Multiple sequence alignment - TraesCS3A01G173500

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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 TraesCS3A01G173500 chr3A 100.000 2183 0 0 1 2183 191838522 191836340 0.000000e+00 4032
1 TraesCS3A01G173500 chr3A 98.462 65 1 0 270 334 191838186 191838250 4.920000e-22 115
2 TraesCS3A01G173500 chr3B 88.381 1007 67 16 401 1363 238496973 238495973 0.000000e+00 1166
3 TraesCS3A01G173500 chr3B 91.270 504 30 9 1662 2159 238495695 238495200 0.000000e+00 675
4 TraesCS3A01G173500 chr3B 87.469 399 19 6 3 400 238497280 238496912 4.310000e-117 431
5 TraesCS3A01G173500 chr3D 92.587 634 30 8 1558 2183 161928308 161927684 0.000000e+00 894
6 TraesCS3A01G173500 chr3D 94.382 356 18 2 949 1303 161929032 161928678 1.470000e-151 545
7 TraesCS3A01G173500 chr3D 88.333 180 15 3 1 180 161929914 161929741 6.110000e-51 211
8 TraesCS3A01G173500 chr3D 75.649 308 44 18 399 677 161929627 161929322 8.180000e-25 124
9 TraesCS3A01G173500 chr4D 92.523 107 6 2 1453 1558 302691330 302691435 3.750000e-33 152
10 TraesCS3A01G173500 chr4D 87.368 95 11 1 1465 1558 469071736 469071830 8.240000e-20 108
11 TraesCS3A01G173500 chr6D 89.091 110 10 2 1452 1559 140221653 140221762 3.780000e-28 135
12 TraesCS3A01G173500 chr2D 92.632 95 6 1 1465 1558 523649484 523649390 3.780000e-28 135
13 TraesCS3A01G173500 chr1B 92.473 93 7 0 1465 1557 115774530 115774438 1.360000e-27 134
14 TraesCS3A01G173500 chr1B 86.667 105 11 3 1453 1556 26300293 26300395 1.770000e-21 113
15 TraesCS3A01G173500 chrUn 90.722 97 8 1 1465 1561 132061890 132061795 6.330000e-26 128
16 TraesCS3A01G173500 chr6A 91.304 92 8 0 1465 1556 563196042 563195951 2.280000e-25 126
17 TraesCS3A01G173500 chr5B 85.185 108 10 4 1456 1559 90828059 90827954 2.960000e-19 106


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 TraesCS3A01G173500 chr3A 191836340 191838522 2182 True 4032.000000 4032 100.00000 1 2183 1 chr3A.!!$R1 2182
1 TraesCS3A01G173500 chr3B 238495200 238497280 2080 True 757.333333 1166 89.04000 3 2159 3 chr3B.!!$R1 2156
2 TraesCS3A01G173500 chr3D 161927684 161929914 2230 True 443.500000 894 87.73775 1 2183 4 chr3D.!!$R1 2182

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
288 294 0.251354 ACTCATCGCAGGTGCAATCT 59.749 50.0 2.33 0.0 42.21 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 2094 0.107643 GGATTACCTCTGGCCTCTGC 59.892 60.0 3.32 0.0 0.0 4.26 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
87 88 1.648467 GGCTTCGCTTGTGTGGATCC 61.648 60.000 4.20 4.20 0.00 3.36
101 102 2.567615 GTGGATCCCTCAGTGTTGTACT 59.432 50.000 9.90 0.00 41.36 2.73
102 103 3.767673 GTGGATCCCTCAGTGTTGTACTA 59.232 47.826 9.90 0.00 37.60 1.82
114 115 7.310664 TCAGTGTTGTACTACTGTTGCTATAC 58.689 38.462 18.35 4.00 43.59 1.47
168 169 1.072965 CAAGGATAGATGCACCCCTCC 59.927 57.143 0.00 0.00 0.00 4.30
180 181 3.473647 CCCTCCATCTGCGCCAGA 61.474 66.667 4.18 8.59 44.99 3.86
181 182 2.108566 CCTCCATCTGCGCCAGAG 59.891 66.667 4.18 3.53 44.08 3.35
194 196 2.607187 CGCCAGAGTTTTACGATCTGT 58.393 47.619 0.00 0.00 39.03 3.41
270 276 3.118665 ACATGGCCCTTGATTTGCATTAC 60.119 43.478 9.62 0.00 0.00 1.89
271 277 2.818921 TGGCCCTTGATTTGCATTACT 58.181 42.857 0.00 0.00 0.00 2.24
272 278 2.760092 TGGCCCTTGATTTGCATTACTC 59.240 45.455 0.00 0.00 0.00 2.59
274 280 3.385755 GGCCCTTGATTTGCATTACTCAT 59.614 43.478 0.00 0.00 0.00 2.90
275 281 4.500375 GGCCCTTGATTTGCATTACTCATC 60.500 45.833 0.00 0.00 0.00 2.92
276 282 4.790766 GCCCTTGATTTGCATTACTCATCG 60.791 45.833 0.00 0.00 0.00 3.84
277 283 4.285292 CCTTGATTTGCATTACTCATCGC 58.715 43.478 0.00 0.00 0.00 4.58
278 284 4.201940 CCTTGATTTGCATTACTCATCGCA 60.202 41.667 0.00 0.00 0.00 5.10
279 285 4.541085 TGATTTGCATTACTCATCGCAG 57.459 40.909 0.00 0.00 35.47 5.18
280 286 3.313249 TGATTTGCATTACTCATCGCAGG 59.687 43.478 0.00 0.00 35.47 4.85
281 287 2.401583 TTGCATTACTCATCGCAGGT 57.598 45.000 0.00 0.00 35.47 4.00
282 288 1.655484 TGCATTACTCATCGCAGGTG 58.345 50.000 0.00 0.00 0.00 4.00
283 289 0.305922 GCATTACTCATCGCAGGTGC 59.694 55.000 0.00 0.00 37.78 5.01
284 290 1.655484 CATTACTCATCGCAGGTGCA 58.345 50.000 2.33 0.00 42.21 4.57
285 291 2.009051 CATTACTCATCGCAGGTGCAA 58.991 47.619 2.33 0.00 42.21 4.08
286 292 2.401583 TTACTCATCGCAGGTGCAAT 57.598 45.000 2.33 0.00 42.21 3.56
287 293 1.939974 TACTCATCGCAGGTGCAATC 58.060 50.000 2.33 0.00 42.21 2.67
288 294 0.251354 ACTCATCGCAGGTGCAATCT 59.749 50.000 2.33 0.00 42.21 2.40
289 295 0.656259 CTCATCGCAGGTGCAATCTG 59.344 55.000 12.46 12.46 42.21 2.90
300 306 3.727419 GCAATCTGCGGCTTGAAAT 57.273 47.368 13.22 0.00 31.71 2.17
301 307 2.000429 GCAATCTGCGGCTTGAAATT 58.000 45.000 13.22 0.00 31.71 1.82
302 308 3.149436 GCAATCTGCGGCTTGAAATTA 57.851 42.857 13.22 0.00 31.71 1.40
335 341 1.452651 AGATTGCACCTGCGATGGG 60.453 57.895 4.66 0.00 44.75 4.00
374 380 3.570926 TTCCTGCAGTACTGTAGTTCG 57.429 47.619 31.09 20.03 40.94 3.95
375 381 2.511659 TCCTGCAGTACTGTAGTTCGT 58.488 47.619 31.09 0.00 40.94 3.85
376 382 2.486982 TCCTGCAGTACTGTAGTTCGTC 59.513 50.000 31.09 11.88 40.94 4.20
