Multiple sequence alignment - TraesCS3A01G217400

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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 TraesCS3A01G217400 chr3A 100.000 2894 0 0 1 2894 396612275 396609382 0.000000e+00 5345.0
1 TraesCS3A01G217400 chr3A 97.059 34 1 0 2188 2221 42081801 42081768 1.120000e-04 58.4
2 TraesCS3A01G217400 chr3A 97.059 34 1 0 2188 2221 42150849 42150816 1.120000e-04 58.4
3 TraesCS3A01G217400 chr3D 93.893 2145 81 11 77 2186 298585476 298583347 0.000000e+00 3190.0
4 TraesCS3A01G217400 chr3D 94.737 38 2 0 19 56 298585506 298585469 3.110000e-05 60.2
5 TraesCS3A01G217400 chr3B 92.201 1436 48 21 707 2097 394089184 394087768 0.000000e+00 1973.0
6 TraesCS3A01G217400 chr3B 88.314 676 28 5 2221 2865 445588749 445589404 0.000000e+00 763.0
7 TraesCS3A01G217400 chr3B 95.070 426 20 1 280 705 394089904 394089480 0.000000e+00 669.0
8 TraesCS3A01G217400 chr3B 98.413 189 3 0 86 274 394090175 394089987 1.660000e-87 333.0
9 TraesCS3A01G217400 chr3B 100.000 32 0 0 2191 2222 481910506 481910537 3.110000e-05 60.2
10 TraesCS3A01G217400 chr2A 95.723 678 8 2 2218 2894 27958346 27959003 0.000000e+00 1072.0
11 TraesCS3A01G217400 chr4D 94.963 675 27 2 2221 2894 440251793 440252461 0.000000e+00 1051.0
12 TraesCS3A01G217400 chr2D 94.370 675 17 4 2221 2894 106288965 106288311 0.000000e+00 1016.0
13 TraesCS3A01G217400 chr2D 93.626 455 8 2 2255 2708 189704635 189704201 0.000000e+00 660.0
14 TraesCS3A01G217400 chr7D 94.540 641 12 3 2255 2894 624768767 624768149 0.000000e+00 968.0
15 TraesCS3A01G217400 chr7A 92.566 686 19 3 2221 2894 733955029 733955694 0.000000e+00 955.0
16 TraesCS3A01G217400 chr6D 91.869 701 24 11 2221 2894 167261560 167262254 0.000000e+00 948.0
17 TraesCS3A01G217400 chr5B 90.674 697 38 10 2221 2894 205446772 205447464 0.000000e+00 902.0
18 TraesCS3A01G217400 chr6B 90.182 713 33 16 2219 2894 566221734 566221022 0.000000e+00 894.0
19 TraesCS3A01G217400 chr6B 93.333 405 27 0 2490 2894 412459175 412459579 1.480000e-167 599.0
20 TraesCS3A01G217400 chr6B 88.785 428 27 11 2221 2627 412458824 412459251 3.330000e-139 505.0
21 TraesCS3A01G217400 chr1B 89.972 718 35 16 2212 2892 473828720 473828003 0.000000e+00 893.0
22 TraesCS3A01G217400 chrUn 91.888 641 11 3 2255 2894 26913364 26913964 0.000000e+00 857.0
23 TraesCS3A01G217400 chr6A 100.000 35 0 0 2214 2248 218956591 218956557 6.690000e-07 65.8
24 TraesCS3A01G217400 chr6A 100.000 35 0 0 2214 2248 552016273 552016239 6.690000e-07 65.8
25 TraesCS3A01G217400 chr5A 100.000 35 0 0 2214 2248 228816653 228816619 6.690000e-07 65.8


