Multiple sequence alignment - TraesCS7D01G294800

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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 TraesCS7D01G294800 chr7D 100.000 4473 0 0 1 4473 369179521 369175049 0.000000e+00 8261.0
1 TraesCS7D01G294800 chr7D 100.000 68 0 0 3624 3691 369175830 369175763 4.700000e-25 126.0
2 TraesCS7D01G294800 chr7D 100.000 68 0 0 3692 3759 369175898 369175831 4.700000e-25 126.0
3 TraesCS7D01G294800 chr7D 96.364 55 2 0 4419 4473 19211630 19211576 1.710000e-14 91.6
4 TraesCS7D01G294800 chr7B 92.101 2532 138 30 5 2507 313421940 313424438 0.000000e+00 3511.0
5 TraesCS7D01G294800 chr7B 97.061 1191 30 4 2503 3691 313424478 313425665 0.000000e+00 2001.0
6 TraesCS7D01G294800 chr7B 92.388 289 16 1 4050 4332 313425991 313426279 1.500000e-109 407.0
7 TraesCS7D01G294800 chr7B 85.827 381 19 10 3692 4050 313425598 313425965 5.460000e-99 372.0
8 TraesCS7D01G294800 chr7B 94.366 71 4 0 4348 4418 313426441 313426511 4.730000e-20 110.0
9 TraesCS7D01G294800 chr7B 96.429 56 2 0 4418 4473 710484147 710484092 4.760000e-15 93.5
10 TraesCS7D01G294800 chr7A 96.971 1882 33 5 648 2509 413116054 413117931 0.000000e+00 3138.0
11 TraesCS7D01G294800 chr7A 95.474 1193 44 7 2503 3691 413117969 413119155 0.000000e+00 1895.0
12 TraesCS7D01G294800 chr7A 93.089 246 16 1 3692 3937 413119088 413119332 4.250000e-95 359.0
13 TraesCS7D01G294800 chr7A 90.816 196 12 3 4077 4266 413121851 413122046 1.600000e-64 257.0
14 TraesCS7D01G294800 chr7A 96.341 82 3 0 3969 4050 413119460 413119541 7.800000e-28 135.0
15 TraesCS7D01G294800 chr5B 98.246 57 1 0 4417 4473 274455479 274455423 2.850000e-17 100.0
16 TraesCS7D01G294800 chr1B 98.246 57 1 0 4417 4473 332872365 332872421 2.850000e-17 100.0
17 TraesCS7D01G294800 chr4B 96.610 59 2 0 4415 4473 598385686 598385628 1.020000e-16 99.0
18 TraesCS7D01G294800 chr6B 98.182 55 1 0 4417 4471 278073228 278073282 3.680000e-16 97.1
19 TraesCS7D01G294800 chr4D 96.491 57 2 0 4417 4473 323149673 323149729 1.320000e-15 95.3
20 TraesCS7D01G294800 chr1A 94.915 59 3 0 4415 4473 19549950 19549892 4.760000e-15 93.5
21 TraesCS7D01G294800 chr2B 94.828 58 2 1 4416 4473 778837721 778837777 6.160000e-14 89.8


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 TraesCS7D01G294800 chr7D 369175049 369179521 4472 True 2837.666667 8261 100.0000 1 4473 3 chr7D.!!$R2 4472
1 TraesCS7D01G294800 chr7B 313421940 313426511 4571 False 1280.200000 3511 92.3486 5 4418 5 chr7B.!!$F1 4413
2 TraesCS7D01G294800 chr7A 413116054 413122046 5992 False 1156.800000 3138 94.5382 648 4266 5 chr7A.!!$F1 3618

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
410 416 0.096281 CGCGCACGGACAAAATACAT 59.904 50.000 8.75 0.0 34.97 2.29 F
451 458 0.453793 CGCATTGGGCCGTCATTTTA 59.546 50.000 0.00 0.0 40.31 1.52 F
881 916 0.818296 CCTATCCCGGATCCATCGAC 59.182 60.000 13.41 0.0 0.00 4.20 F
1419 1459 2.079158 CACTGCAATGAGGGTACTGTG 58.921 52.381 0.00 0.0 0.00 3.66 F
2649 2734 3.369147 CCTACGCATCTGACAAGAAACTG 59.631 47.826 0.00 0.0 35.59 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1459 3.828875 AACTAAGATCAGTAGCAGGGC 57.171 47.619 0.00 0.00 0.00 5.19 R
1525 1565 5.104527 AGCACTTGCATATAAACTAGACCCA 60.105 40.000 3.62 0.00 45.16 4.51 R
2631 2716 1.532437 TGCAGTTTCTTGTCAGATGCG 59.468 47.619 0.00 0.00 35.93 4.73 R
2890 2975 1.044790 AAATGCATACCCAGGGCTGC 61.045 55.000 21.98 21.98 35.89 5.25 R
3964 4079 0.107410 TGTGACCGATTACATGCCCC 60.107 55.000 0.00 0.00 0.00 5.80 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
31 32 2.362760 TCTTGTAGGGCGGCGGTA 60.363 61.111 9.78 0.00 0.00 4.02
67 68 0.535780 CTGTGGCTTCCAGCTTGTCA 60.536 55.000 0.00 0.00 41.99 3.58
87 88 1.228675 CCTGCACCTTCCTTTGGCT 60.229 57.895 0.00 0.00 0.00 4.75
110 111 3.113260 CCCTCTTGGCCGACTAAATAG 57.887 52.381 0.00 0.00 0.00 1.73
125 126 2.495366 AATAGTCCGTTGCGCGTCCA 62.495 55.000 8.43 0.00 39.32 4.02
129 130 3.418913 CCGTTGCGCGTCCATCAA 61.419 61.111 8.43 0.00 39.32 2.57
136 137 1.696832 GCGCGTCCATCAACTCCTTC 61.697 60.000 8.43 0.00 0.00 3.46
139 140 1.734465 GCGTCCATCAACTCCTTCTTG 59.266 52.381 0.00 0.00 0.00 3.02
140 141 2.350522 CGTCCATCAACTCCTTCTTGG 58.649 52.381 0.00 0.00 37.10 3.61
141 142 2.716217 GTCCATCAACTCCTTCTTGGG 58.284 52.381 0.00 0.00 36.20 4.12
143 144 1.005215 CCATCAACTCCTTCTTGGGCT 59.995 52.381 0.00 0.00 36.20 5.19
144 145 2.089980 CATCAACTCCTTCTTGGGCTG 58.910 52.381 0.00 0.00 36.20 4.85
145 146 0.401738 TCAACTCCTTCTTGGGCTGG 59.598 55.000 0.00 0.00 36.20 4.85