377 383 2.506865 CTGCAGTACTGTAGTTCGTCG 58.493 52.381 27.30 6.31 38.30 5.12
378 384 1.875514 TGCAGTACTGTAGTTCGTCGT 59.124 47.619 23.44 0.00 0.00 4.34
379 385 2.096069 TGCAGTACTGTAGTTCGTCGTC 60.096 50.000 23.44 3.51 0.00 4.20
380 386 2.727298 GCAGTACTGTAGTTCGTCGTCC 60.727 54.545 23.44 0.00 0.00 4.79
381 387 2.079925 AGTACTGTAGTTCGTCGTCCC 58.920 52.381 0.00 0.00 0.00 4.46
382 388 1.806542 GTACTGTAGTTCGTCGTCCCA 59.193 52.381 0.00 0.00 0.00 4.37
383 389 1.542492 ACTGTAGTTCGTCGTCCCAT 58.458 50.000 0.00 0.00 0.00 4.00
384 390 1.201647 ACTGTAGTTCGTCGTCCCATG 59.798 52.381 0.00 0.00 0.00 3.66
385 391 1.201647 CTGTAGTTCGTCGTCCCATGT 59.798 52.381 0.00 0.00 0.00 3.21
386 392 2.421073 CTGTAGTTCGTCGTCCCATGTA 59.579 50.000 0.00 0.00 0.00 2.29
387 393 3.018856 TGTAGTTCGTCGTCCCATGTAT 58.981 45.455 0.00 0.00 0.00 2.29
388 394 2.865343 AGTTCGTCGTCCCATGTATC 57.135 50.000 0.00 0.00 0.00 2.24
389 395 2.376109 AGTTCGTCGTCCCATGTATCT 58.624 47.619 0.00 0.00 0.00 1.98
390 396 2.758979 AGTTCGTCGTCCCATGTATCTT 59.241 45.455 0.00 0.00 0.00 2.40
391 397 3.949754 AGTTCGTCGTCCCATGTATCTTA 59.050 43.478 0.00 0.00 0.00 2.10
392 398 4.583489 AGTTCGTCGTCCCATGTATCTTAT 59.417 41.667 0.00 0.00 0.00 1.73
393 399 4.499037 TCGTCGTCCCATGTATCTTATG 57.501 45.455 0.00 0.00 0.00 1.90
394 400 3.887110 TCGTCGTCCCATGTATCTTATGT 59.113 43.478 0.00 0.00 0.00 2.29
395 401 4.023450 TCGTCGTCCCATGTATCTTATGTC 60.023 45.833 0.00 0.00 0.00 3.06
396 402 4.261447 CGTCGTCCCATGTATCTTATGTCA 60.261 45.833 0.00 0.00 0.00 3.58
397 403 5.223382 GTCGTCCCATGTATCTTATGTCAG 58.777 45.833 0.00 0.00 0.00 3.51
398 404 4.893524 TCGTCCCATGTATCTTATGTCAGT 59.106 41.667 0.00 0.00 0.00 3.41
399 405 5.009710 TCGTCCCATGTATCTTATGTCAGTC 59.990 44.000 0.00 0.00 0.00 3.51
400 406 5.223382 GTCCCATGTATCTTATGTCAGTCG 58.777 45.833 0.00 0.00 0.00 4.18
401 407 5.009710 GTCCCATGTATCTTATGTCAGTCGA 59.990 44.000 0.00 0.00 0.00 4.20
402 408 5.775195 TCCCATGTATCTTATGTCAGTCGAT 59.225 40.000 0.00 0.00 0.00 3.59
403 409 6.071896 TCCCATGTATCTTATGTCAGTCGATC 60.072 42.308 0.00 0.00 0.00 3.69
404 410 6.071672 CCCATGTATCTTATGTCAGTCGATCT 60.072 42.308 0.00 0.00 0.00 2.75
405 411 7.374272 CCATGTATCTTATGTCAGTCGATCTT 58.626 38.462 0.00 0.00 0.00 2.40
406 412 8.515414 CCATGTATCTTATGTCAGTCGATCTTA 58.485 37.037 0.00 0.00 0.00 2.10
407 413 9.553418 CATGTATCTTATGTCAGTCGATCTTAG 57.447 37.037 0.00 0.00 0.00 2.18
408 414 8.904099 TGTATCTTATGTCAGTCGATCTTAGA 57.096 34.615 0.00 0.00 0.00 2.10
409 415 9.338622 TGTATCTTATGTCAGTCGATCTTAGAA 57.661 33.333 0.00 0.00 0.00 2.10
410 416 9.601971 GTATCTTATGTCAGTCGATCTTAGAAC 57.398 37.037 0.00 0.00 0.00 3.01
411 417 7.625828 TCTTATGTCAGTCGATCTTAGAACA 57.374 36.000 0.00 0.00 0.00 3.18
412 418 8.226819 TCTTATGTCAGTCGATCTTAGAACAT 57.773 34.615 0.00 0.00 0.00 2.71
413 419 8.346300 TCTTATGTCAGTCGATCTTAGAACATC 58.654 37.037 0.00 0.00 0.00 3.06
414 420 5.897377 TGTCAGTCGATCTTAGAACATCA 57.103 39.130 0.00 0.00 0.00 3.07
415 421 6.456795 TGTCAGTCGATCTTAGAACATCAT 57.543 37.500 0.00 0.00 0.00 2.45
416 422 6.867550 TGTCAGTCGATCTTAGAACATCATT 58.132 36.000 0.00 0.00 0.00 2.57
417 423 7.323420 TGTCAGTCGATCTTAGAACATCATTT 58.677 34.615 0.00 0.00 0.00 2.32
418 424 7.489435 TGTCAGTCGATCTTAGAACATCATTTC 59.511 37.037 0.00 0.00 0.00 2.17
419 425 6.980978 TCAGTCGATCTTAGAACATCATTTCC 59.019 38.462 0.00 0.00 0.00 3.13
420 426 6.983307 CAGTCGATCTTAGAACATCATTTCCT 59.017 38.462 0.00 0.00 0.00 3.36
421 427 8.138074 CAGTCGATCTTAGAACATCATTTCCTA 58.862 37.037 0.00 0.00 0.00 2.94
422 428 8.138712 AGTCGATCTTAGAACATCATTTCCTAC 58.861 37.037 0.00 0.00 0.00 3.18
423 429 7.921214 GTCGATCTTAGAACATCATTTCCTACA 59.079 37.037 0.00 0.00 0.00 2.74
424 430 8.138074 TCGATCTTAGAACATCATTTCCTACAG 58.862 37.037 0.00 0.00 0.00 2.74
425 431 7.923344 CGATCTTAGAACATCATTTCCTACAGT 59.077 37.037 0.00 0.00 0.00 3.55
428 434 9.256228 TCTTAGAACATCATTTCCTACAGTACT 57.744 33.333 0.00 0.00 0.00 2.73
429 435 9.307121 CTTAGAACATCATTTCCTACAGTACTG 57.693 37.037 21.44 21.44 0.00 2.74
430 436 6.109359 AGAACATCATTTCCTACAGTACTGC 58.891 40.000 22.90 0.52 0.00 4.40
431 437 5.420725 ACATCATTTCCTACAGTACTGCA 57.579 39.130 22.90 9.40 0.00 4.41
432 438 5.423015 ACATCATTTCCTACAGTACTGCAG 58.577 41.667 22.90 18.84 0.00 4.41
433 439 4.471904 TCATTTCCTACAGTACTGCAGG 57.528 45.455 29.64 29.64 43.87 4.85
434 440 3.838317 TCATTTCCTACAGTACTGCAGGT 59.162 43.478 32.31 17.19 43.18 4.00
435 441 3.955650 TTTCCTACAGTACTGCAGGTC 57.044 47.619 32.31 10.42 43.18 3.85
502 516 3.743132 TGAGGTCCCCACATAATAACCT 58.257 45.455 0.00 0.00 39.76 3.50
601 633 6.634805 TCGCTTCTTCAATTATCTCTGAAGT 58.365 36.000 10.64 0.00 45.75 3.01
610 642 8.777865 TCAATTATCTCTGAAGTTTGGTAGTG 57.222 34.615 0.00 0.00 0.00 2.74
615 647 6.109156 TCTCTGAAGTTTGGTAGTGCATTA 57.891 37.500 0.00 0.00 0.00 1.90
616 648 6.711277 TCTCTGAAGTTTGGTAGTGCATTAT 58.289 36.000 0.00 0.00 0.00 1.28
644 677 3.501062 CACATGGAAGATGCAATATCGCT 59.499 43.478 0.00 0.00 0.00 4.93
652 686 6.036517 GGAAGATGCAATATCGCTGTATTAGG 59.963 42.308 0.00 0.00 0.00 2.69
