Multiple sequence alignment - TraesCS7D01G548200

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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 TraesCS7D01G548200 chr7D 100.000 4074 0 0 1 4074 633807565 633803492 0.000000e+00 7524.0
1 TraesCS7D01G548200 chr7D 97.458 472 10 2 3280 3751 248612714 248613183 0.000000e+00 804.0
2 TraesCS7D01G548200 chr7D 86.779 416 34 5 2864 3274 633674820 633674421 1.040000e-120 444.0
3 TraesCS7D01G548200 chr7D 94.059 202 11 1 3853 4053 633674738 633674537 5.120000e-79 305.0
4 TraesCS7D01G548200 chr7D 91.304 207 18 0 2946 3152 633803713 633803507 2.400000e-72 283.0
5 TraesCS7D01G548200 chr7D 91.304 207 18 0 3853 4059 633804620 633804414 2.400000e-72 283.0
6 TraesCS7D01G548200 chr7B 86.900 3565 259 107 1 3420 750602760 750606261 0.000000e+00 3805.0
7 TraesCS7D01G548200 chr7B 85.228 1205 120 29 1679 2846 750443887 750442704 0.000000e+00 1186.0
8 TraesCS7D01G548200 chr7B 84.184 1176 99 38 2356 3521 750430574 750429476 0.000000e+00 1061.0
9 TraesCS7D01G548200 chr7B 87.774 638 56 13 2811 3435 750442709 750442081 0.000000e+00 726.0
10 TraesCS7D01G548200 chr7B 86.709 632 63 10 2649 3277 750416021 750415408 0.000000e+00 682.0
11 TraesCS7D01G548200 chr7B 93.556 450 24 3 1880 2327 750431018 750430572 0.000000e+00 665.0
12 TraesCS7D01G548200 chr7B 90.909 209 17 1 3853 4059 750442573 750442365 3.100000e-71 279.0
13 TraesCS7D01G548200 chr7B 90.821 207 19 0 3853 4059 750430035 750429829 1.120000e-70 278.0
14 TraesCS7D01G548200 chr7B 85.663 279 19 9 3146 3424 750211492 750211235 1.440000e-69 274.0
15 TraesCS7D01G548200 chr7B 90.000 210 18 1 3853 4059 750605796 750606005 6.710000e-68 268.0
16 TraesCS7D01G548200 chr7B 88.406 207 21 2 3853 4059 750415733 750415530 3.150000e-61 246.0
17 TraesCS7D01G548200 chr7A 84.590 3569 294 126 51 3521 732798438 732801848 0.000000e+00 3308.0
18 TraesCS7D01G548200 chr7A 87.111 1125 101 17 2160 3254 732864102 732862992 0.000000e+00 1234.0
19 TraesCS7D01G548200 chr7A 83.784 407 47 12 1616 2013 732864505 732864109 6.430000e-98 368.0
20 TraesCS7D01G548200 chr7A 84.348 345 38 8 2661 3003 732806734 732807064 1.410000e-84 324.0
21 TraesCS7D01G548200 chr7A 93.720 207 13 0 3853 4059 732863299 732863093 1.100000e-80 311.0
22 TraesCS7D01G548200 chr7A 88.889 207 23 0 3853 4059 732801289 732801495 5.230000e-64 255.0
23 TraesCS7D01G548200 chr7A 92.105 114 8 1 3149 3262 732932116 732932228 4.210000e-35 159.0
24 TraesCS7D01G548200 chr7A 95.652 92 3 1 3963 4053 733029497 733029588 3.280000e-31 147.0
25 TraesCS7D01G548200 chr7A 83.871 93 10 4 3673 3762 732802094 732802184 2.610000e-12 84.2
26 TraesCS7D01G548200 chr3D 97.177 673 14 3 3077 3749 15609528 15608861 0.000000e+00 1133.0
27 TraesCS7D01G548200 chr3D 97.899 476 8 1 3280 3755 130791928 130792401 0.000000e+00 822.0
28 TraesCS7D01G548200 chr3D 96.186 236 8 1 3280 3515 522366659 522366425 6.390000e-103 385.0
