Multiple sequence alignment - TraesCS1B01G047800

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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 TraesCS1B01G047800 chr1B 100.000 2786 0 0 1 2786 28026113 28023328 0.000000e+00 5145.0
1 TraesCS1B01G047800 chr1B 82.129 263 27 13 2533 2785 35138502 35138250 1.010000e-49 207.0
2 TraesCS1B01G047800 chr1B 93.233 133 8 1 2038 2170 373383274 373383405 7.870000e-46 195.0
3 TraesCS1B01G047800 chr1B 100.000 28 0 0 2 29 28026085 28026112 5.000000e-03 52.8
4 TraesCS1B01G047800 chr1D 88.643 1946 114 43 153 2064 18894813 18892941 0.000000e+00 2270.0
5 TraesCS1B01G047800 chr1D 90.476 105 9 1 26 129 18895167 18895063 1.350000e-28 137.0
6 TraesCS1B01G047800 chr1A 91.634 1542 79 16 528 2049 20890130 20888619 0.000000e+00 2087.0
7 TraesCS1B01G047800 chr1A 89.130 322 18 9 220 528 20890535 20890218 4.350000e-103 385.0
8 TraesCS1B01G047800 chr7B 94.819 637 19 6 2161 2786 672378643 672379276 0.000000e+00 981.0
9 TraesCS1B01G047800 chr7B 94.643 616 19 7 2183 2786 672331075 672331688 0.000000e+00 942.0
10 TraesCS1B01G047800 chr7B 93.724 478 12 4 2169 2644 672376574 672377035 0.000000e+00 701.0
11 TraesCS1B01G047800 chr7B 93.515 478 12 5 2169 2644 672284737 672285197 0.000000e+00 693.0
12 TraesCS1B01G047800 chr7B 93.082 477 15 10 2169 2644 672349978 672350437 0.000000e+00 682.0
13 TraesCS1B01G047800 chr7B 92.469 478 10 6 2169 2644 672329009 672329462 0.000000e+00 660.0
14 TraesCS1B01G047800 chr7B 93.125 160 2 2 2636 2786 672378651 672378492 2.790000e-55 226.0
15 TraesCS1B01G047800 chr7B 91.824 159 4 2 2637 2786 672331078 672330920 2.170000e-51 213.0
16 TraesCS1B01G047800 chr7B 93.431 137 8 1 2038 2174 110548119 110547984 4.710000e-48 202.0
17 TraesCS1B01G047800 chr7B 78.431 153 27 1 1307 1459 241757740 241757594 8.210000e-16 95.3
18 TraesCS1B01G047800 chr5B 94.444 630 24 4 2167 2786 310000914 310001542 0.000000e+00 959.0
19 TraesCS1B01G047800 chr5B 87.627 687 70 7 1102 1776 518810113 518810796 0.000000e+00 784.0
20 TraesCS1B01G047800 chr5B 83.951 162 24 2 1613 1773 512213142 512213302 1.340000e-33 154.0
21 TraesCS1B01G047800 chr5B 79.904 209 33 9 1571 1773 656926286 656926491 8.040000e-31 145.0
22 TraesCS1B01G047800 chr5D 87.110 706 75 9 1084 1776 429577516 429578218 0.000000e+00 785.0
23 TraesCS1B01G047800 chr5D 82.222 630 82 17 2174 2785 47805215 47804598 1.480000e-142 516.0
24 TraesCS1B01G047800 chr5D 93.233 133 8 1 2038 2170 474089082 474088951 7.870000e-46 195.0
25 TraesCS1B01G047800 chr5D 74.400 500 87 29 1302 1773 520910185 520910671 2.850000e-40 176.0
26 TraesCS1B01G047800 chr5A 87.110 706 75 8 1084 1776 545530728 545531430 0.000000e+00 785.0
27 TraesCS1B01G047800 chr5A 76.976 291 51 14 1494 1773 649441861 649442146 4.810000e-33 152.0
28 TraesCS1B01G047800 chr4B 91.115 574 20 7 2224 2786 399197085 399197638 0.000000e+00 749.0
