Multiple sequence alignment - TraesCS6A01G126900

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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 TraesCS6A01G126900 chr6A 100.000 4364 0 0 1 4364 100230130 100225767 0.000000e+00 8059.0
1 TraesCS6A01G126900 chr6A 84.866 2491 341 25 1078 3559 100738076 100740539 0.000000e+00 2479.0
2 TraesCS6A01G126900 chr6A 85.745 2357 319 12 1263 3606 100797548 100799900 0.000000e+00 2475.0
3 TraesCS6A01G126900 chr6A 83.862 2429 366 18 1199 3606 100755377 100757800 0.000000e+00 2290.0
4 TraesCS6A01G126900 chr6A 85.537 242 25 5 3928 4161 100800037 100800276 1.210000e-60 244.0
5 TraesCS6A01G126900 chr6A 92.537 134 10 0 4158 4291 100800437 100800570 4.450000e-45 193.0
6 TraesCS6A01G126900 chr6A 91.791 134 11 0 4158 4291 100758355 100758488 2.070000e-43 187.0
7 TraesCS6A01G126900 chr6A 76.031 388 52 24 55 418 100754090 100754460 3.490000e-36 163.0
8 TraesCS6A01G126900 chr6A 96.000 75 1 1 3607 3679 501014592 501014518 2.130000e-23 121.0
9 TraesCS6A01G126900 chr6D 95.221 3264 116 16 363 3606 83161307 83158064 0.000000e+00 5127.0
10 TraesCS6A01G126900 chr6D 83.229 2391 378 23 1179 3559 83046947 83044570 0.000000e+00 2172.0
11 TraesCS6A01G126900 chr6D 84.000 1825 278 12 1199 3018 83525237 83527052 0.000000e+00 1740.0
12 TraesCS6A01G126900 chr6D 90.671 343 26 6 3672 4009 83158087 83157746 6.660000e-123 451.0
13 TraesCS6A01G126900 chr6D 90.343 321 22 5 6 325 83161619 83161307 3.140000e-111 412.0
14 TraesCS6A01G126900 chr6D 95.673 208 7 2 4158 4364 83156368 83156162 2.520000e-87 333.0
15 TraesCS6A01G126900 chr6D 77.149 442 58 25 6 424 83523885 83524306 2.640000e-52 217.0
16 TraesCS6A01G126900 chr6D 96.053 76 1 1 3606 3679 95118124 95118049 5.930000e-24 122.0
17 TraesCS6A01G126900 chr6D 95.122 41 1 1 4252 4291 83527421 83527461 3.640000e-06 63.9
18 TraesCS6A01G126900 chr6B 96.179 2800 97 7 691 3485 158163584 158160790 0.000000e+00 4569.0
19 TraesCS6A01G126900 chr6B 84.279 2519 348 27 1050 3559 159377793 159380272 0.000000e+00 2414.0
20 TraesCS6A01G126900 chr6B 84.268 2282 339 19 1262 3536 159395982 159398250 0.000000e+00 2207.0
21 TraesCS6A01G126900 chr6B 90.909 726 31 16 6 706 158165550 158164835 0.000000e+00 942.0
22 TraesCS6A01G126900 chr6B 85.748 421 30 11 3678 4095 158153211 158152818 6.750000e-113 418.0
23 TraesCS6A01G126900 chr6B 77.252 444 57 26 6 424 159394057 159394481 2.040000e-53 220.0
24 TraesCS6A01G126900 chr6B 85.987 157 10 7 4210 4364 158152778 158152632 1.620000e-34 158.0
25 TraesCS6A01G126900 chr3B 94.602 352 18 1 3255 3606 680860917 680860567 1.070000e-150 544.0
26 TraesCS6A01G126900 chr7D 96.053 76 1 1 3606 3679 224440068 224440143 5.930000e-24 122.0
27 TraesCS6A01G126900 chr7D 96.000 75 1 1 3607 3679 366101819 366101893 2.130000e-23 121.0
28 TraesCS6A01G126900 chr5D 88.182 110 4 2 466 566 455825408 455825299 5.930000e-24 122.0
