Multiple sequence alignment - TraesCS4D01G057300

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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 TraesCS4D01G057300 chr4D 100.000 3284 0 0 1 3284 32347608 32350891 0.000000e+00 6065
1 TraesCS4D01G057300 chr4B 90.780 2885 174 39 1 2858 46939359 46942178 0.000000e+00 3770
2 TraesCS4D01G057300 chr4B 92.188 192 12 3 2893 3084 46942175 46942363 5.400000e-68 268
3 TraesCS4D01G057300 chr4A 91.934 2244 124 33 652 2865 570270308 570268092 0.000000e+00 3088
4 TraesCS4D01G057300 chr4A 90.372 592 45 8 1 585 570270891 570270305 0.000000e+00 767
5 TraesCS4D01G057300 chr4A 88.081 344 28 9 2905 3243 570268093 570267758 2.370000e-106 396


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 TraesCS4D01G057300 chr4D 32347608 32350891 3283 False 6065 6065 100.000 1 3284 1 chr4D.!!$F1 3283
1 TraesCS4D01G057300 chr4B 46939359 46942363 3004 False 2019 3770 91.484 1 3084 2 chr4B.!!$F1 3083
2 TraesCS4D01G057300 chr4A 570267758 570270891 3133 True 1417 3088 90.129 1 3243 3 chr4A.!!$R1 3242

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
599 611 0.042131 TGGTACTCCCTCCGTTCCAT 59.958 55.0 0.00 0.0 28.53 3.41 F
960 973 0.112412 GGAAGGCTTCAGGGGTTTCA 59.888 55.0 27.17 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1868 0.108520 GGGTTGGACGACGCATTAGA 60.109 55.0 0.0 0.0 33.16 2.10 R
2685 2728 0.537143 CAACCTAGGCTGCACCACAA 60.537 55.0 9.3 0.0 43.14 3.33 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
123 125 2.591715 GGGTGTTCGTGCTGCTGT 60.592 61.111 0.00 0.00 0.00 4.40
226 231 7.445945 CCTACACTTAGGCTATGCTTATTTCT 58.554 38.462 7.29 0.00 38.72 2.52
259 264 1.398390 CCCGAAGCTCAAATCTTTCCG 59.602 52.381 0.00 0.00 0.00 4.30
269 274 6.825721 AGCTCAAATCTTTCCGTTGATTATCT 59.174 34.615 0.00 0.00 33.17 1.98
273 278 9.884636 TCAAATCTTTCCGTTGATTATCTTAGA 57.115 29.630 0.00 0.00 33.17 2.10
280 285 6.931838 TCCGTTGATTATCTTAGACTGTTGT 58.068 36.000 0.00 0.00 0.00 3.32
282 287 6.811665 CCGTTGATTATCTTAGACTGTTGTGA 59.188 38.462 0.00 0.00 0.00 3.58
295 300 5.934625 AGACTGTTGTGATGTTAGGTGATTC 59.065 40.000 0.00 0.00 0.00 2.52
300 305 5.147330 TGTGATGTTAGGTGATTCGAGTT 57.853 39.130 0.00 0.00 0.00 3.01
303 308 5.289675 GTGATGTTAGGTGATTCGAGTTCTG 59.710 44.000 0.00 0.00 0.00 3.02
308 314 2.027745 AGGTGATTCGAGTTCTGCATGT 60.028 45.455 0.00 0.00 0.00 3.21
310 316 3.189287 GGTGATTCGAGTTCTGCATGTTT 59.811 43.478 0.00 0.00 0.00 2.83
329 335 5.296748 TGTTTTCTTTAGGCCATTTCAAGC 58.703 37.500 5.01 0.00 0.00 4.01
333 339 4.016444 TCTTTAGGCCATTTCAAGCGAAT 58.984 39.130 5.01 0.00 0.00 3.34
336 342 2.170166 AGGCCATTTCAAGCGAATTGA 58.830 42.857 5.01 0.00 46.31 2.57
353 362 6.524586 GCGAATTGATTTACCTCTGTTTCTTG 59.475 38.462 0.00 0.00 0.00 3.02
361 370 7.941431 TTTACCTCTGTTTCTTGTGGTTTAA 57.059 32.000 0.00 0.00 33.02 1.52
362 371 5.830000 ACCTCTGTTTCTTGTGGTTTAAC 57.170 39.130 0.00 0.00 0.00 2.01
363 372 5.258051 ACCTCTGTTTCTTGTGGTTTAACA 58.742 37.500 0.00 0.00 0.00 2.41
