Multiple sequence alignment - TraesCS6B01G379700

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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 TraesCS6B01G379700 chr6B 100.000 5831 0 0 1 5831 654741177 654735347 0.000000e+00 10768
1 TraesCS6B01G379700 chr6A 93.407 5142 195 75 744 5831 579444845 579439794 0.000000e+00 7485
2 TraesCS6B01G379700 chr6A 84.426 610 81 11 8 612 609958558 609959158 6.510000e-164 588
3 TraesCS6B01G379700 chr6D 93.865 3374 148 28 1912 5244 433483001 433479646 0.000000e+00 5029
4 TraesCS6B01G379700 chr6D 94.844 1280 44 13 603 1875 433484266 433483002 0.000000e+00 1978
5 TraesCS6B01G379700 chr6D 83.581 1212 110 52 4652 5831 433479649 433478495 0.000000e+00 1053
6 TraesCS6B01G379700 chr6D 90.364 550 48 3 59 606 16769120 16769666 0.000000e+00 717
7 TraesCS6B01G379700 chr6D 90.833 240 19 3 3521 3757 440639733 440639494 9.430000e-83 318
8 TraesCS6B01G379700 chr6D 87.313 134 15 1 1 132 16768996 16769129 1.010000e-32 152
9 TraesCS6B01G379700 chr2D 91.887 604 46 2 3 604 63998309 63998911 0.000000e+00 841
10 TraesCS6B01G379700 chr2D 88.226 603 55 8 3 604 107105773 107105186 0.000000e+00 706
11 TraesCS6B01G379700 chr2D 89.627 241 22 3 3517 3755 645896534 645896773 2.640000e-78 303
12 TraesCS6B01G379700 chr2D 87.764 237 25 4 3517 3750 620601791 620601556 2.070000e-69 274
13 TraesCS6B01G379700 chr4A 91.837 539 40 4 75 611 720085299 720084763 0.000000e+00 749
14 TraesCS6B01G379700 chr5D 89.256 605 53 4 3 604 500847147 500846552 0.000000e+00 747
15 TraesCS6B01G379700 chr7D 88.284 606 57 6 3 604 73225633 73225038 0.000000e+00 713
16 TraesCS6B01G379700 chr7D 88.264 605 53 7 3 604 560895452 560894863 0.000000e+00 708
17 TraesCS6B01G379700 chr7D 85.075 201 20 9 5636 5831 104092790 104092595 4.610000e-46 196
18 TraesCS6B01G379700 chr1B 85.062 569 68 14 45 606 68250954 68250396 1.100000e-156 564
19 TraesCS6B01G379700 chr1D 86.166 253 29 5 3509 3757 217297429 217297679 9.630000e-68 268
20 TraesCS6B01G379700 chr1A 86.777 242 28 4 3517 3755 14115611 14115851 3.460000e-67 267
21 TraesCS6B01G379700 chr1A 85.542 249 34 2 3508 3755 112946485 112946732 5.800000e-65 259
22 TraesCS6B01G379700 chr2B 86.585 246 25 7 3517 3759 272768485 272768245 1.250000e-66 265
23 TraesCS6B01G379700 chr7B 86.000 200 20 7 5636 5831 61911105 61910910 2.130000e-49 207
