Multiple sequence alignment - TraesCS5A01G387400

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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 TraesCS5A01G387400 chr5A 100.000 6612 0 0 1 6612 584547196 584553807 0.000000e+00 12211
1 TraesCS5A01G387400 chr5A 81.061 132 23 2 6479 6610 584548806 584548935 3.260000e-18 104
2 TraesCS5A01G387400 chr5D 91.330 4129 259 41 3 4074 464104176 464108262 0.000000e+00 5550
3 TraesCS5A01G387400 chr5D 86.893 3380 345 37 775 4082 474823395 474820042 0.000000e+00 3698
4 TraesCS5A01G387400 chr5D 91.945 2483 163 15 4153 6612 464108310 464110778 0.000000e+00 3443
5 TraesCS5A01G387400 chr5D 85.516 1726 191 31 4159 5841 474820037 474818328 0.000000e+00 1748
6 TraesCS5A01G387400 chr5D 76.744 258 44 9 6368 6610 464105640 464105896 5.380000e-26 130
7 TraesCS5A01G387400 chr5B 91.138 3216 216 26 905 4069 571200660 571203857 0.000000e+00 4296
8 TraesCS5A01G387400 chr5B 84.319 3195 367 65 3075 6167 582108291 582105129 0.000000e+00 3001
9 TraesCS5A01G387400 chr5B 91.561 1884 139 9 4153 6028 571203890 571205761 0.000000e+00 2580
10 TraesCS5A01G387400 chr5B 85.948 1466 152 33 1645 3068 582117200 582115747 0.000000e+00 1517
11 TraesCS5A01G387400 chr5B 90.339 797 44 18 1 792 571199518 571200286 0.000000e+00 1014
12 TraesCS5A01G387400 chr5B 75.309 243 40 13 6372 6612 582117327 582117103 1.520000e-16 99
13 TraesCS5A01G387400 chr2D 84.440 3856 462 68 4 3786 551824511 551820721 0.000000e+00 3670
14 TraesCS5A01G387400 chr2D 83.538 2600 283 71 117 2675 577352914 577350419 0.000000e+00 2296
15 TraesCS5A01G387400 chr2D 83.477 1979 218 53 117 2072 577357177 577355285 0.000000e+00 1742
16 TraesCS5A01G387400 chr2D 83.064 1978 227 51 117 2072 577361453 577359562 0.000000e+00 1698
17 TraesCS5A01G387400 chr2D 81.198 718 76 24 4202 4906 551809100 551808429 2.110000e-144 523
18 TraesCS5A01G387400 chr2D 82.215 596 85 16 4497 5082 577342128 577341544 1.660000e-135 494
19 TraesCS5A01G387400 chr2D 83.371 439 47 11 5231 5665 551714272 551713856 3.740000e-102 383
20 TraesCS5A01G387400 chr2D 93.274 223 13 2 6390 6612 551705145 551704925 1.780000e-85 327
21 TraesCS5A01G387400 chr2D 79.694 458 61 12 2751 3183 577344485 577344035 1.080000e-77 302
22 TraesCS5A01G387400 chr2D 78.439 487 56 26 5707 6162 551706037 551705569 8.450000e-69 272
23 TraesCS5A01G387400 chr2A 82.334 4036 544 86 4 3974 692274336 692270405 0.000000e+00 3347
24 TraesCS5A01G387400 chr2A 82.645 3682 496 68 364 3974 692359937 692356328 0.000000e+00 3127
25 TraesCS5A01G387400 chr2A 82.787 1679 212 40 1036 2675 715437452 715435812 0.000000e+00 1428
26 TraesCS5A01G387400 chr2A 82.628 1560 226 20 2447 3974 692328250 692326704 0.000000e+00 1338
27 TraesCS5A01G387400 chr2A 81.302 722 100 18 1723 2426 692343492 692342788 2.690000e-153 553
28 TraesCS5A01G387400 chr2A 82.353 595 84 16 4497 5081 715422434 715421851 1.280000e-136 497
29 TraesCS5A01G387400 chr2A 79.694 719 87 23 4202 4906 692270238 692269565 1.300000e-126 464
30 TraesCS5A01G387400 chr7A 87.172 2323 219 30 600 2886 660067786 660070065 0.000000e+00 2566
31 TraesCS5A01G387400 chr7A 83.876 2090 194 62 4153 6171 660082240 660084257 0.000000e+00 1860
32 TraesCS5A01G387400 chr7A 84.984 1232 155 14 2882 4087 660081004 660082231 0.000000e+00 1223
33 TraesCS5A01G387400 chr7B 86.476 2307 252 25 1826 4083 626566803 626564508 0.000000e+00 2477
34 TraesCS5A01G387400 chr7B 84.740 2097 210 59 4153 6171 626564499 626562435 0.000000e+00 1999
35 TraesCS5A01G387400 chr7B 85.581 1179 135 18 603 1769 626567976 626566821 0.000000e+00 1203
36 TraesCS5A01G387400 chr2B 82.272 2606 323 77 117 2675 694487614 694485101 0.000000e+00 2124
37 TraesCS5A01G387400 chr2B 83.560 1618 203 41 1088 2668 722379782 722378191 0.000000e+00 1456
38 TraesCS5A01G387400 chr2B 82.095 592 83 18 4497 5077 694420839 694420260 9.970000e-133 484
39 TraesCS5A01G387400 chr7D 87.782 1465 130 28 4211 5638 570988183 570989635 0.000000e+00 1668
40 TraesCS5A01G387400 chr7D 86.468 1005 124 4 3076 4074 570978339 570979337 0.000000e+00 1092
41 TraesCS5A01G387400 chr7D 84.436 559 47 17 5641 6169 570992328 570992876 1.270000e-141 514
42 TraesCS5A01G387400 chr7D 92.208 154 11 1 3 155 570953753 570953906 4.020000e-52 217
43 TraesCS5A01G387400 chrUn 83.436 1298 144 32 713 1998 421373946 421372708 0.000000e+00 1140


