Multiple sequence alignment - TraesCS5D01G395300

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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 TraesCS5D01G395300 chr5D 100.000 4236 0 0 1 4236 462993834 462989599 0.000000e+00 7823.0
1 TraesCS5D01G395300 chr5D 100.000 3525 0 0 4531 8055 462989304 462985780 0.000000e+00 6510.0
2 TraesCS5D01G395300 chr5D 75.986 279 54 12 2770 3041 463175612 463175340 1.820000e-26 132.0
3 TraesCS5D01G395300 chr5B 95.233 4258 150 24 1 4236 569553570 569549344 0.000000e+00 6689.0
4 TraesCS5D01G395300 chr5B 94.142 2629 89 21 4532 7132 569549264 569546673 0.000000e+00 3941.0
5 TraesCS5D01G395300 chr5B 83.057 785 48 25 7145 7880 569546595 569545847 1.140000e-177 634.0
6 TraesCS5D01G395300 chr5B 99.242 132 1 0 7922 8053 569545844 569545713 1.040000e-58 239.0
7 TraesCS5D01G395300 chr5B 75.986 279 54 11 2770 3041 570055539 570055267 1.820000e-26 132.0
8 TraesCS5D01G395300 chr5B 100.000 31 0 0 7108 7138 569546663 569546633 3.140000e-04 58.4
9 TraesCS5D01G395300 chr5A 96.905 3522 90 8 729 4236 582967422 582963906 0.000000e+00 5882.0
10 TraesCS5D01G395300 chr5A 94.238 2638 99 17 4531 7138 582963835 582961221 0.000000e+00 3980.0
11 TraesCS5D01G395300 chr5A 89.985 659 44 9 1 645 582968547 582967897 0.000000e+00 832.0
12 TraesCS5D01G395300 chr5A 85.261 441 44 12 7620 8053 582959787 582959361 1.240000e-117 435.0
13 TraesCS5D01G395300 chr5A 85.714 84 8 3 7372 7455 582960471 582960392 1.440000e-12 86.1
14 TraesCS5D01G395300 chr7B 81.124 747 87 30 5637 6366 15810400 15809691 4.250000e-152 549.0


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 TraesCS5D01G395300 chr5D 462985780 462993834 8054 True 7166.50 7823 100.0000 1 8055 2 chr5D.!!$R2 8054
1 TraesCS5D01G395300 chr5B 569545713 569553570 7857 True 2312.28 6689 94.3348 1 8053 5 chr5B.!!$R2 8052
2 TraesCS5D01G395300 chr5A 582959361 582968547 9186 True 2243.02 5882 90.4206 1 8053 5 chr5A.!!$R1 8052
3 TraesCS5D01G395300 chr7B 15809691 15810400 709 True 549.00 549 81.1240 5637 6366 1 chr7B.!!$R1 729

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
912 1327 0.034896 ACGCGGTCCTTGTTCATTCT 59.965 50.0 12.47 0.0 0.00 2.40 F
1674 2092 0.725117 AAAAGGCGCGAATAGAACCG 59.275 50.0 12.10 0.0 0.00 4.44 F
2923 3345 1.610554 GAATTGCTGCAGGTGGGCAT 61.611 55.0 17.12 0.0 43.97 4.40 F
3647 4070 0.323087 ATGTTGCAGCAGCTCCATCA 60.323 50.0 9.71 0.0 42.74 3.07 F
4611 5037 0.034960 GGCTCCCTTCTCCTTCAACC 60.035 60.0 0.00 0.0 0.00 3.77 F
5131 5582 0.748005 GCAAGGCTCGGAATAAGGCA 60.748 55.0 0.00 0.0 41.51 4.75 F
6251 6718 0.319728 TCTCTGGTGTTCTGCTGCTC 59.680 55.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2576 2.100584 CACACCACAAAGCTAAAAGGCA 59.899 45.455 0.00 0.00 34.17 4.75 R
3626 4049 0.611062 ATGGAGCTGCTGCAACATGT 60.611 50.000 27.28 8.19 42.74 3.21 R
4587 5010 1.561542 GAAGGAGAAGGGAGCCATCAA 59.438 52.381 0.00 0.00 0.00 2.57 R
5071 5522 1.425066 AGGCCATCTTCAGGTTCAACA 59.575 47.619 5.01 0.00 0.00 3.33 R
5688 6143 1.606668 CAAAGTTGTACACCCATGCGT 59.393 47.619 0.00 0.00 0.00 5.24 R
6898 7365 1.078567 GGAGAGAGCAGCACCTTGG 60.079 63.158 0.00 0.00 0.00 3.61 R
