Multiple sequence alignment - TraesCS5A01G168700

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 TraesCS5A01G168700 chr5A 100.000 4613 0 0 1 4613 359695115 359699727 0.000000e+00 8519.0
1 TraesCS5A01G168700 chr5A 82.886 298 34 14 2 290 32671693 32671404 7.660000e-63 252.0
2 TraesCS5A01G168700 chr5D 91.077 3295 167 51 1 3214 270240451 270243699 0.000000e+00 4338.0
3 TraesCS5A01G168700 chr5D 94.685 1317 61 8 3211 4524 270243727 270245037 0.000000e+00 2036.0
4 TraesCS5A01G168700 chr5D 85.000 280 29 11 7 279 421372838 421373111 5.880000e-69 272.0
5 TraesCS5A01G168700 chr5D 84.397 282 30 12 7 279 42912252 42911976 9.840000e-67 265.0
6 TraesCS5A01G168700 chr5D 73.401 297 74 4 4153 4446 356663156 356663450 6.310000e-19 106.0
7 TraesCS5A01G168700 chr5B 90.600 2702 145 41 549 3214 307262731 307265359 0.000000e+00 3482.0
8 TraesCS5A01G168700 chr5B 91.957 1405 72 19 3211 4613 307265387 307266752 0.000000e+00 1930.0
9 TraesCS5A01G168700 chr5B 80.769 312 46 11 17 318 680969946 680969639 9.980000e-57 231.0
10 TraesCS5A01G168700 chr3A 85.911 291 28 9 2 283 111078163 111077877 9.700000e-77 298.0
11 TraesCS5A01G168700 chr1A 84.106 302 33 12 2 292 506295174 506294877 1.260000e-70 278.0
12 TraesCS5A01G168700 chr1A 94.231 52 3 0 457 508 431930256 431930205 3.830000e-11 80.5
13 TraesCS5A01G168700 chr7D 84.138 290 35 8 2 290 549130492 549130213 2.120000e-68 270.0
14 TraesCS5A01G168700 chr7D 80.978 184 25 7 77 255 87427105 87426927 2.240000e-28 137.0
15 TraesCS5A01G168700 chr7D 95.833 48 2 0 459 506 131625040 131624993 1.380000e-10 78.7
16 TraesCS5A01G168700 chr2A 84.000 300 29 14 2 291 150446461 150446171 2.120000e-68 270.0
17 TraesCS5A01G168700 chr6A 84.698 281 28 10 3 274 585496050 585495776 2.740000e-67 267.0
18 TraesCS5A01G168700 chr7A 83.444 302 32 15 2 291 20733300 20733595 9.840000e-67 265.0
19 TraesCS5A01G168700 chr3D 82.781 302 33 15 2 289 156205729 156205433 7.660000e-63 252.0
20 TraesCS5A01G168700 chr6D 94.643 56 1 1 458 513 437322689 437322636 8.220000e-13 86.1
21 TraesCS5A01G168700 chr6B 96.078 51 2 0 458 508 662088004 662087954 2.960000e-12 84.2
22 TraesCS5A01G168700 chrUn 100.000 28 0 0 481 508 11255513 11255540 8.000000e-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 TraesCS5A01G168700 chr5A 359695115 359699727 4612 False 8519 8519 100.0000 1 4613 1 chr5A.!!$F1 4612
1 TraesCS5A01G168700 chr5D 270240451 270245037 4586 False 3187 4338 92.8810 1 4524 2 chr5D.!!$F3 4523
2 TraesCS5A01G168700 chr5B 307262731 307266752 4021 False 2706 3482 91.2785 549 4613 2 chr5B.!!$F1 4064

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
803 848 0.855349 CTTCGCTATGTGTGATCCGC 59.145 55.0 0.00 0.00 34.87 5.54 F
