Multiple sequence alignment - TraesCS5B01G098300

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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 TraesCS5B01G098300 chr5B 100.000 3692 0 0 1 3692 130513731 130510040 0.000000e+00 6818.0
1 TraesCS5B01G098300 chr5B 87.097 186 23 1 3502 3686 441573112 441572927 3.740000e-50 209.0
2 TraesCS5B01G098300 chr5B 93.478 46 2 1 3440 3484 130510220 130510175 2.380000e-07 67.6
3 TraesCS5B01G098300 chr5A 90.840 2500 127 48 739 3185 127612919 127610469 0.000000e+00 3254.0
4 TraesCS5B01G098300 chr5A 91.481 763 56 7 4 761 127613845 127613087 0.000000e+00 1040.0
5 TraesCS5B01G098300 chr5A 87.302 189 21 3 3500 3686 474760818 474760631 2.890000e-51 213.0
6 TraesCS5B01G098300 chr5D 91.636 2188 117 30 739 2908 118457383 118455244 0.000000e+00 2966.0
7 TraesCS5B01G098300 chr5D 91.656 767 54 7 1 761 118458323 118457561 0.000000e+00 1053.0
8 TraesCS5B01G098300 chr5D 94.128 562 19 4 2900 3448 118454586 118454026 0.000000e+00 843.0
9 TraesCS5B01G098300 chr5D 94.089 203 11 1 3490 3692 118453391 118453190 1.290000e-79 307.0
10 TraesCS5B01G098300 chr5D 85.784 204 22 3 3490 3692 365319232 365319035 3.740000e-50 209.0
11 TraesCS5B01G098300 chr4A 86.207 203 27 1 3490 3692 546392678 546392477 6.210000e-53 219.0
12 TraesCS5B01G098300 chr4A 85.000 200 28 1 3495 3692 709190402 709190601 6.250000e-48 202.0
13 TraesCS5B01G098300 chr3D 86.207 203 27 1 3490 3692 457240436 457240235 6.210000e-53 219.0
14 TraesCS5B01G098300 chr2A 85.427 199 29 0 3494 3692 631198167 631197969 1.340000e-49 207.0
15 TraesCS5B01G098300 chr2B 84.729 203 26 1 3490 3692 42935006 42934809 8.090000e-47 198.0
16 TraesCS5B01G098300 chr4D 84.348 115 15 3 3335 3448 28545988 28546100 3.900000e-20 110.0
17 TraesCS5B01G098300 chr7A 89.231 65 5 2 2228 2291 182859552 182859489 3.060000e-11 80.5
18 TraesCS5B01G098300 chr7B 87.273 55 6 1 3057 3110 678734586 678734532 1.110000e-05 62.1
19 TraesCS5B01G098300 chr7B 81.081 74 9 5 2254 2323 484508370 484508298 2.000000e-03 54.7
20 TraesCS5B01G098300 chr6B 97.059 34 1 0 3071 3104 618856076 618856043 1.430000e-04 58.4
21 TraesCS5B01G098300 chr4B 100.000 30 0 0 2251 2280 560661431 560661402 5.150000e-04 56.5


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 TraesCS5B01G098300 chr5B 130510040 130513731 3691 True 3442.80 6818 96.73900 1 3692 2 chr5B.!!$R2 3691
1 TraesCS5B01G098300 chr5A 127610469 127613845 3376 True 2147.00 3254 91.16050 4 3185 2 chr5A.!!$R2 3181
2 TraesCS5B01G098300 chr5D 118453190 118458323 5133 True 1292.25 2966 92.87725 1 3692 4 chr5D.!!$R2 3691

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
733 740 1.280133 TGAGCCAAGTTGATCCTCCAG 59.720 52.381 3.87 0.0 0.0 3.86 F
2238 2483 1.134037 TCGGTAAGTTTTGCCAGTGGT 60.134 47.619 11.74 0.0 34.8 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 2500 0.252012 TTTTGTAGGGGGTGCCATGG 60.252 55.0 7.63 7.63 0.00 3.66 R
3243 4182 0.038618 GGCAAATTGGGTTGTCCGAC 60.039 55.0 0.00 0.00 38.76 4.79 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
34 35 4.275196 AGCCGAACTTTTGACCTTAGTTTC 59.725 41.667 0.00 0.00 32.58 2.78
65 66 3.289407 TCCCTGTGTTGTGATTGTGAA 57.711 42.857 0.00 0.00 0.00 3.18
110 115 8.626526 ACAATGTGTTGGGTAGTTAAGTTAAAG 58.373 33.333 0.00 0.00 39.70 1.85
117 122 4.643334 GGGTAGTTAAGTTAAAGGGCATGG 59.357 45.833 0.00 0.00 0.00 3.66
