Multiple sequence alignment - TraesCS2B01G517000

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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 TraesCS2B01G517000 chr2B 100.000 3284 0 0 1 3284 712002679 711999396 0.000000e+00 6065
1 TraesCS2B01G517000 chr2B 80.054 1113 191 21 580 1678 712359929 712358834 0.000000e+00 797
2 TraesCS2B01G517000 chr2B 74.845 970 209 27 581 1539 712830329 712829384 1.100000e-109 407
3 TraesCS2B01G517000 chr2B 87.815 238 29 0 1 238 689777423 689777660 2.500000e-71 279
4 TraesCS2B01G517000 chr2B 87.440 207 24 2 39 244 712009229 712009024 1.520000e-58 237
5 TraesCS2B01G517000 chr2B 84.328 134 21 0 2031 2164 712774780 712774647 7.390000e-27 132
6 TraesCS2B01G517000 chr2A 91.864 3331 155 33 2 3284 723101701 723098439 0.000000e+00 4543
7 TraesCS2B01G517000 chr2A 78.190 1105 196 25 580 1678 723511837 723510772 0.000000e+00 664
8 TraesCS2B01G517000 chr2A 77.519 1032 186 32 681 1673 723195024 723194000 2.200000e-161 579
9 TraesCS2B01G517000 chr2A 81.407 398 61 11 540 928 723134154 723133761 2.460000e-81 313
10 TraesCS2B01G517000 chr2A 87.083 240 31 0 1 240 712539040 712539279 4.180000e-69 272
11 TraesCS2B01G517000 chr2A 76.265 514 111 9 1028 1539 723578663 723578159 2.510000e-66 263
12 TraesCS2B01G517000 chr2A 85.656 244 35 0 1 244 723134622 723134379 1.170000e-64 257
13 TraesCS2B01G517000 chr2A 80.793 328 52 8 1 319 723512259 723511934 2.530000e-61 246
14 TraesCS2B01G517000 chr2D 91.528 2219 92 20 1 2191 588498828 588496678 0.000000e+00 2968
15 TraesCS2B01G517000 chr2D 92.560 1129 52 12 2185 3283 588491402 588490276 0.000000e+00 1591
16 TraesCS2B01G517000 chr2D 79.137 1112 196 26 580 1678 588735703 588734615 0.000000e+00 736
17 TraesCS2B01G517000 chr2D 87.395 238 30 0 1 238 573952135 573952372 1.160000e-69 274
18 TraesCS2B01G517000 chr2D 81.155 329 51 7 1 319 588736222 588735895 1.510000e-63 254


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 TraesCS2B01G517000 chr2B 711999396 712002679 3283 True 6065 6065 100.0000 1 3284 1 chr2B.!!$R1 3283
1 TraesCS2B01G517000 chr2B 712358834 712359929 1095 True 797 797 80.0540 580 1678 1 chr2B.!!$R3 1098
2 TraesCS2B01G517000 chr2B 712829384 712830329 945 True 407 407 74.8450 581 1539 1 chr2B.!!$R5 958
3 TraesCS2B01G517000 chr2A 723098439 723101701 3262 True 4543 4543 91.8640 2 3284 1 chr2A.!!$R1 3282
4 TraesCS2B01G517000 chr2A 723194000 723195024 1024 True 579 579 77.5190 681 1673 1 chr2A.!!$R2 992
