Multiple sequence alignment - TraesCS2A01G372300

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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 TraesCS2A01G372300 chr2A 100.000 3041 0 0 1 3041 615121988 615118948 0.000000e+00 5616.0
1 TraesCS2A01G372300 chr1D 95.340 2425 102 7 1 2415 70104281 70106704 0.000000e+00 3842.0
2 TraesCS2A01G372300 chr1D 92.410 2174 107 25 614 2778 70129569 70131693 0.000000e+00 3048.0
3 TraesCS2A01G372300 chr1D 94.862 1810 85 5 614 2415 70123956 70125765 0.000000e+00 2820.0
4 TraesCS2A01G372300 chr1D 94.754 1811 86 6 614 2415 70122832 70124642 0.000000e+00 2809.0
5 TraesCS2A01G372300 chr1D 94.641 1810 89 5 614 2415 70109386 70111195 0.000000e+00 2798.0
6 TraesCS2A01G372300 chr1D 94.530 1810 91 5 614 2415 70107140 70108949 0.000000e+00 2787.0
7 TraesCS2A01G372300 chr1D 94.527 1809 92 4 614 2415 70126202 70128010 0.000000e+00 2785.0
8 TraesCS2A01G372300 chr1D 94.475 1810 92 5 614 2415 70111631 70113440 0.000000e+00 2782.0
9 TraesCS2A01G372300 chr1D 93.189 323 21 1 2662 2983 70131698 70132020 9.870000e-130 473.0
10 TraesCS2A01G372300 chr1D 91.228 57 5 0 2985 3041 94267531 94267475 9.040000e-11 78.7
11 TraesCS2A01G372300 chr7A 93.153 2293 143 9 697 2983 199319353 199321637 0.000000e+00 3352.0
12 TraesCS2A01G372300 chr7A 93.109 2293 132 12 697 2983 199314757 199317029 0.000000e+00 3336.0
13 TraesCS2A01G372300 chr7A 93.022 2293 136 10 697 2983 199317054 199319328 0.000000e+00 3326.0
14 TraesCS2A01G372300 chr7A 92.673 2293 140 13 697 2983 199312462 199314732 0.000000e+00 3278.0
15 TraesCS2A01G372300 chr7A 93.831 697 37 5 183 876 199301120 199301813 0.000000e+00 1044.0
16 TraesCS2A01G372300 chr7A 83.301 1036 117 20 1773 2769 568903234 568904252 0.000000e+00 904.0
17 TraesCS2A01G372300 chr7A 84.036 664 77 11 655 1298 568903234 568903888 2.000000e-171 612.0
18 TraesCS2A01G372300 chr7A 93.583 187 12 0 1 187 199282040 199282226 2.310000e-71 279.0
19 TraesCS2A01G372300 chr7A 77.615 478 71 24 11 472 495166489 495166946 1.080000e-64 257.0
20 TraesCS2A01G372300 chr7A 88.462 156 16 2 2828 2981 495169441 495169596 1.440000e-43 187.0
21 TraesCS2A01G372300 chr7A 86.139 101 9 5 2884 2981 29852220 29852122 1.490000e-18 104.0
22 TraesCS2A01G372300 chr3A 90.007 1501 115 18 1300 2771 576911276 576912770 0.000000e+00 1908.0
23 TraesCS2A01G372300 chr3A 85.714 672 71 13 655 1303 284300119 284300788 0.000000e+00 686.0
24 TraesCS2A01G372300 chr6B 88.441 1315 101 25 1503 2771 262865385 262866694 0.000000e+00 1539.0
25 TraesCS2A01G372300 chr6B 92.308 65 5 0 2977 3041 601605267 601605203 3.230000e-15 93.5
26 TraesCS2A01G372300 chr6B 92.857 56 4 0 2986 3041 348912538 348912593 6.990000e-12 82.4
27 TraesCS2A01G372300 chr3B 77.263 475 75 24 11 472 401512233 401512687 6.510000e-62 248.0
