Multiple sequence alignment - TraesCS1A01G347600

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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 TraesCS1A01G347600 chr1A 100.000 3910 0 0 1 3910 533444241 533448150 0.000000e+00 7221
1 TraesCS1A01G347600 chr1A 93.927 247 15 0 652 898 533439657 533439903 1.330000e-99 374
2 TraesCS1A01G347600 chr1A 76.453 671 130 23 2059 2721 533257884 533257234 4.840000e-89 339
3 TraesCS1A01G347600 chr1A 75.070 710 141 24 2016 2719 533265414 533264735 8.210000e-77 298
4 TraesCS1A01G347600 chr1B 95.458 2510 87 13 1401 3898 591107675 591110169 0.000000e+00 3978
5 TraesCS1A01G347600 chr1B 78.533 750 133 21 135 868 557407464 557408201 5.920000e-128 468
6 TraesCS1A01G347600 chr1B 74.366 710 150 23 2016 2721 589920485 589919804 1.380000e-69 274
7 TraesCS1A01G347600 chr1D 94.003 2568 86 36 1382 3910 436187345 436189883 0.000000e+00 3827
8 TraesCS1A01G347600 chr1D 91.847 417 24 5 901 1316 436186860 436187267 1.220000e-159 573
9 TraesCS1A01G347600 chr1D 76.444 675 127 25 2051 2721 436098021 436097375 1.740000e-88 337
10 TraesCS1A01G347600 chr6A 95.419 895 33 3 1 889 163150481 163151373 0.000000e+00 1419
11 TraesCS1A01G347600 chr6A 95.142 247 12 0 652 898 163145896 163146142 1.320000e-104 390
12 TraesCS1A01G347600 chr7D 92.062 907 53 6 1 901 611636337 611635444 0.000000e+00 1258
13 TraesCS1A01G347600 chr7D 93.496 246 16 0 653 898 611640922 611640677 2.220000e-97 366
14 TraesCS1A01G347600 chr7D 75.597 377 78 12 2395 2764 48356818 48357187 1.440000e-39 174
15 TraesCS1A01G347600 chr3B 91.704 904 68 2 1 898 43603188 43604090 0.000000e+00 1247
16 TraesCS1A01G347600 chr3B 91.602 905 68 4 1 898 829498207 829497304 0.000000e+00 1243
17 TraesCS1A01G347600 chr3A 91.481 763 58 2 143 899 99480863 99481624 0.000000e+00 1042
18 TraesCS1A01G347600 chr3A 92.517 147 11 0 1 147 99406014 99406160 1.100000e-50 211
19 TraesCS1A01G347600 chr7B 85.888 907 98 8 3 901 608917448 608916564 0.000000e+00 939
20 TraesCS1A01G347600 chr2B 84.402 936 114 13 3 912 79683570 79682641 0.000000e+00 891
21 TraesCS1A01G347600 chr2B 73.462 1089 212 59 1693 2750 6178985 6180027 4.840000e-89 339
22 TraesCS1A01G347600 chr3D 88.941 642 61 3 3 638 603732459 603731822 0.000000e+00 784
23 TraesCS1A01G347600 chr3D 76.524 328 75 2 2397 2723 387709411 387709085 1.120000e-40 178
24 TraesCS1A01G347600 chr2D 78.636 557 97 19 2202 2750 5268030 5268572 2.240000e-92 350
25 TraesCS1A01G347600 chr5D 75.645 698 137 30 2053 2732 65009539 65010221 2.270000e-82 316
