Multiple sequence alignment - TraesCS2B01G596200

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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 TraesCS2B01G596200 chr2B 100.000 3594 0 0 1 3594 779637212 779633619 0.000000e+00 6637
1 TraesCS2B01G596200 chr2B 95.606 2822 105 10 366 3170 779418863 779416044 0.000000e+00 4506
2 TraesCS2B01G596200 chr2B 95.572 2823 106 11 366 3170 779393164 779390343 0.000000e+00 4503
3 TraesCS2B01G596200 chr2B 95.501 2823 108 10 366 3170 779425317 779422496 0.000000e+00 4492
4 TraesCS2B01G596200 chr2B 95.500 2822 108 10 366 3170 779412414 779409595 0.000000e+00 4490
5 TraesCS2B01G596200 chr2B 95.500 2822 108 10 366 3170 779431772 779428953 0.000000e+00 4490
6 TraesCS2B01G596200 chr2B 95.250 2821 115 11 366 3168 779444648 779441829 0.000000e+00 4449
7 TraesCS2B01G596200 chr2B 94.326 2820 141 9 366 3170 779675596 779672781 0.000000e+00 4303
8 TraesCS2B01G596200 chr2B 94.735 2754 126 9 434 3170 779566442 779563691 0.000000e+00 4265
9 TraesCS2B01G596200 chr2B 95.215 2675 112 6 512 3170 779554893 779552219 0.000000e+00 4217
10 TraesCS2B01G596200 chr2B 94.816 2662 116 10 523 3170 779537767 779535114 0.000000e+00 4132
11 TraesCS2B01G596200 chr2B 95.538 1255 44 1 1928 3170 779654670 779653416 0.000000e+00 1997
12 TraesCS2B01G596200 chr2B 94.832 387 17 2 1 386 779669301 779668917 5.130000e-168 601
13 TraesCS2B01G596200 chr2B 94.574 387 17 3 1 386 779444973 779444590 2.390000e-166 595
14 TraesCS2B01G596200 chr2B 94.574 387 17 3 1 386 779506902 779506519 2.390000e-166 595
15 TraesCS2B01G596200 chr2B 94.330 388 18 4 1 386 779560398 779560013 3.090000e-165 592
16 TraesCS2B01G596200 chr2B 96.848 349 11 0 3167 3515 779563137 779562789 5.170000e-163 584
17 TraesCS2B01G596200 chr2B 94.057 387 20 3 1 386 779576034 779575650 5.170000e-163 584
18 TraesCS2B01G596200 chr2B 96.562 349 12 0 3167 3515 779402465 779402117 2.410000e-161 579
19 TraesCS2B01G596200 chr2B 96.562 349 12 0 3167 3515 779409041 779408693 2.410000e-161 579
20 TraesCS2B01G596200 chr2B 96.562 349 12 0 3167 3515 779415490 779415142 2.410000e-161 579
21 TraesCS2B01G596200 chr2B 96.286 350 12 1 3167 3515 779421942 779421593 1.120000e-159 573
22 TraesCS2B01G596200 chr2B 97.222 72 0 1 3523 3594 782876574 782876643 1.750000e-23 121
23 TraesCS2B01G596200 chr2B 97.059 68 0 1 3527 3594 782750632 782750697 2.930000e-21 113
24 TraesCS2B01G596200 chr2D 95.600 2818 107 10 366 3170 635313515 635310702 0.000000e+00 4501
25 TraesCS2B01G596200 chr2D 95.422 2818 112 9 366 3170 635287494 635284681 0.000000e+00 4473
