Multiple sequence alignment - TraesCS7A01G137800

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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 TraesCS7A01G137800 chr7A 100.000 3957 0 0 1 3957 90452962 90456918 0.000000e+00 7308.0
1 TraesCS7A01G137800 chr7A 83.651 630 97 1 1086 1709 90487260 90487889 4.400000e-164 588.0
2 TraesCS7A01G137800 chr7A 80.656 610 74 30 1835 2412 90487890 90488487 2.180000e-117 433.0
3 TraesCS7A01G137800 chr7A 85.817 416 46 9 3508 3918 195412116 195411709 2.830000e-116 429.0
4 TraesCS7A01G137800 chr7A 85.560 277 32 3 1592 1862 368537277 368537551 2.330000e-72 283.0
5 TraesCS7A01G137800 chr7A 92.308 65 4 1 531 594 689907122 689907186 1.510000e-14 91.6
6 TraesCS7A01G137800 chr7A 87.719 57 4 3 331 385 25858553 25858608 3.300000e-06 63.9
7 TraesCS7A01G137800 chr7D 90.501 2916 173 47 580 3441 89273852 89276717 0.000000e+00 3755.0
8 TraesCS7A01G137800 chr7D 81.778 1125 171 22 1126 2227 89473632 89474745 0.000000e+00 911.0
9 TraesCS7A01G137800 chr7D 80.607 1284 145 54 1303 2492 89280401 89281674 0.000000e+00 896.0
10 TraesCS7A01G137800 chr7D 79.315 788 132 20 999 1766 41933245 41934021 1.260000e-144 523.0
11 TraesCS7A01G137800 chr7D 89.276 373 27 7 81 452 89268032 89268392 4.660000e-124 455.0
12 TraesCS7A01G137800 chr7D 82.090 469 51 16 851 1310 89278714 89279158 1.740000e-98 370.0
13 TraesCS7A01G137800 chr7D 90.551 127 9 3 3 129 89267908 89268031 8.800000e-37 165.0
14 TraesCS7A01G137800 chr7D 84.524 168 23 3 2225 2391 89474776 89474941 3.160000e-36 163.0
15 TraesCS7A01G137800 chr7D 82.386 176 29 2 2806 2980 89475009 89475183 6.850000e-33 152.0
16 TraesCS7A01G137800 chr7B 88.783 2942 191 61 570 3441 40180724 40183596 0.000000e+00 3476.0
17 TraesCS7A01G137800 chr7B 82.473 639 100 5 1086 1717 40292918 40293551 2.080000e-152 549.0
18 TraesCS7A01G137800 chr7B 87.041 463 41 8 78 533 40180164 40180614 4.560000e-139 505.0
19 TraesCS7A01G137800 chr7B 80.707 622 69 31 1823 2412 40294753 40295355 1.690000e-118 436.0
20 TraesCS7A01G137800 chr7B 93.590 78 3 2 3 79 40180006 40180082 8.990000e-22 115.0
21 TraesCS7A01G137800 chr7B 93.151 73 5 0 2806 2878 40295383 40295455 1.500000e-19 108.0
22 TraesCS7A01G137800 chrUn 88.123 1827 115 30 1645 3423 30439657 30437885 0.000000e+00 2078.0
23 TraesCS7A01G137800 chrUn 94.158 736 34 6 866 1598 30440802 30440073 0.000000e+00 1112.0
24 TraesCS7A01G137800 chrUn 80.882 1292 164 48 863 2106 30433191 30431935 0.000000e+00 941.0
25 TraesCS7A01G137800 chrUn 85.765 281 31 5 2105 2383 30431897 30431624 5.000000e-74 289.0
26 TraesCS7A01G137800 chr5A 80.328 1281 165 53 876 2106 666944765 666943522 0.000000e+00 889.0
27 TraesCS7A01G137800 chr5A 94.458 415 15 7 3508 3919 560612531 560612122 2.010000e-177 632.0
28 TraesCS7A01G137800 chr5A 94.217 415 14 6 3508 3919 293507526 293507933 3.360000e-175 625.0
29 TraesCS7A01G137800 chr5A 91.346 416 27 8 3508 3918 535244425 535244014 9.600000e-156 560.0
30 TraesCS7A01G137800 chr5A 84.588 279 34 5 2105 2381 666943484 666943213 6.520000e-68 268.0
31 TraesCS7A01G137800 chr5A 96.429 56 2 0 533 588 673005847 673005792 4.210000e-15 93.5
32 TraesCS7A01G137800 chr2B 87.129 808 72 9 2480 3269 195926741 195925948 0.000000e+00 887.0
33 TraesCS7A01G137800 chr2B 83.580 810 78 26 2480 3269 711159952 711160726 0.000000e+00 708.0
34 TraesCS7A01G137800 chr2B 86.697 436 44 8 1937 2366 711159384 711159811 4.630000e-129 472.0
35 TraesCS7A01G137800 chr2B 85.948 427 35 4 2856 3266 790894067 790893650 2.180000e-117 433.0
36 TraesCS7A01G137800 chr2B 91.133 203 18 0 1979 2181 195927341 195927139 3.900000e-70 276.0
37 TraesCS7A01G137800 chr2B 93.333 60 2 2 531 589 540926350 540926408 1.960000e-13 87.9
38 TraesCS7A01G137800 chr2B 87.931 58 4 3 331 387 788033578 788033633 9.180000e-07 65.8
39 TraesCS7A01G137800 chr6D 95.204 417 13 5 3507 3918 11770519 11770933 0.000000e+00 652.0
40 TraesCS7A01G137800 chr6D 92.289 415 27 5 3507 3918 29754791 29755203 5.700000e-163 584.0
41 TraesCS7A01G137800 chr6D 92.364 275 20 1 2401 2674 277049953 277050227 1.330000e-104 390.0
42 TraesCS7A01G137800 chr6D 96.429 56 1 1 531 585 194007086 194007031 1.510000e-14 91.6
43 TraesCS7A01G137800 chr4A 94.673 413 17 5 3507 3918 620981162 620980754 1.550000e-178 636.0
44 TraesCS7A01G137800 chr4A 94.652 374 15 5 3547 3918 594001560 594001930 3.430000e-160 575.0
45 TraesCS7A01G137800 chr4A 78.841 794 131 27 999 1766 648999065 648998283 5.900000e-138 501.0
46 TraesCS7A01G137800 chr6A 93.976 415 20 5 3507 3918 465233589 465233177 1.210000e-174 623.0
47 TraesCS7A01G137800 chr6A 94.828 58 3 0 531 588 525608035 525608092 1.510000e-14 91.6
48 TraesCS7A01G137800 chr2D 89.545 440 39 7 3507 3942 359387135 359387571 5.780000e-153 551.0
49 TraesCS7A01G137800 chr3D 89.607 433 34 6 1937 2366 103678430 103678854 1.250000e-149 540.0
50 TraesCS7A01G137800 chr3D 96.429 56 1 1 531 585 61798117 61798062 1.510000e-14 91.6
51 TraesCS7A01G137800 chr3D 87.500 64 1 5 327 386 32259792 32259852 2.550000e-07 67.6
52 TraesCS7A01G137800 chr3A 91.273 275 23 1 2400 2674 19634492 19634765 1.340000e-99 374.0