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 TraesCS3A01G217400 chr3A 396609382 396612275 2893 True 5345.000000 5345 100.000 1 2894 1 chr3A.!!$R3 2893
1 TraesCS3A01G217400 chr3D 298583347 298585506 2159 True 1625.100000 3190 94.315 19 2186 2 chr3D.!!$R1 2167
2 TraesCS3A01G217400 chr3B 394087768 394090175 2407 True 991.666667 1973 95.228 86 2097 3 chr3B.!!$R1 2011
3 TraesCS3A01G217400 chr3B 445588749 445589404 655 False 763.000000 763 88.314 2221 2865 1 chr3B.!!$F1 644
4 TraesCS3A01G217400 chr2A 27958346 27959003 657 False 1072.000000 1072 95.723 2218 2894 1 chr2A.!!$F1 676
5 TraesCS3A01G217400 chr4D 440251793 440252461 668 False 1051.000000 1051 94.963 2221 2894 1 chr4D.!!$F1 673
6 TraesCS3A01G217400 chr2D 106288311 106288965 654 True 1016.000000 1016 94.370 2221 2894 1 chr2D.!!$R1 673
7 TraesCS3A01G217400 chr7D 624768149 624768767 618 True 968.000000 968 94.540 2255 2894 1 chr7D.!!$R1 639
8 TraesCS3A01G217400 chr7A 733955029 733955694 665 False 955.000000 955 92.566 2221 2894 1 chr7A.!!$F1 673
9 TraesCS3A01G217400 chr6D 167261560 167262254 694 False 948.000000 948 91.869 2221 2894 1 chr6D.!!$F1 673
10 TraesCS3A01G217400 chr5B 205446772 205447464 692 False 902.000000 902 90.674 2221 2894 1 chr5B.!!$F1 673
11 TraesCS3A01G217400 chr6B 566221022 566221734 712 True 894.000000 894 90.182 2219 2894 1 chr6B.!!$R1 675
12 TraesCS3A01G217400 chr6B 412458824 412459579 755 False 552.000000 599 91.059 2221 2894 2 chr6B.!!$F1 673
13 TraesCS3A01G217400 chr1B 473828003 473828720 717 True 893.000000 893 89.972 2212 2892 1 chr1B.!!$R1 680
14 TraesCS3A01G217400 chrUn 26913364 26913964 600 False 857.000000 857 91.888 2255 2894 1 chrUn.!!$F1 639

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
76 77 0.036164 AAGTGTTGCGTGATAGGCCA 59.964 50.0 5.01 0.0 0.0 5.36 F
77 78 0.391661 AGTGTTGCGTGATAGGCCAG 60.392 55.0 5.01 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 1568 3.423154 CTGCAACCGCCTTCCGTC 61.423 66.667 0.00 0.00 37.32 4.79 R
1979 2412 3.753294 ATCCGGTAATGAGTCATGACC 57.247 47.619 25.16 25.16 40.98 4.02 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
17 18 2.046892 CACCGTCCTGAAGCCCTG 60.047 66.667 0.00 0.00 0.00 4.45
22 23 0.249073 CGTCCTGAAGCCCTGTATCG 60.249 60.000 0.00 0.00 0.00 2.92
25 26 2.103263 GTCCTGAAGCCCTGTATCGATT 59.897 50.000 1.71 0.00 0.00 3.34
56 57 4.390909 ACCGAGTAAAAATTAAGGCTGTCG 59.609 41.667 0.00 0.00 0.00 4.35
57 58 4.628333 CCGAGTAAAAATTAAGGCTGTCGA 59.372 41.667 0.00 0.00 0.00 4.20
58 59 5.121142 CCGAGTAAAAATTAAGGCTGTCGAA 59.879 40.000 0.00 0.00 0.00 3.71
