Multiple sequence alignment - TraesCS4A01G162100

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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 TraesCS4A01G162100 chr4A 100.000 3098 0 0 1 3098 353089596 353092693 0.000000e+00 5722.0
1 TraesCS4A01G162100 chr4A 87.313 1340 130 13 1087 2422 353098824 353100127 0.000000e+00 1496.0
2 TraesCS4A01G162100 chr4A 90.010 1051 88 7 2 1043 353097774 353098816 0.000000e+00 1343.0
3 TraesCS4A01G162100 chr4A 85.772 745 65 14 780 1490 242346609 242347346 0.000000e+00 750.0
4 TraesCS4A01G162100 chr4A 83.941 741 81 23 780 1490 242386127 242386859 0.000000e+00 675.0
5 TraesCS4A01G162100 chr4A 89.647 425 35 3 690 1105 361180168 361179744 1.640000e-147 532.0
6 TraesCS4A01G162100 chr4A 90.083 121 9 1 975 1095 397791394 397791277 1.490000e-33 154.0
7 TraesCS4A01G162100 chr2A 85.784 3088 319 51 33 3095 282287279 282284287 0.000000e+00 3160.0
8 TraesCS4A01G162100 chr2A 87.235 2358 248 19 1 2327 282263268 282260933 0.000000e+00 2638.0
9 TraesCS4A01G162100 chr2A 94.915 59 2 1 1085 1143 355229591 355229648 1.180000e-14 91.6
10 TraesCS4A01G162100 chr2A 94.915 59 2 1 1085 1143 355251946 355252003 1.180000e-14 91.6
11 TraesCS4A01G162100 chr2A 100.000 35 0 0 1153 1187 275352027 275351993 7.170000e-07 65.8
12 TraesCS4A01G162100 chr7A 86.317 1257 143 26 1852 3098 529378166 529376929 0.000000e+00 1341.0
13 TraesCS4A01G162100 chr7A 84.804 204 29 2 2895 3098 365261220 365261019 1.460000e-48 204.0
14 TraesCS4A01G162100 chr7A 86.014 143 17 3 1570 1711 448613677 448613537 1.920000e-32 150.0
15 TraesCS4A01G162100 chr6A 84.086 1263 162 32 1851 3097 252159532 252158293 0.000000e+00 1182.0
16 TraesCS4A01G162100 chr6A 79.267 955 153 32 1 942 458118378 458119300 2.620000e-175 625.0
17 TraesCS4A01G162100 chr6A 79.457 847 136 32 1 833 282784055 282784877 1.610000e-157 566.0
18 TraesCS4A01G162100 chr6A 79.339 847 137 33 1 833 282842915 282843737 7.500000e-156 560.0
19 TraesCS4A01G162100 chr6A 86.026 458 48 8 780 1221 303197865 303197408 7.770000e-131 477.0
20 TraesCS4A01G162100 chr6A 91.594 345 29 0 598 942 458080828 458081172 7.770000e-131 477.0
21 TraesCS4A01G162100 chr6A 83.364 547 50 19 975 1486 303196876 303196336 4.680000e-128 468.0
22 TraesCS4A01G162100 chr1B 83.218 1305 178 38 1818 3098 508629247 508630534 0.000000e+00 1158.0
23 TraesCS4A01G162100 chr1B 80.531 565 91 16 2 558 335057583 335058136 1.720000e-112 416.0
24 TraesCS4A01G162100 chr2B 82.745 1275 165 45 1849 3096 564890426 564889180 0.000000e+00 1085.0
25 TraesCS4A01G162100 chr2B 80.590 1288 202 40 1835 3098 372808429 372807166 0.000000e+00 950.0
26 TraesCS4A01G162100 chr6D 82.110 1308 190 38 1811 3098 364469427 364470710 0.000000e+00 1079.0
