Multiple sequence alignment - TraesCS5D01G086400

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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 TraesCS5D01G086400 chr5D 100.000 4706 0 0 1 4706 91630775 91626070 0.000000e+00 8691.0
1 TraesCS5D01G086400 chr5D 96.817 377 12 0 1 377 91614366 91613990 8.590000e-177 630.0
2 TraesCS5D01G086400 chr5D 95.491 377 16 1 1 377 91840956 91840581 6.740000e-168 601.0
3 TraesCS5D01G086400 chr5D 99.000 100 1 0 532 631 91613995 91613896 3.740000e-41 180.0
4 TraesCS5D01G086400 chr5D 95.000 100 5 0 532 631 91840586 91840487 1.750000e-34 158.0
5 TraesCS5D01G086400 chr5D 78.607 201 29 8 2415 2602 509439280 509439081 2.300000e-23 121.0
6 TraesCS5D01G086400 chr5D 78.155 206 31 7 2410 2602 509443806 509443602 8.270000e-23 119.0
7 TraesCS5D01G086400 chr5A 95.045 2583 78 15 738 3288 85288048 85285484 0.000000e+00 4015.0
8 TraesCS5D01G086400 chr5A 97.347 1206 31 1 3283 4487 85271841 85270636 0.000000e+00 2049.0
9 TraesCS5D01G086400 chr5A 96.552 377 13 0 1 377 85263371 85262995 4.000000e-175 625.0
10 TraesCS5D01G086400 chr5A 94.430 377 21 0 1 377 85290971 85290595 8.780000e-162 580.0
11 TraesCS5D01G086400 chr5A 97.309 223 6 0 4484 4706 85270329 85270107 3.440000e-101 379.0
12 TraesCS5D01G086400 chr5A 97.959 98 2 0 532 629 85263000 85262903 2.250000e-38 171.0
13 TraesCS5D01G086400 chr5A 96.939 98 3 0 532 629 85289233 85289136 1.050000e-36 165.0
14 TraesCS5D01G086400 chr5A 91.262 103 4 4 651 749 85288232 85288131 8.210000e-28 135.0
15 TraesCS5D01G086400 chr5A 77.778 207 32 8 2409 2602 636641959 636641754 1.070000e-21 115.0
16 TraesCS5D01G086400 chr5B 94.960 377 19 0 1 377 96885496 96885120 4.060000e-165 592.0
17 TraesCS5D01G086400 chr5B 99.000 100 1 0 532 631 96885125 96885026 3.740000e-41 180.0
18 TraesCS5D01G086400 chr5B 78.537 205 30 6 2411 2602 639966285 639966082 6.400000e-24 122.0
19 TraesCS5D01G086400 chr5B 78.469 209 29 9 2409 2602 639970018 639969811 6.400000e-24 122.0
20 TraesCS5D01G086400 chr5B 78.155 206 30 8 2411 2602 640125659 640125455 2.980000e-22 117.0
21 TraesCS5D01G086400 chr4B 94.611 167 9 0 366 532 63753837 63754003 4.670000e-65 259.0
22 TraesCS5D01G086400 chr3A 95.122 164 8 0 370 533 659527391 659527228 4.670000e-65 259.0
23 TraesCS5D01G086400 chr2D 95.062 162 8 0 370 531 445733832 445733671 6.040000e-64 255.0
24 TraesCS5D01G086400 chr2D 94.479 163 8 1 370 532 81574924 81575085 2.810000e-62 250.0
25 TraesCS5D01G086400 chr2D 96.226 53 2 0 4527 4579 559218345 559218397 2.330000e-13 87.9
26 TraesCS5D01G086400 chr3D 94.479 163 9 0 370 532 238999414 238999576 7.820000e-63 252.0
27 TraesCS5D01G086400 chr3D 94.479 163 9 0 369 531 410670062 410670224 7.820000e-63 252.0
28 TraesCS5D01G086400 chr3D 94.479 163 9 0 370 532 540255705 540255543 7.820000e-63 252.0
29 TraesCS5D01G086400 chr3B 93.976 166 9 1 366 531 183601083 183601247 2.810000e-62 250.0
30 TraesCS5D01G086400 chr7D 90.608 181 16 1 354 534 419198834 419199013 6.090000e-59 239.0
31 TraesCS5D01G086400 chrUn 77.833 203 31 6 2412 2600 80172433 80172635 3.850000e-21 113.0
32 TraesCS5D01G086400 chr6B 81.250 144 21 2 2465 2602 46671520 46671377 1.380000e-20 111.0


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 TraesCS5D01G086400 chr5D 91626070 91630775 4705 True 8691.00 8691 100.000 1 4706 1 chr5D.!!$R1 4705
1 TraesCS5D01G086400 chr5A 85285484 85290971 5487 True 1223.75 4015 94.419 1 3288 4 chr5A.!!$R4 3287
2 TraesCS5D01G086400 chr5A 85270107 85271841 1734 True 1214.00 2049 97.328 3283 4706 2 chr5A.!!$R3 1423

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
384 385 0.252103 TTGCTACTCCCTCCGTTCCT 60.252 55.000 0.00 0.00 0.00 3.36 F
736 2826 0.899717 GACATGGCATGGTGTTGGGT 60.900 55.000 29.49 7.54 33.60 4.51 F
1388 3580 0.911769 AGGTTTGCCGATCAGATCCA 59.088 50.000 4.73 0.00 40.50 3.41 F
1824 4016 1.615883 AGTGAGCGGCATCTTATCGAT 59.384 47.619 2.16 2.16 0.00 3.59 F
3420 5639 1.410850 GGAGATGGATTGCCGAGGGA 61.411 60.000 0.00 0.00 36.79 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1375 3567 0.179062 AGTTGCTGGATCTGATCGGC 60.179 55.0 19.96 19.96 0.00 5.54 R
1570 3762 0.456221 TTCACCGGATCGCTCTCTTC 59.544 55.0 9.46 0.00 0.00 2.87 R
