Multiple sequence alignment - TraesCS3A01G277100

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 TraesCS3A01G277100 chr3A 100.000 4904 0 0 1 4904 507130807 507125904 0.000000e+00 9057.0
1 TraesCS3A01G277100 chr3B 92.974 3743 162 47 490 4183 499814151 499810461 0.000000e+00 5361.0
2 TraesCS3A01G277100 chr3B 87.797 631 22 17 4313 4904 499807390 499806776 0.000000e+00 688.0
3 TraesCS3A01G277100 chr3B 96.269 134 3 1 4185 4318 499810386 499810255 8.260000e-53 219.0
4 TraesCS3A01G277100 chr3B 100.000 29 0 0 5 33 74291764 74291736 2.000000e-03 54.7
5 TraesCS3A01G277100 chr3D 94.915 2891 94 21 1307 4184 384577555 384574705 0.000000e+00 4475.0
6 TraesCS3A01G277100 chr3D 91.612 763 42 13 489 1248 384578301 384577558 0.000000e+00 1035.0
7 TraesCS3A01G277100 chr3D 92.369 498 35 3 1 498 384578871 384578377 0.000000e+00 706.0
8 TraesCS3A01G277100 chr3D 82.549 510 40 18 4185 4677 384574664 384574187 2.130000e-108 403.0
9 TraesCS3A01G277100 chr3D 96.429 224 3 1 4681 4904 384568629 384568411 1.000000e-96 364.0
10 TraesCS3A01G277100 chr6B 100.000 28 0 0 5 32 36204632 36204659 9.000000e-03 52.8


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 TraesCS3A01G277100 chr3A 507125904 507130807 4903 True 9057.000000 9057 100.000000 1 4904 1 chr3A.!!$R1 4903
1 TraesCS3A01G277100 chr3B 499806776 499814151 7375 True 2089.333333 5361 92.346667 490 4904 3 chr3B.!!$R2 4414
2 TraesCS3A01G277100 chr3D 384574187 384578871 4684 True 1654.750000 4475 90.361250 1 4677 4 chr3D.!!$R2 4676

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
327 328 0.039978 ATAGCCGTCGCTTGATCTCG 60.040 55.0 0.0 0.0 45.55 4.04 F
378 379 0.040058 TCATTTGCCACCTCCATGCT 59.960 50.0 0.0 0.0 0.00 3.79 F
604 689 0.107945 GAACATTCCTCGCTGCTCCT 60.108 55.0 0.0 0.0 0.00 3.69 F
885 994 0.178935 CTCTCTCATCCTCCCCTCCC 60.179 65.0 0.0 0.0 0.00 4.30 F
2057 2177 0.451783 GCGTGATTGATCCCAACACC 59.548 55.0 0.0 0.0 34.72 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1207 1321 0.392327 CACCATCACGGCACCATACA 60.392 55.000 0.00 0.0 39.03 2.29 R
2034 2154 0.394216 TTGGGATCAATCACGCCCTG 60.394 55.000 0.00 0.0 41.28 4.45 R
2198 2318 0.532573 TCTGAGCATTGTCCGGAGTC 59.467 55.000 3.06 0.0 0.00 3.36 R
2648 2768 0.893270 TTCCAGCACCACCAAATCCG 60.893 55.000 0.00 0.0 0.00 4.18 R
4036 4180 1.267532 CGCAGCGATGTACATCCAAAC 60.268 52.381 26.33 15.1 34.40 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
26 27 4.941263 CGACACTTATTTTTGGATGGAGGA 59.059 41.667 0.00 0.00 0.00 3.71
47 48 9.894783 GGAGGAAGTATAAGTTTCTTTTTCAAC 57.105 33.333 0.00 0.00 0.00 3.18
80 81 9.614792 GTAAGAGGTGGTTCATATAAGTTTCAT 57.385 33.333 0.00 0.00 0.00 2.57
81 82 8.738645 AAGAGGTGGTTCATATAAGTTTCATC 57.261 34.615 0.00 0.00 0.00 2.92
82 83 7.283329 AGAGGTGGTTCATATAAGTTTCATCC 58.717 38.462 0.00 0.00 0.00 3.51
83 84 7.127955 AGAGGTGGTTCATATAAGTTTCATCCT 59.872 37.037 0.00 0.00 0.00 3.24
100 101 7.865706 TTCATCCTTAGGAGTATTTCAAAGC 57.134 36.000 7.19 0.00 34.05 3.51
123 124 4.677250 CGTCGGAGTAAGATTTAAGCCACT 60.677 45.833 0.00 0.00 0.00 4.00
