Multiple sequence alignment - TraesCS3B01G470300

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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 TraesCS3B01G470300 chr3B 100.000 4938 0 0 1 4938 718293821 718288884 0.000000e+00 9119
1 TraesCS3B01G470300 chr3A 90.240 4826 263 91 1 4727 678504639 678499923 0.000000e+00 6111
2 TraesCS3B01G470300 chr3D 89.929 4786 248 95 94 4724 542386273 542381567 0.000000e+00 5952
3 TraesCS3B01G470300 chr3D 93.953 215 13 0 4724 4938 542381521 542381307 4.770000e-85 326


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 TraesCS3B01G470300 chr3B 718288884 718293821 4937 True 9119 9119 100.000 1 4938 1 chr3B.!!$R1 4937
1 TraesCS3B01G470300 chr3A 678499923 678504639 4716 True 6111 6111 90.240 1 4727 1 chr3A.!!$R1 4726
2 TraesCS3B01G470300 chr3D 542381307 542386273 4966 True 3139 5952 91.941 94 4938 2 chr3D.!!$R1 4844

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
411 422 0.032017 AGGTACCACTGCCCTCCTAG 60.032 60.000 15.94 0.0 0.00 3.02 F
482 497 0.037419 GCTACCACCCCGTTAAACGA 60.037 55.000 0.00 0.0 46.05 3.85 F
805 857 0.100325 CGCACACAGCCAACAAAGAA 59.900 50.000 0.00 0.0 41.38 2.52 F
1166 1255 0.179070 GCTCTTCATCCGTTCCCCTC 60.179 60.000 0.00 0.0 0.00 4.30 F
1871 1991 0.109132 GCCAAGGTGCCGAAATTCAG 60.109 55.000 0.00 0.0 0.00 3.02 F
2276 2410 3.119316 CCCTAGAGCGCATAAGTATCCTG 60.119 52.174 11.47 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1424 0.305313 GCAAGCAAACGAACCGTGTA 59.695 50.000 0.00 0.00 39.99 2.90 R
1383 1484 0.965439 CAAGCAAAAACGATGGGGGA 59.035 50.000 0.00 0.00 0.00 4.81 R
1706 1820 2.093983 GAGTAGTGCAAACGCGCG 59.906 61.111 30.96 30.96 44.77 6.86 R
3163 3298 1.529010 CACAAGGCCACCTGCAGAA 60.529 57.895 17.39 0.00 43.89 3.02 R
3289 3424 1.002069 TTCCATTCAGCACCATCCCT 58.998 50.000 0.00 0.00 0.00 4.20 R
4275 4412 0.179936 GCTCAGTTCTGGGGAGATGG 59.820 60.000 1.77 0.00 0.00 3.51 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
42 44 3.998672 GCAACGGGGTCGACCAGA 61.999 66.667 34.40 0.00 42.91 3.86
59 61 4.935578 ACCAGAAAGAATAAAGAAGGGGG 58.064 43.478 0.00 0.00 0.00 5.40
62 64 5.196695 CAGAAAGAATAAAGAAGGGGGAGG 58.803 45.833 0.00 0.00 0.00 4.30
63 65 4.230733 AGAAAGAATAAAGAAGGGGGAGGG 59.769 45.833 0.00 0.00 0.00 4.30
64 66 2.503824 AGAATAAAGAAGGGGGAGGGG 58.496 52.381 0.00 0.00 0.00 4.79
65 67 1.499438 GAATAAAGAAGGGGGAGGGGG 59.501 57.143 0.00 0.00 0.00 5.40
80 82 1.839894 GGGGGATGATGAGGGACAC 59.160 63.158 0.00 0.00 0.00 3.67
83 85 1.051812 GGGATGATGAGGGACACGAT 58.948 55.000 0.00 0.00 0.00 3.73
85 87 1.967066 GGATGATGAGGGACACGATCT 59.033 52.381 0.00 0.00 0.00 2.75
100 102 1.647213 CGATCTGTACCAAACACGACG 59.353 52.381 0.00 0.00 33.45 5.12
122 124 0.456628 GACCTCGGTAGACAAGCTCC 59.543 60.000 0.00 0.00 0.00 4.70
181 183 1.270274 GATGCATGCAACAGTTGTGGA 59.730 47.619 26.68 7.76 0.00 4.02
185 187 1.948834 CATGCAACAGTTGTGGAGTCA 59.051 47.619 14.88 3.54 0.00 3.41
189 191 2.917933 CAACAGTTGTGGAGTCAGGAA 58.082 47.619 4.99 0.00 0.00 3.36
196 198 4.770010 AGTTGTGGAGTCAGGAAAACAAAA 59.230 37.500 0.00 0.00 30.06 2.44
197 199 4.981806 TGTGGAGTCAGGAAAACAAAAG 57.018 40.909 0.00 0.00 0.00 2.27
217 219 2.584965 AGGATGGAGAAGAGAGGAGACA 59.415 50.000 0.00 0.00 0.00 3.41
218 220 3.207321 AGGATGGAGAAGAGAGGAGACAT 59.793 47.826 0.00 0.00 0.00 3.06
228 230 5.194473 AGAGAGGAGACATAGTGGTACAA 57.806 43.478 0.00 0.00 44.16 2.41
236 238 1.141053 CATAGTGGTACAAGAGGGGGC 59.859 57.143 0.00 0.00 44.16 5.80
255 264 5.437060 GGGGCACATAAGAGAAAGACAATA 58.563 41.667 0.00 0.00 0.00 1.90
262 271 6.543831 ACATAAGAGAAAGACAATATGGCACC 59.456 38.462 0.00 0.00 0.00 5.01
265 274 4.225942 AGAGAAAGACAATATGGCACCTCA 59.774 41.667 0.00 0.00 0.00 3.86
280 289 4.161001 GGCACCTCATGGATCTTGAAAATT 59.839 41.667 0.00 0.00 37.04 1.82
292 301 8.202811 TGGATCTTGAAAATTGACAAAATCACA 58.797 29.630 10.94 6.18 36.92 3.58
302 311 1.679153 ACAAAATCACAACGGACACCC 59.321 47.619 0.00 0.00 0.00 4.61
305 314 0.183971 AATCACAACGGACACCCCAA 59.816 50.000 0.00 0.00 34.14 4.12
308 317 1.161843 CACAACGGACACCCCAATAC 58.838 55.000 0.00 0.00 34.14 1.89