153 158 1.344438 CCAACCTCTTTCCAAAAGGGC 59.656 52.381 0.00 0.00 36.21 5.19
155 160 2.634453 CAACCTCTTTCCAAAAGGGCAT 59.366 45.455 0.00 0.00 36.21 4.40
213 218 6.599638 GCATAAACACAGAGTAGGGATCTTTT 59.400 38.462 0.00 0.00 0.00 2.27
218 223 3.777522 ACAGAGTAGGGATCTTTTCTGGG 59.222 47.826 13.59 0.00 36.96 4.45
241 246 3.244561 TGAGTCCTGGTCTCATGGTTTTC 60.245 47.826 17.83 0.00 37.07 2.29
249 254 4.825085 TGGTCTCATGGTTTTCTTTGGTAC 59.175 41.667 0.00 0.00 0.00 3.34
259 264 6.935771 TGGTTTTCTTTGGTACGCTCTTATAA 59.064 34.615 0.00 0.00 0.00 0.98
338 344 6.661805 TGATGTAGTCCTTTTACCAATTTCCC 59.338 38.462 0.00 0.00 0.00 3.97
340 346 4.376225 AGTCCTTTTACCAATTTCCCGA 57.624 40.909 0.00 0.00 0.00 5.14
369 375 5.284079 TCAGCAAAGCATTTTTCTCAAGTC 58.716 37.500 0.00 0.00 35.03 3.01
435 441 9.150348 CATCATTTGTTAATCCCTTTTACCAAC 57.850 33.333 0.00 0.00 0.00 3.77
444 450 5.126699 TCCCTTTTACCAACACAAGGTTA 57.873 39.130 0.00 0.00 40.54 2.85
446 452 5.360429 TCCCTTTTACCAACACAAGGTTAAC 59.640 40.000 0.00 0.00 40.54 2.01
471 477 4.517832 AGTAAACTTTTTAAGGGCAGTCGG 59.482 41.667 0.00 0.00 0.00 4.79
579 586 1.324383 CACACCCCTAAACACAACCC 58.676 55.000 0.00 0.00 0.00 4.11
599 606 3.453424 CCGGTGTCGTAATCATCAATGA 58.547 45.455 0.00 0.00 36.53 2.57
671 678 4.513318 GCTGAGACCAACTATGCCTAATTC 59.487 45.833 0.00 0.00 0.00 2.17
678 685 4.511826 CCAACTATGCCTAATTCTCCGAAC 59.488 45.833 0.00 0.00 0.00 3.95
682 689 2.972625 TGCCTAATTCTCCGAACTGTG 58.027 47.619 0.00 0.00 0.00 3.66
690 697 3.303881 TCTCCGAACTGTGAACATGAG 57.696 47.619 0.00 0.00 0.00 2.90
722 729 4.946157 CCATTCTGTTAGATTGAGCCAAGT 59.054 41.667 0.00 0.00 29.56 3.16
733 740 1.280133 TGAGCCAAGTTGATCCTCCAG 59.720 52.381 3.87 0.00 0.00 3.86
794 1002 3.799917 GCAGCCTACTTGTTTTGCATTGT 60.800 43.478 0.00 0.00 0.00 2.71
864 1072 3.010420 GAGTGCCAACTTAGTTCATCCC 58.990 50.000 0.00 0.00 36.52 3.85
865 1073 2.644798 AGTGCCAACTTAGTTCATCCCT 59.355 45.455 0.00 0.00 30.14 4.20
866 1074 3.074538 AGTGCCAACTTAGTTCATCCCTT 59.925 43.478 0.00 0.00 30.14 3.95
867 1075 3.826729 GTGCCAACTTAGTTCATCCCTTT 59.173 43.478 0.00 0.00 0.00 3.11
890 1098 4.344102 TCTTCTCAGAAAAGGAAACCGAGA 59.656 41.667 0.00 0.00 0.00 4.04
903 1111 5.001874 GGAAACCGAGAACTTCCAGTTTAT 58.998 41.667 0.00 0.00 38.80 1.40
923 1131 7.934120 AGTTTATGACATTACCAGCTATTCCTC 59.066 37.037 0.00 0.00 0.00 3.71
924 1132 4.689612 TGACATTACCAGCTATTCCTCC 57.310 45.455 0.00 0.00 0.00 4.30
925 1133 4.037222 TGACATTACCAGCTATTCCTCCA 58.963 43.478 0.00 0.00 0.00 3.86
926 1134 4.473196 TGACATTACCAGCTATTCCTCCAA 59.527 41.667 0.00 0.00 0.00 3.53
927 1135 5.132648 TGACATTACCAGCTATTCCTCCAAT 59.867 40.000 0.00 0.00 0.00 3.16
928 1136 6.018433 ACATTACCAGCTATTCCTCCAATT 57.982 37.500 0.00 0.00 0.00 2.32
951 1162 9.744468 AATTAAAGAAACTAAGAAACATTGCGT 57.256 25.926 0.00 0.00 0.00 5.24
974 1202 9.894783 GCGTTCTATCTTGTTAACTATGAGATA 57.105 33.333 7.22 12.24 0.00 1.98
1081 1309 7.119699 TGGTATGTGCTTCTTGACTTTTATCAG 59.880 37.037 0.00 0.00 0.00 2.90
1197 1425 1.786937 TTTTGCTGAAGGGGCTGAAA 58.213 45.000 0.00 0.00 0.00 2.69
1238 1467 3.295973 ACTTGGCTCAGGTTTGCTTAAA 58.704 40.909 0.00 0.00 0.00 1.52
1277 1506 8.952278 TCTTTCAAAGCTACTGTCACTTTTTAA 58.048 29.630 5.51 2.37 31.43 1.52
1310 1540 5.381757 AGCAGGGTAAATGTTCTGTGTAAA 58.618 37.500 0.00 0.00 0.00 2.01
