Multiple sequence alignment - TraesCS7A01G532300

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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 TraesCS7A01G532300 chr7A 100.000 3525 0 0 1 3525 711173631 711170107 0.000000e+00 6510.0
1 TraesCS7A01G532300 chr7A 89.470 1472 150 5 1058 2528 710959320 710957853 0.000000e+00 1855.0
2 TraesCS7A01G532300 chr7A 89.113 248 24 2 413 660 710960058 710959814 4.420000e-79 305.0
3 TraesCS7A01G532300 chr7A 76.000 250 39 16 817 1061 710959685 710959452 3.720000e-20 110.0
4 TraesCS7A01G532300 chr7B 90.408 2012 167 17 670 2677 711489882 711487893 0.000000e+00 2623.0
5 TraesCS7A01G532300 chr7B 90.318 1570 135 8 1094 2649 711475566 711477132 0.000000e+00 2041.0
6 TraesCS7A01G532300 chr7B 89.331 628 51 11 52 667 711490858 711490235 0.000000e+00 774.0
7 TraesCS7A01G532300 chr7B 90.126 557 51 3 62 615 711474675 711475230 0.000000e+00 721.0
8 TraesCS7A01G532300 chr7B 86.047 172 13 8 707 874 711475253 711475417 1.300000e-39 174.0
9 TraesCS7A01G532300 chr7D 92.367 1808 130 5 870 2677 617378359 617376560 0.000000e+00 2567.0
10 TraesCS7A01G532300 chr7D 88.834 1612 153 14 922 2533 617197160 617198744 0.000000e+00 1954.0
11 TraesCS7A01G532300 chr7D 94.540 641 34 1 2885 3525 574674441 574675080 0.000000e+00 989.0
12 TraesCS7A01G532300 chr7D 90.561 392 32 4 278 667 617379406 617379018 6.750000e-142 514.0
13 TraesCS7A01G532300 chr7D 89.324 281 21 6 1 280 617384062 617383790 9.370000e-91 344.0
14 TraesCS7A01G532300 chr7D 90.347 259 18 4 408 660 617196757 617197014 2.030000e-87 333.0
15 TraesCS7A01G532300 chr7D 91.477 176 13 1 667 842 617378981 617378808 1.260000e-59 241.0
16 TraesCS7A01G532300 chr7D 94.815 135 5 1 736 870 617378811 617378679 3.570000e-50 209.0
17 TraesCS7A01G532300 chrUn 87.664 1297 145 9 1216 2503 241849815 241848525 0.000000e+00 1495.0
18 TraesCS7A01G532300 chrUn 100.000 31 0 0 963 993 427577804 427577834 1.370000e-04 58.4
19 TraesCS7A01G532300 chrUn 100.000 31 0 0 963 993 460760366 460760336 1.370000e-04 58.4
20 TraesCS7A01G532300 chr4A 87.355 1297 149 11 1216 2503 599612138 599613428 0.000000e+00 1472.0
21 TraesCS7A01G532300 chr4A 82.085 1295 212 18 1214 2502 24557443 24556163 0.000000e+00 1088.0
22 TraesCS7A01G532300 chr2D 97.642 848 20 0 2678 3525 628171297 628170450 0.000000e+00 1456.0
23 TraesCS7A01G532300 chr4D 97.524 848 21 0 2678 3525 389492679 389491832 0.000000e+00 1450.0
24 TraesCS7A01G532300 chr4D 82.071 1294 208 22 1214 2499 443206670 443207947 0.000000e+00 1083.0
25 TraesCS7A01G532300 chr3A 97.300 852 18 3 2673 3522 747055280 747056128 0.000000e+00 1441.0
