Multiple sequence alignment - TraesCS2B01G226100

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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 TraesCS2B01G226100 chr2B 100.000 3983 0 0 1 3983 216938112 216942094 0.000000e+00 7356
1 TraesCS2B01G226100 chr2B 95.213 188 9 0 1292 1479 24866220 24866033 8.370000e-77 298
2 TraesCS2B01G226100 chr2D 91.927 1796 82 25 2225 3983 159850666 159852435 0.000000e+00 2455
3 TraesCS2B01G226100 chr2D 94.221 571 16 7 736 1293 159849144 159849710 0.000000e+00 856
4 TraesCS2B01G226100 chr2D 92.416 567 30 6 1496 2050 159849722 159850287 0.000000e+00 797
5 TraesCS2B01G226100 chr2D 85.908 738 83 13 1 728 159823642 159824368 0.000000e+00 767
6 TraesCS2B01G226100 chr2D 78.695 521 85 17 226 728 56296972 56296460 1.380000e-84 324
7 TraesCS2B01G226100 chr2D 93.182 176 9 1 2048 2223 159850448 159850620 5.110000e-64 255
8 TraesCS2B01G226100 chr2A 90.757 1677 106 30 1692 3345 171077523 171079173 0.000000e+00 2193
9 TraesCS2B01G226100 chr2A 92.326 821 51 8 3170 3983 171079089 171079904 0.000000e+00 1157
10 TraesCS2B01G226100 chr2A 87.752 694 68 11 1 682 171076120 171076808 0.000000e+00 795
11 TraesCS2B01G226100 chr2A 92.543 523 22 7 782 1293 171076843 171077359 0.000000e+00 734
12 TraesCS2B01G226100 chr2A 82.387 511 68 16 226 728 720375623 720375127 3.680000e-115 425
13 TraesCS2B01G226100 chr2A 95.187 187 9 0 1293 1479 640918834 640918648 3.010000e-76 296
14 TraesCS2B01G226100 chr2A 93.750 192 12 0 1288 1479 587740017 587739826 5.040000e-74 289
15 TraesCS2B01G226100 chr2A 85.380 171 14 3 1486 1647 171077354 171077522 2.460000e-37 167
16 TraesCS2B01G226100 chr4D 84.024 507 72 7 229 730 7915089 7915591 2.780000e-131 479
17 TraesCS2B01G226100 chr7D 81.797 434 62 6 226 645 113175204 113174774 8.190000e-92 348
18 TraesCS2B01G226100 chr6D 79.070 516 84 16 231 728 382343674 382344183 2.290000e-87 333
19 TraesCS2B01G226100 chr6D 75.591 508 88 28 234 728 8344234 8343750 6.700000e-53 219
20 TraesCS2B01G226100 chr1A 77.820 532 97 15 226 742 556085993 556086518 3.870000e-80 309
21 TraesCS2B01G226100 chr1A 94.681 188 10 0 1292 1479 499932277 499932464 3.890000e-75 292
22 TraesCS2B01G226100 chr7A 94.681 188 10 0 1292 1479 198415635 198415448 3.890000e-75 292
23 TraesCS2B01G226100 chr7A 94.149 188 11 0 1292 1479 605841955 605842142 1.810000e-73 287
24 TraesCS2B01G226100 chr7A 76.103 544 100 20 219 742 694104233 694104766 1.420000e-64 257
25 TraesCS2B01G226100 chr4B 94.681 188 10 0 1292 1479 617384527 617384340 3.890000e-75 292
26 TraesCS2B01G226100 chr4B 76.578 491 89 18 245 728 622120712 622121183 3.070000e-61 246
27 TraesCS2B01G226100 chr3A 94.681 188 10 0 1292 1479 12743531 12743718 3.890000e-75 292
28 TraesCS2B01G226100 chr6A 93.333 195 12 1 1286 1479 584038436 584038630 1.810000e-73 287
29 TraesCS2B01G226100 chr5D 79.215 433 74 12 230 650 249996948 249997376 1.810000e-73 287
30 TraesCS2B01G226100 chr6B 77.108 498 90 16 241 730 478880757 478881238 2.360000e-67 267
31 TraesCS2B01G226100 chr5B 75.498 502 96 19 248 742 216404972 216404491 1.860000e-53 220


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 TraesCS2B01G226100 chr2B 216938112 216942094 3982 False 7356.00 7356 100.0000 1 3983 1 chr2B.!!$F1 3982
1 TraesCS2B01G226100 chr2D 159849144 159852435 3291 False 1090.75 2455 92.9365 736 3983 4 chr2D.!!$F2 3247
2 TraesCS2B01G226100 chr2D 159823642 159824368 726 False 767.00 767 85.9080 1 728 1 chr2D.!!$F1 727
3 TraesCS2B01G226100 chr2D 56296460 56296972 512 True 324.00 324 78.6950 226 728 1 chr2D.!!$R1 502
4 TraesCS2B01G226100 chr2A 171076120 171079904 3784 False 1009.20 2193 89.7516 1 3983 5 chr2A.!!$F1 3982
5 TraesCS2B01G226100 chr4D 7915089 7915591 502 False 479.00 479 84.0240 229 730 1 chr4D.!!$F1 501
6 TraesCS2B01G226100 chr6D 382343674 382344183 509 False 333.00 333 79.0700 231 728 1 chr6D.!!$F1 497
7 TraesCS2B01G226100 chr1A 556085993 556086518 525 False 309.00 309 77.8200 226 742 1 chr1A.!!$F2 516
8 TraesCS2B01G226100 chr7A 694104233 694104766 533 False 257.00 257 76.1030 219 742 1 chr7A.!!$F2 523

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
961 1016 0.162507 CGTCAGTGCGCAAGAAGAAG 59.837 55.0 14.00 6.42 43.02 2.85 F
1399 1468 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.0 0.00 0.00 0.00 3.24 F
1451 1520 0.039437 CATTATAGGCGCCTCGTCGT 60.039 55.0 36.73 17.21 36.23 4.34 F
1452 1521 0.240411 ATTATAGGCGCCTCGTCGTC 59.760 55.0 36.73 0.00 36.23 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2470 0.032416 GGGACAGTCTAGGCCTGGTA 60.032 60.000 17.99 0.0 34.16 3.25 R
2229 2528 0.252375 ACGGCTAAGGTAAGGGGACA 60.252 55.000 0.00 0.0 0.00 4.02 R
2672 2975 1.414550 GGTCTTGCCTCTCCTGGTATC 59.585 57.143 0.00 0.0 0.00 2.24 R
3326 3739 3.055094 ACCCGAATGCTCAGTACAAATCT 60.055 43.478 0.00 0.0 0.00 2.40 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 4.541213 ACGTCACCACCTCCATCT 57.459 55.556 0.00 0.00 0.00 2.90
25 26 1.774254 ACCACCTCCATCTGAACAACA 59.226 47.619 0.00 0.00 0.00 3.33
65 69 6.990349 CCTAATCCAAACTACATACCGAACAT 59.010 38.462 0.00 0.00 0.00 2.71
147 153 0.471211 ACCTTGACAACGGGAGGAGA 60.471 55.000 0.67 0.00 33.47 3.71