24 TraesCS6B01G379700 chr7A 85.075 201 20 9 5636 5831 108238608 108238413 4.610000e-46 196


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 TraesCS6B01G379700 chr6B 654735347 654741177 5830 True 10768.000000 10768 100.000000 1 5831 1 chr6B.!!$R1 5830
1 TraesCS6B01G379700 chr6A 579439794 579444845 5051 True 7485.000000 7485 93.407000 744 5831 1 chr6A.!!$R1 5087
2 TraesCS6B01G379700 chr6A 609958558 609959158 600 False 588.000000 588 84.426000 8 612 1 chr6A.!!$F1 604
3 TraesCS6B01G379700 chr6D 433478495 433484266 5771 True 2686.666667 5029 90.763333 603 5831 3 chr6D.!!$R2 5228
4 TraesCS6B01G379700 chr6D 16768996 16769666 670 False 434.500000 717 88.838500 1 606 2 chr6D.!!$F1 605
5 TraesCS6B01G379700 chr2D 63998309 63998911 602 False 841.000000 841 91.887000 3 604 1 chr2D.!!$F1 601
6 TraesCS6B01G379700 chr2D 107105186 107105773 587 True 706.000000 706 88.226000 3 604 1 chr2D.!!$R1 601
7 TraesCS6B01G379700 chr4A 720084763 720085299 536 True 749.000000 749 91.837000 75 611 1 chr4A.!!$R1 536
8 TraesCS6B01G379700 chr5D 500846552 500847147 595 True 747.000000 747 89.256000 3 604 1 chr5D.!!$R1 601
9 TraesCS6B01G379700 chr7D 73225038 73225633 595 True 713.000000 713 88.284000 3 604 1 chr7D.!!$R1 601
10 TraesCS6B01G379700 chr7D 560894863 560895452 589 True 708.000000 708 88.264000 3 604 1 chr7D.!!$R3 601
11 TraesCS6B01G379700 chr1B 68250396 68250954 558 True 564.000000 564 85.062000 45 606 1 chr1B.!!$R1 561

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
825 916 0.104120 CTGTTCGTGGTGACCAGTGA 59.896 55.000 3.58 2.98 32.78 3.41 F
1410 1501 0.109179 TCGTCGTCATGGTTAACGGG 60.109 55.000 5.01 0.00 39.31 5.28 F
2249 2352 0.457851 AGAAGGAGACGCAGAATCGG 59.542 55.000 0.00 0.00 0.00 4.18 F
2839 2943 2.716217 ACTGGAGCCTTGAACTATTGC 58.284 47.619 0.00 0.00 0.00 3.56 F
3094 3199 3.874383 TTGTCCCTGAACTCAATTGGA 57.126 42.857 5.42 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1987 1.404391 CGGTGCTCAGTTACGTCCTAT 59.596 52.381 0.00 0.00 0.00 2.57 R
3361 3467 1.481772 ACATTGCAGCAAAACAGGTGT 59.518 42.857 12.97 7.97 39.13 4.16 R
3720 3831 2.698274 TCTATATGCAAGGCCACTTCGA 59.302 45.455 5.01 0.00 33.81 3.71 R
4713 4844 3.065648 TCCACAGTTGAACGTTTTAAGGC 59.934 43.478 0.46 0.00 0.00 4.35 R
4927 5064 1.287442 TGGCCTGCCAGGAAATCAATA 59.713 47.619 16.85 0.00 41.89 1.90 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
