Multiple sequence alignment - TraesCS6B01G302600

Loading Multiple Alignment...

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 TraesCS6B01G302600 chr6B 100.000 2540 0 0 1 2540 542232904 542230365 0.000000e+00 4691
1 TraesCS6B01G302600 chr6B 94.737 95 3 2 2035 2128 181295 181388 2.040000e-31 147
2 TraesCS6B01G302600 chr6D 94.008 1185 45 10 106 1271 360688466 360687289 0.000000e+00 1772
3 TraesCS6B01G302600 chr6D 92.084 758 31 10 1269 2009 360687246 360686501 0.000000e+00 1040
4 TraesCS6B01G302600 chr6A 91.533 874 38 12 418 1271 501801957 501801100 0.000000e+00 1171
5 TraesCS6B01G302600 chr6A 87.268 809 42 25 1269 2037 501801057 501800270 0.000000e+00 867
6 TraesCS6B01G302600 chr6A 90.356 477 38 8 7 476 501802486 501802011 9.980000e-174 619
7 TraesCS6B01G302600 chr7B 93.765 417 24 2 2125 2539 285368867 285369283 2.150000e-175 625
8 TraesCS6B01G302600 chr7B 93.301 418 26 2 2125 2540 285365158 285365575 1.290000e-172 616
9 TraesCS6B01G302600 chr7B 93.204 103 4 3 2036 2136 185296612 185296511 5.660000e-32 148
10 TraesCS6B01G302600 chr5B 93.079 419 27 2 2124 2540 161979795 161980213 1.670000e-171 612
11 TraesCS6B01G302600 chr5B 91.148 418 35 2 2125 2540 161976070 161976487 1.320000e-157 566
12 TraesCS6B01G302600 chr5B 91.071 112 6 4 2039 2147 520061858 520061748 5.660000e-32 148
13 TraesCS6B01G302600 chr5B 92.381 105 4 4 2035 2136 692127401 692127504 2.040000e-31 147
14 TraesCS6B01G302600 chr5A 90.931 419 36 2 2124 2540 253470777 253471195 1.710000e-156 562
15 TraesCS6B01G302600 chrUn 90.692 419 37 2 2124 2540 118006400 118006818 7.940000e-155 556
16 TraesCS6B01G302600 chrUn 90.453 419 38 2 2124 2540 72665074 72664656 3.690000e-153 551
17 TraesCS6B01G302600 chrUn 90.476 420 37 2 2124 2540 107963690 107963271 3.690000e-153 551
18 TraesCS6B01G302600 chr4A 90.692 419 36 2 2125 2540 267208541 267208123 2.860000e-154 555
19 TraesCS6B01G302600 chr4A 93.069 101 5 2 2029 2128 728114283 728114382 2.040000e-31 147
20 TraesCS6B01G302600 chr4D 94.000 100 3 3 2039 2136 37604145 37604047 5.660000e-32 148
21 TraesCS6B01G302600 chr3B 93.204 103 3 4 2037 2136 752076633 752076532 5.660000e-32 148
22 TraesCS6B01G302600 chr1B 93.204 103 3 4 2037 2136 463667338 463667237 5.660000e-32 148
23 TraesCS6B01G302600 chr1B 93.878 98 3 3 2032 2128 11133325 11133420 7.320000e-31 145


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 TraesCS6B01G302600 chr6B 542230365 542232904 2539 True 4691.000000 4691 100.0000 1 2540 1 chr6B.!!$R1 2539
1 TraesCS6B01G302600 chr6D 360686501 360688466 1965 True 1406.000000 1772 93.0460 106 2009 2 chr6D.!!$R1 1903
2 TraesCS6B01G302600 chr6A 501800270 501802486 2216 True 885.666667 1171 89.7190 7 2037 3 chr6A.!!$R1 2030
3 TraesCS6B01G302600 chr7B 285365158 285369283 4125 False 620.500000 625 93.5330 2125 2540 2 chr7B.!!$F1 415
4 TraesCS6B01G302600 chr5B 161976070 161980213 4143 False 589.000000 612 92.1135 2124 2540 2 chr5B.!!$F2 416