59 60 6.241385 CGAGTAAAAATTAAGGCTGTCGAAG 58.759 40.000 0.00 0.00 0.00 3.79
60 61 6.128634 CGAGTAAAAATTAAGGCTGTCGAAGT 60.129 38.462 0.00 0.00 0.00 3.01
61 62 6.899114 AGTAAAAATTAAGGCTGTCGAAGTG 58.101 36.000 0.00 0.00 0.00 3.16
62 63 5.767816 AAAAATTAAGGCTGTCGAAGTGT 57.232 34.783 0.00 0.00 0.00 3.55
63 64 5.767816 AAAATTAAGGCTGTCGAAGTGTT 57.232 34.783 0.00 0.00 0.00 3.32
64 65 4.749245 AATTAAGGCTGTCGAAGTGTTG 57.251 40.909 0.00 0.00 0.00 3.33
65 66 1.508632 TAAGGCTGTCGAAGTGTTGC 58.491 50.000 0.00 0.00 0.00 4.17
66 67 1.498865 AAGGCTGTCGAAGTGTTGCG 61.499 55.000 0.00 0.00 0.00 4.85
67 68 2.244651 GGCTGTCGAAGTGTTGCGT 61.245 57.895 0.00 0.00 0.00 5.24
68 69 1.083401 GCTGTCGAAGTGTTGCGTG 60.083 57.895 0.00 0.00 0.00 5.34
69 70 1.487452 GCTGTCGAAGTGTTGCGTGA 61.487 55.000 0.00 0.00 0.00 4.35
70 71 1.139989 CTGTCGAAGTGTTGCGTGAT 58.860 50.000 0.00 0.00 0.00 3.06
71 72 2.324860 CTGTCGAAGTGTTGCGTGATA 58.675 47.619 0.00 0.00 0.00 2.15
72 73 2.324860 TGTCGAAGTGTTGCGTGATAG 58.675 47.619 0.00 0.00 0.00 2.08
73 74 1.654105 GTCGAAGTGTTGCGTGATAGG 59.346 52.381 0.00 0.00 0.00 2.57
74 75 0.370273 CGAAGTGTTGCGTGATAGGC 59.630 55.000 0.00 0.00 0.00 3.93
75 76 0.727398 GAAGTGTTGCGTGATAGGCC 59.273 55.000 0.00 0.00 0.00 5.19
76 77 0.036164 AAGTGTTGCGTGATAGGCCA 59.964 50.000 5.01 0.00 0.00 5.36
77 78 0.391661 AGTGTTGCGTGATAGGCCAG 60.392 55.000 5.01 0.00 0.00 4.85
78 79 1.078497 TGTTGCGTGATAGGCCAGG 60.078 57.895 5.01 0.00 0.00 4.45
79 80 2.124736 TTGCGTGATAGGCCAGGC 60.125 61.111 5.01 1.26 45.17 4.85
80 81 2.669133 TTGCGTGATAGGCCAGGCT 61.669 57.895 12.43 5.23 45.18 4.58
81 82 2.590007 GCGTGATAGGCCAGGCTG 60.590 66.667 12.43 7.75 42.63 4.85
82 83 2.903357 CGTGATAGGCCAGGCTGT 59.097 61.111 12.43 0.03 0.00 4.40
83 84 1.227380 CGTGATAGGCCAGGCTGTC 60.227 63.158 12.43 11.27 0.00 3.51
84 85 1.227380 GTGATAGGCCAGGCTGTCG 60.227 63.158 12.43 0.00 0.00 4.35
121 122 1.138036 CGCAACGTATGGGTCGAGA 59.862 57.895 0.00 0.00 37.22 4.04
145 146 4.559300 GCAAGGTAGCTTTGATTTTGCTGA 60.559 41.667 3.96 0.00 37.17 4.26
296 377 1.460504 GCTAGTAGTTTTGGTGCCCC 58.539 55.000 0.00 0.00 0.00 5.80
297 378 1.271707 GCTAGTAGTTTTGGTGCCCCA 60.272 52.381 0.00 0.00 39.65 4.96
299 380 1.923356 AGTAGTTTTGGTGCCCCATG 58.077 50.000 0.00 0.00 41.49 3.66
313 394 1.287739 CCCCATGCCTTTCCCTAAGAA 59.712 52.381 0.00 0.00 35.80 2.52
323 404 4.221482 CCTTTCCCTAAGAAAAAGCAGCAT 59.779 41.667 0.00 0.00 43.84 3.79
503 584 1.169577 ACAACACACGCAAAACCTCA 58.830 45.000 0.00 0.00 0.00 3.86
511 592 1.741145 ACGCAAAACCTCAAACTTCGT 59.259 42.857 0.00 0.00 0.00 3.85
514 595 2.357952 GCAAAACCTCAAACTTCGTCCT 59.642 45.455 0.00 0.00 0.00 3.85
