Multiple sequence alignment - TraesCS4A01G436700

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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 TraesCS4A01G436700 chr4A 100.000 2525 0 0 1 2525 706536515 706539039 0.000000e+00 4663.0
1 TraesCS4A01G436700 chr4A 98.387 186 3 0 1877 2062 706545225 706545410 6.730000e-86 327.0
2 TraesCS4A01G436700 chr7D 93.494 1491 84 8 386 1870 23095678 23094195 0.000000e+00 2204.0
3 TraesCS4A01G436700 chr7D 86.486 370 34 5 1 369 23096388 23096034 2.350000e-105 392.0
4 TraesCS4A01G436700 chr7D 78.544 261 47 8 39 299 42555367 42555618 2.010000e-36 163.0
5 TraesCS4A01G436700 chr7D 79.769 173 33 1 42 214 579543475 579543645 9.480000e-25 124.0
6 TraesCS4A01G436700 chr7A 93.304 1359 75 11 523 1877 23692540 23691194 0.000000e+00 1991.0
7 TraesCS4A01G436700 chr7A 89.773 528 48 4 1 524 23699707 23699182 0.000000e+00 671.0
8 TraesCS4A01G436700 chr7A 85.081 677 62 18 1878 2520 681512338 681511667 0.000000e+00 654.0
9 TraesCS4A01G436700 chr7A 79.325 237 46 3 63 299 41882131 41882364 2.010000e-36 163.0
10 TraesCS4A01G436700 chr3B 93.333 240 11 2 1871 2110 3796152 3796386 1.440000e-92 350.0
11 TraesCS4A01G436700 chr3B 92.500 240 13 2 1871 2110 4694654 4694888 3.110000e-89 339.0
12 TraesCS4A01G436700 chr3B 94.737 190 8 2 1877 2066 4701475 4701662 6.830000e-76 294.0
13 TraesCS4A01G436700 chr3B 94.211 190 9 2 1877 2066 3802996 3803183 3.180000e-74 289.0
14 TraesCS4A01G436700 chr5A 89.333 225 18 6 1877 2097 185833941 185834163 6.880000e-71 278.0
15 TraesCS4A01G436700 chr7B 90.385 208 16 4 1878 2083 610001870 610002075 1.150000e-68 270.0
16 TraesCS4A01G436700 chr7B 77.070 157 27 8 97 249 74484319 74484168 5.790000e-12 82.4
17 TraesCS4A01G436700 chrUn 89.952 209 18 3 1878 2085 85127900 85128106 1.490000e-67 267.0
18 TraesCS4A01G436700 chr6B 88.393 224 21 5 1877 2097 181115302 181115523 5.360000e-67 265.0
19 TraesCS4A01G436700 chr5D 81.897 116 19 2 65 179 525969932 525969818 2.070000e-16 97.1
20 TraesCS4A01G436700 chr1B 77.419 155 32 3 100 253 622484405 622484253 3.460000e-14 89.8
21 TraesCS4A01G436700 chr6A 77.099 131 29 1 101 230 17582848 17582718 9.690000e-10 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 TraesCS4A01G436700 chr4A 706536515 706539039 2524 False 4663 4663 100.000 1 2525 1 chr4A.!!$F1 2524
1 TraesCS4A01G436700 chr7D 23094195 23096388 2193 True 1298 2204 89.990 1 1870 2 chr7D.!!$R1 1869
2 TraesCS4A01G436700 chr7A 23691194 23692540 1346 True 1991 1991 93.304 523 1877 1 chr7A.!!$R1 1354
3 TraesCS4A01G436700 chr7A 23699182 23699707 525 True 671 671 89.773 1 524 1 chr7A.!!$R2 523
4 TraesCS4A01G436700 chr7A 681511667 681512338 671 True 654 654 85.081 1878 2520 1 chr7A.!!$R3 642

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
