Multiple sequence alignment - TraesCS3D01G105600

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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 TraesCS3D01G105600 chr3D 100.000 3110 0 0 1 3110 58090790 58087681 0.000000e+00 5744.0
1 TraesCS3D01G105600 chr3D 83.348 1111 164 15 1020 2112 568234950 568236057 0.000000e+00 1007.0
2 TraesCS3D01G105600 chr3D 81.834 1123 178 16 1013 2112 567664772 567663653 0.000000e+00 920.0
3 TraesCS3D01G105600 chr3D 80.989 1173 202 11 911 2065 566954521 566955690 0.000000e+00 911.0
4 TraesCS3D01G105600 chr3D 81.629 1105 174 17 1020 2111 569119521 569118433 0.000000e+00 889.0
5 TraesCS3D01G105600 chr3D 79.808 1144 190 20 1000 2112 566742660 566743793 0.000000e+00 795.0
6 TraesCS3D01G105600 chr3D 77.739 1132 184 36 1027 2112 567691092 567689983 1.570000e-177 632.0
7 TraesCS3D01G105600 chr3D 75.841 1159 218 37 991 2112 567902720 567903853 1.640000e-147 532.0
8 TraesCS3D01G105600 chr3D 82.246 552 64 19 2526 3074 567663124 567662604 2.200000e-121 446.0
9 TraesCS3D01G105600 chr3D 80.065 617 103 11 1010 1625 567485635 567486232 1.020000e-119 440.0
10 TraesCS3D01G105600 chr3D 79.636 604 110 11 1519 2112 568111390 568111990 3.710000e-114 422.0
11 TraesCS3D01G105600 chr3D 76.943 759 145 23 1364 2110 520097356 520096616 3.730000e-109 405.0
12 TraesCS3D01G105600 chr3D 82.020 406 54 11 2080 2484 567663646 567663259 8.320000e-86 327.0
13 TraesCS3D01G105600 chr3D 82.817 355 46 9 2131 2484 568236111 568236451 1.400000e-78 303.0
14 TraesCS3D01G105600 chr3D 91.892 185 13 2 1022 1205 520595042 520595225 1.110000e-64 257.0
15 TraesCS3D01G105600 chr3D 86.878 221 23 5 982 1196 565830729 565830949 3.100000e-60 243.0
16 TraesCS3D01G105600 chr3D 85.646 209 27 1 988 1196 568181131 568181336 1.880000e-52 217.0
17 TraesCS3D01G105600 chr3D 84.475 219 29 2 988 1205 568007121 568006907 8.740000e-51 211.0
18 TraesCS3D01G105600 chr3D 79.386 228 30 13 2131 2357 569466088 569465877 8.990000e-31 145.0
19 TraesCS3D01G105600 chr3D 86.992 123 9 3 211 332 58083497 58083381 7.000000e-27 132.0
20 TraesCS3D01G105600 chr3A 93.809 1809 72 21 747 2524 66914467 66912668 0.000000e+00 2684.0
21 TraesCS3D01G105600 chr3A 92.869 589 27 6 2526 3110 66912486 66911909 0.000000e+00 841.0
22 TraesCS3D01G105600 chr3A 79.671 1156 177 31 997 2112 701351702 701352839 0.000000e+00 780.0
23 TraesCS3D01G105600 chr3A 75.166 753 162 21 1366 2107 700739674 700740412 6.430000e-87 331.0
24 TraesCS3D01G105600 chr3A 92.202 218 11 4 529 744 67011976 67011763 1.400000e-78 303.0
25 TraesCS3D01G105600 chr3A 91.743 218 12 4 529 744 66921354 66921141 6.520000e-77 298.0
26 TraesCS3D01G105600 chr3A 83.451 284 31 9 52 332 66922059 66921789 1.850000e-62 250.0
