Multiple sequence alignment - TraesCS7A01G469200

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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 TraesCS7A01G469200 chr7A 100.000 1462 0 0 827 2288 665427555 665429016 0.000000e+00 2700.0
1 TraesCS7A01G469200 chr7A 86.536 713 60 18 829 1521 664999632 665000328 0.000000e+00 752.0
2 TraesCS7A01G469200 chr7A 100.000 348 0 0 1 348 665426729 665427076 0.000000e+00 643.0
3 TraesCS7A01G469200 chr7A 82.172 746 70 41 827 1535 664415158 664414439 1.180000e-162 582.0
4 TraesCS7A01G469200 chr7A 91.803 61 5 0 287 347 664374387 664374327 4.050000e-13 86.1
5 TraesCS7A01G469200 chr7D 93.885 1292 46 14 827 2103 575441454 575442727 0.000000e+00 1917.0
6 TraesCS7A01G469200 chr7D 87.377 713 55 19 827 1519 575408206 575408903 0.000000e+00 785.0
7 TraesCS7A01G469200 chr7D 82.888 748 67 35 827 1535 574764328 574763603 1.160000e-172 616.0
8 TraesCS7A01G469200 chr7D 81.892 740 69 38 827 1521 574774335 574773616 4.270000e-157 564.0
9 TraesCS7A01G469200 chr7D 92.023 351 15 8 10 348 575440984 575441333 4.420000e-132 481.0
10 TraesCS7A01G469200 chr7D 91.667 132 7 4 216 346 574764578 574764450 1.810000e-41 180.0
11 TraesCS7A01G469200 chr7B 90.049 824 54 16 1291 2103 636984350 636985156 0.000000e+00 1042.0
12 TraesCS7A01G469200 chr7B 96.815 471 10 2 827 1296 636983774 636984240 0.000000e+00 782.0
13 TraesCS7A01G469200 chr7B 85.133 713 62 19 827 1520 636940211 636940898 0.000000e+00 689.0
14 TraesCS7A01G469200 chr7B 86.327 490 44 11 827 1306 634647545 634647069 1.570000e-141 512.0
15 TraesCS7A01G469200 chr7B 90.698 344 18 10 13 347 636983318 636983656 1.610000e-121 446.0
16 TraesCS7A01G469200 chr7B 80.332 422 64 11 1537 1948 707824805 707824393 3.690000e-78 302.0
17 TraesCS7A01G469200 chr7B 89.394 132 10 4 216 347 634647762 634647635 1.820000e-36 163.0
18 TraesCS7A01G469200 chr7B 89.565 115 10 2 233 347 634580200 634580088 6.590000e-31 145.0
19 TraesCS7A01G469200 chr7B 98.305 59 1 0 2100 2158 19066501 19066559 1.120000e-18 104.0
20 TraesCS7A01G469200 chrUn 82.767 412 50 9 1537 1938 324024235 324024635 4.680000e-92 348.0
21 TraesCS7A01G469200 chrUn 84.021 194 23 3 2095 2288 150940971 150941156 1.810000e-41 180.0
22 TraesCS7A01G469200 chrUn 84.021 194 23 3 2095 2288 297263492 297263677 1.810000e-41 180.0
23 TraesCS7A01G469200 chr6B 83.735 332 46 3 1610 1940 703398993 703399317 7.940000e-80 307.0
24 TraesCS7A01G469200 chr3B 81.395 387 59 11 1537 1916 758056714 758056334 1.030000e-78 303.0
25 TraesCS7A01G469200 chr3B 81.481 243 29 9 1704 1941 804840814 804841045 3.880000e-43 185.0
26 TraesCS7A01G469200 chr2D 84.244 311 38 9 1565 1868 76750793 76750487 2.220000e-75 292.0
27 TraesCS7A01G469200 chr2A 83.591 323 37 9 1626 1944 77237464 77237154 2.880000e-74 289.0
