Multiple sequence alignment - TraesCS7A01G101000

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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 TraesCS7A01G101000 chr7A 100.000 4578 0 0 1 4578 62094829 62090252 0.000000e+00 8455
1 TraesCS7A01G101000 chr7A 94.233 1023 44 2 1516 2523 62008880 62009902 0.000000e+00 1548
2 TraesCS7A01G101000 chr7A 93.237 828 48 3 2537 3356 62015061 62015888 0.000000e+00 1212
3 TraesCS7A01G101000 chr7A 92.112 786 43 8 564 1335 62008096 62008876 0.000000e+00 1090
4 TraesCS7A01G101000 chr7A 84.890 589 62 9 3348 3927 62019298 62019868 1.850000e-158 569
5 TraesCS7A01G101000 chr7A 97.222 144 3 1 1353 1496 474564362 474564504 4.580000e-60 243
6 TraesCS7A01G101000 chr7D 95.044 2260 85 7 1501 3735 57849753 57847496 0.000000e+00 3528
7 TraesCS7A01G101000 chr7D 90.152 1848 122 21 2102 3927 57702989 57704798 0.000000e+00 2350
8 TraesCS7A01G101000 chr7D 90.185 1355 101 16 3 1335 57701074 57702418 0.000000e+00 1736
9 TraesCS7A01G101000 chr7D 92.680 847 31 10 3733 4578 57829331 57828515 0.000000e+00 1192
10 TraesCS7A01G101000 chr7D 92.768 802 41 9 564 1354 57850543 57849748 0.000000e+00 1144
11 TraesCS7A01G101000 chr7D 93.194 573 25 1 1516 2074 57702422 57702994 0.000000e+00 830
12 TraesCS7A01G101000 chr7D 79.690 581 78 20 3 568 59941240 59941795 2.580000e-102 383
13 TraesCS7A01G101000 chr5A 89.726 584 23 22 3998 4578 483046875 483047424 0.000000e+00 712
14 TraesCS7A01G101000 chr5D 83.750 560 67 8 3 551 444955409 444955955 4.090000e-140 508
15 TraesCS7A01G101000 chr5D 81.771 576 89 9 3 567 394834838 394834268 6.940000e-128 468
16 TraesCS7A01G101000 chr5D 79.000 500 75 21 4012 4501 7630422 7629943 9.560000e-82 315
17 TraesCS7A01G101000 chr5D 82.895 304 40 8 3 305 486993487 486993779 3.510000e-66 263
18 TraesCS7A01G101000 chr3D 82.777 569 82 10 6 566 464321569 464321009 1.140000e-135 494
19 TraesCS7A01G101000 chr3D 81.865 386 51 16 4196 4573 241396435 241396061 1.600000e-79 307
20 TraesCS7A01G101000 chr1D 81.961 571 88 12 3 564 217139288 217139852 1.930000e-128 470
21 TraesCS7A01G101000 chr1D 81.930 570 86 12 3 564 95444495 95443935 2.490000e-127 466
22 TraesCS7A01G101000 chr2B 81.707 574 88 12 1 566 17832057 17831493 3.230000e-126 462
23 TraesCS7A01G101000 chr2B 81.143 350 48 15 4231 4573 142890218 142889880 9.770000e-67 265
24 TraesCS7A01G101000 chr2A 82.246 552 73 15 3 544 676406473 676405937 1.940000e-123 453
25 TraesCS7A01G101000 chr2A 82.203 472 62 13 3 459 417072738 417073202 2.000000e-103 387
26 TraesCS7A01G101000 chr2A 81.818 396 60 7 3 388 194477680 194478073 5.710000e-84 322
27 TraesCS7A01G101000 chr2A 81.682 333 49 11 4245 4573 648157486 648157162 2.720000e-67 267
28 TraesCS7A01G101000 chr2A 92.593 81 6 0 3921 4001 587158362 587158282 2.890000e-22 117
29 TraesCS7A01G101000 chr4D 81.207 580 91 14 3 567 385489447 385488871 6.980000e-123 451
30 TraesCS7A01G101000 chr4D 95.918 147 5 1 1354 1500 2103353 2103498 2.130000e-58 237
31 TraesCS7A01G101000 chr4D 95.918 147 5 1 1356 1502 65847649 65847504 2.130000e-58 237
32 TraesCS7A01G101000 chr5B 81.942 515 63 13 3 505 401001343 401000847 4.260000e-110 409
33 TraesCS7A01G101000 chr5B 79.130 460 63 18 3 446 592724055 592724497 2.080000e-73 287
34 TraesCS7A01G101000 chr5B 91.139 79 7 0 3923 4001 441067884 441067806 1.740000e-19 108
35 TraesCS7A01G101000 chr5B 84.416 77 10 2 1501 1576 554644145 554644220 1.770000e-09 75
36 TraesCS7A01G101000 chr1B 78.976 547 81 22 4040 4575 618990988 618991511 4.390000e-90 342
37 TraesCS7A01G101000 chr3B 77.720 579 86 29 5 564 55368492 55367938 9.560000e-82 315
38 TraesCS7A01G101000 chr3B 81.865 386 51 16 4196 4573 338596484 338596110 1.600000e-79 307
39 TraesCS7A01G101000 chr2D 81.197 351 47 13 4231 4573 197520219 197520558 9.770000e-67 265
40 TraesCS7A01G101000 chr2D 96.622 148 4 1 1354 1501 597957104 597956958 1.270000e-60 244
41 TraesCS7A01G101000 chr2D 96.503 143 4 1 1354 1496 406152091 406151950 7.660000e-58 235
42 TraesCS7A01G101000 chr2D 94.631 149 7 1 1348 1496 406184059 406183912 3.560000e-56 230
43 TraesCS7A01G101000 chr2D 93.421 76 5 0 3926 4001 624812124 624812049 3.740000e-21 113
44 TraesCS7A01G101000 chr2D 90.361 83 7 1 3919 4001 32060190 32060109 1.740000e-19 108
45 TraesCS7A01G101000 chr3A 80.682 352 47 17 4231 4573 1713645 1713984 2.110000e-63 254
46 TraesCS7A01G101000 chr6A 95.804 143 5 1 1354 1496 226075810 226075669 3.560000e-56 230
47 TraesCS7A01G101000 chr6A 94.558 147 7 1 1354 1500 168092048 168091903 4.610000e-55 226
48 TraesCS7A01G101000 chr6B 94.595 148 7 1 1354 1501 26372874 26372728 1.280000e-55 228
49 TraesCS7A01G101000 chr6B 92.308 78 6 0 3924 4001 160912384 160912461 1.350000e-20 111
50 TraesCS7A01G101000 chr6D 92.208 77 6 0 3925 4001 141924996 141924920 4.840000e-20 110
51 TraesCS7A01G101000 chr4B 92.208 77 6 0 3925 4001 621424695 621424771 4.840000e-20 110
52 TraesCS7A01G101000 chr1A 89.535 86 7 2 3917 4001 264217597 264217513 1.740000e-19 108


