Multiple sequence alignment - TraesCS2A01G037200

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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 TraesCS2A01G037200 chr2A 100.000 3375 0 0 1 3375 15873900 15877274 0.000000e+00 6233.0
1 TraesCS2A01G037200 chr2D 87.705 2253 153 52 422 2628 13682039 13679865 0.000000e+00 2512.0
2 TraesCS2A01G037200 chr2D 91.392 546 35 7 1 543 13682792 13682256 0.000000e+00 737.0
3 TraesCS2A01G037200 chr2B 88.947 1538 112 28 1872 3375 24921837 24920324 0.000000e+00 1845.0
4 TraesCS2A01G037200 chr2B 89.401 868 49 26 990 1828 24923040 24922187 0.000000e+00 1053.0
5 TraesCS2A01G037200 chr2B 82.821 553 55 12 1 546 24949535 24949016 3.070000e-125 459.0
6 TraesCS2A01G037200 chr2B 78.947 266 46 6 1 259 24929617 24929355 4.480000e-39 172.0
7 TraesCS2A01G037200 chr7A 86.673 1103 103 24 2305 3375 353260040 353261130 0.000000e+00 1182.0
8 TraesCS2A01G037200 chr6A 86.310 1103 107 26 2305 3375 214878818 214877728 0.000000e+00 1160.0
9 TraesCS2A01G037200 chr6A 89.875 721 48 15 1395 2109 31917800 31918501 0.000000e+00 904.0
10 TraesCS2A01G037200 chr1A 84.859 1103 102 30 2305 3375 449794344 449793275 0.000000e+00 1051.0
11 TraesCS2A01G037200 chr1A 83.731 922 104 25 2305 3194 42804869 42805776 0.000000e+00 830.0
12 TraesCS2A01G037200 chr4B 97.222 36 1 0 1307 1342 22807894 22807859 1.010000e-05 62.1


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 TraesCS2A01G037200 chr2A 15873900 15877274 3374 False 6233.0 6233 100.0000 1 3375 1 chr2A.!!$F1 3374
1 TraesCS2A01G037200 chr2D 13679865 13682792 2927 True 1624.5 2512 89.5485 1 2628 2 chr2D.!!$R1 2627
2 TraesCS2A01G037200 chr2B 24920324 24923040 2716 True 1449.0 1845 89.1740 990 3375 2 chr2B.!!$R3 2385
3 TraesCS2A01G037200 chr2B 24949016 24949535 519 True 459.0 459 82.8210 1 546 1 chr2B.!!$R2 545
4 TraesCS2A01G037200 chr7A 353260040 353261130 1090 False 1182.0 1182 86.6730 2305 3375 1 chr7A.!!$F1 1070
5 TraesCS2A01G037200 chr6A 214877728 214878818 1090 True 1160.0 1160 86.3100 2305 3375 1 chr6A.!!$R1 1070
6 TraesCS2A01G037200 chr6A 31917800 31918501 701 False 904.0 904 89.8750 1395 2109 1 chr6A.!!$F1 714
7 TraesCS2A01G037200 chr1A 449793275 449794344 1069 True 1051.0 1051 84.8590 2305 3375 1 chr1A.!!$R1 1070
8 TraesCS2A01G037200 chr1A 42804869 42805776 907 False 830.0 830 83.7310 2305 3194 1 chr1A.!!$F1 889

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
755 1097 0.180171 ATGCGGATTGAACGATGGGA 59.820 50.0 0.0 0.0 0.0 4.37 F
756 1098 0.742990 TGCGGATTGAACGATGGGAC 60.743 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 3014 0.037447 ACAGCCTCCTCCTGAAAAGC 59.963 55.0 0.0 0.0 34.47 3.51 R
2418 3130 0.247736 ATGTGCTGAAGGGAGTCGAC 59.752 55.0 7.7 7.7 0.00 4.20 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
110 111 4.000988 GAGCTTTGACGGTAAGAATCCAA 58.999 43.478 0.00 0.00 0.00 3.53
121 122 5.570844 CGGTAAGAATCCAAAGGAGGAGAAA 60.571 44.000 0.00 0.00 41.90 2.52
