Multiple sequence alignment - TraesCS3B01G363400

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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 TraesCS3B01G363400 chr3B 100.000 3860 0 0 1 3860 574830968 574827109 0.000000e+00 7129
1 TraesCS3B01G363400 chr3D 88.454 3499 217 89 1 3368 438644497 438641055 0.000000e+00 4050
2 TraesCS3B01G363400 chr3D 88.184 2395 166 53 1568 3860 438642906 438640527 0.000000e+00 2747
3 TraesCS3B01G363400 chr3D 83.556 450 56 9 1 437 553166608 553167052 4.640000e-109 405
4 TraesCS3B01G363400 chr3D 82.664 473 52 16 1 448 43036054 43036521 3.620000e-105 392
5 TraesCS3B01G363400 chr3A 90.899 1758 125 24 549 2292 577636662 577634926 0.000000e+00 2327
6 TraesCS3B01G363400 chr3A 95.205 855 32 5 2517 3368 577634924 577634076 0.000000e+00 1343
7 TraesCS3B01G363400 chr3A 91.143 350 21 6 3376 3725 577634036 577633697 2.100000e-127 466
8 TraesCS3B01G363400 chr5B 87.333 450 50 5 3 448 484803539 484803985 3.440000e-140 508
9 TraesCS3B01G363400 chr6D 84.382 461 54 9 1 448 36059175 36059630 1.650000e-118 436
10 TraesCS3B01G363400 chr6A 82.937 463 57 17 1 448 34212882 34212427 7.770000e-107 398
11 TraesCS3B01G363400 chr7D 82.174 460 51 21 1 437 617269626 617270077 2.190000e-97 366
12 TraesCS3B01G363400 chr1D 82.989 435 41 9 1 431 352375961 352375556 2.830000e-96 363
13 TraesCS3B01G363400 chr1B 81.425 463 61 17 1 444 594055432 594054976 4.740000e-94 355
14 TraesCS3B01G363400 chr4B 80.892 471 59 23 1 448 586470750 586470288 3.690000e-90 342
15 TraesCS3B01G363400 chr2D 80.093 216 35 6 239 448 637744524 637744311 1.860000e-33 154


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 TraesCS3B01G363400 chr3B 574827109 574830968 3859 True 7129.000000 7129 100.000000 1 3860 1 chr3B.!!$R1 3859
1 TraesCS3B01G363400 chr3D 438640527 438644497 3970 True 3398.500000 4050 88.319000 1 3860 2 chr3D.!!$R1 3859
2 TraesCS3B01G363400 chr3A 577633697 577636662 2965 True 1378.666667 2327 92.415667 549 3725 3 chr3A.!!$R1 3176

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
312 333 0.178992 CGGGCCCCACATGTCATAAT 60.179 55.0 18.66 0.0 0.00 1.28 F
677 707 0.454600 GGAGTGACATCGCGGTAGAA 59.545 55.0 6.13 0.0 0.00 2.10 F
1888 1962 0.391793 CCGAGAAAGTCTCAAGGGCC 60.392 60.0 0.00 0.0 43.55 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1510 0.235926 GAGCACCACGAACTGCTTTC 59.764 55.0 6.86 0.0 43.94 2.62 R
2021 2111 0.319900 CCAGACTGACAGAACCGGTG 60.320 60.0 8.52 0.0 0.00 4.94 R
3193 3315 0.871057 CACACACACACACACACACA 59.129 50.0 0.00 0.0 0.00 3.72 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
96 97 2.626743 CCATCATTCCAAGAAGGCATCC 59.373 50.000 0.00 0.00 37.29 3.51
144 145 4.933064 CGACGATGGCGAGCTCCC 62.933 72.222 8.47 11.08 41.64 4.30
203 204 2.574399 GGTGAGCGAGAGTGGGAC 59.426 66.667 0.00 0.00 0.00 4.46
231 252 1.000955 CTAAGCACCTGGTCAGAACGT 59.999 52.381 0.00 0.00 0.00 3.99
254 275 1.654105 CGTTCTAACAGCCGTCATCAC 59.346 52.381 0.00 0.00 0.00 3.06
312 333 0.178992 CGGGCCCCACATGTCATAAT 60.179 55.000 18.66 0.00 0.00 1.28
340 361 5.741982 GCTTAAAATGTAACGATTCGGCAAT 59.258 36.000 11.29 0.00 0.00 3.56
357 380 2.298729 GCAATTAGGGTTTGGAACAGCA 59.701 45.455 0.00 0.00 42.39 4.41
418 442 4.873827 TGATAGTTTGTTGGAACGATAGCC 59.126 41.667 0.00 0.00 42.67 3.93
