Multiple sequence alignment - TraesCS4D01G235900

Loading Multiple Alignment...

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 TraesCS4D01G235900 chr4D 100.000 3249 0 0 1 3249 397159443 397156195 0.000000e+00 6000.0
1 TraesCS4D01G235900 chr4D 81.349 1201 162 26 1106 2272 488666096 488664924 0.000000e+00 920.0
2 TraesCS4D01G235900 chr4D 100.000 30 0 0 2352 2381 488664533 488664504 4.530000e-04 56.5
3 TraesCS4D01G235900 chr4A 93.767 1845 80 12 549 2382 54406465 54404645 0.000000e+00 2737.0
4 TraesCS4D01G235900 chr4A 85.853 516 28 15 1 501 54407044 54406559 1.040000e-139 507.0
5 TraesCS4D01G235900 chr4B 94.750 1200 45 5 1188 2382 489294396 489293210 0.000000e+00 1851.0
6 TraesCS4D01G235900 chr4B 91.369 869 63 6 2383 3248 139533714 139532855 0.000000e+00 1179.0
7 TraesCS4D01G235900 chr4B 94.313 633 23 5 549 1174 489295207 489294581 0.000000e+00 957.0
8 TraesCS4D01G235900 chr4B 82.104 1017 137 22 1106 2107 626068871 626067885 0.000000e+00 828.0
9 TraesCS4D01G235900 chr4B 80.215 1208 146 43 1126 2272 639452147 639453322 0.000000e+00 821.0
10 TraesCS4D01G235900 chr4B 92.731 509 22 7 1 503 489295814 489295315 0.000000e+00 721.0
11 TraesCS4D01G235900 chr4B 81.511 741 87 28 1126 1854 667343688 667344390 6.090000e-157 564.0
12 TraesCS4D01G235900 chr4B 84.634 410 45 8 1700 2094 667263801 667264207 3.040000e-105 392.0
13 TraesCS4D01G235900 chr4B 78.502 414 43 23 1901 2272 667345419 667345828 2.520000e-56 230.0
14 TraesCS4D01G235900 chr4B 81.720 279 33 13 1357 1620 667263235 667263510 1.960000e-52 217.0
15 TraesCS4D01G235900 chr4B 100.000 33 0 0 2352 2384 626067298 626067266 9.730000e-06 62.1
16 TraesCS4D01G235900 chr7D 93.873 865 49 4 2384 3248 264774318 264773458 0.000000e+00 1301.0
17 TraesCS4D01G235900 chr3D 94.152 855 48 2 2387 3241 8874480 8873628 0.000000e+00 1301.0
18 TraesCS4D01G235900 chr6B 93.056 864 56 4 2380 3241 620626623 620625762 0.000000e+00 1260.0
19 TraesCS4D01G235900 chr6B 91.879 862 67 3 2383 3242 151907751 151908611 0.000000e+00 1201.0
20 TraesCS4D01G235900 chr6B 89.474 57 3 2 467 523 76149747 76149800 5.820000e-08 69.4
21 TraesCS4D01G235900 chr5D 93.015 859 59 1 2384 3242 537650564 537651421 0.000000e+00 1253.0
22 TraesCS4D01G235900 chr5D 90.741 54 5 0 467 520 351335591 351335644 4.500000e-09 73.1
23 TraesCS4D01G235900 chrUn 92.567 861 61 3 2383 3241 12189317 12190176 0.000000e+00 1232.0
