Multiple sequence alignment - TraesCS5B01G401700

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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 TraesCS5B01G401700 chr5B 100.000 4139 0 0 1 4139 578534339 578538477 0.000000e+00 7644.0
1 TraesCS5B01G401700 chr5D 93.422 4211 142 46 1 4139 472231647 472235794 0.000000e+00 6117.0
2 TraesCS5B01G401700 chr5D 87.547 265 33 0 2109 2373 303407552 303407816 1.450000e-79 307.0
3 TraesCS5B01G401700 chr5D 94.964 139 7 0 3979 4117 549703909 549704047 6.970000e-53 219.0
4 TraesCS5B01G401700 chr5D 90.370 135 9 2 3979 4113 362655988 362656118 1.530000e-39 174.0
5 TraesCS5B01G401700 chr5D 88.462 104 9 2 3890 3990 449629261 449629158 5.620000e-24 122.0
6 TraesCS5B01G401700 chr5D 83.333 114 6 2 3890 3990 298070745 298070632 4.410000e-15 93.5
7 TraesCS5B01G401700 chr5A 86.397 2448 210 68 1488 3872 591439405 591441792 0.000000e+00 2562.0
8 TraesCS5B01G401700 chr5A 86.484 910 78 22 573 1455 591438524 591439415 0.000000e+00 957.0
9 TraesCS5B01G401700 chr5A 94.775 555 16 3 1 555 591392173 591392714 0.000000e+00 852.0
10 TraesCS5B01G401700 chr5A 87.658 316 30 5 7 313 591437981 591438296 3.930000e-95 359.0
11 TraesCS5B01G401700 chr5A 93.296 179 8 2 379 555 591438295 591438471 1.140000e-65 261.0
12 TraesCS5B01G401700 chr5A 90.566 106 10 0 1832 1937 603998490 603998385 1.550000e-29 141.0
13 TraesCS5B01G401700 chr5A 97.260 73 2 0 573 645 591392767 591392839 1.560000e-24 124.0
14 TraesCS5B01G401700 chr2B 82.498 1057 138 31 1588 2644 37325665 37324656 0.000000e+00 883.0
15 TraesCS5B01G401700 chr2B 90.580 138 13 0 3979 4116 768127677 768127814 2.540000e-42 183.0
16 TraesCS5B01G401700 chr1B 82.492 891 116 26 1201 2083 533759059 533758201 0.000000e+00 745.0
17 TraesCS5B01G401700 chr1B 82.235 895 115 28 1201 2083 640478827 640477965 0.000000e+00 732.0
18 TraesCS5B01G401700 chr1B 81.967 122 9 2 3882 3990 58862887 58862766 1.580000e-14 91.6
19 TraesCS5B01G401700 chr1B 93.103 58 3 1 3887 3943 45121824 45121767 2.650000e-12 84.2
20 TraesCS5B01G401700 chr6D 88.302 265 31 0 2109 2373 79884311 79884047 6.680000e-83 318.0
21 TraesCS5B01G401700 chr3D 87.970 266 31 1 2109 2373 536420291 536420556 3.110000e-81 313.0
22 TraesCS5B01G401700 chr3D 87.547 265 32 1 2109 2373 19630324 19630587 5.200000e-79 305.0
23 TraesCS5B01G401700 chr1A 80.386 311 42 10 1198 1496 551506568 551506871 6.970000e-53 219.0
24 TraesCS5B01G401700 chr1A 89.286 84 2 3 312 389 11617140 11617222 9.470000e-17 99.0
25 TraesCS5B01G401700 chr1A 81.373 102 7 4 3890 3980 269092670 269092770 5.740000e-09 73.1
