Multiple sequence alignment - TraesCS2A01G251700

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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 TraesCS2A01G251700 chr2A 100.000 2414 0 0 1 2414 381504520 381502107 0.000000e+00 4458.0
1 TraesCS2A01G251700 chr2D 87.507 1833 48 56 459 2254 303515655 303513967 0.000000e+00 1949.0
2 TraesCS2A01G251700 chr2D 96.875 224 3 1 1 224 303515960 303515741 2.930000e-99 372.0
3 TraesCS2A01G251700 chr2D 85.083 181 17 4 269 449 533780272 533780102 2.470000e-40 176.0
4 TraesCS2A01G251700 chr2D 87.857 140 7 5 2281 2414 303513977 303513842 3.210000e-34 156.0
5 TraesCS2A01G251700 chr2B 86.968 1458 68 46 995 2414 372089273 372087900 0.000000e+00 1528.0
6 TraesCS2A01G251700 chr2B 88.337 523 17 17 459 964 372089766 372089271 2.670000e-164 588.0
7 TraesCS2A01G251700 chr2B 92.544 228 4 2 1 227 372090088 372089873 5.010000e-82 315.0
8 TraesCS2A01G251700 chr3D 87.135 171 12 6 274 444 575732533 575732373 4.100000e-43 185.0
9 TraesCS2A01G251700 chr3D 86.826 167 12 2 274 440 83491916 83492072 6.860000e-41 178.0
10 TraesCS2A01G251700 chr3D 86.310 168 13 7 274 441 299744336 299744493 8.870000e-40 174.0
11 TraesCS2A01G251700 chr7D 85.795 176 16 8 274 448 42837461 42837294 6.860000e-41 178.0
12 TraesCS2A01G251700 chr7D 86.826 167 12 7 274 440 449448695 449448851 6.860000e-41 178.0
13 TraesCS2A01G251700 chr7D 86.047 172 13 8 274 444 179219920 179220081 8.870000e-40 174.0
14 TraesCS2A01G251700 chr7D 85.227 176 17 6 269 444 513211716 513211550 3.190000e-39 172.0
15 TraesCS2A01G251700 chr4D 85.246 183 14 6 269 450 466669271 466669441 2.470000e-40 176.0
16 TraesCS2A01G251700 chr1A 80.833 120 21 2 1296 1414 562902781 562902899 2.560000e-15 93.5
17 TraesCS2A01G251700 chr3B 80.328 122 20 4 1296 1415 379654012 379654131 3.310000e-14 89.8
18 TraesCS2A01G251700 chr1B 81.416 113 17 4 1307 1417 649670511 649670621 3.310000e-14 89.8
19 TraesCS2A01G251700 chr1B 80.672 119 19 4 1299 1415 651286856 651286740 3.310000e-14 89.8
20 TraesCS2A01G251700 chr5B 80.734 109 17 4 1306 1412 328274092 328274198 5.530000e-12 82.4
21 TraesCS2A01G251700 chr1D 79.032 124 22 4 1296 1417 469795846 469795967 5.530000e-12 82.4
22 TraesCS2A01G251700 chr6D 78.992 119 21 4 1299 1415 17042690 17042574 7.160000e-11 78.7


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 TraesCS2A01G251700 chr2A 381502107 381504520 2413 True 4458.000000 4458 100.000000 1 2414 1 chr2A.!!$R1 2413
1 TraesCS2A01G251700 chr2D 303513842 303515960 2118 True 825.666667 1949 90.746333 1 2414 3 chr2D.!!$R2 2413
2 TraesCS2A01G251700 chr2B 372087900 372090088 2188 True 810.333333 1528 89.283000 1 2414 3 chr2B.!!$R1 2413

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
156 157 0.321653 GTGTCCATGCTTCGTTCCCT 60.322 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1707 0.318869 AACACACCATGCATTGCACG 60.319 50.0 14.66 5.42 43.04 5.34 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
135 136 1.206745 CGACGCTTGTCTTGTCACGT 61.207 55.000 0.00 0.00 40.61 4.49
148 149 0.944311 GTCACGTCGTGTCCATGCTT 60.944 55.000 23.82 0.00 34.79 3.91
154 155 0.669318 TCGTGTCCATGCTTCGTTCC 60.669 55.000 0.00 0.00 0.00 3.62
155 156 1.635663 CGTGTCCATGCTTCGTTCCC 61.636 60.000 0.00 0.00 0.00 3.97
156 157 0.321653 GTGTCCATGCTTCGTTCCCT 60.322 55.000 0.00 0.00 0.00 4.20
157 158 0.400213 TGTCCATGCTTCGTTCCCTT 59.600 50.000 0.00 0.00 0.00 3.95
224 225 6.486657 GCCTGCAGATACATGTAAATTCCTAA 59.513 38.462 17.39 0.00 0.00 2.69
225 226 7.308229 GCCTGCAGATACATGTAAATTCCTAAG 60.308 40.741 17.39 1.52 0.00 2.18
226 227 7.716998 CCTGCAGATACATGTAAATTCCTAAGT 59.283 37.037 17.39 0.00 0.00 2.24
235 295 7.232534 ACATGTAAATTCCTAAGTTTGAAGGCA 59.767 33.333 0.00 0.00 32.55 4.75
258 331 9.382275 GGCACATTGGTTCATTATAAAGAAAAT 57.618 29.630 4.78 0.74 0.00 1.82
272 345 9.834628 TTATAAAGAAAATAGTTTTGCTGACCG 57.165 29.630 0.00 0.00 30.64 4.79
273 346 6.385649 AAAGAAAATAGTTTTGCTGACCGA 57.614 33.333 0.00 0.00 30.64 4.69
274 347 5.613358 AGAAAATAGTTTTGCTGACCGAG 57.387 39.130 0.00 0.00 28.91 4.63
275 348 5.305585 AGAAAATAGTTTTGCTGACCGAGA 58.694 37.500 0.00 0.00 28.91 4.04
276 349 5.179555 AGAAAATAGTTTTGCTGACCGAGAC 59.820 40.000 0.00 0.00 28.91 3.36
277 350 3.963428 ATAGTTTTGCTGACCGAGACT 57.037 42.857 0.00 0.00 0.00 3.24
278 351 2.622064 AGTTTTGCTGACCGAGACTT 57.378 45.000 0.00 0.00 0.00 3.01
279 352 2.484889 AGTTTTGCTGACCGAGACTTC 58.515 47.619 0.00 0.00 0.00 3.01
