Multiple sequence alignment - TraesCS1D01G247000

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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 TraesCS1D01G247000 chr1D 100.000 3086 0 0 1 3086 339736243 339733158 0.000000e+00 5699.0
1 TraesCS1D01G247000 chr1D 93.617 94 6 0 1047 1140 339572809 339572716 1.150000e-29 141.0
2 TraesCS1D01G247000 chr1B 88.271 1330 94 20 59 1374 454611746 454610465 0.000000e+00 1535.0
3 TraesCS1D01G247000 chr1B 89.710 758 21 18 1358 2090 454610443 454609718 0.000000e+00 915.0
4 TraesCS1D01G247000 chr1B 80.065 617 80 34 2492 3086 454607664 454607069 4.760000e-113 418.0
5 TraesCS1D01G247000 chr1B 94.565 92 5 0 1047 1138 454543570 454543479 3.210000e-30 143.0
6 TraesCS1D01G247000 chr1B 81.356 118 22 0 255 372 549619667 549619550 2.530000e-16 97.1
7 TraesCS1D01G247000 chr1A 81.302 1690 176 79 1497 3086 439687885 439686236 0.000000e+00 1242.0
8 TraesCS1D01G247000 chr1A 87.500 456 46 6 741 1189 439688402 439687951 1.640000e-142 516.0
9 TraesCS1D01G247000 chr1A 95.652 92 4 0 1047 1138 439622126 439622035 6.890000e-32 148.0
10 TraesCS1D01G247000 chr1A 86.923 130 12 2 516 640 439690403 439690274 1.150000e-29 141.0
11 TraesCS1D01G247000 chr1A 78.182 165 28 4 69 228 555976827 555976988 7.040000e-17 99.0
12 TraesCS1D01G247000 chr7B 77.101 476 81 20 1 466 246503632 246504089 1.840000e-62 250.0
13 TraesCS1D01G247000 chr7B 76.336 393 74 17 11 392 750572915 750572531 3.140000e-45 193.0
14 TraesCS1D01G247000 chr7B 77.477 333 62 10 101 426 961171 961497 1.460000e-43 187.0
15 TraesCS1D01G247000 chr7B 84.545 110 10 4 1535 1640 586981939 586981833 5.440000e-18 102.0
16 TraesCS1D01G247000 chr7B 100.000 28 0 0 194 221 716967801 716967828 6.000000e-03 52.8
17 TraesCS1D01G247000 chr7A 80.106 377 32 29 804 1168 617742635 617742290 1.110000e-59 241.0
18 TraesCS1D01G247000 chr7A 77.689 251 46 7 131 378 729281085 729280842 8.920000e-31 145.0
19 TraesCS1D01G247000 chr7A 77.291 251 45 8 131 378 729312424 729312183 1.490000e-28 137.0
20 TraesCS1D01G247000 chr7A 86.458 96 4 7 1551 1641 617741790 617741699 2.530000e-16 97.1
21 TraesCS1D01G247000 chr7A 84.536 97 5 6 1551 1641 625546106 625546014 1.520000e-13 87.9
22 TraesCS1D01G247000 chr7A 85.526 76 0 4 1555 1623 625620537 625620466 5.520000e-08 69.4
23 TraesCS1D01G247000 chr6B 79.191 346 47 23 2437 2765 682689833 682690170 1.860000e-52 217.0
24 TraesCS1D01G247000 chr6B 78.840 293 40 18 2482 2765 703569319 703569040 8.790000e-41 178.0
25 TraesCS1D01G247000 chr6B 86.111 72 10 0 392 463 716340400 716340471 9.170000e-11 78.7
26 TraesCS1D01G247000 chr3A 80.612 294 39 15 2482 2765 617006631 617006916 8.670000e-51 211.0
27 TraesCS1D01G247000 chr3A 78.154 325 47 19 2437 2747 440610951 440610637 5.250000e-43 185.0
28 TraesCS1D01G247000 chr4D 76.659 437 67 20 2299 2726 390759978 390759568 3.120000e-50 209.0
29 TraesCS1D01G247000 chr4D 76.201 437 68 25 2299 2726 448608249 448608658 6.750000e-47 198.0
30 TraesCS1D01G247000 chr5D 75.625 480 84 17 8 463 548259310 548259780 1.120000e-49 207.0
31 TraesCS1D01G247000 chr5D 75.325 308 50 14 166 457 491661536 491661833 1.160000e-24 124.0
32 TraesCS1D01G247000 chr5D 80.189 106 14 5 8 108 14081571 14081468 4.270000e-09 73.1
33 TraesCS1D01G247000 chr6D 79.667 300 36 20 2482 2765 75754023 75754313 3.140000e-45 193.0
34 TraesCS1D01G247000 chr6D 77.299 348 58 19 2448 2784 75024244 75024581 5.250000e-43 185.0
35 TraesCS1D01G247000 chr5B 76.842 380 63 13 69 440 665766186 665765824 1.130000e-44 191.0
36 TraesCS1D01G247000 chr5B 75.798 376 72 13 11 378 541095613 541095249 4.090000e-39 172.0
37 TraesCS1D01G247000 chr7D 86.286 175 15 8 1003 1168 543631052 543630878 6.800000e-42 182.0
38 TraesCS1D01G247000 chr7D 74.123 456 90 15 43 481 588469173 588469617 2.460000e-36 163.0
39 TraesCS1D01G247000 chr7D 75.266 376 73 14 8 374 154201902 154202266 8.860000e-36 161.0
40 TraesCS1D01G247000 chr7D 78.486 251 44 5 131 378 636847130 636847373 4.120000e-34 156.0
41 TraesCS1D01G247000 chr7D 75.150 334 65 11 69 392 579044020 579044345 1.150000e-29 141.0
42 TraesCS1D01G247000 chr7D 75.920 299 46 14 12 296 38660183 38659897 2.500000e-26 130.0
43 TraesCS1D01G247000 chr7D 83.333 120 19 1 257 376 564071805 564071687 3.250000e-20 110.0