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
84 86 0.036010 CGCTGAAGGTTCCCTCATGT 60.036 55.0 0.0 0.0 30.89 3.21 F
1188 1331 0.038709 GGAGGAGAAGATCGGCATCG 60.039 60.0 0.0 0.0 33.75 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1676 0.108186 TCAAGCCTGCGTACATCTGG 60.108 55.0 0.0 0.0 0.0 3.86 R
2455 6454 0.810031 CCATAACTCAACGCTCCGGG 60.810 60.0 0.0 0.0 0.0 5.73 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
23 24 5.662456 GAGACTACCCTTTGACATCTAACC 58.338 45.833 0.00 0.00 0.00 2.85
29 30 2.678336 CCTTTGACATCTAACCGCCTTC 59.322 50.000 0.00 0.00 0.00 3.46
62 64 2.142761 ACCAGAGTGCAGTGGCTGA 61.143 57.895 10.96 0.00 41.91 4.26
84 86 0.036010 CGCTGAAGGTTCCCTCATGT 60.036 55.000 0.00 0.00 30.89 3.21
119 121 7.389330 TCGATGTGGTCTTGAAATAAAAGCTTA 59.611 33.333 0.00 0.00 0.00 3.09
136 138 5.464030 AGCTTACCTTTACAAGAGAACGA 57.536 39.130 0.00 0.00 0.00 3.85
203 205 8.919661 GCTGAACAATCTTTAATTTCCTTTCTG 58.080 33.333 0.00 0.00 0.00 3.02
286 290 6.084326 TGTAATTTTCCTTTGAAGTGCTCC 57.916 37.500 0.00 0.00 0.00 4.70
287 291 5.833131 TGTAATTTTCCTTTGAAGTGCTCCT 59.167 36.000 0.00 0.00 0.00 3.69
295 299 4.500375 CCTTTGAAGTGCTCCTTTTTCCTG 60.500 45.833 0.00 0.00 32.03 3.86
306 310 4.079253 TCCTTTTTCCTGGTATTCAGTGC 58.921 43.478 0.00 0.00 41.83 4.40
313 317 3.134623 TCCTGGTATTCAGTGCTGTATGG 59.865 47.826 0.00 0.00 41.83 2.74
338 349 9.256477 GGAATAATACGATGACAGTACATTTCA 57.744 33.333 0.00 0.00 0.00 2.69
353 364 5.999205 ACATTTCAGTGCATTTTCCCATA 57.001 34.783 0.00 0.00 0.00 2.74
357 368 3.700538 TCAGTGCATTTTCCCATAAGCT 58.299 40.909 0.00 0.00 0.00 3.74
359 370 4.158394 TCAGTGCATTTTCCCATAAGCTTC 59.842 41.667 0.00 0.00 0.00 3.86
462 529 0.253044 AACCATGGTGATCGGGACTG 59.747 55.000 20.60 0.00 0.00 3.51
464 531 1.524002 CATGGTGATCGGGACTGCT 59.476 57.895 0.00 0.00 0.00 4.24
465 532 0.107508 CATGGTGATCGGGACTGCTT 60.108 55.000 0.00 0.00 0.00 3.91
472 539 2.171237 TGATCGGGACTGCTTGAATGAT 59.829 45.455 0.00 0.00 0.00 2.45
491 613 7.879677 TGAATGATATGCCGACTTCATCTAAAT 59.120 33.333 0.00 0.00 0.00 1.40
510 633 4.388577 AATAGGGGAAAGTTTGTCTGCT 57.611 40.909 0.00 0.00 0.00 4.24
530 653 3.235195 CTCTAGTTGACTGAAACCGTCG 58.765 50.000 0.00 0.00 34.17 5.12
544 667 1.732259 ACCGTCGCATTTCTCATGTTC 59.268 47.619 0.00 0.00 0.00 3.18
545 668 2.002586 CCGTCGCATTTCTCATGTTCT 58.997 47.619 0.00 0.00 0.00 3.01
632 755 1.291877 CCGCACCCTTTCTGTTCGAG 61.292 60.000 0.00 0.00 0.00 4.04
640 763 3.056107 CCCTTTCTGTTCGAGGATACACA 60.056 47.826 0.00 0.00 41.41 3.72
645 768 4.806330 TCTGTTCGAGGATACACAGAAAC 58.194 43.478 11.88 0.00 42.09 2.78
654 777 4.285260 AGGATACACAGAAACCCGTTAACT 59.715 41.667 3.71 0.00 41.41 2.24
841 969 2.427506 GCTTGGAAGAATCAACGAGGT 58.572 47.619 0.00 0.00 0.00 3.85
862 990 0.528470 GACCCCTCAAGTCACTCGAG 59.472 60.000 11.84 11.84 34.27 4.04
863 991 1.216710 CCCCTCAAGTCACTCGAGC 59.783 63.158 13.61 0.00 0.00 5.03
