Multiple sequence alignment - TraesCS1B01G403600

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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 TraesCS1B01G403600 chr1B 100.000 2738 0 0 1 2738 633137940 633135203 0.000000e+00 5057.0
1 TraesCS1B01G403600 chr1D 92.231 2008 113 27 584 2584 460866504 460864533 0.000000e+00 2804.0
2 TraesCS1B01G403600 chr1D 94.129 528 20 6 60 587 460867100 460866584 0.000000e+00 793.0
3 TraesCS1B01G403600 chr1D 92.308 65 4 1 2664 2728 460864325 460864262 1.040000e-14 91.6
4 TraesCS1B01G403600 chr1A 93.266 1871 92 19 60 1929 551982736 551980899 0.000000e+00 2726.0
5 TraesCS1B01G403600 chr1A 93.443 61 3 1 2668 2728 551980000 551979941 3.760000e-14 89.8
6 TraesCS1B01G403600 chr2D 78.689 183 35 4 1507 1687 111336769 111336949 4.790000e-23 119.0
7 TraesCS1B01G403600 chr2B 78.142 183 36 4 1507 1687 161419823 161420003 2.230000e-21 113.0
8 TraesCS1B01G403600 chr2A 77.596 183 37 4 1507 1687 111426138 111426318 1.040000e-19 108.0


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 TraesCS1B01G403600 chr1B 633135203 633137940 2737 True 5057.000000 5057 100.000000 1 2738 1 chr1B.!!$R1 2737
1 TraesCS1B01G403600 chr1D 460864262 460867100 2838 True 1229.533333 2804 92.889333 60 2728 3 chr1D.!!$R1 2668
2 TraesCS1B01G403600 chr1A 551979941 551982736 2795 True 1407.900000 2726 93.354500 60 2728 2 chr1A.!!$R1 2668

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
621 705 1.283793 GTGAACTGCAGCGCAACAT 59.716 52.632 15.27 0.0 38.41 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2571 2752 0.180171 ACTGCAAGCACCACAGTACA 59.82 50.0 0.0 0.0 42.65 2.9 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
37 38 9.899661 ACAAGTATATACAACTCTAATTTGCCA 57.100 29.630 15.18 0.00 0.00 4.92
55 56 9.777297 AATTTGCCATTATGTTTAAAGACTGTT 57.223 25.926 0.00 0.00 0.00 3.16
56 57 9.777297 ATTTGCCATTATGTTTAAAGACTGTTT 57.223 25.926 0.00 0.00 0.00 2.83
104 105 7.010923 GCAAAATGATCCAAACACAACTGTTTA 59.989 33.333 0.00 0.00 46.88 2.01
134 135 9.494271 TCTACTCAATTGCCATATGTATTCTTC 57.506 33.333 0.00 0.00 0.00 2.87
142 143 8.523915 TTGCCATATGTATTCTTCATGTTCTT 57.476 30.769 1.24 0.00 0.00 2.52
209 210 2.096466 TGCTTTGCGTGATGTTCTAACG 60.096 45.455 0.00 0.00 40.22 3.18
270 271 9.489084 TCTGGACGTATCCTTGATAAATTAATG 57.511 33.333 0.00 0.00 46.43 1.90
312 313 7.751768 ATATATCAAGCCCTTTTACTGCTTC 57.248 36.000 0.00 0.00 43.10 3.86
