Multiple sequence alignment - TraesCS1D01G279600

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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 TraesCS1D01G279600 chr1D 100.000 3718 0 0 1 3718 377573344 377569627 0.000000e+00 6866
1 TraesCS1D01G279600 chr1D 88.950 181 20 0 506 686 463333443 463333263 1.340000e-54 224
2 TraesCS1D01G279600 chr1D 86.528 193 23 3 496 686 21448385 21448576 3.760000e-50 209
3 TraesCS1D01G279600 chr1B 91.198 2931 187 28 683 3565 504507650 504504743 0.000000e+00 3917
4 TraesCS1D01G279600 chr1B 88.115 244 6 6 1 221 504508865 504508622 6.120000e-68 268
5 TraesCS1D01G279600 chr1B 90.323 93 2 2 220 306 504507902 504507811 8.440000e-22 115
6 TraesCS1D01G279600 chr1A 89.703 3059 160 74 726 3718 478258990 478256021 0.000000e+00 3760
7 TraesCS1D01G279600 chr1A 88.966 290 17 7 34 309 478259403 478259115 9.890000e-91 344
8 TraesCS1D01G279600 chr1A 89.881 168 11 2 313 474 478259158 478258991 1.050000e-50 211
9 TraesCS1D01G279600 chr5B 87.766 188 21 2 499 685 707382011 707382197 6.250000e-53 219
10 TraesCS1D01G279600 chr7A 87.709 179 22 0 500 678 675583292 675583470 3.760000e-50 209
11 TraesCS1D01G279600 chr2D 86.772 189 23 2 499 686 499895174 499894987 3.760000e-50 209
12 TraesCS1D01G279600 chr5A 86.243 189 24 2 499 686 1773439 1773626 1.750000e-48 204
13 TraesCS1D01G279600 chr4D 86.243 189 25 1 499 686 12695891 12696079 1.750000e-48 204
14 TraesCS1D01G279600 chr3A 86.243 189 25 1 499 686 10238956 10238768 1.750000e-48 204
15 TraesCS1D01G279600 chrUn 84.314 204 27 3 487 686 51420763 51420561 1.050000e-45 195


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 TraesCS1D01G279600 chr1D 377569627 377573344 3717 True 6866.000000 6866 100.000000 1 3718 1 chr1D.!!$R1 3717
1 TraesCS1D01G279600 chr1B 504504743 504508865 4122 True 1433.333333 3917 89.878667 1 3565 3 chr1B.!!$R1 3564
2 TraesCS1D01G279600 chr1A 478256021 478259403 3382 True 1438.333333 3760 89.516667 34 3718 3 chr1A.!!$R1 3684

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
309 1070 0.032130 TCAGTGCCTGACGAAGACAC 59.968 55.0 0.00 0.00 35.39 3.67 F
310 1071 0.032678 CAGTGCCTGACGAAGACACT 59.967 55.0 6.14 6.14 42.09 3.55 F
311 1072 0.032678 AGTGCCTGACGAAGACACTG 59.967 55.0 10.05 0.00 39.97 3.66 F
315 1076 0.032678 CCTGACGAAGACACTGCACT 59.967 55.0 0.00 0.00 0.00 4.40 F
714 1476 0.108396 TACAGCAGCCAGAGTGCAAA 59.892 50.0 0.00 0.00 43.82 3.68 F
2274 3058 0.178068 AAGAAGTCTGGTGCGTGTGT 59.822 50.0 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 3029 0.251634 CAGACTTCTTCCTGGGCTCC 59.748 60.000 0.00 0.00 0.00 4.70 R
2274 3058 2.485835 CCAAAACAGGTGTTACGAGGGA 60.486 50.000 0.00 0.00 37.25 4.20 R
2352 3136 1.946267 CGAAAGACACCAAACGGGG 59.054 57.895 0.00 0.00 42.91 5.73 R
2431 3215 2.261671 CCGAGGTCGTCCAGGTTG 59.738 66.667 0.51 0.00 37.74 3.77 R
2562 3347 0.321919 TGATCAAGGCCTCTGTGCAC 60.322 55.000 5.23 10.75 0.00 4.57 R
3664 4520 0.179000 CGTTCCTTCCAGCTATGCCT 59.821 55.000 0.00 0.00 0.00 4.75 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
72 83 3.968180 GCGACTTTAATGCGCTGC 58.032 55.556 9.73 0.00 46.53 5.25
111 122 6.496911 ACACAACTTAAATTCCCAAAGCCTAT 59.503 34.615 0.00 0.00 0.00 2.57
112 123 6.813152 CACAACTTAAATTCCCAAAGCCTATG 59.187 38.462 0.00 0.00 0.00 2.23
115 126 7.640597 ACTTAAATTCCCAAAGCCTATGTAC 57.359 36.000 0.00 0.00 0.00 2.90
309 1070 0.032130 TCAGTGCCTGACGAAGACAC 59.968 55.000 0.00 0.00 35.39 3.67
310 1071 0.032678 CAGTGCCTGACGAAGACACT 59.967 55.000 6.14 6.14 42.09 3.55
311 1072 0.032678 AGTGCCTGACGAAGACACTG 59.967 55.000 10.05 0.00 39.97 3.66
312 1073 1.300931 TGCCTGACGAAGACACTGC 60.301 57.895 0.00 0.00 0.00 4.40
313 1074 1.300931 GCCTGACGAAGACACTGCA 60.301 57.895 0.00 0.00 0.00 4.41
314 1075 1.560860 GCCTGACGAAGACACTGCAC 61.561 60.000 0.00 0.00 0.00 4.57
315 1076 0.032678 CCTGACGAAGACACTGCACT 59.967 55.000 0.00 0.00 0.00 4.40
316 1077 1.135046 CTGACGAAGACACTGCACTG 58.865 55.000 0.00 0.00 0.00 3.66
317 1078 0.875908 TGACGAAGACACTGCACTGC 60.876 55.000 0.00 0.00 0.00 4.40
318 1079 0.875908 GACGAAGACACTGCACTGCA 60.876 55.000 3.11 3.11 36.92 4.41
319 1080 1.154205 ACGAAGACACTGCACTGCAC 61.154 55.000 0.00 0.00 33.79 4.57
320 1081 0.877649 CGAAGACACTGCACTGCACT 60.878 55.000 0.00 0.00 33.79 4.40
321 1082 0.585357 GAAGACACTGCACTGCACTG 59.415 55.000 0.00 4.38 33.79 3.66
322 1083 0.816825 AAGACACTGCACTGCACTGG 60.817 55.000 13.31 2.18 33.79 4.00
323 1084 1.524621 GACACTGCACTGCACTGGT 60.525 57.895 13.31 6.44 33.79 4.00
324 1085 1.077501 ACACTGCACTGCACTGGTT 60.078 52.632 13.31 0.00 33.79 3.67
325 1086 0.680921 ACACTGCACTGCACTGGTTT 60.681 50.000 13.31 0.00 33.79 3.27
326 1087 1.308047 CACTGCACTGCACTGGTTTA 58.692 50.000 0.00 0.00 33.79 2.01
327 1088 1.265095 CACTGCACTGCACTGGTTTAG 59.735 52.381 0.00 0.00 33.79 1.85
328 1089 0.877071 CTGCACTGCACTGGTTTAGG 59.123 55.000 0.00 0.00 33.79 2.69
329 1090 0.182537 TGCACTGCACTGGTTTAGGT 59.817 50.000 0.00 0.00 31.71 3.08
