Multiple sequence alignment - TraesCS7B01G330300

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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 TraesCS7B01G330300 chr7B 100.000 2621 0 0 1 2621 585623434 585620814 0.000000e+00 4841.0
1 TraesCS7B01G330300 chr7B 88.889 243 17 7 1655 1893 354390183 354390419 9.180000e-75 291.0
2 TraesCS7B01G330300 chr7B 89.394 198 17 3 2425 2621 616834444 616834250 2.010000e-61 246.0
3 TraesCS7B01G330300 chr7B 88.372 129 14 1 2226 2353 616825178 616825050 1.260000e-33 154.0
4 TraesCS7B01G330300 chr7B 81.250 112 15 5 2472 2580 377820013 377819905 4.650000e-13 86.1
5 TraesCS7B01G330300 chr3B 90.139 933 84 8 1 928 96620938 96620009 0.000000e+00 1206.0
6 TraesCS7B01G330300 chr3B 89.931 725 65 7 931 1651 96619782 96619062 0.000000e+00 928.0
7 TraesCS7B01G330300 chr7A 83.415 1019 107 41 1655 2621 18093032 18092024 0.000000e+00 889.0
8 TraesCS7B01G330300 chr7A 78.014 141 24 5 2483 2621 190018331 190018196 6.010000e-12 82.4
9 TraesCS7B01G330300 chr1B 91.446 643 50 4 1 638 47252880 47253522 0.000000e+00 878.0
10 TraesCS7B01G330300 chr1B 94.783 230 10 1 1426 1655 564446529 564446756 8.920000e-95 357.0
11 TraesCS7B01G330300 chr2A 86.887 755 73 11 1884 2618 768846939 768847687 0.000000e+00 822.0
12 TraesCS7B01G330300 chr2A 93.750 240 13 2 1655 1893 768846675 768846913 2.480000e-95 359.0
13 TraesCS7B01G330300 chr2A 80.169 237 38 7 2382 2618 40375134 40375361 4.490000e-38 169.0
14 TraesCS7B01G330300 chr3A 86.246 698 75 13 1884 2573 723332814 723332130 0.000000e+00 737.0
15 TraesCS7B01G330300 chr3A 91.919 297 22 2 1337 1633 69260681 69260387 5.220000e-112 414.0
16 TraesCS7B01G330300 chr3A 83.668 398 59 5 2221 2618 257287763 257288154 1.150000e-98 370.0
17 TraesCS7B01G330300 chr3A 84.848 264 23 9 1655 1913 723333086 723332835 1.560000e-62 250.0
18 TraesCS7B01G330300 chr2D 93.991 466 21 5 1191 1652 13639546 13639084 0.000000e+00 699.0
19 TraesCS7B01G330300 chr4B 84.736 511 53 17 1883 2374 644284367 644283863 3.030000e-134 488.0
20 TraesCS7B01G330300 chr2B 91.566 249 20 1 2081 2329 768915045 768915292 2.500000e-90 342.0
21 TraesCS7B01G330300 chr2B 90.763 249 22 1 2081 2329 768791158 768791405 5.410000e-87 331.0
22 TraesCS7B01G330300 chr1A 92.523 214 16 0 1335 1548 536235416 536235203 9.110000e-80 307.0
23 TraesCS7B01G330300 chr1A 78.838 241 41 8 2381 2618 32258407 32258640 1.260000e-33 154.0
