Multiple sequence alignment - TraesCS5A01G440500

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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 TraesCS5A01G440500 chr5A 100.000 4777 0 0 1 4777 621844909 621849685 0.000000e+00 8822
1 TraesCS5A01G440500 chr5A 76.915 901 166 27 2498 3380 537125012 537124136 1.560000e-129 473
2 TraesCS5A01G440500 chr5D 89.051 3352 238 66 1116 4400 497818859 497822148 0.000000e+00 4037
3 TraesCS5A01G440500 chr5D 86.264 1325 166 12 1 1315 40727058 40725740 0.000000e+00 1424
4 TraesCS5A01G440500 chr5D 75.602 1496 279 62 2559 4006 47531058 47532515 0.000000e+00 662
5 TraesCS5A01G440500 chr5D 77.636 939 162 31 2462 3380 423535405 423534495 1.180000e-145 527
6 TraesCS5A01G440500 chr5D 83.333 222 22 10 4556 4764 497822424 497822643 1.750000e-44 191
7 TraesCS5A01G440500 chr2D 87.922 1333 146 13 8 1328 69500141 69498812 0.000000e+00 1555
8 TraesCS5A01G440500 chr2D 86.426 1385 176 11 1 1376 388514446 388513065 0.000000e+00 1506
9 TraesCS5A01G440500 chr2D 79.000 300 38 16 1489 1769 108316260 108315967 1.060000e-41 182
10 TraesCS5A01G440500 chr5B 87.322 1333 158 8 1 1326 108839079 108840407 0.000000e+00 1515
11 TraesCS5A01G440500 chr5B 90.492 894 58 15 2258 3130 616957966 616958853 0.000000e+00 1155
12 TraesCS5A01G440500 chr5B 86.625 800 84 15 3608 4394 616958850 616959639 0.000000e+00 863
13 TraesCS5A01G440500 chr2B 86.599 1388 164 18 6 1376 105904114 105902732 0.000000e+00 1513
14 TraesCS5A01G440500 chr2B 80.952 273 41 11 1502 1769 655518307 655518041 6.270000e-49 206
15 TraesCS5A01G440500 chr6A 85.508 1387 187 8 1 1376 448359228 448360611 0.000000e+00 1435
16 TraesCS5A01G440500 chr6A 84.964 1390 194 12 1 1379 604257773 604256388 0.000000e+00 1395
17 TraesCS5A01G440500 chr6A 77.329 1535 239 59 2564 4065 17947374 17945916 0.000000e+00 806
18 TraesCS5A01G440500 chr6A 79.355 310 45 8 3481 3786 616884434 616884140 2.920000e-47 200
19 TraesCS5A01G440500 chr6A 80.224 268 51 2 3490 3756 616902727 616902461 2.920000e-47 200
20 TraesCS5A01G440500 chr3B 85.447 1388 184 14 1 1375 370939656 370941038 0.000000e+00 1428
21 TraesCS5A01G440500 chr3B 79.500 200 33 8 1489 1683 564773473 564773277 8.340000e-28 135
22 TraesCS5A01G440500 chr7B 84.831 1391 197 9 1 1379 91981328 91979940 0.000000e+00 1387
23 TraesCS5A01G440500 chr7B 75.931 752 147 23 2655 3380 594121928 594122671 5.880000e-94 355
24 TraesCS5A01G440500 chr7D 76.762 1149 228 23 2646 3763 566520007 566521147 1.470000e-169 606
25 TraesCS5A01G440500 chr7D 77.584 861 155 24 2501 3341 602291785 602292627 2.000000e-133 486
26 TraesCS5A01G440500 chr7D 75.584 856 143 39 2558 3380 602286753 602287575 3.510000e-96 363
27 TraesCS5A01G440500 chr7D 75.360 763 133 25 2647 3380 549794669 549795405 2.770000e-82 316
28 TraesCS5A01G440500 chr7D 76.241 282 37 15 1511 1769 100856764 100856490 6.490000e-24 122
29 TraesCS5A01G440500 chr1D 75.071 1412 269 49 2661 4032 458875921 458877289 8.910000e-162 580
30 TraesCS5A01G440500 chr3A 75.298 1344 255 42 2456 3751 629063641 629064955 5.360000e-159 571
31 TraesCS5A01G440500 chr3D 75.037 1350 250 45 2456 3751 560281083 560279767 3.250000e-151 545
32 TraesCS5A01G440500 chr3D 80.342 234 28 13 1505 1726 432543970 432543743 1.380000e-35 161
33 TraesCS5A01G440500 chr1A 74.496 1388 273 48 2662 4029 551307466 551308792 1.180000e-145 527
34 TraesCS5A01G440500 chrUn 77.816 861 159 20 2501 3344 87219756 87220601 1.980000e-138 503
35 TraesCS5A01G440500 chrUn 74.022 1355 262 49 2456 3756 221377421 221378739 2.010000e-128 470
36 TraesCS5A01G440500 chrUn 73.948 1355 263 49 2456 3756 225550546 225551864 9.360000e-127 464
37 TraesCS5A01G440500 chrUn 73.801 1355 265 50 2456 3756 306578357 306577039 2.030000e-123 453
38 TraesCS5A01G440500 chrUn 74.786 1051 192 37 2749 3756 285617452 285618472 5.760000e-109 405
39 TraesCS5A01G440500 chrUn 77.778 675 109 15 3102 3756 387971865 387971212 1.250000e-100 377
40 TraesCS5A01G440500 chr1B 77.121 896 170 29 2875 3751 630741600 630742479 2.000000e-133 486
41 TraesCS5A01G440500 chr7A 74.096 1355 261 49 2456 3756 5794955 5796273 4.330000e-130 475
42 TraesCS5A01G440500 chr7A 75.858 758 147 21 2655 3381 635277611 635278363 2.110000e-93 353
43 TraesCS5A01G440500 chr7A 82.292 288 37 12 1489 1769 56711909 56711629 2.220000e-58 237
44 TraesCS5A01G440500 chr7A 79.866 298 39 13 1489 1769 56657086 56656793 1.050000e-46 198
45 TraesCS5A01G440500 chr6B 72.586 1481 303 61 2661 4081 718597780 718596343 1.610000e-104 390
46 TraesCS5A01G440500 chr6B 83.158 380 46 8 3017 3384 30341692 30341319 9.910000e-87 331
47 TraesCS5A01G440500 chr6B 81.387 274 33 13 1489 1751 20205888 20205622 1.740000e-49 207
48 TraesCS5A01G440500 chr6B 79.514 288 31 13 1489 1753 632189954 632189672 3.800000e-41 180
49 TraesCS5A01G440500 chr6D 81.800 489 65 17 2865 3344 472909746 472910219 5.800000e-104 388
50 TraesCS5A01G440500 chr6D 83.392 283 47 0 3481 3763 472931949 472932231 3.670000e-66 263
51 TraesCS5A01G440500 chr6D 76.054 522 95 21 2874 3380 472931408 472931914 1.330000e-60 244
52 TraesCS5A01G440500 chr6D 74.008 504 117 14 2866 3360 464652591 464653089 4.880000e-45 193


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 TraesCS5A01G440500 chr5A 621844909 621849685 4776 False 8822.0 8822 100.0000 1 4777 1 chr5A.!!$F1 4776
1 TraesCS5A01G440500 chr5A 537124136 537125012 876 True 473.0 473 76.9150 2498 3380 1 chr5A.!!$R1 882
