Multiple sequence alignment - TraesCS6B01G155400

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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 TraesCS6B01G155400 chr6B 100.000 2681 0 0 1 2681 158164042 158161362 0.000000e+00 4951
1 TraesCS6B01G155400 chr6B 84.524 1861 265 16 820 2672 159377793 159379638 0.000000e+00 1820
2 TraesCS6B01G155400 chr6B 86.255 1637 209 13 1055 2681 158149775 158148145 0.000000e+00 1762
3 TraesCS6B01G155400 chr6B 86.157 1647 205 21 1048 2681 159402088 159403724 0.000000e+00 1757
4 TraesCS6B01G155400 chr6D 96.903 2228 59 7 459 2681 83160970 83158748 0.000000e+00 3723
5 TraesCS6B01G155400 chr6D 86.752 1638 199 17 1055 2681 83124706 83123076 0.000000e+00 1807
6 TraesCS6B01G155400 chr6D 85.143 1750 246 14 940 2681 83046957 83045214 0.000000e+00 1779
7 TraesCS6B01G155400 chr6D 86.177 1635 209 14 1048 2672 83540620 83542247 0.000000e+00 1751
8 TraesCS6B01G155400 chr6A 96.095 2228 77 7 459 2681 100229440 100227218 0.000000e+00 3624
9 TraesCS6B01G155400 chr6A 85.628 1823 252 10 866 2681 100738095 100739914 0.000000e+00 1906
10 TraesCS6B01G155400 chr6A 81.414 382 57 10 1 375 24249456 24249082 1.560000e-77 300
11 TraesCS6B01G155400 chr6A 86.441 177 22 2 1 176 484080680 484080505 2.720000e-45 193
12 TraesCS6B01G155400 chr2B 86.499 437 52 6 1 433 5440704 5440271 8.690000e-130 473
13 TraesCS6B01G155400 chr2B 89.831 177 18 0 1 177 768458203 768458379 7.470000e-56 228
14 TraesCS6B01G155400 chr7A 86.215 428 46 8 1 422 506287428 506287848 4.070000e-123 451
15 TraesCS6B01G155400 chrUn 85.476 420 52 7 1 412 26663010 26662592 1.910000e-116 429
16 TraesCS6B01G155400 chrUn 88.318 214 24 1 226 438 93758658 93758445 3.430000e-64 255
17 TraesCS6B01G155400 chr1B 84.862 436 51 7 1 431 58085969 58085544 2.470000e-115 425
18 TraesCS6B01G155400 chr1B 79.872 467 52 28 1 430 377662881 377663342 1.210000e-78 303
19 TraesCS6B01G155400 chr1B 85.388 219 25 5 219 431 73038691 73038908 1.250000e-53 220
20 TraesCS6B01G155400 chr4A 82.045 440 62 16 1 430 516180611 516180179 2.540000e-95 359
21 TraesCS6B01G155400 chr4A 79.511 327 43 16 124 430 667095812 667095490 7.520000e-51 211
22 TraesCS6B01G155400 chr3D 86.611 239 28 4 209 444 421292340 421292103 7.360000e-66 261
23 TraesCS6B01G155400 chr3D 94.366 142 7 1 1 142 421292472 421292332 1.620000e-52 217
24 TraesCS6B01G155400 chr3B 84.071 226 28 5 219 437 144212094 144212318 7.520000e-51 211
25 TraesCS6B01G155400 chr4B 84.834 211 29 3 219 426 5806581 5806791 2.700000e-50 209


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 TraesCS6B01G155400 chr6B 158161362 158164042 2680 True 4951 4951 100.000 1 2681 1 chr6B.!!$R2 2680
1 TraesCS6B01G155400 chr6B 159377793 159379638 1845 False 1820 1820 84.524 820 2672 1 chr6B.!!$F1 1852
2 TraesCS6B01G155400 chr6B 158148145 158149775 1630 True 1762 1762 86.255 1055 2681 1 chr6B.!!$R1 1626
3 TraesCS6B01G155400 chr6B 159402088 159403724 1636 False 1757 1757 86.157 1048 2681 1 chr6B.!!$F2 1633
