Multiple sequence alignment - TraesCS1B01G333500

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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 TraesCS1B01G333500 chr1B 100.000 3221 0 0 1 3221 560021274 560018054 0.000000e+00 5949.0
1 TraesCS1B01G333500 chr1B 89.623 106 2 2 2890 2995 337573637 337573733 3.370000e-25 126.0
2 TraesCS1B01G333500 chr1B 97.143 35 1 0 2942 2976 337573598 337573632 3.470000e-05 60.2
3 TraesCS1B01G333500 chr1D 91.443 2454 143 31 777 3218 414568622 414566224 0.000000e+00 3306.0
4 TraesCS1B01G333500 chr1D 84.406 699 48 22 68 750 414569342 414568689 5.860000e-177 630.0
5 TraesCS1B01G333500 chr1A 90.954 1205 69 18 1725 2900 511450304 511449111 0.000000e+00 1585.0
6 TraesCS1B01G333500 chr1A 88.928 569 46 8 735 1295 511451818 511451259 0.000000e+00 686.0
7 TraesCS1B01G333500 chr1A 88.304 342 23 6 2888 3221 511449090 511448758 8.380000e-106 394.0
8 TraesCS1B01G333500 chr1A 93.617 94 5 1 10 102 511452912 511452819 4.330000e-29 139.0
9 TraesCS1B01G333500 chr2D 82.061 1388 191 37 888 2238 33544437 33545803 0.000000e+00 1131.0
10 TraesCS1B01G333500 chr2D 81.506 1341 199 32 928 2238 33340632 33341953 0.000000e+00 1057.0
11 TraesCS1B01G333500 chr7B 79.879 1317 227 24 952 2244 680541731 680540429 0.000000e+00 929.0
12 TraesCS1B01G333500 chr7B 81.297 925 125 26 1310 2226 732713329 732712445 0.000000e+00 706.0
13 TraesCS1B01G333500 chr7D 79.300 1372 242 29 897 2244 601494463 601493110 0.000000e+00 922.0
14 TraesCS1B01G333500 chr7D 79.106 1297 240 20 962 2237 601699824 601698538 0.000000e+00 865.0
15 TraesCS1B01G333500 chr7D 78.244 1310 248 30 952 2237 601439688 601438392 0.000000e+00 806.0
16 TraesCS1B01G333500 chr7D 77.590 1303 260 20 952 2234 601463649 601462359 0.000000e+00 760.0
17 TraesCS1B01G333500 chr7D 77.614 1291 248 32 971 2237 601410819 601409546 0.000000e+00 745.0
18 TraesCS1B01G333500 chr7A 77.422 1311 256 33 952 2237 693197915 693196620 0.000000e+00 745.0
19 TraesCS1B01G333500 chr7A 82.432 222 21 6 1004 1225 725925506 725925709 9.180000e-41 178.0
20 TraesCS1B01G333500 chr6A 88.679 106 3 2 2890 2995 11915237 11915333 1.570000e-23 121.0
21 TraesCS1B01G333500 chr6A 97.143 35 1 0 2942 2976 11915198 11915232 3.470000e-05 60.2
22 TraesCS1B01G333500 chr3A 88.679 106 3 2 2890 2995 233469952 233470048 1.570000e-23 121.0
23 TraesCS1B01G333500 chr3A 97.143 35 1 0 2942 2976 233469913 233469947 3.470000e-05 60.2
24 TraesCS1B01G333500 chr4B 86.792 106 5 2 2890 2995 6833954 6833858 3.400000e-20 110.0


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 TraesCS1B01G333500 chr1B 560018054 560021274 3220 True 5949 5949 100.00000 1 3221 1 chr1B.!!$R1 3220
