Multiple sequence alignment - TraesCS1D01G218200

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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 TraesCS1D01G218200 chr1D 100.000 4588 0 0 1 4588 304837565 304842152 0.000000e+00 8473.0
1 TraesCS1D01G218200 chr1B 90.789 2649 151 26 385 3002 411987431 411990017 0.000000e+00 3454.0
2 TraesCS1D01G218200 chr1B 90.652 1027 42 27 2986 3967 411990037 411991054 0.000000e+00 1315.0
3 TraesCS1D01G218200 chr1A 91.522 2076 124 24 389 2435 381818984 381821036 0.000000e+00 2811.0
4 TraesCS1D01G218200 chr1A 90.201 1143 39 24 2632 3731 381821406 381822518 0.000000e+00 1423.0
5 TraesCS1D01G218200 chr1A 89.919 248 15 9 35 281 381818709 381818947 1.240000e-80 311.0
6 TraesCS1D01G218200 chr1A 85.549 173 19 4 3796 3967 381822965 381823132 4.720000e-40 176.0
7 TraesCS1D01G218200 chr5D 92.793 555 36 2 4038 4588 272356444 272355890 0.000000e+00 800.0
8 TraesCS1D01G218200 chr5D 91.712 555 42 2 4036 4586 212952980 212952426 0.000000e+00 767.0
9 TraesCS1D01G218200 chr5D 89.286 56 6 0 1076 1131 475302757 475302812 2.290000e-08 71.3
10 TraesCS1D01G218200 chr4D 92.714 549 34 4 4041 4586 385587094 385586549 0.000000e+00 787.0
11 TraesCS1D01G218200 chr4D 92.532 549 35 4 4041 4586 5724190 5724735 0.000000e+00 782.0
12 TraesCS1D01G218200 chr4D 91.607 560 39 7 4032 4586 468586662 468586106 0.000000e+00 767.0
13 TraesCS1D01G218200 chr7D 92.405 553 36 4 4038 4586 561873404 561873954 0.000000e+00 784.0
14 TraesCS1D01G218200 chr7D 92.182 550 38 3 4042 4588 410122333 410121786 0.000000e+00 773.0
15 TraesCS1D01G218200 chr6D 92.532 549 38 1 4041 4586 17972248 17972796 0.000000e+00 784.0
16 TraesCS1D01G218200 chrUn 91.712 555 42 2 4036 4586 320692162 320692716 0.000000e+00 767.0
17 TraesCS1D01G218200 chr6B 80.113 709 106 23 1734 2421 128035685 128034991 3.190000e-136 496.0
18 TraesCS1D01G218200 chr6B 80.113 709 106 23 1734 2421 128066880 128066186 3.190000e-136 496.0
19 TraesCS1D01G218200 chr6B 80.000 710 106 23 1734 2421 128075299 128074604 4.120000e-135 492.0
20 TraesCS1D01G218200 chr6B 79.972 709 106 24 1734 2421 128053428 128052735 1.480000e-134 490.0
21 TraesCS1D01G218200 chr6B 79.972 709 107 23 1734 2421 128062702 128062008 1.480000e-134 490.0
22 TraesCS1D01G218200 chr6B 80.000 710 105 25 1734 2421 128071188 128070494 1.480000e-134 490.0
23 TraesCS1D01G218200 chr6B 79.096 708 115 24 1734 2421 128076343 128075649 1.500000e-124 457.0
24 TraesCS1D01G218200 chr2A 77.953 254 37 14 1271 1511 196291611 196291364 1.720000e-29 141.0
25 TraesCS1D01G218200 chr4A 77.559 254 38 14 1271 1511 586651473 586651226 8.010000e-28 135.0
26 TraesCS1D01G218200 chr4A 76.987 239 38 13 1271 1498 456397495 456397263 2.240000e-23 121.0
27 TraesCS1D01G218200 chr5B 89.286 56 6 0 1076 1131 582578570 582578625 2.290000e-08 71.3
28 TraesCS1D01G218200 chr5A 89.286 56 6 0 1076 1131 594571173 594571228 2.290000e-08 71.3


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 TraesCS1D01G218200 chr1D 304837565 304842152 4587 False 8473.00 8473 100.00000 1 4588 1 chr1D.!!$F1 4587
1 TraesCS1D01G218200 chr1B 411987431 411991054 3623 False 2384.50 3454 90.72050 385 3967 2 chr1B.!!$F1 3582
2 TraesCS1D01G218200 chr1A 381818709 381823132 4423 False 1180.25 2811 89.29775 35 3967 4 chr1A.!!$F1 3932
3 TraesCS1D01G218200 chr5D 272355890 272356444 554 True 800.00 800 92.79300 4038 4588 1 chr5D.!!$R2 550
4 TraesCS1D01G218200 chr5D 212952426 212952980 554 True 767.00 767 91.71200 4036 4586 1 chr5D.!!$R1 550
5 TraesCS1D01G218200 chr4D 385586549 385587094 545 True 787.00 787 92.71400 4041 4586 1 chr4D.!!$R1 545
6 TraesCS1D01G218200 chr4D 5724190 5724735 545 False 782.00 782 92.53200 4041 4586 1 chr4D.!!$F1 545
7 TraesCS1D01G218200 chr4D 468586106 468586662 556 True 767.00 767 91.60700 4032 4586 1 chr4D.!!$R2 554
8 TraesCS1D01G218200 chr7D 561873404 561873954 550 False 784.00 784 92.40500 4038 4586 1 chr7D.!!$F1 548
9 TraesCS1D01G218200 chr7D 410121786 410122333 547 True 773.00 773 92.18200 4042 4588 1 chr7D.!!$R1 546
10 TraesCS1D01G218200 chr6D 17972248 17972796 548 False 784.00 784 92.53200 4041 4586 1 chr6D.!!$F1 545
11 TraesCS1D01G218200 chrUn 320692162 320692716 554 False 767.00 767 91.71200 4036 4586 1 chrUn.!!$F1 550
12 TraesCS1D01G218200 chr6B 128034991 128035685 694 True 496.00 496 80.11300 1734 2421 1 chr6B.!!$R1 687
13 TraesCS1D01G218200 chr6B 128052735 128053428 693 True 490.00 490 79.97200 1734 2421 1 chr6B.!!$R2 687
14 TraesCS1D01G218200 chr6B 128062008 128076343 14335 True 485.00 496 79.83620 1734 2421 5 chr6B.!!$R3 687

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
922 944 0.318441 TCTGAGTTGGTGCTTCTCCG 59.682 55.000 0.00 0.0 0.00 4.63 F
2397 16079 0.033920 CTCCAGCATACATAGCGCCA 59.966 55.000 2.29 0.0 37.01 5.69 F
2879 16755 1.141665 CGTGATGCTCATCGGGTCA 59.858 57.895 5.51 0.0 40.63 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2823 16699 0.527565 GACCAAACGTCCGCTACCTA 59.472 55.000 0.0 0.0 35.23 3.08 R
3249 17170 0.733150 GGTTAGGCACGATTGAAGGC 59.267 55.000 0.0 0.0 0.00 4.35 R
3809 18154 1.135972 CCACTGCAAAATCGTTCCTCG 60.136 52.381 0.0 0.0 41.41 4.63 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
20 21 3.889196 TGCAGTACATGAAACGTTTCC 57.111 42.857 32.14 19.18 36.36 3.13
21 22 3.472652 TGCAGTACATGAAACGTTTCCT 58.527 40.909 32.14 22.85 36.36 3.36
22 23 4.633175 TGCAGTACATGAAACGTTTCCTA 58.367 39.130 32.14 18.86 36.36 2.94
