Multiple sequence alignment - TraesCS2B01G245200

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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 TraesCS2B01G245200 chr2B 100.000 3541 0 0 1 3541 249368113 249371653 0.000000e+00 6540
1 TraesCS2B01G245200 chr7D 89.000 3009 306 13 539 3541 603898887 603895898 0.000000e+00 3699
2 TraesCS2B01G245200 chr1D 86.787 2770 352 9 776 3541 42882631 42879872 0.000000e+00 3075
3 TraesCS2B01G245200 chr6D 89.509 2259 225 10 1288 3541 334312636 334314887 0.000000e+00 2848
4 TraesCS2B01G245200 chr6D 88.181 753 75 4 539 1291 334251096 334251834 0.000000e+00 885
5 TraesCS2B01G245200 chr3D 83.201 3012 465 32 545 3541 610016587 610013602 0.000000e+00 2721
6 TraesCS2B01G245200 chr2D 82.741 3013 465 32 539 3540 6071513 6074481 0.000000e+00 2632
7 TraesCS2B01G245200 chr2A 79.006 1991 383 29 1570 3538 66525613 66527590 0.000000e+00 1328
8 TraesCS2B01G245200 chr2A 78.163 1415 267 34 2151 3541 755429946 755428550 0.000000e+00 863
9 TraesCS2B01G245200 chr1A 98.893 542 6 0 1 542 505746182 505746723 0.000000e+00 968
10 TraesCS2B01G245200 chr7A 98.893 542 4 1 1 542 663781066 663781605 0.000000e+00 966
11 TraesCS2B01G245200 chr7A 98.524 542 6 1 1 542 663785758 663786297 0.000000e+00 955
12 TraesCS2B01G245200 chr3B 98.891 541 6 0 1 541 463098740 463098200 0.000000e+00 966
13 TraesCS2B01G245200 chr3A 98.708 542 4 2 1 542 8701690 8701152 0.000000e+00 959
14 TraesCS2B01G245200 chr7B 98.521 541 8 0 4 544 689931637 689931097 0.000000e+00 955
15 TraesCS2B01G245200 chr1B 98.004 551 9 2 1 549 138849494 138850044 0.000000e+00 955
16 TraesCS2B01G245200 chrUn 98.336 541 9 0 1 541 289009910 289009370 0.000000e+00 950
17 TraesCS2B01G245200 chrUn 98.336 541 9 0 1 541 326904455 326903915 0.000000e+00 950
18 TraesCS2B01G245200 chr5D 73.978 1199 270 37 2351 3531 565272723 565271549 6.970000e-122 448
19 TraesCS2B01G245200 chr5A 73.388 1210 292 28 2348 3541 652945682 652946877 1.180000e-114 424


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 TraesCS2B01G245200 chr2B 249368113 249371653 3540 False 6540 6540 100.000 1 3541 1 chr2B.!!$F1 3540
1 TraesCS2B01G245200 chr7D 603895898 603898887 2989 True 3699 3699 89.000 539 3541 1 chr7D.!!$R1 3002
2 TraesCS2B01G245200 chr1D 42879872 42882631 2759 True 3075 3075 86.787 776 3541 1 chr1D.!!$R1 2765
3 TraesCS2B01G245200 chr6D 334312636 334314887 2251 False 2848 2848 89.509 1288 3541 1 chr6D.!!$F2 2253
4 TraesCS2B01G245200 chr6D 334251096 334251834 738 False 885 885 88.181 539 1291 1 chr6D.!!$F1 752
5 TraesCS2B01G245200 chr3D 610013602 610016587 2985 True 2721 2721 83.201 545 3541 1 chr3D.!!$R1 2996
6 TraesCS2B01G245200 chr2D 6071513 6074481 2968 False 2632 2632 82.741 539 3540 1 chr2D.!!$F1 3001
