Multiple sequence alignment - TraesCS6A01G345500

Loading Multiple Alignment...

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 TraesCS6A01G345500 chr6A 100.000 3155 0 0 1 3155 579112671 579109517 0.000000e+00 5827.0
1 TraesCS6A01G345500 chr6A 97.149 912 26 0 2244 3155 420952263 420953174 0.000000e+00 1541.0
2 TraesCS6A01G345500 chr6A 96.495 913 28 1 2247 3155 186999837 187000749 0.000000e+00 1506.0
3 TraesCS6A01G345500 chr6A 86.681 901 100 13 411 1306 579025198 579024313 0.000000e+00 981.0
4 TraesCS6A01G345500 chr6A 85.590 916 113 10 1334 2247 579024316 579023418 0.000000e+00 942.0
5 TraesCS6A01G345500 chr6A 88.916 415 43 1 1 415 579034272 579033861 2.810000e-140 508.0
6 TraesCS6A01G345500 chr6A 80.457 481 75 10 468 947 579767818 579768280 1.800000e-92 350.0
7 TraesCS6A01G345500 chr6B 88.803 1545 151 8 63 1597 653852699 653851167 0.000000e+00 1875.0
8 TraesCS6A01G345500 chr6B 88.357 1546 153 13 63 1597 653185174 653183645 0.000000e+00 1832.0
9 TraesCS6A01G345500 chr6B 83.721 1204 164 17 1055 2246 653772682 653771499 0.000000e+00 1109.0
10 TraesCS6A01G345500 chr6B 83.993 1187 145 18 1055 2238 653711373 653710229 0.000000e+00 1098.0
11 TraesCS6A01G345500 chr6B 82.690 1011 119 27 1073 2056 653310131 653309150 0.000000e+00 846.0
12 TraesCS6A01G345500 chr6B 86.600 597 74 5 1653 2247 653851150 653850558 0.000000e+00 654.0
13 TraesCS6A01G345500 chr6B 85.531 622 80 7 1631 2247 653108506 653107890 2.650000e-180 641.0
14 TraesCS6A01G345500 chr6B 85.149 606 79 5 1649 2247 653220197 653220798 7.480000e-171 610.0
15 TraesCS6A01G345500 chr6B 85.435 563 73 4 1689 2247 653183610 653183053 7.590000e-161 577.0
16 TraesCS6A01G345500 chr6B 79.697 857 120 36 101 930 653230088 653229259 1.270000e-158 569.0
17 TraesCS6A01G345500 chr6B 79.405 874 122 22 64 929 653712363 653711540 5.910000e-157 564.0
18 TraesCS6A01G345500 chr6B 79.200 875 132 26 96 946 653110060 653109212 2.120000e-156 562.0
19 TraesCS6A01G345500 chr6B 83.750 560 80 8 1046 1602 653109053 653108502 1.300000e-143 520.0
20 TraesCS6A01G345500 chr6B 79.108 785 106 23 96 873 653763339 653762606 3.660000e-134 488.0
21 TraesCS6A01G345500 chr6B 77.791 869 130 26 1 863 653784086 653783275 7.920000e-131 477.0
22 TraesCS6A01G345500 chr6B 78.561 681 113 21 1495 2158 655077838 655078502 4.870000e-113 418.0
23 TraesCS6A01G345500 chr6B 78.650 637 92 24 96 710 653338137 653337523 1.780000e-102 383.0