1357 1590 4.018050 AGGAAAGCATTACCCTTCTGTCAT 60.018 41.667 0.00 0.00 28.44 3.06
1367 1600 3.007398 ACCCTTCTGTCATTCTGTCAGTC 59.993 47.826 0.00 0.00 35.53 3.51
1388 1621 8.044908 TCAGTCTAATAGTTCAAAATGGTACCC 58.955 37.037 10.07 0.00 0.00 3.69
1389 1622 7.827236 CAGTCTAATAGTTCAAAATGGTACCCA 59.173 37.037 10.07 0.00 38.19 4.51
1402 1635 4.066646 TGGTACCCATTGATCATACACG 57.933 45.455 10.07 0.00 0.00 4.49
1435 1668 7.400599 AATGCCAGCATCAAATAGTATATGG 57.599 36.000 5.44 0.00 35.31 2.74
1474 1707 8.298140 CCGTATCCCAGTTTATTTTGTTAAACA 58.702 33.333 9.11 0.00 42.11 2.83
1590 1828 7.767659 TCTGAAATATCACTCAAATCTGGTCAG 59.232 37.037 0.00 0.00 0.00 3.51
1603 1841 2.205022 TGGTCAGGCCAGATTTTCTG 57.795 50.000 5.01 0.00 43.61 3.02
1604 1842 1.425066 TGGTCAGGCCAGATTTTCTGT 59.575 47.619 5.01 0.00 42.80 3.41
1609 1847 4.762251 GTCAGGCCAGATTTTCTGTAAGTT 59.238 41.667 5.01 0.00 42.80 2.66
1622 1860 9.696917 ATTTTCTGTAAGTTAAAAAGAGCATGG 57.303 29.630 0.00 0.00 33.76 3.66
1623 1861 7.817418 TTCTGTAAGTTAAAAAGAGCATGGT 57.183 32.000 0.00 0.00 33.76 3.55
1626 1864 7.284489 TCTGTAAGTTAAAAAGAGCATGGTGTT 59.716 33.333 0.00 0.39 33.76 3.32
1643 1881 4.681942 TGGTGTTTTGTCTTTGTTTTCACG 59.318 37.500 0.00 0.00 0.00 4.35
1660 1898 8.332464 TGTTTTCACGTAGAGAAGTAAATGTTG 58.668 33.333 0.00 0.00 38.51 3.33
1661 1899 8.545420 GTTTTCACGTAGAGAAGTAAATGTTGA 58.455 33.333 0.00 0.00 38.51 3.18
1662 1900 7.869016 TTCACGTAGAGAAGTAAATGTTGAG 57.131 36.000 0.00 0.00 30.97 3.02
1663 1901 7.210718 TCACGTAGAGAAGTAAATGTTGAGA 57.789 36.000 0.00 0.00 0.00 3.27
1664 1902 7.654568 TCACGTAGAGAAGTAAATGTTGAGAA 58.345 34.615 0.00 0.00 0.00 2.87
1665 1903 8.304596 TCACGTAGAGAAGTAAATGTTGAGAAT 58.695 33.333 0.00 0.00 0.00 2.40
1666 1904 8.376203 CACGTAGAGAAGTAAATGTTGAGAATG 58.624 37.037 0.00 0.00 0.00 2.67
1667 1905 8.304596 ACGTAGAGAAGTAAATGTTGAGAATGA 58.695 33.333 0.00 0.00 0.00 2.57
1668 1906 9.307121 CGTAGAGAAGTAAATGTTGAGAATGAT 57.693 33.333 0.00 0.00 0.00 2.45
1705 1943 8.816640 AGTCAACGAATTGAAAATGCTTTTAT 57.183 26.923 0.00 0.00 46.40 1.40
1706 1944 9.906660 AGTCAACGAATTGAAAATGCTTTTATA 57.093 25.926 0.00 0.00 46.40 0.98
1707 1945 9.937577 GTCAACGAATTGAAAATGCTTTTATAC 57.062 29.630 0.00 0.00 46.40 1.47
1708 1946 9.684448 TCAACGAATTGAAAATGCTTTTATACA 57.316 25.926 0.00 0.00 41.99 2.29
1771 2010 5.251700 ACCTCAGGAACATTACAAGGATCTT 59.748 40.000 0.00 0.00 0.00 2.40
1846 2085 7.065085 CCTGTAGTCTGCATGGTATATATTTGC 59.935 40.741 0.00 7.28 0.00 3.68
1888 2127 5.572511 TGCAACTTCGCATTTTGATCAATAC 59.427 36.000 9.40 0.00 36.86 1.89
1946 2189 4.512914 GCCTGGGAGGGTGATGGC 62.513 72.222 0.00 0.00 35.37 4.40
1955 2198 2.560119 GGGTGATGGCGTTGTTGCA 61.560 57.895 0.00 0.00 36.28 4.08
2000 2243 2.062636 ACTAACCCCCTTCAAGCTGAA 58.937 47.619 0.00 0.00 34.79 3.02
2066 2310 1.767759 CACCCATCCTTTCCATGTCC 58.232 55.000 0.00 0.00 0.00 4.02
2089 2333 7.549488 GTCCTCACACTATTATTTGCAGTACTT 59.451 37.037 0.00 0.00 0.00 2.24
2095 2339 8.721478 ACACTATTATTTGCAGTACTTCTGTTG 58.279 33.333 0.00 0.00 45.23 3.33
2106 2350 7.381948 TGCAGTACTTCTGTTGCATTTTATTTG 59.618 33.333 0.00 0.00 45.23 2.32
2138 2382 6.239714 CCTCTATTTGCACCCTCTATGTGTAT 60.240 42.308 0.00 0.00 36.11 2.29
2159 2403 9.438291 GTGTATCAAAGAAATTATCATGGAACG 57.562 33.333 0.00 0.00 0.00 3.95
2238 2483 1.134037 TCGGTAAGTTTTGCCAGTGGT 60.134 47.619 11.74 0.00 34.80 4.16
