Multiple sequence alignment - TraesCS1B01G403700

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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 TraesCS1B01G403700 chr1B 100.000 3719 0 0 1 3719 633140234 633136516 0.000000e+00 6868.0
1 TraesCS1B01G403700 chr1D 92.569 1588 93 13 766 2345 460868777 460867207 0.000000e+00 2255.0
2 TraesCS1B01G403700 chr1D 95.740 845 28 8 2878 3719 460866504 460865665 0.000000e+00 1354.0
3 TraesCS1B01G403700 chr1D 94.129 528 20 6 2354 2881 460867100 460866584 0.000000e+00 793.0
4 TraesCS1B01G403700 chr1D 85.659 258 35 2 1 257 460869413 460869157 1.700000e-68 270.0
5 TraesCS1B01G403700 chr1D 87.574 169 15 3 340 504 280704942 280705108 1.360000e-44 191.0
6 TraesCS1B01G403700 chr1D 92.857 42 3 0 570 611 460868937 460868896 1.120000e-05 62.1
7 TraesCS1B01G403700 chr1A 90.043 1617 80 38 761 2345 551984404 551982837 0.000000e+00 2019.0
8 TraesCS1B01G403700 chr1A 93.270 1367 69 13 2354 3719 551982736 551981392 0.000000e+00 1993.0
9 TraesCS1B01G403700 chr1A 87.047 193 21 2 314 503 252511666 252511857 8.090000e-52 215.0
10 TraesCS1B01G403700 chr1A 89.610 77 8 0 642 718 534564754 534564678 8.500000e-17 99.0
11 TraesCS1B01G403700 chr1A 87.500 64 6 1 502 563 551985089 551985026 5.150000e-09 73.1
12 TraesCS1B01G403700 chr5B 89.123 285 14 8 236 505 527760641 527760359 4.600000e-89 339.0
13 TraesCS1B01G403700 chr5B 89.744 78 8 0 642 719 682121627 682121550 2.360000e-17 100.0
14 TraesCS1B01G403700 chr5B 88.462 78 9 0 642 719 603154615 603154538 1.100000e-15 95.3
15 TraesCS1B01G403700 chr5B 88.406 69 6 2 60 127 505377854 505377921 8.560000e-12 82.4
16 TraesCS1B01G403700 chr5B 84.746 59 8 1 34 92 563604029 563603972 1.440000e-04 58.4
17 TraesCS1B01G403700 chr3A 90.204 245 19 3 263 503 17857213 17857456 7.750000e-82 315.0
18 TraesCS1B01G403700 chr4A 89.231 260 13 4 253 503 352482007 352481754 1.000000e-80 311.0
19 TraesCS1B01G403700 chr4A 89.744 78 8 0 642 719 249649364 249649441 2.360000e-17 100.0
20 TraesCS1B01G403700 chr2B 88.716 257 14 6 262 504 45729546 45729801 2.170000e-77 300.0
21 TraesCS1B01G403700 chr2B 87.624 202 24 1 1873 2074 76099486 76099286 2.230000e-57 233.0
22 TraesCS1B01G403700 chr2B 85.345 232 22 5 283 505 166665564 166665336 2.890000e-56 230.0
23 TraesCS1B01G403700 chr7A 87.170 265 19 6 253 503 150586756 150587019 1.690000e-73 287.0
24 TraesCS1B01G403700 chr5A 87.597 258 12 10 261 504 568680112 568679861 7.860000e-72 281.0
25 TraesCS1B01G403700 chr2A 86.873 259 20 7 255 500 69310956 69311213 1.020000e-70 278.0
26 TraesCS1B01G403700 chr2A 83.333 216 25 8 294 505 681097890 681097682 4.900000e-44 189.0
27 TraesCS1B01G403700 chr2A 89.744 78 8 0 642 719 127198482 127198405 2.360000e-17 100.0
28 TraesCS1B01G403700 chr5D 85.551 263 24 4 255 504 449691471 449691210 2.850000e-66 263.0
29 TraesCS1B01G403700 chr5D 91.237 194 13 3 265 455 434580406 434580214 1.020000e-65 261.0
30 TraesCS1B01G403700 chr5D 82.422 256 37 6 254 504 226557179 226556927 2.250000e-52 217.0
31 TraesCS1B01G403700 chr5D 89.744 78 8 0 642 719 539890109 539890032 2.360000e-17 100.0
32 TraesCS1B01G403700 chr7D 82.490 257 35 8 254 505 198869176 198869427 2.250000e-52 217.0
33 TraesCS1B01G403700 chr7D 90.411 73 7 0 647 719 207183740 207183812 3.060000e-16 97.1
34 TraesCS1B01G403700 chr2D 85.000 200 17 6 280 473 116492209 116492017 1.360000e-44 191.0
35 TraesCS1B01G403700 chrUn 81.279 219 32 6 294 506 22157778 22157563 6.390000e-38 169.0
36 TraesCS1B01G403700 chrUn 81.132 106 17 3 6 109 402525398 402525294 8.560000e-12 82.4
37 TraesCS1B01G403700 chrUn 82.000 100 15 3 6 103 474083782 474083880 8.560000e-12 82.4
38 TraesCS1B01G403700 chr3B 83.333 120 10 9 636 745 12407684 12407565 6.570000e-18 102.0
39 TraesCS1B01G403700 chr7B 81.967 122 16 6 1 119 509563156 509563274 8.500000e-17 99.0
40 TraesCS1B01G403700 chr6D 87.654 81 10 0 641 721 428647295 428647375 1.100000e-15 95.3
41 TraesCS1B01G403700 chr4D 81.132 106 17 3 6 109 254812938 254812834 8.560000e-12 82.4
42 TraesCS1B01G403700 chr4D 82.000 100 15 3 6 103 267717319 267717417 8.560000e-12 82.4
43 TraesCS1B01G403700 chr4D 82.000 100 15 3 6 103 498075990 498076088 8.560000e-12 82.4
44 TraesCS1B01G403700 chr4D 81.818 99 15 3 7 103 212574573 212574670 3.080000e-11 80.5


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 TraesCS1B01G403700 chr1B 633136516 633140234 3718 True 6868.00 6868 100.0000 1 3719 1 chr1B.!!$R1 3718
1 TraesCS1B01G403700 chr1D 460865665 460869413 3748 True 946.82 2255 92.1908 1 3719 5 chr1D.!!$R1 3718
2 TraesCS1B01G403700 chr1A 551981392 551985089 3697 True 1361.70 2019 90.2710 502 3719 3 chr1A.!!$R2 3217

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
40 41 0.099791 GTGGTGTTTGTTCGGTGGTG 59.900 55.0 0.00 0.0 0.0 4.17 F
1173 1810 0.463620 GATCTGGACTCTGGAGGTGC 59.536 60.0 2.58 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1954 0.036388 GTCGTCCCCTTGCTCAATCA 60.036 55.0 0.0 0.0 0.0 2.57 R
2778 3563 0.548031 TCATCTGACATTGGCTCCCC 59.452 55.0 0.0 0.0 0.0 4.81 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
19 20 0.316032 CGACGGCTCGTTCTACTAGC 60.316 60.000 1.80 0.00 41.37 3.42
