 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
562 616 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
563 617 6.620877 AACGCTCTTATATTATGGGATGGA 57.379 37.500 0.00 0.00 0.00 3.41
564 618 7.687941 AAAACGCTCTTATATTATGGGATGG 57.312 36.000 0.00 0.00 0.00 3.51
586 640 8.712285 AATATTAGAGCGCACTAGTGTAAAAA 57.288 30.769 23.44 11.26 0.00 1.94
587 641 9.976511 ATAATATTAGAGCGCACTAGTGTAAAA 57.023 29.630 23.44 10.32 0.00 1.52
588 642 9.406828 CATAATATTAGAGCGCACTAGTGTAAA 57.593 33.333 23.44 9.70 0.00 2.01
589 643 8.027189 CCATAATATTAGAGCGCACTAGTGTAA 58.973 37.037 23.44 13.79 0.00 2.41
590 644 7.362660 CCCATAATATTAGAGCGCACTAGTGTA 60.363 40.741 23.44 11.49 0.00 2.90
591 645 6.390721 CCATAATATTAGAGCGCACTAGTGT 58.609 40.000 23.44 9.95 0.00 3.55
592 646 5.807520 CCCATAATATTAGAGCGCACTAGTG 59.192 44.000 18.93 18.93 0.00 2.74
593 647 5.715279 TCCCATAATATTAGAGCGCACTAGT 59.285 40.000 11.47 12.92 0.00 2.57
594 648 6.037098 GTCCCATAATATTAGAGCGCACTAG 58.963 44.000 11.47 0.00 0.00 2.57
595 649 5.392703 CGTCCCATAATATTAGAGCGCACTA 60.393 44.000 11.47 11.04 0.00 2.74
596 650 4.618460 CGTCCCATAATATTAGAGCGCACT 60.618 45.833 13.06 13.06 0.00 4.40
597 651 3.612860 CGTCCCATAATATTAGAGCGCAC 59.387 47.826 11.47 2.25 0.00 5.34
598 652 3.368013 CCGTCCCATAATATTAGAGCGCA 60.368 47.826 11.47 0.00 0.00 6.09
599 653 3.119245 TCCGTCCCATAATATTAGAGCGC 60.119 47.826 0.00 0.00 0.00 5.92
600 654 4.440250 CCTCCGTCCCATAATATTAGAGCG 60.440 50.000 1.02 2.06 0.00 5.03
601 655 4.141914 CCCTCCGTCCCATAATATTAGAGC 60.142 50.000 1.02 0.00 0.00 4.09
602 656 5.269991 TCCCTCCGTCCCATAATATTAGAG 58.730 45.833 1.02 0.87 0.00 2.43
603 657 5.222484 ACTCCCTCCGTCCCATAATATTAGA 60.222 44.000 1.02 0.00 0.00 2.10
604 658 5.024118 ACTCCCTCCGTCCCATAATATTAG 58.976 45.833 1.02 0.00 0.00 1.73
605 659 5.019657 ACTCCCTCCGTCCCATAATATTA 57.980 43.478 0.00 0.00 0.00 0.98
606 660 3.870559 ACTCCCTCCGTCCCATAATATT 58.129 45.455 0.00 0.00 0.00 1.28
607 661 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
608 662 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
609 663 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
610 664 4.474303 TTATACTCCCTCCGTCCCATAA 57.526 45.455 0.00 0.00 0.00 1.90
611 665 4.687262 ATTATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
612 666 3.562108 ATTATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
613 667 3.339713 AATTATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
614 668 4.837298 ACTAAATTATACTCCCTCCGTCCC 59.163 45.833 0.00 0.00 0.00 4.46
615 669 6.041296 TCAACTAAATTATACTCCCTCCGTCC 59.959 42.308 0.00 0.00 0.00 4.79
