Multiple sequence alignment - TraesCS4D01G117200

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 TraesCS4D01G117200 chr4D 100.000 3781 0 0 1 3781 97963406 97959626 0.000000e+00 6983
1 TraesCS4D01G117200 chr4D 87.116 2018 204 27 904 2912 97970281 97968311 0.000000e+00 2235
2 TraesCS4D01G117200 chr4D 79.774 1419 249 26 1387 2787 98015418 98014020 0.000000e+00 996
3 TraesCS4D01G117200 chr4D 77.778 1368 219 44 1398 2740 435198744 435197437 0.000000e+00 763
4 TraesCS4D01G117200 chr4B 96.696 2270 52 7 869 3117 139549319 139547052 0.000000e+00 3755
5 TraesCS4D01G117200 chr4B 86.236 2216 234 38 866 3047 139572284 139570106 0.000000e+00 2337
6 TraesCS4D01G117200 chr4B 91.304 690 27 9 3099 3781 139546970 139546307 0.000000e+00 911
7 TraesCS4D01G117200 chr4B 90.924 628 46 10 121 739 139564253 139563628 0.000000e+00 833
8 TraesCS4D01G117200 chr4B 81.600 250 29 13 199 432 139564783 139564535 1.390000e-44 191
9 TraesCS4D01G117200 chr4B 95.062 81 4 0 757 837 139549398 139549318 1.100000e-25 128
10 TraesCS4D01G117200 chr1B 83.253 2484 317 58 905 3330 487405524 487407966 0.000000e+00 2191
11 TraesCS4D01G117200 chr4A 95.021 1406 44 15 868 2255 478209460 478210857 0.000000e+00 2185
12 TraesCS4D01G117200 chr4A 96.778 869 25 3 2251 3117 478216299 478217166 0.000000e+00 1447
13 TraesCS4D01G117200 chr4A 79.733 1421 249 26 1387 2784 478191411 478192815 0.000000e+00 992
14 TraesCS4D01G117200 chr4A 88.467 711 45 31 3096 3778 478217216 478217917 0.000000e+00 824
15 TraesCS4D01G117200 chr1D 84.761 2159 267 39 969 3095 363861164 363863292 0.000000e+00 2108
16 TraesCS4D01G117200 chr1A 84.660 2047 265 27 894 2915 463218522 463220544 0.000000e+00 1995
17 TraesCS4D01G117200 chr3D 79.902 1428 206 39 888 2291 134964470 134963100 0.000000e+00 972
18 TraesCS4D01G117200 chr6B 78.756 1431 230 43 888 2289 134838188 134839573 0.000000e+00 891
19 TraesCS4D01G117200 chr3B 79.023 1249 199 40 1387 2598 706754884 706756106 0.000000e+00 797


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 TraesCS4D01G117200 chr4D 97959626 97963406 3780 True 6983.0 6983 100.0000 1 3781 1 chr4D.!!$R1 3780
1 TraesCS4D01G117200 chr4D 97968311 97970281 1970 True 2235.0 2235 87.1160 904 2912 1 chr4D.!!$R2 2008
2 TraesCS4D01G117200 chr4D 98014020 98015418 1398 True 996.0 996 79.7740 1387 2787 1 chr4D.!!$R3 1400
3 TraesCS4D01G117200 chr4D 435197437 435198744 1307 True 763.0 763 77.7780 1398 2740 1 chr4D.!!$R4 1342
4 TraesCS4D01G117200 chr4B 139570106 139572284 2178 True 2337.0 2337 86.2360 866 3047 1 chr4B.!!$R1 2181
5 TraesCS4D01G117200 chr4B 139546307 139549398 3091 True 1598.0 3755 94.3540 757 3781 3 chr4B.!!$R2 3024
6 TraesCS4D01G117200 chr4B 139563628 139564783 1155 True 512.0 833 86.2620 121 739 2 chr4B.!!$R3 618
7 TraesCS4D01G117200 chr1B 487405524 487407966 2442 False 2191.0 2191 83.2530 905 3330 1 chr1B.!!$F1 2425
8 TraesCS4D01G117200 chr4A 478209460 478210857 1397 False 2185.0 2185 95.0210 868 2255 1 chr4A.!!$F2 1387
