Multiple sequence alignment - TraesCS4A01G077300

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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 TraesCS4A01G077300 chr4A 100.000 4154 0 0 1 4154 76426179 76422026 0.000000e+00 7672.0
1 TraesCS4A01G077300 chr4D 91.789 3410 181 45 2 3367 394858120 394854766 0.000000e+00 4654.0
2 TraesCS4A01G077300 chr4D 89.313 524 31 12 3367 3873 394854347 394853832 5.860000e-178 634.0
3 TraesCS4A01G077300 chr4D 93.725 255 11 2 3895 4149 394853838 394853589 1.090000e-100 377.0
4 TraesCS4A01G077300 chr4B 92.685 2365 106 30 1036 3364 485557161 485554828 0.000000e+00 3347.0
5 TraesCS4A01G077300 chr4B 92.152 790 46 10 3367 4154 485554783 485554008 0.000000e+00 1101.0
6 TraesCS4A01G077300 chr4B 92.991 214 13 2 757 968 485557646 485557433 1.120000e-80 311.0
7 TraesCS4A01G077300 chr4B 81.115 323 44 8 329 651 485558098 485557793 4.150000e-60 243.0
8 TraesCS4A01G077300 chr5B 88.136 59 6 1 25 83 62970056 62970113 7.450000e-08 69.4


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 TraesCS4A01G077300 chr4A 76422026 76426179 4153 True 7672.000000 7672 100.00000 1 4154 1 chr4A.!!$R1 4153
1 TraesCS4A01G077300 chr4D 394853589 394858120 4531 True 1888.333333 4654 91.60900 2 4149 3 chr4D.!!$R1 4147
2 TraesCS4A01G077300 chr4B 485554008 485558098 4090 True 1250.500000 3347 89.73575 329 4154 4 chr4B.!!$R1 3825

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
469 483 0.176910 TGCAGAAGTGGTCGTCAACA 59.823 50.000 0.00 0.00 0.0 3.33 F
526 540 0.607489 GAGCAACATCAGCCACCAGT 60.607 55.000 0.00 0.00 0.0 4.00 F
1029 1135 1.075600 CTCCACCTCCCTCTCCCTC 60.076 68.421 0.00 0.00 0.0 4.30 F
1935 2248 2.257371 GAAGGCCGGGCGAAAAAC 59.743 61.111 23.81 7.79 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2235 0.241481 TGTAATGTTTTTCGCCCGGC 59.759 50.0 0.00 0.0 0.00 6.13 R
1994 2307 0.687757 AGGTAGCTCCGATTCTGCCA 60.688 55.0 0.00 0.0 41.99 4.92 R
2029 2342 1.996786 CTATGCCAAACAGCCAGCCG 61.997 60.0 0.00 0.0 0.00 5.52 R
3320 3659 0.103208 CGGAGCAGGTAGTAGCAAGG 59.897 60.0 1.58 0.0 0.00 3.61 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
264 269 0.467844 TAGGCCCAAATCATGCGCAT 60.468 50.000 19.28 19.28 34.39 4.73
292 297 1.142314 GCGGGTGCGTGTAATCCTA 59.858 57.895 0.00 0.00 0.00 2.94
319 324 2.232208 GCCTTCTTTTAGCAGGTGCAAT 59.768 45.455 4.48 0.00 45.16 3.56
321 326 4.800582 GCCTTCTTTTAGCAGGTGCAATTT 60.801 41.667 4.48 0.00 45.16 1.82
322 327 5.299949 CCTTCTTTTAGCAGGTGCAATTTT 58.700 37.500 4.48 0.00 45.16 1.82
346 360 0.945099 TGCATTCGCGGTTGTTTACA 59.055 45.000 6.13 0.00 42.97 2.41
352 366 1.062873 CGCGGTTGTTTACATTGGCG 61.063 55.000 0.00 7.28 33.89 5.69
354 368 1.600912 GCGGTTGTTTACATTGGCGTT 60.601 47.619 0.00 0.00 0.00 4.84
