Multiple sequence alignment - TraesCS7D01G219000

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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 TraesCS7D01G219000 chr7D 100.000 4707 0 0 1 4707 179524303 179519597 0.000000e+00 8693.0
1 TraesCS7D01G219000 chr7D 84.683 1371 189 15 2260 3620 179508973 179507614 0.000000e+00 1349.0
2 TraesCS7D01G219000 chr7D 81.795 1549 244 22 2096 3628 179536199 179534673 0.000000e+00 1264.0
3 TraesCS7D01G219000 chr7D 83.575 895 117 22 1166 2045 179510088 179509209 0.000000e+00 811.0
4 TraesCS7D01G219000 chr7D 82.167 886 143 13 1151 2030 179537090 179536214 0.000000e+00 747.0
5 TraesCS7D01G219000 chr7D 81.016 827 146 8 2285 3110 94114619 94113803 0.000000e+00 647.0
6 TraesCS7D01G219000 chr7D 83.111 225 32 2 1190 1414 94116018 94115800 2.870000e-47 200.0
7 TraesCS7D01G219000 chr7B 95.867 4065 130 17 669 4707 145712119 145708067 0.000000e+00 6541.0
8 TraesCS7D01G219000 chr7B 85.508 1318 172 13 2311 3620 145697361 145696055 0.000000e+00 1358.0
9 TraesCS7D01G219000 chr7B 81.931 963 158 12 2180 3140 145739730 145738782 0.000000e+00 800.0
10 TraesCS7D01G219000 chr7B 82.517 898 128 22 1166 2045 145698712 145697826 0.000000e+00 761.0
11 TraesCS7D01G219000 chr7B 81.893 845 142 8 2270 3113 48050342 48049508 0.000000e+00 702.0
12 TraesCS7D01G219000 chr7B 86.506 415 48 4 3219 3632 145738673 145738266 2.580000e-122 449.0
13 TraesCS7D01G219000 chr7B 87.427 342 20 5 1 325 145725770 145725435 5.750000e-99 372.0
14 TraesCS7D01G219000 chr7B 83.967 368 59 0 1646 2013 145740243 145739876 2.080000e-93 353.0
15 TraesCS7D01G219000 chr7B 79.920 249 42 5 1180 1427 48052956 48052715 4.840000e-40 176.0
16 TraesCS7D01G219000 chr7B 100.000 28 0 0 1165 1192 145790025 145789998 9.000000e-03 52.8
17 TraesCS7D01G219000 chr7A 96.121 1521 56 3 2406 3925 183918191 183916673 0.000000e+00 2479.0
18 TraesCS7D01G219000 chr7A 80.400 2500 390 63 1165 3620 183858669 183856226 0.000000e+00 1810.0
19 TraesCS7D01G219000 chr7A 94.459 1155 38 9 1261 2409 183920896 183919762 0.000000e+00 1755.0
20 TraesCS7D01G219000 chr7A 82.414 1450 222 21 2180 3619 183950214 183948788 0.000000e+00 1234.0
21 TraesCS7D01G219000 chr7A 89.241 725 59 10 550 1263 183929329 183928613 0.000000e+00 889.0
22 TraesCS7D01G219000 chr7A 81.271 881 143 18 1167 2043 183951206 183950344 0.000000e+00 693.0
23 TraesCS7D01G219000 chr7A 90.744 497 32 8 4218 4707 183905882 183905393 0.000000e+00 651.0
24 TraesCS7D01G219000 chr7A 89.137 313 14 9 3927 4222 183911361 183911052 5.750000e-99 372.0
25 TraesCS7D01G219000 chr7A 85.621 306 25 4 1 290 183929930 183929628 2.130000e-78 303.0
26 TraesCS7D01G219000 chr6D 81.560 846 146 6 2285 3125 445893889 445894729 0.000000e+00 689.0
27 TraesCS7D01G219000 chr6D 78.571 406 61 18 3219 3605 445894865 445895263 1.310000e-60 244.0
28 TraesCS7D01G219000 chr6D 77.751 409 64 19 1180 1570 445852291 445852690 4.740000e-55 226.0
29 TraesCS7D01G219000 chr6D 77.037 405 69 13 3219 3605 445840191 445840589 1.330000e-50 211.0
30 TraesCS7D01G219000 chr6D 87.805 82 10 0 1920 2001 445955975 445956056 3.880000e-16 97.1
31 TraesCS7D01G219000 chr6A 81.420 845 149 6 2285 3125 592549779 592550619 0.000000e+00 684.0
32 TraesCS7D01G219000 chr6A 80.357 392 63 10 3219 3597 592580016 592580406 7.710000e-73 285.0
33 TraesCS7D01G219000 chr6A 77.531 405 68 17 1179 1570 592548390 592548784 6.130000e-54 222.0
34 TraesCS7D01G219000 chr6B 81.206 846 149 9 2285 3125 672894441 672895281 0.000000e+00 673.0
35 TraesCS7D01G219000 chr6B 77.857 420 78 10 3219 3624 673698624 673699042 3.640000e-61 246.0
36 TraesCS7D01G219000 chr6B 76.675 403 73 14 1180 1570 673024674 673025067 2.220000e-48 204.0
37 TraesCS7D01G219000 chr6B 76.296 405 71 21 1180 1570 673545861 673545468 4.810000e-45 193.0
38 TraesCS7D01G219000 chr6B 81.731 208 34 4 1648 1853 673366254 673366049 2.250000e-38 171.0


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 TraesCS7D01G219000 chr7D 179519597 179524303 4706 True 8693.0 8693 100.000000 1 4707 1 chr7D.!!$R1 4706