330 1091 1.318576 GCACTGCACTGGTTTAGGTT 58.681 50.000 0.00 0.00 0.00 3.50
331 1092 1.681264 GCACTGCACTGGTTTAGGTTT 59.319 47.619 0.00 0.00 0.00 3.27
332 1093 2.287608 GCACTGCACTGGTTTAGGTTTC 60.288 50.000 0.00 0.00 0.00 2.78
333 1094 2.032030 CACTGCACTGGTTTAGGTTTCG 60.032 50.000 0.00 0.00 0.00 3.46
334 1095 1.535462 CTGCACTGGTTTAGGTTTCGG 59.465 52.381 0.00 0.00 0.00 4.30
335 1096 1.134037 TGCACTGGTTTAGGTTTCGGT 60.134 47.619 0.00 0.00 0.00 4.69
336 1097 1.534163 GCACTGGTTTAGGTTTCGGTC 59.466 52.381 0.00 0.00 0.00 4.79
337 1098 2.841215 CACTGGTTTAGGTTTCGGTCA 58.159 47.619 0.00 0.00 0.00 4.02
338 1099 2.806244 CACTGGTTTAGGTTTCGGTCAG 59.194 50.000 0.00 0.00 0.00 3.51
339 1100 2.436911 ACTGGTTTAGGTTTCGGTCAGT 59.563 45.455 0.00 0.00 0.00 3.41
340 1101 2.806244 CTGGTTTAGGTTTCGGTCAGTG 59.194 50.000 0.00 0.00 0.00 3.66
341 1102 1.534163 GGTTTAGGTTTCGGTCAGTGC 59.466 52.381 0.00 0.00 0.00 4.40
342 1103 1.534163 GTTTAGGTTTCGGTCAGTGCC 59.466 52.381 0.00 0.00 0.00 5.01
343 1104 1.053424 TTAGGTTTCGGTCAGTGCCT 58.947 50.000 2.74 0.00 0.00 4.75
344 1105 1.927487 TAGGTTTCGGTCAGTGCCTA 58.073 50.000 2.74 0.00 0.00 3.93
345 1106 1.053424 AGGTTTCGGTCAGTGCCTAA 58.947 50.000 2.74 0.00 0.00 2.69
346 1107 1.154197 GGTTTCGGTCAGTGCCTAAC 58.846 55.000 2.74 6.16 0.00 2.34
347 1108 0.788391 GTTTCGGTCAGTGCCTAACG 59.212 55.000 2.74 0.00 0.00 3.18
348 1109 0.675083 TTTCGGTCAGTGCCTAACGA 59.325 50.000 0.00 0.00 0.00 3.85
349 1110 0.675083 TTCGGTCAGTGCCTAACGAA 59.325 50.000 0.00 0.00 37.91 3.85
352 1113 1.711206 GGTCAGTGCCTAACGAAGAC 58.289 55.000 0.00 0.00 32.57 3.01
358 1119 3.997021 CAGTGCCTAACGAAGACAGAAAT 59.003 43.478 0.00 0.00 0.00 2.17
384 1146 3.381590 GCCTTTCCCGCTATTCTGATTTT 59.618 43.478 0.00 0.00 0.00 1.82
388 1150 3.541632 TCCCGCTATTCTGATTTTGGTC 58.458 45.455 0.00 0.00 0.00 4.02
415 1177 2.481568 GTGGGTTCAGCTACCGTTTAAC 59.518 50.000 0.00 0.00 39.18 2.01
423 1185 3.007635 AGCTACCGTTTAACAATCTGGC 58.992 45.455 0.00 0.00 0.00 4.85
427 1189 1.202031 CCGTTTAACAATCTGGCGAGC 60.202 52.381 0.00 0.00 0.00 5.03
433 1195 3.390521 AATCTGGCGAGCGGGTGA 61.391 61.111 0.00 0.00 0.00 4.02
470 1232 8.236586 ACATGGCGCACATAATAAATGTAATAG 58.763 33.333 10.83 0.00 37.84 1.73
529 1291 9.745018 TTGAGAAAACTTCCAATCTATTCATCT 57.255 29.630 0.00 0.00 0.00 2.90
530 1292 9.745018 TGAGAAAACTTCCAATCTATTCATCTT 57.255 29.630 0.00 0.00 0.00 2.40
532 1294 9.745018 AGAAAACTTCCAATCTATTCATCTTCA 57.255 29.630 0.00 0.00 0.00 3.02
536 1298 9.690913 AACTTCCAATCTATTCATCTTCAATCA 57.309 29.630 0.00 0.00 0.00 2.57
537 1299 9.863650 ACTTCCAATCTATTCATCTTCAATCAT 57.136 29.630 0.00 0.00 0.00 2.45
539 1301 8.631480 TCCAATCTATTCATCTTCAATCATGG 57.369 34.615 0.00 0.00 0.00 3.66
540 1302 8.222637 TCCAATCTATTCATCTTCAATCATGGT 58.777 33.333 0.00 0.00 0.00 3.55
541 1303 9.511272 CCAATCTATTCATCTTCAATCATGGTA 57.489 33.333 0.00 0.00 0.00 3.25
549 1311 9.551734 TTCATCTTCAATCATGGTAATACAGAG 57.448 33.333 0.00 0.00 0.00 3.35
550 1312 8.152898 TCATCTTCAATCATGGTAATACAGAGG 58.847 37.037 0.00 0.00 0.00 3.69
551 1313 7.675161 TCTTCAATCATGGTAATACAGAGGA 57.325 36.000 0.00 0.00 0.00 3.71
552 1314 7.500992 TCTTCAATCATGGTAATACAGAGGAC 58.499 38.462 0.00 0.00 0.00 3.85
553 1315 6.806668 TCAATCATGGTAATACAGAGGACA 57.193 37.500 0.00 0.00 0.00 4.02
554 1316 7.379059 TCAATCATGGTAATACAGAGGACAT 57.621 36.000 0.00 0.00 0.00 3.06
555 1317 7.445121 TCAATCATGGTAATACAGAGGACATC 58.555 38.462 0.00 0.00 0.00 3.06
556 1318 7.071071 TCAATCATGGTAATACAGAGGACATCA 59.929 37.037 0.00 0.00 0.00 3.07
557 1319 6.410942 TCATGGTAATACAGAGGACATCAG 57.589 41.667 0.00 0.00 0.00 2.90
558 1320 6.136155 TCATGGTAATACAGAGGACATCAGA 58.864 40.000 0.00 0.00 0.00 3.27
559 1321 6.611236 TCATGGTAATACAGAGGACATCAGAA 59.389 38.462 0.00 0.00 0.00 3.02
560 1322 6.867519 TGGTAATACAGAGGACATCAGAAA 57.132 37.500 0.00 0.00 0.00 2.52
561 1323 7.437713 TGGTAATACAGAGGACATCAGAAAT 57.562 36.000 0.00 0.00 0.00 2.17
562 1324 8.547481 TGGTAATACAGAGGACATCAGAAATA 57.453 34.615 0.00 0.00 0.00 1.40
563 1325 8.988060 TGGTAATACAGAGGACATCAGAAATAA 58.012 33.333 0.00 0.00 0.00 1.40
590 1352 7.812690 AAAATTATATCCAGGTCCGTAAACC 57.187 36.000 0.00 0.00 39.80 3.27
591 1353 6.503560 AATTATATCCAGGTCCGTAAACCA 57.496 37.500 2.23 0.00 42.12 3.67
592 1354 6.697641 ATTATATCCAGGTCCGTAAACCAT 57.302 37.500 2.23 0.00 42.12 3.55
593 1355 4.618920 ATATCCAGGTCCGTAAACCATC 57.381 45.455 2.23 0.00 42.12 3.51
594 1356 1.946984 TCCAGGTCCGTAAACCATCT 58.053 50.000 2.23 0.00 42.12 2.90
595 1357 3.104519 TCCAGGTCCGTAAACCATCTA 57.895 47.619 2.23 0.00 42.12 1.98
596 1358 3.028850 TCCAGGTCCGTAAACCATCTAG 58.971 50.000 2.23 0.00 42.12 2.43
597 1359 2.764572 CCAGGTCCGTAAACCATCTAGT 59.235 50.000 2.23 0.00 42.12 2.57
598 1360 3.430374 CCAGGTCCGTAAACCATCTAGTG 60.430 52.174 2.23 0.00 42.12 2.74
599 1361 3.446161 CAGGTCCGTAAACCATCTAGTGA 59.554 47.826 2.23 0.00 42.12 3.41
600 1362 4.099573 CAGGTCCGTAAACCATCTAGTGAT 59.900 45.833 2.23 0.00 42.12 3.06
616 1378 7.881775 TCTAGTGATGACTATAAGCACTGAA 57.118 36.000 4.69 0.00 39.84 3.02