384 393 2.290323 ACAAATGAGTGTAGAGGTGCCC 60.290 50.000 0.00 0.00 0.00 5.36
459 468 2.218759 CGGCGTTGATTAGTGCTATGTC 59.781 50.000 0.00 0.00 0.00 3.06
470 479 0.260816 TGCTATGTCGGGGGAGTAGT 59.739 55.000 0.00 0.00 0.00 2.73
506 518 1.331756 CCACACACTCTGCTGTTGTTC 59.668 52.381 0.00 0.00 0.00 3.18
551 563 5.005094 TCGTTTCAGAAAATTAACCCGGAT 58.995 37.500 0.73 0.00 0.00 4.18
579 591 3.153369 TGGTACACATGGCTTGATTGT 57.847 42.857 7.45 4.80 0.00 2.71
580 592 3.495331 TGGTACACATGGCTTGATTGTT 58.505 40.909 7.45 0.00 0.00 2.83
588 600 2.790433 TGGCTTGATTGTTGGTACTCC 58.210 47.619 0.00 0.00 0.00 3.85
594 606 1.553704 GATTGTTGGTACTCCCTCCGT 59.446 52.381 0.00 0.00 0.00 4.69
595 607 1.426751 TTGTTGGTACTCCCTCCGTT 58.573 50.000 0.00 0.00 0.00 4.44
597 609 0.248565 GTTGGTACTCCCTCCGTTCC 59.751 60.000 0.00 0.00 0.00 3.62
598 610 0.178926 TTGGTACTCCCTCCGTTCCA 60.179 55.000 0.00 0.00 31.17 3.53
599 611 0.042131 TGGTACTCCCTCCGTTCCAT 59.958 55.000 0.00 0.00 28.53 3.41
600 612 0.464452 GGTACTCCCTCCGTTCCATG 59.536 60.000 0.00 0.00 0.00 3.66
601 613 0.179081 GTACTCCCTCCGTTCCATGC 60.179 60.000 0.00 0.00 0.00 4.06
602 614 1.335132 TACTCCCTCCGTTCCATGCC 61.335 60.000 0.00 0.00 0.00 4.40
603 615 2.609299 TCCCTCCGTTCCATGCCA 60.609 61.111 0.00 0.00 0.00 4.92
607 619 1.308069 CCTCCGTTCCATGCCAGTTG 61.308 60.000 0.00 0.00 0.00 3.16
608 620 0.606401 CTCCGTTCCATGCCAGTTGT 60.606 55.000 0.00 0.00 0.00 3.32
619 631 1.804151 TGCCAGTTGTCGCTGATTTAC 59.196 47.619 0.00 0.00 38.70 2.01
625 637 5.178623 CCAGTTGTCGCTGATTTACTACAAA 59.821 40.000 0.00 0.00 38.70 2.83
626 638 6.299604 CAGTTGTCGCTGATTTACTACAAAG 58.700 40.000 0.00 0.00 38.70 2.77
627 639 5.408604 AGTTGTCGCTGATTTACTACAAAGG 59.591 40.000 0.00 0.00 0.00 3.11
632 644 4.330074 CGCTGATTTACTACAAAGGGACAG 59.670 45.833 0.00 0.00 0.00 3.51
723 735 3.191162 TGCATAGCTTGTTTCATGTGACC 59.809 43.478 0.00 0.00 0.00 4.02
804 816 8.599055 TTGCTTGTGACAAGATAGATATGATC 57.401 34.615 27.97 6.84 0.00 2.92
912 925 3.305813 GGTGTTCAGTGTCGAGGTTGATA 60.306 47.826 0.00 0.00 0.00 2.15
915 928 4.167268 GTTCAGTGTCGAGGTTGATACTC 58.833 47.826 0.00 0.00 38.12 2.59
924 937 4.462834 TCGAGGTTGATACTCATCTGTTGT 59.537 41.667 0.00 0.00 34.66 3.32
933 946 6.650807 TGATACTCATCTGTTGTTTGACCTTC 59.349 38.462 0.00 0.00 31.93 3.46
958 971 1.354705 GTAGGAAGGCTTCAGGGGTTT 59.645 52.381 27.17 7.18 0.00 3.27
959 972 0.405973 AGGAAGGCTTCAGGGGTTTC 59.594 55.000 27.17 8.48 0.00 2.78
960 973 0.112412 GGAAGGCTTCAGGGGTTTCA 59.888 55.000 27.17 0.00 0.00 2.69
961 974 1.539157 GAAGGCTTCAGGGGTTTCAG 58.461 55.000 21.99 0.00 0.00 3.02
975 988 2.552743 GGTTTCAGTAACAGGTTGCTCC 59.447 50.000 0.00 0.00 38.55 4.70
983 996 1.898574 CAGGTTGCTCCGTTGCCTT 60.899 57.895 0.00 0.00 41.99 4.35
995 1008 5.353394 TCCGTTGCCTTGATAGACTAATT 57.647 39.130 0.00 0.00 0.00 1.40
1119 1132 5.165961 TGCTCTACCAAGTAAAGCATTCT 57.834 39.130 0.00 0.00 38.01 2.40
1251 1264 2.273449 CCAGCAAAGGAGGCCGAT 59.727 61.111 0.00 0.00 0.00 4.18
1275 1288 1.142060 TCAACACTGGATGAACGGGTT 59.858 47.619 0.00 0.00 0.00 4.11
