Multiple sequence alignment - TraesCS5D01G339900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G339900 chr5D 100.000 5445 0 0 1 5445 428669636 428675080 0.000000e+00 10056.0
1 TraesCS5D01G339900 chr5D 85.304 3409 474 23 1140 4527 428593106 428596508 0.000000e+00 3494.0
2 TraesCS5D01G339900 chr5D 84.350 3559 501 29 988 4527 428512207 428515728 0.000000e+00 3435.0
3 TraesCS5D01G339900 chr5D 83.766 3431 496 46 1136 4527 428565631 428569039 0.000000e+00 3193.0
4 TraesCS5D01G339900 chr5B 94.493 4721 193 40 161 4834 517796828 517801528 0.000000e+00 7215.0
5 TraesCS5D01G339900 chr5B 84.389 3600 512 31 988 4563 517774900 517778473 0.000000e+00 3489.0
6 TraesCS5D01G339900 chr5B 84.050 3467 495 34 1136 4563 517694498 517697945 0.000000e+00 3286.0
7 TraesCS5D01G339900 chr5B 94.346 283 11 2 4997 5275 517801526 517801807 3.900000e-116 429.0
8 TraesCS5D01G339900 chr5B 93.640 283 13 2 4997 5275 517813958 517814239 8.440000e-113 418.0
9 TraesCS5D01G339900 chr5B 92.883 281 11 5 4556 4834 517811262 517811535 3.060000e-107 399.0
10 TraesCS5D01G339900 chr5B 92.883 281 11 3 4556 4834 517813687 517813960 3.060000e-107 399.0
11 TraesCS5D01G339900 chr5B 91.873 283 18 2 4997 5275 517811533 517811814 1.840000e-104 390.0
12 TraesCS5D01G339900 chr5A 94.327 4442 205 13 28 4451 544451937 544456349 0.000000e+00 6763.0
13 TraesCS5D01G339900 chr5A 84.497 3509 489 35 1000 4466 544502346 544505841 0.000000e+00 3415.0
14 TraesCS5D01G339900 chr5A 86.119 2118 277 14 2406 4511 544246346 544248458 0.000000e+00 2266.0
15 TraesCS5D01G339900 chr5A 83.914 1722 253 15 1131 2834 544158653 544160368 0.000000e+00 1624.0
16 TraesCS5D01G339900 chr5A 83.086 1750 262 22 1017 2749 544461637 544463369 0.000000e+00 1561.0
17 TraesCS5D01G339900 chr5A 92.214 989 56 13 4458 5445 544511326 544512294 0.000000e+00 1380.0
18 TraesCS5D01G339900 chr5A 82.133 1444 220 23 981 2411 544244113 544245531 0.000000e+00 1203.0
19 TraesCS5D01G339900 chr5A 100.000 32 0 0 5414 5445 544458445 544458476 5.890000e-05 60.2
20 TraesCS5D01G339900 chr7A 85.915 71 10 0 4182 4252 3141241 3141311 5.850000e-10 76.8


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 TraesCS5D01G339900 chr5D 428669636 428675080 5444 False 10056.000000 10056 100.00000 1 5445 1 chr5D.!!$F4 5444
1 TraesCS5D01G339900 chr5D 428593106 428596508 3402 False 3494.000000 3494 85.30400 1140 4527 1 chr5D.!!$F3 3387
2 TraesCS5D01G339900 chr5D 428512207 428515728 3521 False 3435.000000 3435 84.35000 988 4527 1 chr5D.!!$F1 3539
3 TraesCS5D01G339900 chr5D 428565631 428569039 3408 False 3193.000000 3193 83.76600 1136 4527 1 chr5D.!!$F2 3391
