Multiple sequence alignment - TraesCS3D01G221500

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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 TraesCS3D01G221500 chr3D 100.000 2773 0 0 1 2773 301849498 301852270 0.000000e+00 5121.0
1 TraesCS3D01G221500 chr3B 93.646 1558 69 8 60 1605 419120675 419119136 0.000000e+00 2302.0
2 TraesCS3D01G221500 chr3B 83.085 603 55 17 1826 2420 419118302 419117739 3.190000e-139 505.0
3 TraesCS3D01G221500 chr3B 93.392 227 12 2 1607 1830 419119088 419118862 1.590000e-87 333.0
4 TraesCS3D01G221500 chr3A 94.590 647 28 2 60 699 433409532 433408886 0.000000e+00 994.0
5 TraesCS3D01G221500 chr3A 86.310 672 81 9 1826 2492 433391652 433390987 0.000000e+00 721.0
6 TraesCS3D01G221500 chr3A 88.088 638 35 18 685 1314 433408867 433408263 0.000000e+00 719.0
7 TraesCS3D01G221500 chr3A 85.878 524 61 10 2250 2769 433391252 433390738 1.880000e-151 545.0
8 TraesCS3D01G221500 chr3A 90.608 181 14 2 1607 1784 433405607 433405427 1.280000e-58 237.0
9 TraesCS3D01G221500 chr3A 96.183 131 3 2 1475 1604 433405790 433405661 2.160000e-51 213.0
10 TraesCS3D01G221500 chr3A 93.939 99 6 0 1381 1479 433408264 433408166 1.720000e-32 150.0
11 TraesCS3D01G221500 chr4A 95.588 68 3 0 1 68 60050436 60050369 2.920000e-20 110.0
12 TraesCS3D01G221500 chr1A 98.387 62 1 0 1 62 70690836 70690775 2.920000e-20 110.0
13 TraesCS3D01G221500 chr1A 96.667 60 2 0 1 60 493087195 493087254 1.760000e-17 100.0
14 TraesCS3D01G221500 chr7A 92.958 71 5 0 1 71 570272577 570272647 1.360000e-18 104.0
15 TraesCS3D01G221500 chr7A 92.958 71 5 0 1 71 570284202 570284272 1.360000e-18 104.0
16 TraesCS3D01G221500 chr7A 96.774 62 2 0 1 62 670899830 670899769 1.360000e-18 104.0
17 TraesCS3D01G221500 chr2D 98.305 59 1 0 2 60 392766505 392766563 1.360000e-18 104.0
18 TraesCS3D01G221500 chr5A 95.312 64 3 0 1 64 290329413 290329476 4.890000e-18 102.0
19 TraesCS3D01G221500 chr4D 95.238 63 3 0 1 63 486181464 486181402 1.760000e-17 100.0
20 TraesCS3D01G221500 chr5B 76.074 163 34 4 2556 2717 420191238 420191080 2.290000e-11 80.5
21 TraesCS3D01G221500 chr1B 100.000 36 0 0 351 386 7406676 7406641 1.780000e-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 TraesCS3D01G221500 chr3D 301849498 301852270 2772 False 5121.000000 5121 100.0000 1 2773 1 chr3D.!!$F1 2772
1 TraesCS3D01G221500 chr3B 419117739 419120675 2936 True 1046.666667 2302 90.0410 60 2420 3 chr3B.!!$R1 2360
2 TraesCS3D01G221500 chr3A 433390738 433391652 914 True 633.000000 721 86.0940 1826 2769 2 chr3A.!!$R1 943
