Multiple sequence alignment - TraesCS3B01G377200

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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 TraesCS3B01G377200 chr3B 100.000 3089 0 0 1 3089 593923480 593920392 0.000000e+00 5705.0
1 TraesCS3B01G377200 chr3D 91.039 2790 99 59 1 2725 452242144 452239441 0.000000e+00 3627.0
2 TraesCS3B01G377200 chr3D 86.216 370 37 7 2723 3088 452239180 452238821 3.740000e-104 388.0
3 TraesCS3B01G377200 chr3A 89.159 2177 97 57 325 2456 594592206 594590124 0.000000e+00 2584.0
4 TraesCS3B01G377200 chr3A 91.218 353 19 5 2573 2913 594589836 594589484 1.300000e-128 470.0
5 TraesCS3B01G377200 chr1B 82.011 189 31 3 1877 2063 533089619 533089806 1.150000e-34 158.0
6 TraesCS3B01G377200 chr1D 81.481 189 32 3 1877 2063 397631164 397631351 5.340000e-33 152.0
7 TraesCS3B01G377200 chr1A 81.481 189 32 3 1877 2063 495130435 495130622 5.340000e-33 152.0
8 TraesCS3B01G377200 chr1A 93.548 62 4 0 1012 1073 495129517 495129578 3.280000e-15 93.5
9 TraesCS3B01G377200 chr7A 80.292 137 22 5 2954 3089 23302529 23302397 7.050000e-17 99.0
10 TraesCS3B01G377200 chr7A 97.143 35 1 0 3055 3089 538339406 538339440 3.330000e-05 60.2
11 TraesCS3B01G377200 chr5B 100.000 28 0 0 3062 3089 643258196 643258223 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 TraesCS3B01G377200 chr3B 593920392 593923480 3088 True 5705.0 5705 100.0000 1 3089 1 chr3B.!!$R1 3088
1 TraesCS3B01G377200 chr3D 452238821 452242144 3323 True 2007.5 3627 88.6275 1 3088 2 chr3D.!!$R1 3087
2 TraesCS3B01G377200 chr3A 594589484 594592206 2722 True 1527.0 2584 90.1885 325 2913 2 chr3A.!!$R1 2588

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
867 914 0.235665 CGAAAACAGCACGCACAGAT 59.764 50.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2193 0.099436 GATTCACCATGCAAGACCGC 59.901 55.0 0.0 0.0 0.0 5.68 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
21 22 3.676742 CGTCTTTACGCTCGGCTC 58.323 61.111 0.00 0.00 43.12 4.70
22 23 2.215604 CGTCTTTACGCTCGGCTCG 61.216 63.158 0.00 0.00 43.12 5.03
23 24 1.136147 GTCTTTACGCTCGGCTCGA 59.864 57.895 0.00 0.00 0.00 4.04
24 25 0.248539 GTCTTTACGCTCGGCTCGAT 60.249 55.000 0.00 0.00 34.61 3.59
26 27 0.248498 CTTTACGCTCGGCTCGATCA 60.248 55.000 0.00 0.00 34.61 2.92
27 28 0.524816 TTTACGCTCGGCTCGATCAC 60.525 55.000 0.00 0.00 34.61 3.06
61 68 5.665459 AGGATTCATTCACTAGTCTTTCGG 58.335 41.667 0.00 0.00 0.00 4.30
71 78 3.948719 TCTTTCGGCCGCCCTGTT 61.949 61.111 23.51 0.00 0.00 3.16