318 327 4.457466 GACACCCCAATACCGATGTAAAT 58.543 43.478 0.00 0.00 0.00 1.40
327 337 6.073222 CCAATACCGATGTAAATGTAGCCTTC 60.073 42.308 0.00 0.00 0.00 3.46
346 356 5.507985 GCCTTCCCATTGAAAGAATAATCCG 60.508 44.000 1.64 0.00 31.06 4.18
348 358 3.563808 TCCCATTGAAAGAATAATCCGCG 59.436 43.478 0.00 0.00 0.00 6.46
351 361 3.918258 TTGAAAGAATAATCCGCGTCG 57.082 42.857 4.92 0.00 0.00 5.12
378 388 2.421424 GCACCATGTGACTTTGATCTCC 59.579 50.000 0.00 0.00 35.23 3.71
384 394 4.743057 TGTGACTTTGATCTCCGATGAT 57.257 40.909 0.00 0.00 0.00 2.45
411 422 0.032017 AGGTACCACTGCCCTCCTAG 60.032 60.000 15.94 0.00 0.00 3.02
414 425 3.854669 CCACTGCCCTCCTAGCCG 61.855 72.222 0.00 0.00 0.00 5.52
416 427 1.756950 CACTGCCCTCCTAGCCGTA 60.757 63.158 0.00 0.00 0.00 4.02
439 454 3.159213 AGCATTGGTTGGTTCTCATCA 57.841 42.857 0.00 0.00 29.87 3.07
449 464 5.010012 GGTTGGTTCTCATCATGAAAACACT 59.990 40.000 6.19 0.00 0.00 3.55
467 482 5.993106 ACACTCTGTTTTTCTCAAGCTAC 57.007 39.130 0.00 0.00 0.00 3.58
471 486 4.134563 TCTGTTTTTCTCAAGCTACCACC 58.865 43.478 0.00 0.00 0.00 4.61
472 487 3.219281 TGTTTTTCTCAAGCTACCACCC 58.781 45.455 0.00 0.00 0.00 4.61
473 488 2.557056 GTTTTTCTCAAGCTACCACCCC 59.443 50.000 0.00 0.00 0.00 4.95
474 489 0.323629 TTTCTCAAGCTACCACCCCG 59.676 55.000 0.00 0.00 0.00 5.73
477 492 0.899720 CTCAAGCTACCACCCCGTTA 59.100 55.000 0.00 0.00 0.00 3.18
478 493 1.276989 CTCAAGCTACCACCCCGTTAA 59.723 52.381 0.00 0.00 0.00 2.01
479 494 1.698532 TCAAGCTACCACCCCGTTAAA 59.301 47.619 0.00 0.00 0.00 1.52
480 495 1.808343 CAAGCTACCACCCCGTTAAAC 59.192 52.381 0.00 0.00 0.00 2.01
482 497 0.037419 GCTACCACCCCGTTAAACGA 60.037 55.000 0.00 0.00 46.05 3.85
483 498 1.405933 GCTACCACCCCGTTAAACGAT 60.406 52.381 0.00 0.00 46.05 3.73
485 500 0.397564 ACCACCCCGTTAAACGATGT 59.602 50.000 0.00 0.00 46.05 3.06
486 501 1.622811 ACCACCCCGTTAAACGATGTA 59.377 47.619 0.00 0.00 46.05 2.29
487 502 2.001872 CCACCCCGTTAAACGATGTAC 58.998 52.381 0.00 0.00 46.05 2.90
489 504 3.065655 CACCCCGTTAAACGATGTACAA 58.934 45.455 0.00 0.00 46.05 2.41
496 511 5.390040 CCGTTAAACGATGTACAATCAGCAA 60.390 40.000 0.00 0.00 46.05 3.91
499 514 2.009774 ACGATGTACAATCAGCAAGGC 58.990 47.619 0.00 0.00 0.00 4.35
500 515 2.009051 CGATGTACAATCAGCAAGGCA 58.991 47.619 0.00 0.00 0.00 4.75
517 532 2.174060 GCAAATTAGCCTACGTGCAC 57.826 50.000 6.82 6.82 32.29 4.57
520 535 2.742053 CAAATTAGCCTACGTGCACACT 59.258 45.455 18.64 8.00 0.00 3.55
532 551 1.102154 TGCACACTTGTTGTCCTTGG 58.898 50.000 0.00 0.00 35.67 3.61
533 552 0.249031 GCACACTTGTTGTCCTTGGC 60.249 55.000 0.00 0.00 35.67 4.52
534 553 1.392589 CACACTTGTTGTCCTTGGCT 58.607 50.000 0.00 0.00 35.67 4.75
535 554 1.334869 CACACTTGTTGTCCTTGGCTC 59.665 52.381 0.00 0.00 35.67 4.70
536 555 0.954452 CACTTGTTGTCCTTGGCTCC 59.046 55.000 0.00 0.00 0.00 4.70
537 556 0.846693 ACTTGTTGTCCTTGGCTCCT 59.153 50.000 0.00 0.00 0.00 3.69
538 557 1.215423 ACTTGTTGTCCTTGGCTCCTT 59.785 47.619 0.00 0.00 0.00 3.36
539 558 1.610522 CTTGTTGTCCTTGGCTCCTTG 59.389 52.381 0.00 0.00 0.00 3.61
553 572 2.222819 GCTCCTTGCTACGTTTCATTCG 60.223 50.000 0.00 0.00 38.95 3.34
581 605 2.095466 CCGGAACACGCACACAATTATT 60.095 45.455 0.00 0.00 42.52 1.40
584 608 4.612712 CGGAACACGCACACAATTATTCTT 60.613 41.667 0.00 0.00 34.82 2.52
594 618 7.361371 CGCACACAATTATTCTTACTTAACCCA 60.361 37.037 0.00 0.00 0.00 4.51
613 637 4.404098 ACCGCACCCATCCCGTTC 62.404 66.667 0.00 0.00 0.00 3.95
656 688 1.153046 CAACCGGAACACCACCACT 60.153 57.895 9.46 0.00 0.00 4.00
657 689 1.153046 AACCGGAACACCACCACTG 60.153 57.895 9.46 0.00 0.00 3.66
658 690 2.978010 CCGGAACACCACCACTGC 60.978 66.667 0.00 0.00 0.00 4.40
663 695 0.882927 GAACACCACCACTGCGCTAA 60.883 55.000 9.73 0.00 0.00 3.09
667 699 0.682852 ACCACCACTGCGCTAAACTA 59.317 50.000 9.73 0.00 0.00 2.24
668 700 1.076332 CCACCACTGCGCTAAACTAC 58.924 55.000 9.73 0.00 0.00 2.73
679 728 3.733077 GCGCTAAACTACCACACGAGTAT 60.733 47.826 0.00 0.00 0.00 2.12
680 729 4.496341 GCGCTAAACTACCACACGAGTATA 60.496 45.833 0.00 0.00 0.00 1.47
681 730 4.966366 CGCTAAACTACCACACGAGTATAC 59.034 45.833 0.00 0.00 0.00 1.47
