Multiple sequence alignment - TraesCS5A01G513100

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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 TraesCS5A01G513100 chr5A 100.000 3485 0 0 1 3485 676962970 676959486 0.000000e+00 6436
1 TraesCS5A01G513100 chr5A 83.968 1366 206 12 906 2260 676951015 676949652 0.000000e+00 1297
2 TraesCS5A01G513100 chr5A 82.641 939 127 13 2565 3470 676951104 676950169 0.000000e+00 798
3 TraesCS5A01G513100 chr5A 82.464 844 144 3 893 1734 676943948 676943107 0.000000e+00 736
4 TraesCS5A01G513100 chr5A 80.924 844 133 11 2648 3464 676943944 676943102 2.930000e-180 641
5 TraesCS5A01G513100 chr4D 92.155 2613 198 3 877 3485 497160187 497157578 0.000000e+00 3683
6 TraesCS5A01G513100 chr4D 84.233 1389 208 7 882 2260 497152474 497151087 0.000000e+00 1341
7 TraesCS5A01G513100 chr4D 84.167 1339 180 7 877 2211 497158435 497157125 0.000000e+00 1269
8 TraesCS5A01G513100 chr4D 85.359 1045 115 11 2475 3485 497160343 497159303 0.000000e+00 1048
9 TraesCS5A01G513100 chr4D 82.854 939 125 15 2565 3470 497152539 497151604 0.000000e+00 809
10 TraesCS5A01G513100 chr4D 83.261 687 50 18 222 880 497161204 497160555 3.900000e-159 571
11 TraesCS5A01G513100 chr4B 89.615 2600 253 5 877 3459 637731684 637729085 0.000000e+00 3290
12 TraesCS5A01G513100 chr4B 84.908 1365 195 6 906 2260 637724106 637722743 0.000000e+00 1369
13 TraesCS5A01G513100 chr4B 84.291 1044 126 11 2476 3485 637731839 637730800 0.000000e+00 985
14 TraesCS5A01G513100 chr4B 84.994 893 68 29 15 876 637732923 637732066 0.000000e+00 846
15 TraesCS5A01G513100 chr4B 82.572 941 124 21 2565 3470 637724195 637723260 0.000000e+00 793
16 TraesCS5A01G513100 chr4B 82.847 857 118 12 877 1732 637729916 637729088 0.000000e+00 741
17 TraesCS5A01G513100 chr2A 77.386 1561 297 43 885 2414 602652779 602651244 0.000000e+00 876
18 TraesCS5A01G513100 chr2A 77.544 855 155 20 2651 3470 602652764 602651912 6.770000e-132 481
19 TraesCS5A01G513100 chr6A 89.888 89 9 0 1928 2016 420103499 420103587 7.900000e-22 115
20 TraesCS5A01G513100 chr3D 84.348 115 17 1 654 768 554729707 554729594 1.020000e-20 111
21 TraesCS5A01G513100 chr3B 83.784 111 12 5 654 761 736841281 736841174 2.210000e-17 100


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 TraesCS5A01G513100 chr5A 676959486 676962970 3484 True 6436.00 6436 100.00000 1 3485 1 chr5A.!!$R1 3484
1 TraesCS5A01G513100 chr5A 676949652 676951104 1452 True 1047.50 1297 83.30450 906 3470 2 chr5A.!!$R3 2564
2 TraesCS5A01G513100 chr5A 676943102 676943948 846 True 688.50 736 81.69400 893 3464 2 chr5A.!!$R2 2571
3 TraesCS5A01G513100 chr4D 497157125 497161204 4079 True 1642.75 3683 86.23550 222 3485 4 chr4D.!!$R2 3263
