Multiple sequence alignment - TraesCS7A01G091700

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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 TraesCS7A01G091700 chr7A 100.000 3784 0 0 1 3784 55895638 55891855 0.000000e+00 6988
1 TraesCS7A01G091700 chr7A 85.870 2753 321 48 131 2831 55883582 55880846 0.000000e+00 2867
2 TraesCS7A01G091700 chr7A 85.770 1293 170 12 1506 2795 55427140 55425859 0.000000e+00 1356
3 TraesCS7A01G091700 chr7A 87.021 1148 143 6 1521 2665 55383717 55382573 0.000000e+00 1290
4 TraesCS7A01G091700 chr7A 82.448 1299 215 9 111 1408 55385054 55383768 0.000000e+00 1123
5 TraesCS7A01G091700 chr7A 81.380 1391 228 22 111 1482 55398031 55396653 0.000000e+00 1105
6 TraesCS7A01G091700 chr7A 83.861 1010 153 8 107 1112 55428477 55427474 0.000000e+00 953
7 TraesCS7A01G091700 chr7A 88.889 108 11 1 3332 3438 55919442 55919335 8.530000e-27 132
8 TraesCS7A01G091700 chr7D 92.936 3695 196 16 129 3784 53509960 53506292 0.000000e+00 5317
9 TraesCS7A01G091700 chr7D 85.927 2750 311 42 131 2831 53498748 53496026 0.000000e+00 2865
10 TraesCS7A01G091700 chr7D 86.461 1263 159 10 1543 2801 53484058 53482804 0.000000e+00 1375
11 TraesCS7A01G091700 chr7D 85.898 1241 163 10 1562 2798 52696501 52697733 0.000000e+00 1312
12 TraesCS7A01G091700 chr7D 86.879 1128 142 6 1521 2645 52822711 52823835 0.000000e+00 1258
13 TraesCS7A01G091700 chr7D 81.719 1373 221 25 131 1482 52796511 52797874 0.000000e+00 1118
14 TraesCS7A01G091700 chr7D 82.894 1251 205 7 158 1405 52821413 52822657 0.000000e+00 1116
15 TraesCS7A01G091700 chr7D 82.344 1280 213 9 131 1408 53427254 53425986 0.000000e+00 1099
16 TraesCS7A01G091700 chr7D 83.861 1010 153 7 107 1112 53485430 53484427 0.000000e+00 953
17 TraesCS7A01G091700 chr7D 83.647 1009 157 5 107 1112 52695219 52696222 0.000000e+00 942
18 TraesCS7A01G091700 chr4A 84.887 2746 347 40 111 2831 668162883 668160181 0.000000e+00 2710
19 TraesCS7A01G091700 chr4A 89.392 1678 145 25 1174 2831 668147914 668146250 0.000000e+00 2082
20 TraesCS7A01G091700 chr4A 82.538 1300 212 11 111 1408 668085966 668084680 0.000000e+00 1129
21 TraesCS7A01G091700 chr4A 81.223 1390 220 27 111 1482 668096514 668095148 0.000000e+00 1083
22 TraesCS7A01G091700 chr4A 83.366 1010 158 7 107 1112 668110355 668109352 0.000000e+00 926
23 TraesCS7A01G091700 chr4A 92.806 139 10 0 3183 3321 668159776 668159638 6.410000e-48 202
24 TraesCS7A01G091700 chr4A 90.741 108 9 1 3592 3699 668155528 668155422 3.940000e-30 143


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 TraesCS7A01G091700 chr7A 55891855 55895638 3783 True 6988.0 6988 100.0000 1 3784 1 chr7A.!!$R3 3783
