Multiple sequence alignment - TraesCS6D01G337900

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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 TraesCS6D01G337900 chr6D 100.000 4845 0 0 2323 7167 438308951 438304107 0.000000e+00 8948.0
1 TraesCS6D01G337900 chr6D 100.000 2090 0 0 1 2090 438311273 438309184 0.000000e+00 3860.0
2 TraesCS6D01G337900 chr6D 96.571 2129 70 3 3605 5731 456598368 456600495 0.000000e+00 3524.0
3 TraesCS6D01G337900 chr6D 100.000 709 0 0 7329 8037 438303945 438303237 0.000000e+00 1310.0
4 TraesCS6D01G337900 chr6D 75.182 548 109 23 76 601 438341650 438341108 4.850000e-57 233.0
5 TraesCS6D01G337900 chr6D 100.000 40 0 0 1415 1454 260734006 260734045 3.110000e-09 75.0
6 TraesCS6D01G337900 chr1D 97.135 2129 52 6 3607 5729 14677931 14675806 0.000000e+00 3585.0
7 TraesCS6D01G337900 chr1D 95.269 2135 91 7 3605 5731 7791176 7793308 0.000000e+00 3374.0
8 TraesCS6D01G337900 chr1D 93.258 89 6 0 6290 6378 484391666 484391578 1.820000e-26 132.0
9 TraesCS6D01G337900 chr7D 98.385 1919 29 2 3814 5731 226719029 226717112 0.000000e+00 3371.0
10 TraesCS6D01G337900 chr7D 98.332 1919 30 2 3814 5731 226711574 226709657 0.000000e+00 3365.0
11 TraesCS6D01G337900 chr7D 97.923 1926 35 5 3814 5736 580238479 580236556 0.000000e+00 3330.0
12 TraesCS6D01G337900 chr7D 93.438 320 15 4 3602 3916 589809710 589810028 3.400000e-128 470.0
13 TraesCS6D01G337900 chr3D 98.176 1919 31 4 3814 5731 608600458 608602373 0.000000e+00 3347.0
14 TraesCS6D01G337900 chr3D 97.975 1926 35 4 3814 5737 51025228 51023305 0.000000e+00 3338.0
15 TraesCS6D01G337900 chr3D 84.537 1080 102 26 2580 3604 313818674 313817605 0.000000e+00 1009.0
16 TraesCS6D01G337900 chr3D 93.396 318 15 4 3604 3916 605184018 605183702 4.390000e-127 466.0
17 TraesCS6D01G337900 chr3D 89.552 335 24 2 5795 6129 313817552 313817229 1.610000e-111 414.0
18 TraesCS6D01G337900 chr3D 82.025 484 55 15 6709 7166 313816691 313816214 4.550000e-102 383.0
19 TraesCS6D01G337900 chr3D 90.909 264 22 2 6129 6390 313817198 313816935 3.570000e-93 353.0
20 TraesCS6D01G337900 chr3D 78.669 586 79 23 838 1415 313820549 313820002 1.660000e-91 348.0
21 TraesCS6D01G337900 chr3D 100.000 42 0 0 1413 1454 536226808 536226849 2.400000e-10 78.7
22 TraesCS6D01G337900 chr3D 100.000 38 0 0 1414 1451 121335112 121335149 4.020000e-08 71.3
23 TraesCS6D01G337900 chr3D 100.000 33 0 0 1414 1446 536227054 536227022 2.420000e-05 62.1
24 TraesCS6D01G337900 chr3D 100.000 29 0 0 1418 1446 121335353 121335325 4.000000e-03 54.7
25 TraesCS6D01G337900 chr2D 98.176 1919 32 3 3814 5731 551423250 551425166 0.000000e+00 3347.0
26 TraesCS6D01G337900 chr2D 89.373 574 36 13 3605 4158 634372077 634371509 0.000000e+00 699.0
27 TraesCS6D01G337900 chr2D 93.691 317 14 4 3605 3916 342120520 342120205 3.400000e-128 470.0
28 TraesCS6D01G337900 chr2D 82.500 120 19 1 134 251 641189992 641189873 3.970000e-18 104.0
29 TraesCS6D01G337900 chr2D 100.000 41 0 0 1414 1454 70030690 70030650 8.650000e-10 76.8
30 TraesCS6D01G337900 chr2D 100.000 34 0 0 1413 1446 70030444 70030477 6.730000e-06 63.9
31 TraesCS6D01G337900 chr2D 100.000 33 0 0 1414 1446 114690844 114690876 2.420000e-05 62.1
32 TraesCS6D01G337900 chr6A 95.264 1288 45 5 2328 3604 586837890 586836608 0.000000e+00 2026.0
33 TraesCS6D01G337900 chr6A 88.785 749 40 16 1 735 586840389 586839671 0.000000e+00 878.0
34 TraesCS6D01G337900 chr6A 89.046 566 45 9 6561 7112 586834007 586833445 0.000000e+00 686.0
35 TraesCS6D01G337900 chr6A 94.688 433 17 5 6129 6556 586836186 586835755 0.000000e+00 667.0
36 TraesCS6D01G337900 chr6A 90.177 509 32 8 868 1369 586839535 586839038 0.000000e+00 647.0
37 TraesCS6D01G337900 chr6A 95.262 401 17 1 5730 6130 586836614 586836216 1.140000e-177 634.0
38 TraesCS6D01G337900 chr6A 92.664 259 15 4 7776 8034 586829310 586829056 3.540000e-98 370.0
39 TraesCS6D01G337900 chr6A 94.037 218 11 2 7568 7784 586829734 586829518 6.010000e-86 329.0
40 TraesCS6D01G337900 chr6A 84.242 330 32 5 1771 2088 586838267 586837946 3.640000e-78 303.0
41 TraesCS6D01G337900 chr6A 82.305 243 43 0 76 318 586852317 586852075 2.270000e-50 211.0
42 TraesCS6D01G337900 chr6A 80.738 244 47 0 91 334 587555991 587556234 2.960000e-44 191.0
43 TraesCS6D01G337900 chr6A 87.671 73 7 2 97 168 586334762 586334691 5.170000e-12 84.2
44 TraesCS6D01G337900 chr6A 95.918 49 1 1 766 813 586839672 586839624 2.400000e-10 78.7
45 TraesCS6D01G337900 chr6B 93.813 1293 57 11 2323 3604 663710124 663708844 0.000000e+00 1923.0
46 TraesCS6D01G337900 chr6B 91.856 835 33 14 6358 7167 663698088 663697264 0.000000e+00 1133.0
47 TraesCS6D01G337900 chr6B 92.496 653 42 4 7329 7979 663697253 663696606 0.000000e+00 928.0
48 TraesCS6D01G337900 chr6B 88.679 371 29 3 442 799 663723273 663722903 2.660000e-119 440.0
49 TraesCS6D01G337900 chr6B 91.566 249 21 0 868 1116 663722817 663722569 2.150000e-90 344.0
50 TraesCS6D01G337900 chr6B 84.848 330 30 5 1771 2088 663710495 663710174 1.680000e-81 315.0
