Multiple sequence alignment - TraesCS7A01G225500

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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 TraesCS7A01G225500 chr7A 100.000 3837 0 0 1 3837 194809802 194805966 0.000000e+00 7086
1 TraesCS7A01G225500 chr7A 87.583 451 51 4 6 453 17392773 17393221 5.680000e-143 518
2 TraesCS7A01G225500 chr7D 93.232 3029 155 22 8 3024 189169476 189172466 0.000000e+00 4412
3 TraesCS7A01G225500 chr7B 95.934 2238 75 7 800 3024 333751112 333753346 0.000000e+00 3615
4 TraesCS7A01G225500 chr7B 86.813 455 56 4 6 459 74298052 74297601 4.420000e-139 505
5 TraesCS7A01G225500 chr7B 87.179 429 49 5 335 761 333750621 333751045 2.070000e-132 483
6 TraesCS7A01G225500 chr3D 95.320 812 35 3 3028 3837 307921135 307921945 0.000000e+00 1286
7 TraesCS7A01G225500 chr3D 93.350 812 52 1 3028 3837 534112500 534113311 0.000000e+00 1199
8 TraesCS7A01G225500 chr2D 94.951 812 39 1 3028 3837 507059745 507060556 0.000000e+00 1271
9 TraesCS7A01G225500 chr2D 93.473 812 51 2 3028 3837 607979607 607980418 0.000000e+00 1205
10 TraesCS7A01G225500 chr4D 94.698 811 41 2 3028 3837 484121232 484120423 0.000000e+00 1258
11 TraesCS7A01G225500 chr3A 94.575 811 43 1 3028 3837 143015611 143014801 0.000000e+00 1253
12 TraesCS7A01G225500 chr6D 93.850 813 46 3 3029 3837 398167437 398168249 0.000000e+00 1221
13 TraesCS7A01G225500 chr5D 93.604 813 48 3 3028 3837 74418160 74417349 0.000000e+00 1210
14 TraesCS7A01G225500 chr4A 93.358 813 51 2 3028 3837 631492646 631491834 0.000000e+00 1199
15 TraesCS7A01G225500 chr5B 88.667 450 46 5 6 453 639761132 639761578 9.370000e-151 544
16 TraesCS7A01G225500 chr5B 87.555 458 52 5 6 460 578440134 578439679 3.400000e-145 525
17 TraesCS7A01G225500 chr5B 87.472 447 51 5 6 450 639761749 639762192 9.510000e-141 510
18 TraesCS7A01G225500 chr5B 84.683 457 68 1 6 460 659629725 659630181 4.520000e-124 455
19 TraesCS7A01G225500 chr6B 87.965 457 52 3 6 460 124390376 124390831 1.570000e-148 536
20 TraesCS7A01G225500 chr3B 87.061 456 57 2 6 460 133084964 133085418 7.350000e-142 514


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 TraesCS7A01G225500 chr7A 194805966 194809802 3836 True 7086 7086 100.0000 1 3837 1 chr7A.!!$R1 3836
1 TraesCS7A01G225500 chr7D 189169476 189172466 2990 False 4412 4412 93.2320 8 3024 1 chr7D.!!$F1 3016
2 TraesCS7A01G225500 chr7B 333750621 333753346 2725 False 2049 3615 91.5565 335 3024 2 chr7B.!!$F1 2689