44 TraesCS1D01G247000 chr7D 100.000 28 0 0 1696 1723 378495333 378495306 6.000000e-03 52.8
45 TraesCS1D01G247000 chr5A 77.044 318 58 9 69 378 105413564 105413254 5.290000e-38 169.0
46 TraesCS1D01G247000 chr5A 73.668 319 76 5 166 481 31002197 31001884 1.940000e-22 117.0
47 TraesCS1D01G247000 chr5A 74.532 267 63 4 255 518 31059359 31059095 9.050000e-21 111.0
48 TraesCS1D01G247000 chr2D 74.573 468 78 21 45 481 325810395 325809938 1.900000e-37 167.0
49 TraesCS1D01G247000 chr2D 75.328 381 70 16 8 378 519343590 519343956 8.860000e-36 161.0
50 TraesCS1D01G247000 chr2D 78.698 169 30 4 210 378 21185599 21185437 1.170000e-19 108.0
51 TraesCS1D01G247000 chr2D 81.132 106 11 6 8 109 13988448 13988548 3.300000e-10 76.8
52 TraesCS1D01G247000 chr3B 75.719 313 65 7 69 376 640705350 640705044 2.480000e-31 147.0
53 TraesCS1D01G247000 chrUn 85.714 91 11 2 282 372 422908410 422908322 9.110000e-16 95.3
54 TraesCS1D01G247000 chr2A 79.439 107 13 6 7 109 450537209 450537310 1.990000e-07 67.6


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 TraesCS1D01G247000 chr1D 339733158 339736243 3085 True 5699 5699 100.000000 1 3086 1 chr1D.!!$R2 3085
1 TraesCS1D01G247000 chr1B 454607069 454611746 4677 True 956 1535 86.015333 59 3086 3 chr1B.!!$R3 3027
2 TraesCS1D01G247000 chr1A 439686236 439690403 4167 True 633 1242 85.241667 516 3086 3 chr1A.!!$R2 2570

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
267 281 0.111639 GCTAGGTCCAACCACCCAAA 59.888 55.0 0.0 0.0 41.95 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 5539 0.37861 GCCTGAAGCGACAAATAGGC 59.621 55.0 0.0 0.0 43.2 3.93 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
23 24 6.702449 ATAGATATAAGATGCACCCAACCA 57.298 37.500 0.00 0.00 0.00 3.67
24 25 5.387113 AGATATAAGATGCACCCAACCAA 57.613 39.130 0.00 0.00 0.00 3.67
25 26 5.957132 AGATATAAGATGCACCCAACCAAT 58.043 37.500 0.00 0.00 0.00 3.16
26 27 7.090319 AGATATAAGATGCACCCAACCAATA 57.910 36.000 0.00 0.00 0.00 1.90
27 28 7.702785 AGATATAAGATGCACCCAACCAATAT 58.297 34.615 0.00 0.00 0.00 1.28
28 29 7.831193 AGATATAAGATGCACCCAACCAATATC 59.169 37.037 0.00 0.00 0.00 1.63
29 30 3.668141 AGATGCACCCAACCAATATCA 57.332 42.857 0.00 0.00 0.00 2.15
30 31 4.188937 AGATGCACCCAACCAATATCAT 57.811 40.909 0.00 0.00 0.00 2.45
31 32 5.323382 AGATGCACCCAACCAATATCATA 57.677 39.130 0.00 0.00 0.00 2.15
32 33 5.319453 AGATGCACCCAACCAATATCATAG 58.681 41.667 0.00 0.00 0.00 2.23
33 34 4.518278 TGCACCCAACCAATATCATAGT 57.482 40.909 0.00 0.00 0.00 2.12
34 35 5.638530 TGCACCCAACCAATATCATAGTA 57.361 39.130 0.00 0.00 0.00 1.82
35 36 5.373222 TGCACCCAACCAATATCATAGTAC 58.627 41.667 0.00 0.00 0.00 2.73
36 37 5.131977 TGCACCCAACCAATATCATAGTACT 59.868 40.000 0.00 0.00 0.00 2.73
37 38 5.701290 GCACCCAACCAATATCATAGTACTC 59.299 44.000 0.00 0.00 0.00 2.59
38 39 5.926542 CACCCAACCAATATCATAGTACTCG 59.073 44.000 0.00 0.00 0.00 4.18
39 40 4.929808 CCCAACCAATATCATAGTACTCGC 59.070 45.833 0.00 0.00 0.00 5.03
40 41 5.510690 CCCAACCAATATCATAGTACTCGCA 60.511 44.000 0.00 0.00 0.00 5.10
41 42 5.405571 CCAACCAATATCATAGTACTCGCAC 59.594 44.000 0.00 0.00 0.00 5.34
42 43 5.784578 ACCAATATCATAGTACTCGCACA 57.215 39.130 0.00 0.00 0.00 4.57
43 44 6.156748 ACCAATATCATAGTACTCGCACAA 57.843 37.500 0.00 0.00 0.00 3.33
44 45 6.578944 ACCAATATCATAGTACTCGCACAAA 58.421 36.000 0.00 0.00 0.00 2.83
45 46 7.045416 ACCAATATCATAGTACTCGCACAAAA 58.955 34.615 0.00 0.00 0.00 2.44
46 47 7.551262 ACCAATATCATAGTACTCGCACAAAAA 59.449 33.333 0.00 0.00 0.00 1.94
93 94 1.933853 GACCAAAGCTATGTGTAGGCG 59.066 52.381 0.00 0.00 0.00 5.52
130 144 4.993029 AAAAGATCAAAACCGTGACCAA 57.007 36.364 0.00 0.00 0.00 3.67
135 149 3.219052 TCAAAACCGTGACCAACAAAC 57.781 42.857 0.00 0.00 0.00 2.93
136 150 2.094649 TCAAAACCGTGACCAACAAACC 60.095 45.455 0.00 0.00 0.00 3.27
141 155 1.468395 CCGTGACCAACAAACCACAAC 60.468 52.381 0.00 0.00 0.00 3.32
143 157 2.159310 CGTGACCAACAAACCACAACAT 60.159 45.455 0.00 0.00 0.00 2.71
145 159 4.249661 GTGACCAACAAACCACAACATTT 58.750 39.130 0.00 0.00 0.00 2.32
154 168 6.616947 ACAAACCACAACATTTACCATATCG 58.383 36.000 0.00 0.00 0.00 2.92
157 171 5.690865 ACCACAACATTTACCATATCGGAT 58.309 37.500 0.00 0.00 38.63 4.18
