Multiple sequence alignment - TraesCS2B01G250200

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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 TraesCS2B01G250200 chr2B 100.000 3005 0 0 1 3005 259687321 259690325 0.000000e+00 5550.0
1 TraesCS2B01G250200 chr2B 74.027 1490 289 76 194 1632 11907835 11909277 4.440000e-143 518.0
2 TraesCS2B01G250200 chr7D 88.441 3028 280 39 1 3003 86071722 86068740 0.000000e+00 3589.0
3 TraesCS2B01G250200 chr7A 87.192 2194 226 25 833 3005 675496841 675499000 0.000000e+00 2444.0
4 TraesCS2B01G250200 chr7A 84.497 2019 283 25 1 2007 102056733 102058733 0.000000e+00 1967.0
5 TraesCS2B01G250200 chr7A 90.732 820 73 2 1 817 675495716 675496535 0.000000e+00 1090.0
6 TraesCS2B01G250200 chr7A 83.039 737 98 12 2296 3005 102059037 102059773 0.000000e+00 643.0
7 TraesCS2B01G250200 chr7A 86.667 60 8 0 232 291 522256118 522256177 1.930000e-07 67.6
8 TraesCS2B01G250200 chr5B 89.870 1155 91 4 1 1155 126445037 126446165 0.000000e+00 1461.0
9 TraesCS2B01G250200 chr5B 91.937 831 61 5 1182 2010 126446495 126447321 0.000000e+00 1158.0
10 TraesCS2B01G250200 chr3B 75.138 1086 223 42 578 1632 232566750 232567819 1.630000e-127 466.0
11 TraesCS2B01G250200 chr3B 76.777 211 47 2 1403 1612 648183354 648183145 1.890000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G250200 chr2B 259687321 259690325 3004 False 5550.0 5550 100.0000 1 3005 1 chr2B.!!$F2 3004
1 TraesCS2B01G250200 chr2B 11907835 11909277 1442 False 518.0 518 74.0270 194 1632 1 chr2B.!!$F1 1438
2 TraesCS2B01G250200 chr7D 86068740 86071722 2982 True 3589.0 3589 88.4410 1 3003 1 chr7D.!!$R1 3002
3 TraesCS2B01G250200 chr7A 675495716 675499000 3284 False 1767.0 2444 88.9620 1 3005 2 chr7A.!!$F3 3004
4 TraesCS2B01G250200 chr7A 102056733 102059773 3040 False 1305.0 1967 83.7680 1 3005 2 chr7A.!!$F2 3004
5 TraesCS2B01G250200 chr5B 126445037 126447321 2284 False 1309.5 1461 90.9035 1 2010 2 chr5B.!!$F1 2009
6 TraesCS2B01G250200 chr3B 232566750 232567819 1069 False 466.0 466 75.1380 578 1632 1 chr3B.!!$F1 1054

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
124 125 0.250234 ATGGCGTGCTTAGCAGAGAA 59.750 50.0 7.34 0.0 40.08 2.87 F
448 469 0.253044 AAGCATACAGTCGGGCACAT 59.747 50.0 0.00 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2618 1.152860 TTTCACCGCTTCAAGGGCA 60.153 52.632 0.00 0.0 0.0 5.36 R
2391 3106 0.179015 TTGTGAAGGGGTTTGCGCTA 60.179 50.000 9.73 0.0 0.0 4.26 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
61 62 5.221106 GCCTAGCAAACATATCAGAAATGCA 60.221 40.000 0.00 0.00 34.89 3.96
124 125 0.250234 ATGGCGTGCTTAGCAGAGAA 59.750 50.000 7.34 0.00 40.08 2.87