27 TraesCS3D01G105600 chr3A 83.451 284 31 9 52 332 67012681 67012411 1.850000e-62 250.0
28 TraesCS3D01G105600 chr3A 87.755 196 24 0 1000 1195 700444814 700444619 2.410000e-56 230.0
29 TraesCS3D01G105600 chr3A 83.962 212 31 3 988 1199 700423430 700423222 1.890000e-47 200.0
30 TraesCS3D01G105600 chr3A 95.181 83 4 0 417 499 66921520 66921438 7.000000e-27 132.0
31 TraesCS3D01G105600 chr3A 95.181 83 4 0 417 499 67012142 67012060 7.000000e-27 132.0
32 TraesCS3D01G105600 chr3A 85.246 122 12 4 2111 2229 701352876 701352994 1.510000e-23 121.0
33 TraesCS3D01G105600 chr3A 91.525 59 5 0 921 979 700444872 700444814 7.150000e-12 82.4
34 TraesCS3D01G105600 chr6A 78.538 1081 182 28 1027 2086 596777193 596776142 0.000000e+00 665.0
35 TraesCS3D01G105600 chr6A 89.205 176 19 0 1020 1195 794637 794462 1.450000e-53 220.0
36 TraesCS3D01G105600 chr3B 83.527 516 60 18 1 502 90991811 90991307 2.830000e-125 459.0
37 TraesCS3D01G105600 chr3B 77.279 757 144 21 1365 2110 684513599 684512860 1.330000e-113 420.0
38 TraesCS3D01G105600 chr3B 92.208 154 9 3 2959 3110 90934009 90933857 6.750000e-52 215.0
39 TraesCS3D01G105600 chr3B 80.795 151 28 1 2283 2433 201999828 201999679 1.960000e-22 117.0
40 TraesCS3D01G105600 chr3B 92.000 75 6 0 531 605 62946631 62946557 4.240000e-19 106.0
41 TraesCS3D01G105600 chr3B 89.535 86 1 2 3025 3110 90979329 90979252 5.490000e-18 102.0
42 TraesCS3D01G105600 chr3B 90.667 75 6 1 2632 2706 684636085 684636012 7.100000e-17 99.0
43 TraesCS3D01G105600 chr1B 87.192 203 26 0 991 1193 41840570 41840772 6.710000e-57 231.0
44 TraesCS3D01G105600 chrUn 78.882 322 51 12 2113 2432 41058204 41058510 5.260000e-48 202.0
45 TraesCS3D01G105600 chrUn 76.875 320 47 22 2131 2443 314515110 314514811 4.150000e-34 156.0
46 TraesCS3D01G105600 chrUn 75.294 340 48 24 2101 2437 41196535 41196229 2.520000e-26 130.0
47 TraesCS3D01G105600 chr4A 78.261 322 48 16 2081 2396 79912 79607 1.470000e-43 187.0
48 TraesCS3D01G105600 chr4B 77.950 322 49 16 2081 2396 121229 120924 6.850000e-42 182.0
49 TraesCS3D01G105600 chr1D 71.853 707 151 29 1519 2195 26269645 26268957 3.210000e-35 159.0
50 TraesCS3D01G105600 chr7A 100.000 28 0 0 2499 2526 123273345 123273318 6.000000e-03 52.8


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 TraesCS3D01G105600 chr3D 58087681 58090790 3109 True 5744.000000 5744 100.000000 1 3110 1 chr3D.!!$R2 3109
1 TraesCS3D01G105600 chr3D 566954521 566955690 1169 False 911.000000 911 80.989000 911 2065 1 chr3D.!!$F4 1154
2 TraesCS3D01G105600 chr3D 569118433 569119521 1088 True 889.000000 889 81.629000 1020 2111 1 chr3D.!!$R6 1091
3 TraesCS3D01G105600 chr3D 566742660 566743793 1133 False 795.000000 795 79.808000 1000 2112 1 chr3D.!!$F3 1112
4 TraesCS3D01G105600 chr3D 568234950 568236451 1501 False 655.000000 1007 83.082500 1020 2484 2 chr3D.!!$F9 1464
