Multiple sequence alignment - TraesCS3B01G119600

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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 TraesCS3B01G119600 chr3B 100.000 4019 0 0 1 4019 89359023 89355005 0.000000e+00 7422.0
1 TraesCS3B01G119600 chr3B 92.257 1679 117 9 1568 3243 89063430 89065098 0.000000e+00 2368.0
2 TraesCS3B01G119600 chr3B 93.027 588 34 4 990 1572 89059387 89059972 0.000000e+00 852.0
3 TraesCS3B01G119600 chr3B 74.816 1493 329 39 1104 2568 576020777 576022250 7.330000e-177 630.0
4 TraesCS3B01G119600 chr3B 74.880 1457 313 40 1076 2510 576049270 576050695 7.380000e-172 614.0
5 TraesCS3B01G119600 chr3B 83.705 448 49 12 3245 3681 89065517 89065951 6.260000e-108 401.0
6 TraesCS3B01G119600 chr3B 83.569 353 28 19 3681 4019 89065985 89066321 1.810000e-78 303.0
7 TraesCS3B01G119600 chr3D 89.140 2965 236 44 889 3808 56710420 56707497 0.000000e+00 3613.0
8 TraesCS3B01G119600 chr3D 89.024 246 19 5 3574 3812 56688415 56688171 8.440000e-77 298.0
9 TraesCS3B01G119600 chr3D 85.200 250 30 5 3247 3490 56688853 56688605 2.400000e-62 250.0
10 TraesCS3B01G119600 chr3D 94.771 153 8 0 3867 4019 56707471 56707319 5.190000e-59 239.0
11 TraesCS3B01G119600 chr3A 92.063 2142 159 8 991 3123 66057015 66059154 0.000000e+00 3003.0
12 TraesCS3B01G119600 chr3A 85.659 781 92 12 3245 4019 66060955 66061721 0.000000e+00 804.0
13 TraesCS3B01G119600 chr3A 87.050 139 12 5 3108 3244 66060773 66060907 6.960000e-33 152.0
14 TraesCS3B01G119600 chr7B 95.133 863 10 7 1 835 456616320 456615462 0.000000e+00 1332.0
15 TraesCS3B01G119600 chr7B 89.167 600 35 21 3 593 605370006 605369428 0.000000e+00 721.0
16 TraesCS3B01G119600 chr7B 81.550 542 68 24 24 558 648041227 648041743 6.210000e-113 418.0
17 TraesCS3B01G119600 chr6D 92.262 840 33 20 3 841 38533916 38534724 0.000000e+00 1162.0
18 TraesCS3B01G119600 chr6D 72.746 1952 437 73 1068 2967 86721412 86723320 1.620000e-158 569.0
19 TraesCS3B01G119600 chr7D 91.215 831 33 12 3 831 2510878 2510086 0.000000e+00 1094.0
20 TraesCS3B01G119600 chr7D 93.286 566 21 10 3 558 45055290 45054732 0.000000e+00 819.0
21 TraesCS3B01G119600 chr7D 92.218 257 11 2 586 834 45054797 45054542 4.940000e-94 355.0
22 TraesCS3B01G119600 chr6B 91.615 811 29 12 23 833 31777332 31778103 0.000000e+00 1085.0
23 TraesCS3B01G119600 chr6B 72.690 1959 438 70 1068 2973 164363006 164364920 7.540000e-157 564.0
24 TraesCS3B01G119600 chr6B 91.667 48 4 0 786 833 439357291 439357244 2.590000e-07 67.6
25 TraesCS3B01G119600 chr5B 87.950 556 50 9 3 558 122420348 122419810 1.220000e-179 640.0
26 TraesCS3B01G119600 chr5D 72.737 1812 433 52 1091 2871 515252583 515250802 1.630000e-153 553.0
