Multiple sequence alignment - TraesCS7B01G276900

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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 TraesCS7B01G276900 chr7B 100.000 3378 0 0 1 3378 506548178 506551555 0.000000e+00 6239.0
1 TraesCS7B01G276900 chr7B 93.542 1053 37 7 2333 3378 145546443 145545415 0.000000e+00 1539.0
2 TraesCS7B01G276900 chr7B 82.967 546 50 23 1 527 465114330 465113809 1.430000e-123 453.0
3 TraesCS7B01G276900 chr1B 96.375 2759 80 12 634 3378 594014822 594017574 0.000000e+00 4523.0
4 TraesCS7B01G276900 chr1B 96.967 2440 58 11 950 3378 649429258 649431692 0.000000e+00 4082.0
5 TraesCS7B01G276900 chr1B 92.807 2141 82 26 634 2712 673447336 673445206 0.000000e+00 3035.0
6 TraesCS7B01G276900 chr1B 95.587 1881 58 12 634 2489 438159774 438161654 0.000000e+00 2990.0
7 TraesCS7B01G276900 chr1B 91.478 1631 76 39 634 2230 61450804 61449203 0.000000e+00 2183.0
8 TraesCS7B01G276900 chr1B 98.083 887 17 0 2492 3378 438161625 438162511 0.000000e+00 1544.0
9 TraesCS7B01G276900 chr1B 86.923 390 17 8 2309 2668 61449202 61448817 1.130000e-109 407.0
10 TraesCS7B01G276900 chr1B 100.000 30 0 0 2492 2521 594016650 594016679 4.710000e-04 56.5
11 TraesCS7B01G276900 chr1B 100.000 30 0 0 2492 2521 649430767 649430796 4.710000e-04 56.5
12 TraesCS7B01G276900 chr1B 100.000 30 0 0 2492 2521 673445484 673445455 4.710000e-04 56.5
13 TraesCS7B01G276900 chr3B 94.805 2098 70 15 634 2712 52631695 52629618 0.000000e+00 3234.0
14 TraesCS7B01G276900 chr3B 94.764 2101 70 16 631 2712 53026233 53028312 0.000000e+00 3234.0
15 TraesCS7B01G276900 chr3B 97.317 671 17 1 2709 3378 53028728 53029398 0.000000e+00 1138.0
16 TraesCS7B01G276900 chr3B 95.492 244 11 0 634 877 52623750 52623993 1.140000e-104 390.0
17 TraesCS7B01G276900 chr3B 94.262 244 14 0 634 877 53033365 53033122 1.140000e-99 374.0
18 TraesCS7B01G276900 chr2B 92.383 2140 79 32 634 2712 453819524 453821640 0.000000e+00 2972.0
19 TraesCS7B01G276900 chr2B 97.500 640 14 1 2739 3378 794529885 794530522 0.000000e+00 1092.0
20 TraesCS7B01G276900 chr2B 96.850 635 20 0 2744 3378 453822386 453823020 0.000000e+00 1062.0
21 TraesCS7B01G276900 chr2B 100.000 30 0 0 2492 2521 453821362 453821391 4.710000e-04 56.5
22 TraesCS7B01G276900 chr5B 95.168 1697 38 8 1702 3378 578450926 578452598 0.000000e+00 2639.0
23 TraesCS7B01G276900 chr5B 94.715 1419 44 7 1967 3378 567004790 567003396 0.000000e+00 2176.0
24 TraesCS7B01G276900 chr5B 100.000 30 0 0 2492 2521 567004297 567004268 4.710000e-04 56.5
25 TraesCS7B01G276900 chr5B 100.000 30 0 0 2492 2521 578451684 578451713 4.710000e-04 56.5
26 TraesCS7B01G276900 chr6B 94.677 1315 45 9 634 1924 169167829 169166516 0.000000e+00 2017.0
27 TraesCS7B01G276900 chr6B 97.971 887 18 0 2492 3378 558312529 558311643 0.000000e+00 1539.0
28 TraesCS7B01G276900 chr6B 97.895 855 18 0 1635 2489 558313354 558312500 0.000000e+00 1480.0
29 TraesCS7B01G276900 chr6B 96.674 872 22 4 918 1786 151206940 151206073 0.000000e+00 1443.0
30 TraesCS7B01G276900 chrUn 93.953 893 37 7 631 1511 371388779 371389666 0.000000e+00 1334.0
31 TraesCS7B01G276900 chrUn 97.317 671 17 1 2709 3378 415919906 415919236 0.000000e+00 1138.0
32 TraesCS7B01G276900 chrUn 97.168 671 18 1 2709 3378 438247095 438247765 0.000000e+00 1133.0
33 TraesCS7B01G276900 chrUn 94.207 656 19 8 2064 2712 211278796 211279439 0.000000e+00 983.0
34 TraesCS7B01G276900 chr2A 90.299 938 72 11 1784 2709 753952781 753953711 0.000000e+00 1210.0
35 TraesCS7B01G276900 chr7A 92.044 641 39 5 1 632 548036397 548037034 0.000000e+00 891.0
36 TraesCS7B01G276900 chr7D 91.311 633 39 8 1 625 480830723 480831347 0.000000e+00 850.0
37 TraesCS7B01G276900 chr7D 81.574 559 51 26 1 527 447758088 447757550 6.740000e-112 414.0


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 TraesCS7B01G276900 chr7B 506548178 506551555 3377 False 6239.00 6239 100.0000 1 3378 1 chr7B.!!$F1 3377
1 TraesCS7B01G276900 chr7B 145545415 145546443 1028 True 1539.00 1539 93.5420 2333 3378 1 chr7B.!!$R1 1045
2 TraesCS7B01G276900 chr7B 465113809 465114330 521 True 453.00 453 82.9670 1 527 1 chr7B.!!$R2 526
3 TraesCS7B01G276900 chr1B 594014822 594017574 2752 False 2289.75 4523 98.1875 634 3378 2 chr1B.!!$F2 2744
4 TraesCS7B01G276900 chr1B 438159774 438162511 2737 False 2267.00 2990 96.8350 634 3378 2 chr1B.!!$F1 2744
5 TraesCS7B01G276900 chr1B 649429258 649431692 2434 False 2069.25 4082 98.4835 950 3378 2 chr1B.!!$F3 2428
6 TraesCS7B01G276900 chr1B 673445206 673447336 2130 True 1545.75 3035 96.4035 634 2712 2 chr1B.!!$R2 2078
7 TraesCS7B01G276900 chr1B 61448817 61450804 1987 True 1295.00 2183 89.2005 634 2668 2 chr1B.!!$R1 2034
8 TraesCS7B01G276900 chr3B 52629618 52631695 2077 True 3234.00 3234 94.8050 634 2712 1 chr3B.!!$R1 2078