27 TraesCS4A01G162100 chr6B 83.767 1152 160 24 1895 3031 651453667 651454806 0.000000e+00 1066.0
28 TraesCS4A01G162100 chr1A 83.000 1200 159 33 1895 3082 187557031 187558197 0.000000e+00 1044.0
29 TraesCS4A01G162100 chr1A 88.800 500 52 4 2 497 324506597 324507096 7.340000e-171 610.0
30 TraesCS4A01G162100 chr1A 92.000 325 25 1 619 942 157581830 157582154 3.640000e-124 455.0
31 TraesCS4A01G162100 chr1A 83.478 345 36 14 1167 1490 119644047 119643703 5.020000e-78 302.0
32 TraesCS4A01G162100 chr1A 85.965 114 11 5 1259 1369 408230139 408230250 1.950000e-22 117.0
33 TraesCS4A01G162100 chr1A 86.111 72 9 1 1071 1142 33811029 33811099 3.310000e-10 76.8
34 TraesCS4A01G162100 chr1A 93.617 47 1 2 1153 1197 447932352 447932398 5.540000e-08 69.4
35 TraesCS4A01G162100 chr1A 93.617 47 1 2 1153 1197 447940098 447940144 5.540000e-08 69.4
36 TraesCS4A01G162100 chr3D 82.273 1258 167 50 1854 3096 209227583 209228799 0.000000e+00 1037.0
37 TraesCS4A01G162100 chr1D 81.451 841 102 37 4 824 230527887 230528693 9.370000e-180 640.0
38 TraesCS4A01G162100 chr1D 83.208 530 67 17 25 541 54670688 54671208 1.680000e-127 466.0
39 TraesCS4A01G162100 chr3A 87.871 404 48 1 539 942 304551648 304551246 1.010000e-129 473.0
40 TraesCS4A01G162100 chr3A 79.511 532 81 22 1831 2356 371319631 371320140 1.370000e-93 353.0
41 TraesCS4A01G162100 chr3A 91.195 159 12 2 539 696 59057169 59057012 6.730000e-52 215.0
42 TraesCS4A01G162100 chr3A 83.478 115 16 2 1260 1372 71449550 71449437 1.520000e-18 104.0
43 TraesCS4A01G162100 chr3B 82.033 551 73 18 1 535 666770633 666770093 2.190000e-121 446.0
44 TraesCS4A01G162100 chr3B 81.193 553 80 16 1 536 642537304 642536759 1.030000e-114 424.0
45 TraesCS4A01G162100 chr2D 81.851 551 79 16 1 535 184854063 184853518 7.880000e-121 444.0
46 TraesCS4A01G162100 chr5D 93.852 244 13 2 719 960 163709721 163709964 1.760000e-97 366.0
47 TraesCS4A01G162100 chr5A 86.531 245 29 2 1234 1478 164067576 164067816 1.830000e-67 267.0
48 TraesCS4A01G162100 chr5A 86.096 187 19 5 1064 1246 152025655 152025838 8.770000e-46 195.0
49 TraesCS4A01G162100 chr5A 87.730 163 18 2 1086 1246 152033537 152033699 4.080000e-44 189.0
50 TraesCS4A01G162100 chr5A 89.796 98 6 3 1702 1795 352929041 352928944 4.200000e-24 122.0
51 TraesCS4A01G162100 chr5A 94.444 54 3 0 1740 1793 362676689 362676636 1.980000e-12 84.2
52 TraesCS4A01G162100 chr4D 92.857 70 5 0 1026 1095 274033168 274033099 5.470000e-18 102.0


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 TraesCS4A01G162100 chr4A 353089596 353092693 3097 False 5722.0 5722 100.0000 1 3098 1 chr4A.!!$F3 3097
1 TraesCS4A01G162100 chr4A 353097774 353100127 2353 False 1419.5 1496 88.6615 2 2422 2 chr4A.!!$F4 2420