617 1379 7.935520 TCTAGTGATGACTATAAGCACTGAAG 58.064 38.462 4.69 0.00 39.84 3.02
618 1380 5.355596 AGTGATGACTATAAGCACTGAAGC 58.644 41.667 0.00 0.00 38.30 3.86
619 1381 4.208047 GTGATGACTATAAGCACTGAAGCG 59.792 45.833 0.00 0.00 40.15 4.68
620 1382 4.097892 TGATGACTATAAGCACTGAAGCGA 59.902 41.667 0.00 0.00 40.15 4.93
621 1383 4.033990 TGACTATAAGCACTGAAGCGAG 57.966 45.455 0.00 0.00 40.15 5.03
622 1384 2.792116 GACTATAAGCACTGAAGCGAGC 59.208 50.000 0.00 0.00 40.15 5.03
623 1385 2.131183 CTATAAGCACTGAAGCGAGCC 58.869 52.381 0.00 0.00 40.15 4.70
624 1386 0.807667 ATAAGCACTGAAGCGAGCCG 60.808 55.000 0.00 0.00 40.15 5.52
625 1387 1.873270 TAAGCACTGAAGCGAGCCGA 61.873 55.000 0.00 0.00 40.15 5.54
626 1388 2.715532 AAGCACTGAAGCGAGCCGAA 62.716 55.000 0.00 0.00 40.15 4.30
627 1389 2.734673 GCACTGAAGCGAGCCGAAG 61.735 63.158 0.00 0.00 0.00 3.79
628 1390 1.080501 CACTGAAGCGAGCCGAAGA 60.081 57.895 0.00 0.00 0.00 2.87
629 1391 1.080434 ACTGAAGCGAGCCGAAGAC 60.080 57.895 0.00 0.00 0.00 3.01
630 1392 2.126463 TGAAGCGAGCCGAAGACG 60.126 61.111 0.00 0.00 39.43 4.18
646 1408 4.505217 CGCAGCGCCGTCAACATC 62.505 66.667 2.29 0.00 0.00 3.06
647 1409 4.166011 GCAGCGCCGTCAACATCC 62.166 66.667 2.29 0.00 0.00 3.51
648 1410 3.499737 CAGCGCCGTCAACATCCC 61.500 66.667 2.29 0.00 0.00 3.85
649 1411 3.706373 AGCGCCGTCAACATCCCT 61.706 61.111 2.29 0.00 0.00 4.20
650 1412 2.746277 GCGCCGTCAACATCCCTT 60.746 61.111 0.00 0.00 0.00 3.95
651 1413 2.750888 GCGCCGTCAACATCCCTTC 61.751 63.158 0.00 0.00 0.00 3.46
652 1414 2.106683 CGCCGTCAACATCCCTTCC 61.107 63.158 0.00 0.00 0.00 3.46
653 1415 1.299976 GCCGTCAACATCCCTTCCT 59.700 57.895 0.00 0.00 0.00 3.36
654 1416 0.744771 GCCGTCAACATCCCTTCCTC 60.745 60.000 0.00 0.00 0.00 3.71
655 1417 0.460284 CCGTCAACATCCCTTCCTCG 60.460 60.000 0.00 0.00 0.00 4.63
656 1418 1.084370 CGTCAACATCCCTTCCTCGC 61.084 60.000 0.00 0.00 0.00 5.03
657 1419 0.744771 GTCAACATCCCTTCCTCGCC 60.745 60.000 0.00 0.00 0.00 5.54
658 1420 1.198094 TCAACATCCCTTCCTCGCCA 61.198 55.000 0.00 0.00 0.00 5.69
659 1421 0.745845 CAACATCCCTTCCTCGCCAG 60.746 60.000 0.00 0.00 0.00 4.85
660 1422 0.909610 AACATCCCTTCCTCGCCAGA 60.910 55.000 0.00 0.00 0.00 3.86
661 1423 1.333636 ACATCCCTTCCTCGCCAGAG 61.334 60.000 0.00 0.00 43.98 3.35
662 1424 1.002274 ATCCCTTCCTCGCCAGAGT 59.998 57.895 0.00 0.00 42.86 3.24
663 1425 1.045911 ATCCCTTCCTCGCCAGAGTC 61.046 60.000 0.00 0.00 42.86 3.36
664 1426 2.492090 CCTTCCTCGCCAGAGTCG 59.508 66.667 0.00 0.00 42.86 4.18
665 1427 2.492090 CTTCCTCGCCAGAGTCGG 59.508 66.667 0.00 0.00 42.86 4.79
666 1428 3.068691 TTCCTCGCCAGAGTCGGG 61.069 66.667 4.73 4.73 42.86 5.14
673 1435 4.800554 CCAGAGTCGGGCAAAACT 57.199 55.556 0.00 0.00 0.00 2.66
674 1436 3.021451 CCAGAGTCGGGCAAAACTT 57.979 52.632 0.00 0.00 0.00 2.66
675 1437 0.593128 CCAGAGTCGGGCAAAACTTG 59.407 55.000 0.00 0.00 0.00 3.16
676 1438 1.308998 CAGAGTCGGGCAAAACTTGT 58.691 50.000 0.00 0.00 0.00 3.16
677 1439 1.676006 CAGAGTCGGGCAAAACTTGTT 59.324 47.619 0.00 0.00 0.00 2.83
678 1440 2.875933 CAGAGTCGGGCAAAACTTGTTA 59.124 45.455 0.00 0.00 0.00 2.41
679 1441 3.502211 CAGAGTCGGGCAAAACTTGTTAT 59.498 43.478 0.00 0.00 0.00 1.89
680 1442 4.693566 CAGAGTCGGGCAAAACTTGTTATA 59.306 41.667 0.00 0.00 0.00 0.98
681 1443 4.935808 AGAGTCGGGCAAAACTTGTTATAG 59.064 41.667 0.00 0.00 0.00 1.31
703 1465 5.764131 AGTAGAACGATAGATTACAGCAGC 58.236 41.667 0.00 0.00 41.38 5.25
714 1476 0.108396 TACAGCAGCCAGAGTGCAAA 59.892 50.000 0.00 0.00 43.82 3.68
718 1480 0.389426 GCAGCCAGAGTGCAAAATGG 60.389 55.000 7.75 7.75 40.86 3.16
745 1507 4.671377 TGCAATAAATCGGAGCACAATTC 58.329 39.130 0.00 0.00 0.00 2.17
756 1522 8.627208 ATCGGAGCACAATTCATAATCTAAAT 57.373 30.769 0.00 0.00 0.00 1.40
794 1561 3.626028 AAAGTTCGGAGCACAATTCAC 57.374 42.857 0.00 0.00 0.00 3.18
798 1565 2.370281 TCGGAGCACAATTCACTCTC 57.630 50.000 0.00 0.00 0.00 3.20
834 1601 8.609176 GTCGGAATATACTTTAGAAATTGTGCA 58.391 33.333 0.00 0.00 0.00 4.57
852 1625 0.452184 CACAGACGAGGTATGCGAGT 59.548 55.000 0.00 0.00 0.00 4.18
858 1631 1.202973 CGAGGTATGCGAGTTGAGCG 61.203 60.000 0.00 0.00 37.44 5.03
879 1652 4.329619 CGTGCTACGGTTCACACA 57.670 55.556 11.80 0.00 38.08 3.72
918 1691 2.221169 TCACTCCACTCACAAATGCAC 58.779 47.619 0.00 0.00 0.00 4.57
920 1693 0.518636 CTCCACTCACAAATGCACGG 59.481 55.000 0.00 0.00 0.00 4.94
921 1694 1.081242 CCACTCACAAATGCACGGC 60.081 57.895 0.00 0.00 0.00 5.68
922 1695 1.653667 CACTCACAAATGCACGGCA 59.346 52.632 0.00 1.01 44.86 5.69
925 1698 1.518056 CTCACAAATGCACGGCAGGT 61.518 55.000 0.00 1.10 43.65 4.00
926 1699 1.106351 TCACAAATGCACGGCAGGTT 61.106 50.000 0.00 0.00 43.65 3.50
927 1700 0.595588 CACAAATGCACGGCAGGTTA 59.404 50.000 0.00 0.00 43.65 2.85
928 1701 1.000827 CACAAATGCACGGCAGGTTAA 60.001 47.619 0.00 0.00 43.65 2.01
1015 1792 4.095932 GGCCTCTCTTTTATAAACCCAACG 59.904 45.833 0.00 0.00 0.00 4.10
1016 1793 4.095932 GCCTCTCTTTTATAAACCCAACGG 59.904 45.833 0.00 0.00 0.00 4.44
1065 1842 1.383799 CCCCAGCTCAAACCCATCA 59.616 57.895 0.00 0.00 0.00 3.07