543 624 1.101635 TGGACCTCATAGCTCGGTCG 61.102 60.000 14.45 0.00 46.35 4.79
720 1096 6.919775 ACTCCTAGCAGATATTTAATCCGT 57.080 37.500 0.00 0.00 0.00 4.69
944 1320 1.634702 CCGAGAAAGTAGCACTCAGC 58.365 55.000 0.00 0.00 46.19 4.26
972 1356 0.523757 GACTAGTCGCTGCCGTTCTC 60.524 60.000 7.22 0.00 35.54 2.87
1175 1568 2.003548 CTGGGAAGGGGAAGGGGAG 61.004 68.421 0.00 0.00 0.00 4.30
1235 1628 1.302511 GACGGAAGCCCAAGAAGCA 60.303 57.895 0.00 0.00 0.00 3.91
1242 1635 3.058160 CCCAAGAAGCAGGCCACG 61.058 66.667 5.01 0.00 0.00 4.94
1644 2061 3.739922 TCCGGTAGGGAGGACGTA 58.260 61.111 0.00 0.00 40.94 3.57
1650 2067 0.745845 GTAGGGAGGACGTAGACGCA 60.746 60.000 1.14 0.00 44.43 5.24
1971 2404 5.871524 AGTCTGCGCTATGATTATGGTATTG 59.128 40.000 9.73 0.00 0.00 1.90
1979 2412 8.058328 CGCTATGATTATGGTATTGATTTAGCG 58.942 37.037 0.00 0.00 42.44 4.26
2112 2557 1.614413 GGTCCGAGGACTCATATGGAC 59.386 57.143 20.27 12.78 44.04 4.02
2113 2558 2.307768 GTCCGAGGACTCATATGGACA 58.692 52.381 14.61 0.00 44.10 4.02
2116 2561 2.035193 CCGAGGACTCATATGGACACAG 59.965 54.545 2.13 0.00 0.00 3.66
2127 2572 0.608130 TGGACACAGATCCCTTGACG 59.392 55.000 0.00 0.00 38.06 4.35
2132 2577 2.492484 ACACAGATCCCTTGACGTACTC 59.508 50.000 0.00 0.00 0.00 2.59
2133 2578 2.755655 CACAGATCCCTTGACGTACTCT 59.244 50.000 0.00 0.00 0.00 3.24
2144 2589 2.165641 TGACGTACTCTAGGTGCCATTG 59.834 50.000 0.00 0.00 0.00 2.82
2148 2593 0.912486 ACTCTAGGTGCCATTGGTCC 59.088 55.000 4.26 7.65 0.00 4.46
2151 2596 0.620556 CTAGGTGCCATTGGTCCACT 59.379 55.000 17.04 8.48 0.00 4.00
2154 2599 1.244019 GGTGCCATTGGTCCACTGAC 61.244 60.000 10.72 0.00 40.98 3.51
2162 2607 1.741770 GGTCCACTGACATGTCGGC 60.742 63.158 30.48 16.19 43.65 5.54
2173 2619 2.143419 ATGTCGGCCCAGGATCCTC 61.143 63.158 12.69 0.00 0.00 3.71
2179 2625 2.134287 GCCCAGGATCCTCGTAGCA 61.134 63.158 12.69 0.00 0.00 3.49
2186 2632 3.006323 CAGGATCCTCGTAGCAAAGCTAT 59.994 47.826 12.69 0.00 43.30 2.97
2187 2633 4.218635 CAGGATCCTCGTAGCAAAGCTATA 59.781 45.833 12.69 0.00 43.30 1.31
2188 2634 5.020132 AGGATCCTCGTAGCAAAGCTATAT 58.980 41.667 9.02 0.00 43.30 0.86
2189 2635 6.095580 CAGGATCCTCGTAGCAAAGCTATATA 59.904 42.308 12.69 0.00 43.30 0.86
2190 2636 6.663953 AGGATCCTCGTAGCAAAGCTATATAA 59.336 38.462 9.02 0.00 43.30 0.98
2191 2637 6.975772 GGATCCTCGTAGCAAAGCTATATAAG 59.024 42.308 3.84 0.00 43.30 1.73
2192 2638 6.268825 TCCTCGTAGCAAAGCTATATAAGG 57.731 41.667 1.68 7.15 43.30 2.69
2193 2639 4.865365 CCTCGTAGCAAAGCTATATAAGGC 59.135 45.833 1.68 0.00 43.30 4.35
2194 2640 5.336849 CCTCGTAGCAAAGCTATATAAGGCT 60.337 44.000 1.68 0.00 43.30 4.58
