Multiple sequence alignment - TraesCS2B01G579400

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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 TraesCS2B01G579400 chr2B 100.000 5546 0 0 1 5546 767370609 767376154 0.000000e+00 10242.0
1 TraesCS2B01G579400 chr2B 83.520 1608 203 34 1905 3493 793980418 793981982 0.000000e+00 1445.0
2 TraesCS2B01G579400 chr2B 84.890 1231 157 11 1902 3106 793921773 793920546 0.000000e+00 1216.0
3 TraesCS2B01G579400 chr2B 87.025 894 102 8 3142 4027 793920173 793919286 0.000000e+00 996.0
4 TraesCS2B01G579400 chr2B 87.361 269 11 11 4703 4957 793916437 793916178 2.530000e-73 287.0
5 TraesCS2B01G579400 chr2B 86.935 199 20 2 5158 5356 793915883 793915691 9.350000e-53 219.0
6 TraesCS2B01G579400 chr2B 80.303 264 38 7 3546 3802 793981999 793982255 2.640000e-43 187.0
7 TraesCS2B01G579400 chr2B 78.421 190 24 9 4465 4641 793918686 793918501 2.110000e-19 108.0
8 TraesCS2B01G579400 chr2D 95.291 5606 127 39 1 5546 625145439 625150967 0.000000e+00 8763.0
9 TraesCS2B01G579400 chr2D 86.696 2255 265 27 1914 4146 635808723 635806482 0.000000e+00 2470.0
10 TraesCS2B01G579400 chr2D 83.907 1249 166 18 2533 3767 636048165 636049392 0.000000e+00 1160.0
11 TraesCS2B01G579400 chr2D 83.557 596 72 15 1921 2511 636047359 636047933 8.180000e-148 534.0
12 TraesCS2B01G579400 chr2D 89.340 394 26 11 975 1363 636043620 636044002 1.080000e-131 481.0
13 TraesCS2B01G579400 chr2D 87.687 268 31 2 3835 4101 635840941 635840675 1.500000e-80 311.0
14 TraesCS2B01G579400 chr2D 84.365 307 23 12 1 301 523167076 523166789 1.520000e-70 278.0
15 TraesCS2B01G579400 chr2D 83.636 275 45 0 1089 1363 635853695 635853421 5.510000e-65 259.0
16 TraesCS2B01G579400 chr2D 80.997 321 33 6 1001 1315 635819882 635819584 4.320000e-56 230.0
17 TraesCS2B01G579400 chr2D 82.160 213 34 4 3999 4209 636049816 636050026 4.410000e-41 180.0
18 TraesCS2B01G579400 chr2D 81.818 198 34 2 3780 3976 636049450 636049646 1.240000e-36 165.0
19 TraesCS2B01G579400 chr2D 93.269 104 5 2 200 301 286002289 286002392 9.620000e-33 152.0
20 TraesCS2B01G579400 chr2D 81.319 91 9 7 1704 1788 635808942 635808854 3.590000e-07 67.6
21 TraesCS2B01G579400 chrUn 84.322 2513 337 38 1977 4452 124673485 124675977 0.000000e+00 2405.0
22 TraesCS2B01G579400 chrUn 82.209 489 76 9 3946 4427 124806281 124806765 1.440000e-110 411.0
23 TraesCS2B01G579400 chrUn 85.284 299 40 4 1001 1297 124667106 124667402 6.980000e-79 305.0
24 TraesCS2B01G579400 chrUn 81.440 361 43 13 4141 4494 124712957 124713300 1.970000e-69 274.0
25 TraesCS2B01G579400 chrUn 83.333 66 11 0 1704 1769 124671707 124671772 1.670000e-05 62.1
26 TraesCS2B01G579400 chr4A 80.775 619 103 13 3093 3702 95338094 95337483 2.340000e-128 470.0
27 TraesCS2B01G579400 chr4A 86.154 195 20 3 1 194 714908551 714908739 2.620000e-48 204.0