26 TraesCS5B01G401700 chr2A 93.333 135 9 0 3982 4116 565077335 565077201 2.520000e-47 200.0
27 TraesCS5B01G401700 chr2A 92.593 135 9 1 3982 4116 143844079 143843946 4.220000e-45 193.0
28 TraesCS5B01G401700 chr2A 90.909 77 5 2 311 385 754467810 754467886 7.320000e-18 102.0
29 TraesCS5B01G401700 chr2A 90.541 74 3 2 311 380 675885097 675885170 1.220000e-15 95.3
30 TraesCS5B01G401700 chr4D 91.971 137 10 1 3982 4117 50663175 50663039 1.520000e-44 191.0
31 TraesCS5B01G401700 chr4D 94.545 55 2 1 3890 3943 66224845 66224899 2.650000e-12 84.2
32 TraesCS5B01G401700 chr7A 90.580 138 12 1 3979 4116 725736860 725736996 9.140000e-42 182.0
33 TraesCS5B01G401700 chr2D 89.209 139 12 3 3979 4116 281670627 281670763 1.980000e-38 171.0
34 TraesCS5B01G401700 chr2D 91.429 70 4 2 311 380 447497036 447496969 1.220000e-15 95.3
35 TraesCS5B01G401700 chr2D 89.706 68 4 3 3878 3943 236114125 236114191 2.650000e-12 84.2
36 TraesCS5B01G401700 chr7D 93.243 74 4 1 312 385 18437347 18437275 1.570000e-19 108.0
37 TraesCS5B01G401700 chr7D 80.833 120 11 3 3883 3990 255305516 255305397 2.650000e-12 84.2
38 TraesCS5B01G401700 chr6B 91.304 69 4 1 312 380 706122030 706121964 4.410000e-15 93.5
39 TraesCS5B01G401700 chr4A 90.411 73 3 2 312 380 540014943 540015015 4.410000e-15 93.5
40 TraesCS5B01G401700 chrUn 84.000 100 3 3 3890 3976 94995892 94995793 2.650000e-12 84.2


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 TraesCS5B01G401700 chr5B 578534339 578538477 4138 False 7644.00 7644 100.00000 1 4139 1 chr5B.!!$F1 4138
1 TraesCS5B01G401700 chr5D 472231647 472235794 4147 False 6117.00 6117 93.42200 1 4139 1 chr5D.!!$F3 4138
2 TraesCS5B01G401700 chr5A 591437981 591441792 3811 False 1034.75 2562 88.45875 7 3872 4 chr5A.!!$F2 3865
3 TraesCS5B01G401700 chr5A 591392173 591392839 666 False 488.00 852 96.01750 1 645 2 chr5A.!!$F1 644
4 TraesCS5B01G401700 chr2B 37324656 37325665 1009 True 883.00 883 82.49800 1588 2644 1 chr2B.!!$R1 1056
5 TraesCS5B01G401700 chr1B 533758201 533759059 858 True 745.00 745 82.49200 1201 2083 1 chr1B.!!$R3 882
6 TraesCS5B01G401700 chr1B 640477965 640478827 862 True 732.00 732 82.23500 1201 2083 1 chr1B.!!$R4 882

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
286 298 0.459899 TAGCACTATGGTCACTGGCG 59.540 55.000 0.00 0.0 0.0 5.69 F
1479 1593 0.111639 TTTTACACCCCCACCTGCTC 59.888 55.000 0.00 0.0 0.0 4.26 F
1578 1715 0.837272 TCCAGGGCCTACATTGCTAC 59.163 55.000 5.28 0.0 0.0 3.58 F
