Multiple sequence alignment - TraesCS1B01G123500

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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 TraesCS1B01G123500 chr1B 100.000 5678 0 0 722 6399 150064534 150058857 0.000000e+00 10486.0
1 TraesCS1B01G123500 chr1B 100.000 41 0 0 1 41 150065255 150065215 6.880000e-10 76.8
2 TraesCS1B01G123500 chr1A 95.503 4937 128 36 1538 6399 103635926 103631009 0.000000e+00 7801.0
3 TraesCS1B01G123500 chr1A 91.226 718 33 16 772 1462 103636650 103635936 0.000000e+00 950.0
4 TraesCS1B01G123500 chr1D 95.924 4220 114 18 2217 6399 101579940 101575742 0.000000e+00 6787.0
5 TraesCS1B01G123500 chr1D 95.559 698 19 3 1537 2230 101580665 101579976 0.000000e+00 1107.0
6 TraesCS1B01G123500 chr1D 94.030 603 25 5 875 1474 101581268 101580674 0.000000e+00 904.0
7 TraesCS1B01G123500 chr1D 89.831 59 0 1 817 875 101581338 101581286 3.200000e-08 71.3
8 TraesCS1B01G123500 chr4B 88.079 453 44 5 5644 6090 630376379 630375931 4.390000e-146 529.0
9 TraesCS1B01G123500 chr4B 95.522 67 3 0 6331 6397 630428564 630428498 2.440000e-19 108.0
10 TraesCS1B01G123500 chr3D 91.954 87 2 5 1501 1585 126949053 126949136 4.050000e-22 117.0
11 TraesCS1B01G123500 chr3B 91.954 87 2 5 1501 1585 181288818 181288901 4.050000e-22 117.0
12 TraesCS1B01G123500 chr3A 90.805 87 3 5 1501 1585 137579567 137579650 1.890000e-20 111.0
13 TraesCS1B01G123500 chr5A 95.522 67 3 0 6331 6397 672416360 672416426 2.440000e-19 108.0
14 TraesCS1B01G123500 chr7B 90.244 82 5 3 1501 1580 142285338 142285258 3.160000e-18 104.0
15 TraesCS1B01G123500 chr7B 89.873 79 5 3 1501 1577 142285269 142285346 1.470000e-16 99.0
16 TraesCS1B01G123500 chr2B 88.889 72 6 2 1503 1573 113263494 113263424 3.180000e-13 87.9
17 TraesCS1B01G123500 chr2A 87.342 79 6 3 1501 1577 445754405 445754329 3.180000e-13 87.9
18 TraesCS1B01G123500 chr4D 96.875 32 1 0 6366 6397 490603480 490603449 3.000000e-03 54.7


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 TraesCS1B01G123500 chr1B 150058857 150065255 6398 True 5281.400 10486 100.0000 1 6399 2 chr1B.!!$R1 6398
1 TraesCS1B01G123500 chr1A 103631009 103636650 5641 True 4375.500 7801 93.3645 772 6399 2 chr1A.!!$R1 5627
2 TraesCS1B01G123500 chr1D 101575742 101581338 5596 True 2217.325 6787 93.8360 817 6399 4 chr1D.!!$R1 5582

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
843 847 0.033504 CCCTACACACAACTCGCAGT 59.966 55.000 0.00 0.0 0.00 4.40 F
2399 2524 0.523519 TGCACACTCGTGTTGCAAAA 59.476 45.000 18.37 0.0 45.50 2.44 F
3161 3316 1.753073 CTGGTGATGGGAGAAAATGCC 59.247 52.381 0.00 0.0 40.61 4.40 F
4057 4217 0.520404 ATGCAGCTTTTGAGTGCTCG 59.480 50.000 0.00 0.0 37.44 5.03 F
4954 5125 0.178964 ACCAAGACACCCCAACATGG 60.179 55.000 0.00 0.0 37.25 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2664 2793 0.475475 CATTAGCTGCATCTCCCCCA 59.525 55.000 1.02 0.0 0.00 4.96 R
3358 3513 2.622470 GGGTCCTTCTAGCTAACTACCG 59.378 54.545 0.00 0.0 0.00 4.02 R
4589 4749 0.250858 CTGGCACCTGAATCCACACA 60.251 55.000 0.00 0.0 0.00 3.72 R
