Multiple sequence alignment - TraesCS5D01G308500

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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 TraesCS5D01G308500 chr5D 100.000 2442 0 0 1 2442 405335786 405333345 0.000000e+00 4510
1 TraesCS5D01G308500 chr5D 86.786 560 49 19 840 1391 440375669 440375127 3.470000e-168 601
2 TraesCS5D01G308500 chr5D 80.235 511 81 11 4 511 286934057 286933564 1.380000e-97 366
3 TraesCS5D01G308500 chr5A 88.115 1077 91 20 759 1823 509043344 509044395 0.000000e+00 1245
4 TraesCS5D01G308500 chr5A 86.339 549 65 9 1 543 509041751 509042295 7.520000e-165 590
5 TraesCS5D01G308500 chr5A 85.663 558 66 14 840 1395 552078674 552078129 2.110000e-160 575
6 TraesCS5D01G308500 chr5A 85.536 560 47 15 840 1391 556534532 556533999 2.740000e-154 555
7 TraesCS5D01G308500 chr5A 88.197 466 42 11 1766 2223 509044384 509044844 5.940000e-151 544
8 TraesCS5D01G308500 chr5A 90.385 156 8 2 2294 2442 509045402 509045557 5.330000e-47 198
9 TraesCS5D01G308500 chr5B 88.695 973 84 17 759 1713 486283585 486282621 0.000000e+00 1164
10 TraesCS5D01G308500 chr5B 97.476 317 8 0 1075 1391 535715413 535715097 2.140000e-150 542
11 TraesCS5D01G308500 chr5B 89.083 229 9 8 2218 2442 486282114 486281898 1.110000e-68 270
12 TraesCS5D01G308500 chr4A 96.594 323 11 0 1068 1390 66148194 66147872 9.940000e-149 536
13 TraesCS5D01G308500 chr1D 97.444 313 8 0 1077 1389 445366814 445366502 3.570000e-148 534
14 TraesCS5D01G308500 chr1D 76.674 433 84 10 88 512 50973981 50974404 8.790000e-55 224
15 TraesCS5D01G308500 chr7B 96.855 318 10 0 1074 1391 589740528 589740211 1.290000e-147 532
16 TraesCS5D01G308500 chr1A 76.940 464 88 11 50 504 50712576 50713029 1.880000e-61 246
17 TraesCS5D01G308500 chr1A 75.155 483 103 10 30 504 50131666 50132139 6.840000e-51 211
18 TraesCS5D01G308500 chr1A 76.190 420 83 10 94 504 50196973 50197384 3.180000e-49 206
19 TraesCS5D01G308500 chr1A 76.092 435 80 16 89 512 50614565 50614986 3.180000e-49 206
20 TraesCS5D01G308500 chr1A 74.948 483 98 17 30 501 50257370 50257840 1.480000e-47 200
21 TraesCS5D01G308500 chr7A 84.071 113 16 2 109 221 18776627 18776737 9.230000e-20 108


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 TraesCS5D01G308500 chr5D 405333345 405335786 2441 True 4510.00 4510 100.000 1 2442 1 chr5D.!!$R2 2441
1 TraesCS5D01G308500 chr5D 440375127 440375669 542 True 601.00 601 86.786 840 1391 1 chr5D.!!$R3 551
2 TraesCS5D01G308500 chr5A 509041751 509045557 3806 False 644.25 1245 88.259 1 2442 4 chr5A.!!$F1 2441
3 TraesCS5D01G308500 chr5A 552078129 552078674 545 True 575.00 575 85.663 840 1395 1 chr5A.!!$R1 555
4 TraesCS5D01G308500 chr5A 556533999 556534532 533 True 555.00 555 85.536 840 1391 1 chr5A.!!$R2 551
5 TraesCS5D01G308500 chr5B 486281898 486283585 1687 True 717.00 1164 88.889 759 2442 2 chr5B.!!$R2 1683

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
742 1653 0.038618 TCATACGCGTCTGTGCAAGT 60.039 50.0 18.63 0.0 34.15 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 2634 0.315886 CAGCCAGCTTGATTTGTGCA 59.684 50.0 0.0 0.0 0.0 4.57 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
32 33 5.353111 AGGCTATCTTCGCTAGAAAGTTTC 58.647 41.667 7.57 7.57 36.22 2.78
39 40 5.800941 TCTTCGCTAGAAAGTTTCGAGAATC 59.199 40.000 24.70 9.84 34.77 2.52
58 59 3.018598 TCGATCGCTTGATTGGAGATC 57.981 47.619 11.09 0.00 36.91 2.75
65 66 3.462021 GCTTGATTGGAGATCGCTAACT 58.538 45.455 0.00 0.00 0.00 2.24
66 67 3.873952 GCTTGATTGGAGATCGCTAACTT 59.126 43.478 0.00 0.00 0.00 2.66
72 73 4.487714 TGGAGATCGCTAACTTTGGATT 57.512 40.909 0.00 0.00 0.00 3.01
74 75 4.635765 TGGAGATCGCTAACTTTGGATTTG 59.364 41.667 0.00 0.00 0.00 2.32
80 81 3.305335 CGCTAACTTTGGATTTGGCAAGT 60.305 43.478 0.00 0.00 0.00 3.16
94 95 1.597027 CAAGTCGGTTCGGTTGCCT 60.597 57.895 0.00 0.00 0.00 4.75
95 96 1.147600 AAGTCGGTTCGGTTGCCTT 59.852 52.632 0.00 0.00 0.00 4.35
133 136 0.474660 AGGGACAAGAGCAAGAGGGT 60.475 55.000 0.00 0.00 0.00 4.34
