Multiple sequence alignment - TraesCS7B01G085100

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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 TraesCS7B01G085100 chr7B 100.000 3133 0 0 1 3133 97191168 97194300 0.000000e+00 5786.0
1 TraesCS7B01G085100 chr7A 92.208 3157 177 34 22 3133 134490246 134493378 0.000000e+00 4403.0
2 TraesCS7B01G085100 chr7D 93.193 2703 118 23 450 3133 135356811 135359466 0.000000e+00 3912.0
3 TraesCS7B01G085100 chr7D 86.635 419 44 9 23 435 135356152 135356564 1.320000e-123 453.0
4 TraesCS7B01G085100 chr7D 91.935 186 10 5 984 1165 135356809 135356625 4.010000e-64 255.0
5 TraesCS7B01G085100 chr6B 75.545 826 157 40 997 1794 613610169 613610977 6.390000e-97 364.0
6 TraesCS7B01G085100 chr6B 78.351 388 75 7 1415 1797 614127914 614128297 3.120000e-60 243.0
7 TraesCS7B01G085100 chr6D 77.325 613 100 25 1217 1797 409288156 409288761 3.010000e-85 326.0
8 TraesCS7B01G085100 chr6D 78.406 389 75 6 1414 1797 408945983 408946367 8.680000e-61 244.0
9 TraesCS7B01G085100 chr6A 79.177 389 72 7 1414 1797 554716443 554716827 8.620000e-66 261.0
10 TraesCS7B01G085100 chr3A 81.102 127 20 4 1228 1352 330698437 330698561 7.150000e-17 99.0
11 TraesCS7B01G085100 chr1D 90.000 70 1 1 741 810 118475725 118475662 5.570000e-13 86.1
12 TraesCS7B01G085100 chr1B 77.966 118 26 0 1419 1536 615744798 615744681 1.210000e-09 75.0
13 TraesCS7B01G085100 chr1A 81.609 87 16 0 1440 1526 545009086 545009000 4.330000e-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 TraesCS7B01G085100 chr7B 97191168 97194300 3132 False 5786.0 5786 100.000 1 3133 1 chr7B.!!$F1 3132
1 TraesCS7B01G085100 chr7A 134490246 134493378 3132 False 4403.0 4403 92.208 22 3133 1 chr7A.!!$F1 3111
2 TraesCS7B01G085100 chr7D 135356152 135359466 3314 False 2182.5 3912 89.914 23 3133 2 chr7D.!!$F1 3110
3 TraesCS7B01G085100 chr6B 613610169 613610977 808 False 364.0 364 75.545 997 1794 1 chr6B.!!$F1 797
4 TraesCS7B01G085100 chr6D 409288156 409288761 605 False 326.0 326 77.325 1217 1797 1 chr6D.!!$F2 580

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
185 189 0.038159 GCCACAGCGTCAGACTAGTT 60.038 55.0 0.00 0.00 0.0 2.24 F
1137 1380 0.250727 TGCCTCAACTTGCTGGTACC 60.251 55.0 4.43 4.43 0.0 3.34 F
1844 2166 0.880718 GCATAGACTTAGCCGGGCAC 60.881 60.0 23.09 6.91 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2256 0.036952 CTCCCTCATCGCAGTGTTGT 60.037 55.000 0.00 0.0 0.00 3.32 R
2003 2325 0.322277 AAGCTGCCATGTCAGTGAGG 60.322 55.000 5.53 0.0 36.49 3.86 R
2959 3287 5.709966 GGTTGCTACCTCTTTAAAACATGG 58.290 41.667 10.33 0.0 41.53 3.66 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
