Multiple sequence alignment - TraesCS2A01G449100

Loading Multiple Alignment...

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 TraesCS2A01G449100 chr2A 100.000 4907 0 0 1 4907 698822746 698827652 0.000000e+00 9062
1 TraesCS2A01G449100 chr2D 93.642 4184 155 37 786 4899 558236688 558240830 0.000000e+00 6150
2 TraesCS2A01G449100 chr2B 92.088 1959 110 21 2966 4899 666651968 666653906 0.000000e+00 2717
3 TraesCS2A01G449100 chr2B 89.532 1882 143 25 28 1877 666649082 666650941 0.000000e+00 2335
4 TraesCS2A01G449100 chr2B 95.283 530 22 2 2018 2546 666650936 666651463 0.000000e+00 837
5 TraesCS2A01G449100 chr2B 90.358 363 32 2 2592 2952 666651624 666651985 1.600000e-129 473
6 TraesCS2A01G449100 chr2B 77.987 745 113 32 26 726 58546930 58547667 2.110000e-113 420
7 TraesCS2A01G449100 chr4D 79.900 602 88 27 41 621 51298415 51297826 1.270000e-110 411
8 TraesCS2A01G449100 chr6D 76.320 625 105 19 28 621 138386772 138387384 1.340000e-75 294
9 TraesCS2A01G449100 chr4A 72.515 513 120 14 29 535 474926317 474926814 3.960000e-31 147
10 TraesCS2A01G449100 chr4A 72.822 482 112 16 29 505 474930493 474930960 3.960000e-31 147
11 TraesCS2A01G449100 chr3D 74.320 331 69 13 277 603 514999066 514999384 5.160000e-25 126


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 TraesCS2A01G449100 chr2A 698822746 698827652 4906 False 9062.0 9062 100.00000 1 4907 1 chr2A.!!$F1 4906
1 TraesCS2A01G449100 chr2D 558236688 558240830 4142 False 6150.0 6150 93.64200 786 4899 1 chr2D.!!$F1 4113
2 TraesCS2A01G449100 chr2B 666649082 666653906 4824 False 1590.5 2717 91.81525 28 4899 4 chr2B.!!$F2 4871
3 TraesCS2A01G449100 chr2B 58546930 58547667 737 False 420.0 420 77.98700 26 726 1 chr2B.!!$F1 700
4 TraesCS2A01G449100 chr4D 51297826 51298415 589 True 411.0 411 79.90000 41 621 1 chr4D.!!$R1 580
5 TraesCS2A01G449100 chr6D 138386772 138387384 612 False 294.0 294 76.32000 28 621 1 chr6D.!!$F1 593

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
311 356 0.106217 GGTAGCTCCTCTCTCTGCCT 60.106 60.0 0.00 0.00 31.16 4.75 F
890 978 0.320374 TGATCCTTCCACGTGTCCAC 59.680 55.0 15.65 0.03 0.00 4.02 F
1069 1170 0.458716 CTCCCCGCGTCTCTTTTCTC 60.459 60.0 4.92 0.00 0.00 2.87 F
1567 1676 1.093972 CGCATACCAGTGCATTTGGA 58.906 50.0 22.63 9.87 45.30 3.53 F
3158 3426 0.621609 TTCCACCGGGGGACTATTTG 59.378 55.0 29.76 0.00 36.46 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1676 0.321919 TCAGCTTCTTCGGCTTGCAT 60.322 50.000 0.0 0.0 38.03 3.96 R
