Multiple sequence alignment - TraesCS3D01G037800

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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 TraesCS3D01G037800 chr3D 100.000 3524 0 0 1 3524 13665749 13662226 0.000000e+00 6508.0
1 TraesCS3D01G037800 chr3D 95.515 602 26 1 178 779 11414912 11415512 0.000000e+00 961.0
2 TraesCS3D01G037800 chr3D 97.222 72 2 0 2989 3060 13662694 13662623 4.780000e-24 122.0
3 TraesCS3D01G037800 chr3D 97.222 72 2 0 3056 3127 13662761 13662690 4.780000e-24 122.0
4 TraesCS3D01G037800 chr3A 91.779 2299 141 15 797 3060 23274177 23276462 0.000000e+00 3155.0
5 TraesCS3D01G037800 chr3A 90.254 472 27 5 3057 3524 23276393 23276849 1.810000e-167 599.0
6 TraesCS3D01G037800 chr3A 91.667 144 12 0 1709 1852 23319999 23320142 2.150000e-47 200.0
7 TraesCS3D01G037800 chr3A 95.349 43 2 0 1890 1932 23275222 23275264 6.310000e-08 69.4
8 TraesCS3D01G037800 chr3B 90.222 2342 150 34 781 3060 20055478 20053154 0.000000e+00 2983.0
9 TraesCS3D01G037800 chr3B 89.111 450 45 1 3060 3505 20053221 20052772 1.110000e-154 556.0
10 TraesCS3D01G037800 chr3B 88.194 144 17 0 1709 1852 20002078 20001935 4.680000e-39 172.0
11 TraesCS3D01G037800 chr3B 78.341 217 34 12 182 393 42064280 42064072 1.030000e-25 128.0
12 TraesCS3D01G037800 chr3B 78.341 217 34 12 182 393 42090674 42090466 1.030000e-25 128.0
13 TraesCS3D01G037800 chr6B 94.366 781 43 1 1 781 23588033 23588812 0.000000e+00 1197.0
14 TraesCS3D01G037800 chr1A 92.811 779 53 3 1 778 466030119 466029343 0.000000e+00 1125.0
15 TraesCS3D01G037800 chrUn 78.341 217 34 12 182 393 305871208 305871000 1.030000e-25 128.0
16 TraesCS3D01G037800 chr5B 77.333 150 17 7 267 399 572164517 572164368 4.880000e-09 73.1


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 TraesCS3D01G037800 chr3D 13662226 13665749 3523 True 2250.666667 6508 98.148000 1 3524 3 chr3D.!!$R1 3523
1 TraesCS3D01G037800 chr3D 11414912 11415512 600 False 961.000000 961 95.515000 178 779 1 chr3D.!!$F1 601
2 TraesCS3D01G037800 chr3A 23274177 23276849 2672 False 1274.466667 3155 92.460667 797 3524 3 chr3A.!!$F2 2727
3 TraesCS3D01G037800 chr3B 20052772 20055478 2706 True 1769.500000 2983 89.666500 781 3505 2 chr3B.!!$R4 2724
4 TraesCS3D01G037800 chr6B 23588033 23588812 779 False 1197.000000 1197 94.366000 1 781 1 chr6B.!!$F1 780
5 TraesCS3D01G037800 chr1A 466029343 466030119 776 True 1125.000000 1125 92.811000 1 778 1 chr1A.!!$R1 777

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
884 886 0.040058 ATGCCCTCAATGCTCCAACA 59.960 50.0 0.00 0.00 0.00 3.33 F
1801 1869 0.037303 TGAGGCTGCTTCCTTGAAGG 59.963 55.0 4.45 4.45 39.76 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2262 0.108396 GCAAGGGTGCCACCATTTTT 59.892 50.0 17.22 1.29 39.55 1.94 R