364 378 1.813753 ATTGGCGTTGTCGATCCGG 60.814 57.895 0.00 0.00 39.71 5.14
404 418 3.806625 ATGCAATGAAGCCATAACACC 57.193 42.857 0.00 0.00 31.59 4.16
406 420 1.742831 GCAATGAAGCCATAACACCGA 59.257 47.619 0.00 0.00 31.59 4.69
416 430 3.120792 CCATAACACCGACCACTAATCG 58.879 50.000 0.00 0.00 39.33 3.34
425 439 2.748605 GACCACTAATCGCCATCTGAG 58.251 52.381 0.00 0.00 0.00 3.35
449 463 2.279741 GATTTGCATCGCCACAGACTA 58.720 47.619 0.00 0.00 0.00 2.59
453 467 0.811219 GCATCGCCACAGACTATGCA 60.811 55.000 0.00 0.00 41.94 3.96
464 478 2.094494 CAGACTATGCAGAAGTGGTCGT 60.094 50.000 9.10 0.00 0.00 4.34
469 483 0.176910 TGCAGAAGTGGTCGTCAACA 59.823 50.000 0.00 0.00 0.00 3.33
498 512 3.573491 GCGCCTTGTCGGTATGCC 61.573 66.667 0.00 0.00 34.25 4.40
503 517 1.299541 CCTTGTCGGTATGCCATGAC 58.700 55.000 0.00 0.67 34.09 3.06
518 532 2.422479 CCATGACCTTGAGCAACATCAG 59.578 50.000 0.00 0.00 0.00 2.90
526 540 0.607489 GAGCAACATCAGCCACCAGT 60.607 55.000 0.00 0.00 0.00 4.00
537 551 1.598701 GCCACCAGTGCCAATCCTTC 61.599 60.000 0.00 0.00 0.00 3.46
539 553 1.171308 CACCAGTGCCAATCCTTCTG 58.829 55.000 0.00 0.00 0.00 3.02
542 556 1.681166 CCAGTGCCAATCCTTCTGAGG 60.681 57.143 0.00 0.00 45.02 3.86
548 562 2.881403 GCCAATCCTTCTGAGGCTTCAA 60.881 50.000 0.00 0.00 43.21 2.69
566 580 4.462508 TCAAGATCATTCACGAGAAGCT 57.537 40.909 1.01 0.00 37.14 3.74
618 632 2.488204 AGGCAGCTTCTTCTCTTTCC 57.512 50.000 0.00 0.00 0.00 3.13
703 805 8.079211 TGCTACTTAATAAAGGTCACAGATCT 57.921 34.615 0.00 0.00 37.01 2.75
793 897 4.261801 CTGAAACGGAAATGACCCATAGT 58.738 43.478 0.00 0.00 0.00 2.12
794 898 5.423704 TGAAACGGAAATGACCCATAGTA 57.576 39.130 0.00 0.00 0.00 1.82
888 993 3.138798 GTGCCTACTCCGCTCCGA 61.139 66.667 0.00 0.00 0.00 4.55
963 1069 4.426313 GGCCTTCTTCCACCCCCG 62.426 72.222 0.00 0.00 0.00 5.73
1029 1135 1.075600 CTCCACCTCCCTCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
1596 1906 3.450457 AGAGACCTCCTGAAATGCTACTG 59.550 47.826 0.00 0.00 0.00 2.74
1651 1961 7.542477 AGTCTGAGTTTATCAACGACATTACTG 59.458 37.037 0.00 0.00 36.19 2.74
1663 1973 5.242434 ACGACATTACTGTGCATTTCCTTA 58.758 37.500 0.00 0.00 35.14 2.69
1697 2007 8.272173 TGTACCGATATGACTAGATGGATATCA 58.728 37.037 4.83 0.00 35.70 2.15
1698 2008 9.290988 GTACCGATATGACTAGATGGATATCAT 57.709 37.037 4.83 0.00 39.13 2.45
1743 2053 5.012664 TCACTAATGGGTACTGCTTTTGAGA 59.987 40.000 0.00 0.00 0.00 3.27
1749 2059 4.227300 TGGGTACTGCTTTTGAGATGGTAT 59.773 41.667 0.00 0.00 0.00 2.73
1750 2060 4.576463 GGGTACTGCTTTTGAGATGGTATG 59.424 45.833 0.00 0.00 0.00 2.39
1765 2075 4.137116 TGGTATGTGTGATGCTTAGACC 57.863 45.455 0.00 0.00 0.00 3.85
1778 2088 7.011482 GTGATGCTTAGACCTTACAATACAAGG 59.989 40.741 0.00 0.00 46.74 3.61