29 TraesCS7D01G548200 chr3D 96.894 161 5 0 3280 3440 578302427 578302587 1.870000e-68 270.0
30 TraesCS7D01G548200 chr5D 97.458 472 10 2 3280 3751 434018457 434018926 0.000000e+00 804.0
31 TraesCS7D01G548200 chr2D 97.166 247 5 2 3505 3751 411145348 411145104 2.270000e-112 416.0
32 TraesCS7D01G548200 chr4D 96.129 155 4 2 3597 3751 14198466 14198314 6.760000e-63 252.0


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 TraesCS7D01G548200 chr7D 633803492 633807565 4073 True 7524.000000 7524 100.000000 1 4074 1 chr7D.!!$R1 4073
1 TraesCS7D01G548200 chr7D 633803507 633804620 1113 True 283.000000 283 91.304000 2946 4059 2 chr7D.!!$R3 1113
2 TraesCS7D01G548200 chr7B 750602760 750606261 3501 False 2036.500000 3805 88.450000 1 4059 2 chr7B.!!$F1 4058
3 TraesCS7D01G548200 chr7B 750442081 750443887 1806 True 730.333333 1186 87.970333 1679 4059 3 chr7B.!!$R4 2380
4 TraesCS7D01G548200 chr7B 750429476 750431018 1542 True 668.000000 1061 89.520333 1880 4059 3 chr7B.!!$R3 2179
5 TraesCS7D01G548200 chr7B 750415408 750416021 613 True 464.000000 682 87.557500 2649 4059 2 chr7B.!!$R2 1410
6 TraesCS7D01G548200 chr7A 732798438 732802184 3746 False 1215.733333 3308 85.783333 51 4059 3 chr7A.!!$F4 4008
7 TraesCS7D01G548200 chr7A 732862992 732864505 1513 True 637.666667 1234 88.205000 1616 4059 3 chr7A.!!$R1 2443
8 TraesCS7D01G548200 chr3D 15608861 15609528 667 True 1133.000000 1133 97.177000 3077 3749 1 chr3D.!!$R1 672

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
895 1020 0.105593 ATGTATGACTCAGCGCAGGG 59.894 55.0 11.47 3.21 0.00 4.45 F
1269 1407 0.109597 AGACGGTTTACCAGTACGCG 60.110 55.0 3.53 3.53 35.14 6.01 F
1657 1795 0.392998 CGGCTGGCTTTGGTATGTCT 60.393 55.0 0.00 0.00 0.00 3.41 F
2337 2507 0.528924 GCAGCTCATCCACATTTGCA 59.471 50.0 0.00 0.00 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2317 2483 0.524816 GCAAATGTGGATGAGCTGCG 60.525 55.000 0.00 0.00 0.00 5.18 R
2884 3152 0.895530 TCTCCACGAATGACTCCACC 59.104 55.000 0.00 0.00 0.00 4.61 R
2923 3191 1.081376 GTCACACGACCTCACCTCG 60.081 63.158 0.00 0.00 36.02 4.63 R
3291 3587 4.309099 CTCCCACACAAATCAATGGTTTG 58.691 43.478 16.61 16.61 41.22 2.93 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
71 78 1.517257 CGCTCGGCTCGAATCAACT 60.517 57.895 0.00 0.00 34.74 3.16
78 85 0.729690 GCTCGAATCAACTGCTTCCC 59.270 55.000 0.00 0.00 0.00 3.97
79 86 1.002366 CTCGAATCAACTGCTTCCCG 58.998 55.000 0.00 0.00 0.00 5.14
124 141 4.322049 CGTCTTCTTCTTCCTCCAGCTTTA 60.322 45.833 0.00 0.00 0.00 1.85
150 172 6.029346 GGAAAAAGATGAAGATTTCCAGCA 57.971 37.500 10.41 0.00 46.43 4.41
151 173 6.458210 GGAAAAAGATGAAGATTTCCAGCAA 58.542 36.000 10.41 0.00 46.43 3.91
284 317 4.624747 CGTACGCACGCAAATCTG 57.375 55.556 0.52 0.00 42.05 2.90
287 320 1.068474 GTACGCACGCAAATCTGTCT 58.932 50.000 0.00 0.00 0.00 3.41