2195 2641 5.470368 TCGTAGCAAAGCTATATAAGGCTG 58.530 41.667 1.68 0.00 43.30 4.85
2196 2642 4.627467 CGTAGCAAAGCTATATAAGGCTGG 59.373 45.833 1.68 2.24 43.30 4.85
2197 2643 3.416156 AGCAAAGCTATATAAGGCTGGC 58.584 45.455 13.93 13.93 36.99 4.85
2198 2644 2.489722 GCAAAGCTATATAAGGCTGGCC 59.510 50.000 3.00 3.00 38.91 5.36
2199 2645 3.754965 CAAAGCTATATAAGGCTGGCCA 58.245 45.455 14.39 4.71 38.91 5.36
2200 2646 4.338879 CAAAGCTATATAAGGCTGGCCAT 58.661 43.478 5.51 4.39 38.91 4.40
2201 2647 5.500234 CAAAGCTATATAAGGCTGGCCATA 58.500 41.667 5.51 6.71 38.91 2.74
2202 2648 5.365021 AAGCTATATAAGGCTGGCCATAG 57.635 43.478 5.51 12.06 38.91 2.23
2203 2649 3.135530 AGCTATATAAGGCTGGCCATAGC 59.864 47.826 22.91 22.91 41.14 2.97
2204 2650 2.698855 ATATAAGGCTGGCCATAGCG 57.301 50.000 5.51 0.00 44.60 4.26
2205 2651 0.613260 TATAAGGCTGGCCATAGCGG 59.387 55.000 5.51 0.00 44.60 5.52
2206 2652 2.129555 ATAAGGCTGGCCATAGCGGG 62.130 60.000 5.51 0.00 44.60 6.13
2209 2655 3.556306 GCTGGCCATAGCGGGGTA 61.556 66.667 5.51 0.00 41.24 3.69
2210 2656 3.114825 GCTGGCCATAGCGGGGTAA 62.115 63.158 5.51 0.00 41.24 2.85
2211 2657 1.227853 CTGGCCATAGCGGGGTAAC 60.228 63.158 5.51 0.00 41.24 2.50
2212 2658 1.978455 CTGGCCATAGCGGGGTAACA 61.978 60.000 5.51 0.00 41.24 2.41
2213 2659 1.349542 TGGCCATAGCGGGGTAACAT 61.350 55.000 0.00 0.00 41.24 2.71
2214 2660 0.688487 GGCCATAGCGGGGTAACATA 59.312 55.000 0.00 0.00 41.24 2.29
2215 2661 1.072648 GGCCATAGCGGGGTAACATAA 59.927 52.381 0.00 0.00 41.24 1.90
2216 2662 2.148768 GCCATAGCGGGGTAACATAAC 58.851 52.381 0.00 0.00 39.74 1.89
2232 2678 4.864726 ACATAACTAGTACTCCCTCCGTT 58.135 43.478 0.00 0.00 0.00 4.44
2276 2722 3.573967 ACATTTTGCGAAAATCACCTCCT 59.426 39.130 2.54 0.00 38.97 3.69
2421 3018 3.283812 TTCTCCCCCTCGTCTCGCT 62.284 63.158 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.105039 GATACAGGGCTTCAGGACGG 59.895 60.000 0.00 0.00 0.00 4.79
3 4 0.249073 CGATACAGGGCTTCAGGACG 60.249 60.000 0.00 0.00 0.00 4.79
4 5 1.112113 TCGATACAGGGCTTCAGGAC 58.888 55.000 0.00 0.00 0.00 3.85
5 6 2.088104 ATCGATACAGGGCTTCAGGA 57.912 50.000 0.00 0.00 0.00 3.86
6 7 2.918712 AATCGATACAGGGCTTCAGG 57.081 50.000 0.00 0.00 0.00 3.86
7 8 5.201713 TCTTAATCGATACAGGGCTTCAG 57.798 43.478 0.00 0.00 0.00 3.02
9 10 6.920569 TTTTCTTAATCGATACAGGGCTTC 57.079 37.500 0.00 0.00 0.00 3.86
10 11 6.095021 GGTTTTTCTTAATCGATACAGGGCTT 59.905 38.462 0.00 0.00 0.00 4.35
11 12 5.589050 GGTTTTTCTTAATCGATACAGGGCT 59.411 40.000 0.00 0.00 0.00 5.19
12 13 5.503520 CGGTTTTTCTTAATCGATACAGGGC 60.504 44.000 0.00 0.00 33.57 5.19
13 14 5.813672 TCGGTTTTTCTTAATCGATACAGGG 59.186 40.000 0.00 0.00 35.86 4.45
