Multiple sequence alignment - TraesCS7A01G497700

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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 TraesCS7A01G497700 chr7A 100.000 4301 0 0 1 4301 688344417 688348717 0.000000e+00 7943.0
1 TraesCS7A01G497700 chr7A 87.916 1804 178 14 983 2765 702610774 702612558 0.000000e+00 2087.0
2 TraesCS7A01G497700 chr7A 82.619 1703 241 33 983 2651 702407443 702409124 0.000000e+00 1454.0
3 TraesCS7A01G497700 chr7A 80.854 1311 187 31 1365 2651 702237726 702238996 0.000000e+00 972.0
4 TraesCS7A01G497700 chr7A 83.444 755 98 11 2322 3052 702984045 702983294 0.000000e+00 676.0
5 TraesCS7A01G497700 chr7A 82.857 350 38 17 3282 3617 702620741 702621082 1.170000e-75 294.0
6 TraesCS7A01G497700 chr7A 81.166 223 34 7 510 729 702237255 702237472 5.720000e-39 172.0
7 TraesCS7A01G497700 chr7A 79.231 260 43 8 2596 2848 703545801 703546056 2.060000e-38 171.0
8 TraesCS7A01G497700 chr7A 89.474 76 5 2 3081 3156 704265402 704265474 4.580000e-15 93.5
9 TraesCS7A01G497700 chr7A 87.500 72 8 1 4161 4231 352910450 352910379 9.910000e-12 82.4
10 TraesCS7A01G497700 chr7B 92.810 3185 167 22 934 4093 672770048 672773195 0.000000e+00 4556.0
11 TraesCS7A01G497700 chr7B 81.684 1698 218 43 983 2651 701457534 701459167 0.000000e+00 1327.0
12 TraesCS7A01G497700 chr7B 81.766 691 77 29 4 688 672768034 672768681 2.280000e-147 532.0
13 TraesCS7A01G497700 chr7B 80.029 696 103 23 1337 2015 701646000 701646676 2.330000e-132 483.0
14 TraesCS7A01G497700 chr7B 83.224 459 50 14 3282 3722 701460138 701460587 3.120000e-106 396.0
15 TraesCS7A01G497700 chr7B 92.857 42 3 0 792 833 672768740 672768781 1.290000e-05 62.1
16 TraesCS7A01G497700 chr7D 95.149 1711 50 14 859 2564 595346602 595348284 0.000000e+00 2669.0
17 TraesCS7A01G497700 chr7D 92.927 1626 72 19 1703 3324 595348282 595349868 0.000000e+00 2326.0
18 TraesCS7A01G497700 chr7D 88.040 1806 178 20 983 2759 612403684 612405480 0.000000e+00 2104.0
19 TraesCS7A01G497700 chr7D 81.704 1995 265 61 1333 3283 612428100 612430038 0.000000e+00 1570.0
20 TraesCS7A01G497700 chr7D 82.943 1706 231 32 983 2651 612325796 612327478 0.000000e+00 1483.0
21 TraesCS7A01G497700 chr7D 81.877 1694 226 34 986 2651 611857524 611855884 0.000000e+00 1352.0
22 TraesCS7A01G497700 chr7D 93.333 780 44 4 3528 4301 595350066 595350843 0.000000e+00 1146.0
23 TraesCS7A01G497700 chr7D 91.357 833 45 10 1 833 595345540 595346345 0.000000e+00 1114.0
24 TraesCS7A01G497700 chr7D 80.916 1310 180 35 1365 2645 611871144 611869876 0.000000e+00 970.0
25 TraesCS7A01G497700 chr7D 78.081 844 156 22 2022 2848 612708062 612708893 1.380000e-139 507.0
26 TraesCS7A01G497700 chr7D 82.713 457 51 16 3285 3722 611854901 611854454 8.730000e-102 381.0
27 TraesCS7A01G497700 chr7D 81.779 461 55 16 3282 3722 612289314 612289765 4.090000e-95 359.0