29 TraesCS1B01G047800 chr4B 93.233 133 8 1 2038 2170 215906666 215906797 7.870000e-46 195.0
30 TraesCS1B01G047800 chr4B 93.233 133 8 1 2038 2170 440130565 440130434 7.870000e-46 195.0
31 TraesCS1B01G047800 chr2A 86.667 630 35 21 2168 2786 386011377 386010786 0.000000e+00 652.0
32 TraesCS1B01G047800 chr3D 84.946 372 25 13 2445 2786 5144510 5144880 5.710000e-92 348.0
33 TraesCS1B01G047800 chr3D 79.825 342 39 14 2450 2785 609603621 609603304 3.610000e-54 222.0
34 TraesCS1B01G047800 chr7A 89.513 267 16 5 2531 2786 108227062 108226797 7.440000e-86 327.0
35 TraesCS1B01G047800 chr7A 84.848 264 22 5 2172 2417 108227408 108227145 1.660000e-62 250.0
36 TraesCS1B01G047800 chr3B 93.233 133 7 2 2038 2170 253225816 253225946 7.870000e-46 195.0
37 TraesCS1B01G047800 chr3B 93.233 133 8 1 2038 2170 597392948 597393079 7.870000e-46 195.0
38 TraesCS1B01G047800 chr4D 93.182 132 8 1 2038 2169 331619267 331619137 2.830000e-45 193.0
39 TraesCS1B01G047800 chr6A 92.481 133 9 1 2038 2170 402258207 402258076 3.660000e-44 189.0
40 TraesCS1B01G047800 chr2B 83.146 178 27 3 1182 1358 198539888 198540063 2.870000e-35 159.0
41 TraesCS1B01G047800 chr7D 70.898 646 135 39 1106 1741 262285897 262286499 4.910000e-18 102.0


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 TraesCS1B01G047800 chr1B 28023328 28026113 2785 True 5145.0 5145 100.0000 1 2786 1 chr1B.!!$R1 2785
1 TraesCS1B01G047800 chr1D 18892941 18895167 2226 True 1203.5 2270 89.5595 26 2064 2 chr1D.!!$R1 2038
2 TraesCS1B01G047800 chr1A 20888619 20890535 1916 True 1236.0 2087 90.3820 220 2049 2 chr1A.!!$R1 1829
3 TraesCS1B01G047800 chr7B 672376574 672379276 2702 False 841.0 981 94.2715 2161 2786 2 chr7B.!!$F4 625
4 TraesCS1B01G047800 chr7B 672329009 672331688 2679 False 801.0 942 93.5560 2169 2786 2 chr7B.!!$F3 617
5 TraesCS1B01G047800 chr5B 310000914 310001542 628 False 959.0 959 94.4440 2167 2786 1 chr5B.!!$F1 619
6 TraesCS1B01G047800 chr5B 518810113 518810796 683 False 784.0 784 87.6270 1102 1776 1 chr5B.!!$F3 674
7 TraesCS1B01G047800 chr5D 429577516 429578218 702 False 785.0 785 87.1100 1084 1776 1 chr5D.!!$F1 692
8 TraesCS1B01G047800 chr5D 47804598 47805215 617 True 516.0 516 82.2220 2174 2785 1 chr5D.!!$R1 611
9 TraesCS1B01G047800 chr5A 545530728 545531430 702 False 785.0 785 87.1100 1084 1776 1 chr5A.!!$F1 692
10 TraesCS1B01G047800 chr4B 399197085 399197638 553 False 749.0 749 91.1150 2224 2786 1 chr4B.!!$F2 562
11 TraesCS1B01G047800 chr2A 386010786 386011377 591 True 652.0 652 86.6670 2168 2786 1 chr2A.!!$R1 618
12 TraesCS1B01G047800 chr7A 108226797 108227408 611 True 288.5 327 87.1805 2172 2786 2 chr7A.!!$R1 614

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
961 1321 0.037326 TTCACCAGTGACGCTCCATC 60.037 55.0 0.0 0.0 39.66 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2661 7276 1.268352 GAAACGGTGTAATTGGCAGCA 59.732 47.619 12.31 0.0 34.37 4.41 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