864 992 1.216710 CCCTCAAGTCACTCGAGCC 59.783 63.158 13.61 0.22 0.00 4.70
865 993 1.153939 CCTCAAGTCACTCGAGCCG 60.154 63.158 13.61 3.95 0.00 5.52
866 994 1.587043 CCTCAAGTCACTCGAGCCGA 61.587 60.000 13.61 6.70 0.00 5.54
965 1093 0.621571 AGCAGCTACCCATTCCTCCA 60.622 55.000 0.00 0.00 0.00 3.86
992 1120 1.292941 CCTCTCCCTCTCCTCCTCCA 61.293 65.000 0.00 0.00 0.00 3.86
993 1121 0.185901 CTCTCCCTCTCCTCCTCCAG 59.814 65.000 0.00 0.00 0.00 3.86
1176 1319 1.000993 GCACAGGAGGAGGAGGAGA 59.999 63.158 0.00 0.00 0.00 3.71
1188 1331 0.038709 GGAGGAGAAGATCGGCATCG 60.039 60.000 0.00 0.00 33.75 3.84
1191 1334 1.068083 GAGAAGATCGGCATCGGCA 59.932 57.895 0.00 0.00 43.71 5.69
1327 1518 3.554692 GCTTCGCCATGGACGACG 61.555 66.667 24.55 23.19 39.67 5.12
1338 1529 3.330853 GACGACGATGATGGCGGC 61.331 66.667 0.00 0.00 0.00 6.53
1485 1676 2.434359 CCGGTTTCTGCGGAGGAC 60.434 66.667 3.37 3.41 0.00 3.85
1587 1781 1.468736 GGCTTGCATTGCAGCTTCTAC 60.469 52.381 23.08 9.96 40.61 2.59
1588 1782 1.471684 GCTTGCATTGCAGCTTCTACT 59.528 47.619 19.32 0.00 40.61 2.57
1589 1783 2.679837 GCTTGCATTGCAGCTTCTACTA 59.320 45.455 19.32 1.01 40.61 1.82
1590 1784 3.486542 GCTTGCATTGCAGCTTCTACTAC 60.487 47.826 19.32 0.00 40.61 2.73
1591 1785 3.616956 TGCATTGCAGCTTCTACTACT 57.383 42.857 7.38 0.00 33.32 2.57
1592 1786 4.736126 TGCATTGCAGCTTCTACTACTA 57.264 40.909 7.38 0.00 33.32 1.82
1616 1810 7.264294 AGATGAGGTTTCTACTTTTCCATCT 57.736 36.000 0.00 0.00 34.98 2.90
1776 2004 1.751924 GTGACCGGAAGAGCAGTCTAT 59.248 52.381 9.46 0.00 30.45 1.98
1887 2138 2.687935 ACCTCGTGTTGCTTTGTTCAAT 59.312 40.909 0.00 0.00 0.00 2.57
1891 2142 5.569059 CCTCGTGTTGCTTTGTTCAATTATC 59.431 40.000 0.00 0.00 0.00 1.75
1905 2156 5.596836 TCAATTATCCTTGGTTTGGATGC 57.403 39.130 5.61 0.00 43.48 3.91
1907 2158 5.662208 TCAATTATCCTTGGTTTGGATGCAT 59.338 36.000 0.00 0.00 43.48 3.96
1928 2179 7.223584 TGCATGTATGTATGTATACTTTGCCT 58.776 34.615 4.17 0.00 39.66 4.75
2037 2288 2.180276 ACTTCATCCCGTAGCTGTCTT 58.820 47.619 0.00 0.00 0.00 3.01
2038 2289 2.567615 ACTTCATCCCGTAGCTGTCTTT 59.432 45.455 0.00 0.00 0.00 2.52
2039 2290 3.008049 ACTTCATCCCGTAGCTGTCTTTT 59.992 43.478 0.00 0.00 0.00 2.27
2040 2291 3.695830 TCATCCCGTAGCTGTCTTTTT 57.304 42.857 0.00 0.00 0.00 1.94
2063 2314 5.883503 TTTTTCATGGTAATACGTGTCCC 57.116 39.130 0.00 0.00 0.00 4.46
2064 2315 4.554960 TTTCATGGTAATACGTGTCCCA 57.445 40.909 0.00 1.78 0.00 4.37
2065 2316 4.764050 TTCATGGTAATACGTGTCCCAT 57.236 40.909 9.71 9.71 36.35 4.00
2066 2317 4.764050 TCATGGTAATACGTGTCCCATT 57.236 40.909 12.04 0.53 33.70 3.16
2067 2318 4.699637 TCATGGTAATACGTGTCCCATTC 58.300 43.478 12.04 0.00 33.70 2.67
2068 2319 4.162509 TCATGGTAATACGTGTCCCATTCA 59.837 41.667 12.04 2.50 33.70 2.57
2069 2320 4.764050 TGGTAATACGTGTCCCATTCAT 57.236 40.909 0.00 0.00 0.00 2.57
2070 2321 5.873146 TGGTAATACGTGTCCCATTCATA 57.127 39.130 0.00 0.00 0.00 2.15
