Multiple sequence alignment - TraesCS3B01G440300

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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 TraesCS3B01G440300 chr3B 100.000 3920 0 0 1 3920 679648637 679644718 0.000000e+00 7239.0
1 TraesCS3B01G440300 chr3D 93.783 3458 155 25 512 3920 516387291 516383845 0.000000e+00 5140.0
2 TraesCS3B01G440300 chr3D 89.231 65 6 1 2482 2546 48365691 48365628 3.250000e-11 80.5
3 TraesCS3B01G440300 chr3A 92.814 3145 185 18 810 3920 651589921 651586784 0.000000e+00 4518.0
4 TraesCS3B01G440300 chr3A 93.980 299 14 2 488 786 651590275 651589981 2.150000e-122 449.0
5 TraesCS3B01G440300 chr3A 90.323 217 20 1 1 216 651590887 651590671 2.310000e-72 283.0
6 TraesCS3B01G440300 chr7A 91.935 186 13 1 2527 2712 717067806 717067623 3.890000e-65 259.0
7 TraesCS3B01G440300 chr7A 94.118 68 3 1 2371 2438 717067868 717067802 6.930000e-18 102.0
8 TraesCS3B01G440300 chr7D 89.655 145 12 1 2569 2713 621613723 621613582 8.650000e-42 182.0
9 TraesCS3B01G440300 chr7D 95.588 68 2 1 2371 2438 621613802 621613736 1.490000e-19 108.0
10 TraesCS3B01G440300 chr7B 90.566 106 6 2 2608 2713 718445362 718445463 1.900000e-28 137.0
11 TraesCS3B01G440300 chr7B 95.238 42 2 0 96 137 627031518 627031559 2.530000e-07 67.6
12 TraesCS3B01G440300 chr6A 83.505 97 14 2 2441 2536 570382447 570382352 5.390000e-14 89.8
13 TraesCS3B01G440300 chr2D 80.220 91 14 3 2460 2548 595290206 595290118 9.090000e-07 65.8
14 TraesCS3B01G440300 chr2D 89.583 48 5 0 2497 2544 492022266 492022219 1.180000e-05 62.1
15 TraesCS3B01G440300 chr2A 80.220 91 14 3 2460 2548 729500624 729500536 9.090000e-07 65.8
16 TraesCS3B01G440300 chr2A 89.583 48 5 0 2497 2544 637222695 637222648 1.180000e-05 62.1
17 TraesCS3B01G440300 chr2B 78.889 90 17 2 2460 2548 723043321 723043233 4.230000e-05 60.2


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 TraesCS3B01G440300 chr3B 679644718 679648637 3919 True 7239 7239 100.000000 1 3920 1 chr3B.!!$R1 3919
1 TraesCS3B01G440300 chr3D 516383845 516387291 3446 True 5140 5140 93.783000 512 3920 1 chr3D.!!$R2 3408
2 TraesCS3B01G440300 chr3A 651586784 651590887 4103 True 1750 4518 92.372333 1 3920 3 chr3A.!!$R1 3919

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
377 459 0.038892 CATTGTGAAGCTGCGCCTTT 60.039 50.0 4.18 0.0 0.0 3.11 F
1459 1627 0.687354 GGAACTCAACTCCTCCTGCA 59.313 55.0 0.00 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 1864 0.039035 TTGGTGTGGGTAATGGAGCC 59.961 55.000 0.00 0.0 46.83 4.70 R
