Multiple sequence alignment - TraesCS6B01G132900

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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 TraesCS6B01G132900 chr6B 100.000 2819 0 0 1 2819 129849898 129852716 0.000000e+00 5206.0
1 TraesCS6B01G132900 chr6B 79.583 1342 240 25 540 1860 129447047 129448375 0.000000e+00 929.0
2 TraesCS6B01G132900 chr6B 78.271 1353 240 46 537 1860 129268709 129270036 0.000000e+00 821.0
3 TraesCS6B01G132900 chr6B 75.411 1338 267 45 540 1847 129237176 129238481 2.420000e-165 592.0
4 TraesCS6B01G132900 chr6B 79.540 435 80 8 1398 1829 129680405 129680833 4.560000e-78 302.0
5 TraesCS6B01G132900 chr6A 91.437 2464 129 42 382 2819 73063469 73065876 0.000000e+00 3306.0
6 TraesCS6B01G132900 chr6A 78.412 1348 247 36 537 1860 72429449 72430776 0.000000e+00 837.0
7 TraesCS6B01G132900 chr6A 81.250 464 78 7 1400 1860 72481183 72481640 1.600000e-97 366.0
8 TraesCS6B01G132900 chr6A 90.717 237 17 4 1 234 73063150 73063384 7.580000e-81 311.0
9 TraesCS6B01G132900 chr6A 83.582 335 50 4 540 873 72488820 72489150 2.730000e-80 309.0
10 TraesCS6B01G132900 chr6A 76.277 607 123 16 540 1134 71948684 71949281 1.270000e-78 303.0
11 TraesCS6B01G132900 chr6A 81.818 99 12 4 254 347 73063370 73063467 8.370000e-11 78.7
12 TraesCS6B01G132900 chr6D 91.951 1640 65 20 381 1970 57893908 57895530 0.000000e+00 2235.0
13 TraesCS6B01G132900 chr6D 90.365 685 41 12 1955 2632 57896143 57896809 0.000000e+00 876.0
14 TraesCS6B01G132900 chr6D 76.993 1317 240 45 540 1834 57514214 57515489 0.000000e+00 695.0
15 TraesCS6B01G132900 chr6D 75.504 1339 264 48 540 1847 57171293 57172598 5.200000e-167 597.0
16 TraesCS6B01G132900 chr6D 82.365 482 73 9 1382 1860 57483275 57483747 2.610000e-110 409.0
17 TraesCS6B01G132900 chr6D 78.548 606 108 17 540 1137 57482430 57483021 2.050000e-101 379.0
18 TraesCS6B01G132900 chr6D 91.139 237 14 5 1 234 57883466 57883698 5.860000e-82 315.0
19 TraesCS6B01G132900 chr6D 90.957 188 16 1 2633 2819 57896779 57896966 4.660000e-63 252.0
20 TraesCS6B01G132900 chr6D 82.530 166 22 6 2401 2561 57179740 57179903 3.790000e-29 139.0
21 TraesCS6B01G132900 chr6D 83.333 144 9 7 254 388 57883684 57883821 4.930000e-23 119.0
22 TraesCS6B01G132900 chr1A 83.117 154 23 3 1861 2012 528671096 528671248 1.360000e-28 137.0
23 TraesCS6B01G132900 chr1B 82.692 156 22 4 1861 2012 581696620 581696774 1.760000e-27 134.0


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 TraesCS6B01G132900 chr6B 129849898 129852716 2818 False 5206.0 5206 100.000000 1 2819 1 chr6B.!!$F5 2818
