Multiple sequence alignment - TraesCS4B01G345000

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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 TraesCS4B01G345000 chr4B 100.000 2393 0 0 1 2393 638308906 638306514 0.000000e+00 4420.0
1 TraesCS4B01G345000 chr4B 95.438 548 22 2 233 779 511263778 511263233 0.000000e+00 870.0
2 TraesCS4B01G345000 chr4B 95.429 350 16 0 430 779 511262608 511262259 2.080000e-155 558.0
3 TraesCS4B01G345000 chr4D 91.748 921 39 8 805 1696 497353785 497352873 0.000000e+00 1245.0
4 TraesCS4B01G345000 chr4D 96.898 548 13 3 233 779 506272254 506271710 0.000000e+00 915.0
5 TraesCS4B01G345000 chr4D 91.582 392 20 5 1751 2140 497352879 497352499 1.630000e-146 529.0
6 TraesCS4B01G345000 chr4D 80.692 549 62 21 1003 1516 497259968 497259429 1.040000e-103 387.0
7 TraesCS4B01G345000 chr4D 78.603 673 59 39 1000 1614 497273966 497273321 1.350000e-97 366.0
8 TraesCS4B01G345000 chr4D 87.766 188 16 3 1 181 497354009 497353822 1.860000e-51 213.0
9 TraesCS4B01G345000 chr4D 81.818 231 27 10 1526 1756 497259264 497259049 1.890000e-41 180.0
10 TraesCS4B01G345000 chr4D 90.678 118 9 2 2277 2393 497351334 497351218 3.180000e-34 156.0
11 TraesCS4B01G345000 chr6B 99.502 602 3 0 178 779 42435124 42434523 0.000000e+00 1096.0
12 TraesCS4B01G345000 chr6B 97.407 270 4 2 233 501 644460475 644460208 7.800000e-125 457.0
13 TraesCS4B01G345000 chr6B 96.491 57 2 0 176 232 273772348 273772292 7.040000e-16 95.3
14 TraesCS4B01G345000 chr6B 92.683 41 2 1 803 842 719771634 719771674 9.240000e-05 58.4
15 TraesCS4B01G345000 chr3B 98.342 603 9 1 177 779 659153146 659152545 0.000000e+00 1057.0
16 TraesCS4B01G345000 chr2A 96.892 547 14 2 233 779 61359919 61359376 0.000000e+00 913.0
17 TraesCS4B01G345000 chr2A 81.868 182 26 5 1003 1177 536313356 536313175 1.920000e-31 147.0
18 TraesCS4B01G345000 chr2A 92.857 56 4 0 178 233 61359996 61359941 5.480000e-12 82.4
19 TraesCS4B01G345000 chr5B 95.636 550 18 4 233 779 126236263 126235717 0.000000e+00 878.0
20 TraesCS4B01G345000 chr5B 84.946 93 14 0 1079 1171 542694761 542694669 7.040000e-16 95.3
21 TraesCS4B01G345000 chr5B 96.429 56 2 0 178 233 453671811 453671756 2.530000e-15 93.5
22 TraesCS4B01G345000 chr5B 84.615 91 14 0 1079 1169 542295573 542295483 9.110000e-15 91.6
23 TraesCS4B01G345000 chr7B 94.526 548 22 3 233 779 564652628 564653168 0.000000e+00 839.0
24 TraesCS4B01G345000 chr5A 80.325 493 65 20 238 706 470161915 470162399 6.330000e-91 344.0
25 TraesCS4B01G345000 chr5A 76.500 400 63 18 1002 1396 698528631 698529004 3.140000e-44 189.0
26 TraesCS4B01G345000 chr5A 85.714 91 13 0 1079 1169 562108418 562108328 1.960000e-16 97.1
27 TraesCS4B01G345000 chr5A 90.769 65 6 0 169 233 606195734 606195798 1.180000e-13 87.9
