Multiple sequence alignment - TraesCS7D01G405400

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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 TraesCS7D01G405400 chr7D 100.000 3717 0 0 1 3717 522919617 522915901 0.000000e+00 6865.0
1 TraesCS7D01G405400 chr7D 81.250 256 38 7 198 445 31567254 31567001 8.140000e-47 198.0
2 TraesCS7D01G405400 chr7D 78.636 220 36 8 224 438 360337323 360337536 6.480000e-28 135.0
3 TraesCS7D01G405400 chr7D 85.393 89 8 4 197 280 146621729 146621641 1.840000e-13 87.9
4 TraesCS7D01G405400 chr7B 92.642 3683 168 33 4 3612 556739194 556735541 0.000000e+00 5204.0
5 TraesCS7D01G405400 chr7B 94.545 165 8 1 3553 3717 556735543 556735380 1.710000e-63 254.0
6 TraesCS7D01G405400 chr7A 93.336 2776 94 33 28 2752 603099682 603096947 0.000000e+00 4017.0
7 TraesCS7D01G405400 chr7A 93.119 218 9 4 2752 2963 603090004 603089787 7.750000e-82 315.0
8 TraesCS7D01G405400 chr2D 80.859 256 41 6 194 442 424828580 424828834 1.050000e-45 195.0
9 TraesCS7D01G405400 chr2D 83.041 171 26 3 282 450 318562626 318562457 6.430000e-33 152.0
10 TraesCS7D01G405400 chr3B 80.786 229 34 8 224 445 92583480 92583705 1.780000e-38 171.0
11 TraesCS7D01G405400 chr3B 75.479 261 44 17 195 442 792682801 792683054 3.920000e-20 110.0
12 TraesCS7D01G405400 chr3A 77.239 268 45 10 192 449 56733190 56733451 3.870000e-30 143.0
13 TraesCS7D01G405400 chr1B 82.424 165 28 1 282 445 268587167 268587331 3.870000e-30 143.0
14 TraesCS7D01G405400 chr1B 81.481 162 21 7 195 349 81373926 81374085 1.400000e-24 124.0
15 TraesCS7D01G405400 chr4A 80.556 108 16 3 3288 3392 647408973 647409078 1.110000e-10 78.7


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 TraesCS7D01G405400 chr7D 522915901 522919617 3716 True 6865 6865 100.0000 1 3717 1 chr7D.!!$R3 3716
1 TraesCS7D01G405400 chr7B 556735380 556739194 3814 True 2729 5204 93.5935 4 3717 2 chr7B.!!$R1 3713
2 TraesCS7D01G405400 chr7A 603096947 603099682 2735 True 4017 4017 93.3360 28 2752 1 chr7A.!!$R2 2724

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
886 934 1.271054 GCTTGTCTTCTCCTGCTCCAA 60.271 52.381 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2743 2801 0.17576 CGTCGATGGTCCCAGATTGT 59.824 55.0 0.0 0.0 0.0 2.71 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
34 35 7.489574 TCAAATTTTGAACTAAAACCATGGC 57.510 32.000 13.04 0.00 40.80 4.40
45 46 7.296628 ACTAAAACCATGGCAACTATTTTGA 57.703 32.000 13.04 0.00 37.61 2.69
