Multiple sequence alignment - TraesCS5B01G331000

Loading Multiple Alignment...

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 TraesCS5B01G331000 chr5B 100.000 3105 0 0 1 3105 515191146 515194250 0.000000e+00 5734
1 TraesCS5B01G331000 chr5B 97.656 384 7 2 174 555 522393836 522394219 0.000000e+00 658
2 TraesCS5B01G331000 chr5D 91.860 1253 65 16 1857 3090 425847161 425848395 0.000000e+00 1714
3 TraesCS5B01G331000 chr5D 87.785 1359 84 38 562 1873 425845815 425847138 0.000000e+00 1515
4 TraesCS5B01G331000 chr5D 92.199 141 6 1 1369 1509 3968028 3967893 8.790000e-46 195
5 TraesCS5B01G331000 chr5A 86.708 1467 104 43 563 1973 540056973 540058404 0.000000e+00 1544
6 TraesCS5B01G331000 chr5A 89.794 872 62 15 2239 3090 540060355 540061219 0.000000e+00 1092
7 TraesCS5B01G331000 chr5A 97.714 350 8 0 212 561 355114778 355114429 1.230000e-168 603
8 TraesCS5B01G331000 chr5A 97.719 263 6 0 1 263 355115039 355114777 1.310000e-123 453
9 TraesCS5B01G331000 chr5A 87.702 309 24 5 1952 2246 540058418 540058726 6.370000e-92 348
10 TraesCS5B01G331000 chr1B 97.691 563 12 1 1 562 659686324 659686886 0.000000e+00 966
11 TraesCS5B01G331000 chr1B 94.671 563 28 2 1 562 645101627 645102188 0.000000e+00 872
12 TraesCS5B01G331000 chr2A 97.509 562 14 0 1 562 257852413 257852974 0.000000e+00 961
13 TraesCS5B01G331000 chr2A 89.062 128 14 0 1353 1480 467183453 467183326 3.200000e-35 159
14 TraesCS5B01G331000 chr2A 94.203 69 3 1 1201 1269 467197888 467197821 1.520000e-18 104
15 TraesCS5B01G331000 chr3B 95.907 562 14 2 1 562 736675788 736676340 0.000000e+00 902
16 TraesCS5B01G331000 chr3B 85.613 563 65 10 6 562 659083129 659082577 7.470000e-161 577
17 TraesCS5B01G331000 chr7B 81.714 350 59 5 215 561 56473343 56472996 1.410000e-73 287
18 TraesCS5B01G331000 chr4A 79.744 390 66 11 174 558 666276060 666275679 1.420000e-68 270
19 TraesCS5B01G331000 chr4A 78.505 321 31 16 1189 1509 360422105 360421823 3.180000e-40 176


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 TraesCS5B01G331000 chr5B 515191146 515194250 3104 False 5734.000000 5734 100.0000 1 3105 1 chr5B.!!$F1 3104
1 TraesCS5B01G331000 chr5D 425845815 425848395 2580 False 1614.500000 1714 89.8225 562 3090 2 chr5D.!!$F1 2528
2 TraesCS5B01G331000 chr5A 540056973 540061219 4246 False 994.666667 1544 88.0680 563 3090 3 chr5A.!!$F1 2527
3 TraesCS5B01G331000 chr5A 355114429 355115039 610 True 528.000000 603 97.7165 1 561 2 chr5A.!!$R1 560
4 TraesCS5B01G331000 chr1B 659686324 659686886 562 False 966.000000 966 97.6910 1 562 1 chr1B.!!$F2 561
5 TraesCS5B01G331000 chr1B 645101627 645102188 561 False 872.000000 872 94.6710 1 562 1 chr1B.!!$F1 561
6 TraesCS5B01G331000 chr2A 257852413 257852974 561 False 961.000000 961 97.5090 1 562 1 chr2A.!!$F1 561