141 142 0.182537 CTATGAAATCCCACCGCCCA 59.817 55.000 0.00 0.00 0.00 5.36
201 202 3.470888 CGCCAGGGAGGGTGGTAG 61.471 72.222 0.00 0.00 37.40 3.18
206 207 1.151899 AGGGAGGGTGGTAGTTGCA 60.152 57.895 0.00 0.00 0.00 4.08
210 211 0.389948 GAGGGTGGTAGTTGCAGACG 60.390 60.000 0.00 0.00 0.00 4.18
214 215 1.539496 GGTGGTAGTTGCAGACGTTCA 60.539 52.381 0.00 0.00 0.00 3.18
222 223 0.606130 TGCAGACGTTCACATGGCAT 60.606 50.000 0.00 0.00 0.00 4.40
245 246 3.849563 TTTAGTTGTGTGGCAGTAGGT 57.150 42.857 0.00 0.00 0.00 3.08
255 256 1.078848 GCAGTAGGTGAGGTGGCAG 60.079 63.158 0.00 0.00 0.00 4.85
272 273 1.135859 GCAGTTTCTTCAGGCGACATG 60.136 52.381 0.00 0.00 0.00 3.21
281 282 2.083774 TCAGGCGACATGACATTTTCC 58.916 47.619 0.00 0.00 0.00 3.13
310 311 7.539366 CCGAGAAGGCAATTTTCGTTTAAAATA 59.461 33.333 11.23 0.00 45.12 1.40
326 327 2.141535 AATAGCCGTCGCTTGATCTC 57.858 50.000 0.00 0.00 45.55 2.75
327 328 0.039978 ATAGCCGTCGCTTGATCTCG 60.040 55.000 0.00 0.00 45.55 4.04
331 332 0.640768 CCGTCGCTTGATCTCGTTTC 59.359 55.000 0.00 0.00 0.00 2.78
342 343 5.657470 TGATCTCGTTTCACAACTCAAAG 57.343 39.130 0.00 0.00 0.00 2.77
344 345 4.857871 TCTCGTTTCACAACTCAAAGTG 57.142 40.909 0.00 0.00 37.10 3.16
349 350 3.713858 TTCACAACTCAAAGTGCCATG 57.286 42.857 0.00 0.00 35.76 3.66
377 378 0.896923 TTCATTTGCCACCTCCATGC 59.103 50.000 0.00 0.00 0.00 4.06
378 379 0.040058 TCATTTGCCACCTCCATGCT 59.960 50.000 0.00 0.00 0.00 3.79
420 421 7.316544 ACAATTACCGATAGTTAAAGCCAAG 57.683 36.000 0.00 0.00 0.00 3.61
460 461 2.029649 CACTGGCAGGAAACAAATCAGG 60.030 50.000 20.34 0.00 0.00 3.86
514 599 1.006571 TCGACACGAGCCAAGGTTC 60.007 57.895 0.00 0.00 0.00 3.62
523 608 0.555769 AGCCAAGGTTCCAAGGTCAA 59.444 50.000 0.00 0.00 0.00 3.18
560 645 1.664965 GAGCTCACGCGTCAACCTT 60.665 57.895 9.86 0.00 42.32 3.50
576 661 1.677552 CTTTAGCCGTGTGGTCCCT 59.322 57.895 0.00 0.00 37.67 4.20
602 687 2.002127 CGAACATTCCTCGCTGCTC 58.998 57.895 0.00 0.00 0.00 4.26
604 689 0.107945 GAACATTCCTCGCTGCTCCT 60.108 55.000 0.00 0.00 0.00 3.69
605 690 1.137086 GAACATTCCTCGCTGCTCCTA 59.863 52.381 0.00 0.00 0.00 2.94
606 691 0.461961 ACATTCCTCGCTGCTCCTAC 59.538 55.000 0.00 0.00 0.00 3.18
607 692 0.249657 CATTCCTCGCTGCTCCTACC 60.250 60.000 0.00 0.00 0.00 3.18
610 695 0.614979 TCCTCGCTGCTCCTACCTTT 60.615 55.000 0.00 0.00 0.00 3.11
656 742 4.899239 CTGCTCGGTCCATCGGCC 62.899 72.222 0.00 0.00 0.00 6.13
722 809 1.219646 GTGCGACCTCCGTTTAAACA 58.780 50.000 18.07 0.00 41.15 2.83
873 965 1.217747 TCAGCCCTCCTCCTCTCTCA 61.218 60.000 0.00 0.00 0.00 3.27
885 994 0.178935 CTCTCTCATCCTCCCCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
894 1003 3.695825 TCCCCTCCCCTCCACTCC 61.696 72.222 0.00 0.00 0.00 3.85
898 1007 1.687493 CCTCCCCTCCACTCCACTC 60.687 68.421 0.00 0.00 0.00 3.51
899 1008 1.079256 CTCCCCTCCACTCCACTCA 59.921 63.158 0.00 0.00 0.00 3.41
900 1009 0.545309 CTCCCCTCCACTCCACTCAA 60.545 60.000 0.00 0.00 0.00 3.02
901 1010 0.836400 TCCCCTCCACTCCACTCAAC 60.836 60.000 0.00 0.00 0.00 3.18
