Multiple sequence alignment - TraesCS4D01G239800

Loading Multiple Alignment...

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 TraesCS4D01G239800 chr4D 100.000 3604 0 0 1 3604 402231300 402234903 0.000000e+00 6656
1 TraesCS4D01G239800 chr4B 90.432 2822 146 70 408 3175 497859603 497862354 0.000000e+00 3602
2 TraesCS4D01G239800 chr4B 92.343 431 15 4 3175 3604 497862388 497862801 6.660000e-167 597
3 TraesCS4D01G239800 chr4B 92.157 408 21 4 1 403 497858864 497859265 1.880000e-157 566
4 TraesCS4D01G239800 chr4A 92.579 2210 93 32 998 3176 59670021 59672190 0.000000e+00 3107
5 TraesCS4D01G239800 chr4A 89.495 990 43 18 1 957 59669050 59670011 0.000000e+00 1195
6 TraesCS4D01G239800 chr4A 92.677 396 12 6 3209 3604 59672286 59672664 4.070000e-154 555
7 TraesCS4D01G239800 chr1A 81.633 245 38 6 2201 2440 550111016 550111258 2.840000e-46 196
8 TraesCS4D01G239800 chr1B 80.658 243 40 6 2203 2440 627098788 627099028 7.950000e-42 182
9 TraesCS4D01G239800 chr1D 80.242 248 32 12 2203 2440 457530372 457530132 1.720000e-38 171


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 TraesCS4D01G239800 chr4D 402231300 402234903 3603 False 6656.000000 6656 100.000000 1 3604 1 chr4D.!!$F1 3603
1 TraesCS4D01G239800 chr4B 497858864 497862801 3937 False 1588.333333 3602 91.644000 1 3604 3 chr4B.!!$F1 3603
2 TraesCS4D01G239800 chr4A 59669050 59672664 3614 False 1619.000000 3107 91.583667 1 3604 3 chr4A.!!$F1 3603

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
447 788 0.038159 AGTGACGCTGCTACAGTTCC 60.038 55.0 0.00 0.00 33.43 3.62 F
788 1161 0.391927 ATTGTGTGCAATGCCATGCC 60.392 50.0 1.53 1.49 45.83 4.40 F
2135 2544 0.250124 CGGCCACCAACAAGTGAGTA 60.250 55.0 2.24 0.00 40.34 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1740 0.251165 ACCGTTCCCACCATTCAAGG 60.251 55.0 0.00 0.00 0.00 3.61 R
2210 2631 0.317938 GCACGATCTCCGCGAGTATT 60.318 55.0 8.23 0.00 43.32 1.89 R
3491 4039 0.253044 ACATCCAGGACATGTTCGGG 59.747 55.0 16.71 16.71 29.75 5.14 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
37 38 5.084519 AGGATAGGCTTTATACATCCACGA 58.915 41.667 12.91 0.00 38.10 4.35
55 56 3.001228 CACGACGGAACAATATGGTGATG 59.999 47.826 0.00 0.00 0.00 3.07
130 135 0.882927 TGTTCTGCCTTGCGTGGTAC 60.883 55.000 0.00 0.00 0.00 3.34
191 197 3.988379 TGGAAGTGTCATTCTTGTTGC 57.012 42.857 0.00 0.00 0.00 4.17
247 253 4.905429 TCTGTTCTATGGCTTGTGCTTTA 58.095 39.130 0.00 0.00 39.59 1.85
331 337 5.358298 GTGACCACACTTCTAAAATGTCC 57.642 43.478 0.00 0.00 42.99 4.02
447 788 0.038159 AGTGACGCTGCTACAGTTCC 60.038 55.000 0.00 0.00 33.43 3.62
507 848 1.337071 TGCGAATGGCCGTTTAAAACA 59.663 42.857 12.53 3.49 42.61 2.83
508 849 2.029828 TGCGAATGGCCGTTTAAAACAT 60.030 40.909 12.53 0.00 42.61 2.71
509 850 3.190744 TGCGAATGGCCGTTTAAAACATA 59.809 39.130 12.53 0.00 42.61 2.29
548 889 1.871039 TGTTAAACGAGGCTGCTTGTC 59.129 47.619 0.00 0.00 0.00 3.18
564 905 5.527033 TGCTTGTCGATGATTCTCTATCTG 58.473 41.667 0.00 0.00 34.17 2.90
594 941 4.925054 CCCTTTATTGAAATATGCATGCGG 59.075 41.667 14.09 2.30 0.00 5.69