5 TraesCS2B01G517000 chr2A 723510772 723512259 1487 True 455 664 79.4915 1 1678 2 chr2A.!!$R5 1677
6 TraesCS2B01G517000 chr2A 723133761 723134622 861 True 285 313 83.5315 1 928 2 chr2A.!!$R4 927
7 TraesCS2B01G517000 chr2A 723578159 723578663 504 True 263 263 76.2650 1028 1539 1 chr2A.!!$R3 511
8 TraesCS2B01G517000 chr2D 588496678 588498828 2150 True 2968 2968 91.5280 1 2191 1 chr2D.!!$R2 2190
9 TraesCS2B01G517000 chr2D 588490276 588491402 1126 True 1591 1591 92.5600 2185 3283 1 chr2D.!!$R1 1098
10 TraesCS2B01G517000 chr2D 588734615 588736222 1607 True 495 736 80.1460 1 1678 2 chr2D.!!$R3 1677

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
391 446 0.323629 CGTGGGCCCTAGTCTTTTGA 59.676 55.0 25.7 0.0 0.0 2.69 F
1614 1813 0.463204 CTGATCATGCTGTCCGGTCT 59.537 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1992 0.106708 GCCATCTGGAACGGCATCTA 59.893 55.0 0.0 0.0 45.52 1.98 R
2514 2753 0.322546 CAGGTCCTAGTTGGGTTGCC 60.323 60.0 0.0 0.0 36.20 4.52 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
269 279 2.794910 CGTTGACGAAGCCATATCGATT 59.205 45.455 1.71 0.00 42.76 3.34
377 432 1.312371 CCAGGGTTTATGTGCGTGGG 61.312 60.000 0.00 0.00 0.00 4.61
388 443 2.221299 TGCGTGGGCCCTAGTCTTT 61.221 57.895 25.70 0.00 38.85 2.52
391 446 0.323629 CGTGGGCCCTAGTCTTTTGA 59.676 55.000 25.70 0.00 0.00 2.69
414 469 4.458295 ACCGACTATATGAACCGACTATGG 59.542 45.833 0.00 0.00 0.00 2.74
469 535 1.899534 GGTCGAGGAGGGATCGGAG 60.900 68.421 0.00 0.00 40.54 4.63
471 537 3.299190 CGAGGAGGGATCGGAGGC 61.299 72.222 0.00 0.00 36.54 4.70
472 538 3.299190 GAGGAGGGATCGGAGGCG 61.299 72.222 0.00 0.00 0.00 5.52
473 539 4.924187 AGGAGGGATCGGAGGCGG 62.924 72.222 0.00 0.00 0.00 6.13
524 590 2.587194 CGGGCCGCTTCTGATCTG 60.587 66.667 15.42 0.00 0.00 2.90
536 652 5.697178 CGCTTCTGATCTGATCTTGATTGAT 59.303 40.000 17.82 0.00 0.00 2.57
537 653 6.128769 CGCTTCTGATCTGATCTTGATTGATC 60.129 42.308 17.82 14.58 42.19 2.92
538 654 6.932400 GCTTCTGATCTGATCTTGATTGATCT 59.068 38.462 17.82 0.00 42.30 2.75
539 655 7.117236 GCTTCTGATCTGATCTTGATTGATCTC 59.883 40.741 17.82 0.00 42.30 2.75
540 656 6.679843 TCTGATCTGATCTTGATTGATCTCG 58.320 40.000 17.82 13.45 42.30 4.04
541 657 6.489361 TCTGATCTGATCTTGATTGATCTCGA 59.511 38.462 17.82 14.61 42.30 4.04
626 765 4.498520 GCTGCAGCGCGTCCTCTA 62.499 66.667 25.23 0.00 0.00 2.43
937 1094 5.360144 GTCAAGCTCAGATACAAGGGTAGTA 59.640 44.000 0.00 0.00 31.88 1.82
980 1167 1.872237 GCTCTGCCCATTACGCGAATA 60.872 52.381 15.93 0.00 0.00 1.75
981 1168 2.688507 CTCTGCCCATTACGCGAATAT 58.311 47.619 15.93 0.00 0.00 1.28