9 TraesCS4D01G117200 chr4A 478216299 478217917 1618 False 1135.5 1447 92.6225 2251 3778 2 chr4A.!!$F3 1527
10 TraesCS4D01G117200 chr4A 478191411 478192815 1404 False 992.0 992 79.7330 1387 2784 1 chr4A.!!$F1 1397
11 TraesCS4D01G117200 chr1D 363861164 363863292 2128 False 2108.0 2108 84.7610 969 3095 1 chr1D.!!$F1 2126
12 TraesCS4D01G117200 chr1A 463218522 463220544 2022 False 1995.0 1995 84.6600 894 2915 1 chr1A.!!$F1 2021
13 TraesCS4D01G117200 chr3D 134963100 134964470 1370 True 972.0 972 79.9020 888 2291 1 chr3D.!!$R1 1403
14 TraesCS4D01G117200 chr6B 134838188 134839573 1385 False 891.0 891 78.7560 888 2289 1 chr6B.!!$F1 1401
15 TraesCS4D01G117200 chr3B 706754884 706756106 1222 False 797.0 797 79.0230 1387 2598 1 chr3B.!!$F1 1211

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
866 1286 0.250770 GCCGACCCCTTCAGAAGTTT 60.251 55.0 9.41 0.0 0.0 2.66 F
883 1303 0.897863 TTTTCGGGACATTGGGCCTG 60.898 55.0 4.53 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2742 3292 0.748450 TCGCCAATAGAACTACCCGG 59.252 55.000 0.00 0.0 0.00 5.73 R
3060 3638 6.429078 TCAAGCCTCATATGAATAGCATCAAC 59.571 38.462 18.89 0.0 38.44 3.18 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
30 31 9.582648 TTTTATAGGGGCAATTAGAATAGTTCC 57.417 33.333 0.00 0.00 0.00 3.62
31 32 8.520119 TTATAGGGGCAATTAGAATAGTTCCT 57.480 34.615 0.00 0.00 0.00 3.36
32 33 5.734031 AGGGGCAATTAGAATAGTTCCTT 57.266 39.130 0.00 0.00 0.00 3.36
33 34 5.449553 AGGGGCAATTAGAATAGTTCCTTG 58.550 41.667 0.00 0.00 0.00 3.61
34 35 5.193728 AGGGGCAATTAGAATAGTTCCTTGA 59.806 40.000 0.00 0.00 0.00 3.02
35 36 5.891551 GGGGCAATTAGAATAGTTCCTTGAA 59.108 40.000 0.00 0.00 0.00 2.69
36 37 6.183360 GGGGCAATTAGAATAGTTCCTTGAAC 60.183 42.308 0.00 0.00 42.25 3.18
37 38 6.458342 GGGCAATTAGAATAGTTCCTTGAACG 60.458 42.308 1.64 0.00 45.96 3.95
38 39 6.458342 GGCAATTAGAATAGTTCCTTGAACGG 60.458 42.308 1.64 0.00 45.96 4.44
39 40 6.458342 GCAATTAGAATAGTTCCTTGAACGGG 60.458 42.308 1.64 0.00 45.96 5.28
41 42 3.178865 AGAATAGTTCCTTGAACGGGGA 58.821 45.455 1.64 0.00 45.96 4.81
43 44 4.227527 AGAATAGTTCCTTGAACGGGGATT 59.772 41.667 1.64 1.70 45.96 3.01
44 45 2.200373 AGTTCCTTGAACGGGGATTG 57.800 50.000 1.64 0.00 45.96 2.67
45 46 0.526211 GTTCCTTGAACGGGGATTGC 59.474 55.000 0.00 0.00 32.81 3.56
46 47 0.404040 TTCCTTGAACGGGGATTGCT 59.596 50.000 0.00 0.00 0.00 3.91
49 50 2.040545 TCCTTGAACGGGGATTGCTAAA 59.959 45.455 0.00 0.00 0.00 1.85
50 51 3.023832 CCTTGAACGGGGATTGCTAAAT 58.976 45.455 0.00 0.00 0.00 1.40
51 52 4.080243 TCCTTGAACGGGGATTGCTAAATA 60.080 41.667 0.00 0.00 0.00 1.40
52 53 4.827284 CCTTGAACGGGGATTGCTAAATAT 59.173 41.667 0.00 0.00 0.00 1.28
53 54 6.001460 CCTTGAACGGGGATTGCTAAATATA 58.999 40.000 0.00 0.00 0.00 0.86
54 55 6.149474 CCTTGAACGGGGATTGCTAAATATAG 59.851 42.308 0.00 0.00 0.00 1.31
78 79 8.621532 AGCATCAGTCAAAAACATAACTAAGA 57.378 30.769 0.00 0.00 0.00 2.10
79 80 9.236006 AGCATCAGTCAAAAACATAACTAAGAT 57.764 29.630 0.00 0.00 0.00 2.40
80 81 9.495754 GCATCAGTCAAAAACATAACTAAGATC 57.504 33.333 0.00 0.00 0.00 2.75