2799 2874 0.588252 CAGACTTTCAGTTGCCACGG 59.412 55.0 0.00 0.00 0.00 4.94 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
82 83 1.841663 CGTGCCCCTGAACAACTTCG 61.842 60.000 0.00 0.00 0.00 3.79
102 103 2.484062 CGCTGTGCCATGAATCCCC 61.484 63.158 0.00 0.00 0.00 4.81
109 110 0.614415 GCCATGAATCCCCAACACCA 60.614 55.000 0.00 0.00 0.00 4.17
160 161 3.559238 ACCGAATGAGATGTGCAAAAC 57.441 42.857 0.00 0.00 0.00 2.43
198 199 0.749454 ATGTGAGGAGATTTGGCGCC 60.749 55.000 22.73 22.73 0.00 6.53
381 382 1.716172 GCCGATTTGAGAACTCCGC 59.284 57.895 0.00 0.00 0.00 5.54
409 411 2.512286 CTGCATCACGGCCGACAT 60.512 61.111 35.90 20.01 0.00 3.06
472 474 1.153745 GCAGTGGAGTACCTGCGAG 60.154 63.158 6.15 0.00 37.04 5.03
596 598 2.537625 GCAACGATGAGGAGAGATTTCG 59.462 50.000 0.00 0.00 0.00 3.46
619 621 1.082104 GCAGTTTCGAAACAGCCGG 60.082 57.895 35.08 22.31 43.13 6.13
651 653 0.545787 ATAGAACCACCCACGACCCA 60.546 55.000 0.00 0.00 0.00 4.51
714 716 3.445518 GACGATGGCTGCCCGATCA 62.446 63.158 21.39 1.07 0.00 2.92
715 717 2.969238 CGATGGCTGCCCGATCAC 60.969 66.667 17.53 0.35 0.00 3.06
753 755 0.602905 CTCGGTTCGCCCAGAAAGTT 60.603 55.000 0.00 0.00 41.10 2.66
775 777 2.583801 CGCGTGCACTTTTTAGATTTCG 59.416 45.455 16.19 0.00 0.00 3.46
781 783 5.401376 GTGCACTTTTTAGATTTCGGGTTTC 59.599 40.000 10.32 0.00 0.00 2.78
782 784 4.615541 GCACTTTTTAGATTTCGGGTTTCG 59.384 41.667 0.00 0.00 40.90 3.46
794 796 3.180613 TCGGGTTTCGAAAAACAAAAGC 58.819 40.909 13.10 0.00 45.44 3.51
795 797 3.119424 TCGGGTTTCGAAAAACAAAAGCT 60.119 39.130 13.10 0.00 45.44 3.74
796 798 4.096081 TCGGGTTTCGAAAAACAAAAGCTA 59.904 37.500 13.10 0.00 45.44 3.32
797 799 4.799428 CGGGTTTCGAAAAACAAAAGCTAA 59.201 37.500 13.10 0.00 45.44 3.09
798 800 5.288952 CGGGTTTCGAAAAACAAAAGCTAAA 59.711 36.000 13.10 0.00 45.44 1.85
843 845 3.328237 AAAGAAAACAACGTGGCGTAG 57.672 42.857 0.00 0.00 39.99 3.51
876 878 1.462616 TTCCGTTCATGCCCTCAATG 58.537 50.000 0.00 0.00 0.00 2.82
877 879 1.031571 TCCGTTCATGCCCTCAATGC 61.032 55.000 0.00 0.00 0.00 3.56
880 882 0.743097 GTTCATGCCCTCAATGCTCC 59.257 55.000 0.00 0.00 0.00 4.70
884 886 0.040058 ATGCCCTCAATGCTCCAACA 59.960 50.000 0.00 0.00 0.00 3.33
1012 1017 4.161295 CGAGGATGGGCCGCAAGA 62.161 66.667 0.00 0.00 43.43 3.02
1085 1114 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
1188 1217 0.389391 ATTCGTCGGATGGAAGCGAT 59.611 50.000 0.00 0.00 0.00 4.58
1313 1366 3.870299 GCCAAGGACAAGAAGAAGGGTAG 60.870 52.174 0.00 0.00 0.00 3.18
1421 1489 0.173708 AGCGAGGGTAAGAAGAAGCG 59.826 55.000 0.00 0.00 0.00 4.68