1014 1204 3.510360 ACAGTAAGATGTACGCCAAGACT 59.490 43.478 0.00 0.00 0.00 3.24
1110 1306 3.188786 GACATGGCGTCGCTGGAC 61.189 66.667 18.11 0.17 39.89 4.02
1208 1404 3.695606 GACGCTGGAGGAGTGCCA 61.696 66.667 0.00 0.00 35.37 4.92
1446 1642 3.744719 CCGTCGGAAGTCGCTCCA 61.745 66.667 4.91 0.00 41.20 3.86
1449 1645 1.444553 GTCGGAAGTCGCTCCAGTG 60.445 63.158 0.00 0.00 39.05 3.66
1566 1765 0.601558 GCGGACTAGACAACCTCACA 59.398 55.000 0.00 0.00 0.00 3.58
1614 1813 0.463204 CTGATCATGCTGTCCGGTCT 59.537 55.000 0.00 0.00 0.00 3.85
1684 1883 4.103153 TGTTCCTTCTGGGTCCATATGATC 59.897 45.833 3.65 0.00 36.25 2.92
1685 1884 2.899900 TCCTTCTGGGTCCATATGATCG 59.100 50.000 3.65 0.00 36.25 3.69
1738 1937 0.888619 GACTGATCTGTCGGACACCA 59.111 55.000 15.85 5.02 34.68 4.17
1767 1981 3.512496 TGGCGAATATGGTACCTATCCA 58.488 45.455 14.36 9.15 39.41 3.41
1768 1982 3.513912 TGGCGAATATGGTACCTATCCAG 59.486 47.826 14.36 2.17 38.42 3.86
1769 1983 3.767673 GGCGAATATGGTACCTATCCAGA 59.232 47.826 14.36 0.00 38.42 3.86
1770 1984 4.406003 GGCGAATATGGTACCTATCCAGAT 59.594 45.833 14.36 0.00 38.34 2.90
1771 1985 5.352284 GCGAATATGGTACCTATCCAGATG 58.648 45.833 14.36 0.00 37.05 2.90
1772 1986 5.682471 GCGAATATGGTACCTATCCAGATGG 60.682 48.000 14.36 0.00 37.05 3.51
1773 1987 5.675538 GAATATGGTACCTATCCAGATGGC 58.324 45.833 14.36 0.00 37.05 4.40
1774 1988 1.338107 TGGTACCTATCCAGATGGCG 58.662 55.000 14.36 0.00 34.44 5.69
1775 1989 1.133294 TGGTACCTATCCAGATGGCGA 60.133 52.381 14.36 0.00 34.44 5.54
1776 1990 1.968493 GGTACCTATCCAGATGGCGAA 59.032 52.381 4.06 0.00 34.44 4.70
1777 1991 2.367567 GGTACCTATCCAGATGGCGAAA 59.632 50.000 4.06 0.00 34.44 3.46
1778 1992 3.008049 GGTACCTATCCAGATGGCGAAAT 59.992 47.826 4.06 0.00 34.44 2.17
1779 1993 4.222145 GGTACCTATCCAGATGGCGAAATA 59.778 45.833 4.06 0.00 34.44 1.40
1780 1994 4.543590 ACCTATCCAGATGGCGAAATAG 57.456 45.455 0.00 0.00 34.44 1.73
1781 1995 4.160329 ACCTATCCAGATGGCGAAATAGA 58.840 43.478 6.81 0.00 34.44 1.98
1782 1996 4.780021 ACCTATCCAGATGGCGAAATAGAT 59.220 41.667 6.81 0.00 34.44 1.98
1783 1997 5.114780 CCTATCCAGATGGCGAAATAGATG 58.885 45.833 6.81 0.00 34.44 2.90
1784 1998 2.771089 TCCAGATGGCGAAATAGATGC 58.229 47.619 0.00 0.00 34.44 3.91
1790 2004 0.586802 GGCGAAATAGATGCCGTTCC 59.413 55.000 0.00 0.00 39.30 3.62
1791 2005 1.295792 GCGAAATAGATGCCGTTCCA 58.704 50.000 0.00 0.00 0.00 3.53
1834 2048 6.196538 CGATATGGATGACGAAACATATACCG 59.803 42.308 0.00 0.00 36.83 4.02
1835 2049 4.922471 TGGATGACGAAACATATACCGA 57.078 40.909 0.00 0.00 0.00 4.69