3 TraesCS7A01G225500 chr3D 307921135 307921945 810 False 1286 1286 95.3200 3028 3837 1 chr3D.!!$F1 809
4 TraesCS7A01G225500 chr3D 534112500 534113311 811 False 1199 1199 93.3500 3028 3837 1 chr3D.!!$F2 809
5 TraesCS7A01G225500 chr2D 507059745 507060556 811 False 1271 1271 94.9510 3028 3837 1 chr2D.!!$F1 809
6 TraesCS7A01G225500 chr2D 607979607 607980418 811 False 1205 1205 93.4730 3028 3837 1 chr2D.!!$F2 809
7 TraesCS7A01G225500 chr4D 484120423 484121232 809 True 1258 1258 94.6980 3028 3837 1 chr4D.!!$R1 809
8 TraesCS7A01G225500 chr3A 143014801 143015611 810 True 1253 1253 94.5750 3028 3837 1 chr3A.!!$R1 809
9 TraesCS7A01G225500 chr6D 398167437 398168249 812 False 1221 1221 93.8500 3029 3837 1 chr6D.!!$F1 808
10 TraesCS7A01G225500 chr5D 74417349 74418160 811 True 1210 1210 93.6040 3028 3837 1 chr5D.!!$R1 809
11 TraesCS7A01G225500 chr4A 631491834 631492646 812 True 1199 1199 93.3580 3028 3837 1 chr4A.!!$R1 809
12 TraesCS7A01G225500 chr5B 639761132 639762192 1060 False 527 544 88.0695 6 453 2 chr5B.!!$F2 447

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
461 1354 0.107800 GAACTCGGGTCTTTAGGCCC 60.108 60.0 9.47 9.47 41.45 5.80 F
916 1840 0.109272 ACAGGCGACATGTCAGTACG 60.109 55.0 24.93 12.65 0.00 3.67 F
2098 3032 0.242825 TTCTGGCACTCCTTACGACG 59.757 55.0 0.00 0.00 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 3315 2.020559 CGCGACGCAGCATTCTTC 59.979 61.111 21.35 0.0 36.85 2.87 R
2500 3434 1.497278 CATGTCCTTGTGAACGCCG 59.503 57.895 0.00 0.0 0.00 6.46 R
3609 4560 0.613853 CCGGACTGGGACTGAAGGTA 60.614 60.000 0.00 0.0 0.00 3.08 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
32 33 9.712305 GCATACATCCATTTTAGTATGAGTACT 57.288 33.333 13.74 0.00 43.94 2.73
130 750 5.393068 AGCTTGATCCTCAATAAATGGGA 57.607 39.130 0.00 0.00 35.59 4.37
159 779 3.956199 CCCTATGCATCACCTGTCAATTT 59.044 43.478 0.19 0.00 0.00 1.82
165 785 4.458989 TGCATCACCTGTCAATTTTAGGAC 59.541 41.667 6.44 0.00 35.55 3.85
166 786 4.142381 GCATCACCTGTCAATTTTAGGACC 60.142 45.833 6.44 0.00 35.55 4.46
171 791 5.711976 CACCTGTCAATTTTAGGACCTGAAT 59.288 40.000 3.53 1.61 35.55 2.57
190 810 0.669318 TTCGGGTCGTTAAGCTGCAG 60.669 55.000 10.11 10.11 0.00 4.41
194 814 1.608283 GGGTCGTTAAGCTGCAGAACT 60.608 52.381 20.43 2.30 0.00 3.01
210 830 0.112218 AACTGCATGCCCAACCACTA 59.888 50.000 16.68 0.00 0.00 2.74
213 833 0.112218 TGCATGCCCAACCACTAAGT 59.888 50.000 16.68 0.00 0.00 2.24
