Multiple sequence alignment - TraesCS6D01G197700

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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 TraesCS6D01G197700 chr6D 100.000 4043 0 0 1 4043 275668734 275664692 0.000000e+00 7467
1 TraesCS6D01G197700 chr6A 91.767 3887 185 66 191 4043 396292674 396288889 0.000000e+00 5280
2 TraesCS6D01G197700 chr6A 87.047 193 12 4 4 184 396293110 396292919 5.300000e-49 206
3 TraesCS6D01G197700 chr6B 94.079 2280 83 14 544 2807 437472305 437470062 0.000000e+00 3415
4 TraesCS6D01G197700 chr6B 92.377 446 23 6 109 546 437472800 437472358 3.430000e-175 625
5 TraesCS6D01G197700 chr6B 95.610 205 9 0 3541 3745 437459413 437459209 3.010000e-86 329
6 TraesCS6D01G197700 chr6B 95.122 205 10 0 3541 3745 437460344 437460140 1.400000e-84 324
7 TraesCS6D01G197700 chr6B 90.336 238 21 2 3069 3306 437459779 437459544 1.090000e-80 311
8 TraesCS6D01G197700 chr6B 90.336 238 21 2 3069 3306 437460710 437460475 1.090000e-80 311
9 TraesCS6D01G197700 chr6B 95.322 171 8 0 3873 4043 437459127 437458957 5.150000e-69 272
10 TraesCS6D01G197700 chr6B 94.079 152 6 1 2809 2957 437469899 437469748 1.130000e-55 228
11 TraesCS6D01G197700 chr6B 92.857 98 7 0 3873 3970 437460058 437459961 4.210000e-30 143
12 TraesCS6D01G197700 chr7A 90.201 1194 90 15 1463 2638 543341168 543342352 0.000000e+00 1531
13 TraesCS6D01G197700 chr7A 87.054 533 58 4 938 1459 543340507 543341039 3.480000e-165 592
14 TraesCS6D01G197700 chr7A 82.171 129 15 6 2994 3119 543343159 543343282 1.990000e-18 104
15 TraesCS6D01G197700 chr7B 89.842 1142 100 5 947 2077 479238246 479237110 0.000000e+00 1452
16 TraesCS6D01G197700 chr7B 87.787 696 53 16 2072 2745 479234525 479233840 0.000000e+00 785
17 TraesCS6D01G197700 chr7B 81.203 133 19 6 2992 3119 479232946 479232815 7.150000e-18 102
18 TraesCS6D01G197700 chr7D 89.326 1143 110 5 945 2077 457150089 457148949 0.000000e+00 1424
19 TraesCS6D01G197700 chr7D 88.075 696 51 17 2072 2745 457148797 457148112 0.000000e+00 797
20 TraesCS6D01G197700 chr7D 81.250 192 19 10 2937 3119 457147472 457147289 5.450000e-29 139
21 TraesCS6D01G197700 chr1A 78.968 252 39 10 1677 1920 483617919 483618164 4.180000e-35 159


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 TraesCS6D01G197700 chr6D 275664692 275668734 4042 True 7467.000000 7467 100.000000 1 4043 1 chr6D.!!$R1 4042
1 TraesCS6D01G197700 chr6A 396288889 396293110 4221 True 2743.000000 5280 89.407000 4 4043 2 chr6A.!!$R1 4039
2 TraesCS6D01G197700 chr6B 437469748 437472800 3052 True 1422.666667 3415 93.511667 109 2957 3 chr6B.!!$R2 2848
3 TraesCS6D01G197700 chr6B 437458957 437460710 1753 True 281.666667 329 93.263833 3069 4043 6 chr6B.!!$R1 974
4 TraesCS6D01G197700 chr7A 543340507 543343282 2775 False 742.333333 1531 86.475333 938 3119 3 chr7A.!!$F1 2181