107 108 5.105797 GCAATTAGAACCCATGTGTCATTGA 60.106 40.000 0.00 0.00 0.00 2.57
168 169 6.382859 AGAACCCCAAGTTGTAAAGTTTGAAT 59.617 34.615 1.45 0.00 37.37 2.57
390 402 4.637483 TTTCTCTGCAAACTTGGTCAAG 57.363 40.909 8.97 8.97 43.79 3.02
399 411 4.803613 GCAAACTTGGTCAAGGTTTGTAAG 59.196 41.667 23.13 12.23 45.33 2.34
445 457 4.424061 TGCACTGCATTATGAAACAGAC 57.576 40.909 0.00 0.00 31.71 3.51
449 461 5.688823 CACTGCATTATGAAACAGACGAAA 58.311 37.500 0.00 0.00 34.25 3.46
886 934 1.271054 GCTTGTCTTCTCCTGCTCCAA 60.271 52.381 0.00 0.00 0.00 3.53
929 977 5.559148 TGGCTTCTTCTTCTTCTTCTTCT 57.441 39.130 0.00 0.00 0.00 2.85
930 978 5.934781 TGGCTTCTTCTTCTTCTTCTTCTT 58.065 37.500 0.00 0.00 0.00 2.52
931 979 5.994668 TGGCTTCTTCTTCTTCTTCTTCTTC 59.005 40.000 0.00 0.00 0.00 2.87
932 980 6.183361 TGGCTTCTTCTTCTTCTTCTTCTTCT 60.183 38.462 0.00 0.00 0.00 2.85
933 981 6.710295 GGCTTCTTCTTCTTCTTCTTCTTCTT 59.290 38.462 0.00 0.00 0.00 2.52
934 982 7.095229 GGCTTCTTCTTCTTCTTCTTCTTCTTC 60.095 40.741 0.00 0.00 0.00 2.87
935 983 7.095229 GCTTCTTCTTCTTCTTCTTCTTCTTCC 60.095 40.741 0.00 0.00 0.00 3.46
936 984 7.366847 TCTTCTTCTTCTTCTTCTTCTTCCA 57.633 36.000 0.00 0.00 0.00 3.53
937 985 7.972301 TCTTCTTCTTCTTCTTCTTCTTCCAT 58.028 34.615 0.00 0.00 0.00 3.41
938 986 9.094578 TCTTCTTCTTCTTCTTCTTCTTCCATA 57.905 33.333 0.00 0.00 0.00 2.74
939 987 9.150348 CTTCTTCTTCTTCTTCTTCTTCCATAC 57.850 37.037 0.00 0.00 0.00 2.39
940 988 8.429237 TCTTCTTCTTCTTCTTCTTCCATACT 57.571 34.615 0.00 0.00 0.00 2.12
941 989 8.527810 TCTTCTTCTTCTTCTTCTTCCATACTC 58.472 37.037 0.00 0.00 0.00 2.59
942 990 6.857956 TCTTCTTCTTCTTCTTCCATACTCG 58.142 40.000 0.00 0.00 0.00 4.18
1022 1072 2.593925 TCCTGAGTCTCTGAGCAGAA 57.406 50.000 8.24 0.00 36.94 3.02
1023 1073 2.445427 TCCTGAGTCTCTGAGCAGAAG 58.555 52.381 8.24 0.00 36.94 2.85
1024 1074 2.170166 CCTGAGTCTCTGAGCAGAAGT 58.830 52.381 8.24 0.00 36.94 3.01
1025 1075 2.562298 CCTGAGTCTCTGAGCAGAAGTT 59.438 50.000 8.24 0.00 36.94 2.66
1063 1117 2.640421 GCTAGCTAGCCGGACGAG 59.360 66.667 31.67 3.36 43.39 4.18
1425 1479 2.489275 CGCCACCAACCAAGTGCTT 61.489 57.895 0.00 0.00 33.75 3.91
1578 1632 0.904865 AGAACCTCACCTCATCGGCA 60.905 55.000 0.00 0.00 35.61 5.69
1755 1809 2.337532 GGCCCGATATACGTGCGT 59.662 61.111 0.00 2.05 45.52 5.24
1866 1920 2.584418 CTCCGCCGCATGACTCTG 60.584 66.667 0.00 0.00 0.00 3.35
2116 2170 3.064987 CTGTACTCGGAGGTGCGGG 62.065 68.421 10.23 0.00 0.00 6.13
2259 2313 0.315568 CGGGCTACTGCTACCTCATC 59.684 60.000 0.00 0.00 39.59 2.92