23 24 5.057819 TGCAGTACATGAAACGTTTCCTAA 58.942 37.500 32.14 18.19 36.36 2.69
24 25 5.527951 TGCAGTACATGAAACGTTTCCTAAA 59.472 36.000 32.14 17.86 36.36 1.85
25 26 5.849604 GCAGTACATGAAACGTTTCCTAAAC 59.150 40.000 32.14 24.40 36.36 2.01
26 27 6.293244 GCAGTACATGAAACGTTTCCTAAACT 60.293 38.462 32.14 25.81 39.23 2.66
27 28 7.636326 CAGTACATGAAACGTTTCCTAAACTT 58.364 34.615 32.14 15.15 39.23 2.66
28 29 8.126700 CAGTACATGAAACGTTTCCTAAACTTT 58.873 33.333 32.14 13.85 39.23 2.66
29 30 8.126700 AGTACATGAAACGTTTCCTAAACTTTG 58.873 33.333 32.14 19.38 39.23 2.77
30 31 6.270064 ACATGAAACGTTTCCTAAACTTTGG 58.730 36.000 32.14 14.18 39.23 3.28
31 32 5.900865 TGAAACGTTTCCTAAACTTTGGT 57.099 34.783 32.14 0.00 39.23 3.67
32 33 5.642686 TGAAACGTTTCCTAAACTTTGGTG 58.357 37.500 32.14 0.00 39.23 4.17
33 34 3.703286 ACGTTTCCTAAACTTTGGTGC 57.297 42.857 1.49 0.00 39.23 5.01
39 40 6.539324 GTTTCCTAAACTTTGGTGCAAAAAC 58.461 36.000 0.00 0.00 38.35 2.43
107 109 3.181435 CCACCCCACCCAAAATTGAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
110 112 4.166919 ACCCCACCCAAAATTGAAAATGAA 59.833 37.500 0.00 0.00 0.00 2.57
113 115 6.238981 CCCCACCCAAAATTGAAAATGAAAAG 60.239 38.462 0.00 0.00 0.00 2.27
114 116 6.545298 CCCACCCAAAATTGAAAATGAAAAGA 59.455 34.615 0.00 0.00 0.00 2.52
115 117 7.067981 CCCACCCAAAATTGAAAATGAAAAGAA 59.932 33.333 0.00 0.00 0.00 2.52
116 118 8.631797 CCACCCAAAATTGAAAATGAAAAGAAT 58.368 29.630 0.00 0.00 0.00 2.40
230 232 3.726291 AAAAATGGTTGTCCGGAAGTG 57.274 42.857 5.23 0.00 36.30 3.16
232 234 3.495434 AAATGGTTGTCCGGAAGTGTA 57.505 42.857 5.23 0.00 36.30 2.90
244 246 3.119602 CCGGAAGTGTAAGTCTCGAATCA 60.120 47.826 0.00 0.00 0.00 2.57
260 262 4.455190 TCGAATCAAACACATCATGCTTGA 59.545 37.500 4.57 4.57 45.19 3.02
270 272 7.458409 ACACATCATGCTTGAACTAATTTCT 57.542 32.000 6.36 0.00 34.96 2.52
281 283 7.518370 GCTTGAACTAATTTCTTCTCGTTCACA 60.518 37.037 0.00 0.00 40.00 3.58
282 284 7.780008 TGAACTAATTTCTTCTCGTTCACAA 57.220 32.000 0.00 0.00 36.72 3.33
283 285 7.851508 TGAACTAATTTCTTCTCGTTCACAAG 58.148 34.615 0.00 0.00 36.72 3.16
284 286 7.494625 TGAACTAATTTCTTCTCGTTCACAAGT 59.505 33.333 0.00 0.00 36.72 3.16
287 289 8.122952 ACTAATTTCTTCTCGTTCACAAGTTTG 58.877 33.333 0.00 0.00 0.00 2.93
288 290 6.677781 ATTTCTTCTCGTTCACAAGTTTGA 57.322 33.333 0.00 0.00 0.00 2.69
289 291 6.677781 TTTCTTCTCGTTCACAAGTTTGAT 57.322 33.333 0.00 0.00 0.00 2.57
290 292 5.657470 TCTTCTCGTTCACAAGTTTGATG 57.343 39.130 0.00 0.00 0.00 3.07
291 293 5.356426 TCTTCTCGTTCACAAGTTTGATGA 58.644 37.500 0.00 0.00 0.00 2.92
292 294 5.991606 TCTTCTCGTTCACAAGTTTGATGAT 59.008 36.000 0.00 0.00 0.00 2.45
293 295 6.483307 TCTTCTCGTTCACAAGTTTGATGATT 59.517 34.615 0.00 0.00 0.00 2.57
294 296 6.618287 TCTCGTTCACAAGTTTGATGATTT 57.382 33.333 0.00 0.00 0.00 2.17
295 297 6.429624 TCTCGTTCACAAGTTTGATGATTTG 58.570 36.000 0.00 0.00 0.00 2.32
296 298 6.038161 TCTCGTTCACAAGTTTGATGATTTGT 59.962 34.615 0.00 0.00 34.31 2.83
297 299 7.225734 TCTCGTTCACAAGTTTGATGATTTGTA 59.774 33.333 0.00 0.00 32.86 2.41
298 300 7.351981 TCGTTCACAAGTTTGATGATTTGTAG 58.648 34.615 0.00 0.00 32.86 2.74
299 301 6.086765 CGTTCACAAGTTTGATGATTTGTAGC 59.913 38.462 0.00 0.00 32.86 3.58
300 302 6.631971 TCACAAGTTTGATGATTTGTAGCA 57.368 33.333 0.00 0.00 32.86 3.49
301 303 7.218228 TCACAAGTTTGATGATTTGTAGCAT 57.782 32.000 0.00 0.00 32.86 3.79
302 304 7.307694 TCACAAGTTTGATGATTTGTAGCATC 58.692 34.615 0.00 0.00 45.28 3.91
303 305 7.175467 TCACAAGTTTGATGATTTGTAGCATCT 59.825 33.333 0.00 0.00 45.28 2.90
304 306 7.811236 CACAAGTTTGATGATTTGTAGCATCTT 59.189 33.333 0.00 0.00 45.28 2.40
305 307 8.025445 ACAAGTTTGATGATTTGTAGCATCTTC 58.975 33.333 0.00 0.00 45.28 2.87
306 308 7.934855 AGTTTGATGATTTGTAGCATCTTCT 57.065 32.000 0.00 0.00 45.28 2.85
307 309 8.345724 AGTTTGATGATTTGTAGCATCTTCTT 57.654 30.769 0.00 0.00 45.28 2.52
308 310 8.800332 AGTTTGATGATTTGTAGCATCTTCTTT 58.200 29.630 0.00 0.00 45.28 2.52
309 311 9.415544 GTTTGATGATTTGTAGCATCTTCTTTT 57.584 29.630 0.00 0.00 45.28 2.27
310 312 9.985730 TTTGATGATTTGTAGCATCTTCTTTTT 57.014 25.926 0.00 0.00 45.28 1.94
339 341 7.482169 AGGTGATTTGTAACATCTAGTCTGA 57.518 36.000 2.71 0.00 0.00 3.27
340 342 8.083828 AGGTGATTTGTAACATCTAGTCTGAT 57.916 34.615 2.71 0.00 0.00 2.90
342 344 9.167311 GGTGATTTGTAACATCTAGTCTGATTT 57.833 33.333 2.71 0.00 0.00 2.17
364 366 2.414250 AAAAAGGAAAGGATGGGCCA 57.586 45.000 9.61 9.61 40.02 5.36
365 367 2.414250 AAAAGGAAAGGATGGGCCAA 57.586 45.000 11.89 0.00 40.02 4.52
366 368 2.647846 AAAGGAAAGGATGGGCCAAT 57.352 45.000 11.89 0.00 40.02 3.16
367 369 3.774842 AAAGGAAAGGATGGGCCAATA 57.225 42.857 11.89 0.00 40.02 1.90
368 370 3.999764 AAGGAAAGGATGGGCCAATAT 57.000 42.857 11.89 0.00 40.02 1.28
369 371 3.532641 AGGAAAGGATGGGCCAATATC 57.467 47.619 11.89 3.07 40.02 1.63
370 372 2.162681 GGAAAGGATGGGCCAATATCG 58.837 52.381 11.89 0.00 40.02 2.92
371 373 2.489073 GGAAAGGATGGGCCAATATCGT 60.489 50.000 11.89 1.99 40.02 3.73
372 374 3.222603 GAAAGGATGGGCCAATATCGTT 58.777 45.455 11.89 9.14 40.02 3.85
373 375 3.312736 AAGGATGGGCCAATATCGTTT 57.687 42.857 11.89 0.00 40.02 3.60
374 376 2.863809 AGGATGGGCCAATATCGTTTC 58.136 47.619 11.89 0.00 40.02 2.78
375 377 1.886542 GGATGGGCCAATATCGTTTCC 59.113 52.381 11.89 6.54 36.34 3.13
376 378 1.535462 GATGGGCCAATATCGTTTCCG 59.465 52.381 11.89 0.00 0.00 4.30
377 379 1.098712 TGGGCCAATATCGTTTCCGC 61.099 55.000 2.13 0.00 0.00 5.54
378 380 1.652563 GGCCAATATCGTTTCCGCC 59.347 57.895 0.00 0.00 0.00 6.13
