Multiple sequence alignment - TraesCS2B01G301800

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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 TraesCS2B01G301800 chr2B 100.000 3432 0 0 2885 6316 425351017 425354448 0.000000e+00 6338.0
1 TraesCS2B01G301800 chr2B 100.000 2549 0 0 1 2549 425348133 425350681 0.000000e+00 4708.0
2 TraesCS2B01G301800 chr2B 85.691 1223 149 16 4115 5328 57665792 57664587 0.000000e+00 1266.0
3 TraesCS2B01G301800 chr2B 84.272 1208 172 15 4126 5328 57673834 57672640 0.000000e+00 1162.0
4 TraesCS2B01G301800 chr2B 91.148 305 25 2 1052 1355 57670087 57669784 4.560000e-111 412.0
5 TraesCS2B01G301800 chr2B 90.397 302 27 2 1052 1352 706414769 706415069 4.590000e-106 396.0
6 TraesCS2B01G301800 chr2B 82.278 316 48 8 3436 3747 706416577 706416888 3.750000e-67 267.0
7 TraesCS2B01G301800 chr2B 86.344 227 30 1 3484 3709 57674472 57674246 4.890000e-61 246.0
8 TraesCS2B01G301800 chr2B 85.782 211 28 2 1654 1864 57669430 57669222 8.240000e-54 222.0
9 TraesCS2B01G301800 chr2B 89.205 176 17 2 3117 3291 706416290 706416464 1.070000e-52 219.0
10 TraesCS2B01G301800 chr2D 96.379 2734 64 13 2934 5652 357699423 357702136 0.000000e+00 4468.0
11 TraesCS2B01G301800 chr2D 94.187 1015 49 8 1537 2549 357698331 357699337 0.000000e+00 1539.0
12 TraesCS2B01G301800 chr2D 85.364 1223 153 16 4115 5328 34989287 34988082 0.000000e+00 1243.0
13 TraesCS2B01G301800 chr2D 95.833 768 14 7 612 1378 357697163 357697913 0.000000e+00 1225.0
14 TraesCS2B01G301800 chr2D 84.578 1219 168 18 4115 5328 585516177 585517380 0.000000e+00 1192.0
15 TraesCS2B01G301800 chr2D 84.483 1218 169 17 4115 5326 585475911 585477114 0.000000e+00 1184.0
16 TraesCS2B01G301800 chr2D 84.507 1207 171 13 4126 5328 34996031 34994837 0.000000e+00 1179.0
17 TraesCS2B01G301800 chr2D 90.268 411 12 8 5926 6316 357702564 357702966 4.370000e-141 512.0
18 TraesCS2B01G301800 chr2D 88.032 376 25 11 979 1352 585473465 585473822 1.630000e-115 427.0
19 TraesCS2B01G301800 chr2D 92.466 292 22 0 1064 1355 585501811 585502102 9.790000e-113 418.0
20 TraesCS2B01G301800 chr2D 91.986 287 23 0 1069 1355 34992145 34991859 2.740000e-108 403.0
21 TraesCS2B01G301800 chr2D 91.409 291 25 0 1065 1355 34998745 34998455 3.550000e-107 399.0
22 TraesCS2B01G301800 chr2D 78.905 493 77 18 1639 2109 585474126 585474613 6.150000e-80 309.0
23 TraesCS2B01G301800 chr2D 91.266 229 10 3 318 537 357696741 357696968 2.860000e-78 303.0
24 TraesCS2B01G301800 chr2D 78.700 446 67 14 1665 2086 585502328 585502769 8.070000e-69 272.0
25 TraesCS2B01G301800 chr2D 89.109 202 22 0 3509 3710 34989901 34989700 1.050000e-62 252.0
26 TraesCS2B01G301800 chr2D 86.344 227 30 1 3484 3709 34996667 34996441 4.890000e-61 246.0
27 TraesCS2B01G301800 chr2D 85.593 236 31 3 3502 3736 585475298 585475531 1.760000e-60 244.0
28 TraesCS2B01G301800 chr2D 89.894 188 17 2 3117 3303 585474941 585475127 2.280000e-59 241.0
29 TraesCS2B01G301800 chr2D 96.350 137 5 0 1375 1511 357698035 357698171 6.370000e-55 226.0
30 TraesCS2B01G301800 chr2D 85.308 211 29 2 1654 1864 34991506 34991298 3.830000e-52 217.0
31 TraesCS2B01G301800 chr2D 87.701 187 22 1 3117 3303 585514990 585515175 3.830000e-52 217.0
32 TraesCS2B01G301800 chr2D 79.747 237 19 12 3 233 357696374 357696587 1.840000e-30 145.0
33 TraesCS2B01G301800 chr2D 91.228 57 5 0 5855 5911 617129295 617129239 1.890000e-10 78.7
34 TraesCS2B01G301800 chr2A 95.457 1629 39 9 4036 5652 478761520 478763125 0.000000e+00 2566.0
35 TraesCS2B01G301800 chr2A 93.641 1148 50 9 2890 4037 478760235 478761359 0.000000e+00 1694.0
36 TraesCS2B01G301800 chr2A 95.768 898 23 8 606 1501 478757857 478758741 0.000000e+00 1434.0
37 TraesCS2B01G301800 chr2A 85.655 1213 149 15 4115 5319 38310562 38309367 0.000000e+00 1253.0
38 TraesCS2B01G301800 chr2A 89.858 848 43 17 1537 2376 478758944 478759756 0.000000e+00 1050.0
39 TraesCS2B01G301800 chr2A 91.584 404 16 7 5926 6316 478763370 478763768 5.570000e-150 542.0
40 TraesCS2B01G301800 chr2A 83.824 544 29 25 32 537 478757302 478757824 4.460000e-126 462.0
41 TraesCS2B01G301800 chr2A 91.065 291 26 0 1065 1355 38314147 38313857 1.650000e-105 394.0
42 TraesCS2B01G301800 chr2A 89.604 202 21 0 3509 3710 38311176 38310975 2.260000e-64 257.0
43 TraesCS2B01G301800 chr2A 83.094 278 41 6 3436 3710 719539375 719539649 1.360000e-61 248.0
44 TraesCS2B01G301800 chr2A 90.341 176 15 2 3117 3291 719539088 719539262 4.930000e-56 230.0
45 TraesCS2B01G301800 chr2A 90.909 132 6 3 5715 5844 478763222 478763349 8.420000e-39 172.0
46 TraesCS2B01G301800 chr1B 92.857 56 3 1 5856 5911 8670202 8670148 5.250000e-11 80.5
47 TraesCS2B01G301800 chr1B 89.655 58 5 1 5859 5915 488821933 488821876 8.780000e-09 73.1