53 TraesCS7A01G137800 chr3A 86.538 52 7 0 341 392 30351124 30351175 1.540000e-04 58.4
54 TraesCS7A01G137800 chr3A 84.746 59 7 2 331 387 716193532 716193474 1.540000e-04 58.4
55 TraesCS7A01G137800 chr2A 90.909 275 24 1 2400 2674 659737165 659737438 6.250000e-98 368.0
56 TraesCS7A01G137800 chr5B 96.429 56 1 1 531 585 528505144 528505199 1.510000e-14 91.6
57 TraesCS7A01G137800 chr1D 94.828 58 3 0 531 588 478352555 478352498 1.510000e-14 91.6
58 TraesCS7A01G137800 chr1D 86.792 53 5 2 332 382 479341833 479341781 1.540000e-04 58.4
59 TraesCS7A01G137800 chr4B 90.000 70 5 2 533 600 607640799 607640730 5.450000e-14 89.8
60 TraesCS7A01G137800 chr1A 86.154 65 7 2 324 388 566491313 566491375 7.100000e-08 69.4
61 TraesCS7A01G137800 chr6B 88.462 52 4 2 340 390 692820767 692820717 1.190000e-05 62.1


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 TraesCS7A01G137800 chr7A 90452962 90456918 3956 False 7308.000000 7308 100.000000 1 3957 1 chr7A.!!$F2 3956
1 TraesCS7A01G137800 chr7A 90487260 90488487 1227 False 510.500000 588 82.153500 1086 2412 2 chr7A.!!$F5 1326
2 TraesCS7A01G137800 chr7D 89273852 89281674 7822 False 1673.666667 3755 84.399333 580 3441 3 chr7D.!!$F3 2861
3 TraesCS7A01G137800 chr7D 41933245 41934021 776 False 523.000000 523 79.315000 999 1766 1 chr7D.!!$F1 767
4 TraesCS7A01G137800 chr7D 89473632 89475183 1551 False 408.666667 911 82.896000 1126 2980 3 chr7D.!!$F4 1854
5 TraesCS7A01G137800 chr7B 40180006 40183596 3590 False 1365.333333 3476 89.804667 3 3441 3 chr7B.!!$F1 3438
6 TraesCS7A01G137800 chr7B 40292918 40295455 2537 False 364.333333 549 85.443667 1086 2878 3 chr7B.!!$F2 1792
7 TraesCS7A01G137800 chrUn 30437885 30440802 2917 True 1595.000000 2078 91.140500 866 3423 2 chrUn.!!$R2 2557
8 TraesCS7A01G137800 chrUn 30431624 30433191 1567 True 615.000000 941 83.323500 863 2383 2 chrUn.!!$R1 1520
9 TraesCS7A01G137800 chr5A 666943213 666944765 1552 True 578.500000 889 82.458000 876 2381 2 chr5A.!!$R4 1505
10 TraesCS7A01G137800 chr2B 711159384 711160726 1342 False 590.000000 708 85.138500 1937 3269 2 chr2B.!!$F3 1332
11 TraesCS7A01G137800 chr2B 195925948 195927341 1393 True 581.500000 887 89.131000 1979 3269 2 chr2B.!!$R2 1290
12 TraesCS7A01G137800 chr4A 648998283 648999065 782 True 501.000000 501 78.841000 999 1766 1 chr4A.!!$R2 767

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
269 354 0.319555 TTGGACGTTTGAGGAGCTCG 60.320 55.000 7.83 0.00 32.35 5.03 F
522 611 0.323302 TGGGCACGCAGATTAACTCA 59.677 50.000 0.00 0.00 0.00 3.41 F
966 1162 0.978146 CCACCCTCCAGTCCTACCAG 60.978 65.000 0.00 0.00 0.00 4.00 F
1551 1804 1.007387 CGCCAAGTTTGTCAAGGGC 60.007 57.895 8.68 8.68 38.04 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1816 0.038159 ACGACGCCAGGAAGAAGAAG 60.038 55.000 0.00 0.00 0.00 2.85 R
1773 2410 0.966920 GTTCACCTCGAGGAGTTGGA 59.033 55.000 37.69 17.93 38.94 3.53 R
1820 3567 1.270550 CCACAGCAAACATCCTGAACC 59.729 52.381 0.00 0.00 33.40 3.62 R
3227 5479 0.250295 TGCCAAACAAGAGAGACCCG 60.250 55.000 0.00 0.00 0.00 5.28 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
71 72 7.424452 GGTCTATTACATAGTTTGTTTTTCGCG 59.576 37.037 0.00 0.00 39.87 5.87
74 75 2.879646 ACATAGTTTGTTTTTCGCGGGA 59.120 40.909 6.13 0.00 33.74 5.14
76 77 2.197792 AGTTTGTTTTTCGCGGGAAC 57.802 45.000 15.20 9.63 0.00 3.62
86 171 8.836268 TGTTTTTCGCGGGAACTATTATATAT 57.164 30.769 15.20 0.00 0.00 0.86
117 202 1.612950 CACAAACAATAGGGTGCAGCA 59.387 47.619 19.06 0.00 0.00 4.41
163 248 3.937079 ACCCGTCGATGAAAGGTAAATTC 59.063 43.478 6.11 0.00 0.00 2.17
164 249 3.000925 CCCGTCGATGAAAGGTAAATTCG 59.999 47.826 6.11 0.00 0.00 3.34
269 354 0.319555 TTGGACGTTTGAGGAGCTCG 60.320 55.000 7.83 0.00 32.35 5.03
272 357 1.006102 ACGTTTGAGGAGCTCGTGG 60.006 57.895 14.78 0.51 32.35 4.94
281 366 4.647611 TGAGGAGCTCGTGGAAAAATAAA 58.352 39.130 14.78 0.00 32.35 1.40
282 367 5.067273 TGAGGAGCTCGTGGAAAAATAAAA 58.933 37.500 14.78 0.00 32.35 1.52
283 368 5.533154 TGAGGAGCTCGTGGAAAAATAAAAA 59.467 36.000 14.78 0.00 32.35 1.94
313 398 7.338196 TGGTCTGTCAAAGTATCTTTCAAAACA 59.662 33.333 0.00 0.00 0.00 2.83
316 401 7.862372 TCTGTCAAAGTATCTTTCAAAACATGC 59.138 33.333 0.00 0.00 0.00 4.06
319 404 6.922957 TCAAAGTATCTTTCAAAACATGCACC 59.077 34.615 0.00 0.00 0.00 5.01
322 407 3.077229 TCTTTCAAAACATGCACCGTG 57.923 42.857 0.00 0.00 0.00 4.94
323 408 2.425312 TCTTTCAAAACATGCACCGTGT 59.575 40.909 0.00 0.00 34.83 4.49
325 410 3.617540 TTCAAAACATGCACCGTGTAG 57.382 42.857 0.00 0.00 31.86 2.74
326 411 2.839975 TCAAAACATGCACCGTGTAGA 58.160 42.857 0.00 0.00 31.86 2.59
327 412 2.546368 TCAAAACATGCACCGTGTAGAC 59.454 45.455 0.00 0.00 31.86 2.59
328 413 2.543777 AAACATGCACCGTGTAGACT 57.456 45.000 0.00 0.00 31.86 3.24
329 414 3.671008 AAACATGCACCGTGTAGACTA 57.329 42.857 0.00 0.00 31.86 2.59
330 415 2.941453 ACATGCACCGTGTAGACTAG 57.059 50.000 0.00 0.00 31.23 2.57
331 416 2.443416 ACATGCACCGTGTAGACTAGA 58.557 47.619 0.00 0.00 31.23 2.43
361 449 0.674581 TGCCACGAGCTCCTCAAATG 60.675 55.000 8.47 0.00 44.23 2.32
373 461 4.557496 GCTCCTCAAATGTCCAAACACTTC 60.557 45.833 0.00 0.00 38.48 3.01
