Multiple sequence alignment - TraesCS1B01G327000

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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 TraesCS1B01G327000 chr1B 100.000 3800 0 0 1 3800 553137253 553141052 0.000000e+00 7018.0
1 TraesCS1B01G327000 chr1B 97.333 750 19 1 2490 3238 579772946 579773695 0.000000e+00 1273.0
2 TraesCS1B01G327000 chr1B 84.148 1186 162 17 1147 2315 631824756 631825932 0.000000e+00 1125.0
3 TraesCS1B01G327000 chr1B 85.849 1060 134 9 1310 2362 637388658 637387608 0.000000e+00 1112.0
4 TraesCS1B01G327000 chr1B 85.900 922 123 5 1446 2360 637478371 637477450 0.000000e+00 976.0
5 TraesCS1B01G327000 chr1B 98.529 204 3 0 3597 3800 579774172 579774375 1.000000e-95 361.0
6 TraesCS1B01G327000 chr1D 92.362 1689 74 22 805 2490 410495157 410496793 0.000000e+00 2353.0
7 TraesCS1B01G327000 chr1D 84.219 1223 168 15 1136 2343 459818712 459817500 0.000000e+00 1166.0
8 TraesCS1B01G327000 chr1D 82.816 1193 167 18 1201 2378 462359215 462358046 0.000000e+00 1033.0
9 TraesCS1B01G327000 chr1D 87.989 741 80 6 1629 2362 410497200 410497938 0.000000e+00 867.0
10 TraesCS1B01G327000 chr1D 83.456 544 77 7 1842 2378 462312977 462312440 9.480000e-136 494.0
11 TraesCS1B01G327000 chr1D 86.813 455 40 7 3 441 410492315 410492765 1.230000e-134 490.0
12 TraesCS1B01G327000 chr1D 83.740 369 34 11 441 803 410492892 410493240 3.660000e-85 326.0
13 TraesCS1B01G327000 chr1A 91.790 1559 81 18 876 2430 506540794 506542309 0.000000e+00 2126.0
14 TraesCS1B01G327000 chr1A 86.947 475 49 7 441 910 506491030 506491496 4.350000e-144 521.0
15 TraesCS1B01G327000 chr1A 86.430 479 51 9 441 913 506477027 506477497 2.620000e-141 512.0
16 TraesCS1B01G327000 chr1A 87.559 426 35 5 3 411 506490452 506490876 9.550000e-131 477.0
17 TraesCS1B01G327000 chr1A 85.619 452 48 8 3 441 506476453 506476900 3.460000e-125 459.0
18 TraesCS1B01G327000 chr1A 94.776 134 7 0 670 803 506540659 506540792 3.850000e-50 209.0
19 TraesCS1B01G327000 chr4B 97.523 767 16 3 2475 3238 366940064 366940830 0.000000e+00 1308.0
20 TraesCS1B01G327000 chr4B 98.136 751 11 3 2490 3238 22220621 22221370 0.000000e+00 1306.0
21 TraesCS1B01G327000 chr4B 98.131 535 8 2 3267 3800 22221647 22222180 0.000000e+00 931.0
22 TraesCS1B01G327000 chr4B 95.545 202 9 0 3599 3800 366941350 366941551 1.320000e-84 324.0
23 TraesCS1B01G327000 chr3B 96.649 776 15 4 2793 3557 759110721 759109946 0.000000e+00 1279.0
24 TraesCS1B01G327000 chr3B 78.769 942 190 10 1297 2233 27035798 27036734 1.160000e-174 623.0
25 TraesCS1B01G327000 chr3B 96.805 313 10 0 2489 2801 759112451 759112139 1.210000e-144 523.0
26 TraesCS1B01G327000 chr3B 96.392 194 5 2 3607 3800 759109693 759109502 6.130000e-83 318.0
27 TraesCS1B01G327000 chr7A 90.714 840 74 4 2962 3799 713224228 713225065 0.000000e+00 1116.0
