Multiple sequence alignment - TraesCS7B01G054100

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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 TraesCS7B01G054100 chr7B 100.000 3290 0 0 1 3290 57270345 57267056 0.000000e+00 6076.0
1 TraesCS7B01G054100 chr7B 82.862 1307 193 23 999 2290 56390348 56389058 0.000000e+00 1144.0
2 TraesCS7B01G054100 chr7B 82.529 1305 203 16 1000 2290 57065930 57067223 0.000000e+00 1123.0
3 TraesCS7B01G054100 chr7B 94.569 534 24 4 2759 3290 207904684 207904154 0.000000e+00 821.0
4 TraesCS7B01G054100 chr7B 88.168 524 57 5 2769 3290 291940128 291939608 1.300000e-173 619.0
5 TraesCS7B01G054100 chr7B 96.000 150 6 0 500 649 629872938 629873087 9.120000e-61 244.0
6 TraesCS7B01G054100 chr7B 80.000 265 20 15 507 742 493863035 493862775 7.300000e-37 165.0
7 TraesCS7B01G054100 chr7D 93.515 1943 67 25 741 2653 100988016 100986103 0.000000e+00 2835.0
8 TraesCS7B01G054100 chr7D 83.602 1305 191 12 999 2290 100307729 100306435 0.000000e+00 1203.0
9 TraesCS7B01G054100 chr7D 82.659 1309 199 18 999 2290 100939542 100940839 0.000000e+00 1134.0
10 TraesCS7B01G054100 chr7D 93.690 523 29 3 2769 3290 46831551 46832070 0.000000e+00 780.0
11 TraesCS7B01G054100 chr7D 88.209 441 28 8 74 495 100988473 100988038 3.790000e-139 505.0
12 TraesCS7B01G054100 chr7D 84.615 91 12 1 1 89 100989163 100989073 4.520000e-14 89.8
13 TraesCS7B01G054100 chr7A 89.728 1947 129 48 741 2638 103116119 103114195 0.000000e+00 2422.0
14 TraesCS7B01G054100 chr7A 84.028 1296 183 12 1010 2290 103071494 103072780 0.000000e+00 1225.0
15 TraesCS7B01G054100 chr7A 92.982 171 7 3 326 495 103116307 103116141 9.120000e-61 244.0
16 TraesCS7B01G054100 chr7A 84.444 135 9 5 2634 2767 103114166 103114043 4.460000e-24 122.0
17 TraesCS7B01G054100 chr7A 90.411 73 6 1 268 339 103116547 103116475 9.720000e-16 95.3
18 TraesCS7B01G054100 chr3B 91.494 1446 114 5 847 2283 560557844 560556399 0.000000e+00 1980.0
19 TraesCS7B01G054100 chr3B 89.382 518 49 6 2775 3290 753914524 753915037 0.000000e+00 647.0
20 TraesCS7B01G054100 chr3B 79.087 263 24 13 507 741 377405361 377405102 5.690000e-33 152.0
21 TraesCS7B01G054100 chr3B 90.110 91 6 2 651 741 703118511 703118424 7.460000e-22 115.0
22 TraesCS7B01G054100 chr3B 93.023 43 3 0 466 508 560558032 560557990 2.740000e-06 63.9
23 TraesCS7B01G054100 chr3D 92.115 1395 102 4 897 2283 428534023 428532629 0.000000e+00 1960.0
24 TraesCS7B01G054100 chr1A 95.985 523 18 2 2769 3290 515952323 515952843 0.000000e+00 846.0
25 TraesCS7B01G054100 chr6B 95.220 523 22 2 2769 3290 51553673 51553153 0.000000e+00 824.0
26 TraesCS7B01G054100 chr6B 90.594 202 18 1 3089 3290 639981749 639981549 1.950000e-67 267.0
27 TraesCS7B01G054100 chr6B 97.902 143 3 0 507 649 76339096 76338954 7.050000e-62 248.0
28 TraesCS7B01G054100 chr6B 97.143 140 4 0 510 649 184891864 184891725 1.530000e-58 237.0
29 TraesCS7B01G054100 chr5B 94.837 523 22 5 2769 3290 643442506 643441988 0.000000e+00 811.0
30 TraesCS7B01G054100 chr5B 97.917 144 3 0 507 650 487639385 487639242 1.960000e-62 250.0
31 TraesCS7B01G054100 chr5B 85.606 264 7 18 504 739 527932103 527932363 7.050000e-62 248.0
32 TraesCS7B01G054100 chr1D 94.264 523 26 3 2769 3290 464276571 464276052 0.000000e+00 797.0
33 TraesCS7B01G054100 chr5D 92.585 499 34 3 2793 3290 304348516 304349012 0.000000e+00 713.0
34 TraesCS7B01G054100 chr4D 91.784 499 38 3 2793 3290 504083083 504083579 0.000000e+00 691.0
35 TraesCS7B01G054100 chr4D 88.304 171 19 1 3120 3290 352540132 352540301 1.550000e-48 204.0
36 TraesCS7B01G054100 chr4D 96.970 33 1 0 1198 1230 442644998 442645030 4.590000e-04 56.5
37 TraesCS7B01G054100 chr5A 95.522 201 8 1 3091 3290 389155806 389155606 1.470000e-83 320.0
38 TraesCS7B01G054100 chr4B 97.902 143 3 0 507 649 453049514 453049372 7.050000e-62 248.0
39 TraesCS7B01G054100 chr1B 97.902 143 3 0 507 649 37568562 37568420 7.050000e-62 248.0
40 TraesCS7B01G054100 chr1B 97.902 143 3 0 507 649 280168263 280168121 7.050000e-62 248.0
41 TraesCS7B01G054100 chr1B 97.902 143 3 0 507 649 660398569 660398711 7.050000e-62 248.0
42 TraesCS7B01G054100 chr1B 90.110 91 6 2 651 741 37568390 37568303 7.460000e-22 115.0
43 TraesCS7B01G054100 chr1B 100.000 28 0 0 2789 2816 152521417 152521390 6.000000e-03 52.8