1 TraesCS7D01G219000 chr7D 179507614 179510088 2474 True 1080.0 1349 84.129000 1166 3620 2 chr7D.!!$R3 2454
2 TraesCS7D01G219000 chr7D 179534673 179537090 2417 True 1005.5 1264 81.981000 1151 3628 2 chr7D.!!$R4 2477
3 TraesCS7D01G219000 chr7D 94113803 94116018 2215 True 423.5 647 82.063500 1190 3110 2 chr7D.!!$R2 1920
4 TraesCS7D01G219000 chr7B 145708067 145712119 4052 True 6541.0 6541 95.867000 669 4707 1 chr7B.!!$R1 4038
5 TraesCS7D01G219000 chr7B 145696055 145698712 2657 True 1059.5 1358 84.012500 1166 3620 2 chr7B.!!$R5 2454
6 TraesCS7D01G219000 chr7B 145738266 145740243 1977 True 534.0 800 84.134667 1646 3632 3 chr7B.!!$R6 1986
7 TraesCS7D01G219000 chr7B 48049508 48052956 3448 True 439.0 702 80.906500 1180 3113 2 chr7B.!!$R4 1933
8 TraesCS7D01G219000 chr7A 183916673 183920896 4223 True 2117.0 2479 95.290000 1261 3925 2 chr7A.!!$R4 2664
9 TraesCS7D01G219000 chr7A 183856226 183858669 2443 True 1810.0 1810 80.400000 1165 3620 1 chr7A.!!$R1 2455
10 TraesCS7D01G219000 chr7A 183948788 183951206 2418 True 963.5 1234 81.842500 1167 3619 2 chr7A.!!$R6 2452
11 TraesCS7D01G219000 chr7A 183928613 183929930 1317 True 596.0 889 87.431000 1 1263 2 chr7A.!!$R5 1262
12 TraesCS7D01G219000 chr6D 445893889 445895263 1374 False 466.5 689 80.065500 2285 3605 2 chr6D.!!$F4 1320
13 TraesCS7D01G219000 chr6A 592548390 592550619 2229 False 453.0 684 79.475500 1179 3125 2 chr6A.!!$F2 1946
14 TraesCS7D01G219000 chr6B 672894441 672895281 840 False 673.0 673 81.206000 2285 3125 1 chr6B.!!$F1 840

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
806 919 0.109964 TTTGGCGCGTCAGCATAAAC 60.110 50.000 15.27 0.00 45.49 2.01 F
1075 1195 1.382146 GTCCCCACGGTGGATCCTA 60.382 63.158 28.36 5.83 40.96 2.94 F
2424 6449 1.448922 GACCCGATCCTCCTGACGAG 61.449 65.000 0.00 0.00 38.46 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 6449 0.463833 CTTGTACCGCCCAGGATTCC 60.464 60.0 0.0 0.0 45.00 3.01 R
2770 6801 0.601841 CGGCTTGGTAAGTGACGGTT 60.602 55.0 0.0 0.0 0.00 4.44 R
4290 8413 0.460987 GATTCAGGTCTGCACCCGAG 60.461 60.0 0.0 0.0 45.12 4.63 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
45 56 2.030412 TCATGCCTCACGCGTTGT 59.970 55.556 10.22 0.00 42.08 3.32
50 61 1.092921 TGCCTCACGCGTTGTCTTTT 61.093 50.000 10.22 0.00 42.08 2.27
69 80 1.961793 TTTATTTCATCCCGCCGGAG 58.038 50.000 5.05 0.00 43.12 4.63
98 115 3.375782 CAGTTTCCCTGCAAAGAAAGG 57.624 47.619 10.28 4.04 32.86 3.11
105 122 1.610522 CCTGCAAAGAAAGGGTCACAG 59.389 52.381 0.00 0.00 0.00 3.66
111 128 5.001232 GCAAAGAAAGGGTCACAGTGTATA 58.999 41.667 0.00 0.00 0.00 1.47
116 133 7.171630 AGAAAGGGTCACAGTGTATACTTAG 57.828 40.000 4.17 0.00 34.07 2.18
121 138 7.384477 AGGGTCACAGTGTATACTTAGTTTTC 58.616 38.462 4.17 0.00 34.07 2.29
150 167 6.459066 TGTTTTGATAGGTGAGAACTGAGAG 58.541 40.000 0.00 0.00 0.00 3.20
185 202 5.708697 TGATCTGAAGGCATAATTAGGCATG 59.291 40.000 22.31 5.47 34.14 4.06
207 224 4.462834 TGAGACTATAGAACATATGCCCGG 59.537 45.833 6.78 0.00 0.00 5.73
212 229 1.502690 AGAACATATGCCCGGTGGTA 58.497 50.000 1.58 0.00 0.00 3.25
215 232 0.468226 ACATATGCCCGGTGGTACTG 59.532 55.000 1.58 0.00 0.00 2.74
228 245 4.603985 GGTGGTACTGTACAAAAACTTGC 58.396 43.478 18.79 0.03 0.00 4.01
231 248 4.944930 TGGTACTGTACAAAAACTTGCACT 59.055 37.500 18.79 0.00 0.00 4.40
232 249 5.065474 TGGTACTGTACAAAAACTTGCACTC 59.935 40.000 18.79 0.00 0.00 3.51
233 250 4.632538 ACTGTACAAAAACTTGCACTCC 57.367 40.909 0.00 0.00 0.00 3.85
234 251 4.270008 ACTGTACAAAAACTTGCACTCCT 58.730 39.130 0.00 0.00 0.00 3.69
242 259 6.183361 ACAAAAACTTGCACTCCTACCTACTA 60.183 38.462 0.00 0.00 0.00 1.82
251 268 5.070580 GCACTCCTACCTACTATCACCAAAT 59.929 44.000 0.00 0.00 0.00 2.32
257 274 8.480501 TCCTACCTACTATCACCAAATTTGTAC 58.519 37.037 16.73 0.00 0.00 2.90
281 298 4.782019 TTTTGCGCATTTCTACAGGAAT 57.218 36.364 12.75 0.00 33.53 3.01
321 431 5.357257 ACGTCATGTATGTCCCATAAGAAC 58.643 41.667 0.00 0.00 0.00 3.01
328 438 2.639065 TGTCCCATAAGAACGGATTGC 58.361 47.619 0.00 0.00 0.00 3.56
343 453 1.734465 GATTGCTTCTTCCGTGGACAG 59.266 52.381 0.00 0.00 0.00 3.51
353 463 0.599558 CCGTGGACAGAGACCGTTTA 59.400 55.000 0.00 0.00 0.00 2.01
