Multiple sequence alignment - TraesCS6A01G293400

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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 TraesCS6A01G293400 chr6A 100.000 4605 0 0 1 4605 524837295 524832691 0.000000e+00 8504.0
1 TraesCS6A01G293400 chr6D 90.905 4662 261 63 1 4605 382729304 382724749 0.000000e+00 6109.0
2 TraesCS6A01G293400 chr6D 97.826 46 1 0 3741 3786 245495195 245495240 3.820000e-11 80.5
3 TraesCS6A01G293400 chr6D 77.778 126 22 5 111 233 303845102 303844980 6.390000e-09 73.1
4 TraesCS6A01G293400 chr6B 92.970 2347 120 21 2291 4605 572505032 572502699 0.000000e+00 3378.0
5 TraesCS6A01G293400 chr6B 89.776 1829 139 24 1 1812 572545410 572543613 0.000000e+00 2298.0
6 TraesCS6A01G293400 chr6B 91.375 1229 75 17 599 1812 572506730 572505518 0.000000e+00 1653.0
7 TraesCS6A01G293400 chr6B 92.820 1156 54 18 2291 3427 572543127 572541982 0.000000e+00 1648.0
8 TraesCS6A01G293400 chr6B 88.561 813 56 15 3811 4605 572495089 572494296 0.000000e+00 952.0
9 TraesCS6A01G293400 chr6B 89.627 617 52 7 1 613 572507360 572506752 0.000000e+00 774.0
10 TraesCS6A01G293400 chr6B 93.077 390 26 1 1936 2324 572505490 572505101 1.860000e-158 569.0
11 TraesCS6A01G293400 chr6B 92.564 390 28 1 1936 2324 572543585 572543196 4.020000e-155 558.0
12 TraesCS6A01G293400 chr6B 97.826 46 1 0 3741 3786 13827569 13827614 3.820000e-11 80.5
13 TraesCS6A01G293400 chr7A 77.485 493 94 16 1 482 531735062 531735548 3.510000e-71 279.0
14 TraesCS6A01G293400 chr7A 86.179 123 13 3 4331 4451 66880937 66881057 3.740000e-26 130.0
15 TraesCS6A01G293400 chr7A 92.424 66 5 0 4358 4423 66742704 66742769 1.360000e-15 95.3
16 TraesCS6A01G293400 chr5A 78.033 305 54 7 4008 4309 639565894 639566188 3.660000e-41 180.0
17 TraesCS6A01G293400 chr5A 83.000 200 32 1 4110 4309 639638037 639638234 3.660000e-41 180.0
18 TraesCS6A01G293400 chr5A 82.632 190 31 1 4110 4299 639490956 639491143 2.850000e-37 167.0
19 TraesCS6A01G293400 chr5A 81.356 118 14 8 167 279 461584802 461584688 6.350000e-14 89.8
20 TraesCS6A01G293400 chr5A 93.103 58 3 1 3729 3786 619169033 619169089 2.950000e-12 84.2
21 TraesCS6A01G293400 chr5D 81.188 202 35 2 4108 4309 511451998 511452196 4.770000e-35 159.0
22 TraesCS6A01G293400 chr1D 75.146 342 73 8 161 498 398557121 398556788 2.870000e-32 150.0
23 TraesCS6A01G293400 chr7B 89.189 74 8 0 4350 4423 4513866 4513939 4.910000e-15 93.5
24 TraesCS6A01G293400 chr3A 80.488 123 19 4 4130 4251 80432299 80432417 6.350000e-14 89.8
25 TraesCS6A01G293400 chr2D 94.828 58 2 1 3008 3064 288967422 288967365 6.350000e-14 89.8
26 TraesCS6A01G293400 chr2D 78.295 129 21 6 108 233 177559937 177560061 4.940000e-10 76.8
27 TraesCS6A01G293400 chr7D 97.826 46 1 0 3741 3786 42640049 42640094 3.820000e-11 80.5