146 147 2.198406 TCAAGGTGACGTTTCAAGTCG 58.802 47.619 0.00 0.00 41.24 4.18
271 272 1.135603 CGTTTGGAGTCGATCGGTACA 60.136 52.381 16.41 7.26 0.00 2.90
274 275 1.830279 TGGAGTCGATCGGTACAAGT 58.170 50.000 16.41 0.00 0.00 3.16
288 289 6.350906 TCGGTACAAGTAATAAATTGAGGGG 58.649 40.000 0.00 0.00 0.00 4.79
330 331 5.005012 GCACATCACATGTTTGTATCATTGC 59.995 40.000 10.13 6.04 42.70 3.56
345 346 4.486125 TCATTGCATGCTACTCAGGTTA 57.514 40.909 20.33 0.00 0.00 2.85
350 351 2.874701 GCATGCTACTCAGGTTATGTGG 59.125 50.000 11.37 0.00 0.00 4.17
356 357 4.562757 GCTACTCAGGTTATGTGGTTGACA 60.563 45.833 0.00 0.00 39.53 3.58
357 358 4.431416 ACTCAGGTTATGTGGTTGACAA 57.569 40.909 0.00 0.00 38.36 3.18
360 361 5.067283 ACTCAGGTTATGTGGTTGACAAAAC 59.933 40.000 0.00 0.00 38.36 2.43
416 419 8.677148 ACCATGTTTCGCTAATACAAAGATAT 57.323 30.769 0.00 0.00 0.00 1.63
457 461 5.920193 TCAAGCTCTCATTTATTTTGGGG 57.080 39.130 0.00 0.00 0.00 4.96
471 475 3.129502 GGGGGAACTTAACGCGCC 61.130 66.667 5.73 0.00 0.00 6.53
502 512 3.764434 TGCCTAAGTTTTGTGTTTGTGGA 59.236 39.130 0.00 0.00 0.00 4.02
503 513 4.220821 TGCCTAAGTTTTGTGTTTGTGGAA 59.779 37.500 0.00 0.00 0.00 3.53
510 670 1.040339 TGTGTTTGTGGAAGTGGGGC 61.040 55.000 0.00 0.00 0.00 5.80
533 693 2.223572 GGGTGTGTGTTGAAAAGAGCAG 60.224 50.000 0.00 0.00 0.00 4.24
593 932 9.546428 AGGTTTAAAATCTCAAAAGTCCAAATG 57.454 29.630 0.00 0.00 0.00 2.32
594 933 9.325198 GGTTTAAAATCTCAAAAGTCCAAATGT 57.675 29.630 0.00 0.00 0.00 2.71
618 957 5.982465 TTTTCTTGCGGGAAAATCAAAAG 57.018 34.783 11.04 0.00 39.37 2.27
619 958 4.664150 TTCTTGCGGGAAAATCAAAAGT 57.336 36.364 0.00 0.00 0.00 2.66
620 959 4.664150 TCTTGCGGGAAAATCAAAAGTT 57.336 36.364 0.00 0.00 0.00 2.66
621 960 4.367450 TCTTGCGGGAAAATCAAAAGTTG 58.633 39.130 0.00 0.00 0.00 3.16
622 961 4.098654 TCTTGCGGGAAAATCAAAAGTTGA 59.901 37.500 0.00 0.00 45.01 3.18
623 962 4.392921 TGCGGGAAAATCAAAAGTTGAA 57.607 36.364 0.00 0.00 43.95 2.69
627 966 6.317391 TGCGGGAAAATCAAAAGTTGAAAAAT 59.683 30.769 0.00 0.00 43.95 1.82
629 968 7.254761 GCGGGAAAATCAAAAGTTGAAAAATCT 60.255 33.333 0.00 0.00 43.95 2.40
631 970 9.720667 GGGAAAATCAAAAGTTGAAAAATCTTG 57.279 29.630 0.00 0.00 43.95 3.02
656 995 9.442047 TGGAAATTTAAAACTTGAAGCTTTGAA 57.558 25.926 0.00 2.73 0.00 2.69
661 1000 7.826260 TTAAAACTTGAAGCTTTGAAGGTTG 57.174 32.000 18.24 2.23 45.82 3.77
663 1002 3.631250 ACTTGAAGCTTTGAAGGTTGGA 58.369 40.909 18.40 1.35 45.82 3.53
665 1004 4.651045 ACTTGAAGCTTTGAAGGTTGGAAT 59.349 37.500 18.40 0.00 45.82 3.01
666 1005 5.129320 ACTTGAAGCTTTGAAGGTTGGAATT 59.871 36.000 18.40 0.00 45.82 2.17
667 1006 5.612725 TGAAGCTTTGAAGGTTGGAATTT 57.387 34.783 12.39 0.00 45.82 1.82
694 1033 3.848272 AAACGTGCAATAGGGTGAATG 57.152 42.857 0.00 0.00 0.00 2.67
699 1038 2.945668 GTGCAATAGGGTGAATGTCCTC 59.054 50.000 0.00 0.00 34.75 3.71
700 1039 2.846206 TGCAATAGGGTGAATGTCCTCT 59.154 45.455 0.00 0.00 34.75 3.69
701 1040 3.209410 GCAATAGGGTGAATGTCCTCTG 58.791 50.000 0.00 0.00 34.75 3.35
