Multiple sequence alignment - TraesCS5B01G395900

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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 TraesCS5B01G395900 chr5B 100.000 3650 0 0 1 3650 572960693 572964342 0.000000e+00 6741
1 TraesCS5B01G395900 chr1B 97.032 2325 44 5 1326 3650 33971038 33973337 0.000000e+00 3888
2 TraesCS5B01G395900 chr5D 89.544 899 52 26 1 888 465725149 465726016 0.000000e+00 1101
3 TraesCS5B01G395900 chr5D 100.000 53 0 0 912 964 465726291 465726343 8.340000e-17 99
4 TraesCS5B01G395900 chr5A 86.717 527 27 19 390 887 586164737 586165249 2.480000e-151 545
5 TraesCS5B01G395900 chr5A 91.667 360 18 3 7 359 586164384 586164738 4.240000e-134 488
6 TraesCS5B01G395900 chr5A 74.797 861 190 21 976 1820 382783726 382784575 2.680000e-96 363
7 TraesCS5B01G395900 chr2D 76.992 665 134 15 979 1629 447150926 447151585 2.680000e-96 363


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 TraesCS5B01G395900 chr5B 572960693 572964342 3649 False 6741.0 6741 100.000 1 3650 1 chr5B.!!$F1 3649
1 TraesCS5B01G395900 chr1B 33971038 33973337 2299 False 3888.0 3888 97.032 1326 3650 1 chr1B.!!$F1 2324
2 TraesCS5B01G395900 chr5D 465725149 465726343 1194 False 600.0 1101 94.772 1 964 2 chr5D.!!$F1 963
3 TraesCS5B01G395900 chr5A 586164384 586165249 865 False 516.5 545 89.192 7 887 2 chr5A.!!$F2 880
4 TraesCS5B01G395900 chr5A 382783726 382784575 849 False 363.0 363 74.797 976 1820 1 chr5A.!!$F1 844
5 TraesCS5B01G395900 chr2D 447150926 447151585 659 False 363.0 363 76.992 979 1629 1 chr2D.!!$F1 650

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
908 962 0.466739 ACGGCGAACCCTTCCTTTTT 60.467 50.0 16.62 0.0 0.00 1.94 F
1262 1566 0.032813 AATGCCTGGGATTGGGACAG 60.033 55.0 13.01 0.0 42.39 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2589 2902 1.133982 CTGTGTCTATCAGCGCAGTCT 59.866 52.381 11.47 0.0 38.14 3.24 R
3027 3340 0.951040 CCAGCTTGGTGACGTTCTCC 60.951 60.000 1.00 0.0 31.35 3.71 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
158 159 1.738030 GCACGCGGTTATAGTGGAAGT 60.738 52.381 12.47 0.00 36.48 3.01
166 167 4.094442 CGGTTATAGTGGAAGTGCTTTTCC 59.906 45.833 11.48 11.48 45.59 3.13
300 308 0.682292 GTGCAGAGGTATCTAGGCCC 59.318 60.000 0.00 0.00 33.22 5.80
301 309 0.563173 TGCAGAGGTATCTAGGCCCT 59.437 55.000 0.00 0.00 33.22 5.19
302 310 1.787058 TGCAGAGGTATCTAGGCCCTA 59.213 52.381 0.00 0.00 33.22 3.53
303 311 2.225142 TGCAGAGGTATCTAGGCCCTAG 60.225 54.545 11.84 11.84 35.57 3.02
304 312 2.041891 GCAGAGGTATCTAGGCCCTAGA 59.958 54.545 22.44 22.44 45.52 2.43
361 370 2.362120 AGCCAATGGAGCAGTGCC 60.362 61.111 12.58 3.03 0.00 5.01
362 371 2.362120 GCCAATGGAGCAGTGCCT 60.362 61.111 12.58 0.00 0.00 4.75