379 381 1.098712 GGCCAATATCGTTTCCGCCA 61.099 55.000 0.00 0.00 34.98 5.69
380 382 0.736053 GCCAATATCGTTTCCGCCAA 59.264 50.000 0.00 0.00 0.00 4.52
381 383 1.133407 GCCAATATCGTTTCCGCCAAA 59.867 47.619 0.00 0.00 0.00 3.28
382 384 2.416162 GCCAATATCGTTTCCGCCAAAA 60.416 45.455 0.00 0.00 0.00 2.44
383 385 3.839293 CCAATATCGTTTCCGCCAAAAA 58.161 40.909 0.00 0.00 0.00 1.94
408 410 7.630242 AAAAGATGAGCCAAGATCGAATTAA 57.370 32.000 0.00 0.00 0.00 1.40
415 417 6.206634 TGAGCCAAGATCGAATTAAAAACTGT 59.793 34.615 0.00 0.00 0.00 3.55
417 419 7.084486 AGCCAAGATCGAATTAAAAACTGTTC 58.916 34.615 0.00 0.00 0.00 3.18
434 440 5.846203 ACTGTTCTTCCATTGACAAAATGG 58.154 37.500 10.27 10.27 46.59 3.16
456 462 7.843490 TGGGATTATAAAGCGATAATACAGC 57.157 36.000 11.22 0.00 35.19 4.40
458 464 6.018994 GGGATTATAAAGCGATAATACAGCGG 60.019 42.308 11.22 0.00 35.19 5.52
462 468 1.714794 AGCGATAATACAGCGGATGC 58.285 50.000 0.00 0.00 43.24 3.91
464 470 1.126846 GCGATAATACAGCGGATGCAC 59.873 52.381 0.00 0.00 46.23 4.57
476 482 1.662629 CGGATGCACTGTCAGAACATC 59.337 52.381 21.57 21.57 37.09 3.06
477 483 1.662629 GGATGCACTGTCAGAACATCG 59.337 52.381 22.23 3.28 38.38 3.84
479 485 3.511699 GATGCACTGTCAGAACATCGTA 58.488 45.455 17.84 0.00 34.13 3.43
480 486 3.592898 TGCACTGTCAGAACATCGTAT 57.407 42.857 6.91 0.00 34.13 3.06
481 487 4.712122 TGCACTGTCAGAACATCGTATA 57.288 40.909 6.91 0.00 34.13 1.47
483 489 4.157840 TGCACTGTCAGAACATCGTATAGT 59.842 41.667 6.91 0.00 34.13 2.12
484 490 4.500837 GCACTGTCAGAACATCGTATAGTG 59.499 45.833 6.91 0.00 34.13 2.74
609 617 1.600107 GGACGTGCCATCTAACCCA 59.400 57.895 0.00 0.00 36.34 4.51
610 618 0.462047 GGACGTGCCATCTAACCCAG 60.462 60.000 0.00 0.00 36.34 4.45
611 619 0.462047 GACGTGCCATCTAACCCAGG 60.462 60.000 0.00 0.00 0.00 4.45
612 620 1.153168 CGTGCCATCTAACCCAGGG 60.153 63.158 2.85 2.85 0.00 4.45
613 621 1.227383 GTGCCATCTAACCCAGGGG 59.773 63.158 11.37 6.87 42.03 4.79
614 622 2.195956 GCCATCTAACCCAGGGGC 59.804 66.667 11.37 0.00 37.76 5.80
699 708 3.281975 TATCACCTGGCCCACCCCT 62.282 63.158 0.00 0.00 33.59 4.79
922 944 0.318441 TCTGAGTTGGTGCTTCTCCG 59.682 55.000 0.00 0.00 0.00 4.63
972 994 1.478631 CCCTTGAAATTCAGGGAGGC 58.521 55.000 23.50 0.00 45.53 4.70
1181 1211 1.228124 CTGGGGTTTGGTCGCTGAA 60.228 57.895 0.00 0.00 0.00 3.02
1190 1220 1.112916 TGGTCGCTGAAGACTGGTGA 61.113 55.000 4.25 0.00 40.76 4.02
1201 1231 1.203050 AGACTGGTGAATTTGGGGGTG 60.203 52.381 0.00 0.00 0.00 4.61
1207 1237 1.273327 GTGAATTTGGGGGTGCTTCTG 59.727 52.381 0.00 0.00 0.00 3.02
1211 1241 1.650242 TTTGGGGGTGCTTCTGGACA 61.650 55.000 0.00 0.00 36.16 4.02
1215 1245 1.632589 GGGGTGCTTCTGGACAAATT 58.367 50.000 0.00 0.00 36.16 1.82
1242 1272 3.751518 TCGATAGATGGTAGCTGTAGCA 58.248 45.455 6.65 0.00 42.17 3.49
1243 1273 3.753797 TCGATAGATGGTAGCTGTAGCAG 59.246 47.826 6.65 0.00 42.17 4.24
1244 1274 3.119673 CGATAGATGGTAGCTGTAGCAGG 60.120 52.174 6.65 0.00 39.96 4.85
1245 1275 1.418334 AGATGGTAGCTGTAGCAGGG 58.582 55.000 6.65 0.00 45.16 4.45
1246 1276 0.394565 GATGGTAGCTGTAGCAGGGG 59.605 60.000 6.65 0.00 45.16 4.79
1257 1287 0.764369 TAGCAGGGGACTATGGCTGG 60.764 60.000 0.00 0.00 40.21 4.85
1428 1458 6.686130 ACTCGTTAGTCGTTTGATAAGTTG 57.314 37.500 0.00 0.00 40.80 3.16
1602 1634 6.099125 TGCTCTGCCAGTTATTAGTAATGGTA 59.901 38.462 5.61 0.00 33.42 3.25
1662 1694 1.916181 ACTGGACCCCTACATTTCAGG 59.084 52.381 0.00 0.00 0.00 3.86
1694 1726 6.303054 TGGTTGGTGATAATGAGTTCAGAAA 58.697 36.000 0.00 0.00 0.00 2.52
1698 1730 8.299570 GTTGGTGATAATGAGTTCAGAAACATT 58.700 33.333 16.19 16.19 37.88 2.71
1703 1735 8.239314 TGATAATGAGTTCAGAAACATTGAAGC 58.761 33.333 19.07 9.45 37.88 3.86
1713 1745 5.702670 CAGAAACATTGAAGCTTGTCCTAGA 59.297 40.000 2.10 0.00 0.00 2.43
1747 1779 9.844790 TGTCTTGATATTCAACTTAGCAAATTG 57.155 29.630 0.00 0.00 32.21 2.32
1795 6982 6.490040 TGCCTTTGCTATAATATGGTCTTTCC 59.510 38.462 0.00 0.00 38.71 3.13
1842 7029 3.499737 CCGACGCACCTTGCCATC 61.500 66.667 0.00 0.00 41.12 3.51
1939 7126 6.314152 GGTTGCTCTTGAACCTACTTATCTTC 59.686 42.308 0.00 0.00 39.94 2.87
1987 7174 6.653020 TCTGAACCATGTCTGCTAACAATAT 58.347 36.000 0.00 0.00 31.81 1.28
2031 7218 2.401583 ATGCGTGTCAATAGGCAAGA 57.598 45.000 0.00 0.00 43.59 3.02
2076 7265 0.543749 GGGTCAGCTACTGCCATTCT 59.456 55.000 9.29 0.00 40.80 2.40
2099 7288 4.888326 TGGTATGCTTTGCCTTTTGAAT 57.112 36.364 0.00 0.00 0.00 2.57
2100 7289 4.819769 TGGTATGCTTTGCCTTTTGAATC 58.180 39.130 0.00 0.00 0.00 2.52
2267 15945 4.575885 TCAAAGGTACTGATGGTTACTGC 58.424 43.478 0.00 0.00 40.86 4.40
2276 15954 5.804639 ACTGATGGTTACTGCTATGTTTCA 58.195 37.500 0.00 0.00 0.00 2.69
2280 15959 6.371548 TGATGGTTACTGCTATGTTTCAAGTC 59.628 38.462 0.00 0.00 0.00 3.01
2282 15961 6.999950 TGGTTACTGCTATGTTTCAAGTCTA 58.000 36.000 0.00 0.00 0.00 2.59
2303 15982 7.398904 AGTCTAGCTAGAATTGACCTTTCTCTT 59.601 37.037 24.85 0.00 35.19 2.85
2322 16001 9.490379 TTTCTCTTTCCTTACTGATCAAGTTAC 57.510 33.333 0.00 0.00 40.56 2.50
2330 16009 7.341256 TCCTTACTGATCAAGTTACCTATCGTT 59.659 37.037 0.00 0.00 40.56 3.85
2331 16010 7.648510 CCTTACTGATCAAGTTACCTATCGTTC 59.351 40.741 0.00 0.00 40.56 3.95
2352 16032 0.664761 TTCAGTCTGCTTTGCTGCAC 59.335 50.000 0.00 0.00 38.12 4.57
2397 16079 0.033920 CTCCAGCATACATAGCGCCA 59.966 55.000 2.29 0.00 37.01 5.69
2403 16085 2.628178 AGCATACATAGCGCCAGAAGTA 59.372 45.455 2.29 0.55 37.01 2.24
2421 16103 8.648968 CCAGAAGTACTTTCGAGAAAAGAATAC 58.351 37.037 10.02 0.00 46.18 1.89