663 697 6.913873 TCGCTGTATTAGGTGTTTATTTCC 57.086 37.500 0.00 0.00 0.00 3.13
666 700 6.483687 GCTGTATTAGGTGTTTATTTCCACG 58.516 40.000 0.00 0.00 32.30 4.94
677 711 0.902531 ATTTCCACGTCCCGATGAGT 59.097 50.000 0.00 0.00 0.00 3.41
747 949 6.877611 AAAACCATGTACTAGTTCAAGGTG 57.122 37.500 24.41 11.16 36.10 4.00
763 965 6.026947 TCAAGGTGCTTAGAGAAGTACTTC 57.973 41.667 25.24 25.24 44.95 3.01
792 994 8.515473 AAAATAAACAGATTGTCGCTTAAACC 57.485 30.769 0.00 0.00 0.00 3.27
804 1008 2.855370 CGCTTAAACCGTTGCTTGTTTT 59.145 40.909 0.00 0.00 36.23 2.43
843 1047 3.701532 CACCGGTGCTTAAGAAAACAA 57.298 42.857 24.02 0.00 0.00 2.83
845 1049 3.018149 ACCGGTGCTTAAGAAAACAACA 58.982 40.909 6.12 0.00 0.00 3.33
846 1050 3.634910 ACCGGTGCTTAAGAAAACAACAT 59.365 39.130 6.12 0.00 0.00 2.71
847 1051 3.980775 CCGGTGCTTAAGAAAACAACATG 59.019 43.478 6.67 0.00 0.00 3.21
849 1053 5.040635 CGGTGCTTAAGAAAACAACATGTT 58.959 37.500 4.92 4.92 43.41 2.71
850 1054 5.173131 CGGTGCTTAAGAAAACAACATGTTC 59.827 40.000 8.48 0.00 40.14 3.18
851 1055 6.039616 GGTGCTTAAGAAAACAACATGTTCA 58.960 36.000 8.48 0.00 40.14 3.18
852 1056 6.701400 GGTGCTTAAGAAAACAACATGTTCAT 59.299 34.615 8.48 0.00 40.14 2.57
885 1089 2.050144 CTCTCTAGGCCCCTTGCATTA 58.950 52.381 0.00 0.00 43.89 1.90
889 1093 3.322862 TCTAGGCCCCTTGCATTATACA 58.677 45.455 0.00 0.00 43.89 2.29
892 1096 2.177669 AGGCCCCTTGCATTATACATGT 59.822 45.455 2.69 2.69 43.89 3.21
897 1101 5.630121 CCCCTTGCATTATACATGTCCTAA 58.370 41.667 0.00 2.22 0.00 2.69
919 1123 7.498900 CCTAATGCAGTTGATCAGTTAATGGTA 59.501 37.037 0.00 0.00 0.00 3.25
929 1133 7.629157 TGATCAGTTAATGGTATTCTTGTGGA 58.371 34.615 0.00 0.00 0.00 4.02
947 1151 9.527157 TCTTGTGGATTATAATGGTTCAGAAAA 57.473 29.630 1.78 0.00 0.00 2.29
972 1202 4.965532 ACTTCCTTATGCTGATACCAGTCT 59.034 41.667 0.00 0.00 42.35 3.24
975 1205 6.313519 TCCTTATGCTGATACCAGTCTTTT 57.686 37.500 0.00 0.00 42.35 2.27
987 1217 3.062042 CCAGTCTTTTTCTTGGCATTGC 58.938 45.455 0.00 0.00 0.00 3.56
1086 1316 1.476652 GGCCCAACAATGTTTGCCTTT 60.477 47.619 22.22 0.00 33.44 3.11
1208 1438 3.181513 CGAGCAAGTGTGGAATGATTGAG 60.182 47.826 0.00 0.00 0.00 3.02
1246 1476 7.333528 TGTATCATCTTGTTGGCTAATTTCC 57.666 36.000 0.00 0.00 0.00 3.13
1307 1546 3.692690 TGCCATGTTTAGTTCTTACCCC 58.307 45.455 0.00 0.00 0.00 4.95
1309 1548 3.562609 GCCATGTTTAGTTCTTACCCCCA 60.563 47.826 0.00 0.00 0.00 4.96
1352 1926 6.882610 ACTTGCTATGTCACATTCTTTTCA 57.117 33.333 0.00 0.00 0.00 2.69
1353 1927 7.458409 ACTTGCTATGTCACATTCTTTTCAT 57.542 32.000 0.00 0.00 0.00 2.57
1354 1928 7.889469 ACTTGCTATGTCACATTCTTTTCATT 58.111 30.769 0.00 0.00 0.00 2.57
1355 1929 9.013229 ACTTGCTATGTCACATTCTTTTCATTA 57.987 29.630 0.00 0.00 0.00 1.90
1358 1932 9.791820 TGCTATGTCACATTCTTTTCATTATTG 57.208 29.630 0.00 0.00 0.00 1.90
1359 1933 8.749499 GCTATGTCACATTCTTTTCATTATTGC 58.251 33.333 0.00 0.00 0.00 3.56
1363 1937 9.791820 TGTCACATTCTTTTCATTATTGCTATG 57.208 29.630 0.00 0.00 0.00 2.23
1364 1938 9.793252 GTCACATTCTTTTCATTATTGCTATGT 57.207 29.630 0.00 0.00 0.00 2.29
1366 1940 9.791820 CACATTCTTTTCATTATTGCTATGTCA 57.208 29.630 0.00 0.00 0.00 3.58
1367 1941 9.793252 ACATTCTTTTCATTATTGCTATGTCAC 57.207 29.630 0.00 0.00 0.00 3.67
1368 1942 9.791820 CATTCTTTTCATTATTGCTATGTCACA 57.208 29.630 0.00 0.00 0.00 3.58
1376 1950 9.791820 TCATTATTGCTATGTCACATTCTTTTG 57.208 29.630 0.00 0.00 0.00 2.44
1377 1951 9.027129 CATTATTGCTATGTCACATTCTTTTGG 57.973 33.333 0.00 0.00 0.00 3.28
1378 1952 6.594788 ATTGCTATGTCACATTCTTTTGGT 57.405 33.333 0.00 0.00 0.00 3.67
1379 1953 5.375417 TGCTATGTCACATTCTTTTGGTG 57.625 39.130 0.00 0.00 0.00 4.17
1380 1954 4.218200 TGCTATGTCACATTCTTTTGGTGG 59.782 41.667 0.00 0.00 33.45 4.61
1381 1955 3.665745 ATGTCACATTCTTTTGGTGGC 57.334 42.857 0.00 0.00 37.64 5.01
1382 1956 1.336440 TGTCACATTCTTTTGGTGGCG 59.664 47.619 0.00 0.00 39.89 5.69
1383 1957 0.313672 TCACATTCTTTTGGTGGCGC 59.686 50.000 0.00 0.00 33.45 6.53
1384 1958 0.314935 CACATTCTTTTGGTGGCGCT 59.685 50.000 7.64 0.00 0.00 5.92
1385 1959 1.039856 ACATTCTTTTGGTGGCGCTT 58.960 45.000 7.64 0.00 0.00 4.68
1386 1960 1.412343 ACATTCTTTTGGTGGCGCTTT 59.588 42.857 7.64 0.00 0.00 3.51
1387 1961 2.625790 ACATTCTTTTGGTGGCGCTTTA 59.374 40.909 7.64 0.00 0.00 1.85
1388 1962 2.785713 TTCTTTTGGTGGCGCTTTAC 57.214 45.000 7.64 4.27 0.00 2.01
1389 1963 1.681538 TCTTTTGGTGGCGCTTTACA 58.318 45.000 7.64 0.00 0.00 2.41
1390 1964 2.025155 TCTTTTGGTGGCGCTTTACAA 58.975 42.857 7.64 5.28 0.00 2.41
1391 1965 2.427453 TCTTTTGGTGGCGCTTTACAAA 59.573 40.909 7.64 11.31 0.00 2.83
1392 1966 3.068873 TCTTTTGGTGGCGCTTTACAAAT 59.931 39.130 7.64 0.00 31.92 2.32
1393 1967 3.460857 TTTGGTGGCGCTTTACAAATT 57.539 38.095 7.64 0.00 0.00 1.82
1394 1968 3.460857 TTGGTGGCGCTTTACAAATTT 57.539 38.095 7.64 0.00 0.00 1.82
1395 1969 4.585955 TTGGTGGCGCTTTACAAATTTA 57.414 36.364 7.64 0.00 0.00 1.40
1396 1970 4.792521 TGGTGGCGCTTTACAAATTTAT 57.207 36.364 7.64 0.00 0.00 1.40
1397 1971 5.140747 TGGTGGCGCTTTACAAATTTATT 57.859 34.783 7.64 0.00 0.00 1.40
1398 1972 5.542779 TGGTGGCGCTTTACAAATTTATTT 58.457 33.333 7.64 0.00 0.00 1.40
