Multiple sequence alignment - TraesCS1A01G049100

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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 TraesCS1A01G049100 chr1A 100.000 3090 0 0 1 3090 30774112 30771023 0.000000e+00 5707.0
1 TraesCS1A01G049100 chr1D 92.920 1483 82 13 1621 3090 31353736 31352264 0.000000e+00 2135.0
2 TraesCS1A01G049100 chr1D 93.850 813 39 2 824 1626 31356298 31355487 0.000000e+00 1214.0
3 TraesCS1A01G049100 chr1D 87.952 830 61 17 1 821 31358891 31358092 0.000000e+00 942.0
4 TraesCS1A01G049100 chr1D 83.871 496 67 9 2426 2915 31060140 31059652 7.810000e-126 460.0
5 TraesCS1A01G049100 chr1D 80.132 302 50 6 2426 2723 30666622 30666327 1.870000e-52 217.0
6 TraesCS1A01G049100 chr1D 83.237 173 22 6 2537 2705 31285596 31285427 5.340000e-33 152.0
7 TraesCS1A01G049100 chr1D 82.424 165 27 2 2743 2906 30265709 30265546 3.210000e-30 143.0
8 TraesCS1A01G049100 chr1D 76.923 247 51 5 2670 2915 30538237 30537996 5.370000e-28 135.0
9 TraesCS1A01G049100 chr1D 77.049 244 47 6 2670 2912 30266031 30265796 6.950000e-27 132.0
10 TraesCS1A01G049100 chr1D 83.333 144 21 3 331 473 425916970 425917111 2.500000e-26 130.0
11 TraesCS1A01G049100 chr1D 86.792 106 14 0 2540 2645 31285718 31285613 5.410000e-23 119.0
12 TraesCS1A01G049100 chr1D 80.000 135 24 3 337 469 357277446 357277579 2.540000e-16 97.1
13 TraesCS1A01G049100 chr1B 89.024 410 38 5 2425 2832 49166572 49166168 4.600000e-138 501.0
14 TraesCS1A01G049100 chr1B 81.212 495 77 11 2426 2915 49642673 49642190 4.830000e-103 385.0
15 TraesCS1A01G049100 chr1B 90.816 98 9 0 2818 2915 49146582 49146485 6.950000e-27 132.0
16 TraesCS1A01G049100 chr1B 90.000 70 7 0 485 554 368504243 368504312 1.180000e-14 91.6
17 TraesCS1A01G049100 chr1B 87.500 72 7 2 485 555 531693108 531693178 7.100000e-12 82.4
18 TraesCS1A01G049100 chr2B 86.525 282 30 5 1 276 476220458 476220179 1.390000e-78 303.0
19 TraesCS1A01G049100 chr5B 84.643 280 37 5 1 276 503117194 503116917 1.090000e-69 274.0
20 TraesCS1A01G049100 chr5B 88.732 71 8 0 485 555 580973867 580973797 1.530000e-13 87.9
21 TraesCS1A01G049100 chr7B 87.903 124 12 3 351 473 218817200 218817079 3.210000e-30 143.0
22 TraesCS1A01G049100 chr7B 85.484 124 14 3 335 457 609762386 609762506 3.230000e-25 126.0
23 TraesCS1A01G049100 chr7B 88.732 71 8 0 485 555 609816378 609816308 1.530000e-13 87.9
24 TraesCS1A01G049100 chr7B 94.595 37 2 0 2146 2182 579282444 579282480 1.200000e-04 58.4
25 TraesCS1A01G049100 chr7A 90.805 87 6 2 2156 2241 521335925 521336010 7.000000e-22 115.0
26 TraesCS1A01G049100 chr4B 83.607 122 18 2 353 473 380012809 380012689 2.520000e-21 113.0
27 TraesCS1A01G049100 chr4B 88.732 71 7 1 485 555 253672348 253672417 5.490000e-13 86.1
28 TraesCS1A01G049100 chrUn 83.471 121 15 5 354 473 238402236 238402120 1.170000e-19 108.0
29 TraesCS1A01G049100 chr4A 80.556 144 25 3 331 473 186735950 186735809 1.170000e-19 108.0
