Multiple sequence alignment - TraesCS5D01G163800

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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 TraesCS5D01G163800 chr5D 100.000 2617 0 0 1 2617 255473942 255476558 0.000000e+00 4833.0
1 TraesCS5D01G163800 chr5D 86.709 790 69 10 1 758 486816894 486817679 0.000000e+00 845.0
2 TraesCS5D01G163800 chr5B 90.821 926 43 22 757 1648 289145546 289144629 0.000000e+00 1201.0
3 TraesCS5D01G163800 chr5B 83.228 793 85 16 1 759 651339478 651338700 0.000000e+00 684.0
4 TraesCS5D01G163800 chr5B 83.985 537 48 21 1690 2214 289144072 289143562 5.070000e-132 481.0
5 TraesCS5D01G163800 chr5B 87.313 402 37 6 2220 2614 285930643 285931037 5.140000e-122 448.0
6 TraesCS5D01G163800 chr5A 85.835 946 87 25 1690 2615 338559558 338560476 0.000000e+00 961.0
7 TraesCS5D01G163800 chr5A 94.727 512 17 6 757 1263 338558081 338558587 0.000000e+00 787.0
8 TraesCS5D01G163800 chr5A 95.408 392 16 2 1259 1648 338558611 338559002 7.950000e-175 623.0
9 TraesCS5D01G163800 chr3D 87.848 790 60 18 1 760 537633560 537634343 0.000000e+00 894.0
10 TraesCS5D01G163800 chr3D 86.100 777 79 18 5 758 513669491 513670261 0.000000e+00 809.0
11 TraesCS5D01G163800 chr3D 85.000 800 73 24 1 760 469241616 469240824 0.000000e+00 769.0
12 TraesCS5D01G163800 chr3D 84.780 795 78 16 1 758 554221841 554222629 0.000000e+00 758.0
13 TraesCS5D01G163800 chr2A 86.599 791 71 7 1 759 444791208 444791995 0.000000e+00 841.0
14 TraesCS5D01G163800 chr2A 83.021 801 84 25 1 762 515939023 515938236 0.000000e+00 678.0
15 TraesCS5D01G163800 chr2A 96.875 32 1 0 1970 2001 276880249 276880218 1.000000e-03 54.7
16 TraesCS5D01G163800 chr2D 86.439 789 72 10 1 758 189373200 189373984 0.000000e+00 832.0
17 TraesCS5D01G163800 chr2D 85.805 789 74 11 1 758 347795902 347796683 0.000000e+00 802.0
18 TraesCS5D01G163800 chr7D 86.242 785 76 12 5 761 28359908 28359128 0.000000e+00 822.0
19 TraesCS5D01G163800 chr6D 86.010 772 79 19 7 758 164816176 164815414 0.000000e+00 800.0
20 TraesCS5D01G163800 chr6D 84.975 792 68 22 5 759 461500073 461500850 0.000000e+00 756.0
21 TraesCS5D01G163800 chr6D 87.797 631 53 5 1 608 41189106 41189735 0.000000e+00 717.0
22 TraesCS5D01G163800 chr7A 85.209 791 75 12 1 758 566985599 566986380 0.000000e+00 774.0
23 TraesCS5D01G163800 chr4D 84.625 800 75 24 1 759 34653808 34653016 0.000000e+00 752.0
24 TraesCS5D01G163800 chr2B 83.480 793 81 26 1 758 64096868 64097645 0.000000e+00 693.0
25 TraesCS5D01G163800 chr1D 86.024 508 39 18 281 759 65093446 65092942 1.390000e-142 516.0
26 TraesCS5D01G163800 chr1D 89.286 308 19 7 458 758 24942386 24942686 8.840000e-100 374.0
27 TraesCS5D01G163800 chr3B 88.312 308 25 5 460 761 671846464 671846162 2.480000e-95 359.0