27 TraesCS3B01G119600 chr2A 84.342 479 57 15 23 495 318022179 318021713 1.700000e-123 453.0
28 TraesCS3B01G119600 chr2A 72.486 1621 358 64 1089 2653 75644328 75642740 3.690000e-120 442.0
29 TraesCS3B01G119600 chr6A 71.758 1951 444 77 1084 2973 104413807 104411903 6.130000e-123 451.0
30 TraesCS3B01G119600 chr1A 90.667 75 4 3 767 839 27386154 27386081 3.310000e-16 97.1
31 TraesCS3B01G119600 chr4B 89.041 73 6 2 767 838 339454753 339454682 5.530000e-14 89.8
32 TraesCS3B01G119600 chr1D 84.932 73 6 4 762 831 23326420 23326490 7.210000e-08 69.4


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 TraesCS3B01G119600 chr3B 89355005 89359023 4018 True 7422.000000 7422 100.000000 1 4019 1 chr3B.!!$R1 4018
1 TraesCS3B01G119600 chr3B 89059387 89066321 6934 False 981.000000 2368 88.139500 990 4019 4 chr3B.!!$F3 3029
2 TraesCS3B01G119600 chr3B 576020777 576022250 1473 False 630.000000 630 74.816000 1104 2568 1 chr3B.!!$F1 1464
3 TraesCS3B01G119600 chr3B 576049270 576050695 1425 False 614.000000 614 74.880000 1076 2510 1 chr3B.!!$F2 1434
4 TraesCS3B01G119600 chr3D 56707319 56710420 3101 True 1926.000000 3613 91.955500 889 4019 2 chr3D.!!$R2 3130
5 TraesCS3B01G119600 chr3D 56688171 56688853 682 True 274.000000 298 87.112000 3247 3812 2 chr3D.!!$R1 565
6 TraesCS3B01G119600 chr3A 66057015 66061721 4706 False 1319.666667 3003 88.257333 991 4019 3 chr3A.!!$F1 3028
7 TraesCS3B01G119600 chr7B 456615462 456616320 858 True 1332.000000 1332 95.133000 1 835 1 chr7B.!!$R1 834
8 TraesCS3B01G119600 chr7B 605369428 605370006 578 True 721.000000 721 89.167000 3 593 1 chr7B.!!$R2 590
9 TraesCS3B01G119600 chr7B 648041227 648041743 516 False 418.000000 418 81.550000 24 558 1 chr7B.!!$F1 534
10 TraesCS3B01G119600 chr6D 38533916 38534724 808 False 1162.000000 1162 92.262000 3 841 1 chr6D.!!$F1 838
11 TraesCS3B01G119600 chr6D 86721412 86723320 1908 False 569.000000 569 72.746000 1068 2967 1 chr6D.!!$F2 1899
12 TraesCS3B01G119600 chr7D 2510086 2510878 792 True 1094.000000 1094 91.215000 3 831 1 chr7D.!!$R1 828
13 TraesCS3B01G119600 chr7D 45054542 45055290 748 True 587.000000 819 92.752000 3 834 2 chr7D.!!$R2 831
14 TraesCS3B01G119600 chr6B 31777332 31778103 771 False 1085.000000 1085 91.615000 23 833 1 chr6B.!!$F1 810
15 TraesCS3B01G119600 chr6B 164363006 164364920 1914 False 564.000000 564 72.690000 1068 2973 1 chr6B.!!$F2 1905
16 TraesCS3B01G119600 chr5B 122419810 122420348 538 True 640.000000 640 87.950000 3 558 1 chr5B.!!$R1 555
17 TraesCS3B01G119600 chr5D 515250802 515252583 1781 True 553.000000 553 72.737000 1091 2871 1 chr5D.!!$R1 1780
18 TraesCS3B01G119600 chr2A 75642740 75644328 1588 True 442.000000 442 72.486000 1089 2653 1 chr2A.!!$R1 1564