1350 1363 1.889105 CGACCCCATTGATGAGCCG 60.889 63.158 0.00 0.00 0.00 5.52
1500 1513 4.521146 AGAGTTTCCATGGTGATGATGTC 58.479 43.478 12.58 0.00 0.00 3.06
1503 1516 4.226846 AGTTTCCATGGTGATGATGTCTCT 59.773 41.667 12.58 0.00 0.00 3.10
1599 1612 1.814394 GTGGATGATGCTTCAACTGCA 59.186 47.619 6.36 0.00 44.95 4.41
1647 1660 1.827969 CACAAGGAGGAGGAAGATCGT 59.172 52.381 0.00 0.00 0.00 3.73
1653 1666 2.312390 GAGGAGGAAGATCGTAAGGCT 58.688 52.381 0.00 0.00 38.47 4.58
1680 1693 3.576550 AGAAGAGTTCTGGAGGTGAGAAC 59.423 47.826 0.00 0.00 46.58 3.01
1683 1696 2.528041 GTTCTGGAGGTGAGAACGTT 57.472 50.000 0.00 0.00 39.87 3.99
1711 1724 0.611618 TGTGGACCATGATGCCCAAC 60.612 55.000 0.00 3.36 0.00 3.77
1728 1741 0.818296 AACTCACGAATCCTCTCCCG 59.182 55.000 0.00 0.00 0.00 5.14
1789 1802 5.396660 GGCACCACCAATTTATCAAATGGAT 60.397 40.000 0.62 0.00 38.03 3.41
1820 1833 1.065126 GGGTCCTGGAGTGAATGGAAG 60.065 57.143 0.00 0.00 0.00 3.46
1830 1843 2.490903 AGTGAATGGAAGCAATGCTGTC 59.509 45.455 9.14 8.59 39.62 3.51
1860 1876 2.411904 GAGGCTTCAGGATCTAATGCG 58.588 52.381 0.00 0.00 0.00 4.73
1926 1942 3.055819 GCAAGACTGATCCAACTCCAGTA 60.056 47.826 0.00 0.00 40.80 2.74
1930 1946 5.738909 AGACTGATCCAACTCCAGTAAATG 58.261 41.667 0.00 0.00 40.80 2.32
1942 1958 4.460263 TCCAGTAAATGTGACAAGCAACT 58.540 39.130 0.00 0.00 0.00 3.16
2016 2032 2.030007 GCCAGTAAATTCAACAGCAGCA 60.030 45.455 0.00 0.00 0.00 4.41
2019 2035 4.082625 CCAGTAAATTCAACAGCAGCATCA 60.083 41.667 0.00 0.00 0.00 3.07
2144 2160 3.634448 ACATCTAGAGACGGAGACAATGG 59.366 47.826 0.00 0.00 0.00 3.16
2177 2193 2.266055 CACCTCTTCCACTCCGGC 59.734 66.667 0.00 0.00 33.14 6.13
2178 2194 3.003763 ACCTCTTCCACTCCGGCC 61.004 66.667 0.00 0.00 33.14 6.13
2337 2353 4.612264 TGACCTGTAAGTTTGTAGGACC 57.388 45.455 0.00 0.00 34.42 4.46
2392 2408 5.228427 GCTTTTTGTGTAAGTTTGGTACGTG 59.772 40.000 0.00 0.00 0.00 4.49
2417 2433 0.798776 CTGCTTCGTGTTTGCCTAGG 59.201 55.000 3.67 3.67 0.00 3.02
2433 2449 2.029290 CCTAGGGTACATCACGGTATGC 60.029 54.545 0.00 0.00 0.00 3.14
2529 2548 0.453390 GCTGCTGGAATGCCAACTAC 59.547 55.000 0.00 0.00 45.41 2.73
2553 2572 3.324846 AGTGACAATGTCTGCCTTGTCTA 59.675 43.478 14.97 1.83 44.83 2.59
2573 2609 5.117592 GTCTATTGTTGTGTTGCTTGCATTC 59.882 40.000 0.00 0.00 0.00 2.67
2588 2624 4.001618 TGCATTCGCATGGCTAGTATTA 57.998 40.909 0.00 0.00 45.36 0.98
2590 2626 3.997021 GCATTCGCATGGCTAGTATTAGT 59.003 43.478 0.00 0.00 38.36 2.24
2645 2687 1.518325 TGTGCGTCGGAATTGAACAT 58.482 45.000 0.00 0.00 0.00 2.71
2647 2689 2.413796 TGTGCGTCGGAATTGAACATAC 59.586 45.455 0.00 0.00 0.00 2.39
2648 2690 1.656594 TGCGTCGGAATTGAACATACG 59.343 47.619 0.00 0.00 0.00 3.06
2685 2728 3.469008 TGAGACACAAACATTCCGTCT 57.531 42.857 0.00 0.00 39.57 4.18
2728 2774 3.131709 AGCTGTTGCAGATACACTTGT 57.868 42.857 0.00 0.00 42.74 3.16
2775 2821 3.174799 GCACAAAGCGTTCTTCTACTG 57.825 47.619 0.00 0.00 0.00 2.74
2814 2865 4.640647 CCCTGGCATCCTAGAAAAAGTTAC 59.359 45.833 0.00 0.00 0.00 2.50