28 TraesCS4B01G345000 chr2B 81.868 182 26 5 1003 1177 472251145 472250964 1.920000e-31 147.0
29 TraesCS4B01G345000 chr2B 91.176 68 3 3 167 233 390949310 390949375 3.280000e-14 89.8
30 TraesCS4B01G345000 chr1A 96.429 56 2 0 178 233 39638057 39638112 2.530000e-15 93.5
31 TraesCS4B01G345000 chr1A 93.651 63 3 1 171 233 57736171 57736232 2.530000e-15 93.5
32 TraesCS4B01G345000 chr5D 84.615 91 14 0 1079 1169 445062753 445062663 9.110000e-15 91.6
33 TraesCS4B01G345000 chr5D 85.057 87 12 1 1083 1169 444976383 444976298 1.180000e-13 87.9


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 TraesCS4B01G345000 chr4B 638306514 638308906 2392 True 4420.00 4420 100.0000 1 2393 1 chr4B.!!$R1 2392
1 TraesCS4B01G345000 chr4B 511262259 511263778 1519 True 714.00 870 95.4335 233 779 2 chr4B.!!$R2 546
2 TraesCS4B01G345000 chr4D 506271710 506272254 544 True 915.00 915 96.8980 233 779 1 chr4D.!!$R2 546
3 TraesCS4B01G345000 chr4D 497351218 497354009 2791 True 535.75 1245 90.4435 1 2393 4 chr4D.!!$R4 2392
4 TraesCS4B01G345000 chr4D 497273321 497273966 645 True 366.00 366 78.6030 1000 1614 1 chr4D.!!$R1 614
5 TraesCS4B01G345000 chr4D 497259049 497259968 919 True 283.50 387 81.2550 1003 1756 2 chr4D.!!$R3 753
6 TraesCS4B01G345000 chr6B 42434523 42435124 601 True 1096.00 1096 99.5020 178 779 1 chr6B.!!$R1 601
7 TraesCS4B01G345000 chr3B 659152545 659153146 601 True 1057.00 1057 98.3420 177 779 1 chr3B.!!$R1 602
8 TraesCS4B01G345000 chr2A 61359376 61359996 620 True 497.70 913 94.8745 178 779 2 chr2A.!!$R2 601
9 TraesCS4B01G345000 chr5B 126235717 126236263 546 True 878.00 878 95.6360 233 779 1 chr5B.!!$R1 546
10 TraesCS4B01G345000 chr7B 564652628 564653168 540 False 839.00 839 94.5260 233 779 1 chr7B.!!$F1 546

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
119 120 0.107993 CCATCGTCCACTGCAGTCAT 60.108 55.0 18.64 1.1 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 3107 0.392461 GTCGGCCATGGTAAGCAAGA 60.392 55.0 14.67 0.0 0.0 3.02 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 2.164219 CCATGACGCTAGCAATTGGTTT 59.836 45.455 16.43 0.00 0.00 3.27
36 37 2.413796 TGACGCTAGCAATTGGTTTACG 59.586 45.455 16.43 17.91 0.00 3.18
41 42 1.803922 GCAATTGGTTTACGGCGCC 60.804 57.895 19.07 19.07 0.00 6.53
73 74 4.854784 TCGCTCGCGACTCCATGC 62.855 66.667 3.71 4.98 44.01 4.06
75 76 2.413351 GCTCGCGACTCCATGCTA 59.587 61.111 3.71 0.00 0.00 3.49
116 117 2.046892 GCCATCGTCCACTGCAGT 60.047 61.111 15.25 15.25 0.00 4.40
119 120 0.107993 CCATCGTCCACTGCAGTCAT 60.108 55.000 18.64 1.10 0.00 3.06
120 121 1.136891 CCATCGTCCACTGCAGTCATA 59.863 52.381 18.64 1.83 0.00 2.15
166 174 6.425721 TGTTTGTTATGTGTAGCTGGTAACTC 59.574 38.462 0.00 0.00 37.61 3.01
591 1596 6.519382 TCAGATGATCTTATGCGAAATCTGT 58.481 36.000 11.47 0.00 38.28 3.41
