Multiple sequence alignment - TraesCS2A01G537600

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 TraesCS2A01G537600 chr2A 100.000 3083 0 0 1 3083 751170981 751174063 0.000000e+00 5694.0
1 TraesCS2A01G537600 chr2A 90.904 1682 127 13 370 2041 751036695 751038360 0.000000e+00 2235.0
2 TraesCS2A01G537600 chr2A 87.959 1063 119 5 991 2048 751013336 751014394 0.000000e+00 1245.0
3 TraesCS2A01G537600 chr2A 88.258 792 81 8 2297 3083 751014959 751015743 0.000000e+00 937.0
4 TraesCS2A01G537600 chr2A 88.792 687 71 5 2401 3083 751048515 751049199 0.000000e+00 837.0
5 TraesCS2A01G537600 chr2A 77.062 994 169 41 2116 3083 719738116 719737156 4.560000e-143 518.0
6 TraesCS2A01G537600 chr2A 91.444 374 31 1 2711 3083 751055333 751055706 2.120000e-141 512.0
7 TraesCS2A01G537600 chr2A 76.747 744 109 41 545 1271 719738810 719738114 1.050000e-94 357.0
8 TraesCS2A01G537600 chr2A 94.196 224 5 4 1 223 751032034 751032250 4.930000e-88 335.0
9 TraesCS2A01G537600 chr2B 89.465 1832 129 18 244 2041 758895744 758897545 0.000000e+00 2255.0
10 TraesCS2A01G537600 chr2B 82.692 1300 187 21 758 2044 706792969 706791695 0.000000e+00 1120.0
11 TraesCS2A01G537600 chr2B 83.036 1008 121 32 2101 3075 706791127 706790137 0.000000e+00 869.0
12 TraesCS2A01G537600 chr2B 87.840 699 75 6 2390 3083 758898332 758899025 0.000000e+00 811.0
13 TraesCS2A01G537600 chr2B 79.323 1064 196 16 993 2041 758666322 758667376 0.000000e+00 725.0
14 TraesCS2A01G537600 chr2B 78.236 1066 202 19 938 1988 707242644 707241594 0.000000e+00 656.0
15 TraesCS2A01G537600 chr2B 81.340 209 37 2 2872 3079 706731247 706731040 5.290000e-38 169.0
16 TraesCS2A01G537600 chr2B 80.000 225 43 2 2856 3079 707240289 707240066 6.840000e-37 165.0
17 TraesCS2A01G537600 chr2B 86.232 138 17 2 247 384 758673569 758673704 6.890000e-32 148.0
18 TraesCS2A01G537600 chr2D 91.275 1616 110 12 429 2041 619572594 619574181 0.000000e+00 2174.0
19 TraesCS2A01G537600 chr2D 78.999 1519 240 40 545 2035 585740889 585739422 0.000000e+00 965.0
20 TraesCS2A01G537600 chr2D 89.542 698 66 6 2390 3083 619575059 619575753 0.000000e+00 878.0
21 TraesCS2A01G537600 chr2D 78.848 1059 210 8 993 2041 619566035 619567089 0.000000e+00 702.0
22 TraesCS2A01G537600 chr2D 80.392 663 111 9 2423 3082 585738365 585737719 1.290000e-133 486.0
23 TraesCS2A01G537600 chr2D 95.327 107 5 0 273 379 619572386 619572492 1.470000e-38 171.0
24 TraesCS2A01G537600 chr2D 89.313 131 12 1 1 129 619571685 619571815 2.460000e-36 163.0
25 TraesCS2A01G537600 chr2D 94.000 50 3 0 328 377 585741073 585741024 3.300000e-10 76.8