28 TraesCS1B01G327000 chr7A 80.425 659 103 14 3146 3800 190397860 190397224 2.660000e-131 479.0
29 TraesCS1B01G327000 chr7A 94.059 303 15 2 2508 2810 713223163 713223462 1.240000e-124 457.0
30 TraesCS1B01G327000 chr7A 91.571 261 21 1 2506 2766 102107102 102107361 3.610000e-95 359.0
31 TraesCS1B01G327000 chr7A 90.968 155 12 2 2810 2962 713223773 713223927 1.380000e-49 207.0
32 TraesCS1B01G327000 chr7A 85.000 80 9 3 3679 3755 66175222 66175143 1.130000e-10 78.7
33 TraesCS1B01G327000 chr7B 97.426 544 11 2 2709 3251 81308458 81307917 0.000000e+00 924.0
34 TraesCS1B01G327000 chr7B 78.617 622 106 13 3181 3796 11087072 11086472 1.660000e-103 387.0
35 TraesCS1B01G327000 chr7B 97.664 214 5 0 3587 3800 81307558 81307345 6.000000e-98 368.0
36 TraesCS1B01G327000 chr7B 96.739 184 6 0 2491 2674 81308642 81308459 1.330000e-79 307.0
37 TraesCS1B01G327000 chr5B 85.420 727 96 8 2809 3529 137280349 137281071 0.000000e+00 747.0
38 TraesCS1B01G327000 chr2A 82.804 756 110 16 2829 3572 650611090 650610343 0.000000e+00 658.0
39 TraesCS1B01G327000 chr4A 80.371 647 92 16 3158 3800 475909355 475908740 3.460000e-125 459.0
40 TraesCS1B01G327000 chr2D 83.846 390 52 9 3189 3571 590060138 590059753 1.000000e-95 361.0
41 TraesCS1B01G327000 chr5A 78.049 164 29 6 3610 3769 546232678 546232838 3.120000e-16 97.1
42 TraesCS1B01G327000 chr2B 80.952 105 13 4 3656 3755 544762368 544762470 4.070000e-10 76.8


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 TraesCS1B01G327000 chr1B 553137253 553141052 3799 False 7018.000000 7018 100.000000 1 3800 1 chr1B.!!$F1 3799
1 TraesCS1B01G327000 chr1B 631824756 631825932 1176 False 1125.000000 1125 84.148000 1147 2315 1 chr1B.!!$F2 1168
2 TraesCS1B01G327000 chr1B 637387608 637388658 1050 True 1112.000000 1112 85.849000 1310 2362 1 chr1B.!!$R1 1052
3 TraesCS1B01G327000 chr1B 637477450 637478371 921 True 976.000000 976 85.900000 1446 2360 1 chr1B.!!$R2 914
4 TraesCS1B01G327000 chr1B 579772946 579774375 1429 False 817.000000 1273 97.931000 2490 3800 2 chr1B.!!$F3 1310
5 TraesCS1B01G327000 chr1D 459817500 459818712 1212 True 1166.000000 1166 84.219000 1136 2343 1 chr1D.!!$R1 1207
6 TraesCS1B01G327000 chr1D 462358046 462359215 1169 True 1033.000000 1033 82.816000 1201 2378 1 chr1D.!!$R3 1177
7 TraesCS1B01G327000 chr1D 410492315 410497938 5623 False 1009.000000 2353 87.726000 3 2490 4 chr1D.!!$F1 2487
8 TraesCS1B01G327000 chr1D 462312440 462312977 537 True 494.000000 494 83.456000 1842 2378 1 chr1D.!!$R2 536
9 TraesCS1B01G327000 chr1A 506540659 506542309 1650 False 1167.500000 2126 93.283000 670 2430 2 chr1A.!!$F3 1760
10 TraesCS1B01G327000 chr1A 506490452 506491496 1044 False 499.000000 521 87.253000 3 910 2 chr1A.!!$F2 907
11 TraesCS1B01G327000 chr1A 506476453 506477497 1044 False 485.500000 512 86.024500 3 913 2 chr1A.!!$F1 910