134 137 0.322008 GGGACAAGAGCAAGAGGGTG 60.322 60.000 0.00 0.00 0.00 4.61
152 155 2.202878 TGCGCTAGCCATCGTTCC 60.203 61.111 9.73 0.00 44.33 3.62
162 165 1.451207 CATCGTTCCGGCATTCCCA 60.451 57.895 0.00 0.00 0.00 4.37
166 169 1.241315 CGTTCCGGCATTCCCAAAGT 61.241 55.000 0.00 0.00 0.00 2.66
168 171 1.743394 GTTCCGGCATTCCCAAAGTAG 59.257 52.381 0.00 0.00 0.00 2.57
180 183 7.614494 CATTCCCAAAGTAGAAATCATTTGGT 58.386 34.615 12.97 0.00 46.67 3.67
197 200 4.836125 TTGGTAGCAAAAGCAAGAAGAG 57.164 40.909 4.54 0.00 33.24 2.85
213 216 1.115467 AGAGTGGCGTCATAGGGAAG 58.885 55.000 0.00 0.00 0.00 3.46
219 222 2.017559 GCGTCATAGGGAAGGCGTCT 62.018 60.000 0.00 0.00 0.00 4.18
223 226 0.824109 CATAGGGAAGGCGTCTGTGA 59.176 55.000 0.00 0.00 0.00 3.58
224 227 0.824759 ATAGGGAAGGCGTCTGTGAC 59.175 55.000 0.00 0.00 0.00 3.67
226 229 1.374758 GGGAAGGCGTCTGTGACTG 60.375 63.158 0.00 0.00 0.00 3.51
227 230 1.374758 GGAAGGCGTCTGTGACTGG 60.375 63.158 0.00 0.00 0.00 4.00
231 234 1.069090 GGCGTCTGTGACTGGTTGA 59.931 57.895 0.00 0.00 0.00 3.18
252 255 8.552034 GGTTGATAGATGGTTATCTTCTTTTCG 58.448 37.037 0.00 0.00 40.79 3.46
259 262 4.758165 TGGTTATCTTCTTTTCGGGTTGTC 59.242 41.667 0.00 0.00 0.00 3.18
277 280 2.877786 TGTCGTGCATGATGTCTTTGTT 59.122 40.909 12.67 0.00 0.00 2.83
287 290 6.201425 GCATGATGTCTTTGTTGATGTGTTTT 59.799 34.615 0.00 0.00 0.00 2.43
289 292 6.861144 TGATGTCTTTGTTGATGTGTTTTCA 58.139 32.000 0.00 0.00 0.00 2.69
290 293 7.490840 TGATGTCTTTGTTGATGTGTTTTCAT 58.509 30.769 0.00 0.00 0.00 2.57
291 294 8.628280 TGATGTCTTTGTTGATGTGTTTTCATA 58.372 29.630 0.00 0.00 0.00 2.15
294 297 7.284261 TGTCTTTGTTGATGTGTTTTCATAGGA 59.716 33.333 0.00 0.00 0.00 2.94
298 301 5.412594 TGTTGATGTGTTTTCATAGGAGCTC 59.587 40.000 4.71 4.71 0.00 4.09
307 310 2.384828 TCATAGGAGCTCCTTTGCGTA 58.615 47.619 39.23 22.14 46.09 4.42
312 315 1.608283 GGAGCTCCTTTGCGTAGTTGT 60.608 52.381 26.25 0.00 38.13 3.32
313 316 2.353406 GGAGCTCCTTTGCGTAGTTGTA 60.353 50.000 26.25 0.00 38.13 2.41
321 324 6.408035 TCCTTTGCGTAGTTGTATTTCCATA 58.592 36.000 0.00 0.00 0.00 2.74
323 326 6.238374 CCTTTGCGTAGTTGTATTTCCATAGG 60.238 42.308 0.00 0.00 0.00 2.57
324 327 5.347620 TGCGTAGTTGTATTTCCATAGGT 57.652 39.130 0.00 0.00 0.00 3.08
325 328 5.736813 TGCGTAGTTGTATTTCCATAGGTT 58.263 37.500 0.00 0.00 0.00 3.50
327 330 5.583457 GCGTAGTTGTATTTCCATAGGTTGT 59.417 40.000 0.00 0.00 0.00 3.32
338 341 3.118038 TCCATAGGTTGTGAGGTTATGCC 60.118 47.826 0.00 0.00 37.58 4.40
362 365 2.840572 GGGTTGGGGGCGTTTGTT 60.841 61.111 0.00 0.00 0.00 2.83
363 366 2.436544 GGGTTGGGGGCGTTTGTTT 61.437 57.895 0.00 0.00 0.00 2.83
365 368 1.885388 GTTGGGGGCGTTTGTTTGC 60.885 57.895 0.00 0.00 0.00 3.68
366 369 2.060980 TTGGGGGCGTTTGTTTGCT 61.061 52.632 0.00 0.00 0.00 3.91
372 375 1.539776 GGCGTTTGTTTGCTTGCTCG 61.540 55.000 0.00 0.00 0.00 5.03
382 385 2.908073 GCTTGCTCGGGTGGTTGTG 61.908 63.158 0.00 0.00 0.00 3.33
383 386 1.227823 CTTGCTCGGGTGGTTGTGA 60.228 57.895 0.00 0.00 0.00 3.58
384 387 1.227823 TTGCTCGGGTGGTTGTGAG 60.228 57.895 0.00 0.00 0.00 3.51
393 396 2.555227 GGGTGGTTGTGAGGATTCATGT 60.555 50.000 0.00 0.00 35.39 3.21
407 410 4.640647 GGATTCATGTTTTGGGAGTAGTCC 59.359 45.833 8.22 8.22 43.05 3.85
410 413 0.759959 TGTTTTGGGAGTAGTCCGCA 59.240 50.000 10.57 7.05 45.05 5.69
457 460 8.568676 TTCATTCGGTTTCTATCAATTAACCA 57.431 30.769 6.41 0.00 39.98 3.67
465 468 7.706607 GGTTTCTATCAATTAACCAGGCAATTC 59.293 37.037 0.00 0.00 39.80 2.17
468 471 7.345691 TCTATCAATTAACCAGGCAATTCTCA 58.654 34.615 0.00 0.00 0.00 3.27
470 473 6.855763 TCAATTAACCAGGCAATTCTCATT 57.144 33.333 0.00 0.00 0.00 2.57
478 481 5.011943 ACCAGGCAATTCTCATTTGCTTAAA 59.988 36.000 8.15 0.00 46.74 1.52
496 499 8.389779 TGCTTAAATAATCGATGAGGCAAATA 57.610 30.769 0.00 0.00 0.00 1.40
543 548 4.655762 AACTTTGCCTCTCCTTTTTGAC 57.344 40.909 0.00 0.00 0.00 3.18
544 549 3.631250 ACTTTGCCTCTCCTTTTTGACA 58.369 40.909 0.00 0.00 0.00 3.58