1476 1544 3.152341 CAAGCTTGAGAAACCTGGACAT 58.848 45.455 22.31 0.00 0.00 3.06
1524 1592 1.493861 TCAAGATCCTGGAGGCTCTG 58.506 55.000 15.23 7.71 39.56 3.35
1797 1865 2.559668 TCAAAATGAGGCTGCTTCCTTG 59.440 45.455 9.40 9.90 36.38 3.61
1801 1869 0.037303 TGAGGCTGCTTCCTTGAAGG 59.963 55.000 4.45 4.45 39.76 3.46
1842 1910 2.057922 AGCAAGGAGAAAACAGAGGGA 58.942 47.619 0.00 0.00 0.00 4.20
1935 2003 3.064324 GCAAAGCAGGCCACCGAT 61.064 61.111 5.01 0.00 0.00 4.18
1944 2012 1.201429 AGGCCACCGATGAGAAGGTT 61.201 55.000 5.01 0.00 39.00 3.50
2145 2213 4.576463 GGAAAGTCTGACAAAGAGAAAGCA 59.424 41.667 10.88 0.00 34.84 3.91
2168 2236 1.417288 GGAGATGCAGAGAGCCCCAT 61.417 60.000 0.00 0.00 44.83 4.00
2194 2262 1.464376 GGAGGCTATGGCTGACGCTA 61.464 60.000 0.00 0.00 38.98 4.26
2233 2301 3.650942 TGCTCTGTTTAAGAAGGAAGGGA 59.349 43.478 0.00 0.00 33.37 4.20
2270 2338 4.644103 AAATGGACACTGATGCTAATGC 57.356 40.909 0.00 0.00 40.20 3.56
2415 2483 1.680860 CCTGATGAGAAGGCATGTGCA 60.681 52.381 7.36 0.00 44.36 4.57
2490 2558 3.664107 CCGATCTGACACAAAGAAGGAA 58.336 45.455 0.00 0.00 31.11 3.36
2563 2631 2.137523 CCCATTTACGCGGTATACCAC 58.862 52.381 21.76 11.30 35.14 4.16
2567 2635 3.425577 TTTACGCGGTATACCACTCTG 57.574 47.619 21.76 6.08 35.14 3.35
2702 2777 0.789687 ATCCAAATTCCACCCACCCA 59.210 50.000 0.00 0.00 0.00 4.51
2713 2788 1.967779 CACCCACCCAAAAAGGTTAGG 59.032 52.381 0.00 0.00 38.39 2.69
2775 2850 8.690203 TGGACATATATCCAGTGTAATTTTGG 57.310 34.615 0.00 0.00 44.14 3.28
2781 2856 2.158385 TCCAGTGTAATTTTGGGCAGGT 60.158 45.455 0.00 0.00 32.76 4.00
2799 2874 1.134371 GGTAGTGAGGCCCTGTGAATC 60.134 57.143 0.00 0.00 0.00 2.52
2851 2926 5.251764 CCAAGGGACATGAGATGGATTATC 58.748 45.833 0.00 0.00 35.97 1.75
2852 2927 5.251764 CAAGGGACATGAGATGGATTATCC 58.748 45.833 3.91 3.91 36.40 2.59
2878 2964 9.932699 CACTCATTTCTTATGCTTCTATTCAAG 57.067 33.333 0.00 0.00 0.00 3.02
2890 2976 6.116126 GCTTCTATTCAAGTATGGTTCCACT 58.884 40.000 0.00 0.00 0.00 4.00
2903 2989 9.435570 AGTATGGTTCCACTGTATTTAGATACT 57.564 33.333 5.14 0.00 39.12 2.12
2920 3007 9.944376 TTTAGATACTCAGTTTTTCTGCAGTAT 57.056 29.630 14.67 0.40 42.65 2.12
2929 3016 6.974622 CAGTTTTTCTGCAGTATTGACTTGTT 59.025 34.615 14.67 0.00 37.36 2.83
2975 3062 5.875910 TCGGTTACTGTTATTGTATTGTGGG 59.124 40.000 0.00 0.00 0.00 4.61
2997 3084 8.137437 GTGGGTGTCAAAATATTATTCAGGATG 58.863 37.037 0.00 0.00 37.54 3.51
3029 3116 6.822442 TGGTGTCTTTGATTGTTACTGTAGA 58.178 36.000 0.00 0.00 0.00 2.59
3030 3117 6.929049 TGGTGTCTTTGATTGTTACTGTAGAG 59.071 38.462 0.00 0.00 0.00 2.43
3031 3118 6.929606 GGTGTCTTTGATTGTTACTGTAGAGT 59.070 38.462 0.00 0.00 36.07 3.24
3032 3119 7.441458 GGTGTCTTTGATTGTTACTGTAGAGTT 59.559 37.037 0.00 0.00 33.21 3.01