87 88 8.286800 TCAAAAACATAACTAAGATCAACACGG 58.713 33.333 0.00 0.00 0.00 4.94
88 89 7.972832 AAAACATAACTAAGATCAACACGGA 57.027 32.000 0.00 0.00 0.00 4.69
95 96 7.972832 AACTAAGATCAACACGGAAAACATA 57.027 32.000 0.00 0.00 0.00 2.29
96 97 7.972832 ACTAAGATCAACACGGAAAACATAA 57.027 32.000 0.00 0.00 0.00 1.90
97 98 8.561738 ACTAAGATCAACACGGAAAACATAAT 57.438 30.769 0.00 0.00 0.00 1.28
98 99 9.010029 ACTAAGATCAACACGGAAAACATAATT 57.990 29.630 0.00 0.00 0.00 1.40
102 103 9.226606 AGATCAACACGGAAAACATAATTAAGA 57.773 29.630 0.00 0.00 0.00 2.10
107 108 9.620660 AACACGGAAAACATAATTAAGATCAAC 57.379 29.630 0.00 0.00 0.00 3.18
108 109 8.788806 ACACGGAAAACATAATTAAGATCAACA 58.211 29.630 0.00 0.00 0.00 3.33
109 110 9.061610 CACGGAAAACATAATTAAGATCAACAC 57.938 33.333 0.00 0.00 0.00 3.32
110 111 8.241367 ACGGAAAACATAATTAAGATCAACACC 58.759 33.333 0.00 0.00 0.00 4.16
112 113 9.573133 GGAAAACATAATTAAGATCAACACCTG 57.427 33.333 0.00 0.00 0.00 4.00
123 124 7.404671 AAGATCAACACCTGTTAAACAAAGT 57.595 32.000 0.00 0.00 36.32 2.66
124 125 6.795399 AGATCAACACCTGTTAAACAAAGTG 58.205 36.000 0.00 0.00 38.01 3.16
129 540 4.525100 ACACCTGTTAAACAAAGTGTTGGT 59.475 37.500 0.00 0.00 40.57 3.67
134 545 7.093684 ACCTGTTAAACAAAGTGTTGGTAATGT 60.094 33.333 0.00 0.00 40.14 2.71
138 549 8.927721 GTTAAACAAAGTGTTGGTAATGTGTTT 58.072 29.630 0.00 0.00 40.14 2.83
235 648 7.315142 TGCTCAAAGGAATGATGTTGATTTAC 58.685 34.615 0.00 0.00 30.06 2.01
251 666 9.990360 TGTTGATTTACAGAAGTATGTGTAAGA 57.010 29.630 0.00 0.00 43.59 2.10
307 722 7.232118 ACAGCTGCTAAATGTATTTTCCTTT 57.768 32.000 15.27 0.00 0.00 3.11
310 725 6.437162 AGCTGCTAAATGTATTTTCCTTTGGA 59.563 34.615 0.00 0.00 0.00 3.53
383 798 6.661805 ACAAAACCTTTAGGACAAGACAAGAA 59.338 34.615 2.06 0.00 38.94 2.52
385 800 7.898014 AAACCTTTAGGACAAGACAAGAAAT 57.102 32.000 2.06 0.00 38.94 2.17
421 837 4.808364 GGTAACAAATGTTGCTTGCTCAAA 59.192 37.500 12.91 0.00 39.94 2.69
424 840 3.132646 ACAAATGTTGCTTGCTCAAAGGA 59.867 39.130 0.00 0.00 36.30 3.36
435 851 4.751767 TGCTCAAAGGAAAAATGTTGGT 57.248 36.364 0.00 0.00 0.00 3.67
455 871 9.357161 TGTTGGTTTGGTAGTTAAGAAATGTAT 57.643 29.630 0.00 0.00 0.00 2.29
464 880 9.310716 GGTAGTTAAGAAATGTATGTGTAGGAC 57.689 37.037 0.00 0.00 0.00 3.85
560 978 8.839947 AAAAAGTGTTGGTAACGTGTTATAAC 57.160 30.769 8.75 8.75 42.51 1.89
665 1083 8.511321 TGCAAAGATGTTGTTATAGTGGTTAAG 58.489 33.333 0.00 0.00 0.00 1.85
838 1258 4.247380 GGAGGCCCATCCAGCGAG 62.247 72.222 6.15 0.00 39.34 5.03
839 1259 3.474570 GAGGCCCATCCAGCGAGT 61.475 66.667 0.00 0.00 37.29 4.18
840 1260 2.041922 AGGCCCATCCAGCGAGTA 60.042 61.111 0.00 0.00 37.29 2.59
841 1261 2.109181 GGCCCATCCAGCGAGTAC 59.891 66.667 0.00 0.00 34.01 2.73
842 1262 2.109181 GCCCATCCAGCGAGTACC 59.891 66.667 0.00 0.00 0.00 3.34
843 1263 2.417516 CCCATCCAGCGAGTACCG 59.582 66.667 0.00 0.00 42.21 4.02
844 1264 2.423898 CCCATCCAGCGAGTACCGT 61.424 63.158 5.79 0.00 41.15 4.83
845 1265 1.515954 CCATCCAGCGAGTACCGTT 59.484 57.895 5.79 0.00 41.15 4.44
846 1266 0.527817 CCATCCAGCGAGTACCGTTC 60.528 60.000 5.79 0.00 41.15 3.95