545 550 4.023291 ACTTTGCCTCTCCTTTTTGACAA 58.977 39.130 0.00 0.00 0.00 3.18
546 551 4.651045 ACTTTGCCTCTCCTTTTTGACAAT 59.349 37.500 0.00 0.00 0.00 2.71
547 552 5.833131 ACTTTGCCTCTCCTTTTTGACAATA 59.167 36.000 0.00 0.00 0.00 1.90
549 554 6.723298 TTGCCTCTCCTTTTTGACAATAAA 57.277 33.333 0.00 0.00 0.00 1.40
551 556 8.415950 TTGCCTCTCCTTTTTGACAATAAATA 57.584 30.769 0.00 0.00 0.00 1.40
553 558 9.034800 TGCCTCTCCTTTTTGACAATAAATATT 57.965 29.630 0.00 0.00 0.00 1.28
661 1572 8.924303 AGGGAAAATAAATAAATAAGACCAGGC 58.076 33.333 0.00 0.00 0.00 4.85
662 1573 8.924303 GGGAAAATAAATAAATAAGACCAGGCT 58.076 33.333 0.00 0.00 0.00 4.58
663 1574 9.967346 GGAAAATAAATAAATAAGACCAGGCTC 57.033 33.333 0.00 0.00 0.00 4.70
664 1575 9.665264 GAAAATAAATAAATAAGACCAGGCTCG 57.335 33.333 0.00 0.00 0.00 5.03
665 1576 8.747538 AAATAAATAAATAAGACCAGGCTCGT 57.252 30.769 0.00 0.00 0.00 4.18
666 1577 7.964604 ATAAATAAATAAGACCAGGCTCGTC 57.035 36.000 3.88 3.88 0.00 4.20
667 1578 2.295253 AAATAAGACCAGGCTCGTCG 57.705 50.000 6.61 0.00 35.33 5.12
668 1579 0.460311 AATAAGACCAGGCTCGTCGG 59.540 55.000 6.61 0.00 35.33 4.79
669 1580 0.395311 ATAAGACCAGGCTCGTCGGA 60.395 55.000 6.61 0.00 35.33 4.55
670 1581 1.310933 TAAGACCAGGCTCGTCGGAC 61.311 60.000 6.61 0.00 35.33 4.79
671 1582 4.131088 GACCAGGCTCGTCGGACC 62.131 72.222 1.91 0.00 0.00 4.46
672 1583 4.680537 ACCAGGCTCGTCGGACCT 62.681 66.667 1.91 1.58 0.00 3.85
675 1586 2.043852 AGGCTCGTCGGACCTGAT 60.044 61.111 1.91 0.00 30.82 2.90
676 1587 2.105128 GGCTCGTCGGACCTGATG 59.895 66.667 1.91 0.00 0.00 3.07
677 1588 2.415608 GGCTCGTCGGACCTGATGA 61.416 63.158 1.91 7.66 33.08 2.92
678 1589 1.226717 GCTCGTCGGACCTGATGAC 60.227 63.158 1.91 0.00 30.92 3.06
679 1590 1.934220 GCTCGTCGGACCTGATGACA 61.934 60.000 1.91 0.00 32.91 3.58
680 1591 0.741326 CTCGTCGGACCTGATGACAT 59.259 55.000 1.91 0.00 32.91 3.06
681 1592 0.738975 TCGTCGGACCTGATGACATC 59.261 55.000 8.59 8.59 32.91 3.06
682 1593 0.741326 CGTCGGACCTGATGACATCT 59.259 55.000 16.25 0.00 32.91 2.90
683 1594 1.268794 CGTCGGACCTGATGACATCTC 60.269 57.143 16.25 5.89 32.91 2.75
684 1595 1.751351 GTCGGACCTGATGACATCTCA 59.249 52.381 16.25 0.00 32.91 3.27
685 1596 2.027385 TCGGACCTGATGACATCTCAG 58.973 52.381 16.25 7.92 39.88 3.35
690 1601 2.685850 CTGATGACATCTCAGGTGCA 57.314 50.000 16.25 0.00 37.15 4.57
691 1602 2.981898 CTGATGACATCTCAGGTGCAA 58.018 47.619 16.25 0.00 37.15 4.08
692 1603 3.340928 CTGATGACATCTCAGGTGCAAA 58.659 45.455 16.25 0.00 37.15 3.68
693 1604 3.753815 TGATGACATCTCAGGTGCAAAA 58.246 40.909 16.25 0.00 0.00 2.44
694 1605 3.754850 TGATGACATCTCAGGTGCAAAAG 59.245 43.478 16.25 0.00 0.00 2.27
695 1606 1.881973 TGACATCTCAGGTGCAAAAGC 59.118 47.619 0.00 0.00 0.00 3.51
696 1607 1.200948 GACATCTCAGGTGCAAAAGCC 59.799 52.381 0.00 0.00 0.00 4.35
697 1608 0.529378 CATCTCAGGTGCAAAAGCCC 59.471 55.000 0.00 0.00 0.00 5.19
698 1609 0.962356 ATCTCAGGTGCAAAAGCCCG 60.962 55.000 0.00 0.00 0.00 6.13
699 1610 2.597217 TCAGGTGCAAAAGCCCGG 60.597 61.111 0.00 0.00 0.00 5.73
700 1611 4.362476 CAGGTGCAAAAGCCCGGC 62.362 66.667 0.00 0.00 0.00 6.13
723 1634 2.443390 GATGCCCATTGCCCAGCT 60.443 61.111 0.00 0.00 40.16 4.24
725 1636 3.305619 ATGCCCATTGCCCAGCTCA 62.306 57.895 0.00 0.00 40.16 4.26
727 1638 1.152694 GCCCATTGCCCAGCTCATA 60.153 57.895 0.00 0.00 0.00 2.15
728 1639 1.458639 GCCCATTGCCCAGCTCATAC 61.459 60.000 0.00 0.00 0.00 2.39
729 1640 1.168407 CCCATTGCCCAGCTCATACG 61.168 60.000 0.00 0.00 0.00 3.06
732 1643 2.593468 ATTGCCCAGCTCATACGCGT 62.593 55.000 19.17 19.17 34.40 6.01
734 1645 2.808315 CCCAGCTCATACGCGTCT 59.192 61.111 18.63 1.73 34.40 4.18
735 1646 1.589993 CCCAGCTCATACGCGTCTG 60.590 63.158 18.63 18.04 34.40 3.51
740 1651 1.351430 GCTCATACGCGTCTGTGCAA 61.351 55.000 32.91 11.82 33.33 4.08
741 1652 0.642291 CTCATACGCGTCTGTGCAAG 59.358 55.000 18.63 5.80 34.15 4.01
742 1653 0.038618 TCATACGCGTCTGTGCAAGT 60.039 50.000 18.63 0.00 34.15 3.16
744 1655 1.194547 CATACGCGTCTGTGCAAGTTT 59.805 47.619 18.63 0.00 34.15 2.66