1 TraesCS6B01G132900 chr6B 129447047 129448375 1328 False 929.0 929 79.583000 540 1860 1 chr6B.!!$F3 1320
2 TraesCS6B01G132900 chr6B 129268709 129270036 1327 False 821.0 821 78.271000 537 1860 1 chr6B.!!$F2 1323
3 TraesCS6B01G132900 chr6B 129237176 129238481 1305 False 592.0 592 75.411000 540 1847 1 chr6B.!!$F1 1307
4 TraesCS6B01G132900 chr6A 73063150 73065876 2726 False 1231.9 3306 87.990667 1 2819 3 chr6A.!!$F5 2818
5 TraesCS6B01G132900 chr6A 72429449 72430776 1327 False 837.0 837 78.412000 537 1860 1 chr6A.!!$F2 1323
6 TraesCS6B01G132900 chr6A 71948684 71949281 597 False 303.0 303 76.277000 540 1134 1 chr6A.!!$F1 594
7 TraesCS6B01G132900 chr6D 57893908 57896966 3058 False 1121.0 2235 91.091000 381 2819 3 chr6D.!!$F6 2438
8 TraesCS6B01G132900 chr6D 57514214 57515489 1275 False 695.0 695 76.993000 540 1834 1 chr6D.!!$F3 1294
9 TraesCS6B01G132900 chr6D 57171293 57172598 1305 False 597.0 597 75.504000 540 1847 1 chr6D.!!$F1 1307
10 TraesCS6B01G132900 chr6D 57482430 57483747 1317 False 394.0 409 80.456500 540 1860 2 chr6D.!!$F4 1320

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
365 371 0.038159 CACTCACCTCGTTCCAGGTC 60.038 60.0 0.0 0.0 44.08 3.85 F
375 381 0.603975 GTTCCAGGTCCAGCACACTC 60.604 60.0 0.0 0.0 0.00 3.51 F
379 385 0.904865 CAGGTCCAGCACACTCCCTA 60.905 60.0 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1742 0.905357 AACAAGCTCATAGGGACGCT 59.095 50.0 0.00 0.0 33.33 5.07 R
1652 1746 2.094182 GTCGTCAACAAGCTCATAGGGA 60.094 50.0 0.00 0.0 0.00 4.20 R
2045 2769 2.229675 CGTGAGCTCTCATTGGCATA 57.770 50.0 16.19 0.0 42.18 3.14 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
19 20 0.676466 CTTACTCGCACCCATTGGCA 60.676 55.000 0.00 0.00 33.59 4.92
24 25 2.973082 GCACCCATTGGCAAGGAC 59.027 61.111 14.30 0.92 33.59 3.85
30 31 1.002134 CATTGGCAAGGACGAGGGT 60.002 57.895 5.89 0.00 0.00 4.34
58 59 3.931907 CCTTCAAGGTGATATGGGTGA 57.068 47.619 0.00 0.00 0.00 4.02
64 65 1.762957 AGGTGATATGGGTGAACTCCG 59.237 52.381 0.00 0.00 0.00 4.63
68 69 2.040009 ATATGGGTGAACTCCGGGCG 62.040 60.000 0.00 0.00 0.00 6.13
129 132 0.304705 CGAAAAAGACAGCACGCACT 59.695 50.000 0.00 0.00 0.00 4.40
131 134 0.381801 AAAAAGACAGCACGCACTGG 59.618 50.000 9.78 0.00 42.21 4.00
149 152 3.652869 ACTGGATTTTTCCTCTCCTCACA 59.347 43.478 0.00 0.00 0.00 3.58
171 174 4.304048 TGGTAATTTTCCTTCGGCCTTA 57.696 40.909 0.00 0.00 0.00 2.69
172 175 4.862371 TGGTAATTTTCCTTCGGCCTTAT 58.138 39.130 0.00 0.00 0.00 1.73