28 TraesCS2B01G579400 chr4A 79.677 310 37 11 4 302 660200770 660201064 3.390000e-47 200.0
29 TraesCS2B01G579400 chr7B 87.338 308 23 7 7 301 673656586 673656282 6.880000e-89 339.0
30 TraesCS2B01G579400 chr7B 83.750 320 32 7 1 301 94763141 94763459 9.090000e-73 285.0
31 TraesCS2B01G579400 chr7B 71.939 923 204 41 2224 3114 685208843 685209742 9.350000e-53 219.0
32 TraesCS2B01G579400 chr7B 71.659 928 208 44 2219 3114 695373519 695372615 7.280000e-49 206.0
33 TraesCS2B01G579400 chr7B 79.412 238 43 6 2219 2453 684944262 684944028 4.450000e-36 163.0
34 TraesCS2B01G579400 chr7B 77.068 266 54 5 2853 3114 697519657 697519919 4.480000e-31 147.0
35 TraesCS2B01G579400 chr7B 93.220 59 4 0 705 763 347997593 347997651 2.750000e-13 87.9
36 TraesCS2B01G579400 chr5B 84.326 319 31 7 1 301 334049681 334049998 1.510000e-75 294.0
37 TraesCS2B01G579400 chr5B 83.228 316 35 8 1 301 707951036 707951348 1.970000e-69 274.0
38 TraesCS2B01G579400 chr3B 83.333 318 33 8 2 301 77162494 77162179 5.470000e-70 276.0
39 TraesCS2B01G579400 chr4B 90.674 193 17 1 1 193 115374115 115373924 7.130000e-64 255.0
40 TraesCS2B01G579400 chr4B 91.005 189 15 2 1 188 560238954 560238767 2.560000e-63 254.0
41 TraesCS2B01G579400 chr4B 91.429 105 7 1 200 302 91736539 91736643 5.790000e-30 143.0
42 TraesCS2B01G579400 chr2A 81.818 308 33 8 17 302 459803644 459803338 2.580000e-58 237.0
43 TraesCS2B01G579400 chr5D 78.767 292 59 1 2211 2502 552734959 552735247 5.670000e-45 193.0
44 TraesCS2B01G579400 chr5D 72.998 437 88 23 3853 4266 552736478 552736907 5.830000e-25 126.0
45 TraesCS2B01G579400 chr6B 94.000 100 4 1 204 301 29777513 29777414 3.460000e-32 150.0
46 TraesCS2B01G579400 chr1B 70.416 649 161 21 3350 3987 169940 169312 7.600000e-19 106.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G579400 chr2B 767370609 767376154 5545 False 10242.00 10242 100.0000 1 5546 1 chr2B.!!$F1 5545
1 TraesCS2B01G579400 chr2B 793980418 793982255 1837 False 816.00 1445 81.9115 1905 3802 2 chr2B.!!$F2 1897
2 TraesCS2B01G579400 chr2B 793915691 793921773 6082 True 565.20 1216 84.9264 1902 5356 5 chr2B.!!$R1 3454
3 TraesCS2B01G579400 chr2D 625145439 625150967 5528 False 8763.00 8763 95.2910 1 5546 1 chr2D.!!$F2 5545
4 TraesCS2B01G579400 chr2D 635806482 635808942 2460 True 1268.80 2470 84.0075 1704 4146 2 chr2D.!!$R5 2442
5 TraesCS2B01G579400 chr2D 636043620 636050026 6406 False 504.00 1160 84.1564 975 4209 5 chr2D.!!$F3 3234
6 TraesCS2B01G579400 chrUn 124671707 124675977 4270 False 1233.55 2405 83.8275 1704 4452 2 chrUn.!!$F4 2748
7 TraesCS2B01G579400 chr4A 95337483 95338094 611 True 470.00 470 80.7750 3093 3702 1 chr4A.!!$R1 609
8 TraesCS2B01G579400 chr7B 685208843 685209742 899 False 219.00 219 71.9390 2224 3114 1 chr7B.!!$F3 890