7 TraesCS2B01G245200 chr2A 66525613 66527590 1977 False 1328 1328 79.006 1570 3538 1 chr2A.!!$F1 1968
8 TraesCS2B01G245200 chr2A 755428550 755429946 1396 True 863 863 78.163 2151 3541 1 chr2A.!!$R1 1390
9 TraesCS2B01G245200 chr1A 505746182 505746723 541 False 968 968 98.893 1 542 1 chr1A.!!$F1 541
10 TraesCS2B01G245200 chr7A 663781066 663781605 539 False 966 966 98.893 1 542 1 chr7A.!!$F1 541
11 TraesCS2B01G245200 chr7A 663785758 663786297 539 False 955 955 98.524 1 542 1 chr7A.!!$F2 541
12 TraesCS2B01G245200 chr3B 463098200 463098740 540 True 966 966 98.891 1 541 1 chr3B.!!$R1 540
13 TraesCS2B01G245200 chr3A 8701152 8701690 538 True 959 959 98.708 1 542 1 chr3A.!!$R1 541
14 TraesCS2B01G245200 chr7B 689931097 689931637 540 True 955 955 98.521 4 544 1 chr7B.!!$R1 540
15 TraesCS2B01G245200 chr1B 138849494 138850044 550 False 955 955 98.004 1 549 1 chr1B.!!$F1 548
16 TraesCS2B01G245200 chrUn 289009370 289009910 540 True 950 950 98.336 1 541 1 chrUn.!!$R1 540
17 TraesCS2B01G245200 chrUn 326903915 326904455 540 True 950 950 98.336 1 541 1 chrUn.!!$R2 540
18 TraesCS2B01G245200 chr5D 565271549 565272723 1174 True 448 448 73.978 2351 3531 1 chr5D.!!$R1 1180
19 TraesCS2B01G245200 chr5A 652945682 652946877 1195 False 424 424 73.388 2348 3541 1 chr5A.!!$F1 1193

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
672 674 0.108615 CCTACGCTGAGGTGGTCAAG 60.109 60.0 0.0 0.0 33.60 3.02 F
1113 1118 0.108424 GGCAGTCTAGCACTCACCAG 60.108 60.0 0.0 0.0 35.83 4.00 F
2136 2150 0.761802 GCCCACCCCAAAATTCACAA 59.238 50.0 0.0 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2081 0.486879 TTTCCATGTCTTTGGGGCCT 59.513 50.000 0.84 0.0 37.37 5.19 R
2141 2155 1.278413 GGGTCTTGGACTTAGTGGGAC 59.722 57.143 0.00 0.0 32.47 4.46 R
3468 3500 1.997791 TGGTCACTACCCACTCTAGGA 59.002 52.381 0.00 0.0 46.16 2.94 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
214 215 8.525316 TGATAATTTGCAGATTCAAGACACAAT 58.475 29.630 5.63 0.00 0.00 2.71
582 583 1.313772 GCTATCCTGCGAGAGTGAGA 58.686 55.000 0.00 0.00 29.59 3.27
588 589 0.393673 CTGCGAGAGTGAGAGGGAGA 60.394 60.000 0.00 0.00 0.00 3.71
636 638 4.660938 AAGGAGTTGTGGCGGGGC 62.661 66.667 0.00 0.00 0.00 5.80
672 674 0.108615 CCTACGCTGAGGTGGTCAAG 60.109 60.000 0.00 0.00 33.60 3.02
675 677 2.360475 GCTGAGGTGGTCAAGGGC 60.360 66.667 0.00 0.00 33.60 5.19
693 695 3.593680 ATGGCAGGCAACAGGGGT 61.594 61.111 0.00 0.00 41.41 4.95
701 703 3.182263 CAACAGGGGTGGGGGTCA 61.182 66.667 0.00 0.00 0.00 4.02
714 716 2.920912 GGTCACCGTGGTGGAGGA 60.921 66.667 18.47 0.00 45.43 3.71
769 771 1.539496 GCGGTCAGGTACACACTCAAA 60.539 52.381 0.00 0.00 0.00 2.69
770 772 2.828877 CGGTCAGGTACACACTCAAAA 58.171 47.619 0.00 0.00 0.00 2.44
788 790 0.978146 AACCCTGGTCAGATCCCGAG 60.978 60.000 0.00 0.00 0.00 4.63
800 802 0.982852 ATCCCGAGCCAATCTGGTGA 60.983 55.000 0.00 0.00 40.46 4.02