28 TraesCS6A01G293400 chr4B 78.295 129 22 5 108 233 502687387 502687512 1.370000e-10 78.7
29 TraesCS6A01G293400 chr2B 95.833 48 2 0 3741 3788 714132784 714132737 1.370000e-10 78.7
30 TraesCS6A01G293400 chr2A 95.833 48 2 0 3741 3788 235370912 235370959 1.370000e-10 78.7
31 TraesCS6A01G293400 chr2A 95.122 41 1 1 3025 3064 114306754 114306714 3.850000e-06 63.9
32 TraesCS6A01G293400 chr3D 89.286 56 6 0 3727 3782 514650532 514650477 2.300000e-08 71.3


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 TraesCS6A01G293400 chr6A 524832691 524837295 4604 True 8504.000000 8504 100.00000 1 4605 1 chr6A.!!$R1 4604
1 TraesCS6A01G293400 chr6D 382724749 382729304 4555 True 6109.000000 6109 90.90500 1 4605 1 chr6D.!!$R2 4604
2 TraesCS6A01G293400 chr6B 572502699 572507360 4661 True 1593.500000 3378 91.76225 1 4605 4 chr6B.!!$R2 4604
3 TraesCS6A01G293400 chr6B 572541982 572545410 3428 True 1501.333333 2298 91.72000 1 3427 3 chr6B.!!$R3 3426
4 TraesCS6A01G293400 chr6B 572494296 572495089 793 True 952.000000 952 88.56100 3811 4605 1 chr6B.!!$R1 794

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
368 372 0.250513 GCTCTTCCAGTCGGAACCAT 59.749 55.000 0.0 0.0 46.79 3.55 F
576 581 0.413832 ACACCTTAGCCCCTCTCTCA 59.586 55.000 0.0 0.0 0.00 3.27 F
1524 1574 0.183492 CATCCCACCATTCCGACCAT 59.817 55.000 0.0 0.0 0.00 3.55 F
2038 2118 0.680061 CCATACCCGAGGCTACTTCC 59.320 60.000 0.0 0.0 0.00 3.46 F
3095 3300 1.137404 CACCACTAATGCCGCAAGC 59.863 57.895 0.0 0.0 44.14 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1336 1.065854 AGCCCAACAGCTAGCTAACTG 60.066 52.381 18.86 20.18 42.70 3.16 R
2038 2118 1.996292 TCTGGTTCGCTTCTTCGATG 58.004 50.000 0.00 0.00 38.37 3.84 R
3153 3358 0.729690 GTCTGAATGCTTCCTTCGCC 59.270 55.000 0.00 0.00 0.00 5.54 R
3463 3668 0.892755 ACGGTTCGGTGCTCTTCATA 59.107 50.000 0.00 0.00 0.00 2.15 R
4058 4271 0.038801 CGACTTCAGTGAGCAGAGCA 60.039 55.000 0.00 0.00 0.00 4.26 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
33 35 8.356657 CCGCTTGGTGGATTTTAATATTATTGA 58.643 33.333 0.00 0.00 34.74 2.57
67 69 8.634444 TCTCAAGGAACTAATGCTTATCTAGTC 58.366 37.037 0.00 0.00 38.49 2.59
222 225 8.642885 GTTCATAAGCATGTCGATACTATCAAG 58.357 37.037 0.00 0.00 33.57 3.02
226 229 6.641169 AGCATGTCGATACTATCAAGAAGA 57.359 37.500 0.00 0.00 0.00 2.87
233 236 8.850156 TGTCGATACTATCAAGAAGATGATGAA 58.150 33.333 0.00 0.00 40.21 2.57
234 237 9.123709 GTCGATACTATCAAGAAGATGATGAAC 57.876 37.037 0.00 0.00 40.21 3.18
302 306 3.515602 ACTGCCCTCAAAAGTCTTCAT 57.484 42.857 0.00 0.00 0.00 2.57
308 312 4.281941 GCCCTCAAAAGTCTTCATTTCCTT 59.718 41.667 0.00 0.00 0.00 3.36
320 324 9.030452 AGTCTTCATTTCCTTCGCTATATCTAT 57.970 33.333 0.00 0.00 0.00 1.98
321 325 9.646427 GTCTTCATTTCCTTCGCTATATCTATT 57.354 33.333 0.00 0.00 0.00 1.73