19 TraesCS3B01G119600 chr6A 104411903 104413807 1904 True 451.000000 451 71.758000 1084 2973 1 chr6A.!!$R1 1889

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
388 401 0.970640 TGCCAGTTTTGATGCTGCAT 59.029 45.000 16.2 16.2 0.0 3.96 F
1356 1432 1.006102 CACCAACTTCTCGTCCGCT 60.006 57.895 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 5497 0.038159 AACGTCTCTGTAGCACCAGC 60.038 55.0 0.00 0.00 42.56 4.85 R
3158 8399 0.037160 TGCATCAGAGGTGCACACAT 59.963 50.0 20.43 3.33 46.76 3.21 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
170 175 2.050077 GACTTTGCTGCAACCGGC 60.050 61.111 15.72 7.77 43.83 6.13
388 401 0.970640 TGCCAGTTTTGATGCTGCAT 59.029 45.000 16.20 16.20 0.00 3.96
693 745 2.788581 CGTGTTGTGCGGTGTTGT 59.211 55.556 0.00 0.00 0.00 3.32
835 887 1.145759 CGCAGATCGCTCGCCTTTTA 61.146 55.000 7.71 0.00 39.08 1.52
841 893 2.981400 TCGCTCGCCTTTTAAAAAGG 57.019 45.000 0.00 0.00 40.39 3.11
842 894 2.496111 TCGCTCGCCTTTTAAAAAGGA 58.504 42.857 11.99 7.49 39.81 3.36
843 895 2.482721 TCGCTCGCCTTTTAAAAAGGAG 59.517 45.455 11.99 14.98 39.81 3.69
844 896 2.225727 CGCTCGCCTTTTAAAAAGGAGT 59.774 45.455 11.99 0.00 39.81 3.85
845 897 3.434299 CGCTCGCCTTTTAAAAAGGAGTA 59.566 43.478 11.99 0.25 39.81 2.59
846 898 4.668431 CGCTCGCCTTTTAAAAAGGAGTAC 60.668 45.833 11.99 5.33 39.81 2.73
847 899 4.454847 GCTCGCCTTTTAAAAAGGAGTACT 59.545 41.667 11.99 0.00 39.81 2.73
848 900 5.048921 GCTCGCCTTTTAAAAAGGAGTACTT 60.049 40.000 11.99 0.00 42.52 2.24
871 923 8.683615 ACTTTGTTAGTAGCTAATAAAATGGGC 58.316 33.333 14.76 3.14 36.89 5.36
872 924 8.817092 TTTGTTAGTAGCTAATAAAATGGGCT 57.183 30.769 14.76 0.00 35.32 5.19
873 925 7.801716 TGTTAGTAGCTAATAAAATGGGCTG 57.198 36.000 14.76 0.00 34.88 4.85
874 926 6.770785 TGTTAGTAGCTAATAAAATGGGCTGG 59.229 38.462 14.76 0.00 34.88 4.85
875 927 4.145052 AGTAGCTAATAAAATGGGCTGGC 58.855 43.478 0.00 0.00 34.88 4.85
876 928 3.030873 AGCTAATAAAATGGGCTGGCA 57.969 42.857 2.88 0.00 31.68 4.92
877 929 2.961062 AGCTAATAAAATGGGCTGGCAG 59.039 45.455 10.94 10.94 31.68 4.85
878 930 2.036346 GCTAATAAAATGGGCTGGCAGG 59.964 50.000 17.64 0.00 0.00 4.85
879 931 2.252535 AATAAAATGGGCTGGCAGGT 57.747 45.000 17.64 0.00 0.00 4.00
880 932 2.252535 ATAAAATGGGCTGGCAGGTT 57.747 45.000 17.64 0.00 0.00 3.50
881 933 1.555967 TAAAATGGGCTGGCAGGTTC 58.444 50.000 17.64 0.00 0.00 3.62
882 934 1.535204 AAAATGGGCTGGCAGGTTCG 61.535 55.000 17.64 0.00 0.00 3.95
887 939 4.742201 GCTGGCAGGTTCGCTCGA 62.742 66.667 17.64 0.00 0.00 4.04
899 951 1.664649 CGCTCGACTCCAGCACAAA 60.665 57.895 0.00 0.00 36.61 2.83
906 958 2.605338 CGACTCCAGCACAAACATTTGG 60.605 50.000 9.09 0.00 42.34 3.28
911 963 2.483363 CCAGCACAAACATTTGGCTTCA 60.483 45.455 14.04 0.00 40.33 3.02