1144 1925 0.250640 CACAGCACTCCTCTGCCTTT 60.251 55.000 0.00 0.00 37.96 3.11
1155 1936 0.606096 TCTGCCTTTCATTCGACGGA 59.394 50.000 0.00 0.00 0.00 4.69
1161 1942 2.162338 TTTCATTCGACGGACGGCCT 62.162 55.000 5.33 0.00 42.82 5.19
1162 1943 2.125673 CATTCGACGGACGGCCTT 60.126 61.111 5.33 0.00 42.82 4.35
1170 1951 3.760035 GGACGGCCTTCTCGCTCA 61.760 66.667 9.40 0.00 0.00 4.26
1223 2004 3.605749 AATGGCGGTGGAGTGGTCG 62.606 63.158 0.00 0.00 0.00 4.79
1328 2109 1.107114 GGAGCGAGAGTGATGAGGAA 58.893 55.000 0.00 0.00 0.00 3.36
1435 2216 7.264373 TCTTGTTCCTTCAATCTTTCTGTTC 57.736 36.000 0.00 0.00 0.00 3.18
1454 2235 1.494189 GCGTGGTTCGTTATGCGTT 59.506 52.632 0.00 0.00 42.13 4.84
1486 2267 1.128692 GGTTCCTGATTGTTCGCTTCG 59.871 52.381 0.00 0.00 0.00 3.79
1489 2270 2.066262 TCCTGATTGTTCGCTTCGTTC 58.934 47.619 0.00 0.00 0.00 3.95
1701 2482 2.267961 GGCCACCCCTACGTCTTG 59.732 66.667 0.00 0.00 0.00 3.02
1812 2593 2.345760 CGGCGTGTACTACCACCCT 61.346 63.158 0.00 0.00 31.47 4.34
1860 2641 2.746947 TACAGGCTGCCAGGGTGAGA 62.747 60.000 22.65 1.52 0.00 3.27
1862 2643 1.927527 AGGCTGCCAGGGTGAGATT 60.928 57.895 22.65 0.00 0.00 2.40
1882 2663 1.136147 CAGTTGCATGGCGCTCTTC 59.864 57.895 7.64 0.00 43.06 2.87
1913 2696 6.592220 GTCTCCTACCTGAAGATTTCTTGTTC 59.408 42.308 0.00 0.00 36.11 3.18
1924 2707 8.292448 TGAAGATTTCTTGTTCTTAACATCTGC 58.708 33.333 0.00 0.00 41.79 4.26
1931 2715 5.493133 TGTTCTTAACATCTGCGTTTGTT 57.507 34.783 3.86 3.86 39.32 2.83
1940 2724 4.326009 ACATCTGCGTTTGTTTTTGTGTTC 59.674 37.500 0.00 0.00 0.00 3.18
2173 2957 4.778143 ATGCGGGCCGTGTTCCTC 62.778 66.667 28.82 9.29 0.00 3.71
2274 3058 0.178068 AAGAAGTCTGGTGCGTGTGT 59.822 50.000 0.00 0.00 0.00 3.72
2317 3101 2.158841 CCGTTCTGGTTGTTGATTACCG 59.841 50.000 0.00 0.00 37.23 4.02
2352 3136 4.025979 CGTCGTTGGTGGCTAAATATTCTC 60.026 45.833 0.00 0.00 0.00 2.87
2431 3215 1.592081 GTCGTGCATGCTCTGAATCTC 59.408 52.381 20.33 2.50 0.00 2.75
2437 3221 2.355132 GCATGCTCTGAATCTCAACCTG 59.645 50.000 11.37 0.00 0.00 4.00
2501 3285 4.625028 TCTTGATCATGGTAAGCATCTCG 58.375 43.478 8.60 0.00 0.00 4.04
2505 3289 1.067060 TCATGGTAAGCATCTCGTCCG 59.933 52.381 0.00 0.00 0.00 4.79
2510 3294 1.135199 GTAAGCATCTCGTCCGGAACA 60.135 52.381 5.23 0.00 0.00 3.18
2511 3295 0.537188 AAGCATCTCGTCCGGAACAT 59.463 50.000 5.23 0.00 0.00 2.71
2513 3297 1.338337 AGCATCTCGTCCGGAACATAG 59.662 52.381 5.23 0.97 0.00 2.23
2514 3298 1.772182 CATCTCGTCCGGAACATAGC 58.228 55.000 5.23 0.00 0.00 2.97
2516 3300 1.471119 TCTCGTCCGGAACATAGCTT 58.529 50.000 5.23 0.00 0.00 3.74
2519 3303 3.004419 TCTCGTCCGGAACATAGCTTATG 59.996 47.826 5.23 0.00 41.88 1.90
2562 3347 1.005748 TGACAGCGAGCTCTGTTGG 60.006 57.895 20.03 4.68 46.40 3.77
2566 3351 2.666190 GCGAGCTCTGTTGGTGCA 60.666 61.111 12.85 0.00 36.95 4.57
2673 3458 0.249322 ACAGTTCGTGAACCCAGTCG 60.249 55.000 9.03 0.00 42.06 4.18
2701 3486 2.641197 ACAATCCGTGTTCTTGGCC 58.359 52.632 0.00 0.00 37.01 5.36
2711 3496 3.056179 CGTGTTCTTGGCCCCATTTAATT 60.056 43.478 0.00 0.00 0.00 1.40
2876 3681 3.626670 GGAGATGGATGAACAAGCAAGAG 59.373 47.826 0.00 0.00 0.00 2.85
2893 3698 6.606069 AGCAAGAGATCCATGTCTAGTAGTA 58.394 40.000 0.00 0.00 29.33 1.82
2894 3699 6.714810 AGCAAGAGATCCATGTCTAGTAGTAG 59.285 42.308 0.00 0.00 29.33 2.57
2895 3700 6.488683 GCAAGAGATCCATGTCTAGTAGTAGT 59.511 42.308 4.51 0.00 29.33 2.73
2896 3701 7.662258 GCAAGAGATCCATGTCTAGTAGTAGTA 59.338 40.741 4.51 0.00 29.33 1.82
2897 3702 9.214957 CAAGAGATCCATGTCTAGTAGTAGTAG 57.785 40.741 5.75 5.75 29.33 2.57
2898 3703 8.500667 AGAGATCCATGTCTAGTAGTAGTAGT 57.499 38.462 11.08 0.00 0.00 2.73
2924 3729 5.243060 GGTTTGTTAGAAGCAATAAGTGGGT 59.757 40.000 0.00 0.00 0.00 4.51
2949 3754 0.394488 TCGGAGGCGAGAGAGATGTT 60.394 55.000 0.00 0.00 0.00 2.71
2970 3775 0.796312 TAGCTGTTTGTAGCAAGCGC 59.204 50.000 0.00 0.00 46.07 5.92
3013 3822 6.715280 AGTGAAATGAGGCTAATCTTGAAGA 58.285 36.000 0.00 0.00 0.00 2.87
3136 3956 2.144952 CCCCCTTTTGCAGCCTTTT 58.855 52.632 0.00 0.00 0.00 2.27
3187 4011 2.172851 TGAATAAGGGCGTTCGTTGT 57.827 45.000 0.00 0.00 0.00 3.32
3188 4012 1.801771 TGAATAAGGGCGTTCGTTGTG 59.198 47.619 0.00 0.00 0.00 3.33
3190 4014 2.747396 ATAAGGGCGTTCGTTGTGTA 57.253 45.000 0.00 0.00 0.00 2.90
3237 4071 8.106247 TGGTTTTTCTTGTAATAGCTAGTTGG 57.894 34.615 0.00 0.00 0.00 3.77
3287 4125 3.029735 GCAACCGCCGCAAAGTTG 61.030 61.111 11.64 11.64 42.95 3.16
3308 4146 6.653740 AGTTGGGCTCGGCTTTATAATAATAC 59.346 38.462 0.00 0.00 0.00 1.89
3311 4149 7.909518 TGGGCTCGGCTTTATAATAATACTAA 58.090 34.615 0.00 0.00 0.00 2.24
3312 4150 8.545472 TGGGCTCGGCTTTATAATAATACTAAT 58.455 33.333 0.00 0.00 0.00 1.73
3313 4151 8.827677 GGGCTCGGCTTTATAATAATACTAATG 58.172 37.037 0.00 0.00 0.00 1.90
3386 4224 7.425606 GCGGTCTCATTTATTTGGTAATGATT 58.574 34.615 0.00 0.00 39.34 2.57
3445 4283 0.692419 CATCTGAGGGGCACTAGGGT 60.692 60.000 0.00 0.00 0.00 4.34
3596 4434 1.070445 CACGGGATCTGCATCTCCC 59.930 63.158 19.38 19.38 46.59 4.30
3620 4459 1.487231 CGTCTGAAAACGACGCCTG 59.513 57.895 0.00 0.00 46.12 4.85