3190 3365 1.355381 TCCCTGATCACCACAATTGCT 59.645 47.619 5.05 0.0 0.00 3.91 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
25 26 2.143925 GGCAACTACACTGTGAAGACC 58.856 52.381 15.86 4.38 0.00 3.85
30 32 0.318360 TACACTGTGAAGACCGCGTG 60.318 55.000 15.86 0.00 36.55 5.34
32 34 2.661537 CTGTGAAGACCGCGTGCA 60.662 61.111 4.92 0.00 0.00 4.57
35 37 3.422303 TGAAGACCGCGTGCATGC 61.422 61.111 21.27 21.27 0.00 4.06
51 53 6.253298 GCGTGCATGCTCTTATAAATCAAAAA 59.747 34.615 23.72 0.00 0.00 1.94
55 57 9.357652 TGCATGCTCTTATAAATCAAAAAGAAC 57.642 29.630 20.33 0.00 0.00 3.01
59 61 6.472486 GCTCTTATAAATCAAAAAGAACGCCC 59.528 38.462 0.00 0.00 0.00 6.13
60 62 6.859017 TCTTATAAATCAAAAAGAACGCCCC 58.141 36.000 0.00 0.00 0.00 5.80
94 96 2.693074 GGTTGGTCTGTGTCCAATGTTT 59.307 45.455 0.79 0.00 45.01 2.83
108 110 3.127030 CCAATGTTTTACTCTTCCTCGCC 59.873 47.826 0.00 0.00 0.00 5.54
112 114 1.250328 TTTACTCTTCCTCGCCGACA 58.750 50.000 0.00 0.00 0.00 4.35
130 132 1.463444 ACAATCGCACCTTAACTTCGC 59.537 47.619 0.00 0.00 0.00 4.70
141 143 2.203972 TAACTTCGCGGGTCTCACGG 62.204 60.000 6.13 0.00 0.00 4.94
142 144 4.052229 CTTCGCGGGTCTCACGGT 62.052 66.667 6.13 0.00 0.00 4.83
171 173 1.455822 TGGACAGGGAAGGGAACAAT 58.544 50.000 0.00 0.00 0.00 2.71
173 175 2.307686 TGGACAGGGAAGGGAACAATAC 59.692 50.000 0.00 0.00 0.00 1.89
175 177 2.235402 GACAGGGAAGGGAACAATACGA 59.765 50.000 0.00 0.00 0.00 3.43
237 319 3.772025 ACATGAAAAGGTTGGTTTGGTCA 59.228 39.130 0.00 0.00 0.00 4.02
242 324 5.877564 TGAAAAGGTTGGTTTGGTCAAATTC 59.122 36.000 0.00 0.00 32.36 2.17
274 356 1.101049 ATAAAGGCGCGGTTGGATGG 61.101 55.000 8.83 0.00 0.00 3.51
286 368 4.962836 GGATGGCCGGCTCCCATG 62.963 72.222 28.56 0.00 42.94 3.66
294 376 2.592308 GGCTCCCATGTCCAGACC 59.408 66.667 0.00 0.00 0.00 3.85
298 380 0.471617 CTCCCATGTCCAGACCCATC 59.528 60.000 0.00 0.00 0.00 3.51
332 414 3.267483 CCGTGTCCGTTTTAAGGATCAT 58.733 45.455 0.00 0.00 40.30 2.45
342 424 8.170894 TCCGTTTTAAGGATCATCATGGAGATG 61.171 40.741 5.68 0.00 43.01 2.90
355 437 1.992557 TGGAGATGCCCTAACACCTTT 59.007 47.619 0.00 0.00 34.97 3.11
368 450 6.404734 CCCTAACACCTTTATCATTGTGAAGC 60.405 42.308 0.00 0.00 33.08 3.86
370 452 5.633830 ACACCTTTATCATTGTGAAGCTG 57.366 39.130 0.00 0.00 33.08 4.24
377 459 0.038892 CATTGTGAAGCTGCGCCTTT 60.039 50.000 4.18 0.00 0.00 3.11