2435 16117 3.814005 AGAATACGACGGCAAGGTAAT 57.186 42.857 0.00 0.00 0.00 1.89
2464 16146 8.669243 CCTCTTTTGACAGTCTATGGTTATTTC 58.331 37.037 1.31 0.00 0.00 2.17
2469 16151 9.436957 TTTGACAGTCTATGGTTATTTCTTCTC 57.563 33.333 1.31 0.00 0.00 2.87
2480 16162 7.322664 TGGTTATTTCTTCTCATTTTGCATCC 58.677 34.615 0.00 0.00 0.00 3.51
2565 16437 4.785511 AGTAACTACTCGTGTTGCATCT 57.214 40.909 0.00 0.00 33.52 2.90
2566 16438 5.892160 AGTAACTACTCGTGTTGCATCTA 57.108 39.130 0.00 0.00 33.52 1.98
2585 16457 9.646522 TGCATCTATAGCATTAGTATCAGGATA 57.353 33.333 0.00 0.00 37.02 2.59
2602 16475 5.489792 AGGATATGTTTCCTGCATCGTAT 57.510 39.130 0.00 0.00 44.63 3.06
2604 16477 7.187824 AGGATATGTTTCCTGCATCGTATAT 57.812 36.000 0.00 0.00 44.63 0.86
2610 16483 8.758633 ATGTTTCCTGCATCGTATATTAGTAC 57.241 34.615 0.00 0.00 0.00 2.73
2742 16618 8.151141 CATAGTGATGCTATCAAAGTTCATGT 57.849 34.615 0.00 0.00 41.69 3.21
2743 16619 9.264719 CATAGTGATGCTATCAAAGTTCATGTA 57.735 33.333 0.00 0.00 41.69 2.29
2745 16621 8.743085 AGTGATGCTATCAAAGTTCATGTATT 57.257 30.769 0.00 0.00 41.69 1.89
2804 16680 4.820716 GCTTCCAACTCTGCATCTTATGAT 59.179 41.667 0.00 0.00 0.00 2.45
2879 16755 1.141665 CGTGATGCTCATCGGGTCA 59.858 57.895 5.51 0.00 40.63 4.02
2959 16835 2.877866 TCGATCCCTCCTCCTTATCAC 58.122 52.381 0.00 0.00 0.00 3.06
2996 16880 1.269936 ACCTTGCTTGAATGCTTGTGC 60.270 47.619 0.00 0.00 40.20 4.57
3015 16935 1.403323 GCTAAGCATGCCTGAAACTCC 59.597 52.381 15.66 0.00 0.00 3.85
3174 17094 2.998316 ACTTCTGCTGCTTATCCTCC 57.002 50.000 0.00 0.00 0.00 4.30
3179 17100 3.878778 TCTGCTGCTTATCCTCCTTTTC 58.121 45.455 0.00 0.00 0.00 2.29
3183 17104 5.079643 TGCTGCTTATCCTCCTTTTCTTTT 58.920 37.500 0.00 0.00 0.00 2.27
3184 17105 5.183904 TGCTGCTTATCCTCCTTTTCTTTTC 59.816 40.000 0.00 0.00 0.00 2.29
3249 17170 7.349711 CAAAAGGCAGAAAACTTTGAATCATG 58.650 34.615 0.00 0.00 37.04 3.07
3254 17175 5.119743 GCAGAAAACTTTGAATCATGCCTTC 59.880 40.000 0.00 0.00 0.00 3.46
3542 17467 4.079850 CTGGCCGAGCTGCAGAGT 62.080 66.667 20.43 2.61 0.00 3.24
3559 17484 2.045242 TGACGACGAGGAGGAGGG 60.045 66.667 0.00 0.00 0.00 4.30
3615 17541 0.108377 TGCATCGCAGTTCATACGGT 60.108 50.000 0.00 0.00 33.32 4.83
3616 17542 0.577269 GCATCGCAGTTCATACGGTC 59.423 55.000 0.00 0.00 0.00 4.79
3617 17543 1.802880 GCATCGCAGTTCATACGGTCT 60.803 52.381 0.00 0.00 0.00 3.85
3644 17597 3.252458 GGAGTACGGTTTGCTGAAACAAT 59.748 43.478 2.50 0.00 42.95 2.71
3687 17647 9.197694 GTATGATACAGATTATGACACCTGTTC 57.802 37.037 0.00 0.00 40.07 3.18
3719 17679 6.953743 CGCTGTGTACATTATTACTGAACAAC 59.046 38.462 0.00 0.00 0.00 3.32
3720 17680 7.359681 CGCTGTGTACATTATTACTGAACAACA 60.360 37.037 0.00 0.00 0.00 3.33
3721 17681 8.450964 GCTGTGTACATTATTACTGAACAACAT 58.549 33.333 0.00 0.00 0.00 2.71
3725 17685 8.787852 TGTACATTATTACTGAACAACATTGCA 58.212 29.630 0.00 0.00 0.00 4.08
3726 17686 9.061610 GTACATTATTACTGAACAACATTGCAC 57.938 33.333 0.00 0.00 0.00 4.57
3729 17689 1.674359 ACTGAACAACATTGCACCGA 58.326 45.000 0.00 0.00 0.00 4.69
3730 17690 2.229792 ACTGAACAACATTGCACCGAT 58.770 42.857 0.00 0.00 0.00 4.18
3732 17692 3.068024 ACTGAACAACATTGCACCGATTT 59.932 39.130 0.00 0.00 0.00 2.17
3733 17693 4.050553 CTGAACAACATTGCACCGATTTT 58.949 39.130 0.00 0.00 0.00 1.82
3734 17694 4.437239 TGAACAACATTGCACCGATTTTT 58.563 34.783 0.00 0.00 0.00 1.94
3764 17752 5.043432 TCCAAGAATAAAAGATGGTGGGGAT 60.043 40.000 0.00 0.00 32.90 3.85
3781 17769 4.654262 TGGGGATATACAGTTCTTCCAGTC 59.346 45.833 0.00 0.00 0.00 3.51
3784 17772 6.284459 GGGATATACAGTTCTTCCAGTCTTG 58.716 44.000 0.00 0.00 0.00 3.02
3785 17773 6.127026 GGGATATACAGTTCTTCCAGTCTTGT 60.127 42.308 0.00 0.00 0.00 3.16
3788 17776 6.867662 ATACAGTTCTTCCAGTCTTGTTTG 57.132 37.500 0.00 0.00 0.00 2.93
3789 17777 4.843728 ACAGTTCTTCCAGTCTTGTTTGA 58.156 39.130 0.00 0.00 0.00 2.69
3791 17779 5.888161 ACAGTTCTTCCAGTCTTGTTTGAAT 59.112 36.000 0.00 0.00 0.00 2.57
3792 17780 6.378280 ACAGTTCTTCCAGTCTTGTTTGAATT 59.622 34.615 0.00 0.00 0.00 2.17
3800 17788 8.402798 TCCAGTCTTGTTTGAATTATTAAGCA 57.597 30.769 0.00 0.00 0.00 3.91
3863 18208 0.322008 CACTCTTGACTCTTGGGGGC 60.322 60.000 0.00 0.00 0.00 5.80
3897 18242 8.041829 TCGAAATTTGGAAAACCGTATGAATA 57.958 30.769 0.00 0.00 0.00 1.75
3931 18292 3.046390 GTGGCGAATCTAGAATCTCACG 58.954 50.000 6.26 3.48 0.00 4.35
3937 18298 5.116377 GCGAATCTAGAATCTCACGATGAAC 59.884 44.000 6.26 0.00 0.00 3.18
3955 18316 9.095065 ACGATGAACAGTATAATTTGGTCTAAC 57.905 33.333 0.00 0.00 32.27 2.34
3972 18333 8.927675 TGGTCTAACCATTGTTATAAGTGTTT 57.072 30.769 0.00 0.00 44.79 2.83
3973 18334 9.005777 TGGTCTAACCATTGTTATAAGTGTTTC 57.994 33.333 0.00 0.00 44.79 2.78
3974 18335 8.456471 GGTCTAACCATTGTTATAAGTGTTTCC 58.544 37.037 0.00 0.00 38.42 3.13
3975 18336 8.456471 GTCTAACCATTGTTATAAGTGTTTCCC 58.544 37.037 0.00 0.00 36.40 3.97
3976 18337 8.387813 TCTAACCATTGTTATAAGTGTTTCCCT 58.612 33.333 0.00 0.00 36.40 4.20
3977 18338 7.849322 AACCATTGTTATAAGTGTTTCCCTT 57.151 32.000 0.00 0.00 31.36 3.95
3978 18339 7.227049 ACCATTGTTATAAGTGTTTCCCTTG 57.773 36.000 0.00 0.00 0.00 3.61
3979 18340 6.780522 ACCATTGTTATAAGTGTTTCCCTTGT 59.219 34.615 0.00 0.00 0.00 3.16
3980 18341 7.289084 ACCATTGTTATAAGTGTTTCCCTTGTT 59.711 33.333 0.00 0.00 0.00 2.83
3981 18342 7.812669 CCATTGTTATAAGTGTTTCCCTTGTTC 59.187 37.037 0.00 0.00 0.00 3.18
3982 18343 8.576442 CATTGTTATAAGTGTTTCCCTTGTTCT 58.424 33.333 0.00 0.00 0.00 3.01
3983 18344 8.528044 TTGTTATAAGTGTTTCCCTTGTTCTT 57.472 30.769 0.00 0.00 0.00 2.52