928 980 1.990799 TCATAGCAGCGTACACACAC 58.009 50.000 0.00 0.00 0.00 3.82
929 981 1.271102 TCATAGCAGCGTACACACACA 59.729 47.619 0.00 0.00 0.00 3.72
933 985 2.066262 AGCAGCGTACACACACATAAC 58.934 47.619 0.00 0.00 0.00 1.89
935 987 2.415168 GCAGCGTACACACACATAACAT 59.585 45.455 0.00 0.00 0.00 2.71
947 999 7.039293 ACACACACATAACATGAGTAGTCCTTA 60.039 37.037 0.00 0.00 32.77 2.69
950 1002 6.098409 ACACATAACATGAGTAGTCCTTAGGG 59.902 42.308 0.00 0.00 32.26 3.53
957 1009 2.515005 GAGTAGTCCTTAGGGGTCCTCT 59.485 54.545 0.00 0.00 34.61 3.69
966 1018 4.079327 CCTTAGGGGTCCTCTACAAGACTA 60.079 50.000 0.00 0.00 34.61 2.59
967 1019 3.385314 AGGGGTCCTCTACAAGACTAC 57.615 52.381 0.00 0.00 33.39 2.73
968 1020 2.653366 AGGGGTCCTCTACAAGACTACA 59.347 50.000 0.00 0.00 33.39 2.74
972 1024 4.082136 GGGTCCTCTACAAGACTACAACAG 60.082 50.000 0.00 0.00 33.39 3.16
973 1025 4.765856 GGTCCTCTACAAGACTACAACAGA 59.234 45.833 0.00 0.00 33.39 3.41
982 1034 2.297597 AGACTACAACAGACCAGCTCAC 59.702 50.000 0.00 0.00 0.00 3.51
1026 1081 2.327343 TGTGCTCATGCTTGTCCGC 61.327 57.895 0.00 2.61 40.48 5.54
1161 1219 3.674050 GACCCCAGACGGCCTCCTA 62.674 68.421 0.00 0.00 0.00 2.94
1356 1432 1.006102 CACCAACTTCTCGTCCGCT 60.006 57.895 0.00 0.00 0.00 5.52
1452 1528 2.766313 CTCGACACCATCCAGAACAAA 58.234 47.619 0.00 0.00 0.00 2.83
1611 5161 1.209504 CAGGTGTGGGTGGATTACGAT 59.790 52.381 0.00 0.00 0.00 3.73
1946 5508 2.153645 CATTGTTCTGCTGGTGCTACA 58.846 47.619 0.00 0.00 40.48 2.74
2411 6012 3.340814 TCATGAAGAGTGGGAGAAAGC 57.659 47.619 0.00 0.00 0.00 3.51
2436 6037 2.034879 CCACCGCGACATCAAAGCT 61.035 57.895 8.23 0.00 0.00 3.74
2445 6046 4.100529 GCGACATCAAAGCTAGTAACGTA 58.899 43.478 0.00 0.00 0.00 3.57
2514 6115 1.370900 GTTGTACGACCACGACGCT 60.371 57.895 1.31 0.00 42.66 5.07
2610 6213 2.548067 CCCTCTTACTGACGTGTTTGCT 60.548 50.000 0.00 0.00 0.00 3.91
2675 6281 7.068716 GCCAGTAAATCCAAATTTAGAGGACAT 59.931 37.037 0.00 0.00 37.87 3.06
2907 6513 0.677288 TGTCACCGACGGATTTGAGT 59.323 50.000 23.38 0.00 34.95 3.41
2934 6540 5.761726 TCAGATGATGACCATAATGCAGAAC 59.238 40.000 0.00 0.00 35.17 3.01
2967 6573 4.635223 ACCAGTTCATCATGACATATCCG 58.365 43.478 0.00 0.00 0.00 4.18
2978 6584 4.736126 TGACATATCCGTCATCAACAGT 57.264 40.909 0.00 0.00 40.94 3.55
2996 6602 3.999001 ACAGTGAGTATTGACAGCACATG 59.001 43.478 0.00 0.00 36.27 3.21
3042 6648 4.063998 TGCATGATCCTCACTGTGATAC 57.936 45.455 11.45 4.20 0.00 2.24
3105 6712 5.034152 CGAGCTTTGTGTTCTTTTTGCTTA 58.966 37.500 0.00 0.00 0.00 3.09
3167 8408 8.915871 AATCTTAACAAATATGATGTGTGCAC 57.084 30.769 10.75 10.75 30.92 4.57
3168 8409 6.851609 TCTTAACAAATATGATGTGTGCACC 58.148 36.000 15.69 6.37 0.00 5.01
3191 8434 0.393808 GATGCAGAGGCGGGGTAAAA 60.394 55.000 0.00 0.00 45.35 1.52