24 TraesCS6A01G345500 chr6B 85.512 283 38 2 647 929 653216192 653216471 3.080000e-75 292.0
25 TraesCS6A01G345500 chr6B 82.026 306 37 10 307 609 653214433 653214723 8.740000e-61 244.0
26 TraesCS6A01G345500 chr7A 97.478 912 23 0 2244 3155 287501243 287502154 0.000000e+00 1557.0
27 TraesCS6A01G345500 chr7A 94.195 913 51 1 2245 3155 716399046 716399958 0.000000e+00 1391.0
28 TraesCS6A01G345500 chr7A 88.889 54 6 0 370 423 666683181 666683128 2.030000e-07 67.6
29 TraesCS6A01G345500 chr1A 97.259 912 24 1 2244 3155 98591800 98592710 0.000000e+00 1544.0
30 TraesCS6A01G345500 chr3A 96.703 910 28 2 2246 3155 46013597 46014504 0.000000e+00 1513.0
31 TraesCS6A01G345500 chr4A 95.895 877 36 0 2279 3155 50419617 50418741 0.000000e+00 1421.0
32 TraesCS6A01G345500 chr4A 91.996 912 69 4 2246 3155 674632223 674631314 0.000000e+00 1277.0
33 TraesCS6A01G345500 chr5B 93.326 914 56 5 2244 3155 62948502 62947592 0.000000e+00 1345.0
34 TraesCS6A01G345500 chr6D 84.725 1198 141 27 1068 2247 432965637 432964464 0.000000e+00 1160.0
35 TraesCS6A01G345500 chr6D 78.349 933 142 30 1 929 432910319 432909443 1.650000e-152 549.0
36 TraesCS6A01G345500 chr6D 78.472 864 131 31 1 838 432966937 432966103 6.030000e-142 514.0
37 TraesCS6A01G345500 chr6D 78.271 833 142 23 116 929 433582024 433582836 1.690000e-137 499.0
38 TraesCS6A01G345500 chr6D 81.850 573 92 4 1051 1623 433582991 433583551 3.680000e-129 472.0
39 TraesCS6A01G345500 chr6D 84.314 153 23 1 96 247 433256028 433255876 7.050000e-32 148.0


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 TraesCS6A01G345500 chr6A 579109517 579112671 3154 True 5827.000000 5827 100.0000 1 3155 1 chr6A.!!$R2 3154
1 TraesCS6A01G345500 chr6A 420952263 420953174 911 False 1541.000000 1541 97.1490 2244 3155 1 chr6A.!!$F2 911
2 TraesCS6A01G345500 chr6A 186999837 187000749 912 False 1506.000000 1506 96.4950 2247 3155 1 chr6A.!!$F1 908
3 TraesCS6A01G345500 chr6A 579023418 579025198 1780 True 961.500000 981 86.1355 411 2247 2 chr6A.!!$R3 1836
4 TraesCS6A01G345500 chr6B 653850558 653852699 2141 True 1264.500000 1875 87.7015 63 2247 2 chr6B.!!$R10 2184
5 TraesCS6A01G345500 chr6B 653183053 653185174 2121 True 1204.500000 1832 86.8960 63 2247 2 chr6B.!!$R8 2184
6 TraesCS6A01G345500 chr6B 653771499 653772682 1183 True 1109.000000 1109 83.7210 1055 2246 1 chr6B.!!$R5 1191