28 TraesCS2A01G372300 chr3B 91.228 57 5 0 2985 3041 260641152 260641096 9.040000e-11 78.7
29 TraesCS2A01G372300 chr3B 92.727 55 2 2 2988 3041 746007484 746007537 9.040000e-11 78.7
30 TraesCS2A01G372300 chr3D 86.449 214 18 3 2779 2983 146132098 146131887 1.100000e-54 224.0
31 TraesCS2A01G372300 chr3D 89.032 155 15 2 2828 2981 398277391 398277238 1.110000e-44 191.0
32 TraesCS2A01G372300 chr7D 94.286 70 1 1 2974 3040 454719863 454719932 1.490000e-18 104.0
33 TraesCS2A01G372300 chr7D 91.228 57 5 0 2985 3041 51378140 51378084 9.040000e-11 78.7
34 TraesCS2A01G372300 chr4B 92.857 56 3 1 2986 3041 327999227 327999281 2.510000e-11 80.5
35 TraesCS2A01G372300 chrUn 91.071 56 5 0 2986 3041 20479939 20479884 3.250000e-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 TraesCS2A01G372300 chr2A 615118948 615121988 3040 True 5616.00 5616 100.00000 1 3041 1 chr2A.!!$R1 3040
1 TraesCS2A01G372300 chr1D 70104281 70113440 9159 False 3052.25 3842 94.74650 1 2415 4 chr1D.!!$F1 2414
2 TraesCS2A01G372300 chr1D 70122832 70132020 9188 False 2387.00 3048 93.94840 614 2983 5 chr1D.!!$F2 2369
3 TraesCS2A01G372300 chr7A 199312462 199321637 9175 False 3323.00 3352 92.98925 697 2983 4 chr7A.!!$F3 2286
4 TraesCS2A01G372300 chr7A 199301120 199301813 693 False 1044.00 1044 93.83100 183 876 1 chr7A.!!$F2 693
5 TraesCS2A01G372300 chr7A 568903234 568904252 1018 False 758.00 904 83.66850 655 2769 2 chr7A.!!$F5 2114
6 TraesCS2A01G372300 chr7A 495166489 495169596 3107 False 222.00 257 83.03850 11 2981 2 chr7A.!!$F4 2970
7 TraesCS2A01G372300 chr3A 576911276 576912770 1494 False 1908.00 1908 90.00700 1300 2771 1 chr3A.!!$F2 1471
8 TraesCS2A01G372300 chr3A 284300119 284300788 669 False 686.00 686 85.71400 655 1303 1 chr3A.!!$F1 648
9 TraesCS2A01G372300 chr6B 262865385 262866694 1309 False 1539.00 1539 88.44100 1503 2771 1 chr6B.!!$F1 1268

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
87 88 1.197721 GAGATCGCGGGGCAAATAATG 59.802 52.381 6.13 0.0 0.00 1.90 F
1013 1180 0.035152 TCAGCTATGGTGGCTTGTGG 60.035 55.000 0.00 0.0 38.03 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1289 0.375106 GATTGCTTCTTCGGCCTTCG 59.625 55.0 0.00 0.0 40.9 3.79 R
2152 10334 0.104120 GGTCCAGCGGCAAAAACTTT 59.896 50.0 1.45 0.0 0.0 2.66 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
87 88 1.197721 GAGATCGCGGGGCAAATAATG 59.802 52.381 6.13 0.00 0.00 1.90
109 111 2.046604 AGCAAGATGAGCAGCGCA 60.047 55.556 11.47 0.00 0.00 6.09
233 235 7.042335 AGTCTTATAGTTCCTTCAAATCACCG 58.958 38.462 0.00 0.00 0.00 4.94
353 366 3.863396 TTACATGTGTTTTCGGTGTCG 57.137 42.857 9.11 0.00 37.82 4.35
383 396 7.492994 GGTACTGAAGATCTAGTCATGGTTTTC 59.507 40.741 1.29 0.00 0.00 2.29
472 485 5.130292 AGTGCATGTCTTCCAGAAAATTG 57.870 39.130 0.00 0.00 0.00 2.32