4 TraesCS5A01G513100 chr4D 497151087 497152539 1452 True 1075.00 1341 83.54350 882 3470 2 chr4D.!!$R1 2588
5 TraesCS5A01G513100 chr4B 637729085 637732923 3838 True 1465.50 3290 85.43675 15 3485 4 chr4B.!!$R2 3470
6 TraesCS5A01G513100 chr4B 637722743 637724195 1452 True 1081.00 1369 83.74000 906 3470 2 chr4B.!!$R1 2564
7 TraesCS5A01G513100 chr2A 602651244 602652779 1535 True 678.50 876 77.46500 885 3470 2 chr2A.!!$R1 2585

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
850 901 0.029567 CAGATAGACACTCGTCCCGC 59.970 60.0 0.0 0.0 43.73 6.13 F
1071 1517 0.109919 TCGTGACGGTTCTCGATGTG 60.110 55.0 4.7 0.0 41.55 3.21 F
1787 2236 0.395724 TACGCTGATGAGGAGAGGCA 60.396 55.0 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2145 0.242825 TCGTAACTGCCGGACTTGAG 59.757 55.0 5.05 0.0 0.00 3.02 R
2277 2729 0.319900 CGGCCATAGATTCCACCGAG 60.320 60.0 2.24 0.0 43.19 4.63 R
3132 3607 0.037590 TAATTGTTGGCCTGGACGCT 59.962 50.0 3.32 0.0 0.00 5.07 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
19 20 0.324943 CACCGGATGTTGAGGGTTCT 59.675 55.000 9.46 0.00 0.00 3.01
21 22 2.170607 CACCGGATGTTGAGGGTTCTAT 59.829 50.000 9.46 0.00 0.00 1.98
41 42 1.393603 TTTTTGCGGTCACCACATCA 58.606 45.000 0.00 0.00 0.00 3.07
42 43 0.950836 TTTTGCGGTCACCACATCAG 59.049 50.000 0.00 0.00 0.00 2.90
95 96 3.821033 ACAAGGCACATGAGTTTTACTCC 59.179 43.478 0.00 0.00 44.44 3.85
103 104 4.202326 ACATGAGTTTTACTCCGGACTTGT 60.202 41.667 0.00 0.00 44.44 3.16
115 116 2.474410 GGACTTGTCACCGATCCTTT 57.526 50.000 3.08 0.00 0.00 3.11
117 118 3.934068 GGACTTGTCACCGATCCTTTTA 58.066 45.455 3.08 0.00 0.00 1.52
133 134 7.467403 CGATCCTTTTAAATAAGAGAGTTGGGC 60.467 40.741 0.00 0.00 0.00 5.36
137 138 5.514500 TTAAATAAGAGAGTTGGGCTGGT 57.486 39.130 0.00 0.00 0.00 4.00
139 140 2.859165 TAAGAGAGTTGGGCTGGTTG 57.141 50.000 0.00 0.00 0.00 3.77
143 144 0.550914 AGAGTTGGGCTGGTTGTCAA 59.449 50.000 0.00 0.00 0.00 3.18
144 145 1.064017 AGAGTTGGGCTGGTTGTCAAA 60.064 47.619 0.00 0.00 0.00 2.69
145 146 1.067060 GAGTTGGGCTGGTTGTCAAAC 59.933 52.381 0.00 0.00 35.40 2.93
146 147 1.111277 GTTGGGCTGGTTGTCAAACT 58.889 50.000 1.59 0.00 36.48 2.66
148 149 2.691011 GTTGGGCTGGTTGTCAAACTTA 59.309 45.455 1.59 0.00 36.48 2.24
149 150 2.582052 TGGGCTGGTTGTCAAACTTAG 58.418 47.619 1.59 0.00 36.48 2.18
150 151 2.173782 TGGGCTGGTTGTCAAACTTAGA 59.826 45.455 1.59 0.00 36.48 2.10
151 152 3.219281 GGGCTGGTTGTCAAACTTAGAA 58.781 45.455 1.59 0.00 36.48 2.10
152 153 3.253432 GGGCTGGTTGTCAAACTTAGAAG 59.747 47.826 1.59 0.00 36.48 2.85
153 154 4.134563 GGCTGGTTGTCAAACTTAGAAGA 58.865 43.478 1.59 0.00 36.48 2.87
154 155 4.214332 GGCTGGTTGTCAAACTTAGAAGAG 59.786 45.833 1.59 0.00 36.48 2.85