902 1011 1.293498 CCCTCCACTCCACTCAACG 59.707 63.158 0.00 0.00 0.00 4.10
904 1013 1.293498 CTCCACTCCACTCAACGGG 59.707 63.158 0.00 0.00 0.00 5.28
957 1066 3.435186 GGACGGCAAGAGCAAGGC 61.435 66.667 0.00 0.00 44.61 4.35
968 1077 2.669569 GCAAGGCCTTGTCAGCGA 60.670 61.111 38.87 0.00 42.31 4.93
1042 1151 1.296755 GGTTTCCGCGTTCCTCTTCC 61.297 60.000 4.92 0.00 0.00 3.46
1101 1215 5.392165 CCTTCAGTTCGTCTTCTGGTACTAG 60.392 48.000 0.00 0.00 33.13 2.57
1102 1216 4.903054 TCAGTTCGTCTTCTGGTACTAGA 58.097 43.478 4.58 4.58 33.13 2.43
1104 1218 6.647229 TCAGTTCGTCTTCTGGTACTAGATA 58.353 40.000 10.02 0.00 33.13 1.98
1193 1307 2.419198 CCGCTGGGTGCTAGCTAG 59.581 66.667 16.84 16.84 39.00 3.42
1194 1308 2.127869 CCGCTGGGTGCTAGCTAGA 61.128 63.158 25.15 6.86 39.00 2.43
1195 1309 1.361993 CGCTGGGTGCTAGCTAGAG 59.638 63.158 25.15 12.96 39.00 2.43
1196 1310 1.388065 CGCTGGGTGCTAGCTAGAGT 61.388 60.000 25.15 0.00 39.00 3.24
1197 1311 1.693627 GCTGGGTGCTAGCTAGAGTA 58.306 55.000 25.15 6.81 38.14 2.59
1207 1321 3.068873 GCTAGCTAGAGTACCTGCAATGT 59.931 47.826 25.15 0.00 0.00 2.71
1215 1329 3.609853 AGTACCTGCAATGTGTATGGTG 58.390 45.455 0.54 0.00 0.00 4.17
1263 1377 4.697798 TCTTTTGGGGGAAATCCAATGAT 58.302 39.130 1.22 0.00 43.01 2.45
1264 1378 4.716287 TCTTTTGGGGGAAATCCAATGATC 59.284 41.667 1.22 0.00 43.01 2.92
1277 1391 5.246981 TCCAATGATCTAATCCCCATGTC 57.753 43.478 0.00 0.00 0.00 3.06
1295 1409 5.072329 CCATGTCCCATGACCTTTATCTACT 59.928 44.000 5.80 0.00 41.01 2.57
1296 1410 6.270000 CCATGTCCCATGACCTTTATCTACTA 59.730 42.308 5.80 0.00 41.01 1.82
1297 1411 6.726490 TGTCCCATGACCTTTATCTACTAC 57.274 41.667 0.00 0.00 41.01 2.73
1312 1426 5.934402 TCTACTACCCAACCTTCAGATTC 57.066 43.478 0.00 0.00 0.00 2.52
1335 1449 6.355747 TCTTTGTTTTTCTGGCATGGAATTT 58.644 32.000 0.00 0.00 0.00 1.82
1336 1450 6.260493 TCTTTGTTTTTCTGGCATGGAATTTG 59.740 34.615 0.00 0.00 0.00 2.32
1337 1451 5.033589 TGTTTTTCTGGCATGGAATTTGT 57.966 34.783 0.00 0.00 0.00 2.83
1338 1452 6.166984 TGTTTTTCTGGCATGGAATTTGTA 57.833 33.333 0.00 0.00 0.00 2.41
1339 1453 6.222389 TGTTTTTCTGGCATGGAATTTGTAG 58.778 36.000 0.00 0.00 0.00 2.74
1344 1458 8.537728 TTTCTGGCATGGAATTTGTAGAATAT 57.462 30.769 0.00 0.00 0.00 1.28
1549 1669 1.708027 GCATCTACGACACCAACGC 59.292 57.895 0.00 0.00 0.00 4.84
1693 1813 4.217159 CTACTACCCGGCCACCGC 62.217 72.222 2.24 0.00 46.86 5.68
1803 1923 2.048222 CGCTCAAGAAGGTCGGCA 60.048 61.111 0.00 0.00 0.00 5.69
2004 2124 2.434884 CGCCCAGCAATGTCTCGT 60.435 61.111 0.00 0.00 0.00 4.18
2034 2154 3.708220 CTCTTCTCGCCGCAGTCCC 62.708 68.421 0.00 0.00 0.00 4.46
2057 2177 0.451783 GCGTGATTGATCCCAACACC 59.548 55.000 0.00 0.00 34.72 4.16
2159 2279 3.048501 CAAGATCATGATCACCGAGACG 58.951 50.000 31.99 11.03 40.22 4.18
2237 2357 7.239763 TCAGACTTACAACACCAATCTGATA 57.760 36.000 0.00 0.00 36.94 2.15
2240 2360 4.630069 ACTTACAACACCAATCTGATACGC 59.370 41.667 0.00 0.00 0.00 4.42
2342 2462 4.162690 AAGCCGGGCATCGAGTCC 62.163 66.667 23.09 0.00 42.43 3.85