7 TraesCS6A01G345500 chr6B 653309150 653310131 981 True 846.000000 846 82.6900 1073 2056 1 chr6B.!!$R2 983
8 TraesCS6A01G345500 chr6B 653710229 653712363 2134 True 831.000000 1098 81.6990 64 2238 2 chr6B.!!$R9 2174
9 TraesCS6A01G345500 chr6B 653107890 653110060 2170 True 574.333333 641 82.8270 96 2247 3 chr6B.!!$R7 2151
10 TraesCS6A01G345500 chr6B 653229259 653230088 829 True 569.000000 569 79.6970 101 930 1 chr6B.!!$R1 829
11 TraesCS6A01G345500 chr6B 653762606 653763339 733 True 488.000000 488 79.1080 96 873 1 chr6B.!!$R4 777
12 TraesCS6A01G345500 chr6B 653783275 653784086 811 True 477.000000 477 77.7910 1 863 1 chr6B.!!$R6 862
13 TraesCS6A01G345500 chr6B 655077838 655078502 664 False 418.000000 418 78.5610 1495 2158 1 chr6B.!!$F1 663
14 TraesCS6A01G345500 chr6B 653337523 653338137 614 True 383.000000 383 78.6500 96 710 1 chr6B.!!$R3 614
15 TraesCS6A01G345500 chr6B 653214433 653220798 6365 False 382.000000 610 84.2290 307 2247 3 chr6B.!!$F2 1940
16 TraesCS6A01G345500 chr7A 287501243 287502154 911 False 1557.000000 1557 97.4780 2244 3155 1 chr7A.!!$F1 911
17 TraesCS6A01G345500 chr7A 716399046 716399958 912 False 1391.000000 1391 94.1950 2245 3155 1 chr7A.!!$F2 910
18 TraesCS6A01G345500 chr1A 98591800 98592710 910 False 1544.000000 1544 97.2590 2244 3155 1 chr1A.!!$F1 911
19 TraesCS6A01G345500 chr3A 46013597 46014504 907 False 1513.000000 1513 96.7030 2246 3155 1 chr3A.!!$F1 909
20 TraesCS6A01G345500 chr4A 50418741 50419617 876 True 1421.000000 1421 95.8950 2279 3155 1 chr4A.!!$R1 876
21 TraesCS6A01G345500 chr4A 674631314 674632223 909 True 1277.000000 1277 91.9960 2246 3155 1 chr4A.!!$R2 909
22 TraesCS6A01G345500 chr5B 62947592 62948502 910 True 1345.000000 1345 93.3260 2244 3155 1 chr5B.!!$R1 911
23 TraesCS6A01G345500 chr6D 432964464 432966937 2473 True 837.000000 1160 81.5985 1 2247 2 chr6D.!!$R3 2246
24 TraesCS6A01G345500 chr6D 432909443 432910319 876 True 549.000000 549 78.3490 1 929 1 chr6D.!!$R1 928
25 TraesCS6A01G345500 chr6D 433582024 433583551 1527 False 485.500000 499 80.0605 116 1623 2 chr6D.!!$F1 1507

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
259 268 0.849417 AGCCATCCCCTCCTTTGATC 59.151 55.0 0.00 0.00 0.00 2.92 F
1034 4020 0.034896 ACGAACAAACTCGGGATGCT 59.965 50.0 0.00 0.00 43.22 3.79 F
1517 4536 0.036732 TTACTCTGGGCCTGCAACAG 59.963 55.0 4.53 0.22 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 6619 0.108186 TGATTCTGTGTAGCGCCCAG 60.108 55.0 2.29 5.66 0.00 4.45 R