775 1783 3.934068 TCCGTCAGTCCTTATTTTGTCC 58.066 45.455 0.00 0.00 0.00 4.02
779 1787 4.627467 CGTCAGTCCTTATTTTGTCCTGAG 59.373 45.833 0.00 0.00 0.00 3.35
780 1788 4.938226 GTCAGTCCTTATTTTGTCCTGAGG 59.062 45.833 0.00 0.00 0.00 3.86
781 1789 4.019321 TCAGTCCTTATTTTGTCCTGAGGG 60.019 45.833 0.00 0.00 0.00 4.30
782 1790 3.267031 AGTCCTTATTTTGTCCTGAGGGG 59.733 47.826 0.00 0.00 0.00 4.79
783 1791 2.580783 TCCTTATTTTGTCCTGAGGGGG 59.419 50.000 0.00 0.00 35.33 5.40
826 1834 1.830368 GCCAATGCACGCAACCAAAC 61.830 55.000 0.00 0.00 37.47 2.93
828 1836 0.869454 CAATGCACGCAACCAAACGT 60.869 50.000 0.00 0.00 44.75 3.99
832 1840 1.010125 CACGCAACCAAACGTCAGG 60.010 57.895 4.80 4.80 41.32 3.86
854 1862 3.492313 CAAAATTGCTCTCCTAACGTGC 58.508 45.455 0.00 0.00 0.00 5.34
928 1952 4.457810 CCTGAAGCGCATCATATAAAACG 58.542 43.478 16.57 1.55 0.00 3.60
959 1983 0.609662 ATTGATTGCCTTGCCACACC 59.390 50.000 0.00 0.00 0.00 4.16
1264 2318 1.307647 CCATTGGGAACAGGAGGGG 59.692 63.158 0.00 0.00 44.54 4.79
1336 2390 2.885861 CCTCGTCCGGGACAAGAG 59.114 66.667 25.80 22.21 32.09 2.85
1350 2404 1.072965 ACAAGAGGAGGCAACCAAGAG 59.927 52.381 3.78 0.00 37.17 2.85
1351 2405 0.695347 AAGAGGAGGCAACCAAGAGG 59.305 55.000 3.78 0.00 42.21 3.69
1352 2406 0.178891 AGAGGAGGCAACCAAGAGGA 60.179 55.000 3.78 0.00 38.69 3.71
1357 2411 1.130054 AGGCAACCAAGAGGAGCTCA 61.130 55.000 17.19 0.00 38.75 4.26
1381 2435 0.616111 AGAGGCGATTGACCTGTCCT 60.616 55.000 1.11 0.00 37.77 3.85
1399 2453 4.586421 TGTCCTTGAAGCTATGATCGATCT 59.414 41.667 25.02 13.51 0.00 2.75
1410 2464 3.242549 TGATCGATCTATCCATGCAGC 57.757 47.619 25.02 0.00 0.00 5.25
1467 2541 4.174009 GTCTTGTGTTTCTGCTATCGCTA 58.826 43.478 0.00 0.00 36.97 4.26
1468 2542 4.031878 GTCTTGTGTTTCTGCTATCGCTAC 59.968 45.833 0.00 0.00 36.97 3.58
1469 2543 2.526077 TGTGTTTCTGCTATCGCTACG 58.474 47.619 0.00 0.00 36.97 3.51
1470 2544 1.255600 GTGTTTCTGCTATCGCTACGC 59.744 52.381 0.00 0.00 36.97 4.42
1475 2549 2.219458 TCTGCTATCGCTACGCTTACT 58.781 47.619 0.00 0.00 36.97 2.24
1522 2603 2.105766 GGCTCTTGATTTGGGCTTGAT 58.894 47.619 0.00 0.00 0.00 2.57
1523 2604 2.159142 GGCTCTTGATTTGGGCTTGATG 60.159 50.000 0.00 0.00 0.00 3.07
1581 2822 9.855021 GCATGGATTGTTACTTTGTTAGTTAAT 57.145 29.630 0.00 0.00 38.33 1.40
1601 2842 0.456221 AAGTCGCTACACTCATCGGG 59.544 55.000 0.00 0.00 0.00 5.14
1670 2911 5.515270 GCCTGTGAATAACTAAATTTTCGGC 59.485 40.000 0.00 0.00 0.00 5.54
1700 2941 4.081697 CGATAATTTCTTGGTTTTGGGGCT 60.082 41.667 0.00 0.00 0.00 5.19
1701 2942 5.568624 CGATAATTTCTTGGTTTTGGGGCTT 60.569 40.000 0.00 0.00 0.00 4.35
1702 2943 2.998316 TTTCTTGGTTTTGGGGCTTG 57.002 45.000 0.00 0.00 0.00 4.01
1704 2945 1.118838 TCTTGGTTTTGGGGCTTGTG 58.881 50.000 0.00 0.00 0.00 3.33