702 1041 3.118261 GCAATAGGGTGAATGTCCTCTGA 60.118 47.826 0.00 0.00 34.75 3.27
704 1043 5.688807 CAATAGGGTGAATGTCCTCTGAAT 58.311 41.667 0.00 0.00 34.75 2.57
705 1044 5.983333 ATAGGGTGAATGTCCTCTGAATT 57.017 39.130 0.00 0.00 34.75 2.17
707 1046 4.338879 AGGGTGAATGTCCTCTGAATTTG 58.661 43.478 0.00 0.00 0.00 2.32
708 1047 3.119352 GGGTGAATGTCCTCTGAATTTGC 60.119 47.826 0.00 0.00 0.00 3.68
753 1095 1.670295 TCAATGCGGATTGAACGATGG 59.330 47.619 27.40 1.55 44.11 3.51
754 1096 1.024271 AATGCGGATTGAACGATGGG 58.976 50.000 0.00 0.00 0.00 4.00
755 1097 0.180171 ATGCGGATTGAACGATGGGA 59.820 50.000 0.00 0.00 0.00 4.37
756 1098 0.742990 TGCGGATTGAACGATGGGAC 60.743 55.000 0.00 0.00 0.00 4.46
776 1118 3.641439 CGATGTCAATGTCGTTCTTCC 57.359 47.619 0.00 0.00 33.42 3.46
778 1120 3.618594 CGATGTCAATGTCGTTCTTCCAT 59.381 43.478 0.00 0.00 33.42 3.41
785 1127 2.131972 TGTCGTTCTTCCATGACGTTG 58.868 47.619 0.00 0.00 35.70 4.10
793 1135 2.498644 TCCATGACGTTGGCCAAATA 57.501 45.000 22.47 7.23 36.66 1.40
799 1141 3.950397 TGACGTTGGCCAAATAGAGATT 58.050 40.909 22.47 0.00 0.00 2.40
806 1149 6.402766 CGTTGGCCAAATAGAGATTTCGTTTA 60.403 38.462 22.47 0.00 32.73 2.01
807 1150 7.309920 GTTGGCCAAATAGAGATTTCGTTTAA 58.690 34.615 22.47 0.00 32.73 1.52
815 1158 9.503399 AAATAGAGATTTCGTTTAAGTTCACCT 57.497 29.630 0.00 0.00 28.60 4.00
817 1160 7.803279 AGAGATTTCGTTTAAGTTCACCTTT 57.197 32.000 0.00 0.00 34.46 3.11
878 1221 1.604378 CCCACTGGGCCAAGTCTAG 59.396 63.158 10.87 1.77 35.35 2.43
945 1290 1.214325 CACTCCATCGTACGGTGCA 59.786 57.895 23.08 7.63 0.00 4.57
1169 1520 4.079850 CTCGGCTCAGCTGGCTGT 62.080 66.667 25.67 0.00 43.96 4.40
1179 1530 4.007644 CTGGCTGTCCGGTGCTGA 62.008 66.667 0.00 0.00 33.91 4.26
1379 1734 5.286438 CGAGGTACGGTAATTCATTCATCA 58.714 41.667 0.00 0.00 38.46 3.07
1427 1803 1.188219 ACAGCTGACGGGATGACACT 61.188 55.000 23.35 0.00 0.00 3.55
1429 1805 1.448540 GCTGACGGGATGACACTGG 60.449 63.158 0.00 0.00 0.00 4.00
1430 1806 1.448540 CTGACGGGATGACACTGGC 60.449 63.158 0.00 0.00 0.00 4.85
1431 1807 2.171209 CTGACGGGATGACACTGGCA 62.171 60.000 0.00 0.00 0.00 4.92
1634 2010 2.591715 GCGGTCTGCACCAACTGT 60.592 61.111 0.00 0.00 44.02 3.55
1641 2017 1.135141 TCTGCACCAACTGTTTTGCAC 60.135 47.619 18.12 0.00 40.01 4.57
1656 2035 3.713858 TTGCACACATTTCAACCTGAG 57.286 42.857 0.00 0.00 0.00 3.35
1658 2037 3.023119 TGCACACATTTCAACCTGAGTT 58.977 40.909 0.00 0.00 36.33 3.01
1818 2204 4.378459 CGGTCAGTGAACAAAATCTTAGCC 60.378 45.833 9.27 0.00 0.00 3.93
1823 2209 4.706962 AGTGAACAAAATCTTAGCCCCATC 59.293 41.667 0.00 0.00 0.00 3.51
1829 2531 5.185828 ACAAAATCTTAGCCCCATCAAACTC 59.814 40.000 0.00 0.00 0.00 3.01
1851 2556 3.812053 CGCTGAATAATCCAAGCTAGCTT 59.188 43.478 24.42 24.42 36.60 3.74
1903 2608 1.654954 CTGCTGTCCTTGCTGATGGC 61.655 60.000 0.00 0.00 42.22 4.40
1981 2686 3.367703 CCAACATCCTGCAATCCAAAGAC 60.368 47.826 0.00 0.00 0.00 3.01
2018 2723 2.441750 AGACCTGAAACAACAAGGGCTA 59.558 45.455 0.00 0.00 36.00 3.93