821 823 3.140814 GAATCCACAAGGGCCGCC 61.141 66.667 0.00 0.00 36.21 6.13
837 839 2.872557 CCACCGTTGCAGCAGATG 59.127 61.111 0.24 0.00 0.00 2.90
848 850 2.336945 CAGCAGATGCATCCAGGTAA 57.663 50.000 23.06 0.00 45.16 2.85
876 878 5.251764 CAAAATATGCAACAATTTGGGGGA 58.748 37.500 0.78 0.00 32.81 4.81
900 902 1.355720 AGCAACTTACAAGGGATGCCT 59.644 47.619 0.00 0.00 35.91 4.75
945 947 3.937706 CTCAGTTCAATTAGTGGCCTCAG 59.062 47.826 3.32 0.00 0.00 3.35
948 950 2.819608 GTTCAATTAGTGGCCTCAGCAA 59.180 45.455 3.32 0.00 42.56 3.91
952 954 4.080356 TCAATTAGTGGCCTCAGCAATACT 60.080 41.667 3.32 0.00 42.56 2.12
953 955 4.510167 ATTAGTGGCCTCAGCAATACTT 57.490 40.909 3.32 0.00 42.56 2.24
954 956 2.119801 AGTGGCCTCAGCAATACTTG 57.880 50.000 3.32 0.00 42.56 3.16
981 983 1.203237 TGCCTAGCTTGCCTGTGATA 58.797 50.000 0.00 0.00 0.00 2.15
991 996 2.226330 TGCCTGTGATACACCAACAAC 58.774 47.619 0.00 0.00 32.73 3.32
992 997 2.226330 GCCTGTGATACACCAACAACA 58.774 47.619 0.00 0.00 32.73 3.33
993 998 2.621055 GCCTGTGATACACCAACAACAA 59.379 45.455 0.00 0.00 32.73 2.83
1014 1019 2.100252 ACAGCAGATGCCAATTATGCAC 59.900 45.455 0.14 0.46 42.38 4.57
1045 1050 0.110056 GCAGATGCAGTTTGGTCACG 60.110 55.000 0.00 0.00 41.59 4.35
1048 1053 2.200170 GATGCAGTTTGGTCACGCCC 62.200 60.000 0.00 0.00 36.04 6.13
1056 1061 4.329545 GGTCACGCCCCAGAGCAA 62.330 66.667 0.00 0.00 32.77 3.91
1092 1097 3.882444 TCAGATGCAAGGATTTGGAGAG 58.118 45.455 0.00 0.00 38.08 3.20
1098 1103 0.627986 AAGGATTTGGAGAGGGGCAG 59.372 55.000 0.00 0.00 0.00 4.85
1110 1115 1.219393 GGGGCAGTCTAGCACTCAC 59.781 63.158 0.00 0.00 38.23 3.51
1113 1118 0.108424 GGCAGTCTAGCACTCACCAG 60.108 60.000 0.00 0.00 35.83 4.00
1132 1137 4.038402 ACCAGCAGATTTCTCAAAACCAAG 59.962 41.667 0.00 0.00 0.00 3.61
1167 1175 3.598299 CAAGAGCTTCTCCCAGAAAGAG 58.402 50.000 0.00 0.00 33.19 2.85
1185 1193 2.376518 AGAGGTGCAAAGGAAATCTGGA 59.623 45.455 0.00 0.00 0.00 3.86
1195 1203 5.511386 AAGGAAATCTGGAGATGACAAGT 57.489 39.130 0.00 0.00 34.49 3.16
1200 1208 5.752036 AATCTGGAGATGACAAGTCTGAA 57.248 39.130 1.53 0.00 34.49 3.02
1253 1262 7.253422 GTGGTCAACTATGATCCAAAAATGAG 58.747 38.462 0.00 0.00 38.00 2.90
1260 1269 9.471702 AACTATGATCCAAAAATGAGAGATGTT 57.528 29.630 0.00 0.00 0.00 2.71
1363 1372 2.446435 GGCACCATATGGACAACTGTT 58.554 47.619 28.77 0.00 38.94 3.16
1364 1373 2.423538 GGCACCATATGGACAACTGTTC 59.576 50.000 28.77 8.49 38.94 3.18
1425 1434 2.620234 TGCTAATGCAGGGCTAGGT 58.380 52.632 9.19 0.00 45.31 3.08
1431 1440 2.907458 ATGCAGGGCTAGGTTTCTTT 57.093 45.000 0.00 0.00 0.00 2.52
1461 1470 1.074405 TCAGATGGCAAAGAGGCTGTT 59.926 47.619 0.00 0.00 44.55 3.16
1470 1479 3.443681 GCAAAGAGGCTGTTAAATGGCTA 59.556 43.478 0.00 0.00 39.23 3.93
1497 1506 2.106566 TCCAATGTTTGTGTGGCTGTT 58.893 42.857 0.00 0.00 32.10 3.16
