Multiple sequence alignment - TraesCS1B01G246100

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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 TraesCS1B01G246100 chr1B 100.000 4217 0 0 1 4217 435359643 435363859 0.000000e+00 7788.0
1 TraesCS1B01G246100 chr1B 87.775 2863 289 31 360 3201 326928110 326925288 0.000000e+00 3291.0
2 TraesCS1B01G246100 chr1B 86.828 2270 262 26 990 3242 442621033 442618784 0.000000e+00 2501.0
3 TraesCS1B01G246100 chr1B 96.667 270 5 3 1 268 326928429 326928162 2.990000e-121 446.0
4 TraesCS1B01G246100 chr1B 94.425 287 6 3 1 277 442621743 442621457 2.330000e-117 433.0
5 TraesCS1B01G246100 chr1B 84.862 218 15 4 286 489 442621924 442621711 1.990000e-48 204.0
6 TraesCS1B01G246100 chr1B 86.391 169 10 5 601 762 442621240 442621078 5.610000e-39 172.0
7 TraesCS1B01G246100 chr1B 91.954 87 7 0 510 596 435926188 435926274 5.730000e-24 122.0
8 TraesCS1B01G246100 chr1A 96.558 3864 113 7 360 4217 407518800 407514951 0.000000e+00 6381.0
9 TraesCS1B01G246100 chr1A 96.809 3228 101 2 990 4217 425257928 425254703 0.000000e+00 5389.0
10 TraesCS1B01G246100 chr1A 95.942 3228 127 3 990 4217 421637974 421641197 0.000000e+00 5232.0
11 TraesCS1B01G246100 chr1A 96.784 3141 83 6 360 3483 406581938 406585077 0.000000e+00 5225.0
12 TraesCS1B01G246100 chr1A 84.499 1858 251 25 1402 3242 417389158 417387321 0.000000e+00 1801.0
13 TraesCS1B01G246100 chr1A 95.962 743 27 3 3475 4217 406597398 406598137 0.000000e+00 1203.0
14 TraesCS1B01G246100 chr1A 93.371 528 27 3 360 881 421637347 421637872 0.000000e+00 774.0
15 TraesCS1B01G246100 chr1A 97.473 277 6 1 1 277 425258770 425258495 4.940000e-129 472.0
16 TraesCS1B01G246100 chr1A 95.139 288 5 5 1 279 406581642 406581929 2.990000e-121 446.0
17 TraesCS1B01G246100 chr1A 94.845 291 6 5 1 282 407519096 407518806 2.990000e-121 446.0
18 TraesCS1B01G246100 chr1A 94.203 276 10 4 6 277 417396534 417396261 2.350000e-112 416.0
19 TraesCS1B01G246100 chr1A 95.833 192 5 1 1 189 421635923 421636114 1.470000e-79 307.0
20 TraesCS1B01G246100 chr1A 86.977 215 14 10 601 808 425258281 425258074 3.280000e-56 230.0
21 TraesCS1B01G246100 chr1A 88.272 162 9 4 832 990 421637761 421637915 7.200000e-43 185.0
22 TraesCS1B01G246100 chr1A 94.643 112 3 1 835 943 407518382 407518271 2.020000e-38 171.0
23 TraesCS1B01G246100 chr1A 90.000 130 9 3 360 489 417396632 417396507 9.380000e-37 165.0
