Multiple sequence alignment - TraesCS3A01G198000

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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 TraesCS3A01G198000 chr3A 100.000 5557 0 0 1 5557 312259492 312253936 0.000000e+00 10262.0
1 TraesCS3A01G198000 chr3A 94.564 2189 111 8 2402 4588 299367062 299369244 0.000000e+00 3376.0
2 TraesCS3A01G198000 chr3A 94.521 2190 110 10 2402 4588 299413365 299415547 0.000000e+00 3371.0
3 TraesCS3A01G198000 chr3A 90.943 1877 127 24 557 2403 299365135 299366998 0.000000e+00 2484.0
4 TraesCS3A01G198000 chr3A 90.890 1877 128 24 557 2403 299411438 299413301 0.000000e+00 2479.0
5 TraesCS3A01G198000 chr3A 94.129 1567 76 9 850 2403 550671108 550669545 0.000000e+00 2370.0
6 TraesCS3A01G198000 chr3A 88.889 567 40 7 456 1000 410045192 410044627 0.000000e+00 676.0
7 TraesCS3A01G198000 chr3A 78.552 359 48 13 289 637 245301055 245301394 5.640000e-50 209.0
8 TraesCS3A01G198000 chr3A 90.968 155 12 1 273 425 410045339 410045185 2.030000e-49 207.0
9 TraesCS3A01G198000 chr3A 91.391 151 13 0 3 153 410045733 410045583 2.030000e-49 207.0
10 TraesCS3A01G198000 chr3A 97.436 117 3 0 158 274 312259220 312259104 3.400000e-47 200.0
11 TraesCS3A01G198000 chr3A 97.436 117 3 0 273 389 312259335 312259219 3.400000e-47 200.0
12 TraesCS3A01G198000 chr3A 92.000 125 8 1 152 274 410045345 410045221 2.060000e-39 174.0
13 TraesCS3A01G198000 chr3A 82.278 158 16 9 4647 4795 144039902 144039748 5.840000e-25 126.0
14 TraesCS3A01G198000 chr3A 90.164 61 4 2 4737 4796 264141077 264141018 1.660000e-10 78.7
15 TraesCS3A01G198000 chr4A 89.269 3187 288 35 2402 5556 327032731 327029567 0.000000e+00 3941.0
16 TraesCS3A01G198000 chr4A 88.437 2309 216 28 2402 4697 548068426 548066156 0.000000e+00 2737.0
17 TraesCS3A01G198000 chr4A 89.246 809 70 11 4760 5557 109516196 109516998 0.000000e+00 996.0
18 TraesCS3A01G198000 chr6D 89.171 3186 247 43 2402 5557 192177161 192174044 0.000000e+00 3882.0
19 TraesCS3A01G198000 chr6D 92.119 2411 155 19 2402 4795 30038602 30036210 0.000000e+00 3367.0
20 TraesCS3A01G198000 chr6D 92.880 1573 94 11 844 2401 30040237 30038668 0.000000e+00 2268.0
21 TraesCS3A01G198000 chr6D 93.537 851 39 6 4718 5557 30036382 30035537 0.000000e+00 1253.0
22 TraesCS3A01G198000 chr6D 81.572 369 56 9 274 633 302688365 302688730 1.510000e-75 294.0
23 TraesCS3A01G198000 chr5A 88.955 3187 287 39 2402 5557 67811076 67814228 0.000000e+00 3875.0
24 TraesCS3A01G198000 chr5A 89.806 1962 152 32 478 2403 67809063 67811012 0.000000e+00 2471.0
25 TraesCS3A01G198000 chrUn 88.277 2414 245 23 2402 4796 284016664 284019058 0.000000e+00 2856.0
26 TraesCS3A01G198000 chrUn 89.144 2091 210 11 2402 4486 343664471 343662392 0.000000e+00 2588.0
27 TraesCS3A01G198000 chrUn 88.082 923 89 16 4651 5557 55650558 55649641 0.000000e+00 1075.0
28 TraesCS3A01G198000 chrUn 89.246 809 71 11 4760 5557 284018975 284019778 0.000000e+00 998.0
29 TraesCS3A01G198000 chrUn 83.007 153 21 4 4647 4795 55650464 55650313 3.490000e-27 134.0
30 TraesCS3A01G198000 chr2A 91.143 1829 114 36 615 2403 58206210 58204390 0.000000e+00 2436.0
31 TraesCS3A01G198000 chr2A 78.873 284 31 22 4647 4913 481280021 481280292 1.240000e-36 165.0
32 TraesCS3A01G198000 chr7A 93.106 1668 98 10 751 2403 647034499 647036164 0.000000e+00 2427.0
33 TraesCS3A01G198000 chr7A 93.015 272 17 1 273 542 647033405 647033676 4.030000e-106 396.0
34 TraesCS3A01G198000 chr7A 91.096 146 11 1 131 274 647033378 647033523 4.390000e-46 196.0
35 TraesCS3A01G198000 chr7A 92.366 131 10 0 3 133 647027634 647027764 2.640000e-43 187.0
36 TraesCS3A01G198000 chr6B 89.269 1929 169 25 499 2401 513259775 513261691 0.000000e+00 2381.0
37 TraesCS3A01G198000 chr6B 90.181 1660 135 14 756 2403 107136637 107134994 0.000000e+00 2137.0
38 TraesCS3A01G198000 chr3B 88.925 921 75 15 4647 5557 379317105 379318008 0.000000e+00 1110.0
39 TraesCS3A01G198000 chr3B 89.651 860 67 13 4713 5557 734461640 734462492 0.000000e+00 1075.0
40 TraesCS3A01G198000 chr7B 88.875 809 72 12 4760 5557 258334233 258333432 0.000000e+00 979.0
41 TraesCS3A01G198000 chr7D 80.429 373 53 9 274 637 181831962 181832323 3.300000e-67 267.0
42 TraesCS3A01G198000 chr2B 83.392 283 31 6 1 269 137884402 137884122 1.200000e-61 248.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G198000 chr3A 312253936 312259492 5556 True 3554.000000 10262 98.290667 1 5557 3 chr3A.!!$R4 5556
1 TraesCS3A01G198000 chr3A 299365135 299369244 4109 False 2930.000000 3376 92.753500 557 4588 2 chr3A.!!$F2 4031
2 TraesCS3A01G198000 chr3A 299411438 299415547 4109 False 2925.000000 3371 92.705500 557 4588 2 chr3A.!!$F3 4031
3 TraesCS3A01G198000 chr3A 550669545 550671108 1563 True 2370.000000 2370 94.129000 850 2403 1 chr3A.!!$R3 1553
4 TraesCS3A01G198000 chr3A 410044627 410045733 1106 True 316.000000 676 90.812000 3 1000 4 chr3A.!!$R5 997
5 TraesCS3A01G198000 chr4A 327029567 327032731 3164 True 3941.000000 3941 89.269000 2402 5556 1 chr4A.!!$R1 3154
6 TraesCS3A01G198000 chr4A 548066156 548068426 2270 True 2737.000000 2737 88.437000 2402 4697 1 chr4A.!!$R2 2295
7 TraesCS3A01G198000 chr4A 109516196 109516998 802 False 996.000000 996 89.246000 4760 5557 1 chr4A.!!$F1 797