7750 9304 0.106335 TTGCAGTTGGTTGGCATTGG 59.894 50.000 0.00 0.00 37.39 3.16 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
87 88 4.202223 ACGGACTAACACATCACAAGAACT 60.202 41.667 0.00 0.00 0.00 3.01
106 107 6.879400 AGAACTGGAGGAGTAATATGACAAC 58.121 40.000 0.00 0.00 33.09 3.32
111 113 5.596772 TGGAGGAGTAATATGACAACATCGA 59.403 40.000 0.00 0.00 37.87 3.59
163 166 4.274950 CGAGAACAAAACCCTAGCAAAAGA 59.725 41.667 0.00 0.00 0.00 2.52
169 172 0.038310 ACCCTAGCAAAAGACTGGGC 59.962 55.000 0.00 0.00 38.23 5.36
171 174 1.341383 CCCTAGCAAAAGACTGGGCAT 60.341 52.381 0.00 0.00 34.59 4.40
179 182 0.179000 AAGACTGGGCATCCACGATC 59.821 55.000 0.00 0.00 38.32 3.69
186 189 2.588877 CATCCACGATCGTGCCCC 60.589 66.667 36.77 0.00 44.16 5.80
187 190 2.764128 ATCCACGATCGTGCCCCT 60.764 61.111 36.77 20.04 44.16 4.79
188 191 3.094062 ATCCACGATCGTGCCCCTG 62.094 63.158 36.77 24.63 44.16 4.45
221 225 3.569701 TGGTTGAGAAGAGTTTCATTGCC 59.430 43.478 0.00 0.00 35.70 4.52
223 227 4.540824 GTTGAGAAGAGTTTCATTGCCAC 58.459 43.478 0.00 0.00 35.70 5.01
227 231 2.610438 AGAGTTTCATTGCCACCCAT 57.390 45.000 0.00 0.00 0.00 4.00
277 281 1.972075 TCGTCCTATGTGGGTTGTTGA 59.028 47.619 0.00 0.00 36.20 3.18
282 286 5.497474 GTCCTATGTGGGTTGTTGATAACT 58.503 41.667 0.00 0.00 36.20 2.24
294 298 8.421002 GGGTTGTTGATAACTAATGCCAAATAT 58.579 33.333 0.00 0.00 0.00 1.28
309 313 5.105797 TGCCAAATATGATGGTTGTTGAGTC 60.106 40.000 9.02 0.00 40.23 3.36
327 331 3.965888 CTGGAAGACAGGGGAAAGG 57.034 57.895 0.00 0.00 43.70 3.11
343 347 6.439058 AGGGGAAAGGAAGAAGATAGATATCG 59.561 42.308 0.00 0.00 37.76 2.92
451 456 8.504005 GTTGCTTGCTAAAATTGACTAACTAGA 58.496 33.333 0.00 0.00 0.00 2.43
472 477 2.978156 ACAATCCATGGGTTGTCACT 57.022 45.000 33.40 14.56 33.53 3.41
498 506 8.111545 TCACATACATATACGGTTAGACCCTAT 58.888 37.037 0.00 0.00 33.75 2.57
675 701 1.140852 CCCCATTCGCTGGTAAGATCA 59.859 52.381 0.00 0.00 44.30 2.92
697 723 1.876322 CGAGGAGCAAATCTCATCCC 58.124 55.000 1.69 0.00 46.76 3.85
700 726 1.773653 AGGAGCAAATCTCATCCCCTC 59.226 52.381 0.00 0.00 43.70 4.30
708 734 0.558220 TCTCATCCCCTCTCCATCGT 59.442 55.000 0.00 0.00 0.00 3.73
709 735 1.062886 TCTCATCCCCTCTCCATCGTT 60.063 52.381 0.00 0.00 0.00 3.85
713 739 0.635009 TCCCCTCTCCATCGTTAGGT 59.365 55.000 0.00 0.00 0.00 3.08
760 1167 3.849951 CCGCCGTGCCCTACATCT 61.850 66.667 0.00 0.00 0.00 2.90
912 1327 0.034896 ACGCGGTCCTTGTTCATTCT 59.965 50.000 12.47 0.00 0.00 2.40
924 1339 5.750067 CCTTGTTCATTCTTTTCTTGGTGTG 59.250 40.000 0.00 0.00 0.00 3.82
953 1369 3.547054 TTTTATCCAGCGACCGGTTAT 57.453 42.857 9.42 0.00 0.00 1.89
993 1409 1.069636 CAACTTCTGTTTCAGCCGCTC 60.070 52.381 0.00 0.00 33.52 5.03
1674 2092 0.725117 AAAAGGCGCGAATAGAACCG 59.275 50.000 12.10 0.00 0.00 4.44
1805 2223 9.474920 TGAAGCTTAATAGTTTTCAACCAAATG 57.525 29.630 0.00 0.00 29.91 2.32
1929 2347 7.624360 AATGTTTGCTTCATCGGTAGATTTA 57.376 32.000 0.00 0.00 34.23 1.40
2172 2590 8.863049 CACAATAAGTTATGCCTTTTAGCTTTG 58.137 33.333 0.00 0.00 0.00 2.77
2223 2641 3.497879 GTGCCATTCTGGTACGGC 58.502 61.111 0.00 0.68 42.97 5.68