12 TraesCS1B01G327000 chr4B 22220621 22222180 1559 False 1118.500000 1306 98.133500 2490 3800 2 chr4B.!!$F1 1310
13 TraesCS1B01G327000 chr4B 366940064 366941551 1487 False 816.000000 1308 96.534000 2475 3800 2 chr4B.!!$F2 1325
14 TraesCS1B01G327000 chr3B 759109502 759112451 2949 True 706.666667 1279 96.615333 2489 3800 3 chr3B.!!$R1 1311
15 TraesCS1B01G327000 chr3B 27035798 27036734 936 False 623.000000 623 78.769000 1297 2233 1 chr3B.!!$F1 936
16 TraesCS1B01G327000 chr7A 713223163 713225065 1902 False 593.333333 1116 91.913667 2508 3799 3 chr7A.!!$F2 1291
17 TraesCS1B01G327000 chr7A 190397224 190397860 636 True 479.000000 479 80.425000 3146 3800 1 chr7A.!!$R2 654
18 TraesCS1B01G327000 chr7B 81307345 81308642 1297 True 533.000000 924 97.276333 2491 3800 3 chr7B.!!$R2 1309
19 TraesCS1B01G327000 chr7B 11086472 11087072 600 True 387.000000 387 78.617000 3181 3796 1 chr7B.!!$R1 615
20 TraesCS1B01G327000 chr5B 137280349 137281071 722 False 747.000000 747 85.420000 2809 3529 1 chr5B.!!$F1 720
21 TraesCS1B01G327000 chr2A 650610343 650611090 747 True 658.000000 658 82.804000 2829 3572 1 chr2A.!!$R1 743
22 TraesCS1B01G327000 chr4A 475908740 475909355 615 True 459.000000 459 80.371000 3158 3800 1 chr4A.!!$R1 642

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
946 3021 0.100682 AGTCGTGTAGCCATAGCGTG 59.899 55.0 0.00 0.00 46.67 5.34 F
1771 3871 0.107017 GGGCTGTCATGTAGCATGGT 60.107 55.0 20.59 1.62 42.88 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 4651 0.388263 GGTGAAGGAGTCGTTCGGAC 60.388 60.0 18.07 12.44 46.45 4.79 R
3009 7172 1.355796 CGTTTTGCGGCGAGACCATA 61.356 55.0 12.98 0.00 39.03 2.74 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
55 56 2.489329 CAAAGAGAAACATGGTCGCCAT 59.511 45.455 5.65 5.65 46.37 4.40
64 65 2.588877 GGTCGCCATCCACCATCG 60.589 66.667 0.00 0.00 32.33 3.84
69 70 2.588877 CCATCCACCATCGCCGAC 60.589 66.667 0.00 0.00 0.00 4.79
71 72 1.592669 CATCCACCATCGCCGACTC 60.593 63.158 0.00 0.00 0.00 3.36
96 97 0.881159 AATCGTTGCGTTCCGAACCA 60.881 50.000 5.67 2.50 36.57 3.67
120 121 2.145397 ATCGTGCCACTAGGAGAAGA 57.855 50.000 0.00 0.00 36.89 2.87
123 124 2.631062 TCGTGCCACTAGGAGAAGAAAA 59.369 45.455 0.00 0.00 36.89 2.29
130 131 5.584251 GCCACTAGGAGAAGAAAAATGAGAG 59.416 44.000 0.00 0.00 36.89 3.20
175 176 3.583882 AAACCGTGGCCCATGGAGG 62.584 63.158 28.89 12.06 42.73 4.30
212 213 1.354337 CCACTCCTTCGTCACATGCG 61.354 60.000 0.00 0.00 0.00 4.73
252 253 7.115378 GTGAGGAACTATCAAATTGCTTTTGTG 59.885 37.037 10.97 6.91 42.14 3.33
264 265 7.437267 CAAATTGCTTTTGTGGATCATCTATCC 59.563 37.037 0.00 0.00 43.70 2.59
285 286 5.575157 TCCTAGATCTTAGGTAGCTCATGG 58.425 45.833 0.00 0.00 36.16 3.66
300 301 4.039004 AGCTCATGGACATCATCTAGTGAC 59.961 45.833 0.00 0.00 40.28 3.67