30 TraesCS1A01G049100 chr7D 90.244 82 7 1 2163 2244 14264647 14264567 4.210000e-19 106.0
31 TraesCS1A01G049100 chr7D 89.157 83 9 0 2159 2241 632508050 632507968 1.520000e-18 104.0
32 TraesCS1A01G049100 chr2D 77.184 206 31 8 351 555 498231605 498231415 4.210000e-19 106.0
33 TraesCS1A01G049100 chr2D 100.000 29 0 0 557 585 544659128 544659100 2.000000e-03 54.7
34 TraesCS1A01G049100 chr3D 87.805 82 10 0 2162 2243 544488074 544488155 2.540000e-16 97.1
35 TraesCS1A01G049100 chr3D 78.472 144 27 4 331 473 77545122 77544982 1.180000e-14 91.6
36 TraesCS1A01G049100 chr5A 94.915 59 2 1 485 543 293396243 293396186 1.180000e-14 91.6
37 TraesCS1A01G049100 chr3A 86.842 76 8 2 2160 2233 736809674 736809599 1.970000e-12 84.2
38 TraesCS1A01G049100 chr6B 87.324 71 9 0 485 555 225831885 225831815 7.100000e-12 82.4


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 TraesCS1A01G049100 chr1A 30771023 30774112 3089 True 5707.000000 5707 100.000 1 3090 1 chr1A.!!$R1 3089
1 TraesCS1A01G049100 chr1D 31352264 31358891 6627 True 1430.333333 2135 91.574 1 3090 3 chr1D.!!$R6 3089

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
27 28 0.179045 GGTATCATTGTGGAGCCGCT 60.179 55.0 0.00 0.0 0.00 5.52 F
365 373 1.191535 GTCTTGGTTTATTGGCCCCC 58.808 55.0 0.00 0.0 0.00 5.40 F
1514 3324 0.977395 GCCCTCTATAGGTTCGGCAT 59.023 55.0 12.55 0.0 41.89 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 3165 0.390472 GAAGAGGCCTTCCACAGACG 60.390 60.0 6.77 0.0 42.24 4.18 R
1711 5277 0.895530 ATAGCCTGCACAGTGTACGT 59.104 50.0 1.61 0.0 0.00 3.57 R
2846 6420 0.616964 ATGAGCCTCTCCACTCTGCA 60.617 55.0 0.00 0.0 33.92 4.41 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
23 24 3.209410 CTTGGAGGTATCATTGTGGAGC 58.791 50.000 0.00 0.00 0.00 4.70
24 25 1.490490 TGGAGGTATCATTGTGGAGCC 59.510 52.381 0.00 0.00 0.00 4.70
27 28 0.179045 GGTATCATTGTGGAGCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
45 46 2.234143 GCTTGCCCTTCCTATCCAATC 58.766 52.381 0.00 0.00 0.00 2.67
57 58 3.440522 CCTATCCAATCGCGTGAGATCTA 59.559 47.826 5.77 0.00 0.00 1.98
69 70 3.367087 CGTGAGATCTACGGGTGAAAACT 60.367 47.826 13.58 0.00 37.86 2.66
80 81 4.638865 ACGGGTGAAAACTTAAGATATGGC 59.361 41.667 10.09 0.00 0.00 4.40
100 101 1.524621 GTGCCAGATCGGGTGATGG 60.525 63.158 13.75 2.90 34.09 3.51
105 106 1.456892 AGATCGGGTGATGGCGGTA 60.457 57.895 0.00 0.00 34.09 4.02
106 107 1.300697 GATCGGGTGATGGCGGTAC 60.301 63.158 0.00 0.00 34.09 3.34
166 168 2.916702 TCCTGACGATGGATCCAATG 57.083 50.000 20.67 16.44 0.00 2.82
204 206 2.736670 AGAGTTTGGGTTTGTCTGCT 57.263 45.000 0.00 0.00 0.00 4.24
207 209 2.887152 GAGTTTGGGTTTGTCTGCTGAT 59.113 45.455 0.00 0.00 0.00 2.90
281 283 5.523188 CCTTCTCTGAGGATTCTTGAATTCG 59.477 44.000 4.59 0.00 39.25 3.34
284 286 2.279741 TGAGGATTCTTGAATTCGCCG 58.720 47.619 0.04 0.00 0.00 6.46
285 287 2.280628 GAGGATTCTTGAATTCGCCGT 58.719 47.619 0.04 0.00 0.00 5.68
