Multiple sequence alignment - TraesCS3B01G237800

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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 TraesCS3B01G237800 chr3B 100.000 5345 0 0 1 5345 373135429 373130085 0.000000e+00 9871
1 TraesCS3B01G237800 chr3B 86.376 367 45 5 4928 5291 526193211 526193575 3.880000e-106 396
2 TraesCS3B01G237800 chr3B 96.063 127 5 0 1 127 606376334 606376208 1.950000e-49 207
3 TraesCS3B01G237800 chr3D 95.442 5397 136 31 1 5345 277134956 277140294 0.000000e+00 8503
4 TraesCS3B01G237800 chr3D 88.959 317 32 2 4971 5285 457242271 457241956 6.490000e-104 388
5 TraesCS3B01G237800 chr3D 82.297 418 58 5 188 590 131225158 131224742 1.100000e-91 348
6 TraesCS3B01G237800 chr3A 94.111 2700 84 16 644 3314 362341799 362339146 0.000000e+00 4036
7 TraesCS3B01G237800 chr3A 94.359 1560 56 15 3312 4846 362339096 362337544 0.000000e+00 2364
8 TraesCS3B01G237800 chr3A 90.930 430 25 3 4845 5261 362337439 362337011 2.790000e-157 566
9 TraesCS3B01G237800 chr3A 87.066 317 38 2 4971 5285 600043766 600043451 6.580000e-94 355
10 TraesCS3B01G237800 chr1D 82.056 496 68 9 111 589 374361234 374360743 2.320000e-108 403
11 TraesCS3B01G237800 chr1D 88.474 321 32 3 4972 5291 309632859 309632543 3.020000e-102 383
12 TraesCS3B01G237800 chr1A 88.925 307 28 4 4977 5283 389251761 389251461 1.820000e-99 374
13 TraesCS3B01G237800 chr1A 96.063 127 5 0 1 127 520861040 520860914 1.950000e-49 207
14 TraesCS3B01G237800 chr6D 87.697 317 31 8 4971 5285 27211558 27211248 3.930000e-96 363
15 TraesCS3B01G237800 chr2D 82.100 419 60 3 187 590 31474659 31475077 1.430000e-90 344
16 TraesCS3B01G237800 chr2D 82.303 356 57 6 4932 5285 485744530 485744179 2.420000e-78 303
17 TraesCS3B01G237800 chr2D 84.946 279 40 2 5008 5285 337308580 337308303 1.130000e-71 281
18 TraesCS3B01G237800 chr1B 82.324 413 56 6 194 590 314634551 314634962 5.130000e-90 342
19 TraesCS3B01G237800 chr1B 81.796 412 60 6 193 589 68274773 68275184 1.110000e-86 331
20 TraesCS3B01G237800 chr1B 96.063 127 5 0 1 127 661438980 661438854 1.950000e-49 207
21 TraesCS3B01G237800 chr7B 81.818 418 60 5 188 590 206536175 206536591 2.380000e-88 337
22 TraesCS3B01G237800 chr2B 81.818 418 59 5 188 589 689050348 689049932 8.580000e-88 335
23 TraesCS3B01G237800 chr7A 81.100 418 63 5 188 590 603143665 603143249 2.400000e-83 320