24 TraesCS4D01G235900 chrUn 82.519 675 82 20 1428 2094 30126390 30125744 7.870000e-156 560.0
25 TraesCS4D01G235900 chr3B 91.820 868 63 6 2383 3248 118787509 118786648 0.000000e+00 1203.0
26 TraesCS4D01G235900 chr5B 91.686 866 71 1 2383 3248 592340409 592339545 0.000000e+00 1199.0
27 TraesCS4D01G235900 chr5B 88.060 67 5 2 439 503 549974425 549974360 3.480000e-10 76.8
28 TraesCS4D01G235900 chr5B 88.136 59 3 3 468 526 411035007 411034953 2.090000e-07 67.6
29 TraesCS4D01G235900 chr5A 83.300 1000 125 19 1106 2094 670426159 670425191 0.000000e+00 883.0
30 TraesCS4D01G235900 chr5A 79.983 1199 141 50 1126 2272 706678504 706677353 0.000000e+00 793.0
31 TraesCS4D01G235900 chr5A 81.364 220 33 5 1693 1908 706705514 706705299 4.310000e-39 172.0
32 TraesCS4D01G235900 chr5A 92.308 52 3 1 467 517 119216153 119216204 4.500000e-09 73.1
33 TraesCS4D01G235900 chr5A 100.000 31 0 0 2352 2382 670424791 670424761 1.260000e-04 58.4
34 TraesCS4D01G235900 chr1D 96.837 411 9 3 1135 1544 394263776 394263369 0.000000e+00 684.0
35 TraesCS4D01G235900 chr7A 90.909 55 1 3 467 521 287218264 287218214 1.620000e-08 71.3
36 TraesCS4D01G235900 chr2D 90.741 54 2 2 468 521 575354250 575354200 5.820000e-08 69.4


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 TraesCS4D01G235900 chr4D 397156195 397159443 3248 True 6000.000000 6000 100.000000 1 3249 1 chr4D.!!$R1 3248
1 TraesCS4D01G235900 chr4D 488664504 488666096 1592 True 488.250000 920 90.674500 1106 2381 2 chr4D.!!$R2 1275
2 TraesCS4D01G235900 chr4A 54404645 54407044 2399 True 1622.000000 2737 89.810000 1 2382 2 chr4A.!!$R1 2381
3 TraesCS4D01G235900 chr4B 139532855 139533714 859 True 1179.000000 1179 91.369000 2383 3248 1 chr4B.!!$R1 865
4 TraesCS4D01G235900 chr4B 489293210 489295814 2604 True 1176.333333 1851 93.931333 1 2382 3 chr4B.!!$R2 2381
5 TraesCS4D01G235900 chr4B 639452147 639453322 1175 False 821.000000 821 80.215000 1126 2272 1 chr4B.!!$F1 1146
6 TraesCS4D01G235900 chr4B 626067266 626068871 1605 True 445.050000 828 91.052000 1106 2384 2 chr4B.!!$R3 1278
7 TraesCS4D01G235900 chr4B 667343688 667345828 2140 False 397.000000 564 80.006500 1126 2272 2 chr4B.!!$F3 1146
8 TraesCS4D01G235900 chr4B 667263235 667264207 972 False 304.500000 392 83.177000 1357 2094 2 chr4B.!!$F2 737