48 TraesCS2B01G301800 chr4B 95.833 48 2 0 5867 5914 630972782 630972735 1.890000e-10 78.7
49 TraesCS2B01G301800 chr7B 95.745 47 2 0 5868 5914 731191040 731191086 6.790000e-10 76.8
50 TraesCS2B01G301800 chr5B 95.652 46 2 0 5866 5911 657589041 657588996 2.440000e-09 75.0
51 TraesCS2B01G301800 chr4A 91.228 57 2 3 5862 5918 667343366 667343313 2.440000e-09 75.0
52 TraesCS2B01G301800 chr6B 93.750 48 3 0 5867 5914 668960221 668960268 8.780000e-09 73.1
53 TraesCS2B01G301800 chr5A 92.157 51 2 2 5865 5914 653056666 653056617 3.160000e-08 71.3


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 TraesCS2B01G301800 chr2B 425348133 425354448 6315 False 5523.000000 6338 100.000000 1 6316 2 chr2B.!!$F1 6315
1 TraesCS2B01G301800 chr2B 57664587 57674472 9885 True 661.600000 1266 86.647400 1052 5328 5 chr2B.!!$R1 4276
2 TraesCS2B01G301800 chr2B 706414769 706416888 2119 False 294.000000 396 87.293333 1052 3747 3 chr2B.!!$F2 2695
3 TraesCS2B01G301800 chr2D 357696374 357702966 6592 False 1202.571429 4468 92.004286 3 6316 7 chr2D.!!$F1 6313
4 TraesCS2B01G301800 chr2D 585514990 585517380 2390 False 704.500000 1192 86.139500 3117 5328 2 chr2D.!!$F4 2211
5 TraesCS2B01G301800 chr2D 34988082 34998745 10663 True 562.714286 1243 87.718143 1065 5328 7 chr2D.!!$R2 4263
6 TraesCS2B01G301800 chr2D 585473465 585477114 3649 False 481.000000 1184 85.381400 979 5326 5 chr2D.!!$F2 4347
7 TraesCS2B01G301800 chr2D 585501811 585502769 958 False 345.000000 418 85.583000 1064 2086 2 chr2D.!!$F3 1022
8 TraesCS2B01G301800 chr2A 478757302 478763768 6466 False 1131.428571 2566 91.577286 32 6316 7 chr2A.!!$F1 6284
9 TraesCS2B01G301800 chr2A 38309367 38314147 4780 True 634.666667 1253 88.774667 1065 5319 3 chr2A.!!$R1 4254
10 TraesCS2B01G301800 chr2A 719539088 719539649 561 False 239.000000 248 86.717500 3117 3710 2 chr2A.!!$F2 593

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
577 666 0.036306 GTATAATCCGGGCCCACCTG 59.964 60.000 24.92 4.73 42.66 4.00 F
892 1151 0.542938 CACAGTCCTCACCTCCTCCA 60.543 60.000 0.00 0.00 0.00 3.86 F
1397 11453 1.811359 AGATTGCTCTGCTTGACTTGC 59.189 47.619 0.00 0.00 0.00 4.01 F
2196 13014 2.118403 TCCCTTTCTTCCCTGTGACT 57.882 50.000 0.00 0.00 0.00 3.41 F
3382 16354 1.272212 GAGGGCGGAAAGAAATTTGCA 59.728 47.619 0.00 0.00 0.00 4.08 F
3423 16395 1.427753 CTTTAACCACCCCTCCCACTT 59.572 52.381 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 11464 0.174617 TCACACGGCAGAATCGCATA 59.825 50.000 0.00 0.0 0.00 3.14 R
2126 12944 2.514803 ACAATGCACCTTGAACTACCC 58.485 47.619 7.04 0.0 0.00 3.69 R
3348 16313 3.756434 TCCGCCCTCAAAACTAAAATGAG 59.244 43.478 0.00 0.0 40.17 2.90 R
3585 16562 2.189594 TGATGGCTCCAAGAAGTGTG 57.810 50.000 0.00 0.0 0.00 3.82 R
4880 18273 1.116308 TGCCATCAGGATTGCCAATG 58.884 50.000 0.00 0.0 36.89 2.82 R
5415 18820 1.467920 ACAGGGCTGCTGCTATTTTC 58.532 50.000 15.64 0.0 39.59 2.29 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
92 98 2.413765 GCCGTCCCGCAACAAAAA 59.586 55.556 0.00 0.00 0.00 1.94
93 99 1.947146 GCCGTCCCGCAACAAAAAC 60.947 57.895 0.00 0.00 0.00 2.43
139 145 8.429641 TGGAAGTAATGTATAAAAGCTAGGGAG 58.570 37.037 0.00 0.00 0.00 4.30
164 170 4.363990 CCACCAGACAGCGAGCGT 62.364 66.667 0.00 0.00 0.00 5.07
213 219 2.726691 CGGCAGTGAAAGCGTACGG 61.727 63.158 18.39 0.00 0.00 4.02
225 231 3.116531 GTACGGCTTCGCACCACC 61.117 66.667 0.00 0.00 37.41 4.61
248 266 4.063967 CCTCACGCCACCGCAGTA 62.064 66.667 0.00 0.00 38.22 2.74
254 272 2.786495 CGCCACCGCAGTAGATCCT 61.786 63.158 0.00 0.00 34.03 3.24
263 288 1.323412 CAGTAGATCCTGGTCCCGAG 58.677 60.000 0.00 0.00 0.00 4.63
280 308 2.356553 GCACCGCACGTGGAACTA 60.357 61.111 18.88 0.00 43.24 2.24
291 319 2.891580 ACGTGGAACTATCAGTCACAGT 59.108 45.455 0.00 0.00 31.75 3.55
306 370 0.969894 ACAGTTCGTTCTCCCTCTGG 59.030 55.000 0.00 0.00 0.00 3.86
333 412 4.735132 CCCACCGACGTGTGCGAT 62.735 66.667 0.00 0.00 42.00 4.58
386 466 0.105913 AGAAGATCTCGAGGTCCCCC 60.106 60.000 22.05 11.23 0.00 5.40
505 594 2.232108 TTTGGGCCCCACGTGGATA 61.232 57.895 36.07 13.55 37.39 2.59
537 626 2.126463 CTCGCTCGGCTTGAACGA 60.126 61.111 0.00 5.23 42.50 3.85
539 628 1.945776 CTCGCTCGGCTTGAACGAAC 61.946 60.000 6.49 0.00 43.91 3.95
540 629 2.470286 GCTCGGCTTGAACGAACG 59.530 61.111 0.00 0.00 40.16 3.95
541 630 2.470286 CTCGGCTTGAACGAACGC 59.530 61.111 0.00 0.00 40.16 4.84
542 631 3.011760 CTCGGCTTGAACGAACGCC 62.012 63.158 0.00 0.00 40.16 5.68
543 632 3.041940 CGGCTTGAACGAACGCCT 61.042 61.111 0.00 0.00 40.34 5.52
544 633 2.861006 GGCTTGAACGAACGCCTC 59.139 61.111 0.00 0.00 39.42 4.70
547 636 0.586802 GCTTGAACGAACGCCTCTTT 59.413 50.000 0.00 0.00 0.00 2.52
548 637 1.796459 GCTTGAACGAACGCCTCTTTA 59.204 47.619 0.00 0.00 0.00 1.85
549 638 2.411160 GCTTGAACGAACGCCTCTTTAC 60.411 50.000 0.00 0.00 0.00 2.01