682 731 5.277047 GCTAAACTACCACACGAGTATACC 58.723 45.833 0.00 0.00 0.00 2.73
683 732 5.163622 GCTAAACTACCACACGAGTATACCA 60.164 44.000 0.00 0.00 0.00 3.25
684 733 4.978083 AACTACCACACGAGTATACCAG 57.022 45.455 0.00 0.00 0.00 4.00
685 734 3.285484 ACTACCACACGAGTATACCAGG 58.715 50.000 0.00 0.00 0.00 4.45
686 735 2.519771 ACCACACGAGTATACCAGGA 57.480 50.000 0.00 0.00 0.00 3.86
687 736 2.376109 ACCACACGAGTATACCAGGAG 58.624 52.381 0.00 0.00 0.00 3.69
688 737 1.681793 CCACACGAGTATACCAGGAGG 59.318 57.143 0.00 0.00 42.21 4.30
689 738 2.651455 CACACGAGTATACCAGGAGGA 58.349 52.381 0.00 0.00 38.69 3.71
690 739 2.619177 CACACGAGTATACCAGGAGGAG 59.381 54.545 0.00 0.00 38.69 3.69
691 740 2.508716 ACACGAGTATACCAGGAGGAGA 59.491 50.000 0.00 0.00 38.69 3.71
692 741 3.138653 ACACGAGTATACCAGGAGGAGAT 59.861 47.826 0.00 0.00 38.69 2.75
693 742 3.754323 CACGAGTATACCAGGAGGAGATC 59.246 52.174 0.00 0.00 38.69 2.75
798 850 4.539083 ACGGACGCACACAGCCAA 62.539 61.111 0.00 0.00 41.38 4.52
799 851 4.012895 CGGACGCACACAGCCAAC 62.013 66.667 0.00 0.00 41.38 3.77
800 852 2.899838 GGACGCACACAGCCAACA 60.900 61.111 0.00 0.00 41.38 3.33
801 853 2.477176 GGACGCACACAGCCAACAA 61.477 57.895 0.00 0.00 41.38 2.83
802 854 1.431440 GACGCACACAGCCAACAAA 59.569 52.632 0.00 0.00 41.38 2.83
803 855 0.592247 GACGCACACAGCCAACAAAG 60.592 55.000 0.00 0.00 41.38 2.77
804 856 1.029408 ACGCACACAGCCAACAAAGA 61.029 50.000 0.00 0.00 41.38 2.52
805 857 0.100325 CGCACACAGCCAACAAAGAA 59.900 50.000 0.00 0.00 41.38 2.52
1111 1199 3.603330 ATCCCCAGGCAAGTCCCCT 62.603 63.158 0.00 0.00 34.51 4.79
1125 1213 1.004436 TCCCCTAACCAATCCCCAAC 58.996 55.000 0.00 0.00 0.00 3.77
1145 1233 1.770518 CCCCCTAATCCCCTTCGCT 60.771 63.158 0.00 0.00 0.00 4.93
1147 1235 1.367840 CCCTAATCCCCTTCGCTCG 59.632 63.158 0.00 0.00 0.00 5.03
1148 1236 1.301009 CCTAATCCCCTTCGCTCGC 60.301 63.158 0.00 0.00 0.00 5.03
1151 1239 0.755698 TAATCCCCTTCGCTCGCTCT 60.756 55.000 0.00 0.00 0.00 4.09
1152 1240 1.617947 AATCCCCTTCGCTCGCTCTT 61.618 55.000 0.00 0.00 0.00 2.85
1154 1242 2.573869 CCCTTCGCTCGCTCTTCA 59.426 61.111 0.00 0.00 0.00 3.02
1156 1244 0.873743 CCCTTCGCTCGCTCTTCATC 60.874 60.000 0.00 0.00 0.00 2.92
1158 1246 1.205485 CTTCGCTCGCTCTTCATCCG 61.205 60.000 0.00 0.00 0.00 4.18
1159 1247 1.934220 TTCGCTCGCTCTTCATCCGT 61.934 55.000 0.00 0.00 0.00 4.69
1160 1248 1.517257 CGCTCGCTCTTCATCCGTT 60.517 57.895 0.00 0.00 0.00 4.44
1166 1255 0.179070 GCTCTTCATCCGTTCCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
1173 1262 2.930777 ATCCGTTCCCCTCCTCTCCG 62.931 65.000 0.00 0.00 0.00 4.63
1201 1290 1.666234 GGATTCGCTCGGATCTGCC 60.666 63.158 10.05 0.00 0.00 4.85
1302 1403 2.323447 GCGGAAATTAGGTCGCGC 59.677 61.111 0.00 0.00 38.82 6.86
1307 1408 0.507358 GAAATTAGGTCGCGCGGATC 59.493 55.000 31.69 19.67 0.00 3.36
1310 1411 1.745320 ATTAGGTCGCGCGGATCCTT 61.745 55.000 32.78 20.64 31.41 3.36
1331 1432 4.973055 TGGCGCGCTTACACGGTT 62.973 61.111 32.29 0.00 0.00 4.44
1332 1433 4.143363 GGCGCGCTTACACGGTTC 62.143 66.667 32.29 5.91 0.00 3.62
1333 1434 4.479121 GCGCGCTTACACGGTTCG 62.479 66.667 26.67 0.00 0.00 3.95
1334 1435 3.101428 CGCGCTTACACGGTTCGT 61.101 61.111 5.56 0.00 42.36 3.85
1335 1436 2.651137 CGCGCTTACACGGTTCGTT 61.651 57.895 5.56 0.00 38.32 3.85
1336 1437 1.566077 GCGCTTACACGGTTCGTTT 59.434 52.632 0.00 0.00 38.32 3.60
1337 1438 0.720173 GCGCTTACACGGTTCGTTTG 60.720 55.000 0.00 0.00 38.32 2.93
1338 1439 0.720173 CGCTTACACGGTTCGTTTGC 60.720 55.000 0.00 0.00 38.32 3.68
1343 1444 1.657181 CACGGTTCGTTTGCTTGCC 60.657 57.895 0.00 0.00 38.32 4.52
1344 1445 2.050442 CGGTTCGTTTGCTTGCCC 60.050 61.111 0.00 0.00 0.00 5.36
1366 1467 2.672651 TGTCGCCGGACTCCGTTA 60.673 61.111 16.35 0.00 46.80 3.18
1380 1481 4.171103 GTTACGGCGGCTCCCCAT 62.171 66.667 13.24 0.00 0.00 4.00
1383 1484 2.487274 TTACGGCGGCTCCCCATTTT 62.487 55.000 13.24 0.00 0.00 1.82
1398 1499 3.333804 CCATTTTCCCCCATCGTTTTTG 58.666 45.455 0.00 0.00 0.00 2.44
1399 1500 2.535012 TTTTCCCCCATCGTTTTTGC 57.465 45.000 0.00 0.00 0.00 3.68
1400 1501 1.710816 TTTCCCCCATCGTTTTTGCT 58.289 45.000 0.00 0.00 0.00 3.91
1402 1503 0.965439 TCCCCCATCGTTTTTGCTTG 59.035 50.000 0.00 0.00 0.00 4.01
