Multiple sequence alignment - TraesCS6A01G143700

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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 TraesCS6A01G143700 chr6A 100.000 3799 0 0 1 3799 120131184 120127386 0.000000e+00 7016.0
1 TraesCS6A01G143700 chr6A 84.399 923 114 13 996 1891 121871004 121871923 0.000000e+00 880.0
2 TraesCS6A01G143700 chr6A 83.965 923 120 12 995 1891 121659032 121659952 0.000000e+00 859.0
3 TraesCS6A01G143700 chr6D 91.374 2736 151 26 434 3121 100569351 100566653 0.000000e+00 3666.0
4 TraesCS6A01G143700 chr6D 85.197 912 117 7 995 1891 101212208 101213116 0.000000e+00 920.0
5 TraesCS6A01G143700 chr6D 84.324 925 117 13 995 1896 101202193 101203112 0.000000e+00 880.0
6 TraesCS6A01G143700 chr6D 82.131 929 131 22 999 1899 25440236 25439315 0.000000e+00 763.0
7 TraesCS6A01G143700 chr6D 96.904 323 8 2 120 442 100570946 100570626 1.200000e-149 540.0
8 TraesCS6A01G143700 chr6D 98.230 113 2 0 1 113 100571155 100571043 8.320000e-47 198.0
9 TraesCS6A01G143700 chr6B 93.797 2386 105 19 735 3109 184725928 184723575 0.000000e+00 3546.0
10 TraesCS6A01G143700 chr6B 91.413 1479 112 3 1463 2941 184706520 184705057 0.000000e+00 2013.0
11 TraesCS6A01G143700 chr6B 91.435 1436 108 4 1506 2941 184699004 184697584 0.000000e+00 1956.0
12 TraesCS6A01G143700 chr6B 91.435 1436 108 3 1506 2941 184701405 184699985 0.000000e+00 1956.0
13 TraesCS6A01G143700 chr6B 91.017 1436 114 5 1506 2941 184704097 184702677 0.000000e+00 1923.0
14 TraesCS6A01G143700 chr6B 84.039 921 117 17 995 1891 185100018 185100932 0.000000e+00 859.0
15 TraesCS6A01G143700 chr6B 83.585 926 122 15 995 1895 185110525 185111445 0.000000e+00 841.0
16 TraesCS6A01G143700 chr6B 85.762 597 34 24 1 568 184726505 184725931 5.470000e-163 584.0
17 TraesCS6A01G143700 chr6B 85.370 540 62 7 3261 3798 184636833 184636309 9.280000e-151 544.0
18 TraesCS6A01G143700 chr6B 82.256 665 74 20 3139 3799 184723577 184722953 5.590000e-148 534.0
19 TraesCS6A01G143700 chr6B 93.878 49 3 0 3034 3082 184683329 184683281 1.460000e-09 75.0
20 TraesCS6A01G143700 chr7A 79.528 635 128 2 2175 2808 16730805 16731438 5.790000e-123 451.0
21 TraesCS6A01G143700 chr1D 79.321 648 131 3 2175 2820 334041486 334040840 5.790000e-123 451.0
22 TraesCS6A01G143700 chr1A 79.353 649 129 5 2175 2820 431977558 431976912 5.790000e-123 451.0
23 TraesCS6A01G143700 chr3A 84.545 110 17 0 3263 3372 649743799 649743908 4.010000e-20 110.0
24 TraesCS6A01G143700 chr3A 87.500 64 8 0 3258 3321 714653547 714653610 1.460000e-09 75.0
25 TraesCS6A01G143700 chr3D 83.051 118 20 0 3263 3380 515192961 515193078 1.440000e-19 108.0
26 TraesCS6A01G143700 chr3B 87.143 70 7 2 3256 3324 462868590 462868522 1.130000e-10 78.7
27 TraesCS6A01G143700 chr3B 90.566 53 2 1 3345 3394 180466282 180466334 2.450000e-07 67.6
28 TraesCS6A01G143700 chr2B 88.889 63 7 0 3562 3624 359933716 359933778 1.130000e-10 78.7
29 TraesCS6A01G143700 chr4D 87.879 66 6 2 3256 3320 319024449 319024385 4.070000e-10 76.8
30 TraesCS6A01G143700 chr2A 86.567 67 7 2 3256 3321 221892468 221892533 5.260000e-09 73.1
31 TraesCS6A01G143700 chr2A 89.091 55 4 2 3256 3309 550527484 550527537 2.450000e-07 67.6