1807 2117 9.150348 CATTATTTGTAGAAATTGGTGGGTTTC 57.850 33.333 2.84 0.00 33.63 2.78
1835 2145 4.333926 GTCAGATTGGCCTGTTAGATCAAC 59.666 45.833 3.32 0.00 37.67 3.18
1836 2146 4.019411 TCAGATTGGCCTGTTAGATCAACA 60.019 41.667 3.32 9.41 44.97 3.33
1837 2147 4.701651 CAGATTGGCCTGTTAGATCAACAA 59.298 41.667 3.32 0.00 46.37 2.83
1839 2149 5.359009 AGATTGGCCTGTTAGATCAACAATG 59.641 40.000 3.32 7.20 46.37 2.82
1840 2150 4.032960 TGGCCTGTTAGATCAACAATGT 57.967 40.909 3.32 0.00 46.37 2.71
1841 2151 4.406456 TGGCCTGTTAGATCAACAATGTT 58.594 39.130 3.32 0.00 46.37 2.71
1844 2157 5.863935 GGCCTGTTAGATCAACAATGTTTTC 59.136 40.000 0.00 0.00 46.37 2.29
1874 2187 2.365105 TGTCCCTTAGGGCTCCGG 60.365 66.667 13.54 0.00 43.94 5.14
1895 2208 7.225725 TCCGGTTCATTAAAAGAAGGTAGAAA 58.774 34.615 0.00 0.00 0.00 2.52
1922 2235 3.430453 TGCCTGGTTAATTTGAGGAAGG 58.570 45.455 0.00 0.00 0.00 3.46
1934 2247 2.986979 GGAAGGCCGGGCGAAAAA 60.987 61.111 23.81 0.00 0.00 1.94
1935 2248 2.257371 GAAGGCCGGGCGAAAAAC 59.743 61.111 23.81 7.79 0.00 2.43
1936 2249 2.519780 AAGGCCGGGCGAAAAACA 60.520 55.556 23.81 0.00 0.00 2.83
1945 2258 3.570559 CGGGCGAAAAACATTACAACAT 58.429 40.909 0.00 0.00 0.00 2.71
1994 2307 4.443266 GCTCCTGCGAGGCTCGTT 62.443 66.667 34.41 0.00 42.81 3.85
2029 2342 2.643933 ACCTAGTCCTTACGCGTTTC 57.356 50.000 20.78 3.82 0.00 2.78
2075 2388 1.072331 AGGGTTCTCATGTTGCGTTCT 59.928 47.619 0.00 0.00 0.00 3.01
2091 2404 3.934579 GCGTTCTTTCGGAGGGTTATTAA 59.065 43.478 0.00 0.00 0.00 1.40
2226 2539 5.695816 TGTCAATTTAGTTTGCATGGAAAGC 59.304 36.000 13.15 8.18 0.00 3.51
2273 2586 6.978659 AGATATATTATGTATTGGACCGCACG 59.021 38.462 0.00 0.00 0.00 5.34
2282 2595 0.317799 TGGACCGCACGCTAACTTTA 59.682 50.000 0.00 0.00 0.00 1.85
2420 2739 3.065095 GCTGCTCATTCCACTTCAAGATC 59.935 47.826 0.00 0.00 0.00 2.75
2427 2746 1.081892 CCACTTCAAGATCCACAGCG 58.918 55.000 0.00 0.00 0.00 5.18
2445 2764 5.063944 CACAGCGCTCATTAGTTAAATCAGT 59.936 40.000 7.13 0.00 0.00 3.41
2460 2779 7.873505 AGTTAAATCAGTCACCTACTTCTGTTC 59.126 37.037 0.00 0.00 35.76 3.18
2602 2921 6.309712 TGAGAATTCAGTCAAAGCTTCAAG 57.690 37.500 8.44 0.00 0.00 3.02
2645 2966 9.678941 TCAGTTAGTAATATATCTTGTGCTTCG 57.321 33.333 0.00 0.00 0.00 3.79
2673 2996 6.704493 GTCATATAAATTTGCCTCACGGTCTA 59.296 38.462 0.00 0.00 0.00 2.59
2730 3056 5.168569 AGATTTGTCTGCATGCAATTCTTG 58.831 37.500 22.88 9.00 33.96 3.02
2820 3159 3.886505 CAGGGTACTGCAGGTTGTTTTAA 59.113 43.478 19.93 0.00 38.01 1.52
2844 3183 3.875134 CACGAACCAAACAACTCCTTAGT 59.125 43.478 0.00 0.00 37.65 2.24
2851 3190 7.234661 ACCAAACAACTCCTTAGTTTTGAAA 57.765 32.000 4.90 0.00 43.60 2.69
2860 3199 8.112016 ACTCCTTAGTTTTGAAATCTTAAGGC 57.888 34.615 1.85 0.00 34.44 4.35