5 TraesCS6D01G197700 chr7B 479232815 479238246 5431 True 779.666667 1452 86.277333 947 3119 3 chr7B.!!$R1 2172
6 TraesCS6D01G197700 chr7D 457147289 457150089 2800 True 786.666667 1424 86.217000 945 3119 3 chr7D.!!$R1 2174

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
56 57 0.034186 TGTCTGGGCCCATGAACATC 60.034 55.0 28.82 12.86 0.00 3.06 F
1306 1630 0.036875 GGGTTTGGACCTGAGGACAG 59.963 60.0 4.99 0.00 45.75 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1719 0.387929 AGACACACACGTCGACCAAT 59.612 50.0 10.58 0.0 40.98 3.16 R
3201 8233 0.250640 CAGCAAGTCCCAAGCACTCT 60.251 55.0 0.00 0.0 0.00 3.24 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
49 50 0.912486 GTAGAGTTGTCTGGGCCCAT 59.088 55.000 28.82 9.58 33.84 4.00
52 53 0.038166 GAGTTGTCTGGGCCCATGAA 59.962 55.000 28.82 15.59 0.00 2.57
56 57 0.034186 TGTCTGGGCCCATGAACATC 60.034 55.000 28.82 12.86 0.00 3.06
78 81 6.546972 TCGCAGTAATTGTTGTGATGTTTA 57.453 33.333 3.90 0.00 0.00 2.01
80 83 7.240674 TCGCAGTAATTGTTGTGATGTTTATC 58.759 34.615 3.90 0.00 0.00 1.75
107 111 4.576873 TCAGCAAAACACGATTTTGGAGTA 59.423 37.500 22.22 0.17 39.19 2.59
108 112 4.911610 CAGCAAAACACGATTTTGGAGTAG 59.088 41.667 22.22 5.47 39.19 2.57
109 113 4.023193 AGCAAAACACGATTTTGGAGTAGG 60.023 41.667 22.22 4.96 39.19 3.18
110 114 4.261447 GCAAAACACGATTTTGGAGTAGGT 60.261 41.667 22.22 0.00 39.19 3.08
112 116 4.345859 AACACGATTTTGGAGTAGGTGA 57.654 40.909 0.00 0.00 0.00 4.02
113 117 4.553330 ACACGATTTTGGAGTAGGTGAT 57.447 40.909 0.00 0.00 0.00 3.06
138 151 2.094597 TGTGATTAGCATGCTGCCAAAC 60.095 45.455 30.42 19.88 46.52 2.93
183 196 2.362077 GTTTCAGTTGAACTGCCCACAT 59.638 45.455 19.99 0.00 45.54 3.21
186 436 3.411446 TCAGTTGAACTGCCCACATTAG 58.589 45.455 19.99 0.00 45.54 1.73
258 513 0.037326 GCCGATTATCTGCCGGATCA 60.037 55.000 5.05 0.00 45.58 2.92
305 560 1.475751 CCATCTCATTCTTCACCCCCG 60.476 57.143 0.00 0.00 0.00 5.73
306 561 0.181350 ATCTCATTCTTCACCCCCGC 59.819 55.000 0.00 0.00 0.00 6.13
390 648 8.394121 CAGATTTCTTAGGTTTCTGATACAAGC 58.606 37.037 0.84 0.00 36.72 4.01
394 654 2.716217 AGGTTTCTGATACAAGCTGGC 58.284 47.619 0.00 0.00 29.56 4.85
413 673 1.202746 GCTAGCATCCTCCCCTTTCTG 60.203 57.143 10.63 0.00 0.00 3.02
419 679 0.772124 TCCTCCCCTTTCTGCTTGGT 60.772 55.000 0.00 0.00 0.00 3.67
455 715 7.816995 TGTATAATTTGATTTGTTCCAAGCACC 59.183 33.333 0.00 0.00 0.00 5.01
500 760 6.017109 CGAAAATACTGTAGAAATCATGGGGG 60.017 42.308 0.00 0.00 0.00 5.40
539 800 5.255443 ACCTTTTATAGAACCACCCCAATCT 59.745 40.000 0.00 0.00 0.00 2.40
688 1005 0.879090 CTGGGTTGGGAAAACGCTAC 59.121 55.000 6.80 0.00 34.63 3.58
742 1059 1.846007 TGTGAAGTGGCTGTTTTGGT 58.154 45.000 0.00 0.00 0.00 3.67
791 1108 2.425143 TTTGATGGTGGATGGAGAGC 57.575 50.000 0.00 0.00 0.00 4.09
854 1171 7.485810 CATTCTGATTTTGTGGCATGATTCTA 58.514 34.615 0.00 0.00 0.00 2.10
909 1226 6.459923 GGACTCCTGGTATATGATTTCTGTC 58.540 44.000 0.00 0.00 0.00 3.51