322 326 2.932130 GAAGGCATCCAGGAGGTCGC 62.932 65.000 2.38 0.00 35.89 5.19
332 340 3.760035 GAGGTCGCCCGCAGAAGA 61.760 66.667 0.00 0.00 35.12 2.87
335 343 2.357034 GTCGCCCGCAGAAGACAA 60.357 61.111 0.00 0.00 34.09 3.18
340 348 1.376037 CCCGCAGAAGACAAGGGTC 60.376 63.158 0.00 0.00 44.66 4.46
364 372 1.083401 CGCAGTCGCACACAAAGTC 60.083 57.895 0.00 0.00 38.40 3.01
411 432 6.315091 TGTGTGAGAGAGAGTAGTGTTAAC 57.685 41.667 0.00 0.00 0.00 2.01
414 435 5.530171 TGTGAGAGAGAGTAGTGTTAACGTT 59.470 40.000 5.88 5.88 0.00 3.99
416 437 5.761726 TGAGAGAGAGTAGTGTTAACGTTGA 59.238 40.000 11.99 0.00 0.00 3.18
417 438 5.999721 AGAGAGAGTAGTGTTAACGTTGAC 58.000 41.667 15.70 15.70 0.00 3.18
418 439 5.530171 AGAGAGAGTAGTGTTAACGTTGACA 59.470 40.000 20.62 20.62 0.00 3.58
423 444 2.557317 AGTGTTAACGTTGACAGGTGG 58.443 47.619 24.33 0.00 0.00 4.61
424 445 1.003223 GTGTTAACGTTGACAGGTGGC 60.003 52.381 24.33 10.08 0.00 5.01
448 596 6.428295 CCCCACACCCAACTTAAATAGATAA 58.572 40.000 0.00 0.00 0.00 1.75
450 598 7.563556 CCCCACACCCAACTTAAATAGATAAAT 59.436 37.037 0.00 0.00 0.00 1.40
480 628 2.096119 CGGTTAAGTAAAGTGGTTGCGG 60.096 50.000 0.00 0.00 0.00 5.69
481 629 2.880268 GGTTAAGTAAAGTGGTTGCGGT 59.120 45.455 0.00 0.00 0.00 5.68
526 674 6.549364 TGTGATGGTTTTATGATATTCACCCC 59.451 38.462 0.00 0.00 0.00 4.95
527 675 6.015434 GTGATGGTTTTATGATATTCACCCCC 60.015 42.308 0.00 0.00 0.00 5.40
550 699 6.838612 CCCTTTTTAGGAAATACCATCATGGA 59.161 38.462 11.90 0.00 40.96 3.41
605 756 4.936685 ATTAAGAAAGCCAGAGGGTCTT 57.063 40.909 0.00 0.00 33.17 3.01
618 769 2.231215 GGGTCTTCATGACTCCATCG 57.769 55.000 0.00 0.00 44.74 3.84
625 776 0.857287 CATGACTCCATCGCATGACG 59.143 55.000 0.00 0.00 41.35 4.35
648 801 4.096984 GCTCACCATGTTTAGCTAAAGCAT 59.903 41.667 19.16 19.53 45.16 3.79
649 802 5.731686 GCTCACCATGTTTAGCTAAAGCATC 60.732 44.000 19.16 8.23 45.16 3.91
650 803 4.640201 TCACCATGTTTAGCTAAAGCATCC 59.360 41.667 19.16 7.87 45.16 3.51
651 804 3.954258 ACCATGTTTAGCTAAAGCATCCC 59.046 43.478 19.16 7.17 45.16 3.85
857 2932 2.494073 CTCCTACGGCTTCCTATCCATC 59.506 54.545 0.00 0.00 0.00 3.51
943 3018 0.381089 ACGAGTCGTGTAGCCATAGC 59.619 55.000 19.16 0.00 39.18 2.97
944 3019 0.657659 CGAGTCGTGTAGCCATAGCG 60.658 60.000 3.82 0.00 46.67 4.26
945 3020 0.381089 GAGTCGTGTAGCCATAGCGT 59.619 55.000 0.00 0.00 46.67 5.07
946 3021 0.100682 AGTCGTGTAGCCATAGCGTG 59.899 55.000 0.00 0.00 46.67 5.34
947 3022 1.226859 TCGTGTAGCCATAGCGTGC 60.227 57.895 0.00 0.00 46.67 5.34
948 3023 1.226974 CGTGTAGCCATAGCGTGCT 60.227 57.895 0.00 0.00 46.67 4.40
949 3024 1.482621 CGTGTAGCCATAGCGTGCTG 61.483 60.000 4.25 0.00 46.67 4.41
950 3025 1.521457 TGTAGCCATAGCGTGCTGC 60.521 57.895 4.25 0.00 46.67 5.25
974 3049 4.202020 CGTGCTGGCCGTCTATATATACAT 60.202 45.833 0.00 0.00 0.00 2.29
1024 3100 7.039504 TGAGAAATAAAGCAAAAGCAATCCTCT 60.040 33.333 0.00 0.00 0.00 3.69