73 74 2.124695 GCTCGGGGCTAGGGTTTG 60.125 66.667 0.00 0.00 38.06 2.93
76 77 4.041762 CGGGGCTAGGGTTTGGCA 62.042 66.667 0.00 0.00 0.00 4.92
77 78 2.362503 GGGGCTAGGGTTTGGCAC 60.363 66.667 0.00 0.00 0.00 5.01
138 178 1.399727 GGCTGATTTTTGACACGGACG 60.400 52.381 0.00 0.00 0.00 4.79
139 179 1.399727 GCTGATTTTTGACACGGACGG 60.400 52.381 0.00 0.00 0.00 4.79
162 202 5.403466 GGCTCAGTTTCTTGTGCTTAATTTG 59.597 40.000 0.00 0.00 37.63 2.32
229 457 8.053355 AGGTAGGTCCTTTCCTATTATTGTTTG 58.947 37.037 12.05 0.00 45.67 2.93
307 568 8.252417 TCAACTAAACAAAAGAACTAAAACCCC 58.748 33.333 0.00 0.00 0.00 4.95
348 609 3.382227 TCAGTTCAACCGTCACTTGACTA 59.618 43.478 7.74 0.00 42.66 2.59
349 610 4.038763 TCAGTTCAACCGTCACTTGACTAT 59.961 41.667 7.74 0.00 42.66 2.12
378 639 3.061697 GTCGTACCCGTTAATCAAGCTTG 59.938 47.826 20.81 20.81 35.01 4.01
481 746 1.229428 CCGATCGGTGGAATTCATGG 58.771 55.000 26.35 0.00 0.00 3.66
521 786 5.220154 CGTACGTGATGACATTAACTTGGTC 60.220 44.000 7.22 0.00 0.00 4.02
543 896 6.704050 GGTCATTACTTTGCCTTTGCTTTTTA 59.296 34.615 0.00 0.00 38.71 1.52
549 902 5.634859 ACTTTGCCTTTGCTTTTTATCATCG 59.365 36.000 0.00 0.00 38.71 3.84
600 957 2.125310 CCCACGCCAAGCATACGA 60.125 61.111 0.00 0.00 0.00 3.43
631 988 7.452630 AATATCGAGTAAGCGTCTTCTTTTC 57.547 36.000 0.00 0.00 0.00 2.29
708 1065 2.715758 CACGCATGCATGTTGACAC 58.284 52.632 26.79 8.94 0.00 3.67
709 1066 0.040246 CACGCATGCATGTTGACACA 60.040 50.000 26.79 0.00 37.31 3.72
710 1067 0.883153 ACGCATGCATGTTGACACAT 59.117 45.000 26.79 2.43 45.18 3.21
751 1108 4.089361 TCTCATCCACGCATCACCTATAT 58.911 43.478 0.00 0.00 0.00 0.86
797 1154 4.368067 TGACCTGCCTACCTTAATTACCT 58.632 43.478 0.00 0.00 0.00 3.08
798 1155 4.407945 TGACCTGCCTACCTTAATTACCTC 59.592 45.833 0.00 0.00 0.00 3.85
820 1177 5.847304 TCTTGTTCATCGATTATCTCCTGG 58.153 41.667 0.00 0.00 0.00 4.45
865 1225 2.054687 TGGCACGTACGTACTTTGAG 57.945 50.000 22.34 7.97 0.00 3.02
866 1226 1.337703 TGGCACGTACGTACTTTGAGT 59.662 47.619 22.34 10.38 0.00 3.41
914 1274 3.967467 AGCCAAGAAAGATGGATGGAT 57.033 42.857 0.00 0.00 40.56 3.41
944 1304 5.346822 CAGGTGTCAATTTGCTTGCTAATTC 59.653 40.000 10.94 4.05 34.66 2.17
961 1321 0.037326 TTCACCAGTGACGCTCCATC 60.037 55.000 0.00 0.00 39.66 3.51
1019 1379 2.592861 GGCCGGCAATGGAGCTAG 60.593 66.667 30.85 0.00 34.17 3.42
1021 1381 2.969238 CCGGCAATGGAGCTAGCG 60.969 66.667 9.55 0.00 34.17 4.26
1024 1384 2.203126 GCAATGGAGCTAGCGCCT 60.203 61.111 33.41 18.83 36.82 5.52
1044 1404 1.446966 GAGGCAGCTCACTCCGTTC 60.447 63.158 3.31 0.00 0.00 3.95
1051 1411 2.282958 TCACTCCGTTCCCGCTCT 60.283 61.111 0.00 0.00 0.00 4.09
1063 1423 2.136878 CCGCTCTACCTGGCCATCT 61.137 63.158 5.51 0.00 0.00 2.90
1856 2232 4.695455 ACAGTGGACATGTATGCAGTTTAC 59.305 41.667 0.00 0.00 0.00 2.01
1857 2233 4.094887 CAGTGGACATGTATGCAGTTTACC 59.905 45.833 0.00 0.00 0.00 2.85