24 TraesCS3B01G237800 chr6B 80.825 412 63 4 193 589 410875675 410876085 5.200000e-80 309
25 TraesCS3B01G237800 chr6B 96.094 128 4 1 1 127 384834048 384834175 1.950000e-49 207
26 TraesCS3B01G237800 chr7D 80.096 417 59 6 188 588 234860790 234861198 6.770000e-74 289
27 TraesCS3B01G237800 chr2A 83.333 312 35 5 125 420 357153693 357154003 6.820000e-69 272
28 TraesCS3B01G237800 chr2A 96.063 127 5 0 1 127 456572231 456572357 1.950000e-49 207
29 TraesCS3B01G237800 chr2A 90.909 55 5 0 4928 4982 613340101 613340047 2.060000e-09 75
30 TraesCS3B01G237800 chr5A 96.850 127 4 0 1 127 81453437 81453311 4.190000e-51 213
31 TraesCS3B01G237800 chr5A 96.063 127 5 0 1 127 3424574 3424700 1.950000e-49 207
32 TraesCS3B01G237800 chr5A 96.063 127 5 0 1 127 703192691 703192817 1.950000e-49 207


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 TraesCS3B01G237800 chr3B 373130085 373135429 5344 True 9871 9871 100.000000 1 5345 1 chr3B.!!$R1 5344
1 TraesCS3B01G237800 chr3D 277134956 277140294 5338 False 8503 8503 95.442000 1 5345 1 chr3D.!!$F1 5344
2 TraesCS3B01G237800 chr3A 362337011 362341799 4788 True 2322 4036 93.133333 644 5261 3 chr3A.!!$R2 4617

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
849 857 0.810648 TATTTGCCGCCTCTGCTTTG 59.189 50.0 0.00 0.00 34.43 2.77 F
1920 1973 0.250038 CATCTGGCCAGGACATACCG 60.250 60.0 32.23 4.54 44.74 4.02 F
2417 2473 0.106015 ACTTTGCAGGCTCCCAAACT 60.106 50.0 5.91 0.00 0.00 2.66 F
2987 3048 0.457337 GCTTCTTGCAAAGCCATCCG 60.457 55.0 11.37 0.00 45.70 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 2445 1.342174 AGCCTGCAAAGTTTGTCATGG 59.658 47.619 16.70 15.99 0.00 3.66 R
3731 3866 4.394729 TCAATTCACAGGGTGGAACTAAC 58.605 43.478 0.00 0.00 36.74 2.34 R
4317 4452 4.088634 TGCCAGCACCAAATAAGAATTCT 58.911 39.130 0.88 0.88 0.00 2.40 R
4774 4914 1.141053 ACTCGGAGCAACTTCCAAAGT 59.859 47.619 4.58 0.00 45.46 2.66 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
109 110 4.236147 CTGAGCCGACATATCATCTTGAG 58.764 47.826 0.00 0.00 0.00 3.02
119 120 7.591426 CGACATATCATCTTGAGATTTACGACA 59.409 37.037 0.00 0.00 31.21 4.35
134 135 3.411808 GACATCACCGTCGTGCTTA 57.588 52.632 0.00 0.00 40.04 3.09
142 143 1.658686 CCGTCGTGCTTAGGAGAGCT 61.659 60.000 0.00 0.00 43.11 4.09
160 161 1.209019 GCTCATCTTGCTCTCTTGGGA 59.791 52.381 0.00 0.00 0.00 4.37