2743 2801 3.074412 GTCTGGGCGAGAAAAGAAATGA 58.926 45.455 0.00 0.00 30.26 2.57
2781 2861 1.676014 CGGCTCGGGAACTTCAAGATT 60.676 52.381 0.00 0.00 0.00 2.40
2782 2862 2.010497 GGCTCGGGAACTTCAAGATTC 58.990 52.381 0.00 0.00 0.00 2.52
2803 2883 1.471676 GGACACTCATCTAGCCGTTGG 60.472 57.143 0.00 0.00 0.00 3.77
2812 2892 4.816385 TCATCTAGCCGTTGGATTGAAATC 59.184 41.667 0.00 0.00 34.66 2.17
2850 2930 0.606401 TTCCAGCTCAAGCCTTTCCG 60.606 55.000 0.00 0.00 43.38 4.30
2872 2952 4.499758 CGTCTACAGTTTATTCCTTCTCGC 59.500 45.833 0.00 0.00 0.00 5.03
2880 2960 1.592400 ATTCCTTCTCGCGACCGTCA 61.592 55.000 3.71 0.00 35.54 4.35
2883 2963 1.874019 CTTCTCGCGACCGTCATGG 60.874 63.158 3.71 0.00 46.41 3.66
2914 2997 2.494918 CCGCCTCTTCCACTACCG 59.505 66.667 0.00 0.00 0.00 4.02
2923 3006 3.371034 TCTTCCACTACCGGATCATCAA 58.629 45.455 9.46 0.00 34.19 2.57
2937 3020 5.241728 CGGATCATCAACATACTCTACCTCA 59.758 44.000 0.00 0.00 0.00 3.86
2958 3041 8.591072 ACCTCAATTCATCATTTCAAACTTCAT 58.409 29.630 0.00 0.00 0.00 2.57
3001 3084 3.899726 ACTCCTTCTATCTCTACCGCAA 58.100 45.455 0.00 0.00 0.00 4.85
3003 3086 4.521256 ACTCCTTCTATCTCTACCGCAATC 59.479 45.833 0.00 0.00 0.00 2.67
3008 3091 4.135306 TCTATCTCTACCGCAATCGAAGT 58.865 43.478 0.00 0.00 38.10 3.01
3016 3099 2.231964 ACCGCAATCGAAGTACCTACAA 59.768 45.455 0.00 0.00 38.10 2.41
3023 3106 7.201496 CGCAATCGAAGTACCTACAAGTAAATT 60.201 37.037 0.00 0.00 38.10 1.82
3025 3108 9.755064 CAATCGAAGTACCTACAAGTAAATTTG 57.245 33.333 0.00 0.00 0.00 2.32
3030 3113 9.492973 GAAGTACCTACAAGTAAATTTGGTGTA 57.507 33.333 0.00 5.75 32.32 2.90
3040 3123 9.965824 CAAGTAAATTTGGTGTATTTCTTGTCT 57.034 29.630 0.00 0.00 32.69 3.41
3049 3132 6.177610 GGTGTATTTCTTGTCTGTAATGGGA 58.822 40.000 0.00 0.00 0.00 4.37
3057 3140 4.054780 TGTCTGTAATGGGAGTAATCGC 57.945 45.455 0.00 0.00 0.00 4.58
3066 3149 2.994186 GGAGTAATCGCCCTTACCAA 57.006 50.000 0.68 0.00 33.02 3.67
3077 3160 6.687081 TCGCCCTTACCAATGTAAAATAAG 57.313 37.500 0.00 0.00 36.54 1.73
3086 3169 7.466746 ACCAATGTAAAATAAGAGCATGTGT 57.533 32.000 0.00 0.00 0.00 3.72
3093 3176 4.708726 AATAAGAGCATGTGTCTTTGCC 57.291 40.909 15.11 0.00 39.72 4.52
3110 3193 0.169009 GCCCATTCACAAGAACTCGC 59.831 55.000 0.00 0.00 36.39 5.03
3146 3229 0.174617 CGCCTCTCCTCTTTCTCACC 59.825 60.000 0.00 0.00 0.00 4.02
3163 3247 1.679680 CACCAGGATTGATGCCACATC 59.320 52.381 0.00 0.55 0.00 3.06
3165 3249 1.475571 CCAGGATTGATGCCACATCGA 60.476 52.381 0.14 0.14 0.00 3.59