28 TraesCS5D01G163800 chr7B 84.615 117 6 5 650 758 46802225 46802113 3.560000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G163800 chr5D 255473942 255476558 2616 False 4833.000000 4833 100.000 1 2617 1 chr5D.!!$F1 2616
1 TraesCS5D01G163800 chr5D 486816894 486817679 785 False 845.000000 845 86.709 1 758 1 chr5D.!!$F2 757
2 TraesCS5D01G163800 chr5B 289143562 289145546 1984 True 841.000000 1201 87.403 757 2214 2 chr5B.!!$R2 1457
3 TraesCS5D01G163800 chr5B 651338700 651339478 778 True 684.000000 684 83.228 1 759 1 chr5B.!!$R1 758
4 TraesCS5D01G163800 chr5A 338558081 338560476 2395 False 790.333333 961 91.990 757 2615 3 chr5A.!!$F1 1858
5 TraesCS5D01G163800 chr3D 537633560 537634343 783 False 894.000000 894 87.848 1 760 1 chr3D.!!$F2 759
6 TraesCS5D01G163800 chr3D 513669491 513670261 770 False 809.000000 809 86.100 5 758 1 chr3D.!!$F1 753
7 TraesCS5D01G163800 chr3D 469240824 469241616 792 True 769.000000 769 85.000 1 760 1 chr3D.!!$R1 759
8 TraesCS5D01G163800 chr3D 554221841 554222629 788 False 758.000000 758 84.780 1 758 1 chr3D.!!$F3 757
9 TraesCS5D01G163800 chr2A 444791208 444791995 787 False 841.000000 841 86.599 1 759 1 chr2A.!!$F1 758
10 TraesCS5D01G163800 chr2A 515938236 515939023 787 True 678.000000 678 83.021 1 762 1 chr2A.!!$R2 761
11 TraesCS5D01G163800 chr2D 189373200 189373984 784 False 832.000000 832 86.439 1 758 1 chr2D.!!$F1 757
12 TraesCS5D01G163800 chr2D 347795902 347796683 781 False 802.000000 802 85.805 1 758 1 chr2D.!!$F2 757
13 TraesCS5D01G163800 chr7D 28359128 28359908 780 True 822.000000 822 86.242 5 761 1 chr7D.!!$R1 756
14 TraesCS5D01G163800 chr6D 164815414 164816176 762 True 800.000000 800 86.010 7 758 1 chr6D.!!$R1 751
15 TraesCS5D01G163800 chr6D 461500073 461500850 777 False 756.000000 756 84.975 5 759 1 chr6D.!!$F2 754
16 TraesCS5D01G163800 chr6D 41189106 41189735 629 False 717.000000 717 87.797 1 608 1 chr6D.!!$F1 607
17 TraesCS5D01G163800 chr7A 566985599 566986380 781 False 774.000000 774 85.209 1 758 1 chr7A.!!$F1 757
18 TraesCS5D01G163800 chr4D 34653016 34653808 792 True 752.000000 752 84.625 1 759 1 chr4D.!!$R1 758
19 TraesCS5D01G163800 chr2B 64096868 64097645 777 False 693.000000 693 83.480 1 758 1 chr2B.!!$F1 757
20 TraesCS5D01G163800 chr1D 65092942 65093446 504 True 516.000000 516 86.024 281 759 1 chr1D.!!$R1 478

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
581 626 0.374758 CAACGCTACCGCTACGACTA 59.625 55.0 0.0 0.0 38.22 2.59 F
1362 1468 0.415429 TCCTGGAAGAGGGAGAAGCT 59.585 55.0 0.0 0.0 43.06 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1708 0.039617 TACACATGTTTTGCAGCGGC 60.040 50.0 0.31 0.31 41.68 6.53 R
2383 3036 0.665298 TGATCAGATGTCTCGCTCGG 59.335 55.0 0.00 0.00 0.00 4.63 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
32 33 2.772691 GCAGGTCCCTCGTCTACGG 61.773 68.421 2.24 0.00 40.29 4.02
70 71 2.507102 CGATGCGTGCCTTCGTCT 60.507 61.111 6.24 0.00 36.63 4.18