157 158 5.611374 TGGTTGTCAAACTTAGAAGAGGAG 58.389 41.667 1.59 0.00 36.48 3.69
178 179 5.248380 AGCATTTTCTCCTCTGTAAAGGT 57.752 39.130 0.00 0.00 37.69 3.50
183 184 8.023706 GCATTTTCTCCTCTGTAAAGGTTTTAG 58.976 37.037 0.00 0.00 37.69 1.85
246 247 7.775053 TTTTTAAGGATTGGTTAGATGCAGT 57.225 32.000 0.00 0.00 0.00 4.40
247 248 7.775053 TTTTAAGGATTGGTTAGATGCAGTT 57.225 32.000 0.00 0.00 0.00 3.16
248 249 8.871629 TTTTAAGGATTGGTTAGATGCAGTTA 57.128 30.769 0.00 0.00 0.00 2.24
249 250 9.474313 TTTTAAGGATTGGTTAGATGCAGTTAT 57.526 29.630 0.00 0.00 0.00 1.89
286 287 1.373590 GCAAATCCGCTCCGCCTAAA 61.374 55.000 0.00 0.00 0.00 1.85
304 305 6.368791 CGCCTAAATTTATCGATCATCCTTGA 59.631 38.462 0.00 0.00 36.00 3.02
346 354 0.537188 ACGTACAGAGGGAGCATTGG 59.463 55.000 0.00 0.00 0.00 3.16
365 373 8.195436 AGCATTGGTTATTCTCTTGATTGATTG 58.805 33.333 0.00 0.00 0.00 2.67
366 374 8.192774 GCATTGGTTATTCTCTTGATTGATTGA 58.807 33.333 0.00 0.00 0.00 2.57
500 516 4.668576 TTTCATTTCGTAGCAGCTTCAG 57.331 40.909 0.00 0.00 0.00 3.02
524 540 3.574749 TCAAGAGATGGAGATCCCTGAG 58.425 50.000 0.00 0.00 35.38 3.35
553 569 1.337823 TGCGTGCTAACCCTTTCTCTC 60.338 52.381 0.00 0.00 0.00 3.20
555 571 2.613223 GCGTGCTAACCCTTTCTCTCTT 60.613 50.000 0.00 0.00 0.00 2.85
561 577 6.207614 GTGCTAACCCTTTCTCTCTTTTTCAT 59.792 38.462 0.00 0.00 0.00 2.57
562 578 6.777580 TGCTAACCCTTTCTCTCTTTTTCATT 59.222 34.615 0.00 0.00 0.00 2.57
563 579 7.040409 TGCTAACCCTTTCTCTCTTTTTCATTC 60.040 37.037 0.00 0.00 0.00 2.67
564 580 7.040409 GCTAACCCTTTCTCTCTTTTTCATTCA 60.040 37.037 0.00 0.00 0.00 2.57
597 614 8.703378 AAAGAATTCTTCTCCAGATCAAGTTT 57.297 30.769 20.71 0.00 39.61 2.66
610 627 5.737757 CAGATCAAGTTTCTCGATGCAAATG 59.262 40.000 0.00 0.00 0.00 2.32
611 628 3.825308 TCAAGTTTCTCGATGCAAATGC 58.175 40.909 0.00 0.00 42.50 3.56
612 629 2.919229 CAAGTTTCTCGATGCAAATGCC 59.081 45.455 2.46 0.00 41.18 4.40
613 630 2.161855 AGTTTCTCGATGCAAATGCCA 58.838 42.857 2.46 0.00 41.18 4.92
617 634 0.379669 CTCGATGCAAATGCCACCTC 59.620 55.000 2.46 0.00 41.18 3.85
618 635 0.322366 TCGATGCAAATGCCACCTCA 60.322 50.000 2.46 0.00 41.18 3.86
619 636 0.527113 CGATGCAAATGCCACCTCAA 59.473 50.000 2.46 0.00 41.18 3.02
620 637 1.067706 CGATGCAAATGCCACCTCAAA 60.068 47.619 2.46 0.00 41.18 2.69
628 645 1.398692 TGCCACCTCAAACCTGAAAC 58.601 50.000 0.00 0.00 0.00 2.78
629 646 0.673985 GCCACCTCAAACCTGAAACC 59.326 55.000 0.00 0.00 0.00 3.27
631 648 1.675552 CACCTCAAACCTGAAACCGT 58.324 50.000 0.00 0.00 0.00 4.83
641 658 2.488937 ACCTGAAACCGTTCGTTTGTTT 59.511 40.909 0.00 0.00 44.88 2.83
645 662 1.619983 AACCGTTCGTTTGTTTGTGC 58.380 45.000 0.00 0.00 0.00 4.57
681 698 1.517257 CGATCTGTCTCGGTGGCAC 60.517 63.158 9.70 9.70 35.03 5.01
