Multiple sequence alignment - TraesCS5D01G148800

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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 TraesCS5D01G148800 chr5D 100.000 3738 0 0 1 3738 238065006 238068743 0.000000e+00 6903.0
1 TraesCS5D01G148800 chr5D 76.471 153 22 10 1206 1351 384348078 384347933 1.860000e-08 71.3
2 TraesCS5D01G148800 chr5B 90.734 3475 160 66 56 3451 267780418 267777027 0.000000e+00 4484.0
3 TraesCS5D01G148800 chr5B 91.111 270 11 2 3469 3738 267776741 267776485 1.650000e-93 353.0
4 TraesCS5D01G148800 chr5B 76.471 153 22 10 1206 1351 461141441 461141296 1.860000e-08 71.3
5 TraesCS5D01G148800 chr5A 92.734 3014 121 37 766 3738 317248598 317245642 0.000000e+00 4263.0
6 TraesCS5D01G148800 chr5A 86.334 761 57 17 1 742 317249709 317248977 0.000000e+00 785.0
7 TraesCS5D01G148800 chr2B 79.303 488 75 18 1219 1697 85177897 85177427 6.020000e-83 318.0
8 TraesCS5D01G148800 chr2B 78.614 505 76 24 1207 1697 85074019 85074505 4.690000e-79 305.0
9 TraesCS5D01G148800 chr2B 87.500 48 6 0 1216 1263 83955340 83955293 5.220000e-04 56.5
10 TraesCS5D01G148800 chr2D 78.615 491 75 19 1216 1697 54317534 54318003 7.850000e-77 298.0
11 TraesCS5D01G148800 chr2D 78.367 490 78 21 1219 1697 54487966 54487494 3.650000e-75 292.0
12 TraesCS5D01G148800 chr2D 85.965 57 8 0 1207 1263 52647005 52647061 1.120000e-05 62.1
13 TraesCS5D01G148800 chr2D 85.000 60 9 0 1204 1263 52852077 52852136 1.120000e-05 62.1
14 TraesCS5D01G148800 chr2A 77.734 503 80 20 1207 1697 54882383 54882865 2.840000e-71 279.0
15 TraesCS5D01G148800 chr2A 85.656 244 30 3 1467 1709 54955222 54954983 6.200000e-63 252.0
16 TraesCS5D01G148800 chr4B 83.588 262 39 4 1438 1697 380653771 380654030 3.730000e-60 243.0
17 TraesCS5D01G148800 chr7B 89.796 49 5 0 1215 1263 316006655 316006607 3.120000e-06 63.9
18 TraesCS5D01G148800 chr7A 89.796 49 5 0 1215 1263 410727038 410727086 3.120000e-06 63.9


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 TraesCS5D01G148800 chr5D 238065006 238068743 3737 False 6903.0 6903 100.0000 1 3738 1 chr5D.!!$F1 3737
1 TraesCS5D01G148800 chr5B 267776485 267780418 3933 True 2418.5 4484 90.9225 56 3738 2 chr5B.!!$R2 3682
2 TraesCS5D01G148800 chr5A 317245642 317249709 4067 True 2524.0 4263 89.5340 1 3738 2 chr5A.!!$R1 3737

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
757 801 0.391528 TAGTTTTTCTACGCCCCGGC 60.392 55.0 0.0 0.0 37.85 6.13 F