28 TraesCS7A01G497700 chr7D 83.133 415 45 18 2800 3193 612405481 612405891 5.290000e-94 355.0
29 TraesCS7A01G497700 chr7D 79.159 523 57 27 3285 3791 611868886 611868400 8.980000e-82 315.0
30 TraesCS7A01G497700 chr7D 77.660 564 59 31 3284 3818 612328404 612328929 9.110000e-72 281.0
31 TraesCS7A01G497700 chr7D 94.220 173 10 0 3392 3564 595349892 595350064 9.170000e-67 265.0
32 TraesCS7A01G497700 chr7D 80.982 326 44 11 3282 3596 612430118 612430436 4.300000e-60 243.0
33 TraesCS7A01G497700 chr7D 82.909 275 38 5 213 487 612284616 612284881 5.560000e-59 239.0
34 TraesCS7A01G497700 chr7D 84.906 212 26 6 6 214 612050399 612050607 4.360000e-50 209.0
35 TraesCS7A01G497700 chr7D 81.860 215 32 6 510 721 612284872 612285082 1.590000e-39 174.0
36 TraesCS7A01G497700 chr7D 84.492 187 16 8 3598 3774 612406490 612406673 5.720000e-39 172.0
37 TraesCS7A01G497700 chr7D 87.407 135 17 0 3190 3324 612405959 612406093 5.760000e-34 156.0
38 TraesCS7A01G497700 chr7D 76.235 324 57 15 2832 3143 611652406 611652091 2.070000e-33 154.0
39 TraesCS7A01G497700 chrUn 84.590 597 53 16 983 1570 87707725 87708291 1.350000e-154 556.0
40 TraesCS7A01G497700 chrUn 84.027 601 61 15 983 1573 324304903 324304328 2.920000e-151 545.0
41 TraesCS7A01G497700 chrUn 83.860 601 62 15 983 1573 324358518 324357943 1.360000e-149 540.0
42 TraesCS7A01G497700 chrUn 83.591 518 50 15 1066 1573 445548116 445547624 1.820000e-123 453.0
43 TraesCS7A01G497700 chrUn 81.978 455 56 14 3282 3717 368812154 368812601 3.160000e-96 363.0
44 TraesCS7A01G497700 chrUn 88.034 117 10 4 100 214 302634830 302634944 7.500000e-28 135.0
45 TraesCS7A01G497700 chr5B 72.956 1468 295 62 1067 2503 689180330 689178934 6.650000e-113 418.0
46 TraesCS7A01G497700 chr5B 88.889 72 7 1 4161 4231 96325906 96325835 2.130000e-13 87.9
47 TraesCS7A01G497700 chr6D 89.189 74 5 3 4160 4231 422072020 422072092 5.920000e-14 89.8
48 TraesCS7A01G497700 chr6D 87.500 72 8 1 4161 4231 171376523 171376594 9.910000e-12 82.4
49 TraesCS7A01G497700 chr2D 88.889 72 7 1 4161 4231 332587134 332587063 2.130000e-13 87.9
50 TraesCS7A01G497700 chr2B 87.671 73 8 1 4160 4231 201440277 201440349 2.760000e-12 84.2
51 TraesCS7A01G497700 chr1B 87.013 77 2 5 4159 4231 137448071 137448143 3.570000e-11 80.5
52 TraesCS7A01G497700 chr3D 82.222 90 13 3 4144 4231 288540212 288540300 1.660000e-09 75.0


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 TraesCS7A01G497700 chr7A 688344417 688348717 4300 False 7943.00 7943 100.000000 1 4301 1 chr7A.!!$F1 4300
1 TraesCS7A01G497700 chr7A 702610774 702612558 1784 False 2087.00 2087 87.916000 983 2765 1 chr7A.!!$F3 1782
2 TraesCS7A01G497700 chr7A 702407443 702409124 1681 False 1454.00 1454 82.619000 983 2651 1 chr7A.!!$F2 1668
