Multiple sequence alignment - TraesCS2A01G291400

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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 TraesCS2A01G291400 chr2A 100.000 3125 0 0 1 3125 502323767 502320643 0.000000e+00 5771.0
1 TraesCS2A01G291400 chr2D 92.162 2845 123 38 288 3079 371690750 371687953 0.000000e+00 3927.0
2 TraesCS2A01G291400 chr2D 82.222 270 8 13 27 295 371691014 371690784 2.460000e-46 196.0
3 TraesCS2A01G291400 chr2D 80.447 179 26 7 2907 3079 628340080 628340255 9.100000e-26 128.0
4 TraesCS2A01G291400 chr2B 91.603 2620 129 35 288 2864 440766201 440763630 0.000000e+00 3535.0
5 TraesCS2A01G291400 chr2B 84.871 271 12 9 30 295 440766477 440766231 2.410000e-61 246.0
6 TraesCS2A01G291400 chr2B 83.077 65 11 0 2904 2968 165095073 165095137 3.370000e-05 60.2
7 TraesCS2A01G291400 chr4A 82.162 185 22 6 2904 3079 31578730 31578548 6.980000e-32 148.0
8 TraesCS2A01G291400 chr7D 76.923 247 30 13 2857 3079 602173961 602174204 7.080000e-22 115.0
9 TraesCS2A01G291400 chr6B 93.182 44 3 0 2926 2969 563477078 563477035 7.230000e-07 65.8


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 TraesCS2A01G291400 chr2A 502320643 502323767 3124 True 5771.0 5771 100.000 1 3125 1 chr2A.!!$R1 3124
1 TraesCS2A01G291400 chr2D 371687953 371691014 3061 True 2061.5 3927 87.192 27 3079 2 chr2D.!!$R1 3052
2 TraesCS2A01G291400 chr2B 440763630 440766477 2847 True 1890.5 3535 88.237 30 2864 2 chr2B.!!$R1 2834

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
390 441 0.093535 GCGGGAAGCGTAACGTAAAC 59.906 55.0 0.00 0.00 35.41 2.01 F
572 628 0.395312 AGACCCGTTGTTACCAGTGG 59.605 55.0 7.91 7.91 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 2004 0.178975 CGGAGAGCCAGTAGGAGGAT 60.179 60.0 0.0 0.0 36.89 3.24 R
2423 2527 0.034756 CATGTCCCGTCTCCAACACA 59.965 55.0 0.0 0.0 0.00 3.72 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
21 22 3.453059 ACTACTACAGTGTACAGGCCT 57.547 47.619 0.00 0.00 35.62 5.19
22 23 3.354467 ACTACTACAGTGTACAGGCCTC 58.646 50.000 0.00 0.00 35.62 4.70
23 24 2.304221 ACTACAGTGTACAGGCCTCA 57.696 50.000 0.00 0.00 0.00 3.86
24 25 2.821437 ACTACAGTGTACAGGCCTCAT 58.179 47.619 0.00 0.00 0.00 2.90
25 26 2.497675 ACTACAGTGTACAGGCCTCATG 59.502 50.000 0.00 0.00 0.00 3.07
97 98 1.082300 CGCTGCTGAGTTTGTGCTG 60.082 57.895 0.00 0.00 0.00 4.41
123 124 2.627515 CCATGGTGATGGTGGAGTAG 57.372 55.000 2.57 0.00 43.98 2.57
124 125 1.475751 CCATGGTGATGGTGGAGTAGC 60.476 57.143 2.57 0.00 43.98 3.58
125 126 1.487976 CATGGTGATGGTGGAGTAGCT 59.512 52.381 0.00 0.00 0.00 3.32
126 127 1.195115 TGGTGATGGTGGAGTAGCTC 58.805 55.000 0.00 0.00 0.00 4.09
127 128 1.273267 TGGTGATGGTGGAGTAGCTCT 60.273 52.381 0.00 0.00 0.00 4.09
215 217 1.737793 GGAATCATGGAACGGACACAC 59.262 52.381 0.00 0.00 0.00 3.82