141 142 5.277974 GCAGAGAATTGCACTTGTTGTAAGA 60.278 40.000 0.00 0.00 43.53 2.10
169 170 4.190772 GGGAACAAAACATGCATATTGGG 58.809 43.478 17.99 5.87 0.00 4.12
309 313 7.287061 TGGAGGTAAACGATCCATCATTTTAT 58.713 34.615 0.00 0.00 38.19 1.40
313 317 8.405531 AGGTAAACGATCCATCATTTTATGTTG 58.594 33.333 0.00 0.00 0.00 3.33
317 321 7.572523 ACGATCCATCATTTTATGTTGTGAT 57.427 32.000 0.00 0.00 0.00 3.06
374 395 1.780503 ACCCATTATCCCTTTGCAGC 58.219 50.000 0.00 0.00 0.00 5.25
375 396 1.006998 ACCCATTATCCCTTTGCAGCA 59.993 47.619 0.00 0.00 0.00 4.41
395 416 3.441572 GCATGCCTGTCTGTCAATAGTTT 59.558 43.478 6.36 0.00 0.00 2.66
405 426 6.016527 TGTCTGTCAATAGTTTCGTGTCTAGT 60.017 38.462 0.00 0.00 0.00 2.57
448 469 0.253044 AAGCATACAGTCGGGCACAT 59.747 50.000 0.00 0.00 0.00 3.21
454 475 0.606401 ACAGTCGGGCACATCAAAGG 60.606 55.000 0.00 0.00 0.00 3.11
469 490 2.685388 TCAAAGGAAACATGTTCACGCA 59.315 40.909 12.39 0.00 0.00 5.24
525 546 2.730550 GGCAAAACCCACTCAATCAG 57.269 50.000 0.00 0.00 0.00 2.90
572 593 3.801594 GTCAAGGAAATTGCGAGCAAAAA 59.198 39.130 14.76 0.00 39.55 1.94
594 615 7.408756 AAATGCTGCTTTTTATGATGACCTA 57.591 32.000 7.60 0.00 0.00 3.08
639 660 0.757188 CTGAGATACGTCCAGCCCCT 60.757 60.000 0.00 0.00 0.00 4.79
734 756 3.739922 TCCATGGGTCGCTGGATT 58.260 55.556 13.02 0.00 36.63 3.01
739 761 1.414181 CATGGGTCGCTGGATTAGTCT 59.586 52.381 0.00 0.00 0.00 3.24
740 762 1.568504 TGGGTCGCTGGATTAGTCTT 58.431 50.000 0.00 0.00 0.00 3.01
846 1158 4.265073 ACATTCCCTGTGCAGTAATCTTC 58.735 43.478 0.00 0.00 36.48 2.87
850 1162 5.957771 TCCCTGTGCAGTAATCTTCTTAT 57.042 39.130 0.00 0.00 0.00 1.73
851 1163 5.674525 TCCCTGTGCAGTAATCTTCTTATG 58.325 41.667 0.00 0.00 0.00 1.90
863 1175 8.216423 AGTAATCTTCTTATGGAATGCTCACAT 58.784 33.333 0.00 0.00 38.49 3.21
880 1192 5.288712 GCTCACATGCATTTTTCATCTTCTG 59.711 40.000 0.00 0.00 0.00 3.02
881 1193 5.716094 TCACATGCATTTTTCATCTTCTGG 58.284 37.500 0.00 0.00 0.00 3.86
886 1198 8.316214 ACATGCATTTTTCATCTTCTGGTTTAT 58.684 29.630 0.00 0.00 0.00 1.40
910 1222 1.818060 CCGCATCTTCCCAATCAAACA 59.182 47.619 0.00 0.00 0.00 2.83
919 1231 1.001181 CCCAATCAAACAGTTGCAGGG 59.999 52.381 0.00 0.00 35.14 4.45
964 1276 6.183360 GCCAAGACTCATAACATTAGAGGGTA 60.183 42.308 0.00 0.00 33.76 3.69
979 1291 3.054361 AGAGGGTATTGAAATCCAGCGTT 60.054 43.478 0.00 0.00 0.00 4.84
1065 1377 7.201723 GGCCAAGTTGATTTGTTTTTCTCAAAT 60.202 33.333 3.87 3.99 44.67 2.32
1128 1440 2.418368 TTGCTGTGAGTGTTTCCAGT 57.582 45.000 0.00 0.00 0.00 4.00
1136 1448 1.422402 GAGTGTTTCCAGTAACCCCCA 59.578 52.381 0.00 0.00 0.00 4.96
1188 1515 3.190349 CCCCCTCCCAAACCACAT 58.810 61.111 0.00 0.00 0.00 3.21