1306 1630 0.036875 GGGTTTGGACCTGAGGACAG 59.963 60.000 4.99 0.00 45.75 3.51
1390 1718 8.682710 GCAACCAGTTTGATATCCTTGTTAATA 58.317 33.333 0.00 0.00 37.39 0.98
1407 1735 5.107414 TGTTAATAATTGGTCGACGTGTGTG 60.107 40.000 9.92 0.00 0.00 3.82
1464 1923 6.220201 GGGTCTTATTCTTCTCTCTGCATAC 58.780 44.000 0.00 0.00 0.00 2.39
1470 1929 1.406898 CTTCTCTCTGCATACGAGCCA 59.593 52.381 0.00 0.00 0.00 4.75
1538 1997 4.629634 TGTTGTGCTAATATGTCCGTTCTG 59.370 41.667 0.00 0.00 0.00 3.02
1558 2017 7.254455 CGTTCTGGTTTGATAGATTATGGTGTC 60.254 40.741 0.00 0.00 0.00 3.67
1660 2119 1.633945 ACCCTTCATGTTACAGACCCC 59.366 52.381 0.00 0.00 0.00 4.95
1728 2187 6.885918 TGGCTGAGACAATTAAATCATCTTCA 59.114 34.615 0.00 0.00 0.00 3.02
1785 2244 0.326264 GAGGGTCCACTGTGATTGCT 59.674 55.000 9.86 0.00 0.00 3.91
2074 2533 3.134804 GGATGTGCCTCAGTACAAGGTAT 59.865 47.826 13.95 7.84 42.20 2.73
2107 5156 6.505272 CCAATTGTTGTTTTGATGCCATTTT 58.495 32.000 4.43 0.00 0.00 1.82
2114 5163 7.094032 TGTTGTTTTGATGCCATTTTTCCTTTT 60.094 29.630 0.00 0.00 0.00 2.27
2422 5496 5.561679 ACCAAAGAACTAGGTGGAAAGATC 58.438 41.667 0.00 0.00 33.57 2.75
2428 5502 3.978610 ACTAGGTGGAAAGATCCTACGT 58.021 45.455 0.00 0.00 46.70 3.57
2689 5784 9.423061 AGAATAATTGAATTGGCTTACACAAAC 57.577 29.630 0.00 0.00 0.00 2.93
2717 5820 7.101054 ACCGATAATTGCTAGTTTGTCTGTAA 58.899 34.615 0.00 0.00 0.00 2.41
2980 7076 7.041984 GGCTAAAGTATCTGTGGCTAATGTTAC 60.042 40.741 0.00 0.00 0.00 2.50
3058 7154 2.203126 GAAGATCAGCAGGCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
3059 7155 3.764160 GAAGATCAGCAGGCCCCGG 62.764 68.421 0.00 0.00 0.00 5.73
3130 8162 6.600388 TGATGTAATAAAATGGCAGCCTCTA 58.400 36.000 14.15 0.00 0.00 2.43
3137 8169 4.228567 GGCAGCCTCTACCGCTCC 62.229 72.222 3.29 0.00 33.17 4.70
3138 8170 4.577246 GCAGCCTCTACCGCTCCG 62.577 72.222 0.00 0.00 33.17 4.63
3163 8195 7.060633 CGCCAACAAAAATAAAAGCTACTGTAG 59.939 37.037 10.48 10.48 0.00 2.74
3200 8232 2.693591 CCGTGATTGGCCTAGTTAGAGA 59.306 50.000 3.32 0.00 0.00 3.10
3201 8233 3.132289 CCGTGATTGGCCTAGTTAGAGAA 59.868 47.826 3.32 0.00 0.00 2.87
3210 8242 4.429108 GCCTAGTTAGAGAAGAGTGCTTG 58.571 47.826 0.00 0.00 33.61 4.01
3220 8252 0.250640 AGAGTGCTTGGGACTTGCTG 60.251 55.000 0.00 0.00 0.00 4.41
3252 8284 2.222678 GTGCTATGATCGCTGAACATGG 59.777 50.000 0.00 8.73 0.00 3.66
3273 8311 5.958321 TGGATACTACTGAGATGGATCTGT 58.042 41.667 0.00 0.00 35.41 3.41
3274 8312 6.377080 TGGATACTACTGAGATGGATCTGTT 58.623 40.000 0.00 0.00 35.41 3.16
3279 8317 2.027745 ACTGAGATGGATCTGTTTGCGT 60.028 45.455 0.00 0.00 37.25 5.24
3288 8326 0.956633 TCTGTTTGCGTAGTCGGAGT 59.043 50.000 0.00 0.00 38.80 3.85
3290 8328 0.386476 TGTTTGCGTAGTCGGAGTGT 59.614 50.000 0.00 0.00 38.80 3.55
3291 8329 0.782384 GTTTGCGTAGTCGGAGTGTG 59.218 55.000 0.00 0.00 38.80 3.82
3292 8330 0.319211 TTTGCGTAGTCGGAGTGTGG 60.319 55.000 0.00 0.00 38.80 4.17
