Multiple sequence alignment - TraesCS7B01G344600

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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 TraesCS7B01G344600 chr7B 100.000 3144 0 0 1 3144 600597845 600594702 0.000000e+00 5806.0
1 TraesCS7B01G344600 chr7D 95.096 2080 80 14 366 2430 554316421 554318493 0.000000e+00 3256.0
2 TraesCS7B01G344600 chr7D 87.027 740 69 13 2418 3143 554318663 554319389 0.000000e+00 809.0
3 TraesCS7B01G344600 chr7D 93.393 333 17 2 3 335 554316097 554316424 3.640000e-134 488.0
4 TraesCS7B01G344600 chr7D 79.630 108 12 7 2444 2548 230490989 230491089 5.630000e-08 69.4
5 TraesCS7B01G344600 chr7D 100.000 32 0 0 2441 2472 182992761 182992730 3.390000e-05 60.2
6 TraesCS7B01G344600 chr3D 82.858 2176 285 58 260 2379 600189042 600186899 0.000000e+00 1871.0
7 TraesCS7B01G344600 chr3D 85.294 136 15 3 46 180 93611684 93611553 5.470000e-28 135.0
8 TraesCS7B01G344600 chr3B 82.729 2067 250 66 385 2372 807374442 807372404 0.000000e+00 1740.0
9 TraesCS7B01G344600 chr4A 76.493 536 122 4 529 1062 738815348 738815881 3.970000e-74 289.0
10 TraesCS7B01G344600 chr4A 92.708 96 5 1 75 170 658070540 658070633 1.520000e-28 137.0
11 TraesCS7B01G344600 chr4A 91.667 96 6 1 75 170 658109521 658109614 7.080000e-27 132.0
12 TraesCS7B01G344600 chr5B 75.524 429 79 13 565 986 9334375 9333966 1.490000e-43 187.0
13 TraesCS7B01G344600 chr4B 91.509 106 7 1 75 180 647648653 647648550 9.090000e-31 145.0
14 TraesCS7B01G344600 chr4B 90.816 98 7 1 73 170 659485920 659485825 2.540000e-26 130.0
15 TraesCS7B01G344600 chr1D 92.857 98 5 1 82 179 9583955 9583860 1.180000e-29 141.0
16 TraesCS7B01G344600 chr1D 95.000 40 1 1 2433 2472 438319046 438319008 9.420000e-06 62.1
17 TraesCS7B01G344600 chr6D 85.106 141 16 3 46 185 30450598 30450462 4.230000e-29 139.0
18 TraesCS7B01G344600 chr6D 87.500 56 3 3 2441 2494 263045188 263045241 9.420000e-06 62.1
19 TraesCS7B01G344600 chr2A 90.816 98 6 2 82 179 251392173 251392267 9.150000e-26 128.0
20 TraesCS7B01G344600 chr1A 82.727 110 19 0 2826 2935 437235818 437235709 7.180000e-17 99.0
21 TraesCS7B01G344600 chr1A 79.348 92 11 7 2441 2529 496646215 496646129 1.220000e-04 58.4
22 TraesCS7B01G344600 chr2D 100.000 34 0 0 2441 2474 628612464 628612497 2.620000e-06 63.9
23 TraesCS7B01G344600 chr6A 94.595 37 2 0 2441 2477 176992702 176992666 1.220000e-04 58.4


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 TraesCS7B01G344600 chr7B 600594702 600597845 3143 True 5806.000000 5806 100.000000 1 3144 1 chr7B.!!$R1 3143
1 TraesCS7B01G344600 chr7D 554316097 554319389 3292 False 1517.666667 3256 91.838667 3 3143 3 chr7D.!!$F2 3140