225 227 2.014554 CGGACACACGTCGGACAAG 61.015 63.158 9.10 2.17 43.30 3.16
242 244 3.596214 ACAAGAACCATGACCATCGTAC 58.404 45.455 0.00 0.00 0.00 3.67
248 250 2.098607 ACCATGACCATCGTACGTGTAG 59.901 50.000 16.05 5.54 0.00 2.74
390 441 0.093535 GCGGGAAGCGTAACGTAAAC 59.906 55.000 0.00 0.00 35.41 2.01
404 455 1.268625 CGTAAACCCTTTTCCCACTGC 59.731 52.381 0.00 0.00 0.00 4.40
443 498 9.832445 TCCAGTAGTAATTTTCATCAACCTATC 57.168 33.333 0.00 0.00 0.00 2.08
523 578 0.958382 TGGCACGGCACCAGTAATTC 60.958 55.000 0.00 0.00 32.06 2.17
556 612 7.478520 TTTTACTTGACACTCTGCTTAAGAC 57.521 36.000 6.67 0.00 0.00 3.01
567 623 2.740447 CTGCTTAAGACCCGTTGTTACC 59.260 50.000 6.67 0.00 0.00 2.85
569 625 2.740447 GCTTAAGACCCGTTGTTACCAG 59.260 50.000 6.67 0.00 0.00 4.00
570 626 3.804759 GCTTAAGACCCGTTGTTACCAGT 60.805 47.826 6.67 0.00 0.00 4.00
571 627 2.249844 AAGACCCGTTGTTACCAGTG 57.750 50.000 0.00 0.00 0.00 3.66
572 628 0.395312 AGACCCGTTGTTACCAGTGG 59.605 55.000 7.91 7.91 0.00 4.00
579 637 2.352814 CGTTGTTACCAGTGGAGAGAGG 60.353 54.545 18.40 0.00 0.00 3.69
665 723 4.785453 GCCCTGACCGAGCCCTTG 62.785 72.222 0.00 0.00 0.00 3.61
690 751 2.074547 TTTCCTTCTTCTACGTGCGG 57.925 50.000 0.00 0.00 0.00 5.69
804 873 3.813724 CCCCTGCCACTCCCATCC 61.814 72.222 0.00 0.00 0.00 3.51
930 999 3.344215 GCGGCAGATCGGCATCAG 61.344 66.667 19.63 8.52 41.26 2.90
944 1013 1.206610 GCATCAGGAGAGCAACTGAGA 59.793 52.381 0.00 0.00 45.87 3.27
946 1015 2.001076 TCAGGAGAGCAACTGAGACA 57.999 50.000 0.00 0.00 38.71 3.41
973 1057 1.331756 GGCACAGCATTACCAAGATCG 59.668 52.381 0.00 0.00 0.00 3.69
986 1073 1.478510 CAAGATCGTAGCACAGGAGGT 59.521 52.381 0.00 0.00 0.00 3.85
1015 1102 1.821332 GGCATGGAGGAGAAAGCGG 60.821 63.158 0.00 0.00 0.00 5.52
1068 1155 1.026718 CGGTGGATCAAGAAGTGGCC 61.027 60.000 0.00 0.00 0.00 5.36
1224 1311 4.796231 CCGCCTTCCTCCGTCACG 62.796 72.222 0.00 0.00 0.00 4.35
1260 1347 3.936203 AACAGGCTCGCCACCGAA 61.936 61.111 11.02 0.00 43.87 4.30
1270 1357 3.546218 GCTCGCCACCGAAAATCTTTATC 60.546 47.826 0.00 0.00 43.87 1.75
1317 1404 2.594303 CCGCACAAGGGCAAGACA 60.594 61.111 0.00 0.00 0.00 3.41
1320 1407 0.957395 CGCACAAGGGCAAGACATCT 60.957 55.000 0.00 0.00 0.00 2.90
1414 1501 2.036731 TGTCGTCCGGGATCACCT 59.963 61.111 0.00 0.00 36.97 4.00
1420 1507 1.753078 TCCGGGATCACCTCTGACG 60.753 63.158 0.00 0.00 36.97 4.35
1611 1698 2.632602 TAGAGGAGCCTGAGAGCCCG 62.633 65.000 0.00 0.00 0.00 6.13
2070 2157 1.301716 GAGCTCCACGTCCAGCAAA 60.302 57.895 15.84 0.00 38.18 3.68
2280 2374 2.897326 TGTCCATTCGAGTCCTGAGAAA 59.103 45.455 0.00 0.00 0.00 2.52
2290 2384 3.096092 AGTCCTGAGAAACTGCTCCTAG 58.904 50.000 0.00 0.00 33.95 3.02
2293 2387 1.484240 CTGAGAAACTGCTCCTAGGGG 59.516 57.143 9.46 6.61 33.95 4.79
