Multiple sequence alignment - TraesCS4B01G142500

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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 TraesCS4B01G142500 chr4B 100.000 2732 0 0 1 2732 188212759 188210028 0.000000e+00 5046.0
1 TraesCS4B01G142500 chr4B 94.737 38 2 0 111 148 28630728 28630691 2.940000e-05 60.2
2 TraesCS4B01G142500 chr4B 94.595 37 0 2 106 142 530463217 530463251 3.800000e-04 56.5
3 TraesCS4B01G142500 chr4D 89.572 2618 101 77 144 2663 124600946 124598403 0.000000e+00 3164.0
4 TraesCS4B01G142500 chr4D 95.588 68 3 0 2665 2732 124598338 124598271 2.880000e-20 110.0
5 TraesCS4B01G142500 chr4A 88.770 2155 79 59 469 2556 446070968 446073026 0.000000e+00 2488.0
6 TraesCS4B01G142500 chr4A 90.157 254 15 8 144 389 446069069 446069320 3.390000e-84 322.0
7 TraesCS4B01G142500 chr4A 95.775 71 3 0 2662 2732 446073431 446073501 6.180000e-22 115.0
8 TraesCS4B01G142500 chr4A 85.714 112 8 3 2 113 446068966 446069069 8.000000e-21 111.0
9 TraesCS4B01G142500 chr4A 90.698 43 3 1 106 148 596062788 596062747 3.800000e-04 56.5
10 TraesCS4B01G142500 chr2B 100.000 32 0 0 111 142 531562858 531562889 2.940000e-05 60.2
11 TraesCS4B01G142500 chr1A 94.737 38 2 0 111 148 342385646 342385683 2.940000e-05 60.2
12 TraesCS4B01G142500 chr7A 92.683 41 2 1 108 148 696538846 696538807 1.060000e-04 58.4
13 TraesCS4B01G142500 chr5B 94.595 37 1 1 106 142 501963937 501963972 3.800000e-04 56.5
14 TraesCS4B01G142500 chr5B 92.500 40 2 1 109 148 654147622 654147660 3.800000e-04 56.5
15 TraesCS4B01G142500 chr1B 94.595 37 1 1 107 142 642731958 642731994 3.800000e-04 56.5


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 TraesCS4B01G142500 chr4B 188210028 188212759 2731 True 5046 5046 100.000 1 2732 1 chr4B.!!$R2 2731
1 TraesCS4B01G142500 chr4D 124598271 124600946 2675 True 1637 3164 92.580 144 2732 2 chr4D.!!$R1 2588
2 TraesCS4B01G142500 chr4A 446068966 446073501 4535 False 759 2488 90.104 2 2732 4 chr4A.!!$F1 2730

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
439 1415 0.034863 GAGAGGAGAGGTGAGACCGT 60.035 60.0 0.0 0.0 44.9 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 3444 1.069204 GGAACACTGACTGACTCTGCA 59.931 52.381 0.0 0.0 0.0 4.41 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
51 52 3.862845 GTCAATTTTGGCGTCAGTTTTGT 59.137 39.130 0.00 0.00 0.00 2.83
52 53 5.038033 GTCAATTTTGGCGTCAGTTTTGTA 58.962 37.500 0.00 0.00 0.00 2.41
53 54 5.038033 TCAATTTTGGCGTCAGTTTTGTAC 58.962 37.500 0.00 0.00 0.00 2.90
54 55 4.911514 ATTTTGGCGTCAGTTTTGTACT 57.088 36.364 0.00 0.00 37.68 2.73
55 56 6.038382 TCAATTTTGGCGTCAGTTTTGTACTA 59.962 34.615 0.00 0.00 34.56 1.82
56 57 4.799419 TTTGGCGTCAGTTTTGTACTAC 57.201 40.909 0.00 0.00 34.56 2.73
89 90 0.840617 GAGAATCTTGGACCTCCCCC 59.159 60.000 0.00 0.00 34.29 5.40
98 99 2.863988 ACCTCCCCCAACCCCAAG 60.864 66.667 0.00 0.00 0.00 3.61