479 503 3.370840 ACATGCTGGCTCCTTCATAAA 57.629 42.857 0.00 0.00 0.00 1.40
628 658 3.403038 AGTAGAACATTCTTGCTTGCGT 58.597 40.909 0.00 0.00 38.70 5.24
647 677 3.043999 GCCAAGCCCGGGTGTAGAT 62.044 63.158 24.63 0.00 0.00 1.98
656 686 0.525668 CGGGTGTAGATGCAGACGAC 60.526 60.000 0.00 0.00 0.00 4.34
657 687 0.530744 GGGTGTAGATGCAGACGACA 59.469 55.000 0.00 0.00 0.00 4.35
677 707 0.454600 GGAGTGACATCGCGGTAGAA 59.545 55.000 6.13 0.00 0.00 2.10
786 816 3.735029 GGCACTGCTCACTGCTGC 61.735 66.667 0.00 0.00 43.25 5.25
819 849 4.063967 AGTCATCCGCGGACGCAA 62.064 61.111 33.75 13.51 42.06 4.85
953 983 1.805945 CTCCGCCTCGAAACCGAAG 60.806 63.158 1.20 0.00 35.44 3.79
954 984 3.488090 CCGCCTCGAAACCGAAGC 61.488 66.667 0.00 0.00 39.42 3.86
955 985 3.488090 CGCCTCGAAACCGAAGCC 61.488 66.667 0.00 0.00 39.59 4.35
992 1022 3.844090 GCAGCGGAGGAGGAGGAC 61.844 72.222 0.00 0.00 0.00 3.85
1221 1257 1.367471 CAACGACCAGGTCTGCTCA 59.633 57.895 17.95 0.00 0.00 4.26
1232 1268 0.458889 GTCTGCTCAGCTCAGCTCAG 60.459 60.000 12.05 1.02 40.39 3.35
1264 1300 2.084546 CTCCCCTACTTTTGCTTTCCG 58.915 52.381 0.00 0.00 0.00 4.30
1265 1301 1.422402 TCCCCTACTTTTGCTTTCCGT 59.578 47.619 0.00 0.00 0.00 4.69
1266 1302 1.810755 CCCCTACTTTTGCTTTCCGTC 59.189 52.381 0.00 0.00 0.00 4.79
1267 1303 2.500229 CCCTACTTTTGCTTTCCGTCA 58.500 47.619 0.00 0.00 0.00 4.35
1268 1304 3.081804 CCCTACTTTTGCTTTCCGTCAT 58.918 45.455 0.00 0.00 0.00 3.06
1270 1306 2.969443 ACTTTTGCTTTCCGTCATCG 57.031 45.000 0.00 0.00 0.00 3.84
1271 1307 1.069227 ACTTTTGCTTTCCGTCATCGC 60.069 47.619 0.00 0.00 35.54 4.58
1273 1309 1.582610 TTTGCTTTCCGTCATCGCCC 61.583 55.000 0.00 0.00 35.54 6.13
1274 1310 2.435938 GCTTTCCGTCATCGCCCA 60.436 61.111 0.00 0.00 35.54 5.36
1275 1311 2.750888 GCTTTCCGTCATCGCCCAC 61.751 63.158 0.00 0.00 35.54 4.61
1358 1429 4.629065 CGACAACTTCGCTAGATTTGAAC 58.371 43.478 0.00 0.00 41.87 3.18
1363 1434 2.691409 TCGCTAGATTTGAACCCCTG 57.309 50.000 0.00 0.00 0.00 4.45
1379 1450 1.817099 CTGGCTCCATCGTCTTGCC 60.817 63.158 0.00 0.00 43.49 4.52
1443 1514 3.670311 CATCAAGTGCTCGATGGAAAG 57.330 47.619 0.00 0.00 36.24 2.62
1444 1515 1.442769 TCAAGTGCTCGATGGAAAGC 58.557 50.000 0.00 0.00 39.02 3.51
1508 1580 2.203056 TGCTCTGCTGTGCACGTT 60.203 55.556 15.21 0.00 37.71 3.99
1510 1582 2.537560 GCTCTGCTGTGCACGTTGT 61.538 57.895 13.13 0.00 33.79 3.32
1526 1598 2.223479 CGTTGTGCTAGGCAAGTTGTTT 60.223 45.455 4.48 0.00 41.47 2.83
1530 1602 2.803956 GTGCTAGGCAAGTTGTTTCGTA 59.196 45.455 4.48 0.00 41.47 3.43
1531 1603 3.435671 GTGCTAGGCAAGTTGTTTCGTAT 59.564 43.478 4.48 0.00 41.47 3.06
1532 1604 4.628333 GTGCTAGGCAAGTTGTTTCGTATA 59.372 41.667 4.48 0.00 41.47 1.47
1535 1607 5.446875 GCTAGGCAAGTTGTTTCGTATAACC 60.447 44.000 4.48 0.00 0.00 2.85
1538 1610 3.739494 CAAGTTGTTTCGTATAACCGCC 58.261 45.455 0.00 0.00 0.00 6.13
1541 1613 2.298411 TGTTTCGTATAACCGCCCTC 57.702 50.000 0.00 0.00 0.00 4.30
1565 1637 1.599606 CCGTCTGCTACTGCCTGACT 61.600 60.000 0.00 0.00 38.54 3.41
1584 1656 6.266558 CCTGACTAGCCTCTACAATTCTACAT 59.733 42.308 0.00 0.00 0.00 2.29
1617 1691 7.931275 CAAGTACTATTGGAAGAATTTAGCCC 58.069 38.462 0.00 0.00 0.00 5.19
1618 1692 6.289064 AGTACTATTGGAAGAATTTAGCCCG 58.711 40.000 0.00 0.00 0.00 6.13
1686 1760 2.436173 GGACCTCTAGGGACAATTCAGG 59.564 54.545 0.20 0.00 40.27 3.86