358 468 2.422479 TGGACAGAGACCGTTTATCTCG 59.578 50.000 0.00 0.00 46.09 4.04
360 470 3.242804 GGACAGAGACCGTTTATCTCGAG 60.243 52.174 5.93 5.93 46.09 4.04
361 471 2.683867 ACAGAGACCGTTTATCTCGAGG 59.316 50.000 13.56 0.00 46.09 4.63
362 472 1.677052 AGAGACCGTTTATCTCGAGGC 59.323 52.381 13.56 0.00 46.09 4.70
363 473 1.404391 GAGACCGTTTATCTCGAGGCA 59.596 52.381 13.56 0.00 33.68 4.75
364 474 1.822990 AGACCGTTTATCTCGAGGCAA 59.177 47.619 13.56 4.00 0.00 4.52
365 475 1.925185 GACCGTTTATCTCGAGGCAAC 59.075 52.381 13.56 11.67 0.00 4.17
366 476 6.455918 GAGACCGTTTATCTCGAGGCAACT 62.456 50.000 13.56 0.25 41.11 3.16
367 477 7.842609 GAGACCGTTTATCTCGAGGCAACTT 62.843 48.000 13.56 3.36 39.43 2.66
381 491 4.853924 GGCAACTTCCTCAATCTTCAAA 57.146 40.909 0.00 0.00 0.00 2.69
382 492 5.397142 GGCAACTTCCTCAATCTTCAAAT 57.603 39.130 0.00 0.00 0.00 2.32
383 493 5.787380 GGCAACTTCCTCAATCTTCAAATT 58.213 37.500 0.00 0.00 0.00 1.82
384 494 5.866092 GGCAACTTCCTCAATCTTCAAATTC 59.134 40.000 0.00 0.00 0.00 2.17
385 495 5.866092 GCAACTTCCTCAATCTTCAAATTCC 59.134 40.000 0.00 0.00 0.00 3.01
387 497 5.316987 ACTTCCTCAATCTTCAAATTCCGT 58.683 37.500 0.00 0.00 0.00 4.69
389 499 6.940298 ACTTCCTCAATCTTCAAATTCCGTTA 59.060 34.615 0.00 0.00 0.00 3.18
391 501 7.553881 TCCTCAATCTTCAAATTCCGTTATC 57.446 36.000 0.00 0.00 0.00 1.75
392 502 6.542370 TCCTCAATCTTCAAATTCCGTTATCC 59.458 38.462 0.00 0.00 0.00 2.59
393 503 6.318648 CCTCAATCTTCAAATTCCGTTATCCA 59.681 38.462 0.00 0.00 0.00 3.41
398 508 6.234920 TCTTCAAATTCCGTTATCCAAGACA 58.765 36.000 0.00 0.00 0.00 3.41
400 510 6.677781 TCAAATTCCGTTATCCAAGACATC 57.322 37.500 0.00 0.00 0.00 3.06
413 523 1.698165 AGACATCGTGTAAGTGTGCG 58.302 50.000 0.00 0.00 0.00 5.34
426 536 1.010238 TGTGCGTGTCAATGTTGCG 60.010 52.632 0.00 0.00 0.00 4.85
431 541 0.862490 CGTGTCAATGTTGCGGTGTA 59.138 50.000 0.00 0.00 0.00 2.90
434 544 3.488489 GTGTCAATGTTGCGGTGTATTC 58.512 45.455 0.00 0.00 0.00 1.75
435 545 3.188460 GTGTCAATGTTGCGGTGTATTCT 59.812 43.478 0.00 0.00 0.00 2.40
441 554 7.060633 GTCAATGTTGCGGTGTATTCTAAAAAG 59.939 37.037 0.00 0.00 0.00 2.27
465 578 7.929941 GAAGGATTCAGGAGTAAATTCAAGT 57.070 36.000 0.00 0.00 46.62 3.16
467 580 9.103861 GAAGGATTCAGGAGTAAATTCAAGTAG 57.896 37.037 0.00 0.00 46.62 2.57
468 581 8.152023 AGGATTCAGGAGTAAATTCAAGTAGT 57.848 34.615 0.00 0.00 0.00 2.73
469 582 9.268282 AGGATTCAGGAGTAAATTCAAGTAGTA 57.732 33.333 0.00 0.00 0.00 1.82
473 586 9.653287 TTCAGGAGTAAATTCAAGTAGTATGTG 57.347 33.333 0.00 0.00 0.00 3.21
474 587 8.258007 TCAGGAGTAAATTCAAGTAGTATGTGG 58.742 37.037 0.00 0.00 0.00 4.17
475 588 8.258007 CAGGAGTAAATTCAAGTAGTATGTGGA 58.742 37.037 0.00 0.00 0.00 4.02
476 589 8.258708 AGGAGTAAATTCAAGTAGTATGTGGAC 58.741 37.037 0.00 0.00 0.00 4.02
477 590 7.494952 GGAGTAAATTCAAGTAGTATGTGGACC 59.505 40.741 0.00 0.00 0.00 4.46
478 591 7.039882 AGTAAATTCAAGTAGTATGTGGACCG 58.960 38.462 0.00 0.00 0.00 4.79
479 592 5.670792 AATTCAAGTAGTATGTGGACCGA 57.329 39.130 0.00 0.00 0.00 4.69
480 593 5.670792 ATTCAAGTAGTATGTGGACCGAA 57.329 39.130 0.00 0.00 0.00 4.30
481 594 5.471556 TTCAAGTAGTATGTGGACCGAAA 57.528 39.130 0.00 0.00 0.00 3.46
482 595 4.813027 TCAAGTAGTATGTGGACCGAAAC 58.187 43.478 0.00 0.00 0.00 2.78
483 596 4.281435 TCAAGTAGTATGTGGACCGAAACA 59.719 41.667 0.00 0.00 0.00 2.83
484 597 4.877378 AGTAGTATGTGGACCGAAACAA 57.123 40.909 0.00 0.00 0.00 2.83
485 598 4.563061 AGTAGTATGTGGACCGAAACAAC 58.437 43.478 0.00 0.00 0.00 3.32
486 599 2.774687 AGTATGTGGACCGAAACAACC 58.225 47.619 0.00 0.00 0.00 3.77
487 600 1.461897 GTATGTGGACCGAAACAACCG 59.538 52.381 0.00 0.00 0.00 4.44
488 601 0.179040 ATGTGGACCGAAACAACCGT 60.179 50.000 0.00 0.00 0.00 4.83
489 602 0.810823 TGTGGACCGAAACAACCGTC 60.811 55.000 0.00 0.00 0.00 4.79
490 603 1.592131 TGGACCGAAACAACCGTCG 60.592 57.895 0.00 0.00 37.01 5.12
513 626 1.235724 GTGACTTGTGCCACCCTTAC 58.764 55.000 0.00 0.00 0.00 2.34
518 631 4.029809 GTGCCACCCTTACCGGCT 62.030 66.667 0.00 0.00 46.39 5.52
520 633 2.035155 GCCACCCTTACCGGCTTT 59.965 61.111 0.00 0.00 42.78 3.51
521 634 2.340328 GCCACCCTTACCGGCTTTG 61.340 63.158 0.00 0.00 42.78 2.77