550 639 1.787012 TGAACGAACGCCTCTTTACC 58.213 50.000 0.00 0.00 0.00 2.85
553 642 2.467566 ACGAACGCCTCTTTACCAAT 57.532 45.000 0.00 0.00 0.00 3.16
556 645 2.606272 CGAACGCCTCTTTACCAATACC 59.394 50.000 0.00 0.00 0.00 2.73
557 646 2.304751 ACGCCTCTTTACCAATACCG 57.695 50.000 0.00 0.00 0.00 4.02
558 647 1.134610 ACGCCTCTTTACCAATACCGG 60.135 52.381 0.00 0.00 0.00 5.28
559 648 1.134610 CGCCTCTTTACCAATACCGGT 60.135 52.381 13.98 13.98 43.46 5.28
560 649 2.101249 CGCCTCTTTACCAATACCGGTA 59.899 50.000 18.46 18.46 40.67 4.02
562 651 4.022068 CGCCTCTTTACCAATACCGGTATA 60.022 45.833 27.03 9.15 41.18 1.47
563 652 5.509501 CGCCTCTTTACCAATACCGGTATAA 60.510 44.000 27.03 14.81 41.18 0.98
564 653 6.470278 GCCTCTTTACCAATACCGGTATAAT 58.530 40.000 27.03 17.02 41.18 1.28
565 654 6.592994 GCCTCTTTACCAATACCGGTATAATC 59.407 42.308 27.03 4.37 41.18 1.75
573 662 3.474000 CGGTATAATCCGGGCCCA 58.526 61.111 24.92 2.47 45.88 5.36
574 663 1.004200 CGGTATAATCCGGGCCCAC 60.004 63.158 24.92 10.41 45.88 4.61
575 664 1.377612 GGTATAATCCGGGCCCACC 59.622 63.158 24.92 16.40 0.00 4.61
576 665 1.131928 GGTATAATCCGGGCCCACCT 61.132 60.000 24.92 5.12 36.97 4.00
577 666 0.036306 GTATAATCCGGGCCCACCTG 59.964 60.000 24.92 4.73 42.66 4.00
578 667 1.774894 TATAATCCGGGCCCACCTGC 61.775 60.000 24.92 0.00 41.53 4.85
606 695 4.840772 CGCAGTTTAGACGAAATCAAACTG 59.159 41.667 17.42 17.42 46.19 3.16
608 697 5.846473 GCAGTTTAGACGAAATCAAACTGTC 59.154 40.000 20.77 12.87 45.79 3.51
609 698 6.511121 GCAGTTTAGACGAAATCAAACTGTCA 60.511 38.462 20.77 0.00 45.79 3.58
747 1005 0.872388 CCGAAAGAAAAGGTCACGGG 59.128 55.000 0.00 0.00 36.64 5.28
892 1151 0.542938 CACAGTCCTCACCTCCTCCA 60.543 60.000 0.00 0.00 0.00 3.86
1378 11309 7.478044 CGTCTTCTTCTCAACGTTACTTAGTAG 59.522 40.741 0.00 0.42 0.00 2.57
1379 11310 8.502387 GTCTTCTTCTCAACGTTACTTAGTAGA 58.498 37.037 0.00 2.79 0.00 2.59
1380 11311 9.228949 TCTTCTTCTCAACGTTACTTAGTAGAT 57.771 33.333 0.00 0.00 0.00 1.98
1381 11312 9.843334 CTTCTTCTCAACGTTACTTAGTAGATT 57.157 33.333 0.00 0.00 0.00 2.40
1382 11313 9.622004 TTCTTCTCAACGTTACTTAGTAGATTG 57.378 33.333 0.00 0.04 0.00 2.67
1383 11314 7.754027 TCTTCTCAACGTTACTTAGTAGATTGC 59.246 37.037 0.00 0.00 0.00 3.56
1397 11453 1.811359 AGATTGCTCTGCTTGACTTGC 59.189 47.619 0.00 0.00 0.00 4.01
1408 11464 2.619074 GCTTGACTTGCTAGGTGGGAAT 60.619 50.000 0.00 0.00 0.00 3.01
1513 11569 4.333926 GGAACTATGACTCTCATTTGTGCC 59.666 45.833 0.00 0.00 38.26 5.01
1516 11572 4.697352 ACTATGACTCTCATTTGTGCCAAC 59.303 41.667 0.00 0.00 38.26 3.77
1518 11574 2.880268 TGACTCTCATTTGTGCCAACTG 59.120 45.455 0.73 0.73 0.00 3.16
1519 11575 2.880890 GACTCTCATTTGTGCCAACTGT 59.119 45.455 5.59 0.00 0.00 3.55
1523 11579 4.713553 TCTCATTTGTGCCAACTGTCTTA 58.286 39.130 5.59 0.00 0.00 2.10
1528 11584 3.788227 TGTGCCAACTGTCTTAGGATT 57.212 42.857 0.00 0.00 0.00 3.01
1530 11586 3.820467 TGTGCCAACTGTCTTAGGATTTG 59.180 43.478 0.00 0.00 0.00 2.32
1531 11587 4.072131 GTGCCAACTGTCTTAGGATTTGA 58.928 43.478 0.00 0.00 0.00 2.69
1534 11590 4.633565 GCCAACTGTCTTAGGATTTGAGAG 59.366 45.833 0.00 0.00 0.00 3.20
1535 11591 5.569630 GCCAACTGTCTTAGGATTTGAGAGA 60.570 44.000 0.00 0.00 0.00 3.10
1613 11961 3.339093 GTTGGGAGTGGGAGGGGG 61.339 72.222 0.00 0.00 0.00 5.40
1651 12003 3.803021 GCAATTGCACCCTTGTCATTGAA 60.803 43.478 25.36 0.00 41.59 2.69
1794 12576 6.112058 AGATGTTAAGAATCCTTCACTGAGC 58.888 40.000 0.00 0.00 33.94 4.26
1888 12670 7.861629 ACCCACTCATCTTATGTTTATCTGAA 58.138 34.615 0.00 0.00 0.00 3.02
1914 12722 7.279981 ACACTTTTTCTTTTTGATTAAGTGGGC 59.720 33.333 14.31 0.00 43.31 5.36
1915 12723 7.495606 CACTTTTTCTTTTTGATTAAGTGGGCT 59.504 33.333 0.00 0.00 39.78 5.19
2126 12944 5.700846 TGCAAAAATAAATTGGCTTGCATG 58.299 33.333 12.48 0.00 42.93 4.06
2128 12946 5.642686 CAAAAATAAATTGGCTTGCATGGG 58.357 37.500 1.34 0.00 0.00 4.00
2196 13014 2.118403 TCCCTTTCTTCCCTGTGACT 57.882 50.000 0.00 0.00 0.00 3.41
2243 13061 9.179909 TGAAACAGTTAACTGAAATTTAGTCCA 57.820 29.630 36.14 18.73 46.59 4.02
2247 13065 7.228706 ACAGTTAACTGAAATTTAGTCCACTGG 59.771 37.037 36.14 8.68 46.59 4.00
2414 13349 5.067674 GCTATGAGTATTTTTGGCACCATCA 59.932 40.000 0.00 0.00 0.00 3.07
2915 15578 3.947612 ATTCAGACCAGGAATGATGCT 57.052 42.857 0.00 0.00 33.88 3.79
2920 15583 4.901250 TCAGACCAGGAATGATGCTATGTA 59.099 41.667 0.00 0.00 0.00 2.29
3007 15923 2.437281 CACAGGGTGGAGCTGAAGATAT 59.563 50.000 0.00 0.00 0.00 1.63
3323 16278 5.722021 TTTTGCCATTTCCTCTAAGGTTC 57.278 39.130 0.00 0.00 36.53 3.62
3348 16313 7.391786 CACTAGTCGTAAGTGAAAATGCATAC 58.608 38.462 0.00 0.00 45.89 2.39
3382 16354 1.272212 GAGGGCGGAAAGAAATTTGCA 59.728 47.619 0.00 0.00 0.00 4.08
3423 16395 1.427753 CTTTAACCACCCCTCCCACTT 59.572 52.381 0.00 0.00 0.00 3.16