3 TraesCS3D01G221500 chr3A 433405427 433409532 4105 True 462.600000 994 92.6816 60 1784 5 chr3A.!!$R2 1724

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
902 950 0.037697 TGCGCAATACACTCCTTCGT 60.038 50.0 8.16 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 5488 0.387239 GGTCGCACCTGCACATTTTC 60.387 55.0 0.0 0.0 42.21 2.29 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
49 50 9.705103 AAGATCCTATGAAAATCCTTTGAATCA 57.295 29.630 0.00 0.00 0.00 2.57
50 51 9.705103 AGATCCTATGAAAATCCTTTGAATCAA 57.295 29.630 0.00 0.00 0.00 2.57
86 87 5.353956 GCCTTTCAAAACAAAAACACAGGAT 59.646 36.000 0.00 0.00 0.00 3.24
90 91 6.959671 TCAAAACAAAAACACAGGATTCAC 57.040 33.333 0.00 0.00 0.00 3.18
94 95 6.391227 AACAAAAACACAGGATTCACTAGG 57.609 37.500 0.00 0.00 0.00 3.02
120 121 2.777459 TCTAGGATGTTCCCTCCCTC 57.223 55.000 0.00 0.00 37.19 4.30
161 167 5.450274 CGCTACTCATATCCCTGATCTGATG 60.450 48.000 0.38 0.00 27.76 3.07
240 246 2.475466 CGGCAGCCAATCAAGCGAT 61.475 57.895 13.30 0.00 34.64 4.58
271 277 5.703978 AAGAGACACATCGGATCTATCAG 57.296 43.478 0.00 0.00 0.00 2.90
389 395 9.352784 CGCAAAAATGATTCCTTAAATTCAGTA 57.647 29.630 0.00 0.00 0.00 2.74
417 423 1.398595 GTTGTGTTTGCAGCTAAGCG 58.601 50.000 0.00 0.00 37.31 4.68
465 471 2.037772 CGGCCATTTCTAGCAGGAGTAT 59.962 50.000 2.24 0.00 0.00 2.12
471 477 1.005630 CTAGCAGGAGTATGGCCGC 60.006 63.158 0.00 0.00 0.00 6.53
552 563 3.188786 GAAGCTGGCGCGTACTGG 61.189 66.667 8.43 0.43 42.32 4.00
553 564 3.934391 GAAGCTGGCGCGTACTGGT 62.934 63.158 8.43 8.31 42.32 4.00
554 565 4.742201 AGCTGGCGCGTACTGGTG 62.742 66.667 8.43 0.00 42.32 4.17
587 598 1.301677 GGAAGGCAAGTGCTTCCTCG 61.302 60.000 19.06 0.00 41.17 4.63
598 609 1.021920 GCTTCCTCGGTGGCTTTCTC 61.022 60.000 0.00 0.00 35.26 2.87
675 686 6.186957 TGACAAATAAGACCCTGCATTACAT 58.813 36.000 0.00 0.00 0.00 2.29
765 808 4.504916 CTGCTGGAGGCCGACGAG 62.505 72.222 0.00 3.75 40.92 4.18
840 888 0.101759 GCGAGGGTCGTGCTACAATA 59.898 55.000 0.00 0.00 42.81 1.90
847 895 3.259064 GGTCGTGCTACAATATGTGTGT 58.741 45.455 0.00 0.00 41.89 3.72
871 919 2.280628 CCACGGGATTCAGTTAAGCTC 58.719 52.381 0.00 0.00 0.00 4.09
892 940 2.346803 TCAACCTCTTCTGCGCAATAC 58.653 47.619 13.05 0.00 0.00 1.89
895 943 1.276421 ACCTCTTCTGCGCAATACACT 59.724 47.619 13.05 0.00 0.00 3.55
896 944 1.929836 CCTCTTCTGCGCAATACACTC 59.070 52.381 13.05 0.00 0.00 3.51
897 945 1.929836 CTCTTCTGCGCAATACACTCC 59.070 52.381 13.05 0.00 0.00 3.85
898 946 1.550524 TCTTCTGCGCAATACACTCCT 59.449 47.619 13.05 0.00 0.00 3.69