4 TraesCS5D01G339900 chr5B 517796828 517801807 4979 False 3822.000000 7215 94.41950 161 5275 2 chr5B.!!$F3 5114
5 TraesCS5D01G339900 chr5B 517774900 517778473 3573 False 3489.000000 3489 84.38900 988 4563 1 chr5B.!!$F2 3575
6 TraesCS5D01G339900 chr5B 517694498 517697945 3447 False 3286.000000 3286 84.05000 1136 4563 1 chr5B.!!$F1 3427
7 TraesCS5D01G339900 chr5B 517811262 517814239 2977 False 401.500000 418 92.81975 4556 5275 4 chr5B.!!$F4 719
8 TraesCS5D01G339900 chr5A 544502346 544505841 3495 False 3415.000000 3415 84.49700 1000 4466 1 chr5A.!!$F2 3466
9 TraesCS5D01G339900 chr5A 544451937 544463369 11432 False 2794.733333 6763 92.47100 28 5445 3 chr5A.!!$F5 5417
10 TraesCS5D01G339900 chr5A 544244113 544248458 4345 False 1734.500000 2266 84.12600 981 4511 2 chr5A.!!$F4 3530
11 TraesCS5D01G339900 chr5A 544158653 544160368 1715 False 1624.000000 1624 83.91400 1131 2834 1 chr5A.!!$F1 1703
12 TraesCS5D01G339900 chr5A 544511326 544512294 968 False 1380.000000 1380 92.21400 4458 5445 1 chr5A.!!$F3 987

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
794 827 0.104855 TCAGCTCACACTCACACACC 59.895 55.0 0.00 0.0 0.0 4.16 F
800 833 0.107703 CACACTCACACACCACCACT 60.108 55.0 0.00 0.0 0.0 4.00 F
1903 1993 0.170561 CACAATGCTCAGCTTCCTGC 59.829 55.0 0.00 0.0 39.0 4.85 F
3861 4783 1.301677 GGCAAAGAAGGACCGCTCTG 61.302 60.0 0.36 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2361 3.949113 GGCCGGATAACTGGTTTTCATAA 59.051 43.478 5.05 0.0 43.99 1.90 R
2403 2493 6.513884 GCTTGTTGTCATTCAGTTCAATGAGA 60.514 38.462 0.00 0.0 42.26 3.27 R
3876 4798 0.253327 GGAGGTAAGTGAGGGCTTGG 59.747 60.000 0.00 0.0 0.00 3.61 R
4870 6896 0.534412 ACTCCGCAGTCATCTTGAGG 59.466 55.000 0.00 0.0 0.00 3.86 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
20 21 2.403252 ATGAGGGACGTTGAATGACC 57.597 50.000 0.00 0.00 0.00 4.02
21 22 1.052617 TGAGGGACGTTGAATGACCA 58.947 50.000 8.09 0.00 0.00 4.02
22 23 1.628340 TGAGGGACGTTGAATGACCAT 59.372 47.619 8.09 0.38 0.00 3.55
23 24 2.039746 TGAGGGACGTTGAATGACCATT 59.960 45.455 8.09 0.00 0.00 3.16
24 25 3.262151 TGAGGGACGTTGAATGACCATTA 59.738 43.478 8.09 0.00 0.00 1.90
25 26 4.080582 TGAGGGACGTTGAATGACCATTAT 60.081 41.667 8.09 0.00 0.00 1.28
26 27 4.855340 AGGGACGTTGAATGACCATTATT 58.145 39.130 8.09 0.00 0.00 1.40
74 75 4.453478 CCATAGTAACGCATGAGCATTCAT 59.547 41.667 0.00 0.00 44.87 2.57
94 95 6.647212 TCATCTAGTTAATGCAAAGACACG 57.353 37.500 0.00 0.00 0.00 4.49
96 97 4.890088 TCTAGTTAATGCAAAGACACGGT 58.110 39.130 0.00 0.00 0.00 4.83