24 TraesCS7B01G330300 chr1A 91.892 74 5 1 1581 1654 536235205 536235133 4.620000e-18 102.0
25 TraesCS7B01G330300 chrUn 83.704 270 34 8 1884 2146 299784243 299783977 2.010000e-61 246.0
26 TraesCS7B01G330300 chrUn 83.704 270 34 8 1884 2146 321632929 321632663 2.010000e-61 246.0
27 TraesCS7B01G330300 chrUn 89.474 133 14 0 2342 2474 76825816 76825948 4.490000e-38 169.0
28 TraesCS7B01G330300 chrUn 91.250 80 7 0 2487 2566 76826003 76826082 2.760000e-20 110.0
29 TraesCS7B01G330300 chr7D 76.426 526 74 27 1655 2143 596617697 596617185 3.370000e-59 239.0
30 TraesCS7B01G330300 chr5A 81.013 79 15 0 505 583 591309686 591309764 2.180000e-06 63.9


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 TraesCS7B01G330300 chr7B 585620814 585623434 2620 True 4841.0 4841 100.0000 1 2621 1 chr7B.!!$R2 2620
1 TraesCS7B01G330300 chr3B 96619062 96620938 1876 True 1067.0 1206 90.0350 1 1651 2 chr3B.!!$R1 1650
2 TraesCS7B01G330300 chr7A 18092024 18093032 1008 True 889.0 889 83.4150 1655 2621 1 chr7A.!!$R1 966
3 TraesCS7B01G330300 chr1B 47252880 47253522 642 False 878.0 878 91.4460 1 638 1 chr1B.!!$F1 637
4 TraesCS7B01G330300 chr2A 768846675 768847687 1012 False 590.5 822 90.3185 1655 2618 2 chr2A.!!$F2 963
5 TraesCS7B01G330300 chr3A 723332130 723333086 956 True 493.5 737 85.5470 1655 2573 2 chr3A.!!$R2 918
6 TraesCS7B01G330300 chr4B 644283863 644284367 504 True 488.0 488 84.7360 1883 2374 1 chr4B.!!$R1 491
7 TraesCS7B01G330300 chr7D 596617185 596617697 512 True 239.0 239 76.4260 1655 2143 1 chr7D.!!$R1 488

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
146 148 0.660488 TGCGCTTATTATGCAACCCG 59.340 50.0 9.73 0.0 35.33 5.28 F
1189 1420 0.026803 GATGCGGCGTTTGATGAGAC 59.973 55.0 9.37 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1617 0.037232 AACGCTCCAGCCTGAAGTAC 60.037 55.0 0.0 0.00 37.91 2.73 R
2363 2696 0.175073 AACGTGCGGATTCTAGGTCC 59.825 55.0 0.0 5.32 0.00 4.46 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
27 28 3.402110 TGTCAACGACAAGAAGATGCAT 58.598 40.909 0.00 0.00 39.78 3.96
33 34 4.323417 ACGACAAGAAGATGCATTGGTTA 58.677 39.130 0.00 0.00 0.00 2.85
65 66 8.145122 GTGGAAATTGTGTATCCCAAAACTTAA 58.855 33.333 0.00 0.00 32.01 1.85
68 69 8.485578 AAATTGTGTATCCCAAAACTTAAGGA 57.514 30.769 7.53 0.00 0.00 3.36
73 74 3.825908 TCCCAAAACTTAAGGATGGCT 57.174 42.857 7.53 0.00 0.00 4.75
114 115 6.588756 CACACTGTTTTAATCTCGCCTTACTA 59.411 38.462 0.00 0.00 0.00 1.82