1509 1518 3.191371 GTGTGGCTGTTATTGAAGAAGGG 59.809 47.826 0.00 0.00 0.00 3.95
1519 1528 3.874383 TTGAAGAAGGGTCCATCACAA 57.126 42.857 0.00 0.00 0.00 3.33
1527 1536 2.154462 GGGTCCATCACAACACAAGAG 58.846 52.381 0.00 0.00 0.00 2.85
1533 1542 3.058432 CCATCACAACACAAGAGCTGAAG 60.058 47.826 0.00 0.00 0.00 3.02
1560 1569 9.525826 AACAATTTCTCTGAGATATGGAAAACT 57.474 29.630 16.42 0.00 31.24 2.66
1599 1608 1.622811 AGGCAGTTGACTGAGAAGAGG 59.377 52.381 14.98 0.00 46.59 3.69
1632 1642 1.822425 TCCCACCTCACCAAAAGGTA 58.178 50.000 0.00 0.00 45.48 3.08
1668 1678 3.205507 AGCTACCCTCCATTAGTCTCAGA 59.794 47.826 0.00 0.00 0.00 3.27
1675 1685 6.112058 CCCTCCATTAGTCTCAGAAAGAAAG 58.888 44.000 0.00 0.00 35.21 2.62
1683 1694 3.045634 TCTCAGAAAGAAAGGGGTGACA 58.954 45.455 0.00 0.00 0.00 3.58
1698 1709 5.770162 AGGGGTGACAGTTTCTTTTGATAAG 59.230 40.000 0.00 0.00 0.00 1.73
1707 1718 6.434028 CAGTTTCTTTTGATAAGTGGGATGGA 59.566 38.462 0.00 0.00 0.00 3.41
1767 1778 1.417890 ACCATGATTCGGATCCCTGTC 59.582 52.381 6.06 2.05 0.00 3.51
1815 1826 4.406972 TCTCAGATCACTTACATCTTGGGG 59.593 45.833 0.00 0.00 0.00 4.96
1816 1827 3.455910 TCAGATCACTTACATCTTGGGGG 59.544 47.826 0.00 0.00 0.00 5.40
1822 1833 3.009033 CACTTACATCTTGGGGGTCTTGA 59.991 47.826 0.00 0.00 0.00 3.02
1824 1835 4.292306 ACTTACATCTTGGGGGTCTTGATT 59.708 41.667 0.00 0.00 0.00 2.57
1887 1898 2.500229 GTTAAAGTGCAGGTGGCTGTA 58.500 47.619 0.00 0.00 45.15 2.74
1896 1907 1.837439 CAGGTGGCTGTAAGGGACATA 59.163 52.381 0.00 0.00 37.45 2.29
1941 1955 5.152623 TGGTAGAGATTGACAAGGAACTG 57.847 43.478 0.00 0.00 40.86 3.16
1950 1964 8.697507 AGATTGACAAGGAACTGTTTCTTATT 57.302 30.769 13.52 4.38 40.86 1.40
1952 1966 9.185192 GATTGACAAGGAACTGTTTCTTATTTG 57.815 33.333 13.52 5.35 40.86 2.32
1953 1967 7.639113 TGACAAGGAACTGTTTCTTATTTGT 57.361 32.000 13.52 8.48 40.86 2.83
1975 1989 3.616956 TCCTTGTTGACATAGCTCCAG 57.383 47.619 0.00 0.00 0.00 3.86
1978 1992 3.438087 CCTTGTTGACATAGCTCCAGTTG 59.562 47.826 0.00 0.00 0.00 3.16
2000 2014 3.815809 CTGGAAGTGTGAACCCAAGTAA 58.184 45.455 0.00 0.00 0.00 2.24
2009 2023 4.348461 TGTGAACCCAAGTAATAGTGGTGA 59.652 41.667 0.00 0.00 32.60 4.02
2025 2039 9.471702 AATAGTGGTGAAGAAAAATCAGATGAT 57.528 29.630 0.00 0.00 36.07 2.45
2037 2051 3.900966 TCAGATGATGACCTGTTGGAG 57.099 47.619 0.00 0.00 37.04 3.86
2055 2069 1.945580 AGGGGAGTCCTGAAAGAGAC 58.054 55.000 9.58 0.00 46.07 3.36
2103 2117 4.743493 TGGAAACTGACAAGAGCAAAAAC 58.257 39.130 0.00 0.00 0.00 2.43
2106 2120 2.031870 ACTGACAAGAGCAAAAACCCC 58.968 47.619 0.00 0.00 0.00 4.95
2136 2150 0.761802 GCCCACCCCAAAATTCACAA 59.238 50.000 0.00 0.00 0.00 3.33
2141 2155 3.882288 CCACCCCAAAATTCACAAAAAGG 59.118 43.478 0.00 0.00 0.00 3.11
2160 2174 1.278413 GGTCCCACTAAGTCCAAGACC 59.722 57.143 0.00 0.00 35.91 3.85
2163 2177 1.657804 CCACTAAGTCCAAGACCCCT 58.342 55.000 0.00 0.00 32.18 4.79