26 TraesCS7A01G532300 chr3A 90.691 333 22 7 2678 3009 603279258 603279582 5.400000e-118 435.0
27 TraesCS7A01G532300 chr1D 92.606 852 56 4 2678 3525 47639026 47639874 0.000000e+00 1218.0
28 TraesCS7A01G532300 chr1D 92.506 854 58 4 2675 3525 463531176 463532026 0.000000e+00 1218.0
29 TraesCS7A01G532300 chr5D 92.308 858 60 4 2671 3525 322189740 322188886 0.000000e+00 1214.0
30 TraesCS7A01G532300 chr3D 92.127 851 61 4 2678 3525 538177883 538178730 0.000000e+00 1195.0
31 TraesCS7A01G532300 chr5B 90.391 843 75 5 2678 3518 448039249 448040087 0.000000e+00 1103.0
32 TraesCS7A01G532300 chr1B 89.714 768 60 13 52 805 667982566 667981804 0.000000e+00 963.0


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 TraesCS7A01G532300 chr7A 711170107 711173631 3524 True 6510.000000 6510 100.000000 1 3525 1 chr7A.!!$R1 3524
1 TraesCS7A01G532300 chr7A 710957853 710960058 2205 True 756.666667 1855 84.861000 413 2528 3 chr7A.!!$R2 2115
2 TraesCS7A01G532300 chr7B 711487893 711490858 2965 True 1698.500000 2623 89.869500 52 2677 2 chr7B.!!$R1 2625
3 TraesCS7A01G532300 chr7B 711474675 711477132 2457 False 978.666667 2041 88.830333 62 2649 3 chr7B.!!$F1 2587
4 TraesCS7A01G532300 chr7D 617196757 617198744 1987 False 1143.500000 1954 89.590500 408 2533 2 chr7D.!!$F2 2125
5 TraesCS7A01G532300 chr7D 574674441 574675080 639 False 989.000000 989 94.540000 2885 3525 1 chr7D.!!$F1 640
6 TraesCS7A01G532300 chr7D 617376560 617379406 2846 True 882.750000 2567 92.305000 278 2677 4 chr7D.!!$R2 2399
7 TraesCS7A01G532300 chrUn 241848525 241849815 1290 True 1495.000000 1495 87.664000 1216 2503 1 chrUn.!!$R1 1287
8 TraesCS7A01G532300 chr4A 599612138 599613428 1290 False 1472.000000 1472 87.355000 1216 2503 1 chr4A.!!$F1 1287
9 TraesCS7A01G532300 chr4A 24556163 24557443 1280 True 1088.000000 1088 82.085000 1214 2502 1 chr4A.!!$R1 1288
10 TraesCS7A01G532300 chr2D 628170450 628171297 847 True 1456.000000 1456 97.642000 2678 3525 1 chr2D.!!$R1 847
11 TraesCS7A01G532300 chr4D 389491832 389492679 847 True 1450.000000 1450 97.524000 2678 3525 1 chr4D.!!$R1 847
12 TraesCS7A01G532300 chr4D 443206670 443207947 1277 False 1083.000000 1083 82.071000 1214 2499 1 chr4D.!!$F1 1285
13 TraesCS7A01G532300 chr3A 747055280 747056128 848 False 1441.000000 1441 97.300000 2673 3522 1 chr3A.!!$F2 849
14 TraesCS7A01G532300 chr1D 47639026 47639874 848 False 1218.000000 1218 92.606000 2678 3525 1 chr1D.!!$F1 847
15 TraesCS7A01G532300 chr1D 463531176 463532026 850 False 1218.000000 1218 92.506000 2675 3525 1 chr1D.!!$F2 850
16 TraesCS7A01G532300 chr5D 322188886 322189740 854 True 1214.000000 1214 92.308000 2671 3525 1 chr5D.!!$R1 854