2022 2727 4.468153 ACCTGAAACAACAAGGGCTAAAAA 59.532 37.500 0.00 0.00 0.00 1.94
2062 2772 3.134804 GGGAGTATGTATGAACCTGCTGT 59.865 47.826 0.00 0.00 0.00 4.40
2148 2858 4.517285 ACATGTCCATATTGACGCTTCTT 58.483 39.130 0.00 0.00 38.11 2.52
2151 2861 4.769688 TGTCCATATTGACGCTTCTTGAT 58.230 39.130 2.76 0.00 38.11 2.57
2166 2876 4.991153 TCTTGATGAGAACATAGCGAGT 57.009 40.909 0.00 0.00 36.82 4.18
2229 2939 7.762588 TCTATAAGGAAGGAGAACCGAATAG 57.237 40.000 0.00 0.00 41.83 1.73
2253 2963 3.604875 AGCAATGCTTTGGATCTTTGG 57.395 42.857 0.00 0.00 33.89 3.28
2260 2971 2.887152 GCTTTGGATCTTTGGTCTGTGT 59.113 45.455 0.00 0.00 0.00 3.72
2265 2976 4.136796 TGGATCTTTGGTCTGTGTTTCTG 58.863 43.478 0.00 0.00 0.00 3.02
2283 2994 9.760660 GTGTTTCTGTTGCTACTATTTATTCTG 57.239 33.333 0.00 0.00 0.00 3.02
2303 3014 8.633075 ATTCTGAACTTGTGTGTTTGTATTTG 57.367 30.769 0.00 0.00 0.00 2.32
2407 3119 3.832704 TGGCGTGACCAGTTATCTG 57.167 52.632 0.00 0.00 46.36 2.90
2418 3130 2.947652 CCAGTTATCTGTGGCATTGGAG 59.052 50.000 0.00 0.00 39.82 3.86
2450 3165 5.580691 CCTTCAGCACATAGTTGTTCGAATA 59.419 40.000 0.00 0.00 32.34 1.75
2456 3171 7.162546 CAGCACATAGTTGTTCGAATAAATTCG 59.837 37.037 12.70 16.93 46.33 3.34
2479 3194 2.843113 AGGAGCTGTAATTCAGAAGGCT 59.157 45.455 0.00 0.00 46.27 4.58
2492 3207 3.769300 TCAGAAGGCTATCTTGTGTGCTA 59.231 43.478 0.00 0.00 44.36 3.49
2522 3237 8.983307 TTTGTTTCGGTTGTATTTAGTTGTTT 57.017 26.923 0.00 0.00 0.00 2.83
2573 3289 4.940654 AGCTTTACTGGCAAAGAGAGATTC 59.059 41.667 1.67 0.00 37.66 2.52
2613 3330 1.402613 ACGGCTGTACCACAAACAAAC 59.597 47.619 0.00 0.00 39.03 2.93
2627 3344 6.472163 CCACAAACAAACACAACAAGACTATC 59.528 38.462 0.00 0.00 0.00 2.08
2658 3375 3.007182 TCCTGGTCGGTTAACTGGTTTAG 59.993 47.826 14.44 7.93 0.00 1.85
2679 3396 9.109393 GTTTAGGAATGTATGATTTGCTAGTGA 57.891 33.333 0.00 0.00 29.25 3.41
2767 3510 2.486548 GCAGAAAAGGAGGTACACCACA 60.487 50.000 10.24 0.00 43.22 4.17
2780 3523 6.779860 AGGTACACCACATTTTCTTACTGAT 58.220 36.000 0.38 0.00 38.89 2.90
2781 3524 6.655003 AGGTACACCACATTTTCTTACTGATG 59.345 38.462 0.38 0.00 38.89 3.07
2782 3525 6.653320 GGTACACCACATTTTCTTACTGATGA 59.347 38.462 0.00 0.00 35.64 2.92
2801 3544 9.935241 ACTGATGAAGTACATATAATCCATGTC 57.065 33.333 0.00 0.00 39.56 3.06
2802 3545 9.376075 CTGATGAAGTACATATAATCCATGTCC 57.624 37.037 0.00 0.00 39.56 4.02
2803 3546 8.879227 TGATGAAGTACATATAATCCATGTCCA 58.121 33.333 0.00 0.00 39.56 4.02
2804 3547 9.896645 GATGAAGTACATATAATCCATGTCCAT 57.103 33.333 0.00 0.00 39.56 3.41
2819 3562 9.784531 ATCCATGTCCATAGTGATTAAAGTTAG 57.215 33.333 0.00 0.00 0.00 2.34
2825 3568 8.870879 GTCCATAGTGATTAAAGTTAGACACAC 58.129 37.037 0.00 0.00 0.00 3.82
2842 3585 1.675641 ACGCCCCTGATGCTTGAAC 60.676 57.895 0.00 0.00 0.00 3.18
2848 3591 1.135972 CCCTGATGCTTGAACGAAACG 60.136 52.381 0.00 0.00 0.00 3.60
2881 3624 4.748892 CAGATTCTGCCGTCTAAAGAGAA 58.251 43.478 0.00 0.00 31.96 2.87