3633 4472 3.005539 GCCTGTGGCCTCTCCTCA 61.006 66.667 3.32 0.00 44.06 3.86
3634 4473 2.985456 CCTGTGGCCTCTCCTCAC 59.015 66.667 3.32 0.00 34.82 3.51
3635 4474 2.664081 CCTGTGGCCTCTCCTCACC 61.664 68.421 3.32 0.00 34.82 4.02
3636 4475 1.611851 CTGTGGCCTCTCCTCACCT 60.612 63.158 3.32 0.00 34.82 4.00
3645 4489 1.078567 CTCCTCACCTTGCTGGCTC 60.079 63.158 0.00 0.00 40.22 4.70
3649 4493 3.429141 CACCTTGCTGGCTCGCTG 61.429 66.667 1.45 0.00 40.22 5.18
3664 4520 3.066190 CTGGGACGGTCCAGCGTA 61.066 66.667 27.32 8.06 46.47 4.42
3670 4526 1.731433 GACGGTCCAGCGTAGGCATA 61.731 60.000 10.48 0.00 43.41 3.14
3676 4532 4.277552 AGCGTAGGCATAGCTGGA 57.722 55.556 10.48 0.00 43.41 3.86
3677 4533 2.516448 AGCGTAGGCATAGCTGGAA 58.484 52.632 10.48 0.00 43.41 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 83 4.882671 AGTTGTGTTCTTTGTACTGCTG 57.117 40.909 0.00 0.00 0.00 4.41
111 122 4.202060 GCATCCTCTCGAGATTTCTGTACA 60.202 45.833 17.03 0.00 0.00 2.90
112 123 4.202060 TGCATCCTCTCGAGATTTCTGTAC 60.202 45.833 17.03 2.03 0.00 2.90
115 126 3.449528 TGCATCCTCTCGAGATTTCTG 57.550 47.619 17.03 12.04 0.00 3.02
263 1019 1.072331 CCTAAACCAGTGCAGTGGAGT 59.928 52.381 40.79 29.28 40.44 3.85
309 1070 0.877071 CCTAAACCAGTGCAGTGCAG 59.123 55.000 20.42 9.88 40.08 4.41
310 1071 0.182537 ACCTAAACCAGTGCAGTGCA 59.817 50.000 15.37 15.37 35.60 4.57
311 1072 1.318576 AACCTAAACCAGTGCAGTGC 58.681 50.000 16.47 8.58 0.00 4.40
312 1073 2.032030 CGAAACCTAAACCAGTGCAGTG 60.032 50.000 14.95 14.95 0.00 3.66
313 1074 2.218603 CGAAACCTAAACCAGTGCAGT 58.781 47.619 0.00 0.00 0.00 4.40
314 1075 1.535462 CCGAAACCTAAACCAGTGCAG 59.465 52.381 0.00 0.00 0.00 4.41
315 1076 1.134037 ACCGAAACCTAAACCAGTGCA 60.134 47.619 0.00 0.00 0.00 4.57
316 1077 1.534163 GACCGAAACCTAAACCAGTGC 59.466 52.381 0.00 0.00 0.00 4.40
317 1078 2.806244 CTGACCGAAACCTAAACCAGTG 59.194 50.000 0.00 0.00 0.00 3.66
318 1079 2.436911 ACTGACCGAAACCTAAACCAGT 59.563 45.455 0.00 0.00 0.00 4.00
319 1080 2.806244 CACTGACCGAAACCTAAACCAG 59.194 50.000 0.00 0.00 0.00 4.00
320 1081 2.841215 CACTGACCGAAACCTAAACCA 58.159 47.619 0.00 0.00 0.00 3.67
321 1082 1.534163 GCACTGACCGAAACCTAAACC 59.466 52.381 0.00 0.00 0.00 3.27
322 1083 1.534163 GGCACTGACCGAAACCTAAAC 59.466 52.381 0.00 0.00 0.00 2.01
323 1084 1.418637 AGGCACTGACCGAAACCTAAA 59.581 47.619 0.00 0.00 37.18 1.85
324 1085 1.053424 AGGCACTGACCGAAACCTAA 58.947 50.000 0.00 0.00 37.18 2.69
325 1086 1.927487 TAGGCACTGACCGAAACCTA 58.073 50.000 0.00 0.00 41.52 3.08
326 1087 1.053424 TTAGGCACTGACCGAAACCT 58.947 50.000 0.00 0.00 41.52 3.50
327 1088 1.154197 GTTAGGCACTGACCGAAACC 58.846 55.000 0.00 0.00 39.19 3.27
328 1089 0.788391 CGTTAGGCACTGACCGAAAC 59.212 55.000 0.00 0.00 42.36 2.78
329 1090 0.675083 TCGTTAGGCACTGACCGAAA 59.325 50.000 0.00 0.00 42.36 3.46
330 1091 0.675083 TTCGTTAGGCACTGACCGAA 59.325 50.000 0.00 0.00 42.36 4.30
331 1092 0.242825 CTTCGTTAGGCACTGACCGA 59.757 55.000 0.00 0.00 42.36 4.69
332 1093 0.242825 TCTTCGTTAGGCACTGACCG 59.757 55.000 0.00 0.00 42.36 4.79
333 1094 1.000506 TGTCTTCGTTAGGCACTGACC 59.999 52.381 0.00 0.00 42.36 4.02
334 1095 2.030185 TCTGTCTTCGTTAGGCACTGAC 60.030 50.000 0.00 0.00 41.89 3.51
335 1096 2.235891 TCTGTCTTCGTTAGGCACTGA 58.764 47.619 0.00 0.00 41.52 3.41
336 1097 2.724977 TCTGTCTTCGTTAGGCACTG 57.275 50.000 0.00 0.00 41.52 3.66
337 1098 3.746045 TTTCTGTCTTCGTTAGGCACT 57.254 42.857 0.00 0.00 46.37 4.40
338 1099 5.358298 AAATTTCTGTCTTCGTTAGGCAC 57.642 39.130 0.00 0.00 32.31 5.01
339 1100 5.757886 CAAAATTTCTGTCTTCGTTAGGCA 58.242 37.500 0.00 0.00 35.72 4.75
340 1101 4.617223 GCAAAATTTCTGTCTTCGTTAGGC 59.383 41.667 0.00 0.00 0.00 3.93
341 1102 5.048713 AGGCAAAATTTCTGTCTTCGTTAGG 60.049 40.000 0.00 0.00 0.00 2.69
342 1103 6.002062 AGGCAAAATTTCTGTCTTCGTTAG 57.998 37.500 0.00 0.00 0.00 2.34
343 1104 6.385649 AAGGCAAAATTTCTGTCTTCGTTA 57.614 33.333 11.81 0.00 33.48 3.18
344 1105 4.918810 AGGCAAAATTTCTGTCTTCGTT 57.081 36.364 0.00 0.00 0.00 3.85
345 1106 4.918810 AAGGCAAAATTTCTGTCTTCGT 57.081 36.364 11.81 0.00 33.48 3.85
346 1107 4.681483 GGAAAGGCAAAATTTCTGTCTTCG 59.319 41.667 15.66 0.00 37.75 3.79
347 1108 4.991056 GGGAAAGGCAAAATTTCTGTCTTC 59.009 41.667 15.66 11.19 37.75 2.87
348 1109 4.501400 CGGGAAAGGCAAAATTTCTGTCTT 60.501 41.667 11.81 11.81 40.40 3.01
349 1110 3.005791 CGGGAAAGGCAAAATTTCTGTCT 59.994 43.478 0.00 0.00 36.96 3.41
352 1113 2.068519 GCGGGAAAGGCAAAATTTCTG 58.931 47.619 0.00 0.00 36.96 3.02
358 1119 2.491693 CAGAATAGCGGGAAAGGCAAAA 59.508 45.455 0.00 0.00 0.00 2.44
384 1146 1.254026 CTGAACCCACTCTACGACCA 58.746 55.000 0.00 0.00 0.00 4.02
388 1150 1.134560 GGTAGCTGAACCCACTCTACG 59.865 57.143 0.00 0.00 33.02 3.51
415 1177 3.197790 CACCCGCTCGCCAGATTG 61.198 66.667 0.00 0.00 0.00 2.67
423 1185 1.656818 AATGGCATTTCACCCGCTCG 61.657 55.000 6.96 0.00 0.00 5.03
427 1189 0.887247 TGTCAATGGCATTTCACCCG 59.113 50.000 10.65 0.00 0.00 5.28
503 1265 9.745018 AGATGAATAGATTGGAAGTTTTCTCAA 57.255 29.630 0.00 0.00 0.00 3.02