8 TraesCS3A01G198000 chr6D 192174044 192177161 3117 True 3882.000000 3882 89.171000 2402 5557 1 chr6D.!!$R1 3155
9 TraesCS3A01G198000 chr6D 30035537 30040237 4700 True 2296.000000 3367 92.845333 844 5557 3 chr6D.!!$R2 4713
10 TraesCS3A01G198000 chr5A 67809063 67814228 5165 False 3173.000000 3875 89.380500 478 5557 2 chr5A.!!$F1 5079
11 TraesCS3A01G198000 chrUn 343662392 343664471 2079 True 2588.000000 2588 89.144000 2402 4486 1 chrUn.!!$R1 2084
12 TraesCS3A01G198000 chrUn 284016664 284019778 3114 False 1927.000000 2856 88.761500 2402 5557 2 chrUn.!!$F1 3155
13 TraesCS3A01G198000 chrUn 55649641 55650558 917 True 604.500000 1075 85.544500 4647 5557 2 chrUn.!!$R2 910
14 TraesCS3A01G198000 chr2A 58204390 58206210 1820 True 2436.000000 2436 91.143000 615 2403 1 chr2A.!!$R1 1788
15 TraesCS3A01G198000 chr7A 647033378 647036164 2786 False 1006.333333 2427 92.405667 131 2403 3 chr7A.!!$F2 2272
16 TraesCS3A01G198000 chr6B 513259775 513261691 1916 False 2381.000000 2381 89.269000 499 2401 1 chr6B.!!$F1 1902
17 TraesCS3A01G198000 chr6B 107134994 107136637 1643 True 2137.000000 2137 90.181000 756 2403 1 chr6B.!!$R1 1647
18 TraesCS3A01G198000 chr3B 379317105 379318008 903 False 1110.000000 1110 88.925000 4647 5557 1 chr3B.!!$F1 910
19 TraesCS3A01G198000 chr3B 734461640 734462492 852 False 1075.000000 1075 89.651000 4713 5557 1 chr3B.!!$F2 844
20 TraesCS3A01G198000 chr7B 258333432 258334233 801 True 979.000000 979 88.875000 4760 5557 1 chr7B.!!$R1 797

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
278 518 0.032815 TGACGTGCCGACAAGATGAA 59.967 50.0 0.0 0.0 0.0 2.57 F
346 586 0.180406 ACAACCGTGCTTCTTGTCCT 59.820 50.0 0.0 0.0 0.0 3.85 F
350 590 0.249868 CCGTGCTTCTTGTCCTGTGA 60.250 55.0 0.0 0.0 0.0 3.58 F
1892 2936 0.404426 GTACCCCAACTTCCTGCCTT 59.596 55.0 0.0 0.0 0.0 4.35 F
3369 4562 0.251916 TTAGCCATGTTCTCACGGGG 59.748 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 3134 0.396811 GCCGCCATCACTAATACCCT 59.603 55.000 0.00 0.0 0.00 4.34 R
2246 3290 0.691078 AGGTACACGCCCATCCATCT 60.691 55.000 0.00 0.0 0.00 2.90 R
2294 3340 1.667154 GGAGCTCGGGAAATTTGGCC 61.667 60.000 7.83 0.0 0.00 5.36 R
3471 4665 1.304134 GGGTAGGGGGCACAGTTTG 60.304 63.158 0.00 0.0 0.00 2.93 R
5083 6566 0.457853 TAGTGCTCACCGTCATTCGC 60.458 55.000 0.00 0.0 38.35 4.70 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
46 47 2.932614 CTGTTGCTTGAACCTCTATCCG 59.067 50.000 0.00 0.00 33.07 4.18
51 52 2.957006 GCTTGAACCTCTATCCGTCCTA 59.043 50.000 0.00 0.00 0.00 2.94
84 85 1.603678 GCCTGGAAAACTACGTCACGA 60.604 52.381 2.91 0.00 0.00 4.35
116 117 7.278868 GTCAGATCTTGTTTAGGTAAGACCATG 59.721 40.741 0.00 0.00 41.95 3.66
117 118 6.037610 CAGATCTTGTTTAGGTAAGACCATGC 59.962 42.308 0.00 0.00 41.95 4.06
129 130 2.250031 AGACCATGCATGCCTTTTTCA 58.750 42.857 21.69 0.00 0.00 2.69
136 137 6.154445 CCATGCATGCCTTTTTCATCTATAC 58.846 40.000 21.69 0.00 0.00 1.47
193 433 5.581874 TCTGTAGATGTATCGACACACGTAA 59.418 40.000 0.00 0.00 37.48 3.18
222 462 0.538516 TGGCCATTAACAACCGTGCT 60.539 50.000 0.00 0.00 0.00 4.40
232 472 0.588252 CAACCGTGCTTCTTGTCCTG 59.412 55.000 0.00 0.00 0.00 3.86
238 478 1.869767 GTGCTTCTTGTCCTGTGAGTG 59.130 52.381 0.00 0.00 0.00 3.51
239 479 0.871057 GCTTCTTGTCCTGTGAGTGC 59.129 55.000 0.00 0.00 0.00 4.40
240 480 1.811558 GCTTCTTGTCCTGTGAGTGCA 60.812 52.381 0.00 0.00 0.00 4.57
241 481 2.564771 CTTCTTGTCCTGTGAGTGCAA 58.435 47.619 0.00 0.00 0.00 4.08
242 482 2.708216 TCTTGTCCTGTGAGTGCAAA 57.292 45.000 0.00 0.00 0.00 3.68
243 483 2.997980 TCTTGTCCTGTGAGTGCAAAA 58.002 42.857 0.00 0.00 0.00 2.44
244 484 3.554934 TCTTGTCCTGTGAGTGCAAAAT 58.445 40.909 0.00 0.00 0.00 1.82
245 485 3.953612 TCTTGTCCTGTGAGTGCAAAATT 59.046 39.130 0.00 0.00 0.00 1.82
246 486 4.402155 TCTTGTCCTGTGAGTGCAAAATTT 59.598 37.500 0.00 0.00 0.00 1.82
247 487 4.734398 TGTCCTGTGAGTGCAAAATTTT 57.266 36.364 0.00 0.00 0.00 1.82
248 488 5.083533 TGTCCTGTGAGTGCAAAATTTTT 57.916 34.783 0.00 0.00 0.00 1.94
249 489 6.214191 TGTCCTGTGAGTGCAAAATTTTTA 57.786 33.333 0.00 0.00 0.00 1.52
250 490 6.634805 TGTCCTGTGAGTGCAAAATTTTTAA 58.365 32.000 0.00 0.00 0.00 1.52
251 491 7.271511 TGTCCTGTGAGTGCAAAATTTTTAAT 58.728 30.769 0.00 0.00 0.00 1.40
252 492 7.437862 TGTCCTGTGAGTGCAAAATTTTTAATC 59.562 33.333 0.00 3.39 0.00 1.75
253 493 7.653311 GTCCTGTGAGTGCAAAATTTTTAATCT 59.347 33.333 0.00 0.00 0.00 2.40
254 494 7.867403 TCCTGTGAGTGCAAAATTTTTAATCTC 59.133 33.333 0.00 7.70 0.00 2.75
255 495 7.652909 CCTGTGAGTGCAAAATTTTTAATCTCA 59.347 33.333 0.00 9.91 0.00 3.27
256 496 8.351495 TGTGAGTGCAAAATTTTTAATCTCAC 57.649 30.769 26.83 26.83 45.01 3.51
257 497 8.351495 GTGAGTGCAAAATTTTTAATCTCACA 57.649 30.769 27.60 13.29 44.52 3.58
258 498 8.816144 GTGAGTGCAAAATTTTTAATCTCACAA 58.184 29.630 27.60 12.31 44.52 3.33
259 499 9.545105 TGAGTGCAAAATTTTTAATCTCACAAT 57.455 25.926 0.00 0.00 0.00 2.71
260 500 9.801714 GAGTGCAAAATTTTTAATCTCACAATG 57.198 29.630 0.00 0.00 0.00 2.82
261 501 9.545105 AGTGCAAAATTTTTAATCTCACAATGA 57.455 25.926 0.00 0.00 0.00 2.57
262 502 9.584839 GTGCAAAATTTTTAATCTCACAATGAC 57.415 29.630 0.00 0.00 0.00 3.06
263 503 8.486383 TGCAAAATTTTTAATCTCACAATGACG 58.514 29.630 0.00 0.00 0.00 4.35
264 504 8.487176 GCAAAATTTTTAATCTCACAATGACGT 58.513 29.630 0.00 0.00 0.00 4.34