2 TraesCS4A01G162100 chr4A 242346609 242347346 737 False 750.0 750 85.7720 780 1490 1 chr4A.!!$F1 710
3 TraesCS4A01G162100 chr4A 242386127 242386859 732 False 675.0 675 83.9410 780 1490 1 chr4A.!!$F2 710
4 TraesCS4A01G162100 chr2A 282284287 282287279 2992 True 3160.0 3160 85.7840 33 3095 1 chr2A.!!$R3 3062
5 TraesCS4A01G162100 chr2A 282260933 282263268 2335 True 2638.0 2638 87.2350 1 2327 1 chr2A.!!$R2 2326
6 TraesCS4A01G162100 chr7A 529376929 529378166 1237 True 1341.0 1341 86.3170 1852 3098 1 chr7A.!!$R3 1246
7 TraesCS4A01G162100 chr6A 252158293 252159532 1239 True 1182.0 1182 84.0860 1851 3097 1 chr6A.!!$R1 1246
8 TraesCS4A01G162100 chr6A 458118378 458119300 922 False 625.0 625 79.2670 1 942 1 chr6A.!!$F4 941
9 TraesCS4A01G162100 chr6A 282784055 282784877 822 False 566.0 566 79.4570 1 833 1 chr6A.!!$F1 832
10 TraesCS4A01G162100 chr6A 282842915 282843737 822 False 560.0 560 79.3390 1 833 1 chr6A.!!$F2 832
11 TraesCS4A01G162100 chr6A 303196336 303197865 1529 True 472.5 477 84.6950 780 1486 2 chr6A.!!$R2 706
12 TraesCS4A01G162100 chr1B 508629247 508630534 1287 False 1158.0 1158 83.2180 1818 3098 1 chr1B.!!$F2 1280
13 TraesCS4A01G162100 chr1B 335057583 335058136 553 False 416.0 416 80.5310 2 558 1 chr1B.!!$F1 556
14 TraesCS4A01G162100 chr2B 564889180 564890426 1246 True 1085.0 1085 82.7450 1849 3096 1 chr2B.!!$R2 1247
15 TraesCS4A01G162100 chr2B 372807166 372808429 1263 True 950.0 950 80.5900 1835 3098 1 chr2B.!!$R1 1263
16 TraesCS4A01G162100 chr6D 364469427 364470710 1283 False 1079.0 1079 82.1100 1811 3098 1 chr6D.!!$F1 1287
17 TraesCS4A01G162100 chr6B 651453667 651454806 1139 False 1066.0 1066 83.7670 1895 3031 1 chr6B.!!$F1 1136
18 TraesCS4A01G162100 chr1A 187557031 187558197 1166 False 1044.0 1044 83.0000 1895 3082 1 chr1A.!!$F3 1187
19 TraesCS4A01G162100 chr3D 209227583 209228799 1216 False 1037.0 1037 82.2730 1854 3096 1 chr3D.!!$F1 1242
20 TraesCS4A01G162100 chr1D 230527887 230528693 806 False 640.0 640 81.4510 4 824 1 chr1D.!!$F2 820
21 TraesCS4A01G162100 chr1D 54670688 54671208 520 False 466.0 466 83.2080 25 541 1 chr1D.!!$F1 516
22 TraesCS4A01G162100 chr3A 371319631 371320140 509 False 353.0 353 79.5110 1831 2356 1 chr3A.!!$F1 525
23 TraesCS4A01G162100 chr3B 666770093 666770633 540 True 446.0 446 82.0330 1 535 1 chr3B.!!$R2 534
24 TraesCS4A01G162100 chr3B 642536759 642537304 545 True 424.0 424 81.1930 1 536 1 chr3B.!!$R1 535
25 TraesCS4A01G162100 chr2D 184853518 184854063 545 True 444.0 444 81.8510 1 535 1 chr2D.!!$R1 534

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
482 516 0.314935 TTACGGAGCGGTTCGAGTTT 59.685 50.0 24.21 1.16 0.00 2.66 F
1034 1084 0.112995 ACATGTGAAGGTGGCCATGT 59.887 50.0 9.72 3.02 42.16 3.21 F