548 692 9.992442 CTAATAAGTATCCTTCCTATCCTGGTA 57.008 37.037 0.00 0.00 31.89 3.25
659 803 8.355169 ACCTATGAATTGTGCATAATCAATGAC 58.645 33.333 9.29 4.28 37.86 3.06
660 804 8.354426 CCTATGAATTGTGCATAATCAATGACA 58.646 33.333 9.29 9.05 37.86 3.58
661 805 7.997107 ATGAATTGTGCATAATCAATGACAC 57.003 32.000 9.29 0.00 40.27 3.67
662 806 6.921914 TGAATTGTGCATAATCAATGACACA 58.078 32.000 9.29 0.33 44.02 3.72
663 807 7.548967 TGAATTGTGCATAATCAATGACACAT 58.451 30.769 9.29 0.00 44.53 3.21
667 811 8.604640 TTGTGCATAATCAATGACACATTTTT 57.395 26.923 4.79 0.00 44.53 1.94
670 814 6.874664 TGCATAATCAATGACACATTTTTGCT 59.125 30.769 9.22 0.00 37.86 3.91
671 815 8.033626 TGCATAATCAATGACACATTTTTGCTA 58.966 29.630 9.22 0.00 37.86 3.49
672 816 9.037737 GCATAATCAATGACACATTTTTGCTAT 57.962 29.630 0.00 0.00 37.86 2.97
677 821 7.828712 TCAATGACACATTTTTGCTATGATGA 58.171 30.769 0.00 0.00 0.00 2.92
682 826 9.738832 TGACACATTTTTGCTATGATGAATATG 57.261 29.630 0.00 0.00 0.00 1.78
683 827 9.740239 GACACATTTTTGCTATGATGAATATGT 57.260 29.630 0.00 0.00 0.00 2.29
743 887 9.421806 TCAGGCATTTTTGTTGTAAAGATAATG 57.578 29.630 0.00 0.00 30.12 1.90
782 948 6.873076 TGGCTTTGCAAATAAGATTAACCTTG 59.127 34.615 13.23 0.00 0.00 3.61
820 987 5.242615 TCAGAGTAGAGGTAGCTATGCAATG 59.757 44.000 7.39 5.35 0.00 2.82
821 988 4.526262 AGAGTAGAGGTAGCTATGCAATGG 59.474 45.833 7.39 0.00 0.00 3.16
822 989 4.227197 AGTAGAGGTAGCTATGCAATGGT 58.773 43.478 7.39 0.00 0.00 3.55
823 990 3.760580 AGAGGTAGCTATGCAATGGTC 57.239 47.619 0.00 0.00 0.00 4.02
824 991 3.041211 AGAGGTAGCTATGCAATGGTCA 58.959 45.455 0.00 0.00 0.00 4.02
825 992 3.649981 AGAGGTAGCTATGCAATGGTCAT 59.350 43.478 0.00 0.00 0.00 3.06
826 993 3.748083 AGGTAGCTATGCAATGGTCATG 58.252 45.455 0.00 0.00 0.00 3.07
827 994 3.137176 AGGTAGCTATGCAATGGTCATGT 59.863 43.478 0.00 0.00 0.00 3.21
830 997 2.947652 AGCTATGCAATGGTCATGTGTC 59.052 45.455 0.00 0.00 0.00 3.67
831 998 2.684374 GCTATGCAATGGTCATGTGTCA 59.316 45.455 0.00 0.00 0.00 3.58
862 1029 4.162509 AGTCTAAGGCTCTAACCACATTCC 59.837 45.833 0.00 0.00 0.00 3.01
902 1069 6.649141 TCTCAACTACGCATATCTGTTTGTTT 59.351 34.615 0.00 0.00 0.00 2.83
929 1096 4.442706 AGCCACGAAATTGAGGTATGTAG 58.557 43.478 0.00 0.00 0.00 2.74
967 1134 6.303903 TGAGAACTGATGATCCAATGAAGA 57.696 37.500 0.00 0.00 0.00 2.87
970 1137 6.347696 AGAACTGATGATCCAATGAAGAGTC 58.652 40.000 0.00 0.00 0.00 3.36
971 1138 5.688814 ACTGATGATCCAATGAAGAGTCA 57.311 39.130 0.00 0.00 38.41 3.41
977 1144 5.319453 TGATCCAATGAAGAGTCAAAGCTT 58.681 37.500 0.00 0.00 37.30 3.74
978 1145 6.475504 TGATCCAATGAAGAGTCAAAGCTTA 58.524 36.000 0.00 0.00 37.30 3.09
981 1148 6.533730 TCCAATGAAGAGTCAAAGCTTAAGA 58.466 36.000 6.67 0.00 37.30 2.10
1013 1180 0.035152 TCAGCTATGGTGGCTTGTGG 60.035 55.000 0.00 0.00 38.03 4.17