742 759 0.179056 CCCACACGTTCCACTTCAGT 60.179 55.000 0.00 0.00 0.00 3.41
751 768 3.406764 GTTCCACTTCAGTTGCATCTCT 58.593 45.455 0.00 0.00 0.00 3.10
761 778 2.894387 GCATCTCTGCCAGCGTCC 60.894 66.667 0.00 0.00 42.88 4.79
850 901 0.029567 CAGATAGACACTCGTCCCGC 59.970 60.000 0.00 0.00 43.73 6.13
852 903 0.739561 GATAGACACTCGTCCCGCTT 59.260 55.000 0.00 0.00 43.73 4.68
853 904 1.134560 GATAGACACTCGTCCCGCTTT 59.865 52.381 0.00 0.00 43.73 3.51
861 912 4.083862 GTCCCGCTTTCCTCCGCT 62.084 66.667 0.00 0.00 0.00 5.52
904 1335 2.558821 CCGCCGCATCGAACAAAA 59.441 55.556 0.00 0.00 0.00 2.44
981 1412 2.279918 AACTTCGCCGTGCTCGTT 60.280 55.556 7.47 0.00 35.01 3.85
985 1416 3.776659 TTCGCCGTGCTCGTTCACA 62.777 57.895 7.47 0.00 36.80 3.58
1071 1517 0.109919 TCGTGACGGTTCTCGATGTG 60.110 55.000 4.70 0.00 41.55 3.21
1077 1523 1.819288 ACGGTTCTCGATGTGAGTCAT 59.181 47.619 0.00 0.00 45.46 3.06
1141 1587 1.640428 GTTCGTCATCGCCAATCTCA 58.360 50.000 0.00 0.00 36.96 3.27
1178 1624 0.677288 TCCGTCGTGTCCTTCAACAT 59.323 50.000 0.00 0.00 0.00 2.71
1326 1772 3.807538 GTACTCGACCAGCGCCGA 61.808 66.667 2.29 4.81 40.61 5.54
1335 1781 2.434884 CAGCGCCGACACAGGAAT 60.435 61.111 2.29 0.00 0.00 3.01
1453 1899 2.203523 TCGTCCCGACCACCTTCA 60.204 61.111 0.00 0.00 0.00 3.02
1488 1937 1.302431 CGGTGAATGGTCAGTGCCA 60.302 57.895 8.45 8.45 43.48 4.92
1658 2107 3.842923 CCAGGAGGCTCGCATCGT 61.843 66.667 8.69 0.00 0.00 3.73
1659 2108 2.185350 CAGGAGGCTCGCATCGTT 59.815 61.111 8.69 0.00 0.00 3.85
1668 2117 3.762992 CGCATCGTTGTCGCGTGT 61.763 61.111 5.77 0.00 43.86 4.49
1696 2145 2.813908 GGGTCCGTGTCATGTCGC 60.814 66.667 0.00 0.00 0.00 5.19
1729 2178 1.650314 TTACGAGAGCCGCATCGACA 61.650 55.000 20.73 8.37 41.40 4.35
1734 2183 1.227380 GAGCCGCATCGACAAGGAT 60.227 57.895 6.12 0.00 0.00 3.24
1787 2236 0.395724 TACGCTGATGAGGAGAGGCA 60.396 55.000 0.00 0.00 0.00 4.75
1829 2278 1.373497 CAAGAGCCGAAGCGACAGT 60.373 57.895 0.00 0.00 46.67 3.55
1875 2324 5.611128 ATGTGTCATTCAGCTACAGAGAT 57.389 39.130 0.00 0.00 0.00 2.75
1972 2424 2.571216 CGGTCGGTGGAGGTTGAGT 61.571 63.158 0.00 0.00 0.00 3.41
1980 2432 2.584391 GGAGGTTGAGTGGGAGCGT 61.584 63.158 0.00 0.00 0.00 5.07
2072 2524 0.459585 GCGGCGATACTCAAGAACCA 60.460 55.000 12.98 0.00 0.00 3.67
2073 2525 1.278238 CGGCGATACTCAAGAACCAC 58.722 55.000 0.00 0.00 0.00 4.16
2076 2528 2.614481 GGCGATACTCAAGAACCACCAA 60.614 50.000 0.00 0.00 0.00 3.67
2226 2678 4.519437 CTCTCCGGCATGAGCGCA 62.519 66.667 11.47 0.00 43.41 6.09
2235 2687 2.281692 ATGAGCGCACACCAGCAA 60.282 55.556 10.42 0.00 35.48 3.91
2277 2729 5.486735 AGATGAATCTGGTGGATGAGATC 57.513 43.478 0.00 0.00 35.42 2.75