4 TraesCS6B01G155400 chr6D 83158748 83160970 2222 True 3723 3723 96.903 459 2681 1 chr6D.!!$R3 2222
5 TraesCS6B01G155400 chr6D 83123076 83124706 1630 True 1807 1807 86.752 1055 2681 1 chr6D.!!$R2 1626
6 TraesCS6B01G155400 chr6D 83045214 83046957 1743 True 1779 1779 85.143 940 2681 1 chr6D.!!$R1 1741
7 TraesCS6B01G155400 chr6D 83540620 83542247 1627 False 1751 1751 86.177 1048 2672 1 chr6D.!!$F1 1624
8 TraesCS6B01G155400 chr6A 100227218 100229440 2222 True 3624 3624 96.095 459 2681 1 chr6A.!!$R2 2222
9 TraesCS6B01G155400 chr6A 100738095 100739914 1819 False 1906 1906 85.628 866 2681 1 chr6A.!!$F1 1815

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
68 69 0.030908 CGATGGAGAGGAACCTACGC 59.969 60.0 0.00 0.00 0.00 4.42 F
434 435 0.036294 GGAGGGAAGGGTTTCACGAG 60.036 60.0 0.00 0.00 41.75 4.18 F
442 443 0.108567 GGGTTTCACGAGAGGAGCTC 60.109 60.0 4.71 4.71 40.38 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 1235 0.439985 CAGCGAAACATCAGTGACCG 59.560 55.0 0.00 0.0 0.00 4.79 R
1305 1308 0.465460 ACAGGTTGAGGCGCAAAAGA 60.465 50.0 10.83 0.0 38.44 2.52 R
1707 1711 0.842030 TCTGGAAGTGCCCCACTGAT 60.842 55.0 0.00 0.0 44.62 2.90 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
57 58 4.451150 GCACGCCCACGATGGAGA 62.451 66.667 5.71 0.00 40.96 3.71
58 59 2.202797 CACGCCCACGATGGAGAG 60.203 66.667 5.71 1.72 40.96 3.20
59 60 3.461773 ACGCCCACGATGGAGAGG 61.462 66.667 5.71 0.00 40.96 3.69
60 61 3.147595 CGCCCACGATGGAGAGGA 61.148 66.667 5.71 0.00 40.96 3.71
61 62 2.721167 CGCCCACGATGGAGAGGAA 61.721 63.158 5.71 0.00 40.96 3.36
62 63 1.153349 GCCCACGATGGAGAGGAAC 60.153 63.158 5.71 0.00 40.96 3.62
63 64 1.522569 CCCACGATGGAGAGGAACC 59.477 63.158 5.71 0.00 40.96 3.62
64 65 0.978146 CCCACGATGGAGAGGAACCT 60.978 60.000 5.71 0.00 40.96 3.50
65 66 1.688311 CCCACGATGGAGAGGAACCTA 60.688 57.143 5.71 0.00 40.96 3.08
66 67 1.409427 CCACGATGGAGAGGAACCTAC 59.591 57.143 0.00 0.00 40.96 3.18
67 68 1.065701 CACGATGGAGAGGAACCTACG 59.934 57.143 0.00 0.00 34.90 3.51
68 69 0.030908 CGATGGAGAGGAACCTACGC 59.969 60.000 0.00 0.00 0.00 4.42
69 70 1.112113 GATGGAGAGGAACCTACGCA 58.888 55.000 0.00 0.00 0.00 5.24
70 71 1.067821 GATGGAGAGGAACCTACGCAG 59.932 57.143 0.00 0.00 0.00 5.18
71 72 1.142097 GGAGAGGAACCTACGCAGC 59.858 63.158 0.00 0.00 0.00 5.25
72 73 1.142097 GAGAGGAACCTACGCAGCC 59.858 63.158 0.00 0.00 0.00 4.85
73 74 2.202756 GAGGAACCTACGCAGCCG 60.203 66.667 0.00 0.00 41.14 5.52
74 75 4.452733 AGGAACCTACGCAGCCGC 62.453 66.667 0.00 0.00 38.22 6.53
76 77 4.752879 GAACCTACGCAGCCGCCA 62.753 66.667 0.00 0.00 38.22 5.69
77 78 4.760047 AACCTACGCAGCCGCCAG 62.760 66.667 0.00 0.00 38.22 4.85
158 159 4.332637 CAAGGCGTGCACCACTGC 62.333 66.667 12.15 8.67 44.52 4.40
181 182 4.246206 CGGCCACGCAGCATCATG 62.246 66.667 2.24 0.00 0.00 3.07
182 183 4.564116 GGCCACGCAGCATCATGC 62.564 66.667 0.00 0.00 45.46 4.06
191 192 2.805546 GCATCATGCACTGCCAGG 59.194 61.111 4.20 0.00 44.26 4.45