1 TraesCS1B01G333500 chr1D 414566224 414569342 3118 True 1968 3306 87.92450 68 3218 2 chr1D.!!$R1 3150
2 TraesCS1B01G333500 chr1A 511448758 511452912 4154 True 701 1585 90.45075 10 3221 4 chr1A.!!$R1 3211
3 TraesCS1B01G333500 chr2D 33544437 33545803 1366 False 1131 1131 82.06100 888 2238 1 chr2D.!!$F2 1350
4 TraesCS1B01G333500 chr2D 33340632 33341953 1321 False 1057 1057 81.50600 928 2238 1 chr2D.!!$F1 1310
5 TraesCS1B01G333500 chr7B 680540429 680541731 1302 True 929 929 79.87900 952 2244 1 chr7B.!!$R1 1292
6 TraesCS1B01G333500 chr7B 732712445 732713329 884 True 706 706 81.29700 1310 2226 1 chr7B.!!$R2 916
7 TraesCS1B01G333500 chr7D 601493110 601494463 1353 True 922 922 79.30000 897 2244 1 chr7D.!!$R4 1347
8 TraesCS1B01G333500 chr7D 601698538 601699824 1286 True 865 865 79.10600 962 2237 1 chr7D.!!$R5 1275
9 TraesCS1B01G333500 chr7D 601438392 601439688 1296 True 806 806 78.24400 952 2237 1 chr7D.!!$R2 1285
10 TraesCS1B01G333500 chr7D 601462359 601463649 1290 True 760 760 77.59000 952 2234 1 chr7D.!!$R3 1282
11 TraesCS1B01G333500 chr7D 601409546 601410819 1273 True 745 745 77.61400 971 2237 1 chr7D.!!$R1 1266
12 TraesCS1B01G333500 chr7A 693196620 693197915 1295 True 745 745 77.42200 952 2237 1 chr7A.!!$R1 1285

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
786 1349 0.177141 AACCTGCGTACACACACACT 59.823 50.0 0.00 0.00 0.0 3.55 F
813 1376 0.527385 GCCGTCAACTTTGCAGCAAA 60.527 50.0 19.55 19.55 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 3278 0.327259 ACATGACCAGCAGCTCACAT 59.673 50.0 0.00 0.00 0.00 3.21 R
2753 4072 0.846693 ACCTGAAAGACTTGGCTGGT 59.153 50.0 11.68 11.68 34.07 4.00 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
104 108 1.366854 GAAATTCGCCGTCCTCACCC 61.367 60.000 0.00 0.00 0.00 4.61
105 109 1.838073 AAATTCGCCGTCCTCACCCT 61.838 55.000 0.00 0.00 0.00 4.34
115 119 1.454847 CCTCACCCTCTCTCCCTCG 60.455 68.421 0.00 0.00 0.00 4.63
132 557 2.982130 GCTCGAGCTCTCCCCAAA 59.018 61.111 29.88 0.00 38.21 3.28
176 601 3.374402 CGCACCTCGTGGTCTCCT 61.374 66.667 6.10 0.00 46.60 3.69
177 602 2.932234 CGCACCTCGTGGTCTCCTT 61.932 63.158 6.10 0.00 46.60 3.36
181 606 0.178958 ACCTCGTGGTCTCCTTCTGT 60.179 55.000 2.61 0.00 44.78 3.41
234 666 2.798262 CGACACGGTTCGACGACC 60.798 66.667 0.00 1.53 41.78 4.79
235 667 2.332514 GACACGGTTCGACGACCA 59.667 61.111 7.06 0.00 39.78 4.02
236 668 2.012948 GACACGGTTCGACGACCAC 61.013 63.158 7.06 4.57 39.78 4.16
237 669 2.333938 CACGGTTCGACGACCACT 59.666 61.111 7.06 0.00 39.78 4.00
238 670 1.728426 CACGGTTCGACGACCACTC 60.728 63.158 7.06 0.00 39.78 3.51