385 473 4.564769 TCCAAACACTTCGAAATTTTGCAC 59.435 37.500 15.44 0.00 0.00 4.57
387 475 2.116366 ACACTTCGAAATTTTGCACGC 58.884 42.857 0.00 0.00 0.00 5.34
399 487 2.010145 TTGCACGCACCTAGAAGATC 57.990 50.000 0.00 0.00 0.00 2.75
408 496 3.181470 GCACCTAGAAGATCCTCTCAACC 60.181 52.174 0.00 0.00 0.00 3.77
412 500 4.037446 CCTAGAAGATCCTCTCAACCTTCG 59.963 50.000 0.00 0.00 38.49 3.79
413 501 3.436243 AGAAGATCCTCTCAACCTTCGT 58.564 45.455 0.00 0.00 38.49 3.85
429 518 2.435059 GTGGTGAAGAGCGAGCCC 60.435 66.667 0.00 0.00 0.00 5.19
436 525 2.214181 GAAGAGCGAGCCCGACTTCA 62.214 60.000 17.57 0.00 43.21 3.02
442 531 1.671742 GAGCCCGACTTCAAGGTGA 59.328 57.895 0.00 0.00 0.00 4.02
445 534 1.374252 CCCGACTTCAAGGTGACGG 60.374 63.158 0.00 0.00 40.03 4.79
460 549 6.980051 AGGTGACGGTGAAAGATATAAAAC 57.020 37.500 0.00 0.00 0.00 2.43
463 552 6.183360 GGTGACGGTGAAAGATATAAAACCTG 60.183 42.308 0.00 0.00 0.00 4.00
482 571 4.041691 ACCTGTGTATCCTTAACAAGCAGT 59.958 41.667 0.00 0.00 0.00 4.40
494 583 6.988580 CCTTAACAAGCAGTATCATGATGAGA 59.011 38.462 18.72 0.00 0.00 3.27
503 592 5.024785 AGTATCATGATGAGATGGCTAGCT 58.975 41.667 18.72 0.00 0.00 3.32
505 594 2.302157 TCATGATGAGATGGCTAGCTGG 59.698 50.000 15.72 0.00 0.00 4.85
522 611 0.323302 TGGGCACGCAGATTAACTCA 59.677 50.000 0.00 0.00 0.00 3.41
525 614 1.405526 GGCACGCAGATTAACTCAGGA 60.406 52.381 0.00 0.00 0.00 3.86
533 622 4.499865 GCAGATTAACTCAGGATCGCTGTA 60.500 45.833 9.98 0.00 0.00 2.74
534 623 4.979197 CAGATTAACTCAGGATCGCTGTAC 59.021 45.833 9.98 0.00 0.00 2.90
535 624 4.890581 AGATTAACTCAGGATCGCTGTACT 59.109 41.667 9.98 0.00 0.00 2.73
536 625 6.017026 CAGATTAACTCAGGATCGCTGTACTA 60.017 42.308 9.98 0.68 0.00 1.82
538 627 4.373348 AACTCAGGATCGCTGTACTAAC 57.627 45.455 9.98 0.00 0.00 2.34
539 628 3.622630 ACTCAGGATCGCTGTACTAACT 58.377 45.455 9.98 0.00 0.00 2.24
540 629 4.017808 ACTCAGGATCGCTGTACTAACTT 58.982 43.478 9.98 0.00 0.00 2.66
541 630 5.191426 ACTCAGGATCGCTGTACTAACTTA 58.809 41.667 9.98 0.00 0.00 2.24
542 631 5.297278 ACTCAGGATCGCTGTACTAACTTAG 59.703 44.000 9.98 0.00 0.00 2.18
543 632 5.191426 TCAGGATCGCTGTACTAACTTAGT 58.809 41.667 6.68 6.68 42.68 2.24
544 633 6.351711 TCAGGATCGCTGTACTAACTTAGTA 58.648 40.000 4.76 4.76 40.14 1.82
559 648 9.227777 ACTAACTTAGTACAAAATTGGGTCATC 57.772 33.333 0.00 0.00 37.23 2.92
560 649 9.449719 CTAACTTAGTACAAAATTGGGTCATCT 57.550 33.333 0.00 0.00 0.00 2.90
563 652 9.975218 ACTTAGTACAAAATTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
567 656 9.308000 AGTACAAAATTGGGTCATCTATTTTGA 57.692 29.630 21.48 9.78 44.64 2.69
568 657 9.921637 GTACAAAATTGGGTCATCTATTTTGAA 57.078 29.630 21.48 0.00 44.64 2.69
571 733 8.434661 CAAAATTGGGTCATCTATTTTGAAACG 58.565 33.333 14.48 0.00 44.64 3.60
593 755 4.652822 GGAGGGAGTACAAGTTTTGTCAT 58.347 43.478 0.00 0.00 44.12 3.06
615 786 8.087750 GTCATTAAAGTGACCATTTCCATCAAA 58.912 33.333 0.00 0.00 42.04 2.69
618 789 9.657419 ATTAAAGTGACCATTTCCATCAAATTC 57.343 29.630 0.00 0.00 31.79 2.17
627 798 6.312918 CCATTTCCATCAAATTCAAGAAGCAG 59.687 38.462 0.00 0.00 31.79 4.24
651 822 8.499162 CAGTGGTGTAATTGACTCTTTTTCTAG 58.501 37.037 0.00 0.00 0.00 2.43
667 838 8.766476 TCTTTTTCTAGTGATCTGATCCTGAAT 58.234 33.333 14.71 0.00 0.00 2.57
779 971 4.948341 TTTTTCTCCCAAGTTTTAGGCC 57.052 40.909 0.00 0.00 0.00 5.19
780 972 2.194201 TTCTCCCAAGTTTTAGGCCG 57.806 50.000 0.00 0.00 0.00 6.13
789 981 1.202770 AGTTTTAGGCCGTGTCTTGCT 60.203 47.619 0.00 0.00 0.00 3.91
823 1015 7.868775 TCAAGAATCAGTGACAAAGAATGAAG 58.131 34.615 0.00 0.00 0.00 3.02
956 1152 2.609610 GTAGCCACCCACCCTCCA 60.610 66.667 0.00 0.00 0.00 3.86
957 1153 2.285368 TAGCCACCCACCCTCCAG 60.285 66.667 0.00 0.00 0.00 3.86
958 1154 3.188355 TAGCCACCCACCCTCCAGT 62.188 63.158 0.00 0.00 0.00 4.00
960 1156 3.330720 CCACCCACCCTCCAGTCC 61.331 72.222 0.00 0.00 0.00 3.85
961 1157 2.203998 CACCCACCCTCCAGTCCT 60.204 66.667 0.00 0.00 0.00 3.85
962 1158 1.080354 CACCCACCCTCCAGTCCTA 59.920 63.158 0.00 0.00 0.00 2.94
963 1159 1.080538 ACCCACCCTCCAGTCCTAC 59.919 63.158 0.00 0.00 0.00 3.18
964 1160 1.689582 CCCACCCTCCAGTCCTACC 60.690 68.421 0.00 0.00 0.00 3.18
965 1161 1.080354 CCACCCTCCAGTCCTACCA 59.920 63.158 0.00 0.00 0.00 3.25
966 1162 0.978146 CCACCCTCCAGTCCTACCAG 60.978 65.000 0.00 0.00 0.00 4.00
967 1163 1.306226 ACCCTCCAGTCCTACCAGC 60.306 63.158 0.00 0.00 0.00 4.85
968 1164 2.427245 CCCTCCAGTCCTACCAGCG 61.427 68.421 0.00 0.00 0.00 5.18
969 1165 2.496817 CTCCAGTCCTACCAGCGC 59.503 66.667 0.00 0.00 0.00 5.92
970 1166 3.075005 TCCAGTCCTACCAGCGCC 61.075 66.667 2.29 0.00 0.00 6.53
971 1167 4.514577 CCAGTCCTACCAGCGCCG 62.515 72.222 2.29 0.00 0.00 6.46
1035 1239 2.361357 ACCTCGGAGTCCTGGTCG 60.361 66.667 15.47 0.00 0.00 4.79
1036 1240 3.827898 CCTCGGAGTCCTGGTCGC 61.828 72.222 7.77 0.00 0.00 5.19
1037 1241 4.180946 CTCGGAGTCCTGGTCGCG 62.181 72.222 7.77 0.00 0.00 5.87
1196 1436 3.925090 GAGGTACGCCATCCCCGG 61.925 72.222 0.00 0.00 37.19 5.73
1551 1804 1.007387 CGCCAAGTTTGTCAAGGGC 60.007 57.895 8.68 8.68 38.04 5.19
1563 1816 1.201429 TCAAGGGCTGGAAGGAGGAC 61.201 60.000 0.00 0.00 0.00 3.85
1745 2373 3.372730 CCACCACCGCAACATGGG 61.373 66.667 0.00 0.00 40.59 4.00