899 947 2.028112 TCTTCTGCGCAATACACTCCTT 60.028 45.455 13.05 0.00 0.00 3.36
900 948 2.010145 TCTGCGCAATACACTCCTTC 57.990 50.000 13.05 0.00 0.00 3.46
901 949 0.647410 CTGCGCAATACACTCCTTCG 59.353 55.000 13.05 0.00 0.00 3.79
902 950 0.037697 TGCGCAATACACTCCTTCGT 60.038 50.000 8.16 0.00 0.00 3.85
903 951 0.645868 GCGCAATACACTCCTTCGTC 59.354 55.000 0.30 0.00 0.00 4.20
904 952 1.736032 GCGCAATACACTCCTTCGTCT 60.736 52.381 0.30 0.00 0.00 4.18
918 966 4.391830 TCCTTCGTCTTCCATTTCGAAATG 59.608 41.667 34.03 34.03 44.12 2.32
919 967 4.154195 CCTTCGTCTTCCATTTCGAAATGT 59.846 41.667 36.20 13.30 43.24 2.71
920 968 4.921470 TCGTCTTCCATTTCGAAATGTC 57.079 40.909 36.20 23.36 43.24 3.06
974 1022 0.179145 AAACGGTCCGCTGATCTACG 60.179 55.000 12.28 0.00 0.00 3.51
979 1027 1.015109 GTCCGCTGATCTACGAGACA 58.985 55.000 9.15 0.00 32.97 3.41
1143 1191 2.027625 CACGTCCTCTTCGGGCAAC 61.028 63.158 0.00 0.00 37.17 4.17
1554 3988 8.542953 GGCATGATTCTCCGATTTTTAAATTTC 58.457 33.333 0.00 0.00 0.00 2.17
1624 4110 4.700700 TCTGTCCAGTATGATTGCATCAG 58.299 43.478 0.00 0.00 43.53 2.90
1653 4141 4.893524 TGTTGTTCTGTTCTCTCTGTCCTA 59.106 41.667 0.00 0.00 0.00 2.94
1683 4171 4.278170 TGGCAGTATGTTGGAACAGAAAAG 59.722 41.667 0.00 0.00 43.04 2.27
1741 4230 4.847757 CACTCTTGCGTGTAACATTTGATG 59.152 41.667 0.00 0.00 35.74 3.07
1805 4294 6.767524 TCAAACTGTTTATTGTCACCAGTT 57.232 33.333 5.31 0.00 45.51 3.16
1821 4310 1.065401 CAGTTTGTGTTGGACGCATGT 59.935 47.619 0.00 0.00 38.53 3.21
1831 4884 1.273886 TGGACGCATGTGTAGCAGTTA 59.726 47.619 12.82 0.00 0.00 2.24
1844 4897 3.705043 AGCAGTTATAGTCGGGTTACG 57.295 47.619 0.00 0.00 46.11 3.18
1873 4926 0.535335 GTTGCGGGTCTAGTGATGGA 59.465 55.000 0.00 0.00 0.00 3.41
1878 4931 2.563179 GCGGGTCTAGTGATGGACATAT 59.437 50.000 0.00 0.00 34.49 1.78
1881 4934 5.710984 CGGGTCTAGTGATGGACATATAAC 58.289 45.833 0.00 0.00 34.49 1.89
1886 4939 6.015010 GTCTAGTGATGGACATATAACTGGCT 60.015 42.308 0.00 0.00 33.19 4.75
1892 4945 4.960938 TGGACATATAACTGGCTGACATC 58.039 43.478 0.00 0.00 0.00 3.06
1893 4946 4.202357 TGGACATATAACTGGCTGACATCC 60.202 45.833 0.00 0.00 0.00 3.51
1905 4959 8.366359 ACTGGCTGACATCCTAATTAAAAATT 57.634 30.769 0.00 0.00 0.00 1.82
1925 4979 2.351706 TGTAGTTGCGACCCCTTTTT 57.648 45.000 0.00 0.00 0.00 1.94
1933 4987 2.959707 TGCGACCCCTTTTTAAACATGT 59.040 40.909 0.00 0.00 0.00 3.21
1962 5017 4.202172 TGCCCCAACTTAAAAACTTACAGC 60.202 41.667 0.00 0.00 0.00 4.40
1963 5018 4.798263 GCCCCAACTTAAAAACTTACAGCC 60.798 45.833 0.00 0.00 0.00 4.85