9 TraesCS7B01G276900 chr3B 53026233 53029398 3165 False 2186.00 3234 96.0405 631 3378 2 chr3B.!!$F2 2747
10 TraesCS7B01G276900 chr2B 453819524 453823020 3496 False 1363.50 2972 96.4110 634 3378 3 chr2B.!!$F2 2744
11 TraesCS7B01G276900 chr2B 794529885 794530522 637 False 1092.00 1092 97.5000 2739 3378 1 chr2B.!!$F1 639
12 TraesCS7B01G276900 chr5B 578450926 578452598 1672 False 1347.75 2639 97.5840 1702 3378 2 chr5B.!!$F1 1676
13 TraesCS7B01G276900 chr5B 567003396 567004790 1394 True 1116.25 2176 97.3575 1967 3378 2 chr5B.!!$R1 1411
14 TraesCS7B01G276900 chr6B 169166516 169167829 1313 True 2017.00 2017 94.6770 634 1924 1 chr6B.!!$R2 1290
15 TraesCS7B01G276900 chr6B 558311643 558313354 1711 True 1509.50 1539 97.9330 1635 3378 2 chr6B.!!$R3 1743
16 TraesCS7B01G276900 chr6B 151206073 151206940 867 True 1443.00 1443 96.6740 918 1786 1 chr6B.!!$R1 868
17 TraesCS7B01G276900 chrUn 371388779 371389666 887 False 1334.00 1334 93.9530 631 1511 1 chrUn.!!$F2 880
18 TraesCS7B01G276900 chrUn 415919236 415919906 670 True 1138.00 1138 97.3170 2709 3378 1 chrUn.!!$R1 669
19 TraesCS7B01G276900 chrUn 438247095 438247765 670 False 1133.00 1133 97.1680 2709 3378 1 chrUn.!!$F3 669
20 TraesCS7B01G276900 chrUn 211278796 211279439 643 False 983.00 983 94.2070 2064 2712 1 chrUn.!!$F1 648
21 TraesCS7B01G276900 chr2A 753952781 753953711 930 False 1210.00 1210 90.2990 1784 2709 1 chr2A.!!$F1 925
22 TraesCS7B01G276900 chr7A 548036397 548037034 637 False 891.00 891 92.0440 1 632 1 chr7A.!!$F1 631
23 TraesCS7B01G276900 chr7D 480830723 480831347 624 False 850.00 850 91.3110 1 625 1 chr7D.!!$F1 624
24 TraesCS7B01G276900 chr7D 447757550 447758088 538 True 414.00 414 81.5740 1 527 1 chr7D.!!$R1 526

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
441 483 0.038618 GTTGCCGGGGAACAACAATC 60.039 55.0 24.37 0.0 44.39 2.67 F
492 534 0.040425 GGGCGTGCTTTATTATGGCG 60.040 55.0 0.00 0.0 0.00 5.69 F
531 573 0.102300 CCGGGCCGAATTTTGAATCC 59.898 55.0 30.79 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1357 1.068121 CCTCCTCCCAGTGTCCTTTT 58.932 55.000 0.0 0.0 0.0 2.27 R
1818 1928 2.233271 CATCAACCCACTGAGCAACTT 58.767 47.619 0.0 0.0 0.0 2.66 R
2521 2806 8.129211 GGGTAGTTTTGCAGATAATCATTACAC 58.871 37.037 0.0 0.0 0.0 2.90 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
113 151 6.183360 CGAAGCGAAGAAGAAGAAGAATGAAT 60.183 38.462 0.00 0.00 0.00 2.57
217 259 1.529713 GAGAGGGTAGGGGAGAGCG 60.530 68.421 0.00 0.00 0.00 5.03
218 260 3.228017 GAGGGTAGGGGAGAGCGC 61.228 72.222 0.00 0.00 0.00 5.92
243 285 3.446365 CGATCATGTCGTCGAGGAG 57.554 57.895 8.30 0.00 45.19 3.69
244 286 0.040870 CGATCATGTCGTCGAGGAGG 60.041 60.000 8.30 1.71 45.19 4.30
245 287 0.318275 GATCATGTCGTCGAGGAGGC 60.318 60.000 8.30 0.00 0.00 4.70
252 294 3.213402 GTCGAGGAGGCGGAGGAG 61.213 72.222 0.00 0.00 0.00 3.69
255 297 3.223589 GAGGAGGCGGAGGAGCTC 61.224 72.222 4.71 4.71 37.29 4.09
258 300 4.200283 GAGGCGGAGGAGCTCGTG 62.200 72.222 14.78 1.21 37.29 4.35
261 303 4.500116 GCGGAGGAGCTCGTGGTC 62.500 72.222 14.78 8.11 39.76 4.02
267 309 3.827898 GAGCTCGTGGTCCTCCGG 61.828 72.222 0.00 0.00 34.87 5.14
286 328 2.663196 ACGAAGTGGTAGCCCTGC 59.337 61.111 0.00 0.00 42.51 4.85
287 329 2.509336 CGAAGTGGTAGCCCTGCG 60.509 66.667 0.00 0.00 0.00 5.18
288 330 2.125106 GAAGTGGTAGCCCTGCGG 60.125 66.667 0.00 0.00 0.00 5.69
307 349 2.903350 AACCCGTGCCGGTTCAAC 60.903 61.111 1.90 0.00 46.80 3.18
308 350 4.941309 ACCCGTGCCGGTTCAACC 62.941 66.667 1.90 0.00 46.80 3.77
309 351 4.939368 CCCGTGCCGGTTCAACCA 62.939 66.667 7.52 0.00 46.80 3.67
310 352 3.353836 CCGTGCCGGTTCAACCAG 61.354 66.667 7.52 0.00 42.73 4.00
311 353 2.590575 CGTGCCGGTTCAACCAGT 60.591 61.111 7.52 0.00 38.47 4.00
312 354 2.604174 CGTGCCGGTTCAACCAGTC 61.604 63.158 7.52 0.00 38.47 3.51
313 355 2.280524 TGCCGGTTCAACCAGTCG 60.281 61.111 7.52 0.00 38.47 4.18
314 356 2.280592 GCCGGTTCAACCAGTCGT 60.281 61.111 7.52 0.00 38.47 4.34
315 357 2.315386 GCCGGTTCAACCAGTCGTC 61.315 63.158 7.52 0.00 38.47 4.20
316 358 2.019951 CCGGTTCAACCAGTCGTCG 61.020 63.158 7.52 0.00 38.47 5.12
317 359 2.654912 CGGTTCAACCAGTCGTCGC 61.655 63.158 7.52 0.00 38.47 5.19
318 360 2.315386 GGTTCAACCAGTCGTCGCC 61.315 63.158 0.01 0.00 38.42 5.54
319 361 2.355363 TTCAACCAGTCGTCGCCG 60.355 61.111 0.00 0.00 0.00 6.46
320 362 2.847754 TTCAACCAGTCGTCGCCGA 61.848 57.895 0.00 0.00 41.73 5.54
347 389 2.998097 CCTTCGGCATCTTCCCCA 59.002 61.111 0.00 0.00 0.00 4.96
348 390 1.533711 CCTTCGGCATCTTCCCCAT 59.466 57.895 0.00 0.00 0.00 4.00
349 391 0.820891 CCTTCGGCATCTTCCCCATG 60.821 60.000 0.00 0.00 0.00 3.66
350 392 0.820891 CTTCGGCATCTTCCCCATGG 60.821 60.000 4.14 4.14 0.00 3.66
351 393 2.908940 CGGCATCTTCCCCATGGC 60.909 66.667 6.09 0.00 42.11 4.40
352 394 2.908940 GGCATCTTCCCCATGGCG 60.909 66.667 6.09 0.00 37.11 5.69