292 294 4.035278 TCTTGAATTCGCCGTTGTTTTT 57.965 36.364 0.04 0.00 0.00 1.94
296 298 4.669318 TGAATTCGCCGTTGTTTTTGTTA 58.331 34.783 0.04 0.00 0.00 2.41
308 310 7.043920 CCGTTGTTTTTGTTATTGTAAGTGGTC 60.044 37.037 0.00 0.00 0.00 4.02
312 314 8.478877 TGTTTTTGTTATTGTAAGTGGTCCATT 58.521 29.630 0.00 0.00 0.00 3.16
313 315 9.968870 GTTTTTGTTATTGTAAGTGGTCCATTA 57.031 29.630 0.00 0.00 0.00 1.90
317 319 8.514330 TGTTATTGTAAGTGGTCCATTAATCC 57.486 34.615 0.00 0.00 0.00 3.01
318 320 8.333235 TGTTATTGTAAGTGGTCCATTAATCCT 58.667 33.333 0.00 0.00 0.00 3.24
321 323 3.737559 AAGTGGTCCATTAATCCTGCA 57.262 42.857 0.00 0.00 0.00 4.41
324 326 2.035066 GTGGTCCATTAATCCTGCATGC 59.965 50.000 11.82 11.82 0.00 4.06
346 354 7.581011 TGCATGCATGTACTATATACTTTCG 57.419 36.000 26.79 0.00 0.00 3.46
361 369 4.499037 ACTTTCGTCTTGGTTTATTGGC 57.501 40.909 0.00 0.00 0.00 4.52
365 373 1.191535 GTCTTGGTTTATTGGCCCCC 58.808 55.000 0.00 0.00 0.00 5.40
369 377 3.077695 TCTTGGTTTATTGGCCCCCTTTA 59.922 43.478 0.00 0.00 0.00 1.85
375 383 7.371043 TGGTTTATTGGCCCCCTTTATATTTA 58.629 34.615 0.00 0.00 0.00 1.40
376 384 7.849904 TGGTTTATTGGCCCCCTTTATATTTAA 59.150 33.333 0.00 0.00 0.00 1.52
475 483 6.696411 TGTTTAAACATGAATCCAATGACCC 58.304 36.000 17.01 0.00 33.17 4.46
476 484 6.496565 TGTTTAAACATGAATCCAATGACCCT 59.503 34.615 17.01 0.00 33.17 4.34
477 485 6.773976 TTAAACATGAATCCAATGACCCTC 57.226 37.500 0.00 0.00 0.00 4.30
478 486 4.320546 AACATGAATCCAATGACCCTCA 57.679 40.909 0.00 0.00 0.00 3.86
479 487 3.894759 ACATGAATCCAATGACCCTCAG 58.105 45.455 0.00 0.00 0.00 3.35
480 488 3.524789 ACATGAATCCAATGACCCTCAGA 59.475 43.478 0.00 0.00 0.00 3.27
481 489 4.018141 ACATGAATCCAATGACCCTCAGAA 60.018 41.667 0.00 0.00 0.00 3.02
482 490 4.656100 TGAATCCAATGACCCTCAGAAA 57.344 40.909 0.00 0.00 0.00 2.52
483 491 4.996793 TGAATCCAATGACCCTCAGAAAA 58.003 39.130 0.00 0.00 0.00 2.29
484 492 5.392995 TGAATCCAATGACCCTCAGAAAAA 58.607 37.500 0.00 0.00 0.00 1.94
571 579 7.213678 TGATCAAAAAGGAACCAATAAACCAC 58.786 34.615 0.00 0.00 0.00 4.16
603 611 6.072563 GGTAGTAGGCTATAGCTACAGACAAC 60.073 46.154 23.53 15.01 41.70 3.32
604 612 5.446860 AGTAGGCTATAGCTACAGACAACA 58.553 41.667 23.53 0.00 41.70 3.33
648 658 1.745489 GTGAATGCACCGGACCTCC 60.745 63.158 9.46 0.00 39.14 4.30
708 718 2.266554 GCTCACGATGACTCCTTTCTG 58.733 52.381 0.00 0.00 0.00 3.02
714 724 2.626840 GATGACTCCTTTCTGGCTCAC 58.373 52.381 0.00 0.00 35.26 3.51
821 831 1.537202 AGCGAGATCAAGTTGTTTGGC 59.463 47.619 2.11 3.31 37.39 4.52
822 832 1.537202 GCGAGATCAAGTTGTTTGGCT 59.463 47.619 2.11 0.00 37.39 4.75
823 833 2.030805 GCGAGATCAAGTTGTTTGGCTT 60.031 45.455 2.11 0.00 37.39 4.35
824 834 3.814945 CGAGATCAAGTTGTTTGGCTTC 58.185 45.455 2.11 0.00 37.39 3.86
825 835 3.250762 CGAGATCAAGTTGTTTGGCTTCA 59.749 43.478 2.11 0.00 37.39 3.02
826 836 4.540824 GAGATCAAGTTGTTTGGCTTCAC 58.459 43.478 2.11 0.00 37.39 3.18
