Multiple sequence alignment - TraesCS2A01G444800

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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 TraesCS2A01G444800 chr2A 100.000 3108 0 0 1 3108 694901061 694904168 0.000000e+00 5740.0
1 TraesCS2A01G444800 chr2A 76.740 1178 235 26 994 2159 694839902 694841052 4.140000e-174 621.0
2 TraesCS2A01G444800 chr2A 100.000 330 0 0 3448 3777 694904508 694904837 8.970000e-171 610.0
3 TraesCS2A01G444800 chr2A 78.455 738 129 20 1463 2197 694864922 694865632 4.450000e-124 455.0
4 TraesCS2A01G444800 chr2A 77.477 222 39 9 3512 3731 491538510 491538722 5.120000e-24 122.0
5 TraesCS2A01G444800 chr2A 98.113 53 1 0 3516 3568 694904528 694904580 4.020000e-15 93.5
6 TraesCS2A01G444800 chr2A 98.113 53 1 0 3468 3520 694904576 694904628 4.020000e-15 93.5
7 TraesCS2A01G444800 chr2B 92.302 1390 76 11 1746 3106 661445853 661447240 0.000000e+00 1945.0
8 TraesCS2A01G444800 chr2B 94.130 988 52 4 765 1751 661444774 661445756 0.000000e+00 1498.0
9 TraesCS2A01G444800 chr2B 76.992 1004 185 30 994 1984 661175711 661176681 2.000000e-147 532.0
10 TraesCS2A01G444800 chr2B 85.185 378 45 5 940 1316 661191806 661192173 9.900000e-101 377.0
11 TraesCS2A01G444800 chr2B 89.286 308 13 2 3468 3775 661447548 661447835 5.960000e-98 368.0
12 TraesCS2A01G444800 chr2B 97.826 46 1 0 614 659 661444730 661444775 3.130000e-11 80.5
13 TraesCS2A01G444800 chr2B 88.235 51 6 0 3537 3587 747347161 747347111 1.130000e-05 62.1
14 TraesCS2A01G444800 chr2B 100.000 32 0 0 3537 3568 661447521 661447552 4.070000e-05 60.2
15 TraesCS2A01G444800 chrUn 90.022 1373 101 18 1746 3097 26258575 26259932 0.000000e+00 1744.0
16 TraesCS2A01G444800 chrUn 93.994 716 40 3 1038 1751 26257763 26258477 0.000000e+00 1081.0
17 TraesCS2A01G444800 chrUn 76.444 1125 217 30 994 2101 26236351 26237444 1.970000e-157 566.0
18 TraesCS2A01G444800 chrUn 84.392 378 48 5 940 1316 26244801 26245168 9.970000e-96 361.0
19 TraesCS2A01G444800 chrUn 94.268 157 7 2 800 956 26257608 26257762 4.880000e-59 239.0
20 TraesCS2A01G444800 chrUn 86.473 207 16 7 3516 3713 26261334 26261537 2.280000e-52 217.0
21 TraesCS2A01G444800 chrUn 84.795 171 26 0 1463 1633 26245195 26245365 5.020000e-39 172.0
22 TraesCS2A01G444800 chrUn 96.154 78 3 0 707 784 26255333 26255410 1.100000e-25 128.0
23 TraesCS2A01G444800 chrUn 92.683 82 2 3 613 690 26255267 26255348 8.570000e-22 115.0
24 TraesCS2A01G444800 chr7D 96.110 617 24 0 1 617 451044592 451045208 0.000000e+00 1007.0
25 TraesCS2A01G444800 chr3D 95.786 617 26 0 1 617 125801813 125802429 0.000000e+00 996.0