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 TraesCS7A01G101000 chr7A 62090252 62094829 4577 True 8455.000000 8455 100.0000 1 4578 1 chr7A.!!$R1 4577
1 TraesCS7A01G101000 chr7A 62008096 62009902 1806 False 1319.000000 1548 93.1725 564 2523 2 chr7A.!!$F2 1959
2 TraesCS7A01G101000 chr7A 62015061 62019868 4807 False 890.500000 1212 89.0635 2537 3927 2 chr7A.!!$F3 1390
3 TraesCS7A01G101000 chr7D 57847496 57850543 3047 True 2336.000000 3528 93.9060 564 3735 2 chr7D.!!$R2 3171
4 TraesCS7A01G101000 chr7D 57701074 57704798 3724 False 1638.666667 2350 91.1770 3 3927 3 chr7D.!!$F2 3924
5 TraesCS7A01G101000 chr7D 57828515 57829331 816 True 1192.000000 1192 92.6800 3733 4578 1 chr7D.!!$R1 845
6 TraesCS7A01G101000 chr7D 59941240 59941795 555 False 383.000000 383 79.6900 3 568 1 chr7D.!!$F1 565
7 TraesCS7A01G101000 chr5A 483046875 483047424 549 False 712.000000 712 89.7260 3998 4578 1 chr5A.!!$F1 580
8 TraesCS7A01G101000 chr5D 444955409 444955955 546 False 508.000000 508 83.7500 3 551 1 chr5D.!!$F1 548
9 TraesCS7A01G101000 chr5D 394834268 394834838 570 True 468.000000 468 81.7710 3 567 1 chr5D.!!$R2 564
10 TraesCS7A01G101000 chr3D 464321009 464321569 560 True 494.000000 494 82.7770 6 566 1 chr3D.!!$R2 560
11 TraesCS7A01G101000 chr1D 217139288 217139852 564 False 470.000000 470 81.9610 3 564 1 chr1D.!!$F1 561
12 TraesCS7A01G101000 chr1D 95443935 95444495 560 True 466.000000 466 81.9300 3 564 1 chr1D.!!$R1 561
13 TraesCS7A01G101000 chr2B 17831493 17832057 564 True 462.000000 462 81.7070 1 566 1 chr2B.!!$R1 565
14 TraesCS7A01G101000 chr2A 676405937 676406473 536 True 453.000000 453 82.2460 3 544 1 chr2A.!!$R3 541
15 TraesCS7A01G101000 chr4D 385488871 385489447 576 True 451.000000 451 81.2070 3 567 1 chr4D.!!$R2 564
16 TraesCS7A01G101000 chr1B 618990988 618991511 523 False 342.000000 342 78.9760 4040 4575 1 chr1B.!!$F1 535
17 TraesCS7A01G101000 chr3B 55367938 55368492 554 True 315.000000 315 77.7200 5 564 1 chr3B.!!$R1 559

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
576 610 1.003003 GATGCTCTTATCCCAGCCTCC 59.997 57.143 0.00 0.0 34.47 4.30 F
1067 1116 0.387239 GCGTTCATGGCACTGGTTTC 60.387 55.000 0.00 0.0 0.00 2.78 F
1433 1482 0.343372 AGATTGAGGTAGAGGCCCCA 59.657 55.000 0.00 0.0 0.00 4.96 F
1434 1483 0.470341 GATTGAGGTAGAGGCCCCAC 59.530 60.000 0.00 0.0 0.00 4.61 F
1435 1484 0.988678 ATTGAGGTAGAGGCCCCACC 60.989 60.000 0.00 4.2 39.61 4.61 F
3323 3435 0.935196 GCTACGGTTTAAGCCCATCG 59.065 55.000 2.36 0.0 32.40 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 1463 0.343372 TGGGGCCTCTACCTCAATCT 59.657 55.000 3.07 0.0 37.21 2.40 R
2825 2929 0.468400 GGCTCGTATGACTCCCCTCT 60.468 60.000 0.00 0.0 0.00 3.69 R
3162 3274 1.656652 CTCGGTTCGCAGAAATGGAT 58.343 50.000 0.00 0.0 45.90 3.41 R
3310 3422 2.650322 TGATTCCCGATGGGCTTAAAC 58.350 47.619 0.00 0.0 43.94 2.01 R
3430 6960 4.020573 ACTGGAGTTTGATCGGTTATGTCA 60.021 41.667 0.00 0.0 0.00 3.58 R
4474 8025 3.553828 TCGAAAGTGTCCCTGACTTTT 57.446 42.857 0.00 0.0 42.42 2.27 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
77 78 7.056844 TCCATCGTTTTCCCTAACAAAATTT 57.943 32.000 0.00 0.00 0.00 1.82
78 79 6.926272 TCCATCGTTTTCCCTAACAAAATTTG 59.074 34.615 3.89 3.89 0.00 2.32
79 80 6.926272 CCATCGTTTTCCCTAACAAAATTTGA 59.074 34.615 13.19 0.00 0.00 2.69
205 223 2.804856 GGCGAGGACAGAGAGAGC 59.195 66.667 0.00 0.00 0.00 4.09
353 383 3.839490 AGATTTGATGCAATTTGGGGTGA 59.161 39.130 0.00 0.00 0.00 4.02
423 454 2.257353 GCCGCATATTTAGGCTGGG 58.743 57.895 0.00 0.00 46.83 4.45
425 456 1.238439 CCGCATATTTAGGCTGGGTG 58.762 55.000 0.00 0.00 0.00 4.61
473 505 3.961414 GGGTCGTTTGAGGGGCCA 61.961 66.667 4.39 0.00 0.00 5.36
479 511 1.761174 GTTTGAGGGGCCAGTCTGA 59.239 57.895 4.39 0.00 0.00 3.27
533 567 1.139058 GTCCACCCAAGCGTATGAGAT 59.861 52.381 0.00 0.00 0.00 2.75
576 610 1.003003 GATGCTCTTATCCCAGCCTCC 59.997 57.143 0.00 0.00 34.47 4.30
586 620 1.153107 CCAGCCTCCGCATCAATCA 60.153 57.895 0.00 0.00 37.52 2.57
627 661 3.057596 TGCAGAATTCAAGCGTTTAAGGG 60.058 43.478 8.44 0.00 0.00 3.95
654 691 4.082517 CAGCTGACTTCTCTTGTGCTAGTA 60.083 45.833 8.42 0.00 0.00 1.82
667 704 6.999272 TCTTGTGCTAGTATTTTGTTAACCCA 59.001 34.615 2.48 0.00 0.00 4.51
682 719 5.104151 TGTTAACCCAAGAGGATATCATGCA 60.104 40.000 4.83 0.00 39.89 3.96
753 793 3.262420 GTTTCTGGTACGCATCATGTCT 58.738 45.455 0.00 0.00 0.00 3.41
766 806 1.155889 CATGTCTTTGTGCCAGCGTA 58.844 50.000 0.00 0.00 0.00 4.42
769 809 1.003839 TCTTTGTGCCAGCGTAGGG 60.004 57.895 0.00 0.00 0.00 3.53
772 812 2.741486 TTTGTGCCAGCGTAGGGTCC 62.741 60.000 0.00 0.00 0.00 4.46
773 813 4.468689 GTGCCAGCGTAGGGTCCC 62.469 72.222 0.00 0.00 0.00 4.46
808 852 3.008375 AGCATCTACCGTTCATGCCATAT 59.992 43.478 9.65 0.00 43.40 1.78
995 1044 4.400567 ACTTGCATTTCTTAATCTCAGGCC 59.599 41.667 0.00 0.00 0.00 5.19
996 1045 3.966979 TGCATTTCTTAATCTCAGGCCA 58.033 40.909 5.01 0.00 0.00 5.36
997 1046 4.539726 TGCATTTCTTAATCTCAGGCCAT 58.460 39.130 5.01 0.00 0.00 4.40
998 1047 4.340097 TGCATTTCTTAATCTCAGGCCATG 59.660 41.667 5.01 0.00 0.00 3.66
1067 1116 0.387239 GCGTTCATGGCACTGGTTTC 60.387 55.000 0.00 0.00 0.00 2.78