838 2638 2.447443 TGGCTTCACGATGACTCTAGT 58.553 47.619 0.00 0.00 0.00 2.57
843 2643 5.448438 GCTTCACGATGACTCTAGTCTATG 58.552 45.833 11.22 4.90 44.99 2.23
1043 2853 1.490574 AGCTCACCCATCTACCACTC 58.509 55.000 0.00 0.00 0.00 3.51
1061 2871 3.434984 CACTCCAAGCTAAGCTCAGTTTC 59.565 47.826 0.00 0.00 38.25 2.78
1062 2872 3.071602 ACTCCAAGCTAAGCTCAGTTTCA 59.928 43.478 0.00 0.00 38.25 2.69
1073 2883 7.171678 GCTAAGCTCAGTTTCAAGTAAGAAAGA 59.828 37.037 0.00 0.00 38.11 2.52
1104 2914 3.882025 GCTTCTTCAGCCGTCCTG 58.118 61.111 0.00 0.00 43.65 3.86
1116 2926 2.101582 AGCCGTCCTGCTACTTATTCTG 59.898 50.000 0.00 0.00 40.56 3.02
1131 2941 3.803082 CTGATGGTTGTGGCCGCG 61.803 66.667 12.58 0.00 0.00 6.46
1242 3052 2.743928 GCCCACCTCGTGCAGAAG 60.744 66.667 0.00 0.00 31.34 2.85
1489 3299 1.078426 ATTCCCTTCGGCAACCTCG 60.078 57.895 0.00 0.00 0.00 4.63
1514 3324 0.977395 GCCCTCTATAGGTTCGGCAT 59.023 55.000 12.55 0.00 41.89 4.40
1515 3325 1.066787 GCCCTCTATAGGTTCGGCATC 60.067 57.143 12.55 0.00 41.89 3.91
1516 3326 2.248248 CCCTCTATAGGTTCGGCATCA 58.752 52.381 0.00 0.00 41.89 3.07
1567 3377 4.385405 AGACACTGAGCGCCTGCC 62.385 66.667 2.29 0.00 44.31 4.85
1695 5261 1.671379 GTCCGCACTTCCCAACTCC 60.671 63.158 0.00 0.00 0.00 3.85
1824 5390 4.451241 CACATGATGGAGGGCTCG 57.549 61.111 0.00 0.00 0.00 5.03
1920 5486 4.806247 CACTTCGACACCTCTAATTGGATC 59.194 45.833 0.00 0.00 0.00 3.36
2017 5583 0.389817 CCTCATGTTCGGCGTGAAGA 60.390 55.000 6.85 0.00 42.05 2.87
2022 5588 2.435938 TTCGGCGTGAAGATGGCC 60.436 61.111 6.85 0.00 43.42 5.36
2046 5612 6.907212 CCGACAATGCATAGAATCTTAACAAC 59.093 38.462 0.00 0.00 0.00 3.32
2051 5617 9.630098 CAATGCATAGAATCTTAACAACAAACT 57.370 29.630 0.00 0.00 0.00 2.66
2054 5620 8.440059 TGCATAGAATCTTAACAACAAACTACG 58.560 33.333 0.00 0.00 0.00 3.51
2109 5675 8.305317 AGCAAGAATAAAAAGTACTCGTAGTCT 58.695 33.333 0.00 0.42 0.00 3.24
2148 5714 2.370849 CCGTAAGTTGGCTATACCCCAT 59.629 50.000 0.00 0.00 37.83 4.00
2189 5763 9.529823 CTTTACCTAAAAATAAAGGGAGGAAGT 57.470 33.333 0.00 0.00 37.18 3.01
2200 5774 8.809468 ATAAAGGGAGGAAGTTTTCATAGTTC 57.191 34.615 0.00 0.00 0.00 3.01
2213 5787 4.913335 TCATAGTTCTCCATACGTCACC 57.087 45.455 0.00 0.00 0.00 4.02
2259 5833 5.878116 TGTTAATCACCGAATCTACAAAGGG 59.122 40.000 0.00 0.00 0.00 3.95
2260 5834 3.560636 ATCACCGAATCTACAAAGGGG 57.439 47.619 0.00 0.00 0.00 4.79
2276 5850 4.735358 GGGGTTCCCAACTCCCGC 62.735 72.222 10.25 0.00 46.85 6.13
2292 5866 1.134367 CCCGCTGTTCGTGAATCTAGA 59.866 52.381 0.00 0.00 36.19 2.43
2296 5870 3.059570 CGCTGTTCGTGAATCTAGAACAC 59.940 47.826 17.78 17.78 46.12 3.32
2304 5878 5.940603 GTGAATCTAGAACACGACATCTG 57.059 43.478 14.52 0.00 0.00 2.90
2311 5885 2.433145 CACGACATCTGGCACGCT 60.433 61.111 0.00 0.00 0.00 5.07
2317 5891 0.253044 ACATCTGGCACGCTTGGTAT 59.747 50.000 0.00 0.00 0.00 2.73
2324 5898 3.334891 ACGCTTGGTATGGGGGCA 61.335 61.111 0.00 0.00 0.00 5.36