1 TraesCS7A01G091700 chr7A 55880846 55883582 2736 True 2867.0 2867 85.8700 131 2831 1 chr7A.!!$R2 2700
2 TraesCS7A01G091700 chr7A 55382573 55385054 2481 True 1206.5 1290 84.7345 111 2665 2 chr7A.!!$R5 2554
3 TraesCS7A01G091700 chr7A 55425859 55428477 2618 True 1154.5 1356 84.8155 107 2795 2 chr7A.!!$R6 2688
4 TraesCS7A01G091700 chr7A 55396653 55398031 1378 True 1105.0 1105 81.3800 111 1482 1 chr7A.!!$R1 1371
5 TraesCS7A01G091700 chr7D 53506292 53509960 3668 True 5317.0 5317 92.9360 129 3784 1 chr7D.!!$R3 3655
6 TraesCS7A01G091700 chr7D 53496026 53498748 2722 True 2865.0 2865 85.9270 131 2831 1 chr7D.!!$R2 2700
7 TraesCS7A01G091700 chr7D 52821413 52823835 2422 False 1187.0 1258 84.8865 158 2645 2 chr7D.!!$F3 2487
8 TraesCS7A01G091700 chr7D 53482804 53485430 2626 True 1164.0 1375 85.1610 107 2801 2 chr7D.!!$R4 2694
9 TraesCS7A01G091700 chr7D 52695219 52697733 2514 False 1127.0 1312 84.7725 107 2798 2 chr7D.!!$F2 2691
10 TraesCS7A01G091700 chr7D 52796511 52797874 1363 False 1118.0 1118 81.7190 131 1482 1 chr7D.!!$F1 1351
11 TraesCS7A01G091700 chr7D 53425986 53427254 1268 True 1099.0 1099 82.3440 131 1408 1 chr7D.!!$R1 1277
12 TraesCS7A01G091700 chr4A 668146250 668147914 1664 True 2082.0 2082 89.3920 1174 2831 1 chr4A.!!$R4 1657
13 TraesCS7A01G091700 chr4A 668159638 668162883 3245 True 1456.0 2710 88.8465 111 3321 2 chr4A.!!$R6 3210
14 TraesCS7A01G091700 chr4A 668084680 668085966 1286 True 1129.0 1129 82.5380 111 1408 1 chr4A.!!$R1 1297
15 TraesCS7A01G091700 chr4A 668095148 668096514 1366 True 1083.0 1083 81.2230 111 1482 1 chr4A.!!$R2 1371
16 TraesCS7A01G091700 chr4A 668109352 668110355 1003 True 926.0 926 83.3660 107 1112 1 chr4A.!!$R3 1005

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
326 342 0.687920 TTCTGTACCCATTCGGCACA 59.312 50.000 0.0 0.0 33.26 4.57 F
1357 1419 1.269051 CGAGCTGACCCAAACAAAACC 60.269 52.381 0.0 0.0 0.00 3.27 F
2553 2634 0.108329 GGGAGAAATCGCCGAACTGA 60.108 55.000 0.0 0.0 36.62 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1672 1749 1.198637 CCTTCTCTTTTGCCAGCTTCG 59.801 52.381 0.00 0.00 0.0 3.79 R
2636 2717 0.329596 GCACCAGTTTCTCCCTCCAT 59.670 55.000 0.00 0.00 0.0 3.41 R
3735 3942 1.462283 CTGAAGTCATGACGGCAACAG 59.538 52.381 19.85 18.79 36.2 3.16 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
24 25 7.595819 TTGTATGGTGAAAAGGACTTGAAAT 57.404 32.000 0.00 0.00 0.00 2.17
25 26 7.214467 TGTATGGTGAAAAGGACTTGAAATC 57.786 36.000 0.00 0.00 0.00 2.17
26 27 6.775142 TGTATGGTGAAAAGGACTTGAAATCA 59.225 34.615 0.00 0.00 0.00 2.57
27 28 5.772825 TGGTGAAAAGGACTTGAAATCAG 57.227 39.130 0.00 0.00 0.00 2.90
28 29 5.445069 TGGTGAAAAGGACTTGAAATCAGA 58.555 37.500 0.00 0.00 0.00 3.27