51 TraesCS6D01G337900 chr6B 88.889 243 17 2 1126 1368 663722382 663722150 2.840000e-74 291.0
52 TraesCS6D01G337900 chr6B 92.157 204 14 1 5837 6040 663706435 663706234 3.670000e-73 287.0
53 TraesCS6D01G337900 chr6B 86.752 234 14 12 196 429 663723585 663723369 2.240000e-60 244.0
54 TraesCS6D01G337900 chr6B 91.473 129 9 2 5728 5855 663708852 663708725 8.290000e-40 176.0
55 TraesCS6D01G337900 chr6B 94.118 85 5 0 6029 6113 663698166 663698082 6.550000e-26 130.0
56 TraesCS6D01G337900 chr3B 87.100 938 90 7 2564 3474 405781741 405782674 0.000000e+00 1033.0
57 TraesCS6D01G337900 chr3B 88.060 335 29 2 5795 6129 405782880 405783203 3.520000e-103 387.0
58 TraesCS6D01G337900 chr3B 90.530 264 23 2 6129 6390 405783234 405783497 1.660000e-91 348.0
59 TraesCS6D01G337900 chr3A 92.240 683 49 3 2564 3245 416311185 416310506 0.000000e+00 965.0
60 TraesCS6D01G337900 chr3A 88.955 335 26 4 5795 6129 416307763 416307440 3.490000e-108 403.0
61 TraesCS6D01G337900 chr3A 81.856 485 54 16 6709 7166 416306903 416306426 2.120000e-100 377.0
62 TraesCS6D01G337900 chr3A 90.909 264 22 2 6129 6390 416307409 416307146 3.570000e-93 353.0
63 TraesCS6D01G337900 chr3A 76.520 592 89 28 838 1415 416312743 416312188 2.210000e-70 278.0
64 TraesCS6D01G337900 chr3A 86.667 225 20 9 2323 2540 416311544 416311323 2.900000e-59 241.0
65 TraesCS6D01G337900 chrUn 92.537 335 15 9 3597 3926 108267103 108266774 9.440000e-129 472.0
66 TraesCS6D01G337900 chrUn 93.691 317 14 4 3605 3916 445538279 445538594 3.400000e-128 470.0
67 TraesCS6D01G337900 chr1B 85.246 61 7 2 7866 7925 673451881 673451940 2.420000e-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 TraesCS6D01G337900 chr6D 438303237 438311273 8036 True 4706.000000 8948 100.000000 1 8037 3 chr6D.!!$R2 8036
1 TraesCS6D01G337900 chr6D 456598368 456600495 2127 False 3524.000000 3524 96.571000 3605 5731 1 chr6D.!!$F2 2126
2 TraesCS6D01G337900 chr6D 438341108 438341650 542 True 233.000000 233 75.182000 76 601 1 chr6D.!!$R1 525
3 TraesCS6D01G337900 chr1D 14675806 14677931 2125 True 3585.000000 3585 97.135000 3607 5729 1 chr1D.!!$R1 2122
4 TraesCS6D01G337900 chr1D 7791176 7793308 2132 False 3374.000000 3374 95.269000 3605 5731 1 chr1D.!!$F1 2126
5 TraesCS6D01G337900 chr7D 226717112 226719029 1917 True 3371.000000 3371 98.385000 3814 5731 1 chr7D.!!$R2 1917
6 TraesCS6D01G337900 chr7D 226709657 226711574 1917 True 3365.000000 3365 98.332000 3814 5731 1 chr7D.!!$R1 1917
7 TraesCS6D01G337900 chr7D 580236556 580238479 1923 True 3330.000000 3330 97.923000 3814 5736 1 chr7D.!!$R3 1922
8 TraesCS6D01G337900 chr3D 608600458 608602373 1915 False 3347.000000 3347 98.176000 3814 5731 1 chr3D.!!$F3 1917
9 TraesCS6D01G337900 chr3D 51023305 51025228 1923 True 3338.000000 3338 97.975000 3814 5737 1 chr3D.!!$R1 1923
10 TraesCS6D01G337900 chr3D 313816214 313820549 4335 True 501.400000 1009 85.138400 838 7166 5 chr3D.!!$R5 6328
11 TraesCS6D01G337900 chr2D 551423250 551425166 1916 False 3347.000000 3347 98.176000 3814 5731 1 chr2D.!!$F3 1917
12 TraesCS6D01G337900 chr2D 634371509 634372077 568 True 699.000000 699 89.373000 3605 4158 1 chr2D.!!$R3 553
13 TraesCS6D01G337900 chr6A 586829056 586840389 11333 True 661.870000 2026 92.008300 1 8034 10 chr6A.!!$R3 8033
14 TraesCS6D01G337900 chr6B 663696606 663698166 1560 True 730.333333 1133 92.823333 6029 7979 3 chr6B.!!$R1 1950
15 TraesCS6D01G337900 chr6B 663706234 663710495 4261 True 675.250000 1923 90.572750 1771 6040 4 chr6B.!!$R2 4269
16 TraesCS6D01G337900 chr6B 663722150 663723585 1435 True 329.750000 440 88.971500 196 1368 4 chr6B.!!$R3 1172
17 TraesCS6D01G337900 chr3B 405781741 405783497 1756 False 589.333333 1033 88.563333 2564 6390 3 chr3B.!!$F1 3826
18 TraesCS6D01G337900 chr3A 416306426 416312743 6317 True 436.166667 965 86.191167 838 7166 6 chr3A.!!$R1 6328

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
539 645 0.466124 GCCTCGTAAGCCATCTCCTT 59.534 55.000 0.00 0.00 37.18 3.36 F
1122 1324 0.613260 TCAAGAAGATCCCCGTGTGG 59.387 55.000 0.00 0.00 0.00 4.17 F
1550 1983 0.394938 TCTCTGGTTGCCGCAACTTA 59.605 50.000 30.09 20.14 43.14 2.24 F
3095 4758 0.321653 GAGGACGGGTCAACTGCATT 60.322 55.000 0.75 0.00 0.00 3.56 F
3652 7681 1.466025 TTTCCGACCTACGCACCAGT 61.466 55.000 0.00 0.00 41.07 4.00 F
4318 8414 3.572255 GGCTCAAAACATTTCCAGTACCA 59.428 43.478 0.00 0.00 0.00 3.25 F
4561 8657 1.962306 GTCAAAGCGGTACCGGCAA 60.962 57.895 33.98 11.47 40.19 4.52 F
6137 12572 1.068333 GCAATGTCTCGGTTGTTGCAT 60.068 47.619 3.76 0.00 43.33 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1983 0.586319 CGGAACAATCGCCGCATTAT 59.414 50.000 0.00 0.00 41.17 1.28 R
3095 4758 1.412710 TGCCAACCAAAATTGCGGTTA 59.587 42.857 10.59 0.00 43.72 2.85 R
3161 4824 2.597217 CACCTTTGCCCGCCTTCA 60.597 61.111 0.00 0.00 0.00 3.02 R
4059 8150 1.006813 TCTGGCTTCTCTCTCCCTCT 58.993 55.000 0.00 0.00 0.00 3.69 R
4544 8640 1.962306 GTTGCCGGTACCGCTTTGA 60.962 57.895 29.15 9.22 38.24 2.69 R
6116 12520 0.725784 GCAACAACCGAGACATTGCG 60.726 55.000 0.00 0.00 36.63 4.85 R