2 TraesCS5A01G440500 chr5D 497818859 497822643 3784 False 2114.0 4037 86.1920 1116 4764 2 chr5D.!!$F2 3648
3 TraesCS5A01G440500 chr5D 40725740 40727058 1318 True 1424.0 1424 86.2640 1 1315 1 chr5D.!!$R1 1314
4 TraesCS5A01G440500 chr5D 47531058 47532515 1457 False 662.0 662 75.6020 2559 4006 1 chr5D.!!$F1 1447
5 TraesCS5A01G440500 chr5D 423534495 423535405 910 True 527.0 527 77.6360 2462 3380 1 chr5D.!!$R2 918
6 TraesCS5A01G440500 chr2D 69498812 69500141 1329 True 1555.0 1555 87.9220 8 1328 1 chr2D.!!$R1 1320
7 TraesCS5A01G440500 chr2D 388513065 388514446 1381 True 1506.0 1506 86.4260 1 1376 1 chr2D.!!$R3 1375
8 TraesCS5A01G440500 chr5B 108839079 108840407 1328 False 1515.0 1515 87.3220 1 1326 1 chr5B.!!$F1 1325
9 TraesCS5A01G440500 chr5B 616957966 616959639 1673 False 1009.0 1155 88.5585 2258 4394 2 chr5B.!!$F2 2136
10 TraesCS5A01G440500 chr2B 105902732 105904114 1382 True 1513.0 1513 86.5990 6 1376 1 chr2B.!!$R1 1370
11 TraesCS5A01G440500 chr6A 448359228 448360611 1383 False 1435.0 1435 85.5080 1 1376 1 chr6A.!!$F1 1375
12 TraesCS5A01G440500 chr6A 604256388 604257773 1385 True 1395.0 1395 84.9640 1 1379 1 chr6A.!!$R2 1378
13 TraesCS5A01G440500 chr6A 17945916 17947374 1458 True 806.0 806 77.3290 2564 4065 1 chr6A.!!$R1 1501
14 TraesCS5A01G440500 chr3B 370939656 370941038 1382 False 1428.0 1428 85.4470 1 1375 1 chr3B.!!$F1 1374
15 TraesCS5A01G440500 chr7B 91979940 91981328 1388 True 1387.0 1387 84.8310 1 1379 1 chr7B.!!$R1 1378
16 TraesCS5A01G440500 chr7B 594121928 594122671 743 False 355.0 355 75.9310 2655 3380 1 chr7B.!!$F1 725
17 TraesCS5A01G440500 chr7D 566520007 566521147 1140 False 606.0 606 76.7620 2646 3763 1 chr7D.!!$F2 1117
18 TraesCS5A01G440500 chr7D 602291785 602292627 842 False 486.0 486 77.5840 2501 3341 1 chr7D.!!$F4 840
19 TraesCS5A01G440500 chr7D 602286753 602287575 822 False 363.0 363 75.5840 2558 3380 1 chr7D.!!$F3 822
20 TraesCS5A01G440500 chr7D 549794669 549795405 736 False 316.0 316 75.3600 2647 3380 1 chr7D.!!$F1 733
21 TraesCS5A01G440500 chr1D 458875921 458877289 1368 False 580.0 580 75.0710 2661 4032 1 chr1D.!!$F1 1371
22 TraesCS5A01G440500 chr3A 629063641 629064955 1314 False 571.0 571 75.2980 2456 3751 1 chr3A.!!$F1 1295
23 TraesCS5A01G440500 chr3D 560279767 560281083 1316 True 545.0 545 75.0370 2456 3751 1 chr3D.!!$R2 1295
24 TraesCS5A01G440500 chr1A 551307466 551308792 1326 False 527.0 527 74.4960 2662 4029 1 chr1A.!!$F1 1367
25 TraesCS5A01G440500 chrUn 87219756 87220601 845 False 503.0 503 77.8160 2501 3344 1 chrUn.!!$F1 843
26 TraesCS5A01G440500 chrUn 221377421 221378739 1318 False 470.0 470 74.0220 2456 3756 1 chrUn.!!$F2 1300
27 TraesCS5A01G440500 chrUn 225550546 225551864 1318 False 464.0 464 73.9480 2456 3756 1 chrUn.!!$F3 1300
28 TraesCS5A01G440500 chrUn 306577039 306578357 1318 True 453.0 453 73.8010 2456 3756 1 chrUn.!!$R1 1300
29 TraesCS5A01G440500 chrUn 285617452 285618472 1020 False 405.0 405 74.7860 2749 3756 1 chrUn.!!$F4 1007
30 TraesCS5A01G440500 chrUn 387971212 387971865 653 True 377.0 377 77.7780 3102 3756 1 chrUn.!!$R2 654
31 TraesCS5A01G440500 chr1B 630741600 630742479 879 False 486.0 486 77.1210 2875 3751 1 chr1B.!!$F1 876
32 TraesCS5A01G440500 chr7A 5794955 5796273 1318 False 475.0 475 74.0960 2456 3756 1 chr7A.!!$F1 1300
33 TraesCS5A01G440500 chr7A 635277611 635278363 752 False 353.0 353 75.8580 2655 3381 1 chr7A.!!$F2 726
34 TraesCS5A01G440500 chr6B 718596343 718597780 1437 True 390.0 390 72.5860 2661 4081 1 chr6B.!!$R4 1420
35 TraesCS5A01G440500 chr6D 472931408 472932231 823 False 253.5 263 79.7230 2874 3763 2 chr6D.!!$F3 889

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
765 778 0.250234 TTGAGAACATGCTCCTCCGG 59.750 55.0 0.00 0.0 33.95 5.14 F
1508 1535 0.035056 AAGATTCAGTTGGGCTCCGG 60.035 55.0 0.00 0.0 0.00 5.14 F
1863 1913 0.107312 AGCATCTGCAGCTAACCAGG 60.107 55.0 9.47 0.0 45.16 4.45 F
2199 2258 0.250684 TCAAGCCCAATGACTTGCGA 60.251 50.0 9.98 0.0 42.41 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1965 0.883370 AGGGTTGTTCTTCGCGTTCC 60.883 55.000 5.77 0.0 0.00 3.62 R
2431 2502 1.280746 CTCAACAGTTGCTGTGCCG 59.719 57.895 8.58 0.0 44.62 5.69 R
3767 4011 0.109873 CGAGTGAGCGTTACTTCCGT 60.110 55.000 0.00 0.0 0.00 4.69 R
4020 4286 2.047655 TAGCGGGGAACTTGCACG 60.048 61.111 0.00 0.0 34.73 5.34 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
34 35 2.453521 ACCGTCAACCAGATAGTAGCA 58.546 47.619 0.00 0.00 0.00 3.49
91 92 4.544651 CAAAGAGGAGCTTTTTCTTCAGC 58.455 43.478 8.25 0.00 44.24 4.26
148 150 5.473066 TTGATGTCATTGTGAGACTCAGA 57.527 39.130 5.10 0.73 36.94 3.27
181 187 3.536956 AGCATGCCAAATCCAAAGATG 57.463 42.857 15.66 0.00 31.29 2.90
193 200 4.976224 TCCAAAGATGATGTGATGCAAG 57.024 40.909 0.00 0.00 0.00 4.01
228 235 3.737559 TGGTGGGCTTCTTAACATGAT 57.262 42.857 0.00 0.00 0.00 2.45
232 239 5.104151 TGGTGGGCTTCTTAACATGATCATA 60.104 40.000 8.15 0.00 0.00 2.15
242 249 9.585369 TTCTTAACATGATCATAATATTGCCCA 57.415 29.630 8.15 0.00 0.00 5.36
293 300 2.159421 CCAATGCATGCAGTCAAGAGAC 60.159 50.000 26.69 0.00 45.31 3.36
368 375 0.886490 CTGCCGCAGTTGGTTCTCTT 60.886 55.000 12.54 0.00 0.00 2.85
370 377 1.202710 TGCCGCAGTTGGTTCTCTTAA 60.203 47.619 0.00 0.00 0.00 1.85
386 393 4.942483 TCTCTTAAGTACTGAGGTCCGAAG 59.058 45.833 0.00 0.00 0.00 3.79
410 417 2.416547 CTCGACCATGGTAGTTGCAAAG 59.583 50.000 19.80 6.05 0.00 2.77
413 420 3.343617 GACCATGGTAGTTGCAAAGCTA 58.656 45.455 19.80 0.00 0.00 3.32