745 1656 0.856641 TACGCGTCTGTGCAAGTTTC 59.143 50.000 18.63 0.00 34.15 2.78
746 1657 0.810031 ACGCGTCTGTGCAAGTTTCT 60.810 50.000 5.58 0.00 34.15 2.52
747 1658 0.383491 CGCGTCTGTGCAAGTTTCTG 60.383 55.000 0.00 0.00 34.15 3.02
748 1659 0.658536 GCGTCTGTGCAAGTTTCTGC 60.659 55.000 0.00 0.00 42.95 4.26
750 1661 1.312815 GTCTGTGCAAGTTTCTGCCT 58.687 50.000 0.00 0.00 41.90 4.75
752 1663 2.224314 GTCTGTGCAAGTTTCTGCCTAC 59.776 50.000 0.00 0.00 41.90 3.18
753 1664 2.104792 TCTGTGCAAGTTTCTGCCTACT 59.895 45.455 0.00 0.00 41.90 2.57
754 1665 2.221169 TGTGCAAGTTTCTGCCTACTG 58.779 47.619 0.00 0.00 41.90 2.74
755 1666 1.537202 GTGCAAGTTTCTGCCTACTGG 59.463 52.381 0.00 0.00 41.90 4.00
894 1815 1.068083 CACTCCCGACCATCCATCG 59.932 63.158 0.00 0.00 39.33 3.84
973 1895 3.491276 CGAACACCGTGGCTATATAACCA 60.491 47.826 0.45 0.45 0.00 3.67
980 1902 3.064931 GTGGCTATATAACCAACCTCGC 58.935 50.000 6.44 0.00 37.79 5.03
988 1910 4.047125 CCAACCTCGCCCCCACAT 62.047 66.667 0.00 0.00 0.00 3.21
1005 1927 0.464373 CATTCCACCACCATCCTCCG 60.464 60.000 0.00 0.00 0.00 4.63
1008 1930 3.716195 CACCACCATCCTCCGCCA 61.716 66.667 0.00 0.00 0.00 5.69
1029 1954 1.898574 GCCACCACTCCCAACACAG 60.899 63.158 0.00 0.00 0.00 3.66
1030 1955 1.898574 CCACCACTCCCAACACAGC 60.899 63.158 0.00 0.00 0.00 4.40
1053 1978 3.775654 CCCACCGGAGAGACAGGC 61.776 72.222 9.46 0.00 37.36 4.85
1063 1988 1.193462 AGAGACAGGCAGAAGCAGCT 61.193 55.000 0.00 0.00 44.61 4.24
1156 2100 2.325082 GGTGCTCCGCGACAACATT 61.325 57.895 8.23 0.00 0.00 2.71
1430 2374 3.876914 CCAGCCAGCAACGAGATAAATTA 59.123 43.478 0.00 0.00 0.00 1.40
1432 2376 5.009010 CCAGCCAGCAACGAGATAAATTATT 59.991 40.000 0.00 0.00 0.00 1.40
1433 2377 6.460123 CCAGCCAGCAACGAGATAAATTATTT 60.460 38.462 0.00 0.00 0.00 1.40
1572 2522 9.696917 ATCGAATTTGGAAATTATAATGCCTTC 57.303 29.630 15.06 8.70 38.64 3.46
1574 2524 8.971321 CGAATTTGGAAATTATAATGCCTTCTG 58.029 33.333 15.06 7.04 38.64 3.02
1582 2532 3.607490 ATAATGCCTTCTGCCCTTGAT 57.393 42.857 0.00 0.00 40.16 2.57
1583 2533 1.772836 AATGCCTTCTGCCCTTGATC 58.227 50.000 0.00 0.00 40.16 2.92
1584 2534 0.627451 ATGCCTTCTGCCCTTGATCA 59.373 50.000 0.00 0.00 40.16 2.92
1593 2543 0.895100 GCCCTTGATCACACCTGCAA 60.895 55.000 0.00 0.00 0.00 4.08
1597 2547 2.619849 CCTTGATCACACCTGCAATCCT 60.620 50.000 0.00 0.00 0.00 3.24
1611 2561 2.758009 CAATCCTTTGCCCTGTTTGTG 58.242 47.619 0.00 0.00 0.00 3.33
1624 2574 3.931468 CCTGTTTGTGTTGATTTGTGCAA 59.069 39.130 0.00 0.00 0.00 4.08
1653 2603 0.824109 TCTTATCAGTGCGTCCCCAG 59.176 55.000 0.00 0.00 0.00 4.45
1684 2634 3.324846 TCAGTGGCTCTGTATCAAACTGT 59.675 43.478 15.49 0.00 43.97 3.55
1685 2635 3.434641 CAGTGGCTCTGTATCAAACTGTG 59.565 47.826 8.37 0.00 39.17 3.66
1687 2637 2.224499 TGGCTCTGTATCAAACTGTGCA 60.224 45.455 9.98 0.00 43.99 4.57
1700 2650 1.338973 ACTGTGCACAAATCAAGCTGG 59.661 47.619 21.98 7.42 0.00 4.85
1702 2652 0.316204 GTGCACAAATCAAGCTGGCT 59.684 50.000 13.17 0.00 0.00 4.75
1726 2676 5.534654 TGTGTTTATTTCTGAAACCTCCCTG 59.465 40.000 4.73 0.00 36.20 4.45
1734 2684 3.321682 TCTGAAACCTCCCTGCATTTTTG 59.678 43.478 0.00 0.00 0.00 2.44
1742 2692 3.303938 TCCCTGCATTTTTGTTCCTCAA 58.696 40.909 0.00 0.00 0.00 3.02
1744 2694 3.809279 CCCTGCATTTTTGTTCCTCAAAC 59.191 43.478 0.00 0.00 44.39 2.93
1745 2695 4.440880 CCTGCATTTTTGTTCCTCAAACA 58.559 39.130 0.00 0.00 46.11 2.83
1756 2706 4.513692 TGTTCCTCAAACACTACCATTTCG 59.486 41.667 0.00 0.00 42.95 3.46
1764 2714 1.331756 CACTACCATTTCGCATCCTGC 59.668 52.381 0.00 0.00 40.69 4.85
1773 2723 2.894387 GCATCCTGCGTCTGCCTC 60.894 66.667 0.00 0.00 41.78 4.70
1780 2730 2.282147 CTGCGTCTGCCTCTGAGGAG 62.282 65.000 27.53 19.41 37.67 3.69
1795 2745 5.245075 CTCTGAGGAGGTGAACTTTAGTTCT 59.755 44.000 19.97 3.89 43.21 3.01
1809 2759 1.843368 AGTTCTGCCCATTCATGTGG 58.157 50.000 0.00 0.00 39.05 4.17
1816 2766 3.985410 CCATTCATGTGGGGTCTGT 57.015 52.632 0.00 0.00 35.55 3.41