7 TraesCS5B01G331000 chr3B 736675788 736676340 552 False 902.000000 902 95.9070 1 562 1 chr3B.!!$F1 561
8 TraesCS5B01G331000 chr3B 659082577 659083129 552 True 577.000000 577 85.6130 6 562 1 chr3B.!!$R1 556

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
762 839 0.038251 TCTACTGACTGCTTGGCACG 60.038 55.0 0.0 0.0 33.79 5.34 F
763 840 0.038251 CTACTGACTGCTTGGCACGA 60.038 55.0 0.0 0.0 33.79 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2246 0.035630 AGCTGATTCGGAGCTGCTTT 60.036 50.0 7.62 0.0 45.28 3.51 R
2188 2431 0.244994 GCTCCTTTGCTGACGAGAGA 59.755 55.0 0.00 0.0 0.00 3.10 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
104 106 5.658468 GTCACGGGACTAGTATAAAAAGCT 58.342 41.667 11.49 0.00 40.99 3.74
124 135 3.288308 CTCGCCTGTTCTCTGCCGT 62.288 63.158 0.00 0.00 0.00 5.68
198 209 2.435938 GTTCGAATCCGGCAGCCA 60.436 61.111 13.30 0.00 36.24 4.75
451 517 9.502145 CAATGCATGTTTATACGTTGTTTAGAT 57.498 29.630 0.00 0.00 0.00 1.98
749 826 6.072064 CCATAACGGATACCTTACCTCTACTG 60.072 46.154 0.00 0.00 36.56 2.74
750 827 4.785346 ACGGATACCTTACCTCTACTGA 57.215 45.455 0.00 0.00 0.00 3.41
751 828 4.459330 ACGGATACCTTACCTCTACTGAC 58.541 47.826 0.00 0.00 0.00 3.51
752 829 4.165758 ACGGATACCTTACCTCTACTGACT 59.834 45.833 0.00 0.00 0.00 3.41
753 830 4.515944 CGGATACCTTACCTCTACTGACTG 59.484 50.000 0.00 0.00 0.00 3.51
754 831 4.278919 GGATACCTTACCTCTACTGACTGC 59.721 50.000 0.00 0.00 0.00 4.40
755 832 3.459710 ACCTTACCTCTACTGACTGCT 57.540 47.619 0.00 0.00 0.00 4.24
756 833 3.780626 ACCTTACCTCTACTGACTGCTT 58.219 45.455 0.00 0.00 0.00 3.91
757 834 3.511934 ACCTTACCTCTACTGACTGCTTG 59.488 47.826 0.00 0.00 0.00 4.01
758 835 3.118956 CCTTACCTCTACTGACTGCTTGG 60.119 52.174 0.00 0.00 0.00 3.61
759 836 0.610687 ACCTCTACTGACTGCTTGGC 59.389 55.000 0.00 0.00 0.00 4.52
760 837 0.610174 CCTCTACTGACTGCTTGGCA 59.390 55.000 0.00 0.00 36.92 4.92
761 838 1.674221 CCTCTACTGACTGCTTGGCAC 60.674 57.143 0.00 0.00 33.79 5.01
762 839 0.038251 TCTACTGACTGCTTGGCACG 60.038 55.000 0.00 0.00 33.79 5.34
763 840 0.038251 CTACTGACTGCTTGGCACGA 60.038 55.000 0.00 0.00 33.79 4.35
764 841 0.608130 TACTGACTGCTTGGCACGAT 59.392 50.000 0.00 0.00 33.79 3.73
765 842 0.608130 ACTGACTGCTTGGCACGATA 59.392 50.000 0.00 0.00 33.79 2.92
766 843 1.002366 CTGACTGCTTGGCACGATAC 58.998 55.000 0.00 0.00 33.79 2.24
767 844 0.391130 TGACTGCTTGGCACGATACC 60.391 55.000 0.00 0.00 33.79 2.73
768 845 0.391130 GACTGCTTGGCACGATACCA 60.391 55.000 0.00 0.00 33.79 3.25
769 846 0.253044 ACTGCTTGGCACGATACCAT 59.747 50.000 0.00 0.00 36.96 3.55
770 847 1.340017 ACTGCTTGGCACGATACCATT 60.340 47.619 0.00 0.00 36.96 3.16
771 848 2.093181 ACTGCTTGGCACGATACCATTA 60.093 45.455 0.00 0.00 36.96 1.90