3 TraesCS7A01G497700 chr7A 702983294 702984045 751 True 676.00 676 83.444000 2322 3052 1 chr7A.!!$R2 730
4 TraesCS7A01G497700 chr7A 702237255 702238996 1741 False 572.00 972 81.010000 510 2651 2 chr7A.!!$F7 2141
5 TraesCS7A01G497700 chr7B 672768034 672773195 5161 False 1716.70 4556 89.144333 4 4093 3 chr7B.!!$F2 4089
6 TraesCS7A01G497700 chr7B 701457534 701460587 3053 False 861.50 1327 82.454000 983 3722 2 chr7B.!!$F3 2739
7 TraesCS7A01G497700 chr7B 701646000 701646676 676 False 483.00 483 80.029000 1337 2015 1 chr7B.!!$F1 678
8 TraesCS7A01G497700 chr7D 595345540 595350843 5303 False 1504.00 2669 93.397200 1 4301 5 chr7D.!!$F4 4300
9 TraesCS7A01G497700 chr7D 612428100 612430436 2336 False 906.50 1570 81.343000 1333 3596 2 chr7D.!!$F8 2263
10 TraesCS7A01G497700 chr7D 612325796 612328929 3133 False 882.00 1483 80.301500 983 3818 2 chr7D.!!$F6 2835
11 TraesCS7A01G497700 chr7D 611854454 611857524 3070 True 866.50 1352 82.295000 986 3722 2 chr7D.!!$R2 2736
12 TraesCS7A01G497700 chr7D 612403684 612406673 2989 False 696.75 2104 85.768000 983 3774 4 chr7D.!!$F7 2791
13 TraesCS7A01G497700 chr7D 611868400 611871144 2744 True 642.50 970 80.037500 1365 3791 2 chr7D.!!$R3 2426
14 TraesCS7A01G497700 chr7D 612708062 612708893 831 False 507.00 507 78.081000 2022 2848 1 chr7D.!!$F3 826
15 TraesCS7A01G497700 chrUn 87707725 87708291 566 False 556.00 556 84.590000 983 1570 1 chrUn.!!$F1 587
16 TraesCS7A01G497700 chrUn 324304328 324304903 575 True 545.00 545 84.027000 983 1573 1 chrUn.!!$R1 590
17 TraesCS7A01G497700 chrUn 324357943 324358518 575 True 540.00 540 83.860000 983 1573 1 chrUn.!!$R2 590
18 TraesCS7A01G497700 chr5B 689178934 689180330 1396 True 418.00 418 72.956000 1067 2503 1 chr5B.!!$R2 1436

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
478 480 0.179018 AACTCCTTGACGCTTGCCTT 60.179 50.0 0.00 0.00 0.00 4.35 F
488 490 0.179113 CGCTTGCCTTCCTCTCTCTC 60.179 60.0 0.00 0.00 0.00 3.20 F
1798 3273 0.312102 TAGCACGATGGAGCTGATCG 59.688 55.0 18.73 18.73 46.55 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 2746 0.778078 TCTTGGGGTTGGGATTGGGA 60.778 55.000 0.00 0.0 0.00 4.37 R
1848 3323 1.351683 ACAACATACGGCCCCAAGTAA 59.648 47.619 0.00 0.0 0.00 2.24 R
3797 6866 0.388006 TCGCCATATATCGCACACGG 60.388 55.000 3.17 0.0 40.63 4.94 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
66 67 1.152819 ACCTATGGCGACGGCTAGA 60.153 57.895 22.70 2.30 39.81 2.43
110 112 7.864379 CCAATGCATTGAGTTATCCTACAAATC 59.136 37.037 35.47 0.00 40.14 2.17
167 169 1.389609 AAGTCGTATGTCCCGGCGAT 61.390 55.000 9.30 0.00 34.56 4.58
207 209 0.390472 GTAGCCAGCGACTTTGCTCT 60.390 55.000 0.00 0.00 45.23 4.09
341 343 1.474330 GACCCAAAGGATCGCCATTT 58.526 50.000 0.00 0.00 36.73 2.32
428 430 7.587028 GTGACGATAAATTCTAGTCTTAGGACG 59.413 40.741 0.00 0.00 46.29 4.79
433 435 5.401531 AATTCTAGTCTTAGGACGCAACA 57.598 39.130 0.00 0.00 46.29 3.33