364 373 2.050350 CCAATGGAGCAGTGCCTGG 61.050 63.158 12.58 7.40 31.21 4.45
365 374 2.362120 AATGGAGCAGTGCCTGGC 60.362 61.111 12.87 12.87 31.21 4.85
366 375 2.915504 AATGGAGCAGTGCCTGGCT 61.916 57.895 21.03 0.00 44.48 4.75
367 376 3.640257 ATGGAGCAGTGCCTGGCTG 62.640 63.158 21.03 11.93 41.22 4.85
533 547 2.352388 GTTCGTGGAATCAAATCCGGA 58.648 47.619 6.61 6.61 42.76 5.14
585 604 1.593933 CGTAGACTCGTAGCTCTCCAC 59.406 57.143 0.00 0.00 0.00 4.02
621 655 2.607750 AGCCTTTCTCCTCCCGCA 60.608 61.111 0.00 0.00 0.00 5.69
707 748 1.153706 GTTCGGCGATTCGGAGGAA 60.154 57.895 11.76 0.00 36.41 3.36
710 751 1.878522 CGGCGATTCGGAGGAAGTG 60.879 63.158 0.00 0.00 35.19 3.16
715 756 1.739371 CGATTCGGAGGAAGTGGGAAC 60.739 57.143 0.00 0.00 35.19 3.62
755 800 4.034048 AGCGCGGATTTTAATTACTGACTG 59.966 41.667 8.83 0.00 0.00 3.51
763 808 9.841880 GGATTTTAATTACTGACTGAACTTTCC 57.158 33.333 0.00 0.00 0.00 3.13
785 830 3.479269 GAGACGCAGGCGAAACGG 61.479 66.667 21.62 0.00 42.83 4.44
789 834 1.356527 GACGCAGGCGAAACGGTATT 61.357 55.000 21.62 0.00 42.83 1.89
811 865 1.069765 CGTGGAGGGAATGGATCGG 59.930 63.158 0.00 0.00 0.00 4.18
813 867 1.004230 TGGAGGGAATGGATCGGGT 59.996 57.895 0.00 0.00 0.00 5.28
816 870 2.591715 GGGAATGGATCGGGTGCG 60.592 66.667 0.00 0.00 0.00 5.34
818 872 3.640000 GAATGGATCGGGTGCGCG 61.640 66.667 0.00 0.00 0.00 6.86
839 893 1.216444 CTCTAAGCGCTGCACCTCA 59.784 57.895 12.58 0.00 0.00 3.86
887 941 2.684843 GCTCGCTTTCACCCAGCTG 61.685 63.158 6.78 6.78 34.88 4.24
888 942 2.669569 TCGCTTTCACCCAGCTGC 60.670 61.111 8.66 0.00 34.88 5.25
889 943 2.979676 CGCTTTCACCCAGCTGCA 60.980 61.111 8.66 0.00 34.88 4.41
890 944 2.647297 GCTTTCACCCAGCTGCAC 59.353 61.111 8.66 0.00 34.15 4.57
891 945 2.949106 CTTTCACCCAGCTGCACG 59.051 61.111 8.66 0.00 0.00 5.34
892 946 2.594303 TTTCACCCAGCTGCACGG 60.594 61.111 8.66 7.11 0.00 4.94
902 956 3.423154 CTGCACGGCGAACCCTTC 61.423 66.667 16.62 0.00 0.00 3.46
904 958 4.699522 GCACGGCGAACCCTTCCT 62.700 66.667 16.62 0.00 0.00 3.36
905 959 2.032071 CACGGCGAACCCTTCCTT 59.968 61.111 16.62 0.00 0.00 3.36
906 960 1.599797 CACGGCGAACCCTTCCTTT 60.600 57.895 16.62 0.00 0.00 3.11
907 961 1.149854 ACGGCGAACCCTTCCTTTT 59.850 52.632 16.62 0.00 0.00 2.27
908 962 0.466739 ACGGCGAACCCTTCCTTTTT 60.467 50.000 16.62 0.00 0.00 1.94
968 1272 8.577296 TGTTCTTAGACATATATACAGGTGAGC 58.423 37.037 0.00 0.00 0.00 4.26
969 1273 8.577296 GTTCTTAGACATATATACAGGTGAGCA 58.423 37.037 0.00 0.00 0.00 4.26
970 1274 8.341892 TCTTAGACATATATACAGGTGAGCAG 57.658 38.462 0.00 0.00 0.00 4.24
971 1275 5.398603 AGACATATATACAGGTGAGCAGC 57.601 43.478 0.00 0.00 0.00 5.25
972 1276 4.835056 AGACATATATACAGGTGAGCAGCA 59.165 41.667 0.00 0.00 0.00 4.41