29 30 5.532406 TGGTGAAAAGGACTTGAAATCAGAG 59.468 40.000 0.00 0.00 0.00 3.35
30 31 5.765182 GGTGAAAAGGACTTGAAATCAGAGA 59.235 40.000 0.00 0.00 0.00 3.10
31 32 6.263168 GGTGAAAAGGACTTGAAATCAGAGAA 59.737 38.462 0.00 0.00 0.00 2.87
32 33 7.040132 GGTGAAAAGGACTTGAAATCAGAGAAT 60.040 37.037 0.00 0.00 0.00 2.40
33 34 9.003658 GTGAAAAGGACTTGAAATCAGAGAATA 57.996 33.333 0.00 0.00 0.00 1.75
34 35 9.573166 TGAAAAGGACTTGAAATCAGAGAATAA 57.427 29.630 0.00 0.00 0.00 1.40
35 36 9.833182 GAAAAGGACTTGAAATCAGAGAATAAC 57.167 33.333 0.00 0.00 0.00 1.89
36 37 7.929941 AAGGACTTGAAATCAGAGAATAACC 57.070 36.000 0.00 0.00 0.00 2.85
37 38 7.020827 AGGACTTGAAATCAGAGAATAACCA 57.979 36.000 0.00 0.00 0.00 3.67
38 39 7.461749 AGGACTTGAAATCAGAGAATAACCAA 58.538 34.615 0.00 0.00 0.00 3.67
39 40 7.609532 AGGACTTGAAATCAGAGAATAACCAAG 59.390 37.037 0.00 0.00 35.81 3.61
40 41 7.607991 GGACTTGAAATCAGAGAATAACCAAGA 59.392 37.037 0.00 0.00 34.37 3.02
41 42 8.558973 ACTTGAAATCAGAGAATAACCAAGAG 57.441 34.615 0.00 0.00 34.37 2.85
42 43 8.378565 ACTTGAAATCAGAGAATAACCAAGAGA 58.621 33.333 0.00 0.00 34.37 3.10
43 44 8.783833 TTGAAATCAGAGAATAACCAAGAGAG 57.216 34.615 0.00 0.00 0.00 3.20
44 45 8.138928 TGAAATCAGAGAATAACCAAGAGAGA 57.861 34.615 0.00 0.00 0.00 3.10
45 46 8.037758 TGAAATCAGAGAATAACCAAGAGAGAC 58.962 37.037 0.00 0.00 0.00 3.36
46 47 7.487822 AATCAGAGAATAACCAAGAGAGACA 57.512 36.000 0.00 0.00 0.00 3.41
47 48 7.673641 ATCAGAGAATAACCAAGAGAGACAT 57.326 36.000 0.00 0.00 0.00 3.06
48 49 7.487822 TCAGAGAATAACCAAGAGAGACATT 57.512 36.000 0.00 0.00 0.00 2.71
49 50 7.551585 TCAGAGAATAACCAAGAGAGACATTC 58.448 38.462 0.00 0.00 0.00 2.67
50 51 7.179160 TCAGAGAATAACCAAGAGAGACATTCA 59.821 37.037 0.00 0.00 0.00 2.57
51 52 7.492020 CAGAGAATAACCAAGAGAGACATTCAG 59.508 40.741 0.00 0.00 0.00 3.02
52 53 7.398618 AGAGAATAACCAAGAGAGACATTCAGA 59.601 37.037 0.00 0.00 0.00 3.27
53 54 7.911651 AGAATAACCAAGAGAGACATTCAGAA 58.088 34.615 0.00 0.00 0.00 3.02
54 55 8.547173 AGAATAACCAAGAGAGACATTCAGAAT 58.453 33.333 0.00 0.00 0.00 2.40
55 56 9.171877 GAATAACCAAGAGAGACATTCAGAATT 57.828 33.333 0.00 0.00 0.00 2.17
56 57 8.729805 ATAACCAAGAGAGACATTCAGAATTC 57.270 34.615 0.00 0.00 0.00 2.17
57 58 6.119240 ACCAAGAGAGACATTCAGAATTCA 57.881 37.500 8.44 0.00 0.00 2.57
58 59 6.719301 ACCAAGAGAGACATTCAGAATTCAT 58.281 36.000 8.44 0.00 0.00 2.57
59 60 6.598457 ACCAAGAGAGACATTCAGAATTCATG 59.402 38.462 8.44 5.51 0.00 3.07
60 61 6.598457 CCAAGAGAGACATTCAGAATTCATGT 59.402 38.462 8.44 8.81 33.72 3.21
61 62 7.120873 CCAAGAGAGACATTCAGAATTCATGTT 59.879 37.037 8.44 1.09 31.10 2.71
62 63 8.512956 CAAGAGAGACATTCAGAATTCATGTTT 58.487 33.333 8.44 4.33 31.10 2.83
