Multiple sequence alignment - TraesCS3A01G510200

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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 TraesCS3A01G510200 chr3A 100.000 2954 0 0 1 2954 730329798 730326845 0.000000e+00 5456
1 TraesCS3A01G510200 chr3A 84.272 1208 90 36 823 1972 730280227 730279062 0.000000e+00 1086
2 TraesCS3A01G510200 chr3A 78.986 947 122 44 1074 1975 730208657 730207743 2.550000e-160 575
3 TraesCS3A01G510200 chr3A 77.244 958 136 49 1075 1975 730178367 730177435 1.230000e-133 486
4 TraesCS3A01G510200 chr5B 96.040 808 29 3 1 807 660956611 660955806 0.000000e+00 1312
5 TraesCS3A01G510200 chr5B 90.796 804 67 6 1 800 398644678 398643878 0.000000e+00 1068
6 TraesCS3A01G510200 chr3B 91.511 966 38 13 1057 1978 807812886 807813851 0.000000e+00 1290
7 TraesCS3A01G510200 chr3B 90.582 807 67 9 1 803 43377170 43376369 0.000000e+00 1061
8 TraesCS3A01G510200 chr3B 89.963 807 69 11 1 800 690725615 690724814 0.000000e+00 1031
9 TraesCS3A01G510200 chr3B 77.450 1153 152 64 882 1975 807930180 807931283 9.120000e-165 590
10 TraesCS3A01G510200 chr3B 79.020 939 125 39 1071 1973 807881921 807882823 7.100000e-161 577
11 TraesCS3A01G510200 chr3B 76.436 679 133 20 2146 2816 323458066 323458725 2.820000e-90 342
12 TraesCS3A01G510200 chr1A 95.533 806 32 2 1 806 539982689 539981888 0.000000e+00 1286
13 TraesCS3A01G510200 chr3D 85.575 1227 91 38 799 1972 600563098 600564291 0.000000e+00 1206
14 TraesCS3A01G510200 chr3D 77.826 1150 149 66 882 1975 600594226 600595325 5.410000e-172 614
15 TraesCS3A01G510200 chr3D 77.360 1144 162 62 882 1975 600607651 600608747 3.280000e-164 588
16 TraesCS3A01G510200 chr3D 78.328 646 114 16 2081 2720 94004853 94005478 7.670000e-106 394
17 TraesCS3A01G510200 chr7B 92.269 802 58 4 1 800 119313803 119313004 0.000000e+00 1134
18 TraesCS3A01G510200 chr7B 75.823 881 186 24 2084 2948 440195070 440195939 3.520000e-114 422
19 TraesCS3A01G510200 chr4B 91.034 803 63 7 1 800 5277232 5276436 0.000000e+00 1075
20 TraesCS3A01G510200 chr1B 90.864 810 62 11 1 804 587025963 587025160 0.000000e+00 1075
21 TraesCS3A01G510200 chr2B 89.988 809 67 11 1 800 36603261 36604064 0.000000e+00 1033
22 TraesCS3A01G510200 chr5D 83.884 968 131 15 1973 2934 286416311 286417259 0.000000e+00 900
23 TraesCS3A01G510200 chr5A 82.825 984 143 17 1973 2948 378578342 378579307 0.000000e+00 857
24 TraesCS3A01G510200 chr4A 79.926 807 134 23 2148 2948 677307234 677306450 4.270000e-158 568