2707 2958 1.261619 GTGCTGACTTGTTCCTTCACG 59.738 52.381 0.0 0.0 0.00 4.35 R
2775 3026 1.468985 CTTCCCTCTCTCTCTTGCGA 58.531 55.000 0.0 0.0 0.00 5.10 R
3438 3706 0.394938 TCGCAAGGTTCAGTTGGCTA 59.605 50.000 0.0 0.0 38.47 3.93 R
4862 5156 0.169230 CACCGAGGAGTTCTGTCTCG 59.831 60.000 0.0 0.0 46.73 4.04 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
79 80 2.172679 TCCGCAATATATACCGGAGCA 58.827 47.619 9.46 0.00 44.13 4.26
159 183 1.369091 CCTTCGGCGACAAATCCCTG 61.369 60.000 10.16 0.00 0.00 4.45
161 185 0.672401 TTCGGCGACAAATCCCTGTC 60.672 55.000 10.16 0.00 41.98 3.51
162 186 1.079127 CGGCGACAAATCCCTGTCT 60.079 57.895 0.00 0.00 43.01 3.41
163 187 0.673644 CGGCGACAAATCCCTGTCTT 60.674 55.000 0.00 0.00 43.01 3.01
164 188 1.087501 GGCGACAAATCCCTGTCTTC 58.912 55.000 2.57 0.00 43.01 2.87
166 190 1.610624 GCGACAAATCCCTGTCTTCCA 60.611 52.381 2.57 0.00 43.01 3.53
272 317 3.043713 CTCGTCGCCTTGCAAGCA 61.044 61.111 21.43 3.89 0.00 3.91
303 348 1.153127 CGAGGTCGGTAGCTCCTCT 60.153 63.158 21.76 4.00 45.60 3.69
307 352 0.181824 GGTCGGTAGCTCCTCTCTCT 59.818 60.000 0.00 0.00 0.00 3.10
311 356 0.106217 GGTAGCTCCTCTCTCTGCCT 60.106 60.000 0.00 0.00 31.16 4.75
314 359 2.357575 GCTCCTCTCTCTGCCTGCA 61.358 63.158 0.00 0.00 0.00 4.41
408 456 0.674895 GCAACTTCGACAGGCTGGAT 60.675 55.000 20.34 0.00 0.00 3.41
413 461 1.945354 TTCGACAGGCTGGATCGGAC 61.945 60.000 22.34 4.56 36.51 4.79
440 489 2.125912 GCGCTCAAGCTTCTCCGA 60.126 61.111 0.00 0.00 39.32 4.55
557 612 0.539051 CTCGCCATCCTCTCCAACTT 59.461 55.000 0.00 0.00 0.00 2.66
563 618 3.274288 CCATCCTCTCCAACTTGCTAAC 58.726 50.000 0.00 0.00 0.00 2.34
649 719 7.602517 AATATTAGTGTGAACTCTGTTCAGC 57.397 36.000 12.64 9.27 0.00 4.26
650 720 2.988010 AGTGTGAACTCTGTTCAGCA 57.012 45.000 12.64 10.92 0.00 4.41
665 751 4.704057 TGTTCAGCAATGTAATATGTGGCA 59.296 37.500 0.00 0.00 0.00 4.92
671 757 4.597079 CAATGTAATATGTGGCACGAACC 58.403 43.478 13.77 0.00 0.00 3.62
687 773 6.018832 GGCACGAACCGCTAGTTTAAATTATA 60.019 38.462 0.00 0.00 39.40 0.98
712 798 6.127952 ACCGTATGTGTTTGTGTTTGTTTACT 60.128 34.615 0.00 0.00 0.00 2.24
713 799 7.065563 ACCGTATGTGTTTGTGTTTGTTTACTA 59.934 33.333 0.00 0.00 0.00 1.82
779 867 2.496111 TCGTAAATTTTGCAGGACGGT 58.504 42.857 8.57 0.00 0.00 4.83
795 883 2.340328 GGTGGTTTGCGGGATCACC 61.340 63.158 0.00 1.12 40.63 4.02