288 321 1.067693 TACGCACGCAAATCTGTCTG 58.932 50.000 0.00 0.00 0.00 3.51
291 324 1.151668 GCACGCAAATCTGTCTGTCT 58.848 50.000 0.00 0.00 0.00 3.41
292 325 2.337583 GCACGCAAATCTGTCTGTCTA 58.662 47.619 0.00 0.00 0.00 2.59
293 326 2.092838 GCACGCAAATCTGTCTGTCTAC 59.907 50.000 0.00 0.00 0.00 2.59
294 327 2.668457 CACGCAAATCTGTCTGTCTACC 59.332 50.000 0.00 0.00 0.00 3.18
296 329 3.006967 ACGCAAATCTGTCTGTCTACCTT 59.993 43.478 0.00 0.00 0.00 3.50
297 330 3.997021 CGCAAATCTGTCTGTCTACCTTT 59.003 43.478 0.00 0.00 0.00 3.11
299 332 4.092091 GCAAATCTGTCTGTCTACCTTTCG 59.908 45.833 0.00 0.00 0.00 3.46
300 333 3.512033 ATCTGTCTGTCTACCTTTCGC 57.488 47.619 0.00 0.00 0.00 4.70
302 335 2.229062 TCTGTCTGTCTACCTTTCGCTG 59.771 50.000 0.00 0.00 0.00 5.18
303 336 1.961394 TGTCTGTCTACCTTTCGCTGT 59.039 47.619 0.00 0.00 0.00 4.40
304 337 2.030185 TGTCTGTCTACCTTTCGCTGTC 60.030 50.000 0.00 0.00 0.00 3.51
307 347 1.000506 TGTCTACCTTTCGCTGTCACC 59.999 52.381 0.00 0.00 0.00 4.02
349 389 6.998802 TCCATCCCGTTCAACAAAAATAAAT 58.001 32.000 0.00 0.00 0.00 1.40
375 415 8.457238 AAGATAGCTTCACTTTTGTTTTCTCT 57.543 30.769 0.00 0.00 0.00 3.10
376 416 8.457238 AGATAGCTTCACTTTTGTTTTCTCTT 57.543 30.769 0.00 0.00 0.00 2.85
377 417 8.907885 AGATAGCTTCACTTTTGTTTTCTCTTT 58.092 29.630 0.00 0.00 0.00 2.52
378 418 9.521503 GATAGCTTCACTTTTGTTTTCTCTTTT 57.478 29.630 0.00 0.00 0.00 2.27
379 419 7.586714 AGCTTCACTTTTGTTTTCTCTTTTG 57.413 32.000 0.00 0.00 0.00 2.44
382 422 7.571059 GCTTCACTTTTGTTTTCTCTTTTGCAA 60.571 33.333 0.00 0.00 0.00 4.08
395 435 1.032014 TTTGCAACTCCTCCTTGTGC 58.968 50.000 0.00 0.00 0.00 4.57
399 439 1.073897 AACTCCTCCTTGTGCCTGC 59.926 57.895 0.00 0.00 0.00 4.85
441 481 8.029642 ACGACTCAGATTACACCTTTTATTTG 57.970 34.615 0.00 0.00 0.00 2.32
444 484 8.918202 ACTCAGATTACACCTTTTATTTGACA 57.082 30.769 0.00 0.00 0.00 3.58
477 522 8.462811 GTCAGATATATAAATCGAGAGGCTCAA 58.537 37.037 18.26 1.72 0.00 3.02
498 543 7.306225 GCTCAACTGTAATTGTTTTTCTCTTGC 60.306 37.037 0.00 0.00 0.00 4.01
597 658 3.070576 GGCAGCCACCCCACAATC 61.071 66.667 6.55 0.00 0.00 2.67
600 661 2.863484 AGCCACCCCACAATCCCA 60.863 61.111 0.00 0.00 0.00 4.37
601 662 2.119391 GCCACCCCACAATCCCAA 59.881 61.111 0.00 0.00 0.00 4.12
603 664 1.464722 CCACCCCACAATCCCAACT 59.535 57.895 0.00 0.00 0.00 3.16
607 671 0.323725 CCCCACAATCCCAACTCCAG 60.324 60.000 0.00 0.00 0.00 3.86
667 739 7.066887 ACCAACAAACAAATTCCCAATCTTTTC 59.933 33.333 0.00 0.00 0.00 2.29
676 748 9.948964 CAAATTCCCAATCTTTTCCTTTCTTAT 57.051 29.630 0.00 0.00 0.00 1.73
787 880 4.563580 GCACACATGTTTTCTCCCTCTCTA 60.564 45.833 0.00 0.00 0.00 2.43
791 884 6.656693 ACACATGTTTTCTCCCTCTCTATTTG 59.343 38.462 0.00 0.00 0.00 2.32
804 897 3.064408 TCTCTATTTGCAGCGCTTGAATG 59.936 43.478 7.50 0.00 0.00 2.67
808 912 2.267188 TTGCAGCGCTTGAATGAATC 57.733 45.000 7.50 0.00 0.00 2.52
811 915 1.533338 GCAGCGCTTGAATGAATCCAG 60.533 52.381 7.50 0.00 0.00 3.86