1236 1299 0.188587 TCCCCTCTATCAGCGGTGAT 59.811 55.0 30.62 30.62 45.82 3.06 F
1239 1302 0.320247 CCTCTATCAGCGGTGATGCC 60.320 60.0 34.11 0.00 43.66 4.40 F
2217 2300 0.725117 CCGTAAGTTAAAGCCCGCTG 59.275 55.0 0.00 0.00 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2013 1.398451 GCGTTATTCGGCCAATCATCG 60.398 52.381 2.24 8.68 40.26 3.84 R
2200 2283 3.990546 GCAGCGGGCTTTAACTTAC 57.009 52.632 0.00 0.00 40.25 2.34 R
2574 2663 4.691175 TGTTATCTCAGCTGCAGAGAATC 58.309 43.478 25.30 18.25 44.56 2.52 R
3953 4081 0.421904 AACCCACCCCTAGAGATGGT 59.578 55.000 0.00 0.00 0.00 3.55 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
309 313 4.718858 TCTACACGTTCAACATTTTCCG 57.281 40.909 0.00 0.00 0.00 4.30
322 326 5.551760 ACATTTTCCGAATGCTTGAGTAG 57.448 39.130 0.00 0.00 0.00 2.57
327 331 6.385649 TTTCCGAATGCTTGAGTAGTTTTT 57.614 33.333 0.00 0.00 0.00 1.94
489 523 2.973899 GGAAGCTGGACTCGCTGA 59.026 61.111 0.00 0.00 37.87 4.26
602 636 3.107642 ACTAACCACCTCGTTCACTTG 57.892 47.619 0.00 0.00 0.00 3.16
689 723 2.689983 CACCAACAAACCAAAGCTCTCT 59.310 45.455 0.00 0.00 0.00 3.10
784 829 3.300667 GATTCATCCGATGCGCGCC 62.301 63.158 30.77 13.55 39.11 6.53
801 846 1.221414 GCCTTCGCTATGTGTGATCC 58.779 55.000 0.00 0.00 34.87 3.36
802 847 1.491670 CCTTCGCTATGTGTGATCCG 58.508 55.000 0.00 0.00 34.87 4.18
803 848 0.855349 CTTCGCTATGTGTGATCCGC 59.145 55.000 0.00 0.00 34.87 5.54
804 849 0.869880 TTCGCTATGTGTGATCCGCG 60.870 55.000 0.00 0.00 41.69 6.46
805 850 2.931386 GCTATGTGTGATCCGCGC 59.069 61.111 0.00 0.00 0.00 6.86
850 895 2.097104 CAGCTTTCGTTGCATGCTTTTG 60.097 45.455 20.33 6.36 0.00 2.44
872 917 1.945354 GCCCGGATCTGACGAGAACA 61.945 60.000 0.73 0.00 0.00 3.18
893 938 2.279120 CGTCCAGATCCGAGCTGC 60.279 66.667 8.20 0.00 32.06 5.25
898 943 1.424493 CCAGATCCGAGCTGCGTTTC 61.424 60.000 8.20 0.00 38.67 2.78
926 971 1.949525 TGGTTTTGAGCTGCTTCTGTC 59.050 47.619 2.53 0.00 0.00 3.51
1021 1075 0.259065 GGGGGAATTCTCCAAGGTCC 59.741 60.000 25.81 3.43 44.51 4.46
1034 1088 2.616510 CCAAGGTCCGCAGATTCTTTCT 60.617 50.000 0.00 0.00 33.90 2.52
1049 1103 7.659390 CAGATTCTTTCTCTGTTCCTGTTACTT 59.341 37.037 0.00 0.00 36.26 2.24
1050 1104 7.659390 AGATTCTTTCTCTGTTCCTGTTACTTG 59.341 37.037 0.00 0.00 0.00 3.16
1051 1105 6.235231 TCTTTCTCTGTTCCTGTTACTTGT 57.765 37.500 0.00 0.00 0.00 3.16
1052 1106 6.650120 TCTTTCTCTGTTCCTGTTACTTGTT 58.350 36.000 0.00 0.00 0.00 2.83
1053 1107 6.538742 TCTTTCTCTGTTCCTGTTACTTGTTG 59.461 38.462 0.00 0.00 0.00 3.33
1055 1109 3.211045 TCTGTTCCTGTTACTTGTTGCC 58.789 45.455 0.00 0.00 0.00 4.52
1056 1110 2.948979 CTGTTCCTGTTACTTGTTGCCA 59.051 45.455 0.00 0.00 0.00 4.92
1057 1111 3.561143 TGTTCCTGTTACTTGTTGCCAT 58.439 40.909 0.00 0.00 0.00 4.40