44 TraesCS7B01G054100 chr2B 97.203 143 4 0 507 649 198448735 198448877 3.280000e-60 243.0
45 TraesCS7B01G054100 chr2B 81.716 268 16 11 502 741 86541392 86541130 3.350000e-45 193.0
46 TraesCS7B01G054100 chr2A 84.746 236 29 5 503 738 237315644 237315872 2.550000e-56 230.0
47 TraesCS7B01G054100 chr4A 82.400 250 12 15 522 742 651161470 651161224 4.330000e-44 189.0
48 TraesCS7B01G054100 chr4A 96.970 33 1 0 1198 1230 24854866 24854834 4.590000e-04 56.5
49 TraesCS7B01G054100 chrUn 96.970 33 1 0 1198 1230 339715609 339715641 4.590000e-04 56.5
50 TraesCS7B01G054100 chrUn 96.970 33 1 0 1198 1230 397315583 397315615 4.590000e-04 56.5


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 TraesCS7B01G054100 chr7B 57267056 57270345 3289 True 6076.000000 6076 100.000000 1 3290 1 chr7B.!!$R2 3289
1 TraesCS7B01G054100 chr7B 56389058 56390348 1290 True 1144.000000 1144 82.862000 999 2290 1 chr7B.!!$R1 1291
2 TraesCS7B01G054100 chr7B 57065930 57067223 1293 False 1123.000000 1123 82.529000 1000 2290 1 chr7B.!!$F1 1290
3 TraesCS7B01G054100 chr7B 207904154 207904684 530 True 821.000000 821 94.569000 2759 3290 1 chr7B.!!$R3 531
4 TraesCS7B01G054100 chr7B 291939608 291940128 520 True 619.000000 619 88.168000 2769 3290 1 chr7B.!!$R4 521
5 TraesCS7B01G054100 chr7D 100306435 100307729 1294 True 1203.000000 1203 83.602000 999 2290 1 chr7D.!!$R1 1291
6 TraesCS7B01G054100 chr7D 100986103 100989163 3060 True 1143.266667 2835 88.779667 1 2653 3 chr7D.!!$R2 2652
7 TraesCS7B01G054100 chr7D 100939542 100940839 1297 False 1134.000000 1134 82.659000 999 2290 1 chr7D.!!$F2 1291
8 TraesCS7B01G054100 chr7D 46831551 46832070 519 False 780.000000 780 93.690000 2769 3290 1 chr7D.!!$F1 521
9 TraesCS7B01G054100 chr7A 103071494 103072780 1286 False 1225.000000 1225 84.028000 1010 2290 1 chr7A.!!$F1 1280
10 TraesCS7B01G054100 chr7A 103114043 103116547 2504 True 720.825000 2422 89.391250 268 2767 4 chr7A.!!$R1 2499
11 TraesCS7B01G054100 chr3B 560556399 560558032 1633 True 1021.950000 1980 92.258500 466 2283 2 chr3B.!!$R3 1817
12 TraesCS7B01G054100 chr3B 753914524 753915037 513 False 647.000000 647 89.382000 2775 3290 1 chr3B.!!$F1 515
13 TraesCS7B01G054100 chr3D 428532629 428534023 1394 True 1960.000000 1960 92.115000 897 2283 1 chr3D.!!$R1 1386
14 TraesCS7B01G054100 chr1A 515952323 515952843 520 False 846.000000 846 95.985000 2769 3290 1 chr1A.!!$F1 521
15 TraesCS7B01G054100 chr6B 51553153 51553673 520 True 824.000000 824 95.220000 2769 3290 1 chr6B.!!$R1 521
16 TraesCS7B01G054100 chr5B 643441988 643442506 518 True 811.000000 811 94.837000 2769 3290 1 chr5B.!!$R2 521
17 TraesCS7B01G054100 chr1D 464276052 464276571 519 True 797.000000 797 94.264000 2769 3290 1 chr1D.!!$R1 521

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
510 1327 0.03438 TACCGCTGTAGACTGAGGCT 60.034 55.0 8.83 0.0 38.07 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 3254 0.250295 GGCAGCAGTGTGTGTAGGAA 60.25 55.0 0.0 0.0 0.0 3.36 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
17 18 2.203070 GCGAATCCACGGGCTCAT 60.203 61.111 0.00 0.00 0.00 2.90
20 21 1.595382 GAATCCACGGGCTCATCGG 60.595 63.158 0.00 0.00 0.00 4.18
50 51 3.648739 AGAGGGGAGAGTTTGTCCTATC 58.351 50.000 0.00 0.00 34.16 2.08
52 53 1.413077 GGGGAGAGTTTGTCCTATCCG 59.587 57.143 0.00 0.00 42.58 4.18
57 58 2.959707 AGAGTTTGTCCTATCCGCCTAG 59.040 50.000 0.00 0.00 0.00 3.02
63 64 2.169330 GTCCTATCCGCCTAGGGTTAG 58.831 57.143 11.72 3.81 39.08 2.34
64 65 2.068181 TCCTATCCGCCTAGGGTTAGA 58.932 52.381 11.72 0.00 39.08 2.10
69 70 1.465200 CCGCCTAGGGTTAGAGGAGC 61.465 65.000 11.72 0.00 34.46 4.70
105 723 1.070038 TTTTCACGGACGGCGTTATC 58.930 50.000 16.19 6.45 0.00 1.75
114 732 4.232221 CGGACGGCGTTATCTTGTATAAT 58.768 43.478 16.19 0.00 0.00 1.28
121 739 5.220228 GGCGTTATCTTGTATAATGCGCTAG 60.220 44.000 9.73 0.00 43.67 3.42
122 740 5.571741 GCGTTATCTTGTATAATGCGCTAGA 59.428 40.000 9.73 0.00 36.95 2.43
151 784 1.078143 AGAATCGTTCTGGGCAGCC 60.078 57.895 1.26 1.26 38.91 4.85
163 796 2.031163 GCAGCCACCGAACTGAGT 59.969 61.111 0.00 0.00 35.90 3.41
180 813 6.551385 ACTGAGTGAATCTTGACACAAATC 57.449 37.500 0.00 0.00 39.18 2.17
262 898 7.664552 AAAGGAATATTTGCATGAATCTCCA 57.335 32.000 0.00 0.00 0.00 3.86
265 901 2.857592 ATTTGCATGAATCTCCACGC 57.142 45.000 0.00 0.00 0.00 5.34
316 954 3.062639 CCTCGTCCAATGAAATTCAGTCG 59.937 47.826 1.10 0.00 31.22 4.18