26 TraesCS2A01G444800 chr4D 94.489 617 33 1 1 617 506096235 506096850 0.000000e+00 950.0
27 TraesCS2A01G444800 chr4D 94.737 38 2 0 3524 3561 458154818 458154855 4.070000e-05 60.2
28 TraesCS2A01G444800 chr4A 91.709 591 45 3 41 629 677313469 677312881 0.000000e+00 817.0
29 TraesCS2A01G444800 chr1A 94.831 445 21 2 1 444 32466397 32466840 0.000000e+00 693.0
30 TraesCS2A01G444800 chr1A 80.978 184 35 0 1018 1201 555129297 555129480 3.040000e-31 147.0
31 TraesCS2A01G444800 chr7A 93.885 278 14 2 1 275 47014911 47015188 2.100000e-112 416.0
32 TraesCS2A01G444800 chr7A 92.674 273 19 1 1 272 7771928 7771656 3.540000e-105 392.0
33 TraesCS2A01G444800 chr7A 87.037 54 7 0 3459 3512 281626935 281626988 1.130000e-05 62.1
34 TraesCS2A01G444800 chr6D 92.667 150 11 0 1 150 202256472 202256323 2.280000e-52 217.0
35 TraesCS2A01G444800 chr1D 78.816 321 50 10 2411 2713 474354119 474354439 2.300000e-47 200.0
36 TraesCS2A01G444800 chr1B 81.522 184 34 0 1018 1201 638682901 638683084 6.530000e-33 152.0
37 TraesCS2A01G444800 chr5D 80.583 206 30 6 3510 3706 443722435 443722639 2.350000e-32 150.0
38 TraesCS2A01G444800 chr6B 76.364 275 48 12 3512 3775 225322060 225322328 8.510000e-27 132.0
39 TraesCS2A01G444800 chr6B 100.000 34 0 0 1750 1783 457468992 457469025 3.150000e-06 63.9
40 TraesCS2A01G444800 chr7B 95.122 82 4 0 1 82 686853384 686853303 3.060000e-26 130.0
41 TraesCS2A01G444800 chr2D 92.208 77 6 0 1 77 275248316 275248240 3.990000e-20 110.0
42 TraesCS2A01G444800 chr3B 90.196 51 2 3 3728 3777 737660150 737660198 3.150000e-06 63.9


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 TraesCS2A01G444800 chr2A 694901061 694904837 3776 False 1634.250000 5740 99.056500 1 3777 4 chr2A.!!$F4 3776
1 TraesCS2A01G444800 chr2A 694839902 694841052 1150 False 621.000000 621 76.740000 994 2159 1 chr2A.!!$F2 1165
2 TraesCS2A01G444800 chr2A 694864922 694865632 710 False 455.000000 455 78.455000 1463 2197 1 chr2A.!!$F3 734
3 TraesCS2A01G444800 chr2B 661444730 661447835 3105 False 790.340000 1945 94.708800 614 3775 5 chr2B.!!$F3 3161
4 TraesCS2A01G444800 chr2B 661175711 661176681 970 False 532.000000 532 76.992000 994 1984 1 chr2B.!!$F1 990
5 TraesCS2A01G444800 chrUn 26255267 26261537 6270 False 587.333333 1744 92.265667 613 3713 6 chrUn.!!$F3 3100
6 TraesCS2A01G444800 chrUn 26236351 26237444 1093 False 566.000000 566 76.444000 994 2101 1 chrUn.!!$F1 1107
7 TraesCS2A01G444800 chrUn 26244801 26245365 564 False 266.500000 361 84.593500 940 1633 2 chrUn.!!$F2 693