108 109 6.864165 TGCAAAGACACGGTTAATTTAAATCC 59.136 34.615 0.10 0.00 0.00 3.01
232 233 6.156429 ACTTCCTCCGATCCAAAGTAAGTATT 59.844 38.462 0.00 0.00 0.00 1.89
241 242 5.764131 TCCAAAGTAAGTATTGCGGTTTTG 58.236 37.500 0.00 0.00 35.15 2.44
328 342 5.234972 TCACAAATATGCATTCACTCTAGCG 59.765 40.000 3.54 0.00 0.00 4.26
491 514 2.273370 TACTGAAAGCACGATCGTCC 57.727 50.000 19.84 10.11 37.60 4.79
501 524 2.350964 GCACGATCGTCCTAGAGAATCC 60.351 54.545 19.84 0.00 33.66 3.01
574 607 2.030717 CGAGATAGCTAGGTCGCACATT 60.031 50.000 12.96 0.00 0.00 2.71
794 827 0.104855 TCAGCTCACACTCACACACC 59.895 55.000 0.00 0.00 0.00 4.16
795 828 0.179076 CAGCTCACACTCACACACCA 60.179 55.000 0.00 0.00 0.00 4.17
797 830 1.160329 GCTCACACTCACACACCACC 61.160 60.000 0.00 0.00 0.00 4.61
798 831 0.177836 CTCACACTCACACACCACCA 59.822 55.000 0.00 0.00 0.00 4.17
800 833 0.107703 CACACTCACACACCACCACT 60.108 55.000 0.00 0.00 0.00 4.00
801 834 0.178068 ACACTCACACACCACCACTC 59.822 55.000 0.00 0.00 0.00 3.51
802 835 0.177836 CACTCACACACCACCACTCA 59.822 55.000 0.00 0.00 0.00 3.41
884 926 3.306818 CGCCGGTATTCTTCTTAGCTAC 58.693 50.000 1.90 0.00 0.00 3.58
889 931 6.544622 CCGGTATTCTTCTTAGCTACTATCG 58.455 44.000 0.00 0.00 0.00 2.92
895 940 6.307031 TCTTCTTAGCTACTATCGCTTCTG 57.693 41.667 0.00 0.00 38.86 3.02
928 973 4.972440 GTCTTTTCTTTCGCATATGCATCC 59.028 41.667 26.52 0.00 42.21 3.51
974 1019 0.236711 GGCGCATGCAGTCATATCAC 59.763 55.000 19.57 0.00 45.35 3.06
975 1020 0.939419 GCGCATGCAGTCATATCACA 59.061 50.000 19.57 0.00 42.15 3.58
986 1031 6.652062 TGCAGTCATATCACATTGATCATACC 59.348 38.462 0.00 0.00 38.26 2.73
1068 1119 2.522436 TTTGCCCTGCTGCTGCTT 60.522 55.556 17.00 0.00 40.48 3.91
1078 1132 1.071228 TGCTGCTGCTTCTTCTTCTCA 59.929 47.619 17.00 0.00 40.48 3.27
1192 1255 2.426522 CGCTTCTCCACTGGAAATCAA 58.573 47.619 0.00 0.00 0.00 2.57
1204 1267 2.296752 TGGAAATCAACCGTCGAGTACA 59.703 45.455 0.00 0.00 0.00 2.90
1205 1268 3.056393 TGGAAATCAACCGTCGAGTACAT 60.056 43.478 0.00 0.00 0.00 2.29
1219 1291 0.392461 GTACATCACGCACATGGGGT 60.392 55.000 0.00 0.00 44.58 4.95
1238 1313 2.179517 CTGGAGAGACGACGGCAC 59.820 66.667 2.19 0.00 0.00 5.01
1326 1408 2.368221 GGTCATCAGAGGAATCTCCCTG 59.632 54.545 0.00 5.35 40.83 4.45
1761 1851 5.152623 TGACAAACCTCAACTATCTGGAG 57.847 43.478 0.00 0.00 0.00 3.86
1774 1864 5.145564 ACTATCTGGAGCTTTCCGGTAATA 58.854 41.667 0.00 0.00 37.42 0.98
1903 1993 0.170561 CACAATGCTCAGCTTCCTGC 59.829 55.000 0.00 0.00 39.00 4.85
2271 2361 9.517868 TTGGCAAATTTGGAAATAATTGATTCT 57.482 25.926 19.47 0.00 0.00 2.40