1218 1846 1.298041 AACTGTTTTGGCGAACGCG 60.298 52.632 3.53 3.53 43.06 6.01
1229 1857 1.813753 CGAACGCGGACCCAATGAT 60.814 57.895 12.47 0.00 0.00 2.45
1247 1875 5.551305 ATGATCGTACAATCAATCAGGGA 57.449 39.130 0.00 0.00 39.04 4.20
1290 1918 0.896940 CCTGCAACCCAGCTTCATGT 60.897 55.000 0.00 0.00 40.36 3.21
1346 1997 4.481368 AACTTTACGATGCCCATCACTA 57.519 40.909 8.79 0.00 37.69 2.74
1363 2015 7.563188 CCCATCACTAAGAGCCTATCTATATGT 59.437 40.741 0.00 0.00 37.23 2.29
1401 2053 3.243771 CGATACTACCTGATGGTTGGACC 60.244 52.174 0.00 0.00 46.05 4.46
1527 2179 4.367023 AAGCTCCACGCCGCGTTA 62.367 61.111 17.45 6.61 38.32 3.18
1544 2196 2.868583 CGTTATTCACATGCCTCCAGAG 59.131 50.000 0.00 0.00 0.00 3.35
1573 2225 2.753452 AGCTCTTGGCATTGTGAATCAG 59.247 45.455 0.00 0.00 44.79 2.90
1605 2257 3.541632 ACGCACTTTCCCGATCATAATT 58.458 40.909 0.00 0.00 0.00 1.40
1637 2289 1.277842 TGAGAAGTATGCTTTCGGCCA 59.722 47.619 2.24 0.00 40.92 5.36
1643 2295 1.436195 TATGCTTTCGGCCATGTCGC 61.436 55.000 2.24 0.00 40.92 5.19
1652 2304 1.750399 GCCATGTCGCCCACTTGAT 60.750 57.895 0.00 0.00 32.87 2.57
1694 2346 7.220683 ACATAATCATCGCATTGTTTTAACTGC 59.779 33.333 0.00 0.00 0.00 4.40
1695 2347 3.832276 TCATCGCATTGTTTTAACTGCC 58.168 40.909 2.48 0.00 29.26 4.85
1801 2453 5.228945 ACAAGCTACAGACACCACTAAAT 57.771 39.130 0.00 0.00 0.00 1.40
1905 2558 0.532640 ACACGCTTGCATCACACAGA 60.533 50.000 0.00 0.00 0.00 3.41
1965 2618 1.608590 CAAACTCCAGTGGCAAACGAT 59.391 47.619 3.51 0.00 0.00 3.73
2015 2685 5.105716 TCACTGCTCTTTAGAATAGCGTTCT 60.106 40.000 11.33 11.33 39.14 3.01
2016 2686 5.578727 CACTGCTCTTTAGAATAGCGTTCTT 59.421 40.000 11.74 0.00 39.14 2.52
2017 2687 5.578727 ACTGCTCTTTAGAATAGCGTTCTTG 59.421 40.000 11.74 4.96 39.14 3.02
2018 2688 5.479306 TGCTCTTTAGAATAGCGTTCTTGT 58.521 37.500 11.74 0.00 39.14 3.16
2019 2689 5.577164 TGCTCTTTAGAATAGCGTTCTTGTC 59.423 40.000 11.74 0.18 39.14 3.18
2020 2690 5.808030 GCTCTTTAGAATAGCGTTCTTGTCT 59.192 40.000 11.74 0.00 0.00 3.41
2021 2691 6.237701 GCTCTTTAGAATAGCGTTCTTGTCTG 60.238 42.308 11.74 3.79 0.00 3.51
2022 2692 6.688578 TCTTTAGAATAGCGTTCTTGTCTGT 58.311 36.000 11.74 0.00 0.00 3.41
2023 2693 6.586463 TCTTTAGAATAGCGTTCTTGTCTGTG 59.414 38.462 11.74 0.00 0.00 3.66
2024 2694 4.258702 AGAATAGCGTTCTTGTCTGTGT 57.741 40.909 2.07 0.00 0.00 3.72
2025 2695 4.238514 AGAATAGCGTTCTTGTCTGTGTC 58.761 43.478 2.07 0.00 0.00 3.67
2026 2696 3.660501 ATAGCGTTCTTGTCTGTGTCA 57.339 42.857 0.00 0.00 0.00 3.58
2027 2697 2.533266 AGCGTTCTTGTCTGTGTCAT 57.467 45.000 0.00 0.00 0.00 3.06
2028 2698 2.838736 AGCGTTCTTGTCTGTGTCATT 58.161 42.857 0.00 0.00 0.00 2.57