3090 5309 0.680921 TAGGGCATTCAGCTGCAACC 60.681 55.0 9.47 7.58 44.12 3.77 R
3633 5852 0.033504 ACCTGCGAATCTTGTCACGT 59.966 50.0 0.00 0.00 0.00 4.49 R
4657 7187 0.038343 CAAAAGGTGTTGGATGCCGG 60.038 55.0 0.00 0.00 0.00 6.13 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
28 29 3.065786 CAGTTCAGACAACTGTGTGCATT 59.934 43.478 6.36 0.00 43.81 3.56
47 48 1.236616 TGGCATTGGCTCAGTGAACG 61.237 55.000 11.84 0.00 40.87 3.95
89 90 2.751806 CTCAGGTTCAGATTTCAAGCCC 59.248 50.000 0.00 0.00 0.00 5.19
114 115 6.471841 CGAGAAAATAGTGATGTCAGTGAGAG 59.528 42.308 0.00 0.00 0.00 3.20
144 145 2.744202 CGGAGATCAAGAAACTTGGTGG 59.256 50.000 10.84 0.00 0.00 4.61
145 146 3.084786 GGAGATCAAGAAACTTGGTGGG 58.915 50.000 10.84 0.00 0.00 4.61
222 223 1.509644 CCCATGACGGCGATCATTGG 61.510 60.000 16.62 18.81 37.20 3.16
236 237 3.845781 TCATTGGATCTAGGAAGGTGC 57.154 47.619 0.00 0.00 0.00 5.01
262 263 4.329545 GTGCCCTCCCAACGCTGA 62.330 66.667 0.00 0.00 0.00 4.26
358 359 4.153117 ACGCTTCATCTCAACTGAATTGTC 59.847 41.667 0.00 0.00 39.54 3.18
373 374 6.545504 TGAATTGTCAGTTCTTTGCTACTC 57.454 37.500 9.24 0.00 0.00 2.59
377 378 3.006967 TGTCAGTTCTTTGCTACTCCCTC 59.993 47.826 0.00 0.00 0.00 4.30
378 379 2.567615 TCAGTTCTTTGCTACTCCCTCC 59.432 50.000 0.00 0.00 0.00 4.30
379 380 1.550976 AGTTCTTTGCTACTCCCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
381 382 1.640917 TCTTTGCTACTCCCTCCGTT 58.359 50.000 0.00 0.00 0.00 4.44
382 383 1.549170 TCTTTGCTACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
383 384 0.611714 TTTGCTACTCCCTCCGTTCC 59.388 55.000 0.00 0.00 0.00 3.62
384 385 0.252103 TTGCTACTCCCTCCGTTCCT 60.252 55.000 0.00 0.00 0.00 3.36
387 388 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
388 389 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
389 390 3.893813 GCTACTCCCTCCGTTCCTAAATA 59.106 47.826 0.00 0.00 0.00 1.40
390 391 4.261952 GCTACTCCCTCCGTTCCTAAATAC 60.262 50.000 0.00 0.00 0.00 1.89
391 392 3.716431 ACTCCCTCCGTTCCTAAATACA 58.284 45.455 0.00 0.00 0.00 2.29
393 394 4.161754 ACTCCCTCCGTTCCTAAATACAAG 59.838 45.833 0.00 0.00 0.00 3.16
394 395 4.098894 TCCCTCCGTTCCTAAATACAAGT 58.901 43.478 0.00 0.00 0.00 3.16
395 396 4.161001 TCCCTCCGTTCCTAAATACAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
398 399 6.171213 CCTCCGTTCCTAAATACAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
399 400 6.092259 CCTCCGTTCCTAAATACAAGTCTTTG 59.908 42.308 0.00 0.00 40.24 2.77
415 416 9.429359 ACAAGTCTTTGTAGAGATTTCACTATG 57.571 33.333 0.00 0.00 45.45 2.23
429 430 4.811969 TCACTATGAAACACATACGGGT 57.188 40.909 0.00 0.00 40.07 5.28
430 431 4.500127 TCACTATGAAACACATACGGGTG 58.500 43.478 3.06 3.06 44.35 4.61
442 443 5.961272 CACATACGGGTGTATATAGATGCA 58.039 41.667 0.00 0.00 39.28 3.96
443 444 6.573434 CACATACGGGTGTATATAGATGCAT 58.427 40.000 0.00 0.00 39.28 3.96
444 445 7.041721 CACATACGGGTGTATATAGATGCATT 58.958 38.462 0.00 0.00 39.28 3.56
445 446 7.549134 CACATACGGGTGTATATAGATGCATTT 59.451 37.037 0.00 0.00 39.28 2.32
446 447 8.100791 ACATACGGGTGTATATAGATGCATTTT 58.899 33.333 0.00 0.00 39.28 1.82
447 448 9.594478 CATACGGGTGTATATAGATGCATTTTA 57.406 33.333 0.00 0.00 39.28 1.52
448 449 9.817809 ATACGGGTGTATATAGATGCATTTTAG 57.182 33.333 0.00 0.00 39.52 1.85
449 450 7.903145 ACGGGTGTATATAGATGCATTTTAGA 58.097 34.615 0.00 0.00 29.77 2.10
450 451 8.035394 ACGGGTGTATATAGATGCATTTTAGAG 58.965 37.037 0.00 0.00 29.77 2.43
451 452 8.035394 CGGGTGTATATAGATGCATTTTAGAGT 58.965 37.037 0.00 0.00 29.77 3.24
472 473 8.885494 AGAGTATAGATTCACTCATTTTGCTC 57.115 34.615 4.70 0.00 42.99 4.26
473 474 7.930865 AGAGTATAGATTCACTCATTTTGCTCC 59.069 37.037 4.70 0.00 42.99 4.70
474 475 5.998454 ATAGATTCACTCATTTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
475 476 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
476 477 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
477 478 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
478 479 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
479 480 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
480 481 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
481 482 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
482 483 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