239 671 2.188829 ACGGTTCGACGACCACTCA 61.189 57.895 7.06 0.00 39.78 3.41
240 672 1.442184 CGGTTCGACGACCACTCAG 60.442 63.158 7.06 0.00 39.78 3.35
280 712 1.470890 CTCTCCGACAGACACCTTCTC 59.529 57.143 0.00 0.00 28.96 2.87
281 713 0.528470 CTCCGACAGACACCTTCTCC 59.472 60.000 0.00 0.00 28.96 3.71
282 714 1.213013 CCGACAGACACCTTCTCCG 59.787 63.158 0.00 0.00 28.96 4.63
283 715 1.444553 CGACAGACACCTTCTCCGC 60.445 63.158 0.00 0.00 28.96 5.54
284 716 1.079750 GACAGACACCTTCTCCGCC 60.080 63.158 0.00 0.00 28.96 6.13
285 717 1.534235 ACAGACACCTTCTCCGCCT 60.534 57.895 0.00 0.00 28.96 5.52
286 718 1.216710 CAGACACCTTCTCCGCCTC 59.783 63.158 0.00 0.00 28.96 4.70
287 719 1.985116 AGACACCTTCTCCGCCTCC 60.985 63.158 0.00 0.00 0.00 4.30
288 720 3.358076 GACACCTTCTCCGCCTCCG 62.358 68.421 0.00 0.00 0.00 4.63
364 804 2.101233 CGCCGTCTCTCTCGTCTCA 61.101 63.158 0.00 0.00 0.00 3.27
411 876 0.949588 CGCATCTGCATCTGGCCTAG 60.950 60.000 3.32 0.00 43.89 3.02
488 959 2.660802 CACCGCCGAGGGTAAACT 59.339 61.111 0.00 0.00 46.96 2.66
499 970 1.521141 GGTAAACTCCTCTCGCCCC 59.479 63.158 0.00 0.00 0.00 5.80
502 973 0.686769 TAAACTCCTCTCGCCCCTCC 60.687 60.000 0.00 0.00 0.00 4.30
552 1023 2.029844 GCACTCGAGGTGGTTCAGC 61.030 63.158 18.41 3.76 45.44 4.26
587 1058 0.394216 AGGCACACACAAAGCACAGA 60.394 50.000 0.00 0.00 0.00 3.41
593 1064 2.423538 ACACACAAAGCACAGAAAGACC 59.576 45.455 0.00 0.00 0.00 3.85
622 1093 5.920903 AGTAGTAGTACCTCAGTAGCAGAG 58.079 45.833 4.02 0.00 0.00 3.35
624 1095 5.031066 AGTAGTACCTCAGTAGCAGAGAG 57.969 47.826 0.00 0.00 35.09 3.20
636 1109 1.068281 AGCAGAGAGACACACACACAG 59.932 52.381 0.00 0.00 0.00 3.66
669 1169 1.227089 CGACGGATGCCCTTCTCTG 60.227 63.158 0.00 0.00 0.00 3.35
680 1180 3.885297 TGCCCTTCTCTGTTCTTCTTTTG 59.115 43.478 0.00 0.00 0.00 2.44
682 1182 4.215185 GCCCTTCTCTGTTCTTCTTTTGAG 59.785 45.833 0.00 0.00 0.00 3.02
686 1186 5.028549 TCTCTGTTCTTCTTTTGAGCTGT 57.971 39.130 0.00 0.00 0.00 4.40
687 1187 6.161855 TCTCTGTTCTTCTTTTGAGCTGTA 57.838 37.500 0.00 0.00 0.00 2.74
688 1188 6.763355 TCTCTGTTCTTCTTTTGAGCTGTAT 58.237 36.000 0.00 0.00 0.00 2.29
689 1189 7.896811 TCTCTGTTCTTCTTTTGAGCTGTATA 58.103 34.615 0.00 0.00 0.00 1.47
690 1190 7.815068 TCTCTGTTCTTCTTTTGAGCTGTATAC 59.185 37.037 0.00 0.00 0.00 1.47
691 1191 7.671302 TCTGTTCTTCTTTTGAGCTGTATACT 58.329 34.615 4.17 0.00 0.00 2.12
692 1192 8.803235 TCTGTTCTTCTTTTGAGCTGTATACTA 58.197 33.333 4.17 0.00 0.00 1.82
693 1193 8.758633 TGTTCTTCTTTTGAGCTGTATACTAC 57.241 34.615 4.17 0.00 0.00 2.73
721 1229 2.389020 CGGCAACTGAGCTGAGCAG 61.389 63.158 7.39 0.00 43.63 4.24
762 1310 8.236586 CAGTTTTACTGCAACACATACATACAT 58.763 33.333 0.00 0.00 39.62 2.29