2029 2699 2.802816 AGCGTTCTTGTCTGTGTCATTC 59.197 45.455 0.00 0.00 0.00 2.67
2030 2700 2.802816 GCGTTCTTGTCTGTGTCATTCT 59.197 45.455 0.00 0.00 0.00 2.40
2044 2714 5.697633 TGTGTCATTCTTAACTACCGGAAAC 59.302 40.000 9.46 0.00 0.00 2.78
2045 2715 5.121298 GTGTCATTCTTAACTACCGGAAACC 59.879 44.000 9.46 0.00 0.00 3.27
2050 2720 5.813513 TCTTAACTACCGGAAACCTCTTT 57.186 39.130 9.46 0.00 0.00 2.52
2065 2735 3.834231 ACCTCTTTCCCAAATGGATTGTG 59.166 43.478 0.00 0.00 44.66 3.33
2069 2739 6.339587 TCTTTCCCAAATGGATTGTGTTAC 57.660 37.500 0.00 0.00 44.66 2.50
2086 2756 9.998106 ATTGTGTTACAACTAGAGATTACAACT 57.002 29.630 0.00 0.00 41.40 3.16
2111 2783 3.694746 GCCACCTAGCCCAAAACC 58.305 61.111 0.00 0.00 0.00 3.27
2115 2787 0.532115 CACCTAGCCCAAAACCATGC 59.468 55.000 0.00 0.00 0.00 4.06
2121 2793 1.974543 CCCAAAACCATGCCTGACC 59.025 57.895 0.00 0.00 0.00 4.02
2127 2799 2.203252 CCATGCCTGACCATCGGG 60.203 66.667 0.00 0.00 45.82 5.14
2142 2814 5.540400 CCATCGGGTCCTACTTATTTGTA 57.460 43.478 0.00 0.00 0.00 2.41
2168 2841 7.433680 TCGAGTGCAAATTTCTAGCATATCTA 58.566 34.615 5.13 0.00 40.78 1.98
2194 2867 6.882610 AGAAACTCAAGTTCATATGCAACA 57.117 33.333 15.69 0.00 37.25 3.33
2212 2895 6.810911 TGCAACAAGTTTACCACATACATTT 58.189 32.000 0.00 0.00 0.00 2.32
2215 2902 6.339587 ACAAGTTTACCACATACATTTGGG 57.660 37.500 0.00 0.00 37.18 4.12
2216 2903 5.167845 CAAGTTTACCACATACATTTGGGC 58.832 41.667 0.00 0.00 37.18 5.36
2237 2925 3.678548 GCGTACAAGTTCAACTTCTAGGG 59.321 47.826 0.00 0.00 36.03 3.53
2239 2927 2.767505 ACAAGTTCAACTTCTAGGGCG 58.232 47.619 0.00 0.00 36.03 6.13
2272 2960 4.580995 GCAACTACTCTACTCCAGCTGATA 59.419 45.833 17.39 1.38 0.00 2.15
2274 2962 4.394729 ACTACTCTACTCCAGCTGATAGC 58.605 47.826 17.39 0.00 42.84 2.97
2294 2982 9.725019 TGATAGCTTGATAGGGTTACAATTATG 57.275 33.333 0.00 0.00 0.00 1.90
2314 3002 7.834068 TTATGACATCTAGAACACAAGCTTC 57.166 36.000 0.00 0.00 0.00 3.86
2353 3068 3.618690 AAGATCACTGCTCCTAACCAC 57.381 47.619 0.00 0.00 0.00 4.16
2368 3083 5.003804 CCTAACCACAGAAGCACTTGTAAT 58.996 41.667 0.00 0.00 0.00 1.89
2369 3084 4.836125 AACCACAGAAGCACTTGTAATG 57.164 40.909 0.00 0.00 0.00 1.90
2382 3097 2.512692 TGTAATGGAATGCTGCCAGT 57.487 45.000 0.00 0.00 39.11 4.00
2410 3125 0.179015 TAGCGCAAACCCCTTCACAA 60.179 50.000 11.47 0.00 0.00 3.33
2435 3150 4.262981 GCCAGATCCTTGATTCAGAGCTAT 60.263 45.833 0.00 0.00 0.00 2.97
2450 3165 9.989296 ATTCAGAGCTATATTATCTGTAGGAGT 57.011 33.333 9.86 0.00 41.01 3.85
2470 3185 2.031495 AGGAGGTTGTTCTAGCTGGT 57.969 50.000 0.00 0.00 0.00 4.00
2472 3187 1.339151 GGAGGTTGTTCTAGCTGGTGG 60.339 57.143 0.00 0.00 0.00 4.61