279 280 0.179032 TTGAGGCAGGTTTGAAGCGA 60.179 50.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2438 0.103208 CGTCGCCCTATTGCTCTCTT 59.897 55.0 0.0 0.0 0.0 2.85 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
35 36 7.096844 CGATTGATTCACTATACTTGTGAGTCG 60.097 40.741 12.32 8.18 46.89 4.18
55 56 3.216292 AGCGGTGTGTTTGGTGGC 61.216 61.111 0.00 0.00 0.00 5.01
56 57 4.279043 GCGGTGTGTTTGGTGGCC 62.279 66.667 0.00 0.00 0.00 5.36
106 107 3.374402 AGGCTGTCTGGTCCGACG 61.374 66.667 8.63 0.00 36.71 5.12
188 189 0.320697 GGTCAGCCCGAGTGTTTAGT 59.679 55.000 0.00 0.00 0.00 2.24
189 190 1.429463 GTCAGCCCGAGTGTTTAGTG 58.571 55.000 0.00 0.00 0.00 2.74
197 198 2.982470 CCGAGTGTTTAGTGACGGTAAC 59.018 50.000 0.00 0.00 36.38 2.50
249 250 2.114625 TCAGTGACCGGTCCGTCT 59.885 61.111 31.19 22.15 33.70 4.18
250 251 0.957395 GTCAGTGACCGGTCCGTCTA 60.957 60.000 31.19 10.01 33.70 2.59
253 254 1.676967 GTGACCGGTCCGTCTACCT 60.677 63.158 31.19 0.00 37.39 3.08
255 256 1.377725 GACCGGTCCGTCTACCTGA 60.378 63.158 24.75 0.00 37.39 3.86
267 268 1.977854 TCTACCTGAGCTTTTGAGGCA 59.022 47.619 0.00 0.00 0.00 4.75
279 280 0.179032 TTGAGGCAGGTTTGAAGCGA 60.179 50.000 0.00 0.00 0.00 4.93
330 331 2.856222 CTGAGATGCCCATCCTTTACC 58.144 52.381 4.72 0.00 38.58 2.85
331 332 2.441001 CTGAGATGCCCATCCTTTACCT 59.559 50.000 4.72 0.00 38.58 3.08
356 358 4.186077 AGAGCCAAGCTAGGTATAGACA 57.814 45.455 0.00 0.00 39.88 3.41
358 360 4.342665 AGAGCCAAGCTAGGTATAGACAAC 59.657 45.833 0.00 0.00 39.88 3.32
389 732 2.204624 TGAGAGAGGGGAGGGGGA 60.205 66.667 0.00 0.00 0.00 4.81
392 735 1.097722 GAGAGAGGGGAGGGGGATAT 58.902 60.000 0.00 0.00 0.00 1.63
466 809 4.343526 TGTGGGTTGATACAAAGTGCAAAT 59.656 37.500 0.00 0.00 0.00 2.32
589 932 8.688151 ACTTGTGTTTTGCTTATTTGGTAAGTA 58.312 29.630 0.00 0.00 41.55 2.24
625 968 4.260334 CGTCGCAACACAATCATCATACAT 60.260 41.667 0.00 0.00 0.00 2.29
626 969 4.965762 GTCGCAACACAATCATCATACATG 59.034 41.667 0.00 0.00 0.00 3.21
723 1066 1.926511 GACAAGGCACGGGCATTCAG 61.927 60.000 13.89 1.53 43.08 3.02
732 1075 2.228822 CACGGGCATTCAGCTAGTTTTT 59.771 45.455 0.00 0.00 44.79 1.94
743 1086 9.436957 CATTCAGCTAGTTTTTAGGTAAGAGAA 57.563 33.333 0.00 0.00 0.00 2.87
802 1146 4.311816 AGACAAAAAGGTGTGCATTGAG 57.688 40.909 1.18 0.00 0.00 3.02
969 1314 4.165779 CCAACATCGTTTCCAGCATTAAC 58.834 43.478 0.00 0.00 0.00 2.01
978 1323 1.643286 TCCAGCATTAACCCCCATGAA 59.357 47.619 0.00 0.00 0.00 2.57
980 1325 1.405105 CAGCATTAACCCCCATGAACG 59.595 52.381 0.00 0.00 0.00 3.95
999 1344 2.534349 ACGTTCGATTGCACGACATATC 59.466 45.455 12.25 0.00 41.97 1.63
1042 1387 2.798680 CTGAAATCATGAGCAGCAAGC 58.201 47.619 0.09 0.00 46.19 4.01
1105 1450 1.002134 AAGAATGGTGACGGCCAGG 60.002 57.895 2.24 0.00 42.47 4.45
1116 1461 1.228124 CGGCCAGGTCACCAAGAAA 60.228 57.895 2.24 0.00 0.00 2.52
1123 1468 3.244561 CCAGGTCACCAAGAAAGAGCTAA 60.245 47.826 0.00 0.00 37.97 3.09