151 155 4.659172 TTCTTGGGCTGGGGCGTG 62.659 66.667 0.00 0.00 39.81 5.34
163 167 1.281656 GGGCGTGTTTTTGAGGACG 59.718 57.895 0.00 0.00 34.93 4.79
164 168 1.281656 GGCGTGTTTTTGAGGACGG 59.718 57.895 0.00 0.00 32.45 4.79
168 172 2.127383 GTTTTTGAGGACGGCGCG 60.127 61.111 6.90 0.00 0.00 6.86
186 190 2.351276 GGGCTTGTCGATGGTGGT 59.649 61.111 0.00 0.00 0.00 4.16
231 236 2.045708 GTTGGCCATGATGTGCGGA 61.046 57.895 6.09 0.00 0.00 5.54
233 238 2.438254 GGCCATGATGTGCGGACA 60.438 61.111 13.59 13.59 36.22 4.02
237 242 0.392863 CCATGATGTGCGGACAGGAA 60.393 55.000 16.77 3.65 34.87 3.36
262 267 2.119611 GGGTGGGAGGGTTTTGGG 59.880 66.667 0.00 0.00 0.00 4.12
266 271 1.484256 GGTGGGAGGGTTTTGGGAAAT 60.484 52.381 0.00 0.00 0.00 2.17
268 273 1.505538 TGGGAGGGTTTTGGGAAATGA 59.494 47.619 0.00 0.00 0.00 2.57
278 283 6.295249 GGTTTTGGGAAATGAAGGAAAATGA 58.705 36.000 0.00 0.00 0.00 2.57
281 286 4.750941 TGGGAAATGAAGGAAAATGAGGT 58.249 39.130 0.00 0.00 0.00 3.85
282 287 4.527816 TGGGAAATGAAGGAAAATGAGGTG 59.472 41.667 0.00 0.00 0.00 4.00
284 289 4.772100 GGAAATGAAGGAAAATGAGGTGGA 59.228 41.667 0.00 0.00 0.00 4.02
285 290 5.423290 GGAAATGAAGGAAAATGAGGTGGAT 59.577 40.000 0.00 0.00 0.00 3.41
286 291 5.927281 AATGAAGGAAAATGAGGTGGATG 57.073 39.130 0.00 0.00 0.00 3.51
287 292 4.387026 TGAAGGAAAATGAGGTGGATGT 57.613 40.909 0.00 0.00 0.00 3.06
288 293 4.081406 TGAAGGAAAATGAGGTGGATGTG 58.919 43.478 0.00 0.00 0.00 3.21
289 294 3.814504 AGGAAAATGAGGTGGATGTGT 57.185 42.857 0.00 0.00 0.00 3.72
309 315 3.574952 CCAACTGGTGGGTCAGGA 58.425 61.111 3.05 0.00 44.64 3.86
320 326 1.002011 GGTCAGGAAGGACAAGGCC 60.002 63.158 0.00 0.00 39.59 5.19
350 356 4.552365 CGCCCGCTCCATGTCCAT 62.552 66.667 0.00 0.00 0.00 3.41
352 358 2.591753 CCCGCTCCATGTCCATGT 59.408 61.111 6.53 0.00 37.11 3.21
356 362 0.249615 CGCTCCATGTCCATGTCGAT 60.250 55.000 6.53 0.00 37.11 3.59
370 376 4.494484 CATGTCGATACAAACCTGACTCA 58.506 43.478 0.00 0.00 39.58 3.41
377 383 8.169268 GTCGATACAAACCTGACTCAAATTTAG 58.831 37.037 0.00 0.00 0.00 1.85
389 395 7.230747 TGACTCAAATTTAGACCTGAAATGGA 58.769 34.615 0.00 0.00 0.00 3.41
396 402 1.078497 ACCTGAAATGGATCGCGCA 60.078 52.632 8.75 0.00 0.00 6.09
402 408 3.657448 AATGGATCGCGCACGGACA 62.657 57.895 8.75 0.00 40.63 4.02
403 409 3.657448 ATGGATCGCGCACGGACAA 62.657 57.895 8.75 0.00 40.63 3.18
404 410 3.115892 GGATCGCGCACGGACAAA 61.116 61.111 8.75 0.00 40.63 2.83
405 411 2.673114 GGATCGCGCACGGACAAAA 61.673 57.895 8.75 0.00 40.63 2.44
406 412 1.423845 GATCGCGCACGGACAAAAT 59.576 52.632 8.75 0.00 40.63 1.82
407 413 0.648441 GATCGCGCACGGACAAAATA 59.352 50.000 8.75 0.00 40.63 1.40
408 414 0.372334 ATCGCGCACGGACAAAATAC 59.628 50.000 8.75 0.00 40.63 1.89
409 415 0.944788 TCGCGCACGGACAAAATACA 60.945 50.000 8.75 0.00 40.63 2.29
410 416 0.096281 CGCGCACGGACAAAATACAT 59.904 50.000 8.75 0.00 34.97 2.29
411 417 1.325037 CGCGCACGGACAAAATACATA 59.675 47.619 8.75 0.00 34.97 2.29
412 418 2.033236 CGCGCACGGACAAAATACATAT 60.033 45.455 8.75 0.00 34.97 1.78
413 419 3.288242 GCGCACGGACAAAATACATATG 58.712 45.455 0.30 0.00 0.00 1.78
414 420 3.288242 CGCACGGACAAAATACATATGC 58.712 45.455 1.58 0.00 0.00 3.14
415 421 3.002246 CGCACGGACAAAATACATATGCT 59.998 43.478 1.58 0.00 0.00 3.79
416 422 4.527564 GCACGGACAAAATACATATGCTC 58.472 43.478 1.58 0.00 0.00 4.26
417 423 4.035091 GCACGGACAAAATACATATGCTCA 59.965 41.667 1.58 0.00 0.00 4.26
418 424 5.277974 GCACGGACAAAATACATATGCTCAT 60.278 40.000 1.58 0.00 0.00 2.90
419 425 6.365839 CACGGACAAAATACATATGCTCATC 58.634 40.000 1.58 0.00 0.00 2.92
420 426 5.470098 ACGGACAAAATACATATGCTCATCC 59.530 40.000 1.58 0.73 0.00 3.51
421 427 5.469760 CGGACAAAATACATATGCTCATCCA 59.530 40.000 1.58 0.00 0.00 3.41
451 458 0.453793 CGCATTGGGCCGTCATTTTA 59.546 50.000 0.00 0.00 40.31 1.52
454 461 2.545742 GCATTGGGCCGTCATTTTATCC 60.546 50.000 0.00 0.00 36.11 2.59
455 462 1.384525 TTGGGCCGTCATTTTATCCG 58.615 50.000 0.00 0.00 0.00 4.18
457 464 1.340211 TGGGCCGTCATTTTATCCGTT 60.340 47.619 0.00 0.00 0.00 4.44
460 467 3.377798 GGGCCGTCATTTTATCCGTTTTA 59.622 43.478 0.00 0.00 0.00 1.52
470 477 7.596995 TCATTTTATCCGTTTTAAGCCAAACAG 59.403 33.333 5.03 0.00 36.58 3.16
472 479 3.974871 TCCGTTTTAAGCCAAACAGAC 57.025 42.857 5.03 0.00 36.58 3.51
477 484 2.165362 TTAAGCCAAACAGACGCGCG 62.165 55.000 30.96 30.96 0.00 6.86
491 498 2.126463 CGCGTGGACAGTCGACAT 60.126 61.111 19.50 5.01 0.00 3.06
496 503 1.601914 CGTGGACAGTCGACATGTTGA 60.602 52.381 19.50 11.98 0.00 3.18
498 505 2.476619 GTGGACAGTCGACATGTTGAAG 59.523 50.000 17.55 14.83 0.00 3.02