112 113 2.107552 ACCCCAAGGATCGAAAACTTGA 59.892 45.455 21.42 0.00 43.13 3.02
113 114 2.749621 CCCCAAGGATCGAAAACTTGAG 59.250 50.000 21.42 12.64 43.13 3.02
114 115 2.749621 CCCAAGGATCGAAAACTTGAGG 59.250 50.000 21.42 17.43 43.13 3.86
115 116 2.162408 CCAAGGATCGAAAACTTGAGGC 59.838 50.000 21.42 0.00 43.13 4.70
116 117 3.077359 CAAGGATCGAAAACTTGAGGCT 58.923 45.455 17.20 0.00 43.13 4.58
117 118 2.704572 AGGATCGAAAACTTGAGGCTG 58.295 47.619 0.00 0.00 0.00 4.85
118 119 1.740025 GGATCGAAAACTTGAGGCTGG 59.260 52.381 0.00 0.00 0.00 4.85
119 120 2.427506 GATCGAAAACTTGAGGCTGGT 58.572 47.619 0.00 0.00 0.00 4.00
120 121 1.878953 TCGAAAACTTGAGGCTGGTC 58.121 50.000 0.00 0.00 0.00 4.02
121 122 1.140052 TCGAAAACTTGAGGCTGGTCA 59.860 47.619 0.00 0.00 0.00 4.02
122 123 1.264288 CGAAAACTTGAGGCTGGTCAC 59.736 52.381 0.00 0.00 0.00 3.67
123 124 2.297701 GAAAACTTGAGGCTGGTCACA 58.702 47.619 0.00 0.00 0.00 3.58
125 126 0.839946 AACTTGAGGCTGGTCACAGT 59.160 50.000 0.00 0.00 46.62 3.55
126 127 0.107456 ACTTGAGGCTGGTCACAGTG 59.893 55.000 0.00 0.00 46.62 3.66
127 128 0.604780 CTTGAGGCTGGTCACAGTGG 60.605 60.000 0.00 0.00 46.62 4.00
128 129 2.055689 TTGAGGCTGGTCACAGTGGG 62.056 60.000 0.00 0.00 46.62 4.61
129 130 3.252284 AGGCTGGTCACAGTGGGG 61.252 66.667 0.00 0.00 46.62 4.96
130 131 3.249189 GGCTGGTCACAGTGGGGA 61.249 66.667 0.00 0.00 46.62 4.81
131 132 2.348998 GCTGGTCACAGTGGGGAG 59.651 66.667 0.00 0.00 46.62 4.30
132 133 3.072476 CTGGTCACAGTGGGGAGG 58.928 66.667 0.00 0.00 39.92 4.30
133 134 1.536418 CTGGTCACAGTGGGGAGGA 60.536 63.158 0.00 0.00 39.92 3.71
134 135 1.074090 TGGTCACAGTGGGGAGGAA 60.074 57.895 0.00 0.00 0.00 3.36
135 136 1.375326 GGTCACAGTGGGGAGGAAC 59.625 63.158 0.00 0.00 0.00 3.62
137 138 0.765510 GTCACAGTGGGGAGGAACTT 59.234 55.000 0.00 0.00 41.55 2.66
138 139 1.975680 GTCACAGTGGGGAGGAACTTA 59.024 52.381 0.00 0.00 41.55 2.24
139 140 2.028020 GTCACAGTGGGGAGGAACTTAG 60.028 54.545 0.00 0.00 41.55 2.18
140 141 2.158219 TCACAGTGGGGAGGAACTTAGA 60.158 50.000 0.00 0.00 41.55 2.10
141 142 2.637872 CACAGTGGGGAGGAACTTAGAA 59.362 50.000 0.00 0.00 41.55 2.10
142 143 3.072476 CACAGTGGGGAGGAACTTAGAAA 59.928 47.826 0.00 0.00 41.55 2.52
158 159 3.884318 AAAAACAAGGCCGGCCAT 58.116 50.000 45.13 34.11 38.92 4.40
164 166 2.117206 AAGGCCGGCCATCAACAA 59.883 55.556 45.13 0.00 38.92 2.83
175 177 1.229428 CATCAACAACAGCACGGTCT 58.771 50.000 0.00 0.00 0.00 3.85
202 204 5.246656 TCAGAAAACAATTCCAAGGCATCAT 59.753 36.000 0.00 0.00 0.00 2.45
260 277 2.615912 GGTCACCTAAGCTGATGAATGC 59.384 50.000 0.00 0.00 0.00 3.56
301 318 5.886474 CAGGTCCCTCTTTATTTTAAGGTCC 59.114 44.000 0.00 0.00 0.00 4.46
308 325 7.337184 CCCTCTTTATTTTAAGGTCCTTCTCAC 59.663 40.741 7.61 0.00 0.00 3.51
319 336 1.996291 TCCTTCTCACTCCCTCTCTCA 59.004 52.381 0.00 0.00 0.00 3.27
320 337 2.025416 TCCTTCTCACTCCCTCTCTCAG 60.025 54.545 0.00 0.00 0.00 3.35