1399 1973 6.688578 TGGTGGCGCTTTACAAATTTATTTA 58.311 32.000 7.64 0.00 0.00 1.40
1400 1974 7.324178 TGGTGGCGCTTTACAAATTTATTTAT 58.676 30.769 7.64 0.00 0.00 1.40
1401 1975 7.819900 TGGTGGCGCTTTACAAATTTATTTATT 59.180 29.630 7.64 0.00 0.00 1.40
1402 1976 8.661257 GGTGGCGCTTTACAAATTTATTTATTT 58.339 29.630 7.64 0.00 0.00 1.40
1425 1999 8.464770 TTTTTCATTATTGCTCCGATTTTGAG 57.535 30.769 0.00 0.00 0.00 3.02
1434 2008 4.088823 CTCCGATTTTGAGCTTTCTTGG 57.911 45.455 0.00 0.00 0.00 3.61
1435 2009 3.750371 TCCGATTTTGAGCTTTCTTGGA 58.250 40.909 0.00 0.00 0.00 3.53
1436 2010 4.141287 TCCGATTTTGAGCTTTCTTGGAA 58.859 39.130 0.00 0.00 0.00 3.53
1437 2011 4.023193 TCCGATTTTGAGCTTTCTTGGAAC 60.023 41.667 0.00 0.00 0.00 3.62
1438 2012 4.022849 CCGATTTTGAGCTTTCTTGGAACT 60.023 41.667 0.00 0.00 0.00 3.01
1439 2013 5.507985 CCGATTTTGAGCTTTCTTGGAACTT 60.508 40.000 0.00 0.00 0.00 2.66
1440 2014 6.293955 CCGATTTTGAGCTTTCTTGGAACTTA 60.294 38.462 0.00 0.00 0.00 2.24
1441 2015 7.138736 CGATTTTGAGCTTTCTTGGAACTTAA 58.861 34.615 0.00 0.00 0.00 1.85
1442 2016 7.324616 CGATTTTGAGCTTTCTTGGAACTTAAG 59.675 37.037 0.00 0.00 0.00 1.85
1443 2017 7.639113 TTTTGAGCTTTCTTGGAACTTAAGA 57.361 32.000 10.09 0.00 32.64 2.10
1444 2018 6.619801 TTGAGCTTTCTTGGAACTTAAGAC 57.380 37.500 10.09 2.77 34.14 3.01
1445 2019 5.063880 TGAGCTTTCTTGGAACTTAAGACC 58.936 41.667 10.09 12.30 34.14 3.85
1446 2020 5.163195 TGAGCTTTCTTGGAACTTAAGACCT 60.163 40.000 10.09 0.00 34.14 3.85
1447 2021 5.696030 AGCTTTCTTGGAACTTAAGACCTT 58.304 37.500 10.09 0.00 34.14 3.50
1448 2022 6.129874 AGCTTTCTTGGAACTTAAGACCTTT 58.870 36.000 10.09 0.00 34.14 3.11
1449 2023 6.607600 AGCTTTCTTGGAACTTAAGACCTTTT 59.392 34.615 10.09 0.00 34.14 2.27
1450 2024 7.124298 AGCTTTCTTGGAACTTAAGACCTTTTT 59.876 33.333 10.09 0.00 34.14 1.94
1477 2051 9.594478 TTTTTGAATTTTCTGGAACTTAAGACC 57.406 29.630 10.09 12.30 0.00 3.85
1478 2052 8.533569 TTTGAATTTTCTGGAACTTAAGACCT 57.466 30.769 10.09 0.00 0.00 3.85
1479 2053 8.533569 TTGAATTTTCTGGAACTTAAGACCTT 57.466 30.769 10.09 0.00 0.00 3.50
1480 2054 7.940850 TGAATTTTCTGGAACTTAAGACCTTG 58.059 34.615 10.09 9.28 0.00 3.61
1481 2055 7.559897 TGAATTTTCTGGAACTTAAGACCTTGT 59.440 33.333 10.09 0.00 0.00 3.16
1482 2056 7.898014 ATTTTCTGGAACTTAAGACCTTGTT 57.102 32.000 10.09 0.00 0.00 2.83
1483 2057 8.990163 ATTTTCTGGAACTTAAGACCTTGTTA 57.010 30.769 10.09 1.35 0.00 2.41
1484 2058 7.797038 TTTCTGGAACTTAAGACCTTGTTAC 57.203 36.000 10.09 0.00 0.00 2.50
1485 2059 5.535333 TCTGGAACTTAAGACCTTGTTACG 58.465 41.667 10.09 0.00 0.00 3.18
1486 2060 4.060205 TGGAACTTAAGACCTTGTTACGC 58.940 43.478 10.09 0.00 0.00 4.42
1487 2061 4.202284 TGGAACTTAAGACCTTGTTACGCT 60.202 41.667 10.09 0.00 0.00 5.07
1488 2062 4.753610 GGAACTTAAGACCTTGTTACGCTT 59.246 41.667 10.09 0.00 0.00 4.68
1489 2063 5.237996 GGAACTTAAGACCTTGTTACGCTTT 59.762 40.000 10.09 0.00 0.00 3.51
1490 2064 6.238566 GGAACTTAAGACCTTGTTACGCTTTT 60.239 38.462 10.09 0.00 0.00 2.27
1491 2065 6.688637 ACTTAAGACCTTGTTACGCTTTTT 57.311 33.333 10.09 0.00 0.00 1.94
1492 2066 7.790823 ACTTAAGACCTTGTTACGCTTTTTA 57.209 32.000 10.09 0.00 0.00 1.52
1493 2067 8.212317 ACTTAAGACCTTGTTACGCTTTTTAA 57.788 30.769 10.09 0.00 0.00 1.52
1494 2068 8.843262 ACTTAAGACCTTGTTACGCTTTTTAAT 58.157 29.630 10.09 0.00 0.00 1.40
1505 2079 9.291664 TGTTACGCTTTTTAATAATATGGTTGC 57.708 29.630 0.00 0.00 0.00 4.17
1506 2080 9.291664 GTTACGCTTTTTAATAATATGGTTGCA 57.708 29.630 0.00 0.00 0.00 4.08
1508 2082 8.351495 ACGCTTTTTAATAATATGGTTGCATG 57.649 30.769 0.00 0.00 0.00 4.06
1509 2083 7.042791 ACGCTTTTTAATAATATGGTTGCATGC 60.043 33.333 11.82 11.82 0.00 4.06
1510 2084 7.042858 CGCTTTTTAATAATATGGTTGCATGCA 60.043 33.333 18.46 18.46 0.00 3.96
1511 2085 8.776470 GCTTTTTAATAATATGGTTGCATGCAT 58.224 29.630 23.37 9.20 0.00 3.96
1513 2087 8.518151 TTTTAATAATATGGTTGCATGCATCG 57.482 30.769 23.37 0.00 0.00 3.84
1514 2088 5.963176 AATAATATGGTTGCATGCATCGA 57.037 34.783 23.37 18.42 0.00 3.59
1515 2089 6.519679 AATAATATGGTTGCATGCATCGAT 57.480 33.333 23.37 23.71 0.00 3.59
1516 2090 4.859304 AATATGGTTGCATGCATCGATT 57.141 36.364 25.11 18.38 0.00 3.34
1517 2091 2.502213 ATGGTTGCATGCATCGATTG 57.498 45.000 23.37 0.00 0.00 2.67
1518 2092 1.461559 TGGTTGCATGCATCGATTGA 58.538 45.000 23.37 0.58 0.00 2.57
1519 2093 2.025898 TGGTTGCATGCATCGATTGAT 58.974 42.857 23.37 0.00 34.28 2.57
1528 2102 0.873054 CATCGATTGATGCAGAGGCC 59.127 55.000 10.05 0.00 45.06 5.19
1529 2103 0.471191 ATCGATTGATGCAGAGGCCA 59.529 50.000 5.01 0.00 40.13 5.36
1530 2104 0.179065 TCGATTGATGCAGAGGCCAG 60.179 55.000 5.01 0.00 40.13 4.85
1531 2105 0.179065 CGATTGATGCAGAGGCCAGA 60.179 55.000 5.01 0.00 40.13 3.86
1532 2106 1.595466 GATTGATGCAGAGGCCAGAG 58.405 55.000 5.01 0.00 40.13 3.35
1533 2107 0.183014 ATTGATGCAGAGGCCAGAGG 59.817 55.000 5.01 0.00 40.13 3.69
1534 2108 1.203441 TTGATGCAGAGGCCAGAGGT 61.203 55.000 5.01 0.00 40.13 3.85
1535 2109 0.325577 TGATGCAGAGGCCAGAGGTA 60.326 55.000 5.01 0.00 40.13 3.08
1536 2110 0.833287 GATGCAGAGGCCAGAGGTAA 59.167 55.000 5.01 0.00 40.13 2.85