2253 2498 2.446036 GGTGGATCTAGCGGGGGT 60.446 66.667 0.00 0.00 0.00 4.95
2254 2499 2.808206 GGTGGATCTAGCGGGGGTG 61.808 68.421 0.00 0.00 0.00 4.61
2255 2500 3.161450 TGGATCTAGCGGGGGTGC 61.161 66.667 0.00 0.00 0.00 5.01
2256 2501 3.942439 GGATCTAGCGGGGGTGCC 61.942 72.222 0.00 0.00 34.65 5.01
2257 2502 3.161450 GATCTAGCGGGGGTGCCA 61.161 66.667 0.00 0.00 34.65 4.92
2345 2599 8.478066 TGTAATGACATAGTGCTATTTCAGACT 58.522 33.333 11.95 4.51 36.19 3.24
2346 2600 9.967346 GTAATGACATAGTGCTATTTCAGACTA 57.033 33.333 11.95 0.00 36.19 2.59
2423 2677 2.418628 CCGACGTATTGAAGTTTGGCAT 59.581 45.455 0.00 0.00 0.00 4.40
2489 2743 4.264638 GTGCACCGCCGTTTGCTT 62.265 61.111 5.22 0.00 39.62 3.91
2511 2766 9.844790 TGCTTTTCAGTTGATTCAGTATTTATG 57.155 29.630 0.00 0.00 0.00 1.90
2527 2782 8.902806 CAGTATTTATGTGGTTATGGTGTGAAT 58.097 33.333 0.00 0.00 0.00 2.57
2528 2783 8.902806 AGTATTTATGTGGTTATGGTGTGAATG 58.097 33.333 0.00 0.00 0.00 2.67
2529 2784 7.716799 ATTTATGTGGTTATGGTGTGAATGT 57.283 32.000 0.00 0.00 0.00 2.71
2588 2843 1.072666 GCACGGCTATTTGCAGCAAC 61.073 55.000 7.54 0.00 43.67 4.17
2704 2964 8.040132 GGCTTATAGAGTGATCTTTGCATATCT 58.960 37.037 0.00 0.00 0.00 1.98
2798 3068 3.646637 ACCAAGTAAAGTAGCCAGTCAGT 59.353 43.478 0.00 0.00 0.00 3.41
2911 3848 6.641169 AAATCTTCCTGTTGAGAACTTTCC 57.359 37.500 0.00 0.00 0.00 3.13
3139 4078 8.367156 ACAATACAATTTTGTTGGCAAGATAGT 58.633 29.630 0.00 0.00 42.35 2.12
3254 4193 0.252197 ATTGCCTAGTCGGACAACCC 59.748 55.000 11.27 0.00 33.62 4.11
3257 4196 0.252197 GCCTAGTCGGACAACCCAAT 59.748 55.000 11.27 0.00 33.16 3.16
3346 4296 6.595772 TTTGAAACATTAAACACATGCACC 57.404 33.333 0.00 0.00 0.00 5.01
3348 4298 6.641169 TGAAACATTAAACACATGCACCTA 57.359 33.333 0.00 0.00 0.00 3.08
3355 4305 7.340232 ACATTAAACACATGCACCTAGATCATT 59.660 33.333 0.00 0.00 0.00 2.57
3358 4308 7.701539 AAACACATGCACCTAGATCATTTTA 57.298 32.000 0.00 0.00 0.00 1.52
3461 4411 6.723298 ATATTGTTCACACAAACCTTTGGA 57.277 33.333 2.94 0.00 46.17 3.53
3462 4412 3.859411 TGTTCACACAAACCTTTGGAC 57.141 42.857 2.94 0.00 42.34 4.02
3464 4414 3.192422 TGTTCACACAAACCTTTGGACAG 59.808 43.478 2.94 0.00 42.34 3.51
3465 4415 3.080300 TCACACAAACCTTTGGACAGT 57.920 42.857 2.94 0.00 42.34 3.55
3466 4416 3.426615 TCACACAAACCTTTGGACAGTT 58.573 40.909 2.94 0.00 42.34 3.16
3467 4417 3.442273 TCACACAAACCTTTGGACAGTTC 59.558 43.478 2.94 0.00 42.34 3.01
3468 4418 3.443681 CACACAAACCTTTGGACAGTTCT 59.556 43.478 2.94 0.00 42.34 3.01
3469 4419 4.082245 CACACAAACCTTTGGACAGTTCTT 60.082 41.667 2.94 0.00 42.34 2.52
3470 4420 4.157840 ACACAAACCTTTGGACAGTTCTTC 59.842 41.667 2.94 0.00 42.34 2.87
3471 4421 3.699538 ACAAACCTTTGGACAGTTCTTCC 59.300 43.478 2.94 0.00 42.34 3.46
3474 4424 2.092592 ACCTTTGGACAGTTCTTCCGTT 60.093 45.455 0.00 0.00 35.70 4.44
3475 4425 2.290641 CCTTTGGACAGTTCTTCCGTTG 59.709 50.000 0.00 0.00 35.70 4.10
3476 4426 1.305201 TTGGACAGTTCTTCCGTTGC 58.695 50.000 0.00 0.00 35.70 4.17
3477 4427 0.468226 TGGACAGTTCTTCCGTTGCT 59.532 50.000 0.00 0.00 35.70 3.91
3478 4428 1.689813 TGGACAGTTCTTCCGTTGCTA 59.310 47.619 0.00 0.00 35.70 3.49
3479 4429 2.288825 TGGACAGTTCTTCCGTTGCTAG 60.289 50.000 0.00 0.00 35.70 3.42
3481 4431 2.731976 GACAGTTCTTCCGTTGCTAGTG 59.268 50.000 0.00 0.00 0.00 2.74
3503 5046 1.376037 GGAGGGCCTCTTTGACGTG 60.376 63.158 31.39 0.00 0.00 4.49
