Multiple sequence alignment - TraesCS5A01G256300

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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 TraesCS5A01G256300 chr5A 100.000 3875 0 0 1 3875 471903127 471907001 0.000000e+00 7156.0
1 TraesCS5A01G256300 chr5B 95.164 2688 107 14 855 3528 438167172 438169850 0.000000e+00 4222.0
2 TraesCS5A01G256300 chr5B 82.336 702 95 20 1 684 438166102 438166792 2.010000e-162 582.0
3 TraesCS5A01G256300 chr5B 95.324 278 9 3 3600 3875 438211853 438212128 4.600000e-119 438.0
4 TraesCS5A01G256300 chr5D 95.533 2037 79 7 886 2914 369377673 369379705 0.000000e+00 3247.0
5 TraesCS5A01G256300 chr5D 94.013 618 33 1 2911 3528 369379896 369380509 0.000000e+00 933.0
6 TraesCS5A01G256300 chr5D 88.679 371 17 13 3517 3875 369381609 369381966 2.770000e-116 429.0
7 TraesCS5A01G256300 chr2D 80.656 884 113 27 2539 3384 2197418 2198281 1.960000e-177 632.0
8 TraesCS5A01G256300 chr2D 85.321 545 60 5 1071 1604 2196337 2196872 2.630000e-151 545.0
9 TraesCS5A01G256300 chr2D 81.873 331 54 3 1645 1969 2196874 2197204 1.370000e-69 274.0
10 TraesCS5A01G256300 chr2D 88.947 190 20 1 2005 2193 2197208 2197397 2.330000e-57 233.0
11 TraesCS5A01G256300 chr3B 88.608 79 9 0 777 855 118809396 118809474 3.190000e-16 97.1
12 TraesCS5A01G256300 chr2A 88.136 59 6 1 806 864 758605539 758605482 6.950000e-08 69.4
13 TraesCS5A01G256300 chr1B 97.222 36 1 0 832 867 165546808 165546773 1.160000e-05 62.1


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 TraesCS5A01G256300 chr5A 471903127 471907001 3874 False 7156.000000 7156 100.000000 1 3875 1 chr5A.!!$F1 3874
1 TraesCS5A01G256300 chr5B 438166102 438169850 3748 False 2402.000000 4222 88.750000 1 3528 2 chr5B.!!$F2 3527
2 TraesCS5A01G256300 chr5D 369377673 369381966 4293 False 1536.333333 3247 92.741667 886 3875 3 chr5D.!!$F1 2989
3 TraesCS5A01G256300 chr2D 2196337 2198281 1944 False 421.000000 632 84.199250 1071 3384 4 chr2D.!!$F1 2313

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
279 289 0.034670 GGCTCAGAAATGTGCCTCCT 60.035 55.0 12.74 0.00 43.04 3.69 F
347 358 0.179000 ACAATGATGGGACGGAGCTC 59.821 55.0 4.71 4.71 0.00 4.09 F
348 359 0.467384 CAATGATGGGACGGAGCTCT 59.533 55.0 14.64 0.00 0.00 4.09 F
1530 1791 0.473326 GGAGGCAGATCCATGCTCTT 59.527 55.0 6.87 0.00 45.75 2.85 F
2211 2477 0.393808 TTATGGGCCGAGCTGGTTTC 60.394 55.0 0.00 0.00 41.21 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1437 0.320374 TCGAGGTTCTTGGATTGCGT 59.680 50.0 0.00 0.0 0.0 5.24 R
1530 1791 0.815213 GCCAGTCACACTTCACAGCA 60.815 55.0 0.00 0.0 0.0 4.41 R
1659 1920 1.368641 CGGAGATCAATGCGTTCCAA 58.631 50.0 0.00 0.0 0.0 3.53 R
2694 2960 0.029035 CTGCAGGCATTTCGATCAGC 59.971 55.0 5.57 0.0 0.0 4.26 R
3812 5428 0.105862 ATAACGGGGAGATCGGTGGA 60.106 55.0 0.00 0.0 0.0 4.02 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
33 34 8.400184 AGAGTGTTTCATGATCAATTTGAGAA 57.600 30.769 0.00 0.56 0.00 2.87
34 35 8.295288 AGAGTGTTTCATGATCAATTTGAGAAC 58.705 33.333 0.00 7.48 0.00 3.01
87 91 4.893608 ACAATAACAGTTGGGGCAATTTC 58.106 39.130 0.00 0.00 33.40 2.17
90 94 1.247567 ACAGTTGGGGCAATTTCTCG 58.752 50.000 0.00 0.00 0.00 4.04
93 97 1.886542 AGTTGGGGCAATTTCTCGAAC 59.113 47.619 0.00 0.00 0.00 3.95
139 143 2.433491 CGACGGTTGGCGATGGAA 60.433 61.111 0.00 0.00 0.00 3.53
140 144 2.736682 CGACGGTTGGCGATGGAAC 61.737 63.158 0.00 0.00 0.00 3.62
141 145 2.359478 ACGGTTGGCGATGGAACC 60.359 61.111 0.00 0.00 38.65 3.62
143 147 2.106683 CGGTTGGCGATGGAACCTC 61.107 63.158 0.00 0.00 39.69 3.85