9 TraesCS2B01G579400 chr7B 695372615 695373519 904 True 206.00 206 71.6590 2219 3114 1 chr7B.!!$R3 895

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
150 151 0.034337 GTCAGTCGGGTTGGTTAGCA 59.966 55.000 0.00 0.0 0.00 3.49 F
517 520 1.078709 CGTGTAGATGCACACCCAAG 58.921 55.000 0.00 0.0 44.88 3.61 F
731 734 1.290491 CGCGTTAACGGTGGGCTTAA 61.290 55.000 27.82 0.0 40.23 1.85 F
1212 1216 1.316706 ACAGGCCTCGTCTAGAGCAC 61.317 60.000 0.00 0.0 45.54 4.40 F
2002 6371 2.099756 TGCTCTCATCTGTATGGTCACG 59.900 50.000 0.00 0.0 33.61 4.35 F
3203 8180 2.108075 TCATTTCTTCAACCAGGAGGCA 59.892 45.455 0.00 0.0 39.06 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 4555 2.038426 TCGGAGAGAGAATTTTGTGCCA 59.962 45.455 0.00 0.0 0.00 4.92 R
1814 4710 4.080687 GCTAGGAATCACCGAGGTATACT 58.919 47.826 2.25 0.0 44.74 2.12 R
2676 7298 5.234466 AGTTGTCACTAGGATCTTGCTTT 57.766 39.130 0.00 0.0 0.00 3.51 R
3203 8180 2.308570 TGCCATGATTGTACCAGTCCTT 59.691 45.455 0.00 0.0 0.00 3.36 R
3328 8342 0.038166 TGGGAACATCTCTTGCCCAC 59.962 55.000 0.00 0.0 43.57 4.61 R
4959 12420 0.404426 GGGGCCCTGAAGTTTGTACT 59.596 55.000 24.38 0.0 35.68 2.73 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
85 86 4.335874 TGGTTTTAAGTTTTGTCGCTGCTA 59.664 37.500 0.00 0.00 0.00 3.49
103 104 6.582295 CGCTGCTATGTGTTTTTCTATGTTTT 59.418 34.615 0.00 0.00 0.00 2.43
145 146 1.764854 ACCAGTCAGTCGGGTTGGT 60.765 57.895 0.00 0.00 41.63 3.67
150 151 0.034337 GTCAGTCGGGTTGGTTAGCA 59.966 55.000 0.00 0.00 0.00 3.49
155 156 2.414785 CGGGTTGGTTAGCATGGCC 61.415 63.158 0.00 0.00 0.00 5.36
216 217 3.509388 TTCTCGCGAGAAGGGAAAC 57.491 52.632 39.93 0.00 42.06 2.78
220 221 1.080705 CGCGAGAAGGGAAACGACT 60.081 57.895 0.00 0.00 34.27 4.18
396 399 1.202758 TGTTGCAGATTTCACGGGTCT 60.203 47.619 0.00 0.00 0.00 3.85
436 439 1.818674 GTTTCCCTTGCCGTCAATGAT 59.181 47.619 0.00 0.00 0.00 2.45
475 478 3.242188 CCGCGTTATACCAACTAACAAGC 60.242 47.826 4.92 0.00 0.00 4.01
476 479 3.540744 CGCGTTATACCAACTAACAAGCG 60.541 47.826 0.00 0.00 34.81 4.68
517 520 1.078709 CGTGTAGATGCACACCCAAG 58.921 55.000 0.00 0.00 44.88 3.61
518 521 1.608025 CGTGTAGATGCACACCCAAGT 60.608 52.381 0.00 0.00 44.88 3.16
519 522 2.353307 CGTGTAGATGCACACCCAAGTA 60.353 50.000 0.00 0.00 44.88 2.24
520 523 3.000727 GTGTAGATGCACACCCAAGTAC 58.999 50.000 0.00 0.00 42.46 2.73
521 524 2.903784 TGTAGATGCACACCCAAGTACT 59.096 45.455 0.00 0.00 0.00 2.73
673 676 3.881688 CACTGGGAGATGATTGGACAATC 59.118 47.826 16.12 16.12 45.55 2.67
731 734 1.290491 CGCGTTAACGGTGGGCTTAA 61.290 55.000 27.82 0.00 40.23 1.85
769 772 5.659440 ATTGTCAAAACCAACAGAGTTGT 57.341 34.783 8.83 0.00 39.87 3.32
812 815 1.899814 ACAGTCCTATCCTTGCGTCAA 59.100 47.619 0.00 0.00 0.00 3.18
898 901 7.078011 ACTTATTTTAGCTGCTTTCTAGTGC 57.922 36.000 7.79 0.00 0.00 4.40