1155 1500 5.071115 GCTCAAGAACCTAGGGATCTACATT 59.929 44.000 14.81 0.00 33.66 2.71
1158 1503 4.298626 AGAACCTAGGGATCTACATTGCA 58.701 43.478 14.81 0.00 33.01 4.08
1160 1505 2.975489 ACCTAGGGATCTACATTGCAGG 59.025 50.000 14.81 0.00 0.00 4.85
1200 1545 3.899360 CCATGGCCAAGATTGATACCAAT 59.101 43.478 10.96 0.00 45.10 3.16
1254 1599 3.702045 GCCTACTATATCGCTCCATCCTT 59.298 47.826 0.00 0.00 0.00 3.36
1366 1711 3.679917 CGGCTACATCACCATTGAAGAGT 60.680 47.826 0.00 0.00 34.61 3.24
1369 1714 4.697352 GCTACATCACCATTGAAGAGTTGT 59.303 41.667 0.00 0.00 34.61 3.32
1428 1773 2.331893 CGTTGAGGAATGCCGCCAA 61.332 57.895 0.00 0.00 39.96 4.52
1446 1791 3.129287 GCCAAATGATCAACAAGGTCGAT 59.871 43.478 0.00 0.00 0.00 3.59
1448 1793 4.156556 CCAAATGATCAACAAGGTCGATGT 59.843 41.667 0.00 0.00 0.00 3.06
1497 1842 0.251354 AGTTCAGCCAGATGATGCGT 59.749 50.000 0.00 0.00 0.00 5.24
1554 1899 1.265236 TGGGAATGGTTCATTGTGGC 58.735 50.000 0.00 0.00 33.90 5.01
1667 2016 6.990349 TGAAACGACCAACTCTTCTCTTTTAT 59.010 34.615 0.00 0.00 0.00 1.40
1688 2038 2.032681 GACGGTGAGGCTGCCTTT 59.967 61.111 24.26 0.05 31.76 3.11
1698 2048 0.244721 GGCTGCCTTTGTCCATGTTC 59.755 55.000 12.43 0.00 0.00 3.18
1761 2112 6.243811 TGGTATTTATCACACAAAACGGTC 57.756 37.500 0.00 0.00 0.00 4.79
1778 2129 1.594331 GTCGGGTGAAGAAGCAAGTT 58.406 50.000 0.00 0.00 0.00 2.66
1801 2152 2.021042 TCCCCCTATCCACTCCTTTGAT 60.021 50.000 0.00 0.00 0.00 2.57
1809 2160 2.092753 TCCACTCCTTTGATGATCCTGC 60.093 50.000 0.00 0.00 0.00 4.85
1814 2165 0.661552 CTTTGATGATCCTGCAGGCG 59.338 55.000 28.91 5.66 34.44 5.52
1870 2221 0.252927 CCCCTCTTCCTCCTCTTGGT 60.253 60.000 0.00 0.00 34.23 3.67
1873 2224 1.650528 CTCTTCCTCCTCTTGGTGGT 58.349 55.000 3.53 0.00 44.94 4.16
1881 2232 3.170717 CTCCTCTTGGTGGTAGGTGTTA 58.829 50.000 0.00 0.00 34.23 2.41
1893 2244 9.369672 TGGTGGTAGGTGTTAAGAAATAAAAAT 57.630 29.630 0.00 0.00 0.00 1.82
1921 2272 2.785269 TCAATTGTATGGGAGGGATGCT 59.215 45.455 5.13 0.00 0.00 3.79
1941 2292 1.279496 TCCCAGGAGATGTCTGTTGG 58.721 55.000 0.00 0.00 0.00 3.77
1942 2293 0.254178 CCCAGGAGATGTCTGTTGGG 59.746 60.000 11.79 11.79 38.84 4.12
1956 2307 0.325272 GTTGGGGAAGAGGTGTCTCC 59.675 60.000 0.00 0.00 40.83 3.71
1957 2308 0.840722 TTGGGGAAGAGGTGTCTCCC 60.841 60.000 0.00 0.00 40.83 4.30
1973 2324 1.228552 CCCCAACACACCCCTTCAG 60.229 63.158 0.00 0.00 0.00 3.02
1975 2326 1.903404 CCAACACACCCCTTCAGCC 60.903 63.158 0.00 0.00 0.00 4.85
1995 2346 3.901844 GCCTGTATATAAGTGGGTCTCCA 59.098 47.826 0.00 0.00 41.58 3.86
2006 2358 0.819582 GGGTCTCCACATTGCAATGG 59.180 55.000 35.85 24.91 40.70 3.16
2014 2366 5.045942 TCTCCACATTGCAATGGAACTAGTA 60.046 40.000 35.85 15.42 44.42 1.82
2022 2374 7.792374 TTGCAATGGAACTAGTAGATCATTC 57.208 36.000 3.59 0.00 0.00 2.67
2024 2376 5.986135 GCAATGGAACTAGTAGATCATTCGT 59.014 40.000 3.59 0.00 0.00 3.85
2025 2377 6.074088 GCAATGGAACTAGTAGATCATTCGTG 60.074 42.308 3.59 2.26 0.00 4.35