32 TraesCS6A01G143700 chr4A 92.000 50 4 0 3267 3316 106578068 106578117 1.890000e-08 71.3


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 TraesCS6A01G143700 chr6A 120127386 120131184 3798 True 7016.000000 7016 100.000000 1 3799 1 chr6A.!!$R1 3798
1 TraesCS6A01G143700 chr6A 121871004 121871923 919 False 880.000000 880 84.399000 996 1891 1 chr6A.!!$F2 895
2 TraesCS6A01G143700 chr6A 121659032 121659952 920 False 859.000000 859 83.965000 995 1891 1 chr6A.!!$F1 896
3 TraesCS6A01G143700 chr6D 100566653 100571155 4502 True 1468.000000 3666 95.502667 1 3121 3 chr6D.!!$R2 3120
4 TraesCS6A01G143700 chr6D 101212208 101213116 908 False 920.000000 920 85.197000 995 1891 1 chr6D.!!$F2 896
5 TraesCS6A01G143700 chr6D 101202193 101203112 919 False 880.000000 880 84.324000 995 1896 1 chr6D.!!$F1 901
6 TraesCS6A01G143700 chr6D 25439315 25440236 921 True 763.000000 763 82.131000 999 1899 1 chr6D.!!$R1 900
7 TraesCS6A01G143700 chr6B 184697584 184706520 8936 True 1962.000000 2013 91.325000 1463 2941 4 chr6B.!!$R3 1478
8 TraesCS6A01G143700 chr6B 184722953 184726505 3552 True 1554.666667 3546 87.271667 1 3799 3 chr6B.!!$R4 3798
9 TraesCS6A01G143700 chr6B 185100018 185100932 914 False 859.000000 859 84.039000 995 1891 1 chr6B.!!$F1 896
10 TraesCS6A01G143700 chr6B 185110525 185111445 920 False 841.000000 841 83.585000 995 1895 1 chr6B.!!$F2 900
11 TraesCS6A01G143700 chr6B 184636309 184636833 524 True 544.000000 544 85.370000 3261 3798 1 chr6B.!!$R1 537
12 TraesCS6A01G143700 chr7A 16730805 16731438 633 False 451.000000 451 79.528000 2175 2808 1 chr7A.!!$F1 633
13 TraesCS6A01G143700 chr1D 334040840 334041486 646 True 451.000000 451 79.321000 2175 2820 1 chr1D.!!$R1 645
14 TraesCS6A01G143700 chr1A 431976912 431977558 646 True 451.000000 451 79.353000 2175 2820 1 chr1A.!!$R1 645

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
877 2299 0.249531 TGACGCACACCGAAAGCTAA 60.250 50.0 0.00 0.00 41.02 3.09 F
986 2409 0.728129 CGCGATCACACGTACACACT 60.728 55.0 0.00 0.00 35.59 3.55 F
2248 11189 0.462581 GCCATGTCGGAGCTCATGAA 60.463 55.0 17.19 4.61 40.07 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 11189 0.108804 CTGCATCACGTTCGGGTACT 60.109 55.0 0.0 0.0 0.00 2.73 R
2255 11196 0.790866 GCGCTTTCTGCATCACGTTC 60.791 55.0 0.0 0.0 43.06 3.95 R
3329 12326 0.165944 CGGCTGCGAAACTTGGTAAG 59.834 55.0 0.0 0.0 0.00 2.34 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
43 44 1.596477 GCCGCTAGCAAGATCCCTG 60.596 63.158 16.45 0.00 42.97 4.45
116 117 1.096386 ACCGAGTCGCTGCTACCTAG 61.096 60.000 7.12 0.00 0.00 3.02
117 118 0.814410 CCGAGTCGCTGCTACCTAGA 60.814 60.000 7.12 0.00 0.00 2.43
118 119 0.584396 CGAGTCGCTGCTACCTAGAG 59.416 60.000 0.00 0.00 0.00 2.43
356 447 1.303317 GTGGATGCAAACGGGACCT 60.303 57.895 0.00 0.00 0.00 3.85
397 488 1.281419 TCCCTTGTATGGAAAGGCGA 58.719 50.000 0.00 0.00 42.52 5.54
401 524 2.009774 CTTGTATGGAAAGGCGACCTG 58.990 52.381 0.00 0.00 32.13 4.00
430 553 1.154016 CTCGGTGCGTCGTCTGATT 60.154 57.895 0.00 0.00 0.00 2.57
431 554 1.134530 CTCGGTGCGTCGTCTGATTC 61.135 60.000 0.00 0.00 0.00 2.52
432 555 1.154016 CGGTGCGTCGTCTGATTCT 60.154 57.895 0.00 0.00 0.00 2.40