21 22 0.733729 ACGGCTCGTTCTACTAGCAG 59.266 55.000 5.82 4.30 38.51 4.24
27 28 2.488545 CTCGTTCTACTAGCAGTGGTGT 59.511 50.000 4.76 4.01 0.00 4.16
32 33 4.682778 TCTACTAGCAGTGGTGTTTGTT 57.317 40.909 4.76 0.00 0.00 2.83
40 41 0.099791 GTGGTGTTTGTTCGGTGGTG 59.900 55.000 0.00 0.00 0.00 4.17
50 51 2.492088 TGTTCGGTGGTGTAGAGATCTG 59.508 50.000 0.00 0.00 0.00 2.90
54 55 3.137728 TCGGTGGTGTAGAGATCTGGATA 59.862 47.826 0.00 0.00 0.00 2.59
56 57 4.082517 CGGTGGTGTAGAGATCTGGATATG 60.083 50.000 0.00 0.00 0.00 1.78
58 59 5.047660 GGTGGTGTAGAGATCTGGATATGAC 60.048 48.000 0.00 0.00 0.00 3.06
60 61 6.266558 GTGGTGTAGAGATCTGGATATGACTT 59.733 42.308 0.00 0.00 0.00 3.01
96 98 9.944376 TTAAGATGCTTTGTACTTCTCATAACT 57.056 29.630 0.00 0.00 0.00 2.24
98 100 8.854614 AGATGCTTTGTACTTCTCATAACTTT 57.145 30.769 0.00 0.00 0.00 2.66
174 176 8.034804 GTGCAATTGAGGGTATTCAACTTAAAT 58.965 33.333 10.34 0.00 39.68 1.40
175 177 8.034215 TGCAATTGAGGGTATTCAACTTAAATG 58.966 33.333 10.34 0.00 39.68 2.32
209 211 7.657023 TGATAAAAACTCTAGAGGTACCTCC 57.343 40.000 33.81 18.53 43.70 4.30
210 212 6.610425 TGATAAAAACTCTAGAGGTACCTCCC 59.390 42.308 33.81 14.98 43.70 4.30
229 231 4.116113 TCCCTAGGACAATTAATGTGGGT 58.884 43.478 11.48 0.00 44.12 4.51
230 232 4.542525 TCCCTAGGACAATTAATGTGGGTT 59.457 41.667 11.48 0.00 44.12 4.11
241 243 6.645884 ATTAATGTGGGTTGGAGGTAGTAA 57.354 37.500 0.00 0.00 0.00 2.24
243 245 5.530176 AATGTGGGTTGGAGGTAGTAAAT 57.470 39.130 0.00 0.00 0.00 1.40
251 253 8.050930 TGGGTTGGAGGTAGTAAATAATTCTTC 58.949 37.037 0.00 0.00 0.00 2.87
280 282 7.582352 ACTTTCTCCGTTTTTATTTACTCTGC 58.418 34.615 0.00 0.00 0.00 4.26
281 283 7.227910 ACTTTCTCCGTTTTTATTTACTCTGCA 59.772 33.333 0.00 0.00 0.00 4.41
282 284 7.681939 TTCTCCGTTTTTATTTACTCTGCAT 57.318 32.000 0.00 0.00 0.00 3.96
283 285 8.780846 TTCTCCGTTTTTATTTACTCTGCATA 57.219 30.769 0.00 0.00 0.00 3.14
284 286 8.958119 TCTCCGTTTTTATTTACTCTGCATAT 57.042 30.769 0.00 0.00 0.00 1.78
285 287 9.391006 TCTCCGTTTTTATTTACTCTGCATATT 57.609 29.630 0.00 0.00 0.00 1.28
296 298 9.686683 ATTTACTCTGCATATTAGTTTTGACCT 57.313 29.630 0.00 0.00 0.00 3.85
299 301 8.723942 ACTCTGCATATTAGTTTTGACCTAAG 57.276 34.615 0.00 0.00 0.00 2.18
300 302 8.322091 ACTCTGCATATTAGTTTTGACCTAAGT 58.678 33.333 0.00 0.00 0.00 2.24
301 303 8.718102 TCTGCATATTAGTTTTGACCTAAGTC 57.282 34.615 0.00 0.00 43.83 3.01
338 340 8.488979 AGTTTTGATCAAGTTTATCGAAAACG 57.511 30.769 8.41 0.00 38.08 3.60
339 341 8.339714 AGTTTTGATCAAGTTTATCGAAAACGA 58.660 29.630 8.41 0.00 38.08 3.85
340 342 9.113876 GTTTTGATCAAGTTTATCGAAAACGAT 57.886 29.630 8.41 9.85 38.08 3.73
341 343 8.874745 TTTGATCAAGTTTATCGAAAACGATC 57.125 30.769 8.41 19.46 35.42 3.69
342 344 7.827819 TGATCAAGTTTATCGAAAACGATCT 57.172 32.000 22.49 0.00 35.42 2.75
343 345 8.920509 TGATCAAGTTTATCGAAAACGATCTA 57.079 30.769 22.49 15.10 35.42 1.98
344 346 9.361315 TGATCAAGTTTATCGAAAACGATCTAA 57.639 29.630 22.49 2.99 35.42 2.10
346 348 9.968743 ATCAAGTTTATCGAAAACGATCTAAAC 57.031 29.630 16.30 16.30 35.42 2.01
347 349 9.199982 TCAAGTTTATCGAAAACGATCTAAACT 57.800 29.630 18.86 18.86 38.10 2.66
348 350 9.807386 CAAGTTTATCGAAAACGATCTAAACTT 57.193 29.630 24.27 24.27 42.07 2.66
351 353 9.801714 GTTTATCGAAAACGATCTAAACTTTCA 57.198 29.630 16.56 0.00 30.44 2.69
352 354 9.801714 TTTATCGAAAACGATCTAAACTTTCAC 57.198 29.630 8.34 0.00 0.00 3.18
353 355 6.831727 TCGAAAACGATCTAAACTTTCACA 57.168 33.333 0.00 0.00 0.00 3.58
354 356 7.236674 TCGAAAACGATCTAAACTTTCACAA 57.763 32.000 0.00 0.00 0.00 3.33
355 357 7.857569 TCGAAAACGATCTAAACTTTCACAAT 58.142 30.769 0.00 0.00 0.00 2.71
356 358 8.980610 TCGAAAACGATCTAAACTTTCACAATA 58.019 29.630 0.00 0.00 0.00 1.90
357 359 9.250986 CGAAAACGATCTAAACTTTCACAATAG 57.749 33.333 0.00 0.00 0.00 1.73
358 360 8.950403 AAAACGATCTAAACTTTCACAATAGC 57.050 30.769 0.00 0.00 0.00 2.97
359 361 7.667043 AACGATCTAAACTTTCACAATAGCA 57.333 32.000 0.00 0.00 0.00 3.49
360 362 7.667043 ACGATCTAAACTTTCACAATAGCAA 57.333 32.000 0.00 0.00 0.00 3.91
361 363 8.094798 ACGATCTAAACTTTCACAATAGCAAA 57.905 30.769 0.00 0.00 0.00 3.68
362 364 8.730680 ACGATCTAAACTTTCACAATAGCAAAT 58.269 29.630 0.00 0.00 0.00 2.32
410 412 9.645128 TGATGATTCTAATGGTATTGATTTGGT 57.355 29.630 0.00 0.00 0.00 3.67
417 419 9.130661 TCTAATGGTATTGATTTGGTATTGTGG 57.869 33.333 0.00 0.00 0.00 4.17
418 420 7.969690 AATGGTATTGATTTGGTATTGTGGA 57.030 32.000 0.00 0.00 0.00 4.02
419 421 8.551682 AATGGTATTGATTTGGTATTGTGGAT 57.448 30.769 0.00 0.00 0.00 3.41
420 422 7.345422 TGGTATTGATTTGGTATTGTGGATG 57.655 36.000 0.00 0.00 0.00 3.51
421 423 6.894654 TGGTATTGATTTGGTATTGTGGATGT 59.105 34.615 0.00 0.00 0.00 3.06
422 424 7.398618 TGGTATTGATTTGGTATTGTGGATGTT 59.601 33.333 0.00 0.00 0.00 2.71
423 425 8.908903 GGTATTGATTTGGTATTGTGGATGTTA 58.091 33.333 0.00 0.00 0.00 2.41
468 470 5.718649 TCAAAGTTTGACTCGAGACAAAG 57.281 39.130 33.03 23.95 39.51 2.77
469 471 4.034048 TCAAAGTTTGACTCGAGACAAAGC 59.966 41.667 33.03 26.85 39.51 3.51
470 472 3.460857 AGTTTGACTCGAGACAAAGCT 57.539 42.857 33.03 28.07 39.51 3.74
471 473 4.585955 AGTTTGACTCGAGACAAAGCTA 57.414 40.909 33.03 16.73 39.51 3.32