502 509 3.531538 ACAGTCGACATGTTGAAGTTGT 58.468 40.909 17.55 17.37 0.00 3.32
510 517 5.901884 CGACATGTTGAAGTTGTTCTTACAC 59.098 40.000 7.36 0.00 36.40 2.90
538 545 5.102313 GTGTCAAAGCCATGGTTATTAAGC 58.898 41.667 14.67 0.00 0.00 3.09
543 550 5.388599 AAGCCATGGTTATTAAGCTAGGT 57.611 39.130 14.67 0.00 0.00 3.08
559 566 5.269459 GCTAGGTGCGTGTCATATATTTG 57.731 43.478 0.00 0.00 0.00 2.32
560 567 4.750098 GCTAGGTGCGTGTCATATATTTGT 59.250 41.667 0.00 0.00 0.00 2.83
561 568 5.236478 GCTAGGTGCGTGTCATATATTTGTT 59.764 40.000 0.00 0.00 0.00 2.83
562 569 5.734855 AGGTGCGTGTCATATATTTGTTC 57.265 39.130 0.00 0.00 0.00 3.18
563 570 5.428253 AGGTGCGTGTCATATATTTGTTCT 58.572 37.500 0.00 0.00 0.00 3.01
564 571 5.523916 AGGTGCGTGTCATATATTTGTTCTC 59.476 40.000 0.00 0.00 0.00 2.87
565 572 5.293324 GGTGCGTGTCATATATTTGTTCTCA 59.707 40.000 0.00 0.00 0.00 3.27
566 573 6.185399 GTGCGTGTCATATATTTGTTCTCAC 58.815 40.000 0.00 0.00 0.00 3.51
636 647 5.499268 CGTAGAGACGTAGAGTACATAGC 57.501 47.826 0.00 0.00 44.31 2.97
637 648 4.981054 CGTAGAGACGTAGAGTACATAGCA 59.019 45.833 0.00 0.00 44.31 3.49
638 649 5.117440 CGTAGAGACGTAGAGTACATAGCAG 59.883 48.000 0.00 0.00 44.31 4.24
639 650 5.026038 AGAGACGTAGAGTACATAGCAGT 57.974 43.478 0.00 0.00 0.00 4.40
640 651 5.430007 AGAGACGTAGAGTACATAGCAGTT 58.570 41.667 0.00 0.00 0.00 3.16
642 653 7.046652 AGAGACGTAGAGTACATAGCAGTTTA 58.953 38.462 0.00 0.00 0.00 2.01
643 654 7.225145 AGAGACGTAGAGTACATAGCAGTTTAG 59.775 40.741 0.00 0.00 0.00 1.85
743 758 3.254035 AAGGGGGCCCGAGAGAGAA 62.254 63.158 17.79 0.00 41.95 2.87
879 914 1.107114 CTCCTATCCCGGATCCATCG 58.893 60.000 13.41 0.00 31.43 3.84
881 916 0.818296 CCTATCCCGGATCCATCGAC 59.182 60.000 13.41 0.00 0.00 4.20
1206 1241 7.867305 TCTTCTTATTGACGTGTCTATCTCT 57.133 36.000 0.00 0.00 0.00 3.10
1297 1337 7.500992 TCTCTGATGTGGTTATTATGGAACTC 58.499 38.462 0.00 0.00 0.00 3.01
1419 1459 2.079158 CACTGCAATGAGGGTACTGTG 58.921 52.381 0.00 0.00 0.00 3.66
1677 1717 7.279758 TGCAGGTTTATTTTTGCATTTATAGGC 59.720 33.333 0.00 0.00 41.23 3.93
1770 1810 8.367911 TGCTTATCCACTGTATCCTTAACATAG 58.632 37.037 0.00 0.00 0.00 2.23
2049 2089 6.257411 TGTTTTGCTTTACATTGTGTGATTGG 59.743 34.615 0.00 0.00 0.00 3.16
2061 2101 3.758023 TGTGTGATTGGTTTAGGATGCTG 59.242 43.478 0.00 0.00 0.00 4.41
2421 2461 6.403964 GCTGTAATTTGATGAAGCATCTGTGA 60.404 38.462 8.66 0.00 41.06 3.58
2566 2651 7.114529 GCTTATGCAGAGATAAATTTGTGATGC 59.885 37.037 0.00 5.01 39.41 3.91
2600 2685 8.322906 TGTTGTTTAGATAACAATCCTGTCTG 57.677 34.615 6.38 0.00 41.51 3.51
2631 2716 8.150945 TCTGTTGCTTTATTATCCAGATCCTAC 58.849 37.037 0.00 0.00 0.00 3.18
2649 2734 3.369147 CCTACGCATCTGACAAGAAACTG 59.631 47.826 0.00 0.00 35.59 3.16
2675 2760 7.415541 GCAGCATCTGATTTTCCACATTAAGTA 60.416 37.037 0.00 0.00 32.44 2.24
2890 2975 9.803315 ACTATATATTCCATACTAACATGTGCG 57.197 33.333 0.00 0.00 0.00 5.34
2925 3010 3.380004 TGCATTTTCGTGAAAGAAGTGGT 59.620 39.130 0.00 0.00 0.00 4.16
3077 3163 6.537301 TCAGTAACAATAGGCTAAAACATCCG 59.463 38.462 0.00 0.00 0.00 4.18
3186 3272 3.457380 AGTGATGATGAGTACATTGGCCT 59.543 43.478 3.32 0.00 36.82 5.19
3361 3447 7.081526 AGTATCTCAGTGCAAATGCTTTTAG 57.918 36.000 6.97 0.33 42.66 1.85
3427 3514 1.535860 CCAAACAGGTTTCAACAGGCG 60.536 52.381 0.00 0.00 0.00 5.52
3488 3575 0.656259 CTGATGCTTGGTCGATGCAG 59.344 55.000 10.16 0.00 38.08 4.41
3497 3584 1.067142 TGGTCGATGCAGTTCAGTACC 60.067 52.381 0.00 0.00 0.00 3.34
3538 3625 2.932614 AGCTGTGCAATAACATCGACTC 59.067 45.455 0.00 0.00 0.00 3.36
3566 3653 0.253894 CATGTGGCTGGGTGATCTGA 59.746 55.000 0.00 0.00 0.00 3.27
3604 3691 3.866379 ATGTGGCGAGCCCTTGCAA 62.866 57.895 12.05 0.00 41.74 4.08
3614 3701 3.864686 CCTTGCAATCGCCCGTCG 61.865 66.667 0.00 0.00 37.32 5.12
3621 3708 0.179145 CAATCGCCCGTCGTAGTTCT 60.179 55.000 0.00 0.00 39.67 3.01
3662 3749 6.941436 AGAAATCTCTGCATCTTTCAGTCTTT 59.059 34.615 10.90 0.00 33.48 2.52
3663 3750 6.497785 AATCTCTGCATCTTTCAGTCTTTG 57.502 37.500 0.00 0.00 33.48 2.77
3664 3751 3.750130 TCTCTGCATCTTTCAGTCTTTGC 59.250 43.478 0.00 0.00 33.48 3.68
3665 3752 3.479489 TCTGCATCTTTCAGTCTTTGCA 58.521 40.909 0.00 0.00 37.73 4.08
3666 3753 3.884693 TCTGCATCTTTCAGTCTTTGCAA 59.115 39.130 0.00 0.00 39.36 4.08
3667 3754 4.521639 TCTGCATCTTTCAGTCTTTGCAAT 59.478 37.500 0.00 0.00 39.36 3.56
3668 3755 5.706833 TCTGCATCTTTCAGTCTTTGCAATA 59.293 36.000 0.00 0.00 39.36 1.90
3669 3756 6.207221 TCTGCATCTTTCAGTCTTTGCAATAA 59.793 34.615 0.00 0.00 39.36 1.40