280 353 1.192534 GTTTTGCTGACCGAGACTTCG 59.807 52.381 0.00 0.00 46.29 3.79
281 354 0.387929 TTTGCTGACCGAGACTTCGT 59.612 50.000 0.00 0.00 45.28 3.85
282 355 0.387929 TTGCTGACCGAGACTTCGTT 59.612 50.000 0.00 0.00 45.28 3.85
283 356 1.241165 TGCTGACCGAGACTTCGTTA 58.759 50.000 0.00 0.00 45.28 3.18
284 357 1.816835 TGCTGACCGAGACTTCGTTAT 59.183 47.619 0.00 0.00 45.28 1.89
285 358 3.011818 TGCTGACCGAGACTTCGTTATA 58.988 45.455 0.00 0.00 45.28 0.98
286 359 3.630769 TGCTGACCGAGACTTCGTTATAT 59.369 43.478 0.00 0.00 45.28 0.86
287 360 4.220572 GCTGACCGAGACTTCGTTATATC 58.779 47.826 0.00 0.00 45.28 1.63
288 361 4.023878 GCTGACCGAGACTTCGTTATATCT 60.024 45.833 0.00 0.00 45.28 1.98
289 362 5.670149 TGACCGAGACTTCGTTATATCTC 57.330 43.478 0.00 0.00 45.28 2.75
290 363 5.121105 TGACCGAGACTTCGTTATATCTCA 58.879 41.667 0.00 0.00 45.28 3.27
291 364 5.236695 TGACCGAGACTTCGTTATATCTCAG 59.763 44.000 0.00 0.00 45.28 3.35
292 365 5.124645 ACCGAGACTTCGTTATATCTCAGT 58.875 41.667 0.00 0.00 45.28 3.41
293 366 5.589452 ACCGAGACTTCGTTATATCTCAGTT 59.411 40.000 0.00 0.00 45.28 3.16
294 367 5.910166 CCGAGACTTCGTTATATCTCAGTTG 59.090 44.000 0.00 0.00 45.28 3.16
295 368 6.238402 CCGAGACTTCGTTATATCTCAGTTGA 60.238 42.308 0.00 0.00 45.28 3.18
296 369 7.356540 CGAGACTTCGTTATATCTCAGTTGAT 58.643 38.462 0.00 0.00 41.84 2.57
297 370 7.322461 CGAGACTTCGTTATATCTCAGTTGATG 59.678 40.741 0.00 0.00 41.84 3.07
298 371 8.001881 AGACTTCGTTATATCTCAGTTGATGT 57.998 34.615 0.00 0.00 0.00 3.06
299 372 8.470805 AGACTTCGTTATATCTCAGTTGATGTT 58.529 33.333 0.00 0.00 0.00 2.71
300 373 9.731819 GACTTCGTTATATCTCAGTTGATGTTA 57.268 33.333 0.00 0.00 0.00 2.41
329 402 9.474920 TTTCTTTAATTTTGCATGAAGATTCGT 57.525 25.926 0.00 0.00 0.00 3.85
331 404 9.554724 TCTTTAATTTTGCATGAAGATTCGTAC 57.445 29.630 0.00 0.00 0.00 3.67
332 405 9.340695 CTTTAATTTTGCATGAAGATTCGTACA 57.659 29.630 0.00 0.00 0.00 2.90
333 406 9.684448 TTTAATTTTGCATGAAGATTCGTACAA 57.316 25.926 0.00 0.00 29.90 2.41
334 407 9.684448 TTAATTTTGCATGAAGATTCGTACAAA 57.316 25.926 8.45 8.45 37.56 2.83
335 408 8.586570 AATTTTGCATGAAGATTCGTACAAAA 57.413 26.923 20.24 20.24 45.78 2.44
336 409 7.993821 TTTTGCATGAAGATTCGTACAAAAA 57.006 28.000 17.53 9.03 42.21 1.94
401 474 9.415008 ACTACTGTATATCATTTGAGTGAGACT 57.585 33.333 0.00 0.00 0.00 3.24
403 476 8.939201 ACTGTATATCATTTGAGTGAGACTTG 57.061 34.615 0.00 0.00 0.00 3.16
404 477 7.984050 ACTGTATATCATTTGAGTGAGACTTGG 59.016 37.037 0.00 0.00 0.00 3.61
405 478 7.851228 TGTATATCATTTGAGTGAGACTTGGT 58.149 34.615 0.00 0.00 0.00 3.67
406 479 8.321353 TGTATATCATTTGAGTGAGACTTGGTT 58.679 33.333 0.00 0.00 0.00 3.67
407 480 9.817809 GTATATCATTTGAGTGAGACTTGGTTA 57.182 33.333 0.00 0.00 0.00 2.85
409 482 7.678947 ATCATTTGAGTGAGACTTGGTTAAG 57.321 36.000 0.00 0.00 39.86 1.85
420 493 4.240175 ACTTGGTTAAGTCTCAGTCGAC 57.760 45.455 7.70 7.70 43.53 4.20
421 494 3.890147 ACTTGGTTAAGTCTCAGTCGACT 59.110 43.478 13.58 13.58 43.53 4.18
422 495 3.917329 TGGTTAAGTCTCAGTCGACTG 57.083 47.619 34.76 34.76 43.14 3.51
423 496 6.438740 ACTTGGTTAAGTCTCAGTCGACTGA 61.439 44.000 38.24 38.24 45.53 3.41
432 505 2.923605 CAGTCGACTGAGACCTAACC 57.076 55.000 36.73 0.00 46.59 2.85
433 506 2.160205 CAGTCGACTGAGACCTAACCA 58.840 52.381 36.73 0.00 46.59 3.67
434 507 2.095161 CAGTCGACTGAGACCTAACCAC 60.095 54.545 36.73 0.00 46.59 4.16
435 508 1.884579 GTCGACTGAGACCTAACCACA 59.115 52.381 8.70 0.00 35.22 4.17
436 509 1.884579 TCGACTGAGACCTAACCACAC 59.115 52.381 0.00 0.00 0.00 3.82
437 510 1.067776 CGACTGAGACCTAACCACACC 60.068 57.143 0.00 0.00 0.00 4.16
438 511 1.275573 GACTGAGACCTAACCACACCC 59.724 57.143 0.00 0.00 0.00 4.61
439 512 1.132817 ACTGAGACCTAACCACACCCT 60.133 52.381 0.00 0.00 0.00 4.34
440 513 2.111255 ACTGAGACCTAACCACACCCTA 59.889 50.000 0.00 0.00 0.00 3.53
441 514 3.170717 CTGAGACCTAACCACACCCTAA 58.829 50.000 0.00 0.00 0.00 2.69
442 515 3.581332 CTGAGACCTAACCACACCCTAAA 59.419 47.826 0.00 0.00 0.00 1.85
443 516 3.975312 TGAGACCTAACCACACCCTAAAA 59.025 43.478 0.00 0.00 0.00 1.52
444 517 4.041198 TGAGACCTAACCACACCCTAAAAG 59.959 45.833 0.00 0.00 0.00 2.27
445 518 4.237018 AGACCTAACCACACCCTAAAAGA 58.763 43.478 0.00 0.00 0.00 2.52
446 519 4.661709 AGACCTAACCACACCCTAAAAGAA 59.338 41.667 0.00 0.00 0.00 2.52
447 520 5.133153 AGACCTAACCACACCCTAAAAGAAA 59.867 40.000 0.00 0.00 0.00 2.52
448 521 5.768752 ACCTAACCACACCCTAAAAGAAAA 58.231 37.500 0.00 0.00 0.00 2.29
449 522 5.831525 ACCTAACCACACCCTAAAAGAAAAG 59.168 40.000 0.00 0.00 0.00 2.27