224 230 3.573772 TTGCCGCTCCTCTCGTGTG 62.574 63.158 0.00 0.00 0.00 3.82
255 263 6.183360 TGCTTTTCTGAGTTTTCTTAGGGTTG 60.183 38.462 0.00 0.00 34.77 3.77
333 342 3.851128 GCCTAGCTCCCGTCCCAC 61.851 72.222 0.00 0.00 0.00 4.61
358 367 0.312416 CTTCTAGCGTCATCGGAGGG 59.688 60.000 0.00 0.00 37.56 4.30
359 368 0.395311 TTCTAGCGTCATCGGAGGGT 60.395 55.000 0.00 0.00 41.87 4.34
400 409 2.904676 CGGATCTCGCGGGATTCGA 61.905 63.158 40.17 5.03 44.78 3.71
406 415 4.647615 CGCGGGATTCGATCGGCT 62.648 66.667 16.41 2.29 42.43 5.52
413 422 2.280628 GGATTCGATCGGCTTTTGTCT 58.719 47.619 16.41 0.00 0.00 3.41
461 480 4.652421 TTTGTTCGTGTGTCTACAGGTA 57.348 40.909 0.00 0.00 41.97 3.08
468 487 2.694109 GTGTGTCTACAGGTAGGATCCC 59.306 54.545 8.55 0.00 37.52 3.85
525 544 1.270839 GCTCTTGTGCACTGGTCCTAA 60.271 52.381 19.41 0.54 0.00 2.69
573 598 4.056050 ACTGTCTACTACAAGTTTTGCCG 58.944 43.478 0.00 0.00 37.74 5.69
589 614 2.128507 CCGGGCTCTAGTGAGGGAC 61.129 68.421 0.00 0.00 40.53 4.46
634 659 3.120408 TCGTCTCGCTTCAGTACTTGTAC 60.120 47.826 0.00 2.94 0.00 2.90
641 666 3.120408 GCTTCAGTACTTGTACTCGTCGA 60.120 47.826 10.16 0.00 0.00 4.20
658 683 5.554070 TCGTCGATAGGTGGTCTATGAATA 58.446 41.667 0.00 0.00 38.71 1.75
760 787 6.469782 AAAAAGATTCTGCAGAAACTGGAA 57.530 33.333 32.27 11.83 37.27 3.53
761 788 6.469782 AAAAGATTCTGCAGAAACTGGAAA 57.530 33.333 32.27 11.10 37.27 3.13
762 789 6.469782 AAAGATTCTGCAGAAACTGGAAAA 57.530 33.333 32.27 10.39 37.27 2.29
763 790 5.702349 AGATTCTGCAGAAACTGGAAAAG 57.298 39.130 31.43 0.00 36.10 2.27
764 791 5.380043 AGATTCTGCAGAAACTGGAAAAGA 58.620 37.500 31.43 8.46 36.10 2.52
765 792 5.829924 AGATTCTGCAGAAACTGGAAAAGAA 59.170 36.000 31.43 8.26 36.10 2.52
766 793 5.913137 TTCTGCAGAAACTGGAAAAGAAA 57.087 34.783 26.61 0.00 30.12 2.52
767 794 5.248870 TCTGCAGAAACTGGAAAAGAAAC 57.751 39.130 15.67 0.00 30.12 2.78
768 795 4.704540 TCTGCAGAAACTGGAAAAGAAACA 59.295 37.500 15.67 0.00 30.12 2.83
769 796 5.360714 TCTGCAGAAACTGGAAAAGAAACAT 59.639 36.000 15.67 0.00 30.12 2.71
770 797 6.545666 TCTGCAGAAACTGGAAAAGAAACATA 59.454 34.615 15.67 0.00 30.12 2.29
771 798 7.068103 TCTGCAGAAACTGGAAAAGAAACATAA 59.932 33.333 15.67 0.00 30.12 1.90
772 799 7.551585 TGCAGAAACTGGAAAAGAAACATAAA 58.448 30.769 0.00 0.00 31.21 1.40
773 800 8.037758 TGCAGAAACTGGAAAAGAAACATAAAA 58.962 29.630 0.00 0.00 31.21 1.52
774 801 8.542953 GCAGAAACTGGAAAAGAAACATAAAAG 58.457 33.333 0.00 0.00 31.21 2.27
775 802 9.801873 CAGAAACTGGAAAAGAAACATAAAAGA 57.198 29.630 0.00 0.00 0.00 2.52
815 870 8.198109 CGAAAAATAGAATACCCTCTCTTCTCA 58.802 37.037 0.00 0.00 31.89 3.27
895 950 2.665089 CGGCTACACCACCCATCCA 61.665 63.158 0.00 0.00 39.03 3.41
928 983 2.365617 TCTTCCTTCTCTTTCAGCGTGT 59.634 45.455 0.00 0.00 0.00 4.49
959 1014 0.939577 GTCGTCAGTGCGCAAGAAGA 60.940 55.000 14.00 18.16 43.02 2.87
960 1015 0.249280 TCGTCAGTGCGCAAGAAGAA 60.249 50.000 21.26 9.74 43.02 2.52
961 1016 0.162507 CGTCAGTGCGCAAGAAGAAG 59.837 55.000 14.00 6.42 43.02 2.85
962 1017 1.221414 GTCAGTGCGCAAGAAGAAGT 58.779 50.000 14.00 0.00 43.02 3.01
1254 1320 5.670485 TGCACTAACTGGTATCCACATTAG 58.330 41.667 10.83 10.83 35.17 1.73
1293 1362 5.754890 ACTGATTTGCGCAAAGAAAAGATTT 59.245 32.000 35.62 19.02 33.32 2.17
1294 1363 6.258507 ACTGATTTGCGCAAAGAAAAGATTTT 59.741 30.769 35.62 18.31 33.32 1.82
1295 1364 7.014092 TGATTTGCGCAAAGAAAAGATTTTT 57.986 28.000 35.62 17.81 33.32 1.94
1319 1388 4.972514 TGAGCATCAGTACAGACACTAG 57.027 45.455 0.00 0.00 42.56 2.57
1320 1389 3.129462 TGAGCATCAGTACAGACACTAGC 59.871 47.826 0.00 0.00 42.56 3.42
1321 1390 2.098280 AGCATCAGTACAGACACTAGCG 59.902 50.000 0.00 0.00 0.00 4.26
1322 1391 2.455032 CATCAGTACAGACACTAGCGC 58.545 52.381 0.00 0.00 0.00 5.92
1323 1392 1.822506 TCAGTACAGACACTAGCGCT 58.177 50.000 17.26 17.26 0.00 5.92
1324 1393 1.738350 TCAGTACAGACACTAGCGCTC 59.262 52.381 16.34 0.00 0.00 5.03
1325 1394 1.468914 CAGTACAGACACTAGCGCTCA 59.531 52.381 16.34 0.00 0.00 4.26
1326 1395 2.098280 CAGTACAGACACTAGCGCTCAT 59.902 50.000 16.34 0.00 0.00 2.90
1327 1396 3.312697 CAGTACAGACACTAGCGCTCATA 59.687 47.826 16.34 0.00 0.00 2.15
1328 1397 4.023622 CAGTACAGACACTAGCGCTCATAT 60.024 45.833 16.34 0.00 0.00 1.78
1329 1398 5.179555 CAGTACAGACACTAGCGCTCATATA 59.820 44.000 16.34 0.00 0.00 0.86
1330 1399 4.491234 ACAGACACTAGCGCTCATATAC 57.509 45.455 16.34 2.43 0.00 1.47
1331 1400 3.883489 ACAGACACTAGCGCTCATATACA 59.117 43.478 16.34 0.00 0.00 2.29
1332 1401 4.222886 CAGACACTAGCGCTCATATACAC 58.777 47.826 16.34 0.00 0.00 2.90
1333 1402 3.058846 AGACACTAGCGCTCATATACACG 60.059 47.826 16.34 0.00 0.00 4.49
1337 1406 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
1338 1407 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
1339 1408 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
1340 1409 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
1341 1410 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
1342 1411 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
1343 1412 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
1344 1413 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
1345 1414 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
