Multiple sequence alignment - TraesCS4B01G278400

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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 TraesCS4B01G278400 chr4B 100.000 3369 0 0 1 3369 561020445 561023813 0.000000e+00 6222.0
1 TraesCS4B01G278400 chr4D 90.746 1837 152 12 853 2680 390755309 390753482 0.000000e+00 2435.0
2 TraesCS4B01G278400 chr4D 90.622 1834 155 7 853 2677 448612939 448614764 0.000000e+00 2418.0
3 TraesCS4B01G278400 chr4D 89.913 1606 147 7 902 2502 448502796 448504391 0.000000e+00 2054.0
4 TraesCS4B01G278400 chr4D 89.516 1612 148 10 902 2502 390860125 390858524 0.000000e+00 2021.0
5 TraesCS4B01G278400 chr4D 87.055 1321 145 18 1236 2543 448152814 448154121 0.000000e+00 1469.0
6 TraesCS4B01G278400 chr4D 91.858 393 32 0 1494 1886 448621859 448622251 1.770000e-152 549.0
7 TraesCS4B01G278400 chr4D 91.250 400 33 2 1494 1891 390732398 390731999 8.220000e-151 544.0
8 TraesCS4B01G278400 chr4D 91.349 393 34 0 1494 1886 390669230 390668838 3.820000e-149 538.0
9 TraesCS4B01G278400 chr4D 92.056 214 15 2 947 1160 448152595 448152806 1.960000e-77 300.0
10 TraesCS4B01G278400 chr4D 85.235 149 19 3 2526 2674 85876574 85876719 2.090000e-32 150.0
11 TraesCS4B01G278400 chr4D 91.589 107 7 2 718 822 390860257 390860151 2.710000e-31 147.0
12 TraesCS4B01G278400 chr4D 91.589 107 7 2 718 822 448502664 448502770 2.710000e-31 147.0
13 TraesCS4B01G278400 chr4D 91.765 85 7 0 635 719 448148168 448148252 5.910000e-23 119.0
14 TraesCS4B01G278400 chr4D 96.429 56 2 0 664 719 390860340 390860285 3.580000e-15 93.5
15 TraesCS4B01G278400 chr4D 94.915 59 3 0 661 719 448502578 448502636 3.580000e-15 93.5
16 TraesCS4B01G278400 chr4A 89.134 1859 160 20 848 2680 19167350 19165508 0.000000e+00 2276.0
17 TraesCS4B01G278400 chr4A 82.950 522 62 22 2675 3184 720557057 720556551 2.380000e-121 446.0
18 TraesCS4B01G278400 chr4A 82.375 522 65 22 2675 3184 719413588 719414094 2.400000e-116 429.0
19 TraesCS4B01G278400 chr4A 95.000 100 5 0 620 719 19167581 19167482 1.250000e-34 158.0
20 TraesCS4B01G278400 chr4A 82.424 165 24 4 2515 2677 521058452 521058613 4.530000e-29 139.0
21 TraesCS4B01G278400 chr6B 98.311 533 9 0 1 533 142803286 142803818 0.000000e+00 935.0
22 TraesCS4B01G278400 chr6B 97.186 533 15 0 1 533 207153339 207153871 0.000000e+00 902.0
23 TraesCS4B01G278400 chr6B 84.375 160 17 6 2518 2674 145548144 145548298 2.090000e-32 150.0
24 TraesCS4B01G278400 chr6B 100.000 28 0 0 692 719 155750105 155750078 6.000000e-03 52.8
25 TraesCS4B01G278400 chr1B 97.561 533 13 0 1 533 395265160 395265692 0.000000e+00 913.0
26 TraesCS4B01G278400 chr5B 97.373 533 14 0 1 533 35185547 35185015 0.000000e+00 907.0
27 TraesCS4B01G278400 chr5B 100.000 28 0 0 692 719 519235624 519235651 6.000000e-03 52.8
28 TraesCS4B01G278400 chr2D 97.186 533 15 0 1 533 203046322 203045790 0.000000e+00 902.0
29 TraesCS4B01G278400 chr3B 96.992 532 16 0 2 533 775663017 775662486 0.000000e+00 894.0
30 TraesCS4B01G278400 chr1A 96.811 533 17 0 1 533 432967360 432967892 0.000000e+00 891.0
31 TraesCS4B01G278400 chr1A 95.294 85 4 0 539 623 581857497 581857581 5.860000e-28 135.0
32 TraesCS4B01G278400 chr1A 91.111 90 7 1 531 620 581856703 581856615 1.640000e-23 121.0
33 TraesCS4B01G278400 chr3D 96.623 533 18 0 1 533 397784706 397784174 0.000000e+00 885.0
34 TraesCS4B01G278400 chr3D 100.000 32 0 0 577 608 83702705 83702674 3.630000e-05 60.2
35 TraesCS4B01G278400 chr1D 96.623 533 18 0 1 533 62578413 62577881 0.000000e+00 885.0
36 TraesCS4B01G278400 chr1D 80.254 709 103 34 2683 3369 56885958 56885265 1.800000e-137 499.0
37 TraesCS4B01G278400 chr1D 85.259 502 51 18 2700 3193 457174285 457173799 2.330000e-136 496.0
38 TraesCS4B01G278400 chr1D 83.890 509 59 19 2700 3194 253100985 253100486 6.580000e-127 464.0
39 TraesCS4B01G278400 chr7D 84.325 504 57 17 2700 3191 598590008 598590501 1.090000e-129 473.0
40 TraesCS4B01G278400 chr6D 83.768 499 61 11 2700 3188 89811715 89812203 3.960000e-124 455.0
41 TraesCS4B01G278400 chr5D 84.114 491 55 17 2708 3186 511614475 511613996 1.430000e-123 453.0
42 TraesCS4B01G278400 chr2B 83.845 489 55 20 2700 3176 40458960 40458484 8.580000e-121 444.0
43 TraesCS4B01G278400 chrUn 82.759 522 63 22 2675 3184 51101144 51100638 1.110000e-119 440.0