1227 1276 1.737735 CATTCTGCTCGACCGTGCA 60.738 57.895 16.47 16.47 41.45 4.57
1241 1290 3.219281 ACCGTGCATTAGTTTGGAGTTT 58.781 40.909 0.00 0.00 0.00 2.66
1286 1335 7.724506 AGACTTCGACCTATGATCTTATGGTAA 59.275 37.037 0.00 0.00 0.00 2.85
1287 1336 7.659186 ACTTCGACCTATGATCTTATGGTAAC 58.341 38.462 0.00 0.00 0.00 2.50
1348 1397 7.893124 TTATTAGGAATAGGTCGTGAAGAGT 57.107 36.000 0.00 0.00 0.00 3.24
1349 1398 5.578005 TTAGGAATAGGTCGTGAAGAGTG 57.422 43.478 0.00 0.00 0.00 3.51
1350 1399 3.698289 AGGAATAGGTCGTGAAGAGTGA 58.302 45.455 0.00 0.00 0.00 3.41
1351 1400 4.087182 AGGAATAGGTCGTGAAGAGTGAA 58.913 43.478 0.00 0.00 0.00 3.18
1352 1401 4.082136 AGGAATAGGTCGTGAAGAGTGAAC 60.082 45.833 0.00 0.00 0.00 3.18
1353 1402 4.082136 GGAATAGGTCGTGAAGAGTGAACT 60.082 45.833 0.00 0.00 33.46 3.01
1354 1403 2.802787 AGGTCGTGAAGAGTGAACTG 57.197 50.000 0.00 0.00 0.00 3.16
1355 1404 2.032620 AGGTCGTGAAGAGTGAACTGT 58.967 47.619 0.00 0.00 0.00 3.55
1356 1405 2.431057 AGGTCGTGAAGAGTGAACTGTT 59.569 45.455 0.00 0.00 31.63 3.16
1357 1406 2.540101 GGTCGTGAAGAGTGAACTGTTG 59.460 50.000 0.00 0.00 28.86 3.33
1358 1407 3.444916 GTCGTGAAGAGTGAACTGTTGA 58.555 45.455 0.00 0.00 28.86 3.18
1359 1408 3.487574 GTCGTGAAGAGTGAACTGTTGAG 59.512 47.826 0.00 0.00 28.86 3.02
1360 1409 3.130516 TCGTGAAGAGTGAACTGTTGAGT 59.869 43.478 0.00 0.00 28.86 3.41
1361 1410 4.337274 TCGTGAAGAGTGAACTGTTGAGTA 59.663 41.667 0.00 0.00 28.86 2.59
1362 1411 5.009710 TCGTGAAGAGTGAACTGTTGAGTAT 59.990 40.000 0.00 0.00 28.86 2.12
1363 1412 5.117745 CGTGAAGAGTGAACTGTTGAGTATG 59.882 44.000 0.00 0.00 28.86 2.39
1364 1413 5.986135 GTGAAGAGTGAACTGTTGAGTATGT 59.014 40.000 0.00 0.00 28.86 2.29
1365 1414 6.480320 GTGAAGAGTGAACTGTTGAGTATGTT 59.520 38.462 0.00 0.00 28.86 2.71
1366 1415 7.652105 GTGAAGAGTGAACTGTTGAGTATGTTA 59.348 37.037 0.00 0.00 28.86 2.41
1367 1416 8.367911 TGAAGAGTGAACTGTTGAGTATGTTAT 58.632 33.333 0.00 0.00 28.86 1.89
1368 1417 9.209175 GAAGAGTGAACTGTTGAGTATGTTATT 57.791 33.333 0.00 0.00 28.86 1.40
1369 1418 9.561069 AAGAGTGAACTGTTGAGTATGTTATTT 57.439 29.630 0.00 0.00 0.00 1.40
1370 1419 8.993121 AGAGTGAACTGTTGAGTATGTTATTTG 58.007 33.333 0.00 0.00 0.00 2.32
1371 1420 8.677148 AGTGAACTGTTGAGTATGTTATTTGT 57.323 30.769 0.00 0.00 0.00 2.83
1372 1421 8.559536 AGTGAACTGTTGAGTATGTTATTTGTG 58.440 33.333 0.00 0.00 0.00 3.33
1373 1422 7.323656 GTGAACTGTTGAGTATGTTATTTGTGC 59.676 37.037 0.00 0.00 0.00 4.57
1374 1423 6.875948 ACTGTTGAGTATGTTATTTGTGCA 57.124 33.333 0.00 0.00 0.00 4.57
1375 1424 7.452880 ACTGTTGAGTATGTTATTTGTGCAT 57.547 32.000 0.00 0.00 0.00 3.96
1376 1425 7.307694 ACTGTTGAGTATGTTATTTGTGCATG 58.692 34.615 0.00 0.00 0.00 4.06
1377 1426 7.040478 ACTGTTGAGTATGTTATTTGTGCATGT 60.040 33.333 0.00 0.00 0.00 3.21
1378 1427 8.329203 TGTTGAGTATGTTATTTGTGCATGTA 57.671 30.769 0.00 0.00 0.00 2.29
1379 1428 8.955388 TGTTGAGTATGTTATTTGTGCATGTAT 58.045 29.630 0.00 0.00 0.00 2.29
1391 1440 7.504924 TTTGTGCATGTATATTAACTAGGCC 57.495 36.000 0.00 0.00 0.00 5.19
1392 1441 5.556915 TGTGCATGTATATTAACTAGGCCC 58.443 41.667 0.00 0.00 0.00 5.80
1393 1442 5.072464 TGTGCATGTATATTAACTAGGCCCA 59.928 40.000 0.00 0.00 0.00 5.36
1394 1443 5.411669 GTGCATGTATATTAACTAGGCCCAC 59.588 44.000 0.00 0.00 0.00 4.61
1395 1444 4.941873 GCATGTATATTAACTAGGCCCACC 59.058 45.833 0.00 0.00 0.00 4.61
1397 1446 6.407202 CATGTATATTAACTAGGCCCACCTC 58.593 44.000 0.00 0.00 46.34 3.85
1398 1447 5.723355 TGTATATTAACTAGGCCCACCTCT 58.277 41.667 0.00 0.00 46.34 3.69
1399 1448 5.778750 TGTATATTAACTAGGCCCACCTCTC 59.221 44.000 0.00 0.00 46.34 3.20
1400 1449 2.942604 TTAACTAGGCCCACCTCTCT 57.057 50.000 0.00 0.00 46.34 3.10
1401 1450 4.554553 ATTAACTAGGCCCACCTCTCTA 57.445 45.455 0.00 0.00 46.34 2.43
1402 1451 2.463047 AACTAGGCCCACCTCTCTAG 57.537 55.000 0.00 0.00 46.34 2.43
1403 1452 1.310877 ACTAGGCCCACCTCTCTAGT 58.689 55.000 0.00 0.00 46.34 2.57
1404 1453 1.646977 ACTAGGCCCACCTCTCTAGTT 59.353 52.381 0.00 0.00 46.34 2.24
1405 1454 2.312390 CTAGGCCCACCTCTCTAGTTC 58.688 57.143 0.00 0.00 46.34 3.01
1406 1455 0.684805 AGGCCCACCTCTCTAGTTCG 60.685 60.000 0.00 0.00 46.34 3.95
1407 1456 1.677637 GGCCCACCTCTCTAGTTCGG 61.678 65.000 0.00 0.00 0.00 4.30
1408 1457 0.971447 GCCCACCTCTCTAGTTCGGT 60.971 60.000 0.00 0.00 0.00 4.69
1409 1458 1.558233 CCCACCTCTCTAGTTCGGTT 58.442 55.000 0.00 0.00 0.00 4.44
1410 1459 1.204941 CCCACCTCTCTAGTTCGGTTG 59.795 57.143 0.00 0.00 0.00 3.77
1411 1460 1.893801 CCACCTCTCTAGTTCGGTTGT 59.106 52.381 0.00 0.00 0.00 3.32
1412 1461 3.087031 CCACCTCTCTAGTTCGGTTGTA 58.913 50.000 0.00 0.00 0.00 2.41
1413 1462 3.700038 CCACCTCTCTAGTTCGGTTGTAT 59.300 47.826 0.00 0.00 0.00 2.29
1414 1463 4.885907 CCACCTCTCTAGTTCGGTTGTATA 59.114 45.833 0.00 0.00 0.00 1.47
1415 1464 5.008811 CCACCTCTCTAGTTCGGTTGTATAG 59.991 48.000 0.00 0.00 0.00 1.31
1416 1465 5.821470 CACCTCTCTAGTTCGGTTGTATAGA 59.179 44.000 0.00 0.00 0.00 1.98
1417 1466 6.487331 CACCTCTCTAGTTCGGTTGTATAGAT 59.513 42.308 0.00 0.00 0.00 1.98
1418 1467 7.013464 CACCTCTCTAGTTCGGTTGTATAGATT 59.987 40.741 0.00 0.00 0.00 2.40