146 148 0.660488 TGCGCTTATTATGCAACCCG 59.340 50.000 9.73 0.00 35.33 5.28
149 151 2.151202 CGCTTATTATGCAACCCGGAT 58.849 47.619 0.73 0.00 0.00 4.18
346 351 1.851304 TGGATTCCAAACAGCCCATC 58.149 50.000 1.94 0.00 0.00 3.51
348 353 2.225343 TGGATTCCAAACAGCCCATCTT 60.225 45.455 1.94 0.00 0.00 2.40
352 357 2.956132 TCCAAACAGCCCATCTTGAAA 58.044 42.857 0.00 0.00 0.00 2.69
361 366 4.927425 CAGCCCATCTTGAAAAATTGTGAG 59.073 41.667 0.00 0.00 0.00 3.51
376 381 3.334583 TGTGAGTCCAAGAGGTAATGC 57.665 47.619 0.00 0.00 35.89 3.56
411 416 6.519679 TGGTTTCAGAATTGATCAATCCAG 57.480 37.500 20.95 13.11 32.27 3.86
438 443 2.088104 ATTATGGGACGAGGCTCTGA 57.912 50.000 13.50 0.00 0.00 3.27
452 457 8.410673 ACGAGGCTCTGATAAGAGATAATTTA 57.589 34.615 11.70 0.00 38.13 1.40
493 498 9.289782 GTCAAGAATCCTAGCAATACCATTATT 57.710 33.333 0.00 0.00 0.00 1.40
583 588 5.061435 CAGCGTATCATATTGAGTGGAATCG 59.939 44.000 0.00 0.00 0.00 3.34
600 605 1.860676 TCGTCGGTTTGGTCTGAAAG 58.139 50.000 0.00 0.00 0.00 2.62
672 678 6.577103 ACTATGTGGAGTTGTGATGTATCAG 58.423 40.000 0.00 0.00 37.51 2.90
717 723 0.779997 AACTTTGCATGGGGTCCTCT 59.220 50.000 0.00 0.00 0.00 3.69
741 747 2.243478 TGCTATGGGGTCTTGGCAAATA 59.757 45.455 0.00 0.00 33.06 1.40
742 748 3.295973 GCTATGGGGTCTTGGCAAATAA 58.704 45.455 0.00 0.00 0.00 1.40
759 765 5.682862 GCAAATAAGCATGTGATTACTTCCG 59.317 40.000 0.00 0.00 0.00 4.30
760 766 6.201517 CAAATAAGCATGTGATTACTTCCGG 58.798 40.000 0.00 0.00 0.00 5.14
796 802 3.455910 TGTCCCCTGGAATGTGAAGATAG 59.544 47.826 0.00 0.00 31.38 2.08
808 814 4.960938 TGTGAAGATAGAAAGCACACACT 58.039 39.130 0.00 0.00 34.85 3.55
824 830 4.805192 CACACACTTTTTGCTTGTGCTTAT 59.195 37.500 0.92 0.00 43.72 1.73
868 874 5.974156 TTGGGACTGATGGATTTGATAGA 57.026 39.130 0.00 0.00 0.00 1.98
878 884 7.937649 TGATGGATTTGATAGAAGCAGAAATG 58.062 34.615 0.00 0.00 0.00 2.32
899 905 5.378230 TGCTTGATGATAAATCTGGGAGT 57.622 39.130 0.00 0.00 0.00 3.85
920 926 7.365652 GGGAGTGAAATACTTGGGAATCTTCTA 60.366 40.741 0.00 0.00 40.53 2.10
953 1184 1.095807 GTGCTAATTCTGGGCCGGAC 61.096 60.000 16.41 0.00 0.00 4.79
956 1187 3.394635 TAATTCTGGGCCGGACCGC 62.395 63.158 24.84 5.38 40.62 5.68
991 1222 6.690194 AGAAATATTCTTAACAGCAGCCTG 57.310 37.500 0.00 0.00 40.04 4.85
1000 1231 7.131907 TCTTAACAGCAGCCTGGTATATTTA 57.868 36.000 0.00 0.00 40.76 1.40
1009 1240 3.660865 CCTGGTATATTTAGTGGCGTCC 58.339 50.000 0.00 0.00 0.00 4.79