772 849 3.141398 CTGCTTGGCACGATACCATTAT 58.859 45.455 0.00 0.00 36.96 1.28
773 850 3.138304 TGCTTGGCACGATACCATTATC 58.862 45.455 0.00 0.00 36.96 1.75
774 851 3.181455 TGCTTGGCACGATACCATTATCT 60.181 43.478 0.00 0.00 36.96 1.98
775 852 3.815401 GCTTGGCACGATACCATTATCTT 59.185 43.478 0.00 0.00 36.96 2.40
776 853 4.083802 GCTTGGCACGATACCATTATCTTC 60.084 45.833 0.00 0.00 36.96 2.87
777 854 4.955811 TGGCACGATACCATTATCTTCT 57.044 40.909 0.00 0.00 33.07 2.85
778 855 5.290493 TGGCACGATACCATTATCTTCTT 57.710 39.130 0.00 0.00 33.07 2.52
779 856 5.297547 TGGCACGATACCATTATCTTCTTC 58.702 41.667 0.00 0.00 33.07 2.87
780 857 4.691216 GGCACGATACCATTATCTTCTTCC 59.309 45.833 0.00 0.00 33.07 3.46
783 860 6.295123 GCACGATACCATTATCTTCTTCCCTA 60.295 42.308 0.00 0.00 33.07 3.53
799 877 0.543749 CCTACCCTTCCTTGGCTCAG 59.456 60.000 0.00 0.00 0.00 3.35
810 905 0.399454 TTGGCTCAGCAGCTCTTCTT 59.601 50.000 0.00 0.00 46.03 2.52
824 919 1.971357 TCTTCTTCGGCTCACCTTTCT 59.029 47.619 0.00 0.00 0.00 2.52
892 1003 4.331168 GCTGCATCTCGATCTGTTTTAGTT 59.669 41.667 0.00 0.00 0.00 2.24
907 1018 8.314021 TCTGTTTTAGTTGATCTAGATCTGCAA 58.686 33.333 28.51 15.70 38.60 4.08
925 1040 1.268899 CAACCAAGCAAGCTTCTCCAG 59.731 52.381 3.97 0.00 33.42 3.86
1038 1166 2.911723 CAGCTCTCAACGTTTACTCGAG 59.088 50.000 11.84 11.84 34.70 4.04
1052 1180 1.609555 ACTCGAGATAATCAGCCGACC 59.390 52.381 21.68 0.00 0.00 4.79
1090 1218 1.974265 TGTTTCGGCACCAGATTTGA 58.026 45.000 0.00 0.00 0.00 2.69
1104 1232 6.206243 CACCAGATTTGAAAAGACTGACTCAT 59.794 38.462 10.16 0.00 32.14 2.90
1540 1680 3.150335 CCTGCTCCGGCTCTAGCA 61.150 66.667 14.24 14.24 46.11 3.49
1542 1682 2.895680 TGCTCCGGCTCTAGCAAG 59.104 61.111 12.79 0.00 45.36 4.01
1543 1683 2.107953 GCTCCGGCTCTAGCAAGG 59.892 66.667 7.94 6.82 44.36 3.61
1544 1684 2.107953 CTCCGGCTCTAGCAAGGC 59.892 66.667 0.00 0.00 44.36 4.35
1548 1688 2.107953 GGCTCTAGCAAGGCGAGG 59.892 66.667 4.07 0.00 44.36 4.63
1549 1689 2.107953 GCTCTAGCAAGGCGAGGG 59.892 66.667 0.00 0.00 41.59 4.30
1550 1690 2.427245 GCTCTAGCAAGGCGAGGGA 61.427 63.158 2.25 0.00 33.63 4.20
1551 1691 1.739049 CTCTAGCAAGGCGAGGGAG 59.261 63.158 0.00 0.00 33.63 4.30
1552 1692 2.107953 CTAGCAAGGCGAGGGAGC 59.892 66.667 0.00 0.00 0.00 4.70
1553 1693 2.364317 TAGCAAGGCGAGGGAGCT 60.364 61.111 0.00 0.00 39.22 4.09
1586 1740 1.890979 GGAGCTGCGGATGGATGTG 60.891 63.158 0.00 0.00 0.00 3.21
1608 1764 1.089481 CCGTTCATGGATCGTGGGTG 61.089 60.000 0.00 0.00 0.00 4.61
1690 1847 6.931840 TGTAACAACAATGTACTGATGCAGTA 59.068 34.615 3.32 3.32 44.77 2.74
1739 1896 6.119536 TCATTTCAGTTCCTTGTGTAGTTGT 58.880 36.000 0.00 0.00 0.00 3.32
1740 1897 7.276658 TCATTTCAGTTCCTTGTGTAGTTGTA 58.723 34.615 0.00 0.00 0.00 2.41
1757 1914 1.165270 GTATGTTGTGTGCCTGGGTC 58.835 55.000 0.00 0.00 0.00 4.46