2874 3213 8.642908 AAATCTTAAGGCTTTGTGTGTTTTAC 57.357 30.769 4.45 0.00 0.00 2.01
2876 3215 6.791303 TCTTAAGGCTTTGTGTGTTTTACTG 58.209 36.000 4.45 0.00 0.00 2.74
2878 3217 2.757868 AGGCTTTGTGTGTTTTACTGCA 59.242 40.909 0.00 0.00 0.00 4.41
2879 3218 2.857748 GGCTTTGTGTGTTTTACTGCAC 59.142 45.455 0.00 0.00 36.26 4.57
2880 3219 3.506810 GCTTTGTGTGTTTTACTGCACA 58.493 40.909 0.00 0.00 42.50 4.57
2881 3220 3.923461 GCTTTGTGTGTTTTACTGCACAA 59.077 39.130 12.68 12.68 45.59 3.33
2967 3306 0.246635 TTCGCCTAGGTGCAAGAGTC 59.753 55.000 18.01 0.00 0.00 3.36
3106 3445 4.737352 GCAAGTTTGAAATGGCAGAGTTCA 60.737 41.667 6.88 6.88 36.88 3.18
3111 3450 5.988310 TTGAAATGGCAGAGTTCATTGAT 57.012 34.783 10.65 0.00 38.41 2.57
3117 3456 3.008266 TGGCAGAGTTCATTGATGAGTCA 59.992 43.478 0.00 0.00 38.19 3.41
3138 3477 1.070134 TCGCTGTACCTTGCTGTTCTT 59.930 47.619 0.00 0.00 0.00 2.52
3175 3514 8.755018 GGTGAAACATTTTTGTAAGACAGATTG 58.245 33.333 0.00 0.00 39.98 2.67
3176 3515 8.268738 GTGAAACATTTTTGTAAGACAGATTGC 58.731 33.333 0.00 0.00 36.32 3.56
3189 3528 4.402793 AGACAGATTGCGTAGACTGGTATT 59.597 41.667 11.83 0.00 35.08 1.89
3198 3537 6.909909 TGCGTAGACTGGTATTATCTACATG 58.090 40.000 10.36 0.00 43.30 3.21
3317 3656 1.404717 CGAGACCATCCCTGTGTCTTG 60.405 57.143 0.00 0.00 39.36 3.02
3318 3657 0.326264 AGACCATCCCTGTGTCTTGC 59.674 55.000 0.00 0.00 35.93 4.01
3319 3658 0.036732 GACCATCCCTGTGTCTTGCA 59.963 55.000 0.00 0.00 0.00 4.08
3365 3706 3.599412 CAAAGGCTTGCATTGCAGT 57.401 47.368 11.76 0.00 40.61 4.40
3479 4240 1.001378 GTCGGCATGTTTATGGATGGC 60.001 52.381 0.00 0.00 40.75 4.40
3516 4278 0.666274 CGCGTTGCTCAGTTCCAGTA 60.666 55.000 0.00 0.00 0.00 2.74
3524 4286 1.005037 CAGTTCCAGTAGTGCGGCA 60.005 57.895 0.00 0.00 0.00 5.69
3540 4302 2.664185 CATCCTCGATGCGGGCAG 60.664 66.667 0.00 0.00 33.17 4.85
3541 4303 2.839632 ATCCTCGATGCGGGCAGA 60.840 61.111 0.00 0.00 0.00 4.26
3542 4304 2.434843 ATCCTCGATGCGGGCAGAA 61.435 57.895 0.00 0.00 0.00 3.02
3543 4305 2.374830 ATCCTCGATGCGGGCAGAAG 62.375 60.000 0.00 0.00 0.00 2.85
3544 4306 3.267860 CTCGATGCGGGCAGAAGC 61.268 66.667 0.00 0.00 41.10 3.86
3777 4555 2.263852 CGCTCTGAGGCTGCTTCA 59.736 61.111 14.02 14.02 0.00 3.02
3808 4586 0.986527 TGGCATCCTTCTTGCTCTCA 59.013 50.000 0.00 0.00 40.03 3.27
3831 4609 3.243134 GGTGAGCGTCTCTATACTCCAAC 60.243 52.174 8.07 0.00 0.00 3.77
3832 4610 3.377485 GTGAGCGTCTCTATACTCCAACA 59.623 47.826 8.07 0.00 0.00 3.33
3838 4616 4.807834 CGTCTCTATACTCCAACAGTACGA 59.192 45.833 0.00 0.00 40.60 3.43
3854 4632 2.125106 GACGCCCTTCGAGCCAAT 60.125 61.111 0.00 0.00 41.67 3.16
3896 4674 5.476091 CTTCAGTGTTAGAGAAGGAAGGT 57.524 43.478 0.00 0.00 36.11 3.50
3897 4675 4.873746 TCAGTGTTAGAGAAGGAAGGTG 57.126 45.455 0.00 0.00 0.00 4.00
