Multiple sequence alignment - TraesCS3B01G034200

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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 TraesCS3B01G034200 chr3B 100.000 2498 0 0 842 3339 16333194 16335691 0.000000e+00 4614.0
1 TraesCS3B01G034200 chr3B 100.000 488 0 0 1 488 16332353 16332840 0.000000e+00 902.0
2 TraesCS3B01G034200 chr3B 92.373 472 30 4 2121 2588 20384840 20384371 0.000000e+00 667.0
3 TraesCS3B01G034200 chr3B 84.167 360 51 4 1281 1640 20383553 20383200 8.870000e-91 344.0
4 TraesCS3B01G034200 chr3B 83.844 359 48 8 1281 1637 16324795 16325145 1.920000e-87 333.0
5 TraesCS3B01G034200 chr3B 79.787 376 57 16 1992 2363 20382975 20382615 4.270000e-64 255.0
6 TraesCS3B01G034200 chr3B 79.467 375 61 11 1992 2363 16326711 16327072 5.530000e-63 252.0
7 TraesCS3B01G034200 chr3B 92.857 42 3 0 3276 3317 85103904 85103863 1.000000e-05 62.1
8 TraesCS3B01G034200 chr3D 92.070 2106 112 21 1265 3339 11600922 11603003 0.000000e+00 2913.0
9 TraesCS3B01G034200 chr3D 93.644 472 23 6 1 472 11599869 11600333 0.000000e+00 699.0
10 TraesCS3B01G034200 chr3D 94.236 347 20 0 842 1188 11600578 11600924 6.340000e-147 531.0
11 TraesCS3B01G034200 chr3D 78.989 376 55 17 1992 2359 11593310 11593669 5.570000e-58 235.0
12 TraesCS3B01G034200 chr3D 78.992 357 48 8 1281 1637 11592750 11593079 5.610000e-53 219.0
13 TraesCS3B01G034200 chr3D 90.000 90 5 3 1182 1267 163993700 163993789 2.720000e-21 113.0
14 TraesCS3B01G034200 chr3D 89.362 94 5 3 1187 1275 611569818 611569911 2.720000e-21 113.0
15 TraesCS3B01G034200 chr3D 90.769 65 4 2 3272 3336 297500338 297500400 5.940000e-13 86.1
16 TraesCS3B01G034200 chr3A 83.333 366 48 10 1281 1640 25388954 25388596 3.210000e-85 326.0
17 TraesCS3B01G034200 chr3A 80.053 376 59 13 1992 2363 25388371 25388008 7.100000e-67 265.0
18 TraesCS3B01G034200 chr3A 87.500 64 4 4 3274 3336 394352966 394353026 1.660000e-08 71.3
19 TraesCS3B01G034200 chr7D 79.921 254 43 7 2216 2469 70821297 70821542 2.650000e-41 180.0
20 TraesCS3B01G034200 chr7D 90.698 86 7 1 1187 1272 104640643 104640727 2.720000e-21 113.0
21 TraesCS3B01G034200 chr7D 89.362 94 5 3 1180 1268 494673687 494673594 2.720000e-21 113.0
22 TraesCS3B01G034200 chr7D 91.667 48 1 2 378 424 60602767 60602722 2.780000e-06 63.9
23 TraesCS3B01G034200 chr7A 86.755 151 19 1 1492 1642 76936009 76936158 2.060000e-37 167.0
24 TraesCS3B01G034200 chr7A 80.905 199 38 0 2216 2414 76936449 76936647 1.240000e-34 158.0
25 TraesCS3B01G034200 chr7A 90.000 90 7 2 1187 1276 381248684 381248771 7.570000e-22 115.0
26 TraesCS3B01G034200 chr7B 80.905 199 38 0 2216 2414 12967338 12967536 1.240000e-34 158.0
27 TraesCS3B01G034200 chr7B 88.542 96 7 3 1176 1267 718351000 718351095 2.720000e-21 113.0
28 TraesCS3B01G034200 chr4D 91.954 87 4 2 1190 1275 384974362 384974278 5.850000e-23 119.0
29 TraesCS3B01G034200 chr5D 89.130 92 6 2 1180 1267 411995123 411995032 9.790000e-21 111.0