812 916 1.741706 CAGCGCTTGAATGAATCCAGT 59.258 47.619 7.50 0.00 0.00 4.00
848 960 3.986006 GTGCCAGGACCGACACGA 61.986 66.667 0.00 0.00 0.00 4.35
851 963 2.258591 CCAGGACCGACACGACAG 59.741 66.667 0.00 0.00 0.00 3.51
852 964 2.430921 CAGGACCGACACGACAGC 60.431 66.667 0.00 0.00 0.00 4.40
853 965 2.597805 AGGACCGACACGACAGCT 60.598 61.111 0.00 0.00 0.00 4.24
855 967 2.022129 GGACCGACACGACAGCTTG 61.022 63.158 0.00 0.00 0.00 4.01
856 968 1.299926 GACCGACACGACAGCTTGT 60.300 57.895 0.00 0.00 0.00 3.16
858 970 1.151777 ACCGACACGACAGCTTGTTG 61.152 55.000 0.00 0.00 37.76 3.33
859 971 0.874175 CCGACACGACAGCTTGTTGA 60.874 55.000 5.25 0.00 35.34 3.18
872 997 6.763355 ACAGCTTGTTGATCTCTTCTTCTTA 58.237 36.000 0.00 0.00 0.00 2.10
874 999 7.333921 ACAGCTTGTTGATCTCTTCTTCTTATG 59.666 37.037 0.00 0.00 0.00 1.90
875 1000 7.333921 CAGCTTGTTGATCTCTTCTTCTTATGT 59.666 37.037 0.00 0.00 0.00 2.29
876 1001 8.535335 AGCTTGTTGATCTCTTCTTCTTATGTA 58.465 33.333 0.00 0.00 0.00 2.29
877 1002 9.323985 GCTTGTTGATCTCTTCTTCTTATGTAT 57.676 33.333 0.00 0.00 0.00 2.29
889 1014 9.190858 CTTCTTCTTATGTATGTATGACTCAGC 57.809 37.037 0.00 0.00 0.00 4.26
893 1018 3.084070 TGTATGTATGACTCAGCGCAG 57.916 47.619 11.47 0.00 0.00 5.18
894 1019 2.223805 TGTATGTATGACTCAGCGCAGG 60.224 50.000 11.47 0.20 0.00 4.85
895 1020 0.105593 ATGTATGACTCAGCGCAGGG 59.894 55.000 11.47 3.21 0.00 4.45
896 1021 1.884926 GTATGACTCAGCGCAGGGC 60.885 63.158 11.47 0.00 44.05 5.19
919 1044 1.073722 CAGGGCAGAGCAGGACAAA 59.926 57.895 0.00 0.00 0.00 2.83
922 1047 1.518903 GGGCAGAGCAGGACAAACAC 61.519 60.000 0.00 0.00 0.00 3.32
926 1051 2.160417 GCAGAGCAGGACAAACACATAC 59.840 50.000 0.00 0.00 0.00 2.39
929 1054 2.484264 GAGCAGGACAAACACATACCAC 59.516 50.000 0.00 0.00 0.00 4.16
930 1055 2.158682 AGCAGGACAAACACATACCACA 60.159 45.455 0.00 0.00 0.00 4.17
1074 1212 2.042537 TCCTCCATCGAGCTGCCT 60.043 61.111 0.00 0.00 34.49 4.75
1093 1231 2.488891 CCTGACAAATTCTCCCACCACA 60.489 50.000 0.00 0.00 0.00 4.17
1145 1283 1.304713 CCAGCAAACCAGAGGCCAT 60.305 57.895 5.01 0.00 0.00 4.40
1152 1290 1.782201 AACCAGAGGCCATCACAGCA 61.782 55.000 5.01 0.00 0.00 4.41
1163 1301 1.495579 ATCACAGCACCTTCAGCCCT 61.496 55.000 0.00 0.00 0.00 5.19
1209 1347 0.537371 CACGGAACCTCCAGGCTTTT 60.537 55.000 0.00 0.00 35.91 2.27
1218 1356 2.597217 CAGGCTTTTGACCCGGCA 60.597 61.111 0.00 0.00 0.00 5.69
1248 1386 4.778143 GCGTCCCTGCCGGTCATT 62.778 66.667 1.90 0.00 0.00 2.57
1269 1407 0.109597 AGACGGTTTACCAGTACGCG 60.110 55.000 3.53 3.53 35.14 6.01
1271 1409 0.109597 ACGGTTTACCAGTACGCGAG 60.110 55.000 15.93 0.00 35.14 5.03
1301 1439 2.058675 CCTCACCGGAACAAGAGGT 58.941 57.895 9.46 0.00 42.10 3.85
1404 1542 2.571216 CGACAGGTCCCAGACGGTT 61.571 63.158 0.00 0.00 32.65 4.44
1407 1545 0.470456 ACAGGTCCCAGACGGTTGTA 60.470 55.000 0.00 0.00 32.65 2.41