1775 1932 4.814900 ACGATCTCCATGCGTGAC 57.185 55.556 7.72 0.00 36.83 3.67
1833 1990 3.181496 TGTGTTGCAACGCAGAAATTACA 60.181 39.130 35.41 21.91 43.79 2.41
1834 1991 3.794028 GTGTTGCAACGCAGAAATTACAA 59.206 39.130 32.56 5.82 40.61 2.41
1838 1995 3.181486 TGCAACGCAGAAATTACAACCAA 60.181 39.130 0.00 0.00 33.32 3.67
1840 1997 4.085107 GCAACGCAGAAATTACAACCAAAG 60.085 41.667 0.00 0.00 0.00 2.77
1844 2001 5.163602 ACGCAGAAATTACAACCAAAGTTCA 60.164 36.000 0.00 0.00 34.31 3.18
1845 2002 5.920273 CGCAGAAATTACAACCAAAGTTCAT 59.080 36.000 0.00 0.00 34.31 2.57
1846 2003 7.081349 CGCAGAAATTACAACCAAAGTTCATA 58.919 34.615 0.00 0.00 34.31 2.15
1864 2021 5.578005 TCATAGTACGAACTTGAGAAGGG 57.422 43.478 0.00 0.00 37.15 3.95
1866 2023 5.357314 TCATAGTACGAACTTGAGAAGGGAG 59.643 44.000 0.00 0.00 37.15 4.30
1909 2103 5.025826 CGGGTAAAACTGACGCATTATTTC 58.974 41.667 0.00 0.00 0.00 2.17
1910 2104 5.391097 CGGGTAAAACTGACGCATTATTTCA 60.391 40.000 0.00 0.00 0.00 2.69
1911 2105 6.027749 GGGTAAAACTGACGCATTATTTCAG 58.972 40.000 0.00 0.00 42.17 3.02
1937 2131 2.753701 CACCAATCGTGTCCCCCA 59.246 61.111 0.00 0.00 37.73 4.96
1950 2144 0.766674 TCCCCCAAGTACACTGCACT 60.767 55.000 0.00 0.00 0.00 4.40
2011 2245 0.447406 CGAGATCAAACAATGGCGCA 59.553 50.000 10.83 0.00 0.00 6.09
2012 2246 1.135717 CGAGATCAAACAATGGCGCAA 60.136 47.619 10.83 0.00 0.00 4.85
2013 2247 2.668001 CGAGATCAAACAATGGCGCAAA 60.668 45.455 10.83 0.00 0.00 3.68
2018 2252 1.070443 CAAACAATGGCGCAAAAGCAG 60.070 47.619 10.83 0.00 39.27 4.24
2028 2262 0.523072 GCAAAAGCAGCTCCGAATCA 59.477 50.000 0.00 0.00 0.00 2.57
2030 2264 0.807496 AAAAGCAGCTCCGAATCAGC 59.193 50.000 0.00 0.00 37.12 4.26
2101 2341 6.149474 GTGCACCATCTAACACTTGTTTAGAT 59.851 38.462 5.22 4.58 39.31 1.98
2106 2346 9.227777 ACCATCTAACACTTGTTTAGATAAACC 57.772 33.333 11.82 0.00 43.64 3.27
2127 2367 1.542492 ACCTGTCCCGTGTACAGTAG 58.458 55.000 0.00 0.00 42.30 2.57
2141 2381 5.919141 GTGTACAGTAGACGAGTCACAAAAT 59.081 40.000 0.00 0.00 0.00 1.82
2147 2387 3.243336 AGACGAGTCACAAAATAGCGAC 58.757 45.455 5.99 0.00 0.00 5.19
2162 2405 0.110373 GCGACGGCTTTGTAGGTTTG 60.110 55.000 0.00 0.00 35.83 2.93
2187 2430 5.897050 TGCTCAGGTAAAACGAAAACAAAT 58.103 33.333 0.00 0.00 0.00 2.32
2188 2431 6.334202 TGCTCAGGTAAAACGAAAACAAATT 58.666 32.000 0.00 0.00 0.00 1.82
2201 2444 5.499139 AAAACAAATTCTCTCGTCAGCAA 57.501 34.783 0.00 0.00 0.00 3.91
2263 4145 9.086336 TGAATTCTGTTTTTCAAAATGACTGAC 57.914 29.630 7.05 0.00 0.00 3.51
2285 4167 5.385198 ACCACAATTCACAATTACTGAGGT 58.615 37.500 0.00 0.00 0.00 3.85
2300 4182 3.780294 ACTGAGGTATGATGCCCTACAAA 59.220 43.478 0.00 0.00 0.00 2.83
2335 4223 0.322187 CCTGGAACCAACCCCTTACG 60.322 60.000 0.00 0.00 0.00 3.18