3670 3757 6.927416 TGCATCTTTCAGTCTTTGCAATAAT 58.073 32.000 0.00 0.00 37.17 1.28
3671 3758 7.380536 TGCATCTTTCAGTCTTTGCAATAATT 58.619 30.769 0.00 0.00 37.17 1.40
3672 3759 7.329962 TGCATCTTTCAGTCTTTGCAATAATTG 59.670 33.333 0.00 0.00 37.17 2.32
3673 3760 7.543172 GCATCTTTCAGTCTTTGCAATAATTGA 59.457 33.333 0.00 1.24 0.00 2.57
3674 3761 9.414295 CATCTTTCAGTCTTTGCAATAATTGAA 57.586 29.630 0.00 7.61 0.00 2.69
3675 3762 8.801715 TCTTTCAGTCTTTGCAATAATTGAAC 57.198 30.769 14.86 2.25 0.00 3.18
3676 3763 8.632679 TCTTTCAGTCTTTGCAATAATTGAACT 58.367 29.630 14.86 4.04 0.00 3.01
3677 3764 9.252962 CTTTCAGTCTTTGCAATAATTGAACTT 57.747 29.630 14.86 0.00 0.00 2.66
3686 3773 9.890352 TTTGCAATAATTGAACTTAATTTTGGC 57.110 25.926 0.00 0.00 32.14 4.52
3687 3774 8.038492 TGCAATAATTGAACTTAATTTTGGCC 57.962 30.769 0.00 0.00 31.14 5.36
3688 3775 7.663081 TGCAATAATTGAACTTAATTTTGGCCA 59.337 29.630 0.00 0.00 31.14 5.36
3689 3776 8.676401 GCAATAATTGAACTTAATTTTGGCCAT 58.324 29.630 6.09 0.00 32.79 4.40
3696 3783 9.956640 TTGAACTTAATTTTGGCCATATCATTT 57.043 25.926 6.09 0.00 0.00 2.32
3705 3792 8.759481 TTTTGGCCATATCATTTACATAGTCA 57.241 30.769 6.09 0.00 0.00 3.41
3706 3793 7.984422 TTGGCCATATCATTTACATAGTCAG 57.016 36.000 6.09 0.00 0.00 3.51
3707 3794 7.315066 TGGCCATATCATTTACATAGTCAGA 57.685 36.000 0.00 0.00 0.00 3.27
3708 3795 7.744733 TGGCCATATCATTTACATAGTCAGAA 58.255 34.615 0.00 0.00 0.00 3.02
3709 3796 8.217111 TGGCCATATCATTTACATAGTCAGAAA 58.783 33.333 0.00 0.00 0.00 2.52
3710 3797 9.236006 GGCCATATCATTTACATAGTCAGAAAT 57.764 33.333 0.00 0.00 0.00 2.17
3727 3814 6.109320 CAGAAATCTCTGCATCTTTCAGTC 57.891 41.667 10.90 0.00 42.66 3.51
3728 3815 5.875910 CAGAAATCTCTGCATCTTTCAGTCT 59.124 40.000 10.90 0.00 42.66 3.24
3729 3816 6.372103 CAGAAATCTCTGCATCTTTCAGTCTT 59.628 38.462 10.90 0.00 42.66 3.01
3787 3874 0.856641 CTGTTGTGTACACGTTCCCG 59.143 55.000 20.61 3.82 40.83 5.14
3805 3892 3.389983 TCCCGTGGAACCTTATATGGAAG 59.610 47.826 11.49 0.00 0.00 3.46
3845 3932 0.318107 GCATTGTGCAGTGAAGCGTT 60.318 50.000 0.00 0.00 44.26 4.84
3855 3942 1.604278 AGTGAAGCGTTTTTGAGCTCC 59.396 47.619 12.15 0.00 43.78 4.70
3907 3994 2.076863 GAGTATTGTGTTTGAGCGCCT 58.923 47.619 2.29 0.00 0.00 5.52
3939 4054 1.719709 GGCGCTATCCAAAACCGTC 59.280 57.895 7.64 0.00 0.00 4.79
3941 4056 0.373716 GCGCTATCCAAAACCGTCAG 59.626 55.000 0.00 0.00 0.00 3.51
3950 4065 2.459934 CAAAACCGTCAGGCTTTGTTC 58.540 47.619 5.52 0.00 44.45 3.18
3952 4067 1.164041 AACCGTCAGGCTTTGTTCGG 61.164 55.000 17.53 17.53 44.30 4.30
3954 4069 1.164041 CCGTCAGGCTTTGTTCGGTT 61.164 55.000 14.05 0.00 39.00 4.44
3955 4070 1.504359 CGTCAGGCTTTGTTCGGTTA 58.496 50.000 0.00 0.00 0.00 2.85
3957 4072 1.193874 GTCAGGCTTTGTTCGGTTACG 59.806 52.381 0.00 0.00 42.74 3.18
3958 4073 0.110373 CAGGCTTTGTTCGGTTACGC 60.110 55.000 0.00 0.00 40.69 4.42
3959 4074 1.208358 GGCTTTGTTCGGTTACGCC 59.792 57.895 0.00 0.00 40.69 5.68
3960 4075 1.208358 GCTTTGTTCGGTTACGCCC 59.792 57.895 0.00 0.00 40.69 6.13
3964 4079 0.247185 TTGTTCGGTTACGCCCTAGG 59.753 55.000 0.06 0.06 40.69 3.02
4009 4191 4.814234 GCTATACAAAATCGATCACACCCA 59.186 41.667 0.00 0.00 0.00 4.51
4045 4227 3.617284 GTTAACCGTTCCCATCCTGATT 58.383 45.455 0.00 0.00 0.00 2.57
4067 4275 1.278985 ACTGCCCATCGACATCTTTGA 59.721 47.619 0.00 0.00 0.00 2.69
4071 4279 3.126831 GCCCATCGACATCTTTGAGTAG 58.873 50.000 0.00 0.00 0.00 2.57
4092 6557 1.302752 GTGTCTGCCTCACATGCCA 60.303 57.895 0.00 0.00 36.05 4.92
4158 6623 0.534203 ACGGTCGTTTCCATTGCTGT 60.534 50.000 0.00 0.00 0.00 4.40
4269 6740 1.144565 CGAGCAGGAGAATCACGCAG 61.145 60.000 0.00 0.00 36.25 5.18
4272 6743 1.900351 CAGGAGAATCACGCAGGGA 59.100 57.895 0.00 0.00 36.25 4.20
4321 6792 9.529325 TTCTCGTCTTTTCGATTGTATTCATAT 57.471 29.630 0.00 0.00 39.12 1.78
4332 6803 7.039434 TCGATTGTATTCATATGCCTTCTCTCT 60.039 37.037 0.00 0.00 0.00 3.10
4333 6804 7.275341 CGATTGTATTCATATGCCTTCTCTCTC 59.725 40.741 0.00 0.00 0.00 3.20
4335 6806 6.990798 TGTATTCATATGCCTTCTCTCTCTG 58.009 40.000 0.00 0.00 0.00 3.35
4336 6807 6.552725 TGTATTCATATGCCTTCTCTCTCTGT 59.447 38.462 0.00 0.00 0.00 3.41
4337 6808 5.946942 TTCATATGCCTTCTCTCTCTGTT 57.053 39.130 0.00 0.00 0.00 3.16
4338 6809 7.609097 ATTCATATGCCTTCTCTCTCTGTTA 57.391 36.000 0.00 0.00 0.00 2.41
4339 6810 6.398234 TCATATGCCTTCTCTCTCTGTTAC 57.602 41.667 0.00 0.00 0.00 2.50
4341 6812 2.515854 TGCCTTCTCTCTCTGTTACGT 58.484 47.619 0.00 0.00 0.00 3.57
4342 6813 2.891580 TGCCTTCTCTCTCTGTTACGTT 59.108 45.455 0.00 0.00 0.00 3.99