2338 2796 0.517316 AAAGTTGGCATCGAACGAGC 59.483 50.000 2.94 6.59 0.00 5.03
2451 2913 4.706035 AGCTGAAGAAGAATATGCAGGAG 58.294 43.478 0.00 0.00 0.00 3.69
2456 2918 2.371510 AGAAGAATATGCAGGAGGCTCC 59.628 50.000 26.42 26.42 45.15 4.70
2471 2933 2.915659 TCCGAACACGGTCAGCCT 60.916 61.111 8.46 0.00 45.96 4.58
2497 2959 0.241213 CCACTGACATCGTCGTGTCT 59.759 55.000 20.72 6.67 46.70 3.41
2498 2960 1.331241 CACTGACATCGTCGTGTCTG 58.669 55.000 21.46 21.46 46.70 3.51
2559 3030 4.529219 TGCGTATCGGGCAGGCTG 62.529 66.667 10.94 10.94 35.04 4.85
2562 3033 2.786495 CGTATCGGGCAGGCTGAGT 61.786 63.158 20.86 0.68 0.00 3.41
2573 3044 2.102553 GCTGAGTCGCCTACGGTC 59.897 66.667 0.00 0.00 40.63 4.79
2596 3067 2.038837 TCGATGACGACGAGCAGGT 61.039 57.895 0.00 0.00 43.81 4.00
2603 3074 2.741092 GACGAGCAGGTTGGTCCA 59.259 61.111 0.00 0.00 41.50 4.02
2711 3186 1.300233 CGCTAGGGATTCGTCCAGC 60.300 63.158 0.00 0.00 0.00 4.85
2757 3232 4.414956 AGGCTCCCGGGATGACCA 62.415 66.667 29.40 8.43 40.22 4.02
2759 3234 2.190578 GCTCCCGGGATGACCAAG 59.809 66.667 27.07 11.90 40.22 3.61
2771 3246 1.451927 GACCAAGATCATGGCGGCA 60.452 57.895 16.34 16.34 44.75 5.69
2810 3285 2.825982 CCCGTGGACCTTGTGACA 59.174 61.111 0.00 0.00 0.00 3.58
2816 3291 2.741878 CGTGGACCTTGTGACAGTTCTT 60.742 50.000 0.00 0.00 0.00 2.52
2837 3312 2.265739 GTCGGTGGCAGCATGAGA 59.734 61.111 17.80 2.57 39.69 3.27
2847 3322 1.065854 GCAGCATGAGAGGGTACAAGT 60.066 52.381 0.00 0.00 39.69 3.16
2891 3366 0.876342 GGGTCGTCATCGCCAATCTC 60.876 60.000 0.00 0.00 35.88 2.75
2966 3441 2.357396 AAGCTCACGCGCATGTCA 60.357 55.556 5.73 0.00 42.32 3.58
2982 3457 2.685380 CAGAGACCGGGAAGGCCT 60.685 66.667 6.32 0.00 46.52 5.19
3010 3485 3.461773 CGCCGTGGAGTCCCTCAT 61.462 66.667 6.74 0.00 31.08 2.90
3035 3510 3.683937 GGCGGCACCAACATTGCT 61.684 61.111 3.07 0.00 40.07 3.91
3048 3523 3.335356 ATTGCTGAGGGGCTCCGTG 62.335 63.158 0.00 0.00 38.33 4.94
3083 3558 3.041940 GACCAACGTCGGCACAGG 61.042 66.667 0.00 0.00 0.00 4.00
3149 3624 1.973281 CAGCGTCCAGGCCAACAAT 60.973 57.895 5.01 0.00 0.00 2.71
3162 3637 2.935238 GCCAACAATTACGAGGAGCTCA 60.935 50.000 17.19 0.00 0.00 4.26
3197 3672 2.587753 CACACGGGCGTTGACTGT 60.588 61.111 0.00 0.00 0.00 3.55
3318 3793 1.586564 GAGAACGAGGCGGTGATCG 60.587 63.158 0.00 0.00 44.36 3.69
3356 3831 2.763292 ATCGGCAGGCAGCTCTCT 60.763 61.111 0.81 0.00 44.79 3.10
3370 3845 1.857965 CTCTCTGTCATGGTCCAGGA 58.142 55.000 1.03 1.03 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.324943 AGAACCCTCAACATCCGGTG 59.675 55.000 0.00 1.37 0.00 4.94
1 2 1.946984 TAGAACCCTCAACATCCGGT 58.053 50.000 0.00 0.00 0.00 5.28
3 4 5.897377 AAAAATAGAACCCTCAACATCCG 57.103 39.130 0.00 0.00 0.00 4.18
81 82 4.315803 ACAAGTCCGGAGTAAAACTCATG 58.684 43.478 13.41 7.01 46.79 3.07