560 1965 1.601903 TGAGGTGTCAATCGCAAACAC 59.398 47.619 0.00 0.00 41.97 3.32
561 1966 1.601903 GAGGTGTCAATCGCAAACACA 59.398 47.619 7.12 0.00 43.96 3.72
568 1973 2.036217 CAATCGCAAACACAACTGTCG 58.964 47.619 0.00 0.00 0.00 4.35
575 1980 4.318475 CGCAAACACAACTGTCGAAGAATA 60.318 41.667 0.00 0.00 39.69 1.75
608 2013 0.387929 AATGACGTGTCACCAGTCGT 59.612 50.000 4.57 0.00 43.11 4.34
609 2014 0.318699 ATGACGTGTCACCAGTCGTG 60.319 55.000 4.57 0.00 43.11 4.35
627 2034 2.203015 GGTGTGTGACGTGGCAGT 60.203 61.111 0.00 0.00 0.00 4.40
651 2065 6.631971 TTTTTCATGTGTGTGCTCTCAATA 57.368 33.333 0.00 0.00 0.00 1.90
699 2117 4.110482 GTTCTCACGTGTTACTGTCAGTT 58.890 43.478 16.51 0.00 0.00 3.16
702 2120 4.336153 TCTCACGTGTTACTGTCAGTTACA 59.664 41.667 18.43 18.43 35.66 2.41
704 2122 5.038683 TCACGTGTTACTGTCAGTTACAAG 58.961 41.667 26.09 26.09 39.13 3.16
719 2137 7.328737 GTCAGTTACAAGTACTTACAGACCATG 59.671 40.741 16.13 3.42 0.00 3.66
728 2146 5.838531 ACTTACAGACCATGCTACTACTC 57.161 43.478 0.00 0.00 0.00 2.59
729 2147 4.645588 ACTTACAGACCATGCTACTACTCC 59.354 45.833 0.00 0.00 0.00 3.85
730 2148 3.390175 ACAGACCATGCTACTACTCCT 57.610 47.619 0.00 0.00 0.00 3.69
771 2193 3.181482 TGCATACAAAATTACATGCCGGG 60.181 43.478 2.18 0.00 42.45 5.73
772 2194 3.380142 CATACAAAATTACATGCCGGGC 58.620 45.455 13.32 13.32 0.00 6.13
773 2195 0.534873 ACAAAATTACATGCCGGGCC 59.465 50.000 17.97 0.00 0.00 5.80
877 2299 0.249531 TGACGCACACCGAAAGCTAA 60.250 50.000 0.00 0.00 41.02 3.09
880 2302 1.132640 GCACACCGAAAGCTAAGCG 59.867 57.895 0.00 0.00 0.00 4.68
940 2363 3.371965 TCAAGATAGTAACCCGCCTCTT 58.628 45.455 0.00 0.00 0.00 2.85
958 2381 5.686124 GCCTCTTGTCAATATAAGACCTGCT 60.686 44.000 5.94 0.00 35.15 4.24
982 2405 2.505337 GCCGCGATCACACGTACA 60.505 61.111 8.23 0.00 35.59 2.90
986 2409 0.728129 CGCGATCACACGTACACACT 60.728 55.000 0.00 0.00 35.59 3.55
988 2411 1.664874 GCGATCACACGTACACACTCA 60.665 52.381 0.00 0.00 35.59 3.41
991 2417 3.575630 GATCACACGTACACACTCACAT 58.424 45.455 0.00 0.00 0.00 3.21
997 2423 1.875996 CGTACACACTCACATTGCCCA 60.876 52.381 0.00 0.00 0.00 5.36
1188 2620 4.451150 GTCATGGCCGACCTCGCA 62.451 66.667 0.00 0.00 38.18 5.10
1587 10492 1.060729 TGATCGGGGACAGGTTTCAA 58.939 50.000 0.00 0.00 0.00 2.69
1614 10519 1.349357 GAGGAGTTCTTGCAGGTCCTT 59.651 52.381 7.75 0.00 37.78 3.36
1781 10719 4.821589 CGAGGACAAGAGGGCCGC 62.822 72.222 0.00 0.00 0.00 6.53
1965 10905 5.458891 CAGCAAGCATAGCATATCTTTTCC 58.541 41.667 0.00 0.00 0.00 3.13
2038 10979 3.745799 TCGTTGAAAACTTAGGATGGCA 58.254 40.909 0.00 0.00 46.99 4.92
2068 11009 1.470098 CTTGCTGGCATGTGGTTCTAC 59.530 52.381 0.00 0.00 0.00 2.59
2112 11053 8.680001 CAATAAGACATCAGGTGAAAATCATCA 58.320 33.333 0.00 0.00 27.47 3.07
2118 11059 7.373493 ACATCAGGTGAAAATCATCAAGTTTC 58.627 34.615 0.00 0.00 41.27 2.78
2248 11189 0.462581 GCCATGTCGGAGCTCATGAA 60.463 55.000 17.19 4.61 40.07 2.57
2255 11196 0.249073 CGGAGCTCATGAAGTACCCG 60.249 60.000 17.19 2.03 0.00 5.28
2339 11280 0.038744 AGGATGACTTGGCCAACCTG 59.961 55.000 20.73 12.06 35.78 4.00
2354 11295 4.807643 GCCAACCTGAAATACCTCAGACTT 60.808 45.833 2.18 0.00 44.82 3.01
2420 11361 3.727258 CCACGGGAGGCCATGGAA 61.727 66.667 18.40 0.00 34.41 3.53