380 462 1.360192 GTGAAGCTGCGCCTTTGTT 59.640 52.632 4.18 0.00 0.00 2.83
386 468 1.646540 CTGCGCCTTTGTTCGTTCA 59.353 52.632 4.18 0.00 0.00 3.18
389 471 0.729140 GCGCCTTTGTTCGTTCATGG 60.729 55.000 0.00 0.00 0.00 3.66
421 507 9.739276 TTCCTCAAAAATATGTGTCTATGTCTT 57.261 29.630 0.00 0.00 0.00 3.01
422 508 9.166173 TCCTCAAAAATATGTGTCTATGTCTTG 57.834 33.333 0.00 0.00 0.00 3.02
465 553 5.020132 AGTGTGGCTAGATCTTAGTCAAGT 58.980 41.667 0.00 0.00 30.27 3.16
494 621 5.613358 ACATGTAAAGAAAAAGGAGCGAG 57.387 39.130 0.00 0.00 0.00 5.03
498 625 5.547465 TGTAAAGAAAAAGGAGCGAGATCA 58.453 37.500 0.00 0.00 0.00 2.92
551 678 1.365699 ACGCACAATGATAACCGGAC 58.634 50.000 9.46 0.00 0.00 4.79
786 916 2.158449 CAGACAGCTGAGCTTTTAACCG 59.842 50.000 23.35 0.00 45.17 4.44
789 929 2.224305 ACAGCTGAGCTTTTAACCGACT 60.224 45.455 23.35 0.00 36.40 4.18
801 941 6.073222 GCTTTTAACCGACTGAGAAATGAGAA 60.073 38.462 0.00 0.00 0.00 2.87
810 950 6.019961 CGACTGAGAAATGAGAAATCTGCTAC 60.020 42.308 0.00 0.00 0.00 3.58
811 951 6.945218 ACTGAGAAATGAGAAATCTGCTACT 58.055 36.000 0.00 0.00 0.00 2.57
835 1002 2.884012 CCTGCGTCTCAGATAGTCAGAT 59.116 50.000 0.00 0.00 45.72 2.90
836 1003 3.058293 CCTGCGTCTCAGATAGTCAGATC 60.058 52.174 0.00 0.00 45.72 2.75
841 1008 5.561919 GCGTCTCAGATAGTCAGATCGAAAT 60.562 44.000 0.00 0.00 0.00 2.17
845 1012 5.847304 TCAGATAGTCAGATCGAAATTGGG 58.153 41.667 0.00 0.00 0.00 4.12
848 1015 2.893637 AGTCAGATCGAAATTGGGTCG 58.106 47.619 0.00 0.00 39.88 4.79
915 1082 1.477558 CCACAAGCCAAAGACTCCAGT 60.478 52.381 0.00 0.00 0.00 4.00
941 1109 4.202080 CGAGTAATTTACCCGACTGGATCA 60.202 45.833 4.65 0.00 37.49 2.92
950 1118 2.093500 CCCGACTGGATCAGTTGATTCA 60.093 50.000 14.87 3.21 45.84 2.57
1114 1282 2.034532 TCGACCTGGGCTACGTGA 59.965 61.111 0.00 0.00 0.00 4.35
1459 1627 0.687354 GGAACTCAACTCCTCCTGCA 59.313 55.000 0.00 0.00 0.00 4.41
1483 1651 2.864471 AACCTCACCGACACGTCCC 61.864 63.158 0.00 0.00 0.00 4.46
1493 1661 1.303074 ACACGTCCCTCTGCTACGA 60.303 57.895 0.00 0.00 39.80 3.43
1530 1698 2.110967 CCATGCCTTGGCTCGACTG 61.111 63.158 13.18 3.20 39.09 3.51
1563 1731 1.704641 GCAAAACCTCCAACTCCCTT 58.295 50.000 0.00 0.00 0.00 3.95
1609 1777 3.103911 CCGCCGGCGTATCGAATC 61.104 66.667 43.12 2.88 37.81 2.52
1678 1846 1.616327 CTCTCCACCACATCCCCCA 60.616 63.158 0.00 0.00 0.00 4.96
1696 1864 0.877649 CACATCCTCGAATGCCTCCG 60.878 60.000 0.00 0.00 0.00 4.63
1884 2052 2.125512 GGCTCGGTGCTGTTCGAT 60.126 61.111 1.77 0.00 42.39 3.59