2071 2322 6.428083 TGGTAATACGTGTCCCATTCATAT 57.572 37.500 0.00 0.00 0.00 1.78
2072 2323 6.460781 TGGTAATACGTGTCCCATTCATATC 58.539 40.000 0.00 0.00 0.00 1.63
2073 2324 6.042208 TGGTAATACGTGTCCCATTCATATCA 59.958 38.462 0.00 0.00 0.00 2.15
2074 2325 7.103641 GGTAATACGTGTCCCATTCATATCAT 58.896 38.462 0.00 0.00 0.00 2.45
2075 2326 8.255206 GGTAATACGTGTCCCATTCATATCATA 58.745 37.037 0.00 0.00 0.00 2.15
2076 2327 9.647797 GTAATACGTGTCCCATTCATATCATAA 57.352 33.333 0.00 0.00 0.00 1.90
2078 2329 8.777865 ATACGTGTCCCATTCATATCATAAAG 57.222 34.615 0.00 0.00 0.00 1.85
2079 2330 6.826668 ACGTGTCCCATTCATATCATAAAGA 58.173 36.000 0.00 0.00 0.00 2.52
2080 2331 7.279615 ACGTGTCCCATTCATATCATAAAGAA 58.720 34.615 0.00 0.00 0.00 2.52
2081 2332 7.226720 ACGTGTCCCATTCATATCATAAAGAAC 59.773 37.037 0.00 0.00 0.00 3.01
2082 2333 7.226523 CGTGTCCCATTCATATCATAAAGAACA 59.773 37.037 0.00 0.00 0.00 3.18
2083 2334 8.902806 GTGTCCCATTCATATCATAAAGAACAA 58.097 33.333 0.00 0.00 0.00 2.83
2084 2335 9.473007 TGTCCCATTCATATCATAAAGAACAAA 57.527 29.630 0.00 0.00 0.00 2.83
2085 2336 9.956720 GTCCCATTCATATCATAAAGAACAAAG 57.043 33.333 0.00 0.00 0.00 2.77
2086 2337 9.699410 TCCCATTCATATCATAAAGAACAAAGT 57.301 29.630 0.00 0.00 0.00 2.66
2096 2347 7.847487 TCATAAAGAACAAAGTACAAGTCACG 58.153 34.615 0.00 0.00 0.00 4.35
2097 2348 7.493320 TCATAAAGAACAAAGTACAAGTCACGT 59.507 33.333 0.00 0.00 0.00 4.49
2098 2349 8.757789 CATAAAGAACAAAGTACAAGTCACGTA 58.242 33.333 0.00 0.00 0.00 3.57
2099 2350 7.599630 AAAGAACAAAGTACAAGTCACGTAA 57.400 32.000 0.00 0.00 0.00 3.18
2100 2351 7.599630 AAGAACAAAGTACAAGTCACGTAAA 57.400 32.000 0.00 0.00 0.00 2.01
2101 2352 7.230466 AGAACAAAGTACAAGTCACGTAAAG 57.770 36.000 0.00 0.00 0.00 1.85
2102 2353 7.037438 AGAACAAAGTACAAGTCACGTAAAGA 58.963 34.615 0.00 0.00 0.00 2.52
2103 2354 6.579491 ACAAAGTACAAGTCACGTAAAGAC 57.421 37.500 0.00 0.00 36.26 3.01
2104 2355 5.521372 ACAAAGTACAAGTCACGTAAAGACC 59.479 40.000 0.00 0.00 36.68 3.85
2105 2356 3.893720 AGTACAAGTCACGTAAAGACCG 58.106 45.455 0.00 0.00 36.68 4.79
2106 2357 3.565482 AGTACAAGTCACGTAAAGACCGA 59.435 43.478 0.00 0.00 36.68 4.69
2107 2358 2.735823 ACAAGTCACGTAAAGACCGAC 58.264 47.619 1.21 0.00 36.68 4.79
2108 2359 2.099592 ACAAGTCACGTAAAGACCGACA 59.900 45.455 1.21 0.00 36.68 4.35
2109 2360 3.243636 ACAAGTCACGTAAAGACCGACAT 60.244 43.478 1.21 0.00 36.68 3.06
2110 2361 2.942710 AGTCACGTAAAGACCGACATG 58.057 47.619 1.21 0.00 36.68 3.21
2111 2362 2.555325 AGTCACGTAAAGACCGACATGA 59.445 45.455 0.00 0.00 36.68 3.07
2112 2363 2.660236 GTCACGTAAAGACCGACATGAC 59.340 50.000 0.00 0.00 0.00 3.06
2113 2364 2.293955 TCACGTAAAGACCGACATGACA 59.706 45.455 0.00 0.00 0.00 3.58
2114 2365 3.054166 CACGTAAAGACCGACATGACAA 58.946 45.455 0.00 0.00 0.00 3.18
2115 2366 3.491639 CACGTAAAGACCGACATGACAAA 59.508 43.478 0.00 0.00 0.00 2.83
2116 2367 4.025563 CACGTAAAGACCGACATGACAAAA 60.026 41.667 0.00 0.00 0.00 2.44
2117 2368 4.025480 ACGTAAAGACCGACATGACAAAAC 60.025 41.667 0.00 0.00 0.00 2.43