1809 3556 1.141053 GAACCCTCCGGCATTGTAGAT 59.859 52.381 0.00 0.00 0.00 1.98
1811 3558 1.134098 ACCCTCCGGCATTGTAGATTG 60.134 52.381 0.00 0.00 0.00 2.67
1814 3561 3.131396 CCTCCGGCATTGTAGATTGTAC 58.869 50.000 0.00 0.00 0.00 2.90
1816 3563 4.380531 CTCCGGCATTGTAGATTGTACAT 58.619 43.478 0.00 0.00 0.00 2.29
1819 3566 4.756642 CCGGCATTGTAGATTGTACATCAT 59.243 41.667 0.00 0.00 0.00 2.45
1820 3567 5.334337 CCGGCATTGTAGATTGTACATCATG 60.334 44.000 0.00 0.00 0.00 3.07
1821 3568 5.334337 CGGCATTGTAGATTGTACATCATGG 60.334 44.000 0.00 0.00 0.00 3.66
1869 3625 3.669536 TGATCTGTGATTTGCAACCGTA 58.330 40.909 0.00 0.00 0.00 4.02
1900 3674 2.989639 CCATGGAGGAAGCCACGA 59.010 61.111 5.56 0.00 41.56 4.35
2217 4163 1.139989 CAACCTACGTGTCACTGCTG 58.860 55.000 0.00 0.00 0.00 4.41
2234 4213 0.673022 CTGCAGGTGAGCTCCTTGTC 60.673 60.000 12.15 6.55 35.37 3.18
2495 4533 4.225340 CCGAGCTCGACGAGACGG 62.225 72.222 36.59 32.27 41.36 4.79
3025 5239 3.301906 CGTCGATCGATCTGCAATTATCC 59.698 47.826 22.50 2.21 42.86 2.59
3040 5268 2.325583 TATCCGCATGTTTCTGGGAC 57.674 50.000 0.00 0.00 0.00 4.46
3085 5328 1.961793 TTCCCACCTTCGTTTCACAG 58.038 50.000 0.00 0.00 0.00 3.66
3202 5454 8.891985 TGAGAGGCAATCTAATCTATGACTAT 57.108 34.615 0.00 0.00 38.84 2.12
3227 5479 3.257469 TCATGAGCTGTGATCTGAACC 57.743 47.619 0.00 0.00 0.00 3.62
3234 5486 0.895530 TGTGATCTGAACCGGGTCTC 59.104 55.000 22.56 10.86 0.00 3.36
3236 5488 1.135333 GTGATCTGAACCGGGTCTCTC 59.865 57.143 22.56 14.54 0.00 3.20
3251 5503 3.304928 GGTCTCTCTTGTTTGGCAATGTG 60.305 47.826 0.00 0.00 36.36 3.21
3262 5514 1.350684 TGGCAATGTGCTAGACCAAGA 59.649 47.619 0.00 0.00 44.28 3.02
3320 5574 3.788227 AATTGCAAGGACACTCTACCA 57.212 42.857 4.94 0.00 0.00 3.25
3328 5582 4.317530 AGGACACTCTACCATCTACACA 57.682 45.455 0.00 0.00 0.00 3.72
3329 5583 4.017808 AGGACACTCTACCATCTACACAC 58.982 47.826 0.00 0.00 0.00 3.82
3360 5614 6.814506 AGAAAAATCTCAATGACAGACCAG 57.185 37.500 0.00 0.00 0.00 4.00
3395 5653 4.141251 GCTCTCCCCCAATTTACCTATTCA 60.141 45.833 0.00 0.00 0.00 2.57
3407 5665 5.514500 TTACCTATTCAGCAACTTTCCCT 57.486 39.130 0.00 0.00 0.00 4.20
3408 5666 3.690460 ACCTATTCAGCAACTTTCCCTG 58.310 45.455 0.00 0.00 0.00 4.45
3454 5712 9.877137 GAAGAATTCTCTCTTTTCTTTTGACTC 57.123 33.333 8.78 0.00 43.23 3.36
3455 5713 8.970859 AGAATTCTCTCTTTTCTTTTGACTCA 57.029 30.769 0.88 0.00 0.00 3.41
3456 5714 8.835439 AGAATTCTCTCTTTTCTTTTGACTCAC 58.165 33.333 0.88 0.00 0.00 3.51
3457 5715 8.511604 AATTCTCTCTTTTCTTTTGACTCACA 57.488 30.769 0.00 0.00 0.00 3.58
3458 5716 7.545362 TTCTCTCTTTTCTTTTGACTCACAG 57.455 36.000 0.00 0.00 0.00 3.66
3459 5717 6.051717 TCTCTCTTTTCTTTTGACTCACAGG 58.948 40.000 0.00 0.00 0.00 4.00
3463 5721 6.129179 TCTTTTCTTTTGACTCACAGGGAAT 58.871 36.000 0.00 0.00 0.00 3.01
3464 5722 5.772825 TTTCTTTTGACTCACAGGGAATG 57.227 39.130 0.00 0.00 0.00 2.67
3467 5725 5.248640 TCTTTTGACTCACAGGGAATGATC 58.751 41.667 0.00 0.00 0.00 2.92
3468 5726 3.634397 TTGACTCACAGGGAATGATCC 57.366 47.619 0.00 0.00 45.77 3.36
3469 5727 2.837947 TGACTCACAGGGAATGATCCT 58.162 47.619 0.00 0.00 45.77 3.24
3470 5728 2.768527 TGACTCACAGGGAATGATCCTC 59.231 50.000 0.00 0.00 45.77 3.71
3471 5729 2.768527 GACTCACAGGGAATGATCCTCA 59.231 50.000 0.00 0.00 45.77 3.86
3473 5731 1.839994 TCACAGGGAATGATCCTCACC 59.160 52.381 0.00 0.00 45.77 4.02
3474 5732 0.833287 ACAGGGAATGATCCTCACCG 59.167 55.000 0.00 0.00 45.77 4.94
3475 5733 0.833287 CAGGGAATGATCCTCACCGT 59.167 55.000 0.00 0.00 45.77 4.83
3476 5734 1.210478 CAGGGAATGATCCTCACCGTT 59.790 52.381 0.00 0.00 45.77 4.44
3477 5735 1.916181 AGGGAATGATCCTCACCGTTT 59.084 47.619 0.00 0.00 45.77 3.60
3478 5736 2.017049 GGGAATGATCCTCACCGTTTG 58.983 52.381 0.00 0.00 45.77 2.93
3479 5737 2.017049 GGAATGATCCTCACCGTTTGG 58.983 52.381 0.00 0.00 42.93 3.28
3481 5739 2.403252 ATGATCCTCACCGTTTGGAC 57.597 50.000 0.00 0.00 39.21 4.02
3482 5740 1.052617 TGATCCTCACCGTTTGGACA 58.947 50.000 0.00 0.00 39.21 4.02
3483 5741 1.001974 TGATCCTCACCGTTTGGACAG 59.998 52.381 0.00 0.00 39.21 3.51
3487 5745 1.333619 CCTCACCGTTTGGACAGTTTG 59.666 52.381 0.00 0.00 39.21 2.93
3488 5746 2.014128 CTCACCGTTTGGACAGTTTGT 58.986 47.619 0.00 0.00 39.21 2.83
3489 5747 2.422127 CTCACCGTTTGGACAGTTTGTT 59.578 45.455 0.00 0.00 39.21 2.83
3490 5748 3.607741 TCACCGTTTGGACAGTTTGTTA 58.392 40.909 0.00 0.00 39.21 2.41
3491 5749 4.200874 TCACCGTTTGGACAGTTTGTTAT 58.799 39.130 0.00 0.00 39.21 1.89
3493 5751 5.236911 TCACCGTTTGGACAGTTTGTTATAC 59.763 40.000 0.00 0.00 39.21 1.47
3494 5752 5.237779 CACCGTTTGGACAGTTTGTTATACT 59.762 40.000 0.00 0.00 39.21 2.12
3497 5755 6.869913 CCGTTTGGACAGTTTGTTATACTAGA 59.130 38.462 0.00 0.00 37.49 2.43
3499 5757 8.380644 CGTTTGGACAGTTTGTTATACTAGATG 58.619 37.037 0.00 0.00 0.00 2.90
3501 5759 8.997621 TTGGACAGTTTGTTATACTAGATGAC 57.002 34.615 0.00 0.00 0.00 3.06
3502 5760 8.129496 TGGACAGTTTGTTATACTAGATGACA 57.871 34.615 0.00 0.00 0.00 3.58
3503 5761 8.590204 TGGACAGTTTGTTATACTAGATGACAA 58.410 33.333 0.00 2.88 0.00 3.18
3504 5762 8.870879 GGACAGTTTGTTATACTAGATGACAAC 58.129 37.037 0.00 1.94 30.71 3.32