389 407 0.037326 CCCTCACACACGCACATACT 60.037 55.000 0.00 0.00 0.00 2.12
390 408 1.203758 CCCTCACACACGCACATACTA 59.796 52.381 0.00 0.00 0.00 1.82
391 409 2.530177 CCTCACACACGCACATACTAG 58.470 52.381 0.00 0.00 0.00 2.57
395 413 3.502979 TCACACACGCACATACTAGTACA 59.497 43.478 4.31 0.00 0.00 2.90
396 414 3.606777 CACACACGCACATACTAGTACAC 59.393 47.826 4.31 0.00 0.00 2.90
397 415 3.253921 ACACACGCACATACTAGTACACA 59.746 43.478 4.31 0.00 0.00 3.72
398 416 3.606777 CACACGCACATACTAGTACACAC 59.393 47.826 4.31 0.00 0.00 3.82
399 417 3.253921 ACACGCACATACTAGTACACACA 59.746 43.478 4.31 0.00 0.00 3.72
425 1401 1.133792 GTGAGGAGAGGAGAGGAGAGG 60.134 61.905 0.00 0.00 0.00 3.69
429 1405 1.421646 GGAGAGGAGAGGAGAGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
436 1412 1.564348 AGAGGAGAGGAGAGGTGAGAC 59.436 57.143 0.00 0.00 0.00 3.36
438 1414 0.750182 GGAGAGGAGAGGTGAGACCG 60.750 65.000 0.00 0.00 44.90 4.79
439 1415 0.034863 GAGAGGAGAGGTGAGACCGT 60.035 60.000 0.00 0.00 44.90 4.83
440 1416 0.322997 AGAGGAGAGGTGAGACCGTG 60.323 60.000 0.00 0.00 44.90 4.94
442 1418 0.322997 AGGAGAGGTGAGACCGTGAG 60.323 60.000 0.00 0.00 44.90 3.51
443 1419 0.322636 GGAGAGGTGAGACCGTGAGA 60.323 60.000 0.00 0.00 44.90 3.27
444 1420 1.091537 GAGAGGTGAGACCGTGAGAG 58.908 60.000 0.00 0.00 44.90 3.20
445 1421 0.402504 AGAGGTGAGACCGTGAGAGT 59.597 55.000 0.00 0.00 44.90 3.24
446 1422 0.806241 GAGGTGAGACCGTGAGAGTC 59.194 60.000 0.00 0.00 44.90 3.36
458 2062 0.178973 TGAGAGTCCCACGAGAACCA 60.179 55.000 0.00 0.00 0.00 3.67
461 2065 0.244178 GAGTCCCACGAGAACCACTC 59.756 60.000 0.00 0.00 41.79 3.51
462 2066 1.186267 AGTCCCACGAGAACCACTCC 61.186 60.000 0.00 0.00 42.18 3.85
463 2067 1.911766 TCCCACGAGAACCACTCCC 60.912 63.158 0.00 0.00 42.18 4.30
464 2068 2.214216 CCCACGAGAACCACTCCCA 61.214 63.158 0.00 0.00 42.18 4.37
465 2069 1.553690 CCCACGAGAACCACTCCCAT 61.554 60.000 0.00 0.00 42.18 4.00
466 2070 0.324943 CCACGAGAACCACTCCCATT 59.675 55.000 0.00 0.00 42.18 3.16
467 2071 1.676014 CCACGAGAACCACTCCCATTC 60.676 57.143 0.00 0.00 42.18 2.67
545 2149 2.962569 GCCCCGTGCTTTCCTTTC 59.037 61.111 0.00 0.00 36.87 2.62
546 2150 2.636412 GCCCCGTGCTTTCCTTTCC 61.636 63.158 0.00 0.00 36.87 3.13
662 2297 1.896465 CTCCCCTTCAGTTCGAGTCTT 59.104 52.381 0.00 0.00 0.00 3.01
664 2299 1.896465 CCCCTTCAGTTCGAGTCTTCT 59.104 52.381 0.00 0.00 0.00 2.85
723 2361 4.162131 GCTCATCCTCTCCTTCTTCTTCTT 59.838 45.833 0.00 0.00 0.00 2.52
724 2362 5.682212 GCTCATCCTCTCCTTCTTCTTCTTC 60.682 48.000 0.00 0.00 0.00 2.87
725 2363 5.588845 TCATCCTCTCCTTCTTCTTCTTCT 58.411 41.667 0.00 0.00 0.00 2.85
726 2364 5.656416 TCATCCTCTCCTTCTTCTTCTTCTC 59.344 44.000 0.00 0.00 0.00 2.87
727 2365 4.349365 TCCTCTCCTTCTTCTTCTTCTCC 58.651 47.826 0.00 0.00 0.00 3.71
728 2366 4.045334 TCCTCTCCTTCTTCTTCTTCTCCT 59.955 45.833 0.00 0.00 0.00 3.69
775 2413 0.250234 TGATTGACTCCTTGCCTCCG 59.750 55.000 0.00 0.00 0.00 4.63