1537 2111 1.419387 GATGCAGAGGCCAGAGGTAAT 59.581 52.381 5.01 0.00 40.13 1.89
1538 2112 0.833287 TGCAGAGGCCAGAGGTAATC 59.167 55.000 5.01 0.00 40.13 1.75
1539 2113 0.107643 GCAGAGGCCAGAGGTAATCC 59.892 60.000 5.01 0.00 0.00 3.01
1540 2114 4.911773 TGCAGAGGCCAGAGGTAATCCT 62.912 54.545 5.01 0.00 43.01 3.24
1626 2201 5.892160 ATTGCTGGAATGATTGATATCCG 57.108 39.130 0.00 0.00 34.60 4.18
1634 2209 3.558931 TGATTGATATCCGTGGCAGTT 57.441 42.857 0.00 0.00 0.00 3.16
1649 2225 3.258372 TGGCAGTTTGTGGTTGTTTAACA 59.742 39.130 0.00 0.00 38.58 2.41
1653 2229 5.164002 GCAGTTTGTGGTTGTTTAACAGTTG 60.164 40.000 0.00 0.00 38.58 3.16
1677 2454 2.858745 TGGTTTACTGGCTTGGAACTC 58.141 47.619 0.00 0.00 0.00 3.01
1690 2467 1.230324 GGAACTCACCACTGTTGCTC 58.770 55.000 0.00 0.00 32.90 4.26
1778 2555 7.437267 GCTTGCAATGCTCATTTAGTCATTATT 59.563 33.333 6.82 0.00 33.18 1.40
1779 2556 9.955208 CTTGCAATGCTCATTTAGTCATTATTA 57.045 29.630 6.82 0.00 33.18 0.98
1780 2557 9.955208 TTGCAATGCTCATTTAGTCATTATTAG 57.045 29.630 6.82 0.00 33.18 1.73
1851 2628 7.119116 TCACATGAAAGTACACACATAATGGAC 59.881 37.037 0.00 0.00 0.00 4.02
1926 2703 5.354842 TCAGAATTCAGATCAGCAGATGT 57.645 39.130 8.44 0.00 33.72 3.06
1965 2742 1.308998 GTCGCACCATCTTATTGGGG 58.691 55.000 0.00 0.00 43.52 4.96
2023 2805 2.880268 TGCTCATGACAGTTCTTGTTGG 59.120 45.455 0.00 0.00 41.05 3.77
2025 2807 2.880268 CTCATGACAGTTCTTGTTGGCA 59.120 45.455 0.00 0.00 41.05 4.92
2082 2864 7.385205 TGAAATCTACCTGAAGTTTCGAAGAAG 59.615 37.037 0.00 0.00 45.90 2.85
2083 2865 6.591750 ATCTACCTGAAGTTTCGAAGAAGA 57.408 37.500 0.00 0.00 45.90 2.87
2084 2866 6.401047 TCTACCTGAAGTTTCGAAGAAGAA 57.599 37.500 0.00 0.00 45.90 2.52
2085 2867 6.448006 TCTACCTGAAGTTTCGAAGAAGAAG 58.552 40.000 0.00 0.00 45.90 2.85
2147 2929 7.502226 CCTTTTGTATCATCTATAGTTTGGCCA 59.498 37.037 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.741344 GCAACAGTAGTACAACACTGAGG 59.259 47.826 21.91 15.65 43.99 3.86
114 115 4.800993 CGTTGTCTGAAGAACTAGGCTATG 59.199 45.833 0.00 0.00 0.00 2.23
168 169 1.061131 CGTAAAACTCTGGCGCAGATG 59.939 52.381 10.83 7.15 39.92 2.90
180 181 3.367087 CGAGGGACACAGATCGTAAAACT 60.367 47.826 0.00 0.00 0.00 2.66
181 182 2.921754 CGAGGGACACAGATCGTAAAAC 59.078 50.000 0.00 0.00 0.00 2.43
194 196 1.367471 CTGTTGCACTCGAGGGACA 59.633 57.895 21.51 14.08 0.00 4.02
270 276 0.656259 CAGATTGCACCTGCGATGAG 59.344 55.000 4.66 0.00 44.75 2.90
271 277 1.371337 GCAGATTGCACCTGCGATGA 61.371 55.000 20.30 0.00 46.03 2.92
272 278 1.063649 GCAGATTGCACCTGCGATG 59.936 57.895 20.30 0.00 46.03 3.84
277 283 2.338015 AAGCCGCAGATTGCACCTG 61.338 57.895 10.16 10.16 45.36 4.00
278 284 2.034687 AAGCCGCAGATTGCACCT 59.965 55.556 1.69 0.00 45.36 4.00
279 285 1.865788 TTCAAGCCGCAGATTGCACC 61.866 55.000 1.69 0.00 45.36 5.01
280 286 0.039256 TTTCAAGCCGCAGATTGCAC 60.039 50.000 1.69 0.00 45.36 4.57
281 287 0.889994 ATTTCAAGCCGCAGATTGCA 59.110 45.000 1.69 0.00 45.36 4.08
282 288 2.000429 AATTTCAAGCCGCAGATTGC 58.000 45.000 0.00 0.00 40.69 3.56
283 289 7.935338 AATTATAATTTCAAGCCGCAGATTG 57.065 32.000 4.81 0.00 0.00 2.67
297 303 7.042523 GCAATCTGCGGCTTGAAATTATAATTT 60.043 33.333 20.77 20.77 36.01 1.82
298 304 6.421801 GCAATCTGCGGCTTGAAATTATAATT 59.578 34.615 13.22 4.81 31.71 1.40
299 305 5.922544 GCAATCTGCGGCTTGAAATTATAAT 59.077 36.000 13.22 0.00 31.71 1.28
300 306 5.280945 GCAATCTGCGGCTTGAAATTATAA 58.719 37.500 13.22 0.00 31.71 0.98
301 307 4.858935 GCAATCTGCGGCTTGAAATTATA 58.141 39.130 13.22 0.00 31.71 0.98
302 308 3.709987 GCAATCTGCGGCTTGAAATTAT 58.290 40.909 13.22 0.00 31.71 1.28
321 327 4.758251 CGACCCATCGCAGGTGCA 62.758 66.667 2.33 0.00 42.43 4.57
335 341 6.292596 GCAGGAAATGATGTTCTAAGATCGAC 60.293 42.308 0.00 0.00 31.80 4.20
374 380 5.196341 TGACATAAGATACATGGGACGAC 57.804 43.478 0.00 0.00 0.00 4.34
375 381 4.893524 ACTGACATAAGATACATGGGACGA 59.106 41.667 0.00 0.00 0.00 4.20
376 382 5.201713 ACTGACATAAGATACATGGGACG 57.798 43.478 0.00 0.00 0.00 4.79
377 383 5.009710 TCGACTGACATAAGATACATGGGAC 59.990 44.000 0.00 0.00 0.00 4.46
378 384 5.137551 TCGACTGACATAAGATACATGGGA 58.862 41.667 0.00 0.00 0.00 4.37
379 385 5.453567 TCGACTGACATAAGATACATGGG 57.546 43.478 0.00 0.00 0.00 4.00
380 386 6.918626 AGATCGACTGACATAAGATACATGG 58.081 40.000 0.00 0.00 0.00 3.66
381 387 9.553418 CTAAGATCGACTGACATAAGATACATG 57.447 37.037 0.00 0.00 0.00 3.21
382 388 9.508642 TCTAAGATCGACTGACATAAGATACAT 57.491 33.333 0.00 0.00 0.00 2.29
383 389 8.904099 TCTAAGATCGACTGACATAAGATACA 57.096 34.615 0.00 0.00 0.00 2.29
384 390 9.601971 GTTCTAAGATCGACTGACATAAGATAC 57.398 37.037 0.00 0.00 0.00 2.24
385 391 9.338622 TGTTCTAAGATCGACTGACATAAGATA 57.661 33.333 0.00 0.00 0.00 1.98
386 392 8.226819 TGTTCTAAGATCGACTGACATAAGAT 57.773 34.615 0.00 0.00 0.00 2.40
387 393 7.625828 TGTTCTAAGATCGACTGACATAAGA 57.374 36.000 0.00 0.00 0.00 2.10
388 394 8.131731 TGATGTTCTAAGATCGACTGACATAAG 58.868 37.037 0.00 0.00 31.80 1.73
389 395 7.996385 TGATGTTCTAAGATCGACTGACATAA 58.004 34.615 0.00 0.00 31.80 1.90
390 396 7.568199 TGATGTTCTAAGATCGACTGACATA 57.432 36.000 0.00 0.00 31.80 2.29