72 79 3.431725 CTTTCGGCCGCCCTGTTC 61.432 66.667 23.51 0.00 0.00 3.18
73 80 3.901797 CTTTCGGCCGCCCTGTTCT 62.902 63.158 23.51 0.00 0.00 3.01
74 81 4.697756 TTCGGCCGCCCTGTTCTG 62.698 66.667 23.51 0.00 0.00 3.02
115 123 1.375140 CAGCCGAGCAAGCAGAGAA 60.375 57.895 0.00 0.00 0.00 2.87
125 137 1.345741 CAAGCAGAGAACCCAGACTGA 59.654 52.381 3.32 0.00 32.90 3.41
142 154 1.300233 GACTGGCCGACCGATCATC 60.300 63.158 0.00 0.00 39.70 2.92
191 203 2.896801 GCACGCTGAACCACCACTG 61.897 63.158 0.00 0.00 0.00 3.66
194 206 2.320587 CGCTGAACCACCACTGCTC 61.321 63.158 0.00 0.00 0.00 4.26
195 207 2.320587 GCTGAACCACCACTGCTCG 61.321 63.158 0.00 0.00 0.00 5.03
272 284 4.275282 GCTTTCAGCGCGCATAAG 57.725 55.556 35.10 29.30 0.00 1.73
299 318 5.511386 AACCTGATGAGAAAGAAGGTCAT 57.489 39.130 0.00 0.00 40.37 3.06
310 329 1.537889 AAGGTCATGTGGGACGGGA 60.538 57.895 0.00 0.00 38.70 5.14
311 330 1.553690 AAGGTCATGTGGGACGGGAG 61.554 60.000 0.00 0.00 38.70 4.30
336 355 2.661718 GAGGGGTGGAAAACAAACAGA 58.338 47.619 0.00 0.00 0.00 3.41
340 359 2.159156 GGGTGGAAAACAAACAGACCAC 60.159 50.000 0.00 0.00 44.50 4.16
448 471 4.532036 CCCTATCCCCTGCCCCCA 62.532 72.222 0.00 0.00 0.00 4.96
489 512 4.149922 ACTCACGTCAATAAACACATCACG 59.850 41.667 0.00 0.00 0.00 4.35
815 862 2.674220 CCTTCCCCTGCACCTCTCC 61.674 68.421 0.00 0.00 0.00 3.71
816 863 1.614824 CTTCCCCTGCACCTCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
817 864 1.613630 TTCCCCTGCACCTCTCCTC 60.614 63.158 0.00 0.00 0.00 3.71
818 865 3.086600 CCCCTGCACCTCTCCTCC 61.087 72.222 0.00 0.00 0.00 4.30
819 866 3.086600 CCCTGCACCTCTCCTCCC 61.087 72.222 0.00 0.00 0.00 4.30
820 867 3.086600 CCTGCACCTCTCCTCCCC 61.087 72.222 0.00 0.00 0.00 4.81
865 912 4.194312 CGAAAACAGCACGCACAG 57.806 55.556 0.00 0.00 0.00 3.66
867 914 0.235665 CGAAAACAGCACGCACAGAT 59.764 50.000 0.00 0.00 0.00 2.90
873 920 1.301953 AGCACGCACAGATCAGCAA 60.302 52.632 0.00 0.00 0.00 3.91
875 922 0.727122 GCACGCACAGATCAGCAAAC 60.727 55.000 0.00 0.00 0.00 2.93
883 930 3.437741 CACAGATCAGCAAACACATAGCA 59.562 43.478 0.00 0.00 0.00 3.49
894 941 1.065109 ACATAGCATACGCGCACGA 59.935 52.632 5.73 0.00 45.49 4.35
897 944 2.677573 ATAGCATACGCGCACGAGCA 62.678 55.000 5.73 0.00 45.49 4.26
898 945 4.271170 GCATACGCGCACGAGCAG 62.271 66.667 5.73 0.49 43.93 4.24
899 946 4.271170 CATACGCGCACGAGCAGC 62.271 66.667 5.73 8.47 43.93 5.25
957 1013 2.989639 CATTCCTCTGCCCGGTGA 59.010 61.111 0.00 0.00 0.00 4.02
970 1026 2.281761 GGTGAGTGGCCAGTGTGG 60.282 66.667 20.47 0.00 41.55 4.17