353 354 4.457949 CCTATTTTAACCGCTCCTGTGTTT 59.542 41.667 0.00 0.00 0.00 2.83
354 355 3.701532 TTTTAACCGCTCCTGTGTTTG 57.298 42.857 0.00 0.00 0.00 2.93
355 356 2.623878 TTAACCGCTCCTGTGTTTGA 57.376 45.000 0.00 0.00 0.00 2.69
356 357 2.851263 TAACCGCTCCTGTGTTTGAT 57.149 45.000 0.00 0.00 0.00 2.57
357 358 2.851263 AACCGCTCCTGTGTTTGATA 57.149 45.000 0.00 0.00 0.00 2.15
358 359 3.350219 AACCGCTCCTGTGTTTGATAT 57.650 42.857 0.00 0.00 0.00 1.63
359 360 4.481368 AACCGCTCCTGTGTTTGATATA 57.519 40.909 0.00 0.00 0.00 0.86
360 361 4.689612 ACCGCTCCTGTGTTTGATATAT 57.310 40.909 0.00 0.00 0.00 0.86
418 419 5.379732 TTGCGTATGATATCGTCCACATA 57.620 39.130 0.00 0.00 0.00 2.29
422 423 6.127730 TGCGTATGATATCGTCCACATATTCT 60.128 38.462 0.00 0.00 0.00 2.40
423 424 6.197282 GCGTATGATATCGTCCACATATTCTG 59.803 42.308 0.00 0.00 0.00 3.02
424 425 7.472543 CGTATGATATCGTCCACATATTCTGA 58.527 38.462 0.00 0.00 0.00 3.27
425 426 7.641802 CGTATGATATCGTCCACATATTCTGAG 59.358 40.741 0.00 0.00 0.00 3.35
426 427 6.901081 TGATATCGTCCACATATTCTGAGT 57.099 37.500 0.00 0.00 0.00 3.41
427 428 7.290110 TGATATCGTCCACATATTCTGAGTT 57.710 36.000 0.00 0.00 0.00 3.01
428 429 7.147976 TGATATCGTCCACATATTCTGAGTTG 58.852 38.462 0.00 0.00 0.00 3.16
621 705 1.283793 GTGAACTGCAGCGCAACAT 59.716 52.632 15.27 0.00 38.41 2.71
857 941 8.601845 ATTCGGTTAGCTTGCTTTTTAAAAAT 57.398 26.923 13.55 1.13 0.00 1.82
926 1010 7.116805 CCTTATGTGTTTTTCCAGCTGATTTTC 59.883 37.037 17.39 1.64 0.00 2.29
998 1082 4.356405 TTTTGAGAGAGAAGCATGACCA 57.644 40.909 0.00 0.00 0.00 4.02
1028 1112 4.764771 TGGGCTCATTGGGCTGGC 62.765 66.667 8.71 0.00 0.00 4.85
1032 1116 1.547472 GGCTCATTGGGCTGGCTTTT 61.547 55.000 8.71 0.00 0.00 2.27
1100 1184 1.333177 TCCAAAACCCAATTCCCACG 58.667 50.000 0.00 0.00 0.00 4.94
1103 1187 1.899142 CAAAACCCAATTCCCACGGAT 59.101 47.619 0.00 0.00 0.00 4.18
1112 1196 1.043116 TTCCCACGGATCATCGCTCT 61.043 55.000 0.00 0.00 0.00 4.09
1666 1750 2.190578 CCGTGATCAAGGGAGGGC 59.809 66.667 18.99 0.00 35.72 5.19
1740 1824 1.852633 AGGTCGTCATGGACTGATCA 58.147 50.000 0.00 0.00 35.97 2.92
1770 1854 4.305769 CATTTCGAGGTGAGATGAGATCC 58.694 47.826 0.00 0.00 40.71 3.36
1773 1857 2.711547 TCGAGGTGAGATGAGATCCCTA 59.288 50.000 0.00 0.00 0.00 3.53
1775 1859 3.443329 CGAGGTGAGATGAGATCCCTATG 59.557 52.174 0.00 0.00 0.00 2.23
1781 1865 1.480137 GATGAGATCCCTATGGCGGAG 59.520 57.143 0.00 0.00 31.41 4.63
1839 1923 5.422666 TGACTTGCTGTAGTGAAATTGTG 57.577 39.130 0.00 0.00 0.00 3.33