1419 1468 7.013464 ACCTCTCTAGTTCGGTTGTATAGATTG 59.987 40.741 0.00 0.00 0.00 2.67
1420 1469 7.228906 CCTCTCTAGTTCGGTTGTATAGATTGA 59.771 40.741 0.00 0.00 0.00 2.57
1421 1470 8.155821 TCTCTAGTTCGGTTGTATAGATTGAG 57.844 38.462 0.00 0.00 0.00 3.02
1422 1471 7.228906 TCTCTAGTTCGGTTGTATAGATTGAGG 59.771 40.741 0.00 0.00 0.00 3.86
1423 1472 5.934402 AGTTCGGTTGTATAGATTGAGGT 57.066 39.130 0.00 0.00 0.00 3.85
1424 1473 7.994911 TCTAGTTCGGTTGTATAGATTGAGGTA 59.005 37.037 0.00 0.00 0.00 3.08
1425 1474 7.040473 AGTTCGGTTGTATAGATTGAGGTAG 57.960 40.000 0.00 0.00 0.00 3.18
1426 1475 6.832384 AGTTCGGTTGTATAGATTGAGGTAGA 59.168 38.462 0.00 0.00 0.00 2.59
1427 1476 6.879276 TCGGTTGTATAGATTGAGGTAGAG 57.121 41.667 0.00 0.00 0.00 2.43
1428 1477 5.768662 TCGGTTGTATAGATTGAGGTAGAGG 59.231 44.000 0.00 0.00 0.00 3.69
1429 1478 5.565045 CGGTTGTATAGATTGAGGTAGAGGC 60.565 48.000 0.00 0.00 0.00 4.70
1430 1479 5.279556 GGTTGTATAGATTGAGGTAGAGGCC 60.280 48.000 0.00 0.00 0.00 5.19
1431 1480 4.417437 TGTATAGATTGAGGTAGAGGCCC 58.583 47.826 0.00 0.00 0.00 5.80
1432 1481 2.400467 TAGATTGAGGTAGAGGCCCC 57.600 55.000 0.00 0.00 0.00 5.80
1433 1482 0.343372 AGATTGAGGTAGAGGCCCCA 59.657 55.000 0.00 0.00 0.00 4.96
1434 1483 0.470341 GATTGAGGTAGAGGCCCCAC 59.530 60.000 0.00 0.00 0.00 4.61
1435 1484 0.988678 ATTGAGGTAGAGGCCCCACC 60.989 60.000 0.00 4.20 39.61 4.61
1449 1498 5.774102 GGCCCCACCTTGTACTTATATAT 57.226 43.478 0.00 0.00 34.51 0.86
1450 1499 6.879367 GGCCCCACCTTGTACTTATATATA 57.121 41.667 0.00 0.00 34.51 0.86
1451 1500 6.647229 GGCCCCACCTTGTACTTATATATAC 58.353 44.000 0.00 0.00 34.51 1.47
1452 1501 6.352479 GGCCCCACCTTGTACTTATATATACC 60.352 46.154 0.00 0.00 34.51 2.73
1453 1502 6.214005 GCCCCACCTTGTACTTATATATACCA 59.786 42.308 0.00 0.00 0.00 3.25
1454 1503 7.092578 GCCCCACCTTGTACTTATATATACCAT 60.093 40.741 0.00 0.00 0.00 3.55
1455 1504 8.265055 CCCCACCTTGTACTTATATATACCATG 58.735 40.741 0.00 0.00 0.00 3.66
1456 1505 7.769044 CCCACCTTGTACTTATATATACCATGC 59.231 40.741 0.00 0.00 0.00 4.06
1457 1506 8.318412 CCACCTTGTACTTATATATACCATGCA 58.682 37.037 0.00 0.00 0.00 3.96
1458 1507 9.151471 CACCTTGTACTTATATATACCATGCAC 57.849 37.037 0.00 0.00 0.00 4.57
1459 1508 8.876181 ACCTTGTACTTATATATACCATGCACA 58.124 33.333 0.00 0.00 0.00 4.57
1460 1509 9.890629 CCTTGTACTTATATATACCATGCACAT 57.109 33.333 0.00 0.00 0.00 3.21
1463 1512 9.161629 TGTACTTATATATACCATGCACATTGC 57.838 33.333 0.00 0.00 45.29 3.56
1473 1522 3.790744 GCACATTGCACCGAATCAA 57.209 47.368 0.00 0.00 44.26 2.57
1474 1523 2.282701 GCACATTGCACCGAATCAAT 57.717 45.000 0.00 0.00 44.26 2.57
1475 1524 3.419264 GCACATTGCACCGAATCAATA 57.581 42.857 0.00 0.00 44.26 1.90
1476 1525 3.108144 GCACATTGCACCGAATCAATAC 58.892 45.455 0.00 0.00 44.26 1.89
1477 1526 3.427368 GCACATTGCACCGAATCAATACA 60.427 43.478 0.00 0.00 44.26 2.29
1478 1527 4.734402 GCACATTGCACCGAATCAATACAT 60.734 41.667 0.00 0.00 44.26 2.29
1479 1528 4.971830 CACATTGCACCGAATCAATACATC 59.028 41.667 0.00 0.00 32.22 3.06
1480 1529 3.942539 TTGCACCGAATCAATACATCG 57.057 42.857 0.00 0.00 36.39 3.84
1481 1530 2.899976 TGCACCGAATCAATACATCGT 58.100 42.857 0.00 0.00 34.90 3.73
1482 1531 2.607180 TGCACCGAATCAATACATCGTG 59.393 45.455 0.00 0.00 34.90 4.35
1483 1532 2.599848 GCACCGAATCAATACATCGTGC 60.600 50.000 0.00 0.00 36.89 5.34
1484 1533 2.607180 CACCGAATCAATACATCGTGCA 59.393 45.455 0.00 0.00 34.90 4.57
1485 1534 3.063316 CACCGAATCAATACATCGTGCAA 59.937 43.478 0.00 0.00 34.90 4.08
1486 1535 3.876914 ACCGAATCAATACATCGTGCAAT 59.123 39.130 0.00 0.00 34.90 3.56
1487 1536 4.335315 ACCGAATCAATACATCGTGCAATT 59.665 37.500 0.00 0.00 34.90 2.32
1488 1537 4.905866 CCGAATCAATACATCGTGCAATTC 59.094 41.667 0.00 0.00 34.90 2.17
1489 1538 5.500825 CGAATCAATACATCGTGCAATTCA 58.499 37.500 0.00 0.00 0.00 2.57
1490 1539 6.138088 CGAATCAATACATCGTGCAATTCAT 58.862 36.000 0.00 0.00 0.00 2.57
1491 1540 7.290118 CGAATCAATACATCGTGCAATTCATA 58.710 34.615 0.00 0.00 0.00 2.15
1492 1541 7.266966 CGAATCAATACATCGTGCAATTCATAC 59.733 37.037 0.00 0.00 0.00 2.39
1493 1542 6.917217 TCAATACATCGTGCAATTCATACA 57.083 33.333 0.00 0.00 0.00 2.29
1494 1543 7.495135 TCAATACATCGTGCAATTCATACAT 57.505 32.000 0.00 0.00 0.00 2.29
1495 1544 7.575365 TCAATACATCGTGCAATTCATACATC 58.425 34.615 0.00 0.00 0.00 3.06
1496 1545 7.442062 TCAATACATCGTGCAATTCATACATCT 59.558 33.333 0.00 0.00 0.00 2.90
1497 1546 7.734924 ATACATCGTGCAATTCATACATCTT 57.265 32.000 0.00 0.00 0.00 2.40
1498 1547 6.052840 ACATCGTGCAATTCATACATCTTC 57.947 37.500 0.00 0.00 0.00 2.87
1499 1548 5.585844 ACATCGTGCAATTCATACATCTTCA 59.414 36.000 0.00 0.00 0.00 3.02
1544 1593 4.913784 TGGTAGGTCCAAAATACCAGTTC 58.086 43.478 4.04 0.00 43.06 3.01
1562 1614 8.336801 ACCAGTTCCTTTTGTAGAATGATAAC 57.663 34.615 0.00 0.00 0.00 1.89
1585 1637 5.163804 ACCAAATTGGCAAAGTTTTCGTTTC 60.164 36.000 12.67 0.00 42.67 2.78
1671 1723 5.761165 TTATCACACATAGCTAGTACGCA 57.239 39.130 0.00 0.00 0.00 5.24
1713 1779 5.127194 TCCAGAAGCTACTTCAACGTATCAT 59.873 40.000 9.80 0.00 42.37 2.45
1722 1788 1.343142 TCAACGTATCATCCCGATGGG 59.657 52.381 4.90 0.00 46.11 4.00