218 838 1.771854 TGCCCAACCACTAAGTCAAGA 59.228 47.619 0.00 0.00 0.00 3.02
240 860 6.306987 AGACTCTCTTTGCTTAAAAATGGGA 58.693 36.000 0.00 0.00 0.00 4.37
249 869 8.831715 TTTGCTTAAAAATGGGAGAGATTTTC 57.168 30.769 0.00 0.00 32.94 2.29
254 874 9.987272 CTTAAAAATGGGAGAGATTTTCACTTT 57.013 29.630 0.00 0.00 32.94 2.66
266 886 3.121030 CACTTTCCGGCCTCTGCG 61.121 66.667 0.00 0.00 38.85 5.18
285 905 1.202639 CGCCAACTAGGGATGCATACA 60.203 52.381 11.97 0.00 38.09 2.29
286 906 2.744823 CGCCAACTAGGGATGCATACAA 60.745 50.000 11.97 0.00 38.09 2.41
295 915 7.122715 ACTAGGGATGCATACAACCATTTTAA 58.877 34.615 11.97 0.00 40.45 1.52
320 940 8.818141 ATATGAGTACCAAGATAAACGTGATG 57.182 34.615 0.00 0.00 0.00 3.07
325 945 4.517285 ACCAAGATAAACGTGATGCTCAT 58.483 39.130 0.00 0.00 0.00 2.90
326 946 4.333649 ACCAAGATAAACGTGATGCTCATG 59.666 41.667 0.00 4.45 39.24 3.07
328 948 5.237996 CCAAGATAAACGTGATGCTCATGAT 59.762 40.000 0.00 0.00 36.89 2.45
329 949 6.238566 CCAAGATAAACGTGATGCTCATGATT 60.239 38.462 0.00 8.47 36.89 2.57
377 997 3.289407 TGATGACTGGTTTCACCACAA 57.711 42.857 0.00 0.00 44.79 3.33
384 1004 3.384467 ACTGGTTTCACCACAAATCAAGG 59.616 43.478 0.00 0.00 44.79 3.61
391 1011 4.468713 TCACCACAAATCAAGGTTGATCA 58.531 39.130 5.68 0.00 46.60 2.92
403 1023 7.680442 TCAAGGTTGATCATCAATAAAACGA 57.320 32.000 2.67 0.00 38.79 3.85
412 1305 7.748683 TGATCATCAATAAAACGAGAAAAACCG 59.251 33.333 0.00 0.00 0.00 4.44
426 1319 2.401583 AAACCGCTGTGCATCATCTA 57.598 45.000 0.00 0.00 0.00 1.98
439 1332 9.438228 CTGTGCATCATCTATCAATTCTAGAAT 57.562 33.333 12.37 12.37 0.00 2.40
450 1343 6.985188 TCAATTCTAGAATTTGAACTCGGG 57.015 37.500 24.94 12.46 38.84 5.14
451 1344 6.472887 TCAATTCTAGAATTTGAACTCGGGT 58.527 36.000 24.94 0.44 38.84 5.28
454 1347 5.740290 TCTAGAATTTGAACTCGGGTCTT 57.260 39.130 0.00 0.00 0.00 3.01
455 1348 6.110411 TCTAGAATTTGAACTCGGGTCTTT 57.890 37.500 0.00 0.00 0.00 2.52
456 1349 7.235935 TCTAGAATTTGAACTCGGGTCTTTA 57.764 36.000 0.00 0.00 0.00 1.85
457 1350 7.321153 TCTAGAATTTGAACTCGGGTCTTTAG 58.679 38.462 0.00 0.00 0.00 1.85
458 1351 5.246307 AGAATTTGAACTCGGGTCTTTAGG 58.754 41.667 0.00 0.00 0.00 2.69
459 1352 2.467566 TTGAACTCGGGTCTTTAGGC 57.532 50.000 0.00 0.00 0.00 3.93
460 1353 0.611714 TGAACTCGGGTCTTTAGGCC 59.388 55.000 0.00 0.00 0.00 5.19
461 1354 0.107800 GAACTCGGGTCTTTAGGCCC 60.108 60.000 9.47 9.47 41.45 5.80