353 395 2.124151 GCATCTTCCCCATGGCGT 60.124 61.111 6.09 0.00 0.00 5.68
354 396 2.484062 GCATCTTCCCCATGGCGTG 61.484 63.158 6.09 0.00 0.00 5.34
355 397 2.124151 ATCTTCCCCATGGCGTGC 60.124 61.111 6.09 0.00 0.00 5.34
356 398 4.776322 TCTTCCCCATGGCGTGCG 62.776 66.667 6.09 0.00 0.00 5.34
392 434 3.515286 CGGAGCTCGGCGACCTTA 61.515 66.667 4.99 0.00 34.75 2.69
393 435 2.413765 GGAGCTCGGCGACCTTAG 59.586 66.667 4.99 0.00 0.00 2.18
394 436 2.416432 GGAGCTCGGCGACCTTAGT 61.416 63.158 4.99 0.00 0.00 2.24
395 437 1.226717 GAGCTCGGCGACCTTAGTG 60.227 63.158 4.99 0.00 0.00 2.74
396 438 2.202756 GCTCGGCGACCTTAGTGG 60.203 66.667 4.99 0.00 42.93 4.00
397 439 2.494918 CTCGGCGACCTTAGTGGG 59.505 66.667 4.99 0.00 41.11 4.61
398 440 2.036098 TCGGCGACCTTAGTGGGA 59.964 61.111 4.99 0.00 41.11 4.37
399 441 1.380785 TCGGCGACCTTAGTGGGAT 60.381 57.895 4.99 0.00 41.11 3.85
400 442 1.227263 CGGCGACCTTAGTGGGATG 60.227 63.158 0.00 0.00 41.11 3.51
401 443 1.146263 GGCGACCTTAGTGGGATGG 59.854 63.158 0.00 0.00 41.11 3.51
402 444 1.146263 GCGACCTTAGTGGGATGGG 59.854 63.158 0.00 0.00 41.11 4.00
403 445 1.335132 GCGACCTTAGTGGGATGGGA 61.335 60.000 0.00 0.00 41.11 4.37
404 446 0.753262 CGACCTTAGTGGGATGGGAG 59.247 60.000 0.00 0.00 41.11 4.30
405 447 1.688311 CGACCTTAGTGGGATGGGAGA 60.688 57.143 0.00 0.00 41.11 3.71
406 448 2.695585 GACCTTAGTGGGATGGGAGAT 58.304 52.381 0.00 0.00 41.11 2.75
407 449 2.370189 GACCTTAGTGGGATGGGAGATG 59.630 54.545 0.00 0.00 41.11 2.90
408 450 1.701847 CCTTAGTGGGATGGGAGATGG 59.298 57.143 0.00 0.00 0.00 3.51
409 451 2.694397 CTTAGTGGGATGGGAGATGGA 58.306 52.381 0.00 0.00 0.00 3.41
410 452 2.887454 TAGTGGGATGGGAGATGGAA 57.113 50.000 0.00 0.00 0.00 3.53
411 453 1.216990 AGTGGGATGGGAGATGGAAC 58.783 55.000 0.00 0.00 0.00 3.62
412 454 1.216990 GTGGGATGGGAGATGGAACT 58.783 55.000 0.00 0.00 0.00 3.01
413 455 1.141858 GTGGGATGGGAGATGGAACTC 59.858 57.143 0.00 0.00 36.31 3.01
414 456 0.394565 GGGATGGGAGATGGAACTCG 59.605 60.000 0.00 0.00 37.74 4.18
415 457 1.414158 GGATGGGAGATGGAACTCGA 58.586 55.000 0.00 0.00 37.74 4.04
416 458 1.342819 GGATGGGAGATGGAACTCGAG 59.657 57.143 11.84 11.84 37.74 4.04
417 459 1.342819 GATGGGAGATGGAACTCGAGG 59.657 57.143 18.41 0.00 37.74 4.63
418 460 0.335019 TGGGAGATGGAACTCGAGGA 59.665 55.000 18.41 0.00 37.74 3.71
419 461 1.036707 GGGAGATGGAACTCGAGGAG 58.963 60.000 18.41 0.00 37.74 3.69
420 462 1.036707 GGAGATGGAACTCGAGGAGG 58.963 60.000 18.41 0.00 37.74 4.30
421 463 1.410365 GGAGATGGAACTCGAGGAGGA 60.410 57.143 18.41 0.00 37.74 3.71
422 464 1.953686 GAGATGGAACTCGAGGAGGAG 59.046 57.143 18.41 0.00 39.97 3.69
427 469 3.701454 ACTCGAGGAGGAGTTGCC 58.299 61.111 18.41 0.00 44.65 4.52
428 470 2.344203 ACTCGAGGAGGAGTTGCCG 61.344 63.158 18.41 0.00 44.65 5.69
429 471 3.068691 TCGAGGAGGAGTTGCCGG 61.069 66.667 0.00 0.00 43.43 6.13
430 472 4.148825 CGAGGAGGAGTTGCCGGG 62.149 72.222 2.18 0.00 43.43 5.73
431 473 3.787001 GAGGAGGAGTTGCCGGGG 61.787 72.222 2.18 0.00 43.43 5.73
432 474 4.332543 AGGAGGAGTTGCCGGGGA 62.333 66.667 2.18 0.00 43.43 4.81
433 475 3.327404 GGAGGAGTTGCCGGGGAA 61.327 66.667 2.18 0.00 43.43 3.97
434 476 2.046217 GAGGAGTTGCCGGGGAAC 60.046 66.667 22.26 22.26 43.43 3.62
435 477 2.852075 AGGAGTTGCCGGGGAACA 60.852 61.111 29.46 1.25 43.43 3.18
436 478 2.114411 GGAGTTGCCGGGGAACAA 59.886 61.111 29.46 7.76 0.00 2.83
437 479 2.265904 GGAGTTGCCGGGGAACAAC 61.266 63.158 29.46 22.02 45.15 3.32
438 480 1.527380 GAGTTGCCGGGGAACAACA 60.527 57.895 29.46 0.00 46.79 3.33
439 481 1.076632 AGTTGCCGGGGAACAACAA 60.077 52.632 29.46 6.32 46.79 2.83
440 482 0.469144 AGTTGCCGGGGAACAACAAT 60.469 50.000 29.46 9.04 46.79 2.71
441 483 0.038618 GTTGCCGGGGAACAACAATC 60.039 55.000 24.37 0.00 44.39 2.67
442 484 0.178975 TTGCCGGGGAACAACAATCT 60.179 50.000 2.18 0.00 0.00 2.40
443 485 0.893270 TGCCGGGGAACAACAATCTG 60.893 55.000 2.18 0.00 0.00 2.90
444 486 1.883021 CCGGGGAACAACAATCTGC 59.117 57.895 0.00 0.00 0.00 4.26
445 487 1.501741 CGGGGAACAACAATCTGCG 59.498 57.895 0.00 0.00 0.00 5.18
446 488 1.234615 CGGGGAACAACAATCTGCGT 61.235 55.000 0.00 0.00 0.00 5.24
447 489 0.521735 GGGGAACAACAATCTGCGTC 59.478 55.000 0.00 0.00 0.00 5.19
448 490 0.521735 GGGAACAACAATCTGCGTCC 59.478 55.000 0.00 0.00 0.00 4.79
449 491 0.165944 GGAACAACAATCTGCGTCCG 59.834 55.000 0.00 0.00 0.00 4.79
450 492 0.452784 GAACAACAATCTGCGTCCGC 60.453 55.000 4.42 4.42 42.35 5.54
451 493 2.096406 CAACAATCTGCGTCCGCG 59.904 61.111 7.22 0.00 45.51 6.46
474 516 2.187946 CAGGAGCTGCGGTTAGGG 59.812 66.667 0.00 0.00 0.00 3.53
475 517 3.083997 AGGAGCTGCGGTTAGGGG 61.084 66.667 0.00 0.00 0.00 4.79
476 518 4.858680 GGAGCTGCGGTTAGGGGC 62.859 72.222 0.00 0.00 0.00 5.80
483 525 2.359478 CGGTTAGGGGCGTGCTTT 60.359 61.111 0.00 0.00 0.00 3.51
484 526 1.078988 CGGTTAGGGGCGTGCTTTA 60.079 57.895 0.00 0.00 0.00 1.85