2649 3071 8.623310 TTTCTTAACGTGATTTCTTGGAAAAC 57.377 30.769 0.00 0.00 0.00 2.43
2690 3112 8.362464 TCCTGAGTTAAGTAGAATTTGAGCTA 57.638 34.615 0.00 0.00 0.00 3.32
2923 3345 1.610554 GAATTGCTGCAGGTGGGCAT 61.611 55.000 17.12 0.00 43.97 4.40
3140 3562 4.799678 AGACGACATTCACAAGTAGACTG 58.200 43.478 0.00 0.00 0.00 3.51
3167 3589 5.703130 AGTTGGAGAGTTTATCAAGAGCAAC 59.297 40.000 0.00 0.00 0.00 4.17
3464 3887 5.163844 GGTGCGAGGTTCTTTTATTCTCTTC 60.164 44.000 0.00 0.00 0.00 2.87
3626 4049 6.151648 ACTGTATACGGCTCTGTTACAACTAA 59.848 38.462 11.79 0.00 0.00 2.24
3647 4070 0.323087 ATGTTGCAGCAGCTCCATCA 60.323 50.000 9.71 0.00 42.74 3.07
3686 4109 8.985315 TCCATACTTCTATGCTTCATTGAATT 57.015 30.769 0.00 2.91 35.75 2.17
3696 4119 6.788684 TGCTTCATTGAATTTTCACCATTG 57.211 33.333 0.00 0.00 36.83 2.82
3813 4236 6.512741 CGGCAACATTACCTATGGAATTACAC 60.513 42.308 0.00 0.00 38.64 2.90
3889 4312 3.689347 TCCACATCTGCAGTTGCTATTT 58.311 40.909 21.97 2.26 42.66 1.40
3898 4321 5.125900 TCTGCAGTTGCTATTTATGCATTGT 59.874 36.000 14.67 0.00 45.08 2.71
3938 4361 6.678568 ATCTCTATTGTGCAGCCTATTAGT 57.321 37.500 0.00 0.00 0.00 2.24
4014 4437 7.344612 ACCAGGGAATTTCTTTAAGTTCAGTTT 59.655 33.333 0.00 0.00 34.05 2.66
4128 4551 2.878526 GCCCAGAAAATTACGAGGTGGT 60.879 50.000 0.00 0.00 0.00 4.16
4180 4603 8.411318 CTGTGTATATTTCAGCAATTTTTCCC 57.589 34.615 0.00 0.00 0.00 3.97
4557 4980 1.043673 AACCCTAGCCGCCACTCTAG 61.044 60.000 0.00 0.00 33.76 2.43
4587 5010 1.630878 CTCCTTCCAGCCTACCACTTT 59.369 52.381 0.00 0.00 0.00 2.66
4611 5037 0.034960 GGCTCCCTTCTCCTTCAACC 60.035 60.000 0.00 0.00 0.00 3.77
4636 5062 1.804396 CGGCACCACCAATTGAAGCA 61.804 55.000 7.12 0.00 39.03 3.91
4774 5200 1.913419 TCCCCCAATCCTAACTCACAC 59.087 52.381 0.00 0.00 0.00 3.82
4778 5204 3.506067 CCCCAATCCTAACTCACACAAAC 59.494 47.826 0.00 0.00 0.00 2.93
4887 5336 3.270877 GCGTGAGGATTTGTCTGGTAAT 58.729 45.455 0.00 0.00 0.00 1.89
4964 5415 5.257345 GTCTGTCTTGACGCTAGAAAAAG 57.743 43.478 0.00 0.00 0.00 2.27
5071 5522 2.434702 AGGAACTCTTCAAGTGGAACGT 59.565 45.455 0.00 0.00 45.86 3.99
5131 5582 0.748005 GCAAGGCTCGGAATAAGGCA 60.748 55.000 0.00 0.00 41.51 4.75
5213 5664 3.935203 CTGCGTACATCCTGATTTCTGTT 59.065 43.478 0.00 0.00 0.00 3.16
5380 5831 2.087646 GGAACTGTTGGAGGAAGCATC 58.912 52.381 0.00 0.00 0.00 3.91
5540 5991 1.939934 TCTTGCGTGGTTCAAGACAAG 59.060 47.619 1.72 0.00 43.34 3.16
5670 6125 1.406614 CCAGCACTCCTCTGATTGGTC 60.407 57.143 0.00 0.00 30.46 4.02
5673 6128 1.134551 GCACTCCTCTGATTGGTCCTC 60.135 57.143 0.00 0.00 0.00 3.71
5674 6129 2.465813 CACTCCTCTGATTGGTCCTCT 58.534 52.381 0.00 0.00 0.00 3.69
5675 6130 2.168106 CACTCCTCTGATTGGTCCTCTG 59.832 54.545 0.00 0.00 0.00 3.35
5677 6132 3.307506 CTCCTCTGATTGGTCCTCTGAT 58.692 50.000 0.00 0.00 0.00 2.90
5680 6135 3.433314 CCTCTGATTGGTCCTCTGATTGG 60.433 52.174 0.00 0.00 0.00 3.16
5681 6136 3.184628 TCTGATTGGTCCTCTGATTGGT 58.815 45.455 0.00 0.00 0.00 3.67
5682 6137 3.054875 TCTGATTGGTCCTCTGATTGGTG 60.055 47.826 0.00 0.00 0.00 4.17
5683 6138 2.019984 GATTGGTCCTCTGATTGGTGC 58.980 52.381 0.00 0.00 0.00 5.01
5684 6139 1.067295 TTGGTCCTCTGATTGGTGCT 58.933 50.000 0.00 0.00 0.00 4.40