25 TraesCS3A01G510200 chr6B 77.719 947 174 24 1973 2905 489847474 489846551 2.000000e-151 545
26 TraesCS3A01G510200 chr2D 80.000 765 122 22 2200 2948 14383416 14382667 1.200000e-148 536
27 TraesCS3A01G510200 chr4D 77.743 638 121 15 2079 2705 435976289 435976916 3.600000e-99 372
28 TraesCS3A01G510200 chr6D 74.685 873 183 30 2095 2948 458999742 459000595 1.300000e-93 353


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 TraesCS3A01G510200 chr3A 730326845 730329798 2953 True 5456 5456 100.000 1 2954 1 chr3A.!!$R4 2953
1 TraesCS3A01G510200 chr3A 730279062 730280227 1165 True 1086 1086 84.272 823 1972 1 chr3A.!!$R3 1149
2 TraesCS3A01G510200 chr3A 730207743 730208657 914 True 575 575 78.986 1074 1975 1 chr3A.!!$R2 901
3 TraesCS3A01G510200 chr3A 730177435 730178367 932 True 486 486 77.244 1075 1975 1 chr3A.!!$R1 900
4 TraesCS3A01G510200 chr5B 660955806 660956611 805 True 1312 1312 96.040 1 807 1 chr5B.!!$R2 806
5 TraesCS3A01G510200 chr5B 398643878 398644678 800 True 1068 1068 90.796 1 800 1 chr5B.!!$R1 799
6 TraesCS3A01G510200 chr3B 807812886 807813851 965 False 1290 1290 91.511 1057 1978 1 chr3B.!!$F2 921
7 TraesCS3A01G510200 chr3B 43376369 43377170 801 True 1061 1061 90.582 1 803 1 chr3B.!!$R1 802
8 TraesCS3A01G510200 chr3B 690724814 690725615 801 True 1031 1031 89.963 1 800 1 chr3B.!!$R2 799
9 TraesCS3A01G510200 chr3B 807930180 807931283 1103 False 590 590 77.450 882 1975 1 chr3B.!!$F4 1093
10 TraesCS3A01G510200 chr3B 807881921 807882823 902 False 577 577 79.020 1071 1973 1 chr3B.!!$F3 902
11 TraesCS3A01G510200 chr3B 323458066 323458725 659 False 342 342 76.436 2146 2816 1 chr3B.!!$F1 670
12 TraesCS3A01G510200 chr1A 539981888 539982689 801 True 1286 1286 95.533 1 806 1 chr1A.!!$R1 805
13 TraesCS3A01G510200 chr3D 600563098 600564291 1193 False 1206 1206 85.575 799 1972 1 chr3D.!!$F2 1173
14 TraesCS3A01G510200 chr3D 600594226 600595325 1099 False 614 614 77.826 882 1975 1 chr3D.!!$F3 1093
15 TraesCS3A01G510200 chr3D 600607651 600608747 1096 False 588 588 77.360 882 1975 1 chr3D.!!$F4 1093
16 TraesCS3A01G510200 chr3D 94004853 94005478 625 False 394 394 78.328 2081 2720 1 chr3D.!!$F1 639
17 TraesCS3A01G510200 chr7B 119313004 119313803 799 True 1134 1134 92.269 1 800 1 chr7B.!!$R1 799
18 TraesCS3A01G510200 chr7B 440195070 440195939 869 False 422 422 75.823 2084 2948 1 chr7B.!!$F1 864