890 978 0.320374 TGATCCTTCCACGTGTCCAC 59.680 55.000 15.65 0.03 0.00 4.02
1056 1157 4.148825 CCACTTCTCCGCTCCCCG 62.149 72.222 0.00 0.00 0.00 5.73
1069 1170 0.458716 CTCCCCGCGTCTCTTTTCTC 60.459 60.000 4.92 0.00 0.00 2.87
1099 1200 3.007506 TGCTTCGGTACTTTCTTCATGGA 59.992 43.478 0.00 0.00 0.00 3.41
1325 1432 7.820578 AGAGTAACTGAGTAACACTGTAACT 57.179 36.000 0.00 0.00 0.00 2.24
1326 1433 7.649973 AGAGTAACTGAGTAACACTGTAACTG 58.350 38.462 0.00 0.00 0.00 3.16
1327 1434 7.284944 AGAGTAACTGAGTAACACTGTAACTGT 59.715 37.037 0.00 0.00 0.00 3.55
1328 1435 8.455903 AGTAACTGAGTAACACTGTAACTGTA 57.544 34.615 0.00 0.00 0.00 2.74
1329 1436 8.906867 AGTAACTGAGTAACACTGTAACTGTAA 58.093 33.333 0.00 0.00 0.00 2.41
1393 1500 3.995199 TGGAGATCCAATTGCTCGTATC 58.005 45.455 0.00 0.00 44.35 2.24
1403 1511 6.701841 TCCAATTGCTCGTATCTTATGAACTC 59.298 38.462 0.00 0.00 0.00 3.01
1444 1553 3.535561 CTGGTGTATAAGTGGAGCTTGG 58.464 50.000 0.00 0.00 38.05 3.61
1495 1604 4.976540 AGTTCTTTAGTACCCAGTTGCT 57.023 40.909 0.00 0.00 0.00 3.91
1567 1676 1.093972 CGCATACCAGTGCATTTGGA 58.906 50.000 22.63 9.87 45.30 3.53
1602 1711 7.521871 AGAAGCTGATCTCAAACAGAAATTT 57.478 32.000 0.00 0.00 36.38 1.82
1799 1909 3.688673 GCTTCTCCCAGTTTTCATCTCTG 59.311 47.826 0.00 0.00 0.00 3.35
1849 1959 3.421844 AGCCTGGTTCATTTAGTGTTCC 58.578 45.455 0.00 0.00 0.00 3.62
1908 2018 8.239314 TGATAATTCTTTGTTCATGTTCTGCTC 58.761 33.333 0.00 0.00 0.00 4.26
1951 2061 1.427020 GCACGCTGAAATGGAGCTC 59.573 57.895 4.71 4.71 34.03 4.09
1957 2067 4.993584 CACGCTGAAATGGAGCTCTAATAT 59.006 41.667 14.64 0.00 34.03 1.28
1999 2109 9.717892 CATATCACTATATCATGCTGAAAATGC 57.282 33.333 0.00 0.00 0.00 3.56
2058 2193 4.864247 AGACACACATGTTTTGTTGAAAGC 59.136 37.500 10.51 0.00 39.95 3.51
2065 2200 2.920490 TGTTTTGTTGAAAGCGCTTGTC 59.080 40.909 25.80 21.59 0.00 3.18
2084 2219 6.366332 GCTTGTCGAGATTCTTTTCAAGTAGA 59.634 38.462 17.97 0.00 34.99 2.59
2194 2329 3.130516 TCACCGATGACATCTTCTGGTAC 59.869 47.826 13.45 0.00 31.39 3.34
2252 2387 9.790389 GATATCTTGTAATCATTAGAGTACCGG 57.210 37.037 0.00 0.00 42.92 5.28
2259 2394 8.464404 TGTAATCATTAGAGTACCGGTATATGC 58.536 37.037 19.19 4.55 42.92 3.14
2461 2597 1.870055 GCCACATGTGCAACCTCAGG 61.870 60.000 20.81 4.49 34.36 3.86
2562 2698 8.266392 TCTACCGAAGAACAAACAAAAAGTTA 57.734 30.769 0.00 0.00 40.26 2.24
2598 2849 7.182817 AGCTCAAAGTCCACATGTAATACTA 57.817 36.000 0.00 0.00 0.00 1.82
2655 2906 7.915293 TGTGTAGGTGGTACAGATTATTTTG 57.085 36.000 0.00 0.00 42.56 2.44