5 TraesCS3D01G105600 chr3D 567689983 567691092 1109 True 632.000000 632 77.739000 1027 2112 1 chr3D.!!$R4 1085
6 TraesCS3D01G105600 chr3D 567662604 567664772 2168 True 564.333333 920 82.033333 1013 3074 3 chr3D.!!$R8 2061
7 TraesCS3D01G105600 chr3D 567902720 567903853 1133 False 532.000000 532 75.841000 991 2112 1 chr3D.!!$F6 1121
8 TraesCS3D01G105600 chr3D 567485635 567486232 597 False 440.000000 440 80.065000 1010 1625 1 chr3D.!!$F5 615
9 TraesCS3D01G105600 chr3D 568111390 568111990 600 False 422.000000 422 79.636000 1519 2112 1 chr3D.!!$F7 593
10 TraesCS3D01G105600 chr3D 520096616 520097356 740 True 405.000000 405 76.943000 1364 2110 1 chr3D.!!$R3 746
11 TraesCS3D01G105600 chr3A 66911909 66914467 2558 True 1762.500000 2684 93.339000 747 3110 2 chr3A.!!$R2 2363
12 TraesCS3D01G105600 chr3A 701351702 701352994 1292 False 450.500000 780 82.458500 997 2229 2 chr3A.!!$F2 1232
13 TraesCS3D01G105600 chr3A 700739674 700740412 738 False 331.000000 331 75.166000 1366 2107 1 chr3A.!!$F1 741
14 TraesCS3D01G105600 chr3A 67011763 67012681 918 True 228.333333 303 90.278000 52 744 3 chr3A.!!$R4 692
15 TraesCS3D01G105600 chr3A 66921141 66922059 918 True 226.666667 298 90.125000 52 744 3 chr3A.!!$R3 692
16 TraesCS3D01G105600 chr6A 596776142 596777193 1051 True 665.000000 665 78.538000 1027 2086 1 chr6A.!!$R2 1059
17 TraesCS3D01G105600 chr3B 90991307 90991811 504 True 459.000000 459 83.527000 1 502 1 chr3B.!!$R4 501
18 TraesCS3D01G105600 chr3B 684512860 684513599 739 True 420.000000 420 77.279000 1365 2110 1 chr3B.!!$R6 745

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
242 260 0.170561 CTTGCTGAACTCAGGCATGC 59.829 55.0 9.9 9.9 43.94 4.06 F
768 1027 0.240945 CTTGCTACAAAACTGGGCCG 59.759 55.0 0.0 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2301 0.393944 AGCAGGAGCACATCACCATG 60.394 55.0 0.0 0.0 45.49 3.66 R
2664 3283 0.397941 AGTTCAGGTGCTGCTTGCTA 59.602 50.0 0.0 0.0 43.37 3.49 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
26 27 0.822811 AGTTGCATGTTGTGGTTGCA 59.177 45.000 0.00 0.00 44.12 4.08
42 43 2.175878 TGCAGCTGAAGAACCTTCTC 57.824 50.000 20.43 0.00 36.28 2.87
50 51 0.977395 AAGAACCTTCTCCTCCACGG 59.023 55.000 0.00 0.00 36.28 4.94
84 88 6.482835 TGACTACTGTGAATGTTTTTGTTCG 58.517 36.000 0.00 0.00 0.00 3.95
86 90 3.105203 ACTGTGAATGTTTTTGTTCGCG 58.895 40.909 0.00 0.00 37.59 5.87
139 143 4.748892 ACAAGAGGATGTATCACGAACTG 58.251 43.478 0.00 0.00 0.00 3.16
156 160 2.653726 ACTGCTGACACCAACATTCAA 58.346 42.857 0.00 0.00 0.00 2.69
163 167 7.890515 TGCTGACACCAACATTCAAATAATAA 58.109 30.769 0.00 0.00 0.00 1.40
164 168 8.530311 TGCTGACACCAACATTCAAATAATAAT 58.470 29.630 0.00 0.00 0.00 1.28