1545 1683 0.765510 ATAATGTCGGAGGGAAGGCC 59.234 55.000 0.00 0.00 0.00 5.19
1656 1794 1.376609 CCGGCTGGCTTTGGTATGTC 61.377 60.000 0.00 0.00 0.00 3.06
1657 1795 0.392998 CGGCTGGCTTTGGTATGTCT 60.393 55.000 0.00 0.00 0.00 3.41
1664 1802 2.162408 GGCTTTGGTATGTCTGCAGTTC 59.838 50.000 14.67 9.03 0.00 3.01
1673 1811 2.783135 TGTCTGCAGTTCCTTTGGATC 58.217 47.619 14.67 0.00 0.00 3.36
1714 1860 9.665719 AACTCTTTTTGGATTTTTCAAGCTTAA 57.334 25.926 0.00 0.00 0.00 1.85
1875 2024 5.763355 ACTGTAGCTAACCTCACATACCTA 58.237 41.667 0.00 0.00 0.00 3.08
2204 2366 3.070446 ACCAAATACAAGGTCTGACGTCA 59.930 43.478 18.88 18.88 30.79 4.35
2218 2380 2.230508 TGACGTCATAGTTGTGGAGTCC 59.769 50.000 15.76 0.73 0.00 3.85
2317 2483 3.507622 ACTATCCGGCCGTAAATAGGTAC 59.492 47.826 28.48 0.00 0.00 3.34
2333 2503 1.656652 GTACGCAGCTCATCCACATT 58.343 50.000 0.00 0.00 0.00 2.71
2337 2507 0.528924 GCAGCTCATCCACATTTGCA 59.471 50.000 0.00 0.00 0.00 4.08
2338 2508 1.469251 GCAGCTCATCCACATTTGCAG 60.469 52.381 0.00 0.00 0.00 4.41
2339 2509 2.089201 CAGCTCATCCACATTTGCAGA 58.911 47.619 0.00 0.00 0.00 4.26
2340 2510 2.490509 CAGCTCATCCACATTTGCAGAA 59.509 45.455 0.00 0.00 0.00 3.02
2341 2511 2.753452 AGCTCATCCACATTTGCAGAAG 59.247 45.455 0.00 0.00 0.00 2.85
2342 2512 2.490903 GCTCATCCACATTTGCAGAAGT 59.509 45.455 0.00 0.00 0.00 3.01
2514 2697 6.413892 TCGATTATATTATGCCAGATGCCAA 58.586 36.000 0.00 0.00 40.16 4.52
2540 2723 4.656041 GCATGATGTAACTGAGCTTTGAC 58.344 43.478 0.00 0.00 0.00 3.18
2587 2773 9.717942 AATAGTGTAAGAATGCCATAGAATCTC 57.282 33.333 0.00 0.00 0.00 2.75
2613 2801 2.266070 TGCAGTAAACCATGCAGGC 58.734 52.632 0.00 0.00 46.97 4.85
2730 2961 7.550551 CACTGTCATAGAACATGTCCTAAATGT 59.449 37.037 0.00 0.00 39.95 2.71
2765 3001 9.248291 ACTAAAAAGTGCTGTTAATCAACATTG 57.752 29.630 0.00 0.00 43.58 2.82
2829 3097 4.432712 CTTTTGTCCTCAAACCAACCAAG 58.567 43.478 0.00 0.00 42.28 3.61
2833 3101 1.064017 TCCTCAAACCAACCAAGCTGT 60.064 47.619 0.00 0.00 0.00 4.40
2923 3191 2.644992 CAACGGAAAGCAGGGTGC 59.355 61.111 0.00 0.00 45.46 5.01
3287 3583 1.102154 CTGTTGGTTCCAGTGCACAA 58.898 50.000 21.04 1.11 0.00 3.33
3288 3584 1.066002 CTGTTGGTTCCAGTGCACAAG 59.934 52.381 21.04 11.05 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.033550 CGGAAACCAAATCGAAACCACA 59.966 45.455 0.00 0.00 0.00 4.17
8 9 2.606065 CCGGAAACCAAATCGAAACCAC 60.606 50.000 0.00 0.00 0.00 4.16
9 10 1.609555 CCGGAAACCAAATCGAAACCA 59.390 47.619 0.00 0.00 0.00 3.67
54 61 2.002127 CAGTTGATTCGAGCCGAGC 58.998 57.895 0.00 0.00 37.14 5.03
55 62 0.459237 AGCAGTTGATTCGAGCCGAG 60.459 55.000 0.00 0.00 37.14 4.63
56 63 0.037326 AAGCAGTTGATTCGAGCCGA 60.037 50.000 0.00 0.00 0.00 5.54
57 64 0.371645 GAAGCAGTTGATTCGAGCCG 59.628 55.000 0.00 0.00 30.44 5.52
58 65 0.729690 GGAAGCAGTTGATTCGAGCC 59.270 55.000 4.27 0.00 41.02 4.70
79 86 1.095600 GCCAGATTTCTTCCGGGAAC 58.904 55.000 5.09 0.00 0.00 3.62