2303 2397 0.474660 CTCCTAGGGGGAAGGATGGG 60.475 65.000 9.46 0.00 44.58 4.00
2304 2398 0.939443 TCCTAGGGGGAAGGATGGGA 60.939 60.000 9.46 0.00 41.91 4.37
2305 2399 0.197145 CCTAGGGGGAAGGATGGGAT 59.803 60.000 0.00 0.00 36.08 3.85
2421 2525 8.279695 TGTTTTATGTTGAATTCATTCGTGTG 57.720 30.769 9.40 0.00 39.62 3.82
2422 2526 6.926280 TTTATGTTGAATTCATTCGTGTGC 57.074 33.333 9.40 0.00 39.62 4.57
2423 2527 4.771590 ATGTTGAATTCATTCGTGTGCT 57.228 36.364 9.40 0.00 39.62 4.40
2424 2528 3.887741 TGTTGAATTCATTCGTGTGCTG 58.112 40.909 9.40 0.00 39.62 4.41
2425 2529 3.314913 TGTTGAATTCATTCGTGTGCTGT 59.685 39.130 9.40 0.00 39.62 4.40
2443 2547 0.673644 GTGTTGGAGACGGGACATGG 60.674 60.000 0.00 0.00 0.00 3.66
2479 2583 7.338957 TGAAAAGGAGAAATTTGGCAATTTGTT 59.661 29.630 0.00 0.00 41.79 2.83
2488 2592 8.674263 AAATTTGGCAATTTGTTCATCAGTTA 57.326 26.923 0.00 0.00 40.48 2.24
2493 2597 7.537715 TGGCAATTTGTTCATCAGTTATGTAG 58.462 34.615 0.00 0.00 36.89 2.74
2494 2598 7.176515 TGGCAATTTGTTCATCAGTTATGTAGT 59.823 33.333 0.00 0.00 36.89 2.73
2495 2599 8.673711 GGCAATTTGTTCATCAGTTATGTAGTA 58.326 33.333 0.00 0.00 36.89 1.82
2496 2600 9.490663 GCAATTTGTTCATCAGTTATGTAGTAC 57.509 33.333 0.00 0.00 36.89 2.73
2523 2627 3.316029 TGTTCTTGTGTGCCTTGATTCAG 59.684 43.478 0.00 0.00 0.00 3.02
2534 2638 5.575606 GTGCCTTGATTCAGTTTTCATGATG 59.424 40.000 0.00 0.00 0.00 3.07
2539 2643 2.905959 TCAGTTTTCATGATGCTGCG 57.094 45.000 13.55 0.00 0.00 5.18
2583 2689 4.000988 CCTGTTAAAGCATCTACAACCGT 58.999 43.478 0.00 0.00 0.00 4.83
2601 2707 2.056577 CGTACCCGTCAAAAGTGAGTC 58.943 52.381 0.00 0.00 33.27 3.36
2625 2731 4.088634 CCCCTCAAATCTCAAATGTCCAA 58.911 43.478 0.00 0.00 0.00 3.53
2645 2751 2.872732 AGTCTACAACCGTCTTCCTCA 58.127 47.619 0.00 0.00 0.00 3.86
2677 2783 8.915057 ATCCTTAAATTCATACACTCTCATGG 57.085 34.615 0.00 0.00 0.00 3.66
2688 2794 5.862924 ACACTCTCATGGAATGTAAAACG 57.137 39.130 0.00 0.00 46.80 3.60
2739 2845 5.400782 TGCAATGTAAAATAAACACACGCAG 59.599 36.000 0.00 0.00 32.22 5.18
2851 2963 6.367969 TGTTCTAAAGGTTTGAACTATCGAGC 59.632 38.462 13.68 0.00 40.27 5.03
2954 3066 3.832615 TTTCTAGCCGATCCCCTAAAC 57.167 47.619 0.00 0.00 0.00 2.01
2958 3070 4.150359 TCTAGCCGATCCCCTAAACTTAG 58.850 47.826 0.00 0.00 0.00 2.18
2959 3071 2.760581 AGCCGATCCCCTAAACTTAGT 58.239 47.619 0.00 0.00 0.00 2.24
3001 3113 2.760634 TGCGTCACATACTCAACCAT 57.239 45.000 0.00 0.00 0.00 3.55
3002 3114 3.878160 TGCGTCACATACTCAACCATA 57.122 42.857 0.00 0.00 0.00 2.74
3003 3115 4.400529 TGCGTCACATACTCAACCATAT 57.599 40.909 0.00 0.00 0.00 1.78
3004 3116 4.765273 TGCGTCACATACTCAACCATATT 58.235 39.130 0.00 0.00 0.00 1.28
3005 3117 5.182487 TGCGTCACATACTCAACCATATTT 58.818 37.500 0.00 0.00 0.00 1.40
3006 3118 5.293324 TGCGTCACATACTCAACCATATTTC 59.707 40.000 0.00 0.00 0.00 2.17