26 TraesCS2B01G596200 chr2D 94.820 946 35 6 2237 3170 635445076 635444133 0.000000e+00 1463
27 TraesCS2B01G596200 chr2D 95.607 387 16 1 1 386 635313843 635313457 1.420000e-173 619
28 TraesCS2B01G596200 chr2D 95.361 388 15 2 1 386 635287822 635287436 6.590000e-172 614
29 TraesCS2B01G596200 chr2D 95.090 387 17 2 1 386 635461060 635460675 3.070000e-170 608
30 TraesCS2B01G596200 chr2D 94.588 388 19 2 1 386 635281372 635280985 1.850000e-167 599
31 TraesCS2B01G596200 chr2D 97.143 350 9 1 3167 3515 635284125 635283776 1.110000e-164 590
32 TraesCS2B01G596200 chr2D 96.866 351 9 1 3167 3515 635413113 635412763 1.440000e-163 586
33 TraesCS2B01G596200 chr2D 96.571 350 11 1 3167 3515 635310146 635309797 2.410000e-161 579
34 TraesCS2B01G596200 chrUn 95.464 2822 110 10 366 3170 280844605 280847425 0.000000e+00 4486
35 TraesCS2B01G596200 chrUn 96.562 349 12 0 3164 3512 280841528 280841876 2.410000e-161 579
36 TraesCS2B01G596200 chrUn 85.246 366 44 6 2814 3170 402332003 402331639 5.670000e-98 368
37 TraesCS2B01G596200 chrUn 92.222 90 3 2 3509 3594 50087582 50087671 1.350000e-24 124
38 TraesCS2B01G596200 chrUn 92.222 90 3 2 3509 3594 50119789 50119700 1.350000e-24 124
39 TraesCS2B01G596200 chr3D 94.253 87 3 1 3510 3594 601179008 601178922 8.100000e-27 132
40 TraesCS2B01G596200 chr7A 97.059 68 0 1 3527 3594 39391688 39391623 2.930000e-21 113
41 TraesCS2B01G596200 chr5B 97.059 68 0 1 3527 3594 389510979 389510914 2.930000e-21 113
42 TraesCS2B01G596200 chr1D 88.889 90 10 0 3505 3594 273555908 273555997 1.050000e-20 111
43 TraesCS2B01G596200 chr1D 89.535 86 7 1 3509 3594 289163294 289163211 1.360000e-19 108


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 TraesCS2B01G596200 chr2B 779633619 779637212 3593 True 6637.000000 6637 100.000000 1 3594 1 chr2B.!!$R7 3593
1 TraesCS2B01G596200 chr2B 779390343 779393164 2821 True 4503.000000 4503 95.572000 366 3170 1 chr2B.!!$R1 2804
2 TraesCS2B01G596200 chr2B 779552219 779554893 2674 True 4217.000000 4217 95.215000 512 3170 1 chr2B.!!$R5 2658
3 TraesCS2B01G596200 chr2B 779535114 779537767 2653 True 4132.000000 4132 94.816000 523 3170 1 chr2B.!!$R4 2647
4 TraesCS2B01G596200 chr2B 779408693 779431772 23079 True 2815.571429 4506 95.931000 366 3515 7 chr2B.!!$R9 3149
5 TraesCS2B01G596200 chr2B 779441829 779444973 3144 True 2522.000000 4449 94.912000 1 3168 2 chr2B.!!$R10 3167
6 TraesCS2B01G596200 chr2B 779668917 779675596 6679 True 2452.000000 4303 94.579000 1 3170 2 chr2B.!!$R12 3169
7 TraesCS2B01G596200 chr2B 779653416 779654670 1254 True 1997.000000 1997 95.538000 1928 3170 1 chr2B.!!$R8 1242