368 372 0.250513 GCTCTTCCAGTCGGAACCAT 59.749 55.000 0.00 0.00 46.79 3.55
369 373 1.339151 GCTCTTCCAGTCGGAACCATT 60.339 52.381 0.00 0.00 46.79 3.16
410 414 1.169661 CCGTTGCAAACCCTAGCACA 61.170 55.000 0.00 0.00 46.28 4.57
419 423 1.221840 CCCTAGCACATTGGAGCGT 59.778 57.895 0.00 0.00 35.61 5.07
421 425 1.148157 CCTAGCACATTGGAGCGTCG 61.148 60.000 0.00 0.00 35.61 5.12
469 473 4.244862 CACTTGGCAAAACTTCTGTTGTT 58.755 39.130 0.00 0.00 36.39 2.83
487 491 4.389664 TGTTCGCTCAGAATTTTCGAAG 57.610 40.909 0.00 0.00 41.49 3.79
498 502 3.790089 ATTTTCGAAGACCCCTCACTT 57.210 42.857 0.00 0.00 34.32 3.16
519 523 8.208224 TCACTTGGAGTTCTGAAGTGTTTATAA 58.792 33.333 1.76 0.00 44.56 0.98
531 535 8.754991 TGAAGTGTTTATAAAGAGGGAAAACA 57.245 30.769 0.00 0.00 37.62 2.83
534 538 6.775629 AGTGTTTATAAAGAGGGAAAACAGCA 59.224 34.615 0.00 0.00 39.83 4.41
535 539 6.861572 GTGTTTATAAAGAGGGAAAACAGCAC 59.138 38.462 0.00 0.00 39.83 4.40
559 564 2.046314 GCTAGGGCTTGGCGAACA 60.046 61.111 0.00 0.00 35.22 3.18
575 580 1.483004 GAACACCTTAGCCCCTCTCTC 59.517 57.143 0.00 0.00 0.00 3.20
576 581 0.413832 ACACCTTAGCCCCTCTCTCA 59.586 55.000 0.00 0.00 0.00 3.27
577 582 1.008938 ACACCTTAGCCCCTCTCTCAT 59.991 52.381 0.00 0.00 0.00 2.90
578 583 2.247635 ACACCTTAGCCCCTCTCTCATA 59.752 50.000 0.00 0.00 0.00 2.15
584 589 1.214673 AGCCCCTCTCTCATACGTACA 59.785 52.381 0.00 0.00 0.00 2.90
632 675 2.876955 CGCGCATGTGGTGGAATT 59.123 55.556 8.75 0.00 0.00 2.17
673 716 7.102346 ACTATCTTTGTTGGATTCACTCTGAG 58.898 38.462 2.45 2.45 0.00 3.35
745 795 3.440522 GTGCTCCCTATGAGTTTTTGGTC 59.559 47.826 0.00 0.00 43.48 4.02
748 798 4.807643 GCTCCCTATGAGTTTTTGGTCAGT 60.808 45.833 0.00 0.00 43.48 3.41
770 820 2.009774 GTCATCACCCTCATTTCCGTG 58.990 52.381 0.00 0.00 0.00 4.94
779 829 4.461431 ACCCTCATTTCCGTGTTTATTTCC 59.539 41.667 0.00 0.00 0.00 3.13
785 835 6.492087 TCATTTCCGTGTTTATTTCCCTTTCT 59.508 34.615 0.00 0.00 0.00 2.52
786 836 6.718522 TTTCCGTGTTTATTTCCCTTTCTT 57.281 33.333 0.00 0.00 0.00 2.52
827 877 6.033966 GCTTCAAATACAACGGAAATAAGGG 58.966 40.000 0.00 0.00 0.00 3.95
828 878 6.518208 TTCAAATACAACGGAAATAAGGGG 57.482 37.500 0.00 0.00 0.00 4.79
946 996 4.749323 TCCGGTAGAGCGGAGAAA 57.251 55.556 18.35 0.00 0.00 2.52
947 997 2.965805 TCCGGTAGAGCGGAGAAAA 58.034 52.632 18.35 0.00 0.00 2.29
948 998 1.481871 TCCGGTAGAGCGGAGAAAAT 58.518 50.000 18.35 0.00 0.00 1.82
949 999 1.407979 TCCGGTAGAGCGGAGAAAATC 59.592 52.381 18.35 0.00 0.00 2.17
960 1010 1.065358 GAGAAAATCGAACGACGGCA 58.935 50.000 0.00 0.00 42.82 5.69
1231 1281 1.339610 CGCTCTACTCCCTCATGAAGG 59.660 57.143 3.72 3.72 45.77 3.46
1284 1334 3.803082 CGCACCATTGGCCGTCAG 61.803 66.667 1.54 0.00 0.00 3.51
1285 1335 2.672996 GCACCATTGGCCGTCAGT 60.673 61.111 1.54 0.00 0.00 3.41
1286 1336 2.690778 GCACCATTGGCCGTCAGTC 61.691 63.158 1.54 0.00 0.00 3.51