899 902 6.881602 ACTTATTTTAGCTGCTTTCTAGTGCT 59.118 34.615 7.79 0.00 37.22 4.40
900 903 5.557891 ATTTTAGCTGCTTTCTAGTGCTG 57.442 39.130 7.79 0.00 35.81 4.41
993 997 9.645059 CTCTCTCAAAACTAATTGTATCTGTCA 57.355 33.333 0.00 0.00 0.00 3.58
1074 1078 4.554036 GCCTCGGCCACCATCTCC 62.554 72.222 2.24 0.00 34.56 3.71
1212 1216 1.316706 ACAGGCCTCGTCTAGAGCAC 61.317 60.000 0.00 0.00 45.54 4.40
1274 1278 2.306341 ATCTTGGATGCTGTCGAGTG 57.694 50.000 0.00 0.00 0.00 3.51
1436 1482 9.693739 TGTTGTTCCATATATATGTTTGAAGGT 57.306 29.630 19.11 0.00 31.82 3.50
1546 3651 5.642491 AGCCTAAACCTACATCGAAACTTTC 59.358 40.000 0.00 0.00 0.00 2.62
1560 3665 5.216648 CGAAACTTTCGCAAGGGAAAATTA 58.783 37.500 10.83 0.00 46.97 1.40
1570 3675 6.432783 TCGCAAGGGAAAATTAGAGAAATTCA 59.567 34.615 0.00 0.00 35.63 2.57
1683 4539 4.037222 TCTGGCTCACATGTATTCCCTTA 58.963 43.478 0.00 0.00 0.00 2.69
1684 4540 4.101585 TCTGGCTCACATGTATTCCCTTAG 59.898 45.833 0.00 0.00 0.00 2.18
1685 4541 4.037222 TGGCTCACATGTATTCCCTTAGA 58.963 43.478 0.00 0.00 0.00 2.10
1686 4542 4.660303 TGGCTCACATGTATTCCCTTAGAT 59.340 41.667 0.00 0.00 0.00 1.98
1814 4710 3.008485 TGTGTGTGTGCCTGATGGTATTA 59.992 43.478 0.00 0.00 35.27 0.98
1880 4776 4.020128 AGAGAACTAGGTTTAGGGCAAGTG 60.020 45.833 0.00 0.00 0.00 3.16
1887 4783 4.740902 AGGTTTAGGGCAAGTGATTTCTT 58.259 39.130 0.00 0.00 0.00 2.52
2002 6371 2.099756 TGCTCTCATCTGTATGGTCACG 59.900 50.000 0.00 0.00 33.61 4.35
2566 7182 3.580458 TGGAAGAAGAACTGGAGAGGAAG 59.420 47.826 0.00 0.00 0.00 3.46
2676 7298 7.802117 TCTCCACTTAAGAAAGGAAAGAAAGA 58.198 34.615 10.09 3.68 37.01 2.52
3203 8180 2.108075 TCATTTCTTCAACCAGGAGGCA 59.892 45.455 0.00 0.00 39.06 4.75
3320 8334 9.512435 GAATTGACAATAACATGATCCAGAAAG 57.488 33.333 0.00 0.00 0.00 2.62
3321 8335 7.395190 TTGACAATAACATGATCCAGAAAGG 57.605 36.000 0.00 0.00 39.47 3.11
3332 8346 1.705186 TCCAGAAAGGAGAAAGGTGGG 59.295 52.381 0.00 0.00 43.07 4.61
3333 8347 1.539157 CAGAAAGGAGAAAGGTGGGC 58.461 55.000 0.00 0.00 0.00 5.36
3334 8348 1.149101 AGAAAGGAGAAAGGTGGGCA 58.851 50.000 0.00 0.00 0.00 5.36
3335 8349 1.499007 AGAAAGGAGAAAGGTGGGCAA 59.501 47.619 0.00 0.00 0.00 4.52
3358 8372 0.966920 ATGTTCCCAGAGACGTTCGT 59.033 50.000 0.00 0.00 0.00 3.85
3410 8429 6.894103 AGCATTGATTACAGGGAAGATTCTTT 59.106 34.615 0.00 0.00 0.00 2.52
3989 9209 4.865365 GGCTCACAGAACTAACACTATCAC 59.135 45.833 0.00 0.00 0.00 3.06
4153 9388 2.843701 CTGCAACAACTTGGTCTCTCT 58.156 47.619 0.00 0.00 0.00 3.10
4423 9658 7.123355 TCCAAACTGGAAAAAGATTCAACAT 57.877 32.000 0.00 0.00 45.00 2.71
4576 10014 3.444034 TGGAATCGGAGTCAGAGTACTTG 59.556 47.826 7.82 0.00 0.00 3.16
4587 10025 2.171448 CAGAGTACTTGCTTATGGCCCT 59.829 50.000 0.00 0.00 40.92 5.19
4754 12205 9.565090 TTGTAAGGAGTACATATATAGTGTCGT 57.435 33.333 0.00 0.00 42.37 4.34
4755 12206 9.212641 TGTAAGGAGTACATATATAGTGTCGTC 57.787 37.037 0.00 0.00 37.81 4.20