192 193 2.782222 GCATCATGCACTGCCAGGG 61.782 63.158 4.20 0.00 44.26 4.45
193 194 2.125326 CATCATGCACTGCCAGGGG 61.125 63.158 0.00 0.00 0.00 4.79
194 195 3.369410 ATCATGCACTGCCAGGGGG 62.369 63.158 0.00 0.00 37.18 5.40
239 240 4.821589 GCCCGCACTCGAAGGAGG 62.822 72.222 0.00 0.00 44.93 4.30
240 241 3.068691 CCCGCACTCGAAGGAGGA 61.069 66.667 7.24 0.00 44.93 3.71
241 242 2.492090 CCGCACTCGAAGGAGGAG 59.508 66.667 0.18 0.00 44.93 3.69
242 243 2.202676 CGCACTCGAAGGAGGAGC 60.203 66.667 0.00 0.00 44.93 4.70
243 244 2.185608 GCACTCGAAGGAGGAGCC 59.814 66.667 0.00 0.00 44.93 4.70
244 245 2.896443 CACTCGAAGGAGGAGCCC 59.104 66.667 0.00 0.00 44.93 5.19
245 246 2.756283 ACTCGAAGGAGGAGCCCG 60.756 66.667 0.00 0.00 44.93 6.13
246 247 4.214327 CTCGAAGGAGGAGCCCGC 62.214 72.222 0.00 0.00 36.61 6.13
267 268 4.873129 GCCTCATCGCGCGGAGAA 62.873 66.667 29.67 14.03 32.87 2.87
268 269 2.656651 CCTCATCGCGCGGAGAAG 60.657 66.667 29.67 21.29 32.87 2.85
269 270 2.656651 CTCATCGCGCGGAGAAGG 60.657 66.667 31.69 12.72 32.87 3.46
270 271 3.126074 CTCATCGCGCGGAGAAGGA 62.126 63.158 31.69 16.68 32.87 3.36
271 272 2.202743 CATCGCGCGGAGAAGGAA 60.203 61.111 31.69 8.20 0.00 3.36
272 273 1.809619 CATCGCGCGGAGAAGGAAA 60.810 57.895 31.69 7.32 0.00 3.13
273 274 1.079405 ATCGCGCGGAGAAGGAAAA 60.079 52.632 31.69 6.44 0.00 2.29
274 275 0.672401 ATCGCGCGGAGAAGGAAAAA 60.672 50.000 31.69 5.82 0.00 1.94
275 276 1.154469 CGCGCGGAGAAGGAAAAAC 60.154 57.895 24.84 0.00 0.00 2.43
276 277 1.209383 GCGCGGAGAAGGAAAAACC 59.791 57.895 8.83 0.00 39.35 3.27
277 278 1.873863 CGCGGAGAAGGAAAAACCC 59.126 57.895 0.00 0.00 40.05 4.11
278 279 1.873863 GCGGAGAAGGAAAAACCCG 59.126 57.895 0.00 0.00 40.05 5.28
279 280 1.873863 CGGAGAAGGAAAAACCCGC 59.126 57.895 0.00 0.00 40.05 6.13
280 281 1.583495 CGGAGAAGGAAAAACCCGCC 61.583 60.000 0.00 0.00 40.05 6.13
281 282 1.248785 GGAGAAGGAAAAACCCGCCC 61.249 60.000 0.00 0.00 40.05 6.13
282 283 1.228769 AGAAGGAAAAACCCGCCCC 60.229 57.895 0.00 0.00 40.05 5.80
283 284 1.532078 GAAGGAAAAACCCGCCCCA 60.532 57.895 0.00 0.00 40.05 4.96
284 285 1.812686 GAAGGAAAAACCCGCCCCAC 61.813 60.000 0.00 0.00 40.05 4.61
285 286 3.307906 GGAAAAACCCGCCCCACC 61.308 66.667 0.00 0.00 0.00 4.61
286 287 2.522193 GAAAAACCCGCCCCACCA 60.522 61.111 0.00 0.00 0.00 4.17
287 288 2.840572 AAAAACCCGCCCCACCAC 60.841 61.111 0.00 0.00 0.00 4.16
288 289 4.926162 AAAACCCGCCCCACCACC 62.926 66.667 0.00 0.00 0.00 4.61
346 347 4.803908 GGCGGCAAGGGAGGAAGG 62.804 72.222 3.07 0.00 0.00 3.46
347 348 3.717294 GCGGCAAGGGAGGAAGGA 61.717 66.667 0.00 0.00 0.00 3.36
348 349 2.586792 CGGCAAGGGAGGAAGGAG 59.413 66.667 0.00 0.00 0.00 3.69
349 350 3.002371 GGCAAGGGAGGAAGGAGG 58.998 66.667 0.00 0.00 0.00 4.30
350 351 1.616628 GGCAAGGGAGGAAGGAGGA 60.617 63.158 0.00 0.00 0.00 3.71
351 352 1.631071 GGCAAGGGAGGAAGGAGGAG 61.631 65.000 0.00 0.00 0.00 3.69
352 353 1.631071 GCAAGGGAGGAAGGAGGAGG 61.631 65.000 0.00 0.00 0.00 4.30
353 354 0.043334 CAAGGGAGGAAGGAGGAGGA 59.957 60.000 0.00 0.00 0.00 3.71
