Multiple sequence alignment - TraesCS2B01G432900

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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 TraesCS2B01G432900 chr2B 100.000 5214 0 0 1 5214 622472671 622477884 0.000000e+00 9629
1 TraesCS2B01G432900 chr2A 94.262 4688 171 42 588 5213 671271494 671276145 0.000000e+00 7077
2 TraesCS2B01G432900 chr2A 84.720 589 62 15 1 587 671270895 671271457 9.800000e-157 564
3 TraesCS2B01G432900 chr2D 93.748 4079 160 38 591 4619 525301819 525297786 0.000000e+00 6032
4 TraesCS2B01G432900 chr2D 91.147 497 26 9 4705 5198 525297787 525297306 0.000000e+00 658
5 TraesCS2B01G432900 chr2D 84.330 351 30 13 238 587 525302190 525301864 2.340000e-83 320
6 TraesCS2B01G432900 chr2D 87.603 242 27 2 1 241 525407323 525407084 1.430000e-70 278


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 TraesCS2B01G432900 chr2B 622472671 622477884 5213 False 9629.000000 9629 100.000000 1 5214 1 chr2B.!!$F1 5213
1 TraesCS2B01G432900 chr2A 671270895 671276145 5250 False 3820.500000 7077 89.491000 1 5213 2 chr2A.!!$F1 5212
2 TraesCS2B01G432900 chr2D 525297306 525302190 4884 True 2336.666667 6032 89.741667 238 5198 3 chr2D.!!$R2 4960

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
75 76 0.108756 GGTCAGAGTGGCTTCGGTAC 60.109 60.0 0.00 0.0 0.00 3.34 F
864 910 0.400213 TGTTTCCTCCACTCGCCATT 59.600 50.0 0.00 0.0 0.00 3.16 F
1140 1187 0.745486 TCGTATCGCTCTTCACCGGA 60.745 55.0 9.46 0.0 0.00 5.14 F
3012 3089 0.320073 TGCTTGCATTTTCTGGCTGC 60.320 50.0 0.00 0.0 36.45 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1856 0.106419 GTTGTTGGTTCAGTCCCCCA 60.106 55.000 0.0 0.0 0.00 4.96 R
2629 2706 2.029918 TCACCAGAACAGATGACTCACG 60.030 50.000 0.0 0.0 0.00 4.35 R
3128 3205 3.634397 TGGACCCATCTGTTGAGAATC 57.366 47.619 0.0 0.0 0.00 2.52 R
4912 5043 0.099259 CCTGCAACATGGCATACGTG 59.901 55.000 0.0 0.0 43.97 4.49 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
21 22 0.543749 GTGCTAGCTTCATCAGGGGT 59.456 55.000 17.23 0.00 0.00 4.95
40 41 3.553508 GGGTACGTGCACAAAGACTTCTA 60.554 47.826 18.64 0.00 0.00 2.10
75 76 0.108756 GGTCAGAGTGGCTTCGGTAC 60.109 60.000 0.00 0.00 0.00 3.34
102 103 7.197017 AGACTAATGAGTAACGACAATAGCAG 58.803 38.462 0.00 0.00 35.45 4.24
111 112 1.546834 GACAATAGCAGGTCGACGAC 58.453 55.000 19.70 19.70 0.00 4.34
121 122 1.572085 GGTCGACGACTCGTTCTGGA 61.572 60.000 25.87 0.00 41.37 3.86
135 136 2.119801 TCTGGAGGTAGTGGTCGTAC 57.880 55.000 0.00 0.00 0.00 3.67