161 162 2.355513 GCTCATCTTGCTCTCTTGGGAA 60.356 50.000 0.00 0.00 0.00 3.97
180 181 5.045213 TGGGAAAACTAGCAATAGATGGTGA 60.045 40.000 0.00 0.00 40.70 4.02
233 234 5.945784 AGGTGCATATGCTAAGAACTTTTGA 59.054 36.000 27.13 0.26 42.66 2.69
237 238 8.642020 GTGCATATGCTAAGAACTTTTGAAAAG 58.358 33.333 27.13 15.59 42.66 2.27
273 279 2.029739 ACACATTGTCGACCACGTATCA 60.030 45.455 14.12 0.00 40.69 2.15
321 327 9.816354 GCTTCCATGTTTGTTGGTAAATATAAT 57.184 29.630 0.00 0.00 35.64 1.28
348 354 9.903682 GAAGAAAATCATGGACAACATATATGG 57.096 33.333 16.96 2.79 37.84 2.74
438 444 2.523015 TCGAGGTAAAATCGAACGAGC 58.477 47.619 2.94 0.00 45.52 5.03
439 445 1.587034 CGAGGTAAAATCGAACGAGCC 59.413 52.381 2.94 0.00 42.76 4.70
440 446 2.613691 GAGGTAAAATCGAACGAGCCA 58.386 47.619 2.94 0.00 0.00 4.75
441 447 2.603560 GAGGTAAAATCGAACGAGCCAG 59.396 50.000 2.94 0.00 0.00 4.85
442 448 2.028385 AGGTAAAATCGAACGAGCCAGT 60.028 45.455 2.94 0.00 0.00 4.00
443 449 3.194116 AGGTAAAATCGAACGAGCCAGTA 59.806 43.478 2.94 0.00 0.00 2.74
444 450 4.117685 GGTAAAATCGAACGAGCCAGTAT 58.882 43.478 2.94 0.00 0.00 2.12
445 451 4.569564 GGTAAAATCGAACGAGCCAGTATT 59.430 41.667 2.94 0.00 0.00 1.89
446 452 4.600012 AAAATCGAACGAGCCAGTATTG 57.400 40.909 2.94 0.00 0.00 1.90
482 488 4.171005 TCGTTTCTTAGTTGACCTATGCG 58.829 43.478 0.00 0.00 0.00 4.73
498 504 5.408604 ACCTATGCGAAGTGTTTAAACTCAG 59.591 40.000 18.72 11.51 0.00 3.35
528 534 9.286946 GTTTCTTTTCGAGTCGATCTCTAATAA 57.713 33.333 17.34 1.74 40.75 1.40
530 536 9.850628 TTCTTTTCGAGTCGATCTCTAATAAAA 57.149 29.630 17.34 9.29 40.75 1.52
531 537 9.286946 TCTTTTCGAGTCGATCTCTAATAAAAC 57.713 33.333 17.34 0.00 40.75 2.43
577 583 2.349912 GCTCACAAGCCTCGAACTTTTC 60.350 50.000 0.00 0.00 43.10 2.29
606 612 4.095036 GCCCTACAAGCAATTGACTAAGAC 59.905 45.833 10.34 0.00 0.00 3.01
634 640 2.221055 GTCGTGCAATCCGAATATGACC 59.779 50.000 0.00 0.00 35.89 4.02
731 738 3.244875 ACCATGTCACCAGCATCAAACTA 60.245 43.478 0.00 0.00 0.00 2.24
849 857 0.810648 TATTTGCCGCCTCTGCTTTG 59.189 50.000 0.00 0.00 34.43 2.77
1014 1028 0.988145 TCGCCATGGAGGATTCCCTT 60.988 55.000 18.40 0.00 44.53 3.95
1229 1243 4.814294 GTGCTCGGTACCGCCTGG 62.814 72.222 29.64 18.39 42.84 4.45
1366 1395 2.432146 GCACCACAGAGATACATGGAGA 59.568 50.000 0.00 0.00 36.04 3.71
1449 1478 1.853319 CCGTGAGACTGTTGCGTTC 59.147 57.895 0.00 0.00 0.00 3.95