3430 16402 2.706190 CCACCCCTCCCACTTCTATAAG 59.294 54.545 0.00 0.00 38.77 1.73
3456 16428 9.941664 GTTAGTTATCATGTGGAATTTCTCATG 57.058 33.333 18.79 18.79 38.96 3.07
3585 16562 3.848726 CCCACACATTGTTAATTGCTCC 58.151 45.455 0.00 0.00 0.00 4.70
3690 16667 3.193267 TCGGAAGCAATGATTTCAAAGGG 59.807 43.478 0.00 0.00 0.00 3.95
4022 17253 8.399425 TGTTCGAAATTTTGTTAGTTCTTAGCA 58.601 29.630 0.00 0.00 0.00 3.49
4345 17738 4.323028 CCAGGCTACCAGTATATCACATGG 60.323 50.000 0.00 0.00 38.83 3.66
4856 18249 2.027745 TGTCATTGCTCCTCTCACCTTC 60.028 50.000 0.00 0.00 0.00 3.46
4880 18273 1.804748 CTTTACTGGACGGCCTTTGAC 59.195 52.381 9.82 0.00 34.31 3.18
5346 18739 7.661536 AATAGACTGTAGCTAGAATGTTGGA 57.338 36.000 0.00 0.00 0.00 3.53
5348 18741 5.911752 AGACTGTAGCTAGAATGTTGGATG 58.088 41.667 0.00 0.00 0.00 3.51
5349 18742 4.446371 ACTGTAGCTAGAATGTTGGATGC 58.554 43.478 0.00 0.00 0.00 3.91
5350 18743 3.808728 TGTAGCTAGAATGTTGGATGCC 58.191 45.455 0.00 0.00 0.00 4.40
5351 18744 3.199727 TGTAGCTAGAATGTTGGATGCCA 59.800 43.478 0.00 0.00 0.00 4.92
5352 18745 2.648059 AGCTAGAATGTTGGATGCCAC 58.352 47.619 0.00 0.00 30.78 5.01
5353 18746 2.025981 AGCTAGAATGTTGGATGCCACA 60.026 45.455 0.00 0.00 30.78 4.17
5415 18820 1.071502 CGTGTAAATCATACTGCGGCG 60.072 52.381 0.51 0.51 0.00 6.46
5430 18835 1.064783 GGCGAAAATAGCAGCAGCC 59.935 57.895 0.00 0.00 43.56 4.85
5465 18872 3.643237 TGATATCTCGACCCCTCTGTTT 58.357 45.455 3.98 0.00 0.00 2.83
5517 18926 5.006552 GCAGTTTTCACATTTTGCTTGCTTA 59.993 36.000 0.00 0.00 0.00 3.09
5527 18936 5.514274 TTTTGCTTGCTTAAGCTAGTGTT 57.486 34.783 30.58 0.00 45.66 3.32
5528 18937 5.514274 TTTGCTTGCTTAAGCTAGTGTTT 57.486 34.783 30.58 0.00 45.66 2.83
5529 18938 5.514274 TTGCTTGCTTAAGCTAGTGTTTT 57.486 34.783 30.58 0.00 45.66 2.43
5530 18939 5.108385 TGCTTGCTTAAGCTAGTGTTTTC 57.892 39.130 30.58 18.08 45.66 2.29
5531 18940 4.578516 TGCTTGCTTAAGCTAGTGTTTTCA 59.421 37.500 30.58 19.93 45.66 2.69
5532 18941 4.912187 GCTTGCTTAAGCTAGTGTTTTCAC 59.088 41.667 30.58 14.18 43.92 3.18
5673 19361 7.361799 GGAAAACTAAATCTCACACGCCTAAAT 60.362 37.037 0.00 0.00 0.00 1.40
5689 19377 1.722011 AAATTGACGCCGACGAATCT 58.278 45.000 0.00 0.00 43.93 2.40
5690 19378 1.278238 AATTGACGCCGACGAATCTC 58.722 50.000 0.00 0.00 43.93 2.75
5691 19379 0.866061 ATTGACGCCGACGAATCTCG 60.866 55.000 0.00 0.00 46.93 4.04
5697 19385 0.640768 GCCGACGAATCTCGAAGTTG 59.359 55.000 2.59 0.00 43.74 3.16
5742 19431 4.741676 GCTCCACACATTTGAAGAAGTTTG 59.258 41.667 0.00 0.00 0.00 2.93
5749 19440 7.805071 CACACATTTGAAGAAGTTTGGTATCTC 59.195 37.037 0.00 0.00 0.00 2.75
5757 19448 2.906354 AGTTTGGTATCTCGTGATGGC 58.094 47.619 10.16 3.30 34.32 4.40
5779 19470 2.228582 TCGAATTGTGGGCACATTTGAG 59.771 45.455 0.00 0.00 41.52 3.02
5805 19496 6.572519 ACAAACTTTAGTACTAACACCGTCA 58.427 36.000 14.96 0.00 0.00 4.35
5815 19506 5.821516 ACTAACACCGTCATTTGAACAAA 57.178 34.783 2.48 2.48 34.46 2.83
5816 19507 5.816919 ACTAACACCGTCATTTGAACAAAG 58.183 37.500 6.18 0.00 33.32 2.77
5817 19508 4.974368 AACACCGTCATTTGAACAAAGA 57.026 36.364 6.18 2.01 33.32 2.52
5818 19509 4.287238 ACACCGTCATTTGAACAAAGAC 57.713 40.909 6.18 10.98 33.32 3.01
5819 19510 3.945285 ACACCGTCATTTGAACAAAGACT 59.055 39.130 17.94 6.86 33.32 3.24
5820 19511 4.201910 ACACCGTCATTTGAACAAAGACTG 60.202 41.667 17.94 15.68 33.32 3.51
5821 19512 3.243068 ACCGTCATTTGAACAAAGACTGC 60.243 43.478 17.94 0.00 33.32 4.40
5822 19513 3.243035 CCGTCATTTGAACAAAGACTGCA 60.243 43.478 17.94 0.00 33.32 4.41
5839 19530 3.280295 CTGCAGCAATCTTCCAAGAGAT 58.720 45.455 0.00 0.00 38.66 2.75
5840 19531 3.014623 TGCAGCAATCTTCCAAGAGATG 58.985 45.455 0.00 0.00 38.66 2.90
5841 19532 3.015327 GCAGCAATCTTCCAAGAGATGT 58.985 45.455 0.00 0.00 38.66 3.06
5842 19533 3.181499 GCAGCAATCTTCCAAGAGATGTG 60.181 47.826 0.00 1.23 38.66 3.21
5843 19534 4.259356 CAGCAATCTTCCAAGAGATGTGA 58.741 43.478 0.00 0.00 38.66 3.58
5844 19535 4.094590 CAGCAATCTTCCAAGAGATGTGAC 59.905 45.833 0.00 0.00 38.66 3.67
5845 19536 4.005650 GCAATCTTCCAAGAGATGTGACA 58.994 43.478 0.00 0.00 38.66 3.58
5851 19542 3.930336 TCCAAGAGATGTGACATGTGAC 58.070 45.455 8.67 8.67 0.00 3.67
5867 19562 9.214957 TGACATGTGACGATTTCTTAATAAAGT 57.785 29.630 1.15 0.00 34.13 2.66
5872 19567 9.362539 TGTGACGATTTCTTAATAAAGTACTCC 57.637 33.333 0.00 0.00 34.13 3.85
5873 19568 8.815189 GTGACGATTTCTTAATAAAGTACTCCC 58.185 37.037 0.00 0.00 34.13 4.30
5874 19569 8.755977 TGACGATTTCTTAATAAAGTACTCCCT 58.244 33.333 0.00 0.00 34.13 4.20
5875 19570 9.247126 GACGATTTCTTAATAAAGTACTCCCTC 57.753 37.037 0.00 0.00 34.13 4.30
5876 19571 8.202811 ACGATTTCTTAATAAAGTACTCCCTCC 58.797 37.037 0.00 0.00 34.13 4.30
5877 19572 7.381678 CGATTTCTTAATAAAGTACTCCCTCCG 59.618 40.741 0.00 0.00 34.13 4.63
5878 19573 7.486407 TTTCTTAATAAAGTACTCCCTCCGT 57.514 36.000 0.00 0.00 34.13 4.69