1705 2946 1.118838 CTTGGTTTTGGGGCTTGTGA 58.881 50.000 0.00 0.00 0.00 3.58
1706 2947 1.484240 CTTGGTTTTGGGGCTTGTGAA 59.516 47.619 0.00 0.00 0.00 3.18
1707 2948 1.799933 TGGTTTTGGGGCTTGTGAAT 58.200 45.000 0.00 0.00 0.00 2.57
1708 2949 2.964209 TGGTTTTGGGGCTTGTGAATA 58.036 42.857 0.00 0.00 0.00 1.75
1709 2950 3.309296 TGGTTTTGGGGCTTGTGAATAA 58.691 40.909 0.00 0.00 0.00 1.40
1714 2955 2.455557 TGGGGCTTGTGAATAACCATG 58.544 47.619 0.00 0.00 0.00 3.66
1719 2960 3.514645 GCTTGTGAATAACCATGCCTTG 58.485 45.455 0.00 0.00 0.00 3.61
1721 2962 4.737054 CTTGTGAATAACCATGCCTTGAC 58.263 43.478 0.00 0.00 0.00 3.18
1752 2993 6.309712 TCAAGCTTGAAGACAGATTTCTTG 57.690 37.500 26.61 0.00 35.90 3.02
1756 2997 5.591877 AGCTTGAAGACAGATTTCTTGTTGT 59.408 36.000 0.00 0.00 35.90 3.32
1757 2998 5.911838 GCTTGAAGACAGATTTCTTGTTGTC 59.088 40.000 0.00 0.00 40.08 3.18
1759 3000 6.851222 TGAAGACAGATTTCTTGTTGTCTC 57.149 37.500 6.47 2.51 46.91 3.36
1760 3001 5.463392 TGAAGACAGATTTCTTGTTGTCTCG 59.537 40.000 6.47 0.00 46.91 4.04
1761 3002 3.743396 AGACAGATTTCTTGTTGTCTCGC 59.257 43.478 0.45 0.00 45.11 5.03
1762 3003 2.808543 ACAGATTTCTTGTTGTCTCGCC 59.191 45.455 0.00 0.00 0.00 5.54
1890 3131 1.910580 CTTACCATGGCCGACCTGGT 61.911 60.000 13.04 19.22 44.64 4.00
1917 3158 1.089920 GTCAAGCTGATGCGGTGATT 58.910 50.000 0.00 0.00 45.42 2.57
1960 3202 5.653507 TGCATGTCTTCATAAGCCAAATTC 58.346 37.500 0.00 0.00 32.47 2.17
2026 3268 1.794222 GCGCCTGTAGCAAAATCGT 59.206 52.632 0.00 0.00 44.04 3.73
2028 3270 0.373716 CGCCTGTAGCAAAATCGTCC 59.626 55.000 0.00 0.00 44.04 4.79
2029 3271 0.373716 GCCTGTAGCAAAATCGTCCG 59.626 55.000 0.00 0.00 42.97 4.79
2030 3272 2.004583 CCTGTAGCAAAATCGTCCGA 57.995 50.000 0.00 0.00 0.00 4.55
2031 3273 1.927174 CCTGTAGCAAAATCGTCCGAG 59.073 52.381 0.00 0.00 0.00 4.63
2048 3290 3.797546 GCGAGCTGCTTGTCTGCC 61.798 66.667 17.76 0.00 41.73 4.85
2051 3293 4.631247 AGCTGCTTGTCTGCCGCA 62.631 61.111 0.00 0.00 43.87 5.69
2061 3303 4.834453 CTGCCGCAGCCTCAGGAG 62.834 72.222 7.61 0.00 38.69 3.69
2063 3305 4.828925 GCCGCAGCCTCAGGAGTC 62.829 72.222 0.00 0.00 0.00 3.36
2064 3306 3.385384 CCGCAGCCTCAGGAGTCA 61.385 66.667 0.00 0.00 0.00 3.41
2065 3307 2.183811 CGCAGCCTCAGGAGTCAG 59.816 66.667 0.00 0.00 0.00 3.51
2066 3308 2.583520 GCAGCCTCAGGAGTCAGG 59.416 66.667 0.00 0.00 0.00 3.86
2070 3312 2.716017 GCCTCAGGAGTCAGGACCG 61.716 68.421 0.00 0.00 30.32 4.79
2077 3319 2.283966 AGTCAGGACCGTCCAGGG 60.284 66.667 19.95 8.72 46.96 4.45
2095 3337 3.156714 TGGCAAGGATGTCACCGT 58.843 55.556 0.00 0.00 35.91 4.83
2099 3341 1.875963 CAAGGATGTCACCGTTGCC 59.124 57.895 0.00 0.00 34.73 4.52
2140 3382 1.583477 GTTTCAAGGAGCAGCTGCC 59.417 57.895 34.39 24.38 43.38 4.85
2141 3383 1.968017 TTTCAAGGAGCAGCTGCCG 60.968 57.895 34.39 17.79 43.38 5.69