44 TraesCS4B01G278400 chr7A 84.146 164 22 3 2516 2677 720003305 720003466 4.500000e-34 156.0
45 TraesCS4B01G278400 chr2A 84.472 161 22 2 2518 2677 409643987 409644145 4.500000e-34 156.0
46 TraesCS4B01G278400 chr2A 83.234 167 21 5 2511 2676 66805782 66805942 2.710000e-31 147.0
47 TraesCS4B01G278400 chr2A 93.258 89 6 0 532 620 410869948 410869860 7.580000e-27 132.0
48 TraesCS4B01G278400 chr2A 95.181 83 4 0 539 621 410870738 410870820 7.580000e-27 132.0
49 TraesCS4B01G278400 chr5A 94.382 89 5 0 532 620 579850024 579849936 1.630000e-28 137.0
50 TraesCS4B01G278400 chr5A 92.683 82 6 0 539 620 579850820 579850901 5.910000e-23 119.0
51 TraesCS4B01G278400 chr6A 93.258 89 6 0 532 620 154034439 154034351 7.580000e-27 132.0
52 TraesCS4B01G278400 chr6A 93.902 82 5 0 539 620 154035234 154035315 1.270000e-24 124.0
53 TraesCS4B01G278400 chr7B 100.000 28 0 0 692 719 411324263 411324236 6.000000e-03 52.8


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 TraesCS4B01G278400 chr4B 561020445 561023813 3368 False 6222.000000 6222 100.000000 1 3369 1 chr4B.!!$F1 3368
1 TraesCS4B01G278400 chr4D 390753482 390755309 1827 True 2435.000000 2435 90.746000 853 2680 1 chr4D.!!$R3 1827
2 TraesCS4B01G278400 chr4D 448612939 448614764 1825 False 2418.000000 2418 90.622000 853 2677 1 chr4D.!!$F3 1824
3 TraesCS4B01G278400 chr4D 448152595 448154121 1526 False 884.500000 1469 89.555500 947 2543 2 chr4D.!!$F5 1596
4 TraesCS4B01G278400 chr4D 448502578 448504391 1813 False 764.833333 2054 92.139000 661 2502 3 chr4D.!!$F6 1841
5 TraesCS4B01G278400 chr4D 390858524 390860340 1816 True 753.833333 2021 92.511333 664 2502 3 chr4D.!!$R4 1838
6 TraesCS4B01G278400 chr4A 19165508 19167581 2073 True 1217.000000 2276 92.067000 620 2680 2 chr4A.!!$R2 2060
7 TraesCS4B01G278400 chr4A 720556551 720557057 506 True 446.000000 446 82.950000 2675 3184 1 chr4A.!!$R1 509
8 TraesCS4B01G278400 chr4A 719413588 719414094 506 False 429.000000 429 82.375000 2675 3184 1 chr4A.!!$F2 509
9 TraesCS4B01G278400 chr6B 142803286 142803818 532 False 935.000000 935 98.311000 1 533 1 chr6B.!!$F1 532
10 TraesCS4B01G278400 chr6B 207153339 207153871 532 False 902.000000 902 97.186000 1 533 1 chr6B.!!$F3 532
11 TraesCS4B01G278400 chr1B 395265160 395265692 532 False 913.000000 913 97.561000 1 533 1 chr1B.!!$F1 532
12 TraesCS4B01G278400 chr5B 35185015 35185547 532 True 907.000000 907 97.373000 1 533 1 chr5B.!!$R1 532
13 TraesCS4B01G278400 chr2D 203045790 203046322 532 True 902.000000 902 97.186000 1 533 1 chr2D.!!$R1 532
14 TraesCS4B01G278400 chr3B 775662486 775663017 531 True 894.000000 894 96.992000 2 533 1 chr3B.!!$R1 531
15 TraesCS4B01G278400 chr1A 432967360 432967892 532 False 891.000000 891 96.811000 1 533 1 chr1A.!!$F1 532
16 TraesCS4B01G278400 chr3D 397784174 397784706 532 True 885.000000 885 96.623000 1 533 1 chr3D.!!$R2 532
17 TraesCS4B01G278400 chr1D 62577881 62578413 532 True 885.000000 885 96.623000 1 533 1 chr1D.!!$R2 532
18 TraesCS4B01G278400 chr1D 56885265 56885958 693 True 499.000000 499 80.254000 2683 3369 1 chr1D.!!$R1 686
19 TraesCS4B01G278400 chrUn 51100638 51101144 506 True 440.000000 440 82.759000 2675 3184 1 chrUn.!!$R1 509

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
601 602 0.179018 ATAATTCGTGCAGGGAGCCC 60.179 55.0 6.56 0.0 44.83 5.19 F
1835 1956 0.313043 CGTTGACGACAGGGTGTACT 59.687 55.0 0.00 0.0 43.02 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2189 0.037605 AGAAAGCGGTAGGTGAACGG 60.038 55.0 0.00 0.0 0.0 4.44 R
2985 3128 0.041833 AAGACTCTCTAGGGCAGCCA 59.958 55.0 15.19 0.0 0.0 4.75 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
55 56 4.004982 GAGAAGCGTGGTTGGGTAAATTA 58.995 43.478 0.00 0.00 0.00 1.40
117 118 3.545703 CCACACCTCTTCTTCAAGTGTT 58.454 45.455 0.00 0.00 39.56 3.32
156 157 6.516527 GCTTTGGAGATCTATCATCGAGAAGT 60.517 42.308 0.00 0.00 0.00 3.01
287 288 1.203287 CTCGTCATGCTCACCTCTTGA 59.797 52.381 0.00 0.00 0.00 3.02
550 551 4.871933 AAAAGGTAATTGGCTCACAAGG 57.128 40.909 0.00 0.00 43.48 3.61
551 552 3.806949 AAGGTAATTGGCTCACAAGGA 57.193 42.857 0.00 0.00 43.48 3.36
552 553 3.073274 AGGTAATTGGCTCACAAGGAC 57.927 47.619 0.00 0.00 43.48 3.85
553 554 2.375174 AGGTAATTGGCTCACAAGGACA 59.625 45.455 0.00 0.00 43.48 4.02