335 973 3.427863 GTCGTCTTCCGTAAACTTTCCTG 59.572 47.826 0.00 0.00 37.94 3.86
364 1181 2.362717 GGAAGAGAACGACCCCTGATAG 59.637 54.545 0.00 0.00 0.00 2.08
400 1217 4.502087 CCACGAGCTCTGAATTCCATATGA 60.502 45.833 12.85 0.00 0.00 2.15
439 1256 1.078848 GCACTGGCGGAGAAGTCAT 60.079 57.895 0.00 0.00 0.00 3.06
460 1277 4.642445 TGAGAAAACGTGTGTACTCTCA 57.358 40.909 4.10 4.10 40.72 3.27
495 1312 6.252015 TCGTCGTCTTCATTCTTAATTTACCG 59.748 38.462 0.00 0.00 0.00 4.02
499 1316 6.183360 CGTCTTCATTCTTAATTTACCGCTGT 60.183 38.462 0.00 0.00 0.00 4.40
507 1324 6.561614 TCTTAATTTACCGCTGTAGACTGAG 58.438 40.000 0.00 0.00 0.00 3.35
509 1326 0.815734 TTACCGCTGTAGACTGAGGC 59.184 55.000 8.83 0.00 38.07 4.70
510 1327 0.034380 TACCGCTGTAGACTGAGGCT 60.034 55.000 8.83 0.00 38.07 4.58
511 1328 1.140589 CCGCTGTAGACTGAGGCTG 59.859 63.158 0.00 0.00 0.00 4.85
512 1329 1.315981 CCGCTGTAGACTGAGGCTGA 61.316 60.000 0.00 0.00 0.00 4.26
513 1330 0.743688 CGCTGTAGACTGAGGCTGAT 59.256 55.000 0.00 0.00 0.00 2.90
514 1331 1.135915 CGCTGTAGACTGAGGCTGATT 59.864 52.381 0.00 0.00 0.00 2.57
515 1332 2.548875 GCTGTAGACTGAGGCTGATTG 58.451 52.381 0.00 0.00 0.00 2.67
516 1333 2.093764 GCTGTAGACTGAGGCTGATTGT 60.094 50.000 0.00 0.00 0.00 2.71
518 1335 4.382040 GCTGTAGACTGAGGCTGATTGTAA 60.382 45.833 0.00 0.00 0.00 2.41
519 1336 5.683509 GCTGTAGACTGAGGCTGATTGTAAT 60.684 44.000 0.00 0.00 0.00 1.89
520 1337 5.664457 TGTAGACTGAGGCTGATTGTAATG 58.336 41.667 0.00 0.00 0.00 1.90
521 1338 4.148128 AGACTGAGGCTGATTGTAATGG 57.852 45.455 0.00 0.00 0.00 3.16
522 1339 3.118112 AGACTGAGGCTGATTGTAATGGG 60.118 47.826 0.00 0.00 0.00 4.00
523 1340 2.846206 ACTGAGGCTGATTGTAATGGGA 59.154 45.455 0.00 0.00 0.00 4.37
524 1341 3.118112 ACTGAGGCTGATTGTAATGGGAG 60.118 47.826 0.00 0.00 0.00 4.30
525 1342 2.846206 TGAGGCTGATTGTAATGGGAGT 59.154 45.455 0.00 0.00 0.00 3.85
526 1343 4.037222 TGAGGCTGATTGTAATGGGAGTA 58.963 43.478 0.00 0.00 0.00 2.59
527 1344 4.660303 TGAGGCTGATTGTAATGGGAGTAT 59.340 41.667 0.00 0.00 0.00 2.12
528 1345 5.221722 TGAGGCTGATTGTAATGGGAGTATC 60.222 44.000 0.00 0.00 0.00 2.24
529 1346 4.660303 AGGCTGATTGTAATGGGAGTATCA 59.340 41.667 0.00 0.00 36.25 2.15
530 1347 5.311649 AGGCTGATTGTAATGGGAGTATCAT 59.688 40.000 0.00 0.00 36.25 2.45
531 1348 6.501805 AGGCTGATTGTAATGGGAGTATCATA 59.498 38.462 0.00 0.00 36.25 2.15
532 1349 6.820656 GGCTGATTGTAATGGGAGTATCATAG 59.179 42.308 0.00 0.00 36.25 2.23
533 1350 6.314896 GCTGATTGTAATGGGAGTATCATAGC 59.685 42.308 0.00 0.00 36.25 2.97
534 1351 7.559335 TGATTGTAATGGGAGTATCATAGCT 57.441 36.000 0.00 0.00 36.25 3.32
535 1352 8.664669 TGATTGTAATGGGAGTATCATAGCTA 57.335 34.615 0.00 0.00 36.25 3.32
536 1353 8.753133 TGATTGTAATGGGAGTATCATAGCTAG 58.247 37.037 0.00 0.00 36.25 3.42
537 1354 8.671987 ATTGTAATGGGAGTATCATAGCTAGT 57.328 34.615 0.00 0.00 36.25 2.57
538 1355 9.769677 ATTGTAATGGGAGTATCATAGCTAGTA 57.230 33.333 0.00 0.00 36.25 1.82
539 1356 9.769677 TTGTAATGGGAGTATCATAGCTAGTAT 57.230 33.333 0.00 0.00 36.25 2.12
540 1357 9.409918 TGTAATGGGAGTATCATAGCTAGTATC 57.590 37.037 0.00 0.00 36.25 2.24
541 1358 9.409918 GTAATGGGAGTATCATAGCTAGTATCA 57.590 37.037 0.00 0.00 36.25 2.15
543 1360 7.888250 TGGGAGTATCATAGCTAGTATCATG 57.112 40.000 0.00 0.00 36.25 3.07
544 1361 6.322456 TGGGAGTATCATAGCTAGTATCATGC 59.678 42.308 0.00 0.00 36.25 4.06
545 1362 6.322456 GGGAGTATCATAGCTAGTATCATGCA 59.678 42.308 0.00 0.00 36.25 3.96
546 1363 7.015098 GGGAGTATCATAGCTAGTATCATGCAT 59.985 40.741 0.00 0.00 36.25 3.96
547 1364 7.866898 GGAGTATCATAGCTAGTATCATGCATG 59.133 40.741 21.07 21.07 36.25 4.06
548 1365 7.208777 AGTATCATAGCTAGTATCATGCATGC 58.791 38.462 22.25 11.82 0.00 4.06
549 1366 4.763073 TCATAGCTAGTATCATGCATGCC 58.237 43.478 22.25 11.72 0.00 4.40
550 1367 4.223477 TCATAGCTAGTATCATGCATGCCA 59.777 41.667 22.25 8.84 0.00 4.92
551 1368 3.497103 AGCTAGTATCATGCATGCCAA 57.503 42.857 22.25 5.34 0.00 4.52
552 1369 3.144506 AGCTAGTATCATGCATGCCAAC 58.855 45.455 22.25 17.59 0.00 3.77
553 1370 3.144506 GCTAGTATCATGCATGCCAACT 58.855 45.455 22.25 22.78 0.00 3.16
554 1371 4.040829 AGCTAGTATCATGCATGCCAACTA 59.959 41.667 22.25 22.70 0.00 2.24
555 1372 4.391216 GCTAGTATCATGCATGCCAACTAG 59.609 45.833 32.38 32.38 37.27 2.57
556 1373 3.748083 AGTATCATGCATGCCAACTAGG 58.252 45.455 22.25 0.00 41.84 3.02