462 1355 1.559965 AACTCGGGTCTTTAGGCCCC 61.560 60.000 13.69 4.83 41.85 5.80
463 1356 1.993391 CTCGGGTCTTTAGGCCCCA 60.993 63.158 13.69 0.00 41.85 4.96
485 1378 6.293955 CCCAAACAGTGATTTGTAGTACTTGG 60.294 42.308 0.00 0.00 37.79 3.61
509 1402 8.458843 TGGTAAGATAACTTTTAAGCTTCATGC 58.541 33.333 0.00 0.00 38.50 4.06
522 1415 0.608035 TTCATGCGTCCTTTGGTCCC 60.608 55.000 0.00 0.00 0.00 4.46
534 1427 3.011257 CCTTTGGTCCCCCTTTCATCTTA 59.989 47.826 0.00 0.00 0.00 2.10
619 1512 7.181305 TGTGTATTACTGTCTCCCTCCAAAATA 59.819 37.037 0.00 0.00 0.00 1.40
625 1518 5.073144 ACTGTCTCCCTCCAAAATAAAGTCA 59.927 40.000 0.00 0.00 0.00 3.41
632 1525 4.866486 CCTCCAAAATAAAGTCAGCATTGC 59.134 41.667 0.00 0.00 0.00 3.56
676 1569 5.108187 TCTCTTCTGGCAATAGAGCAATT 57.892 39.130 16.64 0.00 36.27 2.32
709 1602 8.335532 TGGATTGATTTTTCGTATCAAACTCT 57.664 30.769 0.00 0.00 43.14 3.24
722 1615 7.042051 TCGTATCAAACTCTTTTTGAGACAAGG 60.042 37.037 19.11 7.85 45.61 3.61
866 1787 2.550830 AGAACATTCTTGCCGAGTGT 57.449 45.000 0.00 0.00 43.52 3.55
867 1788 3.678056 AGAACATTCTTGCCGAGTGTA 57.322 42.857 2.48 0.00 41.16 2.90
898 1822 3.603532 TCTGTTTGAGATGCAGATCCAC 58.396 45.455 0.00 0.00 34.72 4.02
916 1840 0.109272 ACAGGCGACATGTCAGTACG 60.109 55.000 24.93 12.65 0.00 3.67
949 1873 1.630878 CCTTCCAGGCTAAGTCACCTT 59.369 52.381 0.00 0.00 32.56 3.50
953 1877 1.160137 CAGGCTAAGTCACCTTGCAC 58.840 55.000 0.00 0.00 32.56 4.57
958 1882 2.548920 GCTAAGTCACCTTGCACTGTCT 60.549 50.000 0.00 0.00 31.89 3.41
999 1923 3.488090 CCGAAAAGGACGGCGAGC 61.488 66.667 16.62 4.71 45.00 5.03
1000 1924 2.736995 CGAAAAGGACGGCGAGCA 60.737 61.111 16.62 0.00 0.00 4.26
1156 2081 0.401738 TTCTGCCCTTCCACTCCAAG 59.598 55.000 0.00 0.00 0.00 3.61
1157 2082 1.676967 CTGCCCTTCCACTCCAAGC 60.677 63.158 0.00 0.00 0.00 4.01
1158 2083 2.361737 GCCCTTCCACTCCAAGCC 60.362 66.667 0.00 0.00 0.00 4.35
1159 2084 2.045926 CCCTTCCACTCCAAGCCG 60.046 66.667 0.00 0.00 0.00 5.52
1160 2085 2.747855 CCTTCCACTCCAAGCCGC 60.748 66.667 0.00 0.00 0.00 6.53
1161 2086 2.747855 CTTCCACTCCAAGCCGCC 60.748 66.667 0.00 0.00 0.00 6.13
1349 2283 3.775654 CCGTCTCTCCACCTGGCC 61.776 72.222 0.00 0.00 34.44 5.36
1654 2588 1.554042 GCGCGAAGAAAACGGAGTCA 61.554 55.000 12.10 0.00 45.00 3.41
1736 2670 0.326048 AGATGAGTGGGAGGTGGAGG 60.326 60.000 0.00 0.00 0.00 4.30
2026 2960 4.400961 GCTCTGTTCGGCCTGGCT 62.401 66.667 19.68 0.00 0.00 4.75
2095 3029 1.134965 CCTCTTCTGGCACTCCTTACG 60.135 57.143 0.00 0.00 0.00 3.18