3926 4704 7.397221 TGTTCTAGACACCATGATCTTCAAAT 58.603 34.615 0.00 0.00 32.00 2.32
3927 4705 7.550551 TGTTCTAGACACCATGATCTTCAAATC 59.449 37.037 0.00 0.00 32.00 2.17
3928 4706 7.186570 TCTAGACACCATGATCTTCAAATCA 57.813 36.000 0.00 0.00 39.85 2.57
3929 4707 7.623630 TCTAGACACCATGATCTTCAAATCAA 58.376 34.615 0.00 0.00 39.04 2.57
3930 4708 6.506500 AGACACCATGATCTTCAAATCAAC 57.493 37.500 0.00 0.00 39.04 3.18
3934 4712 4.264532 ACCATGATCTTCAAATCAACCCCT 60.265 41.667 0.00 0.00 39.04 4.79
3985 4763 3.282021 GCATCTGCCATGACCTTCTTTA 58.718 45.455 0.00 0.00 34.31 1.85
4028 4806 3.003275 TCACCATTCAAGCTTTGTTCGTC 59.997 43.478 0.00 0.00 0.00 4.20
4054 4832 2.164422 TGACTACTCTTGGATGCTCGTG 59.836 50.000 0.00 0.00 0.00 4.35
4064 4842 1.068541 GGATGCTCGTGGTGGTTTTTC 60.069 52.381 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 127 8.780249 CAAGAATTTGAAAAATGCTCTTGGATT 58.220 29.630 14.10 0.00 36.33 3.01
127 129 7.499292 TCAAGAATTTGAAAAATGCTCTTGGA 58.501 30.769 18.24 9.17 40.26 3.53
128 130 7.718272 TCAAGAATTTGAAAAATGCTCTTGG 57.282 32.000 18.24 7.82 40.26 3.61
173 178 8.811017 TGCTTCATAATGTTAAGGATTTCCAAA 58.189 29.630 0.00 0.00 38.89 3.28
292 297 2.508526 CTGCTAAAAGAAGGCAGGTGT 58.491 47.619 6.31 0.00 46.51 4.16
297 302 1.247567 GCACCTGCTAAAAGAAGGCA 58.752 50.000 0.45 0.00 45.62 4.75
321 326 1.203928 CAACCGCGAATGCAACAAAA 58.796 45.000 8.23 0.00 42.97 2.44
322 327 0.101399 ACAACCGCGAATGCAACAAA 59.899 45.000 8.23 0.00 42.97 2.83
332 346 0.238817 GCCAATGTAAACAACCGCGA 59.761 50.000 8.23 0.00 0.00 5.87
346 360 1.813753 CCGGATCGACAACGCCAAT 60.814 57.895 0.00 0.00 39.58 3.16
364 378 2.386660 GCTGAGCTTCCAGTGTCGC 61.387 63.158 0.00 0.00 36.57 5.19
404 418 1.067060 TCAGATGGCGATTAGTGGTCG 59.933 52.381 0.00 0.00 41.77 4.79
406 420 2.111384 ACTCAGATGGCGATTAGTGGT 58.889 47.619 0.00 0.00 0.00 4.16
416 430 3.581024 TGCAAATCAAACTCAGATGGC 57.419 42.857 0.00 0.00 0.00 4.40
425 439 1.987770 CTGTGGCGATGCAAATCAAAC 59.012 47.619 0.00 0.00 0.00 2.93
449 463 1.202639 TGTTGACGACCACTTCTGCAT 60.203 47.619 0.00 0.00 0.00 3.96
453 467 1.873591 GCAATGTTGACGACCACTTCT 59.126 47.619 0.00 0.00 0.00 2.85
464 478 1.669502 GCGCTGAATTGGCAATGTTGA 60.670 47.619 14.47 0.00 0.00 3.18
469 483 0.108520 CAAGGCGCTGAATTGGCAAT 60.109 50.000 6.96 6.96 0.00 3.56
498 512 2.159421 GCTGATGTTGCTCAAGGTCATG 60.159 50.000 0.00 0.00 0.00 3.07
503 517 0.524862 GTGGCTGATGTTGCTCAAGG 59.475 55.000 0.00 0.00 0.00 3.61
526 540 2.391226 AGCCTCAGAAGGATTGGCA 58.609 52.632 0.00 0.00 46.67 4.92
537 551 3.309138 CGTGAATGATCTTGAAGCCTCAG 59.691 47.826 0.00 0.00 31.69 3.35
539 553 3.525537 TCGTGAATGATCTTGAAGCCTC 58.474 45.455 0.00 0.00 0.00 4.70
542 556 4.493872 GCTTCTCGTGAATGATCTTGAAGC 60.494 45.833 0.00 0.00 44.90 3.86