2064 2232 1.407437 GCCAACGAGGTGGAGATCATT 60.407 52.381 11.99 0.00 41.65 2.57
2178 2346 0.452987 TCGTGTACGACTACATGCCC 59.547 55.000 2.55 0.00 44.22 5.36
2268 2436 4.945645 AGGAGTGTGGTCCTCGAA 57.054 55.556 0.00 0.00 44.25 3.71
2269 2437 3.143010 AGGAGTGTGGTCCTCGAAA 57.857 52.632 0.00 0.00 44.25 3.46
2619 2787 1.078848 GTGGATGCTCGTCAAGGCT 60.079 57.895 0.00 0.00 0.00 4.58
2781 2949 2.373707 GCTGAGGATGCTGGAGGGT 61.374 63.158 0.00 0.00 0.00 4.34
2838 3006 0.384669 CGTACGGACAGAGAATCCCC 59.615 60.000 7.57 0.00 33.66 4.81
2845 3013 2.104170 GACAGAGAATCCCCTTCGACT 58.896 52.381 0.00 0.00 38.98 4.18
2846 3014 2.498078 GACAGAGAATCCCCTTCGACTT 59.502 50.000 0.00 0.00 38.98 3.01
2877 3045 1.006102 CTTCAGTGCCTCGTCGGTT 60.006 57.895 0.00 0.00 34.25 4.44
2975 3143 7.195374 AGCTGGACTGGAATTTATGTACTTA 57.805 36.000 0.00 0.00 0.00 2.24
3020 3189 6.823678 ACTACAACTTGTAACTGAAGTTCG 57.176 37.500 0.00 0.00 40.83 3.95
3069 3240 4.004314 TGGTGTAAATGGATTGTGTACCG 58.996 43.478 0.00 0.00 0.00 4.02
3097 3268 3.689161 TCTTGTGCTGAAATACCGAATGG 59.311 43.478 0.00 0.00 42.84 3.16
3099 3270 3.884895 TGTGCTGAAATACCGAATGGAT 58.115 40.909 0.00 0.00 39.21 3.41
3106 3277 6.347725 GCTGAAATACCGAATGGATCATGTAC 60.348 42.308 0.00 0.00 39.21 2.90
3110 3281 7.873719 AATACCGAATGGATCATGTACAAAA 57.126 32.000 0.00 0.00 39.21 2.44
3111 3282 8.463930 AATACCGAATGGATCATGTACAAAAT 57.536 30.769 0.00 0.00 39.21 1.82
3112 3283 6.135290 ACCGAATGGATCATGTACAAAATG 57.865 37.500 0.00 0.00 39.21 2.32
3113 3284 4.977963 CCGAATGGATCATGTACAAAATGC 59.022 41.667 0.00 2.48 37.49 3.56
3114 3285 4.671964 CGAATGGATCATGTACAAAATGCG 59.328 41.667 0.00 0.00 0.00 4.73
3115 3286 4.572985 ATGGATCATGTACAAAATGCGG 57.427 40.909 0.00 0.00 0.00 5.69
3116 3287 3.615155 TGGATCATGTACAAAATGCGGA 58.385 40.909 0.00 0.00 0.00 5.54
3122 3293 6.018589 TCATGTACAAAATGCGGAATGAAA 57.981 33.333 0.00 0.00 0.00 2.69
3123 3294 6.629128 TCATGTACAAAATGCGGAATGAAAT 58.371 32.000 0.00 0.00 0.00 2.17
3155 3329 7.724287 TCACATCAAATCAAGATTTTCCACAA 58.276 30.769 5.34 0.00 38.84 3.33
3161 3335 9.044150 TCAAATCAAGATTTTCCACAATGTTTC 57.956 29.630 5.34 0.00 38.84 2.78
3190 3365 5.640357 GTCATTACAAACTATTCACCGTCCA 59.360 40.000 0.00 0.00 0.00 4.02
3198 3373 1.909700 ATTCACCGTCCAGCAATTGT 58.090 45.000 7.40 0.00 0.00 2.71
3237 3412 4.708177 ACATGCAGATACAATACCAGTCC 58.292 43.478 0.00 0.00 0.00 3.85
