Multiple sequence alignment - TraesCS4B01G255900

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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 TraesCS4B01G255900 chr4B 100.000 4701 0 0 1 4701 520886299 520890999 0.000000e+00 8682.0
1 TraesCS4B01G255900 chr4A 93.509 3559 145 38 983 4471 39545353 39541811 0.000000e+00 5214.0
2 TraesCS4B01G255900 chr4A 85.079 382 47 8 1 380 39547352 39546979 9.550000e-102 381.0
3 TraesCS4B01G255900 chr4A 83.024 377 45 8 432 808 39546963 39546606 1.630000e-84 324.0
4 TraesCS4B01G255900 chr4A 87.500 248 11 1 4474 4701 39541767 39541520 7.750000e-68 268.0
5 TraesCS4B01G255900 chr4D 94.144 2698 96 23 1820 4471 425225151 425227832 0.000000e+00 4050.0
6 TraesCS4B01G255900 chr4D 94.545 880 40 3 878 1751 425224271 425225148 0.000000e+00 1352.0
7 TraesCS4B01G255900 chr4D 88.699 876 72 10 1 867 425223362 425224219 0.000000e+00 1044.0
8 TraesCS4B01G255900 chr4D 90.097 414 29 5 1030 1443 425212331 425212732 1.160000e-145 527.0
9 TraesCS4B01G255900 chr4D 88.843 242 8 5 4474 4701 425227876 425228112 3.580000e-71 279.0
10 TraesCS4B01G255900 chr1D 81.818 198 33 3 7 203 437990497 437990302 3.760000e-36 163.0
11 TraesCS4B01G255900 chr7B 74.877 203 47 4 1 202 581247783 581247982 6.480000e-14 89.8
12 TraesCS4B01G255900 chr6A 86.585 82 8 3 86 166 10004926 10004847 2.330000e-13 87.9
13 TraesCS4B01G255900 chr6D 87.879 66 8 0 89 154 256971064 256970999 1.400000e-10 78.7
14 TraesCS4B01G255900 chr6D 93.333 45 3 0 9 53 545831 545787 3.040000e-07 67.6
15 TraesCS4B01G255900 chr1B 76.027 146 31 3 9 152 635983811 635983668 6.530000e-09 73.1
16 TraesCS4B01G255900 chr5A 100.000 29 0 0 9 37 632196234 632196262 2.000000e-03 54.7
17 TraesCS4B01G255900 chr2D 100.000 29 0 0 13 41 640585269 640585241 2.000000e-03 54.7


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 TraesCS4B01G255900 chr4B 520886299 520890999 4700 False 8682.00 8682 100.00000 1 4701 1 chr4B.!!$F1 4700
1 TraesCS4B01G255900 chr4A 39541520 39547352 5832 True 1546.75 5214 87.27800 1 4701 4 chr4A.!!$R1 4700
2 TraesCS4B01G255900 chr4D 425223362 425228112 4750 False 1681.25 4050 91.55775 1 4701 4 chr4D.!!$F2 4700

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
818 850 0.034767 ACTAGTGATCGGTCGGGTGA 60.035 55.0 0.00 0.0 0.00 4.02 F
1200 2396 0.901124 TCAAGGCAAGCTCTCTCTCC 59.099 55.0 0.00 0.0 0.00 3.71 F
1561 2757 1.272807 ATCCATTTGCTGCCAGCTTT 58.727 45.0 18.96 0.0 42.97 3.51 F
3385 4632 0.179161 AGAAGGCTCGAACGACATCG 60.179 55.0 0.00 0.0 44.04 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 3618 1.404583 GGCATCACAAGCATCAAACCC 60.405 52.381 0.00 0.0 0.00 4.11 R
2418 3632 2.616960 CTGTAGCGTACAAAGGCATCA 58.383 47.619 0.00 0.0 38.38 3.07 R
3424 4671 0.533308 AACTTGTTACTGGCGCGGAA 60.533 50.000 8.83 0.0 0.00 4.30 R
4471 5747 0.029300 CGAACCAAGCACCAACACAG 59.971 55.000 0.00 0.0 0.00 3.66 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