616 670 7.047460 TCAACTAAATTATACTCCCTCCGTC 57.953 40.000 0.00 0.00 0.00 4.79
617 671 7.427989 TTCAACTAAATTATACTCCCTCCGT 57.572 36.000 0.00 0.00 0.00 4.69
618 672 8.904099 AATTCAACTAAATTATACTCCCTCCG 57.096 34.615 0.00 0.00 0.00 4.63
713 767 6.896021 AGCTAGATCCATTTTTCATGATGG 57.104 37.500 6.72 6.72 43.36 3.51
715 769 8.974238 TGAAAAGCTAGATCCATTTTTCATGAT 58.026 29.630 15.34 0.00 40.68 2.45
722 776 7.869429 CACAAACTGAAAAGCTAGATCCATTTT 59.131 33.333 0.00 0.00 0.00 1.82
790 844 8.226112 TGAGTAAATTCCACTTTTTACCCCTTA 58.774 33.333 0.00 0.00 38.49 2.69
799 853 9.959721 TCTAGCTTATGAGTAAATTCCACTTTT 57.040 29.630 0.00 0.00 0.00 2.27
803 857 9.982651 TGTATCTAGCTTATGAGTAAATTCCAC 57.017 33.333 0.00 0.00 0.00 4.02
833 887 1.926510 GCAACAAAAACCAGAGCACAC 59.073 47.619 0.00 0.00 0.00 3.82
911 965 9.817809 CAAGCAATAGGTAGTACAGAAGATTAA 57.182 33.333 2.06 0.00 0.00 1.40
912 966 8.978472 ACAAGCAATAGGTAGTACAGAAGATTA 58.022 33.333 2.06 0.00 0.00 1.75
913 967 7.852263 ACAAGCAATAGGTAGTACAGAAGATT 58.148 34.615 2.06 0.00 0.00 2.40
914 968 7.425224 ACAAGCAATAGGTAGTACAGAAGAT 57.575 36.000 2.06 0.00 0.00 2.40
915 969 6.852420 ACAAGCAATAGGTAGTACAGAAGA 57.148 37.500 2.06 0.00 0.00 2.87
916 970 8.634444 AGATACAAGCAATAGGTAGTACAGAAG 58.366 37.037 2.06 0.00 0.00 2.85
917 971 8.534954 AGATACAAGCAATAGGTAGTACAGAA 57.465 34.615 2.06 0.00 0.00 3.02
918 972 7.778382 TGAGATACAAGCAATAGGTAGTACAGA 59.222 37.037 2.06 0.00 0.00 3.41
919 973 7.941919 TGAGATACAAGCAATAGGTAGTACAG 58.058 38.462 2.06 0.00 0.00 2.74
920 974 7.891498 TGAGATACAAGCAATAGGTAGTACA 57.109 36.000 2.06 0.00 0.00 2.90
923 977 9.314133 TGATATGAGATACAAGCAATAGGTAGT 57.686 33.333 0.00 0.00 0.00 2.73
924 978 9.800433 CTGATATGAGATACAAGCAATAGGTAG 57.200 37.037 0.00 0.00 0.00 3.18
925 979 9.314133 ACTGATATGAGATACAAGCAATAGGTA 57.686 33.333 0.00 0.00 0.00 3.08
926 980 8.200024 ACTGATATGAGATACAAGCAATAGGT 57.800 34.615 0.00 0.00 0.00 3.08
931 985 9.702494 CAAGATACTGATATGAGATACAAGCAA 57.298 33.333 0.00 0.00 0.00 3.91
969 1026 4.300189 TGTGCAACCTACACATGAAAAC 57.700 40.909 0.00 0.00 42.88 2.43
1104 1161 2.674796 ATGCAAGGTCGAGTTCTACC 57.325 50.000 0.00 0.00 35.91 3.18
1315 1372 9.582431 CTCAACATTTTTAGCATCAATCTGAAT 57.418 29.630 0.00 0.00 0.00 2.57
1368 1425 2.819608 CAGCTTAGCTTTAACCTTGCCA 59.180 45.455 3.00 0.00 36.40 4.92
1574 1642 3.243035 ACACATGACCATTTTCACACACG 60.243 43.478 0.00 0.00 0.00 4.49
1593 1661 2.196749 CATGCTAGTGACGGATGACAC 58.803 52.381 0.00 0.00 40.42 3.67
1835 1903 7.829706 AGTTCATTTATAAGTTCCCTGGAAGTC 59.170 37.037 6.72 0.00 36.84 3.01