158 172 5.530915 ACCACAACATTTACCATATCGGATG 59.469 40.000 0.00 0.00 38.63 3.51
160 174 4.518970 ACAACATTTACCATATCGGATGCC 59.481 41.667 0.00 0.00 38.63 4.40
162 176 4.724399 ACATTTACCATATCGGATGCCAA 58.276 39.130 0.00 0.00 38.63 4.52
164 178 4.431416 TTTACCATATCGGATGCCAACT 57.569 40.909 0.00 0.00 38.63 3.16
167 181 4.207891 ACCATATCGGATGCCAACTATC 57.792 45.455 0.00 0.00 38.63 2.08
180 194 3.190079 CCAACTATCTCATGACACCACG 58.810 50.000 0.00 0.00 0.00 4.94
181 195 3.368427 CCAACTATCTCATGACACCACGT 60.368 47.826 0.00 0.00 0.00 4.49
203 217 4.682860 GTGGACGACGAGATTCTTTAACAA 59.317 41.667 0.00 0.00 0.00 2.83
210 224 5.699839 ACGAGATTCTTTAACAACAATGCC 58.300 37.500 0.00 0.00 0.00 4.40
241 255 2.029369 TGACGTTTAACCGCCGCT 59.971 55.556 0.00 0.00 0.00 5.52
242 256 1.594836 TGACGTTTAACCGCCGCTT 60.595 52.632 0.00 0.00 0.00 4.68
243 257 1.159098 TGACGTTTAACCGCCGCTTT 61.159 50.000 0.00 0.00 0.00 3.51
248 262 1.888958 TTTAACCGCCGCTTTCGTCG 61.889 55.000 0.00 0.00 36.78 5.12
253 267 3.255379 GCCGCTTTCGTCGCTAGG 61.255 66.667 0.00 0.00 0.00 3.02
262 276 1.445582 CGTCGCTAGGTCCAACCAC 60.446 63.158 0.00 0.00 41.95 4.16
263 277 1.079336 GTCGCTAGGTCCAACCACC 60.079 63.158 0.00 0.00 41.95 4.61
264 278 2.267961 CGCTAGGTCCAACCACCC 59.732 66.667 0.00 0.00 41.95 4.61
265 279 2.589157 CGCTAGGTCCAACCACCCA 61.589 63.158 0.00 0.00 41.95 4.51
266 280 1.765074 GCTAGGTCCAACCACCCAA 59.235 57.895 0.00 0.00 41.95 4.12
267 281 0.111639 GCTAGGTCCAACCACCCAAA 59.888 55.000 0.00 0.00 41.95 3.28
268 282 1.886655 GCTAGGTCCAACCACCCAAAG 60.887 57.143 0.00 0.00 41.95 2.77
269 283 0.111639 TAGGTCCAACCACCCAAAGC 59.888 55.000 0.00 0.00 41.95 3.51
276 290 1.693606 CAACCACCCAAAGCCAGAATT 59.306 47.619 0.00 0.00 0.00 2.17
279 293 3.790126 ACCACCCAAAGCCAGAATTTAT 58.210 40.909 0.00 0.00 0.00 1.40
294 308 7.922811 GCCAGAATTTATATTTTCACCCAGAAG 59.077 37.037 0.00 0.00 37.57 2.85
304 318 1.203300 TCACCCAGAAGATCCAGTCCA 60.203 52.381 0.00 0.00 0.00 4.02
311 325 4.202440 CCAGAAGATCCAGTCCAAGCATAT 60.202 45.833 0.00 0.00 0.00 1.78
315 329 1.788229 TCCAGTCCAAGCATATCCGA 58.212 50.000 0.00 0.00 0.00 4.55
317 331 1.506493 CAGTCCAAGCATATCCGAGC 58.494 55.000 0.00 0.00 0.00 5.03
326 340 3.813443 AGCATATCCGAGCAATGACTTT 58.187 40.909 0.00 0.00 0.00 2.66
329 343 5.237344 AGCATATCCGAGCAATGACTTTAAC 59.763 40.000 0.00 0.00 0.00 2.01
340 354 7.951591 AGCAATGACTTTAACAAGGTAACAAT 58.048 30.769 0.00 0.00 41.41 2.71
372 386 7.164122 ACATCATCATTGCTAGGTATAACCAG 58.836 38.462 0.00 0.00 41.95 4.00
376 390 4.653801 TCATTGCTAGGTATAACCAGCTCA 59.346 41.667 9.65 0.00 41.95 4.26
377 391 4.672587 TTGCTAGGTATAACCAGCTCAG 57.327 45.455 9.65 0.00 41.95 3.35
381 395 6.075315 TGCTAGGTATAACCAGCTCAGATAA 58.925 40.000 9.65 0.00 41.95 1.75
382 396 6.209589 TGCTAGGTATAACCAGCTCAGATAAG 59.790 42.308 9.65 0.00 41.95 1.73
383 397 6.434652 GCTAGGTATAACCAGCTCAGATAAGA 59.565 42.308 0.44 0.00 41.95 2.10
384 398 7.123547 GCTAGGTATAACCAGCTCAGATAAGAT 59.876 40.741 0.44 0.00 41.95 2.40
395 409 4.379394 GCTCAGATAAGATGTAGGCTCGAG 60.379 50.000 8.45 8.45 0.00 4.04
429 443 1.078497 GGCACCACCATCGACATCA 60.078 57.895 0.00 0.00 38.86 3.07
430 444 0.464373 GGCACCACCATCGACATCAT 60.464 55.000 0.00 0.00 38.86 2.45
431 445 1.382522 GCACCACCATCGACATCATT 58.617 50.000 0.00 0.00 0.00 2.57
432 446 1.745087 GCACCACCATCGACATCATTT 59.255 47.619 0.00 0.00 0.00 2.32
433 447 2.942376 GCACCACCATCGACATCATTTA 59.058 45.455 0.00 0.00 0.00 1.40
434 448 3.565482 GCACCACCATCGACATCATTTAT 59.435 43.478 0.00 0.00 0.00 1.40
435 449 4.754618 GCACCACCATCGACATCATTTATA 59.245 41.667 0.00 0.00 0.00 0.98
436 450 5.412594 GCACCACCATCGACATCATTTATAT 59.587 40.000 0.00 0.00 0.00 0.86
437 451 6.621380 GCACCACCATCGACATCATTTATATG 60.621 42.308 0.00 0.00 0.00 1.78
438 452 6.427853 CACCACCATCGACATCATTTATATGT 59.572 38.462 0.00 0.00 40.23 2.29
439 453 6.998074 ACCACCATCGACATCATTTATATGTT 59.002 34.615 0.00 0.00 37.69 2.71
440 454 8.154203 ACCACCATCGACATCATTTATATGTTA 58.846 33.333 0.00 0.00 37.69 2.41
441 455 9.166173 CCACCATCGACATCATTTATATGTTAT 57.834 33.333 0.00 0.00 37.69 1.89
443 457 9.087424 ACCATCGACATCATTTATATGTTATCG 57.913 33.333 0.00 0.24 37.69 2.92
444 458 8.058328 CCATCGACATCATTTATATGTTATCGC 58.942 37.037 0.00 0.00 37.69 4.58
445 459 8.811378 CATCGACATCATTTATATGTTATCGCT 58.189 33.333 0.00 0.00 37.69 4.93