265 505 9.782028 CAAAATTTTTAATCTCACAATGACGTG 57.218 29.630 0.00 0.00 38.29 4.49
266 506 7.566858 AATTTTTAATCTCACAATGACGTGC 57.433 32.000 0.00 0.00 36.80 5.34
267 507 4.678509 TTTAATCTCACAATGACGTGCC 57.321 40.909 0.00 0.00 36.80 5.01
268 508 1.078709 AATCTCACAATGACGTGCCG 58.921 50.000 0.00 0.00 36.80 5.69
269 509 0.246360 ATCTCACAATGACGTGCCGA 59.754 50.000 0.00 0.00 36.80 5.54
270 510 0.666274 TCTCACAATGACGTGCCGAC 60.666 55.000 0.00 0.00 36.80 4.79
271 511 0.943835 CTCACAATGACGTGCCGACA 60.944 55.000 0.00 2.25 36.80 4.35
272 512 0.530870 TCACAATGACGTGCCGACAA 60.531 50.000 0.00 0.00 35.18 3.18
273 513 0.110688 CACAATGACGTGCCGACAAG 60.111 55.000 0.00 0.00 35.18 3.16
274 514 0.249699 ACAATGACGTGCCGACAAGA 60.250 50.000 0.00 0.00 35.18 3.02
275 515 1.078709 CAATGACGTGCCGACAAGAT 58.921 50.000 0.00 0.00 35.18 2.40
276 516 1.078709 AATGACGTGCCGACAAGATG 58.921 50.000 0.00 0.00 35.18 2.90
277 517 0.246360 ATGACGTGCCGACAAGATGA 59.754 50.000 0.00 0.00 35.18 2.92
278 518 0.032815 TGACGTGCCGACAAGATGAA 59.967 50.000 0.00 0.00 0.00 2.57
279 519 1.337728 TGACGTGCCGACAAGATGAAT 60.338 47.619 0.00 0.00 0.00 2.57
280 520 2.094442 TGACGTGCCGACAAGATGAATA 60.094 45.455 0.00 0.00 0.00 1.75
281 521 3.123804 GACGTGCCGACAAGATGAATAT 58.876 45.455 0.00 0.00 0.00 1.28
282 522 4.202070 TGACGTGCCGACAAGATGAATATA 60.202 41.667 0.00 0.00 0.00 0.86
283 523 4.299155 ACGTGCCGACAAGATGAATATAG 58.701 43.478 1.50 0.00 0.00 1.31
284 524 4.202121 ACGTGCCGACAAGATGAATATAGT 60.202 41.667 1.50 0.00 0.00 2.12
285 525 4.745125 CGTGCCGACAAGATGAATATAGTT 59.255 41.667 0.00 0.00 0.00 2.24
286 526 5.234329 CGTGCCGACAAGATGAATATAGTTT 59.766 40.000 0.00 0.00 0.00 2.66
287 527 6.422223 GTGCCGACAAGATGAATATAGTTTG 58.578 40.000 0.00 0.00 0.00 2.93
288 528 6.037172 GTGCCGACAAGATGAATATAGTTTGT 59.963 38.462 0.00 0.00 0.00 2.83
289 529 7.223971 GTGCCGACAAGATGAATATAGTTTGTA 59.776 37.037 0.00 0.00 0.00 2.41
290 530 7.438160 TGCCGACAAGATGAATATAGTTTGTAG 59.562 37.037 0.00 0.00 0.00 2.74
291 531 7.652105 GCCGACAAGATGAATATAGTTTGTAGA 59.348 37.037 0.00 0.00 0.00 2.59
292 532 9.698309 CCGACAAGATGAATATAGTTTGTAGAT 57.302 33.333 0.00 0.00 0.00 1.98
304 544 9.894783 ATATAGTTTGTAGATGTATCGACACAC 57.105 33.333 0.00 13.18 41.12 3.82
305 545 5.093457 AGTTTGTAGATGTATCGACACACG 58.907 41.667 0.00 0.00 43.31 4.49
306 546 4.690184 TTGTAGATGTATCGACACACGT 57.310 40.909 0.00 0.00 41.12 4.49
307 547 5.799681 TTGTAGATGTATCGACACACGTA 57.200 39.130 0.00 0.00 41.12 3.57
308 548 5.799681 TGTAGATGTATCGACACACGTAA 57.200 39.130 0.00 0.00 37.48 3.18
309 549 6.367686 TGTAGATGTATCGACACACGTAAT 57.632 37.500 0.00 0.00 37.48 1.89
310 550 6.424683 TGTAGATGTATCGACACACGTAATC 58.575 40.000 0.00 0.00 37.48 1.75
311 551 5.752892 AGATGTATCGACACACGTAATCT 57.247 39.130 0.00 0.00 38.76 2.40
312 552 6.856135 AGATGTATCGACACACGTAATCTA 57.144 37.500 0.00 0.00 38.76 1.98
313 553 6.656945 AGATGTATCGACACACGTAATCTAC 58.343 40.000 0.00 0.00 38.76 2.59
314 554 5.160699 TGTATCGACACACGTAATCTACC 57.839 43.478 0.00 0.00 43.13 3.18
315 555 4.877823 TGTATCGACACACGTAATCTACCT 59.122 41.667 0.00 0.00 43.13 3.08
316 556 4.978083 ATCGACACACGTAATCTACCTT 57.022 40.909 0.00 0.00 43.13 3.50
317 557 4.771590 TCGACACACGTAATCTACCTTT 57.228 40.909 0.00 0.00 43.13 3.11
318 558 5.125100 TCGACACACGTAATCTACCTTTT 57.875 39.130 0.00 0.00 43.13 2.27
319 559 4.919168 TCGACACACGTAATCTACCTTTTG 59.081 41.667 0.00 0.00 43.13 2.44
320 560 4.090930 CGACACACGTAATCTACCTTTTGG 59.909 45.833 0.00 0.00 40.53 3.28
321 561 3.749609 ACACACGTAATCTACCTTTTGGC 59.250 43.478 0.00 0.00 45.59 4.52
322 562 3.126343 CACACGTAATCTACCTTTTGGCC 59.874 47.826 0.00 0.00 45.59 5.36
323 563 3.244630 ACACGTAATCTACCTTTTGGCCA 60.245 43.478 0.00 0.00 45.59 5.36
324 564 3.945285 CACGTAATCTACCTTTTGGCCAT 59.055 43.478 6.09 0.00 45.59 4.40
325 565 4.398044 CACGTAATCTACCTTTTGGCCATT 59.602 41.667 6.09 0.00 45.59 3.16
326 566 5.587043 CACGTAATCTACCTTTTGGCCATTA 59.413 40.000 6.09 0.00 45.59 1.90
327 567 6.094325 CACGTAATCTACCTTTTGGCCATTAA 59.906 38.462 6.09 3.07 45.59 1.40
328 568 6.094464 ACGTAATCTACCTTTTGGCCATTAAC 59.906 38.462 6.09 0.00 45.59 2.01
329 569 6.094325 CGTAATCTACCTTTTGGCCATTAACA 59.906 38.462 6.09 0.00 45.59 2.41
330 570 6.926630 AATCTACCTTTTGGCCATTAACAA 57.073 33.333 6.09 0.00 45.59 2.83
331 571 5.715434 TCTACCTTTTGGCCATTAACAAC 57.285 39.130 6.09 0.00 45.59 3.32
332 572 3.762407 ACCTTTTGGCCATTAACAACC 57.238 42.857 6.09 0.00 45.59 3.77
333 573 2.036604 ACCTTTTGGCCATTAACAACCG 59.963 45.455 6.09 0.00 45.59 4.44
334 574 2.036604 CCTTTTGGCCATTAACAACCGT 59.963 45.455 6.09 0.00 0.00 4.83
335 575 2.802787 TTTGGCCATTAACAACCGTG 57.197 45.000 6.09 0.00 0.00 4.94
336 576 0.315568 TTGGCCATTAACAACCGTGC 59.684 50.000 6.09 0.00 0.00 5.34
337 577 0.538516 TGGCCATTAACAACCGTGCT 60.539 50.000 0.00 0.00 0.00 4.40
338 578 0.601057 GGCCATTAACAACCGTGCTT 59.399 50.000 0.00 0.00 0.00 3.91
339 579 1.402325 GGCCATTAACAACCGTGCTTC 60.402 52.381 0.00 0.00 0.00 3.86
340 580 1.539827 GCCATTAACAACCGTGCTTCT 59.460 47.619 0.00 0.00 0.00 2.85
341 581 2.030274 GCCATTAACAACCGTGCTTCTT 60.030 45.455 0.00 0.00 0.00 2.52
342 582 3.564511 CCATTAACAACCGTGCTTCTTG 58.435 45.455 0.00 0.00 0.00 3.02