1836 2050 5.462530 TGGATGACGAAACATATACCGAT 57.537 39.130 0.00 0.00 0.00 4.18
1837 2051 5.466819 TGGATGACGAAACATATACCGATC 58.533 41.667 0.00 0.00 0.00 3.69
1838 2052 5.010213 TGGATGACGAAACATATACCGATCA 59.990 40.000 0.00 0.00 0.00 2.92
1839 2053 5.924254 GGATGACGAAACATATACCGATCAA 59.076 40.000 0.00 0.00 0.00 2.57
1840 2054 6.089551 GGATGACGAAACATATACCGATCAAG 59.910 42.308 0.00 0.00 0.00 3.02
1841 2055 6.139048 TGACGAAACATATACCGATCAAGA 57.861 37.500 0.00 0.00 0.00 3.02
1842 2056 6.745116 TGACGAAACATATACCGATCAAGAT 58.255 36.000 0.00 0.00 0.00 2.40
1843 2057 6.640907 TGACGAAACATATACCGATCAAGATG 59.359 38.462 0.00 0.00 0.00 2.90
1844 2058 5.405571 ACGAAACATATACCGATCAAGATGC 59.594 40.000 0.00 0.00 0.00 3.91
1845 2059 5.635280 CGAAACATATACCGATCAAGATGCT 59.365 40.000 0.00 0.00 0.00 3.79
1850 2064 2.540265 ACCGATCAAGATGCTGATCC 57.460 50.000 7.80 0.00 46.06 3.36
1999 2225 0.742505 TGGCGTCAAGGATAGTACCG 59.257 55.000 0.00 0.00 34.73 4.02
2000 2226 0.031721 GGCGTCAAGGATAGTACCGG 59.968 60.000 0.00 0.00 34.73 5.28
2034 2260 0.177836 TGTGGCATATGGACGTCAGG 59.822 55.000 18.91 0.00 0.00 3.86
2172 2398 0.874390 CGTTAGCAGCTTGGCTTGAA 59.126 50.000 0.00 0.00 42.71 2.69
2177 2403 1.283793 CAGCTTGGCTTGAACCACG 59.716 57.895 0.00 0.00 40.19 4.94
2327 2554 5.967088 TGCCTGCACTTGTAAAAAGTAAAA 58.033 33.333 0.00 0.00 0.00 1.52
2428 2655 7.754851 TTTCTCTGTTAAATTTGTACCTCCC 57.245 36.000 0.00 0.00 0.00 4.30
2514 2753 3.364889 TCTTAGTGACAGTTGGACACG 57.635 47.619 0.00 0.00 39.19 4.49
2666 2937 7.662604 CAGATAGCACAATACATCTGCATAA 57.337 36.000 0.00 0.00 38.35 1.90
2667 2938 8.091385 CAGATAGCACAATACATCTGCATAAA 57.909 34.615 0.00 0.00 38.35 1.40
2668 2939 8.562052 CAGATAGCACAATACATCTGCATAAAA 58.438 33.333 0.00 0.00 38.35 1.52
2669 2940 8.781196 AGATAGCACAATACATCTGCATAAAAG 58.219 33.333 0.00 0.00 33.06 2.27
2670 2941 8.681486 ATAGCACAATACATCTGCATAAAAGA 57.319 30.769 0.00 0.00 33.06 2.52
2671 2942 7.395190 AGCACAATACATCTGCATAAAAGAA 57.605 32.000 0.00 0.00 33.06 2.52
2672 2943 7.829725 AGCACAATACATCTGCATAAAAGAAA 58.170 30.769 0.00 0.00 33.06 2.52
2673 2944 7.972277 AGCACAATACATCTGCATAAAAGAAAG 59.028 33.333 0.00 0.00 33.06 2.62
2674 2945 7.253883 GCACAATACATCTGCATAAAAGAAAGC 60.254 37.037 0.00 0.00 0.00 3.51
2675 2946 7.756272 CACAATACATCTGCATAAAAGAAAGCA 59.244 33.333 0.00 0.00 35.43 3.91
2913 3200 6.073003 CGCTATCCAAGAAATCCTGGTAAATC 60.073 42.308 0.00 0.00 0.00 2.17
2945 3232 5.918608 ACATTCGCCTACTATTCAGAACAT 58.081 37.500 0.00 0.00 0.00 2.71