2016 6767 0.178990 GGTGCCCTTTGAGGTTGTCT 60.179 55.0 0.00 0.00 31.93 3.41 R
2410 7187 0.383949 ATTGTGGCGTGCGTCTTTTT 59.616 45.0 0.00 0.00 0.00 1.94 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
31 32 1.669115 CTCCACACTTGGCTCCACG 60.669 63.158 0.00 0.00 43.56 4.94
34 35 3.168528 ACACTTGGCTCCACGGGT 61.169 61.111 0.00 0.00 0.00 5.28
38 39 0.907704 ACTTGGCTCCACGGGTGATA 60.908 55.000 0.00 0.00 0.00 2.15
47 48 4.742440 GCTCCACGGGTGATATGTTTGATA 60.742 45.833 0.00 0.00 0.00 2.15
50 51 5.762711 TCCACGGGTGATATGTTTGATATTG 59.237 40.000 0.00 0.00 0.00 1.90
68 69 9.642327 TTGATATTGTTCTCAAACATGAATTGG 57.358 29.630 0.00 0.00 44.59 3.16
108 109 3.859650 GCATGCACTCATACATGGC 57.140 52.632 14.21 0.00 43.13 4.40
118 119 3.586174 ACTCATACATGGCCATAGCATCT 59.414 43.478 20.30 0.00 42.56 2.90
156 164 6.359804 TGATTTCTGCTATCAATACAAGCCT 58.640 36.000 0.00 0.00 35.33 4.58
172 180 3.810310 AGCCTGATAGTTGCTACTGAC 57.190 47.619 11.27 5.49 35.78 3.51
250 259 2.588925 AGTTTACCTAGCCATCCCCT 57.411 50.000 0.00 0.00 0.00 4.79
259 268 0.849417 AGCCATCCCCTCCTTTGATC 59.151 55.000 0.00 0.00 0.00 2.92
271 280 4.141824 CCTCCTTTGATCTTCCTGGTAGAC 60.142 50.000 5.07 1.37 0.00 2.59
272 281 3.775316 TCCTTTGATCTTCCTGGTAGACC 59.225 47.826 5.07 0.00 0.00 3.85
274 283 4.226168 CCTTTGATCTTCCTGGTAGACCTT 59.774 45.833 5.07 0.00 36.82 3.50
275 284 5.280727 CCTTTGATCTTCCTGGTAGACCTTT 60.281 44.000 5.07 0.00 36.82 3.11
279 288 6.889198 TGATCTTCCTGGTAGACCTTTTATG 58.111 40.000 5.07 0.00 36.82 1.90
289 298 9.110502 CTGGTAGACCTTTTATGGAAATAAGAC 57.889 37.037 0.00 0.00 36.82 3.01
290 299 8.832735 TGGTAGACCTTTTATGGAAATAAGACT 58.167 33.333 0.00 0.00 36.82 3.24
368 380 2.632377 TGCATTTCTAAAGGCTCGGAG 58.368 47.619 12.61 0.00 45.16 4.63
529 556 3.246619 CGACAAGTAGAGAAGCAACCTC 58.753 50.000 0.00 0.00 0.00 3.85
530 557 3.246619 GACAAGTAGAGAAGCAACCTCG 58.753 50.000 0.00 0.00 35.88 4.63
569 596 5.534278 TGTTCAGAAATAACATGAAGGCACA 59.466 36.000 0.00 0.00 33.83 4.57
625 2104 2.499289 TGGCAGTTGGACAACATGTTTT 59.501 40.909 8.77 1.70 43.47 2.43
735 2214 2.287427 CGCCGACGTTATCACTAAGGAT 60.287 50.000 0.00 0.00 33.53 3.24
752 2231 7.279981 CACTAAGGATACCATCAAATTCGTCAA 59.720 37.037 0.00 0.00 37.17 3.18
815 2294 4.820173 CAGGATGATTGCAGATGAGCTTTA 59.180 41.667 0.00 0.00 39.69 1.85