457 471 1.810151 GTTATCGCTGCCACTTTTCCA 59.190 47.619 0.00 0.00 0.00 3.53
478 492 4.261155 CCACTATCCCAACAATTACATGCG 60.261 45.833 0.00 0.00 0.00 4.73
482 496 5.689383 ATCCCAACAATTACATGCGATAC 57.311 39.130 0.00 0.00 0.00 2.24
511 525 0.868406 GCCGCTGCATAACTATCCAC 59.132 55.000 0.00 0.00 37.47 4.02
527 541 7.444629 ACTATCCACATGCATTATCATCAAC 57.555 36.000 0.00 0.00 0.00 3.18
602 616 5.525745 CACCTGCATTAATATGTACGGTCAA 59.474 40.000 0.00 0.00 31.07 3.18
612 630 4.577834 ATGTACGGTCAAAACCTTTTGG 57.422 40.909 9.99 0.00 45.68 3.28
771 2562 6.508880 CGCCGATCGATAAATCACTAACAAAA 60.509 38.462 18.66 0.00 41.67 2.44
786 2577 2.620242 ACAAAACCACTGCAAGCTTTG 58.380 42.857 0.00 0.00 37.60 2.77
892 2690 4.240888 CGATGGATCGCAGATGAAATACT 58.759 43.478 0.00 0.00 45.12 2.12
893 2691 4.325741 CGATGGATCGCAGATGAAATACTC 59.674 45.833 0.00 0.00 45.12 2.59
894 2692 3.995199 TGGATCGCAGATGAAATACTCC 58.005 45.455 0.00 0.00 45.12 3.85
897 2695 5.059833 GGATCGCAGATGAAATACTCCTTT 58.940 41.667 0.00 0.00 45.12 3.11
926 2724 3.518998 CTCGATCCGGTCCGCACT 61.519 66.667 5.50 0.00 0.00 4.40
985 2783 4.448363 GCTAAACGGAATTAGCGTTAGG 57.552 45.455 12.16 0.00 45.77 2.69
1195 2993 1.825090 TAAGAACCATGCAGTGCAGG 58.175 50.000 24.20 23.32 43.65 4.85
1237 3035 5.505159 CGTACGTAGAGCCTATGAACATCAA 60.505 44.000 7.22 0.00 0.00 2.57
1263 3061 7.088589 AGCGTCAATGTTATAAGCTTTCATT 57.911 32.000 3.20 8.43 0.00 2.57
1264 3062 7.538575 AGCGTCAATGTTATAAGCTTTCATTT 58.461 30.769 3.20 0.00 0.00 2.32
1265 3063 7.698130 AGCGTCAATGTTATAAGCTTTCATTTC 59.302 33.333 3.20 6.35 0.00 2.17
1266 3064 7.698130 GCGTCAATGTTATAAGCTTTCATTTCT 59.302 33.333 3.20 0.00 0.00 2.52
1267 3065 9.003112 CGTCAATGTTATAAGCTTTCATTTCTG 57.997 33.333 3.20 1.78 0.00 3.02
1268 3066 8.801913 GTCAATGTTATAAGCTTTCATTTCTGC 58.198 33.333 3.20 0.00 0.00 4.26
1270 3068 9.362539 CAATGTTATAAGCTTTCATTTCTGCTT 57.637 29.630 3.20 0.00 45.94 3.91
1271 3069 8.922058 ATGTTATAAGCTTTCATTTCTGCTTG 57.078 30.769 3.20 0.00 44.21 4.01
1272 3070 7.315142 TGTTATAAGCTTTCATTTCTGCTTGG 58.685 34.615 3.20 0.00 44.21 3.61
1275 3073 3.766545 AGCTTTCATTTCTGCTTGGGTA 58.233 40.909 0.00 0.00 30.96 3.69
1276 3074 3.507622 AGCTTTCATTTCTGCTTGGGTAC 59.492 43.478 0.00 0.00 30.96 3.34
1277 3075 3.255642 GCTTTCATTTCTGCTTGGGTACA 59.744 43.478 0.00 0.00 0.00 2.90
1278 3076 4.798574 CTTTCATTTCTGCTTGGGTACAC 58.201 43.478 0.00 0.00 0.00 2.90
1279 3077 2.790433 TCATTTCTGCTTGGGTACACC 58.210 47.619 0.00 0.00 40.81 4.16
1453 3289 6.071728 TGCATTTCCTTTTCTTGAGAGGAATC 60.072 38.462 14.13 9.58 45.99 2.52
1635 3471 4.606961 GGCAAAAATACCACCATCATACG 58.393 43.478 0.00 0.00 0.00 3.06
1673 3509 7.661536 TTCTATAGCTACTGGACTTGATTGT 57.338 36.000 0.00 0.00 0.00 2.71
1674 3510 8.762481 TTCTATAGCTACTGGACTTGATTGTA 57.238 34.615 0.00 0.00 0.00 2.41
1675 3511 8.397575 TCTATAGCTACTGGACTTGATTGTAG 57.602 38.462 0.00 0.00 35.17 2.74
1718 3579 8.887036 AGTTTGAAGTTTGAAGTTTGAAGTTT 57.113 26.923 0.00 0.00 0.00 2.66
1719 3580 8.764287 AGTTTGAAGTTTGAAGTTTGAAGTTTG 58.236 29.630 0.00 0.00 0.00 2.93
1720 3581 8.760569 GTTTGAAGTTTGAAGTTTGAAGTTTGA 58.239 29.630 0.00 0.00 0.00 2.69
1721 3582 8.879342 TTGAAGTTTGAAGTTTGAAGTTTGAA 57.121 26.923 0.00 0.00 0.00 2.69
1755 3616 6.932356 TCGTTCATACTACTACTTGGTAGG 57.068 41.667 9.14 0.00 42.29 3.18
1821 3685 0.391793 GCCTGGGAGGAAAGAGAACG 60.392 60.000 0.00 0.00 37.67 3.95
1843 3707 6.827727 ACGGGAATGAGCAATATAGTTAAGT 58.172 36.000 0.00 0.00 0.00 2.24
1903 3788 4.766404 ATAAAAACGTGAGGAAGCCTTG 57.234 40.909 0.00 0.00 31.76 3.61
1904 3789 2.341846 AAAACGTGAGGAAGCCTTGA 57.658 45.000 0.00 0.00 31.76 3.02
1905 3790 2.568623 AAACGTGAGGAAGCCTTGAT 57.431 45.000 0.00 0.00 31.76 2.57
1906 3791 2.568623 AACGTGAGGAAGCCTTGATT 57.431 45.000 0.00 0.00 31.76 2.57
1907 3792 3.695830 AACGTGAGGAAGCCTTGATTA 57.304 42.857 0.00 0.00 31.76 1.75
1908 3793 2.973945 ACGTGAGGAAGCCTTGATTAC 58.026 47.619 0.00 0.00 31.76 1.89
1924 3809 7.359181 GCCTTGATTACTTTGCACATGTAAAAC 60.359 37.037 0.00 7.41 31.25 2.43
1984 3869 2.817258 CCGAACACACACCCAATTACAT 59.183 45.455 0.00 0.00 0.00 2.29
1990 3875 8.237949 CGAACACACACCCAATTACATTAATAA 58.762 33.333 0.00 0.00 0.00 1.40
1991 3876 9.567848 GAACACACACCCAATTACATTAATAAG 57.432 33.333 0.00 0.00 0.00 1.73