8 TraesCS2A01G444800 chr7D 451044592 451045208 616 False 1007.000000 1007 96.110000 1 617 1 chr7D.!!$F1 616
9 TraesCS2A01G444800 chr3D 125801813 125802429 616 False 996.000000 996 95.786000 1 617 1 chr3D.!!$F1 616
10 TraesCS2A01G444800 chr4D 506096235 506096850 615 False 950.000000 950 94.489000 1 617 1 chr4D.!!$F2 616
11 TraesCS2A01G444800 chr4A 677312881 677313469 588 True 817.000000 817 91.709000 41 629 1 chr4A.!!$R1 588

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
906 3094 0.036732 ATCTGCCGCTTCAGGTTTCA 59.963 50.0 0.0 0.0 34.91 2.69 F
971 3159 0.661187 CATTCTGCAACACACGCACC 60.661 55.0 0.0 0.0 35.08 5.01 F
1266 3456 0.684535 TTCTCAGTCCCATCAACGCA 59.315 50.0 0.0 0.0 0.00 5.24 F
2495 4805 0.815734 TAGCAAGCACTCTACGGGTC 59.184 55.0 0.0 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 4719 0.825010 GGCCCCTGCTTGACATATGG 60.825 60.000 7.80 0.00 37.74 2.74 R
2660 4970 1.808945 CACCAAGGCAGCTTTCAGTAG 59.191 52.381 0.00 0.00 0.00 2.57 R
2719 5029 1.885049 TATTCTTGGGAGCAGGCTCT 58.115 50.000 19.67 2.11 42.38 4.09 R
3521 6898 1.961793 CCCTCGTCAAAAGGAACACA 58.038 50.000 0.00 0.00 35.83 3.72 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
48 49 6.043590 AGCAAGATATAGTGGGTCATCAATCA 59.956 38.462 0.00 0.00 0.00 2.57
61 62 7.232330 TGGGTCATCAATCAAAGTACAAATCAA 59.768 33.333 0.00 0.00 0.00 2.57
103 104 2.103094 CGGCCCTATCAACATTCAGAGA 59.897 50.000 0.00 0.00 0.00 3.10
107 108 5.237048 GCCCTATCAACATTCAGAGATCTC 58.763 45.833 15.29 15.29 0.00 2.75
128 130 8.712228 ATCTCTCAACTTTTTCCAATAAACCT 57.288 30.769 0.00 0.00 0.00 3.50
200 202 5.043903 CGAATGTCTTCAGTATACACCTGG 58.956 45.833 5.50 0.00 0.00 4.45
286 288 1.089481 CCATGTAGCGTTCGCCACAT 61.089 55.000 20.93 20.93 42.36 3.21
414 416 2.094762 ACGGTTCCACTCAATGTAGC 57.905 50.000 0.00 0.00 0.00 3.58
482 484 4.816385 GCAACGAAATCTTCCATATCTCCA 59.184 41.667 0.00 0.00 0.00 3.86
483 485 5.277538 GCAACGAAATCTTCCATATCTCCAC 60.278 44.000 0.00 0.00 0.00 4.02
691 697 2.061028 GCAGTGTTGCTAATTTGCACC 58.939 47.619 14.23 8.26 46.95 5.01
692 698 2.318578 CAGTGTTGCTAATTTGCACCG 58.681 47.619 14.23 0.00 43.20 4.94
693 699 1.269448 AGTGTTGCTAATTTGCACCGG 59.731 47.619 14.23 0.00 43.20 5.28
694 700 0.600557 TGTTGCTAATTTGCACCGGG 59.399 50.000 14.23 0.00 43.20 5.73
695 701 0.735978 GTTGCTAATTTGCACCGGGC 60.736 55.000 14.23 7.25 43.20 6.13
696 702 0.897863 TTGCTAATTTGCACCGGGCT 60.898 50.000 14.23 0.00 43.20 5.19
697 703 1.139520 GCTAATTTGCACCGGGCTG 59.860 57.895 6.32 0.00 45.15 4.85
698 704 1.139520 CTAATTTGCACCGGGCTGC 59.860 57.895 6.32 8.50 45.15 5.25
