Multiple sequence alignment - TraesCS7B01G037200

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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 TraesCS7B01G037200 chr7B 100.000 7600 0 0 1 7600 36431795 36439394 0.000000e+00 14035.0
1 TraesCS7B01G037200 chr7B 88.616 1546 143 13 4346 5882 36434778 36436299 0.000000e+00 1849.0
2 TraesCS7B01G037200 chr7B 88.616 1546 143 13 2984 4505 36436140 36437676 0.000000e+00 1849.0
3 TraesCS7B01G037200 chr7B 85.149 1239 130 18 5301 6533 36434518 36435708 0.000000e+00 1219.0
4 TraesCS7B01G037200 chr7B 85.149 1239 130 18 2724 3914 36437095 36438327 0.000000e+00 1219.0
5 TraesCS7B01G037200 chr7B 85.802 979 112 12 4346 5297 36437349 36438327 0.000000e+00 1013.0
6 TraesCS7B01G037200 chr7B 88.754 578 65 0 3928 4505 36434528 36435105 0.000000e+00 708.0
7 TraesCS7B01G037200 chr7B 88.754 578 65 0 2734 3311 36435722 36436299 0.000000e+00 708.0
8 TraesCS7B01G037200 chr7A 95.116 6900 276 17 1 6859 88950016 88956895 0.000000e+00 10818.0
9 TraesCS7B01G037200 chr7A 88.853 1534 153 10 4346 5873 88953004 88954525 0.000000e+00 1869.0
10 TraesCS7B01G037200 chr7A 88.810 1546 143 11 2984 4505 88954375 88955914 0.000000e+00 1869.0
11 TraesCS7B01G037200 chr7A 85.553 1239 140 14 5303 6535 88952746 88953951 0.000000e+00 1260.0
12 TraesCS7B01G037200 chr7A 84.597 1240 135 26 2724 3914 88955333 88956565 0.000000e+00 1181.0
13 TraesCS7B01G037200 chr7A 86.140 974 111 11 5555 6528 88954375 88955324 0.000000e+00 1029.0
14 TraesCS7B01G037200 chr7A 84.709 981 119 13 4346 5297 88955587 88956565 0.000000e+00 952.0
15 TraesCS7B01G037200 chr7A 88.421 760 54 15 6857 7595 88962647 88963393 0.000000e+00 885.0
16 TraesCS7B01G037200 chr7A 87.329 584 68 4 2719 3302 88953948 88954525 0.000000e+00 664.0
17 TraesCS7B01G037200 chr7A 87.195 328 42 0 4178 4505 88954375 88954702 2.590000e-99 374.0
18 TraesCS7B01G037200 chr7D 93.584 6001 316 31 894 6859 87431218 87437184 0.000000e+00 8885.0
19 TraesCS7B01G037200 chr7D 88.788 1543 155 10 4346 5882 87433306 87434836 0.000000e+00 1875.0
20 TraesCS7B01G037200 chr7D 87.970 1488 152 9 2984 4447 87434677 87436161 0.000000e+00 1731.0
21 TraesCS7B01G037200 chr7D 85.576 1241 140 15 5301 6535 87433046 87434253 0.000000e+00 1264.0
22 TraesCS7B01G037200 chr7D 84.753 1233 128 19 2724 3914 87435635 87436849 0.000000e+00 1181.0
23 TraesCS7B01G037200 chr7D 84.995 973 110 12 4346 5297 87435892 87436849 0.000000e+00 955.0
24 TraesCS7B01G037200 chr7D 84.474 979 128 12 5555 6533 87434677 87435631 0.000000e+00 944.0
25 TraesCS7B01G037200 chr7D 89.100 578 63 0 3928 4505 87433056 87433633 0.000000e+00 719.0
26 TraesCS7B01G037200 chr7D 81.874 651 71 24 54 663 87430008 87430652 8.800000e-139 505.0