1706 1780 1.997606 GGCAACTCAATGCTGCATTTC 59.002 47.619 24.28 9.71 45.68 2.17
1729 1803 5.007626 TCGTGCCAAATTCAGCTATTATGTC 59.992 40.000 0.00 0.00 0.00 3.06
1753 1827 3.319122 GTGAAGTTCTGCCTTGAAATGGT 59.681 43.478 4.17 0.00 32.80 3.55
1767 1841 5.068234 TGAAATGGTAGTCTCCTAACACG 57.932 43.478 0.00 0.00 43.49 4.49
1788 1862 8.658499 ACACGTATTAGTTGTTTCTCTCTTTT 57.342 30.769 0.00 0.00 0.00 2.27
1804 1878 9.737427 TTCTCTCTTTTGAATCAGATATACGTC 57.263 33.333 0.00 0.00 0.00 4.34
1825 1899 3.822735 TCTTCTTCCCTAACGACGAGAAA 59.177 43.478 0.00 0.00 0.00 2.52
1882 1956 0.671796 TGAACGCCGAGAAAGTCTCA 59.328 50.000 6.12 0.00 43.55 3.27
1888 1962 0.391793 CCGAGAAAGTCTCAAGGGCC 60.392 60.000 0.00 0.00 43.55 5.80
1930 2004 2.568509 CCTCACCCCATTTGCAAAATCT 59.431 45.455 17.19 0.00 0.00 2.40
1936 2010 5.532032 CACCCCATTTGCAAAATCTTTTCTT 59.468 36.000 17.19 0.00 0.00 2.52
1982 2072 1.617322 GGAGGTTTTCCAGGTTGGTC 58.383 55.000 0.00 0.00 46.01 4.02
1983 2073 1.617322 GAGGTTTTCCAGGTTGGTCC 58.383 55.000 0.00 0.00 43.73 4.46
1996 2086 2.046507 GGTCCTGCTCCTGCACTG 60.047 66.667 0.00 0.00 45.31 3.66
1998 2088 1.544825 GGTCCTGCTCCTGCACTGTA 61.545 60.000 0.00 0.00 45.31 2.74
2002 2092 2.040278 TCCTGCTCCTGCACTGTAATTT 59.960 45.455 0.00 0.00 45.31 1.82
2003 2093 2.163010 CCTGCTCCTGCACTGTAATTTG 59.837 50.000 0.00 0.00 45.31 2.32
2016 2106 3.906998 TGTAATTTGACCGGCACATTTG 58.093 40.909 0.00 0.00 30.08 2.32
2026 2116 1.503542 GCACATTTGCTCTCACCGG 59.496 57.895 0.00 0.00 46.17 5.28
2028 2118 1.238439 CACATTTGCTCTCACCGGTT 58.762 50.000 2.97 0.00 0.00 4.44
2029 2119 1.197721 CACATTTGCTCTCACCGGTTC 59.802 52.381 2.97 0.00 0.00 3.62
2030 2120 1.072331 ACATTTGCTCTCACCGGTTCT 59.928 47.619 2.97 0.00 0.00 3.01
2031 2121 1.466167 CATTTGCTCTCACCGGTTCTG 59.534 52.381 2.97 0.00 0.00 3.02
2034 2124 1.112916 TGCTCTCACCGGTTCTGTCA 61.113 55.000 2.97 0.00 0.00 3.58
2035 2125 0.389166 GCTCTCACCGGTTCTGTCAG 60.389 60.000 2.97 0.00 0.00 3.51
2292 2386 5.363562 AGCAATATGGTGAACATCAGAGA 57.636 39.130 0.00 0.00 41.03 3.10
2293 2387 5.366460 AGCAATATGGTGAACATCAGAGAG 58.634 41.667 0.00 0.00 41.03 3.20
2294 2388 4.024218 GCAATATGGTGAACATCAGAGAGC 60.024 45.833 0.00 0.00 41.03 4.09
2298 2394 2.634453 TGGTGAACATCAGAGAGCAGAA 59.366 45.455 0.00 0.00 0.00 3.02
2299 2395 3.262660 TGGTGAACATCAGAGAGCAGAAT 59.737 43.478 0.00 0.00 0.00 2.40
2300 2396 3.622163 GGTGAACATCAGAGAGCAGAATG 59.378 47.826 0.00 0.00 40.87 2.67
2308 2404 4.573900 TCAGAGAGCAGAATGTTTTCCTC 58.426 43.478 0.00 0.00 39.31 3.71
2309 2405 4.040829 TCAGAGAGCAGAATGTTTTCCTCA 59.959 41.667 0.00 0.00 39.31 3.86
2310 2406 4.153835 CAGAGAGCAGAATGTTTTCCTCAC 59.846 45.833 0.00 0.00 39.31 3.51
2317 2413 7.224297 AGCAGAATGTTTTCCTCACTAGTTAA 58.776 34.615 0.00 0.00 39.31 2.01
2318 2414 7.885399 AGCAGAATGTTTTCCTCACTAGTTAAT 59.115 33.333 0.00 0.00 39.31 1.40
2319 2415 8.515414 GCAGAATGTTTTCCTCACTAGTTAATT 58.485 33.333 0.00 0.00 39.31 1.40
2369 2465 2.028748 GCATCAACCATTGCCTTTGTCT 60.029 45.455 0.00 0.00 32.66 3.41
2403 2499 9.950680 TTCACTTCATCTTAATTTGTTCACTTC 57.049 29.630 0.00 0.00 0.00 3.01
2447 2556 3.320541 CAGACCCATTTTAGGCACAAACA 59.679 43.478 0.00 0.00 0.00 2.83
2456 2565 7.710475 CCATTTTAGGCACAAACAAATATAGGG 59.290 37.037 0.00 0.00 0.00 3.53
2460 2569 3.181476 GGCACAAACAAATATAGGGCAGG 60.181 47.826 0.00 0.00 0.00 4.85