9 TraesCS4D01G235900 chr7D 264773458 264774318 860 True 1301.000000 1301 93.873000 2384 3248 1 chr7D.!!$R1 864
10 TraesCS4D01G235900 chr3D 8873628 8874480 852 True 1301.000000 1301 94.152000 2387 3241 1 chr3D.!!$R1 854
11 TraesCS4D01G235900 chr6B 620625762 620626623 861 True 1260.000000 1260 93.056000 2380 3241 1 chr6B.!!$R1 861
12 TraesCS4D01G235900 chr6B 151907751 151908611 860 False 1201.000000 1201 91.879000 2383 3242 1 chr6B.!!$F2 859
13 TraesCS4D01G235900 chr5D 537650564 537651421 857 False 1253.000000 1253 93.015000 2384 3242 1 chr5D.!!$F2 858
14 TraesCS4D01G235900 chrUn 12189317 12190176 859 False 1232.000000 1232 92.567000 2383 3241 1 chrUn.!!$F1 858
15 TraesCS4D01G235900 chrUn 30125744 30126390 646 True 560.000000 560 82.519000 1428 2094 1 chrUn.!!$R1 666
16 TraesCS4D01G235900 chr3B 118786648 118787509 861 True 1203.000000 1203 91.820000 2383 3248 1 chr3B.!!$R1 865
17 TraesCS4D01G235900 chr5B 592339545 592340409 864 True 1199.000000 1199 91.686000 2383 3248 1 chr5B.!!$R3 865
18 TraesCS4D01G235900 chr5A 706677353 706678504 1151 True 793.000000 793 79.983000 1126 2272 1 chr5A.!!$R1 1146
19 TraesCS4D01G235900 chr5A 670424761 670426159 1398 True 470.700000 883 91.650000 1106 2382 2 chr5A.!!$R3 1276

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
293 309 0.107654 GGTCCCTCCAGAAATGTCGG 60.108 60.0 0.0 0.0 35.97 4.79 F
1654 2251 0.108992 GTGGCTGCATTCATGTGGTG 60.109 55.0 0.5 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 3566 0.041833 CACCCCTCTCCTCTCCTTGA 59.958 60.0 0.0 0.0 0.00 3.02 R
2732 4762 0.250510 TGGCACGGTAGATGCAACAA 60.251 50.0 0.0 0.0 45.27 2.83 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
54 55 2.298163 GGTCCGGAACAGTTGTCTTCTA 59.702 50.000 16.61 0.00 0.00 2.10
55 56 3.315418 GTCCGGAACAGTTGTCTTCTAC 58.685 50.000 5.23 0.00 0.00 2.59
56 57 3.005578 GTCCGGAACAGTTGTCTTCTACT 59.994 47.826 5.23 0.00 0.00 2.57
263 279 4.776322 TGCCCTCCAACGCCATCG 62.776 66.667 0.00 0.00 42.43 3.84
269 285 0.953471 CTCCAACGCCATCGGAACAA 60.953 55.000 0.00 0.00 40.69 2.83
293 309 0.107654 GGTCCCTCCAGAAATGTCGG 60.108 60.000 0.00 0.00 35.97 4.79
298 314 0.389817 CTCCAGAAATGTCGGCGTCA 60.390 55.000 9.58 9.58 0.00 4.35
311 327 1.711206 GGCGTCACTTCAACCTACTC 58.289 55.000 0.00 0.00 0.00 2.59
330 346 1.748493 TCTGCACACCCTTCACAAAAC 59.252 47.619 0.00 0.00 0.00 2.43
389 405 5.591099 GATCATTCCACAAACAAACACACT 58.409 37.500 0.00 0.00 0.00 3.55