3505 5763 8.773404 ACAGTTTGTTATACTAGATGACAACC 57.227 34.615 0.00 0.00 30.71 3.77
3506 5764 7.822822 ACAGTTTGTTATACTAGATGACAACCC 59.177 37.037 0.00 0.21 30.71 4.11
3507 5765 7.010183 CAGTTTGTTATACTAGATGACAACCCG 59.990 40.741 0.00 0.00 30.71 5.28
3509 5767 5.202765 TGTTATACTAGATGACAACCCGGA 58.797 41.667 0.73 0.00 0.00 5.14
3523 6297 2.428622 CGGAGGGGAACGTTTGGT 59.571 61.111 0.46 0.00 0.00 3.67
3533 6307 1.971481 AACGTTTGGTTCCTGGGTAC 58.029 50.000 0.00 0.00 31.79 3.34
3538 6312 3.625764 CGTTTGGTTCCTGGGTACATATG 59.374 47.826 0.00 0.00 0.00 1.78
3539 6313 4.595986 GTTTGGTTCCTGGGTACATATGT 58.404 43.478 13.93 13.93 0.00 2.29
3631 6405 9.856162 AGAAAAACTTAACCTTCCATTGTACTA 57.144 29.630 0.00 0.00 0.00 1.82
3636 6410 9.939802 AACTTAACCTTCCATTGTACTAGTAAG 57.060 33.333 3.61 0.00 0.00 2.34
3680 6454 9.942850 AAAATTCCTCTTTGACTTCTTTTCAAA 57.057 25.926 0.00 0.00 39.99 2.69
3712 6486 7.623268 AATTTTCAGTCAAAATAGCGTGAAC 57.377 32.000 0.00 0.00 42.86 3.18
3716 6490 4.211164 TCAGTCAAAATAGCGTGAACAGTG 59.789 41.667 0.00 0.00 0.00 3.66
3719 6493 3.496884 TCAAAATAGCGTGAACAGTGACC 59.503 43.478 0.00 0.00 0.00 4.02
3721 6495 4.530710 AAATAGCGTGAACAGTGACCTA 57.469 40.909 0.00 0.00 0.00 3.08
3724 6498 5.847111 ATAGCGTGAACAGTGACCTATAA 57.153 39.130 0.00 0.00 0.00 0.98
3725 6499 4.737855 AGCGTGAACAGTGACCTATAAT 57.262 40.909 0.00 0.00 0.00 1.28
3726 6500 5.847111 AGCGTGAACAGTGACCTATAATA 57.153 39.130 0.00 0.00 0.00 0.98
3727 6501 5.833082 AGCGTGAACAGTGACCTATAATAG 58.167 41.667 0.00 0.00 0.00 1.73
3728 6502 4.444720 GCGTGAACAGTGACCTATAATAGC 59.555 45.833 0.00 0.00 0.00 2.97
3729 6503 5.588240 CGTGAACAGTGACCTATAATAGCA 58.412 41.667 0.00 0.00 0.00 3.49
3730 6504 6.040247 CGTGAACAGTGACCTATAATAGCAA 58.960 40.000 0.00 0.00 0.00 3.91
3731 6505 6.533723 CGTGAACAGTGACCTATAATAGCAAA 59.466 38.462 0.00 0.00 0.00 3.68
3733 6507 9.542462 GTGAACAGTGACCTATAATAGCAAATA 57.458 33.333 0.00 0.00 0.00 1.40
3750 6524 7.338440 AGCAAATAAATTTTGTCTTCTTCGC 57.662 32.000 0.00 0.00 0.00 4.70
3751 6525 7.147976 AGCAAATAAATTTTGTCTTCTTCGCT 58.852 30.769 0.00 0.00 0.00 4.93
3752 6526 7.115378 AGCAAATAAATTTTGTCTTCTTCGCTG 59.885 33.333 0.00 0.00 0.00 5.18
3753 6527 7.096065 GCAAATAAATTTTGTCTTCTTCGCTGT 60.096 33.333 0.00 0.00 0.00 4.40
3754 6528 7.858052 AATAAATTTTGTCTTCTTCGCTGTG 57.142 32.000 0.00 0.00 0.00 3.66
3771 6545 7.428282 TCGCTGTGAAGTCAATGTAATTTAA 57.572 32.000 0.00 0.00 31.22 1.52
3772 6546 7.866729 TCGCTGTGAAGTCAATGTAATTTAAA 58.133 30.769 0.00 0.00 31.22 1.52
3773 6547 8.511321 TCGCTGTGAAGTCAATGTAATTTAAAT 58.489 29.630 0.00 0.00 31.22 1.40
3774 6548 9.128107 CGCTGTGAAGTCAATGTAATTTAAATT 57.872 29.630 17.18 17.18 31.22 1.82
3801 6575 9.767684 TTTTGTGAAAATTCATATACTAGTGCG 57.232 29.630 5.39 0.00 39.73 5.34
3802 6576 6.943981 TGTGAAAATTCATATACTAGTGCGC 58.056 36.000 5.39 0.00 39.73 6.09
3805 6579 7.584123 GTGAAAATTCATATACTAGTGCGCAAG 59.416 37.037 14.00 10.16 39.73 4.01
3806 6580 7.279981 TGAAAATTCATATACTAGTGCGCAAGT 59.720 33.333 14.00 16.58 33.38 3.16
3808 6582 8.657074 AAATTCATATACTAGTGCGCAAGTAA 57.343 30.769 22.10 13.54 41.68 2.24
3818 6592 4.124238 AGTGCGCAAGTAAGTCAAGTTTA 58.876 39.130 14.00 0.00 41.68 2.01
3821 6595 5.564127 GTGCGCAAGTAAGTCAAGTTTATTC 59.436 40.000 14.00 0.00 41.68 1.75
3822 6596 5.468746 TGCGCAAGTAAGTCAAGTTTATTCT 59.531 36.000 8.16 0.00 41.68 2.40
3905 6679 5.562298 GTACATATGTACCCAGGAACCAT 57.438 43.478 28.48 0.00 43.73 3.55
3906 6680 5.937111 GTACATATGTACCCAGGAACCATT 58.063 41.667 28.48 0.00 43.73 3.16
3907 6681 4.792068 ACATATGTACCCAGGAACCATTG 58.208 43.478 6.56 0.00 0.00 2.82
3928 6702 3.094484 GGTATTTCCCATGACAACCCA 57.906 47.619 0.00 0.00 0.00 4.51
3929 6703 2.758423 GGTATTTCCCATGACAACCCAC 59.242 50.000 0.00 0.00 0.00 4.61
3930 6704 2.692709 ATTTCCCATGACAACCCACA 57.307 45.000 0.00 0.00 0.00 4.17
3933 6707 4.329638 TTTCCCATGACAACCCACATAT 57.670 40.909 0.00 0.00 0.00 1.78
3936 6710 3.011144 TCCCATGACAACCCACATATTGT 59.989 43.478 0.00 0.00 41.70 2.71
3937 6711 3.768757 CCCATGACAACCCACATATTGTT 59.231 43.478 0.00 0.00 39.13 2.83
3938 6712 4.381825 CCCATGACAACCCACATATTGTTG 60.382 45.833 0.00 0.00 43.76 3.33
3946 6720 6.686630 CAACCCACATATTGTTGTTGTATGT 58.313 36.000 9.82 0.00 39.05 2.29
3949 6723 6.491745 ACCCACATATTGTTGTTGTATGTTGA 59.508 34.615 0.00 0.00 37.04 3.18
3950 6724 7.014711 ACCCACATATTGTTGTTGTATGTTGAA 59.985 33.333 0.00 0.00 37.04 2.69
3951 6725 7.541783 CCCACATATTGTTGTTGTATGTTGAAG 59.458 37.037 0.00 0.00 37.04 3.02
3952 6726 8.081633 CCACATATTGTTGTTGTATGTTGAAGT 58.918 33.333 0.00 0.00 37.04 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 8.601476 GGAGAAAAATATATAATAGTTCCCGCG 58.399 37.037 0.00 0.00 0.00 6.46
86 171 5.221422 CCCTATTGTTTGTGCAGGAGAAAAA 60.221 40.000 0.00 0.00 0.00 1.94
98 183 1.993956 TGCTGCACCCTATTGTTTGT 58.006 45.000 0.00 0.00 0.00 2.83
117 202 1.957113 GCTAAGCCTGGGTGCAGAAAT 60.957 52.381 0.00 0.00 0.00 2.17
203 288 5.926542 CACACACCTAAAAGATTCTCTCGAA 59.073 40.000 0.00 0.00 0.00 3.71
205 290 5.119279 CACACACACCTAAAAGATTCTCTCG 59.881 44.000 0.00 0.00 0.00 4.04
206 291 5.992217 ACACACACACCTAAAAGATTCTCTC 59.008 40.000 0.00 0.00 0.00 3.20