242 260 0.170561 CTTGCTGAACTCAGGCATGC 59.829 55.000 9.90 9.90 43.94 4.06
271 289 9.555727 AGAACTACAGTAGAATAGAGATCAGAC 57.444 37.037 14.94 0.00 0.00 3.51
300 318 0.385751 ATGGCTAGTGATGACGACGG 59.614 55.000 0.00 0.00 0.00 4.79
344 392 6.824196 AGTGTCATGAACTCTACTAATCTCGA 59.176 38.462 0.00 0.00 30.04 4.04
360 408 3.939066 TCTCGAGGTGGAAATCCTTTTC 58.061 45.455 13.56 0.00 40.48 2.29
391 439 7.785028 TGTAGGCTGGATCTCTTTAATCTCTTA 59.215 37.037 0.00 0.00 0.00 2.10
413 461 9.803315 TCTTAATTGCTACAGTACATACTTCTG 57.197 33.333 0.00 0.00 33.46 3.02
414 462 9.587772 CTTAATTGCTACAGTACATACTTCTGT 57.412 33.333 0.00 0.00 43.46 3.41
459 661 1.559682 ACTACCACCTGCCCAAGTATG 59.440 52.381 0.00 0.00 0.00 2.39
480 682 4.625028 TGTATCGGAAGCTTCATGAGATG 58.375 43.478 27.02 8.07 0.00 2.90
499 702 7.546358 TGAGATGTTTTTCTTTTCTTGCTTGA 58.454 30.769 0.00 0.00 0.00 3.02
507 725 2.727123 TTTCTTGCTTGACCAGACCA 57.273 45.000 0.00 0.00 0.00 4.02
510 728 1.211703 TCTTGCTTGACCAGACCACAA 59.788 47.619 0.00 0.00 0.00 3.33
511 729 2.158623 TCTTGCTTGACCAGACCACAAT 60.159 45.455 0.00 0.00 0.00 2.71
521 739 1.732259 CAGACCACAATAACCAGCGTC 59.268 52.381 0.00 0.00 0.00 5.19
568 825 5.735285 TCATGGTAGCATCTATCTTCTGG 57.265 43.478 3.96 0.00 0.00 3.86
599 856 1.014564 GGGCGTCAGACTGTTAGTGC 61.015 60.000 1.59 1.06 0.00 4.40
642 899 2.889503 CGGCTACTGCTGCTCTGC 60.890 66.667 0.00 0.16 38.88 4.26
676 935 1.528129 CTCGCCAAGAGCTTTCCTTT 58.472 50.000 0.00 0.00 40.54 3.11
709 968 1.273606 GGGCCAAGAGCTTTTCCTTTC 59.726 52.381 4.39 0.00 43.05 2.62
710 969 2.242926 GGCCAAGAGCTTTTCCTTTCT 58.757 47.619 0.00 0.00 43.05 2.52
711 970 2.630098 GGCCAAGAGCTTTTCCTTTCTT 59.370 45.455 0.00 0.00 43.05 2.52
715 974 5.235186 GCCAAGAGCTTTTCCTTTCTTTTTC 59.765 40.000 0.00 0.00 38.99 2.29
733 992 2.034687 TTGAGCTGGGCCAAGAGC 59.965 61.111 12.85 12.16 42.60 4.09
738 997 0.897401 AGCTGGGCCAAGAGCTTTTC 60.897 55.000 12.85 0.00 43.15 2.29
744 1003 3.099905 GGGCCAAGAGCTTTTCCTATTT 58.900 45.455 4.39 0.00 43.05 1.40
745 1004 3.515502 GGGCCAAGAGCTTTTCCTATTTT 59.484 43.478 4.39 0.00 43.05 1.82
746 1005 4.709886 GGGCCAAGAGCTTTTCCTATTTTA 59.290 41.667 4.39 0.00 43.05 1.52
747 1006 5.394224 GGGCCAAGAGCTTTTCCTATTTTAC 60.394 44.000 4.39 0.00 43.05 2.01
748 1007 5.332707 GCCAAGAGCTTTTCCTATTTTACG 58.667 41.667 0.00 0.00 38.99 3.18
749 1008 5.332707 CCAAGAGCTTTTCCTATTTTACGC 58.667 41.667 0.00 0.00 0.00 4.42
750 1009 5.123979 CCAAGAGCTTTTCCTATTTTACGCT 59.876 40.000 0.00 0.00 0.00 5.07
754 1013 4.459337 AGCTTTTCCTATTTTACGCTTGCT 59.541 37.500 0.00 0.00 0.00 3.91
768 1027 0.240945 CTTGCTACAAAACTGGGCCG 59.759 55.000 0.00 0.00 0.00 6.13
790 1049 1.967319 CCCAAATGCAGCCGTACTAT 58.033 50.000 0.00 0.00 0.00 2.12
791 1050 2.297701 CCCAAATGCAGCCGTACTATT 58.702 47.619 0.00 0.00 0.00 1.73