108 110 1.672356 GGCAAGTCTGGTGCGATGT 60.672 57.895 0.00 0.00 43.18 3.06
158 160 2.672996 GCCCGGTGCTGACAACAT 60.673 61.111 0.00 0.00 36.87 2.71
267 270 4.363990 CCTCGACACCACTGCGCT 62.364 66.667 9.73 0.00 0.00 5.92
366 370 0.865111 CCACAACGTTCTTCGCATGA 59.135 50.000 0.00 0.00 44.19 3.07
581 626 0.374758 CAACGCTACCGCTACGACTA 59.625 55.000 0.00 0.00 38.22 2.59
587 633 2.514592 CCGCTACGACTACGGGGA 60.515 66.667 0.00 0.00 43.23 4.81
660 722 9.936759 GAGTTATTTCCATCTTTATCTCTAGGG 57.063 37.037 0.00 0.00 0.00 3.53
707 775 5.804692 ACTCAATATATACTCGAGGCTCG 57.195 43.478 30.10 30.10 42.10 5.03
720 788 4.338012 TCGAGGCTCGGTAATATATCCAA 58.662 43.478 33.93 9.46 40.88 3.53
723 791 5.566032 CGAGGCTCGGTAATATATCCAACAA 60.566 44.000 28.52 0.00 36.00 2.83
724 792 5.548406 AGGCTCGGTAATATATCCAACAAC 58.452 41.667 0.00 0.00 0.00 3.32
822 895 4.080863 AGCCTACTATTTCTGGGTCACAAG 60.081 45.833 0.00 0.00 0.00 3.16
825 901 4.098914 ACTATTTCTGGGTCACAAGCAA 57.901 40.909 0.00 0.00 0.00 3.91
833 909 1.338020 GGGTCACAAGCAAACTTCCTG 59.662 52.381 0.00 0.00 32.29 3.86
884 960 4.022935 ACGTGAATGAATTGTCAGTTGCAT 60.023 37.500 0.00 0.00 37.14 3.96
960 1038 3.567797 GATTCAGGAGGCACGCGC 61.568 66.667 5.73 0.00 37.44 6.86
981 1059 5.243954 GCGCATATATATGTGGAGGGATCTA 59.756 44.000 28.78 0.00 42.75 1.98
1018 1096 3.650950 GCACTTGGCAGGGAGGGA 61.651 66.667 0.44 0.00 43.97 4.20
1136 1214 2.260247 CGTGGAGACGGGTGAGTTA 58.740 57.895 0.00 0.00 42.18 2.24
1288 1394 2.170166 TGGCAGCTAGGTTCCATTTTG 58.830 47.619 9.37 0.00 0.00 2.44
1350 1456 3.072468 CGGCGGTACCTCCTGGAA 61.072 66.667 18.71 0.00 37.04 3.53
1362 1468 0.415429 TCCTGGAAGAGGGAGAAGCT 59.585 55.000 0.00 0.00 43.06 3.74
1368 1474 2.124778 GAGGGAGAAGCTGCAGCC 60.125 66.667 34.39 20.47 43.38 4.85
1369 1475 4.093291 AGGGAGAAGCTGCAGCCG 62.093 66.667 34.39 0.00 43.38 5.52
1470 1579 8.076178 GGCGCATAACTTATACTGATTGATTTT 58.924 33.333 10.83 0.00 0.00 1.82
1527 1636 4.006989 TGTTACTGCACAAGTTGTTGACT 58.993 39.130 5.57 0.00 40.56 3.41
1575 1690 1.004560 TGCTTCTCTGCGGAACCAG 60.005 57.895 0.00 0.00 35.36 4.00
1593 1708 1.935873 CAGTATGGTCCACGCATCAAG 59.064 52.381 0.00 0.00 0.00 3.02
1596 1711 3.499737 GGTCCACGCATCAAGCCG 61.500 66.667 0.00 0.00 41.38 5.52
1620 1735 6.089283 CGCTGCAAAACATGTGTATAAATGTT 59.911 34.615 0.00 2.33 46.35 2.71
1622 1737 8.920665 GCTGCAAAACATGTGTATAAATGTTAA 58.079 29.630 8.30 0.00 44.24 2.01
1704 2337 7.094075 ACAGCTATATTTTATGGGCATGTCATG 60.094 37.037 8.56 8.56 0.00 3.07
1733 2366 3.112075 GCACTTAGCAGCGACGCA 61.112 61.111 23.70 0.00 44.79 5.24
1734 2367 2.772189 CACTTAGCAGCGACGCAC 59.228 61.111 23.70 13.74 0.00 5.34
1735 2368 2.432628 ACTTAGCAGCGACGCACC 60.433 61.111 23.70 12.08 0.00 5.01
1736 2369 2.432456 CTTAGCAGCGACGCACCA 60.432 61.111 23.70 0.00 0.00 4.17