2465 2574 5.422012 ACAAACAAATATAGGGCAGGGAAAG 59.578 40.000 0.00 0.00 0.00 2.62
2481 2590 6.808704 GCAGGGAAAGAATGACAATCTTTTAC 59.191 38.462 17.48 13.68 44.81 2.01
2484 2593 9.093458 AGGGAAAGAATGACAATCTTTTACATT 57.907 29.630 17.48 0.00 44.81 2.71
2487 2596 9.912634 GAAAGAATGACAATCTTTTACATTCCA 57.087 29.630 17.48 0.00 44.81 3.53
2490 2599 8.734386 AGAATGACAATCTTTTACATTCCAGTC 58.266 33.333 0.00 0.00 44.13 3.51
2494 2603 8.160765 TGACAATCTTTTACATTCCAGTCCTAA 58.839 33.333 0.00 0.00 0.00 2.69
2599 2708 6.917217 ACAATAGCTACTGAATCTTGCTTC 57.083 37.500 9.58 0.00 35.47 3.86
2663 2772 4.911390 ACACCCTCTCCATTTTTCAGTAG 58.089 43.478 0.00 0.00 0.00 2.57
2889 3011 4.399303 ACAAACTGAAGGAACCAAGAACAG 59.601 41.667 0.00 0.00 0.00 3.16
2902 3024 3.070015 CCAAGAACAGGGTGATTTTTGCT 59.930 43.478 0.00 0.00 0.00 3.91
2963 3085 5.473504 GGAGAAAACTGGTATTGCTTCAAGA 59.526 40.000 0.00 0.00 0.00 3.02
3026 3148 7.389053 GGATTCTTAATAAGCTGAGTGTATGGG 59.611 40.741 0.00 0.00 0.00 4.00
3102 3224 2.684881 CAGAACAGAAACTGGTGTGCTT 59.315 45.455 1.35 0.00 35.76 3.91
3164 3286 7.432869 TCATTTGAACGAACCATTCTTGAAAT 58.567 30.769 0.00 0.00 0.00 2.17
3193 3315 0.179084 CTGGTCCTGACGTTGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
3205 3331 1.265635 GTTGTGTGTGTGTGTGTGTGT 59.734 47.619 0.00 0.00 0.00 3.72
3206 3332 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3207 3333 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3208 3334 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3209 3335 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3210 3336 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3211 3337 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
3212 3338 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3213 3339 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
3223 3349 3.216292 GTGTGTGGTGGTGGTGGC 61.216 66.667 0.00 0.00 0.00 5.01
3243 3369 3.126858 GGCATGCGTGATGAACTTCTTTA 59.873 43.478 12.44 0.00 33.31 1.85
3267 3423 2.568546 ACATGGTGGATCCTGGAGTA 57.431 50.000 14.23 0.00 37.07 2.59
3269 3425 2.293184 ACATGGTGGATCCTGGAGTAGT 60.293 50.000 14.23 0.31 37.07 2.73
3336 3492 9.603921 TTTAGTATTACCTCCGTTTGGAATTAG 57.396 33.333 0.00 0.00 45.87 1.73
3343 3499 2.232941 TCCGTTTGGAATTAGCTCTCGT 59.767 45.455 0.00 0.00 42.85 4.18
3345 3501 3.250744 CGTTTGGAATTAGCTCTCGTGA 58.749 45.455 0.00 0.00 0.00 4.35
3355 3511 3.229276 AGCTCTCGTGACTCATTTCAG 57.771 47.619 0.00 0.00 0.00 3.02
3368 3524 6.204688 TGACTCATTTCAGCGACAGTTAATTT 59.795 34.615 0.00 0.00 0.00 1.82
3373 3561 3.664107 TCAGCGACAGTTAATTTCAGCT 58.336 40.909 0.00 0.00 0.00 4.24
3382 3570 7.224753 CGACAGTTAATTTCAGCTACATACCAT 59.775 37.037 0.00 0.00 0.00 3.55
3489 3678 0.179048 TGCTGGATATCTTGCCGGTG 60.179 55.000 1.90 0.00 32.98 4.94
3534 3723 6.815089 ACTCTTATCACTAGCTTCCATCTTG 58.185 40.000 0.00 0.00 0.00 3.02
3581 3770 2.481276 CGGAGATGCGGAGTTATGACAA 60.481 50.000 0.00 0.00 0.00 3.18
3608 3798 6.588719 TTGCAAAGCTAACCTAACATGATT 57.411 33.333 0.00 0.00 0.00 2.57
3633 3823 1.952296 GGCCTGAATTATGGAGCTGTG 59.048 52.381 0.00 0.00 0.00 3.66
3734 3925 4.460948 GACCAGGTCGTCCTAACAATAA 57.539 45.455 3.05 0.00 43.07 1.40
3763 3954 3.370104 AGCTAACAGCATCCAGAGTACT 58.630 45.455 0.00 0.00 45.56 2.73