781 2419 2.683933 TCCTTGCCTCCGACTCCC 60.684 66.667 0.00 0.00 0.00 4.30
790 2428 1.304217 TCCGACTCCCCACTCACTC 60.304 63.158 0.00 0.00 0.00 3.51
802 2440 1.131638 ACTCACTCTTCTTGGTGGCA 58.868 50.000 0.00 0.00 34.57 4.92
803 2441 1.071385 ACTCACTCTTCTTGGTGGCAG 59.929 52.381 0.00 0.00 34.57 4.85
822 2460 4.153296 GGCAGAGCTTCTTCTTTCTGTTAC 59.847 45.833 0.00 0.00 39.33 2.50
830 2468 4.049186 TCTTCTTTCTGTTACGTGTCAGC 58.951 43.478 14.21 0.00 0.00 4.26
834 2472 3.728076 TTCTGTTACGTGTCAGCTTCT 57.272 42.857 14.21 0.00 0.00 2.85
837 2475 2.731976 CTGTTACGTGTCAGCTTCTTCC 59.268 50.000 0.00 0.00 0.00 3.46
868 2506 4.495422 GTCCGAGCTTTCTAGATTCAACA 58.505 43.478 0.00 0.00 0.00 3.33
873 2511 4.764172 AGCTTTCTAGATTCAACATCGCT 58.236 39.130 0.00 0.00 0.00 4.93
878 2516 4.115516 TCTAGATTCAACATCGCTTCTGC 58.884 43.478 0.00 0.00 0.00 4.26
950 2589 2.028839 TGAATCCGAGTTAGTTTGCCGA 60.029 45.455 0.00 0.00 0.00 5.54
951 2590 2.005971 ATCCGAGTTAGTTTGCCGAC 57.994 50.000 0.00 0.00 0.00 4.79
952 2591 0.963962 TCCGAGTTAGTTTGCCGACT 59.036 50.000 0.00 0.00 0.00 4.18
953 2592 1.342174 TCCGAGTTAGTTTGCCGACTT 59.658 47.619 0.00 0.00 0.00 3.01
954 2593 1.459592 CCGAGTTAGTTTGCCGACTTG 59.540 52.381 0.00 0.00 0.00 3.16
955 2594 1.136336 CGAGTTAGTTTGCCGACTTGC 60.136 52.381 0.00 0.00 0.00 4.01
956 2595 1.197036 GAGTTAGTTTGCCGACTTGCC 59.803 52.381 0.00 0.00 0.00 4.52
957 2596 0.110373 GTTAGTTTGCCGACTTGCCG 60.110 55.000 0.00 0.00 0.00 5.69
971 2610 1.537202 CTTGCCGTGGAAGAAAGGAAG 59.463 52.381 0.00 0.00 0.00 3.46
985 2630 3.488090 GAAGAGAAACCGCCGGCG 61.488 66.667 41.00 41.00 39.44 6.46
1203 2852 4.634703 TTCAAGAAGCCGCCCGCA 62.635 61.111 0.00 0.00 41.38 5.69
1497 3155 2.773993 TGGAGAAATCGTACAACCCC 57.226 50.000 0.00 0.00 0.00 4.95
1765 3435 4.083802 GCTTTTGTTAACTCGTCTGATGCT 60.084 41.667 7.22 0.00 0.00 3.79
1819 3489 4.485554 CGTAGCCTCTGTGCTGTC 57.514 61.111 5.02 0.00 42.77 3.51
1900 3570 5.488919 AGGAACTGAGAACTTGGGATCAATA 59.511 40.000 0.00 0.00 37.18 1.90
1908 3578 9.312904 TGAGAACTTGGGATCAATATTTTCTTT 57.687 29.630 0.00 0.00 31.75 2.52
1936 3606 9.375974 ACTATCTGTATCTGTAGTCTCTAGTCT 57.624 37.037 0.00 0.00 0.00 3.24
1937 3607 9.856488 CTATCTGTATCTGTAGTCTCTAGTCTC 57.144 40.741 0.00 0.00 0.00 3.36
1938 3608 7.907841 TCTGTATCTGTAGTCTCTAGTCTCT 57.092 40.000 0.00 0.00 0.00 3.10
1939 3609 8.999905 TCTGTATCTGTAGTCTCTAGTCTCTA 57.000 38.462 0.00 0.00 0.00 2.43
1940 3610 9.074576 TCTGTATCTGTAGTCTCTAGTCTCTAG 57.925 40.741 0.00 0.00 0.00 2.43
1941 3611 8.771521 TGTATCTGTAGTCTCTAGTCTCTAGT 57.228 38.462 4.13 0.00 0.00 2.57
1942 3612 8.853126 TGTATCTGTAGTCTCTAGTCTCTAGTC 58.147 40.741 4.13 0.00 0.00 2.59
2038 3718 8.822652 TGCACTCTTATGTTATGTATGATGAG 57.177 34.615 0.00 0.00 0.00 2.90
2050 3735 8.454106 GTTATGTATGATGAGCATAAATGGACC 58.546 37.037 3.72 0.00 40.97 4.46