416 436 3.786576 CGCGTACTGATTCAGTAGAACTG 59.213 47.826 23.59 13.48 45.88 3.16
419 439 3.238108 ACTGATTCAGTAGAACTGCCG 57.762 47.619 17.63 0.00 45.54 5.69
446 466 5.981315 CCATCCATCAATGTAACAATTGCTC 59.019 40.000 5.05 0.00 37.44 4.26
522 621 7.700022 TTAGAGGGAGTACTTTCTAGTGAAC 57.300 40.000 0.00 0.00 35.78 3.18
524 623 5.013258 AGGGAGTACTTTCTAGTGAACCT 57.987 43.478 0.00 0.00 35.78 3.50
525 624 6.011805 AGAGGGAGTACTTTCTAGTGAACCTA 60.012 42.308 0.00 0.00 35.78 3.08
526 625 5.951148 AGGGAGTACTTTCTAGTGAACCTAC 59.049 44.000 0.00 0.00 35.78 3.18
527 626 5.951148 GGGAGTACTTTCTAGTGAACCTACT 59.049 44.000 0.00 0.00 35.78 2.57
528 627 6.127675 GGGAGTACTTTCTAGTGAACCTACTG 60.128 46.154 0.00 0.00 35.78 2.74
529 628 6.658391 GGAGTACTTTCTAGTGAACCTACTGA 59.342 42.308 0.00 0.00 35.78 3.41
530 629 7.176340 GGAGTACTTTCTAGTGAACCTACTGAA 59.824 40.741 0.00 0.00 35.78 3.02
531 630 8.474710 AGTACTTTCTAGTGAACCTACTGAAA 57.525 34.615 0.00 0.00 35.78 2.69
532 631 8.921205 AGTACTTTCTAGTGAACCTACTGAAAA 58.079 33.333 0.00 0.00 35.78 2.29
533 632 9.708092 GTACTTTCTAGTGAACCTACTGAAAAT 57.292 33.333 0.00 0.00 35.78 1.82
535 634 9.057089 ACTTTCTAGTGAACCTACTGAAAATTG 57.943 33.333 0.00 0.00 32.60 2.32
536 635 9.273016 CTTTCTAGTGAACCTACTGAAAATTGA 57.727 33.333 0.00 0.00 32.60 2.57
537 636 9.793259 TTTCTAGTGAACCTACTGAAAATTGAT 57.207 29.630 0.00 0.00 31.32 2.57
538 637 8.777865 TCTAGTGAACCTACTGAAAATTGATG 57.222 34.615 0.00 0.00 32.19 3.07
539 638 8.593679 TCTAGTGAACCTACTGAAAATTGATGA 58.406 33.333 0.00 0.00 32.19 2.92
540 639 7.440523 AGTGAACCTACTGAAAATTGATGAC 57.559 36.000 0.00 0.00 0.00 3.06
541 640 6.431234 AGTGAACCTACTGAAAATTGATGACC 59.569 38.462 0.00 0.00 0.00 4.02
542 641 6.431234 GTGAACCTACTGAAAATTGATGACCT 59.569 38.462 0.00 0.00 0.00 3.85
543 642 6.655003 TGAACCTACTGAAAATTGATGACCTC 59.345 38.462 0.00 0.00 0.00 3.85
544 643 5.178797 ACCTACTGAAAATTGATGACCTCG 58.821 41.667 0.00 0.00 0.00 4.63
545 644 5.178797 CCTACTGAAAATTGATGACCTCGT 58.821 41.667 0.00 0.00 0.00 4.18
546 645 5.292101 CCTACTGAAAATTGATGACCTCGTC 59.708 44.000 0.00 0.00 0.00 4.20
547 646 3.679980 ACTGAAAATTGATGACCTCGTCG 59.320 43.478 0.00 0.00 34.95 5.12
556 655 3.377656 ACCTCGTCGGTCAAGCAT 58.622 55.556 0.00 0.00 44.93 3.79
557 656 1.215647 ACCTCGTCGGTCAAGCATC 59.784 57.895 0.00 0.00 44.93 3.91
576 675 2.874014 TCCATGCACACTTTCAATCCA 58.126 42.857 0.00 0.00 0.00 3.41