3193 8436 2.044555 GCAGAGGCGGGGTAAAACC 61.045 63.158 0.00 0.00 37.60 3.27
3202 8445 2.936316 CGGGGTAAAACCGTCATTTTG 58.064 47.619 0.00 0.00 46.03 2.44
3203 8446 2.553172 CGGGGTAAAACCGTCATTTTGA 59.447 45.455 0.00 0.00 46.03 2.69
3204 8447 3.004524 CGGGGTAAAACCGTCATTTTGAA 59.995 43.478 0.00 0.00 46.03 2.69
3205 8448 4.552355 GGGGTAAAACCGTCATTTTGAAG 58.448 43.478 0.00 0.00 39.83 3.02
3208 8451 5.918576 GGGTAAAACCGTCATTTTGAAGAAG 59.081 40.000 0.00 0.00 39.83 2.85
3213 8456 8.541133 AAAACCGTCATTTTGAAGAAGAAAAA 57.459 26.923 0.00 0.00 30.56 1.94
3255 8915 8.972458 ACACCAACATATAAGTGCATACATAA 57.028 30.769 0.00 0.00 33.46 1.90
3342 9002 7.394359 GGCCAGAATTATATGGACAACACATAT 59.606 37.037 0.00 0.00 45.88 1.78
3356 9020 7.255139 GGACAACACATATAATTACTGCCCTTC 60.255 40.741 0.00 0.00 0.00 3.46
3454 9120 8.641498 ATCCAACAAATATGGCTTTCTATAGG 57.359 34.615 0.00 0.00 37.88 2.57
3461 9127 7.394144 AATATGGCTTTCTATAGGTTGAGGT 57.606 36.000 0.00 0.00 0.00 3.85
3465 9131 5.059833 GGCTTTCTATAGGTTGAGGTGATG 58.940 45.833 0.00 0.00 0.00 3.07
3472 9138 7.275183 TCTATAGGTTGAGGTGATGACATTTG 58.725 38.462 0.00 0.00 0.00 2.32
3485 9151 8.085296 GGTGATGACATTTGGTACATTTTTACA 58.915 33.333 0.00 0.00 39.30 2.41
3539 9272 2.027745 CACTTATATCCGGCCTCTGCAT 60.028 50.000 0.00 0.00 40.13 3.96
3552 9285 3.303593 GCCTCTGCATCAACACAATATCG 60.304 47.826 0.00 0.00 37.47 2.92
3654 9465 1.474879 CAACAAAACCAACCACGGACT 59.525 47.619 0.00 0.00 0.00 3.85
3704 9552 3.315191 ACCACCTCACAAAGTTGATTTCG 59.685 43.478 0.00 0.00 0.00 3.46
3748 9601 0.560688 ACCCATCTCTCTCCTCCCTC 59.439 60.000 0.00 0.00 0.00 4.30
3749 9602 0.859760 CCCATCTCTCTCCTCCCTCT 59.140 60.000 0.00 0.00 0.00 3.69
3768 9621 4.321527 CCTCTGCTTTCACATTTTTCCTCC 60.322 45.833 0.00 0.00 0.00 4.30
3777 9630 8.713708 TTTCACATTTTTCCTCCCATACTTTA 57.286 30.769 0.00 0.00 0.00 1.85
3823 9676 2.114670 CGCCATGGGTTAGCCACAG 61.115 63.158 15.13 0.80 36.17 3.66
3829 9682 1.561643 TGGGTTAGCCACAGAGAGAG 58.438 55.000 0.00 0.00 36.17 3.20
3834 9687 4.406003 GGGTTAGCCACAGAGAGAGAAATA 59.594 45.833 0.00 0.00 36.17 1.40
3879 9741 8.261522 AGACTTTTATCAGAGACAACCTATTCC 58.738 37.037 0.00 0.00 0.00 3.01
3921 9783 4.836125 ACAAACAACACATCCATCAGTC 57.164 40.909 0.00 0.00 0.00 3.51
3970 9839 2.181021 GCGAGGTAGGTGTCCACG 59.819 66.667 0.00 0.00 40.78 4.94
4008 9877 1.172180 CCTTGGTGTTGTGCGGATGT 61.172 55.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 93 6.910536 AATCCGAAGACATTAGTAGCAAAG 57.089 37.500 0.00 0.00 0.00 2.77
135 139 0.249953 TCAAGACGCCGGTAGCAAAA 60.250 50.000 1.90 0.00 44.04 2.44
177 182 3.823873 ACATGATACGGTGGAAGCAAAAA 59.176 39.130 0.00 0.00 0.00 1.94
693 745 2.600475 GCCCGCGTCTTCGTCAAAA 61.600 57.895 4.92 0.00 39.49 2.44