3261 3436 5.686159 CTGATATTTCAGCTCCAATGGTC 57.314 43.478 0.00 0.00 42.79 4.02
3278 3454 3.997762 TGGTCGTGCAAACTTACAGTAT 58.002 40.909 0.00 0.00 0.00 2.12
3285 3461 4.396166 GTGCAAACTTACAGTATGGCAGAT 59.604 41.667 0.00 0.00 43.62 2.90
3287 3463 4.635765 GCAAACTTACAGTATGGCAGATCA 59.364 41.667 0.00 0.00 43.62 2.92
3377 3553 8.377681 ACTACGTATAACATGTTCAATTGTTCG 58.622 33.333 15.85 11.59 37.29 3.95
3414 3590 2.699954 ACGAAGGATACAACTGGCAAG 58.300 47.619 0.00 0.00 41.41 4.01
3420 3596 3.372349 AGGATACAACTGGCAAGATGCAT 60.372 43.478 0.00 0.00 43.05 3.96
3519 3695 4.033776 GGGTGGCTAGGCTGCACA 62.034 66.667 18.18 0.00 34.04 4.57
3702 3891 8.609176 ACTAATGCAAATATAACTTGTACACGG 58.391 33.333 4.21 0.00 0.00 4.94
3708 3897 0.032403 TAACTTGTACACGGTGCGCT 59.968 50.000 9.73 0.00 0.00 5.92
3750 3948 4.759793 TCCCCCACTCTATGCTCTATTA 57.240 45.455 0.00 0.00 0.00 0.98
3751 3949 5.087923 TCCCCCACTCTATGCTCTATTAA 57.912 43.478 0.00 0.00 0.00 1.40
3752 3950 5.665701 TCCCCCACTCTATGCTCTATTAAT 58.334 41.667 0.00 0.00 0.00 1.40
3753 3951 6.091555 TCCCCCACTCTATGCTCTATTAATT 58.908 40.000 0.00 0.00 0.00 1.40
3765 3963 5.344665 TGCTCTATTAATTTGCGTGTTTTGC 59.655 36.000 0.00 0.00 0.00 3.68
3877 4077 2.287644 CGTTGAGTGTGAGTGCATTCAA 59.712 45.455 14.07 1.98 40.91 2.69
3887 4087 3.189910 TGAGTGCATTCAACTCATTCAGC 59.810 43.478 9.78 0.00 35.81 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.059665 TGATTTATAAGAGCATGCACGCG 60.060 43.478 21.98 3.53 36.85 6.01
30 32 8.526681 CGTTCTTTTTGATTTATAAGAGCATGC 58.473 33.333 10.51 10.51 30.96 4.06
32 34 7.702348 GGCGTTCTTTTTGATTTATAAGAGCAT 59.298 33.333 0.00 0.00 30.96 3.79
35 37 6.972901 GGGGCGTTCTTTTTGATTTATAAGAG 59.027 38.462 0.00 0.00 0.00 2.85
51 53 1.682684 ATGAGACTCGGGGCGTTCT 60.683 57.895 0.00 0.00 0.00 3.01
55 57 2.202797 CACATGAGACTCGGGGCG 60.203 66.667 0.00 0.00 0.00 6.13
59 61 0.391661 CCAACCCACATGAGACTCGG 60.392 60.000 0.00 0.00 0.00 4.63
60 62 0.321671 ACCAACCCACATGAGACTCG 59.678 55.000 0.00 0.00 0.00 4.18
94 96 1.250328 TTGTCGGCGAGGAAGAGTAA 58.750 50.000 11.20 0.00 0.00 2.24
108 110 2.222508 CGAAGTTAAGGTGCGATTGTCG 60.223 50.000 0.00 0.00 43.89 4.35
141 143 2.509336 CTGTCCATGTCCGGCGAC 60.509 66.667 9.30 5.41 39.66 5.19
142 144 3.770040 CCTGTCCATGTCCGGCGA 61.770 66.667 9.30 0.00 0.00 5.54
145 147 1.221840 CTTCCCTGTCCATGTCCGG 59.778 63.158 0.00 0.00 0.00 5.14
171 173 0.540365 ACCCGTCCTCCAAGTTCGTA 60.540 55.000 0.00 0.00 0.00 3.43