554 555 2.488153 GGTAATTGGCTCACAAGGACAC 59.512 50.000 0.00 0.00 43.48 3.67
555 556 2.363306 AATTGGCTCACAAGGACACA 57.637 45.000 0.00 0.00 43.48 3.72
556 557 2.592102 ATTGGCTCACAAGGACACAT 57.408 45.000 0.00 0.00 43.48 3.21
557 558 1.608055 TTGGCTCACAAGGACACATG 58.392 50.000 0.00 0.00 33.18 3.21
558 559 0.250858 TGGCTCACAAGGACACATGG 60.251 55.000 0.00 0.00 0.00 3.66
559 560 1.589716 GGCTCACAAGGACACATGGC 61.590 60.000 0.00 0.00 0.00 4.40
560 561 1.915614 GCTCACAAGGACACATGGCG 61.916 60.000 0.00 0.00 0.00 5.69
561 562 0.320683 CTCACAAGGACACATGGCGA 60.321 55.000 0.00 0.00 0.00 5.54
562 563 0.324614 TCACAAGGACACATGGCGAT 59.675 50.000 0.00 0.00 0.00 4.58
563 564 0.729116 CACAAGGACACATGGCGATC 59.271 55.000 0.00 0.00 0.00 3.69
564 565 0.615331 ACAAGGACACATGGCGATCT 59.385 50.000 0.00 0.00 0.00 2.75
565 566 1.003580 ACAAGGACACATGGCGATCTT 59.996 47.619 0.00 0.00 0.00 2.40
566 567 2.086869 CAAGGACACATGGCGATCTTT 58.913 47.619 0.00 0.00 0.00 2.52
567 568 2.489329 CAAGGACACATGGCGATCTTTT 59.511 45.455 0.00 0.00 0.00 2.27
568 569 3.627395 AGGACACATGGCGATCTTTTA 57.373 42.857 0.00 0.00 0.00 1.52
569 570 4.156455 AGGACACATGGCGATCTTTTAT 57.844 40.909 0.00 0.00 0.00 1.40
570 571 4.526970 AGGACACATGGCGATCTTTTATT 58.473 39.130 0.00 0.00 0.00 1.40
571 572 4.336433 AGGACACATGGCGATCTTTTATTG 59.664 41.667 0.00 0.00 0.00 1.90
572 573 4.498009 GGACACATGGCGATCTTTTATTGG 60.498 45.833 0.00 0.00 0.00 3.16
573 574 3.181487 ACACATGGCGATCTTTTATTGGC 60.181 43.478 0.00 0.00 0.00 4.52
574 575 2.362077 ACATGGCGATCTTTTATTGGCC 59.638 45.455 0.00 0.00 40.88 5.36
575 576 1.398692 TGGCGATCTTTTATTGGCCC 58.601 50.000 0.00 0.00 39.78 5.80
576 577 1.064017 TGGCGATCTTTTATTGGCCCT 60.064 47.619 0.00 0.00 39.78 5.19
577 578 1.338020 GGCGATCTTTTATTGGCCCTG 59.662 52.381 0.00 0.00 34.54 4.45
578 579 1.269257 GCGATCTTTTATTGGCCCTGC 60.269 52.381 0.00 0.00 0.00 4.85
579 580 2.023673 CGATCTTTTATTGGCCCTGCA 58.976 47.619 0.00 0.00 0.00 4.41
580 581 2.223572 CGATCTTTTATTGGCCCTGCAC 60.224 50.000 0.00 0.00 0.00 4.57
581 582 2.300956 TCTTTTATTGGCCCTGCACA 57.699 45.000 0.00 0.00 0.00 4.57
582 583 2.603021 TCTTTTATTGGCCCTGCACAA 58.397 42.857 0.00 0.00 0.00 3.33
583 584 3.172339 TCTTTTATTGGCCCTGCACAAT 58.828 40.909 0.00 5.69 40.21 2.71
584 585 4.348486 TCTTTTATTGGCCCTGCACAATA 58.652 39.130 0.00 3.95 38.24 1.90
585 586 4.774726 TCTTTTATTGGCCCTGCACAATAA 59.225 37.500 13.37 13.37 43.76 1.40
586 587 5.424895 TCTTTTATTGGCCCTGCACAATAAT 59.575 36.000 16.48 0.00 44.40 1.28
587 588 5.690464 TTTATTGGCCCTGCACAATAATT 57.310 34.783 16.48 0.00 44.40 1.40
588 589 3.825143 ATTGGCCCTGCACAATAATTC 57.175 42.857 0.00 0.00 35.67 2.17
589 590 1.102154 TGGCCCTGCACAATAATTCG 58.898 50.000 0.00 0.00 0.00 3.34
590 591 1.102978 GGCCCTGCACAATAATTCGT 58.897 50.000 0.00 0.00 0.00 3.85
591 592 1.202290 GGCCCTGCACAATAATTCGTG 60.202 52.381 0.00 0.00 36.18 4.35
598 599 3.680642 CACAATAATTCGTGCAGGGAG 57.319 47.619 6.56 0.00 0.00 4.30
599 600 2.017049 ACAATAATTCGTGCAGGGAGC 58.983 47.619 6.56 0.00 45.96 4.70
600 601 1.334869 CAATAATTCGTGCAGGGAGCC 59.665 52.381 6.56 0.00 44.83 4.70
601 602 0.179018 ATAATTCGTGCAGGGAGCCC 60.179 55.000 6.56 0.00 44.83 5.19
611 612 4.486503 GGGAGCCCTGCAGCTGAG 62.487 72.222 20.43 11.85 45.15 3.35
616 617 4.355720 CCCTGCAGCTGAGCCCAA 62.356 66.667 20.43 0.00 0.00 4.12
617 618 3.060615 CCTGCAGCTGAGCCCAAC 61.061 66.667 20.43 0.00 0.00 3.77
618 619 3.060615 CTGCAGCTGAGCCCAACC 61.061 66.667 20.43 0.00 0.00 3.77
722 778 2.010043 GCGTTGGATGGATGGTTACGT 61.010 52.381 0.00 0.00 0.00 3.57
740 796 3.334751 CGTCGCGGTTGCAGACAA 61.335 61.111 6.13 0.00 41.50 3.18
808 867 2.159226 CGAGACTTGGATGGGTACTGAC 60.159 54.545 0.00 0.00 0.00 3.51
809 868 2.168728 GAGACTTGGATGGGTACTGACC 59.831 54.545 0.00 0.00 46.13 4.02
820 879 3.772060 GGTACTGACCGTATTTCGACT 57.228 47.619 0.00 0.00 42.86 4.18
821 880 4.102035 GGTACTGACCGTATTTCGACTT 57.898 45.455 0.00 0.00 42.86 3.01
822 881 4.488879 GGTACTGACCGTATTTCGACTTT 58.511 43.478 0.00 0.00 42.86 2.66
823 882 4.925646 GGTACTGACCGTATTTCGACTTTT 59.074 41.667 0.00 0.00 42.86 2.27
824 883 5.406477 GGTACTGACCGTATTTCGACTTTTT 59.594 40.000 0.00 0.00 42.86 1.94
867 926 3.599343 TCGACTTGGATGGTTGATTCAG 58.401 45.455 0.00 0.00 0.00 3.02