847 1267 0.866061 CATCCAGCGAGTACCGTTCG 60.866 60.000 5.79 2.64 41.15 3.95
852 1272 2.575262 CGAGTACCGTTCGCCGAC 60.575 66.667 0.00 0.00 39.56 4.79
853 1273 2.202531 GAGTACCGTTCGCCGACC 60.203 66.667 0.00 0.00 39.56 4.79
854 1274 3.690108 GAGTACCGTTCGCCGACCC 62.690 68.421 0.00 0.00 39.56 4.46
855 1275 4.801624 GTACCGTTCGCCGACCCC 62.802 72.222 0.00 0.00 39.56 4.95
859 1279 4.367023 CGTTCGCCGACCCCTTCA 62.367 66.667 0.00 0.00 39.56 3.02
860 1280 2.434359 GTTCGCCGACCCCTTCAG 60.434 66.667 0.00 0.00 0.00 3.02
861 1281 2.602267 TTCGCCGACCCCTTCAGA 60.602 61.111 0.00 0.00 0.00 3.27
862 1282 2.211410 TTCGCCGACCCCTTCAGAA 61.211 57.895 0.00 0.00 0.00 3.02
863 1283 2.125512 CGCCGACCCCTTCAGAAG 60.126 66.667 2.78 2.78 0.00 2.85
864 1284 2.943978 CGCCGACCCCTTCAGAAGT 61.944 63.158 9.41 0.00 0.00 3.01
865 1285 1.375326 GCCGACCCCTTCAGAAGTT 59.625 57.895 9.41 0.00 0.00 2.66
866 1286 0.250770 GCCGACCCCTTCAGAAGTTT 60.251 55.000 9.41 0.00 0.00 2.66
867 1287 1.818131 GCCGACCCCTTCAGAAGTTTT 60.818 52.381 9.41 0.00 0.00 2.43
883 1303 0.897863 TTTTCGGGACATTGGGCCTG 60.898 55.000 4.53 0.00 0.00 4.85
1086 1519 2.056223 GGACCCGGACGAGATGGAA 61.056 63.158 0.73 0.00 0.00 3.53
1395 1844 4.827087 CGGCGCATCACCTCTGCT 62.827 66.667 10.83 0.00 37.48 4.24
1610 2082 3.155167 CCTCACCCGCCTCTACCC 61.155 72.222 0.00 0.00 0.00 3.69
2051 2557 5.047448 TCCATTTGTTCCATTGGTGTACATG 60.047 40.000 0.00 0.00 0.00 3.21
2340 2886 4.274214 GCATCATACTGTGAATTGCTGCTA 59.726 41.667 0.00 0.00 38.96 3.49
2706 3256 1.072173 TGGTCACTGGGTGTTCTGATG 59.928 52.381 0.00 0.00 34.79 3.07
2742 3292 1.072331 TGGGGAACTTCAAGAGAGCAC 59.928 52.381 0.00 0.00 0.00 4.40
2754 3304 1.284198 AGAGAGCACCGGGTAGTTCTA 59.716 52.381 6.32 0.00 0.00 2.10
3057 3635 5.496387 GTCTGATGAGAATTACATTGCACG 58.504 41.667 0.00 0.00 0.00 5.34
3060 3638 6.018507 TCTGATGAGAATTACATTGCACGATG 60.019 38.462 0.00 0.00 0.00 3.84
3064 3642 5.411053 TGAGAATTACATTGCACGATGTTGA 59.589 36.000 9.22 0.54 40.54 3.18
3117 3695 2.296471 CGGGGATAGTAGTAACAGCTGG 59.704 54.545 19.93 0.00 0.00 4.85
3118 3696 2.037381 GGGGATAGTAGTAACAGCTGGC 59.963 54.545 19.93 7.87 0.00 4.85
3120 3698 3.243907 GGGATAGTAGTAACAGCTGGCAG 60.244 52.174 19.93 10.94 0.00 4.85
3122 3700 4.282195 GGATAGTAGTAACAGCTGGCAGAT 59.718 45.833 20.86 9.84 0.00 2.90
3176 3854 4.614284 GTGTTCTGTTCTGATTGATTTGCG 59.386 41.667 0.00 0.00 0.00 4.85
3298 3977 3.181397 TCGCAACGTGCTAAGGTAATAC 58.819 45.455 8.07 0.00 42.25 1.89
3336 4015 4.210331 CAAGGGCATGCCTAAGAATAGTT 58.790 43.478 34.70 12.14 36.10 2.24
3337 4016 5.104109 ACAAGGGCATGCCTAAGAATAGTTA 60.104 40.000 34.70 0.00 36.10 2.24
3338 4017 5.234466 AGGGCATGCCTAAGAATAGTTAG 57.766 43.478 34.70 0.00 36.10 2.34
3339 4018 4.660771 AGGGCATGCCTAAGAATAGTTAGT 59.339 41.667 34.70 1.25 36.10 2.24
3359 4038 2.597510 GTCCAGGCGGCCAAACTT 60.598 61.111 23.09 0.00 0.00 2.66
3362 4041 2.356194 CAGGCGGCCAAACTTTGC 60.356 61.111 23.09 0.00 0.00 3.68
3364 4043 2.356194 GGCGGCCAAACTTTGCTG 60.356 61.111 15.62 0.00 36.92 4.41