801 1060 1.591619 GCCGTACTATTTTGTCTCCGC 59.408 52.381 0.00 0.00 0.00 5.54
826 1086 3.697542 GAGAGACAGAGAGGAAACCTACC 59.302 52.174 0.00 0.00 31.76 3.18
898 1160 1.523758 GAGAGAGAGGATCGAGAGCC 58.476 60.000 0.00 0.00 42.67 4.70
899 1161 0.250295 AGAGAGAGGATCGAGAGCCG 60.250 60.000 1.40 0.00 42.82 5.52
1351 1658 3.458189 CTCTTACGCACCTGGAATAAGG 58.542 50.000 0.00 0.00 43.57 2.69
1668 2041 0.951525 TGGTATTTGACACCACCGCG 60.952 55.000 0.00 0.00 41.17 6.46
1710 2083 4.023707 CACTCTCCAATTGTTTCTGACCAC 60.024 45.833 4.43 0.00 0.00 4.16
1841 2221 1.081041 CCTTTAAACGCCGGGTTGC 60.081 57.895 2.18 0.00 39.30 4.17
1899 2285 2.832838 TCTGGAGATTGTTGGGAGCTA 58.167 47.619 0.00 0.00 0.00 3.32
1915 2301 2.290093 GAGCTAATGCCTGCATCTTGTC 59.710 50.000 4.89 0.00 40.80 3.18
2071 2460 6.040842 AGTTTCACATAACTTGTTTCTGGCAT 59.959 34.615 0.00 0.00 36.00 4.40
2127 2558 3.257933 CCGAAGGCTGTTGAGTGC 58.742 61.111 0.00 0.00 46.14 4.40
2267 2700 0.602905 GCTCTGGCTGTTACGGTGTT 60.603 55.000 0.00 0.00 35.22 3.32
2268 2701 1.337447 GCTCTGGCTGTTACGGTGTTA 60.337 52.381 0.00 0.00 35.22 2.41
2269 2702 2.334838 CTCTGGCTGTTACGGTGTTAC 58.665 52.381 0.00 0.00 0.00 2.50
2386 2820 9.205513 AGGATCTATAATGTTTTCCAATTGCTT 57.794 29.630 0.00 0.00 0.00 3.91
2512 2946 9.988815 CAATTGCTAGTCAATAGTATTACCTCT 57.011 33.333 11.24 0.00 44.23 3.69
2530 3146 6.636454 ACCTCTGTCCCAAATTAGTATCAA 57.364 37.500 0.00 0.00 0.00 2.57
2611 3230 3.645884 CATGTGCTTCCTGTTCCTTTTG 58.354 45.455 0.00 0.00 0.00 2.44
2613 3232 3.096092 TGTGCTTCCTGTTCCTTTTGTT 58.904 40.909 0.00 0.00 0.00 2.83
2614 3233 3.119173 TGTGCTTCCTGTTCCTTTTGTTG 60.119 43.478 0.00 0.00 0.00 3.33
2615 3234 3.096092 TGCTTCCTGTTCCTTTTGTTGT 58.904 40.909 0.00 0.00 0.00 3.32
2616 3235 4.097286 GTGCTTCCTGTTCCTTTTGTTGTA 59.903 41.667 0.00 0.00 0.00 2.41
2617 3236 4.338118 TGCTTCCTGTTCCTTTTGTTGTAG 59.662 41.667 0.00 0.00 0.00 2.74
2618 3237 4.261614 GCTTCCTGTTCCTTTTGTTGTAGG 60.262 45.833 0.00 0.00 0.00 3.18
2619 3238 3.219281 TCCTGTTCCTTTTGTTGTAGGC 58.781 45.455 0.00 0.00 0.00 3.93
2645 3264 7.198306 TGTAGCTTATGATGATTTGATGCAG 57.802 36.000 0.00 0.00 0.00 4.41
2664 3283 8.380867 TGATGCAGATTATCATCCTTATTGACT 58.619 33.333 0.00 0.00 38.57 3.41
2766 3385 5.559770 TCTTGTTCATTGCATCTGGTTAGA 58.440 37.500 0.00 0.00 37.35 2.10
2777 3396 7.320443 TGCATCTGGTTAGATATTGAAACAC 57.680 36.000 0.00 0.00 41.71 3.32
2855 3474 8.125978 TCACTTTAGATGCTTTCCATTTCAAT 57.874 30.769 0.00 0.00 33.29 2.57
2932 3551 4.109766 TGTACAGGCTCATATCGAAAACG 58.890 43.478 0.00 0.00 0.00 3.60
3003 3622 5.220854 CCTCGTGTCTTTGTTTGTCTTTGAT 60.221 40.000 0.00 0.00 0.00 2.57
3013 3632 8.861033 TTTGTTTGTCTTTGATCTGAAGAATG 57.139 30.769 11.90 0.00 35.11 2.67
3014 3633 7.572523 TGTTTGTCTTTGATCTGAAGAATGT 57.427 32.000 11.90 0.00 35.11 2.71