2426 11367 1.649271 GGGAGGCCATGGAATCCTGT 61.649 60.000 26.29 2.69 32.18 4.00
2561 11502 2.736719 CGAGTCTGGCATCATCGACTTT 60.737 50.000 7.64 0.00 36.90 2.66
2729 11670 0.325671 AGGTCGACATGGTGGAGGAT 60.326 55.000 18.91 0.00 0.00 3.24
2862 11803 3.118738 AGTCCTTTGTCTCTGACGTTGTT 60.119 43.478 0.00 0.00 34.95 2.83
2971 11939 4.963318 TGCATTTAAATCACAAACCCCA 57.037 36.364 0.00 0.00 0.00 4.96
3025 11999 8.586570 TTTGTCGAATCACTTTATTTGCAAAT 57.413 26.923 26.72 26.72 30.27 2.32
3113 12087 1.063912 CATGTCACACACACACCACAC 59.936 52.381 0.00 0.00 38.04 3.82
3115 12089 0.446222 GTCACACACACACCACACAC 59.554 55.000 0.00 0.00 0.00 3.82
3121 12095 2.395360 ACACACCACACACACACGC 61.395 57.895 0.00 0.00 0.00 5.34
3122 12096 3.192230 ACACCACACACACACGCG 61.192 61.111 3.53 3.53 0.00 6.01
3123 12097 4.589700 CACCACACACACACGCGC 62.590 66.667 5.73 0.00 0.00 6.86
3147 12121 3.772560 CGCGCGCACACACACATA 61.773 61.111 32.61 0.00 0.00 2.29
3169 12143 8.999431 ACATAGTTATAAATTATGCAACCTCCG 58.001 33.333 13.98 0.00 35.26 4.63
3176 12150 3.576078 TTATGCAACCTCCGATCCATT 57.424 42.857 0.00 0.00 0.00 3.16
3180 12154 3.278574 TGCAACCTCCGATCCATTTTAG 58.721 45.455 0.00 0.00 0.00 1.85
3189 12163 5.928976 TCCGATCCATTTTAGATGTGACAT 58.071 37.500 0.00 0.00 0.00 3.06
3199 12173 9.726232 CATTTTAGATGTGACATAAATGACCAG 57.274 33.333 19.90 1.37 35.88 4.00
3200 12174 9.685276 ATTTTAGATGTGACATAAATGACCAGA 57.315 29.630 0.00 0.00 0.00 3.86
3203 12177 4.632327 TGTGACATAAATGACCAGACCA 57.368 40.909 0.00 0.00 0.00 4.02
3204 12178 4.578871 TGTGACATAAATGACCAGACCAG 58.421 43.478 0.00 0.00 0.00 4.00
3207 12181 3.347216 ACATAAATGACCAGACCAGCAC 58.653 45.455 0.00 0.00 0.00 4.40
3213 12187 2.172483 GACCAGACCAGCACGTCCAT 62.172 60.000 0.00 0.00 32.91 3.41
3239 12213 1.272490 CCGCCGATAGCAAGGAATAGA 59.728 52.381 0.00 0.00 44.04 1.98
3248 12222 6.925718 CGATAGCAAGGAATAGAAGAACATGA 59.074 38.462 0.00 0.00 0.00 3.07
3253 12227 6.631314 GCAAGGAATAGAAGAACATGAGAGGA 60.631 42.308 0.00 0.00 0.00 3.71
3254 12228 6.729690 AGGAATAGAAGAACATGAGAGGAG 57.270 41.667 0.00 0.00 0.00 3.69
3286 12260 2.014857 CGAGGACGAGTAGAACATGGA 58.985 52.381 0.00 0.00 42.66 3.41
3318 12315 2.953188 TTGGGTCCCAAGAAGGTCA 58.047 52.632 20.15 0.00 38.75 4.02
3319 12316 0.476771 TTGGGTCCCAAGAAGGTCAC 59.523 55.000 20.15 0.00 38.75 3.67
3320 12317 1.379146 GGGTCCCAAGAAGGTCACC 59.621 63.158 1.78 0.00 37.60 4.02
3321 12318 1.423794 GGGTCCCAAGAAGGTCACCA 61.424 60.000 1.78 0.00 39.30 4.17
3322 12319 0.036875 GGTCCCAAGAAGGTCACCAG 59.963 60.000 0.00 0.00 38.03 4.00
3323 12320 0.606673 GTCCCAAGAAGGTCACCAGC 60.607 60.000 0.00 0.00 34.66 4.85
3324 12321 1.059584 TCCCAAGAAGGTCACCAGCA 61.060 55.000 0.00 0.00 34.66 4.41
3325 12322 0.890996 CCCAAGAAGGTCACCAGCAC 60.891 60.000 0.00 0.00 34.66 4.40
3326 12323 0.890996 CCAAGAAGGTCACCAGCACC 60.891 60.000 0.00 0.00 0.00 5.01
3327 12324 0.179020 CAAGAAGGTCACCAGCACCA 60.179 55.000 0.00 0.00 36.23 4.17
3328 12325 0.773644 AAGAAGGTCACCAGCACCAT 59.226 50.000 0.00 0.00 36.23 3.55
3329 12326 0.326264 AGAAGGTCACCAGCACCATC 59.674 55.000 0.00 0.00 36.23 3.51
3336 12333 1.702401 TCACCAGCACCATCTTACCAA 59.298 47.619 0.00 0.00 0.00 3.67