3366 4045 2.730094 CGGCCAAACTTTGCTGCT 59.270 55.556 2.24 0.00 0.00 4.24
3367 4046 1.662446 CGGCCAAACTTTGCTGCTG 60.662 57.895 2.24 0.00 0.00 4.41
3368 4047 1.957695 GGCCAAACTTTGCTGCTGC 60.958 57.895 8.89 8.89 40.20 5.25
3369 4048 1.068585 GCCAAACTTTGCTGCTGCT 59.931 52.632 17.00 0.00 40.48 4.24
3370 4049 0.314935 GCCAAACTTTGCTGCTGCTA 59.685 50.000 17.00 6.36 40.48 3.49
3371 4050 1.668047 GCCAAACTTTGCTGCTGCTAG 60.668 52.381 17.00 15.10 40.48 3.42
3415 4125 3.309682 TCTGCACGCAATGATAAAGTAGC 59.690 43.478 0.00 0.00 0.00 3.58
3453 4163 2.617308 CACAGCTTCTTCATGGCCTATG 59.383 50.000 3.32 6.57 38.17 2.23
3454 4164 2.507058 ACAGCTTCTTCATGGCCTATGA 59.493 45.455 3.32 9.06 43.92 2.15
3455 4165 3.137913 ACAGCTTCTTCATGGCCTATGAT 59.862 43.478 15.69 0.00 44.90 2.45
3456 4166 4.142790 CAGCTTCTTCATGGCCTATGATT 58.857 43.478 15.69 0.59 44.90 2.57
3457 4167 5.163163 ACAGCTTCTTCATGGCCTATGATTA 60.163 40.000 15.69 7.09 44.90 1.75
3458 4168 5.944599 CAGCTTCTTCATGGCCTATGATTAT 59.055 40.000 15.69 0.00 44.90 1.28
3491 4201 7.681939 TCAGTTGCGAAAAATAAGGTTATCT 57.318 32.000 0.00 0.00 0.00 1.98
3495 4205 8.357402 AGTTGCGAAAAATAAGGTTATCTTGTT 58.643 29.630 0.00 0.00 38.24 2.83
3636 4347 1.141053 ACGAGAGGAAACCACAAGCTT 59.859 47.619 0.00 0.00 0.00 3.74
3778 4489 2.232452 CAGTTCTTCCTGATCTGTCCGT 59.768 50.000 0.00 0.00 37.59 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.520119 AGGAACTATTCTAATTGCCCCTATAA 57.480 34.615 0.00 0.00 36.02 0.98
8 9 7.073725 TCAAGGAACTATTCTAATTGCCCCTAT 59.926 37.037 0.00 0.00 38.49 2.57
9 10 6.388689 TCAAGGAACTATTCTAATTGCCCCTA 59.611 38.462 0.00 0.00 38.49 3.53
11 12 5.445964 TCAAGGAACTATTCTAATTGCCCC 58.554 41.667 0.00 0.00 38.49 5.80
12 13 6.458342 CGTTCAAGGAACTATTCTAATTGCCC 60.458 42.308 7.43 0.00 38.49 5.36
14 15 6.458342 CCCGTTCAAGGAACTATTCTAATTGC 60.458 42.308 7.43 0.00 38.49 3.56
15 16 6.038271 CCCCGTTCAAGGAACTATTCTAATTG 59.962 42.308 7.43 0.00 38.49 2.32
16 17 6.069847 TCCCCGTTCAAGGAACTATTCTAATT 60.070 38.462 7.43 0.00 38.49 1.40
18 19 4.778958 TCCCCGTTCAAGGAACTATTCTAA 59.221 41.667 7.43 0.00 38.49 2.10
19 20 4.355549 TCCCCGTTCAAGGAACTATTCTA 58.644 43.478 7.43 0.00 38.49 2.10
20 21 3.178865 TCCCCGTTCAAGGAACTATTCT 58.821 45.455 7.43 0.00 38.49 2.40
24 25 2.617021 GCAATCCCCGTTCAAGGAACTA 60.617 50.000 7.43 0.00 38.49 2.24
28 29 1.281419 TAGCAATCCCCGTTCAAGGA 58.719 50.000 0.00 0.00 36.36 3.36
29 30 2.122783 TTAGCAATCCCCGTTCAAGG 57.877 50.000 0.00 0.00 0.00 3.61
30 31 7.133891 CTATATTTAGCAATCCCCGTTCAAG 57.866 40.000 0.00 0.00 0.00 3.02
52 53 9.719355 TCTTAGTTATGTTTTTGACTGATGCTA 57.281 29.630 0.00 0.00 0.00 3.49
53 54 8.621532 TCTTAGTTATGTTTTTGACTGATGCT 57.378 30.769 0.00 0.00 0.00 3.79
54 55 9.495754 GATCTTAGTTATGTTTTTGACTGATGC 57.504 33.333 0.00 0.00 0.00 3.91
61 62 8.286800 CCGTGTTGATCTTAGTTATGTTTTTGA 58.713 33.333 0.00 0.00 0.00 2.69
62 63 8.286800 TCCGTGTTGATCTTAGTTATGTTTTTG 58.713 33.333 0.00 0.00 0.00 2.44
64 65 7.972832 TCCGTGTTGATCTTAGTTATGTTTT 57.027 32.000 0.00 0.00 0.00 2.43