1413 1825 0.391395 CAGCTCCAACTCTGCTCTGG 60.391 60.0 0.0 0.0 34.51 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 2038 0.036875 GCTTGCCCCTGTAGAACACT 59.963 55.0 0.0 0.0 0.0 3.55 R
2921 3367 0.539669 GGTGGACAAGGGAAGGGTTG 60.540 60.0 0.0 0.0 0.0 3.77 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
31 32 2.832733 AGTCCTACCTCAGCTTTGGTAC 59.167 50.000 9.81 4.85 37.74 3.34
34 35 4.650131 GTCCTACCTCAGCTTTGGTACTAT 59.350 45.833 9.81 0.00 37.74 2.12
37 38 5.010213 CCTACCTCAGCTTTGGTACTATCTC 59.990 48.000 9.81 0.00 37.74 2.75
43 44 5.059833 CAGCTTTGGTACTATCTCCAATCC 58.940 45.833 0.00 0.00 42.25 3.01
51 52 7.815383 TGGTACTATCTCCAATCCATTTCAAT 58.185 34.615 0.00 0.00 0.00 2.57
62 63 8.190122 TCCAATCCATTTCAATTATCGTTGAAG 58.810 33.333 2.80 0.00 45.67 3.02
64 65 6.507958 TCCATTTCAATTATCGTTGAAGCA 57.492 33.333 2.80 0.00 45.67 3.91
92 93 9.836864 ATGTATCTAGATGCACTTCAATGTTAA 57.163 29.630 23.58 0.00 36.29 2.01
124 127 7.439955 TGGAGTATTAATTATTGGCACGTGTAG 59.560 37.037 18.38 0.00 0.00 2.74
167 170 3.636929 TACGGCCAGCACCCCATTG 62.637 63.158 2.24 0.00 0.00 2.82
169 172 2.604382 GGCCAGCACCCCATTGTT 60.604 61.111 0.00 0.00 0.00 2.83
181 184 5.016173 CACCCCATTGTTCCTTATCTGAAA 58.984 41.667 0.00 0.00 0.00 2.69
260 272 1.106285 GCACATGAAATCTGGACCCC 58.894 55.000 0.00 0.00 0.00 4.95
280 292 2.097466 CCGCCATTAATCAACTCCACAC 59.903 50.000 0.00 0.00 0.00 3.82
282 294 3.190327 CGCCATTAATCAACTCCACACAA 59.810 43.478 0.00 0.00 0.00 3.33
284 296 4.458989 GCCATTAATCAACTCCACACAAGA 59.541 41.667 0.00 0.00 0.00 3.02
381 420 4.700365 GCCCGCAAGACGCCAAAC 62.700 66.667 0.00 0.00 41.76 2.93
492 535 6.770303 ACCAAAAGAAAAGAAGAGAAGAGAGG 59.230 38.462 0.00 0.00 0.00 3.69
602 646 4.373116 CGTACGCACACAGGGGCT 62.373 66.667 0.52 0.00 33.80 5.19
717 761 2.297701 TGCGCTCCAAGGATTAATTCC 58.702 47.619 9.73 0.00 45.85 3.01
737 781 2.544685 CGGTGTGAATCTAGGCTTGAG 58.455 52.381 4.72 0.00 0.00 3.02
743 787 6.166982 GTGTGAATCTAGGCTTGAGTAGTTT 58.833 40.000 4.72 0.00 0.00 2.66
745 789 7.173390 GTGTGAATCTAGGCTTGAGTAGTTTTT 59.827 37.037 4.72 0.00 0.00 1.94
746 790 7.387948 TGTGAATCTAGGCTTGAGTAGTTTTTC 59.612 37.037 4.72 2.62 0.00 2.29
748 792 8.812972 TGAATCTAGGCTTGAGTAGTTTTTCTA 58.187 33.333 4.72 0.00 0.00 2.10
749 793 9.089601 GAATCTAGGCTTGAGTAGTTTTTCTAC 57.910 37.037 4.72 0.00 46.68 2.59
756 800 1.362768 GTAGTTTTTCTACGCCCCGG 58.637 55.000 0.00 0.00 39.42 5.73
757 801 0.391528 TAGTTTTTCTACGCCCCGGC 60.392 55.000 0.00 0.00 37.85 6.13
758 802 1.967494 GTTTTTCTACGCCCCGGCA 60.967 57.895 6.52 0.00 42.06 5.69
759 803 1.673009 TTTTTCTACGCCCCGGCAG 60.673 57.895 6.52 1.40 42.06 4.85