1059 1115 0.032952 ACGCGTGGTTCTTCAAGCTA 59.967 50.000 12.93 0.00 39.39 3.32
1950 2027 0.036577 CCATGGAGGAGATGATCGCC 60.037 60.000 5.56 7.15 41.22 5.54
1968 2045 1.446792 CGAGAACGGCATCTGCACT 60.447 57.895 4.33 0.00 44.36 4.40
2070 2147 2.839098 CATATCTGGGCCGGCCTT 59.161 61.111 42.70 26.73 36.10 4.35
2101 2178 2.158986 AGCATGTAGTAGCAAGCAGAGG 60.159 50.000 0.00 0.00 35.77 3.69
2104 2181 2.808919 TGTAGTAGCAAGCAGAGGAGT 58.191 47.619 0.00 0.00 0.00 3.85
2105 2182 2.493675 TGTAGTAGCAAGCAGAGGAGTG 59.506 50.000 0.00 0.00 0.00 3.51
2106 2183 0.248843 AGTAGCAAGCAGAGGAGTGC 59.751 55.000 0.00 0.00 44.35 4.40
2112 2189 2.813042 GCAGAGGAGTGCTCGTGC 60.813 66.667 16.07 16.07 40.54 5.34
2113 2190 2.505777 CAGAGGAGTGCTCGTGCG 60.506 66.667 5.96 0.00 43.34 5.34
2114 2191 2.673341 AGAGGAGTGCTCGTGCGA 60.673 61.111 5.96 0.00 43.34 5.10
2115 2192 2.049185 AGAGGAGTGCTCGTGCGAT 61.049 57.895 5.96 0.00 43.34 4.58
2116 2193 1.875813 GAGGAGTGCTCGTGCGATG 60.876 63.158 4.84 0.00 43.34 3.84
2200 2283 8.443953 AATTAGCTCTTGTTAATGCTCCTAAG 57.556 34.615 0.00 0.00 37.02 2.18
2252 2341 0.392336 TGTGAAGCCAAAACCATGCC 59.608 50.000 0.00 0.00 0.00 4.40
2313 2403 3.071479 GCTCCCGAACATCAACTGTAAA 58.929 45.455 0.00 0.00 36.98 2.01
2314 2404 3.500680 GCTCCCGAACATCAACTGTAAAA 59.499 43.478 0.00 0.00 36.98 1.52
2315 2405 4.023536 GCTCCCGAACATCAACTGTAAAAA 60.024 41.667 0.00 0.00 36.98 1.94
2347 2437 0.865769 CGTACAAGTGAACAGTGGGC 59.134 55.000 0.00 0.00 0.00 5.36
2350 2440 1.095228 ACAAGTGAACAGTGGGCGTG 61.095 55.000 0.00 0.00 0.00 5.34
2363 2453 4.816385 CAGTGGGCGTGATAACTGATAAAT 59.184 41.667 0.00 0.00 42.09 1.40
2391 2481 5.196341 TGGTAGAACCGCAGAAGTATATG 57.804 43.478 0.00 0.00 42.58 1.78
2445 2540 2.163818 TACTGTTGTTGGGCTCGAAG 57.836 50.000 0.00 0.00 0.00 3.79
2447 2542 1.134220 ACTGTTGTTGGGCTCGAAGAA 60.134 47.619 0.00 0.00 34.09 2.52
2448 2543 1.532868 CTGTTGTTGGGCTCGAAGAAG 59.467 52.381 0.00 0.00 34.09 2.85
2449 2544 1.134220 TGTTGTTGGGCTCGAAGAAGT 60.134 47.619 0.00 0.00 34.09 3.01
2541 2668 9.661563 TCAGTACTTCAGTTGAAACTTTTAAGA 57.338 29.630 12.96 0.00 37.08 2.10
2542 2669 9.922305 CAGTACTTCAGTTGAAACTTTTAAGAG 57.078 33.333 12.96 0.00 37.08 2.85
2543 2670 9.886132 AGTACTTCAGTTGAAACTTTTAAGAGA 57.114 29.630 12.96 0.00 37.08 3.10
2641 2907 0.109132 CGGGCAACAAATCTTGGAGC 60.109 55.000 0.00 0.00 39.74 4.70
2688 2959 0.247736 CTTGCGTGGTAGCTTCCTCT 59.752 55.000 11.05 0.00 38.13 3.69
2881 3421 9.909644 GGTAATACACTTGATAATACGTGAGAT 57.090 33.333 0.00 0.00 0.00 2.75