763 1311 8.236586 AGTTTTACTGCAACACATACATACATG 58.763 33.333 0.00 0.00 0.00 3.21
772 1335 3.316029 CACATACATACATGGCCAACCTG 59.684 47.826 10.96 6.36 36.63 4.00
774 1337 1.031571 ACATACATGGCCAACCTGCG 61.032 55.000 10.96 0.00 36.63 5.18
775 1338 1.031571 CATACATGGCCAACCTGCGT 61.032 55.000 10.96 2.88 36.63 5.24
786 1349 0.177141 AACCTGCGTACACACACACT 59.823 50.000 0.00 0.00 0.00 3.55
787 1350 0.529773 ACCTGCGTACACACACACTG 60.530 55.000 0.00 0.00 0.00 3.66
788 1351 1.221466 CCTGCGTACACACACACTGG 61.221 60.000 0.00 0.00 0.00 4.00
789 1352 1.831389 CTGCGTACACACACACTGGC 61.831 60.000 0.00 0.00 0.00 4.85
790 1353 1.885388 GCGTACACACACACTGGCA 60.885 57.895 0.00 0.00 0.00 4.92
791 1354 1.831389 GCGTACACACACACTGGCAG 61.831 60.000 14.16 14.16 0.00 4.85
792 1355 0.529773 CGTACACACACACTGGCAGT 60.530 55.000 15.88 15.88 0.00 4.40
813 1376 0.527385 GCCGTCAACTTTGCAGCAAA 60.527 50.000 19.55 19.55 0.00 3.68
860 1427 3.162202 TCCACATTGCACAAACAACTG 57.838 42.857 0.00 0.00 31.03 3.16
861 1428 1.593933 CCACATTGCACAAACAACTGC 59.406 47.619 0.00 0.00 31.03 4.40
875 1442 7.862372 CACAAACAACTGCTTAACTACAATCAT 59.138 33.333 0.00 0.00 0.00 2.45
909 1476 4.941263 ACAGTTTGTACTTGCTTGTCTTCA 59.059 37.500 0.00 0.00 30.26 3.02
969 1546 0.882927 AACTAAAGCTTGCCGCGACA 60.883 50.000 8.23 0.00 45.59 4.35
984 1561 1.361668 CGACATTTCAGCTGACCGGG 61.362 60.000 18.03 9.05 0.00 5.73
1071 1650 6.744175 ATCATGGACAAGATACTCATCAGT 57.256 37.500 0.00 0.00 36.55 3.41
1080 1659 1.990799 TACTCATCAGTTTGCCGTCG 58.009 50.000 0.00 0.00 33.62 5.12
1270 1864 4.111053 GGCCTTTCCTCCCGGGTC 62.111 72.222 22.86 0.52 36.25 4.46
1272 1866 2.285442 CCTTTCCTCCCGGGTCCT 60.285 66.667 22.86 0.00 36.25 3.85
1291 1888 2.163010 CCTGAACATCGCTTGCAGAATT 59.837 45.455 0.00 0.00 0.00 2.17
1535 2155 2.664851 CGACAAGCCGAGGCACAA 60.665 61.111 17.18 0.00 44.88 3.33
1827 3095 1.185618 CGACTCCCAGGTCCACTTCA 61.186 60.000 0.00 0.00 33.07 3.02
1890 3158 3.279434 GGCTTTCAAGTACCGGATTGAT 58.721 45.455 9.46 0.00 35.47 2.57
2004 3278 2.031245 CGATGTGGCTGTGCTAAACAAA 60.031 45.455 0.00 0.00 38.67 2.83
2268 3570 4.184629 CTCTTCCTACTTGTACCACATGC 58.815 47.826 0.00 0.00 0.00 4.06
2272 3574 4.034410 TCCTACTTGTACCACATGCCATA 58.966 43.478 0.00 0.00 0.00 2.74
2419 3725 8.695456 TGTTATTCTAGATCTCTTACATGTGCA 58.305 33.333 9.11 0.00 0.00 4.57
2433 3739 4.139786 ACATGTGCAGTCTGTTTGATTCT 58.860 39.130 0.00 0.00 0.00 2.40
2434 3740 4.581824 ACATGTGCAGTCTGTTTGATTCTT 59.418 37.500 0.00 0.00 0.00 2.52
2449 3755 1.355796 TTCTTAATGTCCGGCGTGCG 61.356 55.000 6.01 0.00 0.00 5.34
2530 3838 8.940397 TGATCTAAGAAATCCTTGGTTCTTTT 57.060 30.769 9.53 0.00 40.37 2.27