1732 1869 1.207089 TGGGCGGAGTACAAGATCAAG 59.793 52.381 0.00 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1737 0.107456 CATTCAGGGATCAGGGTCCG 59.893 60.0 0.00 0.00 39.26 4.79 R
2443 2586 0.824759 GGAGGACAACCGTATCAGCT 59.175 55.0 0.00 0.00 41.83 4.24 R
2504 2647 4.583907 GGAGTTACCACTACCATAGACTCC 59.416 50.0 3.74 3.74 43.37 3.85 R
3522 3688 7.908193 TTTTGAAACAAAGATAGAAGAACGC 57.092 32.0 0.00 0.00 0.00 4.84 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
98 99 7.092716 CAGCCTGAAACTTTATGCTAAACATT 58.907 34.615 0.00 0.00 40.38 2.71
175 180 0.899720 TAGTCTTAGCCCGGGTGTTG 59.100 55.000 24.63 10.80 0.00 3.33
259 264 6.595326 CGCTTCTATCTGGAATATGGCATTTA 59.405 38.462 4.78 0.00 0.00 1.40
263 268 9.676861 TTCTATCTGGAATATGGCATTTATCTG 57.323 33.333 4.78 0.00 0.00 2.90
286 298 0.459899 TAGCACTATGGTCACTGGCG 59.540 55.000 0.00 0.00 0.00 5.69
287 299 1.079127 GCACTATGGTCACTGGCGT 60.079 57.895 0.00 0.00 0.00 5.68
298 310 2.046892 CTGGCGTGTCCTCCCTTG 60.047 66.667 0.00 0.00 35.26 3.61
353 365 3.553105 ACTCGTCGTGGTTTTAGTTCAAC 59.447 43.478 0.00 0.00 0.00 3.18
386 398 3.958798 TGGAACGGAGGGAGTATAAGAAG 59.041 47.826 0.00 0.00 0.00 2.85
387 399 4.213513 GGAACGGAGGGAGTATAAGAAGA 58.786 47.826 0.00 0.00 0.00 2.87
388 400 4.648307 GGAACGGAGGGAGTATAAGAAGAA 59.352 45.833 0.00 0.00 0.00 2.52
555 567 2.724454 CTCTCTTCTTACCCAGACCGA 58.276 52.381 0.00 0.00 0.00 4.69
801 898 2.930168 CGCAGCGCTGTATTTTTCC 58.070 52.632 35.80 17.13 0.00 3.13
805 902 3.317150 GCAGCGCTGTATTTTTCCTTTT 58.683 40.909 35.80 0.00 0.00 2.27
806 903 4.481463 GCAGCGCTGTATTTTTCCTTTTA 58.519 39.130 35.80 0.00 0.00 1.52
807 904 4.920927 GCAGCGCTGTATTTTTCCTTTTAA 59.079 37.500 35.80 0.00 0.00 1.52
809 906 5.059221 CAGCGCTGTATTTTTCCTTTTAACG 59.941 40.000 29.24 0.00 0.00 3.18
810 907 4.201456 GCGCTGTATTTTTCCTTTTAACGC 60.201 41.667 0.00 0.00 0.00 4.84
824 926 6.312918 TCCTTTTAACGCTAGAAACTGCATAG 59.687 38.462 0.00 0.00 0.00 2.23
825 927 6.092259 CCTTTTAACGCTAGAAACTGCATAGT 59.908 38.462 0.00 0.00 39.32 2.12
826 928 7.277098 CCTTTTAACGCTAGAAACTGCATAGTA 59.723 37.037 0.00 0.00 35.69 1.82
827 929 7.515957 TTTAACGCTAGAAACTGCATAGTAC 57.484 36.000 0.00 0.00 35.69 2.73
828 930 4.043037 ACGCTAGAAACTGCATAGTACC 57.957 45.455 0.00 0.00 35.69 3.34
829 931 3.446161 ACGCTAGAAACTGCATAGTACCA 59.554 43.478 0.00 0.00 35.69 3.25
830 932 4.045104 CGCTAGAAACTGCATAGTACCAG 58.955 47.826 0.00 0.00 35.69 4.00
831 933 4.202020 CGCTAGAAACTGCATAGTACCAGA 60.202 45.833 0.00 0.00 35.69 3.86
848 950 8.896722 AGTACCAGATTAGAAGTAGGAAAAGA 57.103 34.615 0.00 0.00 0.00 2.52
849 956 9.322769 AGTACCAGATTAGAAGTAGGAAAAGAA 57.677 33.333 0.00 0.00 0.00 2.52