5685 6140 1.951209 TGGTCCTCTGATTGGTGCTA 58.049 50.000 0.00 0.00 0.00 3.49
5686 6141 2.265367 TGGTCCTCTGATTGGTGCTAA 58.735 47.619 0.00 0.00 0.00 3.09
5687 6142 2.846206 TGGTCCTCTGATTGGTGCTAAT 59.154 45.455 0.00 0.00 0.00 1.73
5688 6143 4.037222 TGGTCCTCTGATTGGTGCTAATA 58.963 43.478 0.00 0.00 0.00 0.98
5802 6257 6.730507 TGCTGAAGTATGGAATATGGAGGATA 59.269 38.462 0.00 0.00 0.00 2.59
6056 6513 7.042051 ACACGCATCATATTTTACTATGGACAC 60.042 37.037 0.00 0.00 31.32 3.67
6204 6665 8.571461 ACTTGAATTATGACATGTGACTGAAT 57.429 30.769 1.15 0.00 0.00 2.57
6215 6676 5.177511 ACATGTGACTGAATGTTGTAGAACG 59.822 40.000 0.00 0.00 33.19 3.95
6226 6693 3.242608 TGTTGTAGAACGCAAAGAACAGC 60.243 43.478 0.00 0.00 34.49 4.40
6227 6694 1.871039 TGTAGAACGCAAAGAACAGCC 59.129 47.619 0.00 0.00 0.00 4.85
6247 6714 2.499289 CCTGTATCTCTGGTGTTCTGCT 59.501 50.000 0.00 0.00 0.00 4.24
6249 6716 2.275318 GTATCTCTGGTGTTCTGCTGC 58.725 52.381 0.00 0.00 0.00 5.25
6251 6718 0.319728 TCTCTGGTGTTCTGCTGCTC 59.680 55.000 0.00 0.00 0.00 4.26
6292 6759 5.701224 TGTCCATAACTGGGTTCTTTTCTT 58.299 37.500 0.00 0.00 43.34 2.52
6293 6760 5.768164 TGTCCATAACTGGGTTCTTTTCTTC 59.232 40.000 0.00 0.00 43.34 2.87
6294 6761 6.004574 GTCCATAACTGGGTTCTTTTCTTCT 58.995 40.000 0.00 0.00 43.34 2.85
6888 7355 4.682401 TGTGCTGTTGTACTGTTGTATACG 59.318 41.667 0.00 0.00 0.00 3.06
6898 7365 3.120060 ACTGTTGTATACGTGTCTCCGAC 60.120 47.826 0.00 0.00 0.00 4.79
6917 7384 1.447489 CAAGGTGCTGCTCTCTCCG 60.447 63.158 0.00 0.00 0.00 4.63
6918 7385 1.910772 AAGGTGCTGCTCTCTCCGT 60.911 57.895 0.00 0.00 0.00 4.69
6919 7386 2.125753 GGTGCTGCTCTCTCCGTG 60.126 66.667 0.00 0.00 0.00 4.94
6920 7387 2.813042 GTGCTGCTCTCTCCGTGC 60.813 66.667 0.00 0.00 0.00 5.34
7008 7475 9.088512 GACTTTAATCGTACATTCAGAGTTCAT 57.911 33.333 0.00 0.00 0.00 2.57
7053 7520 7.433708 TGTGTTTATTCTGTGATTTGTCGAT 57.566 32.000 0.00 0.00 0.00 3.59
7062 7529 5.754890 TCTGTGATTTGTCGATATGATGGTG 59.245 40.000 0.00 0.00 0.00 4.17
7106 7573 3.096791 GCAACTGCGAGATGGAGC 58.903 61.111 0.00 0.00 40.21 4.70
7140 7672 1.294068 TGGAACAGGGGAGGCTATACT 59.706 52.381 0.00 0.00 0.00 2.12
7143 7675 4.358918 TGGAACAGGGGAGGCTATACTATA 59.641 45.833 0.00 0.00 0.00 1.31
7161 7693 2.990740 TACCCCTTTCCTGCATTTGT 57.009 45.000 0.00 0.00 0.00 2.83
7303 8276 7.218963 GCGCTGGAGATTTAAGATTTTTGTAAG 59.781 37.037 0.00 0.00 0.00 2.34
7455 8472 2.216046 ACACTGCCATCATTCGCATAG 58.784 47.619 0.00 0.00 33.78 2.23
7462 8479 3.589988 CCATCATTCGCATAGGGTACTC 58.410 50.000 0.00 0.00 0.00 2.59
7485 8502 7.380602 ACTCGCAAAATTCTTCTTTTCATTCTG 59.619 33.333 0.00 0.00 0.00 3.02
7504 8535 5.227569 TCTGAACCACTTATGCTTCAGAA 57.772 39.130 11.01 0.00 43.52 3.02
7510 8541 4.133078 CCACTTATGCTTCAGAATCCTCC 58.867 47.826 0.00 0.00 0.00 4.30
7527 8558 8.363390 AGAATCCTCCTTTTCACATTTTCTTTC 58.637 33.333 0.00 0.00 0.00 2.62
7535 8566 9.377312 CCTTTTCACATTTTCTTTCCTAAACAA 57.623 29.630 0.00 0.00 0.00 2.83
7583 8614 4.442706 TCCATTCCTTCGATCTGTAAAGC 58.557 43.478 0.00 0.00 0.00 3.51
7585 8616 4.446371 CATTCCTTCGATCTGTAAAGCCT 58.554 43.478 0.00 0.00 0.00 4.58