699 705 2.283472 CTAATTTGCACCGGGCTGCC 62.283 60.000 11.05 11.05 45.15 4.85
741 747 5.003160 TGCAAGTTGACATATTACAGCAGT 58.997 37.500 7.16 0.00 0.00 4.40
757 763 6.115448 ACAGCAGTCATTAAGTAAACCTCT 57.885 37.500 0.00 0.00 0.00 3.69
834 3022 7.363793 CCCTAACTTAATGTGGAAAATGAAGGG 60.364 40.741 0.00 0.00 0.00 3.95
906 3094 0.036732 ATCTGCCGCTTCAGGTTTCA 59.963 50.000 0.00 0.00 34.91 2.69
947 3135 1.134175 CCGCACAAACATATCCCCAAC 59.866 52.381 0.00 0.00 0.00 3.77
971 3159 0.661187 CATTCTGCAACACACGCACC 60.661 55.000 0.00 0.00 35.08 5.01
980 3168 4.295119 ACACGCACCTCACCGGAC 62.295 66.667 9.46 0.00 36.31 4.79
991 3179 4.250170 ACCGGACCACCCTCCAGT 62.250 66.667 9.46 0.00 0.00 4.00
1241 3431 0.990374 AGAACTGAGGCCTGCAAGAT 59.010 50.000 12.00 0.00 34.07 2.40
1266 3456 0.684535 TTCTCAGTCCCATCAACGCA 59.315 50.000 0.00 0.00 0.00 5.24
1302 3492 1.342496 TGTCAGCTCAAGGTCAGAGTG 59.658 52.381 0.00 0.00 35.55 3.51
1332 3522 1.490574 AGCACAGGGAGGTCTATGTC 58.509 55.000 0.00 0.00 0.00 3.06
1461 3651 2.950309 GGAGAACGATGGTAGCACTAGA 59.050 50.000 0.00 0.00 0.00 2.43
1476 3666 3.320879 TAGAGCTGCTGGTGCTGGC 62.321 63.158 7.01 0.00 41.30 4.85
1500 3690 4.974368 TTCTGATGTCGGTGTTTTTGTT 57.026 36.364 0.00 0.00 0.00 2.83
1675 3867 4.882671 TCTCAACTCTGTTTTTGAGCAC 57.117 40.909 6.48 0.00 45.65 4.40
1690 3882 4.316205 TGAGCACTACTCTTTTTGACGA 57.684 40.909 0.00 0.00 46.41 4.20
1692 3884 4.506654 TGAGCACTACTCTTTTTGACGAAC 59.493 41.667 0.00 0.00 46.41 3.95
1693 3885 4.439057 AGCACTACTCTTTTTGACGAACA 58.561 39.130 0.00 0.00 0.00 3.18
1801 4111 2.759191 ACGTCGAAGAACCCTTTAACC 58.241 47.619 5.05 0.00 39.69 2.85
1820 4130 7.605410 TTAACCGGTCACTATTTTGATCTTC 57.395 36.000 8.04 0.00 0.00 2.87
1837 4147 2.923426 TTCCCATCGCGCCTGATGAC 62.923 60.000 22.15 0.00 46.98 3.06
1847 4157 1.134877 CGCCTGATGACTCAGTCACAT 60.135 52.381 10.48 0.00 45.65 3.21
1858 4168 4.487804 ACTCAGTCACATATATGCTCCCT 58.512 43.478 12.79 1.31 0.00 4.20
1879 4189 4.008330 CTGAGAACTTGCATCCTCAACAT 58.992 43.478 8.50 0.00 35.52 2.71
1890 4200 4.142622 GCATCCTCAACATGAAAACGATGA 60.143 41.667 15.85 3.12 0.00 2.92
1933 4243 8.794335 ATGTTAAGATTAAGGTTCTTCAGACC 57.206 34.615 0.00 0.00 35.19 3.85
1957 4267 4.000988 AGGACAATTCATCGGTGTTGTAC 58.999 43.478 6.32 6.32 36.00 2.90
2016 4326 2.418368 TTGCTAAGCATACCACTGGG 57.582 50.000 0.00 0.00 38.76 4.45
2086 4396 6.480320 GTGGACAATCTTTACAGTAGCATAGG 59.520 42.308 0.00 0.00 0.00 2.57
2092 4402 6.808321 TCTTTACAGTAGCATAGGTGGATT 57.192 37.500 0.00 0.00 0.00 3.01
2117 4427 2.373224 GAAGAATTCTTGAGGCCAGGG 58.627 52.381 25.12 0.00 43.23 4.45