102 119 3.694043 AAGCTGGAGGAAGAAGAAGAC 57.306 47.619 0.00 0.00 0.00 3.01
147 169 3.261250 CTGGACAAGCTGGATTGCT 57.739 52.632 0.00 0.00 46.40 3.91
194 221 4.267690 GGGAAAAGAAAGAAACACGCTTTG 59.732 41.667 0.00 0.00 35.83 2.77
195 222 4.430007 GGGAAAAGAAAGAAACACGCTTT 58.570 39.130 0.00 0.00 38.22 3.51
196 223 3.181479 GGGGAAAAGAAAGAAACACGCTT 60.181 43.478 0.00 0.00 0.00 4.68
197 224 2.361119 GGGGAAAAGAAAGAAACACGCT 59.639 45.455 0.00 0.00 0.00 5.07
198 225 2.361119 AGGGGAAAAGAAAGAAACACGC 59.639 45.455 0.00 0.00 0.00 5.34
199 226 4.499188 GGAAGGGGAAAAGAAAGAAACACG 60.499 45.833 0.00 0.00 0.00 4.49
200 227 4.649674 AGGAAGGGGAAAAGAAAGAAACAC 59.350 41.667 0.00 0.00 0.00 3.32
202 229 5.871396 AAGGAAGGGGAAAAGAAAGAAAC 57.129 39.130 0.00 0.00 0.00 2.78
284 317 2.030185 TGACAGCGAAAGGTAGACAGAC 60.030 50.000 0.00 0.00 41.81 3.51
287 320 1.000506 GGTGACAGCGAAAGGTAGACA 59.999 52.381 0.00 0.00 41.81 3.41
288 321 1.711206 GGTGACAGCGAAAGGTAGAC 58.289 55.000 0.00 0.00 41.81 2.59
291 324 1.373748 GCGGTGACAGCGAAAGGTA 60.374 57.895 29.64 0.00 42.41 3.08
292 325 2.665185 GCGGTGACAGCGAAAGGT 60.665 61.111 29.64 0.00 42.41 3.50
293 326 3.423154 GGCGGTGACAGCGAAAGG 61.423 66.667 29.64 1.58 42.41 3.11
294 327 3.423154 GGGCGGTGACAGCGAAAG 61.423 66.667 29.64 1.97 42.41 2.62
296 329 4.980805 GTGGGCGGTGACAGCGAA 62.981 66.667 29.64 11.82 42.41 4.70
321 361 0.037590 TGTTGAACGGGATGGAAGGG 59.962 55.000 0.00 0.00 0.00 3.95
323 363 4.314740 TTTTTGTTGAACGGGATGGAAG 57.685 40.909 0.00 0.00 0.00 3.46
349 389 9.561069 AGAGAAAACAAAAGTGAAGCTATCTTA 57.439 29.630 0.00 0.00 31.48 2.10
372 412 3.004106 CACAAGGAGGAGTTGCAAAAGAG 59.996 47.826 0.00 0.00 0.00 2.85
373 413 2.951642 CACAAGGAGGAGTTGCAAAAGA 59.048 45.455 0.00 0.00 0.00 2.52
375 415 1.408702 GCACAAGGAGGAGTTGCAAAA 59.591 47.619 0.00 0.00 0.00 2.44
376 416 1.032014 GCACAAGGAGGAGTTGCAAA 58.968 50.000 0.00 0.00 0.00 3.68
377 417 0.823356 GGCACAAGGAGGAGTTGCAA 60.823 55.000 0.00 0.00 0.00 4.08
378 418 1.228245 GGCACAAGGAGGAGTTGCA 60.228 57.895 0.00 0.00 0.00 4.08
379 419 1.073897 AGGCACAAGGAGGAGTTGC 59.926 57.895 0.00 0.00 0.00 4.17
382 422 2.753029 GCAGGCACAAGGAGGAGT 59.247 61.111 0.00 0.00 0.00 3.85
399 439 4.147449 TCTGCTCCGTGGCATCCG 62.147 66.667 0.00 0.00 41.63 4.18
410 450 3.430931 GTGTAATCTGAGTCGTCTGCTC 58.569 50.000 0.00 0.00 0.00 4.26
411 451 2.164624 GGTGTAATCTGAGTCGTCTGCT 59.835 50.000 0.00 0.00 0.00 4.24
418 458 8.999431 TGTCAAATAAAAGGTGTAATCTGAGTC 58.001 33.333 0.00 0.00 0.00 3.36
458 498 6.412362 ACAGTTGAGCCTCTCGATTTATAT 57.588 37.500 0.00 0.00 32.35 0.86
467 512 5.948992 AAACAATTACAGTTGAGCCTCTC 57.051 39.130 0.00 0.00 33.37 3.20
477 522 6.463995 TGGCAAGAGAAAAACAATTACAGT 57.536 33.333 0.00 0.00 0.00 3.55
498 543 3.788937 CTCCTGCAGCCAATAATTTTGG 58.211 45.455 8.66 12.43 42.37 3.28
597 658 1.078848 CGGAGAAGCTGGAGTTGGG 60.079 63.158 0.00 0.00 0.00 4.12