24 TraesCS1B01G246100 chr1A 92.857 112 5 1 832 940 406582353 406582464 4.360000e-35 159.0
25 TraesCS1B01G246100 chr1A 94.737 95 5 0 185 279 421637244 421637338 9.450000e-32 148.0
26 TraesCS1B01G246100 chr1D 95.602 3229 136 5 990 4217 322380989 322384212 0.000000e+00 5171.0
27 TraesCS1B01G246100 chr1D 86.784 2270 263 25 990 3242 328445991 328443742 0.000000e+00 2495.0
28 TraesCS1B01G246100 chr1D 87.912 2126 223 15 995 3116 323636496 323638591 0.000000e+00 2471.0
29 TraesCS1B01G246100 chr1D 93.645 535 21 3 360 881 322380353 322380887 0.000000e+00 787.0
30 TraesCS1B01G246100 chr1D 95.789 285 6 4 1 279 322380060 322380344 4.970000e-124 455.0
31 TraesCS1B01G246100 chr1D 92.500 280 7 6 1 277 328453249 328452981 5.110000e-104 388.0
32 TraesCS1B01G246100 chr1D 87.442 215 14 7 601 808 328446361 328446153 7.050000e-58 235.0
33 TraesCS1B01G246100 chr1D 91.045 134 6 2 832 959 322380773 322380906 4.330000e-40 176.0
34 TraesCS1B01G246100 chr1D 87.671 146 10 4 360 504 323635378 323635516 3.370000e-36 163.0
35 TraesCS1B01G246100 chr1D 89.231 130 10 2 360 489 322379967 322380092 4.360000e-35 159.0
36 TraesCS1B01G246100 chr3B 92.778 360 23 2 3860 4217 169901543 169901901 6.250000e-143 518.0
37 TraesCS1B01G246100 chr3B 89.912 228 21 2 3630 3857 169901205 169901430 4.120000e-75 292.0
38 TraesCS1B01G246100 chr7B 92.857 56 4 0 3873 3928 276178124 276178069 9.720000e-12 82.4
39 TraesCS1B01G246100 chr6B 92.857 56 4 0 3873 3928 35811971 35811916 9.720000e-12 82.4
40 TraesCS1B01G246100 chr6A 92.857 56 4 0 3873 3928 50238891 50238946 9.720000e-12 82.4


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 TraesCS1B01G246100 chr1B 435359643 435363859 4216 False 7788.000000 7788 100.000000 1 4217 1 chr1B.!!$F1 4216
1 TraesCS1B01G246100 chr1B 326925288 326928429 3141 True 1868.500000 3291 92.221000 1 3201 2 chr1B.!!$R1 3200
2 TraesCS1B01G246100 chr1B 442618784 442621924 3140 True 827.500000 2501 88.126500 1 3242 4 chr1B.!!$R2 3241
3 TraesCS1B01G246100 chr1A 407514951 407519096 4145 True 2332.666667 6381 95.348667 1 4217 3 chr1A.!!$R2 4216
4 TraesCS1B01G246100 chr1A 425254703 425258770 4067 True 2030.333333 5389 93.753000 1 4217 3 chr1A.!!$R4 4216
5 TraesCS1B01G246100 chr1A 406581642 406585077 3435 False 1943.333333 5225 94.926667 1 3483 3 chr1A.!!$F2 3482