354 355 0.341609 AAGGGAGGAAGGAGGAGGAG 59.658 60.000 0.00 0.00 0.00 3.69
355 356 1.074850 GGGAGGAAGGAGGAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
356 357 1.074850 GGAGGAAGGAGGAGGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
357 358 1.074850 GAGGAAGGAGGAGGAGGGG 60.075 68.421 0.00 0.00 0.00 4.79
358 359 1.550374 AGGAAGGAGGAGGAGGGGA 60.550 63.158 0.00 0.00 0.00 4.81
359 360 1.074850 GGAAGGAGGAGGAGGGGAG 60.075 68.421 0.00 0.00 0.00 4.30
360 361 1.074850 GAAGGAGGAGGAGGGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
361 362 3.339951 AAGGAGGAGGAGGGGAGGC 62.340 68.421 0.00 0.00 0.00 4.70
362 363 4.890306 GGAGGAGGAGGGGAGGCC 62.890 77.778 0.00 0.00 0.00 5.19
389 390 2.757145 GGGGGATCTAGGCTCCCTCC 62.757 70.000 22.99 19.26 46.39 4.30
390 391 4.551148 GGATCTAGGCTCCCTCCC 57.449 66.667 0.00 0.00 34.61 4.30
391 392 1.608046 GGATCTAGGCTCCCTCCCG 60.608 68.421 0.00 0.00 34.61 5.14
392 393 1.608046 GATCTAGGCTCCCTCCCGG 60.608 68.421 0.00 0.00 34.61 5.73
393 394 3.837213 ATCTAGGCTCCCTCCCGGC 62.837 68.421 0.00 0.00 34.61 6.13
429 430 2.045242 GCGGGAGGGAAGGGTTTC 60.045 66.667 0.00 0.00 0.00 2.78
430 431 2.902457 GCGGGAGGGAAGGGTTTCA 61.902 63.158 0.00 0.00 34.90 2.69
431 432 1.002502 CGGGAGGGAAGGGTTTCAC 60.003 63.158 0.00 0.00 36.96 3.18
432 433 1.002502 GGGAGGGAAGGGTTTCACG 60.003 63.158 0.00 0.00 41.75 4.35
433 434 1.486145 GGGAGGGAAGGGTTTCACGA 61.486 60.000 0.00 0.00 41.75 4.35
434 435 0.036294 GGAGGGAAGGGTTTCACGAG 60.036 60.000 0.00 0.00 41.75 4.18
435 436 0.974383 GAGGGAAGGGTTTCACGAGA 59.026 55.000 0.00 0.00 41.75 4.04
436 437 0.977395 AGGGAAGGGTTTCACGAGAG 59.023 55.000 0.00 0.00 41.75 3.20
437 438 0.036294 GGGAAGGGTTTCACGAGAGG 60.036 60.000 0.00 0.00 34.90 3.69
438 439 0.974383 GGAAGGGTTTCACGAGAGGA 59.026 55.000 0.00 0.00 34.90 3.71
439 440 1.066787 GGAAGGGTTTCACGAGAGGAG 60.067 57.143 0.00 0.00 34.90 3.69
440 441 0.321996 AAGGGTTTCACGAGAGGAGC 59.678 55.000 0.00 0.00 0.00 4.70
441 442 0.543174 AGGGTTTCACGAGAGGAGCT 60.543 55.000 0.00 0.00 0.00 4.09
442 443 0.108567 GGGTTTCACGAGAGGAGCTC 60.109 60.000 4.71 4.71 40.38 4.09
443 444 0.108567 GGTTTCACGAGAGGAGCTCC 60.109 60.000 26.22 26.22 40.70 4.70
444 445 0.456995 GTTTCACGAGAGGAGCTCCG 60.457 60.000 26.95 17.09 40.70 4.63
445 446 2.214181 TTTCACGAGAGGAGCTCCGC 62.214 60.000 27.43 27.43 40.70 5.54
446 447 4.544689 CACGAGAGGAGCTCCGCG 62.545 72.222 30.66 30.66 40.70 6.46
447 448 4.779966 ACGAGAGGAGCTCCGCGA 62.780 66.667 35.52 0.00 40.70 5.87
448 449 3.509757 CGAGAGGAGCTCCGCGAA 61.510 66.667 29.55 0.00 40.70 4.70
449 450 2.885861 GAGAGGAGCTCCGCGAAA 59.114 61.111 27.99 0.00 40.98 3.46
450 451 1.226831 GAGAGGAGCTCCGCGAAAG 60.227 63.158 27.99 5.80 40.98 2.62
451 452 2.202810 GAGGAGCTCCGCGAAAGG 60.203 66.667 26.95 0.00 42.08 3.11
452 453 4.459089 AGGAGCTCCGCGAAAGGC 62.459 66.667 26.95 6.04 42.08 4.35
596 597 4.184629 GCTCTTCTCCAAATCATGTACGT 58.815 43.478 0.00 0.00 0.00 3.57