2336 4224 0.688487 CTGGAACCAACCCCTTACGA 59.312 55.000 0.00 0.00 0.00 3.43
2368 4256 8.638565 CATTATTCTCACCAAAACGAAATGAAC 58.361 33.333 0.00 0.00 0.00 3.18
2388 4276 6.500041 TGAACAAATAAAGGTAGCACACAAC 58.500 36.000 0.00 0.00 0.00 3.32
2406 4296 0.595588 ACGCACTCACTCTCTCTGTG 59.404 55.000 0.00 0.00 36.82 3.66
2463 4357 2.775911 TGGATCTCCAGCTTGACAAG 57.224 50.000 11.02 11.02 42.01 3.16
2469 4363 2.639347 TCTCCAGCTTGACAAGGATCAA 59.361 45.455 16.80 0.00 37.08 2.57
2472 4366 5.045651 TCTCCAGCTTGACAAGGATCAATTA 60.046 40.000 16.80 0.00 37.93 1.40
2621 4515 1.737816 GCGCCATGCAAGGAATCAT 59.262 52.632 13.26 0.00 45.45 2.45
2622 4516 0.318445 GCGCCATGCAAGGAATCATC 60.318 55.000 13.26 0.00 45.45 2.92
2623 4517 1.026584 CGCCATGCAAGGAATCATCA 58.973 50.000 13.26 0.00 0.00 3.07
2636 4530 9.760077 GCAAGGAATCATCAATCATTAAGATTT 57.240 29.630 0.00 0.00 44.48 2.17
2724 4624 4.770795 AGGTACTTACAGCCATGATGTTC 58.229 43.478 8.55 0.00 33.09 3.18
3033 4937 6.701400 GCCTGGCAATTAAATGAAACGATTAT 59.299 34.615 15.17 0.00 0.00 1.28
3047 4956 9.817809 ATGAAACGATTATAGTGAGTAACATGT 57.182 29.630 0.00 0.00 0.00 3.21
3060 4969 9.204570 AGTGAGTAACATGTATACTTCACAAAC 57.795 33.333 25.78 16.98 35.82 2.93
3061 4970 8.984764 GTGAGTAACATGTATACTTCACAAACA 58.015 33.333 23.23 14.47 34.79 2.83
3085 4994 3.959495 AGGTTGCTATCACATTCCCAT 57.041 42.857 0.00 0.00 0.00 4.00
3090 4999 6.840705 AGGTTGCTATCACATTCCCATAAAAT 59.159 34.615 0.00 0.00 0.00 1.82
3091 5000 8.004215 AGGTTGCTATCACATTCCCATAAAATA 58.996 33.333 0.00 0.00 0.00 1.40
3092 5001 8.806146 GGTTGCTATCACATTCCCATAAAATAT 58.194 33.333 0.00 0.00 0.00 1.28
3093 5002 9.846248 GTTGCTATCACATTCCCATAAAATATC 57.154 33.333 0.00 0.00 0.00 1.63
3094 5003 8.267620 TGCTATCACATTCCCATAAAATATCG 57.732 34.615 0.00 0.00 0.00 2.92
3095 5004 8.100164 TGCTATCACATTCCCATAAAATATCGA 58.900 33.333 0.00 0.00 0.00 3.59
3096 5005 8.607459 GCTATCACATTCCCATAAAATATCGAG 58.393 37.037 0.00 0.00 0.00 4.04
3097 5006 9.658799 CTATCACATTCCCATAAAATATCGAGT 57.341 33.333 0.00 0.00 0.00 4.18
3098 5007 8.924511 ATCACATTCCCATAAAATATCGAGTT 57.075 30.769 0.00 0.00 0.00 3.01
3099 5008 8.153479 TCACATTCCCATAAAATATCGAGTTG 57.847 34.615 0.00 0.00 0.00 3.16
3100 5009 7.990314 TCACATTCCCATAAAATATCGAGTTGA 59.010 33.333 0.00 0.00 0.00 3.18
3101 5010 8.285394 CACATTCCCATAAAATATCGAGTTGAG 58.715 37.037 0.00 0.00 0.00 3.02
3102 5011 7.445402 ACATTCCCATAAAATATCGAGTTGAGG 59.555 37.037 0.00 0.00 0.00 3.86
3103 5012 6.494666 TCCCATAAAATATCGAGTTGAGGT 57.505 37.500 0.00 0.00 0.00 3.85
3104 5013 6.895782 TCCCATAAAATATCGAGTTGAGGTT 58.104 36.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 5.643379 TTTTTATACTAGTCCCGTGACGT 57.357 39.130 3.64 0.00 46.51 4.34
104 106 1.293498 GGCAGAGAACAGGCGAGAA 59.707 57.895 0.00 0.00 0.00 2.87