1035 1202 2.480416 GCGGATGTGTCTCAGACCTAAG 60.480 54.545 1.24 0.00 0.00 2.18
1044 1211 2.069273 CTCAGACCTAAGTTGTTGCCG 58.931 52.381 0.00 0.00 0.00 5.69
1082 1249 3.914426 TCATCCTAGCTTGGAGGAAAC 57.086 47.619 25.72 0.00 46.19 2.78
1087 1254 0.321298 TAGCTTGGAGGAAACGGTGC 60.321 55.000 0.00 0.00 0.00 5.01
1122 1289 2.035442 GCAGGGCGAAGAAGTGGAC 61.035 63.158 0.00 0.00 0.00 4.02
1128 1295 1.627550 GCGAAGAAGTGGACGAAGGC 61.628 60.000 0.00 0.00 0.00 4.35
1158 1342 0.114168 ATCTCTGCCTCCCTATCGCT 59.886 55.000 0.00 0.00 0.00 4.93
1169 1353 1.227089 CTATCGCTGCGTCCTGCTT 60.227 57.895 22.48 2.41 46.63 3.91
1196 1380 1.357137 TGTCACCTTAGTCATGGCCA 58.643 50.000 8.56 8.56 0.00 5.36
1227 1411 4.946157 CCTCATGCTACTGATTTGAACCTT 59.054 41.667 0.00 0.00 0.00 3.50
1246 1430 3.704061 CCTTCCCTACTCTTCTTCTCCTG 59.296 52.174 0.00 0.00 0.00 3.86
1258 1442 3.073735 CTCCTGGGCTGCTCGAGT 61.074 66.667 15.13 0.00 0.00 4.18
1266 1450 1.373999 GCTGCTCGAGTGCTTCAGT 60.374 57.895 15.13 0.00 0.00 3.41
1269 1453 1.739562 GCTCGAGTGCTTCAGTGGG 60.740 63.158 15.13 0.00 0.00 4.61
1362 1548 6.821388 AGAATATGCTTACCAGGTGTTAGAG 58.179 40.000 0.76 0.00 0.00 2.43
1445 1631 9.724839 GTCAGTTTATTTTGTAGTTAGTTTGCA 57.275 29.630 0.00 0.00 0.00 4.08
1480 1666 6.700081 ACATGATCATCTGCATATTTTGTTGC 59.300 34.615 4.86 0.00 39.33 4.17
1621 1812 8.975439 GTTCGATAATATATGACGTTTTCTGGT 58.025 33.333 0.00 0.00 0.00 4.00
1664 1855 6.267928 ACGTCTTATATTATGGGACAGAAGCT 59.732 38.462 9.73 0.00 45.00 3.74
1847 3166 7.276218 CCATAAATACACAGTCAGGCATTTTTG 59.724 37.037 0.00 0.00 0.00 2.44
1855 3174 6.312426 CACAGTCAGGCATTTTTGTTGTAAAA 59.688 34.615 0.00 0.00 0.00 1.52
1944 4447 3.312890 AGAGGTAGCTATGCAATGGTCT 58.687 45.455 0.00 0.00 0.00 3.85
1975 4482 7.342026 TCACATCATTAGTCTAAGGCTCTAACA 59.658 37.037 0.00 0.00 0.00 2.41
2017 4524 5.284864 ACATCTCAACTACGCATATCTGTG 58.715 41.667 0.00 0.00 38.87 3.66
2026 5657 1.935873 CGCATATCTGTGTGTTCCAGG 59.064 52.381 0.00 0.00 0.00 4.45
2091 5722 7.400439 AGAATTGATGATCCAAAGAAGAGTCA 58.600 34.615 0.00 0.00 0.00 3.41
2115 10297 1.266989 CTCGAGCATCACATAGCCGTA 59.733 52.381 0.00 0.00 33.17 4.02
2152 10334 1.591703 GCGGATGTGTCTCAGACCA 59.408 57.895 1.24 0.05 0.00 4.02
2174 10356 2.122167 TTTTTGCCGCTGGACCGTT 61.122 52.632 0.00 0.00 0.00 4.44
2279 11584 0.771755 TCTCTGCCTCCCTATCGCTA 59.228 55.000 0.00 0.00 0.00 4.26
2284 11589 1.170919 GCCTCCCTATCGCTACGTCA 61.171 60.000 0.00 0.00 0.00 4.35
2361 13926 2.168521 TGAACCTGCCCTATTCTTCTCG 59.831 50.000 0.00 0.00 0.00 4.04
2418 17450 1.765314 CGACAGGGAAGGAAGGATCAT 59.235 52.381 0.00 0.00 0.00 2.45
2536 17576 6.556974 AAGAAGAGATGGATCATGTGAGAA 57.443 37.500 0.00 0.00 0.00 2.87
2557 17597 3.625649 AAGAGACCAGCTTTGATCCTC 57.374 47.619 0.00 0.00 0.00 3.71
