Multiple sequence alignment - TraesCS7A01G008800

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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 TraesCS7A01G008800 chr7A 100.000 3261 0 0 1 3261 3861198 3857938 0.000000e+00 6023.0
1 TraesCS7A01G008800 chr7A 78.112 233 42 6 1325 1549 34519296 34519065 4.390000e-29 139.0
2 TraesCS7A01G008800 chr7A 85.870 92 10 3 165 254 97912758 97912668 9.630000e-16 95.3
3 TraesCS7A01G008800 chr4A 90.312 2405 137 55 323 2674 739586217 739588578 0.000000e+00 3062.0
4 TraesCS7A01G008800 chr4A 92.857 546 24 3 2730 3261 739588683 739589227 0.000000e+00 778.0
5 TraesCS7A01G008800 chr4A 90.751 173 12 2 2 170 739585971 739586143 9.100000e-56 228.0
6 TraesCS7A01G008800 chr4A 77.682 233 43 6 1325 1549 691247057 691247288 2.040000e-27 134.0
7 TraesCS7A01G008800 chr4A 87.500 88 8 3 169 254 738802939 738802853 7.450000e-17 99.0
8 TraesCS7A01G008800 chr4A 90.909 55 5 0 271 325 739586150 739586204 1.250000e-09 75.0
9 TraesCS7A01G008800 chr7D 88.536 2582 161 69 522 3015 4027301 4024767 0.000000e+00 3003.0
10 TraesCS7A01G008800 chr7D 90.814 479 29 3 2 465 4027790 4027312 7.680000e-176 627.0
11 TraesCS7A01G008800 chr7D 77.444 266 46 10 1302 1560 420742663 420742405 2.620000e-31 147.0
12 TraesCS7A01G008800 chr7D 95.294 85 4 0 3177 3261 4024730 4024646 5.680000e-28 135.0
13 TraesCS7A01G008800 chr7D 87.500 88 7 4 169 254 619757854 619757939 7.450000e-17 99.0
14 TraesCS7A01G008800 chr7D 100.000 29 0 0 483 511 4027307 4027279 2.000000e-03 54.7
15 TraesCS7A01G008800 chr6D 84.836 244 35 2 1319 1561 310888070 310887828 9.040000e-61 244.0
16 TraesCS7A01G008800 chr6B 84.836 244 35 2 1319 1561 515577927 515578169 9.040000e-61 244.0
17 TraesCS7A01G008800 chr6A 84.836 244 35 2 1319 1561 447178897 447178655 9.040000e-61 244.0
18 TraesCS7A01G008800 chr6A 87.778 90 10 1 166 255 115022793 115022881 1.600000e-18 104.0
19 TraesCS7A01G008800 chr7B 77.444 266 46 10 1302 1560 436787606 436787348 2.620000e-31 147.0
20 TraesCS7A01G008800 chr7B 86.364 88 8 4 169 254 559634417 559634332 3.460000e-15 93.5
21 TraesCS7A01G008800 chr4B 94.048 84 4 1 171 254 598404826 598404908 3.420000e-25 126.0
22 TraesCS7A01G008800 chr5B 86.207 87 12 0 168 254 463778074 463778160 9.630000e-16 95.3
23 TraesCS7A01G008800 chr2A 86.364 88 8 4 169 254 627260647 627260562 3.460000e-15 93.5


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 TraesCS7A01G008800 chr7A 3857938 3861198 3260 True 6023.000 6023 100.00000 1 3261 1 chr7A.!!$R1 3260
1 TraesCS7A01G008800 chr4A 739585971 739589227 3256 False 1035.750 3062 91.20725 2 3261 4 chr4A.!!$F2 3259