30 TraesCS3B01G034200 chr1D 87.755 98 7 3 1187 1280 337065189 337065285 3.520000e-20 110.0
31 TraesCS3B01G034200 chr2A 94.118 51 3 0 2189 2239 741990045 741989995 9.930000e-11 78.7
32 TraesCS3B01G034200 chr2A 92.105 38 2 1 382 419 78767716 78767752 6.000000e-03 52.8
33 TraesCS3B01G034200 chr5A 94.737 38 1 1 382 419 626263458 626263494 1.290000e-04 58.4
34 TraesCS3B01G034200 chr5A 100.000 29 0 0 381 409 17596714 17596742 2.000000e-03 54.7
35 TraesCS3B01G034200 chr6D 100.000 29 0 0 381 409 472968563 472968535 2.000000e-03 54.7
36 TraesCS3B01G034200 chr6D 92.105 38 2 1 381 418 389333972 389334008 6.000000e-03 52.8
37 TraesCS3B01G034200 chr5B 92.105 38 2 1 382 419 591493524 591493560 6.000000e-03 52.8


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 TraesCS3B01G034200 chr3B 16332353 16335691 3338 False 2758.0 4614 100.000000 1 3339 2 chr3B.!!$F2 3338
1 TraesCS3B01G034200 chr3B 20382615 20384840 2225 True 422.0 667 85.442333 1281 2588 3 chr3B.!!$R2 1307
2 TraesCS3B01G034200 chr3B 16324795 16327072 2277 False 292.5 333 81.655500 1281 2363 2 chr3B.!!$F1 1082
3 TraesCS3B01G034200 chr3D 11599869 11603003 3134 False 1381.0 2913 93.316667 1 3339 3 chr3D.!!$F5 3338
4 TraesCS3B01G034200 chr3D 11592750 11593669 919 False 227.0 235 78.990500 1281 2359 2 chr3D.!!$F4 1078
5 TraesCS3B01G034200 chr3A 25388008 25388954 946 True 295.5 326 81.693000 1281 2363 2 chr3A.!!$R1 1082

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
882 883 2.384382 CAAGAATGAAACGGCACACAC 58.616 47.619 0.0 0.0 0.0 3.82 F
1073 1074 0.246086 GCAAATCCCGGCATGTGAAA 59.754 50.000 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 3627 0.673333 ATGGCGCGTTCATGTTGAGA 60.673 50.0 8.43 0.00 0.0 3.27 R
2566 4074 0.811616 CCTCTAGATGCCGGCACAAC 60.812 60.0 35.50 25.14 0.0 3.32 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
144 145 6.939132 ATTTGAAGTGAGAGCCATCATAAG 57.061 37.500 0.00 0.00 0.00 1.73
149 150 6.942005 TGAAGTGAGAGCCATCATAAGAAAAA 59.058 34.615 0.00 0.00 0.00 1.94
150 151 6.998968 AGTGAGAGCCATCATAAGAAAAAG 57.001 37.500 0.00 0.00 0.00 2.27
341 342 8.463930 AGGTGAACTCAATGAAATTAGTCAAA 57.536 30.769 0.00 0.00 32.46 2.69
412 413 9.549078 TTATATGCACTACATTATGAAACCGAA 57.451 29.630 0.00 0.00 40.38 4.30
413 414 6.942532 ATGCACTACATTATGAAACCGAAT 57.057 33.333 0.00 0.00 34.40 3.34
430 431 6.519679 ACCGAATGGAGTTTAATTTAACCC 57.480 37.500 3.79 5.96 39.21 4.11
882 883 2.384382 CAAGAATGAAACGGCACACAC 58.616 47.619 0.00 0.00 0.00 3.82
1053 1054 2.685017 ACCTCGCCATGCTCTCCA 60.685 61.111 0.00 0.00 0.00 3.86
1064 1065 1.821332 GCTCTCCAGCAAATCCCGG 60.821 63.158 0.00 0.00 46.06 5.73
1073 1074 0.246086 GCAAATCCCGGCATGTGAAA 59.754 50.000 0.00 0.00 0.00 2.69
1085 1086 1.126846 CATGTGAAAGTTCTCGCCGTC 59.873 52.381 0.00 0.00 0.00 4.79
1088 1089 1.292541 GAAAGTTCTCGCCGTCCCT 59.707 57.895 0.00 0.00 0.00 4.20
1188 1189 5.678142 TCCCATCCATTGGTATTTGGTAT 57.322 39.130 1.86 0.00 44.83 2.73