6190 12625 1.967319 AATGGTGTCTTTGCAGTCGT 58.033 45.000 0.00 0.00 0.00 4.34 R
7518 19449 0.036105 ACTCGCATTGTGCTCATGGA 60.036 50.000 0.00 0.00 42.25 3.41 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
53 54 3.887716 AGCCTGTGCAATAATCAAGATCC 59.112 43.478 0.00 0.00 41.13 3.36
59 60 5.483231 TGTGCAATAATCAAGATCCCCAAAA 59.517 36.000 0.00 0.00 0.00 2.44
107 108 5.618056 ATGCTTACATCTTGTGTGAGTTG 57.382 39.130 2.62 0.00 44.09 3.16
346 348 4.528002 CTGCAAGCAAGTGAAGCG 57.472 55.556 0.00 0.00 37.01 4.68
347 349 1.728426 CTGCAAGCAAGTGAAGCGC 60.728 57.895 0.00 0.00 37.01 5.92
348 350 2.332514 GCAAGCAAGTGAAGCGCA 59.667 55.556 11.47 0.00 37.01 6.09
349 351 1.080974 GCAAGCAAGTGAAGCGCAT 60.081 52.632 11.47 0.00 37.01 4.73
363 365 0.986992 GCGCATGCATGTCAGAAAAC 59.013 50.000 26.79 7.51 42.15 2.43
367 369 3.490155 CGCATGCATGTCAGAAAACAAAA 59.510 39.130 26.79 0.00 31.81 2.44
377 379 9.520204 CATGTCAGAAAACAAAAATGTTCTAGT 57.480 29.630 0.00 0.00 31.81 2.57
416 419 1.207329 AGGGACGGCTGCTAGTTAAAG 59.793 52.381 0.00 0.00 0.00 1.85
429 432 7.466590 GCTGCTAGTTAAAGGAGATTGATTGAC 60.467 40.741 0.25 0.00 37.12 3.18
431 434 7.766278 TGCTAGTTAAAGGAGATTGATTGACTC 59.234 37.037 0.00 0.00 0.00 3.36
432 435 7.043059 GCTAGTTAAAGGAGATTGATTGACTCG 60.043 40.741 0.00 0.00 0.00 4.18
433 436 6.702329 AGTTAAAGGAGATTGATTGACTCGT 58.298 36.000 0.00 0.00 0.00 4.18
435 438 5.869753 AAAGGAGATTGATTGACTCGTTG 57.130 39.130 0.00 0.00 38.28 4.10
439 442 4.003648 GAGATTGATTGACTCGTTGGGTT 58.996 43.478 0.00 0.00 0.00 4.11
492 597 2.129785 GCCCCATGCAGATTCCCAC 61.130 63.158 0.00 0.00 40.77 4.61
539 645 0.466124 GCCTCGTAAGCCATCTCCTT 59.534 55.000 0.00 0.00 37.18 3.36
562 668 3.550431 CATCGTCCGGGCCCATCT 61.550 66.667 24.92 0.00 0.00 2.90
563 669 2.768344 ATCGTCCGGGCCCATCTT 60.768 61.111 24.92 0.00 0.00 2.40
608 723 1.600058 TTGCCCTCCATCTCAATCCT 58.400 50.000 0.00 0.00 0.00 3.24
635 750 2.329379 GGCGATCGATGGAATAGACAC 58.671 52.381 21.57 0.00 28.34 3.67
643 761 4.115516 CGATGGAATAGACACAACTCAGG 58.884 47.826 0.00 0.00 0.00 3.86
670 788 1.006832 GTGTGCGTGTTCTGTTCAGT 58.993 50.000 0.00 0.00 0.00 3.41
674 792 1.400142 TGCGTGTTCTGTTCAGTTTGG 59.600 47.619 0.00 0.00 0.00 3.28
680 798 3.128349 GTTCTGTTCAGTTTGGCTCGTA 58.872 45.455 0.00 0.00 0.00 3.43
693 811 1.335689 GGCTCGTATACTTGTAGGCGG 60.336 57.143 0.56 0.00 0.00 6.13
701 819 3.659089 CTTGTAGGCGGGTGGGTCG 62.659 68.421 0.00 0.00 0.00 4.79
715 833 3.248171 GTCGCCGCGATCACAGTC 61.248 66.667 20.03 0.00 38.42 3.51
741 859 2.108776 TCGGATTCGGATAGGGTTAGGA 59.891 50.000 0.00 0.00 36.95 2.94
751 870 0.689055 AGGGTTAGGAAACACCGTCC 59.311 55.000 0.00 0.00 40.09 4.79
753 872 1.293963 GGTTAGGAAACACCGTCCGC 61.294 60.000 0.00 0.00 44.74 5.54
759 878 1.505425 GAAACACCGTCCGCTAAACT 58.495 50.000 0.00 0.00 0.00 2.66
800 919 3.621394 GTCCAAGCGCGATCGAGC 61.621 66.667 32.62 32.62 41.21 5.03
833 1012 3.818773 GACTCGATTTCTTCCCAAAACCA 59.181 43.478 0.00 0.00 0.00 3.67
834 1013 4.211920 ACTCGATTTCTTCCCAAAACCAA 58.788 39.130 0.00 0.00 0.00 3.67
930 1126 0.899720 CTCGCCCCCTACAACTTACA 59.100 55.000 0.00 0.00 0.00 2.41
934 1130 1.612462 GCCCCCTACAACTTACACACC 60.612 57.143 0.00 0.00 0.00 4.16
1058 1260 3.054503 CTCGTCGTCTCCACCCGT 61.055 66.667 0.00 0.00 0.00 5.28
1104 1306 2.501610 CCTAGGCCAGCGAGGTTC 59.498 66.667 5.01 0.00 40.61 3.62
1119 1321 1.279271 AGGTTCAAGAAGATCCCCGTG 59.721 52.381 0.00 0.00 36.88 4.94
1120 1322 1.003233 GGTTCAAGAAGATCCCCGTGT 59.997 52.381 0.00 0.00 31.08 4.49
1121 1323 2.076863 GTTCAAGAAGATCCCCGTGTG 58.923 52.381 0.00 0.00 0.00 3.82
1122 1324 0.613260 TCAAGAAGATCCCCGTGTGG 59.387 55.000 0.00 0.00 0.00 4.17
1123 1325 1.026718 CAAGAAGATCCCCGTGTGGC 61.027 60.000 0.00 0.00 0.00 5.01
1124 1326 1.488705 AAGAAGATCCCCGTGTGGCA 61.489 55.000 0.00 0.00 0.00 4.92
1144 1523 2.534038 TGGCACCCACTGAAGTACA 58.466 52.632 0.00 0.00 0.00 2.90
1145 1524 1.064003 TGGCACCCACTGAAGTACAT 58.936 50.000 0.00 0.00 0.00 2.29
1146 1525 1.271325 TGGCACCCACTGAAGTACATG 60.271 52.381 0.00 0.00 0.00 3.21
1331 1733 1.243902 GCTCTCTCGGATGACCCTAG 58.756 60.000 0.00 0.00 0.00 3.02
1333 1735 0.847373 TCTCTCGGATGACCCTAGCT 59.153 55.000 0.00 0.00 0.00 3.32
1334 1736 2.039216 CTCTCTCGGATGACCCTAGCTA 59.961 54.545 0.00 0.00 0.00 3.32
1371 1774 5.994250 AGGTCTTCTGCATGCTAGAATTTA 58.006 37.500 23.66 14.38 33.99 1.40
1427 1832 5.837829 GAGGATCTAGGGAGAATATCAGGT 58.162 45.833 0.00 0.00 34.61 4.00
1428 1833 5.588845 AGGATCTAGGGAGAATATCAGGTG 58.411 45.833 0.00 0.00 34.61 4.00
1429 1834 4.161377 GGATCTAGGGAGAATATCAGGTGC 59.839 50.000 0.00 0.00 34.61 5.01
1430 1835 4.477536 TCTAGGGAGAATATCAGGTGCT 57.522 45.455 0.00 0.00 0.00 4.40
1432 1837 2.334023 AGGGAGAATATCAGGTGCTCC 58.666 52.381 0.00 0.00 43.40 4.70
1433 1838 1.001406 GGGAGAATATCAGGTGCTCCG 59.999 57.143 0.00 0.00 44.71 4.63
1434 1839 1.001406 GGAGAATATCAGGTGCTCCGG 59.999 57.143 0.00 0.00 36.18 5.14
1435 1840 1.689273 GAGAATATCAGGTGCTCCGGT 59.311 52.381 0.00 0.00 39.05 5.28
1436 1841 2.891580 GAGAATATCAGGTGCTCCGGTA 59.108 50.000 0.00 0.00 39.05 4.02