1862 1891 3.937778 TGCAGATGATGAGGAATTGGA 57.062 42.857 0.00 0.00 0.00 3.53
1873 1902 7.642186 TGATGAGGAATTGGAAGAGGATTTTA 58.358 34.615 0.00 0.00 0.00 1.52
1910 1963 2.158564 GGGAGAATGAATCATCTGGCCA 60.159 50.000 4.71 4.71 0.00 5.36
1911 1964 3.147629 GGAGAATGAATCATCTGGCCAG 58.852 50.000 27.87 27.87 0.00 4.85
1912 1965 3.147629 GAGAATGAATCATCTGGCCAGG 58.852 50.000 32.23 17.56 0.00 4.45
1913 1966 2.781757 AGAATGAATCATCTGGCCAGGA 59.218 45.455 32.23 22.35 0.00 3.86
1914 1967 2.653234 ATGAATCATCTGGCCAGGAC 57.347 50.000 32.23 16.50 0.00 3.85
1915 1968 1.288188 TGAATCATCTGGCCAGGACA 58.712 50.000 32.23 14.37 0.00 4.02
1916 1969 1.848388 TGAATCATCTGGCCAGGACAT 59.152 47.619 32.23 16.17 0.00 3.06
1917 1970 3.047857 TGAATCATCTGGCCAGGACATA 58.952 45.455 32.23 13.54 0.00 2.29
1918 1971 3.181451 TGAATCATCTGGCCAGGACATAC 60.181 47.826 32.23 19.07 0.00 2.39
1919 1972 1.131638 TCATCTGGCCAGGACATACC 58.868 55.000 32.23 0.00 39.35 2.73
1920 1973 0.250038 CATCTGGCCAGGACATACCG 60.250 60.000 32.23 4.54 44.74 4.02
1921 1974 0.691078 ATCTGGCCAGGACATACCGT 60.691 55.000 32.23 4.99 44.74 4.83
1922 1975 1.153369 CTGGCCAGGACATACCGTG 60.153 63.158 26.14 0.00 44.74 4.94
1923 1976 1.899437 CTGGCCAGGACATACCGTGT 61.899 60.000 26.14 0.00 45.83 4.49
1949 2002 5.233263 TGAATTTGCTTTCAACGCCTAAAAC 59.767 36.000 0.00 0.00 32.82 2.43
2070 2123 2.009774 GTGGAATGGAATGAGACACCG 58.990 52.381 0.00 0.00 0.00 4.94
2080 2133 1.812922 GAGACACCGCTGCCTGATG 60.813 63.158 0.00 0.00 0.00 3.07
2389 2445 5.300286 AGAAGCACTGACATTAAATATGCCC 59.700 40.000 0.00 0.00 31.94 5.36
2417 2473 0.106015 ACTTTGCAGGCTCCCAAACT 60.106 50.000 5.91 0.00 0.00 2.66
2943 3004 2.656560 GCGAGGAGCCGTATCATATT 57.343 50.000 0.00 0.00 40.81 1.28
2987 3048 0.457337 GCTTCTTGCAAAGCCATCCG 60.457 55.000 11.37 0.00 45.70 4.18
2994 3055 3.502191 TGCAAAGCCATCCGTTTTATC 57.498 42.857 0.00 0.00 0.00 1.75
3193 3254 4.217118 AGAAGTTTTTATGTCTGCCTGCAG 59.783 41.667 12.91 12.91 44.86 4.41
3217 3278 9.821662 CAGTATTCATTATGCATTACTGTGATG 57.178 33.333 19.25 8.09 31.76 3.07
3385 3498 6.455360 AACTGTTGAGTTGTTCACATGATT 57.545 33.333 0.00 0.00 41.12 2.57
3390 3503 7.318893 TGTTGAGTTGTTCACATGATTTGAAA 58.681 30.769 0.00 0.00 34.78 2.69
3391 3504 7.980662 TGTTGAGTTGTTCACATGATTTGAAAT 59.019 29.630 0.00 0.00 34.78 2.17
3392 3505 9.462174 GTTGAGTTGTTCACATGATTTGAAATA 57.538 29.630 0.00 0.00 34.78 1.40