2891 3634 5.625721 GCCGTCTAAAGAGAAAAAGAAAAGC 59.374 40.000 0.00 0.00 31.96 3.51
3023 3770 1.636148 ACATGATGCCAAAAGCCAGT 58.364 45.000 0.00 0.00 42.71 4.00
3027 3774 1.075374 TGATGCCAAAAGCCAGTACCT 59.925 47.619 0.00 0.00 42.71 3.08
3035 3782 1.764571 AAGCCAGTACCTTCACCGCA 61.765 55.000 0.00 0.00 0.00 5.69
3118 3865 4.522114 TGACATGGAACTGTGAAGTTTCA 58.478 39.130 2.20 2.20 41.06 2.69
3161 3908 2.165301 GTGATATATCGCCGCCCGC 61.165 63.158 14.27 0.00 36.73 6.13
3194 3941 5.694995 TCTTGGGGACATCATTTCTTATCC 58.305 41.667 0.00 0.00 42.32 2.59
3213 3964 1.351017 CCCTGCAAGTGTTCTTCCCTA 59.649 52.381 0.00 0.00 0.00 3.53
3214 3965 2.025887 CCCTGCAAGTGTTCTTCCCTAT 60.026 50.000 0.00 0.00 0.00 2.57
3230 3981 3.846588 TCCCTATTTCTTGGAGACAGCTT 59.153 43.478 0.00 0.00 44.54 3.74
3288 4040 5.527951 TCCATGTTTTCTCATTGGTTTTCG 58.472 37.500 0.00 0.00 0.00 3.46
3307 4059 1.865970 CGCAGCTTCAGATCAGGATTC 59.134 52.381 0.00 0.00 0.00 2.52
3332 4084 3.381335 AGATCCGGCCTCCTTACTTTTA 58.619 45.455 0.00 0.00 0.00 1.52
3357 4109 3.218453 GGAGTGCAGAGATCTACAGCTA 58.782 50.000 12.86 0.49 0.00 3.32
3367 4119 3.392616 AGATCTACAGCTAATGGGTTGGG 59.607 47.826 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 4.829492 CACCTTGAAATGTTTCTCCTCCTT 59.171 41.667 6.99 0.00 38.02 3.36
121 122 4.398044 ACTTGAAACGTCACCTTGAAATGT 59.602 37.500 0.00 0.00 31.90 2.71
146 147 3.692406 AGCCTCGACGGGGTTGTC 61.692 66.667 16.76 0.00 32.66 3.18
288 289 3.005261 TGTGCATGTGTTAAATGGGTGAC 59.995 43.478 0.00 0.00 0.00 3.67
294 295 6.325849 CATGTGATGTGCATGTGTTAAATG 57.674 37.500 0.00 0.00 38.96 2.32
330 331 4.142609 ACCACATAACCTGAGTAGCATG 57.857 45.455 0.00 0.00 0.00 4.06
345 346 4.016444 ACTCTGTGTTTTGTCAACCACAT 58.984 39.130 14.48 2.17 33.90 3.21
350 351 3.119849 ACTGCACTCTGTGTTTTGTCAAC 60.120 43.478 0.00 0.00 35.75 3.18
356 357 7.094634 CCATATTTCTACTGCACTCTGTGTTTT 60.095 37.037 0.00 0.00 35.75 2.43
357 358 6.372659 CCATATTTCTACTGCACTCTGTGTTT 59.627 38.462 0.00 0.00 35.75 2.83
360 361 4.272018 GCCATATTTCTACTGCACTCTGTG 59.728 45.833 0.00 0.00 36.51 3.66
446 450 4.321082 CGCGTTAAGTTCCCCCAAAATAAA 60.321 41.667 0.00 0.00 0.00 1.40
457 461 4.243270 AGATATATGGCGCGTTAAGTTCC 58.757 43.478 8.43 0.00 0.00 3.62
510 670 1.333619 CTCTTTTCAACACACACCCCG 59.666 52.381 0.00 0.00 0.00 5.73
514 674 4.094887 TCTTCTGCTCTTTTCAACACACAC 59.905 41.667 0.00 0.00 0.00 3.82
568 907 9.325198 ACATTTGGACTTTTGAGATTTTAAACC 57.675 29.630 0.00 0.00 0.00 3.27
595 934 5.877564 ACTTTTGATTTTCCCGCAAGAAAAA 59.122 32.000 13.15 1.39 45.94 1.94
597 936 5.017294 ACTTTTGATTTTCCCGCAAGAAA 57.983 34.783 0.00 0.00 43.02 2.52
598 937 4.664150 ACTTTTGATTTTCCCGCAAGAA 57.336 36.364 0.00 0.00 43.02 2.52
599 938 4.098654 TCAACTTTTGATTTTCCCGCAAGA 59.901 37.500 0.00 0.00 34.81 3.02
600 939 4.367450 TCAACTTTTGATTTTCCCGCAAG 58.633 39.130 0.00 0.00 34.08 4.01
601 940 4.392921 TCAACTTTTGATTTTCCCGCAA 57.607 36.364 0.00 0.00 34.08 4.85
602 941 4.392921 TTCAACTTTTGATTTTCCCGCA 57.607 36.364 0.00 0.00 39.84 5.69