5879 19574 7.486407 TTCTTAATAAAGTACTCCCTCCGTT 57.514 36.000 0.00 0.00 34.13 4.44
5880 19575 7.105241 TCTTAATAAAGTACTCCCTCCGTTC 57.895 40.000 0.00 0.00 34.13 3.95
5881 19576 4.382345 AATAAAGTACTCCCTCCGTTCG 57.618 45.455 0.00 0.00 0.00 3.95
5882 19577 1.915141 AAAGTACTCCCTCCGTTCGA 58.085 50.000 0.00 0.00 0.00 3.71
5883 19578 1.915141 AAGTACTCCCTCCGTTCGAA 58.085 50.000 0.00 0.00 0.00 3.71
5884 19579 1.915141 AGTACTCCCTCCGTTCGAAA 58.085 50.000 0.00 0.00 0.00 3.46
5885 19580 2.242043 AGTACTCCCTCCGTTCGAAAA 58.758 47.619 0.00 0.00 0.00 2.29
5886 19581 2.830321 AGTACTCCCTCCGTTCGAAAAT 59.170 45.455 0.00 0.00 0.00 1.82
5887 19582 4.019174 AGTACTCCCTCCGTTCGAAAATA 58.981 43.478 0.00 0.00 0.00 1.40
5888 19583 3.242549 ACTCCCTCCGTTCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
5889 19584 2.830321 ACTCCCTCCGTTCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
5890 19585 3.260128 ACTCCCTCCGTTCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
5891 19586 3.592059 TCCCTCCGTTCGAAAATACTTG 58.408 45.455 0.00 0.00 0.00 3.16
5892 19587 3.007182 TCCCTCCGTTCGAAAATACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
5893 19588 3.370061 CCCTCCGTTCGAAAATACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
5894 19589 3.991773 CCTCCGTTCGAAAATACTTGTCA 59.008 43.478 0.00 0.00 0.00 3.58
5895 19590 4.630069 CCTCCGTTCGAAAATACTTGTCAT 59.370 41.667 0.00 0.00 0.00 3.06
5896 19591 5.121768 CCTCCGTTCGAAAATACTTGTCATT 59.878 40.000 0.00 0.00 0.00 2.57
5897 19592 6.311935 CCTCCGTTCGAAAATACTTGTCATTA 59.688 38.462 0.00 0.00 0.00 1.90
5898 19593 7.148540 CCTCCGTTCGAAAATACTTGTCATTAA 60.149 37.037 0.00 0.00 0.00 1.40
5899 19594 8.085720 TCCGTTCGAAAATACTTGTCATTAAA 57.914 30.769 0.00 0.00 0.00 1.52
5900 19595 8.557864 TCCGTTCGAAAATACTTGTCATTAAAA 58.442 29.630 0.00 0.00 0.00 1.52
5901 19596 9.337091 CCGTTCGAAAATACTTGTCATTAAAAT 57.663 29.630 0.00 0.00 0.00 1.82
5915 19610 8.854979 TGTCATTAAAATAGATGAAAATGGCG 57.145 30.769 0.00 0.00 34.34 5.69
5916 19611 7.920151 TGTCATTAAAATAGATGAAAATGGCGG 59.080 33.333 0.00 0.00 34.34 6.13
5917 19612 8.134895 GTCATTAAAATAGATGAAAATGGCGGA 58.865 33.333 0.00 0.00 34.34 5.54
5918 19613 8.352201 TCATTAAAATAGATGAAAATGGCGGAG 58.648 33.333 0.00 0.00 29.82 4.63
5919 19614 5.520376 AAAATAGATGAAAATGGCGGAGG 57.480 39.130 0.00 0.00 0.00 4.30
5920 19615 2.638480 TAGATGAAAATGGCGGAGGG 57.362 50.000 0.00 0.00 0.00 4.30
5921 19616 0.918983 AGATGAAAATGGCGGAGGGA 59.081 50.000 0.00 0.00 0.00 4.20
5922 19617 1.133976 AGATGAAAATGGCGGAGGGAG 60.134 52.381 0.00 0.00 0.00 4.30
5923 19618 0.625849 ATGAAAATGGCGGAGGGAGT 59.374 50.000 0.00 0.00 0.00 3.85
5924 19619 1.281419 TGAAAATGGCGGAGGGAGTA 58.719 50.000 0.00 0.00 0.00 2.59
6005 19702 2.872245 GTGCAGTTGACTTAGTTGAGCA 59.128 45.455 0.00 0.00 0.00 4.26
6018 19715 3.525537 AGTTGAGCAATACAGATCACGG 58.474 45.455 0.00 0.00 33.03 4.94
6033 19730 2.040939 TCACGGGTCCACTTTGACTTA 58.959 47.619 0.00 0.00 35.54 2.24
6035 19732 1.764134 ACGGGTCCACTTTGACTTACA 59.236 47.619 0.00 0.00 35.54 2.41
6036 19733 2.140717 CGGGTCCACTTTGACTTACAC 58.859 52.381 0.00 0.00 35.54 2.90
6037 19734 2.140717 GGGTCCACTTTGACTTACACG 58.859 52.381 0.00 0.00 35.54 4.49
6039 19736 3.057734 GGTCCACTTTGACTTACACGAG 58.942 50.000 0.00 0.00 35.54 4.18
6040 19737 3.243636 GGTCCACTTTGACTTACACGAGA 60.244 47.826 0.00 0.00 35.54 4.04
6042 19739 4.807304 GTCCACTTTGACTTACACGAGAAA 59.193 41.667 0.00 0.00 32.39 2.52
6043 19740 5.465724 GTCCACTTTGACTTACACGAGAAAT 59.534 40.000 0.00 0.00 32.39 2.17
6045 19742 6.643770 TCCACTTTGACTTACACGAGAAATAC 59.356 38.462 0.00 0.00 0.00 1.89
6046 19743 6.422701 CCACTTTGACTTACACGAGAAATACA 59.577 38.462 0.00 0.00 0.00 2.29
6047 19744 7.359264 CCACTTTGACTTACACGAGAAATACAG 60.359 40.741 0.00 0.00 0.00 2.74
6060 19757 7.797123 CACGAGAAATACAGTAGTTCCAAAAAC 59.203 37.037 15.56 2.76 33.56 2.43
6128 19831 2.987125 GCCACCACGTCATACCCT 59.013 61.111 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.726791 ACGCTAATCAACAACGCAGAG 59.273 47.619 0.00 0.00 0.00 3.35
8 9 3.185594 GTGTGTTGCTACGCTAATCAACA 59.814 43.478 12.87 2.93 44.23 3.33
25 26 1.068417 TTCTACCGCTTGCGTGTGT 59.932 52.632 13.97 7.35 0.00 3.72
131 137 0.537653 GTGGGTCTTGTCTCCCTAGC 59.462 60.000 0.00 0.00 43.74 3.42
139 145 0.603975 GCTGTCTGGTGGGTCTTGTC 60.604 60.000 0.00 0.00 0.00 3.18
246 264 0.755698 TGCTCGGGACCAGGATCTAC 60.756 60.000 0.00 0.00 0.00 2.59
247 265 0.755698 GTGCTCGGGACCAGGATCTA 60.756 60.000 0.00 0.00 0.00 1.98
248 266 2.060980 GTGCTCGGGACCAGGATCT 61.061 63.158 0.00 0.00 0.00 2.75
263 288 1.693083 GATAGTTCCACGTGCGGTGC 61.693 60.000 10.91 0.00 45.62 5.01
268 293 1.993370 GTGACTGATAGTTCCACGTGC 59.007 52.381 10.91 0.00 0.00 5.34
273 298 3.572682 ACGAACTGTGACTGATAGTTCCA 59.427 43.478 9.86 0.00 45.50 3.53