17 TraesCS7A01G532300 chr3D 538177883 538178730 847 False 1195.000000 1195 92.127000 2678 3525 1 chr3D.!!$F1 847
18 TraesCS7A01G532300 chr5B 448039249 448040087 838 False 1103.000000 1103 90.391000 2678 3518 1 chr5B.!!$F1 840
19 TraesCS7A01G532300 chr1B 667981804 667982566 762 True 963.000000 963 89.714000 52 805 1 chr1B.!!$R1 753

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
81 82 0.250295 TCAGTGCCAAAGGAAGACCG 60.250 55.0 0.0 0.0 41.83 4.79 F
356 362 0.611896 AATTTGCCCCCACTTCCTCG 60.612 55.0 0.0 0.0 0.00 4.63 F
1995 3009 0.611062 ACGTCGGGATCAACCTCAGA 60.611 55.0 0.0 0.0 38.98 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 2616 0.617535 TGATGTCGACCAGGGATGGT 60.618 55.0 14.12 0.00 46.40 3.55 R
2128 3142 0.474660 GGGATGTAGGGCCTGATCCT 60.475 60.0 30.70 12.35 35.61 3.24 R
3273 4308 6.434018 AATCTTGAAGATGCACTTAAGAGC 57.566 37.5 16.90 16.90 39.13 4.09 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
23 24 6.957984 AATCACTCGCATCATGATATACAC 57.042 37.500 8.15 0.00 32.74 2.90
24 25 5.712152 TCACTCGCATCATGATATACACT 57.288 39.130 8.15 0.00 0.00 3.55
25 26 6.089249 TCACTCGCATCATGATATACACTT 57.911 37.500 8.15 0.00 0.00 3.16
26 27 7.214467 TCACTCGCATCATGATATACACTTA 57.786 36.000 8.15 0.00 0.00 2.24
27 28 7.657336 TCACTCGCATCATGATATACACTTAA 58.343 34.615 8.15 0.00 0.00 1.85
28 29 8.141268 TCACTCGCATCATGATATACACTTAAA 58.859 33.333 8.15 0.00 0.00 1.52
29 30 8.764287 CACTCGCATCATGATATACACTTAAAA 58.236 33.333 8.15 0.00 0.00 1.52
30 31 9.325198 ACTCGCATCATGATATACACTTAAAAA 57.675 29.630 8.15 0.00 0.00 1.94
81 82 0.250295 TCAGTGCCAAAGGAAGACCG 60.250 55.000 0.00 0.00 41.83 4.79
109 110 1.376543 TCGAGACTACCCTAGCAACG 58.623 55.000 0.00 0.00 0.00 4.10
183 187 5.941788 ACAAGTGGGATTATTAGTCCATCC 58.058 41.667 7.46 0.00 37.49 3.51
205 209 5.104374 CCTATTTTGTGCATCGCATCTTTT 58.896 37.500 0.00 0.00 41.91 2.27
233 237 3.559069 ACATCATCCTGGCTACCATTTG 58.441 45.455 0.00 0.00 30.82 2.32
289 295 4.162690 GGCTCTGGGGCGTACTGG 62.163 72.222 0.00 0.00 0.00 4.00
347 353 2.223443 ACCCTTGCAATTTGCCCCC 61.223 57.895 18.27 0.00 44.23 5.40
356 362 0.611896 AATTTGCCCCCACTTCCTCG 60.612 55.000 0.00 0.00 0.00 4.63
359 365 4.785453 GCCCCCACTTCCTCGCTG 62.785 72.222 0.00 0.00 0.00 5.18
373 379 2.354259 CTCGCTGGCTCTTCAAGAAAT 58.646 47.619 0.00 0.00 0.00 2.17
374 380 2.746362 CTCGCTGGCTCTTCAAGAAATT 59.254 45.455 0.00 0.00 0.00 1.82
385 391 7.087007 GCTCTTCAAGAAATTTTTAGGTCCAG 58.913 38.462 0.00 0.00 0.00 3.86
398 404 8.477419 TTTTTAGGTCCAGTTGAAGAATCAAT 57.523 30.769 0.00 0.00 46.67 2.57
554 567 4.993584 GCCTATGATGACTTCGTCAATCAT 59.006 41.667 17.50 17.50 45.96 2.45