36 37 2.464682 GCAAACTCTGAGCGAGCAT 58.535 52.632 4.19 0.00 43.85 3.79
44 45 1.066645 TCTGAGCGAGCATGTGACATT 60.067 47.619 0.00 0.00 0.00 2.71
45 46 1.736126 CTGAGCGAGCATGTGACATTT 59.264 47.619 0.00 0.00 0.00 2.32
47 48 2.095617 TGAGCGAGCATGTGACATTTTG 60.096 45.455 0.00 0.00 0.00 2.44
48 49 2.153645 AGCGAGCATGTGACATTTTGA 58.846 42.857 0.00 0.00 0.00 2.69
51 52 2.485426 CGAGCATGTGACATTTTGAGGT 59.515 45.455 0.00 0.00 0.00 3.85
52 53 3.058016 CGAGCATGTGACATTTTGAGGTT 60.058 43.478 0.00 0.00 0.00 3.50
53 54 4.479619 GAGCATGTGACATTTTGAGGTTC 58.520 43.478 0.00 0.00 0.00 3.62
54 55 3.890756 AGCATGTGACATTTTGAGGTTCA 59.109 39.130 0.00 0.00 0.00 3.18
56 57 4.549458 CATGTGACATTTTGAGGTTCACC 58.451 43.478 0.00 0.00 0.00 4.02
57 58 3.625853 TGTGACATTTTGAGGTTCACCA 58.374 40.909 0.00 0.00 38.89 4.17
62 66 6.538381 GTGACATTTTGAGGTTCACCATTTTT 59.462 34.615 0.00 0.00 38.89 1.94
72 76 5.897250 AGGTTCACCATTTTTAGAACTTGGT 59.103 36.000 0.00 0.00 41.27 3.67
91 95 1.110442 TGTTGTCCAGCAAACCTTGG 58.890 50.000 0.00 0.00 39.03 3.61
121 125 1.490490 TGTCCAATCCTGTATCCTGCC 59.510 52.381 0.00 0.00 0.00 4.85
124 128 1.349026 CCAATCCTGTATCCTGCCGAT 59.651 52.381 0.00 0.00 34.73 4.18
156 160 6.946340 TGTAGCTTCACTGAATAATCTGGAA 58.054 36.000 0.00 0.00 0.00 3.53
171 175 2.169561 TCTGGAAGCATTATACGCCACA 59.830 45.455 0.00 0.00 0.00 4.17
172 176 2.545526 CTGGAAGCATTATACGCCACAG 59.454 50.000 0.00 0.00 0.00 3.66
185 189 0.038159 GCCACAGCGTCAGACTAGTT 60.038 55.000 0.00 0.00 0.00 2.24
201 205 0.671781 AGTTGCTAGCAGCCACGAAG 60.672 55.000 25.76 0.00 41.27 3.79
210 214 1.308998 CAGCCACGAAGTTTCTTGGT 58.691 50.000 15.99 2.67 45.47 3.67
214 218 2.876550 GCCACGAAGTTTCTTGGTTACT 59.123 45.455 15.99 0.00 45.47 2.24
239 244 5.121611 TGTTATATTCTGTGCCTTGAACACG 59.878 40.000 0.00 0.00 41.03 4.49
271 276 6.936335 TCACTTGCTTCATTCAGAGTTTCATA 59.064 34.615 0.00 0.00 0.00 2.15
272 277 7.020010 CACTTGCTTCATTCAGAGTTTCATAC 58.980 38.462 0.00 0.00 0.00 2.39
273 278 6.712095 ACTTGCTTCATTCAGAGTTTCATACA 59.288 34.615 0.00 0.00 0.00 2.29
280 285 7.453393 TCATTCAGAGTTTCATACACCTTTCT 58.547 34.615 0.00 0.00 0.00 2.52
307 313 2.360165 CCCTATCCTGTGCAATTTCAGC 59.640 50.000 0.00 0.00 0.00 4.26
325 333 2.158449 CAGCAAGGAAACAGAGTAAGCG 59.842 50.000 0.00 0.00 0.00 4.68
330 338 5.753921 GCAAGGAAACAGAGTAAGCGTATAT 59.246 40.000 0.00 0.00 0.00 0.86
333 341 5.047847 GGAAACAGAGTAAGCGTATATGCA 58.952 41.667 18.91 0.00 37.31 3.96
337 345 5.043903 ACAGAGTAAGCGTATATGCACAAG 58.956 41.667 18.91 6.10 37.31 3.16
340 348 5.980116 AGAGTAAGCGTATATGCACAAGAAG 59.020 40.000 18.91 0.00 37.31 2.85
341 349 3.951979 AAGCGTATATGCACAAGAAGC 57.048 42.857 18.91 0.00 37.31 3.86