26 TraesCS2A01G537600 chr2D 79.808 104 17 4 839 940 619565460 619565561 4.260000e-09 73.1


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 TraesCS2A01G537600 chr2A 751170981 751174063 3082 False 5694.000000 5694 100.000000 1 3083 1 chr2A.!!$F5 3082
1 TraesCS2A01G537600 chr2A 751036695 751038360 1665 False 2235.000000 2235 90.904000 370 2041 1 chr2A.!!$F2 1671
2 TraesCS2A01G537600 chr2A 751013336 751015743 2407 False 1091.000000 1245 88.108500 991 3083 2 chr2A.!!$F6 2092
3 TraesCS2A01G537600 chr2A 751048515 751049199 684 False 837.000000 837 88.792000 2401 3083 1 chr2A.!!$F3 682
4 TraesCS2A01G537600 chr2A 719737156 719738810 1654 True 437.500000 518 76.904500 545 3083 2 chr2A.!!$R1 2538
5 TraesCS2A01G537600 chr2B 758895744 758899025 3281 False 1533.000000 2255 88.652500 244 3083 2 chr2B.!!$F3 2839
6 TraesCS2A01G537600 chr2B 706790137 706792969 2832 True 994.500000 1120 82.864000 758 3075 2 chr2B.!!$R2 2317
7 TraesCS2A01G537600 chr2B 758666322 758667376 1054 False 725.000000 725 79.323000 993 2041 1 chr2B.!!$F1 1048
8 TraesCS2A01G537600 chr2B 707240066 707242644 2578 True 410.500000 656 79.118000 938 3079 2 chr2B.!!$R3 2141
9 TraesCS2A01G537600 chr2D 619571685 619575753 4068 False 846.500000 2174 91.364250 1 3083 4 chr2D.!!$F2 3082
10 TraesCS2A01G537600 chr2D 585737719 585741073 3354 True 509.266667 965 84.463667 328 3082 3 chr2D.!!$R1 2754
11 TraesCS2A01G537600 chr2D 619565460 619567089 1629 False 387.550000 702 79.328000 839 2041 2 chr2D.!!$F1 1202

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
696 1217 0.108585 ATTCAGTCAGGCAACACCGT 59.891 50.0 0.0 0.0 46.52 4.83 F
1569 2579 0.399949 ACTCCTTGGGTGGTGACTCA 60.400 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2995 0.242825 CCTTGACCACAATGCAGCTG 59.757 55.0 10.11 10.11 35.37 4.24 R
2863 4909 0.555769 TTCCTTGCCACCTTCCAGTT 59.444 50.0 0.00 0.00 0.00 3.16 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
42 43 8.744568 TCACATATGAACATATTTAGGTGCAA 57.255 30.769 10.38 2.07 28.19 4.08
65 66 9.639601 GCAACTATATTGTGCAGATACTACATA 57.360 33.333 0.00 0.00 0.00 2.29
74 75 8.424274 TGTGCAGATACTACATATTTTGACAG 57.576 34.615 0.00 0.00 0.00 3.51
77 78 7.710907 TGCAGATACTACATATTTTGACAGGAC 59.289 37.037 0.00 0.00 0.00 3.85
78 79 7.710907 GCAGATACTACATATTTTGACAGGACA 59.289 37.037 0.00 0.00 0.00 4.02
133 160 6.294564 CGATACCACCTAACATATGTACAGCT 60.295 42.308 9.21 0.00 0.00 4.24
134 161 5.693769 ACCACCTAACATATGTACAGCTT 57.306 39.130 9.21 0.00 0.00 3.74