19 TraesCS3A01G510200 chr4B 5276436 5277232 796 True 1075 1075 91.034 1 800 1 chr4B.!!$R1 799
20 TraesCS3A01G510200 chr1B 587025160 587025963 803 True 1075 1075 90.864 1 804 1 chr1B.!!$R1 803
21 TraesCS3A01G510200 chr2B 36603261 36604064 803 False 1033 1033 89.988 1 800 1 chr2B.!!$F1 799
22 TraesCS3A01G510200 chr5D 286416311 286417259 948 False 900 900 83.884 1973 2934 1 chr5D.!!$F1 961
23 TraesCS3A01G510200 chr5A 378578342 378579307 965 False 857 857 82.825 1973 2948 1 chr5A.!!$F1 975
24 TraesCS3A01G510200 chr4A 677306450 677307234 784 True 568 568 79.926 2148 2948 1 chr4A.!!$R1 800
25 TraesCS3A01G510200 chr6B 489846551 489847474 923 True 545 545 77.719 1973 2905 1 chr6B.!!$R1 932
26 TraesCS3A01G510200 chr2D 14382667 14383416 749 True 536 536 80.000 2200 2948 1 chr2D.!!$R1 748
27 TraesCS3A01G510200 chr4D 435976289 435976916 627 False 372 372 77.743 2079 2705 1 chr4D.!!$F1 626
28 TraesCS3A01G510200 chr6D 458999742 459000595 853 False 353 353 74.685 2095 2948 1 chr6D.!!$F1 853

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
709 726 1.229177 TGTGGCTACTCCTGGCTGA 60.229 57.895 0.64 0.0 35.26 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2673 0.037232 ACTCGCAACTAGAGGCCAAC 60.037 55.0 5.01 0.0 39.9 3.77 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
113 116 5.073144 TCCCCCTAATATCCATGTGTTTCTC 59.927 44.000 0.00 0.00 0.00 2.87
371 377 6.404074 GCTGTAAACTTGATTTCTGCTGCTAT 60.404 38.462 0.00 0.00 0.00 2.97
605 613 2.100989 CTGTAGGGAGTTCGTAGCCTT 58.899 52.381 0.00 0.00 0.00 4.35
629 638 2.755549 CGCTGGTAGTTCCTATAGGGGT 60.756 54.545 18.97 6.34 37.07 4.95
701 718 6.049149 TGTAATAATTCTGCTGTGGCTACTC 58.951 40.000 0.64 0.00 39.59 2.59
709 726 1.229177 TGTGGCTACTCCTGGCTGA 60.229 57.895 0.64 0.00 35.26 4.26
728 745 4.683432 GCCGAGAGCTGTGAACTT 57.317 55.556 0.00 0.00 38.99 2.66
848 865 7.608153 TCATAAAATTTCTCTACCGAGTGTCA 58.392 34.615 0.00 0.00 38.45 3.58
854 871 2.423892 TCTCTACCGAGTGTCATCAAGC 59.576 50.000 0.00 0.00 38.45 4.01
938 966 2.283298 CAATCCTCACCGTCCATCTTG 58.717 52.381 0.00 0.00 0.00 3.02
1042 1085 5.032220 CGTTGATCACGTACATTAGCTACA 58.968 41.667 0.00 0.00 44.49 2.74
1044 1087 6.198403 CGTTGATCACGTACATTAGCTACATT 59.802 38.462 0.00 0.00 44.49 2.71
1045 1088 7.253983 CGTTGATCACGTACATTAGCTACATTT 60.254 37.037 0.00 0.00 44.49 2.32
1046 1089 7.463469 TGATCACGTACATTAGCTACATTTG 57.537 36.000 0.00 0.00 0.00 2.32
1047 1090 5.712217 TCACGTACATTAGCTACATTTGC 57.288 39.130 0.00 0.00 0.00 3.68