973 1277 5.047448 AGACATATATACAGGTGAGCAGCAG 60.047 44.000 0.00 0.00 0.00 4.24
974 1278 2.540265 ATATACAGGTGAGCAGCAGC 57.460 50.000 0.00 0.00 45.24 5.25
1003 1307 1.524621 GGCATCACTCCGGACATGG 60.525 63.158 0.00 0.00 0.00 3.66
1005 1309 1.091771 GCATCACTCCGGACATGGTG 61.092 60.000 16.77 16.77 0.00 4.17
1007 1311 0.617535 ATCACTCCGGACATGGTGGA 60.618 55.000 18.43 8.35 0.00 4.02
1011 1315 4.838152 CCGGACATGGTGGAGCGG 62.838 72.222 0.00 0.00 0.00 5.52
1026 1330 4.082523 CGGGTGGTGGAGCGTGAT 62.083 66.667 0.00 0.00 0.00 3.06
1029 1333 1.741770 GGTGGTGGAGCGTGATCAC 60.742 63.158 16.21 16.21 0.00 3.06
1032 1336 2.261671 GTGGAGCGTGATCACCGT 59.738 61.111 20.03 7.29 0.00 4.83
1036 1340 1.359459 GGAGCGTGATCACCGTTTCC 61.359 60.000 20.03 18.58 0.00 3.13
1037 1341 1.359459 GAGCGTGATCACCGTTTCCC 61.359 60.000 20.03 2.94 0.00 3.97
1038 1342 1.375523 GCGTGATCACCGTTTCCCT 60.376 57.895 20.03 0.00 0.00 4.20
1039 1343 1.635663 GCGTGATCACCGTTTCCCTG 61.636 60.000 20.03 3.89 0.00 4.45
1040 1344 1.635663 CGTGATCACCGTTTCCCTGC 61.636 60.000 20.03 0.00 0.00 4.85
1042 1346 2.046314 ATCACCGTTTCCCTGCCG 60.046 61.111 0.00 0.00 0.00 5.69
1044 1348 4.323477 CACCGTTTCCCTGCCGGA 62.323 66.667 5.05 0.00 44.41 5.14
1074 1378 2.747855 GCGCCCTGTTTCCCTGAG 60.748 66.667 0.00 0.00 0.00 3.35
1077 1381 1.915078 CGCCCTGTTTCCCTGAGGAT 61.915 60.000 0.00 0.00 43.54 3.24
1079 1383 1.272704 GCCCTGTTTCCCTGAGGATTT 60.273 52.381 0.00 0.00 43.54 2.17
1090 1394 3.137913 CCCTGAGGATTTCATCATCACCT 59.862 47.826 0.00 0.00 44.18 4.00
1095 1399 2.033801 GGATTTCATCATCACCTTGGCG 59.966 50.000 0.00 0.00 0.00 5.69
1098 1402 0.839277 TCATCATCACCTTGGCGGAT 59.161 50.000 0.00 0.00 36.31 4.18
1128 1432 0.530870 GCGACCTGGTCTATGAAGGC 60.531 60.000 23.49 13.96 34.18 4.35
1134 1438 2.993539 GGTCTATGAAGGCCGCTTC 58.006 57.895 0.00 0.00 37.86 3.86
1143 1447 2.579684 AAGGCCGCTTCATCGAGGTC 62.580 60.000 0.00 0.00 0.00 3.85
1146 1450 2.103143 CGCTTCATCGAGGTCGCT 59.897 61.111 0.00 0.00 39.60 4.93
1152 1456 3.461773 ATCGAGGTCGCTGGGGTG 61.462 66.667 0.00 0.00 39.60 4.61
1153 1457 3.957435 ATCGAGGTCGCTGGGGTGA 62.957 63.158 0.00 0.00 39.60 4.02
1154 1458 3.691342 CGAGGTCGCTGGGGTGAA 61.691 66.667 0.00 0.00 33.47 3.18
1155 1459 2.266055 GAGGTCGCTGGGGTGAAG 59.734 66.667 0.00 0.00 33.47 3.02
1170 1474 2.034221 AAGTTTCAGCTCCGCCCC 59.966 61.111 0.00 0.00 0.00 5.80
1216 1520 0.036294 GGTGTGGAGGTTCTACTGCC 60.036 60.000 0.00 0.00 0.00 4.85
1218 1522 0.830444 TGTGGAGGTTCTACTGCCGT 60.830 55.000 0.00 0.00 0.00 5.68
1221 1525 0.108756 GGAGGTTCTACTGCCGTGTC 60.109 60.000 0.00 0.00 0.00 3.67
1223 1527 2.092882 GGTTCTACTGCCGTGTCGC 61.093 63.158 0.00 0.00 0.00 5.19
1224 1528 1.080705 GTTCTACTGCCGTGTCGCT 60.081 57.895 0.00 0.00 0.00 4.93