2172 2186 0.250901 CCAAGACCCCTGTGGAACTG 60.251 60.000 0.00 0.00 38.04 3.16
2218 2234 3.669023 GCAAAGTGCAATACTGAGTCTGC 60.669 47.826 11.46 11.46 44.26 4.26
2222 2238 4.136796 AGTGCAATACTGAGTCTGCAAAA 58.863 39.130 19.83 0.22 45.71 2.44
2243 2259 7.296660 CAAAATGACTCTCACATGAAGAAGAC 58.703 38.462 0.00 0.15 0.00 3.01
2248 2264 4.244066 CTCTCACATGAAGAAGACTGTGG 58.756 47.826 0.00 0.00 39.51 4.17
2259 2275 6.316390 TGAAGAAGACTGTGGAGAAGAAAAAC 59.684 38.462 0.00 0.00 0.00 2.43
2268 2284 4.276183 GTGGAGAAGAAAAACCCTGAAGAC 59.724 45.833 0.00 0.00 0.00 3.01
2292 2308 3.441572 ACATTGCTATTCAACTGCTGGAC 59.558 43.478 0.00 0.00 37.53 4.02
2362 2384 3.625649 AACCACAAAAGCACAAATGGT 57.374 38.095 0.00 0.00 42.22 3.55
2657 2684 0.322008 CAGAGTGTTTCCTCCCTGCC 60.322 60.000 0.00 0.00 31.53 4.85
2745 2772 1.431633 TCAGTAGAGACCACCCTGGAA 59.568 52.381 0.00 0.00 40.96 3.53
2838 2866 6.096282 TGGTAGTTAGCTTATTTTGGAATGCC 59.904 38.462 0.00 0.00 0.00 4.40
2889 2917 2.565841 GCTGTGGGTAAGCTCATTAGG 58.434 52.381 0.00 0.00 37.69 2.69
2996 3027 4.144297 GGTAGATATTCTTGGCATTGGCA 58.856 43.478 9.11 9.11 43.71 4.92
3196 3228 8.604640 AGAGTTCATCAATGAGCTACATAATG 57.395 34.615 9.03 1.38 46.31 1.90
3201 3233 9.836864 TTCATCAATGAGCTACATAATGTAGTT 57.163 29.630 0.00 0.00 45.12 2.24
3255 3287 4.082190 GGGGACTTCAATTTGGTTAGAAGC 60.082 45.833 0.00 0.00 40.77 3.86
3257 3289 5.185828 GGGACTTCAATTTGGTTAGAAGCAT 59.814 40.000 0.00 0.00 40.77 3.79
3272 3304 4.405548 AGAAGCATTGAGGAGAAAAGCTT 58.594 39.130 0.00 0.00 42.82 3.74
3297 3329 5.163258 TGGAAATGTTAACTTGCATTGGGTT 60.163 36.000 7.22 0.00 35.72 4.11
3333 3365 7.214460 TGACTGGGTCAATAAATATGGGTTA 57.786 36.000 0.00 0.00 39.78 2.85
3378 3410 5.589831 AGGAAGTTTACTTGGGCCAATAAT 58.410 37.500 21.25 11.08 36.11 1.28
3513 3545 3.140519 CCCCTCTAGTGGTAGATACTGGT 59.859 52.174 9.90 0.00 34.63 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 215 4.453136 GCGACTTCAACCATAGGTTTGTTA 59.547 41.667 0.00 0.00 44.33 2.41
533 534 2.823154 GGTGTGAATTTTTCGGATGGGA 59.177 45.455 0.00 0.00 0.00 4.37
582 583 1.760086 CGCCTGGATCTGTCTCCCT 60.760 63.158 0.00 0.00 34.12 4.20
588 589 1.561643 TCTTCTTCGCCTGGATCTGT 58.438 50.000 0.00 0.00 0.00 3.41
663 665 3.070576 GCCATGCCCTTGACCACC 61.071 66.667 0.00 0.00 0.00 4.61
672 674 3.766691 CTGTTGCCTGCCATGCCC 61.767 66.667 0.00 0.00 0.00 5.36
675 677 3.072468 CCCCTGTTGCCTGCCATG 61.072 66.667 0.00 0.00 0.00 3.66
701 703 2.923035 CACCTCCTCCACCACGGT 60.923 66.667 0.00 0.00 35.57 4.83
714 716 3.319198 CCACGGCCAGTACCACCT 61.319 66.667 2.24 0.00 0.00 4.00
749 751 0.032952 TTGAGTGTGTACCTGACCGC 59.967 55.000 0.00 0.00 0.00 5.68
753 755 2.775384 AGGGTTTTGAGTGTGTACCTGA 59.225 45.455 0.00 0.00 0.00 3.86
769 771 0.978146 CTCGGGATCTGACCAGGGTT 60.978 60.000 0.00 0.00 0.00 4.11