2027 2379 6.132791 TGGAACTAGTAGATCATTCGTGTC 57.867 41.667 3.59 0.00 0.00 3.67
2028 2380 5.886474 TGGAACTAGTAGATCATTCGTGTCT 59.114 40.000 3.59 0.00 0.00 3.41
2029 2381 6.038382 TGGAACTAGTAGATCATTCGTGTCTC 59.962 42.308 3.59 0.00 0.00 3.36
2031 2383 7.201750 GGAACTAGTAGATCATTCGTGTCTCTT 60.202 40.741 3.59 0.00 0.00 2.85
2032 2384 7.633193 ACTAGTAGATCATTCGTGTCTCTTT 57.367 36.000 3.59 0.00 0.00 2.52
2034 2386 8.524487 ACTAGTAGATCATTCGTGTCTCTTTTT 58.476 33.333 3.59 0.00 0.00 1.94
2074 2426 3.985008 ACTACAACACGTTATCAGCACA 58.015 40.909 0.00 0.00 0.00 4.57
2075 2427 4.566004 ACTACAACACGTTATCAGCACAT 58.434 39.130 0.00 0.00 0.00 3.21
2076 2428 5.716094 ACTACAACACGTTATCAGCACATA 58.284 37.500 0.00 0.00 0.00 2.29
2077 2429 5.805486 ACTACAACACGTTATCAGCACATAG 59.195 40.000 0.00 0.00 0.00 2.23
2078 2430 4.816392 ACAACACGTTATCAGCACATAGA 58.184 39.130 0.00 0.00 0.00 1.98
2085 2437 4.277174 CGTTATCAGCACATAGACTCTCCT 59.723 45.833 0.00 0.00 0.00 3.69
2086 2438 5.470437 CGTTATCAGCACATAGACTCTCCTA 59.530 44.000 0.00 0.00 0.00 2.94
2087 2439 6.017026 CGTTATCAGCACATAGACTCTCCTAA 60.017 42.308 0.00 0.00 0.00 2.69
2088 2440 7.367285 GTTATCAGCACATAGACTCTCCTAAG 58.633 42.308 0.00 0.00 0.00 2.18
2089 2441 5.117406 TCAGCACATAGACTCTCCTAAGA 57.883 43.478 0.00 0.00 0.00 2.10
2104 2464 2.288518 CCTAAGAGAGCAATAGGGCGAC 60.289 54.545 0.00 0.00 39.27 5.19
2105 2465 0.103208 AAGAGAGCAATAGGGCGACG 59.897 55.000 0.00 0.00 39.27 5.12
2106 2466 1.300233 GAGAGCAATAGGGCGACGG 60.300 63.158 0.00 0.00 39.27 4.79
2107 2467 2.017559 GAGAGCAATAGGGCGACGGT 62.018 60.000 0.00 0.00 39.27 4.83
2108 2468 1.153429 GAGCAATAGGGCGACGGTT 60.153 57.895 0.00 0.00 39.27 4.44
2110 2470 1.448893 GCAATAGGGCGACGGTTGA 60.449 57.895 0.00 0.00 0.00 3.18
2111 2471 0.814010 GCAATAGGGCGACGGTTGAT 60.814 55.000 0.00 0.00 0.00 2.57
2112 2472 1.663695 CAATAGGGCGACGGTTGATT 58.336 50.000 0.00 0.00 0.00 2.57
2113 2473 1.597663 CAATAGGGCGACGGTTGATTC 59.402 52.381 0.00 0.00 0.00 2.52
2114 2474 1.120530 ATAGGGCGACGGTTGATTCT 58.879 50.000 0.00 0.00 0.00 2.40
2115 2475 0.899720 TAGGGCGACGGTTGATTCTT 59.100 50.000 0.00 0.00 0.00 2.52
2116 2476 0.036306 AGGGCGACGGTTGATTCTTT 59.964 50.000 0.00 0.00 0.00 2.52
2117 2477 0.446616 GGGCGACGGTTGATTCTTTC 59.553 55.000 0.00 0.00 0.00 2.62
2118 2478 0.094730 GGCGACGGTTGATTCTTTCG 59.905 55.000 0.00 0.00 0.00 3.46
2119 2479 0.518559 GCGACGGTTGATTCTTTCGC 60.519 55.000 0.00 0.00 44.22 4.70
2120 2480 1.068474 CGACGGTTGATTCTTTCGCT 58.932 50.000 0.00 0.00 0.00 4.93
2122 2482 2.066262 GACGGTTGATTCTTTCGCTCA 58.934 47.619 0.00 0.00 0.00 4.26
2123 2483 1.798813 ACGGTTGATTCTTTCGCTCAC 59.201 47.619 0.00 0.00 0.00 3.51
2124 2484 2.069273 CGGTTGATTCTTTCGCTCACT 58.931 47.619 0.00 0.00 0.00 3.41
2126 2486 3.067106 GGTTGATTCTTTCGCTCACTGA 58.933 45.455 0.00 0.00 0.00 3.41