1865 2241 7.721402 ACATGTATGCAGTTTACCTTTTTCAA 58.279 30.769 0.00 0.00 0.00 2.69
1911 2291 8.702163 AAAAAGGGATTACAAATCTTTATGCG 57.298 30.769 0.11 0.00 0.00 4.73
1914 2294 6.357367 AGGGATTACAAATCTTTATGCGTCT 58.643 36.000 0.11 0.00 0.00 4.18
2053 2439 9.399797 TGATTATTTCTTCAGCAATGTATGACT 57.600 29.630 0.00 0.00 0.00 3.41
2059 2445 5.422012 TCTTCAGCAATGTATGACTACTCCA 59.578 40.000 0.00 0.00 0.00 3.86
2064 2450 5.600069 AGCAATGTATGACTACTCCATCTCA 59.400 40.000 0.00 0.00 0.00 3.27
2065 2451 5.925397 GCAATGTATGACTACTCCATCTCAG 59.075 44.000 0.00 0.00 0.00 3.35
2066 2452 6.453943 CAATGTATGACTACTCCATCTCAGG 58.546 44.000 0.00 0.00 0.00 3.86
2067 2453 5.130705 TGTATGACTACTCCATCTCAGGT 57.869 43.478 0.00 0.00 0.00 4.00
2068 2454 4.889995 TGTATGACTACTCCATCTCAGGTG 59.110 45.833 0.00 0.00 0.00 4.00
2069 2455 3.739401 TGACTACTCCATCTCAGGTGA 57.261 47.619 0.00 0.00 0.00 4.02
2070 2456 4.256983 TGACTACTCCATCTCAGGTGAT 57.743 45.455 0.00 0.00 0.00 3.06
2071 2457 3.956848 TGACTACTCCATCTCAGGTGATG 59.043 47.826 0.00 4.73 42.38 3.07
2072 2458 4.211125 GACTACTCCATCTCAGGTGATGA 58.789 47.826 11.73 0.00 44.71 2.92
2073 2459 4.813809 ACTACTCCATCTCAGGTGATGAT 58.186 43.478 11.73 2.04 44.71 2.45
2074 2460 4.832266 ACTACTCCATCTCAGGTGATGATC 59.168 45.833 11.73 0.00 44.71 2.92
2075 2461 2.627221 ACTCCATCTCAGGTGATGATCG 59.373 50.000 11.73 3.97 44.71 3.69
2076 2462 1.966354 TCCATCTCAGGTGATGATCGG 59.034 52.381 11.73 5.54 44.71 4.18
2077 2463 1.966354 CCATCTCAGGTGATGATCGGA 59.034 52.381 11.73 0.00 44.71 4.55
2078 2464 2.288702 CCATCTCAGGTGATGATCGGAC 60.289 54.545 11.73 0.00 44.71 4.79
2079 2465 2.143876 TCTCAGGTGATGATCGGACA 57.856 50.000 0.00 0.00 37.28 4.02
2080 2466 2.670939 TCTCAGGTGATGATCGGACAT 58.329 47.619 0.00 0.00 37.28 3.06
2081 2467 2.363359 TCTCAGGTGATGATCGGACATG 59.637 50.000 0.00 0.00 37.28 3.21
2082 2468 1.413812 TCAGGTGATGATCGGACATGG 59.586 52.381 0.00 0.00 31.12 3.66
2083 2469 1.139654 CAGGTGATGATCGGACATGGT 59.860 52.381 0.00 0.00 0.00 3.55
2084 2470 1.839994 AGGTGATGATCGGACATGGTT 59.160 47.619 0.00 0.00 0.00 3.67
2085 2471 2.239654 AGGTGATGATCGGACATGGTTT 59.760 45.455 0.00 0.00 0.00 3.27
2086 2472 3.454447 AGGTGATGATCGGACATGGTTTA 59.546 43.478 0.00 0.00 0.00 2.01
2087 2473 3.809832 GGTGATGATCGGACATGGTTTAG 59.190 47.826 0.00 0.00 0.00 1.85
2088 2474 4.442706 GTGATGATCGGACATGGTTTAGT 58.557 43.478 0.00 0.00 0.00 2.24
2089 2475 4.876107 GTGATGATCGGACATGGTTTAGTT 59.124 41.667 0.00 0.00 0.00 2.24
2090 2476 6.046593 GTGATGATCGGACATGGTTTAGTTA 58.953 40.000 0.00 0.00 0.00 2.24
2091 2477 6.537301 GTGATGATCGGACATGGTTTAGTTAA 59.463 38.462 0.00 0.00 0.00 2.01
2092 2478 7.226720 GTGATGATCGGACATGGTTTAGTTAAT 59.773 37.037 0.00 0.00 0.00 1.40
2093 2479 7.773224 TGATGATCGGACATGGTTTAGTTAATT 59.227 33.333 0.00 0.00 0.00 1.40
2094 2480 7.931578 TGATCGGACATGGTTTAGTTAATTT 57.068 32.000 0.00 0.00 0.00 1.82