28 TraesCS7A01G469200 chr4A 79.952 419 60 18 1536 1941 584660593 584661000 1.030000e-73 287.0
29 TraesCS7A01G469200 chr4A 89.167 120 12 1 2169 2288 642443666 642443548 5.090000e-32 148.0
30 TraesCS7A01G469200 chr4A 79.459 185 14 7 2085 2265 601790698 601790862 2.400000e-20 110.0
31 TraesCS7A01G469200 chr5B 78.662 314 35 9 1533 1828 7998754 7999053 1.810000e-41 180.0
32 TraesCS7A01G469200 chr5B 92.793 111 8 0 2169 2279 614057974 614057864 6.540000e-36 161.0
33 TraesCS7A01G469200 chr5B 92.793 111 8 0 2169 2279 614058399 614058289 6.540000e-36 161.0
34 TraesCS7A01G469200 chr5B 82.682 179 10 1 2100 2278 632326489 632326646 3.060000e-29 139.0
35 TraesCS7A01G469200 chr5B 98.305 59 1 0 2100 2158 614058448 614058390 1.120000e-18 104.0
36 TraesCS7A01G469200 chr6D 90.833 120 11 0 2169 2288 185286899 185287018 6.540000e-36 161.0
37 TraesCS7A01G469200 chr5D 92.727 110 7 1 2169 2278 503797492 503797600 8.460000e-35 158.0
38 TraesCS7A01G469200 chr5D 98.305 59 1 0 2100 2158 503797443 503797501 1.120000e-18 104.0
39 TraesCS7A01G469200 chr3D 91.964 112 9 0 2169 2280 576709752 576709641 8.460000e-35 158.0
40 TraesCS7A01G469200 chr3D 90.000 120 12 0 2169 2288 596408277 596408158 3.040000e-34 156.0
41 TraesCS7A01G469200 chr3D 95.385 65 3 0 2094 2158 576709807 576709743 1.120000e-18 104.0
42 TraesCS7A01G469200 chr3D 98.305 59 1 0 2100 2158 596408326 596408268 1.120000e-18 104.0
43 TraesCS7A01G469200 chr2B 83.425 181 9 2 2100 2280 140626364 140626205 5.090000e-32 148.0
44 TraesCS7A01G469200 chr2B 82.778 180 10 2 2101 2280 122072018 122072176 8.520000e-30 141.0


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 TraesCS7A01G469200 chr7A 665426729 665429016 2287 False 1671.500000 2700 100.000000 1 2288 2 chr7A.!!$F2 2287
1 TraesCS7A01G469200 chr7A 664999632 665000328 696 False 752.000000 752 86.536000 829 1521 1 chr7A.!!$F1 692
2 TraesCS7A01G469200 chr7A 664414439 664415158 719 True 582.000000 582 82.172000 827 1535 1 chr7A.!!$R2 708
3 TraesCS7A01G469200 chr7D 575440984 575442727 1743 False 1199.000000 1917 92.954000 10 2103 2 chr7D.!!$F2 2093
4 TraesCS7A01G469200 chr7D 575408206 575408903 697 False 785.000000 785 87.377000 827 1519 1 chr7D.!!$F1 692
5 TraesCS7A01G469200 chr7D 574773616 574774335 719 True 564.000000 564 81.892000 827 1521 1 chr7D.!!$R1 694
6 TraesCS7A01G469200 chr7D 574763603 574764578 975 True 398.000000 616 87.277500 216 1535 2 chr7D.!!$R2 1319
7 TraesCS7A01G469200 chr7B 636983318 636985156 1838 False 756.666667 1042 92.520667 13 2103 3 chr7B.!!$F3 2090
8 TraesCS7A01G469200 chr7B 636940211 636940898 687 False 689.000000 689 85.133000 827 1520 1 chr7B.!!$F2 693