2152 3394 4.479993 GCTGCCGCCTGAGGTGAT 62.480 66.667 14.80 0.00 34.74 3.06
2153 3395 2.202987 CTGCCGCCTGAGGTGATC 60.203 66.667 14.80 5.48 34.74 2.92
2154 3396 4.147449 TGCCGCCTGAGGTGATCG 62.147 66.667 14.80 0.86 34.74 3.69
2155 3397 4.148825 GCCGCCTGAGGTGATCGT 62.149 66.667 14.80 0.00 34.74 3.73
2156 3398 2.105128 CCGCCTGAGGTGATCGTC 59.895 66.667 14.80 0.00 34.74 4.20
2157 3399 2.278206 CGCCTGAGGTGATCGTCG 60.278 66.667 6.07 0.00 34.74 5.12
2158 3400 2.583593 GCCTGAGGTGATCGTCGC 60.584 66.667 0.00 0.00 0.00 5.19
2174 3416 3.105659 GCCATGCGCTTCCTCTTC 58.894 61.111 9.73 0.00 0.00 2.87
2175 3417 1.746615 GCCATGCGCTTCCTCTTCA 60.747 57.895 9.73 0.00 0.00 3.02
2176 3418 1.308069 GCCATGCGCTTCCTCTTCAA 61.308 55.000 9.73 0.00 0.00 2.69
2177 3419 0.731417 CCATGCGCTTCCTCTTCAAG 59.269 55.000 9.73 0.00 0.00 3.02
2178 3420 0.098376 CATGCGCTTCCTCTTCAAGC 59.902 55.000 9.73 0.00 42.51 4.01
2179 3421 0.321919 ATGCGCTTCCTCTTCAAGCA 60.322 50.000 9.73 0.00 45.66 3.91
2180 3422 0.952497 TGCGCTTCCTCTTCAAGCAG 60.952 55.000 9.73 0.00 45.66 4.24
2181 3423 1.642952 GCGCTTCCTCTTCAAGCAGG 61.643 60.000 0.00 0.00 45.66 4.85
2182 3424 0.036952 CGCTTCCTCTTCAAGCAGGA 60.037 55.000 5.35 2.40 45.66 3.86
2183 3425 1.406614 CGCTTCCTCTTCAAGCAGGAT 60.407 52.381 6.47 0.00 45.66 3.24
2184 3426 2.015587 GCTTCCTCTTCAAGCAGGATG 58.984 52.381 6.47 9.25 44.87 3.51
2185 3427 2.355513 GCTTCCTCTTCAAGCAGGATGA 60.356 50.000 16.49 0.75 44.87 2.92
2186 3428 3.269178 CTTCCTCTTCAAGCAGGATGAC 58.731 50.000 10.73 0.00 38.66 3.06
2187 3429 1.205655 TCCTCTTCAAGCAGGATGACG 59.794 52.381 2.40 0.00 39.69 4.35
2188 3430 1.205655 CCTCTTCAAGCAGGATGACGA 59.794 52.381 0.00 0.00 39.69 4.20
2189 3431 2.266554 CTCTTCAAGCAGGATGACGAC 58.733 52.381 0.00 0.00 39.69 4.34
2190 3432 1.066858 TCTTCAAGCAGGATGACGACC 60.067 52.381 0.00 0.00 39.69 4.79
2191 3433 0.389817 TTCAAGCAGGATGACGACCG 60.390 55.000 0.00 0.00 39.69 4.79
2217 3459 1.019278 GGCCGTCGAAAATGAGCTCA 61.019 55.000 20.79 20.79 0.00 4.26
2224 3466 1.594862 CGAAAATGAGCTCATCGACCC 59.405 52.381 28.83 14.96 35.10 4.46
2246 3488 1.541588 GGAGGTGAACATGCTTTGGAC 59.458 52.381 0.00 0.00 0.00 4.02
2257 3499 2.665165 TGCTTTGGACCATGAGTTTGT 58.335 42.857 0.00 0.00 0.00 2.83
2275 3517 2.429478 TGTGAATGATGGAGCTGTGTG 58.571 47.619 0.00 0.00 0.00 3.82
2313 4635 2.731571 GGCTGATGTGCTCCGGGTA 61.732 63.158 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.306847 TGCTAGCGTCATGGTCATAGA 58.693 47.619 10.77 0.00 0.00 1.98
7 8 3.751479 ATTGCTAGCGTCATGGTCATA 57.249 42.857 10.77 0.00 0.00 2.15
11 12 1.340017 ACCAATTGCTAGCGTCATGGT 60.340 47.619 21.61 21.61 34.98 3.55
13 14 3.492421 AAACCAATTGCTAGCGTCATG 57.508 42.857 10.77 6.45 0.00 3.07
19 20 1.531058 CGCCGTAAACCAATTGCTAGC 60.531 52.381 8.10 8.10 0.00 3.42