1048 1091 5.416083 TCACGTACATTAGCTACATTTGCT 58.584 37.500 0.00 0.00 43.79 3.91
1049 1092 6.566141 TCACGTACATTAGCTACATTTGCTA 58.434 36.000 0.00 0.00 41.46 3.49
1050 1093 6.474427 TCACGTACATTAGCTACATTTGCTAC 59.526 38.462 0.00 0.00 41.95 3.58
1051 1094 6.254804 CACGTACATTAGCTACATTTGCTACA 59.745 38.462 0.00 0.00 41.95 2.74
1052 1095 6.814644 ACGTACATTAGCTACATTTGCTACAA 59.185 34.615 0.00 0.00 41.95 2.41
1053 1096 7.010183 ACGTACATTAGCTACATTTGCTACAAG 59.990 37.037 0.00 0.00 41.95 3.16
1054 1097 6.124088 ACATTAGCTACATTTGCTACAAGC 57.876 37.500 0.00 0.00 41.95 4.01
1067 1110 1.129251 CTACAAGCAAGCATCACCACG 59.871 52.381 0.00 0.00 0.00 4.94
1069 1112 1.155889 CAAGCAAGCATCACCACGTA 58.844 50.000 0.00 0.00 0.00 3.57
1072 1115 1.156736 GCAAGCATCACCACGTACTT 58.843 50.000 0.00 0.00 0.00 2.24
1077 1120 3.000727 AGCATCACCACGTACTTTTAGC 58.999 45.455 0.00 0.00 0.00 3.09
1141 1184 0.798776 CAACACCGATGAGTGCTTCC 59.201 55.000 0.00 0.00 41.67 3.46
1170 1213 1.275291 AGGACCATGTACTCCAACACG 59.725 52.381 0.00 0.00 30.75 4.49
1380 1450 3.731728 AGGCACGGGCATGGACAT 61.732 61.111 13.89 0.00 43.71 3.06
1381 1451 3.520862 GGCACGGGCATGGACATG 61.521 66.667 13.89 7.91 43.71 3.21
1382 1452 3.520862 GCACGGGCATGGACATGG 61.521 66.667 3.77 0.70 40.72 3.66
1386 1468 2.123164 GGGCATGGACATGGGCAT 60.123 61.111 13.63 0.00 39.16 4.40
1461 1552 4.821589 GAGTGCTTCGGCGGAGGG 62.822 72.222 18.39 0.00 45.37 4.30
1484 1575 0.988832 CAGGGGCAAGGGTACTACAA 59.011 55.000 0.00 0.00 0.00 2.41
1485 1576 1.065418 CAGGGGCAAGGGTACTACAAG 60.065 57.143 0.00 0.00 0.00 3.16
1486 1577 1.203389 AGGGGCAAGGGTACTACAAGA 60.203 52.381 0.00 0.00 0.00 3.02
1590 1703 8.231692 TCAATCAATTAACCTCACTCAACAAA 57.768 30.769 0.00 0.00 0.00 2.83
1597 1715 7.581213 TTAACCTCACTCAACAAATCAACAT 57.419 32.000 0.00 0.00 0.00 2.71
1602 1720 7.231317 ACCTCACTCAACAAATCAACATTACAT 59.769 33.333 0.00 0.00 0.00 2.29
1603 1721 7.539710 CCTCACTCAACAAATCAACATTACATG 59.460 37.037 0.00 0.00 0.00 3.21
1604 1722 7.369607 TCACTCAACAAATCAACATTACATGG 58.630 34.615 0.00 0.00 33.60 3.66
1657 1784 1.405105 TCTTTGAACTTGGTGTGCAGC 59.595 47.619 0.00 0.00 35.26 5.25
1687 1814 1.248785 CGAGGTGAAGAAGGACCCGA 61.249 60.000 0.00 0.00 32.03 5.14
1841 2022 4.499188 GCAACTGAGTAATCATGCATGCAT 60.499 41.667 27.46 27.46 37.08 3.96
1986 2189 1.895020 TTCGTGCTACTTGGGCCGAT 61.895 55.000 0.00 0.00 34.45 4.18