179 182 2.452505 TCCTTCGGCCTTATTTTTGGG 58.547 47.619 0.00 0.00 0.00 4.12
182 185 3.450817 CCTTCGGCCTTATTTTTGGGAAT 59.549 43.478 0.00 0.00 0.00 3.01
183 186 4.647399 CCTTCGGCCTTATTTTTGGGAATA 59.353 41.667 0.00 0.00 0.00 1.75
185 188 5.845391 TCGGCCTTATTTTTGGGAATAAG 57.155 39.130 0.00 9.36 43.98 1.73
193 196 9.078990 CCTTATTTTTGGGAATAAGATACTCCC 57.921 37.037 15.36 0.00 45.79 4.30
309 314 3.340928 CGGAACCCTAGGAAATTCGTTT 58.659 45.455 11.48 0.00 0.00 3.60
337 343 2.175035 TTTTCCCTCGATCCGCCGTT 62.175 55.000 0.00 0.00 0.00 4.44
347 353 4.418328 CCGCCGTTCCATTCCCCA 62.418 66.667 0.00 0.00 0.00 4.96
348 354 3.131478 CGCCGTTCCATTCCCCAC 61.131 66.667 0.00 0.00 0.00 4.61
349 355 2.355115 GCCGTTCCATTCCCCACT 59.645 61.111 0.00 0.00 0.00 4.00
350 356 1.749258 GCCGTTCCATTCCCCACTC 60.749 63.158 0.00 0.00 0.00 3.51
351 357 1.682849 CCGTTCCATTCCCCACTCA 59.317 57.895 0.00 0.00 0.00 3.41
352 358 0.676782 CCGTTCCATTCCCCACTCAC 60.677 60.000 0.00 0.00 0.00 3.51
353 359 0.676782 CGTTCCATTCCCCACTCACC 60.677 60.000 0.00 0.00 0.00 4.02
354 360 0.698818 GTTCCATTCCCCACTCACCT 59.301 55.000 0.00 0.00 0.00 4.00
355 361 0.991920 TTCCATTCCCCACTCACCTC 59.008 55.000 0.00 0.00 0.00 3.85
356 362 1.221840 CCATTCCCCACTCACCTCG 59.778 63.158 0.00 0.00 0.00 4.63
357 363 1.553690 CCATTCCCCACTCACCTCGT 61.554 60.000 0.00 0.00 0.00 4.18
358 364 0.324943 CATTCCCCACTCACCTCGTT 59.675 55.000 0.00 0.00 0.00 3.85
359 365 0.613777 ATTCCCCACTCACCTCGTTC 59.386 55.000 0.00 0.00 0.00 3.95
360 366 1.477685 TTCCCCACTCACCTCGTTCC 61.478 60.000 0.00 0.00 0.00 3.62
361 367 2.214216 CCCCACTCACCTCGTTCCA 61.214 63.158 0.00 0.00 0.00 3.53
362 368 1.293498 CCCACTCACCTCGTTCCAG 59.707 63.158 0.00 0.00 0.00 3.86
363 369 1.293498 CCACTCACCTCGTTCCAGG 59.707 63.158 0.00 0.00 39.80 4.45
365 371 0.038159 CACTCACCTCGTTCCAGGTC 60.038 60.000 0.00 0.00 44.08 3.85
366 372 1.186267 ACTCACCTCGTTCCAGGTCC 61.186 60.000 0.00 0.00 44.08 4.46
367 373 1.152419 TCACCTCGTTCCAGGTCCA 60.152 57.895 0.00 0.00 44.08 4.02
368 374 1.185618 TCACCTCGTTCCAGGTCCAG 61.186 60.000 0.00 0.00 44.08 3.86
369 375 2.266055 CCTCGTTCCAGGTCCAGC 59.734 66.667 0.00 0.00 0.00 4.85
370 376 2.583441 CCTCGTTCCAGGTCCAGCA 61.583 63.158 0.00 0.00 0.00 4.41
371 377 1.374758 CTCGTTCCAGGTCCAGCAC 60.375 63.158 0.00 0.00 0.00 4.40
372 378 2.099652 CTCGTTCCAGGTCCAGCACA 62.100 60.000 0.00 0.00 0.00 4.57
373 379 1.961277 CGTTCCAGGTCCAGCACAC 60.961 63.158 0.00 0.00 0.00 3.82
374 380 1.451936 GTTCCAGGTCCAGCACACT 59.548 57.895 0.00 0.00 0.00 3.55