2098 3032 0.242825 TTCTGGCACTCCTTACGACG 59.757 55.000 0.00 0.00 0.00 5.12
2381 3315 4.586618 CTCACAGGTCGGAGCTTG 57.413 61.111 7.04 9.49 0.00 4.01
2592 3526 3.248266 GCCTTCATGATTTCAGCAACAC 58.752 45.455 0.00 0.00 0.00 3.32
2730 3664 3.549471 CGATCAGTATGCATCGATTAGCC 59.451 47.826 0.19 0.00 43.66 3.93
2766 3700 1.949525 GGTGTTGCTGTGTTGTCATCT 59.050 47.619 0.00 0.00 0.00 2.90
2822 3756 7.156876 CCTGCTTGGTCTGTAATTTTGAATA 57.843 36.000 0.00 0.00 0.00 1.75
2893 3828 9.855021 GTTTGTGCTCCACTTTGTTTATATATT 57.145 29.630 0.00 0.00 35.11 1.28
2922 3859 7.127955 TCCCTGAAAAGGCTTTAGATCTAGATT 59.872 37.037 13.77 0.00 0.00 2.40
3016 3960 8.948145 GCAGATAGCAGAAGATTATTCATGAAT 58.052 33.333 23.75 23.75 44.79 2.57
3039 3983 4.699637 TCATCTAGAACGTGTTTGGTTGT 58.300 39.130 0.00 0.00 0.00 3.32
3063 4007 4.644685 AGTTTGGAACAGTACTTGCATTGT 59.355 37.500 0.00 0.00 42.39 2.71
3077 4021 5.889853 ACTTGCATTGTATGTCCATCTCAAT 59.110 36.000 0.00 5.41 0.00 2.57
3100 4044 5.076182 TCCAACCTGATTGCTGAAATACAA 58.924 37.500 0.00 0.00 36.93 2.41
3102 4046 4.685169 ACCTGATTGCTGAAATACAACG 57.315 40.909 0.00 0.00 0.00 4.10
3116 4060 2.099141 ACAACGTCATATGCAGCAGT 57.901 45.000 0.00 0.00 0.00 4.40
3150 4094 3.344215 GCCTGCATCGCATCGAGG 61.344 66.667 0.00 0.00 39.91 4.63
3249 4197 0.100503 AACAGCGTTTGTGTTCTGCC 59.899 50.000 0.00 0.00 40.74 4.85
3252 4200 1.008538 GCGTTTGTGTTCTGCCCAG 60.009 57.895 0.00 0.00 0.00 4.45
3318 4267 2.166050 ACAGCAACATCACAACAGCAAA 59.834 40.909 0.00 0.00 0.00 3.68
3386 4336 9.968870 AGCAAACTACTTAACTAGATAGCATAC 57.031 33.333 0.00 0.00 0.00 2.39
3405 4355 5.719173 CATACTCTAGATTAAGAGCAGGGC 58.281 45.833 0.00 0.00 45.81 5.19
3462 4412 5.012975 ACCTGGCCAAAATATGAACATGTTT 59.987 36.000 13.36 0.00 34.29 2.83
3609 4560 2.161808 CGAGTCGTGGTTGTAGATCTGT 59.838 50.000 5.18 0.00 0.00 3.41
3659 4610 3.210528 GACGAGGTCGCCGAGGAT 61.211 66.667 0.00 0.00 44.43 3.24
3766 4717 0.035881 CCTCTTGTTGGCTGAGAGCA 59.964 55.000 0.00 0.00 44.75 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.816385 ACTAAAATGGATGTATGCAGGACG 59.184 41.667 0.00 0.00 0.00 4.79
1 2 7.661437 TCATACTAAAATGGATGTATGCAGGAC 59.339 37.037 0.00 0.00 40.90 3.85
2 3 7.744733 TCATACTAAAATGGATGTATGCAGGA 58.255 34.615 0.00 0.00 40.90 3.86
3 4 7.663081 ACTCATACTAAAATGGATGTATGCAGG 59.337 37.037 0.00 0.00 40.90 4.85
4 5 8.613060 ACTCATACTAAAATGGATGTATGCAG 57.387 34.615 0.00 0.00 40.90 4.41