1994 2197 0.107017 ACTTGGGCCGATTCATCTGG 60.107 55.000 0.00 0.00 0.00 3.86
2005 2208 3.484229 CGATTCATCTGGAGTTTGTTCGC 60.484 47.826 0.00 0.00 0.00 4.70
2015 2218 0.599204 GTTTGTTCGCTGTCGAGGGA 60.599 55.000 0.00 0.00 46.34 4.20
2033 2236 2.173569 GGGATAGACTTGCAACTGGGAT 59.826 50.000 0.00 0.00 0.00 3.85
2050 2254 1.064979 GGATAAAAGAAGGCCGGACCA 60.065 52.381 1.76 0.00 43.14 4.02
2124 2380 1.582610 GGCCCAAATTGCGAGTCGAA 61.583 55.000 18.61 1.43 0.00 3.71
2135 2391 1.798813 GCGAGTCGAATTTGGACTTGT 59.201 47.619 22.41 2.13 44.41 3.16
2167 2426 2.250635 AAAGGTTGGGCCCCAGTTGT 62.251 55.000 22.27 0.00 38.26 3.32
2170 2429 1.456705 GTTGGGCCCCAGTTGTGAA 60.457 57.895 22.27 0.00 33.81 3.18
2176 2435 0.321653 GCCCCAGTTGTGAATCGAGT 60.322 55.000 0.00 0.00 0.00 4.18
2180 2439 2.547855 CCCAGTTGTGAATCGAGTGTGA 60.548 50.000 0.00 0.00 0.00 3.58
2185 2444 2.754472 TGTGAATCGAGTGTGAACCTG 58.246 47.619 0.00 0.00 0.00 4.00
2212 2472 2.349532 GGAACAAGAAAAGTTCGAGCCG 60.350 50.000 0.00 0.00 44.78 5.52
2235 2495 1.385756 TTGTGAGTCGACGGTGGACA 61.386 55.000 22.50 6.95 36.87 4.02
2242 2502 0.244450 TCGACGGTGGACATGTAACC 59.756 55.000 16.84 16.84 0.00 2.85
2340 2657 0.321564 TGCGAATCAAGGGTGGACTG 60.322 55.000 0.00 0.00 0.00 3.51
2343 2660 0.329596 GAATCAAGGGTGGACTGGCT 59.670 55.000 0.00 0.00 0.00 4.75
2355 2672 3.748568 GTGGACTGGCTACTCAGAAAAAG 59.251 47.826 0.00 0.00 38.11 2.27
2356 2673 3.244561 TGGACTGGCTACTCAGAAAAAGG 60.245 47.826 0.00 0.00 38.11 3.11
2435 2861 1.745320 AAGTTGCGAGTCGAGGGTGT 61.745 55.000 18.61 0.00 0.00 4.16
2446 2872 1.414919 TCGAGGGTGTACTTGCAAGTT 59.585 47.619 35.20 17.77 40.37 2.66
2483 2910 3.482783 GCAGTTGCGAGTCGAGGC 61.483 66.667 18.61 7.60 0.00 4.70
2520 3250 6.895782 TCCAACTTGGATAAAATAGGTCGAT 58.104 36.000 6.39 0.00 42.67 3.59
2543 3273 0.892358 TAGTTGCGAGTCGAGGGTGT 60.892 55.000 18.61 0.00 0.00 4.16
2558 3288 1.541670 GGGTGTACTTGCAACTCGGAA 60.542 52.381 0.00 0.00 0.00 4.30
2601 3332 2.432628 GTCGAGGGTGGACTTGCG 60.433 66.667 0.00 0.00 0.00 4.85
2657 3390 5.567138 ATCGATGGTGGACTTTCAATTTC 57.433 39.130 0.00 0.00 0.00 2.17
2666 3399 4.568760 TGGACTTTCAATTTCGCCAAAAAC 59.431 37.500 0.00 0.00 0.00 2.43
2667 3400 4.025229 GGACTTTCAATTTCGCCAAAAACC 60.025 41.667 0.00 0.00 0.00 3.27
2668 3401 4.508662 ACTTTCAATTTCGCCAAAAACCA 58.491 34.783 0.00 0.00 0.00 3.67
2735 3474 0.108329 AATGTCGGGTCTAGTTGCGG 60.108 55.000 0.00 0.00 0.00 5.69
2738 3477 2.125673 CGGGTCTAGTTGCGGGTG 60.126 66.667 0.00 0.00 0.00 4.61