3293 8331 1.457823 TTGCGTAGTCGGAGTGTGGT 61.458 55.000 0.00 0.00 38.80 4.16
3294 8332 1.288127 GCGTAGTCGGAGTGTGGTT 59.712 57.895 0.00 0.00 37.56 3.67
3295 8333 0.319297 GCGTAGTCGGAGTGTGGTTT 60.319 55.000 0.00 0.00 37.56 3.27
3296 8334 1.870993 GCGTAGTCGGAGTGTGGTTTT 60.871 52.381 0.00 0.00 37.56 2.43
3297 8335 2.056577 CGTAGTCGGAGTGTGGTTTTC 58.943 52.381 0.00 0.00 0.00 2.29
3298 8336 2.288030 CGTAGTCGGAGTGTGGTTTTCT 60.288 50.000 0.00 0.00 0.00 2.52
3299 8337 3.058016 CGTAGTCGGAGTGTGGTTTTCTA 60.058 47.826 0.00 0.00 0.00 2.10
3300 8338 4.380233 CGTAGTCGGAGTGTGGTTTTCTAT 60.380 45.833 0.00 0.00 0.00 1.98
3301 8339 3.926616 AGTCGGAGTGTGGTTTTCTATG 58.073 45.455 0.00 0.00 0.00 2.23
3302 8340 3.576982 AGTCGGAGTGTGGTTTTCTATGA 59.423 43.478 0.00 0.00 0.00 2.15
3303 8341 4.223032 AGTCGGAGTGTGGTTTTCTATGAT 59.777 41.667 0.00 0.00 0.00 2.45
3304 8342 4.567159 GTCGGAGTGTGGTTTTCTATGATC 59.433 45.833 0.00 0.00 0.00 2.92
3305 8343 4.466370 TCGGAGTGTGGTTTTCTATGATCT 59.534 41.667 0.00 0.00 0.00 2.75
3306 8344 5.046591 TCGGAGTGTGGTTTTCTATGATCTT 60.047 40.000 0.00 0.00 0.00 2.40
3307 8345 5.643777 CGGAGTGTGGTTTTCTATGATCTTT 59.356 40.000 0.00 0.00 0.00 2.52
3308 8346 6.149474 CGGAGTGTGGTTTTCTATGATCTTTT 59.851 38.462 0.00 0.00 0.00 2.27
3309 8347 7.308589 CGGAGTGTGGTTTTCTATGATCTTTTT 60.309 37.037 0.00 0.00 0.00 1.94
3337 8375 7.282585 TGAGGTAATGGTTTTCTATGATCTGG 58.717 38.462 0.00 0.00 0.00 3.86
3384 8422 9.677567 TTTGAACTGCAAAAATGTCTTATACTC 57.322 29.630 0.00 0.00 43.18 2.59
3385 8423 7.816640 TGAACTGCAAAAATGTCTTATACTCC 58.183 34.615 0.00 0.00 0.00 3.85
3386 8424 6.422776 ACTGCAAAAATGTCTTATACTCCG 57.577 37.500 0.00 0.00 0.00 4.63
3387 8425 5.938125 ACTGCAAAAATGTCTTATACTCCGT 59.062 36.000 0.00 0.00 0.00 4.69
3388 8426 7.101054 ACTGCAAAAATGTCTTATACTCCGTA 58.899 34.615 0.00 0.00 0.00 4.02
3397 8435 9.978044 AATGTCTTATACTCCGTATTTAGGAAC 57.022 33.333 0.00 0.00 37.32 3.62
3409 8447 8.508875 TCCGTATTTAGGAACTTGAAATGAAAC 58.491 33.333 0.00 0.00 41.75 2.78
3411 8449 9.672086 CGTATTTAGGAACTTGAAATGAAACAA 57.328 29.630 0.00 0.00 41.75 2.83
3414 8452 5.576447 AGGAACTTGAAATGAAACAACGT 57.424 34.783 0.00 0.00 27.25 3.99
3415 8453 5.339990 AGGAACTTGAAATGAAACAACGTG 58.660 37.500 0.00 0.00 27.25 4.49
3417 8455 5.575218 GGAACTTGAAATGAAACAACGTGTT 59.425 36.000 0.00 0.00 43.41 3.32
3418 8456 6.388259 AACTTGAAATGAAACAACGTGTTG 57.612 33.333 11.02 11.02 40.14 3.33
3435 8473 8.723311 CAACGTGTTGTATTTAGGATTTAGGAA 58.277 33.333 4.58 0.00 35.92 3.36
3436 8474 8.260270 ACGTGTTGTATTTAGGATTTAGGAAC 57.740 34.615 0.00 0.00 0.00 3.62
3437 8475 7.879160 ACGTGTTGTATTTAGGATTTAGGAACA 59.121 33.333 0.00 0.00 0.00 3.18
3449 8494 4.884668 TTTAGGAACAGAGGGTGTACTG 57.115 45.455 0.00 0.00 39.03 2.74
3471 8516 0.659957 GAGACGAATTGGCCATGCTC 59.340 55.000 6.09 2.32 0.00 4.26
3504 8549 2.818751 TGCATTCCCGGGTTTTATCT 57.181 45.000 22.86 0.00 0.00 1.98