1854 1938 2.957402 TTGTGGAGAAACTGATGGCT 57.043 45.000 0.00 0.00 0.00 4.75
1859 1943 2.373169 TGGAGAAACTGATGGCTCTGTT 59.627 45.455 0.00 4.32 43.09 3.16
1944 2120 4.946445 TGCAATGTGTGACATTTGATTGT 58.054 34.783 13.26 0.00 45.80 2.71
1945 2121 4.745620 TGCAATGTGTGACATTTGATTGTG 59.254 37.500 13.26 0.00 45.80 3.33
1954 2130 5.514914 GTGACATTTGATTGTGTTGTTTCGT 59.485 36.000 0.00 0.00 0.00 3.85
2034 2210 5.769662 ACTGTCCATTTTATTCAGCAAGTCA 59.230 36.000 0.00 0.00 0.00 3.41
2040 2216 8.855110 TCCATTTTATTCAGCAAGTCAAGTTAA 58.145 29.630 0.00 0.00 0.00 2.01
2063 2239 6.091123 ACGATTTTAGACGTAGATGCAAAC 57.909 37.500 0.00 0.00 40.92 2.93
2081 2257 4.625742 GCAAACGTGATCTACTTTCTGCTA 59.374 41.667 0.00 0.00 30.05 3.49
2093 2269 5.604758 ACTTTCTGCTATGCTCTGTATGA 57.395 39.130 0.00 0.00 0.00 2.15
2096 2272 6.482641 ACTTTCTGCTATGCTCTGTATGAATG 59.517 38.462 0.00 0.00 0.00 2.67
2098 2274 6.356186 TCTGCTATGCTCTGTATGAATGAT 57.644 37.500 0.00 0.00 0.00 2.45
2100 2276 7.899973 TCTGCTATGCTCTGTATGAATGATAA 58.100 34.615 0.00 0.00 0.00 1.75
2101 2277 7.816513 TCTGCTATGCTCTGTATGAATGATAAC 59.183 37.037 0.00 0.00 0.00 1.89
2103 2279 8.098912 TGCTATGCTCTGTATGAATGATAACAT 58.901 33.333 0.00 0.00 38.50 2.71
2104 2280 9.591792 GCTATGCTCTGTATGAATGATAACATA 57.408 33.333 0.00 0.00 35.50 2.29
2106 2282 7.873739 TGCTCTGTATGAATGATAACATACG 57.126 36.000 13.70 10.37 46.53 3.06
2107 2283 7.433680 TGCTCTGTATGAATGATAACATACGT 58.566 34.615 13.70 0.00 46.53 3.57
2108 2284 7.382218 TGCTCTGTATGAATGATAACATACGTG 59.618 37.037 0.00 10.68 46.53 4.49
2121 2297 3.031736 ACATACGTGGCTCTACCTTGAT 58.968 45.455 0.00 0.00 40.22 2.57
2131 2307 3.935828 GCTCTACCTTGATTGGAACTGAC 59.064 47.826 0.00 0.00 0.00 3.51
2149 2325 1.940613 GACTCCTTGTGTGTTGGTGTC 59.059 52.381 0.00 0.00 37.26 3.67
2152 2328 3.131396 CTCCTTGTGTGTTGGTGTCTAC 58.869 50.000 0.00 0.00 0.00 2.59
2160 2336 6.174760 TGTGTGTTGGTGTCTACTAGTTTTT 58.825 36.000 0.00 0.00 0.00 1.94
2184 2361 8.659925 TTTTTATCTGCACACATCACAAAATT 57.340 26.923 0.00 0.00 0.00 1.82
2188 2365 2.620585 TGCACACATCACAAAATTCGGA 59.379 40.909 0.00 0.00 0.00 4.55
2194 2371 5.185635 ACACATCACAAAATTCGGATTCCAT 59.814 36.000 3.09 0.00 0.00 3.41
2207 2384 9.759473 AATTCGGATTCCATTATTCCATAGAAT 57.241 29.630 3.09 0.00 44.95 2.40
2208 2385 8.792830 TTCGGATTCCATTATTCCATAGAATC 57.207 34.615 3.09 0.00 41.91 2.52
2216 2393 7.667219 TCCATTATTCCATAGAATCAAGGAAGC 59.333 37.037 0.00 0.00 42.84 3.86