3338 12335 1.705186 ACCAGCACCATCTTACCAAGT 59.295 47.619 0.00 0.00 0.00 3.16
3339 12336 2.108250 ACCAGCACCATCTTACCAAGTT 59.892 45.455 0.00 0.00 0.00 2.66
3342 12339 3.074412 AGCACCATCTTACCAAGTTTCG 58.926 45.455 0.00 0.00 0.00 3.46
3343 12340 2.414161 GCACCATCTTACCAAGTTTCGC 60.414 50.000 0.00 0.00 0.00 4.70
3393 12390 1.269831 CGGAGGCTATTCTTCCCTTCG 60.270 57.143 0.00 0.00 40.96 3.79
3396 12393 2.431057 GAGGCTATTCTTCCCTTCGTCA 59.569 50.000 0.00 0.00 0.00 4.35
3397 12394 3.041946 AGGCTATTCTTCCCTTCGTCAT 58.958 45.455 0.00 0.00 0.00 3.06
3412 12409 4.990543 TCGTCATGAAGTTTCACACATC 57.009 40.909 8.54 0.00 40.49 3.06
3420 12417 0.112412 GTTTCACACATCCCCAGGGT 59.888 55.000 4.22 0.00 36.47 4.34
3423 12420 0.475632 TCACACATCCCCAGGGTTCT 60.476 55.000 4.22 0.00 36.47 3.01
3433 12430 1.237285 CCAGGGTTCTTGAACGGCTG 61.237 60.000 7.32 0.00 0.00 4.85
3552 12550 8.270799 CGGAAATATGTCAAAATGCAATGAATC 58.729 33.333 0.00 0.00 0.00 2.52
3613 12611 6.752815 TGAAAGTCGTCCAATTTGTTTAAACC 59.247 34.615 15.59 0.00 0.00 3.27
3637 12635 5.819059 TGCATCAAATTTCTTTGTTTTGGC 58.181 33.333 0.00 0.00 42.02 4.52
3662 12660 5.765677 TGAATTCCGTTTGAAATGTGACCTA 59.234 36.000 2.27 0.00 36.33 3.08
3672 12671 2.922740 ATGTGACCTACGTTTGTGGT 57.077 45.000 0.00 0.00 33.84 4.16
3676 12675 3.132646 TGTGACCTACGTTTGTGGTTAGT 59.867 43.478 0.00 0.00 32.11 2.24
3699 12698 5.614324 TTTGGATGACCGACTCTCATATT 57.386 39.130 0.00 0.00 39.42 1.28
3701 12700 5.966742 TGGATGACCGACTCTCATATTAG 57.033 43.478 0.00 0.00 39.42 1.73
3707 12709 3.564644 ACCGACTCTCATATTAGTGTCCG 59.435 47.826 11.59 8.77 36.91 4.79
3708 12710 3.556513 CGACTCTCATATTAGTGTCCGC 58.443 50.000 11.59 0.00 36.91 5.54
3744 12746 1.884579 GGTCGGCGAAGAGATATGGTA 59.115 52.381 12.92 0.00 0.00 3.25
3762 12764 2.701951 GGTATCCGTATGAAGGGTCCAA 59.298 50.000 0.00 0.00 32.23 3.53
3767 12769 2.027561 CCGTATGAAGGGTCCAAGTTGA 60.028 50.000 3.87 0.00 0.00 3.18
3798 12800 3.446516 AGTTGTATACTCCCTCCGTTCAC 59.553 47.826 4.17 0.00 28.23 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.461516 AGCCACACTCATCGATGCAG 60.462 55.000 20.81 18.97 0.00 4.41
43 44 0.742281 ACAGCCACACTCATCGATGC 60.742 55.000 20.81 7.03 0.00 3.91
116 117 7.915923 CCAAAGAAAAGAAAAGGACAAGTACTC 59.084 37.037 0.00 0.00 0.00 2.59
117 118 7.147897 CCCAAAGAAAAGAAAAGGACAAGTACT 60.148 37.037 0.00 0.00 0.00 2.73
118 119 6.978659 CCCAAAGAAAAGAAAAGGACAAGTAC 59.021 38.462 0.00 0.00 0.00 2.73
356 447 0.537828 GGGTGGTCCGTTTTGGCTTA 60.538 55.000 0.00 0.00 37.80 3.09
401 524 4.012895 CACCGAGTGCACAACCGC 62.013 66.667 21.04 1.67 0.00 5.68
430 553 2.566913 GCGTCTAGACTCCAGATCAGA 58.433 52.381 20.34 0.00 0.00 3.27
431 554 1.262950 CGCGTCTAGACTCCAGATCAG 59.737 57.143 20.34 3.05 0.00 2.90
432 555 1.134491 TCGCGTCTAGACTCCAGATCA 60.134 52.381 20.34 0.00 0.00 2.92
560 1965 5.446473 GCATCCTGTTATTCTTCGACAGTTG 60.446 44.000 0.00 0.00 39.23 3.16
561 1966 4.631813 GCATCCTGTTATTCTTCGACAGTT 59.368 41.667 0.00 0.00 39.23 3.16
568 1973 4.906065 TGCATGCATCCTGTTATTCTTC 57.094 40.909 18.46 0.00 0.00 2.87
575 1980 1.133598 CGTCATTGCATGCATCCTGTT 59.866 47.619 23.37 0.00 0.00 3.16
608 2013 3.748660 CTGCCACGTCACACACCCA 62.749 63.158 0.00 0.00 0.00 4.51