1227 1531 0.661552 TCTACTGCCGTGTCGCTATC 59.338 55.000 0.00 0.00 0.00 2.08
1262 1566 0.032813 AATGCCTGGGATTGGGACAG 60.033 55.000 13.01 0.00 42.39 3.51
1263 1567 1.217057 ATGCCTGGGATTGGGACAGT 61.217 55.000 0.00 0.00 42.39 3.55
1276 1580 1.004440 GACAGTGTCCAGGAGGTGC 60.004 63.158 12.54 0.00 35.89 5.01
1287 1591 1.005215 CAGGAGGTGCTTGGGAAGAAT 59.995 52.381 0.00 0.00 0.00 2.40
1296 1600 1.203994 CTTGGGAAGAATTGCTGGCTG 59.796 52.381 0.00 0.00 36.31 4.85
1299 1603 0.813821 GGAAGAATTGCTGGCTGGAC 59.186 55.000 0.00 0.00 31.69 4.02
1302 1606 0.034670 AGAATTGCTGGCTGGACCTC 60.035 55.000 0.00 0.00 40.22 3.85
1305 1609 0.106819 ATTGCTGGCTGGACCTCATC 60.107 55.000 0.00 0.00 40.22 2.92
1311 1615 2.279120 CTGGACCTCATCGAGCGC 60.279 66.667 0.00 0.00 0.00 5.92
1317 1621 2.491621 CTCATCGAGCGCCAGTCA 59.508 61.111 2.29 0.00 0.00 3.41
1319 1623 1.416813 CTCATCGAGCGCCAGTCAAC 61.417 60.000 2.29 0.00 0.00 3.18
1320 1624 2.125512 ATCGAGCGCCAGTCAACC 60.126 61.111 2.29 0.00 0.00 3.77
1322 1626 2.842394 ATCGAGCGCCAGTCAACCAG 62.842 60.000 2.29 0.00 0.00 4.00
1402 1706 1.065854 CCCGAGCCTCAGACTTCAATT 60.066 52.381 0.00 0.00 0.00 2.32
1426 1730 5.541845 TGATCCATCGTCCTGATATTGTTC 58.458 41.667 0.00 0.00 34.83 3.18
1552 1856 4.776322 CACCATCCGCGAGCCCAA 62.776 66.667 8.23 0.00 0.00 4.12
1587 1900 1.604604 GCACATACACACACAAGGGT 58.395 50.000 0.00 0.00 0.00 4.34
1872 2185 3.449737 CCATTTGTCTCCCGTTAGAGGTA 59.550 47.826 0.00 0.00 34.46 3.08
1928 2241 2.594303 CCCGGCAGCACAAGACAA 60.594 61.111 0.00 0.00 0.00 3.18
2001 2314 2.240162 CTAGGGAACAGGCCGACCAC 62.240 65.000 0.00 0.00 39.06 4.16
2141 2454 1.203441 TTGCCACCTCAGGAGCTCAT 61.203 55.000 17.19 5.25 0.00 2.90
2196 2509 3.728292 GAAGGAGGCTGGGGGCATG 62.728 68.421 0.00 0.00 44.01 4.06
2368 2681 0.179034 CAGCTATGAGTTGCCTCCCC 60.179 60.000 0.00 0.00 36.86 4.81
2448 2761 3.161450 GCGATGGCCTGGGACCTA 61.161 66.667 3.32 0.00 0.00 3.08
2452 2765 1.694169 ATGGCCTGGGACCTACCTG 60.694 63.158 3.32 0.00 38.98 4.00
2541 2854 1.132977 TCTGGACCTGAGGTGGTGTTA 60.133 52.381 9.89 0.00 41.00 2.41
2589 2902 1.236026 ACCATCCCCCTCCTGGACTA 61.236 60.000 0.00 0.00 33.94 2.59
2616 2929 1.139654 GCTGATAGACACAGGGATGCA 59.860 52.381 0.00 0.00 36.09 3.96
2617 2930 2.420547 GCTGATAGACACAGGGATGCAA 60.421 50.000 0.00 0.00 36.09 4.08
2627 2940 3.446161 CACAGGGATGCAAGATCATTTGT 59.554 43.478 0.00 0.00 0.00 2.83
2719 3032 3.197790 CAGCGATCACGGCAAGGG 61.198 66.667 0.00 0.00 40.15 3.95
2770 3083 5.011943 AGGCAGTTCATTGGAAAAATTGCTA 59.988 36.000 0.00 0.00 34.13 3.49
2777 3090 5.418840 TCATTGGAAAAATTGCTACCCTCTC 59.581 40.000 0.00 0.00 0.00 3.20
2832 3145 1.304962 TCCCTCACCTCGCAAGCTA 60.305 57.895 0.00 0.00 37.18 3.32