2858 2912 5.007682 GGTGTGGTGTTGAAGGTGTATATT 58.992 41.667 0.00 0.00 0.00 1.28
2859 2913 6.174760 GGTGTGGTGTTGAAGGTGTATATTA 58.825 40.000 0.00 0.00 0.00 0.98
2860 2914 6.655848 GGTGTGGTGTTGAAGGTGTATATTAA 59.344 38.462 0.00 0.00 0.00 1.40
2861 2915 7.148306 GGTGTGGTGTTGAAGGTGTATATTAAG 60.148 40.741 0.00 0.00 0.00 1.85
2862 2916 7.389607 GTGTGGTGTTGAAGGTGTATATTAAGT 59.610 37.037 0.00 0.00 0.00 2.24
2863 2917 8.595421 TGTGGTGTTGAAGGTGTATATTAAGTA 58.405 33.333 0.00 0.00 0.00 2.24
2864 2918 9.609346 GTGGTGTTGAAGGTGTATATTAAGTAT 57.391 33.333 0.00 0.00 0.00 2.12
2945 2999 2.568090 GGCAACCTGGCAATGTCG 59.432 61.111 0.00 0.00 43.14 4.35
2958 3012 1.958579 CAATGTCGCCATCCAATCCAT 59.041 47.619 0.00 0.00 0.00 3.41
2959 3013 3.148412 CAATGTCGCCATCCAATCCATA 58.852 45.455 0.00 0.00 0.00 2.74
3012 3067 4.158786 TCCATTGATTGTGTTCATGGGTT 58.841 39.130 0.00 0.00 31.10 4.11
3107 3162 3.181485 CGTACAAAAGAAAACCCTTGCCA 60.181 43.478 0.00 0.00 0.00 4.92
3111 3166 2.452600 AAGAAAACCCTTGCCACAGA 57.547 45.000 0.00 0.00 0.00 3.41
3112 3167 1.692411 AGAAAACCCTTGCCACAGAC 58.308 50.000 0.00 0.00 0.00 3.51
3113 3168 1.064017 AGAAAACCCTTGCCACAGACA 60.064 47.619 0.00 0.00 0.00 3.41
3115 3170 1.331214 AAACCCTTGCCACAGACATG 58.669 50.000 0.00 0.00 0.00 3.21
3116 3171 0.185901 AACCCTTGCCACAGACATGT 59.814 50.000 0.00 0.00 41.57 3.21
3117 3172 0.250901 ACCCTTGCCACAGACATGTC 60.251 55.000 18.47 18.47 37.65 3.06
3118 3173 0.962356 CCCTTGCCACAGACATGTCC 60.962 60.000 22.21 7.15 37.65 4.02
3120 3175 1.608055 CTTGCCACAGACATGTCCAA 58.392 50.000 22.21 16.35 37.65 3.53
3124 3179 1.001378 GCCACAGACATGTCCAACAAC 60.001 52.381 22.21 4.54 37.65 3.32
3141 3196 2.048222 CGGAGCAAGCGAGGTTGA 60.048 61.111 17.82 0.00 0.00 3.18
3147 3202 0.317854 GCAAGCGAGGTTGACCAAAC 60.318 55.000 17.82 0.00 38.89 2.93
3149 3204 1.608590 CAAGCGAGGTTGACCAAACAT 59.391 47.619 9.17 0.00 40.86 2.71
3150 3205 1.523758 AGCGAGGTTGACCAAACATC 58.476 50.000 2.56 0.00 44.34 3.06
3182 3237 2.740714 GACCTGAATCACGTGCGGC 61.741 63.158 11.67 2.43 0.00 6.53
3184 3239 3.499737 CTGAATCACGTGCGGCCC 61.500 66.667 11.67 0.00 0.00 5.80
3191 3246 4.778143 ACGTGCGGCCCCTTGATC 62.778 66.667 0.00 0.00 0.00 2.92
3193 3248 2.044946 GTGCGGCCCCTTGATCTT 60.045 61.111 0.00 0.00 0.00 2.40
3194 3249 1.223487 GTGCGGCCCCTTGATCTTA 59.777 57.895 0.00 0.00 0.00 2.10
3197 3252 1.239347 GCGGCCCCTTGATCTTATTC 58.761 55.000 0.00 0.00 0.00 1.75
3202 3257 2.560105 GCCCCTTGATCTTATTCATGGC 59.440 50.000 0.00 0.00 38.81 4.40
3236 3291 2.094545 ACATCGAAAATTGCTCCTTGGC 60.095 45.455 0.00 0.00 0.00 4.52
3243 3298 0.995024 ATTGCTCCTTGGCTGGTACT 59.005 50.000 0.00 0.00 0.00 2.73
3244 3299 0.324943 TTGCTCCTTGGCTGGTACTC 59.675 55.000 0.00 0.00 0.00 2.59
3245 3300 1.222113 GCTCCTTGGCTGGTACTCC 59.778 63.158 0.00 0.00 0.00 3.85
3246 3301 1.908483 CTCCTTGGCTGGTACTCCC 59.092 63.158 0.00 0.00 0.00 4.30
3247 3302 0.618968 CTCCTTGGCTGGTACTCCCT 60.619 60.000 0.00 0.00 0.00 4.20
3248 3303 0.617820 TCCTTGGCTGGTACTCCCTC 60.618 60.000 0.00 0.00 0.00 4.30