5290 5461 0.537188 CTGTCTTGTACTCGGCCCAT 59.463 55.000 0.00 0.0 0.00 4.00 R
6279 6455 1.599606 ATCAGCGGACGTGCTCTTCT 61.600 55.000 5.27 0.0 45.23 2.85 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
18 19 2.437625 TTAGGCAGATCGGTAGGCC 58.562 57.895 0.00 0.00 46.77 5.19
20 21 3.942439 GGCAGATCGGTAGGCCCC 61.942 72.222 0.00 0.00 40.55 5.80
21 22 3.942439 GCAGATCGGTAGGCCCCC 61.942 72.222 0.00 0.00 0.00 5.40
22 23 2.445845 CAGATCGGTAGGCCCCCA 60.446 66.667 0.00 0.00 0.00 4.96
23 24 2.446036 AGATCGGTAGGCCCCCAC 60.446 66.667 0.00 0.00 0.00 4.61
24 25 3.925090 GATCGGTAGGCCCCCACG 61.925 72.222 0.00 0.00 0.00 4.94
36 37 3.917760 CCCACGCCCGGAGATCTC 61.918 72.222 14.75 14.75 0.00 2.75
37 38 3.147595 CCACGCCCGGAGATCTCA 61.148 66.667 23.85 0.00 0.00 3.27
38 39 2.415010 CACGCCCGGAGATCTCAG 59.585 66.667 23.85 19.50 0.00 3.35
39 40 3.532155 ACGCCCGGAGATCTCAGC 61.532 66.667 23.85 20.11 0.00 4.26
40 41 4.637489 CGCCCGGAGATCTCAGCG 62.637 72.222 28.07 28.07 38.24 5.18
740 741 1.359848 CCAAGTCGAAAGATCACGGG 58.640 55.000 0.00 0.00 45.19 5.28
741 742 1.359848 CAAGTCGAAAGATCACGGGG 58.640 55.000 0.00 0.00 45.19 5.73
742 743 0.249398 AAGTCGAAAGATCACGGGGG 59.751 55.000 0.00 0.00 45.19 5.40
756 757 2.034221 GGGGGTCAGCAACTCACC 59.966 66.667 0.00 0.00 0.00 4.02
757 758 2.829384 GGGGGTCAGCAACTCACCA 61.829 63.158 0.00 0.00 31.06 4.17
758 759 1.600916 GGGGTCAGCAACTCACCAC 60.601 63.158 0.00 0.00 31.06 4.16
759 760 1.451936 GGGTCAGCAACTCACCACT 59.548 57.895 0.00 0.00 31.06 4.00
760 761 0.603975 GGGTCAGCAACTCACCACTC 60.604 60.000 0.00 0.00 31.06 3.51
761 762 0.394565 GGTCAGCAACTCACCACTCT 59.605 55.000 0.00 0.00 0.00 3.24
762 763 1.618837 GGTCAGCAACTCACCACTCTA 59.381 52.381 0.00 0.00 0.00 2.43
763 764 2.353208 GGTCAGCAACTCACCACTCTAG 60.353 54.545 0.00 0.00 0.00 2.43
764 765 1.273606 TCAGCAACTCACCACTCTAGC 59.726 52.381 0.00 0.00 0.00 3.42
765 766 1.001293 CAGCAACTCACCACTCTAGCA 59.999 52.381 0.00 0.00 0.00 3.49
766 767 1.274728 AGCAACTCACCACTCTAGCAG 59.725 52.381 0.00 0.00 0.00 4.24
767 768 1.001406 GCAACTCACCACTCTAGCAGT 59.999 52.381 0.00 0.00 34.67 4.40
796 797 9.813826 TTCTCTCTCTTCATGTCCATATATACA 57.186 33.333 0.00 0.00 0.00 2.29
811 815 0.399233 ATACAGCCACTCTCCCCTCC 60.399 60.000 0.00 0.00 0.00 4.30
812 816 2.856039 TACAGCCACTCTCCCCTCCG 62.856 65.000 0.00 0.00 0.00 4.63
835 839 1.061546 GGAAGACCCCCTACACACAA 58.938 55.000 0.00 0.00 0.00 3.33
836 840 1.271217 GGAAGACCCCCTACACACAAC 60.271 57.143 0.00 0.00 0.00 3.32
837 841 1.697982 GAAGACCCCCTACACACAACT 59.302 52.381 0.00 0.00 0.00 3.16
838 842 1.349067 AGACCCCCTACACACAACTC 58.651 55.000 0.00 0.00 0.00 3.01
839 843 0.037605 GACCCCCTACACACAACTCG 60.038 60.000 0.00 0.00 0.00 4.18
840 844 1.375523 CCCCCTACACACAACTCGC 60.376 63.158 0.00 0.00 0.00 5.03
842 846 0.670546 CCCCTACACACAACTCGCAG 60.671 60.000 0.00 0.00 0.00 5.18
843 847 0.033504 CCCTACACACAACTCGCAGT 59.966 55.000 0.00 0.00 0.00 4.40
844 848 1.271379 CCCTACACACAACTCGCAGTA 59.729 52.381 0.00 0.00 0.00 2.74