2956 3243 7.020827 ACTATTCAGAACATTTCCCTGAAGA 57.979 36.000 0.00 0.00 46.17 2.87
2988 3275 4.151157 GGCTATCAGCAAAAGCAAACAAAG 59.849 41.667 0.00 0.00 44.75 2.77
2995 3282 5.120519 CAGCAAAAGCAAACAAAGAGAACAA 59.879 36.000 0.00 0.00 0.00 2.83
3028 3315 9.385902 GAAAATCCAACATATGTTATGACATCG 57.614 33.333 20.39 6.10 42.83 3.84
3048 3335 3.501828 TCGGATGAAATATTGAATGGGCG 59.498 43.478 0.00 0.00 0.00 6.13
3049 3336 3.366273 CGGATGAAATATTGAATGGGCGG 60.366 47.826 0.00 0.00 0.00 6.13
3050 3337 3.826157 GGATGAAATATTGAATGGGCGGA 59.174 43.478 0.00 0.00 0.00 5.54
3051 3338 4.321230 GGATGAAATATTGAATGGGCGGAC 60.321 45.833 0.00 0.00 0.00 4.79
3052 3339 2.616376 TGAAATATTGAATGGGCGGACG 59.384 45.455 0.00 0.00 0.00 4.79
3053 3340 2.341846 AATATTGAATGGGCGGACGT 57.658 45.000 0.00 0.00 0.00 4.34
3054 3341 1.593196 ATATTGAATGGGCGGACGTG 58.407 50.000 0.00 0.00 0.00 4.49
3056 3343 2.191786 ATTGAATGGGCGGACGTGGA 62.192 55.000 0.00 0.00 0.00 4.02
3072 3360 2.035449 CGTGGAGTCCAGAACACTAACA 59.965 50.000 13.61 0.00 32.34 2.41
3140 3436 3.325753 GTCCCAGCAGCCTCCTGT 61.326 66.667 0.00 0.00 41.26 4.00
3142 3438 1.229496 TCCCAGCAGCCTCCTGTTA 60.229 57.895 0.00 0.00 41.26 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
269 279 1.142748 CAAACAACCCTGCGGCAAA 59.857 52.632 3.44 0.00 0.00 3.68
377 432 1.275573 AGTCGGTCAAAAGACTAGGGC 59.724 52.381 0.00 0.00 44.93 5.19
388 443 3.949754 AGTCGGTTCATATAGTCGGTCAA 59.050 43.478 0.00 0.00 0.00 3.18
391 446 4.458295 CCATAGTCGGTTCATATAGTCGGT 59.542 45.833 0.00 0.00 0.00 4.69
392 447 4.458295 ACCATAGTCGGTTCATATAGTCGG 59.542 45.833 0.00 0.00 34.91 4.79
393 448 5.624344 ACCATAGTCGGTTCATATAGTCG 57.376 43.478 0.00 0.00 34.91 4.18
440 506 2.950309 CCTCCTCGACCTCTTAATCGAA 59.050 50.000 0.00 0.00 46.01 3.71
475 541 4.736896 ACGCTTCCGAGTTCCGCC 62.737 66.667 0.00 0.00 38.29 6.13
476 542 3.479269 CACGCTTCCGAGTTCCGC 61.479 66.667 0.00 0.00 38.29 5.54
477 543 2.087009 GTCACGCTTCCGAGTTCCG 61.087 63.158 0.00 0.00 38.29 4.30
478 544 0.389948 ATGTCACGCTTCCGAGTTCC 60.390 55.000 0.00 0.00 38.29 3.62
479 545 2.273370 TATGTCACGCTTCCGAGTTC 57.727 50.000 0.00 0.00 38.29 3.01
480 546 2.736144 TTATGTCACGCTTCCGAGTT 57.264 45.000 0.00 0.00 38.29 3.01
481 547 2.736144 TTTATGTCACGCTTCCGAGT 57.264 45.000 0.00 0.00 38.29 4.18
482 548 2.222819 GCTTTTATGTCACGCTTCCGAG 60.223 50.000 0.00 0.00 38.29 4.63
524 590 3.661728 CGTCGTCGAGATCAATCAAGATC 59.338 47.826 0.00 0.00 43.73 2.75
539 655 2.643790 CCATCGTCGTCGTCGTCG 60.644 66.667 14.18 14.18 46.06 5.12