3984 18345 9.629878 TTGTTATAAGTGTTTCCCTTGTTCTTA 57.370 29.630 0.00 0.00 0.00 2.10
3985 18346 9.059260 TGTTATAAGTGTTTCCCTTGTTCTTAC 57.941 33.333 0.00 0.00 0.00 2.34
3986 18347 6.796705 ATAAGTGTTTCCCTTGTTCTTACG 57.203 37.500 0.00 0.00 0.00 3.18
3987 18348 3.473625 AGTGTTTCCCTTGTTCTTACGG 58.526 45.455 0.00 0.00 0.00 4.02
3988 18349 3.135167 AGTGTTTCCCTTGTTCTTACGGA 59.865 43.478 0.00 0.00 0.00 4.69
3989 18350 4.070009 GTGTTTCCCTTGTTCTTACGGAT 58.930 43.478 0.00 0.00 0.00 4.18
3990 18351 4.153655 GTGTTTCCCTTGTTCTTACGGATC 59.846 45.833 0.00 0.00 0.00 3.36
3991 18352 4.041198 TGTTTCCCTTGTTCTTACGGATCT 59.959 41.667 0.00 0.00 0.00 2.75
3992 18353 4.467198 TTCCCTTGTTCTTACGGATCTC 57.533 45.455 0.00 0.00 0.00 2.75
3993 18354 3.709587 TCCCTTGTTCTTACGGATCTCT 58.290 45.455 0.00 0.00 0.00 3.10
3994 18355 4.863548 TCCCTTGTTCTTACGGATCTCTA 58.136 43.478 0.00 0.00 0.00 2.43
3995 18356 5.266788 TCCCTTGTTCTTACGGATCTCTAA 58.733 41.667 0.00 0.00 0.00 2.10
3996 18357 5.897824 TCCCTTGTTCTTACGGATCTCTAAT 59.102 40.000 0.00 0.00 0.00 1.73
3997 18358 6.040616 TCCCTTGTTCTTACGGATCTCTAATC 59.959 42.308 0.00 0.00 0.00 1.75
3998 18359 5.915758 CCTTGTTCTTACGGATCTCTAATCG 59.084 44.000 0.00 0.00 0.00 3.34
3999 18360 6.238676 CCTTGTTCTTACGGATCTCTAATCGA 60.239 42.308 0.00 0.00 0.00 3.59
4000 18361 6.879276 TGTTCTTACGGATCTCTAATCGAT 57.121 37.500 0.00 0.00 0.00 3.59
4001 18362 6.900189 TGTTCTTACGGATCTCTAATCGATC 58.100 40.000 0.00 0.00 37.21 3.69
4020 18381 9.681062 AATCGATCCTCTAAAATTTTAAGTGGA 57.319 29.630 20.76 20.76 0.00 4.02
4021 18382 8.718102 TCGATCCTCTAAAATTTTAAGTGGAG 57.282 34.615 21.81 18.38 0.00 3.86
4022 18383 8.319146 TCGATCCTCTAAAATTTTAAGTGGAGT 58.681 33.333 21.81 15.55 0.00 3.85
4023 18384 9.595823 CGATCCTCTAAAATTTTAAGTGGAGTA 57.404 33.333 21.81 11.61 0.00 2.59
4034 18395 7.754851 TTTTAAGTGGAGTAAAAGGCTTAGG 57.245 36.000 0.00 0.00 0.00 2.69
4089 18454 2.032528 CACATCACCCACACGCCT 59.967 61.111 0.00 0.00 0.00 5.52
4110 18475 1.199789 TCATCACTCATTTTGCCACGC 59.800 47.619 0.00 0.00 0.00 5.34
4123 18488 2.363683 TGCCACGCATGAACATATGAA 58.636 42.857 10.38 0.00 31.71 2.57
4150 18515 5.748152 CAGCAGAAATCTTTTTGGTTTTCGA 59.252 36.000 0.00 0.00 31.72 3.71
4244 18609 4.773149 ACGAGATCTTCAAAACTAGACCCT 59.227 41.667 0.00 0.00 0.00 4.34
4267 18633 8.620416 CCCTATGTTGATATGTTTCGATGAAAA 58.380 33.333 0.00 0.00 33.14 2.29
4284 18650 7.066284 TCGATGAAAAATTCTTTTGCCCAAAAA 59.934 29.630 7.50 0.00 39.49 1.94
4334 18700 8.896320 TGTCATAGTGCTTAAACTAAAGTTGA 57.104 30.769 0.00 0.00 38.44 3.18
4359 18725 7.145323 ACATGTGGCAATTTTAGTTTGTAGAC 58.855 34.615 0.00 0.00 0.00 2.59
4385 18751 7.411804 CCATGGCAATTTTAGTTTTTCGATGAC 60.412 37.037 0.00 0.00 0.00 3.06
4456 18822 9.248291 CCATAACAATTTTAAGTGCATGTATCC 57.752 33.333 0.00 0.00 0.00 2.59
4475 18841 8.076910 TGTATCCTGGCAATTTTGATTTATGT 57.923 30.769 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.472652 AGGAAACGTTTCATGTACTGCA 58.527 40.909 34.79 0.00 38.92 4.41
1 2 5.600908 TTAGGAAACGTTTCATGTACTGC 57.399 39.130 34.79 18.93 38.92 4.40
2 3 7.186021 AGTTTAGGAAACGTTTCATGTACTG 57.814 36.000 34.79 0.00 45.88 2.74
3 4 7.797038 AAGTTTAGGAAACGTTTCATGTACT 57.203 32.000 34.79 29.48 45.88 2.73
4 5 7.377662 CCAAAGTTTAGGAAACGTTTCATGTAC 59.622 37.037 34.79 28.18 45.88 2.90
5 6 7.067251 ACCAAAGTTTAGGAAACGTTTCATGTA 59.933 33.333 34.79 22.41 45.88 2.29
6 7 6.127563 ACCAAAGTTTAGGAAACGTTTCATGT 60.128 34.615 34.79 23.29 45.88 3.21
7 8 6.198216 CACCAAAGTTTAGGAAACGTTTCATG 59.802 38.462 34.79 19.58 45.88 3.07
8 9 6.270064 CACCAAAGTTTAGGAAACGTTTCAT 58.730 36.000 34.79 31.72 45.88 2.57
9 10 5.642686 CACCAAAGTTTAGGAAACGTTTCA 58.357 37.500 34.79 18.17 45.88 2.69
10 11 4.501559 GCACCAAAGTTTAGGAAACGTTTC 59.498 41.667 28.83 28.83 45.88 2.78
11 12 4.082136 TGCACCAAAGTTTAGGAAACGTTT 60.082 37.500 14.57 14.57 45.88 3.60
12 13 3.444388 TGCACCAAAGTTTAGGAAACGTT 59.556 39.130 0.00 0.00 45.88 3.99
13 14 3.018149 TGCACCAAAGTTTAGGAAACGT 58.982 40.909 10.03 0.00 45.88 3.99
14 15 3.701532 TGCACCAAAGTTTAGGAAACG 57.298 42.857 10.03 0.00 45.88 3.60
15 16 6.370442 AGTTTTTGCACCAAAGTTTAGGAAAC 59.630 34.615 10.03 9.19 41.69 2.78
16 17 6.370166 CAGTTTTTGCACCAAAGTTTAGGAAA 59.630 34.615 10.03 4.85 34.72 3.13
17 18 5.872070 CAGTTTTTGCACCAAAGTTTAGGAA 59.128 36.000 10.03 0.00 34.72 3.36
18 19 5.186021 TCAGTTTTTGCACCAAAGTTTAGGA 59.814 36.000 10.03 0.00 34.72 2.94
19 20 5.415221 TCAGTTTTTGCACCAAAGTTTAGG 58.585 37.500 0.00 0.00 34.72 2.69
20 21 6.959671 TTCAGTTTTTGCACCAAAGTTTAG 57.040 33.333 0.00 0.00 34.72 1.85
21 22 7.730364 TTTTCAGTTTTTGCACCAAAGTTTA 57.270 28.000 0.00 0.00 34.72 2.01
22 23 6.625873 TTTTCAGTTTTTGCACCAAAGTTT 57.374 29.167 0.00 0.00 34.72 2.66
23 24 6.625873 TTTTTCAGTTTTTGCACCAAAGTT 57.374 29.167 0.00 0.00 34.72 2.66
82 84 1.979389 AATTTTGGGTGGGGTGGGGT 61.979 55.000 0.00 0.00 0.00 4.95
86 88 3.567478 TTTTCAATTTTGGGTGGGGTG 57.433 42.857 0.00 0.00 0.00 4.61
87 89 3.718956 TCATTTTCAATTTTGGGTGGGGT 59.281 39.130 0.00 0.00 0.00 4.95
88 90 4.363991 TCATTTTCAATTTTGGGTGGGG 57.636 40.909 0.00 0.00 0.00 4.96
107 109 9.778741 AGTACATCACTTCTTGTATTCTTTTCA 57.221 29.630 0.00 0.00 31.59 2.69
110 112 8.375506 TGGAGTACATCACTTCTTGTATTCTTT 58.624 33.333 0.00 0.00 37.72 2.52
113 115 9.250624 GTATGGAGTACATCACTTCTTGTATTC 57.749 37.037 0.00 0.00 41.03 1.75
114 116 8.758829 TGTATGGAGTACATCACTTCTTGTATT 58.241 33.333 0.00 0.00 41.03 1.89
115 117 8.306313 TGTATGGAGTACATCACTTCTTGTAT 57.694 34.615 0.00 0.00 41.03 2.29