562 583 6.228616 TGACTTCGTCAATCATAATACCCA 57.771 37.500 0.00 0.00 39.78 4.51
599 620 4.528596 TCAGAGGAGCTTATAAGGGTATGC 59.471 45.833 14.28 0.00 0.00 3.14
619 642 2.475519 GCTGTACATGTGCGCGTTTATT 60.476 45.455 9.11 0.00 0.00 1.40
660 683 1.070376 CATGTGAGCGTCTGTGTTGTG 60.070 52.381 0.00 0.00 0.00 3.33
705 1078 8.647796 TGCTCTTATATTTCTTTATCGAGGGAA 58.352 33.333 0.00 0.00 0.00 3.97
753 1127 4.493547 CCCAAAAGAGCGCAAAATCAATA 58.506 39.130 11.47 0.00 0.00 1.90
757 1131 6.957077 CCAAAAGAGCGCAAAATCAATAATTG 59.043 34.615 11.47 1.17 0.00 2.32
758 1132 5.707411 AAGAGCGCAAAATCAATAATTGC 57.293 34.783 11.47 0.00 44.50 3.56
777 1180 1.593196 CGCCTCTGTTTTCCTGTTCA 58.407 50.000 0.00 0.00 0.00 3.18
826 1330 2.780643 CCGAGTCGCAACAGCATG 59.219 61.111 7.12 0.00 46.00 4.06
874 1698 4.715520 AGTGATATGCTTGCGTTAATCG 57.284 40.909 0.00 0.00 43.12 3.34
954 1811 7.170658 TGACTACAAATTAATGCTTTGTTTGCC 59.829 33.333 10.13 9.87 42.58 4.52
1015 1882 7.618502 AATTAAGACACACACACACACTAAA 57.381 32.000 0.00 0.00 0.00 1.85
1046 1913 7.148390 GCTCATAAAGGAAAGAGTACTTCCAAC 60.148 40.741 13.40 0.00 35.05 3.77
1203 2208 2.526545 GCTCATCAGCTACATCCGC 58.473 57.895 0.00 0.00 43.09 5.54
1212 2217 1.146930 CTACATCCGCCCAGTGCAT 59.853 57.895 0.00 0.00 41.33 3.96
1230 2235 1.589716 ATCTGTTCTTTGCAGCCGCC 61.590 55.000 0.00 0.00 37.32 6.13
1465 2479 3.405592 TACATCCCGACGCACGAGC 62.406 63.158 0.00 0.00 45.77 5.03
1487 2501 2.989639 CACCCTCGAGAATGCCCA 59.010 61.111 15.71 0.00 0.00 5.36
1491 2505 2.185350 CTCGAGAATGCCCACGCT 59.815 61.111 6.58 0.00 35.36 5.07
1534 2548 1.445095 GCCATCGATGACCTGCTCT 59.555 57.895 26.86 0.00 0.00 4.09
1538 2552 1.039068 ATCGATGACCTGCTCTCCAG 58.961 55.000 0.00 0.00 41.41 3.86
1564 2578 2.764128 TCGCCCCAGACTCCATCC 60.764 66.667 0.00 0.00 0.00 3.51
1566 2580 3.083997 GCCCCAGACTCCATCCGT 61.084 66.667 0.00 0.00 0.00 4.69
1596 2610 0.761187 TCAACTGCAGCCTCTTCTGT 59.239 50.000 15.27 0.00 36.49 3.41
1602 2616 2.061220 CAGCCTCTTCTGTCCCACA 58.939 57.895 0.00 0.00 0.00 4.17
1641 2655 5.456548 TCATCGTGAACAAGTACAACCTA 57.543 39.130 0.00 0.00 0.00 3.08
1706 2720 2.764128 GGGGCTCATCTCCGTGGA 60.764 66.667 0.00 0.00 0.00 4.02
1707 2721 2.367202 GGGGCTCATCTCCGTGGAA 61.367 63.158 0.00 0.00 0.00 3.53
1767 2781 4.357947 GCGCTGGTCGTCTCCACA 62.358 66.667 0.00 0.00 41.07 4.17
1830 2844 1.002134 GCTCCTGCCAAACTGCCTA 60.002 57.895 0.00 0.00 0.00 3.93
1917 2931 1.081641 CGTCGTACGCACCTTCACT 60.082 57.895 11.24 0.00 33.65 3.41
1927 2941 2.664851 CCTTCACTGGCGCGAACA 60.665 61.111 12.10 7.09 0.00 3.18
1995 3009 0.611062 ACGTCGGGATCAACCTCAGA 60.611 55.000 0.00 0.00 38.98 3.27
2061 3075 2.683933 AGGATCGGGCCACTCGTT 60.684 61.111 4.39 0.00 0.00 3.85