1189 1190 6.036926 TCCCATCCATTGGTATTTGGTATT 57.963 37.500 1.86 0.00 44.83 1.89
1190 1191 6.074648 TCCCATCCATTGGTATTTGGTATTC 58.925 40.000 1.86 0.00 44.83 1.75
1192 1193 5.245977 CCATCCATTGGTATTTGGTATTCCC 59.754 44.000 1.86 0.00 40.99 3.97
1193 1194 5.742562 TCCATTGGTATTTGGTATTCCCT 57.257 39.130 1.86 0.00 34.48 4.20
1194 1195 5.701224 TCCATTGGTATTTGGTATTCCCTC 58.299 41.667 1.86 0.00 34.48 4.30
1195 1196 4.832823 CCATTGGTATTTGGTATTCCCTCC 59.167 45.833 0.00 0.00 0.00 4.30
1196 1197 3.849563 TGGTATTTGGTATTCCCTCCG 57.150 47.619 0.00 0.00 0.00 4.63
1197 1198 3.116959 TGGTATTTGGTATTCCCTCCGT 58.883 45.455 0.00 0.00 0.00 4.69
1198 1199 3.135167 TGGTATTTGGTATTCCCTCCGTC 59.865 47.826 0.00 0.00 0.00 4.79
1199 1200 3.495629 GGTATTTGGTATTCCCTCCGTCC 60.496 52.174 0.00 0.00 0.00 4.79
1200 1201 0.913924 TTTGGTATTCCCTCCGTCCC 59.086 55.000 0.00 0.00 0.00 4.46
1201 1202 0.252789 TTGGTATTCCCTCCGTCCCA 60.253 55.000 0.00 0.00 0.00 4.37
1203 1204 1.221007 TGGTATTCCCTCCGTCCCATA 59.779 52.381 0.00 0.00 0.00 2.74
1204 1205 1.900486 GGTATTCCCTCCGTCCCATAG 59.100 57.143 0.00 0.00 0.00 2.23
1205 1206 2.606378 GTATTCCCTCCGTCCCATAGT 58.394 52.381 0.00 0.00 0.00 2.12
1206 1207 3.501019 GGTATTCCCTCCGTCCCATAGTA 60.501 52.174 0.00 0.00 0.00 1.82
1207 1208 3.562108 ATTCCCTCCGTCCCATAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
1209 1210 4.474303 TTCCCTCCGTCCCATAGTATAA 57.526 45.455 0.00 0.00 0.00 0.98
1210 1211 4.043608 TCCCTCCGTCCCATAGTATAAG 57.956 50.000 0.00 0.00 0.00 1.73
1211 1212 3.659195 TCCCTCCGTCCCATAGTATAAGA 59.341 47.826 0.00 0.00 0.00 2.10
1212 1213 4.017808 CCCTCCGTCCCATAGTATAAGAG 58.982 52.174 0.00 0.00 0.00 2.85
1213 1214 3.444388 CCTCCGTCCCATAGTATAAGAGC 59.556 52.174 0.00 0.00 0.00 4.09
1214 1215 4.079970 CTCCGTCCCATAGTATAAGAGCA 58.920 47.826 0.00 0.00 0.00 4.26
1216 1217 5.084519 TCCGTCCCATAGTATAAGAGCATT 58.915 41.667 0.00 0.00 0.00 3.56
1217 1218 5.542635 TCCGTCCCATAGTATAAGAGCATTT 59.457 40.000 0.00 0.00 0.00 2.32
1257 1258 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
1258 1259 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
1260 1261 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
1261 1262 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
1262 1263 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
1263 1264 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
1264 1265 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
1265 1266 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1266 1267 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
1267 1268 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
1268 1269 1.526315 TATGGGACGGAGGGAGTAGA 58.474 55.000 0.00 0.00 0.00 2.59
1272 1273 1.688627 GGGACGGAGGGAGTAGAACAT 60.689 57.143 0.00 0.00 0.00 2.71
1391 1403 3.255149 ACGAACTTGACGAGTATGGAGTT 59.745 43.478 0.00 0.00 37.72 3.01
1434 1446 1.810151 CTTACATCCACAACGGTTGGG 59.190 52.381 23.51 20.05 38.61 4.12