343 583 3.004315 CCATTAACAACCGTGCTTCTTGT 59.996 43.478 0.00 0.00 0.00 3.16
344 584 3.955771 TTAACAACCGTGCTTCTTGTC 57.044 42.857 0.00 0.00 0.00 3.18
345 585 1.021968 AACAACCGTGCTTCTTGTCC 58.978 50.000 0.00 0.00 0.00 4.02
346 586 0.180406 ACAACCGTGCTTCTTGTCCT 59.820 50.000 0.00 0.00 0.00 3.85
347 587 0.588252 CAACCGTGCTTCTTGTCCTG 59.412 55.000 0.00 0.00 0.00 3.86
348 588 0.180406 AACCGTGCTTCTTGTCCTGT 59.820 50.000 0.00 0.00 0.00 4.00
349 589 0.532862 ACCGTGCTTCTTGTCCTGTG 60.533 55.000 0.00 0.00 0.00 3.66
350 590 0.249868 CCGTGCTTCTTGTCCTGTGA 60.250 55.000 0.00 0.00 0.00 3.58
397 637 2.359848 ACGTGCCGACAAGCTATATACA 59.640 45.455 1.50 0.00 0.00 2.29
415 655 9.442033 CTATATACAAACTTCATCGACGTACAA 57.558 33.333 0.00 0.00 0.00 2.41
422 662 9.160576 CAAACTTCATCGACGTACAATTTTTAA 57.839 29.630 0.00 0.00 0.00 1.52
423 663 8.928844 AACTTCATCGACGTACAATTTTTAAG 57.071 30.769 0.00 0.00 0.00 1.85
424 664 8.301730 ACTTCATCGACGTACAATTTTTAAGA 57.698 30.769 0.00 0.00 0.00 2.10
425 665 8.932791 ACTTCATCGACGTACAATTTTTAAGAT 58.067 29.630 0.00 0.00 0.00 2.40
426 666 9.409949 CTTCATCGACGTACAATTTTTAAGATC 57.590 33.333 0.00 0.00 0.00 2.75
427 667 8.468720 TCATCGACGTACAATTTTTAAGATCA 57.531 30.769 0.00 0.00 0.00 2.92
428 668 8.927721 TCATCGACGTACAATTTTTAAGATCAA 58.072 29.630 0.00 0.00 0.00 2.57
429 669 9.702726 CATCGACGTACAATTTTTAAGATCAAT 57.297 29.630 0.00 0.00 0.00 2.57
455 695 9.515226 TTTTGTTTTACCTATAAGATGCTCACT 57.485 29.630 0.00 0.00 0.00 3.41
456 696 9.515226 TTTGTTTTACCTATAAGATGCTCACTT 57.485 29.630 0.00 0.00 0.00 3.16
457 697 9.515226 TTGTTTTACCTATAAGATGCTCACTTT 57.485 29.630 0.00 0.00 0.00 2.66
458 698 9.515226 TGTTTTACCTATAAGATGCTCACTTTT 57.485 29.630 0.00 0.00 0.00 2.27
484 762 7.238486 AGACACAGACTTACATCTTTCTCAT 57.762 36.000 0.00 0.00 0.00 2.90
597 886 1.199558 GTCTCTTACTGTCGGCGTTCT 59.800 52.381 6.85 0.00 0.00 3.01
607 908 4.785453 GGCGTTCTGGGGAGCCTG 62.785 72.222 0.00 0.00 45.67 4.85
729 1706 0.527817 GGCTTCGTCCGTCATTCGAT 60.528 55.000 0.00 0.00 42.86 3.59
987 2003 1.796017 TATATGGGCTTGGTCCGTCA 58.204 50.000 0.00 0.00 0.00 4.35
1006 2022 4.495844 CGTCATTCGACAGTGATGCTACTA 60.496 45.833 0.00 0.00 42.74 1.82
1162 2201 0.541392 CGGGATCATCACTTCCACCA 59.459 55.000 0.00 0.00 33.43 4.17
1163 2202 1.065491 CGGGATCATCACTTCCACCAA 60.065 52.381 0.00 0.00 33.43 3.67
1232 2274 8.114331 TCCTGTAATTTCATACGTATACCGAT 57.886 34.615 7.96 0.00 40.70 4.18
1346 2388 8.706322 AAAACACCTATTTGAACCTGATACTT 57.294 30.769 0.00 0.00 0.00 2.24
1364 2406 2.040278 ACTTGTGAGCTAGCCAATCCAA 59.960 45.455 12.13 8.84 0.00 3.53
1402 2444 1.195442 TACCACACGGCCATCCTGAA 61.195 55.000 2.24 0.00 34.57 3.02
1515 2557 5.930209 ACCCTTGGGACACATATGATATT 57.070 39.130 13.39 0.00 39.29 1.28
1553 2595 5.429762 TGGGAGAATCATGAGGTTGAATACT 59.570 40.000 0.09 0.00 36.25 2.12
1569 2611 4.225942 TGAATACTCTCCAATGCCTCTTGT 59.774 41.667 0.00 0.00 0.00 3.16
1797 2839 5.695363 CACTTCTTGATATGCATCAGATCGT 59.305 40.000 0.19 0.00 42.11 3.73
1892 2936 0.404426 GTACCCCAACTTCCTGCCTT 59.596 55.000 0.00 0.00 0.00 4.35
2008 3052 5.683876 TTGCTACCAAGAGCTTAGAAGAT 57.316 39.130 0.00 0.00 43.27 2.40
2060 3104 2.434359 GGCTTTGCCGCTACGTCT 60.434 61.111 0.00 0.00 39.62 4.18
2191 3235 2.070783 TCACTTCGGCGAATTTGTACC 58.929 47.619 23.96 0.00 0.00 3.34
2226 3270 6.012745 GCCCCTCATTCATACATAGGATTTT 58.987 40.000 0.00 0.00 0.00 1.82
2426 3602 7.201617 CGAGGGCTTTCTTAATTTCTATTCGTT 60.202 37.037 0.00 0.00 0.00 3.85
2472 3648 1.395635 ACTATCACCGCCGATGTGTA 58.604 50.000 0.00 0.00 35.25 2.90
2557 3733 2.730934 TTTCTCCTCTAGCGAGCCTA 57.269 50.000 0.00 0.00 35.90 3.93
2893 4073 2.816087 CAACATGTTCAGTCCCTTGAGG 59.184 50.000 8.48 0.00 0.00 3.86
2926 4106 7.015098 AGACACCTATTACAGATCAATGGAGAG 59.985 40.741 0.00 0.00 0.00 3.20
3007 4187 0.520404 GAGCTCAAGCACATGTGTGG 59.480 55.000 26.01 15.72 45.72 4.17
3099 4292 2.032550 GCTACGACGAGGCAATGTACTA 59.967 50.000 0.00 0.00 0.00 1.82
3210 4403 1.893137 AGACGCAGACAATCTACACCA 59.107 47.619 0.00 0.00 0.00 4.17
3280 4473 3.866883 TCGCCCAAGAATCCAATTTTC 57.133 42.857 0.00 0.00 0.00 2.29
3309 4502 4.199310 CAATAACATTGGATGGTCCGTCT 58.801 43.478 10.99 0.00 40.17 4.18
3369 4562 0.251916 TTAGCCATGTTCTCACGGGG 59.748 55.000 0.00 0.00 0.00 5.73
3370 4563 0.907704 TAGCCATGTTCTCACGGGGT 60.908 55.000 0.00 0.00 36.51 4.95
3404 4598 2.744202 CCTTGGTGACCTCTTCGATTTG 59.256 50.000 2.11 0.00 0.00 2.32
3408 4602 2.289444 GGTGACCTCTTCGATTTGTCCA 60.289 50.000 0.00 0.00 0.00 4.02
3500 4694 0.470268 CCCCTACCCCTAGTGCTCTC 60.470 65.000 0.00 0.00 0.00 3.20
3534 4728 8.380099 TGTCAACTTTACCTGGTAGTTCATTAT 58.620 33.333 11.21 0.00 30.08 1.28
3669 4872 3.009033 CCCTGAGGTGATGGTAGTTTCAA 59.991 47.826 0.00 0.00 0.00 2.69
3863 5066 1.549203 CTAAGGTGCAGGCCATGTTT 58.451 50.000 5.01 0.00 0.00 2.83
3864 5067 1.895131 CTAAGGTGCAGGCCATGTTTT 59.105 47.619 5.01 0.00 0.00 2.43
3884 5087 3.713826 TTCGGGCTTATTGACCTTTCT 57.286 42.857 0.00 0.00 43.44 2.52
3898 5101 2.306219 ACCTTTCTAGGAAGTTGGAGGC 59.694 50.000 9.99 0.00 45.05 4.70
3993 5196 0.776810 TGGCCATGAGGTTTCCAAGA 59.223 50.000 0.00 0.00 37.19 3.02
4002 5206 6.833416 CCATGAGGTTTCCAAGACCATAATTA 59.167 38.462 0.00 0.00 39.71 1.40
4017 5221 7.072454 AGACCATAATTAAGGACTTATCTGCCA 59.928 37.037 13.56 0.00 0.00 4.92