32 33 7.346175 TGTTGGATAAGGCCTAAACATAGACTA 59.654 37.037 5.16 0.00 0.00 2.59
87 88 3.253230 GGCCATTATTTCACACACTTGC 58.747 45.455 0.00 0.00 0.00 4.01
92 93 5.984926 CCATTATTTCACACACTTGCAGTTT 59.015 36.000 0.00 0.00 0.00 2.66
162 163 6.311200 GCTTGAATATAGCAAACAAACCCAAG 59.689 38.462 0.00 0.00 38.51 3.61
166 167 7.870445 TGAATATAGCAAACAAACCCAAGAAAC 59.130 33.333 0.00 0.00 0.00 2.78
176 178 4.400529 AACCCAAGAAACGCAAGAAAAT 57.599 36.364 0.00 0.00 43.62 1.82
220 222 7.611467 TGGTGTATGATCAAGTTGAAAGCTATT 59.389 33.333 10.14 0.00 0.00 1.73
251 253 3.510459 AGCTAAAACTTGAAAGCCCCAT 58.490 40.909 0.00 0.00 35.54 4.00
313 315 4.702831 TGGGAATTTGAAAGTGAAAAGGC 58.297 39.130 0.00 0.00 0.00 4.35
318 320 5.966636 ATTTGAAAGTGAAAAGGCGAAAC 57.033 34.783 0.00 0.00 0.00 2.78
385 387 4.020218 CCAACAGAGAAGATGGTCCACTTA 60.020 45.833 0.00 0.00 0.00 2.24
388 420 6.187727 ACAGAGAAGATGGTCCACTTAAAA 57.812 37.500 0.00 0.00 0.00 1.52
392 424 7.609532 CAGAGAAGATGGTCCACTTAAAAGAAT 59.390 37.037 0.00 0.00 0.00 2.40
393 425 8.826765 AGAGAAGATGGTCCACTTAAAAGAATA 58.173 33.333 0.00 0.00 0.00 1.75
394 426 8.794335 AGAAGATGGTCCACTTAAAAGAATAC 57.206 34.615 0.00 0.00 0.00 1.89
395 427 8.383175 AGAAGATGGTCCACTTAAAAGAATACA 58.617 33.333 0.00 0.00 0.00 2.29
396 428 8.567285 AAGATGGTCCACTTAAAAGAATACAG 57.433 34.615 0.00 0.00 0.00 2.74
397 429 7.918076 AGATGGTCCACTTAAAAGAATACAGA 58.082 34.615 0.00 0.00 0.00 3.41
398 430 8.043710 AGATGGTCCACTTAAAAGAATACAGAG 58.956 37.037 0.00 0.00 0.00 3.35
399 431 7.311092 TGGTCCACTTAAAAGAATACAGAGA 57.689 36.000 0.00 0.00 0.00 3.10
400 432 7.741785 TGGTCCACTTAAAAGAATACAGAGAA 58.258 34.615 0.00 0.00 0.00 2.87
401 433 7.878127 TGGTCCACTTAAAAGAATACAGAGAAG 59.122 37.037 0.00 0.00 0.00 2.85
402 434 8.095169 GGTCCACTTAAAAGAATACAGAGAAGA 58.905 37.037 0.00 0.00 0.00 2.87
403 435 9.660180 GTCCACTTAAAAGAATACAGAGAAGAT 57.340 33.333 0.00 0.00 0.00 2.40
404 436 9.658799 TCCACTTAAAAGAATACAGAGAAGATG 57.341 33.333 0.00 0.00 0.00 2.90
405 437 8.887717 CCACTTAAAAGAATACAGAGAAGATGG 58.112 37.037 0.00 0.00 0.00 3.51
406 438 9.442047 CACTTAAAAGAATACAGAGAAGATGGT 57.558 33.333 0.00 0.00 0.00 3.55
407 439 9.660180 ACTTAAAAGAATACAGAGAAGATGGTC 57.340 33.333 0.00 0.00 0.00 4.02
408 440 8.703604 TTAAAAGAATACAGAGAAGATGGTCG 57.296 34.615 0.00 0.00 0.00 4.79
409 441 4.314740 AGAATACAGAGAAGATGGTCGC 57.685 45.455 0.00 0.00 0.00 5.19
410 442 2.783828 ATACAGAGAAGATGGTCGCG 57.216 50.000 0.00 0.00 0.00 5.87
411 443 0.100682 TACAGAGAAGATGGTCGCGC 59.899 55.000 0.00 0.00 0.00 6.86
412 444 1.880340 CAGAGAAGATGGTCGCGCC 60.880 63.158 0.00 6.97 37.90 6.53
420 452 2.668212 TGGTCGCGCCAAAGGAAG 60.668 61.111 17.94 0.00 45.94 3.46
421 453 3.431725 GGTCGCGCCAAAGGAAGG 61.432 66.667 13.61 0.00 37.17 3.46
422 454 3.431725 GTCGCGCCAAAGGAAGGG 61.432 66.667 0.00 0.00 0.00 3.95
423 455 3.632080 TCGCGCCAAAGGAAGGGA 61.632 61.111 0.00 0.00 0.00 4.20
424 456 3.127533 CGCGCCAAAGGAAGGGAG 61.128 66.667 0.00 0.00 0.00 4.30