3033 3120 8.827677 GTGTCTTTGATTGTTACTGTAGAGTTT 58.172 33.333 0.00 0.00 33.21 2.66
3034 3121 9.042008 TGTCTTTGATTGTTACTGTAGAGTTTC 57.958 33.333 0.00 0.00 33.21 2.78
3035 3122 9.262358 GTCTTTGATTGTTACTGTAGAGTTTCT 57.738 33.333 0.00 0.00 33.21 2.52
3039 3126 9.909644 TTGATTGTTACTGTAGAGTTTCTAGTC 57.090 33.333 0.00 0.00 33.21 2.59
3040 3127 9.074576 TGATTGTTACTGTAGAGTTTCTAGTCA 57.925 33.333 0.00 0.00 33.21 3.41
3048 3135 9.915629 ACTGTAGAGTTTCTAGTCATTTTAGTG 57.084 33.333 0.00 0.00 28.01 2.74
3050 3137 9.909644 TGTAGAGTTTCTAGTCATTTTAGTGAC 57.090 33.333 0.00 0.00 46.90 3.67
3062 3149 7.816640 GTCATTTTAGTGACTTGCATTTAGGA 58.183 34.615 0.00 0.00 43.96 2.94
3063 3150 8.462016 GTCATTTTAGTGACTTGCATTTAGGAT 58.538 33.333 0.00 0.00 43.96 3.24
3064 3151 8.461222 TCATTTTAGTGACTTGCATTTAGGATG 58.539 33.333 0.00 0.00 0.00 3.51
3065 3152 7.994425 TTTTAGTGACTTGCATTTAGGATGA 57.006 32.000 0.00 0.00 0.00 2.92
3066 3153 7.994425 TTTAGTGACTTGCATTTAGGATGAA 57.006 32.000 0.00 0.00 0.00 2.57
3067 3154 7.994425 TTAGTGACTTGCATTTAGGATGAAA 57.006 32.000 0.00 0.00 0.00 2.69
3068 3155 6.259550 AGTGACTTGCATTTAGGATGAAAC 57.740 37.500 0.00 0.00 0.00 2.78
3069 3156 6.006449 AGTGACTTGCATTTAGGATGAAACT 58.994 36.000 0.00 0.00 0.00 2.66
3070 3157 6.072286 AGTGACTTGCATTTAGGATGAAACTG 60.072 38.462 0.00 0.00 0.00 3.16
3071 3158 5.064441 ACTTGCATTTAGGATGAAACTGC 57.936 39.130 0.00 0.00 0.00 4.40
3072 3159 4.768968 ACTTGCATTTAGGATGAAACTGCT 59.231 37.500 0.00 0.00 0.00 4.24
3073 3160 4.707030 TGCATTTAGGATGAAACTGCTG 57.293 40.909 0.00 0.00 0.00 4.41
3074 3161 3.444742 TGCATTTAGGATGAAACTGCTGG 59.555 43.478 0.00 0.00 0.00 4.85
3075 3162 3.445096 GCATTTAGGATGAAACTGCTGGT 59.555 43.478 0.00 0.00 0.00 4.00
3076 3163 4.676196 GCATTTAGGATGAAACTGCTGGTG 60.676 45.833 0.00 0.00 0.00 4.17
3077 3164 3.788227 TTAGGATGAAACTGCTGGTGT 57.212 42.857 0.00 0.00 0.00 4.16
3078 3165 2.191128 AGGATGAAACTGCTGGTGTC 57.809 50.000 0.00 0.00 32.91 3.67
3079 3166 1.701847 AGGATGAAACTGCTGGTGTCT 59.298 47.619 0.00 0.00 33.45 3.41
3080 3167 2.107204 AGGATGAAACTGCTGGTGTCTT 59.893 45.455 0.00 0.00 33.45 3.01
3081 3168 2.887152 GGATGAAACTGCTGGTGTCTTT 59.113 45.455 0.00 0.00 33.45 2.52
3082 3169 3.304928 GGATGAAACTGCTGGTGTCTTTG 60.305 47.826 0.00 0.00 33.45 2.77
3083 3170 2.997980 TGAAACTGCTGGTGTCTTTGA 58.002 42.857 0.00 0.00 33.45 2.69
3084 3171 3.554934 TGAAACTGCTGGTGTCTTTGAT 58.445 40.909 0.00 0.00 33.45 2.57
3085 3172 3.953612 TGAAACTGCTGGTGTCTTTGATT 59.046 39.130 0.00 0.00 33.45 2.57
3086 3173 3.996150 AACTGCTGGTGTCTTTGATTG 57.004 42.857 0.00 0.00 0.00 2.67
3087 3174 2.936202 ACTGCTGGTGTCTTTGATTGT 58.064 42.857 0.00 0.00 0.00 2.71