116 118 7.712204 TGTATGGAGTACATCACTTCTTGTA 57.288 36.000 0.00 0.00 41.03 2.41
117 119 6.605471 TGTATGGAGTACATCACTTCTTGT 57.395 37.500 0.00 0.00 41.03 3.16
187 189 2.315925 TCAAGATCGATCAAGTGGGC 57.684 50.000 26.47 0.00 0.00 5.36
227 229 5.597806 TGTGTTTGATTCGAGACTTACACT 58.402 37.500 17.25 0.00 36.51 3.55
228 230 5.900339 TGTGTTTGATTCGAGACTTACAC 57.100 39.130 12.43 12.43 36.19 2.90
230 232 6.706055 TGATGTGTTTGATTCGAGACTTAC 57.294 37.500 0.00 0.00 0.00 2.34
232 234 5.391310 GCATGATGTGTTTGATTCGAGACTT 60.391 40.000 0.00 0.00 0.00 3.01
244 246 8.362639 AGAAATTAGTTCAAGCATGATGTGTTT 58.637 29.630 0.00 0.00 38.86 2.83
260 262 7.787725 ACTTGTGAACGAGAAGAAATTAGTT 57.212 32.000 4.67 0.00 0.00 2.24
270 272 6.618287 AATCATCAAACTTGTGAACGAGAA 57.382 33.333 4.67 0.00 0.00 2.87
281 283 8.345724 AGAAGATGCTACAAATCATCAAACTT 57.654 30.769 5.22 0.00 41.02 2.66
282 284 7.934855 AGAAGATGCTACAAATCATCAAACT 57.065 32.000 5.22 0.00 41.02 2.66
283 285 8.976986 AAAGAAGATGCTACAAATCATCAAAC 57.023 30.769 5.22 0.00 41.02 2.93
284 286 9.985730 AAAAAGAAGATGCTACAAATCATCAAA 57.014 25.926 5.22 0.00 41.02 2.69
310 312 9.431887 GACTAGATGTTACAAATCACCTTGTAA 57.568 33.333 0.00 5.12 45.19 2.41
311 313 8.812972 AGACTAGATGTTACAAATCACCTTGTA 58.187 33.333 0.00 0.00 40.08 2.41
312 314 7.604164 CAGACTAGATGTTACAAATCACCTTGT 59.396 37.037 0.00 0.00 42.20 3.16
313 315 7.819415 TCAGACTAGATGTTACAAATCACCTTG 59.181 37.037 0.00 0.00 0.00 3.61
314 316 7.907389 TCAGACTAGATGTTACAAATCACCTT 58.093 34.615 0.00 0.00 0.00 3.50
315 317 7.482169 TCAGACTAGATGTTACAAATCACCT 57.518 36.000 0.00 0.00 0.00 4.00
316 318 8.723942 AATCAGACTAGATGTTACAAATCACC 57.276 34.615 0.00 0.00 0.00 4.02
350 352 2.162681 CGATATTGGCCCATCCTTTCC 58.837 52.381 0.00 0.00 35.26 3.13
352 354 3.312736 AACGATATTGGCCCATCCTTT 57.687 42.857 0.00 0.00 35.26 3.11
353 355 3.222603 GAAACGATATTGGCCCATCCTT 58.777 45.455 0.00 0.00 35.26 3.36
354 356 2.489073 GGAAACGATATTGGCCCATCCT 60.489 50.000 0.00 0.00 35.26 3.24
355 357 1.886542 GGAAACGATATTGGCCCATCC 59.113 52.381 0.00 0.00 0.00 3.51
383 385 6.521151 AATTCGATCTTGGCTCATCTTTTT 57.479 33.333 0.00 0.00 0.00 1.94
387 389 7.337942 AGTTTTTAATTCGATCTTGGCTCATCT 59.662 33.333 0.00 0.00 0.00 2.90
408 410 8.200364 CATTTTGTCAATGGAAGAACAGTTTT 57.800 30.769 0.00 0.00 0.00 2.43
434 440 6.755141 TCCGCTGTATTATCGCTTTATAATCC 59.245 38.462 0.00 0.00 34.60 3.01
444 450 1.126846 GTGCATCCGCTGTATTATCGC 59.873 52.381 0.00 0.00 39.64 4.58
456 462 1.662629 GATGTTCTGACAGTGCATCCG 59.337 52.381 20.82 0.00 39.58 4.18
458 464 2.341257 ACGATGTTCTGACAGTGCATC 58.659 47.619 21.20 21.20 39.58 3.91
462 468 5.037385 CCACTATACGATGTTCTGACAGTG 58.963 45.833 1.59 0.00 39.58 3.66
464 470 4.338400 TCCCACTATACGATGTTCTGACAG 59.662 45.833 0.00 0.00 39.58 3.51
829 839 5.836358 AGAGGCGGAGAAAAATATAGAGAGT 59.164 40.000 0.00 0.00 0.00 3.24
1181 1211 1.158007 ACCCCCAAATTCACCAGTCT 58.842 50.000 0.00 0.00 0.00 3.24
1190 1220 0.486879 TCCAGAAGCACCCCCAAATT 59.513 50.000 0.00 0.00 0.00 1.82
1201 1231 4.876107 TCGAGGATTAATTTGTCCAGAAGC 59.124 41.667 10.39 0.00 36.96 3.86
1207 1237 7.162082 ACCATCTATCGAGGATTAATTTGTCC 58.838 38.462 0.00 1.56 34.64 4.02
1211 1241 8.037758 CAGCTACCATCTATCGAGGATTAATTT 58.962 37.037 0.00 0.00 0.00 1.82
1215 1245 5.571285 ACAGCTACCATCTATCGAGGATTA 58.429 41.667 0.00 0.00 0.00 1.75
1241 1271 1.414061 CCTCCAGCCATAGTCCCCTG 61.414 65.000 0.00 0.00 0.00 4.45
1242 1272 1.074167 CCTCCAGCCATAGTCCCCT 60.074 63.158 0.00 0.00 0.00 4.79
1243 1273 0.988678 AACCTCCAGCCATAGTCCCC 60.989 60.000 0.00 0.00 0.00 4.81
1244 1274 0.919710 AAACCTCCAGCCATAGTCCC 59.080 55.000 0.00 0.00 0.00 4.46
1245 1275 1.282157 ACAAACCTCCAGCCATAGTCC 59.718 52.381 0.00 0.00 0.00 3.85
1246 1276 2.290323 ACACAAACCTCCAGCCATAGTC 60.290 50.000 0.00 0.00 0.00 2.59
1257 1287 1.956477 ACATCCAGCAACACAAACCTC 59.044 47.619 0.00 0.00 0.00 3.85
1363 1393 5.745227 ACCTCCTTGAATCGTATGATGTTT 58.255 37.500 0.00 0.00 34.24 2.83
1428 1458 8.723942 ACCAATCTAATGTAACTGAGAATCAC 57.276 34.615 0.00 0.00 42.56 3.06
1662 1694 5.680619 TCATTATCACCAACCATAGTCACC 58.319 41.667 0.00 0.00 0.00 4.02
1665 1697 7.047891 TGAACTCATTATCACCAACCATAGTC 58.952 38.462 0.00 0.00 0.00 2.59
1694 1726 5.564550 ACATTCTAGGACAAGCTTCAATGT 58.435 37.500 0.00 0.00 0.00 2.71
1698 1730 4.774726 AGAGACATTCTAGGACAAGCTTCA 59.225 41.667 0.00 0.00 33.23 3.02
1703 1735 5.913137 AGACAGAGACATTCTAGGACAAG 57.087 43.478 0.00 0.00 33.83 3.16
1747 1779 9.508567 GGCAGTTCAATTTTATCTAAAGATGAC 57.491 33.333 2.66 0.00 36.05 3.06
1769 1801 7.308830 GGAAAGACCATATTATAGCAAAGGCAG 60.309 40.741 0.00 0.00 39.75 4.85
1795 6982 3.438297 AACCTGTCCTCGATTGATACG 57.562 47.619 0.00 0.00 0.00 3.06
1842 7029 1.534163 CCAGCAGCATATTCCATGACG 59.466 52.381 0.00 0.00 0.00 4.35
1935 7122 6.159172 AGATAGCCTGGTGATATAGGAAGA 57.841 41.667 0.00 0.00 36.11 2.87
1939 7126 8.986991 AGAATAAAGATAGCCTGGTGATATAGG 58.013 37.037 0.00 0.00 37.14 2.57
2010 7197 4.071961 TCTTGCCTATTGACACGCATAT 57.928 40.909 0.00 0.00 0.00 1.78
2031 7218 6.769512 TGAAAGTAGTTGCTGGAAGAAGTAT 58.230 36.000 0.00 0.00 34.07 2.12
2076 7265 5.991933 TTCAAAAGGCAAAGCATACCATA 57.008 34.783 0.00 0.00 0.00 2.74
2083 7272 3.384146 TGACAGATTCAAAAGGCAAAGCA 59.616 39.130 0.00 0.00 0.00 3.91
2099 7288 8.825745 GGTTTTGCATTTATTTTCTTTGACAGA 58.174 29.630 0.00 0.00 0.00 3.41
2100 7289 8.069574 GGGTTTTGCATTTATTTTCTTTGACAG 58.930 33.333 0.00 0.00 0.00 3.51
2256 7455 6.595716 AGACTTGAAACATAGCAGTAACCATC 59.404 38.462 0.00 0.00 0.00 3.51