4799 12250 4.323417 TCATGCACTTCCGTTTCTGTATT 58.677 39.130 0.00 0.00 0.00 1.89
4800 12251 4.759693 TCATGCACTTCCGTTTCTGTATTT 59.240 37.500 0.00 0.00 0.00 1.40
4801 12252 4.742438 TGCACTTCCGTTTCTGTATTTC 57.258 40.909 0.00 0.00 0.00 2.17
4802 12253 4.130857 TGCACTTCCGTTTCTGTATTTCA 58.869 39.130 0.00 0.00 0.00 2.69
4803 12254 4.024387 TGCACTTCCGTTTCTGTATTTCAC 60.024 41.667 0.00 0.00 0.00 3.18
4886 12337 7.849804 TCTTCTCTACACAATATTTCCTTGC 57.150 36.000 0.00 0.00 0.00 4.01
4959 12420 8.780846 TCAACACTCAAAGAAAACTTACTACA 57.219 30.769 0.00 0.00 0.00 2.74
4960 12421 8.879759 TCAACACTCAAAGAAAACTTACTACAG 58.120 33.333 0.00 0.00 0.00 2.74
4961 12422 8.665685 CAACACTCAAAGAAAACTTACTACAGT 58.334 33.333 0.00 0.00 0.00 3.55
4962 12423 9.880157 AACACTCAAAGAAAACTTACTACAGTA 57.120 29.630 0.00 0.00 0.00 2.74
4964 12425 9.309516 CACTCAAAGAAAACTTACTACAGTACA 57.690 33.333 0.00 0.00 0.00 2.90
4965 12426 9.880157 ACTCAAAGAAAACTTACTACAGTACAA 57.120 29.630 0.00 0.00 0.00 2.41
4973 12434 8.658499 AAACTTACTACAGTACAAACTTCAGG 57.342 34.615 0.00 0.00 31.97 3.86
4974 12435 6.756221 ACTTACTACAGTACAAACTTCAGGG 58.244 40.000 0.00 0.00 31.97 4.45
4975 12436 4.004196 ACTACAGTACAAACTTCAGGGC 57.996 45.455 0.00 0.00 31.97 5.19
4976 12437 2.271944 ACAGTACAAACTTCAGGGCC 57.728 50.000 0.00 0.00 31.97 5.80
4977 12438 1.202891 ACAGTACAAACTTCAGGGCCC 60.203 52.381 16.46 16.46 31.97 5.80
4989 12450 3.683034 AGGGCCCCTGATCACTATT 57.317 52.632 21.43 0.00 29.57 1.73
4991 12452 2.217776 AGGGCCCCTGATCACTATTTT 58.782 47.619 21.43 0.00 29.57 1.82
4992 12453 3.403322 AGGGCCCCTGATCACTATTTTA 58.597 45.455 21.43 0.00 29.57 1.52
4993 12454 3.395941 AGGGCCCCTGATCACTATTTTAG 59.604 47.826 21.43 0.00 29.57 1.85
4995 12456 4.386424 GGGCCCCTGATCACTATTTTAGTT 60.386 45.833 12.23 0.00 36.76 2.24
4996 12457 5.163131 GGGCCCCTGATCACTATTTTAGTTA 60.163 44.000 12.23 0.00 36.76 2.24
4997 12458 5.763698 GGCCCCTGATCACTATTTTAGTTAC 59.236 44.000 0.00 0.00 36.76 2.50
4999 12460 6.579865 CCCCTGATCACTATTTTAGTTACGT 58.420 40.000 0.00 0.00 36.76 3.57
5019 12549 0.541863 AGTACAATTCCGAGGGCCTG 59.458 55.000 12.95 2.92 0.00 4.85
5074 12606 1.137086 TGATGCTAGCTCGTCCCTTTC 59.863 52.381 17.23 0.20 0.00 2.62
5134 12703 3.758554 ACAACAACAGCAACTCTTCAGTT 59.241 39.130 0.00 0.00 44.26 3.16
5184 12753 0.321346 TCTGATCCAGCAAAGCGTCA 59.679 50.000 0.00 0.00 0.00 4.35
5259 12828 5.073311 TCTTCCGAACAGAGAAAGGTATG 57.927 43.478 0.00 0.00 0.00 2.39
5364 12933 6.759272 AGTGAAGTAAGAAGTGCAATAGTGA 58.241 36.000 0.00 0.00 0.00 3.41
5451 13020 3.936453 TGGTGAAGTGATACGGTATTTGC 59.064 43.478 1.57 0.00 0.00 3.68
5477 13046 0.250513 AAGGGTGAGATTCCGACAGC 59.749 55.000 0.00 0.00 0.00 4.40
