Multiple sequence alignment - TraesCS6A01G356400

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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 TraesCS6A01G356400 chr6A 100.000 3164 0 0 1 3164 587562177 587565340 0.000000e+00 5843.0
1 TraesCS6A01G356400 chr6A 82.324 611 64 24 2586 3164 587700472 587699874 1.020000e-134 490.0
2 TraesCS6A01G356400 chr6A 86.261 444 37 14 2246 2678 587762629 587762199 8.000000e-126 460.0
3 TraesCS6A01G356400 chr6A 88.321 274 15 13 2210 2478 586878198 586878459 2.370000e-81 313.0
4 TraesCS6A01G356400 chr6A 80.338 473 41 21 1768 2230 586877750 586878180 8.520000e-81 311.0
5 TraesCS6A01G356400 chr6A 93.421 152 10 0 1648 1799 586877591 586877742 3.180000e-55 226.0
6 TraesCS6A01G356400 chr6A 87.143 70 5 3 967 1034 586876765 586876832 3.380000e-10 76.8
7 TraesCS6A01G356400 chr6D 91.830 1530 82 21 1651 3164 438805030 438806532 0.000000e+00 2093.0
8 TraesCS6A01G356400 chr6D 88.427 769 88 1 1 769 221297574 221296807 0.000000e+00 926.0
9 TraesCS6A01G356400 chr6D 89.583 720 39 15 958 1666 438802882 438803576 0.000000e+00 881.0
10 TraesCS6A01G356400 chr6D 87.400 627 52 14 1768 2382 438460898 438461509 0.000000e+00 695.0
11 TraesCS6A01G356400 chr6B 87.605 1315 100 23 1881 3164 663840261 663841543 0.000000e+00 1467.0
12 TraesCS6A01G356400 chr6B 83.610 543 59 12 1768 2301 663800502 663801023 1.710000e-132 483.0
13 TraesCS6A01G356400 chr6B 86.364 352 29 7 1453 1799 608038253 608038590 1.790000e-97 366.0
14 TraesCS6A01G356400 chr6B 82.198 455 54 15 2728 3164 664002302 664001857 1.790000e-97 366.0
15 TraesCS6A01G356400 chr6B 78.147 572 61 33 2589 3121 664029126 664028580 3.960000e-79 305.0
16 TraesCS6A01G356400 chr1A 92.364 956 70 2 1 956 11068713 11067761 0.000000e+00 1358.0
17 TraesCS6A01G356400 chr5A 91.979 960 75 2 1 959 631713102 631714060 0.000000e+00 1345.0
18 TraesCS6A01G356400 chr5A 79.878 164 33 0 1794 1957 439556186 439556023 1.540000e-23 121.0
19 TraesCS6A01G356400 chr5D 90.890 966 85 2 1 966 349361245 349360283 0.000000e+00 1293.0
20 TraesCS6A01G356400 chr5D 84.982 566 82 3 391 955 200496023 200495460 3.540000e-159 571.0
21 TraesCS6A01G356400 chr2B 82.795 959 157 8 1 956 278434437 278435390 0.000000e+00 850.0
22 TraesCS6A01G356400 chr4B 80.251 957 183 5 3 957 638313010 638313962 0.000000e+00 715.0
23 TraesCS6A01G356400 chrUn 80.940 745 114 10 215 958 50268817 50269534 5.920000e-157 564.0
24 TraesCS6A01G356400 chrUn 86.455 347 44 3 613 958 473461904 473461560 8.280000e-101 377.0
25 TraesCS6A01G356400 chr7A 81.507 584 96 12 379 957 576420392 576420968 1.330000e-128 470.0
26 TraesCS6A01G356400 chr7A 81.100 582 103 7 379 957 658689624 658689047 2.880000e-125 459.0
27 TraesCS6A01G356400 chr7B 80.796 578 63 21 1241 1799 651561119 651561667 2.940000e-110 409.0