6 TraesCS1B01G246100 chr1A 417387321 417389158 1837 True 1801.000000 1801 84.499000 1402 3242 1 chr1A.!!$R1 1840
7 TraesCS1B01G246100 chr1A 421635923 421641197 5274 False 1329.200000 5232 93.631000 1 4217 5 chr1A.!!$F3 4216
8 TraesCS1B01G246100 chr1A 406597398 406598137 739 False 1203.000000 1203 95.962000 3475 4217 1 chr1A.!!$F1 742
9 TraesCS1B01G246100 chr1D 328443742 328446361 2619 True 1365.000000 2495 87.113000 601 3242 2 chr1D.!!$R2 2641
10 TraesCS1B01G246100 chr1D 322379967 322384212 4245 False 1349.600000 5171 93.062400 1 4217 5 chr1D.!!$F1 4216
11 TraesCS1B01G246100 chr1D 323635378 323638591 3213 False 1317.000000 2471 87.791500 360 3116 2 chr1D.!!$F2 2756
12 TraesCS1B01G246100 chr3B 169901205 169901901 696 False 405.000000 518 91.345000 3630 4217 2 chr3B.!!$F1 587

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
279 1639 0.764890 TGCTTTGCAGGGACTAGTGT 59.235 50.0 0.00 0.0 36.02 3.55 F
450 1817 0.884704 CACTTCCTTCCACCACCACG 60.885 60.0 0.00 0.0 0.00 4.94 F
2379 4583 0.034337 CAAGCAAAGCCAGTGCCAAT 59.966 50.0 0.56 0.0 43.27 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 3589 1.004745 CTTGGCCATAGTTGGTGTCCT 59.995 52.381 6.09 0.00 45.57 3.85 R
2400 4604 0.179000 GAGATGGATGGACGCCAAGT 59.821 55.000 2.68 0.00 39.21 3.16 R
3709 5913 0.600057 CAGGCAAACCTCTCCTTTGC 59.400 55.000 7.23 7.23 46.34 3.68 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
55 243 2.015456 TGGAAGCTCAACCTCTCTCA 57.985 50.000 0.00 0.00 0.00 3.27
183 1509 2.356673 ACGCGGTCGAACCTTTCC 60.357 61.111 12.47 0.00 35.66 3.13
279 1639 0.764890 TGCTTTGCAGGGACTAGTGT 59.235 50.000 0.00 0.00 36.02 3.55
294 1654 6.487299 GACTAGTGTCCAAATCCTAATCCT 57.513 41.667 0.00 0.00 37.24 3.24
295 1655 7.598759 GACTAGTGTCCAAATCCTAATCCTA 57.401 40.000 0.00 0.00 37.24 2.94
296 1656 7.989947 ACTAGTGTCCAAATCCTAATCCTAA 57.010 36.000 0.00 0.00 0.00 2.69
297 1657 8.568617 ACTAGTGTCCAAATCCTAATCCTAAT 57.431 34.615 0.00 0.00 0.00 1.73
298 1658 8.432805 ACTAGTGTCCAAATCCTAATCCTAATG 58.567 37.037 0.00 0.00 0.00 1.90
299 1659 6.064717 AGTGTCCAAATCCTAATCCTAATGC 58.935 40.000 0.00 0.00 0.00 3.56
300 1660 6.064717 GTGTCCAAATCCTAATCCTAATGCT 58.935 40.000 0.00 0.00 0.00 3.79
301 1661 6.547510 GTGTCCAAATCCTAATCCTAATGCTT 59.452 38.462 0.00 0.00 0.00 3.91
302 1662 7.068716 GTGTCCAAATCCTAATCCTAATGCTTT 59.931 37.037 0.00 0.00 0.00 3.51