2894 3434 1.202043 CGTGAGATCGTCGTGCTAAGT 60.202 52.381 0.00 0.00 0.00 2.24
2913 3453 7.710907 TGCTAAGTCAACATACCAGATTGATAC 59.289 37.037 0.00 0.00 34.98 2.24
2948 3488 7.095187 ACAGAAATACTCAAAAATCAGACGTCC 60.095 37.037 13.01 0.00 0.00 4.79
2952 3492 3.679980 ACTCAAAAATCAGACGTCCGATG 59.320 43.478 14.82 6.01 0.00 3.84
2958 3498 2.933495 TCAGACGTCCGATGTTTAGG 57.067 50.000 13.01 0.00 0.00 2.69
2961 3501 1.480954 AGACGTCCGATGTTTAGGCAT 59.519 47.619 13.01 0.00 0.00 4.40
2962 3502 1.593006 GACGTCCGATGTTTAGGCATG 59.407 52.381 3.51 0.00 0.00 4.06
2963 3503 1.206132 ACGTCCGATGTTTAGGCATGA 59.794 47.619 0.00 0.00 0.00 3.07
2964 3504 1.593006 CGTCCGATGTTTAGGCATGAC 59.407 52.381 0.00 0.00 0.00 3.06
2965 3505 2.627945 GTCCGATGTTTAGGCATGACA 58.372 47.619 0.00 0.00 0.00 3.58
2967 3507 3.438781 GTCCGATGTTTAGGCATGACAAA 59.561 43.478 0.00 0.00 0.00 2.83
2968 3508 4.075682 TCCGATGTTTAGGCATGACAAAA 58.924 39.130 0.00 0.00 0.00 2.44
2969 3509 4.704540 TCCGATGTTTAGGCATGACAAAAT 59.295 37.500 0.00 0.00 0.00 1.82
2970 3510 5.036737 CCGATGTTTAGGCATGACAAAATC 58.963 41.667 0.00 0.00 0.00 2.17
2971 3511 4.730042 CGATGTTTAGGCATGACAAAATCG 59.270 41.667 9.18 9.18 0.00 3.34
2972 3512 5.447144 CGATGTTTAGGCATGACAAAATCGA 60.447 40.000 15.81 0.00 29.59 3.59
2973 3513 5.295431 TGTTTAGGCATGACAAAATCGAG 57.705 39.130 0.00 0.00 0.00 4.04
2974 3514 4.098416 GTTTAGGCATGACAAAATCGAGC 58.902 43.478 0.00 0.00 0.00 5.03
2985 3525 5.627367 TGACAAAATCGAGCGTTTTTAATGG 59.373 36.000 10.25 3.31 0.00 3.16
2990 3530 7.964545 AAATCGAGCGTTTTTAATGGTAATC 57.035 32.000 0.00 0.00 0.00 1.75
2991 3531 6.671614 ATCGAGCGTTTTTAATGGTAATCA 57.328 33.333 0.00 0.00 0.00 2.57
2992 3532 6.483385 TCGAGCGTTTTTAATGGTAATCAA 57.517 33.333 0.00 0.00 0.00 2.57
2994 3534 6.797995 TCGAGCGTTTTTAATGGTAATCAAAC 59.202 34.615 0.00 0.00 0.00 2.93
3002 3542 2.645730 TGGTAATCAAACATTGGCGC 57.354 45.000 0.00 0.00 0.00 6.53
3004 3544 1.131504 GGTAATCAAACATTGGCGCGA 59.868 47.619 12.10 0.00 0.00 5.87
3005 3545 2.173964 GTAATCAAACATTGGCGCGAC 58.826 47.619 12.10 8.22 0.00 5.19
3032 3573 4.679654 GTCAAATTAGTTTTCCAAGCACGG 59.320 41.667 0.00 0.00 0.00 4.94
3033 3574 3.297830 AATTAGTTTTCCAAGCACGGC 57.702 42.857 0.00 0.00 0.00 5.68
3036 3577 1.039856 AGTTTTCCAAGCACGGCAAT 58.960 45.000 0.00 0.00 0.00 3.56
3047 3588 1.421382 CACGGCAATTTTCTGGCAAG 58.579 50.000 0.00 0.00 41.82 4.01
3059 3600 3.490439 TCTGGCAAGACATTGAACTGA 57.510 42.857 0.00 0.00 38.83 3.41
3069 3610 6.037786 AGACATTGAACTGAGACGGATTTA 57.962 37.500 0.00 0.00 0.00 1.40