3187 3271 6.697455 TCGACAATTATCATCTCCTTTTCGAG 59.303 38.462 0.00 0.00 0.00 4.04
3198 3282 0.934496 CTTTTCGAGTGTGTGCCGAA 59.066 50.000 0.00 0.00 40.04 4.30
3200 3284 0.653636 TTTCGAGTGTGTGCCGAAAC 59.346 50.000 0.00 0.00 44.17 2.78
3226 3310 5.735766 AGTTTCTACCATGGAAGCTCTTAC 58.264 41.667 21.47 5.87 30.51 2.34
3229 3313 3.706594 TCTACCATGGAAGCTCTTACTGG 59.293 47.826 21.47 8.06 31.92 4.00
3256 3340 2.623416 ACACTGATGTGACTTGTCTCGA 59.377 45.455 3.03 0.00 46.55 4.04
3257 3341 3.240884 CACTGATGTGACTTGTCTCGAG 58.759 50.000 5.93 5.93 46.55 4.04
3258 3342 2.230025 ACTGATGTGACTTGTCTCGAGG 59.770 50.000 13.56 0.00 0.00 4.63
3273 3357 1.202302 TCGAGGCTCAACTGCTAATCG 60.202 52.381 15.95 0.00 35.99 3.34
3282 3366 0.253044 ACTGCTAATCGTGGCCACAT 59.747 50.000 34.16 22.84 0.00 3.21
3283 3367 1.340017 ACTGCTAATCGTGGCCACATT 60.340 47.619 34.16 29.38 0.00 2.71
3284 3368 1.064505 CTGCTAATCGTGGCCACATTG 59.935 52.381 34.16 22.88 0.00 2.82
3316 3400 9.002600 GGAAATTGATTCAACCAAAAAGCTAAT 57.997 29.630 0.15 0.00 39.98 1.73
3350 3434 8.770010 TTTCTTCAAATTAAGGTTCCCTGTAA 57.230 30.769 0.00 0.00 32.13 2.41
3366 3450 4.563580 CCCTGTAATGATCTATCCCGTTGG 60.564 50.000 0.00 0.00 0.00 3.77
3375 3459 2.241176 TCTATCCCGTTGGCCAAAGAAT 59.759 45.455 30.02 23.12 0.00 2.40
3388 3472 5.104109 TGGCCAAAGAATAAGTACATAGCCT 60.104 40.000 0.61 0.00 36.47 4.58
3392 3476 7.229506 GCCAAAGAATAAGTACATAGCCTGAAT 59.770 37.037 0.00 0.00 0.00 2.57
3460 3544 0.672711 GGACAACCCAACGAGGTAGC 60.673 60.000 0.00 0.00 40.05 3.58
3462 3546 0.034896 ACAACCCAACGAGGTAGCAG 59.965 55.000 0.00 0.00 40.05 4.24
3468 3552 0.108138 CAACGAGGTAGCAGGGGAAG 60.108 60.000 0.00 0.00 0.00 3.46
3469 3553 0.252103 AACGAGGTAGCAGGGGAAGA 60.252 55.000 0.00 0.00 0.00 2.87
3473 3557 0.644937 AGGTAGCAGGGGAAGAGGAT 59.355 55.000 0.00 0.00 0.00 3.24
3483 3567 0.695347 GGAAGAGGATGGGGCTATGG 59.305 60.000 0.00 0.00 0.00 2.74
3490 3574 0.106519 GATGGGGCTATGGCAAGTGT 60.107 55.000 2.58 0.00 40.87 3.55
3492 3576 0.611618 TGGGGCTATGGCAAGTGTTG 60.612 55.000 2.58 0.00 40.87 3.33
3495 3579 0.109132 GGCTATGGCAAGTGTTGTGC 60.109 55.000 2.58 0.00 41.45 4.57
3503 3587 0.586256 CAAGTGTTGTGCGTGTGACG 60.586 55.000 0.00 0.00 45.88 4.35
3505 3589 3.568743 TGTTGTGCGTGTGACGGC 61.569 61.111 0.00 0.00 42.82 5.68
3506 3590 3.568743 GTTGTGCGTGTGACGGCA 61.569 61.111 0.00 0.00 42.82 5.69
3507 3591 2.820037 TTGTGCGTGTGACGGCAA 60.820 55.556 0.00 0.00 42.82 4.52