483 484 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
484 485 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
485 486 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
486 487 1.466856 TTGCTCCGTATGTAGTCCGT 58.533 50.000 0.00 0.00 0.00 4.69
487 488 2.330440 TGCTCCGTATGTAGTCCGTA 57.670 50.000 0.00 0.00 0.00 4.02
488 489 2.216046 TGCTCCGTATGTAGTCCGTAG 58.784 52.381 0.00 0.00 0.00 3.51
489 490 2.216898 GCTCCGTATGTAGTCCGTAGT 58.783 52.381 0.00 0.00 0.00 2.73
490 491 3.181466 TGCTCCGTATGTAGTCCGTAGTA 60.181 47.826 0.00 0.00 0.00 1.82
491 492 3.431572 GCTCCGTATGTAGTCCGTAGTAG 59.568 52.174 0.00 0.00 0.00 2.57
492 493 4.797604 GCTCCGTATGTAGTCCGTAGTAGA 60.798 50.000 0.00 0.00 0.00 2.59
493 494 5.276461 TCCGTATGTAGTCCGTAGTAGAA 57.724 43.478 0.00 0.00 0.00 2.10
494 495 5.858381 TCCGTATGTAGTCCGTAGTAGAAT 58.142 41.667 0.00 0.00 0.00 2.40
495 496 6.993079 TCCGTATGTAGTCCGTAGTAGAATA 58.007 40.000 0.00 0.00 0.00 1.75
496 497 7.615403 TCCGTATGTAGTCCGTAGTAGAATAT 58.385 38.462 0.00 0.00 0.00 1.28
497 498 7.761704 TCCGTATGTAGTCCGTAGTAGAATATC 59.238 40.741 0.00 0.00 0.00 1.63
498 499 7.763528 CCGTATGTAGTCCGTAGTAGAATATCT 59.236 40.741 0.00 0.00 0.00 1.98
499 500 9.794685 CGTATGTAGTCCGTAGTAGAATATCTA 57.205 37.037 0.00 0.00 0.00 1.98
524 525 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
525 526 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
526 527 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
527 528 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
528 529 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
529 530 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
530 531 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
562 1770 0.917533 AGCATCTCCAGCCAGAACAT 59.082 50.000 0.00 0.00 0.00 2.71
569 1777 2.943690 CTCCAGCCAGAACATGATCAAG 59.056 50.000 0.00 0.00 0.00 3.02
596 1804 3.093057 TCAGCTCTACCTCCTCAAGAAC 58.907 50.000 0.00 0.00 0.00 3.01
671 2761 6.267471 AGCTGCTCTAGATGCTCTTATAAGTT 59.733 38.462 12.19 0.00 0.00 2.66
703 2793 2.741878 GCAGTTTAGGGAGCGCTGATAA 60.742 50.000 18.48 8.14 0.00 1.75
713 2803 2.408050 AGCGCTGATAACGATGGATTC 58.592 47.619 10.39 0.00 0.00 2.52
733 2823 1.666599 CGTTGACATGGCATGGTGTTG 60.667 52.381 29.49 13.52 33.60 3.33
734 2824 0.967662 TTGACATGGCATGGTGTTGG 59.032 50.000 29.49 4.81 33.60 3.77
736 2826 0.899717 GACATGGCATGGTGTTGGGT 60.900 55.000 29.49 7.54 33.60 4.51
764 2951 7.661847 GGTGTAGTGGGGATAAGATTAATCAAG 59.338 40.741 17.56 0.00 0.00 3.02
765 2952 7.173390 GTGTAGTGGGGATAAGATTAATCAAGC 59.827 40.741 17.56 7.73 0.00 4.01
766 2953 6.521527 AGTGGGGATAAGATTAATCAAGCT 57.478 37.500 17.56 2.04 29.66 3.74
767 2954 7.633018 AGTGGGGATAAGATTAATCAAGCTA 57.367 36.000 17.56 4.08 28.03 3.32
768 2955 7.684529 AGTGGGGATAAGATTAATCAAGCTAG 58.315 38.462 17.56 0.00 28.03 3.42
814 3002 3.044986 CCACTTCAACGCATTGACTTTG 58.955 45.455 0.00 0.00 44.66 2.77
847 3035 1.344226 GGCCAAGCATCGAAAAACGC 61.344 55.000 0.00 0.00 42.26 4.84
930 3118 3.205338 CATCGTGTTGCAATATCCCTGA 58.795 45.455 0.59 0.00 0.00 3.86
976 3164 4.406456 TCACAATCCAGCCACTAAACATT 58.594 39.130 0.00 0.00 0.00 2.71
978 3166 4.022068 CACAATCCAGCCACTAAACATTGT 60.022 41.667 0.00 0.00 34.16 2.71
985 3173 2.162408 GCCACTAAACATTGTGAGGAGC 59.838 50.000 0.00 0.00 36.38 4.70
986 3174 3.411446 CCACTAAACATTGTGAGGAGCA 58.589 45.455 0.00 0.00 36.38 4.26
993 3181 1.277580 ATTGTGAGGAGCAGGGAGGG 61.278 60.000 0.00 0.00 0.00 4.30
1128 3317 1.542547 GGCGTCAAGAAGAAGGTGGAA 60.543 52.381 0.00 0.00 0.00 3.53
1162 3351 4.818642 AGAGCTGATCACCATCAATATCG 58.181 43.478 0.00 0.00 38.63 2.92
1176 3365 3.321111 TCAATATCGCCCTGGAGAAGTAC 59.679 47.826 0.00 0.00 0.00 2.73
1224 3416 2.125512 AGCGCCTGGATGAACGAC 60.126 61.111 2.29 0.00 0.00 4.34
1225 3417 3.554692 GCGCCTGGATGAACGACG 61.555 66.667 0.00 0.00 0.00 5.12
1306 3498 2.446994 AACCACCCGGGAGTGTCA 60.447 61.111 32.02 0.00 41.15 3.58
1320 3512 2.438434 GTCACCGGCATCAAGGGG 60.438 66.667 0.00 0.00 0.00 4.79
1324 3516 3.801997 CCGGCATCAAGGGGCTCT 61.802 66.667 0.00 0.00 0.00 4.09
1370 3562 7.658179 TGAAGAAGCTTAAATATCGCCATAG 57.342 36.000 0.00 0.00 0.00 2.23
1374 3566 6.998673 AGAAGCTTAAATATCGCCATAGGTTT 59.001 34.615 0.00 0.00 0.00 3.27
1375 3567 6.560253 AGCTTAAATATCGCCATAGGTTTG 57.440 37.500 0.00 0.00 0.00 2.93