157 161 3.527641 CCTCGACTAGGGCTGGAC 58.472 66.667 0.00 0.00 42.32 4.02
159 163 1.451567 CTCGACTAGGGCTGGACGA 60.452 63.158 0.00 0.00 36.21 4.20
162 166 3.412879 GACTAGGGCTGGACGACGC 62.413 68.421 0.00 0.00 0.00 5.19
163 167 4.208686 CTAGGGCTGGACGACGCC 62.209 72.222 0.00 0.00 45.55 5.68
171 175 4.609247 GGACGACGCCGGATCTCG 62.609 72.222 5.05 10.17 40.78 4.04
216 220 0.535102 GGATGTAGGGCCGACAATGG 60.535 60.000 23.42 0.00 0.00 3.16
241 251 1.093496 GGGTTACTTGGCCGATTCCG 61.093 60.000 0.00 0.00 0.00 4.30
279 289 0.034670 GGCTCAGAAATGTGCCTCCT 60.035 55.000 12.74 0.00 43.04 3.69
281 291 2.284190 GCTCAGAAATGTGCCTCCTAC 58.716 52.381 0.00 0.00 0.00 3.18
290 300 0.530870 GTGCCTCCTACGCCATCTTC 60.531 60.000 0.00 0.00 0.00 2.87
330 341 1.371183 CAGCGAAAGGGACCTCACA 59.629 57.895 0.00 0.00 0.00 3.58
332 343 0.693049 AGCGAAAGGGACCTCACAAT 59.307 50.000 0.00 0.00 0.00 2.71
336 347 2.679837 CGAAAGGGACCTCACAATGATG 59.320 50.000 0.00 0.00 0.00 3.07
347 358 0.179000 ACAATGATGGGACGGAGCTC 59.821 55.000 4.71 4.71 0.00 4.09
348 359 0.467384 CAATGATGGGACGGAGCTCT 59.533 55.000 14.64 0.00 0.00 4.09
364 375 0.529337 CTCTGCGATGGTAGCCACAG 60.529 60.000 0.00 0.00 35.80 3.66
383 394 1.004745 AGGGGCAGTGAAAACGATGAT 59.995 47.619 0.00 0.00 0.00 2.45
389 400 3.725010 GCAGTGAAAACGATGATTCCGAC 60.725 47.826 0.00 0.00 0.00 4.79
390 401 3.431912 CAGTGAAAACGATGATTCCGACA 59.568 43.478 0.00 0.00 0.00 4.35
392 403 3.432252 GTGAAAACGATGATTCCGACACT 59.568 43.478 0.00 0.00 0.00 3.55
394 405 2.010145 AACGATGATTCCGACACTGG 57.990 50.000 0.00 0.00 0.00 4.00
462 473 3.221222 CCCGAGGGGTGAGATGTC 58.779 66.667 0.00 0.00 38.25 3.06
463 474 1.685765 CCCGAGGGGTGAGATGTCA 60.686 63.158 0.00 0.00 38.25 3.58
477 488 6.376978 GTGAGATGTCAGGATTGAAAAGTTG 58.623 40.000 0.00 0.00 34.49 3.16
480 491 5.474876 AGATGTCAGGATTGAAAAGTTGACC 59.525 40.000 0.00 0.00 35.08 4.02
483 494 5.299279 TGTCAGGATTGAAAAGTTGACCTTC 59.701 40.000 0.00 0.00 35.08 3.46
484 495 5.532779 GTCAGGATTGAAAAGTTGACCTTCT 59.467 40.000 0.00 0.00 34.49 2.85
527 538 5.301555 GGATGGACTAGAAGGTGCTTAATC 58.698 45.833 0.00 0.00 0.00 1.75
528 539 5.071115 GGATGGACTAGAAGGTGCTTAATCT 59.929 44.000 0.00 0.00 0.00 2.40
531 542 7.490657 TGGACTAGAAGGTGCTTAATCTTTA 57.509 36.000 0.00 0.00 0.00 1.85
532 543 7.556844 TGGACTAGAAGGTGCTTAATCTTTAG 58.443 38.462 0.00 0.00 0.00 1.85
533 544 7.399191 TGGACTAGAAGGTGCTTAATCTTTAGA 59.601 37.037 0.00 0.00 0.00 2.10
535 546 9.825109 GACTAGAAGGTGCTTAATCTTTAGAAT 57.175 33.333 0.00 0.00 0.00 2.40
573 589 4.608170 ATTTGACTTATGTGGGATGGGT 57.392 40.909 0.00 0.00 0.00 4.51
601 619 2.541556 GCCCTTGCTACTCTCTTAACG 58.458 52.381 0.00 0.00 33.53 3.18
603 621 3.771798 CCCTTGCTACTCTCTTAACGAC 58.228 50.000 0.00 0.00 0.00 4.34
617 636 7.982224 TCTCTTAACGACTTTCTAATCGATCA 58.018 34.615 0.00 0.00 40.86 2.92
620 639 9.582431 TCTTAACGACTTTCTAATCGATCAAAT 57.418 29.630 0.00 0.00 40.86 2.32
630 649 8.908786 TTCTAATCGATCAAATTAGCCATTCT 57.091 30.769 15.36 0.00 36.88 2.40
631 650 8.908786 TCTAATCGATCAAATTAGCCATTCTT 57.091 30.769 15.36 0.00 36.88 2.52
703 759 9.778741 TTTTAATGCTATGAACTACCTATGGAG 57.221 33.333 0.00 0.00 0.00 3.86
705 761 5.791336 TGCTATGAACTACCTATGGAGTG 57.209 43.478 0.00 0.00 0.00 3.51
711 767 5.989477 TGAACTACCTATGGAGTGAAATGG 58.011 41.667 0.00 0.00 0.00 3.16
712 768 4.423625 ACTACCTATGGAGTGAAATGGC 57.576 45.455 0.00 0.00 0.00 4.40
723 779 4.293415 GAGTGAAATGGCTGAACAAACAG 58.707 43.478 0.00 0.00 40.43 3.16