1042 1273 4.970003 CGTGTTTGGAGAGAAAATGTGTTC 59.030 41.667 0.00 0.00 0.00 3.18
1063 1294 2.341452 CTGATCATGCAGCCATGGG 58.659 57.895 15.13 0.00 47.00 4.00
1096 1327 7.255139 GGTTATAACTATGAACAATGTCAGGGC 60.255 40.741 15.05 0.00 0.00 5.19
1107 1338 2.746279 TGTCAGGGCTTTGAGGAAAA 57.254 45.000 0.00 0.00 0.00 2.29
1111 1342 4.202567 TGTCAGGGCTTTGAGGAAAATAGT 60.203 41.667 0.00 0.00 0.00 2.12
1112 1343 4.767409 GTCAGGGCTTTGAGGAAAATAGTT 59.233 41.667 0.00 0.00 0.00 2.24
1113 1344 4.766891 TCAGGGCTTTGAGGAAAATAGTTG 59.233 41.667 0.00 0.00 0.00 3.16
1114 1345 4.524328 CAGGGCTTTGAGGAAAATAGTTGT 59.476 41.667 0.00 0.00 0.00 3.32
1117 1348 5.461526 GGCTTTGAGGAAAATAGTTGTGAC 58.538 41.667 0.00 0.00 0.00 3.67
1118 1349 5.009610 GGCTTTGAGGAAAATAGTTGTGACA 59.990 40.000 0.00 0.00 0.00 3.58
1175 1406 4.620982 TCACCTGTATCAATGTAGATGCG 58.379 43.478 0.00 0.00 33.91 4.73
1177 1408 2.738846 CCTGTATCAATGTAGATGCGGC 59.261 50.000 0.00 0.00 36.17 6.53
1189 1420 0.026803 GATGCGGCGTTTGATGAGAC 59.973 55.000 9.37 0.00 0.00 3.36
1201 1432 4.655762 TTGATGAGACTACTGAATCCGG 57.344 45.455 0.00 0.00 0.00 5.14
1203 1434 1.847328 TGAGACTACTGAATCCGGCA 58.153 50.000 0.00 0.00 0.00 5.69
1218 1449 1.078848 GGCAGTGTAGGAGCAGTGG 60.079 63.158 0.00 0.00 39.50 4.00
1222 1453 1.078848 GTGTAGGAGCAGTGGCCAG 60.079 63.158 5.11 0.00 42.56 4.85
1247 1480 0.768221 ATATGGGGAGTCATGGCGGT 60.768 55.000 0.00 0.00 0.00 5.68
1315 1550 2.100252 GCTATGGCTGTTACGTGGACTA 59.900 50.000 0.00 0.00 35.22 2.59
1337 1572 2.690786 CATTGGCAAATGAGTTGGGTG 58.309 47.619 8.21 0.00 45.17 4.61
1341 1576 3.300388 TGGCAAATGAGTTGGGTGTAAA 58.700 40.909 0.00 0.00 37.73 2.01
1342 1577 3.068873 TGGCAAATGAGTTGGGTGTAAAC 59.931 43.478 0.00 0.00 37.73 2.01
1343 1578 3.068873 GGCAAATGAGTTGGGTGTAAACA 59.931 43.478 0.00 0.00 37.73 2.83
1344 1579 4.298332 GCAAATGAGTTGGGTGTAAACAG 58.702 43.478 0.00 0.00 37.73 3.16
1382 1617 2.099141 TTGTCTTGAAGCCATCGAGG 57.901 50.000 0.00 0.00 39.68 4.63
1394 1629 1.202463 CCATCGAGGTACTTCAGGCTG 60.202 57.143 8.58 8.58 41.55 4.85
1398 1633 0.176910 GAGGTACTTCAGGCTGGAGC 59.823 60.000 22.92 7.29 41.55 4.70
1399 1634 1.153549 GGTACTTCAGGCTGGAGCG 60.154 63.158 22.92 1.10 43.26 5.03
1414 1649 2.392933 GAGCGTTCTCCTCTACATCG 57.607 55.000 0.00 0.00 33.19 3.84
1416 1651 0.595310 GCGTTCTCCTCTACATCGGC 60.595 60.000 0.00 0.00 0.00 5.54
1452 1687 9.551734 TTATGATGATATATGCATTCAGGCTAC 57.448 33.333 3.54 0.00 34.04 3.58