740 1113 4.513442 ACTTACAATAATTCAGCGGCAGA 58.487 39.130 1.45 0.00 0.00 4.26
741 1114 4.941263 ACTTACAATAATTCAGCGGCAGAA 59.059 37.500 10.30 10.30 0.00 3.02
742 1115 5.065218 ACTTACAATAATTCAGCGGCAGAAG 59.935 40.000 13.27 2.43 0.00 2.85
788 1161 0.391927 ATTGTGTGCAATGCCATGCC 60.392 50.000 1.53 1.49 45.83 4.40
792 1165 1.590525 GTGCAATGCCATGCCATCG 60.591 57.895 1.53 0.00 45.83 3.84
878 1268 2.356069 CTGTTGATCTCATCTCCGTCGA 59.644 50.000 0.00 0.00 0.00 4.20
879 1269 2.356069 TGTTGATCTCATCTCCGTCGAG 59.644 50.000 0.00 0.00 37.48 4.04
988 1378 3.230245 CGCTGGCTAGGGAGAGGG 61.230 72.222 8.58 0.00 39.07 4.30
1315 1705 2.861006 GCGTCTCCGGCACTTTTC 59.139 61.111 0.00 0.00 33.68 2.29
1330 1720 0.603707 TTTTCTCCAGGTCAGCAGCG 60.604 55.000 0.00 0.00 0.00 5.18
1331 1721 3.596066 TTCTCCAGGTCAGCAGCGC 62.596 63.158 0.00 0.00 0.00 5.92
1332 1722 4.383861 CTCCAGGTCAGCAGCGCA 62.384 66.667 11.47 0.00 0.00 6.09
1333 1723 3.677284 CTCCAGGTCAGCAGCGCAT 62.677 63.158 11.47 0.00 0.00 4.73
1346 1736 2.827190 CGCATGCAGCCACCTCAT 60.827 61.111 19.57 0.00 41.38 2.90
1347 1737 2.805546 GCATGCAGCCACCTCATG 59.194 61.111 14.21 0.00 40.23 3.07
1348 1738 2.050350 GCATGCAGCCACCTCATGT 61.050 57.895 14.21 0.00 39.64 3.21
1350 1740 0.454600 CATGCAGCCACCTCATGTTC 59.545 55.000 0.00 0.00 34.48 3.18
1358 1755 2.165030 GCCACCTCATGTTCCTTGAATG 59.835 50.000 0.00 0.00 0.00 2.67
1361 1758 3.192001 CACCTCATGTTCCTTGAATGGTG 59.808 47.826 0.00 0.00 36.85 4.17
1363 1760 2.756760 CTCATGTTCCTTGAATGGTGGG 59.243 50.000 0.00 0.00 0.00 4.61
1370 1767 1.003812 CCTTGAATGGTGGGAACGGTA 59.996 52.381 0.00 0.00 0.00 4.02
1371 1768 2.553466 CCTTGAATGGTGGGAACGGTAA 60.553 50.000 0.00 0.00 0.00 2.85
1372 1769 2.953284 TGAATGGTGGGAACGGTAAA 57.047 45.000 0.00 0.00 0.00 2.01
1373 1770 2.506444 TGAATGGTGGGAACGGTAAAC 58.494 47.619 0.00 0.00 0.00 2.01
1377 1774 1.232119 GGTGGGAACGGTAAACACTG 58.768 55.000 8.30 0.00 32.88 3.66
1379 1776 0.470766 TGGGAACGGTAAACACTGCT 59.529 50.000 0.00 0.00 0.00 4.24
1380 1777 1.693062 TGGGAACGGTAAACACTGCTA 59.307 47.619 0.00 0.00 0.00 3.49
1381 1778 2.104451 TGGGAACGGTAAACACTGCTAA 59.896 45.455 0.00 0.00 0.00 3.09
1382 1779 3.140623 GGGAACGGTAAACACTGCTAAA 58.859 45.455 0.00 0.00 0.00 1.85
1384 1781 4.530388 GGAACGGTAAACACTGCTAAAAC 58.470 43.478 0.00 0.00 0.00 2.43
1386 1783 4.541085 ACGGTAAACACTGCTAAAACAC 57.459 40.909 0.00 0.00 0.00 3.32
1397 1806 5.395486 CACTGCTAAAACACGCTACTTTTTC 59.605 40.000 0.00 0.00 0.00 2.29
1415 1824 2.732468 CAGATGGCGATCGCGAGG 60.732 66.667 31.76 18.33 43.06 4.63
1673 2082 2.915659 ACGTGGTTCCTCGCCTCA 60.916 61.111 12.23 0.00 0.00 3.86
2111 2520 1.003355 CTTCGTCATGCCCTGGTGT 60.003 57.895 0.00 0.00 0.00 4.16
2135 2544 0.250124 CGGCCACCAACAAGTGAGTA 60.250 55.000 2.24 0.00 40.34 2.59
2136 2545 1.523758 GGCCACCAACAAGTGAGTAG 58.476 55.000 0.00 0.00 40.34 2.57
2137 2546 1.202770 GGCCACCAACAAGTGAGTAGT 60.203 52.381 0.00 0.00 40.34 2.73
2138 2547 2.143925 GCCACCAACAAGTGAGTAGTC 58.856 52.381 0.00 0.00 40.34 2.59
2139 2548 2.224305 GCCACCAACAAGTGAGTAGTCT 60.224 50.000 0.00 0.00 40.34 3.24