451 517 4.653868 TGGGGCTAATCGTTACAAAAAGA 58.346 39.130 0.00 0.00 0.00 2.52
506 572 3.569194 TTACATGCGGATTGGTACCAT 57.431 42.857 17.17 5.96 0.00 3.55
541 607 4.048504 GCGGAGTTAATTGCACAAAAGTT 58.951 39.130 0.00 0.00 0.00 2.66
715 792 1.618876 ATCCGTTATGGTCGTGGCCA 61.619 55.000 0.00 0.00 43.48 5.36
723 800 4.812653 AGAGGTAAGGTATCCGTTATGGT 58.187 43.478 0.00 0.00 39.52 3.55
727 804 6.058183 GTCAGTAGAGGTAAGGTATCCGTTA 58.942 44.000 0.00 0.00 0.00 3.18
749 826 0.391130 TGGTATCGTGCCAAGCAGTC 60.391 55.000 0.00 0.00 40.08 3.51
750 827 0.253044 ATGGTATCGTGCCAAGCAGT 59.747 50.000 0.00 0.00 40.08 4.40
751 828 1.382522 AATGGTATCGTGCCAAGCAG 58.617 50.000 0.00 0.00 40.08 4.24
752 829 2.700722 TAATGGTATCGTGCCAAGCA 57.299 45.000 0.00 0.00 39.72 3.91
753 830 3.403038 AGATAATGGTATCGTGCCAAGC 58.597 45.455 0.00 0.00 41.03 4.01
754 831 5.300752 AGAAGATAATGGTATCGTGCCAAG 58.699 41.667 0.00 0.00 41.03 3.61
755 832 5.290493 AGAAGATAATGGTATCGTGCCAA 57.710 39.130 0.00 0.00 41.03 4.52
756 833 4.955811 AGAAGATAATGGTATCGTGCCA 57.044 40.909 0.00 0.00 41.03 4.92
757 834 4.691216 GGAAGAAGATAATGGTATCGTGCC 59.309 45.833 0.00 0.00 41.03 5.01
758 835 4.691216 GGGAAGAAGATAATGGTATCGTGC 59.309 45.833 0.00 0.00 41.03 5.34
759 836 6.102897 AGGGAAGAAGATAATGGTATCGTG 57.897 41.667 0.00 0.00 41.03 4.35
760 837 6.210984 GGTAGGGAAGAAGATAATGGTATCGT 59.789 42.308 0.00 0.00 41.03 3.73
761 838 6.351117 GGGTAGGGAAGAAGATAATGGTATCG 60.351 46.154 0.00 0.00 41.03 2.92
762 839 6.731448 AGGGTAGGGAAGAAGATAATGGTATC 59.269 42.308 0.00 0.00 37.04 2.24
763 840 6.644882 AGGGTAGGGAAGAAGATAATGGTAT 58.355 40.000 0.00 0.00 0.00 2.73
764 841 6.051946 AGGGTAGGGAAGAAGATAATGGTA 57.948 41.667 0.00 0.00 0.00 3.25
765 842 4.909284 AGGGTAGGGAAGAAGATAATGGT 58.091 43.478 0.00 0.00 0.00 3.55
766 843 5.221945 GGAAGGGTAGGGAAGAAGATAATGG 60.222 48.000 0.00 0.00 0.00 3.16
767 844 5.608860 AGGAAGGGTAGGGAAGAAGATAATG 59.391 44.000 0.00 0.00 0.00 1.90
768 845 5.805135 AGGAAGGGTAGGGAAGAAGATAAT 58.195 41.667 0.00 0.00 0.00 1.28
769 846 5.236425 AGGAAGGGTAGGGAAGAAGATAA 57.764 43.478 0.00 0.00 0.00 1.75
770 847 4.920781 AGGAAGGGTAGGGAAGAAGATA 57.079 45.455 0.00 0.00 0.00 1.98
771 848 3.783082 CAAGGAAGGGTAGGGAAGAAGAT 59.217 47.826 0.00 0.00 0.00 2.40
772 849 3.182152 CAAGGAAGGGTAGGGAAGAAGA 58.818 50.000 0.00 0.00 0.00 2.87
773 850 2.239907 CCAAGGAAGGGTAGGGAAGAAG 59.760 54.545 0.00 0.00 0.00 2.85
774 851 2.275466 CCAAGGAAGGGTAGGGAAGAA 58.725 52.381 0.00 0.00 0.00 2.52
775 852 1.966845 CCAAGGAAGGGTAGGGAAGA 58.033 55.000 0.00 0.00 0.00 2.87
776 853 0.256177 GCCAAGGAAGGGTAGGGAAG 59.744 60.000 0.00 0.00 0.00 3.46
777 854 0.178843 AGCCAAGGAAGGGTAGGGAA 60.179 55.000 0.00 0.00 37.68 3.97
778 855 0.620700 GAGCCAAGGAAGGGTAGGGA 60.621 60.000 0.00 0.00 40.02 4.20