346 354 3.485051 CGTATATGCACAAGAAGCGCAAA 60.485 43.478 11.47 0.00 39.01 3.68
347 355 3.574284 ATATGCACAAGAAGCGCAAAA 57.426 38.095 11.47 0.00 39.01 2.44
366 374 6.074409 CGCAAAATTTCAAGTCAAAGCATACA 60.074 34.615 0.00 0.00 0.00 2.29
368 376 7.285788 CAAAATTTCAAGTCAAAGCATACAGC 58.714 34.615 0.00 0.00 46.19 4.40
397 405 3.306156 GCTCTATCATCCGGTTACCTTCC 60.306 52.174 0.00 0.00 0.00 3.46
399 407 1.492764 ATCATCCGGTTACCTTCCGT 58.507 50.000 0.00 0.00 45.63 4.69
411 419 5.474532 GGTTACCTTCCGTTTCCATAAAACT 59.525 40.000 0.00 0.00 44.25 2.66
434 442 3.795688 ACAGGCTTCAGATGAAAAGGA 57.204 42.857 0.00 0.00 33.07 3.36
435 443 4.104383 ACAGGCTTCAGATGAAAAGGAA 57.896 40.909 0.00 0.00 33.07 3.36
436 444 4.473444 ACAGGCTTCAGATGAAAAGGAAA 58.527 39.130 0.00 0.00 33.07 3.13
679 922 1.956477 GTCAACAGAACCAAGTGCCAT 59.044 47.619 0.00 0.00 0.00 4.40
681 924 3.568007 GTCAACAGAACCAAGTGCCATAA 59.432 43.478 0.00 0.00 0.00 1.90
682 925 4.218417 GTCAACAGAACCAAGTGCCATAAT 59.782 41.667 0.00 0.00 0.00 1.28
684 927 5.304101 TCAACAGAACCAAGTGCCATAATTT 59.696 36.000 0.00 0.00 0.00 1.82
685 928 5.806654 ACAGAACCAAGTGCCATAATTTT 57.193 34.783 0.00 0.00 0.00 1.82
721 964 2.227036 AGACAAGACCCCAGCCCAG 61.227 63.158 0.00 0.00 0.00 4.45
771 1014 3.808728 GCAACAAGCTATCTACCATGGA 58.191 45.455 21.47 0.67 41.15 3.41
847 1090 2.778299 TGTCTAGCATGGTGTTGTTCC 58.222 47.619 7.89 0.00 0.00 3.62
853 1096 2.906389 AGCATGGTGTTGTTCCTCTAGA 59.094 45.455 0.00 0.00 0.00 2.43
922 1165 1.548582 CCAGCAATCCCAAAGACAGGT 60.549 52.381 0.00 0.00 0.00 4.00
925 1168 1.737793 GCAATCCCAAAGACAGGTACG 59.262 52.381 0.00 0.00 0.00 3.67
944 1187 1.276622 GCTAAGGTGTGAAGGGGAGA 58.723 55.000 0.00 0.00 0.00 3.71
947 1190 1.059913 AAGGTGTGAAGGGGAGACAG 58.940 55.000 0.00 0.00 0.00 3.51
951 1194 1.902508 GTGTGAAGGGGAGACAGATCA 59.097 52.381 0.00 0.00 0.00 2.92
958 1201 2.035632 GGGGAGACAGATCATCTCGTT 58.964 52.381 16.58 0.00 43.07 3.85
965 1208 0.753262 AGATCATCTCGTTTCCCCCG 59.247 55.000 0.00 0.00 0.00 5.73
970 1213 0.908180 ATCTCGTTTCCCCCGTCCTT 60.908 55.000 0.00 0.00 0.00 3.36
974 1217 4.024545 TTTCCCCCGTCCTTCCGC 62.025 66.667 0.00 0.00 0.00 5.54
990 1233 2.902608 TCCGCCATTGACCTATCCTAT 58.097 47.619 0.00 0.00 0.00 2.57
1056 1299 2.286197 AAGGGCCCCTGGACTACC 60.286 66.667 21.43 0.00 32.13 3.18
1059 1302 3.155167 GGCCCCTGGACTACCGAG 61.155 72.222 0.00 0.00 39.42 4.63
1079 1322 3.030291 AGGAAGACGAGAAGCTCATGAT 58.970 45.455 0.00 0.00 0.00 2.45
1137 1380 0.250727 TGCCTCAACTTGCTGGTACC 60.251 55.000 4.43 4.43 0.00 3.34
1141 1384 1.880027 CTCAACTTGCTGGTACCCAAC 59.120 52.381 10.07 0.00 30.80 3.77
1142 1385 1.213182 TCAACTTGCTGGTACCCAACA 59.787 47.619 10.07 1.60 30.80 3.33