576 1393 3.874392 GCAACTTTGATAAGGTGGCAT 57.126 42.857 5.22 0.00 46.95 4.40
577 1394 4.981806 GCAACTTTGATAAGGTGGCATA 57.018 40.909 5.22 0.00 46.95 3.14
578 1395 4.925068 GCAACTTTGATAAGGTGGCATAG 58.075 43.478 5.22 0.00 46.95 2.23
579 1396 4.640201 GCAACTTTGATAAGGTGGCATAGA 59.360 41.667 5.22 0.00 46.95 1.98
580 1397 5.125417 GCAACTTTGATAAGGTGGCATAGAA 59.875 40.000 5.22 0.00 46.95 2.10
581 1398 6.183360 GCAACTTTGATAAGGTGGCATAGAAT 60.183 38.462 5.22 0.00 46.95 2.40
582 1399 7.631377 GCAACTTTGATAAGGTGGCATAGAATT 60.631 37.037 5.22 0.00 46.95 2.17
583 1400 8.902806 CAACTTTGATAAGGTGGCATAGAATTA 58.097 33.333 0.00 0.00 43.89 1.40
584 1401 9.474313 AACTTTGATAAGGTGGCATAGAATTAA 57.526 29.630 0.00 0.00 35.61 1.40
585 1402 9.474313 ACTTTGATAAGGTGGCATAGAATTAAA 57.526 29.630 0.00 0.00 35.61 1.52
588 1405 9.639563 TTGATAAGGTGGCATAGAATTAAATGA 57.360 29.630 0.00 0.00 0.00 2.57
589 1406 9.639563 TGATAAGGTGGCATAGAATTAAATGAA 57.360 29.630 0.00 0.00 0.00 2.57
591 1408 7.961326 AAGGTGGCATAGAATTAAATGAAGT 57.039 32.000 0.00 0.00 0.00 3.01
593 1410 9.474313 AAGGTGGCATAGAATTAAATGAAGTAA 57.526 29.630 0.00 0.00 0.00 2.24
594 1411 9.125026 AGGTGGCATAGAATTAAATGAAGTAAG 57.875 33.333 0.00 0.00 0.00 2.34
595 1412 9.120538 GGTGGCATAGAATTAAATGAAGTAAGA 57.879 33.333 0.00 0.00 0.00 2.10
646 1463 9.856488 ACCGTATCATAATAAATGCTACACTAG 57.144 33.333 0.00 0.00 0.00 2.57
647 1464 9.856488 CCGTATCATAATAAATGCTACACTAGT 57.144 33.333 0.00 0.00 0.00 2.57
662 1479 9.926158 TGCTACACTAGTACTCTATGATACTAC 57.074 37.037 0.00 0.00 33.65 2.73
663 1480 9.369904 GCTACACTAGTACTCTATGATACTACC 57.630 40.741 0.00 0.00 33.65 3.18
718 1535 8.422577 TCATACACTAGTATCATATGCAAGGT 57.577 34.615 0.00 0.00 38.88 3.50
719 1536 9.528489 TCATACACTAGTATCATATGCAAGGTA 57.472 33.333 0.00 0.00 38.88 3.08
720 1537 9.794685 CATACACTAGTATCATATGCAAGGTAG 57.205 37.037 0.00 0.00 38.88 3.18
721 1538 7.841282 ACACTAGTATCATATGCAAGGTAGT 57.159 36.000 0.00 0.00 0.00 2.73
722 1539 8.935614 ACACTAGTATCATATGCAAGGTAGTA 57.064 34.615 0.00 0.00 0.00 1.82
723 1540 8.794553 ACACTAGTATCATATGCAAGGTAGTAC 58.205 37.037 0.00 0.00 0.00 2.73
724 1541 9.015367 CACTAGTATCATATGCAAGGTAGTACT 57.985 37.037 0.00 0.00 0.00 2.73
728 1545 9.589461 AGTATCATATGCAAGGTAGTACTAACT 57.411 33.333 14.98 14.98 39.91 2.24
737 1554 9.417561 TGCAAGGTAGTACTAACTTATGATACT 57.582 33.333 28.45 5.84 40.84 2.12
744 1561 7.869800 AGTACTAACTTATGATACTACCACGC 58.130 38.462 0.00 0.00 29.00 5.34
745 1562 6.081872 ACTAACTTATGATACTACCACGCC 57.918 41.667 0.00 0.00 0.00 5.68
746 1563 5.832060 ACTAACTTATGATACTACCACGCCT 59.168 40.000 0.00 0.00 0.00 5.52
747 1564 7.000472 ACTAACTTATGATACTACCACGCCTA 59.000 38.462 0.00 0.00 0.00 3.93
864 1752 2.596046 AAATGCCACCAACCGCGA 60.596 55.556 8.23 0.00 0.00 5.87
907 1807 4.950475 GCCTTCCTGCTTCTATTTAAACCT 59.050 41.667 0.00 0.00 0.00 3.50
1176 2098 4.241555 GCCGACGCCATGAGGGAT 62.242 66.667 0.00 0.00 40.01 3.85
1351 2273 3.743636 TGCCGTGCGACGAGATGA 61.744 61.111 0.00 0.00 46.05 2.92
1626 2554 1.114722 ACGACCACCCGGAGTACAAA 61.115 55.000 0.73 0.00 35.59 2.83
1929 2860 1.831652 CTGTGGAGGAGGTGGTGTCC 61.832 65.000 0.00 0.00 0.00 4.02
2318 3254 4.212636 GCATGCCGTAAATTAAGGACGTAT 59.787 41.667 6.36 0.00 34.81 3.06
2352 3306 1.516161 CTGCCATGCATGCGTATACT 58.484 50.000 21.69 0.00 38.13 2.12
2370 3324 2.426522 ACTCTGCATGCATGTACGTTT 58.573 42.857 26.79 5.86 0.00 3.60
2409 3363 7.959718 TTGCTCTTCGTTAATTACTACTACG 57.040 36.000 1.12 1.12 0.00 3.51
2437 3394 6.641176 TGTGTATGTGAATATGAACGTGTC 57.359 37.500 0.00 0.00 0.00 3.67
2441 3398 2.921121 TGTGAATATGAACGTGTCGAGC 59.079 45.455 0.00 0.00 0.00 5.03
2443 3400 0.921347 AATATGAACGTGTCGAGCGC 59.079 50.000 0.00 0.00 0.00 5.92
2447 3404 4.280494 AACGTGTCGAGCGCTGGT 62.280 61.111 18.48 0.00 0.00 4.00
2448 3405 4.702081 ACGTGTCGAGCGCTGGTC 62.702 66.667 18.48 13.02 0.00 4.02
2457 3414 4.396854 GCGCTGGTCGGTAAGTAG 57.603 61.111 0.00 0.00 38.94 2.57
2458 3415 1.877165 GCGCTGGTCGGTAAGTAGC 60.877 63.158 0.00 0.00 38.94 3.58
2463 3425 0.177141 TGGTCGGTAAGTAGCCATGC 59.823 55.000 0.00 0.00 0.00 4.06
2468 3430 2.963101 TCGGTAAGTAGCCATGCATAGT 59.037 45.455 0.00 0.00 0.00 2.12
2469 3431 3.386726 TCGGTAAGTAGCCATGCATAGTT 59.613 43.478 0.00 0.00 0.00 2.24
2471 3433 4.451900 GGTAAGTAGCCATGCATAGTTGT 58.548 43.478 0.00 0.00 0.00 3.32