27 TraesCS7B01G037200 chr7D 89.835 364 17 7 6857 7206 87437428 87437785 4.180000e-122 449.0
28 TraesCS7B01G037200 chr7D 87.688 398 32 5 7205 7598 87437950 87438334 1.500000e-121 448.0
29 TraesCS7B01G037200 chr7D 93.827 162 10 0 4514 4675 87433306 87433467 2.120000e-60 244.0
30 TraesCS7B01G037200 chr7D 92.308 117 8 1 665 781 87430723 87430838 1.700000e-36 165.0
31 TraesCS7B01G037200 chr7D 87.755 49 6 0 883 931 87430833 87430881 2.960000e-04 58.4
32 TraesCS7B01G037200 chrUn 95.592 1293 40 7 178 1466 304728323 304727044 0.000000e+00 2056.0
33 TraesCS7B01G037200 chr6B 90.909 858 69 7 894 1750 653209170 653208321 0.000000e+00 1144.0
34 TraesCS7B01G037200 chr6B 82.828 99 15 2 795 892 646201781 646201684 3.780000e-13 87.9
35 TraesCS7B01G037200 chr6B 80.556 108 18 1 3454 3561 563290377 563290273 6.320000e-11 80.5
36 TraesCS7B01G037200 chr5B 89.744 858 75 6 894 1750 43247384 43248229 0.000000e+00 1085.0
37 TraesCS7B01G037200 chr2A 90.677 665 49 3 1083 1747 628687852 628688503 0.000000e+00 872.0
38 TraesCS7B01G037200 chr2A 93.077 130 7 2 894 1022 628687729 628687857 1.010000e-43 189.0
39 TraesCS7B01G037200 chr2A 86.076 79 11 0 780 858 496476592 496476670 1.360000e-12 86.1
40 TraesCS7B01G037200 chr2A 79.646 113 20 3 776 886 205917941 205917830 2.270000e-10 78.7
41 TraesCS7B01G037200 chr2B 92.110 507 36 3 1244 1750 108536962 108537464 0.000000e+00 712.0
42 TraesCS7B01G037200 chr2B 89.859 355 32 4 894 1246 108528130 108528482 3.230000e-123 453.0
43 TraesCS7B01G037200 chr2B 87.671 73 9 0 797 869 6995501 6995573 1.360000e-12 86.1
44 TraesCS7B01G037200 chr2D 88.320 488 47 7 894 1376 3458915 3459397 1.840000e-160 577.0
45 TraesCS7B01G037200 chr2D 92.267 375 29 0 1374 1748 3571769 3572143 4.040000e-147 532.0
46 TraesCS7B01G037200 chr3B 90.943 265 18 2 1486 1750 735246156 735246414 1.210000e-92 351.0
47 TraesCS7B01G037200 chr3B 86.022 93 12 1 797 889 167246350 167246441 1.750000e-16 99.0
48 TraesCS7B01G037200 chr1B 90.099 101 10 0 780 880 428722561 428722461 1.720000e-26 132.0
49 TraesCS7B01G037200 chr1B 76.623 231 35 10 7222 7439 621538825 621539049 8.060000e-20 110.0
50 TraesCS7B01G037200 chr1A 75.321 312 54 17 7222 7518 276305733 276305430 2.230000e-25 128.0
51 TraesCS7B01G037200 chr1A 78.571 126 15 7 7236 7349 311065491 311065616 1.060000e-08 73.1
52 TraesCS7B01G037200 chr1A 97.143 35 1 0 853 887 108695979 108696013 8.240000e-05 60.2
53 TraesCS7B01G037200 chr6A 81.081 148 28 0 1472 1619 606121461 606121314 1.340000e-22 119.0
54 TraesCS7B01G037200 chr4A 75.083 301 48 16 7260 7546 623066642 623066929 1.730000e-21 115.0
55 TraesCS7B01G037200 chr5D 80.000 95 18 1 797 891 352931049 352931142 1.370000e-07 69.4
56 TraesCS7B01G037200 chr5A 77.419 124 21 6 7245 7365 118803004 118803123 4.920000e-07 67.6