890 953 7.119407 TCAGCTGGTCGTTCTATATATACTGAC 59.881 40.741 15.13 0.00 0.00 3.51
917 1016 1.538135 ACGTAGGGGGAGCAAAGGT 60.538 57.895 0.00 0.00 0.00 3.50
935 1034 0.533308 GTGCAAGAACCCCACGTACA 60.533 55.000 0.00 0.00 0.00 2.90
943 1042 3.383825 AGAACCCCACGTACAAGCTATAG 59.616 47.826 0.00 0.00 0.00 1.31
999 1102 2.432628 CGAGAACAGGTCGCCACC 60.433 66.667 0.00 0.00 44.19 4.61
1048 1151 2.413351 CGTCGGCGATGTGAGGAT 59.587 61.111 20.53 0.00 41.33 3.24
1135 1242 0.721718 GATGCACGGTGTACAAGCTC 59.278 55.000 10.24 0.00 0.00 4.09
1269 1388 2.928361 CGACCAGTTCGTGTGCAC 59.072 61.111 10.75 10.75 43.24 4.57
1305 1424 1.967597 GCTTTCTACAAGGACGCGGC 61.968 60.000 12.47 7.53 0.00 6.53
1366 1485 2.363975 GGTGACCGTATGCCCTCCA 61.364 63.158 0.00 0.00 0.00 3.86
1368 1487 1.610967 TGACCGTATGCCCTCCACA 60.611 57.895 0.00 0.00 0.00 4.17
1447 1566 1.211190 GACCGACTACGACCGCTTT 59.789 57.895 0.00 0.00 42.66 3.51
1468 1587 7.430441 GCTTTAACTACAAATTTGTTCCCTCA 58.570 34.615 27.66 8.91 42.35 3.86
1565 1684 1.153289 CTGCCCATCCTTGTCTCGG 60.153 63.158 0.00 0.00 0.00 4.63
1593 1712 2.140138 TGCATCCCGACGGATCCAT 61.140 57.895 17.49 0.00 46.77 3.41
1597 1716 1.824852 CATCCCGACGGATCCATCATA 59.175 52.381 17.49 0.00 46.77 2.15
1729 1848 3.716195 CTGGATGCGTGGGTGGGA 61.716 66.667 0.00 0.00 0.00 4.37
1774 1895 0.390472 TCGCCGTGTGCAATGTCATA 60.390 50.000 0.00 0.00 41.33 2.15
1788 1909 0.933509 GTCATATCACCCGACGACGC 60.934 60.000 0.64 0.00 38.29 5.19
1814 1935 1.224592 GAATGCCCGACCTGGACAT 59.775 57.895 0.00 0.00 42.00 3.06
1819 1940 2.656069 CCCGACCTGGACATCCGTT 61.656 63.158 0.00 0.00 42.00 4.44
1822 1943 0.736325 CGACCTGGACATCCGTTGAC 60.736 60.000 0.00 0.00 39.43 3.18
1835 1956 0.313043 CGTTGACGACAGGGTGTACT 59.687 55.000 0.00 0.00 43.02 2.73
1882 2003 1.555075 GTGAGCCTCACTTACATGGGA 59.445 52.381 17.57 0.00 43.73 4.37
1957 2078 3.837578 GAGTCCAGGACGCGGATA 58.162 61.111 14.32 0.00 37.67 2.59
2018 2139 3.998672 GTGAGGTTCGGGCGGTGA 61.999 66.667 0.00 0.00 0.00 4.02
2068 2189 1.270550 CACTGGGAGTTGGAATGTTGC 59.729 52.381 0.00 0.00 0.00 4.17
2118 2239 3.139077 CCTGTTGCCTACGTTTCTCTTT 58.861 45.455 0.00 0.00 0.00 2.52
2123 2244 4.707030 TGCCTACGTTTCTCTTTATCGA 57.293 40.909 0.00 0.00 0.00 3.59
2128 2249 1.587034 CGTTTCTCTTTATCGACGGCC 59.413 52.381 0.00 0.00 0.00 6.13
2152 2273 1.202770 GCTGTTCCGGTGCCCTAATAT 60.203 52.381 0.00 0.00 0.00 1.28
2180 2301 2.742589 CCCTTAGCAAGACTTTTCGACC 59.257 50.000 0.00 0.00 0.00 4.79
2192 2313 7.565323 AGACTTTTCGACCGTCTACTATAAT 57.435 36.000 8.26 0.00 36.33 1.28
2275 2396 0.389391 CGCTAGGTGATCCACGGATT 59.611 55.000 0.00 0.00 34.83 3.01
2439 2572 4.056092 GAGGAATCCTCGTATCCGTTTT 57.944 45.455 14.22 0.00 41.08 2.43
2467 2601 3.258228 CCGCTCAAACAACCAAAAACTT 58.742 40.909 0.00 0.00 0.00 2.66
2469 2603 3.305897 CGCTCAAACAACCAAAAACTTCC 59.694 43.478 0.00 0.00 0.00 3.46
2495 2629 2.608261 CCTGTGAGTCCGAGACTTGAAC 60.608 54.545 7.80 7.75 43.53 3.18
2521 2655 6.149807 GGACACCGACCATATTTTGACTTTTA 59.850 38.462 0.00 0.00 0.00 1.52
2523 2657 8.117813 ACACCGACCATATTTTGACTTTTATT 57.882 30.769 0.00 0.00 0.00 1.40
2524 2658 8.581578 ACACCGACCATATTTTGACTTTTATTT 58.418 29.630 0.00 0.00 0.00 1.40
2596 2730 2.684374 ACATGAATGCATACACGCACAT 59.316 40.909 0.00 0.00 46.56 3.21
2597 2731 3.129113 ACATGAATGCATACACGCACATT 59.871 39.130 0.00 0.00 46.56 2.71
2601 2735 4.815846 TGAATGCATACACGCACATTCTAT 59.184 37.500 0.00 0.00 46.56 1.98
2603 2737 3.130633 TGCATACACGCACATTCTATCC 58.869 45.455 0.00 0.00 36.86 2.59
2605 2739 2.502213 TACACGCACATTCTATCCCG 57.498 50.000 0.00 0.00 0.00 5.14
2610 2745 2.288457 ACGCACATTCTATCCCGATGAG 60.288 50.000 0.00 0.00 0.00 2.90
2630 2765 1.679139 CATCTCCGAGAGACTGAGCT 58.321 55.000 4.07 0.00 41.76 4.09
2635 2770 1.153862 CGAGAGACTGAGCTGGCAC 60.154 63.158 0.00 0.00 0.00 5.01
2657 2792 6.904011 GCACATCATCTTGAGATTTTACGAAG 59.096 38.462 0.00 0.00 31.21 3.79
2658 2793 7.413438 GCACATCATCTTGAGATTTTACGAAGT 60.413 37.037 0.00 0.00 37.29 3.01
2677 2812 1.370172 CATCGTAGGCGCCTCGTAC 60.370 63.158 36.73 25.13 38.14 3.67
2680 2815 2.178890 CGTAGGCGCCTCGTACTCT 61.179 63.158 36.73 9.44 34.73 3.24
2681 2816 1.648174 GTAGGCGCCTCGTACTCTC 59.352 63.158 36.73 10.37 34.23 3.20
2747 2885 2.656947 TTCTGGCTTGCCTTGTACTT 57.343 45.000 13.18 0.00 0.00 2.24