222 307 2.232208 TGAAATTTGGCACACACACACA 59.768 40.909 0.00 0.00 39.29 3.72
223 308 2.886081 TGAAATTTGGCACACACACAC 58.114 42.857 0.00 0.00 39.29 3.82
224 309 3.194329 TCTTGAAATTTGGCACACACACA 59.806 39.130 0.00 0.00 39.29 3.72
225 310 3.779759 TCTTGAAATTTGGCACACACAC 58.220 40.909 0.00 0.00 39.29 3.82
226 311 4.669206 ATCTTGAAATTTGGCACACACA 57.331 36.364 0.00 0.00 39.29 3.72
227 312 7.512297 CAAATATCTTGAAATTTGGCACACAC 58.488 34.615 0.00 0.00 39.29 3.82
256 341 1.878953 TTTCCACGAGCTCCTCAAAC 58.121 50.000 8.47 0.00 0.00 2.93
269 354 9.929722 GACAGACCAAAATTTTTATTTTTCCAC 57.070 29.630 0.00 0.00 31.96 4.02
281 366 9.750125 GAAAGATACTTTGACAGACCAAAATTT 57.250 29.630 1.41 0.00 35.83 1.82
282 367 8.912988 TGAAAGATACTTTGACAGACCAAAATT 58.087 29.630 1.41 0.00 35.83 1.82
283 368 8.463930 TGAAAGATACTTTGACAGACCAAAAT 57.536 30.769 1.41 0.00 35.83 1.82
313 398 4.737855 AAATCTAGTCTACACGGTGCAT 57.262 40.909 8.30 0.00 0.00 3.96
338 426 0.603707 TGAGGAGCTCGTGGCAAAAG 60.604 55.000 14.78 0.00 44.79 2.27
361 449 4.564769 TGCAAAATTTCGAAGTGTTTGGAC 59.435 37.500 21.64 12.50 31.36 4.02
373 461 2.095969 TCTAGGTGCGTGCAAAATTTCG 60.096 45.455 0.00 0.00 0.00 3.46
412 500 2.435059 GGGCTCGCTCTTCACCAC 60.435 66.667 0.00 0.00 0.00 4.16
413 501 4.069232 CGGGCTCGCTCTTCACCA 62.069 66.667 0.00 0.00 0.00 4.17
429 518 0.031585 TCACCGTCACCTTGAAGTCG 59.968 55.000 0.00 0.00 0.00 4.18
436 525 6.373495 GGTTTTATATCTTTCACCGTCACCTT 59.627 38.462 0.00 0.00 0.00 3.50
442 531 6.235664 ACACAGGTTTTATATCTTTCACCGT 58.764 36.000 0.00 0.00 0.00 4.83
445 534 9.614792 AGGATACACAGGTTTTATATCTTTCAC 57.385 33.333 0.00 0.00 41.41 3.18
460 549 4.579869 ACTGCTTGTTAAGGATACACAGG 58.420 43.478 0.00 0.00 41.41 4.00
463 552 7.710907 TCATGATACTGCTTGTTAAGGATACAC 59.289 37.037 0.00 0.00 41.41 2.90
482 571 4.161754 CCAGCTAGCCATCTCATCATGATA 59.838 45.833 12.13 0.00 0.00 2.15
494 583 4.864334 GCGTGCCCAGCTAGCCAT 62.864 66.667 12.13 0.00 0.00 4.40
503 592 0.323302 TGAGTTAATCTGCGTGCCCA 59.677 50.000 0.00 0.00 0.00 5.36
505 594 1.009829 CCTGAGTTAATCTGCGTGCC 58.990 55.000 0.00 0.00 0.00 5.01
512 601 4.890581 AGTACAGCGATCCTGAGTTAATCT 59.109 41.667 15.51 0.00 44.64 2.40
513 602 5.189659 AGTACAGCGATCCTGAGTTAATC 57.810 43.478 15.51 0.00 44.64 1.75
533 622 9.227777 GATGACCCAATTTTGTACTAAGTTAGT 57.772 33.333 19.15 19.15 42.68 2.24
534 623 9.449719 AGATGACCCAATTTTGTACTAAGTTAG 57.550 33.333 8.41 8.41 0.00 2.34
536 625 9.975218 ATAGATGACCCAATTTTGTACTAAGTT 57.025 29.630 0.00 0.00 0.00 2.66
541 630 9.308000 TCAAAATAGATGACCCAATTTTGTACT 57.692 29.630 15.19 0.00 44.18 2.73
542 631 9.921637 TTCAAAATAGATGACCCAATTTTGTAC 57.078 29.630 15.19 0.00 44.18 2.90
544 633 9.271828 GTTTCAAAATAGATGACCCAATTTTGT 57.728 29.630 15.19 0.00 44.18 2.83
545 634 8.434661 CGTTTCAAAATAGATGACCCAATTTTG 58.565 33.333 11.32 11.32 44.73 2.44
546 635 7.602265 CCGTTTCAAAATAGATGACCCAATTTT 59.398 33.333 0.00 0.00 33.07 1.82
547 636 7.039363 TCCGTTTCAAAATAGATGACCCAATTT 60.039 33.333 0.00 0.00 0.00 1.82
548 637 6.435904 TCCGTTTCAAAATAGATGACCCAATT 59.564 34.615 0.00 0.00 0.00 2.32
549 638 5.949354 TCCGTTTCAAAATAGATGACCCAAT 59.051 36.000 0.00 0.00 0.00 3.16
550 639 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
551 640 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
552 641 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
553 642 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
554 643 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
555 644 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
556 645 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
557 646 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
558 647 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
559 648 5.484715 TGTACTCCCTCCGTTTCAAAATAG 58.515 41.667 0.00 0.00 0.00 1.73
560 649 5.486735 TGTACTCCCTCCGTTTCAAAATA 57.513 39.130 0.00 0.00 0.00 1.40
563 652 3.135167 ACTTGTACTCCCTCCGTTTCAAA 59.865 43.478 0.00 0.00 0.00 2.69
565 654 2.322658 ACTTGTACTCCCTCCGTTTCA 58.677 47.619 0.00 0.00 0.00 2.69
566 655 3.397849 AACTTGTACTCCCTCCGTTTC 57.602 47.619 0.00 0.00 0.00 2.78
567 656 3.851458 AAACTTGTACTCCCTCCGTTT 57.149 42.857 0.00 0.00 0.00 3.60
568 657 3.118149 ACAAAACTTGTACTCCCTCCGTT 60.118 43.478 0.00 0.00 43.27 4.44
571 733 4.081322 TGACAAAACTTGTACTCCCTCC 57.919 45.455 0.00 0.00 45.52 4.30
593 755 8.646004 TGAATTTGATGGAAATGGTCACTTTAA 58.354 29.630 0.00 0.00 34.30 1.52
615 786 5.769662 TCAATTACACCACTGCTTCTTGAAT 59.230 36.000 0.00 0.00 0.00 2.57
618 789 4.516698 AGTCAATTACACCACTGCTTCTTG 59.483 41.667 0.00 0.00 0.00 3.02
627 798 8.283291 CACTAGAAAAAGAGTCAATTACACCAC 58.717 37.037 0.00 0.00 0.00 4.16
651 822 3.071312 AGCTGGATTCAGGATCAGATCAC 59.929 47.826 12.66 2.13 41.19 3.06
667 838 9.224267 GCATATTCTTTCATTAATAGAGCTGGA 57.776 33.333 0.00 0.00 0.00 3.86
761 953 1.422402 ACGGCCTAAAACTTGGGAGAA 59.578 47.619 0.00 0.00 32.08 2.87
763 955 1.165270 CACGGCCTAAAACTTGGGAG 58.835 55.000 0.00 0.00 32.08 4.30
765 957 0.879090 GACACGGCCTAAAACTTGGG 59.121 55.000 0.00 0.00 0.00 4.12
766 958 1.892209 AGACACGGCCTAAAACTTGG 58.108 50.000 0.00 0.00 0.00 3.61