1737 2370 1.811266 CTTAGCAGCGACGCACCAT 60.811 57.895 23.70 7.34 0.00 3.55
1738 2371 0.527600 CTTAGCAGCGACGCACCATA 60.528 55.000 23.70 6.30 0.00 2.74
1739 2372 0.104120 TTAGCAGCGACGCACCATAT 59.896 50.000 23.70 4.00 0.00 1.78
1740 2373 0.597377 TAGCAGCGACGCACCATATG 60.597 55.000 23.70 11.36 0.00 1.78
1741 2374 2.173669 GCAGCGACGCACCATATGT 61.174 57.895 23.70 0.00 0.00 2.29
1742 2375 1.705337 GCAGCGACGCACCATATGTT 61.705 55.000 23.70 0.00 0.00 2.71
1743 2376 0.026674 CAGCGACGCACCATATGTTG 59.973 55.000 23.70 3.95 0.00 3.33
1744 2377 0.391130 AGCGACGCACCATATGTTGT 60.391 50.000 23.70 0.00 0.00 3.32
1746 2379 1.257936 GCGACGCACCATATGTTGTAG 59.742 52.381 16.42 0.00 0.00 2.74
1754 2387 6.645003 ACGCACCATATGTTGTAGTATATGTG 59.355 38.462 1.95 0.00 36.16 3.21
1756 2389 7.810759 CGCACCATATGTTGTAGTATATGTGTA 59.189 37.037 1.95 0.00 36.16 2.90
1757 2390 8.922676 GCACCATATGTTGTAGTATATGTGTAC 58.077 37.037 1.95 0.00 36.16 2.90
1758 2391 9.974980 CACCATATGTTGTAGTATATGTGTACA 57.025 33.333 1.24 0.00 36.16 2.90
1818 2451 2.004583 TGCTATGTGTTCGCCACTAC 57.995 50.000 6.61 0.00 44.81 2.73
1827 2462 4.817464 TGTGTTCGCCACTACTGTATTTTT 59.183 37.500 6.61 0.00 44.81 1.94
1853 2488 3.906846 TGGTGGTTATTGGGAAGCAAATT 59.093 39.130 0.00 0.00 38.47 1.82
1854 2489 5.087323 TGGTGGTTATTGGGAAGCAAATTA 58.913 37.500 0.00 0.00 38.47 1.40
1855 2490 5.544176 TGGTGGTTATTGGGAAGCAAATTAA 59.456 36.000 0.00 0.00 38.47 1.40
1856 2491 6.214412 TGGTGGTTATTGGGAAGCAAATTAAT 59.786 34.615 0.00 0.00 38.47 1.40
1862 2497 6.813293 ATTGGGAAGCAAATTAATAAGCCT 57.187 33.333 8.06 0.00 0.00 4.58
1870 2505 6.974965 AGCAAATTAATAAGCCTCTACATGC 58.025 36.000 8.06 0.00 0.00 4.06
1879 2514 1.952367 GCCTCTACATGCTTTGCACCT 60.952 52.381 0.00 0.00 43.04 4.00
1886 2521 4.870123 ACATGCTTTGCACCTCATTTTA 57.130 36.364 0.00 0.00 43.04 1.52
1993 2631 2.880890 ACACCAACACAATCTCAAGAGC 59.119 45.455 0.00 0.00 0.00 4.09
1998 2636 6.006449 ACCAACACAATCTCAAGAGCTATTT 58.994 36.000 0.00 0.00 0.00 1.40
2013 2651 9.770097 CAAGAGCTATTTAAGACATCAAGGATA 57.230 33.333 0.00 0.00 0.00 2.59
2015 2653 8.928448 AGAGCTATTTAAGACATCAAGGATACA 58.072 33.333 0.00 0.00 41.41 2.29
2016 2654 9.717942 GAGCTATTTAAGACATCAAGGATACAT 57.282 33.333 0.00 0.00 41.41 2.29
2121 2767 3.073062 ACAAGATAGGTGCTCCAACAACT 59.927 43.478 7.70 0.00 41.53 3.16
2137 2783 5.240183 CCAACAACTATGCATCTAGAATGGG 59.760 44.000 0.19 0.00 0.00 4.00
2158 2804 0.458543 ACGACTCATAAGCACCGCAG 60.459 55.000 0.00 0.00 0.00 5.18
2173 2819 1.827789 GCAGTTGCTGGACCCAACA 60.828 57.895 13.94 2.92 43.74 3.33
2178 2824 0.817634 TTGCTGGACCCAACAACTCG 60.818 55.000 1.06 0.00 28.54 4.18
2187 2833 1.271379 CCCAACAACTCGGGTCAGATT 60.271 52.381 0.00 0.00 37.70 2.40
2191 2837 4.503910 CAACAACTCGGGTCAGATTATGA 58.496 43.478 0.00 0.00 34.79 2.15
2204 2850 6.173339 GTCAGATTATGAGTTTTCACCCTGA 58.827 40.000 0.00 0.00 39.07 3.86