28 TraesCS6A01G356400 chr7B 80.796 578 63 21 1241 1799 651736131 651736679 2.940000e-110 409.0
29 TraesCS6A01G356400 chr3B 80.104 578 66 22 1241 1799 588909503 588910050 4.950000e-103 385.0
30 TraesCS6A01G356400 chr5B 79.268 164 34 0 1794 1957 397838078 397837915 7.170000e-22 115.0


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 TraesCS6A01G356400 chr6A 587562177 587565340 3163 False 5843.0 5843 100.00000 1 3164 1 chr6A.!!$F1 3163
1 TraesCS6A01G356400 chr6A 587699874 587700472 598 True 490.0 490 82.32400 2586 3164 1 chr6A.!!$R1 578
2 TraesCS6A01G356400 chr6A 586876765 586878459 1694 False 231.7 313 87.30575 967 2478 4 chr6A.!!$F2 1511
3 TraesCS6A01G356400 chr6D 438802882 438806532 3650 False 1487.0 2093 90.70650 958 3164 2 chr6D.!!$F2 2206
4 TraesCS6A01G356400 chr6D 221296807 221297574 767 True 926.0 926 88.42700 1 769 1 chr6D.!!$R1 768
5 TraesCS6A01G356400 chr6D 438460898 438461509 611 False 695.0 695 87.40000 1768 2382 1 chr6D.!!$F1 614
6 TraesCS6A01G356400 chr6B 663840261 663841543 1282 False 1467.0 1467 87.60500 1881 3164 1 chr6B.!!$F3 1283
7 TraesCS6A01G356400 chr6B 663800502 663801023 521 False 483.0 483 83.61000 1768 2301 1 chr6B.!!$F2 533
8 TraesCS6A01G356400 chr6B 664028580 664029126 546 True 305.0 305 78.14700 2589 3121 1 chr6B.!!$R2 532
9 TraesCS6A01G356400 chr1A 11067761 11068713 952 True 1358.0 1358 92.36400 1 956 1 chr1A.!!$R1 955
10 TraesCS6A01G356400 chr5A 631713102 631714060 958 False 1345.0 1345 91.97900 1 959 1 chr5A.!!$F1 958
11 TraesCS6A01G356400 chr5D 349360283 349361245 962 True 1293.0 1293 90.89000 1 966 1 chr5D.!!$R2 965
12 TraesCS6A01G356400 chr5D 200495460 200496023 563 True 571.0 571 84.98200 391 955 1 chr5D.!!$R1 564
13 TraesCS6A01G356400 chr2B 278434437 278435390 953 False 850.0 850 82.79500 1 956 1 chr2B.!!$F1 955
14 TraesCS6A01G356400 chr4B 638313010 638313962 952 False 715.0 715 80.25100 3 957 1 chr4B.!!$F1 954
15 TraesCS6A01G356400 chrUn 50268817 50269534 717 False 564.0 564 80.94000 215 958 1 chrUn.!!$F1 743
16 TraesCS6A01G356400 chr7A 576420392 576420968 576 False 470.0 470 81.50700 379 957 1 chr7A.!!$F1 578
17 TraesCS6A01G356400 chr7A 658689047 658689624 577 True 459.0 459 81.10000 379 957 1 chr7A.!!$R1 578
18 TraesCS6A01G356400 chr7B 651561119 651561667 548 False 409.0 409 80.79600 1241 1799 1 chr7B.!!$F1 558
19 TraesCS6A01G356400 chr7B 651736131 651736679 548 False 409.0 409 80.79600 1241 1799 1 chr7B.!!$F2 558
20 TraesCS6A01G356400 chr3B 588909503 588910050 547 False 385.0 385 80.10400 1241 1799 1 chr3B.!!$F1 558

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
987 993 0.03779 AGAAGAAGAGCCAGACACGC 60.038 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2794 4592 0.10339 TGACAGCGACGAGGTTTTCA 59.897 50.0 0.0 0.0 0.0 2.69 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