2128 2488 2.328473 TGATTCTTTCGCTCACTGACG 58.672 47.619 0.00 0.00 0.00 4.35
2129 2489 1.656095 GATTCTTTCGCTCACTGACGG 59.344 52.381 0.00 0.00 0.00 4.79
2130 2490 0.671796 TTCTTTCGCTCACTGACGGA 59.328 50.000 0.00 0.00 0.00 4.69
2131 2491 0.241213 TCTTTCGCTCACTGACGGAG 59.759 55.000 0.00 0.00 35.47 4.63
2137 2497 3.425578 CTCACTGACGGAGCGATTT 57.574 52.632 0.00 0.00 0.00 2.17
2138 2498 1.272781 CTCACTGACGGAGCGATTTC 58.727 55.000 0.00 0.00 0.00 2.17
2139 2499 0.601057 TCACTGACGGAGCGATTTCA 59.399 50.000 0.00 0.00 0.00 2.69
2140 2500 1.204704 TCACTGACGGAGCGATTTCAT 59.795 47.619 0.00 0.00 0.00 2.57
2169 2530 3.008157 AGGAAAATCAATTGGCATGCACA 59.992 39.130 21.36 12.37 0.00 4.57
2208 2569 2.615240 GGTGGCAATGGATTTGTTTCCC 60.615 50.000 0.00 0.00 37.65 3.97
2273 2653 0.952010 TTGCTAAAGGCGACGGTTCC 60.952 55.000 0.00 0.00 45.43 3.62
2285 2665 1.244019 ACGGTTCCATCAGCCTTTGC 61.244 55.000 0.00 0.00 37.95 3.68
2329 2709 2.046023 TGGAGCATGGCCGAAGTG 60.046 61.111 0.00 0.00 0.00 3.16
2446 2826 9.665719 TTATGAGCATGTACTAGTTTTGAATGA 57.334 29.630 0.00 0.00 0.00 2.57
2448 2828 8.032952 TGAGCATGTACTAGTTTTGAATGAAG 57.967 34.615 0.00 0.00 0.00 3.02
2465 2845 6.549364 TGAATGAAGGAACTAACCATTGTGTT 59.451 34.615 0.00 0.00 38.49 3.32
2466 2846 7.721842 TGAATGAAGGAACTAACCATTGTGTTA 59.278 33.333 0.00 0.00 38.49 2.41
2467 2847 8.650143 AATGAAGGAACTAACCATTGTGTTAT 57.350 30.769 0.00 0.00 38.49 1.89
2468 2848 7.447374 TGAAGGAACTAACCATTGTGTTATG 57.553 36.000 0.00 0.00 38.49 1.90
2470 2850 7.504238 TGAAGGAACTAACCATTGTGTTATGTT 59.496 33.333 0.00 0.00 38.49 2.71
2471 2851 7.448748 AGGAACTAACCATTGTGTTATGTTC 57.551 36.000 17.59 17.59 37.66 3.18
2472 2852 6.148811 AGGAACTAACCATTGTGTTATGTTCG 59.851 38.462 18.21 0.00 38.30 3.95
2473 2853 6.072893 GGAACTAACCATTGTGTTATGTTCGT 60.073 38.462 18.21 0.00 38.30 3.85
2474 2854 6.476243 ACTAACCATTGTGTTATGTTCGTC 57.524 37.500 0.00 0.00 30.75 4.20
2485 2865 2.405892 ATGTTCGTCTTTGTTGCTGC 57.594 45.000 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.302345 ACAAGTATAGTGAATCAATCGTAGTTG 57.698 33.333 15.56 15.56 0.00 3.16
35 36 1.355210 CACCAAACACACCGCTGAC 59.645 57.895 0.00 0.00 0.00 3.51
55 56 5.865552 ACAAATTGCATCAAATCTTCGAAGG 59.134 36.000 24.37 8.95 0.00 3.46
56 57 6.583427 TCACAAATTGCATCAAATCTTCGAAG 59.417 34.615 19.35 19.35 0.00 3.79
179 180 3.638160 TCCTGTTACCGTCACTAAACACT 59.362 43.478 0.00 0.00 0.00 3.55
181 182 3.553508 GCTCCTGTTACCGTCACTAAACA 60.554 47.826 0.00 0.00 0.00 2.83
188 189 1.972198 CAGGCTCCTGTTACCGTCA 59.028 57.895 7.75 0.00 39.10 4.35
189 190 4.913126 CAGGCTCCTGTTACCGTC 57.087 61.111 7.75 0.00 39.10 4.79
236 237 1.676635 CAGGTAGACGGACCGGTCA 60.677 63.158 34.40 12.40 44.88 4.02
249 250 1.003580 CCTGCCTCAAAAGCTCAGGTA 59.996 52.381 7.11 0.58 37.16 3.08
250 251 0.251077 CCTGCCTCAAAAGCTCAGGT 60.251 55.000 7.11 0.00 37.16 4.00