2956 3269 2.346803 GCGTCAAGCTAGGTTTCATCA 58.653 47.619 3.96 0.00 44.04 3.07
3095 3408 2.572284 GCTACAGCTTCCGGACGT 59.428 61.111 1.83 1.41 38.21 4.34
3163 3476 1.200020 CTTCCTTCGTTTGACCATGCC 59.800 52.381 0.00 0.00 0.00 4.40
3203 3516 6.484364 AGTTTCCAATGATTTGTTGTCCTT 57.516 33.333 0.00 0.00 0.00 3.36
3227 3540 4.581409 TGAACCTTAAGTTTACTGTTGGGC 59.419 41.667 0.97 0.00 39.40 5.36
3252 3565 1.533711 GGGCTGCCATGTATCCTGT 59.466 57.895 22.05 0.00 0.00 4.00
3256 3569 1.202336 GCTGCCATGTATCCTGTTTGC 60.202 52.381 0.00 0.00 0.00 3.68
3257 3570 1.406539 CTGCCATGTATCCTGTTTGCC 59.593 52.381 0.00 0.00 0.00 4.52
3258 3571 1.005805 TGCCATGTATCCTGTTTGCCT 59.994 47.619 0.00 0.00 0.00 4.75
3259 3572 1.406539 GCCATGTATCCTGTTTGCCTG 59.593 52.381 0.00 0.00 0.00 4.85
3260 3573 2.026641 CCATGTATCCTGTTTGCCTGG 58.973 52.381 0.00 0.00 0.00 4.45
3263 3576 1.427368 TGTATCCTGTTTGCCTGGGTT 59.573 47.619 0.00 0.00 33.14 4.11
3264 3577 2.158385 TGTATCCTGTTTGCCTGGGTTT 60.158 45.455 0.00 0.00 33.14 3.27
3265 3578 1.632589 ATCCTGTTTGCCTGGGTTTC 58.367 50.000 0.00 0.00 33.14 2.78
3266 3579 0.260230 TCCTGTTTGCCTGGGTTTCA 59.740 50.000 0.00 0.00 33.14 2.69
3267 3580 0.389025 CCTGTTTGCCTGGGTTTCAC 59.611 55.000 0.00 0.00 0.00 3.18
3268 3581 0.389025 CTGTTTGCCTGGGTTTCACC 59.611 55.000 0.00 0.00 37.60 4.02
3277 3590 2.600470 GGTTTCACCCACCCAGGC 60.600 66.667 0.00 0.00 35.39 4.85
3278 3591 2.520968 GTTTCACCCACCCAGGCT 59.479 61.111 0.00 0.00 35.39 4.58
3279 3592 1.152546 GTTTCACCCACCCAGGCTT 60.153 57.895 0.00 0.00 35.39 4.35
3280 3593 1.152567 TTTCACCCACCCAGGCTTG 60.153 57.895 0.00 0.00 35.39 4.01
3281 3594 1.650242 TTTCACCCACCCAGGCTTGA 61.650 55.000 0.00 0.00 35.39 3.02
3282 3595 1.434513 TTCACCCACCCAGGCTTGAT 61.435 55.000 0.00 0.00 35.39 2.57
3283 3596 1.379044 CACCCACCCAGGCTTGATC 60.379 63.158 0.00 0.00 35.39 2.92
3284 3597 1.542375 ACCCACCCAGGCTTGATCT 60.542 57.895 0.00 0.00 35.39 2.75
3285 3598 1.142688 ACCCACCCAGGCTTGATCTT 61.143 55.000 0.00 0.00 35.39 2.40
3286 3599 0.682209 CCCACCCAGGCTTGATCTTG 60.682 60.000 0.00 0.00 35.39 3.02
3287 3600 0.038744 CCACCCAGGCTTGATCTTGT 59.961 55.000 0.00 0.00 0.00 3.16
3288 3601 1.171308 CACCCAGGCTTGATCTTGTG 58.829 55.000 0.00 0.00 0.00 3.33
3289 3602 0.610232 ACCCAGGCTTGATCTTGTGC 60.610 55.000 0.00 0.00 0.00 4.57
3367 3680 2.486548 GGTTGAATAATAGGGCGAGGCA 60.487 50.000 0.00 0.00 0.00 4.75
3550 3863 4.680237 CTGTTGGCGCTCGGACCA 62.680 66.667 7.64 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 149 2.084546 GCGGAAAAGCACTTCCACTAT 58.915 47.619 15.00 0.00 44.52 2.12
212 213 2.753043 TACCTCGGGTCAGGCGTC 60.753 66.667 0.00 0.00 36.98 5.19
300 308 2.490115 GCATGACCCGGATCTAGTCTAG 59.510 54.545 0.73 0.00 0.00 2.43