2218 2395 8.512956 CATTATTCCATAGAATCAAGGAAGCAG 58.487 37.037 0.00 0.00 42.84 4.24
2298 2475 9.283768 TGAATGTATGAACCATATGATTACCAC 57.716 33.333 3.65 0.00 0.00 4.16
2325 2502 2.397751 GCTGCGAGCATTGTGGTAT 58.602 52.632 0.00 0.00 41.89 2.73
2326 2503 0.734889 GCTGCGAGCATTGTGGTATT 59.265 50.000 0.00 0.00 41.89 1.89
2329 2506 1.472082 TGCGAGCATTGTGGTATTTGG 59.528 47.619 0.00 0.00 0.00 3.28
2376 2553 7.439056 CAGGTTCAAAGTTTTTCATAATGCTGT 59.561 33.333 0.00 0.00 0.00 4.40
2393 2570 4.759782 TGCTGTATTCTCTTAGTTGCCTC 58.240 43.478 0.00 0.00 0.00 4.70
2478 2657 9.773328 TTTAAAAGATGAGATAAGAAACATGCG 57.227 29.630 0.00 0.00 0.00 4.73
2490 2669 3.254166 AGAAACATGCGCTGAAATGACTT 59.746 39.130 9.73 3.34 0.00 3.01
2491 2670 2.907910 ACATGCGCTGAAATGACTTC 57.092 45.000 9.73 0.00 34.31 3.01
2496 2675 1.129437 GCGCTGAAATGACTTCTGACC 59.871 52.381 0.00 0.00 35.54 4.02
2506 2685 1.129437 GACTTCTGACCGCAATTGAGC 59.871 52.381 10.34 0.00 0.00 4.26
2515 2694 1.202114 CCGCAATTGAGCTGCCTTTTA 59.798 47.619 10.34 0.00 36.40 1.52
2518 2697 3.305094 CGCAATTGAGCTGCCTTTTATTG 59.695 43.478 10.34 1.54 36.40 1.90
2519 2698 4.497300 GCAATTGAGCTGCCTTTTATTGA 58.503 39.130 10.34 0.00 33.51 2.57
2527 2706 5.482006 AGCTGCCTTTTATTGATTTTGGAC 58.518 37.500 0.00 0.00 0.00 4.02
2528 2707 5.246883 AGCTGCCTTTTATTGATTTTGGACT 59.753 36.000 0.00 0.00 0.00 3.85
2529 2708 5.349543 GCTGCCTTTTATTGATTTTGGACTG 59.650 40.000 0.00 0.00 0.00 3.51
2571 2752 5.625197 GCATGCATTTGGTTCCTTGTTAGAT 60.625 40.000 14.21 0.00 0.00 1.98
2584 2765 4.563580 CCTTGTTAGATGTACTGTGGTGCT 60.564 45.833 0.00 0.00 0.00 4.40
2585 2766 4.617253 TGTTAGATGTACTGTGGTGCTT 57.383 40.909 0.00 0.00 0.00 3.91
2586 2767 4.314961 TGTTAGATGTACTGTGGTGCTTG 58.685 43.478 0.00 0.00 0.00 4.01
2587 2768 1.813513 AGATGTACTGTGGTGCTTGC 58.186 50.000 0.00 0.00 0.00 4.01
2588 2769 1.072173 AGATGTACTGTGGTGCTTGCA 59.928 47.619 0.00 0.00 0.00 4.08
2589 2770 1.466167 GATGTACTGTGGTGCTTGCAG 59.534 52.381 0.00 0.00 36.41 4.41
2625 2838 4.527944 TCAAGTTTGGTGTAATGTGGTGA 58.472 39.130 0.00 0.00 0.00 4.02
2638 2851 3.586470 TGTGGTGACCAGTTAACCAAT 57.414 42.857 3.58 0.00 45.26 3.16
2656 2869 6.870971 ACCAATTACAGATTTGTACAACGT 57.129 33.333 8.07 6.13 39.44 3.99
2719 3048 5.065218 ACATTCACATATCTCGGAGCAAAAC 59.935 40.000 0.00 0.00 0.00 2.43
2722 3051 2.093658 ACATATCTCGGAGCAAAACGGT 60.094 45.455 0.00 0.00 0.00 4.83