29 TraesCS6A01G126900 chr5D 96.000 75 1 1 3607 3679 348295768 348295694 2.130000e-23 121.0
30 TraesCS6A01G126900 chr5D 94.805 77 2 1 3605 3679 301720568 301720492 7.670000e-23 119.0
31 TraesCS6A01G126900 chr4D 95.946 74 1 1 3608 3679 359240312 359240239 7.670000e-23 119.0
32 TraesCS6A01G126900 chr3D 95.890 73 1 1 3606 3676 175837109 175837181 2.760000e-22 117.0
33 TraesCS6A01G126900 chr3D 95.890 73 1 1 3606 3676 176106133 176106205 2.760000e-22 117.0


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 TraesCS6A01G126900 chr6A 100225767 100230130 4363 True 8059.000000 8059 100.000000 1 4364 1 chr6A.!!$R1 4363
1 TraesCS6A01G126900 chr6A 100738076 100740539 2463 False 2479.000000 2479 84.866000 1078 3559 1 chr6A.!!$F1 2481
2 TraesCS6A01G126900 chr6A 100797548 100800570 3022 False 970.666667 2475 87.939667 1263 4291 3 chr6A.!!$F3 3028
3 TraesCS6A01G126900 chr6A 100754090 100758488 4398 False 880.000000 2290 83.894667 55 4291 3 chr6A.!!$F2 4236
4 TraesCS6A01G126900 chr6D 83044570 83046947 2377 True 2172.000000 2172 83.229000 1179 3559 1 chr6D.!!$R1 2380
5 TraesCS6A01G126900 chr6D 83156162 83161619 5457 True 1580.750000 5127 92.977000 6 4364 4 chr6D.!!$R3 4358
6 TraesCS6A01G126900 chr6D 83523885 83527461 3576 False 673.633333 1740 85.423667 6 4291 3 chr6D.!!$F1 4285
7 TraesCS6A01G126900 chr6B 158160790 158165550 4760 True 2755.500000 4569 93.544000 6 3485 2 chr6B.!!$R2 3479
8 TraesCS6A01G126900 chr6B 159377793 159380272 2479 False 2414.000000 2414 84.279000 1050 3559 1 chr6B.!!$F1 2509
9 TraesCS6A01G126900 chr6B 159394057 159398250 4193 False 1213.500000 2207 80.760000 6 3536 2 chr6B.!!$F2 3530
10 TraesCS6A01G126900 chr6B 158152632 158153211 579 True 288.000000 418 85.867500 3678 4364 2 chr6B.!!$R1 686

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
868 2608 0.108186 ACATCTCGCGAATCTGCCAA 60.108 50.0 11.33 0.0 0.0 4.52 F
1686 3784 0.974010 CAACCCCTACACGGCCTCTA 60.974 60.0 0.00 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 4012 0.035317 TGTTGTAGCCAGCACAGAGG 59.965 55.0 0.0 0.0 0.00 3.69 R
3615 5737 0.115152 AAGGGGGAAGCCCTTCTTTG 59.885 55.0 0.0 0.0 43.38 2.77 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
162 177 2.239402 TGGCACAGCTTCTCATCCAATA 59.761 45.455 0.00 0.00 0.00 1.90
283 320 6.208797 GGTTTAAGGAAAAGGATGTAGCTGTT 59.791 38.462 0.00 0.00 0.00 3.16
285 322 3.600388 AGGAAAAGGATGTAGCTGTTCG 58.400 45.455 0.00 0.00 0.00 3.95
296 333 6.755141 GGATGTAGCTGTTCGACAAATAAGTA 59.245 38.462 0.00 0.00 34.04 2.24
395 445 1.486726 GGGTAGGTGTGCATAGCTTCT 59.513 52.381 20.50 0.00 31.05 2.85
449 898 6.600882 ACCGACTAAATGAAACTAGGAAGA 57.399 37.500 0.00 0.00 0.00 2.87
463 912 7.800300 AACTAGGAAGATAGGACAAGACTTT 57.200 36.000 0.00 0.00 0.00 2.66
544 1002 0.935898 GATGCTGGATGCTGAGAACG 59.064 55.000 0.00 0.00 43.37 3.95