921 949 2.355837 CACTACCACACACGCGCT 60.356 61.111 5.73 0.00 0.00 5.92
1040 1083 4.719369 GGCGCGACAAGAGACGGT 62.719 66.667 12.10 0.00 33.59 4.83
1046 1089 0.663568 CGACAAGAGACGGTGACCAC 60.664 60.000 1.11 0.00 0.00 4.16
1182 1225 1.671054 CTTCCGTGCCGTCAACCAT 60.671 57.895 0.00 0.00 0.00 3.55
1194 1237 3.965258 AACCATGGCGTGCCTCCA 61.965 61.111 13.04 0.00 38.09 3.86
1326 1369 2.861006 GGCTTCAACGGCGACTTC 59.139 61.111 16.62 0.00 0.00 3.01
1483 1530 8.943909 ATAATAAGAACTGTACTGCCTTGTAC 57.056 34.615 14.19 0.00 42.10 2.90
1484 1531 4.957684 AAGAACTGTACTGCCTTGTACT 57.042 40.909 11.28 0.00 42.22 2.73
1485 1532 4.522722 AGAACTGTACTGCCTTGTACTC 57.477 45.455 11.28 3.71 42.22 2.59
1486 1533 3.057456 AGAACTGTACTGCCTTGTACTCG 60.057 47.826 11.28 6.67 42.22 4.18
1487 1534 1.067776 ACTGTACTGCCTTGTACTCGC 60.068 52.381 11.28 0.00 42.22 5.03
1488 1535 0.963225 TGTACTGCCTTGTACTCGCA 59.037 50.000 11.28 0.00 42.22 5.10
1489 1536 1.341852 TGTACTGCCTTGTACTCGCAA 59.658 47.619 11.28 0.00 42.22 4.85
1490 1537 2.224090 TGTACTGCCTTGTACTCGCAAA 60.224 45.455 11.28 0.00 42.22 3.68
1491 1538 1.961793 ACTGCCTTGTACTCGCAAAA 58.038 45.000 0.00 0.00 30.85 2.44
1492 1539 2.294074 ACTGCCTTGTACTCGCAAAAA 58.706 42.857 0.00 0.00 30.85 1.94
1526 1573 9.685005 CTGTACACTAATATAAGACGTTTTTGC 57.315 33.333 0.00 0.00 0.00 3.68
1527 1574 9.205719 TGTACACTAATATAAGACGTTTTTGCA 57.794 29.630 0.00 0.00 0.00 4.08
1528 1575 9.685005 GTACACTAATATAAGACGTTTTTGCAG 57.315 33.333 0.00 0.00 0.00 4.41
1529 1576 8.319143 ACACTAATATAAGACGTTTTTGCAGT 57.681 30.769 0.00 0.00 0.00 4.40
1530 1577 8.780249 ACACTAATATAAGACGTTTTTGCAGTT 58.220 29.630 0.00 0.00 0.00 3.16
1531 1578 9.262472 CACTAATATAAGACGTTTTTGCAGTTC 57.738 33.333 0.00 0.00 0.00 3.01
1532 1579 8.995220 ACTAATATAAGACGTTTTTGCAGTTCA 58.005 29.630 0.00 0.00 0.00 3.18
1533 1580 9.820229 CTAATATAAGACGTTTTTGCAGTTCAA 57.180 29.630 0.00 0.00 0.00 2.69
1535 1582 9.691362 AATATAAGACGTTTTTGCAGTTCAATT 57.309 25.926 0.00 0.00 34.12 2.32
1536 1583 5.701029 AAGACGTTTTTGCAGTTCAATTG 57.299 34.783 0.00 0.00 34.12 2.32
1537 1584 4.743493 AGACGTTTTTGCAGTTCAATTGT 58.257 34.783 5.13 0.00 34.12 2.71
1538 1585 5.167845 AGACGTTTTTGCAGTTCAATTGTT 58.832 33.333 5.13 0.00 34.12 2.83
1539 1586 5.062058 AGACGTTTTTGCAGTTCAATTGTTG 59.938 36.000 5.13 4.40 34.12 3.33
1540 1587 4.926238 ACGTTTTTGCAGTTCAATTGTTGA 59.074 33.333 5.13 0.00 38.04 3.18
1541 1588 5.406780 ACGTTTTTGCAGTTCAATTGTTGAA 59.593 32.000 5.13 1.24 46.68 2.69
1561 1608 9.409312 TGTTGAACTGCAAAATGTCTTATATTG 57.591 29.630 0.00 0.00 38.44 1.90
1631 1678 8.687292 ACATCAGTGAAGCATCATTATACATT 57.313 30.769 0.00 0.00 38.01 2.71
1670 1717 4.158394 TGGTTTCTTAATCCTGCAAGCATC 59.842 41.667 0.00 0.00 0.00 3.91
1715 1762 4.651503 ACATACTAGTGCTGTATTCAGGCT 59.348 41.667 5.39 0.00 41.57 4.58
1876 1926 3.758554 GCTCCACCGCCATTAATTATCAT 59.241 43.478 0.00 0.00 0.00 2.45
2186 2262 2.592993 CCAGACCGACATGTGGGGT 61.593 63.158 28.01 22.02 36.58 4.95
2318 2443 1.141657 TGCACAGAGGACTTTCTGCTT 59.858 47.619 3.10 0.00 46.77 3.91