731 787 5.243426 TGGCTGAACAAACAGACTAAAAC 57.757 39.130 0.00 0.00 45.26 2.43
734 790 5.915196 GGCTGAACAAACAGACTAAAACATC 59.085 40.000 0.00 0.00 42.12 3.06
737 793 7.254932 GCTGAACAAACAGACTAAAACATCTCT 60.255 37.037 0.00 0.00 39.94 3.10
791 910 9.498176 TGAACACTTTTTAGTACTCCCTTTATC 57.502 33.333 0.00 0.00 0.00 1.75
793 912 9.722184 AACACTTTTTAGTACTCCCTTTATCTC 57.278 33.333 0.00 0.00 0.00 2.75
795 914 9.892130 CACTTTTTAGTACTCCCTTTATCTCAT 57.108 33.333 0.00 0.00 0.00 2.90
826 945 5.635549 ATCGTTTTGCAAACTAAAACAGC 57.364 34.783 12.39 0.00 44.28 4.40
827 946 4.739195 TCGTTTTGCAAACTAAAACAGCT 58.261 34.783 12.39 0.00 44.28 4.24
829 948 5.061560 TCGTTTTGCAAACTAAAACAGCTTG 59.938 36.000 12.39 0.00 44.28 4.01
836 955 5.247340 CAAACTAAAACAGCTTGCAAAACG 58.753 37.500 0.00 0.00 0.00 3.60
837 956 3.443976 ACTAAAACAGCTTGCAAAACGG 58.556 40.909 0.00 0.00 0.00 4.44
838 957 2.378445 AAAACAGCTTGCAAAACGGT 57.622 40.000 0.00 0.00 0.00 4.83
839 958 1.921243 AAACAGCTTGCAAAACGGTC 58.079 45.000 0.00 0.00 0.00 4.79
840 959 1.102978 AACAGCTTGCAAAACGGTCT 58.897 45.000 0.00 0.00 0.00 3.85
841 960 1.102978 ACAGCTTGCAAAACGGTCTT 58.897 45.000 0.00 0.00 0.00 3.01
842 961 2.294074 ACAGCTTGCAAAACGGTCTTA 58.706 42.857 0.00 0.00 0.00 2.10
844 963 4.069304 ACAGCTTGCAAAACGGTCTTATA 58.931 39.130 0.00 0.00 0.00 0.98
846 965 5.183140 ACAGCTTGCAAAACGGTCTTATATT 59.817 36.000 0.00 0.00 0.00 1.28
848 967 6.687105 CAGCTTGCAAAACGGTCTTATATTAC 59.313 38.462 0.00 0.00 0.00 1.89
850 969 5.721876 TGCAAAACGGTCTTATATTACGG 57.278 39.130 0.00 0.00 0.00 4.02
851 970 4.571580 TGCAAAACGGTCTTATATTACGGG 59.428 41.667 0.00 0.00 0.00 5.28
852 971 4.810491 GCAAAACGGTCTTATATTACGGGA 59.190 41.667 0.00 0.00 0.00 5.14
877 1108 5.667466 GGAGGAAGTATTTGTGAACGGATA 58.333 41.667 0.00 0.00 0.00 2.59
880 1111 6.942976 AGGAAGTATTTGTGAACGGATAGAA 58.057 36.000 0.00 0.00 0.00 2.10
943 1193 1.162181 TCGCTGTATACGGACCCTCG 61.162 60.000 16.15 8.86 0.00 4.63
951 1201 3.744719 CGGACCCTCGTTCTCGCA 61.745 66.667 0.00 0.00 36.96 5.10
958 1208 1.475441 CCTCGTTCTCGCATTCTCGC 61.475 60.000 0.00 0.00 36.96 5.03
1061 1311 1.183030 TACCGACACACCAGACCCTG 61.183 60.000 0.00 0.00 0.00 4.45
1131 1381 1.826054 CCTCGATCTCCTGGACGCT 60.826 63.158 0.00 0.00 0.00 5.07
1183 1437 1.820519 ACTCGTTCATAACCGCCTGTA 59.179 47.619 0.00 0.00 0.00 2.74
1331 1588 3.110178 GCGGAAGGTGTTCGACGG 61.110 66.667 0.00 0.00 32.92 4.79
1530 1791 0.473326 GGAGGCAGATCCATGCTCTT 59.527 55.000 6.87 0.00 45.75 2.85
1545 1806 1.262683 GCTCTTGCTGTGAAGTGTGAC 59.737 52.381 0.00 0.00 36.03 3.67
1578 1839 2.202878 TATGTTGGGAGCGCGCTC 60.203 61.111 44.84 44.84 42.04 5.03
1659 1920 2.637872 TGACTCGAAGAATGGGGTTTCT 59.362 45.455 0.00 0.00 37.56 2.52
1725 1986 0.725686 CTGCTCTGATGACCTTTGCG 59.274 55.000 0.00 0.00 0.00 4.85
1920 2186 0.745486 CAGGGAGCATGATTGACGCA 60.745 55.000 0.00 0.00 0.00 5.24
1939 2205 4.834394 CGCAAGAAAGGTGTTTGACCGTA 61.834 47.826 0.00 0.00 46.64 4.02
1955 2221 4.039973 TGACCGTATGGACAATAAGGATCC 59.960 45.833 8.33 2.48 41.53 3.36
1962 2228 6.575244 ATGGACAATAAGGATCCAGTTACA 57.425 37.500 15.82 7.96 45.53 2.41
2194 2460 6.874664 TCATTATGTTACGGTTGTTGCTCTTA 59.125 34.615 0.00 0.00 0.00 2.10
2196 2462 5.545658 ATGTTACGGTTGTTGCTCTTATG 57.454 39.130 0.00 0.00 0.00 1.90
2211 2477 0.393808 TTATGGGCCGAGCTGGTTTC 60.394 55.000 0.00 0.00 41.21 2.78
2637 2903 1.656095 GTGCTTCTGCGTGTAGATGAC 59.344 52.381 5.29 0.00 43.34 3.06
2727 2993 2.125952 GCAGGGGCAACAATTCGC 60.126 61.111 0.00 0.00 40.72 4.70