2211 2857 4.451900 TGAGTTTTCACCCTGAAGAGAAC 58.548 43.478 0.00 0.00 37.70 3.01
2215 2861 4.342862 TTTCACCCTGAAGAGAACTCTG 57.657 45.455 5.06 0.00 40.36 3.35
2216 2862 3.244887 TCACCCTGAAGAGAACTCTGA 57.755 47.619 5.06 0.00 40.36 3.27
2251 2897 2.305927 AGGTCCTTCAACGATGGAATGT 59.694 45.455 0.00 0.00 37.57 2.71
2260 2906 4.154015 TCAACGATGGAATGTCATGTCAAC 59.846 41.667 0.00 0.00 0.00 3.18
2265 2911 2.288518 TGGAATGTCATGTCAACGACGA 60.289 45.455 0.00 0.00 34.95 4.20
2278 2924 2.583593 GACGACATCGCCAGGCTC 60.584 66.667 10.54 0.00 44.43 4.70
2290 2936 2.945008 CGCCAGGCTCAATTAATGAAGA 59.055 45.455 10.54 0.00 37.67 2.87
2315 2961 3.775316 GGACCTAGAGTTTTCATCCCTGA 59.225 47.826 0.00 0.00 0.00 3.86
2377 3030 0.468226 TGTCGAGCACTCCAAACCTT 59.532 50.000 0.00 0.00 0.00 3.50
2381 3034 1.032014 GAGCACTCCAAACCTTTGCA 58.968 50.000 0.00 0.00 36.86 4.08
2383 3036 0.249447 GCACTCCAAACCTTTGCACC 60.249 55.000 0.00 0.00 36.86 5.01
2389 3042 2.551912 AAACCTTTGCACCCGAGCG 61.552 57.895 0.00 0.00 37.31 5.03
2397 3050 3.069980 GCACCCGAGCGAGACATCT 62.070 63.158 0.00 0.00 0.00 2.90
2398 3051 1.226802 CACCCGAGCGAGACATCTG 60.227 63.158 0.00 0.00 0.00 2.90
2403 3056 1.269174 CCGAGCGAGACATCTGATCAT 59.731 52.381 0.00 0.00 0.00 2.45
2406 3059 1.269174 AGCGAGACATCTGATCATCGG 59.731 52.381 14.12 1.99 0.00 4.18
2418 3071 0.753262 ATCATCGGACTGTGCTACCC 59.247 55.000 0.00 0.00 0.00 3.69
2420 3073 1.064240 TCATCGGACTGTGCTACCCTA 60.064 52.381 0.00 0.00 0.00 3.53
2447 3100 2.884639 CCAATATGGAGGCTAAAACCCG 59.115 50.000 0.00 0.00 40.96 5.28
2453 3106 2.967397 GGCTAAAACCCGCCAACC 59.033 61.111 0.00 0.00 45.59 3.77
2470 3123 1.056700 ACCTTGCGCCCCATAGAGAT 61.057 55.000 4.18 0.00 0.00 2.75
2486 3139 0.916358 AGATGGTTAGCAGCCTGGGT 60.916 55.000 0.00 0.00 0.00 4.51
2509 3163 5.061808 GTCGCGCCGTTGAGATAAATATTAT 59.938 40.000 0.00 0.00 0.00 1.28
2518 3172 7.836493 CGTTGAGATAAATATTATCGATGCACG 59.164 37.037 8.54 0.00 44.09 5.34
2553 3207 0.249447 CGCAGATCGCCTCCATACAA 60.249 55.000 4.37 0.00 37.30 2.41
2554 3208 1.506493 GCAGATCGCCTCCATACAAG 58.494 55.000 0.00 0.00 32.94 3.16
2559 3213 2.447408 TCGCCTCCATACAAGGACTA 57.553 50.000 0.00 0.00 35.83 2.59
2571 3225 7.068348 TCCATACAAGGACTAGTAAGATGTGTC 59.932 40.741 0.00 0.00 31.23 3.67
2572 3226 5.312120 ACAAGGACTAGTAAGATGTGTCG 57.688 43.478 0.00 0.00 0.00 4.35
2573 3227 4.765856 ACAAGGACTAGTAAGATGTGTCGT 59.234 41.667 0.00 0.00 0.00 4.34
2574 3228 5.106237 ACAAGGACTAGTAAGATGTGTCGTC 60.106 44.000 0.00 0.00 0.00 4.20
2575 3229 4.846040 AGGACTAGTAAGATGTGTCGTCT 58.154 43.478 0.00 0.00 0.00 4.18
2576 3230 5.254901 AGGACTAGTAAGATGTGTCGTCTT 58.745 41.667 0.00 8.84 41.76 3.01
2577 3231 5.354792 AGGACTAGTAAGATGTGTCGTCTTC 59.645 44.000 0.00 1.92 39.90 2.87
2578 3232 5.123502 GGACTAGTAAGATGTGTCGTCTTCA 59.876 44.000 0.00 0.00 39.90 3.02