2095 2481 7.757526 TGATCGGACATGGTTTAGTTAATTTG 58.242 34.615 0.00 0.00 0.00 2.32
2096 2482 7.608376 TGATCGGACATGGTTTAGTTAATTTGA 59.392 33.333 0.00 0.00 0.00 2.69
2097 2483 7.747155 TCGGACATGGTTTAGTTAATTTGAA 57.253 32.000 0.00 0.00 0.00 2.69
2098 2484 8.343168 TCGGACATGGTTTAGTTAATTTGAAT 57.657 30.769 0.00 0.00 0.00 2.57
2099 2485 8.455682 TCGGACATGGTTTAGTTAATTTGAATC 58.544 33.333 0.00 0.00 0.00 2.52
2100 2486 8.240682 CGGACATGGTTTAGTTAATTTGAATCA 58.759 33.333 0.00 0.00 0.00 2.57
2101 2487 9.353999 GGACATGGTTTAGTTAATTTGAATCAC 57.646 33.333 0.00 0.00 0.00 3.06
2102 2488 8.964420 ACATGGTTTAGTTAATTTGAATCACG 57.036 30.769 0.00 0.00 0.00 4.35
2103 2489 8.573035 ACATGGTTTAGTTAATTTGAATCACGT 58.427 29.630 0.00 0.00 0.00 4.49
2118 2504 9.599866 TTTGAATCACGTATCATTTAGATGACT 57.400 29.630 0.00 0.00 44.64 3.41
2119 2505 9.599866 TTGAATCACGTATCATTTAGATGACTT 57.400 29.630 0.00 0.00 44.64 3.01
2120 2506 9.034544 TGAATCACGTATCATTTAGATGACTTG 57.965 33.333 0.00 0.00 44.64 3.16
2121 2507 9.249457 GAATCACGTATCATTTAGATGACTTGA 57.751 33.333 0.00 0.00 44.64 3.02
2122 2508 9.599866 AATCACGTATCATTTAGATGACTTGAA 57.400 29.630 0.00 0.00 44.64 2.69
2123 2509 8.634475 TCACGTATCATTTAGATGACTTGAAG 57.366 34.615 0.00 0.00 44.64 3.02
2124 2510 7.706607 TCACGTATCATTTAGATGACTTGAAGG 59.293 37.037 0.00 0.00 44.64 3.46
2125 2511 7.706607 CACGTATCATTTAGATGACTTGAAGGA 59.293 37.037 0.00 0.00 44.64 3.36
2126 2512 8.424918 ACGTATCATTTAGATGACTTGAAGGAT 58.575 33.333 0.00 0.00 44.64 3.24
2127 2513 8.706936 CGTATCATTTAGATGACTTGAAGGATG 58.293 37.037 0.00 0.00 44.64 3.51
2128 2514 9.553064 GTATCATTTAGATGACTTGAAGGATGT 57.447 33.333 0.00 0.00 44.64 3.06
2129 2515 8.674263 ATCATTTAGATGACTTGAAGGATGTC 57.326 34.615 0.00 0.00 44.64 3.06
2130 2516 7.855375 TCATTTAGATGACTTGAAGGATGTCT 58.145 34.615 0.00 0.00 37.37 3.41
2131 2517 8.981659 TCATTTAGATGACTTGAAGGATGTCTA 58.018 33.333 0.00 0.00 37.37 2.59
2132 2518 9.775854 CATTTAGATGACTTGAAGGATGTCTAT 57.224 33.333 0.00 0.00 35.16 1.98
2133 2519 9.995003 ATTTAGATGACTTGAAGGATGTCTATC 57.005 33.333 0.00 0.00 31.38 2.08
2155 2541 6.697641 TCCAAGTGGGAGTTCTTAAGTAAT 57.302 37.500 1.63 0.00 42.15 1.89
2156 2542 7.801893 TCCAAGTGGGAGTTCTTAAGTAATA 57.198 36.000 1.63 0.00 42.15 0.98
2157 2543 8.388656 TCCAAGTGGGAGTTCTTAAGTAATAT 57.611 34.615 1.63 0.00 42.15 1.28
2158 2544 9.496710 TCCAAGTGGGAGTTCTTAAGTAATATA 57.503 33.333 1.63 0.00 42.15 0.86
2311 6833 1.598130 CAATTCCCGCTCGATCCCC 60.598 63.158 0.00 0.00 0.00 4.81
2377 6984 2.515057 AAGGCCACGTTGCGACAA 60.515 55.556 5.01 0.00 0.00 3.18
2454 7062 1.379044 CCATGTTCCCAGCCAGGTC 60.379 63.158 0.00 0.00 34.66 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.140814 GAAATCCCTGGCCACCGC 61.141 66.667 0.00 0.00 0.00 5.68
26 27 2.046285 GTGAAATCCCTGGCCACCG 61.046 63.158 0.00 0.00 0.00 4.94
27 28 2.046285 CGTGAAATCCCTGGCCACC 61.046 63.158 0.00 0.00 0.00 4.61