3505 8550 3.094484 TGCATTCCCGGGTTTTATCTT 57.906 42.857 22.86 0.00 0.00 2.40
3546 8591 4.377431 CGAAAGTCAGGAATCTTGAAACCG 60.377 45.833 0.00 0.00 0.00 4.44
3595 8640 3.921677 TCAGTCTCGTAAACACCATTCC 58.078 45.455 0.00 0.00 0.00 3.01
3685 8733 2.855963 GCAGCGGAAAACATCATCAATG 59.144 45.455 0.00 0.00 41.48 2.82
3727 8775 3.058450 CACGACACGGTTAACACCATAA 58.942 45.455 8.10 0.00 44.53 1.90
3731 8779 4.628333 CGACACGGTTAACACCATAAGAAT 59.372 41.667 8.10 0.00 44.53 2.40
3732 8780 5.806502 CGACACGGTTAACACCATAAGAATA 59.193 40.000 8.10 0.00 44.53 1.75
3733 8781 6.237648 CGACACGGTTAACACCATAAGAATAC 60.238 42.308 8.10 0.00 44.53 1.89
3734 8782 5.577945 ACACGGTTAACACCATAAGAATACG 59.422 40.000 8.10 0.00 44.53 3.06
3735 8783 5.577945 CACGGTTAACACCATAAGAATACGT 59.422 40.000 8.10 0.00 44.53 3.57
3736 8784 6.751425 CACGGTTAACACCATAAGAATACGTA 59.249 38.462 8.10 0.00 44.53 3.57
3737 8785 7.436080 CACGGTTAACACCATAAGAATACGTAT 59.564 37.037 8.10 1.14 44.53 3.06
3738 8786 8.629158 ACGGTTAACACCATAAGAATACGTATA 58.371 33.333 8.83 0.00 44.53 1.47
3739 8787 9.462174 CGGTTAACACCATAAGAATACGTATAA 57.538 33.333 8.83 0.00 44.53 0.98
3743 8791 7.941795 ACACCATAAGAATACGTATAACTGC 57.058 36.000 8.83 0.00 0.00 4.40
3744 8792 7.723324 ACACCATAAGAATACGTATAACTGCT 58.277 34.615 8.83 0.00 0.00 4.24
3745 8793 8.202137 ACACCATAAGAATACGTATAACTGCTT 58.798 33.333 8.83 9.84 0.00 3.91
3746 8794 9.042008 CACCATAAGAATACGTATAACTGCTTT 57.958 33.333 8.83 0.20 0.00 3.51
3747 8795 9.609346 ACCATAAGAATACGTATAACTGCTTTT 57.391 29.630 8.83 0.00 0.00 2.27
3750 8798 6.823678 AGAATACGTATAACTGCTTTTCCG 57.176 37.500 8.83 0.00 0.00 4.30
3751 8799 5.233689 AGAATACGTATAACTGCTTTTCCGC 59.766 40.000 8.83 0.00 0.00 5.54
3752 8800 2.690786 ACGTATAACTGCTTTTCCGCA 58.309 42.857 0.00 0.00 38.40 5.69
3753 8801 3.068560 ACGTATAACTGCTTTTCCGCAA 58.931 40.909 0.00 0.00 39.80 4.85
3754 8802 3.499157 ACGTATAACTGCTTTTCCGCAAA 59.501 39.130 0.00 0.00 39.80 3.68
3755 8803 4.023878 ACGTATAACTGCTTTTCCGCAAAA 60.024 37.500 0.00 0.00 39.80 2.44
3756 8804 4.912766 CGTATAACTGCTTTTCCGCAAAAA 59.087 37.500 0.00 0.00 39.80 1.94
3871 8919 1.599047 CTCATTCCTCACCGTGGCT 59.401 57.895 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.128282 CCACGAGAAACAACTACAAATGCTAT 60.128 38.462 0.00 0.00 0.00 2.97
3 4 5.178623 CCACGAGAAACAACTACAAATGCTA 59.821 40.000 0.00 0.00 0.00 3.49
5 6 4.219033 CCACGAGAAACAACTACAAATGC 58.781 43.478 0.00 0.00 0.00 3.56
6 7 4.219033 GCCACGAGAAACAACTACAAATG 58.781 43.478 0.00 0.00 0.00 2.32
7 8 3.252458 GGCCACGAGAAACAACTACAAAT 59.748 43.478 0.00 0.00 0.00 2.32
8 9 2.614983 GGCCACGAGAAACAACTACAAA 59.385 45.455 0.00 0.00 0.00 2.83
9 10 2.215196 GGCCACGAGAAACAACTACAA 58.785 47.619 0.00 0.00 0.00 2.41
18 19 0.963962 AACTCTACGGCCACGAGAAA 59.036 50.000 17.05 0.00 44.60 2.52
49 50 4.513318 TCACAACAATTACTGCGATGTTCA 59.487 37.500 0.00 0.00 33.97 3.18