547 1008 1.975363 GCTGGATGCTGAGAACGTGC 61.975 60.000 0.00 0.00 38.95 5.34
578 1049 2.757868 GAGCTAGTCGAGGCCATATGAT 59.242 50.000 5.01 0.00 0.00 2.45
582 1053 3.883830 AGTCGAGGCCATATGATGATC 57.116 47.619 5.01 0.00 0.00 2.92
833 2572 3.555547 TCTCCAAATCATGTACGCGAATG 59.444 43.478 15.93 13.82 0.00 2.67
868 2608 0.108186 ACATCTCGCGAATCTGCCAA 60.108 50.000 11.33 0.00 0.00 4.52
1134 2879 1.202940 AGAGCAGGTTGTTCCTTTCCC 60.203 52.381 0.00 0.00 45.67 3.97
1139 2884 1.071857 AGGTTGTTCCTTTCCCGTCTC 59.928 52.381 0.00 0.00 45.67 3.36
1233 3331 2.787473 TTCTCGAGGAAACCATGCAT 57.213 45.000 13.56 0.00 0.00 3.96
1406 3504 1.751544 GCCTCACAGCATCATGGCA 60.752 57.895 0.00 0.00 40.04 4.92
1416 3514 1.402968 GCATCATGGCAAATCGACACT 59.597 47.619 0.00 0.00 33.05 3.55
1460 3558 2.237143 TCACCTGCAACCAAGATAGGAG 59.763 50.000 0.00 0.00 32.86 3.69
1571 3669 2.636412 CCCAGAACTCGCTGTCCGA 61.636 63.158 0.00 0.00 45.15 4.55
1675 3773 1.992557 AGTTGCCATCTTCAACCCCTA 59.007 47.619 2.65 0.00 43.45 3.53
1686 3784 0.974010 CAACCCCTACACGGCCTCTA 60.974 60.000 0.00 0.00 0.00 2.43
1914 4012 4.091365 GGTAATTGCTTGGCGTTGAAATTC 59.909 41.667 0.00 0.00 0.00 2.17
1918 4016 1.541588 GCTTGGCGTTGAAATTCCTCT 59.458 47.619 0.00 0.00 0.00 3.69
2011 4109 5.640732 TCTCGTTACCTAACAATCGGTTAC 58.359 41.667 0.00 0.00 40.96 2.50
2037 4135 2.689471 AGCGCTAAATGGCATCATCAAA 59.311 40.909 8.99 0.00 32.24 2.69
2464 4563 7.762615 CCCTTACAAATATCACGAGAACACTTA 59.237 37.037 0.00 0.00 0.00 2.24
2676 4775 2.094545 GCAAGGCAATCAACTAACTGGG 60.095 50.000 0.00 0.00 0.00 4.45
2862 4962 9.645128 TTCAGTCCATTTATCCAATACATCAAT 57.355 29.630 0.00 0.00 0.00 2.57
3131 5231 5.607939 TCTAATAATGACTTCGAAGGCCA 57.392 39.130 27.85 23.28 31.13 5.36
3183 5284 4.428294 TCCAGATTCTAGCTTTGATGGG 57.572 45.455 0.00 0.00 0.00 4.00
3259 5360 2.069273 GTCCAGAGTTCATCAACACCG 58.931 52.381 0.00 0.00 34.60 4.94
3284 5385 2.973945 AGAGATTGGCCGTAAAGTCAC 58.026 47.619 0.00 0.00 0.00 3.67
3377 5479 4.577834 TTGGCTAAAACCTTGTAACTGC 57.422 40.909 0.00 0.00 0.00 4.40
3411 5522 4.771590 AACCGTTACGTGATCTCAAGTA 57.228 40.909 3.52 2.44 39.24 2.24
3501 5613 5.779922 TGCTATCTTGAGTTAGTGACGTTT 58.220 37.500 0.00 0.00 0.00 3.60
3551 5664 3.138304 TGATTAGCAAGTGAGCAACGTT 58.862 40.909 0.00 0.00 36.85 3.99
3559 5672 3.173668 AGTGAGCAACGTTAACAGTGA 57.826 42.857 0.00 0.00 0.00 3.41
3561 5674 1.864711 TGAGCAACGTTAACAGTGAGC 59.135 47.619 0.00 11.67 0.00 4.26
3563 5676 2.480419 GAGCAACGTTAACAGTGAGCAT 59.520 45.455 19.62 11.31 0.00 3.79
3564 5677 2.480419 AGCAACGTTAACAGTGAGCATC 59.520 45.455 19.62 3.33 0.00 3.91
3588 5710 9.905713 ATCATTGTACTCCATGTAACTATTTGT 57.094 29.630 0.00 0.00 32.25 2.83
3630 5752 5.738619 TTTTTATCAAAGAAGGGCTTCCC 57.261 39.130 0.00 0.00 45.90 3.97
3640 5762 3.007542 GGCTTCCCCCTTCCGATT 58.992 61.111 0.00 0.00 0.00 3.34
3641 5763 1.306633 GGCTTCCCCCTTCCGATTT 59.693 57.895 0.00 0.00 0.00 2.17