41 42 2.098298 CGAGCAATTCCGTTGGCG 59.902 61.111 0.00 0.00 38.29 5.69
141 142 6.292923 AGTTACCAGCTACACATAACAAACA 58.707 36.000 0.00 0.00 0.00 2.83
144 145 6.354794 AGAGTTACCAGCTACACATAACAA 57.645 37.500 0.00 0.00 0.00 2.83
146 147 8.943909 ATTAAGAGTTACCAGCTACACATAAC 57.056 34.615 0.00 0.00 0.00 1.89
166 174 1.611673 CCGGCCCTGGCTATGATTAAG 60.612 57.143 8.29 0.00 41.60 1.85
803 1811 3.682885 TTGCGTGCATTGGCTGGG 61.683 61.111 0.00 0.00 41.91 4.45
817 1825 0.179124 TTTGCCTGACGTTTGGTTGC 60.179 50.000 9.08 0.00 0.00 4.17
893 1917 0.250727 CTTCAGGGAGCCCGTTTTGA 60.251 55.000 0.00 0.00 41.95 2.69
901 1925 2.899339 GATGCGCTTCAGGGAGCC 60.899 66.667 17.62 0.00 39.51 4.70
902 1926 0.250038 TATGATGCGCTTCAGGGAGC 60.250 55.000 27.07 0.91 39.29 4.70
928 1952 1.064621 AATCAATCACGCATGCGGC 59.935 52.632 39.95 3.93 44.69 6.53
959 1983 3.562973 AGTGGATATGGAGTACGTACACG 59.437 47.826 26.55 0.00 46.33 4.49
1245 2299 1.380380 CCCTCCTGTTCCCAATGGC 60.380 63.158 0.00 0.00 0.00 4.40
1246 2300 1.307647 CCCCTCCTGTTCCCAATGG 59.692 63.158 0.00 0.00 0.00 3.16
1248 2302 3.856093 CCCCCTCCTGTTCCCAAT 58.144 61.111 0.00 0.00 0.00 3.16
1336 2390 1.377856 GCTCCTCTTGGTTGCCTCC 60.378 63.158 0.00 0.00 34.23 4.30
1350 2404 2.185608 GCCTCTTCCGTGAGCTCC 59.814 66.667 12.15 1.40 33.02 4.70
1351 2405 2.010582 ATCGCCTCTTCCGTGAGCTC 62.011 60.000 6.82 6.82 33.02 4.09
1352 2406 1.608717 AATCGCCTCTTCCGTGAGCT 61.609 55.000 0.00 0.00 33.02 4.09
1357 2411 1.218316 GGTCAATCGCCTCTTCCGT 59.782 57.895 0.00 0.00 0.00 4.69
1381 2435 6.840780 TGGATAGATCGATCATAGCTTCAA 57.159 37.500 26.47 5.43 0.00 2.69
1399 2453 2.224378 GGAACTAGCTGCTGCATGGATA 60.224 50.000 18.42 0.00 42.74 2.59
1475 2549 7.016268 AGCCAGCATAAGTATTTAACCTAGCTA 59.984 37.037 0.00 0.00 0.00 3.32
1522 2603 2.231235 TGAAGATCGAGCAAGTACAGCA 59.769 45.455 2.38 0.00 0.00 4.41
1523 2604 2.857152 CTGAAGATCGAGCAAGTACAGC 59.143 50.000 2.38 0.00 0.00 4.40
1581 2822 1.674441 CCCGATGAGTGTAGCGACTTA 59.326 52.381 0.00 0.00 0.00 2.24
1582 2823 0.456221 CCCGATGAGTGTAGCGACTT 59.544 55.000 0.00 0.00 0.00 3.01
1583 2824 0.393944 TCCCGATGAGTGTAGCGACT 60.394 55.000 0.00 0.00 0.00 4.18
1601 2842 4.214119 TGCAAGCAGTTACAGACAAAGATC 59.786 41.667 0.00 0.00 0.00 2.75
1670 2911 1.956477 CCAAGAAATTATCGGCCAGGG 59.044 52.381 2.24 0.00 0.00 4.45
1700 2941 3.190327 CGTCAAGGCATGGTTATTCACAA 59.810 43.478 0.00 0.00 0.00 3.33
1701 2942 2.746904 CGTCAAGGCATGGTTATTCACA 59.253 45.455 0.00 0.00 0.00 3.58
1702 2943 2.747446 ACGTCAAGGCATGGTTATTCAC 59.253 45.455 0.00 0.00 0.00 3.18
1704 2945 3.063997 CAGACGTCAAGGCATGGTTATTC 59.936 47.826 19.50 0.00 0.00 1.75
1705 2946 3.009723 CAGACGTCAAGGCATGGTTATT 58.990 45.455 19.50 0.00 0.00 1.40
1706 2947 2.236146 TCAGACGTCAAGGCATGGTTAT 59.764 45.455 19.50 0.00 0.00 1.89