2258 7457 5.865085 AGACTTGAAACATAGCAGTAACCA 58.135 37.500 0.00 0.00 0.00 3.67
2267 15945 9.809096 TCAATTCTAGCTAGACTTGAAACATAG 57.191 33.333 35.84 19.09 44.05 2.23
2276 15954 7.398904 AGAGAAAGGTCAATTCTAGCTAGACTT 59.601 37.037 23.17 20.31 37.26 3.01
2280 15959 7.494298 GGAAAGAGAAAGGTCAATTCTAGCTAG 59.506 40.741 15.01 15.01 37.26 3.42
2282 15961 6.012945 AGGAAAGAGAAAGGTCAATTCTAGCT 60.013 38.462 0.00 0.00 37.26 3.32
2322 16001 4.116747 AGCAGACTGAAAGAACGATAGG 57.883 45.455 6.65 0.00 37.86 2.57
2330 16009 1.605710 GCAGCAAAGCAGACTGAAAGA 59.394 47.619 6.65 0.00 37.43 2.52
2331 16010 1.335810 TGCAGCAAAGCAGACTGAAAG 59.664 47.619 6.65 0.00 40.11 2.62
2352 16032 4.810491 CCAACTGTTGATTTTGGTTTGGAG 59.190 41.667 21.49 0.00 35.91 3.86
2397 16079 8.295288 TCGTATTCTTTTCTCGAAAGTACTTCT 58.705 33.333 8.95 0.00 44.17 2.85
2403 16085 4.620184 CCGTCGTATTCTTTTCTCGAAAGT 59.380 41.667 0.00 0.00 44.17 2.66
2435 16117 6.681729 ACCATAGACTGTCAAAAGAGGTAA 57.318 37.500 10.88 0.00 0.00 2.85
2440 16122 9.793259 AAGAAATAACCATAGACTGTCAAAAGA 57.207 29.630 10.88 0.00 0.00 2.52
2450 16132 9.508567 GCAAAATGAGAAGAAATAACCATAGAC 57.491 33.333 0.00 0.00 0.00 2.59
2454 16136 7.983484 GGATGCAAAATGAGAAGAAATAACCAT 59.017 33.333 0.00 0.00 0.00 3.55
2464 16146 5.646793 TCTCTCTTGGATGCAAAATGAGAAG 59.353 40.000 17.39 12.09 0.00 2.85
2469 16151 5.381174 TGTTCTCTCTTGGATGCAAAATG 57.619 39.130 0.00 0.00 0.00 2.32
2536 16232 7.654520 TGCAACACGAGTAGTTACTTTTCTAAT 59.345 33.333 0.00 0.00 36.50 1.73
2557 16429 8.253810 TCCTGATACTAATGCTATAGATGCAAC 58.746 37.037 3.21 0.00 44.01 4.17
2585 16457 8.585881 AGTACTAATATACGATGCAGGAAACAT 58.414 33.333 0.00 0.00 0.00 2.71
2610 16483 6.582677 AGCTATAATGCTACTGTACTCCAG 57.417 41.667 0.00 0.00 42.10 3.86
2622 16495 5.877012 CGGATCATTGGTAAGCTATAATGCT 59.123 40.000 0.00 0.00 46.40 3.79
2623 16496 5.643777 ACGGATCATTGGTAAGCTATAATGC 59.356 40.000 0.00 0.00 32.14 3.56
2628 16501 3.815401 GCAACGGATCATTGGTAAGCTAT 59.185 43.478 10.10 0.00 0.00 2.97
2629 16502 3.202906 GCAACGGATCATTGGTAAGCTA 58.797 45.455 10.10 0.00 0.00 3.32
2722 16598 9.176460 TCAAATACATGAACTTTGATAGCATCA 57.824 29.630 0.00 0.00 34.80 3.07
2724 16600 9.961265 CATCAAATACATGAACTTTGATAGCAT 57.039 29.630 22.31 9.02 43.93 3.79
2725 16601 8.959548 ACATCAAATACATGAACTTTGATAGCA 58.040 29.630 22.31 7.09 43.93 3.49
2726 16602 9.793252 AACATCAAATACATGAACTTTGATAGC 57.207 29.630 22.31 0.00 43.93 2.97
2734 16610 9.412460 ACCATGATAACATCAAATACATGAACT 57.588 29.630 0.00 0.00 43.50 3.01
2737 16613 9.631257 AGAACCATGATAACATCAAATACATGA 57.369 29.630 0.00 0.00 43.50 3.07
2738 16614 9.673454 CAGAACCATGATAACATCAAATACATG 57.327 33.333 0.00 0.00 43.50 3.21
2739 16615 9.631257 TCAGAACCATGATAACATCAAATACAT 57.369 29.630 0.00 0.00 43.50 2.29
2740 16616 9.112725 CTCAGAACCATGATAACATCAAATACA 57.887 33.333 0.00 0.00 43.50 2.29
2741 16617 9.330063 TCTCAGAACCATGATAACATCAAATAC 57.670 33.333 0.00 0.00 43.50 1.89
2743 16619 8.847196 CATCTCAGAACCATGATAACATCAAAT 58.153 33.333 0.00 0.00 43.50 2.32
2744 16620 7.830697 ACATCTCAGAACCATGATAACATCAAA 59.169 33.333 0.00 0.00 43.50 2.69
2745 16621 7.341030 ACATCTCAGAACCATGATAACATCAA 58.659 34.615 0.00 0.00 43.50 2.57
2822 16698 0.529378 ACCAAACGTCCGCTACCTAG 59.471 55.000 0.00 0.00 0.00 3.02
2823 16699 0.527565 GACCAAACGTCCGCTACCTA 59.472 55.000 0.00 0.00 35.23 3.08
2879 16755 0.843984 CGGGGTCCTCAAATGGGTAT 59.156 55.000 0.00 0.00 0.00 2.73
2959 16835 0.895559 GGTGCTGAACAAGGGAAGGG 60.896 60.000 0.00 0.00 0.00 3.95
2996 16880 1.667724 CGGAGTTTCAGGCATGCTTAG 59.332 52.381 18.92 7.92 0.00 2.18
3002 16886 1.833630 TGAGATCGGAGTTTCAGGCAT 59.166 47.619 0.00 0.00 0.00 4.40
3015 16935 0.314578 GTGCATTCGCGTTGAGATCG 60.315 55.000 5.77 0.00 42.97 3.69
3158 17078 3.521126 AGAAAAGGAGGATAAGCAGCAGA 59.479 43.478 0.00 0.00 0.00 4.26
3183 17104 8.209802 TCCTTGGAAGTTACTAATAAACAGGA 57.790 34.615 0.00 0.00 0.00 3.86
3184 17105 8.857694 TTCCTTGGAAGTTACTAATAAACAGG 57.142 34.615 0.00 0.00 0.00 4.00
3249 17170 0.733150 GGTTAGGCACGATTGAAGGC 59.267 55.000 0.00 0.00 0.00 4.35
3254 17175 3.252215 TCACTTTTGGTTAGGCACGATTG 59.748 43.478 0.00 0.00 0.00 2.67
3485 17410 1.375523 GGCCGACGACTTGGACATT 60.376 57.895 0.00 0.00 31.69 2.71
3542 17467 2.045242 CCCTCCTCCTCGTCGTCA 60.045 66.667 0.00 0.00 0.00 4.35
3611 17537 0.959372 CCGTACTCCAGACAGACCGT 60.959 60.000 0.00 0.00 0.00 4.83
3613 17539 1.254954 AACCGTACTCCAGACAGACC 58.745 55.000 0.00 0.00 0.00 3.85
3615 17541 1.000506 GCAAACCGTACTCCAGACAGA 59.999 52.381 0.00 0.00 0.00 3.41
3616 17542 1.000955 AGCAAACCGTACTCCAGACAG 59.999 52.381 0.00 0.00 0.00 3.51
3617 17543 1.045407 AGCAAACCGTACTCCAGACA 58.955 50.000 0.00 0.00 0.00 3.41
3644 17597 3.068448 TCATACGCTTCGTGGCCTTATTA 59.932 43.478 3.32 0.00 41.39 0.98
3687 17647 9.331106 CAGTAATAATGTACACAGCGATAGTAG 57.669 37.037 0.00 0.00 39.35 2.57
3734 17694 8.802267 CCACCATCTTTTATTCTTGGAAGTTAA 58.198 33.333 0.00 0.00 0.00 2.01
3735 17695 7.396055 CCCACCATCTTTTATTCTTGGAAGTTA 59.604 37.037 0.00 0.00 0.00 2.24
3736 17696 6.211384 CCCACCATCTTTTATTCTTGGAAGTT 59.789 38.462 0.00 0.00 0.00 2.66
3737 17697 5.716703 CCCACCATCTTTTATTCTTGGAAGT 59.283 40.000 0.00 0.00 0.00 3.01
3738 17698 5.127682 CCCCACCATCTTTTATTCTTGGAAG 59.872 44.000 0.00 0.00 0.00 3.46
3739 17699 5.022787 CCCCACCATCTTTTATTCTTGGAA 58.977 41.667 0.00 0.00 0.00 3.53
3740 17700 4.293634 TCCCCACCATCTTTTATTCTTGGA 59.706 41.667 0.00 0.00 0.00 3.53