2489 3451 8.706936 CATAGTTGTATGCTGCTATCTTACAAG 58.293 37.037 0.00 0.00 35.87 3.16
2490 3452 5.525378 AGTTGTATGCTGCTATCTTACAAGC 59.475 40.000 0.00 0.00 35.87 4.01
2492 3454 6.405278 TGTATGCTGCTATCTTACAAGCTA 57.595 37.500 0.00 0.00 39.53 3.32
2493 3455 6.450545 TGTATGCTGCTATCTTACAAGCTAG 58.549 40.000 0.00 0.00 39.53 3.42
2494 3456 5.543507 ATGCTGCTATCTTACAAGCTAGT 57.456 39.130 0.00 0.00 39.53 2.57
2495 3457 6.656632 ATGCTGCTATCTTACAAGCTAGTA 57.343 37.500 0.00 0.00 39.53 1.82
2496 3458 5.833082 TGCTGCTATCTTACAAGCTAGTAC 58.167 41.667 0.00 0.00 39.53 2.73
2497 3459 5.359860 TGCTGCTATCTTACAAGCTAGTACA 59.640 40.000 0.00 0.00 39.53 2.90
2513 3481 8.447924 AGCTAGTACATGTAATAAGACTCGAA 57.552 34.615 13.54 0.00 0.00 3.71
2544 3516 2.236146 ACTTGGGCATGTGTAATCTCGA 59.764 45.455 0.00 0.00 0.00 4.04
2547 3519 2.224281 TGGGCATGTGTAATCTCGATCC 60.224 50.000 0.00 0.00 0.00 3.36
2579 3552 4.740235 GCTAGCTAAGCCGAGTGG 57.260 61.111 7.70 0.00 46.25 4.00
2648 3621 2.097791 ACGTCGCTCTACTTTGAGATCC 59.902 50.000 0.00 0.00 36.23 3.36
2651 3624 2.690497 TCGCTCTACTTTGAGATCCTGG 59.310 50.000 0.00 0.00 36.23 4.45
2653 3626 3.131223 CGCTCTACTTTGAGATCCTGGAA 59.869 47.826 0.00 0.00 36.23 3.53
2654 3627 4.382040 CGCTCTACTTTGAGATCCTGGAAA 60.382 45.833 0.00 0.00 36.23 3.13
2655 3628 5.679601 GCTCTACTTTGAGATCCTGGAAAT 58.320 41.667 0.00 0.00 36.23 2.17
2656 3629 6.118852 GCTCTACTTTGAGATCCTGGAAATT 58.881 40.000 0.00 0.00 36.23 1.82
2657 3630 6.038050 GCTCTACTTTGAGATCCTGGAAATTG 59.962 42.308 0.00 0.00 36.23 2.32
2658 3631 7.020827 TCTACTTTGAGATCCTGGAAATTGT 57.979 36.000 0.00 0.00 0.00 2.71
2703 3707 1.351017 ACCATGTGAATTCGGACACCT 59.649 47.619 0.04 0.00 36.35 4.00
2705 3709 2.819608 CCATGTGAATTCGGACACCTTT 59.180 45.455 0.04 0.00 36.35 3.11
2707 3711 1.606668 TGTGAATTCGGACACCTTTGC 59.393 47.619 0.04 0.00 36.35 3.68
2708 3712 1.880027 GTGAATTCGGACACCTTTGCT 59.120 47.619 0.04 0.00 0.00 3.91
2709 3713 1.879380 TGAATTCGGACACCTTTGCTG 59.121 47.619 0.04 0.00 0.00 4.41
2710 3714 1.200020 GAATTCGGACACCTTTGCTGG 59.800 52.381 0.00 0.00 0.00 4.85
2711 3715 0.110486 ATTCGGACACCTTTGCTGGT 59.890 50.000 0.00 0.00 41.77 4.00
2717 3721 4.625350 ACCTTTGCTGGTGCCATT 57.375 50.000 0.00 0.00 39.17 3.16
2718 3722 3.763931 ACCTTTGCTGGTGCCATTA 57.236 47.368 0.00 0.00 39.17 1.90
2719 3723 2.236489 ACCTTTGCTGGTGCCATTAT 57.764 45.000 0.00 0.00 39.17 1.28
2720 3724 3.380471 ACCTTTGCTGGTGCCATTATA 57.620 42.857 0.00 0.00 39.17 0.98
2721 3725 3.914771 ACCTTTGCTGGTGCCATTATAT 58.085 40.909 0.00 0.00 39.17 0.86
2730 3734 4.133820 TGGTGCCATTATATTTCTCGTGG 58.866 43.478 0.00 0.00 0.00 4.94
2739 3743 8.660373 CCATTATATTTCTCGTGGCTTAAGATC 58.340 37.037 6.67 0.00 0.00 2.75
2747 3751 2.271800 GTGGCTTAAGATCTGGACGTG 58.728 52.381 6.67 0.00 0.00 4.49
2751 3756 2.798680 CTTAAGATCTGGACGTGGTCG 58.201 52.381 0.00 0.00 43.34 4.79
2892 3899 2.099405 CACCCCAATCGTTGCCTTATT 58.901 47.619 0.00 0.00 0.00 1.40
2913 3921 9.447157 CTTATTTTCTCCTTCATCTTCTCAACT 57.553 33.333 0.00 0.00 0.00 3.16
2936 3944 4.748102 TGCTCGTTCGTTTCTTATCTGTTT 59.252 37.500 0.00 0.00 0.00 2.83
3127 4135 1.809619 GGCTGCTTGCGTCGTCATA 60.810 57.895 0.00 0.00 44.05 2.15
3275 4283 4.697756 CGCCGGAGCTGGAACCAA 62.698 66.667 5.05 0.00 36.60 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.455959 TCTCCCCTCTAGGCTTCGC 60.456 63.158 0.00 0.00 0.00 4.70
50 51 1.465200 GCTCCTCTAACCCTAGGCGG 61.465 65.000 2.05 0.00 32.55 6.13
52 53 1.465200 CGGCTCCTCTAACCCTAGGC 61.465 65.000 2.05 0.00 32.55 3.93
57 58 1.732308 CGTACGGCTCCTCTAACCC 59.268 63.158 7.57 0.00 0.00 4.11
63 64 1.206523 GTTATTGCGTACGGCTCCTC 58.793 55.000 18.39 0.00 44.05 3.71
64 65 0.533491 TGTTATTGCGTACGGCTCCT 59.467 50.000 18.39 1.82 44.05 3.69
69 70 5.613983 CGTGAAAATATGTTATTGCGTACGG 59.386 40.000 18.39 0.00 0.00 4.02
105 723 5.802451 ACGATGATCTAGCGCATTATACAAG 59.198 40.000 11.47 4.34 43.14 3.16
114 732 2.099098 TCTGAAACGATGATCTAGCGCA 59.901 45.455 11.47 0.00 43.14 6.09
121 739 5.957910 AGAACGATTCTGAAACGATGATC 57.042 39.130 23.80 15.53 38.91 2.92
151 784 3.430218 GTCAAGATTCACTCAGTTCGGTG 59.570 47.826 0.00 0.00 35.06 4.94
163 796 7.815840 TGGTTAAGATTTGTGTCAAGATTCA 57.184 32.000 0.00 0.00 0.00 2.57
180 813 4.690748 TCGCTTGATTGAGACTTGGTTAAG 59.309 41.667 0.00 0.00 39.86 1.85
242 878 4.913924 GCGTGGAGATTCATGCAAATATTC 59.086 41.667 0.23 0.00 45.94 1.75