2710 3620 7.112287 TGACGAGTATTTATTTTGCAAACAACG 59.888 33.333 12.39 11.26 34.87 4.10
2814 3724 4.715297 AGTGAGATACCGGTAGAAATTGGT 59.285 41.667 20.91 0.00 38.51 3.67
3046 3964 1.851304 TGGCAATTTAGCTTCCCTGG 58.149 50.000 0.00 0.00 34.17 4.45
3360 4278 7.346751 TCATAGGAAAAGGCATGAAAATACC 57.653 36.000 0.00 0.00 0.00 2.73
3861 4783 1.301677 GGCAAAGAAGGACCGCTCTG 61.302 60.000 0.36 0.00 0.00 3.35
3976 4898 5.904362 AGATGCTGGTTACAAAGGATTTC 57.096 39.130 0.00 0.00 35.03 2.17
4002 4924 4.638421 TCGGATTTCGGTATTGCAAGAATT 59.362 37.500 4.94 0.00 39.77 2.17
4032 4954 2.774007 GATTCGTCAAATTGGAGTGCG 58.226 47.619 0.00 0.00 0.00 5.34
4255 5192 0.329261 TGGGCAAACATCCAGGAGAG 59.671 55.000 0.00 0.00 0.00 3.20
4324 5261 6.920817 AGAAATTTTGGATAAACGACTTCCC 58.079 36.000 0.00 0.00 0.00 3.97
4330 5267 1.205417 GATAAACGACTTCCCCGACCA 59.795 52.381 0.00 0.00 0.00 4.02
4400 5340 2.160205 GCCTAACTCCTTCACCCAAAC 58.840 52.381 0.00 0.00 0.00 2.93
4483 5434 6.326064 ACTCTTGCAGATGTATCATCTTAGGT 59.674 38.462 9.19 5.93 0.00 3.08
4534 6407 1.903877 TAGCTGTCCAAGGCCTGCTC 61.904 60.000 15.70 3.69 37.16 4.26
4740 6766 3.788227 TGACTGCCCAAGTGAAATACT 57.212 42.857 0.00 0.00 40.07 2.12
4741 6767 4.901197 TGACTGCCCAAGTGAAATACTA 57.099 40.909 0.00 0.00 40.07 1.82
4742 6768 4.575885 TGACTGCCCAAGTGAAATACTAC 58.424 43.478 0.00 0.00 40.07 2.73
4816 6842 7.967908 ACCTCAACTTCTCTTCTAATTCTTCA 58.032 34.615 0.00 0.00 0.00 3.02
4837 6863 9.516314 TCTTCACGTCATTCAATAGTAATACTG 57.484 33.333 2.68 0.00 0.00 2.74
4838 6864 8.642908 TTCACGTCATTCAATAGTAATACTGG 57.357 34.615 2.68 0.00 0.00 4.00
4839 6865 6.700081 TCACGTCATTCAATAGTAATACTGGC 59.300 38.462 2.68 0.00 0.00 4.85
4850 6876 4.651778 AGTAATACTGGCAAGTGCAAAGA 58.348 39.130 3.21 0.00 44.36 2.52
4872 6898 1.059913 AGCACCTTACTGCAACTCCT 58.940 50.000 0.00 0.00 39.86 3.69
4882 6908 2.636893 ACTGCAACTCCTCAAGATGACT 59.363 45.455 0.00 0.00 29.49 3.41
4883 6909 3.001414 CTGCAACTCCTCAAGATGACTG 58.999 50.000 0.00 0.00 29.49 3.51
4884 6910 1.736681 GCAACTCCTCAAGATGACTGC 59.263 52.381 0.00 0.00 29.49 4.40
4885 6911 1.998315 CAACTCCTCAAGATGACTGCG 59.002 52.381 0.00 0.00 29.49 5.18
4908 6934 6.183360 GCGGAGTTAAAAGGTACAATTCTCTC 60.183 42.308 0.00 0.00 0.00 3.20
4909 6935 7.097834 CGGAGTTAAAAGGTACAATTCTCTCT 58.902 38.462 0.00 0.00 0.00 3.10
4943 6969 0.550914 AACAGAGTTTCAGCCACCCA 59.449 50.000 0.00 0.00 0.00 4.51
4950 6976 2.569404 AGTTTCAGCCACCCAAAAACAA 59.431 40.909 0.00 0.00 33.37 2.83
4965 7026 7.039993 ACCCAAAAACAATACCAGAGTGATTAC 60.040 37.037 0.00 0.00 0.00 1.89
4978 7039 5.003804 AGAGTGATTACGAAAACAGGCAAT 58.996 37.500 0.00 0.00 0.00 3.56