375 381 0.603975 GTTCCAGGTCCAGCACACTC 60.604 60.000 0.00 0.00 0.00 3.51
376 382 1.768684 TTCCAGGTCCAGCACACTCC 61.769 60.000 0.00 0.00 0.00 3.85
377 383 2.348998 CAGGTCCAGCACACTCCC 59.651 66.667 0.00 0.00 0.00 4.30
378 384 2.205462 AGGTCCAGCACACTCCCT 59.795 61.111 0.00 0.00 0.00 4.20
379 385 0.904865 CAGGTCCAGCACACTCCCTA 60.905 60.000 0.00 0.00 0.00 3.53
657 699 2.997897 ACCGAGCGCTCCTTCCTT 60.998 61.111 30.66 6.55 0.00 3.36
805 856 1.001376 ACCTACTCCTTCGTCCCCC 59.999 63.158 0.00 0.00 0.00 5.40
840 891 4.388499 GTGTGGGTCCCGTGCGAT 62.388 66.667 2.65 0.00 0.00 4.58
925 983 1.731709 TCTGCGATCCATTGTTTCGTG 59.268 47.619 7.15 2.69 35.40 4.35
980 1041 1.078848 CACTCCAGGAGAAAGGCCG 60.079 63.158 24.45 0.00 33.32 6.13
983 1044 4.803908 CCAGGAGAAAGGCCGCCC 62.804 72.222 5.55 0.00 0.00 6.13
986 1047 4.035102 GGAGAAAGGCCGCCCTGT 62.035 66.667 5.55 0.00 41.90 4.00
1182 1273 2.069273 CGAAACTTCAGAGGTTGCGAT 58.931 47.619 18.91 0.00 45.46 4.58
1289 1380 5.058490 CACAAGGAAAATGGAGTTTTGCAT 58.942 37.500 7.35 0.00 46.81 3.96
1533 1627 1.272147 GGCCAGTCTTCCAAGGAATGT 60.272 52.381 0.00 0.00 33.28 2.71
1648 1742 4.464008 AGATCAGCTGGACTTTGTTGAAA 58.536 39.130 15.13 0.00 0.00 2.69
1652 1746 1.065551 GCTGGACTTTGTTGAAAGCGT 59.934 47.619 0.00 0.00 42.19 5.07
1935 2030 4.124351 CACCCGCGTTCGAGCCTA 62.124 66.667 4.92 0.00 38.10 3.93
1953 2049 1.549243 TAGGCTCCGCATGGTGTGAA 61.549 55.000 0.00 0.00 36.30 3.18
1988 2712 5.930837 TCTTAATTAATTTGCCACAGGGG 57.069 39.130 5.91 0.00 40.85 4.79
2030 2754 1.055849 TAAGAACAGAGCAGTGGCCA 58.944 50.000 0.00 0.00 42.56 5.36
2031 2755 0.183492 AAGAACAGAGCAGTGGCCAA 59.817 50.000 7.24 0.00 42.56 4.52
2032 2756 0.183492 AGAACAGAGCAGTGGCCAAA 59.817 50.000 7.24 0.00 42.56 3.28
2045 2769 2.497273 GTGGCCAAATTGGTTAGAGCAT 59.503 45.455 7.24 0.00 40.46 3.79
2054 2778 5.717078 ATTGGTTAGAGCATATGCCAATG 57.283 39.130 23.96 0.00 42.82 2.82
2055 2779 4.436113 TGGTTAGAGCATATGCCAATGA 57.564 40.909 23.96 4.53 43.38 2.57
2117 2841 4.537135 TGCCTCACTTCTACCTAAACAG 57.463 45.455 0.00 0.00 0.00 3.16
2125 2849 6.436218 TCACTTCTACCTAAACAGCATACAGA 59.564 38.462 0.00 0.00 0.00 3.41
2126 2850 7.124298 TCACTTCTACCTAAACAGCATACAGAT 59.876 37.037 0.00 0.00 0.00 2.90
2127 2851 7.766278 CACTTCTACCTAAACAGCATACAGATT 59.234 37.037 0.00 0.00 0.00 2.40
2128 2852 8.322091 ACTTCTACCTAAACAGCATACAGATTT 58.678 33.333 0.00 0.00 0.00 2.17
2129 2853 9.167311 CTTCTACCTAAACAGCATACAGATTTT 57.833 33.333 0.00 0.00 0.00 1.82
2130 2854 8.492673 TCTACCTAAACAGCATACAGATTTTG 57.507 34.615 0.00 0.00 0.00 2.44