301 309 2.108425 AGCATGACCCGGATCTAGTCTA 59.892 50.000 0.73 0.00 0.00 2.59
302 310 1.133325 AGCATGACCCGGATCTAGTCT 60.133 52.381 0.73 0.00 0.00 3.24
303 311 1.333177 AGCATGACCCGGATCTAGTC 58.667 55.000 0.73 1.05 0.00 2.59
304 312 2.677542 TAGCATGACCCGGATCTAGT 57.322 50.000 0.73 0.00 0.00 2.57
342 351 1.378250 GCACTGCTCCATTGGCTCT 60.378 57.895 0.00 0.00 0.00 4.09
564 583 1.219646 GGAGAGCTACGAGTCTACGG 58.780 60.000 0.00 0.00 37.61 4.02
621 655 0.596577 TAGCTGTTTGTCTCGCTCGT 59.403 50.000 0.00 0.00 34.14 4.18
693 734 1.521681 CCACTTCCTCCGAATCGCC 60.522 63.158 0.00 0.00 0.00 5.54
707 748 0.898789 AGTCATCGACGGTTCCCACT 60.899 55.000 0.00 0.00 37.67 4.00
710 751 1.810030 GCAGTCATCGACGGTTCCC 60.810 63.158 0.00 0.00 37.67 3.97
715 756 1.874019 CTTCCGCAGTCATCGACGG 60.874 63.158 3.66 3.66 46.97 4.79
755 800 0.736672 GCGTCTCCGAGGGAAAGTTC 60.737 60.000 0.00 0.00 35.63 3.01
779 824 2.414138 CCTCCACGACAAATACCGTTTC 59.586 50.000 0.00 0.00 36.83 2.78
785 830 2.943033 CCATTCCCTCCACGACAAATAC 59.057 50.000 0.00 0.00 0.00 1.89
789 834 1.209504 GATCCATTCCCTCCACGACAA 59.790 52.381 0.00 0.00 0.00 3.18
820 874 2.125350 AGGTGCAGCGCTTAGAGC 60.125 61.111 7.50 9.24 38.02 4.09
821 875 0.390340 TTGAGGTGCAGCGCTTAGAG 60.390 55.000 20.22 0.00 0.00 2.43
822 876 0.250234 ATTGAGGTGCAGCGCTTAGA 59.750 50.000 20.22 4.86 0.00 2.10
823 877 1.089920 AATTGAGGTGCAGCGCTTAG 58.910 50.000 20.22 0.00 0.00 2.18
824 878 0.804364 CAATTGAGGTGCAGCGCTTA 59.196 50.000 20.22 9.07 0.00 3.09
825 879 1.582968 CAATTGAGGTGCAGCGCTT 59.417 52.632 20.22 4.81 0.00 4.68
828 882 0.597568 TTTCCAATTGAGGTGCAGCG 59.402 50.000 10.78 0.00 0.00 5.18
839 893 7.427989 ACAGAATAGCCATCATTTTCCAATT 57.572 32.000 0.00 0.00 0.00 2.32
887 941 4.699522 AGGAAGGGTTCGCCGTGC 62.700 66.667 0.00 0.00 38.45 5.34
888 942 1.170290 AAAAGGAAGGGTTCGCCGTG 61.170 55.000 0.00 0.00 38.45 4.94
889 943 0.466739 AAAAAGGAAGGGTTCGCCGT 60.467 50.000 0.00 0.00 38.45 5.68
890 944 2.337361 AAAAAGGAAGGGTTCGCCG 58.663 52.632 0.00 0.00 38.45 6.46
908 962 4.158025 TGGTTCGCCTGTGTTTTCTAAAAA 59.842 37.500 0.00 0.00 38.36 1.94
909 963 3.695060 TGGTTCGCCTGTGTTTTCTAAAA 59.305 39.130 0.00 0.00 38.36 1.52
910 964 3.280295 TGGTTCGCCTGTGTTTTCTAAA 58.720 40.909 0.00 0.00 38.36 1.85
980 1284 2.202987 CCGGAGTGATGCCAGAGC 60.203 66.667 0.00 0.00 40.48 4.09
981 1285 1.142748 GTCCGGAGTGATGCCAGAG 59.857 63.158 3.06 0.00 0.00 3.35
982 1286 0.977627 ATGTCCGGAGTGATGCCAGA 60.978 55.000 3.06 0.00 0.00 3.86
983 1287 0.812811 CATGTCCGGAGTGATGCCAG 60.813 60.000 3.06 0.00 0.00 4.85
984 1288 1.221566 CATGTCCGGAGTGATGCCA 59.778 57.895 3.06 0.00 0.00 4.92
985 1289 1.524621 CCATGTCCGGAGTGATGCC 60.525 63.158 3.06 0.00 0.00 4.40
986 1290 1.091771 CACCATGTCCGGAGTGATGC 61.092 60.000 14.71 0.00 31.79 3.91