8 TraesCS2B01G596200 chr2B 779560013 779566442 6429 True 1813.666667 4265 95.304333 1 3515 3 chr2B.!!$R11 3514
9 TraesCS2B01G596200 chr2D 635309797 635313843 4046 True 1899.666667 4501 95.926000 1 3515 3 chr2D.!!$R5 3514
10 TraesCS2B01G596200 chr2D 635280985 635287822 6837 True 1569.000000 4473 95.628500 1 3515 4 chr2D.!!$R4 3514
11 TraesCS2B01G596200 chr2D 635444133 635445076 943 True 1463.000000 1463 94.820000 2237 3170 1 chr2D.!!$R2 933
12 TraesCS2B01G596200 chrUn 280841528 280847425 5897 False 2532.500000 4486 96.013000 366 3512 2 chrUn.!!$F2 3146

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
333 334 0.107643 TGGCAATGGTCGTCAACTCA 59.892 50.0 0.0 0.0 0.00 3.41 F
338 339 0.320421 ATGGTCGTCAACTCAACCGG 60.320 55.0 0.0 0.0 34.39 5.28 F
2004 8101 0.106708 TTGGAGACCTGTCACAGCAC 59.893 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 7584 1.134848 CAGAGTAGCTCTTGCCTGACC 60.135 57.143 0.00 0.0 38.99 4.02 R
2006 8103 2.038820 CCCATTTTTGGCCTTGTGATGT 59.961 45.455 3.32 0.0 0.00 3.06 R
2960 21959 0.249699 TACCGGCAATGGATGTAGCG 60.250 55.000 0.00 0.0 0.00 4.26 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
204 205 3.364964 GGCCTCACATTAAACGAGTGTTG 60.365 47.826 0.00 0.00 38.62 3.33
289 290 3.326733 TTTGTTCACAACATCGAACGG 57.673 42.857 0.00 0.00 43.59 4.44
291 292 0.865769 GTTCACAACATCGAACGGCT 59.134 50.000 0.00 0.00 32.87 5.52
292 293 1.136336 GTTCACAACATCGAACGGCTC 60.136 52.381 0.00 0.00 32.87 4.70
303 304 3.276846 ACGGCTCGTTGTGTTGGC 61.277 61.111 0.00 0.00 36.35 4.52
305 306 2.331451 GGCTCGTTGTGTTGGCAC 59.669 61.111 0.00 0.00 45.44 5.01
306 307 2.331451 GCTCGTTGTGTTGGCACC 59.669 61.111 0.00 0.00 44.65 5.01
307 308 2.477176 GCTCGTTGTGTTGGCACCA 61.477 57.895 0.00 0.00 44.65 4.17
308 309 1.999071 GCTCGTTGTGTTGGCACCAA 61.999 55.000 0.00 0.00 44.65 3.67
310 311 0.453793 TCGTTGTGTTGGCACCAAAG 59.546 50.000 3.10 0.00 44.65 2.77
311 312 0.527385 CGTTGTGTTGGCACCAAAGG 60.527 55.000 3.10 0.00 44.65 3.11
312 313 0.534873 GTTGTGTTGGCACCAAAGGT 59.465 50.000 3.10 0.00 44.65 3.50
315 316 1.959985 TGTGTTGGCACCAAAGGTATG 59.040 47.619 3.10 0.00 44.65 2.39
316 317 1.272212 GTGTTGGCACCAAAGGTATGG 59.728 52.381 3.10 0.00 46.38 2.74
317 318 0.246360 GTTGGCACCAAAGGTATGGC 59.754 55.000 3.10 0.00 44.75 4.40
320 321 1.194218 GGCACCAAAGGTATGGCAAT 58.806 50.000 0.00 0.00 44.75 3.56
322 323 1.134729 GCACCAAAGGTATGGCAATGG 60.135 52.381 0.00 0.00 44.75 3.16
324 325 2.166254 CACCAAAGGTATGGCAATGGTC 59.834 50.000 0.00 0.00 44.75 4.02
328 329 0.908910 AGGTATGGCAATGGTCGTCA 59.091 50.000 0.00 0.00 0.00 4.35
330 331 1.400494 GGTATGGCAATGGTCGTCAAC 59.600 52.381 0.00 0.00 0.00 3.18