1404 1505 0.678950 CCCCATCGTTTTTGCTTGGT 59.321 50.000 0.00 0.00 0.00 3.67
1407 1508 1.526464 CCATCGTTTTTGCTTGGTTGC 59.474 47.619 0.00 0.00 0.00 4.17
1460 1562 4.980805 GGCGTGCGACACAGGGAA 62.981 66.667 9.95 0.00 33.40 3.97
1461 1563 3.712881 GCGTGCGACACAGGGAAC 61.713 66.667 9.95 0.00 33.40 3.62
1464 1575 4.980805 TGCGACACAGGGAACGGC 62.981 66.667 0.00 0.00 0.00 5.68
1493 1604 4.463879 CCGCACTGCTAGCCTGCT 62.464 66.667 24.41 0.00 0.00 4.24
1494 1605 2.889503 CGCACTGCTAGCCTGCTC 60.890 66.667 24.41 6.89 0.00 4.26
1495 1606 2.889503 GCACTGCTAGCCTGCTCG 60.890 66.667 21.58 3.87 0.00 5.03
1511 1622 1.405661 GCTCGTTCCCTCCTCGAAATT 60.406 52.381 0.00 0.00 33.32 1.82
1537 1648 7.971168 TGTTTGTTAATGCCACTATTTTATCCG 59.029 33.333 0.00 0.00 0.00 4.18
1636 1750 3.236137 GAACGAGGCGCGACGTAC 61.236 66.667 25.18 10.94 44.57 3.67
1656 1770 6.973474 ACGTACAGACTATTTTAGAGCATGTC 59.027 38.462 0.00 0.00 0.00 3.06
1658 1772 7.649705 CGTACAGACTATTTTAGAGCATGTCAT 59.350 37.037 0.00 0.00 0.00 3.06
1701 1815 9.347240 CATATCCTGATTAAGTTGACTTTGGAT 57.653 33.333 1.20 9.71 37.40 3.41
1706 1820 0.598065 AAGTTGACTTTGGATGCGCC 59.402 50.000 4.18 0.00 30.82 6.53
1768 1887 3.004862 ACGAACGGGAAATGGTGATTAC 58.995 45.455 0.00 0.00 0.00 1.89
1816 1935 2.956987 CTGCAAGCCTTGAACGGG 59.043 61.111 9.04 0.00 0.00 5.28
1841 1961 9.678941 GGATAGAAAAAGGAAACAAGTTTACTG 57.321 33.333 10.97 0.00 42.60 2.74
1850 1970 5.063564 GGAAACAAGTTTACTGGATCGCTAG 59.936 44.000 0.67 0.00 32.11 3.42
1871 1991 0.109132 GCCAAGGTGCCGAAATTCAG 60.109 55.000 0.00 0.00 0.00 3.02
1900 2033 3.385111 GGTGAACAACATACCCCACAAAA 59.615 43.478 0.00 0.00 0.00 2.44
2019 2152 6.385759 TGCTTACAGTTTGGGGATTATCTCTA 59.614 38.462 0.00 0.00 0.00 2.43
2091 2224 4.451435 GGTTTCCTGCGGATAAAGCTATAC 59.549 45.833 12.53 0.00 35.28 1.47
2108 2241 7.639162 AGCTATACTAAAATCAACGATTCCG 57.361 36.000 0.00 0.00 42.50 4.30
2123 2256 5.285798 CGATTCCGTTGGTTAAAAAGCTA 57.714 39.130 0.00 0.00 0.00 3.32
2276 2410 3.119316 CCCTAGAGCGCATAAGTATCCTG 60.119 52.174 11.47 0.00 0.00 3.86
2444 2579 7.164803 GCTTTATTTGATCAGGCTACCTCTAT 58.835 38.462 0.00 0.00 0.00 1.98
2655 2790 6.822667 TCAGAATTCTTCTATTGCTTTGCA 57.177 33.333 4.86 0.00 38.11 4.08
2758 2893 5.250543 TGATTATTGTGGAGAAAGGACTGGA 59.749 40.000 0.00 0.00 0.00 3.86
3205 3340 4.164030 TGCTTATTGGATCTTAGCCACAGA 59.836 41.667 0.00 0.00 34.56 3.41
3289 3424 2.028112 GGCATGGTCAAGAGTGTCAGTA 60.028 50.000 0.00 0.00 0.00 2.74
3367 3502 5.684626 GCGAAATGATGGAAATCATGAAGTC 59.315 40.000 0.00 0.00 40.81 3.01
3457 3592 4.583871 CTCTAAATTTCAGGTCACAGCCT 58.416 43.478 0.00 0.00 39.99 4.58
3619 3754 0.743097 GGAAGATCATGCTTGTGGGC 59.257 55.000 0.00 0.00 0.00 5.36
3631 3766 3.225798 GTGGGCCTGCTGTGCAAA 61.226 61.111 4.53 0.00 38.41 3.68
3793 3928 0.254178 TCATGCTCTCCTTGAAGGCC 59.746 55.000 6.30 0.00 34.61 5.19
3853 3988 1.376037 GGAGTGGCAGAAGGTTCCG 60.376 63.158 0.00 0.00 0.00 4.30
3911 4046 2.992273 GCATGTGGCACGGCATTCA 61.992 57.895 23.76 1.89 43.97 2.57
4061 4196 8.945481 AATTCATGTCAAAGTGATTGTTTTCA 57.055 26.923 0.00 0.00 40.11 2.69
4091 4226 0.039527 AAGCAATCGGACCGTTTTGC 60.040 50.000 31.69 31.69 42.37 3.68
4098 4233 1.202557 TCGGACCGTTTTGCTACTGTT 60.203 47.619 14.79 0.00 0.00 3.16
4111 4246 7.759489 TTTGCTACTGTTGGTTTTATCATCT 57.241 32.000 0.00 0.00 0.00 2.90
4213 4348 6.940739 AGAGCAGACATCTGTTACTGTATTT 58.059 36.000 10.50 0.00 45.45 1.40
4214 4349 7.038659 AGAGCAGACATCTGTTACTGTATTTC 58.961 38.462 10.50 0.00 45.45 2.17
4246 4383 2.031068 TGTTCCGTTGTTGTCATGTTCG 59.969 45.455 0.00 0.00 0.00 3.95
4283 4420 2.175715 ACTAAATCTTGGGCCATCTCCC 59.824 50.000 7.26 0.00 46.73 4.30
4383 4550 2.093306 TGCTTGTAGTGTAATGCGCT 57.907 45.000 9.73 0.00 41.45 5.92
4405 4572 4.968259 TGATACAGTAATATGGTGGTGCC 58.032 43.478 0.00 0.00 37.90 5.01
4480 4647 2.937149 CACCAAGATGAGATGCTGACAG 59.063 50.000 0.00 0.00 0.00 3.51
4481 4648 2.836372 ACCAAGATGAGATGCTGACAGA 59.164 45.455 6.65 0.00 0.00 3.41
4557 4724 1.037493 AACGCAGGTTCCTTTTTCCC 58.963 50.000 0.00 0.00 0.00 3.97
4592 4759 3.369921 CAGGAAAACTGCCAGGCC 58.630 61.111 9.64 0.00 40.97 5.19
