Multiple sequence alignment - TraesCS6A01G173400

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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 TraesCS6A01G173400 chr6A 100.000 3989 0 0 1 3989 185317962 185321950 0.000000e+00 7367
1 TraesCS6A01G173400 chr6B 92.247 3147 168 37 1 3127 240399681 240402771 0.000000e+00 4390
2 TraesCS6A01G173400 chr6B 91.468 879 49 9 3118 3989 240402806 240403665 0.000000e+00 1184
3 TraesCS6A01G173400 chr6D 91.419 2086 103 24 1919 3989 141136225 141138249 0.000000e+00 2791
4 TraesCS6A01G173400 chr6D 93.586 1185 53 9 762 1936 141135038 141136209 0.000000e+00 1746
5 TraesCS6A01G173400 chr6D 90.639 673 39 7 115 775 141134362 141135022 0.000000e+00 872
6 TraesCS6A01G173400 chr6D 93.902 82 5 0 1 82 141134277 141134358 1.510000e-24 124
7 TraesCS6A01G173400 chr2D 79.512 205 30 7 579 776 473167979 473167780 6.950000e-28 135
8 TraesCS6A01G173400 chr7B 79.397 199 23 10 594 778 395413664 395413470 1.510000e-24 124
9 TraesCS6A01G173400 chr7B 80.606 165 21 6 577 731 711876845 711877008 2.520000e-22 117
10 TraesCS6A01G173400 chr3D 83.206 131 20 2 587 716 114650085 114649956 7.000000e-23 119
11 TraesCS6A01G173400 chr2B 78.977 176 23 9 566 731 539337163 539337334 1.520000e-19 108
12 TraesCS6A01G173400 chr2B 80.000 150 20 4 587 726 335806312 335806461 7.050000e-18 102
13 TraesCS6A01G173400 chr1B 79.870 154 20 7 587 731 26269554 26269403 7.050000e-18 102
14 TraesCS6A01G173400 chr3B 76.777 211 28 11 587 781 15854523 15854318 9.120000e-17 99


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 TraesCS6A01G173400 chr6A 185317962 185321950 3988 False 7367.00 7367 100.0000 1 3989 1 chr6A.!!$F1 3988
1 TraesCS6A01G173400 chr6B 240399681 240403665 3984 False 2787.00 4390 91.8575 1 3989 2 chr6B.!!$F1 3988
2 TraesCS6A01G173400 chr6D 141134277 141138249 3972 False 1383.25 2791 92.3865 1 3989 4 chr6D.!!$F1 3988

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
941 983 0.249657 GAGATAAGGGGAGCACGCTG 60.250 60.0 0.00 0.0 42.22 5.18 F
1779 1839 0.321919 TGTGCACATTCCTCCTCTGC 60.322 55.0 17.42 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2442 2546 1.469703 CGAAATGGAGCTGCATGACAA 59.53 47.619 22.38 0.0 0.0 3.18 R
3574 3737 0.730265 CTTCGGTCGGTCTCTCTCTG 59.27 60.000 0.00 0.0 0.0 3.35 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