331 332 2.356135 GTATGGCAATGGTCGTCAACT 58.644 47.619 0.00 0.00 0.00 3.16
332 333 1.453155 ATGGCAATGGTCGTCAACTC 58.547 50.000 0.00 0.00 0.00 3.01
333 334 0.107643 TGGCAATGGTCGTCAACTCA 59.892 50.000 0.00 0.00 0.00 3.41
334 335 1.234821 GGCAATGGTCGTCAACTCAA 58.765 50.000 0.00 0.00 0.00 3.02
335 336 1.069227 GGCAATGGTCGTCAACTCAAC 60.069 52.381 0.00 0.00 0.00 3.18
336 337 1.069227 GCAATGGTCGTCAACTCAACC 60.069 52.381 0.00 0.00 0.00 3.77
337 338 1.194547 CAATGGTCGTCAACTCAACCG 59.805 52.381 0.00 0.00 34.39 4.44
338 339 0.320421 ATGGTCGTCAACTCAACCGG 60.320 55.000 0.00 0.00 34.39 5.28
353 354 3.282557 CCGGAGGCAAAACCAAAAC 57.717 52.632 0.00 0.00 46.14 2.43
355 356 1.537990 CCGGAGGCAAAACCAAAACTG 60.538 52.381 0.00 0.00 46.14 3.16
359 360 3.368948 GGAGGCAAAACCAAAACTGAACA 60.369 43.478 0.00 0.00 43.14 3.18
360 361 4.441792 GAGGCAAAACCAAAACTGAACAT 58.558 39.130 0.00 0.00 43.14 2.71
361 362 4.441792 AGGCAAAACCAAAACTGAACATC 58.558 39.130 0.00 0.00 43.14 3.06
362 363 4.162131 AGGCAAAACCAAAACTGAACATCT 59.838 37.500 0.00 0.00 43.14 2.90
364 365 6.045955 GGCAAAACCAAAACTGAACATCTTA 58.954 36.000 0.00 0.00 38.86 2.10
370 6462 6.795399 ACCAAAACTGAACATCTTACAACTG 58.205 36.000 0.00 0.00 0.00 3.16
486 6578 9.014297 TCCTTCTGAGATAATTGTTTCCTTTTC 57.986 33.333 0.00 0.00 0.00 2.29
721 6813 5.622770 AGTTTCCAATACCAACAATCGAC 57.377 39.130 0.00 0.00 0.00 4.20
726 6818 3.504134 CCAATACCAACAATCGACCAACA 59.496 43.478 0.00 0.00 0.00 3.33
887 6979 0.550914 TGGCCCATGAAGGATACCAC 59.449 55.000 0.00 0.00 41.22 4.16
916 7010 1.893808 CCCCCATACACGAGCATGC 60.894 63.158 10.51 10.51 0.00 4.06
923 7017 0.469494 TACACGAGCATGCCATCCAT 59.531 50.000 15.66 0.00 33.39 3.41
1027 7121 4.953579 AGGGTGTTACAGTGTTGATTGTTT 59.046 37.500 0.00 0.00 0.00 2.83
1039 7133 0.609662 GATTGTTTGTGCTGGGCCAT 59.390 50.000 6.72 0.00 0.00 4.40
1155 7249 2.706555 CGTATGATCGCCTCAAGCTA 57.293 50.000 0.00 0.00 40.39 3.32
1162 7256 1.474330 TCGCCTCAAGCTACATCTCA 58.526 50.000 0.00 0.00 40.39 3.27
1199 7293 2.040278 AGTTGCCACACATGTCATACCT 59.960 45.455 0.00 0.00 0.00 3.08
1200 7294 3.263170 AGTTGCCACACATGTCATACCTA 59.737 43.478 0.00 0.00 0.00 3.08
1347 7441 0.602562 AATGTTGGTCCATTGTGGCG 59.397 50.000 0.00 0.00 37.47 5.69
1424 7518 3.005554 CAAGTGGTGAGAATAGTGCAGG 58.994 50.000 0.00 0.00 0.00 4.85
1459 7553 6.503560 TGTTCCCTAGACTGGAAAACTTTA 57.496 37.500 1.00 0.00 43.24 1.85
1462 7556 6.503560 TCCCTAGACTGGAAAACTTTACAA 57.496 37.500 0.00 0.00 28.96 2.41
1490 7584 4.160439 TGTTATCCACTCCTCAAGCTACAG 59.840 45.833 0.00 0.00 0.00 2.74
1755 7850 9.911788 AAAGAGATGGACTGTTTTATATCACAT 57.088 29.630 0.00 0.00 38.64 3.21