485 527 0.463116 CGGTTAGGGGCGTGCTTTAT 60.463 55.000 0.00 0.00 0.00 1.40
486 528 1.758936 GGTTAGGGGCGTGCTTTATT 58.241 50.000 0.00 0.00 0.00 1.40
487 529 2.742530 CGGTTAGGGGCGTGCTTTATTA 60.743 50.000 0.00 0.00 0.00 0.98
488 530 3.483421 GGTTAGGGGCGTGCTTTATTAT 58.517 45.455 0.00 0.00 0.00 1.28
489 531 3.252458 GGTTAGGGGCGTGCTTTATTATG 59.748 47.826 0.00 0.00 0.00 1.90
490 532 1.981256 AGGGGCGTGCTTTATTATGG 58.019 50.000 0.00 0.00 0.00 2.74
491 533 0.313987 GGGGCGTGCTTTATTATGGC 59.686 55.000 0.00 0.00 0.00 4.40
492 534 0.040425 GGGCGTGCTTTATTATGGCG 60.040 55.000 0.00 0.00 0.00 5.69
493 535 0.941542 GGCGTGCTTTATTATGGCGA 59.058 50.000 0.00 0.00 0.00 5.54
494 536 1.333791 GGCGTGCTTTATTATGGCGAC 60.334 52.381 0.00 0.00 0.00 5.19
495 537 1.656429 GCGTGCTTTATTATGGCGACG 60.656 52.381 0.00 0.00 35.44 5.12
496 538 1.591158 CGTGCTTTATTATGGCGACGT 59.409 47.619 0.00 0.00 0.00 4.34
497 539 2.347292 CGTGCTTTATTATGGCGACGTC 60.347 50.000 5.18 5.18 0.00 4.34
498 540 2.033151 GTGCTTTATTATGGCGACGTCC 60.033 50.000 10.58 2.55 0.00 4.79
499 541 1.191647 GCTTTATTATGGCGACGTCCG 59.808 52.381 10.58 6.51 42.21 4.79
512 554 3.195698 GTCCGCTGGCAACCGATC 61.196 66.667 8.57 0.00 0.00 3.69
513 555 4.467084 TCCGCTGGCAACCGATCC 62.467 66.667 8.57 0.00 0.00 3.36
524 566 2.203153 CCGATCCGGGCCGAATTT 60.203 61.111 30.79 8.69 44.15 1.82
525 567 1.822186 CCGATCCGGGCCGAATTTT 60.822 57.895 30.79 6.63 44.15 1.82
526 568 1.355210 CGATCCGGGCCGAATTTTG 59.645 57.895 30.79 9.73 0.00 2.44
527 569 1.092921 CGATCCGGGCCGAATTTTGA 61.093 55.000 30.79 15.64 0.00 2.69
528 570 1.099689 GATCCGGGCCGAATTTTGAA 58.900 50.000 30.79 2.02 0.00 2.69
529 571 1.681264 GATCCGGGCCGAATTTTGAAT 59.319 47.619 30.79 7.10 0.00 2.57
530 572 1.099689 TCCGGGCCGAATTTTGAATC 58.900 50.000 30.79 0.00 0.00 2.52
531 573 0.102300 CCGGGCCGAATTTTGAATCC 59.898 55.000 30.79 0.00 0.00 3.01
532 574 0.248458 CGGGCCGAATTTTGAATCCG 60.248 55.000 24.41 0.00 0.00 4.18
533 575 0.102300 GGGCCGAATTTTGAATCCGG 59.898 55.000 0.00 0.00 42.74 5.14
536 578 2.475200 CCGAATTTTGAATCCGGCTC 57.525 50.000 0.00 0.00 33.47 4.70
537 579 1.065551 CCGAATTTTGAATCCGGCTCC 59.934 52.381 0.00 0.00 33.47 4.70
538 580 1.268032 CGAATTTTGAATCCGGCTCCG 60.268 52.381 0.00 0.48 39.44 4.63
539 581 1.743394 GAATTTTGAATCCGGCTCCGT 59.257 47.619 7.59 0.00 37.81 4.69
540 582 1.834188 ATTTTGAATCCGGCTCCGTT 58.166 45.000 7.59 0.00 37.81 4.44
541 583 0.878416 TTTTGAATCCGGCTCCGTTG 59.122 50.000 7.59 0.00 37.81 4.10
542 584 0.958382 TTTGAATCCGGCTCCGTTGG 60.958 55.000 7.59 0.00 37.81 3.77
543 585 2.513897 GAATCCGGCTCCGTTGGG 60.514 66.667 7.59 0.00 37.81 4.12
544 586 4.109675 AATCCGGCTCCGTTGGGG 62.110 66.667 7.59 0.00 37.81 4.96
547 589 3.708544 CCGGCTCCGTTGGGGTTA 61.709 66.667 7.59 0.00 37.81 2.85
548 590 2.348243 CGGCTCCGTTGGGGTTAA 59.652 61.111 0.00 0.00 37.00 2.01
549 591 1.743995 CGGCTCCGTTGGGGTTAAG 60.744 63.158 0.00 0.00 37.00 1.85
550 592 1.378119 GGCTCCGTTGGGGTTAAGG 60.378 63.158 0.00 0.00 37.00 2.69
551 593 2.044555 GCTCCGTTGGGGTTAAGGC 61.045 63.158 0.00 0.00 37.00 4.35
552 594 1.743995 CTCCGTTGGGGTTAAGGCG 60.744 63.158 0.00 0.00 37.00 5.52
553 595 2.748647 CCGTTGGGGTTAAGGCGG 60.749 66.667 0.00 0.00 0.00 6.13
554 596 2.748647 CGTTGGGGTTAAGGCGGG 60.749 66.667 0.00 0.00 0.00 6.13
555 597 2.361992 GTTGGGGTTAAGGCGGGG 60.362 66.667 0.00 0.00 0.00 5.73
556 598 2.532199 TTGGGGTTAAGGCGGGGA 60.532 61.111 0.00 0.00 0.00 4.81
557 599 2.608550 TTGGGGTTAAGGCGGGGAG 61.609 63.158 0.00 0.00 0.00 4.30
558 600 3.805497 GGGGTTAAGGCGGGGAGG 61.805 72.222 0.00 0.00 0.00 4.30
559 601 3.805497 GGGTTAAGGCGGGGAGGG 61.805 72.222 0.00 0.00 0.00 4.30
560 602 2.689771 GGTTAAGGCGGGGAGGGA 60.690 66.667 0.00 0.00 0.00 4.20
561 603 2.588439 GTTAAGGCGGGGAGGGAC 59.412 66.667 0.00 0.00 0.00 4.46
562 604 3.078836 TTAAGGCGGGGAGGGACG 61.079 66.667 0.00 0.00 0.00 4.79
592 634 4.250431 GGTGCGTGCGTGCTTGTT 62.250 61.111 1.52 0.00 35.36 2.83
593 635 2.277884 GTGCGTGCGTGCTTGTTT 60.278 55.556 1.52 0.00 35.36 2.83
594 636 2.277820 TGCGTGCGTGCTTGTTTG 60.278 55.556 1.52 0.00 35.36 2.93
595 637 2.024022 GCGTGCGTGCTTGTTTGA 59.976 55.556 0.00 0.00 0.00 2.69
596 638 1.370414 GCGTGCGTGCTTGTTTGAT 60.370 52.632 0.00 0.00 0.00 2.57
597 639 0.934436 GCGTGCGTGCTTGTTTGATT 60.934 50.000 0.00 0.00 0.00 2.57
598 640 1.044725 CGTGCGTGCTTGTTTGATTC 58.955 50.000 0.00 0.00 0.00 2.52
599 641 1.334059 CGTGCGTGCTTGTTTGATTCT 60.334 47.619 0.00 0.00 0.00 2.40
600 642 2.046313 GTGCGTGCTTGTTTGATTCTG 58.954 47.619 0.00 0.00 0.00 3.02
601 643 1.946081 TGCGTGCTTGTTTGATTCTGA 59.054 42.857 0.00 0.00 0.00 3.27
602 644 2.357323 TGCGTGCTTGTTTGATTCTGAA 59.643 40.909 0.00 0.00 0.00 3.02
603 645 3.004629 TGCGTGCTTGTTTGATTCTGAAT 59.995 39.130 1.81 1.81 0.00 2.57
604 646 3.605486 GCGTGCTTGTTTGATTCTGAATC 59.395 43.478 20.74 20.74 38.40 2.52