1437 1842 2.894126 AGAATATCAGGTGCTCCGGTAG 59.106 50.000 0.00 0.00 39.05 3.18
1449 1854 2.239400 CTCCGGTAGCACCTGATGATA 58.761 52.381 0.00 0.00 35.66 2.15
1450 1855 2.628178 CTCCGGTAGCACCTGATGATAA 59.372 50.000 0.00 0.00 35.66 1.75
1451 1856 2.628178 TCCGGTAGCACCTGATGATAAG 59.372 50.000 0.00 0.00 35.66 1.73
1452 1857 2.289072 CCGGTAGCACCTGATGATAAGG 60.289 54.545 0.00 0.00 40.93 2.69
1454 1859 3.572682 CGGTAGCACCTGATGATAAGGTA 59.427 47.826 0.00 0.00 46.58 3.08
1457 1862 5.482175 GGTAGCACCTGATGATAAGGTAGAT 59.518 44.000 0.00 0.00 46.58 1.98
1459 1864 7.343316 GGTAGCACCTGATGATAAGGTAGATAT 59.657 40.741 0.00 0.00 46.58 1.63
1471 1876 9.032624 TGATAAGGTAGATATAACCTAAGCACC 57.967 37.037 9.17 0.00 46.85 5.01
1475 1880 9.443365 AAGGTAGATATAACCTAAGCACCTTAA 57.557 33.333 9.17 0.00 46.85 1.85
1484 1889 6.879367 ACCTAAGCACCTTAATTAGTACCA 57.121 37.500 0.00 0.00 0.00 3.25
1485 1890 6.647229 ACCTAAGCACCTTAATTAGTACCAC 58.353 40.000 0.00 0.00 0.00 4.16
1508 1913 6.591834 CACAAAGTAAGATGGTCACTAGGAAG 59.408 42.308 0.00 0.00 0.00 3.46
1529 1939 4.284178 AGGATACGTAGCTTGGTTCCTTA 58.716 43.478 11.10 0.00 46.39 2.69
1533 1966 3.163467 ACGTAGCTTGGTTCCTTAGTCT 58.837 45.455 0.00 0.00 0.00 3.24
1550 1983 0.394938 TCTCTGGTTGCCGCAACTTA 59.605 50.000 30.09 20.14 43.14 2.24
1554 1987 3.616219 TCTGGTTGCCGCAACTTATAAT 58.384 40.909 30.09 0.00 43.14 1.28
1555 1988 3.376859 TCTGGTTGCCGCAACTTATAATG 59.623 43.478 30.09 15.05 43.14 1.90
1556 1989 2.159310 TGGTTGCCGCAACTTATAATGC 60.159 45.455 30.09 14.87 43.14 3.56
1562 1995 2.969443 GCAACTTATAATGCGGCGAT 57.031 45.000 12.98 0.00 32.17 4.58
1563 1996 3.268013 GCAACTTATAATGCGGCGATT 57.732 42.857 12.98 10.37 32.17 3.34
1564 1997 2.973224 GCAACTTATAATGCGGCGATTG 59.027 45.455 12.98 1.25 32.17 2.67
1565 1998 3.548014 GCAACTTATAATGCGGCGATTGT 60.548 43.478 12.98 8.68 32.17 2.71
1566 1999 4.597079 CAACTTATAATGCGGCGATTGTT 58.403 39.130 12.98 5.54 0.00 2.83
1567 2000 4.468095 ACTTATAATGCGGCGATTGTTC 57.532 40.909 12.98 0.00 0.00 3.18
1568 2001 3.250040 ACTTATAATGCGGCGATTGTTCC 59.750 43.478 12.98 0.00 0.00 3.62
1583 2531 5.003496 CGATTGTTCCGCGTATATGTAGATG 59.997 44.000 4.92 0.00 0.00 2.90
1588 2536 4.993905 TCCGCGTATATGTAGATGGATTG 58.006 43.478 4.92 0.00 0.00 2.67
1633 2593 7.992754 AGAGAAATCCCTCATGTATTTATGC 57.007 36.000 0.00 0.00 35.68 3.14
1634 2594 7.753630 AGAGAAATCCCTCATGTATTTATGCT 58.246 34.615 0.00 0.00 35.68 3.79
1646 2606 8.836413 TCATGTATTTATGCTGTTAGCTTAACC 58.164 33.333 0.00 2.69 42.97 2.85
1648 2608 8.746052 TGTATTTATGCTGTTAGCTTAACCAT 57.254 30.769 0.00 0.00 42.97 3.55
1660 2620 8.035394 TGTTAGCTTAACCATTACTCTTCTCTG 58.965 37.037 0.00 0.00 37.88 3.35
1665 2625 8.608317 GCTTAACCATTACTCTTCTCTGATTTC 58.392 37.037 0.00 0.00 0.00 2.17
1670 2630 8.816894 ACCATTACTCTTCTCTGATTTCTAACA 58.183 33.333 0.00 0.00 0.00 2.41
1671 2631 9.658799 CCATTACTCTTCTCTGATTTCTAACAA 57.341 33.333 0.00 0.00 0.00 2.83
1693 2653 6.995686 ACAACTGTATAGGATCAACAACAACA 59.004 34.615 0.00 0.00 0.00 3.33
1695 2655 7.435068 ACTGTATAGGATCAACAACAACAAC 57.565 36.000 0.00 0.00 0.00 3.32
1696 2656 6.995686 ACTGTATAGGATCAACAACAACAACA 59.004 34.615 0.00 0.00 0.00 3.33
1700 2660 5.200368 AGGATCAACAACAACAACAATCC 57.800 39.130 0.00 0.00 33.21 3.01
1710 2670 6.695278 ACAACAACAACAATCCGATACTTTTG 59.305 34.615 0.00 0.00 0.00 2.44
1713 2673 7.357303 ACAACAACAATCCGATACTTTTGTAC 58.643 34.615 0.00 0.00 37.78 2.90
1764 2724 8.651391 TTCATAGTCTGTTTGTTTTTAGACGA 57.349 30.769 0.00 0.00 43.19 4.20
1777 2737 4.742438 TTTAGACGAACCAATGTCAAGC 57.258 40.909 0.00 0.00 37.58 4.01
1781 2741 1.603802 ACGAACCAATGTCAAGCACAG 59.396 47.619 0.00 0.00 38.85 3.66
1804 2764 3.318017 CTTCAACAGTGGTTAGGAGACG 58.682 50.000 0.00 0.00 34.87 4.18
1819 2779 1.258982 GAGACGCAATCACTATTGGCG 59.741 52.381 0.00 0.00 42.39 5.69
1834 2796 8.361889 TCACTATTGGCGCTATAGTAAATTACA 58.638 33.333 24.86 3.31 36.84 2.41
1842 2804 6.278363 CGCTATAGTAAATTACAGTGTGGGT 58.722 40.000 5.88 0.00 0.00 4.51
1848 2810 0.476338 ATTACAGTGTGGGTGGTGCA 59.524 50.000 5.88 0.00 0.00 4.57
1889 3391 8.848474 TCAGAAGAAAAGGTTAGAAATACCTG 57.152 34.615 0.00 0.00 45.17 4.00
1898 3400 8.581253 AAGGTTAGAAATACCTGAAATTGGAG 57.419 34.615 0.00 0.00 45.17 3.86
1923 3425 9.993454 AGTATAGAAACTTTTTCGAAGGTTACT 57.007 29.630 11.58 9.07 0.00 2.24
2003 3522 7.609760 TTGCAGAAACGTCTCATGTAATATT 57.390 32.000 0.00 0.00 28.78 1.28
2088 3623 4.398988 GTGATCAATAGTGTGGGCATCAAA 59.601 41.667 0.00 0.00 0.00 2.69
2394 3930 8.113173 TGGTTTTTGTTGTTAGTTTACTCAGT 57.887 30.769 0.00 0.00 0.00 3.41
2643 4305 2.227388 GCAGTGAGGATGGAAGTTTGTG 59.773 50.000 0.00 0.00 0.00 3.33
2692 4354 6.120507 AGAAGAGCAAGTATGGAAGACTTT 57.879 37.500 0.00 0.00 34.90 2.66
2695 4357 8.325046 AGAAGAGCAAGTATGGAAGACTTTTAT 58.675 33.333 0.00 0.00 34.90 1.40
2919 4582 9.630098 CAGCTTTCATTAGTGATACAAAAACAT 57.370 29.630 0.00 0.00 33.56 2.71
2977 4640 7.342769 TCAAAATCATTCAATGCATCTAGCT 57.657 32.000 0.00 0.00 45.94 3.32
2978 4641 8.454570 TCAAAATCATTCAATGCATCTAGCTA 57.545 30.769 0.00 0.00 45.94 3.32