609 2014 2.972505 CTGCCACGTCACACACCC 60.973 66.667 0.00 0.00 0.00 4.61
641 2055 0.179702 CAGCCTGCCTATTGAGAGCA 59.820 55.000 0.00 0.00 34.79 4.26
647 2061 1.607628 GCTTGATCAGCCTGCCTATTG 59.392 52.381 0.00 0.00 43.65 1.90
682 2096 4.802039 ACTTGTAACTGACAGTAACACGTG 59.198 41.667 15.48 15.48 39.88 4.49
699 2117 5.995565 AGCATGGTCTGTAAGTACTTGTA 57.004 39.130 18.56 5.97 33.76 2.41
702 2120 6.890814 AGTAGTAGCATGGTCTGTAAGTACTT 59.109 38.462 13.68 13.68 30.25 2.24
704 2122 6.238703 GGAGTAGTAGCATGGTCTGTAAGTAC 60.239 46.154 0.00 1.00 33.76 2.73
719 2137 5.163499 ACAGCTTGTCATAAGGAGTAGTAGC 60.163 44.000 0.00 0.00 0.00 3.58
771 2193 2.256461 CTCTTTGGCGTTGCAGGC 59.744 61.111 3.41 3.41 37.19 4.85
772 2194 2.956987 CCTCTTTGGCGTTGCAGG 59.043 61.111 0.00 0.00 0.00 4.85
877 2299 2.116366 GCGTGAACAAACAAATTCGCT 58.884 42.857 0.00 0.00 39.43 4.93
880 2302 1.137287 CGCGCGTGAACAAACAAATTC 60.137 47.619 24.19 0.00 0.00 2.17
940 2363 5.109210 CGTCAAGCAGGTCTTATATTGACA 58.891 41.667 14.15 0.00 44.13 3.58
969 2392 1.976728 GTGAGTGTGTACGTGTGATCG 59.023 52.381 0.00 0.00 0.00 3.69
978 2401 1.535462 GTGGGCAATGTGAGTGTGTAC 59.465 52.381 0.00 0.00 0.00 2.90
979 2402 1.544537 GGTGGGCAATGTGAGTGTGTA 60.545 52.381 0.00 0.00 0.00 2.90
982 2405 0.112995 ATGGTGGGCAATGTGAGTGT 59.887 50.000 0.00 0.00 0.00 3.55
986 2409 0.323633 CTCCATGGTGGGCAATGTGA 60.324 55.000 12.58 0.00 38.32 3.58
988 2411 1.683365 GCTCCATGGTGGGCAATGT 60.683 57.895 12.58 0.00 38.32 2.71
991 2417 1.607178 CTTGCTCCATGGTGGGCAA 60.607 57.895 27.01 27.01 45.07 4.52
997 2423 2.840651 AGTAAGTAGCTTGCTCCATGGT 59.159 45.455 12.58 0.00 31.08 3.55
1587 10492 0.988063 GCAAGAACTCCTCCCTCCTT 59.012 55.000 0.00 0.00 0.00 3.36
1614 10519 2.604686 AGCTTGACGCCCTCCTCA 60.605 61.111 0.00 0.00 40.39 3.86
1788 10726 1.096386 CGTCCACTAGGTCCTCTCCG 61.096 65.000 0.00 0.00 35.89 4.63
1965 10905 2.240493 AGTCACGTGGAAGTGGAAAG 57.760 50.000 17.00 0.00 42.10 2.62
2038 10979 0.610174 TGCCAGCAAGAGATCGAGTT 59.390 50.000 0.00 0.00 0.00 3.01
2068 11009 3.981071 TTGACATGTGGTCCCTAGAAG 57.019 47.619 1.15 0.00 46.38 2.85
2098 11039 6.729690 TTGGAAACTTGATGATTTTCACCT 57.270 33.333 0.00 0.00 30.74 4.00
2248 11189 0.108804 CTGCATCACGTTCGGGTACT 60.109 55.000 0.00 0.00 0.00 2.73
2255 11196 0.790866 GCGCTTTCTGCATCACGTTC 60.791 55.000 0.00 0.00 43.06 3.95
2339 11280 7.301068 CTTGATGACAAGTCTGAGGTATTTC 57.699 40.000 1.53 0.00 45.73 2.17
2390 11331 1.153449 CCGTGGAATAAGCAGCGGA 60.153 57.895 0.00 0.00 41.45 5.54
2420 11361 4.905456 TCATACCCGAGGATTTTACAGGAT 59.095 41.667 0.00 0.00 0.00 3.24
2426 11367 3.738899 GCACGTCATACCCGAGGATTTTA 60.739 47.826 0.00 0.00 0.00 1.52
2561 11502 0.963962 ACTCGAAGTCCGTGCCTTTA 59.036 50.000 0.00 0.00 39.75 1.85
2729 11670 2.802724 CCGGACGGTGATGCCCATA 61.803 63.158 0.00 0.00 0.00 2.74
2862 11803 9.981114 ACATTACATCATAAGTATCGACATTCA 57.019 29.630 0.00 0.00 0.00 2.57
2893 11834 4.082625 TGCAATGGTGTTTCTGATGATGTC 60.083 41.667 0.00 0.00 0.00 3.06
2907 11848 8.761575 AATTTGATAGTAAACTTGCAATGGTG 57.238 30.769 0.00 0.00 0.00 4.17
2941 11907 9.749490 GTTTGTGATTTAAATGCAATTGATCAG 57.251 29.630 10.34 0.00 36.10 2.90