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 TraesCS5A01G387400 chr5A 584547196 584553807 6611 False 12211.0 12211 100.000000 1 6612 1 chr5A.!!$F1 6611
1 TraesCS5A01G387400 chr5D 464104176 464110778 6602 False 3041.0 5550 86.673000 3 6612 3 chr5D.!!$F1 6609
2 TraesCS5A01G387400 chr5D 474818328 474823395 5067 True 2723.0 3698 86.204500 775 5841 2 chr5D.!!$R1 5066
3 TraesCS5A01G387400 chr5B 582105129 582108291 3162 True 3001.0 3001 84.319000 3075 6167 1 chr5B.!!$R1 3092
4 TraesCS5A01G387400 chr5B 571199518 571205761 6243 False 2630.0 4296 91.012667 1 6028 3 chr5B.!!$F1 6027
5 TraesCS5A01G387400 chr5B 582115747 582117327 1580 True 808.0 1517 80.628500 1645 6612 2 chr5B.!!$R2 4967
6 TraesCS5A01G387400 chr2D 551820721 551824511 3790 True 3670.0 3670 84.440000 4 3786 1 chr2D.!!$R3 3782
7 TraesCS5A01G387400 chr2D 577350419 577361453 11034 True 1912.0 2296 83.359667 117 2675 3 chr2D.!!$R6 2558
8 TraesCS5A01G387400 chr2D 551808429 551809100 671 True 523.0 523 81.198000 4202 4906 1 chr2D.!!$R2 704
9 TraesCS5A01G387400 chr2D 577341544 577344485 2941 True 398.0 494 80.954500 2751 5082 2 chr2D.!!$R5 2331
10 TraesCS5A01G387400 chr2D 551704925 551706037 1112 True 299.5 327 85.856500 5707 6612 2 chr2D.!!$R4 905
11 TraesCS5A01G387400 chr2A 692356328 692359937 3609 True 3127.0 3127 82.645000 364 3974 1 chr2A.!!$R3 3610
12 TraesCS5A01G387400 chr2A 692269565 692274336 4771 True 1905.5 3347 81.014000 4 4906 2 chr2A.!!$R6 4902
13 TraesCS5A01G387400 chr2A 715435812 715437452 1640 True 1428.0 1428 82.787000 1036 2675 1 chr2A.!!$R5 1639
14 TraesCS5A01G387400 chr2A 692326704 692328250 1546 True 1338.0 1338 82.628000 2447 3974 1 chr2A.!!$R1 1527
15 TraesCS5A01G387400 chr2A 692342788 692343492 704 True 553.0 553 81.302000 1723 2426 1 chr2A.!!$R2 703
16 TraesCS5A01G387400 chr2A 715421851 715422434 583 True 497.0 497 82.353000 4497 5081 1 chr2A.!!$R4 584
17 TraesCS5A01G387400 chr7A 660067786 660070065 2279 False 2566.0 2566 87.172000 600 2886 1 chr7A.!!$F1 2286
18 TraesCS5A01G387400 chr7A 660081004 660084257 3253 False 1541.5 1860 84.430000 2882 6171 2 chr7A.!!$F2 3289
19 TraesCS5A01G387400 chr7B 626562435 626567976 5541 True 1893.0 2477 85.599000 603 6171 3 chr7B.!!$R1 5568
20 TraesCS5A01G387400 chr2B 694485101 694487614 2513 True 2124.0 2124 82.272000 117 2675 1 chr2B.!!$R2 2558
21 TraesCS5A01G387400 chr2B 722378191 722379782 1591 True 1456.0 1456 83.560000 1088 2668 1 chr2B.!!$R3 1580
22 TraesCS5A01G387400 chr2B 694420260 694420839 579 True 484.0 484 82.095000 4497 5077 1 chr2B.!!$R1 580
23 TraesCS5A01G387400 chr7D 570978339 570979337 998 False 1092.0 1092 86.468000 3076 4074 1 chr7D.!!$F2 998
24 TraesCS5A01G387400 chr7D 570988183 570992876 4693 False 1091.0 1668 86.109000 4211 6169 2 chr7D.!!$F3 1958
25 TraesCS5A01G387400 chrUn 421372708 421373946 1238 True 1140.0 1140 83.436000 713 1998 1 chrUn.!!$R1 1285

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
467 479 0.036732 TTGCAAAGTCCATCGAGCCT 59.963 50.0 0.00 0.0 0.00 4.58 F
468 480 0.391661 TGCAAAGTCCATCGAGCCTC 60.392 55.0 0.00 0.0 0.00 4.70 F
871 908 0.395036 TTTGAGTGTGTGTGTGGGGG 60.395 55.0 0.00 0.0 0.00 5.40 F
2022 10914 0.469144 AGGAGAGGGAGGATCGAAGC 60.469 60.0 0.00 0.0 34.37 3.86 F
3064 12006 0.671781 GCAGTGCAAGGACATCGACT 60.672 55.0 11.09 0.0 0.00 4.18 F
3420 12434 0.179150 CTGCGGAGAGGAAGAACTCG 60.179 60.0 0.00 0.0 42.31 4.18 F
3455 12470 0.548510 GATCCAACTTCTGGGGGAGG 59.451 60.0 0.00 0.0 46.44 4.30 F
3681 12721 0.610232 CCCAAGAAGTCCAAGGCTGG 60.610 60.0 0.00 0.0 45.08 4.85 F
3927 13001 0.742635 CGAGGGGAAAAGCTCTGCTC 60.743 60.0 0.00 0.0 38.25 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 6245 0.393077 ACACAAGTTCCACTCGAGGG 59.607 55.000 18.41 13.63 0.00 4.30 R
1646 6248 0.742505 ACGACACAAGTTCCACTCGA 59.257 50.000 0.00 0.00 0.00 4.04 R
2086 10978 2.625314 GCTGCCCTTGTTCTTCTTTCTT 59.375 45.455 0.00 0.00 0.00 2.52 R
3328 12342 0.031010 AACCTAGCCCTCTTCCCGAT 60.031 55.000 0.00 0.00 0.00 4.18 R
4452 14286 0.109723 AAAGGGTGCGCTTACAGGAA 59.890 50.000 9.73 0.00 0.00 3.36 R
4453 14287 0.109723 AAAAGGGTGCGCTTACAGGA 59.890 50.000 9.73 0.00 0.00 3.86 R
4947 14808 1.026718 GGTTGTTCTCCATGGCGAGG 61.027 60.000 6.96 0.00 0.00 4.63 R
5565 15457 2.218953 GCAAGATGCACCATGGATTG 57.781 50.000 21.47 8.56 44.26 2.67 R
5724 18307 0.726827 TCTAAGAGGCGCGCAAAATG 59.273 50.000 34.42 17.28 0.00 2.32 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