2 TraesCS7A01G008800 chr7D 4024646 4027790 3144 True 954.925 3003 93.66100 2 3261 4 chr7D.!!$R2 3259

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
662 686 0.107993 TGCCTCTCAGCATGTGTAGC 60.108 55.0 0.00 0.00 38.00 3.58 F
1807 1880 0.190069 ATGGGCCCTTCATGCATGAT 59.810 50.0 29.13 9.73 36.56 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2288 1.443702 CGATGTTGAGGTCGACGCA 60.444 57.895 9.92 7.58 40.11 5.24 R
2691 2785 1.909700 TTTGTTCCCTGACATGAGGC 58.090 50.000 0.00 0.00 0.00 4.70 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
116 119 3.754955 CATGTTGAGATGATGTGTGTGC 58.245 45.455 0.00 0.00 0.00 4.57
117 120 2.848691 TGTTGAGATGATGTGTGTGCA 58.151 42.857 0.00 0.00 0.00 4.57
189 194 8.487028 GGATATACTCCTTCCGATCCATAATTT 58.513 37.037 0.00 0.00 41.29 1.82
195 200 6.184068 TCCTTCCGATCCATAATTTTTGTCA 58.816 36.000 0.00 0.00 0.00 3.58
197 202 7.996066 TCCTTCCGATCCATAATTTTTGTCATA 59.004 33.333 0.00 0.00 0.00 2.15
282 287 1.167851 ATGTTCCCTTGCACATGACG 58.832 50.000 0.00 0.00 32.19 4.35
294 299 2.030335 GCACATGACGATGCGTATTTGA 59.970 45.455 0.00 0.00 41.37 2.69
397 420 2.389449 ATGCCCACCAGCCAGCTAT 61.389 57.895 0.00 0.00 0.00 2.97
478 501 9.507329 CAAGTGCTTATATATGACCCAACTATT 57.493 33.333 0.00 0.00 0.00 1.73
480 503 9.507329 AGTGCTTATATATGACCCAACTATTTG 57.493 33.333 0.00 0.00 0.00 2.32
518 541 4.213270 TGCAAATACAAGTAGCACAGACAC 59.787 41.667 0.00 0.00 0.00 3.67
521 544 6.092122 GCAAATACAAGTAGCACAGACACATA 59.908 38.462 0.00 0.00 0.00 2.29
522 545 7.201644 GCAAATACAAGTAGCACAGACACATAT 60.202 37.037 0.00 0.00 0.00 1.78
523 546 9.313118 CAAATACAAGTAGCACAGACACATATA 57.687 33.333 0.00 0.00 0.00 0.86
535 558 9.698309 GCACAGACACATATATAAGTTCACTAT 57.302 33.333 0.00 0.00 0.00 2.12
570 593 3.059352 AGAGCAGGGACAAACATACAC 57.941 47.619 0.00 0.00 0.00 2.90
662 686 0.107993 TGCCTCTCAGCATGTGTAGC 60.108 55.000 0.00 0.00 38.00 3.58
715 739 3.941483 CTCCCAGCATTACCACTACTTTG 59.059 47.826 0.00 0.00 0.00 2.77
773 801 5.265958 AGACACATCTAGGCATGCTTGCT 62.266 47.826 22.27 8.96 40.32 3.91
790 818 1.202498 TGCTTGCTCGATCTCCATCAG 60.202 52.381 0.00 0.00 0.00 2.90
840 868 4.898320 TGCTTATGTGTATAGATGGGCAG 58.102 43.478 0.00 0.00 0.00 4.85
843 871 5.869888 GCTTATGTGTATAGATGGGCAGTAC 59.130 44.000 0.00 0.00 0.00 2.73
844 872 6.295349 GCTTATGTGTATAGATGGGCAGTACT 60.295 42.308 0.00 0.00 0.00 2.73
845 873 7.612065 TTATGTGTATAGATGGGCAGTACTT 57.388 36.000 0.00 0.00 0.00 2.24
846 874 5.950544 TGTGTATAGATGGGCAGTACTTT 57.049 39.130 0.00 0.00 0.00 2.66
881 909 3.748083 TCTTTTGCTGTCTTCTCTGCAT 58.252 40.909 0.00 0.00 40.70 3.96
908 936 3.980134 TGCATGCTTCATTTTTACACACG 59.020 39.130 20.33 0.00 0.00 4.49