139 209 1.489560 GGAGGTAGCGGCCCCATATT 61.490 60.000 0.00 0.00 0.00 1.28
155 225 1.548081 TATTGTCTGGTTCCGGTCGA 58.452 50.000 0.00 0.00 0.00 4.20
286 371 0.251653 TGGAGAAGTAGGGCGTCAGT 60.252 55.000 0.00 0.00 0.00 3.41
289 374 1.185618 AGAAGTAGGGCGTCAGTGCA 61.186 55.000 0.00 0.00 36.28 4.57
297 382 2.029288 GCGTCAGTGCAGCAGCTTA 61.029 57.895 1.76 0.00 42.74 3.09
303 388 2.149578 CAGTGCAGCAGCTTAGAACTT 58.850 47.619 1.76 0.00 42.74 2.66
314 399 0.314935 TTAGAACTTCGGCGGTCGTT 59.685 50.000 7.21 8.08 40.32 3.85
333 418 3.838271 GCGTCATCCAGAGGCGGA 61.838 66.667 0.00 0.00 46.68 5.54
416 502 0.179100 ATCTCAATCCAGCGTGACGG 60.179 55.000 7.25 0.00 0.00 4.79
489 575 3.864789 ATCAGTCAAGTCAAACCACCT 57.135 42.857 0.00 0.00 0.00 4.00
712 803 5.606348 AGTAAACATTTTTGAGGGTGCAA 57.394 34.783 0.00 0.00 0.00 4.08
713 804 6.173427 AGTAAACATTTTTGAGGGTGCAAT 57.827 33.333 0.00 0.00 0.00 3.56
714 805 6.591001 AGTAAACATTTTTGAGGGTGCAATT 58.409 32.000 0.00 0.00 0.00 2.32
715 806 7.731054 AGTAAACATTTTTGAGGGTGCAATTA 58.269 30.769 0.00 0.00 0.00 1.40
716 807 7.872483 AGTAAACATTTTTGAGGGTGCAATTAG 59.128 33.333 0.00 0.00 0.00 1.73
719 810 7.716799 ACATTTTTGAGGGTGCAATTAGATA 57.283 32.000 0.00 0.00 0.00 1.98
722 813 2.833794 TGAGGGTGCAATTAGATACGC 58.166 47.619 0.00 0.00 0.00 4.42
725 816 3.988517 GAGGGTGCAATTAGATACGCTAC 59.011 47.826 0.00 0.00 36.61 3.58
755 846 1.476891 TGTCGACTAGGTCTTGATGCC 59.523 52.381 17.92 0.00 0.00 4.40
795 886 1.906333 GCCCCAATGGTCGTGGTTT 60.906 57.895 0.00 0.00 34.01 3.27
803 894 0.531090 TGGTCGTGGTTTTCTGTCCG 60.531 55.000 0.00 0.00 0.00 4.79
825 916 0.104120 CTGTTCGTGGTGACCAGTGA 59.896 55.000 3.58 2.98 32.78 3.41
877 968 1.030457 ACGAAGTCGACCACTCAAGT 58.970 50.000 13.01 0.29 29.74 3.16
882 973 0.319641 GTCGACCACTCAAGTGTCCC 60.320 60.000 3.51 0.00 44.21 4.46
887 978 1.342074 CCACTCAAGTGTCCCTGAGA 58.658 55.000 9.19 0.00 44.21 3.27
888 979 1.694150 CCACTCAAGTGTCCCTGAGAA 59.306 52.381 9.19 0.00 44.21 2.87
1410 1501 0.109179 TCGTCGTCATGGTTAACGGG 60.109 55.000 5.01 0.00 39.31 5.28
1437 1528 1.913419 GGAAGGTGGGTGGAAGATACA 59.087 52.381 0.00 0.00 0.00 2.29
1443 1534 2.832129 GTGGGTGGAAGATACACTCTCA 59.168 50.000 0.00 0.00 40.01 3.27
1468 1559 3.745975 TCTATTTTATTCGCGATGGCCAG 59.254 43.478 13.05 0.00 35.02 4.85
1673 1771 6.808829 TGACTTCAAATTCTGTTGATTTGCT 58.191 32.000 5.03 0.00 37.36 3.91
1676 1774 6.698766 ACTTCAAATTCTGTTGATTTGCTGAC 59.301 34.615 5.03 0.00 37.36 3.51