2769 3035 2.233566 TGGGGATTGCCACTCTGCT 61.234 57.895 0.00 0.00 38.87 4.24
2914 3180 3.303132 GCGTTTATGAATCTACAAGGCCG 60.303 47.826 0.00 0.00 0.00 6.13
3012 3472 0.380378 GTTGACAGAGCAAACCGCAA 59.620 50.000 0.00 0.00 46.13 4.85
3015 3475 1.785041 GACAGAGCAAACCGCAAGCA 61.785 55.000 0.00 0.00 46.13 3.91
3016 3476 1.174712 ACAGAGCAAACCGCAAGCAT 61.175 50.000 0.00 0.00 46.13 3.79
3017 3477 0.731514 CAGAGCAAACCGCAAGCATG 60.732 55.000 0.00 0.00 46.13 4.06
3091 3573 8.049117 AGAAGACATGTGCTTTCATCCTTATAA 58.951 33.333 1.15 0.00 0.00 0.98
3153 3635 1.065199 TGTCTGCATGATTCCTGGGAC 60.065 52.381 0.00 0.00 0.00 4.46
3305 3802 2.124277 GGAACCTAATTTCCGCACCT 57.876 50.000 0.00 0.00 35.92 4.00
3343 3840 9.834628 GAGAGAGAACAATTTAGATATCCGTAG 57.165 37.037 0.00 0.00 0.00 3.51
3361 3858 4.171754 CGTAGTTCTACAAGTGTAAGGCC 58.828 47.826 0.00 0.00 0.00 5.19
3409 3906 3.135712 TGTGCATTTCAGGGTATATCGGT 59.864 43.478 0.00 0.00 0.00 4.69
3416 3913 2.367567 TCAGGGTATATCGGTTTCAGCC 59.632 50.000 0.00 0.00 0.00 4.85
3455 3952 4.433283 GCAATGCACGTTGATTTTGCTAAG 60.433 41.667 9.53 0.00 37.18 2.18
3494 3991 4.183865 TGATGATGGCTCTTTTGTAGTCG 58.816 43.478 0.00 0.00 0.00 4.18
3528 4025 1.254975 TTTCGGTCCATGCTCCTCGA 61.255 55.000 0.00 0.00 0.00 4.04
3529 4026 1.945354 TTCGGTCCATGCTCCTCGAC 61.945 60.000 0.00 0.00 0.00 4.20
3530 4027 2.710902 CGGTCCATGCTCCTCGACA 61.711 63.158 0.00 0.00 0.00 4.35
3532 4029 0.460987 GGTCCATGCTCCTCGACAAG 60.461 60.000 0.00 0.00 0.00 3.16
3569 5178 1.024046 CATGTCGCCAACGGATCCAA 61.024 55.000 13.41 0.00 40.63 3.53
3574 5183 1.861542 CGCCAACGGATCCAAGCAAA 61.862 55.000 13.41 0.00 34.97 3.68
3579 5188 1.600023 ACGGATCCAAGCAAAAACGA 58.400 45.000 13.41 0.00 0.00 3.85
3580 5189 1.950909 ACGGATCCAAGCAAAAACGAA 59.049 42.857 13.41 0.00 0.00 3.85
3581 5190 2.287368 ACGGATCCAAGCAAAAACGAAC 60.287 45.455 13.41 0.00 0.00 3.95
3582 5191 2.315901 GGATCCAAGCAAAAACGAACG 58.684 47.619 6.95 0.00 0.00 3.95
3604 5213 1.136690 TGTTAAACGAGCACTGCGAG 58.863 50.000 0.00 0.00 0.00 5.03
3609 5218 0.666577 AACGAGCACTGCGAGTTACC 60.667 55.000 13.19 0.00 33.27 2.85
3625 5234 3.623060 AGTTACCAGCATGCATTCGTTAG 59.377 43.478 21.98 1.25 31.97 2.34
3626 5235 2.401583 ACCAGCATGCATTCGTTAGA 57.598 45.000 21.98 0.00 31.97 2.10
3627 5236 2.283298 ACCAGCATGCATTCGTTAGAG 58.717 47.619 21.98 0.00 31.97 2.43
3628 5237 2.283298 CCAGCATGCATTCGTTAGAGT 58.717 47.619 21.98 0.00 31.97 3.24
3631 5240 4.337763 CAGCATGCATTCGTTAGAGTTTC 58.662 43.478 21.98 0.00 0.00 2.78
3637 5249 7.148755 GCATGCATTCGTTAGAGTTTCAAAAAT 60.149 33.333 14.21 0.00 0.00 1.82
3640 5252 9.737427 TGCATTCGTTAGAGTTTCAAAAATAAA 57.263 25.926 0.00 0.00 0.00 1.40
3809 5425 2.296945 TAATGCATGCTCCCCCACCC 62.297 60.000 20.33 0.00 0.00 4.61
3811 5427 4.512914 GCATGCTCCCCCACCCTC 62.513 72.222 11.37 0.00 0.00 4.30
3812 5428 2.693864 CATGCTCCCCCACCCTCT 60.694 66.667 0.00 0.00 0.00 3.69
3813 5429 2.367512 ATGCTCCCCCACCCTCTC 60.368 66.667 0.00 0.00 0.00 3.20
3814 5430 4.741239 TGCTCCCCCACCCTCTCC 62.741 72.222 0.00 0.00 0.00 3.71
3815 5431 4.741239 GCTCCCCCACCCTCTCCA 62.741 72.222 0.00 0.00 0.00 3.86
3816 5432 2.689034 CTCCCCCACCCTCTCCAC 60.689 72.222 0.00 0.00 0.00 4.02
3817 5433 4.348495 TCCCCCACCCTCTCCACC 62.348 72.222 0.00 0.00 0.00 4.61
3819 5435 4.715130 CCCCACCCTCTCCACCGA 62.715 72.222 0.00 0.00 0.00 4.69
3839 5455 3.631227 CGATCTCCCCGTTATATACTCCC 59.369 52.174 0.00 0.00 0.00 4.30
3841 5457 3.771216 TCTCCCCGTTATATACTCCCAC 58.229 50.000 0.00 0.00 0.00 4.61