1455 1690 8.200120 TGATGATATATGCATTCAGGCTACTAC 58.800 37.037 3.54 0.00 34.04 2.73
1456 1691 6.878317 TGATATATGCATTCAGGCTACTACC 58.122 40.000 3.54 0.00 34.04 3.18
1482 1717 6.959671 TGGCAAAGTTTGTTTTAGTTTCTG 57.040 33.333 16.70 0.00 0.00 3.02
1485 1720 7.757624 TGGCAAAGTTTGTTTTAGTTTCTGTAG 59.242 33.333 16.70 0.00 0.00 2.74
1540 1775 3.653835 AAAGAGGCTGAGATTAACCCC 57.346 47.619 0.00 0.00 0.00 4.95
1566 1801 3.788672 GGGTTGATGAGCCACCTAG 57.211 57.895 0.00 0.00 45.52 3.02
1578 1813 5.020795 TGAGCCACCTAGTTTCATAGTACA 58.979 41.667 0.00 0.00 0.00 2.90
1580 1815 6.156256 TGAGCCACCTAGTTTCATAGTACATT 59.844 38.462 0.00 0.00 0.00 2.71
1610 1845 7.171653 TGTGGATGATGTAACTACCATTTGAA 58.828 34.615 0.00 0.00 0.00 2.69
1613 1848 8.902806 TGGATGATGTAACTACCATTTGAATTC 58.097 33.333 0.00 0.00 0.00 2.17
1704 1939 8.391106 CAATTTTCACCGGTTTGTTTTTCATTA 58.609 29.630 2.97 0.00 0.00 1.90
1713 1948 9.432077 CCGGTTTGTTTTTCATTAATTTTTCTG 57.568 29.630 0.00 0.00 0.00 3.02
2166 2487 9.898152 AATTTACATTTTGTTTTGAGGGAAGAA 57.102 25.926 0.00 0.00 0.00 2.52
2171 2492 9.325198 ACATTTTGTTTTGAGGGAAGAAATTAC 57.675 29.630 0.00 0.00 0.00 1.89
2329 2662 3.751518 GTGAATGGTGGAGTGGTTTAGT 58.248 45.455 0.00 0.00 0.00 2.24
2334 2667 1.405121 GGTGGAGTGGTTTAGTAGGCG 60.405 57.143 0.00 0.00 0.00 5.52
2363 2696 0.852777 CGTCTCTGTTGTGTGTTCGG 59.147 55.000 0.00 0.00 0.00 4.30
2396 2734 4.204573 TCCGCACGTTTTGTTTAATTTTCG 59.795 37.500 0.00 0.00 0.00 3.46
2400 2738 5.343603 CACGTTTTGTTTAATTTTCGCTCG 58.656 37.500 0.00 0.00 0.00 5.03
2404 2742 2.566036 TGTTTAATTTTCGCTCGCACG 58.434 42.857 0.00 0.00 0.00 5.34
2455 2807 2.376518 TGAAGAAAATGGCACCTCTCCT 59.623 45.455 0.00 0.00 0.00 3.69
2467 2819 3.192799 CTCTCCTACGCCAAGAGGA 57.807 57.895 0.00 0.00 39.63 3.71
2576 2928 2.831770 CCCCATGCGCCTAGTCAT 59.168 61.111 4.18 0.00 0.00 3.06
2585 2937 1.521681 GCCTAGTCATCGCGGCTTT 60.522 57.895 6.13 0.00 39.42 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.279935 ATTTCCACCACGCTAACCAA 57.720 45.000 0.00 0.00 0.00 3.67
33 34 2.264005 TACACAATTTCCACCACGCT 57.736 45.000 0.00 0.00 0.00 5.07
65 66 0.106519 CCGAAATCCCAAGCCATCCT 60.107 55.000 0.00 0.00 0.00 3.24
68 69 0.557729 ATCCCGAAATCCCAAGCCAT 59.442 50.000 0.00 0.00 0.00 4.40
73 74 0.995803 TGTGGATCCCGAAATCCCAA 59.004 50.000 9.90 0.42 43.99 4.12
114 115 7.148407 GCATAATAAGCGCATACCTGTTTAGAT 60.148 37.037 11.47 0.00 0.00 1.98
146 148 4.642885 AGTACTCTAGCACACAGAGAATCC 59.357 45.833 6.38 0.00 41.80 3.01