3015 3634 7.642669 TGTTTGTCTTTGATCTGAAGAATGTC 58.357 34.615 11.90 3.54 35.11 3.06
3016 3635 7.500227 TGTTTGTCTTTGATCTGAAGAATGTCT 59.500 33.333 11.90 0.00 35.11 3.41
3018 3637 7.430992 TGTCTTTGATCTGAAGAATGTCTTG 57.569 36.000 11.90 0.00 36.73 3.02
3019 3638 7.219322 TGTCTTTGATCTGAAGAATGTCTTGA 58.781 34.615 11.90 0.00 36.73 3.02
3020 3639 7.881751 TGTCTTTGATCTGAAGAATGTCTTGAT 59.118 33.333 11.90 0.00 36.73 2.57
3021 3640 8.728833 GTCTTTGATCTGAAGAATGTCTTGATT 58.271 33.333 11.90 0.00 36.73 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.853307 GCAACCACAACATGCAACTAGAC 60.853 47.826 0.00 0.00 39.81 2.59
26 27 1.905894 GGAGGAGAAGGTTCTTCAGCT 59.094 52.381 9.87 0.00 37.73 4.24
42 43 1.553248 TCATGAACTAACCCGTGGAGG 59.447 52.381 0.00 0.00 40.63 4.30
50 51 6.874134 ACATTCACAGTAGTCATGAACTAACC 59.126 38.462 0.00 0.00 42.11 2.85
84 88 2.366859 GAGCTTCGCATTTACAATCGC 58.633 47.619 0.00 0.00 0.00 4.58
86 90 3.242870 CCTGGAGCTTCGCATTTACAATC 60.243 47.826 0.00 0.00 0.00 2.67
105 109 1.230635 CCTCTTGTCAACACGCCCTG 61.231 60.000 0.00 0.00 0.00 4.45
109 113 1.512926 ACATCCTCTTGTCAACACGC 58.487 50.000 0.00 0.00 0.00 5.34
139 143 8.931385 ATTATTATTTGAATGTTGGTGTCAGC 57.069 30.769 0.00 0.00 0.00 4.26
163 167 9.407380 CAGAATCTGCCTATCTATCTACTGTAT 57.593 37.037 0.00 0.00 0.00 2.29
164 168 8.800370 CAGAATCTGCCTATCTATCTACTGTA 57.200 38.462 0.00 0.00 0.00 2.74
165 169 7.701539 CAGAATCTGCCTATCTATCTACTGT 57.298 40.000 0.00 0.00 0.00 3.55
184 202 3.456277 CCCTAGTCCCTACTTTGCAGAAT 59.544 47.826 0.00 0.00 37.15 2.40
192 210 2.653366 TCAGTGTCCCTAGTCCCTACTT 59.347 50.000 0.00 0.00 37.15 2.24
242 260 9.554395 TGATCTCTATTCTACTGTAGTTCTCAG 57.446 37.037 14.11 7.01 38.68 3.35
251 269 5.067273 CCCGTCTGATCTCTATTCTACTGT 58.933 45.833 0.00 0.00 0.00 3.55
271 289 1.378514 ACTAGCCATTTGTGCCCCG 60.379 57.895 0.00 0.00 0.00 5.73
300 318 4.213482 ACACTATCGTTTTTCAGTTCCTGC 59.787 41.667 0.00 0.00 0.00 4.85
315 333 8.779303 AGATTAGTAGAGTTCATGACACTATCG 58.221 37.037 0.00 0.00 34.61 2.92
324 342 6.434596 CACCTCGAGATTAGTAGAGTTCATG 58.565 44.000 15.71 0.00 0.00 3.07
401 449 2.954318 TCCGGCCTACAGAAGTATGTAC 59.046 50.000 0.00 0.00 34.56 2.90
404 452 3.555168 GGAATCCGGCCTACAGAAGTATG 60.555 52.174 0.00 0.00 0.00 2.39
405 453 2.633481 GGAATCCGGCCTACAGAAGTAT 59.367 50.000 0.00 0.00 0.00 2.12
406 454 2.037144 GGAATCCGGCCTACAGAAGTA 58.963 52.381 0.00 0.00 0.00 2.24
407 455 0.831307 GGAATCCGGCCTACAGAAGT 59.169 55.000 0.00 0.00 0.00 3.01
409 457 0.539986 GTGGAATCCGGCCTACAGAA 59.460 55.000 0.00 0.00 0.00 3.02
410 458 0.325296 AGTGGAATCCGGCCTACAGA 60.325 55.000 0.00 0.00 0.00 3.41
411 459 0.179073 CAGTGGAATCCGGCCTACAG 60.179 60.000 0.00 0.00 0.00 2.74
413 461 0.462047 CACAGTGGAATCCGGCCTAC 60.462 60.000 0.00 0.00 0.00 3.18