2561 17601 4.968080 AGAGACCAGCTTTGATCCTCTATT 59.032 41.667 0.00 0.00 0.00 1.73
2565 17605 4.141528 ACCAGCTTTGATCCTCTATTGGAG 60.142 45.833 6.34 0.00 39.78 3.86
2614 17665 7.236640 TGCCTAGTCCATATTGTCCATGTATTA 59.763 37.037 0.00 0.00 0.00 0.98
2619 17670 9.354673 AGTCCATATTGTCCATGTATTAAAAGG 57.645 33.333 0.00 0.00 0.00 3.11
2651 17702 3.585289 TGTGGCTCCTGGAGTTTGTATTA 59.415 43.478 23.92 1.80 31.39 0.98
2674 17840 8.958119 TTACTCTTGGATTTGGATATGTGTAC 57.042 34.615 0.00 0.00 0.00 2.90
2743 17910 3.122948 GCATCAGTTCGTACGTGATTGTT 59.877 43.478 16.05 5.16 0.00 2.83
2775 18144 7.704271 TCAAACAATACGTGTCCATGTTTTTA 58.296 30.769 9.91 1.64 40.98 1.52
2806 18176 6.814954 ATATGTGTCCATGTAGTTCTTCCT 57.185 37.500 0.00 0.00 32.29 3.36
2810 18180 3.646162 TGTCCATGTAGTTCTTCCTGTGT 59.354 43.478 0.00 0.00 0.00 3.72
2828 18198 3.583526 TGTGTGCCCTAGTGTTATGGTTA 59.416 43.478 0.00 0.00 0.00 2.85
2973 18344 3.126858 GCATATGTGGACAAACGTGATGT 59.873 43.478 6.94 6.94 0.00 3.06
2983 18354 6.127980 TGGACAAACGTGATGTCTTGTTTTAA 60.128 34.615 25.17 3.31 45.13 1.52
2984 18355 6.915843 GGACAAACGTGATGTCTTGTTTTAAT 59.084 34.615 25.17 0.00 45.13 1.40
2985 18356 7.434013 GGACAAACGTGATGTCTTGTTTTAATT 59.566 33.333 25.17 0.00 45.13 1.40
2986 18357 9.440784 GACAAACGTGATGTCTTGTTTTAATTA 57.559 29.630 21.30 0.00 43.03 1.40
2987 18358 9.959749 ACAAACGTGATGTCTTGTTTTAATTAT 57.040 25.926 1.64 0.00 32.58 1.28
3009 18380 9.941325 ATTATATAATAGATGGCTATGAGCTGC 57.059 33.333 6.16 0.00 41.99 5.25
3010 18381 5.954153 ATAATAGATGGCTATGAGCTGCT 57.046 39.130 0.00 0.00 41.99 4.24
3011 18382 3.613494 ATAGATGGCTATGAGCTGCTG 57.387 47.619 7.01 0.00 41.99 4.41
3012 18383 0.250381 AGATGGCTATGAGCTGCTGC 60.250 55.000 7.01 7.62 41.99 5.25
3013 18384 4.641474 ATAGATGGCTATGAGCTGCTGCT 61.641 47.826 18.93 18.93 41.99 4.24
3014 18385 6.662986 ATAGATGGCTATGAGCTGCTGCTG 62.663 50.000 23.89 9.49 40.84 4.41
3025 18396 2.165319 CTGCTGCTGCTGCTATATGA 57.835 50.000 27.67 9.42 40.48 2.15
3026 18397 2.701107 CTGCTGCTGCTGCTATATGAT 58.299 47.619 27.67 0.00 40.48 2.45
3027 18398 2.416893 CTGCTGCTGCTGCTATATGATG 59.583 50.000 27.67 7.99 40.48 3.07
3028 18399 2.038033 TGCTGCTGCTGCTATATGATGA 59.962 45.455 27.67 5.79 40.48 2.92
3029 18400 3.072211 GCTGCTGCTGCTATATGATGAA 58.928 45.455 22.10 0.00 40.48 2.57
3030 18401 3.690139 GCTGCTGCTGCTATATGATGAAT 59.310 43.478 22.10 0.00 40.48 2.57
3031 18402 4.156190 GCTGCTGCTGCTATATGATGAATT 59.844 41.667 22.10 0.00 40.48 2.17
3032 18403 5.622770 TGCTGCTGCTATATGATGAATTG 57.377 39.130 17.00 0.00 40.48 2.32
3033 18404 5.310451 TGCTGCTGCTATATGATGAATTGA 58.690 37.500 17.00 0.00 40.48 2.57
3034 18405 5.944007 TGCTGCTGCTATATGATGAATTGAT 59.056 36.000 17.00 0.00 40.48 2.57
3035 18406 7.107542 TGCTGCTGCTATATGATGAATTGATA 58.892 34.615 17.00 0.00 40.48 2.15