472 474 4.945246 AGTTTGACTCGAGACAAAGCTAA 58.055 39.130 33.03 16.41 39.51 3.09
473 475 5.542779 AGTTTGACTCGAGACAAAGCTAAT 58.457 37.500 33.03 15.99 39.51 1.73
474 476 6.688578 AGTTTGACTCGAGACAAAGCTAATA 58.311 36.000 33.03 15.18 39.51 0.98
475 477 7.324178 AGTTTGACTCGAGACAAAGCTAATAT 58.676 34.615 33.03 16.09 39.51 1.28
476 478 7.276658 AGTTTGACTCGAGACAAAGCTAATATG 59.723 37.037 33.03 0.00 39.51 1.78
477 479 5.043903 TGACTCGAGACAAAGCTAATATGC 58.956 41.667 21.68 0.00 0.00 3.14
478 480 4.045104 ACTCGAGACAAAGCTAATATGCG 58.955 43.478 21.68 0.00 38.13 4.73
479 481 4.202020 ACTCGAGACAAAGCTAATATGCGA 60.202 41.667 21.68 0.00 38.13 5.10
480 482 4.678622 TCGAGACAAAGCTAATATGCGAA 58.321 39.130 0.00 0.00 38.13 4.70
481 483 4.740205 TCGAGACAAAGCTAATATGCGAAG 59.260 41.667 0.00 0.00 38.13 3.79
482 484 4.504461 CGAGACAAAGCTAATATGCGAAGT 59.496 41.667 0.00 0.00 38.13 3.01
483 485 5.685954 CGAGACAAAGCTAATATGCGAAGTA 59.314 40.000 0.00 0.00 38.13 2.24
484 486 6.198403 CGAGACAAAGCTAATATGCGAAGTAA 59.802 38.462 0.00 0.00 38.13 2.24
485 487 7.253983 CGAGACAAAGCTAATATGCGAAGTAAA 60.254 37.037 0.00 0.00 38.13 2.01
486 488 8.438676 AGACAAAGCTAATATGCGAAGTAAAT 57.561 30.769 0.00 0.00 38.13 1.40
487 489 9.542462 AGACAAAGCTAATATGCGAAGTAAATA 57.458 29.630 0.00 0.00 38.13 1.40
493 495 9.646336 AGCTAATATGCGAAGTAAATAAAAACG 57.354 29.630 0.00 0.00 38.13 3.60
494 496 9.429600 GCTAATATGCGAAGTAAATAAAAACGT 57.570 29.630 0.00 0.00 0.00 3.99
497 499 9.925268 AATATGCGAAGTAAATAAAAACGTAGG 57.075 29.630 0.00 0.00 0.00 3.18
498 500 6.168164 TGCGAAGTAAATAAAAACGTAGGG 57.832 37.500 0.00 0.00 0.00 3.53
499 501 5.931146 TGCGAAGTAAATAAAAACGTAGGGA 59.069 36.000 0.00 0.00 0.00 4.20
500 502 6.091169 TGCGAAGTAAATAAAAACGTAGGGAG 59.909 38.462 0.00 0.00 0.00 4.30
506 508 9.208022 AGTAAATAAAAACGTAGGGAGTACAAC 57.792 33.333 0.00 0.00 0.00 3.32
522 524 7.284944 GGGAGTACAACTCTAGCTAAACAGATA 59.715 40.741 6.99 0.00 44.46 1.98
606 1155 3.571401 AGTCCAAACTCCTTTTGCTCATG 59.429 43.478 0.00 0.00 43.03 3.07
611 1160 6.267471 TCCAAACTCCTTTTGCTCATGTTTAT 59.733 34.615 0.00 0.00 43.03 1.40
612 1161 6.366877 CCAAACTCCTTTTGCTCATGTTTATG 59.633 38.462 0.00 0.00 43.03 1.90
613 1162 6.655078 AACTCCTTTTGCTCATGTTTATGT 57.345 33.333 0.00 0.00 35.73 2.29
614 1163 6.655078 ACTCCTTTTGCTCATGTTTATGTT 57.345 33.333 0.00 0.00 35.73 2.71
615 1164 6.449698 ACTCCTTTTGCTCATGTTTATGTTG 58.550 36.000 0.00 0.00 35.73 3.33
616 1165 5.229423 TCCTTTTGCTCATGTTTATGTTGC 58.771 37.500 0.00 0.00 35.73 4.17
617 1166 4.989797 CCTTTTGCTCATGTTTATGTTGCA 59.010 37.500 0.00 0.00 40.26 4.08
618 1167 5.640357 CCTTTTGCTCATGTTTATGTTGCAT 59.360 36.000 0.00 0.00 40.94 3.96
619 1168 6.148150 CCTTTTGCTCATGTTTATGTTGCATT 59.852 34.615 0.00 0.00 40.94 3.56
620 1169 6.469139 TTTGCTCATGTTTATGTTGCATTG 57.531 33.333 0.00 0.00 40.94 2.82
621 1170 3.927758 TGCTCATGTTTATGTTGCATTGC 59.072 39.130 0.46 0.46 38.67 3.56
646 1277 4.848757 CAACTCTGCAAAACAAGTACTCC 58.151 43.478 0.00 0.00 0.00 3.85
647 1278 4.150897 ACTCTGCAAAACAAGTACTCCA 57.849 40.909 0.00 0.00 0.00 3.86
648 1279 4.718961 ACTCTGCAAAACAAGTACTCCAT 58.281 39.130 0.00 0.00 0.00 3.41
649 1280 4.757149 ACTCTGCAAAACAAGTACTCCATC 59.243 41.667 0.00 0.00 0.00 3.51
650 1281 4.713553 TCTGCAAAACAAGTACTCCATCA 58.286 39.130 0.00 0.00 0.00 3.07
651 1282 4.756642 TCTGCAAAACAAGTACTCCATCAG 59.243 41.667 0.00 0.00 0.00 2.90
652 1283 4.460263 TGCAAAACAAGTACTCCATCAGT 58.540 39.130 0.00 0.00 39.41 3.41
653 1284 4.887071 TGCAAAACAAGTACTCCATCAGTT 59.113 37.500 0.00 0.00 36.43 3.16
654 1285 5.359576 TGCAAAACAAGTACTCCATCAGTTT 59.640 36.000 0.00 0.00 36.43 2.66
655 1286 5.915196 GCAAAACAAGTACTCCATCAGTTTC 59.085 40.000 0.00 0.00 36.43 2.78
656 1287 6.459573 GCAAAACAAGTACTCCATCAGTTTCA 60.460 38.462 0.00 0.00 36.43 2.69
657 1288 7.479980 CAAAACAAGTACTCCATCAGTTTCAA 58.520 34.615 0.00 0.00 36.43 2.69
658 1289 7.639113 AAACAAGTACTCCATCAGTTTCAAA 57.361 32.000 0.00 0.00 36.43 2.69
659 1290 7.639113 AACAAGTACTCCATCAGTTTCAAAA 57.361 32.000 0.00 0.00 36.43 2.44
660 1291 7.823745 ACAAGTACTCCATCAGTTTCAAAAT 57.176 32.000 0.00 0.00 36.43 1.82
661 1292 8.918202 ACAAGTACTCCATCAGTTTCAAAATA 57.082 30.769 0.00 0.00 36.43 1.40
662 1293 9.520515 ACAAGTACTCCATCAGTTTCAAAATAT 57.479 29.630 0.00 0.00 36.43 1.28
702 1333 8.879342 ATTTCAATACAGACTACATACAGAGC 57.121 34.615 0.00 0.00 0.00 4.09
703 1334 7.404671 TTCAATACAGACTACATACAGAGCA 57.595 36.000 0.00 0.00 0.00 4.26
704 1335 7.404671 TCAATACAGACTACATACAGAGCAA 57.595 36.000 0.00 0.00 0.00 3.91
705 1336 7.836842 TCAATACAGACTACATACAGAGCAAA 58.163 34.615 0.00 0.00 0.00 3.68
706 1337 8.311109 TCAATACAGACTACATACAGAGCAAAA 58.689 33.333 0.00 0.00 0.00 2.44
707 1338 9.102757 CAATACAGACTACATACAGAGCAAAAT 57.897 33.333 0.00 0.00 0.00 1.82
708 1339 6.974932 ACAGACTACATACAGAGCAAAATG 57.025 37.500 0.00 0.00 0.00 2.32
709 1340 5.877012 ACAGACTACATACAGAGCAAAATGG 59.123 40.000 0.00 0.00 0.00 3.16
710 1341 5.295292 CAGACTACATACAGAGCAAAATGGG 59.705 44.000 0.00 0.00 0.00 4.00
711 1342 5.045578 AGACTACATACAGAGCAAAATGGGT 60.046 40.000 0.00 0.00 0.00 4.51
712 1343 6.156256 AGACTACATACAGAGCAAAATGGGTA 59.844 38.462 0.00 0.00 0.00 3.69