425 457 2.351276 GCGCCAAAGGAAGGGAGA 59.649 61.111 0.00 0.00 0.00 3.71
426 458 1.303317 GCGCCAAAGGAAGGGAGAA 60.303 57.895 0.00 0.00 0.00 2.87
427 459 1.587043 GCGCCAAAGGAAGGGAGAAC 61.587 60.000 0.00 0.00 0.00 3.01
428 460 0.036875 CGCCAAAGGAAGGGAGAACT 59.963 55.000 0.00 0.00 0.00 3.01
429 461 1.539157 GCCAAAGGAAGGGAGAACTG 58.461 55.000 0.00 0.00 0.00 3.16
430 462 1.202940 GCCAAAGGAAGGGAGAACTGT 60.203 52.381 0.00 0.00 0.00 3.55
440 472 2.158143 AGGGAGAACTGTAGAAGGTGGT 60.158 50.000 0.00 0.00 0.00 4.16
509 541 0.459585 CGACGTGGGGGTATGAACAG 60.460 60.000 0.00 0.00 0.00 3.16
572 604 2.915604 AGGAAGACACATGGAGGAACAT 59.084 45.455 0.00 0.00 0.00 2.71
574 606 4.723789 AGGAAGACACATGGAGGAACATAT 59.276 41.667 0.00 0.00 0.00 1.78
575 607 5.192522 AGGAAGACACATGGAGGAACATATT 59.807 40.000 0.00 0.00 0.00 1.28
620 652 9.366216 CCTAAATGTTTAAGGGCTAAAATGAAC 57.634 33.333 0.00 0.00 31.22 3.18
632 664 6.462347 GGGCTAAAATGAACAAGAGAAAACCA 60.462 38.462 0.00 0.00 0.00 3.67
639 671 4.573201 TGAACAAGAGAAAACCAGTAACCG 59.427 41.667 0.00 0.00 0.00 4.44
653 685 5.591067 ACCAGTAACCGAGAAAATGAAAACA 59.409 36.000 0.00 0.00 0.00 2.83
654 686 5.912955 CCAGTAACCGAGAAAATGAAAACAC 59.087 40.000 0.00 0.00 0.00 3.32
658 690 6.885735 AACCGAGAAAATGAAAACACAAAG 57.114 33.333 0.00 0.00 0.00 2.77
661 693 6.183360 ACCGAGAAAATGAAAACACAAAGCTA 60.183 34.615 0.00 0.00 0.00 3.32
675 707 0.949105 AAGCTAGGAAACACGCACGG 60.949 55.000 0.00 0.00 0.00 4.94
808 840 9.906660 CCACAAGATATCTCTTAACTAGTGATC 57.093 37.037 5.51 0.00 39.78 2.92
809 841 9.605955 CACAAGATATCTCTTAACTAGTGATCG 57.394 37.037 5.51 0.00 39.78 3.69
810 842 8.788806 ACAAGATATCTCTTAACTAGTGATCGG 58.211 37.037 5.51 0.00 39.78 4.18
811 843 8.788806 CAAGATATCTCTTAACTAGTGATCGGT 58.211 37.037 5.51 0.00 39.78 4.69
814 846 3.875727 TCTCTTAACTAGTGATCGGTCGG 59.124 47.826 0.00 0.00 0.00 4.79
817 849 0.815734 AACTAGTGATCGGTCGGGTG 59.184 55.000 0.00 0.00 0.00 4.61
818 850 0.034767 ACTAGTGATCGGTCGGGTGA 60.035 55.000 0.00 0.00 0.00 4.02
867 939 3.264706 TGGAATTGACGATAACCTTCCCA 59.735 43.478 0.00 0.00 32.90 4.37
870 942 2.754946 TGACGATAACCTTCCCACAC 57.245 50.000 0.00 0.00 0.00 3.82
871 943 1.972075 TGACGATAACCTTCCCACACA 59.028 47.619 0.00 0.00 0.00 3.72
872 944 2.369203 TGACGATAACCTTCCCACACAA 59.631 45.455 0.00 0.00 0.00 3.33
873 945 3.181453 TGACGATAACCTTCCCACACAAA 60.181 43.478 0.00 0.00 0.00 2.83
874 946 3.816523 GACGATAACCTTCCCACACAAAA 59.183 43.478 0.00 0.00 0.00 2.44
1200 2396 0.901124 TCAAGGCAAGCTCTCTCTCC 59.099 55.000 0.00 0.00 0.00 3.71
1344 2540 4.758251 CTCCACACCATCGCCGCA 62.758 66.667 0.00 0.00 0.00 5.69
1364 2560 1.692519 ACAGGTGCTCCGTCTTTACTT 59.307 47.619 0.00 0.00 39.05 2.24
1365 2561 2.104281 ACAGGTGCTCCGTCTTTACTTT 59.896 45.455 0.00 0.00 39.05 2.66
1523 2719 2.224670 TGGATAGGGCAACGAGTTGTTT 60.225 45.455 16.14 6.16 42.31 2.83
1561 2757 1.272807 ATCCATTTGCTGCCAGCTTT 58.727 45.000 18.96 0.00 42.97 3.51