1143 1386 2.158534 TCAACTTGCTGGTACCCAACAT 60.159 45.455 10.07 0.00 29.25 2.71
1144 1387 3.073209 TCAACTTGCTGGTACCCAACATA 59.927 43.478 10.07 0.00 29.25 2.29
1145 1388 4.016444 CAACTTGCTGGTACCCAACATAT 58.984 43.478 10.07 0.00 29.25 1.78
1146 1389 3.620488 ACTTGCTGGTACCCAACATATG 58.380 45.455 10.07 0.00 29.25 1.78
1187 1475 2.165030 CCTCATGCACATTTCCTTCACC 59.835 50.000 0.00 0.00 0.00 4.02
1188 1476 2.821378 CTCATGCACATTTCCTTCACCA 59.179 45.455 0.00 0.00 0.00 4.17
1192 1480 3.295093 TGCACATTTCCTTCACCAAGAA 58.705 40.909 0.00 0.00 34.41 2.52
1193 1481 3.896888 TGCACATTTCCTTCACCAAGAAT 59.103 39.130 0.00 0.00 35.25 2.40
1194 1482 4.240096 GCACATTTCCTTCACCAAGAATG 58.760 43.478 0.00 0.00 35.25 2.67
1195 1483 4.262164 GCACATTTCCTTCACCAAGAATGT 60.262 41.667 0.00 0.00 37.46 2.71
1196 1484 5.739935 GCACATTTCCTTCACCAAGAATGTT 60.740 40.000 0.00 0.00 35.99 2.71
1197 1485 5.693104 CACATTTCCTTCACCAAGAATGTTG 59.307 40.000 0.00 0.00 35.99 3.33
1198 1486 5.363580 ACATTTCCTTCACCAAGAATGTTGT 59.636 36.000 0.00 0.00 35.20 3.32
1199 1487 5.930837 TTTCCTTCACCAAGAATGTTGTT 57.069 34.783 0.00 0.00 35.25 2.83
1200 1488 5.514274 TTCCTTCACCAAGAATGTTGTTC 57.486 39.130 0.00 0.00 35.25 3.18
1212 1501 8.090214 CCAAGAATGTTGTTCACCATATTTTCT 58.910 33.333 0.00 0.00 0.00 2.52
1328 1617 1.210478 GAGCAAACCATCCTCCAGCTA 59.790 52.381 0.00 0.00 0.00 3.32
1363 1652 3.676646 GGCAACAAGTACTAACTACACCG 59.323 47.826 0.00 0.00 33.75 4.94
1379 1673 5.983720 ACTACACCGACATTCTATTGCATAC 59.016 40.000 0.00 0.00 0.00 2.39
1386 1680 6.090493 CCGACATTCTATTGCATACATCTCAG 59.910 42.308 0.00 0.00 0.00 3.35
1393 1687 9.788889 TTCTATTGCATACATCTCAGATGAATT 57.211 29.630 22.08 1.34 0.00 2.17
1595 1914 2.665185 GCACTCGCCAACCTTCGT 60.665 61.111 0.00 0.00 0.00 3.85
1688 2010 1.810755 CTCCAGTACGTGCAGTCACTA 59.189 52.381 6.38 0.00 40.99 2.74
1807 2129 1.135460 GCAGATGCTTTCTCCAAGTGC 60.135 52.381 0.00 0.00 38.21 4.40
1844 2166 0.880718 GCATAGACTTAGCCGGGCAC 60.881 60.000 23.09 6.91 0.00 5.01
1855 2177 2.126307 CGGGCACGTGTCTCAGAG 60.126 66.667 21.13 3.08 34.81 3.35
1927 2249 5.629020 CGGGTTCACATAACAATGTTGAAAG 59.371 40.000 9.15 0.00 31.37 2.62
1934 2256 6.696583 CACATAACAATGTTGAAAGCAGTGAA 59.303 34.615 9.15 0.00 35.75 3.18
1937 2259 5.070770 ACAATGTTGAAAGCAGTGAACAA 57.929 34.783 0.00 0.00 35.75 2.83
1975 2297 1.339291 GAACAGCAGCAAGAAAAGGCT 59.661 47.619 0.00 0.00 42.06 4.58
2003 2325 1.423921 TCTGAAAACTCCCTTCCACCC 59.576 52.381 0.00 0.00 0.00 4.61
2084 2406 0.606604 TCAGTAGTCCGTTTCCCAGC 59.393 55.000 0.00 0.00 0.00 4.85
2099 2421 0.462759 CCAGCTGGTCGGAAATCCTC 60.463 60.000 25.53 0.00 0.00 3.71
2171 2493 3.889815 AGCTTGAATTGCATACTAGCCA 58.110 40.909 14.05 0.00 34.19 4.75