135 162 5.428253 ACCACCTAACATATGTACAGCTTG 58.572 41.667 9.21 8.87 0.00 4.01
138 165 6.037172 CCACCTAACATATGTACAGCTTGTTC 59.963 42.308 18.58 0.00 33.03 3.18
141 168 7.334421 ACCTAACATATGTACAGCTTGTTCAAG 59.666 37.037 18.58 13.50 31.60 3.02
144 171 7.744087 ACATATGTACAGCTTGTTCAAGAAA 57.256 32.000 6.56 0.00 31.60 2.52
145 172 7.584987 ACATATGTACAGCTTGTTCAAGAAAC 58.415 34.615 6.56 7.92 31.60 2.78
146 173 7.228507 ACATATGTACAGCTTGTTCAAGAAACA 59.771 33.333 6.56 12.19 46.11 2.83
189 255 1.542915 AGATGCACATGGCTCACAAAC 59.457 47.619 0.00 0.00 45.15 2.93
270 720 4.973055 CGTTCAACGTCCCCGGCA 62.973 66.667 0.39 0.00 36.74 5.69
271 721 2.359478 GTTCAACGTCCCCGGCAT 60.359 61.111 0.00 0.00 38.78 4.40
272 722 1.969589 GTTCAACGTCCCCGGCATT 60.970 57.895 0.00 0.00 38.78 3.56
273 723 1.673009 TTCAACGTCCCCGGCATTC 60.673 57.895 0.00 0.00 38.78 2.67
274 724 3.496131 CAACGTCCCCGGCATTCG 61.496 66.667 0.00 0.00 38.78 3.34
379 829 4.016444 TGATGGTAACTCATTTCTTGGCC 58.984 43.478 0.00 0.00 37.61 5.36
390 870 4.278170 TCATTTCTTGGCCTACTTGTTGTG 59.722 41.667 3.32 0.00 0.00 3.33
395 875 0.872388 GGCCTACTTGTTGTGAACCG 59.128 55.000 0.00 0.00 0.00 4.44
435 915 4.499696 CGGTGCTCTCCAATTTCAGTTTTT 60.500 41.667 0.00 0.00 0.00 1.94
436 916 4.746611 GGTGCTCTCCAATTTCAGTTTTTG 59.253 41.667 0.00 0.00 0.00 2.44
450 951 8.873215 TTTCAGTTTTTGTTGTAGTTGTGAAA 57.127 26.923 0.00 0.00 0.00 2.69
605 1124 1.473677 TGGCGCAGATTTTCTTCATGG 59.526 47.619 10.83 0.00 0.00 3.66
624 1143 3.986006 GACAGTGACCGACGCCCA 61.986 66.667 0.00 0.00 0.00 5.36
658 1179 2.574018 CGGGACAGGTGACAGCTGA 61.574 63.158 34.85 0.00 45.98 4.26
659 1180 1.892819 CGGGACAGGTGACAGCTGAT 61.893 60.000 34.85 21.39 45.98 2.90
669 1190 2.999355 GTGACAGCTGATGAGTTTCTCC 59.001 50.000 23.35 0.00 0.00 3.71
696 1217 0.108585 ATTCAGTCAGGCAACACCGT 59.891 50.000 0.00 0.00 46.52 4.83
697 1218 0.531974 TTCAGTCAGGCAACACCGTC 60.532 55.000 0.00 0.00 46.52 4.79
698 1219 2.029073 AGTCAGGCAACACCGTCG 59.971 61.111 0.00 0.00 46.52 5.12
699 1220 3.041940 GTCAGGCAACACCGTCGG 61.042 66.667 10.48 10.48 46.52 4.79
880 1424 7.448420 CACATCAGGAATACCAATACTCTGAT 58.552 38.462 0.00 0.00 39.98 2.90
952 1508 6.035866 CAGTCTGAAGCATCTTCATAGTTCAC 59.964 42.308 9.39 2.01 0.00 3.18
1060 2064 3.953612 ACTGATTTGTTTCTGCAACTCCA 59.046 39.130 0.00 0.00 36.21 3.86
1120 2124 3.430790 CGACAGGCTCATCTCAAATGGTA 60.431 47.826 0.00 0.00 0.00 3.25
1395 2405 1.421646 CTGGACTCTGGGAACTTGGTT 59.578 52.381 0.00 0.00 0.00 3.67
1444 2454 0.747283 GCAGAGCTTCCATCACCCAG 60.747 60.000 0.00 0.00 0.00 4.45