2765 2903 9.862371 CTTGTACTTCAAGTAGATCATGTACTT 57.138 33.333 1.26 1.26 45.89 2.24
2781 2919 7.993101 TCATGTACTTCTATATATACGCCCAC 58.007 38.462 0.00 0.00 0.00 4.61
2824 2962 2.993863 ACTATTCCACCAAACCCCTCTT 59.006 45.455 0.00 0.00 0.00 2.85
2827 2965 1.529744 TCCACCAAACCCCTCTTTCT 58.470 50.000 0.00 0.00 0.00 2.52
2849 2987 6.373759 TCTCTTCTAACATGGTATCAGCCTA 58.626 40.000 0.00 0.00 0.00 3.93
2853 2991 2.910688 ACATGGTATCAGCCTAACCG 57.089 50.000 0.00 0.00 35.98 4.44
2854 2992 2.394632 ACATGGTATCAGCCTAACCGA 58.605 47.619 0.00 0.00 35.98 4.69
2855 2993 2.972713 ACATGGTATCAGCCTAACCGAT 59.027 45.455 0.00 0.00 35.98 4.18
2856 2994 3.006967 ACATGGTATCAGCCTAACCGATC 59.993 47.826 0.00 0.00 35.98 3.69
2857 2995 1.968493 TGGTATCAGCCTAACCGATCC 59.032 52.381 0.00 0.00 35.98 3.36
2869 3011 2.280186 CGATCCAACCCTAGCCGC 60.280 66.667 0.00 0.00 0.00 6.53
2870 3012 2.111251 GATCCAACCCTAGCCGCC 59.889 66.667 0.00 0.00 0.00 6.13
2871 3013 3.809374 GATCCAACCCTAGCCGCCG 62.809 68.421 0.00 0.00 0.00 6.46
2969 3112 1.565067 CCCGTACCTAGGGTTTGTCT 58.435 55.000 14.81 0.00 43.89 3.41
2973 3116 1.626825 GTACCTAGGGTTTGTCTGCCA 59.373 52.381 14.81 0.00 37.09 4.92
2977 3120 1.347707 CTAGGGTTTGTCTGCCAGTCA 59.652 52.381 0.00 0.00 0.00 3.41
2983 3126 0.953727 TTGTCTGCCAGTCATGTTGC 59.046 50.000 0.00 0.00 0.00 4.17
2985 3128 0.607489 GTCTGCCAGTCATGTTGCCT 60.607 55.000 0.00 0.00 0.00 4.75
3015 3160 3.512033 AGAGAGTCTTTTTCCGATCCG 57.488 47.619 0.00 0.00 0.00 4.18
3022 3167 3.933332 GTCTTTTTCCGATCCGTTGATCT 59.067 43.478 0.00 0.00 44.40 2.75
3037 3182 4.322349 CGTTGATCTGGGTTTCTCTCTCTT 60.322 45.833 0.00 0.00 0.00 2.85
3040 3185 1.273606 TCTGGGTTTCTCTCTCTTGCG 59.726 52.381 0.00 0.00 0.00 4.85
3041 3186 0.321671 TGGGTTTCTCTCTCTTGCGG 59.678 55.000 0.00 0.00 0.00 5.69
3059 3204 1.931172 CGGGTCGCTTTAATCGATGTT 59.069 47.619 0.00 0.00 38.29 2.71
3099 3247 1.200716 TCTAAGATCGGTTTGCGTCGT 59.799 47.619 0.00 0.00 0.00 4.34
3134 3283 2.291043 CCCCCACACGCCTCTACTT 61.291 63.158 0.00 0.00 0.00 2.24
3137 3286 1.153823 CCACACGCCTCTACTTCGG 60.154 63.158 0.00 0.00 0.00 4.30
3164 3313 3.541713 GATCGGCCGGCCTCTTCT 61.542 66.667 41.01 21.42 0.00 2.85
3213 3374 3.740397 CGTCCGTACGTCTGCCCA 61.740 66.667 15.21 0.00 44.21 5.36
3215 3376 3.740397 TCCGTACGTCTGCCCACG 61.740 66.667 15.21 0.00 45.65 4.94
3223 3384 4.662961 TCTGCCCACGTGTCGCTG 62.663 66.667 21.22 20.23 0.00 5.18
3225 3386 4.961511 TGCCCACGTGTCGCTGTC 62.962 66.667 21.22 0.00 0.00 3.51
3284 3445 2.009774 CATCAACCCCACGTTCATCTC 58.990 52.381 0.00 0.00 29.93 2.75
3316 3477 3.870538 TCATGCTTATTCCTGCAGGAT 57.129 42.857 35.42 25.29 43.51 3.24
3319 3480 1.565759 TGCTTATTCCTGCAGGATGGT 59.434 47.619 35.42 24.77 44.98 3.55
3331 3492 0.618458 AGGATGGTGCGTAATGGTGT 59.382 50.000 0.00 0.00 0.00 4.16
3336 3497 2.418692 TGGTGCGTAATGGTGTAACTG 58.581 47.619 0.00 0.00 36.74 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 3.719268 TGCATAGTGGACAAAGACCAT 57.281 42.857 0.00 0.00 39.69 3.55
117 118 4.591498 TCTCCAAAGCCTAAGAGTGTAACA 59.409 41.667 0.00 0.00 41.43 2.41
156 157 0.759959 TTGACGTGAGGTAGCCCAAA 59.240 50.000 0.00 0.00 0.00 3.28
287 288 1.600023 TTCGCTCGTTCCAAATGGTT 58.400 45.000 0.00 0.00 36.34 3.67
533 534 2.488153 GTGTCCTTGTGAGCCAATTACC 59.512 50.000 0.00 0.00 31.20 2.85
534 535 3.146066 TGTGTCCTTGTGAGCCAATTAC 58.854 45.455 0.00 0.00 31.20 1.89
535 536 3.500448 TGTGTCCTTGTGAGCCAATTA 57.500 42.857 0.00 0.00 31.20 1.40
536 537 2.363306 TGTGTCCTTGTGAGCCAATT 57.637 45.000 0.00 0.00 31.20 2.32
537 538 2.165167 CATGTGTCCTTGTGAGCCAAT 58.835 47.619 0.00 0.00 31.20 3.16
538 539 1.608055 CATGTGTCCTTGTGAGCCAA 58.392 50.000 0.00 0.00 0.00 4.52
539 540 0.250858 CCATGTGTCCTTGTGAGCCA 60.251 55.000 0.00 0.00 0.00 4.75
540 541 1.589716 GCCATGTGTCCTTGTGAGCC 61.590 60.000 0.00 0.00 0.00 4.70
541 542 1.878775 GCCATGTGTCCTTGTGAGC 59.121 57.895 0.00 0.00 0.00 4.26
542 543 0.320683 TCGCCATGTGTCCTTGTGAG 60.321 55.000 0.00 0.00 0.00 3.51
543 544 0.324614 ATCGCCATGTGTCCTTGTGA 59.675 50.000 0.00 0.00 0.00 3.58
544 545 0.729116 GATCGCCATGTGTCCTTGTG 59.271 55.000 0.00 0.00 0.00 3.33
545 546 0.615331 AGATCGCCATGTGTCCTTGT 59.385 50.000 0.00 0.00 0.00 3.16
546 547 1.742761 AAGATCGCCATGTGTCCTTG 58.257 50.000 0.00 0.00 0.00 3.61