2256 2580 7.378181 AGGTTTATTTTTCATGCACTTGTAGG 58.622 34.615 0.00 0.00 0.00 3.18
2381 2705 5.234752 GGTTGTTCTTCCTTTCTCTCTCTC 58.765 45.833 0.00 0.00 0.00 3.20
2382 2706 5.011635 GGTTGTTCTTCCTTTCTCTCTCTCT 59.988 44.000 0.00 0.00 0.00 3.10
2407 2731 5.567823 GCCACTATATCTTAGTTCCTGGAGC 60.568 48.000 1.81 1.81 0.00 4.70
2478 2802 4.692625 ACAAATGGTGCGATGATATAGCTC 59.307 41.667 0.00 0.00 0.00 4.09
2482 2806 2.181205 GTGCGATGATATAGCTCGAGC 58.819 52.381 30.01 30.01 42.49 5.03
2501 2825 1.333702 GCGACAACATGCGTGAAAGAA 60.334 47.619 14.17 0.00 0.00 2.52
2502 2826 2.852901 GCGACAACATGCGTGAAAGAAA 60.853 45.455 14.17 0.00 0.00 2.52
2534 2858 1.078848 CTGCTACCACACCAGAGGC 60.079 63.158 0.00 0.00 0.00 4.70
2554 2880 9.365906 CAGAGGCCATCTATCATATAGTAGAAT 57.634 37.037 5.01 0.00 36.10 2.40
2959 3287 4.083271 CCTCCAAGAAATTGACTCCGAAAC 60.083 45.833 0.00 0.00 0.00 2.78
2996 3324 4.034048 GGTAGCAACCTAACATCAACATCG 59.966 45.833 0.00 0.00 43.08 3.84
2998 3326 4.517285 AGCAACCTAACATCAACATCGAT 58.483 39.130 0.00 0.00 0.00 3.59
3104 3432 6.266558 ACCAATTACTCCACTTGCAAAATACA 59.733 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.632251 TCAGAGTTTGCGCGGATATAAAAA 59.368 37.500 8.83 0.00 0.00 1.94
6 7 4.185394 TCAGAGTTTGCGCGGATATAAAA 58.815 39.130 8.83 0.00 0.00 1.52
7 8 3.787785 TCAGAGTTTGCGCGGATATAAA 58.212 40.909 8.83 0.00 0.00 1.40
8 9 3.381045 CTCAGAGTTTGCGCGGATATAA 58.619 45.455 8.83 0.00 0.00 0.98
9 10 2.862530 GCTCAGAGTTTGCGCGGATATA 60.863 50.000 8.83 0.00 0.00 0.86
10 11 1.858091 CTCAGAGTTTGCGCGGATAT 58.142 50.000 8.83 0.00 0.00 1.63
11 12 0.806102 GCTCAGAGTTTGCGCGGATA 60.806 55.000 8.83 0.00 0.00 2.59
12 13 2.103042 GCTCAGAGTTTGCGCGGAT 61.103 57.895 8.83 0.00 0.00 4.18
13 14 2.738521 GCTCAGAGTTTGCGCGGA 60.739 61.111 8.83 0.00 0.00 5.54
26 27 1.812235 AAATGTCACATGCTCGCTCA 58.188 45.000 0.00 0.00 0.00 4.26
33 34 3.983344 GTGAACCTCAAAATGTCACATGC 59.017 43.478 0.00 0.00 0.00 4.06
36 37 3.625853 TGGTGAACCTCAAAATGTCACA 58.374 40.909 0.37 0.00 36.82 3.58
44 45 7.654022 AGTTCTAAAAATGGTGAACCTCAAA 57.346 32.000 0.37 0.00 39.45 2.69
45 46 7.417342 CCAAGTTCTAAAAATGGTGAACCTCAA 60.417 37.037 0.37 0.00 39.45 3.02
47 48 6.040504 ACCAAGTTCTAAAAATGGTGAACCTC 59.959 38.462 0.37 0.00 42.57 3.85
48 49 5.897250 ACCAAGTTCTAAAAATGGTGAACCT 59.103 36.000 0.37 0.00 42.57 3.50
54 55 6.406512 GGACAACACCAAGTTCTAAAAATGGT 60.407 38.462 0.00 0.00 44.95 3.55
56 57 6.568869 TGGACAACACCAAGTTCTAAAAATG 58.431 36.000 0.00 0.00 38.74 2.32
57 58 6.682861 GCTGGACAACACCAAGTTCTAAAAAT 60.683 38.462 0.00 0.00 38.74 1.82
62 66 2.171659 TGCTGGACAACACCAAGTTCTA 59.828 45.455 0.00 0.00 38.74 2.10