2945 11913 6.429385 GGGGTTTGTGATTTAAATGCAATTGA 59.571 34.615 10.34 0.00 36.10 2.57
2957 11925 1.047801 GGTGCTGGGGTTTGTGATTT 58.952 50.000 0.00 0.00 0.00 2.17
2971 11939 1.106351 TTGTTTGGCGTCATGGTGCT 61.106 50.000 0.00 0.00 0.00 4.40
3025 11999 7.878127 GGTGGCTGCAATATAGATAGAACTTTA 59.122 37.037 0.50 0.00 0.00 1.85
3029 12003 5.799213 AGGTGGCTGCAATATAGATAGAAC 58.201 41.667 0.50 0.00 0.00 3.01
3088 12062 3.138304 GGTGTGTGTGTGACATGTATGT 58.862 45.455 0.00 0.00 45.16 2.29
3093 12067 1.063912 GTGTGGTGTGTGTGTGACATG 59.936 52.381 0.00 0.00 36.78 3.21
3103 12077 2.395360 GCGTGTGTGTGTGGTGTGT 61.395 57.895 0.00 0.00 0.00 3.72
3104 12078 2.403186 GCGTGTGTGTGTGGTGTG 59.597 61.111 0.00 0.00 0.00 3.82
3105 12079 3.192230 CGCGTGTGTGTGTGGTGT 61.192 61.111 0.00 0.00 0.00 4.16
3106 12080 4.589700 GCGCGTGTGTGTGTGGTG 62.590 66.667 8.43 0.00 0.00 4.17
3130 12104 3.684809 CTATGTGTGTGTGCGCGCG 62.685 63.158 28.44 28.44 38.36 6.86
3131 12105 2.096406 CTATGTGTGTGTGCGCGC 59.904 61.111 27.26 27.26 36.27 6.86
3135 12109 9.169468 GCATAATTTATAACTATGTGTGTGTGC 57.831 33.333 12.28 0.00 0.00 4.57
3143 12117 8.999431 CGGAGGTTGCATAATTTATAACTATGT 58.001 33.333 12.28 0.00 0.00 2.29
3147 12121 7.390718 GGATCGGAGGTTGCATAATTTATAACT 59.609 37.037 0.00 0.00 0.00 2.24
3166 12140 5.351948 TGTCACATCTAAAATGGATCGGA 57.648 39.130 0.00 0.00 0.00 4.55
3168 12142 9.603298 CATTTATGTCACATCTAAAATGGATCG 57.397 33.333 13.52 0.00 33.03 3.69
3176 12150 7.552687 GGTCTGGTCATTTATGTCACATCTAAA 59.447 37.037 0.00 0.00 0.00 1.85
3180 12154 5.185454 TGGTCTGGTCATTTATGTCACATC 58.815 41.667 0.00 0.00 0.00 3.06
3189 12163 1.346395 ACGTGCTGGTCTGGTCATTTA 59.654 47.619 0.00 0.00 0.00 1.40
3199 12173 3.127533 GCCATGGACGTGCTGGTC 61.128 66.667 18.40 12.59 36.18 4.02
3200 12174 4.722700 GGCCATGGACGTGCTGGT 62.723 66.667 18.40 1.80 32.42 4.00
3222 12196 5.601662 TGTTCTTCTATTCCTTGCTATCGG 58.398 41.667 0.00 0.00 0.00 4.18
3230 12204 6.099557 CCTCCTCTCATGTTCTTCTATTCCTT 59.900 42.308 0.00 0.00 0.00 3.36
3232 12206 5.741673 GCCTCCTCTCATGTTCTTCTATTCC 60.742 48.000 0.00 0.00 0.00 3.01
3239 12213 0.539051 CGGCCTCCTCTCATGTTCTT 59.461 55.000 0.00 0.00 0.00 2.52
3248 12222 2.598985 CTATCGGCGGCCTCCTCT 60.599 66.667 18.34 0.00 0.00 3.69
3272 12246 1.802880 CGGCCTTCCATGTTCTACTCG 60.803 57.143 0.00 0.00 0.00 4.18
3307 12304 0.890996 GGTGCTGGTGACCTTCTTGG 60.891 60.000 2.11 0.00 42.93 3.61
3308 12305 0.179020 TGGTGCTGGTGACCTTCTTG 60.179 55.000 2.11 0.00 34.26 3.02
3309 12306 0.773644 ATGGTGCTGGTGACCTTCTT 59.226 50.000 2.11 0.00 34.26 2.52
3310 12307 0.326264 GATGGTGCTGGTGACCTTCT 59.674 55.000 2.11 0.00 35.64 2.85
3311 12308 0.326264 AGATGGTGCTGGTGACCTTC 59.674 55.000 2.11 0.00 37.73 3.46
3312 12309 0.773644 AAGATGGTGCTGGTGACCTT 59.226 50.000 2.11 0.00 34.26 3.50
3313 12310 1.279271 GTAAGATGGTGCTGGTGACCT 59.721 52.381 2.11 0.00 34.26 3.85
3314 12311 1.679032 GGTAAGATGGTGCTGGTGACC 60.679 57.143 0.00 0.00 0.00 4.02
3315 12312 1.003118 TGGTAAGATGGTGCTGGTGAC 59.997 52.381 0.00 0.00 0.00 3.67
3316 12313 1.357137 TGGTAAGATGGTGCTGGTGA 58.643 50.000 0.00 0.00 0.00 4.02
3317 12314 2.086869 CTTGGTAAGATGGTGCTGGTG 58.913 52.381 0.00 0.00 0.00 4.17