540 656 2.943034 GCCATCGTCGTCGTCGTC 60.943 66.667 11.41 0.00 38.33 4.20
541 657 4.806481 CGCCATCGTCGTCGTCGT 62.806 66.667 11.41 0.00 38.33 4.34
980 1167 1.472878 TCTTACTGTCGCTTCGCTCAT 59.527 47.619 0.00 0.00 0.00 2.90
981 1168 0.879090 TCTTACTGTCGCTTCGCTCA 59.121 50.000 0.00 0.00 0.00 4.26
1014 1204 2.496341 CGGAAGATCAGCCGCTGA 59.504 61.111 24.90 24.90 44.99 4.26
1020 1210 3.267860 CGGCAGCGGAAGATCAGC 61.268 66.667 0.00 0.00 37.86 4.26
1110 1306 4.504916 CTCCCGAGGCAGAGCGTG 62.505 72.222 0.00 0.00 0.00 5.34
1208 1404 1.411977 CCGTGATCTCCTTGATGCTCT 59.588 52.381 0.00 0.00 35.14 4.09
1446 1642 1.153939 GCTGATGAGCGTCGTCACT 60.154 57.895 0.00 0.00 37.48 3.41
1566 1765 2.365370 CCCTGGAGGCTCAGCTCT 60.365 66.667 17.69 0.00 33.64 4.09
1590 1789 0.254178 GGACAGCATGATCAGTGGGT 59.746 55.000 0.09 0.00 39.69 4.51
1614 1813 4.314440 AGAAGCAAGGCGGCGACA 62.314 61.111 18.30 0.00 39.27 4.35
1684 1883 2.221749 CAGACAAATCGTATGCCATCCG 59.778 50.000 0.00 0.00 28.36 4.18
1685 1884 3.466836 TCAGACAAATCGTATGCCATCC 58.533 45.455 0.00 0.00 36.74 3.51
1738 1937 5.003804 GGTACCATATTCGCCATCTGAATT 58.996 41.667 7.15 0.00 37.28 2.17
1767 1981 1.070758 ACGGCATCTATTTCGCCATCT 59.929 47.619 0.00 0.00 46.60 2.90
1768 1982 1.512926 ACGGCATCTATTTCGCCATC 58.487 50.000 0.00 0.00 46.60 3.51
1769 1983 1.873591 GAACGGCATCTATTTCGCCAT 59.126 47.619 0.00 0.00 46.60 4.40
1770 1984 1.295792 GAACGGCATCTATTTCGCCA 58.704 50.000 0.00 0.00 46.60 5.69
1771 1985 0.586802 GGAACGGCATCTATTTCGCC 59.413 55.000 0.00 0.00 42.64 5.54
1772 1986 1.261619 CTGGAACGGCATCTATTTCGC 59.738 52.381 0.00 0.00 0.00 4.70
1773 1987 2.821546 TCTGGAACGGCATCTATTTCG 58.178 47.619 0.00 0.00 32.53 3.46
1774 1988 3.499918 CCATCTGGAACGGCATCTATTTC 59.500 47.826 0.00 0.00 37.39 2.17
1775 1989 3.480470 CCATCTGGAACGGCATCTATTT 58.520 45.455 0.00 0.00 37.39 1.40
1776 1990 2.811873 GCCATCTGGAACGGCATCTATT 60.812 50.000 0.00 0.00 45.52 1.73
1777 1991 1.271054 GCCATCTGGAACGGCATCTAT 60.271 52.381 0.00 0.00 45.52 1.98
1778 1992 0.106708 GCCATCTGGAACGGCATCTA 59.893 55.000 0.00 0.00 45.52 1.98
1779 1993 1.153086 GCCATCTGGAACGGCATCT 60.153 57.895 0.00 0.00 45.52 2.90
1780 1994 3.425422 GCCATCTGGAACGGCATC 58.575 61.111 0.00 0.00 45.52 3.91
1783 1997 0.388520 GTTTTGCCATCTGGAACGGC 60.389 55.000 0.00 7.26 46.43 5.68
1784 1998 0.958091 TGTTTTGCCATCTGGAACGG 59.042 50.000 0.00 0.00 37.39 4.44
1785 1999 1.879380 TCTGTTTTGCCATCTGGAACG 59.121 47.619 0.00 0.00 37.39 3.95
1786 2000 3.841643 CATCTGTTTTGCCATCTGGAAC 58.158 45.455 0.00 0.00 37.39 3.62