654 753 5.874810 CAGTTTCAGATAACAAATCCTCCGA 59.125 40.000 0.00 0.00 0.00 4.55
664 763 4.770795 ACAAATCCTCCGAGTGGAATTAG 58.229 43.478 0.00 0.00 45.87 1.73
700 799 3.664107 GGAGCTGTGATGTCAACACTAA 58.336 45.455 13.66 0.00 38.81 2.24
791 894 1.815408 GCCTTCTTCTCAACAGCACCA 60.815 52.381 0.00 0.00 0.00 4.17
866 969 3.058363 CAGCAAGTCAAGAAAGAAGAGCC 60.058 47.826 0.00 0.00 0.00 4.70
868 971 2.464157 AGTCAAGAAAGAAGAGCCGG 57.536 50.000 0.00 0.00 0.00 6.13
869 972 0.799393 GTCAAGAAAGAAGAGCCGGC 59.201 55.000 21.89 21.89 0.00 6.13
894 997 2.849294 AGAGAACAGAGGTTTGAGGC 57.151 50.000 0.00 0.00 37.36 4.70
902 1005 2.746362 CAGAGGTTTGAGGCATGTCTTC 59.254 50.000 0.00 0.00 0.00 2.87
935 1038 9.825109 AATTCTACTTCTCTATAAGCTTGGTTC 57.175 33.333 9.86 0.00 0.00 3.62
966 1069 4.394795 GCTTGTGAGCGTATGTTTAACTG 58.605 43.478 0.00 0.00 39.48 3.16
990 1093 0.676151 GCTCTTCTTCTGTGGGCAGG 60.676 60.000 0.00 0.00 42.78 4.85
991 1094 0.689623 CTCTTCTTCTGTGGGCAGGT 59.310 55.000 0.00 0.00 42.78 4.00
992 1095 0.397941 TCTTCTTCTGTGGGCAGGTG 59.602 55.000 0.00 0.00 42.78 4.00
993 1096 0.607489 CTTCTTCTGTGGGCAGGTGG 60.607 60.000 0.00 0.00 42.78 4.61
1067 1177 3.131396 GTCCTAATTACCTGTGGCATCG 58.869 50.000 0.00 0.00 0.00 3.84
1093 1203 8.915654 GGAAAGTTAACATGCTGTGAATTTAAG 58.084 33.333 8.61 0.00 0.00 1.85
1094 1204 8.816640 AAAGTTAACATGCTGTGAATTTAAGG 57.183 30.769 8.61 0.00 0.00 2.69
1095 1205 7.524717 AGTTAACATGCTGTGAATTTAAGGT 57.475 32.000 8.61 0.00 0.00 3.50
1169 1282 1.281867 CATGTACCAGCAAGAAGGGGA 59.718 52.381 0.00 0.00 0.00 4.81
1172 1285 1.134068 GTACCAGCAAGAAGGGGATCC 60.134 57.143 1.92 1.92 0.00 3.36
1173 1286 1.228510 CCAGCAAGAAGGGGATCCC 59.771 63.158 23.95 23.95 45.90 3.85
1242 1540 1.069358 GGCCATCAGGAGCAGTACTAC 59.931 57.143 0.00 0.00 36.89 2.73
1243 1541 1.757118 GCCATCAGGAGCAGTACTACA 59.243 52.381 0.00 0.00 36.89 2.74
1244 1542 2.482142 GCCATCAGGAGCAGTACTACAC 60.482 54.545 0.00 0.00 36.89 2.90
1294 1592 1.372748 CCATCTCGCAGCTCCGATC 60.373 63.158 0.00 0.00 36.54 3.69
1343 1641 4.296265 GAACCTGCCGTTCGGATT 57.704 55.556 15.69 3.16 41.51 3.01
1626 2220 3.540211 CCTCAAGAAGGTGCGTGAT 57.460 52.632 0.00 0.00 40.67 3.06
1654 2251 0.108992 GTGGCTGCATTCATGTGGTG 60.109 55.000 0.50 0.00 0.00 4.17
1956 3566 0.807496 GCGCTCCTGAAAATCTGCTT 59.193 50.000 0.00 0.00 0.00 3.91