1327 1377 1.002366 CTCGTCAGCAATGTAGTGGC 58.998 55.000 0.00 0.00 0.00 5.01
1343 1393 2.983592 GCGGTGGTTGGACTTGGG 60.984 66.667 0.00 0.00 0.00 4.12
1346 1396 3.670377 GTGGTTGGACTTGGGCGC 61.670 66.667 0.00 0.00 0.00 6.53
1370 1420 2.015243 ATGGTGGAGGCCATGGATGG 62.015 60.000 18.40 0.85 46.63 3.51
1476 1526 1.202782 TCGAGAGGATAAGAGACCCCG 60.203 57.143 0.00 0.00 0.00 5.73
1515 1565 0.994247 TGAGCAGTTCATCCCACCAT 59.006 50.000 0.00 0.00 0.00 3.55
1516 1566 1.355381 TGAGCAGTTCATCCCACCATT 59.645 47.619 0.00 0.00 0.00 3.16
1524 1574 0.183492 CATCCCACCATTCCGACCAT 59.817 55.000 0.00 0.00 0.00 3.55
1526 1576 0.912006 TCCCACCATTCCGACCATCA 60.912 55.000 0.00 0.00 0.00 3.07
1529 1579 1.141657 CCACCATTCCGACCATCATCT 59.858 52.381 0.00 0.00 0.00 2.90
1544 1594 3.773860 TCATCTCTTCTTCGTCAGCTC 57.226 47.619 0.00 0.00 0.00 4.09
1560 1611 5.374898 GTCAGCTCTTTTGTTCGATAACAC 58.625 41.667 0.00 0.00 45.18 3.32
1574 1628 6.662414 TCGATAACACATTTCTTTAGCTGG 57.338 37.500 0.00 0.00 0.00 4.85
1584 1638 9.774742 CACATTTCTTTAGCTGGTTAATTAGTC 57.225 33.333 0.00 0.00 0.00 2.59
1586 1640 8.956426 CATTTCTTTAGCTGGTTAATTAGTCCA 58.044 33.333 0.00 9.90 0.00 4.02
1599 1659 7.715249 GGTTAATTAGTCCAGTAGCATCAATCA 59.285 37.037 0.00 0.00 0.00 2.57
1602 1662 4.558226 AGTCCAGTAGCATCAATCACAA 57.442 40.909 0.00 0.00 0.00 3.33
1641 1717 5.644977 AAGGTTATGCTTTTACCTTCAGC 57.355 39.130 11.01 0.00 46.58 4.26
1669 1745 4.388165 CCTCTGATTCGATGATTTGATCGG 59.612 45.833 0.00 0.00 44.41 4.18
1706 1782 5.573337 ATCAAGGAAGCAGAAGCATTAAC 57.427 39.130 0.00 0.00 45.49 2.01
1836 1916 8.051535 ACTTGTGATAATTCAGATCCATTGAGT 58.948 33.333 0.00 0.00 30.85 3.41
1891 1971 7.604657 TTTTTCCTTTAGGTTTGCCATTCTA 57.395 32.000 0.00 0.00 37.19 2.10
2038 2118 0.680061 CCATACCCGAGGCTACTTCC 59.320 60.000 0.00 0.00 0.00 3.46
2108 2188 1.364626 GGAGCATCACCTCAAGCACG 61.365 60.000 0.00 0.00 36.25 5.34
2109 2189 1.364626 GAGCATCACCTCAAGCACGG 61.365 60.000 0.00 0.00 33.17 4.94
2191 2271 2.102252 CAGATACCTGGCTGAGAGGTTC 59.898 54.545 0.00 0.00 41.31 3.62
2241 2321 4.914983 TCTCTTGCCACATCTCTGAAAAT 58.085 39.130 0.00 0.00 0.00 1.82
2269 2349 3.243873 TGTCAAGGTTCAGTGTCTGCTAG 60.244 47.826 0.00 0.00 0.00 3.42
2325 2407 5.835582 TCATAGCATCCAGGATCTCTGATA 58.164 41.667 0.00 0.00 46.18 2.15
2326 2408 6.259123 TCATAGCATCCAGGATCTCTGATAA 58.741 40.000 0.00 0.26 46.18 1.75
2327 2409 6.727697 TCATAGCATCCAGGATCTCTGATAAA 59.272 38.462 0.00 0.00 46.18 1.40
2328 2410 5.901413 AGCATCCAGGATCTCTGATAAAA 57.099 39.130 0.00 0.00 46.18 1.52
2329 2411 5.619220 AGCATCCAGGATCTCTGATAAAAC 58.381 41.667 0.00 0.00 46.18 2.43
2330 2412 5.131642 AGCATCCAGGATCTCTGATAAAACA 59.868 40.000 0.00 0.00 46.18 2.83
2430 2620 6.525629 ACCGCTTATCTTAAGCTACATGAAT 58.474 36.000 15.14 0.00 40.94 2.57