9 TraesCS7A01G469200 chr7B 634647069 634647762 693 True 337.500000 512 87.860500 216 1306 2 chr7B.!!$R3 1090

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
193 208 1.045407 AATCTAGCGGCCGGTTCATA 58.955 50.0 37.09 16.88 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1746 0.179045 GTAGCGGGGATGCAATGTCT 60.179 55.0 0.0 0.0 37.31 3.41 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
54 55 7.462571 AAAAACCCAGGTACATGTCTAATTC 57.537 36.000 0.00 0.00 0.00 2.17
59 60 4.202161 CCAGGTACATGTCTAATTCGCTCT 60.202 45.833 0.00 0.00 0.00 4.09
60 61 4.979197 CAGGTACATGTCTAATTCGCTCTC 59.021 45.833 0.00 0.00 0.00 3.20
68 69 4.097135 TGTCTAATTCGCTCTCTGAAGGAG 59.903 45.833 0.00 0.00 43.12 3.69
78 79 5.534207 CTCTCTGAAGGAGCATACATCTT 57.466 43.478 0.00 0.00 41.60 2.40
79 80 5.273674 TCTCTGAAGGAGCATACATCTTG 57.726 43.478 0.00 0.00 41.60 3.02
87 100 3.559242 GGAGCATACATCTTGAGAAGCAC 59.441 47.826 0.00 0.00 0.00 4.40
90 103 4.634883 AGCATACATCTTGAGAAGCACAAG 59.365 41.667 0.00 0.00 43.92 3.16
193 208 1.045407 AATCTAGCGGCCGGTTCATA 58.955 50.000 37.09 16.88 0.00 2.15
947 967 3.100671 AGCTAACAGGTAACAGCTAGCT 58.899 45.455 12.68 12.68 42.41 3.32
948 968 4.279145 AGCTAACAGGTAACAGCTAGCTA 58.721 43.478 18.86 0.00 43.36 3.32
949 969 4.896482 AGCTAACAGGTAACAGCTAGCTAT 59.104 41.667 18.86 12.13 43.36 2.97
950 970 6.069331 AGCTAACAGGTAACAGCTAGCTATA 58.931 40.000 18.86 11.04 43.36 1.31
1047 1076 2.518587 TCGGATCGGGTGAGCGAT 60.519 61.111 0.00 0.00 0.00 4.58
1366 1536 1.879380 CGATTCCTTGGTGCTGTTGAA 59.121 47.619 0.00 0.00 0.00 2.69
1399 1569 3.255149 TCCTACACCACGTTTCTTCTCTC 59.745 47.826 0.00 0.00 0.00 3.20
1462 1645 2.988493 GTTGCCATATGTGTGCACTTTG 59.012 45.455 19.41 8.06 33.31 2.77
1491 1674 6.819146 TGCACATTGTAATTTACGGATAGACA 59.181 34.615 2.30 0.00 0.00 3.41
1559 1746 1.206132 CGTGGCTATTCTACACCCACA 59.794 52.381 8.60 0.00 44.71 4.17
1569 1756 2.305635 TCTACACCCACAGACATTGCAT 59.694 45.455 0.00 0.00 0.00 3.96
1584 1771 3.120086 GCATCCCCGCTACACCCAT 62.120 63.158 0.00 0.00 0.00 4.00
1598 1785 6.183360 CGCTACACCCATGATTGAAAACTTAT 60.183 38.462 0.00 0.00 0.00 1.73
1635 1823 3.356529 AATCCGGAACTTTGCAGATCT 57.643 42.857 9.01 0.00 0.00 2.75
1660 1849 6.208402 TGATTAGAGCAAATGTTTTAGGTGCA 59.792 34.615 0.00 0.00 37.68 4.57
1667 1856 5.442402 CAAATGTTTTAGGTGCATGCAAAC 58.558 37.500 24.58 21.96 0.00 2.93
1671 1860 4.808364 TGTTTTAGGTGCATGCAAACTTTC 59.192 37.500 24.58 8.71 0.00 2.62
1792 1981 5.484173 TTCATATGGAGTTCATTCGTTGC 57.516 39.130 2.13 0.00 37.30 4.17
1798 1987 5.545658 TGGAGTTCATTCGTTGCTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
1803 1992 2.863740 TCATTCGTTGCTATTTCGCGAT 59.136 40.909 10.88 0.00 0.00 4.58
1907 2113 6.746104 TTTGATTTTACTGTTCATTGCGTG 57.254 33.333 0.00 0.00 0.00 5.34