3393 3506 9.462174 TTGAGTTGTTCACATGATTTGAAATAC 57.538 29.630 0.00 1.51 34.78 1.89
3394 3507 8.628280 TGAGTTGTTCACATGATTTGAAATACA 58.372 29.630 0.00 0.00 34.78 2.29
3396 3509 9.985730 AGTTGTTCACATGATTTGAAATACATT 57.014 25.926 0.00 0.00 34.78 2.71
3636 3771 5.612725 ACTTTGTGGAAAATGGAATGTGT 57.387 34.783 0.00 0.00 0.00 3.72
3692 3827 5.861251 TGGTACGTGATTTGCAAAATCATTC 59.139 36.000 17.19 9.31 38.71 2.67
3731 3866 7.396540 AGAAGTGAAATAGCCTGGTAAAATG 57.603 36.000 0.00 0.00 0.00 2.32
4042 4177 7.934855 AAAGACAGATCAAATTCTAGCATGT 57.065 32.000 0.00 0.00 0.00 3.21
4142 4277 4.711846 GGCTGAAGAAGGGGATAAAAATGT 59.288 41.667 0.00 0.00 0.00 2.71
4145 4280 6.405176 GCTGAAGAAGGGGATAAAAATGTCAG 60.405 42.308 0.00 0.00 0.00 3.51
4174 4309 0.536260 ACAGAGATCAGCTCCACTGC 59.464 55.000 0.00 0.00 46.76 4.40
4231 4366 2.656947 TCCAAGTTCAGACCCAAAGG 57.343 50.000 0.00 0.00 40.04 3.11
4317 4452 4.341806 TCAGAGGCTTCAAGAATTTTGCAA 59.658 37.500 0.00 0.00 0.00 4.08
4468 4603 3.555547 GCTTGTTTTGGTACTTTTGGCTG 59.444 43.478 0.00 0.00 0.00 4.85
4576 4711 5.828299 TGGTTACCAAGAAAGTTCACAAG 57.172 39.130 0.00 0.00 0.00 3.16
4774 4914 9.460019 TCTCACATATGATTCATTTTAACCACA 57.540 29.630 10.38 0.00 33.22 4.17
4999 5257 0.036952 CAGTGACCGGACAAGCATCT 60.037 55.000 9.46 0.00 0.00 2.90
5049 5308 6.426633 CCCTATTTTCAAAACACCAAATCCAC 59.573 38.462 0.00 0.00 0.00 4.02
5192 5451 8.850156 AGTGCATAACTGATAAAACAAAAGACT 58.150 29.630 0.00 0.00 37.88 3.24
5308 5570 6.092259 GCTCATCATCATCATCATCATTTCGA 59.908 38.462 0.00 0.00 0.00 3.71
5328 5590 1.974236 ACATCCTCATCCTCCGAATCC 59.026 52.381 0.00 0.00 0.00 3.01
5334 5596 2.495270 CTCATCCTCCGAATCCGATGAT 59.505 50.000 0.00 0.00 40.11 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 0.456221 CTCCTAAGCACGACGGTGAT 59.544 55.000 0.00 0.00 46.53 3.06
142 143 4.074970 GTTTTCCCAAGAGAGCAAGATGA 58.925 43.478 0.00 0.00 0.00 2.92
160 161 8.184192 CGAAAATCACCATCTATTGCTAGTTTT 58.816 33.333 0.00 0.00 0.00 2.43
161 162 7.336931 ACGAAAATCACCATCTATTGCTAGTTT 59.663 33.333 0.00 0.00 0.00 2.66
201 202 5.951747 TCTTAGCATATGCACCTTCCTTTTT 59.048 36.000 28.62 6.68 45.16 1.94
207 208 6.442513 AAAGTTCTTAGCATATGCACCTTC 57.557 37.500 28.62 13.93 45.16 3.46
241 242 8.181573 GTGGTCGACAATGTGTTAAATATCATT 58.818 33.333 18.91 0.00 0.00 2.57
243 244 6.183360 CGTGGTCGACAATGTGTTAAATATCA 60.183 38.462 18.91 0.00 39.71 2.15