1679 2875 9.131791 ACTCAACTACATTTCTTTACATTTGGT 57.868 29.630 0.00 0.00 0.00 3.67
1685 2881 6.512297 ACATTTCTTTACATTTGGTGGTGAC 58.488 36.000 0.00 0.00 0.00 3.67
1697 2893 1.636988 GTGGTGACGCATAGGTGTAC 58.363 55.000 0.00 0.00 41.67 2.90
1699 2895 1.897133 TGGTGACGCATAGGTGTACTT 59.103 47.619 0.00 0.00 38.01 2.24
1700 2896 2.268298 GGTGACGCATAGGTGTACTTG 58.732 52.381 0.00 0.00 38.01 3.16
1701 2897 2.353406 GGTGACGCATAGGTGTACTTGT 60.353 50.000 0.00 0.00 38.01 3.16
1702 2898 3.119388 GGTGACGCATAGGTGTACTTGTA 60.119 47.826 0.00 0.00 38.01 2.41
1703 2899 4.441079 GGTGACGCATAGGTGTACTTGTAT 60.441 45.833 0.00 0.00 38.01 2.29
1705 2901 4.158949 TGACGCATAGGTGTACTTGTATGT 59.841 41.667 0.00 0.00 38.01 2.29
1724 2920 9.783081 TTGTATGTCATAATCTGCATATCTTGT 57.217 29.630 0.00 0.00 31.28 3.16
1784 2980 6.697892 GCAGGCACTAGTTATTTACTGTCTAG 59.302 42.308 0.00 0.00 37.73 2.43
1864 3066 2.710377 TCCGCACATGCTTTGATAAGT 58.290 42.857 1.82 0.00 39.32 2.24
1962 3164 4.433186 TGATAAAATTCAGGCACAACGG 57.567 40.909 0.00 0.00 0.00 4.44
2215 3429 2.305927 TCCTGAAGATTTCCCTGTCACC 59.694 50.000 0.00 0.00 0.00 4.02
2388 3602 2.880890 CTCCGGCCTCTTGGATAAATTG 59.119 50.000 0.00 0.00 32.83 2.32
2418 3632 4.020307 CCATTTAAGGGGTTTGATGCTTGT 60.020 41.667 0.00 0.00 0.00 3.16
2556 3775 5.630661 ACCTATGCGTATAGTGTCAGATC 57.369 43.478 17.72 0.00 35.51 2.75
2565 3784 6.292381 GCGTATAGTGTCAGATCACCAAATTC 60.292 42.308 0.00 0.00 38.91 2.17
3167 4414 3.312146 TCGTTTTGGTTCCCTTTTACGAC 59.688 43.478 0.00 0.00 32.58 4.34
3252 4499 1.271597 GGGACCATTCTTGTGAGCTGT 60.272 52.381 0.00 0.00 0.00 4.40
3268 4515 1.661112 GCTGTTCACCTGAGCGTATTC 59.339 52.381 0.00 0.00 0.00 1.75
3276 4523 2.271800 CCTGAGCGTATTCTGGTTGTC 58.728 52.381 0.00 0.00 33.05 3.18
3385 4632 0.179161 AGAAGGCTCGAACGACATCG 60.179 55.000 0.00 0.00 44.04 3.84
3424 4671 6.496911 ACACTGCCCAGAAACCTTATAAAATT 59.503 34.615 1.69 0.00 0.00 1.82
3441 4688 0.802494 ATTTCCGCGCCAGTAACAAG 59.198 50.000 0.00 0.00 0.00 3.16
3445 4692 1.149987 CCGCGCCAGTAACAAGTTTA 58.850 50.000 0.00 0.00 0.00 2.01
3544 4791 2.929724 CCTCCTCCATCCTCTATCCCTA 59.070 54.545 0.00 0.00 0.00 3.53
3631 4878 2.459060 TTCGCCATCTTTACGGTGAA 57.541 45.000 0.44 0.44 46.75 3.18
3632 4879 2.684001 TCGCCATCTTTACGGTGAAT 57.316 45.000 0.00 0.00 38.83 2.57
3633 4880 2.546778 TCGCCATCTTTACGGTGAATC 58.453 47.619 0.00 0.00 38.83 2.52
3636 4883 3.312421 CGCCATCTTTACGGTGAATCAAT 59.688 43.478 0.00 0.00 34.58 2.57
3637 4884 4.601019 GCCATCTTTACGGTGAATCAATG 58.399 43.478 0.00 0.00 0.00 2.82
3638 4885 4.335315 GCCATCTTTACGGTGAATCAATGA 59.665 41.667 0.00 0.00 0.00 2.57
3639 4886 5.009010 GCCATCTTTACGGTGAATCAATGAT 59.991 40.000 0.00 0.00 0.00 2.45
3640 4887 6.432936 CCATCTTTACGGTGAATCAATGATG 58.567 40.000 0.00 8.42 34.66 3.07
3641 4888 6.260714 CCATCTTTACGGTGAATCAATGATGA 59.739 38.462 13.67 0.00 40.57 2.92
3643 4890 8.992073 CATCTTTACGGTGAATCAATGATGATA 58.008 33.333 0.00 0.00 45.60 2.15