1908 2114 4.793071 TGATTTTACTGTTCATTGCGTGG 58.207 39.130 0.00 0.00 0.00 4.94
1909 2115 3.634568 TTTTACTGTTCATTGCGTGGG 57.365 42.857 0.00 0.00 0.00 4.61
1910 2116 2.264005 TTACTGTTCATTGCGTGGGT 57.736 45.000 0.00 0.00 0.00 4.51
1911 2117 1.518325 TACTGTTCATTGCGTGGGTG 58.482 50.000 0.00 0.00 0.00 4.61
1912 2118 1.081242 CTGTTCATTGCGTGGGTGC 60.081 57.895 0.00 0.00 0.00 5.01
1913 2119 1.794151 CTGTTCATTGCGTGGGTGCA 61.794 55.000 0.00 0.00 44.61 4.57
1914 2120 1.177895 TGTTCATTGCGTGGGTGCAT 61.178 50.000 0.00 0.00 45.78 3.96
1915 2121 0.456653 GTTCATTGCGTGGGTGCATC 60.457 55.000 0.00 0.00 45.78 3.91
1916 2122 0.892814 TTCATTGCGTGGGTGCATCA 60.893 50.000 0.00 0.00 45.78 3.07
1917 2123 0.892814 TCATTGCGTGGGTGCATCAA 60.893 50.000 0.00 0.00 45.78 2.57
1918 2124 0.038435 CATTGCGTGGGTGCATCAAA 60.038 50.000 0.00 0.00 45.78 2.69
1919 2125 0.038343 ATTGCGTGGGTGCATCAAAC 60.038 50.000 0.00 0.00 45.78 2.93
1920 2126 2.126888 GCGTGGGTGCATCAAACG 60.127 61.111 17.36 17.36 37.32 3.60
1921 2127 2.903547 GCGTGGGTGCATCAAACGT 61.904 57.895 21.06 0.00 36.65 3.99
1929 2135 1.361993 GCATCAAACGTGGGTGCAA 59.638 52.632 17.90 0.00 37.00 4.08
2067 2276 0.679505 GGCCTGAGATATACGCCACA 59.320 55.000 0.00 0.00 39.50 4.17
2143 2352 9.474313 AAGTAAATGATGGGTTAATTAGAAGCA 57.526 29.630 0.00 0.00 0.00 3.91
2144 2353 9.474313 AGTAAATGATGGGTTAATTAGAAGCAA 57.526 29.630 0.00 0.00 0.00 3.91
2145 2354 9.736023 GTAAATGATGGGTTAATTAGAAGCAAG 57.264 33.333 0.00 0.00 0.00 4.01
2146 2355 8.593945 AAATGATGGGTTAATTAGAAGCAAGA 57.406 30.769 0.00 0.00 0.00 3.02
2147 2356 7.814264 ATGATGGGTTAATTAGAAGCAAGAG 57.186 36.000 0.00 0.00 0.00 2.85
2148 2357 6.957631 TGATGGGTTAATTAGAAGCAAGAGA 58.042 36.000 0.00 0.00 0.00 3.10
2149 2358 7.402054 TGATGGGTTAATTAGAAGCAAGAGAA 58.598 34.615 0.00 0.00 0.00 2.87
2150 2359 8.055181 TGATGGGTTAATTAGAAGCAAGAGAAT 58.945 33.333 0.00 0.00 0.00 2.40
2151 2360 8.829373 ATGGGTTAATTAGAAGCAAGAGAATT 57.171 30.769 0.00 0.00 0.00 2.17
2152 2361 9.920946 ATGGGTTAATTAGAAGCAAGAGAATTA 57.079 29.630 0.00 0.00 0.00 1.40
2153 2362 9.396022 TGGGTTAATTAGAAGCAAGAGAATTAG 57.604 33.333 0.00 0.00 0.00 1.73
2154 2363 9.397280 GGGTTAATTAGAAGCAAGAGAATTAGT 57.603 33.333 0.00 0.00 0.00 2.24
2161 2370 7.061566 AGAAGCAAGAGAATTAGTCTATCCC 57.938 40.000 0.00 0.00 36.41 3.85
2162 2371 6.843861 AGAAGCAAGAGAATTAGTCTATCCCT 59.156 38.462 0.00 0.00 36.41 4.20
2163 2372 8.007742 AGAAGCAAGAGAATTAGTCTATCCCTA 58.992 37.037 0.00 0.00 36.41 3.53
2164 2373 8.554490 AAGCAAGAGAATTAGTCTATCCCTAA 57.446 34.615 0.00 0.00 36.41 2.69
2165 2374 8.554490 AGCAAGAGAATTAGTCTATCCCTAAA 57.446 34.615 0.00 0.00 36.41 1.85
2166 2375 8.993424 AGCAAGAGAATTAGTCTATCCCTAAAA 58.007 33.333 0.00 0.00 36.41 1.52
2167 2376 9.614792 GCAAGAGAATTAGTCTATCCCTAAAAA 57.385 33.333 0.00 0.00 36.41 1.94