4667 4852 3.608316 TGCAAGGCATATTTTTGGGTC 57.392 42.857 0.00 0.00 31.71 4.46
4673 4858 1.797348 GCATATTTTTGGGTCGCCACG 60.797 52.381 0.00 0.00 0.00 4.94
4685 4870 0.102481 TCGCCACGAAGATAAGGAGC 59.898 55.000 0.00 0.00 31.06 4.70
4687 4872 1.337071 CGCCACGAAGATAAGGAGCTA 59.663 52.381 0.00 0.00 0.00 3.32
4731 4962 4.600012 GTGCTATTCATACTTTGCACGT 57.400 40.909 0.00 0.00 40.67 4.49
4732 4963 4.969816 GTGCTATTCATACTTTGCACGTT 58.030 39.130 0.00 0.00 40.67 3.99
4738 4969 8.070171 GCTATTCATACTTTGCACGTTTCATAT 58.930 33.333 0.00 0.00 0.00 1.78
4741 4972 9.716507 ATTCATACTTTGCACGTTTCATATTAC 57.283 29.630 0.00 0.00 0.00 1.89
4763 4994 9.712305 ATTACGAAAGTTATATCATGGAGGAAG 57.288 33.333 0.00 0.00 46.40 3.46
4797 5028 0.324943 AGAAGGAACATCCACACCCG 59.675 55.000 0.00 0.00 39.61 5.28
4798 5029 0.036306 GAAGGAACATCCACACCCGT 59.964 55.000 0.00 0.00 39.61 5.28
4803 5034 2.159382 GAACATCCACACCCGTGAAAT 58.841 47.619 0.96 0.00 46.80 2.17
4831 5062 0.031585 CTTCGACACGACACCCTTGA 59.968 55.000 0.00 0.00 34.89 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.423154 CCCGTTGCGCTTGTCTCC 61.423 66.667 9.73 0.00 0.00 3.71
39 41 5.196695 CCTCCCCCTTCTTTATTCTTTCTG 58.803 45.833 0.00 0.00 0.00 3.02
42 44 3.272285 CCCCTCCCCCTTCTTTATTCTTT 59.728 47.826 0.00 0.00 0.00 2.52
62 64 1.839894 GTGTCCCTCATCATCCCCC 59.160 63.158 0.00 0.00 0.00 5.40
63 65 1.048724 TCGTGTCCCTCATCATCCCC 61.049 60.000 0.00 0.00 0.00 4.81
64 66 1.001406 GATCGTGTCCCTCATCATCCC 59.999 57.143 0.00 0.00 0.00 3.85
65 67 1.967066 AGATCGTGTCCCTCATCATCC 59.033 52.381 0.00 0.00 0.00 3.51
70 72 2.032620 GGTACAGATCGTGTCCCTCAT 58.967 52.381 0.00 0.00 40.94 2.90
71 73 1.272258 TGGTACAGATCGTGTCCCTCA 60.272 52.381 0.00 0.40 40.94 3.86
74 76 2.289195 TGTTTGGTACAGATCGTGTCCC 60.289 50.000 0.00 1.65 42.39 4.46
80 82 1.647213 CGTCGTGTTTGGTACAGATCG 59.353 52.381 0.00 0.00 42.39 3.69
83 85 2.293955 TCATCGTCGTGTTTGGTACAGA 59.706 45.455 0.00 0.00 42.39 3.41
85 87 2.396601 GTCATCGTCGTGTTTGGTACA 58.603 47.619 0.00 0.00 0.00 2.90
90 92 0.708370 CGAGGTCATCGTCGTGTTTG 59.292 55.000 0.00 0.00 46.62 2.93
91 93 3.102515 CGAGGTCATCGTCGTGTTT 57.897 52.632 0.00 0.00 46.62 2.83
100 102 1.751924 AGCTTGTCTACCGAGGTCATC 59.248 52.381 0.00 0.00 28.77 2.92
122 124 1.081376 GGCATCGATCCGACGGTAG 60.081 63.158 14.79 6.72 39.18 3.18
169 171 2.620251 TCCTGACTCCACAACTGTTG 57.380 50.000 18.44 18.44 0.00 3.33
171 173 3.279434 GTTTTCCTGACTCCACAACTGT 58.721 45.455 0.00 0.00 0.00 3.55
173 175 3.644966 TGTTTTCCTGACTCCACAACT 57.355 42.857 0.00 0.00 0.00 3.16
181 183 4.803452 TCCATCCTTTTGTTTTCCTGACT 58.197 39.130 0.00 0.00 0.00 3.41
185 187 5.705400 TCTTCTCCATCCTTTTGTTTTCCT 58.295 37.500 0.00 0.00 0.00 3.36
189 191 5.073691 TCCTCTCTTCTCCATCCTTTTGTTT 59.926 40.000 0.00 0.00 0.00 2.83
196 198 2.584965 TGTCTCCTCTCTTCTCCATCCT 59.415 50.000 0.00 0.00 0.00 3.24
197 199 3.025322 TGTCTCCTCTCTTCTCCATCC 57.975 52.381 0.00 0.00 0.00 3.51
217 219 1.274184 TGCCCCCTCTTGTACCACTAT 60.274 52.381 0.00 0.00 0.00 2.12
218 220 0.117541 TGCCCCCTCTTGTACCACTA 59.882 55.000 0.00 0.00 0.00 2.74
228 230 2.270434 TTCTCTTATGTGCCCCCTCT 57.730 50.000 0.00 0.00 0.00 3.69
236 238 7.412853 GTGCCATATTGTCTTTCTCTTATGTG 58.587 38.462 0.00 0.00 0.00 3.21
255 264 1.848388 TCAAGATCCATGAGGTGCCAT 59.152 47.619 0.00 0.00 35.89 4.40
262 271 8.821147 TTTTGTCAATTTTCAAGATCCATGAG 57.179 30.769 0.00 0.00 0.00 2.90
265 274 9.211485 GTGATTTTGTCAATTTTCAAGATCCAT 57.789 29.630 14.55 0.00 38.90 3.41
280 289 2.356382 GGTGTCCGTTGTGATTTTGTCA 59.644 45.455 0.00 0.00 0.00 3.58
292 301 1.193462 TCGGTATTGGGGTGTCCGTT 61.193 55.000 0.00 0.00 41.58 4.44
302 311 5.305585 AGGCTACATTTACATCGGTATTGG 58.694 41.667 0.00 0.00 0.00 3.16
305 314 5.512576 GGGAAGGCTACATTTACATCGGTAT 60.513 44.000 0.00 0.00 0.00 2.73
308 317 3.139077 GGGAAGGCTACATTTACATCGG 58.861 50.000 0.00 0.00 0.00 4.18
318 327 4.380843 TTCTTTCAATGGGAAGGCTACA 57.619 40.909 0.00 0.00 36.72 2.74
327 337 3.315191 ACGCGGATTATTCTTTCAATGGG 59.685 43.478 12.47 0.00 0.00 4.00
346 356 2.742372 ATGGTGCCTTGTCGACGC 60.742 61.111 11.62 9.03 0.00 5.19