275 303 5.462405 AGAACGAACTGTGACTGATAGTTC 58.538 41.667 14.09 14.09 45.06 3.01
280 308 2.028930 GGGAGAACGAACTGTGACTGAT 60.029 50.000 0.00 0.00 0.00 2.90
386 466 1.391485 CCGTGAATCTTGCTCGAACTG 59.609 52.381 0.00 0.00 0.00 3.16
497 586 4.508128 CGTGCCGGCTATCCACGT 62.508 66.667 29.70 0.00 45.08 4.49
537 626 2.624636 CGGTATTGGTAAAGAGGCGTT 58.375 47.619 0.00 0.00 0.00 4.84
539 628 1.134610 ACCGGTATTGGTAAAGAGGCG 60.135 52.381 4.49 0.00 41.55 5.52
540 629 2.704464 ACCGGTATTGGTAAAGAGGC 57.296 50.000 4.49 0.00 41.55 4.70
557 646 1.131928 AGGTGGGCCCGGATTATACC 61.132 60.000 19.37 17.34 38.74 2.73
558 647 0.036306 CAGGTGGGCCCGGATTATAC 59.964 60.000 19.37 7.55 38.74 1.47
559 648 1.774894 GCAGGTGGGCCCGGATTATA 61.775 60.000 19.37 0.00 38.74 0.98
560 649 3.133365 GCAGGTGGGCCCGGATTAT 62.133 63.158 19.37 0.00 38.74 1.28
577 666 3.497031 GTCTAAACTGCGCCGGGC 61.497 66.667 9.54 9.54 43.96 6.13
578 667 3.186047 CGTCTAAACTGCGCCGGG 61.186 66.667 4.18 0.00 0.00 5.73
579 668 1.286354 TTTCGTCTAAACTGCGCCGG 61.286 55.000 4.18 0.00 0.00 6.13
580 669 0.719465 ATTTCGTCTAAACTGCGCCG 59.281 50.000 4.18 0.00 0.00 6.46
581 670 1.730064 TGATTTCGTCTAAACTGCGCC 59.270 47.619 4.18 0.00 0.00 6.53
582 671 3.449322 TTGATTTCGTCTAAACTGCGC 57.551 42.857 0.00 0.00 0.00 6.09
583 672 4.840772 CAGTTTGATTTCGTCTAAACTGCG 59.159 41.667 13.57 0.00 42.25 5.18
584 673 5.748592 ACAGTTTGATTTCGTCTAAACTGC 58.251 37.500 21.68 0.00 46.21 4.40
587 676 8.609478 TTTTGACAGTTTGATTTCGTCTAAAC 57.391 30.769 0.00 0.00 30.28 2.01
623 880 5.610552 CGTTCAGACGTTCAGAGTTTGATTC 60.611 44.000 0.00 0.00 44.08 2.52
677 935 2.751436 CAATGCGGACCCACCTGG 60.751 66.667 0.00 0.00 41.37 4.45
747 1005 1.147153 GACATGTGGGGCCTAGAGC 59.853 63.158 1.15 0.00 42.60 4.09
1378 11309 1.811359 AGCAAGTCAAGCAGAGCAATC 59.189 47.619 0.00 0.00 0.00 2.67
1379 11310 1.906990 AGCAAGTCAAGCAGAGCAAT 58.093 45.000 0.00 0.00 0.00 3.56
1380 11311 2.420642 CTAGCAAGTCAAGCAGAGCAA 58.579 47.619 0.00 0.00 0.00 3.91
1381 11312 1.338484 CCTAGCAAGTCAAGCAGAGCA 60.338 52.381 0.00 0.00 0.00 4.26
1382 11313 1.338579 ACCTAGCAAGTCAAGCAGAGC 60.339 52.381 0.00 0.00 0.00 4.09
1383 11314 2.344950 CACCTAGCAAGTCAAGCAGAG 58.655 52.381 0.00 0.00 0.00 3.35
1397 11453 4.248859 CAGAATCGCATATTCCCACCTAG 58.751 47.826 5.40 0.00 0.00 3.02
1408 11464 0.174617 TCACACGGCAGAATCGCATA 59.825 50.000 0.00 0.00 0.00 3.14
1513 11569 9.474920 GATATCTCTCAAATCCTAAGACAGTTG 57.525 37.037 0.00 0.00 0.00 3.16
1516 11572 9.695526 CAAGATATCTCTCAAATCCTAAGACAG 57.304 37.037 5.51 0.00 0.00 3.51
1523 11579 7.075851 TGCATCAAGATATCTCTCAAATCCT 57.924 36.000 5.51 0.00 0.00 3.24
1528 11584 4.903649 TCCCTGCATCAAGATATCTCTCAA 59.096 41.667 5.51 0.00 0.00 3.02
1530 11586 5.480642 TTCCCTGCATCAAGATATCTCTC 57.519 43.478 5.51 0.00 0.00 3.20
1531 11587 5.310068 ACATTCCCTGCATCAAGATATCTCT 59.690 40.000 5.51 0.00 0.00 3.10
1534 11590 7.750229 TTAACATTCCCTGCATCAAGATATC 57.250 36.000 0.00 0.00 0.00 1.63
1535 11591 8.716674 ATTTAACATTCCCTGCATCAAGATAT 57.283 30.769 0.00 0.00 0.00 1.63
1613 11961 2.830772 TTGCGAGCAATCATAGCAAC 57.169 45.000 6.39 0.00 42.02 4.17
1668 12020 5.242393 GCCACCTGCATCAACAGAAATATAT 59.758 40.000 0.00 0.00 40.25 0.86
1669 12021 4.580167 GCCACCTGCATCAACAGAAATATA 59.420 41.667 0.00 0.00 40.25 0.86
1672 12024 1.547372 GCCACCTGCATCAACAGAAAT 59.453 47.619 0.00 0.00 40.25 2.17
1794 12576 4.577693 ACAAACATGAATCCGATCATCCAG 59.422 41.667 0.00 0.00 37.96 3.86
1864 12646 7.770433 TGTTCAGATAAACATAAGATGAGTGGG 59.230 37.037 0.00 0.00 34.31 4.61
1865 12647 8.607459 GTGTTCAGATAAACATAAGATGAGTGG 58.393 37.037 0.00 0.00 40.96 4.00
1888 12670 7.279981 GCCCACTTAATCAAAAAGAAAAAGTGT 59.720 33.333 15.55 0.00 43.97 3.55
1914 12722 8.592998 GTTCATATTAGACACGTCCAAGTTAAG 58.407 37.037 0.00 0.00 0.00 1.85
1915 12723 7.546667 GGTTCATATTAGACACGTCCAAGTTAA 59.453 37.037 0.00 0.00 0.00 2.01
1965 12779 5.116180 TCAATTACCATCACCTAGCGAAAG 58.884 41.667 0.00 0.00 0.00 2.62
1969 12783 5.989168 TGTAATCAATTACCATCACCTAGCG 59.011 40.000 9.74 0.00 41.41 4.26
2126 12944 2.514803 ACAATGCACCTTGAACTACCC 58.485 47.619 7.04 0.00 0.00 3.69
2128 12946 5.438761 AGAAACAATGCACCTTGAACTAC 57.561 39.130 7.04 0.00 0.00 2.73
2223 13041 7.228706 CACCAGTGGACTAAATTTCAGTTAACT 59.771 37.037 18.40 1.12 0.00 2.24
2236 13054 7.636413 GCCCTATTTATTACACCAGTGGACTAA 60.636 40.741 18.40 10.70 34.19 2.24
2243 13061 6.127451 GCAAAAGCCCTATTTATTACACCAGT 60.127 38.462 0.00 0.00 0.00 4.00
2247 13065 7.488322 TCATGCAAAAGCCCTATTTATTACAC 58.512 34.615 0.00 0.00 0.00 2.90
2414 13349 7.472334 AAAGAAGTTGCATTGATGGTTAGAT 57.528 32.000 0.00 0.00 0.00 1.98
2884 15547 6.235231 TCCTGGTCTGAATACAATAGAACC 57.765 41.667 0.00 0.00 0.00 3.62
2885 15548 7.987458 TCATTCCTGGTCTGAATACAATAGAAC 59.013 37.037 0.00 0.00 31.42 3.01