523 636 2.035155 ACCCTTACCGGCTTTGCC 59.965 61.111 0.00 0.00 46.75 4.52
532 645 2.354343 GGCTTTGCCTCTGCCTCT 59.646 61.111 0.73 0.00 46.69 3.69
533 646 1.748500 GGCTTTGCCTCTGCCTCTC 60.749 63.158 0.73 0.00 46.69 3.20
534 647 1.002868 GCTTTGCCTCTGCCTCTCA 60.003 57.895 0.00 0.00 36.33 3.27
535 648 0.607489 GCTTTGCCTCTGCCTCTCAA 60.607 55.000 0.00 0.00 36.33 3.02
536 649 1.451067 CTTTGCCTCTGCCTCTCAAG 58.549 55.000 0.00 0.00 36.33 3.02
537 650 0.607489 TTTGCCTCTGCCTCTCAAGC 60.607 55.000 0.00 0.00 36.33 4.01
538 651 2.511145 GCCTCTGCCTCTCAAGCG 60.511 66.667 0.00 0.00 0.00 4.68
539 652 2.977178 CCTCTGCCTCTCAAGCGT 59.023 61.111 0.00 0.00 0.00 5.07
540 653 1.294780 CCTCTGCCTCTCAAGCGTT 59.705 57.895 0.00 0.00 0.00 4.84
541 654 1.018226 CCTCTGCCTCTCAAGCGTTG 61.018 60.000 0.00 0.00 0.00 4.10
542 655 0.320247 CTCTGCCTCTCAAGCGTTGT 60.320 55.000 0.00 0.00 0.00 3.32
543 656 0.319900 TCTGCCTCTCAAGCGTTGTC 60.320 55.000 0.00 0.00 0.00 3.18
544 657 1.621301 CTGCCTCTCAAGCGTTGTCG 61.621 60.000 0.00 0.00 40.37 4.35
545 658 1.664965 GCCTCTCAAGCGTTGTCGT 60.665 57.895 0.00 0.00 39.49 4.34
546 659 1.618640 GCCTCTCAAGCGTTGTCGTC 61.619 60.000 0.00 0.00 39.49 4.20
547 660 1.009389 CCTCTCAAGCGTTGTCGTCC 61.009 60.000 0.00 0.00 39.49 4.79
548 661 0.318699 CTCTCAAGCGTTGTCGTCCA 60.319 55.000 0.00 0.00 39.49 4.02
554 667 1.300697 GCGTTGTCGTCCACCTCTT 60.301 57.895 0.00 0.00 39.49 2.85
566 679 4.035792 CGTCCACCTCTTCTACATCACTAG 59.964 50.000 0.00 0.00 0.00 2.57
575 688 7.094162 CCTCTTCTACATCACTAGAGAACAACA 60.094 40.741 0.00 0.00 35.48 3.33
577 690 8.082852 TCTTCTACATCACTAGAGAACAACAAC 58.917 37.037 0.00 0.00 0.00 3.32
578 691 7.526142 TCTACATCACTAGAGAACAACAACT 57.474 36.000 0.00 0.00 0.00 3.16
579 692 8.631480 TCTACATCACTAGAGAACAACAACTA 57.369 34.615 0.00 0.00 0.00 2.24
605 718 8.112099 ACTATAACTAGAAAAATGTACGTGCG 57.888 34.615 0.00 0.00 0.00 5.34
606 719 3.717350 ACTAGAAAAATGTACGTGCGC 57.283 42.857 0.00 0.00 0.00 6.09
618 731 3.609373 TGTACGTGCGCAGAATAAAGTAC 59.391 43.478 12.22 16.02 35.23 2.73
619 732 2.955614 ACGTGCGCAGAATAAAGTACT 58.044 42.857 12.22 0.00 0.00 2.73
620 733 4.100707 ACGTGCGCAGAATAAAGTACTA 57.899 40.909 12.22 0.00 0.00 1.82
623 736 4.027621 CGTGCGCAGAATAAAGTACTAGTG 60.028 45.833 12.22 0.00 0.00 2.74
628 741 5.051153 GCAGAATAAAGTACTAGTGCTCCC 58.949 45.833 14.27 2.60 0.00 4.30
630 743 3.729862 ATAAAGTACTAGTGCTCCCGC 57.270 47.619 14.27 0.00 0.00 6.13
680 793 4.796231 CTCGTTCCGCCCACTCCG 62.796 72.222 0.00 0.00 0.00 4.63
724 837 2.162681 CCCTTCCGCTTGATGAACTTT 58.837 47.619 0.00 0.00 0.00 2.66
738 851 2.749076 TGAACTTTGATGGCATTCTCCG 59.251 45.455 0.00 0.00 0.00 4.63
806 919 0.109964 TTTGGCGCGTCAGCATAAAC 60.110 50.000 15.27 0.00 45.49 2.01
828 941 1.648467 GAAGGTCAATCTGCCGGCAC 61.648 60.000 29.03 15.18 0.00 5.01
868 981 7.009440 GGCATTTTCTCTTTTCAAATTTACGC 58.991 34.615 0.00 0.00 0.00 4.42
954 1071 2.765699 AGATCTTCAGCAGGGAAGTCTC 59.234 50.000 11.11 9.66 43.72 3.36
1075 1195 1.382146 GTCCCCACGGTGGATCCTA 60.382 63.158 28.36 5.83 40.96 2.94
1283 1406 2.290847 AGGACACTGATGACGCCAT 58.709 52.632 0.00 0.00 35.29 4.40
2149 3116 2.548480 GTGTCAGGAAGGTTGCAAGTAC 59.452 50.000 0.00 0.00 0.00 2.73
2380 4831 2.664081 GGGTGGAGTCTGGCAGGAG 61.664 68.421 15.73 0.00 0.00 3.69
2424 6449 1.448922 GACCCGATCCTCCTGACGAG 61.449 65.000 0.00 0.00 38.46 4.18
3196 7282 2.683867 AGAGAACGGTGAGGACGATAAG 59.316 50.000 0.00 0.00 34.93 1.73
3447 7552 1.694696 ACTGGAGTGGAAGGACAAGAC 59.305 52.381 0.00 0.00 0.00 3.01
3457 7562 2.545537 AGGACAAGACGAAAAGGTCC 57.454 50.000 0.00 0.00 46.54 4.46
3509 7614 0.461693 GCTGGATTTGCTCGCTCTCT 60.462 55.000 0.00 0.00 0.00 3.10
3633 7738 1.474077 GGCATTCCTGTGTTCACATCC 59.526 52.381 6.09 0.00 0.00 3.51
3651 7756 2.250924 TCCTGATGACAGTTCTCAGCA 58.749 47.619 7.50 0.00 42.05 4.41
3657 7762 1.816863 GACAGTTCTCAGCACCCGGA 61.817 60.000 0.73 0.00 0.00 5.14
3721 7826 2.989840 GGCATAGTTAGCTGCAGTATCG 59.010 50.000 16.64 1.88 40.18 2.92
3824 7930 6.323739 TGCCAAAATTCAAGGTAGTTTCTCTT 59.676 34.615 0.00 0.00 0.00 2.85
3825 7931 7.147742 TGCCAAAATTCAAGGTAGTTTCTCTTT 60.148 33.333 0.00 0.00 0.00 2.52