4120 5324 4.766404 AGCTTAAACTGGAAATGGAACG 57.234 40.909 0.00 0.00 0.00 3.95
4181 5385 6.268847 AGAAGAACTTGGTGAAGACTCTACAT 59.731 38.462 0.00 0.00 32.98 2.29
4229 5433 7.120432 ACAAGGCTTGCTAAATTTGAACAAAAA 59.880 29.630 26.45 0.00 33.56 1.94
4594 5820 5.790593 ACGGTTTAAGCTTATGAAGTCTGA 58.209 37.500 7.08 0.00 0.00 3.27
4600 5826 5.683876 AAGCTTATGAAGTCTGAAGCCTA 57.316 39.130 0.00 0.00 44.32 3.93
4699 5927 4.875561 TTTTTGTGCCCCAGTTTATACC 57.124 40.909 0.00 0.00 0.00 2.73
4703 5931 3.124066 TGTGCCCCAGTTTATACCCATA 58.876 45.455 0.00 0.00 0.00 2.74
4704 5932 3.724738 TGTGCCCCAGTTTATACCCATAT 59.275 43.478 0.00 0.00 0.00 1.78
4725 5953 9.541143 CCATATGGGTGTGGTTTATTTTTATTC 57.459 33.333 14.52 0.00 32.36 1.75
4757 5985 9.778993 TTATGTCACAGTTTATACTCGTAAGTC 57.221 33.333 0.00 0.00 36.92 3.01
4758 5986 6.309436 TGTCACAGTTTATACTCGTAAGTCG 58.691 40.000 0.00 0.00 36.92 4.18
4759 5987 6.073058 TGTCACAGTTTATACTCGTAAGTCGT 60.073 38.462 0.00 0.00 40.80 4.34
4760 5988 6.798959 GTCACAGTTTATACTCGTAAGTCGTT 59.201 38.462 0.00 0.00 40.80 3.85
4761 5989 6.798476 TCACAGTTTATACTCGTAAGTCGTTG 59.202 38.462 0.00 0.00 40.80 4.10
4762 5990 6.033196 CACAGTTTATACTCGTAAGTCGTTGG 59.967 42.308 0.00 0.00 40.80 3.77
4764 5992 6.468319 CAGTTTATACTCGTAAGTCGTTGGAG 59.532 42.308 0.00 0.00 40.80 3.86
4766 5994 7.334421 AGTTTATACTCGTAAGTCGTTGGAGTA 59.666 37.037 2.15 2.15 42.45 2.59
4767 5995 7.792374 TTATACTCGTAAGTCGTTGGAGTAT 57.208 36.000 14.25 14.25 46.76 2.12
4773 6002 7.699812 ACTCGTAAGTCGTTGGAGTATATTTTC 59.300 37.037 0.00 0.00 36.28 2.29
4848 6092 8.396390 TCTCATCACAGTTTATACTCGTAAGTC 58.604 37.037 0.00 0.00 36.92 3.01
4849 6093 8.047413 TCATCACAGTTTATACTCGTAAGTCA 57.953 34.615 0.00 0.00 36.92 3.41
4911 6394 7.556275 TGAGGGTATGGAGTATCATTTTGTTTC 59.444 37.037 0.00 0.00 36.25 2.78
4914 6397 9.574516 GGGTATGGAGTATCATTTTGTTTCTAT 57.425 33.333 0.00 0.00 36.25 1.98
4930 6413 7.786178 TGTTTCTATTCAAGCATAATAGCGT 57.214 32.000 7.49 0.00 37.02 5.07
4969 6452 1.520787 CGGTGGCGGACAATACTCC 60.521 63.158 0.00 0.00 0.00 3.85
4982 6465 5.429130 GACAATACTCCTTGTTAGGGGAAG 58.571 45.833 0.00 0.00 45.85 3.46
4988 6471 5.098663 ACTCCTTGTTAGGGGAAGTTATCA 58.901 41.667 0.00 0.00 45.85 2.15
5010 6493 6.573434 TCATGTATGCACCACTAGAGTAAAG 58.427 40.000 0.00 0.00 0.00 1.85
5083 6566 4.000325 TCTGTCGTGTAACATTCATTGGG 59.000 43.478 0.00 0.00 35.74 4.12
5127 6610 3.118112 TCTCCTTGCTTGAATGATCTCCC 60.118 47.826 0.00 0.00 0.00 4.30
5153 6636 2.250939 CGCTTGTCAAAGGCACGGA 61.251 57.895 0.00 0.00 33.68 4.69
5172 6655 4.649674 ACGGAACATTCTAGCCTGATAAGA 59.350 41.667 0.00 0.00 0.00 2.10
5185 6668 7.722949 AGCCTGATAAGATTCCAAATTTTGA 57.277 32.000 10.72 0.00 0.00 2.69
5425 6908 2.279741 TCATGCCACTCACGCTTATTC 58.720 47.619 0.00 0.00 0.00 1.75
5468 6951 9.921637 TTAACAATTTGCAGAGGGTTTTATTAG 57.078 29.630 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.277174 AGCAACAGCCATTATATTAAAGGAC 57.723 36.000 0.00 0.00 0.00 3.85
19 20 2.819608 GAGGTTCAAGCAACAGCCATTA 59.180 45.455 0.00 0.00 36.61 1.90
25 26 2.932614 CGGATAGAGGTTCAAGCAACAG 59.067 50.000 0.00 0.00 36.61 3.16
46 47 2.110365 AGGCTCCCTACACCTATAGGAC 59.890 54.545 26.01 0.00 44.12 3.85
51 52 0.941963 TCCAGGCTCCCTACACCTAT 59.058 55.000 0.00 0.00 29.64 2.57
84 85 2.930826 AAACAAGATCTGACCCACGT 57.069 45.000 0.00 0.00 0.00 4.49
116 117 5.632347 GCATGTATAGATGAAAAAGGCATGC 59.368 40.000 13.79 9.90 45.88 4.06
117 118 5.854866 CGCATGTATAGATGAAAAAGGCATG 59.145 40.000 13.79 1.28 35.62 4.06
129 130 5.604758 ATGATACTGGCGCATGTATAGAT 57.395 39.130 19.61 13.64 30.49 1.98
136 137 5.654497 TCTAATCTATGATACTGGCGCATG 58.346 41.667 10.83 3.03 0.00 4.06
168 408 4.575236 ACGTGTGTCGATACATCTACAGAT 59.425 41.667 18.34 0.00 42.86 2.90
185 425 3.126343 GGCCAAAAGGTAGATTACGTGTG 59.874 47.826 0.00 0.00 0.00 3.82
186 426 3.244630 TGGCCAAAAGGTAGATTACGTGT 60.245 43.478 0.61 0.00 0.00 4.49
193 433 5.186992 GGTTGTTAATGGCCAAAAGGTAGAT 59.813 40.000 10.96 0.00 0.00 1.98
222 462 2.708216 TTGCACTCACAGGACAAGAA 57.292 45.000 0.00 0.00 0.00 2.52
232 472 8.351495 TGTGAGATTAAAAATTTTGCACTCAC 57.649 30.769 28.95 28.95 46.31 3.51
238 478 8.487176 ACGTCATTGTGAGATTAAAAATTTTGC 58.513 29.630 3.73 0.00 0.00 3.68
239 479 9.782028 CACGTCATTGTGAGATTAAAAATTTTG 57.218 29.630 3.73 0.00 42.55 2.44
240 480 8.487176 GCACGTCATTGTGAGATTAAAAATTTT 58.513 29.630 0.00 0.00 42.55 1.82
241 481 7.116233 GGCACGTCATTGTGAGATTAAAAATTT 59.884 33.333 0.00 0.00 42.55 1.82
242 482 6.586082 GGCACGTCATTGTGAGATTAAAAATT 59.414 34.615 0.00 0.00 42.55 1.82
243 483 6.092748 GGCACGTCATTGTGAGATTAAAAAT 58.907 36.000 0.00 0.00 42.55 1.82
244 484 5.457140 GGCACGTCATTGTGAGATTAAAAA 58.543 37.500 0.00 0.00 42.55 1.94
245 485 5.041951 GGCACGTCATTGTGAGATTAAAA 57.958 39.130 0.00 0.00 42.55 1.52
246 486 4.678509 GGCACGTCATTGTGAGATTAAA 57.321 40.909 0.00 0.00 42.55 1.52
263 503 6.037172 ACAAACTATATTCATCTTGTCGGCAC 59.963 38.462 0.00 0.00 0.00 5.01
264 504 6.112734 ACAAACTATATTCATCTTGTCGGCA 58.887 36.000 0.00 0.00 0.00 5.69
265 505 6.604735 ACAAACTATATTCATCTTGTCGGC 57.395 37.500 0.00 0.00 0.00 5.54
266 506 9.698309 ATCTACAAACTATATTCATCTTGTCGG 57.302 33.333 0.00 0.00 0.00 4.79
278 518 9.894783 GTGTGTCGATACATCTACAAACTATAT 57.105 33.333 18.34 0.00 37.59 0.86