1756 7851 8.899427 AGAGATGGACTGTTTTATATCACATG 57.101 34.615 0.00 0.00 0.00 3.21
1777 7872 8.598924 CACATGCAAACAACTAAGATACTAGAG 58.401 37.037 0.00 0.00 0.00 2.43
1794 7890 5.880901 ACTAGAGGAACCACATGACAAAAT 58.119 37.500 0.00 0.00 0.00 1.82
1863 7960 5.560953 GCATACTTCAAAAGAGGTGTGACAC 60.561 44.000 7.29 7.29 0.00 3.67
1926 8023 0.603065 GTTTGGGGATGACACTTGCC 59.397 55.000 0.00 0.00 0.00 4.52
1973 8070 1.915141 AAACTCCTTGTGATGGCAGG 58.085 50.000 0.00 0.00 0.00 4.85
1974 8071 1.067295 AACTCCTTGTGATGGCAGGA 58.933 50.000 0.00 0.00 0.00 3.86
2004 8101 0.106708 TTGGAGACCTGTCACAGCAC 59.893 55.000 0.00 0.00 0.00 4.40
2006 8103 1.660355 GAGACCTGTCACAGCACGA 59.340 57.895 0.00 0.00 0.00 4.35
2065 8162 0.036732 AGAAACAGGCCGATCTGCAA 59.963 50.000 11.45 0.00 38.26 4.08
2242 8339 8.000780 AGATCAAGGGCAACATAGTTAAATTC 57.999 34.615 0.00 0.00 39.74 2.17
2351 8448 4.037690 GCTTGTGTTTGAACATGTCTGAC 58.962 43.478 0.00 0.00 41.59 3.51
2406 8503 8.911918 TCAGCTAACAAGGTCTATTTGTTTTA 57.088 30.769 8.43 0.00 44.04 1.52
2495 8592 3.806949 AAGGTGAAAATGGGCTCTACA 57.193 42.857 0.00 0.00 0.00 2.74
2694 21692 8.999431 CACCTTTGTATCTAGCTTTTAGACAAA 58.001 33.333 12.21 12.21 0.00 2.83
2924 21922 3.630312 GCGTGTTTACCCCATCAACATAT 59.370 43.478 0.00 0.00 33.15 1.78
2954 21953 3.388024 GGAGGTAGTAATCACATCAGCCA 59.612 47.826 0.00 0.00 0.00 4.75
2955 21954 4.040952 GGAGGTAGTAATCACATCAGCCAT 59.959 45.833 0.00 0.00 0.00 4.40
2958 21957 7.321717 AGGTAGTAATCACATCAGCCATAAT 57.678 36.000 0.00 0.00 0.00 1.28
2960 21959 7.880195 AGGTAGTAATCACATCAGCCATAATTC 59.120 37.037 0.00 0.00 0.00 2.17
2961 21960 6.791887 AGTAATCACATCAGCCATAATTCG 57.208 37.500 0.00 0.00 0.00 3.34
3044 22061 0.397941 GCATCTGCATGGGGTAGCTA 59.602 55.000 0.00 0.00 41.59 3.32
3266 24857 5.241403 AGTGATTGATGTTGGGACTGTTA 57.759 39.130 0.00 0.00 0.00 2.41
3465 25057 9.270576 CTGACTCAAATGCGCAATTATATATTC 57.729 33.333 17.11 4.47 0.00 1.75
3512 25104 1.801178 GAAGGCGGCTACTTGCATATC 59.199 52.381 13.71 0.00 45.15 1.63
3515 25107 2.834549 AGGCGGCTACTTGCATATCTAT 59.165 45.455 11.03 0.00 45.15 1.98
3516 25108 3.118956 AGGCGGCTACTTGCATATCTATC 60.119 47.826 11.03 0.00 45.15 2.08
3517 25109 3.118956 GGCGGCTACTTGCATATCTATCT 60.119 47.826 0.00 0.00 45.15 1.98
3519 25111 5.221342 GGCGGCTACTTGCATATCTATCTAT 60.221 44.000 0.00 0.00 45.15 1.98
3520 25112 5.918011 GCGGCTACTTGCATATCTATCTATC 59.082 44.000 0.00 0.00 45.15 2.08
3521 25113 6.238897 GCGGCTACTTGCATATCTATCTATCT 60.239 42.308 0.00 0.00 45.15 1.98
3522 25114 7.041030 GCGGCTACTTGCATATCTATCTATCTA 60.041 40.741 0.00 0.00 45.15 1.98