1843 1909 4.159506 GGTAATGCTTCTCTCTGTCTGAGT 59.840 45.833 6.63 0.00 43.13 3.41
1876 1942 9.146586 CCTTGATTCATGGATATTTTCCCTAAA 57.853 33.333 12.18 0.00 44.77 1.85
1923 1989 8.143193 ACAAACAAGTGCAAATGAAGAATATCA 58.857 29.630 6.97 0.00 0.00 2.15
2089 2188 5.548181 GGATACCGGAGTTCTTTAAGGAT 57.452 43.478 9.46 0.00 0.00 3.24
2090 2189 5.298347 GGATACCGGAGTTCTTTAAGGATG 58.702 45.833 9.46 0.00 0.00 3.51
2091 2190 5.070047 GGATACCGGAGTTCTTTAAGGATGA 59.930 44.000 9.46 0.00 0.00 2.92
2092 2191 4.903045 ACCGGAGTTCTTTAAGGATGAA 57.097 40.909 9.46 0.00 0.00 2.57
2093 2192 5.437191 ACCGGAGTTCTTTAAGGATGAAT 57.563 39.130 9.46 0.00 0.00 2.57
2094 2193 5.429130 ACCGGAGTTCTTTAAGGATGAATC 58.571 41.667 9.46 0.00 0.00 2.52
2095 2194 5.189934 ACCGGAGTTCTTTAAGGATGAATCT 59.810 40.000 9.46 0.00 0.00 2.40
2096 2195 5.525378 CCGGAGTTCTTTAAGGATGAATCTG 59.475 44.000 0.00 0.00 0.00 2.90
2097 2196 6.109359 CGGAGTTCTTTAAGGATGAATCTGT 58.891 40.000 0.00 0.00 0.00 3.41
2098 2197 6.595716 CGGAGTTCTTTAAGGATGAATCTGTT 59.404 38.462 0.00 0.00 0.00 3.16
2099 2198 7.413438 CGGAGTTCTTTAAGGATGAATCTGTTG 60.413 40.741 0.00 0.00 0.00 3.33
2100 2199 7.607991 GGAGTTCTTTAAGGATGAATCTGTTGA 59.392 37.037 0.00 0.00 0.00 3.18
2101 2200 8.558973 AGTTCTTTAAGGATGAATCTGTTGAG 57.441 34.615 0.00 0.00 0.00 3.02
2102 2201 8.378565 AGTTCTTTAAGGATGAATCTGTTGAGA 58.621 33.333 0.00 0.00 0.00 3.27
2103 2202 8.663911 GTTCTTTAAGGATGAATCTGTTGAGAG 58.336 37.037 0.00 0.00 0.00 3.20
2104 2203 8.138928 TCTTTAAGGATGAATCTGTTGAGAGA 57.861 34.615 0.00 0.00 0.00 3.10
2105 2204 8.037758 TCTTTAAGGATGAATCTGTTGAGAGAC 58.962 37.037 0.00 0.00 0.00 3.36
2106 2205 4.751767 AGGATGAATCTGTTGAGAGACC 57.248 45.455 0.00 0.00 0.00 3.85
2152 2251 2.854967 AGGATCCATGGACAGGAACAAT 59.145 45.455 18.99 0.00 38.93 2.71
2227 2326 4.471904 TGCTCTTCTTAATCACACGGAT 57.528 40.909 0.00 0.00 38.05 4.18
2356 2455 5.947228 TTGCAGGTACATTCTTTCTCTTG 57.053 39.130 0.00 0.00 0.00 3.02
2535 2634 4.777896 ACTATCTCTGAAACTACAAGCCCA 59.222 41.667 0.00 0.00 0.00 5.36
2569 2671 4.837093 TGCTGTAGGCCTATACTTGTTT 57.163 40.909 17.38 0.00 40.92 2.83
2820 2924 1.144276 TCGTGGCCACAGTTTTCGA 59.856 52.632 34.16 21.25 0.00 3.71
2825 2929 2.034053 GTGGCCACAGTTTTCGATGAAA 59.966 45.455 31.23 0.00 0.00 2.69
2829 2933 3.365364 GCCACAGTTTTCGATGAAAGAGG 60.365 47.826 0.00 0.00 32.93 3.69
2833 2937 3.686726 CAGTTTTCGATGAAAGAGGGGAG 59.313 47.826 0.00 0.00 32.93 4.30
2842 2946 3.024547 TGAAAGAGGGGAGTCATACGAG 58.975 50.000 0.00 0.00 0.00 4.18
2849 2953 2.421529 GGGGAGTCATACGAGCCATTTT 60.422 50.000 0.00 0.00 0.00 1.82
2894 2998 4.645535 AGAAGCAAACACAGAAGCTGATA 58.354 39.130 0.82 0.00 37.41 2.15
2921 3025 3.127030 CGGCCACTATTTTCTTCCTCAAC 59.873 47.826 2.24 0.00 0.00 3.18
3149 3261 4.119862 TCTCACAGGTCGAGAAAACAAAG 58.880 43.478 0.00 0.00 36.59 2.77
3162 3274 9.489084 TCGAGAAAACAAAGAAGATGATCTTAA 57.511 29.630 7.82 0.00 38.69 1.85
3180 3292 2.107950 AATCCATTTCTGCGAACCGA 57.892 45.000 0.00 0.00 0.00 4.69
3310 3422 3.214250 GATCCCAGAGGCGCTACGG 62.214 68.421 7.64 2.77 0.00 4.02
3323 3435 0.935196 GCTACGGTTTAAGCCCATCG 59.065 55.000 2.36 0.00 32.40 3.84
3430 6960 5.357032 GTCTGAATTATTTTGTCGTGGGGAT 59.643 40.000 0.00 0.00 0.00 3.85
3484 7014 1.607467 AGCCAAAAGGCTCGCCAAT 60.607 52.632 11.02 0.00 41.97 3.16
3628 7167 6.546403 TGGAGTAAGATCAACTACTCGCTTAT 59.454 38.462 16.92 0.00 39.68 1.73
3827 7366 8.908903 GGATGTATTATGTTGGAATTAACCACA 58.091 33.333 0.00 0.00 39.85 4.17
3905 7444 8.848182 AGTAGTAAGATTTAGATGTCCTAACCG 58.152 37.037 0.00 0.00 37.10 4.44
3911 7450 6.606395 AGATTTAGATGTCCTAACCGTGTAGT 59.394 38.462 0.00 0.00 37.10 2.73
3929 7468 6.807230 CGTGTAGTTCAGCTTGTCTTATACTT 59.193 38.462 0.00 0.00 0.00 2.24
3931 7470 7.275999 GTGTAGTTCAGCTTGTCTTATACTTCC 59.724 40.741 0.00 0.00 0.00 3.46
3932 7471 6.613153 AGTTCAGCTTGTCTTATACTTCCT 57.387 37.500 0.00 0.00 0.00 3.36
3940 7479 2.292845 GTCTTATACTTCCTCCGTCCCG 59.707 54.545 0.00 0.00 0.00 5.14
3972 7511 9.317827 AGTGTCTCAACTTTATACTAACCCTAA 57.682 33.333 0.00 0.00 0.00 2.69
4010 7549 4.353777 AGTTTGAGACACTAGGGCTCATA 58.646 43.478 16.53 11.06 38.35 2.15
4011 7550 4.965532 AGTTTGAGACACTAGGGCTCATAT 59.034 41.667 16.53 6.42 38.35 1.78
4261 7802 8.334632 CAAAAACCACACATACCAAAATTTCTC 58.665 33.333 0.00 0.00 0.00 2.87
4376 7926 2.427095 GCATTGGCCTAAACCGATTTCT 59.573 45.455 3.32 0.00 30.81 2.52
4474 8025 4.598022 TGGATTATCAAGTTGCCATGTCA 58.402 39.130 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 178 0.806492 GACTTCATCTTCGACCCGGC 60.806 60.000 0.00 0.00 0.00 6.13
331 361 3.839490 TCACCCCAAATTGCATCAAATCT 59.161 39.130 0.00 0.00 0.00 2.40
353 383 2.521224 GACCCGATAGCCCGACCT 60.521 66.667 0.00 0.00 0.00 3.85
408 439 2.880890 CTCACACCCAGCCTAAATATGC 59.119 50.000 0.00 0.00 0.00 3.14
423 454 2.032681 GACCAGCACCCCTCACAC 59.967 66.667 0.00 0.00 0.00 3.82
425 456 2.348998 CTGACCAGCACCCCTCAC 59.651 66.667 0.00 0.00 0.00 3.51
448 480 2.504367 CCTCAAACGACCCTCAAACAT 58.496 47.619 0.00 0.00 0.00 2.71
449 481 1.476110 CCCTCAAACGACCCTCAAACA 60.476 52.381 0.00 0.00 0.00 2.83