2165 3821 6.419771 CATGATCAGAAGATTGACATGTTCG 58.580 40.000 0.00 0.00 37.68 3.95
2197 3857 0.677288 TCGAAGAGGGCTTTTCGTCA 59.323 50.000 14.53 0.00 44.68 4.35
2237 3897 1.326213 CCTGACCGTGGCTCTCAGAT 61.326 60.000 6.58 0.00 34.46 2.90
2257 3917 6.793492 AGATGTTTCAGCTGAAAGTAGAAC 57.207 37.500 36.07 25.66 43.82 3.01
2272 3932 5.007385 AGTAGAACGGAAGCGATTTGTAT 57.993 39.130 0.00 0.00 0.00 2.29
2309 4253 1.961793 TTTCTGAGTTTGGTCACGGG 58.038 50.000 0.00 0.00 0.00 5.28
2345 4289 4.629634 CAGTGTTGTGTGAAGTCTGTAACA 59.370 41.667 0.00 0.00 0.00 2.41
2422 4448 1.767672 CCCCCAGCCTCTGCATCTA 60.768 63.158 0.00 0.00 41.13 1.98
2423 4449 1.348008 CCCCCAGCCTCTGCATCTAA 61.348 60.000 0.00 0.00 41.13 2.10
2437 4463 3.777478 GCATCTAAACAATGCATGCAGT 58.223 40.909 26.69 21.79 46.93 4.40
2529 4556 4.737946 GCAACATCTGTCGCTACTCCTATT 60.738 45.833 0.00 0.00 0.00 1.73
2553 4582 4.993584 CAGTTGATGTAGGGATGCTGATAC 59.006 45.833 0.00 0.00 0.00 2.24
2555 4584 5.367937 AGTTGATGTAGGGATGCTGATACTT 59.632 40.000 0.00 0.00 0.00 2.24
2611 4640 5.342866 ACCTAACATCTAAGACCTGAGGTT 58.657 41.667 5.21 0.00 39.84 3.50
2667 4696 4.373116 TCCGGCGCACTCCTCAAC 62.373 66.667 10.83 0.00 0.00 3.18
2732 4762 6.118170 CACCAATCCATCTTCAGAGTTGTAT 58.882 40.000 0.00 0.00 0.00 2.29
2758 4788 1.384989 ATCTACCGTGCCAGGTCTCG 61.385 60.000 3.27 0.00 44.68 4.04
2844 4875 3.044305 GCGCTGAAACTCCGCAGT 61.044 61.111 0.00 0.00 46.32 4.40
2889 4920 0.733150 GCCTTGCGGTAGATGAAACC 59.267 55.000 0.00 0.00 0.00 3.27
2976 5007 0.319211 TCGAAGGCGTTGTCATCGTT 60.319 50.000 0.00 0.00 38.98 3.85
3060 5092 0.033504 AACGACGATGCCTCAACAGT 59.966 50.000 0.00 0.00 0.00 3.55
3141 5173 4.492160 GCGCCACCACGATCTCGA 62.492 66.667 6.60 0.00 43.02 4.04
3148 5180 1.356979 CCACGATCTCGACGCTGAT 59.643 57.895 6.60 3.47 43.02 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.622740 GCTTCAAATCAAAGCGCAAATAGT 59.377 37.500 11.47 0.00 39.71 2.12
55 56 5.122328 GCTTCAAATCAAAGCGCAAATAG 57.878 39.130 11.47 0.00 39.71 1.73
263 279 0.325272 GGAGGGACCTGACTTGTTCC 59.675 60.000 0.00 0.00 35.41 3.62
269 285 1.912043 CATTTCTGGAGGGACCTGACT 59.088 52.381 0.00 0.00 44.30 3.41
293 309 2.329379 CAGAGTAGGTTGAAGTGACGC 58.671 52.381 0.00 0.00 0.00 5.19
298 314 2.224305 GGTGTGCAGAGTAGGTTGAAGT 60.224 50.000 0.00 0.00 0.00 3.01
311 327 1.750778 AGTTTTGTGAAGGGTGTGCAG 59.249 47.619 0.00 0.00 0.00 4.41
330 346 0.608130 TGTTGGAGTGATCGGGACAG 59.392 55.000 0.00 0.00 0.00 3.51