1824 2774 2.319025 TGTGGGGTCTGTGTCTGATA 57.681 50.000 0.00 0.00 0.00 2.15
1825 2775 2.832838 TGTGGGGTCTGTGTCTGATAT 58.167 47.619 0.00 0.00 0.00 1.63
1832 2834 4.631813 GGGTCTGTGTCTGATATTGTGTTC 59.368 45.833 0.00 0.00 0.00 3.18
1841 2843 6.057533 GTCTGATATTGTGTTCCATCCATGA 58.942 40.000 0.00 0.00 0.00 3.07
1842 2844 6.713903 GTCTGATATTGTGTTCCATCCATGAT 59.286 38.462 0.00 0.00 0.00 2.45
1843 2845 7.879677 GTCTGATATTGTGTTCCATCCATGATA 59.120 37.037 0.00 0.00 0.00 2.15
1846 2848 9.016438 TGATATTGTGTTCCATCCATGATATTG 57.984 33.333 0.00 0.00 0.00 1.90
1848 2850 6.453926 TTGTGTTCCATCCATGATATTGTG 57.546 37.500 0.00 0.00 0.00 3.33
1849 2851 5.508567 TGTGTTCCATCCATGATATTGTGT 58.491 37.500 0.00 0.00 0.00 3.72
1850 2852 5.589855 TGTGTTCCATCCATGATATTGTGTC 59.410 40.000 0.00 0.00 0.00 3.67
1851 2853 5.589855 GTGTTCCATCCATGATATTGTGTCA 59.410 40.000 0.00 0.00 0.00 3.58
1853 2855 5.892524 TCCATCCATGATATTGTGTCAGA 57.107 39.130 0.00 0.00 0.00 3.27
1854 2856 6.251255 TCCATCCATGATATTGTGTCAGAA 57.749 37.500 0.00 0.00 0.00 3.02
1882 2884 3.495670 ACTGTTCGAGATCTACACTGC 57.504 47.619 0.00 0.00 0.00 4.40
1896 2898 2.746269 ACACTGCACATGTCAAAATGC 58.254 42.857 0.00 0.00 38.59 3.56
2004 3013 6.026513 GCTCAGTTGATTTCTATTTCTGCAC 58.973 40.000 0.00 0.00 0.00 4.57
2019 3028 3.190079 TCTGCACGATGCTGAATCTTAC 58.810 45.455 13.95 0.00 46.01 2.34
2030 3045 4.451096 TGCTGAATCTTACCAGTTCGTTTC 59.549 41.667 0.00 0.00 33.19 2.78
2099 3115 4.394729 CTGTCTGGTTTTGCCTTTACCTA 58.605 43.478 0.00 0.00 38.35 3.08
2133 3149 2.139118 GCCATCGCCTTCAATAGAGTC 58.861 52.381 0.00 0.00 0.00 3.36
2143 3159 3.689872 TCAATAGAGTCCAGGTAGCCT 57.310 47.619 0.00 0.00 0.00 4.58
2150 3166 0.977395 GTCCAGGTAGCCTTGTGACT 59.023 55.000 0.00 0.00 0.00 3.41
2167 3183 2.223782 TGACTTGCCTGCATTTTGTGTC 60.224 45.455 0.00 0.00 0.00 3.67
2181 3197 4.901197 TTTGTGTCTGCCTCTGGTATTA 57.099 40.909 0.00 0.00 0.00 0.98
2197 3213 7.402054 TCTGGTATTACTGTGTTTCATCCATT 58.598 34.615 0.00 0.00 0.00 3.16
2199 3215 9.173021 CTGGTATTACTGTGTTTCATCCATTTA 57.827 33.333 0.00 0.00 0.00 1.40
2257 3624 3.097877 TCGGCTTGATGCATACAGTAG 57.902 47.619 0.00 0.00 45.15 2.57
2274 3641 6.054860 ACAGTAGAAACATGGTTAGCAGAT 57.945 37.500 0.00 0.00 0.00 2.90
2275 3642 6.109359 ACAGTAGAAACATGGTTAGCAGATC 58.891 40.000 0.00 0.00 0.00 2.75
2276 3643 6.070538 ACAGTAGAAACATGGTTAGCAGATCT 60.071 38.462 0.00 0.00 0.00 2.75
2277 3644 6.257411 CAGTAGAAACATGGTTAGCAGATCTG 59.743 42.308 18.84 18.84 0.00 2.90
2279 3646 5.181748 AGAAACATGGTTAGCAGATCTGTC 58.818 41.667 23.38 15.41 0.00 3.51
2280 3647 4.558226 AACATGGTTAGCAGATCTGTCA 57.442 40.909 23.38 13.94 0.00 3.58
2281 3648 4.134379 ACATGGTTAGCAGATCTGTCAG 57.866 45.455 23.38 8.17 0.00 3.51
2282 3649 3.517100 ACATGGTTAGCAGATCTGTCAGT 59.483 43.478 23.38 9.04 0.00 3.41
2284 3651 3.930336 TGGTTAGCAGATCTGTCAGTTG 58.070 45.455 23.38 0.00 0.00 3.16
2285 3652 2.675348 GGTTAGCAGATCTGTCAGTTGC 59.325 50.000 23.38 8.59 35.09 4.17
2405 3944 7.332926 CGAATACTTCTTTATCCTCATCCATGG 59.667 40.741 4.97 4.97 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.096311 TCGATTCTCGAAACTTTCTAGCG 58.904 43.478 0.00 0.00 46.90 4.26
32 33 2.154580 CCAATCAAGCGATCGATTCTCG 59.845 50.000 21.57 7.49 42.10 4.04
39 40 1.718178 CGATCTCCAATCAAGCGATCG 59.282 52.381 11.69 11.69 44.65 3.69
46 47 4.635765 CCAAAGTTAGCGATCTCCAATCAA 59.364 41.667 0.00 0.00 0.00 2.57
47 48 4.081142 TCCAAAGTTAGCGATCTCCAATCA 60.081 41.667 0.00 0.00 0.00 2.57
58 59 3.244976 CTTGCCAAATCCAAAGTTAGCG 58.755 45.455 0.00 0.00 0.00 4.26
65 66 1.698506 ACCGACTTGCCAAATCCAAA 58.301 45.000 0.00 0.00 0.00 3.28
66 67 1.611491 GAACCGACTTGCCAAATCCAA 59.389 47.619 0.00 0.00 0.00 3.53
72 73 1.153127 AACCGAACCGACTTGCCAA 60.153 52.632 0.00 0.00 0.00 4.52
74 75 2.943653 CAACCGAACCGACTTGCC 59.056 61.111 0.00 0.00 0.00 4.52
80 81 0.680618 TTAGAAGGCAACCGAACCGA 59.319 50.000 0.00 0.00 37.17 4.69
94 95 3.261897 CCTGACTGCCTTCTCCTTTAGAA 59.738 47.826 0.00 0.00 42.07 2.10