348 358 0.602638 TCACATGGTGCCTTGTCGAC 60.603 55.000 9.11 9.11 32.98 4.20
351 361 1.609208 AAGTCACATGGTGCCTTGTC 58.391 50.000 6.76 0.00 30.41 3.18
378 388 1.541233 GGTACCTTCAGCCCATCATCG 60.541 57.143 4.06 0.00 0.00 3.84
384 394 2.066340 CAGTGGTACCTTCAGCCCA 58.934 57.895 14.36 0.00 0.00 5.36
411 422 0.109319 CCAACCAATGCTTGTACGGC 60.109 55.000 4.03 4.03 0.00 5.68
414 425 3.568007 TGAGAACCAACCAATGCTTGTAC 59.432 43.478 0.00 0.00 0.00 2.90
416 427 2.665165 TGAGAACCAACCAATGCTTGT 58.335 42.857 0.00 0.00 0.00 3.16
449 464 4.134563 GGTGGTAGCTTGAGAAAAACAGA 58.865 43.478 0.00 0.00 0.00 3.41
467 482 2.001872 GTACATCGTTTAACGGGGTGG 58.998 52.381 17.59 5.61 42.81 4.61
471 486 4.493545 GCTGATTGTACATCGTTTAACGGG 60.494 45.833 17.59 12.28 42.81 5.28
472 487 4.092237 TGCTGATTGTACATCGTTTAACGG 59.908 41.667 17.59 4.97 42.81 4.44
473 488 5.198116 TGCTGATTGTACATCGTTTAACG 57.802 39.130 11.60 11.60 44.19 3.18
474 489 6.021596 CCTTGCTGATTGTACATCGTTTAAC 58.978 40.000 0.00 0.00 0.00 2.01
477 492 3.119849 GCCTTGCTGATTGTACATCGTTT 60.120 43.478 0.00 0.00 0.00 3.60
478 493 2.420022 GCCTTGCTGATTGTACATCGTT 59.580 45.455 0.00 0.00 0.00 3.85
479 494 2.009774 GCCTTGCTGATTGTACATCGT 58.990 47.619 0.00 0.00 0.00 3.73
480 495 2.009051 TGCCTTGCTGATTGTACATCG 58.991 47.619 0.00 0.00 0.00 3.84
482 497 5.410355 AATTTGCCTTGCTGATTGTACAT 57.590 34.783 0.00 0.00 0.00 2.29
483 498 4.870123 AATTTGCCTTGCTGATTGTACA 57.130 36.364 0.00 0.00 0.00 2.90
485 500 4.997565 GCTAATTTGCCTTGCTGATTGTA 58.002 39.130 0.00 0.00 0.00 2.41
486 501 3.853475 GCTAATTTGCCTTGCTGATTGT 58.147 40.909 0.00 0.00 0.00 2.71
499 514 2.742053 AGTGTGCACGTAGGCTAATTTG 59.258 45.455 13.13 0.00 36.20 2.32
500 515 3.053831 AGTGTGCACGTAGGCTAATTT 57.946 42.857 13.13 0.00 36.20 1.82
517 532 0.954452 GGAGCCAAGGACAACAAGTG 59.046 55.000 0.00 0.00 0.00 3.16
520 535 1.691196 CAAGGAGCCAAGGACAACAA 58.309 50.000 0.00 0.00 0.00 2.83
532 551 2.222819 CGAATGAAACGTAGCAAGGAGC 60.223 50.000 0.00 0.00 46.19 4.70
533 552 2.222819 GCGAATGAAACGTAGCAAGGAG 60.223 50.000 0.00 0.00 0.00 3.69
534 553 1.730064 GCGAATGAAACGTAGCAAGGA 59.270 47.619 0.00 0.00 0.00 3.36
535 554 1.732259 AGCGAATGAAACGTAGCAAGG 59.268 47.619 0.00 0.00 0.00 3.61
536 555 2.222819 GGAGCGAATGAAACGTAGCAAG 60.223 50.000 0.00 0.00 0.00 4.01
537 556 1.730064 GGAGCGAATGAAACGTAGCAA 59.270 47.619 0.00 0.00 0.00 3.91
538 557 1.337354 TGGAGCGAATGAAACGTAGCA 60.337 47.619 0.00 0.00 0.00 3.49
539 558 1.355971 TGGAGCGAATGAAACGTAGC 58.644 50.000 0.00 0.00 0.00 3.58
581 605 1.693062 TGCGGTGTGGGTTAAGTAAGA 59.307 47.619 0.00 0.00 0.00 2.10
584 608 0.035176 GGTGCGGTGTGGGTTAAGTA 59.965 55.000 0.00 0.00 0.00 2.24
613 637 4.025401 GGGTTGCTTGTCGTGCCG 62.025 66.667 0.00 0.00 0.00 5.69
644 676 0.882927 TTAGCGCAGTGGTGGTGTTC 60.883 55.000 11.47 0.00 36.50 3.18
656 688 0.314618 TCGTGTGGTAGTTTAGCGCA 59.685 50.000 11.47 0.00 43.49 6.09
657 689 0.989890 CTCGTGTGGTAGTTTAGCGC 59.010 55.000 0.00 0.00 37.21 5.92
658 690 2.342910 ACTCGTGTGGTAGTTTAGCG 57.657 50.000 0.00 0.00 0.00 4.26
663 695 3.698040 CCTGGTATACTCGTGTGGTAGTT 59.302 47.826 2.25 0.00 0.00 2.24
667 699 2.376109 CTCCTGGTATACTCGTGTGGT 58.624 52.381 2.25 0.00 0.00 4.16
668 700 1.681793 CCTCCTGGTATACTCGTGTGG 59.318 57.143 2.25 0.00 0.00 4.17
683 732 1.977293 GCTTTGCGGGATCTCCTCCT 61.977 60.000 0.00 0.00 44.28 3.69
684 733 1.524849 GCTTTGCGGGATCTCCTCC 60.525 63.158 0.00 0.00 44.11 4.30
685 734 4.132999 GCTTTGCGGGATCTCCTC 57.867 61.111 0.00 0.00 35.95 3.71
733 785 2.158449 GCTGGATTATATGCTGTGCGTC 59.842 50.000 0.00 0.00 0.00 5.19
734 786 2.146342 GCTGGATTATATGCTGTGCGT 58.854 47.619 0.00 0.00 0.00 5.24
784 836 0.592247 CTTTGTTGGCTGTGTGCGTC 60.592 55.000 0.00 0.00 44.05 5.19
787 839 1.135141 TGTTCTTTGTTGGCTGTGTGC 60.135 47.619 0.00 0.00 41.94 4.57
790 842 3.229276 TGTTGTTCTTTGTTGGCTGTG 57.771 42.857 0.00 0.00 0.00 3.66
791 843 3.951775 TTGTTGTTCTTTGTTGGCTGT 57.048 38.095 0.00 0.00 0.00 4.40
792 844 4.493547 TCTTTGTTGTTCTTTGTTGGCTG 58.506 39.130 0.00 0.00 0.00 4.85
793 845 4.462483 TCTCTTTGTTGTTCTTTGTTGGCT 59.538 37.500 0.00 0.00 0.00 4.75