66 67 7.972832 TTTCCGTGTTGATCTTAGTTATGTT 57.027 32.000 0.00 0.00 0.00 2.71
67 68 7.442969 TGTTTTCCGTGTTGATCTTAGTTATGT 59.557 33.333 0.00 0.00 0.00 2.29
68 69 7.802738 TGTTTTCCGTGTTGATCTTAGTTATG 58.197 34.615 0.00 0.00 0.00 1.90
70 71 7.972832 ATGTTTTCCGTGTTGATCTTAGTTA 57.027 32.000 0.00 0.00 0.00 2.24
79 80 9.004717 TGATCTTAATTATGTTTTCCGTGTTGA 57.995 29.630 0.00 0.00 0.00 3.18
80 81 9.619316 TTGATCTTAATTATGTTTTCCGTGTTG 57.381 29.630 0.00 0.00 0.00 3.33
81 82 9.620660 GTTGATCTTAATTATGTTTTCCGTGTT 57.379 29.630 0.00 0.00 0.00 3.32
82 83 8.788806 TGTTGATCTTAATTATGTTTTCCGTGT 58.211 29.630 0.00 0.00 0.00 4.49
84 85 8.241367 GGTGTTGATCTTAATTATGTTTTCCGT 58.759 33.333 0.00 0.00 0.00 4.69
85 86 8.458843 AGGTGTTGATCTTAATTATGTTTTCCG 58.541 33.333 0.00 0.00 0.00 4.30
96 97 9.965824 CTTTGTTTAACAGGTGTTGATCTTAAT 57.034 29.630 5.59 0.00 38.90 1.40
97 98 8.962679 ACTTTGTTTAACAGGTGTTGATCTTAA 58.037 29.630 5.59 0.00 38.90 1.85
98 99 8.402472 CACTTTGTTTAACAGGTGTTGATCTTA 58.598 33.333 18.05 0.00 38.90 2.10
99 100 7.093945 ACACTTTGTTTAACAGGTGTTGATCTT 60.094 33.333 22.73 8.00 40.86 2.40
100 101 6.377146 ACACTTTGTTTAACAGGTGTTGATCT 59.623 34.615 22.73 8.49 40.86 2.75
102 103 6.524101 ACACTTTGTTTAACAGGTGTTGAT 57.476 33.333 22.73 9.23 40.86 2.57
107 108 5.066968 ACCAACACTTTGTTTAACAGGTG 57.933 39.130 21.82 21.82 38.77 4.00
108 109 6.837471 TTACCAACACTTTGTTTAACAGGT 57.163 33.333 7.80 7.80 38.77 4.00
109 110 7.221838 CACATTACCAACACTTTGTTTAACAGG 59.778 37.037 0.00 0.00 38.77 4.00
110 111 7.757624 ACACATTACCAACACTTTGTTTAACAG 59.242 33.333 0.00 0.00 38.77 3.16
112 113 8.468720 AACACATTACCAACACTTTGTTTAAC 57.531 30.769 0.00 0.00 38.77 2.01
115 116 9.490379 TTTAAACACATTACCAACACTTTGTTT 57.510 25.926 0.00 0.00 38.77 2.83
116 117 9.490379 TTTTAAACACATTACCAACACTTTGTT 57.510 25.926 0.00 0.00 42.08 2.83
117 118 9.490379 TTTTTAAACACATTACCAACACTTTGT 57.510 25.926 0.00 0.00 0.00 2.83
120 121 9.660180 ACATTTTTAAACACATTACCAACACTT 57.340 25.926 0.00 0.00 0.00 3.16
203 616 7.649533 ACATCATTCCTTTGAGCATTCAATA 57.350 32.000 0.00 0.00 42.60 1.90
265 680 6.458210 CAGCTGTATCTTTTCCAACCATTTT 58.542 36.000 5.25 0.00 0.00 1.82
280 695 8.159344 AGGAAAATACATTTAGCAGCTGTATC 57.841 34.615 16.64 0.00 35.57 2.24
286 701 6.630071 TCCAAAGGAAAATACATTTAGCAGC 58.370 36.000 0.00 0.00 0.00 5.25
383 798 9.127277 ACATTTGTTACCACTAGTTTGTACATT 57.873 29.630 0.00 0.00 0.00 2.71
385 800 8.399425 CAACATTTGTTACCACTAGTTTGTACA 58.601 33.333 0.00 0.00 36.32 2.90
409 825 4.768583 ACATTTTTCCTTTGAGCAAGCAA 58.231 34.783 0.00 0.00 0.00 3.91
416 832 5.879777 ACCAAACCAACATTTTTCCTTTGAG 59.120 36.000 0.00 0.00 0.00 3.02
421 837 6.553953 AACTACCAAACCAACATTTTTCCT 57.446 33.333 0.00 0.00 0.00 3.36
424 840 9.945904 TTTCTTAACTACCAAACCAACATTTTT 57.054 25.926 0.00 0.00 0.00 1.94
455 871 8.100164 TGATTTACATTCATCAAGTCCTACACA 58.900 33.333 0.00 0.00 0.00 3.72
528 945 6.145696 CACGTTACCAACACTTTTTCCAAAAA 59.854 34.615 0.00 0.00 36.53 1.94
586 1004 6.384886 AGGTGGACCGGTTCTTATTTAGATAA 59.615 38.462 15.59 0.00 42.08 1.75