615 617 3.964909 CGTGAATCGTCCATCACAGATA 58.035 45.455 6.70 0.00 44.84 1.98
619 621 5.580691 GTGAATCGTCCATCACAGATAACAA 59.419 40.000 1.30 0.00 44.19 2.83
629 631 3.857665 TCACAGATAACAATCTCGCGAAC 59.142 43.478 11.33 0.00 0.00 3.95
773 775 3.834610 CGTCCTCGTAAGTCAAACTGAT 58.165 45.455 0.00 0.00 39.48 2.90
857 859 6.691754 TTTTCATCACTGCTCACTACAAAA 57.308 33.333 0.00 0.00 0.00 2.44
863 865 3.059597 CACTGCTCACTACAAAAAGACCG 60.060 47.826 0.00 0.00 0.00 4.79
864 866 2.480419 CTGCTCACTACAAAAAGACCGG 59.520 50.000 0.00 0.00 0.00 5.28
912 914 3.954258 CAGGTTGTTCCTTTCCTGTCTTT 59.046 43.478 0.00 0.00 45.67 2.52
1034 1037 0.319211 CGCTCACACAGGAACGGTTA 60.319 55.000 0.00 0.00 31.98 2.85
1066 1069 1.134220 TCTTCGGTTTGGCTCTTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
1081 1084 4.265893 TCTTGTGTTACTGGTTTGCTTGA 58.734 39.130 0.00 0.00 0.00 3.02
1232 1235 2.027192 TCACCTGCAACCAAGATAGGAC 60.027 50.000 0.00 0.00 32.86 3.85
1281 1284 1.213296 GCCTAAAGGGGTCCATCTCA 58.787 55.000 0.00 0.00 35.18 3.27
1383 1386 0.179702 TGTCATCCAGCAGCATCCTC 59.820 55.000 0.00 0.00 0.00 3.71
1484 1487 6.692486 AGGTACTGAACATCTCAAGTAACTG 58.308 40.000 0.00 0.00 35.82 3.16
1707 1711 1.134250 TCAGTGCTGGCTACAACAACA 60.134 47.619 0.00 0.00 0.00 3.33
1716 1720 1.812571 GCTACAACAACATCAGTGGGG 59.187 52.381 0.00 0.00 0.00 4.96
1845 1849 4.044571 TCACCCTTGATCTTGGGAAGAATT 59.955 41.667 24.03 4.15 46.15 2.17
1846 1850 4.774200 CACCCTTGATCTTGGGAAGAATTT 59.226 41.667 24.03 3.56 46.15 1.82
2081 2088 1.197721 GACTTCACTGGCACAATTCCG 59.802 52.381 0.00 0.00 38.70 4.30
2204 2211 7.903145 TCTGCTTTCTATCACTTGTTAACCTA 58.097 34.615 2.48 0.00 0.00 3.08
2372 2379 6.764308 ATGAGTTATTGTTCAATGTCTGGG 57.236 37.500 8.11 0.00 0.00 4.45
2559 2566 4.022589 CGGAGATGCCAATGCTAAAATCAT 60.023 41.667 0.00 0.00 38.71 2.45
2580 2587 1.921982 TAAGATTGCAGCAAAGGCCA 58.078 45.000 12.97 0.00 42.56 5.36
2602 2609 2.489329 TCTTTGAGCTGCCTGTTTATGC 59.511 45.455 0.00 0.00 0.00 3.14
2628 2636 6.187727 TCAGTCCATTTATCCAATACCTCC 57.812 41.667 0.00 0.00 0.00 4.30
2675 2683 9.403110 GTGCTTAATCTAGCCATCAATAAATTG 57.597 33.333 0.00 0.00 40.49 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 4.451150 TCTCCATCGTGGGCGTGC 62.451 66.667 4.52 0.00 38.32 5.34
41 42 2.202797 CTCTCCATCGTGGGCGTG 60.203 66.667 4.52 0.00 38.32 5.34
42 43 3.461773 CCTCTCCATCGTGGGCGT 61.462 66.667 4.52 0.00 38.32 5.68
43 44 2.721167 TTCCTCTCCATCGTGGGCG 61.721 63.158 4.52 0.00 38.32 6.13
44 45 1.153349 GTTCCTCTCCATCGTGGGC 60.153 63.158 4.52 0.00 38.32 5.36
45 46 0.978146 AGGTTCCTCTCCATCGTGGG 60.978 60.000 4.52 0.00 38.32 4.61
46 47 1.409427 GTAGGTTCCTCTCCATCGTGG 59.591 57.143 0.00 0.00 39.43 4.94
47 48 1.065701 CGTAGGTTCCTCTCCATCGTG 59.934 57.143 0.00 0.00 0.00 4.35
48 49 1.390565 CGTAGGTTCCTCTCCATCGT 58.609 55.000 0.00 0.00 0.00 3.73
49 50 0.030908 GCGTAGGTTCCTCTCCATCG 59.969 60.000 0.00 0.00 0.00 3.84
50 51 1.067821 CTGCGTAGGTTCCTCTCCATC 59.932 57.143 0.00 0.00 0.00 3.51