3249 3304 0.618968 CCTTGGCTGGTACTCCCTCT 60.619 60.000 0.00 0.00 0.00 3.69
3250 3305 0.539051 CTTGGCTGGTACTCCCTCTG 59.461 60.000 0.00 0.00 0.00 3.35
3251 3306 0.178903 TTGGCTGGTACTCCCTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
3252 3307 0.614979 TGGCTGGTACTCCCTCTGTC 60.615 60.000 0.00 0.00 0.00 3.51
3253 3308 1.668101 GGCTGGTACTCCCTCTGTCG 61.668 65.000 0.00 0.00 0.00 4.35
3254 3309 0.966370 GCTGGTACTCCCTCTGTCGT 60.966 60.000 0.00 0.00 0.00 4.34
3255 3310 0.811915 CTGGTACTCCCTCTGTCGTG 59.188 60.000 0.00 0.00 0.00 4.35
3256 3311 0.402887 TGGTACTCCCTCTGTCGTGA 59.597 55.000 0.00 0.00 0.00 4.35
3257 3312 1.005569 TGGTACTCCCTCTGTCGTGAT 59.994 52.381 0.00 0.00 0.00 3.06
3258 3313 1.677052 GGTACTCCCTCTGTCGTGATC 59.323 57.143 0.00 0.00 0.00 2.92
3259 3314 1.677052 GTACTCCCTCTGTCGTGATCC 59.323 57.143 0.00 0.00 0.00 3.36
3260 3315 0.039764 ACTCCCTCTGTCGTGATCCA 59.960 55.000 0.00 0.00 0.00 3.41
3261 3316 1.186200 CTCCCTCTGTCGTGATCCAA 58.814 55.000 0.00 0.00 0.00 3.53
3262 3317 1.550524 CTCCCTCTGTCGTGATCCAAA 59.449 52.381 0.00 0.00 0.00 3.28
3263 3318 1.275291 TCCCTCTGTCGTGATCCAAAC 59.725 52.381 0.00 0.00 0.00 2.93
3264 3319 1.350193 CCTCTGTCGTGATCCAAACG 58.650 55.000 0.00 0.00 42.36 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.223340 GCGACTATTCAACCTTGGCATG 60.223 50.000 0.00 0.00 0.00 4.06
13 14 2.017049 GCGACTATTCAACCTTGGCAT 58.983 47.619 0.00 0.00 0.00 4.40
123 125 0.249120 CACCAACATCCTAGCGACCA 59.751 55.000 0.00 0.00 0.00 4.02
226 231 2.838202 AGCTTCGGGGAAGAAGTAATCA 59.162 45.455 9.43 0.00 46.82 2.57
259 264 9.155975 ACATCACAACAGTCTAAGATAATCAAC 57.844 33.333 0.00 0.00 0.00 3.18
269 274 6.413783 TCACCTAACATCACAACAGTCTAA 57.586 37.500 0.00 0.00 0.00 2.10
273 278 4.690748 CGAATCACCTAACATCACAACAGT 59.309 41.667 0.00 0.00 0.00 3.55
280 285 5.410924 CAGAACTCGAATCACCTAACATCA 58.589 41.667 1.23 0.00 0.00 3.07
282 287 4.184629 GCAGAACTCGAATCACCTAACAT 58.815 43.478 1.23 0.00 0.00 2.71
295 300 5.385617 CCTAAAGAAAACATGCAGAACTCG 58.614 41.667 0.00 0.00 0.00 4.18
300 305 3.495331 TGGCCTAAAGAAAACATGCAGA 58.505 40.909 3.32 0.00 0.00 4.26
303 308 5.237048 TGAAATGGCCTAAAGAAAACATGC 58.763 37.500 3.32 0.00 0.00 4.06
308 314 4.279671 TCGCTTGAAATGGCCTAAAGAAAA 59.720 37.500 3.32 0.00 0.00 2.29
310 316 3.417101 TCGCTTGAAATGGCCTAAAGAA 58.583 40.909 3.32 0.00 0.00 2.52
329 335 7.535258 CACAAGAAACAGAGGTAAATCAATTCG 59.465 37.037 0.00 0.00 0.00 3.34
333 339 6.126409 ACCACAAGAAACAGAGGTAAATCAA 58.874 36.000 0.00 0.00 0.00 2.57
336 342 8.410912 GTTAAACCACAAGAAACAGAGGTAAAT 58.589 33.333 0.00 0.00 0.00 1.40
362 371 2.744202 GGCACCTCTACACTCATTTGTG 59.256 50.000 0.00 0.00 43.07 3.33
363 372 3.059352 GGCACCTCTACACTCATTTGT 57.941 47.619 0.00 0.00 0.00 2.83
384 393 1.110442 TTCCACAAAACACCCAGCAG 58.890 50.000 0.00 0.00 0.00 4.24
459 468 1.380785 TACTGCCACTACTCCCCCG 60.381 63.158 0.00 0.00 0.00 5.73
470 479 2.030007 GTGTGGTACGTTACTACTGCCA 60.030 50.000 0.00 0.00 40.38 4.92