767 959 2.604614 GCAAGACACGGCCTAAAACTTG 60.605 50.000 16.47 16.47 37.09 3.16
768 960 1.607148 GCAAGACACGGCCTAAAACTT 59.393 47.619 0.00 0.00 0.00 2.66
769 961 1.202770 AGCAAGACACGGCCTAAAACT 60.203 47.619 0.00 0.00 0.00 2.66
771 963 1.975660 AAGCAAGACACGGCCTAAAA 58.024 45.000 0.00 0.00 0.00 1.52
772 964 2.695359 CTAAGCAAGACACGGCCTAAA 58.305 47.619 0.00 0.00 0.00 1.85
773 965 1.674817 GCTAAGCAAGACACGGCCTAA 60.675 52.381 0.00 0.00 0.00 2.69
774 966 0.108329 GCTAAGCAAGACACGGCCTA 60.108 55.000 0.00 0.00 0.00 3.93
775 967 1.376037 GCTAAGCAAGACACGGCCT 60.376 57.895 0.00 0.00 0.00 5.19
776 968 1.234615 TTGCTAAGCAAGACACGGCC 61.235 55.000 0.00 0.00 43.99 6.13
777 969 2.244000 TTGCTAAGCAAGACACGGC 58.756 52.632 0.00 0.00 43.99 5.68
789 981 7.509141 TGTCACTGATTCTTGAATTTGCTAA 57.491 32.000 0.00 0.00 0.00 3.09
844 1036 3.195698 GCCGTGTGCCTTCCGATC 61.196 66.667 0.00 0.00 0.00 3.69
1323 1563 2.738521 CCGAAGTGGGTGAGCACG 60.739 66.667 0.00 0.00 0.00 5.34
1551 1804 5.305764 AGGAAGAAGAAGTCCTCCTTCCAG 61.306 50.000 18.19 0.00 43.72 3.86
1563 1816 0.038159 ACGACGCCAGGAAGAAGAAG 60.038 55.000 0.00 0.00 0.00 2.85
1725 2353 2.034066 ATGTTGCGGTGGTGGAGG 59.966 61.111 0.00 0.00 0.00 4.30
1773 2410 0.966920 GTTCACCTCGAGGAGTTGGA 59.033 55.000 37.69 17.93 38.94 3.53
1809 3556 5.178096 ACATCCTGAACCATGATGTACAA 57.822 39.130 13.54 0.00 43.87 2.41
1811 3558 5.677091 GCAAACATCCTGAACCATGATGTAC 60.677 44.000 14.88 7.35 44.53 2.90
1814 3561 3.446161 AGCAAACATCCTGAACCATGATG 59.554 43.478 9.58 9.58 40.55 3.07
1816 3563 2.821378 CAGCAAACATCCTGAACCATGA 59.179 45.455 0.00 0.00 0.00 3.07
1819 3566 1.955778 CACAGCAAACATCCTGAACCA 59.044 47.619 0.00 0.00 33.40 3.67
1820 3567 1.270550 CCACAGCAAACATCCTGAACC 59.729 52.381 0.00 0.00 33.40 3.62
1821 3568 2.229792 TCCACAGCAAACATCCTGAAC 58.770 47.619 0.00 0.00 33.40 3.18
1869 3625 1.596203 CATGGCGGCATCAGATCGT 60.596 57.895 23.19 0.00 0.00 3.73
1918 3698 4.003788 CGTCACCTTCCCTGCCGT 62.004 66.667 0.00 0.00 0.00 5.68
2082 3881 2.040544 ATCTTTGCTTGTCGCGGGG 61.041 57.895 6.13 0.00 43.27 5.73
2217 4163 1.376553 GGACAAGGAGCTCACCTGC 60.377 63.158 17.19 1.21 40.49 4.85
2234 4213 2.193306 GCAAGAATAATGCACACGGG 57.807 50.000 0.00 0.00 43.29 5.28
2260 4245 3.251479 TCGATCAATCCAGACCAACAG 57.749 47.619 0.00 0.00 0.00 3.16
2527 4568 1.429423 CCGCGCCTTCATTTTCCTC 59.571 57.895 0.00 0.00 0.00 3.71
3025 5239 2.480555 GCGTCCCAGAAACATGCG 59.519 61.111 0.00 0.00 0.00 4.73
3040 5268 2.402388 CCAAAGATCAGCAGCGCG 59.598 61.111 0.00 0.00 0.00 6.86
3202 5454 6.317140 GGTTCAGATCACAGCTCATGAAAATA 59.683 38.462 0.00 0.00 0.00 1.40
3208 5460 1.931841 CGGTTCAGATCACAGCTCATG 59.068 52.381 0.00 0.00 0.00 3.07
3209 5461 1.134580 CCGGTTCAGATCACAGCTCAT 60.135 52.381 0.00 0.00 0.00 2.90
3227 5479 0.250295 TGCCAAACAAGAGAGACCCG 60.250 55.000 0.00 0.00 0.00 5.28
3234 5486 2.806608 AGCACATTGCCAAACAAGAG 57.193 45.000 0.00 0.00 46.52 2.85
3236 5488 3.568538 GTCTAGCACATTGCCAAACAAG 58.431 45.455 0.00 0.00 46.52 3.16
3251 5503 3.704061 ACCTCTGAGAATCTTGGTCTAGC 59.296 47.826 6.17 0.00 34.92 3.42
3262 5514 9.838339 AATAATCATACGAAAACCTCTGAGAAT 57.162 29.630 6.17 0.00 0.00 2.40
3309 5563 3.439476 ACGTGTGTAGATGGTAGAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
3314 5568 2.703416 ACGACGTGTGTAGATGGTAGA 58.297 47.619 0.00 0.00 0.00 2.59
3320 5574 7.597743 AGATTTTTCTTTACGACGTGTGTAGAT 59.402 33.333 11.56 0.00 0.00 1.98
3328 5582 7.042321 TGTCATTGAGATTTTTCTTTACGACGT 60.042 33.333 5.52 5.52 0.00 4.34
3329 5583 7.287950 TGTCATTGAGATTTTTCTTTACGACG 58.712 34.615 0.00 0.00 0.00 5.12
3395 5653 4.740902 AGGTAAATTCAGGGAAAGTTGCT 58.259 39.130 0.00 0.00 0.00 3.91
3407 5665 5.738619 TCAGTGCAGAGTAGGTAAATTCA 57.261 39.130 0.00 0.00 0.00 2.57
3408 5666 6.398918 TCTTCAGTGCAGAGTAGGTAAATTC 58.601 40.000 0.00 0.00 0.00 2.17
3441 5699 5.890985 TCATTCCCTGTGAGTCAAAAGAAAA 59.109 36.000 0.00 0.00 0.00 2.29
3442 5700 5.445069 TCATTCCCTGTGAGTCAAAAGAAA 58.555 37.500 0.00 0.00 0.00 2.52
3443 5701 5.047566 TCATTCCCTGTGAGTCAAAAGAA 57.952 39.130 0.00 0.00 0.00 2.52
3444 5702 4.705110 TCATTCCCTGTGAGTCAAAAGA 57.295 40.909 0.00 0.00 0.00 2.52
3445 5703 4.397417 GGATCATTCCCTGTGAGTCAAAAG 59.603 45.833 0.00 0.00 35.84 2.27
3447 5705 3.588842 AGGATCATTCCCTGTGAGTCAAA 59.411 43.478 0.00 0.00 43.76 2.69
3451 5709 2.837947 TGAGGATCATTCCCTGTGAGT 58.162 47.619 0.00 0.00 42.56 3.41
3463 5721 3.611305 ACTGTCCAAACGGTGAGGATCA 61.611 50.000 5.28 5.22 43.50 2.92
3464 5722 1.002087 ACTGTCCAAACGGTGAGGATC 59.998 52.381 5.28 0.00 43.50 3.36
3467 5725 1.333619 CAAACTGTCCAAACGGTGAGG 59.666 52.381 0.00 0.00 44.41 3.86
3468 5726 2.014128 ACAAACTGTCCAAACGGTGAG 58.986 47.619 0.00 0.00 44.41 3.51
3469 5727 2.116827 ACAAACTGTCCAAACGGTGA 57.883 45.000 0.00 0.00 44.41 4.02
3470 5728 2.931512 AACAAACTGTCCAAACGGTG 57.068 45.000 0.00 0.00 44.41 4.94
3473 5731 7.878477 TCTAGTATAACAAACTGTCCAAACG 57.122 36.000 0.00 0.00 0.00 3.60
3474 5732 9.431887 TCATCTAGTATAACAAACTGTCCAAAC 57.568 33.333 0.00 0.00 0.00 2.93
3475 5733 9.431887 GTCATCTAGTATAACAAACTGTCCAAA 57.568 33.333 0.00 0.00 0.00 3.28
3476 5734 8.590204 TGTCATCTAGTATAACAAACTGTCCAA 58.410 33.333 0.00 0.00 0.00 3.53