3642 5764 0.324368 GGCTTCCCCCTTCCGATTTT 60.324 55.000 0.00 0.00 0.00 1.82
3643 5765 1.103803 GCTTCCCCCTTCCGATTTTC 58.896 55.000 0.00 0.00 0.00 2.29
3644 5766 1.615919 GCTTCCCCCTTCCGATTTTCA 60.616 52.381 0.00 0.00 0.00 2.69
3645 5767 2.950418 GCTTCCCCCTTCCGATTTTCAT 60.950 50.000 0.00 0.00 0.00 2.57
3646 5768 3.365472 CTTCCCCCTTCCGATTTTCATT 58.635 45.455 0.00 0.00 0.00 2.57
3647 5769 4.532834 CTTCCCCCTTCCGATTTTCATTA 58.467 43.478 0.00 0.00 0.00 1.90
3648 5770 3.893521 TCCCCCTTCCGATTTTCATTAC 58.106 45.455 0.00 0.00 0.00 1.89
3649 5771 3.526019 TCCCCCTTCCGATTTTCATTACT 59.474 43.478 0.00 0.00 0.00 2.24
3650 5772 3.632145 CCCCCTTCCGATTTTCATTACTG 59.368 47.826 0.00 0.00 0.00 2.74
3651 5773 4.523083 CCCCTTCCGATTTTCATTACTGA 58.477 43.478 0.00 0.00 0.00 3.41
3652 5774 4.947388 CCCCTTCCGATTTTCATTACTGAA 59.053 41.667 0.00 0.00 39.62 3.02
3653 5775 5.417580 CCCCTTCCGATTTTCATTACTGAAA 59.582 40.000 4.26 4.26 46.92 2.69
3664 5786 6.869315 TTCATTACTGAAAACCAACATCGA 57.131 33.333 0.00 0.00 38.43 3.59
3665 5787 6.236017 TCATTACTGAAAACCAACATCGAC 57.764 37.500 0.00 0.00 0.00 4.20
3666 5788 5.180492 TCATTACTGAAAACCAACATCGACC 59.820 40.000 0.00 0.00 0.00 4.79
3667 5789 2.925724 ACTGAAAACCAACATCGACCA 58.074 42.857 0.00 0.00 0.00 4.02
3668 5790 3.283751 ACTGAAAACCAACATCGACCAA 58.716 40.909 0.00 0.00 0.00 3.67
3669 5791 3.697045 ACTGAAAACCAACATCGACCAAA 59.303 39.130 0.00 0.00 0.00 3.28
3670 5792 4.202010 ACTGAAAACCAACATCGACCAAAG 60.202 41.667 0.00 0.00 0.00 2.77
3671 5793 3.697045 TGAAAACCAACATCGACCAAAGT 59.303 39.130 0.00 0.00 0.00 2.66
3672 5794 4.882427 TGAAAACCAACATCGACCAAAGTA 59.118 37.500 0.00 0.00 0.00 2.24
3673 5795 5.533154 TGAAAACCAACATCGACCAAAGTAT 59.467 36.000 0.00 0.00 0.00 2.12
3674 5796 6.039941 TGAAAACCAACATCGACCAAAGTATT 59.960 34.615 0.00 0.00 0.00 1.89
3675 5797 6.399639 AAACCAACATCGACCAAAGTATTT 57.600 33.333 0.00 0.00 40.26 1.40
3696 5818 9.946165 GTATTTGCCAGTATTTACTTTGATACC 57.054 33.333 0.00 0.00 33.46 2.73
3722 5844 5.263599 TGCATAGGGTGATGAATGTTTCTT 58.736 37.500 0.00 0.00 0.00 2.52
3726 5848 7.577426 GCATAGGGTGATGAATGTTTCTTTTGA 60.577 37.037 0.00 0.00 0.00 2.69
3744 5872 5.762179 TTTGATAGTTGACCAGAGGACAT 57.238 39.130 0.00 0.00 0.00 3.06
3750 5878 8.588472 TGATAGTTGACCAGAGGACATATAATG 58.412 37.037 0.00 0.00 0.00 1.90
3765 5893 6.208644 ACATATAATGAGCAAAATCGCCAAC 58.791 36.000 0.00 0.00 0.00 3.77
3794 5922 2.260247 GCAATCTGCAGTCTGGCAA 58.740 52.632 14.67 0.00 44.40 4.52
3798 5926 1.531423 ATCTGCAGTCTGGCAAACTG 58.469 50.000 16.57 16.57 44.40 3.16
3821 5950 7.119846 ACTGAAATCTGTAACTATTTGCAGTCC 59.880 37.037 10.02 1.36 43.79 3.85
3905 6034 5.839262 TTGTGTAACTATTTGCAGACTCG 57.161 39.130 0.00 0.00 38.04 4.18
3906 6035 3.678072 TGTGTAACTATTTGCAGACTCGC 59.322 43.478 0.00 0.00 38.04 5.03
3953 6082 1.597742 CCAGGGTCGCAATTATCCAG 58.402 55.000 0.00 0.00 0.00 3.86
3957 6086 2.366916 AGGGTCGCAATTATCCAGAGAG 59.633 50.000 0.00 0.00 0.00 3.20