107 108 4.579647 AAACACCATCCTATTACCCGTT 57.420 40.909 0.00 0.00 0.00 4.44
112 113 2.550208 CCATCCTATTACCCGTTGAGGC 60.550 54.545 0.00 0.00 39.21 4.70
113 114 1.125633 TCCTATTACCCGTTGAGGCC 58.874 55.000 0.00 0.00 39.21 5.19
118 119 2.400269 TTACCCGTTGAGGCCGCTTT 62.400 55.000 8.34 0.00 39.21 3.51
167 168 3.245016 CCAGGCAGCTATTATTCCCATCA 60.245 47.826 0.00 0.00 0.00 3.07
184 185 1.974875 CATTGCAGCTGCCCTGACA 60.975 57.895 34.64 13.43 44.64 3.58
219 220 5.598417 TGAATAGCTAGACCATAGCAGACAA 59.402 40.000 9.37 0.00 42.68 3.18
222 223 2.804933 GCTAGACCATAGCAGACAAGGC 60.805 54.545 0.00 0.00 40.14 4.35
481 482 5.007234 ACGATGTTTTTGTCGACAATGAGAA 59.993 36.000 30.10 18.84 40.11 2.87
516 517 7.961326 AATCTTAAAGATAGGCAACCATGTT 57.039 32.000 0.00 0.00 32.89 2.71
519 520 7.601856 TCTTAAAGATAGGCAACCATGTTTTG 58.398 34.615 0.00 0.00 37.17 2.44
527 528 2.287308 GCAACCATGTTTTGCGTAGACA 60.287 45.455 12.14 0.00 40.01 3.41
537 538 2.232756 TGCGTAGACATTGTGTGTGT 57.767 45.000 0.00 0.00 42.36 3.72
553 554 4.457603 GTGTGTGTTTGTGCCTCCATATAA 59.542 41.667 0.00 0.00 0.00 0.98
556 557 6.127758 TGTGTGTTTGTGCCTCCATATAATTC 60.128 38.462 0.00 0.00 0.00 2.17
567 568 7.505585 TGCCTCCATATAATTCTTTTTAGGGTG 59.494 37.037 0.00 0.00 0.00 4.61
577 578 1.909700 TTTTAGGGTGCCTGCAAGAG 58.090 50.000 0.00 0.00 34.07 2.85
587 588 2.957680 TGCCTGCAAGAGAAAACAATGA 59.042 40.909 0.00 0.00 34.07 2.57
689 702 7.730364 TCTTCTTGTAAGCTTGGTAAGAAAG 57.270 36.000 23.09 18.89 37.05 2.62
745 758 5.102313 GGCAATTTGTTTCTAGGAAATCCG 58.898 41.667 0.00 0.00 42.08 4.18
747 760 5.800438 GCAATTTGTTTCTAGGAAATCCGAC 59.200 40.000 0.00 0.00 42.08 4.79
793 835 2.875672 GCTCAATACACAGCAACTCCCA 60.876 50.000 0.00 0.00 35.56 4.37
826 868 2.588877 CCGCTAATCACGGCCCAG 60.589 66.667 0.00 0.00 44.90 4.45
875 917 2.202690 CGCTATTCCCGACGCACA 60.203 61.111 0.00 0.00 0.00 4.57
876 918 2.230940 CGCTATTCCCGACGCACAG 61.231 63.158 0.00 0.00 0.00 3.66
877 919 2.526120 GCTATTCCCGACGCACAGC 61.526 63.158 0.00 0.00 0.00 4.40
938 980 1.364171 CCGAGATAAGGGGAGCACG 59.636 63.158 0.00 0.00 0.00 5.34
939 981 1.300233 CGAGATAAGGGGAGCACGC 60.300 63.158 0.00 0.00 0.00 5.34
940 982 1.739338 CGAGATAAGGGGAGCACGCT 61.739 60.000 0.00 0.00 45.42 5.07
941 983 0.249657 GAGATAAGGGGAGCACGCTG 60.250 60.000 0.00 0.00 42.22 5.18