1787 2001 2.231964 GCATCTGTTTTGCCATCTGGAA 59.768 45.455 0.00 0.00 37.39 3.53
1788 2002 1.820519 GCATCTGTTTTGCCATCTGGA 59.179 47.619 0.00 0.00 37.39 3.86
1789 2003 2.288961 GCATCTGTTTTGCCATCTGG 57.711 50.000 0.00 0.00 33.95 3.86
1810 2024 7.255569 TCGGTATATGTTTCGTCATCCATATC 58.744 38.462 0.00 0.00 33.69 1.63
1815 2029 5.466819 TGATCGGTATATGTTTCGTCATCC 58.533 41.667 0.00 0.00 0.00 3.51
1835 2049 3.073209 AGCATCTGGATCAGCATCTTGAT 59.927 43.478 0.00 0.00 40.40 2.57
1836 2050 2.438392 AGCATCTGGATCAGCATCTTGA 59.562 45.455 0.00 0.00 0.00 3.02
1837 2051 2.550180 CAGCATCTGGATCAGCATCTTG 59.450 50.000 0.00 0.00 0.00 3.02
1838 2052 2.438392 TCAGCATCTGGATCAGCATCTT 59.562 45.455 0.00 0.00 31.51 2.40
1839 2053 2.047830 TCAGCATCTGGATCAGCATCT 58.952 47.619 0.00 0.00 31.51 2.90
1840 2054 2.545537 TCAGCATCTGGATCAGCATC 57.454 50.000 0.00 0.00 31.51 3.91
1841 2055 2.950309 GTTTCAGCATCTGGATCAGCAT 59.050 45.455 0.00 0.00 31.51 3.79
1842 2056 2.290450 TGTTTCAGCATCTGGATCAGCA 60.290 45.455 0.00 0.00 31.51 4.41
1843 2057 2.355132 CTGTTTCAGCATCTGGATCAGC 59.645 50.000 0.00 0.00 28.84 4.26
1844 2058 3.870274 TCTGTTTCAGCATCTGGATCAG 58.130 45.455 6.79 6.79 28.84 2.90
1845 2059 3.516700 TCTCTGTTTCAGCATCTGGATCA 59.483 43.478 0.00 0.00 31.51 2.92
1850 2064 1.998315 CGGTCTCTGTTTCAGCATCTG 59.002 52.381 0.00 0.00 0.00 2.90
1946 2172 2.050144 TGTCCTTGGGCTCCATATCTC 58.950 52.381 0.00 0.00 31.53 2.75
2034 2260 0.390340 TCAGACTGCGATCCAAGCAC 60.390 55.000 0.00 0.00 40.01 4.40
2172 2398 4.040095 GCTAGTTTATTATCCTCCCGTGGT 59.960 45.833 0.00 0.00 0.00 4.16
2177 2403 6.838382 TCCTTTGCTAGTTTATTATCCTCCC 58.162 40.000 0.00 0.00 0.00 4.30
2263 2490 6.430308 GCAGGCTAGTTAAAAGTTACTCCTTT 59.570 38.462 0.00 0.00 36.23 3.11
2356 2583 1.540118 TGTATCTGGTGTGCCCCCA 60.540 57.895 0.00 0.00 0.00 4.96
2426 2653 1.674221 CGCCTCTTGAAGACTTGAGGG 60.674 57.143 17.45 5.46 44.46 4.30
2427 2654 1.674221 CCGCCTCTTGAAGACTTGAGG 60.674 57.143 13.38 13.38 46.38 3.86
2428 2655 1.674221 CCCGCCTCTTGAAGACTTGAG 60.674 57.143 0.00 0.00 0.00 3.02
2514 2753 0.322546 CAGGTCCTAGTTGGGTTGCC 60.323 60.000 0.00 0.00 36.20 4.52
2660 2931 5.415389 TGTGCTATCTGCTTTCTTTTATGCA 59.585 36.000 0.00 0.00 43.37 3.96
2661 2932 5.741040 GTGTGCTATCTGCTTTCTTTTATGC 59.259 40.000 0.00 0.00 43.37 3.14
2662 2933 6.845302 TGTGTGCTATCTGCTTTCTTTTATG 58.155 36.000 0.00 0.00 43.37 1.90
2663 2934 7.452880 TTGTGTGCTATCTGCTTTCTTTTAT 57.547 32.000 0.00 0.00 43.37 1.40
2664 2935 6.875948 TTGTGTGCTATCTGCTTTCTTTTA 57.124 33.333 0.00 0.00 43.37 1.52