26 TraesCS1A01G347600 chr7A 76.864 389 72 16 2385 2764 51091523 51091902 1.840000e-48 204
27 TraesCS1A01G347600 chr7A 76.533 375 72 14 2398 2764 51202348 51202714 1.430000e-44 191


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 TraesCS1A01G347600 chr1A 533444241 533448150 3909 False 7221 7221 100.000 1 3910 1 chr1A.!!$F2 3909
1 TraesCS1A01G347600 chr1A 533257234 533257884 650 True 339 339 76.453 2059 2721 1 chr1A.!!$R1 662
2 TraesCS1A01G347600 chr1A 533264735 533265414 679 True 298 298 75.070 2016 2719 1 chr1A.!!$R2 703
3 TraesCS1A01G347600 chr1B 591107675 591110169 2494 False 3978 3978 95.458 1401 3898 1 chr1B.!!$F2 2497
4 TraesCS1A01G347600 chr1B 557407464 557408201 737 False 468 468 78.533 135 868 1 chr1B.!!$F1 733
5 TraesCS1A01G347600 chr1B 589919804 589920485 681 True 274 274 74.366 2016 2721 1 chr1B.!!$R1 705
6 TraesCS1A01G347600 chr1D 436186860 436189883 3023 False 2200 3827 92.925 901 3910 2 chr1D.!!$F1 3009
7 TraesCS1A01G347600 chr1D 436097375 436098021 646 True 337 337 76.444 2051 2721 1 chr1D.!!$R1 670
8 TraesCS1A01G347600 chr6A 163150481 163151373 892 False 1419 1419 95.419 1 889 1 chr6A.!!$F2 888
9 TraesCS1A01G347600 chr7D 611635444 611636337 893 True 1258 1258 92.062 1 901 1 chr7D.!!$R1 900
10 TraesCS1A01G347600 chr3B 43603188 43604090 902 False 1247 1247 91.704 1 898 1 chr3B.!!$F1 897
11 TraesCS1A01G347600 chr3B 829497304 829498207 903 True 1243 1243 91.602 1 898 1 chr3B.!!$R1 897
12 TraesCS1A01G347600 chr3A 99480863 99481624 761 False 1042 1042 91.481 143 899 1 chr3A.!!$F2 756
13 TraesCS1A01G347600 chr7B 608916564 608917448 884 True 939 939 85.888 3 901 1 chr7B.!!$R1 898
14 TraesCS1A01G347600 chr2B 79682641 79683570 929 True 891 891 84.402 3 912 1 chr2B.!!$R1 909
15 TraesCS1A01G347600 chr2B 6178985 6180027 1042 False 339 339 73.462 1693 2750 1 chr2B.!!$F1 1057
16 TraesCS1A01G347600 chr3D 603731822 603732459 637 True 784 784 88.941 3 638 1 chr3D.!!$R2 635
17 TraesCS1A01G347600 chr2D 5268030 5268572 542 False 350 350 78.636 2202 2750 1 chr2D.!!$F1 548
18 TraesCS1A01G347600 chr5D 65009539 65010221 682 False 316 316 75.645 2053 2732 1 chr5D.!!$F1 679

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
675 701 0.674895 ACAGAATCGCAGCAACTCCC 60.675 55.0 0.00 0.0 0.00 4.30 F
1365 1395 0.030369 ATCTCACCGCGAATACCGAC 59.970 55.0 8.23 0.0 41.76 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1774 2.044555 CACCGAGCGGAGGTAGTCA 61.045 63.158 16.83 0.0 40.59 3.41 R
3087 3216 0.792640 GCTGTGTGATGTTGAGACCG 59.207 55.000 0.00 0.0 0.00 4.79 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