1909 2844 0.107557 ACGCGGATAATTTTCCCGGT 60.108 50.0 12.47 12.36 43.17 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 2725 0.962356 AGAGAAGCCCATTTGCCACG 60.962 55.000 0.0 0.0 0.0 4.94 R
1934 2869 1.533625 TCTCGCCCACTCCAATTTTG 58.466 50.000 0.0 0.0 0.0 2.44 R
2860 3851 1.734465 GTTGCTCTCTTTGACCCATCG 59.266 52.381 0.0 0.0 0.0 3.84 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
107 112 2.134201 TCGTGATGCGGATGACATAC 57.866 50.000 7.35 0.00 41.72 2.39
110 115 2.287849 CGTGATGCGGATGACATACTCT 60.288 50.000 7.35 0.00 36.85 3.24
114 119 3.990318 TGCGGATGACATACTCTAGTG 57.010 47.619 0.00 0.00 0.00 2.74
157 166 6.231258 AGTTGACATGAGCATGATAAGAGA 57.769 37.500 16.70 0.00 41.20 3.10
218 234 6.349860 CGATGATAATGGGAATGATGCAATGT 60.350 38.462 0.00 0.00 0.00 2.71
253 269 4.957327 TGATCTGGCAATTCATGGAAATGA 59.043 37.500 0.00 0.00 0.00 2.57
256 272 2.824936 TGGCAATTCATGGAAATGACGT 59.175 40.909 0.00 0.00 33.52 4.34
330 349 3.712907 CGGTGACCGGGTTCCCAT 61.713 66.667 17.80 0.00 44.15 4.00
420 450 5.688823 TCTCATACAACAAAAGCATTCGTG 58.311 37.500 0.00 0.00 0.00 4.35
482 516 0.314935 TTACGGAGCGGTTCGAGTTT 59.685 50.000 24.21 1.16 0.00 2.66
504 545 5.899631 TGGTAAAGGAAGTAGGTGTTCTT 57.100 39.130 0.00 0.00 0.00 2.52
510 551 2.638363 GGAAGTAGGTGTTCTTGGGACT 59.362 50.000 0.00 0.00 0.00 3.85
543 584 6.825213 TGGAAGTAGTAGTACACATGTCGTAT 59.175 38.462 10.33 0.00 0.00 3.06
634 675 1.284408 GTCAAAAATCACGGCGGCA 59.716 52.632 13.24 0.00 0.00 5.69
651 692 2.411748 CGGCAGTAGTTGTACACATGTG 59.588 50.000 24.25 24.25 0.00 3.21
660 701 4.219944 AGTTGTACACATGTGGTAGTCGAT 59.780 41.667 28.64 8.56 34.19 3.59
914 955 0.946221 GCACACCCACAGAGTCTTCG 60.946 60.000 0.00 0.00 0.00 3.79
962 1003 1.303317 GTCTCGGTGGTGGCCAAAT 60.303 57.895 7.24 0.00 34.18 2.32
1003 1053 2.068519 GTGTGTTCGATGCACTGATGA 58.931 47.619 17.59 0.00 37.70 2.92
1020 1070 4.641396 TGATGACCGAAGAAGAAACATGT 58.359 39.130 0.00 0.00 0.00 3.21
1034 1084 0.112995 ACATGTGAAGGTGGCCATGT 59.887 50.000 9.72 3.02 42.16 3.21
1151 1249 2.234613 GCAAGCAGCGAACAGTACA 58.765 52.632 0.00 0.00 0.00 2.90
1160 1269 0.250124 CGAACAGTACAGGGGTTGCA 60.250 55.000 0.00 0.00 0.00 4.08
1264 2180 1.213296 GGGACCCTATGCTGGAAGAA 58.787 55.000 2.09 0.00 34.07 2.52
1265 2181 1.141858 GGGACCCTATGCTGGAAGAAG 59.858 57.143 2.09 0.00 34.07 2.85
1266 2182 2.119495 GGACCCTATGCTGGAAGAAGA 58.881 52.381 0.00 0.00 34.07 2.87
1281 2197 4.020662 GGAAGAAGAAGAAGCAGAGGAAGA 60.021 45.833 0.00 0.00 0.00 2.87
1286 2202 2.317371 AGAAGCAGAGGAAGAGGTCA 57.683 50.000 0.00 0.00 0.00 4.02
1422 2338 0.900182 TGAGAAGAAGAGCTCCGGCA 60.900 55.000 10.93 0.00 41.70 5.69
1450 2366 3.069980 GCTGACGACGGCAGGAGAT 62.070 63.158 30.86 0.00 46.56 2.75