2328 2453 6.211584 AGAGGACTTTCTGCTTAGTACAATGA 59.788 38.462 0.00 0.00 0.00 2.57
2338 2463 6.230472 TGCTTAGTACAATGATGTCTTGTGT 58.770 36.000 0.00 0.00 41.05 3.72
2399 2524 0.523519 TGCACACTCGTGTTGCAAAA 59.476 45.000 18.37 0.00 45.50 2.44
2552 2680 7.814264 ATATAATTCAAGCCAAAGTGAGAGG 57.186 36.000 0.00 0.00 0.00 3.69
2576 2704 9.998106 AGGTGTAGCTAATGTATAAATCGAAAT 57.002 29.630 0.00 0.00 0.00 2.17
2653 2781 9.515226 AACTCCAAACAGATGTAGCTAATTTAA 57.485 29.630 0.00 0.00 0.00 1.52
2799 2928 8.907222 ACTTCAATATGCACACATATGTATCA 57.093 30.769 8.32 7.14 46.58 2.15
2800 2929 9.511272 ACTTCAATATGCACACATATGTATCAT 57.489 29.630 8.32 13.43 46.58 2.45
2814 2945 9.766754 ACATATGTATCATCTTCAGATAGGTCT 57.233 33.333 6.56 0.00 32.63 3.85
2854 2985 6.058183 GGGAATACATGAGCACATAGTTTCT 58.942 40.000 0.00 0.00 35.09 2.52
2993 3138 6.018262 GTGACACAACAAACTTGATAGCTACA 60.018 38.462 0.00 0.00 0.00 2.74
3084 3229 6.070538 TGGAAAAGGAAAACACAGGAAAATCA 60.071 34.615 0.00 0.00 0.00 2.57
3109 3264 8.439286 CAGTCTTAGCTAAGAAATTTGACTCAC 58.561 37.037 32.50 18.22 43.30 3.51
3161 3316 1.753073 CTGGTGATGGGAGAAAATGCC 59.247 52.381 0.00 0.00 40.61 4.40
3180 3335 2.939103 GCCCACAGATGTTAAGCTACAG 59.061 50.000 0.00 0.00 0.00 2.74
3358 3513 7.228706 TGAAAGGGACAATAAAACACTCTCTTC 59.771 37.037 0.00 0.00 0.00 2.87
3706 3865 2.312390 GGCCCCAGTTGAAGTACAAAA 58.688 47.619 0.00 0.00 40.36 2.44
3970 4130 2.102252 TGCCCACTGGAAATTTTGTCAC 59.898 45.455 0.00 0.00 0.00 3.67
3991 4151 1.220206 CCCAGCTGCATCTCGACTT 59.780 57.895 8.66 0.00 0.00 3.01
4016 4176 6.258160 ACAAAGAAACGAATATAGCATGTGC 58.742 36.000 0.00 0.00 42.49 4.57
4057 4217 0.520404 ATGCAGCTTTTGAGTGCTCG 59.480 50.000 0.00 0.00 37.44 5.03
4589 4749 0.744414 CGGACATCAACGGCAAGGAT 60.744 55.000 0.00 0.00 0.00 3.24
4590 4750 0.734889 GGACATCAACGGCAAGGATG 59.265 55.000 7.47 7.47 43.08 3.51
4591 4751 3.650647 ACATCAACGGCAAGGATGT 57.349 47.368 8.55 8.55 44.91 3.06
4616 4776 1.123861 TTCAGGTGCCAGCAGACTCT 61.124 55.000 0.00 0.00 0.00 3.24
4665 4825 4.416516 TCTCCTTCAGGTAGTCACATCAA 58.583 43.478 0.00 0.00 36.34 2.57
4678 4838 9.469807 GGTAGTCACATCAATTAATCTGAGTAG 57.530 37.037 0.00 0.00 0.00 2.57
4794 4954 5.789574 TCTGGGACCAACCATAAATACTT 57.210 39.130 0.00 0.00 40.36 2.24
4945 5116 6.930667 TGAAAACTAGTTTACCAAGACACC 57.069 37.500 20.83 2.47 31.63 4.16
4954 5125 0.178964 ACCAAGACACCCCAACATGG 60.179 55.000 0.00 0.00 37.25 3.66
5049 5220 4.751600 TCACATCTGAAGCTGTGTAAGTTG 59.248 41.667 12.58 0.00 41.43 3.16
5070 5241 2.162408 GGCCTAACAGCACAAATCACTC 59.838 50.000 0.00 0.00 0.00 3.51
5095 5266 8.423349 TCATCCTTGATGATTTGTTTTGTCTTT 58.577 29.630 2.73 0.00 43.11 2.52
5112 5283 6.114187 TGTCTTTTCTTCTCATCTGCCTTA 57.886 37.500 0.00 0.00 0.00 2.69
5168 5339 1.470285 GCGTCCGGCACAGAGTAATTA 60.470 52.381 0.00 0.00 42.87 1.40
5236 5407 1.081094 CACTGCATGCACGAATCTCA 58.919 50.000 18.46 0.00 0.00 3.27
5520 5691 7.094890 CCAGAAATCTCAGTATTATGATGGTGC 60.095 40.741 0.00 0.00 0.00 5.01
5808 5981 1.719780 GTAGTGTCGTCCGCAAGAAAG 59.280 52.381 0.00 0.00 43.02 2.62