2118 2369 4.210537 CGTAAAGACCGACATGACAAAACT 59.789 41.667 0.00 0.00 0.00 2.66
2119 2370 5.403166 CGTAAAGACCGACATGACAAAACTA 59.597 40.000 0.00 0.00 0.00 2.24
2120 2371 6.074195 CGTAAAGACCGACATGACAAAACTAA 60.074 38.462 0.00 0.00 0.00 2.24
2121 2372 6.687081 AAAGACCGACATGACAAAACTAAA 57.313 33.333 0.00 0.00 0.00 1.85
2122 2373 6.687081 AAGACCGACATGACAAAACTAAAA 57.313 33.333 0.00 0.00 0.00 1.52
2123 2374 6.687081 AGACCGACATGACAAAACTAAAAA 57.313 33.333 0.00 0.00 0.00 1.94
2146 2397 4.352893 TGATGAGGACATGACTACCTTGA 58.647 43.478 0.00 0.00 36.82 3.02
2297 6294 2.035321 GCCCAAGAGAAGATAGAGTCCG 59.965 54.545 0.00 0.00 0.00 4.79
2299 6296 3.954904 CCCAAGAGAAGATAGAGTCCGAA 59.045 47.826 0.00 0.00 0.00 4.30
2307 6304 6.542821 AGAAGATAGAGTCCGAATCTCTCAT 58.457 40.000 12.19 2.25 41.66 2.90
2344 6341 1.341209 CAGACTGCACAGACACACCTA 59.659 52.381 4.31 0.00 0.00 3.08
2451 6450 8.443953 CAACCCAATTGGAATCAACTTAAAAA 57.556 30.769 26.60 0.00 35.48 1.94
2455 6454 6.347321 CCAATTGGAATCAACTTAAAAACCGC 60.347 38.462 20.50 0.00 35.48 5.68
2505 6504 0.397564 TGACACTGCAGCAGAATCCA 59.602 50.000 29.70 16.52 35.18 3.41
2513 6512 3.159472 TGCAGCAGAATCCAAGTCAAAT 58.841 40.909 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.662456 GGTTAGATGTCAAAGGGTAGTCTC 58.338 45.833 0.00 0.00 0.00 3.36
1 2 4.159879 CGGTTAGATGTCAAAGGGTAGTCT 59.840 45.833 0.00 0.00 0.00 3.24
2 3 4.430908 CGGTTAGATGTCAAAGGGTAGTC 58.569 47.826 0.00 0.00 0.00 2.59
3 4 3.369157 GCGGTTAGATGTCAAAGGGTAGT 60.369 47.826 0.00 0.00 0.00 2.73
4 5 3.195661 GCGGTTAGATGTCAAAGGGTAG 58.804 50.000 0.00 0.00 0.00 3.18
5 6 2.093341 GGCGGTTAGATGTCAAAGGGTA 60.093 50.000 0.00 0.00 0.00 3.69
29 30 4.568359 CACTCTGGTGTTGATTTAGATCCG 59.432 45.833 0.00 0.00 38.54 4.18
35 37 3.814842 CACTGCACTCTGGTGTTGATTTA 59.185 43.478 0.00 0.00 44.65 1.40
59 61 1.743252 GGAACCTTCAGCGGCTCAG 60.743 63.158 0.00 0.00 0.00 3.35
84 86 1.895798 AGACCACATCGAAGAAGCAGA 59.104 47.619 0.00 0.00 43.58 4.26
119 121 4.341520 AGAGTGTCGTTCTCTTGTAAAGGT 59.658 41.667 0.00 0.00 46.24 3.50
136 138 7.257722 CCACAAGACAAAATAAAACAGAGTGT 58.742 34.615 0.00 0.00 0.00 3.55
229 233 6.894339 TTAAAAACTTTCCATGACCTCTCC 57.106 37.500 0.00 0.00 0.00 3.71
273 277 4.500375 CCAGGAAAAAGGAGCACTTCAAAG 60.500 45.833 0.00 0.00 38.85 2.77
295 299 7.986085 ATTATTCCATACAGCACTGAATACC 57.014 36.000 4.31 0.00 0.00 2.73
306 310 9.343103 GTACTGTCATCGTATTATTCCATACAG 57.657 37.037 0.00 0.00 37.29 2.74
338 349 3.129287 CGAAGCTTATGGGAAAATGCACT 59.871 43.478 0.00 0.00 0.00 4.40
339 350 3.438360 CGAAGCTTATGGGAAAATGCAC 58.562 45.455 0.00 0.00 0.00 4.57
353 364 2.036992 CTGATAGGCTCATCCGAAGCTT 59.963 50.000 0.00 0.00 40.77 3.74
357 368 5.019470 ACATATCTGATAGGCTCATCCGAA 58.981 41.667 9.09 0.00 40.77 4.30
359 370 4.998671 ACATATCTGATAGGCTCATCCG 57.001 45.455 9.09 0.00 40.77 4.18
402 413 3.333680 AGATTCATTGTGTAGGTTGGGGT 59.666 43.478 0.00 0.00 0.00 4.95