3644 4891 9.730705 ATCTTTACGGTGAATCAATGATGATAT 57.269 29.630 0.00 0.00 45.60 1.63
3699 4948 8.475331 AAGTTGTATCAGTTACACCGATTTAG 57.525 34.615 0.00 0.00 40.53 1.85
3707 4956 4.463186 AGTTACACCGATTTAGTGCTCTCT 59.537 41.667 0.00 0.00 38.87 3.10
3708 4957 3.963428 ACACCGATTTAGTGCTCTCTT 57.037 42.857 0.00 0.00 38.87 2.85
3810 5063 0.693622 TGGAAATGGGGCACGTTCTA 59.306 50.000 0.00 0.00 0.00 2.10
3862 5115 2.200170 AAAGAGGCGGCAAATGCGTC 62.200 55.000 13.08 0.00 45.08 5.19
3867 5120 3.088914 CGGCAAATGCGTCGATCA 58.911 55.556 0.00 0.00 43.26 2.92
3874 5127 1.560923 AATGCGTCGATCACTACTGC 58.439 50.000 0.00 0.00 0.00 4.40
3942 5197 1.074775 AATGACAAAGCAGGCCCGA 59.925 52.632 0.00 0.00 0.00 5.14
3980 5236 2.034221 ACCTTCCTCGCTTTGCCC 59.966 61.111 0.00 0.00 0.00 5.36
4230 5495 1.008206 AGCTTCTCAGTCTCAGGGGAT 59.992 52.381 0.00 0.00 0.00 3.85
4231 5496 2.246067 AGCTTCTCAGTCTCAGGGGATA 59.754 50.000 0.00 0.00 0.00 2.59
4232 5497 2.364002 GCTTCTCAGTCTCAGGGGATAC 59.636 54.545 0.00 0.00 0.00 2.24
4297 5562 3.403057 GCTTTGCTCGTCGTCGCA 61.403 61.111 7.65 7.65 36.96 5.10
4373 5638 0.966370 GTCCTCAGCCTCAGGTACGT 60.966 60.000 0.00 0.00 32.20 3.57
4393 5658 0.598065 ACGCAATGAAAACTGCCTCC 59.402 50.000 0.00 0.00 35.01 4.30
4415 5680 3.137533 GTTTGCTGTTCTCTCTCTTGCT 58.862 45.455 0.00 0.00 0.00 3.91
4419 5684 2.417243 GCTGTTCTCTCTCTTGCTCTCC 60.417 54.545 0.00 0.00 0.00 3.71
4425 5690 2.424601 CTCTCTCTTGCTCTCCTGTCAG 59.575 54.545 0.00 0.00 0.00 3.51
4464 5740 2.484770 CCTGTTCCGTTTCTTCTGTCCA 60.485 50.000 0.00 0.00 0.00 4.02
4467 5743 2.526304 TCCGTTTCTTCTGTCCAGTG 57.474 50.000 0.00 0.00 0.00 3.66
4469 5745 2.169769 TCCGTTTCTTCTGTCCAGTGTT 59.830 45.455 0.00 0.00 0.00 3.32
4471 5747 2.286418 CGTTTCTTCTGTCCAGTGTTGC 60.286 50.000 0.00 0.00 0.00 4.17
4497 5813 1.879380 TGGTGCTTGGTTCGATCTTTG 59.121 47.619 0.00 0.00 0.00 2.77
4594 5930 2.800544 TCTTTCGCTCTCTTTTTGACGG 59.199 45.455 0.00 0.00 0.00 4.79
4690 6026 6.047511 AGTTATCTGCATAGCTCCAATAGG 57.952 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 9.686683 GTGAAATAATGGCCAGATATAGGTTAT 57.313 33.333 13.05 4.80 0.00 1.89
62 63 4.603131 AGTGTGTGAAATAATGGCCAGAT 58.397 39.130 13.05 4.01 0.00 2.90
132 133 7.334171 GGTTTGTTTGCTATATTCAAGCCATTT 59.666 33.333 0.00 0.00 38.56 2.32
162 163 3.789224 ACGTGTCAATTTTCTTGCGTTTC 59.211 39.130 0.00 0.00 0.00 2.78
166 167 2.713976 GTCACGTGTCAATTTTCTTGCG 59.286 45.455 16.51 0.00 0.00 4.85
171 173 6.305399 CCATTACATGTCACGTGTCAATTTTC 59.695 38.462 18.96 0.87 0.00 2.29
176 178 3.496507 CACCATTACATGTCACGTGTCAA 59.503 43.478 18.96 3.57 0.00 3.18
234 236 2.688477 TGGATGGGGCTTTCAAGTTTT 58.312 42.857 0.00 0.00 0.00 2.43
251 253 7.474474 AAGGAGTTTTATGGGGTAATATGGA 57.526 36.000 0.00 0.00 0.00 3.41
313 315 2.434359 GTCGCCTCCCCAGTTTCG 60.434 66.667 0.00 0.00 0.00 3.46
318 320 0.323629 TTAGTTTGTCGCCTCCCCAG 59.676 55.000 0.00 0.00 0.00 4.45