173 175 1.374252 CACCCGTCCTCCAAGTTCG 60.374 63.158 0.00 0.00 0.00 3.95
175 177 2.430367 GCACCCGTCCTCCAAGTT 59.570 61.111 0.00 0.00 0.00 2.66
202 204 9.449719 CAACCTTTTCATGTAACCTAGTCTAAT 57.550 33.333 0.00 0.00 0.00 1.73
224 306 4.400529 AGTGAATTTGACCAAACCAACC 57.599 40.909 0.00 0.00 32.51 3.77
227 309 8.887717 CATTTTAAAGTGAATTTGACCAAACCA 58.112 29.630 4.78 0.00 32.51 3.67
242 324 5.454232 CCGCGCCTTTATACATTTTAAAGTG 59.546 40.000 8.99 8.99 35.72 3.16
274 356 4.864334 CTGGACATGGGAGCCGGC 62.864 72.222 21.89 21.89 0.00 6.13
281 363 1.533711 GGATGGGTCTGGACATGGG 59.466 63.158 0.00 0.00 0.00 4.00
283 365 1.524621 GCGGATGGGTCTGGACATG 60.525 63.158 3.10 0.00 0.00 3.21
286 368 3.014085 TTCGCGGATGGGTCTGGAC 62.014 63.158 6.13 0.00 0.00 4.02
310 392 2.037511 TGATCCTTAAAACGGACACGGT 59.962 45.455 0.00 0.00 45.80 4.83
332 414 1.490490 GGTGTTAGGGCATCTCCATGA 59.510 52.381 0.00 0.00 36.21 3.07
342 424 4.947388 TCACAATGATAAAGGTGTTAGGGC 59.053 41.667 0.00 0.00 33.17 5.19
345 427 7.246311 CAGCTTCACAATGATAAAGGTGTTAG 58.754 38.462 13.57 0.00 40.53 2.34
346 428 6.349280 GCAGCTTCACAATGATAAAGGTGTTA 60.349 38.462 18.80 0.00 44.77 2.41
347 429 5.565439 GCAGCTTCACAATGATAAAGGTGTT 60.565 40.000 18.80 0.00 44.77 3.32
348 430 4.082571 GCAGCTTCACAATGATAAAGGTGT 60.083 41.667 18.80 0.00 44.77 4.16
368 450 0.238289 ATGAACGAACAAAGGCGCAG 59.762 50.000 10.83 0.00 0.00 5.18
370 452 0.729140 CCATGAACGAACAAAGGCGC 60.729 55.000 0.00 0.00 0.00 6.53
397 479 8.950210 ACAAGACATAGACACATATTTTTGAGG 58.050 33.333 0.00 0.00 0.00 3.86
406 488 9.516314 CGAGATTAAACAAGACATAGACACATA 57.484 33.333 0.00 0.00 0.00 2.29
444 530 5.016831 TCACTTGACTAAGATCTAGCCACA 58.983 41.667 0.00 0.00 37.36 4.17
459 547 8.682128 TTTCTTTACATGTTTTGTCACTTGAC 57.318 30.769 2.30 2.19 44.97 3.18
465 553 7.491048 GCTCCTTTTTCTTTACATGTTTTGTCA 59.509 33.333 2.30 0.00 39.87 3.58
469 557 6.801575 TCGCTCCTTTTTCTTTACATGTTTT 58.198 32.000 2.30 0.00 0.00 2.43
470 558 6.262273 TCTCGCTCCTTTTTCTTTACATGTTT 59.738 34.615 2.30 0.00 0.00 2.83
476 564 6.508721 CGATGATCTCGCTCCTTTTTCTTTAC 60.509 42.308 0.00 0.00 41.14 2.01
479 567 3.868077 CGATGATCTCGCTCCTTTTTCTT 59.132 43.478 0.00 0.00 41.14 2.52
481 569 3.850657 CGATGATCTCGCTCCTTTTTC 57.149 47.619 0.00 0.00 41.14 2.29
494 621 2.286559 CGTCGCCACGTCGATGATC 61.287 63.158 12.58 0.00 45.47 2.92
498 625 4.771356 CACCGTCGCCACGTCGAT 62.771 66.667 2.55 0.00 45.17 3.59
536 663 2.930950 CCCATGTCCGGTTATCATTGT 58.069 47.619 0.00 0.00 0.00 2.71