2226 4536 5.525378 CCTTATAAGCAAGATATCGATGGCC 59.475 44.000 8.54 0.00 0.00 5.36
2280 4590 1.597854 CTTGCACGTTGCTGGGAGA 60.598 57.895 10.54 0.00 45.31 3.71
2409 4719 2.262423 AGAAAGTGGCACTGGAGAAC 57.738 50.000 22.83 9.07 0.00 3.01
2435 4745 3.726144 AAGCAGGGGCCTCAGAGC 61.726 66.667 4.79 5.90 42.56 4.09
2446 4756 2.559440 GCCTCAGAGCTTCATGGTTAG 58.441 52.381 0.00 0.00 0.00 2.34
2448 4758 3.133003 GCCTCAGAGCTTCATGGTTAGTA 59.867 47.826 0.00 0.00 0.00 1.82
2451 4761 4.744570 TCAGAGCTTCATGGTTAGTAACG 58.255 43.478 6.94 0.00 0.00 3.18
2462 4772 7.423199 TCATGGTTAGTAACGATCTACATGTC 58.577 38.462 18.84 0.00 0.00 3.06
2485 4795 1.276421 TCCTCTGTCCTTAGCAAGCAC 59.724 52.381 0.00 0.00 0.00 4.40
2495 4805 0.815734 TAGCAAGCACTCTACGGGTC 59.184 55.000 0.00 0.00 0.00 4.46
2511 4821 2.354704 CGGGTCATTAGTGAAGCCAAGA 60.355 50.000 0.00 0.00 35.80 3.02
2646 4956 3.568538 CGCTAACTTTGCTGATTTTGCT 58.431 40.909 0.00 0.00 0.00 3.91
2651 4961 5.772825 AACTTTGCTGATTTTGCTACAGA 57.227 34.783 0.00 0.00 34.07 3.41
2719 5029 2.672996 GCGCTTCTGCCTCCCAAA 60.673 61.111 0.00 0.00 35.36 3.28
2795 5106 2.094700 TGAAGCCACTACGTTGCTCTAG 60.095 50.000 0.00 0.00 33.36 2.43
2879 5201 8.870160 TTGTTGAATTTGAGTTTGGAGTTATG 57.130 30.769 0.00 0.00 0.00 1.90
2889 5211 8.263940 TGAGTTTGGAGTTATGTTAATGCTAC 57.736 34.615 0.00 0.00 0.00 3.58
2891 5213 8.268850 AGTTTGGAGTTATGTTAATGCTACTG 57.731 34.615 0.00 0.00 0.00 2.74
2905 5239 2.496070 TGCTACTGTAAAGACGCTCCAT 59.504 45.455 0.00 0.00 0.00 3.41
3024 5360 5.868801 ACAACACAACCAAATCAACAAAGAG 59.131 36.000 0.00 0.00 0.00 2.85
3106 5452 3.282885 CCTTCCATTTAGCACTTCTCCC 58.717 50.000 0.00 0.00 0.00 4.30
3107 5453 2.691409 TCCATTTAGCACTTCTCCCG 57.309 50.000 0.00 0.00 0.00 5.14
3506 6883 4.000988 TGACGAGGGCTTTGAAATAAGAC 58.999 43.478 0.00 0.00 32.10 3.01
3536 6913 7.922505 TTGAATATTTGTGTTCCTTTTGACG 57.077 32.000 0.00 0.00 0.00 4.35
3599 6976 7.022979 ACACGTTATTAAATTTTCCTAACCGC 58.977 34.615 0.00 0.00 0.00 5.68
3684 7068 5.667539 TGGAACTCCAACATTTTTGACAA 57.332 34.783 0.00 0.00 44.35 3.18
3685 7069 5.659463 TGGAACTCCAACATTTTTGACAAG 58.341 37.500 0.00 0.00 44.35 3.16
3686 7070 5.186797 TGGAACTCCAACATTTTTGACAAGT 59.813 36.000 0.00 0.00 44.35 3.16
3687 7071 5.748630 GGAACTCCAACATTTTTGACAAGTC 59.251 40.000 0.00 0.00 35.64 3.01
3688 7072 6.405842 GGAACTCCAACATTTTTGACAAGTCT 60.406 38.462 1.53 0.00 35.64 3.24
3689 7073 6.530019 ACTCCAACATTTTTGACAAGTCTT 57.470 33.333 1.53 0.00 0.00 3.01
3690 7074 7.639113 ACTCCAACATTTTTGACAAGTCTTA 57.361 32.000 1.53 0.00 0.00 2.10
3691 7075 8.062065 ACTCCAACATTTTTGACAAGTCTTAA 57.938 30.769 1.53 0.00 0.00 1.85