2979 4642 8.565416 TCAAAATCATTCAATGCATCTAGCTAG 58.435 33.333 15.01 15.01 45.94 3.42
2992 4655 4.362470 TCTAGCTAGTAGGTAATCGGCA 57.638 45.455 20.10 0.00 0.00 5.69
3095 4758 0.321653 GAGGACGGGTCAACTGCATT 60.322 55.000 0.75 0.00 0.00 3.56
3161 4824 2.806244 GCGATTCACGGGCTGTAATATT 59.194 45.455 0.00 0.00 42.83 1.28
3304 4998 8.531530 GGTATGTTATTCAAATTTGCGATGAAC 58.468 33.333 13.54 12.08 36.03 3.18
3343 5346 9.831737 GTGTATCATGGAGCAATTTATATGTTC 57.168 33.333 0.00 0.00 0.00 3.18
3387 5390 2.001872 TCATGTCAGTAATGCACGCTG 58.998 47.619 7.45 7.45 0.00 5.18
3402 5405 5.533482 TGCACGCTGGTTAATTTTACATTT 58.467 33.333 0.00 0.00 0.00 2.32
3437 5440 5.992217 GTCAAATGGAGTACTGGACATATCC 59.008 44.000 0.00 0.00 46.48 2.59
3597 7626 9.669353 CACTGTTAGTATTTCATTGGATAATGC 57.331 33.333 0.00 0.00 42.71 3.56
3598 7627 9.407380 ACTGTTAGTATTTCATTGGATAATGCA 57.593 29.630 0.00 0.00 42.71 3.96
3614 7643 7.036644 TGGATAATGCATCTATTGTAGGGGAAT 60.037 37.037 0.00 0.00 33.78 3.01
3652 7681 1.466025 TTTCCGACCTACGCACCAGT 61.466 55.000 0.00 0.00 41.07 4.00
4111 8203 4.153117 GCACTTGTATGTGAGAAAGAGTGG 59.847 45.833 0.00 0.00 40.12 4.00
4302 8398 7.716799 ACTGAAAATATTTATGTGGGCTCAA 57.283 32.000 0.01 0.00 0.00 3.02
4318 8414 3.572255 GGCTCAAAACATTTCCAGTACCA 59.428 43.478 0.00 0.00 0.00 3.25
4544 8640 5.687285 GTGAATTTCATCTGCGAAAAACAGT 59.313 36.000 1.78 0.00 38.33 3.55
4561 8657 1.962306 GTCAAAGCGGTACCGGCAA 60.962 57.895 33.98 11.47 40.19 4.52
4644 8740 3.117888 GGCACCCTCCAAGAATTATCAGA 60.118 47.826 0.00 0.00 0.00 3.27
5066 9163 4.036734 ACACTTTGTCCACTATGCAAGTTG 59.963 41.667 0.00 0.00 35.76 3.16
5199 9297 4.174762 CGAGTATATCTCTCCATCGTCGA 58.825 47.826 0.00 0.00 40.75 4.20
5484 9582 4.420522 AACATTGTGCCCTCAAAATTGT 57.579 36.364 0.00 0.00 27.72 2.71
5492 9590 3.326006 TGCCCTCAAAATTGTTGGCATAA 59.674 39.130 19.82 5.66 44.57 1.90
5894 12298 5.872617 TGGTAAATCAGTTCGGTATGTCTTG 59.127 40.000 0.00 0.00 0.00 3.02
5935 12339 3.073678 CGGATGATCACAAACCAGACAA 58.926 45.455 0.00 0.00 0.00 3.18
6017 12421 3.935203 CTGACACTGGTTATGTGGTGATC 59.065 47.826 0.00 0.00 39.52 2.92
6058 12462 5.526115 AGCACATGTTTGTTGAAAGATCTG 58.474 37.500 0.00 0.00 32.34 2.90
6116 12520 1.272872 TGGAGGGTAGGTGGTGTACTC 60.273 57.143 0.00 0.00 0.00 2.59
6137 12572 1.068333 GCAATGTCTCGGTTGTTGCAT 60.068 47.619 3.76 0.00 43.33 3.96
6203 12638 9.582223 GCTATTATTTATAACGACTGCAAAGAC 57.418 33.333 0.00 0.00 0.00 3.01
6216 12651 4.036734 ACTGCAAAGACACCATTACACAAG 59.963 41.667 0.00 0.00 0.00 3.16
6236 12671 3.941629 AGAATGCCCTAGGTCCTGATAA 58.058 45.455 8.29 0.00 0.00 1.75
6282 12717 5.077134 AGGGCAATTTACTCAAGCATTTC 57.923 39.130 0.00 0.00 0.00 2.17
6286 12721 5.876460 GGCAATTTACTCAAGCATTTCCAAT 59.124 36.000 0.00 0.00 0.00 3.16
6721 15046 8.154203 TGGAACAAAGTGAGTAATATGAGTTGA 58.846 33.333 0.00 0.00 31.92 3.18
6739 15066 6.549364 TGAGTTGAAACAAATAGGGACATGTT 59.451 34.615 0.00 0.00 37.59 2.71
6741 15068 7.791029 AGTTGAAACAAATAGGGACATGTTTT 58.209 30.769 0.00 0.00 43.77 2.43
6751 15078 9.747898 AAATAGGGACATGTTTTTGTCATACTA 57.252 29.630 0.00 6.26 46.32 1.82
6842 15169 7.785033 CCAATTTGGTTTGAGCCTTATATTCT 58.215 34.615 7.31 0.00 31.35 2.40
6885 15222 5.401033 TTTCACGATTTGCAATTTGTTGG 57.599 34.783 10.81 2.98 0.00 3.77
6906 15243 3.756434 GGCTTGTGCAAAGTTACCATCTA 59.244 43.478 0.00 0.00 41.91 1.98
7034 15400 2.610232 GCCGTTGCATTTGTGAAGGAAT 60.610 45.455 0.00 0.00 37.47 3.01
7365 19296 0.028110 GGATTTCATCGCTTGCGTCC 59.972 55.000 14.70 9.27 0.00 4.79
7400 19331 4.719026 ATTGGCACATGTCTCCATAGAT 57.281 40.909 15.03 5.64 39.30 1.98
7402 19333 3.040477 TGGCACATGTCTCCATAGATCA 58.960 45.455 11.31 0.00 33.30 2.92
7426 19357 7.618117 TCACATATACCACTTGACCTCTTTCTA 59.382 37.037 0.00 0.00 0.00 2.10
7446 19377 2.625639 AGAATTATCTCGCCCATCCCT 58.374 47.619 0.00 0.00 0.00 4.20
7447 19378 2.304180 AGAATTATCTCGCCCATCCCTG 59.696 50.000 0.00 0.00 0.00 4.45
7459 19390 0.466922 CATCCCTGCCCCTTCATGTC 60.467 60.000 0.00 0.00 0.00 3.06
7512 19443 0.532640 CGCATATGCCACACCAGCTA 60.533 55.000 21.77 0.00 37.91 3.32
7513 19444 1.879372 CGCATATGCCACACCAGCTAT 60.879 52.381 21.77 0.00 37.91 2.97
7545 19476 1.400242 GCACAATGCGAGTCCTTCAAC 60.400 52.381 0.00 0.00 31.71 3.18
7563 19494 9.924650 TCCTTCAACATAAAAGTAGACTTAGTC 57.075 33.333 3.85 3.85 34.61 2.59
7655 19587 7.656707 AATTAAAAATGGTTGTCTGCATCAC 57.343 32.000 0.00 0.00 0.00 3.06
7691 19623 3.224269 CGGGGGTTTAACCTTCTTTTCA 58.776 45.455 14.27 0.00 38.64 2.69
7698 19630 7.065324 GGGGTTTAACCTTCTTTTCAAAACAAG 59.935 37.037 14.27 0.00 38.64 3.16
7757 19689 6.440965 AGGTAAAGAAGAGGCGGCTATATATT 59.559 38.462 13.24 7.18 0.00 1.28
7893 20042 8.682936 TCTTATTGAATGAAATAAGGAGAGCC 57.317 34.615 15.37 0.00 44.74 4.70
7941 20091 5.818136 ATAAAATCAGTCACCATGTTCGG 57.182 39.130 0.00 0.00 0.00 4.30
7949 20099 0.719465 CACCATGTTCGGTAGCGTTC 59.281 55.000 14.79 9.09 37.07 3.95
8034 20184 5.156355 CGCAGCAAGTTGATTGAATAGTTT 58.844 37.500 7.16 0.00 41.83 2.66
8035 20185 5.630680 CGCAGCAAGTTGATTGAATAGTTTT 59.369 36.000 7.16 0.00 41.83 2.43