1058 1112 4.720046 TGTTCCTGTTACTTGTTGCCATA 58.280 39.130 0.00 0.00 0.00 2.74
1059 1113 4.517453 TGTTCCTGTTACTTGTTGCCATAC 59.483 41.667 0.00 0.00 0.00 2.39
1069 1123 4.456911 ACTTGTTGCCATACATTCTGACTG 59.543 41.667 0.00 0.00 0.00 3.51
1072 1126 2.358957 TGCCATACATTCTGACTGCAC 58.641 47.619 0.00 0.00 0.00 4.57
1075 1129 2.349580 CCATACATTCTGACTGCACGTG 59.650 50.000 12.28 12.28 0.00 4.49
1087 1141 3.064207 ACTGCACGTGTTTACATTCGAT 58.936 40.909 18.38 0.00 0.00 3.59
1090 1144 4.215201 TGCACGTGTTTACATTCGATTTG 58.785 39.130 18.38 0.00 0.00 2.32
1091 1145 3.057609 GCACGTGTTTACATTCGATTTGC 59.942 43.478 18.38 0.00 0.00 3.68
1092 1146 4.215201 CACGTGTTTACATTCGATTTGCA 58.785 39.130 7.58 0.00 0.00 4.08
1102 1156 3.617540 TTCGATTTGCACGTTCATTGT 57.382 38.095 0.00 0.00 0.00 2.71
1104 1158 4.733972 TCGATTTGCACGTTCATTGTTA 57.266 36.364 0.00 0.00 0.00 2.41
1105 1159 5.289917 TCGATTTGCACGTTCATTGTTAT 57.710 34.783 0.00 0.00 0.00 1.89
1106 1160 5.085390 TCGATTTGCACGTTCATTGTTATG 58.915 37.500 0.00 0.00 0.00 1.90
1107 1161 5.085390 CGATTTGCACGTTCATTGTTATGA 58.915 37.500 0.00 0.00 39.00 2.15
1108 1162 5.225743 CGATTTGCACGTTCATTGTTATGAG 59.774 40.000 0.00 0.00 41.60 2.90
1109 1163 4.418013 TTGCACGTTCATTGTTATGAGG 57.582 40.909 0.00 0.00 41.60 3.86
1110 1164 2.746904 TGCACGTTCATTGTTATGAGGG 59.253 45.455 0.00 0.00 41.60 4.30
1120 1174 3.998913 TGTTATGAGGGTGATCTTGCA 57.001 42.857 0.00 0.00 0.00 4.08
1123 1177 2.414994 ATGAGGGTGATCTTGCACAG 57.585 50.000 0.00 0.00 40.52 3.66
1125 1179 3.595819 GGGTGATCTTGCACAGCC 58.404 61.111 7.43 7.43 45.06 4.85
1126 1180 2.401766 GGGTGATCTTGCACAGCCG 61.402 63.158 7.43 0.00 43.06 5.52
1133 1187 1.317613 TCTTGCACAGCCGAATTTGT 58.682 45.000 0.00 0.00 0.00 2.83
1151 1205 3.855255 TGTGTCCCAAGAACTGATCAA 57.145 42.857 0.00 0.00 0.00 2.57
1153 1207 4.326826 TGTGTCCCAAGAACTGATCAATC 58.673 43.478 0.00 0.00 0.00 2.67
1155 1209 2.939103 GTCCCAAGAACTGATCAATCGG 59.061 50.000 0.00 0.00 39.11 4.18
1163 1217 2.513753 ACTGATCAATCGGTTTGCCAA 58.486 42.857 0.00 0.00 43.59 4.52
1165 1219 3.320541 ACTGATCAATCGGTTTGCCAAAA 59.679 39.130 0.00 0.00 43.59 2.44
1193 1249 4.243007 TGTCGACCATGCATAGATGTAG 57.757 45.455 14.12 0.00 0.00 2.74
1194 1250 3.636764 TGTCGACCATGCATAGATGTAGT 59.363 43.478 14.12 0.00 0.00 2.73
1196 1252 5.476945 TGTCGACCATGCATAGATGTAGTAT 59.523 40.000 14.12 0.00 0.00 2.12
1206 1269 9.845740 ATGCATAGATGTAGTATAAACCAAACA 57.154 29.630 0.00 0.00 0.00 2.83
1207 1270 9.674068 TGCATAGATGTAGTATAAACCAAACAA 57.326 29.630 0.00 0.00 0.00 2.83
1221 1284 6.707440 AACCAAACAATTTTTGATTTCCCC 57.293 33.333 12.02 0.00 0.00 4.81
1226 1289 8.102676 CCAAACAATTTTTGATTTCCCCTCTAT 58.897 33.333 12.02 0.00 0.00 1.98