3508 3592 2.399356 TTGTGCGTGTGACGGCAAA 61.399 52.632 0.00 0.00 42.82 3.68
3520 3612 1.743394 GACGGCAAATTAGGAACCCAG 59.257 52.381 0.00 0.00 0.00 4.45
3525 3617 2.492088 GCAAATTAGGAACCCAGGACAC 59.508 50.000 0.00 0.00 0.00 3.67
3539 3631 1.130613 GACACGACGACATGCTTGC 59.869 57.895 0.00 0.00 0.00 4.01
3549 3641 1.298563 CATGCTTGCGCCATTACCG 60.299 57.895 4.18 0.00 34.43 4.02
3587 3679 6.078202 TGGACATTATCAGATCGAGACTTC 57.922 41.667 0.00 0.00 0.00 3.01
3623 3770 3.561725 GGCAATGCTAACATAGAGTGGTC 59.438 47.826 4.82 0.00 34.62 4.02
3634 3781 0.032678 AGAGTGGTCGTCTTGTGCTG 59.967 55.000 0.00 0.00 0.00 4.41
3644 3791 0.770499 TCTTGTGCTGGTCCAATCCA 59.230 50.000 0.00 0.00 36.00 3.41
3651 3798 3.378427 GTGCTGGTCCAATCCATTCTAAC 59.622 47.826 0.00 0.00 36.84 2.34
3656 3803 3.003689 GGTCCAATCCATTCTAACATGCG 59.996 47.826 0.00 0.00 0.00 4.73
3673 3820 6.464895 ACATGCGTTACAATTTTCCATTTG 57.535 33.333 0.00 0.00 0.00 2.32
3686 3833 9.263538 CAATTTTCCATTTGATTTCTCTTGACA 57.736 29.630 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.280677 CCCTCAGTTTCAAAATAGTTGCCA 59.719 41.667 0.00 0.00 0.00 4.92
34 35 7.452880 TGATCCCTCAGTTTCAAAATAGTTG 57.547 36.000 0.00 0.00 0.00 3.16
45 46 4.080863 GGTCACACTATGATCCCTCAGTTT 60.081 45.833 0.00 0.00 40.28 2.66
107 108 7.048512 CGATTTTAAGGGAAGAACCTATGACT 58.951 38.462 0.00 0.00 40.87 3.41
168 169 8.768397 TCTTTAGAGGGAGTGCATTTTAAGATA 58.232 33.333 0.00 0.00 0.00 1.98
180 181 5.663556 AGGGAGTATTTCTTTAGAGGGAGTG 59.336 44.000 0.00 0.00 0.00 3.51
301 313 7.640852 ACGTCTTGTGATATATCTAGTGACAC 58.359 38.462 13.79 0.00 0.00 3.67
390 402 9.642327 TTTCTGAAAAGTTAAACCTTACAAACC 57.358 29.630 0.00 0.00 0.00 3.27
430 442 6.142817 ACACTTTTCGTCTGTTTCATAATGC 58.857 36.000 0.00 0.00 0.00 3.56
445 457 4.377897 ACTCCCTCTGTAAACACTTTTCG 58.622 43.478 0.00 0.00 0.00 3.46
449 461 5.479724 GGTACTACTCCCTCTGTAAACACTT 59.520 44.000 0.00 0.00 0.00 3.16
564 610 4.562757 CCCGTTGGTTTCTGAACAGATCTA 60.563 45.833 5.34 0.00 37.29 1.98
645 693 4.684623 GGTGGATCAACCCATGGG 57.315 61.111 30.23 30.23 38.66 4.00
886 934 5.337813 GCCAATGAGAATTTGAGATTGGGTT 60.338 40.000 15.61 0.00 42.24 4.11
929 977 5.621555 GCAGAGTTGTACGAGTATGGAAGAA 60.622 44.000 13.28 0.00 0.00 2.52
930 978 4.142447 GCAGAGTTGTACGAGTATGGAAGA 60.142 45.833 13.28 0.00 0.00 2.87
931 979 4.106197 GCAGAGTTGTACGAGTATGGAAG 58.894 47.826 13.28 0.00 0.00 3.46
932 980 3.762288 AGCAGAGTTGTACGAGTATGGAA 59.238 43.478 13.28 0.00 0.00 3.53
933 981 3.353557 AGCAGAGTTGTACGAGTATGGA 58.646 45.455 13.28 0.00 0.00 3.41