1968 5023 3.749609 ACTTAAAAACTTACAGCCGCGAT 59.250 39.130 8.23 0.00 0.00 4.58
2047 5102 1.370609 TTCAAAACTTGCGGTCACGA 58.629 45.000 0.00 0.00 44.60 4.35
2048 5103 1.588674 TCAAAACTTGCGGTCACGAT 58.411 45.000 0.00 0.00 44.60 3.73
2088 5143 6.873076 TGAAGTTGCAATCCCATATGAAAAAC 59.127 34.615 0.59 0.00 0.00 2.43
2094 5149 4.654091 ATCCCATATGAAAAACCTTGCG 57.346 40.909 3.65 0.00 0.00 4.85
2120 5175 3.494223 GCCACCCCCATTTAAATATGCAC 60.494 47.826 0.00 0.00 0.00 4.57
2146 5201 1.028905 CCTCCCTTGAAAACGTGCAA 58.971 50.000 0.00 0.00 0.00 4.08
2153 5208 1.471964 TGAAAACGTGCAATTGCGAC 58.528 45.000 24.58 20.59 45.83 5.19
2159 5214 2.361104 TGCAATTGCGACCTCCCC 60.361 61.111 24.58 0.00 45.83 4.81
2185 5240 0.250166 ACTTGCAGTTACGACCCCAC 60.250 55.000 0.00 0.00 0.00 4.61
2187 5242 0.034337 TTGCAGTTACGACCCCACTC 59.966 55.000 0.00 0.00 0.00 3.51
2188 5243 1.116536 TGCAGTTACGACCCCACTCA 61.117 55.000 0.00 0.00 0.00 3.41
2207 5262 4.705023 ACTCAAAACTTGTAGTTGCAACCT 59.295 37.500 25.62 15.12 38.66 3.50
2214 5276 4.461081 ACTTGTAGTTGCAACCTTGTTTGA 59.539 37.500 25.62 3.80 0.00 2.69
2217 5279 5.587289 TGTAGTTGCAACCTTGTTTGAATC 58.413 37.500 25.62 0.00 0.00 2.52
2281 5343 7.221838 CGAATCCTTTTTGAAAACTTGCAGTTA 59.778 33.333 0.00 0.00 37.47 2.24
2301 5363 7.581476 CAGTTACGACACCATTATGAAAACTT 58.419 34.615 0.00 0.00 0.00 2.66
2383 5445 2.875933 CGACCCTCACTAAAAACTTGCA 59.124 45.455 0.00 0.00 0.00 4.08
2389 5451 4.040445 TCACTAAAAACTTGCAGTTGCC 57.960 40.909 1.06 0.00 38.66 4.52
2394 5456 0.681175 AAACTTGCAGTTGCCATCCC 59.319 50.000 1.06 0.00 38.66 3.85
2442 5504 1.411394 CTTGAAAATGTGCAGGTGCG 58.589 50.000 0.00 0.00 45.83 5.34
2457 5519 1.923395 TGCGACCTCCCCCTGAAAT 60.923 57.895 0.00 0.00 0.00 2.17
2493 5555 4.959839 ACCCCATTTGAAACTTGTAGTTGT 59.040 37.500 0.00 0.00 38.66 3.32
2494 5556 5.163457 ACCCCATTTGAAACTTGTAGTTGTG 60.163 40.000 0.00 0.00 38.66 3.33
2521 5583 6.327154 CCCGTTTGAAAAACTTGTAGTTTCT 58.673 36.000 5.37 0.00 46.78 2.52
2531 5593 2.754946 TGTAGTTTCTACGCCCCTTG 57.245 50.000 3.10 0.00 0.00 3.61
2537 5599 1.900245 TTCTACGCCCCTTGAAAACC 58.100 50.000 0.00 0.00 0.00 3.27
2538 5600 0.766131 TCTACGCCCCTTGAAAACCA 59.234 50.000 0.00 0.00 0.00 3.67
2556 5618 2.485426 ACCAGCATTCGAACACATGAAG 59.515 45.455 0.00 0.00 0.00 3.02
2563 5625 1.525197 TCGAACACATGAAGTTGCGAC 59.475 47.619 11.86 0.00 0.00 5.19
2581 5644 2.875933 CGACCCTCACTAAAAACTTGCA 59.124 45.455 0.00 0.00 0.00 4.08
2590 5653 4.048504 ACTAAAAACTTGCAATTGCGACC 58.951 39.130 24.58 0.00 45.83 4.79