65 66 1.537397 AGACTGCTCTGCCCTTCCA 60.537 57.895 0.00 0.00 0.00 3.53
299 316 2.342279 CTTTGGCGGACGAGGTGA 59.658 61.111 0.00 0.00 0.00 4.02
393 416 2.124570 GATCGTGGCCTGCACCAT 60.125 61.111 3.32 0.00 43.01 3.55
423 446 3.073735 CGCCAGGGAGAGCTCTGT 61.074 66.667 23.91 1.98 41.23 3.41
507 530 1.134340 TCAACCAAACGCAGGTACACT 60.134 47.619 0.00 0.00 38.76 3.55
675 701 0.674895 ACAGAATCGCAGCAACTCCC 60.675 55.000 0.00 0.00 0.00 4.30
685 711 2.280524 CAACTCCCCGCGTCACAA 60.281 61.111 4.92 0.00 0.00 3.33
745 771 2.175202 GAGGAAGAAGGAGCACAGAGA 58.825 52.381 0.00 0.00 0.00 3.10
920 949 6.735694 GCAAATCAACACCACTTGTATTGACT 60.736 38.462 0.00 0.00 37.51 3.41
921 950 6.959639 AATCAACACCACTTGTATTGACTT 57.040 33.333 0.00 0.00 37.51 3.01
922 951 6.959639 ATCAACACCACTTGTATTGACTTT 57.040 33.333 0.00 0.00 37.51 2.66
923 952 6.767524 TCAACACCACTTGTATTGACTTTT 57.232 33.333 0.00 0.00 37.51 2.27
964 993 2.347490 CGGGTCCAACCACTCAGG 59.653 66.667 0.00 0.00 41.02 3.86
987 1016 2.096318 TCGCGTTTAAAATGAACCGACC 60.096 45.455 5.77 0.00 30.48 4.79
1008 1037 2.804212 CGTCCGTCCCACTAGTGTTTTT 60.804 50.000 21.18 0.00 0.00 1.94
1047 1076 2.431057 ACCTCGGTGATGATCTGTAACC 59.569 50.000 0.00 0.00 0.00 2.85
1077 1106 3.134574 TGTGACGGTATTTGAAAGCCT 57.865 42.857 0.00 0.00 0.00 4.58
1079 1108 3.886505 TGTGACGGTATTTGAAAGCCTTT 59.113 39.130 0.00 0.00 0.00 3.11
1080 1109 4.226761 GTGACGGTATTTGAAAGCCTTTG 58.773 43.478 0.00 0.00 0.00 2.77
1093 1122 5.533154 TGAAAGCCTTTGTTTTTAGGATCGA 59.467 36.000 0.00 0.00 33.13 3.59
1095 1124 7.392113 TGAAAGCCTTTGTTTTTAGGATCGATA 59.608 33.333 0.00 0.00 33.13 2.92
1099 1128 8.190784 AGCCTTTGTTTTTAGGATCGATATTTG 58.809 33.333 0.00 0.00 33.13 2.32
1129 1158 2.735151 AGCCCTAACCCTAAATGTTGC 58.265 47.619 0.00 0.00 0.00 4.17
1230 1260 3.435671 CCACCGGAATACAAGTTTCAGAC 59.564 47.826 9.46 0.00 0.00 3.51
1257 1287 4.379243 CCCGCCGCAAGACTCTGT 62.379 66.667 0.00 0.00 43.02 3.41
1267 1297 4.989168 CCGCAAGACTCTGTTAGTTAGTTT 59.011 41.667 0.00 0.00 39.07 2.66
1277 1307 9.837525 ACTCTGTTAGTTAGTTTAGTACAATCG 57.162 33.333 0.00 0.00 33.35 3.34
1287 1317 4.924305 TTAGTACAATCGGCGAACCTAT 57.076 40.909 15.93 1.07 0.00 2.57
1293 1323 0.314302 ATCGGCGAACCTATTCTCGG 59.686 55.000 15.93 0.00 35.60 4.63
1307 1337 8.575649 ACCTATTCTCGGTTCAAAAATACAAT 57.424 30.769 0.00 0.00 0.00 2.71
1316 1346 6.531240 CGGTTCAAAAATACAATCTTGGATGG 59.469 38.462 0.00 0.00 30.50 3.51
1318 1348 7.331687 GGTTCAAAAATACAATCTTGGATGGTG 59.668 37.037 0.00 0.00 30.50 4.17
1320 1350 8.187913 TCAAAAATACAATCTTGGATGGTGAA 57.812 30.769 0.00 0.00 30.50 3.18