2 TraesCS7B01G344600 chr3D 600186899 600189042 2143 True 1871.000000 1871 82.858000 260 2379 1 chr3D.!!$R2 2119
3 TraesCS7B01G344600 chr3B 807372404 807374442 2038 True 1740.000000 1740 82.729000 385 2372 1 chr3B.!!$R1 1987
4 TraesCS7B01G344600 chr4A 738815348 738815881 533 False 289.000000 289 76.493000 529 1062 1 chr4A.!!$F3 533

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
761 798 0.178767 TGATCATGAAGCTCACCCCG 59.821 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2514 2840 0.323269 TTCGGGATTTGAGCATGGCA 60.323 50.0 0.0 0.0 0.0 4.92 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
42 43 2.050836 AACACCTGGCGGTCACATCA 62.051 55.000 0.00 0.00 43.24 3.07
57 58 8.194104 GCGGTCACATCATCTATTTCTAGATAT 58.806 37.037 0.00 0.00 41.78 1.63
256 257 2.432510 GGACAGGACTACAGCTAGCATT 59.567 50.000 18.83 5.33 0.00 3.56
257 258 3.637229 GGACAGGACTACAGCTAGCATTA 59.363 47.826 18.83 6.32 0.00 1.90
258 259 4.261825 GGACAGGACTACAGCTAGCATTAG 60.262 50.000 18.83 17.73 0.00 1.73
335 336 1.265236 AGCTCACTGAGTAAGCTGCT 58.735 50.000 9.97 0.00 44.41 4.24
336 337 2.451490 AGCTCACTGAGTAAGCTGCTA 58.549 47.619 9.97 0.00 44.41 3.49
337 338 2.426738 AGCTCACTGAGTAAGCTGCTAG 59.573 50.000 9.97 0.00 44.41 3.42
338 339 2.808244 CTCACTGAGTAAGCTGCTAGC 58.192 52.381 8.10 8.10 42.84 3.42
339 340 5.291178 GCTCACTGAGTAAGCTGCTAGCT 62.291 52.174 17.23 3.89 42.01 3.32
367 368 2.072298 GCTAAACAGACCAGCACTCTG 58.928 52.381 4.27 4.27 40.97 3.35
368 369 2.072298 CTAAACAGACCAGCACTCTGC 58.928 52.381 5.47 0.00 45.46 4.26
465 487 3.555956 GGTACAGTCATGCGGTTTGATAG 59.444 47.826 0.00 0.00 0.00 2.08
503 525 6.053632 AGGAATAATGATCGGATATGTGCA 57.946 37.500 0.00 0.00 0.00 4.57
761 798 0.178767 TGATCATGAAGCTCACCCCG 59.821 55.000 0.00 0.00 0.00 5.73
804 841 1.481819 CTGCAACAACAGCGCCAAAC 61.482 55.000 2.29 0.00 33.85 2.93
905 942 2.233922 CGGGTCTAACATCAAGAGTGGT 59.766 50.000 0.00 0.00 0.00 4.16
941 978 2.100631 AATCTTCGACGGCCGCAAG 61.101 57.895 28.58 23.74 38.37 4.01
975 1012 3.119096 GCGCCAACGTCTTCCTCC 61.119 66.667 0.00 0.00 42.83 4.30
986 1023 1.977544 CTTCCTCCTGTCCGACGGT 60.978 63.158 14.79 0.00 0.00 4.83
1013 1050 2.117156 CGCCAATGAAGCCAGGGAG 61.117 63.158 0.00 0.00 0.00 4.30
1014 1051 1.304282 GCCAATGAAGCCAGGGAGA 59.696 57.895 0.00 0.00 0.00 3.71
1015 1052 1.034292 GCCAATGAAGCCAGGGAGAC 61.034 60.000 0.00 0.00 0.00 3.36
1071 1108 0.460987 CGGCAAGGACTCAGATCACC 60.461 60.000 0.00 0.00 0.00 4.02
1077 1114 3.474798 AGGACTCAGATCACCAGGTAA 57.525 47.619 0.00 0.00 0.00 2.85
1078 1115 3.100671 AGGACTCAGATCACCAGGTAAC 58.899 50.000 0.00 0.00 0.00 2.50