909 937 3.980775 GCATGCTTCATTTTTACACACGT 59.019 39.130 11.37 0.00 0.00 4.49
910 938 4.088496 GCATGCTTCATTTTTACACACGTC 59.912 41.667 11.37 0.00 0.00 4.34
911 939 4.884458 TGCTTCATTTTTACACACGTCA 57.116 36.364 0.00 0.00 0.00 4.35
913 941 4.095036 TGCTTCATTTTTACACACGTCACA 59.905 37.500 0.00 0.00 0.00 3.58
914 942 5.031578 GCTTCATTTTTACACACGTCACAA 58.968 37.500 0.00 0.00 0.00 3.33
915 943 5.685511 GCTTCATTTTTACACACGTCACAAT 59.314 36.000 0.00 0.00 0.00 2.71
916 944 6.853872 GCTTCATTTTTACACACGTCACAATA 59.146 34.615 0.00 0.00 0.00 1.90
917 945 7.377397 GCTTCATTTTTACACACGTCACAATAA 59.623 33.333 0.00 0.00 0.00 1.40
918 946 9.393249 CTTCATTTTTACACACGTCACAATAAT 57.607 29.630 0.00 0.00 0.00 1.28
924 952 9.600646 TTTTACACACGTCACAATAATACAATG 57.399 29.630 0.00 0.00 0.00 2.82
927 955 8.710835 ACACACGTCACAATAATACAATGATA 57.289 30.769 0.00 0.00 0.00 2.15
984 1012 5.148651 CCTTACAGGTTTAGCTGTACACT 57.851 43.478 18.42 0.00 36.01 3.55
989 1017 4.528596 ACAGGTTTAGCTGTACACTGATCT 59.471 41.667 12.50 3.69 31.30 2.75
992 1020 6.920758 CAGGTTTAGCTGTACACTGATCTATC 59.079 42.308 0.00 0.00 0.00 2.08
997 1025 3.315470 GCTGTACACTGATCTATCGGACA 59.685 47.826 5.80 0.00 36.97 4.02
998 1026 4.202020 GCTGTACACTGATCTATCGGACAA 60.202 45.833 5.80 0.00 36.97 3.18
999 1027 5.244785 TGTACACTGATCTATCGGACAAC 57.755 43.478 5.80 1.75 36.97 3.32
1000 1028 4.703093 TGTACACTGATCTATCGGACAACA 59.297 41.667 5.80 3.98 36.97 3.33
1001 1029 5.359860 TGTACACTGATCTATCGGACAACAT 59.640 40.000 5.80 0.00 36.97 2.71
1002 1030 4.686972 ACACTGATCTATCGGACAACATG 58.313 43.478 5.80 0.00 36.97 3.21
1003 1031 4.402474 ACACTGATCTATCGGACAACATGA 59.598 41.667 0.00 0.00 36.97 3.07
1004 1032 4.981054 CACTGATCTATCGGACAACATGAG 59.019 45.833 0.00 0.00 36.97 2.90
1010 1042 0.320683 TCGGACAACATGAGTGGCAG 60.321 55.000 0.00 0.00 0.00 4.85
1050 1082 4.583086 GGTTTTCGGTTCCACCCA 57.417 55.556 0.00 0.00 33.75 4.51
1053 1085 0.386476 GTTTTCGGTTCCACCCAACC 59.614 55.000 0.00 0.00 42.34 3.77
1065 1097 1.201429 ACCCAACCGATGAGGAGCTT 61.201 55.000 0.00 0.00 45.00 3.74
1071 1103 0.467384 CCGATGAGGAGCTTGTGGAT 59.533 55.000 0.00 0.00 45.00 3.41
1095 1127 2.747855 CTCCGCAAGAAGGTGGCC 60.748 66.667 0.00 0.00 38.34 5.36
1098 1130 3.121030 CGCAAGAAGGTGGCCTCG 61.121 66.667 3.32 0.00 43.02 4.63
1101 1133 1.078848 CAAGAAGGTGGCCTCGAGG 60.079 63.158 27.83 27.83 30.89 4.63
1158 1190 3.898123 TCTACAAGATAGAGCCATGGGAC 59.102 47.826 15.13 0.00 0.00 4.46
1219 1286 3.441222 TGCAGTCCAATTAGCAATGACAG 59.559 43.478 0.00 0.00 33.48 3.51
1224 1291 5.945784 AGTCCAATTAGCAATGACAGCTTAA 59.054 36.000 0.00 0.00 43.25 1.85
1230 1297 8.400947 CAATTAGCAATGACAGCTTAATGTAGT 58.599 33.333 0.00 0.00 43.25 2.73