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 TraesCS7B01G037200 chr7B 36431795 36439394 7599 False 14035.000000 14035 100.000000 1 7600 1 chr7B.!!$F1 7599
1 TraesCS7B01G037200 chr7B 36434518 36438327 3809 False 1223.571429 1849 87.262857 2724 6533 7 chr7B.!!$F2 3809
2 TraesCS7B01G037200 chr7A 88950016 88956895 6879 False 10818.000000 10818 95.116000 1 6859 1 chr7A.!!$F1 6858
3 TraesCS7B01G037200 chr7A 88952746 88956565 3819 False 1149.750000 1869 86.648250 2719 6535 8 chr7A.!!$F3 3816
4 TraesCS7B01G037200 chr7A 88962647 88963393 746 False 885.000000 885 88.421000 6857 7595 1 chr7A.!!$F2 738
5 TraesCS7B01G037200 chr7D 87430008 87437184 7176 False 2403.350000 8885 88.880250 54 6859 4 chr7D.!!$F1 6805
6 TraesCS7B01G037200 chr7D 87433046 87438334 5288 False 981.000000 1875 87.700600 2724 7598 10 chr7D.!!$F2 4874
7 TraesCS7B01G037200 chrUn 304727044 304728323 1279 True 2056.000000 2056 95.592000 178 1466 1 chrUn.!!$R1 1288
8 TraesCS7B01G037200 chr6B 653208321 653209170 849 True 1144.000000 1144 90.909000 894 1750 1 chr6B.!!$R3 856
9 TraesCS7B01G037200 chr5B 43247384 43248229 845 False 1085.000000 1085 89.744000 894 1750 1 chr5B.!!$F1 856
10 TraesCS7B01G037200 chr2A 628687729 628688503 774 False 530.500000 872 91.877000 894 1747 2 chr2A.!!$F2 853
11 TraesCS7B01G037200 chr2B 108536962 108537464 502 False 712.000000 712 92.110000 1244 1750 1 chr2B.!!$F3 506

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
41 42 0.826256 AAAACCCTCCCAGAAACCGC 60.826 55.0 0.00 0.0 0.0 5.68 F
1173 1567 0.872021 CTGGCGCGACACTATTCCTC 60.872 60.0 12.71 0.0 0.0 3.71 F
2312 2724 1.101331 CCCTGGCAGATTCAAAGCTC 58.899 55.0 17.94 0.0 0.0 4.09 F
2329 2741 0.737367 CTCCGCGCTGACATTGAAGA 60.737 55.0 5.56 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1788 0.036022 GATAGATGCTCCAGGTGGGC 59.964 60.000 0.00 0.0 36.21 5.36 R
2329 2741 0.100503 AGCAAACACGCTTTTTCGCT 59.899 45.000 0.00 0.0 39.99 4.93 R
6544 6980 1.483827 AGAGCAAGATCATCTCGGCAA 59.516 47.619 12.43 0.0 31.57 4.52 R
6668 7115 7.849804 TCTTATTACTTTGCAGGAATCAGTC 57.150 36.000 0.00 0.0 35.01 3.51 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
34 35 1.165270 CAACGCTAAAACCCTCCCAG 58.835 55.000 0.00 0.00 0.00 4.45
35 36 1.061546 AACGCTAAAACCCTCCCAGA 58.938 50.000 0.00 0.00 0.00 3.86
41 42 0.826256 AAAACCCTCCCAGAAACCGC 60.826 55.000 0.00 0.00 0.00 5.68
136 149 1.869690 GCGGGTTCTTGCTCTTGTC 59.130 57.895 0.00 0.00 0.00 3.18
167 200 4.309950 GGCGACCGGACCAACAGT 62.310 66.667 9.46 0.00 0.00 3.55
170 203 2.604174 CGACCGGACCAACAGTTGC 61.604 63.158 9.46 0.00 0.00 4.17
323 368 1.439543 AGTAGGGATGGGGATCTTGC 58.560 55.000 0.00 0.00 0.00 4.01
379 435 8.700439 AATCTGCAAGTTTTTAACCCTTACTA 57.300 30.769 0.00 0.00 33.76 1.82