54 55 0.677842 ACTGGAGAACACGGTACCAC 59.322 55.000 13.54 0.00 0.00 4.16
238 243 0.476771 ACGGAACACCCTCAACCAAT 59.523 50.000 0.00 0.00 0.00 3.16
259 264 3.945640 GGGCCTAAAATAGACCCTCAA 57.054 47.619 0.84 0.00 44.39 3.02
267 272 7.993758 GCCTAAAATAGACCCTCAATAGAAGTT 59.006 37.037 0.00 0.00 0.00 2.66
318 323 3.539338 GCCTGGAATTGGGCCTATT 57.461 52.632 13.12 13.12 42.30 1.73
382 394 7.904558 AAAAATGGACTTTCCTTTCTTCTCT 57.095 32.000 0.00 0.00 37.46 3.10
395 407 1.132849 TCTTCTCTCAAGTCCCACCCA 60.133 52.381 0.00 0.00 0.00 4.51
447 459 2.044630 CCCCCTTTATAACCCCCAAACA 59.955 50.000 0.00 0.00 0.00 2.83
467 479 0.036732 TTGCAAAGTCCATCGAGCCT 59.963 50.000 0.00 0.00 0.00 4.58
468 480 0.391661 TGCAAAGTCCATCGAGCCTC 60.392 55.000 0.00 0.00 0.00 4.70
469 481 1.092345 GCAAAGTCCATCGAGCCTCC 61.092 60.000 0.00 0.00 0.00 4.30
498 511 2.037620 GCAACCAACCATGTTGGCCA 62.038 55.000 22.49 0.00 42.67 5.36
512 534 4.464008 TGTTGGCCATCATCTAAATCTCC 58.536 43.478 12.62 0.00 0.00 3.71
521 543 7.549839 CCATCATCTAAATCTCCTCTCTCATC 58.450 42.308 0.00 0.00 0.00 2.92
522 544 7.398047 CCATCATCTAAATCTCCTCTCTCATCT 59.602 40.741 0.00 0.00 0.00 2.90
523 545 8.809066 CATCATCTAAATCTCCTCTCTCATCTT 58.191 37.037 0.00 0.00 0.00 2.40
525 547 9.874195 TCATCTAAATCTCCTCTCTCATCTTAA 57.126 33.333 0.00 0.00 0.00 1.85
531 553 9.438163 AAATCTCCTCTCTCATCTTAATCTCTT 57.562 33.333 0.00 0.00 0.00 2.85
532 554 8.641498 ATCTCCTCTCTCATCTTAATCTCTTC 57.359 38.462 0.00 0.00 0.00 2.87
533 555 7.815383 TCTCCTCTCTCATCTTAATCTCTTCT 58.185 38.462 0.00 0.00 0.00 2.85
534 556 7.939039 TCTCCTCTCTCATCTTAATCTCTTCTC 59.061 40.741 0.00 0.00 0.00 2.87
535 557 7.815383 TCCTCTCTCATCTTAATCTCTTCTCT 58.185 38.462 0.00 0.00 0.00 3.10
536 558 7.939039 TCCTCTCTCATCTTAATCTCTTCTCTC 59.061 40.741 0.00 0.00 0.00 3.20
537 559 7.095060 CCTCTCTCATCTTAATCTCTTCTCTCG 60.095 44.444 0.00 0.00 0.00 4.04
538 560 7.279615 TCTCTCATCTTAATCTCTTCTCTCGT 58.720 38.462 0.00 0.00 0.00 4.18
543 565 6.352682 TCTTAATCTCTTCTCTCGTCTTCG 57.647 41.667 0.00 0.00 38.55 3.79
573 595 0.623723 GAATGCCCCTTGGAGTGGTA 59.376 55.000 0.00 0.00 0.00 3.25
615 637 3.799137 TTTAAAGTGATTCACGACGCC 57.201 42.857 11.01 0.00 39.64 5.68
773 796 9.046296 GGTTGTATCCATGTTCATAGTTTCTAG 57.954 37.037 0.00 0.00 0.00 2.43
840 867 8.388103 CGGTTTTCTTGATAAGATTGACGTATT 58.612 33.333 0.00 0.00 37.38 1.89
858 895 5.154932 CGTATTCGTCTTCTCACTTTGAGT 58.845 41.667 3.19 0.00 44.58 3.41
860 897 4.386867 TTCGTCTTCTCACTTTGAGTGT 57.613 40.909 7.85 0.00 46.03 3.55
862 899 3.130516 TCGTCTTCTCACTTTGAGTGTGT 59.869 43.478 7.85 0.00 46.03 3.72
864 901 4.184629 GTCTTCTCACTTTGAGTGTGTGT 58.815 43.478 7.85 0.00 46.03 3.72
865 902 4.033358 GTCTTCTCACTTTGAGTGTGTGTG 59.967 45.833 7.85 0.00 46.03 3.82
866 903 3.610040 TCTCACTTTGAGTGTGTGTGT 57.390 42.857 7.85 0.00 46.03 3.72
867 904 3.261580 TCTCACTTTGAGTGTGTGTGTG 58.738 45.455 7.85 0.00 46.03 3.82
868 905 2.352651 CTCACTTTGAGTGTGTGTGTGG 59.647 50.000 7.85 0.00 46.03 4.17
869 906 1.401552 CACTTTGAGTGTGTGTGTGGG 59.598 52.381 0.00 0.00 41.19 4.61
870 907 1.024271 CTTTGAGTGTGTGTGTGGGG 58.976 55.000 0.00 0.00 0.00 4.96
871 908 0.395036 TTTGAGTGTGTGTGTGGGGG 60.395 55.000 0.00 0.00 0.00 5.40
1091 1385 6.939132 AATGCTACCTTTTCTCTCATGATG 57.061 37.500 0.00 0.00 0.00 3.07
1359 5941 9.552114 GATGAATATATAGAAATGTGCAAGTGC 57.448 33.333 0.00 0.00 42.50 4.40
1385 5967 4.581077 TGCCAAAATATTATGCATGCGA 57.419 36.364 14.09 0.00 0.00 5.10
1431 6029 9.394767 AGCATTCATTTATGATGTGTACTTGTA 57.605 29.630 0.00 0.00 36.56 2.41
1533 6135 4.829064 TGTTGGTTGTTAGATCTGCAAC 57.171 40.909 24.69 24.69 41.02 4.17
1538 6140 5.830912 TGGTTGTTAGATCTGCAACAAAAG 58.169 37.500 29.36 0.00 43.97 2.27
1540 6142 5.009610 GGTTGTTAGATCTGCAACAAAAGGA 59.990 40.000 29.36 9.94 43.97 3.36
1541 6143 5.689383 TGTTAGATCTGCAACAAAAGGAC 57.311 39.130 5.18 0.00 31.93 3.85
1545 6147 5.489792 AGATCTGCAACAAAAGGACTCTA 57.510 39.130 0.00 0.00 0.00 2.43
1547 6149 4.415881 TCTGCAACAAAAGGACTCTACA 57.584 40.909 0.00 0.00 0.00 2.74
1548 6150 4.973168 TCTGCAACAAAAGGACTCTACAT 58.027 39.130 0.00 0.00 0.00 2.29
1549 6151 4.756642 TCTGCAACAAAAGGACTCTACATG 59.243 41.667 0.00 0.00 0.00 3.21
1624 6226 9.146270 CAGAACAAAAATACAAAATTGAAAGCG 57.854 29.630 0.00 0.00 0.00 4.68
1626 6228 9.484326 GAACAAAAATACAAAATTGAAAGCGTT 57.516 25.926 0.00 0.00 0.00 4.84