303 1663 7.068593 TGTCCAAATCCTAATCCTAATGCTTTG 59.931 37.037 0.00 0.00 0.00 2.77
304 1664 7.285401 GTCCAAATCCTAATCCTAATGCTTTGA 59.715 37.037 0.00 0.00 0.00 2.69
305 1665 8.006564 TCCAAATCCTAATCCTAATGCTTTGAT 58.993 33.333 0.00 0.00 0.00 2.57
306 1666 8.645110 CCAAATCCTAATCCTAATGCTTTGATT 58.355 33.333 0.00 0.00 0.00 2.57
309 1669 7.042797 TCCTAATCCTAATGCTTTGATTTGC 57.957 36.000 4.04 0.00 0.00 3.68
310 1670 6.835488 TCCTAATCCTAATGCTTTGATTTGCT 59.165 34.615 4.04 0.00 0.00 3.91
311 1671 7.998383 TCCTAATCCTAATGCTTTGATTTGCTA 59.002 33.333 4.04 0.00 0.00 3.49
312 1672 8.078596 CCTAATCCTAATGCTTTGATTTGCTAC 58.921 37.037 4.04 0.00 0.00 3.58
313 1673 7.651027 AATCCTAATGCTTTGATTTGCTACT 57.349 32.000 0.00 0.00 0.00 2.57
314 1674 6.441093 TCCTAATGCTTTGATTTGCTACTG 57.559 37.500 0.00 0.00 0.00 2.74
315 1675 6.179756 TCCTAATGCTTTGATTTGCTACTGA 58.820 36.000 0.00 0.00 0.00 3.41
316 1676 6.830324 TCCTAATGCTTTGATTTGCTACTGAT 59.170 34.615 0.00 0.00 0.00 2.90
317 1677 7.340232 TCCTAATGCTTTGATTTGCTACTGATT 59.660 33.333 0.00 0.00 0.00 2.57
318 1678 7.977853 CCTAATGCTTTGATTTGCTACTGATTT 59.022 33.333 0.00 0.00 0.00 2.17
319 1679 9.362539 CTAATGCTTTGATTTGCTACTGATTTT 57.637 29.630 0.00 0.00 0.00 1.82
320 1680 8.611654 AATGCTTTGATTTGCTACTGATTTTT 57.388 26.923 0.00 0.00 0.00 1.94
321 1681 7.410800 TGCTTTGATTTGCTACTGATTTTTG 57.589 32.000 0.00 0.00 0.00 2.44
322 1682 6.073657 TGCTTTGATTTGCTACTGATTTTTGC 60.074 34.615 0.00 0.00 0.00 3.68
323 1683 6.073657 GCTTTGATTTGCTACTGATTTTTGCA 60.074 34.615 0.00 0.00 0.00 4.08
324 1684 7.360607 GCTTTGATTTGCTACTGATTTTTGCAT 60.361 33.333 0.00 0.00 33.50 3.96
325 1685 7.585286 TTGATTTGCTACTGATTTTTGCATC 57.415 32.000 0.00 0.00 33.50 3.91
326 1686 6.689554 TGATTTGCTACTGATTTTTGCATCA 58.310 32.000 0.00 0.00 33.50 3.07
327 1687 7.153315 TGATTTGCTACTGATTTTTGCATCAA 58.847 30.769 0.00 0.00 32.63 2.57
328 1688 7.656542 TGATTTGCTACTGATTTTTGCATCAAA 59.343 29.630 0.00 0.00 32.63 2.69
329 1689 7.966246 TTTGCTACTGATTTTTGCATCAAAT 57.034 28.000 4.45 4.45 33.19 2.32
330 1690 9.656040 ATTTGCTACTGATTTTTGCATCAAATA 57.344 25.926 4.73 0.00 33.19 1.40
331 1691 9.486497 TTTGCTACTGATTTTTGCATCAAATAA 57.514 25.926 4.73 0.00 33.19 1.40
332 1692 9.486497 TTGCTACTGATTTTTGCATCAAATAAA 57.514 25.926 4.73 0.00 33.19 1.40
333 1693 9.486497 TGCTACTGATTTTTGCATCAAATAAAA 57.514 25.926 4.73 0.08 33.19 1.52