1236 1303 7.675870 GCAATGACAGCTTAATGTAGTCTTGAG 60.676 40.741 11.13 0.00 32.25 3.02
1237 1304 6.346477 TGACAGCTTAATGTAGTCTTGAGT 57.654 37.500 0.00 0.00 32.25 3.41
1238 1305 6.390721 TGACAGCTTAATGTAGTCTTGAGTC 58.609 40.000 0.00 0.00 32.25 3.36
1239 1306 6.209589 TGACAGCTTAATGTAGTCTTGAGTCT 59.790 38.462 0.00 0.00 32.25 3.24
1240 1307 6.998802 ACAGCTTAATGTAGTCTTGAGTCTT 58.001 36.000 0.00 0.00 0.00 3.01
1241 1308 6.870965 ACAGCTTAATGTAGTCTTGAGTCTTG 59.129 38.462 0.00 0.00 0.00 3.02
1242 1309 7.093354 CAGCTTAATGTAGTCTTGAGTCTTGA 58.907 38.462 0.00 0.00 0.00 3.02
1243 1310 7.062839 CAGCTTAATGTAGTCTTGAGTCTTGAC 59.937 40.741 7.65 7.65 0.00 3.18
1244 1311 6.868864 GCTTAATGTAGTCTTGAGTCTTGACA 59.131 38.462 15.01 2.46 33.56 3.58
1245 1312 7.385205 GCTTAATGTAGTCTTGAGTCTTGACAA 59.615 37.037 15.01 0.00 33.56 3.18
1246 1313 8.589335 TTAATGTAGTCTTGAGTCTTGACAAC 57.411 34.615 15.01 0.00 33.56 3.32
1247 1314 5.592104 TGTAGTCTTGAGTCTTGACAACA 57.408 39.130 15.01 0.83 33.56 3.33
1248 1315 5.348986 TGTAGTCTTGAGTCTTGACAACAC 58.651 41.667 15.01 10.96 33.56 3.32
1249 1316 4.471904 AGTCTTGAGTCTTGACAACACA 57.528 40.909 15.01 0.00 33.56 3.72
1250 1317 4.832248 AGTCTTGAGTCTTGACAACACAA 58.168 39.130 15.01 3.87 33.56 3.33
1251 1318 5.245531 AGTCTTGAGTCTTGACAACACAAA 58.754 37.500 15.01 0.00 33.56 2.83
1252 1319 5.882557 AGTCTTGAGTCTTGACAACACAAAT 59.117 36.000 15.01 0.00 33.56 2.32
1255 1322 8.181573 GTCTTGAGTCTTGACAACACAAATTAA 58.818 33.333 3.49 0.00 29.01 1.40
1330 1398 1.685421 GCCTGAGGAGGAGCAGAGT 60.685 63.158 0.65 0.00 42.93 3.24
1454 1522 2.022195 CCATCTATGCAAAGCACTGCT 58.978 47.619 10.88 0.00 43.04 4.24
1558 1626 1.646189 GCCTCGAGACCAATGAGAAC 58.354 55.000 15.71 0.00 31.31 3.01
1586 1654 7.812133 CCTCCACAGGCAAGCTATAGCTATG 62.812 52.000 27.11 24.15 41.40 2.23
1630 1699 3.073274 TCTCTGTCCATCTTGACTCGA 57.927 47.619 0.00 0.00 36.21 4.04
1648 1721 4.811557 ACTCGAATATAAACCTGCAAGCTC 59.188 41.667 0.00 0.00 0.00 4.09
1735 1808 3.933332 GGGTGTTCAAGAAGAGATTACCG 59.067 47.826 0.00 0.00 0.00 4.02
1756 1829 5.654650 ACCGACAACAAGAAGAGATCTAGAT 59.345 40.000 4.47 4.47 37.42 1.98
1807 1880 0.190069 ATGGGCCCTTCATGCATGAT 59.810 50.000 29.13 9.73 36.56 2.45
1834 1907 0.841961 CTCCCATGAGAGGAATGCCA 59.158 55.000 0.00 0.00 41.42 4.92
1884 1957 1.421268 ACACCTCCAGATGCTCAACAA 59.579 47.619 0.00 0.00 0.00 2.83
1897 1970 3.133901 TGCTCAACAACACCTACAAGAGA 59.866 43.478 0.00 0.00 0.00 3.10
1951 2024 5.220989 CCATCATCATGTTCTCAACACCATC 60.221 44.000 0.00 0.00 45.50 3.51
2113 2186 3.492829 GGAGAGTTCTGGACAAGTTCGTT 60.493 47.826 0.00 0.00 0.00 3.85
2116 2189 1.668751 GTTCTGGACAAGTTCGTTGCA 59.331 47.619 0.00 0.00 40.15 4.08