1885 1953 6.983984 TCATCTTCTCTAGATCTTGATGCAG 58.016 40.000 7.34 4.63 41.78 4.41
2120 2188 5.016831 TCCTGACTTACTTCTGCTGATACA 58.983 41.667 0.00 0.00 0.00 2.29
2127 2195 5.992217 TCTCTTTTTCCTGACTTACTTCTGC 59.008 40.000 0.00 0.00 0.00 4.26
2234 2302 3.636300 TGCACCTTACTTCAGCATTTTGT 59.364 39.130 0.00 0.00 0.00 2.83
2331 2399 4.657013 GACAATTCCCTCTCCAAAAGACT 58.343 43.478 0.00 0.00 0.00 3.24
2519 2587 4.818534 ATTGGTGTCTGCTAATAATGCG 57.181 40.909 0.00 0.00 0.00 4.73
2575 2643 2.357637 CTCTCTAGGCCTTCAACTCGAG 59.642 54.545 12.58 11.84 0.00 4.04
2586 2654 1.335496 CTGTAACGAGCTCTCTAGGCC 59.665 57.143 12.85 0.00 0.00 5.19
2606 2674 5.880332 TGATACTTTCACATGGTTAGCTTCC 59.120 40.000 0.00 0.00 0.00 3.46
2628 2696 3.074390 AGACCAATGTCCTTGATGGTTGA 59.926 43.478 0.00 0.00 45.85 3.18
2666 2734 4.282068 CAAGTTTCGTGACCAATTCAGTG 58.718 43.478 0.00 0.00 33.71 3.66
2761 2834 6.493802 GGAATGGGAGGTAAAAAGAAGAGTTT 59.506 38.462 0.00 0.00 0.00 2.66
2763 2836 5.313506 AGGAATGGGAGGTAAAAAGAAGAGT 59.686 40.000 0.00 0.00 0.00 3.24
2769 2842 6.187682 ACATACAGGAATGGGAGGTAAAAAG 58.812 40.000 0.00 0.00 0.00 2.27
2772 2845 5.251932 TGAACATACAGGAATGGGAGGTAAA 59.748 40.000 0.00 0.00 0.00 2.01
2777 2850 5.413833 GCATATGAACATACAGGAATGGGAG 59.586 44.000 6.97 0.00 0.00 4.30
2779 2852 5.182570 CAGCATATGAACATACAGGAATGGG 59.817 44.000 6.97 0.00 0.00 4.00
2836 2910 9.567776 TCAATATCCTGTTCTTCTTTGTTAACA 57.432 29.630 3.59 3.59 0.00 2.41
2854 2928 3.266510 TGCACCTGTGAGTCAATATCC 57.733 47.619 0.51 0.00 0.00 2.59
2869 2943 4.215613 CCTTAACACTAGTTCCTTTGCACC 59.784 45.833 0.00 0.00 39.15 5.01
2904 2978 8.094798 TCTTTACCAGTAGCATTTTTGTACAG 57.905 34.615 0.00 0.00 0.00 2.74
2990 3064 9.525826 AAATTAGAGAGAAATCTCACCACATTT 57.474 29.630 12.65 7.93 45.21 2.32
3021 3095 5.377478 CACTTTACTTCAAAGAAGAGGGGT 58.623 41.667 13.23 4.66 45.62 4.95
3023 3097 4.821805 TGCACTTTACTTCAAAGAAGAGGG 59.178 41.667 13.23 3.32 45.62 4.30
3087 3161 2.383442 TAGGGGCTGGAGTATGTCTC 57.617 55.000 0.00 0.00 42.07 3.36
3088 3162 3.663136 TCTATAGGGGCTGGAGTATGTCT 59.337 47.826 0.00 0.00 0.00 3.41
3122 3196 2.504244 GAGGACTGACGAACGCGG 60.504 66.667 12.47 0.00 43.17 6.46
3124 3198 2.504244 CGGAGGACTGACGAACGC 60.504 66.667 0.00 0.00 0.00 4.84
3125 3199 2.504244 GCGGAGGACTGACGAACG 60.504 66.667 0.00 0.00 0.00 3.95
3152 3226 4.819761 TAAGGCCTGCTCTGCGCG 62.820 66.667 5.69 0.00 43.27 6.86
3153 3227 2.436646 TTAAGGCCTGCTCTGCGC 60.437 61.111 5.69 0.00 39.77 6.09
3154 3228 2.109126 GGTTAAGGCCTGCTCTGCG 61.109 63.158 5.69 0.00 0.00 5.18
3155 3229 0.609131 TTGGTTAAGGCCTGCTCTGC 60.609 55.000 5.69 0.00 0.00 4.26