72 76 1.110442 CCAAGGTTTGCTGGACAACA 58.890 50.000 0.00 0.00 38.23 3.33
91 95 2.227388 CAGGATTGGACAAACAGCTGAC 59.773 50.000 23.35 5.94 0.00 3.51
121 125 5.008118 TCAGTGAAGCTACATCAGAGTATCG 59.992 44.000 0.00 0.00 42.67 2.92
124 128 6.782082 ATTCAGTGAAGCTACATCAGAGTA 57.218 37.500 11.91 0.00 0.00 2.59
171 175 1.133407 GCTAGCAACTAGTCTGACGCT 59.867 52.381 10.63 11.02 36.53 5.07
172 176 1.135373 TGCTAGCAACTAGTCTGACGC 60.135 52.381 16.84 0.00 36.53 5.19
175 179 1.478510 GGCTGCTAGCAACTAGTCTGA 59.521 52.381 19.86 0.00 44.75 3.27
179 183 0.108615 CGTGGCTGCTAGCAACTAGT 60.109 55.000 19.86 0.00 43.00 2.57
185 189 0.250295 AAACTTCGTGGCTGCTAGCA 60.250 50.000 18.22 18.22 44.75 3.49
210 214 8.726988 GTTCAAGGCACAGAATATAACAAGTAA 58.273 33.333 0.00 0.00 0.00 2.24
214 218 6.348132 CGTGTTCAAGGCACAGAATATAACAA 60.348 38.462 0.00 0.00 36.71 2.83
225 229 0.605319 GGATCCGTGTTCAAGGCACA 60.605 55.000 0.00 0.00 36.71 4.57
239 244 4.012374 TGAATGAAGCAAGTGAAGGATCC 58.988 43.478 2.48 2.48 0.00 3.36
271 276 5.131142 CAGGATAGGGAACATAGAAAGGTGT 59.869 44.000 0.00 0.00 0.00 4.16
272 277 5.131142 ACAGGATAGGGAACATAGAAAGGTG 59.869 44.000 0.00 0.00 0.00 4.00
273 278 5.131142 CACAGGATAGGGAACATAGAAAGGT 59.869 44.000 0.00 0.00 0.00 3.50
280 285 5.387113 AATTGCACAGGATAGGGAACATA 57.613 39.130 0.00 0.00 0.00 2.29
307 313 6.292381 GCATATACGCTTACTCTGTTTCCTTG 60.292 42.308 0.00 0.00 0.00 3.61
333 341 4.432712 ACTTGAAATTTTGCGCTTCTTGT 58.567 34.783 9.73 4.22 0.00 3.16
337 345 5.388225 TTTGACTTGAAATTTTGCGCTTC 57.612 34.783 9.73 3.90 0.00 3.86
340 348 3.001127 TGCTTTGACTTGAAATTTTGCGC 59.999 39.130 0.00 0.00 0.00 6.09
341 349 4.775440 TGCTTTGACTTGAAATTTTGCG 57.225 36.364 0.00 0.00 0.00 4.85
346 354 5.156355 CGCTGTATGCTTTGACTTGAAATT 58.844 37.500 0.00 0.00 40.11 1.82
347 355 4.726416 CGCTGTATGCTTTGACTTGAAAT 58.274 39.130 0.00 0.00 40.11 2.17
369 377 1.342819 ACCGGATGATAGAGCTTCAGC 59.657 52.381 9.46 0.00 42.49 4.26
370 378 3.742433 AACCGGATGATAGAGCTTCAG 57.258 47.619 9.46 0.00 0.00 3.02
372 380 3.574826 AGGTAACCGGATGATAGAGCTTC 59.425 47.826 9.46 0.00 37.17 3.86
399 407 8.325787 TCTGAAGCCTGTATAGTTTTATGGAAA 58.674 33.333 0.00 0.00 0.00 3.13
411 419 6.560003 TCCTTTTCATCTGAAGCCTGTATA 57.440 37.500 0.00 0.00 35.21 1.47
685 928 8.564574 GTCTTGTCTGTGTCCATACAATAAAAA 58.435 33.333 0.00 0.00 37.14 1.94
692 935 2.301870 GGGTCTTGTCTGTGTCCATACA 59.698 50.000 0.00 0.00 0.00 2.29
750 993 3.561725 GTCCATGGTAGATAGCTTGTTGC 59.438 47.826 12.58 0.00 43.29 4.17
766 1009 4.418013 TTGCGTTCACTTTATGTCCATG 57.582 40.909 0.00 0.00 0.00 3.66
767 1010 5.401550 CATTTGCGTTCACTTTATGTCCAT 58.598 37.500 0.00 0.00 0.00 3.41