1041 3117 1.227883 CTCTCCGGCCGTCTAGCTA 60.228 63.158 26.12 2.72 0.00 3.32
1072 3148 1.795768 GAGCAGTCGATCAACACCAA 58.204 50.000 0.00 0.00 0.00 3.67
1073 3149 2.143122 GAGCAGTCGATCAACACCAAA 58.857 47.619 0.00 0.00 0.00 3.28
1074 3150 2.146342 AGCAGTCGATCAACACCAAAG 58.854 47.619 0.00 0.00 0.00 2.77
1075 3151 1.400242 GCAGTCGATCAACACCAAAGC 60.400 52.381 0.00 0.00 0.00 3.51
1076 3152 2.146342 CAGTCGATCAACACCAAAGCT 58.854 47.619 0.00 0.00 0.00 3.74
1077 3153 2.549754 CAGTCGATCAACACCAAAGCTT 59.450 45.455 0.00 0.00 0.00 3.74
1078 3154 2.549754 AGTCGATCAACACCAAAGCTTG 59.450 45.455 0.00 0.00 0.00 4.01
1079 3155 1.266718 TCGATCAACACCAAAGCTTGC 59.733 47.619 0.00 0.00 0.00 4.01
1080 3156 1.689959 GATCAACACCAAAGCTTGCG 58.310 50.000 0.00 0.00 0.00 4.85
1081 3157 0.318955 ATCAACACCAAAGCTTGCGC 60.319 50.000 0.00 0.00 0.00 6.09
1103 3179 2.167398 CTGATTGTCCGGTGGGTCGT 62.167 60.000 0.00 0.00 33.83 4.34
1104 3180 1.447314 GATTGTCCGGTGGGTCGTC 60.447 63.158 0.00 0.00 33.83 4.20
1105 3181 3.291101 ATTGTCCGGTGGGTCGTCG 62.291 63.158 0.00 0.00 33.83 5.12
1107 3183 4.712425 GTCCGGTGGGTCGTCGTG 62.712 72.222 0.00 0.00 33.83 4.35
1109 3185 3.364441 CCGGTGGGTCGTCGTGTA 61.364 66.667 0.00 0.00 0.00 2.90
1112 3188 1.373371 GGTGGGTCGTCGTGTAACC 60.373 63.158 0.00 0.00 0.00 2.85
1115 3191 4.876652 GGTCGTCGTGTAACCCTC 57.123 61.111 0.00 0.00 0.00 4.30
1116 3192 1.154150 GGTCGTCGTGTAACCCTCG 60.154 63.158 0.00 0.00 0.00 4.63
1117 3193 1.154150 GTCGTCGTGTAACCCTCGG 60.154 63.158 0.00 0.00 0.00 4.63
1118 3194 2.505557 CGTCGTGTAACCCTCGGC 60.506 66.667 0.00 0.00 0.00 5.54
1119 3195 2.505557 GTCGTGTAACCCTCGGCG 60.506 66.667 0.00 0.00 0.00 6.46
1120 3196 2.985282 TCGTGTAACCCTCGGCGT 60.985 61.111 6.85 0.00 0.00 5.68
1121 3197 2.807895 CGTGTAACCCTCGGCGTG 60.808 66.667 6.85 3.87 0.00 5.34
1122 3198 2.652530 GTGTAACCCTCGGCGTGA 59.347 61.111 10.96 0.00 0.00 4.35
1144 3220 4.498520 ACGGTGCGATCTCTGCGG 62.499 66.667 0.00 0.00 34.24 5.69
1544 3644 2.034221 GACAGCGGGGCTTTCCTT 59.966 61.111 0.00 0.00 36.40 3.36
1748 3848 2.611225 GGAACCTCAAGATCTGCGAT 57.389 50.000 0.00 0.00 0.00 4.58
1771 3871 0.107017 GGGCTGTCATGTAGCATGGT 60.107 55.000 20.59 1.62 42.88 3.55
1956 4056 1.134401 TGGATCACCTCAGCGAAATCC 60.134 52.381 0.00 0.00 37.04 3.01
1982 4082 0.537143 TTCTTGGCACGGCAGACATT 60.537 50.000 0.00 0.00 0.00 2.71
2025 4125 2.125106 GGCGGCTACCAAGTGGAG 60.125 66.667 3.83 0.00 38.94 3.86
2129 4229 1.446272 GTTCGAGGTCTTGAGCGGG 60.446 63.158 0.00 0.00 0.00 6.13
2343 4463 2.902705 AAGCAGGAGTTGTTCGTGTA 57.097 45.000 0.00 0.00 42.33 2.90
2371 4491 3.997681 CCACCACACACATATTGTAACGA 59.002 43.478 0.00 0.00 35.67 3.85
2396 4517 3.110447 TGCAATTTGGTTTCTTGCTCC 57.890 42.857 7.85 0.00 44.29 4.70
2416 4537 5.656859 GCTCCTAATTTGGGGTTCAACTAAT 59.343 40.000 7.67 0.00 34.67 1.73