551 678 0.107508 ATGTCTTCTGGTCGCCCATG 60.108 55.000 0.00 0.00 40.90 3.66
588 715 5.792741 GCAGAAGAACTGGCTGATCTATAT 58.207 41.667 4.66 0.00 45.82 0.86
589 716 5.207110 GCAGAAGAACTGGCTGATCTATA 57.793 43.478 4.66 0.00 45.82 1.31
590 717 4.070630 GCAGAAGAACTGGCTGATCTAT 57.929 45.455 4.66 0.00 45.82 1.98
655 782 2.915659 TCACGGGGCTCGACAGTT 60.916 61.111 16.65 0.00 42.43 3.16
656 783 3.374402 CTCACGGGGCTCGACAGT 61.374 66.667 16.65 0.00 42.43 3.55
657 784 3.057547 CTCTCACGGGGCTCGACAG 62.058 68.421 16.65 8.77 42.43 3.51
786 916 7.041107 AGTAGCAGATTTCTCATTTCTCAGTC 58.959 38.462 0.00 0.00 0.00 3.51
789 929 7.180322 AGAGTAGCAGATTTCTCATTTCTCA 57.820 36.000 0.00 0.00 0.00 3.27
801 941 1.407258 GACGCAGGAGAGTAGCAGATT 59.593 52.381 0.00 0.00 0.00 2.40
810 950 2.548057 GACTATCTGAGACGCAGGAGAG 59.452 54.545 6.35 4.28 44.98 3.20
811 951 2.092914 TGACTATCTGAGACGCAGGAGA 60.093 50.000 6.35 0.00 44.98 3.71
835 1002 2.098233 GCGAGCGACCCAATTTCGA 61.098 57.895 2.27 0.00 38.85 3.71
836 1003 2.025359 GAGCGAGCGACCCAATTTCG 62.025 60.000 0.00 0.00 39.56 3.46
841 1008 3.303135 AGTGAGCGAGCGACCCAA 61.303 61.111 0.00 0.00 0.00 4.12
890 1057 2.203684 CTTTGGCTTGTGGGGGCT 60.204 61.111 0.00 0.00 0.00 5.19
905 1072 1.629043 TTACTCGGCACTGGAGTCTT 58.371 50.000 0.00 0.00 43.39 3.01
941 1109 4.818546 CAGAAGGTGTGAACTGAATCAACT 59.181 41.667 0.00 0.00 32.90 3.16
950 1118 1.583054 GCGAACAGAAGGTGTGAACT 58.417 50.000 0.00 0.00 40.26 3.01
1095 1263 2.035312 ACGTAGCCCAGGTCGAGT 59.965 61.111 0.00 0.00 0.00 4.18
1395 1563 4.657824 ACGTACTGCGCGGCTGTT 62.658 61.111 18.15 0.00 46.11 3.16
1459 1627 1.837051 TGTCGGTGAGGTTGGAGCT 60.837 57.895 0.00 0.00 0.00 4.09
1483 1651 1.063327 CGAGGCAGTCGTAGCAGAG 59.937 63.158 0.00 0.00 44.20 3.35
1549 1717 1.351350 GCAGTTAAGGGAGTTGGAGGT 59.649 52.381 0.00 0.00 0.00 3.85
1563 1731 1.203994 GCGGTGAGGTAGAAGCAGTTA 59.796 52.381 0.00 0.00 0.00 2.24
1647 1815 2.103340 GAGAGAGCGAGGCCGAAC 59.897 66.667 0.00 0.00 38.22 3.95
1678 1846 1.443407 CGGAGGCATTCGAGGATGT 59.557 57.895 0.00 0.00 0.00 3.06
1696 1864 0.039035 TTGGTGTGGGTAATGGAGCC 59.961 55.000 0.00 0.00 46.83 4.70
1812 1980 1.004679 GGACAAACCGCGGTTCCTA 60.005 57.895 41.09 0.00 37.35 2.94
1851 2019 4.619227 CCGGTGTTGGGTCGCTGT 62.619 66.667 0.00 0.00 0.00 4.40
1920 2088 2.589492 GCCGATGATGTTCCGCTCG 61.589 63.158 0.00 0.00 0.00 5.03
2130 2298 2.821366 CTGCTGCCATGGTCGTCC 60.821 66.667 14.67 0.00 0.00 4.79