3512 5055 3.659786 CCTCTTTGACGTGACATTGGTA 58.340 45.455 0.00 0.00 0.00 3.25
3521 5064 2.166829 GTGACATTGGTATTGCCCACA 58.833 47.619 0.00 0.00 33.14 4.17
3545 5088 2.572290 ACCTTTTGGACAGTTCTTCCG 58.428 47.619 0.00 0.00 44.07 4.30
3581 5124 4.218417 GCAATCAACTGAACCCAACATACT 59.782 41.667 0.00 0.00 0.00 2.12
3598 5141 7.972277 CCAACATACTTGGAAATCTTCTTGATG 59.028 37.037 0.00 0.00 42.06 3.07
3605 5148 4.460382 TGGAAATCTTCTTGATGCTCCAAC 59.540 41.667 7.06 0.00 41.35 3.77
3641 5184 0.603975 GTGTCCTCCACAGTTGGCTC 60.604 60.000 0.00 0.00 43.56 4.70
3645 5188 0.248843 CCTCCACAGTTGGCTCTCTC 59.751 60.000 0.00 0.00 43.56 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.487120 ACTAAGGTCAAAAGTTCGGCT 57.513 42.857 0.00 0.00 0.00 5.52
13 14 4.319261 CGGAAACTAAGGTCAAAAGTTCGG 60.319 45.833 0.00 0.00 32.42 4.30
15 16 4.534168 GCGGAAACTAAGGTCAAAAGTTC 58.466 43.478 0.00 0.00 32.42 3.01
73 74 6.052360 ACCCAACACATTGTTACAATTTTCC 58.948 36.000 7.97 0.00 38.77 3.13
75 76 7.787028 ACTACCCAACACATTGTTACAATTTT 58.213 30.769 7.97 0.00 38.77 1.82
117 122 2.155279 GTTGGAAGAGGAACTTGGCTC 58.845 52.381 0.00 0.00 41.55 4.70
213 218 0.251832 GAGACCAGGACTCACCCAGA 60.252 60.000 13.51 0.00 40.05 3.86
218 223 1.270907 ACCATGAGACCAGGACTCAC 58.729 55.000 22.06 0.00 45.19 3.51
241 246 9.189723 GTAGGTTATTATAAGAGCGTACCAAAG 57.810 37.037 12.86 0.00 0.00 2.77
249 254 7.659186 AGTTCTGGTAGGTTATTATAAGAGCG 58.341 38.462 0.00 0.00 0.00 5.03
259 264 7.112779 CCATTTCTGAAGTTCTGGTAGGTTAT 58.887 38.462 9.59 0.00 0.00 1.89
338 344 5.834239 AAAATGCTTTGCTGAATCTTTCG 57.166 34.783 0.00 0.00 0.00 3.46
340 346 6.987992 TGAGAAAAATGCTTTGCTGAATCTTT 59.012 30.769 0.00 0.00 29.74 2.52
386 392 4.936802 ACTTCACTGAGTACCATCTACCT 58.063 43.478 0.00 0.00 0.00 3.08
397 403 8.627208 ATTAACAAATGATGACTTCACTGAGT 57.373 30.769 8.47 0.00 37.11 3.41
435 441 9.857957 TTAAAAAGTTTACTGGTTAACCTTGTG 57.142 29.630 24.78 14.24 36.82 3.33
444 450 5.659525 ACTGCCCTTAAAAAGTTTACTGGTT 59.340 36.000 0.00 0.00 0.00 3.67
446 452 5.562113 CGACTGCCCTTAAAAAGTTTACTGG 60.562 44.000 0.00 0.00 0.00 4.00
500 506 5.699097 TCTTGGGTAGCAAACAAATGTAC 57.301 39.130 0.00 0.00 0.00 2.90
526 532 5.904362 ACTGAGTTTATTTCCTTGGATGC 57.096 39.130 0.00 0.00 0.00 3.91
544 550 2.226330 GTGTGGCCACATGTTTACTGA 58.774 47.619 39.53 11.67 43.97 3.41
631 638 5.023452 TCTCAGCTTGGTAAAGAGGTGATA 58.977 41.667 5.81 0.00 45.86 2.15
671 678 3.032017 ACTCATGTTCACAGTTCGGAG 57.968 47.619 0.00 0.00 0.00 4.63
678 685 4.999311 TGGAGAATCAACTCATGTTCACAG 59.001 41.667 0.00 0.00 38.51 3.66
682 689 6.373774 ACAGAATGGAGAATCAACTCATGTTC 59.626 38.462 0.00 0.00 43.62 3.18
690 697 8.498054 TCAATCTAACAGAATGGAGAATCAAC 57.502 34.615 0.00 0.00 43.62 3.18
733 740 8.627208 AGTGATACATCAATTATTGGACATCC 57.373 34.615 5.02 0.00 38.75 3.51
771 979 1.691196 TGCAAAACAAGTAGGCTGCT 58.309 45.000 0.00 0.00 0.00 4.24
779 987 4.819769 ACAACAGACAATGCAAAACAAGT 58.180 34.783 0.00 0.00 0.00 3.16
794 1002 6.003326 TCTTTCAGGCATCAAATACAACAGA 58.997 36.000 0.00 0.00 0.00 3.41
828 1036 4.973168 TGGCACTCTTAGATGAAACAACT 58.027 39.130 0.00 0.00 0.00 3.16
839 1047 5.582665 GGATGAACTAAGTTGGCACTCTTAG 59.417 44.000 24.55 24.55 43.27 2.18
864 1072 5.527582 TCGGTTTCCTTTTCTGAGAAGAAAG 59.472 40.000 9.33 4.49 38.76 2.62
865 1073 5.433526 TCGGTTTCCTTTTCTGAGAAGAAA 58.566 37.500 9.33 4.57 36.17 2.52