3947 8054 7.272978 TCTTTTTGGGAGTGTCTATATAGCAC 58.727 38.462 20.57 20.57 33.52 4.40
3952 8059 5.536538 TGGGAGTGTCTATATAGCACTCTTG 59.463 44.000 35.09 9.73 45.70 3.02
3953 8060 5.770663 GGGAGTGTCTATATAGCACTCTTGA 59.229 44.000 35.09 11.36 45.70 3.02
4040 8147 4.625800 GCTCGGGCTCAACAGAAT 57.374 55.556 0.00 0.00 35.22 2.40
4085 8192 5.748152 TCTTTTTGCAAGAAAATTCTGGTCG 59.252 36.000 3.79 0.00 37.65 4.79
4094 8201 4.211374 AGAAAATTCTGGTCGTTGTCGAAG 59.789 41.667 0.00 0.00 40.99 3.79
4095 8202 7.255287 AGAAAATTCTGGTCGTTGTCGAAGC 62.255 44.000 0.00 0.00 40.99 3.86
4100 8207 4.238385 TCGTTGTCGAAGCGGAAG 57.762 55.556 0.00 0.00 43.34 3.46
4102 8209 0.937699 TCGTTGTCGAAGCGGAAGTG 60.938 55.000 0.00 0.00 43.34 3.16
4104 8211 1.214367 GTTGTCGAAGCGGAAGTGAA 58.786 50.000 0.00 0.00 0.00 3.18
4145 8268 4.965532 ACCTGTTCTTAGATATCTGGTGCT 59.034 41.667 15.79 0.00 0.00 4.40
4202 8325 5.063060 CCGGTACATCTGCAGTTTACTTTAC 59.937 44.000 14.67 6.70 0.00 2.01
4249 8372 7.182817 TCACTAATGCTAGTATGTTGGAGTT 57.817 36.000 0.00 0.00 36.14 3.01
4285 8408 6.461110 CAACTCCTTTGCCTCATGAATATT 57.539 37.500 0.00 0.00 0.00 1.28
4287 8410 5.136105 ACTCCTTTGCCTCATGAATATTCC 58.864 41.667 12.90 0.00 0.00 3.01
4288 8411 4.136796 TCCTTTGCCTCATGAATATTCCG 58.863 43.478 12.90 4.49 0.00 4.30
4289 8412 4.136796 CCTTTGCCTCATGAATATTCCGA 58.863 43.478 12.90 8.46 0.00 4.55
4290 8413 4.023707 CCTTTGCCTCATGAATATTCCGAC 60.024 45.833 12.90 0.56 0.00 4.79
4291 8414 4.422073 TTGCCTCATGAATATTCCGACT 57.578 40.909 12.90 0.00 0.00 4.18
4292 8415 3.995199 TGCCTCATGAATATTCCGACTC 58.005 45.455 12.90 3.37 0.00 3.36
4315 8438 0.325933 TGCAGACCTGAATCCAGTGG 59.674 55.000 1.40 1.40 38.74 4.00
4386 8509 1.982958 AGGATTGGAGTAAACACCGGT 59.017 47.619 0.00 0.00 0.00 5.28
4388 8511 2.353323 GATTGGAGTAAACACCGGTCC 58.647 52.381 2.59 0.56 0.00 4.46
4412 8535 3.487563 AAAAATTGGCGAGACGGATTC 57.512 42.857 0.00 0.00 0.00 2.52
4476 8600 9.086336 CCACTAAAAATATACCACATGCAAAAG 57.914 33.333 0.00 0.00 0.00 2.27
4496 8620 6.730960 AAAGCAAACAATATGGCTCAATTG 57.269 33.333 0.00 0.00 38.71 2.32
4575 8699 8.498054 GCTACATGCTACATGGTATGAATTAT 57.502 34.615 11.91 0.00 38.95 1.28
4576 8700 8.950210 GCTACATGCTACATGGTATGAATTATT 58.050 33.333 11.91 0.00 38.95 1.40
4626 8751 6.127897 CCTTTTCTGTCAAGAGAAAACACACT 60.128 38.462 10.12 0.00 43.72 3.55
4627 8752 6.817765 TTTCTGTCAAGAGAAAACACACTT 57.182 33.333 0.25 0.00 38.69 3.16
4629 8754 5.487433 TCTGTCAAGAGAAAACACACTTCA 58.513 37.500 0.00 0.00 0.00 3.02
4630 8755 5.351465 TCTGTCAAGAGAAAACACACTTCAC 59.649 40.000 0.00 0.00 0.00 3.18
4631 8756 5.245531 TGTCAAGAGAAAACACACTTCACT 58.754 37.500 0.00 0.00 0.00 3.41
4632 8757 5.705441 TGTCAAGAGAAAACACACTTCACTT 59.295 36.000 0.00 0.00 35.09 3.16
4642 8767 6.604735 AACACACTTCACTTGAGACATAAC 57.395 37.500 0.00 0.00 0.00 1.89
4671 8796 9.740710 ATTAGTAATGCTTTACCTCAAAGAAGT 57.259 29.630 16.52 0.40 45.62 3.01
4673 8798 8.779354 AGTAATGCTTTACCTCAAAGAAGTAG 57.221 34.615 16.52 0.00 45.62 2.57
4678 8803 6.269307 TGCTTTACCTCAAAGAAGTAGTAGGT 59.731 38.462 0.00 0.00 45.62 3.08
4686 8811 7.256012 CCTCAAAGAAGTAGTAGGTCAGAAGTT 60.256 40.741 0.00 0.00 0.00 2.66
4698 8823 1.957177 TCAGAAGTTCTGCTCGAGTGT 59.043 47.619 25.31 0.00 43.95 3.55
4699 8824 2.057316 CAGAAGTTCTGCTCGAGTGTG 58.943 52.381 19.55 4.77 37.72 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 61 1.210967 ACTCCGGCGGGATGAAATAAA 59.789 47.619 27.98 0.52 42.83 1.40
67 78 1.569479 GGGAAACTGCGCTGTGACTC 61.569 60.000 21.17 16.21 0.00 3.36
69 80 1.598130 AGGGAAACTGCGCTGTGAC 60.598 57.895 21.17 16.29 0.00 3.67
89 106 6.231211 AGTATACACTGTGACCCTTTCTTTG 58.769 40.000 15.86 0.00 32.25 2.77
97 114 6.309737 CGAAAACTAAGTATACACTGTGACCC 59.690 42.308 15.86 0.00 34.36 4.46
98 115 6.309737 CCGAAAACTAAGTATACACTGTGACC 59.690 42.308 15.86 0.00 34.36 4.02
105 122 9.720667 AAAACAAACCGAAAACTAAGTATACAC 57.279 29.630 5.50 0.00 0.00 2.90
111 128 8.132995 CCTATCAAAACAAACCGAAAACTAAGT 58.867 33.333 0.00 0.00 0.00 2.24
116 133 6.267070 TCACCTATCAAAACAAACCGAAAAC 58.733 36.000 0.00 0.00 0.00 2.43
121 138 5.238650 AGTTCTCACCTATCAAAACAAACCG 59.761 40.000 0.00 0.00 0.00 4.44