51 52 1.115467 CTGCGTAGGTTCCTCTCCAT 58.885 55.000 0.00 0.00 0.00 3.41
52 53 1.605058 GCTGCGTAGGTTCCTCTCCA 61.605 60.000 1.76 0.00 0.00 3.86
53 54 1.142097 GCTGCGTAGGTTCCTCTCC 59.858 63.158 1.76 0.00 0.00 3.71
54 55 1.142097 GGCTGCGTAGGTTCCTCTC 59.858 63.158 1.76 0.00 0.00 3.20
55 56 2.711922 CGGCTGCGTAGGTTCCTCT 61.712 63.158 1.76 0.00 0.00 3.69
56 57 2.202756 CGGCTGCGTAGGTTCCTC 60.203 66.667 1.76 0.00 0.00 3.71
57 58 4.452733 GCGGCTGCGTAGGTTCCT 62.453 66.667 0.00 0.00 0.00 3.36
59 60 4.752879 TGGCGGCTGCGTAGGTTC 62.753 66.667 12.29 0.00 44.10 3.62
60 61 4.760047 CTGGCGGCTGCGTAGGTT 62.760 66.667 12.29 0.00 44.10 3.50
164 165 4.246206 CATGATGCTGCGTGGCCG 62.246 66.667 0.00 0.00 37.07 6.13
165 166 4.564116 GCATGATGCTGCGTGGCC 62.564 66.667 10.72 0.00 40.96 5.36
166 167 3.817655 TGCATGATGCTGCGTGGC 61.818 61.111 19.19 0.78 45.31 5.01
167 168 2.101575 GTGCATGATGCTGCGTGG 59.898 61.111 19.19 0.00 45.31 4.94
168 169 1.226295 CAGTGCATGATGCTGCGTG 60.226 57.895 19.19 6.72 45.31 5.34
169 170 3.047718 GCAGTGCATGATGCTGCGT 62.048 57.895 19.19 0.00 45.31 5.24
170 171 2.277949 GCAGTGCATGATGCTGCG 60.278 61.111 19.19 7.50 45.31 5.18
172 173 1.433471 CTGGCAGTGCATGATGCTG 59.567 57.895 19.19 10.51 45.31 4.41
173 174 1.753078 CCTGGCAGTGCATGATGCT 60.753 57.895 19.19 0.00 45.31 3.79
174 175 2.782222 CCCTGGCAGTGCATGATGC 61.782 63.158 18.61 11.12 45.29 3.91
175 176 2.125326 CCCCTGGCAGTGCATGATG 61.125 63.158 18.61 0.61 0.00 3.07
176 177 2.277737 CCCCTGGCAGTGCATGAT 59.722 61.111 18.61 0.00 0.00 2.45
177 178 4.051167 CCCCCTGGCAGTGCATGA 62.051 66.667 18.61 0.00 0.00 3.07
222 223 4.821589 CCTCCTTCGAGTGCGGGC 62.822 72.222 0.00 0.00 38.28 6.13
223 224 3.068691 TCCTCCTTCGAGTGCGGG 61.069 66.667 0.00 0.00 38.28 6.13
224 225 2.492090 CTCCTCCTTCGAGTGCGG 59.508 66.667 0.00 0.00 38.28 5.69
225 226 2.202676 GCTCCTCCTTCGAGTGCG 60.203 66.667 0.00 0.00 33.93 5.34
226 227 2.185608 GGCTCCTCCTTCGAGTGC 59.814 66.667 0.00 0.00 33.93 4.40
227 228 2.896443 GGGCTCCTCCTTCGAGTG 59.104 66.667 0.00 0.00 33.93 3.51
228 229 2.756283 CGGGCTCCTCCTTCGAGT 60.756 66.667 0.00 0.00 33.93 4.18
229 230 4.214327 GCGGGCTCCTCCTTCGAG 62.214 72.222 0.00 0.00 35.72 4.04
250 251 4.873129 TTCTCCGCGCGATGAGGC 62.873 66.667 34.63 0.00 37.48 4.70
251 252 2.656651 CTTCTCCGCGCGATGAGG 60.657 66.667 34.63 23.44 39.23 3.86
252 253 2.613739 TTCCTTCTCCGCGCGATGAG 62.614 60.000 34.63 28.55 0.00 2.90
253 254 2.220615 TTTCCTTCTCCGCGCGATGA 62.221 55.000 34.63 24.83 0.00 2.92
254 255 1.358725 TTTTCCTTCTCCGCGCGATG 61.359 55.000 34.63 22.84 0.00 3.84
255 256 0.672401 TTTTTCCTTCTCCGCGCGAT 60.672 50.000 34.63 0.00 0.00 4.58
256 257 1.301087 TTTTTCCTTCTCCGCGCGA 60.301 52.632 34.63 16.66 0.00 5.87
257 258 1.154469 GTTTTTCCTTCTCCGCGCG 60.154 57.895 25.67 25.67 0.00 6.86
258 259 1.209383 GGTTTTTCCTTCTCCGCGC 59.791 57.895 0.00 0.00 0.00 6.86
259 260 1.873863 GGGTTTTTCCTTCTCCGCG 59.126 57.895 0.00 0.00 36.25 6.46
260 261 1.873863 CGGGTTTTTCCTTCTCCGC 59.126 57.895 0.00 0.00 36.25 5.54