760 804 4.770874 TTTCTACGCCCCGGCAGC 62.771 66.667 6.52 0.00 42.06 5.25
796 1195 4.592485 CCTCGTGAGGCAGAATATAACT 57.408 45.455 2.38 0.00 42.44 2.24
797 1196 4.950050 CCTCGTGAGGCAGAATATAACTT 58.050 43.478 2.38 0.00 42.44 2.66
798 1197 4.985409 CCTCGTGAGGCAGAATATAACTTC 59.015 45.833 2.38 0.00 42.44 3.01
799 1198 5.451937 CCTCGTGAGGCAGAATATAACTTCA 60.452 44.000 2.38 0.00 42.44 3.02
800 1199 5.592054 TCGTGAGGCAGAATATAACTTCAG 58.408 41.667 0.00 0.00 0.00 3.02
818 1217 2.232208 TCAGTACACTCCACTGATGCAG 59.768 50.000 1.17 0.00 45.68 4.41
819 1218 2.232208 CAGTACACTCCACTGATGCAGA 59.768 50.000 0.82 0.00 45.10 4.26
820 1219 2.495270 AGTACACTCCACTGATGCAGAG 59.505 50.000 0.82 0.00 35.18 3.35
821 1220 0.612229 ACACTCCACTGATGCAGAGG 59.388 55.000 4.76 4.76 42.25 3.69
822 1221 0.743701 CACTCCACTGATGCAGAGGC 60.744 60.000 6.09 0.00 41.01 4.70
847 1246 7.201565 GCAGACAAGTTCATTAGTCTTGGTATC 60.202 40.741 8.59 0.00 41.64 2.24
860 1259 6.842676 AGTCTTGGTATCTGAAAAGAAAGGT 58.157 36.000 0.00 0.00 30.85 3.50
861 1260 7.974504 AGTCTTGGTATCTGAAAAGAAAGGTA 58.025 34.615 0.00 0.00 30.85 3.08
862 1261 8.437575 AGTCTTGGTATCTGAAAAGAAAGGTAA 58.562 33.333 0.00 0.00 30.85 2.85
921 1320 0.466739 TTCTGCCCCTCGCGATACTA 60.467 55.000 10.36 0.00 42.08 1.82
953 1352 2.023771 CTCGCTGCTGACTCGCAAA 61.024 57.895 0.00 0.00 39.80 3.68
954 1353 1.953353 CTCGCTGCTGACTCGCAAAG 61.953 60.000 0.00 0.00 39.80 2.77
955 1354 2.023771 CGCTGCTGACTCGCAAAGA 61.024 57.895 0.00 0.00 39.80 2.52
1080 1489 2.581726 CTTCTCCTCCTCCTCCCGCT 62.582 65.000 0.00 0.00 0.00 5.52
1138 1547 1.453155 CAGCCCACACCAACTCATAC 58.547 55.000 0.00 0.00 0.00 2.39
1384 1796 6.793505 ACTAAAACTAATCGACTCCATCCT 57.206 37.500 0.00 0.00 0.00 3.24
1413 1825 0.391395 CAGCTCCAACTCTGCTCTGG 60.391 60.000 0.00 0.00 34.51 3.86
1687 2107 2.959372 CACGAGTACCGCCTCACA 59.041 61.111 0.00 0.00 43.32 3.58
1736 2156 0.401105 AGGATCCTCCATGAGGGTGG 60.401 60.000 9.02 0.00 44.18 4.61
1863 2292 8.412608 TCGACTTAATTGTTTGCATTTGAAAA 57.587 26.923 0.00 0.00 0.00 2.29
1865 2294 7.318674 CGACTTAATTGTTTGCATTTGAAAAGC 59.681 33.333 0.00 0.00 0.00 3.51
1892 2321 8.877864 TGTTTAATCAGTGAATTAATCTGGGT 57.122 30.769 0.00 0.00 32.62 4.51
1993 2426 1.132849 TCCTCCTCTGACCAGGAACAA 60.133 52.381 0.00 0.00 42.35 2.83
2047 2483 0.876777 CGCAGAACAACCACACCGTA 60.877 55.000 0.00 0.00 0.00 4.02
2302 2744 4.644954 GGCAACAAACGCTACACTATAAC 58.355 43.478 0.00 0.00 0.00 1.89
2305 2747 6.311723 GCAACAAACGCTACACTATAACAAT 58.688 36.000 0.00 0.00 0.00 2.71