4979 7040 5.046910 AGTGATTACGAAAACAGGCAATG 57.953 39.130 0.00 0.00 0.00 2.82
4981 7042 3.505680 TGATTACGAAAACAGGCAATGCT 59.494 39.130 4.82 0.00 0.00 3.79
5008 7069 6.813152 CAGGCATATGATGAATCACGTACATA 59.187 38.462 6.97 0.00 40.03 2.29
5009 7070 7.331687 CAGGCATATGATGAATCACGTACATAA 59.668 37.037 6.97 0.00 40.03 1.90
5034 7095 2.907634 TGAAGCAACACACCGAACTAA 58.092 42.857 0.00 0.00 0.00 2.24
5095 9581 1.813178 TGCAAAACAGTGTTCCGACAA 59.187 42.857 9.40 0.00 37.57 3.18
5285 9780 4.641094 CCCTGAAATCGACAGAGTAGTACT 59.359 45.833 1.37 1.37 37.54 2.73
5346 9841 4.217550 GGAGAGGGAATCTAGAAGTCATCG 59.782 50.000 0.00 0.00 38.84 3.84
5349 9844 3.892588 AGGGAATCTAGAAGTCATCGTCC 59.107 47.826 0.00 0.00 0.00 4.79
5370 9865 1.026718 CCTCCTCGGCCATGTGTTTC 61.027 60.000 2.24 0.00 0.00 2.78
5373 9868 3.367051 CTCGGCCATGTGTTTCGCG 62.367 63.158 2.24 0.00 0.00 5.87
5400 9895 2.776440 TCCTGCTGGAGCCTCTCT 59.224 61.111 8.48 0.00 41.18 3.10
5412 9907 2.021722 CCTCTCTCGCCTCTTCTCG 58.978 63.158 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.039746 TGGTCATTCAACGTCCCTCATT 59.960 45.455 0.00 0.00 0.00 2.57
2 3 1.052617 TGGTCATTCAACGTCCCTCA 58.947 50.000 0.00 0.00 0.00 3.86
3 4 2.403252 ATGGTCATTCAACGTCCCTC 57.597 50.000 0.00 0.00 0.00 4.30
5 6 4.036380 GGAATAATGGTCATTCAACGTCCC 59.964 45.833 0.00 0.00 34.66 4.46
6 7 4.638421 TGGAATAATGGTCATTCAACGTCC 59.362 41.667 0.00 2.87 34.66 4.79
7 8 5.811399 TGGAATAATGGTCATTCAACGTC 57.189 39.130 0.00 0.00 34.66 4.34
8 9 7.054124 AGTATGGAATAATGGTCATTCAACGT 58.946 34.615 0.00 0.00 34.66 3.99
9 10 7.496529 AGTATGGAATAATGGTCATTCAACG 57.503 36.000 0.00 0.00 34.66 4.10
12 13 9.013229 GCATTAGTATGGAATAATGGTCATTCA 57.987 33.333 0.00 0.00 38.99 2.57
13 14 9.013229 TGCATTAGTATGGAATAATGGTCATTC 57.987 33.333 0.00 0.00 38.99 2.67
14 15 8.796475 GTGCATTAGTATGGAATAATGGTCATT 58.204 33.333 7.11 1.65 38.99 2.57
15 16 7.944000 TGTGCATTAGTATGGAATAATGGTCAT 59.056 33.333 7.11 0.00 38.99 3.06
16 17 7.286313 TGTGCATTAGTATGGAATAATGGTCA 58.714 34.615 7.11 0.00 38.99 4.02
17 18 7.744087 TGTGCATTAGTATGGAATAATGGTC 57.256 36.000 7.11 0.00 38.99 4.02
18 19 8.710749 ATTGTGCATTAGTATGGAATAATGGT 57.289 30.769 7.11 0.00 38.99 3.55
60 61 5.912360 TTAACTAGATGAATGCTCATGCG 57.088 39.130 0.00 0.00 42.60 4.73
74 75 4.890088 ACCGTGTCTTTGCATTAACTAGA 58.110 39.130 0.00 0.00 0.00 2.43
232 233 4.722361 AGGTTAAACTTTCAAAACCGCA 57.278 36.364 0.00 0.00 44.90 5.69
328 342 6.578545 CACTAATAATGTTTGTGTGTGCAGTC 59.421 38.462 0.00 0.00 0.00 3.51
491 514 1.339610 CACTGCTCCGGGATTCTCTAG 59.660 57.143 0.00 0.00 0.00 2.43