7657 9208 5.396213 CCAACAAGGATTTTGGAAGGAAACA 60.396 40.000 0.00 0.00 44.51 2.83
7710 9263 4.879545 TGTGGTTTTCTGTTCTAGTGTTCC 59.120 41.667 0.00 0.00 0.00 3.62
7722 9276 7.331026 TGTTCTAGTGTTCCTGAATTCCTATG 58.669 38.462 2.27 0.00 0.00 2.23
7741 9295 2.925724 TGTTCCAAACATGACCGAAGT 58.074 42.857 0.00 0.00 36.25 3.01
7742 9296 3.283751 TGTTCCAAACATGACCGAAGTT 58.716 40.909 0.00 0.00 36.25 2.66
7750 9304 3.131396 ACATGACCGAAGTTTGTCTGAC 58.869 45.455 0.00 0.00 32.67 3.51
7761 9315 1.327303 TTGTCTGACCAATGCCAACC 58.673 50.000 5.17 0.00 0.00 3.77
7792 9359 1.209621 TCCCCTGAAATTCTACCGGG 58.790 55.000 6.32 0.00 0.00 5.73
7798 9365 3.937079 CCTGAAATTCTACCGGGTTGTAC 59.063 47.826 4.31 0.00 0.00 2.90
7857 9424 1.550524 TCAGCCACTAATCAACGAGCT 59.449 47.619 0.00 0.00 0.00 4.09
7870 9437 2.672874 CAACGAGCTGATCCGATGAAAA 59.327 45.455 0.00 0.00 31.58 2.29
7880 9447 3.126001 TCCGATGAAAAAGCAGACAGT 57.874 42.857 0.00 0.00 0.00 3.55
7882 9449 3.994392 TCCGATGAAAAAGCAGACAGTAC 59.006 43.478 0.00 0.00 0.00 2.73
7898 9465 5.069914 AGACAGTACACATCACTACAACCAA 59.930 40.000 0.00 0.00 0.00 3.67
7904 9471 6.131544 ACACATCACTACAACCAAAAGAAC 57.868 37.500 0.00 0.00 0.00 3.01
7914 9481 4.830600 ACAACCAAAAGAACACGGGATATT 59.169 37.500 0.00 0.00 0.00 1.28
7920 9487 4.684484 AAGAACACGGGATATTCCTACC 57.316 45.455 0.00 0.00 36.57 3.18
8054 9624 4.413800 GCGCCCGTTTCGCCATTT 62.414 61.111 0.00 0.00 46.18 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.585748 TTTCTTGTCTTCGCTTCAACG 57.414 42.857 0.00 0.00 0.00 4.10
87 88 5.596772 TCGATGTTGTCATATTACTCCTCCA 59.403 40.000 0.00 0.00 34.06 3.86
106 107 0.105964 TTTCGCCCCATAGGTCGATG 59.894 55.000 0.00 0.00 41.61 3.84
111 113 1.283613 TGTTGATTTCGCCCCATAGGT 59.716 47.619 0.00 0.00 38.26 3.08
163 166 2.359169 ACGATCGTGGATGCCCAGT 61.359 57.895 22.06 0.00 44.55 4.00
169 172 2.588877 GGGGCACGATCGTGGATG 60.589 66.667 40.19 22.02 45.49 3.51
171 174 3.770040 CAGGGGCACGATCGTGGA 61.770 66.667 40.19 0.00 45.49 4.02
186 189 2.426738 TCTCAACCAACAAAAGTGGCAG 59.573 45.455 0.00 0.00 40.02 4.85
187 190 2.451490 TCTCAACCAACAAAAGTGGCA 58.549 42.857 0.00 0.00 40.02 4.92
188 191 3.130340 TCTTCTCAACCAACAAAAGTGGC 59.870 43.478 0.00 0.00 40.02 5.01
189 192 4.399303 ACTCTTCTCAACCAACAAAAGTGG 59.601 41.667 0.00 0.00 42.28 4.00
191 194 6.208599 TGAAACTCTTCTCAACCAACAAAAGT 59.791 34.615 0.00 0.00 32.33 2.66
221 225 3.623060 CCTTCGTATCAAAGTGATGGGTG 59.377 47.826 0.94 0.00 37.70 4.61
223 227 3.871594 GTCCTTCGTATCAAAGTGATGGG 59.128 47.826 0.94 0.00 37.70 4.00
227 231 4.929211 CACATGTCCTTCGTATCAAAGTGA 59.071 41.667 0.00 0.00 0.00 3.41
277 281 9.146586 ACAACCATCATATTTGGCATTAGTTAT 57.853 29.630 0.00 0.00 37.81 1.89
282 286 7.123997 ACTCAACAACCATCATATTTGGCATTA 59.876 33.333 0.00 0.00 37.81 1.90
294 298 3.390967 TCTTCCAGACTCAACAACCATCA 59.609 43.478 0.00 0.00 0.00 3.07
309 313 1.362224 TCCTTTCCCCTGTCTTCCAG 58.638 55.000 0.00 0.00 41.15 3.86
317 321 5.903198 ATCTATCTTCTTCCTTTCCCCTG 57.097 43.478 0.00 0.00 0.00 4.45
325 329 8.328758 AGATGACTCGATATCTATCTTCTTCCT 58.671 37.037 0.34 0.00 32.13 3.36
326 330 8.506168 AGATGACTCGATATCTATCTTCTTCC 57.494 38.462 0.34 0.00 32.13 3.46