2131 2855 8.100791 TCTACCTAAACAGCATACAGATTTTGT 58.899 33.333 0.00 0.00 43.96 2.83
2132 2856 7.524717 ACCTAAACAGCATACAGATTTTGTT 57.475 32.000 0.00 0.00 41.29 2.83
2133 2857 7.951591 ACCTAAACAGCATACAGATTTTGTTT 58.048 30.769 5.82 5.82 41.29 2.83
2134 2858 8.421002 ACCTAAACAGCATACAGATTTTGTTTT 58.579 29.630 5.83 0.00 41.29 2.43
2135 2859 9.260002 CCTAAACAGCATACAGATTTTGTTTTT 57.740 29.630 5.83 0.00 41.29 1.94
2230 2955 1.426215 ACTTCCCCCGTTAACCATGTT 59.574 47.619 0.00 0.00 0.00 2.71
2264 2990 3.259064 GCGTGCTTCACTGTCCTAATTA 58.741 45.455 0.00 0.00 31.34 1.40
2304 3030 9.638239 TTATTGTTTCATGCTATTTTGAGAACC 57.362 29.630 0.00 0.00 0.00 3.62
2316 3042 7.118971 GCTATTTTGAGAACCTATCTAGCCATG 59.881 40.741 0.00 0.00 38.96 3.66
2343 3069 7.537596 AGGTGGTCATGATTTATTTTTGTCA 57.462 32.000 0.00 0.00 0.00 3.58
2349 3075 8.586273 GGTCATGATTTATTTTTGTCATGTTCG 58.414 33.333 0.00 0.00 45.02 3.95
2393 3119 9.171877 TGCCAGTTAAAGAAAACAAATTCATTT 57.828 25.926 0.00 0.00 0.00 2.32
2418 3144 2.896685 AGGAGGAAAGGCATCTCTATCG 59.103 50.000 0.00 0.00 0.00 2.92
2588 3317 4.630111 TGGAACATTTGAAAGCATGAACC 58.370 39.130 0.00 0.00 0.00 3.62
2589 3318 3.674753 GGAACATTTGAAAGCATGAACCG 59.325 43.478 0.00 0.00 0.00 4.44
2715 3446 5.870433 TGGAAGCATATTTCTGTTGCATTTG 59.130 36.000 0.00 0.00 38.84 2.32
2717 3448 4.761975 AGCATATTTCTGTTGCATTTGGG 58.238 39.130 0.00 0.00 38.84 4.12
2726 3457 0.392336 TTGCATTTGGGTGACTTGCC 59.608 50.000 0.00 0.00 32.39 4.52
2728 3459 1.202989 TGCATTTGGGTGACTTGCCTA 60.203 47.619 0.00 0.00 32.39 3.93
2742 3473 8.182227 GGTGACTTGCCTATTATGAGTTTTAAC 58.818 37.037 0.00 0.00 0.00 2.01
2774 3505 1.813513 CAGGGATCAACTCGCTTTGT 58.186 50.000 0.00 0.00 44.22 2.83
2777 3508 2.814336 AGGGATCAACTCGCTTTGTTTC 59.186 45.455 0.00 0.00 44.22 2.78
2778 3509 2.552315 GGGATCAACTCGCTTTGTTTCA 59.448 45.455 0.00 0.00 34.11 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.529948 TCGTCACACCCTCGTCCTT 60.530 57.895 0.00 0.00 0.00 3.36
24 25 1.080705 GAAGGTCGTCACACCCTCG 60.081 63.158 0.00 0.00 37.09 4.63
58 59 2.926242 TTCCTTCCGCCCGGAGTT 60.926 61.111 0.73 0.00 46.06 3.01
64 65 4.840005 CTCCGCTTCCTTCCGCCC 62.840 72.222 0.00 0.00 0.00 6.13
68 69 1.537135 CGATCTTCTCCGCTTCCTTCC 60.537 57.143 0.00 0.00 0.00 3.46
117 120 0.593128 AAAATCCAGTGCGTGCTGTC 59.407 50.000 7.40 0.00 34.84 3.51
129 132 4.568380 CCATGTGAGGAGAGGAAAAATCCA 60.568 45.833 0.00 0.00 35.45 3.41
131 134 4.593956 ACCATGTGAGGAGAGGAAAAATC 58.406 43.478 0.00 0.00 0.00 2.17