1707 2948 1.621317 TCAGACGTCAAGGCATGGTTA 59.379 47.619 19.50 0.00 0.00 2.85
1708 2949 0.396435 TCAGACGTCAAGGCATGGTT 59.604 50.000 19.50 0.00 0.00 3.67
1709 2950 0.615331 ATCAGACGTCAAGGCATGGT 59.385 50.000 19.50 0.00 0.00 3.55
1719 2960 3.990469 TCTTCAAGCTTGAATCAGACGTC 59.010 43.478 35.40 7.70 45.26 4.34
1721 2962 3.742882 TGTCTTCAAGCTTGAATCAGACG 59.257 43.478 33.60 25.32 45.26 4.18
1749 2990 1.081892 CTCATGGGCGAGACAACAAG 58.918 55.000 0.00 0.00 34.79 3.16
1752 2993 0.745845 ATGCTCATGGGCGAGACAAC 60.746 55.000 14.07 0.00 34.79 3.32
1756 2997 1.368950 GCTATGCTCATGGGCGAGA 59.631 57.895 20.50 0.76 34.79 4.04
1757 2998 2.025969 CGCTATGCTCATGGGCGAG 61.026 63.158 14.07 13.83 42.38 5.03
1758 2999 2.029518 CGCTATGCTCATGGGCGA 59.970 61.111 14.07 1.98 42.38 5.54
1759 3000 3.720193 GCGCTATGCTCATGGGCG 61.720 66.667 14.07 19.49 42.53 6.13
1760 3001 1.919956 GATGCGCTATGCTCATGGGC 61.920 60.000 11.75 11.75 46.63 5.36
1761 3002 0.604511 TGATGCGCTATGCTCATGGG 60.605 55.000 9.73 0.00 46.63 4.00
1762 3003 1.232119 TTGATGCGCTATGCTCATGG 58.768 50.000 9.73 0.00 46.63 3.66
1797 3038 0.889186 CAAGCTAGTGTTGCCCGGTT 60.889 55.000 0.00 0.00 0.00 4.44
1866 3107 0.392461 GTCGGCCATGGTAAGCAAGA 60.392 55.000 14.67 0.00 0.00 3.02
1890 3131 1.073025 ATCAGCTTGACCGGTGCAA 59.927 52.632 14.63 15.29 32.68 4.08
1897 3138 0.745845 ATCACCGCATCAGCTTGACC 60.746 55.000 0.00 0.00 39.10 4.02
2004 3246 1.644786 ATTTTGCTACAGGCGCGACC 61.645 55.000 9.25 10.36 45.43 4.79
2006 3248 1.692148 CGATTTTGCTACAGGCGCGA 61.692 55.000 12.10 0.00 45.43 5.87
2011 3253 1.927174 CTCGGACGATTTTGCTACAGG 59.073 52.381 0.00 0.00 0.00 4.00
2031 3273 3.797546 GGCAGACAAGCAGCTCGC 61.798 66.667 0.00 0.47 42.91 5.03
2048 3290 2.183811 CTGACTCCTGAGGCTGCG 59.816 66.667 1.04 0.00 37.35 5.18
2051 3293 1.305718 GGTCCTGACTCCTGAGGCT 60.306 63.158 1.04 0.00 37.35 4.58
2059 3301 2.352032 CCCTGGACGGTCCTGACTC 61.352 68.421 29.17 4.47 37.65 3.36
2060 3302 2.283966 CCCTGGACGGTCCTGACT 60.284 66.667 29.17 0.00 37.65 3.41
2061 3303 2.603776 ACCCTGGACGGTCCTGAC 60.604 66.667 29.17 5.51 37.65 3.51
2062 3304 2.603473 CACCCTGGACGGTCCTGA 60.603 66.667 29.17 10.83 37.65 3.86
2063 3305 3.706373 CCACCCTGGACGGTCCTG 61.706 72.222 26.41 24.58 40.96 3.86
2066 3308 3.901797 CTTGCCACCCTGGACGGTC 62.902 68.421 0.00 0.00 40.96 4.79
2070 3312 1.379044 CATCCTTGCCACCCTGGAC 60.379 63.158 0.00 0.00 40.96 4.02
2077 3319 0.889186 AACGGTGACATCCTTGCCAC 60.889 55.000 0.00 0.00 35.67 5.01
2099 3341 3.414700 GTGAAGGTGTCCAGCGCG 61.415 66.667 0.00 0.00 0.00 6.86
2140 3382 2.278206 CGACGATCACCTCAGGCG 60.278 66.667 0.00 0.00 0.00 5.52
2141 3383 2.583593 GCGACGATCACCTCAGGC 60.584 66.667 0.00 0.00 0.00 4.85
2142 3384 2.021068 ATGGCGACGATCACCTCAGG 62.021 60.000 0.00 0.00 0.00 3.86