2534 3842 3.005791 AGAAATCCTTGGTTCTTTTGCCG 59.994 43.478 0.00 0.00 29.67 5.69
2540 3848 0.736053 TGGTTCTTTTGCCGTGTGTC 59.264 50.000 0.00 0.00 0.00 3.67
2541 3849 0.316689 GGTTCTTTTGCCGTGTGTCG 60.317 55.000 0.00 0.00 39.52 4.35
2625 3938 4.991056 GTGTAGAAAGTGCTGAAGATGTGA 59.009 41.667 0.00 0.00 0.00 3.58
2649 3965 7.341512 TGATCTCCTGTAGCAAGATAGATATGG 59.658 40.741 0.00 0.00 30.04 2.74
2674 3991 4.712337 GGTCCTCTGTTCATCTTTCTCCTA 59.288 45.833 0.00 0.00 0.00 2.94
2725 4043 2.738587 TGGTCCAGTTTGTAGCCAAA 57.261 45.000 0.00 0.00 38.22 3.28
2741 4060 7.422399 TGTAGCCAAACTGTAAAAGAATTGTC 58.578 34.615 0.00 0.00 0.00 3.18
2752 4071 2.113860 AGAATTGTCCATCACCGGTG 57.886 50.000 29.26 29.26 0.00 4.94
2753 4072 1.628340 AGAATTGTCCATCACCGGTGA 59.372 47.619 37.79 37.79 44.59 4.02
2791 4110 3.259123 AGGTTTCCAGCCATGAAATTGTC 59.741 43.478 0.00 0.00 34.50 3.18
2886 4205 5.928976 TCAATGTTCCAGGATCGTATCATT 58.071 37.500 0.00 0.00 0.00 2.57
2943 4295 2.498167 GCAGAAGGAACACATCACAGT 58.502 47.619 0.00 0.00 0.00 3.55
2944 4296 2.880890 GCAGAAGGAACACATCACAGTT 59.119 45.455 0.00 0.00 0.00 3.16
2945 4297 3.058639 GCAGAAGGAACACATCACAGTTC 60.059 47.826 0.00 0.00 42.51 3.01
2946 4298 4.129380 CAGAAGGAACACATCACAGTTCA 58.871 43.478 7.49 0.00 44.46 3.18
2947 4299 4.024556 CAGAAGGAACACATCACAGTTCAC 60.025 45.833 7.49 0.00 44.46 3.18
2948 4300 3.558931 AGGAACACATCACAGTTCACA 57.441 42.857 7.49 0.00 44.46 3.58
2949 4301 3.470709 AGGAACACATCACAGTTCACAG 58.529 45.455 7.49 0.00 44.46 3.66
2998 4350 2.892374 TCAGCACATTCTGATACCGTG 58.108 47.619 0.00 0.00 38.11 4.94
2999 4351 1.935873 CAGCACATTCTGATACCGTGG 59.064 52.381 0.00 0.00 36.19 4.94
3000 4352 1.831106 AGCACATTCTGATACCGTGGA 59.169 47.619 0.00 0.00 0.00 4.02
3001 4353 2.435805 AGCACATTCTGATACCGTGGAT 59.564 45.455 0.00 0.00 0.00 3.41
3002 4354 3.118261 AGCACATTCTGATACCGTGGATT 60.118 43.478 0.00 0.00 0.00 3.01
3004 4356 3.002656 CACATTCTGATACCGTGGATTGC 59.997 47.826 0.00 0.00 0.00 3.56
3085 4443 1.469079 CGAAACATCCGGGGAAAATGC 60.469 52.381 0.00 0.00 0.00 3.56
3092 4450 1.074727 TCCGGGGAAAATGCTCTCAAA 59.925 47.619 0.00 0.00 0.00 2.69
3093 4451 2.102578 CCGGGGAAAATGCTCTCAAAT 58.897 47.619 0.00 0.00 0.00 2.32
3099 4457 7.417342 CCGGGGAAAATGCTCTCAAATAATTTA 60.417 37.037 0.00 0.00 0.00 1.40
3144 4502 4.290093 ACATCTAGTCACTGGCCAGATAA 58.710 43.478 39.19 19.93 0.00 1.75
3215 4574 5.772169 AGGAAGAAAGAATGGAAGGAAACAG 59.228 40.000 0.00 0.00 0.00 3.16
3218 4577 7.039434 GGAAGAAAGAATGGAAGGAAACAGAAT 60.039 37.037 0.00 0.00 0.00 2.40
3219 4578 8.940397 AAGAAAGAATGGAAGGAAACAGAATA 57.060 30.769 0.00 0.00 0.00 1.75