1531 1543 0.682532 TGTCTGCAGCTCGAGAGGAT 60.683 55.000 18.75 0.00 0.00 3.24
1565 1577 2.044650 GCTTCAGCATGGCCTCCA 60.045 61.111 3.32 0.00 41.59 3.86
1594 1606 3.737172 GGCAACGCGATGGCACTT 61.737 61.111 32.70 3.93 44.66 3.16
1616 1628 1.623811 TGGAGCTGAACCTCAAGTACC 59.376 52.381 0.00 0.00 33.47 3.34
1645 1657 5.511571 CCTCTACGAGTATGTACACACATG 58.488 45.833 7.10 0.60 45.17 3.21
1941 3433 5.690816 GAGACCGGAAATCTCAAGTTTTTC 58.309 41.667 9.46 0.00 41.95 2.29
1991 3488 3.784701 AGTAACCACACTCTCTATGCG 57.215 47.619 0.00 0.00 0.00 4.73
2048 3545 3.325425 TCGTCAAGGTTAGGATTGTCCAA 59.675 43.478 0.00 0.00 39.61 3.53
2108 3605 1.224069 CGCTGCCGGATCATAAGGTG 61.224 60.000 5.05 0.00 0.00 4.00
2123 3627 7.716799 TCATAAGGTGAAGCAATTGGTATTT 57.283 32.000 11.15 0.00 32.78 1.40
2141 3645 0.882484 TTCTCAACATGAACGCGCCA 60.882 50.000 5.73 4.84 0.00 5.69
2195 3701 4.943093 CACTATTGATCAATCCCACACACA 59.057 41.667 23.95 3.07 32.50 3.72
2389 3897 9.988350 AAGTTATTCTAGTTAATTTCATGTGCG 57.012 29.630 0.00 0.00 0.00 5.34
2400 3908 8.785101 GTTAATTTCATGTGCGTTGTATTGTAG 58.215 33.333 0.00 0.00 0.00 2.74
2429 3937 1.026718 GTTCGCCCCTCTGGATGTTG 61.027 60.000 0.00 0.00 35.39 3.33
2443 3951 8.096414 CCTCTGGATGTTGGTTGATTAAAAATT 58.904 33.333 0.00 0.00 0.00 1.82
2451 3959 9.239002 TGTTGGTTGATTAAAAATTAGTGAACG 57.761 29.630 0.00 0.00 0.00 3.95
2489 3997 7.862512 TGTAATTTACCAAAGTATTACCCCG 57.137 36.000 4.17 0.00 28.88 5.73
2494 4002 4.506937 ACCAAAGTATTACCCCGCAATA 57.493 40.909 0.00 0.00 0.00 1.90
2545 4053 1.966451 GTCTGGGTGCCCTTGTTCG 60.966 63.158 8.91 0.00 36.94 3.95
2591 4099 1.941668 GCCGGCATCTAGAGGTAATGC 60.942 57.143 24.80 6.49 43.95 3.56
2634 4142 2.032030 CCTACACTCCAAAGCAAACACG 60.032 50.000 0.00 0.00 0.00 4.49
2637 4145 1.400142 CACTCCAAAGCAAACACGACA 59.600 47.619 0.00 0.00 0.00 4.35
2643 4151 3.440173 CCAAAGCAAACACGACATATCCT 59.560 43.478 0.00 0.00 0.00 3.24
2673 4181 6.208599 TCTCCCATATCTTTCAAACCAAACAC 59.791 38.462 0.00 0.00 0.00 3.32
2675 4183 6.496565 TCCCATATCTTTCAAACCAAACACAT 59.503 34.615 0.00 0.00 0.00 3.21
2686 4194 5.456921 AACCAAACACATGATATCCTCCT 57.543 39.130 0.00 0.00 0.00 3.69
2687 4195 4.785301 ACCAAACACATGATATCCTCCTG 58.215 43.478 0.00 0.00 0.00 3.86
2695 4203 8.455903 ACACATGATATCCTCCTGTATTTTTG 57.544 34.615 0.00 0.00 31.76 2.44
2696 4204 8.274322 ACACATGATATCCTCCTGTATTTTTGA 58.726 33.333 0.00 0.00 31.76 2.69
2697 4205 9.293404 CACATGATATCCTCCTGTATTTTTGAT 57.707 33.333 0.00 0.00 31.76 2.57
2731 4239 2.509052 TGCAAACGCTATATCGAGCT 57.491 45.000 2.48 0.00 40.51 4.09
2739 4247 7.437912 CAAACGCTATATCGAGCTAATACAAC 58.562 38.462 2.48 0.00 40.51 3.32
2753 4261 2.799126 TACAACCCCAATGAGCGAAT 57.201 45.000 0.00 0.00 0.00 3.34
2755 4263 3.297134 ACAACCCCAATGAGCGAATAT 57.703 42.857 0.00 0.00 0.00 1.28
2758 4266 2.057922 ACCCCAATGAGCGAATATCCT 58.942 47.619 0.00 0.00 0.00 3.24
2765 4273 5.167121 CAATGAGCGAATATCCTACCTCTG 58.833 45.833 0.00 0.00 0.00 3.35