600 661 2.665603 GCCGGAGAAGCTGGAGTT 59.334 61.111 5.05 0.00 46.81 3.01
601 662 3.394836 GGCCGGAGAAGCTGGAGT 61.395 66.667 5.05 0.00 46.81 3.85
603 664 3.706373 GTGGCCGGAGAAGCTGGA 61.706 66.667 5.05 0.00 46.81 3.86
607 671 4.785453 CTGGGTGGCCGGAGAAGC 62.785 72.222 5.05 0.00 0.00 3.86
629 693 1.873698 TTGTTGGTGCTTACCTCGTC 58.126 50.000 0.00 0.00 0.00 4.20
642 714 6.940831 AAAGATTGGGAATTTGTTTGTTGG 57.059 33.333 0.00 0.00 0.00 3.77
676 748 6.112734 GTCAGGGTCAACATGTGATGTATAA 58.887 40.000 0.00 0.00 44.07 0.98
678 750 4.019411 TGTCAGGGTCAACATGTGATGTAT 60.019 41.667 0.00 0.00 44.07 2.29
684 764 3.003689 GTCTTTGTCAGGGTCAACATGTG 59.996 47.826 0.00 0.00 0.00 3.21
685 765 3.214328 GTCTTTGTCAGGGTCAACATGT 58.786 45.455 0.00 0.00 0.00 3.21
686 766 2.224079 CGTCTTTGTCAGGGTCAACATG 59.776 50.000 0.00 0.00 0.00 3.21
687 767 2.158813 ACGTCTTTGTCAGGGTCAACAT 60.159 45.455 0.00 0.00 0.00 2.71
787 880 2.728690 TTCATTCAAGCGCTGCAAAT 57.271 40.000 12.58 8.60 0.00 2.32
791 884 0.452987 TGGATTCATTCAAGCGCTGC 59.547 50.000 12.58 0.00 0.00 5.25
804 897 5.812127 GGTTGGCATAAATTGAACTGGATTC 59.188 40.000 0.00 0.00 37.88 2.52
808 912 3.510719 CGGTTGGCATAAATTGAACTGG 58.489 45.455 0.00 0.00 0.00 4.00
811 915 1.917303 CGCGGTTGGCATAAATTGAAC 59.083 47.619 0.00 0.00 43.84 3.18
812 916 1.542030 ACGCGGTTGGCATAAATTGAA 59.458 42.857 12.47 0.00 43.84 2.69
815 919 0.457681 GCACGCGGTTGGCATAAATT 60.458 50.000 12.47 0.00 43.84 1.82
847 959 5.237048 AGAAGAAGAGATCAACAAGCTGTC 58.763 41.667 0.00 0.00 0.00 3.51
848 960 5.226194 AGAAGAAGAGATCAACAAGCTGT 57.774 39.130 0.00 0.00 0.00 4.40
851 963 7.608308 ACATAAGAAGAAGAGATCAACAAGC 57.392 36.000 0.00 0.00 0.00 4.01
872 997 3.553715 CCTGCGCTGAGTCATACATACAT 60.554 47.826 16.65 0.00 0.00 2.29
874 999 2.398498 CCTGCGCTGAGTCATACATAC 58.602 52.381 16.65 0.00 0.00 2.39
875 1000 1.341209 CCCTGCGCTGAGTCATACATA 59.659 52.381 16.65 0.00 0.00 2.29
876 1001 0.105593 CCCTGCGCTGAGTCATACAT 59.894 55.000 16.65 0.00 0.00 2.29
877 1002 1.517361 CCCTGCGCTGAGTCATACA 59.483 57.895 16.65 0.00 0.00 2.29
878 1003 1.884926 GCCCTGCGCTGAGTCATAC 60.885 63.158 16.65 0.00 0.00 2.39
879 1004 2.302199 CTGCCCTGCGCTGAGTCATA 62.302 60.000 16.65 0.00 38.65 2.15
896 1021 4.798344 CTGCTCTGCCCTGCCCTG 62.798 72.222 0.00 0.00 0.00 4.45
899 1024 4.792804 GTCCTGCTCTGCCCTGCC 62.793 72.222 0.00 0.00 0.00 4.85
906 1031 2.744202 GGTATGTGTTTGTCCTGCTCTG 59.256 50.000 0.00 0.00 0.00 3.35
908 1033 2.484264 GTGGTATGTGTTTGTCCTGCTC 59.516 50.000 0.00 0.00 0.00 4.26
909 1034 2.158682 TGTGGTATGTGTTTGTCCTGCT 60.159 45.455 0.00 0.00 0.00 4.24
911 1036 3.629855 TGTTGTGGTATGTGTTTGTCCTG 59.370 43.478 0.00 0.00 0.00 3.86
919 1044 1.142870 AGCTGGTGTTGTGGTATGTGT 59.857 47.619 0.00 0.00 0.00 3.72
922 1047 1.003580 AGGAGCTGGTGTTGTGGTATG 59.996 52.381 0.00 0.00 0.00 2.39
926 1051 1.302832 GGAGGAGCTGGTGTTGTGG 60.303 63.158 0.00 0.00 0.00 4.17