1627 6229 9.833182 AACAAAAATACAAAATTGAAAGCGTTT 57.167 22.222 0.00 0.00 0.00 3.60
1628 6230 9.484326 ACAAAAATACAAAATTGAAAGCGTTTC 57.516 25.926 0.00 4.24 40.08 2.78
1643 6245 7.537306 TGAAAGCGTTTCATTTGTAGATTTAGC 59.463 33.333 8.47 0.00 44.21 3.09
1644 6246 5.880341 AGCGTTTCATTTGTAGATTTAGCC 58.120 37.500 0.00 0.00 0.00 3.93
1645 6247 5.034797 GCGTTTCATTTGTAGATTTAGCCC 58.965 41.667 0.00 0.00 0.00 5.19
1646 6248 5.163652 GCGTTTCATTTGTAGATTTAGCCCT 60.164 40.000 0.00 0.00 0.00 5.19
1647 6249 6.487103 CGTTTCATTTGTAGATTTAGCCCTC 58.513 40.000 0.00 0.00 0.00 4.30
1648 6250 6.487103 GTTTCATTTGTAGATTTAGCCCTCG 58.513 40.000 0.00 0.00 0.00 4.63
1747 10629 7.661536 ATTGTATTGCAGAGAGAAGTACCTA 57.338 36.000 0.00 0.00 0.00 3.08
1804 10686 6.431198 AAAAACAGTATAACACTATGGGCG 57.569 37.500 0.00 0.00 34.98 6.13
1817 10699 5.720041 ACACTATGGGCGTGGTAGATAATAT 59.280 40.000 0.00 0.00 36.71 1.28
1933 10816 3.426829 GGAGAAGCAAAATTCCTCGAAGC 60.427 47.826 0.00 0.00 0.00 3.86
1970 10853 5.245977 AGAACAAGGAGGAGAAAGAGAAGAG 59.754 44.000 0.00 0.00 0.00 2.85
2022 10914 0.469144 AGGAGAGGGAGGATCGAAGC 60.469 60.000 0.00 0.00 34.37 3.86
2137 11041 9.500785 AAATTGAGAAAGAGAAAGTAGAGGAAG 57.499 33.333 0.00 0.00 0.00 3.46
2216 11141 5.946377 AGGATAAGGACCAGAATGACAAAAC 59.054 40.000 0.00 0.00 39.69 2.43
2235 11160 4.590850 AACAAATTGCCCTCACTTCTTC 57.409 40.909 0.00 0.00 0.00 2.87
2239 11164 1.434188 TTGCCCTCACTTCTTCAGGA 58.566 50.000 0.00 0.00 0.00 3.86
2306 11232 8.359642 TCTTGATTCATAACAACAAAGAAAGGG 58.640 33.333 0.00 0.00 0.00 3.95
2321 11247 7.724061 ACAAAGAAAGGGCTAACTCATTTTAGA 59.276 33.333 0.00 0.00 31.60 2.10
2511 11440 7.312154 TGTTTGAAACATGGACTATACAATGC 58.688 34.615 6.66 0.00 36.25 3.56
2702 11638 6.321435 GCACTATAGGAAGGCAAGGTTAAATT 59.679 38.462 4.43 0.00 0.00 1.82
2749 11688 4.637968 CTCGACGTGTTCAACCATTATTG 58.362 43.478 0.00 0.00 0.00 1.90
2796 11735 3.266772 TGCAGACCATTCCAGTAGGATTT 59.733 43.478 0.00 0.00 45.26 2.17
2823 11762 6.659242 ACAAATACTTGGAAGATTGTACAGGG 59.341 38.462 0.00 0.00 36.82 4.45
2861 11800 1.110442 CCAAGCGGGAATAAATGGCA 58.890 50.000 0.00 0.00 40.01 4.92
2894 11833 1.880941 AAAATCTCCGGGGAGCTACT 58.119 50.000 11.27 0.00 41.71 2.57
2940 11879 0.817654 TCTCTGACAATCGCATCGGT 59.182 50.000 0.00 0.00 0.00 4.69
2946 11885 2.210116 GACAATCGCATCGGTTATGGT 58.790 47.619 0.00 0.00 35.99 3.55
3032 11971 2.239400 CTGTGAGGATCCCTATGCGTA 58.761 52.381 8.55 0.00 31.76 4.42
3064 12006 0.671781 GCAGTGCAAGGACATCGACT 60.672 55.000 11.09 0.00 0.00 4.18
3070 12033 1.021390 CAAGGACATCGACTGGCACC 61.021 60.000 0.00 0.00 32.82 5.01
3071 12034 1.480212 AAGGACATCGACTGGCACCA 61.480 55.000 0.00 0.00 32.82 4.17
3119 12085 4.305769 CCTCAAGAAGAAGACACTCACAG 58.694 47.826 0.00 0.00 0.00 3.66
3260 12274 1.069091 CAGTGAATGTCGCATGTGCAA 60.069 47.619 0.00 0.00 42.21 4.08
3261 12275 1.814394 AGTGAATGTCGCATGTGCAAT 59.186 42.857 0.00 0.00 42.21 3.56
3420 12434 0.179150 CTGCGGAGAGGAAGAACTCG 60.179 60.000 0.00 0.00 42.31 4.18
3455 12470 0.548510 GATCCAACTTCTGGGGGAGG 59.451 60.000 0.00 0.00 46.44 4.30
3488 12503 5.277828 GCGATAGTTTGGCAGGTAATTAAGG 60.278 44.000 0.00 0.00 39.35 2.69
3553 12588 7.552848 ACGTGTAGTACTTTTTACGTGTATG 57.447 36.000 18.91 0.00 42.31 2.39
3590 12625 8.537049 TGGCTTGATTTTGTAAAATGATTCTG 57.463 30.769 7.27 0.00 38.64 3.02
3622 12658 6.327934 TGTTATCGAGCTAACCTTTGTCTAC 58.672 40.000 6.49 0.00 31.83 2.59
3626 12662 3.365666 CGAGCTAACCTTTGTCTACGTGA 60.366 47.826 0.00 0.00 0.00 4.35
3681 12721 0.610232 CCCAAGAAGTCCAAGGCTGG 60.610 60.000 0.00 0.00 45.08 4.85
3754 12794 5.460646 AGTGACAATTTTGCAGGTAATTCG 58.539 37.500 0.00 0.00 0.00 3.34
3771 12811 8.437575 AGGTAATTCGGAATAACCATTAGATGT 58.562 33.333 3.22 0.00 38.90 3.06
3927 13001 0.742635 CGAGGGGAAAAGCTCTGCTC 60.743 60.000 0.00 0.00 38.25 4.26
3948 13022 8.506168 TGCTCCTCCTTTAATTGTTTATACTG 57.494 34.615 0.00 0.00 0.00 2.74
3974 13048 6.403092 GGTCTTCTTCTTCAGCATCTAAAAGC 60.403 42.308 0.00 0.00 0.00 3.51
4074 13202 6.821665 AGTAGAACTTGTTTACACACACACAT 59.178 34.615 0.00 0.00 30.32 3.21
4082 13210 7.971183 TGTTTACACACACACATACATACAT 57.029 32.000 0.00 0.00 0.00 2.29
4084 13212 9.660180 TGTTTACACACACACATACATACATAT 57.340 29.630 0.00 0.00 0.00 1.78
4197 13325 8.794335 TCGAGCTATTTATATTCTCTGCTAGA 57.206 34.615 0.00 0.00 0.00 2.43
4243 13513 8.502738 ACTGTAAAATGGTTCCTATCCATATGT 58.497 33.333 1.24 0.00 43.85 2.29