899 1006 4.864704 ATTTGGGTTGCAATACGTCTTT 57.135 36.364 0.59 0.00 0.00 2.52
943 1050 3.716601 GATAAGGTTCAGAGAGCAGCTC 58.283 50.000 15.25 15.25 44.29 4.09
957 1064 0.839477 CAGCTCAACGCAAAAACACG 59.161 50.000 0.00 0.00 42.61 4.49
961 1068 1.507120 CTCAACGCAAAAACACGAACG 59.493 47.619 0.00 0.00 0.00 3.95
986 1093 3.382832 CCTCCCGCTTCACTCCGT 61.383 66.667 0.00 0.00 0.00 4.69
1014 1121 3.451894 GCCATGGCGGAAACCCTG 61.452 66.667 23.48 0.00 36.56 4.45
1271 1381 1.507141 CGCCCTCCGCCATTCATAAC 61.507 60.000 0.00 0.00 0.00 1.89
1278 1388 1.032014 CGCCATTCATAACCCCCAAG 58.968 55.000 0.00 0.00 0.00 3.61
1302 1412 2.652095 CCTGCTTCCGGGTCCGTAA 61.652 63.158 0.00 0.00 37.81 3.18
1306 1416 1.271488 TGCTTCCGGGTCCGTAATTTT 60.271 47.619 0.00 0.00 37.81 1.82
1307 1417 1.814394 GCTTCCGGGTCCGTAATTTTT 59.186 47.619 0.00 0.00 37.81 1.94
1308 1418 2.414957 GCTTCCGGGTCCGTAATTTTTG 60.415 50.000 0.00 0.00 37.81 2.44
1309 1419 1.823797 TCCGGGTCCGTAATTTTTGG 58.176 50.000 0.00 0.00 37.81 3.28
1310 1420 1.073603 TCCGGGTCCGTAATTTTTGGT 59.926 47.619 0.00 0.00 37.81 3.67
1311 1421 1.887854 CCGGGTCCGTAATTTTTGGTT 59.112 47.619 8.67 0.00 37.81 3.67
1314 1424 4.379708 CCGGGTCCGTAATTTTTGGTTAAG 60.380 45.833 8.67 0.00 37.81 1.85
1315 1425 4.216042 CGGGTCCGTAATTTTTGGTTAAGT 59.784 41.667 0.55 0.00 34.35 2.24
1316 1426 5.411053 CGGGTCCGTAATTTTTGGTTAAGTA 59.589 40.000 0.55 0.00 34.35 2.24
1317 1427 6.093909 CGGGTCCGTAATTTTTGGTTAAGTAT 59.906 38.462 0.55 0.00 34.35 2.12
1318 1428 7.361971 CGGGTCCGTAATTTTTGGTTAAGTATT 60.362 37.037 0.55 0.00 34.35 1.89
1319 1429 8.306038 GGGTCCGTAATTTTTGGTTAAGTATTT 58.694 33.333 0.00 0.00 0.00 1.40
1342 1452 0.867746 TCTGTGTGCAGCAATTCGAC 59.132 50.000 0.00 0.00 42.29 4.20
1452 1562 1.448540 GCTCCCGGTGACACTGATG 60.449 63.158 16.28 6.76 0.00 3.07
1461 1571 4.635765 CCGGTGACACTGATGTTGATATTT 59.364 41.667 16.28 0.00 39.95 1.40
1465 1575 7.692291 CGGTGACACTGATGTTGATATTTTTAC 59.308 37.037 8.88 0.00 39.95 2.01
1466 1576 8.511321 GGTGACACTGATGTTGATATTTTTACA 58.489 33.333 5.39 0.00 39.95 2.41
1468 1578 8.511321 TGACACTGATGTTGATATTTTTACACC 58.489 33.333 0.00 0.00 39.95 4.16
1479 1593 0.111639 TTTTACACCCCCACCTGCTC 59.888 55.000 0.00 0.00 0.00 4.26
1527 1664 2.810274 TGCATCTTCAGTCAAGTCAAGC 59.190 45.455 0.00 0.00 33.27 4.01
1563 1700 2.028839 TGCAAGCATTTTGACCATCCAG 60.029 45.455 0.00 0.00 0.00 3.86
1572 1709 2.544768 GACCATCCAGGGCCTACAT 58.455 57.895 5.28 0.00 40.85 2.29
1573 1710 0.846693 GACCATCCAGGGCCTACATT 59.153 55.000 5.28 0.00 40.85 2.71