3036 18407 7.773690 TGCTGCTGCTATATGATGAATTGATAT 59.226 33.333 17.00 0.00 40.48 1.63
3037 18408 8.070769 GCTGCTGCTATATGATGAATTGATATG 58.929 37.037 8.53 0.00 36.03 1.78
3038 18409 9.326413 CTGCTGCTATATGATGAATTGATATGA 57.674 33.333 0.00 0.00 0.00 2.15
3039 18410 9.326413 TGCTGCTATATGATGAATTGATATGAG 57.674 33.333 0.00 0.00 0.00 2.90
3040 18411 8.283992 GCTGCTATATGATGAATTGATATGAGC 58.716 37.037 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.760047 CCGCGGTTCCACCCTCTG 62.760 72.222 19.50 0.00 33.75 3.35
15 16 1.665916 CTCATGGACCATAGCCGCG 60.666 63.158 6.67 0.00 0.00 6.46
87 88 0.656785 GCTGCTCATCTTGCTGCTAC 59.343 55.000 0.00 0.00 46.79 3.58
109 111 1.149174 CAATAGTGGCCGCCCTCAT 59.851 57.895 14.07 0.00 0.00 2.90
314 325 8.934825 ACATGTAAAATTTCAACCATTGTATGC 58.065 29.630 0.00 0.00 0.00 3.14
346 357 2.421073 TCTTCAGTACCATACGACACCG 59.579 50.000 0.00 0.00 42.50 4.94
353 366 7.231722 ACCATGACTAGATCTTCAGTACCATAC 59.768 40.741 0.00 0.00 0.00 2.39
472 485 9.899226 AAACAATGAAAAAGAAGCTGATAGTAC 57.101 29.630 0.00 0.00 0.00 2.73
494 507 4.262617 TGTAAGGGTGCGCATATTAAACA 58.737 39.130 15.91 11.72 0.00 2.83
504 517 2.311124 AGTAGATTGTAAGGGTGCGC 57.689 50.000 0.00 0.00 0.00 6.09
689 833 9.733556 TGTGTACTTATGGAATTGTACAGAATT 57.266 29.630 0.00 0.00 41.83 2.17
691 835 8.372459 ACTGTGTACTTATGGAATTGTACAGAA 58.628 33.333 0.00 0.00 41.83 3.02
692 836 7.903145 ACTGTGTACTTATGGAATTGTACAGA 58.097 34.615 0.00 0.00 41.83 3.41
693 837 7.817478 TGACTGTGTACTTATGGAATTGTACAG 59.183 37.037 0.00 0.00 41.83 2.74
694 838 7.672240 TGACTGTGTACTTATGGAATTGTACA 58.328 34.615 0.00 0.00 40.27 2.90
709 853 4.568152 ACAAAAATGCCTGACTGTGTAC 57.432 40.909 0.00 0.00 0.00 2.90
710 854 4.400884 ACAACAAAAATGCCTGACTGTGTA 59.599 37.500 0.00 0.00 0.00 2.90
758 903 6.313658 CCAAGGTTAATCTTATTTGCAAAGCC 59.686 38.462 18.19 3.18 0.00 4.35
820 987 5.423015 AGACTAATGATGTGACACATGACC 58.577 41.667 25.45 11.78 39.27 4.02
821 988 7.223582 CCTTAGACTAATGATGTGACACATGAC 59.776 40.741 25.45 12.49 39.27 3.06
822 989 7.267857 CCTTAGACTAATGATGTGACACATGA 58.732 38.462 25.45 17.98 39.27 3.07
823 990 6.018425 GCCTTAGACTAATGATGTGACACATG 60.018 42.308 25.45 12.83 39.27 3.21
824 991 6.051717 GCCTTAGACTAATGATGTGACACAT 58.948 40.000 20.95 20.95 42.43 3.21
825 992 5.187772 AGCCTTAGACTAATGATGTGACACA 59.812 40.000 11.41 11.41 0.00 3.72
826 993 5.665459 AGCCTTAGACTAATGATGTGACAC 58.335 41.667 0.00 0.00 0.00 3.67
827 994 5.658634 AGAGCCTTAGACTAATGATGTGACA 59.341 40.000 2.03 0.00 0.00 3.58
830 997 6.926272 GGTTAGAGCCTTAGACTAATGATGTG 59.074 42.308 2.03 0.00 0.00 3.21
831 998 6.611642 TGGTTAGAGCCTTAGACTAATGATGT 59.388 38.462 2.03 0.00 0.00 3.06
862 1029 6.915300 CGTAGTTGAGATGTTAGATTCTCCAG 59.085 42.308 0.00 0.00 38.05 3.86