3843 5459 2.179645 TCCCCGTTATATACTCCCACCA 59.820 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.944061 ACAGTTCTCAAATTGATCATGAAACA 58.056 30.769 0.00 0.13 0.00 2.83
60 61 3.257873 TGCCCCAACTGTTATTGTTCATG 59.742 43.478 0.00 0.00 0.00 3.07
72 76 1.533625 TCGAGAAATTGCCCCAACTG 58.466 50.000 0.00 0.00 0.00 3.16
73 77 1.886542 GTTCGAGAAATTGCCCCAACT 59.113 47.619 0.00 0.00 0.00 3.16
120 124 3.186047 CCATCGCCAACCGTCGTC 61.186 66.667 0.00 0.00 38.35 4.20
124 128 2.359478 GGTTCCATCGCCAACCGT 60.359 61.111 0.00 0.00 38.35 4.83
125 129 2.046314 AGGTTCCATCGCCAACCG 60.046 61.111 0.00 0.00 45.92 4.44
129 133 0.681887 TAGTCGAGGTTCCATCGCCA 60.682 55.000 0.00 0.00 39.98 5.69
139 143 1.380112 GTCCAGCCCTAGTCGAGGT 60.380 63.158 0.00 0.00 45.03 3.85
140 144 2.482333 CGTCCAGCCCTAGTCGAGG 61.482 68.421 0.00 0.00 46.25 4.63
141 145 1.451567 TCGTCCAGCCCTAGTCGAG 60.452 63.158 0.00 0.00 0.00 4.04
143 147 2.799371 GTCGTCCAGCCCTAGTCG 59.201 66.667 0.00 0.00 0.00 4.18
153 157 3.515286 GAGATCCGGCGTCGTCCA 61.515 66.667 9.28 0.00 33.95 4.02
163 167 4.637489 CTCCAGGCGCGAGATCCG 62.637 72.222 12.10 0.00 42.21 4.18
174 178 2.202987 GCATGAGTCGCCTCCAGG 60.203 66.667 0.00 0.00 36.86 4.45
175 179 2.584418 CGCATGAGTCGCCTCCAG 60.584 66.667 0.00 0.00 36.86 3.86
186 190 1.695114 CCTACATCCCCACCGCATGA 61.695 60.000 0.00 0.00 0.00 3.07
189 193 3.087253 CCCTACATCCCCACCGCA 61.087 66.667 0.00 0.00 0.00 5.69
193 197 2.766651 TCGGCCCTACATCCCCAC 60.767 66.667 0.00 0.00 0.00 4.61
194 198 2.766651 GTCGGCCCTACATCCCCA 60.767 66.667 0.00 0.00 0.00 4.96
198 202 0.535102 CCCATTGTCGGCCCTACATC 60.535 60.000 6.42 0.00 0.00 3.06
222 226 1.093496 CGGAATCGGCCAAGTAACCC 61.093 60.000 2.24 0.00 0.00 4.11
245 255 4.874977 GCCCTAGCTGGTCGACGC 62.875 72.222 9.92 8.46 35.50 5.19
255 265 1.020437 GCACATTTCTGAGCCCTAGC 58.980 55.000 0.00 0.00 33.40 3.42
264 274 1.009829 GCGTAGGAGGCACATTTCTG 58.990 55.000 0.00 0.00 0.00 3.02
265 275 0.107654 GGCGTAGGAGGCACATTTCT 60.108 55.000 0.00 0.00 36.61 2.52
266 276 0.392461 TGGCGTAGGAGGCACATTTC 60.392 55.000 0.00 0.00 41.94 2.17
273 283 1.300233 CGAAGATGGCGTAGGAGGC 60.300 63.158 0.00 0.00 37.19 4.70
279 289 0.174845 CCAACCTCGAAGATGGCGTA 59.825 55.000 0.00 0.00 33.89 4.42
281 291 3.799753 CCAACCTCGAAGATGGCG 58.200 61.111 0.00 0.00 33.89 5.69
290 300 0.810031 AATCGAATCGGCCAACCTCG 60.810 55.000 2.24 5.30 33.60 4.63
330 341 0.467384 CAGAGCTCCGTCCCATCATT 59.533 55.000 10.93 0.00 0.00 2.57
332 343 2.725312 GCAGAGCTCCGTCCCATCA 61.725 63.158 10.93 0.00 0.00 3.07
336 347 3.532155 ATCGCAGAGCTCCGTCCC 61.532 66.667 10.93 0.00 43.63 4.46
347 358 1.522355 CCTGTGGCTACCATCGCAG 60.522 63.158 0.00 0.00 40.16 5.18
348 359 2.584064 CCTGTGGCTACCATCGCA 59.416 61.111 0.00 0.00 35.28 5.10
364 375 1.463674 ATCATCGTTTTCACTGCCCC 58.536 50.000 0.00 0.00 0.00 5.80
368 379 3.431912 TGTCGGAATCATCGTTTTCACTG 59.568 43.478 0.00 0.00 0.00 3.66
383 394 2.338620 CACTCGCCAGTGTCGGAA 59.661 61.111 2.94 0.00 44.63 4.30
390 401 1.533469 GGTCTACCACACTCGCCAGT 61.533 60.000 0.00 0.00 35.64 4.00
392 403 1.532078 TGGTCTACCACACTCGCCA 60.532 57.895 0.00 0.00 42.01 5.69
401 412 4.610605 TCTCGACAAATTTGGTCTACCA 57.389 40.909 21.74 0.00 45.94 3.25
404 415 5.995282 ACAACATCTCGACAAATTTGGTCTA 59.005 36.000 21.74 8.47 33.11 2.59
418 429 2.346847 GCTCTAGCAACACAACATCTCG 59.653 50.000 0.00 0.00 41.59 4.04
447 458 0.684479 TCCTGACATCTCACCCCTCG 60.684 60.000 0.00 0.00 0.00 4.63
462 473 7.510549 TTAGAAGGTCAACTTTTCAATCCTG 57.489 36.000 0.00 0.00 40.21 3.86