150 167 3.790123 GCCTTCAGATCAAACGCTATTGC 60.790 47.826 0.00 0.00 0.00 3.56
158 175 6.039717 TGCCTAATTATGCCTTCAGATCAAAC 59.960 38.462 9.84 0.00 0.00 2.93
185 202 4.463186 ACCGGGCATATGTTCTATAGTCTC 59.537 45.833 6.32 0.00 0.00 3.36
199 216 1.113788 GTACAGTACCACCGGGCATA 58.886 55.000 6.32 0.00 37.90 3.14
202 219 0.035176 TTTGTACAGTACCACCGGGC 59.965 55.000 6.32 0.00 37.90 6.13
207 224 5.032220 GTGCAAGTTTTTGTACAGTACCAC 58.968 41.667 8.30 2.32 45.67 4.16
215 232 4.820173 AGGTAGGAGTGCAAGTTTTTGTAC 59.180 41.667 0.00 1.04 46.42 2.90
228 245 6.732896 ATTTGGTGATAGTAGGTAGGAGTG 57.267 41.667 0.00 0.00 0.00 3.51
231 248 7.504926 ACAAATTTGGTGATAGTAGGTAGGA 57.495 36.000 21.74 0.00 0.00 2.94
232 249 8.483758 AGTACAAATTTGGTGATAGTAGGTAGG 58.516 37.037 21.74 0.00 0.00 3.18
233 250 9.886132 AAGTACAAATTTGGTGATAGTAGGTAG 57.114 33.333 21.74 0.00 0.00 3.18
265 282 6.791887 ATGTGATATTCCTGTAGAAATGCG 57.208 37.500 0.00 0.00 38.21 4.73
292 402 5.607939 TGGGACATACATGACGTAGAAAT 57.392 39.130 0.00 0.00 32.28 2.17
328 438 1.067495 GGTCTCTGTCCACGGAAGAAG 60.067 57.143 0.00 0.00 0.00 2.85
336 446 3.731264 CGAGATAAACGGTCTCTGTCCAC 60.731 52.174 2.16 0.00 39.92 4.02
343 453 1.404391 TGCCTCGAGATAAACGGTCTC 59.596 52.381 15.71 0.00 38.95 3.36
360 470 4.853924 TTTGAAGATTGAGGAAGTTGCC 57.146 40.909 0.00 0.00 0.00 4.52
361 471 5.866092 GGAATTTGAAGATTGAGGAAGTTGC 59.134 40.000 0.00 0.00 0.00 4.17
362 472 6.088824 CGGAATTTGAAGATTGAGGAAGTTG 58.911 40.000 0.00 0.00 0.00 3.16
363 473 5.770162 ACGGAATTTGAAGATTGAGGAAGTT 59.230 36.000 0.00 0.00 0.00 2.66
364 474 5.316987 ACGGAATTTGAAGATTGAGGAAGT 58.683 37.500 0.00 0.00 0.00 3.01
365 475 5.886960 ACGGAATTTGAAGATTGAGGAAG 57.113 39.130 0.00 0.00 0.00 3.46
366 476 7.067008 GGATAACGGAATTTGAAGATTGAGGAA 59.933 37.037 0.00 0.00 0.00 3.36
367 477 6.542370 GGATAACGGAATTTGAAGATTGAGGA 59.458 38.462 0.00 0.00 0.00 3.71
369 479 7.320443 TGGATAACGGAATTTGAAGATTGAG 57.680 36.000 0.00 0.00 0.00 3.02
371 481 7.698130 GTCTTGGATAACGGAATTTGAAGATTG 59.302 37.037 0.00 0.00 0.00 2.67
372 482 7.393234 TGTCTTGGATAACGGAATTTGAAGATT 59.607 33.333 0.00 0.00 0.00 2.40
373 483 6.884295 TGTCTTGGATAACGGAATTTGAAGAT 59.116 34.615 0.00 0.00 0.00 2.40
375 485 6.494893 TGTCTTGGATAACGGAATTTGAAG 57.505 37.500 0.00 0.00 0.00 3.02
377 487 5.293324 CGATGTCTTGGATAACGGAATTTGA 59.707 40.000 0.00 0.00 0.00 2.69
378 488 5.064707 ACGATGTCTTGGATAACGGAATTTG 59.935 40.000 0.00 0.00 0.00 2.32
380 490 4.570772 CACGATGTCTTGGATAACGGAATT 59.429 41.667 0.00 0.00 0.00 2.17
381 491 4.119862 CACGATGTCTTGGATAACGGAAT 58.880 43.478 0.00 0.00 0.00 3.01
382 492 3.056393 ACACGATGTCTTGGATAACGGAA 60.056 43.478 0.00 0.00 0.00 4.30
383 493 2.494471 ACACGATGTCTTGGATAACGGA 59.506 45.455 0.00 0.00 0.00 4.69
384 494 2.888594 ACACGATGTCTTGGATAACGG 58.111 47.619 0.00 0.00 0.00 4.44
385 495 5.004440 CACTTACACGATGTCTTGGATAACG 59.996 44.000 0.00 0.00 0.00 3.18
387 497 5.867174 CACACTTACACGATGTCTTGGATAA 59.133 40.000 0.00 0.00 0.00 1.75
389 499 4.245660 CACACTTACACGATGTCTTGGAT 58.754 43.478 0.00 0.00 0.00 3.41
391 501 2.157668 GCACACTTACACGATGTCTTGG 59.842 50.000 0.00 0.00 0.00 3.61
392 502 2.159973 CGCACACTTACACGATGTCTTG 60.160 50.000 0.00 0.00 0.00 3.02
393 503 2.058798 CGCACACTTACACGATGTCTT 58.941 47.619 0.00 0.00 0.00 3.01
398 508 1.269361 TGACACGCACACTTACACGAT 60.269 47.619 0.00 0.00 0.00 3.73
400 510 0.924777 TTGACACGCACACTTACACG 59.075 50.000 0.00 0.00 0.00 4.49
413 523 3.188460 AGAATACACCGCAACATTGACAC 59.812 43.478 0.00 0.00 0.00 3.67
426 536 8.678199 CCTGAATCCTTCTTTTTAGAATACACC 58.322 37.037 0.00 0.00 0.00 4.16
441 554 7.929941 ACTTGAATTTACTCCTGAATCCTTC 57.070 36.000 0.00 0.00 0.00 3.46
449 562 8.258007 TCCACATACTACTTGAATTTACTCCTG 58.742 37.037 0.00 0.00 0.00 3.86
455 568 7.172868 TCGGTCCACATACTACTTGAATTTA 57.827 36.000 0.00 0.00 0.00 1.40
456 569 6.045072 TCGGTCCACATACTACTTGAATTT 57.955 37.500 0.00 0.00 0.00 1.82
461 574 4.562082 TGTTTCGGTCCACATACTACTTG 58.438 43.478 0.00 0.00 0.00 3.16
462 575 4.877378 TGTTTCGGTCCACATACTACTT 57.123 40.909 0.00 0.00 0.00 2.24