244 245 6.182634 CGTGGTCGACAATGTGTTAAATATC 58.817 40.000 18.91 0.00 39.71 1.63
246 247 4.989797 ACGTGGTCGACAATGTGTTAAATA 59.010 37.500 17.11 0.00 40.62 1.40
247 248 3.810941 ACGTGGTCGACAATGTGTTAAAT 59.189 39.130 17.11 0.00 40.62 1.40
257 263 6.210796 CCTAATTATGATACGTGGTCGACAA 58.789 40.000 18.91 2.10 40.62 3.18
262 268 5.148651 AGGCCTAATTATGATACGTGGTC 57.851 43.478 1.29 0.00 0.00 4.02
273 279 9.072375 GAAGCTTGAAGATTTAGGCCTAATTAT 57.928 33.333 25.70 16.99 0.00 1.28
438 444 5.644644 GAGTTGATTTTGAGCCAATACTGG 58.355 41.667 0.00 0.00 46.65 4.00
439 445 5.106555 ACGAGTTGATTTTGAGCCAATACTG 60.107 40.000 0.00 0.00 0.00 2.74
440 446 5.003804 ACGAGTTGATTTTGAGCCAATACT 58.996 37.500 0.00 0.00 0.00 2.12
441 447 5.296813 ACGAGTTGATTTTGAGCCAATAC 57.703 39.130 0.00 0.00 0.00 1.89
442 448 5.957842 AACGAGTTGATTTTGAGCCAATA 57.042 34.783 0.00 0.00 0.00 1.90
443 449 4.853924 AACGAGTTGATTTTGAGCCAAT 57.146 36.364 0.00 0.00 0.00 3.16
444 450 4.338118 AGAAACGAGTTGATTTTGAGCCAA 59.662 37.500 0.00 0.00 0.00 4.52
445 451 3.882888 AGAAACGAGTTGATTTTGAGCCA 59.117 39.130 0.00 0.00 0.00 4.75
446 452 4.489679 AGAAACGAGTTGATTTTGAGCC 57.510 40.909 0.00 0.00 0.00 4.70
447 453 6.659776 ACTAAGAAACGAGTTGATTTTGAGC 58.340 36.000 0.00 0.00 0.00 4.26
457 463 5.638234 GCATAGGTCAACTAAGAAACGAGTT 59.362 40.000 0.00 0.00 36.31 3.01
458 464 5.169295 GCATAGGTCAACTAAGAAACGAGT 58.831 41.667 0.00 0.00 34.79 4.18
459 465 4.265556 CGCATAGGTCAACTAAGAAACGAG 59.734 45.833 0.00 0.00 34.79 4.18
475 481 5.671329 GCTGAGTTTAAACACTTCGCATAGG 60.671 44.000 20.06 0.01 0.00 2.57
482 488 5.405331 AACGAGCTGAGTTTAAACACTTC 57.595 39.130 20.06 9.70 0.00 3.01
565 571 2.742589 GGGCTGTAAGAAAAGTTCGAGG 59.257 50.000 0.00 0.00 34.07 4.63
571 577 4.072839 GCTTGTAGGGCTGTAAGAAAAGT 58.927 43.478 0.00 0.00 34.07 2.66
577 583 4.009675 TCAATTGCTTGTAGGGCTGTAAG 58.990 43.478 0.00 0.00 33.87 2.34
606 612 4.147322 GATTGCACGACGCCACCG 62.147 66.667 0.00 0.00 41.33 4.94
634 640 3.910568 AATCTGGGAAGCTCTTCTCTG 57.089 47.619 10.50 9.88 40.64 3.35
731 738 8.838649 AAATTAGGGTGAACAGGCTAAAATAT 57.161 30.769 0.00 0.00 0.00 1.28
849 857 0.037734 AGGAAACCCCATTGTCGTCC 59.962 55.000 0.00 0.00 37.41 4.79
918 932 2.373335 AGGATATCGAGCAGTGGTCT 57.627 50.000 19.47 5.12 0.00 3.85
1229 1243 1.481363 CTCCTAAGTCCTTTCCCCGTC 59.519 57.143 0.00 0.00 0.00 4.79