144 145 3.696051 GGTAGTGGTCGTACATAGTCCAA 59.304 47.826 0.00 0.00 0.00 3.53
151 152 5.067413 TGGTCGTACATAGTCCAAGAATCTC 59.933 44.000 0.00 0.00 0.00 2.75
186 187 8.410673 TTCATTATGGTTAAGGTGCTTTGTAA 57.589 30.769 0.00 0.00 0.00 2.41
193 194 6.206634 TGGTTAAGGTGCTTTGTAATTCTGAG 59.793 38.462 0.00 0.00 0.00 3.35
200 201 6.239036 GGTGCTTTGTAATTCTGAGGAACTTT 60.239 38.462 0.00 0.00 41.55 2.66
203 204 9.077885 TGCTTTGTAATTCTGAGGAACTTTTAT 57.922 29.630 0.00 0.00 41.55 1.40
252 253 3.400255 AGACTGACCTCGCCTTTTAAAC 58.600 45.455 0.00 0.00 0.00 2.01
280 281 5.240623 CCGAGCCTGATATAGCTAAGATAGG 59.759 48.000 0.00 5.37 40.11 2.57
282 283 6.320164 CGAGCCTGATATAGCTAAGATAGGTT 59.680 42.308 14.91 10.98 40.11 3.50
392 393 1.157513 TGGTACCTCAGCCACCAGA 59.842 57.895 14.36 0.00 37.42 3.86
426 427 2.026262 GGTTTGGCTCCTTGGTATCTCA 60.026 50.000 0.00 0.00 0.00 3.27
427 428 3.561313 GGTTTGGCTCCTTGGTATCTCAA 60.561 47.826 0.00 0.00 0.00 3.02
428 429 4.273318 GTTTGGCTCCTTGGTATCTCAAT 58.727 43.478 0.00 0.00 0.00 2.57
429 430 3.845781 TGGCTCCTTGGTATCTCAATC 57.154 47.619 0.00 0.00 0.00 2.67
430 431 3.387962 TGGCTCCTTGGTATCTCAATCT 58.612 45.455 0.00 0.00 0.00 2.40
431 432 3.389329 TGGCTCCTTGGTATCTCAATCTC 59.611 47.826 0.00 0.00 0.00 2.75
462 463 7.128573 AGGAGGAATATTCTTTCATTGAGAGGT 59.871 37.037 14.95 0.00 0.00 3.85
466 467 9.784531 GGAATATTCTTTCATTGAGAGGTGATA 57.215 33.333 14.95 2.67 0.00 2.15
487 488 7.493971 GTGATATTTTCATAGATAGCGAGGCAT 59.506 37.037 0.00 0.00 36.54 4.40
490 491 6.590234 TTTTCATAGATAGCGAGGCATCTA 57.410 37.500 0.00 10.14 35.22 1.98
492 493 7.881775 TTTCATAGATAGCGAGGCATCTATA 57.118 36.000 15.53 0.00 37.32 1.31
505 506 4.065088 GGCATCTATAATGGCTTCGTCAA 58.935 43.478 4.51 0.00 40.85 3.18
509 510 6.148480 GCATCTATAATGGCTTCGTCAATCTT 59.852 38.462 0.00 0.00 0.00 2.40
512 513 9.950496 ATCTATAATGGCTTCGTCAATCTTAAT 57.050 29.630 0.00 0.00 0.00 1.40
519 520 8.763049 TGGCTTCGTCAATCTTAATATCTATG 57.237 34.615 0.00 0.00 0.00 2.23
522 523 7.819900 GCTTCGTCAATCTTAATATCTATGGGT 59.180 37.037 0.00 0.00 0.00 4.51
546 547 5.742063 TCAGTCTCTCGAAGGTACTCATAA 58.258 41.667 0.00 0.00 38.49 1.90
554 555 7.723324 TCTCGAAGGTACTCATAAAAATAGGG 58.277 38.462 0.00 0.00 38.49 3.53
566 567 2.843401 AAATAGGGTGTGCGTGTGTA 57.157 45.000 0.00 0.00 0.00 2.90
587 588 2.557490 ACGTTCAGAGAAGGGAGTGTAC 59.443 50.000 4.73 0.00 0.00 2.90
588 589 2.820787 CGTTCAGAGAAGGGAGTGTACT 59.179 50.000 0.00 0.00 0.00 2.73