1321 1351 8.306038 TCAAAAATACAATCTTGGATGGTGAAG 58.694 33.333 0.00 0.00 30.50 3.02
1322 1352 8.306038 CAAAAATACAATCTTGGATGGTGAAGA 58.694 33.333 0.00 0.00 30.50 2.87
1323 1353 8.599624 AAAATACAATCTTGGATGGTGAAGAT 57.400 30.769 0.00 0.00 40.02 2.40
1324 1354 8.599624 AAATACAATCTTGGATGGTGAAGATT 57.400 30.769 0.00 0.00 45.59 2.40
1325 1355 8.599624 AATACAATCTTGGATGGTGAAGATTT 57.400 30.769 0.00 0.00 43.34 2.17
1326 1356 9.699410 AATACAATCTTGGATGGTGAAGATTTA 57.301 29.630 0.00 0.00 43.34 1.40
1327 1357 9.699410 ATACAATCTTGGATGGTGAAGATTTAA 57.301 29.630 0.00 0.00 43.34 1.52
1328 1358 8.421249 ACAATCTTGGATGGTGAAGATTTAAA 57.579 30.769 0.00 0.00 43.34 1.52
1329 1359 8.526147 ACAATCTTGGATGGTGAAGATTTAAAG 58.474 33.333 0.00 0.00 43.34 1.85
1330 1360 8.742777 CAATCTTGGATGGTGAAGATTTAAAGA 58.257 33.333 0.00 0.00 43.34 2.52
1331 1361 7.928307 TCTTGGATGGTGAAGATTTAAAGAG 57.072 36.000 0.00 0.00 0.00 2.85
1332 1362 6.886459 TCTTGGATGGTGAAGATTTAAAGAGG 59.114 38.462 0.00 0.00 0.00 3.69
1333 1363 5.509498 TGGATGGTGAAGATTTAAAGAGGG 58.491 41.667 0.00 0.00 0.00 4.30
1334 1364 5.015178 TGGATGGTGAAGATTTAAAGAGGGT 59.985 40.000 0.00 0.00 0.00 4.34
1335 1365 5.952347 GGATGGTGAAGATTTAAAGAGGGTT 59.048 40.000 0.00 0.00 0.00 4.11
1336 1366 6.437477 GGATGGTGAAGATTTAAAGAGGGTTT 59.563 38.462 0.00 0.00 0.00 3.27
1337 1367 7.614192 GGATGGTGAAGATTTAAAGAGGGTTTA 59.386 37.037 0.00 0.00 0.00 2.01
1338 1368 7.754851 TGGTGAAGATTTAAAGAGGGTTTAC 57.245 36.000 0.00 0.00 0.00 2.01
1339 1369 7.523415 TGGTGAAGATTTAAAGAGGGTTTACT 58.477 34.615 0.00 0.00 0.00 2.24
1340 1370 7.447238 TGGTGAAGATTTAAAGAGGGTTTACTG 59.553 37.037 0.00 0.00 0.00 2.74
1341 1371 7.447545 GGTGAAGATTTAAAGAGGGTTTACTGT 59.552 37.037 0.00 0.00 0.00 3.55
1342 1372 8.847196 GTGAAGATTTAAAGAGGGTTTACTGTT 58.153 33.333 0.00 0.00 0.00 3.16
1352 1382 7.407393 AGAGGGTTTACTGTTAGTATCTCAC 57.593 40.000 0.00 0.00 29.64 3.51
1356 1386 2.846039 ACTGTTAGTATCTCACCGCG 57.154 50.000 0.00 0.00 0.00 6.46
1365 1395 0.030369 ATCTCACCGCGAATACCGAC 59.970 55.000 8.23 0.00 41.76 4.79
1392 1457 4.454847 GTCATCTGGCATACATGGAATCTG 59.545 45.833 0.00 0.00 0.00 2.90
1393 1458 2.854963 TCTGGCATACATGGAATCTGC 58.145 47.619 0.00 0.00 0.00 4.26
1394 1459 2.173143 TCTGGCATACATGGAATCTGCA 59.827 45.455 4.44 0.00 34.56 4.41
1399 1467 0.809636 TACATGGAATCTGCACGGCG 60.810 55.000 4.80 4.80 0.00 6.46
1480 1548 2.439701 CATGGTGGAGCTGGCCAG 60.440 66.667 29.34 29.34 38.95 4.85
2307 2388 4.501285 AGGAGATCGCCGTCGGGA 62.501 66.667 14.38 9.13 36.13 5.14
2849 2942 7.726033 TCTTAGAGATCTTTAGAGCCTGTTT 57.274 36.000 0.00 0.00 0.00 2.83