4343 6814 4.077108 TGCCTTCTCTCTCTGTTACGTTA 58.923 43.478 0.00 0.00 0.00 3.18
4345 6816 4.674885 GCCTTCTCTCTCTGTTACGTTACC 60.675 50.000 1.74 0.00 0.00 2.85
4371 6988 5.540911 AGCGAATGAACCAAACAAAATCAT 58.459 33.333 0.00 0.00 32.36 2.45
4414 7031 0.247185 TGCGGGGTAAACTCGTTAGG 59.753 55.000 0.00 0.00 0.00 2.69
4418 7035 1.406477 GGGGTAAACTCGTTAGGGCAG 60.406 57.143 0.00 0.00 0.00 4.85
4419 7036 1.406477 GGGTAAACTCGTTAGGGCAGG 60.406 57.143 0.00 0.00 0.00 4.85
4420 7037 1.406477 GGTAAACTCGTTAGGGCAGGG 60.406 57.143 0.00 0.00 0.00 4.45
4421 7038 0.251073 TAAACTCGTTAGGGCAGGGC 59.749 55.000 0.00 0.00 0.00 5.19
4445 7062 2.043953 GGCAAAATCCGAGGCCCT 60.044 61.111 0.00 0.00 40.55 5.19
4446 7063 2.418083 GGCAAAATCCGAGGCCCTG 61.418 63.158 0.00 0.00 40.55 4.45
4447 7064 1.678970 GCAAAATCCGAGGCCCTGT 60.679 57.895 0.00 0.00 0.00 4.00
4448 7065 1.937546 GCAAAATCCGAGGCCCTGTG 61.938 60.000 0.00 0.00 0.00 3.66
4449 7066 1.678970 AAAATCCGAGGCCCTGTGC 60.679 57.895 0.00 0.00 40.16 4.57
4450 7067 2.424842 AAAATCCGAGGCCCTGTGCA 62.425 55.000 0.00 0.00 43.89 4.57
4451 7068 2.424842 AAATCCGAGGCCCTGTGCAA 62.425 55.000 0.00 0.00 43.89 4.08
4452 7069 2.424842 AATCCGAGGCCCTGTGCAAA 62.425 55.000 0.00 0.00 43.89 3.68
4453 7070 2.424842 ATCCGAGGCCCTGTGCAAAA 62.425 55.000 0.00 0.00 43.89 2.44
4454 7071 2.644992 CGAGGCCCTGTGCAAAAC 59.355 61.111 0.00 0.00 43.89 2.43
4455 7072 1.898574 CGAGGCCCTGTGCAAAACT 60.899 57.895 0.00 0.00 43.89 2.66
4456 7073 0.605319 CGAGGCCCTGTGCAAAACTA 60.605 55.000 0.00 0.00 43.89 2.24
4457 7074 1.616159 GAGGCCCTGTGCAAAACTAA 58.384 50.000 0.00 0.00 43.89 2.24
4458 7075 1.960689 GAGGCCCTGTGCAAAACTAAA 59.039 47.619 0.00 0.00 43.89 1.85
4459 7076 2.364002 GAGGCCCTGTGCAAAACTAAAA 59.636 45.455 0.00 0.00 43.89 1.52
4460 7077 2.769095 AGGCCCTGTGCAAAACTAAAAA 59.231 40.909 0.00 0.00 43.89 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.473520 AAGAGGCCGCCATCGTGG 62.474 66.667 13.15 0.25 43.08 4.94
1 2 2.572095 TACAAGAGGCCGCCATCGTG 62.572 60.000 13.15 15.69 0.00 4.35
2 3 2.298158 CTACAAGAGGCCGCCATCGT 62.298 60.000 13.15 5.63 0.00 3.73
3 4 1.592669 CTACAAGAGGCCGCCATCG 60.593 63.158 13.15 0.00 0.00 3.84
67 68 1.228675 CCAAAGGAAGGTGCAGGCT 60.229 57.895 0.00 0.00 0.00 4.58
74 75 0.846870 AGGGCTAGCCAAAGGAAGGT 60.847 55.000 34.09 4.70 37.98 3.50
75 76 0.106967 GAGGGCTAGCCAAAGGAAGG 60.107 60.000 34.09 0.00 37.98 3.46
115 116 2.032634 GGAGTTGATGGACGCGCAA 61.033 57.895 5.73 0.00 0.00 4.85
125 126 1.005215 CCAGCCCAAGAAGGAGTTGAT 59.995 52.381 0.00 0.00 41.22 2.57
129 130 2.234296 CCCCAGCCCAAGAAGGAGT 61.234 63.158 0.00 0.00 41.22 3.85
136 137 4.974721 AACACGCCCCAGCCCAAG 62.975 66.667 0.00 0.00 34.57 3.61
139 140 3.230990 AAAAACACGCCCCAGCCC 61.231 61.111 0.00 0.00 34.57 5.19
140 141 2.028925 CAAAAACACGCCCCAGCC 59.971 61.111 0.00 0.00 34.57 4.85
141 142 1.007387 CTCAAAAACACGCCCCAGC 60.007 57.895 0.00 0.00 0.00 4.85
143 144 1.104577 GTCCTCAAAAACACGCCCCA 61.105 55.000 0.00 0.00 0.00 4.96
144 145 1.658114 GTCCTCAAAAACACGCCCC 59.342 57.895 0.00 0.00 0.00 5.80
145 146 1.281656 CGTCCTCAAAAACACGCCC 59.718 57.895 0.00 0.00 0.00 6.13
151 155 2.127383 CGCGCCGTCCTCAAAAAC 60.127 61.111 0.00 0.00 0.00 2.43
168 172 2.438434 CCACCATCGACAAGCCCC 60.438 66.667 0.00 0.00 0.00 5.80
199 203 4.676586 CAACGCGCCAAACCCGTC 62.677 66.667 5.73 0.00 33.59 4.79
223 228 2.034879 CGCTTTCCTGTCCGCACAT 61.035 57.895 0.00 0.00 0.00 3.21
224 229 2.664851 CGCTTTCCTGTCCGCACA 60.665 61.111 0.00 0.00 0.00 4.57
231 236 3.626924 ACCCGCTCGCTTTCCTGT 61.627 61.111 0.00 0.00 0.00 4.00
233 238 4.394712 CCACCCGCTCGCTTTCCT 62.395 66.667 0.00 0.00 0.00 3.36
262 267 5.982890 TCCACCTCATTTTCCTTCATTTC 57.017 39.130 0.00 0.00 0.00 2.17
266 271 4.081406 CACATCCACCTCATTTTCCTTCA 58.919 43.478 0.00 0.00 0.00 3.02
268 273 4.082125 GACACATCCACCTCATTTTCCTT 58.918 43.478 0.00 0.00 0.00 3.36
281 286 3.723772 CCAGTTGGTGACACATCCA 57.276 52.632 8.08 0.00 42.67 3.41
294 300 0.401395 TCCTTCCTGACCCACCAGTT 60.401 55.000 0.00 0.00 32.43 3.16
300 306 1.779061 GCCTTGTCCTTCCTGACCCA 61.779 60.000 0.00 0.00 34.25 4.51
301 307 1.002011 GCCTTGTCCTTCCTGACCC 60.002 63.158 0.00 0.00 34.25 4.46
304 310 2.592993 CCGGCCTTGTCCTTCCTGA 61.593 63.158 0.00 0.00 0.00 3.86
333 339 4.552365 ATGGACATGGAGCGGGCG 62.552 66.667 0.00 0.00 0.00 6.13
335 341 1.524621 GACATGGACATGGAGCGGG 60.525 63.158 15.94 0.00 42.91 6.13
343 349 4.081142 TCAGGTTTGTATCGACATGGACAT 60.081 41.667 0.00 0.00 34.86 3.06
347 353 3.861840 AGTCAGGTTTGTATCGACATGG 58.138 45.455 0.00 0.00 34.86 3.66