3958 6087 2.548920 GGGTCGCAATTATCCAGAGAGG 60.549 54.545 0.00 0.00 39.47 3.69
4043 7270 1.676967 CAGCTGCTCCCTGGTTTCC 60.677 63.158 0.00 0.00 0.00 3.13
4045 7272 1.000396 GCTGCTCCCTGGTTTCCAT 60.000 57.895 0.00 0.00 30.82 3.41
4057 7286 4.127171 CTGGTTTCCATAATACCTCGGTG 58.873 47.826 0.00 0.00 30.82 4.94
4095 7324 1.153147 GGCCTTGGTCGAATCTCCC 60.153 63.158 0.00 0.00 0.00 4.30
4138 7367 4.754667 GACCAACGGAGGCGGGAC 62.755 72.222 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.336667 CACGTCATGTGCACTATGTCA 58.663 47.619 19.41 0.00 42.70 3.58
143 158 5.279384 CAATTATTGGATGAGAAGCTGTGC 58.721 41.667 0.00 0.00 0.00 4.57
162 177 7.069331 TGGTGTATGTTGTTCTCTTTTCCAATT 59.931 33.333 0.00 0.00 0.00 2.32
174 192 6.910433 CAGTAAACAAGTGGTGTATGTTGTTC 59.090 38.462 0.15 0.00 41.19 3.18
175 193 6.376018 ACAGTAAACAAGTGGTGTATGTTGTT 59.624 34.615 0.00 0.00 43.30 2.83
296 333 5.385198 TGAGCAGGTCAAAACTATTTTCCT 58.615 37.500 0.00 0.00 33.32 3.36
309 357 1.476833 GGGTTTGACTTGAGCAGGTCA 60.477 52.381 10.85 10.85 44.17 4.02
327 375 1.143073 GCCTACAGGGGTTAGATTGGG 59.857 57.143 0.00 0.00 35.18 4.12
434 882 8.261522 GTCTTGTCCTATCTTCCTAGTTTCATT 58.738 37.037 0.00 0.00 0.00 2.57
449 898 5.333566 TTTCCCCAAAAGTCTTGTCCTAT 57.666 39.130 0.00 0.00 0.00 2.57
463 912 3.007831 GCTTGGTCAAATGATTTCCCCAA 59.992 43.478 13.89 13.89 31.97 4.12
544 1002 2.734079 GACTAGCTCTTCAAGTGTGCAC 59.266 50.000 10.75 10.75 0.00 4.57
547 1008 3.497118 CTCGACTAGCTCTTCAAGTGTG 58.503 50.000 0.00 0.00 0.00 3.82
578 1049 7.800155 TGATGGAATAATTTGTTAGCGATCA 57.200 32.000 0.00 0.00 0.00 2.92
582 1053 6.559810 TGGTTGATGGAATAATTTGTTAGCG 58.440 36.000 0.00 0.00 0.00 4.26
783 2522 0.192566 TGAGGTAGGTGAAGGGGTGT 59.807 55.000 0.00 0.00 0.00 4.16
784 2523 1.210478 CATGAGGTAGGTGAAGGGGTG 59.790 57.143 0.00 0.00 0.00 4.61
833 2572 1.863454 GATGTGATCTGTGATGGACGC 59.137 52.381 0.00 0.00 0.00 5.19
876 2616 5.715439 AATTCACCTTGTGATGATCCCTA 57.285 39.130 0.00 0.00 42.40 3.53
973 2715 0.677288 TTCCGAGGACGTTGATGTGT 59.323 50.000 0.00 0.00 37.88 3.72
1134 2879 2.851235 CTGATGAAGAAAGAGCGAGACG 59.149 50.000 0.00 0.00 0.00 4.18
1139 2884 6.238049 CCAAACTATCTGATGAAGAAAGAGCG 60.238 42.308 0.00 0.00 38.79 5.03
1233 3331 1.683385 CTGTGTGAGTGACTGAGTGGA 59.317 52.381 0.00 0.00 0.00 4.02
1406 3504 2.287915 GTGCAACAGTCAGTGTCGATTT 59.712 45.455 0.00 0.00 39.03 2.17
1416 3514 0.813610 CTTCCCACGTGCAACAGTCA 60.814 55.000 10.91 0.00 35.74 3.41
1460 3558 0.798776 CAGCGAAACATCAGTGACCC 59.201 55.000 0.00 0.00 0.00 4.46
1571 3669 2.042979 ACTAATTCCAGTGGCAACCCAT 59.957 45.455 3.51 0.00 44.51 4.00
1675 3773 0.039326 AGTACCTGTAGAGGCCGTGT 59.961 55.000 5.68 0.00 44.33 4.49
1686 3784 6.267928 AGTTACTTGAGATGTTCAGTACCTGT 59.732 38.462 0.00 0.00 37.07 4.00
1914 4012 0.035317 TGTTGTAGCCAGCACAGAGG 59.965 55.000 0.00 0.00 0.00 3.69