2850 2943 8.824756 TCTTAGAGATCTTTAGAGCCTGTTTA 57.175 34.615 0.00 0.00 0.00 2.01
2851 2944 8.908903 TCTTAGAGATCTTTAGAGCCTGTTTAG 58.091 37.037 0.00 0.00 0.00 1.85
2852 2945 8.824756 TTAGAGATCTTTAGAGCCTGTTTAGA 57.175 34.615 0.00 0.00 0.00 2.10
2854 2947 7.552459 AGAGATCTTTAGAGCCTGTTTAGAAC 58.448 38.462 0.00 0.00 0.00 3.01
2855 2948 7.179338 AGAGATCTTTAGAGCCTGTTTAGAACA 59.821 37.037 0.00 0.00 39.52 3.18
2951 3051 1.067060 TCGATGAATTCTGACGGCGAT 59.933 47.619 16.62 0.00 0.00 4.58
2952 3052 1.453524 CGATGAATTCTGACGGCGATC 59.546 52.381 16.62 8.31 0.00 3.69
2953 3053 2.473816 GATGAATTCTGACGGCGATCA 58.526 47.619 16.62 12.87 0.00 2.92
2954 3054 1.640428 TGAATTCTGACGGCGATCAC 58.360 50.000 16.62 2.37 0.00 3.06
3023 3150 4.507512 GGAAGAACTTGACCCCTTCTCAAT 60.508 45.833 0.00 0.00 36.28 2.57
3039 3166 8.954350 CCCTTCTCAATTATGATCATATTCCAC 58.046 37.037 16.06 0.00 34.37 4.02
3059 3186 5.353956 TCCACACATCAACAGCAACATATAC 59.646 40.000 0.00 0.00 0.00 1.47
3060 3187 5.123661 CCACACATCAACAGCAACATATACA 59.876 40.000 0.00 0.00 0.00 2.29
3061 3188 6.023435 CACACATCAACAGCAACATATACAC 58.977 40.000 0.00 0.00 0.00 2.90
3062 3189 5.704978 ACACATCAACAGCAACATATACACA 59.295 36.000 0.00 0.00 0.00 3.72
3063 3190 6.023435 CACATCAACAGCAACATATACACAC 58.977 40.000 0.00 0.00 0.00 3.82
3064 3191 5.704978 ACATCAACAGCAACATATACACACA 59.295 36.000 0.00 0.00 0.00 3.72
3087 3216 3.507786 AGTCCAAACAAAAACGAGCAAC 58.492 40.909 0.00 0.00 0.00 4.17
3105 3234 2.154854 ACGGTCTCAACATCACACAG 57.845 50.000 0.00 0.00 0.00 3.66
3136 3265 9.976511 ATGAAAAAGAATGCATGTTATCCTATG 57.023 29.630 0.00 0.00 0.00 2.23
3146 3275 3.884895 TGTTATCCTATGGTGGCACAAG 58.115 45.455 20.82 12.83 44.16 3.16
3162 3291 3.428045 GCACAAGAAACAACACAAGCTCT 60.428 43.478 0.00 0.00 0.00 4.09
3207 3336 0.178068 CCGGACCCAATCACTACCAG 59.822 60.000 0.00 0.00 0.00 4.00
3293 3424 8.662141 GTGTTTCCGTCTGTGTATAATTACAAT 58.338 33.333 0.00 0.00 39.96 2.71
3367 3498 3.003480 CAGTTACTTAGCCTTGTGCCTC 58.997 50.000 0.00 0.00 42.71 4.70
3444 3575 6.373774 CCATAAACCATATTCAGGAGATCAGC 59.626 42.308 0.00 0.00 0.00 4.26
3585 3716 1.561542 TGATCCCCAGCTTCCTTTCTC 59.438 52.381 0.00 0.00 0.00 2.87
3594 3725 4.142049 CCAGCTTCCTTTCTCGAGTATCTT 60.142 45.833 13.13 0.00 0.00 2.40
3595 3726 5.067936 CCAGCTTCCTTTCTCGAGTATCTTA 59.932 44.000 13.13 0.00 0.00 2.10
3601 3732 6.931838 TCCTTTCTCGAGTATCTTAAGCAAA 58.068 36.000 13.13 0.54 0.00 3.68
3609 3740 5.445142 CGAGTATCTTAAGCAAAGCAGTGTG 60.445 44.000 0.00 0.00 34.97 3.82