261 262 1.583495 GGCGGGTTTTTCCTTCTCCG 61.583 60.000 0.00 0.00 40.33 4.63
262 263 1.248785 GGGCGGGTTTTTCCTTCTCC 61.249 60.000 0.00 0.00 36.25 3.71
263 264 1.248785 GGGGCGGGTTTTTCCTTCTC 61.249 60.000 0.00 0.00 36.25 2.87
264 265 1.228769 GGGGCGGGTTTTTCCTTCT 60.229 57.895 0.00 0.00 36.25 2.85
265 266 1.532078 TGGGGCGGGTTTTTCCTTC 60.532 57.895 0.00 0.00 36.25 3.46
266 267 1.835267 GTGGGGCGGGTTTTTCCTT 60.835 57.895 0.00 0.00 36.25 3.36
267 268 2.203582 GTGGGGCGGGTTTTTCCT 60.204 61.111 0.00 0.00 36.25 3.36
268 269 3.307906 GGTGGGGCGGGTTTTTCC 61.308 66.667 0.00 0.00 0.00 3.13
269 270 2.522193 TGGTGGGGCGGGTTTTTC 60.522 61.111 0.00 0.00 0.00 2.29
270 271 2.840572 GTGGTGGGGCGGGTTTTT 60.841 61.111 0.00 0.00 0.00 1.94
271 272 4.926162 GGTGGTGGGGCGGGTTTT 62.926 66.667 0.00 0.00 0.00 2.43
329 330 4.803908 CCTTCCTCCCTTGCCGCC 62.804 72.222 0.00 0.00 0.00 6.13
330 331 3.689002 CTCCTTCCTCCCTTGCCGC 62.689 68.421 0.00 0.00 0.00 6.53
331 332 2.586792 CTCCTTCCTCCCTTGCCG 59.413 66.667 0.00 0.00 0.00 5.69
332 333 1.616628 TCCTCCTTCCTCCCTTGCC 60.617 63.158 0.00 0.00 0.00 4.52
333 334 1.631071 CCTCCTCCTTCCTCCCTTGC 61.631 65.000 0.00 0.00 0.00 4.01
334 335 0.043334 TCCTCCTCCTTCCTCCCTTG 59.957 60.000 0.00 0.00 0.00 3.61
335 336 0.341609 CTCCTCCTCCTTCCTCCCTT 59.658 60.000 0.00 0.00 0.00 3.95
336 337 1.598856 CCTCCTCCTCCTTCCTCCCT 61.599 65.000 0.00 0.00 0.00 4.20
337 338 1.074850 CCTCCTCCTCCTTCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
338 339 1.074850 CCCTCCTCCTCCTTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
339 340 1.074850 CCCCTCCTCCTCCTTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
340 341 1.550374 TCCCCTCCTCCTCCTTCCT 60.550 63.158 0.00 0.00 0.00 3.36
341 342 1.074850 CTCCCCTCCTCCTCCTTCC 60.075 68.421 0.00 0.00 0.00 3.46
342 343 1.074850 CCTCCCCTCCTCCTCCTTC 60.075 68.421 0.00 0.00 0.00 3.46
343 344 3.124088 CCTCCCCTCCTCCTCCTT 58.876 66.667 0.00 0.00 0.00 3.36
344 345 3.773154 GCCTCCCCTCCTCCTCCT 61.773 72.222 0.00 0.00 0.00 3.69
345 346 4.890306 GGCCTCCCCTCCTCCTCC 62.890 77.778 0.00 0.00 0.00 4.30
373 374 1.608046 CGGGAGGGAGCCTAGATCC 60.608 68.421 5.60 5.60 37.39 3.36
374 375 4.105388 CGGGAGGGAGCCTAGATC 57.895 66.667 0.00 0.00 31.76 2.75
411 412 3.971109 GAAACCCTTCCCTCCCGCG 62.971 68.421 0.00 0.00 0.00 6.46
412 413 2.045242 GAAACCCTTCCCTCCCGC 60.045 66.667 0.00 0.00 0.00 6.13
413 414 1.002502 GTGAAACCCTTCCCTCCCG 60.003 63.158 0.00 0.00 0.00 5.14
414 415 1.002502 CGTGAAACCCTTCCCTCCC 60.003 63.158 0.00 0.00 0.00 4.30
415 416 0.036294 CTCGTGAAACCCTTCCCTCC 60.036 60.000 0.00 0.00 0.00 4.30
416 417 0.974383 TCTCGTGAAACCCTTCCCTC 59.026 55.000 0.00 0.00 0.00 4.30
417 418 0.977395 CTCTCGTGAAACCCTTCCCT 59.023 55.000 0.00 0.00 0.00 4.20
418 419 0.036294 CCTCTCGTGAAACCCTTCCC 60.036 60.000 0.00 0.00 0.00 3.97
419 420 0.974383 TCCTCTCGTGAAACCCTTCC 59.026 55.000 0.00 0.00 0.00 3.46
420 421 1.673329 GCTCCTCTCGTGAAACCCTTC 60.673 57.143 0.00 0.00 0.00 3.46