428 435 1.516110 AGCTAACCATGGCATCTCCT 58.484 50.000 13.04 0.00 35.08 3.69
485 492 3.873361 ACGAATCAATGACTGTGCCATAG 59.127 43.478 0.00 0.00 0.00 2.23
497 504 3.585247 CCATAGGCAGGCATCCCT 58.415 61.111 0.00 0.00 44.25 4.20
507 514 4.175337 GCATCCCTAGTGCGGCCA 62.175 66.667 2.24 0.00 32.29 5.36
518 525 2.747460 GCGGCCATGCACTTCTGA 60.747 61.111 2.24 0.00 34.15 3.27
537 544 4.471025 TCTGATAACCAGAGAAGCCAATCA 59.529 41.667 0.00 0.00 46.38 2.57
545 552 2.309755 AGAGAAGCCAATCATTCCCACA 59.690 45.455 0.00 0.00 0.00 4.17
547 554 2.042162 AGAAGCCAATCATTCCCACAGT 59.958 45.455 0.00 0.00 0.00 3.55
628 640 0.665835 TCTTGCGCATCCAAAAACGT 59.334 45.000 12.75 0.00 0.00 3.99
721 734 1.159713 TGTTGCAGTTGAGCACTCGG 61.160 55.000 0.00 0.00 45.61 4.63
765 778 0.250234 TTGAGAACATGCTCCTCCGG 59.750 55.000 0.00 0.00 33.95 5.14
812 825 2.159254 TGCATCATTGTCGTCTCATCGA 60.159 45.455 0.00 0.00 37.51 3.59
817 831 5.500645 TCATTGTCGTCTCATCGAAGTAT 57.499 39.130 0.00 0.00 41.47 2.12
818 832 5.273944 TCATTGTCGTCTCATCGAAGTATG 58.726 41.667 0.00 0.00 41.47 2.39
835 855 2.579787 GTCGTCCGATGAGCCGTG 60.580 66.667 0.00 0.00 0.00 4.94
842 862 2.721167 CGATGAGCCGTGGGAGGAA 61.721 63.158 0.00 0.00 0.00 3.36
855 875 2.092429 TGGGAGGAATCAACATACTGCC 60.092 50.000 0.00 0.00 39.74 4.85
874 894 5.541101 ACTGCCCGTATATGTACTCCAAATA 59.459 40.000 0.00 0.00 0.00 1.40
902 922 3.056607 CCATTGCTACAAACAAGAAGGGG 60.057 47.826 0.00 0.00 0.00 4.79
1013 1033 1.859302 ACGAAGATGGAGGAGAAGCT 58.141 50.000 0.00 0.00 0.00 3.74
1014 1034 3.019799 ACGAAGATGGAGGAGAAGCTA 57.980 47.619 0.00 0.00 0.00 3.32
1162 1187 2.039624 ATGGAGTCGCAGGGTCCT 59.960 61.111 0.00 0.00 32.12 3.85
1228 1253 1.227823 TGTGCGGACTCCCACAAAG 60.228 57.895 8.99 0.00 38.87 2.77
1256 1282 4.358851 CCACTTTTGTCTTCATTTTGCGA 58.641 39.130 0.00 0.00 0.00 5.10
1264 1290 5.692814 TGTCTTCATTTTGCGAGAGAAATG 58.307 37.500 3.15 3.15 42.03 2.32
1309 1336 1.634960 TACAGACCGTGTTGGATGGA 58.365 50.000 0.00 0.00 40.94 3.41
1346 1373 3.555547 CAGTATGATCCGAACAATTGCGA 59.444 43.478 5.05 0.00 39.69 5.10
1376 1403 4.461119 TCCGTCTTGGAGATGCCT 57.539 55.556 0.00 0.00 43.74 4.75
1414 1441 8.081633 TGAAAGCAATAAATGTTGTTCGAATCT 58.918 29.630 0.00 0.00 0.00 2.40
1431 1458 2.103153 TCTGGGGACAAGTGTCTTCT 57.897 50.000 11.07 0.00 44.20 2.85
1449 1476 6.071984 GTCTTCTTGACCTCCATCCTCTATA 58.928 44.000 0.00 0.00 39.69 1.31
1462 1489 8.561536 TCCATCCTCTATATTGGAGTTGTTAA 57.438 34.615 0.00 0.00 35.63 2.01
1478 1505 9.702494 GGAGTTGTTAATGTTGTAGTAGTAAGT 57.298 33.333 0.00 0.00 0.00 2.24
1491 1518 8.362860 TGTAGTAGTAAGTAGCATCTACGAAG 57.637 38.462 0.00 0.00 38.12 3.79
1497 1524 7.644490 AGTAAGTAGCATCTACGAAGATTCAG 58.356 38.462 0.00 0.00 40.65 3.02
1508 1535 0.035056 AAGATTCAGTTGGGCTCCGG 60.035 55.000 0.00 0.00 0.00 5.14
1539 1566 5.465532 TGCTCCTGCATGTGAAAAATTAA 57.534 34.783 0.00 0.00 45.31 1.40
1540 1567 5.851720 TGCTCCTGCATGTGAAAAATTAAA 58.148 33.333 0.00 0.00 45.31 1.52
1626 1653 2.355197 ACTGCAAAGTTTTGGGCAAAC 58.645 42.857 6.72 0.00 44.73 2.93
1640 1667 7.396540 TTTGGGCAAACATGTTAAACATTTT 57.603 28.000 12.39 0.00 36.53 1.82
1643 1670 6.769822 TGGGCAAACATGTTAAACATTTTGAT 59.230 30.769 12.39 0.00 36.53 2.57
1646 1673 8.011106 GGCAAACATGTTAAACATTTTGATCTG 58.989 33.333 12.39 2.22 36.53 2.90
1666 1694 8.203485 TGATCTGTAAAAAGGCAAATTTGAACT 58.797 29.630 22.31 15.04 0.00 3.01
1668 1696 7.781056 TCTGTAAAAAGGCAAATTTGAACTCT 58.219 30.769 22.31 9.63 0.00 3.24
1669 1697 7.920682 TCTGTAAAAAGGCAAATTTGAACTCTC 59.079 33.333 22.31 2.62 0.00 3.20
1683 1711 9.533831 AATTTGAACTCTCAATGTTACCCTAAT 57.466 29.630 0.00 0.00 41.22 1.73
1710 1740 4.718858 TTTCACCGACGAAACAATACTG 57.281 40.909 0.00 0.00 30.00 2.74
1712 1742 2.066262 CACCGACGAAACAATACTGCT 58.934 47.619 0.00 0.00 0.00 4.24
1722 1752 2.066262 ACAATACTGCTCCGTTTCACG 58.934 47.619 0.00 0.00 42.11 4.35
1740 1770 4.930963 TCACGTGAAAATTGTCAAGCATT 58.069 34.783 17.62 0.00 31.04 3.56
1741 1771 4.975502 TCACGTGAAAATTGTCAAGCATTC 59.024 37.500 17.62 0.00 31.04 2.67
1760 1790 5.689819 CATTCTTGCTACACTACCACAAAC 58.310 41.667 0.00 0.00 0.00 2.93
1768 1798 3.892284 ACACTACCACAAACATCCACAA 58.108 40.909 0.00 0.00 0.00 3.33
1769 1799 4.469657 ACACTACCACAAACATCCACAAT 58.530 39.130 0.00 0.00 0.00 2.71
1770 1800 4.892934 ACACTACCACAAACATCCACAATT 59.107 37.500 0.00 0.00 0.00 2.32
1771 1801 5.362430 ACACTACCACAAACATCCACAATTT 59.638 36.000 0.00 0.00 0.00 1.82
1772 1802 6.127196 ACACTACCACAAACATCCACAATTTT 60.127 34.615 0.00 0.00 0.00 1.82
1773 1803 6.760770 CACTACCACAAACATCCACAATTTTT 59.239 34.615 0.00 0.00 0.00 1.94
1811 1861 3.662759 TTTGACCACTTTTCCAGGAGT 57.337 42.857 0.00 0.00 0.00 3.85
1817 1867 5.061721 ACCACTTTTCCAGGAGTAAATGT 57.938 39.130 0.00 0.00 0.00 2.71
1822 1872 3.343941 TTCCAGGAGTAAATGTTCCCG 57.656 47.619 0.00 0.00 33.83 5.14
1840 1890 4.103103 GAGCCAAAACGCCGCTCC 62.103 66.667 0.00 0.00 42.59 4.70
1863 1913 0.107312 AGCATCTGCAGCTAACCAGG 60.107 55.000 9.47 0.00 45.16 4.45
1864 1914 0.393537 GCATCTGCAGCTAACCAGGT 60.394 55.000 9.47 0.00 41.59 4.00
1865 1915 6.959588 TTAGCATCTGCAGCTAACCAGGTG 62.960 50.000 9.47 14.03 46.40 4.00
1877 1927 1.302033 CCAGGTGCACAGAGACCAC 60.302 63.158 20.43 0.00 34.36 4.16
1901 1951 4.496670 CCCGAGTGGCTCTTAACG 57.503 61.111 0.00 0.00 0.00 3.18
1964 2016 7.377766 TGTAAATACAGATGCAGAAAGTTCC 57.622 36.000 0.00 0.00 0.00 3.62
1967 2019 7.472334 AAATACAGATGCAGAAAGTTCCAAT 57.528 32.000 0.00 0.00 0.00 3.16
1972 2024 5.182570 CAGATGCAGAAAGTTCCAATCTCAA 59.817 40.000 0.00 0.00 0.00 3.02