463 576 4.562143 GGTTGTTTCGGTCCACATACTACT 60.562 45.833 0.00 0.00 0.00 2.57
464 577 3.681417 GGTTGTTTCGGTCCACATACTAC 59.319 47.826 0.00 0.00 0.00 2.73
465 578 3.614630 CGGTTGTTTCGGTCCACATACTA 60.615 47.826 0.00 0.00 0.00 1.82
466 579 2.774687 GGTTGTTTCGGTCCACATACT 58.225 47.619 0.00 0.00 0.00 2.12
467 580 1.461897 CGGTTGTTTCGGTCCACATAC 59.538 52.381 0.00 0.00 0.00 2.39
468 581 1.070445 ACGGTTGTTTCGGTCCACATA 59.930 47.619 0.00 0.00 0.00 2.29
469 582 0.179040 ACGGTTGTTTCGGTCCACAT 60.179 50.000 0.00 0.00 0.00 3.21
470 583 0.810823 GACGGTTGTTTCGGTCCACA 60.811 55.000 0.00 0.00 33.54 4.17
471 584 1.824272 CGACGGTTGTTTCGGTCCAC 61.824 60.000 0.00 0.00 35.30 4.02
472 585 1.592131 CGACGGTTGTTTCGGTCCA 60.592 57.895 0.00 0.00 35.30 4.02
473 586 3.237290 CGACGGTTGTTTCGGTCC 58.763 61.111 0.00 0.00 35.30 4.46
484 597 0.808453 CACAAGTCACAACCGACGGT 60.808 55.000 15.37 15.37 40.98 4.83
485 598 1.931551 CACAAGTCACAACCGACGG 59.068 57.895 13.61 13.61 40.98 4.79
486 599 1.275657 GCACAAGTCACAACCGACG 59.724 57.895 0.00 0.00 40.98 5.12
487 600 1.092921 TGGCACAAGTCACAACCGAC 61.093 55.000 0.00 0.00 31.92 4.79
488 601 1.222113 TGGCACAAGTCACAACCGA 59.778 52.632 0.00 0.00 31.92 4.69
489 602 3.820590 TGGCACAAGTCACAACCG 58.179 55.556 0.00 0.00 31.92 4.44
495 608 0.109723 GGTAAGGGTGGCACAAGTCA 59.890 55.000 20.82 0.00 44.16 3.41
496 609 0.953960 CGGTAAGGGTGGCACAAGTC 60.954 60.000 20.82 5.72 44.16 3.01
497 610 1.072505 CGGTAAGGGTGGCACAAGT 59.927 57.895 20.82 5.69 44.16 3.16
498 611 1.674322 CCGGTAAGGGTGGCACAAG 60.674 63.158 20.82 1.93 44.16 3.16
518 631 0.607489 GCTTGAGAGGCAGAGGCAAA 60.607 55.000 0.00 0.00 43.71 3.68
520 633 2.667418 GCTTGAGAGGCAGAGGCA 59.333 61.111 0.00 0.00 43.71 4.75
521 634 2.511145 CGCTTGAGAGGCAGAGGC 60.511 66.667 0.00 0.00 40.13 4.70
523 636 0.320247 ACAACGCTTGAGAGGCAGAG 60.320 55.000 5.01 0.00 0.00 3.35
524 637 0.319900 GACAACGCTTGAGAGGCAGA 60.320 55.000 5.01 0.00 0.00 4.26
525 638 1.621301 CGACAACGCTTGAGAGGCAG 61.621 60.000 5.01 0.00 0.00 4.85
526 639 1.664649 CGACAACGCTTGAGAGGCA 60.665 57.895 5.01 0.00 0.00 4.75
527 640 1.618640 GACGACAACGCTTGAGAGGC 61.619 60.000 0.00 0.00 43.96 4.70
528 641 1.009389 GGACGACAACGCTTGAGAGG 61.009 60.000 0.00 0.00 43.96 3.69
529 642 0.318699 TGGACGACAACGCTTGAGAG 60.319 55.000 0.00 0.00 43.96 3.20
530 643 0.596600 GTGGACGACAACGCTTGAGA 60.597 55.000 0.00 0.00 43.96 3.27
531 644 1.557443 GGTGGACGACAACGCTTGAG 61.557 60.000 0.00 2.19 43.96 3.02
532 645 1.593209 GGTGGACGACAACGCTTGA 60.593 57.895 0.00 0.00 43.96 3.02
533 646 1.557443 GAGGTGGACGACAACGCTTG 61.557 60.000 0.00 0.00 43.31 4.01
534 647 1.300697 GAGGTGGACGACAACGCTT 60.301 57.895 0.00 0.00 43.31 4.68
535 648 2.201022 AGAGGTGGACGACAACGCT 61.201 57.895 0.00 0.00 42.48 5.07
536 649 1.282930 GAAGAGGTGGACGACAACGC 61.283 60.000 0.00 0.00 43.31 4.84
537 650 0.314302 AGAAGAGGTGGACGACAACG 59.686 55.000 0.00 0.00 43.31 4.10
538 651 2.295349 TGTAGAAGAGGTGGACGACAAC 59.705 50.000 0.00 0.00 36.91 3.32
539 652 2.589720 TGTAGAAGAGGTGGACGACAA 58.410 47.619 0.00 0.00 0.00 3.18
540 653 2.281539 TGTAGAAGAGGTGGACGACA 57.718 50.000 0.00 0.00 0.00 4.35
541 654 2.753452 TGATGTAGAAGAGGTGGACGAC 59.247 50.000 0.00 0.00 0.00 4.34
542 655 2.753452 GTGATGTAGAAGAGGTGGACGA 59.247 50.000 0.00 0.00 0.00 4.20
543 656 2.755655 AGTGATGTAGAAGAGGTGGACG 59.244 50.000 0.00 0.00 0.00 4.79
544 657 5.194432 TCTAGTGATGTAGAAGAGGTGGAC 58.806 45.833 0.00 0.00 0.00 4.02
545 658 5.191921 TCTCTAGTGATGTAGAAGAGGTGGA 59.808 44.000 0.00 0.00 35.47 4.02
546 659 5.441500 TCTCTAGTGATGTAGAAGAGGTGG 58.558 45.833 0.00 0.00 35.47 4.61
547 660 6.375736 TGTTCTCTAGTGATGTAGAAGAGGTG 59.624 42.308 0.00 0.00 35.47 4.00
548 661 6.486056 TGTTCTCTAGTGATGTAGAAGAGGT 58.514 40.000 0.00 0.00 35.47 3.85
554 667 7.526142 AGTTGTTGTTCTCTAGTGATGTAGA 57.474 36.000 0.00 0.00 0.00 2.59
579 692 8.589629 CGCACGTACATTTTTCTAGTTATAGTT 58.410 33.333 0.00 0.00 0.00 2.24
598 711 4.100707 AGTACTTTATTCTGCGCACGTA 57.899 40.909 5.66 0.00 0.00 3.57
600 713 4.027621 CACTAGTACTTTATTCTGCGCACG 60.028 45.833 5.66 2.75 0.00 5.34
605 718 5.051153 GGGAGCACTAGTACTTTATTCTGC 58.949 45.833 0.00 0.00 0.00 4.26