414 462 1.622607 CCACAGTGGAATCCGGCCTA 61.623 60.000 15.35 0.00 40.96 3.93
415 463 2.671070 CACAGTGGAATCCGGCCT 59.329 61.111 0.00 0.00 0.00 5.19
416 464 2.438434 CCACAGTGGAATCCGGCC 60.438 66.667 15.35 0.00 40.96 6.13
417 465 2.252072 TAGCCACAGTGGAATCCGGC 62.252 60.000 24.96 5.68 40.96 6.13
418 466 0.462047 GTAGCCACAGTGGAATCCGG 60.462 60.000 24.96 0.00 40.96 5.14
459 661 4.626042 ACATCTCATGAAGCTTCCGATAC 58.374 43.478 23.42 0.00 0.00 2.24
480 682 6.035005 GTCTGGTCAAGCAAGAAAAGAAAAAC 59.965 38.462 0.00 0.00 0.00 2.43
499 702 1.610624 CGCTGGTTATTGTGGTCTGGT 60.611 52.381 0.00 0.00 0.00 4.00
507 725 0.241749 TCGACGACGCTGGTTATTGT 59.758 50.000 1.48 0.00 39.58 2.71
510 728 0.098376 GACTCGACGACGCTGGTTAT 59.902 55.000 1.48 0.00 39.58 1.89
511 729 1.499056 GACTCGACGACGCTGGTTA 59.501 57.895 1.48 0.00 39.58 2.85
521 739 0.030908 GCCATAAGGAGGACTCGACG 59.969 60.000 0.00 0.00 36.89 5.12
568 825 1.732259 CTGACGCCCATTGACTTGTAC 59.268 52.381 0.00 0.00 0.00 2.90
599 856 0.734889 GTCGAGGGATGCAATGGTTG 59.265 55.000 0.00 0.00 0.00 3.77
616 873 2.874780 CAGTAGCCGCGACACGTC 60.875 66.667 8.23 0.00 41.42 4.34
642 899 4.821589 GAGGAGAGCAACCCGGCG 62.822 72.222 0.00 0.00 39.27 6.46
647 904 1.743252 CTTGGCGAGGAGAGCAACC 60.743 63.158 0.00 0.00 36.08 3.77
648 905 0.739112 CTCTTGGCGAGGAGAGCAAC 60.739 60.000 1.29 0.00 36.06 4.17
694 953 7.840931 TCAAGAAAAAGAAAGGAAAAGCTCTT 58.159 30.769 0.00 0.00 0.00 2.85
709 968 1.331214 TGGCCCAGCTCAAGAAAAAG 58.669 50.000 0.00 0.00 0.00 2.27
710 969 1.688197 CTTGGCCCAGCTCAAGAAAAA 59.312 47.619 0.00 0.00 38.29 1.94
711 970 1.133513 TCTTGGCCCAGCTCAAGAAAA 60.134 47.619 11.93 0.00 40.23 2.29
715 974 2.045131 GCTCTTGGCCCAGCTCAAG 61.045 63.158 0.00 6.56 37.80 3.02
733 992 6.837992 TGTAGCAAGCGTAAAATAGGAAAAG 58.162 36.000 0.00 0.00 0.00 2.27
738 997 6.523201 CAGTTTTGTAGCAAGCGTAAAATAGG 59.477 38.462 7.16 0.00 0.00 2.57
744 1003 2.550606 CCCAGTTTTGTAGCAAGCGTAA 59.449 45.455 0.00 0.00 0.00 3.18
745 1004 2.147958 CCCAGTTTTGTAGCAAGCGTA 58.852 47.619 0.00 0.00 0.00 4.42
746 1005 0.951558 CCCAGTTTTGTAGCAAGCGT 59.048 50.000 0.00 0.00 0.00 5.07
747 1006 0.387239 GCCCAGTTTTGTAGCAAGCG 60.387 55.000 0.00 0.00 0.00 4.68
748 1007 0.038251 GGCCCAGTTTTGTAGCAAGC 60.038 55.000 0.00 0.00 0.00 4.01
749 1008 0.240945 CGGCCCAGTTTTGTAGCAAG 59.759 55.000 0.00 0.00 0.00 4.01
750 1009 0.179015 TCGGCCCAGTTTTGTAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
754 1013 1.302993 GGCTCGGCCCAGTTTTGTA 60.303 57.895 0.00 0.00 44.06 2.41
768 1027 1.748879 TACGGCTGCATTTGGGCTC 60.749 57.895 0.50 0.00 34.04 4.70
790 1049 1.244816 TCTCTCTCGCGGAGACAAAA 58.755 50.000 19.22 6.65 45.20 2.44
791 1050 2.942641 TCTCTCTCGCGGAGACAAA 58.057 52.632 19.22 8.55 45.20 2.83
801 1060 2.422127 GGTTTCCTCTCTGTCTCTCTCG 59.578 54.545 0.00 0.00 0.00 4.04