506 518 0.833287 ACCAACTCCCGAGGATCATG 59.167 55.000 0.00 0.00 33.17 3.07
579 591 0.178926 TGGAACGGAGGGAGTACCAA 60.179 55.000 0.00 0.00 43.89 3.67
580 592 0.042131 ATGGAACGGAGGGAGTACCA 59.958 55.000 0.00 0.00 43.89 3.25
588 600 1.002134 AACTGGCATGGAACGGAGG 60.002 57.895 0.00 0.00 0.00 4.30
594 606 1.073025 AGCGACAACTGGCATGGAA 59.927 52.632 0.00 0.00 0.00 3.53
595 607 1.672030 CAGCGACAACTGGCATGGA 60.672 57.895 0.00 0.00 33.85 3.41
597 609 0.806868 AATCAGCGACAACTGGCATG 59.193 50.000 0.00 0.00 38.26 4.06
598 610 1.538047 AAATCAGCGACAACTGGCAT 58.462 45.000 0.00 0.00 38.26 4.40
599 611 1.804151 GTAAATCAGCGACAACTGGCA 59.196 47.619 0.00 0.00 38.26 4.92
600 612 2.076863 AGTAAATCAGCGACAACTGGC 58.923 47.619 0.00 0.00 38.26 4.85
601 613 4.242475 TGTAGTAAATCAGCGACAACTGG 58.758 43.478 0.00 0.00 38.26 4.00
602 614 5.839262 TTGTAGTAAATCAGCGACAACTG 57.161 39.130 0.00 0.00 39.12 3.16
603 615 5.408604 CCTTTGTAGTAAATCAGCGACAACT 59.591 40.000 0.00 0.00 0.00 3.16
607 619 4.329256 GTCCCTTTGTAGTAAATCAGCGAC 59.671 45.833 0.00 0.00 0.00 5.19
608 620 4.020928 TGTCCCTTTGTAGTAAATCAGCGA 60.021 41.667 0.00 0.00 0.00 4.93
619 631 6.174720 TCCATATTAGCTGTCCCTTTGTAG 57.825 41.667 0.00 0.00 0.00 2.74
625 637 2.368875 CCGTTCCATATTAGCTGTCCCT 59.631 50.000 0.00 0.00 0.00 4.20
626 638 2.367567 TCCGTTCCATATTAGCTGTCCC 59.632 50.000 0.00 0.00 0.00 4.46
627 639 3.555168 CCTCCGTTCCATATTAGCTGTCC 60.555 52.174 0.00 0.00 0.00 4.02
632 644 1.003233 CCCCCTCCGTTCCATATTAGC 59.997 57.143 0.00 0.00 0.00 3.09
723 735 2.162681 GGAGACAATTTGGGGACAGTG 58.837 52.381 0.78 0.00 44.54 3.66
868 880 3.282021 CAGGTGGGATAGAACAACATGG 58.718 50.000 0.00 0.00 0.00 3.66
912 925 5.041191 AGAAGGTCAAACAACAGATGAGT 57.959 39.130 0.00 0.00 0.00 3.41
915 928 5.240183 ACATGAGAAGGTCAAACAACAGATG 59.760 40.000 0.00 0.00 39.19 2.90
933 946 2.158842 CCCTGAAGCCTTCCTACATGAG 60.159 54.545 0.00 0.00 0.00 2.90
958 971 1.045407 ACGGAGCAACCTGTTACTGA 58.955 50.000 0.00 0.00 36.31 3.41
959 972 1.531149 CAACGGAGCAACCTGTTACTG 59.469 52.381 0.00 0.00 35.13 2.74
960 973 1.878953 CAACGGAGCAACCTGTTACT 58.121 50.000 0.00 0.00 35.13 2.24
961 974 0.237498 GCAACGGAGCAACCTGTTAC 59.763 55.000 0.00 0.00 35.13 2.50
983 996 9.658799 GCCTCAGCATTATTAATTAGTCTATCA 57.341 33.333 0.00 0.00 39.53 2.15
1119 1132 4.913335 ATATGCCGTCTTCTTCTCGTAA 57.087 40.909 0.00 0.00 0.00 3.18
1251 1264 2.131972 CGTTCATCCAGTGTTGACGAA 58.868 47.619 0.00 0.00 34.30 3.85
1275 1288 3.020274 CTCCTCATTCTCTTCGTCCTCA 58.980 50.000 0.00 0.00 0.00 3.86
1350 1363 0.543749 CCTCATCCTTGTCCAGGTCC 59.456 60.000 0.00 0.00 44.37 4.46
1449 1462 1.107114 CCTCCTGAGAGCGCTCTTTA 58.893 55.000 38.41 28.05 40.61 1.85
1500 1513 2.854777 GTCATGTGTTACAGCGCTAGAG 59.145 50.000 10.99 0.00 0.00 2.43
1503 1516 1.404986 GGGTCATGTGTTACAGCGCTA 60.405 52.381 10.99 0.00 0.00 4.26
1647 1660 4.282496 CAGAACTCTTCTCCCTAGCCTTA 58.718 47.826 0.00 0.00 38.11 2.69
1653 1666 2.655407 ACCTCCAGAACTCTTCTCCCTA 59.345 50.000 0.00 0.00 38.11 3.53
1680 1693 2.285083 TGGTCCACAGAACTTGAAACG 58.715 47.619 0.00 0.00 0.00 3.60