2579 3233 6.183360 GGACTAGTAAGATGTGTCGTCTTCAT 60.183 42.308 0.00 2.09 39.90 2.57
2581 3235 5.644977 AGTAAGATGTGTCGTCTTCATCA 57.355 39.130 7.38 0.00 39.90 3.07
2584 3238 4.725790 AGATGTGTCGTCTTCATCATCA 57.274 40.909 15.38 0.00 39.96 3.07
2615 3269 6.521162 GGGAACAAGTAAAATTCATGGTTGT 58.479 36.000 0.00 0.00 0.00 3.32
2616 3270 6.645003 GGGAACAAGTAAAATTCATGGTTGTC 59.355 38.462 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.517832 GGACCTGCACGAGCTGTAT 59.482 57.895 6.36 0.00 42.74 2.29
70 71 2.420568 GGCCCGGAGACACGTCATA 61.421 63.158 0.73 0.00 0.00 2.15
96 98 0.032815 TGACGAAACATCGCACCAGA 59.967 50.000 0.00 0.00 36.44 3.86
108 110 3.813166 GGACAAAGATGGAGTTGACGAAA 59.187 43.478 0.00 0.00 0.00 3.46
119 121 0.721718 GCGAAGACGGACAAAGATGG 59.278 55.000 0.00 0.00 40.15 3.51
152 154 0.955428 AAGGCACGCATCGATGTTGT 60.955 50.000 25.47 20.56 0.00 3.32
158 160 1.650314 TAGACGAAGGCACGCATCGA 61.650 55.000 19.11 0.00 39.73 3.59
267 270 1.141019 GGCGCCGAGTTAGTCATGA 59.859 57.895 12.58 0.00 0.00 3.07
366 370 1.028868 GTAGCCGTGGTCGAGGTAGT 61.029 60.000 0.00 0.00 39.71 2.73
518 562 3.283751 CGGTCAGACTGGAGAGAATAGT 58.716 50.000 1.81 0.00 0.00 2.12
581 626 7.093289 CCAAATATATCTCTAACATCTCCCCGT 60.093 40.741 0.00 0.00 0.00 5.28
650 710 2.679082 GCAAGACACCCCCTAGAGATA 58.321 52.381 0.00 0.00 0.00 1.98
707 775 7.065443 GGCGGAATAGTTGTTGGATATATTACC 59.935 40.741 0.00 0.00 0.00 2.85
720 788 1.409661 GGGGATTGGCGGAATAGTTGT 60.410 52.381 0.00 0.00 0.00 3.32
723 791 0.697854 AGGGGGATTGGCGGAATAGT 60.698 55.000 0.00 0.00 0.00 2.12
724 792 0.036875 GAGGGGGATTGGCGGAATAG 59.963 60.000 0.00 0.00 0.00 1.73
801 874 4.192317 GCTTGTGACCCAGAAATAGTAGG 58.808 47.826 0.00 0.00 0.00 3.18
822 895 1.474077 CCATAGCCACAGGAAGTTTGC 59.526 52.381 0.00 0.00 0.00 3.68
825 901 2.375174 TGTTCCATAGCCACAGGAAGTT 59.625 45.455 0.00 0.00 41.74 2.66
833 909 2.368439 TCTTGCATGTTCCATAGCCAC 58.632 47.619 0.00 0.00 0.00 5.01
884 960 6.937465 TGTTTGCATATACCTGTGTTTAGACA 59.063 34.615 0.00 0.00 0.00 3.41
960 1038 6.728164 CCCCTAGATCCCTCCACATATATATG 59.272 46.154 19.21 19.21 39.55 1.78
1018 1096 3.604582 CTTGATTCTTTCGCTCCTCCTT 58.395 45.455 0.00 0.00 0.00 3.36
1055 1133 1.663379 CCAGCCATGTCCTCGTCGTA 61.663 60.000 0.00 0.00 0.00 3.43
1136 1214 2.826725 GCGCTTCATATAGTACTCCCCT 59.173 50.000 0.00 0.00 0.00 4.79
1288 1394 1.293498 CCCGACCGATCCATCCATC 59.707 63.158 0.00 0.00 0.00 3.51
1350 1456 2.668120 GGCTGCAGCTTCTCCCTCT 61.668 63.158 35.82 0.00 41.70 3.69
1533 1642 8.512138 GCAGCTATACTAACAAAAGGAAAAGAA 58.488 33.333 0.00 0.00 0.00 2.52
1534 1643 7.883311 AGCAGCTATACTAACAAAAGGAAAAGA 59.117 33.333 0.00 0.00 0.00 2.52
1535 1644 8.045176 AGCAGCTATACTAACAAAAGGAAAAG 57.955 34.615 0.00 0.00 0.00 2.27
1550 1665 1.338337 TCCGCAGAGAAGCAGCTATAC 59.662 52.381 0.00 0.00 0.00 1.47