400 456 5.600484 ACTAGAACATTATGTCAGGGGAGAG 59.400 44.000 0.00 0.00 0.00 3.20
401 457 4.624913 AGAACATTATGTCAGGGGAGAGA 58.375 43.478 0.00 0.00 0.00 3.10
402 458 4.653341 AGAACATTATGTCAGGGGAGAGAG 59.347 45.833 0.00 0.00 0.00 3.20
403 459 4.271807 ACATTATGTCAGGGGAGAGAGA 57.728 45.455 0.00 0.00 0.00 3.10
437 493 4.044336 TGTGTTCCAGTTGCAAAGAATG 57.956 40.909 0.00 0.00 0.00 2.67
460 516 4.851558 GCATGTAAATGGTTCAGTCGAAAC 59.148 41.667 0.00 0.00 39.47 2.78
592 649 6.639686 CCATATTTGTGCTGTCATTAAGATGC 59.360 38.462 0.00 0.00 33.14 3.91
663 720 3.398954 TCAGTTCAGCGTGTTTGTTTC 57.601 42.857 0.00 0.00 0.00 2.78
744 870 6.551975 TGATTGATGATTGGCTTCATACCATT 59.448 34.615 3.93 0.00 36.48 3.16
745 871 6.795144 TTGATGATTGGCTTCATACCATTT 57.205 33.333 3.93 0.00 36.48 2.32
814 940 4.385825 AGGAATTAGTTGACGCTCAAACA 58.614 39.130 2.65 0.00 38.22 2.83
1040 1434 6.070710 GGGAAGGTACAGAGTAAGAATGTTCT 60.071 42.308 0.00 0.00 39.74 3.01
1041 1435 6.814146 GGAAGGTACAGAGTAAGAATGTTCTG 59.186 42.308 0.00 0.00 42.07 3.02
1047 1441 5.112686 CAGAGTAAGAATGTTCTGGCCTAC 58.887 45.833 3.32 0.00 37.65 3.18
1057 1451 1.068753 CTGGCCTACGATGGAGCAG 59.931 63.158 3.32 0.00 0.00 4.24
1173 1567 0.872021 CTGGCGCGACACTATTCCTC 60.872 60.000 12.71 0.00 0.00 3.71
1328 1731 8.880244 ACATACCAAGCATAGTTATCTATTCCA 58.120 33.333 0.00 0.00 34.98 3.53
1329 1732 9.896645 CATACCAAGCATAGTTATCTATTCCAT 57.103 33.333 0.00 0.00 34.98 3.41
1360 1772 6.405176 CCAGGGTTTCTATGAAATTTCTCAGC 60.405 42.308 18.64 6.23 0.00 4.26
1376 1788 4.676546 TCTCAGCGACATGTCTTTGATAG 58.323 43.478 22.95 14.14 0.00 2.08
1475 1887 5.702865 TGTCAGCAATTTTCTGTAATGCTC 58.297 37.500 0.00 0.00 33.48 4.26
1480 1892 7.033791 CAGCAATTTTCTGTAATGCTCTGAAT 58.966 34.615 0.00 0.00 0.00 2.57
1494 1906 3.829026 GCTCTGAATTTTTCCCTTCCTGT 59.171 43.478 0.00 0.00 0.00 4.00
1511 1923 6.013032 CCTTCCTGTCATATTATGGGAGACAT 60.013 42.308 3.89 0.00 43.68 3.06
1612 2024 6.882610 AGTGAATTTGAAGATGCTGTACAA 57.117 33.333 0.00 0.00 0.00 2.41
1909 2321 3.534357 TGGTTCATTGAAAAGCCCCTA 57.466 42.857 0.00 0.00 0.00 3.53
1928 2340 4.656112 CCCTATCAAACATGTACCTCCTCT 59.344 45.833 0.00 0.00 0.00 3.69
1937 2349 2.176889 TGTACCTCCTCTAGTGTTGGC 58.823 52.381 0.00 0.00 0.00 4.52
2013 2425 6.024664 CACAGAGAGTTACAACTAGACATCG 58.975 44.000 0.00 0.00 39.88 3.84
2111 2523 1.637553 ACCCAAGAAGCAGTGGATGAT 59.362 47.619 0.00 0.00 37.03 2.45
2113 2525 3.118112 ACCCAAGAAGCAGTGGATGATAG 60.118 47.826 0.00 0.00 37.03 2.08
2144 2556 9.094578 ACTGATGATTATATACCACTACAGCTT 57.905 33.333 0.00 0.00 0.00 3.74
2180 2592 6.132791 TCAGACGGTGTTGATACTCTATTC 57.867 41.667 0.00 0.00 0.00 1.75
2269 2681 2.673775 TTCCACCAACCATGTGTCAT 57.326 45.000 0.00 0.00 31.71 3.06
2312 2724 1.101331 CCCTGGCAGATTCAAAGCTC 58.899 55.000 17.94 0.00 0.00 4.09