713 1344 6.717289 ACTACATACAGAGCAAAATGGGTAA 58.283 36.000 0.00 0.00 0.00 2.85
714 1345 7.172342 ACTACATACAGAGCAAAATGGGTAAA 58.828 34.615 0.00 0.00 0.00 2.01
715 1346 7.834181 ACTACATACAGAGCAAAATGGGTAAAT 59.166 33.333 0.00 0.00 0.00 1.40
716 1347 7.100458 ACATACAGAGCAAAATGGGTAAATC 57.900 36.000 0.00 0.00 0.00 2.17
717 1348 6.891908 ACATACAGAGCAAAATGGGTAAATCT 59.108 34.615 0.00 0.00 0.00 2.40
718 1349 8.052748 ACATACAGAGCAAAATGGGTAAATCTA 58.947 33.333 0.00 0.00 0.00 1.98
719 1350 8.902806 CATACAGAGCAAAATGGGTAAATCTAA 58.097 33.333 0.00 0.00 0.00 2.10
720 1351 7.775053 ACAGAGCAAAATGGGTAAATCTAAA 57.225 32.000 0.00 0.00 0.00 1.85
721 1352 8.189119 ACAGAGCAAAATGGGTAAATCTAAAA 57.811 30.769 0.00 0.00 0.00 1.52
722 1353 8.815912 ACAGAGCAAAATGGGTAAATCTAAAAT 58.184 29.630 0.00 0.00 0.00 1.82
733 1364 9.403583 TGGGTAAATCTAAAATATGTCCAAGAC 57.596 33.333 0.00 0.00 0.00 3.01
734 1365 9.628500 GGGTAAATCTAAAATATGTCCAAGACT 57.372 33.333 0.00 0.00 33.15 3.24
748 1379 7.724305 TGTCCAAGACTTTGTATGTAGAAAC 57.276 36.000 0.00 0.00 33.15 2.78
749 1380 6.422701 TGTCCAAGACTTTGTATGTAGAAACG 59.577 38.462 0.00 0.00 33.15 3.60
750 1381 5.929992 TCCAAGACTTTGTATGTAGAAACGG 59.070 40.000 0.00 0.00 32.21 4.44
751 1382 5.929992 CCAAGACTTTGTATGTAGAAACGGA 59.070 40.000 0.00 0.00 32.21 4.69
752 1383 6.090898 CCAAGACTTTGTATGTAGAAACGGAG 59.909 42.308 0.00 0.00 32.21 4.63
753 1384 5.721232 AGACTTTGTATGTAGAAACGGAGG 58.279 41.667 0.00 0.00 0.00 4.30
754 1385 4.828829 ACTTTGTATGTAGAAACGGAGGG 58.171 43.478 0.00 0.00 0.00 4.30
755 1386 4.529377 ACTTTGTATGTAGAAACGGAGGGA 59.471 41.667 0.00 0.00 0.00 4.20
756 1387 4.730949 TTGTATGTAGAAACGGAGGGAG 57.269 45.455 0.00 0.00 0.00 4.30
757 1388 3.705051 TGTATGTAGAAACGGAGGGAGT 58.295 45.455 0.00 0.00 0.00 3.85
758 1389 4.091549 TGTATGTAGAAACGGAGGGAGTT 58.908 43.478 0.00 0.00 0.00 3.01
759 1390 3.611766 ATGTAGAAACGGAGGGAGTTG 57.388 47.619 0.00 0.00 31.43 3.16
777 1408 6.239629 GGGAGTTGACGATAGGATTTCCTTAT 60.240 42.308 4.08 0.00 46.09 1.73
779 1410 8.532819 GGAGTTGACGATAGGATTTCCTTATAT 58.467 37.037 4.08 0.00 46.09 0.86
807 1438 9.892130 AAAAAGTAGACGATAGGATTTCTGAAT 57.108 29.630 0.00 0.00 43.77 2.57
832 1463 3.441500 AAAAGAGAAAAGGCCGAGGAT 57.558 42.857 0.00 0.00 0.00 3.24
846 1477 1.673168 GAGGATGAGCAGGCGAAAAT 58.327 50.000 0.00 0.00 0.00 1.82
896 1530 3.064987 CTAGACCAGGTCCACCGCG 62.065 68.421 16.72 0.00 42.08 6.46
900 1534 4.003788 CCAGGTCCACCGCGAAGT 62.004 66.667 8.23 0.00 42.08 3.01
980 1614 2.270850 CCCAAATCTCGCCCGGAA 59.729 61.111 0.73 0.00 0.00 4.30
982 1616 1.376609 CCCAAATCTCGCCCGGAAAG 61.377 60.000 0.73 0.00 0.00 2.62
989 1624 2.202810 CGCCCGGAAAGAGAGAGC 60.203 66.667 0.73 0.00 0.00 4.09
1173 1810 0.463620 GATCTGGACTCTGGAGGTGC 59.536 60.000 2.58 0.00 0.00 5.01
1183 1820 1.572085 CTGGAGGTGCGCTCAGTTTG 61.572 60.000 9.73 0.00 0.00 2.93
1222 1860 1.068741 AGGTTTGATCCGAGCGTATCC 59.931 52.381 0.00 0.00 0.00 2.59
1224 1862 1.116308 TTTGATCCGAGCGTATCCCA 58.884 50.000 0.00 0.00 0.00 4.37
1246 1884 5.391310 CCATGGATCATTAGCGTAATTGCTC 60.391 44.000 5.56 0.00 45.87 4.26
1338 1988 2.347755 GGACGACGACTTTGGAATTAGC 59.652 50.000 0.00 0.00 0.00 3.09
1339 1989 1.990563 ACGACGACTTTGGAATTAGCG 59.009 47.619 0.00 0.00 0.00 4.26
1377 2027 5.818136 ATGATGCGCTAACAACTTTACAT 57.182 34.783 9.73 0.00 0.00 2.29
1379 2029 6.102006 TGATGCGCTAACAACTTTACATAC 57.898 37.500 9.73 0.00 0.00 2.39
1418 2068 0.618458 GCTGGGTGGTGGACTGATTA 59.382 55.000 0.00 0.00 0.00 1.75
1465 2115 4.080919 TGCTAGGTTGAGATGCATTGTACT 60.081 41.667 0.00 0.00 0.00 2.73
1466 2116 5.128663 TGCTAGGTTGAGATGCATTGTACTA 59.871 40.000 0.00 0.00 0.00 1.82
1467 2117 5.463724 GCTAGGTTGAGATGCATTGTACTAC 59.536 44.000 0.00 0.63 0.00 2.73
1468 2118 4.770795 AGGTTGAGATGCATTGTACTACC 58.229 43.478 0.00 9.27 0.00 3.18
1469 2119 4.471386 AGGTTGAGATGCATTGTACTACCT 59.529 41.667 16.52 16.52 0.00 3.08
1470 2120 4.572389 GGTTGAGATGCATTGTACTACCTG 59.428 45.833 0.00 0.00 0.00 4.00
1533 2215 1.141657 TGGGCATGCCTCTTAGATGTC 59.858 52.381 34.70 15.31 36.10 3.06
1563 2245 5.972382 CACTAGGTGTATCTAGTTTTCGAGC 59.028 44.000 2.12 0.00 45.32 5.03
1564 2246 5.651139 ACTAGGTGTATCTAGTTTTCGAGCA 59.349 40.000 0.00 0.00 45.32 4.26
1579 2261 2.957006 TCGAGCAGAAGGGGTATAGAAC 59.043 50.000 0.00 0.00 0.00 3.01
1606 2290 3.620821 GCTCTTGTTGGTTCTCTATGCTC 59.379 47.826 0.00 0.00 0.00 4.26
1614 2298 2.946329 GGTTCTCTATGCTCGAGACTCA 59.054 50.000 18.75 4.98 37.26 3.41
1677 2363 5.283294 ACTATTTTAACGTGTTTGGTTGGC 58.717 37.500 0.00 0.00 0.00 4.52
1679 2365 0.248539 TTAACGTGTTTGGTTGGCGC 60.249 50.000 0.00 0.00 0.00 6.53
1683 2369 2.441164 TGTTTGGTTGGCGCTGGT 60.441 55.556 7.64 0.00 0.00 4.00
1693 2379 2.238942 TGGCGCTGGTCATACATAAG 57.761 50.000 7.64 0.00 0.00 1.73
1808 2494 9.597681 TTTCGACTATAAGGAATTACCCTAGAT 57.402 33.333 0.00 0.00 40.05 1.98
1842 2528 9.688091 TTATCTGCTATTTAACCAAACATGGTA 57.312 29.630 0.12 0.00 42.20 3.25
1984 2670 8.149631 TGATAATGATGGTAGCATCTATTGGA 57.850 34.615 29.49 13.27 33.01 3.53
1993 2679 2.158696 AGCATCTATTGGACTCTTGGCC 60.159 50.000 0.00 0.00 0.00 5.36
2044 2730 5.902613 TTGATAGTTGGAGCAGGATTTTG 57.097 39.130 0.00 0.00 0.00 2.44