440 451 0.251916 TCCCGATCACCATGGTTGTC 59.748 55.000 16.84 14.97 0.00 3.18
449 516 0.036388 TTCAAGCAGTCCCGATCACC 60.036 55.000 0.00 0.00 0.00 4.02
462 529 3.561310 TGAAGTCGGCATATCATTCAAGC 59.439 43.478 0.00 0.00 0.00 4.01
464 531 5.614308 AGATGAAGTCGGCATATCATTCAA 58.386 37.500 4.77 0.00 32.90 2.69
465 532 5.219343 AGATGAAGTCGGCATATCATTCA 57.781 39.130 4.77 0.00 32.90 2.57
472 539 5.046591 CCCCTATTTAGATGAAGTCGGCATA 60.047 44.000 0.00 0.00 0.00 3.14
491 613 2.979678 AGAGCAGACAAACTTTCCCCTA 59.020 45.455 0.00 0.00 0.00 3.53
510 633 2.606308 GCGACGGTTTCAGTCAACTAGA 60.606 50.000 0.00 0.00 38.46 2.43
530 653 4.572389 ACCGACATAGAACATGAGAAATGC 59.428 41.667 0.00 0.00 0.00 3.56
544 667 2.926200 CAGTTGCAGAGAACCGACATAG 59.074 50.000 0.00 0.00 0.00 2.23
545 668 2.353704 CCAGTTGCAGAGAACCGACATA 60.354 50.000 0.00 0.00 0.00 2.29
568 691 0.873721 GACTAGTCGATCGGGTAGCC 59.126 60.000 16.41 0.00 0.00 3.93
632 755 4.572909 AGTTAACGGGTTTCTGTGTATCC 58.427 43.478 0.00 0.00 31.84 2.59
640 763 4.566278 GGGTGGATTAGTTAACGGGTTTCT 60.566 45.833 0.00 0.00 0.00 2.52
645 768 1.481772 TCGGGTGGATTAGTTAACGGG 59.518 52.381 0.00 0.00 0.00 5.28
654 777 2.901192 TCTTGTGTCTTCGGGTGGATTA 59.099 45.455 0.00 0.00 0.00 1.75
841 969 1.241990 CGAGTGACTTGAGGGGTCGA 61.242 60.000 0.00 0.00 36.58 4.20
953 1081 0.186873 GCATGGATGGAGGAATGGGT 59.813 55.000 0.00 0.00 0.00 4.51
965 1093 0.473501 GAGAGGGAGAGGGCATGGAT 60.474 60.000 0.00 0.00 0.00 3.41
993 1121 4.166011 GCGCAAGACATCGGTGGC 62.166 66.667 0.30 0.00 43.02 5.01
1176 1319 2.590007 GCTGCCGATGCCGATCTT 60.590 61.111 0.00 0.00 38.22 2.40
1248 1391 2.757508 TCCAGCAGCTCCTCGAGG 60.758 66.667 26.32 26.32 0.00 4.63
1470 1661 1.376037 CTGGTCCTCCGCAGAAACC 60.376 63.158 0.00 0.00 36.30 3.27
1473 1664 0.904865 ACATCTGGTCCTCCGCAGAA 60.905 55.000 0.00 0.00 36.30 3.02
1485 1676 0.108186 TCAAGCCTGCGTACATCTGG 60.108 55.000 0.00 0.00 0.00 3.86
1565 1759 2.482296 GAAGCTGCAATGCAAGCCGT 62.482 55.000 20.23 12.22 38.41 5.68
1587 1781 8.750298 TGGAAAAGTAGAAACCTCATCTAGTAG 58.250 37.037 0.00 0.00 33.05 2.57
1588 1782 8.660295 TGGAAAAGTAGAAACCTCATCTAGTA 57.340 34.615 0.00 0.00 33.05 1.82
1589 1783 7.554959 TGGAAAAGTAGAAACCTCATCTAGT 57.445 36.000 0.00 0.00 35.13 2.57
1590 1784 8.482128 AGATGGAAAAGTAGAAACCTCATCTAG 58.518 37.037 0.00 0.00 30.33 2.43
1591 1785 8.260818 CAGATGGAAAAGTAGAAACCTCATCTA 58.739 37.037 0.00 0.00 0.00 1.98
1592 1786 7.108847 CAGATGGAAAAGTAGAAACCTCATCT 58.891 38.462 0.00 0.00 0.00 2.90
1616 1810 1.900486 TGCAATGACCAAATGATGCCA 59.100 42.857 0.00 0.00 33.01 4.92
1716 1944 3.500680 TGATTAAACTGAAACCCGCTGTC 59.499 43.478 0.00 0.00 0.00 3.51
1776 2004 8.125978 TCAGGGTTCTTAACTCGAACTATTTA 57.874 34.615 6.16 0.00 40.37 1.40
1887 2138 4.352009 ACATGCATCCAAACCAAGGATAA 58.648 39.130 0.00 0.00 43.90 1.75
1891 2142 3.448301 ACATACATGCATCCAAACCAAGG 59.552 43.478 0.00 0.00 0.00 3.61