95 96 2.834549 CCTGACTGCCTTCTCCTTTAGA 59.165 50.000 0.00 0.00 0.00 2.10
111 112 1.338579 CCTCTTGCTCTTGTCCCTGAC 60.339 57.143 0.00 0.00 0.00 3.51
112 113 0.979665 CCTCTTGCTCTTGTCCCTGA 59.020 55.000 0.00 0.00 0.00 3.86
133 136 1.809619 GAACGATGGCTAGCGCACA 60.810 57.895 11.47 2.95 39.81 4.57
134 137 2.526120 GGAACGATGGCTAGCGCAC 61.526 63.158 11.47 1.61 39.81 5.34
152 155 3.694072 TGATTTCTACTTTGGGAATGCCG 59.306 43.478 0.00 0.00 33.83 5.69
162 165 9.696917 CTTTTGCTACCAAATGATTTCTACTTT 57.303 29.630 0.00 0.00 40.40 2.66
197 200 1.523938 GCCTTCCCTATGACGCCAC 60.524 63.158 0.00 0.00 0.00 5.01
213 216 0.320771 ATCAACCAGTCACAGACGCC 60.321 55.000 0.00 0.00 37.67 5.68
219 222 4.908601 AACCATCTATCAACCAGTCACA 57.091 40.909 0.00 0.00 0.00 3.58
223 226 7.682787 AGAAGATAACCATCTATCAACCAGT 57.317 36.000 0.00 0.00 40.81 4.00
224 227 8.970859 AAAGAAGATAACCATCTATCAACCAG 57.029 34.615 0.00 0.00 40.81 4.00
226 229 8.552034 CGAAAAGAAGATAACCATCTATCAACC 58.448 37.037 0.00 0.00 40.81 3.77
227 230 8.552034 CCGAAAAGAAGATAACCATCTATCAAC 58.448 37.037 0.00 0.00 40.81 3.18
231 234 7.138054 ACCCGAAAAGAAGATAACCATCTAT 57.862 36.000 0.00 0.00 40.81 1.98
252 255 0.447801 GACATCATGCACGACAACCC 59.552 55.000 0.00 0.00 0.00 4.11
259 262 3.541071 TCAACAAAGACATCATGCACG 57.459 42.857 0.00 0.00 0.00 5.34
277 280 4.225942 AGGAGCTCCTATGAAAACACATCA 59.774 41.667 34.40 0.00 46.48 3.07
294 297 3.611766 ATACAACTACGCAAAGGAGCT 57.388 42.857 0.00 0.00 32.63 4.09
298 301 5.560966 ATGGAAATACAACTACGCAAAGG 57.439 39.130 0.00 0.00 0.00 3.11
307 310 6.180472 CCTCACAACCTATGGAAATACAACT 58.820 40.000 0.00 0.00 0.00 3.16
312 315 6.770785 GCATAACCTCACAACCTATGGAAATA 59.229 38.462 0.00 0.00 0.00 1.40
313 316 5.594317 GCATAACCTCACAACCTATGGAAAT 59.406 40.000 0.00 0.00 0.00 2.17
338 341 4.796495 GCCCCCAACCCGCTACAG 62.796 72.222 0.00 0.00 0.00 2.74
348 351 1.617947 AAGCAAACAAACGCCCCCAA 61.618 50.000 0.00 0.00 0.00 4.12
362 365 2.192861 CAACCACCCGAGCAAGCAA 61.193 57.895 0.00 0.00 0.00 3.91
363 366 2.594303 CAACCACCCGAGCAAGCA 60.594 61.111 0.00 0.00 0.00 3.91
365 368 1.227823 TCACAACCACCCGAGCAAG 60.228 57.895 0.00 0.00 0.00 4.01
366 369 1.227823 CTCACAACCACCCGAGCAA 60.228 57.895 0.00 0.00 0.00 3.91
372 375 2.094675 CATGAATCCTCACAACCACCC 58.905 52.381 0.00 0.00 33.30 4.61
382 385 5.501156 ACTACTCCCAAAACATGAATCCTC 58.499 41.667 0.00 0.00 0.00 3.71
383 386 5.501156 GACTACTCCCAAAACATGAATCCT 58.499 41.667 0.00 0.00 0.00 3.24
384 387 4.640647 GGACTACTCCCAAAACATGAATCC 59.359 45.833 0.00 0.00 0.00 3.01
393 396 0.323629 CCTGCGGACTACTCCCAAAA 59.676 55.000 0.00 0.00 31.93 2.44
407 410 0.876777 TTACAACACGACCACCTGCG 60.877 55.000 0.00 0.00 0.00 5.18
410 413 0.249573 CCGTTACAACACGACCACCT 60.250 55.000 0.00 0.00 43.15 4.00
465 468 7.536622 GCCTCATCGATTATTTAAGCAAATGAG 59.463 37.037 14.73 14.73 39.12 2.90
468 471 7.275888 TGCCTCATCGATTATTTAAGCAAAT 57.724 32.000 0.00 0.00 38.02 2.32
470 473 6.691754 TTGCCTCATCGATTATTTAAGCAA 57.308 33.333 0.00 2.06 34.41 3.91
527 532 6.916360 ATTTATTGTCAAAAAGGAGAGGCA 57.084 33.333 0.00 0.00 0.00 4.75
640 1551 8.747538 ACGAGCCTGGTCTTATTTATTTATTT 57.252 30.769 0.00 0.00 0.00 1.40
642 1553 6.645415 CGACGAGCCTGGTCTTATTTATTTAT 59.355 38.462 5.31 0.00 32.24 1.40
643 1554 5.981315 CGACGAGCCTGGTCTTATTTATTTA 59.019 40.000 5.31 0.00 32.24 1.40
646 1557 3.243771 CCGACGAGCCTGGTCTTATTTAT 60.244 47.826 5.31 0.00 32.24 1.40
648 1559 1.134788 CCGACGAGCCTGGTCTTATTT 60.135 52.381 5.31 0.00 32.24 1.40
649 1560 0.460311 CCGACGAGCCTGGTCTTATT 59.540 55.000 5.31 0.00 32.24 1.40
650 1561 0.395311 TCCGACGAGCCTGGTCTTAT 60.395 55.000 5.31 0.00 32.24 1.73
651 1562 1.001764 TCCGACGAGCCTGGTCTTA 60.002 57.895 5.31 0.00 32.24 2.10
653 1564 3.063084 GTCCGACGAGCCTGGTCT 61.063 66.667 5.31 0.00 32.24 3.85
654 1565 4.131088 GGTCCGACGAGCCTGGTC 62.131 72.222 0.00 0.00 0.00 4.02
655 1566 4.680537 AGGTCCGACGAGCCTGGT 62.681 66.667 8.94 0.00 37.19 4.00
656 1567 4.135153 CAGGTCCGACGAGCCTGG 62.135 72.222 21.97 9.67 44.36 4.45