3589 27808 8.480133 ACCTATACTAATTTGTGACTCCCTAG 57.520 38.462 2.59 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
267 268 4.099120 CCGTTCGATGTTGTGAACAAAAA 58.901 39.130 0.00 0.00 45.86 1.94
269 270 2.539953 GCCGTTCGATGTTGTGAACAAA 60.540 45.455 0.00 0.00 45.86 2.83
270 271 1.003331 GCCGTTCGATGTTGTGAACAA 60.003 47.619 6.00 0.00 45.86 2.83
271 272 0.584396 GCCGTTCGATGTTGTGAACA 59.416 50.000 6.00 0.00 43.59 3.18
272 273 0.865769 AGCCGTTCGATGTTGTGAAC 59.134 50.000 0.00 0.00 40.77 3.18
273 274 1.144969 GAGCCGTTCGATGTTGTGAA 58.855 50.000 0.00 0.00 0.00 3.18
286 287 3.276846 GCCAACACAACGAGCCGT 61.277 61.111 0.00 0.00 43.97 5.68
287 288 3.276091 TGCCAACACAACGAGCCG 61.276 61.111 0.00 0.00 0.00 5.52
288 289 2.331451 GTGCCAACACAACGAGCC 59.669 61.111 0.00 0.00 46.61 4.70
297 298 1.626686 CCATACCTTTGGTGCCAACA 58.373 50.000 2.72 0.00 36.19 3.33
298 299 0.246360 GCCATACCTTTGGTGCCAAC 59.754 55.000 2.72 0.00 39.11 3.77
300 301 0.178950 TTGCCATACCTTTGGTGCCA 60.179 50.000 0.00 0.00 39.11 4.92
301 302 1.134729 CATTGCCATACCTTTGGTGCC 60.135 52.381 0.00 0.00 39.11 5.01
302 303 1.134729 CCATTGCCATACCTTTGGTGC 60.135 52.381 0.00 0.00 39.11 5.01
303 304 2.166254 GACCATTGCCATACCTTTGGTG 59.834 50.000 0.00 0.00 37.58 4.17
305 306 1.405105 CGACCATTGCCATACCTTTGG 59.595 52.381 0.00 0.00 39.94 3.28
306 307 2.091541 ACGACCATTGCCATACCTTTG 58.908 47.619 0.00 0.00 0.00 2.77
307 308 2.290641 TGACGACCATTGCCATACCTTT 60.291 45.455 0.00 0.00 0.00 3.11
308 309 1.280710 TGACGACCATTGCCATACCTT 59.719 47.619 0.00 0.00 0.00 3.50
310 311 1.400494 GTTGACGACCATTGCCATACC 59.600 52.381 0.00 0.00 0.00 2.73
311 312 2.351726 GAGTTGACGACCATTGCCATAC 59.648 50.000 0.00 0.00 0.00 2.39
312 313 2.027653 TGAGTTGACGACCATTGCCATA 60.028 45.455 0.00 0.00 0.00 2.74
315 316 1.069227 GTTGAGTTGACGACCATTGCC 60.069 52.381 0.00 0.00 0.00 4.52
316 317 1.069227 GGTTGAGTTGACGACCATTGC 60.069 52.381 0.00 0.00 42.26 3.56
317 318 1.194547 CGGTTGAGTTGACGACCATTG 59.805 52.381 0.00 0.00 42.68 2.82
320 321 1.068417 CCGGTTGAGTTGACGACCA 59.932 57.895 0.00 0.00 42.68 4.02
322 323 0.666577 CCTCCGGTTGAGTTGACGAC 60.667 60.000 0.00 0.00 39.65 4.34
324 325 2.027625 GCCTCCGGTTGAGTTGACG 61.028 63.158 0.00 0.00 39.65 4.35
328 329 1.029681 GTTTTGCCTCCGGTTGAGTT 58.970 50.000 0.00 0.00 39.65 3.01
330 331 0.821711 TGGTTTTGCCTCCGGTTGAG 60.822 55.000 0.00 0.00 41.07 3.02
331 332 0.395862 TTGGTTTTGCCTCCGGTTGA 60.396 50.000 0.00 0.00 38.35 3.18
332 333 0.461961 TTTGGTTTTGCCTCCGGTTG 59.538 50.000 0.00 0.00 38.35 3.77
333 334 1.134640 GTTTTGGTTTTGCCTCCGGTT 60.135 47.619 0.00 0.00 38.35 4.44
334 335 0.462375 GTTTTGGTTTTGCCTCCGGT 59.538 50.000 0.00 0.00 38.35 5.28