934 982 3.378742 AGAGCAGAGTTGTACGAGTATGG 59.621 47.826 13.28 0.00 0.00 2.74
935 983 4.142578 ACAGAGCAGAGTTGTACGAGTATG 60.143 45.833 8.03 8.03 0.00 2.39
936 984 4.011023 ACAGAGCAGAGTTGTACGAGTAT 58.989 43.478 0.00 0.00 0.00 2.12
937 985 3.188667 CACAGAGCAGAGTTGTACGAGTA 59.811 47.826 0.00 0.00 0.00 2.59
938 986 2.030717 CACAGAGCAGAGTTGTACGAGT 60.031 50.000 0.00 0.00 0.00 4.18
939 987 2.590073 CACAGAGCAGAGTTGTACGAG 58.410 52.381 0.00 0.00 0.00 4.18
940 988 1.335964 GCACAGAGCAGAGTTGTACGA 60.336 52.381 0.00 0.00 44.79 3.43
941 989 1.063806 GCACAGAGCAGAGTTGTACG 58.936 55.000 0.00 0.00 44.79 3.67
1023 1073 1.406205 GCTAGCTCCCTCCAGTGAAAC 60.406 57.143 7.70 0.00 0.00 2.78
1024 1074 0.905357 GCTAGCTCCCTCCAGTGAAA 59.095 55.000 7.70 0.00 0.00 2.69
1025 1075 1.323271 CGCTAGCTCCCTCCAGTGAA 61.323 60.000 13.93 0.00 0.00 3.18
1082 1136 2.684374 GCCATGCACATCATCACAGTAA 59.316 45.455 0.00 0.00 31.79 2.24
1266 1320 1.367840 GAGCGTGGTGGAGTTGACT 59.632 57.895 0.00 0.00 0.00 3.41
1521 1575 3.626154 CGAAGGGTAGTCGAAGCTC 57.374 57.895 0.00 0.00 41.02 4.09
1557 1611 1.186200 CCGATGAGGTGAGGTTCTGA 58.814 55.000 0.00 0.00 34.51 3.27
1578 1632 1.153745 GTCGATGGAGTGAAGCGCT 60.154 57.895 2.64 2.64 0.00 5.92
1620 1674 0.809385 AGAGCGCGAAGTAGTTGCTA 59.191 50.000 12.10 0.00 35.73 3.49
1780 1834 0.537653 GCTCCCTCCTTCTGGTACAC 59.462 60.000 0.00 0.00 34.23 2.90
1971 2025 3.479269 GGCACGCAGACGCTGTAC 61.479 66.667 8.32 0.00 45.53 2.90
2721 2779 1.508632 TTTCTTTTCTCGCCCAGACG 58.491 50.000 0.00 0.00 0.00 4.18
2743 2801 0.175760 CGTCGATGGTCCCAGATTGT 59.824 55.000 0.00 0.00 0.00 2.71
2781 2861 0.393944 ACGGCTAGATGAGTGTCCGA 60.394 55.000 7.96 0.00 40.04 4.55
2782 2862 0.456221 AACGGCTAGATGAGTGTCCG 59.544 55.000 0.00 0.00 42.24 4.79
2803 2883 4.513198 TGGAAACCGTTGGATTTCAATC 57.487 40.909 10.73 0.00 37.73 2.67
2812 2892 1.209127 GACGCATGGAAACCGTTGG 59.791 57.895 0.00 0.00 35.06 3.77
2821 2901 1.219124 GAGCTGGAAGACGCATGGA 59.781 57.895 0.00 0.00 34.07 3.41
2822 2902 0.674581 TTGAGCTGGAAGACGCATGG 60.675 55.000 0.00 0.00 34.07 3.66
2850 2930 4.499758 CGCGAGAAGGAATAAACTGTAGAC 59.500 45.833 0.00 0.00 0.00 2.59
2897 2977 2.494918 CGGTAGTGGAAGAGGCGG 59.505 66.667 0.00 0.00 0.00 6.13
2899 2979 0.389757 GATCCGGTAGTGGAAGAGGC 59.610 60.000 0.00 0.00 42.46 4.70
2901 2981 2.959030 TGATGATCCGGTAGTGGAAGAG 59.041 50.000 0.00 0.00 42.46 2.85
2902 2982 3.026707 TGATGATCCGGTAGTGGAAGA 57.973 47.619 0.00 0.00 42.46 2.87