1578 1715 0.837272 TCCAGGGCCTACATTGCTAC 59.163 55.000 5.28 0.00 0.00 3.58
1583 1720 3.763897 CAGGGCCTACATTGCTACTTTTT 59.236 43.478 5.28 0.00 0.00 1.94
1584 1721 3.763897 AGGGCCTACATTGCTACTTTTTG 59.236 43.478 2.82 0.00 0.00 2.44
1585 1722 3.511699 GGCCTACATTGCTACTTTTTGC 58.488 45.455 0.00 0.00 0.00 3.68
1640 1777 8.132995 TGAATGATGTATCTGCAATTGTGATTC 58.867 33.333 16.92 13.63 0.00 2.52
1641 1778 6.051646 TGATGTATCTGCAATTGTGATTCG 57.948 37.500 16.92 0.00 0.00 3.34
1642 1779 5.585844 TGATGTATCTGCAATTGTGATTCGT 59.414 36.000 16.92 14.05 0.00 3.85
1732 1869 1.207089 TGGGCGGAGTACAAGATCAAG 59.793 52.381 0.00 0.00 0.00 3.02
1800 1937 6.915300 TGAAGTTCGTGGACATTTATTTTGTG 59.085 34.615 0.00 0.00 0.00 3.33
2008 2149 1.826720 TCCACTACCTTCGGCGTTTAT 59.173 47.619 6.85 0.00 0.00 1.40
2016 2157 2.869801 CCTTCGGCGTTTATCTGCATTA 59.130 45.455 6.85 0.00 0.00 1.90
2043 2184 5.249163 TGATGCCCTTATAGTATGATGCACT 59.751 40.000 0.00 0.00 0.00 4.40
2062 2203 4.558095 GCACTGCATCTGTTTTGACTTCAT 60.558 41.667 0.00 0.00 0.00 2.57
2329 2472 4.127171 CAGGGTCATGAAAAGGTATACCG 58.873 47.826 16.31 0.37 42.08 4.02
2504 2647 2.416547 CAGCTGGTTCAGGTATGTTTCG 59.583 50.000 5.57 0.00 40.40 3.46
2518 2661 5.301298 GGTATGTTTCGGAGTCTATGGTAGT 59.699 44.000 0.00 0.00 0.00 2.73
2524 2667 4.202441 TCGGAGTCTATGGTAGTGGTAAC 58.798 47.826 0.00 0.00 0.00 2.50
3522 3688 2.554806 TGAACGTGATGGTAGTAGCG 57.445 50.000 0.00 0.00 0.00 4.26
3753 3949 1.885887 CTTCCATCTGCCGAACCAAAA 59.114 47.619 0.00 0.00 0.00 2.44
3793 3989 9.119418 TGTGATCAATGTTAAGAGAAGTTTGAA 57.881 29.630 0.00 0.00 0.00 2.69
3908 4104 0.177141 TAGGGATGAAAACGGAGCGG 59.823 55.000 0.00 0.00 0.00 5.52
3935 4131 4.439057 GGACGAAATTGAGTGCTACCATA 58.561 43.478 0.00 0.00 0.00 2.74
4086 4295 7.716799 ATGAATTGGTTACATGGCTAGAAAA 57.283 32.000 0.00 0.00 0.00 2.29
4087 4296 7.716799 TGAATTGGTTACATGGCTAGAAAAT 57.283 32.000 0.00 0.00 0.00 1.82
4113 4322 8.681486 AATATGATTATGTCAGCAACTTAGCA 57.319 30.769 0.00 0.00 40.92 3.49
4114 4323 8.859236 ATATGATTATGTCAGCAACTTAGCAT 57.141 30.769 0.00 0.00 40.92 3.79
4115 4324 9.948964 ATATGATTATGTCAGCAACTTAGCATA 57.051 29.630 0.00 0.00 40.92 3.14
4116 4325 8.681486 ATGATTATGTCAGCAACTTAGCATAA 57.319 30.769 0.00 0.00 40.92 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 1.180456 TCGACGGGGTAGCAAGAACA 61.180 55.000 0.00 0.00 0.00 3.18
175 180 1.552226 CCGCAATGATCAATGTGCAC 58.448 50.000 17.21 10.75 36.80 4.57
259 264 4.467795 AGTGACCATAGTGCTACAACAGAT 59.532 41.667 0.00 0.00 0.00 2.90
263 268 3.262420 CCAGTGACCATAGTGCTACAAC 58.738 50.000 0.00 0.00 0.00 3.32