770 772 1.381872 CTCGGGATCTGACCAGGGT 60.382 63.158 0.00 0.00 0.00 4.34
788 790 2.019984 GATTCAGGTCACCAGATTGGC 58.980 52.381 0.00 0.00 42.67 4.52
800 802 1.384191 GGCCCTTGTGGATTCAGGT 59.616 57.895 0.00 0.00 35.39 4.00
837 839 6.507023 CATATTTTGGAAGTTACCTGGATGC 58.493 40.000 0.00 0.00 0.00 3.91
848 850 6.430616 CCCAAATTGTTGCATATTTTGGAAGT 59.569 34.615 24.70 0.00 45.87 3.01
858 860 1.830477 GCTCCCCCAAATTGTTGCATA 59.170 47.619 0.00 0.00 33.01 3.14
864 866 0.704076 TGCTAGCTCCCCCAAATTGT 59.296 50.000 17.23 0.00 0.00 2.71
876 878 3.878778 CATCCCTTGTAAGTTGCTAGCT 58.121 45.455 17.23 0.00 0.00 3.32
909 911 2.905415 ACTGAGGAAATTGCATCCCA 57.095 45.000 1.05 0.00 37.71 4.37
948 950 2.945890 GCTAGGCAAACCAGGCAAGTAT 60.946 50.000 0.00 0.00 39.06 2.12
952 954 0.178964 AAGCTAGGCAAACCAGGCAA 60.179 50.000 0.00 0.00 37.91 4.52
953 955 0.895100 CAAGCTAGGCAAACCAGGCA 60.895 55.000 0.00 0.00 37.91 4.75
954 956 1.885871 CAAGCTAGGCAAACCAGGC 59.114 57.895 0.00 0.00 39.06 4.85
955 957 1.598701 GGCAAGCTAGGCAAACCAGG 61.599 60.000 11.85 0.00 39.06 4.45
956 958 0.610232 AGGCAAGCTAGGCAAACCAG 60.610 55.000 11.85 0.00 39.06 4.00
957 959 0.895100 CAGGCAAGCTAGGCAAACCA 60.895 55.000 11.85 0.00 39.06 3.67
958 960 0.895559 ACAGGCAAGCTAGGCAAACC 60.896 55.000 11.85 0.00 36.37 3.27
959 961 0.242017 CACAGGCAAGCTAGGCAAAC 59.758 55.000 11.85 0.00 36.37 2.93
960 962 0.110295 TCACAGGCAAGCTAGGCAAA 59.890 50.000 11.85 0.00 36.37 3.68
981 983 1.832883 TCTGCTGTTGTTGTTGGTGT 58.167 45.000 0.00 0.00 0.00 4.16
991 996 3.120792 GCATAATTGGCATCTGCTGTTG 58.879 45.455 1.70 0.00 41.70 3.33
992 997 2.761767 TGCATAATTGGCATCTGCTGTT 59.238 40.909 1.70 0.00 41.70 3.16
993 998 2.100252 GTGCATAATTGGCATCTGCTGT 59.900 45.455 9.44 0.00 44.11 4.40
1037 1042 4.329545 GCTCTGGGGCGTGACCAA 62.330 66.667 0.00 0.00 42.05 3.67
1045 1050 1.079612 GTTGCATTTGCTCTGGGGC 60.080 57.895 3.94 0.00 42.66 5.80
1048 1053 0.245539 CCAGGTTGCATTTGCTCTGG 59.754 55.000 18.23 18.23 42.59 3.86
1056 1061 3.382546 GCATCTGATTACCAGGTTGCATT 59.617 43.478 0.00 0.00 44.49 3.56
1092 1097 1.219393 GTGAGTGCTAGACTGCCCC 59.781 63.158 0.00 0.00 33.83 5.80
1098 1103 0.891373 TCTGCTGGTGAGTGCTAGAC 59.109 55.000 0.00 0.00 0.00 2.59
1110 1115 4.279169 TCTTGGTTTTGAGAAATCTGCTGG 59.721 41.667 0.00 0.00 0.00 4.85
1113 1118 5.695851 TCTCTTGGTTTTGAGAAATCTGC 57.304 39.130 0.00 0.00 36.52 4.26
1158 1166 2.276732 TCCTTTGCACCTCTTTCTGG 57.723 50.000 0.00 0.00 0.00 3.86
1161 1169 4.321527 CCAGATTTCCTTTGCACCTCTTTC 60.322 45.833 0.00 0.00 0.00 2.62
1167 1175 2.795329 TCTCCAGATTTCCTTTGCACC 58.205 47.619 0.00 0.00 0.00 5.01
1185 1193 4.282957 TGAGAGCTTTCAGACTTGTCATCT 59.717 41.667 2.15 0.00 0.00 2.90
1253 1262 9.579768 CTCCACAGTTATAGCATATAACATCTC 57.420 37.037 17.50 0.00 37.05 2.75
1260 1269 7.525526 GCTGGTTCTCCACAGTTATAGCATATA 60.526 40.741 0.00 0.00 39.03 0.86