463 474 8.533569 TTTTAGAAGGTCAACTTTTCAATCCT 57.466 30.769 0.00 0.00 40.21 3.24
490 501 5.324832 AGTCCATCCCCGATTCATTTAAT 57.675 39.130 0.00 0.00 0.00 1.40
491 502 4.788925 AGTCCATCCCCGATTCATTTAA 57.211 40.909 0.00 0.00 0.00 1.52
492 503 5.152193 TCTAGTCCATCCCCGATTCATTTA 58.848 41.667 0.00 0.00 0.00 1.40
493 504 3.973973 TCTAGTCCATCCCCGATTCATTT 59.026 43.478 0.00 0.00 0.00 2.32
494 505 3.587498 TCTAGTCCATCCCCGATTCATT 58.413 45.455 0.00 0.00 0.00 2.57
496 507 2.767644 TCTAGTCCATCCCCGATTCA 57.232 50.000 0.00 0.00 0.00 2.57
497 508 2.300437 CCTTCTAGTCCATCCCCGATTC 59.700 54.545 0.00 0.00 0.00 2.52
498 509 2.330216 CCTTCTAGTCCATCCCCGATT 58.670 52.381 0.00 0.00 0.00 3.34
499 510 1.220750 ACCTTCTAGTCCATCCCCGAT 59.779 52.381 0.00 0.00 0.00 4.18
500 511 0.635009 ACCTTCTAGTCCATCCCCGA 59.365 55.000 0.00 0.00 0.00 5.14
501 512 0.753262 CACCTTCTAGTCCATCCCCG 59.247 60.000 0.00 0.00 0.00 5.73
502 513 0.470341 GCACCTTCTAGTCCATCCCC 59.530 60.000 0.00 0.00 0.00 4.81
503 514 1.501582 AGCACCTTCTAGTCCATCCC 58.498 55.000 0.00 0.00 0.00 3.85
504 515 4.755266 TTAAGCACCTTCTAGTCCATCC 57.245 45.455 0.00 0.00 0.00 3.51
505 516 6.168270 AGATTAAGCACCTTCTAGTCCATC 57.832 41.667 0.00 0.00 0.00 3.51
506 517 6.567602 AAGATTAAGCACCTTCTAGTCCAT 57.432 37.500 0.00 0.00 0.00 3.41
554 570 4.785914 TCTAACCCATCCCACATAAGTCAA 59.214 41.667 0.00 0.00 0.00 3.18
558 574 4.040952 CCTCTCTAACCCATCCCACATAAG 59.959 50.000 0.00 0.00 0.00 1.73
567 583 1.141858 CAAGGGCCTCTCTAACCCATC 59.858 57.143 6.46 0.00 46.88 3.51
573 589 2.023888 AGAGTAGCAAGGGCCTCTCTAA 60.024 50.000 17.54 0.00 43.67 2.10
601 619 8.142994 TGGCTAATTTGATCGATTAGAAAGTC 57.857 34.615 22.86 10.99 38.69 3.01
603 621 9.604626 GAATGGCTAATTTGATCGATTAGAAAG 57.395 33.333 22.86 8.08 38.69 2.62
620 639 9.234827 GGTAGTACCTTTTAAAAGAATGGCTAA 57.765 33.333 26.11 4.35 38.28 3.09
678 697 8.934697 ACTCCATAGGTAGTTCATAGCATTAAA 58.065 33.333 0.00 0.00 34.15 1.52
684 703 6.406692 TTCACTCCATAGGTAGTTCATAGC 57.593 41.667 0.00 0.00 0.00 2.97
685 704 7.875041 CCATTTCACTCCATAGGTAGTTCATAG 59.125 40.741 0.00 0.00 0.00 2.23
689 745 4.816925 GCCATTTCACTCCATAGGTAGTTC 59.183 45.833 0.00 0.00 0.00 3.01
696 752 4.264253 TGTTCAGCCATTTCACTCCATAG 58.736 43.478 0.00 0.00 0.00 2.23
697 753 4.299586 TGTTCAGCCATTTCACTCCATA 57.700 40.909 0.00 0.00 0.00 2.74
698 754 3.159213 TGTTCAGCCATTTCACTCCAT 57.841 42.857 0.00 0.00 0.00 3.41
699 755 2.655090 TGTTCAGCCATTTCACTCCA 57.345 45.000 0.00 0.00 0.00 3.86
701 757 4.036734 TCTGTTTGTTCAGCCATTTCACTC 59.963 41.667 0.00 0.00 35.63 3.51
703 759 4.044426 GTCTGTTTGTTCAGCCATTTCAC 58.956 43.478 0.00 0.00 35.63 3.18
705 761 4.574599 AGTCTGTTTGTTCAGCCATTTC 57.425 40.909 0.00 0.00 35.63 2.17
711 767 6.729187 AGATGTTTTAGTCTGTTTGTTCAGC 58.271 36.000 0.00 0.00 35.63 4.26
712 768 8.147642 AGAGATGTTTTAGTCTGTTTGTTCAG 57.852 34.615 0.00 0.00 36.85 3.02
762 818 6.896883 AGGGAGTACTAAAAAGTGTTCAACT 58.103 36.000 0.00 0.00 42.60 3.16
763 819 7.563888 AAGGGAGTACTAAAAAGTGTTCAAC 57.436 36.000 0.00 0.00 0.00 3.18
764 820 9.856162 ATAAAGGGAGTACTAAAAAGTGTTCAA 57.144 29.630 0.00 0.00 0.00 2.69
765 821 9.498176 GATAAAGGGAGTACTAAAAAGTGTTCA 57.502 33.333 0.00 0.00 0.00 3.18
766 822 9.722184 AGATAAAGGGAGTACTAAAAAGTGTTC 57.278 33.333 0.00 0.00 0.00 3.18
802 921 6.312672 AGCTGTTTTAGTTTGCAAAACGATTT 59.687 30.769 14.67 0.00 44.91 2.17
803 922 5.810074 AGCTGTTTTAGTTTGCAAAACGATT 59.190 32.000 14.67 0.35 44.91 3.34
805 924 4.739195 AGCTGTTTTAGTTTGCAAAACGA 58.261 34.783 14.67 2.13 44.91 3.85