3808 4000 6.291955 CCGCAATCTTTTAATTGTGATGATGC 60.292 38.462 10.78 0.00 45.63 3.91
3809 4001 6.474427 CGCAATCTTTTAATTGTGATGATGCT 59.526 34.615 4.57 0.00 45.63 3.79
3810 4002 7.514591 CGCAATCTTTTAATTGTGATGATGCTG 60.515 37.037 4.57 0.00 45.63 4.41
3811 4003 7.277098 GCAATCTTTTAATTGTGATGATGCTGT 59.723 33.333 0.00 0.00 38.60 4.40
3812 4004 8.592155 CAATCTTTTAATTGTGATGATGCTGTG 58.408 33.333 0.00 0.00 32.97 3.66
3813 4005 7.451501 TCTTTTAATTGTGATGATGCTGTGA 57.548 32.000 0.00 0.00 0.00 3.58
3814 4006 8.058667 TCTTTTAATTGTGATGATGCTGTGAT 57.941 30.769 0.00 0.00 0.00 3.06
3815 4007 7.971722 TCTTTTAATTGTGATGATGCTGTGATG 59.028 33.333 0.00 0.00 0.00 3.07
3817 4009 2.793288 TGTGATGATGCTGTGATGGT 57.207 45.000 0.00 0.00 0.00 3.55
3828 4027 3.580895 TGCTGTGATGGTTTCTGGTAGTA 59.419 43.478 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.362800 GCTCCGACGACGACAACAC 61.363 63.158 9.28 0.00 42.66 3.32
51 52 1.909141 GAGAGCTCCGACGACGACAA 61.909 60.000 10.93 0.00 42.66 3.18
96 97 3.997064 CTTCCTCGTCGCTGGCCAG 62.997 68.421 29.34 29.34 0.00 4.85
102 103 2.756283 CCTCCCTTCCTCGTCGCT 60.756 66.667 0.00 0.00 0.00 4.93
144 145 2.682494 TCCGTTCTCCCCTTCCCG 60.682 66.667 0.00 0.00 0.00 5.14
219 240 2.050351 ACGCGACGTTCTGACCAG 60.050 61.111 15.93 0.00 36.35 4.00
231 252 1.443194 GACGGCTGTTAGAACGCGA 60.443 57.895 15.93 0.00 32.13 5.87
270 291 1.879380 CGTCAAGATTCTGTTGGCCAA 59.121 47.619 16.05 16.05 0.00 4.52
276 297 0.673644 CCGCCCGTCAAGATTCTGTT 60.674 55.000 0.00 0.00 0.00 3.16
280 301 3.202706 GCCCGCCCGTCAAGATTC 61.203 66.667 0.00 0.00 0.00 2.52
312 333 4.570935 GAATCGTTACATTTTAAGCGCGA 58.429 39.130 12.10 0.00 0.00 5.87
340 361 2.303175 GTGTGCTGTTCCAAACCCTAA 58.697 47.619 0.00 0.00 0.00 2.69
395 418 4.873827 GGCTATCGTTCCAACAAACTATCA 59.126 41.667 0.00 0.00 0.00 2.15
396 419 5.006746 CAGGCTATCGTTCCAACAAACTATC 59.993 44.000 0.00 0.00 0.00 2.08
397 420 4.876107 CAGGCTATCGTTCCAACAAACTAT 59.124 41.667 0.00 0.00 0.00 2.12
398 421 4.250464 CAGGCTATCGTTCCAACAAACTA 58.750 43.478 0.00 0.00 0.00 2.24
399 422 3.074412 CAGGCTATCGTTCCAACAAACT 58.926 45.455 0.00 0.00 0.00 2.66
400 423 2.812011 ACAGGCTATCGTTCCAACAAAC 59.188 45.455 0.00 0.00 0.00 2.93
401 424 3.134574 ACAGGCTATCGTTCCAACAAA 57.865 42.857 0.00 0.00 0.00 2.83
404 428 4.034048 CACATTACAGGCTATCGTTCCAAC 59.966 45.833 0.00 0.00 0.00 3.77
412 436 7.625828 AAAAACTACCACATTACAGGCTATC 57.374 36.000 0.00 0.00 0.00 2.08
440 464 9.767684 CAGCATGTTCGTAATGAAAAGTAAATA 57.232 29.630 0.00 0.00 38.60 1.40
448 472 3.081061 AGCCAGCATGTTCGTAATGAAA 58.919 40.909 0.00 0.00 38.60 2.69
465 489 4.774124 CTCATGACTTTATGAAGGAGCCA 58.226 43.478 1.95 0.00 36.69 4.75
479 503 1.242076 GTGGCTTGTTGCTCATGACT 58.758 50.000 0.00 0.00 42.39 3.41
500 524 6.240894 TCTTGCTCCCATGGATGATATTTAC 58.759 40.000 15.22 0.00 0.00 2.01
504 528 3.308259 GCTCTTGCTCCCATGGATGATAT 60.308 47.826 15.22 0.00 36.03 1.63
535 565 2.166459 GCCCAAAGTAGGAAAGAATGGC 59.834 50.000 0.00 0.00 0.00 4.40
594 624 4.041740 TGTTCTACTAGCTGCAATACCG 57.958 45.455 1.02 0.00 0.00 4.02
628 658 4.028490 CTACACCCGGGCTTGGCA 62.028 66.667 24.08 3.89 0.00 4.92
647 677 1.106944 TGTCACTCCTGTCGTCTGCA 61.107 55.000 0.00 0.00 0.00 4.41
656 686 0.248661 CTACCGCGATGTCACTCCTG 60.249 60.000 8.23 0.00 0.00 3.86
657 687 0.393944 TCTACCGCGATGTCACTCCT 60.394 55.000 8.23 0.00 0.00 3.69