385 387 5.582665 GCGACCATCTTCTCTGTATTCTTTT 59.417 40.000 0.00 0.00 0.00 2.27
388 420 3.243234 CGCGACCATCTTCTCTGTATTCT 60.243 47.826 0.00 0.00 0.00 2.40
392 424 0.100682 GCGCGACCATCTTCTCTGTA 59.899 55.000 12.10 0.00 0.00 2.74
393 425 1.153745 GCGCGACCATCTTCTCTGT 60.154 57.895 12.10 0.00 0.00 3.41
394 426 1.880340 GGCGCGACCATCTTCTCTG 60.880 63.158 12.10 0.00 38.86 3.35
395 427 2.351244 TGGCGCGACCATCTTCTCT 61.351 57.895 10.82 0.00 46.36 3.10
396 428 2.184322 TGGCGCGACCATCTTCTC 59.816 61.111 10.82 0.00 46.36 2.87
404 436 3.431725 CCTTCCTTTGGCGCGACC 61.432 66.667 10.82 11.50 39.84 4.79
405 437 3.431725 CCCTTCCTTTGGCGCGAC 61.432 66.667 12.10 8.22 0.00 5.19
406 438 3.605749 CTCCCTTCCTTTGGCGCGA 62.606 63.158 12.10 0.00 0.00 5.87
407 439 3.127533 CTCCCTTCCTTTGGCGCG 61.128 66.667 0.00 0.00 0.00 6.86
408 440 1.303317 TTCTCCCTTCCTTTGGCGC 60.303 57.895 0.00 0.00 0.00 6.53
409 441 0.036875 AGTTCTCCCTTCCTTTGGCG 59.963 55.000 0.00 0.00 0.00 5.69
410 442 1.202940 ACAGTTCTCCCTTCCTTTGGC 60.203 52.381 0.00 0.00 0.00 4.52
411 443 2.959465 ACAGTTCTCCCTTCCTTTGG 57.041 50.000 0.00 0.00 0.00 3.28
412 444 4.891992 TCTACAGTTCTCCCTTCCTTTG 57.108 45.455 0.00 0.00 0.00 2.77
413 445 4.287326 CCTTCTACAGTTCTCCCTTCCTTT 59.713 45.833 0.00 0.00 0.00 3.11
414 446 3.841255 CCTTCTACAGTTCTCCCTTCCTT 59.159 47.826 0.00 0.00 0.00 3.36
415 447 3.181405 ACCTTCTACAGTTCTCCCTTCCT 60.181 47.826 0.00 0.00 0.00 3.36
416 448 3.055747 CACCTTCTACAGTTCTCCCTTCC 60.056 52.174 0.00 0.00 0.00 3.46
417 449 3.055747 CCACCTTCTACAGTTCTCCCTTC 60.056 52.174 0.00 0.00 0.00 3.46
418 450 2.907042 CCACCTTCTACAGTTCTCCCTT 59.093 50.000 0.00 0.00 0.00 3.95
419 451 2.158143 ACCACCTTCTACAGTTCTCCCT 60.158 50.000 0.00 0.00 0.00 4.20
420 452 2.028020 CACCACCTTCTACAGTTCTCCC 60.028 54.545 0.00 0.00 0.00 4.30
421 453 2.028020 CCACCACCTTCTACAGTTCTCC 60.028 54.545 0.00 0.00 0.00 3.71
422 454 2.633481 ACCACCACCTTCTACAGTTCTC 59.367 50.000 0.00 0.00 0.00 2.87
423 455 2.633481 GACCACCACCTTCTACAGTTCT 59.367 50.000 0.00 0.00 0.00 3.01
424 456 2.609737 CGACCACCACCTTCTACAGTTC 60.610 54.545 0.00 0.00 0.00 3.01
425 457 1.343465 CGACCACCACCTTCTACAGTT 59.657 52.381 0.00 0.00 0.00 3.16
426 458 0.966920 CGACCACCACCTTCTACAGT 59.033 55.000 0.00 0.00 0.00 3.55
427 459 0.389948 GCGACCACCACCTTCTACAG 60.390 60.000 0.00 0.00 0.00 2.74
428 460 1.669440 GCGACCACCACCTTCTACA 59.331 57.895 0.00 0.00 0.00 2.74
429 461 1.079336 GGCGACCACCACCTTCTAC 60.079 63.158 0.00 0.00 0.00 2.59
430 462 2.642254 CGGCGACCACCACCTTCTA 61.642 63.158 0.00 0.00 0.00 2.10
466 498 4.452455 CCGTTGCATCCTCCTATTATTGTC 59.548 45.833 0.00 0.00 0.00 3.18
509 541 2.429069 CTTGTTTTCCGCCAGCGC 60.429 61.111 6.50 0.00 38.24 5.92
609 641 7.203218 ACTGGTTTTCTCTTGTTCATTTTAGC 58.797 34.615 0.00 0.00 0.00 3.09
620 652 4.628074 TCTCGGTTACTGGTTTTCTCTTG 58.372 43.478 0.00 0.00 0.00 3.02
632 664 6.687081 TGTGTTTTCATTTTCTCGGTTACT 57.313 33.333 0.00 0.00 0.00 2.24