149 151 4.652822 TCAGTACTCTAGCACACAGAGAA 58.347 43.478 6.38 0.00 41.80 2.87
194 196 7.767198 CCACTTTTCATCCTTGCATTCAATATT 59.233 33.333 0.00 0.00 0.00 1.28
346 351 6.183360 ACCTCTTGGACTCACAATTTTTCAAG 60.183 38.462 0.00 0.00 37.04 3.02
348 353 5.200483 ACCTCTTGGACTCACAATTTTTCA 58.800 37.500 0.00 0.00 37.04 2.69
352 357 5.183904 GCATTACCTCTTGGACTCACAATTT 59.816 40.000 0.00 0.00 37.04 1.82
361 366 3.004752 ACATGGCATTACCTCTTGGAC 57.995 47.619 0.00 0.00 40.22 4.02
411 416 4.038883 AGCCTCGTCCCATAATACAGTAAC 59.961 45.833 0.00 0.00 0.00 2.50
452 457 1.240641 TTGACGCGTCAATTGCCCAT 61.241 50.000 42.01 3.54 43.90 4.00
493 498 6.828273 CACAAAATCCTCCATACCATTCTGTA 59.172 38.462 0.00 0.00 0.00 2.74
500 505 2.042297 TGCCACAAAATCCTCCATACCA 59.958 45.455 0.00 0.00 0.00 3.25
554 559 6.659242 TCCACTCAATATGATACGCTGATCTA 59.341 38.462 0.00 0.00 0.00 1.98
570 575 2.742053 CAAACCGACGATTCCACTCAAT 59.258 45.455 0.00 0.00 0.00 2.57
583 588 4.625972 TTTTCTTTCAGACCAAACCGAC 57.374 40.909 0.00 0.00 0.00 4.79
600 605 4.702131 ACTGCCTGGTCTATCAACATTTTC 59.298 41.667 0.00 0.00 0.00 2.29
656 662 6.674694 ATCTTTGCTGATACATCACAACTC 57.325 37.500 6.68 0.00 32.05 3.01
717 723 1.904771 CCAAGACCCCATAGCACGA 59.095 57.895 0.00 0.00 0.00 4.35
741 747 3.270877 GACCGGAAGTAATCACATGCTT 58.729 45.455 9.46 0.00 0.00 3.91
742 748 2.236146 TGACCGGAAGTAATCACATGCT 59.764 45.455 9.46 0.00 0.00 3.79
759 765 2.104963 GGGGACATCTAGGACATTGACC 59.895 54.545 0.00 0.00 0.00 4.02
760 766 3.041946 AGGGGACATCTAGGACATTGAC 58.958 50.000 0.00 0.00 0.00 3.18
842 848 6.879367 ATCAAATCCATCAGTCCCAATTTT 57.121 33.333 0.00 0.00 0.00 1.82
878 884 5.371526 TCACTCCCAGATTTATCATCAAGC 58.628 41.667 0.00 0.00 0.00 4.01
883 889 9.347240 CAAGTATTTCACTCCCAGATTTATCAT 57.653 33.333 0.00 0.00 36.04 2.45
891 897 3.526899 TCCCAAGTATTTCACTCCCAGA 58.473 45.455 0.00 0.00 36.04 3.86
920 926 4.910458 ATTAGCACCGCCCTCTATATTT 57.090 40.909 0.00 0.00 0.00 1.40
925 931 1.412710 CAGAATTAGCACCGCCCTCTA 59.587 52.381 0.00 0.00 0.00 2.43
926 932 0.179000 CAGAATTAGCACCGCCCTCT 59.821 55.000 0.00 0.00 0.00 3.69
927 933 0.815615 CCAGAATTAGCACCGCCCTC 60.816 60.000 0.00 0.00 0.00 4.30
928 934 1.224592 CCAGAATTAGCACCGCCCT 59.775 57.895 0.00 0.00 0.00 5.19
929 935 1.823899 CCCAGAATTAGCACCGCCC 60.824 63.158 0.00 0.00 0.00 6.13
953 1184 8.728088 AGAATATTTCTTTTATATTTGCGCGG 57.272 30.769 8.83 0.00 36.36 6.46
984 1215 2.814336 GCCACTAAATATACCAGGCTGC 59.186 50.000 9.56 0.00 37.67 5.25