942 984 1.889573 GATAAGGGGAGCACGCTGC 60.890 63.158 1.35 1.35 45.46 5.25
1204 1261 2.868583 CTCGACGATTCCTACTTCGGTA 59.131 50.000 0.00 0.00 39.61 4.02
1216 1273 2.365095 CTTCGGTACCAGATCCCGCC 62.365 65.000 13.54 0.00 41.46 6.13
1243 1300 2.480587 CCGTTTAATTCCCCCGAATTGC 60.481 50.000 8.07 0.00 46.07 3.56
1274 1331 3.845781 TGGTTCTGCCCTAGATTGATC 57.154 47.619 0.00 0.00 34.80 2.92
1311 1368 2.866762 GGATTGCGAGTATGTGACCTTC 59.133 50.000 0.00 0.00 0.00 3.46
1337 1394 3.303395 GCGTTGCTTCTGATTATGTAGGC 60.303 47.826 0.00 0.00 0.00 3.93
1410 1467 1.457738 CGTGTTCATCGCTCTCTACG 58.542 55.000 0.00 0.00 0.00 3.51
1456 1513 3.073798 TGGTATGCCACATATACAAGGGG 59.926 47.826 0.00 0.00 40.46 4.79
1463 1520 4.141574 GCCACATATACAAGGGGTCTGTAA 60.142 45.833 0.00 0.00 0.00 2.41
1581 1641 9.822185 AATAATGGGCAATTTAGAGTGAAATTC 57.178 29.630 0.00 0.00 36.99 2.17
1606 1666 9.645059 TCACTGTCATTGTTTGTTTGAATTAAA 57.355 25.926 0.00 0.00 0.00 1.52
1638 1698 7.386573 GTGGTGGGAATTTAACATTTAAGGTTG 59.613 37.037 5.20 0.00 0.00 3.77
1641 1701 8.769891 GTGGGAATTTAACATTTAAGGTTGTTG 58.230 33.333 5.20 0.00 36.75 3.33
1779 1839 0.321919 TGTGCACATTCCTCCTCTGC 60.322 55.000 17.42 0.00 0.00 4.26
1822 1882 0.464554 GTGTGGATTAGCTCTGCCCC 60.465 60.000 0.00 0.00 0.00 5.80
1880 1941 9.060347 CCTATTTATGAAACTATGATGTGCTGT 57.940 33.333 0.00 0.00 0.00 4.40
1886 1947 6.230472 TGAAACTATGATGTGCTGTTGTACT 58.770 36.000 0.00 0.00 0.00 2.73
1900 1961 1.438651 TGTACTGCTCATTGTTCCGC 58.561 50.000 0.00 0.00 0.00 5.54
2006 2099 4.682787 TGCCTATCAGACAACGTCTTATG 58.317 43.478 0.00 0.00 41.37 1.90
2082 2175 2.385013 TCCGATGATGTCACTTGTGG 57.615 50.000 0.64 0.00 0.00 4.17
2094 2187 2.367567 TCACTTGTGGTCCTCTTGTACC 59.632 50.000 0.64 0.00 36.24 3.34
2095 2188 2.104111 CACTTGTGGTCCTCTTGTACCA 59.896 50.000 0.00 0.00 43.47 3.25
2096 2189 2.775384 ACTTGTGGTCCTCTTGTACCAA 59.225 45.455 0.00 0.00 46.97 3.67
2097 2190 3.201266 ACTTGTGGTCCTCTTGTACCAAA 59.799 43.478 0.00 0.00 46.97 3.28
2098 2191 4.141251 ACTTGTGGTCCTCTTGTACCAAAT 60.141 41.667 0.00 0.00 46.97 2.32
2099 2192 3.750371 TGTGGTCCTCTTGTACCAAATG 58.250 45.455 0.00 0.00 46.97 2.32
2100 2193 2.488153 GTGGTCCTCTTGTACCAAATGC 59.512 50.000 0.00 0.00 46.97 3.56
2101 2194 2.375174 TGGTCCTCTTGTACCAAATGCT 59.625 45.455 0.00 0.00 42.74 3.79