28 29 0.608035 TTCGTGAAATCCCTGGCCAC 60.608 55.000 0.00 0.00 0.00 5.01
29 30 0.322456 CTTCGTGAAATCCCTGGCCA 60.322 55.000 4.71 4.71 0.00 5.36
30 31 0.035439 TCTTCGTGAAATCCCTGGCC 60.035 55.000 0.00 0.00 0.00 5.36
31 32 1.373570 CTCTTCGTGAAATCCCTGGC 58.626 55.000 0.00 0.00 0.00 4.85
101 103 2.833913 CCATTCCCCCTCCATCCCG 61.834 68.421 0.00 0.00 0.00 5.14
106 108 0.925720 AATCAGCCATTCCCCCTCCA 60.926 55.000 0.00 0.00 0.00 3.86
111 113 2.566724 TGTCAAAAATCAGCCATTCCCC 59.433 45.455 0.00 0.00 0.00 4.81
112 114 3.588955 GTGTCAAAAATCAGCCATTCCC 58.411 45.455 0.00 0.00 0.00 3.97
138 178 4.773323 ATTAAGCACAAGAAACTGAGCC 57.227 40.909 0.00 0.00 33.87 4.70
139 179 6.208644 TCAAATTAAGCACAAGAAACTGAGC 58.791 36.000 0.00 0.00 33.61 4.26
210 438 5.524535 CCCCCAAACAATAATAGGAAAGGA 58.475 41.667 0.00 0.00 0.00 3.36
307 568 7.276218 TGAACTGACAAGAGAAAAATGCAAAAG 59.724 33.333 0.00 0.00 0.00 2.27
348 609 7.750229 TGATTAACGGGTACGACTATCTTAT 57.250 36.000 0.00 0.00 44.60 1.73
349 610 7.566760 TTGATTAACGGGTACGACTATCTTA 57.433 36.000 0.00 0.00 44.60 2.10
477 742 2.713011 GTACGTACGTCAGTAGCCATG 58.287 52.381 26.53 0.00 32.77 3.66
500 765 4.637276 TGACCAAGTTAATGTCATCACGT 58.363 39.130 0.00 0.00 34.28 4.49
501 766 5.801350 ATGACCAAGTTAATGTCATCACG 57.199 39.130 8.34 0.00 44.21 4.35
502 767 8.268850 AGTAATGACCAAGTTAATGTCATCAC 57.731 34.615 12.58 9.86 46.16 3.06
503 768 8.862325 AAGTAATGACCAAGTTAATGTCATCA 57.138 30.769 12.58 0.21 46.16 3.07
506 771 7.367285 GCAAAGTAATGACCAAGTTAATGTCA 58.633 34.615 4.98 4.98 42.65 3.58
521 786 8.309163 TGATAAAAAGCAAAGGCAAAGTAATG 57.691 30.769 0.00 0.00 44.61 1.90
543 896 6.423001 CGATCCATGCATCATATAACGATGAT 59.577 38.462 16.01 2.02 45.51 2.45
549 902 5.979517 TCGATCGATCCATGCATCATATAAC 59.020 40.000 19.51 0.00 0.00 1.89
608 965 6.797454 AGAAAAGAAGACGCTTACTCGATAT 58.203 36.000 0.00 0.00 0.00 1.63
692 1049 3.706287 ATGTGTCAACATGCATGCG 57.294 47.368 26.53 17.58 45.51 4.73
700 1057 4.884458 TTAAAGCGAACATGTGTCAACA 57.116 36.364 0.00 0.00 41.58 3.33
701 1058 8.447787 AAATATTAAAGCGAACATGTGTCAAC 57.552 30.769 0.00 0.00 0.00 3.18
702 1059 9.469807 AAAAATATTAAAGCGAACATGTGTCAA 57.530 25.926 0.00 0.00 0.00 3.18
751 1108 4.472108 GGGTAGATAGCTAGCTAGAGAGGA 59.528 50.000 27.42 7.09 43.09 3.71
797 1154 5.221521 CCCAGGAGATAATCGATGAACAAGA 60.222 44.000 0.00 0.00 0.00 3.02
798 1155 4.993584 CCCAGGAGATAATCGATGAACAAG 59.006 45.833 0.00 0.00 0.00 3.16
820 1177 6.171213 ACTAAACAAAGTAGGTAGATGCACC 58.829 40.000 0.00 0.00 39.02 5.01
865 1225 9.422196 GATGTTTATTTATAGCGTGTCAAAGAC 57.578 33.333 0.00 0.00 0.00 3.01
866 1226 9.157104 TGATGTTTATTTATAGCGTGTCAAAGA 57.843 29.630 0.00 0.00 0.00 2.52
912 1272 3.242870 GCAAATTGACACCTGGATCGATC 60.243 47.826 17.36 17.36 0.00 3.69
913 1273 2.684881 GCAAATTGACACCTGGATCGAT 59.315 45.455 0.00 0.00 0.00 3.59
914 1274 2.083774 GCAAATTGACACCTGGATCGA 58.916 47.619 0.00 0.00 0.00 3.59
944 1304 1.448540 GGATGGAGCGTCACTGGTG 60.449 63.158 0.00 0.00 0.00 4.17