2329 2741 0.737367 CTCCGCGCTGACATTGAAGA 60.737 55.000 5.56 0.00 0.00 2.87
2476 2888 4.704833 GCGGAGGGCACAGCAGAA 62.705 66.667 0.00 0.00 42.87 3.02
2481 2893 1.860484 GAGGGCACAGCAGAACAAGC 61.860 60.000 0.00 0.00 0.00 4.01
2487 2899 2.229792 CACAGCAGAACAAGCCCTTTA 58.770 47.619 0.00 0.00 0.00 1.85
2506 2918 6.404184 CCCTTTACATGTGATAATCGTGCAAA 60.404 38.462 9.11 0.00 0.00 3.68
2507 2919 7.026562 CCTTTACATGTGATAATCGTGCAAAA 58.973 34.615 9.11 0.00 0.00 2.44
2576 2988 4.504858 ACTATTCATTTGTCTGGGACGAC 58.495 43.478 0.00 0.00 34.95 4.34
2577 2989 2.920724 TTCATTTGTCTGGGACGACA 57.079 45.000 0.00 0.00 39.28 4.35
2591 3003 3.600388 GGACGACAACAGAAGATCCAAT 58.400 45.455 0.00 0.00 0.00 3.16
6558 6994 0.031857 CGAGCTTGCCGAGATGATCT 59.968 55.000 0.00 0.00 0.00 2.75
6602 7038 1.347707 GACATGGAACCTCACTGACCA 59.652 52.381 0.00 0.00 35.09 4.02
6695 7143 8.680903 ACTGATTCCTGCAAAGTAATAAGATTG 58.319 33.333 0.00 0.00 0.00 2.67
6716 7164 6.854496 TTGTCTGAACTTGTGTATGTAACC 57.146 37.500 0.00 0.00 0.00 2.85
6727 7175 5.496556 TGTGTATGTAACCCTTTCTGGATG 58.503 41.667 0.00 0.00 38.35 3.51
6787 7236 9.661563 ATTACTGTAACAAATAATTCTCGGTGA 57.338 29.630 1.73 0.00 0.00 4.02
6814 7263 1.601903 CCTTGTGTTTACTTGCGCTGA 59.398 47.619 9.73 0.00 0.00 4.26
6834 7287 2.308866 GACTGGGGTTATGGGGATATGG 59.691 54.545 0.00 0.00 0.00 2.74
6861 7560 1.753078 CTGATCTGGTCGTCGGGGA 60.753 63.158 0.00 0.00 0.00 4.81
6911 7610 0.240945 GGCAAATGACGGTGAACAGG 59.759 55.000 0.00 0.00 0.00 4.00
6947 7646 0.109086 CTGGTGCGTCGATCTTCACT 60.109 55.000 0.00 0.00 0.00 3.41
6948 7647 0.317160 TGGTGCGTCGATCTTCACTT 59.683 50.000 0.00 0.00 0.00 3.16
6949 7648 0.992802 GGTGCGTCGATCTTCACTTC 59.007 55.000 0.00 0.00 0.00 3.01
6950 7649 1.668919 GGTGCGTCGATCTTCACTTCA 60.669 52.381 0.00 0.00 0.00 3.02
6951 7650 2.263077 GTGCGTCGATCTTCACTTCAT 58.737 47.619 0.00 0.00 0.00 2.57
6958 7657 3.136763 CGATCTTCACTTCATCCATGGG 58.863 50.000 13.02 0.00 0.00 4.00
6993 7692 2.202797 CATCTCCCACTCGGCGTG 60.203 66.667 6.85 7.20 43.41 5.34
7039 7738 0.739813 CGTCGATTTCTCCGGGCTTT 60.740 55.000 0.00 0.00 0.00 3.51
7106 7808 3.258622 CCCTCCCGAATAAGTAGATCACC 59.741 52.174 0.00 0.00 0.00 4.02
7109 7811 2.296471 CCCGAATAAGTAGATCACCGCT 59.704 50.000 0.00 0.00 0.00 5.52
7111 7813 4.474113 CCGAATAAGTAGATCACCGCTAC 58.526 47.826 0.00 0.00 38.76 3.58
7239 8126 4.899239 CTCGACGCTGGGATGGCC 62.899 72.222 0.00 0.00 0.00 5.36
7243 8130 3.746949 GACGCTGGGATGGCCTCTG 62.747 68.421 3.32 0.00 0.00 3.35
7256 8143 2.037687 CTCTGGGCAATTGGGGCA 59.962 61.111 7.72 0.00 34.52 5.36
7257 8144 1.382146 CTCTGGGCAATTGGGGCAT 60.382 57.895 7.72 0.00 34.52 4.40
7258 8145 1.682451 CTCTGGGCAATTGGGGCATG 61.682 60.000 7.72 0.00 34.52 4.06