1377 3569 5.699097 TTAAATATCGCCATAGGTTTGCC 57.301 39.130 0.00 0.00 0.00 4.52
1378 3570 1.808411 ATATCGCCATAGGTTTGCCG 58.192 50.000 0.00 0.00 40.50 5.69
1388 3580 0.911769 AGGTTTGCCGATCAGATCCA 59.088 50.000 4.73 0.00 40.50 3.41
1419 3611 2.365582 GCCCTTGTGAACGGAACATAT 58.634 47.619 0.00 0.00 0.00 1.78
1464 3656 2.012673 GATGACTGCAATCCTGGTGTC 58.987 52.381 0.00 0.00 0.00 3.67
1570 3762 6.422100 AGAATTAATCAGTCGGTTCATCGATG 59.578 38.462 19.61 19.61 41.40 3.84
1578 3770 2.123342 CGGTTCATCGATGAAGAGAGC 58.877 52.381 35.04 24.05 46.44 4.09
1594 3786 2.125512 GCGATCCGGTGAAGCAGT 60.126 61.111 0.00 0.00 0.00 4.40
1617 3809 2.749621 CAGGGTTGTCTCTATTGTTGGC 59.250 50.000 0.00 0.00 0.00 4.52
1671 3863 8.398665 GCTAATCAGGTGTACCAGAAAATTAAG 58.601 37.037 3.56 0.00 35.11 1.85
1674 3866 5.073965 TCAGGTGTACCAGAAAATTAAGGGT 59.926 40.000 3.56 0.00 38.89 4.34
1676 3868 6.943718 CAGGTGTACCAGAAAATTAAGGGTAA 59.056 38.462 3.56 0.00 35.99 2.85
1707 3899 5.610398 TGTTCTGCTTTTGTCTCTGTATCA 58.390 37.500 0.00 0.00 0.00 2.15
1710 3902 4.022329 TCTGCTTTTGTCTCTGTATCACGA 60.022 41.667 0.00 0.00 0.00 4.35
1718 3910 4.142447 TGTCTCTGTATCACGAAAGCCTAC 60.142 45.833 0.00 0.00 0.00 3.18
1736 3928 4.708177 CCTACCATGGTTAACATCCTGAG 58.292 47.826 25.38 9.87 37.84 3.35
1748 3940 3.424640 TCCTGAGGGATTTGCTCCT 57.575 52.632 0.00 0.00 44.28 3.69
1763 3955 2.003301 GCTCCTGGAAATCGAGAACAC 58.997 52.381 0.00 0.00 0.00 3.32
1824 4016 1.615883 AGTGAGCGGCATCTTATCGAT 59.384 47.619 2.16 2.16 0.00 3.59
1842 4034 3.504134 TCGATAGGCTAAGAGCACATCTC 59.496 47.826 0.00 0.00 44.75 2.75
1848 4040 3.873952 GGCTAAGAGCACATCTCGAAAAT 59.126 43.478 0.21 0.00 44.75 1.82
1849 4041 4.025313 GGCTAAGAGCACATCTCGAAAATC 60.025 45.833 0.21 0.00 44.75 2.17
1871 4063 6.463995 TCAAAGGTAAACTGCTCAAATTGT 57.536 33.333 0.00 0.00 0.00 2.71
1971 4163 9.989869 GCCACAAATAAACTAGATTAGAAACTC 57.010 33.333 0.00 0.00 0.00 3.01
2086 4278 5.130145 ACAGTATTTATGAGAAGAGCAGGCT 59.870 40.000 0.00 0.00 0.00 4.58
2104 4296 2.833943 GGCTCCCCTTCAATGAAACAAT 59.166 45.455 0.00 0.00 0.00 2.71
2127 4319 4.263550 TGGCCAATAAGCACTAACTGGTAA 60.264 41.667 0.61 0.00 0.00 2.85
2394 4590 4.546570 AGTTTTTATTGACTCAAAGCGCC 58.453 39.130 2.29 0.00 0.00 6.53
2501 4712 2.364972 TCCTCGCATCAGGAGTATCA 57.635 50.000 0.00 0.00 37.68 2.15
2621 4838 7.849804 ACAGAACATAACAGACCATATGAAC 57.150 36.000 3.65 0.00 34.38 3.18
2661 4880 9.829507 TTTTGGTTTCTCAAATGTTGATATGTT 57.170 25.926 0.00 0.00 39.30 2.71
2687 4906 9.587772 TCTAAATTAGCTACATCTCAACTCAAC 57.412 33.333 0.00 0.00 0.00 3.18
2725 4944 5.183713 CAGCCCTCAAATGTCAAAATCAGTA 59.816 40.000 0.00 0.00 0.00 2.74
2770 4989 9.353999 GGTTTTGTAGATGGTTTTGAATGATAC 57.646 33.333 0.00 0.00 0.00 2.24
2830 5049 6.764308 ACAACTCATGTCATTTCCTTATGG 57.236 37.500 0.00 0.00 37.96 2.74
2973 5192 5.989168 CCATGGCAGTAGAATAATTACGACA 59.011 40.000 0.00 0.00 0.00 4.35
3210 5429 3.181449 TGTTGGCTAGCAAACCTGTAAGA 60.181 43.478 28.25 8.48 34.07 2.10
3393 5612 9.565213 GAAGATTACATCATTGGCAAATATAGC 57.435 33.333 3.01 0.00 0.00 2.97
3396 5615 9.350357 GATTACATCATTGGCAAATATAGCTTG 57.650 33.333 3.01 0.00 0.00 4.01
3417 5636 2.613977 GGTATGGAGATGGATTGCCGAG 60.614 54.545 0.00 0.00 36.79 4.63
3420 5639 1.410850 GGAGATGGATTGCCGAGGGA 61.411 60.000 0.00 0.00 36.79 4.20
3531 5750 7.592533 CAGGAATTTAAATATGATGGTGAAGCG 59.407 37.037 0.01 0.00 0.00 4.68
3633 5852 1.407851 GCTCAGCACATCCCATCTCAA 60.408 52.381 0.00 0.00 0.00 3.02
3634 5853 2.286872 CTCAGCACATCCCATCTCAAC 58.713 52.381 0.00 0.00 0.00 3.18
3652 5871 0.033504 ACGTGACAAGATTCGCAGGT 59.966 50.000 0.00 0.00 0.00 4.00
3674 5894 8.400947 CAGGTTGTACATCCATAAAAAGATGAG 58.599 37.037 22.15 0.00 42.04 2.90
3703 5923 3.009723 CCGAGGTATCACAGCAAAACAT 58.990 45.455 0.00 0.00 0.00 2.71
3743 5963 2.683968 TCACTTCATGTGTTCGGTAGC 58.316 47.619 0.00 0.00 46.27 3.58
3795 6015 9.001542 ACCTACAGATTCTTCGTGTACTATATC 57.998 37.037 0.00 0.00 0.00 1.63
3919 6139 4.385643 CCCAATCCAAATCAGGAAGCTAGA 60.386 45.833 0.00 0.00 41.92 2.43
3920 6140 4.578105 CCAATCCAAATCAGGAAGCTAGAC 59.422 45.833 0.00 0.00 41.92 2.59
3957 6177 4.547671 TGACCTAAGAGGAAGTGGGATAG 58.452 47.826 0.00 0.00 37.67 2.08
4123 6343 3.631227 GGGAAGGATCTGCAGAATTTGAG 59.369 47.826 22.50 0.00 0.00 3.02