5823 5996 6.038161 CCGCAAGAAAGTACATATGATTGGAA 59.962 38.462 10.38 0.00 43.02 3.53
6116 6290 5.564550 AGCAAACAGTCTGATAAGGTTCAT 58.435 37.500 6.91 0.00 0.00 2.57
6176 6352 8.511604 AAGAAGAAAAAGAGTCATGAAACTCA 57.488 30.769 14.93 0.00 46.65 3.41
6199 6375 5.878406 AACATTTTCACAACATAACCCCA 57.122 34.783 0.00 0.00 0.00 4.96
6201 6377 6.240549 ACATTTTCACAACATAACCCCAAA 57.759 33.333 0.00 0.00 0.00 3.28
6203 6379 7.286313 ACATTTTCACAACATAACCCCAAATT 58.714 30.769 0.00 0.00 0.00 1.82
6301 6477 3.069980 GAGCACGTCCGCTGATCCT 62.070 63.158 4.95 0.00 44.01 3.24
6353 6529 7.390440 TGTTAGTTTGGATGTCTTTGGTAGATG 59.610 37.037 0.00 0.00 34.79 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.119574 GGGCCTACCGATCTGCCTAA 61.120 60.000 0.84 0.00 43.50 2.69
1 2 1.533273 GGGCCTACCGATCTGCCTA 60.533 63.158 0.84 0.00 43.50 3.93
2 3 2.844839 GGGCCTACCGATCTGCCT 60.845 66.667 0.84 0.00 43.50 4.75
3 4 3.942439 GGGGCCTACCGATCTGCC 61.942 72.222 0.84 0.00 43.26 4.85
4 5 3.942439 GGGGGCCTACCGATCTGC 61.942 72.222 0.84 0.00 41.60 4.26
5 6 2.445845 TGGGGGCCTACCGATCTG 60.446 66.667 0.84 0.00 41.60 2.90
6 7 2.446036 GTGGGGGCCTACCGATCT 60.446 66.667 0.84 0.00 41.60 2.75
7 8 3.925090 CGTGGGGGCCTACCGATC 61.925 72.222 0.84 0.12 41.60 3.69
19 20 3.917760 GAGATCTCCGGGCGTGGG 61.918 72.222 12.00 0.00 0.00 4.61
20 21 3.144120 CTGAGATCTCCGGGCGTGG 62.144 68.421 20.03 0.00 0.00 4.94
21 22 2.415010 CTGAGATCTCCGGGCGTG 59.585 66.667 20.03 0.00 0.00 5.34
22 23 3.532155 GCTGAGATCTCCGGGCGT 61.532 66.667 20.03 0.00 0.00 5.68
23 24 4.637489 CGCTGAGATCTCCGGGCG 62.637 72.222 27.33 27.33 36.45 6.13
721 722 1.359848 CCCGTGATCTTTCGACTTGG 58.640 55.000 0.00 0.00 0.00 3.61
722 723 1.359848 CCCCGTGATCTTTCGACTTG 58.640 55.000 0.00 0.00 0.00 3.16
723 724 0.249398 CCCCCGTGATCTTTCGACTT 59.751 55.000 0.00 0.00 0.00 3.01
724 725 1.898154 CCCCCGTGATCTTTCGACT 59.102 57.895 0.00 0.00 0.00 4.18
725 726 4.515404 CCCCCGTGATCTTTCGAC 57.485 61.111 0.00 0.00 0.00 4.20
739 740 2.034221 GGTGAGTTGCTGACCCCC 59.966 66.667 0.00 0.00 31.59 5.40
740 741 1.600916 GTGGTGAGTTGCTGACCCC 60.601 63.158 2.54 0.00 36.94 4.95
741 742 0.603975 GAGTGGTGAGTTGCTGACCC 60.604 60.000 2.54 0.00 36.94 4.46
742 743 0.394565 AGAGTGGTGAGTTGCTGACC 59.605 55.000 0.00 0.00 38.23 4.02
743 744 2.928731 GCTAGAGTGGTGAGTTGCTGAC 60.929 54.545 0.00 0.00 0.00 3.51
744 745 1.273606 GCTAGAGTGGTGAGTTGCTGA 59.726 52.381 0.00 0.00 0.00 4.26
745 746 1.001293 TGCTAGAGTGGTGAGTTGCTG 59.999 52.381 0.00 0.00 0.00 4.41
746 747 1.274728 CTGCTAGAGTGGTGAGTTGCT 59.725 52.381 0.00 0.00 0.00 3.91
747 748 1.001406 ACTGCTAGAGTGGTGAGTTGC 59.999 52.381 0.00 0.00 31.75 4.17
748 749 4.562347 AATCACTGCTAGAGTGGTGAGTTG 60.562 45.833 17.05 0.00 46.05 3.16
749 750 3.580458 AATCACTGCTAGAGTGGTGAGTT 59.420 43.478 17.05 8.37 46.05 3.01
750 751 3.169099 AATCACTGCTAGAGTGGTGAGT 58.831 45.455 17.05 10.42 46.05 3.41
751 752 3.446873 AGAATCACTGCTAGAGTGGTGAG 59.553 47.826 17.05 0.00 46.05 3.51
752 753 3.435275 AGAATCACTGCTAGAGTGGTGA 58.565 45.455 17.05 13.10 46.05 4.02