245 881 2.287644 CGCGTGGAGATTCATGCAAATA 59.712 45.455 6.16 0.00 46.74 1.40
253 889 1.014044 GTTGCTCGCGTGGAGATTCA 61.014 55.000 5.77 0.00 46.23 2.57
262 898 3.636043 CAACGGTGTTGCTCGCGT 61.636 61.111 5.77 0.00 0.00 6.01
265 901 2.052237 GCACAACGGTGTTGCTCG 60.052 61.111 1.53 0.00 46.95 5.03
316 954 8.538409 TTATTACAGGAAAGTTTACGGAAGAC 57.462 34.615 4.86 0.00 0.00 3.01
335 973 5.105023 AGGGGTCGTTCTCTTCCTTTATTAC 60.105 44.000 0.00 0.00 0.00 1.89
364 1181 1.318576 CTCGTGGAATTAATGGGGGC 58.681 55.000 0.00 0.00 0.00 5.80
400 1217 3.360533 CGCACTTTCTACATCGTCGTAT 58.639 45.455 0.00 0.00 0.00 3.06
439 1256 4.642445 TGAGAGTACACACGTTTTCTCA 57.358 40.909 0.00 0.00 39.29 3.27
460 1277 1.001597 GAAGACGACGACTGGACACTT 60.002 52.381 0.00 0.00 0.00 3.16
495 1312 2.093764 ACAATCAGCCTCAGTCTACAGC 60.094 50.000 0.00 0.00 0.00 4.40
499 1316 4.101585 CCCATTACAATCAGCCTCAGTCTA 59.898 45.833 0.00 0.00 0.00 2.59
507 1324 4.973168 TGATACTCCCATTACAATCAGCC 58.027 43.478 0.00 0.00 0.00 4.85
509 1326 7.619050 AGCTATGATACTCCCATTACAATCAG 58.381 38.462 0.00 0.00 0.00 2.90
510 1327 7.559335 AGCTATGATACTCCCATTACAATCA 57.441 36.000 0.00 0.00 0.00 2.57
511 1328 8.754080 ACTAGCTATGATACTCCCATTACAATC 58.246 37.037 0.00 0.00 0.00 2.67
512 1329 8.671987 ACTAGCTATGATACTCCCATTACAAT 57.328 34.615 0.00 0.00 0.00 2.71
513 1330 9.769677 ATACTAGCTATGATACTCCCATTACAA 57.230 33.333 0.00 0.00 0.00 2.41
514 1331 9.409918 GATACTAGCTATGATACTCCCATTACA 57.590 37.037 0.00 0.00 0.00 2.41
515 1332 9.409918 TGATACTAGCTATGATACTCCCATTAC 57.590 37.037 0.00 0.00 0.00 1.89
518 1335 7.015098 GCATGATACTAGCTATGATACTCCCAT 59.985 40.741 0.00 0.00 0.00 4.00
519 1336 6.322456 GCATGATACTAGCTATGATACTCCCA 59.678 42.308 0.00 0.00 0.00 4.37
520 1337 6.322456 TGCATGATACTAGCTATGATACTCCC 59.678 42.308 0.00 0.00 0.00 4.30
521 1338 7.340122 TGCATGATACTAGCTATGATACTCC 57.660 40.000 0.00 0.00 0.00 3.85
522 1339 7.381948 GCATGCATGATACTAGCTATGATACTC 59.618 40.741 30.64 1.38 0.00 2.59
523 1340 7.208777 GCATGCATGATACTAGCTATGATACT 58.791 38.462 30.64 0.00 0.00 2.12
524 1341 6.423302 GGCATGCATGATACTAGCTATGATAC 59.577 42.308 30.64 5.71 0.00 2.24
525 1342 6.098695 TGGCATGCATGATACTAGCTATGATA 59.901 38.462 30.64 0.00 0.00 2.15
526 1343 5.104652 TGGCATGCATGATACTAGCTATGAT 60.105 40.000 30.64 0.00 0.00 2.45
527 1344 4.223477 TGGCATGCATGATACTAGCTATGA 59.777 41.667 30.64 0.00 0.00 2.15
528 1345 4.510571 TGGCATGCATGATACTAGCTATG 58.489 43.478 30.64 0.23 0.00 2.23
529 1346 4.831674 TGGCATGCATGATACTAGCTAT 57.168 40.909 30.64 0.00 0.00 2.97
530 1347 4.040829 AGTTGGCATGCATGATACTAGCTA 59.959 41.667 30.64 7.90 0.00 3.32
531 1348 3.144506 GTTGGCATGCATGATACTAGCT 58.855 45.455 30.64 0.00 0.00 3.32
532 1349 3.144506 AGTTGGCATGCATGATACTAGC 58.855 45.455 30.64 12.56 0.00 3.42
533 1350 4.934001 CCTAGTTGGCATGCATGATACTAG 59.066 45.833 31.40 31.40 36.03 2.57
534 1351 4.898320 CCTAGTTGGCATGCATGATACTA 58.102 43.478 30.64 25.87 0.00 1.82
535 1352 3.748083 CCTAGTTGGCATGCATGATACT 58.252 45.455 30.64 26.11 0.00 2.12
548 1365 5.010282 ACCTTATCAAAGTTGCCTAGTTGG 58.990 41.667 0.00 0.00 39.35 3.77
549 1366 5.106157 CCACCTTATCAAAGTTGCCTAGTTG 60.106 44.000 0.00 0.00 0.00 3.16
550 1367 5.010282 CCACCTTATCAAAGTTGCCTAGTT 58.990 41.667 0.00 0.00 0.00 2.24
551 1368 4.589908 CCACCTTATCAAAGTTGCCTAGT 58.410 43.478 0.00 0.00 0.00 2.57
552 1369 3.378427 GCCACCTTATCAAAGTTGCCTAG 59.622 47.826 0.00 0.00 0.00 3.02
553 1370 3.245087 TGCCACCTTATCAAAGTTGCCTA 60.245 43.478 0.00 0.00 0.00 3.93
554 1371 2.171003 GCCACCTTATCAAAGTTGCCT 58.829 47.619 0.00 0.00 0.00 4.75
555 1372 1.892474 TGCCACCTTATCAAAGTTGCC 59.108 47.619 0.00 0.00 0.00 4.52
556 1373 3.874392 ATGCCACCTTATCAAAGTTGC 57.126 42.857 0.00 0.00 0.00 4.17
557 1374 6.757897 TTCTATGCCACCTTATCAAAGTTG 57.242 37.500 0.00 0.00 0.00 3.16
558 1375 7.961326 AATTCTATGCCACCTTATCAAAGTT 57.039 32.000 0.00 0.00 0.00 2.66
559 1376 9.474313 TTTAATTCTATGCCACCTTATCAAAGT 57.526 29.630 0.00 0.00 0.00 2.66
562 1379 9.639563 TCATTTAATTCTATGCCACCTTATCAA 57.360 29.630 0.00 0.00 0.00 2.57
563 1380 9.639563 TTCATTTAATTCTATGCCACCTTATCA 57.360 29.630 0.00 0.00 0.00 2.15
565 1382 9.646522 ACTTCATTTAATTCTATGCCACCTTAT 57.353 29.630 0.00 0.00 0.00 1.73
567 1384 7.961326 ACTTCATTTAATTCTATGCCACCTT 57.039 32.000 0.00 0.00 0.00 3.50
568 1385 9.125026 CTTACTTCATTTAATTCTATGCCACCT 57.875 33.333 0.00 0.00 0.00 4.00