1346 1415 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
1347 1416 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
1348 1417 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
1349 1418 2.890474 CGCGCATACACTCACCCC 60.890 66.667 8.75 0.00 0.00 4.95
1350 1419 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
1351 1420 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
1352 1421 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
1353 1422 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
1354 1423 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
1355 1424 2.102420 CGCATACACTCACCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
1356 1425 3.431626 CGCATACACTCACCCCTATGAAA 60.432 47.826 0.00 0.00 0.00 2.69
1357 1426 4.130118 GCATACACTCACCCCTATGAAAG 58.870 47.826 0.00 0.00 0.00 2.62
1358 1427 2.789409 ACACTCACCCCTATGAAAGC 57.211 50.000 0.00 0.00 0.00 3.51
1359 1428 1.985159 ACACTCACCCCTATGAAAGCA 59.015 47.619 0.00 0.00 0.00 3.91
1360 1429 2.290323 ACACTCACCCCTATGAAAGCAC 60.290 50.000 0.00 0.00 0.00 4.40
1361 1430 1.066143 ACTCACCCCTATGAAAGCACG 60.066 52.381 0.00 0.00 0.00 5.34
1362 1431 0.392461 TCACCCCTATGAAAGCACGC 60.392 55.000 0.00 0.00 0.00 5.34
1363 1432 1.449601 ACCCCTATGAAAGCACGCG 60.450 57.895 3.53 3.53 0.00 6.01
1364 1433 2.709475 CCCTATGAAAGCACGCGC 59.291 61.111 5.73 0.00 38.99 6.86
1365 1434 2.321060 CCTATGAAAGCACGCGCG 59.679 61.111 30.96 30.96 45.49 6.86
1366 1435 2.350091 CTATGAAAGCACGCGCGC 60.350 61.111 32.58 23.91 45.49 6.86
1367 1436 3.082379 CTATGAAAGCACGCGCGCA 62.082 57.895 32.58 19.24 45.49 6.09
1368 1437 3.361455 TATGAAAGCACGCGCGCAC 62.361 57.895 32.58 22.59 45.49 5.34
1380 1449 3.078836 GCGCACACCCTACCCCTA 61.079 66.667 0.30 0.00 0.00 3.53
1381 1450 2.440817 GCGCACACCCTACCCCTAT 61.441 63.158 0.30 0.00 0.00 2.57
1382 1451 1.445942 CGCACACCCTACCCCTATG 59.554 63.158 0.00 0.00 0.00 2.23
1383 1452 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
1384 1453 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
1385 1454 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
1386 1455 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
1387 1456 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
1388 1457 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
1389 1458 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
1390 1459 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
1391 1460 1.343069 CTACCCCTATGAGCACCTCC 58.657 60.000 0.00 0.00 0.00 4.30
1392 1461 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
1393 1462 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
1394 1463 1.467678 CCCCTATGAGCACCTCCGAG 61.468 65.000 0.00 0.00 0.00 4.63
1395 1464 0.468214 CCCTATGAGCACCTCCGAGA 60.468 60.000 0.00 0.00 0.00 4.04
1396 1465 0.958091 CCTATGAGCACCTCCGAGAG 59.042 60.000 0.00 0.00 0.00 3.20
1397 1466 1.477740 CCTATGAGCACCTCCGAGAGA 60.478 57.143 0.00 0.00 0.00 3.10
1398 1467 1.606668 CTATGAGCACCTCCGAGAGAC 59.393 57.143 0.00 0.00 0.00 3.36
1399 1468 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
1400 1469 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
1401 1470 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
1402 1471 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
1403 1472 1.806568 CACCTCCGAGAGACTGAGC 59.193 63.158 0.00 0.00 0.00 4.26
1404 1473 1.379309 ACCTCCGAGAGACTGAGCC 60.379 63.158 0.00 0.00 0.00 4.70
1405 1474 2.477176 CCTCCGAGAGACTGAGCCG 61.477 68.421 0.00 0.00 0.00 5.52
1406 1475 2.438614 TCCGAGAGACTGAGCCGG 60.439 66.667 0.00 0.00 41.36 6.13
1407 1476 4.200283 CCGAGAGACTGAGCCGGC 62.200 72.222 21.89 21.89 33.47 6.13
1408 1477 3.443925 CGAGAGACTGAGCCGGCA 61.444 66.667 31.54 7.98 0.00 5.69
1409 1478 2.780094 CGAGAGACTGAGCCGGCAT 61.780 63.158 31.54 14.28 0.00 4.40
1410 1479 1.448119 CGAGAGACTGAGCCGGCATA 61.448 60.000 31.54 16.21 0.00 3.14
1411 1480 0.965439 GAGAGACTGAGCCGGCATAT 59.035 55.000 31.54 8.11 0.00 1.78
1412 1481 0.965439 AGAGACTGAGCCGGCATATC 59.035 55.000 31.54 18.63 0.00 1.63
1413 1482 0.965439 GAGACTGAGCCGGCATATCT 59.035 55.000 31.54 24.11 0.00 1.98
1414 1483 1.342819 GAGACTGAGCCGGCATATCTT 59.657 52.381 31.54 6.18 0.00 2.40
1415 1484 1.342819 AGACTGAGCCGGCATATCTTC 59.657 52.381 31.54 16.99 0.00 2.87
1416 1485 1.342819 GACTGAGCCGGCATATCTTCT 59.657 52.381 31.54 4.27 0.00 2.85
1417 1486 1.765314 ACTGAGCCGGCATATCTTCTT 59.235 47.619 31.54 3.33 0.00 2.52
1418 1487 2.141517 CTGAGCCGGCATATCTTCTTG 58.858 52.381 31.54 9.45 0.00 3.02
1419 1488 1.762370 TGAGCCGGCATATCTTCTTGA 59.238 47.619 31.54 0.00 0.00 3.02
1420 1489 2.170397 TGAGCCGGCATATCTTCTTGAA 59.830 45.455 31.54 0.00 0.00 2.69
1421 1490 3.206150 GAGCCGGCATATCTTCTTGAAA 58.794 45.455 31.54 0.00 0.00 2.69
1422 1491 3.817647 GAGCCGGCATATCTTCTTGAAAT 59.182 43.478 31.54 0.06 0.00 2.17
1423 1492 4.210331 AGCCGGCATATCTTCTTGAAATT 58.790 39.130 31.54 0.00 0.00 1.82
1424 1493 4.646492 AGCCGGCATATCTTCTTGAAATTT 59.354 37.500 31.54 0.00 0.00 1.82
1425 1494 5.827797 AGCCGGCATATCTTCTTGAAATTTA 59.172 36.000 31.54 0.00 0.00 1.40
1426 1495 6.491403 AGCCGGCATATCTTCTTGAAATTTAT 59.509 34.615 31.54 0.00 0.00 1.40