2634 3079 0.041839 CTTGCTTGCTGTGTCGTGAC 60.042 55.000 0.00 0.00 0.00 3.67
2721 3166 7.957992 ACGGGGGTTTATTGTGAAATAAATA 57.042 32.000 6.85 0.00 37.09 1.40
2777 3222 7.880105 TGCGATGATCATCATATATCCTAGAC 58.120 38.462 30.13 10.34 37.20 2.59
2778 3223 7.040132 TGCGATGATCATCATATATCCTAGACC 60.040 40.741 30.13 3.60 37.20 3.85
2779 3224 7.176515 GCGATGATCATCATATATCCTAGACCT 59.823 40.741 30.13 0.00 37.20 3.85
2884 3329 3.794481 TGGCGTACCCAGCACTAA 58.206 55.556 0.00 0.00 39.18 2.24
2899 3344 2.224314 GCACTAATTAATGAGCGAGGCC 59.776 50.000 0.00 0.00 0.00 5.19
2921 3367 2.881352 GCTAGCGTGTGCGGTCTC 60.881 66.667 0.00 0.00 46.65 3.36
2953 3399 1.534476 TCCACCGTACAGCCAGGAA 60.534 57.895 0.00 0.00 0.00 3.36
3009 3458 2.131776 TTGTCACCGGAAACCAAAGT 57.868 45.000 9.46 0.00 0.00 2.66
3057 3506 3.410960 GCTCCAGGGCCAATAGAAG 57.589 57.895 6.18 0.00 0.00 2.85
3135 3585 2.512515 AGATGAAGAAGGCGGCGC 60.513 61.111 26.17 26.17 0.00 6.53
3172 3622 4.991687 ACTGCTGCTGAACTTACTTTAGTC 59.008 41.667 13.69 0.00 0.00 2.59
3261 3714 6.001449 TCCTCCATTAGGTTAATCACAAGG 57.999 41.667 0.00 0.00 46.62 3.61
3289 3752 5.102953 TCCCTATTGGAGACACAGATTTG 57.897 43.478 0.00 0.00 42.67 2.32
3290 3753 4.536090 TCCCTATTGGAGACACAGATTTGT 59.464 41.667 0.00 0.00 42.67 2.83
3291 3754 5.014123 TCCCTATTGGAGACACAGATTTGTT 59.986 40.000 0.00 0.00 42.67 2.83
3337 3800 3.676598 CGAACCATCGTGTACCATACCAA 60.677 47.826 0.00 0.00 44.06 3.67
3338 3801 3.536956 ACCATCGTGTACCATACCAAG 57.463 47.619 0.00 0.00 0.00 3.61
3339 3802 2.210116 CCATCGTGTACCATACCAAGC 58.790 52.381 0.00 0.00 0.00 4.01
3340 3803 2.210116 CATCGTGTACCATACCAAGCC 58.790 52.381 0.00 0.00 0.00 4.35
3557 4291 1.456145 TCGCCGGATAGCCTAACCA 60.456 57.895 5.05 0.00 0.00 3.67
3611 4345 6.632672 GCTGAGGGTGGTTAAGATAAGAATGA 60.633 42.308 0.00 0.00 0.00 2.57
3634 4368 1.137872 CGTCCTAATCAGGCTTCAGCT 59.862 52.381 0.00 0.00 42.30 4.24
3652 4386 2.745102 GCTTAGGCTTAGCTAAGTCGG 58.255 52.381 29.42 22.99 42.48 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.010213 GGAGATAGTACCAAAGCTGAGGTAG 59.990 48.000 15.74 0.00 40.83 3.18
18 19 5.344743 TTGGAGATAGTACCAAAGCTGAG 57.655 43.478 0.00 0.00 42.18 3.35
31 32 9.224267 ACGATAATTGAAATGGATTGGAGATAG 57.776 33.333 0.00 0.00 0.00 2.08
34 35 7.555914 TCAACGATAATTGAAATGGATTGGAGA 59.444 33.333 0.00 0.00 35.65 3.71
37 38 7.043192 GCTTCAACGATAATTGAAATGGATTGG 60.043 37.037 2.85 0.00 45.52 3.16
43 44 7.699391 ACATCTGCTTCAACGATAATTGAAATG 59.301 33.333 2.85 5.96 45.52 2.32