416 436 1.901591 ACATTGATGGATGGATCGGC 58.098 50.000 0.00 0.00 0.00 5.54
419 439 6.643770 GCAATTGTTACATTGATGGATGGATC 59.356 38.462 7.40 0.00 0.00 3.36
522 621 5.178797 ACGAGGTCATCAATTTTCAGTAGG 58.821 41.667 0.00 0.00 0.00 3.18
524 623 4.862574 CGACGAGGTCATCAATTTTCAGTA 59.137 41.667 0.00 0.00 32.09 2.74
525 624 3.679980 CGACGAGGTCATCAATTTTCAGT 59.320 43.478 0.00 0.00 32.09 3.41
526 625 3.062639 CCGACGAGGTCATCAATTTTCAG 59.937 47.826 0.00 0.00 34.51 3.02
527 626 3.000041 CCGACGAGGTCATCAATTTTCA 59.000 45.455 0.00 0.00 34.51 2.69
528 627 3.658351 CCGACGAGGTCATCAATTTTC 57.342 47.619 0.00 0.00 34.51 2.29
541 640 0.179100 ATGGATGCTTGACCGACGAG 60.179 55.000 0.00 0.00 0.00 4.18
542 641 0.460109 CATGGATGCTTGACCGACGA 60.460 55.000 0.00 0.00 0.00 4.20
543 642 2.009108 CATGGATGCTTGACCGACG 58.991 57.895 0.00 0.00 0.00 5.12
556 655 2.874014 TGGATTGAAAGTGTGCATGGA 58.126 42.857 0.00 0.00 0.00 3.41
557 656 3.006110 ACTTGGATTGAAAGTGTGCATGG 59.994 43.478 0.00 0.00 36.52 3.66
571 670 2.498167 GCTGACAGTGACACTTGGATT 58.502 47.619 5.04 0.00 0.00 3.01
576 675 1.571919 GTTCGCTGACAGTGACACTT 58.428 50.000 18.17 0.00 33.97 3.16
791 894 1.227853 GTGGTGTGAACTTCCGGCT 60.228 57.895 0.00 0.00 0.00 5.52
866 969 2.125512 CTGTTCTCTTCCCGGCCG 60.126 66.667 21.04 21.04 0.00 6.13
868 971 1.219393 CCTCTGTTCTCTTCCCGGC 59.781 63.158 0.00 0.00 0.00 6.13
869 972 0.977395 AACCTCTGTTCTCTTCCCGG 59.023 55.000 0.00 0.00 0.00 5.73
894 997 6.808008 AGTAGAATTTGTGGTGAAGACATG 57.192 37.500 0.00 0.00 0.00 3.21
902 1005 8.821894 GCTTATAGAGAAGTAGAATTTGTGGTG 58.178 37.037 0.00 0.00 0.00 4.17
934 1037 1.588597 CTCACAAGCGCAGAGGAGA 59.411 57.895 11.47 0.00 0.00 3.71
935 1038 2.099431 GCTCACAAGCGCAGAGGAG 61.099 63.158 11.47 12.36 39.10 3.69
966 1069 2.421619 CCCACAGAAGAAGAGCTTGAC 58.578 52.381 0.00 0.00 36.83 3.18
990 1093 0.811281 GTTGCTCCATTACTGGCCAC 59.189 55.000 0.00 0.00 42.80 5.01
991 1094 0.323360 GGTTGCTCCATTACTGGCCA 60.323 55.000 4.71 4.71 42.80 5.36
992 1095 0.323360 TGGTTGCTCCATTACTGGCC 60.323 55.000 0.00 0.00 42.80 5.36
993 1096 1.544724 TTGGTTGCTCCATTACTGGC 58.455 50.000 0.00 0.00 46.60 4.85
1093 1203 3.873910 TGCAAGAAGAGCTTATACCACC 58.126 45.455 0.00 0.00 34.31 4.61
1094 1204 5.220931 CCATTGCAAGAAGAGCTTATACCAC 60.221 44.000 4.94 0.00 34.31 4.16
1095 1205 4.883585 CCATTGCAAGAAGAGCTTATACCA 59.116 41.667 4.94 0.00 34.31 3.25