279 519 8.066000 CGTGTGTCGATACATCTACAAACTATA 58.934 37.037 18.34 0.00 38.11 1.31
280 520 6.910972 CGTGTGTCGATACATCTACAAACTAT 59.089 38.462 18.34 0.00 38.11 2.12
281 521 6.128200 ACGTGTGTCGATACATCTACAAACTA 60.128 38.462 18.34 0.00 38.11 2.24
282 522 5.093457 CGTGTGTCGATACATCTACAAACT 58.907 41.667 18.34 0.00 38.11 2.66
283 523 4.855388 ACGTGTGTCGATACATCTACAAAC 59.145 41.667 18.34 6.98 42.86 2.93
284 524 5.050644 ACGTGTGTCGATACATCTACAAA 57.949 39.130 18.34 0.00 42.86 2.83
285 525 4.690184 ACGTGTGTCGATACATCTACAA 57.310 40.909 18.34 0.00 42.86 2.41
286 526 5.799681 TTACGTGTGTCGATACATCTACA 57.200 39.130 18.34 0.00 42.86 2.74
287 527 6.656945 AGATTACGTGTGTCGATACATCTAC 58.343 40.000 18.34 4.53 42.86 2.59
288 528 6.856135 AGATTACGTGTGTCGATACATCTA 57.144 37.500 18.34 7.86 42.86 1.98
289 529 5.752892 AGATTACGTGTGTCGATACATCT 57.247 39.130 18.34 13.06 42.86 2.90
290 530 5.850128 GGTAGATTACGTGTGTCGATACATC 59.150 44.000 18.34 11.01 42.86 3.06
291 531 5.530171 AGGTAGATTACGTGTGTCGATACAT 59.470 40.000 18.34 5.98 42.86 2.29
292 532 4.877823 AGGTAGATTACGTGTGTCGATACA 59.122 41.667 11.30 11.30 42.86 2.29
293 533 5.415415 AGGTAGATTACGTGTGTCGATAC 57.585 43.478 5.21 5.21 42.86 2.24
294 534 6.441093 AAAGGTAGATTACGTGTGTCGATA 57.559 37.500 0.00 0.00 42.86 2.92
295 535 4.978083 AAGGTAGATTACGTGTGTCGAT 57.022 40.909 0.00 0.00 42.86 3.59
296 536 4.771590 AAAGGTAGATTACGTGTGTCGA 57.228 40.909 0.00 0.00 42.86 4.20
297 537 4.090930 CCAAAAGGTAGATTACGTGTGTCG 59.909 45.833 0.00 0.00 46.00 4.35
298 538 4.142966 GCCAAAAGGTAGATTACGTGTGTC 60.143 45.833 0.00 0.00 0.00 3.67
299 539 3.749609 GCCAAAAGGTAGATTACGTGTGT 59.250 43.478 0.00 0.00 0.00 3.72
300 540 3.126343 GGCCAAAAGGTAGATTACGTGTG 59.874 47.826 0.00 0.00 0.00 3.82
301 541 3.244630 TGGCCAAAAGGTAGATTACGTGT 60.245 43.478 0.61 0.00 0.00 4.49
302 542 3.340034 TGGCCAAAAGGTAGATTACGTG 58.660 45.455 0.61 0.00 0.00 4.49
303 543 3.706600 TGGCCAAAAGGTAGATTACGT 57.293 42.857 0.61 0.00 0.00 3.57
304 544 6.094325 TGTTAATGGCCAAAAGGTAGATTACG 59.906 38.462 10.96 0.00 0.00 3.18
305 545 7.399245 TGTTAATGGCCAAAAGGTAGATTAC 57.601 36.000 10.96 0.00 0.00 1.89
306 546 7.093684 GGTTGTTAATGGCCAAAAGGTAGATTA 60.094 37.037 10.96 0.00 0.00 1.75
307 547 6.295632 GGTTGTTAATGGCCAAAAGGTAGATT 60.296 38.462 10.96 0.00 0.00 2.40
308 548 5.186992 GGTTGTTAATGGCCAAAAGGTAGAT 59.813 40.000 10.96 0.00 0.00 1.98
309 549 4.525100 GGTTGTTAATGGCCAAAAGGTAGA 59.475 41.667 10.96 0.00 0.00 2.59
310 550 4.617298 CGGTTGTTAATGGCCAAAAGGTAG 60.617 45.833 10.96 0.00 0.00 3.18
311 551 3.256136 CGGTTGTTAATGGCCAAAAGGTA 59.744 43.478 10.96 0.00 0.00 3.08
312 552 2.036604 CGGTTGTTAATGGCCAAAAGGT 59.963 45.455 10.96 0.00 0.00 3.50
313 553 2.036604 ACGGTTGTTAATGGCCAAAAGG 59.963 45.455 10.96 0.00 0.00 3.11
314 554 3.056304 CACGGTTGTTAATGGCCAAAAG 58.944 45.455 10.96 0.00 0.00 2.27
315 555 2.803492 GCACGGTTGTTAATGGCCAAAA 60.803 45.455 10.96 4.29 0.00 2.44
316 556 1.269831 GCACGGTTGTTAATGGCCAAA 60.270 47.619 10.96 0.00 0.00 3.28
317 557 0.315568 GCACGGTTGTTAATGGCCAA 59.684 50.000 10.96 0.00 0.00 4.52
318 558 0.538516 AGCACGGTTGTTAATGGCCA 60.539 50.000 8.56 8.56 0.00 5.36
319 559 0.601057 AAGCACGGTTGTTAATGGCC 59.399 50.000 0.00 0.00 0.00 5.36
320 560 1.539827 AGAAGCACGGTTGTTAATGGC 59.460 47.619 0.00 0.00 0.00 4.40
321 561 3.004315 ACAAGAAGCACGGTTGTTAATGG 59.996 43.478 0.00 0.00 30.07 3.16
322 562 4.219033 GACAAGAAGCACGGTTGTTAATG 58.781 43.478 0.00 0.00 34.55 1.90
323 563 3.252458 GGACAAGAAGCACGGTTGTTAAT 59.748 43.478 0.00 0.00 34.55 1.40
324 564 2.614983 GGACAAGAAGCACGGTTGTTAA 59.385 45.455 0.00 0.00 34.55 2.01
325 565 2.158871 AGGACAAGAAGCACGGTTGTTA 60.159 45.455 0.00 0.00 34.55 2.41
326 566 1.021968 GGACAAGAAGCACGGTTGTT 58.978 50.000 0.00 0.00 34.55 2.83
327 567 0.180406 AGGACAAGAAGCACGGTTGT 59.820 50.000 0.00 0.00 37.12 3.32
328 568 0.588252 CAGGACAAGAAGCACGGTTG 59.412 55.000 0.00 0.00 0.00 3.77
329 569 0.180406 ACAGGACAAGAAGCACGGTT 59.820 50.000 0.00 0.00 0.00 4.44
330 570 0.532862 CACAGGACAAGAAGCACGGT 60.533 55.000 0.00 0.00 0.00 4.83
331 571 0.249868 TCACAGGACAAGAAGCACGG 60.250 55.000 0.00 0.00 0.00 4.94
332 572 1.143305 CTCACAGGACAAGAAGCACG 58.857 55.000 0.00 0.00 0.00 5.34
333 573 1.869767 CACTCACAGGACAAGAAGCAC 59.130 52.381 0.00 0.00 0.00 4.40
334 574 1.811558 GCACTCACAGGACAAGAAGCA 60.812 52.381 0.00 0.00 0.00 3.91
335 575 0.871057 GCACTCACAGGACAAGAAGC 59.129 55.000 0.00 0.00 0.00 3.86
336 576 2.245159 TGCACTCACAGGACAAGAAG 57.755 50.000 0.00 0.00 0.00 2.85
337 577 2.708216 TTGCACTCACAGGACAAGAA 57.292 45.000 0.00 0.00 0.00 2.52
338 578 2.708216 TTTGCACTCACAGGACAAGA 57.292 45.000 0.00 0.00 0.00 3.02
339 579 3.781079 TTTTTGCACTCACAGGACAAG 57.219 42.857 0.00 0.00 0.00 3.16
340 580 4.734398 AATTTTTGCACTCACAGGACAA 57.266 36.364 0.00 0.00 0.00 3.18
341 581 4.734398 AAATTTTTGCACTCACAGGACA 57.266 36.364 0.00 0.00 0.00 4.02
342 582 7.653311 AGATTAAAATTTTTGCACTCACAGGAC 59.347 33.333 9.06 0.00 0.00 3.85
343 583 7.725251 AGATTAAAATTTTTGCACTCACAGGA 58.275 30.769 9.06 0.00 0.00 3.86
344 584 7.652909 TGAGATTAAAATTTTTGCACTCACAGG 59.347 33.333 9.06 0.00 0.00 4.00
345 585 8.482429 GTGAGATTAAAATTTTTGCACTCACAG 58.518 33.333 29.14 0.00 45.80 3.66