2184 2605 2.867333 CTTTGCATGCTCCGCTGCTG 62.867 60.000 20.33 0.00 39.16 4.41
2210 2631 4.299796 GGGTCCCTTTGCAGCCCA 62.300 66.667 0.00 0.00 39.13 5.36
2351 2772 2.960129 GGATACAAGCCGGCGTCG 60.960 66.667 23.20 16.08 0.00 5.12
2386 2807 4.367023 TGAACGGGAGAACGCCGG 62.367 66.667 0.00 0.00 37.37 6.13
2477 2898 0.896479 TCTACTGCACGTACCCAGCA 60.896 55.000 9.23 4.00 36.72 4.41
2483 2904 1.079819 CACGTACCCAGCAGACAGG 60.080 63.158 0.00 0.00 0.00 4.00
2508 2929 2.263852 CGCAGAAGGCAGCTCTGA 59.736 61.111 14.42 0.00 42.51 3.27
2516 2937 4.233635 GCAGCTCTGATTGCGCCG 62.234 66.667 4.18 0.00 35.28 6.46
2535 2956 2.408050 CGGAAGAACAGGACTGTGAAG 58.592 52.381 5.63 0.00 44.13 3.02
2617 3038 7.168972 CAGAAGTGACTAGCAACATATCTAAGC 59.831 40.741 0.00 0.00 0.00 3.09
2618 3039 6.471233 AGTGACTAGCAACATATCTAAGCA 57.529 37.500 0.00 0.00 0.00 3.91
2619 3040 7.060383 AGTGACTAGCAACATATCTAAGCAT 57.940 36.000 0.00 0.00 0.00 3.79
2620 3041 8.183104 AGTGACTAGCAACATATCTAAGCATA 57.817 34.615 0.00 0.00 0.00 3.14
2622 3043 8.300286 GTGACTAGCAACATATCTAAGCATAGA 58.700 37.037 0.38 0.38 42.23 1.98
2624 3045 9.299963 GACTAGCAACATATCTAAGCATAGATG 57.700 37.037 19.27 9.36 46.15 2.90
2625 3046 9.029368 ACTAGCAACATATCTAAGCATAGATGA 57.971 33.333 19.27 6.25 46.15 2.92
2626 3047 9.866798 CTAGCAACATATCTAAGCATAGATGAA 57.133 33.333 19.27 3.19 46.15 2.57
2629 3050 9.770503 GCAACATATCTAAGCATAGATGAAATG 57.229 33.333 19.27 16.52 46.15 2.32
2636 3057 7.955918 TCTAAGCATAGATGAAATGACTAGCA 58.044 34.615 0.00 0.00 33.17 3.49
2637 3058 8.424133 TCTAAGCATAGATGAAATGACTAGCAA 58.576 33.333 0.00 0.00 33.17 3.91
2638 3059 6.857777 AGCATAGATGAAATGACTAGCAAC 57.142 37.500 0.00 0.00 0.00 4.17
2639 3060 6.351711 AGCATAGATGAAATGACTAGCAACA 58.648 36.000 0.00 0.00 0.00 3.33
2640 3061 6.996879 AGCATAGATGAAATGACTAGCAACAT 59.003 34.615 0.00 0.00 0.00 2.71
2641 3062 8.152898 AGCATAGATGAAATGACTAGCAACATA 58.847 33.333 0.00 0.00 0.00 2.29
2642 3063 8.944029 GCATAGATGAAATGACTAGCAACATAT 58.056 33.333 0.00 0.00 0.00 1.78
2649 3070 9.534565 TGAAATGACTAGCAACATATCTAAGAC 57.465 33.333 0.00 0.00 0.00 3.01
2650 3071 9.757227 GAAATGACTAGCAACATATCTAAGACT 57.243 33.333 0.00 0.00 0.00 3.24
2653 3074 7.877003 TGACTAGCAACATATCTAAGACTAGC 58.123 38.462 0.00 0.00 31.22 3.42
2654 3075 7.040340 TGACTAGCAACATATCTAAGACTAGCC 60.040 40.741 0.00 0.00 31.22 3.93
2655 3076 6.778069 ACTAGCAACATATCTAAGACTAGCCA 59.222 38.462 0.00 0.00 31.22 4.75
2656 3077 6.485830 AGCAACATATCTAAGACTAGCCAA 57.514 37.500 0.00 0.00 0.00 4.52
2667 3090 7.001674 TCTAAGACTAGCCAAATGGACAAAAA 58.998 34.615 2.98 0.00 37.39 1.94
2739 3201 8.503458 ACAGCCATATATTCAAGAATAGATGC 57.497 34.615 22.67 18.91 44.97 3.91
2740 3202 8.105197 ACAGCCATATATTCAAGAATAGATGCA 58.895 33.333 22.67 0.00 44.97 3.96
2741 3203 8.953313 CAGCCATATATTCAAGAATAGATGCAA 58.047 33.333 22.67 0.00 44.97 4.08
2742 3204 9.696572 AGCCATATATTCAAGAATAGATGCAAT 57.303 29.630 22.67 12.81 44.97 3.56
2748 3210 9.831737 ATATTCAAGAATAGATGCAATTTACGC 57.168 29.630 8.34 0.00 36.79 4.42