753 754 3.446873 AGAGAATCACTGCTAGAGTGGTG 59.553 47.826 17.05 9.32 46.05 4.17
757 758 5.116084 AGAGAGAGAATCACTGCTAGAGT 57.884 43.478 0.00 0.00 35.72 3.24
758 759 5.589855 TGAAGAGAGAGAATCACTGCTAGAG 59.410 44.000 0.00 0.00 35.72 2.43
759 760 5.504853 TGAAGAGAGAGAATCACTGCTAGA 58.495 41.667 0.00 0.00 35.72 2.43
760 761 5.833406 TGAAGAGAGAGAATCACTGCTAG 57.167 43.478 0.00 0.00 35.72 3.42
761 762 5.655974 ACATGAAGAGAGAGAATCACTGCTA 59.344 40.000 0.00 0.00 35.72 3.49
762 763 4.467082 ACATGAAGAGAGAGAATCACTGCT 59.533 41.667 0.00 0.00 35.72 4.24
763 764 4.757594 ACATGAAGAGAGAGAATCACTGC 58.242 43.478 0.00 0.00 35.72 4.40
764 765 5.105432 TGGACATGAAGAGAGAGAATCACTG 60.105 44.000 0.00 0.00 35.72 3.66
765 766 5.022122 TGGACATGAAGAGAGAGAATCACT 58.978 41.667 0.00 0.00 39.29 3.41
766 767 5.336150 TGGACATGAAGAGAGAGAATCAC 57.664 43.478 0.00 0.00 37.82 3.06
767 768 7.852550 ATATGGACATGAAGAGAGAGAATCA 57.147 36.000 0.00 0.00 37.82 2.57
770 771 9.813826 TGTATATATGGACATGAAGAGAGAGAA 57.186 33.333 0.00 0.00 0.00 2.87
811 815 1.196104 TGTAGGGGGTCTTCCAACCG 61.196 60.000 0.00 0.00 40.46 4.44
812 816 0.327259 GTGTAGGGGGTCTTCCAACC 59.673 60.000 0.00 0.00 38.69 3.77
840 844 3.316588 ACACTATGATCGAGCTGGTACTG 59.683 47.826 0.90 0.00 0.00 2.74
842 846 3.304794 GGACACTATGATCGAGCTGGTAC 60.305 52.174 0.90 0.00 0.00 3.34
843 847 2.885266 GGACACTATGATCGAGCTGGTA 59.115 50.000 0.90 0.00 0.00 3.25
844 848 1.683917 GGACACTATGATCGAGCTGGT 59.316 52.381 0.90 0.00 0.00 4.00
921 949 3.133901 AGAGAGAGAGAGAGTATGTGCGA 59.866 47.826 0.00 0.00 0.00 5.10
925 964 4.473196 TGTGGAGAGAGAGAGAGAGTATGT 59.527 45.833 0.00 0.00 0.00 2.29
993 1036 2.435234 GGCACCACCATCGCGTTA 60.435 61.111 5.77 0.00 38.86 3.18
1029 1072 1.362717 CGTGGTCACCGTCTCTTGT 59.637 57.895 0.00 0.00 0.00 3.16
1040 1083 2.280797 GTGGAAGCAGCGTGGTCA 60.281 61.111 0.00 0.00 0.00 4.02
1324 1367 2.758089 GGTACTCGAGCTCGCCGAA 61.758 63.158 30.97 13.17 39.60 4.30
1326 1369 3.203412 AGGTACTCGAGCTCGCCG 61.203 66.667 30.97 24.30 39.60 6.46
1380 1423 2.581354 GTGTCGATGGAGCTGGCT 59.419 61.111 0.00 0.00 0.00 4.75
1462 1509 5.335426 CGAGTACAAGGCAGTACAGTTCTTA 60.335 44.000 18.36 0.00 45.25 2.10
1463 1510 4.558898 CGAGTACAAGGCAGTACAGTTCTT 60.559 45.833 18.36 1.54 45.25 2.52
1465 1512 3.243336 CGAGTACAAGGCAGTACAGTTC 58.757 50.000 18.36 9.28 45.25 3.01
1466 1513 2.609737 GCGAGTACAAGGCAGTACAGTT 60.610 50.000 18.36 2.71 45.25 3.16
1467 1514 1.067776 GCGAGTACAAGGCAGTACAGT 60.068 52.381 18.36 3.30 45.25 3.55
1468 1515 1.067846 TGCGAGTACAAGGCAGTACAG 60.068 52.381 18.36 13.65 45.25 2.74
1469 1516 0.963225 TGCGAGTACAAGGCAGTACA 59.037 50.000 18.36 0.29 45.25 2.90
1470 1517 2.074547 TTGCGAGTACAAGGCAGTAC 57.925 50.000 11.02 11.02 43.61 2.73
1471 1518 2.823924 TTTGCGAGTACAAGGCAGTA 57.176 45.000 0.00 0.00 38.04 2.74
1472 1519 1.961793 TTTTGCGAGTACAAGGCAGT 58.038 45.000 0.00 0.00 38.04 4.40
1510 1557 9.128107 CAATTGAACTGCAAAAACGTCTTATAT 57.872 29.630 0.00 0.00 40.48 0.86
1513 1560 6.326375 ACAATTGAACTGCAAAAACGTCTTA 58.674 32.000 13.59 0.00 40.48 2.10