548 562 2.762887 TCCAGCTTCTCGTGAATGATCT 59.237 45.455 0.00 0.00 0.00 2.75
566 580 3.814625 TGTGCTTCTACATTGTGTTCCA 58.185 40.909 0.00 0.00 0.00 3.53
618 632 3.879682 CACACATGGCGCCCGATG 61.880 66.667 26.77 23.81 0.00 3.84
766 870 4.080807 TGGGTCATTTCCGTTTCAGCTATA 60.081 41.667 0.00 0.00 0.00 1.31
888 993 4.250305 GTGTGGGTGTGGGAGCGT 62.250 66.667 0.00 0.00 0.00 5.07
947 1053 3.623703 GACGGGGGTGGAAGAAGGC 62.624 68.421 0.00 0.00 0.00 4.35
950 1056 1.559065 GGATGACGGGGGTGGAAGAA 61.559 60.000 0.00 0.00 0.00 2.52
1006 1112 2.169590 GAGAGGGAGGTGGAGGTGGA 62.170 65.000 0.00 0.00 0.00 4.02
1029 1135 1.153469 GAAGAGAGGGCAGAAGGCG 60.153 63.158 0.00 0.00 46.16 5.52
1086 1396 1.001520 GGTTTGGGAAATTTGGGGTCG 59.998 52.381 0.00 0.00 0.00 4.79
1173 1483 4.398319 TCTCTATGATGTCGTCTATGGCA 58.602 43.478 0.00 0.00 0.00 4.92
1582 1892 4.514441 CAGATAAGGCAGTAGCATTTCAGG 59.486 45.833 0.00 0.00 43.04 3.86
1596 1906 3.528597 AGAGACGAAACCAGATAAGGC 57.471 47.619 0.00 0.00 0.00 4.35
1651 1961 7.431084 CGGTACAATTTATGTAAGGAAATGCAC 59.569 37.037 0.00 0.00 45.81 4.57
1697 2007 6.870965 GTGAATCAATAAGGACGCAGAGATAT 59.129 38.462 0.00 0.00 0.00 1.63
1698 2008 6.040955 AGTGAATCAATAAGGACGCAGAGATA 59.959 38.462 0.00 0.00 0.00 1.98
1699 2009 5.053145 GTGAATCAATAAGGACGCAGAGAT 58.947 41.667 0.00 0.00 0.00 2.75
1700 2010 4.160439 AGTGAATCAATAAGGACGCAGAGA 59.840 41.667 0.00 0.00 0.00 3.10
1701 2011 4.437239 AGTGAATCAATAAGGACGCAGAG 58.563 43.478 0.00 0.00 0.00 3.35
1743 2053 4.410228 AGGTCTAAGCATCACACATACCAT 59.590 41.667 0.00 0.00 0.00 3.55
1749 2059 4.882842 TGTAAGGTCTAAGCATCACACA 57.117 40.909 0.00 0.00 0.00 3.72
1750 2060 6.816640 TGTATTGTAAGGTCTAAGCATCACAC 59.183 38.462 0.00 0.00 0.00 3.82
1778 2088 6.534793 CCCACCAATTTCTACAAATAATGTGC 59.465 38.462 0.00 0.00 43.77 4.57
1807 2117 1.843368 ACAGGCCAATCTGACCATTG 58.157 50.000 5.01 0.00 38.11 2.82
1835 2145 4.026640 CACGGCTTCAACAAGAAAACATTG 60.027 41.667 0.00 0.00 35.40 2.82
1836 2146 4.111916 CACGGCTTCAACAAGAAAACATT 58.888 39.130 0.00 0.00 35.40 2.71
1837 2147 3.130340 ACACGGCTTCAACAAGAAAACAT 59.870 39.130 0.00 0.00 35.40 2.71
1839 2149 3.105937 GACACGGCTTCAACAAGAAAAC 58.894 45.455 0.00 0.00 35.40 2.43
1840 2150 2.098443 GGACACGGCTTCAACAAGAAAA 59.902 45.455 0.00 0.00 35.40 2.29
1841 2151 1.673920 GGACACGGCTTCAACAAGAAA 59.326 47.619 0.00 0.00 35.40 2.52
1844 2157 0.535102 AGGGACACGGCTTCAACAAG 60.535 55.000 0.00 0.00 0.00 3.16
1922 2235 0.241481 TGTAATGTTTTTCGCCCGGC 59.759 50.000 0.00 0.00 0.00 6.13
1934 2247 3.495331 TCTTGTGGGCATGTTGTAATGT 58.505 40.909 0.00 0.00 0.00 2.71
1935 2248 4.517952 TTCTTGTGGGCATGTTGTAATG 57.482 40.909 0.00 0.00 0.00 1.90
1936 2249 4.081531 CCATTCTTGTGGGCATGTTGTAAT 60.082 41.667 0.00 0.00 35.55 1.89