605 647 4.614535 GCGTGCTTGTTTGATTCTGAATCT 60.615 41.667 25.83 0.00 38.72 2.40
606 648 4.849926 CGTGCTTGTTTGATTCTGAATCTG 59.150 41.667 25.83 12.82 38.72 2.90
607 649 5.159209 GTGCTTGTTTGATTCTGAATCTGG 58.841 41.667 25.83 13.05 38.72 3.86
608 650 4.171754 GCTTGTTTGATTCTGAATCTGGC 58.828 43.478 25.83 17.05 38.72 4.85
609 651 4.082354 GCTTGTTTGATTCTGAATCTGGCT 60.082 41.667 25.83 0.00 38.72 4.75
610 652 5.633830 TTGTTTGATTCTGAATCTGGCTC 57.366 39.130 25.83 14.45 38.72 4.70
611 653 3.686241 TGTTTGATTCTGAATCTGGCTCG 59.314 43.478 25.83 0.00 38.72 5.03
612 654 2.609427 TGATTCTGAATCTGGCTCGG 57.391 50.000 25.83 0.00 38.72 4.63
613 655 1.833630 TGATTCTGAATCTGGCTCGGT 59.166 47.619 25.83 0.00 38.72 4.69
614 656 2.237143 TGATTCTGAATCTGGCTCGGTT 59.763 45.455 25.83 0.00 38.72 4.44
615 657 2.859165 TTCTGAATCTGGCTCGGTTT 57.141 45.000 0.00 0.00 0.00 3.27
616 658 2.099141 TCTGAATCTGGCTCGGTTTG 57.901 50.000 0.00 0.00 0.00 2.93
617 659 1.089920 CTGAATCTGGCTCGGTTTGG 58.910 55.000 0.00 0.00 0.00 3.28
618 660 0.960364 TGAATCTGGCTCGGTTTGGC 60.960 55.000 0.00 0.00 0.00 4.52
619 661 0.678048 GAATCTGGCTCGGTTTGGCT 60.678 55.000 0.00 0.00 0.00 4.75
620 662 0.251341 AATCTGGCTCGGTTTGGCTT 60.251 50.000 0.00 0.00 0.00 4.35
621 663 0.678048 ATCTGGCTCGGTTTGGCTTC 60.678 55.000 0.00 0.00 0.00 3.86
622 664 1.302832 CTGGCTCGGTTTGGCTTCT 60.303 57.895 0.00 0.00 0.00 2.85
623 665 0.890996 CTGGCTCGGTTTGGCTTCTT 60.891 55.000 0.00 0.00 0.00 2.52
624 666 0.467290 TGGCTCGGTTTGGCTTCTTT 60.467 50.000 0.00 0.00 0.00 2.52
625 667 1.202830 TGGCTCGGTTTGGCTTCTTTA 60.203 47.619 0.00 0.00 0.00 1.85
626 668 2.092323 GGCTCGGTTTGGCTTCTTTAT 58.908 47.619 0.00 0.00 0.00 1.40
627 669 2.159379 GGCTCGGTTTGGCTTCTTTATG 60.159 50.000 0.00 0.00 0.00 1.90
628 670 2.747446 GCTCGGTTTGGCTTCTTTATGA 59.253 45.455 0.00 0.00 0.00 2.15
629 671 3.190535 GCTCGGTTTGGCTTCTTTATGAA 59.809 43.478 0.00 0.00 0.00 2.57
632 674 5.007034 TCGGTTTGGCTTCTTTATGAATCA 58.993 37.500 0.00 0.00 33.71 2.57
701 743 1.194547 CACTACATTTGTTGCGCGTCT 59.805 47.619 8.43 0.00 0.00 4.18
943 995 1.891811 CTCTGCTCTGTCCTCTGTTGA 59.108 52.381 0.00 0.00 0.00 3.18
1305 1357 7.097834 TGCATGAAATATGTTGCATTTGAAGA 58.902 30.769 0.00 0.00 39.98 2.87
1343 1395 5.192522 AGGAGGTTCTATGGATGTGATGTTT 59.807 40.000 0.00 0.00 0.00 2.83
1345 1397 5.440610 AGGTTCTATGGATGTGATGTTTCC 58.559 41.667 0.00 0.00 0.00 3.13
1691 1767 4.961438 AATTGAAGCATTGACCCTGTTT 57.039 36.364 0.00 0.00 0.00 2.83
1818 1928 4.233632 TGCAGGATGGTATTGATTGTGA 57.766 40.909 0.00 0.00 35.86 3.58
2370 2640 6.119240 TGAGAAGATCAAGTCAATCCTTGT 57.881 37.500 0.00 0.00 42.01 3.16
2480 2759 7.294720 TGGGAATCCACCTAGTTATGTAATGAT 59.705 37.037 0.09 0.00 38.32 2.45
2778 3882 6.722129 AGTTCTGAACCATACTAGTTCTCAGT 59.278 38.462 16.48 0.00 43.28 3.41
2971 4075 5.373222 ACCAAATTGTGCACTGACTAGTTA 58.627 37.500 19.41 0.00 34.07 2.24
2994 4098 4.290196 ACCACTAGCATAAAAGTAACCCCA 59.710 41.667 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 151 7.094075 CCCTCAGTTCTTTCATTCATTCATTCA 60.094 37.037 0.00 0.00 0.00 2.57
133 175 2.722201 GCTCCACGGTACCCCTCAG 61.722 68.421 6.25 0.00 0.00 3.35
134 176 2.682494 GCTCCACGGTACCCCTCA 60.682 66.667 6.25 0.00 0.00 3.86
226 268 0.318275 GCCTCCTCGACGACATGATC 60.318 60.000 0.00 0.00 0.00 2.92
227 269 1.736586 GCCTCCTCGACGACATGAT 59.263 57.895 0.00 0.00 0.00 2.45
228 270 2.761195 CGCCTCCTCGACGACATGA 61.761 63.158 0.00 0.00 0.00 3.07
229 271 2.278206 CGCCTCCTCGACGACATG 60.278 66.667 0.00 0.00 0.00 3.21
230 272 3.518998 CCGCCTCCTCGACGACAT 61.519 66.667 0.00 0.00 0.00 3.06
231 273 4.710167 TCCGCCTCCTCGACGACA 62.710 66.667 0.00 0.00 0.00 4.35
232 274 3.878519 CTCCGCCTCCTCGACGAC 61.879 72.222 0.00 0.00 0.00 4.34
235 277 3.213402 CTCCTCCGCCTCCTCGAC 61.213 72.222 0.00 0.00 0.00 4.20
238 280 3.223589 GAGCTCCTCCGCCTCCTC 61.224 72.222 0.87 0.00 0.00 3.71
241 283 4.200283 CACGAGCTCCTCCGCCTC 62.200 72.222 8.47 0.00 0.00 4.70
244 286 4.500116 GACCACGAGCTCCTCCGC 62.500 72.222 8.47 0.00 0.00 5.54
245 287 3.827898 GGACCACGAGCTCCTCCG 61.828 72.222 8.47 0.00 0.00 4.63
246 288 2.363147 AGGACCACGAGCTCCTCC 60.363 66.667 8.47 7.18 30.37 4.30
247 289 3.202467 GAGGACCACGAGCTCCTC 58.798 66.667 8.47 8.24 44.59 3.71
248 290 2.363147 GGAGGACCACGAGCTCCT 60.363 66.667 8.47 0.00 39.81 3.69
249 291 3.827898 CGGAGGACCACGAGCTCC 61.828 72.222 8.47 0.00 35.59 4.70
262 304 1.807886 CTACCACTTCGTCCCGGAG 59.192 63.158 0.73 0.00 38.61 4.63
263 305 2.345760 GCTACCACTTCGTCCCGGA 61.346 63.158 0.73 0.00 0.00 5.14
264 306 2.183555 GCTACCACTTCGTCCCGG 59.816 66.667 0.00 0.00 0.00 5.73
265 307 2.183555 GGCTACCACTTCGTCCCG 59.816 66.667 0.00 0.00 0.00 5.14
266 308 1.988406 AGGGCTACCACTTCGTCCC 60.988 63.158 0.00 0.00 40.13 4.46
267 309 1.218316 CAGGGCTACCACTTCGTCC 59.782 63.158 0.00 0.00 40.13 4.79
268 310 1.448013 GCAGGGCTACCACTTCGTC 60.448 63.158 0.00 0.00 40.13 4.20