603 942 5.726729 TTTTCAACTTTTGATTTTCCCGC 57.273 34.783 0.00 0.00 39.84 6.13
605 944 9.720667 CAAGATTTTTCAACTTTTGATTTTCCC 57.279 29.630 0.00 0.00 39.84 3.97
606 945 9.720667 CCAAGATTTTTCAACTTTTGATTTTCC 57.279 29.630 0.00 0.00 39.84 3.13
627 966 9.665719 AAAGCTTCAAGTTTTAAATTTCCAAGA 57.334 25.926 0.00 0.00 26.56 3.02
629 968 9.442047 TCAAAGCTTCAAGTTTTAAATTTCCAA 57.558 25.926 0.00 0.00 27.42 3.53
631 970 9.920826 CTTCAAAGCTTCAAGTTTTAAATTTCC 57.079 29.630 0.00 0.00 27.42 3.13
633 972 9.448438 ACCTTCAAAGCTTCAAGTTTTAAATTT 57.552 25.926 0.00 0.00 27.42 1.82
636 975 7.333174 CCAACCTTCAAAGCTTCAAGTTTTAAA 59.667 33.333 0.00 0.00 27.42 1.52
639 978 5.046663 TCCAACCTTCAAAGCTTCAAGTTTT 60.047 36.000 0.00 0.00 0.00 2.43
644 983 5.612725 AATTCCAACCTTCAAAGCTTCAA 57.387 34.783 0.00 0.00 0.00 2.69
667 1006 4.806247 CACCCTATTGCACGTTTTGAAAAA 59.194 37.500 0.00 0.00 0.00 1.94
671 1010 2.852449 TCACCCTATTGCACGTTTTGA 58.148 42.857 0.00 0.00 0.00 2.69
673 1012 3.572255 ACATTCACCCTATTGCACGTTTT 59.428 39.130 0.00 0.00 0.00 2.43
677 1016 1.670811 GGACATTCACCCTATTGCACG 59.329 52.381 0.00 0.00 0.00 5.34
678 1017 2.945668 GAGGACATTCACCCTATTGCAC 59.054 50.000 0.00 0.00 31.84 4.57
680 1019 3.118261 TCAGAGGACATTCACCCTATTGC 60.118 47.826 0.00 0.00 31.84 3.56
685 1024 4.338879 CAAATTCAGAGGACATTCACCCT 58.661 43.478 0.00 0.00 35.02 4.34
687 1026 3.119352 GGCAAATTCAGAGGACATTCACC 60.119 47.826 0.00 0.00 0.00 4.02
694 1033 2.814336 ACTTTCGGCAAATTCAGAGGAC 59.186 45.455 0.00 0.00 0.00 3.85
699 1038 5.964887 TTTCAAACTTTCGGCAAATTCAG 57.035 34.783 0.00 0.00 0.00 3.02
700 1039 5.872070 AGTTTTCAAACTTTCGGCAAATTCA 59.128 32.000 0.00 0.00 46.52 2.57
701 1040 6.344572 AGTTTTCAAACTTTCGGCAAATTC 57.655 33.333 0.00 0.00 46.52 2.17
736 1078 0.180171 TCCCATCGTTCAATCCGCAT 59.820 50.000 0.00 0.00 0.00 4.73
740 1082 1.867233 CATCGTCCCATCGTTCAATCC 59.133 52.381 0.00 0.00 0.00 3.01
749 1091 1.860950 CGACATTGACATCGTCCCATC 59.139 52.381 0.00 0.00 33.63 3.51
750 1092 1.939974 CGACATTGACATCGTCCCAT 58.060 50.000 0.00 0.00 33.63 4.00
751 1093 3.434258 CGACATTGACATCGTCCCA 57.566 52.632 0.00 0.00 33.63 4.37
756 1098 2.993220 TGGAAGAACGACATTGACATCG 59.007 45.455 0.00 0.00 43.97 3.84
771 1113 0.109532 TTGGCCAACGTCATGGAAGA 59.890 50.000 16.05 0.00 43.54 2.87
776 1118 3.270027 TCTCTATTTGGCCAACGTCATG 58.730 45.455 20.35 7.43 0.00 3.07
778 1120 3.627395 ATCTCTATTTGGCCAACGTCA 57.373 42.857 20.35 3.25 0.00 4.35
785 1127 7.085052 ACTTAAACGAAATCTCTATTTGGCC 57.915 36.000 0.00 0.00 35.41 5.36
793 1135 7.803279 AAAGGTGAACTTAAACGAAATCTCT 57.197 32.000 0.00 0.00 38.85 3.10
864 1207 3.274288 GTTCAATCTAGACTTGGCCCAG 58.726 50.000 0.00 0.00 0.00 4.45
865 1208 2.354704 CGTTCAATCTAGACTTGGCCCA 60.355 50.000 0.00 0.00 0.00 5.36
871 1214 5.391736 CGAGTACACCGTTCAATCTAGACTT 60.392 44.000 0.00 0.00 0.00 3.01
873 1216 4.093998 TCGAGTACACCGTTCAATCTAGAC 59.906 45.833 0.00 0.00 0.00 2.59
875 1218 4.094590 ACTCGAGTACACCGTTCAATCTAG 59.905 45.833 18.46 0.00 0.00 2.43