130 750 2.582636 AGGTGATGCATAGGGGTTTTCT 59.417 45.455 0.00 0.00 0.00 2.52
141 761 5.126061 GTCCTAAAATTGACAGGTGATGCAT 59.874 40.000 0.00 0.00 0.00 3.96
143 763 4.142381 GGTCCTAAAATTGACAGGTGATGC 60.142 45.833 0.00 0.00 33.09 3.91
165 785 1.664151 GCTTAACGACCCGAATTCAGG 59.336 52.381 6.14 6.14 0.00 3.86
166 786 2.348666 CAGCTTAACGACCCGAATTCAG 59.651 50.000 6.22 0.00 0.00 3.02
171 791 0.669318 CTGCAGCTTAACGACCCGAA 60.669 55.000 0.00 0.00 0.00 4.30
190 810 1.181098 AGTGGTTGGGCATGCAGTTC 61.181 55.000 21.36 6.82 0.00 3.01
194 814 0.112218 ACTTAGTGGTTGGGCATGCA 59.888 50.000 21.36 0.00 0.00 3.96
210 830 7.865706 TTTTAAGCAAAGAGAGTCTTGACTT 57.134 32.000 4.67 8.61 36.71 3.01
213 833 7.255590 CCCATTTTTAAGCAAAGAGAGTCTTGA 60.256 37.037 0.00 0.00 36.71 3.02
218 838 6.306987 TCTCCCATTTTTAAGCAAAGAGAGT 58.693 36.000 0.00 0.00 0.00 3.24
240 860 2.040412 AGGCCGGAAAGTGAAAATCTCT 59.960 45.455 5.05 0.00 0.00 3.10
249 869 3.121030 CGCAGAGGCCGGAAAGTG 61.121 66.667 5.05 0.00 36.38 3.16
266 886 2.618709 GTTGTATGCATCCCTAGTTGGC 59.381 50.000 0.19 0.00 0.00 4.52
274 894 8.584157 TCATATTAAAATGGTTGTATGCATCCC 58.416 33.333 0.19 0.00 34.38 3.85
295 915 7.385205 GCATCACGTTTATCTTGGTACTCATAT 59.615 37.037 0.00 0.00 0.00 1.78
391 1011 5.856455 CAGCGGTTTTTCTCGTTTTATTGAT 59.144 36.000 0.00 0.00 0.00 2.57
400 1020 1.092921 TGCACAGCGGTTTTTCTCGT 61.093 50.000 0.00 0.00 0.00 4.18
401 1021 0.238289 ATGCACAGCGGTTTTTCTCG 59.762 50.000 0.00 0.00 0.00 4.04
403 1023 1.317613 TGATGCACAGCGGTTTTTCT 58.682 45.000 0.00 0.00 0.00 2.52
412 1305 5.943706 AGAATTGATAGATGATGCACAGC 57.056 39.130 0.00 0.00 34.85 4.40
426 1319 7.112779 ACCCGAGTTCAAATTCTAGAATTGAT 58.887 34.615 27.25 12.98 40.57 2.57
439 1332 2.551504 GGCCTAAAGACCCGAGTTCAAA 60.552 50.000 0.00 0.00 0.00 2.69
450 1343 1.886542 CACTGTTTGGGGCCTAAAGAC 59.113 52.381 16.04 6.41 0.00 3.01
451 1344 1.777878 TCACTGTTTGGGGCCTAAAGA 59.222 47.619 16.04 13.70 0.00 2.52
454 1347 2.896685 CAAATCACTGTTTGGGGCCTAA 59.103 45.455 0.84 0.00 35.86 2.69
455 1348 2.158385 ACAAATCACTGTTTGGGGCCTA 60.158 45.455 0.84 0.00 42.07 3.93
456 1349 1.341080 CAAATCACTGTTTGGGGCCT 58.659 50.000 0.84 0.00 35.86 5.19
457 1350 1.047801 ACAAATCACTGTTTGGGGCC 58.952 50.000 0.00 0.00 42.07 5.80
458 1351 2.890945 ACTACAAATCACTGTTTGGGGC 59.109 45.455 4.63 0.00 42.07 5.80
459 1352 5.313712 AGTACTACAAATCACTGTTTGGGG 58.686 41.667 0.00 0.16 42.07 4.96