3318 12315 1.705186 ACTTGGTAAGATGGTGCTGGT 59.295 47.619 0.00 0.00 0.00 4.00
3319 12316 2.496899 ACTTGGTAAGATGGTGCTGG 57.503 50.000 0.00 0.00 0.00 4.85
3320 12317 3.120199 CGAAACTTGGTAAGATGGTGCTG 60.120 47.826 0.00 0.00 0.00 4.41
3321 12318 3.074412 CGAAACTTGGTAAGATGGTGCT 58.926 45.455 0.00 0.00 0.00 4.40
3322 12319 2.414161 GCGAAACTTGGTAAGATGGTGC 60.414 50.000 0.00 0.00 0.00 5.01
3323 12320 2.811431 TGCGAAACTTGGTAAGATGGTG 59.189 45.455 0.00 0.00 0.00 4.17
3324 12321 3.074412 CTGCGAAACTTGGTAAGATGGT 58.926 45.455 0.00 0.00 0.00 3.55
3325 12322 2.159517 GCTGCGAAACTTGGTAAGATGG 60.160 50.000 0.00 0.00 0.00 3.51
3326 12323 2.159517 GGCTGCGAAACTTGGTAAGATG 60.160 50.000 0.00 0.00 0.00 2.90
3327 12324 2.084546 GGCTGCGAAACTTGGTAAGAT 58.915 47.619 0.00 0.00 0.00 2.40
3328 12325 1.519408 GGCTGCGAAACTTGGTAAGA 58.481 50.000 0.00 0.00 0.00 2.10
3329 12326 0.165944 CGGCTGCGAAACTTGGTAAG 59.834 55.000 0.00 0.00 0.00 2.34
3336 12333 2.357517 CTCACCGGCTGCGAAACT 60.358 61.111 0.00 0.00 0.00 2.66
3338 12335 3.825160 AAGCTCACCGGCTGCGAAA 62.825 57.895 0.00 0.00 42.24 3.46
3339 12336 4.314440 AAGCTCACCGGCTGCGAA 62.314 61.111 0.00 0.00 42.24 4.70
3372 12369 1.070914 GAAGGGAAGAATAGCCTCCGG 59.929 57.143 0.00 0.00 0.00 5.14
3393 12390 3.191371 GGGGATGTGTGAAACTTCATGAC 59.809 47.826 0.00 0.00 39.73 3.06
3396 12393 3.424703 CTGGGGATGTGTGAAACTTCAT 58.575 45.455 0.00 0.00 39.73 2.57
3397 12394 2.488891 CCTGGGGATGTGTGAAACTTCA 60.489 50.000 0.00 0.00 38.04 3.02
3409 12406 1.839424 GTTCAAGAACCCTGGGGATG 58.161 55.000 18.88 10.06 38.96 3.51
3410 12407 0.328258 CGTTCAAGAACCCTGGGGAT 59.672 55.000 18.88 5.19 38.03 3.85
3411 12408 1.758592 CGTTCAAGAACCCTGGGGA 59.241 57.895 18.88 0.48 38.03 4.81
3412 12409 1.303317 CCGTTCAAGAACCCTGGGG 60.303 63.158 18.88 7.87 38.03 4.96
3420 12417 0.884704 GCTCACCAGCCGTTCAAGAA 60.885 55.000 0.00 0.00 40.14 2.52
3433 12430 2.033141 TCAGGCAGCAAGCTCACC 59.967 61.111 0.00 0.00 44.79 4.02
3524 12521 3.433709 TGCATTTTGACATATTTCCGCG 58.566 40.909 0.00 0.00 0.00 6.46
3590 12588 6.754675 CAGGTTTAAACAAATTGGACGACTTT 59.245 34.615 19.57 0.00 0.00 2.66
3594 12592 4.098044 TGCAGGTTTAAACAAATTGGACGA 59.902 37.500 19.57 0.00 0.00 4.20
3596 12594 5.988561 TGATGCAGGTTTAAACAAATTGGAC 59.011 36.000 19.57 0.20 0.00 4.02
3613 12611 5.910723 GCCAAAACAAAGAAATTTGATGCAG 59.089 36.000 7.66 0.00 36.41 4.41
3637 12635 4.917415 GGTCACATTTCAAACGGAATTCAG 59.083 41.667 7.93 5.85 34.91 3.02
3662 12660 4.641094 TCATCCAAAACTAACCACAAACGT 59.359 37.500 0.00 0.00 0.00 3.99
3672 12671 4.282449 TGAGAGTCGGTCATCCAAAACTAA 59.718 41.667 0.00 0.00 0.00 2.24
3676 12675 3.981071 ATGAGAGTCGGTCATCCAAAA 57.019 42.857 0.00 0.00 27.81 2.44
3728 12730 2.492484 ACGGATACCATATCTCTTCGCC 59.508 50.000 0.00 0.00 0.00 5.54
3732 12734 6.381420 CCCTTCATACGGATACCATATCTCTT 59.619 42.308 0.00 0.00 0.00 2.85
3744 12746 2.478292 ACTTGGACCCTTCATACGGAT 58.522 47.619 0.00 0.00 0.00 4.18
3762 12764 8.251721 GGAGTATACAACTACATCTGTTCAACT 58.748 37.037 5.50 0.00 39.11 3.16
3767 12769 6.324254 GGAGGGAGTATACAACTACATCTGTT 59.676 42.308 5.50 0.00 46.98 3.16


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

AutoCloner maintained by Alex Coulton.