7293 8180 3.083997 CCTAGGTCTTGGGCGGCT 61.084 66.667 9.56 0.00 0.00 5.52
7297 8184 4.021925 GGTCTTGGGCGGCTCTGT 62.022 66.667 9.56 0.00 0.00 3.41
7404 8292 5.317733 TGTTCGAATTGAAGTTTGGTTGT 57.682 34.783 0.00 0.00 37.23 3.32
7416 8304 0.808125 TTGGTTGTGTGTGAGTGCAC 59.192 50.000 9.40 9.40 45.35 4.57
7443 8331 2.276869 GGTGAGCAACCCCAATTCC 58.723 57.895 0.00 0.00 44.02 3.01
7446 8334 0.251742 TGAGCAACCCCAATTCCAGG 60.252 55.000 0.00 0.00 0.00 4.45
7465 8353 6.267635 TCCAGGGATTTCCATTCCAAAATTA 58.732 36.000 0.00 0.00 38.24 1.40
7479 8367 9.889128 CATTCCAAAATTACAATTACCTTCCAT 57.111 29.630 0.00 0.00 0.00 3.41
7493 8381 4.416516 ACCTTCCATTTAGGTTTCCCTTG 58.583 43.478 0.00 0.00 43.45 3.61
7537 8425 0.255890 GCCATGCTCCTCCCAAGTAA 59.744 55.000 0.00 0.00 0.00 2.24
7558 8446 8.828688 AGTAACTAGTTTGATGTTCCTGTAAC 57.171 34.615 14.49 0.37 38.67 2.50
7598 8486 6.575162 ACTATCACTTTTGTTAAAGCAGGG 57.425 37.500 0.00 0.00 43.72 4.45
7599 8487 6.303839 ACTATCACTTTTGTTAAAGCAGGGA 58.696 36.000 0.00 0.00 43.72 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.165270 CTGGGAGGGTTTTAGCGTTG 58.835 55.000 0.00 0.00 0.00 4.10
17 18 1.061546 TTCTGGGAGGGTTTTAGCGT 58.938 50.000 0.00 0.00 0.00 5.07
34 35 2.543067 ATCCCCTGCTCTGCGGTTTC 62.543 60.000 0.00 0.00 32.22 2.78
35 36 2.543067 GATCCCCTGCTCTGCGGTTT 62.543 60.000 0.00 0.00 32.22 3.27
41 42 2.801631 GGACGGATCCCCTGCTCTG 61.802 68.421 6.06 0.00 39.39 3.35
117 130 1.901650 GACAAGAGCAAGAACCCGCG 61.902 60.000 0.00 0.00 0.00 6.46
122 135 2.262423 ACCCTGACAAGAGCAAGAAC 57.738 50.000 0.00 0.00 0.00 3.01
136 149 1.890041 TCGCCGTTGTGAAACCCTG 60.890 57.895 0.00 0.00 34.36 4.45
157 190 2.983592 CCCCGCAACTGTTGGTCC 60.984 66.667 21.01 4.80 0.00 4.46
166 199 2.180159 TAGAGAAGGCACCCCGCAAC 62.180 60.000 0.00 0.00 45.17 4.17
167 200 1.899437 CTAGAGAAGGCACCCCGCAA 61.899 60.000 0.00 0.00 45.17 4.85
170 203 2.501610 GCTAGAGAAGGCACCCCG 59.498 66.667 0.00 0.00 35.76 5.73
323 368 1.455383 AACGCCTGCCTGAAAACCAG 61.455 55.000 0.00 0.00 42.55 4.00
379 435 4.624913 TCTCTCCCCTGACATAATGTTCT 58.375 43.478 0.00 0.00 0.00 3.01
400 456 3.051081 ACACAAGATGCAGAGGTTCTC 57.949 47.619 0.00 0.00 0.00 2.87
401 457 3.406764 GAACACAAGATGCAGAGGTTCT 58.593 45.455 0.00 0.00 32.59 3.01
402 458 2.485814 GGAACACAAGATGCAGAGGTTC 59.514 50.000 0.00 0.39 34.08 3.62
403 459 2.158623 TGGAACACAAGATGCAGAGGTT 60.159 45.455 0.00 0.00 0.00 3.50
416 472 4.044336 CATTCTTTGCAACTGGAACACA 57.956 40.909 0.00 0.00 0.00 3.72
437 493 4.678509 TTCGACTGAACCATTTACATGC 57.321 40.909 0.00 0.00 0.00 4.06
460 516 3.601435 TGATTTTGCAATGAAGCATGGG 58.399 40.909 0.00 0.00 45.19 4.00
539 595 6.827586 ACACTTTTCAGTTTGACTAACCAA 57.172 33.333 0.00 0.00 37.46 3.67
592 649 1.486439 GCATGAAACACAAACACGGG 58.514 50.000 0.00 0.00 0.00 5.28