2026 2078 1.024271 TCAGTCAAGTGCTGTTTGGC 58.976 50.000 0.00 0.00 35.60 4.52
2038 2090 4.330620 GTGCTGTTTGGCATTCCATAAATG 59.669 41.667 0.00 0.00 46.37 2.32
2039 2091 4.222366 TGCTGTTTGGCATTCCATAAATGA 59.778 37.500 2.07 0.00 46.54 2.57
2048 2100 9.820725 TTGGCATTCCATAAATGAAAATTCTAG 57.179 29.630 2.07 0.00 46.54 2.43
2049 2101 8.423349 TGGCATTCCATAAATGAAAATTCTAGG 58.577 33.333 2.07 0.00 46.54 3.02
2051 2103 7.874528 GCATTCCATAAATGAAAATTCTAGGGG 59.125 37.037 2.07 0.00 46.54 4.79
2063 2115 6.977244 AAATTCTAGGGGGATATAGCACAT 57.023 37.500 0.00 0.00 0.00 3.21
2121 2180 7.202016 TGAAAATTCAGCTCGATTTACACTT 57.798 32.000 4.68 0.00 32.50 3.16
2153 2212 4.247380 CCCTGAGCGATGGGCCTC 62.247 72.222 4.53 0.00 45.17 4.70
2154 2213 4.247380 CCTGAGCGATGGGCCTCC 62.247 72.222 4.53 0.00 45.17 4.30
2161 2220 1.454479 CGATGGGCCTCCTTTGCAT 60.454 57.895 4.53 0.00 0.00 3.96
2194 2253 2.967270 GCCTTCAAGCCCAATGACT 58.033 52.632 0.00 0.00 0.00 3.41
2197 2256 1.067354 CCTTCAAGCCCAATGACTTGC 60.067 52.381 9.98 0.00 42.41 4.01
2198 2257 0.597568 TTCAAGCCCAATGACTTGCG 59.402 50.000 9.98 0.00 42.41 4.85
2199 2258 0.250684 TCAAGCCCAATGACTTGCGA 60.251 50.000 9.98 0.00 42.41 5.10
2201 2260 1.203052 CAAGCCCAATGACTTGCGAAT 59.797 47.619 3.68 0.00 37.11 3.34
2203 2262 1.203052 AGCCCAATGACTTGCGAATTG 59.797 47.619 0.00 0.00 0.00 2.32
2204 2263 1.067635 GCCCAATGACTTGCGAATTGT 60.068 47.619 0.00 0.00 30.84 2.71
2229 2299 2.542550 TGTTAACCCTAGCTGTAGGCA 58.457 47.619 2.48 0.00 44.39 4.75
2317 2387 4.148825 GCGGGTGGAGCGTCATCT 62.149 66.667 0.00 0.00 0.00 2.90
2345 2415 2.733593 GCGACTTCGTTCGGTGCT 60.734 61.111 0.00 0.00 42.22 4.40
2383 2453 1.685224 CAGGTTTGCCCCTCAGCTA 59.315 57.895 0.00 0.00 34.57 3.32
2396 2467 0.966179 TCAGCTACCGCAAACTCTCA 59.034 50.000 0.00 0.00 39.10 3.27
2446 2517 3.595758 GGCGGCACAGCAACTGTT 61.596 61.111 3.07 0.00 42.59 3.16
2468 2561 2.274104 GGCGGCAATCCCAGGTTA 59.726 61.111 3.07 0.00 0.00 2.85
2496 2589 1.103398 GCCCATTGATCCCAACTCCG 61.103 60.000 0.00 0.00 34.72 4.63
2523 2619 4.094887 TCTGAAATTTAGGAGCGTGAATGC 59.905 41.667 0.00 0.00 0.00 3.56
2822 2926 0.370273 GCGCCGACTACATTTCTGTG 59.630 55.000 0.00 0.00 36.79 3.66
3293 3498 3.739810 CGTCCAGCATCATACAGATCAAG 59.260 47.826 0.00 0.00 33.72 3.02
3423 3643 3.119919 GGAGCAAGAACAAGCAGATGAAG 60.120 47.826 0.00 0.00 0.00 3.02
3424 3644 2.228343 AGCAAGAACAAGCAGATGAAGC 59.772 45.455 0.00 0.00 0.00 3.86
3425 3645 2.228343 GCAAGAACAAGCAGATGAAGCT 59.772 45.455 0.00 0.00 45.97 3.74
3426 3646 3.822996 CAAGAACAAGCAGATGAAGCTG 58.177 45.455 0.00 0.00 42.53 4.24
3427 3647 3.137446 AGAACAAGCAGATGAAGCTGT 57.863 42.857 0.00 0.00 42.53 4.40
3431 3651 4.484537 ACAAGCAGATGAAGCTGTAGAT 57.515 40.909 0.00 0.00 42.53 1.98
3561 3805 4.002906 TGTGAAAAGCGGTTATCTGAGT 57.997 40.909 0.00 0.00 0.00 3.41
3574 3818 5.419542 GTTATCTGAGTGCATAGGTGTGAA 58.580 41.667 0.00 0.00 0.00 3.18
3585 3829 1.961277 GGTGTGAACTCGGTGGCAG 60.961 63.158 0.00 0.00 0.00 4.85
3719 3963 3.187227 GCTGGGAGCATATAATCACAACG 59.813 47.826 0.00 0.00 41.89 4.10
3808 4055 6.617879 TCGGCATATATATGGTACGCATATC 58.382 40.000 21.50 3.65 34.32 1.63
3838 4099 2.671888 CTCAAGTGACAGTAGCTGCATG 59.328 50.000 4.12 2.24 34.37 4.06
3839 4100 1.129998 CAAGTGACAGTAGCTGCATGC 59.870 52.381 11.82 11.82 43.29 4.06
3938 4201 3.686241 TGCTGAATCTGAAGAATCCAACG 59.314 43.478 0.00 0.00 0.00 4.10
3972 4237 5.044179 ACTGTCCCTTTCATGGAATGGATAA 60.044 40.000 13.31 5.41 46.73 1.75
4020 4286 3.435566 CATTGATCTGCATCACAGCAAC 58.564 45.455 0.00 0.00 46.76 4.17
4045 4313 2.742589 CAAGTTCCCCGCTAGTCTTTTC 59.257 50.000 0.00 0.00 0.00 2.29
4082 4352 6.435430 TCTGTGCATTAATTGTGTCATACC 57.565 37.500 0.00 0.00 0.00 2.73
4340 4617 3.473625 TGGAGAGATGCATGCACTAATG 58.526 45.455 25.37 0.00 0.00 1.90
4382 4659 3.120025 CGAGATATGATCACTCCTGGTCG 60.120 52.174 0.00 0.26 28.79 4.79
4400 4677 2.938798 TGGGGCAGGGGTGTAAGG 60.939 66.667 0.00 0.00 0.00 2.69
4402 4679 2.939353 GGGCAGGGGTGTAAGGGT 60.939 66.667 0.00 0.00 0.00 4.34
4403 4680 1.617233 GGGCAGGGGTGTAAGGGTA 60.617 63.158 0.00 0.00 0.00 3.69
4405 4682 0.912968 GGCAGGGGTGTAAGGGTAGT 60.913 60.000 0.00 0.00 0.00 2.73
4408 4685 0.912968 AGGGGTGTAAGGGTAGTGCC 60.913 60.000 0.00 0.00 0.00 5.01
4409 4686 1.202769 GGGGTGTAAGGGTAGTGCCA 61.203 60.000 0.00 0.00 39.65 4.92
4410 4687 0.694196 GGGTGTAAGGGTAGTGCCAA 59.306 55.000 0.00 0.00 39.65 4.52
4411 4688 1.074244 GGGTGTAAGGGTAGTGCCAAA 59.926 52.381 0.00 0.00 39.65 3.28
4412 4689 2.156917 GGTGTAAGGGTAGTGCCAAAC 58.843 52.381 0.00 0.00 39.65 2.93
4421 4698 2.730094 GTGCCAAACACCAGCTGG 59.270 61.111 31.60 31.60 44.02 4.85
4442 4875 0.252193 TGGGAAGAATTGCTTGGGGG 60.252 55.000 0.00 0.00 36.83 5.40
4458 4891 1.304381 GGGTGCTTGGCCTGAATGA 60.304 57.895 3.32 0.00 0.00 2.57
4496 4929 0.468029 CCTCAAGGCCAAACACCAGT 60.468 55.000 5.01 0.00 0.00 4.00
4512 4945 1.691196 CAGTTGGTTCTGAAGGCCAA 58.309 50.000 5.01 8.04 39.66 4.52
4514 4947 2.629617 CAGTTGGTTCTGAAGGCCAAAT 59.370 45.455 5.01 9.64 42.98 2.32
4517 4950 2.802719 TGGTTCTGAAGGCCAAATACC 58.197 47.619 5.01 5.13 0.00 2.73
4519 4952 2.755103 GGTTCTGAAGGCCAAATACCAG 59.245 50.000 5.01 2.60 0.00 4.00
4520 4953 2.128771 TCTGAAGGCCAAATACCAGC 57.871 50.000 5.01 0.00 0.00 4.85
4521 4954 1.635487 TCTGAAGGCCAAATACCAGCT 59.365 47.619 5.01 0.00 0.00 4.24
4522 4955 2.843730 TCTGAAGGCCAAATACCAGCTA 59.156 45.455 5.01 0.00 0.00 3.32
4523 4956 3.118261 TCTGAAGGCCAAATACCAGCTAG 60.118 47.826 5.01 0.00 0.00 3.42