1445 2455 0.617413 CAGAGCTTCCATCACCCAGT 59.383 55.000 0.00 0.00 0.00 4.00
1569 2579 0.399949 ACTCCTTGGGTGGTGACTCA 60.400 55.000 0.00 0.00 0.00 3.41
1744 2764 0.888619 TGTCTCTAACGGCTCACCAG 59.111 55.000 0.00 0.00 34.57 4.00
1769 2789 1.371337 CGCATGGTGCTGCACTACAT 61.371 55.000 29.54 22.13 42.25 2.29
1810 2830 3.364964 GGCGTGGAACAACAACTCATTAG 60.365 47.826 0.00 0.00 44.16 1.73
1871 2891 1.895707 GCTATGCTTCATGCGGCCT 60.896 57.895 0.00 1.32 46.63 5.19
1893 2913 3.687212 TGTTTGGCTATTGTGATACCACG 59.313 43.478 0.00 0.00 46.06 4.94
1896 2916 2.158827 TGGCTATTGTGATACCACGCAT 60.159 45.455 0.00 0.00 46.06 4.73
1921 2941 2.314647 GCGACGTGCAAGTGCCTTA 61.315 57.895 10.87 0.00 45.45 2.69
1936 2956 7.391554 GCAAGTGCCTTAATGGATATGAATCTA 59.608 37.037 0.00 0.00 38.35 1.98
1975 2995 4.442753 CCCTAGGATGTCAGAGAAAGAAGC 60.443 50.000 11.48 0.00 0.00 3.86
2024 3044 5.856126 TTCGTTACCTTGCTTAACATGAG 57.144 39.130 0.00 0.00 30.95 2.90
2028 3048 5.246307 GTTACCTTGCTTAACATGAGGACT 58.754 41.667 0.00 0.00 31.59 3.85
2041 3061 0.966920 GAGGACTCCCGACAAGTTCA 59.033 55.000 0.00 0.00 37.58 3.18
2044 3064 1.676014 GGACTCCCGACAAGTTCATGG 60.676 57.143 0.00 0.00 0.00 3.66
2048 3068 1.001974 TCCCGACAAGTTCATGGTCAG 59.998 52.381 0.00 0.00 0.00 3.51
2061 3608 2.597578 TGGTCAGCTCACTACTACCA 57.402 50.000 0.00 0.00 32.70 3.25
2063 3610 2.225041 TGGTCAGCTCACTACTACCAGT 60.225 50.000 0.00 0.00 31.91 4.00
2065 3612 3.258622 GGTCAGCTCACTACTACCAGTTT 59.741 47.826 0.00 0.00 0.00 2.66
2068 3615 3.433615 CAGCTCACTACTACCAGTTTTGC 59.566 47.826 0.00 0.00 0.00 3.68
2078 3644 2.339769 ACCAGTTTTGCTCTCCCTACT 58.660 47.619 0.00 0.00 0.00 2.57
2081 3647 4.349930 ACCAGTTTTGCTCTCCCTACTTTA 59.650 41.667 0.00 0.00 0.00 1.85
2082 3648 4.938226 CCAGTTTTGCTCTCCCTACTTTAG 59.062 45.833 0.00 0.00 0.00 1.85
2095 3661 5.962031 TCCCTACTTTAGATCAAAGGCAGTA 59.038 40.000 16.73 5.38 46.77 2.74
2096 3662 6.615726 TCCCTACTTTAGATCAAAGGCAGTAT 59.384 38.462 16.73 3.61 46.77 2.12
2097 3663 6.931840 CCCTACTTTAGATCAAAGGCAGTATC 59.068 42.308 16.73 0.00 46.77 2.24
2101 3667 7.051000 ACTTTAGATCAAAGGCAGTATCCTTC 58.949 38.462 16.73 0.00 46.77 3.46
2110 3720 3.390639 AGGCAGTATCCTTCTTCATCAGG 59.609 47.826 0.00 0.00 30.82 3.86
2114 3724 5.163405 GCAGTATCCTTCTTCATCAGGTGTA 60.163 44.000 0.00 0.00 0.00 2.90
2118 3728 6.566079 ATCCTTCTTCATCAGGTGTATTCA 57.434 37.500 0.00 0.00 0.00 2.57
2120 3730 6.409704 TCCTTCTTCATCAGGTGTATTCAAG 58.590 40.000 0.00 0.00 0.00 3.02
2127 3746 8.918202 TTCATCAGGTGTATTCAAGTTTTACT 57.082 30.769 0.00 0.00 0.00 2.24
2139 3758 8.986477 ATTCAAGTTTTACTATTTCACATGGC 57.014 30.769 0.00 0.00 0.00 4.40