3678 3809 1.434188 TCCCTTGCTCTCCAAAGTCA 58.566 50.000 0.00 0.00 31.94 3.41
3763 3894 4.277423 CGGTTTACCTGGTTTCAGAAATGT 59.723 41.667 3.84 0.00 43.49 2.71
3841 3972 0.685097 TTAGTTCCTGCGCCAGAACT 59.315 50.000 31.98 31.98 36.56 3.01
3903 4036 5.327091 CAGTTACCTTCTTTGCAATGATCG 58.673 41.667 15.04 10.64 0.00 3.69
3904 4037 4.396166 AGTTACCTTCTTTGCAATGATCGG 59.604 41.667 15.04 18.30 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
299 316 1.335689 GGACTCGCTTGACAAGTACGT 60.336 52.381 16.39 10.32 0.00 3.57
393 416 1.444672 CTGGCGGATCTGCATCAGA 59.555 57.895 27.26 5.22 44.99 3.27
507 530 1.169661 ATTCCGCGCAAAACACCTCA 61.170 50.000 8.75 0.00 0.00 3.86
658 684 1.078143 GGGGAGTTGCTGCGATTCT 60.078 57.895 11.57 0.00 0.00 2.40
675 701 1.667830 ACATCCTGTTGTGACGCGG 60.668 57.895 12.47 0.00 0.00 6.46
685 711 1.825474 CCTCTCGTTACCACATCCTGT 59.175 52.381 0.00 0.00 0.00 4.00
745 771 9.927081 ACATTATTCTCTGGAATACAATCCTTT 57.073 29.630 0.00 0.00 42.15 3.11
920 949 2.226330 AGCGTTGATGTGGCACTAAAA 58.774 42.857 19.83 7.23 0.00 1.52
921 950 1.890876 AGCGTTGATGTGGCACTAAA 58.109 45.000 19.83 7.60 0.00 1.85
922 951 1.890876 AAGCGTTGATGTGGCACTAA 58.109 45.000 19.83 8.67 0.00 2.24
923 952 2.289133 TGTAAGCGTTGATGTGGCACTA 60.289 45.455 19.83 5.69 0.00 2.74
964 993 3.777161 GTCGGTTCATTTTAAACGCGATC 59.223 43.478 15.93 0.00 39.40 3.69
987 1016 0.316204 AAACACTAGTGGGACGGACG 59.684 55.000 26.12 0.00 34.19 4.79
1008 1037 4.095185 CGAGGTGGGCGTAAATTTTATCAA 59.905 41.667 0.00 0.00 0.00 2.57
1012 1041 2.290197 ACCGAGGTGGGCGTAAATTTTA 60.290 45.455 0.00 0.00 44.64 1.52
1017 1046 1.546589 ATCACCGAGGTGGGCGTAAA 61.547 55.000 20.79 1.48 45.43 2.01
1019 1048 2.363276 ATCACCGAGGTGGGCGTA 60.363 61.111 20.79 2.91 45.43 4.42
1020 1049 4.082523 CATCACCGAGGTGGGCGT 62.083 66.667 20.79 3.94 45.43 5.68
1021 1050 2.978452 GATCATCACCGAGGTGGGCG 62.978 65.000 20.79 10.44 45.43 6.13
1028 1057 3.801114 TGGTTACAGATCATCACCGAG 57.199 47.619 0.00 0.00 0.00 4.63
1053 1082 4.083003 GGCTTTCAAATACCGTCACATTGA 60.083 41.667 0.00 0.00 0.00 2.57
1054 1083 4.082787 AGGCTTTCAAATACCGTCACATTG 60.083 41.667 0.00 0.00 0.00 2.82
1093 1122 8.046708 GGGTTAGGGCTTTCAAAATTCAAATAT 58.953 33.333 0.00 0.00 0.00 1.28
1095 1124 6.044287 AGGGTTAGGGCTTTCAAAATTCAAAT 59.956 34.615 0.00 0.00 0.00 2.32
1099 1128 6.599356 TTAGGGTTAGGGCTTTCAAAATTC 57.401 37.500 0.00 0.00 0.00 2.17
1147 1176 4.335594 GTGAGCAGAGTAAAACCACAACTT 59.664 41.667 0.00 0.00 0.00 2.66
1149 1178 3.877508 AGTGAGCAGAGTAAAACCACAAC 59.122 43.478 0.00 0.00 0.00 3.32
1246 1276 9.127006 GTACTAAACTAACTAACAGAGTCTTGC 57.873 37.037 0.00 0.00 37.44 4.01