4524 4957 2.576191 TGAAGGCCAAATACCAGCTAGT 59.424 45.455 5.01 0.00 0.00 2.57
4525 4958 3.010138 TGAAGGCCAAATACCAGCTAGTT 59.990 43.478 5.01 0.00 0.00 2.24
4526 4959 3.283259 AGGCCAAATACCAGCTAGTTC 57.717 47.619 5.01 0.00 0.00 3.01
4527 4960 2.846827 AGGCCAAATACCAGCTAGTTCT 59.153 45.455 5.01 0.00 0.00 3.01
4528 4961 2.945668 GGCCAAATACCAGCTAGTTCTG 59.054 50.000 0.00 0.00 0.00 3.02
4529 4962 3.370527 GGCCAAATACCAGCTAGTTCTGA 60.371 47.826 0.00 0.00 36.19 3.27
4530 4963 4.261801 GCCAAATACCAGCTAGTTCTGAA 58.738 43.478 0.00 0.00 36.19 3.02
4531 4964 4.333926 GCCAAATACCAGCTAGTTCTGAAG 59.666 45.833 0.00 0.00 36.19 3.02
4532 4965 4.878397 CCAAATACCAGCTAGTTCTGAAGG 59.122 45.833 0.00 0.00 36.19 3.46
4533 4966 3.828875 ATACCAGCTAGTTCTGAAGGC 57.171 47.619 0.00 0.00 36.19 4.35
4534 4967 0.615850 ACCAGCTAGTTCTGAAGGCC 59.384 55.000 0.00 0.00 36.19 5.19
4535 4968 0.615331 CCAGCTAGTTCTGAAGGCCA 59.385 55.000 5.01 0.00 36.19 5.36
4536 4969 1.677217 CCAGCTAGTTCTGAAGGCCAC 60.677 57.143 5.01 0.00 36.19 5.01
4537 4970 1.002430 CAGCTAGTTCTGAAGGCCACA 59.998 52.381 5.01 3.66 36.19 4.17
4538 4971 1.912043 AGCTAGTTCTGAAGGCCACAT 59.088 47.619 5.01 0.00 0.00 3.21
4539 4972 3.107601 AGCTAGTTCTGAAGGCCACATA 58.892 45.455 5.01 0.00 0.00 2.29
4540 4973 3.118592 AGCTAGTTCTGAAGGCCACATAC 60.119 47.826 5.01 6.40 0.00 2.39
4541 4974 2.789409 AGTTCTGAAGGCCACATACC 57.211 50.000 5.01 0.00 0.00 2.73
4542 4975 1.985159 AGTTCTGAAGGCCACATACCA 59.015 47.619 5.01 0.00 0.00 3.25
4543 4976 2.375174 AGTTCTGAAGGCCACATACCAA 59.625 45.455 5.01 0.00 0.00 3.67
4544 4977 2.488153 GTTCTGAAGGCCACATACCAAC 59.512 50.000 5.01 2.62 0.00 3.77
4545 4978 1.985159 TCTGAAGGCCACATACCAACT 59.015 47.619 5.01 0.00 0.00 3.16
4546 4979 2.086869 CTGAAGGCCACATACCAACTG 58.913 52.381 5.01 0.00 0.00 3.16
4547 4980 1.271871 TGAAGGCCACATACCAACTGG 60.272 52.381 5.01 0.00 42.17 4.00
4548 4981 1.004277 GAAGGCCACATACCAACTGGA 59.996 52.381 5.01 0.00 38.94 3.86
4549 4982 1.072266 AGGCCACATACCAACTGGAA 58.928 50.000 5.01 0.00 38.94 3.53
4550 4983 1.427368 AGGCCACATACCAACTGGAAA 59.573 47.619 5.01 0.00 38.94 3.13
4551 4984 2.158385 AGGCCACATACCAACTGGAAAA 60.158 45.455 5.01 0.00 38.94 2.29
4552 4985 2.831526 GGCCACATACCAACTGGAAAAT 59.168 45.455 1.86 0.00 38.94 1.82
4553 4986 3.368323 GGCCACATACCAACTGGAAAATG 60.368 47.826 1.86 5.96 38.94 2.32
4554 4987 3.258123 GCCACATACCAACTGGAAAATGT 59.742 43.478 1.86 6.54 37.20 2.71
4591 5024 7.913297 GCTTCTAGTACTCTTATCTGTGTCTTG 59.087 40.741 0.00 0.00 0.00 3.02
4595 5028 7.768807 AGTACTCTTATCTGTGTCTTGTTCT 57.231 36.000 0.00 0.00 0.00 3.01
4601 5034 7.279615 TCTTATCTGTGTCTTGTTCTGGAAAA 58.720 34.615 0.00 0.00 0.00 2.29
4607 5040 7.773224 TCTGTGTCTTGTTCTGGAAAAGAATTA 59.227 33.333 0.00 0.00 46.53 1.40
4611 5044 9.793259 TGTCTTGTTCTGGAAAAGAATTATAGT 57.207 29.630 0.00 0.00 46.53 2.12
4619 5052 9.231297 TCTGGAAAAGAATTATAGTTCTTGGTG 57.769 33.333 20.23 11.24 45.18 4.17
4652 5085 4.193090 TCACCACGTGTGTTAATTTCACT 58.807 39.130 15.65 0.00 45.61 3.41
4656 5089 5.124138 ACCACGTGTGTTAATTTCACTTGAA 59.876 36.000 15.65 0.00 34.71 2.69
4723 5172 7.652105 GGTGTTAAAACCATTCTTTTCTTCCTC 59.348 37.037 10.17 0.00 40.22 3.71
4733 5182 7.121315 CCATTCTTTTCTTCCTCTTCCGTTTAT 59.879 37.037 0.00 0.00 0.00 1.40
4739 5188 6.150396 TCTTCCTCTTCCGTTTATCTCATC 57.850 41.667 0.00 0.00 0.00 2.92
4744 5193 5.751028 CCTCTTCCGTTTATCTCATCTCAAC 59.249 44.000 0.00 0.00 0.00 3.18
4745 5194 6.280855 TCTTCCGTTTATCTCATCTCAACA 57.719 37.500 0.00 0.00 0.00 3.33
4746 5195 6.878317 TCTTCCGTTTATCTCATCTCAACAT 58.122 36.000 0.00 0.00 0.00 2.71
4747 5196 6.758416 TCTTCCGTTTATCTCATCTCAACATG 59.242 38.462 0.00 0.00 0.00 3.21
4748 5197 5.359756 TCCGTTTATCTCATCTCAACATGG 58.640 41.667 0.00 0.00 0.00 3.66
4749 5198 5.128663 TCCGTTTATCTCATCTCAACATGGA 59.871 40.000 0.00 0.00 0.00 3.41
4750 5199 5.817296 CCGTTTATCTCATCTCAACATGGAA 59.183 40.000 0.00 0.00 0.00 3.53
4764 5217 5.190330 TCAACATGGAAGAGATGAAGATGGA 59.810 40.000 0.00 0.00 0.00 3.41
4765 5218 5.033589 ACATGGAAGAGATGAAGATGGAC 57.966 43.478 0.00 0.00 0.00 4.02
4766 5219 3.808466 TGGAAGAGATGAAGATGGACG 57.192 47.619 0.00 0.00 0.00 4.79
4767 5220 3.365472 TGGAAGAGATGAAGATGGACGA 58.635 45.455 0.00 0.00 0.00 4.20
4768 5221 3.963374 TGGAAGAGATGAAGATGGACGAT 59.037 43.478 0.00 0.00 0.00 3.73
4769 5222 4.202192 TGGAAGAGATGAAGATGGACGATG 60.202 45.833 0.00 0.00 0.00 3.84
4770 5223 3.383620 AGAGATGAAGATGGACGATGC 57.616 47.619 0.00 0.00 0.00 3.91
4771 5224 2.057316 GAGATGAAGATGGACGATGCG 58.943 52.381 0.00 0.00 0.00 4.73
4772 5225 1.410517 AGATGAAGATGGACGATGCGT 59.589 47.619 0.00 0.00 45.10 5.24
4773 5226 2.623416 AGATGAAGATGGACGATGCGTA 59.377 45.455 0.00 0.00 41.37 4.42
4774 5227 3.256879 AGATGAAGATGGACGATGCGTAT 59.743 43.478 0.00 0.00 41.37 3.06
4775 5228 3.452755 TGAAGATGGACGATGCGTATT 57.547 42.857 0.00 0.00 41.37 1.89
4776 5229 3.792401 TGAAGATGGACGATGCGTATTT 58.208 40.909 0.00 0.00 41.37 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.049186 CTGGTTGACGGTATTTATCCTCG 58.951 47.826 0.00 0.00 0.00 4.63
11 12 4.647853 TGCTACTATCTGGTTGACGGTATT 59.352 41.667 0.00 0.00 0.00 1.89
55 56 5.567823 GCTCCTCTTTGCCACTATACTATCC 60.568 48.000 0.00 0.00 0.00 2.59
91 92 2.250939 TCGTTGTTTGCGAGGCTGG 61.251 57.895 0.00 0.00 34.11 4.85
144 146 2.585330 TGCTTTCTTTGGCATGTCTGA 58.415 42.857 0.00 0.00 33.23 3.27
181 187 3.189910 TCTTGAAGCACTTGCATCACATC 59.810 43.478 8.58 0.00 46.58 3.06