2906 2986 2.979814 TGTTGATGATCCGGTAGTGG 57.020 50.000 0.00 0.00 0.00 4.00
2907 2987 5.010112 AGAGTATGTTGATGATCCGGTAGTG 59.990 44.000 0.00 0.00 0.00 2.74
2914 2997 6.656632 TGAGGTAGAGTATGTTGATGATCC 57.343 41.667 0.00 0.00 0.00 3.36
2923 3006 9.553064 GAAATGATGAATTGAGGTAGAGTATGT 57.447 33.333 0.00 0.00 0.00 2.29
2972 3055 7.228906 CGGTAGAGATAGAAGGAGTTGATACAA 59.771 40.741 0.00 0.00 0.00 2.41
2973 3056 6.711194 CGGTAGAGATAGAAGGAGTTGATACA 59.289 42.308 0.00 0.00 0.00 2.29
2993 3076 2.865343 AGGTACTTCGATTGCGGTAG 57.135 50.000 0.00 0.00 38.28 3.18
3001 3084 8.098912 ACCAAATTTACTTGTAGGTACTTCGAT 58.901 33.333 0.00 0.00 41.75 3.59
3003 3086 7.172019 ACACCAAATTTACTTGTAGGTACTTCG 59.828 37.037 0.00 0.00 41.75 3.79
3016 3099 9.131791 ACAGACAAGAAATACACCAAATTTACT 57.868 29.630 0.00 0.00 0.00 2.24
3023 3106 6.432783 CCCATTACAGACAAGAAATACACCAA 59.567 38.462 0.00 0.00 0.00 3.67
3025 3108 6.177610 TCCCATTACAGACAAGAAATACACC 58.822 40.000 0.00 0.00 0.00 4.16
3030 3113 7.495934 CGATTACTCCCATTACAGACAAGAAAT 59.504 37.037 0.00 0.00 0.00 2.17
3040 3123 2.404559 AGGGCGATTACTCCCATTACA 58.595 47.619 0.00 0.00 43.03 2.41
3049 3132 3.926058 ACATTGGTAAGGGCGATTACT 57.074 42.857 10.03 0.00 36.19 2.24
3057 3140 7.639113 TGCTCTTATTTTACATTGGTAAGGG 57.361 36.000 0.00 0.00 40.40 3.95
3066 3149 7.756722 GCAAAGACACATGCTCTTATTTTACAT 59.243 33.333 6.66 0.00 39.46 2.29
3077 3160 1.180029 ATGGGCAAAGACACATGCTC 58.820 50.000 0.00 0.00 43.45 4.26
3086 3169 3.565307 AGTTCTTGTGAATGGGCAAAGA 58.435 40.909 0.00 0.00 34.40 2.52
3093 3176 3.193157 CAAGCGAGTTCTTGTGAATGG 57.807 47.619 0.00 0.00 38.81 3.16
3110 3193 2.093973 AGGCGACAGATACCAGAACAAG 60.094 50.000 0.00 0.00 0.00 3.16
3146 3229 1.600957 GTCGATGTGGCATCAATCCTG 59.399 52.381 9.40 0.00 0.00 3.86
3163 3247 6.477033 ACTCGAAAAGGAGATGATAATTGTCG 59.523 38.462 0.00 0.00 37.49 4.35
3165 3249 7.065085 CACACTCGAAAAGGAGATGATAATTGT 59.935 37.037 0.00 0.00 37.49 2.71
3187 3271 1.014352 AACTCAGTTTCGGCACACAC 58.986 50.000 0.00 0.00 0.00 3.82
3198 3282 4.042187 AGCTTCCATGGTAGAAACTCAGTT 59.958 41.667 21.61 0.00 0.00 3.16
3200 3284 4.081198 AGAGCTTCCATGGTAGAAACTCAG 60.081 45.833 21.61 2.29 38.39 3.35
3256 3340 1.406069 CCACGATTAGCAGTTGAGCCT 60.406 52.381 0.00 0.00 34.23 4.58
3257 3341 1.009829 CCACGATTAGCAGTTGAGCC 58.990 55.000 0.00 0.00 34.23 4.70
3258 3342 0.375106 GCCACGATTAGCAGTTGAGC 59.625 55.000 0.00 0.00 0.00 4.26
3282 3366 5.306419 TGGTTGAATCAATTTCCATGGACAA 59.694 36.000 15.91 12.52 33.04 3.18