1514 1561 5.167845 ACAATTGAACTGCAAAAACGTCTT 58.832 33.333 13.59 0.00 40.48 3.01
1515 1562 4.743493 ACAATTGAACTGCAAAAACGTCT 58.257 34.783 13.59 0.00 40.48 4.18
1516 1563 5.061560 TCAACAATTGAACTGCAAAAACGTC 59.938 36.000 13.59 0.00 40.48 4.34
1517 1564 4.926238 TCAACAATTGAACTGCAAAAACGT 59.074 33.333 13.59 0.00 40.48 3.99
1518 1565 5.447478 TCAACAATTGAACTGCAAAAACG 57.553 34.783 13.59 0.00 40.48 3.60
1529 1576 6.817641 AGACATTTTGCAGTTCAACAATTGAA 59.182 30.769 13.59 0.00 46.68 2.69
1530 1577 6.339730 AGACATTTTGCAGTTCAACAATTGA 58.660 32.000 13.59 0.00 38.04 2.57
1531 1578 6.592798 AGACATTTTGCAGTTCAACAATTG 57.407 33.333 3.24 3.24 33.73 2.32
1532 1579 8.891671 ATAAGACATTTTGCAGTTCAACAATT 57.108 26.923 0.00 0.00 33.73 2.32
1534 1581 9.979578 AATATAAGACATTTTGCAGTTCAACAA 57.020 25.926 0.00 0.00 33.73 2.83
1535 1582 9.409312 CAATATAAGACATTTTGCAGTTCAACA 57.591 29.630 0.00 0.00 33.73 3.33
1536 1583 8.863049 CCAATATAAGACATTTTGCAGTTCAAC 58.137 33.333 0.00 0.00 33.73 3.18
1537 1584 8.584157 ACCAATATAAGACATTTTGCAGTTCAA 58.416 29.630 0.00 0.00 0.00 2.69
1538 1585 8.028354 CACCAATATAAGACATTTTGCAGTTCA 58.972 33.333 0.00 0.00 0.00 3.18
1539 1586 8.028938 ACACCAATATAAGACATTTTGCAGTTC 58.971 33.333 0.00 0.00 0.00 3.01
1540 1587 7.895759 ACACCAATATAAGACATTTTGCAGTT 58.104 30.769 0.00 0.00 0.00 3.16
1541 1588 7.466746 ACACCAATATAAGACATTTTGCAGT 57.533 32.000 0.00 0.00 0.00 4.40
1542 1589 8.458052 TGTACACCAATATAAGACATTTTGCAG 58.542 33.333 0.00 0.00 0.00 4.41
1543 1590 8.341892 TGTACACCAATATAAGACATTTTGCA 57.658 30.769 0.00 0.00 0.00 4.08
1544 1591 8.673711 TCTGTACACCAATATAAGACATTTTGC 58.326 33.333 0.00 0.00 0.00 3.68
1550 1597 6.895756 ACTCCTCTGTACACCAATATAAGACA 59.104 38.462 0.00 0.00 0.00 3.41
1631 1678 5.310451 AGAAACCATTAGAACGTTAGGCAA 58.690 37.500 0.00 0.00 0.00 4.52
1647 1694 3.495331 TGCTTGCAGGATTAAGAAACCA 58.505 40.909 0.00 0.00 0.00 3.67
1670 1717 7.593875 TGTTTCATGTTTGAAGGTTTTCTTG 57.406 32.000 0.00 0.00 42.60 3.02
1715 1762 0.969149 CTAGTGTCACTGGCAGGTGA 59.031 55.000 20.34 16.27 42.96 4.02
1752 1799 6.015180 ACCAGACTGTTATGTAGTAAAACCGA 60.015 38.462 0.93 0.00 0.00 4.69
1792 1842 5.249393 ACTGTCTTTCTCTCTCTCTCTCTCT 59.751 44.000 0.00 0.00 0.00 3.10
1793 1843 5.352569 CACTGTCTTTCTCTCTCTCTCTCTC 59.647 48.000 0.00 0.00 0.00 3.20
1794 1844 5.221925 ACACTGTCTTTCTCTCTCTCTCTCT 60.222 44.000 0.00 0.00 0.00 3.10
1795 1845 5.003804 ACACTGTCTTTCTCTCTCTCTCTC 58.996 45.833 0.00 0.00 0.00 3.20
1876 1926 5.572885 GCTTTGAAACCCTCTGGACCTAATA 60.573 44.000 0.00 0.00 34.81 0.98
1970 2020 4.655027 CTTTGGATGTTGATCATGTCACG 58.345 43.478 0.00 0.00 36.32 4.35
2189 2265 9.412898 ATGCCCACATATATCACCTCTCTAGGA 62.413 44.444 0.00 0.00 39.02 2.94
2328 2453 6.892658 TTTTTGCCTGTATACACAAGACAT 57.107 33.333 0.08 0.00 33.22 3.06
2434 2560 4.072839 GGCAAAACAAGAAGTAGCTAGGT 58.927 43.478 0.00 0.00 0.00 3.08
2523 2649 9.859427 CTCACTTTGGCTTGAATTATATTTTCA 57.141 29.630 0.00 0.00 0.00 2.69
2663 2792 1.075050 CATTAGCTGCATCTCCCCCAT 59.925 52.381 1.02 0.00 0.00 4.00