1427 1496 6.583806 GCCGGCATATCTTCTTGAAATTTATG 59.416 38.462 24.80 0.00 0.00 1.90
1428 1497 7.522073 GCCGGCATATCTTCTTGAAATTTATGA 60.522 37.037 24.80 0.00 0.00 2.15
1429 1498 8.352201 CCGGCATATCTTCTTGAAATTTATGAA 58.648 33.333 0.00 0.00 0.00 2.57
1430 1499 9.390795 CGGCATATCTTCTTGAAATTTATGAAG 57.609 33.333 15.45 15.45 36.44 3.02
1443 1512 8.289618 TGAAATTTATGAAGTCATTATAGGCGC 58.710 33.333 0.00 0.00 37.76 6.53
1444 1513 6.743575 ATTTATGAAGTCATTATAGGCGCC 57.256 37.500 21.89 21.89 37.76 6.53
1445 1514 5.483685 TTATGAAGTCATTATAGGCGCCT 57.516 39.130 34.85 34.85 37.76 5.52
1446 1515 3.386768 TGAAGTCATTATAGGCGCCTC 57.613 47.619 36.73 17.40 0.00 4.70
1447 1516 2.288213 TGAAGTCATTATAGGCGCCTCG 60.288 50.000 36.73 17.43 0.00 4.63
1448 1517 1.329256 AGTCATTATAGGCGCCTCGT 58.671 50.000 36.73 25.29 0.00 4.18
1449 1518 1.269998 AGTCATTATAGGCGCCTCGTC 59.730 52.381 36.73 16.85 0.00 4.20
1450 1519 0.240145 TCATTATAGGCGCCTCGTCG 59.760 55.000 36.73 18.98 36.23 5.12
1451 1520 0.039437 CATTATAGGCGCCTCGTCGT 60.039 55.000 36.73 17.21 36.23 4.34
1452 1521 0.240411 ATTATAGGCGCCTCGTCGTC 59.760 55.000 36.73 0.00 36.23 4.20
1453 1522 2.109538 TTATAGGCGCCTCGTCGTCG 62.110 60.000 36.73 0.00 39.34 5.12
1454 1523 2.976692 TATAGGCGCCTCGTCGTCGA 62.977 60.000 36.73 14.03 44.12 4.20
1475 1544 3.460648 GGAACGTCTCCTCCCATTG 57.539 57.895 8.87 0.00 41.61 2.82
1476 1545 0.902531 GGAACGTCTCCTCCCATTGA 59.097 55.000 8.87 0.00 41.61 2.57
1477 1546 1.278127 GGAACGTCTCCTCCCATTGAA 59.722 52.381 8.87 0.00 41.61 2.69
1478 1547 2.290071 GGAACGTCTCCTCCCATTGAAA 60.290 50.000 8.87 0.00 41.61 2.69
1479 1548 3.610911 GAACGTCTCCTCCCATTGAAAT 58.389 45.455 0.00 0.00 0.00 2.17
1480 1549 3.721087 ACGTCTCCTCCCATTGAAATT 57.279 42.857 0.00 0.00 0.00 1.82
1481 1550 4.034285 ACGTCTCCTCCCATTGAAATTT 57.966 40.909 0.00 0.00 0.00 1.82
1482 1551 5.174037 ACGTCTCCTCCCATTGAAATTTA 57.826 39.130 0.00 0.00 0.00 1.40
1483 1552 4.941873 ACGTCTCCTCCCATTGAAATTTAC 59.058 41.667 0.00 0.00 0.00 2.01
1484 1553 4.034048 CGTCTCCTCCCATTGAAATTTACG 59.966 45.833 0.00 0.00 0.00 3.18
1485 1554 5.183228 GTCTCCTCCCATTGAAATTTACGA 58.817 41.667 0.00 0.00 0.00 3.43
1486 1555 5.646360 GTCTCCTCCCATTGAAATTTACGAA 59.354 40.000 0.00 0.00 0.00 3.85
1487 1556 5.880332 TCTCCTCCCATTGAAATTTACGAAG 59.120 40.000 0.00 0.00 0.00 3.79
1488 1557 5.811190 TCCTCCCATTGAAATTTACGAAGA 58.189 37.500 0.00 0.00 0.00 2.87
1489 1558 6.423182 TCCTCCCATTGAAATTTACGAAGAT 58.577 36.000 0.00 0.00 0.00 2.40
1490 1559 6.889722 TCCTCCCATTGAAATTTACGAAGATT 59.110 34.615 0.00 0.00 0.00 2.40
1527 1603 3.440872 AGAGTAGCAGTAGTTTCTGACGG 59.559 47.826 0.00 0.00 37.61 4.79
1530 1606 3.963428 AGCAGTAGTTTCTGACGGAAT 57.037 42.857 0.00 0.00 37.61 3.01
1563 1639 6.601332 TCATGTGTCTACCCTTTTTCTTTCT 58.399 36.000 0.00 0.00 0.00 2.52
1648 1732 6.367695 TGTCGCGTGATTCCCATAAATATTAG 59.632 38.462 5.77 0.00 0.00 1.73
1650 1734 6.367695 TCGCGTGATTCCCATAAATATTAGTG 59.632 38.462 5.77 0.00 0.00 2.74
1713 1800 7.548780 ACAGTACAACGAGTAAAACCTTAACAA 59.451 33.333 0.00 0.00 33.72 2.83
1717 1804 7.819644 ACAACGAGTAAAACCTTAACAAGTTT 58.180 30.769 0.00 0.00 0.00 2.66
1731 1818 5.712152 AACAAGTTTGCTGATTCTTAGGG 57.288 39.130 0.00 0.00 0.00 3.53
1732 1819 4.729868 ACAAGTTTGCTGATTCTTAGGGT 58.270 39.130 0.00 0.00 0.00 4.34
1737 1824 6.515832 AGTTTGCTGATTCTTAGGGTTTTTG 58.484 36.000 0.00 0.00 0.00 2.44
1743 1830 7.279758 TGCTGATTCTTAGGGTTTTTGTTTTTG 59.720 33.333 0.00 0.00 0.00 2.44
1744 1831 7.494298 GCTGATTCTTAGGGTTTTTGTTTTTGA 59.506 33.333 0.00 0.00 0.00 2.69
1812 1903 7.528481 TGCAATCTTTGAACATGCAATATTC 57.472 32.000 0.00 0.00 43.39 1.75
1871 1962 2.364324 ACTTTGGACGTGAGAGCAGTTA 59.636 45.455 0.00 0.00 0.00 2.24
1881 1972 4.267214 CGTGAGAGCAGTTAGATGTTGATG 59.733 45.833 0.00 0.00 0.00 3.07
1884 1975 4.190001 AGAGCAGTTAGATGTTGATGCAG 58.810 43.478 0.00 0.00 36.15 4.41
1954 2046 9.804758 TTTTAAATCTTTACCGAGAAAAGCAAA 57.195 25.926 0.00 0.00 34.58 3.68
2069 2324 6.650807 TCATACAAGAGTGAGAAACAATCCAC 59.349 38.462 0.00 0.00 43.50 4.02
2081 2336 7.835682 TGAGAAACAATCCACAGGAATATTGAT 59.164 33.333 0.00 0.00 34.34 2.57
2082 2337 8.004087 AGAAACAATCCACAGGAATATTGATG 57.996 34.615 0.00 0.00 34.34 3.07
2083 2338 7.835682 AGAAACAATCCACAGGAATATTGATGA 59.164 33.333 0.00 0.00 34.34 2.92
2178 2433 9.393512 GATTCTTATGGGAATTATCTGATCCAG 57.606 37.037 0.00 0.00 36.24 3.86
2204 2459 1.098050 CCTTCGAAAGATGGCTTGGG 58.902 55.000 0.00 0.00 46.60 4.12
2210 2465 3.964688 TCGAAAGATGGCTTGGGTATCTA 59.035 43.478 0.00 0.00 33.79 1.98
2215 2470 6.460103 AAGATGGCTTGGGTATCTATTCAT 57.540 37.500 0.00 0.00 31.83 2.57
2229 2528 5.340891 TCTATTCATACCAGGCCTAGACT 57.659 43.478 3.98 0.00 0.00 3.24
2264 2563 4.010667 AGCCGTGGTTTGTTTCACTATA 57.989 40.909 0.00 0.00 0.00 1.31
2266 2565 4.394920 AGCCGTGGTTTGTTTCACTATATG 59.605 41.667 0.00 0.00 0.00 1.78
2267 2566 4.658071 CCGTGGTTTGTTTCACTATATGC 58.342 43.478 0.00 0.00 0.00 3.14
2271 2574 6.260050 CGTGGTTTGTTTCACTATATGCCTAT 59.740 38.462 0.00 0.00 0.00 2.57
2308 2611 0.676782 CCGTCCCCTTTGACATGTCC 60.677 60.000 22.85 5.91 34.88 4.02
2313 2616 1.686115 CCCCTTTGACATGTCCCCATC 60.686 57.143 22.85 0.00 0.00 3.51
2360 2663 1.369692 CAAGGCCACACAGACGGTA 59.630 57.895 5.01 0.00 0.00 4.02