1710 1808 6.811954 TGAATTGGACCTTTTTAGTTTGGAC 58.188 36.000 0.00 0.00 0.00 4.02
1818 1921 4.698575 GACACTTCAGAGTTCAGAGGTTT 58.301 43.478 0.00 0.00 32.54 3.27
1819 1922 5.104259 ACACTTCAGAGTTCAGAGGTTTT 57.896 39.130 0.00 0.00 32.54 2.43
1846 1949 1.614903 TGCCTTCAGCTGAATGTTTGG 59.385 47.619 28.57 24.59 44.23 3.28
1904 2007 0.806868 TAGGACGTAACTGAGCACCG 59.193 55.000 2.71 0.00 0.00 4.94
2070 2173 6.873605 TGGTAGAACTTGATACACATGTCTTG 59.126 38.462 0.00 0.00 36.16 3.02
2172 2275 5.858381 TGGCTGAAGAGGTATCATCATTAC 58.142 41.667 0.00 0.00 33.01 1.89
2202 2305 4.158025 TGGCAGTGTTCTAGTAGTTCTAGC 59.842 45.833 0.00 0.00 44.10 3.42
2222 2325 4.311816 GCCACTGCTAAAATATGCATGT 57.688 40.909 10.16 0.00 38.59 3.21
2249 2352 0.457851 AGAAGGAGACGCAGAATCGG 59.542 55.000 0.00 0.00 0.00 4.18
2272 2376 6.765989 CGGGGAAATAACAGATCAAACTGATA 59.234 38.462 0.00 0.00 37.20 2.15
2273 2377 7.445402 CGGGGAAATAACAGATCAAACTGATAT 59.555 37.037 0.00 0.00 37.20 1.63
2335 2439 6.208599 AGGAAATTTGCGGAAAATCTCTGTTA 59.791 34.615 6.08 0.00 37.51 2.41
2490 2594 3.973425 AGCTGGCTTAGAACCAATGAAT 58.027 40.909 0.00 0.00 36.56 2.57
2552 2656 7.393515 GTGGAATAAACAAGTAAGATTCAGGGT 59.606 37.037 0.00 0.00 0.00 4.34
2561 2665 8.822805 ACAAGTAAGATTCAGGGTTATCTTGTA 58.177 33.333 0.00 0.00 40.38 2.41
2756 2860 5.625251 CATTTGTCATATCGCCTTGCTATC 58.375 41.667 0.00 0.00 0.00 2.08
2836 2940 6.378280 CCAATTAAACTGGAGCCTTGAACTAT 59.622 38.462 1.48 0.00 35.85 2.12
2839 2943 2.716217 ACTGGAGCCTTGAACTATTGC 58.284 47.619 0.00 0.00 0.00 3.56
2909 3013 9.704098 GAACGAAGTAGCCTAATTTTCTAAATG 57.296 33.333 0.00 0.00 45.00 2.32
2997 3101 5.759059 TCATTTCCTTGCCATAGACTGATT 58.241 37.500 0.00 0.00 0.00 2.57
3003 3107 5.053145 CCTTGCCATAGACTGATTCTACAC 58.947 45.833 0.00 0.00 39.78 2.90
3094 3199 3.874383 TTGTCCCTGAACTCAATTGGA 57.126 42.857 5.42 0.00 0.00 3.53
3096 3201 4.387026 TGTCCCTGAACTCAATTGGAAT 57.613 40.909 5.42 0.00 0.00 3.01
3335 3441 7.502226 GGGAAATTCATGTACCAACTCATGATA 59.498 37.037 0.00 2.17 46.03 2.15
3473 3579 8.318412 TGCAAATATAACATATGACCGTATCCT 58.682 33.333 10.38 0.00 0.00 3.24
3564 3671 9.553064 AGGCTACTTCATATTTTTATGTCTCAG 57.447 33.333 0.00 0.00 0.00 3.35
3639 3749 9.013490 GTATGTCATTAGATGCACATTTGAAAC 57.987 33.333 0.00 0.00 34.86 2.78
4101 4216 7.363705 CCCTGAAGGTAACAATCATTGCAATTA 60.364 37.037 9.83 1.64 41.41 1.40