63 64 9.730705 AAGAGAGACATTCAGAATTCATGTTTA 57.269 29.630 8.44 0.00 31.10 2.01
64 65 9.160496 AGAGAGACATTCAGAATTCATGTTTAC 57.840 33.333 8.44 5.20 31.10 2.01
65 66 9.160496 GAGAGACATTCAGAATTCATGTTTACT 57.840 33.333 8.44 9.09 31.10 2.24
78 79 9.793252 AATTCATGTTTACTATCAAAGACATGC 57.207 29.630 8.88 0.00 42.32 4.06
79 80 7.920160 TCATGTTTACTATCAAAGACATGCA 57.080 32.000 8.88 0.00 42.32 3.96
80 81 8.334263 TCATGTTTACTATCAAAGACATGCAA 57.666 30.769 8.88 0.00 42.32 4.08
81 82 8.959548 TCATGTTTACTATCAAAGACATGCAAT 58.040 29.630 8.88 0.00 42.32 3.56
84 85 9.225436 TGTTTACTATCAAAGACATGCAATACA 57.775 29.630 0.00 0.00 0.00 2.29
116 117 9.653287 TTTCTTCATACGATTCTTAGAACATGT 57.347 29.630 0.00 0.00 0.00 3.21
124 125 6.183360 ACGATTCTTAGAACATGTATCCAGCT 60.183 38.462 0.00 0.00 0.00 4.24
125 126 6.364706 CGATTCTTAGAACATGTATCCAGCTC 59.635 42.308 0.00 0.00 0.00 4.09
126 127 6.798427 TTCTTAGAACATGTATCCAGCTCT 57.202 37.500 0.00 0.00 0.00 4.09
188 198 2.676463 GCCTACAGGTCAGAAGCTCTTG 60.676 54.545 0.00 0.00 37.57 3.02
229 242 6.073314 CCCTAGCCCTACAACATAGTACTAA 58.927 44.000 6.70 0.00 0.00 2.24
257 273 3.273654 TCTGGGACCTCCGGGAGT 61.274 66.667 22.07 10.66 42.31 3.85
258 274 3.077556 CTGGGACCTCCGGGAGTG 61.078 72.222 22.07 15.50 38.27 3.51
285 301 4.641645 CACGACCTGGCTGCCCAA 62.642 66.667 17.53 0.00 41.58 4.12
287 303 2.597217 CGACCTGGCTGCCCAAAA 60.597 61.111 17.53 0.00 41.58 2.44
310 326 1.542915 GTGTGGCAATGTCAGCATTCT 59.457 47.619 0.00 0.00 42.91 2.40
326 342 0.687920 TTCTGTACCCATTCGGCACA 59.312 50.000 0.00 0.00 33.26 4.57
358 374 2.229062 GCTTCCAAGAACCCTTTAGTGC 59.771 50.000 0.00 0.00 0.00 4.40
409 425 2.093816 CCTCAACCGAAGTTAGGGTACC 60.094 54.545 2.17 2.17 42.06 3.34
515 537 2.073816 ACTGGTTTCGACGCCTTAATG 58.926 47.619 6.08 0.00 0.00 1.90
593 615 2.094597 TGCTATGCTTGCAATGGTTGTC 60.095 45.455 0.00 0.00 37.51 3.18
602 624 1.878102 GCAATGGTTGTCGGACTCACT 60.878 52.381 9.88 0.00 0.00 3.41
683 705 5.069119 TGATGCAAGTAGTATCGAAGATGGT 59.931 40.000 0.00 0.00 45.12 3.55
743 765 4.937620 GTGTCAGGAAATGTCAGCTCATTA 59.062 41.667 1.38 0.00 37.09 1.90
770 792 5.069251 CACCTTATCCTTACCAGTACCAGAG 59.931 48.000 0.00 0.00 0.00 3.35
801 823 4.841246 ACTCTACCATCCAGTCTTTCAGTT 59.159 41.667 0.00 0.00 0.00 3.16
872 894 6.860080 TCGTTCCTATGTTAACTCTACAAGG 58.140 40.000 7.22 4.96 0.00 3.61
1044 1066 1.584380 CTGCAACTGCTCTCAAGGCC 61.584 60.000 0.00 0.00 42.66 5.19
1357 1419 1.269051 CGAGCTGACCCAAACAAAACC 60.269 52.381 0.00 0.00 0.00 3.27
1413 1477 7.063780 AGCAATCAAATTATTTTGCACACTAGC 59.936 33.333 13.19 0.00 45.26 3.42
1423 1487 2.734723 ACACTAGCTGCGCACGTG 60.735 61.111 12.28 12.28 37.14 4.49