4253 13523 9.965902 GGTTCCTATCCATATGTTCTTATCATT 57.034 33.333 1.24 0.00 0.00 2.57
4393 14195 5.598005 TCAATTCCCAATGTTCAACAAGAGT 59.402 36.000 0.00 0.00 0.00 3.24
4431 14233 3.944015 CCTGGCAGAGGTAAATCTCTTTG 59.056 47.826 17.94 0.00 41.76 2.77
4452 14286 3.722101 TGTTTCTTCCTTCCTTCCTTCCT 59.278 43.478 0.00 0.00 0.00 3.36
4453 14287 4.168088 TGTTTCTTCCTTCCTTCCTTCCTT 59.832 41.667 0.00 0.00 0.00 3.36
4454 14288 4.642466 TTCTTCCTTCCTTCCTTCCTTC 57.358 45.455 0.00 0.00 0.00 3.46
4455 14289 2.913617 TCTTCCTTCCTTCCTTCCTTCC 59.086 50.000 0.00 0.00 0.00 3.46
4542 14385 7.862873 GCCTGATAGTTTGCATCTTTTTATACC 59.137 37.037 0.00 0.00 0.00 2.73
4636 14479 4.575973 GCCATGGAGAGGGCGCAT 62.576 66.667 18.40 0.00 39.75 4.73
4742 14595 9.829507 ATCAATTCAATTTCTTCTCTCGATAGT 57.170 29.630 0.00 0.00 37.40 2.12
4744 14597 9.699985 CAATTCAATTTCTTCTCTCGATAGTTG 57.300 33.333 0.00 0.00 37.40 3.16
4745 14598 9.658799 AATTCAATTTCTTCTCTCGATAGTTGA 57.341 29.630 0.00 0.00 37.40 3.18
4746 14599 8.467402 TTCAATTTCTTCTCTCGATAGTTGAC 57.533 34.615 0.00 0.00 37.40 3.18
4747 14600 7.602753 TCAATTTCTTCTCTCGATAGTTGACA 58.397 34.615 0.00 0.00 37.40 3.58
4748 14601 7.542477 TCAATTTCTTCTCTCGATAGTTGACAC 59.458 37.037 0.00 0.00 37.40 3.67
4749 14602 5.959618 TTCTTCTCTCGATAGTTGACACA 57.040 39.130 0.00 0.00 37.40 3.72
4750 14603 6.516739 TTCTTCTCTCGATAGTTGACACAT 57.483 37.500 0.00 0.00 37.40 3.21
5084 14945 3.061848 CGCCCCAAAACCTCGCAT 61.062 61.111 0.00 0.00 0.00 4.73
5086 14947 1.714899 CGCCCCAAAACCTCGCATAG 61.715 60.000 0.00 0.00 0.00 2.23
5130 14993 3.922240 GGCGTTTTGATCTAGTGTCGTTA 59.078 43.478 0.00 0.00 0.00 3.18
5148 15021 6.110707 GTCGTTAATGAACCTTTCCATCCTA 58.889 40.000 0.00 0.00 31.28 2.94
5150 15023 7.282450 GTCGTTAATGAACCTTTCCATCCTATT 59.718 37.037 0.00 0.00 31.28 1.73
5229 15112 7.556275 TGGATTAAGGAAAAGGTAAGCATGTAG 59.444 37.037 0.00 0.00 0.00 2.74
5252 15135 5.309282 AGACTTTCCTTTCTTCTCCATGTCT 59.691 40.000 0.00 0.00 0.00 3.41
5309 15196 8.882282 TGTCGAATTCCCTTTATATATAACCCA 58.118 33.333 4.61 0.00 0.00 4.51
5360 15248 1.137872 TGCCACAACCAACCATTTGAC 59.862 47.619 0.00 0.00 34.24 3.18
5378 15266 7.040617 CCATTTGACTTGGATGGATCTCTTATG 60.041 40.741 0.00 0.00 42.31 1.90
5411 15299 1.303282 GAATCGAAGCCCCCTTGGT 59.697 57.895 0.00 0.00 36.04 3.67
5504 15396 4.762251 TGTGTATCAGATCTATGCTAGCGT 59.238 41.667 15.08 15.08 0.00 5.07
5565 15457 6.688578 TCAATCGGCTTAGGATTCTATACAC 58.311 40.000 0.00 0.00 31.98 2.90
5594 15486 4.393834 TGGTGCATCTTGCTTTTGTACTA 58.606 39.130 0.00 0.00 45.31 1.82
5608 15500 4.986054 TTGTACTACTTCCCACCACAAT 57.014 40.909 0.00 0.00 0.00 2.71
5639 18222 7.307811 GGTGTATCCATATTCCTAGTTTTTCGC 60.308 40.741 0.00 0.00 35.97 4.70
5672 18255 5.798132 AGTTCAGCATAGATCAACTTGTGA 58.202 37.500 0.00 0.00 41.67 3.58
5691 18274 7.233757 ACTTGTGAGATGTAACTAGAGGTTTCT 59.766 37.037 0.00 0.00 39.17 2.52
5724 18307 8.037758 TGACAAGATTGACTTATCCTTCTTCTC 58.962 37.037 0.00 0.00 37.03 2.87
5733 18316 3.772060 ATCCTTCTTCTCATTTTGCGC 57.228 42.857 0.00 0.00 0.00 6.09
5842 18441 0.750850 TAGTCCATCGGTTGCTAGCC 59.249 55.000 13.29 0.00 0.00 3.93
5863 18462 4.216257 GCCAGTTATTAGGCCATACATGTG 59.784 45.833 9.11 0.00 45.18 3.21
5967 18580 4.973396 TGCACAACAGAATGATCGAATTC 58.027 39.130 2.20 2.20 39.69 2.17
6056 18680 5.799276 GCACATGCTAGTGGATACATCAGAT 60.799 44.000 10.37 0.00 44.02 2.90
6057 18681 7.239620 GCACATGCTAGTGGATACATCAGATT 61.240 42.308 10.37 0.00 44.02 2.40
6071 18695 3.593442 TCAGATTGGGTGTCAAAACCT 57.407 42.857 0.00 0.00 40.35 3.50
6087 18711 8.041323 TGTCAAAACCTTATTTCCTAGCTAGAG 58.959 37.037 22.70 12.09 0.00 2.43
6103 18727 8.444783 CCTAGCTAGAGGGATGTATACAGATAT 58.555 40.741 22.70 0.00 32.39 1.63
6143 18767 4.142403 GCTAGGCTGCAACACAAAATATGA 60.142 41.667 0.50 0.00 0.00 2.15
6229 19167 4.429108 AAAAAGGTGTGACCATTTTCACG 58.571 39.130 3.46 0.00 43.26 4.35
6237 19175 4.226761 GTGACCATTTTCACGCCTAAAAG 58.773 43.478 0.00 0.00 36.79 2.27
6245 19183 1.067364 TCACGCCTAAAAGACGTCACA 59.933 47.619 19.50 0.00 38.09 3.58
6248 19186 1.393539 CGCCTAAAAGACGTCACATGG 59.606 52.381 19.50 13.39 0.00 3.66
6252 19190 1.686355 AAAAGACGTCACATGGGCAA 58.314 45.000 19.50 0.00 0.00 4.52
6278 19216 5.163784 GCGTGACCTATTTAGGAAAAGAACC 60.164 44.000 10.61 0.00 46.63 3.62
6287 19225 0.600057 GGAAAAGAACCAGCCAGCTG 59.400 55.000 12.78 12.78 43.26 4.24
6319 19257 3.493503 GTGTGTGACTAAAGTGCACTACC 59.506 47.826 22.01 8.23 34.07 3.18