14 15 6.534079 ACTCGGTTTTTCTTAATCGATACAGG 59.466 38.462 0.00 0.00 39.64 4.00
15 16 7.521509 ACTCGGTTTTTCTTAATCGATACAG 57.478 36.000 0.00 0.00 39.64 2.74
16 17 8.984891 TTACTCGGTTTTTCTTAATCGATACA 57.015 30.769 0.00 0.00 39.64 2.29
25 26 9.681692 GCCTTAATTTTTACTCGGTTTTTCTTA 57.318 29.630 0.00 0.00 0.00 2.10
56 57 0.727398 GGCCTATCACGCAACACTTC 59.273 55.000 0.00 0.00 0.00 3.01
57 58 0.036164 TGGCCTATCACGCAACACTT 59.964 50.000 3.32 0.00 0.00 3.16
58 59 0.391661 CTGGCCTATCACGCAACACT 60.392 55.000 3.32 0.00 0.00 3.55
59 60 1.369091 CCTGGCCTATCACGCAACAC 61.369 60.000 3.32 0.00 0.00 3.32
60 61 1.078497 CCTGGCCTATCACGCAACA 60.078 57.895 3.32 0.00 0.00 3.33
61 62 2.472909 GCCTGGCCTATCACGCAAC 61.473 63.158 7.66 0.00 0.00 4.17
62 63 2.124736 GCCTGGCCTATCACGCAA 60.125 61.111 7.66 0.00 0.00 4.85
63 64 3.083349 AGCCTGGCCTATCACGCA 61.083 61.111 16.57 0.00 0.00 5.24
64 65 2.590007 CAGCCTGGCCTATCACGC 60.590 66.667 16.57 0.00 0.00 5.34
65 66 1.227380 GACAGCCTGGCCTATCACG 60.227 63.158 16.57 0.00 0.00 4.35
66 67 1.227380 CGACAGCCTGGCCTATCAC 60.227 63.158 16.57 0.61 0.00 3.06
67 68 0.975556 TTCGACAGCCTGGCCTATCA 60.976 55.000 16.57 0.00 0.00 2.15
68 69 0.249657 CTTCGACAGCCTGGCCTATC 60.250 60.000 16.57 9.64 0.00 2.08
69 70 0.978146 ACTTCGACAGCCTGGCCTAT 60.978 55.000 16.57 0.00 0.00 2.57
70 71 1.609501 ACTTCGACAGCCTGGCCTA 60.610 57.895 16.57 0.00 0.00 3.93
71 72 2.925170 ACTTCGACAGCCTGGCCT 60.925 61.111 16.57 0.00 0.00 5.19
72 73 2.743928 CACTTCGACAGCCTGGCC 60.744 66.667 16.57 0.00 0.00 5.36
73 74 1.598130 AACACTTCGACAGCCTGGC 60.598 57.895 11.65 11.65 0.00 4.85
74 75 1.845809 GCAACACTTCGACAGCCTGG 61.846 60.000 0.00 0.00 0.00 4.45
75 76 1.571460 GCAACACTTCGACAGCCTG 59.429 57.895 0.00 0.00 0.00 4.85
76 77 1.956170 CGCAACACTTCGACAGCCT 60.956 57.895 0.00 0.00 0.00 4.58
77 78 2.244651 ACGCAACACTTCGACAGCC 61.245 57.895 0.00 0.00 0.00 4.85
78 79 1.083401 CACGCAACACTTCGACAGC 60.083 57.895 0.00 0.00 0.00 4.40
79 80 1.139989 ATCACGCAACACTTCGACAG 58.860 50.000 0.00 0.00 0.00 3.51
80 81 2.324860 CTATCACGCAACACTTCGACA 58.675 47.619 0.00 0.00 0.00 4.35
81 82 1.654105 CCTATCACGCAACACTTCGAC 59.346 52.381 0.00 0.00 0.00 4.20
82 83 1.990799 CCTATCACGCAACACTTCGA 58.009 50.000 0.00 0.00 0.00 3.71
83 84 0.370273 GCCTATCACGCAACACTTCG 59.630 55.000 0.00 0.00 0.00 3.79
84 85 0.727398 GGCCTATCACGCAACACTTC 59.273 55.000 0.00 0.00 0.00 3.01
121 122 3.575687 AGCAAAATCAAAGCTACCTTGCT 59.424 39.130 10.73 10.73 46.40 3.91
145 146 2.076863 GCATTGCGACTTCCTACTTGT 58.923 47.619 0.00 0.00 0.00 3.16
296 377 4.021192 TGCTTTTTCTTAGGGAAAGGCATG 60.021 41.667 10.87 0.00 43.68 4.06