1233 1296 1.694696 GATTTCCCCTCTATCAGCGGT 59.305 52.381 0.00 0.00 0.00 5.68
1236 1299 0.188587 TCCCCTCTATCAGCGGTGAT 59.811 55.000 30.62 30.62 45.82 3.06
1239 1302 0.320247 CCTCTATCAGCGGTGATGCC 60.320 60.000 34.11 0.00 43.66 4.40
1252 1315 3.244215 CGGTGATGCCCTATGATAACTGT 60.244 47.826 0.00 0.00 0.00 3.55
1260 1323 4.780815 CCCTATGATAACTGTGAGCCAAA 58.219 43.478 0.00 0.00 0.00 3.28
1344 1407 9.120538 CACCTAGTTATGTTAATTGGCTGTTAT 57.879 33.333 0.00 0.00 0.00 1.89
1392 1455 3.417101 TCGTGTAAATTGGGCTGTCAAT 58.583 40.909 0.00 0.00 38.84 2.57
1395 1458 4.082787 CGTGTAAATTGGGCTGTCAATTCT 60.083 41.667 11.44 6.93 43.93 2.40
1396 1459 5.564651 CGTGTAAATTGGGCTGTCAATTCTT 60.565 40.000 11.44 3.48 43.93 2.52
1398 1461 6.705825 GTGTAAATTGGGCTGTCAATTCTTTT 59.294 34.615 11.44 3.30 43.93 2.27
1486 1562 5.523438 AGCTTAACTACTCCACATAGAGC 57.477 43.478 0.00 0.00 37.39 4.09
1489 1565 3.784701 AACTACTCCACATAGAGCACG 57.215 47.619 0.00 0.00 37.39 5.34
1567 1643 8.627208 AGATTTTGATTTTCAGAAGCAGAGTA 57.373 30.769 0.00 0.00 30.47 2.59
1568 1644 9.071276 AGATTTTGATTTTCAGAAGCAGAGTAA 57.929 29.630 0.00 0.00 30.47 2.24
1569 1645 9.683069 GATTTTGATTTTCAGAAGCAGAGTAAA 57.317 29.630 0.00 0.00 28.84 2.01
1570 1646 9.688592 ATTTTGATTTTCAGAAGCAGAGTAAAG 57.311 29.630 0.00 0.00 0.00 1.85
1571 1647 7.807977 TTGATTTTCAGAAGCAGAGTAAAGT 57.192 32.000 0.00 0.00 0.00 2.66
1612 1688 3.895656 GCTAAAGGGAAAAAGACCAAGGT 59.104 43.478 0.00 0.00 0.00 3.50
1800 1876 8.474577 GCTTTCAATTGATAAATATGAAGTGCG 58.525 33.333 9.40 0.00 32.21 5.34
1877 1953 1.272147 ACACAGGAATCTTGCCCTTCC 60.272 52.381 0.00 0.00 41.07 3.46
1937 2013 3.495001 GTGTTGCTGTGAAGTACTTCTCC 59.505 47.826 30.47 22.22 40.14 3.71
2042 2120 7.223058 CGAAGGTAATTCATTCAGTCTGTAC 57.777 40.000 0.00 0.00 37.83 2.90
2217 2300 0.725117 CCGTAAGTTAAAGCCCGCTG 59.275 55.000 0.00 0.00 0.00 5.18
2380 2464 7.771183 ACAAAGAGCATTAGTTGAACAGAAAA 58.229 30.769 0.00 0.00 0.00 2.29
2457 2541 1.382522 CCTGAATGTCCAATGACCGG 58.617 55.000 0.00 0.00 41.01 5.28
2458 2542 1.065491 CCTGAATGTCCAATGACCGGA 60.065 52.381 9.46 0.00 41.01 5.14
2461 2545 3.696045 TGAATGTCCAATGACCGGAAAT 58.304 40.909 9.46 0.00 41.01 2.17
2574 2663 7.891561 TGGATTTACCTTTGACACCTATTTTG 58.108 34.615 0.00 0.00 39.86 2.44
2875 2964 4.276926 GCACTTGAGAACTTGGACTTGATT 59.723 41.667 0.00 0.00 0.00 2.57
2943 3032 9.453572 TCTTGTGATCTATGCTAAATTTGAGTT 57.546 29.630 0.00 0.00 0.00 3.01
3005 3098 3.620929 GCATCATACTCTTGTGCCATG 57.379 47.619 0.00 0.00 0.00 3.66
3040 3133 6.365518 TGCAGCATGTTTATGTTGTATTGTTG 59.634 34.615 0.00 0.00 44.49 3.33
3090 3183 1.836802 GGAGCTCTCATGGAGTTTCCT 59.163 52.381 14.64 8.19 43.62 3.36