1918 4016 0.182537 AGGTTGTTGTAGCCAGCACA 59.817 50.000 0.00 0.00 30.94 4.57
2011 4109 1.002033 GATGCCATTTAGCGCTCCTTG 60.002 52.381 16.34 9.96 34.65 3.61
2037 4135 3.864789 AGGGTGACAAGATTTGTGAGT 57.135 42.857 0.00 0.00 45.52 3.41
2174 4273 2.300433 TGAGATTTGTGCAGTTGCTGT 58.700 42.857 5.62 0.00 42.66 4.40
2175 4274 3.570926 ATGAGATTTGTGCAGTTGCTG 57.429 42.857 5.62 0.00 42.66 4.41
2464 4563 3.796111 TCCTGGAACTCTCAAGGATCTT 58.204 45.455 0.00 0.00 45.65 2.40
2543 4642 6.570692 AGATTCTCAAAACCATCAATGATGC 58.429 36.000 17.27 0.00 38.59 3.91
2546 4645 7.764141 TGAAGATTCTCAAAACCATCAATGA 57.236 32.000 0.00 0.00 0.00 2.57
2628 4727 7.552050 AAATAACATCCCCAAATTTGTGAGA 57.448 32.000 16.73 10.30 0.00 3.27
2676 4775 3.142174 GCTAATCCAGTCAGGTATTGGC 58.858 50.000 0.00 0.00 34.96 4.52
3121 5221 3.278574 CAGTTGGAATATGGCCTTCGAA 58.721 45.455 3.32 0.00 0.00 3.71
3131 5231 0.466189 CTGGCCCGCAGTTGGAATAT 60.466 55.000 0.00 0.00 0.00 1.28
3183 5284 2.698274 AGGACCACACAATTTTGGGTTC 59.302 45.455 0.00 4.91 43.56 3.62
3259 5360 1.459450 TTACGGCCAATCTCTTTGCC 58.541 50.000 2.24 0.00 33.73 4.52
3284 5385 0.318120 ACCAAAGGCGATTGCAAAGG 59.682 50.000 1.71 5.41 45.35 3.11
3377 5479 1.821216 AACGGTTTGGGCAGTGATAG 58.179 50.000 0.00 0.00 0.00 2.08
3411 5522 1.202818 GGTCTTGCTGAACTGGGAACT 60.203 52.381 0.00 0.00 0.00 3.01
3501 5613 6.764379 TCTGTTACATGGAGTACAACAATGA 58.236 36.000 12.35 0.00 30.54 2.57
3538 5651 3.527533 TCACTGTTAACGTTGCTCACTT 58.472 40.909 11.99 0.00 0.00 3.16
3551 5664 5.046663 TGGAGTACAATGATGCTCACTGTTA 60.047 40.000 5.76 0.00 32.36 2.41
3559 5672 5.994250 AGTTACATGGAGTACAATGATGCT 58.006 37.500 9.42 3.01 30.91 3.79
3563 5676 9.733556 AACAAATAGTTACATGGAGTACAATGA 57.266 29.630 9.42 0.00 39.09 2.57
3564 5677 9.988350 GAACAAATAGTTACATGGAGTACAATG 57.012 33.333 0.00 0.00 41.51 2.82
3565 5678 9.733556 TGAACAAATAGTTACATGGAGTACAAT 57.266 29.630 0.00 0.00 41.51 2.71
3566 5679 9.214957 CTGAACAAATAGTTACATGGAGTACAA 57.785 33.333 0.00 0.00 41.51 2.41
3568 5681 8.773404 ACTGAACAAATAGTTACATGGAGTAC 57.227 34.615 0.00 0.00 41.51 2.73
3570 5683 9.959721 AATACTGAACAAATAGTTACATGGAGT 57.040 29.630 0.00 0.00 41.51 3.85
3608 5730 4.530553 GGGGAAGCCCTTCTTTGATAAAAA 59.469 41.667 7.85 0.00 44.66 1.94
3609 5731 4.093743 GGGGAAGCCCTTCTTTGATAAAA 58.906 43.478 7.85 0.00 44.66 1.52
3610 5732 3.565670 GGGGGAAGCCCTTCTTTGATAAA 60.566 47.826 7.85 0.00 44.66 1.40
3611 5733 2.024369 GGGGGAAGCCCTTCTTTGATAA 60.024 50.000 7.85 0.00 44.66 1.75
3612 5734 1.569072 GGGGGAAGCCCTTCTTTGATA 59.431 52.381 7.85 0.00 44.66 2.15
3613 5735 0.336392 GGGGGAAGCCCTTCTTTGAT 59.664 55.000 7.85 0.00 44.66 2.57
3614 5736 0.776080 AGGGGGAAGCCCTTCTTTGA 60.776 55.000 7.85 0.00 44.66 2.69
3615 5737 0.115152 AAGGGGGAAGCCCTTCTTTG 59.885 55.000 0.00 0.00 43.38 2.77
3616 5738 2.581524 AAGGGGGAAGCCCTTCTTT 58.418 52.632 0.00 0.00 43.38 2.52
3617 5739 4.377149 AAGGGGGAAGCCCTTCTT 57.623 55.556 0.00 4.46 43.38 2.52