353 1713 4.877323 AAAACGCTAACTATGGCTTAGC 57.123 40.909 7.29 6.73 41.82 3.09
354 1714 3.821421 AACGCTAACTATGGCTTAGCT 57.179 42.857 3.59 0.00 42.68 3.32
355 1715 3.372660 ACGCTAACTATGGCTTAGCTC 57.627 47.619 3.59 0.00 42.68 4.09
356 1716 2.036089 ACGCTAACTATGGCTTAGCTCC 59.964 50.000 3.59 0.00 42.68 4.70
357 1717 2.678324 GCTAACTATGGCTTAGCTCCG 58.322 52.381 3.59 0.00 41.93 4.63
358 1718 2.678324 CTAACTATGGCTTAGCTCCGC 58.322 52.381 3.59 0.00 0.00 5.54
371 1731 5.286320 GCTTAGCTCCGCTTTTGATTTTAAC 59.714 40.000 0.00 0.00 40.44 2.01
391 1751 7.817418 TTAACTTAGCTGAAACTGAAACCAT 57.183 32.000 0.00 0.00 0.00 3.55
450 1817 0.884704 CACTTCCTTCCACCACCACG 60.885 60.000 0.00 0.00 0.00 4.94
661 2163 1.068753 CACAGGAGCATCTAGGCGG 59.931 63.158 0.00 0.00 39.27 6.13
869 2837 2.038814 TTTGCTGCTCTCCACCGTGA 62.039 55.000 0.00 0.00 0.00 4.35
1115 3298 4.388465 CCTCTCTCCAGGCCATCA 57.612 61.111 5.01 0.00 0.00 3.07
1406 3589 2.424842 AAAGATGCCGGGCTGTGGAA 62.425 55.000 21.46 0.00 0.00 3.53
1557 3746 2.123342 GCACGCTGCAACAACAAATTA 58.877 42.857 0.00 0.00 44.26 1.40
1671 3860 1.226542 CAGTCATGCCTCAGCCCAT 59.773 57.895 0.00 0.00 38.69 4.00
1734 3923 0.328258 ACTTGGCCATGTACAGGGTC 59.672 55.000 23.84 23.84 37.39 4.46
1740 3929 1.959042 CCATGTACAGGGTCTGCATC 58.041 55.000 18.47 0.00 34.37 3.91
2025 4214 1.007038 CGTTGTGCAGCTTGGCAAT 60.007 52.632 0.00 0.00 46.93 3.56
2078 4273 0.320247 ACTGCGAACTCAAGCTCCAG 60.320 55.000 0.00 0.00 0.00 3.86
2302 4506 3.300388 CTTCTGGAGGACTATGGCAGTA 58.700 50.000 0.00 0.00 37.72 2.74
2313 4517 4.078537 ACTATGGCAGTAATGTTGTGCAA 58.921 39.130 0.00 0.00 39.05 4.08
2379 4583 0.034337 CAAGCAAAGCCAGTGCCAAT 59.966 50.000 0.56 0.00 43.27 3.16
2382 4586 0.249996 GCAAAGCCAGTGCCAATGTT 60.250 50.000 0.00 0.00 38.69 2.71
2398 4602 8.458843 GTGCCAATGTTATATACAAGAACACTT 58.541 33.333 0.00 0.00 40.89 3.16
2411 4615 2.158871 AGAACACTTTACTTGGCGTCCA 60.159 45.455 0.00 0.00 0.00 4.02
2424 4628 1.447643 CGTCCATCCATCTCCCACC 59.552 63.158 0.00 0.00 0.00 4.61
2459 4663 4.155733 CCGCGGTCCCAGCACATA 62.156 66.667 19.50 0.00 34.19 2.29
2811 5015 5.046529 GTGTATGACCTTAGCATCACTGAG 58.953 45.833 0.00 0.00 0.00 3.35
2877 5081 4.673298 ATTGCGCGTGACCCGACA 62.673 61.111 8.43 0.00 39.56 4.35
2952 5156 0.317160 TAACAGTGCCACTCAGGACG 59.683 55.000 0.00 0.00 41.22 4.79
3039 5243 1.352083 TGGAGGTTCCCAAGTCTCTG 58.648 55.000 0.00 0.00 35.03 3.35