794 846 4.562789 GTCTCTTTGTTGTTCTTTGTTGGC 59.437 41.667 0.00 0.00 0.00 4.52
795 847 5.572896 GTGTCTCTTTGTTGTTCTTTGTTGG 59.427 40.000 0.00 0.00 0.00 3.77
796 848 6.088085 GTGTGTCTCTTTGTTGTTCTTTGTTG 59.912 38.462 0.00 0.00 0.00 3.33
797 849 6.149633 GTGTGTCTCTTTGTTGTTCTTTGTT 58.850 36.000 0.00 0.00 0.00 2.83
798 850 5.616866 CGTGTGTCTCTTTGTTGTTCTTTGT 60.617 40.000 0.00 0.00 0.00 2.83
799 851 4.788100 CGTGTGTCTCTTTGTTGTTCTTTG 59.212 41.667 0.00 0.00 0.00 2.77
800 852 4.671766 GCGTGTGTCTCTTTGTTGTTCTTT 60.672 41.667 0.00 0.00 0.00 2.52
801 853 3.181510 GCGTGTGTCTCTTTGTTGTTCTT 60.182 43.478 0.00 0.00 0.00 2.52
802 854 2.351726 GCGTGTGTCTCTTTGTTGTTCT 59.648 45.455 0.00 0.00 0.00 3.01
803 855 2.538939 GGCGTGTGTCTCTTTGTTGTTC 60.539 50.000 0.00 0.00 0.00 3.18
804 856 1.400494 GGCGTGTGTCTCTTTGTTGTT 59.600 47.619 0.00 0.00 0.00 2.83
805 857 1.014352 GGCGTGTGTCTCTTTGTTGT 58.986 50.000 0.00 0.00 0.00 3.32
865 917 0.167689 CTTTTCTCTCGCTGCCTTGC 59.832 55.000 0.00 0.00 0.00 4.01
866 918 0.167689 GCTTTTCTCTCGCTGCCTTG 59.832 55.000 0.00 0.00 0.00 3.61
943 1027 4.154347 GCCTCTGTGCCCCTCTCG 62.154 72.222 0.00 0.00 0.00 4.04
944 1028 4.154347 CGCCTCTGTGCCCCTCTC 62.154 72.222 0.00 0.00 0.00 3.20
1111 1199 2.097967 GGGGGTTGGGGATTGGTTA 58.902 57.895 0.00 0.00 0.00 2.85
1131 1219 0.319125 GAGCGAGCGAAGGGGATTAG 60.319 60.000 0.00 0.00 0.00 1.73
1133 1221 1.617947 AAGAGCGAGCGAAGGGGATT 61.618 55.000 0.00 0.00 0.00 3.01
1134 1222 2.022240 GAAGAGCGAGCGAAGGGGAT 62.022 60.000 0.00 0.00 0.00 3.85
1136 1224 2.202810 GAAGAGCGAGCGAAGGGG 60.203 66.667 0.00 0.00 0.00 4.79
1139 1227 1.205485 CGGATGAAGAGCGAGCGAAG 61.205 60.000 0.00 0.00 0.00 3.79
1140 1228 1.226688 CGGATGAAGAGCGAGCGAA 60.227 57.895 0.00 0.00 0.00 4.70
1143 1231 1.148759 GGAACGGATGAAGAGCGAGC 61.149 60.000 0.00 0.00 0.00 5.03
1145 1233 1.515954 GGGAACGGATGAAGAGCGA 59.484 57.895 0.00 0.00 0.00 4.93
1147 1235 0.179070 GAGGGGAACGGATGAAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
1148 1236 0.466124 GGAGGGGAACGGATGAAGAG 59.534 60.000 0.00 0.00 0.00 2.85
1151 1239 0.042731 AGAGGAGGGGAACGGATGAA 59.957 55.000 0.00 0.00 0.00 2.57
1152 1240 0.397254 GAGAGGAGGGGAACGGATGA 60.397 60.000 0.00 0.00 0.00 2.92
1154 1242 1.075151 GGAGAGGAGGGGAACGGAT 60.075 63.158 0.00 0.00 0.00 4.18
1156 1244 3.148279 CGGAGAGGAGGGGAACGG 61.148 72.222 0.00 0.00 0.00 4.44
1158 1246 3.839432 CGCGGAGAGGAGGGGAAC 61.839 72.222 0.00 0.00 0.00 3.62
1278 1379 4.293626 CTAATTTCCGCGCCGCCG 62.294 66.667 2.28 0.00 37.57 6.46
1279 1380 3.949047 CCTAATTTCCGCGCCGCC 61.949 66.667 2.28 0.00 0.00 6.13
1280 1381 3.164390 GACCTAATTTCCGCGCCGC 62.164 63.158 0.00 0.00 0.00 6.53
1281 1382 2.867091 CGACCTAATTTCCGCGCCG 61.867 63.158 0.00 0.00 0.00 6.46
1323 1424 0.305313 GCAAGCAAACGAACCGTGTA 59.695 50.000 0.00 0.00 39.99 2.90
1325 1426 1.657181 GGCAAGCAAACGAACCGTG 60.657 57.895 0.00 0.00 39.99 4.94
1327 1428 2.050442 GGGCAAGCAAACGAACCG 60.050 61.111 0.00 0.00 0.00 4.44
1328 1429 2.050442 CGGGCAAGCAAACGAACC 60.050 61.111 0.00 0.00 0.00 3.62
1329 1430 2.729491 GCGGGCAAGCAAACGAAC 60.729 61.111 7.11 0.00 37.05 3.95
1330 1431 4.320928 CGCGGGCAAGCAAACGAA 62.321 61.111 0.00 0.00 36.85 3.85
1366 1467 4.360405 AAAATGGGGAGCCGCCGT 62.360 61.111 0.81 1.39 39.47 5.68
1376 1477 1.567357 AAACGATGGGGGAAAATGGG 58.433 50.000 0.00 0.00 0.00 4.00
1378 1479 2.741517 GCAAAAACGATGGGGGAAAATG 59.258 45.455 0.00 0.00 0.00 2.32
1380 1481 2.043227 AGCAAAAACGATGGGGGAAAA 58.957 42.857 0.00 0.00 0.00 2.29
1383 1484 0.965439 CAAGCAAAAACGATGGGGGA 59.035 50.000 0.00 0.00 0.00 4.81
1404 1505 2.360600 CCAAATCGACCGGGGCAA 60.361 61.111 6.32 0.00 0.00 4.52
1489 1600 1.595993 TTCGAGGAGGGAACGAGCAG 61.596 60.000 0.00 0.00 37.36 4.24
1492 1603 2.271800 CAATTTCGAGGAGGGAACGAG 58.728 52.381 0.00 0.00 37.36 4.18
1493 1604 1.621814 ACAATTTCGAGGAGGGAACGA 59.378 47.619 0.00 0.00 0.00 3.85
1494 1605 2.094762 ACAATTTCGAGGAGGGAACG 57.905 50.000 0.00 0.00 0.00 3.95
1495 1606 3.568430 ACAAACAATTTCGAGGAGGGAAC 59.432 43.478 0.00 0.00 0.00 3.62
1511 1622 7.971168 CGGATAAAATAGTGGCATTAACAAACA 59.029 33.333 0.00 0.00 0.00 2.83