2466 4587 3.438297 ACTACTATGCTTGCCGTGTAG 57.562 47.619 11.42 11.42 35.07 2.74
2530 4651 5.696724 CAGTCGGCAGGATTTTAGTAATAGG 59.303 44.000 0.00 0.00 0.00 2.57
3001 7164 1.611491 TGGAACAAAATTCACCTCGCC 59.389 47.619 0.00 0.00 31.92 5.54
3009 7172 0.839946 ATTCACCTCGCCTGGCTATT 59.160 50.000 17.92 0.00 0.00 1.73
3156 7324 2.257207 CTTTGACAGGAGTGGGAGGTA 58.743 52.381 0.00 0.00 0.00 3.08
3206 7375 9.565090 TTCTATGTGAAGAGCATGCTAATTTAT 57.435 29.630 22.74 13.22 0.00 1.40
3238 7408 4.424626 AGCTGATAACATGTGTACAGACG 58.575 43.478 22.00 0.00 0.00 4.18
3251 7421 6.033966 TGTGTACAGACGCTATGATAACTTG 58.966 40.000 0.00 0.00 36.98 3.16
3252 7422 5.459107 GTGTACAGACGCTATGATAACTTGG 59.541 44.000 0.00 0.00 33.03 3.61
3290 7708 6.759356 TGTTGTAATACATCACCGATAACTGG 59.241 38.462 0.40 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.579410 ACGTGAACCTTTTGCCCTAT 57.421 45.000 0.00 0.00 0.00 2.57
11 12 2.477754 CGGTTTCTCCTTTACGTGAACC 59.522 50.000 0.00 0.00 0.00 3.62
55 56 3.458163 GGAGTCGGCGATGGTGGA 61.458 66.667 14.79 0.00 0.00 4.02
69 70 2.476185 GGAACGCAACGATTCATTGGAG 60.476 50.000 0.00 0.00 0.00 3.86
71 72 1.895051 GGAACGCAACGATTCATTGG 58.105 50.000 0.00 0.00 0.00 3.16
120 121 8.477419 TTGTCTAAATGGTTCCTCTCATTTTT 57.523 30.769 6.60 0.00 41.83 1.94
123 124 7.461749 TCTTTGTCTAAATGGTTCCTCTCATT 58.538 34.615 0.00 0.00 35.37 2.57
130 131 5.461526 GCACTTCTTTGTCTAAATGGTTCC 58.538 41.667 0.00 0.00 0.00 3.62
175 176 5.391312 AGTGGATGTAGGCAAAATTTGTC 57.609 39.130 1.48 1.48 34.90 3.18
212 213 1.369091 CCTCACCCTGCGCAATGTAC 61.369 60.000 13.05 0.00 0.00 2.90
224 225 4.273318 AGCAATTTGATAGTTCCTCACCC 58.727 43.478 0.00 0.00 0.00 4.61
264 265 6.007076 TGTCCATGAGCTACCTAAGATCTAG 58.993 44.000 0.00 0.00 41.41 2.43
271 272 5.150715 AGATGATGTCCATGAGCTACCTAA 58.849 41.667 0.00 0.00 35.17 2.69
275 276 5.242615 TCACTAGATGATGTCCATGAGCTAC 59.757 44.000 0.00 0.00 35.17 3.58
285 286 4.791411 GCCTTCTCGTCACTAGATGATGTC 60.791 50.000 0.00 0.00 43.81 3.06
300 301 1.333636 ACCTCCTGGATGCCTTCTCG 61.334 60.000 0.00 0.00 37.04 4.04
322 326 1.376037 GACCCTTGTCTTCTGCGGG 60.376 63.158 0.00 0.00 38.53 6.13
349 357 0.928229 GAACGACTTTGTGTGCGACT 59.072 50.000 0.00 0.00 0.00 4.18
360 368 3.328382 TCCCATTTGATCGAACGACTT 57.672 42.857 0.00 0.00 0.00 3.01
364 372 3.058914 GCCTATTCCCATTTGATCGAACG 60.059 47.826 0.00 0.00 0.00 3.95
411 432 4.263572 TGGGGCCACCTGTCAACG 62.264 66.667 0.20 0.00 41.11 4.10
414 435 3.884774 GTGTGGGGCCACCTGTCA 61.885 66.667 0.20 1.26 45.63 3.58
423 444 1.639722 ATTTAAGTTGGGTGTGGGGC 58.360 50.000 0.00 0.00 0.00 5.80
424 445 4.310022 TCTATTTAAGTTGGGTGTGGGG 57.690 45.455 0.00 0.00 0.00 4.96
448 596 7.863877 CCACTTTACTTAACCGCTACAAAAATT 59.136 33.333 0.00 0.00 0.00 1.82
450 598 6.318396 ACCACTTTACTTAACCGCTACAAAAA 59.682 34.615 0.00 0.00 0.00 1.94