2158 2844 9.740710 GACCCTTGGATGCTATTTTATATACTT 57.259 33.333 0.00 0.00 0.00 2.24
2265 2951 5.240403 GGATCCAGATGAGTTCTTATTTGGC 59.760 44.000 6.95 0.00 29.93 4.52
2398 3183 7.010923 GCAAAATGATCCAAACACAACTGTTTA 59.989 33.333 0.00 0.00 46.88 2.01
2428 3213 9.494271 TCTACTCAATTGCCATATGTATTCTTC 57.506 33.333 0.00 0.00 0.00 2.87
2436 3221 8.523915 TTGCCATATGTATTCTTCATGTTCTT 57.476 30.769 1.24 0.00 0.00 2.52
2503 3288 2.096466 TGCTTTGCGTGATGTTCTAACG 60.096 45.455 0.00 0.00 40.22 3.18
2564 3349 9.489084 TCTGGACGTATCCTTGATAAATTAATG 57.511 33.333 0.00 0.00 46.43 1.90
2606 3391 7.751768 ATATATCAAGCCCTTTTACTGCTTC 57.248 36.000 0.00 0.00 43.10 3.86
2647 3432 4.457949 CCTATTTTAACCGCTCCTGTGTTT 59.542 41.667 0.00 0.00 0.00 2.83
2648 3433 3.701532 TTTTAACCGCTCCTGTGTTTG 57.298 42.857 0.00 0.00 0.00 2.93
2649 3434 2.623878 TTAACCGCTCCTGTGTTTGA 57.376 45.000 0.00 0.00 0.00 2.69
2650 3435 2.851263 TAACCGCTCCTGTGTTTGAT 57.149 45.000 0.00 0.00 0.00 2.57
2651 3436 2.851263 AACCGCTCCTGTGTTTGATA 57.149 45.000 0.00 0.00 0.00 2.15
2652 3437 3.350219 AACCGCTCCTGTGTTTGATAT 57.650 42.857 0.00 0.00 0.00 1.63
2653 3438 4.481368 AACCGCTCCTGTGTTTGATATA 57.519 40.909 0.00 0.00 0.00 0.86
2654 3439 4.689612 ACCGCTCCTGTGTTTGATATAT 57.310 40.909 0.00 0.00 0.00 0.86
2712 3497 5.379732 TTGCGTATGATATCGTCCACATA 57.620 39.130 0.00 0.00 0.00 2.29
2722 3507 7.147976 TGATATCGTCCACATATTCTGAGTTG 58.852 38.462 0.00 0.00 0.00 3.16
2723 3508 4.801330 TCGTCCACATATTCTGAGTTGT 57.199 40.909 0.00 0.00 0.00 3.32
2724 3509 4.494484 TCGTCCACATATTCTGAGTTGTG 58.506 43.478 8.75 8.75 39.29 3.33
2725 3510 4.219725 TCGTCCACATATTCTGAGTTGTGA 59.780 41.667 14.43 3.30 41.50 3.58
2726 3511 4.564372 CGTCCACATATTCTGAGTTGTGAG 59.436 45.833 14.43 7.82 41.50 3.51
2727 3512 5.482908 GTCCACATATTCTGAGTTGTGAGT 58.517 41.667 14.43 0.00 41.50 3.41
2728 3513 5.934625 GTCCACATATTCTGAGTTGTGAGTT 59.065 40.000 14.43 0.00 41.50 3.01
2915 3783 1.283793 GTGAACTGCAGCGCAACAT 59.716 52.632 15.27 0.00 38.41 2.71
3151 4019 8.601845 ATTCGGTTAGCTTGCTTTTTAAAAAT 57.398 26.923 13.55 1.13 0.00 1.82
3220 4088 7.116805 CCTTATGTGTTTTTCCAGCTGATTTTC 59.883 37.037 17.39 1.64 0.00 2.29
3292 4160 4.356405 TTTTGAGAGAGAAGCATGACCA 57.644 40.909 0.00 0.00 0.00 4.02
3322 4190 4.764771 TGGGCTCATTGGGCTGGC 62.765 66.667 8.71 0.00 0.00 4.85
3326 4194 1.547472 GGCTCATTGGGCTGGCTTTT 61.547 55.000 8.71 0.00 0.00 2.27
3394 4262 1.333177 TCCAAAACCCAATTCCCACG 58.667 50.000 0.00 0.00 0.00 4.94
3397 4265 1.899142 CAAAACCCAATTCCCACGGAT 59.101 47.619 0.00 0.00 0.00 4.18
3406 4274 1.043116 TTCCCACGGATCATCGCTCT 61.043 55.000 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.531149 CCGAACAAACACCACTGCTAG 59.469 52.381 0.00 0.00 0.00 3.42
17 18 0.393808 ACCGAACAAACACCACTGCT 60.394 50.000 0.00 0.00 0.00 4.24
19 20 0.380378 CCACCGAACAAACACCACTG 59.620 55.000 0.00 0.00 0.00 3.66
21 22 0.099791 CACCACCGAACAAACACCAC 59.900 55.000 0.00 0.00 0.00 4.16
27 28 3.576982 AGATCTCTACACCACCGAACAAA 59.423 43.478 0.00 0.00 0.00 2.83
32 33 1.283905 TCCAGATCTCTACACCACCGA 59.716 52.381 0.00 0.00 0.00 4.69
175 177 8.561738 TCTAGAGTTTTTATCAATGGTTCACC 57.438 34.615 0.00 0.00 0.00 4.02
190 192 4.696040 AGGGAGGTACCTCTAGAGTTTT 57.304 45.455 35.12 13.43 42.38 2.43
194 196 3.328637 GTCCTAGGGAGGTACCTCTAGAG 59.671 56.522 35.12 27.24 44.19 2.43
196 198 3.054576 TGTCCTAGGGAGGTACCTCTAG 58.945 54.545 35.12 28.33 44.19 2.43
209 211 4.644685 CCAACCCACATTAATTGTCCTAGG 59.355 45.833 0.82 0.82 36.00 3.02
210 212 5.505780 TCCAACCCACATTAATTGTCCTAG 58.494 41.667 0.00 0.00 36.00 3.02
219 221 6.451292 TTTACTACCTCCAACCCACATTAA 57.549 37.500 0.00 0.00 0.00 1.40
254 256 8.715088 GCAGAGTAAATAAAAACGGAGAAAGTA 58.285 33.333 0.00 0.00 0.00 2.24
255 257 7.227910 TGCAGAGTAAATAAAAACGGAGAAAGT 59.772 33.333 0.00 0.00 0.00 2.66
256 258 7.581476 TGCAGAGTAAATAAAAACGGAGAAAG 58.419 34.615 0.00 0.00 0.00 2.62
257 259 7.499321 TGCAGAGTAAATAAAAACGGAGAAA 57.501 32.000 0.00 0.00 0.00 2.52
258 260 7.681939 ATGCAGAGTAAATAAAAACGGAGAA 57.318 32.000 0.00 0.00 0.00 2.87
259 261 8.958119 ATATGCAGAGTAAATAAAAACGGAGA 57.042 30.769 0.00 0.00 0.00 3.71
270 272 9.686683 AGGTCAAAACTAATATGCAGAGTAAAT 57.313 29.630 0.00 0.00 0.00 1.40
273 275 9.817809 CTTAGGTCAAAACTAATATGCAGAGTA 57.182 33.333 0.00 0.00 30.69 2.59
274 276 8.322091 ACTTAGGTCAAAACTAATATGCAGAGT 58.678 33.333 0.00 0.00 30.69 3.24
275 277 8.723942 ACTTAGGTCAAAACTAATATGCAGAG 57.276 34.615 0.00 0.00 30.69 3.35
276 278 8.718102 GACTTAGGTCAAAACTAATATGCAGA 57.282 34.615 0.00 0.00 41.75 4.26
331 333 9.250986 CTATTGTGAAAGTTTAGATCGTTTTCG 57.749 33.333 0.00 0.00 45.64 3.46
332 334 9.052080 GCTATTGTGAAAGTTTAGATCGTTTTC 57.948 33.333 0.00 0.00 0.00 2.29
333 335 8.564574 TGCTATTGTGAAAGTTTAGATCGTTTT 58.435 29.630 0.00 0.00 0.00 2.43
334 336 8.094798 TGCTATTGTGAAAGTTTAGATCGTTT 57.905 30.769 0.00 0.00 0.00 3.60
335 337 7.667043 TGCTATTGTGAAAGTTTAGATCGTT 57.333 32.000 0.00 0.00 0.00 3.85
336 338 7.667043 TTGCTATTGTGAAAGTTTAGATCGT 57.333 32.000 0.00 0.00 0.00 3.73
384 386 9.645128 ACCAAATCAATACCATTAGAATCATCA 57.355 29.630 0.00 0.00 0.00 3.07
391 393 9.130661 CCACAATACCAAATCAATACCATTAGA 57.869 33.333 0.00 0.00 0.00 2.10