589 590 3.119779 CGTTCAGAGAAGGGAGTGTACTC 60.120 52.174 3.43 3.43 42.14 2.59
620 662 1.153628 GCGGCCGTCACAGAATAGT 60.154 57.895 28.70 0.00 0.00 2.12
649 691 9.915629 ACGCCACAAAGTAATAATAAAATTTGA 57.084 25.926 0.00 0.00 33.14 2.69
724 768 2.683211 ACAGCCCATCCAGAAAAAGT 57.317 45.000 0.00 0.00 0.00 2.66
740 784 9.726438 CCAGAAAAAGTAGGAAAGAAGAAGATA 57.274 33.333 0.00 0.00 0.00 1.98
777 822 5.221541 TGTGTTGTTCCACCTTTTCTGTTTT 60.222 36.000 0.00 0.00 34.35 2.43
795 841 3.296322 TTTGGCCTTTAATTGTCTGCG 57.704 42.857 3.32 0.00 0.00 5.18
864 910 0.400213 TGTTTCCTCCACTCGCCATT 59.600 50.000 0.00 0.00 0.00 3.16
1114 1161 2.049063 GCACGGCTCTGTTCGTCT 60.049 61.111 0.00 0.00 37.53 4.18
1140 1187 0.745486 TCGTATCGCTCTTCACCGGA 60.745 55.000 9.46 0.00 0.00 5.14
1233 1280 3.570550 ACTTTGGCCGTTTTACTGCATAA 59.429 39.130 0.00 0.00 29.40 1.90
1234 1281 4.038162 ACTTTGGCCGTTTTACTGCATAAA 59.962 37.500 0.00 0.00 29.40 1.40
1236 1283 4.792521 TGGCCGTTTTACTGCATAAAAT 57.207 36.364 13.50 0.00 43.12 1.82
1237 1284 5.899120 TGGCCGTTTTACTGCATAAAATA 57.101 34.783 13.50 0.00 43.12 1.40
1238 1285 5.885881 TGGCCGTTTTACTGCATAAAATAG 58.114 37.500 13.50 11.44 43.12 1.73
1362 1412 0.949105 GCCTGTCACACCGTAACCTG 60.949 60.000 0.00 0.00 0.00 4.00
1365 1419 2.352421 CCTGTCACACCGTAACCTGTAG 60.352 54.545 0.00 0.00 0.00 2.74
1367 1421 3.159472 TGTCACACCGTAACCTGTAGAT 58.841 45.455 0.00 0.00 0.00 1.98
1421 1492 4.319984 CCGTTTTCCTTGTAAACTAGCCAC 60.320 45.833 0.00 0.00 34.20 5.01
1439 1511 5.709966 AGCCACTCGAAAATTTAATTGTCC 58.290 37.500 2.59 0.00 0.00 4.02
1460 1534 5.287992 GTCCGGTTGAAAGATTACTAAGTCG 59.712 44.000 0.00 0.00 0.00 4.18
1676 1751 4.020839 TCAAGTCCGTCCCTTTAAACTAGG 60.021 45.833 0.00 0.00 0.00 3.02
1694 1769 2.851195 AGGTTGTGAAGAGCGACAAAT 58.149 42.857 0.00 0.00 33.96 2.32
1745 1820 2.956799 TTTCAGCTGCTGTGCCGGAA 62.957 55.000 27.24 11.81 32.61 4.30
1781 1856 4.442192 GGCTACTTGCTGATTGCTACTAGT 60.442 45.833 0.00 0.00 43.37 2.57
2357 2432 3.243002 GCTTCTATCCTTGTCAAGCATGC 60.243 47.826 10.51 10.51 39.45 4.06
2456 2533 9.229784 CATTGTATTTATCTGCTTTAGTGCAAG 57.770 33.333 0.00 0.00 42.83 4.01
2467 2544 1.144969 TAGTGCAAGCAGTTACGTGC 58.855 50.000 7.80 0.00 44.08 5.34
2497 2574 5.491982 ACCTGAACATCTGGTTGTCTAATC 58.508 41.667 3.38 0.00 44.87 1.75
2543 2620 5.141182 TGGTAGCCTCATTTGTTGGTTAAA 58.859 37.500 0.00 0.00 0.00 1.52
2647 2724 2.732412 ACGTGAGTCATCTGTTCTGG 57.268 50.000 0.00 0.00 44.19 3.86