2610 5673 5.562113 CGACCCCATTTCAAACTTGTAGTTC 60.562 44.000 0.00 0.00 37.47 3.01
2614 5677 3.974871 TTTCAAACTTGTAGTTCCGGC 57.025 42.857 0.00 0.00 37.47 6.13
2616 5679 0.879090 CAAACTTGTAGTTCCGGCCC 59.121 55.000 0.00 0.00 37.47 5.80
2623 5686 1.303806 TAGTTCCGGCCCCTTTTGC 60.304 57.895 0.00 0.00 0.00 3.68
2632 5695 1.408127 GGCCCCTTTTGCAAAACTTGT 60.408 47.619 20.46 0.00 0.00 3.16
2644 5707 4.095782 TGCAAAACTTGTAGTTGTGACTCC 59.904 41.667 12.70 0.00 44.33 3.85
2686 5749 3.372206 CGACCCTTCTTGAATACTTGCAG 59.628 47.826 0.00 0.00 0.00 4.41
2713 5776 4.309099 GACCAACATTTGAACACATGCAT 58.691 39.130 0.00 0.00 0.00 3.96
2770 5833 8.140112 AGGATATAGGATAAATCGATATGCCC 57.860 38.462 0.00 0.00 30.96 5.36
2771 5834 7.734865 AGGATATAGGATAAATCGATATGCCCA 59.265 37.037 0.00 0.00 30.96 5.36
2772 5835 7.819900 GGATATAGGATAAATCGATATGCCCAC 59.180 40.741 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.705103 TGATTCAAAGGATTTTCATAGGATCTT 57.295 29.630 0.00 0.00 35.03 2.40
24 25 9.705103 TTGATTCAAAGGATTTTCATAGGATCT 57.295 29.630 0.00 0.00 35.03 2.75
41 42 4.074970 GCTGAGGGTCTCTTTGATTCAAA 58.925 43.478 11.19 11.19 0.00 2.69
42 43 3.560025 GGCTGAGGGTCTCTTTGATTCAA 60.560 47.826 0.00 0.00 0.00 2.69
43 44 2.026822 GGCTGAGGGTCTCTTTGATTCA 60.027 50.000 0.00 0.00 0.00 2.57
44 45 2.238395 AGGCTGAGGGTCTCTTTGATTC 59.762 50.000 0.00 0.00 0.00 2.52
45 46 2.273619 AGGCTGAGGGTCTCTTTGATT 58.726 47.619 0.00 0.00 0.00 2.57
46 47 1.963985 AGGCTGAGGGTCTCTTTGAT 58.036 50.000 0.00 0.00 0.00 2.57
47 48 1.734655 AAGGCTGAGGGTCTCTTTGA 58.265 50.000 0.00 0.00 0.00 2.69
48 49 2.224621 TGAAAGGCTGAGGGTCTCTTTG 60.225 50.000 0.00 0.00 0.00 2.77
49 50 2.057922 TGAAAGGCTGAGGGTCTCTTT 58.942 47.619 0.00 0.00 0.00 2.52
50 51 1.734655 TGAAAGGCTGAGGGTCTCTT 58.265 50.000 0.00 0.00 0.00 2.85
51 52 1.734655 TTGAAAGGCTGAGGGTCTCT 58.265 50.000 0.00 0.00 0.00 3.10
52 53 2.554462 GTTTTGAAAGGCTGAGGGTCTC 59.446 50.000 0.00 0.00 0.00 3.36
53 54 2.091885 TGTTTTGAAAGGCTGAGGGTCT 60.092 45.455 0.00 0.00 0.00 3.85
54 55 2.306847 TGTTTTGAAAGGCTGAGGGTC 58.693 47.619 0.00 0.00 0.00 4.46
55 56 2.452600 TGTTTTGAAAGGCTGAGGGT 57.547 45.000 0.00 0.00 0.00 4.34
56 57 3.817709 TTTGTTTTGAAAGGCTGAGGG 57.182 42.857 0.00 0.00 0.00 4.30
57 58 4.934602 TGTTTTTGTTTTGAAAGGCTGAGG 59.065 37.500 0.00 0.00 0.00 3.86
58 59 5.407995 TGTGTTTTTGTTTTGAAAGGCTGAG 59.592 36.000 0.00 0.00 0.00 3.35
86 87 6.023603 ACATCCTAGAAGTTTCCCTAGTGAA 58.976 40.000 0.00 0.00 32.54 3.18
90 91 5.163290 GGGAACATCCTAGAAGTTTCCCTAG 60.163 48.000 18.17 0.00 34.04 3.02