450 523 6.066032 CCTAACCACACCCTAAAAGAAAAGA 58.934 40.000 0.00 0.00 0.00 2.52
451 524 6.206829 CCTAACCACACCCTAAAAGAAAAGAG 59.793 42.308 0.00 0.00 0.00 2.85
452 525 5.125367 ACCACACCCTAAAAGAAAAGAGT 57.875 39.130 0.00 0.00 0.00 3.24
453 526 6.256643 ACCACACCCTAAAAGAAAAGAGTA 57.743 37.500 0.00 0.00 0.00 2.59
454 527 6.060136 ACCACACCCTAAAAGAAAAGAGTAC 58.940 40.000 0.00 0.00 0.00 2.73
455 528 6.126565 ACCACACCCTAAAAGAAAAGAGTACT 60.127 38.462 0.00 0.00 0.00 2.73
456 529 7.071572 ACCACACCCTAAAAGAAAAGAGTACTA 59.928 37.037 0.00 0.00 0.00 1.82
457 530 8.101419 CCACACCCTAAAAGAAAAGAGTACTAT 58.899 37.037 0.00 0.00 0.00 2.12
592 680 1.747709 TTCCTTCTCCTCGTCTACGG 58.252 55.000 2.24 0.00 40.29 4.02
600 688 1.068055 TCCTCGTCTACGGACAAAAGC 60.068 52.381 2.24 0.00 42.21 3.51
601 689 1.067776 CCTCGTCTACGGACAAAAGCT 60.068 52.381 2.24 0.00 42.21 3.74
602 690 2.163010 CCTCGTCTACGGACAAAAGCTA 59.837 50.000 2.24 0.00 42.21 3.32
621 709 4.477780 GCTACTACCGCATAGCTCTTTAG 58.522 47.826 0.00 0.00 40.59 1.85
643 731 1.840737 TGCTCCTCGCTTTACTCTCT 58.159 50.000 0.00 0.00 40.11 3.10
644 732 3.000684 TGCTCCTCGCTTTACTCTCTA 57.999 47.619 0.00 0.00 40.11 2.43
645 733 3.556999 TGCTCCTCGCTTTACTCTCTAT 58.443 45.455 0.00 0.00 40.11 1.98
646 734 3.566322 TGCTCCTCGCTTTACTCTCTATC 59.434 47.826 0.00 0.00 40.11 2.08
647 735 3.818773 GCTCCTCGCTTTACTCTCTATCT 59.181 47.826 0.00 0.00 35.14 1.98
648 736 4.083484 GCTCCTCGCTTTACTCTCTATCTC 60.083 50.000 0.00 0.00 35.14 2.75
818 906 3.193263 CCATCACACTTCCATTCGAGAG 58.807 50.000 0.00 0.00 0.00 3.20
819 907 3.118992 CCATCACACTTCCATTCGAGAGA 60.119 47.826 0.00 0.00 39.20 3.10
820 908 3.577649 TCACACTTCCATTCGAGAGAC 57.422 47.619 0.00 0.00 41.84 3.36
821 909 2.890945 TCACACTTCCATTCGAGAGACA 59.109 45.455 0.00 0.00 41.84 3.41
822 910 2.989840 CACACTTCCATTCGAGAGACAC 59.010 50.000 0.00 0.00 41.84 3.67
823 911 2.628178 ACACTTCCATTCGAGAGACACA 59.372 45.455 0.00 0.00 41.84 3.72
957 1053 1.880186 CTAGCTAGCTAGGCGAGGC 59.120 63.158 34.95 7.57 41.58 4.70
980 1076 2.440430 CGGCGAGGGAGAAGGAGA 60.440 66.667 0.00 0.00 0.00 3.71
981 1077 2.052690 CGGCGAGGGAGAAGGAGAA 61.053 63.158 0.00 0.00 0.00 2.87
982 1078 1.819905 GGCGAGGGAGAAGGAGAAG 59.180 63.158 0.00 0.00 0.00 2.85
983 1079 1.681486 GGCGAGGGAGAAGGAGAAGG 61.681 65.000 0.00 0.00 0.00 3.46
984 1080 0.684805 GCGAGGGAGAAGGAGAAGGA 60.685 60.000 0.00 0.00 0.00 3.36
985 1081 1.398692 CGAGGGAGAAGGAGAAGGAG 58.601 60.000 0.00 0.00 0.00 3.69
986 1082 1.064314 CGAGGGAGAAGGAGAAGGAGA 60.064 57.143 0.00 0.00 0.00 3.71
987 1083 2.621929 CGAGGGAGAAGGAGAAGGAGAA 60.622 54.545 0.00 0.00 0.00 2.87
988 1084 3.031013 GAGGGAGAAGGAGAAGGAGAAG 58.969 54.545 0.00 0.00 0.00 2.85
989 1085 2.385417 AGGGAGAAGGAGAAGGAGAAGT 59.615 50.000 0.00 0.00 0.00 3.01
990 1086 3.598782 AGGGAGAAGGAGAAGGAGAAGTA 59.401 47.826 0.00 0.00 0.00 2.24
991 1087 3.958147 GGGAGAAGGAGAAGGAGAAGTAG 59.042 52.174 0.00 0.00 0.00 2.57
1498 1601 3.181518 CGTTTACTTTGTGTGTTGGTCGT 60.182 43.478 0.00 0.00 0.00 4.34
1499 1602 4.336932 GTTTACTTTGTGTGTTGGTCGTC 58.663 43.478 0.00 0.00 0.00 4.20
1500 1603 2.396590 ACTTTGTGTGTTGGTCGTCT 57.603 45.000 0.00 0.00 0.00 4.18
1501 1604 2.706890 ACTTTGTGTGTTGGTCGTCTT 58.293 42.857 0.00 0.00 0.00 3.01
1502 1605 3.078837 ACTTTGTGTGTTGGTCGTCTTT 58.921 40.909 0.00 0.00 0.00 2.52
1557 1694 3.807538 GCCTGTGGCTGTGCGATG 61.808 66.667 0.73 0.00 46.69 3.84
1558 1695 3.129502 CCTGTGGCTGTGCGATGG 61.130 66.667 0.00 0.00 0.00 3.51
1559 1696 2.046988 CTGTGGCTGTGCGATGGA 60.047 61.111 0.00 0.00 0.00 3.41
1560 1697 1.450848 CTGTGGCTGTGCGATGGAT 60.451 57.895 0.00 0.00 0.00 3.41
1561 1698 1.712018 CTGTGGCTGTGCGATGGATG 61.712 60.000 0.00 0.00 0.00 3.51
1562 1699 2.124612 TGGCTGTGCGATGGATGG 60.125 61.111 0.00 0.00 0.00 3.51
1563 1700 2.190313 GGCTGTGCGATGGATGGA 59.810 61.111 0.00 0.00 0.00 3.41
1564 1701 2.182842 GGCTGTGCGATGGATGGAC 61.183 63.158 0.00 0.00 0.00 4.02
1565 1702 2.528743 GCTGTGCGATGGATGGACG 61.529 63.158 0.00 0.00 0.00 4.79
1569 1706 3.630148 GCGATGGATGGACGCGTG 61.630 66.667 20.70 0.00 42.65 5.34
1570 1707 3.630148 CGATGGATGGACGCGTGC 61.630 66.667 24.88 24.88 0.00 5.34
1571 1708 3.630148 GATGGATGGACGCGTGCG 61.630 66.667 25.71 13.39 46.03 5.34
1662 1799 1.714899 GCCTTGTCAGTTGCGTGTGT 61.715 55.000 0.00 0.00 0.00 3.72
1663 1800 0.732571 CCTTGTCAGTTGCGTGTGTT 59.267 50.000 0.00 0.00 0.00 3.32
1664 1801 1.132262 CCTTGTCAGTTGCGTGTGTTT 59.868 47.619 0.00 0.00 0.00 2.83