2102 2195 3.181434 TGGTCCTCTTGTACCAAATGCTT 60.181 43.478 0.00 0.00 42.74 3.91
2103 2196 4.042311 TGGTCCTCTTGTACCAAATGCTTA 59.958 41.667 0.00 0.00 42.74 3.09
2104 2197 5.193679 GGTCCTCTTGTACCAAATGCTTAT 58.806 41.667 0.00 0.00 35.73 1.73
2105 2198 5.652452 GGTCCTCTTGTACCAAATGCTTATT 59.348 40.000 0.00 0.00 35.73 1.40
2106 2199 6.404734 GGTCCTCTTGTACCAAATGCTTATTG 60.405 42.308 0.00 0.00 35.73 1.90
2107 2200 6.151144 GTCCTCTTGTACCAAATGCTTATTGT 59.849 38.462 0.00 0.00 0.00 2.71
2108 2201 7.335924 GTCCTCTTGTACCAAATGCTTATTGTA 59.664 37.037 0.00 0.00 0.00 2.41
2109 2202 7.335924 TCCTCTTGTACCAAATGCTTATTGTAC 59.664 37.037 0.00 0.00 0.00 2.90
2126 2219 9.950680 CTTATTGTACCAAATGCTTATTGTAGG 57.049 33.333 0.00 0.00 0.00 3.18
2203 2303 6.992063 TTTCCTCTTCTCATTCTTGCATAC 57.008 37.500 0.00 0.00 0.00 2.39
2317 2421 2.906691 TTGTGTTCAAGGCCATTTGG 57.093 45.000 5.01 0.00 38.53 3.28
2328 2432 3.963129 AGGCCATTTGGAAATCGAGTAA 58.037 40.909 5.01 0.00 37.39 2.24
2411 2515 5.183904 GTGCCATTTTCTACTTCCACTGATT 59.816 40.000 0.00 0.00 0.00 2.57
2423 2527 4.842531 TCCACTGATTTGCCTCTGAATA 57.157 40.909 0.00 0.00 0.00 1.75
2442 2546 9.170890 TCTGAATACCTTCCATTATATTGTCCT 57.829 33.333 0.00 0.00 0.00 3.85
2538 2642 3.064545 GCAACATCTCACAGAAGGTATGC 59.935 47.826 0.00 0.00 0.00 3.14
2548 2652 3.823873 ACAGAAGGTATGCGAGATCCTAG 59.176 47.826 0.00 0.00 0.00 3.02
2556 2660 1.036707 GCGAGATCCTAGTGCCTCTT 58.963 55.000 0.00 0.00 0.00 2.85
2597 2701 5.528043 TGATCTGCATCTTCCTAGAACTC 57.472 43.478 0.00 0.00 33.20 3.01
2630 2734 8.837788 TTTTCTATATGCTCACAATCGATGAT 57.162 30.769 0.00 0.00 0.00 2.45
2633 2737 5.857822 ATATGCTCACAATCGATGATGTG 57.142 39.130 19.71 19.71 0.00 3.21
2745 2849 1.376553 GGGCGAGAAGAAGCTTGCT 60.377 57.895 2.10 0.00 43.42 3.91
2895 2999 2.609737 GGGTAACAGGAGAACACACTCG 60.610 54.545 0.00 0.00 36.57 4.18
2916 3020 3.481453 GGAGAATATTGAGCAACCCTCC 58.519 50.000 0.00 0.00 39.98 4.30
3016 3120 5.279206 CCAACTGCTATCTATCGGACATCTT 60.279 44.000 0.00 0.00 0.00 2.40
3020 3124 5.073428 TGCTATCTATCGGACATCTTCTGT 58.927 41.667 0.00 0.00 42.15 3.41
3039 3143 9.683069 TCTTCTGTTTTATTTTCTGAATGAAGC 57.317 29.630 0.00 0.00 35.89 3.86
3227 3383 4.082026 CACTCCTTCCAAATTTGATGGTCC 60.082 45.833 19.86 0.00 39.09 4.46
3229 3385 4.088634 TCCTTCCAAATTTGATGGTCCTG 58.911 43.478 19.86 0.26 39.09 3.86