884 2545 5.581085 CAGGTAGCTGGTTTACTACAACATC 59.419 44.000 14.29 0.00 40.45 3.06
961 2625 5.593010 ACGTCATCAAAGAAGCTAGGATAC 58.407 41.667 0.00 0.00 0.00 2.24
964 2628 6.529220 GTCATCAAAGAAGCTAGGATACCAT 58.471 40.000 0.00 0.00 37.17 3.55
980 2701 5.162980 GGATACCATGGGATTTTCCTTAGGT 60.163 44.000 18.09 0.00 37.40 3.08
983 3561 4.045334 ACCATGGGATTTTCCTTAGGTGAA 59.955 41.667 18.09 0.00 36.57 3.18
1031 4017 3.507233 TGTACTACGAACAAACTCGGGAT 59.493 43.478 0.00 0.00 43.22 3.85
1034 4020 0.034896 ACGAACAAACTCGGGATGCT 59.965 50.000 0.00 0.00 43.22 3.79
1128 4117 2.435059 GTTGCTGAGGCGAGGGAC 60.435 66.667 0.00 0.00 42.25 4.46
1149 4138 2.057137 TTGCTTCCCACATATGCTCC 57.943 50.000 1.58 0.00 0.00 4.70
1161 4150 2.787473 TATGCTCCAACTGGACCAAG 57.213 50.000 0.00 0.00 39.78 3.61
1243 4239 2.592287 GGGTCGGCCGTTTGTTGA 60.592 61.111 27.15 0.00 34.97 3.18
1261 4257 1.297664 GAGATGCAGATGTGACAGGC 58.702 55.000 0.00 0.00 0.00 4.85
1268 4264 2.745482 GCAGATGTGACAGGCTGATGAT 60.745 50.000 23.66 7.12 0.00 2.45
1306 4302 3.631145 TGAGACAAAGCTCATTGTTGC 57.369 42.857 5.30 2.31 43.31 4.17
1376 4378 2.281517 TCGTTTGCTTGACCGAAAGAA 58.718 42.857 0.00 0.00 0.00 2.52
1377 4379 2.286833 TCGTTTGCTTGACCGAAAGAAG 59.713 45.455 0.00 0.00 0.00 2.85
1400 4408 4.081322 AGAATGTTGAAGTACCAACGGT 57.919 40.909 9.51 0.00 46.89 4.83
1455 4474 0.615331 CAAGCAGTGGAGGCCTAAGA 59.385 55.000 4.42 0.00 0.00 2.10
1474 4493 2.031870 GAAAAGGCACAACTTCCCTGT 58.968 47.619 0.00 0.00 0.00 4.00
1517 4536 0.036732 TTACTCTGGGCCTGCAACAG 59.963 55.000 4.53 0.22 0.00 3.16
1518 4537 1.127567 TACTCTGGGCCTGCAACAGT 61.128 55.000 4.53 6.41 34.02 3.55
1519 4538 1.673665 CTCTGGGCCTGCAACAGTC 60.674 63.158 4.53 0.00 34.02 3.51
1602 4626 0.467290 ACCCACACCACCAACATGAC 60.467 55.000 0.00 0.00 0.00 3.06
1605 4632 0.586319 CACACCACCAACATGACGAC 59.414 55.000 0.00 0.00 0.00 4.34
1623 4650 1.352622 ACCCTCCTCAGCAAACACCA 61.353 55.000 0.00 0.00 0.00 4.17
1624 4651 0.178992 CCCTCCTCAGCAAACACCAA 60.179 55.000 0.00 0.00 0.00 3.67
1625 4652 0.954452 CCTCCTCAGCAAACACCAAC 59.046 55.000 0.00 0.00 0.00 3.77
1626 4653 1.679139 CTCCTCAGCAAACACCAACA 58.321 50.000 0.00 0.00 0.00 3.33
1627 4654 1.334869 CTCCTCAGCAAACACCAACAC 59.665 52.381 0.00 0.00 0.00 3.32
1628 4655 0.385390 CCTCAGCAAACACCAACACC 59.615 55.000 0.00 0.00 0.00 4.16
1652 6388 2.035442 GTGGCCGACCTTCTTCTGC 61.035 63.158 0.00 0.00 36.63 4.26