606 719 5.282510 CGGGAGCACTAGTACTTTATTCTG 58.717 45.833 0.00 0.00 0.00 3.02
639 752 3.416156 AGACAATGGAGAAGAAACTGCC 58.584 45.455 0.00 0.00 0.00 4.85
680 793 0.521291 TGCAATGTAGCCGAAACAGC 59.479 50.000 0.00 0.00 0.00 4.40
724 837 2.203056 CGCCGGAGAATGCCATCA 60.203 61.111 5.05 0.00 0.00 3.07
738 851 2.247437 GCCATGTCGGAATCTCGCC 61.247 63.158 0.00 0.00 36.56 5.54
806 919 1.808133 GCCGGCAGATTGACCTTCTAG 60.808 57.143 24.80 0.00 0.00 2.43
868 981 2.483876 CATGACTACCTGGCATAACGG 58.516 52.381 0.00 0.00 43.93 4.44
931 1048 2.765699 GACTTCCCTGCTGAAGATCTCT 59.234 50.000 15.12 0.00 43.60 3.10
932 1049 2.765699 AGACTTCCCTGCTGAAGATCTC 59.234 50.000 15.12 5.63 43.60 2.75
933 1050 2.765699 GAGACTTCCCTGCTGAAGATCT 59.234 50.000 15.12 13.20 43.60 2.75
934 1051 2.481104 CGAGACTTCCCTGCTGAAGATC 60.481 54.545 15.12 11.67 43.60 2.75
1075 1195 0.041238 TTGATCTCAGGACCCGGAGT 59.959 55.000 0.73 0.00 38.91 3.85
2149 3116 0.671781 CGCAGACTTGGAGTCCTTGG 60.672 60.000 11.33 3.02 46.18 3.61
2424 6449 0.463833 CTTGTACCGCCCAGGATTCC 60.464 60.000 0.00 0.00 45.00 3.01
2770 6801 0.601841 CGGCTTGGTAAGTGACGGTT 60.602 55.000 0.00 0.00 0.00 4.44
3196 7282 4.439305 TTGCTTGGCATATGTTGTCTTC 57.561 40.909 4.29 0.00 38.76 2.87
3447 7552 1.070134 TGAGTGTGAGGGACCTTTTCG 59.930 52.381 0.00 0.00 0.00 3.46
3509 7614 3.899981 CTGCTGCGTAGGCCACCAA 62.900 63.158 5.01 0.00 38.85 3.67
3633 7738 2.344950 GGTGCTGAGAACTGTCATCAG 58.655 52.381 14.54 14.54 46.18 2.90
3651 7756 2.308185 GGAGGAGGATTTTCCGGGT 58.692 57.895 0.00 0.00 42.75 5.28
3657 7762 3.654273 TCCTGTATCGGAGGAGGATTTT 58.346 45.455 0.00 0.00 34.49 1.82
3721 7826 2.623416 GCACACTGATAATAAAGGGGGC 59.377 50.000 0.00 0.00 39.46 5.80
3844 7951 2.441001 TCAAATTGGGGCACAAAATGGT 59.559 40.909 6.13 0.00 43.46 3.55
3928 8035 5.326283 AGAGTGCTATATAGACACTCCCA 57.674 43.478 34.35 16.33 46.52 4.37
3947 8054 4.381292 GGCCAATTGGAAATCAGTCAAGAG 60.381 45.833 29.02 0.00 37.39 2.85
3952 8059 3.259123 AGTTGGCCAATTGGAAATCAGTC 59.741 43.478 29.02 7.29 37.39 3.51
3953 8060 3.007182 CAGTTGGCCAATTGGAAATCAGT 59.993 43.478 28.48 6.40 37.39 3.41
4001 8108 1.668419 GAGCCAGCAATTACACGGAT 58.332 50.000 0.00 0.00 0.00 4.18
4040 8147 9.759473 AAAAGAAATATCCTCTTCCATCTTCAA 57.241 29.630 1.57 0.00 31.85 2.69
4085 8192 1.214367 TTCACTTCCGCTTCGACAAC 58.786 50.000 0.00 0.00 0.00 3.32
4100 8207 6.817140 AGGTGTAGAGAAAAACGGATATTCAC 59.183 38.462 0.00 0.00 0.00 3.18
4102 8209 6.817140 ACAGGTGTAGAGAAAAACGGATATTC 59.183 38.462 0.00 0.00 0.00 1.75
4104 8211 6.295719 ACAGGTGTAGAGAAAAACGGATAT 57.704 37.500 0.00 0.00 0.00 1.63
4145 8268 2.158813 AGAAGAAACCCGACAAAGCTGA 60.159 45.455 0.00 0.00 0.00 4.26
4249 8372 1.063266 AGGAGTTGCCCTTTTTGGTCA 60.063 47.619 0.00 0.00 37.37 4.02
4268 8391 4.818546 AGTCGGAATATTCATGAGGCAAAG 59.181 41.667 17.07 0.00 0.00 2.77
4287 8410 3.374402 AGGTCTGCACCCGAGTCG 61.374 66.667 5.29 5.29 45.12 4.18
4288 8411 1.816863 TTCAGGTCTGCACCCGAGTC 61.817 60.000 0.00 0.00 45.12 3.36
4289 8412 1.194781 ATTCAGGTCTGCACCCGAGT 61.195 55.000 0.00 0.00 45.12 4.18
4290 8413 0.460987 GATTCAGGTCTGCACCCGAG 60.461 60.000 0.00 0.00 45.12 4.63
4291 8414 1.596934 GATTCAGGTCTGCACCCGA 59.403 57.895 0.00 0.00 45.12 5.14
4292 8415 1.450312 GGATTCAGGTCTGCACCCG 60.450 63.158 0.00 0.00 45.12 5.28
4300 8423 2.154462 CACAACCACTGGATTCAGGTC 58.846 52.381 5.84 0.00 44.99 3.85
4315 8438 0.584876 GCGTGTGAACCTACCACAAC 59.415 55.000 0.00 0.00 44.91 3.32
4341 8464 2.506231 TCGGCCACTTACCATGGATTAA 59.494 45.455 21.47 6.70 39.87 1.40
4399 8522 1.931841 GGTAAAAGAATCCGTCTCGCC 59.068 52.381 0.00 0.00 34.56 5.54
4412 8535 6.014840 TCAGGGATAGTTATAGGCGGTAAAAG 60.015 42.308 0.00 0.00 0.00 2.27
4476 8600 3.933955 TGCAATTGAGCCATATTGTTTGC 59.066 39.130 10.34 0.00 38.85 3.68
4614 8739 5.351465 TGTCTCAAGTGAAGTGTGTTTTCTC 59.649 40.000 0.00 0.00 0.00 2.87
4655 8780 7.893658 TGACCTACTACTTCTTTGAGGTAAAG 58.106 38.462 0.00 0.00 45.77 1.85
4657 8782 7.236529 TCTGACCTACTACTTCTTTGAGGTAA 58.763 38.462 0.00 0.00 37.43 2.85


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

AutoCloner maintained by Alex Coulton.