1024 1384 3.385384 CGGAGTGAGCTGCCTCCA 61.385 66.667 22.08 4.03 46.31 3.86
1044 1404 3.164269 ATGGCCAGGTAGAGCGGG 61.164 66.667 13.05 0.00 0.00 6.13
1051 1411 2.270434 AGGAAGAAGATGGCCAGGTA 57.730 50.000 13.05 0.00 0.00 3.08
1063 1423 2.107041 TTGGCGCCGAGAAGGAAGAA 62.107 55.000 23.90 2.74 45.00 2.52
1098 1458 0.976641 TGGTGAAGCTGAAGGACGAT 59.023 50.000 0.00 0.00 0.00 3.73
1099 1459 0.756294 TTGGTGAAGCTGAAGGACGA 59.244 50.000 0.00 0.00 0.00 4.20
1575 1947 2.674033 TTGCAGGCGCTCTTGCAT 60.674 55.556 26.40 0.00 39.64 3.96
1885 2265 9.796120 CGCATAAAGATTTGTAATCCCTTTTTA 57.204 29.630 0.00 0.00 0.00 1.52
1967 2347 6.883756 TCATCCATTTTGTGCTACTGATTACA 59.116 34.615 0.00 0.00 0.00 2.41
2027 2412 9.399797 AGTCATACATTGCTGAAGAAATAATCA 57.600 29.630 0.00 0.00 0.00 2.57
2049 2435 3.739401 TCACCTGAGATGGAGTAGTCA 57.261 47.619 0.00 0.00 0.00 3.41
2050 2436 4.211125 TCATCACCTGAGATGGAGTAGTC 58.789 47.826 4.33 0.00 44.30 2.59
2051 2437 4.256983 TCATCACCTGAGATGGAGTAGT 57.743 45.455 4.33 0.00 44.30 2.73
2052 2438 4.082841 CGATCATCACCTGAGATGGAGTAG 60.083 50.000 4.33 0.00 44.30 2.57
2053 2439 3.823304 CGATCATCACCTGAGATGGAGTA 59.177 47.826 4.33 0.00 44.30 2.59
2054 2440 2.627221 CGATCATCACCTGAGATGGAGT 59.373 50.000 4.33 0.00 44.30 3.85
2059 2445 2.670939 TGTCCGATCATCACCTGAGAT 58.329 47.619 0.00 0.00 37.28 2.75
2064 2450 1.500474 ACCATGTCCGATCATCACCT 58.500 50.000 0.00 0.00 0.00 4.00
2065 2451 2.332063 AACCATGTCCGATCATCACC 57.668 50.000 0.00 0.00 0.00 4.02
2066 2452 4.442706 ACTAAACCATGTCCGATCATCAC 58.557 43.478 0.00 0.00 0.00 3.06
2067 2453 4.753516 ACTAAACCATGTCCGATCATCA 57.246 40.909 0.00 0.00 0.00 3.07
2068 2454 7.730364 ATTAACTAAACCATGTCCGATCATC 57.270 36.000 0.00 0.00 0.00 2.92
2069 2455 8.405531 CAAATTAACTAAACCATGTCCGATCAT 58.594 33.333 0.00 0.00 0.00 2.45
2070 2456 7.608376 TCAAATTAACTAAACCATGTCCGATCA 59.392 33.333 0.00 0.00 0.00 2.92
2071 2457 7.981142 TCAAATTAACTAAACCATGTCCGATC 58.019 34.615 0.00 0.00 0.00 3.69
2072 2458 7.931578 TCAAATTAACTAAACCATGTCCGAT 57.068 32.000 0.00 0.00 0.00 4.18
2073 2459 7.747155 TTCAAATTAACTAAACCATGTCCGA 57.253 32.000 0.00 0.00 0.00 4.55
2074 2460 8.240682 TGATTCAAATTAACTAAACCATGTCCG 58.759 33.333 0.00 0.00 0.00 4.79
2075 2461 9.353999 GTGATTCAAATTAACTAAACCATGTCC 57.646 33.333 0.00 0.00 0.00 4.02
2076 2462 9.061610 CGTGATTCAAATTAACTAAACCATGTC 57.938 33.333 0.00 0.00 0.00 3.06
2077 2463 8.573035 ACGTGATTCAAATTAACTAAACCATGT 58.427 29.630 0.00 0.00 0.00 3.21
2078 2464 8.964420 ACGTGATTCAAATTAACTAAACCATG 57.036 30.769 0.00 0.00 0.00 3.66
2092 2478 9.599866 AGTCATCTAAATGATACGTGATTCAAA 57.400 29.630 0.00 0.00 43.62 2.69
2093 2479 9.599866 AAGTCATCTAAATGATACGTGATTCAA 57.400 29.630 0.00 0.00 43.62 2.69
2094 2480 9.034544 CAAGTCATCTAAATGATACGTGATTCA 57.965 33.333 0.00 0.00 43.62 2.57
2095 2481 9.249457 TCAAGTCATCTAAATGATACGTGATTC 57.751 33.333 0.00 0.00 43.62 2.52