8036 20186 6.183359 CGCAGCAAGTTGATTGAATAGTTTTC 60.183 38.462 7.16 0.00 41.83 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.578423 GCACAGGCTTCTCTTGTGC 59.422 57.895 14.56 14.56 46.74 4.57
53 54 6.655078 TCCTCATTTCTCTTTTCTTTTGGG 57.345 37.500 0.00 0.00 0.00 4.12
59 60 7.170965 TGCTACAATCCTCATTTCTCTTTTCT 58.829 34.615 0.00 0.00 0.00 2.52
107 108 4.228567 GTAGGAGCGAGGCCCTGC 62.229 72.222 8.73 8.73 32.93 4.85
346 348 5.406767 TTTTTGTTTTCTGACATGCATGC 57.593 34.783 26.53 18.59 0.00 4.06
347 349 6.950545 ACATTTTTGTTTTCTGACATGCATG 58.049 32.000 25.09 25.09 0.00 4.06
348 350 7.496591 AGAACATTTTTGTTTTCTGACATGCAT 59.503 29.630 0.00 0.00 31.35 3.96
349 351 6.817641 AGAACATTTTTGTTTTCTGACATGCA 59.182 30.769 0.00 0.00 31.35 3.96
363 365 7.252708 TCATGCATGCTACTAGAACATTTTTG 58.747 34.615 22.25 0.00 0.00 2.44
367 369 5.007039 CGTTCATGCATGCTACTAGAACATT 59.993 40.000 22.25 0.00 35.00 2.71
377 379 2.554142 CTCCTTCGTTCATGCATGCTA 58.446 47.619 22.25 9.44 0.00 3.49
416 419 2.939103 CCCAACGAGTCAATCAATCTCC 59.061 50.000 0.00 0.00 0.00 3.71
429 432 1.538512 TCGAGTGAGTAACCCAACGAG 59.461 52.381 0.00 0.00 0.00 4.18
431 434 1.978542 CTCGAGTGAGTAACCCAACG 58.021 55.000 3.62 0.00 37.46 4.10
492 597 2.128128 GCTTCGCACGTTCGTGTG 60.128 61.111 25.98 25.98 44.96 3.82
513 618 2.666989 GGCTTACGAGGCGAAGAAG 58.333 57.895 0.00 0.00 38.80 2.85
525 630 1.941325 CCGACAAGGAGATGGCTTAC 58.059 55.000 0.00 0.00 45.00 2.34
635 750 1.079543 CACCCTCTCGCCTGAGTTG 60.080 63.158 0.84 0.00 43.09 3.16
643 761 4.664677 ACACGCACACCCTCTCGC 62.665 66.667 0.00 0.00 0.00 5.03
670 788 3.735820 CGCCTACAAGTATACGAGCCAAA 60.736 47.826 0.00 0.00 0.00 3.28
674 792 1.335689 CCCGCCTACAAGTATACGAGC 60.336 57.143 0.00 0.00 0.00 5.03
680 798 0.619543 ACCCACCCGCCTACAAGTAT 60.620 55.000 0.00 0.00 0.00 2.12
701 819 0.249073 ATACAGACTGTGATCGCGGC 60.249 55.000 18.58 8.04 0.00 6.53
704 822 1.333931 TCCGATACAGACTGTGATCGC 59.666 52.381 25.69 0.00 35.07 4.58
710 828 2.651455 TCCGAATCCGATACAGACTGT 58.349 47.619 13.68 13.68 38.22 3.55
713 831 3.128938 CCCTATCCGAATCCGATACAGAC 59.871 52.174 0.00 0.00 38.22 3.51
715 833 3.090037 ACCCTATCCGAATCCGATACAG 58.910 50.000 0.00 0.00 38.22 2.74
741 859 2.802247 GTTAGTTTAGCGGACGGTGTTT 59.198 45.455 6.68 0.00 0.00 2.83
751 870 1.737793 CTTGGCCCAGTTAGTTTAGCG 59.262 52.381 0.00 0.00 0.00 4.26
753 872 2.092323 GGCTTGGCCCAGTTAGTTTAG 58.908 52.381 5.61 0.00 44.06 1.85
800 919 0.249398 AATCGAGTCCTTGTTCCCCG 59.751 55.000 0.00 0.00 0.00 5.73
807 986 3.334583 TGGGAAGAAATCGAGTCCTTG 57.665 47.619 0.00 0.00 0.00 3.61
833 1012 6.000246 TCCTGGCTTTTTGGAAGAAAAATT 58.000 33.333 0.00 0.00 0.00 1.82
834 1013 5.628797 TCCTGGCTTTTTGGAAGAAAAAT 57.371 34.783 0.00 0.00 0.00 1.82
865 1053 3.006728 TCCGGGCGTGATTTCCCT 61.007 61.111 0.00 0.00 40.41 4.20
958 1154 2.115343 AAATCAAGCTTCTCCGGTCC 57.885 50.000 0.00 0.00 0.00 4.46
980 1176 1.771854 TCTAAACAGCCTCCAACACCA 59.228 47.619 0.00 0.00 0.00 4.17
987 1183 1.383523 GCACCATCTAAACAGCCTCC 58.616 55.000 0.00 0.00 0.00 4.30
1018 1214 0.985490 GAGGCCTCCTGGTCCTTCAT 60.985 60.000 23.19 0.00 39.18 2.57
1058 1260 2.403378 GCCCTCGTTATTGCCGCAA 61.403 57.895 8.55 8.55 0.00 4.85
1104 1306 1.026718 GCCACACGGGGATCTTCTTG 61.027 60.000 0.00 0.00 37.04 3.02
1134 1513 1.671850 CGGAACCGCATGTACTTCAGT 60.672 52.381 0.00 0.00 0.00 3.41
1172 1551 1.278172 CGATGATGCGTCGACCATCC 61.278 60.000 28.70 19.55 44.49 3.51
1290 1688 1.276622 GAGGTTACCTCTTCCAGCCA 58.723 55.000 23.05 0.00 46.41 4.75
1415 1820 1.689273 ACCGGAGCACCTGATATTCTC 59.311 52.381 9.46 0.00 0.00 2.87
1416 1821 1.794714 ACCGGAGCACCTGATATTCT 58.205 50.000 9.46 0.00 0.00 2.40
1417 1822 3.305398 CTACCGGAGCACCTGATATTC 57.695 52.381 9.46 0.00 0.00 1.75
1429 1834 1.043816 ATCATCAGGTGCTACCGGAG 58.956 55.000 9.46 1.84 45.30 4.63
1430 1835 2.375014 TATCATCAGGTGCTACCGGA 57.625 50.000 9.46 9.70 46.11 5.14
1432 1837 2.365617 ACCTTATCATCAGGTGCTACCG 59.634 50.000 0.00 0.00 43.52 4.02
1433 1838 4.833380 TCTACCTTATCATCAGGTGCTACC 59.167 45.833 0.19 0.00 44.89 3.18
1434 1839 6.597832 ATCTACCTTATCATCAGGTGCTAC 57.402 41.667 0.19 0.00 44.89 3.58
1435 1840 9.990868 TTATATCTACCTTATCATCAGGTGCTA 57.009 33.333 0.19 0.00 44.89 3.49
1436 1841 8.754080 GTTATATCTACCTTATCATCAGGTGCT 58.246 37.037 0.19 0.00 44.89 4.40
1437 1842 7.982354 GGTTATATCTACCTTATCATCAGGTGC 59.018 40.741 0.19 0.00 44.89 5.01
1445 1850 9.032624 GGTGCTTAGGTTATATCTACCTTATCA 57.967 37.037 13.11 5.46 43.45 2.15
1449 1854 7.932683 AAGGTGCTTAGGTTATATCTACCTT 57.067 36.000 13.11 0.00 43.45 3.50
1459 1864 8.260114 GTGGTACTAATTAAGGTGCTTAGGTTA 58.740 37.037 0.00 0.00 0.00 2.85
1474 1879 8.380099 TGACCATCTTACTTTGTGGTACTAATT 58.620 33.333 0.00 0.00 44.56 1.40
1475 1880 7.822822 GTGACCATCTTACTTTGTGGTACTAAT 59.177 37.037 0.00 0.00 44.56 1.73
1477 1882 6.495872 AGTGACCATCTTACTTTGTGGTACTA 59.504 38.462 0.00 0.00 44.56 1.82
1478 1883 5.307196 AGTGACCATCTTACTTTGTGGTACT 59.693 40.000 0.00 0.00 44.56 2.73
1479 1884 5.548406 AGTGACCATCTTACTTTGTGGTAC 58.452 41.667 0.00 0.00 44.56 3.34