866 1074 5.031066 TCGGTTTCCTTTTCTGAGAAGAA 57.969 39.130 9.33 0.00 0.00 2.52
867 1075 4.344102 TCTCGGTTTCCTTTTCTGAGAAGA 59.656 41.667 9.33 0.00 39.61 2.87
903 1111 4.037222 TGGAGGAATAGCTGGTAATGTCA 58.963 43.478 0.00 0.00 0.00 3.58
924 1132 9.993881 CGCAATGTTTCTTAGTTTCTTTAATTG 57.006 29.630 0.00 0.00 0.00 2.32
925 1133 9.744468 ACGCAATGTTTCTTAGTTTCTTTAATT 57.256 25.926 0.00 0.00 0.00 1.40
926 1134 9.744468 AACGCAATGTTTCTTAGTTTCTTTAAT 57.256 25.926 0.00 0.00 37.59 1.40
927 1135 9.228636 GAACGCAATGTTTCTTAGTTTCTTTAA 57.771 29.630 0.00 0.00 42.09 1.52
928 1136 8.617809 AGAACGCAATGTTTCTTAGTTTCTTTA 58.382 29.630 0.00 0.00 42.09 1.85
976 1204 9.474920 CTGCACAAAATAAAAATCCAGTTAAGA 57.525 29.630 0.00 0.00 0.00 2.10
984 1212 5.793817 ACCTCCTGCACAAAATAAAAATCC 58.206 37.500 0.00 0.00 0.00 3.01
1081 1309 9.522804 TGAAACAAATAACAGATACCAAAACAC 57.477 29.630 0.00 0.00 0.00 3.32
1111 1339 9.553064 CAGGCAGAGACTATTATGTTTTATCTT 57.447 33.333 0.00 0.00 0.00 2.40
1123 1351 3.452627 CCAACCTACAGGCAGAGACTATT 59.547 47.826 0.00 0.00 39.32 1.73
1131 1359 1.561643 TCTCTCCAACCTACAGGCAG 58.438 55.000 0.00 0.00 39.32 4.85
1197 1425 2.430694 GTCTTTGGGGCACTGAAAAAGT 59.569 45.455 0.00 0.00 40.93 2.66
1328 1561 6.317391 CAGAAGGGTAATGCTTTCCTTTAGAG 59.683 42.308 6.73 0.00 39.46 2.43
1357 1590 9.219603 CCATTTTGAACTATTAGACTGACAGAA 57.780 33.333 10.08 0.00 0.00 3.02
1388 1621 6.429791 TTTAACCACCGTGTATGATCAATG 57.570 37.500 0.00 0.00 0.00 2.82
1389 1622 7.479980 CATTTTAACCACCGTGTATGATCAAT 58.520 34.615 0.00 0.00 0.00 2.57
1391 1624 5.163703 GCATTTTAACCACCGTGTATGATCA 60.164 40.000 0.00 0.00 0.00 2.92
1392 1625 5.270853 GCATTTTAACCACCGTGTATGATC 58.729 41.667 0.00 0.00 0.00 2.92
1393 1626 4.097286 GGCATTTTAACCACCGTGTATGAT 59.903 41.667 0.00 0.00 0.00 2.45
1394 1627 3.440872 GGCATTTTAACCACCGTGTATGA 59.559 43.478 0.00 0.00 0.00 2.15
1395 1628 3.191581 TGGCATTTTAACCACCGTGTATG 59.808 43.478 0.00 0.00 0.00 2.39
1396 1629 3.422796 TGGCATTTTAACCACCGTGTAT 58.577 40.909 0.00 0.00 0.00 2.29
1398 1631 1.611491 CTGGCATTTTAACCACCGTGT 59.389 47.619 0.00 0.00 0.00 4.49
1399 1632 1.668628 GCTGGCATTTTAACCACCGTG 60.669 52.381 0.00 0.00 0.00 4.94
1400 1633 0.601057 GCTGGCATTTTAACCACCGT 59.399 50.000 0.00 0.00 0.00 4.83
1401 1634 0.600557 TGCTGGCATTTTAACCACCG 59.399 50.000 0.00 0.00 0.00 4.94
1402 1635 2.233431 TGATGCTGGCATTTTAACCACC 59.767 45.455 9.52 0.00 36.70 4.61
1432 1665 1.398692 ACGGTGTTCTTTTGTGCCAT 58.601 45.000 0.00 0.00 0.00 4.40
1435 1668 2.095415 GGGATACGGTGTTCTTTTGTGC 60.095 50.000 0.00 0.00 37.60 4.57
1441 1674 3.782656 AAACTGGGATACGGTGTTCTT 57.217 42.857 0.00 0.00 39.10 2.52
1521 1756 2.429971 TGGCTGACACATGCAAAGAAAA 59.570 40.909 0.00 0.00 0.00 2.29
1528 1763 1.520600 CTGCTTGGCTGACACATGCA 61.521 55.000 5.18 5.18 43.76 3.96
1571 1808 3.118261 GGCCTGACCAGATTTGAGTGATA 60.118 47.826 0.00 0.00 38.86 2.15
1572 1809 2.356535 GGCCTGACCAGATTTGAGTGAT 60.357 50.000 0.00 0.00 38.86 3.06
1573 1810 1.003580 GGCCTGACCAGATTTGAGTGA 59.996 52.381 0.00 0.00 38.86 3.41
1575 1812 1.067295 TGGCCTGACCAGATTTGAGT 58.933 50.000 3.32 0.00 46.36 3.41
1576 1813 3.963733 TGGCCTGACCAGATTTGAG 57.036 52.632 3.32 0.00 46.36 3.02
1603 1841 8.539674 CAAAACACCATGCTCTTTTTAACTTAC 58.460 33.333 0.00 0.00 0.00 2.34
1604 1842 8.254508 ACAAAACACCATGCTCTTTTTAACTTA 58.745 29.630 0.00 0.00 0.00 2.24