3088 3175 3.290710 ACTGCTGGTGTCTTTGATTGTT 58.709 40.909 0.00 0.00 0.00 2.83
3089 3176 4.460263 ACTGCTGGTGTCTTTGATTGTTA 58.540 39.130 0.00 0.00 0.00 2.41
3090 3177 4.275936 ACTGCTGGTGTCTTTGATTGTTAC 59.724 41.667 0.00 0.00 0.00 2.50
3091 3178 4.460263 TGCTGGTGTCTTTGATTGTTACT 58.540 39.130 0.00 0.00 0.00 2.24
3092 3179 4.275689 TGCTGGTGTCTTTGATTGTTACTG 59.724 41.667 0.00 0.00 0.00 2.74
3093 3180 4.275936 GCTGGTGTCTTTGATTGTTACTGT 59.724 41.667 0.00 0.00 0.00 3.55
3094 3181 5.468746 GCTGGTGTCTTTGATTGTTACTGTA 59.531 40.000 0.00 0.00 0.00 2.74
3095 3182 6.347725 GCTGGTGTCTTTGATTGTTACTGTAG 60.348 42.308 0.00 0.00 0.00 2.74
3134 3221 9.727859 TTTTAGTGACTTGCATGTAACCTTATA 57.272 29.630 15.03 0.84 0.00 0.98
3213 3300 7.974675 AGTGAATTTAATATCGTGTTGACAGG 58.025 34.615 0.00 0.00 0.00 4.00
3304 3399 3.966665 TCATTTTCTGTTGCTTCCCCTTT 59.033 39.130 0.00 0.00 0.00 3.11
3305 3400 4.408596 TCATTTTCTGTTGCTTCCCCTTTT 59.591 37.500 0.00 0.00 0.00 2.27
3336 3431 8.134895 CCTAGAAAGAACAACTGTTGCATTTTA 58.865 33.333 19.82 8.65 38.56 1.52
3346 3441 8.194104 ACAACTGTTGCATTTTAGTTCATGTTA 58.806 29.630 19.82 0.00 31.47 2.41
3349 3444 6.155827 TGTTGCATTTTAGTTCATGTTAGCC 58.844 36.000 0.00 0.00 0.00 3.93
3351 3446 6.194796 TGCATTTTAGTTCATGTTAGCCTC 57.805 37.500 0.00 0.00 0.00 4.70
3354 3449 7.609918 TGCATTTTAGTTCATGTTAGCCTCTAA 59.390 33.333 0.00 0.00 0.00 2.10
3365 3460 6.481434 TGTTAGCCTCTAATTCTTAGGTCC 57.519 41.667 0.00 0.00 34.00 4.46
3447 3542 6.265196 ACATGCAAATTCAGTTGGAAGTTCTA 59.735 34.615 2.25 0.00 41.50 2.10
3449 3544 7.288810 TGCAAATTCAGTTGGAAGTTCTAAT 57.711 32.000 4.86 0.00 41.50 1.73
3517 3612 1.327303 TGTGTTGGGAGGTTCATTGC 58.673 50.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 2.919229 CTCATTCGGTTGATTTTGCTGC 59.081 45.455 0.00 0.00 0.00 5.25
160 161 1.062525 GGGCGATTTTGCTGTAGCG 59.937 57.895 0.00 0.00 45.83 4.26
198 199 1.755380 AGGATTCCTAGGGTTCGAACG 59.245 52.381 21.34 7.92 28.47 3.95
224 225 3.315949 GGGTGGTGGCGGACTGTA 61.316 66.667 0.00 0.00 0.00 2.74
409 411 3.998672 GGAACCGACCGCTCACCA 61.999 66.667 0.00 0.00 0.00 4.17
571 573 2.020720 TCTCTCCTCATCGTTGCTCTC 58.979 52.381 0.00 0.00 0.00 3.20
582 584 0.826715 CAGCCCGAAATCTCTCCTCA 59.173 55.000 0.00 0.00 0.00 3.86
596 598 0.040067 CTGTTTCGAAACTGCAGCCC 60.040 55.000 33.94 12.23 39.59 5.19
619 621 1.557651 GTTCTATCCTCGTTCGTGGC 58.442 55.000 8.20 0.00 0.00 5.01
656 658 2.355986 CCTGGTCGGGATCGGTTCA 61.356 63.158 0.00 0.00 36.95 3.18
753 755 3.663233 CGAAATCTAAAAAGTGCACGCGA 60.663 43.478 15.93 3.40 0.00 5.87
775 777 6.650239 TTTAGCTTTTGTTTTTCGAAACCC 57.350 33.333 10.79 4.57 31.87 4.11
843 845 2.531376 CGGAATTTCGCGTAGGCCC 61.531 63.158 5.77 2.68 35.02 5.80