435 437 3.418995 TCTAGTCTTAGGACGCAACACT 58.581 45.455 0.00 0.00 46.29 3.55
436 438 2.440539 AGTCTTAGGACGCAACACTG 57.559 50.000 0.00 0.00 46.29 3.66
459 461 2.660064 GCTCTTCGCCTTCCTCCCA 61.660 63.158 0.00 0.00 0.00 4.37
474 476 0.250295 TCCCAACTCCTTGACGCTTG 60.250 55.000 0.00 0.00 0.00 4.01
478 480 0.179018 AACTCCTTGACGCTTGCCTT 60.179 50.000 0.00 0.00 0.00 4.35
483 485 0.321122 CTTGACGCTTGCCTTCCTCT 60.321 55.000 0.00 0.00 0.00 3.69
484 486 0.320771 TTGACGCTTGCCTTCCTCTC 60.321 55.000 0.00 0.00 0.00 3.20
485 487 1.188219 TGACGCTTGCCTTCCTCTCT 61.188 55.000 0.00 0.00 0.00 3.10
487 489 0.902516 ACGCTTGCCTTCCTCTCTCT 60.903 55.000 0.00 0.00 0.00 3.10
488 490 0.179113 CGCTTGCCTTCCTCTCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
489 491 1.194218 GCTTGCCTTCCTCTCTCTCT 58.806 55.000 0.00 0.00 0.00 3.10
491 493 2.965147 GCTTGCCTTCCTCTCTCTCTAT 59.035 50.000 0.00 0.00 0.00 1.98
492 494 3.005791 GCTTGCCTTCCTCTCTCTCTATC 59.994 52.174 0.00 0.00 0.00 2.08
493 495 4.473444 CTTGCCTTCCTCTCTCTCTATCT 58.527 47.826 0.00 0.00 0.00 1.98
494 496 4.098914 TGCCTTCCTCTCTCTCTATCTC 57.901 50.000 0.00 0.00 0.00 2.75
495 497 3.721575 TGCCTTCCTCTCTCTCTATCTCT 59.278 47.826 0.00 0.00 0.00 3.10
496 498 4.202461 TGCCTTCCTCTCTCTCTATCTCTC 60.202 50.000 0.00 0.00 0.00 3.20
497 499 4.042187 GCCTTCCTCTCTCTCTATCTCTCT 59.958 50.000 0.00 0.00 0.00 3.10
498 500 5.799213 CCTTCCTCTCTCTCTATCTCTCTC 58.201 50.000 0.00 0.00 0.00 3.20
499 501 5.545723 CCTTCCTCTCTCTCTATCTCTCTCT 59.454 48.000 0.00 0.00 0.00 3.10
500 502 6.295575 CCTTCCTCTCTCTCTATCTCTCTCTC 60.296 50.000 0.00 0.00 0.00 3.20
501 503 5.970289 TCCTCTCTCTCTATCTCTCTCTCT 58.030 45.833 0.00 0.00 0.00 3.10
502 504 6.013379 TCCTCTCTCTCTATCTCTCTCTCTC 58.987 48.000 0.00 0.00 0.00 3.20
549 551 3.023832 CCTCCTCCGTTGGCAAATTTAT 58.976 45.455 0.00 0.00 0.00 1.40
689 694 2.356793 CCTCATCCATCGCCTCGC 60.357 66.667 0.00 0.00 0.00 5.03
691 696 3.153781 TCATCCATCGCCTCGCCA 61.154 61.111 0.00 0.00 0.00 5.69
721 738 2.935201 CTCATCTTCTTGCTAGCACACC 59.065 50.000 19.17 0.00 0.00 4.16
730 747 3.064987 CTAGCACACCCCGGACGAG 62.065 68.421 0.73 0.00 0.00 4.18
746 763 1.134530 CGAGGCGCTAAGTCAAGACG 61.135 60.000 7.64 0.00 36.20 4.18
748 765 0.818296 AGGCGCTAAGTCAAGACGAT 59.182 50.000 7.64 0.00 36.20 3.73
751 768 2.464865 GCGCTAAGTCAAGACGATGAT 58.535 47.619 0.00 0.00 36.20 2.45
754 771 4.598062 CGCTAAGTCAAGACGATGATACA 58.402 43.478 0.00 0.00 36.20 2.29
769 786 8.039603 ACGATGATACAAGCTTCATTGTTTTA 57.960 30.769 11.66 0.00 41.91 1.52
833 850 8.815565 TTTTGAGGCAAACTTATATGTCCATA 57.184 30.769 0.00 0.00 32.79 2.74
1684 3159 1.979693 GACGTCAGGGTCAGCTCCT 60.980 63.158 11.55 0.00 36.91 3.69
1701 3176 4.121669 TCGTCGCTGCAGGAGCTC 62.122 66.667 17.12 4.71 46.64 4.09
1798 3273 0.312102 TAGCACGATGGAGCTGATCG 59.688 55.000 18.73 18.73 46.55 3.69