3070 3611 6.644347 AGACATTGAACTGAGACGGATTTAT 58.356 36.000 0.00 0.00 0.00 1.40
3082 3623 1.872952 CGGATTTATCATGCTCGCCAA 59.127 47.619 0.00 0.00 0.00 4.52
3088 3629 4.875544 TTATCATGCTCGCCAACTAAAC 57.124 40.909 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.684479 TCTGGGTCCTGGTGATCGAG 60.684 60.000 0.00 0.00 31.58 4.04
20 21 0.684479 CTCTGGGTCCTGGTGATCGA 60.684 60.000 0.00 0.00 0.00 3.59
21 22 1.680522 CCTCTGGGTCCTGGTGATCG 61.681 65.000 0.00 0.00 0.00 3.69
22 23 0.325671 TCCTCTGGGTCCTGGTGATC 60.326 60.000 0.00 0.00 0.00 2.92
23 24 0.344790 ATCCTCTGGGTCCTGGTGAT 59.655 55.000 0.00 0.00 0.00 3.06
24 25 0.119155 AATCCTCTGGGTCCTGGTGA 59.881 55.000 0.00 0.00 0.00 4.02
26 27 0.119155 TGAATCCTCTGGGTCCTGGT 59.881 55.000 0.00 0.00 0.00 4.00
27 28 1.516110 ATGAATCCTCTGGGTCCTGG 58.484 55.000 0.00 0.00 0.00 4.45
71 78 4.156622 CGTCCGTACGCGCTCAGA 62.157 66.667 10.49 0.00 43.12 3.27
125 137 2.815308 GATGATCGGTCGGCCAGT 59.185 61.111 6.96 0.00 34.09 4.00
142 154 2.082366 GGCACATCAACTTTGCGCG 61.082 57.895 0.00 0.00 37.11 6.86
191 203 2.732843 GCCTGCGAGATAGCGAGC 60.733 66.667 0.00 0.00 40.67 5.03
269 281 9.284968 CCTTCTTTCTCATCAGGTTTTTACTTA 57.715 33.333 0.00 0.00 0.00 2.24
272 284 7.228706 TGACCTTCTTTCTCATCAGGTTTTTAC 59.771 37.037 0.00 0.00 38.01 2.01
310 329 1.462627 TTTTCCACCCCTCCCGACT 60.463 57.895 0.00 0.00 0.00 4.18
311 330 1.303074 GTTTTCCACCCCTCCCGAC 60.303 63.158 0.00 0.00 0.00 4.79
312 331 1.354168 TTGTTTTCCACCCCTCCCGA 61.354 55.000 0.00 0.00 0.00 5.14
313 332 0.468400 TTTGTTTTCCACCCCTCCCG 60.468 55.000 0.00 0.00 0.00 5.14
314 333 1.045407 GTTTGTTTTCCACCCCTCCC 58.955 55.000 0.00 0.00 0.00 4.30
315 334 1.686587 CTGTTTGTTTTCCACCCCTCC 59.313 52.381 0.00 0.00 0.00 4.30
316 335 2.361119 GTCTGTTTGTTTTCCACCCCTC 59.639 50.000 0.00 0.00 0.00 4.30
336 355 6.814954 AGTAATAGGATTGACATGAGTGGT 57.185 37.500 0.00 0.00 0.00 4.16
340 359 9.868277 GGAAGATAGTAATAGGATTGACATGAG 57.132 37.037 0.00 0.00 0.00 2.90
430 453 4.533794 GGGGGCAGGGGATAGGGT 62.534 72.222 0.00 0.00 0.00 4.34
448 471 4.447389 GTGAGTGCGTTTAAAATTGGCAAT 59.553 37.500 6.96 6.96 35.10 3.56
477 500 0.390603 CTCCCGGCGTGATGTGTTTA 60.391 55.000 6.01 0.00 0.00 2.01
489 512 0.393132 CTTTCCTTTCCTCTCCCGGC 60.393 60.000 0.00 0.00 0.00 6.13
572 601 3.450578 GGTATTTGCTTCGACGATGGTA 58.549 45.455 12.12 0.00 0.00 3.25
815 862 2.443016 CACGAGGAGGAGGGGGAG 60.443 72.222 0.00 0.00 0.00 4.30
816 863 4.779733 GCACGAGGAGGAGGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