3041 5245 1.552792 GGAGGTTCCCAAGTCTCTGAG 59.447 57.143 0.00 0.00 0.00 3.35
3131 5335 2.753966 GCAGGCATCGCAATGTCGT 61.754 57.895 0.00 0.00 42.53 4.34
3255 5459 5.109210 GTGACATATGACGTTGGAGAATCA 58.891 41.667 10.38 0.00 36.25 2.57
3394 5598 8.933653 TCTGAATTACTTTTTCCTTTTCCCAAT 58.066 29.630 0.00 0.00 0.00 3.16
3510 5714 4.978099 CCCTCATATGGGTATATGCCATC 58.022 47.826 12.29 0.00 43.77 3.51
3589 5793 7.440556 TGAGCTATTGATGATAAACTTGCTCTC 59.559 37.037 0.00 0.00 42.26 3.20
3590 5794 6.709846 AGCTATTGATGATAAACTTGCTCTCC 59.290 38.462 0.00 0.00 0.00 3.71
3595 5799 6.475504 TGATGATAAACTTGCTCTCCTTTCA 58.524 36.000 0.00 0.00 0.00 2.69
3665 5869 2.432444 TGACTATTTCGGGTGCTTTGG 58.568 47.619 0.00 0.00 0.00 3.28
3675 5879 5.105567 TCGGGTGCTTTGGAATTAGATTA 57.894 39.130 0.00 0.00 0.00 1.75
3709 5913 9.722184 ATTAAGGTCATCATCAATCTACATGAG 57.278 33.333 0.00 0.00 32.53 2.90
3749 5953 5.177696 CCTGAATACTCGTAGCTAAATTGGC 59.822 44.000 0.00 0.00 0.00 4.52
3844 6141 8.753497 AAATTGAGTCTTGACTTTTAAGAGGT 57.247 30.769 4.67 0.00 35.03 3.85
4010 6325 0.882927 TAGACCTTGCCAACACACGC 60.883 55.000 0.00 0.00 0.00 5.34
4084 6399 3.445450 CCTCAGTAGTGCTACATGAGTGT 59.555 47.826 22.21 0.00 38.35 3.55
4099 6414 7.088589 ACATGAGTGTAGATTTATGTTTGCC 57.911 36.000 0.00 0.00 36.63 4.52
4143 6458 3.492102 TTGCTGATGCTATTCCCCTAC 57.508 47.619 0.00 0.00 40.48 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
279 1639 7.353525 TCAAAGCATTAGGATTAGGATTTGGA 58.646 34.615 0.00 0.00 0.00 3.53
283 1643 8.146412 GCAAATCAAAGCATTAGGATTAGGATT 58.854 33.333 0.00 0.00 33.01 3.01
284 1644 7.508296 AGCAAATCAAAGCATTAGGATTAGGAT 59.492 33.333 0.00 0.00 33.01 3.24
286 1646 7.047460 AGCAAATCAAAGCATTAGGATTAGG 57.953 36.000 0.00 0.00 33.01 2.69
287 1647 8.844244 AGTAGCAAATCAAAGCATTAGGATTAG 58.156 33.333 0.00 0.00 33.01 1.73
288 1648 8.623903 CAGTAGCAAATCAAAGCATTAGGATTA 58.376 33.333 0.00 0.00 33.01 1.75
289 1649 7.340232 TCAGTAGCAAATCAAAGCATTAGGATT 59.660 33.333 0.00 0.00 34.83 3.01
290 1650 6.830324 TCAGTAGCAAATCAAAGCATTAGGAT 59.170 34.615 0.00 0.00 0.00 3.24
291 1651 6.179756 TCAGTAGCAAATCAAAGCATTAGGA 58.820 36.000 0.00 0.00 0.00 2.94
292 1652 6.441093 TCAGTAGCAAATCAAAGCATTAGG 57.559 37.500 0.00 0.00 0.00 2.69
293 1653 8.922058 AAATCAGTAGCAAATCAAAGCATTAG 57.078 30.769 0.00 0.00 0.00 1.73
294 1654 9.709495 AAAAATCAGTAGCAAATCAAAGCATTA 57.291 25.926 0.00 0.00 0.00 1.90