2707 2958 4.804665 GCGGAAGTACAGAGAAATAGGAAC 59.195 45.833 0.00 0.00 0.00 3.62
2709 2960 5.392811 CGGAAGTACAGAGAAATAGGAACGT 60.393 44.000 0.00 0.00 0.00 3.99
2775 3026 2.267006 CAGGTGCGTCTCTGCCAT 59.733 61.111 0.00 0.00 0.00 4.40
2852 3105 9.578576 CCCTATTTGATTATTCAATCTCCTCAA 57.421 33.333 1.11 0.00 41.38 3.02
2860 3113 4.437682 TTCAATCTCCTCAAACACCAGT 57.562 40.909 0.00 0.00 0.00 4.00
2951 3205 5.441718 TCTTTGACATCCAATTCCTAGCT 57.558 39.130 0.00 0.00 34.23 3.32
2955 3209 5.028549 TGACATCCAATTCCTAGCTCTTC 57.971 43.478 0.00 0.00 0.00 2.87
2960 3214 6.950619 ACATCCAATTCCTAGCTCTTCTTTTT 59.049 34.615 0.00 0.00 0.00 1.94
3144 3412 5.639082 CCTTGTTCTATTGGCAATTTTCCAC 59.361 40.000 19.21 8.99 32.45 4.02
3158 3426 0.621609 TTCCACCGGGGGACTATTTG 59.378 55.000 29.76 0.00 36.46 2.32
3219 3487 6.828502 TTAGATACATTGCTGAATGACGAC 57.171 37.500 3.92 0.00 41.49 4.34
3438 3706 2.705658 TCAGACACTGGGTGACAAGATT 59.294 45.455 4.62 0.00 36.96 2.40
3492 3760 0.670546 CCCGATTGAAGCGTGTCACT 60.671 55.000 1.17 0.00 0.00 3.41
3633 3906 6.149474 TGCTTTGGCTTAAGTACTCTCAAATC 59.851 38.462 4.02 0.64 39.59 2.17
3700 3976 9.553064 AAACAATTTTTACATGGTCAATGCTAA 57.447 25.926 0.00 0.00 40.22 3.09
3727 4003 8.533657 TGCTGGAAGTATGAATCAATGAAATTT 58.466 29.630 0.00 0.00 30.84 1.82
3858 4134 6.377996 CACTGGATGATAATGGAGTTTTGGAA 59.622 38.462 0.00 0.00 0.00 3.53
3918 4194 7.734924 AAGTGCAACATAATGATCATATCGT 57.265 32.000 9.04 3.36 41.43 3.73
3922 4198 6.705381 TGCAACATAATGATCATATCGTGTGA 59.295 34.615 9.04 0.00 0.00 3.58
3923 4199 7.388500 TGCAACATAATGATCATATCGTGTGAT 59.612 33.333 9.04 0.00 38.94 3.06
3950 4226 0.179020 TTTGCCAGGTGAGTCACTGG 60.179 55.000 25.48 25.48 36.48 4.00
4012 4289 5.295787 GTGTAGTCAACAATGAACCTTGTCA 59.704 40.000 0.00 0.00 40.63 3.58
4271 4553 9.519191 TCTGTTGTGTACTAGTACCACTAATAA 57.481 33.333 26.41 11.70 35.26 1.40
4287 4574 8.107095 ACCACTAATAATAGACAATGGTGTGTT 58.893 33.333 0.00 0.00 38.41 3.32
4299 4586 7.826744 AGACAATGGTGTGTTTGGTTTAAATTT 59.173 29.630 0.00 0.00 38.41 1.82
4349 4636 5.533528 TCGGAATGGTATCGACTAGAAATCA 59.466 40.000 0.00 0.00 0.00 2.57
4465 4753 5.295787 TCAACATATTAGAATTGGTGACCGC 59.704 40.000 0.00 0.00 32.38 5.68
4488 4776 2.048444 AGCTGTGTGGCATAGGATTG 57.952 50.000 0.00 0.00 34.17 2.67
4544 4834 5.382618 AATTGCCTGAAGAATGAGAACAC 57.617 39.130 0.00 0.00 0.00 3.32