768 1011 4.793071 CATTTGCGTTCACTTTATGTCCA 58.207 39.130 0.00 0.00 0.00 4.02
769 1012 3.608073 GCATTTGCGTTCACTTTATGTCC 59.392 43.478 0.00 0.00 0.00 4.02
770 1013 4.806056 GCATTTGCGTTCACTTTATGTC 57.194 40.909 0.00 0.00 0.00 3.06
800 1043 6.564709 TCATTCAAGTGGAAAAGACTGATG 57.435 37.500 0.00 0.00 39.39 3.07
847 1090 5.220815 GCTTGCTGATCCATGTTTTCTAGAG 60.221 44.000 0.00 0.00 0.00 2.43
853 1096 2.250031 TGGCTTGCTGATCCATGTTTT 58.750 42.857 0.00 0.00 0.00 2.43
922 1165 0.899720 CCCCTTCACACCTTAGCGTA 59.100 55.000 0.00 0.00 0.00 4.42
925 1168 1.066071 GTCTCCCCTTCACACCTTAGC 60.066 57.143 0.00 0.00 0.00 3.09
944 1187 1.486726 GGGGGAAACGAGATGATCTGT 59.513 52.381 0.00 0.00 0.00 3.41
947 1190 0.464452 ACGGGGGAAACGAGATGATC 59.536 55.000 0.00 0.00 34.93 2.92
951 1194 0.908180 AAGGACGGGGGAAACGAGAT 60.908 55.000 0.00 0.00 34.93 2.75
965 1208 0.539986 TAGGTCAATGGCGGAAGGAC 59.460 55.000 0.00 0.00 0.00 3.85
970 1213 2.391926 TAGGATAGGTCAATGGCGGA 57.608 50.000 0.00 0.00 0.00 5.54
974 1217 8.094284 TGATGGATAATAGGATAGGTCAATGG 57.906 38.462 0.00 0.00 0.00 3.16
1056 1299 0.805614 TGAGCTTCTCGTCTTCCTCG 59.194 55.000 0.00 0.00 32.35 4.63
1059 1302 2.949451 TCATGAGCTTCTCGTCTTCC 57.051 50.000 0.00 0.00 32.35 3.46
1079 1322 1.141657 GGCCATGCTTCTGGATGTAGA 59.858 52.381 0.00 0.00 39.90 2.59
1141 1384 5.697178 CAGAGAAAGAGAGATGTGCCATATG 59.303 44.000 0.00 0.00 0.00 1.78
1142 1385 5.742546 GCAGAGAAAGAGAGATGTGCCATAT 60.743 44.000 0.00 0.00 0.00 1.78
1143 1386 4.442612 GCAGAGAAAGAGAGATGTGCCATA 60.443 45.833 0.00 0.00 0.00 2.74
1144 1387 3.682155 GCAGAGAAAGAGAGATGTGCCAT 60.682 47.826 0.00 0.00 0.00 4.40
1145 1388 2.354503 GCAGAGAAAGAGAGATGTGCCA 60.355 50.000 0.00 0.00 0.00 4.92
1146 1389 2.278854 GCAGAGAAAGAGAGATGTGCC 58.721 52.381 0.00 0.00 0.00 5.01
1149 1392 3.439154 TGAGGCAGAGAAAGAGAGATGT 58.561 45.455 0.00 0.00 0.00 3.06
1150 1393 4.373527 CATGAGGCAGAGAAAGAGAGATG 58.626 47.826 0.00 0.00 0.00 2.90
1151 1394 3.181463 GCATGAGGCAGAGAAAGAGAGAT 60.181 47.826 0.00 0.00 43.97 2.75
1187 1475 9.480053 AAGAAAATATGGTGAACAACATTCTTG 57.520 29.630 10.59 0.00 39.80 3.02
1192 1480 7.215789 TGCAAAGAAAATATGGTGAACAACAT 58.784 30.769 10.20 10.20 42.28 2.71
1193 1481 6.577103 TGCAAAGAAAATATGGTGAACAACA 58.423 32.000 0.00 0.00 0.00 3.33
1194 1482 6.146021 CCTGCAAAGAAAATATGGTGAACAAC 59.854 38.462 0.00 0.00 0.00 3.32
1195 1483 6.222389 CCTGCAAAGAAAATATGGTGAACAA 58.778 36.000 0.00 0.00 0.00 2.83
1196 1484 5.782047 CCTGCAAAGAAAATATGGTGAACA 58.218 37.500 0.00 0.00 0.00 3.18
1197 1485 4.627035 GCCTGCAAAGAAAATATGGTGAAC 59.373 41.667 0.00 0.00 0.00 3.18
1198 1486 4.322650 GGCCTGCAAAGAAAATATGGTGAA 60.323 41.667 0.00 0.00 0.00 3.18