2749 3211 5.737353 TCAAGAATAGATGCAATTTACGCG 58.263 37.500 3.53 3.53 0.00 6.01
2750 3212 4.133856 AGAATAGATGCAATTTACGCGC 57.866 40.909 5.73 0.00 0.00 6.86
2751 3213 3.809832 AGAATAGATGCAATTTACGCGCT 59.190 39.130 5.73 0.00 0.00 5.92
2752 3214 4.988540 AGAATAGATGCAATTTACGCGCTA 59.011 37.500 5.73 0.00 0.00 4.26
2753 3215 5.639506 AGAATAGATGCAATTTACGCGCTAT 59.360 36.000 5.73 0.00 33.59 2.97
2754 3216 6.811665 AGAATAGATGCAATTTACGCGCTATA 59.188 34.615 5.73 0.00 32.58 1.31
2755 3217 4.647291 AGATGCAATTTACGCGCTATAC 57.353 40.909 5.73 0.00 0.00 1.47
2756 3218 4.055360 AGATGCAATTTACGCGCTATACA 58.945 39.130 5.73 0.00 0.00 2.29
2757 3219 3.852471 TGCAATTTACGCGCTATACAG 57.148 42.857 5.73 0.00 0.00 2.74
2758 3220 2.033236 TGCAATTTACGCGCTATACAGC 60.033 45.455 5.73 3.20 44.90 4.40
2759 3221 2.661979 GCAATTTACGCGCTATACAGCC 60.662 50.000 5.73 0.00 45.64 4.85
2760 3222 2.519377 ATTTACGCGCTATACAGCCA 57.481 45.000 5.73 0.00 45.64 4.75
2761 3223 2.519377 TTTACGCGCTATACAGCCAT 57.481 45.000 5.73 0.00 45.64 4.40
2762 3224 3.646611 TTTACGCGCTATACAGCCATA 57.353 42.857 5.73 0.00 45.64 2.74
2763 3225 3.861276 TTACGCGCTATACAGCCATAT 57.139 42.857 5.73 0.00 45.64 1.78
2764 3226 1.996292 ACGCGCTATACAGCCATATG 58.004 50.000 5.73 0.00 45.64 1.78
2765 3227 1.272490 ACGCGCTATACAGCCATATGT 59.728 47.619 5.73 0.00 45.64 2.29
2766 3228 2.288825 ACGCGCTATACAGCCATATGTT 60.289 45.455 5.73 0.00 45.64 2.71
2767 3229 2.345641 CGCGCTATACAGCCATATGTTC 59.654 50.000 5.56 0.00 45.64 3.18
2768 3230 3.325870 GCGCTATACAGCCATATGTTCA 58.674 45.455 0.00 0.00 45.64 3.18
2769 3231 3.745975 GCGCTATACAGCCATATGTTCAA 59.254 43.478 0.00 0.00 45.64 2.69
2770 3232 4.143030 GCGCTATACAGCCATATGTTCAAG 60.143 45.833 0.00 0.00 45.64 3.02
2771 3233 4.389992 CGCTATACAGCCATATGTTCAAGG 59.610 45.833 1.24 0.00 45.64 3.61
2781 3243 4.518211 CCATATGTTCAAGGCAAGATCTCC 59.482 45.833 0.00 0.00 0.00 3.71
2782 3244 2.496899 TGTTCAAGGCAAGATCTCCC 57.503 50.000 0.00 0.00 0.00 4.30
2806 3268 7.068593 CCCATGCAATTCTTAATCCTCTAAACA 59.931 37.037 0.00 0.00 0.00 2.83
2842 3322 2.434336 CACCCCTGATTTCCAGTATCGA 59.566 50.000 0.00 0.00 41.33 3.59
2914 3397 7.611213 AAAATGTTAGATGGGACTAAACGAG 57.389 36.000 0.00 0.00 34.74 4.18
2932 3415 3.069158 ACGAGCACACAAGTTAACTAGGT 59.931 43.478 8.92 7.76 0.00 3.08
3207 3755 5.692115 TGAGCATAATTCACAAGGGTCTA 57.308 39.130 0.00 0.00 0.00 2.59
3226 3774 6.063404 GGTCTATAATAGGCTACGGCTAGAT 58.937 44.000 0.00 2.66 43.64 1.98
3279 3827 1.528129 GCTGCAAGAGCTACCAAGTT 58.472 50.000 0.00 0.00 45.21 2.66
3364 3912 1.555075 AGGGAAAGCGAGATGTTGCTA 59.445 47.619 4.77 0.00 43.28 3.49
3365 3913 1.936547 GGGAAAGCGAGATGTTGCTAG 59.063 52.381 4.77 0.00 43.28 3.42
3366 3914 1.328986 GGAAAGCGAGATGTTGCTAGC 59.671 52.381 8.10 8.10 43.28 3.42
3367 3915 2.275318 GAAAGCGAGATGTTGCTAGCT 58.725 47.619 17.23 0.00 46.64 3.32
3368 3916 1.649664 AAGCGAGATGTTGCTAGCTG 58.350 50.000 17.23 0.00 44.43 4.24
3369 3917 0.820226 AGCGAGATGTTGCTAGCTGA 59.180 50.000 17.23 1.37 43.71 4.26
3415 3963 6.549364 TGTCCAAAAGAAACAGTACCATGAAT 59.451 34.615 0.00 0.00 0.00 2.57