3741 17701 4.609301 TCCCCACCATCTTTTATTCTTGG 58.391 43.478 0.00 0.00 0.00 3.61
3764 17752 7.732025 TCAAACAAGACTGGAAGAACTGTATA 58.268 34.615 0.00 0.00 37.43 1.47
3788 17776 9.042008 TCCTCGTTAGAACATGCTTAATAATTC 57.958 33.333 0.00 0.00 0.00 2.17
3789 17777 8.958119 TCCTCGTTAGAACATGCTTAATAATT 57.042 30.769 0.00 0.00 0.00 1.40
3791 17779 7.009815 CGTTCCTCGTTAGAACATGCTTAATAA 59.990 37.037 12.84 0.00 43.07 1.40
3792 17780 6.474427 CGTTCCTCGTTAGAACATGCTTAATA 59.526 38.462 12.84 0.00 43.07 0.98
3800 17788 5.390567 GCAAAATCGTTCCTCGTTAGAACAT 60.391 40.000 12.84 5.54 43.07 2.71
3806 18151 3.185594 CACTGCAAAATCGTTCCTCGTTA 59.814 43.478 0.00 0.00 40.80 3.18
3809 18154 1.135972 CCACTGCAAAATCGTTCCTCG 60.136 52.381 0.00 0.00 41.41 4.63
3863 18208 1.265635 TCCAAATTTCGAACTGTGGCG 59.734 47.619 17.74 0.00 0.00 5.69
3897 18242 5.126067 AGATTCGCCACTGCAAATTATACT 58.874 37.500 0.00 0.00 37.32 2.12
3955 18316 7.227049 ACAAGGGAAACACTTATAACAATGG 57.773 36.000 0.00 0.00 0.00 3.16
3967 18328 3.469739 TCCGTAAGAACAAGGGAAACAC 58.530 45.455 0.00 0.00 43.02 3.32
3968 18329 3.842007 TCCGTAAGAACAAGGGAAACA 57.158 42.857 0.00 0.00 43.02 2.83
3969 18330 4.576879 AGATCCGTAAGAACAAGGGAAAC 58.423 43.478 0.00 0.00 43.02 2.78
3970 18331 4.530946 AGAGATCCGTAAGAACAAGGGAAA 59.469 41.667 0.00 0.00 43.02 3.13
3971 18332 4.094476 AGAGATCCGTAAGAACAAGGGAA 58.906 43.478 0.00 0.00 43.02 3.97
3972 18333 3.709587 AGAGATCCGTAAGAACAAGGGA 58.290 45.455 0.00 0.00 43.02 4.20
3973 18334 5.593679 TTAGAGATCCGTAAGAACAAGGG 57.406 43.478 0.00 0.00 43.02 3.95
3974 18335 5.915758 CGATTAGAGATCCGTAAGAACAAGG 59.084 44.000 0.00 0.00 43.02 3.61
3975 18336 6.726230 TCGATTAGAGATCCGTAAGAACAAG 58.274 40.000 0.00 0.00 43.02 3.16
3976 18337 6.688637 TCGATTAGAGATCCGTAAGAACAA 57.311 37.500 0.00 0.00 43.02 2.83
3977 18338 6.879276 ATCGATTAGAGATCCGTAAGAACA 57.121 37.500 0.00 0.00 43.02 3.18
3994 18355 9.681062 TCCACTTAAAATTTTAGAGGATCGATT 57.319 29.630 17.27 0.00 42.67 3.34
3995 18356 9.331282 CTCCACTTAAAATTTTAGAGGATCGAT 57.669 33.333 19.63 0.00 42.67 3.59
3996 18357 8.319146 ACTCCACTTAAAATTTTAGAGGATCGA 58.681 33.333 20.42 0.00 42.67 3.59
3997 18358 8.494016 ACTCCACTTAAAATTTTAGAGGATCG 57.506 34.615 20.42 15.00 42.67 3.69
4008 18369 8.803235 CCTAAGCCTTTTACTCCACTTAAAATT 58.197 33.333 0.00 0.00 30.07 1.82
4009 18370 7.948447 ACCTAAGCCTTTTACTCCACTTAAAAT 59.052 33.333 0.00 0.00 30.07 1.82
4010 18371 7.292319 ACCTAAGCCTTTTACTCCACTTAAAA 58.708 34.615 0.00 0.00 0.00 1.52
4011 18372 6.844829 ACCTAAGCCTTTTACTCCACTTAAA 58.155 36.000 0.00 0.00 0.00 1.52
4012 18373 6.443995 ACCTAAGCCTTTTACTCCACTTAA 57.556 37.500 0.00 0.00 0.00 1.85
4013 18374 6.443995 AACCTAAGCCTTTTACTCCACTTA 57.556 37.500 0.00 0.00 0.00 2.24
4014 18375 4.995624 ACCTAAGCCTTTTACTCCACTT 57.004 40.909 0.00 0.00 0.00 3.16
4015 18376 4.995624 AACCTAAGCCTTTTACTCCACT 57.004 40.909 0.00 0.00 0.00 4.00
4016 18377 5.121298 CGTAAACCTAAGCCTTTTACTCCAC 59.879 44.000 0.00 0.00 34.77 4.02
4017 18378 5.011943 TCGTAAACCTAAGCCTTTTACTCCA 59.988 40.000 0.00 0.00 34.77 3.86
4018 18379 5.482006 TCGTAAACCTAAGCCTTTTACTCC 58.518 41.667 0.00 0.00 34.77 3.85
4019 18380 7.425577 TTTCGTAAACCTAAGCCTTTTACTC 57.574 36.000 0.00 0.00 34.77 2.59
4020 18381 7.806409 TTTTCGTAAACCTAAGCCTTTTACT 57.194 32.000 0.00 0.00 34.77 2.24
4021 18382 8.131100 AGTTTTTCGTAAACCTAAGCCTTTTAC 58.869 33.333 10.72 0.00 33.96 2.01
4022 18383 8.224389 AGTTTTTCGTAAACCTAAGCCTTTTA 57.776 30.769 10.72 0.00 0.00 1.52
4023 18384 7.104043 AGTTTTTCGTAAACCTAAGCCTTTT 57.896 32.000 10.72 0.00 0.00 2.27
4024 18385 6.704289 AGTTTTTCGTAAACCTAAGCCTTT 57.296 33.333 10.72 0.00 0.00 3.11
4025 18386 7.518848 CGTTAGTTTTTCGTAAACCTAAGCCTT 60.519 37.037 5.06 0.00 31.46 4.35
4026 18387 6.073602 CGTTAGTTTTTCGTAAACCTAAGCCT 60.074 38.462 5.06 0.00 31.46 4.58
4027 18388 6.073369 CGTTAGTTTTTCGTAAACCTAAGCC 58.927 40.000 5.06 0.00 31.46 4.35
4028 18389 6.649436 ACGTTAGTTTTTCGTAAACCTAAGC 58.351 36.000 5.06 1.60 31.46 3.09
4029 18390 7.042791 TGGACGTTAGTTTTTCGTAAACCTAAG 60.043 37.037 5.06 3.55 37.92 2.18
4030 18391 6.758886 TGGACGTTAGTTTTTCGTAAACCTAA 59.241 34.615 10.72 6.41 37.92 2.69
4034 18395 5.672426 GTGTGGACGTTAGTTTTTCGTAAAC 59.328 40.000 0.00 7.51 37.92 2.01
4065 18427 1.285641 GTGGGTGATGTGCAAACGG 59.714 57.895 0.00 0.00 0.00 4.44
4089 18454 2.351641 GCGTGGCAAAATGAGTGATGAA 60.352 45.455 0.00 0.00 0.00 2.57
4110 18475 9.181805 GATTTCTGCTGATTTCATATGTTCATG 57.818 33.333 1.90 0.00 0.00 3.07
4123 18488 7.042523 CGAAAACCAAAAAGATTTCTGCTGATT 60.043 33.333 0.00 0.00 31.29 2.57
4267 18633 7.723172 TCATGGTAATTTTTGGGCAAAAGAATT 59.277 29.630 10.34 10.34 40.83 2.17
4268 18634 7.230027 TCATGGTAATTTTTGGGCAAAAGAAT 58.770 30.769 0.00 0.00 40.83 2.40
4284 18650 6.646267 ACTACGGTGTAAACATCATGGTAAT 58.354 36.000 0.00 0.00 0.00 1.89
4287 18653 4.546829 ACTACGGTGTAAACATCATGGT 57.453 40.909 0.00 0.00 0.00 3.55
4334 18700 7.145323 GTCTACAAACTAAAATTGCCACATGT 58.855 34.615 0.00 0.00 0.00 3.21
4359 18725 6.589523 TCATCGAAAAACTAAAATTGCCATGG 59.410 34.615 7.63 7.63 0.00 3.66
4385 18751 2.161609 GGTCAAAGTACTGGAATTGCCG 59.838 50.000 0.00 0.00 40.66 5.69
4434 18800 7.322664 CCAGGATACATGCACTTAAAATTGTT 58.677 34.615 0.00 0.00 41.41 2.83
4456 18822 6.483385 TGCAACATAAATCAAAATTGCCAG 57.517 33.333 4.47 0.00 41.31 4.85
4475 18841 5.726980 AAGAAATTAGACTTGCCATGCAA 57.273 34.783 1.13 1.13 46.80 4.08


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

AutoCloner maintained by Alex Coulton.