2438 2741 2.174639 TGTTTTCTCCTTGGCCTCTTGA 59.825 45.455 3.32 0.00 0.00 3.02
2447 2750 3.307199 CCTTGGCCTCTTGAATGCAAATT 60.307 43.478 3.32 0.00 32.73 1.82
2469 2772 2.650322 GTTTCCCTGTTGGACAGTTCA 58.350 47.619 7.26 0.00 45.11 3.18
2564 2867 1.792949 GGTATACATTTCCTGCGAGCG 59.207 52.381 5.01 0.00 0.00 5.03
2577 2880 4.694102 GAGCGCTCTCGAAGGTAC 57.306 61.111 29.88 0.00 38.10 3.34
2584 2887 2.159226 CGCTCTCGAAGGTACCATCTTT 60.159 50.000 15.94 0.00 38.10 2.52
2599 2902 0.693049 TCTTTGTCTCTTGCTCCCCC 59.307 55.000 0.00 0.00 0.00 5.40
2603 2906 1.920835 GTCTCTTGCTCCCCCAGGT 60.921 63.158 0.00 0.00 0.00 4.00
2620 2923 5.452776 CCCCAGGTTACAGAAAAGAAAAACC 60.453 44.000 0.00 0.00 37.28 3.27
2647 2950 0.608130 ACAGCAGTGCGTTCCTGATA 59.392 50.000 10.00 0.00 31.38 2.15
2663 2966 8.512138 CGTTCCTGATAATTTCTTAACCTGTTT 58.488 33.333 0.00 0.00 0.00 2.83
2827 3133 8.281212 TGCAGAAGAAAAATATTTACCTCTCC 57.719 34.615 0.01 0.00 0.00 3.71
2828 3134 7.065803 TGCAGAAGAAAAATATTTACCTCTCCG 59.934 37.037 0.01 0.00 0.00 4.63
2862 3168 8.070034 TCTTTTTGGCATATGATCAGAAATGT 57.930 30.769 6.97 0.00 0.00 2.71
2883 3189 5.228665 TGTGACCATACGAAAATGTACGAA 58.771 37.500 0.00 0.00 0.00 3.85
3021 3327 5.480642 AGGATATGATTGCTTCACTCGAT 57.519 39.130 0.00 0.00 37.11 3.59
3165 3491 6.639686 CACTTGATGATTTTTGTCCTGTGAAG 59.360 38.462 0.00 0.00 0.00 3.02
3234 3562 1.552337 AGTGTGCCTGTGTCCTCTATG 59.448 52.381 0.00 0.00 0.00 2.23
3250 3578 7.933577 TGTCCTCTATGCTAAGATTTGTATTGG 59.066 37.037 0.00 0.00 0.00 3.16
3293 3706 6.726035 ACGTGTGATAATTTTGTTTGTTCG 57.274 33.333 0.00 0.00 0.00 3.95
3319 3732 2.621763 CAGTGTGCCTGTGTTCTCC 58.378 57.895 0.00 0.00 36.37 3.71
3326 3739 3.580895 TGTGCCTGTGTTCTCCATACTAA 59.419 43.478 0.00 0.00 0.00 2.24
3356 3769 2.673368 CTGAGCATTCGGGTTTACTGAC 59.327 50.000 0.00 0.00 33.15 3.51
3357 3770 2.301870 TGAGCATTCGGGTTTACTGACT 59.698 45.455 0.00 0.00 33.15 3.41
3455 3870 5.536554 AACAACACGTCATGATCAAGATC 57.463 39.130 3.62 3.12 38.29 2.75
3481 3896 1.997606 GGGTAAACGTCATGTCGAAGG 59.002 52.381 19.02 0.00 34.70 3.46
3484 3899 2.536761 AAACGTCATGTCGAAGGGAA 57.463 45.000 19.02 0.00 34.70 3.97
3514 3929 0.394352 GGCCGAATGTCTGAACCCAT 60.394 55.000 0.00 0.00 0.00 4.00
3578 3995 1.466167 CCTGTTCCAATCTGCTGAACG 59.534 52.381 0.00 0.00 40.92 3.95
3613 4030 1.066858 GCTTCCTGTCTTCGACCATCA 60.067 52.381 0.00 0.00 0.00 3.07
3748 4167 4.245660 CTGTTGGAAAGCTCGACTCATTA 58.754 43.478 0.00 0.00 0.00 1.90
3755 4174 6.037500 TGGAAAGCTCGACTCATTATTCATTG 59.962 38.462 0.00 0.00 0.00 2.82
3760 4179 7.246311 AGCTCGACTCATTATTCATTGTTTTG 58.754 34.615 0.00 0.00 0.00 2.44
3877 4297 0.727398 GCAGTATGACAAACCCGAGC 59.273 55.000 0.00 0.00 39.69 5.03
3890 4312 3.730761 CGAGCACTGCAAGGCCAC 61.731 66.667 5.01 0.00 39.30 5.01
3892 4314 4.208403 AGCACTGCAAGGCCACCA 62.208 61.111 5.01 0.00 39.30 4.17
3894 4316 2.730094 CACTGCAAGGCCACCAAC 59.270 61.111 5.01 0.00 39.30 3.77
3895 4317 2.906897 ACTGCAAGGCCACCAACG 60.907 61.111 5.01 0.00 39.30 4.10
3911 4333 3.142951 CCAACGGTTGACCAAGTTGATA 58.857 45.455 21.88 0.00 44.64 2.15
3914 4336 2.370849 ACGGTTGACCAAGTTGATACCT 59.629 45.455 3.87 0.00 35.14 3.08
3919 4341 5.535030 GGTTGACCAAGTTGATACCTTCTTT 59.465 40.000 3.87 0.00 35.64 2.52
3921 4343 4.518970 TGACCAAGTTGATACCTTCTTTGC 59.481 41.667 3.87 0.00 0.00 3.68
3925 4347 6.206829 ACCAAGTTGATACCTTCTTTGCTTAC 59.793 38.462 3.87 0.00 0.00 2.34
3928 4350 7.440523 AGTTGATACCTTCTTTGCTTACTTG 57.559 36.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.355596 GTTTTGGTTCCATGATGTTGTTCA 58.644 37.500 0.00 0.00 0.00 3.18
25 26 5.588845 TGGATTAGGTTTTGGTTCCATGAT 58.411 37.500 0.00 0.00 0.00 2.45
147 153 1.638589 CTCCCCTCTCCGGATCTCTAT 59.361 57.143 3.57 0.00 33.16 1.98
224 230 7.761651 AAGAAAACTCAGAAAAGCATCAAAC 57.238 32.000 0.00 0.00 0.00 2.93
255 263 1.133407 CGTCTCTCTAAGCAGGACACC 59.867 57.143 0.00 0.00 0.00 4.16
333 342 1.565305 GATGACGCTAGAAGCACCAG 58.435 55.000 0.00 0.00 42.58 4.00
358 367 2.038387 AGACAAACCTCCACACACAC 57.962 50.000 0.00 0.00 0.00 3.82
359 368 2.639065 GAAGACAAACCTCCACACACA 58.361 47.619 0.00 0.00 0.00 3.72
400 409 1.535462 CACCGAAAGACAAAAGCCGAT 59.465 47.619 0.00 0.00 0.00 4.18
406 415 3.216187 TGGATCCACCGAAAGACAAAA 57.784 42.857 11.44 0.00 42.61 2.44
485 504 3.015677 CAACCGCCGTCGTTGAAA 58.984 55.556 0.66 0.00 32.47 2.69
510 529 0.400213 CCCTTTAGGACCAGTGCACA 59.600 55.000 21.04 0.00 38.24 4.57
525 544 1.355720 AGTTGTCATGCTAAGGCCCTT 59.644 47.619 0.00 0.00 37.74 3.95
538 557 1.410004 AGACAGTCGGGAAGTTGTCA 58.590 50.000 6.29 0.00 41.74 3.58
573 598 1.045911 CCAGTCCCTCACTAGAGCCC 61.046 65.000 0.00 0.00 40.68 5.19
634 659 3.400255 TCATAGACCACCTATCGACGAG 58.600 50.000 3.01 0.00 35.96 4.18
786 841 9.813446 GAAGAGAGGGTATTCTATTTTTCGTTA 57.187 33.333 0.00 0.00 29.34 3.18
808 863 0.986527 TGGCTGAAGGCATGAGAAGA 59.013 50.000 1.88 0.00 46.12 2.87
895 950 2.507471 AGAAGGAAGAGATGCGGGATTT 59.493 45.455 0.00 0.00 0.00 2.17
947 1002 2.280183 CGAGATACTTCTTCTTGCGCAC 59.720 50.000 11.12 0.00 30.30 5.34
959 1014 1.405821 CAAGAGGACGGCGAGATACTT 59.594 52.381 16.62 9.42 0.00 2.24
960 1015 1.025812 CAAGAGGACGGCGAGATACT 58.974 55.000 16.62 0.00 0.00 2.12