601 1019 0.460311 CTTAGCACTAGGTGGACCGG 59.540 60.000 0.00 0.00 42.08 5.28
603 1021 1.861982 TCCTTAGCACTAGGTGGACC 58.138 55.000 0.00 0.00 33.64 4.46
746 1166 9.281075 GACCGCAAAATTATACTTTTAACGATT 57.719 29.630 17.25 8.94 32.74 3.34
747 1167 8.671028 AGACCGCAAAATTATACTTTTAACGAT 58.329 29.630 17.25 6.85 32.74 3.73
748 1168 7.958567 CAGACCGCAAAATTATACTTTTAACGA 59.041 33.333 17.25 0.00 32.74 3.85
749 1169 7.217447 CCAGACCGCAAAATTATACTTTTAACG 59.783 37.037 12.27 12.27 31.71 3.18
750 1170 8.024865 ACCAGACCGCAAAATTATACTTTTAAC 58.975 33.333 0.95 0.00 0.00 2.01
751 1171 8.113173 ACCAGACCGCAAAATTATACTTTTAA 57.887 30.769 0.95 0.00 0.00 1.52
752 1172 7.413219 CGACCAGACCGCAAAATTATACTTTTA 60.413 37.037 0.95 0.00 0.00 1.52
753 1173 6.584185 ACCAGACCGCAAAATTATACTTTT 57.416 33.333 0.00 0.00 0.00 2.27
754 1174 5.163794 CGACCAGACCGCAAAATTATACTTT 60.164 40.000 0.00 0.00 0.00 2.66
755 1175 4.331717 CGACCAGACCGCAAAATTATACTT 59.668 41.667 0.00 0.00 0.00 2.24
808 1228 2.751436 CCTCCCAATGGGCACGTG 60.751 66.667 14.88 12.28 43.94 4.49
835 1255 2.575262 GTCGGCGAACGGTACTCG 60.575 66.667 12.92 0.00 44.45 4.18
836 1256 2.202531 GGTCGGCGAACGGTACTC 60.203 66.667 12.92 0.00 44.45 2.59
837 1257 3.752339 GGGTCGGCGAACGGTACT 61.752 66.667 19.88 0.00 44.45 2.73
838 1258 4.801624 GGGGTCGGCGAACGGTAC 62.802 72.222 19.88 4.45 44.45 3.34
842 1262 4.367023 TGAAGGGGTCGGCGAACG 62.367 66.667 19.88 0.00 46.11 3.95
843 1263 2.434359 CTGAAGGGGTCGGCGAAC 60.434 66.667 18.34 18.34 0.00 3.95
844 1264 2.167398 CTTCTGAAGGGGTCGGCGAA 62.167 60.000 12.92 0.00 31.99 4.70
845 1265 2.602267 TTCTGAAGGGGTCGGCGA 60.602 61.111 4.99 4.99 31.99 5.54
846 1266 2.125512 CTTCTGAAGGGGTCGGCG 60.126 66.667 9.57 0.00 31.99 6.46
847 1267 0.250770 AAACTTCTGAAGGGGTCGGC 60.251 55.000 20.61 0.00 31.99 5.54
848 1268 2.152016 GAAAACTTCTGAAGGGGTCGG 58.848 52.381 20.61 0.00 0.00 4.79
849 1269 1.798813 CGAAAACTTCTGAAGGGGTCG 59.201 52.381 20.61 19.07 0.00 4.79
850 1270 2.152016 CCGAAAACTTCTGAAGGGGTC 58.848 52.381 20.61 12.67 0.00 4.46
851 1271 1.202891 CCCGAAAACTTCTGAAGGGGT 60.203 52.381 20.61 5.64 33.97 4.95
852 1272 1.073284 TCCCGAAAACTTCTGAAGGGG 59.927 52.381 20.61 18.97 37.98 4.79
853 1273 2.152016 GTCCCGAAAACTTCTGAAGGG 58.848 52.381 20.61 12.22 38.73 3.95
854 1274 2.846193 TGTCCCGAAAACTTCTGAAGG 58.154 47.619 20.61 3.48 0.00 3.46
855 1275 4.320494 CCAATGTCCCGAAAACTTCTGAAG 60.320 45.833 15.59 15.59 0.00 3.02
856 1276 3.568007 CCAATGTCCCGAAAACTTCTGAA 59.432 43.478 0.00 0.00 0.00 3.02
857 1277 3.146066 CCAATGTCCCGAAAACTTCTGA 58.854 45.455 0.00 0.00 0.00 3.27
858 1278 2.228822 CCCAATGTCCCGAAAACTTCTG 59.771 50.000 0.00 0.00 0.00 3.02
859 1279 2.514803 CCCAATGTCCCGAAAACTTCT 58.485 47.619 0.00 0.00 0.00 2.85
860 1280 1.067846 GCCCAATGTCCCGAAAACTTC 60.068 52.381 0.00 0.00 0.00 3.01
861 1281 0.966179 GCCCAATGTCCCGAAAACTT 59.034 50.000 0.00 0.00 0.00 2.66
862 1282 0.898326 GGCCCAATGTCCCGAAAACT 60.898 55.000 0.00 0.00 0.00 2.66
863 1283 0.898326 AGGCCCAATGTCCCGAAAAC 60.898 55.000 0.00 0.00 0.00 2.43