2208 2417 7.766219 TCCACGTTAATCAGAAAATACTAGC 57.234 36.000 0.00 0.00 0.00 3.42
2209 2418 6.759827 TCCACGTTAATCAGAAAATACTAGCC 59.240 38.462 0.00 0.00 0.00 3.93
2210 2419 6.018180 CCACGTTAATCAGAAAATACTAGCCC 60.018 42.308 0.00 0.00 0.00 5.19
2211 2420 6.761714 CACGTTAATCAGAAAATACTAGCCCT 59.238 38.462 0.00 0.00 0.00 5.19
2212 2421 7.924412 CACGTTAATCAGAAAATACTAGCCCTA 59.076 37.037 0.00 0.00 0.00 3.53
2213 2422 8.142551 ACGTTAATCAGAAAATACTAGCCCTAG 58.857 37.037 0.88 0.88 39.04 3.02
2214 2423 8.358148 CGTTAATCAGAAAATACTAGCCCTAGA 58.642 37.037 9.20 0.00 36.97 2.43
2217 2426 8.734593 AATCAGAAAATACTAGCCCTAGATCT 57.265 34.615 9.20 0.00 36.97 2.75
2218 2427 7.531857 TCAGAAAATACTAGCCCTAGATCTG 57.468 40.000 5.18 12.13 36.97 2.90
2219 2428 6.495181 TCAGAAAATACTAGCCCTAGATCTGG 59.505 42.308 5.18 1.30 36.97 3.86
2220 2429 6.268847 CAGAAAATACTAGCCCTAGATCTGGT 59.731 42.308 5.18 0.00 36.97 4.00
2221 2430 6.847036 AGAAAATACTAGCCCTAGATCTGGTT 59.153 38.462 5.18 0.00 36.97 3.67
2222 2431 6.426646 AAATACTAGCCCTAGATCTGGTTG 57.573 41.667 5.18 0.00 36.97 3.77
2223 2432 2.683768 ACTAGCCCTAGATCTGGTTGG 58.316 52.381 5.18 1.53 36.97 3.77
2224 2433 2.022918 ACTAGCCCTAGATCTGGTTGGT 60.023 50.000 5.18 2.21 36.97 3.67
2225 2434 1.501582 AGCCCTAGATCTGGTTGGTC 58.498 55.000 5.18 0.00 0.00 4.02
2226 2435 1.008938 AGCCCTAGATCTGGTTGGTCT 59.991 52.381 5.18 0.00 0.00 3.85
2227 2436 1.840635 GCCCTAGATCTGGTTGGTCTT 59.159 52.381 5.18 0.00 0.00 3.01
2228 2437 2.239907 GCCCTAGATCTGGTTGGTCTTT 59.760 50.000 5.18 0.00 0.00 2.52
2229 2438 3.308473 GCCCTAGATCTGGTTGGTCTTTT 60.308 47.826 5.18 0.00 0.00 2.27
2230 2439 4.080526 GCCCTAGATCTGGTTGGTCTTTTA 60.081 45.833 5.18 0.00 0.00 1.52
2231 2440 5.572885 GCCCTAGATCTGGTTGGTCTTTTAA 60.573 44.000 5.18 0.00 0.00 1.52
2232 2441 6.481643 CCCTAGATCTGGTTGGTCTTTTAAA 58.518 40.000 5.18 0.00 0.00 1.52
2233 2442 6.946009 CCCTAGATCTGGTTGGTCTTTTAAAA 59.054 38.462 5.18 0.00 0.00 1.52
2234 2443 7.615757 CCCTAGATCTGGTTGGTCTTTTAAAAT 59.384 37.037 5.18 0.00 0.00 1.82
2235 2444 9.025041 CCTAGATCTGGTTGGTCTTTTAAAATT 57.975 33.333 5.18 0.00 0.00 1.82
2261 2470 8.923609 ATAATCATCTGACTGTTAGATATGCG 57.076 34.615 13.88 3.60 33.30 4.73
2262 2471 5.774498 TCATCTGACTGTTAGATATGCGT 57.226 39.130 13.88 0.00 33.30 5.24
2263 2472 6.877611 TCATCTGACTGTTAGATATGCGTA 57.122 37.500 13.88 0.00 33.30 4.42
2264 2473 7.272037 TCATCTGACTGTTAGATATGCGTAA 57.728 36.000 13.88 0.00 33.30 3.18
2265 2474 7.139392 TCATCTGACTGTTAGATATGCGTAAC 58.861 38.462 13.88 0.00 33.30 2.50
2266 2475 6.445357 TCTGACTGTTAGATATGCGTAACA 57.555 37.500 0.00 0.00 36.91 2.41
2267 2476 7.039313 TCTGACTGTTAGATATGCGTAACAT 57.961 36.000 0.00 0.00 38.23 2.71
2268 2477 8.161699 TCTGACTGTTAGATATGCGTAACATA 57.838 34.615 0.00 0.00 45.25 2.29