1366 1395 1.304134 GAACCCCGGCCACTTGATT 60.304 57.895 2.24 0.00 0.00 2.57
1449 1478 4.410400 GCCCCCAACTCCTCCACG 62.410 72.222 0.00 0.00 0.00 4.94
1620 1649 4.629634 CCATAGTTCAGCATTGACGTTGTA 59.370 41.667 0.00 0.00 31.71 2.41
1736 1765 5.064452 CCATCAACTGAGTGCTGATCTAAAC 59.936 44.000 0.00 0.00 29.80 2.01
1739 1768 3.771479 ACCATCAACTGAGTGCTGATCTA 59.229 43.478 0.00 0.00 29.80 1.98
1862 1891 7.661847 CCAACACTCTGTTAGTAAAATCCTCTT 59.338 37.037 0.00 0.00 38.77 2.85
1873 1902 1.978580 CTCCCCCAACACTCTGTTAGT 59.021 52.381 0.00 0.00 38.77 2.24
1913 1966 7.681114 TGAAAGCAAATTCAGACACGGTATGT 61.681 38.462 0.00 0.00 38.14 2.29
1914 1967 4.685169 AAGCAAATTCAGACACGGTATG 57.315 40.909 0.00 0.00 0.00 2.39
1915 1968 4.759693 TGAAAGCAAATTCAGACACGGTAT 59.240 37.500 0.00 0.00 34.50 2.73
1916 1969 4.130857 TGAAAGCAAATTCAGACACGGTA 58.869 39.130 0.00 0.00 34.50 4.02
1917 1970 2.948979 TGAAAGCAAATTCAGACACGGT 59.051 40.909 0.00 0.00 34.50 4.83
1918 1971 3.624326 TGAAAGCAAATTCAGACACGG 57.376 42.857 0.00 0.00 34.50 4.94
1919 1972 3.418619 CGTTGAAAGCAAATTCAGACACG 59.581 43.478 7.65 7.65 40.21 4.49
1920 1973 3.180387 GCGTTGAAAGCAAATTCAGACAC 59.820 43.478 0.00 0.00 40.21 3.67
1921 1974 3.371168 GCGTTGAAAGCAAATTCAGACA 58.629 40.909 0.00 0.00 40.21 3.41
1922 1975 2.726241 GGCGTTGAAAGCAAATTCAGAC 59.274 45.455 5.34 0.00 40.21 3.51
1923 1976 2.622942 AGGCGTTGAAAGCAAATTCAGA 59.377 40.909 5.34 0.00 40.21 3.27
1924 1977 3.017265 AGGCGTTGAAAGCAAATTCAG 57.983 42.857 5.34 0.00 40.21 3.02
1925 1978 4.576216 TTAGGCGTTGAAAGCAAATTCA 57.424 36.364 5.34 0.00 37.53 2.57
1926 1979 5.462068 AGTTTTAGGCGTTGAAAGCAAATTC 59.538 36.000 5.34 0.00 35.42 2.17
1927 1980 5.356426 AGTTTTAGGCGTTGAAAGCAAATT 58.644 33.333 5.34 0.00 35.42 1.82
1928 1981 4.944048 AGTTTTAGGCGTTGAAAGCAAAT 58.056 34.783 5.34 0.00 35.42 2.32
1929 1982 4.379339 AGTTTTAGGCGTTGAAAGCAAA 57.621 36.364 5.34 0.00 35.42 3.68
1930 1983 5.502153 TTAGTTTTAGGCGTTGAAAGCAA 57.498 34.783 5.34 0.00 36.08 3.91
1931 1984 5.502153 TTTAGTTTTAGGCGTTGAAAGCA 57.498 34.783 5.34 0.00 36.08 3.91
1932 1985 4.915667 CCTTTAGTTTTAGGCGTTGAAAGC 59.084 41.667 0.00 0.00 0.00 3.51
1933 1986 6.308371 TCCTTTAGTTTTAGGCGTTGAAAG 57.692 37.500 0.00 0.00 0.00 2.62
1949 2002 6.591834 CAGTACAAGATCACTGGTTCCTTTAG 59.408 42.308 0.00 0.00 38.79 1.85