987 1218 3.064931 GACGCCACTAAATATACCAGGC 58.935 50.000 0.00 0.00 37.32 4.85
991 1222 3.254166 TCGAGGACGCCACTAAATATACC 59.746 47.826 0.00 0.00 39.58 2.73
1000 1231 0.172803 GTATTGTCGAGGACGCCACT 59.827 55.000 0.00 0.00 39.58 4.00
1009 1240 3.571571 TCTCCAAACACGTATTGTCGAG 58.428 45.455 11.09 10.81 37.51 4.04
1016 1247 5.763204 ACACATTTTCTCTCCAAACACGTAT 59.237 36.000 0.00 0.00 0.00 3.06
1071 1302 7.499232 AGCCCTGACATTGTTCATAGTTATAAC 59.501 37.037 7.57 7.57 0.00 1.89
1079 1310 4.661222 TCAAAGCCCTGACATTGTTCATA 58.339 39.130 0.00 0.00 0.00 2.15
1089 1320 4.336280 ACTATTTTCCTCAAAGCCCTGAC 58.664 43.478 0.00 0.00 0.00 3.51
1096 1327 8.925161 TTTTGTCACAACTATTTTCCTCAAAG 57.075 30.769 0.00 0.00 0.00 2.77
1157 1388 2.409715 CGCCGCATCTACATTGATACAG 59.590 50.000 0.00 0.00 0.00 2.74
1168 1399 1.136110 TCTCATCAAACGCCGCATCTA 59.864 47.619 0.00 0.00 0.00 1.98
1169 1400 0.108186 TCTCATCAAACGCCGCATCT 60.108 50.000 0.00 0.00 0.00 2.90
1175 1406 3.232213 TCAGTAGTCTCATCAAACGCC 57.768 47.619 0.00 0.00 0.00 5.68
1177 1408 4.500837 CGGATTCAGTAGTCTCATCAAACG 59.499 45.833 0.00 0.00 0.00 3.60
1189 1420 2.223829 CCTACACTGCCGGATTCAGTAG 60.224 54.545 5.05 9.93 42.38 2.57
1201 1432 1.743252 GCCACTGCTCCTACACTGC 60.743 63.158 0.00 0.00 33.53 4.40
1203 1434 1.536418 TGGCCACTGCTCCTACACT 60.536 57.895 0.00 0.00 37.74 3.55
1218 1449 0.622665 CTCCCCATATCATCCCTGGC 59.377 60.000 0.00 0.00 0.00 4.85
1222 1453 2.240667 CCATGACTCCCCATATCATCCC 59.759 54.545 0.00 0.00 30.58 3.85
1247 1480 5.624509 GCATATACGACCCTCTCATTGCATA 60.625 44.000 0.00 0.00 0.00 3.14
1254 1487 4.343814 TCAATTGCATATACGACCCTCTCA 59.656 41.667 0.00 0.00 0.00 3.27
1280 1513 1.131126 CCATAGCTTCAGTTGTTGCCG 59.869 52.381 0.00 0.00 0.00 5.69
1302 1535 2.933492 GCCAATGCTAGTCCACGTAACA 60.933 50.000 0.00 0.00 33.53 2.41
1304 1537 1.276705 TGCCAATGCTAGTCCACGTAA 59.723 47.619 0.00 0.00 38.71 3.18
1308 1543 2.754552 TCATTTGCCAATGCTAGTCCAC 59.245 45.455 5.64 0.00 39.90 4.02
1315 1550 1.276989 CCCAACTCATTTGCCAATGCT 59.723 47.619 5.64 0.00 39.90 3.79
1359 1594 1.328680 CGATGGCTTCAAGACAATCCG 59.671 52.381 0.00 0.00 36.42 4.18
1382 1617 0.037232 AACGCTCCAGCCTGAAGTAC 60.037 55.000 0.00 0.00 37.91 2.73
1398 1633 1.025812 AGCCGATGTAGAGGAGAACG 58.974 55.000 0.00 0.00 0.00 3.95
1399 1634 1.537135 GCAGCCGATGTAGAGGAGAAC 60.537 57.143 0.00 0.00 0.00 3.01
1405 1640 0.678395 ATGGAGCAGCCGATGTAGAG 59.322 55.000 0.00 0.00 40.66 2.43