1994 2307 0.687757 AGGTAGCTCCGATTCTGCCA 60.688 55.000 0.00 0.00 41.99 4.92
2029 2342 1.996786 CTATGCCAAACAGCCAGCCG 61.997 60.000 0.00 0.00 0.00 5.52
2075 2388 8.810990 ACATGTTAATTAATAACCCTCCGAAA 57.189 30.769 0.31 0.00 42.74 3.46
2091 2404 6.877855 TGTAAATGGCAATGCAACATGTTAAT 59.122 30.769 11.53 5.45 0.00 1.40
2161 2474 7.828712 TCATTCAACAATTTGCTATCACATCA 58.171 30.769 0.00 0.00 32.17 3.07
2311 2628 7.648039 ACAAGAGTATACTACCCTTCTTGAG 57.352 40.000 25.34 9.92 39.17 3.02
2312 2629 9.710818 ATAACAAGAGTATACTACCCTTCTTGA 57.289 33.333 25.34 12.43 39.17 3.02
2329 2646 7.386851 TGACTCAGGGACTAAAATAACAAGAG 58.613 38.462 0.00 0.00 36.02 2.85
2394 2713 2.026542 TGAAGTGGAATGAGCAGCATCT 60.027 45.455 0.00 0.00 35.78 2.90
2420 2739 4.332543 TGATTTAACTAATGAGCGCTGTGG 59.667 41.667 18.48 4.13 0.00 4.17
2427 2746 7.982354 AGTAGGTGACTGATTTAACTAATGAGC 59.018 37.037 0.00 0.00 43.88 4.26
2445 2764 7.406031 AGATTAATCGAACAGAAGTAGGTGA 57.594 36.000 9.78 0.00 0.00 4.02
2460 2779 4.726416 ACTTTGCAGCACAAGATTAATCG 58.274 39.130 18.55 0.00 40.06 3.34
2635 2956 8.577939 CAAATTTATATGACAACGAAGCACAAG 58.422 33.333 0.00 0.00 0.00 3.16
2641 2962 7.429340 GTGAGGCAAATTTATATGACAACGAAG 59.571 37.037 0.00 0.00 0.00 3.79
2642 2963 7.247728 GTGAGGCAAATTTATATGACAACGAA 58.752 34.615 0.00 0.00 0.00 3.85
2643 2964 6.456315 CGTGAGGCAAATTTATATGACAACGA 60.456 38.462 0.00 0.00 38.45 3.85
2644 2965 5.676744 CGTGAGGCAAATTTATATGACAACG 59.323 40.000 0.00 0.00 32.91 4.10
2693 3016 5.409826 CAGACAAATCTTACCAACCTGACTC 59.590 44.000 0.00 0.00 30.42 3.36
2764 3090 2.260869 CGAGGTGTGGCAAGGTTGG 61.261 63.158 0.00 0.00 0.00 3.77
2820 3159 3.208747 AGGAGTTGTTTGGTTCGTGAT 57.791 42.857 0.00 0.00 0.00 3.06
2844 3183 7.327214 ACACACAAAGCCTTAAGATTTCAAAA 58.673 30.769 3.36 0.00 0.00 2.44
2851 3190 7.425606 CAGTAAAACACACAAAGCCTTAAGAT 58.574 34.615 3.36 0.00 0.00 2.40
2911 3250 6.754675 TCGATCGAATTATAAAACTGAGCACA 59.245 34.615 16.99 0.00 0.00 4.57
2912 3251 7.161829 TCGATCGAATTATAAAACTGAGCAC 57.838 36.000 16.99 0.00 0.00 4.40
2967 3306 3.866651 ACCTTGATCCAAGAAGATGACG 58.133 45.455 8.16 0.00 43.42 4.35
3106 3445 3.386078 AGGTACAGCGATGACTCATCAAT 59.614 43.478 8.12 3.96 40.54 2.57
3111 3450 1.404181 GCAAGGTACAGCGATGACTCA 60.404 52.381 8.12 0.00 0.00 3.41
3117 3456 1.276421 AGAACAGCAAGGTACAGCGAT 59.724 47.619 0.00 0.00 36.75 4.58
3175 3514 7.022384 GTCATGTAGATAATACCAGTCTACGC 58.978 42.308 7.13 0.00 44.50 4.42
3176 3515 7.095313 ACGTCATGTAGATAATACCAGTCTACG 60.095 40.741 7.13 0.00 44.50 3.51
3189 3528 4.974275 GCTCGCTTAAACGTCATGTAGATA 59.026 41.667 0.00 0.00 0.00 1.98
3270 3609 5.757320 CAGATAGGTTAGGAAACAGATGCAG 59.243 44.000 0.00 0.00 37.34 4.41
3271 3610 5.396772 CCAGATAGGTTAGGAAACAGATGCA 60.397 44.000 0.00 0.00 37.34 3.96