2481 2679 7.343833 ACCTTTCTGCATATTGATGATTCCTTT 59.656 33.333 0.00 0.00 34.73 3.11
2527 2725 6.646240 TGCTAATTTGGAGCTTTTTCAATGAC 59.354 34.615 0.69 0.00 40.76 3.06
2624 2822 3.959535 ATTCGTTGGGTTCATGCAAAT 57.040 38.095 0.00 0.00 0.00 2.32
2657 2855 1.275010 GGGTTGCCACCGAATTCATTT 59.725 47.619 6.22 0.00 45.39 2.32
2812 3012 5.825151 CCTCAATAATCTTGGAAAGGGAGAC 59.175 44.000 0.00 0.00 46.24 3.36
2814 3014 6.180472 TCAATAATCTTGGAAAGGGAGACAC 58.820 40.000 0.00 0.00 46.24 3.67
2895 3095 5.743026 TGAAGCGACAAAACAATAACTGA 57.257 34.783 0.00 0.00 0.00 3.41
2921 3121 8.534333 TCTTGATCTTACACAATTGTAGTGAC 57.466 34.615 11.53 1.19 39.44 3.67
3001 3201 9.320352 GCCAAGGACTTTGAAAAATAAGTAAAA 57.680 29.630 0.00 0.00 39.21 1.52
3095 3300 1.137404 CACCACTAATGCCGCAAGC 59.863 57.895 0.00 0.00 44.14 4.01
3153 3358 2.545526 AGCACGAGCAATAATCGGATTG 59.454 45.455 13.37 0.00 44.36 2.67
3279 3484 6.310224 CCTGGTAACACAACTGTTTTGAAAAG 59.690 38.462 13.18 4.02 46.17 2.27
3311 3516 6.725246 ACATCTAACTTCGTTTCCTTTTGTG 58.275 36.000 0.00 0.00 0.00 3.33
3380 3585 4.327680 AGCGAAATTTACTGAAGCTCCTT 58.672 39.130 0.00 0.00 0.00 3.36
3386 3591 7.278868 CGAAATTTACTGAAGCTCCTTATCTGT 59.721 37.037 0.00 0.00 0.00 3.41
3463 3668 1.760613 TCACCCGTTCTGTTCACTCTT 59.239 47.619 0.00 0.00 0.00 2.85
3523 3728 2.733945 GATCTGGAGGAGGCGCTC 59.266 66.667 7.64 2.45 0.00 5.03
3595 3800 0.032952 GAACGGTCACTGCCACTGTA 59.967 55.000 0.00 0.00 32.78 2.74
3754 3960 4.346730 TCCCTCCGTTAGTGATCTAAACA 58.653 43.478 0.00 0.00 37.81 2.83
3757 3963 5.103000 CCTCCGTTAGTGATCTAAACACTG 58.897 45.833 10.24 0.00 46.15 3.66
3871 4078 5.458041 ACAAATTTCAACCAGGATGACAG 57.542 39.130 0.00 0.00 39.69 3.51
3872 4079 5.139727 ACAAATTTCAACCAGGATGACAGA 58.860 37.500 0.00 0.00 39.69 3.41
3998 4207 6.895756 TGATACGCTATCCCATATCCTAGTTT 59.104 38.462 0.00 0.00 34.26 2.66
4004 4213 7.012894 CGCTATCCCATATCCTAGTTTCTAGAG 59.987 44.444 5.49 0.00 0.00 2.43
4005 4214 8.056400 GCTATCCCATATCCTAGTTTCTAGAGA 58.944 40.741 5.49 0.00 0.00 3.10
4069 4282 2.675056 CCAGCGTTGCTCTGCTCAC 61.675 63.158 0.00 0.00 40.03 3.51
4083 4296 3.288308 CTCACTGAAGTCGCCGCCT 62.288 63.158 0.00 0.00 0.00 5.52
4174 4387 4.803426 GAGTGGGCGCTCTCGGTG 62.803 72.222 9.62 0.00 35.95 4.94
4205 4418 1.094785 GCCGTCATTGTTGTAGCCAT 58.905 50.000 0.00 0.00 0.00 4.40
4486 4702 2.152830 GAGAGGCCGTAGTCGATGTAT 58.847 52.381 0.00 0.00 39.71 2.29
4488 4704 2.293677 AGAGGCCGTAGTCGATGTATTG 59.706 50.000 0.00 0.00 39.71 1.90
4527 4755 0.684479 TAGCAGGAGTCGGCATCTGT 60.684 55.000 10.49 2.25 36.54 3.41
4535 4763 0.666274 GTCGGCATCTGTCGTGTCAA 60.666 55.000 3.93 0.00 44.53 3.18
4576 4804 3.594775 CCAGCTTGCGTGCAACCA 61.595 61.111 2.58 0.00 34.99 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 7.341805 AGCATTAGTTCCTTGAGATATGTTGT 58.658 34.615 0.00 0.00 0.00 3.32