961 1016 0.595310 GCAAGAGGACGGCGAGATAC 60.595 60.000 16.62 0.00 0.00 2.24
962 1017 0.752009 AGCAAGAGGACGGCGAGATA 60.752 55.000 16.62 0.00 0.00 1.98
1294 1363 5.368145 AGTGTCTGTACTGATGCTCAAAAA 58.632 37.500 5.69 0.00 0.00 1.94
1295 1364 4.960938 AGTGTCTGTACTGATGCTCAAAA 58.039 39.130 5.69 0.00 0.00 2.44
1296 1365 4.607293 AGTGTCTGTACTGATGCTCAAA 57.393 40.909 5.69 0.00 0.00 2.69
1297 1366 4.380973 GCTAGTGTCTGTACTGATGCTCAA 60.381 45.833 5.69 0.00 32.19 3.02
1298 1367 3.129462 GCTAGTGTCTGTACTGATGCTCA 59.871 47.826 5.69 0.00 32.19 4.26
1299 1368 3.701241 GCTAGTGTCTGTACTGATGCTC 58.299 50.000 5.69 0.00 32.19 4.26
1300 1369 2.098280 CGCTAGTGTCTGTACTGATGCT 59.902 50.000 5.69 9.32 32.19 3.79
1301 1370 2.455032 CGCTAGTGTCTGTACTGATGC 58.545 52.381 5.69 2.65 32.19 3.91
1302 1371 2.098280 AGCGCTAGTGTCTGTACTGATG 59.902 50.000 8.99 0.00 32.19 3.07
1303 1372 2.356382 GAGCGCTAGTGTCTGTACTGAT 59.644 50.000 11.50 0.00 32.19 2.90
1304 1373 1.738350 GAGCGCTAGTGTCTGTACTGA 59.262 52.381 11.50 0.00 32.19 3.41
1305 1374 1.468914 TGAGCGCTAGTGTCTGTACTG 59.531 52.381 11.50 0.00 32.19 2.74
1306 1375 1.822506 TGAGCGCTAGTGTCTGTACT 58.177 50.000 11.50 0.00 34.71 2.73
1307 1376 2.853731 ATGAGCGCTAGTGTCTGTAC 57.146 50.000 11.50 0.00 0.00 2.90
1308 1377 5.049612 GTGTATATGAGCGCTAGTGTCTGTA 60.050 44.000 11.50 0.00 0.00 2.74
1309 1378 3.883489 TGTATATGAGCGCTAGTGTCTGT 59.117 43.478 11.50 0.00 0.00 3.41
1310 1379 4.222886 GTGTATATGAGCGCTAGTGTCTG 58.777 47.826 11.50 0.00 0.00 3.51
1311 1380 3.058846 CGTGTATATGAGCGCTAGTGTCT 60.059 47.826 11.50 2.58 0.00 3.41
1312 1381 3.227147 CGTGTATATGAGCGCTAGTGTC 58.773 50.000 11.50 0.00 0.00 3.67
1313 1382 2.604855 GCGTGTATATGAGCGCTAGTGT 60.605 50.000 11.50 2.52 45.48 3.55
1314 1383 1.979469 GCGTGTATATGAGCGCTAGTG 59.021 52.381 11.50 0.00 45.48 2.74
1315 1384 1.399855 CGCGTGTATATGAGCGCTAGT 60.400 52.381 11.50 4.22 46.56 2.57
1316 1385 1.251355 CGCGTGTATATGAGCGCTAG 58.749 55.000 11.50 0.00 46.56 3.42
1317 1386 3.378013 CGCGTGTATATGAGCGCTA 57.622 52.632 11.50 0.00 46.56 4.26
1318 1387 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
1321 1390 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
1322 1391 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
1323 1392 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
1324 1393 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
1325 1394 3.305964 GTGAGTGTATGCGCGTGTATAT 58.694 45.455 13.61 0.00 0.00 0.86
1326 1395 2.542205 GGTGAGTGTATGCGCGTGTATA 60.542 50.000 13.61 2.40 0.00 1.47
1327 1396 1.556564 GTGAGTGTATGCGCGTGTAT 58.443 50.000 13.61 4.63 0.00 2.29
1328 1397 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
1329 1398 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
1330 1399 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
1331 1400 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
1332 1401 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
1333 1402 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
1334 1403 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
1335 1404 3.838244 TTCATAGGGGTGAGTGTATGC 57.162 47.619 0.00 0.00 0.00 3.14
1336 1405 4.130118 GCTTTCATAGGGGTGAGTGTATG 58.870 47.826 0.00 0.00 0.00 2.39
1337 1406 3.780294 TGCTTTCATAGGGGTGAGTGTAT 59.220 43.478 0.00 0.00 0.00 2.29
1338 1407 3.055385 GTGCTTTCATAGGGGTGAGTGTA 60.055 47.826 0.00 0.00 0.00 2.90
1339 1408 1.985159 TGCTTTCATAGGGGTGAGTGT 59.015 47.619 0.00 0.00 0.00 3.55
1340 1409 2.359900 GTGCTTTCATAGGGGTGAGTG 58.640 52.381 0.00 0.00 0.00 3.51
1341 1410 1.066143 CGTGCTTTCATAGGGGTGAGT 60.066 52.381 0.00 0.00 0.00 3.41
1342 1411 1.656652 CGTGCTTTCATAGGGGTGAG 58.343 55.000 0.00 0.00 0.00 3.51
1343 1412 0.392461 GCGTGCTTTCATAGGGGTGA 60.392 55.000 0.00 0.00 0.00 4.02
1344 1413 1.705337 CGCGTGCTTTCATAGGGGTG 61.705 60.000 0.00 0.00 0.00 4.61
1345 1414 1.449601 CGCGTGCTTTCATAGGGGT 60.450 57.895 0.00 0.00 0.00 4.95
1346 1415 2.823829 GCGCGTGCTTTCATAGGGG 61.824 63.158 15.02 0.00 38.39 4.79
1347 1416 2.709475 GCGCGTGCTTTCATAGGG 59.291 61.111 15.02 0.00 38.39 3.53
1348 1417 2.321060 CGCGCGTGCTTTCATAGG 59.679 61.111 24.19 0.00 39.65 2.57
1349 1418 2.350091 GCGCGCGTGCTTTCATAG 60.350 61.111 35.43 2.14 39.65 2.23
1350 1419 3.115253 TGCGCGCGTGCTTTCATA 61.115 55.556 40.02 20.34 39.65 2.15
1351 1420 4.741781 GTGCGCGCGTGCTTTCAT 62.742 61.111 40.02 0.00 39.65 2.57
1363 1432 2.440817 ATAGGGGTAGGGTGTGCGC 61.441 63.158 0.00 0.00 0.00 6.09
1364 1433 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
1365 1434 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
1366 1435 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
1367 1436 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
1368 1437 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
1369 1438 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
1370 1439 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
1371 1440 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
1372 1441 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
1373 1442 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
1374 1443 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