2069 3775 4.533707 GGACCATCATCCCAGATCAGAATA 59.466 45.833 0.00 0.00 31.94 1.75
2134 3840 6.012508 TCTCTTCCTCTTTTGATGGGTTGTAT 60.013 38.462 0.00 0.00 0.00 2.29
2540 4250 6.679146 GCAAAGATCTTTAGGCCTTTCTAAGC 60.679 42.308 20.07 10.77 31.73 3.09
2558 4268 1.777272 AGCCCCAACTCAAAAGTCTCT 59.223 47.619 0.00 0.00 33.48 3.10
2565 4275 6.321435 CCCCAACTCAAAAGTCTCTAGTTTTT 59.679 38.462 0.00 0.00 36.34 1.94
2620 4579 9.803507 TTGATATATTCTCATTGCCTTCTTCAT 57.196 29.630 0.00 0.00 0.00 2.57
2621 4580 9.227777 TGATATATTCTCATTGCCTTCTTCATG 57.772 33.333 0.00 0.00 0.00 3.07
2624 4583 3.349927 TCTCATTGCCTTCTTCATGTGG 58.650 45.455 0.00 0.00 0.00 4.17
2717 4739 4.546570 TCACGTGTTCTACTCTGATTGTG 58.453 43.478 16.51 0.00 0.00 3.33
2726 4748 5.680619 TCTACTCTGATTGTGTTGGTTTGT 58.319 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.998377 GCCAAAATTGACTTACACCATTTATTT 58.002 29.630 0.00 0.00 0.00 1.40
18 19 4.987912 CGCCAAAATTGACTTACACCATTT 59.012 37.500 0.00 0.00 0.00 2.32
19 20 4.038642 ACGCCAAAATTGACTTACACCATT 59.961 37.500 0.00 0.00 0.00 3.16
20 21 3.572255 ACGCCAAAATTGACTTACACCAT 59.428 39.130 0.00 0.00 0.00 3.55
21 22 2.952978 ACGCCAAAATTGACTTACACCA 59.047 40.909 0.00 0.00 0.00 4.17
22 23 3.003897 TGACGCCAAAATTGACTTACACC 59.996 43.478 0.00 0.00 0.00 4.16
23 24 4.217754 TGACGCCAAAATTGACTTACAC 57.782 40.909 0.00 0.00 0.00 2.90
29 30 3.862845 ACAAAACTGACGCCAAAATTGAC 59.137 39.130 0.00 0.00 0.00 3.18
52 53 9.875708 AAGATTCTCTCTCACCAATATAGTAGT 57.124 33.333 0.00 0.00 31.03 2.73
54 55 9.083422 CCAAGATTCTCTCTCACCAATATAGTA 57.917 37.037 0.00 0.00 31.03 1.82
55 56 7.786943 TCCAAGATTCTCTCTCACCAATATAGT 59.213 37.037 0.00 0.00 31.03 2.12
56 57 8.087750 GTCCAAGATTCTCTCTCACCAATATAG 58.912 40.741 0.00 0.00 31.03 1.31
89 90 2.514803 AGTTTTCGATCCTTGGGGTTG 58.485 47.619 0.00 0.00 0.00 3.77
98 99 1.740025 CCAGCCTCAAGTTTTCGATCC 59.260 52.381 0.00 0.00 0.00 3.36
112 113 3.252284 CCCCACTGTGACCAGCCT 61.252 66.667 9.86 0.00 42.81 4.58
113 114 3.249189 TCCCCACTGTGACCAGCC 61.249 66.667 9.86 0.00 42.81 4.85
114 115 2.348998 CTCCCCACTGTGACCAGC 59.651 66.667 9.86 0.00 42.81 4.85
115 116 1.127567 TTCCTCCCCACTGTGACCAG 61.128 60.000 9.86 1.37 44.68 4.00
116 117 1.074090 TTCCTCCCCACTGTGACCA 60.074 57.895 9.86 0.00 0.00 4.02
117 118 1.128188 AGTTCCTCCCCACTGTGACC 61.128 60.000 9.86 0.00 0.00 4.02
118 119 0.765510 AAGTTCCTCCCCACTGTGAC 59.234 55.000 9.86 0.00 0.00 3.67
119 120 2.158219 TCTAAGTTCCTCCCCACTGTGA 60.158 50.000 9.86 0.00 0.00 3.58
120 121 2.257207 TCTAAGTTCCTCCCCACTGTG 58.743 52.381 0.00 0.00 0.00 3.66
121 122 2.715763 TCTAAGTTCCTCCCCACTGT 57.284 50.000 0.00 0.00 0.00 3.55
122 123 4.367039 TTTTCTAAGTTCCTCCCCACTG 57.633 45.455 0.00 0.00 0.00 3.66
141 142 1.118356 TGATGGCCGGCCTTGTTTTT 61.118 50.000 43.34 20.25 36.94 1.94
142 143 1.118356 TTGATGGCCGGCCTTGTTTT 61.118 50.000 43.34 22.00 36.94 2.43