2664 2793 0.475475 CATTAGCTGCATCTCCCCCA 59.525 55.000 1.02 0.00 0.00 4.96
2675 2804 7.807977 ATTAGTCCCACAATAACATTAGCTG 57.192 36.000 0.00 0.00 0.00 4.24
2798 2927 5.956068 TCGATGAGACCTATCTGAAGATG 57.044 43.478 2.99 0.00 34.34 2.90
2799 2928 8.642935 TTAATCGATGAGACCTATCTGAAGAT 57.357 34.615 0.00 0.00 34.34 2.40
2800 2929 8.465273 TTTAATCGATGAGACCTATCTGAAGA 57.535 34.615 0.00 0.00 34.34 2.87
2836 2967 5.106948 CGTTTCAGAAACTATGTGCTCATGT 60.107 40.000 21.24 5.03 39.23 3.21
2993 3138 1.817087 ATCTCTCATGCCCATCCTGT 58.183 50.000 0.00 0.00 0.00 4.00
3084 3229 7.604545 GGTGAGTCAAATTTCTTAGCTAAGACT 59.395 37.037 31.25 23.69 41.64 3.24
3109 3264 2.528564 TCTTTCCCAGGCAGAAATTGG 58.471 47.619 0.00 0.00 33.01 3.16
3180 3335 7.925483 AGATCTTATCTGTTATGTTCAGTCAGC 59.075 37.037 0.00 0.00 38.44 4.26
3358 3513 2.622470 GGGTCCTTCTAGCTAACTACCG 59.378 54.545 0.00 0.00 0.00 4.02
3706 3865 5.893824 GGACCATTTTTATTCCCATCAGACT 59.106 40.000 0.00 0.00 0.00 3.24
3991 4151 7.406553 GCACATGCTATATTCGTTTCTTTGTA 58.593 34.615 0.00 0.00 38.21 2.41
4057 4217 4.361451 AGATTTTGACCGATTGATGCAC 57.639 40.909 0.00 0.00 0.00 4.57
4589 4749 0.250858 CTGGCACCTGAATCCACACA 60.251 55.000 0.00 0.00 0.00 3.72
4590 4750 1.589716 GCTGGCACCTGAATCCACAC 61.590 60.000 0.00 0.00 0.00 3.82
4591 4751 1.303561 GCTGGCACCTGAATCCACA 60.304 57.895 0.00 0.00 0.00 4.17
4616 4776 2.980568 ACATTGACGAAATAGGCCGAA 58.019 42.857 0.00 0.00 0.00 4.30
4710 4870 9.994432 CAGTTCCTATAAAGCATAGTTTTTCTG 57.006 33.333 0.00 0.00 35.71 3.02
4945 5116 7.920160 AAAATAAGCAAAATACCATGTTGGG 57.080 32.000 0.00 0.00 43.37 4.12
4980 5151 1.134068 GGGTACTTGAGGGAATCCAGC 60.134 57.143 0.09 0.00 34.83 4.85
4988 5159 2.766828 CTGGTAAGAGGGTACTTGAGGG 59.233 54.545 0.00 0.00 0.00 4.30
5049 5220 2.162408 GAGTGATTTGTGCTGTTAGGCC 59.838 50.000 0.00 0.00 0.00 5.19
5070 5241 8.597662 AAAGACAAAACAAATCATCAAGGATG 57.402 30.769 0.00 0.00 41.00 3.51
5095 5266 8.321353 TGAAAAGTATAAGGCAGATGAGAAGAA 58.679 33.333 0.00 0.00 0.00 2.52
5112 5283 5.416952 CCATTTGTCAGAGCCTGAAAAGTAT 59.583 40.000 6.48 0.00 42.46 2.12
5290 5461 0.537188 CTGTCTTGTACTCGGCCCAT 59.463 55.000 0.00 0.00 0.00 4.00
5380 5551 3.428045 CCTCTTATTTTCCTTTGCTGCCG 60.428 47.826 0.00 0.00 0.00 5.69
5520 5691 1.599071 GTCATGGACACACACACACTG 59.401 52.381 0.00 0.00 32.09 3.66
5808 5981 7.819644 TGCTGCATATTTCCAATCATATGTAC 58.180 34.615 0.00 0.00 36.23 2.90
6029 6203 6.678857 ACTAAGAAACTCAATCTAATCCCCCT 59.321 38.462 0.00 0.00 0.00 4.79
6107 6281 2.441750 GGTATCCCCAGCATGAACCTTA 59.558 50.000 0.00 0.00 39.69 2.69
6176 6352 6.240549 TGGGGTTATGTTGTGAAAATGTTT 57.759 33.333 0.00 0.00 0.00 2.83
6199 6375 9.981114 CTGAGGTTTTTGTTTACCTGATAATTT 57.019 29.630 0.00 0.00 44.65 1.82
6201 6377 7.947890 TCCTGAGGTTTTTGTTTACCTGATAAT 59.052 33.333 0.00 0.00 44.65 1.28
6203 6379 6.843752 TCCTGAGGTTTTTGTTTACCTGATA 58.156 36.000 0.00 0.00 44.65 2.15
6279 6455 1.599606 ATCAGCGGACGTGCTCTTCT 61.600 55.000 5.27 0.00 45.23 2.85


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

AutoCloner maintained by Alex Coulton.