779 856 0.914417 TGAGCCAAGGAAGGGTAGGG 60.914 60.000 0.00 0.00 40.02 3.53
780 857 0.543749 CTGAGCCAAGGAAGGGTAGG 59.456 60.000 0.00 0.00 40.02 3.18
783 860 2.134630 CTGCTGAGCCAAGGAAGGGT 62.135 60.000 0.23 0.00 43.27 4.34
799 877 1.079543 TGAGCCGAAGAAGAGCTGC 60.080 57.895 0.00 0.00 36.87 5.25
810 905 2.347490 GGCAGAAAGGTGAGCCGA 59.653 61.111 0.00 0.00 40.50 5.54
824 919 4.170468 ACAGGAAAGAGAAAGAAAGGCA 57.830 40.909 0.00 0.00 0.00 4.75
892 1003 3.198417 TGCTTGGTTGCAGATCTAGATCA 59.802 43.478 29.83 11.42 40.22 2.92
907 1018 3.336122 CTGGAGAAGCTTGCTTGGT 57.664 52.632 12.92 0.00 0.00 3.67
1038 1166 0.394565 AGCAGGGTCGGCTGATTATC 59.605 55.000 0.00 0.00 40.80 1.75
1052 1180 2.588314 GCGGCTGATCTGAGCAGG 60.588 66.667 22.84 9.55 41.08 4.85
1090 1218 6.212388 ACACTCCATCTATGAGTCAGTCTTTT 59.788 38.462 0.00 0.00 0.00 2.27
1104 1232 5.253330 GGATTTCAAACCACACTCCATCTA 58.747 41.667 0.00 0.00 0.00 1.98
1540 1680 2.739996 CCATCAGCTCCCTCGCCTT 61.740 63.158 0.00 0.00 0.00 4.35
1542 1682 4.925861 GCCATCAGCTCCCTCGCC 62.926 72.222 0.00 0.00 38.99 5.54
1543 1683 3.687321 TTGCCATCAGCTCCCTCGC 62.687 63.158 0.00 0.00 44.23 5.03
1544 1684 1.523258 CTTGCCATCAGCTCCCTCG 60.523 63.158 0.00 0.00 44.23 4.63
1545 1685 1.153005 CCTTGCCATCAGCTCCCTC 60.153 63.158 0.00 0.00 44.23 4.30
1546 1686 3.004951 CCTTGCCATCAGCTCCCT 58.995 61.111 0.00 0.00 44.23 4.20
1548 1688 3.207669 CGCCTTGCCATCAGCTCC 61.208 66.667 0.00 0.00 44.23 4.70
1549 1689 2.124983 TCGCCTTGCCATCAGCTC 60.125 61.111 0.00 0.00 44.23 4.09
1550 1690 2.124819 CTCGCCTTGCCATCAGCT 60.125 61.111 0.00 0.00 44.23 4.24
1551 1691 3.207669 CCTCGCCTTGCCATCAGC 61.208 66.667 0.00 0.00 44.14 4.26
1552 1692 2.515523 CCCTCGCCTTGCCATCAG 60.516 66.667 0.00 0.00 0.00 2.90
1553 1693 3.008517 TCCCTCGCCTTGCCATCA 61.009 61.111 0.00 0.00 0.00 3.07
1586 1740 2.180204 CACGATCCATGAACGGGCC 61.180 63.158 0.00 0.00 32.29 5.80
1717 1874 7.719633 ACATACAACTACACAAGGAACTGAAAT 59.280 33.333 0.00 0.00 40.86 2.17
1739 1896 0.767998 TGACCCAGGCACACAACATA 59.232 50.000 0.00 0.00 0.00 2.29
1740 1897 0.823356 GTGACCCAGGCACACAACAT 60.823 55.000 8.72 0.00 36.31 2.71
1775 1932 2.605849 GCGTATAAACTTCTCACGCG 57.394 50.000 3.53 3.53 46.85 6.01
1780 1937 5.496657 CGAACTGAACGCGTATAAACTTCTC 60.497 44.000 14.46 3.04 0.00 2.87
1805 1962 2.567151 GCGTTGCAACACAAGCACG 61.567 57.895 28.01 14.14 42.54 5.34
1840 1997 5.805994 CCCTTCTCAAGTTCGTACTATGAAC 59.194 44.000 11.77 11.77 42.81 3.18
1844 2001 4.098196 GCTCCCTTCTCAAGTTCGTACTAT 59.902 45.833 0.00 0.00 33.17 2.12
1845 2002 3.442977 GCTCCCTTCTCAAGTTCGTACTA 59.557 47.826 0.00 0.00 33.17 1.82
1846 2003 2.231721 GCTCCCTTCTCAAGTTCGTACT 59.768 50.000 0.00 0.00 35.68 2.73