2097 3111 2.770589 GCTCCTCTTCGCGCTCTCT 61.771 63.158 5.56 0.00 0.00 3.10
2157 3171 0.669077 CCTACATCCCGGACTTCTCG 59.331 60.000 0.73 0.00 0.00 4.04
2160 3174 0.611062 ACATCCCGGACTTCTCGACA 60.611 55.000 0.73 0.00 0.00 4.35
2219 3233 0.865218 GTCATCGACGAGCTGCAGAG 60.865 60.000 20.43 10.37 0.00 3.35
2265 3279 4.194720 GAGGCGTCGCGGATGACT 62.195 66.667 11.75 6.00 40.00 3.41
2370 3384 1.813753 CCGCGTTTGGATGATCGGT 60.814 57.895 4.92 0.00 32.93 4.69
2415 3432 1.295101 CGTGGTGTGGGAGTGCATA 59.705 57.895 0.00 0.00 0.00 3.14
2422 3439 1.026718 GTGGGAGTGCATACAGCCAC 61.027 60.000 0.00 0.00 44.83 5.01
2429 3446 2.676608 CATACAGCCACCTGCCCA 59.323 61.111 0.00 0.00 43.02 5.36
2533 3565 3.813166 CACTACATAATAAACCCAGCCCG 59.187 47.826 0.00 0.00 0.00 6.13
2555 3587 2.409975 ACGGTGGTCTAAACATGAACG 58.590 47.619 0.00 0.00 0.00 3.95
2562 3594 6.370718 GGTGGTCTAAACATGAACGATAAACT 59.629 38.462 0.00 0.00 0.00 2.66
2576 3608 5.287226 ACGATAAACTCCATATGGTCGTTC 58.713 41.667 22.96 14.33 36.47 3.95
2580 3612 2.747177 ACTCCATATGGTCGTTCCTGA 58.253 47.619 21.28 0.00 37.07 3.86
2638 3671 2.095853 ACGTACGTACCATGTAACCGAG 59.904 50.000 21.41 3.95 0.00 4.63
2639 3672 2.454055 GTACGTACCATGTAACCGAGC 58.546 52.381 15.00 0.00 0.00 5.03
2681 3714 1.066929 CGATGTGTGTGATGGACAGGA 60.067 52.381 0.00 0.00 34.28 3.86
2927 3962 4.826733 TCTACCAAAAAGCAGCATTCTTCA 59.173 37.500 0.00 0.00 0.00 3.02
3236 4271 2.072298 CTGCAGAAAAAGTAGCTCGCT 58.928 47.619 8.42 0.00 0.00 4.93
3273 4308 7.875041 AGTCCATCAATATCTTTATGTTCTCCG 59.125 37.037 0.00 0.00 0.00 4.63
3338 4373 2.358957 CTTGTCATCCAAGGATCGCAA 58.641 47.619 0.00 6.65 45.70 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.278172 AGTGTATATCATGATGCGAGTGAT 57.722 37.500 18.72 4.39 36.60 3.06
2 3 5.712152 AGTGTATATCATGATGCGAGTGA 57.288 39.130 18.72 0.00 0.00 3.41
28 29 8.090214 CCAAACACCTATCTGATTGATGTTTTT 58.910 33.333 18.03 0.98 34.08 1.94
29 30 7.451255 TCCAAACACCTATCTGATTGATGTTTT 59.549 33.333 18.03 5.46 34.08 2.43
30 31 6.947733 TCCAAACACCTATCTGATTGATGTTT 59.052 34.615 15.79 15.79 35.67 2.83
31 32 6.375455 GTCCAAACACCTATCTGATTGATGTT 59.625 38.462 6.08 6.08 36.65 2.71
32 33 5.882557 GTCCAAACACCTATCTGATTGATGT 59.117 40.000 0.00 0.00 36.65 3.06
33 34 5.882000 TGTCCAAACACCTATCTGATTGATG 59.118 40.000 0.00 0.00 36.65 3.07
34 35 6.065976 TGTCCAAACACCTATCTGATTGAT 57.934 37.500 0.00 0.00 39.11 2.57
35 36 5.497464 TGTCCAAACACCTATCTGATTGA 57.503 39.130 0.00 0.00 0.00 2.57
48 49 2.552155 GGCACTGATAGGTGTCCAAACA 60.552 50.000 0.00 0.00 39.21 2.83
49 50 2.084546 GGCACTGATAGGTGTCCAAAC 58.915 52.381 0.00 0.00 39.21 2.93