94 95 4.384318 GGAGGGAACATCCTAGAAGTTTCC 60.384 50.000 9.85 9.85 38.69 3.13
120 121 2.807045 GTGCCGTCGAGTGAGCAG 60.807 66.667 0.00 0.00 35.56 4.24
161 167 2.216898 AGCACACTTCTCTCTGCAAAC 58.783 47.619 0.00 0.00 31.71 2.93
240 246 3.684305 CCGATGTGTCTCTTTTGTATGCA 59.316 43.478 0.00 0.00 0.00 3.96
285 291 4.871993 AGTTCTGAATGATTCGATGTGC 57.128 40.909 0.18 0.00 0.00 4.57
389 395 1.018910 GCAAACACAACCAGGTACGT 58.981 50.000 0.00 0.00 0.00 3.57
417 423 1.218316 CAAGGTCACGGGCTACTCC 59.782 63.158 0.00 0.00 0.00 3.85
465 471 3.531207 CTCTCAGATCCGCGGCCA 61.531 66.667 23.51 4.04 0.00 5.36
471 477 2.132996 AGCTGCCCTCTCAGATCCG 61.133 63.158 0.00 0.00 36.19 4.18
552 563 2.358247 CCACGGCACTACCACCAC 60.358 66.667 0.00 0.00 39.03 4.16
553 564 2.107041 CTTCCACGGCACTACCACCA 62.107 60.000 0.00 0.00 39.03 4.17
554 565 1.375523 CTTCCACGGCACTACCACC 60.376 63.158 0.00 0.00 39.03 4.61
587 598 1.273886 AGAAGAGTCGAGAAAGCCACC 59.726 52.381 0.00 0.00 0.00 4.61
598 609 3.053455 GTGGAACTGTTGAGAAGAGTCG 58.947 50.000 0.00 0.00 33.33 4.18
675 686 9.567776 TCCTCACTAATCTTGTTTGAAATACAA 57.432 29.630 0.00 0.00 36.65 2.41
760 803 1.080434 GTGACCAGAGTGGCTCGTC 60.080 63.158 0.00 0.00 42.67 4.20
761 804 1.528292 GAGTGACCAGAGTGGCTCGT 61.528 60.000 0.00 0.00 42.67 4.18
762 805 1.214062 GAGTGACCAGAGTGGCTCG 59.786 63.158 0.00 0.00 42.67 5.03
763 806 0.037790 GTGAGTGACCAGAGTGGCTC 60.038 60.000 0.00 0.00 42.67 4.70
764 807 0.760567 TGTGAGTGACCAGAGTGGCT 60.761 55.000 0.00 0.00 42.67 4.75
765 808 0.601311 GTGTGAGTGACCAGAGTGGC 60.601 60.000 0.00 0.00 42.67 5.01
825 873 2.607635 CACACATATTGTAGCACGACCC 59.392 50.000 0.00 0.00 35.67 4.46
847 895 1.646912 TAACTGAATCCCGTGGTGGA 58.353 50.000 0.00 0.00 42.00 4.02
871 919 1.446907 ATTGCGCAGAAGAGGTTGAG 58.553 50.000 11.31 0.00 0.00 3.02
892 940 2.668457 CGAAATGGAAGACGAAGGAGTG 59.332 50.000 0.00 0.00 0.00 3.51
895 943 3.671008 TTCGAAATGGAAGACGAAGGA 57.329 42.857 0.00 0.00 39.27 3.36
896 944 4.651994 CATTTCGAAATGGAAGACGAAGG 58.348 43.478 33.59 11.38 43.54 3.46
918 966 5.639506 TCAGATGAAGAAATTCAGGAACGAC 59.360 40.000 0.00 0.00 34.02 4.34
919 967 5.793817 TCAGATGAAGAAATTCAGGAACGA 58.206 37.500 0.00 0.00 34.02 3.85
920 968 6.238320 GGATCAGATGAAGAAATTCAGGAACG 60.238 42.308 0.00 0.00 34.02 3.95
933 981 1.759445 ACACCTCGGGATCAGATGAAG 59.241 52.381 0.00 0.00 0.00 3.02
974 1022 8.417884 GGATATTAATATGGGAGCTAGTGTCTC 58.582 40.741 12.74 0.00 0.00 3.36
979 1027 7.620094 ACGAAGGATATTAATATGGGAGCTAGT 59.380 37.037 12.74 0.95 0.00 2.57