3692 7076 8.527810 ACTCCAACATTTTTGACAAGTCTTAAA 58.472 29.630 1.53 2.96 0.00 1.52
3693 7077 9.364989 CTCCAACATTTTTGACAAGTCTTAAAA 57.635 29.630 12.59 12.59 32.69 1.52
3694 7078 9.712305 TCCAACATTTTTGACAAGTCTTAAAAA 57.288 25.926 11.25 11.25 36.71 1.94
3695 7079 9.753669 CCAACATTTTTGACAAGTCTTAAAAAC 57.246 29.630 11.14 0.00 35.58 2.43
3771 7158 9.499585 GTAAAACTTGGAGAAACTCTGTAAAAC 57.500 33.333 0.00 0.00 0.00 2.43
3775 7162 9.457436 AACTTGGAGAAACTCTGTAAAACTTAA 57.543 29.630 0.00 0.00 0.00 1.85
3776 7163 9.628500 ACTTGGAGAAACTCTGTAAAACTTAAT 57.372 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.065102 CTTGCTCAAATCCCTGCATCG 59.935 52.381 0.00 0.00 35.27 3.84
12 13 5.180868 CACTATATCTTGCTCAAATCCCTGC 59.819 44.000 0.00 0.00 0.00 4.85
48 49 5.941788 ACTGGAGGAGTTGATTTGTACTTT 58.058 37.500 0.00 0.00 0.00 2.66
61 62 0.251653 TTCGGCTGTACTGGAGGAGT 60.252 55.000 1.65 0.00 38.88 3.85
103 104 8.712228 AGGTTTATTGGAAAAAGTTGAGAGAT 57.288 30.769 0.00 0.00 0.00 2.75
128 130 5.819379 AGCGCAGATGATTTGAGAAAATCTA 59.181 36.000 11.47 1.10 39.33 1.98
137 139 1.431488 GCCGAGCGCAGATGATTTGA 61.431 55.000 11.47 0.00 37.47 2.69
142 144 4.819761 GTGGCCGAGCGCAGATGA 62.820 66.667 11.47 0.00 40.31 2.92
200 202 1.399440 CATACTGCATGTCCTGTGTGC 59.601 52.381 0.00 0.00 39.26 4.57
286 288 3.010138 CCCAGGGAAAGTCAAGGTTCATA 59.990 47.826 0.00 0.00 0.00 2.15
332 334 0.889186 CGGCTGCTAACCCAGTTTGT 60.889 55.000 0.00 0.00 35.28 2.83
337 339 1.745489 GGTTCGGCTGCTAACCCAG 60.745 63.158 19.97 0.00 39.43 4.45
414 416 7.224753 ACATAATTTTACTGTACGATCAGCCTG 59.775 37.037 10.40 0.00 38.84 4.85
482 484 4.739793 TCCTTCAAATCCCATTGTCAAGT 58.260 39.130 0.00 0.00 0.00 3.16
483 485 5.927281 ATCCTTCAAATCCCATTGTCAAG 57.073 39.130 0.00 0.00 0.00 3.02
678 684 1.304052 AGCCCGGTGCAAATTAGCA 60.304 52.632 15.92 0.00 44.83 3.49
679 685 1.139520 CAGCCCGGTGCAAATTAGC 59.860 57.895 15.92 1.74 44.83 3.09
680 686 1.139520 GCAGCCCGGTGCAAATTAG 59.860 57.895 13.70 0.00 43.41 1.73
681 687 2.347322 GGCAGCCCGGTGCAAATTA 61.347 57.895 19.47 0.00 45.93 1.40
682 688 3.694538 GGCAGCCCGGTGCAAATT 61.695 61.111 19.47 0.00 45.93 1.82
688 694 3.995506 CTAAAGGGGCAGCCCGGTG 62.996 68.421 25.18 8.67 46.66 4.94
689 695 3.728373 CTAAAGGGGCAGCCCGGT 61.728 66.667 25.18 11.58 46.66 5.28
690 696 3.728373 ACTAAAGGGGCAGCCCGG 61.728 66.667 25.18 13.48 46.66 5.73
691 697 2.438434 CACTAAAGGGGCAGCCCG 60.438 66.667 25.18 12.65 46.66 6.13
692 698 1.076727 AACACTAAAGGGGCAGCCC 59.923 57.895 24.23 24.23 44.51 5.19
693 699 1.877576 GCAACACTAAAGGGGCAGCC 61.878 60.000 1.26 1.26 0.00 4.85