1665 1802 2.176369 CTTGTCAGTTGCGTGTGTTTG 58.824 47.619 0.00 0.00 0.00 2.93
1666 1803 1.160989 TGTCAGTTGCGTGTGTTTGT 58.839 45.000 0.00 0.00 0.00 2.83
1667 1804 1.135831 TGTCAGTTGCGTGTGTTTGTG 60.136 47.619 0.00 0.00 0.00 3.33
1668 1805 1.135803 GTCAGTTGCGTGTGTTTGTGT 60.136 47.619 0.00 0.00 0.00 3.72
1699 1836 7.859325 TTTTTAGGTGATGGTTATCTAGCAC 57.141 36.000 0.00 0.00 39.96 4.40
1701 1838 3.031736 AGGTGATGGTTATCTAGCACGT 58.968 45.455 0.31 0.00 41.23 4.49
1702 1839 4.212716 AGGTGATGGTTATCTAGCACGTA 58.787 43.478 0.00 0.00 41.23 3.57
1703 1840 4.037684 AGGTGATGGTTATCTAGCACGTAC 59.962 45.833 0.00 0.00 41.23 3.67
1704 1841 4.037684 GGTGATGGTTATCTAGCACGTACT 59.962 45.833 0.00 0.00 41.23 2.73
1705 1842 5.240183 GGTGATGGTTATCTAGCACGTACTA 59.760 44.000 0.00 0.00 41.23 1.82
1706 1843 6.372185 GTGATGGTTATCTAGCACGTACTAG 58.628 44.000 15.53 15.53 40.92 2.57
1707 1844 6.017275 GTGATGGTTATCTAGCACGTACTAGT 60.017 42.308 19.84 11.38 40.50 2.57
1708 1845 6.544931 TGATGGTTATCTAGCACGTACTAGTT 59.455 38.462 19.84 15.02 40.50 2.24
1709 1846 6.369059 TGGTTATCTAGCACGTACTAGTTC 57.631 41.667 19.84 10.24 40.50 3.01
1710 1847 5.007039 TGGTTATCTAGCACGTACTAGTTCG 59.993 44.000 19.84 18.88 40.50 3.95
1711 1848 5.007136 GGTTATCTAGCACGTACTAGTTCGT 59.993 44.000 20.20 20.20 40.50 3.85
1712 1849 6.457528 GGTTATCTAGCACGTACTAGTTCGTT 60.458 42.308 22.83 13.38 40.50 3.85
1713 1850 7.254455 GGTTATCTAGCACGTACTAGTTCGTTA 60.254 40.741 22.83 13.76 40.50 3.18
1714 1851 5.456192 TCTAGCACGTACTAGTTCGTTAC 57.544 43.478 22.83 17.71 40.50 2.50
1715 1852 4.929211 TCTAGCACGTACTAGTTCGTTACA 59.071 41.667 22.83 10.81 40.50 2.41
1716 1853 4.075763 AGCACGTACTAGTTCGTTACAG 57.924 45.455 22.83 13.69 38.23 2.74
1717 1854 3.748048 AGCACGTACTAGTTCGTTACAGA 59.252 43.478 22.83 0.00 38.23 3.41
1718 1855 4.087265 GCACGTACTAGTTCGTTACAGAG 58.913 47.826 22.83 12.73 38.23 3.35
1719 1856 4.377841 GCACGTACTAGTTCGTTACAGAGT 60.378 45.833 22.83 0.00 38.23 3.24
1720 1857 5.312054 CACGTACTAGTTCGTTACAGAGTC 58.688 45.833 22.83 0.00 38.23 3.36
1721 1858 4.991056 ACGTACTAGTTCGTTACAGAGTCA 59.009 41.667 20.20 0.00 36.93 3.41
1722 1859 5.119898 ACGTACTAGTTCGTTACAGAGTCAG 59.880 44.000 20.20 0.00 36.93 3.51
1723 1860 5.347093 CGTACTAGTTCGTTACAGAGTCAGA 59.653 44.000 13.17 0.00 0.00 3.27
1724 1861 5.866335 ACTAGTTCGTTACAGAGTCAGAG 57.134 43.478 0.00 0.00 0.00 3.35
1725 1862 5.307204 ACTAGTTCGTTACAGAGTCAGAGT 58.693 41.667 0.00 0.00 0.00 3.24
1726 1863 4.491234 AGTTCGTTACAGAGTCAGAGTG 57.509 45.455 0.00 0.00 0.00 3.51
1734 1871 2.242926 CAGAGTCAGAGTGGAGTGGAA 58.757 52.381 0.00 0.00 0.00 3.53
1782 1919 4.327898 CAGACCAACAATGTAATGCAATGC 59.672 41.667 0.00 0.00 31.33 3.56
1783 1920 4.021280 AGACCAACAATGTAATGCAATGCA 60.021 37.500 11.44 11.44 44.86 3.96
1784 1921 4.639334 ACCAACAATGTAATGCAATGCAA 58.361 34.783 13.45 0.00 43.62 4.08
1785 1922 5.247084 ACCAACAATGTAATGCAATGCAAT 58.753 33.333 13.45 6.50 43.62 3.56
1786 1923 5.122554 ACCAACAATGTAATGCAATGCAATG 59.877 36.000 13.45 6.39 43.62 2.82
1787 1924 5.351740 CCAACAATGTAATGCAATGCAATGA 59.648 36.000 13.45 0.00 43.62 2.57
1788 1925 6.128254 CCAACAATGTAATGCAATGCAATGAA 60.128 34.615 13.45 0.00 43.62 2.57
1812 1949 0.738975 AGCAAGCTAGCATGCACATG 59.261 50.000 37.55 16.77 42.32 3.21
1814 1951 0.248907 CAAGCTAGCATGCACATGGC 60.249 55.000 21.98 13.08 45.13 4.40
1896 2033 8.581253 TCATCTCTATCCATGTTCGTGTATAT 57.419 34.615 0.00 0.00 0.00 0.86
1897 2034 9.681062 TCATCTCTATCCATGTTCGTGTATATA 57.319 33.333 0.00 0.00 0.00 0.86
1898 2035 9.723447 CATCTCTATCCATGTTCGTGTATATAC 57.277 37.037 5.89 5.89 0.00 1.47
1899 2036 9.688091 ATCTCTATCCATGTTCGTGTATATACT 57.312 33.333 13.89 0.00 0.00 2.12
1904 2041 7.688478 TCCATGTTCGTGTATATACTTTTCG 57.312 36.000 13.89 12.25 0.00 3.46
1905 2042 7.482474 TCCATGTTCGTGTATATACTTTTCGA 58.518 34.615 13.89 13.97 0.00 3.71
1906 2043 7.975058 TCCATGTTCGTGTATATACTTTTCGAA 59.025 33.333 20.10 20.10 34.38 3.71
1907 2044 8.597227 CCATGTTCGTGTATATACTTTTCGAAA 58.403 33.333 22.83 6.47 37.52 3.46
1908 2045 9.961266 CATGTTCGTGTATATACTTTTCGAAAA 57.039 29.630 21.35 21.35 37.52 2.29
1922 2059 8.703823 ACTTTTCGAAAAATGTTCGTGTATAC 57.296 30.769 22.67 0.00 42.09 1.47
1923 2060 8.553696 ACTTTTCGAAAAATGTTCGTGTATACT 58.446 29.630 22.67 0.00 42.09 2.12
1924 2061 8.702408 TTTTCGAAAAATGTTCGTGTATACTG 57.298 30.769 20.56 0.00 42.09 2.74
1925 2062 5.849858 TCGAAAAATGTTCGTGTATACTGC 58.150 37.500 5.40 0.00 42.09 4.40
1926 2063 5.636121 TCGAAAAATGTTCGTGTATACTGCT 59.364 36.000 5.40 0.00 42.09 4.24