67 69 4.184629 CACAAGAACCTTTCGGGAGATAG 58.815 47.826 0.00 0.00 39.57 2.08
90 92 4.141756 ACATTTCATTTCCTTTGGTGCACA 60.142 37.500 20.43 1.62 0.00 4.57
129 131 2.229792 TGGCCAACACTTGTCTTCATC 58.770 47.619 0.61 0.00 0.00 2.92
191 194 5.725110 ATCGACATGCTTATGAACTCAAC 57.275 39.130 0.00 0.00 0.00 3.18
222 225 5.526479 TCAGCATAGCTTGTTCATCATCTTC 59.474 40.000 0.00 0.00 36.40 2.87
226 229 4.778579 ACTCAGCATAGCTTGTTCATCAT 58.221 39.130 0.00 0.00 36.40 2.45
233 236 5.312079 AGAAAGAAACTCAGCATAGCTTGT 58.688 37.500 0.00 0.00 36.40 3.16
234 237 5.876612 AGAAAGAAACTCAGCATAGCTTG 57.123 39.130 0.00 0.00 36.40 4.01
283 286 4.321527 GGAAATGAAGACTTTTGAGGGCAG 60.322 45.833 0.00 0.00 0.00 4.85
320 324 7.305474 GCATCTCCGAAGATTTGAAAGTTAAA 58.695 34.615 0.00 0.00 40.38 1.52
321 325 6.128007 GGCATCTCCGAAGATTTGAAAGTTAA 60.128 38.462 0.00 0.00 40.38 2.01
331 335 1.211457 AGCTTGGCATCTCCGAAGATT 59.789 47.619 0.00 0.00 40.38 2.40
368 372 6.291377 GGTTATATCTGGATGAACTGCTCAA 58.709 40.000 8.82 0.00 37.67 3.02
369 373 5.509670 CGGTTATATCTGGATGAACTGCTCA 60.510 44.000 8.82 0.00 38.81 4.26
410 414 2.898729 AGAATGATCGACGCTCCAAT 57.101 45.000 0.00 0.00 0.00 3.16
419 423 3.066342 GTGGTTCCGAGTAGAATGATCGA 59.934 47.826 0.00 0.00 38.72 3.59
421 425 3.132289 TGGTGGTTCCGAGTAGAATGATC 59.868 47.826 0.00 0.00 39.52 2.92
469 473 2.993899 GGTCTTCGAAAATTCTGAGCGA 59.006 45.455 0.00 0.00 0.00 4.93
487 491 1.002544 CAGAACTCCAAGTGAGGGGTC 59.997 57.143 0.00 0.00 43.09 4.46
498 502 7.878127 CCTCTTTATAAACACTTCAGAACTCCA 59.122 37.037 0.00 0.00 0.00 3.86
519 523 1.543429 CCTCGTGCTGTTTTCCCTCTT 60.543 52.381 0.00 0.00 0.00 2.85
535 539 4.899239 CAAGCCCTAGCCGCCTCG 62.899 72.222 0.00 0.00 41.25 4.63
559 564 2.753507 CGTATGAGAGAGGGGCTAAGGT 60.754 54.545 0.00 0.00 0.00 3.50
656 699 5.560722 TTTACCTCAGAGTGAATCCAACA 57.439 39.130 0.00 0.00 0.00 3.33
710 760 2.914289 AGCACCTATGGCTCAGGC 59.086 61.111 5.05 0.00 36.81 4.85
745 795 3.441572 GGAAATGAGGGTGATGACAACTG 59.558 47.826 0.00 0.00 33.68 3.16
748 798 2.039746 ACGGAAATGAGGGTGATGACAA 59.960 45.455 0.00 0.00 0.00 3.18
815 865 0.978907 ACACGTCCCCTTATTTCCGT 59.021 50.000 0.00 0.00 0.00 4.69
824 874 0.252284 AGGATTCTGACACGTCCCCT 60.252 55.000 0.00 0.00 0.00 4.79
827 877 3.458189 CCAATAGGATTCTGACACGTCC 58.542 50.000 0.00 0.00 36.89 4.79
828 878 2.866762 GCCAATAGGATTCTGACACGTC 59.133 50.000 0.00 0.00 36.89 4.34
940 990 0.369248 GCCGTCGTTCGATTTTCTCC 59.631 55.000 0.00 0.00 42.86 3.71
941 991 1.059264 CTGCCGTCGTTCGATTTTCTC 59.941 52.381 0.00 0.00 42.86 2.87
942 992 1.068474 CTGCCGTCGTTCGATTTTCT 58.932 50.000 0.00 0.00 42.86 2.52
943 993 1.059264 CTCTGCCGTCGTTCGATTTTC 59.941 52.381 0.00 0.00 42.86 2.29
944 994 1.068474 CTCTGCCGTCGTTCGATTTT 58.932 50.000 0.00 0.00 42.86 1.82