3289 3445 3.070159 TCTTCTGAGTAACTTGTGCAGCT 59.930 43.478 0.00 0.00 0.00 4.24
3304 3460 2.260434 GCTAGCGGACCGACAACA 59.740 61.111 20.50 0.00 0.00 3.33
3326 3489 3.998913 TTACCCTGTGATCATGAGCAA 57.001 42.857 16.53 5.51 0.00 3.91
3336 3499 4.037208 GTGATCATGAGCAATAAACCTGGG 59.963 45.833 16.53 0.00 0.00 4.45
3352 3515 5.852282 ACCTGGGCAAACATTATGTAATC 57.148 39.130 0.00 0.00 0.00 1.75
3355 3518 5.010012 CCTGGGCAAACATTATGTAATCTCC 59.990 44.000 0.00 0.00 0.00 3.71
3367 3530 4.837093 TGTAATCTCCGTTGGGATTCTT 57.163 40.909 0.00 0.00 42.83 2.52
3368 3531 5.943349 TGTAATCTCCGTTGGGATTCTTA 57.057 39.130 0.00 0.00 42.83 2.10
3369 3532 6.302535 TGTAATCTCCGTTGGGATTCTTAA 57.697 37.500 0.00 0.00 42.83 1.85
3408 3571 1.150081 CTCCATCTGCACATCCCCC 59.850 63.158 0.00 0.00 0.00 5.40
3409 3572 2.203252 CCATCTGCACATCCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
3410 3573 2.903855 CATCTGCACATCCCCCGC 60.904 66.667 0.00 0.00 0.00 6.13
3413 3576 2.497792 ATCTGCACATCCCCCGCAAA 62.498 55.000 0.00 0.00 34.75 3.68
3414 3577 2.676121 TGCACATCCCCCGCAAAG 60.676 61.111 0.00 0.00 31.46 2.77
3574 3737 7.988028 ACAATTAGCAGTACCTATCTTTTCTCC 59.012 37.037 0.00 0.00 0.00 3.71
3605 3768 2.163815 CCGACCGAAGCCTATACCTATG 59.836 54.545 0.00 0.00 0.00 2.23
3690 3853 6.483307 ACCGGTGATATGATACATTTCACAAG 59.517 38.462 24.49 19.51 38.71 3.16
3706 3869 4.043750 TCACAAGTTTACGTACAGAACCG 58.956 43.478 0.00 0.00 0.00 4.44
3927 4092 1.445582 GTCGAAGGCGGTGTCGATT 60.446 57.895 8.42 0.00 46.91 3.34
3938 4103 0.031721 GTGTCGATTACGGGCTAGGG 59.968 60.000 0.00 0.00 40.21 3.53
3968 4133 1.586564 GTCGTCGATCGGCAAGAGG 60.587 63.158 21.12 2.60 44.22 3.69
3972 4137 1.076995 TCGATCGGCAAGAGGGAGA 60.077 57.895 16.41 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.794278 TGCGAAGAGAATGGTACTACAA 57.206 40.909 0.00 0.00 0.00 2.41
16 17 2.535984 CGTCATGCGAAGAGAATGGTAC 59.464 50.000 3.85 0.00 44.77 3.34
41 42 5.412594 AGTGATTAGCATTTGTTCACATCGT 59.587 36.000 4.42 0.00 39.27 3.73
45 46 7.331934 GTCTAGAGTGATTAGCATTTGTTCACA 59.668 37.037 0.00 0.00 39.27 3.58
82 83 4.454504 CGGGTAATAGGATGGTGTTTATGC 59.545 45.833 0.00 0.00 0.00 3.14
107 108 0.038166 ATTTCCTCAAAGCGGCCTCA 59.962 50.000 0.00 0.00 0.00 3.86
112 113 5.063204 TGTCCATATATTTCCTCAAAGCGG 58.937 41.667 0.00 0.00 0.00 5.52