1095 1147 5.041951 GGTAACTGCTCGATCTATCTCTG 57.958 47.826 0.00 0.00 0.00 3.35
1096 1148 3.641437 AACTGCTCGATCTATCTCTGC 57.359 47.619 0.00 0.00 0.00 4.26
1102 1166 3.342719 CTCGATCTATCTCTGCCTAGCA 58.657 50.000 0.00 0.00 36.92 3.49
1110 1174 1.552337 TCTCTGCCTAGCAAAGTCCAG 59.448 52.381 0.00 0.00 38.41 3.86
1121 1196 2.623416 GCAAAGTCCAGCTGTTTAAGGT 59.377 45.455 13.81 0.00 36.97 3.50
1137 1212 7.629157 TGTTTAAGGTGGTGATAGATGATGAA 58.371 34.615 0.00 0.00 0.00 2.57
1147 1222 6.879993 GGTGATAGATGATGAAGCTGATGATT 59.120 38.462 0.00 0.00 0.00 2.57
1149 1224 9.433153 GTGATAGATGATGAAGCTGATGATTTA 57.567 33.333 0.00 0.00 0.00 1.40
1152 1227 7.925043 AGATGATGAAGCTGATGATTTATCC 57.075 36.000 0.00 0.00 34.86 2.59
1153 1228 6.885376 AGATGATGAAGCTGATGATTTATCCC 59.115 38.462 0.00 0.00 34.86 3.85
1154 1229 5.944135 TGATGAAGCTGATGATTTATCCCA 58.056 37.500 0.00 0.00 34.86 4.37
1156 1231 7.008332 TGATGAAGCTGATGATTTATCCCATT 58.992 34.615 0.00 0.00 34.86 3.16
1240 1331 1.070786 GTCGAACCTGACCAAGCCA 59.929 57.895 0.00 0.00 32.61 4.75
1777 1874 0.814457 AGAAGCTGATCGACTCGCTT 59.186 50.000 14.41 14.41 42.40 4.68
1822 1919 1.153005 GCTCATGGCCTCCAAGGAG 60.153 63.158 3.32 9.20 37.67 3.69
1900 1997 3.691342 CGGTTCGCTGACAGGGGA 61.691 66.667 18.48 8.10 0.00 4.81
2262 2396 3.387050 ACGCCCCTAAAATCCTAGTACTG 59.613 47.826 5.39 0.00 0.00 2.74
2266 2400 5.011840 GCCCCTAAAATCCTAGTACTGGTAG 59.988 48.000 5.39 0.00 0.00 3.18
2267 2401 6.141790 CCCCTAAAATCCTAGTACTGGTAGT 58.858 44.000 5.39 0.00 0.00 2.73
2268 2402 7.300658 CCCCTAAAATCCTAGTACTGGTAGTA 58.699 42.308 5.39 0.00 0.00 1.82
2383 2528 3.151710 CCCCCACGGATGCGTCTA 61.152 66.667 10.14 0.00 0.00 2.59
2390 2535 2.540515 CACGGATGCGTCTACATTCTT 58.459 47.619 10.14 0.00 0.00 2.52
2401 2546 7.298122 TGCGTCTACATTCTTTTTCTCATTTC 58.702 34.615 0.00 0.00 0.00 2.17
2422 2567 9.260002 CATTTCTGTATTTTAACCAGCTTGTTT 57.740 29.630 8.67 0.00 0.00 2.83
2424 2569 9.738832 TTTCTGTATTTTAACCAGCTTGTTTAC 57.261 29.630 8.67 5.99 0.00 2.01
2439 2765 8.076178 CAGCTTGTTTACTTTACATTAAGCACT 58.924 33.333 0.00 0.00 32.15 4.40
2468 2794 2.507339 TGCTTGCCAACTAAACTTGC 57.493 45.000 0.00 0.00 0.00 4.01
2477 2803 1.165270 ACTAAACTTGCCATCCACGC 58.835 50.000 0.00 0.00 0.00 5.34
2478 2804 1.164411 CTAAACTTGCCATCCACGCA 58.836 50.000 0.00 0.00 0.00 5.24
2485 2811 0.251634 TGCCATCCACGCATCACTAA 59.748 50.000 0.00 0.00 0.00 2.24
2488 2814 2.477863 GCCATCCACGCATCACTAAAAC 60.478 50.000 0.00 0.00 0.00 2.43
2495 2821 1.535028 CGCATCACTAAAACTGCCACA 59.465 47.619 0.00 0.00 0.00 4.17
2501 2827 5.392767 TCACTAAAACTGCCACACAAAAA 57.607 34.783 0.00 0.00 0.00 1.94