2144 2217 3.879295 GCTTAGTAATGATGCAGCCAAGA 59.121 43.478 0.00 0.00 0.00 3.02
2194 2267 0.392706 TTCAGCTCAACGAGAAGGCA 59.607 50.000 0.00 0.00 0.00 4.75
2215 2288 4.082571 GCACAAGAGTTGGCAACTGATTAT 60.083 41.667 35.57 17.26 43.03 1.28
2282 2355 2.480555 CAGCGGCACCAATCGAAC 59.519 61.111 1.45 0.00 0.00 3.95
2532 2607 6.460676 GGAGACCATAAAGGCTTCATGAATTG 60.461 42.308 12.09 0.00 43.14 2.32
2601 2676 6.018262 TGTTGGTTTCTCAACGAACTTGATAG 60.018 38.462 12.34 0.00 46.44 2.08
2602 2677 4.451096 TGGTTTCTCAACGAACTTGATAGC 59.549 41.667 0.00 0.00 38.26 2.97
2609 2684 4.511454 TCAACGAACTTGATAGCCATATGC 59.489 41.667 0.00 0.00 33.65 3.14
2610 2685 3.403038 ACGAACTTGATAGCCATATGCC 58.597 45.455 0.00 0.00 42.71 4.40
2611 2686 2.413112 CGAACTTGATAGCCATATGCCG 59.587 50.000 0.00 0.00 42.71 5.69
2612 2687 2.479566 ACTTGATAGCCATATGCCGG 57.520 50.000 0.00 0.00 42.71 6.13
2666 2748 6.374333 ACCGACTGTGCTCATTTTTATAACAT 59.626 34.615 0.00 0.00 0.00 2.71
2703 2873 3.758755 TGCTATAAGCCTCATGTCAGG 57.241 47.619 0.00 0.00 41.51 3.86
2734 2904 4.773323 AATTCAGCAGACTAAACCTTGC 57.227 40.909 0.00 0.00 0.00 4.01
2736 2906 3.423539 TCAGCAGACTAAACCTTGCAT 57.576 42.857 0.00 0.00 0.00 3.96
2737 2907 3.076621 TCAGCAGACTAAACCTTGCATG 58.923 45.455 0.00 0.00 0.00 4.06
2738 2908 2.816087 CAGCAGACTAAACCTTGCATGT 59.184 45.455 0.00 0.00 0.00 3.21
2750 2920 6.803154 AACCTTGCATGTTTCTAGTACTTC 57.197 37.500 0.00 0.00 0.00 3.01
2790 2972 3.838120 TGACAACGTGAAGATCTAGCAG 58.162 45.455 0.00 0.00 0.00 4.24
2794 2976 4.101942 CAACGTGAAGATCTAGCAGAGAC 58.898 47.826 0.00 0.00 36.87 3.36
2942 3125 2.725221 AGGGTGAGCCATCATTCTTC 57.275 50.000 2.50 0.00 37.87 2.87
2981 3164 7.307493 TGTGAGTATGCATTTAGTTCATCAC 57.693 36.000 3.54 8.57 0.00 3.06
3022 3208 6.599244 CAGAAACAAAGGGCTATGATGAAGTA 59.401 38.462 0.00 0.00 0.00 2.24
3074 3260 7.991084 TGATTATATACGTACAGTGGTAGCT 57.009 36.000 0.00 0.00 0.00 3.32
3133 3319 6.543831 CACCAAGAAAATTATCTAGGTCCCTG 59.456 42.308 0.00 0.00 0.00 4.45
3199 3385 2.497273 GCATGGGCCTGAAATGTTAGTT 59.503 45.455 4.53 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 8.615211 CATGCATGTACTTACAATAGACACATT 58.385 33.333 18.91 0.00 39.99 2.71
77 80 8.196802 TCAACATGCATGTACTTACAATAGAC 57.803 34.615 31.55 0.00 40.80 2.59
79 82 8.424274 TCTCAACATGCATGTACTTACAATAG 57.576 34.615 31.55 16.83 40.80 1.73
81 84 7.553760 TCATCTCAACATGCATGTACTTACAAT 59.446 33.333 31.55 15.66 40.80 2.71
171 176 6.184068 TGACAAAAATTATGGATCGGAAGGA 58.816 36.000 0.00 0.00 0.00 3.36
224 229 5.292101 CCTCTGTTCCATAATTCTTGTCGTC 59.708 44.000 0.00 0.00 0.00 4.20
227 232 5.745227 TCCCTCTGTTCCATAATTCTTGTC 58.255 41.667 0.00 0.00 0.00 3.18