2350 5924 1.663135 GGTTCGATCTGCTTCAAGCTC 59.337 52.381 11.57 0.00 42.97 4.09
2351 5925 2.341257 GTTCGATCTGCTTCAAGCTCA 58.659 47.619 11.57 0.00 42.97 4.26
2353 5927 2.819115 TCGATCTGCTTCAAGCTCATC 58.181 47.619 11.57 10.54 42.97 2.92
2355 5929 2.796031 CGATCTGCTTCAAGCTCATCTC 59.204 50.000 11.57 0.00 42.97 2.75
2357 5931 3.248495 TCTGCTTCAAGCTCATCTCTG 57.752 47.619 11.57 0.00 42.97 3.35
2392 5966 1.251527 ACTCCGTCATCGCCAAGTCT 61.252 55.000 0.00 0.00 35.54 3.24
2417 5991 0.037303 TGGCTCCCAAGAAGAAGCTG 59.963 55.000 0.00 0.00 0.00 4.24
2425 5999 2.814336 CCAAGAAGAAGCTGGTGGTAAC 59.186 50.000 0.00 0.00 0.00 2.50
2514 6088 2.483014 TGGTAACATGCCGTTAAGCT 57.517 45.000 0.00 0.00 46.17 3.74
2532 6106 3.618351 AGCTGATTGGATCCAAGTTCTG 58.382 45.455 29.98 25.23 39.47 3.02
2535 6109 2.041485 TGATTGGATCCAAGTTCTGGCA 59.959 45.455 29.98 16.13 45.98 4.92
2564 6138 6.765915 AGAGAGGCTAATTTCAAAATGGTC 57.234 37.500 0.00 0.00 0.00 4.02
2595 6169 9.936759 GGAAGGAACCATTTATTTAATTGTTGA 57.063 29.630 0.00 0.00 33.57 3.18
2773 6347 2.320339 GATGCGAGCTTGGCAAGAGC 62.320 60.000 30.45 27.35 44.66 4.09
2779 6353 2.576298 GCTTGGCAAGAGCTCCAAT 58.424 52.632 30.45 0.00 41.10 3.16
2790 6364 0.396695 AGCTCCAATGCTTGATGGGG 60.397 55.000 0.00 0.00 40.93 4.96
2796 6370 2.624029 CCAATGCTTGATGGGGTTAGGT 60.624 50.000 0.00 0.00 32.87 3.08
2821 6395 1.614413 GAGAGAGTTGTGACCGAGGTT 59.386 52.381 0.00 0.00 0.00 3.50
2888 6462 8.260818 TCATCAAATTCCTTAGTCTTCCTACTG 58.739 37.037 0.00 0.00 0.00 2.74
2894 6468 9.765295 AATTCCTTAGTCTTCCTACTGTACTAA 57.235 33.333 0.00 0.00 33.06 2.24
2896 6470 6.827762 TCCTTAGTCTTCCTACTGTACTAAGC 59.172 42.308 15.54 5.95 44.10 3.09
2914 6488 7.524717 ACTAAGCATGGTAGAAACAAATTGT 57.475 32.000 0.00 0.00 0.00 2.71
2915 6489 7.951591 ACTAAGCATGGTAGAAACAAATTGTT 58.048 30.769 5.41 5.41 43.41 2.83
2968 6544 9.398538 AGAGATCACTGTAGGTTAGTTTAGTAG 57.601 37.037 0.00 0.00 0.00 2.57
2990 6566 3.113043 AGTTACCTAGGGATGTTGGGAC 58.887 50.000 14.81 0.00 0.00 4.46
3021 6599 6.596703 GTTTAGGTCGTTGTAATCAAGGTTC 58.403 40.000 0.00 0.00 39.51 3.62
3026 6604 5.163854 GGTCGTTGTAATCAAGGTTCAGATG 60.164 44.000 0.00 0.00 39.51 2.90
3038 6616 5.426689 AGGTTCAGATGCACAAGATAAGA 57.573 39.130 0.00 0.00 0.00 2.10
3060 6638 7.881775 AGACAAATTTGTAAAGTGAAGAGGT 57.118 32.000 23.33 0.00 42.43 3.85
3085 6663 9.368674 GTTCACTAAATTCCCTAGTCTTTCTAC 57.631 37.037 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.064324 GGCAAGCGGCTCCACAAT 61.064 61.111 1.45 0.00 44.01 2.71
23 24 1.227973 GGATAGGAAGGGCAAGCGG 60.228 63.158 0.00 0.00 0.00 5.52
24 25 0.107214 TTGGATAGGAAGGGCAAGCG 60.107 55.000 0.00 0.00 0.00 4.68
27 28 1.476833 GCGATTGGATAGGAAGGGCAA 60.477 52.381 0.00 0.00 0.00 4.52
45 46 1.298413 CACCCGTAGATCTCACGCG 60.298 63.158 3.53 3.53 38.07 6.01
57 58 4.638865 GCCATATCTTAAGTTTTCACCCGT 59.361 41.667 1.63 0.00 0.00 5.28
105 106 2.552373 GGAGGAAAACGATGTTGAGGGT 60.552 50.000 0.00 0.00 0.00 4.34