4175 6395 6.829849 TGAGCATACTTATTGTGATGATGGA 58.170 36.000 0.00 0.00 0.00 3.41
4262 6482 0.669625 GTTGTGGTCCTCCTACGTGC 60.670 60.000 0.00 0.00 34.23 5.34
4265 6485 0.108756 GTGGTCCTCCTACGTGCTTC 60.109 60.000 0.00 0.00 34.23 3.86
4278 6498 0.745845 GTGCTTCGCAGATCCATGGT 60.746 55.000 12.58 0.00 40.08 3.55
4301 6521 3.827898 CCTCCGCGTCTCCTCCAC 61.828 72.222 4.92 0.00 0.00 4.02
4346 6566 5.324784 GGGATGACAATTTACCCTTGTTC 57.675 43.478 0.00 0.00 36.98 3.18
4352 6572 3.824443 ACAATTTACCCTTGTTCCCGAAG 59.176 43.478 0.00 0.00 33.10 3.79
4410 6630 7.599998 ACTTAGATTTTGGTGTTGATCAAATGC 59.400 33.333 10.35 3.28 32.11 3.56
4443 6663 0.593128 GCACATGCTCGAAGGTTTGT 59.407 50.000 0.00 0.00 38.21 2.83
4511 7041 0.108424 GACTCTCGGTCAGCTGCAAT 60.108 55.000 9.47 0.00 43.94 3.56
4633 7163 2.391616 TTCGATGCAGATGAAGCACT 57.608 45.000 0.00 0.00 45.95 4.40
4657 7187 9.080097 ACTCTCTACATATGGTTGTATAGGTTC 57.920 37.037 7.80 0.00 31.94 3.62
4676 7206 0.038343 CCGGCATCCAACACCTTTTG 60.038 55.000 0.00 0.00 0.00 2.44
4677 7207 0.667184 CGGCATCCAACACCTTTTGC 60.667 55.000 0.00 0.00 0.00 3.68
4692 7222 5.851177 CACCTTTTGCGTCTTAACTACATTG 59.149 40.000 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.236616 CGTTCACTGAGCCAATGCCA 61.237 55.000 0.00 0.00 38.69 4.92
35 36 1.963338 AAGCAGCGTTCACTGAGCC 60.963 57.895 0.00 0.00 40.25 4.70
89 90 6.325596 TCTCACTGACATCACTATTTTCTCG 58.674 40.000 0.00 0.00 0.00 4.04
114 115 0.813210 CTTGATCTCCGGCTTCCAGC 60.813 60.000 0.00 0.00 41.46 4.85
122 123 2.744202 CACCAAGTTTCTTGATCTCCGG 59.256 50.000 10.54 0.00 0.00 5.14
172 173 1.747355 GCCCTGATTCTGTTGTGATGG 59.253 52.381 0.00 0.00 0.00 3.51
178 179 1.470098 CCGAAAGCCCTGATTCTGTTG 59.530 52.381 0.00 0.00 0.00 3.33
179 180 1.826385 CCGAAAGCCCTGATTCTGTT 58.174 50.000 0.00 0.00 0.00 3.16
248 249 4.410400 GGGTCAGCGTTGGGAGGG 62.410 72.222 0.00 0.00 0.00 4.30
262 263 1.075536 GGAAGTCATTTGGGTCAGGGT 59.924 52.381 0.00 0.00 0.00 4.34
337 338 5.618056 TGACAATTCAGTTGAGATGAAGC 57.382 39.130 0.00 0.00 39.86 3.86
358 359 2.675317 CGGAGGGAGTAGCAAAGAACTG 60.675 54.545 0.00 0.00 0.00 3.16
370 371 3.716431 TGTATTTAGGAACGGAGGGAGT 58.284 45.455 0.00 0.00 0.00 3.85
373 374 4.161754 AGACTTGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
377 378 6.796705 ACAAAGACTTGTATTTAGGAACGG 57.203 37.500 0.00 0.00 44.14 4.44
378 379 8.752766 TCTACAAAGACTTGTATTTAGGAACG 57.247 34.615 0.00 0.00 44.95 3.95
379 380 9.924650 TCTCTACAAAGACTTGTATTTAGGAAC 57.075 33.333 0.00 0.00 44.95 3.62
390 391 9.645059 TCATAGTGAAATCTCTACAAAGACTTG 57.355 33.333 0.00 0.00 38.61 3.16
394 395 9.996554 TGTTTCATAGTGAAATCTCTACAAAGA 57.003 29.630 8.21 0.00 46.55 2.52
400 401 9.516314 CGTATGTGTTTCATAGTGAAATCTCTA 57.484 33.333 8.21 0.00 46.55 2.43
401 402 7.492669 CCGTATGTGTTTCATAGTGAAATCTCT 59.507 37.037 8.21 0.00 46.55 3.10
402 403 7.254455 CCCGTATGTGTTTCATAGTGAAATCTC 60.254 40.741 8.21 4.96 46.55 2.75
403 404 6.538742 CCCGTATGTGTTTCATAGTGAAATCT 59.461 38.462 8.21 0.00 46.55 2.40
404 405 6.315393 ACCCGTATGTGTTTCATAGTGAAATC 59.685 38.462 8.21 6.17 46.55 2.17
419 420 5.961272 TGCATCTATATACACCCGTATGTG 58.039 41.667 0.00 0.00 38.79 3.21
420 421 6.791867 ATGCATCTATATACACCCGTATGT 57.208 37.500 0.00 0.00 38.79 2.29
421 422 8.492673 AAAATGCATCTATATACACCCGTATG 57.507 34.615 0.00 0.00 38.79 2.39
423 424 9.027202 TCTAAAATGCATCTATATACACCCGTA 57.973 33.333 0.00 0.00 0.00 4.02
425 426 8.035394 ACTCTAAAATGCATCTATATACACCCG 58.965 37.037 0.00 0.00 0.00 5.28
446 447 9.973450 GAGCAAAATGAGTGAATCTATACTCTA 57.027 33.333 0.00 0.00 42.86 2.43
447 448 7.930865 GGAGCAAAATGAGTGAATCTATACTCT 59.069 37.037 0.00 0.00 42.86 3.24
448 449 7.095857 CGGAGCAAAATGAGTGAATCTATACTC 60.096 40.741 0.00 0.00 42.77 2.59
449 450 6.703607 CGGAGCAAAATGAGTGAATCTATACT 59.296 38.462 0.00 0.00 0.00 2.12
450 451 6.480320 ACGGAGCAAAATGAGTGAATCTATAC 59.520 38.462 0.00 0.00 0.00 1.47
451 452 6.582636 ACGGAGCAAAATGAGTGAATCTATA 58.417 36.000 0.00 0.00 0.00 1.31
452 453 5.431765 ACGGAGCAAAATGAGTGAATCTAT 58.568 37.500 0.00 0.00 0.00 1.98
453 454 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
454 455 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
455 456 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