902 1069 2.224523 ACCTCAATTTCGTGGCTTCTGA 60.225 45.455 0.00 0.00 0.00 3.27
929 1096 5.760253 TCAGTTCTCAGGTTTGTTCATCTTC 59.240 40.000 0.00 0.00 0.00 2.87
967 1134 6.317391 GGCTATGTGATTCTTAAGCTTTGACT 59.683 38.462 3.20 0.00 0.00 3.41
970 1137 5.065218 ACGGCTATGTGATTCTTAAGCTTTG 59.935 40.000 3.20 0.00 0.00 2.77
971 1138 5.186198 ACGGCTATGTGATTCTTAAGCTTT 58.814 37.500 3.20 0.00 0.00 3.51
977 1144 3.717707 GCTGACGGCTATGTGATTCTTA 58.282 45.455 0.00 0.00 38.06 2.10
978 1145 2.555199 GCTGACGGCTATGTGATTCTT 58.445 47.619 0.00 0.00 38.06 2.52
1013 1180 1.153549 GGTCTGAGACACATCCGCC 60.154 63.158 15.33 0.00 33.68 6.13
1035 1202 4.025401 CGGTCCAGCGGCAACAAC 62.025 66.667 1.45 0.00 0.00 3.32
1044 1211 1.084289 GAATGTAACCACGGTCCAGC 58.916 55.000 0.00 0.00 0.00 4.85
1082 1249 0.603707 ATGCATATCTTCCCGCACCG 60.604 55.000 0.00 0.00 37.17 4.94
1122 1289 0.375106 GATTGCTTCTTCGGCCTTCG 59.625 55.000 0.00 0.00 40.90 3.79
1158 1342 2.093500 ACATATTGAGAAGCAGGACGCA 60.093 45.455 0.00 0.00 46.13 5.24
1169 1353 6.686378 GCCATGACTAAGGTGACATATTGAGA 60.686 42.308 0.00 0.00 0.00 3.27
1227 1411 2.023888 CCCAGGAGAAGAAGAGTAGGGA 60.024 54.545 0.00 0.00 35.81 4.20
1246 1430 2.817396 GAAGCACTCGAGCAGCCC 60.817 66.667 22.36 13.42 36.85 5.19
1258 1442 1.529010 CAAGGCACCCACTGAAGCA 60.529 57.895 0.00 0.00 0.00 3.91
1280 1464 1.079057 GTCCTTCCTTCCCTGTCGC 60.079 63.158 0.00 0.00 0.00 5.19
1287 1471 3.174779 ACTTACTCTGGTCCTTCCTTCC 58.825 50.000 0.00 0.00 37.07 3.46
1289 1473 9.900112 ATATTATACTTACTCTGGTCCTTCCTT 57.100 33.333 0.00 0.00 37.07 3.36
1617 1808 5.219633 GTTTTTGGCATTGTGTACTACCAG 58.780 41.667 0.00 0.00 0.00 4.00
1621 1812 4.817464 AGACGTTTTTGGCATTGTGTACTA 59.183 37.500 0.00 0.00 0.00 1.82
1737 1929 8.443176 ACATTACATAGGTGAATTCATCTCCAT 58.557 33.333 24.35 11.06 42.95 3.41
1745 1939 9.831737 GATTATGCACATTACATAGGTGAATTC 57.168 33.333 0.00 0.00 33.03 2.17
1944 4447 5.109210 CCTTAGACTAATGATGTGACGCAA 58.891 41.667 0.00 0.00 0.00 4.85
1975 4482 8.270030 TGAGATGTTAGATTCTCCATGAATGTT 58.730 33.333 0.00 0.00 44.70 2.71
2017 4524 0.534203 TTTCGTGGCTCCTGGAACAC 60.534 55.000 16.92 16.92 0.00 3.32
2026 5657 1.659098 CGTACCTCAATTTCGTGGCTC 59.341 52.381 0.00 0.00 0.00 4.70
2091 5722 1.000385 GCTATGTGATGCTCGAGCTCT 60.000 52.381 35.27 23.60 42.66 4.09
2152 10334 0.104120 GGTCCAGCGGCAAAAACTTT 59.896 50.000 1.45 0.00 0.00 2.66
2174 10356 5.396772 CCTCCAAGCTAGGATGAATGTAACA 60.397 44.000 0.00 0.00 36.99 2.41
2279 11584 3.132824 TGACATATTGAGGAGCATGACGT 59.867 43.478 0.00 0.00 0.00 4.34
2284 11589 4.785346 AAGGTGACATATTGAGGAGCAT 57.215 40.909 0.00 0.00 0.00 3.79
2396 13966 1.555533 GATCCTTCCTTCCCTGTCGTT 59.444 52.381 0.00 0.00 0.00 3.85
2473 17505 0.174617 CCCTTGCCACACACGTTTTT 59.825 50.000 0.00 0.00 0.00 1.94