2031 2084 8.464404 CATTCCACAATTTCATCATAACTGACT 58.536 33.333 0.00 0.00 33.22 3.41
2080 2133 8.451908 AAAAATGGTATATTCAGTACCTCAGC 57.548 34.615 4.20 0.00 41.73 4.26
2135 2188 5.581126 ACAAGAAGAAGCAACATGTGAAA 57.419 34.783 0.00 0.00 0.00 2.69
2389 2445 1.342174 AGCCTGCAAAGTTTGTCATGG 59.658 47.619 16.70 15.99 0.00 3.66
2417 2473 3.713826 AATGCCGTTTTCTCTTCCCTA 57.286 42.857 0.00 0.00 0.00 3.53
2942 3003 9.553418 CAATTCAACGTACATTACATCATTCAA 57.447 29.630 0.00 0.00 0.00 2.69
2943 3004 7.696035 GCAATTCAACGTACATTACATCATTCA 59.304 33.333 0.00 0.00 0.00 2.57
3217 3278 6.891624 CATACATACATGGACATGCACTAAC 58.108 40.000 11.96 0.00 42.39 2.34
3458 3593 6.258507 ACATCAAAACAAACAGAAAGGAATGC 59.741 34.615 0.00 0.00 0.00 3.56
3636 3771 9.206870 GAAAATTTGCATTTATCACCTCTGAAA 57.793 29.630 0.00 0.00 31.89 2.69
3731 3866 4.394729 TCAATTCACAGGGTGGAACTAAC 58.605 43.478 0.00 0.00 36.74 2.34
4060 4195 6.590234 TGTATACATATGCTTCTCGATGGT 57.410 37.500 0.08 0.00 0.00 3.55
4142 4277 5.877012 GCTGATCTCTGTTTATTTGGACTGA 59.123 40.000 0.00 0.00 0.00 3.41
4145 4280 5.295540 GGAGCTGATCTCTGTTTATTTGGAC 59.704 44.000 0.00 0.00 41.60 4.02
4317 4452 4.088634 TGCCAGCACCAAATAAGAATTCT 58.911 39.130 0.88 0.88 0.00 2.40
4367 4502 5.661312 TGTAGTCTACAGGTATCAAAGGCAT 59.339 40.000 8.70 0.00 34.06 4.40
4539 4674 6.184580 TGGTAACCAAAAACTATACGCATG 57.815 37.500 0.00 0.00 0.00 4.06
4576 4711 7.433425 CACTTAGCCTAATTCTGCAAAATAAGC 59.567 37.037 0.00 0.00 0.00 3.09
4669 4809 5.772825 TCTAATGCTACAAATGATTGGCC 57.227 39.130 0.00 0.00 41.01 5.36
4672 4812 9.823098 GCTTAGATCTAATGCTACAAATGATTG 57.177 33.333 15.47 0.04 42.46 2.67
4774 4914 1.141053 ACTCGGAGCAACTTCCAAAGT 59.859 47.619 4.58 0.00 45.46 2.66
4862 5108 8.733458 TGGAATCAAGTATCAAGATTCAACAAG 58.267 33.333 14.14 0.00 45.82 3.16
4924 5170 5.361571 TCCGTGGTTGTAGATGCTCTAATAA 59.638 40.000 0.00 0.00 29.58 1.40
4992 5250 4.248058 GCAAATGCCAAGTTTAGATGCTT 58.752 39.130 0.00 0.00 34.31 3.91
4999 5257 3.462021 GTGGTTGCAAATGCCAAGTTTA 58.538 40.909 8.72 0.00 41.18 2.01
5049 5308 2.068716 CGACGTGCATGTGTTTGCG 61.069 57.895 18.17 9.55 45.77 4.85
5184 5443 9.884465 CTGGAAATCAGTAAACTTAGTCTTTTG 57.116 33.333 0.00 0.00 38.64 2.44
5215 5474 0.865111 TTGTCGAGCAAATGTGGACG 59.135 50.000 0.00 0.00 33.53 4.79
5308 5570 1.974236 GGATTCGGAGGATGAGGATGT 59.026 52.381 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.