876 878 1.689959 CGCTGTGAATTTGTTGGAGC 58.310 50.000 0.00 0.00 0.00 4.70
877 879 1.001487 TGCGCTGTGAATTTGTTGGAG 60.001 47.619 9.73 0.00 0.00 3.86
880 882 0.780002 GCTGCGCTGTGAATTTGTTG 59.220 50.000 16.05 0.00 0.00 3.33
884 886 1.286880 GTGGCTGCGCTGTGAATTT 59.713 52.632 16.05 0.00 0.00 1.82
1047 1052 2.776913 GGCGGAAGACTCCTCCTCG 61.777 68.421 0.00 0.00 42.61 4.63
1209 1238 2.655685 GCCTCGGCGTCGATCTTC 60.656 66.667 14.65 0.00 45.04 2.87
1367 1435 2.604686 AGAGTGCCTTCTCCGCCA 60.605 61.111 0.00 0.00 35.28 5.69
1494 1562 2.295909 CAGGATCTTGATCTCGTCCTCC 59.704 54.545 0.00 0.76 37.20 4.30
1524 1592 3.723348 GCCTTGACGTGGCGAACC 61.723 66.667 0.00 0.00 41.03 3.62
1572 1640 2.259204 CCACCAACCGCAGCAATG 59.741 61.111 0.00 0.00 0.00 2.82
1596 1664 2.249844 TGGTGACGTTCTTCCTTTCC 57.750 50.000 0.00 0.00 0.00 3.13
1797 1865 1.271597 TGCTCCTTCTTCTTGCCCTTC 60.272 52.381 0.00 0.00 0.00 3.46
1801 1869 1.003003 AGTCTGCTCCTTCTTCTTGCC 59.997 52.381 0.00 0.00 0.00 4.52
1814 1882 3.071602 TGTTTTCTCCTTGCTAGTCTGCT 59.928 43.478 0.00 0.00 0.00 4.24
1842 1910 2.158534 TGCTGTACCACCCTTTGAATGT 60.159 45.455 0.00 0.00 0.00 2.71
1871 1939 4.569023 CATCGGCGCTAGCGGTGA 62.569 66.667 35.86 18.78 46.35 4.02
1935 2003 5.745312 TGCTATCTTCTTCAACCTTCTCA 57.255 39.130 0.00 0.00 0.00 3.27
1944 2012 2.092753 CCTGCCCTTGCTATCTTCTTCA 60.093 50.000 0.00 0.00 38.71 3.02
2028 2096 1.748591 GCATCGCCTTCCAATTCCTCT 60.749 52.381 0.00 0.00 0.00 3.69
2145 2213 1.050204 GGCTCTCTGCATCTCCATCT 58.950 55.000 0.00 0.00 45.15 2.90
2194 2262 0.108396 GCAAGGGTGCCACCATTTTT 59.892 50.000 17.22 1.29 39.55 1.94
2233 2301 7.286316 AGTGTCCATTTTCTCTTCATGAGTTTT 59.714 33.333 0.00 0.00 43.13 2.43
2270 2338 4.139420 CTTTGCGCGTGCCTCTCG 62.139 66.667 19.87 0.00 41.78 4.04
2310 2378 4.720273 ACATAAGAGGTAAGGTTGGGGTAG 59.280 45.833 0.00 0.00 0.00 3.18
2415 2483 4.213513 GCCTCTTGATCTTGGATTCCAAT 58.786 43.478 18.28 4.90 43.07 3.16
2435 2503 2.999355 CTCAACTCAGCTACTCTTTGCC 59.001 50.000 0.00 0.00 0.00 4.52
2490 2558 6.488006 GCAATCCTATGAATATGTTGGTCACT 59.512 38.462 0.00 0.00 0.00 3.41
2563 2631 7.268586 ACATAATAACACAGGAGTAAGCAGAG 58.731 38.462 0.00 0.00 0.00 3.35
2623 2691 3.474600 AGTAGGATGCATCACATTGAGC 58.525 45.455 27.25 8.02 39.84 4.26
2702 2777 4.948004 CCGCCTAATCTTCCTAACCTTTTT 59.052 41.667 0.00 0.00 0.00 1.94
2713 2788 1.202698 ACCTGCATCCGCCTAATCTTC 60.203 52.381 0.00 0.00 37.32 2.87
2775 2850 2.689034 AGGGCCTCACTACCTGCC 60.689 66.667 0.00 0.00 43.26 4.85
2781 2856 1.204146 GGATTCACAGGGCCTCACTA 58.796 55.000 0.95 0.00 0.00 2.74
2799 2874 0.588252 CAGACTTTCAGTTGCCACGG 59.412 55.000 0.00 0.00 0.00 4.94