2280 2489 6.812481 ATGCGTAACATATATAGCATCGTG 57.188 37.500 0.37 0.00 40.78 4.35
2281 2490 5.099575 TGCGTAACATATATAGCATCGTGG 58.900 41.667 0.00 0.00 0.00 4.94
2282 2491 5.100259 GCGTAACATATATAGCATCGTGGT 58.900 41.667 0.00 0.00 0.00 4.16
2283 2492 6.127952 TGCGTAACATATATAGCATCGTGGTA 60.128 38.462 0.00 0.63 34.60 3.25
2284 2493 6.748658 GCGTAACATATATAGCATCGTGGTAA 59.251 38.462 0.00 0.00 33.73 2.85
2285 2494 7.253552 GCGTAACATATATAGCATCGTGGTAAC 60.254 40.741 0.00 0.00 33.73 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.570672 TGACACAAACTCTAGTACTAGGTG 57.429 41.667 26.06 24.64 34.06 4.00
4 5 7.392494 TCATGACACAAACTCTAGTACTAGG 57.608 40.000 26.06 19.31 34.06 3.02
7 8 8.958119 TTTTTCATGACACAAACTCTAGTACT 57.042 30.769 0.00 0.00 0.00 2.73
59 60 4.958581 TCTCAAGATGTATGCTCCTTCAGA 59.041 41.667 0.00 0.00 0.00 3.27
60 61 5.273674 TCTCAAGATGTATGCTCCTTCAG 57.726 43.478 0.00 0.00 0.00 3.02
68 69 4.730035 GCTTGTGCTTCTCAAGATGTATGC 60.730 45.833 11.41 0.00 43.17 3.14
1366 1536 3.695060 CGTGGTGTAGGAGAGTCAACTAT 59.305 47.826 0.00 0.00 0.00 2.12
1399 1569 5.205759 ACCAGAGAAATCAAAAGGCAAAG 57.794 39.130 0.00 0.00 0.00 2.77
1462 1645 9.594038 CTATCCGTAAATTACAATGTGCATTAC 57.406 33.333 3.91 2.04 0.00 1.89
1546 1733 3.244875 TGCAATGTCTGTGGGTGTAGAAT 60.245 43.478 0.00 0.00 0.00 2.40
1559 1746 0.179045 GTAGCGGGGATGCAATGTCT 60.179 55.000 0.00 0.00 37.31 3.41
1569 1756 0.986019 AATCATGGGTGTAGCGGGGA 60.986 55.000 0.00 0.00 0.00 4.81
1619 1807 5.111989 TCTAATCAGATCTGCAAAGTTCCG 58.888 41.667 18.36 0.00 0.00 4.30
1621 1809 5.583854 TGCTCTAATCAGATCTGCAAAGTTC 59.416 40.000 18.36 10.18 29.35 3.01
1635 1823 6.208402 TGCACCTAAAACATTTGCTCTAATCA 59.792 34.615 0.00 0.00 34.18 2.57
1660 1849 0.749649 TTGGCCACGAAAGTTTGCAT 59.250 45.000 3.88 0.00 46.40 3.96
1667 1856 3.303990 CGGATATCATTTGGCCACGAAAG 60.304 47.826 3.88 0.00 0.00 2.62
1671 1860 1.800586 CTCGGATATCATTTGGCCACG 59.199 52.381 3.88 1.77 0.00 4.94
1739 1928 1.428869 ACTCTTGCTCTTCACCCACT 58.571 50.000 0.00 0.00 0.00 4.00
1747 1936 8.632679 TGAAATGAAATACAAACTCTTGCTCTT 58.367 29.630 0.00 0.00 35.84 2.85
1792 1981 4.402583 TGCAAAGTTTGATCGCGAAATAG 58.597 39.130 19.82 0.00 0.00 1.73
1907 2113 1.901464 ACCCACGTTTGATGCACCC 60.901 57.895 0.00 0.00 0.00 4.61
1908 2114 1.285641 CACCCACGTTTGATGCACC 59.714 57.895 0.00 0.00 0.00 5.01
1909 2115 1.371635 GCACCCACGTTTGATGCAC 60.372 57.895 0.00 0.00 36.30 4.57
1910 2116 1.387295 TTGCACCCACGTTTGATGCA 61.387 50.000 8.92 8.92 44.19 3.96
1911 2117 0.939106 GTTGCACCCACGTTTGATGC 60.939 55.000 4.35 4.35 36.81 3.91
1912 2118 0.318614 GGTTGCACCCACGTTTGATG 60.319 55.000 0.00 0.00 30.04 3.07
1913 2119 0.753479 TGGTTGCACCCACGTTTGAT 60.753 50.000 0.00 0.00 37.50 2.57