993 1297 3.770040 CGCTCCACCATGTCCGGA 61.770 66.667 0.00 0.00 0.00 5.14
1003 1307 4.394712 CTCCACCACCCGCTCCAC 62.395 72.222 0.00 0.00 0.00 4.02
1011 1315 1.741770 GTGATCACGCTCCACCACC 60.742 63.158 10.69 0.00 0.00 4.61
1019 1323 1.375523 GGGAAACGGTGATCACGCT 60.376 57.895 19.33 3.94 34.00 5.07
1022 1326 1.305930 GGCAGGGAAACGGTGATCAC 61.306 60.000 17.91 17.91 0.00 3.06
1026 1330 4.323477 CCGGCAGGGAAACGGTGA 62.323 66.667 0.00 0.00 42.53 4.02
1029 1333 3.702048 TCTCCGGCAGGGAAACGG 61.702 66.667 2.05 0.00 46.61 4.44
1032 1336 4.388499 GCGTCTCCGGCAGGGAAA 62.388 66.667 2.05 0.00 46.61 3.13
1040 1344 4.778415 CGACCACAGCGTCTCCGG 62.778 72.222 0.00 0.00 33.68 5.14
1049 1353 4.988598 AACAGGGCGCGACCACAG 62.989 66.667 36.60 24.86 42.05 3.66
1051 1355 3.723348 GAAACAGGGCGCGACCAC 61.723 66.667 36.60 14.97 42.05 4.16
1062 1366 4.592942 TGATGAAATCCTCAGGGAAACAG 58.407 43.478 0.00 0.00 44.73 3.16
1065 1369 5.195940 GTGATGATGAAATCCTCAGGGAAA 58.804 41.667 0.00 0.00 46.31 3.13
1074 1378 2.033801 CGCCAAGGTGATGATGAAATCC 59.966 50.000 0.00 0.00 44.73 3.01
1077 1381 1.004161 TCCGCCAAGGTGATGATGAAA 59.996 47.619 0.23 0.00 41.99 2.69
1079 1383 0.839277 ATCCGCCAAGGTGATGATGA 59.161 50.000 0.23 0.00 41.99 2.92
1128 1432 2.956964 GCGACCTCGATGAAGCGG 60.957 66.667 0.00 0.00 43.02 5.52
1143 1447 1.856265 GCTGAAACTTCACCCCAGCG 61.856 60.000 0.00 0.00 40.40 5.18
1146 1450 0.110486 GGAGCTGAAACTTCACCCCA 59.890 55.000 0.00 0.00 32.90 4.96
1191 1495 0.179018 AGAACCTCCACACCTTGTGC 60.179 55.000 0.50 0.00 46.51 4.57
1200 1504 0.389948 CACGGCAGTAGAACCTCCAC 60.390 60.000 0.00 0.00 0.00 4.02
1230 1534 3.869272 GCATTCAGCGGCAGACGG 61.869 66.667 1.45 0.00 44.51 4.79
1262 1566 1.302832 CCAAGCACCTCCTGGACAC 60.303 63.158 0.00 0.00 37.04 3.67
1263 1567 2.528818 CCCAAGCACCTCCTGGACA 61.529 63.158 0.00 0.00 37.04 4.02
1272 1576 1.067354 CAGCAATTCTTCCCAAGCACC 60.067 52.381 0.00 0.00 0.00 5.01
1276 1580 1.203994 CAGCCAGCAATTCTTCCCAAG 59.796 52.381 0.00 0.00 0.00 3.61
1287 1591 1.300963 GATGAGGTCCAGCCAGCAA 59.699 57.895 0.00 0.00 40.61 3.91
1296 1600 3.781770 CTGGCGCTCGATGAGGTCC 62.782 68.421 7.64 0.00 0.00 4.46
1299 1603 2.279120 GACTGGCGCTCGATGAGG 60.279 66.667 7.64 0.00 0.00 3.86
1302 1606 2.456119 GGTTGACTGGCGCTCGATG 61.456 63.158 7.64 0.00 0.00 3.84
1305 1609 3.114616 CTGGTTGACTGGCGCTCG 61.115 66.667 7.64 0.30 0.00 5.03
1311 1615 0.397941 TCCTCTTGCTGGTTGACTGG 59.602 55.000 0.00 0.00 0.00 4.00
1317 1621 0.846693 ACCTGTTCCTCTTGCTGGTT 59.153 50.000 0.00 0.00 31.79 3.67
1319 1623 0.397941 TGACCTGTTCCTCTTGCTGG 59.602 55.000 0.00 0.00 0.00 4.85
1320 1624 1.805869 CTGACCTGTTCCTCTTGCTG 58.194 55.000 0.00 0.00 0.00 4.41