569 1386 9.120538 TCTTACTTCATTTAATTCTATGCCACC 57.879 33.333 0.00 0.00 0.00 4.61
584 1401 9.206690 TGATACTCAATCCTCTCTTACTTCATT 57.793 33.333 0.00 0.00 33.22 2.57
585 1402 8.774546 TGATACTCAATCCTCTCTTACTTCAT 57.225 34.615 0.00 0.00 33.22 2.57
586 1403 8.774546 ATGATACTCAATCCTCTCTTACTTCA 57.225 34.615 0.00 0.00 33.22 3.02
592 1409 9.544579 TCATGATATGATACTCAATCCTCTCTT 57.455 33.333 0.00 0.00 33.59 2.85
620 1437 9.856488 CTAGTGTAGCATTTATTATGATACGGT 57.144 33.333 8.18 0.00 42.05 4.83
621 1438 9.856488 ACTAGTGTAGCATTTATTATGATACGG 57.144 33.333 0.00 2.94 42.05 4.02
636 1453 9.926158 GTAGTATCATAGAGTACTAGTGTAGCA 57.074 37.037 5.39 0.00 34.91 3.49
637 1454 9.369904 GGTAGTATCATAGAGTACTAGTGTAGC 57.630 40.741 5.39 0.00 34.91 3.58
692 1509 9.040259 ACCTTGCATATGATACTAGTGTATGAT 57.960 33.333 6.97 0.00 39.29 2.45
693 1510 8.422577 ACCTTGCATATGATACTAGTGTATGA 57.577 34.615 6.97 0.00 39.29 2.15
694 1511 9.794685 CTACCTTGCATATGATACTAGTGTATG 57.205 37.037 6.97 9.68 39.29 2.39
695 1512 9.535170 ACTACCTTGCATATGATACTAGTGTAT 57.465 33.333 6.97 0.00 41.65 2.29
696 1513 8.935614 ACTACCTTGCATATGATACTAGTGTA 57.064 34.615 6.97 0.00 0.00 2.90
697 1514 7.841282 ACTACCTTGCATATGATACTAGTGT 57.159 36.000 6.97 0.00 0.00 3.55
698 1515 9.015367 AGTACTACCTTGCATATGATACTAGTG 57.985 37.037 6.97 0.00 0.00 2.74
702 1519 9.589461 AGTTAGTACTACCTTGCATATGATACT 57.411 33.333 6.97 0.00 31.21 2.12
711 1528 9.417561 AGTATCATAAGTTAGTACTACCTTGCA 57.582 33.333 19.75 4.39 33.17 4.08
718 1535 8.993121 GCGTGGTAGTATCATAAGTTAGTACTA 58.007 37.037 0.00 0.00 33.17 1.82
719 1536 7.040823 GGCGTGGTAGTATCATAAGTTAGTACT 60.041 40.741 0.00 0.00 35.68 2.73
720 1537 7.040823 AGGCGTGGTAGTATCATAAGTTAGTAC 60.041 40.741 0.00 0.00 0.00 2.73
721 1538 7.000472 AGGCGTGGTAGTATCATAAGTTAGTA 59.000 38.462 0.00 0.00 0.00 1.82
722 1539 5.832060 AGGCGTGGTAGTATCATAAGTTAGT 59.168 40.000 0.00 0.00 0.00 2.24
723 1540 6.328641 AGGCGTGGTAGTATCATAAGTTAG 57.671 41.667 0.00 0.00 0.00 2.34
724 1541 7.822161 TTAGGCGTGGTAGTATCATAAGTTA 57.178 36.000 0.00 0.00 0.00 2.24
725 1542 6.720112 TTAGGCGTGGTAGTATCATAAGTT 57.280 37.500 0.00 0.00 0.00 2.66
726 1543 6.720112 TTTAGGCGTGGTAGTATCATAAGT 57.280 37.500 0.00 0.00 0.00 2.24
727 1544 7.375834 TGATTTAGGCGTGGTAGTATCATAAG 58.624 38.462 0.00 0.00 0.00 1.73
728 1545 7.292713 TGATTTAGGCGTGGTAGTATCATAA 57.707 36.000 0.00 0.00 0.00 1.90
729 1546 6.904463 TGATTTAGGCGTGGTAGTATCATA 57.096 37.500 0.00 0.00 0.00 2.15
730 1547 5.801531 TGATTTAGGCGTGGTAGTATCAT 57.198 39.130 0.00 0.00 0.00 2.45
731 1548 5.069914 ACATGATTTAGGCGTGGTAGTATCA 59.930 40.000 0.00 0.00 0.00 2.15
732 1549 5.539048 ACATGATTTAGGCGTGGTAGTATC 58.461 41.667 0.00 0.00 0.00 2.24
733 1550 5.539048 GACATGATTTAGGCGTGGTAGTAT 58.461 41.667 0.00 0.00 0.00 2.12
734 1551 4.498513 CGACATGATTTAGGCGTGGTAGTA 60.499 45.833 0.00 0.00 0.00 1.82
735 1552 3.737047 CGACATGATTTAGGCGTGGTAGT 60.737 47.826 0.00 0.00 0.00 2.73
736 1553 2.794910 CGACATGATTTAGGCGTGGTAG 59.205 50.000 0.00 0.00 0.00 3.18
737 1554 2.166870 ACGACATGATTTAGGCGTGGTA 59.833 45.455 0.00 0.00 0.00 3.25
738 1555 1.066430 ACGACATGATTTAGGCGTGGT 60.066 47.619 0.00 0.00 0.00 4.16
739 1556 1.651987 ACGACATGATTTAGGCGTGG 58.348 50.000 0.00 0.00 0.00 4.94
740 1557 2.285026 CGAACGACATGATTTAGGCGTG 60.285 50.000 0.00 0.00 31.84 5.34
741 1558 1.924524 CGAACGACATGATTTAGGCGT 59.075 47.619 0.00 0.00 0.00 5.68
742 1559 1.257936 CCGAACGACATGATTTAGGCG 59.742 52.381 0.00 0.00 0.00 5.52
743 1560 2.540101 CTCCGAACGACATGATTTAGGC 59.460 50.000 0.00 0.00 0.00 3.93
744 1561 2.540101 GCTCCGAACGACATGATTTAGG 59.460 50.000 0.00 0.00 0.00 2.69
745 1562 3.448686 AGCTCCGAACGACATGATTTAG 58.551 45.455 0.00 0.00 0.00 1.85
746 1563 3.444916 GAGCTCCGAACGACATGATTTA 58.555 45.455 0.87 0.00 0.00 1.40
747 1564 2.271800 GAGCTCCGAACGACATGATTT 58.728 47.619 0.87 0.00 0.00 2.17
873 1761 4.115199 GGAAGGCGCCATGGAGGT 62.115 66.667 31.54 1.71 40.61 3.85
1343 2265 1.000993 AGCAGGTCCCTCATCTCGT 59.999 57.895 0.00 0.00 0.00 4.18
1488 2410 1.179814 ACGTCTCGAAGAAGTGGGCT 61.180 55.000 0.00 0.00 35.66 5.19
1761 2692 3.201297 CACACGCACTGCCACACA 61.201 61.111 0.00 0.00 0.00 3.72
1911 2842 1.841556 GGACACCACCTCCTCCACA 60.842 63.158 0.00 0.00 0.00 4.17
2318 3254 0.250295 GGCAGCAGTGTGTGTAGGAA 60.250 55.000 0.00 0.00 0.00 3.36