945 995 0.242825 TCTCTGCCGTCGTTCGATTT 59.757 50.000 0.00 0.00 42.86 2.17
946 996 0.242825 TTCTCTGCCGTCGTTCGATT 59.757 50.000 0.00 0.00 42.86 3.34
947 997 0.242825 TTTCTCTGCCGTCGTTCGAT 59.757 50.000 0.00 0.00 42.86 3.59
948 998 0.031043 TTTTCTCTGCCGTCGTTCGA 59.969 50.000 4.60 0.00 42.86 3.71
949 999 1.059264 GATTTTCTCTGCCGTCGTTCG 59.941 52.381 0.00 0.00 39.52 3.95
960 1010 4.219288 GGAAATGCTGTGGTGATTTTCTCT 59.781 41.667 0.00 0.00 0.00 3.10
1268 1318 2.672996 ACTGACGGCCAATGGTGC 60.673 61.111 2.24 0.00 0.00 5.01
1283 1333 2.234908 CCCAACAGCTAGCTAACTGACT 59.765 50.000 26.87 12.83 37.35 3.41
1284 1334 2.622436 CCCAACAGCTAGCTAACTGAC 58.378 52.381 26.87 0.80 37.35 3.51
1285 1335 1.066143 GCCCAACAGCTAGCTAACTGA 60.066 52.381 26.87 0.00 37.35 3.41
1286 1336 1.065854 AGCCCAACAGCTAGCTAACTG 60.066 52.381 18.86 20.18 42.70 3.16
1327 1377 2.983592 GCCCAAGTCCAACCACCG 60.984 66.667 0.00 0.00 0.00 4.94
1346 1396 3.716195 TGGCCTCCACCATCACGG 61.716 66.667 3.32 0.00 42.50 4.94
1370 1420 1.087771 CCGCCGTCCTGGATAACAAC 61.088 60.000 0.00 0.00 42.00 3.32
1476 1526 2.093106 ACAGTCAGGGTAGACGATGTC 58.907 52.381 0.00 0.00 43.24 3.06
1515 1565 3.181486 CGAAGAAGAGATGATGGTCGGAA 60.181 47.826 0.00 0.00 0.00 4.30
1516 1566 2.359214 CGAAGAAGAGATGATGGTCGGA 59.641 50.000 0.00 0.00 0.00 4.55
1524 1574 3.351740 AGAGCTGACGAAGAAGAGATGA 58.648 45.455 0.00 0.00 0.00 2.92
1526 1576 4.799564 AAAGAGCTGACGAAGAAGAGAT 57.200 40.909 0.00 0.00 0.00 2.75
1529 1579 4.060038 ACAAAAGAGCTGACGAAGAAGA 57.940 40.909 0.00 0.00 0.00 2.87
1560 1611 8.956426 TGGACTAATTAACCAGCTAAAGAAATG 58.044 33.333 6.88 0.00 0.00 2.32
1574 1628 8.552034 GTGATTGATGCTACTGGACTAATTAAC 58.448 37.037 0.00 0.00 0.00 2.01
1602 1662 8.135529 GCATAACCTTCTCACTGTAAACTTTTT 58.864 33.333 0.00 0.00 0.00 1.94
1607 1667 6.803154 AAGCATAACCTTCTCACTGTAAAC 57.197 37.500 0.00 0.00 0.00 2.01
1622 1682 4.082787 TGCAGCTGAAGGTAAAAGCATAAC 60.083 41.667 20.43 0.00 39.47 1.89
1641 1717 2.591571 TCATCGAATCAGAGGTGCAG 57.408 50.000 0.00 0.00 0.00 4.41
1669 1745 6.564873 GCTTCCTTGATAATTCAGTATCGTGC 60.565 42.308 0.00 0.00 33.83 5.34
1682 1758 6.658816 TGTTAATGCTTCTGCTTCCTTGATAA 59.341 34.615 0.00 0.00 40.48 1.75
1706 1782 2.164827 TGCTCAACATAAGCAAGCCATG 59.835 45.455 0.00 3.50 46.29 3.66
1861 1941 7.213678 TGGCAAACCTAAAGGAAAAATAACTG 58.786 34.615 2.23 0.00 38.94 3.16
1873 1953 8.225603 ACATATGTAGAATGGCAAACCTAAAG 57.774 34.615 6.56 0.00 36.63 1.85
1891 1971 3.206150 GCATGTCTTCCGGAACATATGT 58.794 45.455 23.38 1.41 0.00 2.29
1917 1997 5.645497 ACAGGAGTTCAGATAAAATGTGCTC 59.355 40.000 0.00 0.00 0.00 4.26
1920 2000 8.103948 AGAAACAGGAGTTCAGATAAAATGTG 57.896 34.615 0.00 0.00 36.84 3.21
1996 2076 2.160417 CCTCTTTGCAATCGACAAGGTC 59.840 50.000 0.00 0.00 0.00 3.85