3416 3964 7.721842 TGTCCAAAAGAAACAGTACCATGAATA 59.278 33.333 0.00 0.00 0.00 1.75
3417 3965 8.021396 GTCCAAAAGAAACAGTACCATGAATAC 58.979 37.037 0.00 0.00 0.00 1.89
3491 4039 3.437049 GCCTTCACATCTGTCCACTAAAC 59.563 47.826 0.00 0.00 0.00 2.01
3503 4051 2.081462 CCACTAAACCCGAACATGTCC 58.919 52.381 0.00 0.00 0.00 4.02
3504 4052 2.290071 CCACTAAACCCGAACATGTCCT 60.290 50.000 0.00 0.00 0.00 3.85
3581 4129 0.314935 CATCCACTGCAAAGCGGTTT 59.685 50.000 6.80 6.80 46.97 3.27
3592 4140 2.125952 GCGGTTTGGGATGCAAGC 60.126 61.111 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.997980 TGCATCACCATATTGTTCCGT 58.002 42.857 0.00 0.00 0.00 4.69
41 42 6.322969 ACAATCTCATGCATCACCATATTGTT 59.677 34.615 0.00 0.00 32.28 2.83
42 43 5.831525 ACAATCTCATGCATCACCATATTGT 59.168 36.000 0.00 5.04 31.78 2.71
55 56 4.978083 ACCAAATCTCACAATCTCATGC 57.022 40.909 0.00 0.00 0.00 4.06
170 176 3.953612 AGCAACAAGAATGACACTTCCAA 59.046 39.130 0.00 0.00 0.00 3.53
171 177 3.554934 AGCAACAAGAATGACACTTCCA 58.445 40.909 0.00 0.00 0.00 3.53
172 178 4.276926 AGAAGCAACAAGAATGACACTTCC 59.723 41.667 0.00 0.00 35.04 3.46
173 179 5.429957 AGAAGCAACAAGAATGACACTTC 57.570 39.130 0.00 0.00 34.88 3.01
191 197 2.547913 TTTGCATGTGCGCATAGAAG 57.452 45.000 15.91 6.51 45.83 2.85
253 259 1.923899 TCCATATTTAACGCGCACGA 58.076 45.000 5.73 0.00 43.93 4.35
331 337 2.673368 GTGAAGCGGTGATAACTTGGAG 59.327 50.000 0.00 0.00 0.00 3.86
447 788 4.872124 TGTTCCACAATGATGAGATCTTCG 59.128 41.667 0.00 0.00 0.00 3.79
507 848 5.828747 ACACAGAATGCGTCGTACTATTAT 58.171 37.500 0.00 0.00 42.53 1.28
508 849 5.239359 ACACAGAATGCGTCGTACTATTA 57.761 39.130 0.00 0.00 42.53 0.98
509 850 4.106029 ACACAGAATGCGTCGTACTATT 57.894 40.909 0.00 0.00 42.53 1.73
548 889 8.310382 AGGGTTAAATCAGATAGAGAATCATCG 58.690 37.037 0.00 0.00 37.82 3.84
594 941 2.174424 AGCATCCCTCAGAAAGATTCCC 59.826 50.000 0.00 0.00 0.00 3.97
740 1113 2.135933 CCGCACGTTTCTCTTCTTCTT 58.864 47.619 0.00 0.00 0.00 2.52
741 1114 1.068741 ACCGCACGTTTCTCTTCTTCT 59.931 47.619 0.00 0.00 0.00 2.85
742 1115 1.192534 CACCGCACGTTTCTCTTCTTC 59.807 52.381 0.00 0.00 0.00 2.87
788 1161 2.284684 GCATCTGCACTCTTCTTCGATG 59.715 50.000 0.00 3.21 41.59 3.84
883 1273 2.757212 TCGCTCTCGAGTGAGTCTC 58.243 57.895 18.27 0.00 42.43 3.36
1315 1705 3.677284 ATGCGCTGCTGACCTGGAG 62.677 63.158 9.73 0.00 0.00 3.86
1330 1720 1.601419 AACATGAGGTGGCTGCATGC 61.601 55.000 11.82 11.82 42.28 4.06
1331 1721 0.454600 GAACATGAGGTGGCTGCATG 59.545 55.000 0.00 0.00 43.70 4.06
1332 1722 0.682209 GGAACATGAGGTGGCTGCAT 60.682 55.000 0.00 0.00 0.00 3.96
1333 1723 1.303561 GGAACATGAGGTGGCTGCA 60.304 57.895 0.00 0.00 0.00 4.41
1336 1726 1.067295 TCAAGGAACATGAGGTGGCT 58.933 50.000 0.00 0.00 30.39 4.75
1337 1727 1.909700 TTCAAGGAACATGAGGTGGC 58.090 50.000 0.00 0.00 37.36 5.01
1339 1729 3.192001 CACCATTCAAGGAACATGAGGTG 59.808 47.826 0.00 0.00 42.70 4.00
1340 1730 3.424703 CACCATTCAAGGAACATGAGGT 58.575 45.455 0.00 0.00 37.36 3.85
1341 1731 2.756760 CCACCATTCAAGGAACATGAGG 59.243 50.000 0.00 0.00 37.36 3.86