158 159 0.813610 CCAGACCGTGCTGTTGTTGA 60.814 55.000 0.00 0.00 34.06 3.18
164 166 1.399744 TTCTGACCAGACCGTGCTGT 61.400 55.000 0.00 0.00 37.14 4.40
175 177 3.069443 GCCTTGGAATTGTTTTCTGACCA 59.931 43.478 0.00 0.00 0.00 4.02
260 277 0.099968 CTGTGGATTGGATTGCAGCG 59.900 55.000 0.00 0.00 0.00 5.18
301 318 3.085952 ACTGAGAGAGGGAGTGAGAAG 57.914 52.381 0.00 0.00 0.00 2.85
319 336 5.234466 ACAAAGCAAGATTGTCCTCTACT 57.766 39.130 0.00 0.00 36.28 2.57
320 337 5.948992 AACAAAGCAAGATTGTCCTCTAC 57.051 39.130 0.00 0.00 39.98 2.59
389 407 3.955551 TCCTCACTGTGTTGTGTGTACTA 59.044 43.478 7.79 0.00 38.90 1.82
390 408 2.764010 TCCTCACTGTGTTGTGTGTACT 59.236 45.455 7.79 0.00 38.90 2.73
391 409 3.123804 CTCCTCACTGTGTTGTGTGTAC 58.876 50.000 7.79 0.00 38.90 2.90
395 413 1.414181 CCTCTCCTCACTGTGTTGTGT 59.586 52.381 7.79 0.00 38.90 3.72
396 414 1.688735 TCCTCTCCTCACTGTGTTGTG 59.311 52.381 7.79 2.00 39.15 3.33
397 415 1.967066 CTCCTCTCCTCACTGTGTTGT 59.033 52.381 7.79 0.00 0.00 3.32
398 416 2.230992 CTCTCCTCTCCTCACTGTGTTG 59.769 54.545 7.79 2.44 0.00 3.33
399 417 2.524306 CTCTCCTCTCCTCACTGTGTT 58.476 52.381 7.79 0.00 0.00 3.32
425 1401 1.091537 CTCTCACGGTCTCACCTCTC 58.908 60.000 0.00 0.00 35.66 3.20
429 1405 1.596895 GGGACTCTCACGGTCTCACC 61.597 65.000 0.00 0.00 34.59 4.02
438 1414 0.244178 GGTTCTCGTGGGACTCTCAC 59.756 60.000 0.00 0.00 0.00 3.51
439 1415 0.178973 TGGTTCTCGTGGGACTCTCA 60.179 55.000 0.00 0.00 0.00 3.27
440 1416 0.244178 GTGGTTCTCGTGGGACTCTC 59.756 60.000 0.00 0.00 0.00 3.20
442 1418 0.244178 GAGTGGTTCTCGTGGGACTC 59.756 60.000 0.00 0.00 33.25 3.36
443 1419 1.186267 GGAGTGGTTCTCGTGGGACT 61.186 60.000 0.00 0.00 43.60 3.85
444 1420 1.292541 GGAGTGGTTCTCGTGGGAC 59.707 63.158 0.00 0.00 43.60 4.46
445 1421 1.911766 GGGAGTGGTTCTCGTGGGA 60.912 63.158 0.00 0.00 43.60 4.37
446 1422 1.553690 ATGGGAGTGGTTCTCGTGGG 61.554 60.000 0.00 0.00 43.60 4.61
458 2062 1.218704 CATGGAATGGGGAATGGGAGT 59.781 52.381 0.00 0.00 41.79 3.85
461 2065 1.123246 GGCATGGAATGGGGAATGGG 61.123 60.000 0.00 0.00 46.86 4.00
462 2066 0.398806 TGGCATGGAATGGGGAATGG 60.399 55.000 0.00 0.00 46.86 3.16
463 2067 1.346395 CATGGCATGGAATGGGGAATG 59.654 52.381 19.80 0.00 46.86 2.67
464 2068 1.061967 ACATGGCATGGAATGGGGAAT 60.062 47.619 29.49 3.29 46.86 3.01
465 2069 0.339162 ACATGGCATGGAATGGGGAA 59.661 50.000 29.49 0.00 46.86 3.97
466 2070 0.397394 CACATGGCATGGAATGGGGA 60.397 55.000 29.49 0.00 46.86 4.81
467 2071 0.397394 TCACATGGCATGGAATGGGG 60.397 55.000 29.49 4.23 46.86 4.96
546 2150 3.478274 GCAGAGAGAGGCAGGGGG 61.478 72.222 0.00 0.00 0.00 5.40
643 2265 1.893801 GAAGACTCGAACTGAAGGGGA 59.106 52.381 0.00 0.00 0.00 4.81
644 2266 1.896465 AGAAGACTCGAACTGAAGGGG 59.104 52.381 0.00 0.00 0.00 4.79
662 2297 4.907875 TCAAAGAAGAGGGAAGGAGAAAGA 59.092 41.667 0.00 0.00 0.00 2.52
664 2299 5.850046 ATCAAAGAAGAGGGAAGGAGAAA 57.150 39.130 0.00 0.00 0.00 2.52