4296 4425 5.384063 AATACTGATCAGAGAGTATGGCG 57.616 43.478 29.27 0.00 35.89 5.69
4361 4491 5.009854 ACTGGTTTTCCACTTTGACATTG 57.990 39.130 0.00 0.00 46.22 2.82
4683 4814 5.945191 TGGTGCATGATTTCTGAATTCTACA 59.055 36.000 7.05 6.26 0.00 2.74
4713 4844 8.292448 ACAAATAGTGTCACTAAATTGCAAGAG 58.708 33.333 26.33 4.77 34.38 2.85
4861 4996 5.560724 CCAGTCTCACCTATTCTTTCCAAA 58.439 41.667 0.00 0.00 0.00 3.28
5026 5177 0.320374 TGTAGACTTGAGTTGGGCCG 59.680 55.000 0.00 0.00 0.00 6.13
5145 5300 3.577848 TGGAACAATGCTTGGTGCTAAAT 59.422 39.130 6.91 0.00 39.69 1.40
5146 5301 3.928375 GGAACAATGCTTGGTGCTAAATG 59.072 43.478 0.00 0.00 43.37 2.32
5147 5302 4.559153 GAACAATGCTTGGTGCTAAATGT 58.441 39.130 1.84 0.00 43.37 2.71
5178 5337 3.101437 TGTTACTGGGTGATGACCGTAT 58.899 45.455 0.00 0.00 44.23 3.06
5184 5343 3.578716 CTGGGTGATGACCGTATAAGGAT 59.421 47.826 12.02 0.00 44.23 3.24
5187 5346 4.755123 GGGTGATGACCGTATAAGGATTTG 59.245 45.833 12.02 0.00 44.23 2.32
5223 5383 4.261197 GTTTGCCAAACTACTGAAGACCAG 60.261 45.833 12.98 0.00 42.04 4.00
5250 5981 5.357257 AGTTTGTCTGTTGATAACGTCTGT 58.643 37.500 0.00 0.00 0.00 3.41
5259 5990 6.893759 TGTTGATAACGTCTGTTTTGTATGG 58.106 36.000 0.00 0.00 39.54 2.74
5267 5998 4.517453 CGTCTGTTTTGTATGGGGAAAGAA 59.483 41.667 0.00 0.00 0.00 2.52
5311 6046 2.119457 CGCAAACTCAGCTGGAAAAAC 58.881 47.619 15.13 0.00 0.00 2.43
5431 6166 2.443016 CTCCTCCCCTCCTGACCG 60.443 72.222 0.00 0.00 0.00 4.79
5459 6194 2.175499 CCTCCCTTGGCAATCTTCCATA 59.825 50.000 0.00 0.00 32.92 2.74
5463 6198 2.621998 CCTTGGCAATCTTCCATAGCTG 59.378 50.000 0.00 0.00 32.92 4.24
5506 6252 2.557924 CAGGAGCATAGCCTAGAGACAG 59.442 54.545 0.00 0.00 33.51 3.51
5507 6253 2.445145 AGGAGCATAGCCTAGAGACAGA 59.555 50.000 0.00 0.00 32.92 3.41
5508 6254 2.556622 GGAGCATAGCCTAGAGACAGAC 59.443 54.545 0.00 0.00 0.00 3.51
5509 6255 3.218453 GAGCATAGCCTAGAGACAGACA 58.782 50.000 0.00 0.00 0.00 3.41
5526 6272 2.239907 AGACATTAGGGAGGACCAAAGC 59.760 50.000 0.00 0.00 43.89 3.51
5533 6279 0.174617 GGAGGACCAAAGCGAGAGAG 59.825 60.000 0.00 0.00 35.97 3.20
5534 6280 0.174617 GAGGACCAAAGCGAGAGAGG 59.825 60.000 0.00 0.00 0.00 3.69
5538 6284 1.261238 ACCAAAGCGAGAGAGGGAGG 61.261 60.000 0.00 0.00 0.00 4.30
5547 6293 2.666317 GAGAGAGGGAGGAGAAAGGAG 58.334 57.143 0.00 0.00 0.00 3.69
5555 6311 2.397597 GAGGAGAAAGGAGGCTGATCT 58.602 52.381 0.00 0.00 0.00 2.75
5557 6313 2.114616 GGAGAAAGGAGGCTGATCTGA 58.885 52.381 3.42 0.00 0.00 3.27