2755 3494 3.356290 GGGTGGAGAGTGTAATTGCAAT 58.644 45.455 5.99 5.99 0.00 3.56
2852 3643 1.814248 GCGAGTTGAGGGTGGACTTTT 60.814 52.381 0.00 0.00 0.00 2.27
2864 3655 5.001874 GGGTGGACTTTTAACTAGGACAAG 58.998 45.833 0.00 0.00 0.00 3.16
2906 3699 1.971167 TCGTGGTGGGATTGCAAGC 60.971 57.895 6.04 6.04 0.00 4.01
2948 3791 1.598130 AGTTGCAAGTCGAGGGTGC 60.598 57.895 0.00 7.73 38.78 5.01
2950 3793 1.073025 TTGCAAGTCGAGGGTGCAT 59.927 52.632 15.90 0.00 46.91 3.96
2951 3794 1.236616 TTGCAAGTCGAGGGTGCATG 61.237 55.000 15.90 0.00 46.91 4.06
2952 3795 3.044059 GCAAGTCGAGGGTGCATGC 62.044 63.158 11.82 11.82 38.19 4.06
2953 3796 2.045926 AAGTCGAGGGTGCATGCC 60.046 61.111 16.68 6.42 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 116 5.124457 ACTCTTATTGTGCACAATTAGCCAG 59.876 40.000 41.08 33.47 43.48 4.85
167 170 2.439507 ACAAGTCAGGTCTTCCACATGT 59.560 45.455 0.00 0.00 38.04 3.21
333 339 8.406172 TCAAGTTTACAGCATCAAAACTTTTC 57.594 30.769 13.29 0.00 46.12 2.29
371 377 6.480763 TGAAACAACCATAAGCTCCATAAGA 58.519 36.000 0.00 0.00 0.00 2.10
448 454 3.946824 AGATATGTCTCCCCACCATCTT 58.053 45.455 0.00 0.00 0.00 2.40
485 493 2.738521 CTTGGGAGTCCACGCACG 60.739 66.667 12.30 0.00 43.94 5.34
629 638 2.546368 CCACCAGAAAACGACGAAATGA 59.454 45.455 0.00 0.00 0.00 2.57
728 745 2.699846 AGCAAAGGCAACCAAAGATCAA 59.300 40.909 0.00 0.00 44.61 2.57
848 865 1.579698 CGACTATGCTGCTGCTTGAT 58.420 50.000 17.00 4.73 40.48 2.57
854 871 0.928922 CTCTTGCGACTATGCTGCTG 59.071 55.000 0.00 0.00 35.36 4.41
876 897 3.703001 ATCCCCTCTATTATTGCACCG 57.297 47.619 0.00 0.00 0.00 4.94
938 966 0.664767 GCGAGTGACAGTGACAGGAC 60.665 60.000 0.00 0.00 0.00 3.85
1029 1072 7.126398 GCTTGTAGCAAATGTAGCTAATGTAC 58.874 38.462 0.00 0.00 45.30 2.90
1046 1089 1.135575 GTGGTGATGCTTGCTTGTAGC 60.136 52.381 0.00 0.00 42.82 3.58
1047 1090 1.129251 CGTGGTGATGCTTGCTTGTAG 59.871 52.381 0.00 0.00 0.00 2.74
1048 1091 1.155889 CGTGGTGATGCTTGCTTGTA 58.844 50.000 0.00 0.00 0.00 2.41
1049 1092 0.819259 ACGTGGTGATGCTTGCTTGT 60.819 50.000 0.00 0.00 0.00 3.16
1050 1093 1.135972 GTACGTGGTGATGCTTGCTTG 60.136 52.381 0.00 0.00 0.00 4.01
1051 1094 1.156736 GTACGTGGTGATGCTTGCTT 58.843 50.000 0.00 0.00 0.00 3.91
1052 1095 0.321671 AGTACGTGGTGATGCTTGCT 59.678 50.000 0.00 0.00 0.00 3.91
1053 1096 1.156736 AAGTACGTGGTGATGCTTGC 58.843 50.000 0.00 0.00 0.00 4.01
1054 1097 3.896648 AAAAGTACGTGGTGATGCTTG 57.103 42.857 0.00 0.00 0.00 4.01