269 311 2.663196 GCAGGGCTACCACTTCGT 59.337 61.111 0.00 0.00 40.13 3.85
270 312 2.509336 CGCAGGGCTACCACTTCG 60.509 66.667 0.00 0.00 40.13 3.79
299 341 2.654912 GCGACGACTGGTTGAACCG 61.655 63.158 10.16 7.23 42.58 4.44
300 342 2.315386 GGCGACGACTGGTTGAACC 61.315 63.158 7.57 7.57 39.22 3.62
301 343 3.241177 GGCGACGACTGGTTGAAC 58.759 61.111 0.00 0.00 31.00 3.18
331 373 0.820891 CCATGGGGAAGATGCCGAAG 60.821 60.000 2.85 0.00 35.59 3.79
332 374 1.227102 CCATGGGGAAGATGCCGAA 59.773 57.895 2.85 0.00 35.59 4.30
333 375 2.918248 CCATGGGGAAGATGCCGA 59.082 61.111 2.85 0.00 35.59 5.54
334 376 2.908940 GCCATGGGGAAGATGCCG 60.909 66.667 15.13 0.00 35.59 5.69
335 377 2.908940 CGCCATGGGGAAGATGCC 60.909 66.667 23.98 0.00 35.59 4.40
336 378 2.124151 ACGCCATGGGGAAGATGC 60.124 61.111 33.50 6.02 35.59 3.91
337 379 2.484062 GCACGCCATGGGGAAGATG 61.484 63.158 33.50 21.69 35.59 2.90
338 380 2.124151 GCACGCCATGGGGAAGAT 60.124 61.111 33.50 9.86 35.59 2.40
339 381 4.776322 CGCACGCCATGGGGAAGA 62.776 66.667 33.50 0.00 37.60 2.87
375 417 3.471244 CTAAGGTCGCCGAGCTCCG 62.471 68.421 20.10 9.65 39.62 4.63
376 418 2.413765 CTAAGGTCGCCGAGCTCC 59.586 66.667 20.10 1.05 39.62 4.70
377 419 1.226717 CACTAAGGTCGCCGAGCTC 60.227 63.158 20.10 2.73 39.62 4.09
378 420 2.711922 CCACTAAGGTCGCCGAGCT 61.712 63.158 13.87 13.87 42.52 4.09
379 421 2.202756 CCACTAAGGTCGCCGAGC 60.203 66.667 8.49 8.49 0.00 5.03
380 422 1.392710 ATCCCACTAAGGTCGCCGAG 61.393 60.000 0.00 0.00 34.66 4.63
381 423 1.380785 ATCCCACTAAGGTCGCCGA 60.381 57.895 0.00 0.00 34.66 5.54
382 424 1.227263 CATCCCACTAAGGTCGCCG 60.227 63.158 0.00 0.00 34.66 6.46
383 425 1.146263 CCATCCCACTAAGGTCGCC 59.854 63.158 0.00 0.00 34.66 5.54
384 426 1.146263 CCCATCCCACTAAGGTCGC 59.854 63.158 0.00 0.00 34.66 5.19
385 427 0.753262 CTCCCATCCCACTAAGGTCG 59.247 60.000 0.00 0.00 34.66 4.79
386 428 2.176247 TCTCCCATCCCACTAAGGTC 57.824 55.000 0.00 0.00 34.66 3.85
387 429 2.412591 CATCTCCCATCCCACTAAGGT 58.587 52.381 0.00 0.00 34.66 3.50
388 430 1.701847 CCATCTCCCATCCCACTAAGG 59.298 57.143 0.00 0.00 37.03 2.69
389 431 2.694397 TCCATCTCCCATCCCACTAAG 58.306 52.381 0.00 0.00 0.00 2.18
390 432 2.777692 GTTCCATCTCCCATCCCACTAA 59.222 50.000 0.00 0.00 0.00 2.24
391 433 2.022035 AGTTCCATCTCCCATCCCACTA 60.022 50.000 0.00 0.00 0.00 2.74
392 434 1.216990 GTTCCATCTCCCATCCCACT 58.783 55.000 0.00 0.00 0.00 4.00
393 435 1.141858 GAGTTCCATCTCCCATCCCAC 59.858 57.143 0.00 0.00 0.00 4.61
394 436 1.511613 GAGTTCCATCTCCCATCCCA 58.488 55.000 0.00 0.00 0.00 4.37
395 437 0.394565 CGAGTTCCATCTCCCATCCC 59.605 60.000 0.00 0.00 0.00 3.85
396 438 1.342819 CTCGAGTTCCATCTCCCATCC 59.657 57.143 3.62 0.00 0.00 3.51
397 439 1.342819 CCTCGAGTTCCATCTCCCATC 59.657 57.143 12.31 0.00 0.00 3.51
398 440 1.062886 TCCTCGAGTTCCATCTCCCAT 60.063 52.381 12.31 0.00 0.00 4.00
399 441 0.335019 TCCTCGAGTTCCATCTCCCA 59.665 55.000 12.31 0.00 0.00 4.37
400 442 1.036707 CTCCTCGAGTTCCATCTCCC 58.963 60.000 12.31 0.00 0.00 4.30
401 443 1.036707 CCTCCTCGAGTTCCATCTCC 58.963 60.000 12.31 0.00 0.00 3.71
402 444 1.953686 CTCCTCCTCGAGTTCCATCTC 59.046 57.143 12.31 0.00 0.00 2.75
403 445 1.286553 ACTCCTCCTCGAGTTCCATCT 59.713 52.381 12.31 0.00 40.23 2.90
404 446 1.770294 ACTCCTCCTCGAGTTCCATC 58.230 55.000 12.31 0.00 40.23 3.51
410 452 2.344203 CGGCAACTCCTCCTCGAGT 61.344 63.158 12.31 0.00 45.12 4.18
411 453 2.492090 CGGCAACTCCTCCTCGAG 59.508 66.667 5.13 5.13 35.88 4.04
412 454 3.068691 CCGGCAACTCCTCCTCGA 61.069 66.667 0.00 0.00 0.00 4.04
413 455 4.148825 CCCGGCAACTCCTCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
414 456 3.787001 CCCCGGCAACTCCTCCTC 61.787 72.222 0.00 0.00 0.00 3.71
415 457 3.864983 TTCCCCGGCAACTCCTCCT 62.865 63.158 0.00 0.00 0.00 3.69
416 458 3.327404 TTCCCCGGCAACTCCTCC 61.327 66.667 0.00 0.00 0.00 4.30
417 459 2.046217 GTTCCCCGGCAACTCCTC 60.046 66.667 0.00 0.00 0.00 3.71
418 460 2.457323 TTGTTCCCCGGCAACTCCT 61.457 57.895 13.86 0.00 0.00 3.69
419 461 2.114411 TTGTTCCCCGGCAACTCC 59.886 61.111 13.86 0.00 0.00 3.85
420 462 1.104577 TTGTTGTTCCCCGGCAACTC 61.105 55.000 19.25 11.39 43.66 3.01
421 463 0.469144 ATTGTTGTTCCCCGGCAACT 60.469 50.000 19.25 2.47 43.66 3.16
422 464 0.038618 GATTGTTGTTCCCCGGCAAC 60.039 55.000 13.80 13.80 43.60 4.17
423 465 0.178975 AGATTGTTGTTCCCCGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
424 466 0.893270 CAGATTGTTGTTCCCCGGCA 60.893 55.000 0.00 0.00 0.00 5.69
425 467 1.883021 CAGATTGTTGTTCCCCGGC 59.117 57.895 0.00 0.00 0.00 6.13
426 468 1.883021 GCAGATTGTTGTTCCCCGG 59.117 57.895 0.00 0.00 0.00 5.73
427 469 1.234615 ACGCAGATTGTTGTTCCCCG 61.235 55.000 0.00 0.00 0.00 5.73
428 470 0.521735 GACGCAGATTGTTGTTCCCC 59.478 55.000 0.00 0.00 0.00 4.81
429 471 0.521735 GGACGCAGATTGTTGTTCCC 59.478 55.000 0.00 0.00 0.00 3.97
