Multiple sequence alignment - TraesCS1B01G255300

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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 TraesCS1B01G255300 chr1B 100.000 3182 0 0 1 3182 449850457 449853638 0.000000e+00 5877.0
1 TraesCS1B01G255300 chr1B 89.937 2236 157 38 698 2881 449977065 449979284 0.000000e+00 2820.0
2 TraesCS1B01G255300 chr1B 84.479 509 51 10 6 489 449976143 449976648 7.990000e-131 477.0
3 TraesCS1B01G255300 chr1B 77.961 726 132 18 1138 1849 449737448 449736737 2.270000e-116 429.0
4 TraesCS1B01G255300 chr1D 88.541 2522 187 53 657 3133 334450787 334453251 0.000000e+00 2963.0
5 TraesCS1B01G255300 chr1D 78.423 723 134 16 1138 1849 334336878 334336167 4.840000e-123 451.0
6 TraesCS1B01G255300 chr1D 88.401 319 33 3 174 489 334449291 334449608 6.440000e-102 381.0
7 TraesCS1B01G255300 chr1A 88.830 1880 144 23 1 1843 432338139 432339989 0.000000e+00 2248.0
8 TraesCS1B01G255300 chr1A 92.709 1207 57 15 664 1843 432484889 432486091 0.000000e+00 1712.0
9 TraesCS1B01G255300 chr1A 84.988 1279 139 33 1944 3181 432486130 432487396 0.000000e+00 1249.0
10 TraesCS1B01G255300 chr1A 79.583 720 128 15 1138 1849 432213010 432212302 6.130000e-137 497.0
11 TraesCS1B01G255300 chr1A 94.378 249 12 2 1944 2190 432340028 432340276 6.440000e-102 381.0
12 TraesCS1B01G255300 chr1A 82.713 376 49 13 2252 2614 432340277 432340649 1.420000e-83 320.0
13 TraesCS1B01G255300 chr1A 90.323 93 9 0 2611 2703 432367344 432367436 4.310000e-24 122.0
14 TraesCS1B01G255300 chr2A 78.328 323 57 10 2442 2761 543987729 543987417 2.500000e-46 196.0
15 TraesCS1B01G255300 chr5D 100.000 28 0 0 3035 3062 51924778 51924805 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 TraesCS1B01G255300 chr1B 449850457 449853638 3181 False 5877.0 5877 100.000000 1 3182 1 chr1B.!!$F1 3181
1 TraesCS1B01G255300 chr1B 449976143 449979284 3141 False 1648.5 2820 87.208000 6 2881 2 chr1B.!!$F2 2875
2 TraesCS1B01G255300 chr1B 449736737 449737448 711 True 429.0 429 77.961000 1138 1849 1 chr1B.!!$R1 711
3 TraesCS1B01G255300 chr1D 334449291 334453251 3960 False 1672.0 2963 88.471000 174 3133 2 chr1D.!!$F1 2959
4 TraesCS1B01G255300 chr1D 334336167 334336878 711 True 451.0 451 78.423000 1138 1849 1 chr1D.!!$R1 711
5 TraesCS1B01G255300 chr1A 432484889 432487396 2507 False 1480.5 1712 88.848500 664 3181 2 chr1A.!!$F3 2517
6 TraesCS1B01G255300 chr1A 432338139 432340649 2510 False 983.0 2248 88.640333 1 2614 3 chr1A.!!$F2 2613