5488 13057 1.194218 TCCGACAGCCAGAATGATGA 58.806 50.000 0.00 0.00 39.69 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.500910 ACTTAAAACCAGTTCACGGAATTTC 58.499 36.000 0.00 0.00 0.00 2.17
85 86 6.533367 ACAACGCAAAACATAGAAAAACACAT 59.467 30.769 0.00 0.00 0.00 3.21
103 104 1.003331 GGATGACGAACAAACAACGCA 60.003 47.619 0.00 0.00 0.00 5.24
145 146 5.542251 TCTGTACATGTATAGGCCATGCTAA 59.458 40.000 24.34 4.28 42.74 3.09
150 151 4.907875 ACCTTCTGTACATGTATAGGCCAT 59.092 41.667 24.34 9.65 0.00 4.40
216 217 3.814268 CCGGCCCATTTGCAGTCG 61.814 66.667 0.00 0.00 0.00 4.18
314 317 6.377327 AAACAATGCTGAATTACTATCCCG 57.623 37.500 0.00 0.00 0.00 5.14
405 408 1.333619 CAAGGGAAACTGTTGACCACG 59.666 52.381 13.95 3.44 0.00 4.94
475 478 1.140407 GACTCTGGGAAATCGACGCG 61.140 60.000 3.53 3.53 0.00 6.01
476 479 0.108804 TGACTCTGGGAAATCGACGC 60.109 55.000 0.00 0.00 0.00 5.19
550 553 8.240267 TGTGGTTTAACAAGCTTAATAACCTT 57.760 30.769 22.12 3.33 0.00 3.50
673 676 4.357142 TGCCGTCTAGCTCGTAATTTAAG 58.643 43.478 0.00 0.00 0.00 1.85
731 734 3.084786 GACAATAAAGTTCAGGCAGGCT 58.915 45.455 0.00 0.00 0.00 4.58
812 815 5.723860 AGAAAGGGAAGGAGCTCAATTAT 57.276 39.130 17.19 0.00 0.00 1.28
873 876 8.041323 AGCACTAGAAAGCAGCTAAAATAAGTA 58.959 33.333 0.00 0.00 36.10 2.24
874 877 6.881602 AGCACTAGAAAGCAGCTAAAATAAGT 59.118 34.615 0.00 0.00 36.10 2.24
875 878 7.185453 CAGCACTAGAAAGCAGCTAAAATAAG 58.815 38.462 0.00 0.00 36.10 1.73
876 879 6.403636 GCAGCACTAGAAAGCAGCTAAAATAA 60.404 38.462 0.00 0.00 39.74 1.40
896 899 1.852633 TGAGCTAGTAAGAGGCAGCA 58.147 50.000 0.00 0.00 36.47 4.41
897 900 3.129871 CAATGAGCTAGTAAGAGGCAGC 58.870 50.000 0.00 0.00 0.00 5.25
898 901 3.129871 GCAATGAGCTAGTAAGAGGCAG 58.870 50.000 0.00 0.00 41.15 4.85
899 902 2.501316 TGCAATGAGCTAGTAAGAGGCA 59.499 45.455 0.00 0.00 45.94 4.75
900 903 3.185246 TGCAATGAGCTAGTAAGAGGC 57.815 47.619 0.00 0.00 45.94 4.70
901 904 4.764172 AGTTGCAATGAGCTAGTAAGAGG 58.236 43.478 0.59 0.00 45.94 3.69
947 951 1.690985 GGGGAGAAGGCTAGGCTGT 60.691 63.158 20.99 10.48 0.00 4.40
993 997 6.770286 ATGGTAATTGGATCCATCACTACT 57.230 37.500 17.06 0.00 37.38 2.57
1212 1216 4.601019 CATATTTAAGCCGCTTGAACAGG 58.399 43.478 16.15 0.80 0.00 4.00
1274 1278 4.397730 TGATCTGCTTCTCTAGACAGTGAC 59.602 45.833 0.00 0.00 32.92 3.67
1429 1475 7.775053 ATGCCAAAATTTCTAGTACCTTCAA 57.225 32.000 0.00 0.00 0.00 2.69
1430 1476 9.120538 GATATGCCAAAATTTCTAGTACCTTCA 57.879 33.333 0.00 0.00 0.00 3.02
1432 1478 9.474313 TTGATATGCCAAAATTTCTAGTACCTT 57.526 29.630 0.00 0.00 0.00 3.50
1434 1480 9.683069 CATTGATATGCCAAAATTTCTAGTACC 57.317 33.333 0.00 0.00 0.00 3.34
1546 3651 6.620678 TGAATTTCTCTAATTTTCCCTTGCG 58.379 36.000 0.00 0.00 36.59 4.85
1560 3665 7.440523 ACAAGATTAGCGTTTGAATTTCTCT 57.559 32.000 0.00 0.00 0.00 3.10
1570 3675 5.682943 TTTGTGCTACAAGATTAGCGTTT 57.317 34.783 0.00 0.00 46.51 3.60
1683 4539 5.450818 TGTGCCAAAAGGGTAATCTATCT 57.549 39.130 0.00 0.00 39.65 1.98