392 394 9.130661 TCCACAATACCAAATCAATACCATTAG 57.869 33.333 0.00 0.00 0.00 1.73
393 395 9.653516 ATCCACAATACCAAATCAATACCATTA 57.346 29.630 0.00 0.00 0.00 1.90
394 396 7.969690 TCCACAATACCAAATCAATACCATT 57.030 32.000 0.00 0.00 0.00 3.16
395 397 7.564660 ACATCCACAATACCAAATCAATACCAT 59.435 33.333 0.00 0.00 0.00 3.55
396 398 6.894654 ACATCCACAATACCAAATCAATACCA 59.105 34.615 0.00 0.00 0.00 3.25
397 399 7.346751 ACATCCACAATACCAAATCAATACC 57.653 36.000 0.00 0.00 0.00 2.73
446 448 4.034048 GCTTTGTCTCGAGTCAAACTTTGA 59.966 41.667 26.74 11.45 37.33 2.69
447 449 4.034510 AGCTTTGTCTCGAGTCAAACTTTG 59.965 41.667 26.74 19.77 31.74 2.77
448 450 4.192317 AGCTTTGTCTCGAGTCAAACTTT 58.808 39.130 26.74 15.58 31.74 2.66
449 451 3.798202 AGCTTTGTCTCGAGTCAAACTT 58.202 40.909 26.74 17.50 31.74 2.66
450 452 3.460857 AGCTTTGTCTCGAGTCAAACT 57.539 42.857 26.74 23.87 31.74 2.66
451 453 5.847670 ATTAGCTTTGTCTCGAGTCAAAC 57.152 39.130 26.74 22.56 31.74 2.93
452 454 6.036083 GCATATTAGCTTTGTCTCGAGTCAAA 59.964 38.462 27.91 27.91 33.44 2.69
453 455 5.520288 GCATATTAGCTTTGTCTCGAGTCAA 59.480 40.000 19.08 19.08 0.00 3.18
454 456 5.043903 GCATATTAGCTTTGTCTCGAGTCA 58.956 41.667 13.13 10.62 0.00 3.41
455 457 4.147306 CGCATATTAGCTTTGTCTCGAGTC 59.853 45.833 13.13 7.62 0.00 3.36
456 458 4.045104 CGCATATTAGCTTTGTCTCGAGT 58.955 43.478 13.13 0.00 0.00 4.18
457 459 4.290969 TCGCATATTAGCTTTGTCTCGAG 58.709 43.478 5.93 5.93 0.00 4.04
458 460 4.301637 TCGCATATTAGCTTTGTCTCGA 57.698 40.909 0.00 0.00 0.00 4.04
459 461 4.504461 ACTTCGCATATTAGCTTTGTCTCG 59.496 41.667 0.00 0.00 0.00 4.04
460 462 5.975410 ACTTCGCATATTAGCTTTGTCTC 57.025 39.130 0.00 0.00 0.00 3.36
461 463 7.843490 TTTACTTCGCATATTAGCTTTGTCT 57.157 32.000 0.00 0.00 0.00 3.41
467 469 9.646336 CGTTTTTATTTACTTCGCATATTAGCT 57.354 29.630 0.00 0.00 0.00 3.32
468 470 9.429600 ACGTTTTTATTTACTTCGCATATTAGC 57.570 29.630 0.00 0.00 0.00 3.09
471 473 9.925268 CCTACGTTTTTATTTACTTCGCATATT 57.075 29.630 0.00 0.00 0.00 1.28
472 474 8.553696 CCCTACGTTTTTATTTACTTCGCATAT 58.446 33.333 0.00 0.00 0.00 1.78
473 475 7.763528 TCCCTACGTTTTTATTTACTTCGCATA 59.236 33.333 0.00 0.00 0.00 3.14
474 476 6.594937 TCCCTACGTTTTTATTTACTTCGCAT 59.405 34.615 0.00 0.00 0.00 4.73
475 477 5.931146 TCCCTACGTTTTTATTTACTTCGCA 59.069 36.000 0.00 0.00 0.00 5.10
476 478 6.091305 ACTCCCTACGTTTTTATTTACTTCGC 59.909 38.462 0.00 0.00 0.00 4.70
477 479 7.586714 ACTCCCTACGTTTTTATTTACTTCG 57.413 36.000 0.00 0.00 0.00 3.79
478 480 9.423061 TGTACTCCCTACGTTTTTATTTACTTC 57.577 33.333 0.00 0.00 0.00 3.01
479 481 9.777297 TTGTACTCCCTACGTTTTTATTTACTT 57.223 29.630 0.00 0.00 0.00 2.24
480 482 9.208022 GTTGTACTCCCTACGTTTTTATTTACT 57.792 33.333 0.00 0.00 0.00 2.24
481 483 9.208022 AGTTGTACTCCCTACGTTTTTATTTAC 57.792 33.333 0.00 0.00 0.00 2.01
482 484 9.423061 GAGTTGTACTCCCTACGTTTTTATTTA 57.577 33.333 0.00 0.00 39.28 1.40
483 485 8.152898 AGAGTTGTACTCCCTACGTTTTTATTT 58.847 33.333 0.00 0.00 46.18 1.40
484 486 7.674120 AGAGTTGTACTCCCTACGTTTTTATT 58.326 34.615 0.00 0.00 46.18 1.40
485 487 7.237209 AGAGTTGTACTCCCTACGTTTTTAT 57.763 36.000 0.00 0.00 46.18 1.40
486 488 6.655078 AGAGTTGTACTCCCTACGTTTTTA 57.345 37.500 0.00 0.00 46.18 1.52
487 489 5.541953 AGAGTTGTACTCCCTACGTTTTT 57.458 39.130 0.00 0.00 46.18 1.94
488 490 5.336293 GCTAGAGTTGTACTCCCTACGTTTT 60.336 44.000 0.00 0.00 46.18 2.43
489 491 4.157472 GCTAGAGTTGTACTCCCTACGTTT 59.843 45.833 0.00 0.00 46.18 3.60
490 492 3.693578 GCTAGAGTTGTACTCCCTACGTT 59.306 47.826 0.00 0.00 46.18 3.99
491 493 3.054508 AGCTAGAGTTGTACTCCCTACGT 60.055 47.826 0.00 0.00 46.18 3.57
492 494 3.543665 AGCTAGAGTTGTACTCCCTACG 58.456 50.000 0.00 0.00 46.18 3.51
493 495 6.376581 TGTTTAGCTAGAGTTGTACTCCCTAC 59.623 42.308 0.00 0.00 46.18 3.18
494 496 6.487828 TGTTTAGCTAGAGTTGTACTCCCTA 58.512 40.000 0.00 0.75 46.18 3.53
495 497 5.331069 TGTTTAGCTAGAGTTGTACTCCCT 58.669 41.667 0.00 1.56 46.18 4.20
496 498 5.418209 TCTGTTTAGCTAGAGTTGTACTCCC 59.582 44.000 0.00 0.00 46.18 4.30
497 499 6.512342 TCTGTTTAGCTAGAGTTGTACTCC 57.488 41.667 0.00 0.00 46.18 3.85
498 500 9.887406 GATATCTGTTTAGCTAGAGTTGTACTC 57.113 37.037 0.00 0.00 45.38 2.59
499 501 8.852135 GGATATCTGTTTAGCTAGAGTTGTACT 58.148 37.037 2.05 0.00 0.00 2.73
500 502 8.083462 GGGATATCTGTTTAGCTAGAGTTGTAC 58.917 40.741 2.05 0.00 0.00 2.90
506 508 6.013379 TGAGGGGATATCTGTTTAGCTAGAG 58.987 44.000 2.05 0.00 0.00 2.43
557 561 0.390124 AGTGCGTTTCGGGACAAGTA 59.610 50.000 0.00 0.00 0.00 2.24
563 567 2.459060 TATCAAAGTGCGTTTCGGGA 57.541 45.000 0.00 0.00 0.00 5.14
564 568 3.488489 CTTTATCAAAGTGCGTTTCGGG 58.512 45.455 0.00 0.00 33.80 5.14
676 1307 8.973378 GCTCTGTATGTAGTCTGTATTGAAATC 58.027 37.037 0.00 0.00 0.00 2.17
677 1308 8.478066 TGCTCTGTATGTAGTCTGTATTGAAAT 58.522 33.333 0.00 0.00 0.00 2.17
678 1309 7.836842 TGCTCTGTATGTAGTCTGTATTGAAA 58.163 34.615 0.00 0.00 0.00 2.69
679 1310 7.404671 TGCTCTGTATGTAGTCTGTATTGAA 57.595 36.000 0.00 0.00 0.00 2.69
680 1311 7.404671 TTGCTCTGTATGTAGTCTGTATTGA 57.595 36.000 0.00 0.00 0.00 2.57
681 1312 8.479313 TTTTGCTCTGTATGTAGTCTGTATTG 57.521 34.615 0.00 0.00 0.00 1.90
682 1313 9.102757 CATTTTGCTCTGTATGTAGTCTGTATT 57.897 33.333 0.00 0.00 0.00 1.89