106 107 2.084546 GGAGGAAAACGATGTTGAGGG 58.915 52.381 0.00 0.00 0.00 4.30
166 168 3.395639 TCTACCATCAAACGTGAACACC 58.604 45.455 0.00 0.00 37.30 4.16
204 206 6.611236 AGAAAAGAAAGAAAAAGGACCCATCA 59.389 34.615 0.00 0.00 0.00 3.07
207 209 6.867519 AAGAAAAGAAAGAAAAAGGACCCA 57.132 33.333 0.00 0.00 0.00 4.51
246 248 0.603707 CAGAGAAGGAAAGCACCGCA 60.604 55.000 0.00 0.00 34.73 5.69
257 259 5.523188 CGAATTCAAGAATCCTCAGAGAAGG 59.477 44.000 6.22 0.00 37.81 3.46
281 283 6.291902 CCACTTACAATAACAAAAACAACGGC 60.292 38.462 0.00 0.00 0.00 5.68
284 286 7.760340 TGGACCACTTACAATAACAAAAACAAC 59.240 33.333 0.00 0.00 0.00 3.32
285 287 7.837863 TGGACCACTTACAATAACAAAAACAA 58.162 30.769 0.00 0.00 0.00 2.83
292 294 8.333235 AGGATTAATGGACCACTTACAATAACA 58.667 33.333 0.00 0.00 0.00 2.41
296 298 5.594317 GCAGGATTAATGGACCACTTACAAT 59.406 40.000 0.00 0.00 0.00 2.71
321 323 7.819415 ACGAAAGTATATAGTACATGCATGCAT 59.181 33.333 27.46 27.46 46.88 3.96
346 354 1.191535 GGGGGCCAATAAACCAAGAC 58.808 55.000 4.39 0.00 0.00 3.01
458 466 3.524789 TCTGAGGGTCATTGGATTCATGT 59.475 43.478 0.00 0.00 0.00 3.21
459 467 4.160642 TCTGAGGGTCATTGGATTCATG 57.839 45.455 0.00 0.00 0.00 3.07
460 468 4.868172 TTCTGAGGGTCATTGGATTCAT 57.132 40.909 0.00 0.00 0.00 2.57
461 469 4.656100 TTTCTGAGGGTCATTGGATTCA 57.344 40.909 0.00 0.00 0.00 2.57
462 470 5.982890 TTTTTCTGAGGGTCATTGGATTC 57.017 39.130 0.00 0.00 0.00 2.52
495 503 9.738832 TGCATGTCATCAAAAATAATATCACTG 57.261 29.630 0.00 0.00 0.00 3.66
544 552 7.877097 TGGTTTATTGGTTCCTTTTTGATCATG 59.123 33.333 0.00 0.00 0.00 3.07
555 563 2.419667 CGTCGTGGTTTATTGGTTCCT 58.580 47.619 0.00 0.00 0.00 3.36
558 566 2.419667 CTCCGTCGTGGTTTATTGGTT 58.580 47.619 0.00 0.00 39.52 3.67
571 579 2.181954 ATAGCCTACTACCTCCGTCG 57.818 55.000 0.00 0.00 0.00 5.12
612 620 4.966965 TCACTAGCTAGCTATTATCGGC 57.033 45.455 24.36 0.00 0.00 5.54
661 671 1.362355 GAGCACGGGTTTTTGGTGG 59.638 57.895 0.00 0.00 32.42 4.61
714 724 2.430921 GACGAGCACCACGTGGAG 60.431 66.667 40.21 32.71 43.97 3.86
791 801 3.245797 CTTGATCTCGCTCTCGACAAAA 58.754 45.455 0.00 0.00 40.21 2.44
843 2643 7.649306 AGCAACTTGTAATCAAATTCAGTGAAC 59.351 33.333 7.96 0.00 32.87 3.18
950 2750 1.663739 GACTACGTGGCTCCACACA 59.336 57.895 18.11 4.90 46.47 3.72
975 2775 0.535335 GACCTGCATGTTCGACCCTA 59.465 55.000 0.00 0.00 0.00 3.53
1027 2837 2.187958 CTTGGAGTGGTAGATGGGTGA 58.812 52.381 0.00 0.00 0.00 4.02
1028 2838 1.407437 GCTTGGAGTGGTAGATGGGTG 60.407 57.143 0.00 0.00 0.00 4.61
1036 2846 2.497675 CTGAGCTTAGCTTGGAGTGGTA 59.502 50.000 8.58 0.00 39.88 3.25
1038 2848 1.277557 ACTGAGCTTAGCTTGGAGTGG 59.722 52.381 8.58 0.00 39.88 4.00
1043 2853 3.817647 ACTTGAAACTGAGCTTAGCTTGG 59.182 43.478 8.58 7.00 39.88 3.61
1061 2871 5.591099 TGGCTTGCTTTTCTTTCTTACTTG 58.409 37.500 0.00 0.00 0.00 3.16
1062 2872 5.852282 TGGCTTGCTTTTCTTTCTTACTT 57.148 34.783 0.00 0.00 0.00 2.24