5558 6314 2.102925 GGAGAAAGGAGGCTGATCTGAG 59.897 54.545 3.42 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.717629 CGCGCGAAGACAGGGACA 62.718 66.667 28.94 0.00 0.00 4.02
139 209 0.245539 GATTCGACCGGAACCAGACA 59.754 55.000 9.46 0.00 37.50 3.41
155 225 2.125106 GCCGCCGAACTCTGGATT 60.125 61.111 0.00 0.00 0.00 3.01
286 371 1.432514 CGAAGTTCTAAGCTGCTGCA 58.567 50.000 18.42 0.88 42.74 4.41
289 374 0.737715 CGCCGAAGTTCTAAGCTGCT 60.738 55.000 0.00 0.00 0.00 4.24
297 382 1.663702 CAACGACCGCCGAAGTTCT 60.664 57.895 0.56 0.00 41.76 3.01
314 399 4.147449 CGCCTCTGGATGACGCCA 62.147 66.667 0.00 0.00 36.30 5.69
397 483 0.179100 CCGTCACGCTGGATTGAGAT 60.179 55.000 0.00 0.00 0.00 2.75
416 502 3.775654 CTGCGGGTGAGTCTCCCC 61.776 72.222 21.97 14.91 41.78 4.81
639 729 5.241728 GGCCTAGATAACCAATCCATTGAAC 59.758 44.000 0.00 0.00 40.14 3.18
645 735 6.584471 TTTAAGGCCTAGATAACCAATCCA 57.416 37.500 5.16 0.00 34.90 3.41
703 794 3.113260 AGCGTATCTAATTGCACCCTC 57.887 47.619 0.00 0.00 0.00 4.30
722 813 1.007336 GTCGACACACAAGGGCGTAG 61.007 60.000 11.55 0.00 0.00 3.51
725 816 0.732880 CTAGTCGACACACAAGGGCG 60.733 60.000 19.50 0.00 0.00 6.13
755 846 2.028112 TCAGATTCGAGGAACCAAGTGG 60.028 50.000 0.00 0.00 42.17 4.00
795 886 4.966005 CGAACAGCTCGGACAGAA 57.034 55.556 0.00 0.00 44.20 3.02
803 894 1.069090 TGGTCACCACGAACAGCTC 59.931 57.895 0.00 0.00 36.00 4.09
825 916 0.035317 TCGTCTTGCTGACATGGCTT 59.965 50.000 0.00 0.00 45.60 4.35
877 968 2.746697 AGAAGCGTTCTCAGGGACA 58.253 52.632 0.00 0.00 34.07 4.02
887 978 2.022129 CGAACGGCTGAGAAGCGTT 61.022 57.895 0.00 0.00 35.51 4.84
888 979 2.214181 ATCGAACGGCTGAGAAGCGT 62.214 55.000 0.00 0.00 35.24 5.07
1237 1328 2.262774 AAATCCAGCCTCTCGCCTGG 62.263 60.000 0.31 0.31 38.78 4.45
1383 1474 0.249073 CCATGACGACGAGGTGATCC 60.249 60.000 0.00 0.00 0.00 3.36
1410 1501 1.218316 CACCCACCTTCCGTAGAGC 59.782 63.158 0.00 0.00 0.00 4.09
1437 1528 6.561614 TCGCGAATAAAATAGAAGTGAGAGT 58.438 36.000 6.20 0.00 0.00 3.24
1443 1534 4.213482 GGCCATCGCGAATAAAATAGAAGT 59.787 41.667 15.24 0.00 35.02 3.01
1468 1559 9.017669 CACGACTCAGTTAATATACCAAACTAC 57.982 37.037 0.00 0.00 32.35 2.73
1641 1739 6.263516 ACAGAATTTGAAGTCATGGATGTG 57.736 37.500 0.00 0.00 0.00 3.21
1673 1771 5.543405 AGGTCCAATTCATTCCAAAATGTCA 59.457 36.000 0.00 0.00 42.46 3.58
1676 1774 7.748691 AAAAGGTCCAATTCATTCCAAAATG 57.251 32.000 0.00 0.00 43.10 2.32