663 720 1.062810 AGCAGGGGAGTTCCTACCTAG 60.063 57.143 0.00 0.00 34.20 3.02
801 927 9.031360 GTATAGATAAATCTGTTTGAGCGTCAA 57.969 33.333 2.66 0.00 37.76 3.18
1040 1434 1.264749 AACTGCTCCATCGTAGGCCA 61.265 55.000 5.01 0.00 0.00 5.36
1041 1435 0.107654 AAACTGCTCCATCGTAGGCC 60.108 55.000 0.00 0.00 0.00 5.19
1057 1451 2.165437 TCAGGTGGTTGCACAGAAAAAC 59.835 45.455 0.00 0.00 0.00 2.43
1098 1492 3.118775 ACGAAAGGCCAAAAAGCTTTCTT 60.119 39.130 13.10 8.16 29.66 2.52
1173 1567 5.032100 GCTTATGCTGCTCAACATCATAG 57.968 43.478 0.00 0.00 38.31 2.23
1190 1584 4.046286 TCAAACACCCCATGAAGCTTAT 57.954 40.909 0.00 0.00 0.00 1.73
1330 1733 9.768215 AGAAATTTCATAGAAACCCTGGAATAA 57.232 29.630 19.99 0.00 0.00 1.40
1331 1734 9.408648 GAGAAATTTCATAGAAACCCTGGAATA 57.591 33.333 19.99 0.00 0.00 1.75
1332 1735 7.895429 TGAGAAATTTCATAGAAACCCTGGAAT 59.105 33.333 19.99 0.00 0.00 3.01
1333 1736 7.237982 TGAGAAATTTCATAGAAACCCTGGAA 58.762 34.615 19.99 0.00 0.00 3.53
1334 1737 6.789268 TGAGAAATTTCATAGAAACCCTGGA 58.211 36.000 19.99 0.00 0.00 3.86
1335 1738 6.405176 GCTGAGAAATTTCATAGAAACCCTGG 60.405 42.308 19.99 0.00 0.00 4.45
1336 1739 6.558909 GCTGAGAAATTTCATAGAAACCCTG 58.441 40.000 19.99 3.61 0.00 4.45
1360 1772 2.609459 GTGGGCTATCAAAGACATGTCG 59.391 50.000 19.85 6.55 33.25 4.35
1376 1788 0.036022 GATAGATGCTCCAGGTGGGC 59.964 60.000 0.00 0.00 36.21 5.36
1475 1887 5.990120 ATGACAGGAAGGGAAAAATTCAG 57.010 39.130 0.00 0.00 0.00 3.02
1480 1892 6.838612 CCCATAATATGACAGGAAGGGAAAAA 59.161 38.462 1.10 0.00 35.81 1.94
1484 1896 4.838403 TCCCATAATATGACAGGAAGGGA 58.162 43.478 1.10 0.00 40.31 4.20
1511 1923 7.386848 GTGAACACAGCAGGAAAAGTATTAGTA 59.613 37.037 0.00 0.00 0.00 1.82
1704 2116 2.975489 CACCCTGGGATCAGTAGCTAAT 59.025 50.000 22.23 0.00 39.31 1.73
1751 2163 5.835113 TCCTTGAAGAAAACAAGTGAAGG 57.165 39.130 0.00 0.00 41.88 3.46
1909 2321 5.721960 ACACTAGAGGAGGTACATGTTTGAT 59.278 40.000 2.30 0.00 0.00 2.57
1928 2340 1.155889 CTGCATGTTCGCCAACACTA 58.844 50.000 0.00 0.00 45.47 2.74
1937 2349 2.023741 GGCGATGCTGCATGTTCG 59.976 61.111 21.53 18.98 36.28 3.95
2013 2425 1.740025 GTTGGACTTAGCCACATCAGC 59.260 52.381 0.00 0.00 37.75 4.26
2144 2556 3.381590 CACCGTCTGAAGTATCATCCTCA 59.618 47.826 0.00 0.00 34.37 3.86
2180 2592 2.287373 GCTCTCATCTCCAAGCAAATCG 59.713 50.000 0.00 0.00 34.86 3.34
2312 2724 1.712081 CTCTTCAATGTCAGCGCGG 59.288 57.895 8.83 0.00 0.00 6.46
2329 2741 0.100503 AGCAAACACGCTTTTTCGCT 59.899 45.000 0.00 0.00 39.99 4.93
2476 2888 5.296780 CGATTATCACATGTAAAGGGCTTGT 59.703 40.000 0.00 0.00 0.00 3.16
2481 2893 4.574421 TGCACGATTATCACATGTAAAGGG 59.426 41.667 0.00 0.00 0.00 3.95
2487 2899 5.806502 CCAATTTTGCACGATTATCACATGT 59.193 36.000 0.00 0.00 0.00 3.21
2506 2918 2.025037 TGAGCTGAAGGCATACCCAATT 60.025 45.455 0.00 0.00 44.79 2.32