1375 1444 1.457643 TCGGAGGTGCTCATAGGGG 60.458 63.158 0.00 0.00 31.08 4.79
1376 1445 0.468214 TCTCGGAGGTGCTCATAGGG 60.468 60.000 4.96 0.00 31.08 3.53
1377 1446 0.958091 CTCTCGGAGGTGCTCATAGG 59.042 60.000 4.96 0.00 31.08 2.57
1378 1447 1.606668 GTCTCTCGGAGGTGCTCATAG 59.393 57.143 4.96 0.00 31.08 2.23
1379 1448 1.213182 AGTCTCTCGGAGGTGCTCATA 59.787 52.381 4.96 0.00 31.08 2.15
1380 1449 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
1381 1450 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
1382 1451 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
1383 1452 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
1384 1453 1.806568 CTCAGTCTCTCGGAGGTGC 59.193 63.158 4.96 0.00 35.32 5.01
1385 1454 1.662438 GGCTCAGTCTCTCGGAGGTG 61.662 65.000 4.96 0.00 38.48 4.00
1386 1455 1.379309 GGCTCAGTCTCTCGGAGGT 60.379 63.158 4.96 0.00 38.48 3.85
1387 1456 2.477176 CGGCTCAGTCTCTCGGAGG 61.477 68.421 4.96 0.00 38.48 4.30
1388 1457 2.477176 CCGGCTCAGTCTCTCGGAG 61.477 68.421 0.00 0.00 42.94 4.63
1389 1458 2.438614 CCGGCTCAGTCTCTCGGA 60.439 66.667 0.00 0.00 42.94 4.55
1390 1459 4.200283 GCCGGCTCAGTCTCTCGG 62.200 72.222 22.15 0.00 43.13 4.63
1391 1460 1.448119 TATGCCGGCTCAGTCTCTCG 61.448 60.000 29.70 0.00 0.00 4.04
1392 1461 0.965439 ATATGCCGGCTCAGTCTCTC 59.035 55.000 29.70 0.00 0.00 3.20
1393 1462 0.965439 GATATGCCGGCTCAGTCTCT 59.035 55.000 29.70 3.16 0.00 3.10
1394 1463 0.965439 AGATATGCCGGCTCAGTCTC 59.035 55.000 29.70 14.92 0.00 3.36
1395 1464 1.342819 GAAGATATGCCGGCTCAGTCT 59.657 52.381 29.70 21.09 0.00 3.24
1396 1465 1.342819 AGAAGATATGCCGGCTCAGTC 59.657 52.381 29.70 19.22 0.00 3.51
1397 1466 1.418334 AGAAGATATGCCGGCTCAGT 58.582 50.000 29.70 13.44 0.00 3.41
1398 1467 2.141517 CAAGAAGATATGCCGGCTCAG 58.858 52.381 29.70 8.47 0.00 3.35
1399 1468 1.762370 TCAAGAAGATATGCCGGCTCA 59.238 47.619 29.70 15.91 0.00 4.26
1400 1469 2.533266 TCAAGAAGATATGCCGGCTC 57.467 50.000 29.70 17.47 0.00 4.70
1401 1470 3.281727 TTTCAAGAAGATATGCCGGCT 57.718 42.857 29.70 15.76 0.00 5.52
1402 1471 4.574599 AATTTCAAGAAGATATGCCGGC 57.425 40.909 22.73 22.73 0.00 6.13
1403 1472 7.874940 TCATAAATTTCAAGAAGATATGCCGG 58.125 34.615 0.00 0.00 0.00 6.13
1404 1473 9.390795 CTTCATAAATTTCAAGAAGATATGCCG 57.609 33.333 16.27 0.00 38.30 5.69
1417 1486 8.289618 GCGCCTATAATGACTTCATAAATTTCA 58.710 33.333 0.00 0.00 35.10 2.69
1418 1487 7.750903 GGCGCCTATAATGACTTCATAAATTTC 59.249 37.037 22.15 0.00 35.10 2.17
1419 1488 7.448469 AGGCGCCTATAATGACTTCATAAATTT 59.552 33.333 31.86 0.00 35.10 1.82
1420 1489 6.942576 AGGCGCCTATAATGACTTCATAAATT 59.057 34.615 31.86 0.00 35.10 1.82
1421 1490 6.476378 AGGCGCCTATAATGACTTCATAAAT 58.524 36.000 31.86 0.00 35.10 1.40
1422 1491 5.865085 AGGCGCCTATAATGACTTCATAAA 58.135 37.500 31.86 0.00 35.10 1.40
1423 1492 5.479306 GAGGCGCCTATAATGACTTCATAA 58.521 41.667 32.97 0.00 35.10 1.90
1424 1493 4.380550 CGAGGCGCCTATAATGACTTCATA 60.381 45.833 32.97 0.00 35.10 2.15
1425 1494 3.615110 CGAGGCGCCTATAATGACTTCAT 60.615 47.826 32.97 0.50 38.41 2.57
1426 1495 2.288213 CGAGGCGCCTATAATGACTTCA 60.288 50.000 32.97 0.00 0.00 3.02
1427 1496 2.288273 ACGAGGCGCCTATAATGACTTC 60.288 50.000 32.97 12.25 0.00 3.01
1428 1497 1.687123 ACGAGGCGCCTATAATGACTT 59.313 47.619 32.97 5.44 0.00 3.01
1429 1498 1.269998 GACGAGGCGCCTATAATGACT 59.730 52.381 32.97 3.02 0.00 3.41
1430 1499 1.699343 GACGAGGCGCCTATAATGAC 58.301 55.000 32.97 14.51 0.00 3.06
1431 1500 0.240145 CGACGAGGCGCCTATAATGA 59.760 55.000 32.97 0.00 0.00 2.57
1432 1501 0.039437 ACGACGAGGCGCCTATAATG 60.039 55.000 32.97 20.45 33.86 1.90
1433 1502 0.240411 GACGACGAGGCGCCTATAAT 59.760 55.000 32.97 15.46 33.86 1.28
1434 1503 1.650912 GACGACGAGGCGCCTATAA 59.349 57.895 32.97 0.00 33.86 0.98
1435 1504 3.337619 GACGACGAGGCGCCTATA 58.662 61.111 32.97 0.00 33.86 1.31
1458 1527 2.762535 TTCAATGGGAGGAGACGTTC 57.237 50.000 0.00 0.00 0.00 3.95
1459 1528 3.721087 ATTTCAATGGGAGGAGACGTT 57.279 42.857 0.00 0.00 0.00 3.99
1460 1529 3.721087 AATTTCAATGGGAGGAGACGT 57.279 42.857 0.00 0.00 0.00 4.34
1461 1530 4.034048 CGTAAATTTCAATGGGAGGAGACG 59.966 45.833 0.00 0.00 0.00 4.18
1462 1531 5.183228 TCGTAAATTTCAATGGGAGGAGAC 58.817 41.667 0.00 0.00 0.00 3.36
1463 1532 5.429681 TCGTAAATTTCAATGGGAGGAGA 57.570 39.130 0.00 0.00 0.00 3.71
1464 1533 5.880332 TCTTCGTAAATTTCAATGGGAGGAG 59.120 40.000 0.00 0.00 0.00 3.69
1465 1534 5.811190 TCTTCGTAAATTTCAATGGGAGGA 58.189 37.500 0.00 0.00 0.00 3.71
1466 1535 6.699575 ATCTTCGTAAATTTCAATGGGAGG 57.300 37.500 0.00 0.00 0.00 4.30
1467 1536 7.761409 TCAATCTTCGTAAATTTCAATGGGAG 58.239 34.615 0.00 0.00 0.00 4.30
1468 1537 7.695480 TCAATCTTCGTAAATTTCAATGGGA 57.305 32.000 0.00 0.00 0.00 4.37
1469 1538 9.450807 GTATCAATCTTCGTAAATTTCAATGGG 57.549 33.333 0.00 0.00 0.00 4.00
1470 1539 9.158364 CGTATCAATCTTCGTAAATTTCAATGG 57.842 33.333 0.00 0.00 0.00 3.16
1471 1540 9.702726 ACGTATCAATCTTCGTAAATTTCAATG 57.297 29.630 0.00 0.00 34.78 2.82
1489 1558 9.668497 ACTGCTACTCTGATATATACGTATCAA 57.332 33.333 12.24 1.57 39.77 2.57
1527 1603 9.950496 AGGGTAGACACATGAATATTATCATTC 57.050 33.333 0.00 0.00 37.96 2.67
1563 1639 3.587061 AGGATACGCATGAATATTCCCCA 59.413 43.478 12.90 0.00 46.39 4.96