346 586 8.351495 GTGAGATTAAAATTTTTGCACTCACA 57.649 30.769 29.14 14.53 45.80 3.58
347 587 8.351495 TGTGAGATTAAAATTTTTGCACTCAC 57.649 30.769 28.41 28.41 46.31 3.51
348 588 8.939201 TTGTGAGATTAAAATTTTTGCACTCA 57.061 26.923 9.06 14.64 0.00 3.41
349 589 9.801714 CATTGTGAGATTAAAATTTTTGCACTC 57.198 29.630 9.06 12.60 0.00 3.51
350 590 9.545105 TCATTGTGAGATTAAAATTTTTGCACT 57.455 25.926 9.06 4.33 0.00 4.40
397 637 9.377383 CTTAAAAATTGTACGTCGATGAAGTTT 57.623 29.630 12.58 4.51 0.00 2.66
429 669 9.515226 AGTGAGCATCTTATAGGTAAAACAAAA 57.485 29.630 0.00 0.00 34.92 2.44
430 670 9.515226 AAGTGAGCATCTTATAGGTAAAACAAA 57.485 29.630 0.00 0.00 34.92 2.83
431 671 9.515226 AAAGTGAGCATCTTATAGGTAAAACAA 57.485 29.630 0.00 0.00 34.92 2.83
432 672 9.515226 AAAAGTGAGCATCTTATAGGTAAAACA 57.485 29.630 0.00 0.00 34.92 2.83
438 678 8.540388 TGTCTTAAAAGTGAGCATCTTATAGGT 58.460 33.333 0.00 0.00 34.92 3.08
439 679 8.821894 GTGTCTTAAAAGTGAGCATCTTATAGG 58.178 37.037 0.00 0.00 34.92 2.57
440 680 9.371136 TGTGTCTTAAAAGTGAGCATCTTATAG 57.629 33.333 0.00 0.00 34.92 1.31
441 681 9.371136 CTGTGTCTTAAAAGTGAGCATCTTATA 57.629 33.333 0.00 0.00 34.92 0.98
442 682 8.097038 TCTGTGTCTTAAAAGTGAGCATCTTAT 58.903 33.333 0.00 0.00 34.92 1.73
443 683 7.385205 GTCTGTGTCTTAAAAGTGAGCATCTTA 59.615 37.037 0.00 0.00 34.92 2.10
444 684 6.203723 GTCTGTGTCTTAAAAGTGAGCATCTT 59.796 38.462 0.00 0.00 34.92 2.40
445 685 5.698545 GTCTGTGTCTTAAAAGTGAGCATCT 59.301 40.000 0.00 0.00 34.92 2.90
446 686 5.698545 AGTCTGTGTCTTAAAAGTGAGCATC 59.301 40.000 0.00 0.00 0.00 3.91
447 687 5.615289 AGTCTGTGTCTTAAAAGTGAGCAT 58.385 37.500 0.00 0.00 0.00 3.79
448 688 5.023533 AGTCTGTGTCTTAAAAGTGAGCA 57.976 39.130 0.00 0.00 0.00 4.26
449 689 5.993106 AAGTCTGTGTCTTAAAAGTGAGC 57.007 39.130 0.00 0.00 0.00 4.26
450 690 8.594881 ATGTAAGTCTGTGTCTTAAAAGTGAG 57.405 34.615 0.00 0.00 0.00 3.51
451 691 8.421784 AGATGTAAGTCTGTGTCTTAAAAGTGA 58.578 33.333 0.00 0.00 0.00 3.41
452 692 8.594881 AGATGTAAGTCTGTGTCTTAAAAGTG 57.405 34.615 0.00 0.00 0.00 3.16
453 693 9.614792 AAAGATGTAAGTCTGTGTCTTAAAAGT 57.385 29.630 0.00 0.00 0.00 2.66
455 695 9.832445 AGAAAGATGTAAGTCTGTGTCTTAAAA 57.168 29.630 0.00 0.00 0.00 1.52
456 696 9.477484 GAGAAAGATGTAAGTCTGTGTCTTAAA 57.523 33.333 0.00 0.00 0.00 1.52
457 697 8.638873 TGAGAAAGATGTAAGTCTGTGTCTTAA 58.361 33.333 0.00 0.00 29.47 1.85
458 698 8.178313 TGAGAAAGATGTAAGTCTGTGTCTTA 57.822 34.615 0.00 0.00 29.47 2.10
459 699 7.055667 TGAGAAAGATGTAAGTCTGTGTCTT 57.944 36.000 0.00 0.00 29.47 3.01
570 859 4.602995 GCCGACAGTAAGAGACTCATTAG 58.397 47.826 5.02 0.00 35.64 1.73
597 886 2.006748 CCCAAATACAGGCTCCCCA 58.993 57.895 0.00 0.00 0.00 4.96
607 908 1.092348 GACGGACCAAGCCCAAATAC 58.908 55.000 0.00 0.00 0.00 1.89
703 1680 0.582005 GACGGACGAAGCCAATATGC 59.418 55.000 0.00 0.00 0.00 3.14
704 1681 1.934589 TGACGGACGAAGCCAATATG 58.065 50.000 0.00 0.00 0.00 1.78
834 1839 6.896613 CGACAGTGATCAAGTCATTAAATTCG 59.103 38.462 22.27 8.08 39.48 3.34
930 1944 3.243201 GCCCGAAAATGATCAAGTCATCC 60.243 47.826 0.00 0.00 46.80 3.51
987 2003 7.849804 AAAAATAGTAGCATCACTGTCGAAT 57.150 32.000 0.00 0.00 0.00 3.34
1112 2151 5.211454 CAGTCTGCAACGAGAGATAGTATG 58.789 45.833 0.00 0.00 0.00 2.39
1269 2311 5.400066 TGATTTAGACGAAGATGGTGTCA 57.600 39.130 0.00 0.00 35.09 3.58
1346 2388 2.239402 TCATTGGATTGGCTAGCTCACA 59.761 45.455 15.72 0.73 0.00 3.58
1364 2406 4.098349 TGGTACGCCTAACTTCGTAATCAT 59.902 41.667 0.00 0.00 41.92 2.45
1402 2444 1.125093 TCCATCCACGTGGTCCAAGT 61.125 55.000 32.74 4.40 40.27 3.16
1515 2557 2.344592 TCTCCCAGCCTAAACCTTTGA 58.655 47.619 0.00 0.00 0.00 2.69
1553 2595 3.776969 AGATACACAAGAGGCATTGGAGA 59.223 43.478 7.29 0.00 34.36 3.71
1569 2611 7.347222 AGACATTAGTACCCCATTCAAGATACA 59.653 37.037 0.00 0.00 0.00 2.29
1613 2655 1.089978 TCCTCACTCCCCTTCAGGTA 58.910 55.000 0.00 0.00 0.00 3.08
1892 2936 2.647299 TGGTCCAAATTTCTAGGAGCCA 59.353 45.455 17.73 13.91 46.55 4.75
2060 3104 2.364560 TGGCCCACCACCAACAAA 59.635 55.556 0.00 0.00 42.67 2.83
2090 3134 0.396811 GCCGCCATCACTAATACCCT 59.603 55.000 0.00 0.00 0.00 4.34
2191 3235 2.072874 ATGAGGGGCCAATCGGATGG 62.073 60.000 4.39 3.33 43.70 3.51
2246 3290 0.691078 AGGTACACGCCCATCCATCT 60.691 55.000 0.00 0.00 0.00 2.90
2294 3340 1.667154 GGAGCTCGGGAAATTTGGCC 61.667 60.000 7.83 0.00 0.00 5.36
2472 3648 6.025539 TCTGGGTGATATGGTTCAGCTATAT 58.974 40.000 3.96 0.00 42.39 0.86
2557 3733 8.345565 GCAATTCCAATTTCGTCTTGAGTATAT 58.654 33.333 0.00 0.00 0.00 0.86
2861 4041 1.944024 GAACATGTTGGTCACGGTTCA 59.056 47.619 17.58 0.00 40.39 3.18
2863 4043 1.946768 CTGAACATGTTGGTCACGGTT 59.053 47.619 17.58 0.00 39.52 4.44
2893 4073 3.954904 TCTGTAATAGGTGTCTCTGCCTC 59.045 47.826 0.00 0.00 36.38 4.70
2944 4124 4.797471 TGAGCAGCAACAACATCATTTAC 58.203 39.130 0.00 0.00 0.00 2.01
3007 4187 4.094887 ACGTGAGACATAATGAAACATGGC 59.905 41.667 0.00 0.00 0.00 4.40
3084 4277 4.890088 TCTGTTTTAGTACATTGCCTCGT 58.110 39.130 0.00 0.00 0.00 4.18
3099 4292 2.762327 CCCAGCTATGGCATTCTGTTTT 59.238 45.455 20.57 0.00 46.19 2.43
3210 4403 2.338809 TCTTCCTGTTCCACATGAGGT 58.661 47.619 9.16 0.00 0.00 3.85
3280 4473 4.711355 ACCATCCAATGTTATTGGTTCAGG 59.289 41.667 17.46 16.04 37.40 3.86
3369 4562 1.474330 CCAAGGCCATGGTCCTTTAC 58.526 55.000 27.87 6.28 41.73 2.01