876 1138 0.598942 TCTCGATCCTCTCTCTCGCG 60.599 60.000 0.00 0.00 32.62 5.87
886 1148 3.532155 GTGGCGGCTCTCGATCCT 61.532 66.667 11.43 0.00 42.43 3.24
887 1149 4.593864 GGTGGCGGCTCTCGATCC 62.594 72.222 11.43 0.00 42.43 3.36
947 1209 4.436998 GAGTGGTGGCGACCTCGG 62.437 72.222 19.42 0.00 43.58 4.63
1086 1348 2.269241 CAGCGGAGGAGGGGTTTC 59.731 66.667 0.00 0.00 0.00 2.78
1899 2285 1.754803 CCATGACAAGATGCAGGCATT 59.245 47.619 8.34 0.00 36.70 3.56
1915 2301 0.393944 AGCAGGAGCACATCACCATG 60.394 55.000 0.00 0.00 45.49 3.66
2071 2460 9.542462 CGAAGAATTGATAACATAACCCTCTAA 57.458 33.333 0.00 0.00 0.00 2.10
2117 2507 2.896801 GCACCACCGCACTCAACAG 61.897 63.158 0.00 0.00 0.00 3.16
2127 2558 0.451783 GCCATTAAGAAGCACCACCG 59.548 55.000 0.00 0.00 0.00 4.94
2201 2634 4.787551 TCAACAAAAGAAAGCTAGTGGGA 58.212 39.130 0.00 0.00 0.00 4.37
2301 2735 1.150536 AGCCACTTCAGCCCGAAAA 59.849 52.632 0.00 0.00 31.71 2.29
2305 2739 4.711949 AGCAGCCACTTCAGCCCG 62.712 66.667 0.00 0.00 0.00 6.13
2367 2801 8.149647 TGAGTCAAAGCAATTGGAAAACATTAT 58.850 29.630 7.72 0.00 39.62 1.28
2368 2802 7.495901 TGAGTCAAAGCAATTGGAAAACATTA 58.504 30.769 7.72 0.00 39.62 1.90
2386 2820 3.819368 TGAAAACAGAGGCATGAGTCAA 58.181 40.909 0.00 0.00 0.00 3.18
2435 2869 8.855804 AGACCAGTATCTAAATTCTAAAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
2491 2925 7.309316 GGGACAGAGGTAATACTATTGACTAGC 60.309 44.444 0.00 0.00 0.00 3.42
2512 2946 8.328758 AGAAGACATTGATACTAATTTGGGACA 58.671 33.333 0.00 0.00 0.00 4.02
2524 2958 9.620259 AATCCCTCTAAAAGAAGACATTGATAC 57.380 33.333 0.00 0.00 0.00 2.24
2611 3230 6.049149 TCATCATAAGCTACAAGCCTACAAC 58.951 40.000 0.00 0.00 43.77 3.32
2613 3232 5.869649 TCATCATAAGCTACAAGCCTACA 57.130 39.130 0.00 0.00 43.77 2.74
2614 3233 7.442364 TCAAATCATCATAAGCTACAAGCCTAC 59.558 37.037 0.00 0.00 43.77 3.18
2615 3234 7.508687 TCAAATCATCATAAGCTACAAGCCTA 58.491 34.615 0.00 0.00 43.77 3.93
2616 3235 6.359804 TCAAATCATCATAAGCTACAAGCCT 58.640 36.000 0.00 0.00 43.77 4.58
2617 3236 6.624352 TCAAATCATCATAAGCTACAAGCC 57.376 37.500 0.00 0.00 43.77 4.35
2618 3237 6.581542 GCATCAAATCATCATAAGCTACAAGC 59.418 38.462 0.00 0.00 42.84 4.01
2619 3238 7.645402 TGCATCAAATCATCATAAGCTACAAG 58.355 34.615 0.00 0.00 0.00 3.16
2645 3264 8.663911 GCTTGCTAGTCAATAAGGATGATAATC 58.336 37.037 0.00 0.00 33.57 1.75
2664 3283 0.397941 AGTTCAGGTGCTGCTTGCTA 59.602 50.000 0.00 0.00 43.37 3.49
2821 3440 9.260002 GGAAAGCATCTAAAGTGAAATGAAAAA 57.740 29.630 0.00 0.00 0.00 1.94
2839 3458 7.848128 AGATTCTTCATTGAAATGGAAAGCAT 58.152 30.769 0.01 0.00 37.03 3.79
2932 3551 2.887152 AGCTGACCAAAACCACTTCATC 59.113 45.455 0.00 0.00 0.00 2.92
3052 3673 9.793259 ATTTAGTATTGAGAGAAACCACTGAAA 57.207 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.