3007 3119 5.293324 GCGTCACATACTCAACCATATTTCA 59.707 40.000 0.00 0.00 0.00 2.69
3008 3120 6.017934 GCGTCACATACTCAACCATATTTCAT 60.018 38.462 0.00 0.00 0.00 2.57
3009 3121 7.467267 GCGTCACATACTCAACCATATTTCATT 60.467 37.037 0.00 0.00 0.00 2.57
3010 3122 8.064222 CGTCACATACTCAACCATATTTCATTC 58.936 37.037 0.00 0.00 0.00 2.67
3011 3123 8.892723 GTCACATACTCAACCATATTTCATTCA 58.107 33.333 0.00 0.00 0.00 2.57
3012 3124 9.460019 TCACATACTCAACCATATTTCATTCAA 57.540 29.630 0.00 0.00 0.00 2.69
3013 3125 9.507280 CACATACTCAACCATATTTCATTCAAC 57.493 33.333 0.00 0.00 0.00 3.18
3014 3126 8.686334 ACATACTCAACCATATTTCATTCAACC 58.314 33.333 0.00 0.00 0.00 3.77
3015 3127 8.685427 CATACTCAACCATATTTCATTCAACCA 58.315 33.333 0.00 0.00 0.00 3.67
3079 3201 1.630369 TGCCACTAGAGCAAGACCAAT 59.370 47.619 9.32 0.00 37.28 3.16
3080 3202 2.040278 TGCCACTAGAGCAAGACCAATT 59.960 45.455 9.32 0.00 37.28 2.32
3081 3203 3.084786 GCCACTAGAGCAAGACCAATTT 58.915 45.455 0.00 0.00 0.00 1.82
3082 3204 3.127721 GCCACTAGAGCAAGACCAATTTC 59.872 47.826 0.00 0.00 0.00 2.17
3083 3205 4.326826 CCACTAGAGCAAGACCAATTTCA 58.673 43.478 0.00 0.00 0.00 2.69
3084 3206 4.154918 CCACTAGAGCAAGACCAATTTCAC 59.845 45.833 0.00 0.00 0.00 3.18
3085 3207 4.999950 CACTAGAGCAAGACCAATTTCACT 59.000 41.667 0.00 0.00 0.00 3.41
3086 3208 5.121454 CACTAGAGCAAGACCAATTTCACTC 59.879 44.000 0.00 0.00 0.00 3.51
3087 3209 3.416156 AGAGCAAGACCAATTTCACTCC 58.584 45.455 0.00 0.00 0.00 3.85
3088 3210 2.489722 GAGCAAGACCAATTTCACTCCC 59.510 50.000 0.00 0.00 0.00 4.30
3089 3211 2.108952 AGCAAGACCAATTTCACTCCCT 59.891 45.455 0.00 0.00 0.00 4.20
3090 3212 2.893489 GCAAGACCAATTTCACTCCCTT 59.107 45.455 0.00 0.00 0.00 3.95
3091 3213 4.079253 GCAAGACCAATTTCACTCCCTTA 58.921 43.478 0.00 0.00 0.00 2.69
3092 3214 4.082733 GCAAGACCAATTTCACTCCCTTAC 60.083 45.833 0.00 0.00 0.00 2.34
3093 3215 3.939066 AGACCAATTTCACTCCCTTACG 58.061 45.455 0.00 0.00 0.00 3.18
3094 3216 3.007635 GACCAATTTCACTCCCTTACGG 58.992 50.000 0.00 0.00 0.00 4.02
3095 3217 2.640826 ACCAATTTCACTCCCTTACGGA 59.359 45.455 0.00 0.00 38.83 4.69
3110 3232 4.561105 CTTACGGAGGATAAGGAATCTGC 58.439 47.826 0.00 0.00 34.75 4.26
3111 3233 2.683768 ACGGAGGATAAGGAATCTGCT 58.316 47.619 0.00 0.00 34.75 4.24
3112 3234 3.845860 ACGGAGGATAAGGAATCTGCTA 58.154 45.455 0.00 0.00 34.75 3.49
3113 3235 3.829601 ACGGAGGATAAGGAATCTGCTAG 59.170 47.826 0.00 0.00 34.75 3.42
3114 3236 3.194542 CGGAGGATAAGGAATCTGCTAGG 59.805 52.174 0.00 0.00 34.75 3.02
3115 3237 4.164204 GGAGGATAAGGAATCTGCTAGGT 58.836 47.826 0.00 0.00 34.75 3.08
3116 3238 4.221924 GGAGGATAAGGAATCTGCTAGGTC 59.778 50.000 0.00 0.00 34.75 3.85
3117 3239 4.164204 AGGATAAGGAATCTGCTAGGTCC 58.836 47.826 0.00 0.00 34.75 4.46
3118 3240 3.904339 GGATAAGGAATCTGCTAGGTCCA 59.096 47.826 0.00 0.00 34.75 4.02