1548 1625 6.257630 GGACAACATGTTGCAATTGTTTTAGT 59.742 34.615 33.23 17.52 44.03 2.24
1714 1791 7.493971 GAAGGAAAGATTCTTCGATCAGAATGA 59.506 37.037 15.39 4.90 42.52 2.57
2520 2601 0.324943 AAGCATAGTTGGTGTCGGCT 59.675 50.000 0.00 0.00 32.86 5.52
2549 2630 1.449601 GCTGGGAGAAATCGCCGAA 60.450 57.895 0.00 0.00 36.62 4.30
2553 2634 0.108329 GGGAGAAATCGCCGAACTGA 60.108 55.000 0.00 0.00 36.62 3.41
2689 2770 2.246719 GCAGAGTGTCTGGTCAAGTT 57.753 50.000 6.09 0.00 44.43 2.66
2835 2922 5.103000 GCGAGTAGTATTGCAAAGAAGAGA 58.897 41.667 1.71 0.00 0.00 3.10
2836 2923 5.231147 GCGAGTAGTATTGCAAAGAAGAGAG 59.769 44.000 1.71 0.00 0.00 3.20
2837 2924 6.556212 CGAGTAGTATTGCAAAGAAGAGAGA 58.444 40.000 1.71 0.00 0.00 3.10
2838 2925 6.690957 CGAGTAGTATTGCAAAGAAGAGAGAG 59.309 42.308 1.71 0.00 0.00 3.20
2839 2926 7.414651 CGAGTAGTATTGCAAAGAAGAGAGAGA 60.415 40.741 1.71 0.00 0.00 3.10
2840 2927 7.771183 AGTAGTATTGCAAAGAAGAGAGAGAG 58.229 38.462 1.71 0.00 0.00 3.20
2841 2928 6.849085 AGTATTGCAAAGAAGAGAGAGAGA 57.151 37.500 1.71 0.00 0.00 3.10
2842 2929 6.866480 AGTATTGCAAAGAAGAGAGAGAGAG 58.134 40.000 1.71 0.00 0.00 3.20
2843 2930 5.999205 ATTGCAAAGAAGAGAGAGAGAGA 57.001 39.130 1.71 0.00 0.00 3.10
2844 2931 5.389859 TTGCAAAGAAGAGAGAGAGAGAG 57.610 43.478 0.00 0.00 0.00 3.20
2845 2932 4.661222 TGCAAAGAAGAGAGAGAGAGAGA 58.339 43.478 0.00 0.00 0.00 3.10
2846 2933 4.701651 TGCAAAGAAGAGAGAGAGAGAGAG 59.298 45.833 0.00 0.00 0.00 3.20
2847 2934 4.943705 GCAAAGAAGAGAGAGAGAGAGAGA 59.056 45.833 0.00 0.00 0.00 3.10
2848 2935 5.065731 GCAAAGAAGAGAGAGAGAGAGAGAG 59.934 48.000 0.00 0.00 0.00 3.20
2849 2936 6.409704 CAAAGAAGAGAGAGAGAGAGAGAGA 58.590 44.000 0.00 0.00 0.00 3.10
2850 2937 5.867903 AGAAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
2851 2938 5.523588 AGAAGAGAGAGAGAGAGAGAGAGA 58.476 45.833 0.00 0.00 0.00 3.10
2852 2939 5.598005 AGAAGAGAGAGAGAGAGAGAGAGAG 59.402 48.000 0.00 0.00 0.00 3.20
2853 2940 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2854 2941 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2855 2942 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
2856 2943 4.648762 AGAGAGAGAGAGAGAGAGAGAGTG 59.351 50.000 0.00 0.00 0.00 3.51
2857 2944 4.357325 AGAGAGAGAGAGAGAGAGAGTGT 58.643 47.826 0.00 0.00 0.00 3.55
2858 2945 4.161189 AGAGAGAGAGAGAGAGAGAGTGTG 59.839 50.000 0.00 0.00 0.00 3.82
3131 3219 6.510536 TGTATCTGCAGTCATCAGATTAGTG 58.489 40.000 14.67 0.00 45.99 2.74
3135 3223 5.418840 TCTGCAGTCATCAGATTAGTGTACA 59.581 40.000 14.67 0.00 35.81 2.90
3184 3272 1.811558 GCTTCAGTGAACCTGCTGTCA 60.812 52.381 0.08 0.00 41.25 3.58
3426 3611 4.137543 CACTTCCTCCTGCTTACAGTTTT 58.862 43.478 0.00 0.00 42.81 2.43