473 505 5.583854 CGGTCATGATTTTCTGATTCAGACT 59.416 40.000 15.90 4.29 40.46 3.24
479 511 5.707298 ACTGTTCGGTCATGATTTTCTGATT 59.293 36.000 0.00 0.00 0.00 2.57
514 548 1.138859 CATCTCATACGCTTGGGTGGA 59.861 52.381 0.45 0.00 0.00 4.02
517 551 0.469917 CCCATCTCATACGCTTGGGT 59.530 55.000 0.00 0.00 41.78 4.51
533 567 0.546747 ATCCGGACCTCTCAAACCCA 60.547 55.000 6.12 0.00 0.00 4.51
586 620 3.181397 GCAATAAATCGCTGTGTGCATT 58.819 40.909 0.00 0.00 43.06 3.56
596 630 4.085924 CGCTTGAATTCTGCAATAAATCGC 60.086 41.667 18.79 1.69 0.00 4.58
627 661 3.185391 GCACAAGAGAAGTCAGCTGTAAC 59.815 47.826 14.67 5.43 0.00 2.50
654 691 8.917088 CATGATATCCTCTTGGGTTAACAAAAT 58.083 33.333 8.10 0.00 36.25 1.82
667 704 3.244009 CGACACCTGCATGATATCCTCTT 60.244 47.826 0.00 0.00 0.00 2.85
753 793 1.302192 GACCCTACGCTGGCACAAA 60.302 57.895 0.00 0.00 38.70 2.83
769 809 1.105759 GCTTCATGCATGGGAGGGAC 61.106 60.000 25.97 8.60 42.31 4.46
808 852 1.610086 CATGGAAGGGCAGGGCAAA 60.610 57.895 0.00 0.00 0.00 3.68
915 961 1.812571 CTTGTGTCCAACCATACAGCC 59.187 52.381 0.00 0.00 0.00 4.85
995 1044 1.676746 CCTCCTCTCCAACATGCATG 58.323 55.000 25.09 25.09 0.00 4.06
996 1045 0.106819 GCCTCCTCTCCAACATGCAT 60.107 55.000 0.00 0.00 0.00 3.96
997 1046 1.300963 GCCTCCTCTCCAACATGCA 59.699 57.895 0.00 0.00 0.00 3.96
998 1047 1.452833 GGCCTCCTCTCCAACATGC 60.453 63.158 0.00 0.00 0.00 4.06
1150 1199 3.569902 CCGAACCGGCAAGTTACC 58.430 61.111 0.00 0.00 41.17 2.85
1252 1301 9.303116 AGATCATAGGTCGAAGTCTAATTATGT 57.697 33.333 0.00 0.00 0.00 2.29
1269 1318 9.838339 ACTCTTTTGTTACCATAAGATCATAGG 57.162 33.333 0.00 0.00 37.79 2.57
1286 1335 3.595173 GCAAACCCAACAACTCTTTTGT 58.405 40.909 0.00 0.00 0.00 2.83
1287 1336 2.935849 GGCAAACCCAACAACTCTTTTG 59.064 45.455 0.00 0.00 0.00 2.44
1348 1397 7.012799 TGCACAAATAACATACTCAACAGTTCA 59.987 33.333 0.00 0.00 33.62 3.18
1349 1398 7.359595 TGCACAAATAACATACTCAACAGTTC 58.640 34.615 0.00 0.00 33.62 3.01
1350 1399 7.270757 TGCACAAATAACATACTCAACAGTT 57.729 32.000 0.00 0.00 33.62 3.16
1351 1400 6.875948 TGCACAAATAACATACTCAACAGT 57.124 33.333 0.00 0.00 36.55 3.55
1352 1401 7.307694 ACATGCACAAATAACATACTCAACAG 58.692 34.615 0.00 0.00 0.00 3.16
1353 1402 7.213216 ACATGCACAAATAACATACTCAACA 57.787 32.000 0.00 0.00 0.00 3.33
1365 1414 9.226606 GGCCTAGTTAATATACATGCACAAATA 57.773 33.333 0.00 0.00 0.00 1.40
1366 1415 7.176690 GGGCCTAGTTAATATACATGCACAAAT 59.823 37.037 0.84 0.00 0.00 2.32
1367 1416 6.488683 GGGCCTAGTTAATATACATGCACAAA 59.511 38.462 0.84 0.00 0.00 2.83
1368 1417 6.001460 GGGCCTAGTTAATATACATGCACAA 58.999 40.000 0.84 0.00 0.00 3.33
1369 1418 5.072464 TGGGCCTAGTTAATATACATGCACA 59.928 40.000 4.53 0.00 0.00 4.57
1370 1419 5.411669 GTGGGCCTAGTTAATATACATGCAC 59.588 44.000 4.53 0.00 0.00 4.57
1371 1420 5.514136 GGTGGGCCTAGTTAATATACATGCA 60.514 44.000 4.53 0.00 0.00 3.96
1372 1421 4.941873 GGTGGGCCTAGTTAATATACATGC 59.058 45.833 4.53 0.00 0.00 4.06
1373 1422 6.374417 AGGTGGGCCTAGTTAATATACATG 57.626 41.667 4.53 0.00 44.90 3.21
1379 1428 8.129745 GAACTAGAGAGGTGGGCCTAGTTAATA 61.130 44.444 4.53 0.00 46.41 0.98
1380 1429 7.372018 GAACTAGAGAGGTGGGCCTAGTTAAT 61.372 46.154 4.53 0.00 46.41 1.40
1381 1430 6.102443 GAACTAGAGAGGTGGGCCTAGTTAA 61.102 48.000 4.53 0.00 46.41 2.01
1382 1431 4.630676 GAACTAGAGAGGTGGGCCTAGTTA 60.631 50.000 4.53 0.00 46.41 2.24
1388 1437 1.677637 CCGAACTAGAGAGGTGGGCC 61.678 65.000 0.00 0.00 30.64 5.80
1389 1438 0.971447 ACCGAACTAGAGAGGTGGGC 60.971 60.000 0.00 0.00 41.92 5.36
1390 1439 1.204941 CAACCGAACTAGAGAGGTGGG 59.795 57.143 0.00 0.00 43.75 4.61
1391 1440 1.893801 ACAACCGAACTAGAGAGGTGG 59.106 52.381 0.00 2.45 37.03 4.61
1392 1441 4.985538 ATACAACCGAACTAGAGAGGTG 57.014 45.455 0.00 0.00 37.03 4.00
1393 1442 5.999044 TCTATACAACCGAACTAGAGAGGT 58.001 41.667 0.00 0.00 38.88 3.85
1394 1443 7.228906 TCAATCTATACAACCGAACTAGAGAGG 59.771 40.741 0.00 0.00 0.00 3.69
1395 1444 8.155821 TCAATCTATACAACCGAACTAGAGAG 57.844 38.462 0.00 0.00 0.00 3.20
1396 1445 7.228906 CCTCAATCTATACAACCGAACTAGAGA 59.771 40.741 0.00 0.00 0.00 3.10
1397 1446 7.013464 ACCTCAATCTATACAACCGAACTAGAG 59.987 40.741 0.00 0.00 0.00 2.43
1398 1447 6.832384 ACCTCAATCTATACAACCGAACTAGA 59.168 38.462 0.00 0.00 0.00 2.43
1399 1448 7.040473 ACCTCAATCTATACAACCGAACTAG 57.960 40.000 0.00 0.00 0.00 2.57
1400 1449 7.994911 TCTACCTCAATCTATACAACCGAACTA 59.005 37.037 0.00 0.00 0.00 2.24
1401 1450 5.934402 ACCTCAATCTATACAACCGAACT 57.066 39.130 0.00 0.00 0.00 3.01
1402 1451 7.035840 TCTACCTCAATCTATACAACCGAAC 57.964 40.000 0.00 0.00 0.00 3.95
1403 1452 6.264744 CCTCTACCTCAATCTATACAACCGAA 59.735 42.308 0.00 0.00 0.00 4.30
1404 1453 5.768662 CCTCTACCTCAATCTATACAACCGA 59.231 44.000 0.00 0.00 0.00 4.69
1405 1454 5.565045 GCCTCTACCTCAATCTATACAACCG 60.565 48.000 0.00 0.00 0.00 4.44
1406 1455 5.279556 GGCCTCTACCTCAATCTATACAACC 60.280 48.000 0.00 0.00 0.00 3.77
1407 1456 5.279556 GGGCCTCTACCTCAATCTATACAAC 60.280 48.000 0.84 0.00 0.00 3.32
1408 1457 4.838986 GGGCCTCTACCTCAATCTATACAA 59.161 45.833 0.84 0.00 0.00 2.41
1409 1458 4.417437 GGGCCTCTACCTCAATCTATACA 58.583 47.826 0.84 0.00 0.00 2.29