247 250 5.867174 CCTCGTTTGGTTCAACTTTCTTTTT 59.133 36.000 0.00 0.00 0.00 1.94
248 251 5.407502 CCTCGTTTGGTTCAACTTTCTTTT 58.592 37.500 0.00 0.00 0.00 2.27
249 252 4.676986 GCCTCGTTTGGTTCAACTTTCTTT 60.677 41.667 0.00 0.00 0.00 2.52
250 253 3.181490 GCCTCGTTTGGTTCAACTTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
251 254 2.357952 GCCTCGTTTGGTTCAACTTTCT 59.642 45.455 0.00 0.00 0.00 2.52
252 255 2.098443 TGCCTCGTTTGGTTCAACTTTC 59.902 45.455 0.00 0.00 0.00 2.62
253 256 2.096248 TGCCTCGTTTGGTTCAACTTT 58.904 42.857 0.00 0.00 0.00 2.66
254 257 1.404035 GTGCCTCGTTTGGTTCAACTT 59.596 47.619 0.00 0.00 0.00 2.66
255 258 1.021968 GTGCCTCGTTTGGTTCAACT 58.978 50.000 0.00 0.00 0.00 3.16
289 292 3.442625 CCAAACGAATTTCCTAGGGTTCC 59.557 47.826 9.46 0.00 0.00 3.62
290 293 4.077108 ACCAAACGAATTTCCTAGGGTTC 58.923 43.478 9.46 10.19 0.00 3.62
291 294 4.108501 ACCAAACGAATTTCCTAGGGTT 57.891 40.909 9.46 0.60 0.00 4.11
292 295 3.801307 ACCAAACGAATTTCCTAGGGT 57.199 42.857 9.46 0.00 0.00 4.34
293 296 4.332828 AGAACCAAACGAATTTCCTAGGG 58.667 43.478 9.46 0.00 0.00 3.53
294 297 5.959618 AAGAACCAAACGAATTTCCTAGG 57.040 39.130 0.82 0.82 0.00 3.02
322 327 4.587189 GGAACGGCGGATCGAGGG 62.587 72.222 13.24 0.00 0.00 4.30
323 328 2.644555 AATGGAACGGCGGATCGAGG 62.645 60.000 13.24 0.00 0.00 4.63
324 329 1.215655 GAATGGAACGGCGGATCGAG 61.216 60.000 13.24 0.00 0.00 4.04
325 330 1.227147 GAATGGAACGGCGGATCGA 60.227 57.895 13.24 7.00 0.00 3.59
326 331 2.244651 GGAATGGAACGGCGGATCG 61.245 63.158 13.24 0.00 0.00 3.69
331 337 3.131478 GTGGGGAATGGAACGGCG 61.131 66.667 4.80 4.80 0.00 6.46
337 343 1.264749 CGAGGTGAGTGGGGAATGGA 61.265 60.000 0.00 0.00 0.00 3.41
347 353 4.621269 ACCTGGAACGAGGTGAGT 57.379 55.556 7.66 0.00 45.20 3.41
352 358 2.266055 GCTGGACCTGGAACGAGG 59.734 66.667 0.00 1.46 39.28 4.63
353 359 1.374758 GTGCTGGACCTGGAACGAG 60.375 63.158 0.00 2.10 0.00 4.18
354 360 2.137528 TGTGCTGGACCTGGAACGA 61.138 57.895 0.00 0.00 0.00 3.85
355 361 1.961277 GTGTGCTGGACCTGGAACG 60.961 63.158 0.00 0.00 0.00 3.95
356 362 0.603975 GAGTGTGCTGGACCTGGAAC 60.604 60.000 0.00 0.00 0.00 3.62
357 363 1.754745 GAGTGTGCTGGACCTGGAA 59.245 57.895 0.00 0.00 0.00 3.53
358 364 2.217038 GGAGTGTGCTGGACCTGGA 61.217 63.158 0.00 0.00 0.00 3.86
359 365 2.348998 GGAGTGTGCTGGACCTGG 59.651 66.667 0.00 0.00 0.00 4.45
360 366 0.904865 TAGGGAGTGTGCTGGACCTG 60.905 60.000 0.00 0.00 0.00 4.00
361 367 0.178903 TTAGGGAGTGTGCTGGACCT 60.179 55.000 0.00 0.00 0.00 3.85
362 368 0.690762 TTTAGGGAGTGTGCTGGACC 59.309 55.000 0.00 0.00 0.00 4.46