3119 3241 4.020662 GGATAAGGAATCTGCTAGGTCCAG 60.021 50.000 0.00 0.00 34.75 3.86
3120 3242 1.799933 AGGAATCTGCTAGGTCCAGG 58.200 55.000 0.00 0.00 32.19 4.45
3121 3243 1.008938 AGGAATCTGCTAGGTCCAGGT 59.991 52.381 0.00 0.00 32.19 4.00
3122 3244 1.840635 GGAATCTGCTAGGTCCAGGTT 59.159 52.381 0.00 0.00 36.41 3.50
3123 3245 2.239907 GGAATCTGCTAGGTCCAGGTTT 59.760 50.000 0.00 0.00 33.99 3.27
3124 3246 3.308473 GGAATCTGCTAGGTCCAGGTTTT 60.308 47.826 0.00 0.00 33.99 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.762823 GAGGCCTGTACACTGTAGTAGTT 59.237 47.826 12.00 0.00 37.60 2.24
1 2 3.245158 TGAGGCCTGTACACTGTAGTAGT 60.245 47.826 12.00 0.00 41.36 2.73
2 3 3.353557 TGAGGCCTGTACACTGTAGTAG 58.646 50.000 12.00 0.00 0.00 2.57
3 4 3.444792 TGAGGCCTGTACACTGTAGTA 57.555 47.619 12.00 0.00 0.00 1.82
4 5 2.304221 TGAGGCCTGTACACTGTAGT 57.696 50.000 12.00 0.00 0.00 2.73
5 6 2.497675 ACATGAGGCCTGTACACTGTAG 59.502 50.000 12.00 0.00 0.00 2.74
6 7 2.496070 GACATGAGGCCTGTACACTGTA 59.504 50.000 12.00 0.00 0.00 2.74
7 8 1.276421 GACATGAGGCCTGTACACTGT 59.724 52.381 12.00 8.71 0.00 3.55
8 9 1.276138 TGACATGAGGCCTGTACACTG 59.724 52.381 12.00 5.48 0.00 3.66
9 10 1.644509 TGACATGAGGCCTGTACACT 58.355 50.000 12.00 0.00 0.00 3.55
10 11 2.283298 CATGACATGAGGCCTGTACAC 58.717 52.381 12.00 0.00 0.00 2.90
11 12 1.908619 ACATGACATGAGGCCTGTACA 59.091 47.619 22.19 1.20 0.00 2.90
12 13 2.283298 CACATGACATGAGGCCTGTAC 58.717 52.381 22.19 0.00 0.00 2.90
13 14 1.407299 GCACATGACATGAGGCCTGTA 60.407 52.381 22.19 0.00 0.00 2.74
14 15 0.679002 GCACATGACATGAGGCCTGT 60.679 55.000 22.19 1.56 0.00 4.00
15 16 1.381928 GGCACATGACATGAGGCCTG 61.382 60.000 30.97 18.28 44.69 4.85
16 17 1.077212 GGCACATGACATGAGGCCT 60.077 57.895 30.97 3.86 44.69 5.19
17 18 2.475466 CGGCACATGACATGAGGCC 61.475 63.158 29.69 29.69 44.66 5.19
18 19 1.709147 GACGGCACATGACATGAGGC 61.709 60.000 23.63 23.63 41.68 4.70
19 20 1.091771 GGACGGCACATGACATGAGG 61.092 60.000 22.19 13.74 0.00 3.86
20 21 1.423721 CGGACGGCACATGACATGAG 61.424 60.000 22.19 15.06 0.00 2.90
21 22 1.447663 CGGACGGCACATGACATGA 60.448 57.895 22.19 0.00 0.00 3.07
22 23 1.695893 GACGGACGGCACATGACATG 61.696 60.000 14.02 14.02 0.00 3.21
23 24 1.447838 GACGGACGGCACATGACAT 60.448 57.895 0.00 0.00 0.00 3.06
24 25 2.048597 GACGGACGGCACATGACA 60.049 61.111 0.00 0.00 0.00 3.58
25 26 3.179265 CGACGGACGGCACATGAC 61.179 66.667 0.00 0.00 38.46 3.06
110 111 2.238084 ACAGAGCTACTCCACCATCA 57.762 50.000 0.00 0.00 0.00 3.07
112 113 2.035632 GCTACAGAGCTACTCCACCAT 58.964 52.381 0.00 0.00 45.98 3.55
113 114 1.475403 GCTACAGAGCTACTCCACCA 58.525 55.000 0.00 0.00 45.98 4.17
124 125 3.131933 AGAATGTACAGCCAGCTACAGAG 59.868 47.826 0.33 0.00 0.00 3.35
125 126 3.099905 AGAATGTACAGCCAGCTACAGA 58.900 45.455 0.33 0.00 0.00 3.41