818 865 3.465403 CTGCACGAGGAGGAGGGG 61.465 72.222 0.00 0.00 0.00 4.79
819 866 2.363018 TCTGCACGAGGAGGAGGG 60.363 66.667 0.96 0.00 33.43 4.30
820 867 3.074999 GCTCTGCACGAGGAGGAGG 62.075 68.421 12.98 0.00 40.25 4.30
861 908 3.437741 TGCTATGTGTTTGCTGATCTGTG 59.562 43.478 1.27 0.00 0.00 3.66
862 909 3.678289 TGCTATGTGTTTGCTGATCTGT 58.322 40.909 1.27 0.00 0.00 3.41
864 911 4.509230 CGTATGCTATGTGTTTGCTGATCT 59.491 41.667 0.00 0.00 0.00 2.75
865 912 4.766007 CGTATGCTATGTGTTTGCTGATC 58.234 43.478 0.00 0.00 0.00 2.92
867 914 2.351418 GCGTATGCTATGTGTTTGCTGA 59.649 45.455 0.00 0.00 38.39 4.26
873 920 0.650512 GTGCGCGTATGCTATGTGTT 59.349 50.000 8.43 0.00 39.65 3.32
875 922 1.199126 CGTGCGCGTATGCTATGTG 59.801 57.895 12.43 0.00 39.65 3.21
894 941 1.672881 GCAAAGAATATGGACGCTGCT 59.327 47.619 0.00 0.00 0.00 4.24
897 944 3.550437 AGAGCAAAGAATATGGACGCT 57.450 42.857 0.00 0.00 0.00 5.07
898 945 3.873952 AGAAGAGCAAAGAATATGGACGC 59.126 43.478 0.00 0.00 0.00 5.19
899 946 5.814705 AGAAGAAGAGCAAAGAATATGGACG 59.185 40.000 0.00 0.00 0.00 4.79
900 947 7.043059 CGTAGAAGAAGAGCAAAGAATATGGAC 60.043 40.741 0.00 0.00 0.00 4.02
902 949 6.980978 TCGTAGAAGAAGAGCAAAGAATATGG 59.019 38.462 0.00 0.00 0.00 2.74
903 950 7.993821 TCGTAGAAGAAGAGCAAAGAATATG 57.006 36.000 0.00 0.00 0.00 1.78
954 1010 2.281761 CCCACACTGGCCACTCAC 60.282 66.667 0.00 0.00 35.79 3.51
957 1013 3.252284 CCTCCCACACTGGCCACT 61.252 66.667 0.00 0.00 35.79 4.00
963 1019 0.749649 CTAGCTAGCCTCCCACACTG 59.250 60.000 12.13 0.00 0.00 3.66
970 1026 2.272447 CCTCCGCTAGCTAGCCTCC 61.272 68.421 34.27 12.39 46.34 4.30
1161 1223 0.950116 GCGGCGTGTAGTAGTAGGAT 59.050 55.000 9.37 0.00 0.00 3.24
1446 1508 2.103538 GCCGAGTCGCCGTCATTA 59.896 61.111 7.12 0.00 0.00 1.90
1524 1586 1.452833 GGAGGTGATCAGCTTGCCC 60.453 63.158 27.10 19.79 39.57 5.36
1705 1770 2.526046 CCGAGAAAGGGGTGGTGGT 61.526 63.158 0.00 0.00 0.00 4.16
1713 1778 1.798813 CTTTGTTCGTCCGAGAAAGGG 59.201 52.381 12.13 0.00 0.00 3.95
1950 2027 1.446792 AGTGCAGATGCCGTTCTCG 60.447 57.895 1.72 0.00 41.18 4.04
2070 2147 0.536724 ACTACATGCTGATGTCCGCA 59.463 50.000 1.64 1.64 42.14 5.69
2101 2178 3.906649 CGCATCGCACGAGCACTC 61.907 66.667 5.50 0.00 42.27 3.51
2106 2183 2.507102 AAGACCGCATCGCACGAG 60.507 61.111 0.00 0.00 0.00 4.18
2107 2184 2.809174 CAAGACCGCATCGCACGA 60.809 61.111 0.00 0.00 0.00 4.35
2108 2185 4.505217 GCAAGACCGCATCGCACG 62.505 66.667 0.00 0.00 0.00 5.34
2109 2186 3.422303 TGCAAGACCGCATCGCAC 61.422 61.111 0.00 0.00 36.86 5.34
2116 2193 0.099436 GATTCACCATGCAAGACCGC 59.901 55.000 0.00 0.00 0.00 5.68