3128 3221 3.056393 GGTAGGCCCCATTTAAAACACAC 60.056 47.826 0.00 0.00 0.00 3.82
3480 3605 3.128242 AGCAGGCAAATTTCTGAATCTCG 59.872 43.478 10.29 0.00 33.11 4.04
3483 3608 3.691609 AGGCAAATTTCTGAATCTCGGTC 59.308 43.478 0.00 0.00 0.00 4.79
3649 3775 2.174639 TCTTTCACCCCTGTGTGTTCAT 59.825 45.455 0.00 0.00 43.26 2.57
3653 3779 0.110486 ACCCCTGTGTGTTCATGGTC 59.890 55.000 0.00 0.00 0.00 4.02
3706 3832 0.814457 AACCAAAAGCGCAACTGTGA 59.186 45.000 11.47 0.00 0.00 3.58
3787 3913 6.122850 TGCATGCTGTGTATCTTACATTTC 57.877 37.500 20.33 0.00 41.34 2.17
3854 3980 4.745620 GCGAACTAACACTCTTCTCAAACT 59.254 41.667 0.00 0.00 0.00 2.66
3953 4081 2.715749 ATGGCCTCATCGATGAAACA 57.284 45.000 27.09 23.73 36.18 2.83
3955 4083 1.017387 GGCCTCATCGATGAAACACC 58.983 55.000 27.09 20.60 36.18 4.16
4014 4142 4.041444 CCTCTGAATTCTTATAGGCAGCCT 59.959 45.833 20.63 20.63 37.71 4.58
4135 4263 9.020731 TGAACTTAATGGGAATAGAGGAAAAAC 57.979 33.333 0.00 0.00 0.00 2.43
4204 4332 2.024655 AGTTGAGATCTACCACCCCGTA 60.025 50.000 0.00 0.00 0.00 4.02
4304 4432 9.290988 TGTCTTCATCTAAGGTAGTGATATCTC 57.709 37.037 3.98 0.00 35.75 2.75
4428 4557 4.361783 CCCTAATTTGGGGACTTTTCCAT 58.638 43.478 16.52 0.00 46.50 3.41
4487 4616 9.928236 GATGCTACATTTTTCTAGAAGAATGTC 57.072 33.333 37.83 29.38 46.53 3.06
4496 4625 8.450578 TTTTCTAGAAGAATGTCTGAAAGCAA 57.549 30.769 5.12 0.00 33.67 3.91
4500 4629 6.793492 AGAAGAATGTCTGAAAGCAACTAC 57.207 37.500 0.00 0.00 0.00 2.73
4539 4668 1.003696 GCTGGAAGTACTCAGGGCTTT 59.996 52.381 12.20 0.00 35.30 3.51
4560 4689 2.038557 TCCCTAAGTTCAACCAGTGAGC 59.961 50.000 0.00 0.00 37.61 4.26
4566 4695 3.825328 AGTTCAACCAGTGAGCTTGAAT 58.175 40.909 11.45 2.76 44.73 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 278 4.613944 ACGTGTAGAAAGATTGTCGAACA 58.386 39.130 0.00 0.00 0.00 3.18
279 283 6.281848 TGTTGAACGTGTAGAAAGATTGTC 57.718 37.500 0.00 0.00 0.00 3.18
285 289 5.619607 CGGAAAATGTTGAACGTGTAGAAAG 59.380 40.000 0.00 0.00 0.00 2.62
428 432 6.813649 AGCCTCTTTTTCTGTTTTCTGTTTTC 59.186 34.615 0.00 0.00 0.00 2.29
433 467 5.039333 CACAGCCTCTTTTTCTGTTTTCTG 58.961 41.667 0.00 0.00 38.85 3.02
435 469 3.798878 GCACAGCCTCTTTTTCTGTTTTC 59.201 43.478 0.00 0.00 38.85 2.29
489 523 1.066858 CACGCCCCTATATCTCGCATT 60.067 52.381 0.00 0.00 0.00 3.56
689 723 0.631753 AAGGGAGAGTGATCGGGAGA 59.368 55.000 0.00 0.00 46.90 3.71
719 761 3.650942 GTGGGAGAGATCTAGAGAGGAGA 59.349 52.174 0.00 0.00 0.00 3.71
720 762 3.244911 GGTGGGAGAGATCTAGAGAGGAG 60.245 56.522 0.00 0.00 0.00 3.69
721 763 2.714250 GGTGGGAGAGATCTAGAGAGGA 59.286 54.545 0.00 0.00 0.00 3.71
784 829 0.855349 GCGGATCACACATAGCGAAG 59.145 55.000 0.00 0.00 0.00 3.79
850 895 3.781770 CTCGTCAGATCCGGGCTGC 62.782 68.421 17.23 12.39 33.45 5.25