3542 3727 5.588240 CGCATATCTATATAGAACCGCCAA 58.412 41.667 16.27 0.00 35.69 4.52
3760 3967 1.337260 GCCGTCATGACTTCAGACAGT 60.337 52.381 22.95 0.00 32.68 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.286546 TGATTTCAAGTCCTTTTCACCATACAA 59.713 33.333 0.00 0.00 0.00 2.41
2 3 7.174946 TCTGATTTCAAGTCCTTTTCACCATAC 59.825 37.037 0.00 0.00 0.00 2.39
3 4 7.230747 TCTGATTTCAAGTCCTTTTCACCATA 58.769 34.615 0.00 0.00 0.00 2.74
4 5 6.070656 TCTGATTTCAAGTCCTTTTCACCAT 58.929 36.000 0.00 0.00 0.00 3.55
6 7 5.765182 TCTCTGATTTCAAGTCCTTTTCACC 59.235 40.000 0.00 0.00 0.00 4.02
7 8 6.867662 TCTCTGATTTCAAGTCCTTTTCAC 57.132 37.500 0.00 0.00 0.00 3.18
8 9 9.573166 TTATTCTCTGATTTCAAGTCCTTTTCA 57.427 29.630 0.00 0.00 0.00 2.69
9 10 9.833182 GTTATTCTCTGATTTCAAGTCCTTTTC 57.167 33.333 0.00 0.00 0.00 2.29
10 11 8.797438 GGTTATTCTCTGATTTCAAGTCCTTTT 58.203 33.333 0.00 0.00 0.00 2.27
11 12 7.944554 TGGTTATTCTCTGATTTCAAGTCCTTT 59.055 33.333 0.00 0.00 0.00 3.11
12 13 7.461749 TGGTTATTCTCTGATTTCAAGTCCTT 58.538 34.615 0.00 0.00 0.00 3.36
13 14 7.020827 TGGTTATTCTCTGATTTCAAGTCCT 57.979 36.000 0.00 0.00 0.00 3.85
14 15 7.607991 TCTTGGTTATTCTCTGATTTCAAGTCC 59.392 37.037 0.00 0.00 33.17 3.85
15 16 8.553459 TCTTGGTTATTCTCTGATTTCAAGTC 57.447 34.615 0.00 0.00 33.17 3.01
16 17 8.378565 TCTCTTGGTTATTCTCTGATTTCAAGT 58.621 33.333 0.00 0.00 33.17 3.16
17 18 8.783833 TCTCTTGGTTATTCTCTGATTTCAAG 57.216 34.615 0.00 0.00 0.00 3.02
18 19 8.597167 TCTCTCTTGGTTATTCTCTGATTTCAA 58.403 33.333 0.00 0.00 0.00 2.69
19 20 8.037758 GTCTCTCTTGGTTATTCTCTGATTTCA 58.962 37.037 0.00 0.00 0.00 2.69
20 21 8.037758 TGTCTCTCTTGGTTATTCTCTGATTTC 58.962 37.037 0.00 0.00 0.00 2.17
21 22 7.911651 TGTCTCTCTTGGTTATTCTCTGATTT 58.088 34.615 0.00 0.00 0.00 2.17
22 23 7.487822 TGTCTCTCTTGGTTATTCTCTGATT 57.512 36.000 0.00 0.00 0.00 2.57
23 24 7.673641 ATGTCTCTCTTGGTTATTCTCTGAT 57.326 36.000 0.00 0.00 0.00 2.90
24 25 7.179160 TGAATGTCTCTCTTGGTTATTCTCTGA 59.821 37.037 0.00 0.00 0.00 3.27
25 26 7.326454 TGAATGTCTCTCTTGGTTATTCTCTG 58.674 38.462 0.00 0.00 0.00 3.35
26 27 7.398618 TCTGAATGTCTCTCTTGGTTATTCTCT 59.601 37.037 0.00 0.00 0.00 3.10
27 28 7.551585 TCTGAATGTCTCTCTTGGTTATTCTC 58.448 38.462 0.00 0.00 0.00 2.87
28 29 7.487822 TCTGAATGTCTCTCTTGGTTATTCT 57.512 36.000 0.00 0.00 0.00 2.40
29 30 8.729805 ATTCTGAATGTCTCTCTTGGTTATTC 57.270 34.615 1.31 0.00 0.00 1.75
30 31 9.171877 GAATTCTGAATGTCTCTCTTGGTTATT 57.828 33.333 3.22 0.00 0.00 1.40
31 32 8.324306 TGAATTCTGAATGTCTCTCTTGGTTAT 58.676 33.333 7.05 0.00 0.00 1.89
32 33 7.679783 TGAATTCTGAATGTCTCTCTTGGTTA 58.320 34.615 7.05 0.00 0.00 2.85
33 34 6.537355 TGAATTCTGAATGTCTCTCTTGGTT 58.463 36.000 7.05 0.00 0.00 3.67