463 611 6.690194 TTTAAACCGCAACCACTTTACTTA 57.310 33.333 0.00 0.00 0.00 2.24
464 612 5.579564 TTTAAACCGCAACCACTTTACTT 57.420 34.783 0.00 0.00 0.00 2.24
480 628 7.092716 TCACATCTACGTCTAGGGTTTTAAAC 58.907 38.462 0.00 0.00 0.00 2.01
481 629 7.230849 TCACATCTACGTCTAGGGTTTTAAA 57.769 36.000 0.00 0.00 0.00 1.52
526 674 7.014615 CCTCCATGATGGTATTTCCTAAAAAGG 59.985 40.741 11.87 2.06 39.03 3.11
527 675 7.561356 ACCTCCATGATGGTATTTCCTAAAAAG 59.439 37.037 11.87 0.00 39.03 2.27
565 715 8.232913 TCTTAATTCCTGTAATTGTTATGCCC 57.767 34.615 0.00 0.00 38.29 5.36
592 743 0.908198 GTCATGAAGACCCTCTGGCT 59.092 55.000 0.00 0.00 41.56 4.75
605 756 1.536709 CGTCATGCGATGGAGTCATGA 60.537 52.381 3.85 0.00 42.79 3.07
618 769 0.523072 AAACATGGTGAGCGTCATGC 59.477 50.000 0.00 0.00 43.12 4.06
625 776 3.440173 TGCTTTAGCTAAACATGGTGAGC 59.560 43.478 12.72 12.72 42.66 4.26
648 801 3.895704 AAAACCTAAAAGAGCAGGGGA 57.104 42.857 0.00 0.00 36.15 4.81
649 802 3.444034 GCTAAAACCTAAAAGAGCAGGGG 59.556 47.826 0.00 0.00 36.15 4.79
650 803 3.444034 GGCTAAAACCTAAAAGAGCAGGG 59.556 47.826 0.00 0.00 36.15 4.45
651 804 4.336280 AGGCTAAAACCTAAAAGAGCAGG 58.664 43.478 0.00 0.00 38.67 4.85
658 811 7.039504 TCGTCTTAGAGAGGCTAAAACCTAAAA 60.040 37.037 0.00 0.00 41.32 1.52
659 812 6.435277 TCGTCTTAGAGAGGCTAAAACCTAAA 59.565 38.462 0.00 0.00 41.32 1.85
660 813 5.948162 TCGTCTTAGAGAGGCTAAAACCTAA 59.052 40.000 0.00 0.00 41.32 2.69
661 814 5.503927 TCGTCTTAGAGAGGCTAAAACCTA 58.496 41.667 0.00 0.00 41.32 3.08
662 815 4.342359 TCGTCTTAGAGAGGCTAAAACCT 58.658 43.478 0.00 0.00 45.04 3.50
663 816 4.715527 TCGTCTTAGAGAGGCTAAAACC 57.284 45.455 0.00 0.00 38.56 3.27
664 817 4.504826 GCATCGTCTTAGAGAGGCTAAAAC 59.495 45.833 9.71 0.00 40.51 2.43
724 883 0.376152 CCAGCACGTCAATCATGAGC 59.624 55.000 0.09 0.00 35.88 4.26
735 894 2.029964 CCGTTACCACCAGCACGT 59.970 61.111 0.00 0.00 0.00 4.49
790 950 2.159747 CGTCGTGTGACTTAGTCGATCA 60.160 50.000 7.92 4.52 43.21 2.92
857 2932 2.222678 GCGTCATATTGCTCTCATGGTG 59.777 50.000 0.00 0.00 0.00 4.17
938 3013 4.228097 GCACGGCAGCACGCTATG 62.228 66.667 0.00 0.00 41.91 2.23
939 3014 4.457496 AGCACGGCAGCACGCTAT 62.457 61.111 0.81 0.00 41.91 2.97
950 3025 0.885879 TATATAGACGGCCAGCACGG 59.114 55.000 2.24 0.00 35.23 4.94
1024 3100 0.178998 AATAGCTAGACGGCCGGAGA 60.179 55.000 31.76 12.71 0.00 3.71
1049 3125 1.446099 GTTGATCGACTGCTCGGCA 60.446 57.895 5.79 0.00 40.58 5.69
1075 3151 1.136147 GGACAATCAGCAGCGCAAG 59.864 57.895 11.47 2.01 43.44 4.01
1076 3152 2.679934 CGGACAATCAGCAGCGCAA 61.680 57.895 11.47 0.00 0.00 4.85
1077 3153 3.120385 CGGACAATCAGCAGCGCA 61.120 61.111 11.47 0.00 0.00 6.09
1078 3154 3.869272 CCGGACAATCAGCAGCGC 61.869 66.667 0.00 0.00 0.00 5.92
1079 3155 2.434884 ACCGGACAATCAGCAGCG 60.435 61.111 9.46 0.00 0.00 5.18