547 548 2.496899 AAAGATCGCCATGTGTCCTT 57.503 45.000 0.00 0.00 0.00 3.36
548 549 2.496899 AAAAGATCGCCATGTGTCCT 57.503 45.000 0.00 0.00 0.00 3.85
549 550 4.498009 CCAATAAAAGATCGCCATGTGTCC 60.498 45.833 0.00 0.00 0.00 4.02
550 551 4.601019 CCAATAAAAGATCGCCATGTGTC 58.399 43.478 0.00 0.00 0.00 3.67
551 552 3.181487 GCCAATAAAAGATCGCCATGTGT 60.181 43.478 0.00 0.00 0.00 3.72
552 553 3.374745 GCCAATAAAAGATCGCCATGTG 58.625 45.455 0.00 0.00 0.00 3.21
553 554 2.362077 GGCCAATAAAAGATCGCCATGT 59.638 45.455 0.00 0.00 36.38 3.21
554 555 2.288395 GGGCCAATAAAAGATCGCCATG 60.288 50.000 4.39 0.00 38.16 3.66
555 556 1.963515 GGGCCAATAAAAGATCGCCAT 59.036 47.619 4.39 0.00 38.16 4.40
556 557 1.064017 AGGGCCAATAAAAGATCGCCA 60.064 47.619 6.18 0.00 38.16 5.69
557 558 1.338020 CAGGGCCAATAAAAGATCGCC 59.662 52.381 6.18 0.00 35.60 5.54
558 559 1.269257 GCAGGGCCAATAAAAGATCGC 60.269 52.381 6.18 0.00 0.00 4.58
559 560 2.023673 TGCAGGGCCAATAAAAGATCG 58.976 47.619 6.18 0.00 0.00 3.69
560 561 2.760092 TGTGCAGGGCCAATAAAAGATC 59.240 45.455 6.18 0.00 0.00 2.75
561 562 2.818921 TGTGCAGGGCCAATAAAAGAT 58.181 42.857 6.18 0.00 0.00 2.40
562 563 2.300956 TGTGCAGGGCCAATAAAAGA 57.699 45.000 6.18 0.00 0.00 2.52
563 564 3.615224 ATTGTGCAGGGCCAATAAAAG 57.385 42.857 6.18 0.00 31.43 2.27
564 565 5.690464 ATTATTGTGCAGGGCCAATAAAA 57.310 34.783 18.56 5.34 40.80 1.52
565 566 5.669477 GAATTATTGTGCAGGGCCAATAAA 58.331 37.500 18.56 7.66 40.80 1.40
566 567 4.202101 CGAATTATTGTGCAGGGCCAATAA 60.202 41.667 17.53 17.53 41.20 1.40
567 568 3.317711 CGAATTATTGTGCAGGGCCAATA 59.682 43.478 6.18 3.95 33.78 1.90
568 569 2.101249 CGAATTATTGTGCAGGGCCAAT 59.899 45.455 6.18 5.69 35.14 3.16
569 570 1.476085 CGAATTATTGTGCAGGGCCAA 59.524 47.619 6.18 0.00 0.00 4.52
570 571 1.102154 CGAATTATTGTGCAGGGCCA 58.898 50.000 6.18 0.00 0.00 5.36
571 572 1.102978 ACGAATTATTGTGCAGGGCC 58.897 50.000 0.00 0.00 0.00 5.80
572 573 2.193306 CACGAATTATTGTGCAGGGC 57.807 50.000 0.00 0.00 34.26 5.19
578 579 2.223340 GCTCCCTGCACGAATTATTGTG 60.223 50.000 0.00 1.63 42.88 3.33
579 580 2.017049 GCTCCCTGCACGAATTATTGT 58.983 47.619 0.00 0.00 42.31 2.71
580 581 1.334869 GGCTCCCTGCACGAATTATTG 59.665 52.381 0.00 0.00 45.15 1.90
581 582 1.680338 GGCTCCCTGCACGAATTATT 58.320 50.000 0.00 0.00 45.15 1.40
582 583 0.179018 GGGCTCCCTGCACGAATTAT 60.179 55.000 0.00 0.00 45.15 1.28
583 584 1.223487 GGGCTCCCTGCACGAATTA 59.777 57.895 0.00 0.00 45.15 1.40
584 585 2.044946 GGGCTCCCTGCACGAATT 60.045 61.111 0.00 0.00 45.15 2.17
594 595 4.486503 CTCAGCTGCAGGGCTCCC 62.487 72.222 17.12 0.00 41.00 4.30
599 600 4.355720 TTGGGCTCAGCTGCAGGG 62.356 66.667 17.12 0.00 34.04 4.45
600 601 3.060615 GTTGGGCTCAGCTGCAGG 61.061 66.667 17.12 0.00 34.04 4.85
601 602 3.060615 GGTTGGGCTCAGCTGCAG 61.061 66.667 10.11 10.11 34.04 4.41
602 603 4.666253 GGGTTGGGCTCAGCTGCA 62.666 66.667 9.47 0.00 34.04 4.41
604 605 4.020617 TCGGGTTGGGCTCAGCTG 62.021 66.667 7.63 7.63 0.00 4.24
605 606 4.021925 GTCGGGTTGGGCTCAGCT 62.022 66.667 0.00 0.00 0.00 4.24
606 607 4.329545 TGTCGGGTTGGGCTCAGC 62.330 66.667 0.00 0.00 0.00 4.26
607 608 2.358737 GTGTCGGGTTGGGCTCAG 60.359 66.667 0.00 0.00 0.00 3.35
608 609 3.164977 TGTGTCGGGTTGGGCTCA 61.165 61.111 0.00 0.00 0.00 4.26
609 610 2.668550 GTGTGTCGGGTTGGGCTC 60.669 66.667 0.00 0.00 0.00 4.70
610 611 3.484806 TGTGTGTCGGGTTGGGCT 61.485 61.111 0.00 0.00 0.00 5.19
611 612 3.284449 GTGTGTGTCGGGTTGGGC 61.284 66.667 0.00 0.00 0.00 5.36
612 613 2.593436 GGTGTGTGTCGGGTTGGG 60.593 66.667 0.00 0.00 0.00 4.12
613 614 1.228124 ATGGTGTGTGTCGGGTTGG 60.228 57.895 0.00 0.00 0.00 3.77
614 615 1.565156 CGATGGTGTGTGTCGGGTTG 61.565 60.000 0.00 0.00 0.00 3.77
615 616 1.301401 CGATGGTGTGTGTCGGGTT 60.301 57.895 0.00 0.00 0.00 4.11
616 617 1.541310 ATCGATGGTGTGTGTCGGGT 61.541 55.000 0.00 0.00 36.14 5.28
617 618 1.083806 CATCGATGGTGTGTGTCGGG 61.084 60.000 17.96 0.00 36.14 5.14
618 619 1.695893 GCATCGATGGTGTGTGTCGG 61.696 60.000 26.00 0.00 36.14 4.79
655 656 1.255859 TCGCAAACACGTTTACGACAG 59.744 47.619 12.65 1.45 41.64 3.51
676 677 1.472276 CGCTCGGATCGAAAACGGAG 61.472 60.000 15.35 15.35 34.74 4.63
722 778 3.776659 TTGTCTGCAACCGCGACGA 62.777 57.895 8.23 0.00 41.50 4.20
736 792 2.696759 CGGCCCGGTTGGATTTGTC 61.697 63.158 0.00 0.00 37.49 3.18