2200 2283 9.178758 GGGAATCTCATATTTATCATACCCAAC 57.821 37.037 0.00 0.00 0.00 3.77
2252 2341 4.382577 GCAAGGTAGAAGGAGAGAAGAAGG 60.383 50.000 0.00 0.00 0.00 3.46
2313 2403 1.026584 GTACGCCCACACCTTGTTTT 58.973 50.000 0.00 0.00 0.00 2.43
2314 2404 0.107116 TGTACGCCCACACCTTGTTT 60.107 50.000 0.00 0.00 0.00 2.83
2315 2405 0.107116 TTGTACGCCCACACCTTGTT 60.107 50.000 0.00 0.00 0.00 2.83
2316 2406 0.534203 CTTGTACGCCCACACCTTGT 60.534 55.000 0.00 0.00 0.00 3.16
2347 2437 8.378172 ACCACCATAATTTATCAGTTATCACG 57.622 34.615 0.00 0.00 0.00 4.35
2363 2453 2.181125 TCTGCGGTTCTACCACCATAA 58.819 47.619 0.00 0.00 38.47 1.90
2382 2472 6.764560 ACCACCGTAATCCAAACATATACTTC 59.235 38.462 0.00 0.00 0.00 3.01
2388 2478 4.715792 TCCTACCACCGTAATCCAAACATA 59.284 41.667 0.00 0.00 0.00 2.29
2389 2479 3.520317 TCCTACCACCGTAATCCAAACAT 59.480 43.478 0.00 0.00 0.00 2.71
2390 2480 2.905085 TCCTACCACCGTAATCCAAACA 59.095 45.455 0.00 0.00 0.00 2.83
2391 2481 3.055602 ACTCCTACCACCGTAATCCAAAC 60.056 47.826 0.00 0.00 0.00 2.93
2456 2551 2.547826 GAAGAGGCAACACGGTATACC 58.452 52.381 12.27 12.27 41.41 2.73
2458 2553 1.135527 CGGAAGAGGCAACACGGTATA 59.864 52.381 0.00 0.00 41.41 1.47
2489 2612 1.947934 AACACGGATTTACGCGCGAC 61.948 55.000 39.36 19.99 37.37 5.19
2555 2682 9.860898 GGCACATCATTTCTCTTAAAAGTTAAT 57.139 29.630 0.00 0.00 0.00 1.40
2556 2683 8.855110 TGGCACATCATTTCTCTTAAAAGTTAA 58.145 29.630 0.00 0.00 0.00 2.01
2557 2684 8.402798 TGGCACATCATTTCTCTTAAAAGTTA 57.597 30.769 0.00 0.00 0.00 2.24
2558 2685 7.288810 TGGCACATCATTTCTCTTAAAAGTT 57.711 32.000 0.00 0.00 0.00 2.66
2559 2686 6.899393 TGGCACATCATTTCTCTTAAAAGT 57.101 33.333 0.00 0.00 0.00 2.66
2641 2907 5.464168 CAATCAAGAAACTACAGGCAAAGG 58.536 41.667 0.00 0.00 0.00 3.11
2688 2959 4.497507 CGATGTCGAGTTATGAGCTACCAA 60.498 45.833 0.00 0.00 43.02 3.67
2695 2966 3.251245 AGCCTACGATGTCGAGTTATGAG 59.749 47.826 9.67 0.00 43.02 2.90
2879 3419 2.592194 TGTTGACTTAGCACGACGATC 58.408 47.619 0.00 0.00 0.00 3.69
2881 3421 2.717580 ATGTTGACTTAGCACGACGA 57.282 45.000 0.00 0.00 0.00 4.20
2921 3461 8.827177 ACGTCTGATTTTTGAGTATTTCTGTA 57.173 30.769 0.00 0.00 0.00 2.74
2924 3464 6.090898 CGGACGTCTGATTTTTGAGTATTTCT 59.909 38.462 20.01 0.00 0.00 2.52
2927 3467 5.475719 TCGGACGTCTGATTTTTGAGTATT 58.524 37.500 23.11 0.00 0.00 1.89
2930 3470 3.380479 TCGGACGTCTGATTTTTGAGT 57.620 42.857 23.11 0.00 0.00 3.41
2933 3473 4.404507 AACATCGGACGTCTGATTTTTG 57.595 40.909 32.46 25.46 39.82 2.44