723 2361 2.091830 ACATGGACATACGGAGAGGAGA 60.092 50.000 0.00 0.00 0.00 3.71
724 2362 2.035193 CACATGGACATACGGAGAGGAG 59.965 54.545 0.00 0.00 0.00 3.69
725 2363 2.031870 CACATGGACATACGGAGAGGA 58.968 52.381 0.00 0.00 0.00 3.71
726 2364 1.757118 ACACATGGACATACGGAGAGG 59.243 52.381 0.00 0.00 0.00 3.69
727 2365 2.690497 AGACACATGGACATACGGAGAG 59.310 50.000 0.00 0.00 0.00 3.20
728 2366 2.688446 GAGACACATGGACATACGGAGA 59.312 50.000 0.00 0.00 0.00 3.71
775 2413 1.931635 AGAAGAGTGAGTGGGGAGTC 58.068 55.000 0.00 0.00 0.00 3.36
781 2419 1.879796 GCCACCAAGAAGAGTGAGTGG 60.880 57.143 2.63 2.63 46.03 4.00
790 2428 1.163554 GAAGCTCTGCCACCAAGAAG 58.836 55.000 0.00 0.00 0.00 2.85
802 2440 4.985409 CACGTAACAGAAAGAAGAAGCTCT 59.015 41.667 0.00 0.00 0.00 4.09
803 2441 4.745620 ACACGTAACAGAAAGAAGAAGCTC 59.254 41.667 0.00 0.00 0.00 4.09
822 2460 0.784778 GAACGGAAGAAGCTGACACG 59.215 55.000 0.00 0.00 0.00 4.49
837 2475 0.736325 AAAGCTCGGACCGATGAACG 60.736 55.000 18.71 6.37 42.18 3.95
873 2511 0.539669 TCCCACTCAGACGAGCAGAA 60.540 55.000 0.00 0.00 43.66 3.02
878 2516 0.322997 ACTCCTCCCACTCAGACGAG 60.323 60.000 0.00 0.00 45.49 4.18
938 2577 0.110373 CGGCAAGTCGGCAAACTAAC 60.110 55.000 0.00 0.00 41.26 2.34
950 2589 0.472471 TCCTTTCTTCCACGGCAAGT 59.528 50.000 0.00 0.00 0.00 3.16
951 2590 1.537202 CTTCCTTTCTTCCACGGCAAG 59.463 52.381 0.00 0.00 0.00 4.01
952 2591 1.142060 TCTTCCTTTCTTCCACGGCAA 59.858 47.619 0.00 0.00 0.00 4.52
953 2592 0.762418 TCTTCCTTTCTTCCACGGCA 59.238 50.000 0.00 0.00 0.00 5.69
954 2593 1.002087 TCTCTTCCTTTCTTCCACGGC 59.998 52.381 0.00 0.00 0.00 5.68
955 2594 3.402628 TTCTCTTCCTTTCTTCCACGG 57.597 47.619 0.00 0.00 0.00 4.94
956 2595 3.498777 GGTTTCTCTTCCTTTCTTCCACG 59.501 47.826 0.00 0.00 0.00 4.94
957 2596 3.498777 CGGTTTCTCTTCCTTTCTTCCAC 59.501 47.826 0.00 0.00 0.00 4.02
985 2630 0.453390 CGCATCTTTTTCTGCCCCTC 59.547 55.000 0.00 0.00 34.89 4.30
991 2636 2.295909 TCAAACCCCGCATCTTTTTCTG 59.704 45.455 0.00 0.00 0.00 3.02
1048 2694 3.894947 GAGCGCGAGGAGGAGGAC 61.895 72.222 12.10 0.00 0.00 3.85
1203 2852 3.450115 GCGTAGGTGGAGGCGAGT 61.450 66.667 0.00 0.00 0.00 4.18
1654 3324 4.460683 GGTGATGTACCCGCCGCA 62.461 66.667 0.00 0.00 44.15 5.69
1695 3365 2.370445 CGAGGGCAAGGGGATGACT 61.370 63.158 0.00 0.00 0.00 3.41
1736 3406 3.284617 ACGAGTTAACAAAAGCCACCTT 58.715 40.909 8.61 0.00 0.00 3.50
1744 3414 5.053811 TCAGCATCAGACGAGTTAACAAAA 58.946 37.500 8.61 0.00 0.00 2.44
1774 3444 1.069204 GGAACACTGACTGACTCTGCA 59.931 52.381 0.00 0.00 0.00 4.41
1775 3445 1.789506 GGAACACTGACTGACTCTGC 58.210 55.000 0.00 0.00 0.00 4.26
1777 3447 1.693627 ACGGAACACTGACTGACTCT 58.306 50.000 0.00 0.00 0.00 3.24
1778 3448 2.034812 AGAACGGAACACTGACTGACTC 59.965 50.000 0.00 0.00 0.00 3.36
1914 3584 7.907841 AGAGACTAGAGACTACAGATACAGA 57.092 40.000 0.00 0.00 0.00 3.41
1915 3585 8.857098 ACTAGAGACTAGAGACTACAGATACAG 58.143 40.741 11.94 0.00 0.00 2.74