193 200 2.165030 CCCACCATCATTCTTGAAGCAC 59.835 50.000 0.00 0.00 34.96 4.40
228 235 6.314120 AGGCTTTACATGGGCAATATTATGA 58.686 36.000 0.00 0.00 0.00 2.15
232 239 4.037923 CGAAGGCTTTACATGGGCAATATT 59.962 41.667 0.00 0.00 0.00 1.28
293 300 2.523902 TGGCCAGGTTTGCTTGGG 60.524 61.111 0.00 0.00 41.64 4.12
354 361 5.539048 TCAGTACTTAAGAGAACCAACTGC 58.461 41.667 10.09 0.00 34.51 4.40
386 393 1.739371 GCAACTACCATGGTCGAGGTC 60.739 57.143 23.76 3.68 39.31 3.85
410 417 1.141657 TGAGGAGATGCCATGGTTAGC 59.858 52.381 14.67 5.93 40.02 3.09
413 420 1.567649 ACATGAGGAGATGCCATGGTT 59.432 47.619 14.67 0.59 41.28 3.67
428 435 2.695147 ACGGATGTATGAGAGCACATGA 59.305 45.455 0.00 0.00 35.55 3.07
485 492 2.203266 GCACTAGGGATGCCTGCC 60.203 66.667 17.38 0.00 37.08 4.85
489 496 4.937431 GGCCGCACTAGGGATGCC 62.937 72.222 9.18 9.18 40.09 4.40
518 525 5.136105 GGAATGATTGGCTTCTCTGGTTAT 58.864 41.667 0.00 0.00 0.00 1.89
537 544 1.352352 CCTGAAGGACACTGTGGGAAT 59.648 52.381 13.09 0.00 37.39 3.01
643 655 1.817099 CCCTGATGCACTCTTCGCC 60.817 63.158 0.00 0.00 0.00 5.54
708 721 1.367840 GGTCACCGAGTGCTCAACT 59.632 57.895 0.00 0.00 43.85 3.16
721 734 1.153349 GGGCTCGATCAAGGGTCAC 60.153 63.158 0.00 0.00 0.00 3.67
812 825 1.067212 GGCTCATCGGACGACATACTT 59.933 52.381 0.00 0.00 0.00 2.24
817 831 3.060000 ACGGCTCATCGGACGACA 61.060 61.111 0.00 0.00 40.66 4.35
818 832 2.579787 CACGGCTCATCGGACGAC 60.580 66.667 0.00 0.00 40.66 4.34
835 855 2.576615 GGCAGTATGTTGATTCCTCCC 58.423 52.381 0.00 0.00 39.31 4.30
842 862 5.483685 ACATATACGGGCAGTATGTTGAT 57.516 39.130 18.70 3.20 45.10 2.57
874 894 5.324409 TCTTGTTTGTAGCAATGGATTCCT 58.676 37.500 3.95 0.00 0.00 3.36
902 922 1.701704 CCGGAGCTGAAAACAATTGC 58.298 50.000 5.05 0.00 0.00 3.56
1048 1068 2.830923 CCCCTGCCAAAAATATGTGTCA 59.169 45.455 0.00 0.00 0.00 3.58
1099 1121 1.224075 TTCTCTCTTGTCGTCGTCGT 58.776 50.000 1.33 0.00 38.33 4.34
1162 1187 1.110518 GCCGACCAAAAACCCTTCCA 61.111 55.000 0.00 0.00 0.00 3.53
1213 1238 2.032681 AGCTTTGTGGGAGTCCGC 59.967 61.111 2.26 0.00 43.64 5.54
1228 1253 1.248486 GAAGACAAAAGTGGGGGAGC 58.752 55.000 0.00 0.00 0.00 4.70
1256 1282 1.218316 GTCCGGACGCCATTTCTCT 59.782 57.895 20.85 0.00 0.00 3.10
1288 1314 2.569853 TCCATCCAACACGGTCTGTATT 59.430 45.455 0.00 0.00 35.57 1.89
1336 1363 5.288804 ACATGTAAAGCTTTCGCAATTGTT 58.711 33.333 16.57 0.00 39.10 2.83
1346 1373 3.502211 CCAAGACGGACATGTAAAGCTTT 59.498 43.478 17.30 17.30 36.56 3.51
1350 1377 4.188247 TCTCCAAGACGGACATGTAAAG 57.812 45.455 0.00 0.00 39.64 1.85
1356 1383 0.179000 GGCATCTCCAAGACGGACAT 59.821 55.000 0.00 0.00 39.64 3.06
1357 1384 0.904865 AGGCATCTCCAAGACGGACA 60.905 55.000 0.00 0.00 39.64 4.02
1414 1441 2.123589 TCAAGAAGACACTTGTCCCCA 58.876 47.619 5.73 0.00 45.85 4.96
1431 1458 5.726560 TCCAATATAGAGGATGGAGGTCAA 58.273 41.667 0.00 0.00 37.05 3.18
1462 1489 8.557864 CGTAGATGCTACTTACTACTACAACAT 58.442 37.037 0.00 0.00 34.81 2.71
1478 1505 5.451937 CCCAACTGAATCTTCGTAGATGCTA 60.452 44.000 10.98 0.00 40.26 3.49
1486 1513 1.339151 GGAGCCCAACTGAATCTTCGT 60.339 52.381 0.00 0.00 0.00 3.85
1487 1514 1.373570 GGAGCCCAACTGAATCTTCG 58.626 55.000 0.00 0.00 0.00 3.79
1491 1518 1.026718 CACCGGAGCCCAACTGAATC 61.027 60.000 9.46 0.00 0.00 2.52
1521 1548 9.947669 TTCAAAATTTAATTTTTCACATGCAGG 57.052 25.926 12.36 0.00 40.27 4.85
1602 1629 2.135139 GCCCAAAACTTTGCAGTTAGC 58.865 47.619 0.00 0.00 42.89 3.09
1606 1633 2.355197 GTTTGCCCAAAACTTTGCAGT 58.645 42.857 0.00 0.00 44.10 4.40
1619 1646 6.610741 TCAAAATGTTTAACATGTTTGCCC 57.389 33.333 24.07 3.54 37.97 5.36
1640 1667 8.203485 AGTTCAAATTTGCCTTTTTACAGATCA 58.797 29.630 13.54 0.00 0.00 2.92
1643 1670 7.781056 AGAGTTCAAATTTGCCTTTTTACAGA 58.219 30.769 13.54 0.00 0.00 3.41
1646 1673 8.419076 TTGAGAGTTCAAATTTGCCTTTTTAC 57.581 30.769 13.54 3.19 40.26 2.01
1653 1681 6.366061 GGTAACATTGAGAGTTCAAATTTGCC 59.634 38.462 13.54 6.45 45.82 4.52
1654 1682 6.366061 GGGTAACATTGAGAGTTCAAATTTGC 59.634 38.462 13.54 0.46 45.82 3.68
1655 1683 7.661040 AGGGTAACATTGAGAGTTCAAATTTG 58.339 34.615 12.15 12.15 45.82 2.32
1740 1770 4.409718 TGTTTGTGGTAGTGTAGCAAGA 57.590 40.909 0.00 0.00 37.99 3.02
1741 1771 4.154195 GGATGTTTGTGGTAGTGTAGCAAG 59.846 45.833 0.00 0.00 37.99 4.01
1746 1776 4.691326 TGTGGATGTTTGTGGTAGTGTA 57.309 40.909 0.00 0.00 0.00 2.90
1785 1818 7.947890 ACTCCTGGAAAAGTGGTCAAATATTTA 59.052 33.333 0.00 0.00 0.00 1.40
1811 1861 2.559231 GTTTTGGCTCCGGGAACATTTA 59.441 45.455 0.00 0.00 0.00 1.40
1817 1867 2.981350 GCGTTTTGGCTCCGGGAA 60.981 61.111 0.00 0.00 0.00 3.97
1822 1872 4.103103 GAGCGGCGTTTTGGCTCC 62.103 66.667 9.37 0.00 45.67 4.70
1842 1892 2.420547 CCTGGTTAGCTGCAGATGCTAA 60.421 50.000 20.43 16.12 46.68 3.09
1863 1913 1.630244 GCGATGTGGTCTCTGTGCAC 61.630 60.000 10.75 10.75 0.00 4.57
1864 1914 1.374631 GCGATGTGGTCTCTGTGCA 60.375 57.895 0.00 0.00 0.00 4.57
1865 1915 2.447887 CGCGATGTGGTCTCTGTGC 61.448 63.158 0.00 0.00 0.00 4.57
1866 1916 2.447887 GCGCGATGTGGTCTCTGTG 61.448 63.158 12.10 0.00 0.00 3.66
1867 1917 2.125912 GCGCGATGTGGTCTCTGT 60.126 61.111 12.10 0.00 0.00 3.41
1868 1918 2.887568 GGCGCGATGTGGTCTCTG 60.888 66.667 12.10 0.00 0.00 3.35
1913 1965 0.883370 AGGGTTGTTCTTCGCGTTCC 60.883 55.000 5.77 0.00 0.00 3.62
1920 1972 7.739498 TTACATAAACTCAGGGTTGTTCTTC 57.261 36.000 0.00 0.00 38.29 2.87
1987 2039 9.748708 TGACTGATTTTCTTTTATCACCAAAAG 57.251 29.630 2.62 2.62 43.73 2.27
2026 2078 8.370182 CCCCCTAGAATTTTCATTTATGGAATG 58.630 37.037 0.00 0.00 45.31 2.67