3317 3656 0.250513 AGCAGGTAGTAGCAAGGTGC 59.749 55.000 1.58 2.83 45.46 5.01
3318 3657 1.134670 GGAGCAGGTAGTAGCAAGGTG 60.135 57.143 1.58 0.00 0.00 4.00
3319 3658 1.196012 GGAGCAGGTAGTAGCAAGGT 58.804 55.000 1.58 0.00 0.00 3.50
3320 3659 0.103208 CGGAGCAGGTAGTAGCAAGG 59.897 60.000 1.58 0.00 0.00 3.61
3445 4206 1.539388 TGCCGACACCTTTTTGCATAG 59.461 47.619 0.00 0.00 0.00 2.23
3453 4214 2.491693 CCATAAACATGCCGACACCTTT 59.508 45.455 0.00 0.00 0.00 3.11
3516 4278 2.107750 CATCGAGGATGCCGCACT 59.892 61.111 0.00 0.00 33.17 4.40
3524 4286 2.374830 CTTCTGCCCGCATCGAGGAT 62.375 60.000 0.00 0.00 0.00 3.24
3538 4300 1.202698 CCTATTCCCTTCCGGCTTCTG 60.203 57.143 0.00 0.00 0.00 3.02
3539 4301 1.132500 CCTATTCCCTTCCGGCTTCT 58.868 55.000 0.00 0.00 0.00 2.85
3540 4302 0.108774 CCCTATTCCCTTCCGGCTTC 59.891 60.000 0.00 0.00 0.00 3.86
3541 4303 0.623617 ACCCTATTCCCTTCCGGCTT 60.624 55.000 0.00 0.00 0.00 4.35
3542 4304 0.623617 AACCCTATTCCCTTCCGGCT 60.624 55.000 0.00 0.00 0.00 5.52
3543 4305 0.179026 GAACCCTATTCCCTTCCGGC 60.179 60.000 0.00 0.00 0.00 6.13
3544 4306 0.472898 GGAACCCTATTCCCTTCCGG 59.527 60.000 0.00 0.00 32.48 5.14
3605 4367 2.358322 ACCGACCACAATGGAAAACT 57.642 45.000 0.84 0.00 40.96 2.66
3739 4517 1.811266 CTCGATTCGGGCACACCTG 60.811 63.158 6.18 0.00 44.63 4.00
3777 4555 0.613012 GGATGCCAACCTCAAAGCCT 60.613 55.000 0.00 0.00 0.00 4.58
3808 4586 2.172930 TGGAGTATAGAGACGCTCACCT 59.827 50.000 9.09 0.47 32.06 4.00
3831 4609 1.226323 CTCGAAGGGCGTCGTACTG 60.226 63.158 8.75 0.00 41.80 2.74
3832 4610 3.048941 GCTCGAAGGGCGTCGTACT 62.049 63.158 8.75 0.00 41.80 2.73
3838 4616 2.436646 CATTGGCTCGAAGGGCGT 60.437 61.111 0.00 0.00 41.80 5.68
3854 4632 1.764854 GGAACCCTATCCCCTCGCA 60.765 63.158 0.00 0.00 33.05 5.10
3896 4674 3.506398 TCATGGTGTCTAGAACAGGACA 58.494 45.455 0.00 0.00 38.97 4.02
3897 4675 4.404073 AGATCATGGTGTCTAGAACAGGAC 59.596 45.833 9.07 5.32 38.97 3.85
3926 4704 2.109834 ACCAATCATCACAAGGGGTTGA 59.890 45.455 0.00 0.00 0.00 3.18
3927 4705 2.528564 ACCAATCATCACAAGGGGTTG 58.471 47.619 0.00 0.00 0.00 3.77
3928 4706 2.899256 CAACCAATCATCACAAGGGGTT 59.101 45.455 0.00 0.00 37.62 4.11
3929 4707 2.158325 ACAACCAATCATCACAAGGGGT 60.158 45.455 0.00 0.00 0.00 4.95
3930 4708 2.231964 CACAACCAATCATCACAAGGGG 59.768 50.000 0.00 0.00 0.00 4.79
3959 4737 1.432251 GTCATGGCAGATGCAGCAC 59.568 57.895 4.07 0.00 44.36 4.40
4000 4778 0.806868 AGCTTGAATGGTGATGCACG 59.193 50.000 0.00 0.00 34.83 5.34
4028 4806 3.997021 AGCATCCAAGAGTAGTCAAAACG 59.003 43.478 0.00 0.00 0.00 3.60
4054 4832 5.006153 AGCTAACAACAAGAAAAACCACC 57.994 39.130 0.00 0.00 0.00 4.61
4064 4842 4.620982 CAAAGGGGAAAGCTAACAACAAG 58.379 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.