2665 2936 5.772825 TTGTGTGCTATCTGCTTTCTTTT 57.227 34.783 0.00 0.00 43.37 2.27
2666 2937 5.972107 ATTGTGTGCTATCTGCTTTCTTT 57.028 34.783 0.00 0.00 43.37 2.52
2667 2938 5.939883 TGTATTGTGTGCTATCTGCTTTCTT 59.060 36.000 0.00 0.00 43.37 2.52
2668 2939 5.491070 TGTATTGTGTGCTATCTGCTTTCT 58.509 37.500 0.00 0.00 43.37 2.52
2669 2940 5.801350 TGTATTGTGTGCTATCTGCTTTC 57.199 39.130 0.00 0.00 43.37 2.62
2670 2941 6.037940 CAGATGTATTGTGTGCTATCTGCTTT 59.962 38.462 0.00 0.00 43.37 3.51
2671 2942 5.526479 CAGATGTATTGTGTGCTATCTGCTT 59.474 40.000 0.00 0.00 43.37 3.91
2672 2943 5.055144 CAGATGTATTGTGTGCTATCTGCT 58.945 41.667 0.00 0.00 43.37 4.24
2673 2944 5.052481 TCAGATGTATTGTGTGCTATCTGC 58.948 41.667 0.00 0.00 40.60 4.26
2674 2945 8.302438 TCTATCAGATGTATTGTGTGCTATCTG 58.698 37.037 0.00 0.00 41.59 2.90
2675 2946 8.414629 TCTATCAGATGTATTGTGTGCTATCT 57.585 34.615 0.00 0.00 0.00 1.98
2676 2947 8.518702 TCTCTATCAGATGTATTGTGTGCTATC 58.481 37.037 0.00 0.00 0.00 2.08
2677 2948 8.414629 TCTCTATCAGATGTATTGTGTGCTAT 57.585 34.615 0.00 0.00 0.00 2.97
2678 2949 7.721399 TCTCTCTATCAGATGTATTGTGTGCTA 59.279 37.037 0.00 0.00 0.00 3.49
2679 2950 6.548993 TCTCTCTATCAGATGTATTGTGTGCT 59.451 38.462 0.00 0.00 0.00 4.40
2680 2951 6.743110 TCTCTCTATCAGATGTATTGTGTGC 58.257 40.000 0.00 0.00 0.00 4.57
2681 2952 8.164058 TCTCTCTCTATCAGATGTATTGTGTG 57.836 38.462 0.00 0.00 0.00 3.82
2682 2953 8.759481 TTCTCTCTCTATCAGATGTATTGTGT 57.241 34.615 0.00 0.00 0.00 3.72
2913 3200 3.786635 AGTAGGCGAATGTTCTTGCTAG 58.213 45.455 0.00 0.00 0.00 3.42
2956 3243 3.939740 TTGCTGATAGCCCTTCTGATT 57.060 42.857 0.00 0.00 41.51 2.57
2988 3275 8.195617 TGTTGGATTTTCATTGTTTTGTTCTC 57.804 30.769 0.00 0.00 0.00 2.87
3028 3315 3.826157 TCCGCCCATTCAATATTTCATCC 59.174 43.478 0.00 0.00 0.00 3.51
3049 3336 0.674534 AGTGTTCTGGACTCCACGTC 59.325 55.000 0.00 0.00 42.07 4.34
3050 3337 1.991121 TAGTGTTCTGGACTCCACGT 58.009 50.000 0.00 0.00 33.14 4.49
3051 3338 2.035449 TGTTAGTGTTCTGGACTCCACG 59.965 50.000 0.00 0.00 33.14 4.94
3052 3339 3.391049 GTGTTAGTGTTCTGGACTCCAC 58.609 50.000 0.00 0.00 0.00 4.02
3053 3340 2.035449 CGTGTTAGTGTTCTGGACTCCA 59.965 50.000 0.00 0.00 0.00 3.86
3054 3341 2.295349 TCGTGTTAGTGTTCTGGACTCC 59.705 50.000 0.00 0.00 0.00 3.85
3056 3343 3.243771 CCTTCGTGTTAGTGTTCTGGACT 60.244 47.826 0.00 0.00 0.00 3.85
3160 3456 5.582269 CCGAATGTCAATTCACAGAGTATGT 59.418 40.000 0.00 0.00 45.43 2.29


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

AutoCloner maintained by Alex Coulton.