1927 2064 6.807720 TCGAAAAATGTTCGTGTATACTGCTA 59.192 34.615 5.40 0.00 42.09 3.49
1960 2099 2.486203 GACGTTTTGATGGGTACATGCA 59.514 45.455 0.00 0.00 37.47 3.96
2138 2310 0.656785 GCGACTGTCCGTAGTAGAGG 59.343 60.000 1.55 0.00 0.00 3.69
2197 2380 1.883544 CAGCAGCAGATCAGAGCCG 60.884 63.158 0.00 0.00 0.00 5.52
2248 2432 0.598065 GCTTGGTTCAAAGGCGTGAT 59.402 50.000 0.00 0.00 0.00 3.06
2322 2511 3.328505 TGTACCGGCTAGTTTTTAGCAC 58.671 45.455 0.00 0.00 42.06 4.40
2324 2513 3.067684 ACCGGCTAGTTTTTAGCACAT 57.932 42.857 0.00 0.00 42.06 3.21
2325 2514 3.418047 ACCGGCTAGTTTTTAGCACATT 58.582 40.909 0.00 0.00 42.06 2.71
2326 2515 3.824443 ACCGGCTAGTTTTTAGCACATTT 59.176 39.130 0.00 0.00 42.06 2.32
2327 2516 4.279922 ACCGGCTAGTTTTTAGCACATTTT 59.720 37.500 0.00 0.00 42.06 1.82
2328 2517 5.221362 ACCGGCTAGTTTTTAGCACATTTTT 60.221 36.000 0.00 0.00 42.06 1.94
2329 2518 6.016108 ACCGGCTAGTTTTTAGCACATTTTTA 60.016 34.615 0.00 0.00 42.06 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 0.669318 GGAACGAAGCATGGACACGA 60.669 55.000 0.00 0.00 0.00 4.35
148 149 1.305887 GGAGGGAGGAAGGGAACGA 60.306 63.158 0.00 0.00 0.00 3.85
154 155 2.040359 GGGAGGGAGGGAGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
155 156 1.074850 GAGGGAGGGAGGGAGGAAG 60.075 68.421 0.00 0.00 0.00 3.46
156 157 2.647949 GGAGGGAGGGAGGGAGGAA 61.648 68.421 0.00 0.00 0.00 3.36
157 158 3.036959 GGAGGGAGGGAGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
224 225 3.030291 TGAACCAATGTGCCTTCAAACT 58.970 40.909 0.00 0.00 0.00 2.66
225 226 3.451141 TGAACCAATGTGCCTTCAAAC 57.549 42.857 0.00 0.00 0.00 2.93
226 227 4.686191 AATGAACCAATGTGCCTTCAAA 57.314 36.364 0.00 0.00 0.00 2.69
258 331 3.650139 GAAGTCTCGGTCAGCAAAACTA 58.350 45.455 0.00 0.00 0.00 2.24
259 332 2.484889 GAAGTCTCGGTCAGCAAAACT 58.515 47.619 0.00 0.00 0.00 2.66
261 334 1.497991 CGAAGTCTCGGTCAGCAAAA 58.502 50.000 0.00 0.00 41.57 2.44
262 335 1.202486 AACGAAGTCTCGGTCAGCAAA 60.202 47.619 0.00 0.00 42.92 3.68
263 336 0.387929 AACGAAGTCTCGGTCAGCAA 59.612 50.000 0.00 0.00 42.92 3.91
264 337 1.241165 TAACGAAGTCTCGGTCAGCA 58.759 50.000 0.00 0.00 42.92 4.41
265 338 2.563471 ATAACGAAGTCTCGGTCAGC 57.437 50.000 0.00 0.00 42.92 4.26
266 339 5.236695 TGAGATATAACGAAGTCTCGGTCAG 59.763 44.000 0.00 0.00 42.92 3.51
267 340 5.121105 TGAGATATAACGAAGTCTCGGTCA 58.879 41.667 0.00 0.00 42.92 4.02
268 341 5.670149 TGAGATATAACGAAGTCTCGGTC 57.330 43.478 0.00 0.00 42.92 4.79
271 344 6.716438 TCAACTGAGATATAACGAAGTCTCG 58.284 40.000 0.00 0.00 45.00 4.04
272 345 8.132362 ACATCAACTGAGATATAACGAAGTCTC 58.868 37.037 0.00 0.00 45.00 3.36
273 346 8.001881 ACATCAACTGAGATATAACGAAGTCT 57.998 34.615 0.00 0.00 45.00 3.24
274 347 8.635877 AACATCAACTGAGATATAACGAAGTC 57.364 34.615 0.00 0.00 45.00 3.01
303 376 9.474920 ACGAATCTTCATGCAAAATTAAAGAAA 57.525 25.926 0.00 0.00 0.00 2.52
305 378 9.554724 GTACGAATCTTCATGCAAAATTAAAGA 57.445 29.630 0.00 0.00 0.00 2.52
306 379 9.340695 TGTACGAATCTTCATGCAAAATTAAAG 57.659 29.630 0.00 0.00 0.00 1.85
307 380 9.684448 TTGTACGAATCTTCATGCAAAATTAAA 57.316 25.926 0.00 0.00 0.00 1.52
308 381 9.684448 TTTGTACGAATCTTCATGCAAAATTAA 57.316 25.926 0.00 0.00 0.00 1.40
309 382 9.684448 TTTTGTACGAATCTTCATGCAAAATTA 57.316 25.926 9.75 0.00 31.77 1.40
310 383 8.586570 TTTTGTACGAATCTTCATGCAAAATT 57.413 26.923 9.75 0.00 31.77 1.82
311 384 8.586570 TTTTTGTACGAATCTTCATGCAAAAT 57.413 26.923 13.09 0.00 34.14 1.82
312 385 7.993821 TTTTTGTACGAATCTTCATGCAAAA 57.006 28.000 9.75 9.75 33.25 2.44
375 448 9.415008 AGTCTCACTCAAATGATATACAGTAGT 57.585 33.333 0.00 0.00 0.00 2.73
378 451 7.984050 CCAAGTCTCACTCAAATGATATACAGT 59.016 37.037 0.00 0.00 0.00 3.55
379 452 7.984050 ACCAAGTCTCACTCAAATGATATACAG 59.016 37.037 0.00 0.00 0.00 2.74
380 453 7.851228 ACCAAGTCTCACTCAAATGATATACA 58.149 34.615 0.00 0.00 0.00 2.29
381 454 8.723942 AACCAAGTCTCACTCAAATGATATAC 57.276 34.615 0.00 0.00 0.00 1.47
383 456 9.388506 CTTAACCAAGTCTCACTCAAATGATAT 57.611 33.333 0.00 0.00 0.00 1.63
384 457 8.375506 ACTTAACCAAGTCTCACTCAAATGATA 58.624 33.333 0.00 0.00 41.25 2.15
385 458 7.227156 ACTTAACCAAGTCTCACTCAAATGAT 58.773 34.615 0.00 0.00 41.25 2.45
386 459 6.591935 ACTTAACCAAGTCTCACTCAAATGA 58.408 36.000 0.00 0.00 41.25 2.57
387 460 6.867662 ACTTAACCAAGTCTCACTCAAATG 57.132 37.500 0.00 0.00 41.25 2.32
413 486 2.095161 GTGGTTAGGTCTCAGTCGACTG 60.095 54.545 34.76 34.76 45.08 3.51
414 487 2.161030 GTGGTTAGGTCTCAGTCGACT 58.839 52.381 13.58 13.58 34.38 4.18