1609 1847 6.463995 AGACAAAACACCATGCTCTTTTTA 57.536 33.333 0.00 0.00 0.00 1.52
1621 1859 4.682401 ACGTGAAAACAAAGACAAAACACC 59.318 37.500 0.00 0.00 0.00 4.16
1622 1860 5.815964 ACGTGAAAACAAAGACAAAACAC 57.184 34.783 0.00 0.00 0.00 3.32
1623 1861 6.900189 TCTACGTGAAAACAAAGACAAAACA 58.100 32.000 0.00 0.00 0.00 2.83
1626 1864 6.971527 TCTCTACGTGAAAACAAAGACAAA 57.028 33.333 0.00 0.00 0.00 2.83
1660 1898 9.202273 GTTGACTCTCACCATTATATCATTCTC 57.798 37.037 0.00 0.00 0.00 2.87
1661 1899 7.869937 CGTTGACTCTCACCATTATATCATTCT 59.130 37.037 0.00 0.00 0.00 2.40
1662 1900 7.867909 TCGTTGACTCTCACCATTATATCATTC 59.132 37.037 0.00 0.00 0.00 2.67
1663 1901 7.726216 TCGTTGACTCTCACCATTATATCATT 58.274 34.615 0.00 0.00 0.00 2.57
1664 1902 7.290110 TCGTTGACTCTCACCATTATATCAT 57.710 36.000 0.00 0.00 0.00 2.45
1665 1903 6.709018 TCGTTGACTCTCACCATTATATCA 57.291 37.500 0.00 0.00 0.00 2.15
1666 1904 8.491152 CAATTCGTTGACTCTCACCATTATATC 58.509 37.037 0.00 0.00 0.00 1.63
1667 1905 8.204160 TCAATTCGTTGACTCTCACCATTATAT 58.796 33.333 0.00 0.00 0.00 0.86
1668 1906 7.552459 TCAATTCGTTGACTCTCACCATTATA 58.448 34.615 0.00 0.00 0.00 0.98
1669 1907 6.406370 TCAATTCGTTGACTCTCACCATTAT 58.594 36.000 0.00 0.00 0.00 1.28
1670 1908 5.789521 TCAATTCGTTGACTCTCACCATTA 58.210 37.500 0.00 0.00 0.00 1.90
1671 1909 4.641396 TCAATTCGTTGACTCTCACCATT 58.359 39.130 0.00 0.00 0.00 3.16
1672 1910 4.271696 TCAATTCGTTGACTCTCACCAT 57.728 40.909 0.00 0.00 0.00 3.55
1673 1911 3.744238 TCAATTCGTTGACTCTCACCA 57.256 42.857 0.00 0.00 0.00 4.17
1674 1912 5.418310 TTTTCAATTCGTTGACTCTCACC 57.582 39.130 0.00 0.00 0.00 4.02
1746 1985 5.964477 AGATCCTTGTAATGTTCCTGAGGTA 59.036 40.000 0.00 0.00 0.00 3.08
1846 2085 8.807667 AAGTTGCAAATATCTTCAGTTCTTTG 57.192 30.769 0.00 0.00 0.00 2.77
1924 2167 0.988678 ATCACCCTCCCAGGCCTTAC 60.989 60.000 0.00 0.00 32.73 2.34
1946 2189 1.510623 GCGAGCTGATGCAACAACG 60.511 57.895 0.00 5.91 42.74 4.10
2000 2243 2.006991 GCCCCTTATGGTCCCTGGT 61.007 63.158 0.00 0.00 0.00 4.00
2018 2261 2.807967 TCCTGTTTGAACTGCAAGATCG 59.192 45.455 0.00 0.00 38.80 3.69
2066 2310 8.598924 CAGAAGTACTGCAAATAATAGTGTGAG 58.401 37.037 3.00 0.00 39.86 3.51
2089 2333 8.149647 AGGTGAAATCAAATAAAATGCAACAGA 58.850 29.630 0.00 0.00 0.00 3.41
2106 2350 4.273318 AGGGTGCAAATAGAGGTGAAATC 58.727 43.478 0.00 0.00 0.00 2.17
2122 2366 5.023533 TCTTTGATACACATAGAGGGTGC 57.976 43.478 0.00 0.00 39.87 5.01
2138 2382 6.806249 GCAACGTTCCATGATAATTTCTTTGA 59.194 34.615 0.00 0.00 0.00 2.69
2159 2403 3.555518 GACGACATTCCTGAAAAGCAAC 58.444 45.455 0.00 0.00 0.00 4.17
2238 2483 3.161450 GCACCCCCGCTAGATCCA 61.161 66.667 0.00 0.00 0.00 3.41
2254 2499 2.796734 TTTGTAGGGGGTGCCATGGC 62.797 60.000 30.54 30.54 42.35 4.40
2255 2500 0.252012 TTTTGTAGGGGGTGCCATGG 60.252 55.000 7.63 7.63 0.00 3.66
2256 2501 1.638529 TTTTTGTAGGGGGTGCCATG 58.361 50.000 0.00 0.00 0.00 3.66
2257 2502 2.187100 CATTTTTGTAGGGGGTGCCAT 58.813 47.619 0.00 0.00 0.00 4.40
2409 2663 4.322057 ACTAGGGATGCCAAACTTCAAT 57.678 40.909 5.86 0.00 0.00 2.57
2489 2743 9.295825 ACCACATAAATACTGAATCAACTGAAA 57.704 29.630 0.00 0.00 0.00 2.69
2511 2766 4.846779 ACAACATTCACACCATAACCAC 57.153 40.909 0.00 0.00 0.00 4.16
2527 2782 2.504367 GCTCCCTTCAAGCTAACAACA 58.496 47.619 0.00 0.00 36.80 3.33
2573 2828 2.489329 TCAAGAGTTGCTGCAAATAGCC 59.511 45.455 17.80 4.24 44.83 3.93