813 932 5.247340 CGTTTTGCAAGCTGTTTTAGTTTG 58.753 37.500 0.00 0.00 46.68 2.93
815 934 3.862845 CCGTTTTGCAAGCTGTTTTAGTT 59.137 39.130 0.00 0.00 0.00 2.24
824 943 5.897377 AATATAAGACCGTTTTGCAAGCT 57.103 34.783 0.00 0.00 0.00 3.74
825 944 5.675444 CGTAATATAAGACCGTTTTGCAAGC 59.325 40.000 0.00 0.00 0.00 4.01
826 945 6.189567 CCGTAATATAAGACCGTTTTGCAAG 58.810 40.000 0.00 0.00 0.00 4.01
827 946 5.064962 CCCGTAATATAAGACCGTTTTGCAA 59.935 40.000 0.00 0.00 0.00 4.08
829 948 4.810491 TCCCGTAATATAAGACCGTTTTGC 59.190 41.667 0.00 0.00 0.00 3.68
830 949 5.051508 CGTCCCGTAATATAAGACCGTTTTG 60.052 44.000 0.00 0.00 0.00 2.44
831 950 5.043248 CGTCCCGTAATATAAGACCGTTTT 58.957 41.667 0.00 0.00 0.00 2.43
833 952 3.004734 CCGTCCCGTAATATAAGACCGTT 59.995 47.826 0.00 0.00 0.00 4.44
834 953 2.554032 CCGTCCCGTAATATAAGACCGT 59.446 50.000 0.00 0.00 0.00 4.83
835 954 2.813754 TCCGTCCCGTAATATAAGACCG 59.186 50.000 0.00 0.00 0.00 4.79
836 955 3.192212 CCTCCGTCCCGTAATATAAGACC 59.808 52.174 0.00 0.00 0.00 3.85
837 956 4.074970 TCCTCCGTCCCGTAATATAAGAC 58.925 47.826 0.00 0.00 0.00 3.01
838 957 4.371624 TCCTCCGTCCCGTAATATAAGA 57.628 45.455 0.00 0.00 0.00 2.10
839 958 4.522022 ACTTCCTCCGTCCCGTAATATAAG 59.478 45.833 0.00 0.00 0.00 1.73
840 959 4.473444 ACTTCCTCCGTCCCGTAATATAA 58.527 43.478 0.00 0.00 0.00 0.98
841 960 4.104383 ACTTCCTCCGTCCCGTAATATA 57.896 45.455 0.00 0.00 0.00 0.86
842 961 2.954792 ACTTCCTCCGTCCCGTAATAT 58.045 47.619 0.00 0.00 0.00 1.28
844 963 2.442236 TACTTCCTCCGTCCCGTAAT 57.558 50.000 0.00 0.00 0.00 1.89
846 965 2.428171 CAAATACTTCCTCCGTCCCGTA 59.572 50.000 0.00 0.00 0.00 4.02
848 967 1.206371 ACAAATACTTCCTCCGTCCCG 59.794 52.381 0.00 0.00 0.00 5.14
850 969 3.604875 TCACAAATACTTCCTCCGTCC 57.395 47.619 0.00 0.00 0.00 4.79
851 970 3.367025 CGTTCACAAATACTTCCTCCGTC 59.633 47.826 0.00 0.00 0.00 4.79
852 971 3.323243 CGTTCACAAATACTTCCTCCGT 58.677 45.455 0.00 0.00 0.00 4.69
918 1152 3.514645 GGTCCGTATACAGCGAGAAAAA 58.485 45.455 3.32 0.00 0.00 1.94
931 1165 1.722636 GCGAGAACGAGGGTCCGTAT 61.723 60.000 0.00 0.00 42.54 3.06
932 1166 2.401766 GCGAGAACGAGGGTCCGTA 61.402 63.158 0.00 0.00 42.54 4.02
951 1201 0.798771 GACGTTCTGCTCGCGAGAAT 60.799 55.000 38.74 14.23 41.32 2.40
958 1208 2.081212 GTGTCCGACGTTCTGCTCG 61.081 63.158 0.00 0.00 0.00 5.03
985 1235 0.745845 CTCATGGAGGTGGCGAAAGG 60.746 60.000 0.00 0.00 0.00 3.11
987 1237 0.690192 TTCTCATGGAGGTGGCGAAA 59.310 50.000 0.00 0.00 0.00 3.46
1183 1437 0.320374 TCGAGGTTCTTGGATTGCGT 59.680 50.000 0.00 0.00 0.00 5.24
1331 1588 1.672881 CCATGTCTTTCCTCCGCATTC 59.327 52.381 0.00 0.00 0.00 2.67
1445 1702 4.974989 ACGTGAACCCGTTCGGCC 62.975 66.667 5.66 0.00 42.28 6.13
1530 1791 0.815213 GCCAGTCACACTTCACAGCA 60.815 55.000 0.00 0.00 0.00 4.41
1545 1806 1.410517 ACATAGACGTCCTCATGCCAG 59.589 52.381 13.01 0.00 0.00 4.85
1578 1839 2.302952 CCGCGCATACATGTCGAGG 61.303 63.158 8.75 12.47 39.28 4.63
1659 1920 1.368641 CGGAGATCAATGCGTTCCAA 58.631 50.000 0.00 0.00 0.00 3.53
1725 1986 2.725221 ACCCATTTCTCAGCATCTCC 57.275 50.000 0.00 0.00 0.00 3.71
1920 2186 3.818773 CCATACGGTCAAACACCTTTCTT 59.181 43.478 0.00 0.00 44.21 2.52
1939 2205 6.575244 TGTAACTGGATCCTTATTGTCCAT 57.425 37.500 14.23 0.00 40.96 3.41
1944 2210 6.828273 TGTTCCATGTAACTGGATCCTTATTG 59.172 38.462 14.23 6.52 44.66 1.90
1955 2221 4.216042 TGAGCATTGTGTTCCATGTAACTG 59.784 41.667 2.65 0.00 0.00 3.16
1962 2228 1.542915 GCTGTGAGCATTGTGTTCCAT 59.457 47.619 0.00 0.00 41.89 3.41
2194 2460 2.044946 GAAACCAGCTCGGCCCAT 60.045 61.111 0.00 0.00 39.03 4.00