876 1219 4.005650 ACTCGAGTACACCGTTCAATCTA 58.994 43.478 18.46 0.00 0.00 1.98
878 1221 2.915463 CACTCGAGTACACCGTTCAATC 59.085 50.000 19.57 0.00 0.00 2.67
945 1290 2.359981 TATCCCTTCGACGATGGAGT 57.640 50.000 26.59 17.61 0.00 3.85
1005 1350 1.392534 GAGGGAGGAGGAGGTGGAA 59.607 63.158 0.00 0.00 0.00 3.53
1169 1520 1.530655 TCAGTCAGTCAGCACCGGA 60.531 57.895 9.46 0.00 0.00 5.14
1176 1527 0.727457 CGCGTCAGTCAGTCAGTCAG 60.727 60.000 0.00 0.00 0.00 3.51
1177 1528 1.282875 CGCGTCAGTCAGTCAGTCA 59.717 57.895 0.00 0.00 0.00 3.41
1178 1529 2.083522 GCGCGTCAGTCAGTCAGTC 61.084 63.158 8.43 0.00 0.00 3.51
1179 1530 2.049985 GCGCGTCAGTCAGTCAGT 60.050 61.111 8.43 0.00 0.00 3.41
1409 1782 0.738762 CAGTGTCATCCCGTCAGCTG 60.739 60.000 7.63 7.63 0.00 4.24
1418 1794 3.518003 GCCATGCCAGTGTCATCC 58.482 61.111 0.00 0.00 0.00 3.51
1634 2010 4.081752 ACTCAGGTTGAAATGTGTGCAAAA 60.082 37.500 0.00 0.00 0.00 2.44
1641 2017 4.320057 GCAGAGAACTCAGGTTGAAATGTG 60.320 45.833 4.64 0.00 35.58 3.21
1656 2035 3.386768 TTACCACACAGAGCAGAGAAC 57.613 47.619 0.00 0.00 0.00 3.01
1658 2037 4.623932 ATTTTACCACACAGAGCAGAGA 57.376 40.909 0.00 0.00 0.00 3.10
1818 2204 4.023707 GGATTATTCAGCGAGTTTGATGGG 60.024 45.833 0.00 0.00 0.00 4.00
1823 2209 4.095483 AGCTTGGATTATTCAGCGAGTTTG 59.905 41.667 0.00 0.00 0.00 2.93
1829 2531 3.397482 AGCTAGCTTGGATTATTCAGCG 58.603 45.455 12.68 0.00 33.10 5.18
1981 2686 5.611374 TCAGGTCTTACAGTTTTCTTCCTG 58.389 41.667 0.00 0.00 40.55 3.86
2000 2705 4.664150 TTTTAGCCCTTGTTGTTTCAGG 57.336 40.909 0.00 0.00 0.00 3.86
2022 2727 4.018960 ACTCCCAGATAAGTGACAGCATTT 60.019 41.667 0.00 0.00 0.00 2.32
2148 2858 2.481969 GGCACTCGCTATGTTCTCATCA 60.482 50.000 0.00 0.00 38.60 3.07
2151 2861 0.894835 TGGCACTCGCTATGTTCTCA 59.105 50.000 0.00 0.00 38.60 3.27
2166 2876 0.320374 CCTGGTTACTCGTCTTGGCA 59.680 55.000 0.00 0.00 0.00 4.92
2229 2939 5.751990 CCAAAGATCCAAAGCATTGCTAATC 59.248 40.000 12.39 12.16 38.25 1.75
2253 2963 6.787085 AATAGTAGCAACAGAAACACAGAC 57.213 37.500 0.00 0.00 0.00 3.51
2265 2976 9.760660 CACAAGTTCAGAATAAATAGTAGCAAC 57.239 33.333 0.00 0.00 0.00 4.17
2283 2994 6.885735 AAGCAAATACAAACACACAAGTTC 57.114 33.333 0.00 0.00 0.00 3.01
2303 3014 0.037447 ACAGCCTCCTCCTGAAAAGC 59.963 55.000 0.00 0.00 34.47 3.51
2389 3100 3.832704 CAGATAACTGGTCACGCCA 57.167 52.632 0.00 0.00 46.95 5.69
2407 3119 2.755929 GAGTCGACTCCAATGCCAC 58.244 57.895 31.24 6.83 37.02 5.01
2418 3130 0.247736 ATGTGCTGAAGGGAGTCGAC 59.752 55.000 7.70 7.70 0.00 4.20
2426 3138 3.325870 TCGAACAACTATGTGCTGAAGG 58.674 45.455 0.00 0.00 40.46 3.46
2450 3165 6.173339 TCTGAATTACAGCTCCTTCGAATTT 58.827 36.000 0.00 0.00 45.38 1.82
2456 3171 3.625313 GCCTTCTGAATTACAGCTCCTTC 59.375 47.826 0.00 0.00 45.38 3.46
2479 3194 9.767684 CGAAACAAAATTATAGCACACAAGATA 57.232 29.630 0.00 0.00 0.00 1.98
2548 3264 5.683876 TCTCTCTTTGCCAGTAAAGCTAT 57.316 39.130 3.62 0.00 37.53 2.97