740 796 1.529152 GAAAACGGCCCGGTTGGATT 61.529 55.000 7.44 0.00 36.69 3.01
781 838 1.479709 CCATCCAAGTCTCGGACTCT 58.520 55.000 6.96 0.00 42.59 3.24
824 883 4.579647 AATACGGCTCCCCTAAGAAAAA 57.420 40.909 0.00 0.00 0.00 1.94
825 884 4.520179 GAAATACGGCTCCCCTAAGAAAA 58.480 43.478 0.00 0.00 0.00 2.29
826 885 3.431207 CGAAATACGGCTCCCCTAAGAAA 60.431 47.826 0.00 0.00 38.46 2.52
827 886 2.101917 CGAAATACGGCTCCCCTAAGAA 59.898 50.000 0.00 0.00 38.46 2.52
828 887 1.684983 CGAAATACGGCTCCCCTAAGA 59.315 52.381 0.00 0.00 38.46 2.10
829 888 1.684983 TCGAAATACGGCTCCCCTAAG 59.315 52.381 0.00 0.00 42.82 2.18
830 889 1.410153 GTCGAAATACGGCTCCCCTAA 59.590 52.381 0.00 0.00 43.76 2.69
831 890 1.035139 GTCGAAATACGGCTCCCCTA 58.965 55.000 0.00 0.00 43.76 3.53
832 891 1.821258 GTCGAAATACGGCTCCCCT 59.179 57.895 0.00 0.00 43.76 4.79
833 892 4.432859 GTCGAAATACGGCTCCCC 57.567 61.111 0.00 0.00 43.76 4.81
867 926 6.553524 GGTCAGTATATATAGAACGACCAGC 58.446 44.000 21.27 0.00 41.08 4.85
917 1016 0.180642 TTGTACGTGGGGTTCTTGCA 59.819 50.000 0.00 0.00 0.00 4.08
935 1034 5.243283 CGGTCCACAACCTATACTATAGCTT 59.757 44.000 0.00 0.00 46.87 3.74
943 1042 1.202336 CGGTCGGTCCACAACCTATAC 60.202 57.143 4.14 0.00 46.87 1.47
1048 1151 4.081185 TCGGATGCGCCTGCTTCA 62.081 61.111 4.18 0.00 44.71 3.02
1172 1291 1.450211 CCGTGGACTCCAAGTGGTT 59.550 57.895 9.82 0.00 34.18 3.67
1268 1387 1.298859 GCGAAGATCTTGTTGCCCGT 61.299 55.000 14.00 0.00 0.00 5.28
1269 1388 1.021390 AGCGAAGATCTTGTTGCCCG 61.021 55.000 14.00 10.06 0.00 6.13
1270 1389 1.168714 AAGCGAAGATCTTGTTGCCC 58.831 50.000 14.00 0.00 0.00 5.36
1339 1458 2.537792 ATACGGTCACCTGCGACGTG 62.538 60.000 0.00 0.00 36.73 4.49
1352 1471 3.031417 GCTGTGGAGGGCATACGGT 62.031 63.158 0.00 0.00 0.00 4.83
1366 1485 3.249189 TCCTTTGGGGCGAGCTGT 61.249 61.111 0.00 0.00 34.39 4.40
1368 1487 4.416738 GCTCCTTTGGGGCGAGCT 62.417 66.667 1.14 0.00 44.52 4.09
1447 1566 7.726291 TCCATTGAGGGAACAAATTTGTAGTTA 59.274 33.333 23.53 6.54 38.10 2.24
1468 1587 1.886655 GCCGGTCCAAGTTTCTCCATT 60.887 52.381 1.90 0.00 0.00 3.16
1593 1712 0.591659 CGCGACGGAGAGGAATATGA 59.408 55.000 0.00 0.00 0.00 2.15
1615 1734 1.604915 GAAGGAGAAGGTGCCCCTC 59.395 63.158 0.00 0.00 41.56 4.30
1726 1845 0.108585 TTTGGTGTGAGCAGAGTCCC 59.891 55.000 0.00 0.00 0.00 4.46
1729 1848 2.301346 CCTTTTTGGTGTGAGCAGAGT 58.699 47.619 0.00 0.00 0.00 3.24
1788 1909 4.776322 TCGGGCATTCACAGCGGG 62.776 66.667 0.00 0.00 0.00 6.13
1814 1935 0.822944 TACACCCTGTCGTCAACGGA 60.823 55.000 2.31 0.00 40.29 4.69
1819 1940 2.275134 TGTAGTACACCCTGTCGTCA 57.725 50.000 0.00 0.00 0.00 4.35
1822 1943 3.698040 ACCTATTGTAGTACACCCTGTCG 59.302 47.826 1.43 0.00 0.00 4.35
1835 1956 3.906720 GTGCCTCTTCCACCTATTGTA 57.093 47.619 0.00 0.00 0.00 2.41
1863 1984 1.951209 TCCCATGTAAGTGAGGCTCA 58.049 50.000 14.43 14.43 0.00 4.26
1882 2003 0.603975 GGAGGCAGAACTCAGCGTTT 60.604 55.000 0.00 0.00 39.27 3.60
1924 2045 2.665052 GGACTCGGTGAAAATGTCGTAC 59.335 50.000 0.00 0.00 0.00 3.67
1957 2078 1.598130 GGTTGCCAGTCGAAGCAGT 60.598 57.895 6.20 0.00 40.73 4.40
2068 2189 0.037605 AGAAAGCGGTAGGTGAACGG 60.038 55.000 0.00 0.00 0.00 4.44
2100 2221 4.860907 TCGATAAAGAGAAACGTAGGCAAC 59.139 41.667 0.00 0.00 0.00 4.17
2102 2223 4.418392 GTCGATAAAGAGAAACGTAGGCA 58.582 43.478 0.00 0.00 0.00 4.75
2104 2225 4.033684 CCGTCGATAAAGAGAAACGTAGG 58.966 47.826 0.00 0.00 0.00 3.18
2128 2249 3.499737 GGCACCGGAACAGCATCG 61.500 66.667 9.46 0.00 0.00 3.84
2152 2273 1.146982 AGTCTTGCTAAGGGCCCAAAA 59.853 47.619 27.56 7.66 40.92 2.44
2196 2317 9.025041 CCCTTTTCTAGTTGAAACCAGATAAAT 57.975 33.333 0.00 0.00 43.55 1.40
2200 2321 4.767409 GCCCTTTTCTAGTTGAAACCAGAT 59.233 41.667 0.00 0.00 43.55 2.90
2206 2327 4.647611 TCATCGCCCTTTTCTAGTTGAAA 58.352 39.130 0.00 0.00 42.33 2.69
2213 2334 4.491676 GCGTATATCATCGCCCTTTTCTA 58.508 43.478 8.12 0.00 45.54 2.10
2403 2536 0.680280 TCCTCCTACCTGACGCTCAC 60.680 60.000 0.00 0.00 0.00 3.51
2439 2572 1.153066 TTGTTTGAGCGGCAGGTGA 60.153 52.632 1.45 0.00 0.00 4.02
2467 2601 0.824595 TCGGACTCACAGGAAACGGA 60.825 55.000 0.00 0.00 0.00 4.69
2469 2603 0.596577 TCTCGGACTCACAGGAAACG 59.403 55.000 0.00 0.00 0.00 3.60
2521 2655 8.359642 AGCATTTGTGTTTGTACTGATGTAAAT 58.640 29.630 0.00 0.00 0.00 1.40
2523 2657 7.270757 AGCATTTGTGTTTGTACTGATGTAA 57.729 32.000 0.00 0.00 0.00 2.41