1199 1487 3.195396 GGCCTGCAAAGAAAATATGGTGA 59.805 43.478 0.00 0.00 0.00 4.02
1200 1488 3.196254 AGGCCTGCAAAGAAAATATGGTG 59.804 43.478 3.11 0.00 0.00 4.17
1212 1501 1.108727 CACCTGTTCAGGCCTGCAAA 61.109 55.000 28.91 15.53 0.00 3.68
1363 1652 8.657729 CATCTGAGATGTATGCAATAGAATGTC 58.342 37.037 14.17 0.00 0.00 3.06
1595 1914 3.753815 TGGTTGCTGATTGATGAACTGA 58.246 40.909 0.00 0.00 0.00 3.41
1688 2010 1.123861 TGGAGGCTGCAGAGTGAAGT 61.124 55.000 20.43 0.00 0.00 3.01
1807 2129 3.627395 TGCCACTAATACCCTCAAGTG 57.373 47.619 0.00 0.00 39.22 3.16
1821 2143 0.753262 CCGGCTAAGTCTATGCCACT 59.247 55.000 14.12 0.00 46.39 4.00
1838 2160 2.126307 CTCTGAGACACGTGCCCG 60.126 66.667 17.22 1.89 40.83 6.13
1844 2166 0.445436 GCATTTGGCTCTGAGACACG 59.555 55.000 13.94 6.06 29.12 4.49
1855 2177 0.380733 GGTAACGCTAGGCATTTGGC 59.619 55.000 0.00 0.00 43.74 4.52
1934 2256 0.036952 CTCCCTCATCGCAGTGTTGT 60.037 55.000 0.00 0.00 0.00 3.32
1937 2259 0.323816 TCTCTCCCTCATCGCAGTGT 60.324 55.000 0.00 0.00 0.00 3.55
1941 2263 0.820226 CTGTTCTCTCCCTCATCGCA 59.180 55.000 0.00 0.00 0.00 5.10
1944 2266 1.473080 GCTGCTGTTCTCTCCCTCATC 60.473 57.143 0.00 0.00 0.00 2.92
1945 2267 0.540923 GCTGCTGTTCTCTCCCTCAT 59.459 55.000 0.00 0.00 0.00 2.90
1975 2297 5.368989 GAAGGGAGTTTTCAGAGAGAAACA 58.631 41.667 0.00 0.00 45.48 2.83
2003 2325 0.322277 AAGCTGCCATGTCAGTGAGG 60.322 55.000 5.53 0.00 36.49 3.86
2099 2421 2.281517 CTCAGCAGCTCTTCATCAAGG 58.718 52.381 0.00 0.00 0.00 3.61
2171 2493 1.039856 ATTCCAAAACGCAAGCCACT 58.960 45.000 0.00 0.00 45.62 4.00
2233 2557 6.868339 AGCCTACAAGTGCATGAAAAATAAAC 59.132 34.615 0.00 0.00 0.00 2.01
2237 2561 4.523943 TGAGCCTACAAGTGCATGAAAAAT 59.476 37.500 0.00 0.00 0.00 1.82
2256 2580 4.953940 ATCTATGGACTCCTTTCTGAGC 57.046 45.455 0.00 0.00 35.72 4.26
2381 2705 5.540337 TCCAGGAACTAAGATATAGTGGCAG 59.460 44.000 0.00 0.00 36.02 4.85
2382 2706 5.464069 TCCAGGAACTAAGATATAGTGGCA 58.536 41.667 0.00 0.00 36.02 4.92
2407 2731 3.059597 CGAGCAACTAGGACAAAACAGTG 60.060 47.826 0.00 0.00 0.00 3.66
2444 2768 6.018589 TCGCACCATTTGTATCAAAATTCA 57.981 33.333 0.00 0.00 0.00 2.57
2478 2802 1.885814 TTCACGCATGTTGTCGCTCG 61.886 55.000 0.00 0.00 0.00 5.03
2482 2806 2.661504 TTCTTTCACGCATGTTGTCG 57.338 45.000 0.00 0.00 0.00 4.35
2554 2880 7.283625 TCAGGCAAGCTTTTCTTTATGTTAA 57.716 32.000 0.00 0.00 31.27 2.01
2959 3287 5.709966 GGTTGCTACCTCTTTAAAACATGG 58.290 41.667 10.33 0.00 41.53 3.66
2996 3324 8.994429 AGCATATAAGCACACATCTTAGTATC 57.006 34.615 2.37 0.00 36.85 2.24
2998 3326 9.261180 GAAAGCATATAAGCACACATCTTAGTA 57.739 33.333 2.37 0.00 36.85 1.82


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

AutoCloner maintained by Alex Coulton.