1414 1649 9.163899 CATATATCATCATAATATGGAGCAGCC 57.836 37.037 0.00 0.00 37.10 4.85
1416 1651 9.720769 TGCATATATCATCATAATATGGAGCAG 57.279 33.333 0.00 0.00 0.00 4.24
1445 1680 2.489938 TTGCCAAAGGTAGTAGCCTG 57.510 50.000 0.00 0.00 39.17 4.85
1446 1681 2.375509 ACTTTGCCAAAGGTAGTAGCCT 59.624 45.455 20.55 0.00 42.82 4.58
1452 1687 7.039270 ACTAAAACAAACTTTGCCAAAGGTAG 58.961 34.615 20.55 10.00 37.47 3.18
1455 1690 6.735678 AACTAAAACAAACTTTGCCAAAGG 57.264 33.333 20.55 6.29 42.82 3.11
1456 1691 7.956943 CAGAAACTAAAACAAACTTTGCCAAAG 59.043 33.333 15.47 15.47 44.10 2.77
1482 1717 7.162082 AGCAACATAATTAGCATCCCTACTAC 58.838 38.462 0.00 0.00 0.00 2.73
1485 1720 5.997746 TGAGCAACATAATTAGCATCCCTAC 59.002 40.000 0.00 0.00 0.00 3.18
1540 1775 1.270550 GGCTCATCAACCCAAACACAG 59.729 52.381 0.00 0.00 0.00 3.66
1552 1787 4.716784 ACTATGAAACTAGGTGGCTCATCA 59.283 41.667 0.00 0.00 0.00 3.07
1566 1801 9.559958 CATCCACAAGAAAATGTACTATGAAAC 57.440 33.333 0.00 0.00 30.84 2.78
1578 1813 7.888021 TGGTAGTTACATCATCCACAAGAAAAT 59.112 33.333 0.00 0.00 0.00 1.82
1580 1815 6.774673 TGGTAGTTACATCATCCACAAGAAA 58.225 36.000 0.00 0.00 0.00 2.52
1610 1845 5.303589 CCATCATGGCTCACTTTATTGGAAT 59.696 40.000 0.00 0.00 0.00 3.01
1613 1848 4.579454 CCATCATGGCTCACTTTATTGG 57.421 45.455 0.00 0.00 0.00 3.16
1652 1887 2.094234 GCAGTATCGGCAACCCATTTTT 60.094 45.455 0.00 0.00 0.00 1.94
1653 1888 1.476488 GCAGTATCGGCAACCCATTTT 59.524 47.619 0.00 0.00 0.00 1.82
1865 2103 1.217882 AATATAAGCCGCGAGTGTGC 58.782 50.000 8.23 0.66 0.00 4.57
2217 2540 3.245284 CAGATACTGCGACCCATTTTACG 59.755 47.826 0.00 0.00 0.00 3.18
2329 2662 1.667724 GAGACGTTAGTAGCACGCCTA 59.332 52.381 0.00 0.00 41.53 3.93
2334 2667 3.669122 CACAACAGAGACGTTAGTAGCAC 59.331 47.826 0.00 0.00 0.00 4.40
2363 2696 0.175073 AACGTGCGGATTCTAGGTCC 59.825 55.000 0.00 5.32 0.00 4.46
2396 2734 3.406361 CACCTGTCACGTGCGAGC 61.406 66.667 11.67 1.49 0.00 5.03
2400 2738 2.251642 GGTTCCACCTGTCACGTGC 61.252 63.158 11.67 6.86 34.73 5.34
2423 2775 6.009589 TGCCATTTTCTTCACCTCTATGAAA 58.990 36.000 0.00 0.00 38.12 2.69
2522 2874 1.273098 GGACCAGGAGAAGAGGGTGTA 60.273 57.143 0.00 0.00 32.77 2.90
2529 2881 1.194781 GCCACTGGACCAGGAGAAGA 61.195 60.000 25.34 0.00 35.51 2.87
2576 2928 1.292571 TTTGCATACGAAAGCCGCGA 61.293 50.000 8.23 0.00 43.32 5.87


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

AutoCloner maintained by Alex Coulton.