1143 1191 3.938637 GAAGAAAGGTGGGCGGGGG 62.939 68.421 0.00 0.00 0.00 5.40
1241 1295 1.645455 CCATGCTCCGCGAATCTTG 59.355 57.895 8.23 4.11 0.00 3.02
1554 3988 0.105555 ATCTGAGAGCAGGAGGAGGG 60.106 60.000 0.00 0.00 42.53 4.30
1624 4110 5.350914 CAGAGAGAACAGAACAACATGATCC 59.649 44.000 0.00 0.00 0.00 3.36
1653 4141 2.375174 TCCAACATACTGCCAACTTCCT 59.625 45.455 0.00 0.00 0.00 3.36
1683 4171 5.574443 GCATTGGAGTAAAAGAAATGCTCAC 59.426 40.000 10.55 0.00 46.03 3.51
1741 4230 2.066262 TCGTTTGTCGAGAAGGATTGC 58.934 47.619 0.00 0.00 44.01 3.56
1795 4284 2.088423 GTCCAACACAAACTGGTGACA 58.912 47.619 0.00 0.00 40.48 3.58
1799 4288 0.678366 TGCGTCCAACACAAACTGGT 60.678 50.000 0.00 0.00 34.11 4.00
1805 4294 1.870402 CTACACATGCGTCCAACACAA 59.130 47.619 0.00 0.00 0.00 3.33
1821 4310 4.035558 CGTAACCCGACTATAACTGCTACA 59.964 45.833 0.00 0.00 39.56 2.74
1852 4905 1.645034 CATCACTAGACCCGCAACTG 58.355 55.000 0.00 0.00 0.00 3.16
1860 4913 6.692486 CCAGTTATATGTCCATCACTAGACC 58.308 44.000 0.00 0.00 31.76 3.85
1873 4926 6.747414 TTAGGATGTCAGCCAGTTATATGT 57.253 37.500 10.34 0.00 0.00 2.29
1878 4931 8.871629 TTTTTAATTAGGATGTCAGCCAGTTA 57.128 30.769 10.34 2.64 0.00 2.24
1881 4934 9.090692 CAAATTTTTAATTAGGATGTCAGCCAG 57.909 33.333 10.34 0.00 0.00 4.85
1892 4945 8.856247 GGTCGCAACTACAAATTTTTAATTAGG 58.144 33.333 0.00 0.00 0.00 2.69
1893 4946 8.856247 GGGTCGCAACTACAAATTTTTAATTAG 58.144 33.333 0.00 0.00 0.00 1.73
1905 4959 2.351706 AAAAGGGGTCGCAACTACAA 57.648 45.000 0.00 0.00 0.00 2.41
1933 4987 6.547930 AGTTTTTAAGTTGGGGCAAAACTA 57.452 33.333 6.56 0.00 42.89 2.24
1938 4992 5.682730 GCTGTAAGTTTTTAAGTTGGGGCAA 60.683 40.000 0.00 0.00 35.30 4.52
1944 4999 3.662186 CGCGGCTGTAAGTTTTTAAGTTG 59.338 43.478 0.00 0.00 35.30 3.16
1962 5017 2.878406 AGTTTTCATAATGGGATCGCGG 59.122 45.455 6.13 0.00 0.00 6.46
1963 5018 4.282068 CAAGTTTTCATAATGGGATCGCG 58.718 43.478 0.00 0.00 0.00 5.87
1968 5023 5.642919 GCAATTGCAAGTTTTCATAATGGGA 59.357 36.000 25.36 0.00 41.59 4.37
2022 5077 3.308323 TGACCGCAAGTTTTGAAAAATGC 59.692 39.130 15.60 15.60 33.04 3.56
2040 5095 4.566987 AGTTTTTAGTGAGGATCGTGACC 58.433 43.478 1.19 0.00 38.61 4.02
2047 5102 6.321181 TGCAACTTCAAGTTTTTAGTGAGGAT 59.679 34.615 0.00 0.00 36.03 3.24
2048 5103 5.650266 TGCAACTTCAAGTTTTTAGTGAGGA 59.350 36.000 0.00 0.00 36.03 3.71
2094 5149 1.353091 TTTAAATGGGGGTGGCAACC 58.647 50.000 14.87 14.87 46.81 3.77
2120 5175 1.266989 GTTTTCAAGGGAGGTCGCAAG 59.733 52.381 0.00 0.00 0.00 4.01
2146 5201 0.404040 TTTCAAGGGGAGGTCGCAAT 59.596 50.000 0.00 0.00 0.00 3.56