1257 1287 6.851609 TCGCCGATTGTACTAAACTAACTAA 58.148 36.000 0.00 0.00 0.00 2.24
1267 1297 4.581824 AGAATAGGTTCGCCGATTGTACTA 59.418 41.667 0.00 0.00 41.66 1.82
1287 1317 7.229707 TCCAAGATTGTATTTTTGAACCGAGAA 59.770 33.333 0.00 0.00 0.00 2.87
1293 1323 8.087750 TCACCATCCAAGATTGTATTTTTGAAC 58.912 33.333 0.00 0.00 0.00 3.18
1302 1332 9.527157 TTTAAATCTTCACCATCCAAGATTGTA 57.473 29.630 7.49 1.92 44.87 2.41
1307 1337 6.886459 CCTCTTTAAATCTTCACCATCCAAGA 59.114 38.462 0.00 0.00 33.18 3.02
1316 1346 8.392372 ACAGTAAACCCTCTTTAAATCTTCAC 57.608 34.615 0.00 0.00 0.00 3.18
1325 1355 9.537852 TGAGATACTAACAGTAAACCCTCTTTA 57.462 33.333 0.00 0.00 33.89 1.85
1326 1356 8.312564 GTGAGATACTAACAGTAAACCCTCTTT 58.687 37.037 0.00 0.00 33.89 2.52
1327 1357 7.093421 GGTGAGATACTAACAGTAAACCCTCTT 60.093 40.741 0.00 0.00 33.89 2.85
1328 1358 6.380560 GGTGAGATACTAACAGTAAACCCTCT 59.619 42.308 0.00 0.00 33.89 3.69
1329 1359 6.571605 GGTGAGATACTAACAGTAAACCCTC 58.428 44.000 0.00 0.00 33.89 4.30
1330 1360 5.126707 CGGTGAGATACTAACAGTAAACCCT 59.873 44.000 0.00 0.00 33.89 4.34
1331 1361 5.346522 CGGTGAGATACTAACAGTAAACCC 58.653 45.833 0.00 0.00 33.89 4.11
1332 1362 4.802563 GCGGTGAGATACTAACAGTAAACC 59.197 45.833 0.00 0.00 33.89 3.27
1333 1363 4.498323 CGCGGTGAGATACTAACAGTAAAC 59.502 45.833 0.00 0.00 33.89 2.01
1334 1364 4.395854 TCGCGGTGAGATACTAACAGTAAA 59.604 41.667 6.13 0.00 33.89 2.01
1335 1365 3.940852 TCGCGGTGAGATACTAACAGTAA 59.059 43.478 6.13 0.00 33.89 2.24
1336 1366 3.534554 TCGCGGTGAGATACTAACAGTA 58.465 45.455 6.13 0.00 34.82 2.74
1337 1367 2.362736 TCGCGGTGAGATACTAACAGT 58.637 47.619 6.13 0.00 0.00 3.55
1338 1368 3.416119 TTCGCGGTGAGATACTAACAG 57.584 47.619 6.13 0.00 0.00 3.16
1339 1369 4.261322 GGTATTCGCGGTGAGATACTAACA 60.261 45.833 6.13 0.00 0.00 2.41
1340 1370 4.225208 GGTATTCGCGGTGAGATACTAAC 58.775 47.826 6.13 0.00 0.00 2.34
1341 1371 3.058708 CGGTATTCGCGGTGAGATACTAA 60.059 47.826 6.13 0.00 0.00 2.24
1342 1372 2.481568 CGGTATTCGCGGTGAGATACTA 59.518 50.000 6.13 0.00 0.00 1.82
1343 1373 1.266175 CGGTATTCGCGGTGAGATACT 59.734 52.381 6.13 0.00 0.00 2.12
1352 1382 2.952783 CACGGTCGGTATTCGCGG 60.953 66.667 6.13 0.00 39.05 6.46
1356 1386 2.460918 CAGATGACACGGTCGGTATTC 58.539 52.381 0.00 0.00 34.95 1.75
1365 1395 1.869132 CATGTATGCCAGATGACACGG 59.131 52.381 0.00 0.00 29.21 4.94
1706 1774 2.044555 CACCGAGCGGAGGTAGTCA 61.045 63.158 16.83 0.00 40.59 3.41
2787 2880 1.225704 GGGATGCTCCACCTTCCTG 59.774 63.158 4.85 0.00 38.64 3.86
2789 2882 2.190578 CGGGATGCTCCACCTTCC 59.809 66.667 4.85 0.00 38.64 3.46