456 457 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
457 458 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
458 459 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
459 460 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
460 461 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
461 462 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
462 463 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
463 464 3.245284 CGGACTACATACGGAGCAAAATG 59.755 47.826 0.00 0.00 0.00 2.32
464 465 3.118884 ACGGACTACATACGGAGCAAAAT 60.119 43.478 0.00 0.00 0.00 1.82
465 466 2.231964 ACGGACTACATACGGAGCAAAA 59.768 45.455 0.00 0.00 0.00 2.44
466 467 1.820519 ACGGACTACATACGGAGCAAA 59.179 47.619 0.00 0.00 0.00 3.68
467 468 1.466856 ACGGACTACATACGGAGCAA 58.533 50.000 0.00 0.00 0.00 3.91
468 469 2.216046 CTACGGACTACATACGGAGCA 58.784 52.381 0.00 0.00 31.15 4.26
469 470 2.216898 ACTACGGACTACATACGGAGC 58.783 52.381 0.00 0.00 42.12 4.70
470 471 4.876125 TCTACTACGGACTACATACGGAG 58.124 47.826 0.00 0.00 43.89 4.63
471 472 4.937201 TCTACTACGGACTACATACGGA 57.063 45.455 0.00 0.00 0.00 4.69
472 473 7.763528 AGATATTCTACTACGGACTACATACGG 59.236 40.741 0.00 0.00 0.00 4.02
473 474 8.700722 AGATATTCTACTACGGACTACATACG 57.299 38.462 0.00 0.00 0.00 3.06
499 500 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
500 501 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
501 502 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
502 503 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
503 504 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
504 505 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
505 506 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
506 507 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
507 508 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
508 509 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
509 510 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
510 511 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
511 512 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
512 513 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
513 514 3.359950 GAAGTACTCCCTCCGTTCCTAA 58.640 50.000 0.00 0.00 0.00 2.69
514 515 2.357569 GGAAGTACTCCCTCCGTTCCTA 60.358 54.545 0.00 0.00 38.44 2.94
515 516 1.619160 GGAAGTACTCCCTCCGTTCCT 60.619 57.143 0.00 0.00 38.44 3.36
516 517 0.822811 GGAAGTACTCCCTCCGTTCC 59.177 60.000 0.00 0.00 38.44 3.62
517 518 1.849977 AGGAAGTACTCCCTCCGTTC 58.150 55.000 0.00 0.00 46.81 3.95
518 519 3.363627 CTTAGGAAGTACTCCCTCCGTT 58.636 50.000 2.82 0.00 46.81 4.44
519 520 2.949508 GCTTAGGAAGTACTCCCTCCGT 60.950 54.545 2.82 0.00 46.81 4.69
520 521 1.682323 GCTTAGGAAGTACTCCCTCCG 59.318 57.143 2.82 0.00 46.81 4.63
521 522 2.960384 GAGCTTAGGAAGTACTCCCTCC 59.040 54.545 2.82 3.63 46.81 4.30
522 523 3.633418 TGAGCTTAGGAAGTACTCCCTC 58.367 50.000 2.82 6.25 46.81 4.30
523 524 3.637769 CTGAGCTTAGGAAGTACTCCCT 58.362 50.000 5.75 5.75 46.81 4.20
524 525 2.101750 GCTGAGCTTAGGAAGTACTCCC 59.898 54.545 7.72 0.00 46.81 4.30
525 526 2.761208 TGCTGAGCTTAGGAAGTACTCC 59.239 50.000 5.83 0.00 45.81 3.85
526 527 4.340950 AGATGCTGAGCTTAGGAAGTACTC 59.659 45.833 5.83 0.00 0.00 2.59
527 528 4.285863 AGATGCTGAGCTTAGGAAGTACT 58.714 43.478 5.83 0.00 0.00 2.73
528 529 4.500716 GGAGATGCTGAGCTTAGGAAGTAC 60.501 50.000 5.83 0.00 0.00 2.73
529 530 3.639094 GGAGATGCTGAGCTTAGGAAGTA 59.361 47.826 5.83 0.00 0.00 2.24
530 531 2.433970 GGAGATGCTGAGCTTAGGAAGT 59.566 50.000 5.83 0.00 0.00 3.01
562 1770 3.345508 AGAGCTGAATGTGCTTGATCA 57.654 42.857 0.00 0.00 41.30 2.92
569 1777 1.484240 AGGAGGTAGAGCTGAATGTGC 59.516 52.381 0.00 0.00 0.00 4.57
596 1804 4.763793 AGGACAACACTTTGATCTCCATTG 59.236 41.667 0.00 0.00 36.48 2.82
671 2761 1.559682 CCTAAACTGCAGCCCCTCTAA 59.440 52.381 15.27 0.00 0.00 2.10
713 2803 0.597568 AACACCATGCCATGTCAACG 59.402 50.000 3.63 0.00 0.00 4.10
715 2805 0.967662 CCAACACCATGCCATGTCAA 59.032 50.000 3.63 0.00 0.00 3.18
733 2823 0.326808 TATCCCCACTACACCCACCC 60.327 60.000 0.00 0.00 0.00 4.61
734 2824 1.489230 CTTATCCCCACTACACCCACC 59.511 57.143 0.00 0.00 0.00 4.61
736 2826 2.953093 TCTTATCCCCACTACACCCA 57.047 50.000 0.00 0.00 0.00 4.51