1848 3323 0.324943 AGGTTTCGTGGCACTGCTAT 59.675 50.000 16.72 0.00 0.00 2.97
1902 3386 1.210931 CATCAACAAGGTGCGGCTG 59.789 57.895 0.00 0.00 0.00 4.85
1903 3387 2.629656 ATCAACAAGGTGCGGCTGC 61.630 57.895 11.65 11.65 43.20 5.25
2182 3690 3.791973 TTGGAGCGTTTGTGTTTCATT 57.208 38.095 0.00 0.00 0.00 2.57
2264 4628 3.684788 TCAGCGGTAATTCTTTGCTCTTC 59.315 43.478 0.00 0.00 32.66 2.87
2512 4905 1.070758 TGAAGCTGTCACAAGAGACCC 59.929 52.381 0.00 0.00 37.73 4.46
2651 5256 9.638239 GCATCCTTCTAGATAAAACAGAGATAG 57.362 37.037 0.00 0.00 0.00 2.08
2717 5334 5.913137 TGCCAATTATAGAGTTTGGTTGG 57.087 39.130 3.16 0.00 41.58 3.77
2826 5451 4.804868 TTGAATGGTGGATTGGTTGATG 57.195 40.909 0.00 0.00 0.00 3.07
2871 5497 7.873195 ACTCAGGCTTCCTTATACCTAAATTT 58.127 34.615 0.00 0.00 0.00 1.82
2872 5498 8.336987 ACTCAGGCTTCCTTATACCTAAATTTT 58.663 33.333 0.00 0.00 0.00 1.82
2920 5546 7.775053 TTATTGATCTTGCCCTACTGTTTTT 57.225 32.000 0.00 0.00 0.00 1.94
2944 5570 4.806247 TGTTTGTATTTGGTTTTCTTGGCG 59.194 37.500 0.00 0.00 0.00 5.69
2968 5596 4.002982 TGAAGTTGTCCCATCTGAATTCG 58.997 43.478 0.04 0.00 0.00 3.34
2981 5609 1.604147 GAATTCGTTGGCCTTGGGGG 61.604 60.000 3.32 0.00 38.36 5.40
3055 5722 7.545265 GTCAGCATGTATTCCTTTTTATTTGCA 59.455 33.333 0.00 0.00 37.40 4.08
3057 5724 8.885722 CAGCATGTATTCCTTTTTATTTGCAAT 58.114 29.630 0.00 0.00 0.00 3.56
3099 5766 6.426980 TGCATCAGTATTCAGTAGCAAAAG 57.573 37.500 0.00 0.00 0.00 2.27
3232 6023 7.865706 ACATATAACTCCACATTTCCTTGTC 57.134 36.000 0.00 0.00 0.00 3.18
3352 6311 4.811498 TGTACTAGCCATATACAGGGTGT 58.189 43.478 7.76 6.73 37.45 4.16
3380 6340 8.950210 CAGATAAATCTTGTATGGTTTCTGTGT 58.050 33.333 0.00 0.00 34.22 3.72
3412 6373 7.620880 ACTATTGAAGTTAATGCACTCTACCA 58.379 34.615 0.00 0.00 33.35 3.25
3455 6438 8.849168 TGATTATCATGTTAAGCCTATGGTTTG 58.151 33.333 8.83 0.00 33.46 2.93
3458 6441 6.509418 TCATGTTAAGCCTATGGTTTGAAC 57.491 37.500 0.00 0.00 33.46 3.18
3591 6629 1.347707 AGATGAACCAAACGGCTCTGA 59.652 47.619 0.00 0.00 0.00 3.27
3752 6821 1.966901 ATTGCGTCGATGGCTGGGTA 61.967 55.000 6.79 0.00 0.00 3.69
3767 6836 3.341823 CTGGGTATGAGATATGCAAGGC 58.658 50.000 0.00 0.00 0.00 4.35
3805 6874 4.980903 GCTTGTTGCCCGTGTGCG 62.981 66.667 0.00 0.00 35.15 5.34
3818 6887 1.350193 GTGTGCGATATATGGCGAGG 58.650 55.000 14.08 0.00 33.95 4.63
3912 6981 2.565391 TGGTTATTCGGCTTGAGTGAGA 59.435 45.455 0.00 0.00 0.00 3.27
3948 7017 2.290464 TGAGTTTGTAACACCGTTGGG 58.710 47.619 0.00 0.00 40.11 4.12
3949 7018 1.002142 GAGTTTGTAACACCGTTGGGC 60.002 52.381 0.00 0.00 36.48 5.36
3950 7019 0.739561 GTTTGTAACACCGTTGGGCA 59.260 50.000 0.00 0.00 36.48 5.36
3965 7034 0.669625 GGGCAGTCTGGTACAACGAC 60.670 60.000 1.14 0.00 38.70 4.34
3966 7035 0.317479 GGCAGTCTGGTACAACGACT 59.683 55.000 1.14 0.07 38.70 4.18