348 354 4.494484 TGAGTCAGGTTTGTATCGACATG 58.506 43.478 0.00 0.00 34.86 3.21
349 355 4.801330 TGAGTCAGGTTTGTATCGACAT 57.199 40.909 0.00 0.00 34.86 3.06
350 356 4.594123 TTGAGTCAGGTTTGTATCGACA 57.406 40.909 0.00 0.00 0.00 4.35
352 358 8.092068 TCTAAATTTGAGTCAGGTTTGTATCGA 58.908 33.333 0.00 0.00 0.00 3.59
356 362 7.444183 CAGGTCTAAATTTGAGTCAGGTTTGTA 59.556 37.037 0.00 1.88 0.00 2.41
370 376 5.220854 CGCGATCCATTTCAGGTCTAAATTT 60.221 40.000 0.00 0.00 0.00 1.82
377 383 1.089481 TGCGCGATCCATTTCAGGTC 61.089 55.000 12.10 0.00 0.00 3.85
389 395 0.372334 GTATTTTGTCCGTGCGCGAT 59.628 50.000 23.45 7.92 41.33 4.58
396 402 5.470098 GGATGAGCATATGTATTTTGTCCGT 59.530 40.000 4.29 0.00 0.00 4.69
402 408 9.066892 ACGTAAATGGATGAGCATATGTATTTT 57.933 29.630 4.29 0.00 0.00 1.82
403 409 8.621532 ACGTAAATGGATGAGCATATGTATTT 57.378 30.769 4.29 3.92 0.00 1.40
404 410 7.063426 CGACGTAAATGGATGAGCATATGTATT 59.937 37.037 4.29 0.00 0.00 1.89
405 411 6.531594 CGACGTAAATGGATGAGCATATGTAT 59.468 38.462 4.29 0.00 0.00 2.29
406 412 5.861787 CGACGTAAATGGATGAGCATATGTA 59.138 40.000 4.29 0.00 0.00 2.29
407 413 4.686091 CGACGTAAATGGATGAGCATATGT 59.314 41.667 4.29 0.00 0.00 2.29
408 414 4.091945 CCGACGTAAATGGATGAGCATATG 59.908 45.833 0.00 0.00 0.00 1.78
409 415 4.245660 CCGACGTAAATGGATGAGCATAT 58.754 43.478 0.00 0.00 0.00 1.78
410 416 3.649073 CCGACGTAAATGGATGAGCATA 58.351 45.455 0.00 0.00 0.00 3.14
411 417 2.483876 CCGACGTAAATGGATGAGCAT 58.516 47.619 0.00 0.00 0.00 3.79
412 418 1.934589 CCGACGTAAATGGATGAGCA 58.065 50.000 0.00 0.00 0.00 4.26
413 419 0.582005 GCCGACGTAAATGGATGAGC 59.418 55.000 0.00 0.00 0.00 4.26
414 420 0.852777 CGCCGACGTAAATGGATGAG 59.147 55.000 0.00 0.00 33.53 2.90
415 421 1.149361 GCGCCGACGTAAATGGATGA 61.149 55.000 0.00 0.00 42.83 2.92
416 422 1.275657 GCGCCGACGTAAATGGATG 59.724 57.895 0.00 0.00 42.83 3.51
417 423 0.531974 ATGCGCCGACGTAAATGGAT 60.532 50.000 4.18 0.00 42.83 3.41
418 424 0.741574 AATGCGCCGACGTAAATGGA 60.742 50.000 4.18 0.00 42.83 3.41
419 425 0.588730 CAATGCGCCGACGTAAATGG 60.589 55.000 4.18 0.00 42.83 3.16
420 426 0.588730 CCAATGCGCCGACGTAAATG 60.589 55.000 4.18 0.00 42.83 2.32
421 427 1.711060 CCCAATGCGCCGACGTAAAT 61.711 55.000 4.18 0.00 42.83 1.40
445 451 7.596995 TCTGTTTGGCTTAAAACGGATAAAATG 59.403 33.333 13.95 0.00 45.87 2.32
454 461 2.041244 GCGTCTGTTTGGCTTAAAACG 58.959 47.619 0.00 0.00 41.92 3.60
455 462 2.041244 CGCGTCTGTTTGGCTTAAAAC 58.959 47.619 0.00 4.05 39.90 2.43
457 464 0.040781 GCGCGTCTGTTTGGCTTAAA 60.041 50.000 8.43 0.00 0.00 1.52
460 467 4.012895 CGCGCGTCTGTTTGGCTT 62.013 61.111 24.19 0.00 0.00 4.35
477 484 2.148916 TCAACATGTCGACTGTCCAC 57.851 50.000 17.92 0.00 0.00 4.02
478 485 2.102420 ACTTCAACATGTCGACTGTCCA 59.898 45.455 17.92 6.11 0.00 4.02
479 486 2.755650 ACTTCAACATGTCGACTGTCC 58.244 47.619 17.92 0.00 0.00 4.02
488 495 5.220777 CGGTGTAAGAACAACTTCAACATGT 60.221 40.000 0.00 0.00 41.46 3.21
491 498 4.505808 TCGGTGTAAGAACAACTTCAACA 58.494 39.130 0.00 0.00 41.46 3.33
496 503 3.463944 CACCTCGGTGTAAGAACAACTT 58.536 45.455 7.93 0.00 41.46 2.66
510 517 1.308069 CCATGGCTTTGACACCTCGG 61.308 60.000 0.00 0.00 0.00 4.63
520 527 5.594317 CACCTAGCTTAATAACCATGGCTTT 59.406 40.000 13.04 5.63 0.00 3.51
538 545 6.701841 AGAACAAATATATGACACGCACCTAG 59.298 38.462 0.00 0.00 0.00 3.02
543 550 5.005299 CGTGAGAACAAATATATGACACGCA 59.995 40.000 0.00 0.00 40.93 5.24
555 562 6.204108 CCCTAAGTTACAACGTGAGAACAAAT 59.796 38.462 8.79 0.00 0.00 2.32
557 564 5.051816 CCCTAAGTTACAACGTGAGAACAA 58.948 41.667 8.79 0.00 0.00 2.83
558 565 4.501915 CCCCTAAGTTACAACGTGAGAACA 60.502 45.833 8.79 0.00 0.00 3.18
559 566 3.992427 CCCCTAAGTTACAACGTGAGAAC 59.008 47.826 0.00 0.00 0.00 3.01
560 567 3.555586 GCCCCTAAGTTACAACGTGAGAA 60.556 47.826 0.00 0.00 0.00 2.87
561 568 2.028748 GCCCCTAAGTTACAACGTGAGA 60.029 50.000 0.00 0.00 0.00 3.27
562 569 2.289195 TGCCCCTAAGTTACAACGTGAG 60.289 50.000 0.00 0.00 0.00 3.51
563 570 1.693062 TGCCCCTAAGTTACAACGTGA 59.307 47.619 0.00 0.00 0.00 4.35
564 571 2.172851 TGCCCCTAAGTTACAACGTG 57.827 50.000 0.00 0.00 0.00 4.49
565 572 4.765813 ATATGCCCCTAAGTTACAACGT 57.234 40.909 0.00 0.00 0.00 3.99
566 573 5.816919 CAAATATGCCCCTAAGTTACAACG 58.183 41.667 0.00 0.00 0.00 4.10
615 626 5.984926 ACTGCTATGTACTCTACGTCTCTAC 59.015 44.000 0.00 0.00 0.00 2.59
616 627 6.159299 ACTGCTATGTACTCTACGTCTCTA 57.841 41.667 0.00 0.00 0.00 2.43
617 628 5.026038 ACTGCTATGTACTCTACGTCTCT 57.974 43.478 0.00 0.00 0.00 3.10
618 629 5.738118 AACTGCTATGTACTCTACGTCTC 57.262 43.478 0.00 0.00 0.00 3.36