126 127 3.131933 AGAGAATGTACAGCCAGCTACAG 59.868 47.826 0.33 0.00 0.00 2.74
127 128 3.099905 AGAGAATGTACAGCCAGCTACA 58.900 45.455 0.33 0.00 0.00 2.74
185 187 4.494199 CGTTCCATGATTCCGTTTTCTAGC 60.494 45.833 0.00 0.00 0.00 3.42
215 217 1.068474 GTCATGGTTCTTGTCCGACG 58.932 55.000 0.00 0.00 0.00 5.12
225 227 1.924524 CACGTACGATGGTCATGGTTC 59.075 52.381 24.41 0.00 32.08 3.62
298 342 7.092079 TGTTCCATTGACATTGTTCATTCATC 58.908 34.615 0.00 0.00 0.00 2.92
325 369 4.537433 GAATCAGGAGCCGCGCCT 62.537 66.667 10.29 10.29 32.88 5.52
387 438 1.744320 GCGCAGTGGGAAAAGGGTTT 61.744 55.000 12.03 0.00 0.00 3.27
390 441 2.597217 TGCGCAGTGGGAAAAGGG 60.597 61.111 5.66 0.00 0.00 3.95
404 455 2.223735 ACTACTGGATAATCGTGGTGCG 60.224 50.000 0.00 0.00 43.01 5.34
421 472 8.138365 TGCGATAGGTTGATGAAAATTACTAC 57.862 34.615 0.00 0.00 0.00 2.73
441 496 3.584406 GCAGTACATCTATCCTGCGAT 57.416 47.619 0.00 0.00 40.67 4.58
460 515 0.315382 GATTGCACGTGCGATGTAGC 60.315 55.000 40.67 25.25 44.75 3.58
461 516 0.998669 TGATTGCACGTGCGATGTAG 59.001 50.000 40.67 4.31 44.75 2.74
523 578 5.293569 AGAGTGTCAAGTAAAAACAACTCGG 59.706 40.000 0.00 0.00 31.88 4.63
567 623 1.516892 GCTCTGCCTCTCTCCACTG 59.483 63.158 0.00 0.00 0.00 3.66
569 625 2.493973 CGCTCTGCCTCTCTCCAC 59.506 66.667 0.00 0.00 0.00 4.02
570 626 3.456365 GCGCTCTGCCTCTCTCCA 61.456 66.667 0.00 0.00 37.76 3.86
571 627 4.567385 CGCGCTCTGCCTCTCTCC 62.567 72.222 5.56 0.00 42.08 3.71
579 637 3.494336 ACTTGATGCGCGCTCTGC 61.494 61.111 33.29 18.20 41.47 4.26
673 731 0.242825 CACCGCACGTAGAAGAAGGA 59.757 55.000 0.00 0.00 0.00 3.36
674 732 1.352156 GCACCGCACGTAGAAGAAGG 61.352 60.000 0.00 0.00 0.00 3.46
690 751 2.125512 AAGGCTCGGTCATCGCAC 60.126 61.111 0.00 0.00 39.05 5.34
725 786 0.383860 CGTCTTTTTGTCCGGTTCGC 60.384 55.000 0.00 0.00 0.00 4.70
804 873 1.153208 GGTGGCAGAGGAGAGCATG 60.153 63.158 0.00 0.00 0.00 4.06
930 999 3.520569 GATCTTGTCTCAGTTGCTCTCC 58.479 50.000 0.00 0.00 0.00 3.71
944 1013 0.322816 AATGCTGTGCCGGATCTTGT 60.323 50.000 5.05 0.00 0.00 3.16
946 1015 1.668419 GTAATGCTGTGCCGGATCTT 58.332 50.000 5.05 0.00 0.00 2.40
973 1057 0.820871 CTCCTCACCTCCTGTGCTAC 59.179 60.000 0.00 0.00 45.03 3.58
993 1080 3.344137 TTTCTCCTCCATGCCCGCC 62.344 63.158 0.00 0.00 0.00 6.13
1043 1130 0.953471 TTCTTGATCCACCGCAACCG 60.953 55.000 0.00 0.00 0.00 4.44
1044 1131 0.804989 CTTCTTGATCCACCGCAACC 59.195 55.000 0.00 0.00 0.00 3.77
1045 1132 1.197721 CACTTCTTGATCCACCGCAAC 59.802 52.381 0.00 0.00 0.00 4.17
1257 1344 4.495844 GCGGTGGAAGGATAAAGATTTTCG 60.496 45.833 0.00 0.00 0.00 3.46
1260 1347 3.053619 AGGCGGTGGAAGGATAAAGATTT 60.054 43.478 0.00 0.00 0.00 2.17
1270 1357 4.785453 GGCAGAGGCGGTGGAAGG 62.785 72.222 0.00 0.00 42.47 3.46
1394 1481 2.362503 TGATCCCGGACGACAGCT 60.363 61.111 0.73 0.00 0.00 4.24