52 53 4.455533 ACATCACAACAATTACTGCGATGT 59.544 37.500 13.12 13.12 37.87 3.06
56 57 7.020602 TGATAAACATCACAACAATTACTGCG 58.979 34.615 0.00 0.00 0.00 5.18
78 81 2.254546 TCGTGTTTTGCTGAGGTGAT 57.745 45.000 0.00 0.00 0.00 3.06
80 83 3.354089 AAATCGTGTTTTGCTGAGGTG 57.646 42.857 0.00 0.00 0.00 4.00
90 94 4.710324 TCACCTACTCCAAAATCGTGTTT 58.290 39.130 0.00 0.00 0.00 2.83
107 111 4.142315 GCATGCTAATCACAAACATCACCT 60.142 41.667 11.37 0.00 0.00 4.00
108 112 4.107622 GCATGCTAATCACAAACATCACC 58.892 43.478 11.37 0.00 0.00 4.02
109 113 4.796830 CAGCATGCTAATCACAAACATCAC 59.203 41.667 22.19 0.00 0.00 3.06
110 114 4.989044 CAGCATGCTAATCACAAACATCA 58.011 39.130 22.19 0.00 0.00 3.07
138 151 1.374758 GGCGTCCAGGTTCTGTCAG 60.375 63.158 0.00 0.00 0.00 3.51
183 196 3.292460 GCTCTAGAGGCTTCTCCACTAA 58.708 50.000 21.23 0.00 37.53 2.24
258 513 2.369394 GGATGCTCACCTCGGAAATTT 58.631 47.619 0.00 0.00 0.00 1.82
305 560 2.818274 CGGGTAACGGGAGCAAGC 60.818 66.667 0.00 0.00 39.42 4.01
306 561 2.818274 GCGGGTAACGGGAGCAAG 60.818 66.667 0.00 0.00 44.51 4.01
390 648 1.059006 AAGGGGAGGATGCTAGCCAG 61.059 60.000 13.29 0.00 0.00 4.85
394 654 1.202746 GCAGAAAGGGGAGGATGCTAG 60.203 57.143 0.00 0.00 0.00 3.42
399 659 0.627986 CCAAGCAGAAAGGGGAGGAT 59.372 55.000 0.00 0.00 0.00 3.24
455 715 1.586154 AAAAATCCTGTCCAGCCGCG 61.586 55.000 0.00 0.00 0.00 6.46
500 760 0.468648 AAGGTCGGATCGGGGATTTC 59.531 55.000 0.00 0.00 0.00 2.17
688 1005 8.482429 ACGTTACTCACTCGTACAAAATAAAAG 58.518 33.333 0.00 0.00 36.05 2.27
742 1059 9.970395 TGTAATCGTTTTGAGAAGTAAAGACTA 57.030 29.630 0.00 0.00 33.58 2.59
770 1087 3.294214 GCTCTCCATCCACCATCAAAAT 58.706 45.455 0.00 0.00 0.00 1.82
771 1088 2.041485 TGCTCTCCATCCACCATCAAAA 59.959 45.455 0.00 0.00 0.00 2.44
772 1089 1.634973 TGCTCTCCATCCACCATCAAA 59.365 47.619 0.00 0.00 0.00 2.69
791 1108 0.534412 AGTCGAGGGAGCATGTCTTG 59.466 55.000 0.00 0.00 0.00 3.02
803 1120 6.146837 CCTCAAAAGCATAATATCAGTCGAGG 59.853 42.308 0.00 0.00 0.00 4.63
854 1171 2.100916 ACGTGAAGCTACTCACACAGTT 59.899 45.455 16.70 0.00 45.03 3.16
897 1214 5.147330 ACAGTGAACGGACAGAAATCATA 57.853 39.130 0.00 0.00 0.00 2.15
1167 1491 2.095314 CGCATCAGCACAAACATACCAA 60.095 45.455 0.00 0.00 42.27 3.67
1306 1630 5.113502 AGTCAGCTCAAGTGCAAAATTAC 57.886 39.130 0.00 0.00 34.99 1.89
1390 1718 1.202486 AGACACACACGTCGACCAATT 60.202 47.619 10.58 0.00 40.98 2.32
1391 1719 0.387929 AGACACACACGTCGACCAAT 59.612 50.000 10.58 0.00 40.98 3.16
1464 1923 4.864247 CCCACAAAAGAATTTATTGGCTCG 59.136 41.667 4.52 0.00 37.28 5.03
1538 1997 6.046593 TGTCGACACCATAATCTATCAAACC 58.953 40.000 15.76 0.00 0.00 3.27
1558 2017 2.282555 CGCTCCAATGTCATACTTGTCG 59.717 50.000 0.00 0.00 0.00 4.35
1604 2063 5.008019 GGTAAGCAATACACACATCCTCATG 59.992 44.000 2.63 0.00 36.14 3.07
1660 2119 3.102515 CGACATCGTATAAGCCCGG 57.897 57.895 0.00 0.00 34.11 5.73