1657 6393 1.204941 GCCGACCTTCTTCTGCTTCTA 59.795 52.381 0.00 0.00 0.00 2.10
1663 6399 5.290643 CGACCTTCTTCTGCTTCTATTTCTG 59.709 44.000 0.00 0.00 0.00 3.02
1670 6406 6.870965 TCTTCTGCTTCTATTTCTGACAAGAC 59.129 38.462 0.00 0.00 29.98 3.01
1674 6410 4.923871 GCTTCTATTTCTGACAAGACGACA 59.076 41.667 0.00 0.00 29.98 4.35
1683 6419 1.595109 CAAGACGACAGCTGCCACA 60.595 57.895 15.27 0.00 0.00 4.17
1686 6426 1.669115 GACGACAGCTGCCACACAT 60.669 57.895 15.27 0.00 0.00 3.21
1725 6465 2.323999 ATTTGGTGGCATCTTTCCCA 57.676 45.000 0.00 0.00 0.00 4.37
1756 6496 3.056322 TCCTGATGATGATACATGGAGCG 60.056 47.826 0.00 0.00 0.00 5.03
1782 6522 5.998363 GGACCTCTACAACAAAGTCAAGAAT 59.002 40.000 0.00 0.00 0.00 2.40
1807 6553 2.776526 ACCAAGCCCTCACCACCA 60.777 61.111 0.00 0.00 0.00 4.17
1808 6554 2.034687 CCAAGCCCTCACCACCAG 59.965 66.667 0.00 0.00 0.00 4.00
1809 6555 2.528818 CCAAGCCCTCACCACCAGA 61.529 63.158 0.00 0.00 0.00 3.86
1851 6597 4.069232 CTGTCGCCGGAAGCTGGA 62.069 66.667 5.05 0.00 40.39 3.86
1873 6619 5.758784 GGATACCTAAGGTTGATACAGTTGC 59.241 44.000 0.00 0.00 37.09 4.17
1897 6643 1.260033 GCGCTACACAGAATCATGAGC 59.740 52.381 0.00 0.00 0.00 4.26
2016 6767 0.543410 TCCTTTACCTGGCTCCGTCA 60.543 55.000 0.00 0.00 0.00 4.35
2138 6904 1.004080 ACATCGCTGCAAGTGCTCT 60.004 52.632 4.69 0.00 46.11 4.09
2248 7018 4.839121 TCTTGGTTGTGAGTGTGTTTACT 58.161 39.130 0.00 0.00 0.00 2.24
2347 7121 1.371183 CACACACACGGAGGTCCAT 59.629 57.895 0.00 0.00 35.14 3.41
2410 7187 2.100584 CAGCACAACAAGCCCTAAAACA 59.899 45.455 0.00 0.00 0.00 2.83
2542 7319 4.077184 GGCGGTGATGACGTCCCA 62.077 66.667 14.12 8.40 0.00 4.37
2677 7454 0.883833 CAAAGCGTCCAGGCAAGAAT 59.116 50.000 0.00 0.00 34.64 2.40
2801 7578 2.034066 CGGAAGCAGGCCCAAAGA 59.966 61.111 0.00 0.00 0.00 2.52
3003 7780 1.304952 CTAAATGGTTCCGGGGCCA 59.695 57.895 17.86 17.86 39.33 5.36
3032 7809 2.504367 GCAATGGCACCGTATAAGGAT 58.496 47.619 12.02 0.00 40.72 3.24
3054 7831 1.215173 TCATGGAGAAATGCCCGGAAT 59.785 47.619 0.73 0.00 0.00 3.01
3110 7887 3.790437 ACCTCCATCGGCAGCAGG 61.790 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.469917 ATATCACCCGTGGAGCCAAG 59.530 55.000 0.00 0.00 0.00 3.61
31 32 8.450578 TGAGAACAATATCAAACATATCACCC 57.549 34.615 0.00 0.00 0.00 4.61
50 51 5.048083 TGGCTACCAATTCATGTTTGAGAAC 60.048 40.000 11.19 0.00 36.29 3.01
58 59 2.493278 GCAACTGGCTACCAATTCATGT 59.507 45.455 0.00 0.00 40.25 3.21