6323 19261 4.283467 TGTGACTAAAGTGCACTACCAGAT 59.717 41.667 22.01 0.00 33.83 2.90
6329 19267 8.494016 ACTAAAGTGCACTACCAGATAAATTC 57.506 34.615 22.01 0.00 0.00 2.17
6330 19268 8.322091 ACTAAAGTGCACTACCAGATAAATTCT 58.678 33.333 22.01 0.00 33.90 2.40
6339 19277 5.290493 ACCAGATAAATTCTATGACCGCA 57.710 39.130 0.00 0.00 31.77 5.69
6487 19425 8.634340 GGAATGACCATTGCAAACAAACTTGC 62.634 42.308 1.71 1.40 43.94 4.01
6507 19445 6.480524 TTGCAAAGTGTGTCATATGTAGAC 57.519 37.500 0.00 2.66 36.55 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 264 8.862325 TCACATGTCAATGGTAAAACTTCTAT 57.138 30.769 0.00 0.00 38.19 1.98
267 272 9.092876 GTTTTTCTTTCACATGTCAATGGTAAA 57.907 29.630 0.00 0.00 38.19 2.01
382 394 3.320610 TTTGAAATGGGTGGGACTTGA 57.679 42.857 0.00 0.00 0.00 3.02
422 434 1.216175 GGGGGTTATAAAGGGGGTCAC 59.784 57.143 0.00 0.00 0.00 3.67
447 459 1.098050 GGCTCGATGGACTTTGCAAT 58.902 50.000 0.00 0.00 0.00 3.56
498 511 8.961293 AAGATGAGAGAGGAGATTTAGATGAT 57.039 34.615 0.00 0.00 0.00 2.45
512 534 7.442364 ACGAGAGAAGAGATTAAGATGAGAGAG 59.558 40.741 0.00 0.00 0.00 3.20
521 543 4.967575 GCGAAGACGAGAGAAGAGATTAAG 59.032 45.833 0.00 0.00 42.66 1.85
522 544 4.636648 AGCGAAGACGAGAGAAGAGATTAA 59.363 41.667 0.00 0.00 42.66 1.40
523 545 4.034626 CAGCGAAGACGAGAGAAGAGATTA 59.965 45.833 0.00 0.00 42.66 1.75
524 546 3.013921 AGCGAAGACGAGAGAAGAGATT 58.986 45.455 0.00 0.00 42.66 2.40
525 547 2.354510 CAGCGAAGACGAGAGAAGAGAT 59.645 50.000 0.00 0.00 42.66 2.75
526 548 1.735018 CAGCGAAGACGAGAGAAGAGA 59.265 52.381 0.00 0.00 42.66 3.10
527 549 1.466950 ACAGCGAAGACGAGAGAAGAG 59.533 52.381 0.00 0.00 42.66 2.85
528 550 1.524848 ACAGCGAAGACGAGAGAAGA 58.475 50.000 0.00 0.00 42.66 2.87
529 551 1.982223 CAACAGCGAAGACGAGAGAAG 59.018 52.381 0.00 0.00 42.66 2.85
530 552 1.607148 TCAACAGCGAAGACGAGAGAA 59.393 47.619 0.00 0.00 42.66 2.87
531 553 1.197949 CTCAACAGCGAAGACGAGAGA 59.802 52.381 0.00 0.00 42.66 3.10
532 554 1.068885 ACTCAACAGCGAAGACGAGAG 60.069 52.381 0.00 0.00 42.66 3.20
533 555 0.952280 ACTCAACAGCGAAGACGAGA 59.048 50.000 0.00 0.00 42.66 4.04
534 556 1.332178 GACTCAACAGCGAAGACGAG 58.668 55.000 0.00 0.00 42.66 4.18
535 557 0.385598 CGACTCAACAGCGAAGACGA 60.386 55.000 0.00 0.00 42.66 4.20
536 558 0.385598 TCGACTCAACAGCGAAGACG 60.386 55.000 0.00 0.00 42.93 4.18
537 559 1.767289 TTCGACTCAACAGCGAAGAC 58.233 50.000 0.00 0.00 38.89 3.01
538 560 2.328473 CATTCGACTCAACAGCGAAGA 58.672 47.619 0.00 0.00 45.60 2.87
543 565 1.648467 GGGGCATTCGACTCAACAGC 61.648 60.000 0.00 0.00 0.00 4.40
601 623 0.108992 TACCAGGCGTCGTGAATCAC 60.109 55.000 2.75 2.75 0.00 3.06
615 637 4.099573 CGGATATACCATAGGGCTTACCAG 59.900 50.000 0.00 0.00 39.41 4.00
773 796 7.320443 TGGATCTATGCACAACTAAAACATC 57.680 36.000 0.00 0.00 0.00 3.06
814 839 6.165659 ACGTCAATCTTATCAAGAAAACCG 57.834 37.500 0.00 0.00 41.63 4.44
912 1196 1.811965 CCAATGCGAGGATGACAACAA 59.188 47.619 0.00 0.00 0.00 2.83
1359 5941 3.715495 TGCATAATATTTTGGCAAGGCG 58.285 40.909 0.00 0.00 0.00 5.52
1385 5967 9.160412 GAATGCTAGGAATATATATAGGGTGGT 57.840 37.037 0.00 0.00 0.00 4.16
1529 6131 5.288543 CTCATGTAGAGTCCTTTTGTTGC 57.711 43.478 0.00 0.00 39.62 4.17
1599 6201 8.878769 ACGCTTTCAATTTTGTATTTTTGTTCT 58.121 25.926 0.00 0.00 0.00 3.01
1600 6202 9.484326 AACGCTTTCAATTTTGTATTTTTGTTC 57.516 25.926 0.00 0.00 0.00 3.18
1602 6204 9.484326 GAAACGCTTTCAATTTTGTATTTTTGT 57.516 25.926 5.85 0.00 39.45 2.83
1603 6205 9.483062 TGAAACGCTTTCAATTTTGTATTTTTG 57.517 25.926 9.68 0.00 45.94 2.44
1618 6220 7.008357 GGCTAAATCTACAAATGAAACGCTTTC 59.992 37.037 4.24 4.24 40.08 2.62
1622 6224 5.034797 GGGCTAAATCTACAAATGAAACGC 58.965 41.667 0.00 0.00 0.00 4.84
1624 6226 6.315393 TCGAGGGCTAAATCTACAAATGAAAC 59.685 38.462 0.00 0.00 0.00 2.78
1626 6228 5.984725 TCGAGGGCTAAATCTACAAATGAA 58.015 37.500 0.00 0.00 0.00 2.57
1627 6229 5.128827 ACTCGAGGGCTAAATCTACAAATGA 59.871 40.000 18.41 0.00 0.00 2.57
1628 6230 5.235186 CACTCGAGGGCTAAATCTACAAATG 59.765 44.000 18.41 0.00 0.00 2.32
1630 6232 4.382685 CCACTCGAGGGCTAAATCTACAAA 60.383 45.833 18.41 0.00 0.00 2.83
1631 6233 3.132289 CCACTCGAGGGCTAAATCTACAA 59.868 47.826 18.41 0.00 0.00 2.41
1636 6238 2.168728 AGTTCCACTCGAGGGCTAAATC 59.831 50.000 18.41 0.00 0.00 2.17
1637 6239 2.188817 AGTTCCACTCGAGGGCTAAAT 58.811 47.619 18.41 6.26 0.00 1.40
1638 6240 1.640917 AGTTCCACTCGAGGGCTAAA 58.359 50.000 18.41 4.32 0.00 1.85