295 1655 8.500773 CAAAAATCAGTAGCAAATCAAAGCATT 58.499 29.630 0.00 0.00 0.00 3.56
296 1656 7.360607 GCAAAAATCAGTAGCAAATCAAAGCAT 60.361 33.333 0.00 0.00 0.00 3.79
297 1657 6.073657 GCAAAAATCAGTAGCAAATCAAAGCA 60.074 34.615 0.00 0.00 0.00 3.91
298 1658 6.073657 TGCAAAAATCAGTAGCAAATCAAAGC 60.074 34.615 0.00 0.00 31.42 3.51
299 1659 7.410800 TGCAAAAATCAGTAGCAAATCAAAG 57.589 32.000 0.00 0.00 31.42 2.77
300 1660 7.656542 TGATGCAAAAATCAGTAGCAAATCAAA 59.343 29.630 0.00 0.00 38.85 2.69
301 1661 7.153315 TGATGCAAAAATCAGTAGCAAATCAA 58.847 30.769 0.00 0.00 38.85 2.57
302 1662 6.689554 TGATGCAAAAATCAGTAGCAAATCA 58.310 32.000 0.00 0.00 38.85 2.57
303 1663 7.585286 TTGATGCAAAAATCAGTAGCAAATC 57.415 32.000 0.00 0.00 37.83 2.17
304 1664 7.966246 TTTGATGCAAAAATCAGTAGCAAAT 57.034 28.000 0.00 0.00 37.83 2.32
305 1665 7.966246 ATTTGATGCAAAAATCAGTAGCAAA 57.034 28.000 0.00 0.00 37.83 3.68
306 1666 9.486497 TTTATTTGATGCAAAAATCAGTAGCAA 57.514 25.926 12.53 0.55 37.83 3.91
307 1667 9.486497 TTTTATTTGATGCAAAAATCAGTAGCA 57.514 25.926 12.53 0.00 37.83 3.49
331 1691 5.231265 GCTAAGCCATAGTTAGCGTTTTT 57.769 39.130 0.00 0.00 42.14 1.94
332 1692 4.877323 GCTAAGCCATAGTTAGCGTTTT 57.123 40.909 0.00 0.00 42.14 2.43
353 1713 6.524586 CAGCTAAGTTAAAATCAAAAGCGGAG 59.475 38.462 0.00 0.00 34.01 4.63
354 1714 6.205853 TCAGCTAAGTTAAAATCAAAAGCGGA 59.794 34.615 0.00 0.00 34.01 5.54
355 1715 6.378582 TCAGCTAAGTTAAAATCAAAAGCGG 58.621 36.000 0.00 0.00 34.01 5.52
356 1716 7.851822 TTCAGCTAAGTTAAAATCAAAAGCG 57.148 32.000 0.00 0.00 34.01 4.68
357 1717 9.249457 AGTTTCAGCTAAGTTAAAATCAAAAGC 57.751 29.630 0.00 0.00 0.00 3.51
371 1731 4.217118 AGCATGGTTTCAGTTTCAGCTAAG 59.783 41.667 0.00 0.00 0.00 2.18
450 1817 2.970974 GAAGTTCCGCTGCTGGTGC 61.971 63.158 9.66 5.24 40.20 5.01
661 2163 3.286751 TGCTGAACCTTGCACGCC 61.287 61.111 0.00 0.00 33.94 5.68
856 2824 0.741221 GTGGAATCACGGTGGAGAGC 60.741 60.000 8.50 0.00 33.87 4.09
869 2837 1.152830 GTGGTGGTGGTGGTGGAAT 59.847 57.895 0.00 0.00 0.00 3.01
1075 3258 1.276705 TGCACCTAGGTCGTTGCATAA 59.723 47.619 18.22 0.00 0.00 1.90
1081 3264 2.663196 GCCTGCACCTAGGTCGTT 59.337 61.111 12.84 0.00 40.11 3.85
1406 3589 1.004745 CTTGGCCATAGTTGGTGTCCT 59.995 52.381 6.09 0.00 45.57 3.85
1557 3746 4.583073 GGATTACGGAATTTGGCACCTATT 59.417 41.667 0.00 0.00 0.00 1.73