108 109 0.178998 AAGGCAGGCAGATGCTATGG 60.179 55.000 4.59 0.00 45.75 2.74
118 119 1.888512 GAAATCAGAACAAGGCAGGCA 59.111 47.619 0.00 0.00 0.00 4.75
156 164 3.875134 TCGATCGTCAGTAGCAACTATCA 59.125 43.478 15.94 0.00 33.48 2.15
243 252 2.782341 AGGAAGATCAAAGGAGGGGATG 59.218 50.000 0.00 0.00 0.00 3.51
250 259 3.775316 GGTCTACCAGGAAGATCAAAGGA 59.225 47.826 0.00 0.00 35.64 3.36
259 268 5.693769 TCCATAAAAGGTCTACCAGGAAG 57.306 43.478 1.26 0.00 38.89 3.46
363 375 0.173481 CGAGTGCAAAGGATCTCCGA 59.827 55.000 0.00 0.00 42.08 4.55
368 380 1.696832 GCGTCCGAGTGCAAAGGATC 61.697 60.000 8.95 2.35 36.34 3.36
569 596 2.821969 GTCACCAAGTTGCCATCTTGAT 59.178 45.455 15.44 0.00 43.17 2.57
625 2104 0.038435 CGTTGTGGCATTGGCATCAA 60.038 50.000 16.56 17.27 43.71 2.57
735 2214 5.697473 TGCTTTTGACGAATTTGATGGTA 57.303 34.783 0.00 0.00 0.00 3.25
884 2545 5.970592 TCAAGAGTGAGATGACCATACTTG 58.029 41.667 0.00 0.00 34.36 3.16
961 2625 4.249638 TCACCTAAGGAAAATCCCATGG 57.750 45.455 4.14 4.14 37.19 3.66
980 2701 2.591923 TGCAAGTAATTGTGGCCTTCA 58.408 42.857 3.32 0.00 0.00 3.02
983 3561 2.528564 ACATGCAAGTAATTGTGGCCT 58.471 42.857 3.32 0.00 0.00 5.19
1128 4117 2.295349 GGAGCATATGTGGGAAGCAATG 59.705 50.000 4.29 0.00 0.00 2.82
1149 4138 3.721087 AGGATTACCTTGGTCCAGTTG 57.279 47.619 0.00 0.00 45.36 3.16
1161 4150 0.912486 AGTGGCAGGTGAGGATTACC 59.088 55.000 0.00 0.00 38.52 2.85
1230 4226 1.154225 GCATCTCAACAAACGGCCG 60.154 57.895 26.86 26.86 0.00 6.13
1243 4239 0.910338 AGCCTGTCACATCTGCATCT 59.090 50.000 0.00 0.00 0.00 2.90
1261 4257 2.679336 TGTCGTTCCAATGCATCATCAG 59.321 45.455 0.00 0.00 0.00 2.90
1268 4264 3.567585 TCTCATTTTGTCGTTCCAATGCA 59.432 39.130 0.00 0.00 0.00 3.96
1306 4302 0.971386 AATTGCCTTGGGTGAAGCAG 59.029 50.000 0.00 0.00 0.00 4.24
1376 4378 4.755123 CCGTTGGTACTTCAACATTCTTCT 59.245 41.667 13.28 0.00 45.16 2.85
1377 4379 4.514066 ACCGTTGGTACTTCAACATTCTTC 59.486 41.667 13.28 0.00 45.16 2.87
1400 4408 3.954200 TCAATGATGCAAGCCTTCACTA 58.046 40.909 0.00 0.00 31.31 2.74
1474 4493 2.343758 GTCGTCTTGGCTCTGGCA 59.656 61.111 0.00 0.00 40.87 4.92
1517 4536 2.412089 GTGTCAGATGTACCTTTGCGAC 59.588 50.000 0.00 0.00 0.00 5.19
1518 4537 2.611971 GGTGTCAGATGTACCTTTGCGA 60.612 50.000 0.00 0.00 0.00 5.10
1519 4538 1.732259 GGTGTCAGATGTACCTTTGCG 59.268 52.381 0.00 0.00 0.00 4.85
1602 4626 0.951040 GTGTTTGCTGAGGAGGGTCG 60.951 60.000 0.00 0.00 0.00 4.79