2530 2856 2.830104 GATTTGCCATGCTCAAATCCC 58.170 47.619 25.48 13.11 46.92 3.85
2531 2857 0.531657 TTTGCCATGCTCAAATCCCG 59.468 50.000 7.11 0.00 0.00 5.14
2534 2860 1.035139 GCCATGCTCAAATCCCGAAT 58.965 50.000 0.00 0.00 0.00 3.34
2555 2881 3.660959 TGTTCGGGATTTATAGGGGTCT 58.339 45.455 0.00 0.00 0.00 3.85
2568 2894 8.893563 TTTATAGGGGTCTTTGTTGAAATCAT 57.106 30.769 0.00 0.00 0.00 2.45
2570 2896 5.473066 AGGGGTCTTTGTTGAAATCATTG 57.527 39.130 0.00 0.00 0.00 2.82
2609 2936 1.269309 CGGTGTTCATTTCGGCCAAAA 60.269 47.619 2.24 0.00 0.00 2.44
2611 2938 2.403259 GTGTTCATTTCGGCCAAAAGG 58.597 47.619 2.24 0.00 0.00 3.11
2612 2939 2.035321 GTGTTCATTTCGGCCAAAAGGA 59.965 45.455 0.00 0.00 0.00 3.36
2613 2940 2.035321 TGTTCATTTCGGCCAAAAGGAC 59.965 45.455 2.34 5.37 29.49 3.85
2615 2942 2.311463 TCATTTCGGCCAAAAGGACAA 58.689 42.857 0.00 0.00 0.00 3.18
2618 2955 2.880963 TTCGGCCAAAAGGACAAAAG 57.119 45.000 2.24 0.00 0.00 2.27
2623 2960 3.677424 CGGCCAAAAGGACAAAAGTTTCA 60.677 43.478 2.24 0.00 0.00 2.69
2653 2990 8.783093 TGAATTTGACTGAGATACAACGATTTT 58.217 29.630 0.00 0.00 0.00 1.82
2706 3044 5.705813 TTATGTGTACTACCGAAATTGCG 57.294 39.130 0.00 0.00 0.00 4.85
2707 3045 3.029320 TGTGTACTACCGAAATTGCGT 57.971 42.857 4.84 0.00 0.00 5.24
2712 3050 5.955496 GTGTACTACCGAAATTGCGTAAATG 59.045 40.000 4.84 0.00 0.00 2.32
2725 3063 6.735263 TTGCGTAAATGTTTTAACCGAAAG 57.265 33.333 0.00 0.00 0.00 2.62
2757 3095 4.574892 TCAGTATGTGCCGAAATTTCTCA 58.425 39.130 15.92 10.54 37.40 3.27
2774 3112 3.646534 TCTCAGATTCCTGGACTGCATA 58.353 45.455 8.96 0.00 40.76 3.14
2805 3143 3.824133 TGGAAGGATTGTCCATATGCTG 58.176 45.455 0.00 0.00 40.33 4.41
2807 3145 4.070716 GGAAGGATTGTCCATATGCTGAG 58.929 47.826 0.00 0.00 39.61 3.35
2810 3148 2.551459 GGATTGTCCATATGCTGAGCAC 59.449 50.000 10.33 0.00 37.74 4.40
2811 3149 2.042686 TTGTCCATATGCTGAGCACC 57.957 50.000 10.33 0.00 43.04 5.01
2855 3193 7.441890 TTTTTGAAGTAGTTGTGTCACAAGA 57.558 32.000 18.70 7.35 39.00 3.02
2856 3194 6.417191 TTTGAAGTAGTTGTGTCACAAGAC 57.583 37.500 18.70 17.94 39.00 3.01
2861 3199 3.914426 AGTTGTGTCACAAGACCTCTT 57.086 42.857 18.70 0.00 44.33 2.85
2864 3202 5.930135 AGTTGTGTCACAAGACCTCTTAAT 58.070 37.500 18.70 0.00 44.33 1.40
2883 3221 8.519799 TCTTAATTTGACACTCTTTCTTTGGT 57.480 30.769 0.00 0.00 0.00 3.67
2887 3225 3.950397 TGACACTCTTTCTTTGGTGTGT 58.050 40.909 2.28 0.00 42.01 3.72
2902 3240 2.802816 GGTGTGTCAGTGTCTCACAATC 59.197 50.000 19.29 11.66 42.39 2.67
2910 3248 5.410746 GTCAGTGTCTCACAATCACATCAAT 59.589 40.000 2.80 0.00 36.74 2.57
2923 3261 1.062258 CATCAATGTGTTGCAACGGC 58.938 50.000 23.79 18.76 41.68 5.68