2512 17552 6.556974 TCTCACATGATCCATCTCTTCTTT 57.443 37.500 0.00 0.00 0.00 2.52
2536 17576 3.586618 AGAGGATCAAAGCTGGTCTCTTT 59.413 43.478 0.00 0.00 37.82 2.52
2614 17665 1.537990 GCCACACGTTTGCATCCTTTT 60.538 47.619 0.00 0.00 0.00 2.27
2619 17670 1.210155 GGAGCCACACGTTTGCATC 59.790 57.895 0.00 0.00 0.00 3.91
2651 17702 6.049149 CGTACACATATCCAAATCCAAGAGT 58.951 40.000 0.00 0.00 0.00 3.24
2743 17910 4.273969 GGACACGTATTGTTTGAGTCCAAA 59.726 41.667 10.15 0.00 39.17 3.28
2798 18168 1.348036 ACTAGGGCACACAGGAAGAAC 59.652 52.381 0.00 0.00 0.00 3.01
2806 18176 1.982226 ACCATAACACTAGGGCACACA 59.018 47.619 0.00 0.00 31.79 3.72
2810 18180 7.037945 TGCATATATAACCATAACACTAGGGCA 60.038 37.037 0.00 0.00 31.79 5.36
2828 18198 5.304778 TGTTGCCACGTTAGATGCATATAT 58.695 37.500 0.00 0.00 33.08 0.86
2934 18305 7.362662 CACATATGCTAATCATTTTTACGCCT 58.637 34.615 1.58 0.00 36.63 5.52
2945 18316 5.064579 CACGTTTGTCCACATATGCTAATCA 59.935 40.000 1.58 0.00 0.00 2.57
2983 18354 9.941325 GCAGCTCATAGCCATCTATTATATAAT 57.059 33.333 12.51 12.51 43.77 1.28
2984 18355 9.152327 AGCAGCTCATAGCCATCTATTATATAA 57.848 33.333 0.00 0.00 43.77 0.98
2985 18356 8.583296 CAGCAGCTCATAGCCATCTATTATATA 58.417 37.037 0.00 0.00 43.77 0.86
2986 18357 7.443477 CAGCAGCTCATAGCCATCTATTATAT 58.557 38.462 0.00 0.00 43.77 0.86
2987 18358 6.684865 GCAGCAGCTCATAGCCATCTATTATA 60.685 42.308 0.00 0.00 43.77 0.98
2988 18359 5.672503 CAGCAGCTCATAGCCATCTATTAT 58.327 41.667 0.00 0.00 43.77 1.28
2989 18360 4.622457 GCAGCAGCTCATAGCCATCTATTA 60.622 45.833 0.00 0.00 43.77 0.98
2990 18361 3.869140 GCAGCAGCTCATAGCCATCTATT 60.869 47.826 0.00 0.00 43.77 1.73
2991 18362 2.354906 GCAGCAGCTCATAGCCATCTAT 60.355 50.000 0.00 0.00 43.77 1.98
2992 18363 1.001746 GCAGCAGCTCATAGCCATCTA 59.998 52.381 0.00 0.00 43.77 1.98
2993 18364 0.250381 GCAGCAGCTCATAGCCATCT 60.250 55.000 0.00 0.00 43.77 2.90
2994 18365 2.245892 GCAGCAGCTCATAGCCATC 58.754 57.895 0.00 0.00 43.77 3.51
2995 18366 4.477413 GCAGCAGCTCATAGCCAT 57.523 55.556 0.00 0.00 43.77 4.40
3006 18377 2.165319 TCATATAGCAGCAGCAGCAG 57.835 50.000 12.92 0.00 45.49 4.24
3007 18378 2.038033 TCATCATATAGCAGCAGCAGCA 59.962 45.455 12.92 0.00 45.49 4.41
3008 18379 2.696506 TCATCATATAGCAGCAGCAGC 58.303 47.619 3.17 0.46 45.49 5.25
3009 18380 5.411669 TCAATTCATCATATAGCAGCAGCAG 59.588 40.000 3.17 0.00 45.49 4.24
3010 18381 5.310451 TCAATTCATCATATAGCAGCAGCA 58.690 37.500 3.17 0.00 45.49 4.41
3011 18382 5.874895 TCAATTCATCATATAGCAGCAGC 57.125 39.130 0.00 0.00 42.56 5.25
3012 18383 9.326413 TCATATCAATTCATCATATAGCAGCAG 57.674 33.333 0.00 0.00 0.00 4.24
3013 18384 9.326413 CTCATATCAATTCATCATATAGCAGCA 57.674 33.333 0.00 0.00 0.00 4.41
3014 18385 8.283992 GCTCATATCAATTCATCATATAGCAGC 58.716 37.037 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.