2360 2480 1.893786 CGAGAGGAACTGGGGACTG 59.106 63.158 0.00 0.00 41.55 3.51
2603 2723 3.181498 TGGTTTCACATGCTTCATATGCG 60.181 43.478 0.00 0.00 0.00 4.73
2633 2753 4.522022 AGCTATTATCAGCAAAATGGAGCC 59.478 41.667 0.00 0.00 44.35 4.70
2670 2790 2.170166 GATTTGGTGGTGCTGGAATGA 58.830 47.619 0.00 0.00 0.00 2.57
2722 2842 6.055231 TGTGCTTACAACAACTACATTGAC 57.945 37.500 0.00 0.00 41.23 3.18
2745 2865 2.161855 TGTAAGGAATGCTTGCACTGG 58.838 47.619 0.69 0.00 0.00 4.00
2746 2866 2.224744 TGTAAGGAATGCTTGCACTGGA 60.225 45.455 0.69 0.00 0.00 3.86
2747 2867 1.542492 AAGGAATGCTTGCACTGGAG 58.458 50.000 0.00 0.00 0.00 3.86
2762 2882 5.539955 TGCACTGGAGTATAATATCTCTGCA 59.460 40.000 0.00 0.00 37.19 4.41
2860 2980 7.036220 GTGCTGACTACAGTGTTTATGATAGT 58.964 38.462 0.00 0.00 45.04 2.12
2861 2981 8.188799 GTGCTGACTACAGTGTTTATGATAGTA 58.811 37.037 0.00 0.00 45.04 1.82
2862 2982 8.406297 TGCTGACTACAGTGTTTATGATAGTAG 58.594 37.037 0.00 0.00 45.04 2.57
2863 2983 8.407064 GCTGACTACAGTGTTTATGATAGTAGT 58.593 37.037 0.00 0.00 45.04 2.73
2892 3016 3.319122 GGTCCTTGACTGAAATTGCAACT 59.681 43.478 0.00 0.00 32.47 3.16
2954 3078 6.719370 ACATGTAGCTGGGTATTTCTTTTGAA 59.281 34.615 0.00 0.00 36.52 2.69
3027 3151 6.804677 AGACTACAGAGAAGATAGTGCATTG 58.195 40.000 0.00 0.00 29.25 2.82
3154 3279 6.719370 TCTGTTAGGTTAGAAAAATGGCATGT 59.281 34.615 0.00 0.00 0.00 3.21
3194 3319 8.915654 TGAGATATGATCGATTCATTTTGTACG 58.084 33.333 13.21 0.00 42.62 3.67
3340 3474 6.415206 AATGGCCTCAATTTGATAATGGAG 57.585 37.500 3.32 0.00 40.26 3.86
3341 3475 4.870636 TGGCCTCAATTTGATAATGGAGT 58.129 39.130 3.32 0.00 39.33 3.85
3342 3476 5.271598 TGGCCTCAATTTGATAATGGAGTT 58.728 37.500 3.32 0.00 39.33 3.01
3343 3477 6.430864 TGGCCTCAATTTGATAATGGAGTTA 58.569 36.000 3.32 0.00 39.33 2.24
3344 3478 6.321181 TGGCCTCAATTTGATAATGGAGTTAC 59.679 38.462 3.32 0.00 39.33 2.50
3346 3480 7.147915 GGCCTCAATTTGATAATGGAGTTACAA 60.148 37.037 0.00 0.00 39.33 2.41
3347 3481 8.416329 GCCTCAATTTGATAATGGAGTTACAAT 58.584 33.333 0.00 0.00 39.33 2.71
3506 3641 3.018423 TGCCTCTGCATCACTACTCTA 57.982 47.619 0.00 0.00 44.23 2.43
3606 3742 7.148171 GCTTTTAGTGTCAGCTGGATAATCTTT 60.148 37.037 15.13 0.00 0.00 2.52
3756 3896 8.531530 CAACAGTTTGCACTAACTATTGTTTTC 58.468 33.333 12.22 0.00 37.61 2.29
3811 3951 1.698506 AAATTCAACCGCCACTCCAA 58.301 45.000 0.00 0.00 0.00 3.53
3936 4077 2.349886 CGCTCTAGTTAGTACGTTCGGT 59.650 50.000 0.00 0.00 0.00 4.69
4016 4157 1.201429 AAGGTGGCAGTAGGGACCTG 61.201 60.000 0.00 0.00 38.86 4.00
4036 4180 7.041780 GGACCTGTTATGCAGTATGTTATTCTG 60.042 40.741 0.00 0.00 43.55 3.02
4038 4182 7.829211 ACCTGTTATGCAGTATGTTATTCTGTT 59.171 33.333 0.00 0.00 43.55 3.16
4271 4488 5.657745 GGGCTTCTACTTTCTAGTAACTCCT 59.342 44.000 0.00 0.00 36.46 3.69
4272 4489 6.183360 GGGCTTCTACTTTCTAGTAACTCCTC 60.183 46.154 0.00 0.00 36.46 3.71
4282 4499 0.896226 GTAACTCCTCTCCGCCTGTT 59.104 55.000 0.00 0.00 0.00 3.16
4291 4508 3.077359 CTCTCCGCCTGTTCATTTTCTT 58.923 45.455 0.00 0.00 0.00 2.52
4335 7422 3.418684 AGTTTTGCTTCGATACACCCT 57.581 42.857 0.00 0.00 0.00 4.34