2477 3192 0.835971 TGTTCTAGCTGGTGGGAGCA 60.836 55.000 0.00 0.00 41.83 4.26
2500 3215 1.529309 TGTGCCACCACACTTGCTA 59.471 52.632 0.00 0.00 46.51 3.49
2528 3243 4.767928 ACGTAACTCTGAGTTGATCCTCTT 59.232 41.667 28.46 5.79 39.11 2.85
2626 3341 2.778299 TGTACATTTCACAGCCTCCAC 58.222 47.619 0.00 0.00 0.00 4.02
2633 3348 0.469892 TCACAGCCTCCACTCTGACA 60.470 55.000 0.00 0.00 34.57 3.58
2664 3379 3.119029 CCACAAAATAATGTCAGCAGGGG 60.119 47.826 0.00 0.00 0.00 4.79
2665 3380 2.497273 ACAAAATAATGTCAGCAGGGGC 59.503 45.455 0.00 0.00 41.61 5.80
2703 3433 4.446719 CCAACGAGTTTTAGTAGGACACAC 59.553 45.833 0.00 0.00 0.00 3.82
2780 3510 4.738998 CCACATGGCGGCCTTGGA 62.739 66.667 30.96 9.40 33.63 3.53
2823 3553 0.388134 TCGCTGGTTCGTAGTCAAGC 60.388 55.000 0.00 0.00 0.00 4.01
2844 3574 1.497161 GACCCACCCTGTATAGCACT 58.503 55.000 0.00 0.00 0.00 4.40
2907 3637 2.305343 AGCAGACCTTGAGCTTGAAGAT 59.695 45.455 0.00 0.00 34.37 2.40
2921 3651 6.223852 AGCTTGAAGATAAAGACGAAGACAA 58.776 36.000 0.00 0.00 0.00 3.18
2939 3669 4.081697 AGACAACTGTTTGGGAAGTTTTGG 60.082 41.667 0.00 0.00 37.00 3.28
2945 3675 1.859302 TTGGGAAGTTTTGGTGCTGT 58.141 45.000 0.00 0.00 0.00 4.40
2972 3702 2.358737 GCCCAACGCAGTGTAGCT 60.359 61.111 0.00 0.00 45.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 5.452255 ACATATTGGACTGGAATGCTTGAT 58.548 37.500 0.00 0.00 0.00 2.57
110 111 3.128465 GTGCAATTCTCTGCTAAGCAC 57.872 47.619 0.00 0.00 43.07 4.40
124 125 5.507817 CCATGTGTCTTACAACAAGTGCAAT 60.508 40.000 0.00 0.00 43.77 3.56
141 142 2.433604 TGCATGTTTTGTTCCCATGTGT 59.566 40.909 0.00 0.00 38.53 3.72
157 158 6.040729 TGTTCCTTCATTACCCAATATGCATG 59.959 38.462 10.16 0.00 0.00 4.06
169 170 9.559958 CATCACAAGTATTTGTTCCTTCATTAC 57.440 33.333 0.08 0.00 45.01 1.89
253 256 2.722201 GCTGGTAGTCGGGGTCCAG 61.722 68.421 11.29 11.29 46.96 3.86
313 317 9.674208 CATCGTTTGTATGCATTTAAAAATCAC 57.326 29.630 3.54 0.00 0.00 3.06
317 321 9.081997 GGATCATCGTTTGTATGCATTTAAAAA 57.918 29.630 3.54 0.00 0.00 1.94
374 395 4.201753 CGAAACTATTGACAGACAGGCATG 60.202 45.833 0.00 0.00 33.13 4.06
375 396 3.935203 CGAAACTATTGACAGACAGGCAT 59.065 43.478 0.00 0.00 33.13 4.40
395 416 3.118884 GCCATCCCTTTTACTAGACACGA 60.119 47.826 0.00 0.00 0.00 4.35
405 426 6.430864 TGATGATAAACTGCCATCCCTTTTA 58.569 36.000 0.00 0.00 36.70 1.52
448 469 2.685388 TGCGTGAACATGTTTCCTTTGA 59.315 40.909 13.36 0.00 0.00 2.69
454 475 3.002246 TCTGTCTTGCGTGAACATGTTTC 59.998 43.478 13.36 8.42 0.00 2.78
469 490 2.344203 CGAGGGCGGTCTCTGTCTT 61.344 63.158 0.00 0.00 0.00 3.01
525 546 2.309755 TGCATCCTGGGATATGGGAATC 59.690 50.000 1.42 0.00 32.93 2.52