1055 1098 3.435671 GCTAAAAGTACGTGGTGATGCTT 59.564 43.478 0.00 0.00 0.00 3.91
1067 1110 0.380733 GCCCGCCATGCTAAAAGTAC 59.619 55.000 0.00 0.00 0.00 2.73
1069 1112 0.254747 TAGCCCGCCATGCTAAAAGT 59.745 50.000 0.00 0.00 38.32 2.66
1072 1115 1.124780 TAGTAGCCCGCCATGCTAAA 58.875 50.000 0.00 0.00 42.57 1.85
1077 1120 1.151777 CGTTGTAGTAGCCCGCCATG 61.152 60.000 0.00 0.00 0.00 3.66
1170 1213 1.428620 GTCGTAGCACTCCTCGGTC 59.571 63.158 0.00 0.00 0.00 4.79
1308 1378 3.792736 TACATGGTCCTGCCGCCC 61.793 66.667 0.00 0.00 41.21 6.13
1393 1475 2.048503 GTCGTTGTGCCCGTAGCT 60.049 61.111 0.00 0.00 44.23 3.32
1461 1552 3.015145 TACCCTTGCCCCTGCTCC 61.015 66.667 0.00 0.00 38.71 4.70
1473 1564 3.442076 CACCTCCTTCTTGTAGTACCCT 58.558 50.000 0.00 0.00 0.00 4.34
1484 1575 2.350514 GCTGCTGCACCTCCTTCT 59.649 61.111 11.11 0.00 39.41 2.85
1485 1576 2.033141 TGCTGCTGCACCTCCTTC 59.967 61.111 14.93 0.00 45.31 3.46
1590 1703 7.678837 ACAAAATTGTCCCATGTAATGTTGAT 58.321 30.769 14.14 2.88 38.97 2.57
1657 1784 1.246056 TTCACCTCGTACCCCTCGTG 61.246 60.000 0.00 0.00 0.00 4.35
1787 1934 1.144057 GGACGGGCATCCTGTACTG 59.856 63.158 0.00 0.00 44.10 2.74
1841 2022 2.203972 GACGATCGGTGGACGTTGGA 62.204 60.000 20.98 0.00 44.69 3.53
1872 2063 6.271566 TGCATGATGCTCTATCGATCTTATC 58.728 40.000 19.19 1.42 45.31 1.75
1902 2097 0.234625 CGTAAGCAACACACGCATGT 59.765 50.000 0.00 0.00 40.80 3.21
1933 2136 5.189659 AGCTTATTGTAGAGACACCGATC 57.810 43.478 0.00 0.00 34.48 3.69
1986 2189 2.807967 CAGCGAACAAACTCCAGATGAA 59.192 45.455 0.00 0.00 0.00 2.57
2005 2208 1.751351 TGCAAGTCTATCCCTCGACAG 59.249 52.381 0.00 0.00 32.68 3.51
2015 2218 6.721318 TCTTTTATCCCAGTTGCAAGTCTAT 58.279 36.000 3.08 1.10 0.00 1.98
2033 2236 2.841881 ACTATGGTCCGGCCTTCTTTTA 59.158 45.455 14.76 0.00 38.35 1.52
2050 2254 1.380524 CACCCTCGACTCGTCACTAT 58.619 55.000 0.00 0.00 0.00 2.12
2075 2279 4.497291 TTTAGTCCCAGTTGTGACTTGT 57.503 40.909 2.67 0.00 41.80 3.16
2102 2358 3.825611 CTCGCAATTTGGGCCCGG 61.826 66.667 19.37 4.99 0.00 5.73
2107 2363 2.916716 CAAATTCGACTCGCAATTTGGG 59.083 45.455 23.87 7.11 42.51 4.12
2112 2368 2.699954 AGTCCAAATTCGACTCGCAAT 58.300 42.857 2.97 0.00 35.68 3.56
2124 2380 2.106857 TGACCCGGTTACAAGTCCAAAT 59.893 45.455 0.00 0.00 0.00 2.32
2167 2426 1.069978 TGCAGGTTCACACTCGATTCA 59.930 47.619 0.00 0.00 0.00 2.57
2170 2429 1.070758 AGTTGCAGGTTCACACTCGAT 59.929 47.619 0.00 0.00 0.00 3.59
2176 2435 1.340502 TGTTCCAGTTGCAGGTTCACA 60.341 47.619 0.00 0.00 0.00 3.58