4406 7493 1.671979 TTAGCCTGCAGATCACATGC 58.328 50.000 17.39 8.12 44.11 4.06
4550 7647 7.500227 TGCGGATGATATTCTCATTTCTCTTTT 59.500 33.333 0.00 0.00 44.83 2.27
4586 7683 9.784531 ATAAATTCTCATTTCTCATGTATCCGT 57.215 29.630 0.00 0.00 34.29 4.69
4587 7684 8.511604 AAATTCTCATTTCTCATGTATCCGTT 57.488 30.769 0.00 0.00 0.00 4.44
4588 7685 6.908870 TTCTCATTTCTCATGTATCCGTTG 57.091 37.500 0.00 0.00 0.00 4.10
4602 7729 0.309612 CCGTTGGTTGTGGTTGTAGC 59.690 55.000 0.00 0.00 0.00 3.58
4656 7783 6.967199 GCCTGTGTAAAAGATGCAATAAGTAC 59.033 38.462 0.00 0.00 0.00 2.73
4658 7785 7.148474 CCTGTGTAAAAGATGCAATAAGTACGT 60.148 37.037 0.00 0.00 0.00 3.57
4659 7786 8.760103 TGTGTAAAAGATGCAATAAGTACGTA 57.240 30.769 0.00 0.00 0.00 3.57
4773 7911 3.509659 GGTACGAATTGCAGGCCC 58.490 61.111 0.00 0.00 0.00 5.80
4774 7912 1.377987 GGTACGAATTGCAGGCCCA 60.378 57.895 0.00 0.00 0.00 5.36
4775 7913 1.376609 GGTACGAATTGCAGGCCCAG 61.377 60.000 0.00 0.00 0.00 4.45
4776 7914 0.676782 GTACGAATTGCAGGCCCAGT 60.677 55.000 0.00 0.00 0.00 4.00
4777 7915 0.676466 TACGAATTGCAGGCCCAGTG 60.676 55.000 0.00 0.00 0.00 3.66
4778 7916 1.973281 CGAATTGCAGGCCCAGTGT 60.973 57.895 0.00 0.00 0.00 3.55
4779 7917 0.676466 CGAATTGCAGGCCCAGTGTA 60.676 55.000 0.00 0.00 0.00 2.90
4780 7918 0.811281 GAATTGCAGGCCCAGTGTAC 59.189 55.000 0.00 0.00 0.00 2.90
4799 7937 0.439985 CATCCAACGTTGCTGACTCG 59.560 55.000 22.93 7.41 0.00 4.18
4818 7956 1.518903 GCAACTCACTGGCTTGGGTC 61.519 60.000 0.00 0.00 26.58 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.314917 ACTTCCTCCATCCAAAAATAAGTGT 58.685 36.000 0.00 0.00 0.00 3.55
19 20 9.807921 TGAAAAAGAAACTTATACTTCCTCCAT 57.192 29.630 0.00 0.00 0.00 3.41
33 34 8.912988 TCTTACATGGATGTTGAAAAAGAAACT 58.087 29.630 0.00 0.00 41.97 2.66
35 36 8.359642 CCTCTTACATGGATGTTGAAAAAGAAA 58.640 33.333 0.00 0.00 41.97 2.52
47 48 4.220693 TGAACCACCTCTTACATGGATG 57.779 45.455 0.00 0.00 36.94 3.51
80 81 5.416271 ACGCTTTGAAATACTCCTAAGGA 57.584 39.130 0.00 0.00 0.00 3.36
81 82 4.267928 CGACGCTTTGAAATACTCCTAAGG 59.732 45.833 0.00 0.00 0.00 2.69
82 83 4.267928 CCGACGCTTTGAAATACTCCTAAG 59.732 45.833 0.00 0.00 0.00 2.18
83 84 4.082081 TCCGACGCTTTGAAATACTCCTAA 60.082 41.667 0.00 0.00 0.00 2.69
97 98 3.864003 GCTTAAATCTTACTCCGACGCTT 59.136 43.478 0.00 0.00 0.00 4.68
100 101 3.550678 GTGGCTTAAATCTTACTCCGACG 59.449 47.826 0.00 0.00 0.00 5.12
123 124 0.106918 GTGGGCGGTGGGATTTCATA 60.107 55.000 0.00 0.00 0.00 2.15
188 189 1.151899 TGCAACTACCACCCTCCCT 60.152 57.895 0.00 0.00 0.00 4.20
201 202 0.385974 GCCATGTGAACGTCTGCAAC 60.386 55.000 0.00 0.00 0.00 4.17
242 243 0.846693 AAGAAACTGCCACCTCACCT 59.153 50.000 0.00 0.00 0.00 4.00
245 246 1.202806 CCTGAAGAAACTGCCACCTCA 60.203 52.381 0.00 0.00 0.00 3.86
255 256 2.143122 TGTCATGTCGCCTGAAGAAAC 58.857 47.619 0.00 0.00 0.00 2.78
272 273 2.633488 CCTTCTCGGAGGGAAAATGTC 58.367 52.381 4.96 0.00 29.67 3.06
281 282 1.398390 CGAAAATTGCCTTCTCGGAGG 59.602 52.381 4.96 0.00 39.93 4.30