3283 3367 4.837298 TGGTTGAATCAATTTCCATGGACA 59.163 37.500 15.91 8.93 33.04 4.02
3284 3368 5.404466 TGGTTGAATCAATTTCCATGGAC 57.596 39.130 15.91 0.19 33.04 4.02
3342 3426 4.127918 ACGGGATAGATCATTACAGGGA 57.872 45.455 0.00 0.00 0.00 4.20
3343 3427 4.563580 CCAACGGGATAGATCATTACAGGG 60.564 50.000 0.00 0.00 35.59 4.45
3344 3428 4.569943 CCAACGGGATAGATCATTACAGG 58.430 47.826 0.00 0.00 35.59 4.00
3350 3434 1.434188 TGGCCAACGGGATAGATCAT 58.566 50.000 0.61 0.00 35.59 2.45
3366 3450 6.055588 TCAGGCTATGTACTTATTCTTTGGC 58.944 40.000 0.00 0.00 0.00 4.52
3460 3544 2.761465 GCCCCATCCTCTTCCCCTG 61.761 68.421 0.00 0.00 0.00 4.45
3462 3546 0.476611 ATAGCCCCATCCTCTTCCCC 60.477 60.000 0.00 0.00 0.00 4.81
3468 3552 0.251077 CTTGCCATAGCCCCATCCTC 60.251 60.000 0.00 0.00 38.69 3.71
3469 3553 0.995675 ACTTGCCATAGCCCCATCCT 60.996 55.000 0.00 0.00 38.69 3.24
3473 3557 0.611618 CAACACTTGCCATAGCCCCA 60.612 55.000 0.00 0.00 38.69 4.96
3483 3567 0.861450 GTCACACGCACAACACTTGC 60.861 55.000 0.00 0.00 36.57 4.01
3490 3574 1.719725 ATTTGCCGTCACACGCACAA 61.720 50.000 0.00 0.00 40.91 3.33
3492 3576 0.236187 TAATTTGCCGTCACACGCAC 59.764 50.000 0.00 0.00 40.91 5.34
3495 3579 1.434555 TCCTAATTTGCCGTCACACG 58.565 50.000 0.00 0.00 42.11 4.49
3503 3587 2.100197 GTCCTGGGTTCCTAATTTGCC 58.900 52.381 0.00 0.00 0.00 4.52
3505 3589 2.747446 CGTGTCCTGGGTTCCTAATTTG 59.253 50.000 0.00 0.00 0.00 2.32
3506 3590 2.640826 TCGTGTCCTGGGTTCCTAATTT 59.359 45.455 0.00 0.00 0.00 1.82
3507 3591 2.027469 GTCGTGTCCTGGGTTCCTAATT 60.027 50.000 0.00 0.00 0.00 1.40
3508 3592 1.553704 GTCGTGTCCTGGGTTCCTAAT 59.446 52.381 0.00 0.00 0.00 1.73
3520 3612 1.781555 CAAGCATGTCGTCGTGTCC 59.218 57.895 3.86 0.00 33.51 4.02
3539 3631 1.202486 TCTCCTTAAGCGGTAATGGCG 60.202 52.381 0.00 0.00 35.00 5.69
3549 3641 5.904362 AATGTCCAACAATCTCCTTAAGC 57.096 39.130 0.00 0.00 0.00 3.09
3587 3679 4.659172 TGCCAACCGCCAAGAGGG 62.659 66.667 0.00 0.00 40.85 4.30
3623 3770 0.798776 GATTGGACCAGCACAAGACG 59.201 55.000 0.00 0.00 0.00 4.18
3634 3781 3.003689 CGCATGTTAGAATGGATTGGACC 59.996 47.826 0.00 0.00 0.00 4.46
3651 3798 6.702972 TCAAATGGAAAATTGTAACGCATG 57.297 33.333 0.00 0.00 0.00 4.06
3673 3820 2.573915 AGGAGGGGTGTCAAGAGAAATC 59.426 50.000 0.00 0.00 0.00 2.17
3686 3833 3.265489 TCTTAAACATCCAAGGAGGGGT 58.735 45.455 5.69 0.00 38.24 4.95


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

AutoCloner maintained by Alex Coulton.