415 488 1.884579 TGTGGTTAGGTCTCAGTCGAC 59.115 52.381 7.70 7.70 0.00 4.20
416 489 1.884579 GTGTGGTTAGGTCTCAGTCGA 59.115 52.381 0.00 0.00 0.00 4.20
417 490 1.067776 GGTGTGGTTAGGTCTCAGTCG 60.068 57.143 0.00 0.00 0.00 4.18
418 491 1.275573 GGGTGTGGTTAGGTCTCAGTC 59.724 57.143 0.00 0.00 0.00 3.51
419 492 1.132817 AGGGTGTGGTTAGGTCTCAGT 60.133 52.381 0.00 0.00 0.00 3.41
420 493 1.645710 AGGGTGTGGTTAGGTCTCAG 58.354 55.000 0.00 0.00 0.00 3.35
421 494 3.263369 TTAGGGTGTGGTTAGGTCTCA 57.737 47.619 0.00 0.00 0.00 3.27
422 495 4.285260 TCTTTTAGGGTGTGGTTAGGTCTC 59.715 45.833 0.00 0.00 0.00 3.36
423 496 4.237018 TCTTTTAGGGTGTGGTTAGGTCT 58.763 43.478 0.00 0.00 0.00 3.85
424 497 4.628963 TCTTTTAGGGTGTGGTTAGGTC 57.371 45.455 0.00 0.00 0.00 3.85
425 498 5.391577 TTTCTTTTAGGGTGTGGTTAGGT 57.608 39.130 0.00 0.00 0.00 3.08
426 499 6.066032 TCTTTTCTTTTAGGGTGTGGTTAGG 58.934 40.000 0.00 0.00 0.00 2.69
427 500 6.771267 ACTCTTTTCTTTTAGGGTGTGGTTAG 59.229 38.462 0.00 0.00 0.00 2.34
428 501 6.665695 ACTCTTTTCTTTTAGGGTGTGGTTA 58.334 36.000 0.00 0.00 0.00 2.85
429 502 5.516044 ACTCTTTTCTTTTAGGGTGTGGTT 58.484 37.500 0.00 0.00 0.00 3.67
430 503 5.125367 ACTCTTTTCTTTTAGGGTGTGGT 57.875 39.130 0.00 0.00 0.00 4.16
431 504 6.296803 AGTACTCTTTTCTTTTAGGGTGTGG 58.703 40.000 0.00 0.00 0.00 4.17
432 505 9.503399 AATAGTACTCTTTTCTTTTAGGGTGTG 57.497 33.333 0.00 0.00 0.00 3.82
452 525 9.734620 GCACATCAGCAAAATCAATTAATAGTA 57.265 29.630 0.00 0.00 0.00 1.82
453 526 7.707893 GGCACATCAGCAAAATCAATTAATAGT 59.292 33.333 0.00 0.00 35.83 2.12
454 527 7.707464 TGGCACATCAGCAAAATCAATTAATAG 59.293 33.333 0.00 0.00 35.83 1.73
455 528 7.492020 GTGGCACATCAGCAAAATCAATTAATA 59.508 33.333 13.86 0.00 44.52 0.98
456 529 6.314400 GTGGCACATCAGCAAAATCAATTAAT 59.686 34.615 13.86 0.00 44.52 1.40
457 530 5.638657 GTGGCACATCAGCAAAATCAATTAA 59.361 36.000 13.86 0.00 44.52 1.40
574 662 0.907486 TCCGTAGACGAGGAGAAGGA 59.093 55.000 3.07 0.00 43.02 3.36
592 680 3.245519 GCTATGCGGTAGTAGCTTTTGTC 59.754 47.826 0.00 0.00 40.06 3.18
600 688 4.477780 GCTAAAGAGCTATGCGGTAGTAG 58.522 47.826 0.00 0.00 45.98 2.57
601 689 4.500603 GCTAAAGAGCTATGCGGTAGTA 57.499 45.455 0.00 0.00 45.98 1.82
602 690 3.372660 GCTAAAGAGCTATGCGGTAGT 57.627 47.619 0.00 0.00 45.98 2.73
643 731 6.262496 CCACTACGGTTACAAGAGATGAGATA 59.738 42.308 0.00 0.00 0.00 1.98
644 732 5.067936 CCACTACGGTTACAAGAGATGAGAT 59.932 44.000 0.00 0.00 0.00 2.75
645 733 4.398358 CCACTACGGTTACAAGAGATGAGA 59.602 45.833 0.00 0.00 0.00 3.27
646 734 4.398358 TCCACTACGGTTACAAGAGATGAG 59.602 45.833 0.00 0.00 35.57 2.90
647 735 4.338012 TCCACTACGGTTACAAGAGATGA 58.662 43.478 0.00 0.00 35.57 2.92
648 736 4.713824 TCCACTACGGTTACAAGAGATG 57.286 45.455 0.00 0.00 35.57 2.90
818 906 1.014352 GAAGGGTGTGTGTGTGTGTC 58.986 55.000 0.00 0.00 0.00 3.67
819 907 0.742990 CGAAGGGTGTGTGTGTGTGT 60.743 55.000 0.00 0.00 0.00 3.72
820 908 0.461163 TCGAAGGGTGTGTGTGTGTG 60.461 55.000 0.00 0.00 0.00 3.82
821 909 0.461339 GTCGAAGGGTGTGTGTGTGT 60.461 55.000 0.00 0.00 0.00 3.72
822 910 1.157870 GGTCGAAGGGTGTGTGTGTG 61.158 60.000 0.00 0.00 0.00 3.82
823 911 1.145377 GGTCGAAGGGTGTGTGTGT 59.855 57.895 0.00 0.00 0.00 3.72
957 1053 4.896829 TCTCCCTCGCCGGCCTAG 62.897 72.222 23.46 18.57 0.00 3.02
966 1062 1.064314 TCTCCTTCTCCTTCTCCCTCG 60.064 57.143 0.00 0.00 0.00 4.63
980 1076 0.250513 CTTGGCGCCTACTTCTCCTT 59.749 55.000 29.70 0.00 0.00 3.36
981 1077 0.614979 TCTTGGCGCCTACTTCTCCT 60.615 55.000 29.70 0.00 0.00 3.69
982 1078 0.466124 ATCTTGGCGCCTACTTCTCC 59.534 55.000 29.70 0.00 0.00 3.71
983 1079 1.134670 ACATCTTGGCGCCTACTTCTC 60.135 52.381 29.70 0.00 0.00 2.87
984 1080 0.905357 ACATCTTGGCGCCTACTTCT 59.095 50.000 29.70 4.38 0.00 2.85
985 1081 1.398390 CAACATCTTGGCGCCTACTTC 59.602 52.381 29.70 0.00 0.00 3.01
986 1082 1.003118 TCAACATCTTGGCGCCTACTT 59.997 47.619 29.70 7.39 0.00 2.24
987 1083 0.613260 TCAACATCTTGGCGCCTACT 59.387 50.000 29.70 6.78 0.00 2.57
988 1084 1.009829 CTCAACATCTTGGCGCCTAC 58.990 55.000 29.70 0.50 0.00 3.18
989 1085 0.107703 CCTCAACATCTTGGCGCCTA 60.108 55.000 29.70 20.51 0.00 3.93
990 1086 1.377725 CCTCAACATCTTGGCGCCT 60.378 57.895 29.70 3.37 0.00 5.52
991 1087 0.749454 ATCCTCAACATCTTGGCGCC 60.749 55.000 22.73 22.73 0.00 6.53
1110 1206 3.470567 GCGCTGAAGACGACCACG 61.471 66.667 0.00 0.00 45.75 4.94
1332 1428 1.599047 CATCACCTTCTCCACGCCT 59.401 57.895 0.00 0.00 0.00 5.52
1456 1559 0.391130 CCGTCGTTGATCACCACCAT 60.391 55.000 0.00 0.00 0.00 3.55