1905 2156 9.151471 GGTAGGCAAAGTATACATACATACATG 57.849 37.037 5.50 0.00 34.42 3.21
1907 2158 7.524202 CGGGTAGGCAAAGTATACATACATACA 60.524 40.741 5.50 0.00 34.42 2.29
1945 2196 1.566077 GTGCACCACGAAACGTACC 59.434 57.895 5.22 0.00 38.32 3.34
1948 2199 2.177580 CAGGTGCACCACGAAACGT 61.178 57.895 36.39 11.61 42.36 3.99
2041 2292 5.314529 TGGGACACGTATTACCATGAAAAA 58.685 37.500 0.00 0.00 0.00 1.94
2042 2293 4.907809 TGGGACACGTATTACCATGAAAA 58.092 39.130 0.00 0.00 0.00 2.29
2043 2294 4.554960 TGGGACACGTATTACCATGAAA 57.445 40.909 0.00 0.00 0.00 2.69
2059 2310 9.956720 CTTTGTTCTTTATGATATGAATGGGAC 57.043 33.333 0.00 0.00 0.00 4.46
2060 2311 9.699410 ACTTTGTTCTTTATGATATGAATGGGA 57.301 29.630 0.00 0.00 0.00 4.37
2070 2321 8.495949 CGTGACTTGTACTTTGTTCTTTATGAT 58.504 33.333 0.00 0.00 0.00 2.45
2071 2322 7.493320 ACGTGACTTGTACTTTGTTCTTTATGA 59.507 33.333 0.00 0.00 0.00 2.15
2072 2323 7.627340 ACGTGACTTGTACTTTGTTCTTTATG 58.373 34.615 0.00 0.00 0.00 1.90
2073 2324 7.781548 ACGTGACTTGTACTTTGTTCTTTAT 57.218 32.000 0.00 0.00 0.00 1.40
2074 2325 8.700722 TTACGTGACTTGTACTTTGTTCTTTA 57.299 30.769 0.00 0.00 0.00 1.85
2075 2326 7.599630 TTACGTGACTTGTACTTTGTTCTTT 57.400 32.000 0.00 0.00 0.00 2.52
2076 2327 7.546667 TCTTTACGTGACTTGTACTTTGTTCTT 59.453 33.333 0.00 0.00 0.00 2.52
2077 2328 7.009907 GTCTTTACGTGACTTGTACTTTGTTCT 59.990 37.037 0.00 0.00 0.00 3.01
2078 2329 7.115553 GTCTTTACGTGACTTGTACTTTGTTC 58.884 38.462 0.00 0.00 0.00 3.18
2079 2330 6.036408 GGTCTTTACGTGACTTGTACTTTGTT 59.964 38.462 0.00 0.00 35.04 2.83
2080 2331 5.521372 GGTCTTTACGTGACTTGTACTTTGT 59.479 40.000 0.00 0.00 35.04 2.83
2081 2332 5.332055 CGGTCTTTACGTGACTTGTACTTTG 60.332 44.000 0.00 0.00 35.04 2.77
2082 2333 4.741676 CGGTCTTTACGTGACTTGTACTTT 59.258 41.667 0.00 0.00 35.04 2.66
2083 2334 4.036734 TCGGTCTTTACGTGACTTGTACTT 59.963 41.667 0.00 0.00 35.04 2.24
2084 2335 3.565482 TCGGTCTTTACGTGACTTGTACT 59.435 43.478 0.00 0.00 35.04 2.73
2085 2336 3.665871 GTCGGTCTTTACGTGACTTGTAC 59.334 47.826 0.00 0.00 35.04 2.90
2086 2337 3.314913 TGTCGGTCTTTACGTGACTTGTA 59.685 43.478 0.00 0.00 34.50 2.41
2087 2338 2.099592 TGTCGGTCTTTACGTGACTTGT 59.900 45.455 0.00 0.00 34.50 3.16
2088 2339 2.734670 TGTCGGTCTTTACGTGACTTG 58.265 47.619 0.00 0.00 34.50 3.16
2089 2340 3.005050 TCATGTCGGTCTTTACGTGACTT 59.995 43.478 0.00 0.00 36.86 3.01
2090 2341 2.555325 TCATGTCGGTCTTTACGTGACT 59.445 45.455 0.00 0.00 36.86 3.41
2091 2342 2.937591 TCATGTCGGTCTTTACGTGAC 58.062 47.619 0.00 0.00 36.86 3.67
2092 2343 2.293955 TGTCATGTCGGTCTTTACGTGA 59.706 45.455 0.00 0.00 38.87 4.35
2093 2344 2.668250 TGTCATGTCGGTCTTTACGTG 58.332 47.619 0.00 0.00 34.57 4.49
2094 2345 3.374220 TTGTCATGTCGGTCTTTACGT 57.626 42.857 0.00 0.00 0.00 3.57
2095 2346 4.210537 AGTTTTGTCATGTCGGTCTTTACG 59.789 41.667 0.00 0.00 0.00 3.18
2096 2347 5.668558 AGTTTTGTCATGTCGGTCTTTAC 57.331 39.130 0.00 0.00 0.00 2.01
2097 2348 7.789273 TTTAGTTTTGTCATGTCGGTCTTTA 57.211 32.000 0.00 0.00 0.00 1.85