1080 3156 2.401766 CCACCGGACAATCAGCAGC 61.402 63.158 9.46 0.00 0.00 5.25
1081 3157 1.746615 CCCACCGGACAATCAGCAG 60.747 63.158 9.46 0.00 0.00 4.24
1082 3158 2.350895 CCCACCGGACAATCAGCA 59.649 61.111 9.46 0.00 0.00 4.41
1103 3179 2.985282 ACGCCGAGGGTTACACGA 60.985 61.111 0.00 0.00 0.00 4.35
1104 3180 2.807895 CACGCCGAGGGTTACACG 60.808 66.667 0.00 0.00 0.00 4.49
1105 3181 1.735559 GTCACGCCGAGGGTTACAC 60.736 63.158 0.00 0.00 0.00 2.90
1106 3182 2.652530 GTCACGCCGAGGGTTACA 59.347 61.111 0.00 0.00 0.00 2.41
1107 3183 2.125793 GGTCACGCCGAGGGTTAC 60.126 66.667 0.00 0.00 0.00 2.50
1108 3184 2.283388 AGGTCACGCCGAGGGTTA 60.283 61.111 0.00 0.00 43.70 2.85
1109 3185 3.692406 GAGGTCACGCCGAGGGTT 61.692 66.667 0.00 0.00 43.70 4.11
1144 3220 3.883489 CCCCATATTTCTCCGAGGAAAAC 59.117 47.826 0.00 0.00 38.46 2.43
1544 3644 1.228831 CCCCACAAACTCCATGGCA 60.229 57.895 6.96 0.00 31.66 4.92
1748 3848 0.909133 TGCTACATGACAGCCCCAGA 60.909 55.000 17.46 0.89 38.29 3.86
1956 4056 1.672356 CCGTGCCAAGAAGGTCCAG 60.672 63.158 0.00 0.00 40.61 3.86
1982 4082 1.033746 CGTAGCCCGACCACTCCTTA 61.034 60.000 0.00 0.00 39.56 2.69
2018 4118 1.630878 CTTCCTAGTTGGCCTCCACTT 59.369 52.381 3.32 0.00 30.78 3.16
2025 4125 2.087646 CAGAAAGCTTCCTAGTTGGCC 58.912 52.381 0.00 0.00 35.26 5.36
2343 4463 4.263462 ACAATATGTGTGTGGTGGTGATCT 60.263 41.667 0.00 0.00 39.72 2.75
2371 4491 3.494251 GCAAGAAACCAAATTGCAATCGT 59.506 39.130 13.38 6.67 46.64 3.73
2440 4561 2.102588 CGGCAAGCATAGTAGTACCCTT 59.897 50.000 0.00 0.00 0.00 3.95
2441 4562 1.687123 CGGCAAGCATAGTAGTACCCT 59.313 52.381 0.00 0.00 0.00 4.34
2443 4564 2.159142 ACACGGCAAGCATAGTAGTACC 60.159 50.000 0.00 0.00 0.00 3.34
2444 4565 3.160777 ACACGGCAAGCATAGTAGTAC 57.839 47.619 0.00 0.00 0.00 2.73
2445 4566 3.317149 CCTACACGGCAAGCATAGTAGTA 59.683 47.826 12.61 0.00 0.00 1.82
2446 4567 2.100916 CCTACACGGCAAGCATAGTAGT 59.899 50.000 12.61 0.00 0.00 2.73
2447 4568 2.361119 TCCTACACGGCAAGCATAGTAG 59.639 50.000 8.90 8.90 0.00 2.57
2448 4569 2.100252 GTCCTACACGGCAAGCATAGTA 59.900 50.000 0.00 0.00 0.00 1.82
2449 4570 1.134788 GTCCTACACGGCAAGCATAGT 60.135 52.381 0.00 0.00 0.00 2.12
2466 4587 8.339714 TCGAATTTACAAATATTTGATCCGTCC 58.660 33.333 30.18 14.08 40.55 4.79
2530 4651 0.388263 GGTGAAGGAGTCGTTCGGAC 60.388 60.000 18.07 12.44 46.45 4.79
2775 4896 7.977293 GCTTTAATAATCCCGTAAAAATGGTGT 59.023 33.333 0.00 0.00 0.00 4.16
3001 7164 1.670087 CGGCGAGACCATAATAGCCAG 60.670 57.143 0.00 0.00 44.34 4.85
3009 7172 1.355796 CGTTTTGCGGCGAGACCATA 61.356 55.000 12.98 0.00 39.03 2.74
3156 7324 2.642171 TCAGGGGTATGGTCTCAACT 57.358 50.000 0.00 0.00 0.00 3.16
3206 7375 6.319405 ACACATGTTATCAGCTAAATGATGCA 59.681 34.615 0.00 0.00 40.16 3.96
3579 8000 2.751436 CAACATGCACCCCCTCCG 60.751 66.667 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.