4600 4890 2.306847 GGATTACCGATTTGGGCATGT 58.693 47.619 0.00 0.00 44.64 3.21
4607 4897 2.228822 CCGATTTGGGCATGTATTAGGC 59.771 50.000 0.00 0.00 34.76 3.93
4630 4920 2.484264 GGTTTGATGAAACTCCGGTGAG 59.516 50.000 11.17 0.00 41.21 3.51
4639 4929 0.252284 ACTCCGGTGAGATGGACCTT 60.252 55.000 11.17 0.00 41.42 3.50
4649 4943 5.598830 GGTGAGATGGACCTTAGATGAGTTA 59.401 44.000 0.00 0.00 0.00 2.24
4703 4997 3.852536 CGTAGTTGTAGCTAGTGTTGCTC 59.147 47.826 0.00 0.00 41.46 4.26
4725 5019 7.557358 TGCTCCATACATGTTGTATCTGAAATT 59.443 33.333 2.30 0.00 41.28 1.82
4747 5041 9.524496 AAATTCGGTATCCCCTATAATAAAACC 57.476 33.333 0.00 0.00 0.00 3.27
4767 5061 5.401531 ACCGAAGTAAATCTCTGCAAGTA 57.598 39.130 0.00 0.00 33.76 2.24
4785 5079 7.589395 TGCAAGTATGTCGTTGAAATGTAATT 58.411 30.769 0.00 0.00 38.98 1.40
4862 5156 0.037447 GGCTTCTAGATGGGCATCCC 59.963 60.000 12.65 0.00 45.71 3.85
4899 5193 2.348666 GGTGTCACATCATAACTGTCGC 59.651 50.000 5.12 0.00 0.00 5.19
4900 5194 2.348666 GTGTCACATCATAACTGTCGCC 59.651 50.000 0.00 0.00 0.00 5.54
4901 5195 2.233676 TGTCACATCATAACTGTCGCCT 59.766 45.455 0.00 0.00 0.00 5.52
4902 5196 2.604914 GTCACATCATAACTGTCGCCTG 59.395 50.000 0.00 0.00 0.00 4.85
4903 5197 2.233676 TCACATCATAACTGTCGCCTGT 59.766 45.455 0.00 0.00 0.00 4.00
4904 5198 2.604914 CACATCATAACTGTCGCCTGTC 59.395 50.000 0.00 0.00 0.00 3.51
4905 5199 1.854743 CATCATAACTGTCGCCTGTCG 59.145 52.381 0.00 0.00 40.15 4.35
4906 5200 0.457853 TCATAACTGTCGCCTGTCGC 60.458 55.000 0.00 0.00 38.27 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.067365 AAAATTATGAGTCGGCCCCC 57.933 50.000 0.00 0.00 0.00 5.40
79 80 2.027469 ACGCGAACCCTAAAATCTCCTT 60.027 45.455 15.93 0.00 0.00 3.36
159 183 0.038801 GCAAAAGGCTGCTGGAAGAC 60.039 55.000 0.00 0.00 39.34 3.01
161 185 1.080974 CGCAAAAGGCTGCTGGAAG 60.081 57.895 0.00 0.00 40.33 3.46
162 186 2.563798 CCGCAAAAGGCTGCTGGAA 61.564 57.895 0.00 0.00 40.33 3.53
163 187 2.985282 CCGCAAAAGGCTGCTGGA 60.985 61.111 0.00 0.00 40.33 3.86
257 302 3.349006 AGTGCTTGCAAGGCGACG 61.349 61.111 27.10 2.48 0.00 5.12
272 317 2.050351 CCTCGTCGTCGTTGCAGT 60.050 61.111 1.33 0.00 38.33 4.40
294 339 0.754957 GCAGGCAGAGAGAGGAGCTA 60.755 60.000 0.00 0.00 0.00 3.32
303 348 2.203832 TCCACCTGCAGGCAGAGA 60.204 61.111 33.06 20.15 46.30 3.10
307 352 3.324930 CTCCTCCACCTGCAGGCA 61.325 66.667 33.06 15.76 39.32 4.75
311 356 3.640407 GCCACTCCTCCACCTGCA 61.640 66.667 0.00 0.00 0.00 4.41