2674 2751 8.097038 TGAAGTGAGGAATATATGAATACAGCC 58.903 37.037 0.00 0.00 0.00 4.85
2699 2776 6.094603 CACATTTTCCTATTAGCTCAGCTGTT 59.905 38.462 10.31 0.00 40.10 3.16
2716 2793 3.059393 GCTGTTGAAAATTTTGCAGGCTC 60.059 43.478 8.47 0.00 0.00 4.70
2928 3005 9.546428 CCCTAAATGGAATTTATGAACATTTCC 57.454 33.333 0.00 8.81 46.47 3.13
3012 3089 0.320073 TGCTTGCATTTTCTGGCTGC 60.320 50.000 0.00 0.00 36.45 5.25
3100 3177 5.871396 ACCTGTAAGACTCTGAAACTTGA 57.129 39.130 0.00 0.00 34.07 3.02
3221 3304 4.527509 TTTGTGTTTCTCTTTTGCACCA 57.472 36.364 0.00 0.00 0.00 4.17
3253 3336 6.780457 ATGTTGAGTATGATTTCCCCAAAG 57.220 37.500 0.00 0.00 0.00 2.77
3720 3803 4.770531 TGTTAGCTGGACGCAGGTATATAT 59.229 41.667 0.00 0.00 42.61 0.86
3824 3907 4.345859 AAAGTGAATTGAGGTACGGTCA 57.654 40.909 0.00 0.00 0.00 4.02
3936 4035 8.696043 TTTAATATGCTAATGGTCTTCATGCT 57.304 30.769 0.00 0.00 35.99 3.79
4132 4231 4.277672 CGAGATGATTTCCATGAAATGCCT 59.722 41.667 6.78 1.94 44.97 4.75
4278 4377 5.777732 TGCAAAGGGAAAGTACATATTTGGT 59.222 36.000 0.00 0.00 0.00 3.67
4599 4698 5.334491 CGGTGTGCTGTCAATTACAACATTA 60.334 40.000 0.00 0.00 36.61 1.90
4601 4700 6.086222 GTGTGCTGTCAATTACAACATTAGG 58.914 40.000 0.00 0.00 36.61 2.69
4607 4706 6.893759 TGTCAATTACAACATTAGGTCGTTG 58.106 36.000 0.00 0.00 46.31 4.10
4639 4738 6.096282 TGCTTACCTGTAGCTTGTTTCTTTTT 59.904 34.615 0.00 0.00 0.00 1.94
4670 4796 1.669115 CTGACGGGGTGTGCTCTTG 60.669 63.158 0.00 0.00 0.00 3.02
4671 4797 2.383245 CTGACGGGGTGTGCTCTTGT 62.383 60.000 0.00 0.00 0.00 3.16
4676 4802 2.303600 ACGGGGTGTGCTCTTGTAATTA 59.696 45.455 0.00 0.00 0.00 1.40
4791 4922 3.508845 ACAAGGCCTAACTGAACATGT 57.491 42.857 5.16 0.00 0.00 3.21
4830 4961 2.184448 CAACTTGGTGCGTTCAAAGTG 58.816 47.619 3.32 0.00 0.00 3.16
4854 4985 6.098409 TGGCCAATTTGTCTGTAACCTTTTAA 59.902 34.615 0.61 0.00 0.00 1.52
4860 4991 6.702716 TTGTCTGTAACCTTTTAACTTGGG 57.297 37.500 0.00 0.00 0.00 4.12
4876 5007 2.323999 TGGGCATGTCTTTTCCCATT 57.676 45.000 0.00 0.00 43.40 3.16
4877 5008 1.901159 TGGGCATGTCTTTTCCCATTG 59.099 47.619 0.00 0.00 43.40 2.82
4896 5027 7.939039 TCCCATTGGAATATTTAGCAACTCTAG 59.061 37.037 3.62 0.00 37.86 2.43
4930 5064 0.523968 GCACGTATGCCATGTTGCAG 60.524 55.000 3.06 0.00 46.97 4.41
5105 5244 7.551585 TCTACATGATTCTTCTTCAGAGAACC 58.448 38.462 0.00 0.00 36.99 3.62
5213 5352 7.349598 AGTCCAGATAAAAACATAGGAAGCAT 58.650 34.615 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.762957 GTACCCCTGATGAAGCTAGCA 59.237 52.381 18.83 0.00 0.00 3.49