1565 1702 3.538201 CATGCATTGCACGCACGC 61.538 61.111 14.66 5.81 43.04 5.34
1566 1703 2.877113 CCATGCATTGCACGCACG 60.877 61.111 14.66 4.31 43.04 5.34
1567 1704 2.089936 CACCATGCATTGCACGCAC 61.090 57.895 14.66 0.00 43.04 5.34
1568 1705 2.258897 CACCATGCATTGCACGCA 59.741 55.556 14.66 12.10 43.04 5.24
1569 1706 2.089936 CACACCATGCATTGCACGC 61.090 57.895 14.66 0.20 43.04 5.34
1570 1707 0.318869 AACACACCATGCATTGCACG 60.319 50.000 14.66 5.42 43.04 5.34
1571 1708 1.141645 CAACACACCATGCATTGCAC 58.858 50.000 14.66 0.00 43.04 4.57
1572 1709 1.000052 CTCAACACACCATGCATTGCA 60.000 47.619 14.72 14.72 44.86 4.08
1573 1710 1.705256 CTCAACACACCATGCATTGC 58.295 50.000 0.00 0.46 0.00 3.56
1574 1711 1.271379 AGCTCAACACACCATGCATTG 59.729 47.619 0.00 0.00 0.00 2.82
1575 1712 1.624336 AGCTCAACACACCATGCATT 58.376 45.000 0.00 0.00 0.00 3.56
1576 1713 1.542915 GAAGCTCAACACACCATGCAT 59.457 47.619 0.00 0.00 0.00 3.96
1637 1774 3.435327 CACGCAACTGACAAGGCTAATTA 59.565 43.478 0.00 0.00 0.00 1.40
1678 1815 4.647853 ACGTGCTAGATAACCATCACCTAA 59.352 41.667 0.00 0.00 33.21 2.69
1688 1825 6.042144 ACGAACTAGTACGTGCTAGATAAC 57.958 41.667 37.12 24.31 40.54 1.89
1697 1834 5.107337 TGACTCTGTAACGAACTAGTACGTG 60.107 44.000 0.00 0.00 42.43 4.49
1698 1835 4.991056 TGACTCTGTAACGAACTAGTACGT 59.009 41.667 0.00 0.00 44.57 3.57
1699 1836 5.347093 TCTGACTCTGTAACGAACTAGTACG 59.653 44.000 0.00 0.00 0.00 3.67
1701 1838 6.368243 CACTCTGACTCTGTAACGAACTAGTA 59.632 42.308 0.00 0.00 0.00 1.82
1702 1839 5.179742 CACTCTGACTCTGTAACGAACTAGT 59.820 44.000 0.00 0.00 0.00 2.57
1703 1840 5.391097 CCACTCTGACTCTGTAACGAACTAG 60.391 48.000 0.00 0.00 0.00 2.57
1704 1841 4.454847 CCACTCTGACTCTGTAACGAACTA 59.545 45.833 0.00 0.00 0.00 2.24
1705 1842 3.253677 CCACTCTGACTCTGTAACGAACT 59.746 47.826 0.00 0.00 0.00 3.01
1706 1843 3.252701 TCCACTCTGACTCTGTAACGAAC 59.747 47.826 0.00 0.00 0.00 3.95
1707 1844 3.483421 TCCACTCTGACTCTGTAACGAA 58.517 45.455 0.00 0.00 0.00 3.85
1708 1845 3.075148 CTCCACTCTGACTCTGTAACGA 58.925 50.000 0.00 0.00 0.00 3.85
1709 1846 2.814919 ACTCCACTCTGACTCTGTAACG 59.185 50.000 0.00 0.00 0.00 3.18
1710 1847 3.057174 CCACTCCACTCTGACTCTGTAAC 60.057 52.174 0.00 0.00 0.00 2.50
1711 1848 3.157881 CCACTCCACTCTGACTCTGTAA 58.842 50.000 0.00 0.00 0.00 2.41
1712 1849 2.375509 TCCACTCCACTCTGACTCTGTA 59.624 50.000 0.00 0.00 0.00 2.74
1713 1850 1.145945 TCCACTCCACTCTGACTCTGT 59.854 52.381 0.00 0.00 0.00 3.41
1714 1851 1.916506 TCCACTCCACTCTGACTCTG 58.083 55.000 0.00 0.00 0.00 3.35
1715 1852 2.524306 CTTCCACTCCACTCTGACTCT 58.476 52.381 0.00 0.00 0.00 3.24
1716 1853 1.548269 CCTTCCACTCCACTCTGACTC 59.452 57.143 0.00 0.00 0.00 3.36
1717 1854 1.148027 TCCTTCCACTCCACTCTGACT 59.852 52.381 0.00 0.00 0.00 3.41
1718 1855 1.633774 TCCTTCCACTCCACTCTGAC 58.366 55.000 0.00 0.00 0.00 3.51
1719 1856 2.630889 ATCCTTCCACTCCACTCTGA 57.369 50.000 0.00 0.00 0.00 3.27
1720 1857 3.370104 AGTATCCTTCCACTCCACTCTG 58.630 50.000 0.00 0.00 0.00 3.35
1721 1858 3.767309 AGTATCCTTCCACTCCACTCT 57.233 47.619 0.00 0.00 0.00 3.24
1722 1859 4.202172 GCTAAGTATCCTTCCACTCCACTC 60.202 50.000 0.00 0.00 31.89 3.51
1723 1860 3.707102 GCTAAGTATCCTTCCACTCCACT 59.293 47.826 0.00 0.00 31.89 4.00
1724 1861 3.181464 GGCTAAGTATCCTTCCACTCCAC 60.181 52.174 0.00 0.00 31.89 4.02
1725 1862 3.039011 GGCTAAGTATCCTTCCACTCCA 58.961 50.000 0.00 0.00 31.89 3.86
1726 1863 3.039011 TGGCTAAGTATCCTTCCACTCC 58.961 50.000 0.00 0.00 31.89 3.85
1734 1871 5.649265 TCTCATCTGATGGCTAAGTATCCT 58.351 41.667 17.06 0.00 0.00 3.24
1742 1879 3.831333 GGTCTGATCTCATCTGATGGCTA 59.169 47.826 17.06 4.21 39.06 3.93
1743 1880 2.633967 GGTCTGATCTCATCTGATGGCT 59.366 50.000 17.06 2.93 39.06 4.75
1744 1881 2.367894 TGGTCTGATCTCATCTGATGGC 59.632 50.000 17.06 5.94 39.06 4.40
1746 1883 5.019785 TGTTGGTCTGATCTCATCTGATG 57.980 43.478 11.42 11.42 39.06 3.07
1747 1884 5.688814 TTGTTGGTCTGATCTCATCTGAT 57.311 39.130 0.00 0.00 39.06 2.90
1748 1885 5.046087 ACATTGTTGGTCTGATCTCATCTGA 60.046 40.000 0.00 0.00 35.29 3.27
1749 1886 5.183969 ACATTGTTGGTCTGATCTCATCTG 58.816 41.667 0.00 0.00 0.00 2.90
1750 1887 5.432680 ACATTGTTGGTCTGATCTCATCT 57.567 39.130 0.00 0.00 0.00 2.90
1751 1888 7.637229 CATTACATTGTTGGTCTGATCTCATC 58.363 38.462 0.00 0.00 0.00 2.92
1752 1889 6.039047 GCATTACATTGTTGGTCTGATCTCAT 59.961 38.462 0.00 0.00 0.00 2.90
1753 1890 5.355071 GCATTACATTGTTGGTCTGATCTCA 59.645 40.000 0.00 0.00 0.00 3.27
1754 1891 5.355071 TGCATTACATTGTTGGTCTGATCTC 59.645 40.000 0.00 0.00 0.00 2.75