1404 1491 2.808315 CCGTCAGAGGTGATCCCG 59.192 66.667 0.00 0.00 38.74 5.14
1524 1611 3.441290 ACCGACTTCCTCCTCGCG 61.441 66.667 0.00 0.00 0.00 5.87
1842 1929 0.731514 GCTGCTGCGTGTACTCGTAA 60.732 55.000 17.63 6.89 0.00 3.18
1917 2004 0.178975 CGGAGAGCCAGTAGGAGGAT 60.179 60.000 0.00 0.00 36.89 3.24
2070 2157 3.100545 GGATGCCGACATGATGGTT 57.899 52.632 0.00 0.00 36.35 3.67
2238 2332 5.186198 ACATATACCAGAACCAAGAACAGC 58.814 41.667 0.00 0.00 0.00 4.40
2290 2384 1.002857 CCATATCCCATCCTTCCCCC 58.997 60.000 0.00 0.00 0.00 5.40
2293 2387 0.332972 GGCCCATATCCCATCCTTCC 59.667 60.000 0.00 0.00 0.00 3.46
2303 2397 1.740025 GCTTAATCTGCGGCCCATATC 59.260 52.381 0.00 0.00 0.00 1.63
2304 2398 1.352352 AGCTTAATCTGCGGCCCATAT 59.648 47.619 0.00 0.00 35.28 1.78
2305 2399 0.764890 AGCTTAATCTGCGGCCCATA 59.235 50.000 0.00 0.00 35.28 2.74
2331 2425 6.089417 GGAACAGAATTACAAAATGAAAGGCG 59.911 38.462 0.00 0.00 0.00 5.52
2421 2525 1.668151 GTCCCGTCTCCAACACAGC 60.668 63.158 0.00 0.00 0.00 4.40
2422 2526 0.321671 ATGTCCCGTCTCCAACACAG 59.678 55.000 0.00 0.00 0.00 3.66
2423 2527 0.034756 CATGTCCCGTCTCCAACACA 59.965 55.000 0.00 0.00 0.00 3.72
2424 2528 0.673644 CCATGTCCCGTCTCCAACAC 60.674 60.000 0.00 0.00 0.00 3.32
2425 2529 1.676968 CCATGTCCCGTCTCCAACA 59.323 57.895 0.00 0.00 0.00 3.33
2443 2547 7.677454 AATTTCTCCTTTTCAATTCAATGCC 57.323 32.000 0.00 0.00 0.00 4.40
2479 2583 7.956328 ACAAGGAGTACTACATAACTGATGA 57.044 36.000 8.10 0.00 39.06 2.92
2488 2592 6.223852 CACACAAGAACAAGGAGTACTACAT 58.776 40.000 8.10 0.00 0.00 2.29
2493 2597 2.548480 GGCACACAAGAACAAGGAGTAC 59.452 50.000 0.00 0.00 0.00 2.73
2494 2598 2.438021 AGGCACACAAGAACAAGGAGTA 59.562 45.455 0.00 0.00 0.00 2.59
2495 2599 1.212935 AGGCACACAAGAACAAGGAGT 59.787 47.619 0.00 0.00 0.00 3.85
2496 2600 1.972872 AGGCACACAAGAACAAGGAG 58.027 50.000 0.00 0.00 0.00 3.69
2497 2601 2.023673 CAAGGCACACAAGAACAAGGA 58.976 47.619 0.00 0.00 0.00 3.36
2498 2602 2.023673 TCAAGGCACACAAGAACAAGG 58.976 47.619 0.00 0.00 0.00 3.61
2523 2627 1.199789 TGGTCGCAGCATCATGAAAAC 59.800 47.619 0.00 0.00 0.00 2.43
2534 2638 2.728922 GTAGTATAGTGTGGTCGCAGC 58.271 52.381 0.00 0.00 0.00 5.25
2539 2643 3.065925 GTCACCCGTAGTATAGTGTGGTC 59.934 52.174 0.00 0.00 0.00 4.02
2583 2689 1.603678 GCGACTCACTTTTGACGGGTA 60.604 52.381 0.00 0.00 0.00 3.69
2601 2707 2.094675 ACATTTGAGATTTGAGGGGCG 58.905 47.619 0.00 0.00 0.00 6.13
2625 2731 2.872732 TGAGGAAGACGGTTGTAGACT 58.127 47.619 0.00 0.00 0.00 3.24
2677 2783 3.609475 TGCGTGTGTTCGTTTTACATTC 58.391 40.909 0.00 0.00 0.00 2.67
2688 2794 7.688989 TGTTTATTTATATCGTTGCGTGTGTTC 59.311 33.333 0.00 0.00 0.00 3.18
2739 2845 6.845280 TGAACTACGTGTGTTTATTTTTACGC 59.155 34.615 0.00 0.00 35.17 4.42
2835 2947 5.803020 AAATGAGCTCGATAGTTCAAACC 57.197 39.130 9.64 0.00 44.80 3.27