8 9 1.090052 GCACGTACCCCTGATGAAGC 61.090 60.000 0.00 0.00 0.00 3.86
11 12 1.188871 TGTGCACGTACCCCTGATGA 61.189 55.000 13.13 0.00 0.00 2.92
21 22 4.579454 ACTAGAAGTCTTTGTGCACGTA 57.421 40.909 13.13 0.00 0.00 3.57
64 65 1.825090 TTAGTCTCGTACCGAAGCCA 58.175 50.000 0.00 0.00 34.74 4.75
75 76 6.357503 GCTATTGTCGTTACTCATTAGTCTCG 59.642 42.308 0.00 0.00 37.15 4.04
77 78 7.096884 TGCTATTGTCGTTACTCATTAGTCT 57.903 36.000 0.00 0.00 37.15 3.24
80 81 6.273825 ACCTGCTATTGTCGTTACTCATTAG 58.726 40.000 0.00 0.00 0.00 1.73
92 93 1.132643 AGTCGTCGACCTGCTATTGTC 59.867 52.381 21.40 0.00 32.18 3.18
108 109 1.130749 CACTACCTCCAGAACGAGTCG 59.869 57.143 11.85 11.85 0.00 4.18
109 110 1.473278 CCACTACCTCCAGAACGAGTC 59.527 57.143 0.00 0.00 0.00 3.36
110 111 1.203025 ACCACTACCTCCAGAACGAGT 60.203 52.381 0.00 0.00 0.00 4.18
111 112 1.473278 GACCACTACCTCCAGAACGAG 59.527 57.143 0.00 0.00 0.00 4.18
121 122 3.054139 TGGACTATGTACGACCACTACCT 60.054 47.826 0.00 0.00 0.00 3.08
169 170 6.349363 CCTCAGAATTACAAAGCACCTTAACC 60.349 42.308 0.00 0.00 0.00 2.85
171 172 6.539173 TCCTCAGAATTACAAAGCACCTTAA 58.461 36.000 0.00 0.00 0.00 1.85
172 173 6.121776 TCCTCAGAATTACAAAGCACCTTA 57.878 37.500 0.00 0.00 0.00 2.69
173 174 4.985538 TCCTCAGAATTACAAAGCACCTT 58.014 39.130 0.00 0.00 0.00 3.50
174 175 4.640771 TCCTCAGAATTACAAAGCACCT 57.359 40.909 0.00 0.00 0.00 4.00
236 237 3.124128 CGGTAAGTTTAAAAGGCGAGGTC 59.876 47.826 0.00 0.00 0.00 3.85
242 243 3.079578 AGGCTCGGTAAGTTTAAAAGGC 58.920 45.455 0.00 0.00 0.00 4.35
252 253 5.648526 TCTTAGCTATATCAGGCTCGGTAAG 59.351 44.000 0.00 0.00 39.65 2.34
280 281 4.490799 CCGAATAGCGTACGTACCAAAAAC 60.491 45.833 19.67 7.20 38.67 2.43
282 283 3.178267 CCGAATAGCGTACGTACCAAAA 58.822 45.455 19.67 3.86 38.67 2.44
338 339 5.058490 CCATCAAAGCACAGGTTGATTTTT 58.942 37.500 0.00 0.00 41.08 1.94
409 410 3.387962 AGATTGAGATACCAAGGAGCCA 58.612 45.455 0.00 0.00 0.00 4.75
462 463 6.935167 TGCCTCGCTATCTATGAAAATATCA 58.065 36.000 0.00 0.00 43.67 2.15
466 467 6.047511 AGATGCCTCGCTATCTATGAAAAT 57.952 37.500 0.00 0.00 32.13 1.82
474 475 4.202202 GCCATTATAGATGCCTCGCTATCT 60.202 45.833 0.00 0.00 37.42 1.98
490 491 9.950496 AGATATTAAGATTGACGAAGCCATTAT 57.050 29.630 0.00 0.00 0.00 1.28
492 493 9.950496 ATAGATATTAAGATTGACGAAGCCATT 57.050 29.630 0.00 0.00 0.00 3.16
505 506 9.836179 AGAGACTGAACCCATAGATATTAAGAT 57.164 33.333 0.00 0.00 0.00 2.40