2524 2658 6.875948 AGCATTTGTGTTTGTACTGATGTA 57.124 33.333 0.00 0.00 0.00 2.29
2566 2700 6.863126 CGTGTATGCATTCATGTAGATGAGTA 59.137 38.462 15.33 0.00 39.81 2.59
2586 2720 2.025898 TCGGGATAGAATGTGCGTGTA 58.974 47.619 0.00 0.00 0.00 2.90
2596 2730 2.828520 GGAGATGCTCATCGGGATAGAA 59.171 50.000 4.41 0.00 42.48 2.10
2597 2731 2.451490 GGAGATGCTCATCGGGATAGA 58.549 52.381 4.41 0.00 42.48 1.98
2601 2735 1.152756 TCGGAGATGCTCATCGGGA 60.153 57.895 4.41 1.53 42.48 5.14
2603 2737 0.240678 CTCTCGGAGATGCTCATCGG 59.759 60.000 8.39 0.00 42.48 4.18
2605 2739 2.030893 CAGTCTCTCGGAGATGCTCATC 60.031 54.545 8.39 1.75 40.98 2.92
2610 2745 0.030638 GCTCAGTCTCTCGGAGATGC 59.969 60.000 8.39 4.64 40.98 3.91
2630 2765 5.065090 CGTAAAATCTCAAGATGATGTGCCA 59.935 40.000 0.00 0.00 34.49 4.92
2635 2770 8.189709 TGACTTCGTAAAATCTCAAGATGATG 57.810 34.615 0.00 0.00 34.49 3.07
2657 2792 1.779025 TACGAGGCGCCTACGATGAC 61.779 60.000 37.37 22.42 43.93 3.06
2658 2793 1.524393 TACGAGGCGCCTACGATGA 60.524 57.895 37.37 24.99 43.93 2.92
2693 2828 8.718656 AGTCTAACCTATGCTTCCAATCTAATT 58.281 33.333 0.00 0.00 0.00 1.40
2698 2835 6.267928 TCCTAGTCTAACCTATGCTTCCAATC 59.732 42.308 0.00 0.00 0.00 2.67
2699 2836 6.143915 TCCTAGTCTAACCTATGCTTCCAAT 58.856 40.000 0.00 0.00 0.00 3.16
2701 2838 5.138758 TCCTAGTCTAACCTATGCTTCCA 57.861 43.478 0.00 0.00 0.00 3.53
2706 2843 9.646427 CAGAATATTTCCTAGTCTAACCTATGC 57.354 37.037 0.00 0.00 33.14 3.14
2781 2919 1.061131 CGTTGTATTGCTTGAGCCTCG 59.939 52.381 0.00 0.00 41.18 4.63
2824 2962 5.663106 AGGCTGATACCATGTTAGAAGAGAA 59.337 40.000 0.00 0.00 0.00 2.87
2827 2965 6.183360 GGTTAGGCTGATACCATGTTAGAAGA 60.183 42.308 0.00 0.00 32.12 2.87
2849 2987 1.912971 GGCTAGGGTTGGATCGGTT 59.087 57.895 0.00 0.00 0.00 4.44
2853 2991 2.111251 GGCGGCTAGGGTTGGATC 59.889 66.667 0.00 0.00 0.00 3.36
2854 2992 3.861797 CGGCGGCTAGGGTTGGAT 61.862 66.667 7.61 0.00 0.00 3.41
2908 3050 4.731853 TGGAGGCCGATCACCCCA 62.732 66.667 0.00 7.49 0.00 4.96
2913 3056 3.230284 GGTCATGGAGGCCGATCA 58.770 61.111 0.00 0.00 28.17 2.92
2947 3090 1.305213 AAACCCTAGGTACGGGCGA 60.305 57.895 8.29 0.00 46.04 5.54
2965 3108 0.890542 GGCAACATGACTGGCAGACA 60.891 55.000 23.66 22.25 39.10 3.41
2973 3116 1.975407 GCAGCCAGGCAACATGACT 60.975 57.895 15.80 0.00 34.86 3.41
2977 3120 2.563013 CTAGGGCAGCCAGGCAACAT 62.563 60.000 15.80 3.14 46.44 2.71
2983 3126 1.382420 ACTCTCTAGGGCAGCCAGG 60.382 63.158 15.19 2.25 0.00 4.45
2985 3128 0.041833 AAGACTCTCTAGGGCAGCCA 59.958 55.000 15.19 0.00 0.00 4.75
3015 3160 4.817318 AGAGAGAGAAACCCAGATCAAC 57.183 45.455 0.00 0.00 0.00 3.18
3022 3167 0.321671 CCGCAAGAGAGAGAAACCCA 59.678 55.000 0.00 0.00 43.02 4.51
3040 3185 4.094442 AGAAAACATCGATTAAAGCGACCC 59.906 41.667 0.00 0.00 40.94 4.46
3041 3186 5.217895 AGAAAACATCGATTAAAGCGACC 57.782 39.130 0.00 0.00 40.94 4.79
3077 3222 2.858344 CGACGCAAACCGATCTTAGATT 59.142 45.455 0.00 0.00 41.02 2.40
3083 3228 1.445582 GGACGACGCAAACCGATCT 60.446 57.895 0.00 0.00 41.02 2.75
3113 3261 3.533079 TAGAGGCGTGTGGGGGTCA 62.533 63.158 0.00 0.00 0.00 4.02
3120 3269 1.805945 GCCGAAGTAGAGGCGTGTG 60.806 63.158 0.00 0.00 44.22 3.82
3121 3270 2.572284 GCCGAAGTAGAGGCGTGT 59.428 61.111 0.00 0.00 44.22 4.49
3206 3367 4.662961 CAGCGACACGTGGGCAGA 62.663 66.667 27.99 0.00 0.00 4.26
3208 3369 4.961511 GACAGCGACACGTGGGCA 62.962 66.667 27.99 0.00 0.00 5.36
3243 3404 2.753043 TAGTCCCGACCGGAGCAC 60.753 66.667 9.46 3.79 43.19 4.40
3244 3405 2.753043 GTAGTCCCGACCGGAGCA 60.753 66.667 9.46 0.00 43.19 4.26
3250 3411 2.418334 GGTTGATGAAGTAGTCCCGACC 60.418 54.545 0.00 0.00 0.00 4.79
3251 3412 2.418334 GGGTTGATGAAGTAGTCCCGAC 60.418 54.545 0.00 0.00 0.00 4.79
3284 3445 3.285215 GCATGATGCTGCCGAGGG 61.285 66.667 10.72 0.00 40.96 4.30
3307 3468 0.464373 ATTACGCACCATCCTGCAGG 60.464 55.000 27.87 27.87 36.94 4.85
3311 3472 1.016627 CACCATTACGCACCATCCTG 58.983 55.000 0.00 0.00 0.00 3.86
3312 3473 0.618458 ACACCATTACGCACCATCCT 59.382 50.000 0.00 0.00 0.00 3.24
3316 3477 2.418692 CAGTTACACCATTACGCACCA 58.581 47.619 0.00 0.00 0.00 4.17
3319 3480 2.418692 CACCAGTTACACCATTACGCA 58.581 47.619 0.00 0.00 0.00 5.24
3324 3485 0.480690 TGGCCACCAGTTACACCATT 59.519 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.