1640 6242 0.895530 CAAGTTCCACTCGAGGGCTA 59.104 55.000 18.41 0.00 0.00 3.93
1641 6243 1.122019 ACAAGTTCCACTCGAGGGCT 61.122 55.000 18.41 1.96 0.00 5.19
1643 6245 0.393077 ACACAAGTTCCACTCGAGGG 59.607 55.000 18.41 13.63 0.00 4.30
1644 6246 1.784525 GACACAAGTTCCACTCGAGG 58.215 55.000 18.41 5.65 0.00 4.63
1645 6247 1.269102 ACGACACAAGTTCCACTCGAG 60.269 52.381 11.84 11.84 0.00 4.04
1646 6248 0.742505 ACGACACAAGTTCCACTCGA 59.257 50.000 0.00 0.00 0.00 4.04
1647 6249 2.410785 TACGACACAAGTTCCACTCG 57.589 50.000 0.00 0.00 0.00 4.18
1648 6250 8.644318 AATATAATACGACACAAGTTCCACTC 57.356 34.615 0.00 0.00 0.00 3.51
1747 10629 6.129179 CCATGATTGGACCTTTACTTATGGT 58.871 40.000 0.00 0.00 46.92 3.55
1804 10686 9.669353 CTTGACATTTTGCATATTATCTACCAC 57.331 33.333 0.00 0.00 0.00 4.16
1817 10699 7.106439 TCTTCTTTTACCTTGACATTTTGCA 57.894 32.000 0.00 0.00 0.00 4.08
1933 10816 5.023533 TCCTTGTTCTTATCCATCTTCCG 57.976 43.478 0.00 0.00 0.00 4.30
2022 10914 8.200120 ACCTTCTTCTCATTTTCCTTTCTTTTG 58.800 33.333 0.00 0.00 0.00 2.44
2082 10974 6.151144 GCTGCCCTTGTTCTTCTTTCTTATTA 59.849 38.462 0.00 0.00 0.00 0.98
2086 10978 2.625314 GCTGCCCTTGTTCTTCTTTCTT 59.375 45.455 0.00 0.00 0.00 2.52
2137 11041 7.775561 TCCCTTCTGCTTATTTATCTCCTTTTC 59.224 37.037 0.00 0.00 0.00 2.29
2216 11141 3.057033 CCTGAAGAAGTGAGGGCAATTTG 60.057 47.826 0.00 0.00 31.62 2.32
2511 11440 9.224267 TCTTTTATCCTTCTCAATGACAGAAAG 57.776 33.333 0.00 0.00 29.36 2.62
2702 11638 5.068855 CACAACCCAAACATGCATATATGGA 59.931 40.000 19.89 12.15 32.32 3.41
2749 11688 9.117145 CAACATATGCCGTCATACAAATTAATC 57.883 33.333 1.58 0.00 37.94 1.75
2796 11735 7.390440 CCTGTACAATCTTCCAAGTATTTGTGA 59.610 37.037 0.00 0.00 31.99 3.58
2861 11800 4.502259 CGGAGATTTTAGCCAGCTCTACAT 60.502 45.833 0.00 0.00 0.00 2.29
2894 11833 1.298157 CTTCCATCCACGCGCAAAGA 61.298 55.000 5.73 0.00 0.00 2.52
3070 12033 2.715046 ACCATCTACATTGGTGCACTG 58.285 47.619 17.98 10.00 45.71 3.66
3091 12054 2.155279 GTCTTCTTCTTGAGGGGCAAC 58.845 52.381 0.00 0.00 31.96 4.17
3092 12055 1.774254 TGTCTTCTTCTTGAGGGGCAA 59.226 47.619 0.00 0.00 34.73 4.52
3139 12105 3.054878 CTGAAGCTTCATTTTGTGGTGC 58.945 45.455 28.57 0.00 36.46 5.01
3260 12274 3.383505 CACTGGTTCCAATGCATCATCAT 59.616 43.478 0.00 0.00 0.00 2.45
3261 12275 2.756207 CACTGGTTCCAATGCATCATCA 59.244 45.455 0.00 0.00 0.00 3.07
3328 12342 0.031010 AACCTAGCCCTCTTCCCGAT 60.031 55.000 0.00 0.00 0.00 4.18
3420 12434 3.309296 TGGATCACTAGATGGACCTTCC 58.691 50.000 0.00 0.00 33.72 3.46
3455 12470 2.286654 GCCAAACTATCGCTTGATGCTC 60.287 50.000 0.00 0.00 40.11 4.26
3488 12503 3.058085 GGTCGATCGATAAGAGGGTTCTC 60.058 52.174 22.50 2.97 40.25 2.87
3553 12588 7.092716 ACAAAATCAAGCCATCTCATAACAAC 58.907 34.615 0.00 0.00 0.00 3.32
3590 12625 6.972722 AGGTTAGCTCGATAACAAGACTATC 58.027 40.000 10.28 0.00 37.38 2.08
3594 12629 5.638234 ACAAAGGTTAGCTCGATAACAAGAC 59.362 40.000 10.28 0.00 37.38 3.01
3622 12658 7.736031 TTCTTCTTACAGTTCGATATTCACG 57.264 36.000 0.00 0.00 0.00 4.35
3626 12662 7.713750 TCCGATTCTTCTTACAGTTCGATATT 58.286 34.615 0.00 0.00 0.00 1.28
3723 12763 5.524646 CCTGCAAAATTGTCACTTGATGTTT 59.475 36.000 0.00 0.00 0.00 2.83
3927 13001 8.053355 AGACCCAGTATAAACAATTAAAGGAGG 58.947 37.037 0.00 0.00 0.00 4.30
3948 13022 3.625649 AGATGCTGAAGAAGAAGACCC 57.374 47.619 0.00 0.00 0.00 4.46
3957 13031 3.684788 GGAACGCTTTTAGATGCTGAAGA 59.315 43.478 0.00 0.00 0.00 2.87
4012 13086 4.046286 TCCTTACCTGCCAAATTGTCAT 57.954 40.909 0.00 0.00 0.00 3.06
4147 13275 9.875691 GATGACACAACATCTAAGCCATATATA 57.124 33.333 0.00 0.00 42.09 0.86
4148 13276 7.547019 CGATGACACAACATCTAAGCCATATAT 59.453 37.037 0.00 0.00 42.86 0.86
4149 13277 6.868339 CGATGACACAACATCTAAGCCATATA 59.132 38.462 0.00 0.00 42.86 0.86
4150 13278 5.698089 CGATGACACAACATCTAAGCCATAT 59.302 40.000 0.00 0.00 42.86 1.78
4151 13279 5.049828 CGATGACACAACATCTAAGCCATA 58.950 41.667 0.00 0.00 42.86 2.74
4204 13334 7.913789 ACCATTTTACAGTATAAGACCAGTGA 58.086 34.615 0.00 0.00 0.00 3.41
4253 13523 3.585289 TGTGGGTAAGGTTCATTAGCTCA 59.415 43.478 0.00 0.00 34.37 4.26
4309 14111 0.466543 TGGTTAAGTCCGTGCACACT 59.533 50.000 18.64 10.96 0.00 3.55
4431 14233 4.374689 AGGAAGGAAGGAAGGAAGAAAC 57.625 45.455 0.00 0.00 0.00 2.78
4452 14286 0.109723 AAAGGGTGCGCTTACAGGAA 59.890 50.000 9.73 0.00 0.00 3.36
4453 14287 0.109723 AAAAGGGTGCGCTTACAGGA 59.890 50.000 9.73 0.00 0.00 3.86