286 298 2.143925 CGAAAAGACAAGGGAGGACAC 58.856 52.381 0.00 0.00 0.00 3.67
287 299 1.071699 CCGAAAAGACAAGGGAGGACA 59.928 52.381 0.00 0.00 0.00 4.02
298 310 3.368220 GGAGGGAGTAGAACCGAAAAGAC 60.368 52.174 0.00 0.00 0.00 3.01
353 365 3.306019 CCCTCCGTTCCAAATTTCCAAAG 60.306 47.826 0.00 0.00 0.00 2.77
477 489 5.712004 TCCCGCATCGTTTCGATAAATATA 58.288 37.500 4.37 0.00 45.19 0.86
571 599 4.164030 TCTGCCCAGCTCAATAATGTTAGA 59.836 41.667 0.00 0.00 0.00 2.10
753 845 4.629200 GGATCAAGCTCAACTCTACACTTG 59.371 45.833 0.00 0.00 36.66 3.16
799 896 4.382291 TGCAGTTTCTAGCGTTAAAAGGA 58.618 39.130 0.00 0.00 0.00 3.36
801 898 7.061752 ACTATGCAGTTTCTAGCGTTAAAAG 57.938 36.000 0.00 0.00 0.00 2.27
805 902 5.125900 TGGTACTATGCAGTTTCTAGCGTTA 59.874 40.000 0.00 0.00 36.14 3.18
806 903 4.081862 TGGTACTATGCAGTTTCTAGCGTT 60.082 41.667 0.00 0.00 36.14 4.84
807 904 3.446161 TGGTACTATGCAGTTTCTAGCGT 59.554 43.478 0.00 0.00 36.14 5.07
809 906 5.263968 TCTGGTACTATGCAGTTTCTAGC 57.736 43.478 0.00 0.00 36.14 3.42
810 907 8.851145 TCTAATCTGGTACTATGCAGTTTCTAG 58.149 37.037 0.00 0.00 36.14 2.43
824 926 9.939802 TTTCTTTTCCTACTTCTAATCTGGTAC 57.060 33.333 0.00 0.00 0.00 3.34
826 928 9.862149 TTTTTCTTTTCCTACTTCTAATCTGGT 57.138 29.630 0.00 0.00 0.00 4.00
849 956 1.580815 CCATGGCAAAGCGTGTTTTT 58.419 45.000 0.00 0.00 0.00 1.94
871 978 5.006941 ACGTATTGCAACCCAAATACGTATC 59.993 40.000 24.40 0.00 43.65 2.24
883 990 4.469552 GTTGGTAAAGACGTATTGCAACC 58.530 43.478 0.00 12.83 0.00 3.77
884 991 4.145997 CGTTGGTAAAGACGTATTGCAAC 58.854 43.478 0.00 0.00 34.75 4.17
899 1006 2.601067 TGACCCTCGCCGTTGGTA 60.601 61.111 0.55 0.00 30.97 3.25
943 1050 0.045419 GCGTTCGTGTTTTTGCGTTG 60.045 50.000 0.00 0.00 0.00 4.10
957 1064 2.776913 CGGGAGGAGAGAGGCGTTC 61.777 68.421 0.00 0.00 0.00 3.95
961 1068 2.762043 AAGCGGGAGGAGAGAGGC 60.762 66.667 0.00 0.00 0.00 4.70
986 1093 3.671410 CCATGGCCAGTGGGGGAA 61.671 66.667 20.58 0.00 37.04 3.97
1263 1373 1.217942 GAGGCCTTGGGGGTTATGAAT 59.782 52.381 6.77 0.00 37.43 2.57
1306 1416 6.975772 GCACACAGACAAAAATACTTAACCAA 59.024 34.615 0.00 0.00 0.00 3.67
1307 1417 6.095580 TGCACACAGACAAAAATACTTAACCA 59.904 34.615 0.00 0.00 0.00 3.67
1308 1418 6.500041 TGCACACAGACAAAAATACTTAACC 58.500 36.000 0.00 0.00 0.00 2.85
1357 1467 1.514553 CGTGCTGATCTCCTGCTGA 59.485 57.895 0.00 0.00 40.01 4.26
1406 1516 0.622136 TGCATGAGGCTGATGAGGTT 59.378 50.000 18.49 0.00 45.15 3.50
1452 1562 5.020795 AGGTGGGGGTGTAAAAATATCAAC 58.979 41.667 0.00 0.00 0.00 3.18
1461 1571 0.770557 AGAGCAGGTGGGGGTGTAAA 60.771 55.000 0.00 0.00 0.00 2.01