3621 5743 3.660092 ATCGGAAGGGGGAAGCCCT 62.660 63.158 2.01 0.00 44.66 5.19
3622 5744 2.224805 AAATCGGAAGGGGGAAGCCC 62.225 60.000 0.00 0.00 44.51 5.19
3623 5745 0.324368 AAAATCGGAAGGGGGAAGCC 60.324 55.000 0.00 0.00 0.00 4.35
3624 5746 1.103803 GAAAATCGGAAGGGGGAAGC 58.896 55.000 0.00 0.00 0.00 3.86
3625 5747 2.507407 TGAAAATCGGAAGGGGGAAG 57.493 50.000 0.00 0.00 0.00 3.46
3626 5748 3.466395 AATGAAAATCGGAAGGGGGAA 57.534 42.857 0.00 0.00 0.00 3.97
3627 5749 3.526019 AGTAATGAAAATCGGAAGGGGGA 59.474 43.478 0.00 0.00 0.00 4.81
3628 5750 3.632145 CAGTAATGAAAATCGGAAGGGGG 59.368 47.826 0.00 0.00 0.00 5.40
3629 5751 4.523083 TCAGTAATGAAAATCGGAAGGGG 58.477 43.478 0.00 0.00 0.00 4.79
3630 5752 6.509418 TTTCAGTAATGAAAATCGGAAGGG 57.491 37.500 15.48 0.00 35.17 3.95
3631 5753 6.806739 GGTTTTCAGTAATGAAAATCGGAAGG 59.193 38.462 27.81 0.00 45.67 3.46
3632 5754 7.367285 TGGTTTTCAGTAATGAAAATCGGAAG 58.633 34.615 27.81 0.00 46.34 3.46
3633 5755 7.278461 TGGTTTTCAGTAATGAAAATCGGAA 57.722 32.000 27.81 13.33 46.34 4.30
3634 5756 6.885952 TGGTTTTCAGTAATGAAAATCGGA 57.114 33.333 27.81 13.94 46.34 4.55
3635 5757 6.920758 TGTTGGTTTTCAGTAATGAAAATCGG 59.079 34.615 27.81 0.00 46.34 4.18
3636 5758 7.922505 TGTTGGTTTTCAGTAATGAAAATCG 57.077 32.000 27.81 0.00 46.34 3.34
3637 5759 8.638565 CGATGTTGGTTTTCAGTAATGAAAATC 58.361 33.333 27.81 27.28 45.67 2.17
3638 5760 8.356657 TCGATGTTGGTTTTCAGTAATGAAAAT 58.643 29.630 27.81 14.80 45.67 1.82
3639 5761 7.646130 GTCGATGTTGGTTTTCAGTAATGAAAA 59.354 33.333 23.18 23.18 43.10 2.29
3640 5762 7.136119 GTCGATGTTGGTTTTCAGTAATGAAA 58.864 34.615 13.98 13.98 36.17 2.69
3641 5763 6.293735 GGTCGATGTTGGTTTTCAGTAATGAA 60.294 38.462 0.56 0.56 0.00 2.57
3642 5764 5.180492 GGTCGATGTTGGTTTTCAGTAATGA 59.820 40.000 0.00 0.00 0.00 2.57
3643 5765 5.049060 TGGTCGATGTTGGTTTTCAGTAATG 60.049 40.000 0.00 0.00 0.00 1.90
3644 5766 5.067273 TGGTCGATGTTGGTTTTCAGTAAT 58.933 37.500 0.00 0.00 0.00 1.89
3645 5767 4.452825 TGGTCGATGTTGGTTTTCAGTAA 58.547 39.130 0.00 0.00 0.00 2.24
3646 5768 4.074627 TGGTCGATGTTGGTTTTCAGTA 57.925 40.909 0.00 0.00 0.00 2.74
3647 5769 2.925724 TGGTCGATGTTGGTTTTCAGT 58.074 42.857 0.00 0.00 0.00 3.41
3648 5770 3.980646 TTGGTCGATGTTGGTTTTCAG 57.019 42.857 0.00 0.00 0.00 3.02
3649 5771 3.697045 ACTTTGGTCGATGTTGGTTTTCA 59.303 39.130 0.00 0.00 0.00 2.69
3650 5772 4.301637 ACTTTGGTCGATGTTGGTTTTC 57.698 40.909 0.00 0.00 0.00 2.29
3651 5773 6.399639 AATACTTTGGTCGATGTTGGTTTT 57.600 33.333 0.00 0.00 0.00 2.43
3652 5774 6.212955 CAAATACTTTGGTCGATGTTGGTTT 58.787 36.000 0.00 0.00 37.01 3.27
3653 5775 5.768317 CAAATACTTTGGTCGATGTTGGTT 58.232 37.500 0.00 0.00 37.01 3.67
3654 5776 4.320935 GCAAATACTTTGGTCGATGTTGGT 60.321 41.667 0.00 0.00 40.94 3.67
3655 5777 4.165779 GCAAATACTTTGGTCGATGTTGG 58.834 43.478 0.00 0.00 40.94 3.77