51 52 8.166422 TCTAGATACATCTGCTTCAACGATAA 57.834 34.615 1.88 0.00 37.76 1.75
62 63 5.536260 TGAAGTGCATCTAGATACATCTGC 58.464 41.667 8.89 7.76 37.76 4.26
64 65 7.733969 ACATTGAAGTGCATCTAGATACATCT 58.266 34.615 8.89 5.76 40.86 2.90
99 102 6.613755 ACACGTGCCAATAATTAATACTCC 57.386 37.500 17.22 0.00 0.00 3.85
124 127 2.103042 GCGTCTCCTGTGTGCCATC 61.103 63.158 0.00 0.00 0.00 3.51
130 133 2.885861 GATCCGCGTCTCCTGTGT 59.114 61.111 4.92 0.00 0.00 3.72
167 170 6.238869 GCCATGGAGAATTTCAGATAAGGAAC 60.239 42.308 18.40 0.00 0.00 3.62
169 172 5.380043 GCCATGGAGAATTTCAGATAAGGA 58.620 41.667 18.40 0.00 0.00 3.36
213 216 1.301009 GACCATAGCTAGCACGGCC 60.301 63.158 18.83 2.38 0.00 6.13
217 220 0.032267 GACCGGACCATAGCTAGCAC 59.968 60.000 18.83 0.80 0.00 4.40
260 272 2.746904 TGTGTGGAGTTGATTAATGGCG 59.253 45.455 0.00 0.00 0.00 5.69
306 345 1.746991 CCGCTGGCTCCTTTCTTCC 60.747 63.158 0.00 0.00 0.00 3.46
381 420 1.575922 CCGCCAATGATATGCACCG 59.424 57.895 0.00 0.00 0.00 4.94
447 486 3.002759 GGTTAGCAATAGTAGCAAGCAGC 59.997 47.826 0.00 0.00 46.19 5.25
602 646 1.846007 AACGGGCAAATGGCTAATCA 58.154 45.000 6.93 0.00 44.01 2.57
717 761 2.093973 ACTCAAGCCTAGATTCACACCG 60.094 50.000 0.00 0.00 0.00 4.94
737 781 1.362768 CCGGGGCGTAGAAAAACTAC 58.637 55.000 0.00 0.00 45.56 2.73
743 787 4.770874 GCTGCCGGGGCGTAGAAA 62.771 66.667 2.18 0.00 45.51 2.52
749 793 3.454587 TAATACTGCTGCCGGGGCG 62.455 63.158 2.18 1.36 45.51 6.13
750 794 1.598130 CTAATACTGCTGCCGGGGC 60.598 63.158 2.18 1.86 42.35 5.80
751 795 0.180406 AACTAATACTGCTGCCGGGG 59.820 55.000 2.18 0.00 0.00 5.73
752 796 2.038387 AAACTAATACTGCTGCCGGG 57.962 50.000 2.18 0.00 0.00 5.73
753 797 2.477863 GCAAAACTAATACTGCTGCCGG 60.478 50.000 0.00 0.00 0.00 6.13
754 798 2.477863 GGCAAAACTAATACTGCTGCCG 60.478 50.000 0.00 0.00 38.59 5.69
756 800 2.755103 AGGGCAAAACTAATACTGCTGC 59.245 45.455 0.00 0.00 35.13 5.25
757 801 3.063997 CGAGGGCAAAACTAATACTGCTG 59.936 47.826 0.00 0.00 35.13 4.41
758 802 3.270877 CGAGGGCAAAACTAATACTGCT 58.729 45.455 0.00 0.00 35.13 4.24
759 803 3.007635 ACGAGGGCAAAACTAATACTGC 58.992 45.455 0.00 0.00 0.00 4.40
760 804 4.250464 TCACGAGGGCAAAACTAATACTG 58.750 43.478 0.00 0.00 0.00 2.74
761 805 4.504858 CTCACGAGGGCAAAACTAATACT 58.495 43.478 0.00 0.00 0.00 2.12
762 806 3.621715 CCTCACGAGGGCAAAACTAATAC 59.378 47.826 5.08 0.00 44.87 1.89
764 808 2.711542 CCTCACGAGGGCAAAACTAAT 58.288 47.619 5.08 0.00 44.87 1.73
798 1197 2.232208 TCTGCATCAGTGGAGTGTACTG 59.768 50.000 0.00 0.00 43.56 2.74
799 1198 2.495270 CTCTGCATCAGTGGAGTGTACT 59.505 50.000 0.00 0.00 43.56 2.73