1099 2909 5.283457 ACCATCAGAATAAGTAGCAGGAC 57.717 43.478 0.00 0.00 0.00 3.85
1104 2914 4.035675 GCCACAACCATCAGAATAAGTAGC 59.964 45.833 0.00 0.00 0.00 3.58
1116 2926 3.799755 GTCGCGGCCACAACCATC 61.800 66.667 6.13 0.00 0.00 3.51
1131 2941 3.737172 GTGTGGCCATGCACCGTC 61.737 66.667 9.72 0.00 0.00 4.79
1226 3036 2.046892 CCTTCTGCACGAGGTGGG 60.047 66.667 0.00 0.00 33.64 4.61
1269 3079 3.142838 ATGGCGGCAGAATGGTGC 61.143 61.111 19.29 0.00 43.19 5.01
1355 3165 0.390472 GAAGAGGCCTTCCACAGACG 60.390 60.000 6.77 0.00 42.24 4.18
1462 3272 1.068250 CGAAGGGAATCCTCTCGGC 59.932 63.158 13.29 0.00 44.07 5.54
1501 3311 3.580904 GCGTGATGCCGAACCTATA 57.419 52.632 0.00 0.00 37.76 1.31
1612 3422 4.087892 CAGCACGACCCCCTCCAG 62.088 72.222 0.00 0.00 0.00 3.86
1711 5277 0.895530 ATAGCCTGCACAGTGTACGT 59.104 50.000 1.61 0.00 0.00 3.57
1712 5278 1.135112 TGATAGCCTGCACAGTGTACG 60.135 52.381 1.61 0.00 0.00 3.67
1713 5279 2.672961 TGATAGCCTGCACAGTGTAC 57.327 50.000 1.61 0.00 0.00 2.90
1735 5301 3.541713 GCCTCCTCCGCCTAGTGG 61.542 72.222 0.00 0.00 33.99 4.00
1821 5387 2.513204 TACGCCTCCTCGGACGAG 60.513 66.667 14.39 14.39 41.63 4.18
1824 5390 3.105852 GACGTACGCCTCCTCGGAC 62.106 68.421 16.72 0.00 39.78 4.79
1836 5402 1.298190 GCGGATGGAGACGACGTAC 60.298 63.158 0.00 0.00 0.00 3.67
1899 5465 4.372656 GGATCCAATTAGAGGTGTCGAAG 58.627 47.826 6.95 0.00 0.00 3.79
2017 5583 2.346766 TTCTATGCATTGTCGGCCAT 57.653 45.000 3.54 0.00 0.00 4.40
2022 5588 7.463544 TGTTGTTAAGATTCTATGCATTGTCG 58.536 34.615 3.54 0.00 0.00 4.35
2023 5589 9.624697 TTTGTTGTTAAGATTCTATGCATTGTC 57.375 29.630 3.54 0.00 0.00 3.18
2046 5612 5.061064 GTCATCTCTGCTTGTACGTAGTTTG 59.939 44.000 0.00 0.00 37.78 2.93
2051 5617 3.353557 AGGTCATCTCTGCTTGTACGTA 58.646 45.455 0.00 0.00 0.00 3.57
2052 5618 2.171840 AGGTCATCTCTGCTTGTACGT 58.828 47.619 0.00 0.00 0.00 3.57
2053 5619 2.949451 AGGTCATCTCTGCTTGTACG 57.051 50.000 0.00 0.00 0.00 3.67
2054 5620 6.109359 ACATTTAGGTCATCTCTGCTTGTAC 58.891 40.000 0.00 0.00 0.00 2.90
2082 5648 9.565213 GACTACGAGTACTTTTTATTCTTGCTA 57.435 33.333 0.00 0.00 0.00 3.49
2128 5694 3.764237 ATGGGGTATAGCCAACTTACG 57.236 47.619 22.07 0.00 39.65 3.18
2168 5734 8.866093 TGAAAACTTCCTCCCTTTATTTTTAGG 58.134 33.333 0.00 0.00 0.00 2.69
2172 5738 9.601810 ACTATGAAAACTTCCTCCCTTTATTTT 57.398 29.630 0.00 0.00 0.00 1.82
2174 5740 9.244292 GAACTATGAAAACTTCCTCCCTTTATT 57.756 33.333 0.00 0.00 0.00 1.40
2175 5741 8.615705 AGAACTATGAAAACTTCCTCCCTTTAT 58.384 33.333 0.00 0.00 0.00 1.40
2179 5745 5.045505 GGAGAACTATGAAAACTTCCTCCCT 60.046 44.000 0.00 0.00 0.00 4.20
2180 5746 5.186942 GGAGAACTATGAAAACTTCCTCCC 58.813 45.833 0.00 0.00 0.00 4.30
2181 5747 5.805728 TGGAGAACTATGAAAACTTCCTCC 58.194 41.667 0.00 0.00 0.00 4.30
2182 5748 7.222999 CGTATGGAGAACTATGAAAACTTCCTC 59.777 40.741 0.00 0.00 0.00 3.71
2189 5763 6.103997 GGTGACGTATGGAGAACTATGAAAA 58.896 40.000 0.00 0.00 0.00 2.29