1480 1885 5.818678 AGTGACCATCTTACTTTGTGGTA 57.181 39.130 0.00 0.00 44.56 3.25
1482 1887 5.046591 TCCTAGTGACCATCTTACTTTGTGG 60.047 44.000 0.00 0.00 37.74 4.17
1483 1888 6.037786 TCCTAGTGACCATCTTACTTTGTG 57.962 41.667 0.00 0.00 0.00 3.33
1484 1889 6.295916 CCTTCCTAGTGACCATCTTACTTTGT 60.296 42.308 0.00 0.00 0.00 2.83
1485 1890 6.070767 TCCTTCCTAGTGACCATCTTACTTTG 60.071 42.308 0.00 0.00 0.00 2.77
1508 1913 3.538634 AAGGAACCAAGCTACGTATCC 57.461 47.619 0.00 0.00 0.00 2.59
1529 1939 1.598130 GTTGCGGCAACCAGAGACT 60.598 57.895 30.48 0.00 38.30 3.24
1533 1966 2.772077 TATAAGTTGCGGCAACCAGA 57.228 45.000 34.95 23.40 44.49 3.86
1550 1983 0.586319 CGGAACAATCGCCGCATTAT 59.414 50.000 0.00 0.00 41.17 1.28
1559 1992 4.469552 TCTACATATACGCGGAACAATCG 58.530 43.478 12.47 0.00 0.00 3.34
1560 1993 5.288712 CCATCTACATATACGCGGAACAATC 59.711 44.000 12.47 0.00 0.00 2.67
1561 1994 5.047590 TCCATCTACATATACGCGGAACAAT 60.048 40.000 12.47 0.00 0.00 2.71
1562 1995 4.278919 TCCATCTACATATACGCGGAACAA 59.721 41.667 12.47 0.00 0.00 2.83
1563 1996 3.822167 TCCATCTACATATACGCGGAACA 59.178 43.478 12.47 0.00 0.00 3.18
1564 1997 4.430137 TCCATCTACATATACGCGGAAC 57.570 45.455 12.47 0.00 0.00 3.62
1565 1998 5.047590 ACAATCCATCTACATATACGCGGAA 60.048 40.000 12.47 0.00 0.00 4.30
1566 1999 4.461431 ACAATCCATCTACATATACGCGGA 59.539 41.667 12.47 0.00 0.00 5.54
1567 2000 4.744570 ACAATCCATCTACATATACGCGG 58.255 43.478 12.47 0.00 0.00 6.46
1568 2001 6.074835 GCATACAATCCATCTACATATACGCG 60.075 42.308 3.53 3.53 0.00 6.01
1569 2002 6.980978 AGCATACAATCCATCTACATATACGC 59.019 38.462 0.00 0.00 0.00 4.42
1631 2591 6.049955 AGAGTAATGGTTAAGCTAACAGCA 57.950 37.500 6.19 0.00 45.56 4.41
1632 2592 6.819146 AGAAGAGTAATGGTTAAGCTAACAGC 59.181 38.462 6.19 0.00 42.84 4.40
1633 2593 8.254508 AGAGAAGAGTAATGGTTAAGCTAACAG 58.745 37.037 6.19 0.00 40.39 3.16
1634 2594 8.035394 CAGAGAAGAGTAATGGTTAAGCTAACA 58.965 37.037 6.19 0.00 40.39 2.41
1648 2608 9.698309 CAGTTGTTAGAAATCAGAGAAGAGTAA 57.302 33.333 0.00 0.00 0.00 2.24
1665 2625 8.771920 TGTTGTTGATCCTATACAGTTGTTAG 57.228 34.615 0.00 0.00 0.00 2.34
1670 2630 7.500892 TGTTGTTGTTGTTGATCCTATACAGTT 59.499 33.333 0.00 0.00 0.00 3.16
1671 2631 6.995686 TGTTGTTGTTGTTGATCCTATACAGT 59.004 34.615 0.00 0.00 0.00 3.55
1672 2632 7.433708 TGTTGTTGTTGTTGATCCTATACAG 57.566 36.000 0.00 0.00 0.00 2.74
1693 2653 7.972832 TGAAGTACAAAAGTATCGGATTGTT 57.027 32.000 0.00 0.00 37.25 2.83
1695 2655 8.664798 TGAATGAAGTACAAAAGTATCGGATTG 58.335 33.333 0.00 0.00 0.00 2.67
1696 2656 8.665685 GTGAATGAAGTACAAAAGTATCGGATT 58.334 33.333 0.00 0.00 0.00 3.01
1700 2660 8.239681 TCAGTGAATGAAGTACAAAAGTATCG 57.760 34.615 0.00 0.00 34.02 2.92
1737 2697 9.710979 CGTCTAAAAACAAACAGACTATGAAAA 57.289 29.630 0.00 0.00 36.17 2.29
1742 2702 7.496591 TGGTTCGTCTAAAAACAAACAGACTAT 59.503 33.333 0.00 0.00 36.17 2.12
1743 2703 6.817641 TGGTTCGTCTAAAAACAAACAGACTA 59.182 34.615 0.00 0.00 36.17 2.59
1744 2704 5.644636 TGGTTCGTCTAAAAACAAACAGACT 59.355 36.000 0.00 0.00 36.17 3.24
1746 2706 6.497785 TTGGTTCGTCTAAAAACAAACAGA 57.502 33.333 0.00 0.00 30.67 3.41
1748 2708 6.622549 ACATTGGTTCGTCTAAAAACAAACA 58.377 32.000 0.00 0.00 36.92 2.83
1749 2709 6.748198 TGACATTGGTTCGTCTAAAAACAAAC 59.252 34.615 0.00 0.00 36.92 2.93
1750 2710 6.853720 TGACATTGGTTCGTCTAAAAACAAA 58.146 32.000 0.00 0.00 36.92 2.83
1754 2714 5.066634 TGCTTGACATTGGTTCGTCTAAAAA 59.933 36.000 0.00 0.00 33.18 1.94
1755 2715 4.576873 TGCTTGACATTGGTTCGTCTAAAA 59.423 37.500 0.00 0.00 33.18 1.52
1756 2716 4.024387 GTGCTTGACATTGGTTCGTCTAAA 60.024 41.667 0.00 0.00 33.18 1.85
1757 2717 3.496884 GTGCTTGACATTGGTTCGTCTAA 59.503 43.478 0.00 0.00 33.18 2.10
1762 2722 1.069022 CCTGTGCTTGACATTGGTTCG 60.069 52.381 0.00 0.00 32.74 3.95
1764 2724 0.675633 GCCTGTGCTTGACATTGGTT 59.324 50.000 0.00 0.00 32.74 3.67
1777 2737 1.392589 AACCACTGTTGAAGCCTGTG 58.607 50.000 0.00 0.00 32.13 3.66
1781 2741 2.038557 TCTCCTAACCACTGTTGAAGCC 59.961 50.000 0.00 0.00 35.87 4.35
1790 2750 1.899814 TGATTGCGTCTCCTAACCACT 59.100 47.619 0.00 0.00 0.00 4.00
1804 2764 3.997021 ACTATAGCGCCAATAGTGATTGC 59.003 43.478 24.53 0.00 41.09 3.56
1819 2779 6.482308 CCACCCACACTGTAATTTACTATAGC 59.518 42.308 7.99 0.00 0.00 2.97
1834 2796 2.123897 GGTTGCACCACCCACACT 60.124 61.111 0.00 0.00 38.42 3.55
1848 2810 6.114187 TCTTCTGATAATGTCACAGTGGTT 57.886 37.500 0.00 0.00 32.22 3.67
1855 2817 9.436957 TCTAACCTTTTCTTCTGATAATGTCAC 57.563 33.333 0.00 0.00 32.22 3.67
1923 3425 9.676861 ATTGATGACTCAGAGACATTTCAATAA 57.323 29.630 20.81 10.46 32.27 1.40
2370 3906 8.024865 ACACTGAGTAAACTAACAACAAAAACC 58.975 33.333 0.00 0.00 0.00 3.27
2468 4007 5.185056 GTGGTGGTTTTATAGGTGCTTGATT 59.815 40.000 0.00 0.00 0.00 2.57
2643 4305 4.621991 TCTGAAGCTAGAATATCCGCAAC 58.378 43.478 0.00 0.00 0.00 4.17
2695 4357 7.679400 GCGTCCATTTTAGATGATTTCATGTCA 60.679 37.037 0.00 0.00 36.57 3.58
2719 4381 6.674066 TCCAAAGAGGTTTATTTGTTTAGCG 58.326 36.000 0.00 0.00 34.49 4.26