2038 2118 1.996292 TCTGGTTCGCTTCTTCGATG 58.004 50.000 0.00 0.00 38.37 3.84
2241 2321 3.938963 GACACTGAACCTTGACAAGACAA 59.061 43.478 16.99 0.00 0.00 3.18
2269 2349 6.443792 AGATTTGATCGTTTACCCAAAACAC 58.556 36.000 0.00 0.00 46.59 3.32
2456 2654 6.896021 AGGAATCATCAATATGCAGAAAGG 57.104 37.500 0.00 0.00 32.76 3.11
2481 2679 7.251321 AGCAAATCCATATAAAAACCAACCA 57.749 32.000 0.00 0.00 0.00 3.67
2527 2725 2.494073 GGCGATAGATCTAGTCCCTTGG 59.506 54.545 8.70 0.00 39.76 3.61
2624 2822 1.227823 CAACCCAGTCGCTTCACCA 60.228 57.895 0.00 0.00 0.00 4.17
2657 2855 1.461091 AAGCAAGGGAGACGACGTCA 61.461 55.000 28.31 0.00 34.60 4.35
2852 3052 8.962111 GCTTCAACATTTTCAGTCTCTTTTAAG 58.038 33.333 0.00 0.00 0.00 1.85
2895 3095 9.155975 GTCACTACAATTGTGTAAGATCAAGAT 57.844 33.333 21.42 0.00 39.75 2.40
3001 3201 5.264395 CTGACTTTGATTTCCCCCTGTAAT 58.736 41.667 0.00 0.00 0.00 1.89
3095 3300 4.094887 ACTGCAGGTGTTTATAGAATTGCG 59.905 41.667 19.93 0.00 33.25 4.85
3153 3358 0.729690 GTCTGAATGCTTCCTTCGCC 59.270 55.000 0.00 0.00 0.00 5.54
3174 3379 1.079057 GGTTCCTCCTGGACGAAGC 60.079 63.158 17.56 17.56 43.06 3.86
3279 3484 4.189639 ACGAAGTTAGATGTCTGAACCC 57.810 45.455 0.00 0.00 37.78 4.11
3380 3585 6.997655 AGTCAATGTGAGTGAGAAACAGATA 58.002 36.000 0.00 0.00 0.00 1.98
3463 3668 0.892755 ACGGTTCGGTGCTCTTCATA 59.107 50.000 0.00 0.00 0.00 2.15
3595 3800 0.905357 GGTGATGCAGTCAGTAGGGT 59.095 55.000 0.00 0.00 37.56 4.34
3754 3960 7.125356 ACTCCCTCCGTAAAGAAATATAACAGT 59.875 37.037 0.00 0.00 0.00 3.55
3757 3963 8.637099 AGTACTCCCTCCGTAAAGAAATATAAC 58.363 37.037 0.00 0.00 0.00 1.89
3817 4023 9.612620 CCACTTATTACAGACTTCAAATGTTTC 57.387 33.333 0.00 0.00 0.00 2.78
3850 4056 5.710513 TCTGTCATCCTGGTTGAAATTTG 57.289 39.130 8.97 0.00 0.00 2.32
3866 4072 7.892778 TTTTACTACATACGCAAATCTGTCA 57.107 32.000 0.00 0.00 0.00 3.58
3998 4207 6.993308 ACTAGTCGAAGCAATACATCTCTAGA 59.007 38.462 0.00 0.00 30.31 2.43
4004 4213 6.037098 AGTGAACTAGTCGAAGCAATACATC 58.963 40.000 0.00 0.00 0.00 3.06
4005 4214 5.967088 AGTGAACTAGTCGAAGCAATACAT 58.033 37.500 0.00 0.00 0.00 2.29
4053 4266 1.667191 CAGTGAGCAGAGCAACGCT 60.667 57.895 0.00 0.00 43.88 5.07
4058 4271 0.038801 CGACTTCAGTGAGCAGAGCA 60.039 55.000 0.00 0.00 0.00 4.26
4069 4282 1.901650 GACAAAGGCGGCGACTTCAG 61.902 60.000 30.48 25.29 26.61 3.02
4083 4296 1.515954 GATCCCTCTCGGCGACAAA 59.484 57.895 4.99 0.00 0.00 2.83
4098 4311 2.067766 ACGAGATCTACGGCTACGATC 58.932 52.381 15.68 0.00 44.60 3.69
4099 4312 2.067766 GACGAGATCTACGGCTACGAT 58.932 52.381 15.68 0.00 44.60 3.73
4194 4407 1.739035 GCGCTCTGTATGGCTACAACA 60.739 52.381 0.00 0.00 37.41 3.33
4343 4559 1.180029 GCCTACTACGACCCTTCACA 58.820 55.000 0.00 0.00 0.00 3.58
4486 4702 3.089874 CCTCTCCCGGATGGCCAA 61.090 66.667 10.96 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.