827 879 6.500910 ACAAAGTACTCCTTTTTAAAAGGCG 58.499 36.000 26.66 23.69 41.51 5.52
845 897 8.683615 GCCCATTTTATTAGCTACTAACAAAGT 58.316 33.333 3.20 0.00 42.62 2.66
846 898 8.903820 AGCCCATTTTATTAGCTACTAACAAAG 58.096 33.333 3.20 0.77 26.73 2.77
847 899 8.682710 CAGCCCATTTTATTAGCTACTAACAAA 58.317 33.333 3.20 0.00 31.23 2.83
848 900 7.284489 CCAGCCCATTTTATTAGCTACTAACAA 59.716 37.037 3.20 3.11 31.23 2.83
849 901 6.770785 CCAGCCCATTTTATTAGCTACTAACA 59.229 38.462 3.20 0.00 31.23 2.41
850 902 6.294010 GCCAGCCCATTTTATTAGCTACTAAC 60.294 42.308 3.20 0.00 31.23 2.34
851 903 5.768164 GCCAGCCCATTTTATTAGCTACTAA 59.232 40.000 0.00 0.00 31.23 2.24
852 904 5.163141 TGCCAGCCCATTTTATTAGCTACTA 60.163 40.000 0.00 0.00 31.23 1.82
853 905 4.145052 GCCAGCCCATTTTATTAGCTACT 58.855 43.478 0.00 0.00 31.23 2.57
854 906 3.888930 TGCCAGCCCATTTTATTAGCTAC 59.111 43.478 0.00 0.00 31.23 3.58
855 907 4.144297 CTGCCAGCCCATTTTATTAGCTA 58.856 43.478 0.00 0.00 31.23 3.32
856 908 2.961062 CTGCCAGCCCATTTTATTAGCT 59.039 45.455 0.00 0.00 0.00 3.32
857 909 2.036346 CCTGCCAGCCCATTTTATTAGC 59.964 50.000 0.00 0.00 0.00 3.09
858 910 3.299503 ACCTGCCAGCCCATTTTATTAG 58.700 45.455 0.00 0.00 0.00 1.73
859 911 3.396685 ACCTGCCAGCCCATTTTATTA 57.603 42.857 0.00 0.00 0.00 0.98
860 912 2.252535 ACCTGCCAGCCCATTTTATT 57.747 45.000 0.00 0.00 0.00 1.40
861 913 2.110578 GAACCTGCCAGCCCATTTTAT 58.889 47.619 0.00 0.00 0.00 1.40
862 914 1.555967 GAACCTGCCAGCCCATTTTA 58.444 50.000 0.00 0.00 0.00 1.52
863 915 1.535204 CGAACCTGCCAGCCCATTTT 61.535 55.000 0.00 0.00 0.00 1.82
864 916 1.978617 CGAACCTGCCAGCCCATTT 60.979 57.895 0.00 0.00 0.00 2.32
865 917 2.361610 CGAACCTGCCAGCCCATT 60.362 61.111 0.00 0.00 0.00 3.16
870 922 4.742201 TCGAGCGAACCTGCCAGC 62.742 66.667 0.00 0.00 34.65 4.85
871 923 2.811317 GTCGAGCGAACCTGCCAG 60.811 66.667 0.00 0.00 34.65 4.85
872 924 3.282745 GAGTCGAGCGAACCTGCCA 62.283 63.158 0.00 0.00 34.65 4.92
873 925 2.507324 GAGTCGAGCGAACCTGCC 60.507 66.667 0.00 0.00 34.65 4.85
874 926 2.507324 GGAGTCGAGCGAACCTGC 60.507 66.667 0.00 0.00 0.00 4.85
875 927 1.153939 CTGGAGTCGAGCGAACCTG 60.154 63.158 14.82 11.75 0.00 4.00
876 928 2.995872 GCTGGAGTCGAGCGAACCT 61.996 63.158 11.61 1.83 0.00 3.50
877 929 2.507324 GCTGGAGTCGAGCGAACC 60.507 66.667 11.61 9.39 0.00 3.62
878 930 2.089349 GTGCTGGAGTCGAGCGAAC 61.089 63.158 20.44 11.44 39.47 3.95
879 931 2.082629 TTGTGCTGGAGTCGAGCGAA 62.083 55.000 20.44 13.44 39.47 4.70
880 932 2.082629 TTTGTGCTGGAGTCGAGCGA 62.083 55.000 20.44 8.39 39.47 4.93
881 933 1.664649 TTTGTGCTGGAGTCGAGCG 60.665 57.895 20.44 0.00 39.47 5.03
882 934 0.880278 TGTTTGTGCTGGAGTCGAGC 60.880 55.000 19.28 19.28 36.95 5.03
883 935 1.800805 ATGTTTGTGCTGGAGTCGAG 58.199 50.000 0.00 0.00 0.00 4.04