1992 3877 8.871629 ACACACACCCAATTACATTAATAAGA 57.128 30.769 0.00 0.00 0.00 2.10
2067 3953 7.281324 TGGGTTTATATAAAGACCACGAATGTG 59.719 37.037 20.05 0.00 46.00 3.21
2175 5558 0.378610 GCCTATTTGTCGCTTCAGGC 59.621 55.000 0.00 0.00 41.57 4.85
2187 5570 1.678101 GCTTCAGGCGCCAATTTCTAT 59.322 47.619 31.54 0.76 0.00 1.98
2198 5581 5.390779 GCGCCAATTTCTATTGTTTTTGCAT 60.391 36.000 0.00 0.00 39.62 3.96
2200 5583 7.172757 CGCCAATTTCTATTGTTTTTGCATAC 58.827 34.615 0.00 0.00 39.62 2.39
2222 5605 1.670406 CGCCTGAAGCAGCTCACTT 60.670 57.895 0.00 0.00 44.04 3.16
2226 5609 1.226686 CTGAAGCAGCTCACTTGCGT 61.227 55.000 0.00 0.00 45.98 5.24
2245 5629 1.153549 GTCTAGTTGGGCGGCTCAG 60.154 63.158 9.56 0.00 0.00 3.35
2274 5658 1.941294 TCCTGTTTTCTTTAACGCGCA 59.059 42.857 5.73 0.00 0.00 6.09
2278 5662 4.487002 TGTTTTCTTTAACGCGCAAAAC 57.513 36.364 17.95 17.95 37.43 2.43
2361 5745 5.379732 TCTTGGAACTGTTTTGTTCGTTT 57.620 34.783 0.00 0.00 45.11 3.60
2362 5746 5.774630 TCTTGGAACTGTTTTGTTCGTTTT 58.225 33.333 0.00 0.00 45.11 2.43
2363 5747 5.859648 TCTTGGAACTGTTTTGTTCGTTTTC 59.140 36.000 0.00 0.00 45.11 2.29
2364 5748 4.487019 TGGAACTGTTTTGTTCGTTTTCC 58.513 39.130 0.00 0.00 45.11 3.13
2365 5749 3.861113 GGAACTGTTTTGTTCGTTTTCCC 59.139 43.478 0.00 0.00 45.11 3.97
2370 5754 5.407084 ACTGTTTTGTTCGTTTTCCCTTTTG 59.593 36.000 0.00 0.00 0.00 2.44
2376 5760 7.958053 TTGTTCGTTTTCCCTTTTGTTTTTA 57.042 28.000 0.00 0.00 0.00 1.52
2378 5762 7.965045 TGTTCGTTTTCCCTTTTGTTTTTATG 58.035 30.769 0.00 0.00 0.00 1.90
2456 5842 6.956299 TCTACTTTTACCTAAATGCGTGAC 57.044 37.500 0.00 0.00 0.00 3.67
2472 5858 4.202202 TGCGTGACCATTTTCTTCCAATTT 60.202 37.500 0.00 0.00 0.00 1.82
2522 5908 7.357951 ACTTTTCTTCAAGATCGATGAACTC 57.642 36.000 0.54 0.00 33.47 3.01
2535 5922 8.812329 AGATCGATGAACTCTTTTCTAAATTCG 58.188 33.333 0.54 0.00 0.00 3.34
2673 6168 9.647797 CTCAAATTCAATGATTTTCCAGATTCA 57.352 29.630 0.66 0.00 0.00 2.57
2679 6174 8.991243 TCAATGATTTTCCAGATTCAATGAAC 57.009 30.769 0.00 0.00 28.01 3.18
2747 6283 8.839310 TTTTCAAATTGGTGAACTTTCTTTCA 57.161 26.923 0.00 0.00 37.24 2.69
2914 6495 9.219603 CATATGTTAACTGAAGGAAGAGTCAAA 57.780 33.333 7.22 0.00 0.00 2.69
2915 6496 9.965902 ATATGTTAACTGAAGGAAGAGTCAAAT 57.034 29.630 7.22 0.00 0.00 2.32
2917 6498 9.793259 ATGTTAACTGAAGGAAGAGTCAAATAA 57.207 29.630 7.22 0.00 0.00 1.40
2918 6499 9.052759 TGTTAACTGAAGGAAGAGTCAAATAAC 57.947 33.333 7.22 0.00 31.71 1.89
2919 6500 9.052759 GTTAACTGAAGGAAGAGTCAAATAACA 57.947 33.333 0.00 0.00 31.56 2.41
2920 6501 7.497925 AACTGAAGGAAGAGTCAAATAACAC 57.502 36.000 0.00 0.00 0.00 3.32
2921 6502 6.831976 ACTGAAGGAAGAGTCAAATAACACT 58.168 36.000 0.00 0.00 0.00 3.55
2927 6508 7.283329 AGGAAGAGTCAAATAACACTGTTTCT 58.717 34.615 0.00 0.00 28.91 2.52
2947 6528 6.852858 TTCTGAATTGTTGTCAACGACATA 57.147 33.333 7.84 0.00 42.40 2.29
2990 6571 2.642254 GCATCTGCCAAGGCTTGCA 61.642 57.895 21.77 19.91 42.51 4.08
2995 6576 0.535335 CTGCCAAGGCTTGCATTCAT 59.465 50.000 21.77 0.00 42.51 2.57
3007 6588 4.274459 GCTTGCATTCATAGTTCGAATCCT 59.726 41.667 0.00 0.00 30.65 3.24
3009 6590 4.129380 TGCATTCATAGTTCGAATCCTGG 58.871 43.478 0.00 0.00 30.65 4.45
3027 6610 1.174783 GGTTCTCCAGTGAGCGACTA 58.825 55.000 0.00 0.00 38.58 2.59
3076 6659 2.803956 CCGGTGTGTTCGAGTATTTTGT 59.196 45.455 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.508030 TTGGTTGGGTGCATCTTATATCTA 57.492 37.500 0.00 0.00 0.00 1.98
2 3 5.387113 TTGGTTGGGTGCATCTTATATCT 57.613 39.130 0.00 0.00 0.00 1.98
3 4 7.611467 TGATATTGGTTGGGTGCATCTTATATC 59.389 37.037 0.00 2.58 0.00 1.63
6 7 5.704354 TGATATTGGTTGGGTGCATCTTAT 58.296 37.500 0.00 0.00 0.00 1.73
7 8 5.122707 TGATATTGGTTGGGTGCATCTTA 57.877 39.130 0.00 0.00 0.00 2.10
8 9 3.979911 TGATATTGGTTGGGTGCATCTT 58.020 40.909 0.00 0.00 0.00 2.40
9 10 3.668141 TGATATTGGTTGGGTGCATCT 57.332 42.857 0.00 0.00 0.00 2.90
10 11 5.072741 ACTATGATATTGGTTGGGTGCATC 58.927 41.667 0.00 0.00 0.00 3.91
11 12 5.065613 ACTATGATATTGGTTGGGTGCAT 57.934 39.130 0.00 0.00 0.00 3.96
12 13 4.518278 ACTATGATATTGGTTGGGTGCA 57.482 40.909 0.00 0.00 0.00 4.57
13 14 5.621193 AGTACTATGATATTGGTTGGGTGC 58.379 41.667 0.00 0.00 0.00 5.01
14 15 5.926542 CGAGTACTATGATATTGGTTGGGTG 59.073 44.000 0.00 0.00 0.00 4.61