391 397 6.456795 TGATGTTCTAAGATCGACTGACAT 57.543 37.500 0.00 6.73 31.80 3.06
392 398 5.897377 TGATGTTCTAAGATCGACTGACA 57.103 39.130 0.00 0.00 31.80 3.58
393 399 7.043059 GGAAATGATGTTCTAAGATCGACTGAC 60.043 40.741 0.00 0.00 31.80 3.51
394 400 6.980978 GGAAATGATGTTCTAAGATCGACTGA 59.019 38.462 0.00 0.00 31.80 3.41
395 401 6.983307 AGGAAATGATGTTCTAAGATCGACTG 59.017 38.462 0.00 0.00 31.80 3.51
396 402 7.118496 AGGAAATGATGTTCTAAGATCGACT 57.882 36.000 0.00 0.00 31.80 4.18
397 403 7.921214 TGTAGGAAATGATGTTCTAAGATCGAC 59.079 37.037 0.00 0.00 31.80 4.20
398 404 8.007405 TGTAGGAAATGATGTTCTAAGATCGA 57.993 34.615 0.00 0.00 31.80 3.59
399 405 7.923344 ACTGTAGGAAATGATGTTCTAAGATCG 59.077 37.037 0.00 0.00 31.80 3.69
402 408 9.256228 AGTACTGTAGGAAATGATGTTCTAAGA 57.744 33.333 0.00 0.00 0.00 2.10
403 409 9.307121 CAGTACTGTAGGAAATGATGTTCTAAG 57.693 37.037 15.06 0.00 0.00 2.18
404 410 7.764443 GCAGTACTGTAGGAAATGATGTTCTAA 59.236 37.037 23.44 0.00 0.00 2.10
405 411 7.093509 TGCAGTACTGTAGGAAATGATGTTCTA 60.094 37.037 23.44 0.00 0.00 2.10
406 412 6.109359 GCAGTACTGTAGGAAATGATGTTCT 58.891 40.000 23.44 0.00 0.00 3.01
407 413 5.874810 TGCAGTACTGTAGGAAATGATGTTC 59.125 40.000 23.44 2.27 0.00 3.18
408 414 5.804639 TGCAGTACTGTAGGAAATGATGTT 58.195 37.500 23.44 0.00 0.00 2.71
409 415 5.420725 TGCAGTACTGTAGGAAATGATGT 57.579 39.130 23.44 0.00 0.00 3.06
410 416 5.980698 CTGCAGTACTGTAGGAAATGATG 57.019 43.478 27.78 5.09 39.23 3.07
419 425 2.423892 ACGATGACCTGCAGTACTGTAG 59.576 50.000 28.31 28.31 41.97 2.74
420 426 2.443416 ACGATGACCTGCAGTACTGTA 58.557 47.619 23.44 18.51 0.00 2.74
421 427 1.257743 ACGATGACCTGCAGTACTGT 58.742 50.000 23.44 3.97 0.00 3.55
422 428 2.263077 GAACGATGACCTGCAGTACTG 58.737 52.381 18.93 18.93 0.00 2.74
423 429 1.204941 GGAACGATGACCTGCAGTACT 59.795 52.381 13.81 0.00 0.00 2.73
424 430 1.067142 TGGAACGATGACCTGCAGTAC 60.067 52.381 13.81 6.70 0.00 2.73
425 431 1.262417 TGGAACGATGACCTGCAGTA 58.738 50.000 13.81 0.00 0.00 2.74
426 432 0.615331 ATGGAACGATGACCTGCAGT 59.385 50.000 13.81 0.11 0.00 4.40
427 433 1.012086 CATGGAACGATGACCTGCAG 58.988 55.000 6.78 6.78 0.00 4.41
428 434 0.324614 ACATGGAACGATGACCTGCA 59.675 50.000 0.00 0.00 0.00 4.41
429 435 2.309528 TACATGGAACGATGACCTGC 57.690 50.000 0.00 0.00 0.00 4.85
430 436 4.327982 AGATACATGGAACGATGACCTG 57.672 45.455 0.00 0.00 0.00 4.00
431 437 6.042093 ACATAAGATACATGGAACGATGACCT 59.958 38.462 9.24 0.00 0.00 3.85
432 438 6.223852 ACATAAGATACATGGAACGATGACC 58.776 40.000 9.24 0.00 0.00 4.02
433 439 6.923508 TGACATAAGATACATGGAACGATGAC 59.076 38.462 9.24 5.02 0.00 3.06
434 440 6.923508 GTGACATAAGATACATGGAACGATGA 59.076 38.462 9.24 0.00 0.00 2.92
435 441 6.925718 AGTGACATAAGATACATGGAACGATG 59.074 38.462 0.00 0.00 0.00 3.84
490 504 7.339212 TGAATCCAGTCCAAAGGTTATTATGTG 59.661 37.037 0.00 0.00 0.00 3.21
502 516 6.303054 TGTTAACTCATGAATCCAGTCCAAA 58.697 36.000 7.22 0.00 0.00 3.28
601 633 7.043961 TGTGTCAAAATAATGCACTACCAAA 57.956 32.000 0.00 0.00 32.34 3.28
610 642 6.019318 GCATCTTCCATGTGTCAAAATAATGC 60.019 38.462 0.00 0.00 0.00 3.56
615 647 5.471556 TTGCATCTTCCATGTGTCAAAAT 57.528 34.783 0.00 0.00 0.00 1.82
616 648 4.933505 TTGCATCTTCCATGTGTCAAAA 57.066 36.364 0.00 0.00 0.00 2.44
644 677 6.594937 GGACGTGGAAATAAACACCTAATACA 59.405 38.462 0.00 0.00 34.18 2.29
666 700 2.604046 ATAACTGCACTCATCGGGAC 57.396 50.000 0.00 0.00 0.00 4.46
696 898 5.355071 TGCTTATGAACAGCCTGATTTGTAG 59.645 40.000 0.00 0.00 36.33 2.74
736 938 6.720288 AGTACTTCTCTAAGCACCTTGAACTA 59.280 38.462 0.00 0.00 36.05 2.24
738 940 5.785243 AGTACTTCTCTAAGCACCTTGAAC 58.215 41.667 0.00 0.00 36.05 3.18
739 941 6.420913 AAGTACTTCTCTAAGCACCTTGAA 57.579 37.500 1.12 0.00 36.05 2.69
740 942 5.335740 CGAAGTACTTCTCTAAGCACCTTGA 60.336 44.000 28.30 0.00 37.44 3.02
763 965 7.775729 AAGCGACAATCTGTTTATTTTTACG 57.224 32.000 0.00 0.00 0.00 3.18
781 983 1.003223 ACAAGCAACGGTTTAAGCGAC 60.003 47.619 23.21 11.45 42.41 5.19
783 985 2.113910 AACAAGCAACGGTTTAAGCG 57.886 45.000 15.11 15.11 45.69 4.68
804 1008 2.660572 TGCTTGGCACCTCTGTTAAAA 58.339 42.857 0.00 0.00 31.71 1.52
841 1045 6.479660 AGGTGCTTGTAAAAATGAACATGTTG 59.520 34.615 17.58 0.00 0.00 3.33
843 1047 6.040842 AGAGGTGCTTGTAAAAATGAACATGT 59.959 34.615 0.00 0.00 0.00 3.21
845 1049 6.491403 AGAGAGGTGCTTGTAAAAATGAACAT 59.509 34.615 0.00 0.00 0.00 2.71
846 1050 5.827797 AGAGAGGTGCTTGTAAAAATGAACA 59.172 36.000 0.00 0.00 0.00 3.18
847 1051 6.319141 AGAGAGGTGCTTGTAAAAATGAAC 57.681 37.500 0.00 0.00 0.00 3.18
849 1053 6.173339 CCTAGAGAGGTGCTTGTAAAAATGA 58.827 40.000 0.00 0.00 38.16 2.57
850 1054 5.163713 GCCTAGAGAGGTGCTTGTAAAAATG 60.164 44.000 0.00 0.00 45.78 2.32
851 1055 4.944317 GCCTAGAGAGGTGCTTGTAAAAAT 59.056 41.667 0.00 0.00 45.78 1.82
852 1056 4.324267 GCCTAGAGAGGTGCTTGTAAAAA 58.676 43.478 0.00 0.00 45.78 1.94
875 1079 7.149569 CATTAGGACATGTATAATGCAAGGG 57.850 40.000 21.37 6.21 32.05 3.95
885 1089 6.594744 TGATCAACTGCATTAGGACATGTAT 58.405 36.000 0.00 0.00 0.00 2.29
889 1093 5.108187 ACTGATCAACTGCATTAGGACAT 57.892 39.130 0.00 0.00 0.00 3.06