335 336 0.750249 AGTTTTGGTTTTGCCTCCGG 59.250 50.000 0.00 0.00 38.35 5.14
336 337 1.407258 TCAGTTTTGGTTTTGCCTCCG 59.593 47.619 0.00 0.00 38.35 4.63
337 338 3.194861 GTTCAGTTTTGGTTTTGCCTCC 58.805 45.455 0.00 0.00 38.35 4.30
338 339 3.855858 TGTTCAGTTTTGGTTTTGCCTC 58.144 40.909 0.00 0.00 38.35 4.70
340 341 4.441792 AGATGTTCAGTTTTGGTTTTGCC 58.558 39.130 0.00 0.00 37.90 4.52
341 342 6.533367 TGTAAGATGTTCAGTTTTGGTTTTGC 59.467 34.615 0.00 0.00 0.00 3.68
342 343 8.379902 GTTGTAAGATGTTCAGTTTTGGTTTTG 58.620 33.333 0.00 0.00 0.00 2.44
343 344 8.311109 AGTTGTAAGATGTTCAGTTTTGGTTTT 58.689 29.630 0.00 0.00 0.00 2.43
344 345 7.759433 CAGTTGTAAGATGTTCAGTTTTGGTTT 59.241 33.333 0.00 0.00 0.00 3.27
348 349 7.432252 GGTTCAGTTGTAAGATGTTCAGTTTTG 59.568 37.037 0.00 0.00 0.00 2.44
350 351 6.238374 CGGTTCAGTTGTAAGATGTTCAGTTT 60.238 38.462 0.00 0.00 0.00 2.66
351 352 5.236478 CGGTTCAGTTGTAAGATGTTCAGTT 59.764 40.000 0.00 0.00 0.00 3.16
352 353 4.750098 CGGTTCAGTTGTAAGATGTTCAGT 59.250 41.667 0.00 0.00 0.00 3.41
353 354 4.152402 CCGGTTCAGTTGTAAGATGTTCAG 59.848 45.833 0.00 0.00 0.00 3.02
355 356 4.312443 TCCGGTTCAGTTGTAAGATGTTC 58.688 43.478 0.00 0.00 0.00 3.18
359 360 2.354805 GCCTCCGGTTCAGTTGTAAGAT 60.355 50.000 0.00 0.00 0.00 2.40
360 361 1.001633 GCCTCCGGTTCAGTTGTAAGA 59.998 52.381 0.00 0.00 0.00 2.10
361 362 1.270625 TGCCTCCGGTTCAGTTGTAAG 60.271 52.381 0.00 0.00 0.00 2.34
362 363 0.759959 TGCCTCCGGTTCAGTTGTAA 59.240 50.000 0.00 0.00 0.00 2.41
364 365 0.106918 TTTGCCTCCGGTTCAGTTGT 60.107 50.000 0.00 0.00 0.00 3.32
370 6462 0.747852 TTTGGTTTTGCCTCCGGTTC 59.252 50.000 0.00 0.00 38.35 3.62
427 6519 2.548904 CCATGTTAACCGGTTTTGTCGA 59.451 45.455 27.64 2.44 0.00 4.20
525 6617 6.451393 TCCAAACACACATTTATAGGCAAAC 58.549 36.000 0.00 0.00 0.00 2.93
580 6672 8.429641 TCAAGTGTTTCTTCCTCTTTGTATACT 58.570 33.333 4.17 0.00 33.63 2.12
682 6774 8.624367 TTGGAAACTTATCGACCATCTTTTTA 57.376 30.769 0.00 0.00 0.00 1.52
721 6813 3.208747 AGGTAGGAAACACACTGTTGG 57.791 47.619 0.00 0.00 40.14 3.77
726 6818 8.380099 TGATACAAAATAGGTAGGAAACACACT 58.620 33.333 0.00 0.00 0.00 3.55
849 6941 5.104982 GGGCCAATCTGTTTTATGGATTGAA 60.105 40.000 4.39 0.00 45.09 2.69
887 6979 6.572509 GCTCGTGTATGGGGGCATATATATAG 60.573 46.154 0.00 0.00 0.00 1.31
916 7010 3.391506 TGCTCGATGAACTATGGATGG 57.608 47.619 0.00 0.00 0.00 3.51
923 7017 3.723260 TGTGTGTTTGCTCGATGAACTA 58.277 40.909 0.00 0.00 0.00 2.24
1108 7202 2.878429 CCAGAGTGACGCGCTACT 59.122 61.111 14.69 14.69 0.00 2.57
1155 7249 4.101585 TCACAGAACTCCTTTGTGAGATGT 59.898 41.667 2.68 0.00 44.39 3.06
1162 7256 2.945668 GCAACTCACAGAACTCCTTTGT 59.054 45.455 0.00 0.00 0.00 2.83