864 1284 0.897863 CAGGCCCAATGTCCCGAAAA 60.898 55.000 0.00 0.00 0.00 2.29
865 1285 1.304052 CAGGCCCAATGTCCCGAAA 60.304 57.895 0.00 0.00 0.00 3.46
866 1286 2.075355 AACAGGCCCAATGTCCCGAA 62.075 55.000 0.00 0.00 0.00 4.30
867 1287 2.478335 GAACAGGCCCAATGTCCCGA 62.478 60.000 0.00 0.00 0.00 5.14
957 1390 1.001631 GGGGATGAGGGTTTTGGGG 59.998 63.158 0.00 0.00 0.00 4.96
1395 1844 4.451150 GCGAGGATGCGGGACACA 62.451 66.667 0.00 0.00 0.00 3.72
1610 2082 2.269241 GGAACTTCCAGAGGCCGG 59.731 66.667 0.00 0.00 36.28 6.13
1660 2132 1.760029 GAGCTCAAGGAGGTTAGGGAG 59.240 57.143 9.40 0.00 40.67 4.30
2340 2886 6.940867 CAGATGTTGATGGATCCTGATACAAT 59.059 38.462 14.23 0.00 34.87 2.71
2706 3256 1.389609 CCCATGCCACCATCTTCAGC 61.390 60.000 0.00 0.00 0.00 4.26
2742 3292 0.748450 TCGCCAATAGAACTACCCGG 59.252 55.000 0.00 0.00 0.00 5.73
3057 3635 6.598457 AGCCTCATATGAATAGCATCAACATC 59.402 38.462 18.89 0.00 38.44 3.06
3060 3638 6.429078 TCAAGCCTCATATGAATAGCATCAAC 59.571 38.462 18.89 0.00 38.44 3.18
3064 3642 6.482524 ACATCAAGCCTCATATGAATAGCAT 58.517 36.000 18.89 8.66 41.08 3.79
3117 3695 4.575236 TCTGAGAGCATCAAAATCATCTGC 59.425 41.667 0.00 0.00 37.52 4.26
3118 3696 6.869315 ATCTGAGAGCATCAAAATCATCTG 57.131 37.500 0.00 0.00 37.52 2.90
3120 3698 6.913132 CACAATCTGAGAGCATCAAAATCATC 59.087 38.462 0.00 0.00 37.52 2.92
3122 3700 5.392703 GCACAATCTGAGAGCATCAAAATCA 60.393 40.000 0.00 0.00 37.52 2.57
3176 3854 6.498304 CCAATAATTGACTTGGCACATCTAC 58.502 40.000 0.00 0.00 39.30 2.59
3336 4015 3.702048 GGCCGCCTGGACACACTA 61.702 66.667 0.71 0.00 45.78 2.74
3359 4038 1.918467 ATGGAGGCTAGCAGCAGCAA 61.918 55.000 18.24 0.00 44.75 3.91
3362 4041 2.627515 TAAATGGAGGCTAGCAGCAG 57.372 50.000 18.24 0.00 44.75 4.24
3364 4043 3.749226 AGAATAAATGGAGGCTAGCAGC 58.251 45.455 18.24 7.31 41.46 5.25
3366 4045 6.686484 TCATAGAATAAATGGAGGCTAGCA 57.314 37.500 18.24 0.00 0.00 3.49
3367 4046 7.563906 AGATCATAGAATAAATGGAGGCTAGC 58.436 38.462 6.04 6.04 0.00 3.42
3368 4047 9.598517 GAAGATCATAGAATAAATGGAGGCTAG 57.401 37.037 0.00 0.00 0.00 3.42
3369 4048 9.331466 AGAAGATCATAGAATAAATGGAGGCTA 57.669 33.333 0.00 0.00 0.00 3.93
3370 4049 8.102047 CAGAAGATCATAGAATAAATGGAGGCT 58.898 37.037 0.00 0.00 0.00 4.58
3371 4050 7.148272 GCAGAAGATCATAGAATAAATGGAGGC 60.148 40.741 0.00 0.00 0.00 4.70
3415 4125 0.038159 GTGACCCTCTGGAACGACAG 60.038 60.000 0.00 0.00 39.84 3.51
3453 4163 6.844696 TCGCAACTGAAGAACCATATAATC 57.155 37.500 0.00 0.00 0.00 1.75
3454 4164 7.624360 TTTCGCAACTGAAGAACCATATAAT 57.376 32.000 0.00 0.00 0.00 1.28
3455 4165 7.441890 TTTTCGCAACTGAAGAACCATATAA 57.558 32.000 0.00 0.00 0.00 0.98
3456 4166 7.441890 TTTTTCGCAACTGAAGAACCATATA 57.558 32.000 0.00 0.00 0.00 0.86
3457 4167 5.957842 TTTTCGCAACTGAAGAACCATAT 57.042 34.783 0.00 0.00 0.00 1.78
3458 4168 5.759506 TTTTTCGCAACTGAAGAACCATA 57.240 34.783 0.00 0.00 0.00 2.74
3491 4201 2.612200 GCCTACAGCACGACAACAA 58.388 52.632 0.00 0.00 42.97 2.83


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

AutoCloner maintained by Alex Coulton.