143 144 1.913722 CTCTTCTGCCCTCATGCCT 59.086 57.895 0.00 0.00 0.00 4.75
239 240 1.000955 GGCTCTTCGACTTCTTGTCCA 59.999 52.381 0.00 0.00 42.49 4.02
305 306 3.316308 GCATATCTGGAAAGCACGGAATT 59.684 43.478 0.00 0.00 0.00 2.17
324 325 1.382522 TTGGCGAGGAATGAATCTGC 58.617 50.000 0.00 0.00 0.00 4.26
435 436 0.390472 CGTGAGACCTCCCTTTCTGC 60.390 60.000 0.00 0.00 0.00 4.26
439 440 1.448717 GACCTCCCTTTCTGCTCGC 60.449 63.158 0.00 0.00 0.00 5.03
497 498 0.867753 CTCTGATGCTACGGTGTCGC 60.868 60.000 0.00 0.00 40.63 5.19
590 591 4.521062 CTCTTCTGGGCGCTCGGG 62.521 72.222 17.93 4.79 0.00 5.14
683 684 6.636447 CGAAGTTATTTTCAACACTGATTGCA 59.364 34.615 0.00 0.00 0.00 4.08
757 758 9.449719 GTGGGTTCTATTCTTTCAGAGATTAAA 57.550 33.333 0.00 0.00 33.49 1.52
801 802 3.698539 TCAACTTGTTTCCAGCATGTTCA 59.301 39.130 0.00 0.00 33.74 3.18
924 925 7.996385 ACTCTGTGTAAGTTTGTTGCTTAATT 58.004 30.769 0.00 0.00 31.22 1.40
978 980 0.393673 GCCCCAGGAAGAAGAAGAGC 60.394 60.000 0.00 0.00 0.00 4.09
984 990 2.301296 CAGGAAGAAGAAGAGCCAGACA 59.699 50.000 0.00 0.00 0.00 3.41
985 991 2.301583 AGGAAGAAGAAGAGCCAGACAC 59.698 50.000 0.00 0.00 0.00 3.67
986 992 2.333014 GAAGAAGAAGAGCCAGACACG 58.667 52.381 0.00 0.00 0.00 4.49
987 993 0.037790 AGAAGAAGAGCCAGACACGC 60.038 55.000 0.00 0.00 0.00 5.34
1096 1144 1.012486 GTCCGTCCAGGCAAGTAACG 61.012 60.000 0.00 0.00 40.77 3.18
1122 1177 1.745890 CCTTCGATCCCCGCATACA 59.254 57.895 0.00 0.00 38.37 2.29
1123 1178 0.321671 CCTTCGATCCCCGCATACAT 59.678 55.000 0.00 0.00 38.37 2.29
1124 1179 1.673033 CCTTCGATCCCCGCATACATC 60.673 57.143 0.00 0.00 38.37 3.06
1125 1180 1.273606 CTTCGATCCCCGCATACATCT 59.726 52.381 0.00 0.00 38.37 2.90
1235 1290 5.802064 TGTGCGCGTTTAGGATTAAATTAG 58.198 37.500 8.43 0.00 31.81 1.73
1238 1293 5.813672 TGCGCGTTTAGGATTAAATTAGTCT 59.186 36.000 8.43 0.00 31.81 3.24
1284 1358 1.808945 CGAGCAGTGGAGCAAGATTTT 59.191 47.619 0.00 0.00 36.85 1.82
1320 1407 4.322273 GGCCTTCAGGAAAAGAAATTCAGG 60.322 45.833 0.00 0.00 37.39 3.86
1346 1433 4.047822 CCGACTGCTCTGTCATAGATTTC 58.952 47.826 7.50 0.00 36.82 2.17
1371 1458 7.341512 TCTCATAGTTGTCATCAAGATCTGACT 59.658 37.037 12.47 3.62 41.83 3.41
1385 1472 4.878397 AGATCTGACTTTTAATCTTGCCGG 59.122 41.667 0.00 0.00 0.00 6.13
1387 1474 3.751175 TCTGACTTTTAATCTTGCCGGTG 59.249 43.478 1.90 0.00 0.00 4.94
1404 1491 1.501169 GTGCACAATTGAACCTTGGC 58.499 50.000 13.17 4.61 0.00 4.52
1405 1492 1.069049 GTGCACAATTGAACCTTGGCT 59.931 47.619 13.17 0.00 0.00 4.75
1504 1594 5.738619 AAAAATTGCGGGAAAACCTATCT 57.261 34.783 0.00 0.00 36.97 1.98
1539 1629 3.426859 CAGTAAGTTCAGAGAACACTGCG 59.573 47.826 13.74 0.00 37.75 5.18
1573 1663 2.167693 CCGCTTGTCCTGTTATCCACTA 59.832 50.000 0.00 0.00 0.00 2.74
1574 1664 3.187700 CGCTTGTCCTGTTATCCACTAC 58.812 50.000 0.00 0.00 0.00 2.73
1575 1665 3.119101 CGCTTGTCCTGTTATCCACTACT 60.119 47.826 0.00 0.00 0.00 2.57