694 700 0.895559 AGCAACACTAAAGGGGCAGC 60.896 55.000 0.00 0.00 0.00 5.25
695 701 2.489938 TAGCAACACTAAAGGGGCAG 57.510 50.000 0.00 0.00 0.00 4.85
696 702 2.961531 TTAGCAACACTAAAGGGGCA 57.038 45.000 0.00 0.00 37.93 5.36
697 703 4.494484 CAAATTAGCAACACTAAAGGGGC 58.506 43.478 0.00 0.00 43.99 5.80
698 704 4.021544 TGCAAATTAGCAACACTAAAGGGG 60.022 41.667 0.00 0.00 43.99 4.79
699 705 5.132897 TGCAAATTAGCAACACTAAAGGG 57.867 39.130 0.00 0.00 43.99 3.95
754 760 6.239176 GGAGTGGATCAGTTACCTTATCAGAG 60.239 46.154 0.00 0.00 0.00 3.35
757 763 5.128827 GTGGAGTGGATCAGTTACCTTATCA 59.871 44.000 0.00 0.00 0.00 2.15
834 3022 1.179174 GGTCCTGCAGTTTTCCCACC 61.179 60.000 13.81 3.12 0.00 4.61
906 3094 3.958860 AAGCGGCAGGAGGTTGCT 61.959 61.111 1.45 0.00 43.57 3.91
933 3121 3.426787 TGTCGTGTTGGGGATATGTTT 57.573 42.857 0.00 0.00 0.00 2.83
947 3135 1.657260 CGTGTGTTGCAGAATGTCGTG 60.657 52.381 0.00 0.00 39.31 4.35
971 3159 3.391382 GGAGGGTGGTCCGGTGAG 61.391 72.222 0.00 0.00 41.52 3.51
980 3168 2.122729 TGGAGGACTGGAGGGTGG 59.877 66.667 0.00 0.00 0.00 4.61
991 3179 3.770040 CGTCGCCATGGTGGAGGA 61.770 66.667 24.82 2.61 40.96 3.71
1056 3245 2.743928 GCGAAGACCACCCTGCTG 60.744 66.667 0.00 0.00 0.00 4.41
1212 3402 0.739112 CCTCAGTTCTGAAGAGGCGC 60.739 60.000 11.41 0.00 42.13 6.53
1241 3431 2.190538 TGATGGGACTGAGAAGCATCA 58.809 47.619 0.00 0.00 0.00 3.07
1287 3477 0.389166 CGTCCACTCTGACCTTGAGC 60.389 60.000 0.00 0.00 35.12 4.26
1302 3492 1.961277 CCTGTGCTTGGTGTCGTCC 60.961 63.158 0.00 0.00 0.00 4.79
1332 3522 3.476646 CAGCTCGTGTCAGCGCAG 61.477 66.667 11.47 0.00 44.82 5.18
1439 3629 1.557099 AGTGCTACCATCGTTCTCCA 58.443 50.000 0.00 0.00 0.00 3.86
1476 3666 4.151070 CAAAAACACCGACATCAGAATCG 58.849 43.478 1.25 1.25 38.08 3.34
1500 3690 4.022589 ACGATGAACTTCACGTCCTCTTTA 60.023 41.667 11.32 0.00 31.95 1.85
1801 4111 4.513442 TGGGAAGATCAAAATAGTGACCG 58.487 43.478 0.00 0.00 0.00 4.79
1820 4130 2.969238 GTCATCAGGCGCGATGGG 60.969 66.667 20.56 10.21 42.58 4.00
1837 4147 4.525874 TCAGGGAGCATATATGTGACTGAG 59.474 45.833 14.14 0.74 0.00 3.35
1847 4157 3.711190 TGCAAGTTCTCAGGGAGCATATA 59.289 43.478 0.00 0.00 0.00 0.86
1858 4168 3.490439 TGTTGAGGATGCAAGTTCTCA 57.510 42.857 0.00 0.00 34.84 3.27
1879 4189 3.689161 GGGTGTGATCATCATCGTTTTCA 59.311 43.478 0.00 0.00 0.00 2.69
1890 4200 7.888021 TCTTAACATTGTTTAGGGTGTGATCAT 59.112 33.333 13.83 0.00 0.00 2.45
1933 4243 3.253188 ACAACACCGATGAATTGTCCTTG 59.747 43.478 0.00 0.00 29.30 3.61
2016 4326 5.073144 TCCCATACCTTTTCACTATGGATCC 59.927 44.000 4.20 4.20 39.52 3.36