2723 3052 3.131577 ACATATCTCGGAGCAAAACGGTA 59.868 43.478 0.00 0.00 0.00 4.02
2724 3053 2.295253 ATCTCGGAGCAAAACGGTAG 57.705 50.000 0.00 0.00 0.00 3.18
2727 3056 2.036217 TCTCGGAGCAAAACGGTAGAAA 59.964 45.455 0.00 0.00 0.00 2.52
2728 3057 3.000727 CTCGGAGCAAAACGGTAGAAAT 58.999 45.455 0.00 0.00 0.00 2.17
2729 3058 4.082081 TCTCGGAGCAAAACGGTAGAAATA 60.082 41.667 0.00 0.00 0.00 1.40
2730 3059 4.567971 TCGGAGCAAAACGGTAGAAATAA 58.432 39.130 0.00 0.00 0.00 1.40
2731 3060 4.996122 TCGGAGCAAAACGGTAGAAATAAA 59.004 37.500 0.00 0.00 0.00 1.40
2732 3061 5.084055 CGGAGCAAAACGGTAGAAATAAAC 58.916 41.667 0.00 0.00 0.00 2.01
2733 3062 5.106830 CGGAGCAAAACGGTAGAAATAAACT 60.107 40.000 0.00 0.00 0.00 2.66
2734 3063 6.312487 GGAGCAAAACGGTAGAAATAAACTC 58.688 40.000 0.00 0.00 0.00 3.01
2735 3064 6.250344 AGCAAAACGGTAGAAATAAACTCC 57.750 37.500 0.00 0.00 0.00 3.85
2736 3065 6.002082 AGCAAAACGGTAGAAATAAACTCCT 58.998 36.000 0.00 0.00 0.00 3.69
2737 3066 6.148976 AGCAAAACGGTAGAAATAAACTCCTC 59.851 38.462 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.899661 TGGCAAATTAGAGTTGTATATACTTGT 57.100 29.630 13.89 1.92 0.00 3.16
29 30 9.777297 AACAGTCTTTAAACATAATGGCAAATT 57.223 25.926 0.00 0.00 0.00 1.82
30 31 9.777297 AAACAGTCTTTAAACATAATGGCAAAT 57.223 25.926 0.00 0.00 0.00 2.32
53 54 9.884465 GCAACATCTATCAAAGGACATATAAAC 57.116 33.333 0.00 0.00 0.00 2.01
54 55 9.625747 TGCAACATCTATCAAAGGACATATAAA 57.374 29.630 0.00 0.00 0.00 1.40
55 56 9.625747 TTGCAACATCTATCAAAGGACATATAA 57.374 29.630 0.00 0.00 0.00 0.98
56 57 9.625747 TTTGCAACATCTATCAAAGGACATATA 57.374 29.630 0.00 0.00 0.00 0.86
57 58 8.523915 TTTGCAACATCTATCAAAGGACATAT 57.476 30.769 0.00 0.00 0.00 1.78
58 59 7.936496 TTTGCAACATCTATCAAAGGACATA 57.064 32.000 0.00 0.00 0.00 2.29
178 179 1.717645 CACGCAAAGCAAAAGCTCATC 59.282 47.619 0.00 0.00 0.00 2.92
209 210 6.258507 AGGACTGCAAATGAAAAATTCACAAC 59.741 34.615 0.00 0.00 43.48 3.32
312 313 1.345715 GGATGGGGGTGGGTACAGAG 61.346 65.000 0.00 0.00 0.00 3.35
382 383 5.242434 TCATACGCAAATCTGGTAAGTGTT 58.758 37.500 0.00 0.00 0.00 3.32
418 419 5.012458 TCCATCAGAACTCACAACTCAGAAT 59.988 40.000 0.00 0.00 0.00 2.40
422 423 4.503817 CCTTCCATCAGAACTCACAACTCA 60.504 45.833 0.00 0.00 0.00 3.41
423 424 3.999663 CCTTCCATCAGAACTCACAACTC 59.000 47.826 0.00 0.00 0.00 3.01
424 425 3.648067 TCCTTCCATCAGAACTCACAACT 59.352 43.478 0.00 0.00 0.00 3.16
425 426 3.999663 CTCCTTCCATCAGAACTCACAAC 59.000 47.826 0.00 0.00 0.00 3.32