2851 2926 8.442632 TGAATAGAAGCATAAGAAATGAGTGG 57.557 34.615 0.00 0.00 0.00 4.00
2852 2927 9.932699 CTTGAATAGAAGCATAAGAAATGAGTG 57.067 33.333 0.00 0.00 0.00 3.51
2853 2928 9.678260 ACTTGAATAGAAGCATAAGAAATGAGT 57.322 29.630 0.00 0.00 0.00 3.41
2859 2937 9.905713 AACCATACTTGAATAGAAGCATAAGAA 57.094 29.630 0.00 0.00 0.00 2.52
2878 2964 9.694137 GAGTATCTAAATACAGTGGAACCATAC 57.306 37.037 0.00 0.00 40.28 2.39
2903 2989 6.318648 ACAAGTCAATACTGCAGAAAAACTGA 59.681 34.615 23.35 10.69 41.55 3.41
2912 2999 7.335422 AGGAAGATTAACAAGTCAATACTGCAG 59.665 37.037 13.48 13.48 35.62 4.41
2920 3007 6.899393 ATTGCAGGAAGATTAACAAGTCAA 57.101 33.333 0.00 0.00 0.00 3.18
2929 3016 7.936847 ACCGACATAATAATTGCAGGAAGATTA 59.063 33.333 0.00 0.00 0.00 1.75
2948 3035 7.065324 CCACAATACAATAACAGTAACCGACAT 59.935 37.037 0.00 0.00 0.00 3.06
2988 3075 3.087031 CACCAGCAGTTTCATCCTGAAT 58.913 45.455 0.00 0.00 36.11 2.57
2997 3084 4.202050 ACAATCAAAGACACCAGCAGTTTC 60.202 41.667 0.00 0.00 0.00 2.78
3038 3125 7.994425 TCCTAAATGCAAGTCACTAAAATGA 57.006 32.000 0.00 0.00 0.00 2.57
3039 3126 8.461222 TCATCCTAAATGCAAGTCACTAAAATG 58.539 33.333 0.00 0.00 0.00 2.32
3040 3127 8.579850 TCATCCTAAATGCAAGTCACTAAAAT 57.420 30.769 0.00 0.00 0.00 1.82
3041 3128 7.994425 TCATCCTAAATGCAAGTCACTAAAA 57.006 32.000 0.00 0.00 0.00 1.52
3042 3129 7.994425 TTCATCCTAAATGCAAGTCACTAAA 57.006 32.000 0.00 0.00 0.00 1.85
3043 3130 7.665559 AGTTTCATCCTAAATGCAAGTCACTAA 59.334 33.333 0.00 0.00 0.00 2.24
3044 3131 7.119699 CAGTTTCATCCTAAATGCAAGTCACTA 59.880 37.037 0.00 0.00 0.00 2.74
3045 3132 6.006449 AGTTTCATCCTAAATGCAAGTCACT 58.994 36.000 0.00 0.00 0.00 3.41
3046 3133 6.088824 CAGTTTCATCCTAAATGCAAGTCAC 58.911 40.000 0.00 0.00 0.00 3.67
3047 3134 5.335897 GCAGTTTCATCCTAAATGCAAGTCA 60.336 40.000 0.00 0.00 32.58 3.41
3048 3135 5.098211 GCAGTTTCATCCTAAATGCAAGTC 58.902 41.667 0.00 0.00 32.58 3.01
3049 3136 4.768968 AGCAGTTTCATCCTAAATGCAAGT 59.231 37.500 10.09 0.00 34.71 3.16
3050 3137 5.100259 CAGCAGTTTCATCCTAAATGCAAG 58.900 41.667 10.09 0.00 34.71 4.01
3051 3138 4.082081 CCAGCAGTTTCATCCTAAATGCAA 60.082 41.667 10.09 0.00 34.71 4.08
3052 3139 3.444742 CCAGCAGTTTCATCCTAAATGCA 59.555 43.478 10.09 0.00 34.71 3.96
3053 3140 3.445096 ACCAGCAGTTTCATCCTAAATGC 59.555 43.478 0.00 0.00 0.00 3.56
3054 3141 4.460382 ACACCAGCAGTTTCATCCTAAATG 59.540 41.667 0.00 0.00 0.00 2.32
3055 3142 4.666512 ACACCAGCAGTTTCATCCTAAAT 58.333 39.130 0.00 0.00 0.00 1.40
3056 3143 4.072131 GACACCAGCAGTTTCATCCTAAA 58.928 43.478 0.00 0.00 0.00 1.85
3057 3144 3.327757 AGACACCAGCAGTTTCATCCTAA 59.672 43.478 0.00 0.00 0.00 2.69
3058 3145 2.906389 AGACACCAGCAGTTTCATCCTA 59.094 45.455 0.00 0.00 0.00 2.94