363 369 2.561478 TTTTAGGGAGTGTGCTGGAC 57.439 50.000 0.00 0.00 0.00 4.02
479 503 2.267642 CCGTCGAGGCCATGGAAA 59.732 61.111 18.40 0.00 0.00 3.13
527 551 1.367471 CCGAGGTCTGTGAGCAACA 59.633 57.895 0.00 0.00 37.22 3.33
657 699 3.109547 CGTTTGCGGTAGCTGCGA 61.110 61.111 0.00 0.00 45.42 5.10
980 1041 2.790433 TGAGTGAATTGGTTACAGGGC 58.210 47.619 0.00 0.00 0.00 5.19
983 1044 3.129287 GGGCATGAGTGAATTGGTTACAG 59.871 47.826 0.00 0.00 0.00 2.74
986 1047 3.448093 TGGGCATGAGTGAATTGGTTA 57.552 42.857 0.00 0.00 0.00 2.85
1182 1273 2.030490 AACAGGACACGCCACGGTAA 62.030 55.000 0.00 0.00 40.02 2.85
1289 1380 1.749063 AGCCAGTACGATCATCGACAA 59.251 47.619 15.60 0.00 43.74 3.18
1347 1438 2.852413 CACATAGATGTCGACAACGTCC 59.148 50.000 24.13 9.45 43.79 4.79
1533 1627 6.455647 CAACGGTATAATATTCTCCAGCTGA 58.544 40.000 17.39 0.00 0.00 4.26
1648 1742 0.905357 AACAAGCTCATAGGGACGCT 59.095 50.000 0.00 0.00 33.33 5.07
1652 1746 2.094182 GTCGTCAACAAGCTCATAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1865 1960 2.721231 CCAACTGGCCAACACACG 59.279 61.111 7.01 0.00 0.00 4.49
1945 2041 3.025322 AGAAACAACCCATTCACACCA 57.975 42.857 0.00 0.00 0.00 4.17
1988 2712 9.274206 CTTAAAACTAGACCAATAGGGATTAGC 57.726 37.037 0.00 0.00 41.15 3.09
1997 2721 8.372459 TGCTCTGTTCTTAAAACTAGACCAATA 58.628 33.333 0.00 0.00 0.00 1.90
1998 2722 7.224297 TGCTCTGTTCTTAAAACTAGACCAAT 58.776 34.615 0.00 0.00 0.00 3.16
2030 2754 6.324512 TCATTGGCATATGCTCTAACCAATTT 59.675 34.615 26.12 5.26 43.54 1.82
2031 2755 5.834742 TCATTGGCATATGCTCTAACCAATT 59.165 36.000 26.12 8.74 43.54 2.32
2032 2756 5.387788 TCATTGGCATATGCTCTAACCAAT 58.612 37.500 26.12 20.81 46.16 3.16
2045 2769 2.229675 CGTGAGCTCTCATTGGCATA 57.770 50.000 16.19 0.00 42.18 3.14
2095 2819 4.624125 GCTGTTTAGGTAGAAGTGAGGCAT 60.624 45.833 0.00 0.00 0.00 4.40
2108 2832 7.524717 AACAAAATCTGTATGCTGTTTAGGT 57.475 32.000 0.00 0.00 37.23 3.08
2132 2856 7.396419 TCGTCGTTTCAAAACAAAAACAAAAA 58.604 26.923 6.45 0.00 38.81 1.94
2133 2857 6.929896 TCGTCGTTTCAAAACAAAAACAAAA 58.070 28.000 6.45 0.00 38.81 2.44
2134 2858 6.506464 TCGTCGTTTCAAAACAAAAACAAA 57.494 29.167 6.45 0.00 38.81 2.83
2135 2859 5.387547 GCTCGTCGTTTCAAAACAAAAACAA 60.388 36.000 6.45 0.00 38.81 2.83
2136 2860 4.088781 GCTCGTCGTTTCAAAACAAAAACA 59.911 37.500 6.45 0.00 38.81 2.83
2137 2861 4.322539 AGCTCGTCGTTTCAAAACAAAAAC 59.677 37.500 6.45 0.00 38.81 2.43
2194 2918 4.484537 GGAAGTTCCCTCCCTTAACTAC 57.515 50.000 11.17 0.00 33.24 2.73