639 671 7.425606 TCCTAGCTTTGTGTTTTCATTTTCTC 58.574 34.615 0.00 0.00 0.00 2.87
653 685 1.602377 GTGCGTGTTTCCTAGCTTTGT 59.398 47.619 0.00 0.00 0.00 2.83
654 686 1.398451 CGTGCGTGTTTCCTAGCTTTG 60.398 52.381 0.00 0.00 0.00 2.77
658 690 1.226030 AACCGTGCGTGTTTCCTAGC 61.226 55.000 0.00 0.00 0.00 3.42
661 693 2.830285 GCAACCGTGCGTGTTTCCT 61.830 57.895 0.00 0.00 41.93 3.36
675 707 1.071699 TGTGGTGTAAGGAGAGGCAAC 59.928 52.381 0.00 0.00 0.00 4.17
729 761 3.165498 GTCGCGTTGTCATGGGAC 58.835 61.111 5.77 6.93 42.71 4.46
794 826 2.947652 CCCGACCGATCACTAGTTAAGA 59.052 50.000 0.00 0.00 0.00 2.10
826 898 0.250338 AGGCTTCCGGTGTTGAGTTC 60.250 55.000 0.00 0.00 0.00 3.01
873 945 5.336451 GCCTGGTTATCGTCAATTCCTTTTT 60.336 40.000 0.00 0.00 0.00 1.94
874 946 4.157840 GCCTGGTTATCGTCAATTCCTTTT 59.842 41.667 0.00 0.00 0.00 2.27
876 948 3.279434 GCCTGGTTATCGTCAATTCCTT 58.721 45.455 0.00 0.00 0.00 3.36
1032 2222 2.338984 GCGACGGTCTGGAACACT 59.661 61.111 6.57 0.00 0.00 3.55
1200 2396 1.448013 GAAACGGAGAGGAAGCGGG 60.448 63.158 0.00 0.00 0.00 6.13
1235 2431 2.742348 TCAGCCGAACACCTTAGGATA 58.258 47.619 4.77 0.00 0.00 2.59
1236 2432 1.568504 TCAGCCGAACACCTTAGGAT 58.431 50.000 4.77 0.00 0.00 3.24
1344 2540 1.339097 AGTAAAGACGGAGCACCTGT 58.661 50.000 0.00 0.00 0.00 4.00
1364 2560 2.316108 TGGTGTGCTACTGACAGAGAA 58.684 47.619 10.08 0.00 0.00 2.87
1365 2561 1.995376 TGGTGTGCTACTGACAGAGA 58.005 50.000 10.08 0.00 0.00 3.10
1495 2691 4.141482 ACTCGTTGCCCTATCCACAATTAT 60.141 41.667 0.00 0.00 0.00 1.28
1498 2694 1.559682 ACTCGTTGCCCTATCCACAAT 59.440 47.619 0.00 0.00 0.00 2.71
1508 2704 1.864029 GCTTCAAACAACTCGTTGCCC 60.864 52.381 9.55 0.00 44.03 5.36
1561 2757 5.876612 ACACGGTTAAACAAAACACAGTA 57.123 34.783 0.00 0.00 0.00 2.74
1643 2839 1.975680 TGTAGTTGAGTTCCCTGTCCC 59.024 52.381 0.00 0.00 0.00 4.46
1679 2875 1.552578 AGTACACCTATGCGTCACCA 58.447 50.000 0.00 0.00 0.00 4.17
1685 2881 4.678622 TGACATACAAGTACACCTATGCG 58.321 43.478 0.00 0.00 0.00 4.73
1699 2895 9.211485 CACAAGATATGCAGATTATGACATACA 57.789 33.333 12.49 0.00 33.60 2.29
1700 2896 8.663025 CCACAAGATATGCAGATTATGACATAC 58.337 37.037 12.49 0.00 33.60 2.39
1701 2897 8.596293 TCCACAAGATATGCAGATTATGACATA 58.404 33.333 12.49 0.00 34.56 2.29
1702 2898 7.455891 TCCACAAGATATGCAGATTATGACAT 58.544 34.615 12.49 0.00 32.65 3.06
1703 2899 6.829849 TCCACAAGATATGCAGATTATGACA 58.170 36.000 12.49 0.00 0.00 3.58
1705 2901 8.789762 CAATTCCACAAGATATGCAGATTATGA 58.210 33.333 12.49 0.00 0.00 2.15
1724 2920 3.348647 TCTTCCAAGATCGCAATTCCA 57.651 42.857 0.00 0.00 0.00 3.53
1784 2980 5.418840 TGAATTGGAATGTTCTTCTTAGCCC 59.581 40.000 0.00 0.00 0.00 5.19
1825 3027 4.322049 GCGGATCTCAAGCTAAGCCTATAA 60.322 45.833 0.00 0.00 0.00 0.98
1864 3066 5.327616 TCGATGAATCCGTTACAGGTTAA 57.672 39.130 0.00 0.00 0.00 2.01
1909 3111 7.436376 CAGTCTCGCATCTATTTGAGTCAATAA 59.564 37.037 6.36 0.00 0.00 1.40
1962 3164 5.886960 AGCAATACTCAATCTGTGAAACC 57.113 39.130 0.00 0.00 35.22 3.27