506 1268 9.745018 TGAAGATGAATAGATTGGAAGTTTTCT 57.255 29.630 0.00 0.00 0.00 2.52
511 1273 9.863650 ATGATTGAAGATGAATAGATTGGAAGT 57.136 29.630 0.00 0.00 0.00 3.01
514 1276 8.222637 ACCATGATTGAAGATGAATAGATTGGA 58.777 33.333 0.00 0.00 0.00 3.53
515 1277 8.405418 ACCATGATTGAAGATGAATAGATTGG 57.595 34.615 0.00 0.00 0.00 3.16
523 1285 9.551734 CTCTGTATTACCATGATTGAAGATGAA 57.448 33.333 0.00 0.00 0.00 2.57
524 1286 8.152898 CCTCTGTATTACCATGATTGAAGATGA 58.847 37.037 0.00 0.00 0.00 2.92
525 1287 8.152898 TCCTCTGTATTACCATGATTGAAGATG 58.847 37.037 0.00 0.00 0.00 2.90
526 1288 8.153550 GTCCTCTGTATTACCATGATTGAAGAT 58.846 37.037 0.00 0.00 0.00 2.40
527 1289 7.125659 TGTCCTCTGTATTACCATGATTGAAGA 59.874 37.037 0.00 0.00 0.00 2.87
528 1290 7.275183 TGTCCTCTGTATTACCATGATTGAAG 58.725 38.462 0.00 0.00 0.00 3.02
529 1291 7.194112 TGTCCTCTGTATTACCATGATTGAA 57.806 36.000 0.00 0.00 0.00 2.69
530 1292 6.806668 TGTCCTCTGTATTACCATGATTGA 57.193 37.500 0.00 0.00 0.00 2.57
531 1293 7.219322 TGATGTCCTCTGTATTACCATGATTG 58.781 38.462 0.00 0.00 0.00 2.67
532 1294 7.290948 TCTGATGTCCTCTGTATTACCATGATT 59.709 37.037 0.00 0.00 0.00 2.57
533 1295 6.784473 TCTGATGTCCTCTGTATTACCATGAT 59.216 38.462 0.00 0.00 0.00 2.45
534 1296 6.136155 TCTGATGTCCTCTGTATTACCATGA 58.864 40.000 0.00 0.00 0.00 3.07
535 1297 6.410942 TCTGATGTCCTCTGTATTACCATG 57.589 41.667 0.00 0.00 0.00 3.66
536 1298 7.437713 TTTCTGATGTCCTCTGTATTACCAT 57.562 36.000 0.00 0.00 0.00 3.55
537 1299 6.867519 TTTCTGATGTCCTCTGTATTACCA 57.132 37.500 0.00 0.00 0.00 3.25
564 1326 9.341078 GGTTTACGGACCTGGATATAATTTTTA 57.659 33.333 0.00 0.00 36.73 1.52
565 1327 7.835181 TGGTTTACGGACCTGGATATAATTTTT 59.165 33.333 0.00 0.00 40.47 1.94
566 1328 7.348033 TGGTTTACGGACCTGGATATAATTTT 58.652 34.615 0.00 0.00 40.47 1.82
567 1329 6.902408 TGGTTTACGGACCTGGATATAATTT 58.098 36.000 0.00 0.00 40.47 1.82
568 1330 6.503560 TGGTTTACGGACCTGGATATAATT 57.496 37.500 0.00 0.00 40.47 1.40
569 1331 6.500751 AGATGGTTTACGGACCTGGATATAAT 59.499 38.462 0.00 0.00 40.47 1.28
570 1332 5.842328 AGATGGTTTACGGACCTGGATATAA 59.158 40.000 0.00 0.00 40.47 0.98
571 1333 5.399991 AGATGGTTTACGGACCTGGATATA 58.600 41.667 0.00 0.00 40.47 0.86
572 1334 4.232091 AGATGGTTTACGGACCTGGATAT 58.768 43.478 0.00 0.00 40.47 1.63
573 1335 3.649843 AGATGGTTTACGGACCTGGATA 58.350 45.455 0.00 0.00 40.47 2.59
574 1336 2.478292 AGATGGTTTACGGACCTGGAT 58.522 47.619 0.00 0.00 40.47 3.41
575 1337 1.946984 AGATGGTTTACGGACCTGGA 58.053 50.000 0.00 0.00 40.47 3.86
576 1338 2.764572 ACTAGATGGTTTACGGACCTGG 59.235 50.000 0.00 0.00 40.47 4.45
577 1339 3.446161 TCACTAGATGGTTTACGGACCTG 59.554 47.826 0.00 0.00 40.47 4.00
578 1340 3.705051 TCACTAGATGGTTTACGGACCT 58.295 45.455 0.00 0.00 40.47 3.85
579 1341 4.369182 CATCACTAGATGGTTTACGGACC 58.631 47.826 0.00 0.00 46.33 4.46
591 1353 8.470657 TTCAGTGCTTATAGTCATCACTAGAT 57.529 34.615 0.00 0.00 38.56 1.98
592 1354 7.469318 GCTTCAGTGCTTATAGTCATCACTAGA 60.469 40.741 0.00 0.00 38.56 2.43
593 1355 6.640499 GCTTCAGTGCTTATAGTCATCACTAG 59.360 42.308 0.00 0.00 38.56 2.57
594 1356 6.507900 GCTTCAGTGCTTATAGTCATCACTA 58.492 40.000 0.00 0.00 39.54 2.74
595 1357 5.355596 GCTTCAGTGCTTATAGTCATCACT 58.644 41.667 0.00 0.00 38.40 3.41
596 1358 4.208047 CGCTTCAGTGCTTATAGTCATCAC 59.792 45.833 0.00 0.00 0.00 3.06
597 1359 4.097892 TCGCTTCAGTGCTTATAGTCATCA 59.902 41.667 0.00 0.00 0.00 3.07
598 1360 4.611943 TCGCTTCAGTGCTTATAGTCATC 58.388 43.478 0.00 0.00 0.00 2.92
599 1361 4.615949 CTCGCTTCAGTGCTTATAGTCAT 58.384 43.478 0.00 0.00 0.00 3.06
600 1362 3.735208 GCTCGCTTCAGTGCTTATAGTCA 60.735 47.826 0.00 0.00 0.00 3.41
601 1363 2.792116 GCTCGCTTCAGTGCTTATAGTC 59.208 50.000 0.00 0.00 0.00 2.59
602 1364 2.482142 GGCTCGCTTCAGTGCTTATAGT 60.482 50.000 0.00 0.00 0.00 2.12
603 1365 2.131183 GGCTCGCTTCAGTGCTTATAG 58.869 52.381 0.00 0.00 0.00 1.31
604 1366 1.536072 CGGCTCGCTTCAGTGCTTATA 60.536 52.381 0.00 0.00 0.00 0.98
605 1367 0.807667 CGGCTCGCTTCAGTGCTTAT 60.808 55.000 0.00 0.00 0.00 1.73
606 1368 1.446099 CGGCTCGCTTCAGTGCTTA 60.446 57.895 0.00 0.00 0.00 3.09
607 1369 2.715532 TTCGGCTCGCTTCAGTGCTT 62.716 55.000 0.00 0.00 0.00 3.91
608 1370 3.226429 TTCGGCTCGCTTCAGTGCT 62.226 57.895 0.00 0.00 0.00 4.40
609 1371 2.734673 CTTCGGCTCGCTTCAGTGC 61.735 63.158 0.00 0.00 0.00 4.40
610 1372 1.080501 TCTTCGGCTCGCTTCAGTG 60.081 57.895 0.00 0.00 0.00 3.66
611 1373 1.080434 GTCTTCGGCTCGCTTCAGT 60.080 57.895 0.00 0.00 0.00 3.41
612 1374 2.155194 CGTCTTCGGCTCGCTTCAG 61.155 63.158 0.00 0.00 0.00 3.02
613 1375 2.126463 CGTCTTCGGCTCGCTTCA 60.126 61.111 0.00 0.00 0.00 3.02
614 1376 3.546397 GCGTCTTCGGCTCGCTTC 61.546 66.667 0.00 0.00 45.29 3.86
625 1387 4.961511 TTGACGGCGCTGCGTCTT 62.962 61.111 29.96 16.13 34.86 3.01
629 1391 4.505217 GATGTTGACGGCGCTGCG 62.505 66.667 18.15 19.17 0.00 5.18
630 1392 4.166011 GGATGTTGACGGCGCTGC 62.166 66.667 18.15 10.02 0.00 5.25
631 1393 3.499737 GGGATGTTGACGGCGCTG 61.500 66.667 16.39 16.39 0.00 5.18