1410 1459 3.770388 GGGGCCTCTACCTCAATCTATAC 59.230 52.174 0.84 0.00 0.00 1.47
1411 1460 3.404769 TGGGGCCTCTACCTCAATCTATA 59.595 47.826 3.07 0.00 37.21 1.31
1412 1461 2.182312 TGGGGCCTCTACCTCAATCTAT 59.818 50.000 3.07 0.00 37.21 1.98
1413 1462 1.578703 TGGGGCCTCTACCTCAATCTA 59.421 52.381 3.07 0.00 37.21 1.98
1414 1463 0.343372 TGGGGCCTCTACCTCAATCT 59.657 55.000 3.07 0.00 37.21 2.40
1415 1464 0.470341 GTGGGGCCTCTACCTCAATC 59.530 60.000 3.07 0.00 43.50 2.67
1416 1465 0.988678 GGTGGGGCCTCTACCTCAAT 60.989 60.000 16.34 0.00 43.50 2.57
1417 1466 1.615424 GGTGGGGCCTCTACCTCAA 60.615 63.158 16.34 0.00 43.50 3.02
1418 1467 2.040606 GGTGGGGCCTCTACCTCA 59.959 66.667 16.34 0.00 38.08 3.86
1419 1468 2.369001 AGGTGGGGCCTCTACCTC 59.631 66.667 19.33 6.40 46.96 3.85
1427 1476 5.774102 ATATATAAGTACAAGGTGGGGCC 57.226 43.478 0.00 0.00 37.58 5.80
1428 1477 6.214005 TGGTATATATAAGTACAAGGTGGGGC 59.786 42.308 0.00 0.00 0.00 5.80
1429 1478 7.801893 TGGTATATATAAGTACAAGGTGGGG 57.198 40.000 0.00 0.00 0.00 4.96
1430 1479 7.769044 GCATGGTATATATAAGTACAAGGTGGG 59.231 40.741 0.00 0.00 0.00 4.61
1431 1480 8.318412 TGCATGGTATATATAAGTACAAGGTGG 58.682 37.037 0.00 0.00 0.00 4.61
1432 1481 9.151471 GTGCATGGTATATATAAGTACAAGGTG 57.849 37.037 0.00 0.00 0.00 4.00
1433 1482 8.876181 TGTGCATGGTATATATAAGTACAAGGT 58.124 33.333 0.00 0.00 0.00 3.50
1434 1483 9.890629 ATGTGCATGGTATATATAAGTACAAGG 57.109 33.333 0.00 0.00 0.00 3.61
1437 1486 9.161629 GCAATGTGCATGGTATATATAAGTACA 57.838 33.333 0.00 2.42 44.26 2.90
1455 1504 2.282701 ATTGATTCGGTGCAATGTGC 57.717 45.000 0.00 0.00 45.29 4.57
1456 1505 4.354071 TGTATTGATTCGGTGCAATGTG 57.646 40.909 0.00 0.00 36.27 3.21
1457 1506 4.260743 CGATGTATTGATTCGGTGCAATGT 60.261 41.667 0.00 0.00 36.27 2.71
1458 1507 4.213674 CGATGTATTGATTCGGTGCAATG 58.786 43.478 0.00 0.00 36.27 2.82
1459 1508 3.876914 ACGATGTATTGATTCGGTGCAAT 59.123 39.130 0.00 0.00 37.20 3.56
1460 1509 3.063316 CACGATGTATTGATTCGGTGCAA 59.937 43.478 0.00 0.00 37.20 4.08
1461 1510 2.607180 CACGATGTATTGATTCGGTGCA 59.393 45.455 0.00 0.00 37.20 4.57
1462 1511 2.599848 GCACGATGTATTGATTCGGTGC 60.600 50.000 0.00 0.00 37.20 5.01
1463 1512 2.607180 TGCACGATGTATTGATTCGGTG 59.393 45.455 0.00 0.00 37.20 4.94
1464 1513 2.899976 TGCACGATGTATTGATTCGGT 58.100 42.857 0.00 0.00 37.20 4.69
1465 1514 3.942539 TTGCACGATGTATTGATTCGG 57.057 42.857 0.00 0.00 37.20 4.30
1466 1515 5.500825 TGAATTGCACGATGTATTGATTCG 58.499 37.500 0.00 0.00 38.76 3.34
1467 1516 8.069574 TGTATGAATTGCACGATGTATTGATTC 58.930 33.333 0.00 0.00 0.00 2.52
1468 1517 7.929159 TGTATGAATTGCACGATGTATTGATT 58.071 30.769 0.00 0.00 0.00 2.57
1469 1518 7.495135 TGTATGAATTGCACGATGTATTGAT 57.505 32.000 0.00 0.00 0.00 2.57
1470 1519 6.917217 TGTATGAATTGCACGATGTATTGA 57.083 33.333 0.00 0.00 0.00 2.57
1471 1520 7.578852 AGATGTATGAATTGCACGATGTATTG 58.421 34.615 0.00 0.00 0.00 1.90
1472 1521 7.734924 AGATGTATGAATTGCACGATGTATT 57.265 32.000 0.00 0.00 0.00 1.89
1473 1522 7.442062 TGAAGATGTATGAATTGCACGATGTAT 59.558 33.333 0.00 0.00 0.00 2.29
1474 1523 6.760770 TGAAGATGTATGAATTGCACGATGTA 59.239 34.615 0.00 0.00 0.00 2.29
1475 1524 5.585844 TGAAGATGTATGAATTGCACGATGT 59.414 36.000 0.00 0.00 0.00 3.06
1476 1525 6.051646 TGAAGATGTATGAATTGCACGATG 57.948 37.500 0.00 0.00 0.00 3.84
1477 1526 6.484308 TCATGAAGATGTATGAATTGCACGAT 59.516 34.615 0.00 0.00 30.84 3.73
1478 1527 5.816777 TCATGAAGATGTATGAATTGCACGA 59.183 36.000 0.00 0.00 30.84 4.35
1479 1528 6.051646 TCATGAAGATGTATGAATTGCACG 57.948 37.500 0.00 0.00 30.84 5.34
1480 1529 7.478322 AGTTCATGAAGATGTATGAATTGCAC 58.522 34.615 8.80 0.00 43.03 4.57
1481 1530 7.634671 AGTTCATGAAGATGTATGAATTGCA 57.365 32.000 8.80 0.00 43.03 4.08
1544 1593 9.369904 CCAATTTGGTTATCATTCTACAAAAGG 57.630 33.333 7.31 0.00 32.44 3.11
1562 1614 4.873768 AACGAAAACTTTGCCAATTTGG 57.126 36.364 11.27 11.27 41.55 3.28
1585 1637 7.259161 GTCTCAACAGTAGATACAACCTAAGG 58.741 42.308 0.00 0.00 0.00 2.69
1699 1765 3.492656 CCATCGGGATGATACGTTGAAGT 60.493 47.826 10.16 0.00 41.20 3.01
1722 1788 1.379576 ATGGCCAGCTCTTCCTTGC 60.380 57.895 13.05 0.00 0.00 4.01
1843 1909 3.135161 TCCATGAATCAAGGAGGAGGA 57.865 47.619 2.70 0.00 27.62 3.71
1879 1945 7.639113 TGTTTGTCACCTAGTTTTGAAGAAT 57.361 32.000 0.00 0.00 0.00 2.40
1891 1957 4.642437 TCATTTGCACTTGTTTGTCACCTA 59.358 37.500 0.00 0.00 0.00 3.08
1902 1968 7.485810 TCCATGATATTCTTCATTTGCACTTG 58.514 34.615 0.00 0.00 34.09 3.16
1923 1989 1.528824 CCATGGGCTTCGACTCCAT 59.471 57.895 2.85 7.35 41.53 3.41
2074 2173 7.607991 TCAACAGATTCATCCTTAAAGAACTCC 59.392 37.037 0.00 0.00 0.00 3.85
2075 2174 8.553459 TCAACAGATTCATCCTTAAAGAACTC 57.447 34.615 0.00 0.00 0.00 3.01
2076 2175 8.378565 TCTCAACAGATTCATCCTTAAAGAACT 58.621 33.333 0.00 0.00 0.00 3.01
2077 2176 8.553459 TCTCAACAGATTCATCCTTAAAGAAC 57.447 34.615 0.00 0.00 0.00 3.01
2078 2177 8.597167 TCTCTCAACAGATTCATCCTTAAAGAA 58.403 33.333 0.00 0.00 0.00 2.52
2079 2178 8.037758 GTCTCTCAACAGATTCATCCTTAAAGA 58.962 37.037 0.00 0.00 0.00 2.52
2080 2179 7.279758 GGTCTCTCAACAGATTCATCCTTAAAG 59.720 40.741 0.00 0.00 0.00 1.85