1458 2374 3.157252 GGCAGGAGATGGAGGCGA 61.157 66.667 0.00 0.00 0.00 5.54
1599 2515 4.458829 AGGCGATGGGGGTCGAGA 62.459 66.667 0.00 0.00 44.06 4.04
1651 2569 4.030452 GAAGTGGCGGCAGTGTGC 62.030 66.667 21.18 9.29 44.08 4.57
1664 2582 1.115930 AGTGTGCAAGGACGAGAGGT 61.116 55.000 0.00 0.00 0.00 3.85
1678 2596 3.201266 ACGAGAGGTAGAGAGTGGAGATT 59.799 47.826 0.00 0.00 0.00 2.40
1684 2602 3.970640 GGTAGAGAGTGGAGATTGGGATT 59.029 47.826 0.00 0.00 0.00 3.01
1694 2612 3.701760 ATTGGGATTGGGCAGGGGC 62.702 63.158 0.00 0.00 40.13 5.80
1711 2635 1.197812 GGCGAGGGTTAGGGTTAGAA 58.802 55.000 0.00 0.00 0.00 2.10
1736 2660 4.364318 GGCTGTGCCTCTAGGAGA 57.636 61.111 0.00 0.00 46.69 3.71
1807 2731 2.267642 GGCTGGATACACGTGGCA 59.732 61.111 21.57 7.60 46.17 4.92
1808 2732 1.376683 GGCTGGATACACGTGGCAA 60.377 57.895 21.57 5.16 46.17 4.52
1809 2733 0.958382 GGCTGGATACACGTGGCAAA 60.958 55.000 21.57 2.38 46.17 3.68
1909 2844 0.107557 ACGCGGATAATTTTCCCGGT 60.108 50.000 12.47 12.36 43.17 5.28
1934 2869 3.242712 CACAAAAATGTGCTCGTTCCAAC 59.757 43.478 0.00 0.00 32.72 3.77
2045 2982 7.254421 GGAAGTGTCCAAAAATGTTGAACATTC 60.254 37.037 22.29 10.40 44.49 2.67
2072 3010 5.198602 AGAGCCTTGATAAGTGGGAAAAT 57.801 39.130 0.00 0.00 0.00 1.82
2096 3035 8.682936 ATAATTATTGGCAAGGTTAGAGAGTG 57.317 34.615 5.96 0.00 0.00 3.51
2305 3264 8.992073 GTTCCAAAAATTAATGATATGATGGCC 58.008 33.333 0.00 0.00 0.00 5.36
2389 3352 3.377172 GGTGACAACGGGAATAAATGGAG 59.623 47.826 0.00 0.00 0.00 3.86
2401 3364 1.302907 AAATGGAGGGCATCTGGAGT 58.697 50.000 0.00 0.00 0.00 3.85
2428 3391 1.691195 TTGGGGCGTCACAACTCTCA 61.691 55.000 0.00 0.00 0.00 3.27
2497 3476 2.300437 AGAAACGGAAGAGGAAGAGGTG 59.700 50.000 0.00 0.00 0.00 4.00
2533 3512 3.062909 TCTTTGACAAACGAGTGAAACCG 59.937 43.478 0.00 0.00 37.80 4.44
2575 3555 8.879342 TGAAAACTTGAAAGAAAGAACACAAA 57.121 26.923 0.00 0.00 0.00 2.83
2589 3569 8.831715 AAAGAACACAAAAGAGTTGAACAAAT 57.168 26.923 0.00 0.00 0.00 2.32
2638 3620 2.276732 AGGAACACCATGTGAACCTG 57.723 50.000 12.91 0.00 39.37 4.00
2675 3657 5.183331 GCTATGAATGATGAGCACAATGGAT 59.817 40.000 0.00 0.00 34.96 3.41
2718 3700 6.710744 ACTCTGGTTGAAACGAGATAAACAAT 59.289 34.615 8.14 0.00 41.80 2.71
2813 3800 4.214986 TGAAAGAGAACACAACACTCCA 57.785 40.909 0.00 0.00 0.00 3.86
2822 3809 4.481368 ACACAACACTCCAGTTAACTGA 57.519 40.909 32.50 18.85 46.59 3.41
2860 3851 3.489785 ACACGATCTTGACAAAACGAGAC 59.510 43.478 6.16 0.00 33.77 3.36
2894 3886 2.172930 AGAGCAACATCATCATGCCTCT 59.827 45.455 0.00 0.00 40.93 3.69
2918 3910 4.568760 GGAACGAAAGAATAGAAGCTGGAG 59.431 45.833 0.00 0.00 0.00 3.86
3063 4061 6.399639 TTCCAATGGTCTTAAGGAAAACAC 57.600 37.500 1.85 0.00 35.57 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 95 3.377346 AGAGTATGTCATCCGCATCAC 57.623 47.619 0.00 0.00 0.00 3.06