2886 15549 8.089625 TCATTCCTGGTCTGAATACAATAGAA 57.910 34.615 0.00 0.00 31.42 2.10
2887 15550 7.675161 TCATTCCTGGTCTGAATACAATAGA 57.325 36.000 0.00 0.00 31.42 1.98
2888 15551 7.094890 GCATCATTCCTGGTCTGAATACAATAG 60.095 40.741 5.34 0.00 31.42 1.73
2937 15600 6.644347 CACTCTCTTTCCAAGCCTAATAAGA 58.356 40.000 0.00 0.00 0.00 2.10
3007 15923 8.974060 AACAGACAAGAGGAACTGTTATTTTA 57.026 30.769 0.00 0.00 46.84 1.52
3032 15953 6.596309 AGTATATGCTGCATAACTAGCTGA 57.404 37.500 24.56 2.45 40.52 4.26
3128 16079 7.096065 GCTAACTTGTTTTCTGCAACCATAAAG 60.096 37.037 0.00 0.00 0.00 1.85
3323 16278 5.839262 TGCATTTTCACTTACGACTAGTG 57.161 39.130 0.00 9.11 43.41 2.74
3348 16313 3.756434 TCCGCCCTCAAAACTAAAATGAG 59.244 43.478 0.00 0.00 40.17 2.90
3430 16402 9.941664 CATGAGAAATTCCACATGATAACTAAC 57.058 33.333 18.79 0.00 41.45 2.34
3456 16428 7.990314 GGGCTAAAGGATAATCCATCTTAGATC 59.010 40.741 0.00 0.00 39.61 2.75
3585 16562 2.189594 TGATGGCTCCAAGAAGTGTG 57.810 50.000 0.00 0.00 0.00 3.82
3690 16667 7.704578 TCAGTATACCTTGTATCCATAGAGC 57.295 40.000 0.00 0.00 0.00 4.09
3883 17113 8.623903 CCATGTTTACTTCAACAGCATATACAT 58.376 33.333 0.00 0.00 40.01 2.29
4345 17738 4.202020 ACATGAACAAGATGAGATGCATGC 60.202 41.667 11.82 11.82 37.34 4.06
4430 17823 7.365295 GGAGGGATACTGTCCTTTACAAATACA 60.365 40.741 0.00 0.00 46.91 2.29
4856 18249 1.745489 GGCCGTCCAGTAAAGCCAG 60.745 63.158 0.00 0.00 43.32 4.85
4880 18273 1.116308 TGCCATCAGGATTGCCAATG 58.884 50.000 0.00 0.00 36.89 2.82
5346 18739 3.941483 CGGTTCTCTTCTATTTGTGGCAT 59.059 43.478 0.00 0.00 0.00 4.40
5348 18741 2.096013 GCGGTTCTCTTCTATTTGTGGC 59.904 50.000 0.00 0.00 0.00 5.01
5349 18742 3.334691 TGCGGTTCTCTTCTATTTGTGG 58.665 45.455 0.00 0.00 0.00 4.17
5350 18743 4.259970 CGATGCGGTTCTCTTCTATTTGTG 60.260 45.833 0.00 0.00 0.00 3.33
5351 18744 3.865745 CGATGCGGTTCTCTTCTATTTGT 59.134 43.478 0.00 0.00 0.00 2.83
5352 18745 3.865745 ACGATGCGGTTCTCTTCTATTTG 59.134 43.478 0.00 0.00 0.00 2.32
5353 18746 3.865745 CACGATGCGGTTCTCTTCTATTT 59.134 43.478 0.00 0.00 0.00 1.40
5415 18820 1.467920 ACAGGGCTGCTGCTATTTTC 58.532 50.000 15.64 0.00 39.59 2.29
5430 18835 6.199908 GTCGAGATATCAACAGAATGAACAGG 59.800 42.308 5.32 0.00 39.69 4.00
5517 18926 5.965922 AGCAAAAAGTGAAAACACTAGCTT 58.034 33.333 0.00 0.00 34.56 3.74
5527 18936 2.348059 CGCAAGCAAGCAAAAAGTGAAA 59.652 40.909 1.32 0.00 0.00 2.69
5528 18937 1.925847 CGCAAGCAAGCAAAAAGTGAA 59.074 42.857 1.32 0.00 0.00 3.18
5529 18938 1.558741 CGCAAGCAAGCAAAAAGTGA 58.441 45.000 1.32 0.00 0.00 3.41
5543 18952 4.796231 AGAGCCGTACCGCGCAAG 62.796 66.667 8.75 0.00 39.71 4.01
5565 18974 1.493772 CGCCCAAGCATATGCAATTG 58.506 50.000 28.62 22.80 45.16 2.32
5673 19361 1.513373 CGAGATTCGTCGGCGTCAA 60.513 57.895 10.18 0.00 39.49 3.18
5689 19377 5.706833 TCACTATACTGTGTACCAACTTCGA 59.293 40.000 0.00 0.00 38.90 3.71
5690 19378 5.946298 TCACTATACTGTGTACCAACTTCG 58.054 41.667 0.00 0.00 38.90 3.79
5691 19379 7.544622 TGATCACTATACTGTGTACCAACTTC 58.455 38.462 0.00 0.00 38.90 3.01
5697 19385 6.574350 AGCTTTGATCACTATACTGTGTACC 58.426 40.000 0.00 0.00 38.90 3.34
5742 19431 0.952280 TCGAGCCATCACGAGATACC 59.048 55.000 0.00 0.00 34.49 2.73
5749 19440 0.374758 CCACAATTCGAGCCATCACG 59.625 55.000 0.00 0.00 0.00 4.35
5757 19448 2.228582 TCAAATGTGCCCACAATTCGAG 59.771 45.455 5.08 0.00 45.41 4.04
5779 19470 7.222611 TGACGGTGTTAGTACTAAAGTTTGTTC 59.777 37.037 16.82 8.43 0.00 3.18
5805 19496 4.389890 TTGCTGCAGTCTTTGTTCAAAT 57.610 36.364 16.64 0.00 0.00 2.32
5815 19506 2.039480 TCTTGGAAGATTGCTGCAGTCT 59.961 45.455 20.31 20.31 31.85 3.24
5816 19507 2.419324 CTCTTGGAAGATTGCTGCAGTC 59.581 50.000 16.64 16.35 33.93 3.51
5817 19508 2.039480 TCTCTTGGAAGATTGCTGCAGT 59.961 45.455 16.64 0.00 33.93 4.40
5818 19509 2.708051 TCTCTTGGAAGATTGCTGCAG 58.292 47.619 10.11 10.11 33.93 4.41
5819 19510 2.865119 TCTCTTGGAAGATTGCTGCA 57.135 45.000 0.00 0.00 33.93 4.41
5820 19511 3.015327 ACATCTCTTGGAAGATTGCTGC 58.985 45.455 0.00 0.00 33.68 5.25
5821 19512 4.094590 GTCACATCTCTTGGAAGATTGCTG 59.905 45.833 0.00 0.00 33.68 4.41
5822 19513 4.260170 GTCACATCTCTTGGAAGATTGCT 58.740 43.478 0.00 0.00 33.68 3.91
5839 19530 8.541133 TTATTAAGAAATCGTCACATGTCACA 57.459 30.769 0.00 0.00 0.00 3.58
5840 19531 9.478019 CTTTATTAAGAAATCGTCACATGTCAC 57.522 33.333 0.00 0.00 32.92 3.67
5841 19532 9.214957 ACTTTATTAAGAAATCGTCACATGTCA 57.785 29.630 0.00 0.00 35.30 3.58
5851 19542 7.381678 CGGAGGGAGTACTTTATTAAGAAATCG 59.618 40.741 0.00 0.00 35.30 3.34
5867 19562 4.019174 AGTATTTTCGAACGGAGGGAGTA 58.981 43.478 0.00 0.00 0.00 2.59
5868 19563 2.830321 AGTATTTTCGAACGGAGGGAGT 59.170 45.455 0.00 0.00 0.00 3.85
5869 19564 3.521947 AGTATTTTCGAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