800 1199 2.417924 CCTCTGCATCAGTGGAGTGTAC 60.418 54.545 8.75 0.00 44.90 2.90
818 1217 4.826556 AGACTAATGAACTTGTCTGCCTC 58.173 43.478 0.00 0.00 38.22 4.70
819 1218 4.899352 AGACTAATGAACTTGTCTGCCT 57.101 40.909 0.00 0.00 38.22 4.75
820 1219 4.154918 CCAAGACTAATGAACTTGTCTGCC 59.845 45.833 0.00 0.00 39.39 4.85
821 1220 4.757149 ACCAAGACTAATGAACTTGTCTGC 59.243 41.667 0.00 0.00 39.39 4.26
822 1221 8.037758 AGATACCAAGACTAATGAACTTGTCTG 58.962 37.037 0.00 0.00 39.39 3.51
823 1222 8.037758 CAGATACCAAGACTAATGAACTTGTCT 58.962 37.037 0.00 0.00 40.95 3.41
824 1223 8.035394 TCAGATACCAAGACTAATGAACTTGTC 58.965 37.037 0.00 0.00 39.19 3.18
825 1224 7.907389 TCAGATACCAAGACTAATGAACTTGT 58.093 34.615 0.00 0.00 39.19 3.16
826 1225 8.777865 TTCAGATACCAAGACTAATGAACTTG 57.222 34.615 0.00 0.00 40.12 3.16
847 1246 8.169268 GTCATCACGTATTACCTTTCTTTTCAG 58.831 37.037 0.00 0.00 0.00 3.02
884 1283 5.163652 GGCAGAATCGGCAACTAATTACTTT 60.164 40.000 7.78 0.00 0.00 2.66
921 1320 3.077907 CGAGGTGGTGGGTGGATT 58.922 61.111 0.00 0.00 0.00 3.01
953 1352 1.001641 GGTGCCATGGCTTGTCTCT 60.002 57.895 35.53 0.00 42.51 3.10
954 1353 0.253044 TAGGTGCCATGGCTTGTCTC 59.747 55.000 35.53 18.11 42.51 3.36
955 1354 0.921896 ATAGGTGCCATGGCTTGTCT 59.078 50.000 35.53 26.15 42.51 3.41
1080 1489 0.541863 GCTAGGTGGCTAGCTGGAAA 59.458 55.000 16.68 0.00 46.32 3.13
1138 1547 1.026718 GCAGGTGGGAACGGAATCAG 61.027 60.000 0.00 0.00 0.00 2.90
1377 1789 2.702478 AGCTGATTGATCGAAGGATGGA 59.298 45.455 0.00 0.00 31.51 3.41
1378 1790 3.065655 GAGCTGATTGATCGAAGGATGG 58.934 50.000 0.00 0.00 31.51 3.51
1384 1796 3.196469 AGAGTTGGAGCTGATTGATCGAA 59.804 43.478 0.00 0.00 30.59 3.71
1618 2038 0.036875 GCTTGCCCCTGTAGAACACT 59.963 55.000 0.00 0.00 0.00 3.55
1786 2208 6.377146 ACTGCTCTTACCAAAGTGAAGAAAAA 59.623 34.615 2.93 0.00 36.00 1.94
1832 2261 7.667043 ATGCAAACAATTAAGTCGAGTAAGA 57.333 32.000 0.00 0.00 0.00 2.10
1865 2294 9.793252 CCCAGATTAATTCACTGATTAAACAAG 57.207 33.333 4.60 0.00 35.70 3.16
1993 2426 0.688418 AGCTCTCCTGCTCATGCTCT 60.688 55.000 0.00 0.00 39.34 4.09
2047 2483 3.064987 CTCCGACTTGGGCGACGAT 62.065 63.158 0.00 0.00 38.76 3.73
2361 2806 4.937201 TTCATGCCGTAGTCATCTACAT 57.063 40.909 6.28 0.00 44.71 2.29
2634 3079 0.590732 CGTTCTTATCGGTCGGTCGG 60.591 60.000 0.00 0.00 0.00 4.79
2754 3199 8.634335 AGGTCTAGGATATATGATGATCATCG 57.366 38.462 26.52 11.27 40.63 3.84
2774 3219 6.154021 TCGAATTAACTAACAAGCCTAGGTCT 59.846 38.462 11.31 5.22 0.00 3.85