2161 3780 5.404946 GCAAACATTTACATGCTCATGAGT 58.595 37.500 23.38 7.54 41.20 3.41
2169 3788 9.433153 CATTTACATGCTCATGAGTCTATATGT 57.567 33.333 23.38 22.81 41.20 2.29
2223 3842 5.221843 ACACTAGATACAACTTGCTTCCCAA 60.222 40.000 0.00 0.00 0.00 4.12
2226 3845 4.666512 AGATACAACTTGCTTCCCAACAT 58.333 39.130 0.00 0.00 0.00 2.71
2228 3847 6.245408 AGATACAACTTGCTTCCCAACATTA 58.755 36.000 0.00 0.00 0.00 1.90
2234 4012 7.226523 ACAACTTGCTTCCCAACATTATTTTTC 59.773 33.333 0.00 0.00 0.00 2.29
2241 4019 8.088365 GCTTCCCAACATTATTTTTCTTGTACT 58.912 33.333 0.00 0.00 0.00 2.73
2280 4080 8.214721 TGTGAGAAGATACAGTATCACAGTAG 57.785 38.462 20.62 0.00 41.37 2.57
2331 4159 0.036294 GTTTCCCTCTCCCTTCCACG 60.036 60.000 0.00 0.00 0.00 4.94
2365 4197 2.102420 TGGCCTGGATATACACACTTCG 59.898 50.000 3.32 0.00 0.00 3.79
2379 4211 6.671614 ACACACTTCGTCAATCAACTTTTA 57.328 33.333 0.00 0.00 0.00 1.52
2381 4213 7.132213 ACACACTTCGTCAATCAACTTTTATG 58.868 34.615 0.00 0.00 0.00 1.90
2384 4216 8.999431 ACACTTCGTCAATCAACTTTTATGTAT 58.001 29.630 0.00 0.00 0.00 2.29
2459 4430 4.021016 ACTGAAGATTGTACTCCCAGTCAC 60.021 45.833 0.00 0.00 32.52 3.67
2568 4591 6.925165 AGTTAATGCCATGTTAATGCATTAGC 59.075 34.615 22.29 22.29 40.19 3.09
2587 4612 7.957484 GCATTAGCGATTAACATAACTGGTATG 59.043 37.037 11.08 11.08 44.61 2.39
2588 4613 7.956420 TTAGCGATTAACATAACTGGTATGG 57.044 36.000 16.53 0.00 43.53 2.74
2618 4643 0.759060 GGCAAGGACCAAACCAAGGT 60.759 55.000 0.00 0.00 43.46 3.50
2619 4644 1.119684 GCAAGGACCAAACCAAGGTT 58.880 50.000 0.00 0.00 40.09 3.50
2623 4648 0.830444 GGACCAAACCAAGGTTCCCC 60.830 60.000 4.73 1.25 40.09 4.81
2625 4650 1.426215 GACCAAACCAAGGTTCCCCTA 59.574 52.381 4.73 0.00 41.56 3.53
2641 4669 3.882888 TCCCCTAAATTTTGCGATGCTAG 59.117 43.478 0.00 0.00 0.00 3.42
2645 4673 5.273944 CCTAAATTTTGCGATGCTAGAACC 58.726 41.667 0.00 0.00 0.00 3.62
2681 4709 8.588472 TGATGGACTATACGATGAGAATTCAAT 58.412 33.333 8.44 0.51 36.78 2.57
2682 4710 9.429359 GATGGACTATACGATGAGAATTCAATT 57.571 33.333 8.44 0.00 36.78 2.32
2683 4711 9.784531 ATGGACTATACGATGAGAATTCAATTT 57.215 29.630 8.44 0.00 36.78 1.82
2735 4763 2.753452 CCTGCTACAGACGGTTTCTCTA 59.247 50.000 0.00 0.00 32.44 2.43
2742 4770 3.833070 ACAGACGGTTTCTCTAACTCCAT 59.167 43.478 0.00 0.00 36.93 3.41
2758 4786 1.180029 CCATTGTGCTTGGAAGAGGG 58.820 55.000 0.00 0.00 36.26 4.30
2863 4909 5.245751 TGAACTATGTAACCACGTAGGGAAA 59.754 40.000 0.00 0.00 45.11 3.13
2900 4946 4.725490 AGGAAGTTGCTGTTAAAAGGCTA 58.275 39.130 0.00 0.00 0.00 3.93