4454 14288 1.816074 TAAAAGGGTGCGCTTACAGG 58.184 50.000 9.73 0.00 0.00 4.00
4455 14289 5.751243 ATAATAAAAGGGTGCGCTTACAG 57.249 39.130 9.73 0.00 0.00 2.74
4555 14398 5.708736 TTAATCCCAGCCTTCTCATAACA 57.291 39.130 0.00 0.00 0.00 2.41
4636 14479 1.485066 GGCCTCTCGGATTTGAACCTA 59.515 52.381 0.00 0.00 0.00 3.08
4744 14597 9.055248 GCGATGCAGATTTTTAATATATGTGTC 57.945 33.333 0.00 0.00 0.00 3.67
4745 14598 8.786898 AGCGATGCAGATTTTTAATATATGTGT 58.213 29.630 0.00 0.00 0.00 3.72
4746 14599 9.270576 GAGCGATGCAGATTTTTAATATATGTG 57.729 33.333 0.00 0.00 0.00 3.21
4747 14600 9.002600 TGAGCGATGCAGATTTTTAATATATGT 57.997 29.630 0.00 0.00 0.00 2.29
4748 14601 9.999009 ATGAGCGATGCAGATTTTTAATATATG 57.001 29.630 0.00 0.00 0.00 1.78
4750 14603 9.830294 CAATGAGCGATGCAGATTTTTAATATA 57.170 29.630 0.00 0.00 0.00 0.86
4793 14646 1.482593 ACTTGTCCGGGATGATCTGTC 59.517 52.381 0.00 0.00 0.00 3.51
4947 14808 1.026718 GGTTGTTCTCCATGGCGAGG 61.027 60.000 6.96 0.00 0.00 4.63
5130 14993 6.725834 ACAACAATAGGATGGAAAGGTTCATT 59.274 34.615 0.00 0.00 0.00 2.57
5192 15068 7.559897 CCTTTTCCTTAATCCAGTAATTAGCCA 59.440 37.037 0.00 0.00 0.00 4.75
5229 15112 5.555966 AGACATGGAGAAGAAAGGAAAGTC 58.444 41.667 0.00 0.00 0.00 3.01
5252 15135 3.980698 CCCTAGGTTATGAAGGGGATTGA 59.019 47.826 8.29 0.00 45.43 2.57
5285 15170 9.328975 TCTGGGTTATATATAAAGGGAATTCGA 57.671 33.333 6.75 0.00 0.00 3.71
5309 15196 4.335416 TCGAGGGATTTTGCAAGATTTCT 58.665 39.130 3.69 5.04 0.00 2.52
5360 15248 5.762218 GGACAACATAAGAGATCCATCCAAG 59.238 44.000 0.00 0.00 0.00 3.61
5378 15266 5.418310 TTCGATTCAAACAAGAGGACAAC 57.582 39.130 0.00 0.00 0.00 3.32
5411 15299 3.383505 TCTTCAAAGTTCAGACGACCTCA 59.616 43.478 0.00 0.00 0.00 3.86
5504 15396 7.041107 GTGCAAATGGGCTAAAGATTCAATTA 58.959 34.615 0.00 0.00 34.04 1.40
5565 15457 2.218953 GCAAGATGCACCATGGATTG 57.781 50.000 21.47 8.56 44.26 2.67
5624 15516 4.823790 ACGTTTGCGAAAAACTAGGAAT 57.176 36.364 11.03 0.00 42.00 3.01
5634 15526 3.787105 GCTGAACTAAAACGTTTGCGAAA 59.213 39.130 15.46 0.00 42.00 3.46
5639 18222 7.518161 TGATCTATGCTGAACTAAAACGTTTG 58.482 34.615 15.46 5.51 0.00 2.93
5672 18255 6.014156 ACTTGCAGAAACCTCTAGTTACATCT 60.014 38.462 0.00 0.00 37.88 2.90
5691 18274 6.072508 GGATAAGTCAATCTTGTCAACTTGCA 60.073 38.462 6.66 0.00 43.16 4.08
5724 18307 0.726827 TCTAAGAGGCGCGCAAAATG 59.273 50.000 34.42 17.28 0.00 2.32
5842 18441 6.318648 ACAACACATGTATGGCCTAATAACTG 59.681 38.462 3.32 0.00 41.63 3.16
6056 18680 5.212745 AGGAAATAAGGTTTTGACACCCAA 58.787 37.500 0.00 0.00 37.58 4.12
6057 18681 4.810345 AGGAAATAAGGTTTTGACACCCA 58.190 39.130 0.00 0.00 37.58 4.51
6071 18695 9.476928 GTATACATCCCTCTAGCTAGGAAATAA 57.523 37.037 20.58 0.00 39.15 1.40
6087 18711 5.882000 TGCATTGCATATCTGTATACATCCC 59.118 40.000 7.38 0.00 31.71 3.85
6103 18727 2.408271 AGCTAGCTACTTGCATTGCA 57.592 45.000 17.69 7.38 45.94 4.08
6187 19124 3.016971 CATGAGGGAGTGGGGCCA 61.017 66.667 4.39 0.00 0.00 5.36
6188 19125 3.017581 ACATGAGGGAGTGGGGCC 61.018 66.667 0.00 0.00 0.00 5.80
6229 19167 1.737793 CCCATGTGACGTCTTTTAGGC 59.262 52.381 17.92 0.00 0.00 3.93
6237 19175 2.860293 CGTTGCCCATGTGACGTC 59.140 61.111 9.11 9.11 0.00 4.34
6245 19183 2.252072 ATAGGTCACGCGTTGCCCAT 62.252 55.000 21.07 13.02 0.00 4.00
6248 19186 1.326548 CTAAATAGGTCACGCGTTGCC 59.673 52.381 10.22 15.35 0.00 4.52
6252 19190 3.598019 TTTCCTAAATAGGTCACGCGT 57.402 42.857 5.58 5.58 44.02 6.01
6263 19201 3.511540 GCTGGCTGGTTCTTTTCCTAAAT 59.488 43.478 0.00 0.00 0.00 1.40
6278 19216 2.046507 GGACTGACCAGCTGGCTG 60.047 66.667 33.06 26.87 43.26 4.85
6287 19225 0.753262 AGTCACACACTGGACTGACC 59.247 55.000 0.00 0.00 42.49 4.02
6293 19231 2.169561 TGCACTTTAGTCACACACTGGA 59.830 45.455 0.00 0.00 36.43 3.86
6319 19257 7.115520 CACTAGTGCGGTCATAGAATTTATCTG 59.884 40.741 10.54 0.00 39.30 2.90
6360 19298 7.423844 TCCATACAAGCTCTTGATAGAAGAA 57.576 36.000 15.74 0.00 42.93 2.52
6401 19339 9.715121 AGACTCCGTCATTACAAAACTAATAAA 57.285 29.630 0.00 0.00 34.60 1.40
6404 19342 7.159372 ACAGACTCCGTCATTACAAAACTAAT 58.841 34.615 0.00 0.00 34.60 1.73
6417 19355 1.073444 ACACTCCTACAGACTCCGTCA 59.927 52.381 0.00 0.00 34.60 4.35
6452 19390 5.589855 TGCAATGGTCATTCCTAACTACATG 59.410 40.000 0.00 0.00 37.07 3.21
6487 19425 6.035435 GCTGAGTCTACATATGACACACTTTG 59.965 42.308 10.38 4.40 36.94 2.77


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

AutoCloner maintained by Alex Coulton.