1916 3586 8.771521 ACTAGAGACTAGAGACTACAGATACA 57.228 38.462 11.94 0.00 0.00 2.29
1919 3589 7.563924 ACAGACTAGAGACTAGAGACTACAGAT 59.436 40.741 11.94 0.00 0.00 2.90
1920 3590 6.893554 ACAGACTAGAGACTAGAGACTACAGA 59.106 42.308 11.94 0.00 0.00 3.41
1921 3591 6.978659 CACAGACTAGAGACTAGAGACTACAG 59.021 46.154 11.94 0.00 0.00 2.74
1922 3592 6.664384 TCACAGACTAGAGACTAGAGACTACA 59.336 42.308 11.94 0.00 0.00 2.74
1923 3593 6.976925 GTCACAGACTAGAGACTAGAGACTAC 59.023 46.154 11.94 1.41 0.00 2.73
1925 3595 5.720041 AGTCACAGACTAGAGACTAGAGACT 59.280 44.000 11.94 11.89 41.51 3.24
1928 3598 6.092122 CACAAGTCACAGACTAGAGACTAGAG 59.908 46.154 11.94 5.01 42.59 2.43
1929 3599 5.935206 CACAAGTCACAGACTAGAGACTAGA 59.065 44.000 11.94 0.00 42.59 2.43
1930 3600 5.935206 TCACAAGTCACAGACTAGAGACTAG 59.065 44.000 0.00 0.00 42.59 2.57
1931 3601 5.701750 GTCACAAGTCACAGACTAGAGACTA 59.298 44.000 0.00 0.00 42.59 2.59
1932 3602 4.517453 GTCACAAGTCACAGACTAGAGACT 59.483 45.833 0.00 0.00 42.59 3.24
1933 3603 4.517453 AGTCACAAGTCACAGACTAGAGAC 59.483 45.833 0.00 13.33 42.59 3.36
1934 3604 4.720046 AGTCACAAGTCACAGACTAGAGA 58.280 43.478 0.00 0.00 42.59 3.10
1935 3605 5.446143 AAGTCACAAGTCACAGACTAGAG 57.554 43.478 0.00 0.00 42.59 2.43
1936 3606 5.854010 AAAGTCACAAGTCACAGACTAGA 57.146 39.130 0.00 0.00 42.59 2.43
1937 3607 6.642950 CCTTAAAGTCACAAGTCACAGACTAG 59.357 42.308 0.00 0.00 42.59 2.57
1938 3608 6.097839 ACCTTAAAGTCACAAGTCACAGACTA 59.902 38.462 0.00 0.00 42.59 2.59
1939 3609 5.104900 ACCTTAAAGTCACAAGTCACAGACT 60.105 40.000 0.00 0.00 45.64 3.24
1940 3610 5.006746 CACCTTAAAGTCACAAGTCACAGAC 59.993 44.000 0.00 0.00 0.00 3.51
1941 3611 5.116180 CACCTTAAAGTCACAAGTCACAGA 58.884 41.667 0.00 0.00 0.00 3.41
1942 3612 4.260784 GCACCTTAAAGTCACAAGTCACAG 60.261 45.833 0.00 0.00 0.00 3.66
2038 3718 3.499338 TGGGATGATGGTCCATTTATGC 58.501 45.455 5.65 9.07 40.17 3.14
2050 3735 9.901172 TTAATGATATTCTGATCTGGGATGATG 57.099 33.333 0.00 0.00 0.00 3.07
2104 3810 4.335874 CCATCAAAAGAGGAAGAGAGCATG 59.664 45.833 0.00 0.00 0.00 4.06
2259 3965 6.019779 TGCAAGGAATTTGTATTACACACC 57.980 37.500 0.00 0.00 39.08 4.16
2347 4056 9.508567 GTGAACAATCTAATTAAAGGATTCTGC 57.491 33.333 0.00 0.00 0.00 4.26
2540 4250 4.625607 ACTAGAGACTTTTGAGTTGGGG 57.374 45.455 0.00 0.00 0.00 4.96
2541 4251 6.944234 AAAACTAGAGACTTTTGAGTTGGG 57.056 37.500 0.00 0.00 30.94 4.12
2565 4275 0.392998 GCTGCGGAGAGAATGGGAAA 60.393 55.000 8.65 0.00 0.00 3.13
2568 4278 2.578163 TTCGCTGCGGAGAGAATGGG 62.578 60.000 23.03 0.00 33.53 4.00
2624 4583 3.196901 GGTGGAACAATTTTATCACCCCC 59.803 47.826 0.00 0.00 44.16 5.40
2634 4593 6.290605 CCATTTCTTTCTGGTGGAACAATTT 58.709 36.000 0.00 0.00 44.16 1.82
2643 4602 1.891150 AGCTGCCATTTCTTTCTGGTG 59.109 47.619 0.00 0.00 34.86 4.17


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

AutoCloner maintained by Alex Coulton.