3979 7048 0.109873 AACGACTACTCCGCTGAACG 60.110 55.000 0.00 0.00 43.15 3.95
3982 7051 2.209064 GACTACTCCGCTGAACGCCA 62.209 60.000 0.00 0.00 41.76 5.69
4010 7079 5.056480 GCCTTGTAAAATTTTGTGCCTCTT 58.944 37.500 13.76 0.00 0.00 2.85
4048 7117 2.184533 TGTAAGGCTTTCGGATCCTCA 58.815 47.619 10.75 0.00 0.00 3.86
4061 7130 2.948315 GGATCCTCAGAATCCTTTGTGC 59.052 50.000 3.84 0.00 0.00 4.57
4079 7148 1.684450 TGCATGCCCATGAACATCATC 59.316 47.619 16.68 0.00 41.20 2.92
4140 7209 0.541392 AACTGCGGTAGATGATGCCA 59.459 50.000 0.00 0.00 32.03 4.92
4234 7307 8.044908 ACGTTGGTTGTAATAACATCTTAGGAT 58.955 33.333 0.00 0.00 34.97 3.24
4258 7331 5.602561 TGAAGGGAGTAGCATTAGCATCTTA 59.397 40.000 0.00 0.00 45.49 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.700368 CTCCTCTCCCCTGTCTGGA 59.300 63.158 0.00 0.00 38.35 3.86
32 33 2.501610 GTCTCCTCCATGACGCCC 59.498 66.667 0.00 0.00 0.00 6.13
66 67 5.594317 GCATTGGTATTGGGAGACATAAACT 59.406 40.000 0.00 0.00 0.00 2.66
167 169 1.040339 AAAAAGTGCACGAAGGGGCA 61.040 50.000 12.01 0.00 39.47 5.36
207 209 4.191544 CTCATTCCATTAACCGAAGAGCA 58.808 43.478 0.00 0.00 0.00 4.26
253 255 8.277918 AGGAAGATGGAAACTAGCAAAAGATAT 58.722 33.333 0.00 0.00 0.00 1.63
308 310 0.828022 TGGGTCGGCACCTAACTATG 59.172 55.000 0.00 0.00 43.22 2.23
320 322 2.513897 GGCGATCCTTTGGGTCGG 60.514 66.667 19.05 3.48 36.97 4.79
321 323 0.748005 AATGGCGATCCTTTGGGTCG 60.748 55.000 14.19 14.19 38.34 4.79
341 343 2.027285 TCGAGCCATTGGATCAAACTCA 60.027 45.455 20.24 0.00 38.11 3.41
409 411 6.810182 GTGTTGCGTCCTAAGACTAGAATTTA 59.190 38.462 0.00 0.00 41.16 1.40
428 430 0.308993 GAAGAGCCACACAGTGTTGC 59.691 55.000 19.80 19.80 39.08 4.17
459 461 0.179018 AAGGCAAGCGTCAAGGAGTT 60.179 50.000 0.00 0.00 0.00 3.01
474 476 4.042187 AGAGAGATAGAGAGAGAGGAAGGC 59.958 50.000 0.00 0.00 0.00 4.35
478 480 5.970289 AGAGAGAGAGATAGAGAGAGAGGA 58.030 45.833 0.00 0.00 0.00 3.71
483 485 5.970289 AGAGGAGAGAGAGAGATAGAGAGA 58.030 45.833 0.00 0.00 0.00 3.10
484 486 6.015918 AGAGAGGAGAGAGAGAGATAGAGAG 58.984 48.000 0.00 0.00 0.00 3.20
485 487 5.970289 AGAGAGGAGAGAGAGAGATAGAGA 58.030 45.833 0.00 0.00 0.00 3.10
487 489 5.970289 AGAGAGAGGAGAGAGAGAGATAGA 58.030 45.833 0.00 0.00 0.00 1.98
488 490 6.015918 AGAGAGAGAGGAGAGAGAGAGATAG 58.984 48.000 0.00 0.00 0.00 2.08
489 491 5.970289 AGAGAGAGAGGAGAGAGAGAGATA 58.030 45.833 0.00 0.00 0.00 1.98
491 493 4.078922 AGAGAGAGAGAGGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
492 494 4.222336 AGAGAGAGAGAGGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
493 495 4.219115 GAGAGAGAGAGAGGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
494 496 3.323403 GGAGAGAGAGAGAGGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
495 497 3.309296 GGAGAGAGAGAGAGGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