7 TraesCS1B01G255300 chr1A 432212302 432213010 708 True 497.0 497 79.583000 1138 1849 1 chr1A.!!$R1 711

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
453 479 0.033796 ACCACCATGGCTGAAGATGG 60.034 55.0 13.04 12.74 42.67 3.51 F
1119 2201 0.322098 CGCTCCAATTACACCCACCA 60.322 55.0 0.00 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 3260 0.813821 GACAGAAATCAAGGGCCTGC 59.186 55.0 6.92 0.0 0.0 4.85 R
2992 4158 0.329596 GTGCCCAGAAATCCCACTCT 59.670 55.0 0.00 0.0 0.0 3.24 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
31 32 6.677781 ATATTATATAACGTGTGCCATGCC 57.322 37.500 0.00 0.00 0.00 4.40
41 43 2.199257 GCCATGCCCCCATCATCA 59.801 61.111 0.00 0.00 0.00 3.07
49 51 1.956477 GCCCCCATCATCACACATAAC 59.044 52.381 0.00 0.00 0.00 1.89
51 53 3.902218 CCCCCATCATCACACATAACTT 58.098 45.455 0.00 0.00 0.00 2.66
87 90 0.038343 GCCATGCAACCACACGATTT 60.038 50.000 0.00 0.00 0.00 2.17
145 148 0.445436 CAAGCATCTGTCGACCAAGC 59.555 55.000 14.12 11.81 0.00 4.01
158 161 1.364901 CCAAGCTGTGTGCCCTTTG 59.635 57.895 0.00 0.00 44.23 2.77
160 163 0.249155 CAAGCTGTGTGCCCTTTGTG 60.249 55.000 0.00 0.00 44.23 3.33
166 169 0.814457 GTGTGCCCTTTGTGACACAA 59.186 50.000 17.02 17.02 44.02 3.33
171 174 2.499289 TGCCCTTTGTGACACAATGTTT 59.501 40.909 21.19 0.00 38.00 2.83
224 246 9.949174 ATTTTCTGGCACACAATTTTATTTTTC 57.051 25.926 0.00 0.00 0.00 2.29
225 247 8.498054 TTTCTGGCACACAATTTTATTTTTCA 57.502 26.923 0.00 0.00 0.00 2.69
247 269 5.472820 TCAAACATGTGTAATGTCTGCATCA 59.527 36.000 0.00 0.00 33.50 3.07
248 270 5.963176 AACATGTGTAATGTCTGCATCAA 57.037 34.783 0.00 0.00 33.50 2.57
286 308 1.549950 GGACATGGGGTTGTGATTGGT 60.550 52.381 0.00 0.00 0.00 3.67
311 333 6.769341 TGTGTCTTAATAGCATCATTCTGCAT 59.231 34.615 0.00 0.00 44.77 3.96
321 343 3.885724 TCATTCTGCATTAGTGACCGA 57.114 42.857 0.00 0.00 0.00 4.69
350 372 2.949644 GCGACATAGTTTTTATGGGGCT 59.050 45.455 0.00 0.00 0.00 5.19
427 449 2.890808 TTGGCTACTTCGCTCTATGG 57.109 50.000 0.00 0.00 0.00 2.74
453 479 0.033796 ACCACCATGGCTGAAGATGG 60.034 55.000 13.04 12.74 42.67 3.51
458 484 0.745486 CATGGCTGAAGATGGTGCGA 60.745 55.000 0.00 0.00 0.00 5.10
541 1471 3.131223 AGATACGTGTGTGCTAGATGCTT 59.869 43.478 0.00 0.00 43.37 3.91
549 1479 4.646492 TGTGTGCTAGATGCTTCTGATCTA 59.354 41.667 12.19 1.81 43.37 1.98
563 1493 7.605309 TGCTTCTGATCTATCATATGCGATTTT 59.395 33.333 0.00 0.00 37.08 1.82
571 1501 7.389232 TCTATCATATGCGATTTTCCATGTCT 58.611 34.615 0.00 0.00 0.00 3.41
597 1527 9.176460 TGTAATCTTGTGATGATGCTAATTTGA 57.824 29.630 0.00 0.00 32.44 2.69