2196 2462 2.193087 TTAGGAAACCAGCTCGGCCC 62.193 60.000 0.00 2.63 39.03 5.80
2637 2903 0.322906 GGTTTGCCTCCCTCTCTTGG 60.323 60.000 0.00 0.00 0.00 3.61
2694 2960 0.029035 CTGCAGGCATTTCGATCAGC 59.971 55.000 5.57 0.00 0.00 4.26
2769 3035 9.323985 CCAAAAACTTTGGAGATGTATTTGAAA 57.676 29.630 11.96 0.00 42.06 2.69
2914 3180 2.488153 GGCTGTTACTGAATCAACCCAC 59.512 50.000 0.00 0.00 0.00 4.61
3015 3475 2.955022 GATCTTCAGGGCCGCAGCAT 62.955 60.000 0.00 0.00 42.56 3.79
3016 3476 3.687321 GATCTTCAGGGCCGCAGCA 62.687 63.158 0.00 0.00 42.56 4.41
3017 3477 2.899339 GATCTTCAGGGCCGCAGC 60.899 66.667 0.00 0.00 38.76 5.25
3018 3478 0.465097 AATGATCTTCAGGGCCGCAG 60.465 55.000 0.00 0.00 0.00 5.18
3091 3573 4.153958 TGCGAAATTTTAGTGATTGCGT 57.846 36.364 0.00 0.00 37.74 5.24
3180 3677 2.028930 AGTGTGTTTCCAGTCGGAGATC 60.029 50.000 0.00 0.00 44.10 2.75
3300 3797 5.028549 TCTCTCTGGAATTTATCAGGTGC 57.971 43.478 0.00 0.00 0.00 5.01
3305 3802 9.745018 AAATTGTTCTCTCTCTGGAATTTATCA 57.255 29.630 0.00 0.00 0.00 2.15
3343 3840 2.344025 CCGGCCTTACACTTGTAGAAC 58.656 52.381 0.00 0.00 0.00 3.01
3361 3858 3.314913 TGCATATGTAGCAAAATCACCCG 59.685 43.478 4.29 0.00 39.39 5.28
3442 3939 3.261390 AGGGCAATGCTTAGCAAAATCAA 59.739 39.130 12.08 0.00 43.62 2.57
3455 3952 1.751927 CAGTCCCAGAGGGCAATGC 60.752 63.158 0.00 0.00 43.94 3.56
3494 3991 0.179272 CGAAAGAACGACGAGCAAGC 60.179 55.000 0.00 0.00 35.09 4.01
3528 4025 1.231928 GGGGTGTTGGGTTCCTTGT 59.768 57.895 0.00 0.00 0.00 3.16
3529 4026 1.901464 CGGGGTGTTGGGTTCCTTG 60.901 63.158 0.00 0.00 0.00 3.61
3530 4027 2.518933 CGGGGTGTTGGGTTCCTT 59.481 61.111 0.00 0.00 0.00 3.36
3553 5162 2.750888 GCTTGGATCCGTTGGCGAC 61.751 63.158 7.39 0.00 41.33 5.19
3561 5170 2.315901 GTTCGTTTTTGCTTGGATCCG 58.684 47.619 7.39 0.00 0.00 4.18
3569 5178 5.834951 GTTTAACAAACGTTCGTTTTTGCT 58.165 33.333 18.46 5.92 36.35 3.91
3582 5191 2.034076 CGCAGTGCTCGTTTAACAAAC 58.966 47.619 14.33 0.00 38.02 2.93
3604 5213 2.919666 AACGAATGCATGCTGGTAAC 57.080 45.000 20.33 3.80 0.00 2.50
3609 5218 4.142838 TGAAACTCTAACGAATGCATGCTG 60.143 41.667 20.33 8.65 0.00 4.41
3625 5234 8.507470 ACGAATGCTCTTTATTTTTGAAACTC 57.493 30.769 0.00 0.00 0.00 3.01
3626 5235 8.871686 AACGAATGCTCTTTATTTTTGAAACT 57.128 26.923 0.00 0.00 0.00 2.66
3631 5240 9.612620 AACTCTAACGAATGCTCTTTATTTTTG 57.387 29.630 0.00 0.00 0.00 2.44
3637 5249 7.956420 TTGAAACTCTAACGAATGCTCTTTA 57.044 32.000 0.00 0.00 0.00 1.85
3640 5252 6.861065 TTTTGAAACTCTAACGAATGCTCT 57.139 33.333 0.00 0.00 0.00 4.09
3754 5370 2.880879 CGATGGAGACGTGCACGG 60.881 66.667 39.21 23.04 44.95 4.94
3809 5425 2.196925 CGGGGAGATCGGTGGAGAG 61.197 68.421 0.00 0.00 0.00 3.20
3810 5426 2.123854 CGGGGAGATCGGTGGAGA 60.124 66.667 0.00 0.00 0.00 3.71
3811 5427 0.754217 TAACGGGGAGATCGGTGGAG 60.754 60.000 0.00 0.00 0.00 3.86
3812 5428 0.105862 ATAACGGGGAGATCGGTGGA 60.106 55.000 0.00 0.00 0.00 4.02
3813 5429 1.624336 TATAACGGGGAGATCGGTGG 58.376 55.000 0.00 0.00 0.00 4.61
3814 5430 4.015084 AGTATATAACGGGGAGATCGGTG 58.985 47.826 0.00 0.00 0.00 4.94
3815 5431 4.268359 GAGTATATAACGGGGAGATCGGT 58.732 47.826 0.00 0.00 0.00 4.69
3816 5432 3.631227 GGAGTATATAACGGGGAGATCGG 59.369 52.174 0.00 0.00 0.00 4.18
3817 5433 3.631227 GGGAGTATATAACGGGGAGATCG 59.369 52.174 0.00 0.00 0.00 3.69
3818 5434 4.401837 GTGGGAGTATATAACGGGGAGATC 59.598 50.000 0.00 0.00 0.00 2.75
3819 5435 4.351127 GTGGGAGTATATAACGGGGAGAT 58.649 47.826 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.