95 96 0.246635 AAGGATCGGTGACAAGTCCG 59.753 55.000 0.00 0.00 46.93 4.79
103 104 7.848128 ACTCTCTTATTTAAAAGGATCGGTGA 58.152 34.615 0.00 0.00 0.00 4.02
115 116 5.514500 ACCAGCCCAACTCTCTTATTTAA 57.486 39.130 0.00 0.00 0.00 1.52
117 118 4.082125 CAACCAGCCCAACTCTCTTATTT 58.918 43.478 0.00 0.00 0.00 1.40
133 134 5.611374 TCCTCTTCTAAGTTTGACAACCAG 58.389 41.667 0.00 0.00 32.70 4.00
137 138 5.290493 TGCTCCTCTTCTAAGTTTGACAA 57.710 39.130 0.00 0.00 0.00 3.18
139 140 6.809630 AAATGCTCCTCTTCTAAGTTTGAC 57.190 37.500 0.00 0.00 0.00 3.18
157 158 5.966742 AACCTTTACAGAGGAGAAAATGC 57.033 39.130 0.00 0.00 39.25 3.56
242 243 7.482654 TGACATTGAGTTGCTATATAACTGC 57.517 36.000 7.12 0.00 38.42 4.40
243 244 7.225341 TGCTGACATTGAGTTGCTATATAACTG 59.775 37.037 7.12 0.00 38.42 3.16
244 245 7.275183 TGCTGACATTGAGTTGCTATATAACT 58.725 34.615 3.03 3.03 40.84 2.24
245 246 7.482654 TGCTGACATTGAGTTGCTATATAAC 57.517 36.000 0.00 0.00 33.22 1.89
246 247 8.504812 TTTGCTGACATTGAGTTGCTATATAA 57.495 30.769 0.00 0.00 33.22 0.98
247 248 8.681486 ATTTGCTGACATTGAGTTGCTATATA 57.319 30.769 0.00 0.00 33.22 0.86
248 249 7.255381 GGATTTGCTGACATTGAGTTGCTATAT 60.255 37.037 0.00 0.00 33.22 0.86
249 250 6.038603 GGATTTGCTGACATTGAGTTGCTATA 59.961 38.462 0.00 0.00 33.22 1.31
286 287 7.521099 GCACAACATCAAGGATGATCGATAAAT 60.521 37.037 12.79 0.00 44.53 1.40
304 305 1.472480 GCGTTAAGGGATGCACAACAT 59.528 47.619 0.00 0.00 43.54 2.71
365 373 4.211374 CGACCCCGACTTCATGAAATAATC 59.789 45.833 9.88 4.39 38.22 1.75
366 374 4.127171 CGACCCCGACTTCATGAAATAAT 58.873 43.478 9.88 0.00 38.22 1.28
367 375 3.196039 TCGACCCCGACTTCATGAAATAA 59.804 43.478 9.88 0.00 40.30 1.40
368 376 2.761767 TCGACCCCGACTTCATGAAATA 59.238 45.455 9.88 0.00 40.30 1.40
500 516 2.705127 AGGGATCTCCATCTCTTGAAGC 59.295 50.000 0.00 0.00 36.27 3.86
524 540 4.735132 TAGCACGCACGGACCTGC 62.735 66.667 6.00 6.00 0.00 4.85
534 550 1.066787 AGAGAGAAAGGGTTAGCACGC 60.067 52.381 0.00 0.00 36.07 5.34
597 614 0.035152 AGGTGGCATTTGCATCGAGA 60.035 50.000 4.74 0.00 44.36 4.04
610 627 0.673985 GGTTTCAGGTTTGAGGTGGC 59.326 55.000 0.00 0.00 34.15 5.01
611 628 0.951558 CGGTTTCAGGTTTGAGGTGG 59.048 55.000 0.00 0.00 34.15 4.61
612 629 1.675552 ACGGTTTCAGGTTTGAGGTG 58.324 50.000 0.00 0.00 34.15 4.00
613 630 2.294979 GAACGGTTTCAGGTTTGAGGT 58.705 47.619 0.00 0.00 34.15 3.85
617 634 2.836479 AACGAACGGTTTCAGGTTTG 57.164 45.000 0.00 0.00 34.41 2.93
618 635 2.488937 ACAAACGAACGGTTTCAGGTTT 59.511 40.909 0.00 1.76 45.60 3.27
619 636 2.086094 ACAAACGAACGGTTTCAGGTT 58.914 42.857 0.00 0.00 45.60 3.50
620 637 1.741528 ACAAACGAACGGTTTCAGGT 58.258 45.000 0.00 0.00 45.60 4.00