643 1573 9.950680 AAAACTTTCACTGTACATGTATTTCTG 57.049 29.630 9.18 3.34 0.00 3.02
646 1576 9.120538 ACTTTCACTGTACATGTATTTCTGTTT 57.879 29.630 9.18 0.00 0.00 2.83
741 1800 2.094494 AGACAAAGCATCGATCGTCAGT 60.094 45.455 15.94 5.51 0.00 3.41
758 1817 3.186409 GTCAGTCTAATTGCAAAGCACGA 59.814 43.478 1.71 0.00 38.71 4.35
825 1895 2.091278 CCACTACTCCACTCCATCCCTA 60.091 54.545 0.00 0.00 0.00 3.53
833 1903 1.072965 CACTCCATCCCTAGGAATGCC 59.927 57.143 11.48 0.00 34.34 4.40
869 1939 5.041951 TGTTTTCTTCCATGTATTGCGAC 57.958 39.130 0.00 0.00 0.00 5.19
1115 2197 2.038387 ACATCGCTCCAATTACACCC 57.962 50.000 0.00 0.00 0.00 4.61
1119 2201 0.322098 CGCTCCAATTACACCCACCA 60.322 55.000 0.00 0.00 0.00 4.17
1134 2221 2.268920 CCATCACCTCCCCGTGTG 59.731 66.667 0.00 0.00 35.18 3.82
1550 2652 2.181021 CTGGAGGTGTACGCGGTC 59.819 66.667 12.47 3.06 0.00 4.79
1553 2655 3.434319 GAGGTGTACGCGGTCCGA 61.434 66.667 17.49 0.00 41.02 4.55
1691 2793 3.529734 AGGAAGATGAGACAGAGGAGGTA 59.470 47.826 0.00 0.00 0.00 3.08
1877 2994 2.941064 ACATCTCATGGCTGAATCAACG 59.059 45.455 0.00 0.00 33.60 4.10
1901 3018 2.916640 CCTTCTTCTTCCATCTCCAGC 58.083 52.381 0.00 0.00 0.00 4.85
1995 3112 5.326200 TCTTTCGGTTACCTCTCATCTTC 57.674 43.478 0.00 0.00 0.00 2.87
2012 3129 2.443255 TCTTCAGTTTCCTTCCTGCCTT 59.557 45.455 0.00 0.00 0.00 4.35
2094 3213 4.968259 TGGCACACTTTGTACATAGAAGT 58.032 39.130 18.69 12.17 34.14 3.01
2108 3227 9.542462 TGTACATAGAAGTAGCAATATTTGGTC 57.458 33.333 0.00 0.00 42.20 4.02
2116 3235 3.686016 AGCAATATTTGGTCGGTGAGTT 58.314 40.909 0.00 0.00 36.50 3.01
2131 3252 6.018180 GTCGGTGAGTTGTTTGAAAGAGTATT 60.018 38.462 0.00 0.00 0.00 1.89
2144 3266 6.620678 TGAAAGAGTATTAAAATGTGCAGGC 58.379 36.000 0.00 0.00 0.00 4.85
2167 3289 4.455533 CCCTTGATTTCTGTCGTGAATGAA 59.544 41.667 0.00 0.00 0.00 2.57
2315 3444 3.770666 AGTATATATGCGATCGCCACAC 58.229 45.455 35.12 22.50 41.09 3.82
2327 3456 1.066215 TCGCCACACTGCATATGAAGT 60.066 47.619 10.87 10.87 33.09 3.01
2346 3475 2.803956 AGTGTGCTTCATTTGCATTTGC 59.196 40.909 0.00 0.00 42.69 3.68
2369 3498 1.506309 TTACGCAGGCAGCACACAAG 61.506 55.000 1.96 0.00 46.13 3.16
2373 3502 2.667536 AGGCAGCACACAAGCTCG 60.668 61.111 0.00 0.00 44.54 5.03
2391 3529 4.162320 AGCTCGGATCTTCACCTTCATAAA 59.838 41.667 0.00 0.00 0.00 1.40
2393 3531 6.042093 AGCTCGGATCTTCACCTTCATAAATA 59.958 38.462 0.00 0.00 0.00 1.40
2394 3532 6.876257 GCTCGGATCTTCACCTTCATAAATAT 59.124 38.462 0.00 0.00 0.00 1.28