677 707 1.408422 GCATGAAACGCTCGCTTTTT 58.592 45.000 0.00 0.00 0.00 1.94
798 828 2.202756 GTCCGCGGATGACTGGTC 60.203 66.667 33.58 12.16 0.00 4.02
850 880 4.988598 CGAGTGGGTTGGCTGCGT 62.989 66.667 0.00 0.00 0.00 5.24
906 936 2.164865 CTGAGCTTGACCTGCGGAGT 62.165 60.000 2.36 0.00 35.28 3.85
992 1022 4.271816 CCGACGCCATCTCCCTCG 62.272 72.222 0.00 0.00 0.00 4.63
1232 1268 1.349357 GTAGGGGAGATTGGGATGAGC 59.651 57.143 0.00 0.00 0.00 4.26
1233 1269 2.983296 AGTAGGGGAGATTGGGATGAG 58.017 52.381 0.00 0.00 0.00 2.90
1234 1270 3.438131 AAGTAGGGGAGATTGGGATGA 57.562 47.619 0.00 0.00 0.00 2.92
1235 1271 4.210331 CAAAAGTAGGGGAGATTGGGATG 58.790 47.826 0.00 0.00 0.00 3.51
1236 1272 3.373110 GCAAAAGTAGGGGAGATTGGGAT 60.373 47.826 0.00 0.00 0.00 3.85
1271 1307 4.899239 GAGCTGGATCCGCGTGGG 62.899 72.222 16.49 1.03 35.24 4.61
1273 1309 2.279120 GAGAGCTGGATCCGCGTG 60.279 66.667 18.56 6.29 0.00 5.34
1274 1310 2.441164 AGAGAGCTGGATCCGCGT 60.441 61.111 18.56 12.37 0.00 6.01
1275 1311 2.027314 CAGAGAGCTGGATCCGCG 59.973 66.667 18.56 0.00 38.51 6.46
1358 1429 2.370445 AAGACGATGGAGCCAGGGG 61.370 63.158 0.00 0.00 0.00 4.79
1363 1434 2.514824 GGGCAAGACGATGGAGCC 60.515 66.667 0.00 0.00 44.48 4.70
1379 1450 2.376808 ACAGAACAGATCGAGCAAGG 57.623 50.000 2.38 0.00 0.00 3.61
1439 1510 0.235926 GAGCACCACGAACTGCTTTC 59.764 55.000 6.86 0.00 43.94 2.62
1442 1513 0.952497 CATGAGCACCACGAACTGCT 60.952 55.000 5.38 5.38 46.63 4.24
1443 1514 1.499056 CATGAGCACCACGAACTGC 59.501 57.895 0.00 0.00 0.00 4.40
1444 1515 1.915614 GCCATGAGCACCACGAACTG 61.916 60.000 0.00 0.00 42.97 3.16
1508 1580 1.601903 CGAAACAACTTGCCTAGCACA 59.398 47.619 0.00 0.00 38.71 4.57
1510 1582 1.961793 ACGAAACAACTTGCCTAGCA 58.038 45.000 0.00 0.00 36.47 3.49
1513 1585 4.626604 CGGTTATACGAAACAACTTGCCTA 59.373 41.667 0.00 0.00 35.47 3.93
1518 1590 2.743664 GGGCGGTTATACGAAACAACTT 59.256 45.455 0.00 0.00 35.47 2.66
1526 1598 0.748450 CAAGGAGGGCGGTTATACGA 59.252 55.000 0.00 0.00 35.47 3.43
1530 1602 2.595655 GGCAAGGAGGGCGGTTAT 59.404 61.111 0.00 0.00 0.00 1.89
1594 1668 6.289064 CGGGCTAAATTCTTCCAATAGTACT 58.711 40.000 0.00 0.00 0.00 2.73
1617 1691 1.141881 ATGGTCGAGCTACTTGGCG 59.858 57.895 16.64 0.00 37.29 5.69
1618 1692 1.432270 GCATGGTCGAGCTACTTGGC 61.432 60.000 16.64 6.58 0.00 4.52
1706 1780 5.173774 ACATAATAGCTGAATTTGGCACG 57.826 39.130 0.00 0.00 0.00 5.34
1729 1803 1.593196 TTCAAGGCAGAACTTCACCG 58.407 50.000 0.00 0.00 0.00 4.94
1753 1827 7.928307 ACAACTAATACGTGTTAGGAGACTA 57.072 36.000 28.58 0.00 43.67 2.59
1788 1862 6.778069 AGGGAAGAAGACGTATATCTGATTCA 59.222 38.462 0.00 0.00 30.73 2.57
1804 1878 3.844577 TTCTCGTCGTTAGGGAAGAAG 57.155 47.619 0.00 0.00 0.00 2.85
1825 1899 3.890527 GATGTGCTTCATCCCCACT 57.109 52.632 10.03 0.00 45.05 4.00
1882 1956 1.194218 GCACAACCAATATGGCCCTT 58.806 50.000 0.00 0.00 42.67 3.95
1888 1962 4.022068 AGGTTCTGTTGCACAACCAATATG 60.022 41.667 10.82 0.00 40.46 1.78
1930 2004 3.897239 TGGCTCCAGTTCTTGAAGAAAA 58.103 40.909 9.51 0.00 35.75 2.29
1936 2010 3.560025 GGATCTTTGGCTCCAGTTCTTGA 60.560 47.826 0.00 0.00 0.00 3.02
1985 2075 2.162408 GGTCAAATTACAGTGCAGGAGC 59.838 50.000 0.00 0.00 42.57 4.70
1986 2076 2.416547 CGGTCAAATTACAGTGCAGGAG 59.583 50.000 0.00 0.00 0.00 3.69
1987 2077 2.422597 CGGTCAAATTACAGTGCAGGA 58.577 47.619 0.00 0.00 0.00 3.86