764 2951 6.533214 CCTTGGAAGGTACAGCTAGCTAGC 62.533 54.167 33.96 33.96 44.12 3.42
765 2952 3.068873 CCTTGGAAGGTACAGCTAGCTAG 59.931 52.174 18.86 16.84 41.41 3.42
766 2953 3.031736 CCTTGGAAGGTACAGCTAGCTA 58.968 50.000 18.86 0.00 41.41 3.32
767 2954 1.834263 CCTTGGAAGGTACAGCTAGCT 59.166 52.381 12.68 12.68 41.41 3.32
768 2955 2.317530 CCTTGGAAGGTACAGCTAGC 57.682 55.000 6.62 6.62 41.41 3.42
792 2979 0.593128 AGTCAATGCGTTGAAGTGGC 59.407 50.000 22.56 10.18 45.38 5.01
814 3002 0.889994 TTGGCCATCAAGATGTGCAC 59.110 50.000 6.09 10.75 37.00 4.57
836 3024 1.602191 GCAATCACGCGTTTTTCGAT 58.398 45.000 10.22 6.03 42.86 3.59
847 3035 3.649073 TCCTTATGATACGGCAATCACG 58.351 45.455 1.96 0.00 38.65 4.35
930 3118 7.399191 TGATGTGGTAGAGGAACTAAACTGTAT 59.601 37.037 0.00 0.00 41.55 2.29
976 3164 2.284921 CCCTCCCTGCTCCTCACA 60.285 66.667 0.00 0.00 0.00 3.58
978 3166 4.421554 CCCCCTCCCTGCTCCTCA 62.422 72.222 0.00 0.00 0.00 3.86
993 3181 3.238197 AACCCCTGCCATCAACCCC 62.238 63.158 0.00 0.00 0.00 4.95
1014 3202 3.005554 AGCACTCACCATGATTTTCTCG 58.994 45.455 0.00 0.00 0.00 4.04
1083 3271 1.705745 ACCTTGGAAAACTCCTCCTCC 59.294 52.381 0.00 0.00 33.77 4.30
1084 3272 2.372172 TGACCTTGGAAAACTCCTCCTC 59.628 50.000 0.00 0.00 33.77 3.71
1085 3273 2.418669 TGACCTTGGAAAACTCCTCCT 58.581 47.619 0.00 0.00 33.77 3.69
1149 3338 1.072173 TCCAGGGCGATATTGATGGTG 59.928 52.381 0.00 0.00 0.00 4.17
1162 3351 1.972660 ATGGCGTACTTCTCCAGGGC 61.973 60.000 0.00 0.00 34.19 5.19
1176 3365 0.952497 CCGGATTCTCCATCATGGCG 60.952 60.000 0.00 0.00 37.47 5.69
1225 3417 3.778360 TATACGCCGCTTCCCGCAC 62.778 63.158 0.00 0.00 39.08 5.34
1306 3498 4.115199 GAGCCCCTTGATGCCGGT 62.115 66.667 1.90 0.00 0.00 5.28
1353 3545 5.154222 GCAAACCTATGGCGATATTTAAGC 58.846 41.667 0.00 0.00 0.00 3.09
1370 3562 1.303309 CTGGATCTGATCGGCAAACC 58.697 55.000 11.28 0.00 0.00 3.27
1374 3566 0.462581 GTTGCTGGATCTGATCGGCA 60.463 55.000 23.29 23.29 37.08 5.69
1375 3567 0.179062 AGTTGCTGGATCTGATCGGC 60.179 55.000 19.96 19.96 0.00 5.54
1377 3569 2.591571 TGAGTTGCTGGATCTGATCG 57.408 50.000 11.28 0.33 0.00 3.69
1378 3570 3.204526 CCTTGAGTTGCTGGATCTGATC 58.795 50.000 9.18 9.18 0.00 2.92
1388 3580 0.825010 CACAAGGGCCTTGAGTTGCT 60.825 55.000 44.20 23.67 43.42 3.91
1419 3611 0.894835 TGTACTTCAGATGCCGCTCA 59.105 50.000 0.00 0.00 0.00 4.26
1464 3656 1.600957 GGATCAATCTCCGTGTGCATG 59.399 52.381 0.00 0.00 0.00 4.06
1570 3762 0.456221 TTCACCGGATCGCTCTCTTC 59.544 55.000 9.46 0.00 0.00 2.87
1578 3770 2.456119 GCACTGCTTCACCGGATCG 61.456 63.158 9.46 0.00 0.00 3.69
1594 3786 3.411446 CAACAATAGAGACAACCCTGCA 58.589 45.455 0.00 0.00 0.00 4.41
1617 3809 1.882623 GTTTTGCCTGAACCTCCAGAG 59.117 52.381 0.00 0.00 36.29 3.35
1671 3863 5.468540 AAGCAGAACAGGAAAATTTACCC 57.531 39.130 0.00 0.00 0.00 3.69
1674 3866 7.781056 AGACAAAAGCAGAACAGGAAAATTTA 58.219 30.769 0.00 0.00 0.00 1.40
1676 3868 6.097412 AGAGACAAAAGCAGAACAGGAAAATT 59.903 34.615 0.00 0.00 0.00 1.82
1707 3899 3.244630 TGTTAACCATGGTAGGCTTTCGT 60.245 43.478 20.12 0.84 0.00 3.85
1710 3902 4.017499 AGGATGTTAACCATGGTAGGCTTT 60.017 41.667 20.12 3.39 32.56 3.51
1718 3910 2.509548 TCCCTCAGGATGTTAACCATGG 59.490 50.000 11.19 11.19 37.19 3.66
1746 3938 2.996621 GTCAGTGTTCTCGATTTCCAGG 59.003 50.000 0.00 0.00 0.00 4.45
1747 3939 3.653344 TGTCAGTGTTCTCGATTTCCAG 58.347 45.455 0.00 0.00 0.00 3.86
1748 3940 3.320826 TCTGTCAGTGTTCTCGATTTCCA 59.679 43.478 0.00 0.00 0.00 3.53
1755 3947 4.984785 TCAGATTTTCTGTCAGTGTTCTCG 59.015 41.667 0.00 0.00 44.58 4.04
1763 3955 7.173907 ACAGGTATTTGTCAGATTTTCTGTCAG 59.826 37.037 4.56 0.00 44.58 3.51
1789 3981 2.745821 GCTCACTGCATGATCTTGTTGA 59.254 45.455 10.05 9.09 42.31 3.18
1824 4016 2.932261 TCGAGATGTGCTCTTAGCCTA 58.068 47.619 0.00 0.00 41.51 3.93
1842 4034 5.757886 TGAGCAGTTTACCTTTGATTTTCG 58.242 37.500 0.00 0.00 0.00 3.46
1848 4040 6.463995 ACAATTTGAGCAGTTTACCTTTGA 57.536 33.333 2.79 0.00 0.00 2.69
1849 4041 6.534793 ACAACAATTTGAGCAGTTTACCTTTG 59.465 34.615 2.79 0.00 36.48 2.77
2057 4249 5.525378 GCTCTTCTCATAAATACTGTGGTGG 59.475 44.000 0.00 0.00 0.00 4.61
2086 4278 2.566724 GCCATTGTTTCATTGAAGGGGA 59.433 45.455 0.00 0.00 0.00 4.81
2104 4296 2.041081 ACCAGTTAGTGCTTATTGGCCA 59.959 45.455 0.00 0.00 0.00 5.36