426 427 3.903714 TCTCCTTCCATCAGAACTCACAA 59.096 43.478 0.00 0.00 0.00 3.33
427 428 3.510459 TCTCCTTCCATCAGAACTCACA 58.490 45.455 0.00 0.00 0.00 3.58
428 429 3.513515 ACTCTCCTTCCATCAGAACTCAC 59.486 47.826 0.00 0.00 0.00 3.51
484 485 0.548031 TCATCTGACATTGGCTCCCC 59.452 55.000 0.00 0.00 0.00 4.81
485 486 2.019984 GTTCATCTGACATTGGCTCCC 58.980 52.381 0.00 0.00 0.00 4.30
491 492 4.713824 ATGCTTGGTTCATCTGACATTG 57.286 40.909 0.00 0.00 0.00 2.82
613 697 3.354089 AGGCATATACAAATGTTGCGC 57.646 42.857 0.00 0.00 0.00 6.09
900 984 5.649782 ATCAGCTGGAAAAACACATAAGG 57.350 39.130 15.13 0.00 0.00 2.69
901 985 7.652909 TGAAAATCAGCTGGAAAAACACATAAG 59.347 33.333 15.13 0.00 0.00 1.73
902 986 7.495901 TGAAAATCAGCTGGAAAAACACATAA 58.504 30.769 15.13 0.00 0.00 1.90
904 988 5.916318 TGAAAATCAGCTGGAAAAACACAT 58.084 33.333 15.13 0.00 0.00 3.21
905 989 5.336150 TGAAAATCAGCTGGAAAAACACA 57.664 34.783 15.13 2.10 0.00 3.72
906 990 6.479660 TCAATGAAAATCAGCTGGAAAAACAC 59.520 34.615 15.13 0.00 0.00 3.32
907 991 6.580788 TCAATGAAAATCAGCTGGAAAAACA 58.419 32.000 15.13 8.22 0.00 2.83
908 992 7.662604 ATCAATGAAAATCAGCTGGAAAAAC 57.337 32.000 15.13 2.55 0.00 2.43
909 993 8.680039 AAATCAATGAAAATCAGCTGGAAAAA 57.320 26.923 15.13 0.00 0.00 1.94
947 1031 9.512588 AAAGCAGCAGTAGCATATAATCTAAAT 57.487 29.630 0.00 0.00 45.49 1.40
960 1044 6.381801 TCTCAAAAATTAAAGCAGCAGTAGC 58.618 36.000 0.00 0.00 42.56 3.58
998 1082 3.719268 TGAGCCCACTATGTTTCATGT 57.281 42.857 0.00 0.00 0.00 3.21
1010 1094 2.757099 CCAGCCCAATGAGCCCAC 60.757 66.667 0.00 0.00 0.00 4.61
1028 1112 6.043243 TCTGGACTTAGGCCCATATAGAAAAG 59.957 42.308 0.00 0.00 0.00 2.27
1032 1116 4.759793 TCTGGACTTAGGCCCATATAGA 57.240 45.455 0.00 0.00 0.00 1.98
1100 1184 0.599728 GCCAGTGAGAGCGATGATCC 60.600 60.000 0.00 0.00 0.00 3.36
1103 1187 2.725312 GGGCCAGTGAGAGCGATGA 61.725 63.158 4.39 0.00 0.00 2.92
1112 1196 2.409984 TAGGGTTCTGGGGCCAGTGA 62.410 60.000 4.39 0.00 43.96 3.41
1596 1680 3.358076 GAGCCCGAGGTCCGTGAAG 62.358 68.421 0.00 0.00 34.29 3.02
1666 1750 2.993853 GGCCTCCTCCTTGGACAG 59.006 66.667 0.00 0.00 40.56 3.51
1740 1824 2.273449 CCTCGAAATGCAGGGGCT 59.727 61.111 0.00 0.00 41.91 5.19
1770 1854 0.463833 GTTCCCAACTCCGCCATAGG 60.464 60.000 0.00 0.00 0.00 2.57
1773 1857 3.495729 AGTTCCCAACTCCGCCAT 58.504 55.556 0.00 0.00 37.02 4.40
1781 1865 2.206576 AGCCAATCTGAGTTCCCAAC 57.793 50.000 0.00 0.00 0.00 3.77