2770 4278 4.772624 AGCGAATATCCTACCTCTGCATAA 59.227 41.667 0.00 0.00 0.00 1.90
2775 4283 8.687242 CGAATATCCTACCTCTGCATAATAAGA 58.313 37.037 0.00 0.00 0.00 2.10
2809 4317 6.435277 ACCAACAAGTCTGATAATGCTTGAAT 59.565 34.615 10.73 0.00 40.30 2.57
2821 4329 3.763097 TGCTTGAATAATGGAGCAACG 57.237 42.857 0.00 0.00 41.72 4.10
2822 4330 3.081061 TGCTTGAATAATGGAGCAACGT 58.919 40.909 0.00 0.00 41.72 3.99
2824 4332 3.731867 GCTTGAATAATGGAGCAACGTGG 60.732 47.826 0.00 0.00 35.29 4.94
2825 4333 3.342377 TGAATAATGGAGCAACGTGGA 57.658 42.857 0.00 0.00 0.00 4.02
2826 4334 3.680490 TGAATAATGGAGCAACGTGGAA 58.320 40.909 0.00 0.00 0.00 3.53
2827 4335 3.689161 TGAATAATGGAGCAACGTGGAAG 59.311 43.478 0.00 0.00 0.00 3.46
2840 4348 4.866508 ACGTGGAAGTTCAAGATCACTA 57.133 40.909 5.01 0.00 0.00 2.74
2844 4352 6.540914 ACGTGGAAGTTCAAGATCACTAAAAA 59.459 34.615 5.01 0.00 0.00 1.94
2861 4372 3.992943 AAAACATCACATCCGTCCCTA 57.007 42.857 0.00 0.00 0.00 3.53
2866 4377 0.396695 TCACATCCGTCCCTAGGTCC 60.397 60.000 8.29 0.00 0.00 4.46
2874 4385 1.280998 CGTCCCTAGGTCCAACCAAAT 59.719 52.381 8.29 0.00 41.95 2.32
2878 4389 5.163280 CGTCCCTAGGTCCAACCAAATATAA 60.163 44.000 8.29 0.00 41.95 0.98
2893 4404 7.892609 ACCAAATATAACCAGACCAAAACTTC 58.107 34.615 0.00 0.00 0.00 3.01
2946 4472 5.220191 CCATGTTTTTATGTCGATTTTGCCG 60.220 40.000 0.00 0.00 0.00 5.69
2996 4522 3.560068 ACCTACACAAAGAGCTTGAAACG 59.440 43.478 0.00 0.00 38.50 3.60
3010 4537 8.999431 AGAGCTTGAAACGATATTTTAGAAACA 58.001 29.630 0.00 0.00 0.00 2.83
3058 4585 2.006888 ACCATCGCCATCGTTTTAGTG 58.993 47.619 0.00 0.00 36.96 2.74
3065 4592 2.095415 GCCATCGTTTTAGTGGGTTGTC 60.095 50.000 0.00 0.00 33.58 3.18
3072 4599 4.319477 CGTTTTAGTGGGTTGTCAGTGATG 60.319 45.833 0.00 0.00 0.00 3.07
3127 4654 5.664457 TGGAATCAGTACAATAGACAGCAG 58.336 41.667 0.00 0.00 0.00 4.24
3128 4655 4.509600 GGAATCAGTACAATAGACAGCAGC 59.490 45.833 0.00 0.00 0.00 5.25
3129 4656 3.150848 TCAGTACAATAGACAGCAGCG 57.849 47.619 0.00 0.00 0.00 5.18
3130 4657 2.752903 TCAGTACAATAGACAGCAGCGA 59.247 45.455 0.00 0.00 0.00 4.93
3131 4658 3.111838 CAGTACAATAGACAGCAGCGAG 58.888 50.000 0.00 0.00 0.00 5.03
3132 4659 1.855360 GTACAATAGACAGCAGCGAGC 59.145 52.381 0.00 0.00 46.19 5.03
3250 4777 1.968493 ACCAGTACCGCCGATCAATAT 59.032 47.619 0.00 0.00 0.00 1.28
3302 4829 2.504367 TCTCGAGAAAAAGGGCCAAAG 58.496 47.619 14.01 0.00 0.00 2.77
3303 4830 1.541588 CTCGAGAAAAAGGGCCAAAGG 59.458 52.381 6.58 0.00 0.00 3.11
3333 4860 5.395214 GCCCCATTTCTATTACCAAACAAGG 60.395 44.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 211 9.938280 ATTACAAGTACACTCTGTTATGCTAAA 57.062 29.630 0.00 0.00 0.00 1.85
882 883 3.628942 TGCCCGCCTATATATAGTGTACG 59.371 47.826 16.78 13.87 0.00 3.67
1053 1054 0.611618 TTCACATGCCGGGATTTGCT 60.612 50.000 16.55 0.00 0.00 3.91
1056 1057 1.923356 ACTTTCACATGCCGGGATTT 58.077 45.000 5.36 0.00 0.00 2.17
1064 1065 0.179215 CGGCGAGAACTTTCACATGC 60.179 55.000 0.00 0.00 0.00 4.06
1073 1074 4.070552 GCAGGGACGGCGAGAACT 62.071 66.667 16.62 2.79 41.07 3.01