1728 2187 4.929808 GGTTCACGAGTGATCTTACAACAT 59.070 41.667 6.77 0.00 39.64 2.71
1785 2244 1.619654 CATCTGGGTCTGGTGCAAAA 58.380 50.000 0.00 0.00 0.00 2.44
2074 2533 6.519382 TCAAAACAACAATTGGCATGTGATA 58.481 32.000 10.83 0.00 34.12 2.15
2107 5156 9.295825 TGCTCAGTCTATCAAAATTAAAAGGAA 57.704 29.630 0.00 0.00 0.00 3.36
2362 5436 4.309933 CTTCAGCACTCTTGTACACATCA 58.690 43.478 0.00 0.00 0.00 3.07
2422 5496 4.162690 GGCCCAGGCTGACGTAGG 62.163 72.222 17.94 9.33 41.60 3.18
2428 5502 3.009115 GGTAGTGGCCCAGGCTGA 61.009 66.667 17.94 0.00 41.60 4.26
2672 5767 4.546570 GGTCAGTTTGTGTAAGCCAATTC 58.453 43.478 0.00 0.00 0.00 2.17
2689 5784 5.812642 AGACAAACTAGCAATTATCGGTCAG 59.187 40.000 0.00 0.00 0.00 3.51
2717 5820 9.974980 ATGTACAAACTGGAAATAATTCGTTTT 57.025 25.926 0.00 0.00 36.36 2.43
2923 6957 3.670625 CCAAGGATACCGAAGAACAACA 58.329 45.455 0.00 0.00 37.17 3.33
2957 7049 8.978472 AGAGTAACATTAGCCACAGATACTTTA 58.022 33.333 0.00 0.00 0.00 1.85
2959 7051 7.425224 AGAGTAACATTAGCCACAGATACTT 57.575 36.000 0.00 0.00 0.00 2.24
2980 7076 0.774908 TACAACCCCAACCCCAAGAG 59.225 55.000 0.00 0.00 0.00 2.85
3058 7154 3.886550 CTCAACAACCCCTGGCCCC 62.887 68.421 0.00 0.00 0.00 5.80
3059 7155 2.283173 CTCAACAACCCCTGGCCC 60.283 66.667 0.00 0.00 0.00 5.80
3137 8169 5.689961 ACAGTAGCTTTTATTTTTGTTGGCG 59.310 36.000 0.00 0.00 0.00 5.69
3138 8170 8.227731 CTACAGTAGCTTTTATTTTTGTTGGC 57.772 34.615 0.00 0.00 0.00 4.52
3163 8195 1.850640 CGGCATACGTATTCGGTGC 59.149 57.895 5.03 7.46 45.13 5.01
3200 8232 0.475906 AGCAAGTCCCAAGCACTCTT 59.524 50.000 0.00 0.00 0.00 2.85
3201 8233 0.250640 CAGCAAGTCCCAAGCACTCT 60.251 55.000 0.00 0.00 0.00 3.24
3220 8252 4.383052 GCGATCATAGCACATACTGTACAC 59.617 45.833 0.00 0.00 34.19 2.90
3252 8284 6.644592 GCAAACAGATCCATCTCAGTAGTATC 59.355 42.308 0.00 0.00 34.22 2.24
3273 8311 0.319211 CCACACTCCGACTACGCAAA 60.319 55.000 0.00 0.00 38.29 3.68
3274 8312 1.287815 CCACACTCCGACTACGCAA 59.712 57.895 0.00 0.00 38.29 4.85
3279 8317 4.768448 TCATAGAAAACCACACTCCGACTA 59.232 41.667 0.00 0.00 0.00 2.59
3309 8347 9.753674 AGATCATAGAAAACCATTACCTCAAAA 57.246 29.630 0.00 0.00 0.00 2.44
3310 8348 9.177608 CAGATCATAGAAAACCATTACCTCAAA 57.822 33.333 0.00 0.00 0.00 2.69
3311 8349 7.775093 CCAGATCATAGAAAACCATTACCTCAA 59.225 37.037 0.00 0.00 0.00 3.02
3312 8350 7.092444 ACCAGATCATAGAAAACCATTACCTCA 60.092 37.037 0.00 0.00 0.00 3.86
3313 8351 7.283329 ACCAGATCATAGAAAACCATTACCTC 58.717 38.462 0.00 0.00 0.00 3.85
3314 8352 7.213178 ACCAGATCATAGAAAACCATTACCT 57.787 36.000 0.00 0.00 0.00 3.08
3315 8353 9.003658 CATACCAGATCATAGAAAACCATTACC 57.996 37.037 0.00 0.00 0.00 2.85
3316 8354 9.561069 ACATACCAGATCATAGAAAACCATTAC 57.439 33.333 0.00 0.00 0.00 1.89
3318 8356 9.479549 AAACATACCAGATCATAGAAAACCATT 57.520 29.630 0.00 0.00 0.00 3.16
3319 8357 9.479549 AAAACATACCAGATCATAGAAAACCAT 57.520 29.630 0.00 0.00 0.00 3.55