572 593 6.377996 TGTTAGGTCATCATAAAAAGCAGCAT 59.622 34.615 0.00 0.00 0.00 3.79
594 615 7.499232 GCATAGTAAGTAACCAAGATGGATGTT 59.501 37.037 2.85 0.00 40.96 2.71
639 660 5.105392 GGTTGATCCAAACAATATGAAGCCA 60.105 40.000 0.00 0.00 35.97 4.75
720 742 1.794714 AGACTAATCCAGCGACCCAT 58.205 50.000 0.00 0.00 0.00 4.00
734 756 4.950361 TGGGATTGGTGGTACTAAGACTA 58.050 43.478 0.00 0.00 0.00 2.59
739 761 3.653836 ACAGTTGGGATTGGTGGTACTAA 59.346 43.478 0.00 0.00 0.00 2.24
740 762 3.253220 ACAGTTGGGATTGGTGGTACTA 58.747 45.455 0.00 0.00 0.00 1.82
881 1193 5.570234 TTGGGAAGATGCGGTTAATAAAC 57.430 39.130 0.00 0.00 34.66 2.01
886 1198 3.358111 TGATTGGGAAGATGCGGTTAA 57.642 42.857 0.00 0.00 0.00 2.01
891 1203 2.489329 ACTGTTTGATTGGGAAGATGCG 59.511 45.455 0.00 0.00 0.00 4.73
910 1222 0.620556 ACGATCCATTCCCTGCAACT 59.379 50.000 0.00 0.00 0.00 3.16
979 1291 2.070028 TGCGTCGTTAAATGCAAGCTA 58.930 42.857 0.00 0.00 38.20 3.32
996 1308 0.949397 CCATCTCATGGGTCATTGCG 59.051 55.000 0.00 0.00 46.86 4.85
1065 1377 4.867086 TCCATATCTGTCCAGTACTGTCA 58.133 43.478 21.18 17.26 0.00 3.58
1128 1440 3.603385 AGGGGTGAATTAAATGGGGGTTA 59.397 43.478 0.00 0.00 0.00 2.85
1218 1846 3.804036 TGATTGTACGATCATTGGGTCC 58.196 45.455 19.99 0.00 31.35 4.46
1229 1857 4.588951 AGCTATCCCTGATTGATTGTACGA 59.411 41.667 0.00 0.00 0.00 3.43
1290 1918 7.087409 TCTAATAACACGACTTACCATTCGA 57.913 36.000 0.00 0.00 38.63 3.71
1327 1977 4.693283 TCTTAGTGATGGGCATCGTAAAG 58.307 43.478 0.00 0.00 40.63 1.85
1346 1997 8.391699 TGTACCACTACATATAGATAGGCTCTT 58.608 37.037 0.00 0.00 35.28 2.85
1363 2015 2.353357 ATCGTCGGGATGTACCACTA 57.647 50.000 0.00 0.00 41.20 2.74
1401 2053 5.052436 CCGCAACATATCAAAAGCATAAACG 60.052 40.000 0.00 0.00 0.00 3.60
1453 2105 2.240160 TGCTATACCCAAACGGTCCAAT 59.760 45.455 0.00 0.00 43.58 3.16
1458 2110 1.676615 CGGTTGCTATACCCAAACGGT 60.677 52.381 9.76 0.00 46.44 4.83
1512 2164 3.151673 GAATAACGCGGCGTGGAGC 62.152 63.158 30.10 15.11 39.99 4.70
1527 2179 3.009916 AGAAACTCTGGAGGCATGTGAAT 59.990 43.478 2.58 0.00 0.00 2.57
1544 2196 3.005155 ACAATGCCAAGAGCTGAAGAAAC 59.995 43.478 0.00 0.00 44.23 2.78
1605 2257 5.128827 AGCATACTTCTCAATCGTTTCCCTA 59.871 40.000 0.00 0.00 0.00 3.53
1613 2265 3.302740 GCCGAAAGCATACTTCTCAATCG 60.303 47.826 0.00 0.00 42.97 3.34
1637 2289 1.463674 GGAAATCAAGTGGGCGACAT 58.536 50.000 1.61 0.00 0.00 3.06
1643 2295 6.373216 TGAACTAATTACGGAAATCAAGTGGG 59.627 38.462 0.00 0.00 0.00 4.61
1675 2327 2.923020 GGGCAGTTAAAACAATGCGATG 59.077 45.455 0.00 0.00 39.58 3.84
1724 2376 2.164865 AACCCAGTCTGCTCTCTGCG 62.165 60.000 0.00 0.00 46.63 5.18
1809 2461 5.902760 TGGGGGCTATGATGCTATAAAAAT 58.097 37.500 0.00 0.00 0.00 1.82