34 35 6.119240 TGAATTCTGAATGTCTCTCTTGGT 57.881 37.500 7.05 0.00 0.00 3.67
35 36 6.598457 ACATGAATTCTGAATGTCTCTCTTGG 59.402 38.462 7.05 0.00 28.38 3.61
36 37 7.612668 ACATGAATTCTGAATGTCTCTCTTG 57.387 36.000 7.05 8.13 28.38 3.02
37 38 8.632906 AAACATGAATTCTGAATGTCTCTCTT 57.367 30.769 7.05 0.00 33.48 2.85
38 39 9.160496 GTAAACATGAATTCTGAATGTCTCTCT 57.840 33.333 7.05 0.00 33.48 3.10
39 40 9.160496 AGTAAACATGAATTCTGAATGTCTCTC 57.840 33.333 7.05 0.00 33.48 3.20
52 53 9.793252 GCATGTCTTTGATAGTAAACATGAATT 57.207 29.630 15.33 0.00 36.72 2.17
53 54 8.959548 TGCATGTCTTTGATAGTAAACATGAAT 58.040 29.630 15.33 0.00 36.72 2.57
54 55 8.334263 TGCATGTCTTTGATAGTAAACATGAA 57.666 30.769 15.33 3.98 36.72 2.57
55 56 7.920160 TGCATGTCTTTGATAGTAAACATGA 57.080 32.000 15.33 1.03 36.72 3.07
58 59 9.225436 TGTATTGCATGTCTTTGATAGTAAACA 57.775 29.630 0.00 0.00 0.00 2.83
90 91 9.653287 ACATGTTCTAAGAATCGTATGAAGAAA 57.347 29.630 0.00 0.00 0.00 2.52
94 95 9.692749 GGATACATGTTCTAAGAATCGTATGAA 57.307 33.333 2.30 0.00 0.00 2.57
95 96 8.856103 TGGATACATGTTCTAAGAATCGTATGA 58.144 33.333 2.30 0.00 46.17 2.15
193 203 4.514577 CTAGGGTGGCGGCGACAG 62.515 72.222 19.67 0.00 0.00 3.51
229 242 1.623542 GGTCCCAGACCCATAAGCGT 61.624 60.000 2.14 0.00 46.19 5.07
257 273 2.358615 GGTCGTGCCATGCTGACA 60.359 61.111 11.91 0.00 36.75 3.58
258 274 2.046892 AGGTCGTGCCATGCTGAC 60.047 61.111 0.00 4.25 40.61 3.51
285 301 2.168106 TGCTGACATTGCCACACTTTTT 59.832 40.909 0.00 0.00 0.00 1.94
287 303 1.401761 TGCTGACATTGCCACACTTT 58.598 45.000 0.00 0.00 0.00 2.66
326 342 1.145738 TCTTGGAAGCAGCCTTTTCCT 59.854 47.619 12.02 0.00 42.67 3.36
358 374 1.378882 CCCGGTCTCATTGCATGTGG 61.379 60.000 0.00 0.00 0.00 4.17
409 425 3.697045 ACCAAGAGTAAGACTGATCTCCG 59.303 47.826 0.00 0.00 32.34 4.63
515 537 7.378181 TGGAAAGTTTATGAAAAGGATCAAGC 58.622 34.615 0.00 0.00 32.06 4.01
593 615 3.506810 CTTCTTGCTCTTAGTGAGTCCG 58.493 50.000 0.00 0.00 44.41 4.79
602 624 5.157940 ACTCAATCTGCTTCTTGCTCTTA 57.842 39.130 0.00 0.00 43.37 2.10
618 640 2.995547 GGCGGTGGGGTACTCAAT 59.004 61.111 0.00 0.00 0.00 2.57
637 659 2.679450 TGCAGAATGAAAAGCATGTGC 58.321 42.857 0.00 0.00 43.29 4.57
770 792 6.465084 AGACTGGATGGTAGAGTTGTAAAAC 58.535 40.000 0.00 0.00 0.00 2.43
801 823 1.186200 ACGAATGAGTAGCTGCAGGA 58.814 50.000 17.12 0.00 0.00 3.86
872 894 4.032900 CCATCTGTATGTGTACTTGCGAAC 59.967 45.833 0.00 0.00 0.00 3.95
1423 1487 4.383948 GCTTTCTGTTTACATTGAAGCAGC 59.616 41.667 14.62 6.51 37.51 5.25
1672 1749 1.198637 CCTTCTCTTTTGCCAGCTTCG 59.801 52.381 0.00 0.00 0.00 3.79
2520 2601 0.911045 TCTCCCAGCAGCATCTCCAA 60.911 55.000 0.00 0.00 0.00 3.53
2549 2630 0.969149 TCAAGCACATCCTCGTCAGT 59.031 50.000 0.00 0.00 0.00 3.41