357 402 4.069232 CTGGCGTTGCGGGAGAGA 62.069 66.667 0.00 0.00 0.00 3.10
382 430 0.671781 CTGTCGAAGTTGCTCCAGGG 60.672 60.000 0.00 0.00 0.00 4.45
478 527 1.513158 CTTCGTCTCCAGTGGCGAT 59.487 57.895 4.88 0.00 33.27 4.58
479 528 2.962569 CTTCGTCTCCAGTGGCGA 59.037 61.111 3.51 5.17 0.00 5.54
486 535 2.047844 GCTGCAGCTTCGTCTCCA 60.048 61.111 31.33 0.00 38.21 3.86
596 654 5.065704 ACCTAGATACGCATCATCATCAC 57.934 43.478 0.00 0.00 33.21 3.06
625 695 7.161404 TGCTGAACAGAGTTCACACTAATATT 58.839 34.615 8.39 0.00 31.22 1.28
629 699 4.400529 TGCTGAACAGAGTTCACACTAA 57.599 40.909 8.39 0.00 31.22 2.24
646 716 3.312146 TCGTGCCACATATTACATTGCTG 59.688 43.478 0.00 0.00 0.00 4.41
647 717 3.540617 TCGTGCCACATATTACATTGCT 58.459 40.909 0.00 0.00 0.00 3.91
648 718 3.961477 TCGTGCCACATATTACATTGC 57.039 42.857 0.00 0.00 0.00 3.56
649 719 4.597079 GGTTCGTGCCACATATTACATTG 58.403 43.478 0.00 0.00 0.00 2.82
650 720 3.311322 CGGTTCGTGCCACATATTACATT 59.689 43.478 0.00 0.00 0.00 2.71
665 751 6.198966 CGGTATAATTTAAACTAGCGGTTCGT 59.801 38.462 13.71 0.00 37.12 3.85
671 757 8.971321 ACACATACGGTATAATTTAAACTAGCG 58.029 33.333 17.34 17.34 40.01 4.26
687 773 4.705337 AACAAACACAAACACATACGGT 57.295 36.364 0.00 0.00 0.00 4.83
734 820 2.165437 ACTAAATTTACGGTACCGCGGA 59.835 45.455 35.90 19.28 44.19 5.54
735 821 2.539476 ACTAAATTTACGGTACCGCGG 58.461 47.619 33.62 26.86 44.19 6.46
736 822 4.582441 AAACTAAATTTACGGTACCGCG 57.418 40.909 33.62 12.23 44.19 6.46
737 823 6.019881 ACGATAAACTAAATTTACGGTACCGC 60.020 38.462 33.62 10.52 44.19 5.68
738 824 7.449934 ACGATAAACTAAATTTACGGTACCG 57.550 36.000 32.22 32.22 46.03 4.02
766 854 0.457851 CAAACCACCGTCCTGCAAAA 59.542 50.000 0.00 0.00 0.00 2.44
958 1046 2.092323 GGAGGAAATGAAAGGGGAACG 58.908 52.381 0.00 0.00 0.00 3.95
1056 1157 0.736672 GGGTCGGAGAAAAGAGACGC 60.737 60.000 0.00 0.00 39.69 5.19
1099 1200 5.245531 TCTGATTCTCAAGCCAATACGTTT 58.754 37.500 0.00 0.00 0.00 3.60
1255 1362 3.660111 GCAGAAGCGGCGGTTGTT 61.660 61.111 30.26 14.14 0.00 2.83
1324 1431 2.027561 TCCGGGAAATCCACACTTACAG 60.028 50.000 0.00 0.00 37.91 2.74
1325 1432 1.979308 TCCGGGAAATCCACACTTACA 59.021 47.619 0.00 0.00 37.91 2.41
1326 1433 2.773993 TCCGGGAAATCCACACTTAC 57.226 50.000 0.00 0.00 37.91 2.34
1327 1434 2.026636 CCTTCCGGGAAATCCACACTTA 60.027 50.000 11.24 0.00 37.91 2.24
1328 1435 1.271926 CCTTCCGGGAAATCCACACTT 60.272 52.381 11.24 0.00 37.91 3.16
1329 1436 0.328258 CCTTCCGGGAAATCCACACT 59.672 55.000 11.24 0.00 37.91 3.55