496 498 2.370189 GGGAGAGAGAGAGAGGAGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
497 499 2.408565 GGGAGAGAGAGAGAGGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
498 500 1.421646 GGGGAGAGAGAGAGAGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
499 501 1.274708 TGGGGAGAGAGAGAGAGGAGA 60.275 57.143 0.00 0.00 0.00 3.71
500 502 1.221635 TGGGGAGAGAGAGAGAGGAG 58.778 60.000 0.00 0.00 0.00 3.69
501 503 1.780309 GATGGGGAGAGAGAGAGAGGA 59.220 57.143 0.00 0.00 0.00 3.71
502 504 1.203050 GGATGGGGAGAGAGAGAGAGG 60.203 61.905 0.00 0.00 0.00 3.69
549 551 3.201487 AGCAATGGATCTGAGGACATTCA 59.799 43.478 0.00 0.00 31.67 2.57
657 662 1.070786 GAGGCAAAGGTCGACACCA 59.929 57.895 18.91 0.00 46.68 4.17
689 694 0.536006 GAAGATGAGGGGGCGAATGG 60.536 60.000 0.00 0.00 0.00 3.16
691 696 1.133976 CAAGAAGATGAGGGGGCGAAT 60.134 52.381 0.00 0.00 0.00 3.34
721 738 4.570663 CTTAGCGCCTCGTCCGGG 62.571 72.222 2.29 0.00 0.00 5.73
730 747 0.924090 CATCGTCTTGACTTAGCGCC 59.076 55.000 2.29 0.00 0.00 6.53
751 768 9.522804 ACGAAAAATAAAACAATGAAGCTTGTA 57.477 25.926 2.10 0.00 38.38 2.41
754 771 8.641499 TCACGAAAAATAAAACAATGAAGCTT 57.359 26.923 0.00 0.00 0.00 3.74
773 790 5.295787 ACATGTAAGCTGTTTTCTTCACGAA 59.704 36.000 0.00 0.00 0.00 3.85
774 791 4.814234 ACATGTAAGCTGTTTTCTTCACGA 59.186 37.500 0.00 0.00 0.00 4.35
775 792 5.050091 AGACATGTAAGCTGTTTTCTTCACG 60.050 40.000 0.00 0.00 0.00 4.35
776 793 6.305693 AGACATGTAAGCTGTTTTCTTCAC 57.694 37.500 0.00 0.00 0.00 3.18
793 810 7.149569 TGCCTCAAAAAGAAAGATAGACATG 57.850 36.000 0.00 0.00 0.00 3.21
845 865 8.668353 GTTGATGTGTGCTAGATTCTCATAAAA 58.332 33.333 0.00 0.00 0.00 1.52
849 869 4.807834 CGTTGATGTGTGCTAGATTCTCAT 59.192 41.667 0.00 0.00 0.00 2.90
851 871 3.000724 GCGTTGATGTGTGCTAGATTCTC 59.999 47.826 0.00 0.00 0.00 2.87
854 874 2.674852 CAGCGTTGATGTGTGCTAGATT 59.325 45.455 0.00 0.00 35.56 2.40
855 875 2.274437 CAGCGTTGATGTGTGCTAGAT 58.726 47.619 0.00 0.00 35.56 1.98
856 876 1.672737 CCAGCGTTGATGTGTGCTAGA 60.673 52.381 0.00 0.00 35.56 2.43
900 1358 2.450886 ACATCCCCTTCTGGTCCTTTTT 59.549 45.455 0.00 0.00 0.00 1.94
1320 2746 0.778078 TCTTGGGGTTGGGATTGGGA 60.778 55.000 0.00 0.00 0.00 4.37
1769 3244 2.613595 TCCATCGTGCTAAATGACATGC 59.386 45.455 0.00 0.00 0.00 4.06
1798 3273 1.968540 GTGCCAAGACAGAGGTGCC 60.969 63.158 0.00 0.00 0.00 5.01
1848 3323 1.351683 ACAACATACGGCCCCAAGTAA 59.648 47.619 0.00 0.00 0.00 2.24
1914 3398 2.988010 TCTGTTCTTGTGTGTCTGCT 57.012 45.000 0.00 0.00 0.00 4.24
2182 3690 1.819753 ATCCGATCCATCCCAAGGAA 58.180 50.000 0.00 0.00 38.93 3.36
2512 4905 1.267806 GCATCCATCATTACTTGCCGG 59.732 52.381 0.00 0.00 0.00 6.13
2717 5334 7.668525 AATTAGCTAATAAATAGGACACGCC 57.331 36.000 19.14 0.00 31.83 5.68
2805 5430 4.414677 TCATCAACCAATCCACCATTCAA 58.585 39.130 0.00 0.00 0.00 2.69
2871 5497 8.721019 AAGAAGATTGTGAAATGCAAAAGAAA 57.279 26.923 0.00 0.00 0.00 2.52