1905 2558 7.971201 TCATTAGTTCATAGATCATCAGGCTT 58.029 34.615 0.00 0.00 0.00 4.35
1965 2618 1.152860 TTTCACCGCTTCAAGGGCA 60.153 52.632 0.00 0.00 0.00 5.36
2015 2685 5.924254 CGGTAGTTAAGAATGACACAGACAA 59.076 40.000 0.00 0.00 0.00 3.18
2016 2686 5.466819 CGGTAGTTAAGAATGACACAGACA 58.533 41.667 0.00 0.00 0.00 3.41
2017 2687 4.863131 CCGGTAGTTAAGAATGACACAGAC 59.137 45.833 0.00 0.00 0.00 3.51
2018 2688 4.768448 TCCGGTAGTTAAGAATGACACAGA 59.232 41.667 0.00 0.00 0.00 3.41
2019 2689 5.068234 TCCGGTAGTTAAGAATGACACAG 57.932 43.478 0.00 0.00 0.00 3.66
2020 2690 5.471556 TTCCGGTAGTTAAGAATGACACA 57.528 39.130 0.00 0.00 0.00 3.72
2021 2691 5.121298 GGTTTCCGGTAGTTAAGAATGACAC 59.879 44.000 0.00 0.00 0.00 3.67
2022 2692 5.012354 AGGTTTCCGGTAGTTAAGAATGACA 59.988 40.000 0.00 0.00 0.00 3.58
2023 2693 5.485620 AGGTTTCCGGTAGTTAAGAATGAC 58.514 41.667 0.00 0.00 0.00 3.06
2024 2694 5.482878 AGAGGTTTCCGGTAGTTAAGAATGA 59.517 40.000 0.00 0.00 0.00 2.57
2025 2695 5.731591 AGAGGTTTCCGGTAGTTAAGAATG 58.268 41.667 0.00 0.00 0.00 2.67
2026 2696 6.370186 AAGAGGTTTCCGGTAGTTAAGAAT 57.630 37.500 0.00 0.00 0.00 2.40
2027 2697 5.813513 AAGAGGTTTCCGGTAGTTAAGAA 57.186 39.130 0.00 0.00 0.00 2.52
2028 2698 5.787380 GAAAGAGGTTTCCGGTAGTTAAGA 58.213 41.667 0.00 0.00 36.77 2.10
2056 2726 9.601217 GTAATCTCTAGTTGTAACACAATCCAT 57.399 33.333 0.00 0.00 40.59 3.41
2069 2739 9.262358 GCCCTAAATAGTTGTAATCTCTAGTTG 57.738 37.037 0.00 0.00 0.00 3.16
2101 2773 1.155859 TCAGGCATGGTTTTGGGCT 59.844 52.632 0.00 0.00 38.02 5.19
2111 2783 2.591753 ACCCGATGGTCAGGCATG 59.408 61.111 0.00 0.00 43.06 4.06
2121 2793 5.862323 CGATACAAATAAGTAGGACCCGATG 59.138 44.000 0.00 0.00 0.00 3.84
2127 2799 6.270815 TGCACTCGATACAAATAAGTAGGAC 58.729 40.000 0.00 0.00 0.00 3.85
2142 2814 6.933521 AGATATGCTAGAAATTTGCACTCGAT 59.066 34.615 4.01 0.00 40.27 3.59
2168 2841 7.661437 TGTTGCATATGAACTTGAGTTTCTACT 59.339 33.333 6.97 0.00 38.56 2.57
2177 2850 7.013750 TGGTAAACTTGTTGCATATGAACTTGA 59.986 33.333 6.97 0.00 0.00 3.02
2178 2851 7.114811 GTGGTAAACTTGTTGCATATGAACTTG 59.885 37.037 6.97 7.72 0.00 3.16
2194 2867 4.082463 CGCCCAAATGTATGTGGTAAACTT 60.082 41.667 0.62 0.00 32.60 2.66
2212 2895 2.158871 AGAAGTTGAACTTGTACGCCCA 60.159 45.455 16.25 0.00 38.80 5.36
2215 2902 3.678548 CCCTAGAAGTTGAACTTGTACGC 59.321 47.826 16.25 0.26 38.80 4.42
2216 2903 3.678548 GCCCTAGAAGTTGAACTTGTACG 59.321 47.826 16.25 9.40 38.80 3.67
2237 2925 1.128513 GTAGTTGCCTTTGTTTGCGC 58.871 50.000 0.00 0.00 0.00 6.09
2239 2927 3.990318 AGAGTAGTTGCCTTTGTTTGC 57.010 42.857 0.00 0.00 0.00 3.68
2272 2960 7.573710 TGTCATAATTGTAACCCTATCAAGCT 58.426 34.615 0.00 0.00 0.00 3.74