2143 3385 0.873312 CATGGCGACGATCACCTCAG 60.873 60.000 0.00 0.00 0.00 3.35
2144 3386 1.141665 CATGGCGACGATCACCTCA 59.858 57.895 0.00 0.00 0.00 3.86
2145 3387 2.240500 GCATGGCGACGATCACCTC 61.241 63.158 0.00 0.00 0.00 3.85
2146 3388 2.202932 GCATGGCGACGATCACCT 60.203 61.111 0.00 0.00 0.00 4.00
2157 3399 1.308069 TTGAAGAGGAAGCGCATGGC 61.308 55.000 11.47 0.00 44.05 4.40
2158 3400 0.731417 CTTGAAGAGGAAGCGCATGG 59.269 55.000 11.47 0.00 0.00 3.66
2159 3401 0.098376 GCTTGAAGAGGAAGCGCATG 59.902 55.000 11.47 0.00 36.74 4.06
2160 3402 2.475666 GCTTGAAGAGGAAGCGCAT 58.524 52.632 11.47 0.00 36.74 4.73
2161 3403 3.972227 GCTTGAAGAGGAAGCGCA 58.028 55.556 11.47 0.00 36.74 6.09
2164 3406 2.015587 CATCCTGCTTGAAGAGGAAGC 58.984 52.381 14.39 0.00 41.78 3.86
2165 3407 3.269178 GTCATCCTGCTTGAAGAGGAAG 58.731 50.000 14.39 11.39 41.78 3.46
2166 3408 2.354103 CGTCATCCTGCTTGAAGAGGAA 60.354 50.000 14.39 1.12 41.78 3.36
2167 3409 1.205655 CGTCATCCTGCTTGAAGAGGA 59.794 52.381 13.27 13.27 42.67 3.71
2168 3410 1.205655 TCGTCATCCTGCTTGAAGAGG 59.794 52.381 0.00 0.23 29.98 3.69
2169 3411 2.266554 GTCGTCATCCTGCTTGAAGAG 58.733 52.381 0.00 0.00 33.31 2.85
2170 3412 1.066858 GGTCGTCATCCTGCTTGAAGA 60.067 52.381 0.00 0.00 30.73 2.87
2171 3413 1.363744 GGTCGTCATCCTGCTTGAAG 58.636 55.000 0.00 0.00 0.00 3.02
2172 3414 0.389817 CGGTCGTCATCCTGCTTGAA 60.390 55.000 0.00 0.00 0.00 2.69
2173 3415 1.215382 CGGTCGTCATCCTGCTTGA 59.785 57.895 0.00 0.00 0.00 3.02
2174 3416 1.811266 CCGGTCGTCATCCTGCTTG 60.811 63.158 0.00 0.00 0.00 4.01
2175 3417 2.579201 CCGGTCGTCATCCTGCTT 59.421 61.111 0.00 0.00 0.00 3.91
2176 3418 3.461773 CCCGGTCGTCATCCTGCT 61.462 66.667 0.00 0.00 0.00 4.24
2178 3420 4.530857 GGCCCGGTCGTCATCCTG 62.531 72.222 0.00 0.00 0.00 3.86
2180 3422 4.832608 GTGGCCCGGTCGTCATCC 62.833 72.222 0.00 0.00 0.00 3.51
2201 3443 2.035342 GTCGATGAGCTCATTTTCGACG 60.035 50.000 36.27 29.25 42.24 5.12
2224 3466 0.523072 CAAAGCATGTTCACCTCCGG 59.477 55.000 0.00 0.00 0.00 5.14
2246 3488 4.439700 GCTCCATCATTCACAAACTCATGG 60.440 45.833 0.00 0.00 0.00 3.66
2257 3499 1.951895 GCCACACAGCTCCATCATTCA 60.952 52.381 0.00 0.00 0.00 2.57
2296 4618 1.227380 CTACCCGGAGCACATCAGC 60.227 63.158 0.73 0.00 0.00 4.26
2309 4631 3.851128 GAGACCCCAGCGCTACCC 61.851 72.222 10.99 0.00 0.00 3.69
2310 4632 2.579684 CTTGAGACCCCAGCGCTACC 62.580 65.000 10.99 0.00 0.00 3.18
2313 4635 3.710722 CCTTGAGACCCCAGCGCT 61.711 66.667 2.64 2.64 0.00 5.92
2319 4641 4.097361 GGGACGCCTTGAGACCCC 62.097 72.222 0.00 0.00 35.00 4.95
2325 4647 0.392461 GCTAACATGGGACGCCTTGA 60.392 55.000 0.00 0.00 0.00 3.02
2353 4675 1.748122 CAGCACCCTGGAGCATGAC 60.748 63.158 8.32 0.00 35.38 3.06


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

AutoCloner maintained by Alex Coulton.