2230 2955 5.582665 AGTGAAGCACGCCAAAAATTAAAAA 59.417 32.000 0.00 0.00 39.64 1.94
2251 2977 4.818005 TCAGCATGCATAATTAGGACAGTG 59.182 41.667 21.98 3.89 34.76 3.66
2252 2978 5.039920 TCAGCATGCATAATTAGGACAGT 57.960 39.130 21.98 0.00 34.76 3.55
2264 2990 5.416639 TGAAACAATAACTCTCAGCATGCAT 59.583 36.000 21.98 1.69 34.76 3.96
2304 3030 4.101585 TGACCACCTTTCATGGCTAGATAG 59.898 45.833 0.00 0.00 41.31 2.08
2316 3042 8.831715 ACAAAAATAAATCATGACCACCTTTC 57.168 30.769 0.00 0.00 0.00 2.62
2338 3064 5.163864 GCATGACAACTATCGAACATGACAA 60.164 40.000 0.00 0.00 37.77 3.18
2393 3119 3.933886 AGAGATGCCTTTCCTCCTATGA 58.066 45.455 0.00 0.00 0.00 2.15
2399 3125 2.036475 TGCGATAGAGATGCCTTTCCTC 59.964 50.000 0.00 0.00 39.76 3.71
2418 3144 4.111916 AGCATAATACGCAAATTTGGTGC 58.888 39.130 19.47 13.26 38.68 5.01
2506 3232 7.979537 CAGTATACAACAATAGTAGCAGGAACA 59.020 37.037 5.50 0.00 0.00 3.18
2589 3318 7.545615 AGTTTAAAACTAAATGCATAAGCTGCC 59.454 33.333 0.00 0.00 44.81 4.85
2656 3387 7.652909 CAGTAATGCCTTTCAAGTGAAATTGAA 59.347 33.333 6.92 2.03 45.12 2.69
2657 3388 7.147312 CAGTAATGCCTTTCAAGTGAAATTGA 58.853 34.615 6.92 0.00 42.44 2.57
2658 3389 6.925165 ACAGTAATGCCTTTCAAGTGAAATTG 59.075 34.615 6.92 3.64 42.44 2.32
2659 3390 6.925165 CACAGTAATGCCTTTCAAGTGAAATT 59.075 34.615 6.92 2.09 42.44 1.82
2660 3391 6.265196 TCACAGTAATGCCTTTCAAGTGAAAT 59.735 34.615 6.92 0.00 42.44 2.17
2661 3392 5.592282 TCACAGTAATGCCTTTCAAGTGAAA 59.408 36.000 6.33 6.33 41.29 2.69
2662 3393 5.129634 TCACAGTAATGCCTTTCAAGTGAA 58.870 37.500 0.00 0.00 31.36 3.18
2663 3394 4.713553 TCACAGTAATGCCTTTCAAGTGA 58.286 39.130 0.00 0.00 0.00 3.41
2664 3395 5.437289 TTCACAGTAATGCCTTTCAAGTG 57.563 39.130 0.00 0.00 0.00 3.16
2665 3396 5.594317 AGTTTCACAGTAATGCCTTTCAAGT 59.406 36.000 0.00 0.00 0.00 3.16
2666 3397 6.076981 AGTTTCACAGTAATGCCTTTCAAG 57.923 37.500 0.00 0.00 0.00 3.02
2667 3398 7.309133 CCATAGTTTCACAGTAATGCCTTTCAA 60.309 37.037 0.00 0.00 0.00 2.69
2674 3405 5.123820 TGCTTCCATAGTTTCACAGTAATGC 59.876 40.000 0.00 0.00 0.00 3.56
2715 3446 4.423625 ACTCATAATAGGCAAGTCACCC 57.576 45.455 0.00 0.00 0.00 4.61
2717 3448 8.947115 AGTTAAAACTCATAATAGGCAAGTCAC 58.053 33.333 0.00 0.00 32.86 3.67
2742 3473 6.709281 AGTTGATCCCTGCAGATATATTCAG 58.291 40.000 17.39 0.00 0.00 3.02
2774 3505 3.435890 CCCAAGTACAAGAACCCCTGAAA 60.436 47.826 0.00 0.00 0.00 2.69
2777 3508 1.886655 GCCCAAGTACAAGAACCCCTG 60.887 57.143 0.00 0.00 0.00 4.45
2778 3509 0.404426 GCCCAAGTACAAGAACCCCT 59.596 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.