3656 5778 4.165779 GGCAAATACTTTGGTCGATGTTG 58.834 43.478 0.00 0.00 40.94 3.33
3657 5779 3.823873 TGGCAAATACTTTGGTCGATGTT 59.176 39.130 0.00 0.00 40.94 2.71
3658 5780 3.417101 TGGCAAATACTTTGGTCGATGT 58.583 40.909 0.00 0.00 40.94 3.06
3659 5781 3.440173 ACTGGCAAATACTTTGGTCGATG 59.560 43.478 0.00 0.00 40.94 3.84
3660 5782 3.686016 ACTGGCAAATACTTTGGTCGAT 58.314 40.909 0.00 0.00 40.94 3.59
3661 5783 3.134574 ACTGGCAAATACTTTGGTCGA 57.865 42.857 2.15 0.00 40.94 4.20
3662 5784 5.560966 AATACTGGCAAATACTTTGGTCG 57.439 39.130 2.15 0.00 40.94 4.79
3663 5785 8.051901 AGTAAATACTGGCAAATACTTTGGTC 57.948 34.615 2.15 0.00 36.82 4.02
3664 5786 8.417273 AAGTAAATACTGGCAAATACTTTGGT 57.583 30.769 2.15 0.00 37.59 3.67
3665 5787 9.139174 CAAAGTAAATACTGGCAAATACTTTGG 57.861 33.333 24.38 15.15 46.89 3.28
3670 5792 9.946165 GGTATCAAAGTAAATACTGGCAAATAC 57.054 33.333 0.00 0.50 36.50 1.89
3671 5793 9.914834 AGGTATCAAAGTAAATACTGGCAAATA 57.085 29.630 0.00 0.00 36.50 1.40
3672 5794 8.823220 AGGTATCAAAGTAAATACTGGCAAAT 57.177 30.769 0.00 0.00 36.50 2.32
3673 5795 9.914834 ATAGGTATCAAAGTAAATACTGGCAAA 57.085 29.630 0.00 0.00 36.50 3.68
3674 5796 9.337396 CATAGGTATCAAAGTAAATACTGGCAA 57.663 33.333 0.00 0.00 36.50 4.52
3675 5797 7.444183 GCATAGGTATCAAAGTAAATACTGGCA 59.556 37.037 0.00 0.00 36.50 4.92
3676 5798 7.444183 TGCATAGGTATCAAAGTAAATACTGGC 59.556 37.037 0.00 0.00 36.50 4.85
3696 5818 6.713903 AGAAACATTCATCACCCTATGCATAG 59.286 38.462 24.33 24.33 0.00 2.23
3722 5844 5.762179 ATGTCCTCTGGTCAACTATCAAA 57.238 39.130 0.00 0.00 0.00 2.69
3726 5848 8.727100 TCATTATATGTCCTCTGGTCAACTAT 57.273 34.615 0.00 0.00 0.00 2.12
3744 5872 4.788201 GCGTTGGCGATTTTGCTCATTATA 60.788 41.667 0.00 0.00 41.33 0.98
3750 5878 3.754091 GCGTTGGCGATTTTGCTC 58.246 55.556 0.00 0.00 41.33 4.26
3765 5893 0.927083 GCAGATTGCTTATGTGCGCG 60.927 55.000 0.00 0.00 42.74 6.86
3794 5922 8.396272 ACTGCAAATAGTTACAGATTTCAGTT 57.604 30.769 10.02 0.00 33.99 3.16
3798 5926 7.377766 TGGACTGCAAATAGTTACAGATTTC 57.622 36.000 10.02 0.00 34.25 2.17
3821 5950 1.817357 TCCTTCACTGCAGATTGCTG 58.183 50.000 23.35 7.93 45.31 4.41
3834 5963 3.861840 CATCGAGCTTTAGGTTCCTTCA 58.138 45.455 0.00 0.00 0.00 3.02
3905 6034 2.035530 AGATGGCTAGACTGCAAAGC 57.964 50.000 0.00 0.00 35.47 3.51
3906 6035 4.764172 AGTTAGATGGCTAGACTGCAAAG 58.236 43.478 0.00 0.00 34.04 2.77
3964 6094 2.548057 TGAATTTTTCTCTCAGCGCGTT 59.452 40.909 8.43 0.00 0.00 4.84
4035 7262 4.127171 CACCGAGGTATTATGGAAACCAG 58.873 47.826 0.00 0.00 36.75 4.00
4043 7270 2.368875 AGCCCTTCACCGAGGTATTATG 59.631 50.000 0.00 0.00 34.88 1.90
4045 7272 2.037144 GAGCCCTTCACCGAGGTATTA 58.963 52.381 0.00 0.00 34.88 0.98
4057 7286 2.508663 GCGTACCGTGAGCCCTTC 60.509 66.667 0.00 0.00 0.00 3.46
4095 7324 4.517934 CCAGGCAGGCAGGGGATG 62.518 72.222 0.00 0.00 0.00 3.51
4302 7795 3.636231 CCCGCAGTCCCACTTCCA 61.636 66.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.