1683 1696 3.855255 TCATGGTCCACAGAACTTGAA 57.145 42.857 0.00 0.00 40.02 2.69
1711 1724 0.752009 TCCGGGAGAGGATTCGTGAG 60.752 60.000 0.00 0.00 34.92 3.51
1728 1741 1.865865 TGTTCTTCAGCTGTTCGTCC 58.134 50.000 14.67 0.00 0.00 4.79
1789 1802 0.621609 CCAGGACCCCGGAATGTAAA 59.378 55.000 0.73 0.00 0.00 2.01
1820 1833 3.512516 GCTCCCCGACAGCATTGC 61.513 66.667 0.00 0.00 36.82 3.56
1839 1852 2.411904 GCATTAGATCCTGAAGCCTCG 58.588 52.381 0.00 0.00 0.00 4.63
1848 1861 1.399714 TGGACGACGCATTAGATCCT 58.600 50.000 0.00 0.00 0.00 3.24
1849 1862 1.859080 GTTGGACGACGCATTAGATCC 59.141 52.381 0.00 0.00 0.00 3.36
1850 1863 1.859080 GGTTGGACGACGCATTAGATC 59.141 52.381 0.00 0.00 0.00 2.75
1852 1868 0.108520 GGGTTGGACGACGCATTAGA 60.109 55.000 0.00 0.00 33.16 2.10
1860 1876 1.535462 CTCATGTTTGGGTTGGACGAC 59.465 52.381 0.00 0.00 0.00 4.34
1942 1958 5.675684 TTACTTGTCACTGATCCAGCATA 57.324 39.130 0.00 0.00 34.37 3.14
2016 2032 5.659440 AGAGTTGTGTTTGGTTGTTTGAT 57.341 34.783 0.00 0.00 0.00 2.57
2019 2035 5.185056 AGCTAAGAGTTGTGTTTGGTTGTTT 59.815 36.000 0.00 0.00 0.00 2.83
2127 2143 0.738975 CGCCATTGTCTCCGTCTCTA 59.261 55.000 0.00 0.00 0.00 2.43
2177 2193 1.062587 CGCCGTCTTCTTTATTGCTGG 59.937 52.381 0.00 0.00 0.00 4.85
2178 2194 1.062587 CCGCCGTCTTCTTTATTGCTG 59.937 52.381 0.00 0.00 0.00 4.41
2337 2353 0.883814 GGCGCTCATCTTGGATGGAG 60.884 60.000 7.64 5.54 0.00 3.86
2367 2383 5.106237 ACGTACCAAACTTACACAAAAAGCA 60.106 36.000 0.00 0.00 0.00 3.91
2392 2408 1.228154 AAACACGAAGCAGGTCCCC 60.228 57.895 0.00 0.00 0.00 4.81
2404 2420 2.277084 GATGTACCCTAGGCAAACACG 58.723 52.381 2.05 0.00 0.00 4.49
2417 2433 2.143122 CCATGCATACCGTGATGTACC 58.857 52.381 0.00 0.00 31.89 3.34
2433 2449 1.816835 GCTCATCACATATGCCCCATG 59.183 52.381 1.58 0.41 0.00 3.66
2529 2548 3.668447 ACAAGGCAGACATTGTCACTAG 58.332 45.455 18.57 6.84 34.62 2.57
2553 2572 2.796031 CGAATGCAAGCAACACAACAAT 59.204 40.909 0.00 0.00 0.00 2.71
2573 2609 4.174411 TGCTACTAATACTAGCCATGCG 57.826 45.455 0.00 0.00 36.54 4.73
2578 2614 5.855045 ACCAACATGCTACTAATACTAGCC 58.145 41.667 0.00 0.00 36.54 3.93
2664 2706 3.804036 AGACGGAATGTTTGTGTCTCAA 58.196 40.909 0.00 0.00 35.04 3.02
2666 2708 3.560068 ACAAGACGGAATGTTTGTGTCTC 59.440 43.478 0.00 0.00 38.87 3.36
2685 2728 0.537143 CAACCTAGGCTGCACCACAA 60.537 55.000 9.30 0.00 43.14 3.33
2728 2774 5.939883 CAGATGGTTGTGATTTCTTACAGGA 59.060 40.000 0.00 0.00 0.00 3.86
2769 2815 6.903534 AGGGATCCAAATAAAGTCTCAGTAGA 59.096 38.462 15.23 0.00 0.00 2.59
2773 2819 5.128919 CCAGGGATCCAAATAAAGTCTCAG 58.871 45.833 15.23 0.00 0.00 3.35
2774 2820 4.628715 GCCAGGGATCCAAATAAAGTCTCA 60.629 45.833 15.23 0.00 0.00 3.27
2775 2821 3.885901 GCCAGGGATCCAAATAAAGTCTC 59.114 47.826 15.23 0.00 0.00 3.36
2814 2865 3.188460 CCGTCCAATACTTTTGTCAGGTG 59.812 47.826 0.00 0.00 0.00 4.00
2888 2942 9.650539 ACGTCACTGATTATATCTAGTACGTAT 57.349 33.333 0.00 0.00 34.42 3.06
2889 2943 8.919661 CACGTCACTGATTATATCTAGTACGTA 58.080 37.037 0.00 0.00 34.42 3.57