460 1353 6.293955 CCAAGTACTACAAATCACTGTTTGGG 60.294 42.308 0.00 0.45 42.07 4.12
461 1354 6.262273 ACCAAGTACTACAAATCACTGTTTGG 59.738 38.462 0.00 0.00 42.07 3.28
462 1355 7.259290 ACCAAGTACTACAAATCACTGTTTG 57.741 36.000 0.00 0.00 43.11 2.93
463 1356 8.967664 TTACCAAGTACTACAAATCACTGTTT 57.032 30.769 0.00 0.00 0.00 2.83
485 1378 8.175716 ACGCATGAAGCTTAAAAGTTATCTTAC 58.824 33.333 0.00 0.00 42.61 2.34
518 1411 4.166144 TCTCCAATAAGATGAAAGGGGGAC 59.834 45.833 0.00 0.00 0.00 4.46
522 1415 8.807948 TTTTAGTCTCCAATAAGATGAAAGGG 57.192 34.615 0.00 0.00 0.00 3.95
567 1460 3.469008 TTCAAATGGTCGCGGATAGAT 57.531 42.857 6.13 0.00 0.00 1.98
573 1466 3.119990 ACAATACTTTCAAATGGTCGCGG 60.120 43.478 6.13 0.00 0.00 6.46
574 1467 3.845775 CACAATACTTTCAAATGGTCGCG 59.154 43.478 0.00 0.00 0.00 5.87
619 1512 3.322828 ACCAAAGATGCAATGCTGACTTT 59.677 39.130 6.82 11.94 0.00 2.66
625 1518 4.275810 AGTGATACCAAAGATGCAATGCT 58.724 39.130 6.82 0.00 0.00 3.79
632 1525 8.954350 AGAGAAAATCAAGTGATACCAAAGATG 58.046 33.333 0.00 0.00 33.73 2.90
676 1569 9.787532 GATACGAAAAATCAATCCAATGAGAAA 57.212 29.630 0.00 0.00 31.76 2.52
709 1602 2.612212 GACTCACGCCTTGTCTCAAAAA 59.388 45.455 0.00 0.00 0.00 1.94
714 1607 3.410098 GAGACTCACGCCTTGTCTC 57.590 57.895 10.95 10.95 46.16 3.36
722 1615 1.429463 AAAATCACGGAGACTCACGC 58.571 50.000 4.53 0.00 0.00 5.34
789 1682 6.348622 CGCACCAGTGGTACATAATACAAAAA 60.349 38.462 16.22 0.00 44.52 1.94
861 1782 7.067615 TCTCAAACAGAGTCAGGATATACACTC 59.932 40.741 0.00 0.00 44.98 3.51
865 1786 6.644592 GCATCTCAAACAGAGTCAGGATATAC 59.355 42.308 0.00 0.00 44.98 1.47
866 1787 6.324770 TGCATCTCAAACAGAGTCAGGATATA 59.675 38.462 0.00 0.00 44.98 0.86
867 1788 5.129980 TGCATCTCAAACAGAGTCAGGATAT 59.870 40.000 0.00 0.00 44.98 1.63
898 1822 0.109272 ACGTACTGACATGTCGCCTG 60.109 55.000 20.54 12.64 0.00 4.85
916 1840 0.391597 TGGAAGGGATCGGCGATTAC 59.608 55.000 24.81 18.92 0.00 1.89
949 1873 2.431683 GGCTTGGGAGACAGTGCA 59.568 61.111 0.00 0.00 33.79 4.57
953 1877 2.026822 AGTATTGTGGCTTGGGAGACAG 60.027 50.000 0.00 0.00 43.03 3.51
958 1882 3.754323 CGTTTAAGTATTGTGGCTTGGGA 59.246 43.478 0.00 0.00 0.00 4.37
1012 1936 1.067354 GCTCACCTTTGCTTTGGATGG 60.067 52.381 0.00 0.00 0.00 3.51
1015 1939 0.106268 TGGCTCACCTTTGCTTTGGA 60.106 50.000 0.00 0.00 36.63 3.53
1177 2102 2.128226 AGGGTTGCAGGGAGGGAT 59.872 61.111 0.00 0.00 0.00 3.85
1349 2283 3.522731 CGGCGAGTCTCCCTCCAG 61.523 72.222 0.00 0.00 36.82 3.86