297 378 4.159557 TGCTTTTTCTTAGGGAAAGGCAT 58.840 39.130 10.87 0.00 43.68 4.40
299 380 3.615110 GCTGCTTTTTCTTAGGGAAAGGC 60.615 47.826 5.83 5.83 43.68 4.35
313 394 1.669999 GCCCCATCGATGCTGCTTTT 61.670 55.000 20.25 0.00 0.00 2.27
511 592 2.225267 TGAGGTCCACATGTCTGTAGGA 60.225 50.000 0.00 0.00 33.14 2.94
514 595 3.384789 GCTATGAGGTCCACATGTCTGTA 59.615 47.826 11.71 0.00 33.14 2.74
543 624 3.302347 CTCACTGAGACGTGGGCCC 62.302 68.421 17.59 17.59 35.63 5.80
662 743 6.533367 GCCAGTAAGAGAAGAGATTTGTACTG 59.467 42.308 0.00 0.00 37.83 2.74
944 1320 2.788407 GCAGCGACTAGTCTCAGTTACG 60.788 54.545 20.34 6.64 0.00 3.18
948 1324 1.649390 CGGCAGCGACTAGTCTCAGT 61.649 60.000 20.34 0.00 0.00 3.41
992 1376 3.688049 TCCTCTCCATCATACACCAGA 57.312 47.619 0.00 0.00 0.00 3.86
993 1377 3.070734 CCTTCCTCTCCATCATACACCAG 59.929 52.174 0.00 0.00 0.00 4.00
1155 1548 4.115199 CCCTTCCCCTTCCCAGCG 62.115 72.222 0.00 0.00 0.00 5.18
1175 1568 3.423154 CTGCAACCGCCTTCCGTC 61.423 66.667 0.00 0.00 37.32 4.79
1206 1599 4.772231 TTCCGTCCCCTCCTCCCG 62.772 72.222 0.00 0.00 0.00 5.14
1472 1889 4.373116 CCGTCACCCAGGACACCG 62.373 72.222 0.00 0.00 37.66 4.94
1643 2060 4.175337 GGGCCATGGCTGCGTCTA 62.175 66.667 34.70 0.00 41.60 2.59
1971 2404 5.177696 GGTAATGAGTCATGACCGCTAAATC 59.822 44.000 21.80 11.61 35.85 2.17
1979 2412 3.753294 ATCCGGTAATGAGTCATGACC 57.247 47.619 25.16 25.16 40.98 4.02
2028 2461 8.052141 TCTACCCCTCTTCTTAAACTACTCTAC 58.948 40.741 0.00 0.00 0.00 2.59
2029 2462 8.167691 TCTACCCCTCTTCTTAAACTACTCTA 57.832 38.462 0.00 0.00 0.00 2.43
2036 2469 5.104900 TGCATCTCTACCCCTCTTCTTAAAC 60.105 44.000 0.00 0.00 0.00 2.01
2112 2557 2.755655 AGAGTACGTCAAGGGATCTGTG 59.244 50.000 0.00 0.00 0.00 3.66
2113 2558 3.088789 AGAGTACGTCAAGGGATCTGT 57.911 47.619 0.00 0.00 0.00 3.41
2116 2561 3.315749 CACCTAGAGTACGTCAAGGGATC 59.684 52.174 0.00 0.00 0.00 3.36
2127 2572 2.158943 GGACCAATGGCACCTAGAGTAC 60.159 54.545 0.00 0.00 0.00 2.73
2132 2577 0.620556 AGTGGACCAATGGCACCTAG 59.379 55.000 15.06 0.00 0.00 3.02
2133 2578 0.327924 CAGTGGACCAATGGCACCTA 59.672 55.000 14.24 2.25 0.00 3.08
2144 2589 1.741770 GCCGACATGTCAGTGGACC 60.742 63.158 24.93 3.81 43.65 4.46
2148 2593 1.742880 CTGGGCCGACATGTCAGTG 60.743 63.158 24.93 13.59 0.00 3.66
2151 2596 1.971505 GATCCTGGGCCGACATGTCA 61.972 60.000 24.93 5.36 0.00 3.58
2154 2599 2.111878 GGATCCTGGGCCGACATG 59.888 66.667 3.84 0.00 0.00 3.21
2162 2607 0.830648 TTTGCTACGAGGATCCTGGG 59.169 55.000 25.63 16.64 0.00 4.45
2173 2619 4.627467 CCAGCCTTATATAGCTTTGCTACG 59.373 45.833 0.00 0.00 44.24 3.51