892 1096 6.543465 CCATTAACTGATCAACTGCATTAGGA 59.457 38.462 0.00 0.00 0.00 2.94
897 1101 7.776969 AGAATACCATTAACTGATCAACTGCAT 59.223 33.333 0.00 0.00 0.00 3.96
905 1109 8.682936 ATCCACAAGAATACCATTAACTGATC 57.317 34.615 0.00 0.00 0.00 2.92
919 1123 9.699410 TTCTGAACCATTATAATCCACAAGAAT 57.301 29.630 0.00 0.00 0.00 2.40
947 1151 6.067217 ACTGGTATCAGCATAAGGAAGTTT 57.933 37.500 1.90 0.00 44.59 2.66
965 1195 3.493176 GCAATGCCAAGAAAAAGACTGGT 60.493 43.478 0.00 0.00 0.00 4.00
987 1217 2.110967 CGCCATGGCTCACTTCTGG 61.111 63.158 33.07 11.50 39.32 3.86
1146 1376 1.418097 TTTCTGCTCCAGCTGGTCCA 61.418 55.000 31.58 25.51 42.66 4.02
1208 1438 9.677567 ACAAGATGATACATACAACAACAAAAC 57.322 29.630 0.00 0.00 0.00 2.43
1350 1924 9.791820 CAAAAGAATGTGACATAGCAATAATGA 57.208 29.630 0.00 0.00 0.00 2.57
1351 1925 9.027129 CCAAAAGAATGTGACATAGCAATAATG 57.973 33.333 0.00 0.00 0.00 1.90
1352 1926 8.752187 ACCAAAAGAATGTGACATAGCAATAAT 58.248 29.630 0.00 0.00 0.00 1.28
1353 1927 8.028354 CACCAAAAGAATGTGACATAGCAATAA 58.972 33.333 0.00 0.00 31.66 1.40
1354 1928 7.362834 CCACCAAAAGAATGTGACATAGCAATA 60.363 37.037 0.00 0.00 31.66 1.90
1355 1929 6.392354 CACCAAAAGAATGTGACATAGCAAT 58.608 36.000 0.00 0.00 31.66 3.56
1356 1930 5.278907 CCACCAAAAGAATGTGACATAGCAA 60.279 40.000 0.00 0.00 31.66 3.91
1357 1931 4.218200 CCACCAAAAGAATGTGACATAGCA 59.782 41.667 0.00 0.00 31.66 3.49
1358 1932 4.737054 CCACCAAAAGAATGTGACATAGC 58.263 43.478 0.00 0.00 31.66 2.97
1359 1933 4.672542 CGCCACCAAAAGAATGTGACATAG 60.673 45.833 0.00 0.00 31.66 2.23
1360 1934 3.190327 CGCCACCAAAAGAATGTGACATA 59.810 43.478 0.00 0.00 31.66 2.29
1361 1935 2.030007 CGCCACCAAAAGAATGTGACAT 60.030 45.455 0.00 0.00 31.66 3.06
1362 1936 1.336440 CGCCACCAAAAGAATGTGACA 59.664 47.619 0.00 0.00 31.66 3.58
1363 1937 1.930371 GCGCCACCAAAAGAATGTGAC 60.930 52.381 0.00 0.00 31.66 3.67
1364 1938 0.313672 GCGCCACCAAAAGAATGTGA 59.686 50.000 0.00 0.00 31.66 3.58
1365 1939 0.314935 AGCGCCACCAAAAGAATGTG 59.685 50.000 2.29 0.00 0.00 3.21
1366 1940 1.039856 AAGCGCCACCAAAAGAATGT 58.960 45.000 2.29 0.00 0.00 2.71
1367 1941 2.153366 AAAGCGCCACCAAAAGAATG 57.847 45.000 2.29 0.00 0.00 2.67
1368 1942 2.625790 TGTAAAGCGCCACCAAAAGAAT 59.374 40.909 2.29 0.00 0.00 2.40
1369 1943 2.025155 TGTAAAGCGCCACCAAAAGAA 58.975 42.857 2.29 0.00 0.00 2.52
1370 1944 1.681538 TGTAAAGCGCCACCAAAAGA 58.318 45.000 2.29 0.00 0.00 2.52
1371 1945 2.500509 TTGTAAAGCGCCACCAAAAG 57.499 45.000 2.29 0.00 0.00 2.27
1372 1946 2.961526 TTTGTAAAGCGCCACCAAAA 57.038 40.000 2.29 0.00 0.00 2.44
1373 1947 3.460857 AATTTGTAAAGCGCCACCAAA 57.539 38.095 2.29 9.17 0.00 3.28
1374 1948 3.460857 AAATTTGTAAAGCGCCACCAA 57.539 38.095 2.29 0.00 0.00 3.67
1375 1949 4.792521 ATAAATTTGTAAAGCGCCACCA 57.207 36.364 2.29 0.00 0.00 4.17
1376 1950 7.764695 ATAAATAAATTTGTAAAGCGCCACC 57.235 32.000 2.29 0.00 0.00 4.61
1399 1973 9.090692 CTCAAAATCGGAGCAATAATGAAAAAT 57.909 29.630 0.00 0.00 0.00 1.82
1400 1974 8.464770 CTCAAAATCGGAGCAATAATGAAAAA 57.535 30.769 0.00 0.00 0.00 1.94
1413 1987 3.753272 TCCAAGAAAGCTCAAAATCGGAG 59.247 43.478 0.00 0.00 35.47 4.63
1414 1988 3.750371 TCCAAGAAAGCTCAAAATCGGA 58.250 40.909 0.00 0.00 0.00 4.55
1415 1989 4.022849 AGTTCCAAGAAAGCTCAAAATCGG 60.023 41.667 0.00 0.00 0.00 4.18
1416 1990 5.113502 AGTTCCAAGAAAGCTCAAAATCG 57.886 39.130 0.00 0.00 0.00 3.34
1417 1991 8.352942 TCTTAAGTTCCAAGAAAGCTCAAAATC 58.647 33.333 1.63 0.00 0.00 2.17
1418 1992 8.138074 GTCTTAAGTTCCAAGAAAGCTCAAAAT 58.862 33.333 1.63 0.00 33.95 1.82
1419 1993 7.416326 GGTCTTAAGTTCCAAGAAAGCTCAAAA 60.416 37.037 1.63 0.00 33.95 2.44
1420 1994 6.039382 GGTCTTAAGTTCCAAGAAAGCTCAAA 59.961 38.462 1.63 0.00 33.95 2.69
1421 1995 5.531287 GGTCTTAAGTTCCAAGAAAGCTCAA 59.469 40.000 1.63 0.00 33.95 3.02
1422 1996 5.063880 GGTCTTAAGTTCCAAGAAAGCTCA 58.936 41.667 1.63 0.00 33.95 4.26
1423 1997 5.309638 AGGTCTTAAGTTCCAAGAAAGCTC 58.690 41.667 16.98 0.00 33.95 4.09
1424 1998 5.311844 AGGTCTTAAGTTCCAAGAAAGCT 57.688 39.130 16.98 2.67 33.95 3.74
1425 1999 6.392625 AAAGGTCTTAAGTTCCAAGAAAGC 57.607 37.500 16.98 0.70 33.95 3.51
1451 2025 9.594478 GGTCTTAAGTTCCAGAAAATTCAAAAA 57.406 29.630 1.63 0.00 0.00 1.94
1452 2026 8.977412 AGGTCTTAAGTTCCAGAAAATTCAAAA 58.023 29.630 16.98 0.00 0.00 2.44
1453 2027 8.533569 AGGTCTTAAGTTCCAGAAAATTCAAA 57.466 30.769 16.98 0.00 0.00 2.69
1454 2028 8.413229 CAAGGTCTTAAGTTCCAGAAAATTCAA 58.587 33.333 16.98 0.00 0.00 2.69
1455 2029 7.559897 ACAAGGTCTTAAGTTCCAGAAAATTCA 59.440 33.333 16.98 0.00 0.00 2.57
1456 2030 7.941919 ACAAGGTCTTAAGTTCCAGAAAATTC 58.058 34.615 16.98 0.00 0.00 2.17
1457 2031 7.898014 ACAAGGTCTTAAGTTCCAGAAAATT 57.102 32.000 16.98 4.11 0.00 1.82
1458 2032 7.898014 AACAAGGTCTTAAGTTCCAGAAAAT 57.102 32.000 16.98 0.00 0.00 1.82
1459 2033 7.011669 CGTAACAAGGTCTTAAGTTCCAGAAAA 59.988 37.037 16.98 2.88 0.00 2.29
1460 2034 6.480981 CGTAACAAGGTCTTAAGTTCCAGAAA 59.519 38.462 16.98 5.39 0.00 2.52
1461 2035 5.987347 CGTAACAAGGTCTTAAGTTCCAGAA 59.013 40.000 16.98 0.00 0.00 3.02