1656 1770 2.842457 TGTTATAGGAGCAGCAGCATG 58.158 47.619 3.17 0.00 45.49 4.06
1658 1772 4.323028 GGATATGTTATAGGAGCAGCAGCA 60.323 45.833 3.17 0.00 45.49 4.41
1660 1774 5.186603 TCAGGATATGTTATAGGAGCAGCAG 59.813 44.000 0.00 0.00 0.00 4.24
1706 1820 2.093983 GAGTAGTGCAAACGCGCG 59.906 61.111 30.96 30.96 44.77 6.86
1768 1887 2.852431 GAACGAGGACGCCGTCAGAG 62.852 65.000 20.08 11.15 43.96 3.35
1816 1935 9.678941 CCAGTAAACTTGTTTCCTTTTTCTATC 57.321 33.333 1.72 0.00 0.00 2.08
1841 1961 2.663188 CCTTGGCGCTAGCGATCC 60.663 66.667 39.52 30.15 46.35 3.36
1871 1991 2.817844 GGTATGTTGTTCACCAGTTCCC 59.182 50.000 0.00 0.00 32.32 3.97
2053 2186 8.389586 CGCAGGAAACCAAGTAAATATTTTAC 57.610 34.615 5.91 3.30 0.00 2.01
2108 2241 9.203421 AGCAAATAACATAGCTTTTTAACCAAC 57.797 29.630 0.00 0.00 32.52 3.77
2123 2256 3.573538 TGGTGAGCACAAGCAAATAACAT 59.426 39.130 2.75 0.00 45.49 2.71
2414 2549 5.526506 AGCCTGATCAAATAAAGCAATCC 57.473 39.130 0.00 0.00 0.00 3.01
2444 2579 4.864633 TGTTACGTCACGTGGTAATAACA 58.135 39.130 14.62 19.76 41.39 2.41
2758 2893 7.287061 TGATCTTCAATAATTCCGGGTTGTAT 58.713 34.615 0.00 0.00 0.00 2.29
2765 2900 6.569226 GCTTCCATGATCTTCAATAATTCCGG 60.569 42.308 0.00 0.00 0.00 5.14
3163 3298 1.529010 CACAAGGCCACCTGCAGAA 60.529 57.895 17.39 0.00 43.89 3.02
3205 3340 6.067217 AGAGGGTTGCATATGTAGAAGTTT 57.933 37.500 4.29 0.00 0.00 2.66
3256 3391 1.222936 CCATGCCTGGACTGACCTC 59.777 63.158 0.97 0.00 46.37 3.85
3289 3424 1.002069 TTCCATTCAGCACCATCCCT 58.998 50.000 0.00 0.00 0.00 4.20
3367 3502 4.737279 CACATATTCTGCACTGAGTCGTAG 59.263 45.833 0.00 0.00 0.00 3.51
3405 3540 1.135575 GCTTGATGCTTGGAGGAAACG 60.136 52.381 0.00 0.00 38.95 3.60
3619 3754 1.226916 TGCGTTTTTGCACAGCAGG 60.227 52.632 0.00 0.00 40.61 4.85
3853 3988 2.413142 GCAAGGGAGCATGCAGTCC 61.413 63.158 21.98 18.56 42.12 3.85
4091 4226 5.580691 TCGCAGATGATAAAACCAACAGTAG 59.419 40.000 0.00 0.00 0.00 2.57
4098 4233 6.150976 ACAAATTCTCGCAGATGATAAAACCA 59.849 34.615 0.00 0.00 33.89 3.67
4111 4246 0.865111 CACCGACACAAATTCTCGCA 59.135 50.000 0.00 0.00 0.00 5.10
4164 4299 2.159517 GCCTTTTGATCGCAGTAACCTG 60.160 50.000 0.00 0.00 41.91 4.00
4213 4348 7.091443 ACAACAACGGAACAAATAAAAGTTGA 58.909 30.769 11.61 0.00 39.60 3.18
4214 4349 7.062371 TGACAACAACGGAACAAATAAAAGTTG 59.938 33.333 0.00 0.00 41.97 3.16
4275 4412 0.179936 GCTCAGTTCTGGGGAGATGG 59.820 60.000 1.77 0.00 0.00 3.51
4283 4420 6.909550 ATTATAGAGTAGGCTCAGTTCTGG 57.090 41.667 0.00 0.00 44.00 3.86
4373 4540 6.589907 CCATATTACTGTATCAGCGCATTACA 59.410 38.462 11.47 13.10 34.37 2.41
4383 4550 4.410555 TGGCACCACCATATTACTGTATCA 59.589 41.667 0.00 0.00 46.36 2.15
4405 4572 2.530460 TCCCCCTTCACCATGAATTG 57.470 50.000 0.00 0.00 35.59 2.32
4480 4647 6.858478 GGAAACTTTTCAAGTATTCAGCAGTC 59.142 38.462 4.18 0.00 41.91 3.51
4481 4648 6.513393 CGGAAACTTTTCAAGTATTCAGCAGT 60.513 38.462 4.18 0.00 41.91 4.40
4557 4724 2.031682 CCTGTCTCGGCAGTTGAAAAAG 60.032 50.000 0.00 0.00 34.84 2.27
4592 4759 2.487986 GGAGGGCTTGAGATATGGTTGG 60.488 54.545 0.00 0.00 0.00 3.77
4632 4817 3.860378 GCCTTGCAATTTCAAATGGACGA 60.860 43.478 0.00 0.00 0.00 4.20
4634 4819 3.401182 TGCCTTGCAATTTCAAATGGAC 58.599 40.909 0.00 0.00 34.76 4.02
4667 4852 0.103208 AGCTCCTTATCTTCGTGGCG 59.897 55.000 0.00 0.00 0.00 5.69
4673 4858 8.258708 TCTTGGTTTACTTAGCTCCTTATCTTC 58.741 37.037 0.00 0.00 0.00 2.87
4685 4870 8.037166 ACGGTACCTTTATCTTGGTTTACTTAG 58.963 37.037 10.90 0.00 37.74 2.18
4687 4872 6.652062 CACGGTACCTTTATCTTGGTTTACTT 59.348 38.462 10.90 0.00 37.74 2.24
4738 4969 8.701895 ACTTCCTCCATGATATAACTTTCGTAA 58.298 33.333 0.00 0.00 0.00 3.18
4741 4972 7.815068 CCTACTTCCTCCATGATATAACTTTCG 59.185 40.741 0.00 0.00 0.00 3.46
4798 5029 5.697178 TCGTGTCGAAGGTGAAATAATTTCA 59.303 36.000 0.00 0.00 39.02 2.69
4803 5034 3.737266 GTGTCGTGTCGAAGGTGAAATAA 59.263 43.478 0.00 0.00 37.72 1.40
4815 5046 1.990563 GTTATCAAGGGTGTCGTGTCG 59.009 52.381 0.00 0.00 0.00 4.35
4903 5134 4.479619 GTGTTTCTGCAATGATCCACTTC 58.520 43.478 0.00 0.00 0.00 3.01
4915 5146 3.334691 GCATGTACTAGGTGTTTCTGCA 58.665 45.455 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.