50 51 1.702401 TGGCACTGATAGGTGTCCAAA 59.298 47.619 0.00 0.00 40.67 3.28
81 82 1.606189 GGGTAGTCTCGATAACGGTCC 59.394 57.143 0.00 0.00 40.21 4.46
125 126 1.202428 GGTCGAGTCATCTTAGCACCC 60.202 57.143 0.00 0.00 0.00 4.61
136 138 3.444034 CCTTCTGTGATAAGGTCGAGTCA 59.556 47.826 0.00 0.00 38.98 3.41
183 187 5.574055 ACAAAAGATGCGATGCACAAAATAG 59.426 36.000 0.00 0.00 43.04 1.73
205 209 4.947388 GGTAGCCAGGATGATGTTTTAACA 59.053 41.667 0.00 0.00 44.06 2.41
233 237 4.764172 ACATGACATGAGAGAAAGTAGCC 58.236 43.478 22.19 0.00 0.00 3.93
347 353 0.739112 GAAGAGCCAGCGAGGAAGTG 60.739 60.000 2.12 0.00 41.22 3.16
356 362 5.866092 CCTAAAAATTTCTTGAAGAGCCAGC 59.134 40.000 0.00 0.00 0.00 4.85
358 364 6.015434 GGACCTAAAAATTTCTTGAAGAGCCA 60.015 38.462 0.00 0.00 0.00 4.75
359 365 6.015434 TGGACCTAAAAATTTCTTGAAGAGCC 60.015 38.462 0.00 0.00 0.00 4.70
373 379 7.889873 TTGATTCTTCAACTGGACCTAAAAA 57.110 32.000 0.00 0.00 36.94 1.94
374 380 7.944554 AGATTGATTCTTCAACTGGACCTAAAA 59.055 33.333 0.00 0.00 44.36 1.52
385 391 7.768120 ACCATCTAGTGAGATTGATTCTTCAAC 59.232 37.037 0.00 0.00 44.36 3.18
398 404 4.232188 ACCTACGAACCATCTAGTGAGA 57.768 45.455 0.00 0.00 35.71 3.27
525 538 2.101415 CGAAGTCATCATAGGCACCTCA 59.899 50.000 0.00 0.00 0.00 3.86
554 567 4.737578 AGAGGCTTAGTCGATGGGTATTA 58.262 43.478 0.00 0.00 0.00 0.98
562 583 2.582052 CCTCTGAGAGGCTTAGTCGAT 58.418 52.381 16.73 0.00 43.29 3.59
599 620 3.383546 AATAAACGCGCACATGTACAG 57.616 42.857 5.73 0.00 0.00 2.74
619 642 7.759433 CACATGTACACACATACACTCAATCTA 59.241 37.037 0.00 0.00 43.73 1.98
660 683 4.967036 AGCAATTTAGATCACTAGGGAGC 58.033 43.478 0.76 0.76 0.00 4.70
731 1105 2.437200 TGATTTTGCGCTCTTTTGGG 57.563 45.000 9.73 0.00 0.00 4.12
753 1127 1.270550 CAGGAAAACAGAGGCGCAATT 59.729 47.619 10.83 0.00 0.00 2.32
757 1131 0.238553 GAACAGGAAAACAGAGGCGC 59.761 55.000 0.00 0.00 0.00 6.53
758 1132 1.593196 TGAACAGGAAAACAGAGGCG 58.407 50.000 0.00 0.00 0.00 5.52
826 1330 2.740055 CACTGTCAGCTCGTGGCC 60.740 66.667 0.00 0.00 43.05 5.36
954 1811 7.928706 AGTGCTTGCACTTATATAGTCTTTAGG 59.071 37.037 20.95 0.00 33.85 2.69
1015 1882 6.898521 AGTACTCTTTCCTTTATGAGCTAGGT 59.101 38.462 0.00 0.00 0.00 3.08
1046 1913 1.464608 TCATGCCGCTCTTTCTTTTCG 59.535 47.619 0.00 0.00 0.00 3.46
1212 2217 2.260869 GGCGGCTGCAAAGAACAGA 61.261 57.895 21.31 0.00 45.35 3.41
1233 2238 4.508128 ATGAGGTACACGGCGGCG 62.508 66.667 31.06 31.06 0.00 6.46
1465 2479 1.364626 GCATTCTCGAGGGTGCAGTG 61.365 60.000 27.03 11.94 37.52 3.66
1487 2501 2.177038 CGAGCTCGAACTCAGCGT 59.823 61.111 32.06 0.00 42.14 5.07
1491 2505 0.949588 AGACGACGAGCTCGAACTCA 60.950 55.000 40.58 0.00 46.14 3.41
1524 2538 0.902048 CTGTCCTGGAGAGCAGGTCA 60.902 60.000 8.03 0.00 40.59 4.02