1850 2007 1.001406 ACTGCTCCCTTCTCAAGTTCG 59.999 52.381 0.00 0.00 0.00 3.95
1864 2021 2.370281 TCCTGTGAATCGAACTGCTC 57.630 50.000 0.00 0.00 0.00 4.26
1866 2023 1.936547 GGATCCTGTGAATCGAACTGC 59.063 52.381 3.84 0.00 0.00 4.40
1937 2131 1.717032 TCTCCCAGTGCAGTGTACTT 58.283 50.000 19.93 0.00 0.00 2.24
2011 2245 0.807496 GCTGATTCGGAGCTGCTTTT 59.193 50.000 2.53 0.00 33.90 2.27
2012 2246 0.035630 AGCTGATTCGGAGCTGCTTT 60.036 50.000 7.62 0.00 45.28 3.51
2013 2247 1.601171 AGCTGATTCGGAGCTGCTT 59.399 52.632 7.62 0.00 45.28 3.91
2030 2264 1.205485 GCTGTCGCGTGCTATCAGAG 61.205 60.000 5.77 0.00 0.00 3.35
2031 2265 1.226688 GCTGTCGCGTGCTATCAGA 60.227 57.895 5.77 0.00 0.00 3.27
2101 2341 0.838608 ACACGGGACAGGTTGGTTTA 59.161 50.000 0.00 0.00 0.00 2.01
2106 2346 3.210857 CTGTACACGGGACAGGTTG 57.789 57.895 8.05 0.00 40.58 3.77
2127 2367 2.026507 CGTCGCTATTTTGTGACTCGTC 59.973 50.000 6.63 0.00 43.10 4.20
2147 2387 1.336755 AGCAACAAACCTACAAAGCCG 59.663 47.619 0.00 0.00 0.00 5.52
2155 2395 4.273969 CGTTTTACCTGAGCAACAAACCTA 59.726 41.667 0.00 0.00 0.00 3.08
2162 2405 4.664188 TGTTTTCGTTTTACCTGAGCAAC 58.336 39.130 0.00 0.00 0.00 4.17
2187 2430 1.337260 GCTCCTTTGCTGACGAGAGAA 60.337 52.381 0.00 0.00 0.00 2.87
2188 2431 0.244994 GCTCCTTTGCTGACGAGAGA 59.755 55.000 0.00 0.00 0.00 3.10
2263 4145 5.964958 ACCTCAGTAATTGTGAATTGTGG 57.035 39.130 0.00 0.00 32.38 4.17
2285 4167 5.448654 AGCAATTCTTTGTAGGGCATCATA 58.551 37.500 0.00 0.00 35.17 2.15
2300 4182 3.362706 TCCAGGTCGTAGTAGCAATTCT 58.637 45.455 0.00 0.00 0.00 2.40
2335 4223 6.747280 CGTTTTGGTGAGAATAATGGAATGTC 59.253 38.462 0.00 0.00 0.00 3.06
2336 4224 6.432783 TCGTTTTGGTGAGAATAATGGAATGT 59.567 34.615 0.00 0.00 0.00 2.71
2368 4256 3.911964 GCGTTGTGTGCTACCTTTATTTG 59.088 43.478 0.00 0.00 0.00 2.32
2388 4276 0.595588 ACACAGAGAGAGTGAGTGCG 59.404 55.000 0.00 0.00 40.16 5.34
2463 4357 3.174799 GCGTTCTGCGATAATTGATCC 57.825 47.619 0.00 0.00 44.77 3.36
2660 4557 4.760715 GCTGATATGCTTGGACATCTCAAT 59.239 41.667 0.00 0.00 34.09 2.57
2661 4558 4.132336 GCTGATATGCTTGGACATCTCAA 58.868 43.478 0.00 0.00 34.09 3.02
2724 4624 2.526304 TGACGGTGGAGAAGTTCAAG 57.474 50.000 5.50 0.00 0.00 3.02
2930 4834 3.435671 GGAACGGTAAGACCAGTTGAATG 59.564 47.826 9.52 0.00 38.47 2.67
3047 4956 8.630054 AGCAACCTTATTGTTTGTGAAGTATA 57.370 30.769 0.00 0.00 0.00 1.47
3050 4959 5.852282 AGCAACCTTATTGTTTGTGAAGT 57.148 34.783 0.00 0.00 0.00 3.01
3060 4969 5.593909 TGGGAATGTGATAGCAACCTTATTG 59.406 40.000 0.00 0.00 0.00 1.90
3061 4970 5.765510 TGGGAATGTGATAGCAACCTTATT 58.234 37.500 0.00 0.00 0.00 1.40
3063 4972 4.853468 TGGGAATGTGATAGCAACCTTA 57.147 40.909 0.00 0.00 0.00 2.69
3077 4986 7.445402 ACCTCAACTCGATATTTTATGGGAATG 59.555 37.037 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.