113 114 6.348786 CCATGTCCATATATTTCCTCAAAGCG 60.349 42.308 0.00 0.00 0.00 4.68
118 119 7.631510 TTCTCCATGTCCATATATTTCCTCA 57.368 36.000 0.00 0.00 0.00 3.86
167 168 0.613853 AATGTCAGGGCAGCTGCAAT 60.614 50.000 37.63 23.65 44.36 3.56
184 185 8.034313 TGGTCTAGCTATTCATCTTTGGTAAT 57.966 34.615 0.00 0.00 0.00 1.89
219 220 0.980231 GATCTGAGTGTCCCAGGCCT 60.980 60.000 0.00 0.00 32.73 5.19
222 223 1.680522 CCCGATCTGAGTGTCCCAGG 61.681 65.000 0.00 0.00 32.73 4.45
319 320 7.759489 CTAGAGAGGATGTGTCTAGCTTAAT 57.241 40.000 0.00 0.00 41.07 1.40
377 378 7.089538 CCACACTCATGTATTTGTTTATTGCA 58.910 34.615 0.00 0.00 36.72 4.08
450 451 4.967575 GTCGACAAAAACATCGTTTCACAT 59.032 37.500 11.55 0.00 39.38 3.21
455 456 5.574082 TCATTGTCGACAAAAACATCGTTT 58.426 33.333 32.69 11.22 39.55 3.60
458 459 5.017484 TCTCATTGTCGACAAAAACATCG 57.983 39.130 32.69 16.89 39.55 3.84
511 512 4.379498 CACACAATGTCTACGCAAAACATG 59.621 41.667 0.00 0.00 34.03 3.21
516 517 2.939756 ACACACACAATGTCTACGCAAA 59.060 40.909 0.00 0.00 40.64 3.68
519 520 3.242608 ACAAACACACACAATGTCTACGC 60.243 43.478 0.00 0.00 40.64 4.42
527 528 1.408702 GGAGGCACAAACACACACAAT 59.591 47.619 0.00 0.00 0.00 2.71
553 554 2.888212 TGCAGGCACCCTAAAAAGAAT 58.112 42.857 0.00 0.00 29.64 2.40
556 557 2.229784 CTCTTGCAGGCACCCTAAAAAG 59.770 50.000 0.00 0.00 29.64 2.27
567 568 3.572584 CTCATTGTTTTCTCTTGCAGGC 58.427 45.455 0.00 0.00 0.00 4.85
577 578 4.525912 ACCAATCAGCCTCATTGTTTTC 57.474 40.909 0.00 0.00 30.40 2.29
587 588 1.188863 GGCATCAAACCAATCAGCCT 58.811 50.000 0.00 0.00 37.67 4.58
745 758 1.866601 GGTTTGCACATGCCAAAAGTC 59.133 47.619 12.15 3.08 41.18 3.01
747 760 1.950828 TGGTTTGCACATGCCAAAAG 58.049 45.000 12.15 0.00 41.18 2.27
793 835 1.000896 CGGGAGTGGGCCAGAATTT 60.001 57.895 6.40 0.00 0.00 1.82
826 868 1.479368 TTGGTGGCAAGGATTTGGGC 61.479 55.000 0.00 0.00 34.79 5.36
913 955 2.498941 CCCTTATCTCGGCGAGGCA 61.499 63.158 33.93 20.30 0.00 4.75
1204 1261 4.760220 AAGGGGGCGGGATCTGGT 62.760 66.667 0.00 0.00 0.00 4.00
1216 1273 1.687054 GGGGGAATTAAACGGAAGGGG 60.687 57.143 0.00 0.00 0.00 4.79
1249 1306 0.696501 TCTAGGGCAGAACCAAACCC 59.303 55.000 0.00 0.00 42.05 4.11
1287 1344 1.134521 GTCACATACTCGCAATCCCCA 60.135 52.381 0.00 0.00 0.00 4.96
1311 1368 1.075542 TAATCAGAAGCAACGCACGG 58.924 50.000 0.00 0.00 0.00 4.94