1654 2588 2.035626 CCCTCACCAACCCGCAAT 59.964 61.111 0.00 0.00 0.00 3.56
1720 2654 2.607750 GCCTCCACCTCCCACTCA 60.608 66.667 0.00 0.00 0.00 3.41
1873 2807 3.318384 TTGGCCAGAGCAGCGGTA 61.318 61.111 5.11 0.00 42.56 4.02
2026 2960 3.691342 CGGTTGCCCTCGTGGAGA 61.691 66.667 4.76 0.00 35.39 3.71
2381 3315 2.020559 CGCGACGCAGCATTCTTC 59.979 61.111 21.35 0.00 36.85 2.87
2470 3404 2.037053 CTCGGCGATGAGGATGAGT 58.963 57.895 11.27 0.00 32.18 3.41
2500 3434 1.497278 CATGTCCTTGTGAACGCCG 59.503 57.895 0.00 0.00 0.00 6.46
2530 3464 2.749044 CCCAGCATTGCTCGCAGT 60.749 61.111 8.54 0.00 36.40 4.40
2592 3526 2.084101 TCATCGTCGTTGCGTTCGG 61.084 57.895 0.00 0.00 0.00 4.30
2719 3653 5.176590 GCTCAAGAACTAAGGCTAATCGATG 59.823 44.000 0.00 0.00 0.00 3.84
2730 3664 3.409026 ACACCCAGCTCAAGAACTAAG 57.591 47.619 0.00 0.00 0.00 2.18
2766 3700 2.029739 CACTGCATGAATCCACTGCAAA 60.030 45.455 0.00 0.00 44.59 3.68
2822 3756 8.143193 TGCACAATTGTCTTTAATTTCACATCT 58.857 29.630 8.48 0.00 0.00 2.90
2893 3828 6.314917 AGATCTAAAGCCTTTTCAGGGAAAA 58.685 36.000 0.00 4.31 41.21 2.29
3016 3960 5.120399 ACAACCAAACACGTTCTAGATGAA 58.880 37.500 0.00 0.00 0.00 2.57
3024 3968 4.099824 CCAAACTACAACCAAACACGTTC 58.900 43.478 0.00 0.00 0.00 3.95
3025 3969 3.757493 TCCAAACTACAACCAAACACGTT 59.243 39.130 0.00 0.00 0.00 3.99
3026 3970 3.345414 TCCAAACTACAACCAAACACGT 58.655 40.909 0.00 0.00 0.00 4.49
3039 3983 5.825679 ACAATGCAAGTACTGTTCCAAACTA 59.174 36.000 0.00 0.00 0.00 2.24
3063 4007 4.721274 TCAGGTTGGATTGAGATGGACATA 59.279 41.667 0.00 0.00 0.00 2.29
3077 4021 4.661222 TGTATTTCAGCAATCAGGTTGGA 58.339 39.130 0.00 0.00 38.29 3.53
3122 4066 0.961019 GATGCAGGCAACCAAACAGA 59.039 50.000 0.00 0.00 37.17 3.41
3249 4197 2.159014 CCATCACATTTGAATGGGCTGG 60.159 50.000 12.81 12.81 46.09 4.85
3252 4200 1.473788 GGCCATCACATTTGAATGGGC 60.474 52.381 19.23 19.23 42.80 5.36
3280 4228 2.743664 GCTGTTGTGCTGATCATGTGTA 59.256 45.455 0.00 0.00 0.00 2.90
3318 4267 7.441760 TCATTACATTGCTTGCTTTGTTTGATT 59.558 29.630 6.39 0.00 0.00 2.57
3386 4336 2.968574 TGGCCCTGCTCTTAATCTAGAG 59.031 50.000 0.00 0.00 43.66 2.43
3405 4355 1.277580 ACAGCAGGGAAGGAGGATGG 61.278 60.000 0.00 0.00 0.00 3.51
3462 4412 2.343758 GGCGAGACTTGTGCTGGA 59.656 61.111 0.00 0.00 0.00 3.86
3609 4560 0.613853 CCGGACTGGGACTGAAGGTA 60.614 60.000 0.00 0.00 0.00 3.08
3655 4606 1.153086 GCCGCCACAAGATCATCCT 60.153 57.895 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.