2063 4373 6.480320 CACCTATGCTACTGTAAAGATTGTCC 59.520 42.308 0.00 0.00 0.00 4.02
2086 4396 6.017400 TCAAGAATTCTTCAGCAAATCCAC 57.983 37.500 17.91 0.00 33.11 4.02
2092 4402 2.821969 GGCCTCAAGAATTCTTCAGCAA 59.178 45.455 24.28 8.73 33.11 3.91
2117 4427 2.275318 GACAGTAGCAAGATCTGGCAC 58.725 52.381 24.11 18.12 37.20 5.01
2204 4514 5.109210 CGGCCATCGATATCTTGCTTATAA 58.891 41.667 2.24 0.00 42.43 0.98
2409 4719 0.825010 GGCCCCTGCTTGACATATGG 60.825 60.000 7.80 0.00 37.74 2.74
2435 4745 7.921214 ACATGTAGATCGTTACTAACCATGAAG 59.079 37.037 15.11 0.00 33.06 3.02
2446 4756 5.299782 AGAGGAAGGACATGTAGATCGTTAC 59.700 44.000 0.00 0.00 0.00 2.50
2448 4758 4.098654 CAGAGGAAGGACATGTAGATCGTT 59.901 45.833 0.00 0.00 0.00 3.85
2451 4761 4.038642 GGACAGAGGAAGGACATGTAGATC 59.961 50.000 0.00 0.00 0.00 2.75
2462 4772 2.679349 GCTTGCTAAGGACAGAGGAAGG 60.679 54.545 5.48 0.00 40.41 3.46
2485 4795 3.491104 GGCTTCACTAATGACCCGTAGAG 60.491 52.174 0.00 0.00 33.38 2.43
2495 4805 6.111382 TCTCTGAATCTTGGCTTCACTAATG 58.889 40.000 0.00 0.00 0.00 1.90
2511 4821 3.652869 TCCACAAGGTCCTTTCTCTGAAT 59.347 43.478 0.00 0.00 35.89 2.57
2646 4956 6.516718 GCTTTCAGTAGCTCCATAATCTGTA 58.483 40.000 0.00 0.00 38.15 2.74
2660 4970 1.808945 CACCAAGGCAGCTTTCAGTAG 59.191 52.381 0.00 0.00 0.00 2.57
2699 5009 4.704833 GGGAGGCAGAAGCGCACA 62.705 66.667 11.47 0.00 43.41 4.57
2700 5010 4.704833 TGGGAGGCAGAAGCGCAC 62.705 66.667 11.47 2.78 43.41 5.34
2719 5029 1.885049 TATTCTTGGGAGCAGGCTCT 58.115 50.000 19.67 2.11 42.38 4.09
2795 5106 7.823149 ATTTCTTGTTCTTATTCTGCAATGC 57.177 32.000 0.00 0.00 0.00 3.56
2849 5164 4.810491 CCAAACTCAAATTCAACAAGGGTG 59.190 41.667 0.00 0.00 0.00 4.61
2879 5201 5.005490 GGAGCGTCTTTACAGTAGCATTAAC 59.995 44.000 0.00 0.00 0.00 2.01
2889 5211 4.327357 CACAGTAATGGAGCGTCTTTACAG 59.673 45.833 15.09 11.56 32.82 2.74
2891 5213 4.491676 TCACAGTAATGGAGCGTCTTTAC 58.508 43.478 0.00 8.81 0.00 2.01
2905 5239 2.897271 AATGGTGCCCATCACAGTAA 57.103 45.000 7.12 0.00 44.40 2.24
3024 5360 2.344025 GTGGTCTACGTGGATTTGGTC 58.656 52.381 4.45 0.00 0.00 4.02
3521 6898 1.961793 CCCTCGTCAAAAGGAACACA 58.038 50.000 0.00 0.00 35.83 3.72
3536 6913 5.921962 ATTGGTCTTATTTCAAAGCCCTC 57.078 39.130 0.00 0.00 0.00 4.30
3581 6958 7.892609 AGTTTCAGCGGTTAGGAAAATTTAAT 58.107 30.769 0.80 0.00 32.85 1.40
3592 6969 8.879759 TCATTTCTATTAAGTTTCAGCGGTTAG 58.120 33.333 0.00 0.00 0.00 2.34
3679 7063 8.736244 ACTTGCTAAAGTTTTTAAGACTTGTCA 58.264 29.630 1.61 0.00 44.47 3.58


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

AutoCloner maintained by Alex Coulton.