421 422 0.321996 GCTCCTCTCGTGAAACCCTT 59.678 55.000 0.00 0.00 0.00 3.95
422 423 0.543174 AGCTCCTCTCGTGAAACCCT 60.543 55.000 0.00 0.00 0.00 4.34
423 424 0.108567 GAGCTCCTCTCGTGAAACCC 60.109 60.000 0.87 0.00 31.20 4.11
424 425 0.108567 GGAGCTCCTCTCGTGAAACC 60.109 60.000 26.25 0.00 42.82 3.27
425 426 0.456995 CGGAGCTCCTCTCGTGAAAC 60.457 60.000 29.73 0.00 42.82 2.78
426 427 1.883732 CGGAGCTCCTCTCGTGAAA 59.116 57.895 29.73 0.00 42.82 2.69
427 428 3.592070 CGGAGCTCCTCTCGTGAA 58.408 61.111 29.73 0.00 42.82 3.18
451 452 2.071844 TACCTATCAGCAGGCGACGC 62.072 60.000 12.43 12.43 39.53 5.19
452 453 0.598562 ATACCTATCAGCAGGCGACG 59.401 55.000 0.00 0.00 39.53 5.12
453 454 2.821991 AATACCTATCAGCAGGCGAC 57.178 50.000 0.00 0.00 39.53 5.19
454 455 3.838244 AAAATACCTATCAGCAGGCGA 57.162 42.857 0.00 0.00 39.53 5.54
455 456 5.057149 AGTTAAAATACCTATCAGCAGGCG 58.943 41.667 0.00 0.00 39.53 5.52
456 457 9.720769 TTATAGTTAAAATACCTATCAGCAGGC 57.279 33.333 0.00 0.00 39.53 4.85
596 597 5.337578 TGTTATCTGTGATGGACGATTCA 57.662 39.130 0.00 0.00 0.00 2.57
615 617 1.298859 GGCAGGTTCGCGAGATTGTT 61.299 55.000 9.59 0.00 41.60 2.83
619 621 2.125512 GTGGCAGGTTCGCGAGAT 60.126 61.111 9.59 0.00 41.60 2.75
646 648 4.598036 AATTCACCTTGTGATGATCCCT 57.402 40.909 0.00 0.00 42.40 4.20
649 651 7.388460 AGAGAAAATTCACCTTGTGATGATC 57.612 36.000 0.00 0.00 42.40 2.92
857 859 2.158519 AGTTTGTTTGATCCCCGGTCTT 60.159 45.455 0.00 0.00 0.00 3.01
863 865 6.264518 TCTGTTCTTTAGTTTGTTTGATCCCC 59.735 38.462 0.00 0.00 0.00 4.81
864 866 7.272037 TCTGTTCTTTAGTTTGTTTGATCCC 57.728 36.000 0.00 0.00 0.00 3.85
912 914 6.820656 GCCAAACTATCTGATGAAGAAAGAGA 59.179 38.462 0.00 0.00 38.79 3.10
1034 1037 3.855159 CCGAAGAAAGGAACGGGAT 57.145 52.632 0.00 0.00 41.41 3.85
1066 1069 4.522789 GGGAGAATTCAAGCAAACCAGTAA 59.477 41.667 8.44 0.00 0.00 2.24
1232 1235 0.439985 CAGCGAAACATCAGTGACCG 59.560 55.000 0.00 0.00 0.00 4.79
1266 1269 0.840722 ACGGTGAGATGGACCCCTTT 60.841 55.000 0.00 0.00 0.00 3.11
1281 1284 1.228154 GAGGTTGCCAAGGAACGGT 60.228 57.895 0.00 0.00 0.00 4.83
1305 1308 0.465460 ACAGGTTGAGGCGCAAAAGA 60.465 50.000 10.83 0.00 38.44 2.52
1383 1386 3.496130 AGTTGAAGCTGACATCAAGAACG 59.504 43.478 0.00 0.00 34.39 3.95
1707 1711 0.842030 TCTGGAAGTGCCCCACTGAT 60.842 55.000 0.00 0.00 44.62 2.90
1716 1720 5.123027 CCTTAAAGAGTTCATCTGGAAGTGC 59.877 44.000 0.00 0.00 39.28 4.40
2081 2088 2.810852 GCTGCAGGAGTATATGCTTTCC 59.189 50.000 17.12 0.00 42.98 3.13
2204 2211 6.761714 GTGTTCTCGTGATATTTGTAAGGGAT 59.238 38.462 0.00 0.00 0.00 3.85
2559 2566 3.630168 TGGCCTTTGCTGCAATCTTATA 58.370 40.909 16.77 0.00 37.74 0.98
2580 2587 3.129988 GCATAAACAGGCAGCTCAAAGAT 59.870 43.478 0.00 0.00 0.00 2.40
2602 2609 7.229506 GGAGGTATTGGATAAATGGACTGAAAG 59.770 40.741 0.00 0.00 42.29 2.62
2646 2654 6.874288 ATTGATGGCTAGATTAAGCACTTC 57.126 37.500 0.00 0.00 44.64 3.01


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

AutoCloner maintained by Alex Coulton.