1782 1919 2.290093 GCTAGCTTGCTAGGCTTCATTG 59.710 50.000 25.23 4.17 40.74 2.82
1783 1920 2.092753 TGCTAGCTTGCTAGGCTTCATT 60.093 45.455 25.23 0.00 40.74 2.57
1784 1921 1.487976 TGCTAGCTTGCTAGGCTTCAT 59.512 47.619 25.23 0.00 40.74 2.57
1785 1922 0.904649 TGCTAGCTTGCTAGGCTTCA 59.095 50.000 25.23 14.75 40.74 3.02
1786 1923 1.872313 CATGCTAGCTTGCTAGGCTTC 59.128 52.381 25.23 12.76 40.74 3.86
1787 1924 1.964552 CATGCTAGCTTGCTAGGCTT 58.035 50.000 25.23 15.06 40.74 4.35
1788 1925 0.534652 GCATGCTAGCTTGCTAGGCT 60.535 55.000 35.69 2.75 41.83 4.58
1881 2018 7.688478 TCGAAAAGTATATACACGAACATGG 57.312 36.000 15.18 0.00 0.00 3.66
1896 2033 9.796062 GTATACACGAACATTTTTCGAAAAGTA 57.204 29.630 21.53 17.13 43.97 2.24
1897 2034 8.553696 AGTATACACGAACATTTTTCGAAAAGT 58.446 29.630 21.53 17.04 43.97 2.66
1898 2035 8.827599 CAGTATACACGAACATTTTTCGAAAAG 58.172 33.333 21.53 14.44 43.97 2.27
1899 2036 7.321746 GCAGTATACACGAACATTTTTCGAAAA 59.678 33.333 19.08 19.08 43.97 2.29
1901 2038 6.146510 AGCAGTATACACGAACATTTTTCGAA 59.853 34.615 11.60 0.00 43.97 3.71
1902 2039 5.636121 AGCAGTATACACGAACATTTTTCGA 59.364 36.000 11.60 0.00 43.97 3.71
1903 2040 5.854157 AGCAGTATACACGAACATTTTTCG 58.146 37.500 5.50 3.52 46.36 3.46
1904 2041 7.960793 AGTAGCAGTATACACGAACATTTTTC 58.039 34.615 5.50 0.00 0.00 2.29
1905 2042 7.900782 AGTAGCAGTATACACGAACATTTTT 57.099 32.000 5.50 0.00 0.00 1.94
1906 2043 8.248945 AGTAGTAGCAGTATACACGAACATTTT 58.751 33.333 5.50 0.00 0.00 1.82
1907 2044 7.769220 AGTAGTAGCAGTATACACGAACATTT 58.231 34.615 5.50 0.00 0.00 2.32
1908 2045 7.066645 TGAGTAGTAGCAGTATACACGAACATT 59.933 37.037 5.50 0.00 0.00 2.71
1909 2046 6.541278 TGAGTAGTAGCAGTATACACGAACAT 59.459 38.462 5.50 0.00 0.00 2.71
1910 2047 5.876460 TGAGTAGTAGCAGTATACACGAACA 59.124 40.000 5.50 0.00 0.00 3.18
1911 2048 6.355397 TGAGTAGTAGCAGTATACACGAAC 57.645 41.667 5.50 0.00 0.00 3.95
1912 2049 6.990341 TTGAGTAGTAGCAGTATACACGAA 57.010 37.500 5.50 0.00 0.00 3.85
1913 2050 7.415229 CAATTGAGTAGTAGCAGTATACACGA 58.585 38.462 5.50 0.00 0.00 4.35
1914 2051 6.637254 CCAATTGAGTAGTAGCAGTATACACG 59.363 42.308 7.12 0.00 0.00 4.49
1915 2052 7.648510 GTCCAATTGAGTAGTAGCAGTATACAC 59.351 40.741 7.12 0.00 0.00 2.90
1916 2053 7.468220 CGTCCAATTGAGTAGTAGCAGTATACA 60.468 40.741 7.12 0.00 0.00 2.29
1917 2054 6.856938 CGTCCAATTGAGTAGTAGCAGTATAC 59.143 42.308 7.12 0.00 0.00 1.47
1918 2055 6.544931 ACGTCCAATTGAGTAGTAGCAGTATA 59.455 38.462 7.12 0.00 0.00 1.47
1919 2056 5.360144 ACGTCCAATTGAGTAGTAGCAGTAT 59.640 40.000 7.12 0.00 0.00 2.12
1920 2057 4.703575 ACGTCCAATTGAGTAGTAGCAGTA 59.296 41.667 7.12 0.00 0.00 2.74
1921 2058 3.510360 ACGTCCAATTGAGTAGTAGCAGT 59.490 43.478 7.12 0.00 0.00 4.40
1922 2059 4.111375 ACGTCCAATTGAGTAGTAGCAG 57.889 45.455 7.12 0.00 0.00 4.24
1923 2060 4.530710 AACGTCCAATTGAGTAGTAGCA 57.469 40.909 7.12 0.00 0.00 3.49
1924 2061 5.407387 TCAAAACGTCCAATTGAGTAGTAGC 59.593 40.000 7.12 0.00 0.00 3.58
1925 2062 7.413000 CCATCAAAACGTCCAATTGAGTAGTAG 60.413 40.741 7.12 0.00 36.59 2.57
1926 2063 6.370442 CCATCAAAACGTCCAATTGAGTAGTA 59.630 38.462 7.12 0.00 36.59 1.82
1927 2064 5.181245 CCATCAAAACGTCCAATTGAGTAGT 59.819 40.000 7.12 0.00 36.59 2.73
1966 2105 5.006153 AGTAGTACAAGTATGCATGCGAA 57.994 39.130 14.09 0.00 0.00 4.70
2024 2166 5.649395 TGCTACGTACTACACCTTCAACTAT 59.351 40.000 0.00 0.00 0.00 2.12
2026 2168 3.822735 TGCTACGTACTACACCTTCAACT 59.177 43.478 0.00 0.00 0.00 3.16
2039 2181 3.499157 TCCACCAACAAAATGCTACGTAC 59.501 43.478 0.00 0.00 0.00 3.67
2040 2182 3.741249 TCCACCAACAAAATGCTACGTA 58.259 40.909 0.00 0.00 0.00 3.57
2041 2183 2.577700 TCCACCAACAAAATGCTACGT 58.422 42.857 0.00 0.00 0.00 3.57
2042 2184 3.634568 TTCCACCAACAAAATGCTACG 57.365 42.857 0.00 0.00 0.00 3.51
2085 2257 0.321653 GTGGACGCATCTTCCCACTT 60.322 55.000 0.00 0.00 44.13 3.16
2138 2310 2.574212 CGTGCGTACGTACCGGTC 60.574 66.667 27.11 1.44 44.99 4.79
2189 2372 1.005037 ACGTTTCATGCGGCTCTGA 60.005 52.632 0.00 1.42 0.00 3.27
2192 2375 1.132640 GTCACGTTTCATGCGGCTC 59.867 57.895 0.00 0.00 0.00 4.70
2197 2380 0.593128 AGGCAAGTCACGTTTCATGC 59.407 50.000 7.97 7.97 0.00 4.06
2224 2408 1.536073 GCCTTTGAACCAAGCCCTCC 61.536 60.000 0.00 0.00 0.00 4.30
2226 2410 1.903404 CGCCTTTGAACCAAGCCCT 60.903 57.895 0.00 0.00 0.00 5.19
2227 2411 2.200337 ACGCCTTTGAACCAAGCCC 61.200 57.895 0.00 0.00 0.00 5.19
2341 2530 2.103094 TCAGATTCTTACCGGCCATGAG 59.897 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.