1693 1780 7.253519 GCAAACTTGTTAAGGTTTTACTCGTTG 60.254 37.037 0.00 0.00 35.93 4.10
1713 1800 6.098266 ACAAAAACCCTAAGAATCAGCAAACT 59.902 34.615 0.00 0.00 0.00 2.66
1717 1804 6.478512 AAACAAAAACCCTAAGAATCAGCA 57.521 33.333 0.00 0.00 0.00 4.41
1764 1853 9.704098 GCAATTTTAGACTTAATAGTACACTGC 57.296 33.333 0.00 0.00 33.84 4.40
1807 1898 6.238484 GCAAACCGAAATCTGCACTAGAATAT 60.238 38.462 0.00 0.00 39.30 1.28
1812 1903 2.483877 TGCAAACCGAAATCTGCACTAG 59.516 45.455 0.00 0.00 39.77 2.57
1825 1916 4.730613 GCTTCATATGTAACCTGCAAACCG 60.731 45.833 1.90 0.00 0.00 4.44
1871 1962 2.803030 AAGCCTCTGCATCAACATCT 57.197 45.000 0.00 0.00 41.13 2.90
1881 1972 6.933521 TCTCATTCATATTTCTAAGCCTCTGC 59.066 38.462 0.00 0.00 37.95 4.26
1920 2011 8.287503 TCTCGGTAAAGATTTAAAAGTTGCTTC 58.712 33.333 0.00 0.00 0.00 3.86
2069 2324 4.659115 TGAGGCCATCATCAATATTCCTG 58.341 43.478 5.01 0.00 31.12 3.86
2081 2336 3.053470 TGGATGAGAAAATGAGGCCATCA 60.053 43.478 5.01 6.42 43.70 3.07
2082 2337 3.559069 TGGATGAGAAAATGAGGCCATC 58.441 45.455 5.01 0.00 31.40 3.51
2083 2338 3.675348 TGGATGAGAAAATGAGGCCAT 57.325 42.857 5.01 0.00 33.66 4.40
2178 2433 3.070302 AGCCATCTTTCGAAGGGACTATC 59.930 47.826 7.49 0.00 38.49 2.08
2183 2438 1.340017 CCAAGCCATCTTTCGAAGGGA 60.340 52.381 7.49 6.42 0.00 4.20
2204 2459 6.893005 AGTCTAGGCCTGGTATGAATAGATAC 59.107 42.308 17.99 1.43 0.00 2.24
2210 2465 3.643792 GACAGTCTAGGCCTGGTATGAAT 59.356 47.826 23.09 8.79 34.16 2.57
2215 2470 0.032416 GGGACAGTCTAGGCCTGGTA 60.032 60.000 17.99 0.00 34.16 3.25
2223 2478 3.637694 GCTAAGGTAAGGGGACAGTCTAG 59.362 52.174 0.00 0.00 0.00 2.43
2229 2528 0.252375 ACGGCTAAGGTAAGGGGACA 60.252 55.000 0.00 0.00 0.00 4.02
2266 2565 4.737054 CCATCGAAAAATATGGCATAGGC 58.263 43.478 13.39 0.00 36.50 3.93
2308 2611 2.940158 TCATGATTTCCTGCAGATGGG 58.060 47.619 17.39 0.00 0.00 4.00
2313 2616 6.971184 GTGAAGTAATTCATGATTTCCTGCAG 59.029 38.462 9.08 6.78 33.02 4.41
2360 2663 8.584157 GGATTCATCTCATACAACTGATAGAGT 58.416 37.037 0.00 0.00 35.94 3.24
2504 2807 5.230942 ACGACAAGATAACTGACAAAGGAG 58.769 41.667 0.00 0.00 0.00 3.69
2564 2867 3.190874 CAAAGATGGTACCTTCGAGAGC 58.809 50.000 19.16 0.00 0.00 4.09
2577 2880 2.363683 GGGAGCAAGAGACAAAGATGG 58.636 52.381 0.00 0.00 0.00 3.51
2584 2887 1.920325 CCTGGGGGAGCAAGAGACA 60.920 63.158 0.00 0.00 33.58 3.41
2599 2902 6.096282 TCCTGGTTTTTCTTTTCTGTAACCTG 59.904 38.462 0.00 0.00 36.76 4.00
2620 2923 1.442769 ACGCACTGCTGTATTTCCTG 58.557 50.000 0.00 0.00 0.00 3.86
2647 2950 8.852135 TCCATTTACGAAACAGGTTAAGAAATT 58.148 29.630 0.00 0.00 0.00 1.82
2663 2966 3.895656 CCTCTCCTGGTATCCATTTACGA 59.104 47.826 0.00 0.00 30.82 3.43
2668 2971 2.196742 TGCCTCTCCTGGTATCCATT 57.803 50.000 0.00 0.00 30.82 3.16
2672 2975 1.414550 GGTCTTGCCTCTCCTGGTATC 59.585 57.143 0.00 0.00 0.00 2.24
2715 3018 3.357504 GCCGTATAAGTGAAGGCGT 57.642 52.632 0.00 0.00 38.28 5.68
2772 3078 6.692486 CATCCTATGCTTATCTTAGAACCGT 58.308 40.000 0.00 0.00 0.00 4.83
2862 3168 5.349270 CCTTTCGTACATTTTCGTATGGTCA 59.651 40.000 0.00 0.00 0.00 4.02
2883 3189 5.560724 TCCAAGTTCTCATTCGAAATCCTT 58.439 37.500 0.00 0.00 0.00 3.36
3086 3412 6.481954 ACGCCGATTATCCTATTCATTTTC 57.518 37.500 0.00 0.00 0.00 2.29
3098 3424 3.846896 CGAGAGAATGTACGCCGATTATC 59.153 47.826 0.00 0.00 0.00 1.75
3145 3471 5.179368 TCGACTTCACAGGACAAAAATCATC 59.821 40.000 0.00 0.00 0.00 2.92
3187 3515 9.566624 GTCAAACATGAACAAACAAAATTATCG 57.433 29.630 0.00 0.00 0.00 2.92
3227 3555 6.150140 GCCCAATACAAATCTTAGCATAGAGG 59.850 42.308 0.00 0.00 0.00 3.69
3234 3562 6.147864 TGAATGCCCAATACAAATCTTAGC 57.852 37.500 0.00 0.00 0.00 3.09
3293 3706 3.924238 CAGGCACACTGTCAAACAC 57.076 52.632 0.00 0.00 42.42 3.32
3319 3732 8.483218 CGAATGCTCAGTACAAATCTTAGTATG 58.517 37.037 0.00 0.00 0.00 2.39
3326 3739 3.055094 ACCCGAATGCTCAGTACAAATCT 60.055 43.478 0.00 0.00 0.00 2.40
3455 3870 2.601763 GACATGACGTTTACCCTTAGCG 59.398 50.000 0.00 0.00 0.00 4.26
3484 3899 0.035056 CATTCGGCCTGAAGGAAGGT 60.035 55.000 14.13 0.00 40.79 3.50
3564 3981 0.095935 CGCTTCGTTCAGCAGATTGG 59.904 55.000 5.17 0.00 40.09 3.16
3578 3995 2.987752 AAGCTATTACGGCCGCTTC 58.012 52.632 28.58 8.73 38.21 3.86
3613 4030 1.923356 ATCCGCCCAAATGTTGTTCT 58.077 45.000 0.00 0.00 0.00 3.01
3748 4167 6.600882 ATCTGAAGCTCCAAAACAATGAAT 57.399 33.333 0.00 0.00 0.00 2.57
3868 4288 1.898574 CCTTGCAGTGCTCGGGTTT 60.899 57.895 17.60 0.00 0.00 3.27
3877 4297 2.730094 GTTGGTGGCCTTGCAGTG 59.270 61.111 3.32 0.00 0.00 3.66
3890 4312 1.384525 TCAACTTGGTCAACCGTTGG 58.615 50.000 11.35 0.00 37.69 3.77
3892 4314 3.143728 GGTATCAACTTGGTCAACCGTT 58.856 45.455 0.00 0.00 39.43 4.44
3894 4316 3.053831 AGGTATCAACTTGGTCAACCG 57.946 47.619 0.00 0.00 39.43 4.44
3895 4317 4.652822 AGAAGGTATCAACTTGGTCAACC 58.347 43.478 0.00 0.00 0.00 3.77
3911 4333 2.294512 GCTGCAAGTAAGCAAAGAAGGT 59.705 45.455 0.00 0.00 45.13 3.50
3921 4343 3.708195 GCATGGTGCTGCAAGTAAG 57.292 52.632 2.77 0.00 40.96 2.34
3928 4350 1.026584 TCACATATGCATGGTGCTGC 58.973 50.000 21.78 0.00 45.31 5.25
3934 4356 6.682423 TTAGAAGTTGTCACATATGCATGG 57.318 37.500 10.16 3.88 36.39 3.66


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

AutoCloner maintained by Alex Coulton.