2922 3034 5.155278 TCGGCTAGAAATGGTCAAAACTA 57.845 39.130 0.00 0.00 0.00 2.24
2930 3042 0.765510 GGGGATCGGCTAGAAATGGT 59.234 55.000 0.00 0.00 0.00 3.55
3003 3115 9.138062 CGTTGAATGAAATATGGTTGAATGAAA 57.862 29.630 0.00 0.00 0.00 2.69
3004 3116 8.518702 TCGTTGAATGAAATATGGTTGAATGAA 58.481 29.630 0.00 0.00 0.00 2.57
3005 3117 7.967854 GTCGTTGAATGAAATATGGTTGAATGA 59.032 33.333 0.00 0.00 0.00 2.57
3006 3118 7.754475 TGTCGTTGAATGAAATATGGTTGAATG 59.246 33.333 0.00 0.00 0.00 2.67
3007 3119 7.825681 TGTCGTTGAATGAAATATGGTTGAAT 58.174 30.769 0.00 0.00 0.00 2.57
3008 3120 7.208225 TGTCGTTGAATGAAATATGGTTGAA 57.792 32.000 0.00 0.00 0.00 2.69
3009 3121 6.809630 TGTCGTTGAATGAAATATGGTTGA 57.190 33.333 0.00 0.00 0.00 3.18
3010 3122 7.009448 CCAATGTCGTTGAATGAAATATGGTTG 59.991 37.037 6.35 0.00 40.37 3.77
3011 3123 7.035004 CCAATGTCGTTGAATGAAATATGGTT 58.965 34.615 6.35 0.00 40.37 3.67
3012 3124 6.376864 TCCAATGTCGTTGAATGAAATATGGT 59.623 34.615 6.35 0.00 40.37 3.55
3013 3125 6.794374 TCCAATGTCGTTGAATGAAATATGG 58.206 36.000 6.35 10.21 40.37 2.74
3014 3126 7.475015 ACTCCAATGTCGTTGAATGAAATATG 58.525 34.615 6.35 0.00 40.37 1.78
3015 3127 7.630242 ACTCCAATGTCGTTGAATGAAATAT 57.370 32.000 6.35 0.00 40.37 1.28
3059 3181 1.055849 TTGGTCTTGCTCTAGTGGCA 58.944 50.000 8.57 8.57 37.97 4.92
3085 3207 4.140758 AGATTCCTTATCCTCCGTAAGGGA 60.141 45.833 10.96 4.11 46.23 4.20
3086 3208 4.021016 CAGATTCCTTATCCTCCGTAAGGG 60.021 50.000 10.96 0.00 46.23 3.95
3088 3210 4.282195 AGCAGATTCCTTATCCTCCGTAAG 59.718 45.833 0.00 0.00 33.45 2.34
3089 3211 4.223953 AGCAGATTCCTTATCCTCCGTAA 58.776 43.478 0.00 0.00 33.45 3.18
3090 3212 3.845860 AGCAGATTCCTTATCCTCCGTA 58.154 45.455 0.00 0.00 33.45 4.02
3091 3213 2.683768 AGCAGATTCCTTATCCTCCGT 58.316 47.619 0.00 0.00 33.45 4.69
3092 3214 3.194542 CCTAGCAGATTCCTTATCCTCCG 59.805 52.174 0.00 0.00 33.45 4.63
3093 3215 4.164204 ACCTAGCAGATTCCTTATCCTCC 58.836 47.826 0.00 0.00 33.45 4.30
3094 3216 4.221924 GGACCTAGCAGATTCCTTATCCTC 59.778 50.000 0.00 0.00 33.45 3.71
3095 3217 4.164204 GGACCTAGCAGATTCCTTATCCT 58.836 47.826 0.00 0.00 33.45 3.24
3096 3218 3.904339 TGGACCTAGCAGATTCCTTATCC 59.096 47.826 0.00 0.00 33.45 2.59
3097 3219 4.020662 CCTGGACCTAGCAGATTCCTTATC 60.021 50.000 0.00 0.00 0.00 1.75
3098 3220 3.906846 CCTGGACCTAGCAGATTCCTTAT 59.093 47.826 0.00 0.00 0.00 1.73
3099 3221 3.309296 CCTGGACCTAGCAGATTCCTTA 58.691 50.000 0.00 0.00 0.00 2.69
3100 3222 2.122768 CCTGGACCTAGCAGATTCCTT 58.877 52.381 0.00 0.00 0.00 3.36
3101 3223 1.008938 ACCTGGACCTAGCAGATTCCT 59.991 52.381 0.00 0.00 0.00 3.36
3102 3224 1.501582 ACCTGGACCTAGCAGATTCC 58.498 55.000 0.00 0.00 0.00 3.01
3103 3225 3.636153 AAACCTGGACCTAGCAGATTC 57.364 47.619 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.