2909 4955 4.546570 CTGTTAAAAGGCTAACCAAGTGC 58.453 43.478 0.00 0.00 39.06 4.40
3000 5046 4.557205 AGTTAGACTTCTTGGTTACTGCG 58.443 43.478 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.734620 AATATGTTCATATGTGAATGTTTTCCG 57.265 29.630 8.23 0.00 45.46 4.30
16 17 8.744568 TGCACCTAAATATGTTCATATGTGAA 57.255 30.769 17.35 0.03 41.89 3.18
38 39 7.496747 TGTAGTATCTGCACAATATAGTTGCA 58.503 34.615 8.84 8.84 0.00 4.08
39 40 7.946655 TGTAGTATCTGCACAATATAGTTGC 57.053 36.000 0.00 0.00 0.00 4.17
83 84 7.568679 CGTCTTGACACGAATTATTGAGTGAAA 60.569 37.037 14.18 8.74 42.69 2.69
84 85 6.128929 CGTCTTGACACGAATTATTGAGTGAA 60.129 38.462 14.18 3.19 42.69 3.18
86 87 5.344933 TCGTCTTGACACGAATTATTGAGTG 59.655 40.000 8.08 8.08 45.64 3.51
99 102 4.171754 GTTAGGTGGTATCGTCTTGACAC 58.828 47.826 1.59 0.00 0.00 3.67
149 176 9.212641 TGCATCTTGCTATACATATTTCTCTTC 57.787 33.333 0.75 0.00 45.31 2.87
151 178 8.152898 TGTGCATCTTGCTATACATATTTCTCT 58.847 33.333 0.00 0.00 45.31 3.10
152 179 8.315391 TGTGCATCTTGCTATACATATTTCTC 57.685 34.615 0.00 0.00 45.31 2.87
154 181 7.966753 CCATGTGCATCTTGCTATACATATTTC 59.033 37.037 0.00 0.00 45.31 2.17
156 183 6.127814 GCCATGTGCATCTTGCTATACATATT 60.128 38.462 0.00 0.00 45.31 1.28
165 192 0.323087 TGAGCCATGTGCATCTTGCT 60.323 50.000 8.58 3.79 45.31 3.91
168 195 1.913778 TTGTGAGCCATGTGCATCTT 58.086 45.000 8.58 0.00 44.83 2.40
170 197 1.270274 TGTTTGTGAGCCATGTGCATC 59.730 47.619 8.58 4.57 44.83 3.91
171 198 1.330234 TGTTTGTGAGCCATGTGCAT 58.670 45.000 8.58 0.00 44.83 3.96
172 199 1.330234 ATGTTTGTGAGCCATGTGCA 58.670 45.000 8.58 0.00 44.83 4.57
173 200 2.489329 AGTATGTTTGTGAGCCATGTGC 59.511 45.455 0.00 0.00 41.71 4.57
175 202 7.466746 AAATAAGTATGTTTGTGAGCCATGT 57.533 32.000 0.00 0.00 0.00 3.21
223 289 6.291377 CGGGCCATCATAGCTATACATATTT 58.709 40.000 5.77 0.00 0.00 1.40
224 290 5.743130 GCGGGCCATCATAGCTATACATATT 60.743 44.000 5.77 0.00 0.00 1.28
226 292 3.069586 GCGGGCCATCATAGCTATACATA 59.930 47.826 5.77 0.00 0.00 2.29
227 293 2.158900 GCGGGCCATCATAGCTATACAT 60.159 50.000 5.77 0.00 0.00 2.29
228 294 1.207089 GCGGGCCATCATAGCTATACA 59.793 52.381 5.77 0.00 0.00 2.29
231 297 1.219124 CGCGGGCCATCATAGCTAT 59.781 57.895 4.39 0.00 0.00 2.97
379 829 2.612212 AGCAACGGTTCACAACAAGTAG 59.388 45.455 0.00 0.00 0.00 2.57
420 900 8.091449 ACAACTACAACAAAAACTGAAATTGGA 58.909 29.630 0.00 0.00 0.00 3.53
435 915 4.013728 AGCAAGGTTTCACAACTACAACA 58.986 39.130 0.00 0.00 32.90 3.33
436 916 4.632538 AGCAAGGTTTCACAACTACAAC 57.367 40.909 0.00 0.00 32.90 3.32
450 951 3.067180 CACAATCAGTCAACAAGCAAGGT 59.933 43.478 0.00 0.00 0.00 3.50