2872 5498 8.721019 AAAGAAGATTGTGAAATGCAAAAGAA 57.279 26.923 0.00 0.00 0.00 2.52
2920 5546 5.292101 CGCCAAGAAAACCAAATACAAACAA 59.708 36.000 0.00 0.00 0.00 2.83
2933 5559 3.964909 ACAACTTCATCGCCAAGAAAAC 58.035 40.909 0.00 0.00 0.00 2.43
2968 5596 2.515979 CCAAACCCCCAAGGCCAAC 61.516 63.158 5.01 0.00 40.58 3.77
2981 5609 3.059120 GCCGAAGAGAGTTTGTACCAAAC 60.059 47.826 10.98 10.98 0.00 2.93
3082 5749 6.115448 ACTGTCCTTTTGCTACTGAATACT 57.885 37.500 0.00 0.00 0.00 2.12
3099 5766 6.937392 ACTTCAGGTAATCTAGAAACTGTCC 58.063 40.000 8.91 1.76 0.00 4.02
3277 6071 5.830912 TCAGTTGAAGCAACCAAACATTAG 58.169 37.500 6.67 0.00 44.49 1.73
3347 6306 6.828785 ACCATACAAGATTTATCTGAACACCC 59.171 38.462 0.00 0.00 37.19 4.61
3352 6311 9.739276 ACAGAAACCATACAAGATTTATCTGAA 57.261 29.630 0.00 0.00 37.19 3.02
3380 6340 5.865013 TGCATTAACTTCAATAGTCGAACGA 59.135 36.000 0.00 0.00 35.54 3.85
3455 6438 5.516090 TGAAACAACGCAAAATAGGAGTTC 58.484 37.500 0.00 0.00 0.00 3.01
3458 6441 5.164061 GCAATGAAACAACGCAAAATAGGAG 60.164 40.000 0.00 0.00 0.00 3.69
3752 6821 2.105477 ACTTCCGCCTTGCATATCTCAT 59.895 45.455 0.00 0.00 0.00 2.90
3767 6836 1.659098 GTCGCCAGTAATCAACTTCCG 59.341 52.381 0.00 0.00 35.76 4.30
3797 6866 0.388006 TCGCCATATATCGCACACGG 60.388 55.000 3.17 0.00 40.63 4.94
3800 6869 0.246360 CCCTCGCCATATATCGCACA 59.754 55.000 3.17 0.00 0.00 4.57
3805 6874 2.296471 CGGATACCCCTCGCCATATATC 59.704 54.545 0.00 0.00 0.00 1.63
3912 6981 7.100458 ACAAACTCATCTTTTGCTGTAGTTT 57.900 32.000 0.00 0.00 37.45 2.66
3948 7017 2.228343 AGTAGTCGTTGTACCAGACTGC 59.772 50.000 19.01 17.83 44.05 4.40
3949 7018 3.119919 GGAGTAGTCGTTGTACCAGACTG 60.120 52.174 19.01 0.00 44.05 3.51
3950 7019 3.080319 GGAGTAGTCGTTGTACCAGACT 58.920 50.000 15.85 15.85 45.85 3.24
3982 7051 4.996758 GCACAAAATTTTACAAGGCCTGAT 59.003 37.500 5.69 0.00 0.00 2.90
4010 7079 6.459573 GCCTTACATGTCTCACTTCACAAAAA 60.460 38.462 0.00 0.00 0.00 1.94
4021 7090 2.565391 TCCGAAAGCCTTACATGTCTCA 59.435 45.455 0.00 0.00 0.00 3.27
4032 7101 1.573108 TTCTGAGGATCCGAAAGCCT 58.427 50.000 5.98 0.00 35.36 4.58
4048 7117 1.188863 GGGCATGCACAAAGGATTCT 58.811 50.000 21.36 0.00 0.00 2.40
4061 7130 2.296190 CCTGATGATGTTCATGGGCATG 59.704 50.000 7.47 0.00 37.20 4.06
4079 7148 1.267806 ACGTTTGAGCTTCATTGCCTG 59.732 47.619 0.00 0.00 0.00 4.85
4127 7196 3.266510 TGTGAAGTGGCATCATCTACC 57.733 47.619 0.00 0.00 0.00 3.18
4132 7201 2.519771 ACCATGTGAAGTGGCATCAT 57.480 45.000 0.00 0.00 40.49 2.45
4140 7209 6.828785 GGGAGTAATGAATTACCATGTGAAGT 59.171 38.462 9.12 0.00 42.71 3.01
4234 7307 3.969976 AGATGCTAATGCTACTCCCTTCA 59.030 43.478 0.00 0.00 40.48 3.02
4235 7308 4.615588 AGATGCTAATGCTACTCCCTTC 57.384 45.455 0.00 0.00 40.48 3.46
4258 7331 1.867363 AATGCTACTCCCTTCGTCCT 58.133 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.