1199 7293 6.325286 TGGTATGTATGTTGGTGCATCTACTA 59.675 38.462 12.73 0.24 0.00 1.82
1200 7294 5.130311 TGGTATGTATGTTGGTGCATCTACT 59.870 40.000 12.73 1.63 0.00 2.57
1347 7441 2.030805 GGTGCACTTTGACATGTCCTTC 60.031 50.000 22.85 6.97 0.00 3.46
1459 7553 4.532126 TGAGGAGTGGATAACATCACTTGT 59.468 41.667 0.00 0.00 43.41 3.16
1462 7556 4.383552 GCTTGAGGAGTGGATAACATCACT 60.384 45.833 0.00 0.00 45.70 3.41
1490 7584 1.134848 CAGAGTAGCTCTTGCCTGACC 60.135 57.143 0.00 0.00 38.99 4.02
1755 7850 7.476540 TCCTCTAGTATCTTAGTTGTTTGCA 57.523 36.000 0.00 0.00 0.00 4.08
1756 7851 7.278203 GGTTCCTCTAGTATCTTAGTTGTTTGC 59.722 40.741 0.00 0.00 0.00 3.68
1768 7863 5.854010 TGTCATGTGGTTCCTCTAGTATC 57.146 43.478 0.00 0.00 0.00 2.24
1770 7865 6.428083 TTTTGTCATGTGGTTCCTCTAGTA 57.572 37.500 0.00 0.00 0.00 1.82
1777 7872 9.271828 AGAAATAAAATTTTGTCATGTGGTTCC 57.728 29.630 13.76 0.00 0.00 3.62
1863 7960 3.077229 TGAATCTGCAACCACAAAACG 57.923 42.857 0.00 0.00 0.00 3.60
1926 8023 2.991250 AGATTCAATGGAAGACGGTGG 58.009 47.619 0.00 0.00 36.25 4.61
2004 8101 2.791383 TTTTTGGCCTTGTGATGTCG 57.209 45.000 3.32 0.00 0.00 4.35
2006 8103 2.038820 CCCATTTTTGGCCTTGTGATGT 59.961 45.455 3.32 0.00 0.00 3.06
2065 8162 5.579047 TCCAACAGTCCCAACATCAATTAT 58.421 37.500 0.00 0.00 0.00 1.28
2242 8339 7.599621 TCAAATGACATTCTTTTACTGCATTGG 59.400 33.333 0.05 0.00 0.00 3.16
2288 8385 2.323939 TTTGCCGTGCTTTTGTATCG 57.676 45.000 0.00 0.00 0.00 2.92
2399 8496 7.523709 GCTCTCACCATTCTGGATTTAAAACAA 60.524 37.037 0.00 0.00 40.96 2.83
2406 8503 3.726557 TGCTCTCACCATTCTGGATTT 57.273 42.857 0.00 0.00 40.96 2.17
2495 8592 4.335647 CCTCGCCAACCCAGCACT 62.336 66.667 0.00 0.00 0.00 4.40
2704 21702 8.428852 GGGGCACATATGAACCTTAAAATAAAT 58.571 33.333 10.38 0.00 0.00 1.40
2924 21922 8.057011 TGATGTGATTACTACCTCCTACAGTTA 58.943 37.037 0.00 0.00 0.00 2.24
2954 21953 3.436704 CGGCAATGGATGTAGCGAATTAT 59.563 43.478 0.00 0.00 0.00 1.28
2955 21954 2.805671 CGGCAATGGATGTAGCGAATTA 59.194 45.455 0.00 0.00 0.00 1.40
2958 21957 0.813610 CCGGCAATGGATGTAGCGAA 60.814 55.000 0.00 0.00 0.00 4.70
2960 21959 0.249699 TACCGGCAATGGATGTAGCG 60.250 55.000 0.00 0.00 0.00 4.26
2961 21960 1.202651 AGTACCGGCAATGGATGTAGC 60.203 52.381 0.00 0.00 0.00 3.58
3126 24158 9.709495 ACCACAAATACACGTTCTAAATAGTAA 57.291 29.630 0.00 0.00 0.00 2.24
3353 24945 7.258441 CGACATTATGAGAGAAAAGGTCTACA 58.742 38.462 0.00 0.00 36.41 2.74
3465 25057 5.799936 CGTCATGTAAGTGCCTTATTTTTGG 59.200 40.000 0.00 0.00 0.00 3.28
3565 27784 8.707796 TCTAGGGAGTCACAAATTAGTATAGG 57.292 38.462 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.