658 1569 2.043852 ATCAGGTCCGACGAGCCT 60.044 61.111 0.00 0.00 37.19 4.58
659 1570 2.105128 CATCAGGTCCGACGAGCC 59.895 66.667 0.00 0.00 37.19 4.70
660 1571 1.226717 GTCATCAGGTCCGACGAGC 60.227 63.158 0.00 0.00 36.73 5.03
661 1572 0.741326 ATGTCATCAGGTCCGACGAG 59.259 55.000 0.00 0.00 32.17 4.18
662 1573 0.738975 GATGTCATCAGGTCCGACGA 59.261 55.000 8.00 0.00 32.17 4.20
663 1574 0.741326 AGATGTCATCAGGTCCGACG 59.259 55.000 15.20 0.00 32.17 5.12
664 1575 1.751351 TGAGATGTCATCAGGTCCGAC 59.249 52.381 15.20 0.00 0.00 4.79
665 1576 2.027385 CTGAGATGTCATCAGGTCCGA 58.973 52.381 15.20 0.00 40.44 4.55
666 1577 2.505628 CTGAGATGTCATCAGGTCCG 57.494 55.000 15.20 0.00 40.44 4.79
671 1582 2.685850 TGCACCTGAGATGTCATCAG 57.314 50.000 15.20 6.07 43.15 2.90
672 1583 3.421919 TTTGCACCTGAGATGTCATCA 57.578 42.857 15.20 0.00 30.18 3.07
673 1584 3.427233 GCTTTTGCACCTGAGATGTCATC 60.427 47.826 4.52 4.52 46.58 2.92
674 1585 2.490903 GCTTTTGCACCTGAGATGTCAT 59.509 45.455 0.00 0.00 46.58 3.06
675 1586 1.881973 GCTTTTGCACCTGAGATGTCA 59.118 47.619 0.00 0.00 46.58 3.58
676 1587 2.626088 GCTTTTGCACCTGAGATGTC 57.374 50.000 0.00 0.00 46.58 3.06
699 1610 2.908940 CAATGGGCATCCTCGGGC 60.909 66.667 0.00 0.00 0.00 6.13
700 1611 2.908940 GCAATGGGCATCCTCGGG 60.909 66.667 0.00 0.00 43.97 5.14
709 1620 1.152694 TATGAGCTGGGCAATGGGC 60.153 57.895 0.00 0.00 43.74 5.36
710 1621 1.168407 CGTATGAGCTGGGCAATGGG 61.168 60.000 0.00 0.00 0.00 4.00
711 1622 1.789078 GCGTATGAGCTGGGCAATGG 61.789 60.000 0.00 0.00 0.00 3.16
712 1623 1.650912 GCGTATGAGCTGGGCAATG 59.349 57.895 0.00 0.00 0.00 2.82
713 1624 1.889105 CGCGTATGAGCTGGGCAAT 60.889 57.895 0.00 0.00 34.40 3.56
723 1634 0.038618 ACTTGCACAGACGCGTATGA 60.039 50.000 37.47 15.20 33.35 2.15
725 1636 1.459592 GAAACTTGCACAGACGCGTAT 59.540 47.619 13.97 5.94 33.35 3.06
727 1638 0.810031 AGAAACTTGCACAGACGCGT 60.810 50.000 13.85 13.85 33.35 6.01
728 1639 0.383491 CAGAAACTTGCACAGACGCG 60.383 55.000 3.53 3.53 33.35 6.01
729 1640 0.658536 GCAGAAACTTGCACAGACGC 60.659 55.000 0.00 0.00 43.53 5.19
732 1643 2.104792 AGTAGGCAGAAACTTGCACAGA 59.895 45.455 0.11 0.00 45.86 3.41
734 1645 2.221169 CAGTAGGCAGAAACTTGCACA 58.779 47.619 0.11 0.00 45.86 4.57
735 1646 1.537202 CCAGTAGGCAGAAACTTGCAC 59.463 52.381 0.11 0.00 45.86 4.57
748 1659 3.545124 TTGCGGTGGTGCCAGTAGG 62.545 63.158 0.00 0.00 36.97 3.18
750 1661 0.752009 TTTTTGCGGTGGTGCCAGTA 60.752 50.000 0.00 0.00 36.97 2.74
752 1663 2.811101 TTTTTGCGGTGGTGCCAG 59.189 55.556 0.00 0.00 36.97 4.85
872 1791 3.480133 GATGGTCGGGAGTGGGGG 61.480 72.222 0.00 0.00 0.00 5.40
894 1815 1.029947 ATTTCCGCCGTTGGATGACC 61.030 55.000 0.00 0.00 38.00 4.02
973 1895 2.355115 GAATGTGGGGGCGAGGTT 59.645 61.111 0.00 0.00 0.00 3.50
980 1902 2.037208 GGTGGTGGAATGTGGGGG 59.963 66.667 0.00 0.00 0.00 5.40
988 1910 2.966732 GCGGAGGATGGTGGTGGAA 61.967 63.158 0.00 0.00 0.00 3.53
1008 1930 2.382770 TGTTGGGAGTGGTGGCTGT 61.383 57.895 0.00 0.00 0.00 4.40
1029 1954 1.144936 CTCTCCGGTGGGATTGAGC 59.855 63.158 0.00 0.00 42.83 4.26
1030 1955 0.461961 GTCTCTCCGGTGGGATTGAG 59.538 60.000 9.74 3.75 42.83 3.02
1156 2100 2.268920 GGCTTCGTGATGCCCTGA 59.731 61.111 14.15 0.00 43.54 3.86
1405 2349 2.866085 ATCTCGTTGCTGGCTGGAGC 62.866 60.000 0.00 0.00 39.62 4.70
1440 2384 6.862090 CGAACCATAGACAAATACTACTAGCC 59.138 42.308 0.00 0.00 0.00 3.93
1446 2390 6.379133 AGACCACGAACCATAGACAAATACTA 59.621 38.462 0.00 0.00 0.00 1.82
1459 2403 1.111116 ACCGAAGAGACCACGAACCA 61.111 55.000 0.00 0.00 0.00 3.67
1563 2510 2.241941 TGATCAAGGGCAGAAGGCATTA 59.758 45.455 0.00 0.00 42.74 1.90
1570 2520 1.067295 AGGTGTGATCAAGGGCAGAA 58.933 50.000 0.00 0.00 0.00 3.02
1572 2522 1.310933 GCAGGTGTGATCAAGGGCAG 61.311 60.000 0.00 0.00 0.00 4.85
1574 2524 0.895100 TTGCAGGTGTGATCAAGGGC 60.895 55.000 0.00 0.00 0.00 5.19
1593 2543 2.086610 ACACAAACAGGGCAAAGGAT 57.913 45.000 0.00 0.00 0.00 3.24
1597 2547 3.902881 AATCAACACAAACAGGGCAAA 57.097 38.095 0.00 0.00 0.00 3.68