1575 1690 0.657840 GCTTGATGCGTGGACCATAC 59.342 55.000 0.00 0.00 0.00 2.39
1593 1708 0.039617 TACACATGTTTTGCAGCGGC 60.040 50.000 0.31 0.31 41.68 6.53
1596 1711 6.949578 ACATTTATACACATGTTTTGCAGC 57.050 33.333 0.00 0.00 28.73 5.25
1648 1763 7.924947 ACTTAGTTACAAGTTAATATCTCCCGC 59.075 37.037 0.00 0.00 35.16 6.13
1676 1814 8.108999 TGACATGCCCATAAAATATAGCTGTAT 58.891 33.333 0.00 0.00 0.00 2.29
1679 1817 6.822667 TGACATGCCCATAAAATATAGCTG 57.177 37.500 0.00 0.00 0.00 4.24
1680 1818 7.400599 CATGACATGCCCATAAAATATAGCT 57.599 36.000 1.71 0.00 0.00 3.32
1704 2337 2.933906 TGCTAAGTGCTAACGTAATGGC 59.066 45.455 0.00 0.00 43.37 4.40
1716 2349 3.112075 TGCGTCGCTGCTAAGTGC 61.112 61.111 19.50 0.00 43.25 4.40
1729 2362 6.645003 CACATATACTACAACATATGGTGCGT 59.355 38.462 20.83 18.73 38.76 5.24
1731 2364 7.962964 ACACATATACTACAACATATGGTGC 57.037 36.000 20.83 0.00 38.76 5.01
1739 2372 9.234827 AGTACACTGTACACATATACTACAACA 57.765 33.333 19.34 0.00 0.00 3.33
1827 2462 3.711704 TGCTTCCCAATAACCACCAAAAA 59.288 39.130 0.00 0.00 0.00 1.94
1835 2470 7.441157 GGCTTATTAATTTGCTTCCCAATAACC 59.559 37.037 10.70 0.00 32.49 2.85
1836 2471 8.204160 AGGCTTATTAATTTGCTTCCCAATAAC 58.796 33.333 10.70 0.00 32.49 1.89
1845 2480 7.286316 AGCATGTAGAGGCTTATTAATTTGCTT 59.714 33.333 0.00 4.99 35.00 3.91
1862 2497 2.857186 TGAGGTGCAAAGCATGTAGA 57.143 45.000 0.00 0.00 41.91 2.59
1870 2505 9.079833 CATAGACAAATAAAATGAGGTGCAAAG 57.920 33.333 0.00 0.00 0.00 2.77
1966 2604 5.227569 TGAGATTGTGTTGGTGTAGATGT 57.772 39.130 0.00 0.00 0.00 3.06
1969 2607 5.541845 CTCTTGAGATTGTGTTGGTGTAGA 58.458 41.667 0.00 0.00 0.00 2.59
1998 2636 8.084985 TGGTTGTATGTATCCTTGATGTCTTA 57.915 34.615 0.00 0.00 0.00 2.10
2035 2673 5.248870 TGCAGTGGTTTCTTCTTCTTTTC 57.751 39.130 0.00 0.00 0.00 2.29
2040 2678 1.949525 TGCTGCAGTGGTTTCTTCTTC 59.050 47.619 16.64 0.00 0.00 2.87
2043 2681 2.159254 TGTTTGCTGCAGTGGTTTCTTC 60.159 45.455 16.64 0.00 0.00 2.87
2045 2683 1.473258 TGTTTGCTGCAGTGGTTTCT 58.527 45.000 16.64 0.00 0.00 2.52
2093 2738 2.170607 GGAGCACCTATCTTGTTGCCTA 59.829 50.000 0.00 0.00 0.00 3.93
2121 2767 4.588951 AGTCGTTCCCATTCTAGATGCATA 59.411 41.667 0.00 0.00 0.00 3.14
2123 2769 2.766263 AGTCGTTCCCATTCTAGATGCA 59.234 45.455 0.00 0.00 0.00 3.96
2137 2783 0.645868 GCGGTGCTTATGAGTCGTTC 59.354 55.000 0.00 0.00 0.00 3.95
2173 2819 5.422214 AAACTCATAATCTGACCCGAGTT 57.578 39.130 0.00 0.00 43.56 3.01
2178 2824 4.640647 GGGTGAAAACTCATAATCTGACCC 59.359 45.833 0.00 0.00 0.00 4.46
2187 2833 6.043243 AGTTCTCTTCAGGGTGAAAACTCATA 59.957 38.462 1.19 0.00 32.54 2.15
2191 2837 4.410555 AGAGTTCTCTTCAGGGTGAAAACT 59.589 41.667 5.36 5.36 37.54 2.66
2204 2850 6.696411 CATGGAGTTTACTCAGAGTTCTCTT 58.304 40.000 8.80 4.87 44.60 2.85
2211 2857 3.055530 ACCTGCATGGAGTTTACTCAGAG 60.056 47.826 13.65 0.00 44.60 3.35