1605 4632 0.178992 TTGGTGTTTGCTGAGGAGGG 60.179 55.000 0.00 0.00 0.00 4.30
1641 6377 6.169800 GTCAGAAATAGAAGCAGAAGAAGGT 58.830 40.000 0.00 0.00 0.00 3.50
1652 6388 5.061560 GCTGTCGTCTTGTCAGAAATAGAAG 59.938 44.000 0.00 0.00 36.02 2.85
1657 6393 3.062763 CAGCTGTCGTCTTGTCAGAAAT 58.937 45.455 5.25 0.00 36.02 2.17
1663 6399 1.300931 TGGCAGCTGTCGTCTTGTC 60.301 57.895 14.71 0.00 0.00 3.18
1670 6406 1.375140 AGATGTGTGGCAGCTGTCG 60.375 57.895 14.71 0.00 42.99 4.35
1674 6410 0.604780 GTGACAGATGTGTGGCAGCT 60.605 55.000 0.00 0.00 45.94 4.24
1704 6444 3.364549 TGGGAAAGATGCCACCAAATAG 58.635 45.455 0.00 0.00 42.90 1.73
1708 6448 0.776810 TCTGGGAAAGATGCCACCAA 59.223 50.000 0.00 0.00 42.90 3.67
1719 6459 2.902608 TCAGGAAGTAGCTCTGGGAAA 58.097 47.619 0.00 0.00 0.00 3.13
1721 6461 2.023984 TCATCAGGAAGTAGCTCTGGGA 60.024 50.000 0.00 0.00 0.00 4.37
1725 6465 6.073981 TGTATCATCATCAGGAAGTAGCTCT 58.926 40.000 0.00 0.00 0.00 4.09
1756 6496 4.602340 TGACTTTGTTGTAGAGGTCCTC 57.398 45.455 11.31 11.31 0.00 3.71
1851 6597 6.349300 CAGCAACTGTATCAACCTTAGGTAT 58.651 40.000 3.55 0.00 33.12 2.73
1873 6619 0.108186 TGATTCTGTGTAGCGCCCAG 60.108 55.000 2.29 5.66 0.00 4.45
1897 6643 1.588824 TTGGCGGCATCTTTGAGCAG 61.589 55.000 14.32 0.00 32.04 4.24
1946 6692 3.077556 ACGCCATCTCCTCGCCTT 61.078 61.111 0.00 0.00 0.00 4.35
2016 6767 0.178990 GGTGCCCTTTGAGGTTGTCT 60.179 55.000 0.00 0.00 31.93 3.41
2123 6889 1.446792 GCTAGAGCACTTGCAGCGA 60.447 57.895 12.17 0.00 45.16 4.93
2138 6904 3.316868 GCAAACTTAAACACCAGTGGCTA 59.683 43.478 9.78 0.00 34.19 3.93
2347 7121 6.436738 TTTGGTGTACTATTGTGGTTCCTA 57.563 37.500 0.00 0.00 0.00 2.94
2410 7187 0.383949 ATTGTGGCGTGCGTCTTTTT 59.616 45.000 0.00 0.00 0.00 1.94
2508 7285 1.539165 CCCTCCTCTCCGATCTCCA 59.461 63.158 0.00 0.00 0.00 3.86
2542 7319 4.733725 TTAGCCGCCCCCAGGACT 62.734 66.667 0.00 0.00 33.47 3.85
2677 7454 0.396556 TAGATGGCTGTGCGTAGGGA 60.397 55.000 0.00 0.00 0.00 4.20
2801 7578 1.529244 GTGCCACTCTGCCCAGTTT 60.529 57.895 0.00 0.00 0.00 2.66
3003 7780 2.115052 TGCCATTGCACCCTCGTT 59.885 55.556 0.00 0.00 44.23 3.85
3045 7822 4.161295 CCTCGAGCATTCCGGGCA 62.161 66.667 6.99 0.00 0.00 5.36
3054 7831 3.695606 GTCCTGGCACCTCGAGCA 61.696 66.667 6.99 0.00 0.00 4.26
3110 7887 4.972875 CTCCTCCAGGACATTGCC 57.027 61.111 0.00 0.00 39.78 4.52


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

AutoCloner maintained by Alex Coulton.