327 331 9.161629 TGAGATGACTCGATATCTATCTTCTTC 57.838 37.037 0.34 0.00 45.25 2.87
343 347 6.310197 CACCGAAAAATCTTTGAGATGACTC 58.690 40.000 0.00 0.00 42.88 3.36
472 477 6.309357 AGGGTCTAACCGTATATGTATGTGA 58.691 40.000 0.00 0.00 39.83 3.58
498 506 4.585162 GCCCTTGTAGAATACTCTAGAGCA 59.415 45.833 19.97 7.49 43.54 4.26
675 701 0.176680 ATGAGATTTGCTCCTCGCGT 59.823 50.000 5.77 0.00 43.26 6.01
697 723 0.669077 CGGACCTAACGATGGAGAGG 59.331 60.000 0.00 0.00 35.05 3.69
700 726 1.067582 GCCGGACCTAACGATGGAG 59.932 63.158 5.05 0.00 0.00 3.86
708 734 1.693627 GAGAGATCTGCCGGACCTAA 58.306 55.000 5.05 0.00 0.00 2.69
709 735 0.178987 GGAGAGATCTGCCGGACCTA 60.179 60.000 5.05 0.00 0.00 3.08
842 1257 0.731855 CGACGAGGAAGAACGGGAAC 60.732 60.000 0.00 0.00 0.00 3.62
912 1327 2.821437 TCAAACCCCACACCAAGAAAA 58.179 42.857 0.00 0.00 0.00 2.29
924 1339 3.020984 TCGCTGGATAAAATCAAACCCC 58.979 45.455 0.00 0.00 0.00 4.95
953 1369 3.042682 TGTGAGGTTCAGTGGGACTTAA 58.957 45.455 0.00 0.00 0.00 1.85
1698 2116 2.479566 AGCCATTTGATGACGTCTGT 57.520 45.000 17.92 5.36 0.00 3.41
1805 2223 7.020602 GCAACCATAACAAAATAAAATGCACC 58.979 34.615 0.00 0.00 0.00 5.01
2158 2576 2.100584 CACACCACAAAGCTAAAAGGCA 59.899 45.455 0.00 0.00 34.17 4.75
2172 2590 5.971763 AGATTATGAGAGAAGTCACACCAC 58.028 41.667 0.00 0.00 0.00 4.16
2334 2752 4.803329 AGAAAGTGCCATGGGAGAATAT 57.197 40.909 15.13 0.00 0.00 1.28
2335 2753 4.721776 AGTAGAAAGTGCCATGGGAGAATA 59.278 41.667 15.13 0.00 0.00 1.75
2923 3345 1.427368 AGCATTTACCTGTCCACCCAA 59.573 47.619 0.00 0.00 0.00 4.12
3140 3562 6.428159 TGCTCTTGATAAACTCTCCAACTTTC 59.572 38.462 0.00 0.00 0.00 2.62
3167 3589 4.574013 GTGCTAGGATCAACATCTGGAAAG 59.426 45.833 0.00 0.00 0.00 2.62
3364 3786 2.363680 CACACAGGTGGCCAAACATAAA 59.636 45.455 7.24 0.00 41.45 1.40
3626 4049 0.611062 ATGGAGCTGCTGCAACATGT 60.611 50.000 27.28 8.19 42.74 3.21
3647 4070 6.787170 AGAAGTATGGAATGGACATGCATAT 58.213 36.000 0.00 0.00 34.31 1.78
3686 4109 8.696374 TGGTAAATAACAAAGTCAATGGTGAAA 58.304 29.630 0.00 0.00 34.87 2.69
3719 4142 6.897966 TGGATTATCTTGTCAGTAAGAGGTCT 59.102 38.462 0.00 0.00 39.81 3.85
3781 4204 5.937540 CCATAGGTAATGTTGCCGAATCATA 59.062 40.000 0.00 0.00 38.06 2.15
3813 4236 8.715998 CATACTCATTATCTTCATTCTTTCCCG 58.284 37.037 0.00 0.00 0.00 5.14
3938 4361 7.393796 ACCGTTGTCAAATTTATATGGGTACAA 59.606 33.333 0.00 0.00 0.00 2.41
4079 4502 9.689976 CAACAAGACATGTAAAAACAATATGGA 57.310 29.630 0.00 0.00 42.99 3.41
4128 4551 2.627699 CAACCTTTTAAGCCCAGCTCAA 59.372 45.455 0.00 0.00 38.25 3.02
4557 4980 3.198853 AGGCTGGAAGGAGATGTAAGAAC 59.801 47.826 0.00 0.00 0.00 3.01
4587 5010 1.561542 GAAGGAGAAGGGAGCCATCAA 59.438 52.381 0.00 0.00 0.00 2.57
4611 5037 2.086251 AATTGGTGGTGCCGCACAAG 62.086 55.000 24.43 0.00 41.21 3.16
4636 5062 4.699522 GGGACGGAAAGCGCCACT 62.700 66.667 2.29 0.00 0.00 4.00
4774 5200 4.622740 GGAGAAATGATTTGCTTCCGTTTG 59.377 41.667 0.00 0.00 0.00 2.93
4778 5204 3.691118 TGAGGAGAAATGATTTGCTTCCG 59.309 43.478 0.00 0.00 0.00 4.30
4882 5331 5.470098 CCTTATGTCATGCCACTACATTACC 59.530 44.000 2.67 0.00 35.54 2.85