1410 1467 3.538591 TGACAGCATTCTCCATGTCATC 58.461 45.455 2.91 0.00 45.18 2.92
1545 1605 9.985730 CTAAATTGCCCATTATTCATTGTATGT 57.014 29.630 0.00 0.00 0.00 2.29
1550 1610 8.415553 TCACTCTAAATTGCCCATTATTCATTG 58.584 33.333 0.00 0.00 0.00 2.82
1606 1666 5.896073 TGTTAAATTCCCACCACCAAATT 57.104 34.783 0.00 0.00 0.00 1.82
1638 1698 3.194062 TGCCTAAAACAAGCAAAGCAAC 58.806 40.909 0.00 0.00 32.56 4.17
1641 1701 1.794701 GCTGCCTAAAACAAGCAAAGC 59.205 47.619 0.00 0.00 35.79 3.51
1779 1839 7.218773 CACTAAAATGCACATTTCTACCAATCG 59.781 37.037 8.94 0.00 39.88 3.34
1822 1882 7.203218 TGTATCCTTACTGATCTCATGAAACG 58.797 38.462 0.00 0.00 0.00 3.60
1880 1941 1.804151 GCGGAACAATGAGCAGTACAA 59.196 47.619 0.00 0.00 0.00 2.41
1886 1947 2.346803 GAGTAAGCGGAACAATGAGCA 58.653 47.619 0.00 0.00 0.00 4.26
2048 2141 7.500992 ACATCATCGGAACTAATATGACAAGT 58.499 34.615 0.00 0.00 31.56 3.16
2053 2146 7.290110 AGTGACATCATCGGAACTAATATGA 57.710 36.000 0.00 0.00 33.20 2.15
2104 2197 7.066525 GCTACCTACAATAAGCATTTGGTACAA 59.933 37.037 0.00 0.00 38.08 2.41
2105 2198 6.540914 GCTACCTACAATAAGCATTTGGTACA 59.459 38.462 0.00 0.00 35.05 2.90
2106 2199 6.766467 AGCTACCTACAATAAGCATTTGGTAC 59.234 38.462 0.00 0.00 37.44 3.34
2107 2200 6.895782 AGCTACCTACAATAAGCATTTGGTA 58.104 36.000 0.00 0.00 37.44 3.25
2108 2201 5.755849 AGCTACCTACAATAAGCATTTGGT 58.244 37.500 0.00 0.00 37.44 3.67
2109 2202 5.822519 TGAGCTACCTACAATAAGCATTTGG 59.177 40.000 0.00 0.00 37.44 3.28
2126 2219 4.794655 GCTCTAGCACCATTACTGAGCTAC 60.795 50.000 0.00 0.00 41.26 3.58
2203 2303 9.971922 AAGTAATTCTTGTTCAGGAATTTTCAG 57.028 29.630 21.45 0.00 40.91 3.02
2304 2408 2.754552 CTCGATTTCCAAATGGCCTTGA 59.245 45.455 3.32 0.00 34.44 3.02
2317 2421 6.229561 AGCTGAAACAGTTTACTCGATTTC 57.770 37.500 0.00 0.00 33.43 2.17
2328 2432 3.146066 TCCGCAAATAGCTGAAACAGTT 58.854 40.909 0.00 0.00 42.61 3.16
2411 2515 4.591321 AATGGAAGGTATTCAGAGGCAA 57.409 40.909 0.00 0.00 37.15 4.52
2423 2527 6.969043 TGACAAGGACAATATAATGGAAGGT 58.031 36.000 0.00 0.00 0.00 3.50
2442 2546 1.469703 CGAAATGGAGCTGCATGACAA 59.530 47.619 22.38 0.00 0.00 3.18
2538 2642 4.261825 CCTTAAAGAGGCACTAGGATCTCG 60.262 50.000 0.00 0.00 41.55 4.04
2556 2660 2.175931 TCAAGTGGACAAAGGGCCTTAA 59.824 45.455 21.25 0.09 0.00 1.85
2597 2701 7.974482 TGTGAGCATATAGAAAATCCATGAG 57.026 36.000 0.00 0.00 0.00 2.90