2215 3429 7.869429 AGACAAGCAAAAGTTAAAATGAGATGG 59.131 33.333 0.00 0.00 0.00 3.51
2388 3602 7.279981 GCATCAAACCCCTTAAATGGAAATAAC 59.720 37.037 0.00 0.00 0.00 1.89
2404 3618 1.404583 GGCATCACAAGCATCAAACCC 60.405 52.381 0.00 0.00 0.00 4.11
2418 3632 2.616960 CTGTAGCGTACAAAGGCATCA 58.383 47.619 0.00 0.00 38.38 3.07
2556 3775 7.259882 ACAAGTGCATGTATATGAATTTGGTG 58.740 34.615 16.71 0.00 41.49 4.17
2565 3784 3.878699 TGCCAGACAAGTGCATGTATATG 59.121 43.478 0.00 0.00 37.36 1.78
3082 4326 6.346919 CGTATCTTTCCAGTGACAACAGAAAG 60.347 42.308 12.74 12.74 43.47 2.62
3167 4414 6.905578 TGTGATGAATGAGAACATCTGTTTG 58.094 36.000 0.00 0.00 42.05 2.93
3252 4499 1.899814 ACCAGAATACGCTCAGGTGAA 59.100 47.619 0.00 0.00 34.19 3.18
3268 4515 1.035139 AGGCTGCAAAAGACAACCAG 58.965 50.000 0.50 0.00 35.71 4.00
3276 4523 3.269178 TGTTTTTCCAAGGCTGCAAAAG 58.731 40.909 0.50 0.00 0.00 2.27
3385 4632 1.374252 AGTGTCATCGGTTCGGCAC 60.374 57.895 0.00 0.00 0.00 5.01
3424 4671 0.533308 AACTTGTTACTGGCGCGGAA 60.533 50.000 8.83 0.00 0.00 4.30
3644 4891 9.627123 CCAAAACCTTTACAGATCATAGGATAA 57.373 33.333 0.00 0.00 32.67 1.75
3699 4948 4.376146 AGTTCAGACTTCAAAGAGAGCAC 58.624 43.478 0.00 0.00 29.87 4.40
3707 4956 4.965814 AGCATCAGAGTTCAGACTTCAAA 58.034 39.130 0.00 0.00 35.88 2.69
3708 4957 4.613925 AGCATCAGAGTTCAGACTTCAA 57.386 40.909 0.00 0.00 35.88 2.69
3801 5053 4.034394 TGCAATCTCATGAATAGAACGTGC 59.966 41.667 0.00 3.98 33.41 5.34
3874 5127 7.608376 TGCTGCCTCTGAATATACTACTACTAG 59.392 40.741 0.00 0.00 0.00 2.57
3942 5197 1.528824 CCTCCATGCATTCCTCCGT 59.471 57.895 0.00 0.00 0.00 4.69
3980 5236 1.079888 GGTGCAGGAAAAATGGCCG 60.080 57.895 0.00 0.00 0.00 6.13
4211 5474 1.494960 ATCCCCTGAGACTGAGAAGC 58.505 55.000 0.00 0.00 0.00 3.86
4230 5495 0.898326 TCTCTCCACCGCTTGCAGTA 60.898 55.000 0.00 0.00 0.00 2.74
4231 5496 1.758440 TTCTCTCCACCGCTTGCAGT 61.758 55.000 0.00 0.00 0.00 4.40
4232 5497 1.004560 TTCTCTCCACCGCTTGCAG 60.005 57.895 0.00 0.00 0.00 4.41
4297 5562 1.898154 CAGGTTCCCTCCGACGAAT 59.102 57.895 0.00 0.00 0.00 3.34
4373 5638 1.810151 GGAGGCAGTTTTCATTGCGTA 59.190 47.619 0.00 0.00 41.17 4.42
4393 5658 2.096516 GCAAGAGAGAGAACAGCAAACG 60.097 50.000 0.00 0.00 0.00 3.60
4415 5680 3.574396 CCTGAACTACAACTGACAGGAGA 59.426 47.826 7.51 0.00 45.02 3.71
4419 5684 4.322080 TCACCTGAACTACAACTGACAG 57.678 45.455 0.00 0.00 0.00 3.51
4464 5740 0.680921 AGCACCAACACAGCAACACT 60.681 50.000 0.00 0.00 0.00 3.55
4467 5743 0.528249 CCAAGCACCAACACAGCAAC 60.528 55.000 0.00 0.00 0.00 4.17
4469 5745 0.969917 AACCAAGCACCAACACAGCA 60.970 50.000 0.00 0.00 0.00 4.41
4471 5747 0.029300 CGAACCAAGCACCAACACAG 59.971 55.000 0.00 0.00 0.00 3.66
4497 5813 1.594862 CCTCGCATCCACGATCTTTTC 59.405 52.381 0.00 0.00 42.02 2.29
4594 5930 0.687354 TGCAGAGAAGAGGACCCAAC 59.313 55.000 0.00 0.00 0.00 3.77
4621 5957 4.441792 ACCAAACATTTCCTTCAAGTTGC 58.558 39.130 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.