2207 4399 2.152016 GCCTTTCTGGGATTATACCGC 58.848 52.381 0.00 0.00 36.00 5.68
2208 4400 3.771577 AGCCTTTCTGGGATTATACCG 57.228 47.619 0.00 0.00 36.00 4.02
2209 4401 6.004574 CCTAAAGCCTTTCTGGGATTATACC 58.995 44.000 0.00 0.00 33.50 2.73
2210 4402 6.004574 CCCTAAAGCCTTTCTGGGATTATAC 58.995 44.000 18.22 0.00 38.22 1.47
2211 4403 5.914716 TCCCTAAAGCCTTTCTGGGATTATA 59.085 40.000 20.45 5.16 39.25 0.98
2212 4404 4.731929 TCCCTAAAGCCTTTCTGGGATTAT 59.268 41.667 20.45 0.00 39.25 1.28
2213 4405 4.116113 TCCCTAAAGCCTTTCTGGGATTA 58.884 43.478 20.45 5.71 39.25 1.75
2341 4533 9.595823 CCGGGAAAAGTATATCGTTTGATATAT 57.404 33.333 7.92 0.00 46.50 0.86
2344 4540 6.819284 ACCGGGAAAAGTATATCGTTTGATA 58.181 36.000 6.32 0.00 41.19 2.15
2365 4561 7.429636 TTTGAGTCAATAAAAACTCCTACCG 57.570 36.000 6.36 0.00 40.98 4.02
2394 4590 4.338879 ACTCCAAATTTCTCCCTGATGTG 58.661 43.478 0.00 0.00 0.00 3.21
2501 4712 5.133221 GGCCAGAGTGTGATTAATGGTTAT 58.867 41.667 0.00 0.00 0.00 1.89
2534 4745 5.517770 GCACTTAAATCTGGTTGATGCATTC 59.482 40.000 0.00 0.00 35.21 2.67
2661 4880 9.587772 GTTGAGTTGAGATGTAGCTAATTTAGA 57.412 33.333 7.63 0.00 0.00 2.10
2682 4901 4.445385 GGCTGCAAATTAAACAGTGTTGAG 59.555 41.667 9.79 0.00 33.87 3.02
2687 4906 3.005684 TGAGGGCTGCAAATTAAACAGTG 59.994 43.478 0.50 0.00 33.87 3.66
2725 4944 4.664688 ACCACCCTCAGAATCTGAATTT 57.335 40.909 14.44 0.00 40.18 1.82
2770 4989 9.796062 GCACACAAATATTAAATTGTTTGACTG 57.204 29.630 16.22 8.05 38.75 3.51
2827 5046 5.373854 AGATTAAAGCTACAAGGGATCCCAT 59.626 40.000 32.69 19.33 38.92 4.00
2830 5049 7.226918 GTGTAAGATTAAAGCTACAAGGGATCC 59.773 40.741 1.92 1.92 0.00 3.36
2973 5192 2.878406 AGCTACTTTGTTGATGCGTGTT 59.122 40.909 0.00 0.00 0.00 3.32
3090 5309 0.680921 TAGGGCATTCAGCTGCAACC 60.681 55.000 9.47 7.58 44.12 3.77
3117 5336 6.328672 GCAGTATATCATCCATAATCCCCTCT 59.671 42.308 0.00 0.00 0.00 3.69
3210 5429 2.843113 CACTCTCTCCCATTCTTCCCTT 59.157 50.000 0.00 0.00 0.00 3.95
3298 5517 5.929058 AGATCACAATAGCTGAGAGACAA 57.071 39.130 0.00 0.00 0.00 3.18
3393 5612 3.152341 GGCAATCCATCTCCATACCAAG 58.848 50.000 0.00 0.00 0.00 3.61
3396 5615 1.347707 TCGGCAATCCATCTCCATACC 59.652 52.381 0.00 0.00 0.00 2.73
3417 5636 1.611491 TGCTTCGGAACAACAAATCCC 59.389 47.619 0.00 0.00 31.73 3.85
3420 5639 2.890311 TCCATGCTTCGGAACAACAAAT 59.110 40.909 0.00 0.00 0.00 2.32
3518 5737 3.949754 ACATGAAATCGCTTCACCATCAT 59.050 39.130 0.00 0.00 46.80 2.45
3520 5739 3.544834 CGACATGAAATCGCTTCACCATC 60.545 47.826 0.00 1.34 46.80 3.51
3633 5852 0.033504 ACCTGCGAATCTTGTCACGT 59.966 50.000 0.00 0.00 0.00 4.49
3634 5853 1.136252 CAACCTGCGAATCTTGTCACG 60.136 52.381 0.00 0.00 0.00 4.35
3652 5871 7.936496 TGCTCATCTTTTTATGGATGTACAA 57.064 32.000 0.00 0.00 39.93 2.41
3674 5894 1.227645 TGATACCTCGGCTGCATGC 60.228 57.895 11.82 11.82 41.94 4.06
3703 5923 5.360999 AGTGAACGGAGATGAGACATATTCA 59.639 40.000 0.00 0.00 0.00 2.57
3743 5963 0.111253 GAGGGGGCATCCAGGTAATG 59.889 60.000 0.00 0.00 37.22 1.90
3839 6059 9.956720 AAATATCTCAAATGAATTAAGCTTCCG 57.043 29.630 0.00 0.00 0.00 4.30
3919 6139 2.884639 AGGTCAAGCGTTTGCAAATAGT 59.115 40.909 16.21 0.00 46.23 2.12
3920 6140 3.559238 AGGTCAAGCGTTTGCAAATAG 57.441 42.857 16.21 13.54 46.23 1.73
3968 6188 7.012421 AGCCGTTTTAGATGAACAATAGATTCC 59.988 37.037 0.00 0.00 0.00 3.01
4123 6343 2.533266 TCCAAGCACTCTCAACTGTC 57.467 50.000 0.00 0.00 0.00 3.51
4175 6395 6.073003 GCTTACAAAGAGCTGTACTGATTTGT 60.073 38.462 22.32 22.32 42.87 2.83
4262 6482 0.463295 AGCACCATGGATCTGCGAAG 60.463 55.000 21.47 0.00 35.98 3.79
4265 6485 0.879400 GAGAGCACCATGGATCTGCG 60.879 60.000 21.47 0.17 35.98 5.18
4278 6498 3.134792 GAGACGCGGAGGAGAGCA 61.135 66.667 12.47 0.00 0.00 4.26
4301 6521 6.423604 CCCTATAACCTTGCAAAACAAACTTG 59.576 38.462 0.00 0.00 37.96 3.16
4410 6630 2.014857 CATGTGCAAGTCTCTCCCATG 58.985 52.381 0.00 0.00 0.00 3.66
4511 7041 5.708544 AGATGCCTTAATGATTGGAATCCA 58.291 37.500 0.00 0.00 36.74 3.41
4633 7163 7.176165 CGGAACCTATACAACCATATGTAGAGA 59.824 40.741 9.88 0.00 44.17 3.10
4657 7187 0.038343 CAAAAGGTGTTGGATGCCGG 60.038 55.000 0.00 0.00 0.00 6.13
4676 7206 5.444745 GCTGACTTCAATGTAGTTAAGACGC 60.445 44.000 7.49 0.00 0.00 5.19
4677 7207 5.633601 TGCTGACTTCAATGTAGTTAAGACG 59.366 40.000 7.49 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.