1340 1447 6.823497 TCTACATAAAGAATAACCTTCCGGG 58.177 40.000 0.00 0.00 41.89 5.73
1393 1500 2.831333 AGCGCTCCATGAGTTCATAAG 58.169 47.619 2.64 0.00 34.26 1.73
1403 1511 0.455633 GCAAGAACAAGCGCTCCATG 60.456 55.000 12.06 8.49 0.00 3.66
1567 1676 0.321919 TCAGCTTCTTCGGCTTGCAT 60.322 50.000 0.00 0.00 38.03 3.96
1617 1726 3.649981 TGCATTTTGGGAATTTGAGGGAA 59.350 39.130 0.00 0.00 0.00 3.97
1724 1834 6.057533 TGGTGCTCCAGATGTAATTATTCAG 58.942 40.000 2.64 0.00 39.03 3.02
1799 1909 5.306532 TCTCTACCACGAGACAATGTAAC 57.693 43.478 0.00 0.00 35.23 2.50
1905 2015 5.237996 TGCTCAATTCATATGCAACTAGAGC 59.762 40.000 18.94 18.94 43.56 4.09
1908 2018 5.559608 CGGTGCTCAATTCATATGCAACTAG 60.560 44.000 0.00 0.00 38.98 2.57
1985 2095 3.061322 GCACAAAGCATTTTCAGCATGA 58.939 40.909 0.00 0.00 44.26 3.07
2058 2193 4.389664 TTGAAAAGAATCTCGACAAGCG 57.610 40.909 0.00 0.00 42.69 4.68
2106 2241 3.053619 GGGAATATGACCTCCACCACTTT 60.054 47.826 0.00 0.00 32.95 2.66
2194 2329 4.114794 CAAAGCTCTGTCCAAAACCAAAG 58.885 43.478 0.00 0.00 0.00 2.77
2301 2437 5.939296 TCTTCACTGCATAATCACATCACAA 59.061 36.000 0.00 0.00 0.00 3.33
2461 2597 5.105392 TGCATGATGGTTTTACATTCCCTTC 60.105 40.000 0.00 0.00 0.00 3.46
2562 2698 3.733337 ACTTTGAGCTTGTTGAGATCGT 58.267 40.909 0.00 0.00 43.77 3.73
2598 2849 5.939883 TGCATCATGCTTAGTTAAGAGTTGT 59.060 36.000 11.84 0.00 45.31 3.32
2655 2906 7.783042 AGACCATAACAACCATCTAGACTAAC 58.217 38.462 0.00 0.00 0.00 2.34
2707 2958 1.261619 GTGCTGACTTGTTCCTTCACG 59.738 52.381 0.00 0.00 0.00 4.35
2709 2960 3.281727 AAGTGCTGACTTGTTCCTTCA 57.718 42.857 0.00 0.00 41.12 3.02
2775 3026 1.468985 CTTCCCTCTCTCTCTTGCGA 58.531 55.000 0.00 0.00 0.00 5.10
2852 3105 4.705023 ACTTCTTACTTGCAAACTGGTGTT 59.295 37.500 0.00 0.00 38.16 3.32
2854 3107 4.900635 ACTTCTTACTTGCAAACTGGTG 57.099 40.909 0.00 0.00 0.00 4.17
2860 3113 9.862371 TTTTGTTCATTACTTCTTACTTGCAAA 57.138 25.926 0.00 0.00 0.00 3.68
2951 3205 3.226777 TGGATTTCCCGCAAAAAGAAGA 58.773 40.909 0.00 0.00 37.93 2.87
2955 3209 3.684305 GGAATTGGATTTCCCGCAAAAAG 59.316 43.478 0.00 0.00 39.46 2.27
2960 3214 2.930950 CTAGGAATTGGATTTCCCGCA 58.069 47.619 0.00 0.00 45.32 5.69
3144 3412 4.768448 AGTTTTTAACAAATAGTCCCCCGG 59.232 41.667 0.00 0.00 0.00 5.73
3158 3426 5.067283 TGCTCAAGGAGGTCAAGTTTTTAAC 59.933 40.000 0.00 0.00 0.00 2.01
3219 3487 1.097547 CAGGCTTACCATCTTGCCCG 61.098 60.000 0.00 0.00 45.94 6.13