326 327 2.159448 TGGCACTTTGAGTTGTGAAACG 60.159 45.455 0.00 0.00 42.39 3.60
327 328 3.502191 TGGCACTTTGAGTTGTGAAAC 57.498 42.857 0.00 0.00 36.38 2.78
331 332 3.713858 TTCATGGCACTTTGAGTTGTG 57.286 42.857 0.00 0.00 37.26 3.33
342 343 4.460948 AATGAACCATCTTTCATGGCAC 57.539 40.909 0.25 0.00 43.95 5.01
344 345 3.619929 GCAAATGAACCATCTTTCATGGC 59.380 43.478 0.25 3.76 43.95 4.40
349 350 3.259123 AGGTGGCAAATGAACCATCTTTC 59.741 43.478 0.00 0.00 45.33 2.62
420 421 5.579511 CCAGTGATTGCATTTTCCAAAGATC 59.420 40.000 0.00 0.00 0.00 2.75
510 595 5.538849 TGGTAAAAATTGACCTTGGAACC 57.461 39.130 1.44 0.00 36.62 3.62
514 599 5.510690 GGGTCTTGGTAAAAATTGACCTTGG 60.511 44.000 9.39 0.00 42.37 3.61
523 608 3.418047 CTCACGGGGTCTTGGTAAAAAT 58.582 45.455 0.00 0.00 0.00 1.82
560 645 1.823169 GACAGGGACCACACGGCTAA 61.823 60.000 0.00 0.00 34.57 3.09
576 661 1.808411 GAGGAATGTTCGCTTGGACA 58.192 50.000 0.00 0.00 0.00 4.02
619 705 1.379044 AGCAGCGGGGAATTTCCTG 60.379 57.895 14.95 7.31 36.57 3.86
659 745 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
713 800 2.578786 AGGGTTGAGGGTGTTTAAACG 58.421 47.619 13.45 0.00 0.00 3.60
722 809 5.128205 GCGTTATAAAATAGGGTTGAGGGT 58.872 41.667 0.00 0.00 0.00 4.34
873 965 2.628465 TGGAGGGGAGGGGAGGAT 60.628 66.667 0.00 0.00 0.00 3.24
885 994 1.293498 CCGTTGAGTGGAGTGGAGG 59.707 63.158 0.00 0.00 0.00 4.30
894 1003 1.507141 GGAAGTGTGCCCGTTGAGTG 61.507 60.000 0.00 0.00 0.00 3.51
957 1066 1.515020 CTCCTCCTCGCTGACAAGG 59.485 63.158 0.00 0.00 0.00 3.61
1042 1151 2.433838 CTCACCCACGAGCAGCAG 60.434 66.667 0.00 0.00 0.00 4.24
1161 1275 3.506108 CGGGAAGCAAGGCATCTG 58.494 61.111 0.00 0.00 0.00 2.90
1193 1307 3.623060 CACCATACACATTGCAGGTACTC 59.377 47.826 0.00 0.00 34.60 2.59
1194 1308 3.609853 CACCATACACATTGCAGGTACT 58.390 45.455 0.00 0.00 43.88 2.73
1195 1309 2.097466 GCACCATACACATTGCAGGTAC 59.903 50.000 0.00 0.00 34.97 3.34
1196 1310 2.364632 GCACCATACACATTGCAGGTA 58.635 47.619 0.00 0.00 34.97 3.08
1197 1311 1.176527 GCACCATACACATTGCAGGT 58.823 50.000 0.00 0.00 34.97 4.00
1207 1321 0.392327 CACCATCACGGCACCATACA 60.392 55.000 0.00 0.00 39.03 2.29
1215 1329 2.813908 GTCGGACACCATCACGGC 60.814 66.667 2.62 0.00 39.03 5.68
1277 1391 4.905456 TGGGTAGTAGATAAAGGTCATGGG 59.095 45.833 0.00 0.00 0.00 4.00
1295 1409 5.319043 ACAAAGAATCTGAAGGTTGGGTA 57.681 39.130 0.00 0.00 0.00 3.69
1296 1410 4.184649 ACAAAGAATCTGAAGGTTGGGT 57.815 40.909 0.00 0.00 0.00 4.51
1297 1411 5.535753 AAACAAAGAATCTGAAGGTTGGG 57.464 39.130 0.00 0.00 0.00 4.12
1312 1426 6.038492 ACAAATTCCATGCCAGAAAAACAAAG 59.962 34.615 0.00 0.00 0.00 2.77
1335 1449 8.669946 TTGATGCGTCCATTTAATATTCTACA 57.330 30.769 2.83 0.00 0.00 2.74
1336 1450 9.546909 CATTGATGCGTCCATTTAATATTCTAC 57.453 33.333 2.83 0.00 0.00 2.59
1337 1451 8.729756 CCATTGATGCGTCCATTTAATATTCTA 58.270 33.333 2.83 0.00 0.00 2.10
1338 1452 7.231317 ACCATTGATGCGTCCATTTAATATTCT 59.769 33.333 2.83 0.00 0.00 2.40
1339 1453 7.326789 CACCATTGATGCGTCCATTTAATATTC 59.673 37.037 2.83 0.00 0.00 1.75