3382 8420 7.843490 TCATTTCAAGTTCCTAAATACGGAG 57.157 36.000 0.00 0.00 0.00 4.63
3383 8421 8.508875 GTTTCATTTCAAGTTCCTAAATACGGA 58.491 33.333 0.00 0.00 0.00 4.69
3384 8422 8.293867 TGTTTCATTTCAAGTTCCTAAATACGG 58.706 33.333 0.00 0.00 0.00 4.02
3385 8423 9.672086 TTGTTTCATTTCAAGTTCCTAAATACG 57.328 29.630 0.00 0.00 0.00 3.06
3387 8425 9.672086 CGTTGTTTCATTTCAAGTTCCTAAATA 57.328 29.630 0.00 0.00 0.00 1.40
3388 8426 8.194769 ACGTTGTTTCATTTCAAGTTCCTAAAT 58.805 29.630 0.00 0.00 0.00 1.40
3409 8447 8.259049 TCCTAAATCCTAAATACAACACGTTG 57.741 34.615 8.35 8.35 45.58 4.10
3411 8449 7.879160 TGTTCCTAAATCCTAAATACAACACGT 59.121 33.333 0.00 0.00 0.00 4.49
3412 8450 8.259049 TGTTCCTAAATCCTAAATACAACACG 57.741 34.615 0.00 0.00 0.00 4.49
3414 8452 9.667107 CTCTGTTCCTAAATCCTAAATACAACA 57.333 33.333 0.00 0.00 0.00 3.33
3415 8453 9.110502 CCTCTGTTCCTAAATCCTAAATACAAC 57.889 37.037 0.00 0.00 0.00 3.32
3417 8455 7.404980 ACCCTCTGTTCCTAAATCCTAAATACA 59.595 37.037 0.00 0.00 0.00 2.29
3418 8456 7.715686 CACCCTCTGTTCCTAAATCCTAAATAC 59.284 40.741 0.00 0.00 0.00 1.89
3419 8457 7.404980 ACACCCTCTGTTCCTAAATCCTAAATA 59.595 37.037 0.00 0.00 0.00 1.40
3420 8458 6.217693 ACACCCTCTGTTCCTAAATCCTAAAT 59.782 38.462 0.00 0.00 0.00 1.40
3421 8459 5.550403 ACACCCTCTGTTCCTAAATCCTAAA 59.450 40.000 0.00 0.00 0.00 1.85
3422 8460 5.098663 ACACCCTCTGTTCCTAAATCCTAA 58.901 41.667 0.00 0.00 0.00 2.69
3423 8461 4.695606 ACACCCTCTGTTCCTAAATCCTA 58.304 43.478 0.00 0.00 0.00 2.94
3424 8462 3.532102 ACACCCTCTGTTCCTAAATCCT 58.468 45.455 0.00 0.00 0.00 3.24
3425 8463 4.470304 AGTACACCCTCTGTTCCTAAATCC 59.530 45.833 0.00 0.00 33.91 3.01
3426 8464 5.046520 ACAGTACACCCTCTGTTCCTAAATC 60.047 44.000 0.00 0.00 41.33 2.17
3435 8473 2.628657 GTCTCAACAGTACACCCTCTGT 59.371 50.000 0.00 0.00 45.21 3.41
3436 8474 2.351835 CGTCTCAACAGTACACCCTCTG 60.352 54.545 0.00 0.00 37.65 3.35
3437 8475 1.887198 CGTCTCAACAGTACACCCTCT 59.113 52.381 0.00 0.00 0.00 3.69
3449 8494 1.468054 GCATGGCCAATTCGTCTCAAC 60.468 52.381 10.96 0.00 0.00 3.18
3504 8549 7.953752 ACTTTCGGGTGAAATGGTTAATAAAA 58.046 30.769 0.00 0.00 42.90 1.52
3505 8550 7.230913 TGACTTTCGGGTGAAATGGTTAATAAA 59.769 33.333 0.00 0.00 42.90 1.40
3523 8568 4.377431 CGGTTTCAAGATTCCTGACTTTCG 60.377 45.833 0.00 0.00 0.00 3.46
3546 8591 1.003116 GTGCTTGATCATGACGATGCC 60.003 52.381 12.54 0.00 33.17 4.40
3595 8640 3.067106 ACGGTACAATTGTCAGCAGAAG 58.933 45.455 15.85 2.21 0.00 2.85
3703 8751 0.042794 GTGTTAACCGTGTCGTGTGC 60.043 55.000 2.48 0.00 0.00 4.57
3727 8775 5.233689 GCGGAAAAGCAGTTATACGTATTCT 59.766 40.000 14.33 9.91 37.05 2.40
3731 8779 3.847542 TGCGGAAAAGCAGTTATACGTA 58.152 40.909 0.00 0.00 42.92 3.57
3732 8780 2.690786 TGCGGAAAAGCAGTTATACGT 58.309 42.857 0.00 0.00 42.92 3.57
3849 8897 0.898320 CACGGTGAGGAATGAGGAGT 59.102 55.000 0.74 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.