1734 3923 1.135199 GCACACCCAAGAATGATGCAG 60.135 52.381 0.00 0.00 0.00 4.41
1740 3929 1.747355 GAGGATGCACACCCAAGAATG 59.253 52.381 7.97 0.00 0.00 2.67
2025 4214 2.046988 CCACTGATGTGCTCGCCA 60.047 61.111 0.00 0.00 42.54 5.69
2078 4273 3.895232 TCCAATACAGAGGAACAGAGC 57.105 47.619 0.00 0.00 0.00 4.09
2302 4506 2.099592 CCACAGTCACTTGCACAACATT 59.900 45.455 0.00 0.00 0.00 2.71
2313 4517 1.002868 GCCATCAGCCACAGTCACT 60.003 57.895 0.00 0.00 34.35 3.41
2382 4586 8.036575 ACGCCAAGTAAAGTGTTCTTGTATATA 58.963 33.333 0.00 0.00 37.45 0.86
2398 4602 1.837439 AGATGGATGGACGCCAAGTAA 59.163 47.619 2.68 0.00 39.21 2.24
2400 4604 0.179000 GAGATGGATGGACGCCAAGT 59.821 55.000 2.68 0.00 39.21 3.16
2411 4615 2.797278 GCGACGGTGGGAGATGGAT 61.797 63.158 0.00 0.00 0.00 3.41
2424 4628 1.493950 GGGATGAGAATGCTGCGACG 61.494 60.000 0.00 0.00 0.00 5.12
2457 4661 1.268992 TTAGCACACCGGGGCTGTAT 61.269 55.000 22.84 8.83 41.25 2.29
2459 4663 2.748058 CTTTAGCACACCGGGGCTGT 62.748 60.000 22.84 8.92 41.25 4.40
2811 5015 3.668447 AGCACATATGTAGCCAGCATAC 58.332 45.455 19.89 0.00 32.43 2.39
2952 5156 0.605319 TGTTCACCGTGAATGGCCTC 60.605 55.000 16.80 4.08 38.79 4.70
3039 5243 0.736053 CTGGGTAGACTCGCACTCTC 59.264 60.000 0.00 0.00 0.00 3.20
3041 5245 0.736053 CTCTGGGTAGACTCGCACTC 59.264 60.000 0.00 0.00 0.00 3.51
3273 5477 7.668525 AATTAAAAGACAGTCGTTTCCCTAG 57.331 36.000 16.60 0.00 31.03 3.02
3394 5598 4.499526 CCTGCAGCAAACACTGTTGATAAA 60.500 41.667 8.66 0.00 38.47 1.40
3542 5746 6.254589 GCTCATATCGGCAGAAAGTATATCAC 59.745 42.308 0.00 0.00 0.00 3.06
3589 5793 8.049721 AGGAACTAATGTAGAGGAAATGAAAGG 58.950 37.037 0.00 0.00 36.02 3.11
3590 5794 9.454859 AAGGAACTAATGTAGAGGAAATGAAAG 57.545 33.333 0.00 0.00 38.49 2.62
3595 5799 9.981460 ATTGAAAGGAACTAATGTAGAGGAAAT 57.019 29.630 0.00 0.00 38.49 2.17
3709 5913 0.600057 CAGGCAAACCTCTCCTTTGC 59.400 55.000 7.23 7.23 46.34 3.68
3749 5953 6.268566 CAGAAAAGAAACACAGGGAGAAAAG 58.731 40.000 0.00 0.00 0.00 2.27
3844 6141 9.976255 GTACAATTACTGCAACGATGTATTTTA 57.024 29.630 0.00 0.00 0.00 1.52
4010 6325 4.158394 CAGAGGAGTTGAGGAAGAAGAGAG 59.842 50.000 0.00 0.00 0.00 3.20
4084 6399 5.827797 GGATCCAGTGGCAAACATAAATCTA 59.172 40.000 6.95 0.00 0.00 1.98
4099 6414 3.266510 TGAAGGATTTCGGATCCAGTG 57.733 47.619 13.41 0.00 40.61 3.66
4143 6458 3.891366 AGTGTCAAGTGATGGGGAAAAAG 59.109 43.478 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.