1342 1732 2.756760 CCCACCATTCAAGGAACATGAG 59.243 50.000 0.00 0.00 37.36 2.90
1343 1733 2.378208 TCCCACCATTCAAGGAACATGA 59.622 45.455 0.00 0.00 32.76 3.07
1344 1734 2.806434 TCCCACCATTCAAGGAACATG 58.194 47.619 0.00 0.00 0.00 3.21
1345 1735 3.541242 TTCCCACCATTCAAGGAACAT 57.459 42.857 0.00 0.00 33.48 2.71
1348 1738 1.546773 CCGTTCCCACCATTCAAGGAA 60.547 52.381 0.00 0.00 36.05 3.36
1350 1740 0.251165 ACCGTTCCCACCATTCAAGG 60.251 55.000 0.00 0.00 0.00 3.61
1358 1755 1.232119 CAGTGTTTACCGTTCCCACC 58.768 55.000 0.00 0.00 0.00 4.61
1361 1758 2.460757 TAGCAGTGTTTACCGTTCCC 57.539 50.000 0.00 0.00 0.00 3.97
1363 1760 4.965762 GTGTTTTAGCAGTGTTTACCGTTC 59.034 41.667 0.00 0.00 0.00 3.95
1370 1767 3.875134 AGTAGCGTGTTTTAGCAGTGTTT 59.125 39.130 0.00 0.00 35.48 2.83
1371 1768 3.463944 AGTAGCGTGTTTTAGCAGTGTT 58.536 40.909 0.00 0.00 35.48 3.32
1372 1769 3.107642 AGTAGCGTGTTTTAGCAGTGT 57.892 42.857 0.00 0.00 35.48 3.55
1373 1770 4.468095 AAAGTAGCGTGTTTTAGCAGTG 57.532 40.909 0.00 0.00 35.48 3.66
1377 1774 4.851010 TGGAAAAAGTAGCGTGTTTTAGC 58.149 39.130 0.00 0.00 0.00 3.09
1379 1776 6.293735 CCATCTGGAAAAAGTAGCGTGTTTTA 60.294 38.462 0.00 0.00 37.39 1.52
1380 1777 5.507315 CCATCTGGAAAAAGTAGCGTGTTTT 60.507 40.000 0.00 0.00 37.39 2.43
1381 1778 4.023193 CCATCTGGAAAAAGTAGCGTGTTT 60.023 41.667 0.00 0.00 37.39 2.83
1382 1779 3.502211 CCATCTGGAAAAAGTAGCGTGTT 59.498 43.478 0.00 0.00 37.39 3.32
1384 1781 2.159517 GCCATCTGGAAAAAGTAGCGTG 60.160 50.000 0.00 0.00 37.39 5.34
1386 1783 1.062587 CGCCATCTGGAAAAAGTAGCG 59.937 52.381 0.00 0.00 37.39 4.26
1397 1806 2.732468 CTCGCGATCGCCATCTGG 60.732 66.667 32.63 18.28 37.98 3.86
1415 1824 3.120385 CCGACGCCGTTAAACCCC 61.120 66.667 0.00 0.00 0.00 4.95
1620 2029 3.681789 GCTGAGAAGCGCGAGTAC 58.318 61.111 12.10 0.00 0.00 2.73
1736 2145 2.526873 ACCACGTCCTTGGCCTCT 60.527 61.111 3.32 0.00 40.77 3.69
2184 2605 0.323451 CAAAGGGACCCCAGTTAGCC 60.323 60.000 7.00 0.00 38.92 3.93
2210 2631 0.317938 GCACGATCTCCGCGAGTATT 60.318 55.000 8.23 0.00 43.32 1.89
2233 2654 4.831307 CCGTCGTCCTCGCCTTCG 62.831 72.222 0.00 0.00 36.96 3.79
2367 2788 2.342648 GGCGTTCTCCCGTTCAGT 59.657 61.111 0.00 0.00 0.00 3.41
2501 2922 3.315142 TTCCGGCGCAATCAGAGCT 62.315 57.895 10.83 0.00 43.21 4.09
2508 2929 2.040544 CCTGTTCTTCCGGCGCAAT 61.041 57.895 10.83 0.00 0.00 3.56
2516 2937 3.753294 TCTTCACAGTCCTGTTCTTCC 57.247 47.619 0.00 0.00 42.83 3.46
2535 2956 6.293735 CCAGTAGCAGTACTAGAAGTAGCATC 60.294 46.154 0.00 0.00 37.40 3.91
2624 3045 9.757227 AGTCTTAGATATGTTGCTAGTCATTTC 57.243 33.333 0.00 0.38 0.00 2.17
2627 3048 8.519526 GCTAGTCTTAGATATGTTGCTAGTCAT 58.480 37.037 0.00 0.00 0.00 3.06
2629 3050 7.040340 TGGCTAGTCTTAGATATGTTGCTAGTC 60.040 40.741 0.00 0.00 32.48 2.59
2630 3051 6.778069 TGGCTAGTCTTAGATATGTTGCTAGT 59.222 38.462 0.00 0.00 0.00 2.57
2631 3052 7.220741 TGGCTAGTCTTAGATATGTTGCTAG 57.779 40.000 0.00 0.00 0.00 3.42
2632 3053 7.597288 TTGGCTAGTCTTAGATATGTTGCTA 57.403 36.000 0.00 0.00 0.00 3.49
2633 3054 6.485830 TTGGCTAGTCTTAGATATGTTGCT 57.514 37.500 0.00 0.00 0.00 3.91