2274 2962 9.784531 AGATGTCATAATTGTAACCCTATCAAG 57.215 33.333 0.00 0.00 0.00 3.02
2294 2982 5.719173 AGAGAAGCTTGTGTTCTAGATGTC 58.281 41.667 2.10 0.00 34.30 3.06
2314 3002 7.536622 GTGATCTTTTAACTGCATCAACAAGAG 59.463 37.037 0.00 0.00 0.00 2.85
2353 3068 4.157289 AGCATTCCATTACAAGTGCTTCTG 59.843 41.667 0.00 0.00 39.68 3.02
2368 3083 1.684629 TGCTACTGGCAGCATTCCA 59.315 52.632 15.89 2.08 46.41 3.53
2369 3084 4.643795 TGCTACTGGCAGCATTCC 57.356 55.556 15.89 0.00 46.41 3.01
2391 3106 0.179015 TTGTGAAGGGGTTTGCGCTA 60.179 50.000 9.73 0.00 0.00 4.26
2394 3109 0.597377 GCTTTGTGAAGGGGTTTGCG 60.597 55.000 0.00 0.00 33.34 4.85
2410 3125 3.684981 GCTCTGAATCAAGGATCTGGCTT 60.685 47.826 0.00 0.00 0.00 4.35
2435 3150 7.823635 ACAACCTCCTACTCCTACAGATAATA 58.176 38.462 0.00 0.00 0.00 0.98
2450 3165 2.832129 CACCAGCTAGAACAACCTCCTA 59.168 50.000 0.00 0.00 0.00 2.94
2458 3173 0.835971 TGCTCCCACCAGCTAGAACA 60.836 55.000 0.00 0.00 40.39 3.18
2470 3185 2.203337 GGCACAACACTGCTCCCA 60.203 61.111 0.00 0.00 37.33 4.37
2472 3187 3.034030 GTGGCACAACACTGCTCC 58.966 61.111 13.86 0.00 44.16 4.70
2500 3215 2.361119 TCAACTCAGAGTTACGTGCTGT 59.639 45.455 15.73 0.00 36.03 4.40
2528 3243 0.319211 CGACAGGGTGCGTCACTTAA 60.319 55.000 9.31 0.00 34.40 1.85
2595 3310 6.238566 GCTGTGAAATGTACATGTAGCATGAT 60.239 38.462 9.63 6.33 0.00 2.45
2602 3317 4.019771 TGGAGGCTGTGAAATGTACATGTA 60.020 41.667 9.63 0.08 0.00 2.29
2606 3321 2.371841 AGTGGAGGCTGTGAAATGTACA 59.628 45.455 0.00 0.00 0.00 2.90
2626 3341 3.407424 TGTGGTCAAATCCTGTCAGAG 57.593 47.619 0.00 0.00 0.00 3.35
2633 3348 7.537596 TGACATTATTTTGTGGTCAAATCCT 57.462 32.000 0.00 0.00 42.14 3.24
2664 3379 2.253603 GTTGGCTGATCATTGTTTCGC 58.746 47.619 0.00 0.00 0.00 4.70
2665 3380 2.159430 TCGTTGGCTGATCATTGTTTCG 59.841 45.455 0.00 0.00 0.00 3.46
2669 3384 2.479566 ACTCGTTGGCTGATCATTGT 57.520 45.000 0.00 0.00 0.00 2.71
2673 3388 4.002906 ACTAAAACTCGTTGGCTGATCA 57.997 40.909 0.00 0.00 0.00 2.92
2802 3532 0.669619 TTGACTACGAACCAGCGACA 59.330 50.000 0.00 0.00 34.83 4.35
2823 3553 1.046472 TGCTATACAGGGTGGGTCCG 61.046 60.000 0.00 0.00 37.00 4.79
2901 3631 6.513180 ACAGTTGTCTTCGTCTTTATCTTCA 58.487 36.000 0.00 0.00 0.00 3.02
2907 3637 4.573201 CCCAAACAGTTGTCTTCGTCTTTA 59.427 41.667 0.00 0.00 32.40 1.85
2921 3651 2.093711 GCACCAAAACTTCCCAAACAGT 60.094 45.455 0.00 0.00 0.00 3.55
2939 3669 1.518903 GGGCTTCACTCCAACAGCAC 61.519 60.000 0.00 0.00 33.64 4.40
2945 3675 1.896660 GCGTTGGGCTTCACTCCAA 60.897 57.895 0.00 0.00 40.36 3.53


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

AutoCloner maintained by Alex Coulton.