2573 3289 9.237846 CAGCCGTACATGTATATATGATTGTAG 57.762 37.037 15.59 1.82 0.00 2.74
2613 3330 6.312426 GGAGAACAGATGATAGTCTTGTTGTG 59.688 42.308 0.00 0.00 0.00 3.33
2627 3344 0.898320 ACCGACCAGGAGAACAGATG 59.102 55.000 0.00 0.00 45.00 2.90
2658 3375 8.844244 AGAAATCACTAGCAAATCATACATTCC 58.156 33.333 0.00 0.00 0.00 3.01
2710 3427 8.812972 TCAAACATAGGTACTGTCTCTAATTGT 58.187 33.333 0.00 0.00 41.52 2.71
2711 3428 9.307121 CTCAAACATAGGTACTGTCTCTAATTG 57.693 37.037 0.00 0.00 41.52 2.32
2712 3429 9.256228 TCTCAAACATAGGTACTGTCTCTAATT 57.744 33.333 0.00 0.00 41.52 1.40
2714 3431 8.645814 TTCTCAAACATAGGTACTGTCTCTAA 57.354 34.615 0.00 0.00 41.52 2.10
2726 3468 6.053650 TCTGCAGATCATTCTCAAACATAGG 58.946 40.000 13.74 0.00 0.00 2.57
2801 3544 7.464178 GCGTGTGTCTAACTTTAATCACTATGG 60.464 40.741 0.00 0.00 0.00 2.74
2802 3545 7.391786 GCGTGTGTCTAACTTTAATCACTATG 58.608 38.462 0.00 0.00 0.00 2.23
2803 3546 6.534079 GGCGTGTGTCTAACTTTAATCACTAT 59.466 38.462 0.00 0.00 0.00 2.12
2804 3547 5.865552 GGCGTGTGTCTAACTTTAATCACTA 59.134 40.000 0.00 0.00 0.00 2.74
2805 3548 4.689345 GGCGTGTGTCTAACTTTAATCACT 59.311 41.667 0.00 0.00 0.00 3.41
2806 3549 4.142966 GGGCGTGTGTCTAACTTTAATCAC 60.143 45.833 0.00 0.00 0.00 3.06
2819 3562 3.127533 GCATCAGGGGCGTGTGTC 61.128 66.667 0.00 0.00 0.00 3.67
2825 3568 2.753966 CGTTCAAGCATCAGGGGCG 61.754 63.158 0.00 0.00 36.08 6.13
2869 3612 8.122952 TCTTGCTTTTCTTTTTCTCTTTAGACG 58.877 33.333 0.00 0.00 0.00 4.18
2906 3649 9.342308 TGTGATATCTCTTGTCTTTTTGTTCTT 57.658 29.630 3.98 0.00 0.00 2.52
2919 3662 7.767659 TGTTGATCCTCTTTGTGATATCTCTTG 59.232 37.037 3.98 0.00 0.00 3.02
2989 3735 5.236047 GGCATCATGTTGCTTTTGTTGTTTA 59.764 36.000 24.11 0.00 42.38 2.01
2993 3739 3.132160 TGGCATCATGTTGCTTTTGTTG 58.868 40.909 24.11 0.00 42.38 3.33
3023 3770 1.071814 GGGTGTTGCGGTGAAGGTA 59.928 57.895 0.00 0.00 0.00 3.08
3027 3774 2.589442 GACGGGTGTTGCGGTGAA 60.589 61.111 0.00 0.00 0.00 3.18
3035 3782 3.109592 TTTCGGCAGGACGGGTGTT 62.110 57.895 0.00 0.00 0.00 3.32
3103 3850 9.567848 TTAAGACAAAATGAAACTTCACAGTTC 57.432 29.630 0.00 0.00 42.89 3.01
3107 3854 7.831753 TGGTTAAGACAAAATGAAACTTCACA 58.168 30.769 0.00 0.00 40.49 3.58
3118 3865 7.607991 ACTCGATCATCTTGGTTAAGACAAAAT 59.392 33.333 0.00 0.00 45.17 1.82
3161 3908 1.003118 TGTCCCCAAGAAATCCAGTCG 59.997 52.381 0.00 0.00 0.00 4.18
3194 3941 2.859165 TAGGGAAGAACACTTGCAGG 57.141 50.000 0.00 0.00 34.46 4.85
3213 3964 4.565236 CCTCTGAAGCTGTCTCCAAGAAAT 60.565 45.833 0.00 0.00 0.00 2.17
3214 3965 3.244353 CCTCTGAAGCTGTCTCCAAGAAA 60.244 47.826 0.00 0.00 0.00 2.52
3230 3981 2.105649 TGTGCAATTGTGGTACCTCTGA 59.894 45.455 14.36 3.38 0.00 3.27
3288 4040 2.873472 CTGAATCCTGATCTGAAGCTGC 59.127 50.000 0.38 0.00 0.00 5.25
3323 4075 4.894784 TCTGCACTCCCTGTAAAAGTAAG 58.105 43.478 0.00 0.00 0.00 2.34
3332 4084 2.291865 TGTAGATCTCTGCACTCCCTGT 60.292 50.000 0.00 0.00 33.67 4.00


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

AutoCloner maintained by Alex Coulton.