1462 2036 5.535333 CGTAACAAGGTCTTAAGTTCCAGA 58.465 41.667 16.98 0.00 0.00 3.86
1463 2037 4.151867 GCGTAACAAGGTCTTAAGTTCCAG 59.848 45.833 16.98 12.64 0.00 3.86
1464 2038 4.060205 GCGTAACAAGGTCTTAAGTTCCA 58.940 43.478 16.98 0.00 0.00 3.53
1465 2039 4.313282 AGCGTAACAAGGTCTTAAGTTCC 58.687 43.478 1.63 6.84 0.00 3.62
1466 2040 5.919272 AAGCGTAACAAGGTCTTAAGTTC 57.081 39.130 1.63 0.00 0.00 3.01
1467 2041 6.688637 AAAAGCGTAACAAGGTCTTAAGTT 57.311 33.333 1.63 0.00 0.00 2.66
1468 2042 6.688637 AAAAAGCGTAACAAGGTCTTAAGT 57.311 33.333 1.63 0.00 0.00 2.24
1479 2053 9.291664 GCAACCATATTATTAAAAAGCGTAACA 57.708 29.630 0.00 0.00 0.00 2.41
1480 2054 9.291664 TGCAACCATATTATTAAAAAGCGTAAC 57.708 29.630 0.00 0.00 0.00 2.50
1482 2056 9.457110 CATGCAACCATATTATTAAAAAGCGTA 57.543 29.630 0.00 0.00 0.00 4.42
1483 2057 7.042791 GCATGCAACCATATTATTAAAAAGCGT 60.043 33.333 14.21 0.00 0.00 5.07
1484 2058 7.042858 TGCATGCAACCATATTATTAAAAAGCG 60.043 33.333 20.30 0.00 0.00 4.68
1485 2059 8.140677 TGCATGCAACCATATTATTAAAAAGC 57.859 30.769 20.30 0.00 0.00 3.51
1487 2061 8.976471 CGATGCATGCAACCATATTATTAAAAA 58.024 29.630 26.68 0.00 0.00 1.94
1488 2062 8.355913 TCGATGCATGCAACCATATTATTAAAA 58.644 29.630 26.68 0.00 0.00 1.52
1489 2063 7.880105 TCGATGCATGCAACCATATTATTAAA 58.120 30.769 26.68 0.00 0.00 1.52
1490 2064 7.446001 TCGATGCATGCAACCATATTATTAA 57.554 32.000 26.68 0.00 0.00 1.40
1491 2065 7.628769 ATCGATGCATGCAACCATATTATTA 57.371 32.000 26.68 0.00 0.00 0.98
1492 2066 5.963176 TCGATGCATGCAACCATATTATT 57.037 34.783 26.68 3.17 0.00 1.40
1493 2067 6.151480 TCAATCGATGCATGCAACCATATTAT 59.849 34.615 26.68 4.06 0.00 1.28
1494 2068 5.472820 TCAATCGATGCATGCAACCATATTA 59.527 36.000 26.68 4.42 0.00 0.98
1495 2069 4.278919 TCAATCGATGCATGCAACCATATT 59.721 37.500 26.68 16.43 0.00 1.28
1496 2070 3.822167 TCAATCGATGCATGCAACCATAT 59.178 39.130 26.68 6.72 0.00 1.78
1497 2071 3.212685 TCAATCGATGCATGCAACCATA 58.787 40.909 26.68 9.53 0.00 2.74
1498 2072 2.025898 TCAATCGATGCATGCAACCAT 58.974 42.857 26.68 13.76 0.00 3.55
1499 2073 1.461559 TCAATCGATGCATGCAACCA 58.538 45.000 26.68 11.67 0.00 3.67
1500 2074 2.390938 CATCAATCGATGCATGCAACC 58.609 47.619 26.68 18.06 42.54 3.77
1510 2084 0.471191 TGGCCTCTGCATCAATCGAT 59.529 50.000 3.32 0.00 40.13 3.59
1511 2085 0.179065 CTGGCCTCTGCATCAATCGA 60.179 55.000 3.32 0.00 40.13 3.59
1512 2086 0.179065 TCTGGCCTCTGCATCAATCG 60.179 55.000 3.32 0.00 40.13 3.34
1513 2087 1.595466 CTCTGGCCTCTGCATCAATC 58.405 55.000 3.32 0.00 40.13 2.67
1514 2088 0.183014 CCTCTGGCCTCTGCATCAAT 59.817 55.000 3.32 0.00 40.13 2.57
1515 2089 1.203441 ACCTCTGGCCTCTGCATCAA 61.203 55.000 3.32 0.00 40.13 2.57
1516 2090 0.325577 TACCTCTGGCCTCTGCATCA 60.326 55.000 3.32 0.00 40.13 3.07
1517 2091 0.833287 TTACCTCTGGCCTCTGCATC 59.167 55.000 3.32 0.00 40.13 3.91
1518 2092 1.419387 GATTACCTCTGGCCTCTGCAT 59.581 52.381 3.32 0.00 40.13 3.96
1519 2093 0.833287 GATTACCTCTGGCCTCTGCA 59.167 55.000 3.32 0.00 40.13 4.41
1520 2094 0.107643 GGATTACCTCTGGCCTCTGC 59.892 60.000 3.32 0.00 0.00 4.26
1521 2095 1.799933 AGGATTACCTCTGGCCTCTG 58.200 55.000 3.32 0.00 44.13 3.35
1553 2127 9.657419 AGTCAAAGAAAAGAATGTGACATTTTT 57.343 25.926 12.62 10.20 38.24 1.94
1554 2128 9.657419 AAGTCAAAGAAAAGAATGTGACATTTT 57.343 25.926 12.62 3.66 38.24 1.82
1555 2129 9.090692 CAAGTCAAAGAAAAGAATGTGACATTT 57.909 29.630 12.62 0.00 38.24 2.32
1556 2130 8.469200 TCAAGTCAAAGAAAAGAATGTGACATT 58.531 29.630 11.10 11.10 38.24 2.71
1557 2131 7.999679 TCAAGTCAAAGAAAAGAATGTGACAT 58.000 30.769 0.00 0.00 38.24 3.06
1626 2201 2.378445 AAACAACCACAAACTGCCAC 57.622 45.000 0.00 0.00 0.00 5.01
1634 2209 7.036220 CCATAACAACTGTTAAACAACCACAA 58.964 34.615 6.40 0.00 42.93 3.33
1649 2225 4.522789 CCAAGCCAGTAAACCATAACAACT 59.477 41.667 0.00 0.00 0.00 3.16
1653 2229 4.765339 AGTTCCAAGCCAGTAAACCATAAC 59.235 41.667 0.00 0.00 0.00 1.89
1677 2454 1.233019 CTTGAGGAGCAACAGTGGTG 58.767 55.000 2.98 2.98 35.00 4.17
1711 2488 6.183360 TGCAGAATCATGAAGCAACTCATAAG 60.183 38.462 0.00 0.00 34.20 1.73
1778 2555 7.255035 GCGACATGGTTGAGAATACTACTACTA 60.255 40.741 0.00 0.00 0.00 1.82
1779 2556 6.459848 GCGACATGGTTGAGAATACTACTACT 60.460 42.308 0.00 0.00 0.00 2.57
1780 2557 5.686397 GCGACATGGTTGAGAATACTACTAC 59.314 44.000 0.00 0.00 0.00 2.73
1926 2703 3.951037 GACAGAGCAGAGAAGGAGACATA 59.049 47.826 0.00 0.00 0.00 2.29
1965 2742 3.910767 GCTGCTATAGCGATTGAAAATGC 59.089 43.478 19.55 7.14 43.63 3.56
2002 2784 2.880268 CCAACAAGAACTGTCATGAGCA 59.120 45.455 0.00 0.00 37.23 4.26
2004 2786 2.880268 TGCCAACAAGAACTGTCATGAG 59.120 45.455 0.00 0.00 37.23 2.90
2082 2864 7.668469 TGGTTAGTTTTCCCCTCTTATTTCTTC 59.332 37.037 0.00 0.00 0.00 2.87
2083 2865 7.532199 TGGTTAGTTTTCCCCTCTTATTTCTT 58.468 34.615 0.00 0.00 0.00 2.52
2084 2866 7.098845 TGGTTAGTTTTCCCCTCTTATTTCT 57.901 36.000 0.00 0.00 0.00 2.52
2085 2867 7.956328 ATGGTTAGTTTTCCCCTCTTATTTC 57.044 36.000 0.00 0.00 0.00 2.17
2143 2925 0.604243 TGTAACGTGTGGACATGGCC 60.604 55.000 12.04 12.04 37.19 5.36


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

AutoCloner maintained by Alex Coulton.