430 472 0.165944 CGGACGCAGATTGTTGTTCC 59.834 55.000 0.00 0.00 0.00 3.62
431 473 0.452784 GCGGACGCAGATTGTTGTTC 60.453 55.000 12.31 0.00 41.49 3.18
432 474 1.574428 GCGGACGCAGATTGTTGTT 59.426 52.632 12.31 0.00 41.49 2.83
433 475 2.667318 CGCGGACGCAGATTGTTGT 61.667 57.895 17.35 0.00 42.06 3.32
434 476 2.096406 CGCGGACGCAGATTGTTG 59.904 61.111 17.35 0.00 42.06 3.33
457 499 2.187946 CCCTAACCGCAGCTCCTG 59.812 66.667 0.00 0.00 34.12 3.86
458 500 3.083997 CCCCTAACCGCAGCTCCT 61.084 66.667 0.00 0.00 0.00 3.69
459 501 4.858680 GCCCCTAACCGCAGCTCC 62.859 72.222 0.00 0.00 0.00 4.70
466 508 0.463116 ATAAAGCACGCCCCTAACCG 60.463 55.000 0.00 0.00 0.00 4.44
467 509 1.758936 AATAAAGCACGCCCCTAACC 58.241 50.000 0.00 0.00 0.00 2.85
468 510 3.252458 CCATAATAAAGCACGCCCCTAAC 59.748 47.826 0.00 0.00 0.00 2.34
469 511 3.482436 CCATAATAAAGCACGCCCCTAA 58.518 45.455 0.00 0.00 0.00 2.69
470 512 2.812613 GCCATAATAAAGCACGCCCCTA 60.813 50.000 0.00 0.00 0.00 3.53
471 513 1.981256 CCATAATAAAGCACGCCCCT 58.019 50.000 0.00 0.00 0.00 4.79
472 514 0.313987 GCCATAATAAAGCACGCCCC 59.686 55.000 0.00 0.00 0.00 5.80
473 515 0.040425 CGCCATAATAAAGCACGCCC 60.040 55.000 0.00 0.00 0.00 6.13
474 516 0.941542 TCGCCATAATAAAGCACGCC 59.058 50.000 0.00 0.00 0.00 5.68
475 517 1.656429 CGTCGCCATAATAAAGCACGC 60.656 52.381 0.00 0.00 0.00 5.34
476 518 1.591158 ACGTCGCCATAATAAAGCACG 59.409 47.619 0.00 0.00 37.20 5.34
477 519 2.033151 GGACGTCGCCATAATAAAGCAC 60.033 50.000 9.92 0.00 0.00 4.40
478 520 2.206750 GGACGTCGCCATAATAAAGCA 58.793 47.619 9.92 0.00 0.00 3.91
479 521 1.191647 CGGACGTCGCCATAATAAAGC 59.808 52.381 9.92 0.00 0.00 3.51
495 537 3.195698 GATCGGTTGCCAGCGGAC 61.196 66.667 9.65 0.76 44.32 4.79
496 538 4.467084 GGATCGGTTGCCAGCGGA 62.467 66.667 9.65 0.00 44.32 5.54
504 546 3.750373 ATTCGGCCCGGATCGGTTG 62.750 63.158 0.73 0.00 46.80 3.77
505 547 2.546114 AAATTCGGCCCGGATCGGTT 62.546 55.000 0.73 2.81 46.80 4.44
506 548 2.546114 AAAATTCGGCCCGGATCGGT 62.546 55.000 0.73 0.00 46.80 4.69
508 550 1.092921 TCAAAATTCGGCCCGGATCG 61.093 55.000 0.73 6.54 0.00 3.69
509 551 1.099689 TTCAAAATTCGGCCCGGATC 58.900 50.000 0.73 0.00 0.00 3.36
510 552 1.681264 GATTCAAAATTCGGCCCGGAT 59.319 47.619 0.73 0.00 0.00 4.18
511 553 1.099689 GATTCAAAATTCGGCCCGGA 58.900 50.000 0.73 0.00 0.00 5.14
512 554 0.102300 GGATTCAAAATTCGGCCCGG 59.898 55.000 1.90 0.00 0.00 5.73
513 555 0.248458 CGGATTCAAAATTCGGCCCG 60.248 55.000 0.00 0.00 0.00 6.13
514 556 0.102300 CCGGATTCAAAATTCGGCCC 59.898 55.000 6.47 0.00 34.17 5.80
515 557 3.641031 CCGGATTCAAAATTCGGCC 57.359 52.632 6.47 0.00 34.17 6.13
517 559 1.065551 GGAGCCGGATTCAAAATTCGG 59.934 52.381 5.05 13.85 43.13 4.30
518 560 1.268032 CGGAGCCGGATTCAAAATTCG 60.268 52.381 5.05 0.00 35.56 3.34
519 561 1.743394 ACGGAGCCGGATTCAAAATTC 59.257 47.619 5.05 0.00 44.69 2.17
520 562 1.834188 ACGGAGCCGGATTCAAAATT 58.166 45.000 5.05 0.00 44.69 1.82
521 563 1.472480 CAACGGAGCCGGATTCAAAAT 59.528 47.619 5.05 0.00 44.69 1.82
522 564 0.878416 CAACGGAGCCGGATTCAAAA 59.122 50.000 5.05 0.00 44.69 2.44
523 565 0.958382 CCAACGGAGCCGGATTCAAA 60.958 55.000 5.05 0.00 44.69 2.69
524 566 1.376683 CCAACGGAGCCGGATTCAA 60.377 57.895 5.05 0.00 44.69 2.69
525 567 2.267642 CCAACGGAGCCGGATTCA 59.732 61.111 5.05 0.00 44.69 2.57
526 568 2.513897 CCCAACGGAGCCGGATTC 60.514 66.667 5.05 0.00 44.69 2.52
527 569 4.109675 CCCCAACGGAGCCGGATT 62.110 66.667 5.05 0.00 44.69 3.01
530 572 3.256824 TTAACCCCAACGGAGCCGG 62.257 63.158 14.07 0.00 44.69 6.13
531 573 1.743995 CTTAACCCCAACGGAGCCG 60.744 63.158 7.48 7.48 46.03 5.52
532 574 1.378119 CCTTAACCCCAACGGAGCC 60.378 63.158 0.00 0.00 34.64 4.70
533 575 2.044555 GCCTTAACCCCAACGGAGC 61.045 63.158 0.00 0.00 34.64 4.70
534 576 1.743995 CGCCTTAACCCCAACGGAG 60.744 63.158 0.00 0.00 34.64 4.63
535 577 2.348243 CGCCTTAACCCCAACGGA 59.652 61.111 0.00 0.00 34.64 4.69
536 578 2.748647 CCGCCTTAACCCCAACGG 60.749 66.667 0.00 0.00 37.81 4.44
537 579 2.748647 CCCGCCTTAACCCCAACG 60.749 66.667 0.00 0.00 0.00 4.10
538 580 2.361992 CCCCGCCTTAACCCCAAC 60.362 66.667 0.00 0.00 0.00 3.77
539 581 2.532199 TCCCCGCCTTAACCCCAA 60.532 61.111 0.00 0.00 0.00 4.12
540 582 3.012722 CTCCCCGCCTTAACCCCA 61.013 66.667 0.00 0.00 0.00 4.96
541 583 3.805497 CCTCCCCGCCTTAACCCC 61.805 72.222 0.00 0.00 0.00 4.95
542 584 3.805497 CCCTCCCCGCCTTAACCC 61.805 72.222 0.00 0.00 0.00 4.11
543 585 2.689771 TCCCTCCCCGCCTTAACC 60.690 66.667 0.00 0.00 0.00 2.85
544 586 2.588439 GTCCCTCCCCGCCTTAAC 59.412 66.667 0.00 0.00 0.00 2.01
545 587 3.078836 CGTCCCTCCCCGCCTTAA 61.079 66.667 0.00 0.00 0.00 1.85
575 617 3.749735 AAACAAGCACGCACGCACC 62.750 57.895 0.00 0.00 0.00 5.01
576 618 2.277884 AAACAAGCACGCACGCAC 60.278 55.556 0.00 0.00 0.00 5.34
577 619 2.057654 ATCAAACAAGCACGCACGCA 62.058 50.000 0.00 0.00 0.00 5.24