2553 2634 4.606071 GCTCAAGCACATCCTCGT 57.394 55.556 0.00 0.00 41.59 4.18
2636 2717 0.329596 GCACCAGTTTCTCCCTCCAT 59.670 55.000 0.00 0.00 0.00 3.41
2835 2922 4.161189 CACACTCTCTCTCTCTCTCTCTCT 59.839 50.000 0.00 0.00 0.00 3.10
2836 2923 4.081420 ACACACTCTCTCTCTCTCTCTCTC 60.081 50.000 0.00 0.00 0.00 3.20
2837 2924 3.840666 ACACACTCTCTCTCTCTCTCTCT 59.159 47.826 0.00 0.00 0.00 3.10
2838 2925 3.935203 CACACACTCTCTCTCTCTCTCTC 59.065 52.174 0.00 0.00 0.00 3.20
2839 2926 3.327757 ACACACACTCTCTCTCTCTCTCT 59.672 47.826 0.00 0.00 0.00 3.10
2840 2927 3.436704 CACACACACTCTCTCTCTCTCTC 59.563 52.174 0.00 0.00 0.00 3.20
2841 2928 3.181445 ACACACACACTCTCTCTCTCTCT 60.181 47.826 0.00 0.00 0.00 3.10
2842 2929 3.058293 CACACACACACTCTCTCTCTCTC 60.058 52.174 0.00 0.00 0.00 3.20
2843 2930 2.884012 CACACACACACTCTCTCTCTCT 59.116 50.000 0.00 0.00 0.00 3.10
2844 2931 2.621055 ACACACACACACTCTCTCTCTC 59.379 50.000 0.00 0.00 0.00 3.20
2845 2932 2.360483 CACACACACACACTCTCTCTCT 59.640 50.000 0.00 0.00 0.00 3.10
2846 2933 2.099921 ACACACACACACACTCTCTCTC 59.900 50.000 0.00 0.00 0.00 3.20
2847 2934 2.103373 ACACACACACACACTCTCTCT 58.897 47.619 0.00 0.00 0.00 3.10
2848 2935 2.196749 CACACACACACACACTCTCTC 58.803 52.381 0.00 0.00 0.00 3.20
2849 2936 1.550524 ACACACACACACACACTCTCT 59.449 47.619 0.00 0.00 0.00 3.10
2850 2937 1.660607 CACACACACACACACACTCTC 59.339 52.381 0.00 0.00 0.00 3.20
2851 2938 1.001974 ACACACACACACACACACTCT 59.998 47.619 0.00 0.00 0.00 3.24
2852 2939 1.128507 CACACACACACACACACACTC 59.871 52.381 0.00 0.00 0.00 3.51
2853 2940 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
2854 2941 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2855 2942 2.070028 GTACACACACACACACACACA 58.930 47.619 0.00 0.00 0.00 3.72
2856 2943 1.059979 CGTACACACACACACACACAC 59.940 52.381 0.00 0.00 0.00 3.82
2857 2944 1.336980 ACGTACACACACACACACACA 60.337 47.619 0.00 0.00 0.00 3.72
2858 2945 1.059979 CACGTACACACACACACACAC 59.940 52.381 0.00 0.00 0.00 3.82
3131 3219 3.566322 AGTGATCGGATACTGCTCTGTAC 59.434 47.826 0.00 0.00 0.00 2.90
3135 3223 4.207955 TGTAAGTGATCGGATACTGCTCT 58.792 43.478 0.00 0.00 0.00 4.09
3184 3272 5.491982 AGAGTTCACAGAAACAACAGAACT 58.508 37.500 5.42 5.42 45.76 3.01
3312 3497 5.163652 GCACAAATCACCTTATTACCTGTCC 60.164 44.000 0.00 0.00 0.00 4.02
3366 3551 7.824289 CCTGAGATTGATCCTTGTAACAAACTA 59.176 37.037 0.00 0.00 0.00 2.24
3688 3894 4.756084 AGCTAAACTGTGCTGAATGAAC 57.244 40.909 0.00 0.00 38.21 3.18
3735 3942 1.462283 CTGAAGTCATGACGGCAACAG 59.538 52.381 19.85 18.79 36.20 3.16


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

AutoCloner maintained by Alex Coulton.