1564 2578 1.007271 AGTTGAGGACGAGCACACG 60.007 57.895 0.00 0.00 39.31 4.49
1566 2580 1.300931 GCAGTTGAGGACGAGCACA 60.301 57.895 0.00 0.00 35.26 4.57
1596 2610 1.923395 GACCAGGGATGGTGTGGGA 60.923 63.158 4.31 0.00 43.24 4.37
1602 2616 0.617535 TGATGTCGACCAGGGATGGT 60.618 55.000 14.12 0.00 46.40 3.55
1641 2655 2.102357 CTACGGATGTCGCAGCGT 59.898 61.111 15.93 0.00 43.89 5.07
1706 2720 3.069778 GGAGGTTCCTGGCGAGTT 58.930 61.111 0.00 0.00 32.53 3.01
1767 2781 0.687354 AGTTTGGCGTGATGGTCTCT 59.313 50.000 0.00 0.00 0.00 3.10
1917 2931 2.248135 ATTGTCGTTGTTCGCGCCA 61.248 52.632 0.00 0.00 39.67 5.69
1927 2941 1.153353 CACCGGTAAGCATTGTCGTT 58.847 50.000 6.87 0.00 0.00 3.85
1995 3009 1.755179 CGATGGCCATCAGGTTCTTT 58.245 50.000 38.08 7.24 37.69 2.52
2097 3111 2.975799 GCCTTCCGTGCCACGAAA 60.976 61.111 20.57 2.99 46.05 3.46
2128 3142 0.474660 GGGATGTAGGGCCTGATCCT 60.475 60.000 30.70 12.35 35.61 3.24
2157 3171 1.068748 CACAGGTGCTTGAATGCTGTC 60.069 52.381 0.00 0.00 0.00 3.51
2370 3384 0.472471 ACTTGAACCCTGAGCCGAAA 59.528 50.000 0.00 0.00 0.00 3.46
2415 3432 3.819652 TTGTGGGCAGGTGGCTGT 61.820 61.111 3.28 0.00 44.01 4.40
2422 3439 2.118076 ATGGGTGTTGTGGGCAGG 59.882 61.111 0.00 0.00 0.00 4.85
2429 3446 3.897122 ACGGCCCATGGGTGTTGT 61.897 61.111 31.58 20.64 37.65 3.32
2505 3522 6.766467 GCTGGGTTTATTATGTAGTGTAAGCT 59.234 38.462 0.00 0.00 0.00 3.74
2506 3523 6.017357 GGCTGGGTTTATTATGTAGTGTAAGC 60.017 42.308 0.00 0.00 0.00 3.09
2507 3524 6.485648 GGGCTGGGTTTATTATGTAGTGTAAG 59.514 42.308 0.00 0.00 0.00 2.34
2533 3565 2.740447 GTTCATGTTTAGACCACCGTCC 59.260 50.000 0.00 0.00 40.12 4.79
2555 3587 5.696724 CAGGAACGACCATATGGAGTTTATC 59.303 44.000 28.77 21.08 42.04 1.75
2562 3594 4.450976 CAAATCAGGAACGACCATATGGA 58.549 43.478 28.77 2.36 42.04 3.41
2568 3600 1.606668 GTTGCAAATCAGGAACGACCA 59.393 47.619 0.00 0.00 42.04 4.02
2576 3608 4.799949 CGATTACAATGGTTGCAAATCAGG 59.200 41.667 0.00 2.68 42.35 3.86
2580 3612 7.771183 AGATAACGATTACAATGGTTGCAAAT 58.229 30.769 0.00 0.00 37.78 2.32
2638 3671 4.549107 GCGAGTGAATGATAAAAGAGACGC 60.549 45.833 0.00 0.00 0.00 5.19
2639 3672 4.316722 CGCGAGTGAATGATAAAAGAGACG 60.317 45.833 0.00 0.00 0.00 4.18
2681 3714 1.271926 CCCCAAATTTCTGGAGACGGT 60.272 52.381 5.07 0.00 38.96 4.83
2883 3918 8.613482 GGTAGAAAATGAGGTCAGTTTATAAGC 58.387 37.037 8.37 3.23 43.10 3.09
3236 4271 9.685276 AAGATATTGATGGACTTGAATTGTGTA 57.315 29.630 0.00 0.00 0.00 2.90
3273 4308 6.434018 AATCTTGAAGATGCACTTAAGAGC 57.566 37.500 16.90 16.90 39.13 4.09
3338 4373 7.514721 TGGTTTCTTGTTTACTTCAGATAGGT 58.485 34.615 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.