107 112 9.462174 TTTTCATAAAATTGCACAACACTAGAG 57.538 29.630 0.00 0.00 0.00 2.43
110 115 9.593134 ACTTTTTCATAAAATTGCACAACACTA 57.407 25.926 0.00 0.00 33.05 2.74
114 119 9.209297 GTCAACTTTTTCATAAAATTGCACAAC 57.791 29.630 0.00 0.00 33.05 3.32
218 234 3.608796 TGCCAGATCATCGAAATGTTGA 58.391 40.909 0.00 0.00 34.32 3.18
253 269 3.241701 CACACTTGTTCTTTTGCAACGT 58.758 40.909 0.00 0.00 0.00 3.99
256 272 3.056962 TCTGCACACTTGTTCTTTTGCAA 60.057 39.130 0.00 0.00 39.36 4.08
420 450 2.579787 CGAGACGATGACCCGTGC 60.580 66.667 0.00 0.00 43.49 5.34
482 516 5.455612 CCAAGAACACCTACTTCCTTTACCA 60.456 44.000 0.00 0.00 0.00 3.25
504 545 1.254026 CTTCCACTACGACAGTCCCA 58.746 55.000 0.00 0.00 34.26 4.37
510 551 5.639506 GTGTACTACTACTTCCACTACGACA 59.360 44.000 0.00 0.00 0.00 4.35
543 584 2.167693 CGATAGCACCACTACTTCCCAA 59.832 50.000 0.00 0.00 32.32 4.12
619 660 0.802494 CTACTGCCGCCGTGATTTTT 59.198 50.000 0.00 0.00 0.00 1.94
634 675 5.335426 CGACTACCACATGTGTACAACTACT 60.335 44.000 23.79 0.00 0.00 2.57
651 692 3.132289 TGGTTCCATCAAGATCGACTACC 59.868 47.826 0.00 0.00 0.00 3.18
660 701 3.330405 TGAGGACATTGGTTCCATCAAGA 59.670 43.478 0.00 0.00 0.00 3.02
914 955 2.757099 TACCCGGAGCCGAAGTCC 60.757 66.667 11.05 0.00 42.83 3.85
920 961 1.968050 AAATCCTGTACCCGGAGCCG 61.968 60.000 0.73 1.06 33.29 5.52
1003 1053 3.815401 CCTTCACATGTTTCTTCTTCGGT 59.185 43.478 0.00 0.00 0.00 4.69
1020 1070 0.539438 GACCAACATGGCCACCTTCA 60.539 55.000 8.16 0.00 42.67 3.02
1079 1138 2.124819 CTCTGCATTGCGCCTCCT 60.125 61.111 4.18 0.00 41.33 3.69
1088 1186 1.147824 CATCGGCCTCCTCTGCATT 59.852 57.895 0.00 0.00 0.00 3.56
1144 1242 0.687354 CTCTGCAACCCCTGTACTGT 59.313 55.000 0.00 0.00 0.00 3.55
1148 1246 1.553690 GCCTCTCTGCAACCCCTGTA 61.554 60.000 0.00 0.00 0.00 2.74
1150 1248 2.045536 GCCTCTCTGCAACCCCTG 60.046 66.667 0.00 0.00 0.00 4.45
1151 1249 3.710722 CGCCTCTCTGCAACCCCT 61.711 66.667 0.00 0.00 0.00 4.79
1160 1269 2.043450 CCTCCACCTCGCCTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
1242 2158 2.022428 TCTTCCAGCATAGGGTCCCTTA 60.022 50.000 17.94 2.42 34.61 2.69
1248 2164 3.454858 TCTTCTTCTTCCAGCATAGGGT 58.545 45.455 0.00 0.00 0.00 4.34
1264 2180 2.831526 GACCTCTTCCTCTGCTTCTTCT 59.168 50.000 0.00 0.00 0.00 2.85
1265 2181 2.564947 TGACCTCTTCCTCTGCTTCTTC 59.435 50.000 0.00 0.00 0.00 2.87
1266 2182 2.301583 GTGACCTCTTCCTCTGCTTCTT 59.698 50.000 0.00 0.00 0.00 2.52
1281 2197 2.185310 GACGCCCCTTCATGTGACCT 62.185 60.000 0.00 0.00 0.00 3.85
1286 2202 2.047274 CACGACGCCCCTTCATGT 60.047 61.111 0.00 0.00 0.00 3.21
1324 2240 1.449246 CTGGCTCTTCCTCGCTTGG 60.449 63.158 0.00 0.00 35.26 3.61
1327 2243 3.080121 CCCTGGCTCTTCCTCGCT 61.080 66.667 0.00 0.00 35.26 4.93