253 254 1.682854 CAAACCTGCCTCAAAAGCTCA 59.317 47.619 0.00 0.00 0.00 4.26
255 256 2.071778 TCAAACCTGCCTCAAAAGCT 57.928 45.000 0.00 0.00 0.00 3.74
267 268 2.668550 GCCGGTCGCTTCAAACCT 60.669 61.111 1.90 0.00 33.14 3.50
303 304 2.614987 GGATGGGCATCTCAGCATAGAC 60.615 54.545 0.00 0.00 37.92 2.59
307 308 0.851469 AAGGATGGGCATCTCAGCAT 59.149 50.000 0.00 0.00 37.92 3.79
313 314 2.492025 TGAGGTAAAGGATGGGCATCT 58.508 47.619 0.00 0.00 37.92 2.90
315 316 4.242811 TCTATGAGGTAAAGGATGGGCAT 58.757 43.478 0.00 0.00 0.00 4.40
330 331 6.094881 GTCTATACCTAGCTTGGCTCTATGAG 59.905 46.154 14.60 2.84 40.44 2.90
331 332 5.946972 GTCTATACCTAGCTTGGCTCTATGA 59.053 44.000 14.60 3.02 40.44 2.15
356 358 5.295292 CCTCTCTCACATTGAATATTGCGTT 59.705 40.000 0.00 0.00 0.00 4.84
358 360 4.212847 CCCTCTCTCACATTGAATATTGCG 59.787 45.833 0.00 0.00 0.00 4.85
389 732 1.424638 CGTGGAACCTCCCTCCATAT 58.575 55.000 0.00 0.00 44.69 1.78
392 735 2.606519 CCGTGGAACCTCCCTCCA 60.607 66.667 0.00 0.00 40.77 3.86
589 932 3.874543 TGTTGCGACGAATATTGCCTTAT 59.125 39.130 0.00 0.00 0.00 1.73
698 1041 1.669115 CCCGTGCCTTGTCACAGAG 60.669 63.158 0.00 0.00 36.80 3.35
700 1043 3.357079 GCCCGTGCCTTGTCACAG 61.357 66.667 0.00 0.00 36.80 3.66
705 1048 1.973281 CTGAATGCCCGTGCCTTGT 60.973 57.895 0.00 0.00 36.33 3.16
723 1066 9.064706 AGGTTTTTCTCTTACCTAAAAACTAGC 57.935 33.333 17.25 6.15 45.62 3.42
732 1075 9.470399 AAAAAGACAAGGTTTTTCTCTTACCTA 57.530 29.630 0.00 0.00 41.33 3.08
802 1146 4.561105 GCCATACTAGCTATTCTGGACAC 58.439 47.826 16.79 0.00 0.00 3.67
839 1183 5.485353 AGAGAGATGGAATTAAGGTGTGTCA 59.515 40.000 0.00 0.00 0.00 3.58
841 1185 6.214412 AGAAGAGAGATGGAATTAAGGTGTGT 59.786 38.462 0.00 0.00 0.00 3.72
952 1297 2.375146 GGGGTTAATGCTGGAAACGAT 58.625 47.619 0.00 0.00 0.00 3.73
969 1314 0.732571 CAATCGAACGTTCATGGGGG 59.267 55.000 26.71 10.34 0.00 5.40
978 1323 1.985334 TATGTCGTGCAATCGAACGT 58.015 45.000 7.20 1.30 41.47 3.99
980 1325 4.448891 CATGATATGTCGTGCAATCGAAC 58.551 43.478 0.48 0.00 41.47 3.95
999 1344 2.423185 TCTTGGCCGTTCTATTTGCATG 59.577 45.455 0.00 0.00 0.00 4.06
1024 1369 1.533338 CCGCTTGCTGCTCATGATTTC 60.533 52.381 0.00 0.00 40.11 2.17
1040 1385 3.461773 CCGACTCATCCACCCGCT 61.462 66.667 0.00 0.00 0.00 5.52
1041 1386 3.432051 CTCCGACTCATCCACCCGC 62.432 68.421 0.00 0.00 0.00 6.13
1042 1387 2.808315 CTCCGACTCATCCACCCG 59.192 66.667 0.00 0.00 0.00 5.28
1105 1450 4.632153 TCACTTAGCTCTTTCTTGGTGAC 58.368 43.478 0.00 0.00 0.00 3.67
1123 1468 3.007398 CCTAGGTTCTTGAGCAACTCACT 59.993 47.826 0.00 0.00 40.46 3.41
1155 1500 3.068064 TCCATCTCGTCGCCTGCA 61.068 61.111 0.00 0.00 0.00 4.41
1158 1503 4.194720 GCGTCCATCTCGTCGCCT 62.195 66.667 0.00 0.00 42.33 5.52
1160 1505 4.531912 TCGCGTCCATCTCGTCGC 62.532 66.667 5.77 0.00 44.23 5.19
1200 1545 1.018752 CGTCGATGCAACCATCACCA 61.019 55.000 0.00 0.00 46.59 4.17
1366 1711 3.705934 TTGCCAGCACGGACCACAA 62.706 57.895 0.00 0.00 36.56 3.33