1344 1458 3.130164 CCACCATTGATGCGTCCATTTAA 59.870 43.478 2.83 0.00 0.00 1.52
1507 1627 1.404717 CGTACTTGATGGACTGCTGCT 60.405 52.381 0.00 0.00 0.00 4.24
1549 1669 1.079127 AAGGCCTTGATGACGTCGG 60.079 57.895 19.73 6.57 0.00 4.79
1693 1813 0.744414 GACGGTGATGTGGGTGATGG 60.744 60.000 0.00 0.00 0.00 3.51
1803 1923 4.197750 GAGATGGTGATCTTCTTGTGCAT 58.802 43.478 0.00 0.00 39.19 3.96
2004 2124 1.201647 CGAGAAGAGGGCGTAGTTCAA 59.798 52.381 5.02 0.00 0.00 2.69
2034 2154 0.394216 TTGGGATCAATCACGCCCTG 60.394 55.000 0.00 0.00 41.28 4.45
2057 2177 3.751175 ACATGTTTGTGTAGACCAATCCG 59.249 43.478 0.00 0.00 33.85 4.18
2198 2318 0.532573 TCTGAGCATTGTCCGGAGTC 59.467 55.000 3.06 0.00 0.00 3.36
2237 2357 1.536766 CTGTCATTGACAACATGGCGT 59.463 47.619 19.44 0.00 42.26 5.68
2240 2360 1.135603 CCGCTGTCATTGACAACATGG 60.136 52.381 19.44 14.15 42.26 3.66
2276 2396 7.067496 GATGTAGACATCTATTTCTTCCCCA 57.933 40.000 14.18 0.00 46.88 4.96
2342 2462 0.900647 ACAGTCCCCAGTTCCTCTCG 60.901 60.000 0.00 0.00 0.00 4.04
2360 2480 2.614229 GGAGCTTTGGTCTGGAGAGAAC 60.614 54.545 0.00 0.00 36.32 3.01
2603 2723 7.221452 CCATTTTGCTGATAATAGCTGTTGAAC 59.779 37.037 5.89 0.00 44.01 3.18
2633 2753 3.129502 CCGCAGGCCACATCAGTG 61.130 66.667 5.01 0.00 46.14 3.66
2645 2765 1.973281 AGCACCACCAAATCCGCAG 60.973 57.895 0.00 0.00 0.00 5.18
2648 2768 0.893270 TTCCAGCACCACCAAATCCG 60.893 55.000 0.00 0.00 0.00 4.18
2670 2790 1.893801 ACTTGGATCTTTCGTCGTCCT 59.106 47.619 0.00 0.00 0.00 3.85
2722 2842 4.171005 CAGTGCAAGCATTCCTTACATTG 58.829 43.478 0.00 0.00 31.06 2.82
2747 2867 9.039870 GCCAGTAATGATGCAGAGATATTATAC 57.960 37.037 0.00 0.00 0.00 1.47
2762 2882 6.006275 ACTACATCCAAAGCCAGTAATGAT 57.994 37.500 0.00 0.00 0.00 2.45
2860 2980 4.942944 TCAGTCAAGGACCTGGATAACTA 58.057 43.478 0.66 0.00 32.18 2.24
2861 2981 3.791320 TCAGTCAAGGACCTGGATAACT 58.209 45.455 0.66 0.00 32.18 2.24
2862 2982 4.553330 TTCAGTCAAGGACCTGGATAAC 57.447 45.455 0.66 0.00 32.18 1.89
2863 2983 5.779241 ATTTCAGTCAAGGACCTGGATAA 57.221 39.130 0.66 0.00 32.18 1.75
2892 3016 8.597167 AGCTAGCATTATATCAATGGACTTACA 58.403 33.333 18.83 0.00 0.00 2.41
2981 3105 8.426881 GTCTCTAGACAAAAAGAAACTCAGTT 57.573 34.615 5.24 0.00 44.18 3.16
3050 3174 8.203485 TGATTAGGCATTCAAAAGTCAAAAGTT 58.797 29.630 0.00 0.00 0.00 2.66
3051 3175 7.725251 TGATTAGGCATTCAAAAGTCAAAAGT 58.275 30.769 0.00 0.00 0.00 2.66
3106 3231 2.107953 GCTAGAAGCGGCAGAGGG 59.892 66.667 1.45 0.00 0.00 4.30
3143 3268 3.196901 ACTGATGATGCACATGCCATTTT 59.803 39.130 0.49 0.00 39.56 1.82
3154 3279 7.095355 CGATCATATCTCAAAACTGATGATGCA 60.095 37.037 0.00 0.00 34.89 3.96
3193 3318 9.494479 CTATGAAATGTTATAGCATAATTGGCG 57.506 33.333 2.17 0.00 36.08 5.69
3194 3319 9.793252 CCTATGAAATGTTATAGCATAATTGGC 57.207 33.333 2.17 0.00 0.00 4.52
3347 3481 9.699410 ACTCCATGATCAAACTTCCATATTAAA 57.301 29.630 0.00 0.00 0.00 1.52
3348 3482 9.699410 AACTCCATGATCAAACTTCCATATTAA 57.301 29.630 0.00 0.00 0.00 1.40
3350 3484 9.125026 GTAACTCCATGATCAAACTTCCATATT 57.875 33.333 0.00 0.00 0.00 1.28