509 510 7.459234 TCGAGAGACTGAACCCATAGATATTA 58.541 38.462 0.00 0.00 33.31 0.98
512 513 5.306114 TCGAGAGACTGAACCCATAGATA 57.694 43.478 0.00 0.00 33.31 1.98
514 515 3.646736 TCGAGAGACTGAACCCATAGA 57.353 47.619 0.00 0.00 33.31 1.98
515 516 3.067461 CCTTCGAGAGACTGAACCCATAG 59.933 52.174 0.00 0.00 41.84 2.23
517 518 1.827969 CCTTCGAGAGACTGAACCCAT 59.172 52.381 0.00 0.00 41.84 4.00
519 520 1.258676 ACCTTCGAGAGACTGAACCC 58.741 55.000 0.00 0.00 41.84 4.11
522 523 4.017177 TGAGTACCTTCGAGAGACTGAA 57.983 45.455 0.00 0.00 41.84 3.02
546 547 1.975660 ACACACGCACACCCTATTTT 58.024 45.000 0.00 0.00 0.00 1.82
566 567 1.705873 ACACTCCCTTCTCTGAACGT 58.294 50.000 0.00 0.00 0.00 3.99
587 588 2.030946 CGGCCGCTAATCTTTCTTTGAG 59.969 50.000 14.67 0.00 0.00 3.02
588 589 2.006888 CGGCCGCTAATCTTTCTTTGA 58.993 47.619 14.67 0.00 0.00 2.69
589 590 1.737793 ACGGCCGCTAATCTTTCTTTG 59.262 47.619 28.58 0.00 0.00 2.77
668 712 2.830704 CTTGTGGCCTACGGTCCGTC 62.831 65.000 22.74 7.07 41.54 4.79
687 731 2.231235 CTGTATGTTGGCCCAACTTTCC 59.769 50.000 26.03 14.35 43.85 3.13
724 768 5.030147 TGGGCTGTATCTTCTTCTTTCCTA 58.970 41.667 0.00 0.00 0.00 2.94
740 784 2.318908 ACAACACAATGAATGGGCTGT 58.681 42.857 0.00 0.00 36.93 4.40
777 822 1.539388 CACGCAGACAATTAAAGGCCA 59.461 47.619 5.01 0.00 0.00 5.36
890 936 2.727647 CGCGCTAGATCGTGGAGC 60.728 66.667 5.56 2.89 36.43 4.70
1114 1161 2.686405 TGAAGAGCGATACGAAGCCTAA 59.314 45.455 0.00 0.00 0.00 2.69
1186 1233 2.030027 TCAGTCACCTGATTGGACCT 57.970 50.000 0.00 0.00 42.80 3.85
1233 1280 8.786826 TTATCCACAATTCTGTCGAACTATTT 57.213 30.769 0.00 0.00 31.64 1.40
1234 1281 8.041323 ACTTATCCACAATTCTGTCGAACTATT 58.959 33.333 0.00 0.00 31.64 1.73
1236 1283 6.931838 ACTTATCCACAATTCTGTCGAACTA 58.068 36.000 0.00 0.00 31.64 2.24
1237 1284 5.794894 ACTTATCCACAATTCTGTCGAACT 58.205 37.500 0.00 0.00 31.64 3.01
1238 1285 6.481954 AACTTATCCACAATTCTGTCGAAC 57.518 37.500 0.00 0.00 31.64 3.95
1353 1403 6.040878 CCTTCAGTTTATCTACAGGTTACGG 58.959 44.000 0.00 0.00 0.00 4.02
1362 1412 6.153000 TCACTCAGTCCCTTCAGTTTATCTAC 59.847 42.308 0.00 0.00 0.00 2.59
1365 1419 5.407407 TCACTCAGTCCCTTCAGTTTATC 57.593 43.478 0.00 0.00 0.00 1.75
1367 1421 5.623956 TTTCACTCAGTCCCTTCAGTTTA 57.376 39.130 0.00 0.00 0.00 2.01
1421 1492 6.375377 TCAACCGGACAATTAAATTTTCGAG 58.625 36.000 9.46 0.00 0.00 4.04
1439 1511 4.863131 AGCGACTTAGTAATCTTTCAACCG 59.137 41.667 0.00 0.00 0.00 4.44