1839 1923 2.746362 CAACAGAGCCATCAGTTTCTCC 59.254 50.000 0.00 0.00 33.30 3.71
1854 1938 5.245301 ACAACTACAGTATACAGGCAACAGA 59.755 40.000 5.50 0.00 41.41 3.41
1859 1943 5.718130 AGGTAACAACTACAGTATACAGGCA 59.282 40.000 5.50 0.00 41.41 4.75
1864 1948 9.129532 ACATCCTAGGTAACAACTACAGTATAC 57.870 37.037 9.08 0.00 41.41 1.47
1870 1954 7.820872 GCTAAAACATCCTAGGTAACAACTACA 59.179 37.037 9.08 0.00 41.41 2.74
1944 2120 4.699637 ACTAGGATCACAACGAAACAACA 58.300 39.130 0.00 0.00 0.00 3.33
1945 2121 6.347160 GGTTACTAGGATCACAACGAAACAAC 60.347 42.308 0.00 0.00 0.00 3.32
1954 2130 3.844211 AGCAAGGGTTACTAGGATCACAA 59.156 43.478 0.00 0.00 0.00 3.33
2002 2178 9.423061 GCTGAATAAAATGGACAGTTGTAAATT 57.577 29.630 0.00 0.00 0.00 1.82
2034 2210 7.543172 TGCATCTACGTCTAAAATCGTTAACTT 59.457 33.333 3.71 0.00 40.70 2.66
2040 2216 5.220154 CGTTTGCATCTACGTCTAAAATCGT 60.220 40.000 0.00 0.00 42.82 3.73
2063 2239 4.615949 AGCATAGCAGAAAGTAGATCACG 58.384 43.478 0.00 0.00 0.00 4.35
2067 2243 5.867903 ACAGAGCATAGCAGAAAGTAGAT 57.132 39.130 0.00 0.00 0.00 1.98
2081 2257 8.090831 ACGTATGTTATCATTCATACAGAGCAT 58.909 33.333 13.24 0.00 43.51 3.79
2093 2269 5.304614 AGGTAGAGCCACGTATGTTATCATT 59.695 40.000 0.00 0.00 40.61 2.57
2096 2272 4.850347 AGGTAGAGCCACGTATGTTATC 57.150 45.455 0.00 0.00 40.61 1.75
2098 2274 4.018490 TCAAGGTAGAGCCACGTATGTTA 58.982 43.478 0.00 0.00 40.61 2.41
2100 2276 2.453521 TCAAGGTAGAGCCACGTATGT 58.546 47.619 0.00 0.00 40.61 2.29
2101 2277 3.735237 ATCAAGGTAGAGCCACGTATG 57.265 47.619 0.00 0.00 40.61 2.39
2103 2279 2.167693 CCAATCAAGGTAGAGCCACGTA 59.832 50.000 0.00 0.00 40.61 3.57
2104 2280 1.066143 CCAATCAAGGTAGAGCCACGT 60.066 52.381 0.00 0.00 40.61 4.49
2105 2281 1.207089 TCCAATCAAGGTAGAGCCACG 59.793 52.381 0.00 0.00 40.61 4.94
2106 2282 3.010420 GTTCCAATCAAGGTAGAGCCAC 58.990 50.000 0.00 0.00 40.61 5.01
2107 2283 2.912956 AGTTCCAATCAAGGTAGAGCCA 59.087 45.455 0.00 0.00 40.61 4.75
2108 2284 3.055094 TCAGTTCCAATCAAGGTAGAGCC 60.055 47.826 0.00 0.00 37.58 4.70
2121 2297 2.238646 ACACACAAGGAGTCAGTTCCAA 59.761 45.455 0.00 0.00 39.84 3.53
2131 2307 2.332063 AGACACCAACACACAAGGAG 57.668 50.000 0.00 0.00 0.00 3.69
2160 2336 7.114670 CGAATTTTGTGATGTGTGCAGATAAAA 59.885 33.333 0.00 0.00 0.00 1.52
2163 2339 5.391843 CCGAATTTTGTGATGTGTGCAGATA 60.392 40.000 0.00 0.00 0.00 1.98
2164 2340 4.478699 CGAATTTTGTGATGTGTGCAGAT 58.521 39.130 0.00 0.00 0.00 2.90
2167 2343 2.620585 TCCGAATTTTGTGATGTGTGCA 59.379 40.909 0.00 0.00 0.00 4.57