658 1179 2.839486 TCAAGCACGGAGAAACTCAT 57.161 45.000 0.00 0.00 31.08 2.90
659 1180 2.839486 ATCAAGCACGGAGAAACTCA 57.161 45.000 0.00 0.00 31.08 3.41
669 1190 0.445436 GCCTGACTGAATCAAGCACG 59.555 55.000 0.00 0.00 43.32 5.34
697 1218 3.941188 ATGCTACATCCGGGGCCG 61.941 66.667 0.00 0.00 39.44 6.13
698 1219 2.281761 CATGCTACATCCGGGGCC 60.282 66.667 0.00 0.00 0.00 5.80
699 1220 1.893808 CACATGCTACATCCGGGGC 60.894 63.158 0.00 0.00 0.00 5.80
880 1424 4.525024 GAGGTAGGAGCTGAAGTACTGTA 58.475 47.826 0.00 0.00 0.00 2.74
952 1508 8.260818 TGAAGAGGAAAGTAAGGAGATATTGTG 58.739 37.037 0.00 0.00 0.00 3.33
1060 2064 0.107654 GCAGGTGTTAGGCGATCCTT 60.108 55.000 0.00 0.00 40.66 3.36
1277 2284 2.697654 ACAAGACAAGATCAGAGCTGC 58.302 47.619 0.00 0.00 0.00 5.25
1444 2454 2.178912 TTTGGGAGAATGGTGTCGAC 57.821 50.000 9.11 9.11 0.00 4.20
1445 2455 4.163268 TCATATTTGGGAGAATGGTGTCGA 59.837 41.667 0.00 0.00 0.00 4.20
1569 2579 1.065854 CAAACGAGGATCTGGAGGCTT 60.066 52.381 0.00 0.00 0.00 4.35
1660 2680 2.487986 GGGACATGATGGGACCTGATTC 60.488 54.545 0.00 0.00 0.00 2.52
1769 2789 1.559368 CAGGAATTTCACCATGCCCA 58.441 50.000 0.00 0.00 0.00 5.36
1810 2830 2.288457 GCTCAAAGAAAACCTCCCAAGC 60.288 50.000 0.00 0.00 0.00 4.01
1871 2891 3.687212 CGTGGTATCACAATAGCCAAACA 59.313 43.478 6.97 0.00 43.79 2.83
1893 2913 2.500369 CACGTCGCAACTGCATGC 60.500 61.111 11.82 11.82 42.21 4.06
1921 2941 9.512588 GTCAAGACCAATAGATTCATATCCATT 57.487 33.333 0.00 0.00 0.00 3.16
1936 2956 4.601857 TCCTAGGGAAAAGTCAAGACCAAT 59.398 41.667 9.46 0.00 0.00 3.16
1975 2995 0.242825 CCTTGACCACAATGCAGCTG 59.757 55.000 10.11 10.11 35.37 4.24
2024 3044 1.676014 CCATGAACTTGTCGGGAGTCC 60.676 57.143 0.00 0.00 0.00 3.85
2028 3048 1.001974 CTGACCATGAACTTGTCGGGA 59.998 52.381 0.00 0.00 32.86 5.14
2041 3061 3.027412 CTGGTAGTAGTGAGCTGACCAT 58.973 50.000 0.00 0.00 34.77 3.55
2044 3064 4.522722 AAACTGGTAGTAGTGAGCTGAC 57.477 45.455 0.00 0.00 0.00 3.51
2048 3068 3.665190 AGCAAAACTGGTAGTAGTGAGC 58.335 45.455 0.00 0.00 0.00 4.26
2061 3608 6.213600 TGATCTAAAGTAGGGAGAGCAAAACT 59.786 38.462 0.00 0.00 32.96 2.66
2063 3610 6.620877 TGATCTAAAGTAGGGAGAGCAAAA 57.379 37.500 0.00 0.00 32.96 2.44
2065 3612 6.352222 CCTTTGATCTAAAGTAGGGAGAGCAA 60.352 42.308 13.21 0.00 42.21 3.91
2068 3615 5.129485 TGCCTTTGATCTAAAGTAGGGAGAG 59.871 44.000 13.21 1.99 43.45 3.20
2095 3661 6.566079 TGAATACACCTGATGAAGAAGGAT 57.434 37.500 0.00 0.00 37.01 3.24
2096 3662 6.013379 ACTTGAATACACCTGATGAAGAAGGA 60.013 38.462 0.00 0.00 37.01 3.36