621 632 6.998968 ACTAAACTGCTATGTACTCTACGT 57.001 37.500 0.00 0.00 0.00 3.57
622 633 9.947669 ATTAACTAAACTGCTATGTACTCTACG 57.052 33.333 0.00 0.00 0.00 3.51
630 641 8.395633 CGCCTTAAATTAACTAAACTGCTATGT 58.604 33.333 0.00 0.00 0.00 2.29
631 642 8.609176 TCGCCTTAAATTAACTAAACTGCTATG 58.391 33.333 0.00 0.00 0.00 2.23
633 644 7.820872 AGTCGCCTTAAATTAACTAAACTGCTA 59.179 33.333 0.00 0.00 0.00 3.49
634 645 6.653740 AGTCGCCTTAAATTAACTAAACTGCT 59.346 34.615 0.00 0.00 0.00 4.24
635 646 6.741358 CAGTCGCCTTAAATTAACTAAACTGC 59.259 38.462 0.00 0.00 0.00 4.40
636 647 7.803724 ACAGTCGCCTTAAATTAACTAAACTG 58.196 34.615 0.00 0.00 36.28 3.16
637 648 7.658575 TGACAGTCGCCTTAAATTAACTAAACT 59.341 33.333 0.00 0.00 0.00 2.66
638 649 7.743400 GTGACAGTCGCCTTAAATTAACTAAAC 59.257 37.037 2.32 0.00 0.00 2.01
639 650 7.441760 TGTGACAGTCGCCTTAAATTAACTAAA 59.558 33.333 11.68 0.00 0.00 1.85
640 651 6.930164 TGTGACAGTCGCCTTAAATTAACTAA 59.070 34.615 11.68 0.00 0.00 2.24
642 653 5.178809 GTGTGACAGTCGCCTTAAATTAACT 59.821 40.000 11.68 0.00 0.00 2.24
643 654 5.379827 GTGTGACAGTCGCCTTAAATTAAC 58.620 41.667 11.68 0.00 0.00 2.01
857 892 2.310779 TGGATCCGGGATAGGAGAAG 57.689 55.000 10.08 0.00 44.55 2.85
879 914 0.310854 CGGACCAACCTGCTTTTGTC 59.689 55.000 0.00 0.00 36.31 3.18
881 916 1.007387 GCGGACCAACCTGCTTTTG 60.007 57.895 0.00 0.00 36.08 2.44
1206 1241 1.330655 GCTTCTCCGAGGTCCCATCA 61.331 60.000 0.00 0.00 0.00 3.07
1419 1459 3.828875 AACTAAGATCAGTAGCAGGGC 57.171 47.619 0.00 0.00 0.00 5.19
1525 1565 5.104527 AGCACTTGCATATAAACTAGACCCA 60.105 40.000 3.62 0.00 45.16 4.51
1677 1717 6.532657 AGGTAATGAAAAGTATAACACCGACG 59.467 38.462 0.00 0.00 0.00 5.12
1770 1810 9.764363 AAACAAATAAAAAGGATCTCCAGAAAC 57.236 29.630 0.00 0.00 38.89 2.78
1842 1882 7.882791 TGATTGATACCTTGTTACACAGTGATT 59.117 33.333 7.81 0.00 0.00 2.57
2049 2089 5.699097 TTGTTACCAACAGCATCCTAAAC 57.301 39.130 0.00 0.00 43.27 2.01
2061 2101 7.312154 TCATAACATGCAGATTTGTTACCAAC 58.688 34.615 11.72 0.00 40.15 3.77
2397 2437 7.080353 TCACAGATGCTTCATCAAATTACAG 57.920 36.000 9.19 0.00 42.72 2.74
2600 2685 6.818644 TCTGGATAATAAAGCAACAGAGTCAC 59.181 38.462 0.00 0.00 0.00 3.67
2631 2716 1.532437 TGCAGTTTCTTGTCAGATGCG 59.468 47.619 0.00 0.00 35.93 4.73
2649 2734 3.795623 ATGTGGAAAATCAGATGCTGC 57.204 42.857 0.00 0.00 0.00 5.25
2675 2760 9.630098 CTGCACAAAACATATTAAGAAACTGAT 57.370 29.630 0.00 0.00 0.00 2.90
2889 2974 3.779850 ATGCATACCCAGGGCTGCG 62.780 63.158 22.77 5.04 37.44 5.18
2890 2975 1.044790 AAATGCATACCCAGGGCTGC 61.045 55.000 21.98 21.98 35.89 5.25
3077 3163 3.334583 TGGTGCTAGTGAGAAACCATC 57.665 47.619 0.00 0.00 36.52 3.51
3361 3447 4.109766 GCCACAACACAAGGAGTTAAAAC 58.890 43.478 0.00 0.00 0.00 2.43
3427 3514 1.337071 TGTTCTGCGGGAGATATCGTC 59.663 52.381 0.00 0.00 0.00 4.20
3604 3691 0.529378 AAAGAACTACGACGGGCGAT 59.471 50.000 11.73 0.00 44.57 4.58
3662 3749 7.663081 TGGCCAAAATTAAGTTCAATTATTGCA 59.337 29.630 0.61 0.00 0.00 4.08
3663 3750 8.038492 TGGCCAAAATTAAGTTCAATTATTGC 57.962 30.769 0.61 0.00 0.00 3.56
3670 3757 9.956640 AAATGATATGGCCAAAATTAAGTTCAA 57.043 25.926 10.96 0.00 0.00 2.69
3679 3766 9.365906 TGACTATGTAAATGATATGGCCAAAAT 57.634 29.630 10.96 6.59 0.00 1.82
3680 3767 8.759481 TGACTATGTAAATGATATGGCCAAAA 57.241 30.769 10.96 0.12 0.00 2.44
3681 3768 8.217111 TCTGACTATGTAAATGATATGGCCAAA 58.783 33.333 10.96 0.00 0.00 3.28
3682 3769 7.744733 TCTGACTATGTAAATGATATGGCCAA 58.255 34.615 10.96 0.00 0.00 4.52
3683 3770 7.315066 TCTGACTATGTAAATGATATGGCCA 57.685 36.000 8.56 8.56 0.00 5.36
3684 3771 8.621532 TTTCTGACTATGTAAATGATATGGCC 57.378 34.615 0.00 0.00 0.00 5.36
3699 3786 7.711772 CTGAAAGATGCAGAGATTTCTGACTAT 59.288 37.037 17.06 7.46 45.51 2.12
3700 3787 7.040494 CTGAAAGATGCAGAGATTTCTGACTA 58.960 38.462 17.06 3.01 45.51 2.59
3701 3788 5.875910 CTGAAAGATGCAGAGATTTCTGACT 59.124 40.000 17.06 9.24 45.51 3.41
3702 3789 5.642919 ACTGAAAGATGCAGAGATTTCTGAC 59.357 40.000 17.06 8.71 45.46 3.51
3703 3790 5.802465 ACTGAAAGATGCAGAGATTTCTGA 58.198 37.500 17.06 3.06 45.46 3.27
3704 3791 5.875910 AGACTGAAAGATGCAGAGATTTCTG 59.124 40.000 8.88 8.88 45.42 3.02
3705 3792 6.052405 AGACTGAAAGATGCAGAGATTTCT 57.948 37.500 13.49 0.00 37.43 2.52
3706 3793 6.740411 AAGACTGAAAGATGCAGAGATTTC 57.260 37.500 0.00 0.72 37.43 2.17
3707 3794 6.569994 GCAAAGACTGAAAGATGCAGAGATTT 60.570 38.462 0.00 0.00 37.43 2.17
3708 3795 5.106237 GCAAAGACTGAAAGATGCAGAGATT 60.106 40.000 0.00 0.00 37.43 2.40
3709 3796 4.395542 GCAAAGACTGAAAGATGCAGAGAT 59.604 41.667 0.00 0.00 37.43 2.75