1088 1089 3.333219 CCTTGGGAGCTGGAGGCA 61.333 66.667 0.00 0.00 44.79 4.75
1118 1119 6.892658 AGTTTTGTATGTTGGCTGATGTTA 57.107 33.333 0.00 0.00 0.00 2.41
1188 1189 4.106825 TCTTATACTATGGGACGGAGGGAA 59.893 45.833 0.00 0.00 0.00 3.97
1189 1190 3.659195 TCTTATACTATGGGACGGAGGGA 59.341 47.826 0.00 0.00 0.00 4.20
1190 1191 4.017808 CTCTTATACTATGGGACGGAGGG 58.982 52.174 0.00 0.00 0.00 4.30
1192 1193 4.079970 TGCTCTTATACTATGGGACGGAG 58.920 47.826 0.00 0.00 0.00 4.63
1193 1194 4.108501 TGCTCTTATACTATGGGACGGA 57.891 45.455 0.00 0.00 0.00 4.69
1194 1195 5.407407 AATGCTCTTATACTATGGGACGG 57.593 43.478 0.00 0.00 0.00 4.79
1195 1196 7.730364 AAAAATGCTCTTATACTATGGGACG 57.270 36.000 0.00 0.00 0.00 4.79
1234 1235 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
1235 1236 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
1236 1237 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
1237 1238 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
1238 1239 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
1239 1240 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
1240 1241 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
1242 1243 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1243 1244 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1244 1245 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1245 1246 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1246 1247 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
1247 1248 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
1248 1249 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
1249 1250 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
1250 1251 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
1251 1252 0.324091 GTTCTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
1252 1253 0.324091 TGTTCTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
1253 1254 1.777941 ATGTTCTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
1254 1255 4.996788 TTAATGTTCTACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
1255 1256 5.209659 AGATTAATGTTCTACTCCCTCCGT 58.790 41.667 0.00 0.00 0.00 4.69
1257 1258 5.302313 ACGAGATTAATGTTCTACTCCCTCC 59.698 44.000 0.00 0.00 0.00 4.30
1258 1259 6.039493 TGACGAGATTAATGTTCTACTCCCTC 59.961 42.308 0.00 0.00 0.00 4.30
1260 1261 6.145338 TGACGAGATTAATGTTCTACTCCC 57.855 41.667 0.00 0.00 0.00 4.30
1261 1262 8.649973 ATTTGACGAGATTAATGTTCTACTCC 57.350 34.615 0.00 0.00 0.00 3.85
1263 1264 9.250624 GCTATTTGACGAGATTAATGTTCTACT 57.749 33.333 0.00 0.00 0.00 2.57
1264 1265 9.250624 AGCTATTTGACGAGATTAATGTTCTAC 57.749 33.333 0.00 0.00 0.00 2.59
1265 1266 9.817809 AAGCTATTTGACGAGATTAATGTTCTA 57.182 29.630 0.00 0.00 0.00 2.10
1266 1267 8.723942 AAGCTATTTGACGAGATTAATGTTCT 57.276 30.769 0.00 0.00 0.00 3.01
1267 1268 8.604035 TGAAGCTATTTGACGAGATTAATGTTC 58.396 33.333 0.00 0.00 0.00 3.18