2215 2861 2.237392 AGGACCTGCATGGAGTTTACTC 59.763 50.000 13.65 1.18 42.14 2.59
2216 2862 2.269940 AGGACCTGCATGGAGTTTACT 58.730 47.619 13.65 2.76 39.71 2.24
2265 2911 2.418368 TTAATTGAGCCTGGCGATGT 57.582 45.000 13.96 0.00 0.00 3.06
2270 2916 4.320057 CGATCTTCATTAATTGAGCCTGGC 60.320 45.833 11.65 11.65 35.27 4.85
2278 2924 7.437748 ACTCTAGGTCCGATCTTCATTAATTG 58.562 38.462 0.00 0.00 0.00 2.32
2290 2936 3.388350 GGGATGAAAACTCTAGGTCCGAT 59.612 47.826 0.00 0.00 0.00 4.18
2315 2961 1.053424 TTGAGTGTAGGGGCGAGTTT 58.947 50.000 0.00 0.00 0.00 2.66
2322 2968 3.338249 CACACATCTTTGAGTGTAGGGG 58.662 50.000 0.00 0.00 46.44 4.79
2356 3009 1.072331 AGGTTTGGAGTGCTCGACATT 59.928 47.619 0.00 0.00 0.00 2.71
2377 3030 2.835701 GATGTCTCGCTCGGGTGCAA 62.836 60.000 0.00 0.00 0.00 4.08
2381 3034 0.753479 ATCAGATGTCTCGCTCGGGT 60.753 55.000 0.00 0.00 0.00 5.28
2383 3036 0.665298 TGATCAGATGTCTCGCTCGG 59.335 55.000 0.00 0.00 0.00 4.63
2389 3042 3.317711 ACAGTCCGATGATCAGATGTCTC 59.682 47.826 0.09 0.00 0.00 3.36
2397 3050 1.409064 GGTAGCACAGTCCGATGATCA 59.591 52.381 0.00 0.00 0.00 2.92
2398 3051 1.269831 GGGTAGCACAGTCCGATGATC 60.270 57.143 0.00 0.00 0.00 2.92
2403 3056 1.547372 GTTTAGGGTAGCACAGTCCGA 59.453 52.381 0.00 0.00 0.00 4.55
2406 3059 2.093606 GGAGGTTTAGGGTAGCACAGTC 60.094 54.545 0.00 0.00 0.00 3.51
2453 3106 2.924185 CATCTCTATGGGGCGCAAG 58.076 57.895 10.83 7.78 43.44 4.01
2470 3123 2.954684 CGACCCAGGCTGCTAACCA 61.955 63.158 9.56 0.00 0.00 3.67
2486 3139 2.495409 TATTTATCTCAACGGCGCGA 57.505 45.000 12.10 2.52 0.00 5.87
2493 3147 7.632515 GCGTGCATCGATAATATTTATCTCAAC 59.367 37.037 11.94 0.00 42.86 3.18
2518 3172 2.480555 CGATTGGAGTGGTTGCGC 59.519 61.111 0.00 0.00 0.00 6.09
2553 3207 4.846040 AGACGACACATCTTACTAGTCCT 58.154 43.478 0.00 0.00 0.00 3.85
2554 3208 5.123502 TGAAGACGACACATCTTACTAGTCC 59.876 44.000 0.00 0.00 36.53 3.85
2559 3213 5.644977 TGATGAAGACGACACATCTTACT 57.355 39.130 18.65 0.00 40.39 2.24
2571 3225 3.062639 CCCGTTTCTTGATGATGAAGACG 59.937 47.826 0.00 0.00 32.37 4.18
2572 3226 4.253685 TCCCGTTTCTTGATGATGAAGAC 58.746 43.478 0.00 0.00 0.00 3.01
2573 3227 4.551702 TCCCGTTTCTTGATGATGAAGA 57.448 40.909 0.00 0.00 0.00 2.87
2574 3228 4.455533 TGTTCCCGTTTCTTGATGATGAAG 59.544 41.667 0.00 0.00 0.00 3.02
2575 3229 4.393834 TGTTCCCGTTTCTTGATGATGAA 58.606 39.130 0.00 0.00 0.00 2.57
2576 3230 4.014569 TGTTCCCGTTTCTTGATGATGA 57.985 40.909 0.00 0.00 0.00 2.92
2577 3231 4.216257 ACTTGTTCCCGTTTCTTGATGATG 59.784 41.667 0.00 0.00 0.00 3.07
2578 3232 4.398319 ACTTGTTCCCGTTTCTTGATGAT 58.602 39.130 0.00 0.00 0.00 2.45
2579 3233 3.815809 ACTTGTTCCCGTTTCTTGATGA 58.184 40.909 0.00 0.00 0.00 2.92
2581 3235 6.702716 TTTTACTTGTTCCCGTTTCTTGAT 57.297 33.333 0.00 0.00 0.00 2.57
2584 3238 7.102847 TGAATTTTACTTGTTCCCGTTTCTT 57.897 32.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.