2927 3265 1.805428 AATGTGTTGCAACGGCCTCC 61.805 55.000 23.79 8.34 40.13 4.30
2940 3278 0.960364 GGCCTCCATTGTTTGCGAGA 60.960 55.000 0.00 0.00 0.00 4.04
2951 3289 1.601903 GTTTGCGAGATTGTGTGTGGA 59.398 47.619 0.00 0.00 0.00 4.02
2960 3298 3.328931 AGATTGTGTGTGGACCAAGATCT 59.671 43.478 0.00 0.00 0.00 2.75
2964 3302 0.798776 GTGTGGACCAAGATCTTGCG 59.201 55.000 27.01 21.61 39.16 4.85
2970 3308 0.593128 ACCAAGATCTTGCGTGCAAC 59.407 50.000 27.01 0.00 39.16 4.17
2975 3313 2.069273 AGATCTTGCGTGCAACTACAC 58.931 47.619 2.58 0.00 37.19 2.90
2976 3314 1.798223 GATCTTGCGTGCAACTACACA 59.202 47.619 2.58 0.00 40.73 3.72
3012 3350 9.847706 CGTGAGTATAGCATGAGATACTATTTT 57.152 33.333 15.94 0.10 38.66 1.82
3041 3379 4.021981 TGCTGTGATGGTATCTATCCTTCG 60.022 45.833 0.00 0.00 33.57 3.79
3049 3387 3.005578 GGTATCTATCCTTCGTGGGTGAC 59.994 52.174 0.00 0.00 36.20 3.67
3074 3412 5.627499 TTTTCAAGACCATTTCTGATCCG 57.373 39.130 0.00 0.00 33.46 4.18
3084 3422 9.095989 AGACCATTTCTGATCCGATAGGTAACC 62.096 44.444 5.91 0.00 46.11 2.85
3118 3458 8.327832 CTTTTCAGCAAAGTAAAAGTGTACTG 57.672 34.615 0.00 0.00 37.67 2.74
3143 3483 1.446907 GATGTGGAGAGTGCACCAAG 58.553 55.000 14.63 0.00 37.97 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.035442 GCTCACGGCCAGGTCTTTC 61.035 63.158 2.24 0.00 34.27 2.62
98 99 9.476202 CACAAGTTATAGCACACTAATAGCATA 57.524 33.333 0.00 0.00 30.45 3.14
100 101 7.327975 ACACAAGTTATAGCACACTAATAGCA 58.672 34.615 0.00 0.00 30.45 3.49
101 102 7.772332 ACACAAGTTATAGCACACTAATAGC 57.228 36.000 0.00 0.00 30.45 2.97
134 135 4.137543 CAAAATATAGCGAGGCCCTTCTT 58.862 43.478 0.00 0.00 0.00 2.52
178 179 6.150140 ACTTAGAGACTGCATGTCCATTTTTC 59.850 38.462 11.24 3.87 46.46 2.29
185 186 2.164624 ACGACTTAGAGACTGCATGTCC 59.835 50.000 11.24 5.25 46.46 4.02
359 360 1.893786 CTAGAACCGGCAGAGTGCT 59.106 57.895 0.00 0.00 44.28 4.40
361 362 1.591703 TGCTAGAACCGGCAGAGTG 59.408 57.895 0.00 0.00 34.22 3.51
367 368 1.592939 GCTAGCTGCTAGAACCGGC 60.593 63.158 34.43 18.46 36.26 6.13
368 369 1.068250 GGCTAGCTGCTAGAACCGG 59.932 63.158 34.43 13.01 42.39 5.28
454 471 3.326747 ACACTCTTGTCTATCAAACCGC 58.673 45.455 0.00 0.00 35.48 5.68
703 740 0.175302 CATGCTGACGAGCTTCTCCT 59.825 55.000 0.00 0.00 46.39 3.69
888 925 4.332828 TCGAGACCACTCTTGATGTTAGA 58.667 43.478 0.00 0.00 40.65 2.10
890 927 4.156190 GTCTCGAGACCACTCTTGATGTTA 59.844 45.833 31.24 0.00 40.65 2.41
931 968 0.671163 TTTTACGATCTTGCGGCCGT 60.671 50.000 28.70 5.80 38.82 5.68
941 978 0.232303 CGCTGCGGGATTTTACGATC 59.768 55.000 15.40 0.00 0.00 3.69
975 1012 2.126307 CTGCAGACCGTCGGACAG 60.126 66.667 20.51 14.98 0.00 3.51