1722 1820 6.684897 TTAGCTAGGTTTTACAGTAACCCA 57.315 37.500 0.00 0.00 44.96 4.51
1818 1921 1.977854 TCAGCTGAAGGCAAGTCCTAA 59.022 47.619 15.67 0.00 46.94 2.69
1819 1922 1.644509 TCAGCTGAAGGCAAGTCCTA 58.355 50.000 15.67 0.00 46.94 2.94
1884 1987 1.404391 CGGTGCTCAGTTACGTCCTAT 59.596 52.381 0.00 0.00 0.00 2.57
1904 2007 3.378112 TGCAGTTATATTTGCAGTGGCTC 59.622 43.478 7.39 0.00 44.72 4.70
2070 2173 8.718102 TCACTACCTGCTCAGATAAATTTTAC 57.282 34.615 0.00 0.00 0.00 2.01
2172 2275 3.733337 ACTAGAACACTGCCAAAGTCAG 58.267 45.455 0.00 0.00 36.83 3.51
2202 2305 5.653507 ACAACATGCATATTTTAGCAGTGG 58.346 37.500 0.00 0.00 44.94 4.00
2222 2325 4.077108 TCTGCGTCTCCTTCTAAGTACAA 58.923 43.478 0.00 0.00 0.00 2.41
2335 2439 3.159213 TCCACCAAGTGAATGAGCAAT 57.841 42.857 0.00 0.00 35.23 3.56
2490 2594 1.804151 GGTGTAGCTGACGCAATGAAA 59.196 47.619 0.00 0.00 40.59 2.69
2552 2656 5.509498 ACCCCAGTACTACGTACAAGATAA 58.491 41.667 0.00 0.00 41.03 1.75
2756 2860 8.461222 TGTTCATGAGCTATTTGTCCATTTTAG 58.539 33.333 11.09 0.00 0.00 1.85
2909 3013 9.890352 GAATTATAAGTGAGAAATGATGCCTTC 57.110 33.333 0.00 0.00 0.00 3.46
2921 3025 9.442062 TGGGTATTGTAGGAATTATAAGTGAGA 57.558 33.333 0.00 0.00 0.00 3.27
2982 3086 5.675684 TGTGTAGAATCAGTCTATGGCAA 57.324 39.130 0.00 0.00 41.00 4.52
2997 3101 7.037586 AGGAGGAAACCATAAAAGATGTGTAGA 60.038 37.037 0.00 0.00 0.00 2.59
3003 3107 5.951747 TGGAAGGAGGAAACCATAAAAGATG 59.048 40.000 0.00 0.00 0.00 2.90
3361 3467 1.481772 ACATTGCAGCAAAACAGGTGT 59.518 42.857 12.97 7.97 39.13 4.16
3623 3730 6.477688 CAGAAAGTTGTTTCAAATGTGCATCT 59.522 34.615 0.00 0.00 44.08 2.90
3682 3793 9.458374 AACTTTGACTTATAATTTTGGTCAACG 57.542 29.630 13.73 14.06 43.50 4.10
3720 3831 2.698274 TCTATATGCAAGGCCACTTCGA 59.302 45.455 5.01 0.00 33.81 3.71
4101 4216 3.384467 AGCTTAAAACACCACAGCACATT 59.616 39.130 0.00 0.00 32.58 2.71
4130 4245 9.747898 TCTATCCCAGCTTTATTAAAAGAACAA 57.252 29.630 2.15 0.00 44.14 2.83
4271 4394 6.703607 CGCCATACTCTCTGATCAGTATTTTT 59.296 38.462 21.92 6.16 34.22 1.94
4296 4425 8.712285 TTAAAAGGACAGTATATACAGTGCAC 57.288 34.615 24.77 9.40 36.70 4.57
4361 4491 7.164122 TCATCTCCTCTGCAATAATAATGTCC 58.836 38.462 0.00 0.00 0.00 4.02
4585 4716 7.119262 CAGGTACCGATTAGTTCAAAAGACAAT 59.881 37.037 6.18 0.00 0.00 2.71
4654 4785 7.994911 AGAATTCAGAAATCATGCACCACTATA 59.005 33.333 8.44 0.00 0.00 1.31