244 249 3.586174 ACATGCATGCATATACTCCCTCT 59.414 43.478 31.73 4.38 34.91 3.69
248 253 3.441572 GGGAACATGCATGCATATACTCC 59.558 47.826 31.73 28.37 34.91 3.85
282 287 9.716507 ATAATGTTGTAAGTTCAAATACGCATC 57.283 29.630 0.00 0.00 0.00 3.91
397 420 7.414222 TGCATCTATGATCATATGTGCTAGA 57.586 36.000 31.38 21.13 35.94 2.43
467 490 7.822658 TGTATTAGTTTGCAAATAGTTGGGTC 58.177 34.615 16.21 0.00 35.10 4.46
478 501 8.138074 TGTATTTGCACTTGTATTAGTTTGCAA 58.862 29.630 0.00 0.00 36.11 4.08
480 503 8.514136 TTGTATTTGCACTTGTATTAGTTTGC 57.486 30.769 0.00 0.00 0.00 3.68
523 546 9.357161 AGCTAGCTACTTGTATAGTGAACTTAT 57.643 33.333 17.69 0.00 37.73 1.73
524 547 8.749026 AGCTAGCTACTTGTATAGTGAACTTA 57.251 34.615 17.69 0.00 37.73 2.24
525 548 7.648039 AGCTAGCTACTTGTATAGTGAACTT 57.352 36.000 17.69 0.00 37.73 2.66
526 549 8.212312 TCTAGCTAGCTACTTGTATAGTGAACT 58.788 37.037 20.67 0.00 37.73 3.01
535 558 4.138290 CCTGCTCTAGCTAGCTACTTGTA 58.862 47.826 20.67 11.34 43.19 2.41
570 593 6.313164 GGTAGATCTCATCATACATGCATGTG 59.687 42.308 36.72 23.63 41.89 3.21
662 686 1.651631 CATTTGTGTGACGCATGCATG 59.348 47.619 22.70 22.70 0.00 4.06
715 739 1.603802 CATGTGATAATGGACGGGTGC 59.396 52.381 0.00 0.00 0.00 5.01
773 801 3.385755 TGAATCTGATGGAGATCGAGCAA 59.614 43.478 2.38 0.00 40.89 3.91
790 818 8.375465 GCATGCTTGTGTTAATTTAACTGAATC 58.625 33.333 11.37 8.46 39.38 2.52
821 849 7.612065 AAGTACTGCCCATCTATACACATAA 57.388 36.000 0.00 0.00 0.00 1.90
824 852 5.950544 AAAGTACTGCCCATCTATACACA 57.049 39.130 0.00 0.00 0.00 3.72
845 873 6.266103 ACAGCAAAAGATCAGATCCAGAAAAA 59.734 34.615 6.80 0.00 0.00 1.94
846 874 5.771666 ACAGCAAAAGATCAGATCCAGAAAA 59.228 36.000 6.80 0.00 0.00 2.29
851 879 4.564782 AGACAGCAAAAGATCAGATCCA 57.435 40.909 6.80 0.00 0.00 3.41
852 880 5.184711 AGAAGACAGCAAAAGATCAGATCC 58.815 41.667 6.80 0.00 0.00 3.36
942 970 9.575868 TGTAAGGTGTATGAAAAATCCAGTTAA 57.424 29.630 0.00 0.00 0.00 2.01
943 971 9.226606 CTGTAAGGTGTATGAAAAATCCAGTTA 57.773 33.333 0.00 0.00 0.00 2.24
944 972 8.110860 CTGTAAGGTGTATGAAAAATCCAGTT 57.889 34.615 0.00 0.00 0.00 3.16
945 973 7.687941 CTGTAAGGTGTATGAAAAATCCAGT 57.312 36.000 0.00 0.00 0.00 4.00
963 991 5.779922 TCAGTGTACAGCTAAACCTGTAAG 58.220 41.667 0.00 0.00 46.52 2.34
966 994 4.528596 AGATCAGTGTACAGCTAAACCTGT 59.471 41.667 0.00 0.23 46.98 4.00
972 1000 5.238868 GTCCGATAGATCAGTGTACAGCTAA 59.761 44.000 0.00 0.00 39.76 3.09
976 1004 5.163652 TGTTGTCCGATAGATCAGTGTACAG 60.164 44.000 0.00 0.00 39.76 2.74
978 1006 5.244785 TGTTGTCCGATAGATCAGTGTAC 57.755 43.478 0.00 0.00 39.76 2.90
983 1011 4.981054 CACTCATGTTGTCCGATAGATCAG 59.019 45.833 0.00 0.00 39.76 2.90