3477 5735 8.129496 TGTCATCTAGTATAACAAACTGTCCA 57.871 34.615 0.00 0.00 0.00 4.02
3478 5736 8.870879 GTTGTCATCTAGTATAACAAACTGTCC 58.129 37.037 0.00 0.00 32.17 4.02
3479 5737 8.870879 GGTTGTCATCTAGTATAACAAACTGTC 58.129 37.037 9.34 0.00 35.26 3.51
3481 5739 7.010183 CGGGTTGTCATCTAGTATAACAAACTG 59.990 40.741 13.59 11.98 37.61 3.16
3482 5740 7.039882 CGGGTTGTCATCTAGTATAACAAACT 58.960 38.462 13.59 0.00 37.61 2.66
3483 5741 6.257193 CCGGGTTGTCATCTAGTATAACAAAC 59.743 42.308 0.00 8.55 36.93 2.93
3487 5745 5.278858 CCTCCGGGTTGTCATCTAGTATAAC 60.279 48.000 0.00 0.00 0.00 1.89
3488 5746 4.831155 CCTCCGGGTTGTCATCTAGTATAA 59.169 45.833 0.00 0.00 0.00 0.98
3489 5747 4.404640 CCTCCGGGTTGTCATCTAGTATA 58.595 47.826 0.00 0.00 0.00 1.47
3490 5748 3.231818 CCTCCGGGTTGTCATCTAGTAT 58.768 50.000 0.00 0.00 0.00 2.12
3491 5749 2.662866 CCTCCGGGTTGTCATCTAGTA 58.337 52.381 0.00 0.00 0.00 1.82
3493 5751 0.753262 CCCTCCGGGTTGTCATCTAG 59.247 60.000 0.00 0.00 38.25 2.43
3494 5752 0.689745 CCCCTCCGGGTTGTCATCTA 60.690 60.000 0.00 0.00 45.50 1.98
3505 5763 2.359478 CCAAACGTTCCCCTCCGG 60.359 66.667 0.00 0.00 0.00 5.14
3506 5764 1.228033 AACCAAACGTTCCCCTCCG 60.228 57.895 0.00 0.00 0.00 4.63
3507 5765 2.637521 GAACCAAACGTTCCCCTCC 58.362 57.895 0.00 0.00 44.46 4.30
3514 5772 1.212441 TGTACCCAGGAACCAAACGTT 59.788 47.619 0.00 0.00 37.41 3.99
3515 5773 0.838608 TGTACCCAGGAACCAAACGT 59.161 50.000 0.00 0.00 0.00 3.99
3516 5774 2.194201 ATGTACCCAGGAACCAAACG 57.806 50.000 0.00 0.00 0.00 3.60
3517 5775 4.595986 ACATATGTACCCAGGAACCAAAC 58.404 43.478 6.56 0.00 0.00 2.93
3603 6377 7.654022 ACAATGGAAGGTTAAGTTTTTCTCA 57.346 32.000 0.00 0.00 0.00 3.27
3604 6378 8.847196 AGTACAATGGAAGGTTAAGTTTTTCTC 58.153 33.333 0.00 0.00 0.00 2.87
3615 6389 9.503399 CTTTTCTTACTAGTACAATGGAAGGTT 57.497 33.333 0.91 0.00 0.00 3.50
3684 6458 7.378461 TCACGCTATTTTGACTGAAAATTTGTC 59.622 33.333 0.00 0.00 40.73 3.18
3686 6460 7.621832 TCACGCTATTTTGACTGAAAATTTG 57.378 32.000 0.00 0.00 40.73 2.32
3690 6464 6.125327 TGTTCACGCTATTTTGACTGAAAA 57.875 33.333 0.00 0.00 37.93 2.29
3693 6467 4.211164 CACTGTTCACGCTATTTTGACTGA 59.789 41.667 0.00 0.00 0.00 3.41
3694 6468 4.211164 TCACTGTTCACGCTATTTTGACTG 59.789 41.667 0.00 0.00 0.00 3.51
3697 6471 3.496884 GGTCACTGTTCACGCTATTTTGA 59.503 43.478 0.00 0.00 0.00 2.69
3698 6472 3.498397 AGGTCACTGTTCACGCTATTTTG 59.502 43.478 0.00 0.00 0.00 2.44
3699 6473 3.740115 AGGTCACTGTTCACGCTATTTT 58.260 40.909 0.00 0.00 0.00 1.82
3703 6477 5.847111 ATTATAGGTCACTGTTCACGCTA 57.153 39.130 0.00 0.00 0.00 4.26
3706 6480 5.588240 TGCTATTATAGGTCACTGTTCACG 58.412 41.667 1.12 0.00 0.00 4.35
3724 6498 9.076596 GCGAAGAAGACAAAATTTATTTGCTAT 57.923 29.630 0.00 0.00 32.93 2.97
3725 6499 8.296713 AGCGAAGAAGACAAAATTTATTTGCTA 58.703 29.630 4.93 0.00 35.05 3.49
3726 6500 7.115378 CAGCGAAGAAGACAAAATTTATTTGCT 59.885 33.333 0.00 1.62 36.76 3.91
3727 6501 7.096065 ACAGCGAAGAAGACAAAATTTATTTGC 60.096 33.333 0.00 0.00 32.93 3.68
3728 6502 8.209869 CACAGCGAAGAAGACAAAATTTATTTG 58.790 33.333 0.00 0.00 35.64 2.32
3729 6503 8.134895 TCACAGCGAAGAAGACAAAATTTATTT 58.865 29.630 0.00 0.00 0.00 1.40
3730 6504 7.648142 TCACAGCGAAGAAGACAAAATTTATT 58.352 30.769 0.00 0.00 0.00 1.40
3731 6505 7.202016 TCACAGCGAAGAAGACAAAATTTAT 57.798 32.000 0.00 0.00 0.00 1.40
3733 6507 5.499139 TCACAGCGAAGAAGACAAAATTT 57.501 34.783 0.00 0.00 0.00 1.82
3775 6549 9.767684 CGCACTAGTATATGAATTTTCACAAAA 57.232 29.630 0.00 0.00 40.49 2.44
3778 6552 6.536941 TGCGCACTAGTATATGAATTTTCACA 59.463 34.615 5.66 0.00 40.49 3.58
3781 6555 7.630924 ACTTGCGCACTAGTATATGAATTTTC 58.369 34.615 11.12 0.00 29.61 2.29
3785 6559 7.434492 ACTTACTTGCGCACTAGTATATGAAT 58.566 34.615 19.70 0.00 34.71 2.57
3788 6562 6.206498 TGACTTACTTGCGCACTAGTATATG 58.794 40.000 19.70 15.27 34.71 1.78
3789 6563 6.387041 TGACTTACTTGCGCACTAGTATAT 57.613 37.500 19.70 12.35 34.71 0.86
3795 6569 3.380479 ACTTGACTTACTTGCGCACTA 57.620 42.857 11.12 0.00 0.00 2.74
3796 6570 2.240493 ACTTGACTTACTTGCGCACT 57.760 45.000 11.12 0.00 0.00 4.40
3799 6573 5.928153 AGAATAAACTTGACTTACTTGCGC 58.072 37.500 0.00 0.00 0.00 6.09
3885 6659 4.386312 CCAATGGTTCCTGGGTACATATGT 60.386 45.833 13.93 13.93 0.00 2.29
3886 6660 4.144297 CCAATGGTTCCTGGGTACATATG 58.856 47.826 0.00 0.00 0.00 1.78
3891 6665 3.588742 CCCAATGGTTCCTGGGTAC 57.411 57.895 0.00 0.00 46.37 3.34
3909 6683 3.426615 TGTGGGTTGTCATGGGAAATAC 58.573 45.455 0.00 0.00 0.00 1.89
3911 6685 2.692709 TGTGGGTTGTCATGGGAAAT 57.307 45.000 0.00 0.00 0.00 2.17
3912 6686 2.692709 ATGTGGGTTGTCATGGGAAA 57.307 45.000 0.00 0.00 0.00 3.13
3914 6688 3.011144 ACAATATGTGGGTTGTCATGGGA 59.989 43.478 0.00 0.00 33.53 4.37
3915 6689 3.364549 ACAATATGTGGGTTGTCATGGG 58.635 45.455 0.00 0.00 33.53 4.00
3922 6696 6.686630 ACATACAACAACAATATGTGGGTTG 58.313 36.000 18.71 18.71 44.75 3.77
3923 6697 6.909550 ACATACAACAACAATATGTGGGTT 57.090 33.333 0.00 0.00 37.97 4.11
3925 6699 6.918626 TCAACATACAACAACAATATGTGGG 58.081 36.000 0.00 0.00 39.05 4.61


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

AutoCloner maintained by Alex Coulton.