872 917 2.835431 CTCGGATCTGGACGGCCT 60.835 66.667 9.82 0.00 34.31 5.19
898 943 0.318120 AGCTCAAAACCAAATGGCGG 59.682 50.000 0.00 0.00 39.32 6.13
926 971 2.351835 CGCACCCAGATAGGTAAGATCG 60.352 54.545 0.00 0.00 38.39 3.69
1021 1075 3.370366 CAGGAACAGAGAAAGAATCTGCG 59.630 47.826 2.96 0.00 46.64 5.18
1034 1088 3.211045 GGCAACAAGTAACAGGAACAGA 58.789 45.455 0.00 0.00 0.00 3.41
1049 1103 2.749076 GCAGTCAGAATGTATGGCAACA 59.251 45.455 0.00 0.00 46.63 3.33
1050 1104 2.749076 TGCAGTCAGAATGTATGGCAAC 59.251 45.455 0.00 0.00 37.40 4.17
1051 1105 2.749076 GTGCAGTCAGAATGTATGGCAA 59.251 45.455 0.00 0.00 37.40 4.52
1052 1106 2.358957 GTGCAGTCAGAATGTATGGCA 58.641 47.619 0.00 0.00 37.40 4.92
1053 1107 1.328680 CGTGCAGTCAGAATGTATGGC 59.671 52.381 0.00 0.00 37.40 4.40
1055 1109 2.995939 ACACGTGCAGTCAGAATGTATG 59.004 45.455 17.22 6.62 37.40 2.39
1056 1110 3.319137 ACACGTGCAGTCAGAATGTAT 57.681 42.857 17.22 0.00 37.40 2.29
1057 1111 2.812358 ACACGTGCAGTCAGAATGTA 57.188 45.000 17.22 0.00 37.40 2.29
1058 1112 1.953559 AACACGTGCAGTCAGAATGT 58.046 45.000 17.22 0.00 37.40 2.71
1059 1113 3.247411 TGTAAACACGTGCAGTCAGAATG 59.753 43.478 17.22 0.00 37.54 2.67
1069 1123 3.057609 GCAAATCGAATGTAAACACGTGC 59.942 43.478 17.22 0.00 0.00 5.34
1072 1126 3.294371 CGTGCAAATCGAATGTAAACACG 59.706 43.478 13.58 13.58 41.72 4.49
1075 1129 4.907010 TGAACGTGCAAATCGAATGTAAAC 59.093 37.500 0.00 0.00 0.00 2.01
1087 1141 4.320861 CCCTCATAACAATGAACGTGCAAA 60.321 41.667 0.00 0.00 0.00 3.68
1090 1144 2.747446 ACCCTCATAACAATGAACGTGC 59.253 45.455 0.00 0.00 0.00 5.34
1091 1145 4.000325 TCACCCTCATAACAATGAACGTG 59.000 43.478 0.00 7.61 33.98 4.49
1092 1146 4.280436 TCACCCTCATAACAATGAACGT 57.720 40.909 0.00 0.00 0.00 3.99
1102 1156 3.877559 CTGTGCAAGATCACCCTCATAA 58.122 45.455 0.00 0.00 36.17 1.90
1104 1158 1.681166 GCTGTGCAAGATCACCCTCAT 60.681 52.381 0.00 0.00 36.17 2.90
1105 1159 0.321919 GCTGTGCAAGATCACCCTCA 60.322 55.000 0.00 0.00 36.17 3.86
1106 1160 1.028868 GGCTGTGCAAGATCACCCTC 61.029 60.000 0.00 0.00 36.17 4.30
1107 1161 1.001641 GGCTGTGCAAGATCACCCT 60.002 57.895 0.00 0.00 36.17 4.34
1108 1162 2.401766 CGGCTGTGCAAGATCACCC 61.402 63.158 0.00 0.00 36.17 4.61
1109 1163 0.955428 TTCGGCTGTGCAAGATCACC 60.955 55.000 0.00 0.00 36.17 4.02
1110 1164 1.089920 ATTCGGCTGTGCAAGATCAC 58.910 50.000 0.00 0.00 37.48 3.06
1120 1174 0.179004 TGGGACACAAATTCGGCTGT 60.179 50.000 0.00 0.00 0.00 4.40
1123 1177 1.243902 TCTTGGGACACAAATTCGGC 58.756 50.000 0.00 0.00 39.29 5.54
1125 1179 3.563808 TCAGTTCTTGGGACACAAATTCG 59.436 43.478 0.00 0.00 39.29 3.34
1126 1180 5.241506 TGATCAGTTCTTGGGACACAAATTC 59.758 40.000 0.00 0.00 39.29 2.17