2507 2919 1.565759 TGAGCTGAAGGCATACCCAAT 59.434 47.619 0.00 0.00 44.79 3.16
2576 2988 7.065563 CCAGAGAACTTATTGGATCTTCTGTTG 59.934 40.741 0.00 0.00 32.34 3.33
2577 2989 7.108847 CCAGAGAACTTATTGGATCTTCTGTT 58.891 38.462 0.00 0.00 32.34 3.16
6544 6980 1.483827 AGAGCAAGATCATCTCGGCAA 59.516 47.619 12.43 0.00 31.57 4.52
6668 7115 7.849804 TCTTATTACTTTGCAGGAATCAGTC 57.150 36.000 0.00 0.00 35.01 3.51
6695 7143 5.548406 AGGGTTACATACACAAGTTCAGAC 58.452 41.667 0.00 0.00 30.22 3.51
6716 7164 4.911390 AGGTACTTGAACATCCAGAAAGG 58.089 43.478 0.00 0.00 27.25 3.11
6727 7175 3.402628 TTCAGGCAGAGGTACTTGAAC 57.597 47.619 0.00 0.00 41.55 3.18
6783 7232 1.620822 AACACAAGGAGGCAATCACC 58.379 50.000 0.00 0.00 0.00 4.02
6787 7236 3.005791 GCAAGTAAACACAAGGAGGCAAT 59.994 43.478 0.00 0.00 0.00 3.56
6814 7263 2.358258 CCATATCCCCATAACCCCAGT 58.642 52.381 0.00 0.00 0.00 4.00
6834 7287 1.537776 CGACCAGATCAGATCACAGGC 60.538 57.143 13.14 1.98 0.00 4.85
6911 7610 2.143419 AGATGGACCGATGCCTCCC 61.143 63.158 0.00 0.00 0.00 4.30
6947 7646 2.981914 GATGCGCCCCCATGGATGAA 62.982 60.000 15.22 0.00 35.39 2.57
6948 7647 3.496309 GATGCGCCCCCATGGATGA 62.496 63.158 15.22 0.00 35.39 2.92
6949 7648 2.987547 GATGCGCCCCCATGGATG 60.988 66.667 15.22 4.53 35.39 3.51
6950 7649 4.648626 CGATGCGCCCCCATGGAT 62.649 66.667 15.22 0.00 35.39 3.41
7039 7738 0.874175 CGCACCTGACGAAACTGACA 60.874 55.000 0.00 0.00 0.00 3.58
7070 7769 3.607370 GAGGGGTCGGTTGTCAGGC 62.607 68.421 0.00 0.00 0.00 4.85
7109 7811 0.968901 ACCACAAGATCGCCTCCGTA 60.969 55.000 0.00 0.00 35.54 4.02
7111 7813 1.079127 AACCACAAGATCGCCTCCG 60.079 57.895 0.00 0.00 0.00 4.63
7141 7843 1.834188 CGCCATTCTTAGGGTTTGGT 58.166 50.000 0.00 0.00 0.00 3.67
7239 8126 1.382146 ATGCCCCAATTGCCCAGAG 60.382 57.895 0.00 0.00 0.00 3.35
7240 8127 1.686455 CATGCCCCAATTGCCCAGA 60.686 57.895 0.00 0.00 0.00 3.86
7243 8130 2.688299 ACCATGCCCCAATTGCCC 60.688 61.111 0.00 0.00 0.00 5.36
7293 8180 4.007644 CACAGCTCCGGGCACAGA 62.008 66.667 15.92 0.00 44.79 3.41
7376 8264 1.195448 ACTTCAATTCGAACAGCAGCG 59.805 47.619 0.00 0.00 0.00 5.18
7404 8292 3.157949 TCCCGGTGCACTCACACA 61.158 61.111 17.98 0.00 44.87 3.72
7416 8304 3.003173 TTGCTCACCTCCTCCCGG 61.003 66.667 0.00 0.00 0.00 5.73
7443 8331 6.945218 TGTAATTTTGGAATGGAAATCCCTG 58.055 36.000 0.00 0.00 36.04 4.45
7465 8353 6.439375 GGGAAACCTAAATGGAAGGTAATTGT 59.561 38.462 0.00 0.00 46.85 2.71
7493 8381 3.056322 AGCAATTTGGAAAGAGCATGACC 60.056 43.478 0.00 0.00 0.00 4.02
7537 8425 5.701290 GCTGTTACAGGAACATCAAACTAGT 59.299 40.000 14.63 0.00 46.95 2.57
7572 8460 6.797033 CCTGCTTTAACAAAAGTGATAGTTCG 59.203 38.462 0.36 0.00 32.52 3.95


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

AutoCloner maintained by Alex Coulton.