2426 3577 4.062293 CGTCAAACACTTACATTCCCTCA 58.938 43.478 0.00 0.00 0.00 3.86
2428 3579 5.334105 CGTCAAACACTTACATTCCCTCAAG 60.334 44.000 0.00 0.00 0.00 3.02
2430 3581 5.763204 TCAAACACTTACATTCCCTCAAGAC 59.237 40.000 0.00 0.00 0.00 3.01
2503 3654 7.615582 TGCATGAACAAAAACATTTAAACCA 57.384 28.000 0.00 0.00 0.00 3.67
2505 3656 7.550551 TGCATGAACAAAAACATTTAAACCAGA 59.449 29.630 0.00 0.00 0.00 3.86
2532 3685 3.787785 TGTACAAGTCACATGTTGTCGT 58.212 40.909 4.20 0.00 37.96 4.34
2558 3711 0.475906 CACCATCCCATCCTTCTCCC 59.524 60.000 0.00 0.00 0.00 4.30
2559 3712 0.046242 ACCATCCCATCCTTCTCCCA 59.954 55.000 0.00 0.00 0.00 4.37
2578 3741 0.890542 ACGTGTGCATTGTGCCATCT 60.891 50.000 0.00 0.00 44.23 2.90
2582 3745 1.962100 TGTGCATTGTGCCATCTTTCA 59.038 42.857 0.00 0.00 44.23 2.69
2591 3755 3.149196 GTGCCATCTTTCAAGGTTCTGA 58.851 45.455 0.00 0.00 0.00 3.27
2595 3759 4.037923 GCCATCTTTCAAGGTTCTGAAACA 59.962 41.667 8.34 0.00 39.74 2.83
2619 3783 8.549731 ACATATGATCATATCTCATGCCTTCTT 58.450 33.333 22.76 0.00 35.12 2.52
2622 3786 4.263018 TCATATCTCATGCCTTCTTCCG 57.737 45.455 0.00 0.00 0.00 4.30
2629 3793 3.944015 CTCATGCCTTCTTCCGAAAATCT 59.056 43.478 0.00 0.00 0.00 2.40
2694 3858 6.039717 AGCCATTTATGCTCGATTATGTGTTT 59.960 34.615 0.00 0.00 32.41 2.83
2703 3867 6.091305 TGCTCGATTATGTGTTTTTCTCTCAG 59.909 38.462 0.00 0.00 0.00 3.35
2709 3873 7.962964 TTATGTGTTTTTCTCTCAGTCGATT 57.037 32.000 0.00 0.00 0.00 3.34
2710 3874 5.907197 TGTGTTTTTCTCTCAGTCGATTC 57.093 39.130 0.00 0.00 0.00 2.52
2754 3918 3.446516 GCCTCCATCTTCTGCTGATTTTT 59.553 43.478 0.00 0.00 0.00 1.94
2780 3944 3.325135 CCTACATACCACCATCTCTTCCC 59.675 52.174 0.00 0.00 0.00 3.97
2785 3949 1.605058 CCACCATCTCTTCCCGACGT 61.605 60.000 0.00 0.00 0.00 4.34
2787 3951 0.611062 ACCATCTCTTCCCGACGTCA 60.611 55.000 17.16 0.00 0.00 4.35
2824 3989 1.000731 CATCTCATCTCGCCCTCTTCC 59.999 57.143 0.00 0.00 0.00 3.46
2825 3990 0.260230 TCTCATCTCGCCCTCTTCCT 59.740 55.000 0.00 0.00 0.00 3.36
2829 3994 0.107459 ATCTCGCCCTCTTCCTTTGC 60.107 55.000 0.00 0.00 0.00 3.68
2834 3999 1.884067 CGCCCTCTTCCTTTGCTTCTT 60.884 52.381 0.00 0.00 0.00 2.52
2840 4005 4.694982 CCTCTTCCTTTGCTTCTTCTTCTC 59.305 45.833 0.00 0.00 0.00 2.87
2841 4006 4.646572 TCTTCCTTTGCTTCTTCTTCTCC 58.353 43.478 0.00 0.00 0.00 3.71
2842 4007 4.349342 TCTTCCTTTGCTTCTTCTTCTCCT 59.651 41.667 0.00 0.00 0.00 3.69
2865 4030 5.121811 TCCATCTCTAGCTTTGCTTGATTC 58.878 41.667 0.00 0.00 39.34 2.52
2874 4039 3.181512 GCTTTGCTTGATTCCTCTTCTCG 60.182 47.826 0.00 0.00 0.00 4.04