2890 2944 7.440556 ACACGTCACTGATTATATCTAGTACGT 59.559 37.037 0.00 0.00 35.15 3.57
2891 2945 7.794880 ACACGTCACTGATTATATCTAGTACG 58.205 38.462 0.00 0.00 32.52 3.67
2893 2947 8.919661 CGTACACGTCACTGATTATATCTAGTA 58.080 37.037 0.00 0.00 34.11 1.82
2894 2948 7.794880 CGTACACGTCACTGATTATATCTAGT 58.205 38.462 0.00 0.00 34.11 2.57
2945 2999 7.894376 CATAAATTGTTATGGATTGGATGGC 57.106 36.000 0.00 0.00 41.98 4.40
2958 3012 3.191581 CACCGGCACACCATAAATTGTTA 59.808 43.478 0.00 0.00 34.57 2.41
2959 3013 2.029470 CACCGGCACACCATAAATTGTT 60.029 45.455 0.00 0.00 34.57 2.83
3012 3067 3.089284 TGGCTGTGAAGAAGATCGAGTA 58.911 45.455 0.00 0.00 0.00 2.59
3067 3122 0.389166 CGATGGCTAGATCGGAAGGC 60.389 60.000 6.04 10.92 41.29 4.35
3107 3162 1.140052 TCCGTTGTTGGACATGTCTGT 59.860 47.619 24.50 0.00 38.67 3.41
3111 3166 0.179032 TGCTCCGTTGTTGGACATGT 60.179 50.000 0.00 0.00 33.48 3.21
3112 3167 0.950836 TTGCTCCGTTGTTGGACATG 59.049 50.000 0.00 0.00 33.48 3.21
3113 3168 1.238439 CTTGCTCCGTTGTTGGACAT 58.762 50.000 0.00 0.00 33.48 3.06
3115 3170 1.282875 GCTTGCTCCGTTGTTGGAC 59.717 57.895 0.00 0.00 33.48 4.02
3116 3171 2.250939 CGCTTGCTCCGTTGTTGGA 61.251 57.895 0.00 0.00 36.37 3.53
3117 3172 2.175184 CTCGCTTGCTCCGTTGTTGG 62.175 60.000 0.00 0.00 0.00 3.77
3118 3173 1.205064 CTCGCTTGCTCCGTTGTTG 59.795 57.895 0.00 0.00 0.00 3.33
3120 3175 2.357517 CCTCGCTTGCTCCGTTGT 60.358 61.111 0.00 0.00 0.00 3.32
3124 3179 2.048222 TCAACCTCGCTTGCTCCG 60.048 61.111 0.00 0.00 0.00 4.63
3141 3196 3.219281 GGTGTACAAGGTGATGTTTGGT 58.781 45.455 0.00 0.00 34.75 3.67
3147 3202 1.674817 GGTCGGGTGTACAAGGTGATG 60.675 57.143 0.00 0.00 0.00 3.07
3149 3204 0.470456 AGGTCGGGTGTACAAGGTGA 60.470 55.000 0.00 0.00 0.00 4.02
3150 3205 0.320421 CAGGTCGGGTGTACAAGGTG 60.320 60.000 0.00 0.00 0.00 4.00
3152 3207 0.682852 TTCAGGTCGGGTGTACAAGG 59.317 55.000 0.00 0.00 0.00 3.61
3182 3237 3.160269 GGCCATGAATAAGATCAAGGGG 58.840 50.000 0.00 0.00 38.36 4.79
3184 3239 4.891756 ACTTGGCCATGAATAAGATCAAGG 59.108 41.667 24.48 0.00 40.35 3.61
3190 3245 5.045651 TCAGAAGACTTGGCCATGAATAAGA 60.046 40.000 24.48 11.67 0.00 2.10
3191 3246 5.188434 TCAGAAGACTTGGCCATGAATAAG 58.812 41.667 24.48 11.89 0.00 1.73
3193 3248 4.842531 TCAGAAGACTTGGCCATGAATA 57.157 40.909 24.48 0.00 0.00 1.75
3194 3249 3.726557 TCAGAAGACTTGGCCATGAAT 57.273 42.857 24.48 9.71 0.00 2.57
3197 3252 2.507484 TGTTCAGAAGACTTGGCCATG 58.493 47.619 16.76 16.76 0.00 3.66
3202 3257 5.673337 TTTTCGATGTTCAGAAGACTTGG 57.327 39.130 0.00 0.00 0.00 3.61
3236 3291 0.811915 CACGACAGAGGGAGTACCAG 59.188 60.000 0.00 0.00 43.89 4.00
3243 3298 1.275291 GTTTGGATCACGACAGAGGGA 59.725 52.381 0.00 0.00 0.00 4.20
3244 3299 1.726853 GTTTGGATCACGACAGAGGG 58.273 55.000 0.00 0.00 0.00 4.30
3245 3300 1.067846 TCGTTTGGATCACGACAGAGG 60.068 52.381 2.89 0.00 41.66 3.69
3246 3301 2.347697 TCGTTTGGATCACGACAGAG 57.652 50.000 2.89 0.00 41.66 3.35


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

AutoCloner maintained by Alex Coulton.