5870 19565 3.007182 ACAAGTATTTTCGAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
5871 19566 3.332034 ACAAGTATTTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
5872 19567 3.991773 TGACAAGTATTTTCGAACGGAGG 59.008 43.478 0.00 0.00 0.00 4.30
5873 19568 5.779806 ATGACAAGTATTTTCGAACGGAG 57.220 39.130 0.00 0.00 0.00 4.63
5874 19569 7.655236 TTAATGACAAGTATTTTCGAACGGA 57.345 32.000 0.00 0.00 0.00 4.69
5875 19570 8.716619 TTTTAATGACAAGTATTTTCGAACGG 57.283 30.769 0.00 0.00 0.00 4.44
5889 19584 9.299963 CGCCATTTTCATCTATTTTAATGACAA 57.700 29.630 0.00 0.00 31.83 3.18
5890 19585 7.920151 CCGCCATTTTCATCTATTTTAATGACA 59.080 33.333 0.00 0.00 31.83 3.58
5891 19586 8.134895 TCCGCCATTTTCATCTATTTTAATGAC 58.865 33.333 0.00 0.00 31.83 3.06
5892 19587 8.231692 TCCGCCATTTTCATCTATTTTAATGA 57.768 30.769 0.00 0.00 0.00 2.57
5893 19588 7.596248 CCTCCGCCATTTTCATCTATTTTAATG 59.404 37.037 0.00 0.00 0.00 1.90
5894 19589 7.255942 CCCTCCGCCATTTTCATCTATTTTAAT 60.256 37.037 0.00 0.00 0.00 1.40
5895 19590 6.040391 CCCTCCGCCATTTTCATCTATTTTAA 59.960 38.462 0.00 0.00 0.00 1.52
5896 19591 5.534654 CCCTCCGCCATTTTCATCTATTTTA 59.465 40.000 0.00 0.00 0.00 1.52
5897 19592 4.342092 CCCTCCGCCATTTTCATCTATTTT 59.658 41.667 0.00 0.00 0.00 1.82
5898 19593 3.891366 CCCTCCGCCATTTTCATCTATTT 59.109 43.478 0.00 0.00 0.00 1.40
5899 19594 3.138283 TCCCTCCGCCATTTTCATCTATT 59.862 43.478 0.00 0.00 0.00 1.73
5900 19595 2.711009 TCCCTCCGCCATTTTCATCTAT 59.289 45.455 0.00 0.00 0.00 1.98
5901 19596 2.104792 CTCCCTCCGCCATTTTCATCTA 59.895 50.000 0.00 0.00 0.00 1.98
5902 19597 0.918983 TCCCTCCGCCATTTTCATCT 59.081 50.000 0.00 0.00 0.00 2.90
5903 19598 1.312815 CTCCCTCCGCCATTTTCATC 58.687 55.000 0.00 0.00 0.00 2.92
5904 19599 0.625849 ACTCCCTCCGCCATTTTCAT 59.374 50.000 0.00 0.00 0.00 2.57
5905 19600 1.281419 TACTCCCTCCGCCATTTTCA 58.719 50.000 0.00 0.00 0.00 2.69
5906 19601 2.640316 ATACTCCCTCCGCCATTTTC 57.360 50.000 0.00 0.00 0.00 2.29
5907 19602 4.322499 CGTATATACTCCCTCCGCCATTTT 60.322 45.833 11.05 0.00 0.00 1.82
5908 19603 3.194968 CGTATATACTCCCTCCGCCATTT 59.805 47.826 11.05 0.00 0.00 2.32
5909 19604 2.758979 CGTATATACTCCCTCCGCCATT 59.241 50.000 11.05 0.00 0.00 3.16
5910 19605 2.291411 ACGTATATACTCCCTCCGCCAT 60.291 50.000 11.05 0.00 0.00 4.40
5911 19606 1.074405 ACGTATATACTCCCTCCGCCA 59.926 52.381 11.05 0.00 0.00 5.69
5912 19607 1.831580 ACGTATATACTCCCTCCGCC 58.168 55.000 11.05 0.00 0.00 6.13
5913 19608 5.338365 CAATTACGTATATACTCCCTCCGC 58.662 45.833 11.05 0.00 0.00 5.54
5914 19609 5.125097 AGCAATTACGTATATACTCCCTCCG 59.875 44.000 11.05 0.00 0.00 4.63
5915 19610 6.152323 TCAGCAATTACGTATATACTCCCTCC 59.848 42.308 11.05 0.00 0.00 4.30
5916 19611 7.154435 TCAGCAATTACGTATATACTCCCTC 57.846 40.000 11.05 0.00 0.00 4.30
5917 19612 7.548097 CATCAGCAATTACGTATATACTCCCT 58.452 38.462 11.05 0.00 0.00 4.20
5918 19613 6.255887 GCATCAGCAATTACGTATATACTCCC 59.744 42.308 11.05 0.00 41.58 4.30
5919 19614 6.255887 GGCATCAGCAATTACGTATATACTCC 59.744 42.308 11.05 0.00 44.61 3.85
5920 19615 6.811665 TGGCATCAGCAATTACGTATATACTC 59.188 38.462 11.05 0.00 44.61 2.59
5921 19616 6.697395 TGGCATCAGCAATTACGTATATACT 58.303 36.000 11.05 1.45 44.61 2.12
5922 19617 6.961359 TGGCATCAGCAATTACGTATATAC 57.039 37.500 2.53 2.53 44.61 1.47
5923 19618 6.370442 GGTTGGCATCAGCAATTACGTATATA 59.630 38.462 0.00 0.00 44.61 0.86
5924 19619 5.181245 GGTTGGCATCAGCAATTACGTATAT 59.819 40.000 0.00 0.00 44.61 0.86
6005 19702 2.467880 AGTGGACCCGTGATCTGTATT 58.532 47.619 0.00 0.00 0.00 1.89
6018 19715 3.057734 CTCGTGTAAGTCAAAGTGGACC 58.942 50.000 0.00 0.00 38.59 4.46
6033 19730 5.717078 TGGAACTACTGTATTTCTCGTGT 57.283 39.130 14.89 0.00 0.00 4.49
6035 19732 7.713942 AGTTTTTGGAACTACTGTATTTCTCGT 59.286 33.333 14.89 0.00 0.00 4.18
6036 19733 8.084590 AGTTTTTGGAACTACTGTATTTCTCG 57.915 34.615 14.89 0.00 0.00 4.04
6037 19734 8.504815 GGAGTTTTTGGAACTACTGTATTTCTC 58.495 37.037 14.89 8.02 0.00 2.87
6039 19736 8.161699 TGGAGTTTTTGGAACTACTGTATTTC 57.838 34.615 8.85 8.85 32.34 2.17
6040 19737 8.528044 TTGGAGTTTTTGGAACTACTGTATTT 57.472 30.769 3.11 0.00 32.34 1.40
6042 19739 8.576442 CATTTGGAGTTTTTGGAACTACTGTAT 58.424 33.333 3.11 0.00 32.34 2.29
6043 19740 7.776030 TCATTTGGAGTTTTTGGAACTACTGTA 59.224 33.333 3.11 0.00 32.34 2.74
6045 19742 7.013274 TCTCATTTGGAGTTTTTGGAACTACTG 59.987 37.037 3.11 0.00 44.40 2.74
6046 19743 7.060421 TCTCATTTGGAGTTTTTGGAACTACT 58.940 34.615 3.11 0.00 44.40 2.57
6047 19744 7.272037 TCTCATTTGGAGTTTTTGGAACTAC 57.728 36.000 0.00 0.00 44.40 2.73
6060 19757 3.730061 GCTGTTCGCATTCTCATTTGGAG 60.730 47.826 0.00 0.00 40.98 3.86
6290 20011 3.744719 CCGGAGGCGACGTTGAGA 61.745 66.667 7.08 0.00 46.14 3.27


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

AutoCloner maintained by Alex Coulton.