3156 3230 1.168714 GTTGGTTAAGGCCTGCTCTG 58.831 55.000 5.69 0.00 0.00 3.35
3157 3231 1.003696 GAGTTGGTTAAGGCCTGCTCT 59.996 52.381 5.69 0.00 32.00 4.09
3158 3232 1.003696 AGAGTTGGTTAAGGCCTGCTC 59.996 52.381 5.69 5.94 33.53 4.26
3159 3233 1.068121 AGAGTTGGTTAAGGCCTGCT 58.932 50.000 5.69 0.00 0.00 4.24
3160 3234 1.168714 CAGAGTTGGTTAAGGCCTGC 58.831 55.000 5.69 0.00 0.00 4.85
3161 3235 1.168714 GCAGAGTTGGTTAAGGCCTG 58.831 55.000 5.69 0.00 0.00 4.85
3162 3236 0.771127 TGCAGAGTTGGTTAAGGCCT 59.229 50.000 0.00 0.00 0.00 5.19
3163 3237 1.616159 TTGCAGAGTTGGTTAAGGCC 58.384 50.000 0.00 0.00 0.00 5.19
3164 3238 3.942130 ATTTGCAGAGTTGGTTAAGGC 57.058 42.857 0.00 0.00 0.00 4.35
3165 3239 4.984161 CACAATTTGCAGAGTTGGTTAAGG 59.016 41.667 11.02 0.00 0.00 2.69
3166 3240 4.984161 CCACAATTTGCAGAGTTGGTTAAG 59.016 41.667 11.02 0.00 0.00 1.85
3167 3241 4.739137 GCCACAATTTGCAGAGTTGGTTAA 60.739 41.667 11.02 0.00 0.00 2.01
3168 3242 3.243704 GCCACAATTTGCAGAGTTGGTTA 60.244 43.478 11.02 0.00 0.00 2.85
3169 3243 2.483538 GCCACAATTTGCAGAGTTGGTT 60.484 45.455 11.02 0.00 0.00 3.67
3170 3244 1.069049 GCCACAATTTGCAGAGTTGGT 59.931 47.619 11.02 0.00 0.00 3.67
3171 3245 1.606224 GGCCACAATTTGCAGAGTTGG 60.606 52.381 0.00 7.00 0.00 3.77
3172 3246 1.342174 AGGCCACAATTTGCAGAGTTG 59.658 47.619 5.01 6.33 0.00 3.16
3173 3247 1.708341 AGGCCACAATTTGCAGAGTT 58.292 45.000 5.01 0.00 0.00 3.01
3174 3248 1.708341 AAGGCCACAATTTGCAGAGT 58.292 45.000 5.01 0.00 0.00 3.24
3175 3249 3.940209 TTAAGGCCACAATTTGCAGAG 57.060 42.857 5.01 0.00 0.00 3.35
3176 3250 3.831333 TGATTAAGGCCACAATTTGCAGA 59.169 39.130 5.01 0.00 0.00 4.26
3177 3251 4.191033 TGATTAAGGCCACAATTTGCAG 57.809 40.909 5.01 0.00 0.00 4.41
3178 3252 4.040217 AGTTGATTAAGGCCACAATTTGCA 59.960 37.500 5.01 0.00 0.00 4.08
3179 3253 4.389687 CAGTTGATTAAGGCCACAATTTGC 59.610 41.667 5.01 0.00 0.00 3.68
3180 3254 4.931002 CCAGTTGATTAAGGCCACAATTTG 59.069 41.667 5.01 6.38 0.00 2.32
3181 3255 4.837860 TCCAGTTGATTAAGGCCACAATTT 59.162 37.500 5.01 0.00 0.00 1.82
3182 3256 4.415596 TCCAGTTGATTAAGGCCACAATT 58.584 39.130 5.01 0.00 0.00 2.32
3183 3257 4.046286 TCCAGTTGATTAAGGCCACAAT 57.954 40.909 5.01 3.01 0.00 2.71
3184 3258 3.517296 TCCAGTTGATTAAGGCCACAA 57.483 42.857 5.01 0.00 0.00 3.33
3185 3259 3.737559 ATCCAGTTGATTAAGGCCACA 57.262 42.857 5.01 0.00 0.00 4.17
3186 3260 3.429410 GCAATCCAGTTGATTAAGGCCAC 60.429 47.826 5.01 0.00 41.85 5.01
3187 3261 2.760092 GCAATCCAGTTGATTAAGGCCA 59.240 45.455 5.01 0.00 41.85 5.36
3188 3262 2.101415 GGCAATCCAGTTGATTAAGGCC 59.899 50.000 0.00 0.00 41.85 5.19