15 16 5.510861 GCGAGTACTATGATATTGGTTGGGT 60.511 44.000 0.00 0.00 0.00 4.51
16 17 4.929808 GCGAGTACTATGATATTGGTTGGG 59.070 45.833 0.00 0.00 0.00 4.12
17 18 5.405571 GTGCGAGTACTATGATATTGGTTGG 59.594 44.000 0.00 0.00 0.00 3.77
18 19 5.983118 TGTGCGAGTACTATGATATTGGTTG 59.017 40.000 0.00 0.00 0.00 3.77
19 20 6.156748 TGTGCGAGTACTATGATATTGGTT 57.843 37.500 0.00 0.00 0.00 3.67
20 21 5.784578 TGTGCGAGTACTATGATATTGGT 57.215 39.130 0.00 0.00 0.00 3.67
21 22 7.477144 TTTTGTGCGAGTACTATGATATTGG 57.523 36.000 0.00 0.00 0.00 3.16
43 44 8.751302 ACTTTTCAATTTAGTCGTGTGTTTTT 57.249 26.923 0.00 0.00 0.00 1.94
50 51 9.968743 GGTCTTATACTTTTCAATTTAGTCGTG 57.031 33.333 0.00 0.00 0.00 4.35
51 52 9.715121 TGGTCTTATACTTTTCAATTTAGTCGT 57.285 29.630 0.00 0.00 0.00 4.34
60 61 9.515226 ACATAGCTTTGGTCTTATACTTTTCAA 57.485 29.630 9.08 0.00 0.00 2.69
61 62 8.946085 CACATAGCTTTGGTCTTATACTTTTCA 58.054 33.333 9.08 0.00 0.00 2.69
109 110 4.158764 TGTTGGTCACGGTTTTGATCTTTT 59.841 37.500 0.00 0.00 0.00 2.27
118 132 1.202817 GTGGTTTGTTGGTCACGGTTT 59.797 47.619 0.00 0.00 0.00 3.27
127 141 4.759782 TGGTAAATGTTGTGGTTTGTTGG 58.240 39.130 0.00 0.00 0.00 3.77
130 144 6.349777 CCGATATGGTAAATGTTGTGGTTTGT 60.350 38.462 0.00 0.00 0.00 2.83
135 149 5.562696 GCATCCGATATGGTAAATGTTGTGG 60.563 44.000 0.00 0.00 39.52 4.17
136 150 5.451908 GCATCCGATATGGTAAATGTTGTG 58.548 41.667 0.00 0.00 39.52 3.33
141 155 4.761739 AGTTGGCATCCGATATGGTAAATG 59.238 41.667 0.00 0.00 39.52 2.32
143 157 4.431416 AGTTGGCATCCGATATGGTAAA 57.569 40.909 0.00 0.00 39.52 2.01
145 159 5.023452 AGATAGTTGGCATCCGATATGGTA 58.977 41.667 0.00 0.00 39.52 3.25
154 168 3.812053 GTGTCATGAGATAGTTGGCATCC 59.188 47.826 0.00 0.00 0.00 3.51
157 171 2.571202 TGGTGTCATGAGATAGTTGGCA 59.429 45.455 0.00 0.00 0.00 4.92
158 172 2.939103 GTGGTGTCATGAGATAGTTGGC 59.061 50.000 0.00 0.00 0.00 4.52
160 174 3.614176 CACGTGGTGTCATGAGATAGTTG 59.386 47.826 7.95 0.00 34.18 3.16
162 176 2.166459 CCACGTGGTGTCATGAGATAGT 59.834 50.000 26.95 0.00 34.18 2.12
164 178 2.165641 GTCCACGTGGTGTCATGAGATA 59.834 50.000 32.74 7.31 36.34 1.98
167 181 1.008875 CGTCCACGTGGTGTCATGAG 61.009 60.000 32.74 12.88 36.34 2.90
180 194 4.232221 TGTTAAAGAATCTCGTCGTCCAC 58.768 43.478 0.00 0.00 0.00 4.02
181 195 4.508461 TGTTAAAGAATCTCGTCGTCCA 57.492 40.909 0.00 0.00 0.00 4.02
196 210 5.841810 CTTCCTGAAGGCATTGTTGTTAAA 58.158 37.500 0.00 0.00 34.87 1.52
210 224 0.969894 ACGTCACTCCCTTCCTGAAG 59.030 55.000 0.00 0.00 38.14 3.02
226 240 1.570967 GAAAGCGGCGGTTAAACGT 59.429 52.632 25.54 8.88 35.98 3.99
241 255 0.037975 GGTTGGACCTAGCGACGAAA 60.038 55.000 0.00 0.00 34.73 3.46
242 256 1.180456 TGGTTGGACCTAGCGACGAA 61.180 55.000 0.00 0.00 39.58 3.85
243 257 1.604308 TGGTTGGACCTAGCGACGA 60.604 57.895 0.00 0.00 39.58 4.20
248 262 0.111639 TTTGGGTGGTTGGACCTAGC 59.888 55.000 0.00 0.00 39.58 3.42
253 267 1.456705 TGGCTTTGGGTGGTTGGAC 60.457 57.895 0.00 0.00 0.00 4.02
262 276 7.495606 GGTGAAAATATAAATTCTGGCTTTGGG 59.504 37.037 3.44 0.00 0.00 4.12
263 277 7.495606 GGGTGAAAATATAAATTCTGGCTTTGG 59.504 37.037 3.44 0.00 0.00 3.28
264 278 8.040132 TGGGTGAAAATATAAATTCTGGCTTTG 58.960 33.333 3.44 0.00 0.00 2.77
265 279 8.144862 TGGGTGAAAATATAAATTCTGGCTTT 57.855 30.769 3.44 0.00 0.00 3.51
266 280 7.619302 TCTGGGTGAAAATATAAATTCTGGCTT 59.381 33.333 3.44 0.00 0.00 4.35
267 281 7.125391 TCTGGGTGAAAATATAAATTCTGGCT 58.875 34.615 3.44 0.00 0.00 4.75
268 282 7.346751 TCTGGGTGAAAATATAAATTCTGGC 57.653 36.000 3.44 0.00 0.00 4.85
269 283 9.189156 TCTTCTGGGTGAAAATATAAATTCTGG 57.811 33.333 3.44 0.00 33.79 3.86
276 290 7.872138 ACTGGATCTTCTGGGTGAAAATATAA 58.128 34.615 0.00 0.00 33.79 0.98
279 293 5.339200 GGACTGGATCTTCTGGGTGAAAATA 60.339 44.000 0.00 0.00 33.79 1.40
294 308 2.300152 TCGGATATGCTTGGACTGGATC 59.700 50.000 0.00 0.00 0.00 3.36
304 318 3.482156 AGTCATTGCTCGGATATGCTT 57.518 42.857 0.00 0.00 0.00 3.91
311 325 3.751175 CCTTGTTAAAGTCATTGCTCGGA 59.249 43.478 0.00 0.00 0.00 4.55
315 329 6.952773 TGTTACCTTGTTAAAGTCATTGCT 57.047 33.333 0.00 0.00 0.00 3.91
346 360 7.517320 TGGTTATACCTAGCAATGATGATGTT 58.483 34.615 0.00 0.00 39.58 2.71
361 375 6.784969 ACATCTTATCTGAGCTGGTTATACCT 59.215 38.462 0.00 0.00 39.58 3.08
372 386 3.504134 TCGAGCCTACATCTTATCTGAGC 59.496 47.826 0.00 0.00 0.00 4.26