1460 1534 2.035066 ACACATGAACAGGCAAGAAAGC 59.965 45.455 0.00 0.00 0.00 3.51
1676 1751 5.968848 TGTAAAATTTGTCGCTCTTCACAAC 59.031 36.000 0.00 0.00 32.19 3.32
1694 1769 7.556275 ACACAGAGAAACCTCAAGATTGTAAAA 59.444 33.333 0.00 0.00 33.16 1.52
1745 1820 3.660865 CAAGTAGCCGGTAGAACTGTTT 58.339 45.455 1.90 0.00 0.00 2.83
1781 1856 0.106419 GTTGTTGGTTCAGTCCCCCA 60.106 55.000 0.00 0.00 0.00 4.96
2357 2432 9.559958 GAAATAACTTCTGTTTGTACATGATGG 57.440 33.333 0.00 0.00 37.59 3.51
2456 2533 2.925563 AGGTTATAACGCACGTAACTGC 59.074 45.455 9.46 0.00 0.00 4.40
2457 2534 4.168014 TCAGGTTATAACGCACGTAACTG 58.832 43.478 9.46 8.33 0.00 3.16
2467 2544 5.642063 ACAACCAGATGTTCAGGTTATAACG 59.358 40.000 9.46 0.00 43.24 3.18
2470 2547 6.620877 AGACAACCAGATGTTCAGGTTATA 57.379 37.500 4.29 0.00 43.24 0.98
2497 2574 2.095567 GCTGACCATGCAACAGTAAGTG 60.096 50.000 12.53 0.00 34.60 3.16
2543 2620 9.942526 ATAAAAGGGAAATCAGGATGTATTCTT 57.057 29.630 0.00 0.00 37.40 2.52
2610 2687 6.523546 ACTCACGTATCGCTATAATGATTTCG 59.476 38.462 0.00 0.00 0.00 3.46
2629 2706 2.029918 TCACCAGAACAGATGACTCACG 60.030 50.000 0.00 0.00 0.00 4.35
2647 2724 8.930760 GCTGTATTCATATATTCCTCACTTCAC 58.069 37.037 0.00 0.00 0.00 3.18
2674 2751 5.587844 ACAGCTGAGCTAATAGGAAAATGTG 59.412 40.000 23.35 0.00 36.40 3.21
2716 2793 7.340699 CGATAATCAAACTTAGTTAGCTGCAG 58.659 38.462 10.11 10.11 0.00 4.41
2928 3005 9.698617 GTTTAGTAAAATATGCGTACTTTCAGG 57.301 33.333 0.00 0.00 30.81 3.86
3012 3089 5.556915 TCTTTTTCACCACCACCATAGTAG 58.443 41.667 0.00 0.00 0.00 2.57
3100 3177 8.195165 TCGATAGGAAAACCTCATTATCTCAT 57.805 34.615 0.00 0.00 0.00 2.90
3128 3205 3.634397 TGGACCCATCTGTTGAGAATC 57.366 47.619 0.00 0.00 0.00 2.52
3253 3336 2.143122 TCATCTCAAACAGCGTGTTCC 58.857 47.619 4.28 0.00 40.14 3.62
3288 3371 9.504708 AAATCCAATCACTGCAAATATCAAAAA 57.495 25.926 0.00 0.00 0.00 1.94
3291 3374 7.549842 CCAAAATCCAATCACTGCAAATATCAA 59.450 33.333 0.00 0.00 0.00 2.57
3364 3447 5.844004 AGTCCTGCTAGTAATAACCAATCG 58.156 41.667 0.00 0.00 0.00 3.34
3803 3886 4.345859 TGACCGTACCTCAATTCACTTT 57.654 40.909 0.00 0.00 0.00 2.66
3936 4035 6.894339 TGTATCGCCTACAGATTTGATAGA 57.106 37.500 0.00 0.00 35.38 1.98
3997 4096 7.327975 TCCGTGTCTGAAATAATACATTGAGT 58.672 34.615 0.00 0.00 0.00 3.41
4132 4231 5.645067 CACTCTTTGGCAGATACAAGATGAA 59.355 40.000 0.00 0.00 0.00 2.57
4278 4377 8.603898 TGTAGTTCCATCATCCTCTTAACTTA 57.396 34.615 0.00 0.00 0.00 2.24
4323 4422 1.364626 GAGCTGACGTGCCAAGGATG 61.365 60.000 0.00 0.00 0.00 3.51