632 1394 3.254024 AAGGGATGTTGACGGCGCT 62.254 57.895 6.90 0.00 0.00 5.92
633 1395 2.746277 AAGGGATGTTGACGGCGC 60.746 61.111 6.90 0.00 0.00 6.53
634 1396 2.106683 GGAAGGGATGTTGACGGCG 61.107 63.158 4.80 4.80 0.00 6.46
635 1397 0.744771 GAGGAAGGGATGTTGACGGC 60.745 60.000 0.00 0.00 0.00 5.68
636 1398 0.460284 CGAGGAAGGGATGTTGACGG 60.460 60.000 0.00 0.00 0.00 4.79
637 1399 1.084370 GCGAGGAAGGGATGTTGACG 61.084 60.000 0.00 0.00 0.00 4.35
638 1400 0.744771 GGCGAGGAAGGGATGTTGAC 60.745 60.000 0.00 0.00 0.00 3.18
639 1401 1.198094 TGGCGAGGAAGGGATGTTGA 61.198 55.000 0.00 0.00 0.00 3.18
640 1402 0.745845 CTGGCGAGGAAGGGATGTTG 60.746 60.000 0.00 0.00 0.00 3.33
641 1403 0.909610 TCTGGCGAGGAAGGGATGTT 60.910 55.000 0.00 0.00 0.00 2.71
642 1404 1.306141 TCTGGCGAGGAAGGGATGT 60.306 57.895 0.00 0.00 0.00 3.06
643 1405 1.333636 ACTCTGGCGAGGAAGGGATG 61.334 60.000 10.29 0.00 41.71 3.51
644 1406 1.002274 ACTCTGGCGAGGAAGGGAT 59.998 57.895 10.29 0.00 41.71 3.85
645 1407 1.682684 GACTCTGGCGAGGAAGGGA 60.683 63.158 10.29 0.00 41.71 4.20
646 1408 2.896443 GACTCTGGCGAGGAAGGG 59.104 66.667 10.29 0.00 41.71 3.95
647 1409 2.492090 CGACTCTGGCGAGGAAGG 59.508 66.667 10.29 0.00 41.71 3.46
648 1410 2.492090 CCGACTCTGGCGAGGAAG 59.508 66.667 10.29 0.00 41.71 3.46
649 1411 3.068691 CCCGACTCTGGCGAGGAA 61.069 66.667 10.29 0.00 41.71 3.36
656 1418 0.593128 CAAGTTTTGCCCGACTCTGG 59.407 55.000 0.00 0.00 0.00 3.86
657 1419 1.308998 ACAAGTTTTGCCCGACTCTG 58.691 50.000 0.00 0.00 0.00 3.35
658 1420 2.052782 AACAAGTTTTGCCCGACTCT 57.947 45.000 0.00 0.00 0.00 3.24
659 1421 4.694037 ACTATAACAAGTTTTGCCCGACTC 59.306 41.667 0.00 0.00 0.00 3.36
660 1422 4.648651 ACTATAACAAGTTTTGCCCGACT 58.351 39.130 0.00 0.00 0.00 4.18
661 1423 5.870978 TCTACTATAACAAGTTTTGCCCGAC 59.129 40.000 0.00 0.00 0.00 4.79
662 1424 6.040209 TCTACTATAACAAGTTTTGCCCGA 57.960 37.500 0.00 0.00 0.00 5.14
663 1425 6.540205 GTTCTACTATAACAAGTTTTGCCCG 58.460 40.000 0.00 0.00 0.00 6.13
664 1426 6.369615 TCGTTCTACTATAACAAGTTTTGCCC 59.630 38.462 0.00 0.00 0.00 5.36
665 1427 7.355332 TCGTTCTACTATAACAAGTTTTGCC 57.645 36.000 0.00 0.00 0.00 4.52
677 1439 8.666573 GCTGCTGTAATCTATCGTTCTACTATA 58.333 37.037 0.00 0.00 0.00 1.31
678 1440 7.362229 GGCTGCTGTAATCTATCGTTCTACTAT 60.362 40.741 0.00 0.00 0.00 2.12
679 1441 6.072618 GGCTGCTGTAATCTATCGTTCTACTA 60.073 42.308 0.00 0.00 0.00 1.82
680 1442 5.278561 GGCTGCTGTAATCTATCGTTCTACT 60.279 44.000 0.00 0.00 0.00 2.57
681 1443 4.918583 GGCTGCTGTAATCTATCGTTCTAC 59.081 45.833 0.00 0.00 0.00 2.59
703 1465 0.523072 CGGACCATTTTGCACTCTGG 59.477 55.000 6.15 6.15 34.84 3.86
714 1476 2.357637 CCGATTTATTGCACGGACCATT 59.642 45.455 5.29 0.00 46.94 3.16
756 1522 8.770828 CCGAACTTTTTCTTCTACACAATTCTA 58.229 33.333 0.00 0.00 0.00 2.10
761 1527 5.007332 GCTCCGAACTTTTTCTTCTACACAA 59.993 40.000 0.00 0.00 0.00 3.33
768 1535 3.963383 TGTGCTCCGAACTTTTTCTTC 57.037 42.857 0.00 0.00 0.00 2.87
822 1589 3.244078 ACCTCGTCTGTGCACAATTTCTA 60.244 43.478 21.98 3.70 0.00 2.10
834 1601 1.135373 CAACTCGCATACCTCGTCTGT 60.135 52.381 0.00 0.00 0.00 3.41
879 1652 2.108976 CTGTGCCTGTGACGGTGT 59.891 61.111 0.00 0.00 0.00 4.16
964 1738 2.764010 GAGGTTTGTGGGGAAACAACTT 59.236 45.455 0.00 0.00 39.70 2.66
966 1740 1.066454 CGAGGTTTGTGGGGAAACAAC 59.934 52.381 0.00 0.00 39.70 3.32
969 1743 1.658114 GCGAGGTTTGTGGGGAAAC 59.342 57.895 0.00 0.00 35.45 2.78
1016 1793 1.075600 CTCACCCTCTCTCTCCCCC 60.076 68.421 0.00 0.00 0.00 5.40
1017 1794 1.760480 GCTCACCCTCTCTCTCCCC 60.760 68.421 0.00 0.00 0.00 4.81
1018 1795 1.000993 TGCTCACCCTCTCTCTCCC 59.999 63.158 0.00 0.00 0.00 4.30
1046 1823 1.384191 GATGGGTTTGAGCTGGGGT 59.616 57.895 0.00 0.00 0.00 4.95
1065 1842 1.367848 AGGAGAGGAGAGGGGAATGTT 59.632 52.381 0.00 0.00 0.00 2.71
1105 1886 2.633488 GCTTATCAGCGGAAAGAGGTT 58.367 47.619 11.00 0.00 35.91 3.50
1144 1925 2.552585 GAAGGCCGTCCGTCGAATGA 62.553 60.000 7.56 0.00 42.86 2.57
1155 1936 1.608717 AATCTGAGCGAGAAGGCCGT 61.609 55.000 0.00 0.00 33.12 5.68
1161 1942 1.153568 CGGGCAATCTGAGCGAGAA 60.154 57.895 0.00 0.00 33.12 2.87
1162 1943 2.496341 CGGGCAATCTGAGCGAGA 59.504 61.111 0.00 0.00 34.25 4.04
1170 1951 1.956629 AATCGTCGTCCGGGCAATCT 61.957 55.000 6.96 0.00 37.11 2.40
1195 1976 3.814268 CCGCCATTTGCTCCACCG 61.814 66.667 0.00 0.00 38.05 4.94
1416 2197 3.186409 CGCGAACAGAAAGATTGAAGGAA 59.814 43.478 0.00 0.00 0.00 3.36
1454 2235 4.382320 GGAACCGGCGCAGGTACA 62.382 66.667 32.41 0.00 45.21 2.90
1486 2267 0.402121 ACCTCCTCCTGCCAAAGAAC 59.598 55.000 0.00 0.00 0.00 3.01
1489 2270 0.322008 GTCACCTCCTCCTGCCAAAG 60.322 60.000 0.00 0.00 0.00 2.77
1521 2302 2.022129 CCCACACAGCGTCGACTTC 61.022 63.158 14.70 5.28 0.00 3.01
1653 2434 2.113774 CTGTTGACCTGCCAGGCA 59.886 61.111 15.23 15.23 39.63 4.75
1657 2438 1.303561 GGATGCTGTTGACCTGCCA 60.304 57.895 0.00 0.00 37.22 4.92
1687 2468 1.736645 CGTGCAAGACGTAGGGGTG 60.737 63.158 0.00 0.00 43.50 4.61
1812 2593 2.379634 CGTGATGAGGTGCGCGAAA 61.380 57.895 12.10 0.00 40.15 3.46