578 620 0.934436 AATCAAACAAGCACGCACGC 60.934 50.000 0.00 0.00 0.00 5.34
579 621 1.044725 GAATCAAACAAGCACGCACG 58.955 50.000 0.00 0.00 0.00 5.34
580 622 2.046313 CAGAATCAAACAAGCACGCAC 58.954 47.619 0.00 0.00 0.00 5.34
581 623 1.946081 TCAGAATCAAACAAGCACGCA 59.054 42.857 0.00 0.00 0.00 5.24
582 624 2.686558 TCAGAATCAAACAAGCACGC 57.313 45.000 0.00 0.00 0.00 5.34
583 625 4.849926 CAGATTCAGAATCAAACAAGCACG 59.150 41.667 22.70 0.00 40.42 5.34
584 626 5.159209 CCAGATTCAGAATCAAACAAGCAC 58.841 41.667 22.70 0.00 40.42 4.40
585 627 4.321452 GCCAGATTCAGAATCAAACAAGCA 60.321 41.667 22.70 0.00 40.42 3.91
586 628 4.082354 AGCCAGATTCAGAATCAAACAAGC 60.082 41.667 22.70 15.11 40.42 4.01
587 629 5.638783 GAGCCAGATTCAGAATCAAACAAG 58.361 41.667 22.70 7.54 40.42 3.16
588 630 4.154737 CGAGCCAGATTCAGAATCAAACAA 59.845 41.667 22.70 0.00 40.42 2.83
589 631 3.686241 CGAGCCAGATTCAGAATCAAACA 59.314 43.478 22.70 0.00 40.42 2.83
590 632 3.064545 CCGAGCCAGATTCAGAATCAAAC 59.935 47.826 22.70 12.09 40.42 2.93
591 633 3.273434 CCGAGCCAGATTCAGAATCAAA 58.727 45.455 22.70 0.00 40.42 2.69
592 634 2.237143 ACCGAGCCAGATTCAGAATCAA 59.763 45.455 22.70 0.00 40.42 2.57
593 635 1.833630 ACCGAGCCAGATTCAGAATCA 59.166 47.619 22.70 0.00 40.42 2.57
594 636 2.611225 ACCGAGCCAGATTCAGAATC 57.389 50.000 14.56 14.56 38.20 2.52
595 637 3.012518 CAAACCGAGCCAGATTCAGAAT 58.987 45.455 0.00 0.00 0.00 2.40
596 638 2.426522 CAAACCGAGCCAGATTCAGAA 58.573 47.619 0.00 0.00 0.00 3.02
597 639 1.339055 CCAAACCGAGCCAGATTCAGA 60.339 52.381 0.00 0.00 0.00 3.27
598 640 1.089920 CCAAACCGAGCCAGATTCAG 58.910 55.000 0.00 0.00 0.00 3.02
599 641 0.960364 GCCAAACCGAGCCAGATTCA 60.960 55.000 0.00 0.00 0.00 2.57
600 642 0.678048 AGCCAAACCGAGCCAGATTC 60.678 55.000 0.00 0.00 0.00 2.52
601 643 0.251341 AAGCCAAACCGAGCCAGATT 60.251 50.000 0.00 0.00 0.00 2.40
602 644 0.678048 GAAGCCAAACCGAGCCAGAT 60.678 55.000 0.00 0.00 0.00 2.90
603 645 1.302511 GAAGCCAAACCGAGCCAGA 60.303 57.895 0.00 0.00 0.00 3.86
604 646 0.890996 AAGAAGCCAAACCGAGCCAG 60.891 55.000 0.00 0.00 0.00 4.85
605 647 0.467290 AAAGAAGCCAAACCGAGCCA 60.467 50.000 0.00 0.00 0.00 4.75
606 648 1.530323 TAAAGAAGCCAAACCGAGCC 58.470 50.000 0.00 0.00 0.00 4.70
607 649 2.747446 TCATAAAGAAGCCAAACCGAGC 59.253 45.455 0.00 0.00 0.00 5.03
608 650 5.123820 TGATTCATAAAGAAGCCAAACCGAG 59.876 40.000 0.00 0.00 41.89 4.63
609 651 5.007034 TGATTCATAAAGAAGCCAAACCGA 58.993 37.500 0.00 0.00 41.89 4.69
610 652 5.309323 TGATTCATAAAGAAGCCAAACCG 57.691 39.130 0.00 0.00 41.89 4.44
611 653 6.587608 CACTTGATTCATAAAGAAGCCAAACC 59.412 38.462 0.00 0.00 41.89 3.27
612 654 7.370383 TCACTTGATTCATAAAGAAGCCAAAC 58.630 34.615 0.00 0.00 41.89 2.93
613 655 7.523293 TCACTTGATTCATAAAGAAGCCAAA 57.477 32.000 0.00 0.00 41.89 3.28
614 656 7.523293 TTCACTTGATTCATAAAGAAGCCAA 57.477 32.000 0.00 0.00 41.89 4.52
615 657 7.707624 ATTCACTTGATTCATAAAGAAGCCA 57.292 32.000 0.00 0.00 41.89 4.75
616 658 7.009907 GCAATTCACTTGATTCATAAAGAAGCC 59.990 37.037 0.00 0.00 41.89 4.35
617 659 7.543172 TGCAATTCACTTGATTCATAAAGAAGC 59.457 33.333 0.00 0.00 42.87 3.86
618 660 8.975410 TGCAATTCACTTGATTCATAAAGAAG 57.025 30.769 0.00 0.00 36.07 2.85
619 661 9.761504 TTTGCAATTCACTTGATTCATAAAGAA 57.238 25.926 0.00 0.00 36.97 2.52
620 662 9.761504 TTTTGCAATTCACTTGATTCATAAAGA 57.238 25.926 0.00 0.00 36.97 2.52
652 694 4.430137 GATGCTTCAGCTTCAAATGTGA 57.570 40.909 9.28 0.00 42.61 3.58
684 726 1.503294 TGAGACGCGCAACAAATGTA 58.497 45.000 5.73 0.00 0.00 2.29
808 850 2.954753 GCCGTCTGGTTTGTGCGAG 61.955 63.158 0.00 0.00 37.67 5.03
861 903 2.597217 TGGAGGGCAACGCTTTGG 60.597 61.111 4.97 0.00 32.81 3.28
1305 1357 1.068121 CCTCCTCCCAGTGTCCTTTT 58.932 55.000 0.00 0.00 0.00 2.27
1343 1395 4.223953 GGATATTACTGACTGACCTGGGA 58.776 47.826 0.00 0.00 0.00 4.37
1345 1397 5.129485 AGTTGGATATTACTGACTGACCTGG 59.871 44.000 0.00 0.00 0.00 4.45
1444 1497 3.758755 TGTTGCATCTTCAGACAGTCT 57.241 42.857 0.00 0.00 0.00 3.24
1818 1928 2.233271 CATCAACCCACTGAGCAACTT 58.767 47.619 0.00 0.00 0.00 2.66
2392 2667 8.656806 AGGCCACATATTAGCTTAACATAACTA 58.343 33.333 5.01 0.00 0.00 2.24
2511 2790 9.265901 GCAGATAATCATTACACTCATTACAGT 57.734 33.333 0.00 0.00 0.00 3.55
2512 2791 9.264719 TGCAGATAATCATTACACTCATTACAG 57.735 33.333 0.00 0.00 0.00 2.74
2520 2805 8.893727 GGTAGTTTTGCAGATAATCATTACACT 58.106 33.333 0.00 0.00 0.00 3.55
2521 2806 8.129211 GGGTAGTTTTGCAGATAATCATTACAC 58.871 37.037 0.00 0.00 0.00 2.90
2778 3882 7.611467 AGCAATTGTGGTTCAGAACTATTATGA 59.389 33.333 13.13 0.00 28.67 2.15
2971 4075 4.290196 TGGGGTTACTTTTATGCTAGTGGT 59.710 41.667 0.00 0.00 0.00 4.16
2994 4098 1.073923 GGTTCCAGAACACCAGGATGT 59.926 52.381 12.32 0.00 42.85 3.06
3313 4428 1.075305 TTCTGCTGCATCTGCCCAA 59.925 52.632 1.31 0.00 41.18 4.12


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

AutoCloner maintained by Alex Coulton.