2891 4056 7.086230 TCTTCTCGTATACTTTCTTGTCCTC 57.914 40.000 0.56 0.00 0.00 3.71
2892 4057 6.657966 TCTTCTCGTATACTTTCTTGTCCTCA 59.342 38.462 0.56 0.00 0.00 3.86
2929 4095 0.984230 TTTCATCACCTCCGCCTCTT 59.016 50.000 0.00 0.00 0.00 2.85
2933 4099 1.065854 CATCACCTCCGCCTCTTCTTT 60.066 52.381 0.00 0.00 0.00 2.52
2957 4123 4.103153 TCTCTTGAGCTTCTCCTTTCCAAA 59.897 41.667 0.00 0.00 0.00 3.28
2961 4127 4.536765 TGAGCTTCTCCTTTCCAAACTTT 58.463 39.130 0.00 0.00 0.00 2.66
2966 4132 5.380900 CTTCTCCTTTCCAAACTTTCTCCT 58.619 41.667 0.00 0.00 0.00 3.69
2967 4133 6.509523 TTCTCCTTTCCAAACTTTCTCCTA 57.490 37.500 0.00 0.00 0.00 2.94
2992 4158 1.207089 GCCGACCTATGCTATATGCCA 59.793 52.381 0.00 0.00 42.00 4.92
3051 4217 1.600957 CACCATCATCATCTTCACCGC 59.399 52.381 0.00 0.00 0.00 5.68
3053 4219 1.475571 CCATCATCATCTTCACCGCCA 60.476 52.381 0.00 0.00 0.00 5.69
3062 4228 0.467384 CTTCACCGCCATCCATCTCT 59.533 55.000 0.00 0.00 0.00 3.10
3063 4229 0.178767 TTCACCGCCATCCATCTCTG 59.821 55.000 0.00 0.00 0.00 3.35
3120 4289 6.127535 ACTGCCATCATTCCAACAAATTCTAG 60.128 38.462 0.00 0.00 0.00 2.43
3121 4290 5.716228 TGCCATCATTCCAACAAATTCTAGT 59.284 36.000 0.00 0.00 0.00 2.57
3133 4302 8.335532 CAACAAATTCTAGTAATGTTGGAGGA 57.664 34.615 16.80 0.00 44.29 3.71
3136 4305 7.607991 ACAAATTCTAGTAATGTTGGAGGACAG 59.392 37.037 0.00 0.00 32.19 3.51
3145 4314 5.712152 ATGTTGGAGGACAGACAATTTTC 57.288 39.130 0.00 0.00 32.19 2.29
3147 4316 3.154827 TGGAGGACAGACAATTTTCCC 57.845 47.619 0.00 0.00 0.00 3.97
3148 4317 2.084546 GGAGGACAGACAATTTTCCCG 58.915 52.381 0.00 0.00 0.00 5.14
3149 4318 2.552373 GGAGGACAGACAATTTTCCCGT 60.552 50.000 0.00 0.00 0.00 5.28
3150 4319 3.146847 GAGGACAGACAATTTTCCCGTT 58.853 45.455 0.00 0.00 0.00 4.44
3157 4326 3.049912 GACAATTTTCCCGTTGACTTGC 58.950 45.455 0.00 0.00 0.00 4.01
3166 4335 2.099098 CCCGTTGACTTGCCCATTTATC 59.901 50.000 0.00 0.00 0.00 1.75
3169 4338 1.388547 TGACTTGCCCATTTATCGGC 58.611 50.000 0.00 0.00 45.92 5.54
3181 4350 0.830648 TTATCGGCACCTCTCTTGGG 59.169 55.000 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.111116 GTGTGATGATGGGGGCATGG 61.111 60.000 0.00 0.00 0.00 3.66
31 32 7.587037 AAATAAGTTATGTGTGATGATGGGG 57.413 36.000 0.00 0.00 0.00 4.96
49 51 8.666573 TGCATGGCAATGTTTGAAATAAATAAG 58.333 29.630 2.31 0.00 34.76 1.73
51 53 8.557592 TTGCATGGCAATGTTTGAAATAAATA 57.442 26.923 2.31 0.00 43.99 1.40
72 74 1.950216 TGCTTAAATCGTGTGGTTGCA 59.050 42.857 0.00 0.00 0.00 4.08
87 90 3.904571 ACGAACACGATTGTACTGCTTA 58.095 40.909 0.00 0.00 33.55 3.09