1230 1528 0.886563 ACGTGGTGTAGTACTGCTCC 59.113 55.000 21.12 21.12 0.00 4.70
1294 1592 2.747855 GCCACCAAAGCTCGGGAG 60.748 66.667 10.38 2.70 0.00 4.30
1343 1641 2.355363 CGTTCTTCACCGTCGCCA 60.355 61.111 0.00 0.00 0.00 5.69
1626 2220 1.804151 GAATGCAGCCACGTTGTCTTA 59.196 47.619 0.00 0.00 0.00 2.10
1654 2251 2.813908 CGCTACGGGCAGTTGGTC 60.814 66.667 0.00 0.00 41.91 4.02
1918 3528 2.129620 CGTGTTCCCCCGGATGATA 58.870 57.895 0.73 0.00 0.00 2.15
1956 3566 0.041833 CACCCCTCTCCTCTCCTTGA 59.958 60.000 0.00 0.00 0.00 3.02
2165 3821 2.160417 CCTCTTCGATCTGCACAAAACC 59.840 50.000 0.00 0.00 0.00 3.27
2197 3857 4.127040 CTCACGAGCTCAGCCGCT 62.127 66.667 15.40 0.00 44.33 5.52
2237 3897 3.807622 CCGTTCTACTTTCAGCTGAAACA 59.192 43.478 32.86 22.94 38.94 2.83
2257 3917 6.771188 AAAGATCTATACAAATCGCTTCCG 57.229 37.500 0.00 0.00 0.00 4.30
2286 4230 3.187227 CCGTGACCAAACTCAGAAATCAG 59.813 47.826 0.00 0.00 0.00 2.90
2287 4231 3.138304 CCGTGACCAAACTCAGAAATCA 58.862 45.455 0.00 0.00 0.00 2.57
2288 4232 2.484264 CCCGTGACCAAACTCAGAAATC 59.516 50.000 0.00 0.00 0.00 2.17
2289 4233 2.504367 CCCGTGACCAAACTCAGAAAT 58.496 47.619 0.00 0.00 0.00 2.17
2290 4234 1.476110 CCCCGTGACCAAACTCAGAAA 60.476 52.381 0.00 0.00 0.00 2.52
2291 4235 0.107831 CCCCGTGACCAAACTCAGAA 59.892 55.000 0.00 0.00 0.00 3.02
2292 4236 1.052124 ACCCCGTGACCAAACTCAGA 61.052 55.000 0.00 0.00 0.00 3.27
2309 4253 3.502211 CACAACACTGGTAGAAATGGACC 59.498 47.826 0.00 0.00 0.00 4.46
2395 4419 4.423209 GGCTGGGGGTCCTCCTCT 62.423 72.222 9.90 0.00 36.78 3.69
2422 4448 3.738830 AAGTGACTGCATGCATTGTTT 57.261 38.095 22.97 9.58 0.00 2.83
2423 4449 3.738830 AAAGTGACTGCATGCATTGTT 57.261 38.095 22.97 5.86 0.00 2.83
2529 4556 3.106827 TCAGCATCCCTACATCAACTGA 58.893 45.455 0.00 0.00 0.00 3.41
2555 4584 3.562609 GGTCTGTTTGGTATTAGGCCCAA 60.563 47.826 0.00 0.00 38.92 4.12
2732 4762 0.250510 TGGCACGGTAGATGCAACAA 60.251 50.000 0.00 0.00 45.27 2.83
2827 4858 3.044305 ACTGCGGAGTTTCAGCGC 61.044 61.111 2.68 0.00 40.49 5.92
2831 4862 1.891919 GTGGCACTGCGGAGTTTCA 60.892 57.895 6.93 5.90 0.00 2.69
3009 5040 2.505407 TCAACATGATCGGGATGTTCCT 59.495 45.455 0.00 0.00 41.16 3.36
3141 5173 1.227380 GCTCGGATCCAATCAGCGT 60.227 57.895 13.41 0.00 0.00 5.07
3148 5180 1.899437 GAGGGTGTGCTCGGATCCAA 61.899 60.000 13.41 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.