929 1054 1.197430 AGGAGGAGGAGCTGGTGTTG 61.197 60.000 0.00 0.00 0.00 3.33
930 1055 0.413832 TAGGAGGAGGAGCTGGTGTT 59.586 55.000 0.00 0.00 0.00 3.32
1074 1212 2.955660 GTTGTGGTGGGAGAATTTGTCA 59.044 45.455 0.00 0.00 0.00 3.58
1093 1231 2.683933 ATCGTCGGGGAGCCTGTT 60.684 61.111 0.00 0.00 0.00 3.16
1119 1257 2.282180 GGTTTGCTGGCGGGAAGA 60.282 61.111 0.00 0.00 0.00 2.87
1145 1283 2.149383 AGGGCTGAAGGTGCTGTGA 61.149 57.895 0.00 0.00 0.00 3.58
1248 1386 1.068333 GCGTACTGGTAAACCGTCTGA 60.068 52.381 0.00 0.00 39.43 3.27
1257 1395 0.168788 CGAACCTCGCGTACTGGTAA 59.831 55.000 5.77 0.00 33.17 2.85
1269 1407 0.670854 GTGAGGTCTTGGCGAACCTC 60.671 60.000 19.98 19.98 46.56 3.85
1271 1409 1.671379 GGTGAGGTCTTGGCGAACC 60.671 63.158 0.00 0.00 0.00 3.62
1386 1524 2.571216 AACCGTCTGGGACCTGTCG 61.571 63.158 7.63 7.63 40.75 4.35
1404 1542 1.234615 GCCAGCCGAGCAAAACTACA 61.235 55.000 0.00 0.00 0.00 2.74
1407 1545 2.113986 AGCCAGCCGAGCAAAACT 59.886 55.556 0.00 0.00 0.00 2.66
1545 1683 3.122297 GAGCATCTCCACATTCTTCTCG 58.878 50.000 0.00 0.00 0.00 4.04
1656 1794 4.836825 TCTTAGATCCAAAGGAACTGCAG 58.163 43.478 13.48 13.48 40.86 4.41
1657 1795 4.908601 TCTTAGATCCAAAGGAACTGCA 57.091 40.909 6.14 0.00 40.86 4.41
1714 1860 2.564062 AGCAGCAACACAAAGCCATAAT 59.436 40.909 0.00 0.00 0.00 1.28
1917 2068 7.444299 ACTTTGGATGTGCAGAATTTACAAAT 58.556 30.769 0.00 0.00 0.00 2.32
2204 2366 4.168101 TCTTTCTGGGACTCCACAACTAT 58.832 43.478 0.00 0.00 38.32 2.12
2218 2380 4.378774 CTGCTGGTCTGATATCTTTCTGG 58.621 47.826 3.98 0.00 0.00 3.86
2317 2483 0.524816 GCAAATGTGGATGAGCTGCG 60.525 55.000 0.00 0.00 0.00 5.18
2333 2503 3.803715 GCACAGAACTCCTACTTCTGCAA 60.804 47.826 7.86 0.00 45.88 4.08
2337 2507 4.899352 AATGCACAGAACTCCTACTTCT 57.101 40.909 0.00 0.00 0.00 2.85
2338 2508 5.470098 TGAAAATGCACAGAACTCCTACTTC 59.530 40.000 0.00 0.00 0.00 3.01
2339 2509 5.376625 TGAAAATGCACAGAACTCCTACTT 58.623 37.500 0.00 0.00 0.00 2.24
2340 2510 4.973168 TGAAAATGCACAGAACTCCTACT 58.027 39.130 0.00 0.00 0.00 2.57
2341 2511 4.378874 GCTGAAAATGCACAGAACTCCTAC 60.379 45.833 6.25 0.00 36.38 3.18
2342 2512 3.753272 GCTGAAAATGCACAGAACTCCTA 59.247 43.478 6.25 0.00 36.38 2.94
2485 2663 9.428097 GCATCTGGCATAATATAATCGATGATA 57.572 33.333 4.89 4.89 43.97 2.15
2514 2697 1.945387 CTCAGTTACATCATGCGCCT 58.055 50.000 4.18 0.00 0.00 5.52
2518 2701 4.154737 TGTCAAAGCTCAGTTACATCATGC 59.845 41.667 0.00 0.00 0.00 4.06
2613 2801 2.412870 TGACAAATACTGGTGCAGTCG 58.587 47.619 0.00 0.00 41.21 4.18
2765 3001 6.280643 ACCTCCTGCAAGAAAATAAAAACAC 58.719 36.000 0.00 0.00 34.07 3.32
2884 3152 0.895530 TCTCCACGAATGACTCCACC 59.104 55.000 0.00 0.00 0.00 4.61
2923 3191 1.081376 GTCACACGACCTCACCTCG 60.081 63.158 0.00 0.00 36.02 4.63
3291 3587 4.309099 CTCCCACACAAATCAATGGTTTG 58.691 43.478 16.61 16.61 41.22 2.93


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

AutoCloner maintained by Alex Coulton.