2096 2482 9.599866 TTCAAGTCATCTAAATGATACGTGATT 57.400 29.630 0.00 0.00 43.62 2.57
2097 2483 9.254133 CTTCAAGTCATCTAAATGATACGTGAT 57.746 33.333 0.00 0.00 43.62 3.06
2098 2484 7.706607 CCTTCAAGTCATCTAAATGATACGTGA 59.293 37.037 0.00 0.00 43.62 4.35
2099 2485 7.706607 TCCTTCAAGTCATCTAAATGATACGTG 59.293 37.037 0.00 0.00 43.62 4.49
2100 2486 7.782049 TCCTTCAAGTCATCTAAATGATACGT 58.218 34.615 0.00 0.00 43.62 3.57
2101 2487 8.706936 CATCCTTCAAGTCATCTAAATGATACG 58.293 37.037 0.00 0.00 43.62 3.06
2102 2488 9.553064 ACATCCTTCAAGTCATCTAAATGATAC 57.447 33.333 0.00 0.00 43.62 2.24
2103 2489 9.770097 GACATCCTTCAAGTCATCTAAATGATA 57.230 33.333 0.00 0.00 43.62 2.15
2104 2490 8.492782 AGACATCCTTCAAGTCATCTAAATGAT 58.507 33.333 0.00 0.00 43.62 2.45
2105 2491 7.855375 AGACATCCTTCAAGTCATCTAAATGA 58.145 34.615 0.00 0.00 39.63 2.57
2106 2492 9.775854 ATAGACATCCTTCAAGTCATCTAAATG 57.224 33.333 0.00 0.00 34.80 2.32
2107 2493 9.995003 GATAGACATCCTTCAAGTCATCTAAAT 57.005 33.333 0.00 0.00 34.80 1.40
2108 2494 8.424918 GGATAGACATCCTTCAAGTCATCTAAA 58.575 37.037 0.00 0.00 46.47 1.85
2109 2495 7.957002 GGATAGACATCCTTCAAGTCATCTAA 58.043 38.462 0.00 0.00 46.47 2.10
2110 2496 7.531857 GGATAGACATCCTTCAAGTCATCTA 57.468 40.000 0.00 0.00 46.47 1.98
2111 2497 6.418057 GGATAGACATCCTTCAAGTCATCT 57.582 41.667 0.00 0.00 46.47 2.90
2124 2510 4.407296 AGAACTCCCACTTGGATAGACATC 59.593 45.833 0.00 0.00 44.07 3.06
2125 2511 4.366267 AGAACTCCCACTTGGATAGACAT 58.634 43.478 0.00 0.00 44.07 3.06
2126 2512 3.791320 AGAACTCCCACTTGGATAGACA 58.209 45.455 0.00 0.00 44.07 3.41
2127 2513 4.828072 AAGAACTCCCACTTGGATAGAC 57.172 45.455 0.00 0.00 44.07 2.59
2128 2514 6.023603 ACTTAAGAACTCCCACTTGGATAGA 58.976 40.000 10.09 0.00 44.07 1.98
2129 2515 6.301169 ACTTAAGAACTCCCACTTGGATAG 57.699 41.667 10.09 0.00 44.07 2.08
2130 2516 7.801893 TTACTTAAGAACTCCCACTTGGATA 57.198 36.000 10.09 0.00 44.07 2.59
2131 2517 6.697641 TTACTTAAGAACTCCCACTTGGAT 57.302 37.500 10.09 0.00 44.07 3.41
2132 2518 6.697641 ATTACTTAAGAACTCCCACTTGGA 57.302 37.500 10.09 0.00 42.41 3.53
2159 2545 9.366216 GGAAATTAGCTTTTCCGTTCAATTAAT 57.634 29.630 12.96 0.00 43.75 1.40
2160 2546 8.751302 GGAAATTAGCTTTTCCGTTCAATTAA 57.249 30.769 12.96 0.00 43.75 1.40
2311 6833 2.845486 CGGAGAGATCGAGCGATAAAG 58.155 52.381 5.24 0.00 34.60 1.85
2377 6984 4.526970 ACATGGGCTTAATCGAGACAAAT 58.473 39.130 0.00 0.00 0.00 2.32
2416 7024 1.676006 GGCCTAATGATGGAAACGTGG 59.324 52.381 0.00 0.00 0.00 4.94
2454 7062 6.566197 ACAGAGAAAACAGGCTTCTATTTG 57.434 37.500 0.00 0.00 33.24 2.32
2506 7114 2.416547 CGACTCCTTGTAAGCACAATGG 59.583 50.000 0.00 0.00 43.58 3.16
2516 7125 4.023980 AGATCATGGTTCGACTCCTTGTA 58.976 43.478 16.03 8.04 33.61 2.41
2661 7276 1.268352 GAAACGGTGTAATTGGCAGCA 59.732 47.619 12.31 0.00 34.37 4.41


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

AutoCloner maintained by Alex Coulton.