1860 2641 4.895854 GCGCCATGCAACTGAAAT 57.104 50.000 0.00 0.00 45.45 2.17
1882 2663 2.231478 TCTTCAGGTAGGAGACGCAAAG 59.769 50.000 0.00 0.00 0.00 2.77
1913 2696 6.034470 ACACAAAAACAAACGCAGATGTTAAG 59.966 34.615 0.00 0.00 39.30 1.85
1924 2707 3.672867 ACTGCAGAACACAAAAACAAACG 59.327 39.130 23.35 0.00 0.00 3.60
1931 2715 5.450412 GGAGATGAAACTGCAGAACACAAAA 60.450 40.000 23.35 0.00 0.00 2.44
1940 2724 3.817084 TGTTTGAGGAGATGAAACTGCAG 59.183 43.478 13.48 13.48 32.01 4.41
2245 3029 0.251634 CAGACTTCTTCCTGGGCTCC 59.748 60.000 0.00 0.00 0.00 4.70
2274 3058 2.485835 CCAAAACAGGTGTTACGAGGGA 60.486 50.000 0.00 0.00 37.25 4.20
2352 3136 1.946267 CGAAAGACACCAAACGGGG 59.054 57.895 0.00 0.00 42.91 5.73
2431 3215 2.261671 CCGAGGTCGTCCAGGTTG 59.738 66.667 0.51 0.00 37.74 3.77
2501 3285 3.131396 CACCATAAGCTATGTTCCGGAC 58.869 50.000 1.83 0.00 34.36 4.79
2510 3294 8.704849 TGCCATTAATTAACACCATAAGCTAT 57.295 30.769 0.00 0.00 0.00 2.97
2511 3295 8.526667 TTGCCATTAATTAACACCATAAGCTA 57.473 30.769 0.00 0.00 0.00 3.32
2513 3297 7.264947 ACTTGCCATTAATTAACACCATAAGC 58.735 34.615 0.00 0.00 0.00 3.09
2519 3303 9.301153 CAGATTAACTTGCCATTAATTAACACC 57.699 33.333 0.00 0.00 33.39 4.16
2562 3347 0.321919 TGATCAAGGCCTCTGTGCAC 60.322 55.000 5.23 10.75 0.00 4.57
2566 3351 0.534412 CGACTGATCAAGGCCTCTGT 59.466 55.000 5.23 3.45 0.00 3.41
2739 3524 7.942990 AGTGCTACTACAACCTAATACAGATC 58.057 38.462 0.00 0.00 0.00 2.75
2876 3681 7.720515 ACCAACTACTACTACTAGACATGGATC 59.279 40.741 0.00 0.00 0.00 3.36
2893 3698 8.685838 TTATTGCTTCTAACAAACCAACTACT 57.314 30.769 0.00 0.00 0.00 2.57
2894 3699 8.565416 ACTTATTGCTTCTAACAAACCAACTAC 58.435 33.333 0.00 0.00 0.00 2.73
2895 3700 8.564574 CACTTATTGCTTCTAACAAACCAACTA 58.435 33.333 0.00 0.00 0.00 2.24
2896 3701 7.425606 CACTTATTGCTTCTAACAAACCAACT 58.574 34.615 0.00 0.00 0.00 3.16
2897 3702 6.640907 CCACTTATTGCTTCTAACAAACCAAC 59.359 38.462 0.00 0.00 0.00 3.77
2898 3703 6.239176 CCCACTTATTGCTTCTAACAAACCAA 60.239 38.462 0.00 0.00 0.00 3.67
2924 3729 0.035343 TCTCTCGCCTCCGAAAGAGA 60.035 55.000 0.00 0.00 46.50 3.10
2949 3754 2.350388 GCGCTTGCTACAAACAGCTAAA 60.350 45.455 0.00 0.00 42.30 1.85
2970 3775 9.775854 ATTTCACTCCAACATTATCATCTCTAG 57.224 33.333 0.00 0.00 0.00 2.43
2971 3776 9.551734 CATTTCACTCCAACATTATCATCTCTA 57.448 33.333 0.00 0.00 0.00 2.43
2973 3778 8.442632 TCATTTCACTCCAACATTATCATCTC 57.557 34.615 0.00 0.00 0.00 2.75
3013 3822 3.840078 ACATGGGCCTTTTATTTCTGCTT 59.160 39.130 4.53 0.00 0.00 3.91
3190 4014 9.927668 AACCATGAAATTTTATTTCTCGTCATT 57.072 25.926 11.98 0.18 0.00 2.57
3211 4045 8.739972 CCAACTAGCTATTACAAGAAAAACCAT 58.260 33.333 0.00 0.00 0.00 3.55
3214 4048 9.000486 ACTCCAACTAGCTATTACAAGAAAAAC 58.000 33.333 0.00 0.00 0.00 2.43
3237 4071 7.903431 AGCAACGAATGAAACGAAATATTACTC 59.097 33.333 0.00 0.00 34.70 2.59
3242 4080 7.218204 GCTAAAGCAACGAATGAAACGAAATAT 59.782 33.333 0.00 0.00 41.59 1.28
3249 4087 2.908626 CCGCTAAAGCAACGAATGAAAC 59.091 45.455 2.44 0.00 42.21 2.78
3275 4113 4.404654 GAGCCCAACTTTGCGGCG 62.405 66.667 0.51 0.51 44.23 6.46
3287 4125 8.827677 CATTAGTATTATTATAAAGCCGAGCCC 58.172 37.037 0.00 0.00 0.00 5.19
3311 4149 8.908786 AACGAGTACAATTCCATTATGATCAT 57.091 30.769 13.81 13.81 0.00 2.45
3312 4150 7.441157 GGAACGAGTACAATTCCATTATGATCA 59.559 37.037 14.62 0.00 41.40 2.92
3313 4151 7.657761 AGGAACGAGTACAATTCCATTATGATC 59.342 37.037 19.27 0.00 43.75 2.92
3316 4154 6.074302 CGAGGAACGAGTACAATTCCATTATG 60.074 42.308 19.27 0.00 43.75 1.90
3322 4160 2.165030 TCCGAGGAACGAGTACAATTCC 59.835 50.000 12.57 12.57 45.77 3.01
3333 4171 2.309528 TCCATTCATTCCGAGGAACG 57.690 50.000 6.73 0.00 36.91 3.95
3386 4224 6.873997 ACACCTTGATTAAGATATGACACGA 58.126 36.000 0.00 0.00 35.92 4.35
3445 4283 6.317642 CACATGACACCCCGATTAAGATAAAA 59.682 38.462 0.00 0.00 0.00 1.52
3524 4362 4.676586 CGCGCACCGGACAAAACC 62.677 66.667 9.46 0.00 0.00 3.27
3596 4434 0.669625 GTCGTTTTCAGACGGGGGAG 60.670 60.000 0.00 0.00 42.98 4.30
3597 4435 1.368579 GTCGTTTTCAGACGGGGGA 59.631 57.895 0.00 0.00 42.98 4.81
3620 4459 1.298014 CAAGGTGAGGAGAGGCCAC 59.702 63.158 5.01 0.00 40.02 5.01
3628 4467 2.947532 CGAGCCAGCAAGGTGAGGA 61.948 63.158 0.03 0.00 40.61 3.71
3629 4468 2.435586 CGAGCCAGCAAGGTGAGG 60.436 66.667 0.03 0.00 40.61 3.86
3633 4472 4.711949 CCAGCGAGCCAGCAAGGT 62.712 66.667 3.80 0.00 40.61 3.50
3635 4474 4.399395 TCCCAGCGAGCCAGCAAG 62.399 66.667 3.80 0.00 40.15 4.01
3636 4475 4.704833 GTCCCAGCGAGCCAGCAA 62.705 66.667 3.80 0.00 40.15 3.91
3649 4493 3.834799 CCTACGCTGGACCGTCCC 61.835 72.222 15.24 0.00 42.20 4.46
3664 4520 0.179000 CGTTCCTTCCAGCTATGCCT 59.821 55.000 0.00 0.00 0.00 4.75
3670 4526 2.750350 CACCCGTTCCTTCCAGCT 59.250 61.111 0.00 0.00 0.00 4.24
3674 4530 2.046217 GAGCCACCCGTTCCTTCC 60.046 66.667 0.00 0.00 0.00 3.46
3675 4531 2.046217 GGAGCCACCCGTTCCTTC 60.046 66.667 0.00 0.00 38.78 3.46
3676 4532 4.016706 CGGAGCCACCCGTTCCTT 62.017 66.667 0.00 0.00 44.23 3.36


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

AutoCloner maintained by Alex Coulton.