1268 1269 8.492673 TGAAGCTATTTGACGAGATTAATGTT 57.507 30.769 0.00 0.00 0.00 2.71
1321 1333 4.689345 CGAAGAACTTGTCCGTCCTAATTT 59.311 41.667 0.00 0.00 0.00 1.82
1367 1379 3.829948 TCCATACTCGTCAAGTTCGTTC 58.170 45.455 0.00 0.00 39.55 3.95
1391 1403 4.681942 GCAACATAAATGGCGTTGTTAACA 59.318 37.500 3.59 3.59 41.60 2.41
1434 1446 5.294060 ACTGCAAACAAACATCATTTTGGTC 59.706 36.000 0.00 0.00 40.25 4.02
1531 1543 2.437180 CCAATGCTCGCAGCCAGA 60.437 61.111 0.00 0.00 41.51 3.86
1565 1577 3.124921 GTTGCCGGTGCGTGCTAT 61.125 61.111 1.90 0.00 41.78 2.97
1594 1606 1.722034 ACTTGAGGTTCAGCTCCAGA 58.278 50.000 12.68 0.00 0.00 3.86
1846 1859 3.567478 AGCTTTGTCCTCAGTCAAACT 57.433 42.857 0.00 0.00 29.74 2.66
1972 3465 2.194271 GCGCATAGAGAGTGTGGTTAC 58.806 52.381 0.30 0.00 0.00 2.50
2048 3545 1.692519 AGTATCCTCGCGCCCTTTATT 59.307 47.619 0.00 0.00 0.00 1.40
2108 3605 7.315142 TCATGTTGAGAAATACCAATTGCTTC 58.685 34.615 0.00 0.31 30.42 3.86
2123 3627 0.673333 ATGGCGCGTTCATGTTGAGA 60.673 50.000 8.43 0.00 0.00 3.27
2171 3675 3.947196 TGTGTGGGATTGATCAATAGTGC 59.053 43.478 20.75 11.99 0.00 4.40
2195 3701 2.836636 TAGAGGAGACCAGCATGAGT 57.163 50.000 0.00 0.00 39.69 3.41
2246 3754 0.976641 TCCTTGTTGAGGCAGACGAT 59.023 50.000 0.00 0.00 45.87 3.73
2365 3873 9.769093 AACGCACATGAAATTAACTAGAATAAC 57.231 29.630 0.00 0.00 0.00 1.89
2371 3879 8.998989 CAATACAACGCACATGAAATTAACTAG 58.001 33.333 0.00 0.00 0.00 2.57
2372 3880 8.508062 ACAATACAACGCACATGAAATTAACTA 58.492 29.630 0.00 0.00 0.00 2.24
2382 3890 8.667987 ATTTTAACTACAATACAACGCACATG 57.332 30.769 0.00 0.00 0.00 3.21
2400 3908 4.036380 CCAGAGGGGCGAACATATTTTAAC 59.964 45.833 0.00 0.00 0.00 2.01
2517 4025 1.774856 GGCACCCAGACACCCTATTAT 59.225 52.381 0.00 0.00 0.00 1.28
2518 4026 1.209621 GGCACCCAGACACCCTATTA 58.790 55.000 0.00 0.00 0.00 0.98
2566 4074 0.811616 CCTCTAGATGCCGGCACAAC 60.812 60.000 35.50 25.14 0.00 3.32
2591 4099 5.006386 GGAGGGAGCCAACAAATATATGAG 58.994 45.833 0.00 0.00 0.00 2.90
2634 4142 9.432982 AAGATATGGGAGATAGAAGGATATGTC 57.567 37.037 0.00 0.00 0.00 3.06
2643 4151 8.101309 TGGTTTGAAAGATATGGGAGATAGAA 57.899 34.615 0.00 0.00 0.00 2.10
2681 4189 7.630242 TGCTCTTTATCAAAAATACAGGAGG 57.370 36.000 0.00 0.00 0.00 4.30
2695 4203 6.722298 GCGTTTGCATGAAAATGCTCTTTATC 60.722 38.462 28.99 4.74 44.86 1.75
2696 4204 5.062558 GCGTTTGCATGAAAATGCTCTTTAT 59.937 36.000 28.99 0.00 44.86 1.40
2697 4205 4.385447 GCGTTTGCATGAAAATGCTCTTTA 59.615 37.500 28.99 0.00 44.86 1.85
2698 4206 3.184986 GCGTTTGCATGAAAATGCTCTTT 59.815 39.130 28.99 0.00 44.86 2.52
2699 4207 2.733026 GCGTTTGCATGAAAATGCTCTT 59.267 40.909 28.99 0.00 44.86 2.85
2700 4208 2.331194 GCGTTTGCATGAAAATGCTCT 58.669 42.857 28.99 0.00 44.86 4.09
2720 4228 6.525578 TGGGGTTGTATTAGCTCGATATAG 57.474 41.667 0.00 0.00 0.00 1.31
2721 4229 6.921486 TTGGGGTTGTATTAGCTCGATATA 57.079 37.500 0.00 0.00 0.00 0.86
2731 4239 3.916359 TCGCTCATTGGGGTTGTATTA 57.084 42.857 0.00 0.00 0.00 0.98