2179 2625 4.664688 ATGGCCAGCCTTATATAGCTTT 57.335 40.909 13.05 0.00 37.18 3.51
2186 2632 0.613260 CCGCTATGGCCAGCCTTATA 59.387 55.000 13.05 0.00 38.37 0.98
2187 2633 1.376466 CCGCTATGGCCAGCCTTAT 59.624 57.895 13.05 0.00 38.37 1.73
2188 2634 2.818169 CCCGCTATGGCCAGCCTTA 61.818 63.158 13.05 7.16 38.37 2.69
2189 2635 4.195334 CCCGCTATGGCCAGCCTT 62.195 66.667 13.05 6.25 38.37 4.35
2192 2638 3.114825 TTACCCCGCTATGGCCAGC 62.115 63.158 13.05 9.59 38.23 4.85
2193 2639 1.227853 GTTACCCCGCTATGGCCAG 60.228 63.158 13.05 0.00 35.87 4.85
2194 2640 1.349542 ATGTTACCCCGCTATGGCCA 61.350 55.000 8.56 8.56 35.87 5.36
2195 2641 0.688487 TATGTTACCCCGCTATGGCC 59.312 55.000 0.00 0.00 35.87 5.36
2196 2642 2.148768 GTTATGTTACCCCGCTATGGC 58.851 52.381 0.00 0.00 35.87 4.40
2197 2643 3.764237 AGTTATGTTACCCCGCTATGG 57.236 47.619 0.00 0.00 37.55 2.74
2198 2644 5.464030 ACTAGTTATGTTACCCCGCTATG 57.536 43.478 0.00 0.00 0.00 2.23
2199 2645 6.310149 AGTACTAGTTATGTTACCCCGCTAT 58.690 40.000 0.00 0.00 0.00 2.97
2200 2646 5.694995 AGTACTAGTTATGTTACCCCGCTA 58.305 41.667 0.00 0.00 0.00 4.26
2201 2647 4.540715 AGTACTAGTTATGTTACCCCGCT 58.459 43.478 0.00 0.00 0.00 5.52
2202 2648 4.261783 GGAGTACTAGTTATGTTACCCCGC 60.262 50.000 0.00 0.00 0.00 6.13
2203 2649 4.279420 GGGAGTACTAGTTATGTTACCCCG 59.721 50.000 0.00 0.00 0.00 5.73
2204 2650 5.462240 AGGGAGTACTAGTTATGTTACCCC 58.538 45.833 0.00 5.32 34.77 4.95
2205 2651 5.538053 GGAGGGAGTACTAGTTATGTTACCC 59.462 48.000 0.00 5.39 0.00 3.69
2206 2652 5.240403 CGGAGGGAGTACTAGTTATGTTACC 59.760 48.000 0.00 0.00 0.00 2.85
2207 2653 5.825151 ACGGAGGGAGTACTAGTTATGTTAC 59.175 44.000 0.00 0.00 0.00 2.50
2208 2654 6.006275 ACGGAGGGAGTACTAGTTATGTTA 57.994 41.667 0.00 0.00 0.00 2.41
2209 2655 4.864726 ACGGAGGGAGTACTAGTTATGTT 58.135 43.478 0.00 0.00 0.00 2.71
2210 2656 4.516652 ACGGAGGGAGTACTAGTTATGT 57.483 45.455 0.00 0.00 0.00 2.29
2211 2657 4.024218 CGAACGGAGGGAGTACTAGTTATG 60.024 50.000 0.00 0.00 0.00 1.90
2212 2658 4.133078 CGAACGGAGGGAGTACTAGTTAT 58.867 47.826 0.00 0.00 0.00 1.89
2213 2659 3.535561 CGAACGGAGGGAGTACTAGTTA 58.464 50.000 0.00 0.00 0.00 2.24
2214 2660 2.363683 CGAACGGAGGGAGTACTAGTT 58.636 52.381 0.00 0.00 0.00 2.24
2215 2661 1.407989 CCGAACGGAGGGAGTACTAGT 60.408 57.143 7.53 0.00 37.50 2.57
2216 2662 1.307097 CCGAACGGAGGGAGTACTAG 58.693 60.000 7.53 0.00 37.50 2.57
2276 2722 2.608752 GCGTAGTTTGTCGGGAGAAAGA 60.609 50.000 0.00 0.00 42.89 2.52
2790 3516 6.042093 TCACCTGTAAATTCAGAAGACAGACT 59.958 38.462 18.11 5.95 39.94 3.24


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

AutoCloner maintained by Alex Coulton.