3370 4563 3.998560 CCAAGGCCATGGTCCTTTA 57.001 52.632 27.87 0.00 41.73 1.85
3408 4602 2.741878 CGCCAAAGGTACAATCCTCGAT 60.742 50.000 0.00 0.00 36.74 3.59
3471 4665 1.304134 GGGTAGGGGGCACAGTTTG 60.304 63.158 0.00 0.00 0.00 2.93
3500 4694 2.299297 AGGTAAAGTTGACAGGAGACCG 59.701 50.000 0.00 0.00 0.00 4.79
3625 4828 2.807967 TCTTGTGAGTGGCGAATTTCTG 59.192 45.455 0.00 0.00 0.00 3.02
3665 4868 3.760151 CCATCTGTGCATCTTTCCTTGAA 59.240 43.478 0.00 0.00 0.00 2.69
3669 4872 2.575279 AGTCCATCTGTGCATCTTTCCT 59.425 45.455 0.00 0.00 0.00 3.36
3695 4898 4.693566 TCCATAAACGTGTCCTTGATGAAC 59.306 41.667 0.00 0.00 0.00 3.18
3831 5034 2.104963 GCACCTTAGCTACCTTAGGCAT 59.895 50.000 8.82 0.00 40.70 4.40
3863 5066 4.028993 AGAAAGGTCAATAAGCCCGAAA 57.971 40.909 0.00 0.00 0.00 3.46
3864 5067 3.713826 AGAAAGGTCAATAAGCCCGAA 57.286 42.857 0.00 0.00 0.00 4.30
3884 5087 1.562672 GGCCAGCCTCCAACTTCCTA 61.563 60.000 0.00 0.00 0.00 2.94
3898 5101 1.673033 CCGTGAACTTAGTCTGGCCAG 60.673 57.143 27.87 27.87 0.00 4.85
3993 5196 7.149202 TGGCAGATAAGTCCTTAATTATGGT 57.851 36.000 15.12 1.83 0.00 3.55
4002 5206 7.200434 TCTTTTCTATGGCAGATAAGTCCTT 57.800 36.000 0.00 0.00 40.94 3.36
4017 5221 5.392380 CCATTTCAGCGCACTTCTTTTCTAT 60.392 40.000 11.47 0.00 0.00 1.98
4146 5350 6.122277 TCACCAAGTTCTTCTGTTCAGATTT 58.878 36.000 3.28 0.00 0.00 2.17
4181 5385 1.472082 CGTTTGCCAGCATTGGTATCA 59.528 47.619 0.00 0.00 46.80 2.15
4229 5433 4.083271 GCTTCAGTCTTTAAATCTGCCGTT 60.083 41.667 12.70 0.00 0.00 4.44
4371 5577 7.038659 GCTACATTTGAAGTGAGACTGAGTAT 58.961 38.462 0.00 0.00 0.00 2.12
4380 5586 7.041780 ACAAAGTACTGCTACATTTGAAGTGAG 60.042 37.037 7.93 0.00 35.40 3.51
4497 5713 7.838079 ATAAATAATGCTTCAGGCCATACAA 57.162 32.000 5.01 0.00 40.92 2.41
4533 5755 6.693978 GGGGAACGTACATGCATTTATAAAAC 59.306 38.462 0.00 0.00 0.00 2.43
4645 5871 9.926158 TCCAACAACTTACGAGTATAAATTGTA 57.074 29.630 0.00 0.00 34.21 2.41
4699 5927 9.541143 GAATAAAAATAAACCACACCCATATGG 57.459 33.333 15.41 15.41 42.13 2.74
4704 5932 9.907229 AAAAAGAATAAAAATAAACCACACCCA 57.093 25.926 0.00 0.00 0.00 4.51
4733 5961 6.965500 CGACTTACGAGTATAAACTGTGACAT 59.035 38.462 0.00 0.00 45.77 3.06
4735 5963 6.310197 ACGACTTACGAGTATAAACTGTGAC 58.690 40.000 0.00 0.00 45.77 3.67
4737 5965 6.033196 CCAACGACTTACGAGTATAAACTGTG 59.967 42.308 0.00 0.00 45.77 3.66
4741 5969 6.317857 ACTCCAACGACTTACGAGTATAAAC 58.682 40.000 0.00 0.00 45.77 2.01
4742 5970 6.500684 ACTCCAACGACTTACGAGTATAAA 57.499 37.500 0.00 0.00 45.77 1.40
4743 5971 7.792374 ATACTCCAACGACTTACGAGTATAA 57.208 36.000 6.30 0.00 45.77 0.98
4746 5974 7.792374 AATATACTCCAACGACTTACGAGTA 57.208 36.000 0.00 0.00 45.77 2.59
4747 5975 6.690194 AATATACTCCAACGACTTACGAGT 57.310 37.500 0.00 0.00 45.77 4.18
4748 5976 7.914346 AGAAAATATACTCCAACGACTTACGAG 59.086 37.037 0.00 0.00 45.77 4.18
4753 5981 9.893305 CAAAAAGAAAATATACTCCAACGACTT 57.107 29.630 0.00 0.00 0.00 3.01
4754 5982 8.021396 GCAAAAAGAAAATATACTCCAACGACT 58.979 33.333 0.00 0.00 0.00 4.18
4755 5983 7.272731 GGCAAAAAGAAAATATACTCCAACGAC 59.727 37.037 0.00 0.00 0.00 4.34
4756 5984 7.309920 GGCAAAAAGAAAATATACTCCAACGA 58.690 34.615 0.00 0.00 0.00 3.85
4757 5985 6.530181 GGGCAAAAAGAAAATATACTCCAACG 59.470 38.462 0.00 0.00 0.00 4.10
4758 5986 6.816640 GGGGCAAAAAGAAAATATACTCCAAC 59.183 38.462 0.00 0.00 0.00 3.77
4759 5987 6.498651 TGGGGCAAAAAGAAAATATACTCCAA 59.501 34.615 0.00 0.00 0.00 3.53
4760 5988 6.019748 TGGGGCAAAAAGAAAATATACTCCA 58.980 36.000 0.00 0.00 0.00 3.86
4761 5989 6.154534 ACTGGGGCAAAAAGAAAATATACTCC 59.845 38.462 0.00 0.00 0.00 3.85
4762 5990 7.170393 ACTGGGGCAAAAAGAAAATATACTC 57.830 36.000 0.00 0.00 0.00 2.59
4764 5992 9.884636 ATAAACTGGGGCAAAAAGAAAATATAC 57.115 29.630 0.00 0.00 0.00 1.47
4766 5994 9.884636 GTATAAACTGGGGCAAAAAGAAAATAT 57.115 29.630 0.00 0.00 0.00 1.28
4767 5995 9.095700 AGTATAAACTGGGGCAAAAAGAAAATA 57.904 29.630 0.00 0.00 33.57 1.40
4773 6002 4.698304 TCGAGTATAAACTGGGGCAAAAAG 59.302 41.667 0.00 0.00 35.56 2.27
4777 6010 2.835764 ACTCGAGTATAAACTGGGGCAA 59.164 45.455 18.46 0.00 35.44 4.52
4823 6067 8.182227 TGACTTACGAGTATAAACTGTGATGAG 58.818 37.037 0.00 0.00 35.56 2.90
4872 6351 6.199376 TCCATACCCTCATGAGTGTAAACTA 58.801 40.000 19.91 1.48 0.00 2.24
4911 6394 8.988934 TCCTTAAACGCTATTATGCTTGAATAG 58.011 33.333 7.89 7.89 39.10 1.73
4914 6397 7.618502 TTCCTTAAACGCTATTATGCTTGAA 57.381 32.000 0.00 0.00 0.00 2.69
4930 6413 7.147811 CCACCGATAAATGGGAAATTCCTTAAA 60.148 37.037 12.28 0.00 36.57 1.52
4969 6452 7.041098 GCATACATGATAACTTCCCCTAACAAG 60.041 40.741 0.00 0.00 0.00 3.16
4982 6465 6.516718 ACTCTAGTGGTGCATACATGATAAC 58.483 40.000 0.00 0.00 0.00 1.89
4988 6471 6.546428 ACTTTACTCTAGTGGTGCATACAT 57.454 37.500 6.80 0.00 0.00 2.29
5010 6493 3.889538 GGGCCCCTACATCATAAAAGAAC 59.110 47.826 12.23 0.00 0.00 3.01
5083 6566 0.457853 TAGTGCTCACCGTCATTCGC 60.458 55.000 0.00 0.00 38.35 4.70
5127 6610 2.307049 CCTTTGACAAGCGCGTTAAAG 58.693 47.619 19.09 19.09 40.39 1.85
5153 6636 7.141758 TGGAATCTTATCAGGCTAGAATGTT 57.858 36.000 0.00 0.00 0.00 2.71
5172 6655 6.431852 CCTTCAGGCATTTCAAAATTTGGAAT 59.568 34.615 8.83 6.42 39.44 3.01
5425 6908 5.728351 TGTTAAAGAAAGTCGTGTCAAGG 57.272 39.130 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.