1071 1108 4.759693 AGAGATAGATCGAGCAGTTACCTG 59.240 45.833 2.38 0.00 41.91 4.00
1077 1114 1.885887 GGCAGAGATAGATCGAGCAGT 59.114 52.381 2.38 0.00 0.00 4.40
1078 1115 2.161855 AGGCAGAGATAGATCGAGCAG 58.838 52.381 2.38 0.00 0.00 4.24
1080 1132 2.097466 GCTAGGCAGAGATAGATCGAGC 59.903 54.545 0.00 0.00 0.00 5.03
1084 1136 5.467035 ACTTTGCTAGGCAGAGATAGATC 57.533 43.478 15.22 0.00 42.32 2.75
1090 1142 1.552337 CTGGACTTTGCTAGGCAGAGA 59.448 52.381 15.22 0.00 42.32 3.10
1093 1145 0.035630 AGCTGGACTTTGCTAGGCAG 60.036 55.000 0.00 0.00 40.61 4.85
1095 1147 0.322008 ACAGCTGGACTTTGCTAGGC 60.322 55.000 19.93 0.00 37.81 3.93
1096 1148 2.191128 AACAGCTGGACTTTGCTAGG 57.809 50.000 19.93 0.00 37.81 3.02
1102 1166 3.222603 CCACCTTAAACAGCTGGACTTT 58.777 45.455 19.93 12.07 0.00 2.66
1110 1174 5.428253 TCATCTATCACCACCTTAAACAGC 58.572 41.667 0.00 0.00 0.00 4.40
1121 1196 5.306160 TCATCAGCTTCATCATCTATCACCA 59.694 40.000 0.00 0.00 0.00 4.17
1122 1197 5.791666 TCATCAGCTTCATCATCTATCACC 58.208 41.667 0.00 0.00 0.00 4.02
1123 1198 7.908827 AATCATCAGCTTCATCATCTATCAC 57.091 36.000 0.00 0.00 0.00 3.06
1126 1201 9.616156 GGATAAATCATCAGCTTCATCATCTAT 57.384 33.333 0.00 0.00 35.11 1.98
1127 1202 8.045507 GGGATAAATCATCAGCTTCATCATCTA 58.954 37.037 0.00 0.00 35.11 1.98
1128 1203 6.885376 GGGATAAATCATCAGCTTCATCATCT 59.115 38.462 0.00 0.00 35.11 2.90
1137 1212 6.658391 GCTAGAAATGGGATAAATCATCAGCT 59.342 38.462 0.00 0.00 35.11 4.24
1147 1222 5.126067 GTTGAGCAGCTAGAAATGGGATAA 58.874 41.667 0.00 0.00 0.00 1.75
1149 1224 3.549794 GTTGAGCAGCTAGAAATGGGAT 58.450 45.455 0.00 0.00 0.00 3.85
1151 1226 1.667724 CGTTGAGCAGCTAGAAATGGG 59.332 52.381 0.00 0.00 0.00 4.00
1152 1227 2.349886 GTCGTTGAGCAGCTAGAAATGG 59.650 50.000 0.00 0.00 0.00 3.16
1153 1228 2.995939 TGTCGTTGAGCAGCTAGAAATG 59.004 45.455 0.00 0.00 0.00 2.32
1154 1229 3.319137 TGTCGTTGAGCAGCTAGAAAT 57.681 42.857 0.00 0.00 0.00 2.17
1156 1231 2.732282 CGATGTCGTTGAGCAGCTAGAA 60.732 50.000 0.00 0.00 34.11 2.10
1198 1289 0.665369 CCACCACGGTACTGAACGTC 60.665 60.000 9.17 0.00 42.04 4.34
1645 1742 2.735772 GGCCTTCCTGATCGCCTCA 61.736 63.158 0.00 0.00 38.41 3.86
2266 2400 7.246171 ACAGATGGATATTGGATGGTAGTAC 57.754 40.000 0.00 0.00 0.00 2.73
2267 2401 7.872061 AACAGATGGATATTGGATGGTAGTA 57.128 36.000 0.00 0.00 0.00 1.82
2268 2402 6.770286 AACAGATGGATATTGGATGGTAGT 57.230 37.500 0.00 0.00 0.00 2.73
2372 2517 4.330074 AGAAAAAGAATGTAGACGCATCCG 59.670 41.667 0.00 0.00 41.14 4.18
2390 2535 9.691362 GCTGGTTAAAATACAGAAATGAGAAAA 57.309 29.630 0.00 0.00 34.21 2.29