2849 2942 8.829612 TGTAACACGACGATAATCTATGTTCTA 58.170 33.333 0.00 0.00 31.65 2.10
2850 2943 7.700505 TGTAACACGACGATAATCTATGTTCT 58.299 34.615 0.00 0.00 31.65 3.01
2851 2944 7.642978 ACTGTAACACGACGATAATCTATGTTC 59.357 37.037 0.00 0.00 31.65 3.18
2852 2945 7.478322 ACTGTAACACGACGATAATCTATGTT 58.522 34.615 0.00 1.46 33.02 2.71
2854 2947 7.909777 AACTGTAACACGACGATAATCTATG 57.090 36.000 0.00 0.00 0.00 2.23
2855 2948 8.804743 CAAAACTGTAACACGACGATAATCTAT 58.195 33.333 0.00 0.00 0.00 1.98
2913 3013 8.729529 TTCATCGACGATGATAATCTAAGTTC 57.270 34.615 34.20 0.00 46.52 3.01
2924 3024 3.977579 CGTCAGAATTCATCGACGATGAT 59.022 43.478 34.20 23.70 46.52 2.45
2988 3114 2.204461 TTCTTCCTCCGCCACGACA 61.204 57.895 0.00 0.00 0.00 4.35
3023 3150 8.977267 TGTTGATGTGTGGAATATGATCATAA 57.023 30.769 19.03 0.05 0.00 1.90
3039 3166 6.023435 GTGTGTATATGTTGCTGTTGATGTG 58.977 40.000 0.00 0.00 0.00 3.21
3059 3186 4.681942 TCGTTTTTGTTTGGACTTTGTGTG 59.318 37.500 0.00 0.00 0.00 3.82
3060 3187 4.872664 TCGTTTTTGTTTGGACTTTGTGT 58.127 34.783 0.00 0.00 0.00 3.72
3061 3188 4.201580 GCTCGTTTTTGTTTGGACTTTGTG 60.202 41.667 0.00 0.00 0.00 3.33
3062 3189 3.924073 GCTCGTTTTTGTTTGGACTTTGT 59.076 39.130 0.00 0.00 0.00 2.83
3063 3190 3.923461 TGCTCGTTTTTGTTTGGACTTTG 59.077 39.130 0.00 0.00 0.00 2.77
3064 3191 4.181309 TGCTCGTTTTTGTTTGGACTTT 57.819 36.364 0.00 0.00 0.00 2.66
3087 3216 0.792640 GCTGTGTGATGTTGAGACCG 59.207 55.000 0.00 0.00 0.00 4.79
3105 3234 2.766345 TGCATTCTTTTTCATGGGGC 57.234 45.000 0.00 0.00 0.00 5.80
3136 3265 1.203523 TGTGTTGTTTCTTGTGCCACC 59.796 47.619 0.00 0.00 0.00 4.61
3146 3275 7.190920 ACTACATTAGAGCTTGTGTTGTTTC 57.809 36.000 0.00 0.00 28.78 2.78
3207 3336 9.216117 TCTTCTCTTTGTATGTAAAGTTTAGGC 57.784 33.333 0.00 0.00 38.49 3.93
3293 3424 4.804108 CCACAAGTTTGTTTGTTCTCACA 58.196 39.130 0.00 0.00 39.17 3.58
3367 3498 0.625849 ACAATAGGGAAGGCCACCAG 59.374 55.000 18.41 6.41 35.15 4.00
3444 3575 1.606350 GCGGAGTCGACACAAAGACG 61.606 60.000 19.50 10.91 41.86 4.18
3585 3716 4.627467 ACACTGCTTTGCTTAAGATACTCG 59.373 41.667 6.67 0.00 35.80 4.18
3594 3725 3.015934 CAATGCACACTGCTTTGCTTA 57.984 42.857 9.19 0.00 46.45 3.09
3595 3726 1.860676 CAATGCACACTGCTTTGCTT 58.139 45.000 9.19 0.00 46.45 3.91
3601 3732 0.883833 GTTAGGCAATGCACACTGCT 59.116 50.000 7.79 0.00 45.31 4.24
3616 3747 2.813908 GCACCGGTCGCCAGTTAG 60.814 66.667 2.59 0.00 0.00 2.34
3678 3809 3.829272 CTTTGCTTGTTGCGCGCCT 62.829 57.895 30.77 0.00 46.63 5.52


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

AutoCloner maintained by Alex Coulton.