2098 2349 6.687081 TTTAGTTTTGTCATGTCGGTCTTT 57.313 33.333 0.00 0.00 0.00 2.52
2099 2350 6.687081 TTTTAGTTTTGTCATGTCGGTCTT 57.313 33.333 0.00 0.00 0.00 3.01
2100 2351 6.687081 TTTTTAGTTTTGTCATGTCGGTCT 57.313 33.333 0.00 0.00 0.00 3.85
2101 2352 7.136119 TCATTTTTAGTTTTGTCATGTCGGTC 58.864 34.615 0.00 0.00 0.00 4.79
2102 2353 7.033530 TCATTTTTAGTTTTGTCATGTCGGT 57.966 32.000 0.00 0.00 0.00 4.69
2103 2354 7.807433 TCATCATTTTTAGTTTTGTCATGTCGG 59.193 33.333 0.00 0.00 0.00 4.79
2104 2355 8.726650 TCATCATTTTTAGTTTTGTCATGTCG 57.273 30.769 0.00 0.00 0.00 4.35
2105 2356 9.132521 CCTCATCATTTTTAGTTTTGTCATGTC 57.867 33.333 0.00 0.00 0.00 3.06
2106 2357 8.859090 TCCTCATCATTTTTAGTTTTGTCATGT 58.141 29.630 0.00 0.00 0.00 3.21
2107 2358 9.132521 GTCCTCATCATTTTTAGTTTTGTCATG 57.867 33.333 0.00 0.00 0.00 3.07
2108 2359 8.859090 TGTCCTCATCATTTTTAGTTTTGTCAT 58.141 29.630 0.00 0.00 0.00 3.06
2109 2360 8.231692 TGTCCTCATCATTTTTAGTTTTGTCA 57.768 30.769 0.00 0.00 0.00 3.58
2110 2361 9.132521 CATGTCCTCATCATTTTTAGTTTTGTC 57.867 33.333 0.00 0.00 31.15 3.18
2111 2362 8.859090 TCATGTCCTCATCATTTTTAGTTTTGT 58.141 29.630 0.00 0.00 31.15 2.83
2112 2363 9.132521 GTCATGTCCTCATCATTTTTAGTTTTG 57.867 33.333 0.00 0.00 31.15 2.44
2113 2364 9.082313 AGTCATGTCCTCATCATTTTTAGTTTT 57.918 29.630 0.00 0.00 31.15 2.43
2114 2365 8.641498 AGTCATGTCCTCATCATTTTTAGTTT 57.359 30.769 0.00 0.00 31.15 2.66
2115 2366 9.167311 GTAGTCATGTCCTCATCATTTTTAGTT 57.833 33.333 0.00 0.00 31.15 2.24
2116 2367 7.770897 GGTAGTCATGTCCTCATCATTTTTAGT 59.229 37.037 0.00 0.00 31.15 2.24
2117 2368 7.989741 AGGTAGTCATGTCCTCATCATTTTTAG 59.010 37.037 0.00 0.00 31.15 1.85
2118 2369 7.861629 AGGTAGTCATGTCCTCATCATTTTTA 58.138 34.615 0.00 0.00 31.15 1.52
2119 2370 6.725364 AGGTAGTCATGTCCTCATCATTTTT 58.275 36.000 0.00 0.00 31.15 1.94
2120 2371 6.319048 AGGTAGTCATGTCCTCATCATTTT 57.681 37.500 0.00 0.00 31.15 1.82
2121 2372 5.965033 AGGTAGTCATGTCCTCATCATTT 57.035 39.130 0.00 0.00 31.15 2.32
2122 2373 5.426509 TCAAGGTAGTCATGTCCTCATCATT 59.573 40.000 0.00 0.00 31.15 2.57
2123 2374 4.964897 TCAAGGTAGTCATGTCCTCATCAT 59.035 41.667 0.00 0.00 31.15 2.45
2185 2436 7.831690 TGTGTATTGTACAAATGTCCCATACAT 59.168 33.333 13.23 0.00 41.30 2.29
2207 2458 8.324191 TCTTTCTCCCTTATCTTCATATGTGT 57.676 34.615 1.90 0.00 0.00 3.72
2297 6294 5.126869 TCTGAGTCCAGAACATGAGAGATTC 59.873 44.000 0.00 0.00 45.74 2.52
2299 6296 4.608269 TCTGAGTCCAGAACATGAGAGAT 58.392 43.478 0.00 0.00 45.74 2.75
2344 6341 4.918810 AGAGTTCTTGGCGTTTTGAATT 57.081 36.364 0.00 0.00 0.00 2.17
2443 6442 1.239296 GCTCCGGGCGGTTTTTAAGT 61.239 55.000 0.00 0.00 36.47 2.24
2455 6454 0.810031 CCATAACTCAACGCTCCGGG 60.810 60.000 0.00 0.00 0.00 5.73
2505 6504 6.379988 ACACCTTTGGACTTGTAATTTGACTT 59.620 34.615 0.00 0.00 0.00 3.01
2513 6512 4.768583 ACGTAACACCTTTGGACTTGTAA 58.231 39.130 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.