2352 3306 1.135717 GCAAACGTACATGCATGCAGA 60.136 47.619 26.69 11.04 42.12 4.26
2370 3324 5.565592 AAGAGCAAATTAATCATGACGCA 57.434 34.783 0.00 0.00 0.00 5.24
2407 3361 7.043656 CGTTCATATTCACATACACATGTACGT 60.044 37.037 0.00 0.00 43.73 3.57
2408 3362 7.043656 ACGTTCATATTCACATACACATGTACG 60.044 37.037 0.00 1.32 43.73 3.67
2409 3363 8.055986 CACGTTCATATTCACATACACATGTAC 58.944 37.037 0.00 0.00 43.73 2.90
2437 3394 1.985447 TACTTACCGACCAGCGCTCG 61.985 60.000 7.13 9.10 39.11 5.03
2441 3398 1.226888 GGCTACTTACCGACCAGCG 60.227 63.158 0.00 0.00 40.47 5.18
2443 3400 1.806623 GCATGGCTACTTACCGACCAG 60.807 57.143 0.00 0.00 33.03 4.00
2447 3404 2.963101 ACTATGCATGGCTACTTACCGA 59.037 45.455 10.16 0.00 0.00 4.69
2448 3405 3.386768 ACTATGCATGGCTACTTACCG 57.613 47.619 10.16 0.00 0.00 4.02
2463 3425 8.593492 TTGTAAGATAGCAGCATACAACTATG 57.407 34.615 0.00 0.00 33.03 2.23
2468 3430 5.674525 AGCTTGTAAGATAGCAGCATACAA 58.325 37.500 0.00 1.90 39.85 2.41
2469 3431 5.282055 AGCTTGTAAGATAGCAGCATACA 57.718 39.130 0.00 0.00 39.85 2.29
2471 3433 6.656632 ACTAGCTTGTAAGATAGCAGCATA 57.343 37.500 14.82 0.00 46.20 3.14
2489 3451 9.512435 TTTTCGAGTCTTATTACATGTACTAGC 57.488 33.333 4.68 0.23 0.00 3.42
2513 3481 4.531732 ACACATGCCCAAGTCCAATATTTT 59.468 37.500 0.00 0.00 0.00 1.82
2544 3516 4.263331 GCTAGCTAGTAGAGAGACTGGGAT 60.263 50.000 21.62 0.00 0.00 3.85
2547 3519 4.351874 AGCTAGCTAGTAGAGAGACTGG 57.648 50.000 17.69 0.00 0.00 4.00
2579 3552 1.510623 CGCAGCAATCAACACGAGC 60.511 57.895 0.00 0.00 0.00 5.03
2648 3621 5.529581 AGTTGGGTACAAACAATTTCCAG 57.470 39.130 11.82 0.00 38.54 3.86
2651 3624 6.974048 ACGTAAAGTTGGGTACAAACAATTTC 59.026 34.615 11.82 5.29 38.54 2.17
2653 3626 6.453926 ACGTAAAGTTGGGTACAAACAATT 57.546 33.333 11.82 9.03 38.54 2.32
2654 3627 7.748691 ATACGTAAAGTTGGGTACAAACAAT 57.251 32.000 0.00 4.33 38.54 2.71
2655 3628 7.712639 TGTATACGTAAAGTTGGGTACAAACAA 59.287 33.333 0.00 3.70 38.54 2.83
2656 3629 7.212976 TGTATACGTAAAGTTGGGTACAAACA 58.787 34.615 0.00 0.00 38.54 2.83
2657 3630 7.650834 TGTATACGTAAAGTTGGGTACAAAC 57.349 36.000 0.00 0.00 38.54 2.93
2658 3631 9.364989 GTATGTATACGTAAAGTTGGGTACAAA 57.635 33.333 6.37 0.00 38.54 2.83
2703 3707 5.221028 CGAGAAATATAATGGCACCAGCAAA 60.221 40.000 0.00 0.00 44.61 3.68
2705 3709 3.814842 CGAGAAATATAATGGCACCAGCA 59.185 43.478 0.00 0.00 44.61 4.41
2707 3711 4.214119 CCACGAGAAATATAATGGCACCAG 59.786 45.833 0.00 0.00 0.00 4.00
2708 3712 4.133820 CCACGAGAAATATAATGGCACCA 58.866 43.478 0.00 0.00 0.00 4.17
2709 3713 4.749245 CCACGAGAAATATAATGGCACC 57.251 45.455 0.00 0.00 0.00 5.01
2713 3717 7.962964 TCTTAAGCCACGAGAAATATAATGG 57.037 36.000 0.00 0.00 0.00 3.16
2714 3718 9.429359 AGATCTTAAGCCACGAGAAATATAATG 57.571 33.333 0.00 0.00 0.00 1.90
2715 3719 9.429359 CAGATCTTAAGCCACGAGAAATATAAT 57.571 33.333 0.00 0.00 0.00 1.28
2716 3720 7.872993 CCAGATCTTAAGCCACGAGAAATATAA 59.127 37.037 0.00 0.00 0.00 0.98
2717 3721 7.232737 TCCAGATCTTAAGCCACGAGAAATATA 59.767 37.037 0.00 0.00 0.00 0.86
2718 3722 6.042093 TCCAGATCTTAAGCCACGAGAAATAT 59.958 38.462 0.00 0.00 0.00 1.28
2719 3723 5.362717 TCCAGATCTTAAGCCACGAGAAATA 59.637 40.000 0.00 0.00 0.00 1.40
2720 3724 4.162320 TCCAGATCTTAAGCCACGAGAAAT 59.838 41.667 0.00 0.00 0.00 2.17
2721 3725 3.513912 TCCAGATCTTAAGCCACGAGAAA 59.486 43.478 0.00 0.00 0.00 2.52
2730 3734 2.541556 GACCACGTCCAGATCTTAAGC 58.458 52.381 0.00 0.00 0.00 3.09
2747 3751 3.708734 CCCAAACGTCGCACGACC 61.709 66.667 16.81 0.68 46.05 4.79
2751 3756 2.126888 CATGCCCAAACGTCGCAC 60.127 61.111 0.00 0.00 34.87 5.34
2821 3828 4.742201 GAGGACCGCTTGCTCGCA 62.742 66.667 0.00 0.00 32.28 5.10
2892 3899 4.999950 GCAGTTGAGAAGATGAAGGAGAAA 59.000 41.667 0.00 0.00 0.00 2.52
2913 3921 3.909430 ACAGATAAGAAACGAACGAGCA 58.091 40.909 0.14 0.00 0.00 4.26
2936 3944 2.970639 CCGGCGTGGAAGAGAGAA 59.029 61.111 6.01 0.00 42.00 2.87
2964 3972 3.074412 GAGCTGAAAATTGGACGAAGGA 58.926 45.455 0.00 0.00 0.00 3.36
3079 4087 3.289834 CTTGGTTGCAGCGGCTGT 61.290 61.111 28.88 0.00 41.91 4.40
3127 4135 4.304413 TGGTTGCTGGCCATGGCT 62.304 61.111 34.70 0.00 41.60 4.75
3199 4207 1.152881 CAGTTCCAGCATAGGGGGC 60.153 63.158 0.00 0.00 0.00 5.80
3263 4271 1.692411 AAAGTGGTTGGTTCCAGCTC 58.308 50.000 5.74 0.93 38.23 4.09


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

AutoCloner maintained by Alex Coulton.