683 1314 7.712639 CCATTTTGCTCTGTATGTAGTCTGTAT 59.287 37.037 0.00 0.00 0.00 2.29
684 1315 7.041721 CCATTTTGCTCTGTATGTAGTCTGTA 58.958 38.462 0.00 0.00 0.00 2.74
685 1316 5.877012 CCATTTTGCTCTGTATGTAGTCTGT 59.123 40.000 0.00 0.00 0.00 3.41
686 1317 5.295292 CCCATTTTGCTCTGTATGTAGTCTG 59.705 44.000 0.00 0.00 0.00 3.51
687 1318 5.045578 ACCCATTTTGCTCTGTATGTAGTCT 60.046 40.000 0.00 0.00 0.00 3.24
688 1319 5.186198 ACCCATTTTGCTCTGTATGTAGTC 58.814 41.667 0.00 0.00 0.00 2.59
689 1320 5.179452 ACCCATTTTGCTCTGTATGTAGT 57.821 39.130 0.00 0.00 0.00 2.73
690 1321 7.624360 TTTACCCATTTTGCTCTGTATGTAG 57.376 36.000 0.00 0.00 0.00 2.74
691 1322 8.052748 AGATTTACCCATTTTGCTCTGTATGTA 58.947 33.333 0.00 0.00 0.00 2.29
692 1323 6.891908 AGATTTACCCATTTTGCTCTGTATGT 59.108 34.615 0.00 0.00 0.00 2.29
693 1324 7.338800 AGATTTACCCATTTTGCTCTGTATG 57.661 36.000 0.00 0.00 0.00 2.39
694 1325 9.474313 TTTAGATTTACCCATTTTGCTCTGTAT 57.526 29.630 0.00 0.00 0.00 2.29
695 1326 8.871629 TTTAGATTTACCCATTTTGCTCTGTA 57.128 30.769 0.00 0.00 0.00 2.74
696 1327 7.775053 TTTAGATTTACCCATTTTGCTCTGT 57.225 32.000 0.00 0.00 0.00 3.41
707 1338 9.403583 GTCTTGGACATATTTTAGATTTACCCA 57.596 33.333 0.00 0.00 32.09 4.51
708 1339 9.628500 AGTCTTGGACATATTTTAGATTTACCC 57.372 33.333 0.52 0.00 34.60 3.69
722 1353 9.431887 GTTTCTACATACAAAGTCTTGGACATA 57.568 33.333 0.00 0.00 36.82 2.29
723 1354 7.117812 CGTTTCTACATACAAAGTCTTGGACAT 59.882 37.037 0.00 0.00 36.82 3.06
724 1355 6.422701 CGTTTCTACATACAAAGTCTTGGACA 59.577 38.462 0.00 0.00 36.82 4.02
725 1356 6.128634 CCGTTTCTACATACAAAGTCTTGGAC 60.129 42.308 0.00 0.00 36.82 4.02
726 1357 5.929992 CCGTTTCTACATACAAAGTCTTGGA 59.070 40.000 0.00 0.00 36.82 3.53
727 1358 5.929992 TCCGTTTCTACATACAAAGTCTTGG 59.070 40.000 0.00 0.00 36.82 3.61
728 1359 6.090898 CCTCCGTTTCTACATACAAAGTCTTG 59.909 42.308 0.00 0.00 38.61 3.02
729 1360 6.164176 CCTCCGTTTCTACATACAAAGTCTT 58.836 40.000 0.00 0.00 0.00 3.01
730 1361 5.337330 CCCTCCGTTTCTACATACAAAGTCT 60.337 44.000 0.00 0.00 0.00 3.24
731 1362 4.868734 CCCTCCGTTTCTACATACAAAGTC 59.131 45.833 0.00 0.00 0.00 3.01
732 1363 4.529377 TCCCTCCGTTTCTACATACAAAGT 59.471 41.667 0.00 0.00 0.00 2.66
733 1364 5.080969 TCCCTCCGTTTCTACATACAAAG 57.919 43.478 0.00 0.00 0.00 2.77
734 1365 4.529377 ACTCCCTCCGTTTCTACATACAAA 59.471 41.667 0.00 0.00 0.00 2.83
735 1366 4.091549 ACTCCCTCCGTTTCTACATACAA 58.908 43.478 0.00 0.00 0.00 2.41
736 1367 3.705051 ACTCCCTCCGTTTCTACATACA 58.295 45.455 0.00 0.00 0.00 2.29
737 1368 4.159135 TCAACTCCCTCCGTTTCTACATAC 59.841 45.833 0.00 0.00 0.00 2.39
738 1369 4.159135 GTCAACTCCCTCCGTTTCTACATA 59.841 45.833 0.00 0.00 0.00 2.29
739 1370 3.056035 GTCAACTCCCTCCGTTTCTACAT 60.056 47.826 0.00 0.00 0.00 2.29
740 1371 2.298163 GTCAACTCCCTCCGTTTCTACA 59.702 50.000 0.00 0.00 0.00 2.74
741 1372 2.670509 CGTCAACTCCCTCCGTTTCTAC 60.671 54.545 0.00 0.00 0.00 2.59
742 1373 1.542915 CGTCAACTCCCTCCGTTTCTA 59.457 52.381 0.00 0.00 0.00 2.10
743 1374 0.317479 CGTCAACTCCCTCCGTTTCT 59.683 55.000 0.00 0.00 0.00 2.52
744 1375 0.316204 TCGTCAACTCCCTCCGTTTC 59.684 55.000 0.00 0.00 0.00 2.78
745 1376 0.974383 ATCGTCAACTCCCTCCGTTT 59.026 50.000 0.00 0.00 0.00 3.60
746 1377 1.749634 CTATCGTCAACTCCCTCCGTT 59.250 52.381 0.00 0.00 0.00 4.44
747 1378 1.390565 CTATCGTCAACTCCCTCCGT 58.609 55.000 0.00 0.00 0.00 4.69
748 1379 0.669077 CCTATCGTCAACTCCCTCCG 59.331 60.000 0.00 0.00 0.00 4.63
749 1380 2.068834 TCCTATCGTCAACTCCCTCC 57.931 55.000 0.00 0.00 0.00 4.30
750 1381 4.501743 GGAAATCCTATCGTCAACTCCCTC 60.502 50.000 0.00 0.00 0.00 4.30
751 1382 3.388350 GGAAATCCTATCGTCAACTCCCT 59.612 47.826 0.00 0.00 0.00 4.20
752 1383 3.388350 AGGAAATCCTATCGTCAACTCCC 59.612 47.826 0.00 0.00 46.48 4.30
753 1384 4.674281 AGGAAATCCTATCGTCAACTCC 57.326 45.455 0.00 0.00 46.48 3.85
801 1432 6.015940 GGCCTTTTCTCTTTTTCAGATTCAGA 60.016 38.462 0.00 0.00 0.00 3.27
802 1433 6.155136 GGCCTTTTCTCTTTTTCAGATTCAG 58.845 40.000 0.00 0.00 0.00 3.02
805 1436 4.827284 TCGGCCTTTTCTCTTTTTCAGATT 59.173 37.500 0.00 0.00 0.00 2.40
806 1437 4.398319 TCGGCCTTTTCTCTTTTTCAGAT 58.602 39.130 0.00 0.00 0.00 2.90
807 1438 3.815401 CTCGGCCTTTTCTCTTTTTCAGA 59.185 43.478 0.00 0.00 0.00 3.27
832 1463 0.393808 GGGGTATTTTCGCCTGCTCA 60.394 55.000 0.00 0.00 37.44 4.26
846 1477 1.574339 CTGAGGGAGGTCTTAGGGGTA 59.426 57.143 0.00 0.00 0.00 3.69
896 1530 1.302271 GACGGGGTTGGGTCACTTC 60.302 63.158 0.00 0.00 33.41 3.01
1197 1835 0.250513 GCTCGGATCAAACCTGGACT 59.749 55.000 0.00 0.00 0.00 3.85
1200 1838 0.174845 TACGCTCGGATCAAACCTGG 59.825 55.000 0.00 0.00 0.00 4.45
1222 1860 4.456911 AGCAATTACGCTAATGATCCATGG 59.543 41.667 4.97 4.97 41.55 3.66
1224 1862 4.389992 CGAGCAATTACGCTAATGATCCAT 59.610 41.667 0.00 0.00 44.01 3.41
1303 1953 0.690192 TCGTCCCCTTGCTCAATCAA 59.310 50.000 0.00 0.00 0.00 2.57
1304 1954 0.036388 GTCGTCCCCTTGCTCAATCA 60.036 55.000 0.00 0.00 0.00 2.57
1305 1955 1.084370 CGTCGTCCCCTTGCTCAATC 61.084 60.000 0.00 0.00 0.00 2.67
1306 1956 1.079127 CGTCGTCCCCTTGCTCAAT 60.079 57.895 0.00 0.00 0.00 2.57
1338 1988 3.887621 TCATAGTTCCAGGAGAAACCG 57.112 47.619 0.00 0.00 44.74 4.44