145 148 0.381801 GTGTCACAAAGGGCACACAG 59.618 55.000 0.00 0.00 39.21 3.66
158 161 5.375417 TGATCCATGAAACATTGTGTCAC 57.625 39.130 11.85 0.23 32.15 3.67
160 163 4.418392 GCTGATCCATGAAACATTGTGTC 58.582 43.478 0.00 0.00 0.00 3.67
224 246 5.701855 TGATGCAGACATTACACATGTTTG 58.298 37.500 0.00 2.00 36.35 2.93
225 247 5.963176 TGATGCAGACATTACACATGTTT 57.037 34.783 0.00 0.00 36.35 2.83
239 261 4.378356 GCGTTGAACTATGTTTGATGCAGA 60.378 41.667 0.00 0.00 0.00 4.26
247 269 1.161843 CCCGGCGTTGAACTATGTTT 58.838 50.000 6.01 0.00 0.00 2.83
248 270 0.675522 CCCCGGCGTTGAACTATGTT 60.676 55.000 6.01 0.00 0.00 2.71
286 308 6.114767 TGCAGAATGATGCTATTAAGACACA 58.885 36.000 4.25 0.00 46.63 3.72
311 333 0.539986 GCCCCTCATTCGGTCACTAA 59.460 55.000 0.00 0.00 0.00 2.24
321 343 3.366052 AAAACTATGTCGCCCCTCATT 57.634 42.857 0.00 0.00 0.00 2.57
362 384 2.141535 AGTCGAAGTTGAGTGAGCAC 57.858 50.000 0.00 0.00 0.00 4.40
453 479 1.930371 GCACCAAAAACTCCATCGCAC 60.930 52.381 0.00 0.00 0.00 5.34
541 1471 7.614494 TGGAAAATCGCATATGATAGATCAGA 58.386 34.615 6.97 0.00 40.64 3.27
549 1479 5.766670 ACAGACATGGAAAATCGCATATGAT 59.233 36.000 6.97 0.00 0.00 2.45
563 1493 6.298441 TCATCACAAGATTACAGACATGGA 57.702 37.500 0.00 0.00 30.20 3.41
571 1501 9.176460 TCAAATTAGCATCATCACAAGATTACA 57.824 29.630 0.00 0.00 30.20 2.41
617 1547 9.950680 CAGAAATACATGTACAGTGAAAGTTTT 57.049 29.630 7.96 0.63 0.00 2.43
619 1549 8.677148 ACAGAAATACATGTACAGTGAAAGTT 57.323 30.769 7.96 0.00 0.00 2.66
623 1553 7.717436 TGGAAACAGAAATACATGTACAGTGAA 59.283 33.333 7.96 0.00 35.01 3.18
741 1800 3.374988 CCTCATCGTGCTTTGCAATTAGA 59.625 43.478 0.00 0.00 41.47 2.10
833 1903 7.102993 TGGAAGAAAACAAAAGAAGGAAAAGG 58.897 34.615 0.00 0.00 0.00 3.11
835 1905 8.100164 ACATGGAAGAAAACAAAAGAAGGAAAA 58.900 29.630 0.00 0.00 0.00 2.29
869 1939 1.600663 CCGACTCCGATTCCATTCTCG 60.601 57.143 0.00 0.00 38.22 4.04
1033 2106 2.553028 GGAGTTGGAGGATTTGCAGTGA 60.553 50.000 0.00 0.00 0.00 3.41
1098 2180 1.408266 GGTGGGTGTAATTGGAGCGAT 60.408 52.381 0.00 0.00 0.00 4.58
1115 2197 2.268920 CACGGGGAGGTGATGGTG 59.731 66.667 0.00 0.00 40.38 4.17
1119 2201 2.291043 GGACACACGGGGAGGTGAT 61.291 63.158 0.00 0.00 40.38 3.06
1349 2436 3.458163 TCAGCGGATGGGTCGACC 61.458 66.667 27.04 27.04 40.81 4.79
1691 2793 3.318006 CTCCTGCTGCTGCTGCTCT 62.318 63.158 27.67 0.00 40.48 4.09
1858 2975 3.548745 TCGTTGATTCAGCCATGAGAT 57.451 42.857 0.00 0.00 36.61 2.75
1901 3018 3.119316 ACTCATCCGTTCTAAGTGCAGAG 60.119 47.826 0.00 0.00 0.00 3.35