884 936 2.254546 AATGTTTGTGCTGGAGTCGA 57.745 45.000 0.00 0.00 0.00 4.20
885 937 2.605338 CCAAATGTTTGTGCTGGAGTCG 60.605 50.000 4.92 0.00 36.45 4.18
886 938 2.863704 GCCAAATGTTTGTGCTGGAGTC 60.864 50.000 4.92 0.00 36.45 3.36
887 939 1.069049 GCCAAATGTTTGTGCTGGAGT 59.931 47.619 4.92 0.00 36.45 3.85
911 963 2.672961 ATGTGTGTGTACGCTGCTAT 57.327 45.000 8.10 0.00 38.15 2.97
928 980 5.602978 ACCCCTAAGGACTACTCATGTTATG 59.397 44.000 0.00 0.00 39.89 1.90
929 981 5.789535 ACCCCTAAGGACTACTCATGTTAT 58.210 41.667 0.00 0.00 39.89 1.89
933 985 2.966516 GGACCCCTAAGGACTACTCATG 59.033 54.545 0.00 0.00 39.89 3.07
935 987 2.244252 GAGGACCCCTAAGGACTACTCA 59.756 54.545 0.00 0.00 39.89 3.41
947 999 2.653366 TGTAGTCTTGTAGAGGACCCCT 59.347 50.000 0.00 0.00 36.03 4.79
950 1002 4.765856 TCTGTTGTAGTCTTGTAGAGGACC 59.234 45.833 0.00 0.00 33.39 4.46
957 1009 3.895656 AGCTGGTCTGTTGTAGTCTTGTA 59.104 43.478 0.00 0.00 0.00 2.41
966 1018 0.839946 AAGGTGAGCTGGTCTGTTGT 59.160 50.000 8.47 0.00 0.00 3.32
967 1019 1.517242 GAAGGTGAGCTGGTCTGTTG 58.483 55.000 8.47 0.00 0.00 3.33
968 1020 0.034059 CGAAGGTGAGCTGGTCTGTT 59.966 55.000 8.47 0.00 0.00 3.16
972 1024 2.435059 GGCGAAGGTGAGCTGGTC 60.435 66.667 0.00 0.00 0.00 4.02
973 1025 4.379243 CGGCGAAGGTGAGCTGGT 62.379 66.667 0.00 0.00 36.18 4.00
982 1034 4.452733 GGTGGAGGACGGCGAAGG 62.453 72.222 16.62 0.00 0.00 3.46
1026 1081 3.941704 AGGCAAATTAGGAAGAGGAGG 57.058 47.619 0.00 0.00 0.00 4.30
1161 1219 2.031163 GTGCCGTTGGTGAGCTCT 59.969 61.111 16.19 0.00 0.00 4.09
1242 1303 2.343758 GAGAAGGACTGCACCGCA 59.656 61.111 0.00 0.00 36.92 5.69
1452 1528 0.237761 CGTTGAGGTCGTCGAACTCT 59.762 55.000 33.71 15.87 45.70 3.24
1611 5161 1.680735 GTGATTTGTGCAACCCTGTGA 59.319 47.619 0.00 0.00 34.36 3.58
1851 5410 2.435938 TTGGATCGTGGCTTCGGC 60.436 61.111 3.35 0.00 40.88 5.54
1935 5497 0.038159 AACGTCTCTGTAGCACCAGC 60.038 55.000 0.00 0.00 42.56 4.85
2246 5808 4.956075 ACACCAGAAACAATTCACCTTTCT 59.044 37.500 0.00 0.00 38.06 2.52
2436 6037 3.873361 CACCATCGAGGAGTACGTTACTA 59.127 47.826 0.00 0.00 39.59 1.82
2445 6046 1.852633 TCATGTCACCATCGAGGAGT 58.147 50.000 0.00 0.00 41.22 3.85
2514 6115 1.152860 ATGTGTGGTTTGCGGGTCA 60.153 52.632 0.00 0.00 0.00 4.02
2610 6213 4.284746 ACTTCAAGAACAAACACCCCAAAA 59.715 37.500 0.00 0.00 0.00 2.44
2675 6281 3.930229 CGATTCGACCAACAATACTTGGA 59.070 43.478 0.00 0.00 43.19 3.53
2907 6513 6.829811 TCTGCATTATGGTCATCATCTGAAAA 59.170 34.615 0.00 0.00 37.30 2.29
2934 6540 4.002982 TGATGAACTGGTCAAATCCTTCG 58.997 43.478 0.00 0.00 40.50 3.79
2967 6573 5.163913 GCTGTCAATACTCACTGTTGATGAC 60.164 44.000 0.00 0.00 34.71 3.06
2978 6584 2.001872 CGCATGTGCTGTCAATACTCA 58.998 47.619 3.25 0.00 39.32 3.41