2634 3055 7.308229 CCATTTGGCTAGTCTTAGATATGTTGC 60.308 40.741 0.00 0.00 0.00 4.17
2635 3056 7.933577 TCCATTTGGCTAGTCTTAGATATGTTG 59.066 37.037 0.00 0.00 34.44 3.33
2636 3057 7.934120 GTCCATTTGGCTAGTCTTAGATATGTT 59.066 37.037 0.00 0.00 34.44 2.71
2637 3058 7.071196 TGTCCATTTGGCTAGTCTTAGATATGT 59.929 37.037 0.00 0.00 34.44 2.29
2638 3059 7.445121 TGTCCATTTGGCTAGTCTTAGATATG 58.555 38.462 0.00 0.00 34.44 1.78
2639 3060 7.618019 TGTCCATTTGGCTAGTCTTAGATAT 57.382 36.000 0.00 0.00 34.44 1.63
2640 3061 7.432148 TTGTCCATTTGGCTAGTCTTAGATA 57.568 36.000 0.00 0.00 34.44 1.98
2641 3062 5.957771 TGTCCATTTGGCTAGTCTTAGAT 57.042 39.130 0.00 0.00 34.44 1.98
2642 3063 5.755409 TTGTCCATTTGGCTAGTCTTAGA 57.245 39.130 0.00 0.00 34.44 2.10
2643 3064 6.817765 TTTTGTCCATTTGGCTAGTCTTAG 57.182 37.500 0.00 0.00 34.44 2.18
2644 3065 7.232534 ACATTTTTGTCCATTTGGCTAGTCTTA 59.767 33.333 0.00 0.00 34.44 2.10
2645 3066 6.041979 ACATTTTTGTCCATTTGGCTAGTCTT 59.958 34.615 0.00 0.00 34.44 3.01
2646 3067 5.539955 ACATTTTTGTCCATTTGGCTAGTCT 59.460 36.000 0.00 0.00 34.44 3.24
2647 3068 5.783111 ACATTTTTGTCCATTTGGCTAGTC 58.217 37.500 0.00 0.00 34.44 2.59
2648 3069 5.806654 ACATTTTTGTCCATTTGGCTAGT 57.193 34.783 0.00 0.00 34.44 2.57
2667 3090 7.934665 TGCGTGGACCTACAAAAATATATACAT 59.065 33.333 0.00 0.00 0.00 2.29
2691 3114 0.457443 GCCTGTAAATTGCCTCCTGC 59.543 55.000 0.00 0.00 41.77 4.85
2724 3186 6.852853 CGCGTAAATTGCATCTATTCTTGAAT 59.147 34.615 0.00 1.35 0.00 2.57
2732 3194 5.867174 TGTATAGCGCGTAAATTGCATCTAT 59.133 36.000 8.43 4.44 34.38 1.98
2733 3195 5.224135 TGTATAGCGCGTAAATTGCATCTA 58.776 37.500 8.43 0.00 0.00 1.98
2734 3196 4.055360 TGTATAGCGCGTAAATTGCATCT 58.945 39.130 8.43 0.00 0.00 2.90
2735 3197 4.383774 TGTATAGCGCGTAAATTGCATC 57.616 40.909 8.43 0.00 0.00 3.91
2736 3198 3.363970 GCTGTATAGCGCGTAAATTGCAT 60.364 43.478 8.43 0.00 40.67 3.96
2737 3199 2.033236 GCTGTATAGCGCGTAAATTGCA 60.033 45.455 8.43 0.00 40.67 4.08
2738 3200 2.560896 GCTGTATAGCGCGTAAATTGC 58.439 47.619 8.43 0.89 40.67 3.56
2750 3212 5.308014 TGCCTTGAACATATGGCTGTATAG 58.692 41.667 7.80 0.00 45.11 1.31
2751 3213 5.303259 TGCCTTGAACATATGGCTGTATA 57.697 39.130 7.80 0.00 45.11 1.47
2752 3214 4.169059 TGCCTTGAACATATGGCTGTAT 57.831 40.909 7.80 0.00 45.11 2.29
2753 3215 3.643199 TGCCTTGAACATATGGCTGTA 57.357 42.857 7.80 0.00 45.11 2.74
2754 3216 2.512692 TGCCTTGAACATATGGCTGT 57.487 45.000 7.80 0.00 45.11 4.40
2755 3217 3.018856 TCTTGCCTTGAACATATGGCTG 58.981 45.455 7.80 0.00 45.11 4.85
2756 3218 3.370840 TCTTGCCTTGAACATATGGCT 57.629 42.857 7.80 0.00 45.11 4.75
2757 3219 3.887716 AGATCTTGCCTTGAACATATGGC 59.112 43.478 7.80 0.00 45.10 4.40
2758 3220 4.518211 GGAGATCTTGCCTTGAACATATGG 59.482 45.833 7.80 0.00 0.00 2.74
2759 3221 4.518211 GGGAGATCTTGCCTTGAACATATG 59.482 45.833 0.00 0.00 33.76 1.78
2760 3222 4.166725 TGGGAGATCTTGCCTTGAACATAT 59.833 41.667 0.00 0.00 38.31 1.78
2761 3223 3.523157 TGGGAGATCTTGCCTTGAACATA 59.477 43.478 0.00 0.00 38.31 2.29