984 1012 4.202151 CCACTCATGTTGTCCGATAGATCA 60.202 45.833 0.00 0.00 39.76 2.92
989 1017 1.552792 TGCCACTCATGTTGTCCGATA 59.447 47.619 0.00 0.00 0.00 2.92
992 1020 1.915614 GCTGCCACTCATGTTGTCCG 61.916 60.000 0.00 0.00 0.00 4.79
997 1025 0.466007 TGTGTGCTGCCACTCATGTT 60.466 50.000 17.81 0.00 42.54 2.71
998 1026 0.887836 CTGTGTGCTGCCACTCATGT 60.888 55.000 17.81 0.00 42.52 3.21
999 1027 1.873863 CTGTGTGCTGCCACTCATG 59.126 57.895 17.81 0.00 42.52 3.07
1000 1028 1.970114 GCTGTGTGCTGCCACTCAT 60.970 57.895 17.81 0.00 42.52 2.90
1001 1029 2.592574 GCTGTGTGCTGCCACTCA 60.593 61.111 17.81 12.19 42.54 3.41
1050 1082 0.036010 CCACAAGCTCCTCATCGGTT 60.036 55.000 0.00 0.00 0.00 4.44
1053 1085 2.322355 AATCCACAAGCTCCTCATCG 57.678 50.000 0.00 0.00 0.00 3.84
1056 1088 3.451178 GGTAGTAATCCACAAGCTCCTCA 59.549 47.826 0.00 0.00 0.00 3.86
1065 1097 1.855295 TGCGGAGGTAGTAATCCACA 58.145 50.000 4.09 0.00 35.14 4.17
1071 1103 2.232941 CACCTTCTTGCGGAGGTAGTAA 59.767 50.000 0.00 0.00 32.72 2.24
1098 1130 2.022934 ACGTTTAGGTCGATCCTCCTC 58.977 52.381 9.44 2.54 44.42 3.71
1101 1133 3.066342 TGATGACGTTTAGGTCGATCCTC 59.934 47.826 9.44 0.00 44.42 3.71
1190 1222 9.081204 TCATTGCTAATTGGACTGCATTATATT 57.919 29.630 0.00 0.00 35.27 1.28
1192 1224 7.501892 TGTCATTGCTAATTGGACTGCATTATA 59.498 33.333 0.00 0.00 35.27 0.98
1193 1225 6.321945 TGTCATTGCTAATTGGACTGCATTAT 59.678 34.615 0.00 0.00 35.27 1.28
1197 1229 3.419943 TGTCATTGCTAATTGGACTGCA 58.580 40.909 0.00 0.00 0.00 4.41
1199 1231 3.693085 AGCTGTCATTGCTAATTGGACTG 59.307 43.478 0.00 0.00 39.21 3.51
1210 1242 6.092670 TCAAGACTACATTAAGCTGTCATTGC 59.907 38.462 0.00 0.00 0.00 3.56
1219 1286 6.868864 TGTCAAGACTCAAGACTACATTAAGC 59.131 38.462 1.53 0.00 33.56 3.09
1224 1291 5.986135 GTGTTGTCAAGACTCAAGACTACAT 59.014 40.000 16.53 0.00 44.90 2.29
1230 1297 6.757897 AATTTGTGTTGTCAAGACTCAAGA 57.242 33.333 13.47 0.00 33.63 3.02
1271 1338 8.840833 TCTGTACACAAATGAATGTAAGCTAA 57.159 30.769 0.00 0.00 33.23 3.09
1273 1340 7.161404 TCTCTGTACACAAATGAATGTAAGCT 58.839 34.615 0.00 0.00 33.23 3.74
1274 1341 7.364522 TCTCTGTACACAAATGAATGTAAGC 57.635 36.000 0.00 0.00 33.23 3.09
1330 1398 2.037251 GTGGCTGAAGAAGTACCAGTCA 59.963 50.000 0.00 0.00 39.84 3.41
1396 1464 1.073722 CTTCCAGAACCCTGCAGCA 59.926 57.895 8.66 0.00 39.07 4.41
1399 1467 2.436109 GCCTTCCAGAACCCTGCA 59.564 61.111 0.00 0.00 39.07 4.41
1402 1470 1.831652 CTGTCGCCTTCCAGAACCCT 61.832 60.000 0.00 0.00 0.00 4.34
1454 1522 1.547675 GGTCTTCCTCATGCCAACCAA 60.548 52.381 0.00 0.00 0.00 3.67
1592 1660 7.094592 GGACAGAGATCGATGTATATCAAGTGA 60.095 40.741 0.54 0.00 32.67 3.41
1598 1666 7.566760 AGATGGACAGAGATCGATGTATATC 57.433 40.000 0.54 0.00 0.00 1.63