4655 4786 6.832384 AGAATTCAGAAATCATGCACCACTAT 59.168 34.615 8.44 0.00 0.00 2.12
4713 4844 3.065648 TCCACAGTTGAACGTTTTAAGGC 59.934 43.478 0.46 0.00 0.00 4.35
4927 5064 1.287442 TGGCCTGCCAGGAAATCAATA 59.713 47.619 16.85 0.00 41.89 1.90
5145 5300 7.727578 TCACCCAGTAACAGAAGATATAACA 57.272 36.000 0.00 0.00 0.00 2.41
5146 5301 8.421784 TCATCACCCAGTAACAGAAGATATAAC 58.578 37.037 0.00 0.00 0.00 1.89
5147 5302 8.421784 GTCATCACCCAGTAACAGAAGATATAA 58.578 37.037 0.00 0.00 0.00 0.98
5201 5360 3.882888 CTGGTCTTCAGTAGTTTGGCAAA 59.117 43.478 8.93 8.93 38.64 3.68
5205 5364 3.070018 CTGCTGGTCTTCAGTAGTTTGG 58.930 50.000 3.51 0.00 46.68 3.28
5237 5398 5.413213 CCCCATACAAAACAGACGTTATCAA 59.587 40.000 0.00 0.00 33.99 2.57
5250 5981 6.042552 TGCTCATTTTCTTTCCCCATACAAAA 59.957 34.615 0.00 0.00 0.00 2.44
5259 5990 5.184671 ACAGATTCTGCTCATTTTCTTTCCC 59.815 40.000 13.64 0.00 34.37 3.97
5267 5998 3.755378 GTGACCACAGATTCTGCTCATTT 59.245 43.478 13.64 0.00 34.37 2.32
5311 6046 5.154222 GCTCTTACAAAGGGAATGTTTTCG 58.846 41.667 0.00 0.00 32.28 3.46
5431 6166 2.129555 TTGCCAAGGGAGGAGCTGTC 62.130 60.000 0.00 0.00 0.00 3.51
5459 6194 1.493871 CTCCCAAGGATCATTCCAGCT 59.506 52.381 0.00 0.00 45.30 4.24
5463 6198 3.320256 GCAATTCTCCCAAGGATCATTCC 59.680 47.826 0.00 0.00 42.96 3.01
5467 6210 2.357465 CCTGCAATTCTCCCAAGGATCA 60.357 50.000 0.00 0.00 0.00 2.92
5468 6211 2.092212 TCCTGCAATTCTCCCAAGGATC 60.092 50.000 0.00 0.00 0.00 3.36
5469 6212 1.925255 TCCTGCAATTCTCCCAAGGAT 59.075 47.619 0.00 0.00 0.00 3.24
5470 6213 1.283029 CTCCTGCAATTCTCCCAAGGA 59.717 52.381 0.00 0.00 0.00 3.36
5506 6252 2.644676 GCTTTGGTCCTCCCTAATGTC 58.355 52.381 0.00 0.00 0.00 3.06
5507 6253 1.065418 CGCTTTGGTCCTCCCTAATGT 60.065 52.381 0.00 0.00 0.00 2.71
5508 6254 1.209504 TCGCTTTGGTCCTCCCTAATG 59.790 52.381 0.00 0.00 0.00 1.90
5509 6255 1.486726 CTCGCTTTGGTCCTCCCTAAT 59.513 52.381 0.00 0.00 0.00 1.73
5526 6272 1.064314 TCCTTTCTCCTCCCTCTCTCG 60.064 57.143 0.00 0.00 0.00 4.04
5533 6279 0.618968 TCAGCCTCCTTTCTCCTCCC 60.619 60.000 0.00 0.00 0.00 4.30
5534 6280 1.416030 GATCAGCCTCCTTTCTCCTCC 59.584 57.143 0.00 0.00 0.00 4.30
5538 6284 2.483538 GCTCAGATCAGCCTCCTTTCTC 60.484 54.545 0.00 0.00 32.76 2.87
5547 6293 1.524165 CAGCCAGCTCAGATCAGCC 60.524 63.158 1.57 0.00 40.65 4.85
5587 6343 1.227383 CTGTACTTGCCCATCCCCC 59.773 63.158 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.