2168 2344 3.281341 TCCGAATTTTGTGATGTGTGC 57.719 42.857 0.00 0.00 0.00 4.57
2182 2359 9.401058 GATTCTATGGAATAATGGAATCCGAAT 57.599 33.333 4.04 0.00 43.46 3.34
2183 2360 8.382405 TGATTCTATGGAATAATGGAATCCGAA 58.618 33.333 16.04 1.36 46.24 4.30
2184 2361 7.917003 TGATTCTATGGAATAATGGAATCCGA 58.083 34.615 16.04 1.90 46.24 4.55
2194 2371 7.577303 ACTGCTTCCTTGATTCTATGGAATAA 58.423 34.615 4.04 0.00 41.68 1.40
2207 2384 1.761449 TTGCACAACTGCTTCCTTGA 58.239 45.000 0.00 0.00 44.57 3.02
2208 2385 2.806608 ATTGCACAACTGCTTCCTTG 57.193 45.000 0.00 0.00 44.57 3.61
2216 2393 3.835378 TGCAGACATATTGCACAACTG 57.165 42.857 0.00 0.00 45.89 3.16
2237 2414 9.394767 TGCAGATAAGAACAGCAGATTTAAATA 57.605 29.630 0.00 0.00 0.00 1.40
2271 2448 9.859152 TGGTAATCATATGGTTCATACATTCAA 57.141 29.630 4.00 0.00 0.00 2.69
2298 2475 2.099062 GCTCGCAGCAATCAACCG 59.901 61.111 0.00 0.00 41.89 4.44
2323 2500 4.832266 AGGTTCAATTGACACTGCCAAATA 59.168 37.500 7.89 0.00 0.00 1.40
2325 2502 3.030291 AGGTTCAATTGACACTGCCAAA 58.970 40.909 7.89 0.00 0.00 3.28
2326 2503 2.665165 AGGTTCAATTGACACTGCCAA 58.335 42.857 7.89 0.00 0.00 4.52
2329 2506 4.681744 TGAAAAGGTTCAATTGACACTGC 58.318 39.130 7.89 4.07 40.87 4.40
2393 2570 9.918630 AAAATTCATCAACAAAATAGGAGTGAG 57.081 29.630 0.00 0.00 0.00 3.51
2459 2638 4.509230 TCAGCGCATGTTTCTTATCTCATC 59.491 41.667 11.47 0.00 0.00 2.92
2462 2641 4.864916 TTCAGCGCATGTTTCTTATCTC 57.135 40.909 11.47 0.00 0.00 2.75
2478 2657 1.129437 GCGGTCAGAAGTCATTTCAGC 59.871 52.381 0.00 0.00 38.31 4.26
2490 2669 1.300971 GCAGCTCAATTGCGGTCAGA 61.301 55.000 0.00 0.00 38.13 3.27
2491 2670 1.136147 GCAGCTCAATTGCGGTCAG 59.864 57.895 0.00 0.00 38.13 3.51
2496 2675 2.634982 TAAAAGGCAGCTCAATTGCG 57.365 45.000 0.00 0.00 42.42 4.85
2506 2685 6.690530 TCAGTCCAAAATCAATAAAAGGCAG 58.309 36.000 0.00 0.00 0.00 4.85
2571 2752 0.180171 ACTGCAAGCACCACAGTACA 59.820 50.000 0.00 0.00 42.65 2.90
2625 2838 7.833285 ACAAATCTGTAATTGGTTAACTGGT 57.167 32.000 5.42 0.00 32.54 4.00
2638 2851 9.152595 TGCATAATACGTTGTACAAATCTGTAA 57.847 29.630 10.51 0.00 39.75 2.41
2653 2866 3.458189 GCTGGAGAACTGCATAATACGT 58.542 45.455 0.00 0.00 42.90 3.57
2662 2875 3.505293 AGAAGAATTTGCTGGAGAACTGC 59.495 43.478 0.00 0.00 43.59 4.40
2700 3029 2.285220 CCGTTTTGCTCCGAGATATGTG 59.715 50.000 0.00 0.00 0.00 3.21
2705 3034 1.822990 TCTACCGTTTTGCTCCGAGAT 59.177 47.619 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.