1339 1989 3.879892 GCATCATAGTTCCAGGAGAAACC 59.120 47.826 0.00 0.00 35.85 3.27
1377 2027 5.007682 GCTACCAAAGGTTCCAATTCAGTA 58.992 41.667 0.00 0.00 37.09 2.74
1379 2029 4.082125 AGCTACCAAAGGTTCCAATTCAG 58.918 43.478 0.00 0.00 37.09 3.02
1418 2068 7.388776 GCAGGAAAATCTAAGCAAATCCTTTTT 59.611 33.333 0.00 0.00 33.68 1.94
1465 2115 0.041238 CCAGTCCAGACTCCCAGGTA 59.959 60.000 0.00 0.00 40.20 3.08
1466 2116 1.229336 CCAGTCCAGACTCCCAGGT 60.229 63.158 0.00 0.00 40.20 4.00
1467 2117 1.992277 CCCAGTCCAGACTCCCAGG 60.992 68.421 0.00 0.00 40.20 4.45
1468 2118 1.992277 CCCCAGTCCAGACTCCCAG 60.992 68.421 0.00 0.00 40.20 4.45
1469 2119 2.122729 CCCCAGTCCAGACTCCCA 59.877 66.667 0.00 0.00 40.20 4.37
1470 2120 2.689034 CCCCCAGTCCAGACTCCC 60.689 72.222 0.00 0.00 40.20 4.30
1563 2245 4.346418 AGCATCAGTTCTATACCCCTTCTG 59.654 45.833 0.00 0.00 0.00 3.02
1564 2246 4.561752 AGCATCAGTTCTATACCCCTTCT 58.438 43.478 0.00 0.00 0.00 2.85
1579 2261 3.672808 AGAGAACCAACAAGAGCATCAG 58.327 45.455 0.00 0.00 37.82 2.90
1606 2290 4.052159 ACAGCTTTCCATATGAGTCTCG 57.948 45.455 3.65 0.00 0.00 4.04
1614 2298 7.944729 ACATTGTCTAAACAGCTTTCCATAT 57.055 32.000 0.00 0.00 36.57 1.78
1665 2351 2.027460 CCAGCGCCAACCAAACAC 59.973 61.111 2.29 0.00 0.00 3.32
1677 2363 4.933330 ACAGTACTTATGTATGACCAGCG 58.067 43.478 0.00 0.00 0.00 5.18
1679 2365 9.947669 GTTACTACAGTACTTATGTATGACCAG 57.052 37.037 0.00 0.00 32.91 4.00
1716 2402 7.984422 ATCATCACACAGAAAACAATCAGTA 57.016 32.000 0.00 0.00 0.00 2.74
1808 2494 6.596106 TGGTTAAATAGCAGATAAGCGAAACA 59.404 34.615 0.00 0.00 40.15 2.83
1813 2499 6.781138 TGTTTGGTTAAATAGCAGATAAGCG 58.219 36.000 0.00 0.00 40.15 4.68
1984 2670 2.736670 ACTTTGACTTGGCCAAGAGT 57.263 45.000 44.50 33.93 40.79 3.24
1993 2679 4.034510 GTGTGGACTGAGAACTTTGACTTG 59.965 45.833 0.00 0.00 0.00 3.16
2044 2730 1.574702 CGGCCAAAACTCCTTCGACC 61.575 60.000 2.24 0.00 0.00 4.79
2114 2800 7.299586 CAAGGGTCAAAATGTTTATGCATTTG 58.700 34.615 3.54 2.05 45.17 2.32
2117 2803 5.248020 TCCAAGGGTCAAAATGTTTATGCAT 59.752 36.000 3.79 3.79 0.00 3.96
2189 2875 9.836076 ATTAATTTAGACTAAAACCAAAGACGC 57.164 29.630 11.57 0.00 0.00 5.19
2347 3033 9.884465 GCAACATCTATCAAAGGACATATAAAC 57.116 33.333 0.00 0.00 0.00 2.01
2348 3034 9.625747 TGCAACATCTATCAAAGGACATATAAA 57.374 29.630 0.00 0.00 0.00 1.40
2351 3037 8.523915 TTTGCAACATCTATCAAAGGACATAT 57.476 30.769 0.00 0.00 0.00 1.78
2472 3257 1.717645 CACGCAAAGCAAAAGCTCATC 59.282 47.619 0.00 0.00 0.00 2.92
2503 3288 6.258507 AGGACTGCAAATGAAAAATTCACAAC 59.741 34.615 0.00 0.00 43.48 3.32
2606 3391 1.345715 GGATGGGGGTGGGTACAGAG 61.346 65.000 0.00 0.00 0.00 3.35
2676 3461 5.242434 TCATACGCAAATCTGGTAAGTGTT 58.758 37.500 0.00 0.00 0.00 3.32
2712 3497 5.012458 TCCATCAGAACTCACAACTCAGAAT 59.988 40.000 0.00 0.00 0.00 2.40
2722 3507 3.513515 ACTCTCCTTCCATCAGAACTCAC 59.486 47.826 0.00 0.00 0.00 3.51
2723 3508 3.766591 GACTCTCCTTCCATCAGAACTCA 59.233 47.826 0.00 0.00 0.00 3.41
2724 3509 4.023291 AGACTCTCCTTCCATCAGAACTC 58.977 47.826 0.00 0.00 0.00 3.01
2725 3510 3.768757 CAGACTCTCCTTCCATCAGAACT 59.231 47.826 0.00 0.00 0.00 3.01
2726 3511 3.766591 TCAGACTCTCCTTCCATCAGAAC 59.233 47.826 0.00 0.00 0.00 3.01
2727 3512 4.053009 TCAGACTCTCCTTCCATCAGAA 57.947 45.455 0.00 0.00 0.00 3.02
2728 3513 3.746792 TCAGACTCTCCTTCCATCAGA 57.253 47.619 0.00 0.00 0.00 3.27
2778 3563 0.548031 TCATCTGACATTGGCTCCCC 59.452 55.000 0.00 0.00 0.00 4.81
2779 3564 2.019984 GTTCATCTGACATTGGCTCCC 58.980 52.381 0.00 0.00 0.00 4.30
2785 3570 4.713824 ATGCTTGGTTCATCTGACATTG 57.286 40.909 0.00 0.00 0.00 2.82
2907 3775 3.354089 AGGCATATACAAATGTTGCGC 57.646 42.857 0.00 0.00 0.00 6.09
3194 4062 5.649782 ATCAGCTGGAAAAACACATAAGG 57.350 39.130 15.13 0.00 0.00 2.69
3195 4063 7.652909 TGAAAATCAGCTGGAAAAACACATAAG 59.347 33.333 15.13 0.00 0.00 1.73
3196 4064 7.495901 TGAAAATCAGCTGGAAAAACACATAA 58.504 30.769 15.13 0.00 0.00 1.90
3198 4066 5.916318 TGAAAATCAGCTGGAAAAACACAT 58.084 33.333 15.13 0.00 0.00 3.21
3199 4067 5.336150 TGAAAATCAGCTGGAAAAACACA 57.664 34.783 15.13 2.10 0.00 3.72
3200 4068 6.479660 TCAATGAAAATCAGCTGGAAAAACAC 59.520 34.615 15.13 0.00 0.00 3.32
3201 4069 6.580788 TCAATGAAAATCAGCTGGAAAAACA 58.419 32.000 15.13 8.22 0.00 2.83
3202 4070 7.662604 ATCAATGAAAATCAGCTGGAAAAAC 57.337 32.000 15.13 2.55 0.00 2.43
3203 4071 8.680039 AAATCAATGAAAATCAGCTGGAAAAA 57.320 26.923 15.13 0.00 0.00 1.94
3241 4109 9.512588 AAAGCAGCAGTAGCATATAATCTAAAT 57.487 29.630 0.00 0.00 45.49 1.40
3254 4122 6.381801 TCTCAAAAATTAAAGCAGCAGTAGC 58.618 36.000 0.00 0.00 42.56 3.58
3292 4160 3.719268 TGAGCCCACTATGTTTCATGT 57.281 42.857 0.00 0.00 0.00 3.21
3304 4172 2.757099 CCAGCCCAATGAGCCCAC 60.757 66.667 0.00 0.00 0.00 4.61
3322 4190 6.043243 TCTGGACTTAGGCCCATATAGAAAAG 59.957 42.308 0.00 0.00 0.00 2.27
3326 4194 4.759793 TCTGGACTTAGGCCCATATAGA 57.240 45.455 0.00 0.00 0.00 1.98
3394 4262 0.599728 GCCAGTGAGAGCGATGATCC 60.600 60.000 0.00 0.00 0.00 3.36
3397 4265 2.725312 GGGCCAGTGAGAGCGATGA 61.725 63.158 4.39 0.00 0.00 2.92
3406 4274 2.409984 TAGGGTTCTGGGGCCAGTGA 62.410 60.000 4.39 0.00 43.96 3.41


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

AutoCloner maintained by Alex Coulton.