376 390 4.076394 GGTCTCGAGCCTACATCTTATCT 58.924 47.826 7.81 0.00 0.00 1.98
377 391 3.120130 CGGTCTCGAGCCTACATCTTATC 60.120 52.174 19.30 0.00 39.00 1.75
381 395 0.820074 CCGGTCTCGAGCCTACATCT 60.820 60.000 19.30 0.00 39.00 2.90
382 396 1.655329 CCGGTCTCGAGCCTACATC 59.345 63.158 19.30 0.00 39.00 3.06
383 397 1.828660 CCCGGTCTCGAGCCTACAT 60.829 63.158 19.30 0.00 39.00 2.29
384 398 2.439701 CCCGGTCTCGAGCCTACA 60.440 66.667 19.30 0.00 39.00 2.74
395 409 4.436998 CCACTCGAGCACCCGGTC 62.437 72.222 13.61 0.00 36.25 4.79
421 435 7.201435 GCAGCGATAACATATAAATGATGTCGA 60.201 37.037 15.30 0.00 45.79 4.20
426 440 6.881065 AGTGGCAGCGATAACATATAAATGAT 59.119 34.615 0.00 0.00 36.54 2.45
429 443 7.510549 AAAGTGGCAGCGATAACATATAAAT 57.489 32.000 0.00 0.00 0.00 1.40
430 444 6.935741 AAAGTGGCAGCGATAACATATAAA 57.064 33.333 0.00 0.00 0.00 1.40
431 445 6.017440 GGAAAAGTGGCAGCGATAACATATAA 60.017 38.462 0.00 0.00 0.00 0.98
432 446 5.468746 GGAAAAGTGGCAGCGATAACATATA 59.531 40.000 0.00 0.00 0.00 0.86
433 447 4.275936 GGAAAAGTGGCAGCGATAACATAT 59.724 41.667 0.00 0.00 0.00 1.78
434 448 3.625764 GGAAAAGTGGCAGCGATAACATA 59.374 43.478 0.00 0.00 0.00 2.29
435 449 2.423538 GGAAAAGTGGCAGCGATAACAT 59.576 45.455 0.00 0.00 0.00 2.71
436 450 1.810151 GGAAAAGTGGCAGCGATAACA 59.190 47.619 0.00 0.00 0.00 2.41
437 451 1.810151 TGGAAAAGTGGCAGCGATAAC 59.190 47.619 0.00 0.00 0.00 1.89
438 452 1.810151 GTGGAAAAGTGGCAGCGATAA 59.190 47.619 0.00 0.00 0.00 1.75
439 453 1.003118 AGTGGAAAAGTGGCAGCGATA 59.997 47.619 0.00 0.00 0.00 2.92
440 454 0.250901 AGTGGAAAAGTGGCAGCGAT 60.251 50.000 0.00 0.00 0.00 4.58
441 455 0.394938 TAGTGGAAAAGTGGCAGCGA 59.605 50.000 0.00 0.00 0.00 4.93
442 456 1.398390 GATAGTGGAAAAGTGGCAGCG 59.602 52.381 0.00 0.00 0.00 5.18
443 457 1.745653 GGATAGTGGAAAAGTGGCAGC 59.254 52.381 0.00 0.00 0.00 5.25
444 458 2.290896 TGGGATAGTGGAAAAGTGGCAG 60.291 50.000 0.00 0.00 0.00 4.85
445 459 1.707989 TGGGATAGTGGAAAAGTGGCA 59.292 47.619 0.00 0.00 0.00 4.92
457 471 4.776349 TCGCATGTAATTGTTGGGATAGT 58.224 39.130 0.00 0.00 0.00 2.12
511 525 8.865590 TTGATTGAAGTTGATGATAATGCATG 57.134 30.769 0.00 0.00 0.00 4.06
527 541 3.909776 TGCAGCTGTTCTTGATTGAAG 57.090 42.857 16.64 0.00 0.00 3.02
602 616 3.135225 GTTTTATGCCGCCAAAAGGTTT 58.865 40.909 1.35 0.00 0.00 3.27
612 630 2.595386 CTTCACAAGGTTTTATGCCGC 58.405 47.619 0.00 0.00 0.00 6.53
771 2562 1.757731 TGCCAAAGCTTGCAGTGGT 60.758 52.632 14.81 0.00 40.80 4.16
786 2577 0.954452 CACCTCCAACTGTTTCTGCC 59.046 55.000 0.00 0.00 0.00 4.85
892 2690 4.455070 TCGAGATCAGAGGGATAAAGGA 57.545 45.455 0.00 0.00 36.00 3.36
893 2691 4.159506 GGATCGAGATCAGAGGGATAAAGG 59.840 50.000 14.21 0.00 39.54 3.11
894 2692 4.142491 CGGATCGAGATCAGAGGGATAAAG 60.142 50.000 14.21 0.00 39.54 1.85
897 2695 2.356227 CCGGATCGAGATCAGAGGGATA 60.356 54.545 14.21 0.00 39.54 2.59
926 2724 3.331150 CATCCGCGCCCATAACTTATAA 58.669 45.455 0.00 0.00 0.00 0.98
1237 3035 6.908825 TGAAAGCTTATAACATTGACGCTTT 58.091 32.000 14.77 14.77 45.52 3.51
1280 3078 8.893219 TTGCTGAAGAAACATGACCTATATAG 57.107 34.615 0.00 2.46 0.00 1.31
1309 3107 5.598769 AGACCTATATGCACGGACTTTTAC 58.401 41.667 0.00 0.00 0.00 2.01
1398 3234 6.741992 CAGACTTGCAGTAAATGTCCAATA 57.258 37.500 0.00 0.00 0.00 1.90
1453 3289 1.526887 CTGCACTAACAGTCCAACACG 59.473 52.381 0.00 0.00 32.78 4.49
1673 3509 9.582648 TCAAACTATATATCCAGTACTGTGCTA 57.417 33.333 21.18 9.87 0.00 3.49
1674 3510 8.478775 TCAAACTATATATCCAGTACTGTGCT 57.521 34.615 21.18 8.03 0.00 4.40
1675 3511 9.197694 CTTCAAACTATATATCCAGTACTGTGC 57.802 37.037 21.18 0.00 0.00 4.57
1708 3569 2.869897 TGGCGTGTTCAAACTTCAAAC 58.130 42.857 0.00 0.00 0.00 2.93
1709 3570 3.577649 TTGGCGTGTTCAAACTTCAAA 57.422 38.095 0.00 0.00 0.00 2.69
1710 3571 3.791973 ATTGGCGTGTTCAAACTTCAA 57.208 38.095 0.00 0.00 0.00 2.69
1711 3572 4.377943 CGATATTGGCGTGTTCAAACTTCA 60.378 41.667 0.00 0.00 0.00 3.02
1712 3573 4.088648 CGATATTGGCGTGTTCAAACTTC 58.911 43.478 0.00 0.00 0.00 3.01
1713 3574 3.500680 ACGATATTGGCGTGTTCAAACTT 59.499 39.130 0.00 0.00 40.94 2.66
1714 3575 3.071479 ACGATATTGGCGTGTTCAAACT 58.929 40.909 0.00 0.00 40.94 2.66
1715 3576 3.465122 ACGATATTGGCGTGTTCAAAC 57.535 42.857 0.00 0.00 40.94 2.93