1914 2120 1.378646 TGGTTGCACCCACGTTTGA 60.379 52.632 0.00 0.00 37.50 2.69
1915 2121 1.226831 GTGGTTGCACCCACGTTTG 60.227 57.895 18.39 0.00 45.03 2.93
1916 2122 3.202467 GTGGTTGCACCCACGTTT 58.798 55.556 18.39 0.00 45.03 3.60
1921 2127 1.493022 AGAAAGTAGTGGTTGCACCCA 59.507 47.619 0.00 0.00 37.50 4.51
1929 2135 2.288886 GCCGAACAGAGAAAGTAGTGGT 60.289 50.000 0.00 0.00 0.00 4.16
2117 2326 9.474313 TGCTTCTAATTAACCCATCATTTACTT 57.526 29.630 0.00 0.00 0.00 2.24
2118 2327 9.474313 TTGCTTCTAATTAACCCATCATTTACT 57.526 29.630 0.00 0.00 0.00 2.24
2119 2328 9.736023 CTTGCTTCTAATTAACCCATCATTTAC 57.264 33.333 0.00 0.00 0.00 2.01
2120 2329 9.693739 TCTTGCTTCTAATTAACCCATCATTTA 57.306 29.630 0.00 0.00 0.00 1.40
2121 2330 8.593945 TCTTGCTTCTAATTAACCCATCATTT 57.406 30.769 0.00 0.00 0.00 2.32
2122 2331 8.055181 TCTCTTGCTTCTAATTAACCCATCATT 58.945 33.333 0.00 0.00 0.00 2.57
2123 2332 7.577303 TCTCTTGCTTCTAATTAACCCATCAT 58.423 34.615 0.00 0.00 0.00 2.45
2124 2333 6.957631 TCTCTTGCTTCTAATTAACCCATCA 58.042 36.000 0.00 0.00 0.00 3.07
2125 2334 7.865706 TTCTCTTGCTTCTAATTAACCCATC 57.134 36.000 0.00 0.00 0.00 3.51
2126 2335 8.829373 AATTCTCTTGCTTCTAATTAACCCAT 57.171 30.769 0.00 0.00 0.00 4.00
2127 2336 9.396022 CTAATTCTCTTGCTTCTAATTAACCCA 57.604 33.333 0.00 0.00 0.00 4.51
2128 2337 9.397280 ACTAATTCTCTTGCTTCTAATTAACCC 57.603 33.333 0.00 0.00 0.00 4.11
2135 2344 8.643324 GGGATAGACTAATTCTCTTGCTTCTAA 58.357 37.037 0.00 0.00 35.55 2.10
2136 2345 8.007742 AGGGATAGACTAATTCTCTTGCTTCTA 58.992 37.037 0.00 0.00 35.55 2.10
2137 2346 6.843861 AGGGATAGACTAATTCTCTTGCTTCT 59.156 38.462 0.00 0.00 35.55 2.85
2138 2347 7.061566 AGGGATAGACTAATTCTCTTGCTTC 57.938 40.000 0.00 0.00 35.55 3.86
2139 2348 8.554490 TTAGGGATAGACTAATTCTCTTGCTT 57.446 34.615 0.00 0.00 35.55 3.91
2140 2349 8.554490 TTTAGGGATAGACTAATTCTCTTGCT 57.446 34.615 0.00 0.00 35.55 3.91
2141 2350 9.614792 TTTTTAGGGATAGACTAATTCTCTTGC 57.385 33.333 0.00 0.00 35.55 4.01
2182 2391 8.827677 GCTAGTATTTTCTGATTAACGTGGAAT 58.172 33.333 0.00 0.00 0.00 3.01
2183 2392 7.279313 GGCTAGTATTTTCTGATTAACGTGGAA 59.721 37.037 0.00 0.00 0.00 3.53
2184 2393 6.759827 GGCTAGTATTTTCTGATTAACGTGGA 59.240 38.462 0.00 0.00 0.00 4.02
2185 2394 6.018180 GGGCTAGTATTTTCTGATTAACGTGG 60.018 42.308 0.00 0.00 0.00 4.94
2186 2395 6.761714 AGGGCTAGTATTTTCTGATTAACGTG 59.238 38.462 0.00 0.00 0.00 4.49
2187 2396 6.885922 AGGGCTAGTATTTTCTGATTAACGT 58.114 36.000 0.00 0.00 0.00 3.99
2188 2397 8.358148 TCTAGGGCTAGTATTTTCTGATTAACG 58.642 37.037 0.00 0.00 34.84 3.18
2191 2400 9.830186 AGATCTAGGGCTAGTATTTTCTGATTA 57.170 33.333 0.00 0.00 34.84 1.75
2192 2401 8.592809 CAGATCTAGGGCTAGTATTTTCTGATT 58.407 37.037 0.00 0.00 34.84 2.57
2193 2402 7.180051 CCAGATCTAGGGCTAGTATTTTCTGAT 59.820 40.741 0.00 0.00 34.84 2.90