1133 1187 3.599343 CGATTGATCAGTTCTTGGGACA 58.401 45.455 0.00 0.00 0.00 4.02
1167 1221 5.357878 ACATCTATGCATGGTCGACATTTTT 59.642 36.000 18.91 0.00 37.84 1.94
1168 1222 4.883585 ACATCTATGCATGGTCGACATTTT 59.116 37.500 18.91 0.00 37.84 1.82
1196 1252 8.055790 AGGGGAAATCAAAAATTGTTTGGTTTA 58.944 29.630 9.94 0.00 41.28 2.01
1206 1269 6.183360 CGCTGATAGAGGGGAAATCAAAAATT 60.183 38.462 0.00 0.00 0.00 1.82
1207 1270 5.300286 CGCTGATAGAGGGGAAATCAAAAAT 59.700 40.000 0.00 0.00 0.00 1.82
1221 1284 0.320247 GGGCATCACCGCTGATAGAG 60.320 60.000 0.00 0.00 40.62 2.43
1226 1289 1.048160 TCATAGGGCATCACCGCTGA 61.048 55.000 0.00 0.00 40.62 4.26
1233 1296 4.503817 GCTCACAGTTATCATAGGGCATCA 60.504 45.833 0.00 0.00 0.00 3.07
1236 1299 2.104792 GGCTCACAGTTATCATAGGGCA 59.895 50.000 0.00 0.00 0.00 5.36
1239 1302 5.674525 TCTTTGGCTCACAGTTATCATAGG 58.325 41.667 0.00 0.00 0.00 2.57
1252 1315 2.645838 AGTTTCAGCTCTTTGGCTCA 57.354 45.000 0.00 0.00 41.00 4.26
1260 1323 0.905357 ATGGCGGTAGTTTCAGCTCT 59.095 50.000 0.00 0.00 0.00 4.09
1344 1407 3.382227 CCAGTGCCATATTGCAAGAATGA 59.618 43.478 20.59 4.61 44.11 2.57
1395 1458 8.559536 CAGCTTCAGTTTACACTTCATAGAAAA 58.440 33.333 0.00 0.00 0.00 2.29
1396 1459 7.931407 TCAGCTTCAGTTTACACTTCATAGAAA 59.069 33.333 0.00 0.00 0.00 2.52
1398 1461 6.993079 TCAGCTTCAGTTTACACTTCATAGA 58.007 36.000 0.00 0.00 0.00 1.98
1486 1562 0.105964 TTTCAGACAGACCACCCGTG 59.894 55.000 0.00 0.00 0.00 4.94
1489 1565 2.633481 ACTAGTTTCAGACAGACCACCC 59.367 50.000 0.00 0.00 0.00 4.61
1567 1643 5.506317 GCATCAAGCAGTGAACTGTAACTTT 60.506 40.000 11.87 0.00 45.45 2.66
1568 1644 4.023707 GCATCAAGCAGTGAACTGTAACTT 60.024 41.667 11.87 4.52 45.45 2.66
1569 1645 3.499918 GCATCAAGCAGTGAACTGTAACT 59.500 43.478 11.87 0.00 45.45 2.24
1570 1646 3.814945 GCATCAAGCAGTGAACTGTAAC 58.185 45.455 11.87 0.00 45.45 2.50
1877 1953 4.213270 TCCAGTAGCAAAATGTTCTTCACG 59.787 41.667 0.00 0.00 0.00 4.35
1937 2013 1.398451 GCGTTATTCGGCCAATCATCG 60.398 52.381 2.24 8.68 40.26 3.84
2042 2120 4.588899 TGGTAAGACAGGAATTCACATGG 58.411 43.478 7.93 0.00 0.00 3.66
2098 2181 8.394877 GTGAATTACAATCGTTGACCAATGATA 58.605 33.333 15.42 3.57 43.96 2.15
2200 2283 3.990546 GCAGCGGGCTTTAACTTAC 57.009 52.632 0.00 0.00 40.25 2.34
2217 2300 8.669243 GGAGTATTACCTGCATTATAAATCAGC 58.331 37.037 10.28 4.46 0.00 4.26
2411 2495 5.103728 TCCTCAATTAGGGCATACAATTGGA 60.104 40.000 10.83 0.10 46.55 3.53
2457 2541 7.386059 ACTTTTCACCCATCCAATAACATTTC 58.614 34.615 0.00 0.00 0.00 2.17
2458 2542 7.315066 ACTTTTCACCCATCCAATAACATTT 57.685 32.000 0.00 0.00 0.00 2.32
2461 2545 6.325028 TGAAACTTTTCACCCATCCAATAACA 59.675 34.615 0.07 0.00 41.88 2.41
2574 2663 4.691175 TGTTATCTCAGCTGCAGAGAATC 58.309 43.478 25.30 18.25 44.56 2.52