1465 1575 4.729918 GCAGAGCAGGTGGGGGTG 62.730 72.222 0.00 0.00 0.00 4.61
1466 1576 4.990910 AGCAGAGCAGGTGGGGGT 62.991 66.667 0.00 0.00 0.00 4.95
1468 1578 2.045536 GAAGCAGAGCAGGTGGGG 60.046 66.667 0.00 0.00 0.00 4.96
1479 1593 5.578727 GGAGTGAACATAGTAACTGAAGCAG 59.421 44.000 0.00 0.00 37.52 4.24
1527 1664 3.688185 TGCTTGCAGAAATCAGCTTAGAG 59.312 43.478 7.30 0.00 0.00 2.43
1563 1700 3.676049 GCAAAAAGTAGCAATGTAGGCCC 60.676 47.826 0.00 0.00 0.00 5.80
1567 1704 4.083537 TCCACGCAAAAAGTAGCAATGTAG 60.084 41.667 0.00 0.00 0.00 2.74
1572 1709 2.227865 GGATCCACGCAAAAAGTAGCAA 59.772 45.455 6.95 0.00 0.00 3.91
1573 1710 1.810151 GGATCCACGCAAAAAGTAGCA 59.190 47.619 6.95 0.00 0.00 3.49
1600 1737 0.107456 CATTCAGGGATCAGGGTCCG 59.893 60.000 0.00 0.00 39.26 4.79
1640 1777 4.368315 TGCTTGATATACAGCCTACAACG 58.632 43.478 3.68 0.00 0.00 4.10
1641 1778 4.752101 CCTGCTTGATATACAGCCTACAAC 59.248 45.833 3.68 0.00 0.00 3.32
1642 1779 4.743651 GCCTGCTTGATATACAGCCTACAA 60.744 45.833 3.68 0.00 0.00 2.41
1732 1869 6.268825 TCTACAGTGAACATGTTAGTCTCC 57.731 41.667 11.95 0.00 32.02 3.71
1800 1937 3.358076 CTCGGACCTCGGAGCCAAC 62.358 68.421 0.00 0.00 36.70 3.77
1999 2140 5.778161 TCATATAATGCAGATAAACGCCG 57.222 39.130 0.00 0.00 0.00 6.46
2016 2157 7.935755 GTGCATCATACTATAAGGGCATCATAT 59.064 37.037 0.00 0.00 32.16 1.78
2039 2180 3.243168 TGAAGTCAAAACAGATGCAGTGC 60.243 43.478 8.58 8.58 0.00 4.40
2040 2181 4.556942 TGAAGTCAAAACAGATGCAGTG 57.443 40.909 0.00 0.00 0.00 3.66
2043 2184 5.997129 TCTGTATGAAGTCAAAACAGATGCA 59.003 36.000 18.65 0.00 42.67 3.96
2329 2472 7.110155 TGGGATTCTAGTGACAAAGGATAAAC 58.890 38.462 0.00 0.00 0.00 2.01
2443 2586 0.824759 GGAGGACAACCGTATCAGCT 59.175 55.000 0.00 0.00 41.83 4.24
2504 2647 4.583907 GGAGTTACCACTACCATAGACTCC 59.416 50.000 3.74 3.74 43.37 3.85
2524 2667 9.323985 TCCATTTTTCTAAAACATTTGTTGGAG 57.676 29.630 0.00 0.00 38.44 3.86
3522 3688 7.908193 TTTTGAAACAAAGATAGAAGAACGC 57.092 32.000 0.00 0.00 0.00 4.84
3793 3989 1.026182 TGCGCTCGGAAATTCTGCAT 61.026 50.000 9.73 0.00 0.00 3.96
3908 4104 2.223377 AGCACTCAATTTCGTCCGTTTC 59.777 45.455 0.00 0.00 0.00 2.78
3913 4109 2.695359 TGGTAGCACTCAATTTCGTCC 58.305 47.619 0.00 0.00 0.00 4.79
3945 4153 7.362660 GGGGTTTCTATATTTGTTTTCGCTTCT 60.363 37.037 0.00 0.00 0.00 2.85
3952 4160 9.430623 CATTTTCGGGGTTTCTATATTTGTTTT 57.569 29.630 0.00 0.00 0.00 2.43
4087 4296 9.777297 TGCTAAGTTGCTGACATAATCATATTA 57.223 29.630 0.00 0.00 36.48 0.98
4111 4320 9.538508 AATTCAAGCTCCTGATTTTATTTATGC 57.461 29.630 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.