2996 6602 0.391263 CCTCCCAACTGTAAGGACGC 60.391 60.000 1.15 0.00 39.30 5.19
3042 6648 3.018598 AGACACAATGACTCAGTCACG 57.981 47.619 10.48 7.10 45.65 4.35
3105 6712 7.552687 ACATCCATTACATCGTACAAAAGTGAT 59.447 33.333 0.00 0.00 0.00 3.06
3158 8399 0.037160 TGCATCAGAGGTGCACACAT 59.963 50.000 20.43 3.33 46.76 3.21
3159 8400 0.604511 CTGCATCAGAGGTGCACACA 60.605 55.000 20.43 2.39 46.76 3.72
3160 8401 0.321034 TCTGCATCAGAGGTGCACAC 60.321 55.000 20.43 12.05 46.76 3.82
3161 8402 2.060370 TCTGCATCAGAGGTGCACA 58.940 52.632 20.43 0.00 46.76 4.57
3213 8456 7.573710 TGTTGGTGTAATGAAGGATATAGCTT 58.426 34.615 0.00 0.00 0.00 3.74
3214 8457 7.136822 TGTTGGTGTAATGAAGGATATAGCT 57.863 36.000 0.00 0.00 0.00 3.32
3228 8471 8.972458 ATGTATGCACTTATATGTTGGTGTAA 57.028 30.769 0.00 0.00 32.90 2.41
3271 8931 9.737427 GCTAACAAGTATACTCGATATATGCAT 57.263 33.333 5.70 3.79 0.00 3.96
3281 8941 9.849607 CATGTATTTTGCTAACAAGTATACTCG 57.150 33.333 5.70 0.00 36.75 4.18
3295 8955 7.790027 TGGCCAATAAATACATGTATTTTGCT 58.210 30.769 36.25 23.35 41.49 3.91
3342 9002 8.090788 AGAATTAGTCAGAAGGGCAGTAATTA 57.909 34.615 0.00 0.00 29.55 1.40
3424 9089 7.910584 AGAAAGCCATATTTGTTGGATCTTTT 58.089 30.769 0.00 0.00 36.26 2.27
3454 9120 4.759693 TGTACCAAATGTCATCACCTCAAC 59.240 41.667 0.00 0.00 0.00 3.18
3520 9253 2.234661 TGATGCAGAGGCCGGATATAAG 59.765 50.000 5.05 0.00 40.13 1.73
3539 9272 6.394809 TGTCTAGCTTTCGATATTGTGTTGA 58.605 36.000 0.00 0.00 0.00 3.18
3552 9285 5.127693 TCTCAGTGTCTTGTCTAGCTTTC 57.872 43.478 0.00 0.00 0.00 2.62
3654 9465 2.064434 TCCATGTCTGTGTTGCCAAA 57.936 45.000 0.00 0.00 0.00 3.28
3704 9552 4.434520 GTCCACTAAGACTAGCATTGGAC 58.565 47.826 2.29 2.29 39.63 4.02
3748 9601 3.321682 TGGGAGGAAAAATGTGAAAGCAG 59.678 43.478 0.00 0.00 0.00 4.24
3749 9602 3.303938 TGGGAGGAAAAATGTGAAAGCA 58.696 40.909 0.00 0.00 0.00 3.91
3768 9621 4.618227 GCTGCAGTTTTGGGTAAAGTATGG 60.618 45.833 16.64 0.00 0.00 2.74
3777 9630 2.051941 CATGGCTGCAGTTTTGGGT 58.948 52.632 16.64 0.00 0.00 4.51
3823 9676 2.380660 CGCGACAGCTATTTCTCTCTC 58.619 52.381 0.00 0.00 42.32 3.20
3829 9682 2.117910 GTCTACCGCGACAGCTATTTC 58.882 52.381 8.23 0.00 42.32 2.17
3834 9687 1.132643 CTAAAGTCTACCGCGACAGCT 59.867 52.381 8.23 3.01 42.32 4.24
3875 9737 1.305213 AAATGGGTGCCTGCGGAAT 60.305 52.632 0.00 0.00 0.00 3.01
3879 9741 1.926511 GAGTCAAATGGGTGCCTGCG 61.927 60.000 0.00 0.00 0.00 5.18
3921 9783 2.124570 CGGGTTGGATGCTCCCAG 60.125 66.667 15.43 7.01 41.12 4.45
3954 9823 1.975407 ACCGTGGACACCTACCTCG 60.975 63.158 0.00 0.00 41.85 4.63
3970 9839 4.910585 CCGGGCCATCGCTACACC 62.911 72.222 4.39 0.00 34.44 4.16


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

AutoCloner maintained by Alex Coulton.