2081 2180 7.038017 AGGTCTCTCAACAGATTCATCCTTAAA 60.038 37.037 0.00 0.00 0.00 1.52
2082 2181 6.441924 AGGTCTCTCAACAGATTCATCCTTAA 59.558 38.462 0.00 0.00 0.00 1.85
2083 2182 5.960811 AGGTCTCTCAACAGATTCATCCTTA 59.039 40.000 0.00 0.00 0.00 2.69
2084 2183 4.782156 AGGTCTCTCAACAGATTCATCCTT 59.218 41.667 0.00 0.00 0.00 3.36
2085 2184 4.360889 AGGTCTCTCAACAGATTCATCCT 58.639 43.478 0.00 0.00 0.00 3.24
2086 2185 4.751767 AGGTCTCTCAACAGATTCATCC 57.248 45.455 0.00 0.00 0.00 3.51
2087 2186 6.872920 ACTTAGGTCTCTCAACAGATTCATC 58.127 40.000 0.00 0.00 0.00 2.92
2088 2187 6.865834 ACTTAGGTCTCTCAACAGATTCAT 57.134 37.500 0.00 0.00 0.00 2.57
2089 2188 6.672266 AACTTAGGTCTCTCAACAGATTCA 57.328 37.500 0.00 0.00 0.00 2.57
2090 2189 6.128418 GCAAACTTAGGTCTCTCAACAGATTC 60.128 42.308 0.00 0.00 0.00 2.52
2091 2190 5.703130 GCAAACTTAGGTCTCTCAACAGATT 59.297 40.000 0.00 0.00 0.00 2.40
2092 2191 5.012561 AGCAAACTTAGGTCTCTCAACAGAT 59.987 40.000 0.00 0.00 0.00 2.90
2093 2192 4.345257 AGCAAACTTAGGTCTCTCAACAGA 59.655 41.667 0.00 0.00 0.00 3.41
2094 2193 4.636249 AGCAAACTTAGGTCTCTCAACAG 58.364 43.478 0.00 0.00 0.00 3.16
2095 2194 4.689612 AGCAAACTTAGGTCTCTCAACA 57.310 40.909 0.00 0.00 0.00 3.33
2096 2195 5.301555 AGAAGCAAACTTAGGTCTCTCAAC 58.698 41.667 0.00 0.00 35.82 3.18
2097 2196 5.305644 AGAGAAGCAAACTTAGGTCTCTCAA 59.694 40.000 0.00 0.00 35.82 3.02
2098 2197 4.835615 AGAGAAGCAAACTTAGGTCTCTCA 59.164 41.667 0.00 0.00 35.82 3.27
2099 2198 5.047660 TGAGAGAAGCAAACTTAGGTCTCTC 60.048 44.000 17.54 17.54 43.66 3.20
2100 2199 4.835615 TGAGAGAAGCAAACTTAGGTCTCT 59.164 41.667 0.77 0.77 37.77 3.10
2101 2200 4.926832 GTGAGAGAAGCAAACTTAGGTCTC 59.073 45.833 0.00 0.00 37.60 3.36
2102 2201 4.345257 TGTGAGAGAAGCAAACTTAGGTCT 59.655 41.667 0.00 0.00 35.82 3.85
2103 2202 4.632153 TGTGAGAGAAGCAAACTTAGGTC 58.368 43.478 0.00 0.00 35.82 3.85
2104 2203 4.689612 TGTGAGAGAAGCAAACTTAGGT 57.310 40.909 0.00 0.00 35.82 3.08
2105 2204 4.084328 CGTTGTGAGAGAAGCAAACTTAGG 60.084 45.833 0.00 0.00 35.82 2.69
2106 2205 4.609336 GCGTTGTGAGAGAAGCAAACTTAG 60.609 45.833 0.00 0.00 35.82 2.18
2152 2251 1.590591 TACCAGCAATAGGCCCTGAA 58.409 50.000 0.00 0.00 46.50 3.02
2227 2326 7.673504 TCCTCCAATGGAATGAACTCAAAATAA 59.326 33.333 2.61 0.00 32.39 1.40
2332 2431 6.071728 CCAAGAGAAAGAATGTACCTGCAAAT 60.072 38.462 0.00 0.00 0.00 2.32
2356 2455 9.579932 ACCATTAATCTAAAGGATCAGAATTCC 57.420 33.333 0.65 0.00 32.76 3.01
2535 2634 3.131046 GCCTACAGCAACATAGCCAAAAT 59.869 43.478 0.00 0.00 42.97 1.82
2820 2924 3.639094 CTCGTATGACTCCCCTCTTTCAT 59.361 47.826 0.00 0.00 33.31 2.57
2825 2929 0.468400 GGCTCGTATGACTCCCCTCT 60.468 60.000 0.00 0.00 0.00 3.69
2829 2933 2.622064 AAATGGCTCGTATGACTCCC 57.378 50.000 0.00 0.00 0.00 4.30
2833 2937 5.640732 ACATTGAAAAATGGCTCGTATGAC 58.359 37.500 3.70 0.00 34.56 3.06
2842 2946 5.620467 GTGTGCATAACATTGAAAAATGGC 58.380 37.500 0.00 0.00 41.97 4.40
2888 2992 3.662247 ATAGTGGCCGTACTTATCAGC 57.338 47.619 0.33 0.00 32.19 4.26
2894 2998 4.019591 AGGAAGAAAATAGTGGCCGTACTT 60.020 41.667 0.33 0.00 32.19 2.24
2921 3025 3.965539 CTGGCGGTCCTGGCTTCTG 62.966 68.421 8.33 0.00 35.06 3.02
3149 3261 7.172190 TCGCAGAAATGGATTAAGATCATCTTC 59.828 37.037 2.18 0.00 37.89 2.87
3162 3274 1.656652 CTCGGTTCGCAGAAATGGAT 58.343 50.000 0.00 0.00 45.90 3.41
3180 3292 2.877708 GCTGCTGTCCTTCCTAAAAGCT 60.878 50.000 0.00 0.00 0.00 3.74
3310 3422 2.650322 TGATTCCCGATGGGCTTAAAC 58.350 47.619 0.00 0.00 43.94 2.01
3323 3435 4.692155 CCAACTTTGCTTGATTTGATTCCC 59.308 41.667 0.00 0.00 0.00 3.97
3325 3437 6.849588 AACCAACTTTGCTTGATTTGATTC 57.150 33.333 0.00 0.00 0.00 2.52
3430 6960 4.020573 ACTGGAGTTTGATCGGTTATGTCA 60.021 41.667 0.00 0.00 0.00 3.58
3468 6998 1.446618 GCATTGGCGAGCCTTTTGG 60.447 57.895 15.75 2.10 44.18 3.28
3484 7014 5.972935 TCCTGTCGATTTTCTATGTTAGCA 58.027 37.500 0.00 0.00 0.00 3.49
3539 7069 3.282021 TGAACTTCTTGCAGTGCTTCTT 58.718 40.909 17.60 0.00 0.00 2.52
3628 7167 5.923733 ACCACAATGAACAAACAGGTAAA 57.076 34.783 0.00 0.00 0.00 2.01
3694 7233 5.105797 CCTCATTACAATGCCAAGTTTGCTA 60.106 40.000 0.16 0.00 36.36 3.49
3827 7366 4.142138 GGACAAGATCGAGACCACTACATT 60.142 45.833 0.00 0.00 0.00 2.71
3905 7444 7.275999 GGAAGTATAAGACAAGCTGAACTACAC 59.724 40.741 0.00 0.00 0.00 2.90
3911 7450 5.394224 CGGAGGAAGTATAAGACAAGCTGAA 60.394 44.000 0.00 0.00 0.00 3.02
3972 7511 9.826574 TGTCTCAAACTTAGTACAACTTTGTAT 57.173 29.630 5.16 0.00 44.59 2.29
3989 7528 3.618690 ATGAGCCCTAGTGTCTCAAAC 57.381 47.619 9.06 0.00 39.88 2.93
4010 7549 2.990740 TTCCTACCCAGCAACCAAAT 57.009 45.000 0.00 0.00 0.00 2.32
4011 7550 2.757894 TTTCCTACCCAGCAACCAAA 57.242 45.000 0.00 0.00 0.00 3.28
4038 7578 2.136026 CCTCCCTAGGGGTTTATTGCT 58.864 52.381 28.19 0.00 44.74 3.91
4120 7661 2.590704 CCCCCTGTTACCATTTGGC 58.409 57.895 0.00 0.00 39.32 4.52
4173 7714 9.486497 CTATGATCTGCTGTGTTATATTTGTCT 57.514 33.333 0.00 0.00 0.00 3.41
4474 8025 3.553828 TCGAAAGTGTCCCTGACTTTT 57.446 42.857 0.00 0.00 42.42 2.27


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

AutoCloner maintained by Alex Coulton.