2256 2424 1.375396 CGCCATTTCGAGGACCACA 60.375 57.895 0.00 0.00 0.00 4.17
2646 2814 2.234414 CTCTTTCTCCAGAAGCAGAGCT 59.766 50.000 5.48 0.00 42.56 4.09
2657 2825 3.068881 CCCGGCACTCTTTCTCCA 58.931 61.111 0.00 0.00 0.00 3.86
2826 2994 2.239681 AGTCGAAGGGGATTCTCTGT 57.760 50.000 0.00 0.00 35.61 3.41
3003 3172 4.667519 ACTCCGAACTTCAGTTACAAGT 57.332 40.909 0.00 0.00 38.56 3.16
3069 3240 5.007626 TCGGTATTTCAGCACAAGATAATGC 59.992 40.000 0.00 0.00 42.39 3.56
3097 3268 5.820131 TCATTCCGCATTTTGTACATGATC 58.180 37.500 0.00 0.00 0.00 2.92
3099 3270 5.635417 TTCATTCCGCATTTTGTACATGA 57.365 34.783 0.00 0.00 0.00 3.07
3106 3277 8.494347 TGAACTTTTATTTCATTCCGCATTTTG 58.506 29.630 0.00 0.00 0.00 2.44
3110 3281 6.686630 TGTGAACTTTTATTTCATTCCGCAT 58.313 32.000 0.00 0.00 35.47 4.73
3111 3282 6.078202 TGTGAACTTTTATTTCATTCCGCA 57.922 33.333 0.00 0.00 35.47 5.69
3112 3283 6.806249 TGATGTGAACTTTTATTTCATTCCGC 59.194 34.615 0.00 0.00 35.47 5.54
3113 3284 8.741101 TTGATGTGAACTTTTATTTCATTCCG 57.259 30.769 0.00 0.00 35.47 4.30
3161 3335 7.015289 CGGTGAATAGTTTGTAATGACAACAG 58.985 38.462 0.00 0.00 45.29 3.16
3190 3365 1.355381 TCCCTGATCACCACAATTGCT 59.645 47.619 5.05 0.00 0.00 3.91
3198 3373 3.156293 CATGTTGTTTCCCTGATCACCA 58.844 45.455 0.00 0.00 0.00 4.17
3278 3454 4.478371 CCGCCTGCTGATCTGCCA 62.478 66.667 20.39 8.85 0.00 4.92
3312 3488 6.515648 CGATACAGTCGGGCTCTAAAAGCT 62.516 50.000 0.00 0.00 45.97 3.74
3313 3489 4.339131 CGATACAGTCGGGCTCTAAAAGC 61.339 52.174 0.00 0.00 46.47 3.51
3336 3512 4.720649 ACGTAGTAGCTTGATGATGTGT 57.279 40.909 0.00 0.00 41.94 3.72
3377 3553 5.237779 TCCTTCGTTTGTTATCTGTTTGGAC 59.762 40.000 0.00 0.00 0.00 4.02
3414 3590 3.057736 GGCTTGTATGTCCATCATGCATC 60.058 47.826 0.00 0.00 45.54 3.91
3420 3596 2.356022 CCACTGGCTTGTATGTCCATCA 60.356 50.000 0.00 0.00 0.00 3.07
3519 3695 1.144057 GATGCCGATCACCTTCCGT 59.856 57.895 0.00 0.00 0.00 4.69
3708 3897 4.506625 GGATAGGGGCACTACATTATGCAA 60.507 45.833 0.00 0.00 43.93 4.08
3765 3963 8.216453 CACCTGAATTTTCATTTTAAAAGAGCG 58.784 33.333 6.79 0.00 36.46 5.03
3827 4027 7.972277 CCTTCCATCAATAAGAAATGTTGACAG 59.028 37.037 0.00 0.00 41.25 3.51
3877 4077 7.400599 ACATACATGAAATTGCTGAATGAGT 57.599 32.000 0.00 0.00 0.00 3.41
3887 4087 9.796062 GTTTTGTTAGCAACATACATGAAATTG 57.204 29.630 0.00 0.00 41.79 2.32


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

AutoCloner maintained by Alex Coulton.