574 607 1.863662 GACAGAGGTCTTCCGCGTCA 61.864 60.000 4.92 0.00 40.99 4.35
681 714 1.267806 ACAGCAGCCTCACATTTTTCG 59.732 47.619 0.00 0.00 0.00 3.46
847 887 2.432628 CGGTGTCCGGAGCAGAAC 60.433 66.667 3.06 0.00 44.15 3.01
866 906 6.022821 GCGATAGTAGCTAAGAAGAATACCG 58.977 44.000 0.00 0.00 39.35 4.02
884 926 6.157904 AGACATGATGATTCAGAAGCGATAG 58.842 40.000 0.00 0.00 34.73 2.08
889 931 7.086230 AGAAAAGACATGATGATTCAGAAGC 57.914 36.000 0.00 0.00 34.73 3.86
895 940 6.317088 TGCGAAAGAAAAGACATGATGATTC 58.683 36.000 0.00 0.00 0.00 2.52
928 973 4.839668 TCCAACAGTAAAAATCAACCGG 57.160 40.909 0.00 0.00 0.00 5.28
974 1019 3.443976 TCACGACGTGGTATGATCAATG 58.556 45.455 26.55 0.00 33.87 2.82
975 1020 3.706698 CTCACGACGTGGTATGATCAAT 58.293 45.455 26.55 0.00 33.87 2.57
986 1031 2.447887 GCCATGAGCTCACGACGTG 61.448 63.158 20.97 21.88 38.99 4.49
1007 1052 2.674380 GCAGTGGCACCTTGGAGG 60.674 66.667 15.27 0.00 42.49 4.30
1008 1053 2.674380 GGCAGTGGCACCTTGGAG 60.674 66.667 15.27 0.00 43.71 3.86
1068 1119 3.871463 GCCTGGAAGCAATGAGAAGAAGA 60.871 47.826 0.00 0.00 0.00 2.87
1192 1255 1.136147 GCGTGATGTACTCGACGGT 59.864 57.895 11.34 0.00 37.64 4.83
1204 1267 2.272146 GGACCCCATGTGCGTGAT 59.728 61.111 0.00 0.00 0.00 3.06
1205 1268 2.927856 AGGACCCCATGTGCGTGA 60.928 61.111 0.00 0.00 40.82 4.35
1219 1291 2.750637 GCCGTCGTCTCTCCAGGA 60.751 66.667 0.00 0.00 0.00 3.86
1280 1362 2.915659 TGGTTCCTCGGCGTGACT 60.916 61.111 10.96 0.00 0.00 3.41
1761 1851 4.113354 CTGACAGACTATTACCGGAAAGC 58.887 47.826 9.46 0.00 0.00 3.51
1903 1993 4.512944 GGTGTGCTGGTTCTGATATATGTG 59.487 45.833 0.00 0.00 0.00 3.21
2271 2361 3.949113 GGCCGGATAACTGGTTTTCATAA 59.051 43.478 5.05 0.00 43.99 1.90
2403 2493 6.513884 GCTTGTTGTCATTCAGTTCAATGAGA 60.514 38.462 0.00 0.00 42.26 3.27
2814 3724 7.398829 TCATCCAATACAGGTTGCTTAACTTA 58.601 34.615 0.00 0.00 0.00 2.24
3027 3945 1.357420 TCCAGGGAAGCTAAATTGCCA 59.643 47.619 0.00 0.00 42.75 4.92
3360 4278 7.142021 ACATAAGCAGAACGACTGATAGTATG 58.858 38.462 15.73 15.45 44.93 2.39
3861 4783 1.745653 GCTTGGGCAACATCTCTTACC 59.254 52.381 0.00 0.00 38.54 2.85
3876 4798 0.253327 GGAGGTAAGTGAGGGCTTGG 59.747 60.000 0.00 0.00 0.00 3.61
3976 4898 2.821546 TGCAATACCGAAATCCGAGAG 58.178 47.619 0.00 0.00 41.76 3.20
4002 4924 5.921408 CCAATTTGACGAATCGGGTTTTAAA 59.079 36.000 7.80 0.00 0.00 1.52
4032 4954 1.301795 GCCATAAGTCCCCGCTAGC 60.302 63.158 4.06 4.06 0.00 3.42
4192 5129 4.695455 ACACCAAAGCTATACACATCACAC 59.305 41.667 0.00 0.00 0.00 3.82
4255 5192 7.810658 TGAGTGAAGAATGAAAAGCTTGTATC 58.189 34.615 0.00 0.00 0.00 2.24
4324 5261 2.434359 GCCTCGGTTTCTGGTCGG 60.434 66.667 0.00 0.00 0.00 4.79