1444 2360 2.841988 GCCTCGCCTCCATCTCCT 60.842 66.667 0.00 0.00 0.00 3.69
1458 2374 3.394836 GCTCGAGTCCAAGGGCCT 61.395 66.667 15.13 0.00 0.00 5.19
1593 2509 4.908877 GTAGGCGCCGCTCTCGAC 62.909 72.222 23.20 7.88 38.10 4.20
1645 2563 1.115930 ACCTCTCGTCCTTGCACACT 61.116 55.000 0.00 0.00 0.00 3.55
1651 2569 2.680841 CACTCTCTACCTCTCGTCCTTG 59.319 54.545 0.00 0.00 0.00 3.61
1652 2570 2.356330 CCACTCTCTACCTCTCGTCCTT 60.356 54.545 0.00 0.00 0.00 3.36
1664 2582 3.969976 CCAATCCCAATCTCCACTCTCTA 59.030 47.826 0.00 0.00 0.00 2.43
1694 2612 3.370209 CCCTTTTCTAACCCTAACCCTCG 60.370 52.174 0.00 0.00 0.00 4.63
1730 2654 3.716872 CCTCTAAGGCCCATTTTCTCCTA 59.283 47.826 0.00 0.00 0.00 2.94
1801 2725 0.962356 AGAGAAGCCCATTTGCCACG 60.962 55.000 0.00 0.00 0.00 4.94
1807 2731 8.554490 TTTATAGTAGAGAGAGAAGCCCATTT 57.446 34.615 0.00 0.00 0.00 2.32
1808 2732 8.007742 TCTTTATAGTAGAGAGAGAAGCCCATT 58.992 37.037 0.00 0.00 0.00 3.16
1809 2733 7.531317 TCTTTATAGTAGAGAGAGAAGCCCAT 58.469 38.462 0.00 0.00 0.00 4.00
1909 2844 3.003275 GGAACGAGCACATTTTTGTGAGA 59.997 43.478 10.14 0.00 42.02 3.27
1934 2869 1.533625 TCTCGCCCACTCCAATTTTG 58.466 50.000 0.00 0.00 0.00 2.44
2045 2982 3.539604 CCACTTATCAAGGCTCTTCCTG 58.460 50.000 0.00 0.00 46.94 3.86
2072 3010 7.857456 TCACTCTCTAACCTTGCCAATAATTA 58.143 34.615 0.00 0.00 0.00 1.40
2096 3035 5.660460 TGGCCTTTTCTTCTTCAAGTTTTC 58.340 37.500 3.32 0.00 0.00 2.29
2213 3166 5.393866 AGGGATGTTAACAATGGTGACTTT 58.606 37.500 13.23 0.00 0.00 2.66
2227 3182 6.059484 GGTCCATTTAAATCGAGGGATGTTA 58.941 40.000 7.92 0.00 31.83 2.41
2305 3264 3.708563 TGCATTGCATCATGTCATCAG 57.291 42.857 7.38 0.00 31.71 2.90
2428 3391 4.339814 GGTCGAGATCTCTTGTAAGTGGAT 59.660 45.833 20.26 0.00 0.00 3.41
2575 3555 6.096001 AGTGCTCTCAAATTTGTTCAACTCTT 59.904 34.615 17.47 0.00 0.00 2.85
2589 3569 4.462834 TCTTTCTATCGGAGTGCTCTCAAA 59.537 41.667 17.04 7.20 42.05 2.69
2638 3620 2.128771 TCATAGCTTTGCAACCTCCC 57.871 50.000 0.00 0.00 0.00 4.30
2675 3657 5.243730 CCAGAGTGGCTTCAATTCCTTTTTA 59.756 40.000 0.00 0.00 0.00 1.52
2718 3700 3.948473 TCCAATTTGTTCTTCCACGTTCA 59.052 39.130 0.00 0.00 0.00 3.18
2813 3800 9.952188 GTTCTTTTCTTGCTTATTCAGTTAACT 57.048 29.630 1.12 1.12 0.00 2.24
2822 3809 7.440523 AGATCGTGTTCTTTTCTTGCTTATT 57.559 32.000 0.00 0.00 0.00 1.40
2860 3851 1.734465 GTTGCTCTCTTTGACCCATCG 59.266 52.381 0.00 0.00 0.00 3.84
2894 3886 4.020573 TCCAGCTTCTATTCTTTCGTTCCA 60.021 41.667 0.00 0.00 0.00 3.53
2918 3910 6.867662 TCTCTGTTCTTTTCTTTCCATCAC 57.132 37.500 0.00 0.00 0.00 3.06
3063 4061 5.104109 TGGTCTTCACCTCATAATTTAGGGG 60.104 44.000 6.25 2.56 44.17 4.79


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

AutoCloner maintained by Alex Coulton.