628 645 0.521659 ACGCACAAACAAACGAACGG 60.522 50.000 0.00 0.00 0.00 4.44
629 646 2.024179 CTACGCACAAACAAACGAACG 58.976 47.619 0.00 0.00 0.00 3.95
631 648 2.030701 GGTCTACGCACAAACAAACGAA 59.969 45.455 0.00 0.00 0.00 3.85
641 658 0.249120 CAGGGATTGGTCTACGCACA 59.751 55.000 0.00 0.00 0.00 4.57
645 662 1.883084 GCGCAGGGATTGGTCTACG 60.883 63.158 0.30 0.00 0.00 3.51
742 759 1.742880 GACGCTGGCAGAGATGCAA 60.743 57.895 25.25 0.00 36.33 4.08
850 901 1.424493 GATGCACGAGCGGAGGAAAG 61.424 60.000 0.00 0.00 46.23 2.62
852 903 1.960040 ATGATGCACGAGCGGAGGAA 61.960 55.000 0.00 0.00 46.23 3.36
853 904 1.960040 AATGATGCACGAGCGGAGGA 61.960 55.000 0.00 0.00 46.23 3.71
861 912 2.189257 CGGGGGAATGATGCACGA 59.811 61.111 0.00 0.00 0.00 4.35
891 1322 2.713976 GACAACTGTTTTGTTCGATGCG 59.286 45.455 0.00 0.00 31.96 4.73
901 1332 2.222953 GCGTCTTGACGACAACTGTTTT 60.223 45.455 24.65 0.00 42.98 2.43
904 1335 0.179121 TGCGTCTTGACGACAACTGT 60.179 50.000 24.65 0.00 42.98 3.55
926 1357 2.420043 CGACGGCCGGGTATTCAT 59.580 61.111 31.76 4.91 33.91 2.57
927 1358 4.517815 GCGACGGCCGGGTATTCA 62.518 66.667 31.76 0.00 39.04 2.57
981 1412 1.997311 CCTGGGAGCCTGGATGTGA 60.997 63.158 0.00 0.00 44.09 3.58
1071 1517 1.613925 TGCCCGCTCATACTATGACTC 59.386 52.381 0.00 0.00 35.06 3.36
1077 1523 4.095782 GTCAATTTTTGCCCGCTCATACTA 59.904 41.667 0.00 0.00 0.00 1.82
1224 1670 2.046892 CTCACGGACAGGGCCTTG 60.047 66.667 14.35 14.35 0.00 3.61
1326 1772 1.079819 CGAGACGGCATTCCTGTGT 60.080 57.895 0.00 0.00 0.00 3.72
1462 1908 0.602638 GACCATTCACCGTCAGCACA 60.603 55.000 0.00 0.00 0.00 4.57
1464 1913 0.320683 CTGACCATTCACCGTCAGCA 60.321 55.000 4.43 0.00 46.78 4.41
1484 1933 1.523154 GCCGAAAGTGTGGATTGGCA 61.523 55.000 0.00 0.00 40.66 4.92
1488 1937 1.156736 CGAAGCCGAAAGTGTGGATT 58.843 50.000 0.00 0.00 36.38 3.01
1696 2145 0.242825 TCGTAACTGCCGGACTTGAG 59.757 55.000 5.05 0.00 0.00 3.02
1746 2195 3.222599 TTCCCCGACCCAGACCGTA 62.223 63.158 0.00 0.00 0.00 4.02
1787 2236 2.026822 ACGGTCAGGATCAGCAAGAAAT 60.027 45.455 0.00 0.00 0.00 2.17
1972 2424 4.682334 TACCCGGACACGCTCCCA 62.682 66.667 0.73 0.00 39.22 4.37
1989 2441 3.157217 GATGTCCTCGGCCGCATCT 62.157 63.158 26.56 9.65 35.96 2.90
2054 2506 1.278238 GTGGTTCTTGAGTATCGCCG 58.722 55.000 0.00 0.00 38.61 6.46
2162 2614 3.553437 CTCTGCCGGTTCGACACGT 62.553 63.158 1.90 0.00 0.00 4.49
2197 2649 2.786495 CGGAGAGCATGTACGCCCT 61.786 63.158 0.00 0.00 0.00 5.19
2226 2678 4.250431 GCGCGTTGTTGCTGGTGT 62.250 61.111 8.43 0.00 0.00 4.16
2235 2687 2.178521 CTCGAGGTAGCGCGTTGT 59.821 61.111 17.35 0.00 0.00 3.32
2271 2723 3.829026 CCATAGATTCCACCGAGATCTCA 59.171 47.826 22.31 2.01 0.00 3.27
2277 2729 0.319900 CGGCCATAGATTCCACCGAG 60.320 60.000 2.24 0.00 43.19 4.63