3459 3594 2.673368 CGAGGATCACAACTGGTTTAGC 59.327 50.000 0.00 0.00 33.17 3.09
3503 3638 4.642437 CACAGCTCATAGGAGAACACTAGA 59.358 45.833 8.95 0.00 44.26 2.43
3506 3641 3.435275 TCACAGCTCATAGGAGAACACT 58.565 45.455 8.95 0.00 44.26 3.55
3606 3742 7.571613 GCAAGCAAGCAATACAAAATCATTGAA 60.572 33.333 0.00 0.00 34.69 2.69
3682 3822 8.939929 GTTCATCACATTTGTAAAGAGAGATCA 58.060 33.333 0.00 0.00 0.00 2.92
3694 3834 2.898612 TGGGCATGTTCATCACATTTGT 59.101 40.909 0.00 0.00 44.40 2.83
3756 3896 4.067896 TGCTGCTGTAAGAAAGAAGAAGG 58.932 43.478 0.00 0.00 34.07 3.46
3811 3951 4.400961 GCTGGAGCCGCTTGGAGT 62.401 66.667 0.00 0.00 34.31 3.85
3936 4077 3.861840 CAATTAGCCTCTCACCTTCGAA 58.138 45.455 0.00 0.00 0.00 3.71
4016 4157 8.673711 TCCAAACAGAATAACATACTGCATAAC 58.326 33.333 0.00 0.00 35.38 1.89
4036 4180 1.267532 CGCAGCGATGTACATCCAAAC 60.268 52.381 26.33 15.10 34.40 2.93
4038 4182 2.676744 CGCAGCGATGTACATCCAA 58.323 52.632 26.33 0.00 34.40 3.53
4246 4463 5.450274 GGAGTTACTAGAAAGTAGAAGCCCG 60.450 48.000 0.00 0.00 39.36 6.13
4271 4488 2.813754 CAAGAAAATGAACAGGCGGAGA 59.186 45.455 0.00 0.00 0.00 3.71
4272 4489 2.813754 TCAAGAAAATGAACAGGCGGAG 59.186 45.455 0.00 0.00 0.00 4.63
4282 4499 8.956426 ACTAACAGTTGAAGTTCAAGAAAATGA 58.044 29.630 18.56 1.30 37.00 2.57
4291 4508 9.880157 ACTAGTAAAACTAACAGTTGAAGTTCA 57.120 29.630 0.08 0.08 38.66 3.18
4501 7598 7.042335 GCATAGTGGAGAACTAACATAACAGT 58.958 38.462 0.00 0.00 44.57 3.55
4502 7599 6.199154 CGCATAGTGGAGAACTAACATAACAG 59.801 42.308 0.00 0.00 44.57 3.16
4584 7681 0.309612 GGCTACAACCACAACCAACG 59.690 55.000 0.00 0.00 0.00 4.10
4586 7683 0.553819 AGGGCTACAACCACAACCAA 59.446 50.000 0.00 0.00 0.00 3.67
4587 7684 0.179004 CAGGGCTACAACCACAACCA 60.179 55.000 0.00 0.00 0.00 3.67
4588 7685 0.179001 ACAGGGCTACAACCACAACC 60.179 55.000 0.00 0.00 0.00 3.77
4602 7729 5.189145 ACCCATACTTAACTTCTACACAGGG 59.811 44.000 0.00 0.00 36.17 4.45
4656 7783 3.608474 GCTTGCAAACCCAAGTTACTACG 60.608 47.826 0.00 0.00 43.17 3.51
4658 7785 2.888414 GGCTTGCAAACCCAAGTTACTA 59.112 45.455 7.71 0.00 43.17 1.82
4659 7786 1.686587 GGCTTGCAAACCCAAGTTACT 59.313 47.619 7.71 0.00 43.17 2.24
4685 7823 2.458006 GAAAGCGGTCGCCAAGTTGG 62.458 60.000 18.17 18.17 43.17 3.77
4773 7911 2.096268 CAGCAACGTTGGATGTACACTG 60.096 50.000 28.33 19.18 0.00 3.66
4774 7912 2.143122 CAGCAACGTTGGATGTACACT 58.857 47.619 28.33 12.10 0.00 3.55
4775 7913 2.096417 GTCAGCAACGTTGGATGTACAC 60.096 50.000 28.33 10.00 0.00 2.90
4776 7914 2.139917 GTCAGCAACGTTGGATGTACA 58.860 47.619 28.33 0.00 0.00 2.90
4777 7915 2.412089 GAGTCAGCAACGTTGGATGTAC 59.588 50.000 28.33 16.14 0.00 2.90
4778 7916 2.683968 GAGTCAGCAACGTTGGATGTA 58.316 47.619 28.33 7.09 0.00 2.29
4779 7917 1.512926 GAGTCAGCAACGTTGGATGT 58.487 50.000 28.33 10.46 0.00 3.06
4780 7918 0.439985 CGAGTCAGCAACGTTGGATG 59.560 55.000 28.33 17.74 0.00 3.51
4799 7937 1.518903 GACCCAAGCCAGTGAGTTGC 61.519 60.000 0.00 0.00 0.00 4.17
4818 7956 2.743636 ACGTGATGAGTAAGGTGTGG 57.256 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.