3320 3588 1.747325 AAATGTGCCACACTGCCACC 61.747 55.000 0.00 0.00 35.11 4.61
3438 3706 0.394938 TCGCAAGGTTCAGTTGGCTA 59.605 50.000 0.00 0.00 38.47 3.93
3492 3760 1.593196 CCTCTTTTTCGACACTGCCA 58.407 50.000 0.00 0.00 0.00 4.92
3633 3906 8.547967 TGAAGAGCCTTTACATTAACTTGTAG 57.452 34.615 0.00 0.00 33.81 2.74
3700 3976 7.649533 TTTCATTGATTCATACTTCCAGCAT 57.350 32.000 0.00 0.00 0.00 3.79
3797 4073 6.147864 TCTGCAAAGTTAAGTGAAAATGCT 57.852 33.333 0.00 0.00 33.87 3.79
3858 4134 1.344763 CCCTGTTCACTCGAGTTTCCT 59.655 52.381 17.26 0.00 0.00 3.36
3866 4142 1.268539 GCACAAAACCCTGTTCACTCG 60.269 52.381 0.00 0.00 0.00 4.18
3950 4226 3.754965 TGCACTATATGAATTCCAGGGC 58.245 45.455 2.27 8.17 36.17 5.19
4012 4289 6.649557 CGAAATACTCCCTGTAGTTTCAGTTT 59.350 38.462 0.00 0.00 39.21 2.66
4271 4553 7.589958 TTAAACCAAACACACCATTGTCTAT 57.410 32.000 0.00 0.00 31.66 1.98
4272 4554 7.406031 TTTAAACCAAACACACCATTGTCTA 57.594 32.000 0.00 0.00 31.66 2.59
4273 4555 5.923733 TTAAACCAAACACACCATTGTCT 57.076 34.783 0.00 0.00 31.66 3.41
4274 4556 7.546778 AATTTAAACCAAACACACCATTGTC 57.453 32.000 0.00 0.00 31.66 3.18
4276 4558 7.912773 GGAAAATTTAAACCAAACACACCATTG 59.087 33.333 0.00 0.00 0.00 2.82
4277 4559 7.831690 AGGAAAATTTAAACCAAACACACCATT 59.168 29.630 10.24 0.00 0.00 3.16
4278 4560 7.342581 AGGAAAATTTAAACCAAACACACCAT 58.657 30.769 10.24 0.00 0.00 3.55
4281 4563 9.589111 TTCTAGGAAAATTTAAACCAAACACAC 57.411 29.630 10.24 0.00 0.00 3.82
4299 4586 5.882557 GCCATCAGTTGATTTCTTCTAGGAA 59.117 40.000 0.00 0.00 31.21 3.36
4349 4636 5.178797 CGAGAAAGATGTCCAAGGTAATGT 58.821 41.667 0.00 0.00 0.00 2.71
4465 4753 3.198409 TCCTATGCCACACAGCTATTG 57.802 47.619 0.00 0.00 0.00 1.90
4593 4883 2.362077 CAAACCTGCCTAATACATGCCC 59.638 50.000 0.00 0.00 0.00 5.36
4600 4890 5.885912 GGAGTTTCATCAAACCTGCCTAATA 59.114 40.000 0.00 0.00 42.72 0.98
4607 4897 2.226437 CACCGGAGTTTCATCAAACCTG 59.774 50.000 9.46 0.00 42.72 4.00
4630 4920 8.189119 AGAATCTAACTCATCTAAGGTCCATC 57.811 38.462 0.00 0.00 0.00 3.51
4703 4997 7.012327 ACCGAATTTCAGATACAACATGTATGG 59.988 37.037 7.68 0.00 43.08 2.74
4747 5041 6.291322 CGACATACTTGCAGAGATTTACTTCG 60.291 42.308 3.37 0.00 0.00 3.79
4785 5079 9.396022 GGTTCCTTTAATCTATGATGAAGTGAA 57.604 33.333 0.00 0.00 0.00 3.18
4862 5156 0.169230 CACCGAGGAGTTCTGTCTCG 59.831 60.000 0.00 0.00 46.73 4.04


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

AutoCloner maintained by Alex Coulton.