3189 3263 2.223572 CGGCAATCCAGTTGATTAAGGC 60.224 50.000 0.00 0.00 41.85 4.35
3190 3264 2.223572 GCGGCAATCCAGTTGATTAAGG 60.224 50.000 0.00 0.00 41.85 2.69
3191 3265 2.684881 AGCGGCAATCCAGTTGATTAAG 59.315 45.455 1.45 0.00 41.85 1.85
3192 3266 2.682856 GAGCGGCAATCCAGTTGATTAA 59.317 45.455 1.45 0.00 41.85 1.40
3193 3267 2.288666 GAGCGGCAATCCAGTTGATTA 58.711 47.619 1.45 0.00 41.85 1.75
3194 3268 1.098050 GAGCGGCAATCCAGTTGATT 58.902 50.000 1.45 0.00 44.67 2.57
3195 3269 0.749454 GGAGCGGCAATCCAGTTGAT 60.749 55.000 1.45 0.00 40.37 2.57
3196 3270 1.377202 GGAGCGGCAATCCAGTTGA 60.377 57.895 1.45 0.00 40.37 3.18
3197 3271 2.753966 CGGAGCGGCAATCCAGTTG 61.754 63.158 1.45 0.00 40.90 3.16
3198 3272 2.436646 CGGAGCGGCAATCCAGTT 60.437 61.111 1.45 0.00 36.57 3.16
3238 3312 4.515404 CGTGTTCGGATTCCCTCC 57.485 61.111 0.00 0.00 41.07 4.30
3254 3388 2.178912 TTTCCTGTCAACTTAGGCCG 57.821 50.000 0.00 0.00 34.00 6.13
3255 3389 3.487372 AGTTTTCCTGTCAACTTAGGCC 58.513 45.455 0.00 0.00 34.00 5.19
3256 3390 4.578928 TGAAGTTTTCCTGTCAACTTAGGC 59.421 41.667 0.00 0.00 42.15 3.93
3366 3500 2.849294 AAAGGAGAGGAGAACTGCAC 57.151 50.000 0.00 0.00 0.00 4.57
3368 3502 2.419436 GGCTAAAGGAGAGGAGAACTGC 60.419 54.545 0.00 0.00 0.00 4.40
3374 3508 3.025322 TGAGAGGCTAAAGGAGAGGAG 57.975 52.381 0.00 0.00 0.00 3.69
3387 3521 2.434428 CCCATGATGCTAATGAGAGGC 58.566 52.381 0.00 0.00 0.00 4.70
3411 3545 1.929836 GCACTAACTTCAGAGCATCCG 59.070 52.381 0.00 0.00 33.66 4.18
3438 3572 0.392193 AGTTCTGCCAGAGCCAATCG 60.392 55.000 4.81 0.00 38.69 3.34
3439 3573 1.471684 CAAGTTCTGCCAGAGCCAATC 59.528 52.381 4.81 0.00 38.69 2.67
3448 3582 2.115910 CCAGCCCAAGTTCTGCCA 59.884 61.111 0.00 0.00 0.00 4.92
3451 3585 1.114722 TTTGCCCAGCCCAAGTTCTG 61.115 55.000 0.00 0.00 0.00 3.02
3468 3602 7.631510 ATGGCTGGGGCTTAATAAAATATTT 57.368 32.000 0.00 0.00 38.73 1.40
3471 3605 7.419634 GGAAAATGGCTGGGGCTTAATAAAATA 60.420 37.037 0.00 0.00 38.73 1.40
3472 3606 5.974156 AAATGGCTGGGGCTTAATAAAAT 57.026 34.783 0.00 0.00 38.73 1.82
3487 3637 6.507023 CGAATATTTTGCTAGGAAAATGGCT 58.493 36.000 32.97 21.49 36.44 4.75
3521 3672 1.514678 TTCGGCAAAATGTCAGCGCT 61.515 50.000 2.64 2.64 0.00 5.92
3527 3678 1.987770 CTGCATGTTCGGCAAAATGTC 59.012 47.619 0.00 0.00 41.39 3.06
3536 3687 1.019278 AGGTAACGCTGCATGTTCGG 61.019 55.000 7.65 0.00 46.39 4.30
3582 3735 1.153188 TGCGGGTATGCATGGACAG 60.153 57.895 10.16 1.24 40.62 3.51
3636 3805 6.591834 GCCTGAGTACAACATATCATGGATAC 59.408 42.308 0.00 0.00 33.60 2.24
3637 3806 6.572314 CGCCTGAGTACAACATATCATGGATA 60.572 42.308 0.00 0.00 33.60 2.59