2630 2734 4.708909 TGCCATATGAAATTACTTGCCACA 59.291 37.500 3.65 0.00 0.00 4.17
2633 2737 4.342092 ACCTGCCATATGAAATTACTTGCC 59.658 41.667 3.65 0.00 0.00 4.52
2895 2999 3.137360 AGGAGGGTTGCTCAATATTCTCC 59.863 47.826 7.25 7.25 39.67 3.71
3016 3120 7.233348 AGGGCTTCATTCAGAAAATAAAACAGA 59.767 33.333 0.00 0.00 35.40 3.41
3020 3124 7.537596 TCAGGGCTTCATTCAGAAAATAAAA 57.462 32.000 0.00 0.00 35.40 1.52
3039 3143 2.680913 CGTCTGCCGCTTTTCAGGG 61.681 63.158 0.00 0.00 0.00 4.45
3289 3445 2.609350 GTAATTGTTGTCGGTCCGCTA 58.391 47.619 6.34 0.00 0.00 4.26
3293 3449 2.081462 CAGGGTAATTGTTGTCGGTCC 58.919 52.381 0.00 0.00 0.00 4.46
3304 3460 4.508551 TGCTCATGATCACAGGGTAATT 57.491 40.909 0.00 0.00 0.00 1.40
3326 3489 7.726033 TTACATAATGTTTGCCCAGGTTTAT 57.274 32.000 0.00 0.00 0.00 1.40
3336 3499 5.971202 CCAACGGAGATTACATAATGTTTGC 59.029 40.000 0.00 0.00 0.00 3.68
3352 3515 8.451908 AAGATTTATTAAGAATCCCAACGGAG 57.548 34.615 9.53 0.00 43.12 4.63
3408 3571 6.526674 GGTGTTATGTTATCTTTTCCTTTGCG 59.473 38.462 0.00 0.00 0.00 4.85
3409 3572 7.602753 AGGTGTTATGTTATCTTTTCCTTTGC 58.397 34.615 0.00 0.00 0.00 3.68
3410 3573 9.981114 AAAGGTGTTATGTTATCTTTTCCTTTG 57.019 29.630 0.00 0.00 39.19 2.77
3574 3737 0.730265 CTTCGGTCGGTCTCTCTCTG 59.270 60.000 0.00 0.00 0.00 3.35
3605 3768 3.554960 GGCTGTTTCATTTGTTCTTCCCC 60.555 47.826 0.00 0.00 0.00 4.81
3690 3853 2.070262 AGCCGGTTCTGTACGTAAAC 57.930 50.000 1.90 0.00 0.00 2.01
3696 3859 3.012518 TCACTAGTAGCCGGTTCTGTAC 58.987 50.000 1.90 0.00 0.00 2.90
3699 3862 1.134560 GGTCACTAGTAGCCGGTTCTG 59.865 57.143 1.90 0.00 0.00 3.02
3706 3869 2.412112 CGCCGGTCACTAGTAGCC 59.588 66.667 1.90 0.00 0.00 3.93
3747 3910 2.962786 CCGGTGTTTGTCGTCGCA 60.963 61.111 0.00 0.00 0.00 5.10
3799 3962 4.596180 GCCGTTGCGCGATCATGG 62.596 66.667 12.10 8.50 44.77 3.66
3818 3981 4.329545 TGTTGGCGGAGTGCTCCC 62.330 66.667 12.20 5.60 46.96 4.30
3872 4035 3.179265 CGAGCTTACGCGTGGTGG 61.179 66.667 24.59 9.31 42.32 4.61
3927 4092 1.902556 GACAAAGCCCTAGCCCGTA 59.097 57.895 0.00 0.00 41.25 4.02
3938 4103 3.774702 GACGACCGCCGACAAAGC 61.775 66.667 0.00 0.00 41.76 3.51
3968 4133 2.971307 CTTCTGAAACCAGAGCTCTCC 58.029 52.381 14.96 1.57 41.27 3.71


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

AutoCloner maintained by Alex Coulton.