2977 4640 9.573166 TTAGTTAGTATTGCCGATTACCTACTA 57.427 33.333 0.00 0.00 0.00 1.82
2978 4641 6.973460 AGTTAGTATTGCCGATTACCTACT 57.027 37.500 0.00 0.00 0.00 2.57
2979 4642 9.136952 CATTAGTTAGTATTGCCGATTACCTAC 57.863 37.037 0.00 0.00 0.00 3.18
3095 4758 1.412710 TGCCAACCAAAATTGCGGTTA 59.587 42.857 10.59 0.00 43.72 2.85
3161 4824 2.597217 CACCTTTGCCCGCCTTCA 60.597 61.111 0.00 0.00 0.00 3.02
3281 4974 7.322664 AGGTTCATCGCAAATTTGAATAACAT 58.677 30.769 22.31 11.67 32.48 2.71
3402 5405 7.872993 CAGTACTCCATTTGACAGAGAAAAGTA 59.127 37.037 0.00 0.00 0.00 2.24
3458 5461 8.896320 TTCTCAAATACACTACTAGTTTGCAA 57.104 30.769 0.00 0.00 31.64 4.08
3494 5547 6.256321 GGCATTTTCAGGTGCTGTTTTATATG 59.744 38.462 0.00 0.00 41.04 1.78
3597 7626 3.755378 GCTGCATTCCCCTACAATAGATG 59.245 47.826 0.00 0.00 0.00 2.90
3598 7627 3.395607 TGCTGCATTCCCCTACAATAGAT 59.604 43.478 0.00 0.00 0.00 1.98
3599 7628 2.777114 TGCTGCATTCCCCTACAATAGA 59.223 45.455 0.00 0.00 0.00 1.98
3600 7629 3.144506 CTGCTGCATTCCCCTACAATAG 58.855 50.000 1.31 0.00 0.00 1.73
3601 7630 2.777114 TCTGCTGCATTCCCCTACAATA 59.223 45.455 1.31 0.00 0.00 1.90
3602 7631 1.565759 TCTGCTGCATTCCCCTACAAT 59.434 47.619 1.31 0.00 0.00 2.71
3603 7632 0.991146 TCTGCTGCATTCCCCTACAA 59.009 50.000 1.31 0.00 0.00 2.41
3652 7681 1.646447 AGTCTCCATAGTGGTCCTGGA 59.354 52.381 0.00 0.00 39.03 3.86
4059 8150 1.006813 TCTGGCTTCTCTCTCCCTCT 58.993 55.000 0.00 0.00 0.00 3.69
4111 8203 1.224870 GAGGGGCTGCCTAAAGGAC 59.775 63.158 19.68 0.00 37.39 3.85
4239 8335 8.015087 TGAAAAATGTCGTCATGAATAGTGAAC 58.985 33.333 0.00 0.00 34.19 3.18
4544 8640 1.962306 GTTGCCGGTACCGCTTTGA 60.962 57.895 29.15 9.22 38.24 2.69
4585 8681 9.289782 TGGAAACTTTTTGGAATTTTCAGAAAA 57.710 25.926 10.80 10.80 34.41 2.29
4644 8740 2.363680 TCAAAATGGTTTCGGCACATGT 59.636 40.909 0.00 0.00 0.00 3.21
5199 9297 2.162681 CGAGTTTGGGATTTGCTCCTT 58.837 47.619 0.00 0.00 44.28 3.36
5215 9313 7.154435 TGTTAAGTAACTTGATAGCTCGAGT 57.846 36.000 15.13 3.51 46.28 4.18
5435 9533 3.218453 ACATTTGTGTTGAATCGACCCA 58.782 40.909 0.00 0.00 0.00 4.51
5492 9590 2.832643 TTCCTGATCATGGGCATGTT 57.167 45.000 0.00 0.00 39.72 2.71
5807 9905 6.307776 ACAGATACTGGTAGATAAGCTGCTA 58.692 40.000 0.90 0.00 35.51 3.49
5863 12267 9.483916 CATACCGAACTGATTTACCATTATGTA 57.516 33.333 0.00 0.00 0.00 2.29
5869 12273 6.235231 AGACATACCGAACTGATTTACCAT 57.765 37.500 0.00 0.00 0.00 3.55
5935 12339 1.663702 CGTTCCCGCTCGTCACTTT 60.664 57.895 0.00 0.00 0.00 2.66
5965 12369 6.001460 CCACTAAATGTAACAACTCCTCCAA 58.999 40.000 0.00 0.00 0.00 3.53
6017 12421 4.142491 TGTGCTTGGTTTTCAACACAGTAG 60.142 41.667 0.00 0.00 39.74 2.57
6040 12444 9.288576 TCAGATAACAGATCTTTCAACAAACAT 57.711 29.630 0.00 0.00 0.00 2.71
6058 12462 7.707893 AGCAAACATTTGGCATTATCAGATAAC 59.292 33.333 4.91 0.00 38.57 1.89
6116 12520 0.725784 GCAACAACCGAGACATTGCG 60.726 55.000 0.00 0.00 36.63 4.85
6190 12625 1.967319 AATGGTGTCTTTGCAGTCGT 58.033 45.000 0.00 0.00 0.00 4.34
6203 12638 3.091545 AGGGCATTCTTGTGTAATGGTG 58.908 45.455 0.00 0.00 35.34 4.17
6216 12651 4.706842 TTTATCAGGACCTAGGGCATTC 57.293 45.455 18.82 2.33 0.00 2.67
6236 12671 2.273557 GCCAAGCGCATTCATGAAATT 58.726 42.857 13.09 0.00 37.47 1.82
6711 15036 8.906867 CATGTCCCTATTTGTTTCAACTCATAT 58.093 33.333 0.00 0.00 0.00 1.78
6739 15066 5.079689 TCACATCCGCTAGTATGACAAAA 57.920 39.130 8.32 0.00 0.00 2.44
6741 15068 4.099419 ACATCACATCCGCTAGTATGACAA 59.901 41.667 8.32 0.00 0.00 3.18
6751 15078 4.142609 AGTTCAATACATCACATCCGCT 57.857 40.909 0.00 0.00 0.00 5.52
6885 15222 3.923017 AGATGGTAACTTTGCACAAGC 57.077 42.857 8.09 0.00 38.52 4.01
6948 15286 7.250569 GGATTTAAATGCAAGATCAAACGAGA 58.749 34.615 14.18 0.00 0.00 4.04
7034 15400 1.987807 GCAGCTTCAGGGCCCATCTA 61.988 60.000 27.56 5.02 0.00 1.98
7365 19296 2.658593 CAATAGACGGAGGCGGCG 60.659 66.667 0.51 0.51 0.00 6.46
7400 19331 6.440647 AGAAAGAGGTCAAGTGGTATATGTGA 59.559 38.462 0.00 0.00 0.00 3.58
7402 19333 6.875972 AGAAAGAGGTCAAGTGGTATATGT 57.124 37.500 0.00 0.00 0.00 2.29
7426 19357 2.304180 CAGGGATGGGCGAGATAATTCT 59.696 50.000 0.00 0.00 33.88 2.40
7446 19377 0.400213 AAAGACGACATGAAGGGGCA 59.600 50.000 0.00 0.00 0.00 5.36
7447 19378 1.087501 GAAAGACGACATGAAGGGGC 58.912 55.000 0.00 0.00 0.00 5.80
7459 19390 1.795286 GCACCAACAGAGAGAAAGACG 59.205 52.381 0.00 0.00 0.00 4.18
7518 19449 0.036105 ACTCGCATTGTGCTCATGGA 60.036 50.000 0.00 0.00 42.25 3.41
7527 19458 2.254546 TGTTGAAGGACTCGCATTGT 57.745 45.000 0.00 0.00 0.00 2.71
7545 19476 9.784680 ACACATACGACTAAGTCTACTTTTATG 57.215 33.333 0.00 4.39 37.40 1.90
7655 19587 0.670162 CCCCGGCTTCTGCATTATTG 59.330 55.000 0.00 0.00 41.91 1.90
7757 19689 3.084646 TATCCCGCCTTCGCCCAA 61.085 61.111 0.00 0.00 0.00 4.12
7821 19969 9.745018 TCCTCAATCAAAGATACAAAAGAGATT 57.255 29.630 0.00 0.00 0.00 2.40
7893 20042 9.781834 TTATTATTATTTTGAAACGAGGCACAG 57.218 29.630 0.00 0.00 0.00 3.66
7941 20091 0.528470 ACAGAGAGCAGGAACGCTAC 59.472 55.000 0.00 0.00 44.01 3.58
7949 20099 0.730834 CGAACGTGACAGAGAGCAGG 60.731 60.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.