2401 2546 9.744468 AAAGTAAACAAGCTGGTTAAAATACAG 57.256 29.630 6.98 0.00 30.39 2.74
2422 2567 9.278978 TGACAAATCAGTGCTTAATGTAAAGTA 57.721 29.630 0.00 0.00 0.00 2.24
2424 2569 9.069078 CATGACAAATCAGTGCTTAATGTAAAG 57.931 33.333 0.00 0.00 38.57 1.85
2430 2575 5.909621 AGCATGACAAATCAGTGCTTAAT 57.090 34.783 0.00 0.00 42.25 1.40
2431 2576 5.463286 CAAGCATGACAAATCAGTGCTTAA 58.537 37.500 18.14 0.00 46.46 1.85
2468 2794 3.009723 AGTTTTAGTGATGCGTGGATGG 58.990 45.455 0.00 0.00 0.00 3.51
2477 2803 4.566545 TTGTGTGGCAGTTTTAGTGATG 57.433 40.909 0.00 0.00 0.00 3.07
2478 2804 5.590530 TTTTGTGTGGCAGTTTTAGTGAT 57.409 34.783 0.00 0.00 0.00 3.06
2501 2827 5.064558 TGAGCATGGCAAATCAAATGTTTT 58.935 33.333 0.00 0.00 0.00 2.43
2502 2828 4.643463 TGAGCATGGCAAATCAAATGTTT 58.357 34.783 0.00 0.00 0.00 2.83
2503 2829 4.274602 TGAGCATGGCAAATCAAATGTT 57.725 36.364 0.00 0.00 0.00 2.71
2504 2830 3.965379 TGAGCATGGCAAATCAAATGT 57.035 38.095 0.00 0.00 0.00 2.71
2505 2831 5.811399 ATTTGAGCATGGCAAATCAAATG 57.189 34.783 24.76 7.23 45.73 2.32
2514 2840 0.323269 TTCGGGATTTGAGCATGGCA 60.323 50.000 0.00 0.00 0.00 4.92
2531 2857 4.981812 ACCCCTATAAATCCCGAACATTC 58.018 43.478 0.00 0.00 0.00 2.67
2534 2860 3.660959 AGACCCCTATAAATCCCGAACA 58.339 45.455 0.00 0.00 0.00 3.18
2548 2874 4.901250 ACAATGATTTCAACAAAGACCCCT 59.099 37.500 0.00 0.00 0.00 4.79
2609 2936 8.093927 TCAAATTCAAGTTGAAACTTTTGTCCT 58.906 29.630 26.83 8.41 46.52 3.85
2611 2938 8.925700 AGTCAAATTCAAGTTGAAACTTTTGTC 58.074 29.630 26.83 23.71 46.52 3.18
2612 2939 8.711457 CAGTCAAATTCAAGTTGAAACTTTTGT 58.289 29.630 26.83 15.60 46.52 2.83
2613 2940 8.924691 TCAGTCAAATTCAAGTTGAAACTTTTG 58.075 29.630 24.48 24.48 46.52 2.44
2615 2942 8.522830 TCTCAGTCAAATTCAAGTTGAAACTTT 58.477 29.630 21.57 15.20 46.52 2.66
2618 2955 9.387123 GTATCTCAGTCAAATTCAAGTTGAAAC 57.613 33.333 21.57 14.78 40.12 2.78
2623 2960 7.441157 TCGTTGTATCTCAGTCAAATTCAAGTT 59.559 33.333 0.00 0.00 0.00 2.66
2698 3036 7.323046 TCGGTTAAAACATTTACGCAATTTC 57.677 32.000 0.00 0.00 0.00 2.17
2725 3063 6.371809 TCGGCACATACTGAAATAATTTCC 57.628 37.500 0.00 0.00 38.90 3.13
2740 3078 4.096984 GGAATCTGAGAAATTTCGGCACAT 59.903 41.667 12.42 5.93 0.00 3.21
2744 3082 3.065925 CCAGGAATCTGAGAAATTTCGGC 59.934 47.826 12.42 9.41 43.49 5.54
2757 3095 3.110705 AGTGTATGCAGTCCAGGAATCT 58.889 45.455 0.00 0.00 0.00 2.40
2805 3143 1.583054 CCTTAGTATTGGCGGTGCTC 58.417 55.000 0.00 0.00 0.00 4.26
2807 3145 2.022520 GCCTTAGTATTGGCGGTGC 58.977 57.895 0.00 0.00 39.71 5.01
2833 3171 5.353123 GGTCTTGTGACACAACTACTTCAAA 59.647 40.000 17.02 0.00 44.61 2.69
2855 3193 8.624776 CAAAGAAAGAGTGTCAAATTAAGAGGT 58.375 33.333 0.00 0.00 0.00 3.85