2097 3663 6.176183 ACTTGAATACACCTGATGAAGAAGG 58.824 40.000 0.00 0.00 39.65 3.46
2101 3667 9.003658 AGTAAAACTTGAATACACCTGATGAAG 57.996 33.333 0.00 0.00 0.00 3.02
2114 3724 8.584157 TGCCATGTGAAATAGTAAAACTTGAAT 58.416 29.630 0.00 0.00 0.00 2.57
2118 3728 8.200792 TGTTTGCCATGTGAAATAGTAAAACTT 58.799 29.630 0.00 0.00 0.00 2.66
2120 3730 7.938563 TGTTTGCCATGTGAAATAGTAAAAC 57.061 32.000 0.00 0.00 0.00 2.43
2127 3746 7.064371 GCATGTAAATGTTTGCCATGTGAAATA 59.936 33.333 15.27 0.00 35.28 1.40
2139 3758 6.849502 AGACTCATGAGCATGTAAATGTTTG 58.150 36.000 22.83 0.00 39.72 2.93
2161 3780 5.808540 GTCACCAAACACGCTAACATATAGA 59.191 40.000 0.00 0.00 0.00 1.98
2169 3788 0.941542 GCAGTCACCAAACACGCTAA 59.058 50.000 0.00 0.00 0.00 3.09
2248 4026 9.725019 TGATACTGTATCTTCTCACAAAACATT 57.275 29.630 23.96 0.00 36.17 2.71
2315 4143 0.410663 TTACGTGGAAGGGAGAGGGA 59.589 55.000 0.00 0.00 0.00 4.20
2385 4217 9.469097 AGACAACAGATAGAATACTTACTCACT 57.531 33.333 0.00 0.00 0.00 3.41
2388 4220 9.026074 GCAAGACAACAGATAGAATACTTACTC 57.974 37.037 0.00 0.00 0.00 2.59
2568 4591 7.878127 AGGAATCCATACCAGTTATGTTAATCG 59.122 37.037 0.61 0.00 36.54 3.34
2587 4612 1.755783 CCTTGCCTGCCAGGAATCC 60.756 63.158 16.85 0.00 37.67 3.01
2588 4613 1.034292 GTCCTTGCCTGCCAGGAATC 61.034 60.000 16.85 0.00 37.67 2.52
2618 4643 3.096092 AGCATCGCAAAATTTAGGGGAA 58.904 40.909 11.73 0.21 0.00 3.97
2619 4644 2.733956 AGCATCGCAAAATTTAGGGGA 58.266 42.857 10.57 10.57 0.00 4.81
2623 4648 4.963953 CGGTTCTAGCATCGCAAAATTTAG 59.036 41.667 0.00 0.00 0.00 1.85
2625 4650 3.427503 CCGGTTCTAGCATCGCAAAATTT 60.428 43.478 0.00 0.00 0.00 1.82
2641 4669 1.275291 TCCATCAGAACTGTCCGGTTC 59.725 52.381 10.38 10.38 44.02 3.62
2645 4673 4.554919 CGTATAGTCCATCAGAACTGTCCG 60.555 50.000 1.73 0.00 0.00 4.79
2700 4728 0.687354 AGCAGGGACAATGTCTTCGT 59.313 50.000 13.53 0.00 32.47 3.85
2742 4770 1.460255 CCCCCTCTTCCAAGCACAA 59.540 57.895 0.00 0.00 0.00 3.33
2758 4786 3.821033 CCTTGTATACTATGCCAAAGCCC 59.179 47.826 4.17 0.00 38.69 5.19
2806 4834 6.599638 ACTGAAAGAATACCTTCCACTATTGC 59.400 38.462 0.00 0.00 37.43 3.56
2843 4881 5.579511 CAGTTTTCCCTACGTGGTTACATAG 59.420 44.000 0.00 0.00 0.00 2.23
2863 4909 0.555769 TTCCTTGCCACCTTCCAGTT 59.444 50.000 0.00 0.00 0.00 3.16
2900 4946 2.373169 TCCTTGATCAGAGCACTTGGTT 59.627 45.455 0.00 0.00 0.00 3.67
2909 4955 3.555527 TGCTCCATTCCTTGATCAGAG 57.444 47.619 0.00 0.00 0.00 3.35
3000 5046 3.077617 GCTTCTCAGCTCCATGGAC 57.922 57.895 11.44 8.29 43.51 4.02


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

AutoCloner maintained by Alex Coulton.