3220 4579 8.572855 AGAAAGAATGGAAGGAAACAGAATAG 57.427 34.615 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.376812 CGTCCACCCAGGGCTAAAC 60.377 63.158 4.91 0.00 40.99 2.01
2 3 3.074281 CGTCCACCCAGGGCTAAA 58.926 61.111 4.91 0.00 40.99 1.85
104 108 2.542907 GCTCGAGCGAGGGAGAGAG 61.543 68.421 23.61 0.00 42.19 3.20
105 109 2.515057 GCTCGAGCGAGGGAGAGA 60.515 66.667 23.61 0.00 42.19 3.10
115 119 1.153469 CTTTGGGGAGAGCTCGAGC 60.153 63.158 30.01 30.01 42.49 5.03
132 557 1.764054 CGAGCTGGATCCCCTTCCT 60.764 63.158 9.90 0.00 36.68 3.36
168 593 1.194781 GCCAGGACAGAAGGAGACCA 61.195 60.000 0.00 0.00 0.00 4.02
170 595 0.248843 CAGCCAGGACAGAAGGAGAC 59.751 60.000 0.00 0.00 0.00 3.36
176 601 2.922503 TCCGCAGCCAGGACAGAA 60.923 61.111 0.00 0.00 31.86 3.02
219 651 2.026590 GTGGTCGTCGAACCGTGT 59.973 61.111 8.02 0.00 42.62 4.49
231 663 4.803426 CGGCTCGGCTGAGTGGTC 62.803 72.222 23.36 6.87 44.48 4.02
261 693 1.535833 GAGAAGGTGTCTGTCGGAGA 58.464 55.000 0.00 0.00 36.41 3.71
411 876 1.401905 CGCCTCTGGTTAATTTGAGCC 59.598 52.381 0.00 0.00 0.00 4.70
488 959 4.144727 GAGGGAGGGGCGAGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
499 970 1.027255 TGAGAAGCGAGACGAGGGAG 61.027 60.000 0.00 0.00 0.00 4.30
502 973 1.137825 GGTGAGAAGCGAGACGAGG 59.862 63.158 0.00 0.00 0.00 4.63
538 1009 0.827925 ACTGAGCTGAACCACCTCGA 60.828 55.000 0.00 0.00 0.00 4.04
587 1058 4.940654 GGTACTACTACTCTGTCGGTCTTT 59.059 45.833 0.00 0.00 0.00 2.52
593 1064 4.757594 ACTGAGGTACTACTACTCTGTCG 58.242 47.826 0.00 0.00 41.55 4.35
622 1093 2.621055 ACTCTCTCTGTGTGTGTGTCTC 59.379 50.000 0.00 0.00 0.00 3.36
624 1095 3.444703 AACTCTCTCTGTGTGTGTGTC 57.555 47.619 0.00 0.00 0.00 3.67
636 1109 1.341606 CGTCGCCTGAAAACTCTCTC 58.658 55.000 0.00 0.00 0.00 3.20
669 1169 8.989653 AGTAGTATACAGCTCAAAAGAAGAAC 57.010 34.615 5.50 0.00 46.26 3.01
680 1180 7.623925 GCCGTATCTGTTAGTAGTATACAGCTC 60.624 44.444 5.50 0.00 46.26 4.09
682 1182 6.072838 TGCCGTATCTGTTAGTAGTATACAGC 60.073 42.308 5.50 0.00 46.26 4.40
686 1186 7.716560 TCAGTTGCCGTATCTGTTAGTAGTATA 59.283 37.037 0.00 0.00 0.00 1.47
687 1187 6.544931 TCAGTTGCCGTATCTGTTAGTAGTAT 59.455 38.462 0.00 0.00 0.00 2.12
688 1188 5.882000 TCAGTTGCCGTATCTGTTAGTAGTA 59.118 40.000 0.00 0.00 0.00 1.82
689 1189 4.703575 TCAGTTGCCGTATCTGTTAGTAGT 59.296 41.667 0.00 0.00 0.00 2.73
690 1190 5.244785 TCAGTTGCCGTATCTGTTAGTAG 57.755 43.478 0.00 0.00 0.00 2.57
691 1191 4.439700 GCTCAGTTGCCGTATCTGTTAGTA 60.440 45.833 0.00 0.00 0.00 1.82
692 1192 3.676324 GCTCAGTTGCCGTATCTGTTAGT 60.676 47.826 0.00 0.00 0.00 2.24
693 1193 2.860735 GCTCAGTTGCCGTATCTGTTAG 59.139 50.000 0.00 0.00 0.00 2.34