1607 1675 3.547813 CGAGTCAAGATGGACAGAGATCG 60.548 52.174 0.00 0.00 40.29 3.69
1630 1699 5.379706 AGAGGAGCTTGCAGGTTTATATT 57.620 39.130 0.00 0.00 0.00 1.28
1735 1808 8.412456 TCATGATCTAGATCTCTTCTTGTTGTC 58.588 37.037 28.51 4.08 38.60 3.18
1756 1829 3.427670 CAGCATGGCGCATCATGA 58.572 55.556 24.97 0.00 45.30 3.07
1855 1928 3.480470 CATCTGGAGGTGTTGTTCTTGT 58.520 45.455 0.00 0.00 0.00 3.16
1884 1957 3.162147 TCAGCTCTCTCTTGTAGGTGT 57.838 47.619 0.00 0.00 39.25 4.16
1915 1988 4.223255 ACATGATGATGGTTTGGCATTTGA 59.777 37.500 0.00 0.00 33.39 2.69
1951 2024 2.029743 GCTCTCTAGCTCGTGAGGG 58.970 63.158 16.34 11.66 45.85 4.30
2116 2189 4.996122 GCTGCATCATTACTAAGCTGAGAT 59.004 41.667 4.63 0.00 0.00 2.75
2144 2217 4.100035 TCCTTCATGAGCATAATCGACACT 59.900 41.667 0.00 0.00 0.00 3.55
2194 2267 4.082571 GCATAATCAGTTGCCAACTCTTGT 60.083 41.667 7.22 0.28 40.46 3.16
2215 2288 1.443702 CGATGTTGAGGTCGACGCA 60.444 57.895 9.92 7.58 40.11 5.24
2512 2587 6.211587 TCACAATTCATGAAGCCTTTATGG 57.788 37.500 14.54 0.00 39.35 2.74
2532 2607 3.733727 CCGTGTTGCCTTTTACAAATCAC 59.266 43.478 0.00 0.00 0.00 3.06
2576 2651 4.004314 TCAAGTTCGTTGAGAAACCAACA 58.996 39.130 0.00 0.00 44.85 3.33
2583 2658 8.846849 GCATATGGCTATCAAGTTCGTTGAGAA 61.847 40.741 4.56 0.00 43.47 2.87
2585 2660 5.333645 GCATATGGCTATCAAGTTCGTTGAG 60.334 44.000 4.56 0.00 43.47 3.02
2602 2677 1.453745 ACAACTGGCCGGCATATGG 60.454 57.895 30.85 16.72 0.00 2.74
2678 2772 2.434336 ACATGAGGCTTATAGCAACGGA 59.566 45.455 0.00 0.00 44.75 4.69
2691 2785 1.909700 TTTGTTCCCTGACATGAGGC 58.090 50.000 0.00 0.00 0.00 4.70
2750 2920 9.702726 CGTTGTCATTTGTACTTCTTATTATGG 57.297 33.333 0.00 0.00 0.00 2.74
2790 2972 8.462811 TGTGATCTAGTTATTCTGAACAGTCTC 58.537 37.037 0.00 0.00 0.00 3.36
2942 3125 4.069300 ACTCACATGCATCCACATAGAG 57.931 45.455 0.00 0.00 37.38 2.43
2981 3164 9.185192 CTTTGTTTCTGTAAAAGAATTAGCTGG 57.815 33.333 0.00 0.00 44.46 4.85
3056 3242 5.371526 AGCTAAGCTACCACTGTACGTATA 58.628 41.667 0.00 0.00 36.99 1.47
3061 3247 2.930682 GCAAGCTAAGCTACCACTGTAC 59.069 50.000 3.96 0.00 38.25 2.90
3064 3250 2.393271 AGCAAGCTAAGCTACCACTG 57.607 50.000 11.52 0.00 41.32 3.66
3066 3252 2.699954 TCAAGCAAGCTAAGCTACCAC 58.300 47.619 13.32 0.00 42.53 4.16
3074 3260 4.097741 ACACACATTGTTCAAGCAAGCTAA 59.902 37.500 0.00 0.00 33.09 3.09
3101 3287 7.386299 CCTAGATAATTTTCTTGGTGATCCTCG 59.614 40.741 15.00 0.00 34.93 4.63
3164 3350 3.181487 GGCCCATGCATTAGTAACTGTTG 60.181 47.826 0.00 0.00 40.13 3.33
3173 3359 2.696707 ACATTTCAGGCCCATGCATTAG 59.303 45.455 0.00 0.00 40.13 1.73


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

AutoCloner maintained by Alex Coulton.