2739 4247 2.867109 AGGATATTCGCTCATTGGGG 57.133 50.000 0.00 0.00 0.00 4.96
2770 4278 5.560724 ACTTGTTGGTAGTGTGCATCTTAT 58.439 37.500 0.00 0.00 0.00 1.73
2775 4283 3.141398 CAGACTTGTTGGTAGTGTGCAT 58.859 45.455 0.00 0.00 31.37 3.96
2783 4291 6.472016 TCAAGCATTATCAGACTTGTTGGTA 58.528 36.000 0.00 0.00 40.29 3.25
2809 4317 2.851263 ACTTCCACGTTGCTCCATTA 57.149 45.000 0.00 0.00 0.00 1.90
2821 4329 7.703328 TGTTTTTAGTGATCTTGAACTTCCAC 58.297 34.615 0.00 0.00 0.00 4.02
2822 4330 7.873719 TGTTTTTAGTGATCTTGAACTTCCA 57.126 32.000 0.00 0.00 0.00 3.53
2824 4332 9.387123 GTGATGTTTTTAGTGATCTTGAACTTC 57.613 33.333 0.00 0.00 0.00 3.01
2825 4333 8.902806 TGTGATGTTTTTAGTGATCTTGAACTT 58.097 29.630 0.00 0.00 0.00 2.66
2826 4334 8.450578 TGTGATGTTTTTAGTGATCTTGAACT 57.549 30.769 0.00 0.00 0.00 3.01
2827 4335 9.334693 GATGTGATGTTTTTAGTGATCTTGAAC 57.665 33.333 0.00 0.00 0.00 3.18
2840 4348 3.154827 AGGGACGGATGTGATGTTTTT 57.845 42.857 0.00 0.00 0.00 1.94
2844 4352 1.343075 ACCTAGGGACGGATGTGATGT 60.343 52.381 14.81 0.00 0.00 3.06
2861 4372 5.506708 GTCTGGTTATATTTGGTTGGACCT 58.493 41.667 0.00 0.00 39.58 3.85
2866 4377 7.666623 AGTTTTGGTCTGGTTATATTTGGTTG 58.333 34.615 0.00 0.00 0.00 3.77
2874 4385 7.007723 ACAATGGAAGTTTTGGTCTGGTTATA 58.992 34.615 0.00 0.00 0.00 0.98
2878 4389 3.642141 ACAATGGAAGTTTTGGTCTGGT 58.358 40.909 0.00 0.00 0.00 4.00
2911 4422 7.307632 CGACATAAAAACATGGCCATTTTTCAA 60.308 33.333 26.04 18.31 38.58 2.69
2979 4505 7.858052 AAAATATCGTTTCAAGCTCTTTGTG 57.142 32.000 0.00 0.00 38.01 3.33
3010 4537 7.334421 GTCCATGTCAAAGTTGTACATGTATCT 59.666 37.037 20.85 5.70 40.71 1.98
3043 4570 1.135803 CAACCCACTAAAACGATGGCG 60.136 52.381 0.00 0.00 44.79 5.69
3046 4573 3.813166 ACTGACAACCCACTAAAACGATG 59.187 43.478 0.00 0.00 0.00 3.84
3058 4585 3.120321 TGTACACATCACTGACAACCC 57.880 47.619 0.00 0.00 0.00 4.11
3065 4592 6.915544 ATGCTAGATTTGTACACATCACTG 57.084 37.500 21.04 12.43 0.00 3.66
3109 4636 2.752903 TCGCTGCTGTCTATTGTACTGA 59.247 45.455 0.00 0.00 0.00 3.41
3122 4649 1.136141 CACTTAACTTGCTCGCTGCTG 60.136 52.381 0.00 0.00 43.37 4.41
3124 4651 1.148310 TCACTTAACTTGCTCGCTGC 58.852 50.000 0.00 0.00 43.25 5.25
3125 4652 2.349886 GGATCACTTAACTTGCTCGCTG 59.650 50.000 0.00 0.00 0.00 5.18
3127 4654 2.346803 TGGATCACTTAACTTGCTCGC 58.653 47.619 0.00 0.00 0.00 5.03
3128 4655 3.242543 GCATGGATCACTTAACTTGCTCG 60.243 47.826 0.00 0.00 33.02 5.03
3129 4656 3.691118 TGCATGGATCACTTAACTTGCTC 59.309 43.478 0.00 0.00 35.70 4.26
3130 4657 3.689347 TGCATGGATCACTTAACTTGCT 58.311 40.909 0.00 0.00 35.70 3.91
3131 4658 4.096833 TCATGCATGGATCACTTAACTTGC 59.903 41.667 25.97 0.00 35.38 4.01
3132 4659 5.823209 TCATGCATGGATCACTTAACTTG 57.177 39.130 25.97 0.00 0.00 3.16
3133 4660 6.839124 TTTCATGCATGGATCACTTAACTT 57.161 33.333 25.97 0.00 0.00 2.66
3303 4830 0.105504 AATAGAAATGGGGCTGGGGC 60.106 55.000 0.00 0.00 37.82 5.80


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

AutoCloner maintained by Alex Coulton.