721 1229 3.813529 AAACTGAGTTGTAGCATTCGC 57.186 42.857 0.00 0.00 38.99 4.70
737 1245 7.737972 TGTATGTATGTGTTGCAGTAAAACT 57.262 32.000 0.00 0.00 0.00 2.66
738 1246 7.484641 CCATGTATGTATGTGTTGCAGTAAAAC 59.515 37.037 0.00 0.00 0.00 2.43
762 1310 2.281208 GTGTACGCAGGTTGGCCA 60.281 61.111 0.00 0.00 37.19 5.36
763 1311 2.281208 TGTGTACGCAGGTTGGCC 60.281 61.111 4.65 0.00 0.00 5.36
772 1335 1.831389 CTGCCAGTGTGTGTGTACGC 61.831 60.000 0.00 0.00 37.82 4.42
774 1337 0.937304 CACTGCCAGTGTGTGTGTAC 59.063 55.000 16.78 0.00 41.19 2.90
775 1338 0.179059 CCACTGCCAGTGTGTGTGTA 60.179 55.000 22.54 0.00 44.50 2.90
788 1351 1.008538 CAAAGTTGACGGCCACTGC 60.009 57.895 2.24 0.00 0.00 4.40
789 1352 1.008538 GCAAAGTTGACGGCCACTG 60.009 57.895 2.24 0.00 0.00 3.66
790 1353 1.447317 CTGCAAAGTTGACGGCCACT 61.447 55.000 2.24 0.00 0.00 4.00
791 1354 1.008538 CTGCAAAGTTGACGGCCAC 60.009 57.895 2.24 0.00 0.00 5.01
792 1355 2.844451 GCTGCAAAGTTGACGGCCA 61.844 57.895 2.24 0.00 33.47 5.36
793 1356 2.050077 GCTGCAAAGTTGACGGCC 60.050 61.111 0.00 0.00 33.47 6.13
860 1427 7.308782 AGCTTACACATGATTGTAGTTAAGC 57.691 36.000 0.00 6.64 33.50 3.09
875 1442 6.238266 GCAAGTACAAACTGTTAGCTTACACA 60.238 38.462 0.43 0.00 35.62 3.72
909 1476 2.758979 CCTTTGGAGCAGCTGAAATCAT 59.241 45.455 20.43 0.00 0.00 2.45
969 1546 1.078143 GAGCCCGGTCAGCTGAAAT 60.078 57.895 20.19 0.35 41.75 2.17
984 1561 3.873883 ATCGTCGTCCGTCGGAGC 61.874 66.667 15.95 8.92 40.32 4.70
996 1575 2.892425 CTTCTGCCCGGCATCGTC 60.892 66.667 13.86 0.00 38.13 4.20
1270 1864 1.159285 TTCTGCAAGCGATGTTCAGG 58.841 50.000 0.00 0.00 0.00 3.86
1272 1866 3.206034 CAATTCTGCAAGCGATGTTCA 57.794 42.857 0.00 0.00 0.00 3.18
1335 1938 2.391616 TGCAGATGTAGAGCTGGTTG 57.608 50.000 7.30 0.00 36.03 3.77
1485 2105 3.068165 TGAGGACGTATAAGCTGGATGTG 59.932 47.826 0.00 0.00 0.00 3.21
1535 2155 0.969149 TGTCGGCATTCTGACTCTGT 59.031 50.000 5.90 0.00 46.36 3.41
1715 2893 1.071385 GCATCCATCGGAATGACTCCT 59.929 52.381 0.00 0.00 42.85 3.69
1827 3095 1.285667 TGCATCACCCAGACATCCATT 59.714 47.619 0.00 0.00 0.00 3.16
1890 3158 1.480212 ATGCCTCCACGGTTGACAGA 61.480 55.000 0.00 0.00 34.25 3.41
2004 3278 0.327259 ACATGACCAGCAGCTCACAT 59.673 50.000 0.00 0.00 0.00 3.21
2050 3324 4.019174 CCTAGGAACTTGCCATCAACATT 58.981 43.478 1.05 0.00 41.75 2.71
2268 3570 4.580167 ACCAAACGATCACATCCAATATGG 59.420 41.667 0.00 0.00 39.43 2.74
2272 3574 2.164219 GCACCAAACGATCACATCCAAT 59.836 45.455 0.00 0.00 0.00 3.16
2415 3721 6.672147 ACATTAAGAATCAAACAGACTGCAC 58.328 36.000 1.25 0.00 0.00 4.57
2419 3725 5.643777 CCGGACATTAAGAATCAAACAGACT 59.356 40.000 0.00 0.00 0.00 3.24