2234 5808 6.542370 CCCTTTGTAGATTCGGTGATTAACAT 59.458 38.462 0.00 0.00 0.00 2.71
2275 5849 4.569801 GTGTTCTAGATTCACGAACAGC 57.430 45.455 16.29 10.44 45.18 4.40
2292 5866 2.317609 GCGTGCCAGATGTCGTGTT 61.318 57.895 0.00 0.00 0.00 3.32
2296 5870 2.743752 CCAAGCGTGCCAGATGTCG 61.744 63.158 0.00 0.00 0.00 4.35
2304 5878 2.828549 CCCCATACCAAGCGTGCC 60.829 66.667 0.00 0.00 0.00 5.01
2311 5885 3.095421 CTGGTGCCCCCATACCAA 58.905 61.111 0.00 0.00 45.65 3.67
2324 5898 2.125512 GCAGATCGAACCGCTGGT 60.126 61.111 0.00 0.00 37.65 4.00
2350 5924 2.662006 TGAAGACGAAGGCAGAGATG 57.338 50.000 0.00 0.00 0.00 2.90
2351 5925 2.223688 CGATGAAGACGAAGGCAGAGAT 60.224 50.000 0.00 0.00 0.00 2.75
2353 5927 1.133216 TCGATGAAGACGAAGGCAGAG 59.867 52.381 0.00 0.00 36.84 3.35
2355 5929 1.135257 AGTCGATGAAGACGAAGGCAG 60.135 52.381 0.00 0.00 45.26 4.85
2357 5931 1.551145 GAGTCGATGAAGACGAAGGC 58.449 55.000 0.00 0.00 45.26 4.35
2417 5991 3.886505 TCACAAGTTCCATTGTTACCACC 59.113 43.478 0.00 0.00 41.41 4.61
2425 5999 6.263516 ACAATCAGATCACAAGTTCCATTG 57.736 37.500 0.00 0.00 36.22 2.82
2485 6059 3.553922 CGGCATGTTACCACCACAATTTT 60.554 43.478 0.00 0.00 0.00 1.82
2532 6106 5.590259 TGAAATTAGCCTCTCTAACAATGCC 59.410 40.000 0.00 0.00 39.86 4.40
2564 6138 5.914898 AAATAAATGGTTCCTTCCCTTCG 57.085 39.130 0.00 0.00 0.00 3.79
2661 6235 2.026169 ACCTCTCTCGGTCTATCACACA 60.026 50.000 0.00 0.00 29.14 3.72
2700 6274 2.701951 GGACCTATTCCACCGTCCATAA 59.298 50.000 0.00 0.00 45.10 1.90
2753 6327 1.003476 TCTTGCCAAGCTCGCATCA 60.003 52.632 9.07 0.00 35.83 3.07
2779 6353 0.623723 GGACCTAACCCCATCAAGCA 59.376 55.000 0.00 0.00 0.00 3.91
2790 6364 3.083293 ACAACTCTCTCTCGGACCTAAC 58.917 50.000 0.00 0.00 0.00 2.34
2796 6370 1.535833 GGTCACAACTCTCTCTCGGA 58.464 55.000 0.00 0.00 0.00 4.55
2821 6395 2.723273 TGCCTCGTCTTGTCTATCTGA 58.277 47.619 0.00 0.00 0.00 3.27
2846 6420 0.616964 ATGAGCCTCTCCACTCTGCA 60.617 55.000 0.00 0.00 33.92 4.41
2888 6462 8.512138 ACAATTTGTTTCTACCATGCTTAGTAC 58.488 33.333 0.00 0.00 0.00 2.73
2968 6544 6.808591 TTGTCCCAACATCCCTAGGTAACTC 61.809 48.000 8.29 0.00 40.49 3.01
2978 6554 1.102978 CGGATTTGTCCCAACATCCC 58.897 55.000 10.11 0.00 32.90 3.85
2990 6566 5.594724 TTACAACGACCTAAACGGATTTG 57.405 39.130 0.00 0.00 36.31 2.32
2992 6568 5.481105 TGATTACAACGACCTAAACGGATT 58.519 37.500 0.00 0.00 36.31 3.01
3000 6576 5.244402 TCTGAACCTTGATTACAACGACCTA 59.756 40.000 0.00 0.00 32.27 3.08
3021 6599 7.811236 ACAAATTTGTCTTATCTTGTGCATCTG 59.189 33.333 18.13 0.00 36.50 2.90
3026 6604 9.463443 ACTTTACAAATTTGTCTTATCTTGTGC 57.537 29.630 26.46 0.00 42.35 4.57
3038 6616 8.062065 TGAACCTCTTCACTTTACAAATTTGT 57.938 30.769 25.99 25.99 37.04 2.83
3054 6632 6.731448 AGACTAGGGAATTTAGTGAACCTCTT 59.269 38.462 0.00 0.00 31.74 2.85
3060 6638 9.322769 AGTAGAAAGACTAGGGAATTTAGTGAA 57.677 33.333 0.00 0.00 31.74 3.18


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

AutoCloner maintained by Alex Coulton.