4330 5267 1.372623 GTCGTTCGCCTCGGTTTCT 60.373 57.895 0.00 0.00 0.00 2.52
4400 5340 4.379652 ACTTTTTGCATAGTTGGCCTTTG 58.620 39.130 3.32 0.00 0.00 2.77
4534 6407 9.289303 AGCAGAAATAGCGTTAATTATTTGTTG 57.711 29.630 7.08 6.86 37.01 3.33
4740 6766 5.071250 ACCCTGTTTAAGTGACATCTGTGTA 59.929 40.000 0.00 0.00 39.09 2.90
4741 6767 4.141482 ACCCTGTTTAAGTGACATCTGTGT 60.141 41.667 0.00 0.00 42.49 3.72
4742 6768 4.389374 ACCCTGTTTAAGTGACATCTGTG 58.611 43.478 0.00 0.00 0.00 3.66
4816 6842 6.578944 TGCCAGTATTACTATTGAATGACGT 58.421 36.000 0.00 0.00 0.00 4.34
4832 6858 1.815003 GCTCTTTGCACTTGCCAGTAT 59.185 47.619 0.00 0.00 42.31 2.12
4834 6860 2.036236 GCTCTTTGCACTTGCCAGT 58.964 52.632 0.00 0.00 42.31 4.00
4870 6896 0.534412 ACTCCGCAGTCATCTTGAGG 59.466 55.000 0.00 0.00 0.00 3.86
4872 6898 3.953712 TTAACTCCGCAGTCATCTTGA 57.046 42.857 0.00 0.00 29.93 3.02
4882 6908 5.310451 AGAATTGTACCTTTTAACTCCGCA 58.690 37.500 0.00 0.00 0.00 5.69
4883 6909 5.642491 AGAGAATTGTACCTTTTAACTCCGC 59.358 40.000 0.00 0.00 0.00 5.54
4884 6910 7.097834 AGAGAGAATTGTACCTTTTAACTCCG 58.902 38.462 0.00 0.00 0.00 4.63
4921 6947 1.312815 GTGGCTGAAACTCTGTTGCT 58.687 50.000 0.00 0.00 0.00 3.91
4943 6969 7.972832 TCGTAATCACTCTGGTATTGTTTTT 57.027 32.000 0.00 0.00 0.00 1.94
4950 6976 6.106673 CCTGTTTTCGTAATCACTCTGGTAT 58.893 40.000 0.00 0.00 0.00 2.73
4965 7026 2.414559 CCTGTAGCATTGCCTGTTTTCG 60.415 50.000 4.70 0.00 0.00 3.46
4979 7040 4.092529 CGTGATTCATCATATGCCTGTAGC 59.907 45.833 0.00 0.00 39.30 3.58
4981 7042 5.213891 ACGTGATTCATCATATGCCTGTA 57.786 39.130 0.00 0.00 39.30 2.74
5009 7070 3.791973 TCGGTGTGTTGCTTCATTTTT 57.208 38.095 0.00 0.00 0.00 1.94
5027 7088 5.007136 GGAAGCTGATTTGAGGATTAGTTCG 59.993 44.000 0.00 0.00 0.00 3.95
5034 7095 2.309755 TGTGGGAAGCTGATTTGAGGAT 59.690 45.455 0.00 0.00 0.00 3.24
5095 9581 1.859302 AATCGAGGAACTGAGAGCCT 58.141 50.000 0.00 0.00 41.55 4.58
5199 9685 7.675962 TTACTCAGTGCGGTTTATTATGTTT 57.324 32.000 0.00 0.00 0.00 2.83
5207 9693 5.483811 TGAATGATTACTCAGTGCGGTTTA 58.516 37.500 0.00 0.00 34.12 2.01
5346 9841 2.444895 ATGGCCGAGGAGGAGGAC 60.445 66.667 0.00 0.00 45.00 3.85
5349 9844 1.903877 AACACATGGCCGAGGAGGAG 61.904 60.000 0.00 0.00 45.00 3.69
5370 9865 1.807573 GCAGGAGGAAGAACTCGCG 60.808 63.158 0.00 0.00 38.39 5.87
5373 9868 1.270907 TCCAGCAGGAGGAAGAACTC 58.729 55.000 0.00 0.00 39.61 3.01
5394 9889 1.444119 CCGAGAAGAGGCGAGAGAGG 61.444 65.000 0.00 0.00 0.00 3.69
5412 9907 3.214328 TCACAAGGAAAAAGAGAGTGCC 58.786 45.455 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.