2038 2090 6.779860 TGTGCTATATCCCCCTAGAATTTTC 58.220 40.000 0.00 0.00 0.00 2.29
2039 2091 6.780198 TGTGCTATATCCCCCTAGAATTTT 57.220 37.500 0.00 0.00 0.00 1.82
2090 2142 8.647143 AAATCGAGCTGAATTTTCAAGAAAAA 57.353 26.923 11.53 0.00 42.71 1.94
2095 2147 7.301054 AGTGTAAATCGAGCTGAATTTTCAAG 58.699 34.615 7.90 0.00 36.64 3.02
2121 2180 9.613428 CATCGCTCAGGGGATATTATTTTATTA 57.387 33.333 0.00 0.00 42.11 0.98
2151 2210 2.095567 CAGTCCACGAAATGCAAAGGAG 60.096 50.000 0.00 0.00 0.00 3.69
2152 2211 1.879380 CAGTCCACGAAATGCAAAGGA 59.121 47.619 0.00 0.00 0.00 3.36
2153 2212 1.879380 TCAGTCCACGAAATGCAAAGG 59.121 47.619 0.00 0.00 0.00 3.11
2154 2213 2.095567 CCTCAGTCCACGAAATGCAAAG 60.096 50.000 0.00 0.00 0.00 2.77
2161 2220 1.415672 AAGGCCCTCAGTCCACGAAA 61.416 55.000 0.00 0.00 0.00 3.46
2194 2253 4.567159 GGGTTAACAACAAACAATTCGCAA 59.433 37.500 8.10 0.00 0.00 4.85
2197 2256 5.627780 GCTAGGGTTAACAACAAACAATTCG 59.372 40.000 8.10 0.00 0.00 3.34
2198 2257 6.640907 CAGCTAGGGTTAACAACAAACAATTC 59.359 38.462 8.10 0.00 0.00 2.17
2199 2258 6.097696 ACAGCTAGGGTTAACAACAAACAATT 59.902 34.615 8.10 0.00 0.00 2.32
2201 2260 4.951094 ACAGCTAGGGTTAACAACAAACAA 59.049 37.500 8.10 0.00 0.00 2.83
2203 2262 5.180680 CCTACAGCTAGGGTTAACAACAAAC 59.819 44.000 8.10 0.00 36.56 2.93
2204 2263 5.310451 CCTACAGCTAGGGTTAACAACAAA 58.690 41.667 8.10 0.00 36.56 2.83
2310 2380 2.697425 CGCCGCAAGAAGATGACG 59.303 61.111 0.00 0.00 43.02 4.35
2311 2381 3.093278 CCGCCGCAAGAAGATGAC 58.907 61.111 0.00 0.00 43.02 3.06
2312 2382 2.819595 GCCGCCGCAAGAAGATGA 60.820 61.111 0.00 0.00 43.02 2.92
2313 2383 4.228097 CGCCGCCGCAAGAAGATG 62.228 66.667 0.00 0.00 43.02 2.90
2314 2384 4.451150 TCGCCGCCGCAAGAAGAT 62.451 61.111 0.00 0.00 43.02 2.40
2317 2387 4.980805 AAGTCGCCGCCGCAAGAA 62.981 61.111 0.00 0.00 43.02 2.52
2360 2430 1.303643 GAGGGGCAAACCTGGTCAG 60.304 63.158 0.00 0.00 42.10 3.51
2372 2442 3.622060 TTTGCGGTAGCTGAGGGGC 62.622 63.158 0.00 0.00 45.42 5.80
2383 2453 2.840974 CGGAATGAGAGTTTGCGGT 58.159 52.632 0.00 0.00 34.75 5.68
2430 2501 2.353839 CAACAGTTGCTGTGCCGC 60.354 61.111 0.00 0.00 44.62 6.53
2431 2502 1.280746 CTCAACAGTTGCTGTGCCG 59.719 57.895 8.58 0.00 44.62 5.69
2433 2504 1.369689 CGCTCAACAGTTGCTGTGC 60.370 57.895 8.58 8.88 44.62 4.57
2434 2505 1.280746 CCGCTCAACAGTTGCTGTG 59.719 57.895 8.58 9.91 44.62 3.66
2436 2507 2.253452 GCCGCTCAACAGTTGCTG 59.747 61.111 8.58 5.22 37.52 4.41
2437 2508 3.349006 CGCCGCTCAACAGTTGCT 61.349 61.111 8.58 0.00 0.00 3.91
2438 2509 4.389576 CCGCCGCTCAACAGTTGC 62.390 66.667 8.58 0.00 0.00 4.17
2439 2510 4.389576 GCCGCCGCTCAACAGTTG 62.390 66.667 6.99 6.99 0.00 3.16
2440 2511 4.927782 TGCCGCCGCTCAACAGTT 62.928 61.111 0.00 0.00 35.36 3.16
2441 2512 4.927782 TTGCCGCCGCTCAACAGT 62.928 61.111 0.00 0.00 35.36 3.55
2442 2513 3.386867 GATTGCCGCCGCTCAACAG 62.387 63.158 0.00 0.00 35.36 3.16
2443 2514 3.430862 GATTGCCGCCGCTCAACA 61.431 61.111 0.00 0.00 35.36 3.33
2468 2561 2.004408 GATCAATGGGCTGAGGGGCT 62.004 60.000 0.00 0.00 40.65 5.19
2496 2589 4.929808 TCACGCTCCTAAATTTCAGAGTTC 59.070 41.667 15.21 3.49 0.00 3.01
2523 2619 6.915300 CACCGAAAATCTATCTACTCAGTCAG 59.085 42.308 0.00 0.00 0.00 3.51
2822 2926 6.149807 CGGAGTCATAGAGAAGGGTTAGATAC 59.850 46.154 0.00 0.00 0.00 2.24
3293 3498 3.068024 TGAACACTTTTGCTTCCATGTCC 59.932 43.478 0.00 0.00 0.00 4.02
3423 3643 6.511444 GCTTCTGACATTTCATCATCTACAGC 60.511 42.308 0.00 0.00 0.00 4.40
3424 3644 6.762187 AGCTTCTGACATTTCATCATCTACAG 59.238 38.462 0.00 0.00 0.00 2.74
3425 3645 6.537660 CAGCTTCTGACATTTCATCATCTACA 59.462 38.462 0.00 0.00 32.44 2.74
3426 3646 6.538021 ACAGCTTCTGACATTTCATCATCTAC 59.462 38.462 0.29 0.00 35.18 2.59
3427 3647 6.537660 CACAGCTTCTGACATTTCATCATCTA 59.462 38.462 0.29 0.00 35.18 1.98
3431 3651 3.754850 CCACAGCTTCTGACATTTCATCA 59.245 43.478 0.29 0.00 35.18 3.07
3561 3805 0.973632 ACCGAGTTCACACCTATGCA 59.026 50.000 0.00 0.00 0.00 3.96
3585 3829 1.451028 CAGCTAGAGCAAGGGTGGC 60.451 63.158 4.01 0.00 45.16 5.01
3692 3936 3.395607 TGATTATATGCTCCCAGCCACTT 59.604 43.478 0.00 0.00 41.51 3.16
3719 3963 3.444388 ACTCGTTCAGAACAGAGGGATAC 59.556 47.826 25.63 0.00 36.80 2.24
3767 4011 0.109873 CGAGTGAGCGTTACTTCCGT 60.110 55.000 0.00 0.00 0.00 4.69
3808 4055 2.900546 ACTGTCACTTGAGGTCTAAGGG 59.099 50.000 0.00 0.00 0.00 3.95
3838 4099 2.838736 TCGCTCTAGAAAATCCCATGC 58.161 47.619 0.00 0.00 0.00 4.06
3839 4100 3.750130 CCATCGCTCTAGAAAATCCCATG 59.250 47.826 0.00 0.00 0.00 3.66
4020 4286 2.047655 TAGCGGGGAACTTGCACG 60.048 61.111 0.00 0.00 34.73 5.34
4045 4313 3.702330 TGCACAGAAATATACGAGGACG 58.298 45.455 0.00 0.00 45.75 4.79
4082 4352 6.363357 GGCTACTAGAAAAACAACAAATGCAG 59.637 38.462 0.00 0.00 0.00 4.41
4297 4571 2.114616 TGCTTTGCTTCCCCTGAAAAA 58.885 42.857 0.00 0.00 0.00 1.94
4346 4623 1.387295 ATCTCGTCGCAGCATCTCCA 61.387 55.000 0.00 0.00 0.00 3.86
4357 4634 3.120025 CCAGGAGTGATCATATCTCGTCG 60.120 52.174 0.00 0.00 0.00 5.12
4382 4659 2.355115 CTTACACCCCTGCCCCAC 59.645 66.667 0.00 0.00 0.00 4.61
4400 4677 0.537371 AGCTGGTGTTTGGCACTACC 60.537 55.000 6.96 6.96 46.86 3.18
4402 4679 0.537143 CCAGCTGGTGTTTGGCACTA 60.537 55.000 25.53 0.00 46.86 2.74
4403 4680 1.829533 CCAGCTGGTGTTTGGCACT 60.830 57.895 25.53 0.00 46.86 4.40
4414 4691 1.547372 CAATTCTTCCCAACCAGCTGG 59.453 52.381 31.60 31.60 42.17 4.85
4415 4692 1.067354 GCAATTCTTCCCAACCAGCTG 60.067 52.381 6.78 6.78 0.00 4.24
4416 4693 1.203100 AGCAATTCTTCCCAACCAGCT 60.203 47.619 0.00 0.00 0.00 4.24