3652 3821 0.533032 AGCTTTCTCCGCCTGAGTAC 59.467 55.000 0.00 0.00 42.12 2.73
3654 3823 0.036858 GAAGCTTTCTCCGCCTGAGT 60.037 55.000 0.00 0.00 42.12 3.41
3671 3842 3.432186 CCTTGCCATCGATAAGGTCTGAA 60.432 47.826 14.80 0.00 36.94 3.02
3672 3843 2.103094 CCTTGCCATCGATAAGGTCTGA 59.897 50.000 14.80 0.00 36.94 3.27
3674 3845 2.918712 CCTTGCCATCGATAAGGTCT 57.081 50.000 14.80 0.00 36.94 3.85
3686 3857 3.551496 CTCCGCTTCCACCTTGCCA 62.551 63.158 0.00 0.00 0.00 4.92
3728 3905 3.014085 GCCCTCGTCGGTGGAATCA 62.014 63.158 5.30 0.00 0.00 2.57
3871 4048 0.882927 TCAAAGGAAACGTCAGGCCG 60.883 55.000 0.00 0.00 0.00 6.13
3979 4221 1.827969 CTTGAGTAGGAGGTGTCCCAG 59.172 57.143 0.00 0.00 45.26 4.45
3993 4235 1.250840 GCCCGCCATTTTCCTTGAGT 61.251 55.000 0.00 0.00 0.00 3.41
3994 4236 0.967380 AGCCCGCCATTTTCCTTGAG 60.967 55.000 0.00 0.00 0.00 3.02
3997 4239 0.324645 ATCAGCCCGCCATTTTCCTT 60.325 50.000 0.00 0.00 0.00 3.36
4048 4300 3.628487 TCACAAGGAGGTTAACAAAACCG 59.372 43.478 8.10 0.00 44.82 4.44
4077 4335 1.979855 ATGTTGCTGCAGTACACCAA 58.020 45.000 20.99 11.67 0.00 3.67
4084 4346 1.882912 TCTTCGAATGTTGCTGCAGT 58.117 45.000 16.64 0.00 0.00 4.40
4095 4357 5.983540 AGGCTGAAATACTCTTCTTCGAAT 58.016 37.500 0.00 0.00 0.00 3.34
4114 4376 3.165875 TGAAGACTAGCACAGTTAGGCT 58.834 45.455 0.00 0.00 43.94 4.58
4115 4377 3.594603 TGAAGACTAGCACAGTTAGGC 57.405 47.619 0.00 0.00 37.72 3.93
4116 4378 5.724328 TCAATGAAGACTAGCACAGTTAGG 58.276 41.667 0.00 0.00 37.72 2.69
4117 4379 7.763528 AGAATCAATGAAGACTAGCACAGTTAG 59.236 37.037 0.00 0.00 37.72 2.34
4118 4380 7.615403 AGAATCAATGAAGACTAGCACAGTTA 58.385 34.615 0.00 0.00 37.72 2.24
4119 4381 6.471146 AGAATCAATGAAGACTAGCACAGTT 58.529 36.000 0.00 0.00 37.72 3.16
4120 4382 6.047511 AGAATCAATGAAGACTAGCACAGT 57.952 37.500 0.00 0.00 41.47 3.55
4131 4393 6.956202 AGCCCAGAAATAGAATCAATGAAG 57.044 37.500 0.00 0.00 0.00 3.02
4315 4588 1.444553 GAAGGACGTCTGCGACAGG 60.445 63.158 16.46 0.00 42.00 4.00
4353 4633 3.552384 AACAGCCGGTTCGTGGGA 61.552 61.111 1.90 0.00 33.35 4.37
4362 4642 3.052082 CAGCAGACCAACAGCCGG 61.052 66.667 0.00 0.00 0.00 6.13
4638 4923 4.516195 GAGTTCCTCGCCGGCCTC 62.516 72.222 23.46 16.59 0.00 4.70
4764 5049 1.601412 GCAAGCTCAAACACAAGCCTC 60.601 52.381 0.00 0.00 39.39 4.70
4772 5059 3.659092 CCGCCGCAAGCTCAAACA 61.659 61.111 0.00 0.00 40.39 2.83
4773 5060 3.353836 TCCGCCGCAAGCTCAAAC 61.354 61.111 0.00 0.00 40.39 2.93
4774 5061 3.353836 GTCCGCCGCAAGCTCAAA 61.354 61.111 0.00 0.00 40.39 2.69


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

AutoCloner maintained by Alex Coulton.