3710 3797 3.750130 GCAAAGACTGAAAGATGCAGAGA 59.250 43.478 0.00 0.00 37.43 3.10
3711 3798 3.501062 TGCAAAGACTGAAAGATGCAGAG 59.499 43.478 0.00 0.00 37.67 3.35
3712 3799 3.479489 TGCAAAGACTGAAAGATGCAGA 58.521 40.909 0.00 0.00 37.67 4.26
3713 3800 3.909776 TGCAAAGACTGAAAGATGCAG 57.090 42.857 0.00 0.00 37.67 4.41
3714 3801 4.859304 ATTGCAAAGACTGAAAGATGCA 57.141 36.364 1.71 0.00 39.50 3.96
3715 3802 7.543172 TCAATTATTGCAAAGACTGAAAGATGC 59.457 33.333 1.71 0.00 37.43 3.91
3716 3803 8.975410 TCAATTATTGCAAAGACTGAAAGATG 57.025 30.769 1.71 0.00 37.43 2.90
3717 3804 9.415544 GTTCAATTATTGCAAAGACTGAAAGAT 57.584 29.630 1.71 0.00 37.43 2.40
3718 3805 8.632679 AGTTCAATTATTGCAAAGACTGAAAGA 58.367 29.630 1.71 0.00 37.43 2.52
3719 3806 8.807667 AGTTCAATTATTGCAAAGACTGAAAG 57.192 30.769 1.71 0.00 42.29 2.62
3728 3815 9.890352 GCCAAAATTAAGTTCAATTATTGCAAA 57.110 25.926 1.71 0.00 0.00 3.68
3729 3816 8.510505 GGCCAAAATTAAGTTCAATTATTGCAA 58.489 29.630 0.00 0.00 0.00 4.08
3787 3874 7.775561 AGATTGAACTTCCATATAAGGTTCCAC 59.224 37.037 8.76 3.22 0.00 4.02
3836 3923 1.660333 CGGAGCTCAAAAACGCTTCAC 60.660 52.381 17.19 0.00 36.45 3.18
3845 3932 2.642154 TAAACCCACGGAGCTCAAAA 57.358 45.000 17.19 0.00 0.00 2.44
3855 3942 6.032670 GCGTAACACAAATAAATAAACCCACG 59.967 38.462 0.00 0.00 0.00 4.94
3939 4054 0.110373 GCGTAACCGAACAAAGCCTG 60.110 55.000 0.00 0.00 35.63 4.85
3941 4056 1.208358 GGCGTAACCGAACAAAGCC 59.792 57.895 0.00 0.00 35.63 4.35
3947 4062 1.142531 CCCTAGGGCGTAACCGAAC 59.857 63.158 16.90 0.00 40.62 3.95
3959 4074 0.324943 CCGATTACATGCCCCCTAGG 59.675 60.000 0.06 0.06 39.47 3.02
3960 4075 1.002087 GACCGATTACATGCCCCCTAG 59.998 57.143 0.00 0.00 0.00 3.02
3964 4079 0.107410 TGTGACCGATTACATGCCCC 60.107 55.000 0.00 0.00 0.00 5.80
3966 4081 1.665679 CACTGTGACCGATTACATGCC 59.334 52.381 0.32 0.00 0.00 4.40
3967 4082 1.062587 GCACTGTGACCGATTACATGC 59.937 52.381 12.86 0.00 0.00 4.06
4029 4211 1.210478 AGTGAATCAGGATGGGAACGG 59.790 52.381 0.00 0.00 36.16 4.44
4045 4227 0.904649 AAGATGTCGATGGGCAGTGA 59.095 50.000 0.00 0.00 0.00 3.41
4067 4275 2.039418 TGTGAGGCAGACACAACTACT 58.961 47.619 9.08 0.00 43.73 2.57
4137 6602 1.442017 GCAATGGAAACGACCGTGC 60.442 57.895 0.00 0.32 36.77 5.34
4151 6616 4.041917 CGGCGGCACAACAGCAAT 62.042 61.111 10.53 0.00 41.85 3.56
4321 6792 2.515854 ACGTAACAGAGAGAGAAGGCA 58.484 47.619 0.00 0.00 0.00 4.75
4332 6803 2.153645 TCGCTCAGGTAACGTAACAGA 58.846 47.619 0.00 0.00 46.39 3.41
4333 6804 2.624316 TCGCTCAGGTAACGTAACAG 57.376 50.000 0.00 0.00 46.39 3.16
4335 6806 3.504863 TCATTCGCTCAGGTAACGTAAC 58.495 45.455 0.00 0.00 46.39 2.50
4336 6807 3.853831 TCATTCGCTCAGGTAACGTAA 57.146 42.857 0.00 0.00 46.39 3.18
4337 6808 3.504863 GTTCATTCGCTCAGGTAACGTA 58.495 45.455 0.00 0.00 46.39 3.57
4338 6809 2.334838 GTTCATTCGCTCAGGTAACGT 58.665 47.619 0.00 0.00 46.39 3.99
4339 6810 1.659098 GGTTCATTCGCTCAGGTAACG 59.341 52.381 0.00 0.00 46.39 3.18
4341 6812 3.410631 TTGGTTCATTCGCTCAGGTAA 57.589 42.857 0.00 0.00 0.00 2.85
4342 6813 3.071479 GTTTGGTTCATTCGCTCAGGTA 58.929 45.455 0.00 0.00 0.00 3.08
4343 6814 1.880027 GTTTGGTTCATTCGCTCAGGT 59.120 47.619 0.00 0.00 0.00 4.00
4345 6816 3.624326 TTGTTTGGTTCATTCGCTCAG 57.376 42.857 0.00 0.00 0.00 3.35
4371 6988 2.432444 CGGCTGTAATGGGACTTTTGA 58.568 47.619 0.00 0.00 0.00 2.69
4405 7022 3.400054 GGCCCTGCCCTAACGAGT 61.400 66.667 0.00 0.00 44.06 4.18
4428 7045 2.043953 AGGGCCTCGGATTTTGCC 60.044 61.111 0.00 0.00 43.26 4.52
4429 7046 1.678970 ACAGGGCCTCGGATTTTGC 60.679 57.895 0.95 0.00 0.00 3.68
4430 7047 1.937546 GCACAGGGCCTCGGATTTTG 61.938 60.000 0.95 0.00 36.11 2.44
4431 7048 1.678970 GCACAGGGCCTCGGATTTT 60.679 57.895 0.95 0.00 36.11 1.82
4432 7049 2.044946 GCACAGGGCCTCGGATTT 60.045 61.111 0.95 0.00 36.11 2.17
4433 7050 2.424842 TTTGCACAGGGCCTCGGATT 62.425 55.000 0.95 0.00 43.89 3.01
4434 7051 2.424842 TTTTGCACAGGGCCTCGGAT 62.425 55.000 0.95 0.00 43.89 4.18
4435 7052 3.126703 TTTTGCACAGGGCCTCGGA 62.127 57.895 0.95 0.00 43.89 4.55
4436 7053 2.597217 TTTTGCACAGGGCCTCGG 60.597 61.111 0.95 0.00 43.89 4.63
4437 7054 0.605319 TAGTTTTGCACAGGGCCTCG 60.605 55.000 0.95 1.63 43.89 4.63
4438 7055 1.616159 TTAGTTTTGCACAGGGCCTC 58.384 50.000 0.95 0.00 43.89 4.70
4439 7056 2.080654 TTTAGTTTTGCACAGGGCCT 57.919 45.000 0.00 0.00 43.89 5.19
4440 7057 2.900716 TTTTAGTTTTGCACAGGGCC 57.099 45.000 0.00 0.00 43.89 5.80


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

AutoCloner maintained by Alex Coulton.