2433 3739 3.492545 GCGCACGCCGGACATTAA 61.493 61.111 5.05 0.00 37.44 1.40
2534 3842 2.987547 TCCCGAGTCCCGACACAC 60.988 66.667 0.00 0.00 41.76 3.82
2541 3849 4.437587 TCCCGAGTCCCGAGTCCC 62.438 72.222 0.00 0.00 41.76 4.46
2542 3850 2.829458 CTCCCGAGTCCCGAGTCC 60.829 72.222 0.00 0.00 41.76 3.85
2543 3851 3.519930 GCTCCCGAGTCCCGAGTC 61.520 72.222 3.71 0.00 41.76 3.36
2544 3852 4.361971 TGCTCCCGAGTCCCGAGT 62.362 66.667 3.71 0.00 41.76 4.18
2545 3853 3.827898 GTGCTCCCGAGTCCCGAG 61.828 72.222 0.00 0.00 41.76 4.63
2625 3938 7.123997 CACCATATCTATCTTGCTACAGGAGAT 59.876 40.741 0.00 0.00 34.67 2.75
2649 3965 4.249661 GAGAAAGATGAACAGAGGACCAC 58.750 47.826 0.00 0.00 0.00 4.16
2674 3991 1.395826 GGTCTGCCCTGTCGCTCTAT 61.396 60.000 0.00 0.00 0.00 1.98
2725 4043 5.181245 CGGTGATGGACAATTCTTTTACAGT 59.819 40.000 0.00 0.00 0.00 3.55
2741 4060 2.436646 GCTGGTCACCGGTGATGG 60.437 66.667 38.11 28.56 42.18 3.51
2752 4071 1.202818 ACCTGAAAGACTTGGCTGGTC 60.203 52.381 11.68 3.01 34.07 4.02
2753 4072 0.846693 ACCTGAAAGACTTGGCTGGT 59.153 50.000 11.68 11.68 34.07 4.00
2886 4205 7.914871 CAGTGTCAACAATACTGAAATGTTTCA 59.085 33.333 7.84 7.84 46.88 2.69
2943 4295 1.872952 CGTTTCTGTGGCATCTGTGAA 59.127 47.619 0.00 0.00 0.00 3.18
2944 4296 1.069978 TCGTTTCTGTGGCATCTGTGA 59.930 47.619 0.00 0.00 0.00 3.58
2945 4297 1.195448 GTCGTTTCTGTGGCATCTGTG 59.805 52.381 0.00 0.00 0.00 3.66
2946 4298 1.202639 TGTCGTTTCTGTGGCATCTGT 60.203 47.619 0.00 0.00 0.00 3.41
2947 4299 1.511850 TGTCGTTTCTGTGGCATCTG 58.488 50.000 0.00 0.00 0.00 2.90
2948 4300 1.873591 GTTGTCGTTTCTGTGGCATCT 59.126 47.619 0.00 0.00 0.00 2.90
2949 4301 1.398451 CGTTGTCGTTTCTGTGGCATC 60.398 52.381 0.00 0.00 0.00 3.91
2984 4336 3.002656 GTGCAATCCACGGTATCAGAATG 59.997 47.826 0.00 0.00 34.22 2.67
2997 4349 0.329261 CTCCCTCCTTGTGCAATCCA 59.671 55.000 0.00 0.00 0.00 3.41
2998 4350 1.034292 GCTCCCTCCTTGTGCAATCC 61.034 60.000 0.00 0.00 0.00 3.01
2999 4351 0.322816 TGCTCCCTCCTTGTGCAATC 60.323 55.000 0.00 0.00 0.00 2.67
3000 4352 0.112995 TTGCTCCCTCCTTGTGCAAT 59.887 50.000 0.00 0.00 38.49 3.56
3001 4353 0.538057 CTTGCTCCCTCCTTGTGCAA 60.538 55.000 0.00 0.00 40.65 4.08
3002 4354 1.073722 CTTGCTCCCTCCTTGTGCA 59.926 57.895 0.00 0.00 0.00 4.57
3004 4356 0.538057 TTGCTTGCTCCCTCCTTGTG 60.538 55.000 0.00 0.00 0.00 3.33
3123 4481 4.944619 TTATCTGGCCAGTGACTAGATG 57.055 45.455 31.58 3.59 31.19 2.90
3125 4483 4.962362 TGAATTATCTGGCCAGTGACTAGA 59.038 41.667 31.58 12.00 0.00 2.43
3144 4502 1.612676 TTGCTTGCTGTGAGCTGAAT 58.387 45.000 0.00 0.00 42.97 2.57


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

AutoCloner maintained by Alex Coulton.