2153 5208 1.615392 CTGCAAGTTTTCAAGGGGAGG 59.385 52.381 0.00 0.00 0.00 4.30
2185 5240 5.248870 AGGTTGCAACTACAAGTTTTGAG 57.751 39.130 27.64 0.00 36.03 3.02
2187 5242 5.167845 ACAAGGTTGCAACTACAAGTTTTG 58.832 37.500 27.64 18.70 36.03 2.44
2188 5243 5.400066 ACAAGGTTGCAACTACAAGTTTT 57.600 34.783 27.64 8.04 36.03 2.43
2207 5262 6.162079 TCACAACTGCAAAAGATTCAAACAA 58.838 32.000 0.00 0.00 0.00 2.83
2214 5276 3.706086 AGGGTTCACAACTGCAAAAGATT 59.294 39.130 0.00 0.00 0.00 2.40
2217 5279 2.689983 AGAGGGTTCACAACTGCAAAAG 59.310 45.455 0.00 0.00 0.00 2.27
2281 5343 7.499321 TTACAAGTTTTCATAATGGTGTCGT 57.501 32.000 0.00 0.00 0.00 4.34
2301 5363 5.713792 TTTTTCAAGGGATCGCAATTACA 57.286 34.783 12.83 0.00 0.00 2.41
2383 5445 4.102996 AGTTTTCAAAATGGGATGGCAACT 59.897 37.500 0.00 0.00 37.61 3.16
2389 5451 5.600908 CTGCAAGTTTTCAAAATGGGATG 57.399 39.130 0.00 0.00 0.00 3.51
2426 5488 0.387239 GGTCGCACCTGCACATTTTC 60.387 55.000 0.00 0.00 42.21 2.29
2442 5504 1.683319 GCAAGATTTCAGGGGGAGGTC 60.683 57.143 0.00 0.00 0.00 3.85
2451 5513 2.578495 GTCGCAACTGCAAGATTTCAG 58.422 47.619 2.12 0.00 42.21 3.02
2457 5519 2.281484 GGGGTCGCAACTGCAAGA 60.281 61.111 2.12 0.00 42.21 3.02
2493 5555 1.134670 CAAGTTTTTCAAACGGGGCCA 60.135 47.619 4.39 0.00 0.00 5.36
2494 5556 1.134640 ACAAGTTTTTCAAACGGGGCC 60.135 47.619 0.00 0.00 0.00 5.80
2521 5583 0.891904 GCTGGTTTTCAAGGGGCGTA 60.892 55.000 0.00 0.00 0.00 4.42
2531 5593 3.347958 TGTGTTCGAATGCTGGTTTTC 57.652 42.857 0.00 0.00 0.00 2.29
2537 5599 3.818961 ACTTCATGTGTTCGAATGCTG 57.181 42.857 0.00 0.00 0.00 4.41
2538 5600 3.610114 GCAACTTCATGTGTTCGAATGCT 60.610 43.478 0.00 0.00 28.92 3.79
2556 5618 2.876550 AGTTTTTAGTGAGGGTCGCAAC 59.123 45.455 0.00 0.00 0.00 4.17
2563 5625 4.448732 GCAATTGCAAGTTTTTAGTGAGGG 59.551 41.667 25.36 0.00 41.59 4.30
2581 5644 2.632512 AGTTTGAAATGGGGTCGCAATT 59.367 40.909 0.00 0.00 0.00 2.32
2590 5653 4.320935 CCGGAACTACAAGTTTGAAATGGG 60.321 45.833 0.00 0.00 38.80 4.00
2610 5673 1.596752 GTTTTGCAAAAGGGGCCGG 60.597 57.895 24.46 0.00 0.00 6.13
2614 5677 4.400529 ACTACAAGTTTTGCAAAAGGGG 57.599 40.909 24.46 17.50 0.00 4.79
2616 5679 5.866633 TCACAACTACAAGTTTTGCAAAAGG 59.133 36.000 24.46 18.15 36.03 3.11
2623 5686 4.036380 GGGGAGTCACAACTACAAGTTTTG 59.964 45.833 0.00 0.55 38.19 2.44
2632 5695 4.445735 CCTTTTCAAGGGGAGTCACAACTA 60.446 45.833 0.00 0.00 45.27 2.24
2686 5749 2.533942 GTGTTCAAATGTTGGTCGCAAC 59.466 45.455 0.00 0.00 35.75 4.17


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

AutoCloner maintained by Alex Coulton.