2875 2964 8.208903 TCAATAATCTCATCAATGCAGAGAAGA 58.791 33.333 6.69 2.00 41.30 2.87
2941 3030 7.335422 ACAGAGGATTATGAAACATGAGACAAC 59.665 37.037 0.00 0.00 0.00 3.32
2943 3032 6.950842 ACAGAGGATTATGAAACATGAGACA 58.049 36.000 0.00 0.00 0.00 3.41
3090 3183 6.240645 GGGGCCTACCTTTTCCCATATATTAA 60.241 42.308 0.84 0.00 40.53 1.40
3128 3221 6.548441 TTAAACCATGTCCTGTAAAACTCG 57.452 37.500 0.00 0.00 0.00 4.18
3363 3488 6.513806 AGAATTATGCTGCACAAATACACA 57.486 33.333 3.57 0.00 0.00 3.72
3364 3489 7.028962 TCAAGAATTATGCTGCACAAATACAC 58.971 34.615 3.57 4.33 0.00 2.90
3480 3605 0.678048 GACAGGAATGTGCAGGGACC 60.678 60.000 0.00 0.00 0.00 4.46
3483 3608 1.843368 AATGACAGGAATGTGCAGGG 58.157 50.000 0.00 0.00 0.00 4.45
3666 3792 3.390521 TGACCGCTACCAGGCCTG 61.391 66.667 26.87 26.87 0.00 4.85
3854 3980 4.946038 CGATAACCGCCCTTTCCA 57.054 55.556 0.00 0.00 0.00 3.53
3902 4030 3.011818 TGCTTGGCAATACAGACATCTG 58.988 45.455 7.36 7.36 42.00 2.90
3903 4031 3.354948 TGCTTGGCAATACAGACATCT 57.645 42.857 0.00 0.00 34.76 2.90
3953 4081 0.421904 AACCCACCCCTAGAGATGGT 59.578 55.000 0.00 0.00 0.00 3.55
3955 4083 1.486726 GACAACCCACCCCTAGAGATG 59.513 57.143 0.00 0.00 0.00 2.90
4014 4142 4.032960 ACATCCCTCTTGCACACATTTA 57.967 40.909 0.00 0.00 0.00 1.40
4072 4200 7.673926 TCCAATGGAGGCTAACTTAGAATTTTT 59.326 33.333 0.00 0.00 0.00 1.94
4108 4236 9.768215 TTTTTCCTCTATTCCCATTAAGTTCAT 57.232 29.630 0.00 0.00 0.00 2.57
4113 4241 7.859325 TCGTTTTTCCTCTATTCCCATTAAG 57.141 36.000 0.00 0.00 0.00 1.85
4135 4263 4.934075 TGCTTGATGACAATCTTCTTCG 57.066 40.909 0.00 0.00 35.37 3.79
4172 4300 4.963318 AGATCTCAACTTCACAACCTCA 57.037 40.909 0.00 0.00 0.00 3.86
4204 4332 4.834496 TGATGGAACCAAAGCTTGAAAGAT 59.166 37.500 0.00 0.00 0.00 2.40
4304 4432 8.200792 AGTAGTTTTAGAGGCTCTCATACATTG 58.799 37.037 22.53 0.00 32.06 2.82
4370 4499 6.606768 AGATGAAGCGACTCAAATCTTTTTC 58.393 36.000 0.00 0.00 0.00 2.29
4373 4502 6.312426 CACTAGATGAAGCGACTCAAATCTTT 59.688 38.462 0.00 0.00 0.00 2.52
4487 4616 5.542779 AGGACAAGTAGTAGTTGCTTTCAG 58.457 41.667 16.19 0.00 31.85 3.02
4496 4625 5.299782 GCACATAGCTAGGACAAGTAGTAGT 59.700 44.000 13.23 0.00 41.15 2.73
4539 4668 2.038557 GCTCACTGGTTGAACTTAGGGA 59.961 50.000 0.00 0.32 32.21 4.20
4574 4703 6.880529 TGCATCGACATTCAACATATATGGAT 59.119 34.615 16.96 2.77 0.00 3.41
4582 4711 3.441222 ACACATGCATCGACATTCAACAT 59.559 39.130 0.00 0.00 0.00 2.71
4584 4713 3.476295 ACACATGCATCGACATTCAAC 57.524 42.857 0.00 0.00 0.00 3.18
4585 4714 4.216042 AGAAACACATGCATCGACATTCAA 59.784 37.500 0.00 0.00 0.00 2.69
4586 4715 3.752747 AGAAACACATGCATCGACATTCA 59.247 39.130 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.