2856 3194 8.078596 CCAAAGAAAGAGTGTCAAATTAAGAGG 58.921 37.037 0.00 0.00 0.00 3.69
2861 3199 7.122055 ACACACCAAAGAAAGAGTGTCAAATTA 59.878 33.333 0.00 0.00 41.35 1.40
2864 3202 4.764823 ACACACCAAAGAAAGAGTGTCAAA 59.235 37.500 0.00 0.00 41.35 2.69
2883 3221 3.118811 TGTGATTGTGAGACACTGACACA 60.119 43.478 16.46 16.46 41.70 3.72
2887 3225 4.605640 TGATGTGATTGTGAGACACTGA 57.394 40.909 0.00 0.00 35.11 3.41
2910 3248 2.904866 GGAGGCCGTTGCAACACA 60.905 61.111 28.01 0.00 40.13 3.72
2919 3257 2.625823 CGCAAACAATGGAGGCCGT 61.626 57.895 0.00 0.00 0.00 5.68
2923 3261 2.489329 ACAATCTCGCAAACAATGGAGG 59.511 45.455 0.00 0.00 31.21 4.30
2927 3265 3.422876 CACACACAATCTCGCAAACAATG 59.577 43.478 0.00 0.00 0.00 2.82
2940 3278 3.795688 AGATCTTGGTCCACACACAAT 57.204 42.857 0.00 0.00 0.00 2.71
2951 3289 0.593128 GTTGCACGCAAGATCTTGGT 59.407 50.000 31.41 24.40 40.74 3.67
2964 3302 4.173256 GCCCATTAATTGTGTAGTTGCAC 58.827 43.478 0.00 0.00 39.65 4.57
2970 3308 3.938963 ACTCACGCCCATTAATTGTGTAG 59.061 43.478 1.69 4.10 32.55 2.74
2975 3313 4.754618 TGCTATACTCACGCCCATTAATTG 59.245 41.667 0.00 0.00 0.00 2.32
2976 3314 4.968259 TGCTATACTCACGCCCATTAATT 58.032 39.130 0.00 0.00 0.00 1.40
3012 3350 7.071196 AGGATAGATACCATCACAGCAAAACTA 59.929 37.037 0.00 0.00 0.00 2.24
3013 3351 6.058183 GGATAGATACCATCACAGCAAAACT 58.942 40.000 0.00 0.00 0.00 2.66
3014 3352 6.058183 AGGATAGATACCATCACAGCAAAAC 58.942 40.000 0.00 0.00 0.00 2.43
3015 3353 6.252599 AGGATAGATACCATCACAGCAAAA 57.747 37.500 0.00 0.00 0.00 2.44
3016 3354 5.894298 AGGATAGATACCATCACAGCAAA 57.106 39.130 0.00 0.00 0.00 3.68
3017 3355 5.509670 CGAAGGATAGATACCATCACAGCAA 60.510 44.000 0.00 0.00 0.00 3.91
3018 3356 4.021981 CGAAGGATAGATACCATCACAGCA 60.022 45.833 0.00 0.00 0.00 4.41
3019 3357 4.021894 ACGAAGGATAGATACCATCACAGC 60.022 45.833 0.00 0.00 0.00 4.40
3020 3358 5.465051 CACGAAGGATAGATACCATCACAG 58.535 45.833 0.00 0.00 0.00 3.66
3041 3379 2.361119 GGTCTTGAAAAAGGTCACCCAC 59.639 50.000 0.00 0.00 0.00 4.61
3049 3387 6.393171 GGATCAGAAATGGTCTTGAAAAAGG 58.607 40.000 0.00 0.00 32.70 3.11
3050 3388 6.072508 TCGGATCAGAAATGGTCTTGAAAAAG 60.073 38.462 0.00 0.00 32.70 2.27
3056 3394 4.993584 CCTATCGGATCAGAAATGGTCTTG 59.006 45.833 0.00 0.00 32.70 3.02
3074 3412 9.626045 CTGAAAAGTGATTTTTGGTTACCTATC 57.374 33.333 2.07 1.72 39.06 2.08
3106 3446 6.001460 CCACATCCTTTCCAGTACACTTTTA 58.999 40.000 0.00 0.00 0.00 1.52
3112 3452 3.515502 CTCTCCACATCCTTTCCAGTACA 59.484 47.826 0.00 0.00 0.00 2.90
3118 3458 1.003580 TGCACTCTCCACATCCTTTCC 59.996 52.381 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.