1988 2078 1.468520 CCGGTCAAATTACAGTGCAGG 59.531 52.381 0.00 0.00 0.00 4.85
1989 2079 1.135689 GCCGGTCAAATTACAGTGCAG 60.136 52.381 1.90 0.00 0.00 4.41
1996 2086 2.666022 GCAAATGTGCCGGTCAAATTAC 59.334 45.455 12.75 6.77 45.68 1.89
1998 2088 1.794512 GCAAATGTGCCGGTCAAATT 58.205 45.000 1.90 5.88 45.68 1.82
2016 2106 0.389166 CTGACAGAACCGGTGAGAGC 60.389 60.000 8.52 0.00 0.00 4.09
2017 2107 0.962489 ACTGACAGAACCGGTGAGAG 59.038 55.000 8.52 0.70 0.00 3.20
2018 2108 0.959553 GACTGACAGAACCGGTGAGA 59.040 55.000 8.52 0.00 0.00 3.27
2019 2109 0.962489 AGACTGACAGAACCGGTGAG 59.038 55.000 8.52 3.30 0.00 3.51
2020 2110 0.673985 CAGACTGACAGAACCGGTGA 59.326 55.000 8.52 0.00 0.00 4.02
2021 2111 0.319900 CCAGACTGACAGAACCGGTG 60.320 60.000 8.52 0.00 0.00 4.94
2022 2112 2.050269 CCAGACTGACAGAACCGGT 58.950 57.895 10.08 0.00 0.00 5.28
2024 2114 1.374758 GGCCAGACTGACAGAACCG 60.375 63.158 10.08 0.00 0.00 4.44
2026 2116 1.346068 AGAAGGCCAGACTGACAGAAC 59.654 52.381 10.08 2.95 0.00 3.01
2028 2118 1.261480 GAGAAGGCCAGACTGACAGA 58.739 55.000 10.08 0.00 0.00 3.41
2029 2119 0.972134 TGAGAAGGCCAGACTGACAG 59.028 55.000 5.01 0.00 0.00 3.51
2030 2120 1.649321 ATGAGAAGGCCAGACTGACA 58.351 50.000 5.01 0.00 0.00 3.58
2031 2121 3.196685 AGTTATGAGAAGGCCAGACTGAC 59.803 47.826 5.01 0.00 0.00 3.51
2034 2124 3.445008 TCAGTTATGAGAAGGCCAGACT 58.555 45.455 5.01 0.00 0.00 3.24
2035 2125 3.895232 TCAGTTATGAGAAGGCCAGAC 57.105 47.619 5.01 0.00 0.00 3.51
2136 2226 4.435651 GCCAATAACGTCTTCTTTTCCTCG 60.436 45.833 0.00 0.00 0.00 4.63
2292 2386 5.234466 ACTAGTGAGGAAAACATTCTGCT 57.766 39.130 0.00 0.00 0.00 4.24
2293 2387 5.948992 AACTAGTGAGGAAAACATTCTGC 57.051 39.130 0.00 0.00 0.00 4.26
2324 2420 9.695526 TGCTATAGAAAGTTCTAACAACGTTTA 57.304 29.630 3.21 0.00 42.55 2.01
2325 2421 8.597662 TGCTATAGAAAGTTCTAACAACGTTT 57.402 30.769 3.21 0.00 42.55 3.60
2326 2422 8.773404 ATGCTATAGAAAGTTCTAACAACGTT 57.227 30.769 3.21 0.00 42.55 3.99
2327 2423 8.033038 TGATGCTATAGAAAGTTCTAACAACGT 58.967 33.333 3.21 0.00 42.55 3.99
2328 2424 8.407457 TGATGCTATAGAAAGTTCTAACAACG 57.593 34.615 3.21 0.00 42.55 4.10
2329 2425 9.974750 GTTGATGCTATAGAAAGTTCTAACAAC 57.025 33.333 3.21 10.02 42.55 3.32
2330 2426 9.162764 GGTTGATGCTATAGAAAGTTCTAACAA 57.837 33.333 3.21 3.68 42.55 2.83
2331 2427 8.318412 TGGTTGATGCTATAGAAAGTTCTAACA 58.682 33.333 3.21 4.98 42.55 2.41
2332 2428 8.718102 TGGTTGATGCTATAGAAAGTTCTAAC 57.282 34.615 3.21 0.00 42.55 2.34
2333 2429 9.905713 AATGGTTGATGCTATAGAAAGTTCTAA 57.094 29.630 3.21 0.00 42.55 2.10
2334 2430 9.330063 CAATGGTTGATGCTATAGAAAGTTCTA 57.670 33.333 3.21 3.33 43.35 2.10
2335 2431 7.201767 GCAATGGTTGATGCTATAGAAAGTTCT 60.202 37.037 3.21 0.00 39.46 3.01
2336 2432 6.914757 GCAATGGTTGATGCTATAGAAAGTTC 59.085 38.462 3.21 0.00 39.46 3.01
2447 2556 6.071320 GTCATTCTTTCCCTGCCCTATATTT 58.929 40.000 0.00 0.00 0.00 1.40
2456 2565 5.397142 AAAGATTGTCATTCTTTCCCTGC 57.603 39.130 14.26 0.00 38.71 4.85
2460 2569 9.358872 GGAATGTAAAAGATTGTCATTCTTTCC 57.641 33.333 18.41 12.62 41.38 3.13
2465 2574 7.970614 GGACTGGAATGTAAAAGATTGTCATTC 59.029 37.037 0.00 0.00 38.70 2.67
2481 2590 9.838339 AATTGTAGAGTATTTAGGACTGGAATG 57.162 33.333 0.00 0.00 0.00 2.67
2497 2606 8.205131 ACACGTTGTTCTTAAAATTGTAGAGT 57.795 30.769 0.00 0.00 0.00 3.24