1995 3112 2.575805 AGAAGGCAGGAAGGAAACTG 57.424 50.000 0.00 0.00 42.68 3.16
2012 3129 1.065701 GCGAGCTTGGTCGAAGATAGA 59.934 52.381 23.47 0.00 42.85 1.98
2094 3213 4.481368 ACTCACCGACCAAATATTGCTA 57.519 40.909 0.00 0.00 0.00 3.49
2108 3227 5.924475 ATACTCTTTCAAACAACTCACCG 57.076 39.130 0.00 0.00 0.00 4.94
2116 3235 9.462174 CTGCACATTTTAATACTCTTTCAAACA 57.538 29.630 0.00 0.00 0.00 2.83
2131 3252 2.300956 TCAAGGGCCTGCACATTTTA 57.699 45.000 6.92 0.00 0.00 1.52
2139 3260 0.813821 GACAGAAATCAAGGGCCTGC 59.186 55.000 6.92 0.00 0.00 4.85
2144 3266 4.002982 TCATTCACGACAGAAATCAAGGG 58.997 43.478 0.00 0.00 0.00 3.95
2167 3289 8.958119 TTACTGAAGTTAGAAAACAGACATGT 57.042 30.769 0.00 0.00 43.15 3.21
2301 3430 3.197790 GCAGTGTGGCGATCGCAT 61.198 61.111 38.00 17.30 44.11 4.73
2346 3475 2.358615 TGCTGCCTGCGTAACCTG 60.359 61.111 0.00 0.00 46.63 4.00
2350 3479 1.506309 CTTGTGTGCTGCCTGCGTAA 61.506 55.000 0.00 0.00 46.63 3.18
2369 3498 2.611225 ATGAAGGTGAAGATCCGAGC 57.389 50.000 0.00 0.00 0.00 5.03
2417 3568 3.991605 CGTTTACGTCTTGAGGGAATG 57.008 47.619 0.00 0.00 34.11 2.67
2430 3581 5.258685 TCTTGATGTGCTAAACGTTTACG 57.741 39.130 16.59 13.29 46.33 3.18
2471 3622 4.325741 TGTTTTTGTTCATGCAACTTGTCG 59.674 37.500 0.00 0.00 35.79 4.35
2503 3654 5.929697 CATGTGACTTGTACATGTGTTCT 57.070 39.130 18.24 0.00 46.37 3.01
2529 3682 2.048597 GGATGGTGCACACGACGA 60.049 61.111 20.43 0.00 0.00 4.20
2532 3685 1.078497 GATGGGATGGTGCACACGA 60.078 57.895 20.43 1.58 0.00 4.35
2578 3741 8.634335 TGATCATATGTTTCAGAACCTTGAAA 57.366 30.769 1.90 0.00 42.93 2.69
2591 3755 9.175312 GAAGGCATGAGATATGATCATATGTTT 57.825 33.333 28.79 16.17 35.64 2.83
2595 3759 8.212312 GGAAGAAGGCATGAGATATGATCATAT 58.788 37.037 25.04 25.04 35.64 1.78
2622 3786 3.181506 GGATTCAGTGGTGCGAGATTTTC 60.182 47.826 0.00 0.00 0.00 2.29
2629 3793 1.811965 CAAATGGATTCAGTGGTGCGA 59.188 47.619 0.00 0.00 0.00 5.10
2651 3815 2.551721 GGCTCATCATGTTGGATCCGAT 60.552 50.000 4.57 0.00 0.00 4.18
2694 3858 6.434652 ACTTAAGGAGAATCGACTGAGAGAAA 59.565 38.462 7.53 0.00 34.37 2.52
2730 3894 1.210538 TCAGCAGAAGATGGAGGCAT 58.789 50.000 0.00 0.00 0.00 4.40
2754 3918 2.965831 GAGATGGTGGTATGTAGGCTCA 59.034 50.000 0.00 0.00 0.00 4.26
2780 3944 1.403493 GCAGAGAGCATATGACGTCG 58.597 55.000 11.62 0.00 44.79 5.12
2808 3973 1.208052 CAAAGGAAGAGGGCGAGATGA 59.792 52.381 0.00 0.00 0.00 2.92
2824 3989 4.013267 TGGAGGAGAAGAAGAAGCAAAG 57.987 45.455 0.00 0.00 0.00 2.77
2825 3990 4.288105 AGATGGAGGAGAAGAAGAAGCAAA 59.712 41.667 0.00 0.00 0.00 3.68