4887 5336 2.172505 CCCCTTATGTCATGCCACTACA 59.827 50.000 0.00 0.00 0.00 2.74
4921 5370 6.037500 CAGACGAATCAGCCTATCAAATGAAA 59.962 38.462 0.00 0.00 0.00 2.69
4958 5407 3.888934 TGCAATGACGCTTCTCTTTTTC 58.111 40.909 0.00 0.00 0.00 2.29
4964 5415 1.916000 GCAAATGCAATGACGCTTCTC 59.084 47.619 7.02 0.00 41.59 2.87
5071 5522 1.425066 AGGCCATCTTCAGGTTCAACA 59.575 47.619 5.01 0.00 0.00 3.33
5131 5582 3.102204 CCCTTCTTTCCCAAGATTGCAT 58.898 45.455 0.00 0.00 38.89 3.96
5380 5831 3.882888 AGTAATATTGCACATCCAACCCG 59.117 43.478 6.31 0.00 0.00 5.28
5620 6071 5.996644 CCAAACCATGGTACCTAACTATCA 58.003 41.667 20.12 0.00 44.85 2.15
5670 6125 2.802816 GCGTATTAGCACCAATCAGAGG 59.197 50.000 0.00 0.00 37.05 3.69
5682 6137 2.828877 TGTACACCCATGCGTATTAGC 58.171 47.619 0.00 0.00 37.71 3.09
5683 6138 4.439057 AGTTGTACACCCATGCGTATTAG 58.561 43.478 0.00 0.00 0.00 1.73
5684 6139 4.475051 AGTTGTACACCCATGCGTATTA 57.525 40.909 0.00 0.00 0.00 0.98
5685 6140 3.343941 AGTTGTACACCCATGCGTATT 57.656 42.857 0.00 0.00 0.00 1.89
5686 6141 3.343941 AAGTTGTACACCCATGCGTAT 57.656 42.857 0.00 0.00 0.00 3.06
5687 6142 2.809119 CAAAGTTGTACACCCATGCGTA 59.191 45.455 0.00 0.00 0.00 4.42
5688 6143 1.606668 CAAAGTTGTACACCCATGCGT 59.393 47.619 0.00 0.00 0.00 5.24
5802 6257 2.092267 TCAGTATTGGCATGCCATCACT 60.092 45.455 38.78 35.16 46.64 3.41
6110 6567 8.680903 CAGCAAAGAAGAAATAACAGGTATGAT 58.319 33.333 0.00 0.00 0.00 2.45
6171 6632 8.030692 CACATGTCATAATTCAAGTTGTTCCAT 58.969 33.333 0.00 0.00 0.00 3.41
6174 6635 8.292448 AGTCACATGTCATAATTCAAGTTGTTC 58.708 33.333 0.00 0.00 0.00 3.18
6183 6644 8.239314 ACAACATTCAGTCACATGTCATAATTC 58.761 33.333 0.00 0.00 32.21 2.17
6204 6665 3.242608 GCTGTTCTTTGCGTTCTACAACA 60.243 43.478 0.00 0.00 32.14 3.33
6215 6676 3.373439 CAGAGATACAGGCTGTTCTTTGC 59.627 47.826 27.24 14.74 0.00 3.68
6226 6693 2.499289 AGCAGAACACCAGAGATACAGG 59.501 50.000 0.00 0.00 0.00 4.00
6227 6694 3.519579 CAGCAGAACACCAGAGATACAG 58.480 50.000 0.00 0.00 0.00 2.74
6247 6714 3.349927 AGCAATATGTGAAGCAAGAGCA 58.650 40.909 0.00 0.00 45.49 4.26
6249 6716 5.306532 ACAAGCAATATGTGAAGCAAGAG 57.693 39.130 0.00 0.00 0.00 2.85
6251 6718 4.082625 TGGACAAGCAATATGTGAAGCAAG 60.083 41.667 0.00 0.00 0.00 4.01
6292 6759 4.492494 TTCTTCTGCATGAGCCATAAGA 57.508 40.909 0.00 0.00 41.13 2.10
6293 6760 4.639310 ACTTTCTTCTGCATGAGCCATAAG 59.361 41.667 0.00 0.00 41.13 1.73
6294 6761 4.592942 ACTTTCTTCTGCATGAGCCATAA 58.407 39.130 0.00 0.00 41.13 1.90
6898 7365 1.078567 GGAGAGAGCAGCACCTTGG 60.079 63.158 0.00 0.00 0.00 3.61
7008 7475 6.658816 ACACAAATTACCAGCATAGTCATCAA 59.341 34.615 0.00 0.00 0.00 2.57
7106 7573 3.132925 CTGTTCCAGGTTGCCAAATTTG 58.867 45.455 11.40 11.40 0.00 2.32
7132 7599 4.081031 GCAGGAAAGGGGTATAGTATAGCC 60.081 50.000 24.52 24.52 0.00 3.93
7133 7600 4.530946 TGCAGGAAAGGGGTATAGTATAGC 59.469 45.833 10.35 10.35 0.00 2.97
7134 7601 6.875972 ATGCAGGAAAGGGGTATAGTATAG 57.124 41.667 0.00 0.00 0.00 1.31
7136 7603 6.126185 ACAAATGCAGGAAAGGGGTATAGTAT 60.126 38.462 0.00 0.00 0.00 2.12
7140 7672 4.601406 ACAAATGCAGGAAAGGGGTATA 57.399 40.909 0.00 0.00 0.00 1.47