1684 4540 6.524101 TTTGTGCCAAAAGGGTAATCTATC 57.476 37.500 0.00 0.00 39.65 2.08
1685 4541 6.926630 TTTTGTGCCAAAAGGGTAATCTAT 57.073 33.333 8.46 0.00 39.65 1.98
1686 4542 6.926630 ATTTTGTGCCAAAAGGGTAATCTA 57.073 33.333 15.24 0.00 39.65 1.98
1699 4555 2.038426 TCGGAGAGAGAATTTTGTGCCA 59.962 45.455 0.00 0.00 0.00 4.92
1814 4710 4.080687 GCTAGGAATCACCGAGGTATACT 58.919 47.826 2.25 0.00 44.74 2.12
1887 4783 6.043938 ACCTCCAAGTTTTTCTAGATACACCA 59.956 38.462 0.00 0.00 0.00 4.17
2676 7298 5.234466 AGTTGTCACTAGGATCTTGCTTT 57.766 39.130 0.00 0.00 0.00 3.51
3007 7641 3.465403 CGCCTAGCCTGCTCACCT 61.465 66.667 0.00 0.00 0.00 4.00
3203 8180 2.308570 TGCCATGATTGTACCAGTCCTT 59.691 45.455 0.00 0.00 0.00 3.36
3320 8334 0.693049 TCTCTTGCCCACCTTTCTCC 59.307 55.000 0.00 0.00 0.00 3.71
3321 8335 2.290577 ACATCTCTTGCCCACCTTTCTC 60.291 50.000 0.00 0.00 0.00 2.87
3322 8336 1.707427 ACATCTCTTGCCCACCTTTCT 59.293 47.619 0.00 0.00 0.00 2.52
3323 8337 2.206576 ACATCTCTTGCCCACCTTTC 57.793 50.000 0.00 0.00 0.00 2.62
3324 8338 2.519013 GAACATCTCTTGCCCACCTTT 58.481 47.619 0.00 0.00 0.00 3.11
3325 8339 1.272147 GGAACATCTCTTGCCCACCTT 60.272 52.381 0.00 0.00 0.00 3.50
3326 8340 0.329596 GGAACATCTCTTGCCCACCT 59.670 55.000 0.00 0.00 0.00 4.00
3327 8341 0.681243 GGGAACATCTCTTGCCCACC 60.681 60.000 0.00 0.00 38.68 4.61
3328 8342 0.038166 TGGGAACATCTCTTGCCCAC 59.962 55.000 0.00 0.00 43.57 4.61
3329 8343 0.329261 CTGGGAACATCTCTTGCCCA 59.671 55.000 0.00 0.00 46.10 5.36
3330 8344 0.620556 TCTGGGAACATCTCTTGCCC 59.379 55.000 0.00 0.00 41.51 5.36
3331 8345 1.556911 TCTCTGGGAACATCTCTTGCC 59.443 52.381 0.00 0.00 41.51 4.52
3332 8346 2.626840 GTCTCTGGGAACATCTCTTGC 58.373 52.381 0.00 0.00 41.51 4.01
3333 8347 2.232452 ACGTCTCTGGGAACATCTCTTG 59.768 50.000 0.00 0.00 41.51 3.02
3334 8348 2.530701 ACGTCTCTGGGAACATCTCTT 58.469 47.619 0.00 0.00 41.51 2.85
3335 8349 2.223803 ACGTCTCTGGGAACATCTCT 57.776 50.000 0.00 0.00 41.51 3.10
3358 8372 8.239314 GCATCATAACTCTGAACAAAAAGATGA 58.761 33.333 0.00 0.00 32.06 2.92
3410 8429 9.906660 GATGAGTGTGTGTAAATTTTCCAATAA 57.093 29.630 0.00 0.00 0.00 1.40
3989 9209 3.792124 GCAACTTTTGAACTTCCACCGAG 60.792 47.826 0.00 0.00 0.00 4.63
4153 9388 3.414193 CCTGGCTGGCTCCATCCA 61.414 66.667 10.69 10.69 39.56 3.41
4423 9658 9.342308 CTTCACCTAAAATATTTCCTGCAGATA 57.658 33.333 17.39 5.61 0.00 1.98
4497 9928 4.020485 GTGTTAGAGAACATAGGTGGTGGT 60.020 45.833 0.00 0.00 46.98 4.16
4498 9929 4.020573 TGTGTTAGAGAACATAGGTGGTGG 60.021 45.833 0.00 0.00 46.98 4.61
4499 9930 5.147330 TGTGTTAGAGAACATAGGTGGTG 57.853 43.478 0.00 0.00 46.98 4.17
4576 10014 3.628032 GTCTCAAGTTAAGGGCCATAAGC 59.372 47.826 6.18 0.00 42.60 3.09
4587 10025 2.436417 GGCATGCAGGTCTCAAGTTAA 58.564 47.619 21.36 0.00 0.00 2.01