1716 3577 3.498777 TGAACGATATTGGCGTGTTCAAA 59.501 39.130 3.82 0.00 44.06 2.69
1717 3578 3.067833 TGAACGATATTGGCGTGTTCAA 58.932 40.909 3.82 0.00 44.06 2.69
1718 3579 2.689646 TGAACGATATTGGCGTGTTCA 58.310 42.857 2.26 2.26 44.61 3.18
1719 3580 3.944422 ATGAACGATATTGGCGTGTTC 57.056 42.857 0.00 0.00 41.75 3.18
1720 3581 4.439057 AGTATGAACGATATTGGCGTGTT 58.561 39.130 0.00 0.00 41.75 3.32
1721 3582 4.054780 AGTATGAACGATATTGGCGTGT 57.945 40.909 0.00 0.00 41.75 4.49
1755 3616 2.038387 AGCCCACGGATAACATCAAC 57.962 50.000 0.00 0.00 0.00 3.18
1821 3685 7.604545 GGAGACTTAACTATATTGCTCATTCCC 59.395 40.741 0.00 0.00 0.00 3.97
1843 3707 2.364970 TGTTCGTCCCTTTAAACGGAGA 59.635 45.455 6.21 4.44 39.31 3.71
1903 3788 6.089417 GGCTGTTTTACATGTGCAAAGTAATC 59.911 38.462 9.11 0.00 0.00 1.75
1904 3789 5.925969 GGCTGTTTTACATGTGCAAAGTAAT 59.074 36.000 9.11 0.00 0.00 1.89
1905 3790 5.068460 AGGCTGTTTTACATGTGCAAAGTAA 59.932 36.000 9.11 0.00 0.00 2.24
1906 3791 4.582656 AGGCTGTTTTACATGTGCAAAGTA 59.417 37.500 9.11 0.00 0.00 2.24
1907 3792 3.384467 AGGCTGTTTTACATGTGCAAAGT 59.616 39.130 9.11 0.00 0.00 2.66
1908 3793 3.981211 AGGCTGTTTTACATGTGCAAAG 58.019 40.909 9.11 0.95 0.00 2.77
1924 3809 3.645884 CTCCAAATCACACAAAAGGCTG 58.354 45.455 0.00 0.00 0.00 4.85
2067 3953 3.814283 CAGCTAGCTTCATCCATTTCCTC 59.186 47.826 16.46 0.00 0.00 3.71
2156 5539 0.378610 GCCTGAAGCGACAAATAGGC 59.621 55.000 0.00 0.00 43.20 3.93
2175 5558 5.588568 TGCAAAAACAATAGAAATTGGCG 57.411 34.783 3.41 0.00 45.72 5.69
2187 5570 0.664767 GCGCCGGTATGCAAAAACAA 60.665 50.000 1.90 0.00 0.00 2.83
2198 5581 4.451150 CTGCTTCAGGCGCCGGTA 62.451 66.667 26.04 16.18 45.43 4.02
2222 5605 2.048597 CGCCCAACTAGACACGCA 60.049 61.111 0.00 0.00 0.00 5.24
2226 5609 1.888436 CTGAGCCGCCCAACTAGACA 61.888 60.000 0.00 0.00 0.00 3.41
2293 5677 5.753438 TGAAAAGCTATAGTAATCACGCCTG 59.247 40.000 0.84 0.00 0.00 4.85
2362 5746 9.508642 ACAAAAGAAACATAAAAACAAAAGGGA 57.491 25.926 0.00 0.00 0.00 4.20
2437 5823 5.560966 ATGGTCACGCATTTAGGTAAAAG 57.439 39.130 0.00 0.00 0.00 2.27
2442 5828 4.079253 AGAAAATGGTCACGCATTTAGGT 58.921 39.130 5.09 0.00 31.56 3.08
2443 5829 4.701956 AGAAAATGGTCACGCATTTAGG 57.298 40.909 5.09 0.00 31.56 2.69
2451 5837 5.175491 CACAAATTGGAAGAAAATGGTCACG 59.825 40.000 0.00 0.00 0.00 4.35
2472 5858 9.920133 TTCATCGATTTTGAAAAATATTCCACA 57.080 25.926 0.00 0.00 38.64 4.17
2494 5880 7.912056 TCATCGATCTTGAAGAAAAGTTCAT 57.088 32.000 0.00 0.00 36.34 2.57
2575 5962 9.778993 CTTCGATATTGAAAACTGTTCATCAAT 57.221 29.630 24.97 24.97 43.08 2.57
2578 5965 9.994432 ATTCTTCGATATTGAAAACTGTTCATC 57.006 29.630 6.84 0.00 0.00 2.92
2731 6267 6.857956 TCGATTTTTGAAAGAAAGTTCACCA 58.142 32.000 0.00 0.00 37.24 4.17
2836 6417 9.474920 TCAAATGAAAGCATTAATTCGAAAACT 57.525 25.926 0.00 0.00 43.71 2.66
2888 6469 8.777865 TTGACTCTTCCTTCAGTTAACATATG 57.222 34.615 8.61 0.00 0.00 1.78
2898 6479 6.708054 ACAGTGTTATTTGACTCTTCCTTCAG 59.292 38.462 0.00 0.00 0.00 3.02
2900 6481 7.497925 AACAGTGTTATTTGACTCTTCCTTC 57.502 36.000 6.75 0.00 0.00 3.46
2914 6495 7.995289 TGACAACAATTCAGAAACAGTGTTAT 58.005 30.769 9.37 0.00 0.00 1.89
2915 6496 7.384439 TGACAACAATTCAGAAACAGTGTTA 57.616 32.000 9.37 0.00 0.00 2.41
2916 6497 6.266168 TGACAACAATTCAGAAACAGTGTT 57.734 33.333 1.64 1.64 0.00 3.32
2917 6498 5.895636 TGACAACAATTCAGAAACAGTGT 57.104 34.783 0.00 0.00 0.00 3.55
2918 6499 5.227805 CGTTGACAACAATTCAGAAACAGTG 59.772 40.000 18.09 0.00 38.32 3.66
2919 6500 5.123186 TCGTTGACAACAATTCAGAAACAGT 59.877 36.000 18.09 0.00 38.32 3.55
2920 6501 5.452302 GTCGTTGACAACAATTCAGAAACAG 59.548 40.000 18.09 0.00 38.32 3.16
2921 6502 5.106515 TGTCGTTGACAACAATTCAGAAACA 60.107 36.000 18.09 5.18 39.78 2.83
2927 6508 4.609559 GCGTATGTCGTTGACAACAATTCA 60.610 41.667 18.09 10.62 45.96 2.57
2990 6571 6.240549 AGAACCAGGATTCGAACTATGAAT 57.759 37.500 0.00 0.00 38.71 2.57
2995 6576 3.437213 TGGAGAACCAGGATTCGAACTA 58.563 45.455 0.00 0.00 41.77 2.24
3007 6588 0.827925 AGTCGCTCACTGGAGAACCA 60.828 55.000 0.00 0.00 44.26 3.67
3009 6590 2.085320 TCTAGTCGCTCACTGGAGAAC 58.915 52.381 0.00 0.00 44.26 3.01
3017 6598 1.813786 AGAGGTGTTCTAGTCGCTCAC 59.186 52.381 0.00 0.00 33.23 3.51
3054 6637 2.803956 CAAAATACTCGAACACACCGGT 59.196 45.455 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.