2829 3994 5.010012 GCTAGAGATGGAGGAGAAGAAGAAG 59.990 48.000 0.00 0.00 0.00 2.85
2834 3999 4.534647 AAGCTAGAGATGGAGGAGAAGA 57.465 45.455 0.00 0.00 0.00 2.87
2840 4005 3.118482 TCAAGCAAAGCTAGAGATGGAGG 60.118 47.826 0.00 0.00 38.25 4.30
2841 4006 4.134379 TCAAGCAAAGCTAGAGATGGAG 57.866 45.455 0.00 0.00 38.25 3.86
2842 4007 4.767578 ATCAAGCAAAGCTAGAGATGGA 57.232 40.909 0.00 0.00 38.25 3.41
2865 4030 6.095720 AGGACAAGAAAGTATACGAGAAGAGG 59.904 42.308 0.00 0.00 0.00 3.69
2874 4039 8.035394 TGAGTTGATGAGGACAAGAAAGTATAC 58.965 37.037 0.00 0.00 0.00 1.47
2913 4079 0.539051 AAGAAGAGGCGGAGGTGATG 59.461 55.000 0.00 0.00 0.00 3.07
2917 4083 1.276705 GAGAAAAGAAGAGGCGGAGGT 59.723 52.381 0.00 0.00 0.00 3.85
2923 4089 3.673902 AGCTCAAGAGAAAAGAAGAGGC 58.326 45.455 0.32 0.00 0.00 4.70
2929 4095 5.559148 AAGGAGAAGCTCAAGAGAAAAGA 57.441 39.130 0.32 0.00 31.08 2.52
2933 4099 3.648067 TGGAAAGGAGAAGCTCAAGAGAA 59.352 43.478 0.32 0.00 31.08 2.87
2957 4123 1.757699 GTCGGCCTGATAGGAGAAAGT 59.242 52.381 0.00 0.00 37.67 2.66
2961 4127 1.146452 TAGGTCGGCCTGATAGGAGA 58.854 55.000 21.58 0.00 46.47 3.71
2966 4132 2.597578 TAGCATAGGTCGGCCTGATA 57.402 50.000 21.58 3.53 46.47 2.15
2967 4133 1.944177 ATAGCATAGGTCGGCCTGAT 58.056 50.000 21.58 4.76 46.47 2.90
2988 4154 3.963733 CAGAAATCCCACTCTGGCA 57.036 52.632 0.00 0.00 35.79 4.92
2992 4158 0.329596 GTGCCCAGAAATCCCACTCT 59.670 55.000 0.00 0.00 0.00 3.24
3018 4184 3.874383 TGATGGTGTTGGAGAGGAAAA 57.126 42.857 0.00 0.00 0.00 2.29
3051 4217 2.395336 TCCTCTCCAGAGATGGATGG 57.605 55.000 5.08 4.13 44.74 3.51
3053 4219 3.072768 GCAATTCCTCTCCAGAGATGGAT 59.927 47.826 5.08 3.21 44.74 3.41
3062 4228 0.694771 AGTGCAGCAATTCCTCTCCA 59.305 50.000 0.00 0.00 0.00 3.86
3063 4229 1.742268 GAAGTGCAGCAATTCCTCTCC 59.258 52.381 22.41 0.00 33.16 3.71
3120 4289 6.575162 AAATTGTCTGTCCTCCAACATTAC 57.425 37.500 0.00 0.00 0.00 1.89
3121 4290 6.208599 GGAAAATTGTCTGTCCTCCAACATTA 59.791 38.462 0.00 0.00 0.00 1.90
3133 4302 3.551846 AGTCAACGGGAAAATTGTCTGT 58.448 40.909 0.00 0.00 0.00 3.41
3136 4305 3.049912 GCAAGTCAACGGGAAAATTGTC 58.950 45.455 0.00 0.00 0.00 3.18
3145 4314 1.540267 TAAATGGGCAAGTCAACGGG 58.460 50.000 0.00 0.00 0.00 5.28
3147 4316 2.223249 CCGATAAATGGGCAAGTCAACG 60.223 50.000 0.00 0.00 0.00 4.10
3148 4317 3.420839 CCGATAAATGGGCAAGTCAAC 57.579 47.619 0.00 0.00 0.00 3.18
3157 4326 1.417890 AGAGAGGTGCCGATAAATGGG 59.582 52.381 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.