1604 2554 4.814147 TCTTGCACAAATCAACACAAACA 58.186 34.783 0.00 0.00 0.00 2.83
1608 2558 3.382855 GCATCTTGCACAAATCAACACA 58.617 40.909 0.00 0.00 44.26 3.72
1624 2574 4.056740 CGCACTGATAAGATTGAGCATCT 58.943 43.478 0.00 0.00 45.03 2.90
1637 2587 0.535335 GAACTGGGGACGCACTGATA 59.465 55.000 0.00 0.00 0.00 2.15
1684 2634 0.315886 CAGCCAGCTTGATTTGTGCA 59.684 50.000 0.00 0.00 0.00 4.57
1685 2635 0.316204 ACAGCCAGCTTGATTTGTGC 59.684 50.000 0.00 0.00 0.00 4.57
1687 2637 1.696063 ACACAGCCAGCTTGATTTGT 58.304 45.000 8.25 0.00 0.00 2.83
1700 2650 5.461526 GGAGGTTTCAGAAATAAACACAGC 58.538 41.667 0.00 0.00 38.34 4.40
1702 2652 5.534654 CAGGGAGGTTTCAGAAATAAACACA 59.465 40.000 0.00 0.00 38.34 3.72
1734 2684 4.612939 GCGAAATGGTAGTGTTTGAGGAAC 60.613 45.833 0.00 0.00 38.78 3.62
1742 2692 3.009723 CAGGATGCGAAATGGTAGTGTT 58.990 45.455 0.00 0.00 0.00 3.32
1787 2737 3.763360 CCACATGAATGGGCAGAACTAAA 59.237 43.478 0.00 0.00 35.95 1.85
1788 2738 3.355378 CCACATGAATGGGCAGAACTAA 58.645 45.455 0.00 0.00 35.95 2.24
1809 2759 4.207891 ACACAATATCAGACACAGACCC 57.792 45.455 0.00 0.00 0.00 4.46
1832 2834 6.713450 TCATTCTGACACAATATCATGGATGG 59.287 38.462 0.00 0.00 0.00 3.51
1843 2845 8.017373 CGAACAGTATTTTCATTCTGACACAAT 58.983 33.333 0.00 0.00 33.18 2.71
1846 2848 7.116376 TCTCGAACAGTATTTTCATTCTGACAC 59.884 37.037 0.00 0.00 33.18 3.67
1848 2850 7.582435 TCTCGAACAGTATTTTCATTCTGAC 57.418 36.000 0.00 0.00 33.18 3.51
1849 2851 8.253810 AGATCTCGAACAGTATTTTCATTCTGA 58.746 33.333 0.00 0.00 33.18 3.27
1850 2852 8.417780 AGATCTCGAACAGTATTTTCATTCTG 57.582 34.615 0.00 0.00 34.68 3.02
1851 2853 9.522804 GTAGATCTCGAACAGTATTTTCATTCT 57.477 33.333 0.00 0.00 0.00 2.40
1853 2855 9.088512 GTGTAGATCTCGAACAGTATTTTCATT 57.911 33.333 0.00 0.00 0.00 2.57
1854 2856 8.470805 AGTGTAGATCTCGAACAGTATTTTCAT 58.529 33.333 0.00 0.00 0.00 2.57
1868 2870 3.111838 GACATGTGCAGTGTAGATCTCG 58.888 50.000 1.15 0.00 0.00 4.04
1882 2884 2.420628 ACACGGCATTTTGACATGTG 57.579 45.000 1.15 0.00 0.00 3.21
2004 3013 3.243877 CGAACTGGTAAGATTCAGCATCG 59.756 47.826 0.00 0.00 37.33 3.84
2019 3028 3.418047 AGGGTAATTGGAAACGAACTGG 58.582 45.455 0.00 0.00 0.00 4.00
2030 3045 0.815095 GCCACGGAAAGGGTAATTGG 59.185 55.000 0.00 0.00 0.00 3.16
2099 3115 2.632377 CGATGGCCATTACACAAGAGT 58.368 47.619 21.84 0.00 0.00 3.24
2123 3139 3.689872 AGGCTACCTGGACTCTATTGA 57.310 47.619 0.00 0.00 29.57 2.57
2125 3141 3.452627 CACAAGGCTACCTGGACTCTATT 59.547 47.826 0.00 0.00 32.13 1.73
2133 3149 1.813513 CAAGTCACAAGGCTACCTGG 58.186 55.000 0.00 0.00 32.13 4.45
2143 3159 2.168106 ACAAAATGCAGGCAAGTCACAA 59.832 40.909 0.00 0.00 0.00 3.33
2150 3166 1.538634 GCAGACACAAAATGCAGGCAA 60.539 47.619 0.00 0.00 39.75 4.52
2167 3183 3.895232 ACACAGTAATACCAGAGGCAG 57.105 47.619 0.00 0.00 0.00 4.85
2181 3197 8.859090 TCTGAAAATAAATGGATGAAACACAGT 58.141 29.630 0.00 0.00 0.00 3.55
2232 3599 1.016627 TATGCATCAAGCCGAACTGC 58.983 50.000 0.19 0.00 44.83 4.40
2257 3624 4.937620 TGACAGATCTGCTAACCATGTTTC 59.062 41.667 22.83 8.43 0.00 2.78
2274 3641 2.810274 GAGATTGCAAGCAACTGACAGA 59.190 45.455 18.24 0.00 38.88 3.41
2275 3642 2.551032 TGAGATTGCAAGCAACTGACAG 59.449 45.455 18.24 0.00 38.88 3.51
2276 3643 2.551032 CTGAGATTGCAAGCAACTGACA 59.449 45.455 18.24 7.44 38.88 3.58
2277 3644 2.551459 ACTGAGATTGCAAGCAACTGAC 59.449 45.455 18.24 3.38 38.88 3.51
2279 3646 2.551032 TCACTGAGATTGCAAGCAACTG 59.449 45.455 18.24 15.41 38.88 3.16
2280 3647 2.854963 TCACTGAGATTGCAAGCAACT 58.145 42.857 18.24 9.26 38.88 3.16
2281 3648 3.189910 TCATCACTGAGATTGCAAGCAAC 59.810 43.478 18.24 10.91 38.88 4.17
2282 3649 3.414269 TCATCACTGAGATTGCAAGCAA 58.586 40.909 18.24 10.19 40.47 3.91
2284 3651 5.746307 TTATCATCACTGAGATTGCAAGC 57.254 39.130 6.58 6.58 33.72 4.01
2405 3944 2.045926 CCCCTGTGTGCAGTAGGC 60.046 66.667 5.50 0.00 41.02 3.93


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

AutoCloner maintained by Alex Coulton.