4657 10097 6.562223 TCCACCCAGGAATAGATTATGAATCA 59.438 38.462 2.27 0.00 45.65 2.57
4753 12204 4.998788 TCAGACACTGTATATGCACTGAC 58.001 43.478 7.47 2.55 32.62 3.51
4754 12205 5.659440 TTCAGACACTGTATATGCACTGA 57.341 39.130 7.47 7.47 34.37 3.41
4755 12206 6.044682 TGATTCAGACACTGTATATGCACTG 58.955 40.000 0.00 3.64 32.61 3.66
4886 12337 2.536761 TGTGGGGTGTAGAAAAGACG 57.463 50.000 0.00 0.00 0.00 4.18
4959 12420 0.404426 GGGGCCCTGAAGTTTGTACT 59.596 55.000 24.38 0.00 35.68 2.73
4960 12421 0.404426 AGGGGCCCTGAAGTTTGTAC 59.596 55.000 28.21 0.00 29.57 2.90
4961 12422 2.877150 AGGGGCCCTGAAGTTTGTA 58.123 52.632 28.21 0.00 29.57 2.41
4962 12423 3.688032 AGGGGCCCTGAAGTTTGT 58.312 55.556 28.21 0.00 29.57 2.83
4972 12433 2.755952 AAAATAGTGATCAGGGGCCC 57.244 50.000 17.12 17.12 0.00 5.80
4973 12434 4.439253 ACTAAAATAGTGATCAGGGGCC 57.561 45.455 0.00 0.00 37.69 5.80
4974 12435 5.465724 CGTAACTAAAATAGTGATCAGGGGC 59.534 44.000 0.00 0.00 39.39 5.80
4975 12436 6.579865 ACGTAACTAAAATAGTGATCAGGGG 58.420 40.000 0.00 0.00 39.39 4.79
4976 12437 8.411683 ACTACGTAACTAAAATAGTGATCAGGG 58.588 37.037 0.00 0.00 39.39 4.45
4988 12449 7.754924 CCTCGGAATTGTACTACGTAACTAAAA 59.245 37.037 0.00 0.00 0.00 1.52
4989 12450 7.250569 CCTCGGAATTGTACTACGTAACTAAA 58.749 38.462 0.00 0.00 0.00 1.85
4991 12452 5.296780 CCCTCGGAATTGTACTACGTAACTA 59.703 44.000 0.00 0.00 0.00 2.24
4992 12453 4.096984 CCCTCGGAATTGTACTACGTAACT 59.903 45.833 0.00 0.00 0.00 2.24
4993 12454 4.354587 CCCTCGGAATTGTACTACGTAAC 58.645 47.826 0.00 0.00 0.00 2.50
4995 12456 2.358898 GCCCTCGGAATTGTACTACGTA 59.641 50.000 0.00 0.00 0.00 3.57
4996 12457 1.135721 GCCCTCGGAATTGTACTACGT 59.864 52.381 0.00 0.00 0.00 3.57
4997 12458 1.537562 GGCCCTCGGAATTGTACTACG 60.538 57.143 0.00 0.00 0.00 3.51
4999 12460 1.760613 CAGGCCCTCGGAATTGTACTA 59.239 52.381 0.00 0.00 0.00 1.82
5008 12538 2.363795 CACTACCAGGCCCTCGGA 60.364 66.667 10.34 0.00 0.00 4.55
5009 12539 3.470888 CCACTACCAGGCCCTCGG 61.471 72.222 0.00 0.00 0.00 4.63
5010 12540 3.470888 CCCACTACCAGGCCCTCG 61.471 72.222 0.00 0.00 0.00 4.63
5037 12567 2.683933 AGGGTAGACTGGCGGTGG 60.684 66.667 2.25 0.00 0.00 4.61
5038 12568 1.330655 ATCAGGGTAGACTGGCGGTG 61.331 60.000 2.25 0.00 38.98 4.94
5040 12570 1.443407 CATCAGGGTAGACTGGCGG 59.557 63.158 0.00 0.00 38.98 6.13
5074 12606 1.136252 GCACAGTGATGTACAACAGCG 60.136 52.381 6.00 3.36 37.31 5.18
5184 12753 4.640789 ATTCTCACGTTCGAAGCTAGAT 57.359 40.909 0.00 0.00 0.00 1.98
5259 12828 1.481363 GCTGGTAGGAGTAGGAACCAC 59.519 57.143 0.00 0.00 37.09 4.16
5364 12933 7.120285 CCATCAATTTATCTTCTGATGCCGTAT 59.880 37.037 5.56 0.00 42.44 3.06
5401 12970 8.410673 AGATTAGTGTTGTCCTGATATATCGT 57.589 34.615 8.19 0.00 0.00 3.73
5451 13020 3.568007 TCGGAATCTCACCCTTGTTTTTG 59.432 43.478 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.