2599 2708 1.274167 AGCATGGATGTGTTGGCAAAG 59.726 47.619 0.00 0.00 0.00 2.77
2663 2772 3.841372 GCGAGTGCATATTTGTAGCGAAC 60.841 47.826 0.00 0.00 42.15 3.95
2889 3011 4.314740 TGTGTAACAGCAAAAATCACCC 57.685 40.909 0.00 0.00 45.67 4.61
2963 3085 3.281727 TGCGATCCTTAAGAATGGCTT 57.718 42.857 9.91 0.00 40.68 4.35
3026 3148 4.660789 ACATGAGGATTTTGCTTATGCC 57.339 40.909 0.00 0.00 35.69 4.40
3164 3286 2.093500 CGTCAGGACCAGAATCATGGAA 60.093 50.000 0.00 0.00 43.57 3.53
3193 3315 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3205 3331 2.273776 CCACCACCACCACACACA 59.726 61.111 0.00 0.00 0.00 3.72
3206 3332 3.216292 GCCACCACCACCACACAC 61.216 66.667 0.00 0.00 0.00 3.82
3207 3333 3.067084 ATGCCACCACCACCACACA 62.067 57.895 0.00 0.00 0.00 3.72
3208 3334 2.203480 ATGCCACCACCACCACAC 60.203 61.111 0.00 0.00 0.00 3.82
3209 3335 2.203466 CATGCCACCACCACCACA 60.203 61.111 0.00 0.00 0.00 4.17
3210 3336 3.683937 GCATGCCACCACCACCAC 61.684 66.667 6.36 0.00 0.00 4.16
3213 3339 4.041917 CACGCATGCCACCACCAC 62.042 66.667 13.15 0.00 0.00 4.16
3223 3349 5.281693 TGTAAAGAAGTTCATCACGCATG 57.718 39.130 5.50 0.00 0.00 4.06
3243 3369 3.122480 TCCAGGATCCACCATGTATTGT 58.878 45.455 15.82 0.00 42.04 2.71
3267 3423 9.953565 TTACCTTGAGTAAATGCTTACAATACT 57.046 29.630 0.00 0.00 40.03 2.12
3336 3492 1.658095 GCTGAAATGAGTCACGAGAGC 59.342 52.381 0.00 0.00 0.00 4.09
3343 3499 2.820059 ACTGTCGCTGAAATGAGTCA 57.180 45.000 0.00 0.00 0.00 3.41
3345 3501 6.204688 TGAAATTAACTGTCGCTGAAATGAGT 59.795 34.615 0.00 0.00 0.00 3.41
3355 3511 4.921470 TGTAGCTGAAATTAACTGTCGC 57.079 40.909 0.00 0.00 0.00 5.19
3368 3524 7.778382 TCAGTCTAAACTATGGTATGTAGCTGA 59.222 37.037 0.00 12.16 33.25 4.26
3373 3561 9.542462 GCATTTCAGTCTAAACTATGGTATGTA 57.458 33.333 0.00 0.00 33.25 2.29
3489 3678 0.933047 GCGTTCCGGAAACAAACAGC 60.933 55.000 20.79 10.88 37.77 4.40
3515 3704 4.716784 ACACCAAGATGGAAGCTAGTGATA 59.283 41.667 2.85 0.00 40.96 2.15
3534 3723 1.069258 GCCTATCCGTGCCTACACC 59.931 63.158 0.00 0.00 44.40 4.16
3581 3770 6.434028 TCATGTTAGGTTAGCTTTGCAATTCT 59.566 34.615 0.00 2.93 0.00 2.40
3608 3798 1.152777 CCATAATTCAGGCCGGCCA 60.153 57.895 45.13 27.61 38.92 5.36
3633 3823 4.133796 GTTGCAGAATGGGGCCGC 62.134 66.667 14.01 14.01 35.86 6.53
3734 3925 5.102953 TGGATGCTGTTAGCTTAATCTGT 57.897 39.130 0.00 0.00 42.97 3.41
3763 3954 4.213906 GCGGTTACAGGCTTTAGTGTTTAA 59.786 41.667 0.00 0.00 0.00 1.52
3808 4000 4.184629 GCTACTACCAGAAACCATCACAG 58.815 47.826 0.00 0.00 0.00 3.66
3809 4001 3.580895 TGCTACTACCAGAAACCATCACA 59.419 43.478 0.00 0.00 0.00 3.58
3810 4002 4.184629 CTGCTACTACCAGAAACCATCAC 58.815 47.826 0.00 0.00 32.03 3.06
3811 4003 3.838317 ACTGCTACTACCAGAAACCATCA 59.162 43.478 0.00 0.00 34.47 3.07
3812 4004 4.184629 CACTGCTACTACCAGAAACCATC 58.815 47.826 0.00 0.00 34.47 3.51
3813 4005 3.055094 CCACTGCTACTACCAGAAACCAT 60.055 47.826 0.00 0.00 34.47 3.55
3814 4006 2.301870 CCACTGCTACTACCAGAAACCA 59.698 50.000 0.00 0.00 34.47 3.67
3815 4007 2.354805 CCCACTGCTACTACCAGAAACC 60.355 54.545 0.00 0.00 34.47 3.27
3817 4009 1.278127 GCCCACTGCTACTACCAGAAA 59.722 52.381 0.00 0.00 36.87 2.52
3828 4027 1.153289 GTCGATGATGCCCACTGCT 60.153 57.895 0.00 0.00 42.00 4.24


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

AutoCloner maintained by Alex Coulton.