2319 2777 0.517316 GCTCGTTCGATGCCAACTTT 59.483 50.000 0.00 0.00 0.00 2.66
2423 2885 5.295292 TGCATATTCTTCTTCAGCTTGTAGC 59.705 40.000 0.00 0.00 42.84 3.58
2444 2906 2.922503 TGTTCGGAGCCTCCTGCA 60.923 61.111 9.52 1.99 44.83 4.41
2445 2907 2.435059 GTGTTCGGAGCCTCCTGC 60.435 66.667 9.52 0.00 41.71 4.85
2456 2918 1.800315 CGTAGGCTGACCGTGTTCG 60.800 63.158 0.00 0.00 42.76 3.95
2471 2933 1.214325 CGATGTCAGTGGTGGCGTA 59.786 57.895 0.00 0.00 0.00 4.42
2582 3053 2.338620 CCAACCTGCTCGTCGTCA 59.661 61.111 0.00 0.00 0.00 4.35
2615 3090 2.426023 GACCGGTTGTCAGCTGGT 59.574 61.111 19.28 19.28 43.85 4.00
2714 3189 1.133253 CACGAGCATGGCGAAGTTG 59.867 57.895 0.00 0.00 0.00 3.16
2757 3232 1.452651 CACCTGCCGCCATGATCTT 60.453 57.895 0.00 0.00 0.00 2.40
2759 3234 2.903855 CCACCTGCCGCCATGATC 60.904 66.667 0.00 0.00 0.00 2.92
2795 3270 1.202533 AGAACTGTCACAAGGTCCACG 60.203 52.381 0.00 0.00 34.15 4.94
2804 3279 1.535226 CCGACGTCAAGAACTGTCACA 60.535 52.381 17.16 0.00 33.69 3.58
2810 3285 1.300697 GCCACCGACGTCAAGAACT 60.301 57.895 17.16 0.00 0.00 3.01
2816 3291 4.002506 ATGCTGCCACCGACGTCA 62.003 61.111 17.16 0.00 0.00 4.35
2837 3312 1.302511 CAGCGCCAACTTGTACCCT 60.303 57.895 2.29 0.00 0.00 4.34
2877 3352 3.324035 GCCGAGATTGGCGATGAC 58.676 61.111 0.00 0.00 46.75 3.06
2897 3372 2.362503 ACGGAGAGGCGGTCATCA 60.363 61.111 0.00 0.00 0.00 3.07
3027 3502 1.000396 GGAGCCCCTCAGCAATGTT 60.000 57.895 0.00 0.00 34.23 2.71
3048 3523 1.815421 CGAGTACCATGGCTGCCAC 60.815 63.158 25.99 11.06 35.80 5.01
3102 3577 4.200283 GCCGTCGGAGAGGAGCAG 62.200 72.222 17.49 0.00 46.48 4.24
3128 3603 4.329545 TTGGCCTGGACGCTGGAC 62.330 66.667 3.32 0.00 0.00 4.02
3132 3607 0.037590 TAATTGTTGGCCTGGACGCT 59.962 50.000 3.32 0.00 0.00 5.07
3139 3614 1.679032 GCTCCTCGTAATTGTTGGCCT 60.679 52.381 3.32 0.00 0.00 5.19
3149 3624 1.735376 GCGGGATGAGCTCCTCGTAA 61.735 60.000 12.15 0.00 44.28 3.18
3181 3656 2.581208 TTCACAGTCAACGCCCGTGT 62.581 55.000 0.00 0.00 0.00 4.49
3195 3670 2.422597 GATCGGTGTTGACCATTCACA 58.577 47.619 0.00 0.00 43.33 3.58
3197 3672 1.349357 TGGATCGGTGTTGACCATTCA 59.651 47.619 0.00 0.00 43.33 2.57
3293 3768 0.249073 CCGCCTCGTTCTCGATGAAT 60.249 55.000 0.00 0.00 45.21 2.57
3318 3793 2.432628 CTGGGTGAACGCGTCCTC 60.433 66.667 14.44 8.36 0.00 3.71
3349 3824 1.193323 CTGGACCATGACAGAGAGCT 58.807 55.000 0.00 0.00 36.86 4.09
3356 3831 1.229625 AGCCTCCTGGACCATGACA 60.230 57.895 0.00 0.00 34.57 3.58
3360 3835 3.474570 GCGAGCCTCCTGGACCAT 61.475 66.667 0.00 0.00 34.57 3.55
3410 3885 1.340658 CAGACTTGACCGACATGACG 58.659 55.000 10.68 10.68 0.00 4.35


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

AutoCloner maintained by Alex Coulton.