1428 1773 4.578871 TGACATCGACCTTGTTGATCATT 58.421 39.130 0.00 0.00 34.75 2.57
1510 1855 4.201822 GCAATAAAGTCAATCCTCACGACC 60.202 45.833 0.00 0.00 0.00 4.79
1511 1856 4.391830 TGCAATAAAGTCAATCCTCACGAC 59.608 41.667 0.00 0.00 0.00 4.34
1667 2016 1.192146 AGGCAGCCTCACCGTCTTTA 61.192 55.000 8.70 0.00 0.00 1.85
1715 2066 8.617809 ACCATTTACAACGTATAATGAATCCAC 58.382 33.333 11.24 0.00 31.29 4.02
1750 2101 0.306533 CTTCACCCGACCGTTTTGTG 59.693 55.000 0.00 0.00 0.00 3.33
1751 2102 0.178533 TCTTCACCCGACCGTTTTGT 59.821 50.000 0.00 0.00 0.00 2.83
1752 2103 1.263217 CTTCTTCACCCGACCGTTTTG 59.737 52.381 0.00 0.00 0.00 2.44
1761 2112 2.287608 GGAAAACTTGCTTCTTCACCCG 60.288 50.000 0.00 0.00 0.00 5.28
1778 2129 2.580783 CAAAGGAGTGGATAGGGGGAAA 59.419 50.000 0.00 0.00 0.00 3.13
1867 2218 8.763984 TTTTTATTTCTTAACACCTACCACCA 57.236 30.769 0.00 0.00 0.00 4.17
1893 2244 8.496916 CATCCCTCCCATACAATTGATCATATA 58.503 37.037 13.59 0.00 0.00 0.86
1896 2247 5.577100 CATCCCTCCCATACAATTGATCAT 58.423 41.667 13.59 0.00 0.00 2.45
1921 2272 1.630369 CCAACAGACATCTCCTGGGAA 59.370 52.381 0.00 0.00 36.03 3.97
1931 2282 1.352352 CACCTCTTCCCCAACAGACAT 59.648 52.381 0.00 0.00 0.00 3.06
1942 2293 0.325272 GTTGGGGAGACACCTCTTCC 59.675 60.000 0.00 0.00 41.33 3.46
1956 2307 1.903404 GCTGAAGGGGTGTGTTGGG 60.903 63.158 0.00 0.00 0.00 4.12
1957 2308 1.903404 GGCTGAAGGGGTGTGTTGG 60.903 63.158 0.00 0.00 0.00 3.77
1973 2324 3.901844 TGGAGACCCACTTATATACAGGC 59.098 47.826 0.00 0.00 37.58 4.85
1995 2346 6.653020 TGATCTACTAGTTCCATTGCAATGT 58.347 36.000 31.87 19.16 34.60 2.71
2006 2358 7.254227 AGAGACACGAATGATCTACTAGTTC 57.746 40.000 0.00 0.00 0.00 3.01
2050 2402 5.803461 TGTGCTGATAACGTGTTGTAGTATC 59.197 40.000 0.00 0.00 0.00 2.24
2052 2404 5.123805 TGTGCTGATAACGTGTTGTAGTA 57.876 39.130 0.00 0.00 0.00 1.82
2053 2405 3.985008 TGTGCTGATAACGTGTTGTAGT 58.015 40.909 0.00 0.00 0.00 2.73
2062 2414 4.277174 AGGAGAGTCTATGTGCTGATAACG 59.723 45.833 0.00 0.00 0.00 3.18
2085 2437 1.337071 CGTCGCCCTATTGCTCTCTTA 59.663 52.381 0.00 0.00 0.00 2.10
2086 2438 0.103208 CGTCGCCCTATTGCTCTCTT 59.897 55.000 0.00 0.00 0.00 2.85
2087 2439 1.736586 CGTCGCCCTATTGCTCTCT 59.263 57.895 0.00 0.00 0.00 3.10
2088 2440 1.300233 CCGTCGCCCTATTGCTCTC 60.300 63.158 0.00 0.00 0.00 3.20
2089 2441 1.614241 AACCGTCGCCCTATTGCTCT 61.614 55.000 0.00 0.00 0.00 4.09
2090 2442 1.153429 AACCGTCGCCCTATTGCTC 60.153 57.895 0.00 0.00 0.00 4.26
2091 2443 1.449601 CAACCGTCGCCCTATTGCT 60.450 57.895 0.00 0.00 0.00 3.91
2092 2444 0.814010 ATCAACCGTCGCCCTATTGC 60.814 55.000 0.00 0.00 0.00 3.56
2098 2458 0.446616 GAAAGAATCAACCGTCGCCC 59.553 55.000 0.00 0.00 0.00 6.13
2104 2464 2.069273 AGTGAGCGAAAGAATCAACCG 58.931 47.619 0.00 0.00 31.51 4.44
2105 2465 3.067106 TCAGTGAGCGAAAGAATCAACC 58.933 45.455 0.00 0.00 31.51 3.77