2704 2964 3.507162 TTGGATCAAGGTTCTTGCAGA 57.493 42.857 0.00 0.00 0.00 4.26
2798 3068 3.814283 GCAATGGTGAAAATTTTGGAGCA 59.186 39.130 8.47 10.53 0.00 4.26
2911 3848 7.827819 TCAAAACATTAACATCCGAGTAGAG 57.172 36.000 0.00 0.00 0.00 2.43
3065 4004 5.686159 AGTGTATGTACGTATGTAGAGCC 57.314 43.478 0.00 0.00 0.00 4.70
3076 4015 8.648097 GCATTCATAAGGATAAGTGTATGTACG 58.352 37.037 0.00 0.00 0.00 3.67
3243 4182 0.038618 GGCAAATTGGGTTGTCCGAC 60.039 55.000 0.00 0.00 38.76 4.79
3275 4214 1.779025 GCTCGGTCAGCGGACGTATA 61.779 60.000 10.95 0.00 45.28 1.47
3355 4305 6.761099 TCCGCTAATTATTGTTTGGCTAAA 57.239 33.333 0.00 0.00 0.00 1.85
3358 4308 5.825679 TGTATCCGCTAATTATTGTTTGGCT 59.174 36.000 0.00 0.00 0.00 4.75
3448 4398 4.440112 GGAAGAACTGTCCAAAGGTTTGTG 60.440 45.833 1.94 0.00 36.45 3.33
3450 4400 3.243068 CGGAAGAACTGTCCAAAGGTTTG 60.243 47.826 0.00 0.00 34.56 2.93
3451 4401 2.949644 CGGAAGAACTGTCCAAAGGTTT 59.050 45.455 0.00 0.00 34.56 3.27
3452 4402 2.092592 ACGGAAGAACTGTCCAAAGGTT 60.093 45.455 0.00 0.00 34.56 3.50
3453 4403 1.489230 ACGGAAGAACTGTCCAAAGGT 59.511 47.619 0.00 0.00 34.56 3.50
3454 4404 2.256117 ACGGAAGAACTGTCCAAAGG 57.744 50.000 0.00 0.00 34.56 3.11
3455 4405 2.287009 GCAACGGAAGAACTGTCCAAAG 60.287 50.000 0.00 0.00 37.07 2.77
3456 4406 1.673920 GCAACGGAAGAACTGTCCAAA 59.326 47.619 0.00 0.00 37.07 3.28
3457 4407 1.134220 AGCAACGGAAGAACTGTCCAA 60.134 47.619 0.00 0.00 37.07 3.53
3459 4409 2.288886 ACTAGCAACGGAAGAACTGTCC 60.289 50.000 0.00 0.00 37.07 4.02
3461 4411 2.755650 CACTAGCAACGGAAGAACTGT 58.244 47.619 0.00 0.00 40.17 3.55
3462 4412 1.461127 GCACTAGCAACGGAAGAACTG 59.539 52.381 0.00 0.00 41.58 3.16
3475 4425 4.840005 GGCCCTCCGTGCACTAGC 62.840 72.222 16.19 9.79 42.57 3.42
3476 4426 3.077556 AGGCCCTCCGTGCACTAG 61.078 66.667 16.19 11.88 37.47 2.57
3477 4427 3.075005 GAGGCCCTCCGTGCACTA 61.075 66.667 16.19 1.63 37.47 2.74
3479 4429 3.553095 AAAGAGGCCCTCCGTGCAC 62.553 63.158 7.26 6.82 37.47 4.57
3481 4431 2.747855 CAAAGAGGCCCTCCGTGC 60.748 66.667 7.26 0.00 37.47 5.34
3483 4433 2.943978 CGTCAAAGAGGCCCTCCGT 61.944 63.158 7.26 0.00 37.47 4.69
3484 4434 2.125512 CGTCAAAGAGGCCCTCCG 60.126 66.667 7.26 0.00 37.47 4.63
3485 4435 1.376037 CACGTCAAAGAGGCCCTCC 60.376 63.158 7.26 0.00 0.00 4.30
3486 4436 0.670854 GTCACGTCAAAGAGGCCCTC 60.671 60.000 1.26 1.26 0.00 4.30
3487 4437 1.371558 GTCACGTCAAAGAGGCCCT 59.628 57.895 0.00 0.00 0.00 5.19
3488 4438 0.321653 ATGTCACGTCAAAGAGGCCC 60.322 55.000 0.00 0.00 0.00 5.80
3503 5046 2.166829 TGTGTGGGCAATACCAATGTC 58.833 47.619 0.00 0.00 43.34 3.06
3512 5055 2.421248 CCAAAAGGTTTGTGTGGGCAAT 60.421 45.455 0.47 0.00 0.00 3.56
3521 5064 4.159693 GGAAGAACTGTCCAAAAGGTTTGT 59.840 41.667 0.47 0.00 35.05 2.83
3581 5124 4.665451 TGGAGCATCAAGAAGATTTCCAA 58.335 39.130 0.00 0.00 41.48 3.53
3598 5141 0.746659 AACTTGTTGGCAGTTGGAGC 59.253 50.000 0.00 0.00 0.00 4.70
3605 5148 3.438360 GACACAGAAAACTTGTTGGCAG 58.562 45.455 0.00 0.00 0.00 4.85
3635 5178 1.895798 CAGTGTACCTGAGAGAGCCAA 59.104 52.381 5.67 0.00 44.49 4.52
3645 5188 4.894784 AGGTGTTTGTATCAGTGTACCTG 58.105 43.478 0.00 5.31 42.97 4.00
3656 5199 5.163663 CGCATTATGGTGAAGGTGTTTGTAT 60.164 40.000 0.00 0.00 0.00 2.29
3663 5206 1.202177 GCACGCATTATGGTGAAGGTG 60.202 52.381 14.76 0.00 36.25 4.00


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

AutoCloner maintained by Alex Coulton.