1263 1272 4.684485 GCTGGTTCTCCACAGTTATAGCAT 60.684 45.833 0.00 0.00 39.03 3.79
1302 1311 1.688197 CACTTTTTGGGCACTGGACAT 59.312 47.619 0.00 0.00 0.00 3.06
1363 1372 0.035036 TGCGGTTTGTACCATTCCGA 59.965 50.000 16.12 3.45 45.31 4.55
1364 1373 0.875728 TTGCGGTTTGTACCATTCCG 59.124 50.000 10.16 10.16 45.31 4.30
1422 1431 7.309621 CCATCTGATTCAATGTGAAAGAAACCT 60.310 37.037 0.00 0.00 40.12 3.50
1425 1434 6.015265 TGCCATCTGATTCAATGTGAAAGAAA 60.015 34.615 0.00 0.00 40.12 2.52
1431 1440 5.011586 TCTTTGCCATCTGATTCAATGTGA 58.988 37.500 11.54 6.08 0.00 3.58
1461 1470 9.814899 CAAACATTGGACATATTTAGCCATTTA 57.185 29.630 0.00 0.00 0.00 1.40
1470 1479 5.011943 AGCCACACAAACATTGGACATATTT 59.988 36.000 0.00 0.00 31.39 1.40
1497 1506 5.222027 TGTTGTGATGGACCCTTCTTCAATA 60.222 40.000 12.11 9.12 0.00 1.90
1509 1518 2.225019 CAGCTCTTGTGTTGTGATGGAC 59.775 50.000 0.00 0.00 0.00 4.02
1519 1528 5.591877 AGAAATTGTTCTTCAGCTCTTGTGT 59.408 36.000 0.00 0.00 41.55 3.72
1527 1536 6.740411 ATCTCAGAGAAATTGTTCTTCAGC 57.260 37.500 3.63 0.00 44.42 4.26
1533 1542 9.780413 GTTTTCCATATCTCAGAGAAATTGTTC 57.220 33.333 3.63 0.00 0.00 3.18
1560 1569 1.001020 CACCTGCCATGGCCAGTTA 60.001 57.895 33.44 14.00 41.09 2.24
1624 1634 7.886338 AGCTCTACCAAATCTTTTACCTTTTG 58.114 34.615 0.00 0.00 0.00 2.44
1661 1671 3.181454 TGTCACCCCTTTCTTTCTGAGAC 60.181 47.826 0.00 0.00 33.02 3.36
1668 1678 4.251103 AGAAACTGTCACCCCTTTCTTT 57.749 40.909 0.00 0.00 30.39 2.52
1675 1685 5.535030 ACTTATCAAAAGAAACTGTCACCCC 59.465 40.000 0.00 0.00 0.00 4.95
1683 1694 6.552008 TCCATCCCACTTATCAAAAGAAACT 58.448 36.000 0.00 0.00 0.00 2.66
1698 1709 1.341156 CCACCTCCTCTCCATCCCAC 61.341 65.000 0.00 0.00 0.00 4.61
1707 1718 1.053264 CAGCATAGGCCACCTCCTCT 61.053 60.000 5.01 0.00 42.56 3.69
1756 1767 2.076863 GAGTTTGTTGACAGGGATCCG 58.923 52.381 5.45 0.00 0.00 4.18
1767 1778 7.707104 AGATTACTTTCCAAGTGAGTTTGTTG 58.293 34.615 0.00 0.00 42.84 3.33
1815 1826 3.378427 GCCAGTCCACATTAATCAAGACC 59.622 47.826 5.18 0.00 0.00 3.85
1816 1827 4.009675 TGCCAGTCCACATTAATCAAGAC 58.990 43.478 0.00 0.00 0.00 3.01
1822 1833 4.508551 TCTCATGCCAGTCCACATTAAT 57.491 40.909 0.00 0.00 0.00 1.40
1824 1835 5.830799 ATATCTCATGCCAGTCCACATTA 57.169 39.130 0.00 0.00 0.00 1.90
1866 1877 0.598065 CAGCCACCTGCACTTTAACC 59.402 55.000 0.00 0.00 44.83 2.85
1896 1907 4.476479 AGCCTTTCTGTAGGGATCTTTGAT 59.524 41.667 0.00 0.00 35.74 2.57
1908 1919 5.023452 TCAATCTCTACCAGCCTTTCTGTA 58.977 41.667 0.00 0.00 41.25 2.74
1941 1955 8.696410 TGTCAACAAGGAAACAAATAAGAAAC 57.304 30.769 0.00 0.00 0.00 2.78
1950 1964 4.518970 GGAGCTATGTCAACAAGGAAACAA 59.481 41.667 0.00 0.00 0.00 2.83
1952 1966 4.072131 TGGAGCTATGTCAACAAGGAAAC 58.928 43.478 0.00 0.00 0.00 2.78
1953 1967 4.202461 ACTGGAGCTATGTCAACAAGGAAA 60.202 41.667 0.00 0.00 0.00 3.13