2762 3224 2.309755 TGGGAGATCTTGCCTTGAACAT 59.690 45.455 0.00 0.00 38.31 2.71
2763 3225 1.704628 TGGGAGATCTTGCCTTGAACA 59.295 47.619 0.00 0.00 38.31 3.18
2764 3226 2.496899 TGGGAGATCTTGCCTTGAAC 57.503 50.000 0.00 0.00 38.31 3.18
2765 3227 2.947243 GCATGGGAGATCTTGCCTTGAA 60.947 50.000 16.61 0.00 42.78 2.69
2766 3228 1.409241 GCATGGGAGATCTTGCCTTGA 60.409 52.381 16.61 0.00 42.78 3.02
2767 3229 1.030457 GCATGGGAGATCTTGCCTTG 58.970 55.000 5.92 9.17 42.95 3.61
2768 3230 0.627451 TGCATGGGAGATCTTGCCTT 59.373 50.000 13.26 1.12 38.31 4.35
2769 3231 0.627451 TTGCATGGGAGATCTTGCCT 59.373 50.000 13.26 0.00 38.31 4.75
2770 3232 1.700955 ATTGCATGGGAGATCTTGCC 58.299 50.000 13.26 3.51 37.11 4.52
2771 3233 2.957006 AGAATTGCATGGGAGATCTTGC 59.043 45.455 9.71 9.71 38.02 4.01
2781 3243 7.999679 TGTTTAGAGGATTAAGAATTGCATGG 58.000 34.615 0.00 0.00 0.00 3.66
2782 3244 9.859427 TTTGTTTAGAGGATTAAGAATTGCATG 57.141 29.630 0.00 0.00 0.00 4.06
2842 3322 3.630769 TCATCTAACTCGTATGCCGTCTT 59.369 43.478 0.00 0.00 37.94 3.01
2888 3369 8.036273 TCGTTTAGTCCCATCTAACATTTTTC 57.964 34.615 0.00 0.00 30.87 2.29
2914 3397 4.213482 CCTTGACCTAGTTAACTTGTGTGC 59.787 45.833 14.49 7.11 0.00 4.57
2932 3415 0.898326 TGTCTGCCGTAGCTCCTTGA 60.898 55.000 0.00 0.00 40.80 3.02
2977 3460 6.790285 TGGTTTATAGAAAGTTGTTCGGTC 57.210 37.500 0.00 0.00 0.00 4.79
3008 3491 4.114794 GGGAATAATTTGTGACAGCATGC 58.885 43.478 10.51 10.51 42.53 4.06
3062 3546 7.816945 ATGGTTGCTCTTATTTTTCATTTCG 57.183 32.000 0.00 0.00 0.00 3.46
3177 3661 9.037737 CCCTTGTGAATTATGCTCATTAATTTG 57.962 33.333 0.00 0.00 0.00 2.32
3178 3662 8.761689 ACCCTTGTGAATTATGCTCATTAATTT 58.238 29.630 0.00 0.00 0.00 1.82
3179 3663 8.310122 ACCCTTGTGAATTATGCTCATTAATT 57.690 30.769 0.00 0.00 0.00 1.40
3181 3665 7.118723 AGACCCTTGTGAATTATGCTCATTAA 58.881 34.615 0.00 0.00 0.00 1.40
3207 3755 6.394025 GCTAATCTAGCCGTAGCCTATTAT 57.606 41.667 7.54 0.00 45.95 1.28
3226 3774 7.441836 TCAACTTCACATACTCTTCAAGCTAA 58.558 34.615 0.00 0.00 0.00 3.09
3302 3850 9.872721 TGATGCATTGATTTATTTGTTGTGTAT 57.127 25.926 0.00 0.00 0.00 2.29
3303 3851 9.702494 TTGATGCATTGATTTATTTGTTGTGTA 57.298 25.926 0.00 0.00 0.00 2.90
3304 3852 8.604640 TTGATGCATTGATTTATTTGTTGTGT 57.395 26.923 0.00 0.00 0.00 3.72
3305 3853 9.880064 TTTTGATGCATTGATTTATTTGTTGTG 57.120 25.926 0.00 0.00 0.00 3.33
3365 3913 9.017669 CAATAATAGATTTTGTCAGCTTTCAGC 57.982 33.333 0.00 0.00 42.84 4.26
3368 3916 9.508567 GGACAATAATAGATTTTGTCAGCTTTC 57.491 33.333 19.91 8.10 46.98 2.62
3369 3917 9.023962 TGGACAATAATAGATTTTGTCAGCTTT 57.976 29.630 19.91 0.00 46.98 3.51
3415 3963 8.757789 CATTTCGTAGTCAACTTTGTTGTAGTA 58.242 33.333 9.78 3.13 0.00 1.82
3416 3964 7.493320 TCATTTCGTAGTCAACTTTGTTGTAGT 59.507 33.333 9.78 3.88 0.00 2.73
3417 3965 7.847487 TCATTTCGTAGTCAACTTTGTTGTAG 58.153 34.615 9.78 0.75 0.00 2.74
3491 4039 0.253044 ACATCCAGGACATGTTCGGG 59.747 55.000 16.71 16.71 29.75 5.14
3581 4129 1.304381 GAAGGGTGCTTGCATCCCA 60.304 57.895 20.04 0.00 43.31 4.37


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

AutoCloner maintained by Alex Coulton.