2194 2403 6.495181 CCAGATCTAGGGCTAGTATTTTCTGA 59.505 42.308 0.00 0.00 34.84 3.27
2195 2404 6.268847 ACCAGATCTAGGGCTAGTATTTTCTG 59.731 42.308 13.60 0.00 34.84 3.02
2196 2405 6.386284 ACCAGATCTAGGGCTAGTATTTTCT 58.614 40.000 13.60 0.00 34.84 2.52
2197 2406 6.673839 ACCAGATCTAGGGCTAGTATTTTC 57.326 41.667 13.60 0.00 34.84 2.29
2198 2407 6.183361 CCAACCAGATCTAGGGCTAGTATTTT 60.183 42.308 13.60 0.00 34.84 1.82
2199 2408 5.308237 CCAACCAGATCTAGGGCTAGTATTT 59.692 44.000 13.60 0.00 34.84 1.40
2200 2409 4.841246 CCAACCAGATCTAGGGCTAGTATT 59.159 45.833 13.60 0.00 34.84 1.89
2201 2410 4.140663 ACCAACCAGATCTAGGGCTAGTAT 60.141 45.833 13.60 0.00 34.84 2.12
2202 2411 3.206866 ACCAACCAGATCTAGGGCTAGTA 59.793 47.826 13.60 0.00 34.84 1.82
2203 2412 2.022918 ACCAACCAGATCTAGGGCTAGT 60.023 50.000 13.60 1.03 34.84 2.57
2204 2413 2.630580 GACCAACCAGATCTAGGGCTAG 59.369 54.545 13.60 0.00 34.56 3.42
2205 2414 2.247635 AGACCAACCAGATCTAGGGCTA 59.752 50.000 8.79 0.00 35.50 3.93
2206 2415 1.008938 AGACCAACCAGATCTAGGGCT 59.991 52.381 13.60 9.78 31.31 5.19
2207 2416 1.501582 AGACCAACCAGATCTAGGGC 58.498 55.000 13.60 7.93 0.00 5.19
2208 2417 4.576330 AAAAGACCAACCAGATCTAGGG 57.424 45.455 13.60 6.81 0.00 3.53
2209 2418 7.996098 TTTTAAAAGACCAACCAGATCTAGG 57.004 36.000 0.00 2.07 0.00 3.02
2236 2445 8.526978 ACGCATATCTAACAGTCAGATGATTAT 58.473 33.333 0.00 0.00 34.58 1.28
2237 2446 7.886338 ACGCATATCTAACAGTCAGATGATTA 58.114 34.615 0.00 0.00 34.58 1.75
2238 2447 6.753180 ACGCATATCTAACAGTCAGATGATT 58.247 36.000 0.00 0.00 34.58 2.57
2239 2448 6.338214 ACGCATATCTAACAGTCAGATGAT 57.662 37.500 0.00 0.00 34.58 2.45
2240 2449 5.774498 ACGCATATCTAACAGTCAGATGA 57.226 39.130 0.00 0.00 34.58 2.92
2241 2450 6.918022 TGTTACGCATATCTAACAGTCAGATG 59.082 38.462 0.00 0.00 34.58 2.90
2242 2451 7.039313 TGTTACGCATATCTAACAGTCAGAT 57.961 36.000 0.00 0.00 36.68 2.90
2243 2452 6.445357 TGTTACGCATATCTAACAGTCAGA 57.555 37.500 0.00 0.00 30.90 3.27
2244 2453 8.972262 ATATGTTACGCATATCTAACAGTCAG 57.028 34.615 1.39 0.00 45.02 3.51
2253 2462 8.568794 ACGATGCTATATATGTTACGCATATCT 58.431 33.333 5.22 0.00 45.02 1.98
2254 2463 8.630840 CACGATGCTATATATGTTACGCATATC 58.369 37.037 5.22 0.00 45.02 1.63
2256 2465 6.915843 CCACGATGCTATATATGTTACGCATA 59.084 38.462 5.22 0.00 43.47 3.14
2257 2466 5.748630 CCACGATGCTATATATGTTACGCAT 59.251 40.000 4.96 4.96 40.42 4.73
2258 2467 5.099575 CCACGATGCTATATATGTTACGCA 58.900 41.667 0.00 0.00 0.00 5.24
2259 2468 5.100259 ACCACGATGCTATATATGTTACGC 58.900 41.667 0.00 0.00 0.00 4.42
2260 2469 7.751793 TGTTACCACGATGCTATATATGTTACG 59.248 37.037 0.00 0.00 0.00 3.18
2261 2470 8.975410 TGTTACCACGATGCTATATATGTTAC 57.025 34.615 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.