3059 3146 1.701847 AGACACCAGCAGTTTCATCCT 59.298 47.619 0.00 0.00 0.00 3.24
3060 3147 2.191128 AGACACCAGCAGTTTCATCC 57.809 50.000 0.00 0.00 0.00 3.51
3061 3148 3.565482 TCAAAGACACCAGCAGTTTCATC 59.435 43.478 0.00 0.00 0.00 2.92
3062 3149 3.554934 TCAAAGACACCAGCAGTTTCAT 58.445 40.909 0.00 0.00 0.00 2.57
3063 3150 2.997980 TCAAAGACACCAGCAGTTTCA 58.002 42.857 0.00 0.00 0.00 2.69
3064 3151 4.202050 ACAATCAAAGACACCAGCAGTTTC 60.202 41.667 0.00 0.00 0.00 2.78
3065 3152 3.701040 ACAATCAAAGACACCAGCAGTTT 59.299 39.130 0.00 0.00 0.00 2.66
3066 3153 3.290710 ACAATCAAAGACACCAGCAGTT 58.709 40.909 0.00 0.00 0.00 3.16
3067 3154 2.936202 ACAATCAAAGACACCAGCAGT 58.064 42.857 0.00 0.00 0.00 4.40
3068 3155 3.996150 AACAATCAAAGACACCAGCAG 57.004 42.857 0.00 0.00 0.00 4.24
3069 3156 4.275689 CAGTAACAATCAAAGACACCAGCA 59.724 41.667 0.00 0.00 0.00 4.41
3070 3157 4.275936 ACAGTAACAATCAAAGACACCAGC 59.724 41.667 0.00 0.00 0.00 4.85
3071 3158 6.929049 TCTACAGTAACAATCAAAGACACCAG 59.071 38.462 0.00 0.00 0.00 4.00
3072 3159 6.822442 TCTACAGTAACAATCAAAGACACCA 58.178 36.000 0.00 0.00 0.00 4.17
3073 3160 6.929606 ACTCTACAGTAACAATCAAAGACACC 59.070 38.462 0.00 0.00 0.00 4.16
3074 3161 7.948278 ACTCTACAGTAACAATCAAAGACAC 57.052 36.000 0.00 0.00 0.00 3.67
3075 3162 8.958119 AAACTCTACAGTAACAATCAAAGACA 57.042 30.769 0.00 0.00 30.14 3.41
3076 3163 9.262358 AGAAACTCTACAGTAACAATCAAAGAC 57.738 33.333 0.00 0.00 30.14 3.01
3080 3167 9.909644 GACTAGAAACTCTACAGTAACAATCAA 57.090 33.333 0.00 0.00 30.14 2.57
3081 3168 9.074576 TGACTAGAAACTCTACAGTAACAATCA 57.925 33.333 0.00 0.00 30.14 2.57
3089 3176 9.915629 CACTAAAATGACTAGAAACTCTACAGT 57.084 33.333 0.00 0.00 0.00 3.55
3091 3178 9.909644 GTCACTAAAATGACTAGAAACTCTACA 57.090 33.333 0.00 0.00 44.71 2.74
3120 3207 9.109393 TGAAAACTGAGATATAAGGTTACATGC 57.891 33.333 0.00 0.00 0.00 4.06
3124 3211 9.162764 TGCTTGAAAACTGAGATATAAGGTTAC 57.837 33.333 0.00 0.00 0.00 2.50
3172 3259 9.853555 TTAAATTCACTTAACTAATCGACCGTA 57.146 29.630 0.00 0.00 0.00 4.02
3272 3367 8.627208 AAGCAACAGAAAATGATCTCTAAGAA 57.373 30.769 0.00 0.00 0.00 2.52
3289 3384 3.193479 GGATACAAAAGGGGAAGCAACAG 59.807 47.826 0.00 0.00 0.00 3.16
3304 3399 7.041372 GCAACAGTTGTTCTTTCTAGGATACAA 60.041 37.037 14.88 0.00 35.83 2.41
3305 3400 6.426937 GCAACAGTTGTTCTTTCTAGGATACA 59.573 38.462 14.88 0.00 35.83 2.29
3354 3449 5.160607 TGTCAAATGTCGGACCTAAGAAT 57.839 39.130 5.55 0.00 33.09 2.40
3447 3542 7.281774 CACCATACTTTAGCATTCTCTGTGATT 59.718 37.037 0.00 0.00 0.00 2.57
3449 3544 6.108687 CACCATACTTTAGCATTCTCTGTGA 58.891 40.000 0.00 0.00 0.00 3.58
3492 3587 2.621055 TGAACCTCCCAACACAATTTCG 59.379 45.455 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.