2180 2439 2.435372 TCTTGTTCCAGTTGCAGGTT 57.565 45.000 0.00 0.00 0.00 3.50
2185 2444 3.791353 CGAACTTTTCTTGTTCCAGTTGC 59.209 43.478 0.00 0.00 40.26 4.17
2212 2472 1.299926 ACCGTCGACTCACAACTGC 60.300 57.895 14.70 0.00 0.00 4.40
2264 2525 0.400213 ACCCTCGATTTGCAACTGGA 59.600 50.000 0.00 0.00 0.00 3.86
2315 2632 2.485122 CCTTGATTCGCAACCGGC 59.515 61.111 0.00 0.00 39.90 6.13
2326 2643 0.912486 GTAGCCAGTCCACCCTTGAT 59.088 55.000 0.00 0.00 0.00 2.57
2340 2657 2.229062 GCCAACCTTTTTCTGAGTAGCC 59.771 50.000 0.00 0.00 0.00 3.93
2355 2672 0.741221 CTCGCAACTAGAGGCCAACC 60.741 60.000 5.01 0.00 32.38 3.77
2356 2673 0.037232 ACTCGCAACTAGAGGCCAAC 60.037 55.000 5.01 0.00 39.90 3.77
2466 2892 3.482783 GCCTCGACTCGCAACTGC 61.483 66.667 0.00 0.00 37.78 4.40
2497 3227 6.204882 GGATCGACCTATTTTATCCAAGTTGG 59.795 42.308 16.36 16.36 36.83 3.77
2512 3242 1.134007 TCGCAACTAGGGATCGACCTA 60.134 52.381 2.12 2.12 42.09 3.08
2520 3250 1.030488 CCTCGACTCGCAACTAGGGA 61.030 60.000 0.00 0.00 37.64 4.20
2577 3308 1.982395 TCCACCCTCGACTCGCAAT 60.982 57.895 0.00 0.00 0.00 3.56
2622 3353 2.439507 ACCATCGATTCATAGTTGGGCT 59.560 45.455 0.00 0.00 32.90 5.19
2629 3362 5.359756 TGAAAGTCCACCATCGATTCATAG 58.640 41.667 0.00 0.00 0.00 2.23
2657 3390 2.126110 GCCCGATGGTTTTTGGCG 60.126 61.111 0.00 0.00 31.55 5.69
2666 3399 4.047125 ACAACTGGGGCCCGATGG 62.047 66.667 19.83 8.54 0.00 3.51
2667 3400 2.751436 CACAACTGGGGCCCGATG 60.751 66.667 19.83 18.47 0.00 3.84
2668 3401 2.933287 TCACAACTGGGGCCCGAT 60.933 61.111 19.83 5.08 0.00 4.18
2725 3464 0.251653 ACTCTCCACCCGCAACTAGA 60.252 55.000 0.00 0.00 0.00 2.43
2735 3474 3.129287 CCATTGCAATTACACTCTCCACC 59.871 47.826 9.83 0.00 0.00 4.61
2738 3477 2.689983 CCCCATTGCAATTACACTCTCC 59.310 50.000 9.83 0.00 0.00 3.71
2782 3569 1.230324 GCAAGTCCACTGTTGAGTCC 58.770 55.000 0.00 0.00 0.00 3.85
2790 3577 0.179020 TCCCAGTTGCAAGTCCACTG 60.179 55.000 3.08 6.14 0.00 3.66
2791 3578 0.773644 ATCCCAGTTGCAAGTCCACT 59.226 50.000 3.08 0.00 0.00 4.00
2830 3621 1.194781 AGTCCACCCTCAACTCGCAT 61.195 55.000 0.00 0.00 0.00 4.73
2852 3643 5.152934 ACCTGACCTTTCTTGTCCTAGTTA 58.847 41.667 0.00 0.00 31.60 2.24
2864 3655 3.760684 TCGTAACTAGGACCTGACCTTTC 59.239 47.826 3.53 0.00 41.00 2.62
2927 3722 2.328099 CCCTCGACTTGCAACTGGC 61.328 63.158 0.00 0.00 45.13 4.85


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

AutoCloner maintained by Alex Coulton.