1975 1989 0.668535 GGGTTCACACTTCCAGCAAC 59.331 55.000 0.00 0.00 0.00 4.17
1978 1992 0.954452 CTTGGGTTCACACTTCCAGC 59.046 55.000 0.00 0.00 0.00 4.85
1989 2003 5.801380 TCTTCACCACTATTACTTGGGTTC 58.199 41.667 0.00 0.00 37.18 3.62
2000 2014 8.900781 CATCATCTGATTTTTCTTCACCACTAT 58.099 33.333 0.00 0.00 31.21 2.12
2009 2023 7.309621 CCAACAGGTCATCATCTGATTTTTCTT 60.310 37.037 0.00 0.00 35.97 2.52
2025 2039 0.836400 GACTCCCCTCCAACAGGTCA 60.836 60.000 0.00 0.00 41.51 4.02
2037 2051 1.645710 TGTCTCTTTCAGGACTCCCC 58.354 55.000 0.00 0.00 34.01 4.81
2067 2081 0.486879 TTTCCATGTCTTTGGGGCCT 59.513 50.000 0.84 0.00 37.37 5.19
2124 2138 4.574421 GTGGGACCTTTTTGTGAATTTTGG 59.426 41.667 0.00 0.00 0.00 3.28
2130 2144 4.862371 ACTTAGTGGGACCTTTTTGTGAA 58.138 39.130 0.00 0.00 0.00 3.18
2136 2150 3.720002 TCTTGGACTTAGTGGGACCTTTT 59.280 43.478 0.00 0.00 0.00 2.27
2141 2155 1.278413 GGGTCTTGGACTTAGTGGGAC 59.722 57.143 0.00 0.00 32.47 4.46
2160 2174 2.162681 GAATTCACCAGTTCCACAGGG 58.837 52.381 0.00 0.00 0.00 4.45
2214 2230 4.644498 TCATGTGAGAGTCATTTTGCAGA 58.356 39.130 0.00 0.00 0.00 4.26
2218 2234 7.172875 AGTCTTCTTCATGTGAGAGTCATTTTG 59.827 37.037 0.00 0.00 0.00 2.44
2222 2238 5.245751 ACAGTCTTCTTCATGTGAGAGTCAT 59.754 40.000 0.00 0.00 0.00 3.06
2243 2259 3.820557 TCAGGGTTTTTCTTCTCCACAG 58.179 45.455 0.00 0.00 0.00 3.66
2248 2264 5.357032 TGTTGTCTTCAGGGTTTTTCTTCTC 59.643 40.000 0.00 0.00 0.00 2.87
2259 2275 4.701651 TGAATAGCAATGTTGTCTTCAGGG 59.298 41.667 0.00 0.00 0.00 4.45
2268 2284 4.082625 TCCAGCAGTTGAATAGCAATGTTG 60.083 41.667 0.00 0.00 39.03 3.33
2292 2308 5.884232 TCCATCAGACTCTTCATCAAATTGG 59.116 40.000 0.00 0.00 0.00 3.16
2391 2413 4.510167 TCCTCCCATCTCTTTTGATTCC 57.490 45.455 0.00 0.00 0.00 3.01
2475 2499 9.914131 AAAAGCAGAAAAGGAGTTATGATTAAC 57.086 29.630 0.00 0.00 38.39 2.01
2586 2613 4.263243 GCTATCCTCCATTTGCCTCATAGT 60.263 45.833 0.00 0.00 0.00 2.12
2820 2848 4.889409 CCTCTGGCATTCCAAAATAAGCTA 59.111 41.667 0.00 0.00 42.91 3.32
3196 3228 2.723273 CCCCAACCAGGAATCAACTAC 58.277 52.381 0.00 0.00 41.22 2.73
3201 3233 2.770130 GGCCCCAACCAGGAATCA 59.230 61.111 0.00 0.00 41.22 2.57
3205 3237 2.798760 ATAGTGGGCCCCAACCAGGA 62.799 60.000 22.27 0.00 41.22 3.86
3255 3287 5.458041 TTCCAAAGCTTTTCTCCTCAATG 57.542 39.130 9.53 0.00 0.00 2.82
3257 3289 5.363580 ACATTTCCAAAGCTTTTCTCCTCAA 59.636 36.000 9.53 0.00 0.00 3.02
3272 3304 5.163258 ACCCAATGCAAGTTAACATTTCCAA 60.163 36.000 8.61 0.00 34.32 3.53
3348 3380 8.052621 TGGCCCAAGTAAACTTCCTATTATAT 57.947 34.615 0.00 0.00 33.11 0.86
3378 3410 3.048600 AGCCATAACCAGCTTATCCTGA 58.951 45.455 0.00 0.00 35.22 3.86
3468 3500 1.997791 TGGTCACTACCCACTCTAGGA 59.002 52.381 0.00 0.00 46.16 2.94
3513 3545 3.153919 GTTCTTTGGTGGTTGGATAGCA 58.846 45.455 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.