4417 4694 1.260544 AGCAATTCTTCCCAACCAGC 58.739 50.000 0.00 0.00 0.00 4.85
4418 4695 2.028748 CCAAGCAATTCTTCCCAACCAG 60.029 50.000 0.00 0.00 31.27 4.00
4420 4697 1.276138 CCCAAGCAATTCTTCCCAACC 59.724 52.381 0.00 0.00 31.27 3.77
4421 4698 1.276138 CCCCAAGCAATTCTTCCCAAC 59.724 52.381 0.00 0.00 31.27 3.77
4422 4699 1.643310 CCCCAAGCAATTCTTCCCAA 58.357 50.000 0.00 0.00 31.27 4.12
4423 4700 0.252193 CCCCCAAGCAATTCTTCCCA 60.252 55.000 0.00 0.00 31.27 4.37
4424 4701 0.252239 ACCCCCAAGCAATTCTTCCC 60.252 55.000 0.00 0.00 31.27 3.97
4426 4703 0.247460 GCACCCCCAAGCAATTCTTC 59.753 55.000 0.00 0.00 31.27 2.87
4427 4704 0.178924 AGCACCCCCAAGCAATTCTT 60.179 50.000 0.00 0.00 34.78 2.52
4442 4875 1.503542 CGTCATTCAGGCCAAGCAC 59.496 57.895 5.01 0.00 0.00 4.40
4496 4929 3.161866 GGTATTTGGCCTTCAGAACCAA 58.838 45.455 3.32 1.80 41.61 3.67
4508 4941 3.873910 TCAGAACTAGCTGGTATTTGGC 58.126 45.455 1.97 0.00 36.55 4.52
4512 4945 3.118223 GGCCTTCAGAACTAGCTGGTATT 60.118 47.826 1.97 0.00 36.55 1.89
4514 4947 1.831736 GGCCTTCAGAACTAGCTGGTA 59.168 52.381 1.97 0.00 36.55 3.25
4517 4950 1.002430 TGTGGCCTTCAGAACTAGCTG 59.998 52.381 3.32 0.00 37.24 4.24
4519 4952 2.409948 ATGTGGCCTTCAGAACTAGC 57.590 50.000 3.32 0.00 0.00 3.42
4520 4953 3.197766 TGGTATGTGGCCTTCAGAACTAG 59.802 47.826 3.32 0.00 0.00 2.57
4521 4954 3.178046 TGGTATGTGGCCTTCAGAACTA 58.822 45.455 3.32 2.01 0.00 2.24
4522 4955 1.985159 TGGTATGTGGCCTTCAGAACT 59.015 47.619 3.32 0.00 0.00 3.01
4523 4956 2.488153 GTTGGTATGTGGCCTTCAGAAC 59.512 50.000 3.32 4.16 0.00 3.01
4524 4957 2.375174 AGTTGGTATGTGGCCTTCAGAA 59.625 45.455 3.32 0.00 0.00 3.02
4525 4958 1.985159 AGTTGGTATGTGGCCTTCAGA 59.015 47.619 3.32 0.00 0.00 3.27
4526 4959 2.086869 CAGTTGGTATGTGGCCTTCAG 58.913 52.381 3.32 0.00 0.00 3.02
4527 4960 1.271871 CCAGTTGGTATGTGGCCTTCA 60.272 52.381 3.32 3.67 0.00 3.02
4528 4961 1.004277 TCCAGTTGGTATGTGGCCTTC 59.996 52.381 3.32 0.00 36.34 3.46
4529 4962 1.072266 TCCAGTTGGTATGTGGCCTT 58.928 50.000 3.32 0.00 36.34 4.35
4530 4963 1.072266 TTCCAGTTGGTATGTGGCCT 58.928 50.000 3.32 0.00 36.34 5.19
4531 4964 1.917872 TTTCCAGTTGGTATGTGGCC 58.082 50.000 0.00 0.00 36.34 5.36
4532 4965 3.258123 ACATTTTCCAGTTGGTATGTGGC 59.742 43.478 12.20 0.00 34.31 5.01
4533 4966 5.710099 AGTACATTTTCCAGTTGGTATGTGG 59.290 40.000 17.93 0.00 35.80 4.17
4534 4967 6.349280 CCAGTACATTTTCCAGTTGGTATGTG 60.349 42.308 17.93 9.18 35.80 3.21
4535 4968 5.710099 CCAGTACATTTTCCAGTTGGTATGT 59.290 40.000 15.23 15.23 37.00 2.29
4536 4969 5.943416 TCCAGTACATTTTCCAGTTGGTATG 59.057 40.000 0.00 4.15 36.34 2.39
4537 4970 6.134535 TCCAGTACATTTTCCAGTTGGTAT 57.865 37.500 0.00 0.00 36.34 2.73
4538 4971 5.570205 TCCAGTACATTTTCCAGTTGGTA 57.430 39.130 0.00 0.00 36.34 3.25
4539 4972 4.447138 TCCAGTACATTTTCCAGTTGGT 57.553 40.909 0.00 0.00 36.34 3.67
4540 4973 5.782893 TTTCCAGTACATTTTCCAGTTGG 57.217 39.130 0.00 0.00 0.00 3.77
4541 4974 6.146021 GCATTTTCCAGTACATTTTCCAGTTG 59.854 38.462 0.00 0.00 0.00 3.16
4542 4975 6.041979 AGCATTTTCCAGTACATTTTCCAGTT 59.958 34.615 0.00 0.00 0.00 3.16
4543 4976 5.539955 AGCATTTTCCAGTACATTTTCCAGT 59.460 36.000 0.00 0.00 0.00 4.00
4544 4977 6.029346 AGCATTTTCCAGTACATTTTCCAG 57.971 37.500 0.00 0.00 0.00 3.86
4545 4978 6.267471 AGAAGCATTTTCCAGTACATTTTCCA 59.733 34.615 0.00 0.00 0.00 3.53
4546 4979 6.691508 AGAAGCATTTTCCAGTACATTTTCC 58.308 36.000 0.00 0.00 0.00 3.13
4547 4980 8.515414 ACTAGAAGCATTTTCCAGTACATTTTC 58.485 33.333 0.00 0.00 0.00 2.29
4548 4981 8.409358 ACTAGAAGCATTTTCCAGTACATTTT 57.591 30.769 0.00 0.00 0.00 1.82
4549 4982 8.947115 GTACTAGAAGCATTTTCCAGTACATTT 58.053 33.333 15.73 0.00 37.74 2.32
4550 4983 8.322091 AGTACTAGAAGCATTTTCCAGTACATT 58.678 33.333 19.93 5.54 39.39 2.71
4551 4984 7.852263 AGTACTAGAAGCATTTTCCAGTACAT 58.148 34.615 19.93 8.73 39.39 2.29
4552 4985 7.178628 AGAGTACTAGAAGCATTTTCCAGTACA 59.821 37.037 19.93 0.00 39.39 2.90
4553 4986 7.548967 AGAGTACTAGAAGCATTTTCCAGTAC 58.451 38.462 13.91 13.91 37.97 2.73
4554 4987 7.719871 AGAGTACTAGAAGCATTTTCCAGTA 57.280 36.000 0.00 0.00 0.00 2.74
4577 5010 7.442364 TCTTTTCCAGAACAAGACACAGATAAG 59.558 37.037 2.77 0.00 0.00 1.73
4595 5028 9.581289 TTCACCAAGAACTATAATTCTTTTCCA 57.419 29.630 6.45 0.00 44.74 3.53
4665 5098 8.799367 GGGTCAGTACATACATACATACATACA 58.201 37.037 0.00 0.00 0.00 2.29
4666 5099 8.799367 TGGGTCAGTACATACATACATACATAC 58.201 37.037 0.00 0.00 0.00 2.39
4667 5100 8.799367 GTGGGTCAGTACATACATACATACATA 58.201 37.037 0.00 0.00 0.00 2.29
4668 5101 7.509318 AGTGGGTCAGTACATACATACATACAT 59.491 37.037 0.00 0.00 0.00 2.29
4669 5102 6.837048 AGTGGGTCAGTACATACATACATACA 59.163 38.462 0.00 0.00 0.00 2.29
4670 5103 7.013942 TGAGTGGGTCAGTACATACATACATAC 59.986 40.741 0.00 0.00 0.00 2.39
4723 5172 6.018425 CCATGTTGAGATGAGATAAACGGAAG 60.018 42.308 0.00 0.00 0.00 3.46
4739 5188 5.527951 CCATCTTCATCTCTTCCATGTTGAG 59.472 44.000 0.00 0.00 0.00 3.02
4744 5193 4.056740 CGTCCATCTTCATCTCTTCCATG 58.943 47.826 0.00 0.00 0.00 3.66
4745 5194 3.963374 TCGTCCATCTTCATCTCTTCCAT 59.037 43.478 0.00 0.00 0.00 3.41
4746 5195 3.365472 TCGTCCATCTTCATCTCTTCCA 58.635 45.455 0.00 0.00 0.00 3.53
4747 5196 4.305769 CATCGTCCATCTTCATCTCTTCC 58.694 47.826 0.00 0.00 0.00 3.46
4748 5197 3.740321 GCATCGTCCATCTTCATCTCTTC 59.260 47.826 0.00 0.00 0.00 2.87
4749 5198 3.726607 GCATCGTCCATCTTCATCTCTT 58.273 45.455 0.00 0.00 0.00 2.85
4750 5199 2.288091 CGCATCGTCCATCTTCATCTCT 60.288 50.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.