7143 7675 1.693606 CAACAAATGCAGGAAAGGGGT 59.306 47.619 0.00 0.00 0.00 4.95
7161 7693 1.202245 GGAAACACGCAACTGAAGCAA 60.202 47.619 0.00 0.00 0.00 3.91
7254 7811 3.003480 AGCAAATAAACGACAGGAGAGC 58.997 45.455 0.00 0.00 0.00 4.09
7303 8276 1.443802 AACTCTTCGCTGCCTAAAGC 58.556 50.000 0.00 0.00 44.14 3.51
7364 8360 3.648067 TCCAAATGCATCTAGGTCTAGGG 59.352 47.826 0.00 0.58 34.06 3.53
7365 8361 4.963318 TCCAAATGCATCTAGGTCTAGG 57.037 45.455 0.00 0.00 34.06 3.02
7366 8362 6.106648 TGATCCAAATGCATCTAGGTCTAG 57.893 41.667 0.00 0.00 34.56 2.43
7367 8363 6.692849 ATGATCCAAATGCATCTAGGTCTA 57.307 37.500 0.00 0.00 0.00 2.59
7368 8364 5.579753 ATGATCCAAATGCATCTAGGTCT 57.420 39.130 0.00 0.00 0.00 3.85
7369 8365 5.879223 CCTATGATCCAAATGCATCTAGGTC 59.121 44.000 0.00 0.00 0.00 3.85
7455 8472 5.372547 AAAGAAGAATTTTGCGAGTACCC 57.627 39.130 0.00 0.00 0.00 3.69
7462 8479 7.627585 TCAGAATGAAAAGAAGAATTTTGCG 57.372 32.000 0.00 0.00 45.97 4.85
7504 8535 6.784473 AGGAAAGAAAATGTGAAAAGGAGGAT 59.216 34.615 0.00 0.00 0.00 3.24
7583 8614 4.580167 TCATCTGAAACAACACCTTGAAGG 59.420 41.667 10.24 10.24 42.49 3.46
7585 8616 6.522625 TTTCATCTGAAACAACACCTTGAA 57.477 33.333 1.28 0.00 38.94 2.69
7652 9203 4.964593 TGGTACCCAAGAACTACTGTTTC 58.035 43.478 10.07 0.00 36.39 2.78
7657 9208 2.238898 GGCATGGTACCCAAGAACTACT 59.761 50.000 10.07 0.00 36.95 2.57
7679 9230 8.812972 ACTAGAACAGAAAACCACAGATATACA 58.187 33.333 0.00 0.00 0.00 2.29
7680 9231 9.088512 CACTAGAACAGAAAACCACAGATATAC 57.911 37.037 0.00 0.00 0.00 1.47
7682 9233 7.680730 ACACTAGAACAGAAAACCACAGATAT 58.319 34.615 0.00 0.00 0.00 1.63
7683 9234 7.062749 ACACTAGAACAGAAAACCACAGATA 57.937 36.000 0.00 0.00 0.00 1.98
7686 9237 5.007724 GGAACACTAGAACAGAAAACCACAG 59.992 44.000 0.00 0.00 0.00 3.66
7722 9276 3.982576 AACTTCGGTCATGTTTGGAAC 57.017 42.857 0.00 0.00 0.00 3.62
7737 9291 2.622942 TGGCATTGGTCAGACAAACTTC 59.377 45.455 2.17 0.00 33.48 3.01
7741 9295 1.686052 GGTTGGCATTGGTCAGACAAA 59.314 47.619 2.17 0.00 33.48 2.83
7742 9296 1.327303 GGTTGGCATTGGTCAGACAA 58.673 50.000 2.17 0.00 34.41 3.18
7750 9304 0.106335 TTGCAGTTGGTTGGCATTGG 59.894 50.000 0.00 0.00 37.39 3.16
7761 9315 3.749665 TTCAGGGGAATTTTGCAGTTG 57.250 42.857 0.00 0.00 0.00 3.16
7792 9359 5.453648 TGCATAATGTTTGGAACGTACAAC 58.546 37.500 5.22 0.00 0.00 3.32
7798 9365 7.195646 ACTATGAATGCATAATGTTTGGAACG 58.804 34.615 0.00 0.00 36.60 3.95
7857 9424 3.673902 TGTCTGCTTTTTCATCGGATCA 58.326 40.909 0.00 0.00 0.00 2.92
7870 9437 4.280929 TGTAGTGATGTGTACTGTCTGCTT 59.719 41.667 0.00 0.00 0.00 3.91
7880 9447 6.824196 TGTTCTTTTGGTTGTAGTGATGTGTA 59.176 34.615 0.00 0.00 0.00 2.90
7882 9449 5.971202 GTGTTCTTTTGGTTGTAGTGATGTG 59.029 40.000 0.00 0.00 0.00 3.21
7898 9465 4.472108 TGGTAGGAATATCCCGTGTTCTTT 59.528 41.667 0.00 0.00 37.19 2.52
7904 9471 4.283467 TGAGATTGGTAGGAATATCCCGTG 59.717 45.833 0.00 0.00 37.19 4.94
7914 9481 4.782691 TCATTTCCTGTGAGATTGGTAGGA 59.217 41.667 0.00 0.00 35.84 2.94
8009 9576 0.250295 CTGTCCAAGAAGCGGTTCCA 60.250 55.000 22.91 12.52 32.48 3.53


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

AutoCloner maintained by Alex Coulton.