2775 3220 6.335777 TCGAATTAACTAACAAGCCTAGGTC 58.664 40.000 11.31 2.66 0.00 3.85
2777 3222 6.570692 TCTCGAATTAACTAACAAGCCTAGG 58.429 40.000 3.67 3.67 0.00 3.02
2778 3223 8.543774 CATTCTCGAATTAACTAACAAGCCTAG 58.456 37.037 0.00 0.00 0.00 3.02
2779 3224 7.011109 GCATTCTCGAATTAACTAACAAGCCTA 59.989 37.037 0.00 0.00 0.00 3.93
2783 3228 8.948853 TTTGCATTCTCGAATTAACTAACAAG 57.051 30.769 0.00 0.00 0.00 3.16
2786 3231 7.806014 TGGTTTTGCATTCTCGAATTAACTAAC 59.194 33.333 0.00 0.00 0.00 2.34
2884 3329 2.292267 CAACAGGCCTCGCTCATTAAT 58.708 47.619 0.00 0.00 0.00 1.40
2899 3344 2.471607 CGCACACGCTAGCAACAG 59.528 61.111 16.45 0.05 35.30 3.16
2921 3367 0.539669 GGTGGACAAGGGAAGGGTTG 60.540 60.000 0.00 0.00 0.00 3.77
2953 3399 2.597305 CGAGCGAGCGTTAGTTAATTGT 59.403 45.455 0.00 0.00 0.00 2.71
3009 3458 3.961480 ATGATGTGTCTTTGAGTCGGA 57.039 42.857 0.00 0.00 0.00 4.55
3014 3463 7.965107 GCCTTAGTTAAATGATGTGTCTTTGAG 59.035 37.037 0.00 0.00 0.00 3.02
3057 3506 2.556287 CGAGCTGACGTTTTGCCC 59.444 61.111 0.00 0.00 0.00 5.36
3135 3585 3.716006 CAGTTGAGCGGCGTGTGG 61.716 66.667 9.37 0.00 0.00 4.17
3282 3745 6.570789 CGCAAGCATAAACAAAAACAAATCTG 59.429 34.615 0.00 0.00 0.00 2.90
3286 3749 4.494855 GCCGCAAGCATAAACAAAAACAAA 60.495 37.500 0.00 0.00 42.97 2.83
3287 3750 3.001736 GCCGCAAGCATAAACAAAAACAA 59.998 39.130 0.00 0.00 42.97 2.83
3288 3751 2.541762 GCCGCAAGCATAAACAAAAACA 59.458 40.909 0.00 0.00 42.97 2.83
3289 3752 2.096466 GGCCGCAAGCATAAACAAAAAC 60.096 45.455 0.00 0.00 46.50 2.43
3290 3753 2.139118 GGCCGCAAGCATAAACAAAAA 58.861 42.857 0.00 0.00 46.50 1.94
3291 3754 1.606737 GGGCCGCAAGCATAAACAAAA 60.607 47.619 0.00 0.00 46.50 2.44
3332 3795 4.854173 TGCATTATCTTCTTGGCTTGGTA 58.146 39.130 0.00 0.00 0.00 3.25
3333 3796 3.698040 CTGCATTATCTTCTTGGCTTGGT 59.302 43.478 0.00 0.00 0.00 3.67
3337 3800 4.500499 ACTCTGCATTATCTTCTTGGCT 57.500 40.909 0.00 0.00 0.00 4.75
3338 3801 6.874288 ATTACTCTGCATTATCTTCTTGGC 57.126 37.500 0.00 0.00 0.00 4.52
3425 3891 0.389817 TCTTTGGTGTGATCGCTCCG 60.390 55.000 19.53 8.24 0.00 4.63
3557 4291 0.165079 CACCTTTTAATCGCGCGTGT 59.835 50.000 30.98 20.60 0.00 4.49
3634 4368 2.692041 GTCCCGACTTAGCTAAGCCTAA 59.308 50.000 29.39 11.69 36.79 2.69
3651 4385 0.603975 GCTTAGGGCATCATCGTCCC 60.604 60.000 0.00 0.00 41.35 4.46
3652 4386 2.919971 GCTTAGGGCATCATCGTCC 58.080 57.895 0.00 0.00 41.35 4.79
3675 4409 9.748708 GCCTGCTTAGAGATAATCTATCATAAG 57.251 37.037 10.99 10.99 40.27 1.73


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

AutoCloner maintained by Alex Coulton.