2106 2466 3.422343 CGTCAGTGAGCGAAAGAATCAAC 60.422 47.826 8.78 0.00 31.51 3.18
2107 2467 2.731451 CGTCAGTGAGCGAAAGAATCAA 59.269 45.455 8.78 0.00 31.51 2.57
2108 2468 2.328473 CGTCAGTGAGCGAAAGAATCA 58.672 47.619 8.78 0.00 0.00 2.57
2110 2470 1.272490 TCCGTCAGTGAGCGAAAGAAT 59.728 47.619 14.17 0.00 0.00 2.40
2111 2471 0.671796 TCCGTCAGTGAGCGAAAGAA 59.328 50.000 14.17 0.00 0.00 2.52
2112 2472 0.241213 CTCCGTCAGTGAGCGAAAGA 59.759 55.000 14.17 5.16 0.00 2.52
2113 2473 1.347817 GCTCCGTCAGTGAGCGAAAG 61.348 60.000 14.17 11.95 45.05 2.62
2114 2474 1.372997 GCTCCGTCAGTGAGCGAAA 60.373 57.895 14.17 4.32 45.05 3.46
2115 2475 2.258591 GCTCCGTCAGTGAGCGAA 59.741 61.111 14.17 0.00 45.05 4.70
2119 2479 1.272781 GAAATCGCTCCGTCAGTGAG 58.727 55.000 0.00 0.00 45.06 3.51
2120 2480 0.601057 TGAAATCGCTCCGTCAGTGA 59.399 50.000 0.00 0.00 45.93 3.41
2122 2482 1.927895 GATGAAATCGCTCCGTCAGT 58.072 50.000 0.00 0.00 31.13 3.41
2134 2494 9.793252 CAATTGATTTTCCTTAGTCGATGAAAT 57.207 29.630 0.00 0.00 0.00 2.17
2136 2496 7.628366 GCCAATTGATTTTCCTTAGTCGATGAA 60.628 37.037 7.12 0.00 0.00 2.57
2137 2497 6.183360 GCCAATTGATTTTCCTTAGTCGATGA 60.183 38.462 7.12 0.00 0.00 2.92
2138 2498 5.973565 GCCAATTGATTTTCCTTAGTCGATG 59.026 40.000 7.12 0.00 0.00 3.84
2139 2499 5.652014 TGCCAATTGATTTTCCTTAGTCGAT 59.348 36.000 7.12 0.00 0.00 3.59
2140 2500 5.007034 TGCCAATTGATTTTCCTTAGTCGA 58.993 37.500 7.12 0.00 0.00 4.20
2142 2502 5.521372 GCATGCCAATTGATTTTCCTTAGTC 59.479 40.000 6.36 0.00 0.00 2.59
2143 2503 5.046448 TGCATGCCAATTGATTTTCCTTAGT 60.046 36.000 16.68 0.00 0.00 2.24
2144 2504 5.292589 GTGCATGCCAATTGATTTTCCTTAG 59.707 40.000 16.68 0.00 0.00 2.18
2145 2505 5.177326 GTGCATGCCAATTGATTTTCCTTA 58.823 37.500 16.68 0.00 0.00 2.69
2169 2530 2.124983 ATCGCGGAGTGCTTGCAT 60.125 55.556 6.13 0.00 43.27 3.96
2236 2616 5.023533 AGCAATTTAGGCAGTCGATTCTA 57.976 39.130 0.00 0.00 0.00 2.10
2329 2709 2.814269 TGATTACGCATCTCTGTGAGC 58.186 47.619 0.00 0.00 36.69 4.26
2446 2826 7.308348 CGAACATAACACAATGGTTAGTTCCTT 60.308 37.037 17.56 0.00 37.65 3.36
2448 2828 6.072893 ACGAACATAACACAATGGTTAGTTCC 60.073 38.462 17.56 0.00 37.65 3.62
2465 2845 3.058983 CAGCAGCAACAAAGACGAACATA 60.059 43.478 0.00 0.00 0.00 2.29
2466 2846 1.949525 AGCAGCAACAAAGACGAACAT 59.050 42.857 0.00 0.00 0.00 2.71
2467 2847 1.063912 CAGCAGCAACAAAGACGAACA 59.936 47.619 0.00 0.00 0.00 3.18
2468 2848 1.330521 TCAGCAGCAACAAAGACGAAC 59.669 47.619 0.00 0.00 0.00 3.95
2470 2850 1.800586 GATCAGCAGCAACAAAGACGA 59.199 47.619 0.00 0.00 0.00 4.20
2471 2851 1.463034 CGATCAGCAGCAACAAAGACG 60.463 52.381 0.00 0.00 0.00 4.18
2472 2852 1.135859 CCGATCAGCAGCAACAAAGAC 60.136 52.381 0.00 0.00 0.00 3.01
2473 2853 1.159285 CCGATCAGCAGCAACAAAGA 58.841 50.000 0.00 0.00 0.00 2.52
2474 2854 0.169672 CCCGATCAGCAGCAACAAAG 59.830 55.000 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.