2939 3479 1.135199 GCCTAAACATCGGACGTCTGA 60.135 52.381 28.31 28.31 35.43 3.27
2941 3481 0.892755 TGCCTAAACATCGGACGTCT 59.107 50.000 16.46 0.00 0.00 4.18
2942 3482 1.593006 CATGCCTAAACATCGGACGTC 59.407 52.381 7.13 7.13 0.00 4.34
2948 3488 4.730042 CGATTTTGTCATGCCTAAACATCG 59.270 41.667 0.00 4.34 0.00 3.84
2952 3492 4.098416 GCTCGATTTTGTCATGCCTAAAC 58.902 43.478 0.00 0.00 0.00 2.01
2958 3498 2.247311 AACGCTCGATTTTGTCATGC 57.753 45.000 0.00 0.00 0.00 4.06
2961 3501 5.627367 CCATTAAAAACGCTCGATTTTGTCA 59.373 36.000 16.71 5.15 33.35 3.58
2962 3502 5.627780 ACCATTAAAAACGCTCGATTTTGTC 59.372 36.000 16.71 0.00 33.35 3.18
2963 3503 5.525199 ACCATTAAAAACGCTCGATTTTGT 58.475 33.333 16.71 6.58 33.35 2.83
2964 3504 7.555639 TTACCATTAAAAACGCTCGATTTTG 57.444 32.000 16.71 6.09 33.35 2.44
2965 3505 8.024285 TGATTACCATTAAAAACGCTCGATTTT 58.976 29.630 13.21 13.21 35.05 1.82
2967 3507 7.079182 TGATTACCATTAAAAACGCTCGATT 57.921 32.000 0.00 0.00 0.00 3.34
2968 3508 6.671614 TGATTACCATTAAAAACGCTCGAT 57.328 33.333 0.00 0.00 0.00 3.59
2969 3509 6.483385 TTGATTACCATTAAAAACGCTCGA 57.517 33.333 0.00 0.00 0.00 4.04
2970 3510 6.579292 TGTTTGATTACCATTAAAAACGCTCG 59.421 34.615 0.00 0.00 31.71 5.03
2971 3511 7.861176 TGTTTGATTACCATTAAAAACGCTC 57.139 32.000 0.00 0.00 31.71 5.03
2972 3512 8.707839 CAATGTTTGATTACCATTAAAAACGCT 58.292 29.630 0.00 0.00 31.71 5.07
2973 3513 7.954786 CCAATGTTTGATTACCATTAAAAACGC 59.045 33.333 0.00 0.00 31.71 4.84
2974 3514 7.954786 GCCAATGTTTGATTACCATTAAAAACG 59.045 33.333 0.00 0.00 31.71 3.60
2985 3525 2.173964 GTCGCGCCAATGTTTGATTAC 58.826 47.619 0.00 0.00 0.00 1.89
2990 3530 0.709467 CATTGTCGCGCCAATGTTTG 59.291 50.000 29.18 10.42 44.24 2.93
2991 3531 3.105514 CATTGTCGCGCCAATGTTT 57.894 47.368 29.18 1.07 44.24 2.83
2992 3532 4.866088 CATTGTCGCGCCAATGTT 57.134 50.000 29.18 1.46 44.24 2.71
3002 3542 7.358352 GCTTGGAAAACTAATTTGACATTGTCG 60.358 37.037 11.97 0.00 34.95 4.35
3004 3544 7.224557 GTGCTTGGAAAACTAATTTGACATTGT 59.775 33.333 0.00 0.00 0.00 2.71
3005 3545 7.566709 GTGCTTGGAAAACTAATTTGACATTG 58.433 34.615 0.00 0.00 0.00 2.82
3032 3573 4.309099 TCAATGTCTTGCCAGAAAATTGC 58.691 39.130 14.87 0.00 36.32 3.56
3033 3574 5.987347 AGTTCAATGTCTTGCCAGAAAATTG 59.013 36.000 14.05 14.05 37.03 2.32
3036 3577 4.644234 TCAGTTCAATGTCTTGCCAGAAAA 59.356 37.500 0.00 0.00 32.11 2.29
3047 3588 6.535150 TGATAAATCCGTCTCAGTTCAATGTC 59.465 38.462 0.00 0.00 0.00 3.06
3059 3600 2.408050 GCGAGCATGATAAATCCGTCT 58.592 47.619 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.