1322 1626 1.294659 CGCTGACCTGTTCCTCTTGC 61.295 60.000 0.00 0.00 0.00 4.01
1402 1706 5.551305 ACAATATCAGGACGATGGATCAA 57.449 39.130 0.00 0.00 35.39 2.57
1587 1900 0.698238 CCTTCACACCCATCCTCCAA 59.302 55.000 0.00 0.00 0.00 3.53
1915 2228 1.593196 TACACCTTGTCTTGTGCTGC 58.407 50.000 0.00 0.00 35.90 5.25
2001 2314 3.067074 CTCATCTGTGAGCTGCTGG 57.933 57.895 7.01 0.00 44.86 4.85
2162 2475 2.568956 TCCTTCTCCATCACAAGGACAG 59.431 50.000 0.00 0.00 40.70 3.51
2328 2641 2.354805 GGTACGTTGCTGGAAGAAGGAT 60.355 50.000 0.00 0.00 34.07 3.24
2368 2681 1.741770 CGTCCAAAGAAGGCGGGAG 60.742 63.158 0.00 0.00 0.00 4.30
2589 2902 1.133982 CTGTGTCTATCAGCGCAGTCT 59.866 52.381 11.47 0.00 38.14 3.24
2616 2929 6.405065 CGATGGATTGTTGGACAAATGATCTT 60.405 38.462 0.00 0.00 41.96 2.40
2617 2930 5.066893 CGATGGATTGTTGGACAAATGATCT 59.933 40.000 0.00 0.00 41.96 2.75
2627 2940 2.187958 ACTCCTCGATGGATTGTTGGA 58.812 47.619 4.39 0.00 45.16 3.53
2647 2960 2.818274 TGCTCGTCTCGCTCGCTA 60.818 61.111 0.00 0.00 0.00 4.26
2719 3032 1.675641 CCAGGTGTAAGGCAGCCAC 60.676 63.158 15.80 4.32 46.08 5.01
2770 3083 1.585651 ATGGAGGAGGACGAGAGGGT 61.586 60.000 0.00 0.00 0.00 4.34
2777 3090 1.182385 GCCTAGGATGGAGGAGGACG 61.182 65.000 14.75 0.00 35.99 4.79
2832 3145 1.683441 CCCCAGTAGGCGGTTCTTT 59.317 57.895 0.00 0.00 0.00 2.52
2946 3259 1.202879 TCAGGGCGTTTGATGAAACCT 60.203 47.619 2.01 0.00 38.65 3.50
2956 3269 2.031157 CGTTGAAATCTTCAGGGCGTTT 60.031 45.455 0.00 0.00 41.38 3.60
3027 3340 0.951040 CCAGCTTGGTGACGTTCTCC 60.951 60.000 1.00 0.00 31.35 3.71
3095 3408 2.202797 GGATCGCTTGCAGCTCGA 60.203 61.111 8.95 8.95 39.60 4.04
3203 3516 5.068067 GCCCAACAGTAAACTTAAGGTTCAA 59.932 40.000 9.55 0.00 37.12 2.69
3267 3580 0.682209 CAAGATCAAGCCTGGGTGGG 60.682 60.000 0.00 0.00 36.00 4.61
3268 3581 0.038744 ACAAGATCAAGCCTGGGTGG 59.961 55.000 0.00 0.00 39.35 4.61
3269 3582 1.171308 CACAAGATCAAGCCTGGGTG 58.829 55.000 0.00 0.00 0.00 4.61
3270 3583 0.610232 GCACAAGATCAAGCCTGGGT 60.610 55.000 0.00 0.00 0.00 4.51
3271 3584 0.609957 TGCACAAGATCAAGCCTGGG 60.610 55.000 0.00 0.00 0.00 4.45
3272 3585 0.524862 GTGCACAAGATCAAGCCTGG 59.475 55.000 13.17 0.00 0.00 4.45
3273 3586 0.524862 GGTGCACAAGATCAAGCCTG 59.475 55.000 20.43 0.00 0.00 4.85
3274 3587 0.403271 AGGTGCACAAGATCAAGCCT 59.597 50.000 20.43 0.00 0.00 4.58
3275 3588 1.251251 AAGGTGCACAAGATCAAGCC 58.749 50.000 20.43 0.00 0.00 4.35
3276 3589 2.035066 ACAAAGGTGCACAAGATCAAGC 59.965 45.455 20.43 0.00 0.00 4.01
3277 3590 3.635331 CACAAAGGTGCACAAGATCAAG 58.365 45.455 20.43 2.18 38.37 3.02
3278 3591 3.713858 CACAAAGGTGCACAAGATCAA 57.286 42.857 20.43 0.00 38.37 2.57
3550 3863 0.533755 GGCAGCAGACACACAGAAGT 60.534 55.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.