4428 4527 2.411547 CGTGGCAGTTTCTTCGATTCAC 60.412 50.000 0.00 0.00 0.00 3.18
4499 4598 7.012704 CCAGTTAGTACGTATAGCTCTTTACCA 59.987 40.741 0.00 0.00 0.00 3.25
4599 4698 3.181494 GGTAAGCAAAACAACAACGACCT 60.181 43.478 0.00 0.00 0.00 3.85
4601 4700 3.789224 CAGGTAAGCAAAACAACAACGAC 59.211 43.478 0.00 0.00 0.00 4.34
4607 4706 4.830826 AGCTACAGGTAAGCAAAACAAC 57.169 40.909 0.00 0.00 0.00 3.32
4610 4709 4.830826 ACAAGCTACAGGTAAGCAAAAC 57.169 40.909 0.00 0.00 0.00 2.43
4639 4738 0.321671 CCGTCAGAAGAAAGAGGGCA 59.678 55.000 0.00 0.00 33.61 5.36
4670 4796 3.128764 GGTTGCCCAAGCTCAGTAATTAC 59.871 47.826 7.57 7.57 40.80 1.89
4671 4797 3.352648 GGTTGCCCAAGCTCAGTAATTA 58.647 45.455 3.16 0.00 40.80 1.40
4676 4802 1.764571 TACGGTTGCCCAAGCTCAGT 61.765 55.000 8.36 2.54 40.80 3.41
4711 4837 1.002544 TCCACACACACACACACAAGA 59.997 47.619 0.00 0.00 0.00 3.02
4712 4838 1.447945 TCCACACACACACACACAAG 58.552 50.000 0.00 0.00 0.00 3.16
4713 4839 1.809547 CTTCCACACACACACACACAA 59.190 47.619 0.00 0.00 0.00 3.33
4746 4875 8.840321 GTTGCATTACCAGACAATAATCATACT 58.160 33.333 0.00 0.00 0.00 2.12
4752 4881 6.627953 GCCTTGTTGCATTACCAGACAATAAT 60.628 38.462 0.00 0.00 30.73 1.28
4791 4922 1.329256 GGAGGCGGCTCAAGTAGATA 58.671 55.000 36.07 0.00 0.00 1.98
4830 4961 4.600692 AAAGGTTACAGACAAATTGGCC 57.399 40.909 0.00 0.00 0.00 5.36
4854 4985 1.632589 GGGAAAAGACATGCCCAAGT 58.367 50.000 0.00 0.00 40.39 3.16
4876 5007 9.422681 AGAGTACTAGAGTTGCTAAATATTCCA 57.577 33.333 0.00 0.00 0.00 3.53
4877 5008 9.685828 CAGAGTACTAGAGTTGCTAAATATTCC 57.314 37.037 0.00 0.00 0.00 3.01
4883 5014 5.704515 ACGACAGAGTACTAGAGTTGCTAAA 59.295 40.000 0.00 0.00 0.00 1.85
4884 5015 5.243981 ACGACAGAGTACTAGAGTTGCTAA 58.756 41.667 0.00 0.00 0.00 3.09
4912 5043 0.099259 CCTGCAACATGGCATACGTG 59.901 55.000 0.00 0.00 43.97 4.49
4913 5044 1.031571 CCCTGCAACATGGCATACGT 61.032 55.000 0.00 0.00 43.97 3.57
4930 5064 2.396590 TCTAACAAAGCCGACATCCC 57.603 50.000 0.00 0.00 0.00 3.85
5019 5155 9.627123 CCTAATGAATGAAGAATTGGGTACTTA 57.373 33.333 0.00 0.00 29.82 2.24
5064 5200 8.798859 ATCATGTAGAAAGCAACAGAAACTAT 57.201 30.769 0.00 0.00 0.00 2.12
5065 5201 8.621532 AATCATGTAGAAAGCAACAGAAACTA 57.378 30.769 0.00 0.00 0.00 2.24
5105 5244 8.993404 ACTTAGTACTTATAGGGGTCACTTAG 57.007 38.462 0.00 0.00 0.00 2.18
5183 5322 9.444600 TTCCTATGTTTTTATCTGGACTAACAC 57.555 33.333 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.