1576 1666 4.097437 CGCTTGTCCTGTTATCCACTACTA 59.903 45.833 0.00 0.00 0.00 1.82
1577 1667 5.349809 GCTTGTCCTGTTATCCACTACTAC 58.650 45.833 0.00 0.00 0.00 2.73
1578 1668 5.127356 GCTTGTCCTGTTATCCACTACTACT 59.873 44.000 0.00 0.00 0.00 2.57
1579 1669 6.680872 GCTTGTCCTGTTATCCACTACTACTC 60.681 46.154 0.00 0.00 0.00 2.59
1580 1670 4.880120 TGTCCTGTTATCCACTACTACTCG 59.120 45.833 0.00 0.00 0.00 4.18
1581 1671 5.121811 GTCCTGTTATCCACTACTACTCGA 58.878 45.833 0.00 0.00 0.00 4.04
1582 1672 5.236911 GTCCTGTTATCCACTACTACTCGAG 59.763 48.000 11.84 11.84 0.00 4.04
1583 1673 5.104610 TCCTGTTATCCACTACTACTCGAGT 60.105 44.000 23.66 23.66 42.69 4.18
1840 3555 3.539604 AGAAGAAGATATGCTGCGCTTT 58.460 40.909 9.73 0.00 0.00 3.51
1904 3619 1.891919 GGAGTCTGCGTGCACCAAA 60.892 57.895 12.15 0.00 0.00 3.28
1913 3628 0.801872 CGTGCACCAAATGGATCGAA 59.198 50.000 12.15 0.00 38.94 3.71
1921 3636 2.353889 CCAAATGGATCGAAGCTCACAG 59.646 50.000 0.00 0.00 37.39 3.66
1966 3681 6.103330 GGTTCAAGGTCTGATTCTTCTCTAC 58.897 44.000 0.00 0.00 32.78 2.59
2000 3715 4.643463 TGTTGCATTTGCTTTCATGGATT 58.357 34.783 3.94 0.00 42.66 3.01
2008 3723 4.811969 TGCTTTCATGGATTTTGCAGAT 57.188 36.364 0.00 0.00 0.00 2.90
2049 3764 4.989168 AGTTAGAGTAGTCGCCTTGTTTTG 59.011 41.667 0.00 0.00 0.00 2.44
2066 3781 5.105752 TGTTTTGCAATGTTGTTCCTGTAC 58.894 37.500 0.00 0.00 0.00 2.90
2084 3807 1.236628 ACGGTTAGCGAGCTCGATAT 58.763 50.000 38.74 24.38 40.06 1.63
2085 3808 1.069159 ACGGTTAGCGAGCTCGATATG 60.069 52.381 38.74 27.82 40.06 1.78
2086 3809 1.729472 CGGTTAGCGAGCTCGATATGG 60.729 57.143 38.74 22.93 40.06 2.74
2087 3810 1.540267 GGTTAGCGAGCTCGATATGGA 59.460 52.381 38.74 19.71 40.06 3.41
2115 3838 8.742125 TCCATGGGAGATAAATTACTGATAGT 57.258 34.615 13.02 0.00 0.00 2.12
2116 3839 8.597167 TCCATGGGAGATAAATTACTGATAGTG 58.403 37.037 13.02 0.00 0.00 2.74
2117 3840 7.335422 CCATGGGAGATAAATTACTGATAGTGC 59.665 40.741 2.85 0.00 0.00 4.40
2130 3855 4.051922 CTGATAGTGCGACTTTATGGGTC 58.948 47.826 0.00 0.00 0.00 4.46
2133 3861 3.350219 AGTGCGACTTTATGGGTCATT 57.650 42.857 0.00 0.00 33.73 2.57
2154 3882 7.492344 GTCATTTGAGAAATGTTCTTGGTGTTT 59.508 33.333 8.50 0.00 46.46 2.83
2160 3889 9.311916 TGAGAAATGTTCTTGGTGTTTATTTTG 57.688 29.630 0.00 0.00 40.87 2.44
2167 3896 5.908341 TCTTGGTGTTTATTTTGTTGTCCC 58.092 37.500 0.00 0.00 0.00 4.46
2198 3930 2.288948 TGTTTGGCATGGAAGATGCAAC 60.289 45.455 8.78 6.07 46.21 4.17
2201 3933 3.015675 TGGCATGGAAGATGCAACATA 57.984 42.857 8.78 0.00 46.21 2.29
2203 3935 2.954318 GGCATGGAAGATGCAACATACT 59.046 45.455 8.78 0.00 46.21 2.12
2204 3936 3.004106 GGCATGGAAGATGCAACATACTC 59.996 47.826 8.78 0.00 46.21 2.59
2205 3937 3.004106 GCATGGAAGATGCAACATACTCC 59.996 47.826 0.00 0.00 44.00 3.85
2206 3938 4.458397 CATGGAAGATGCAACATACTCCT 58.542 43.478 0.00 0.00 0.00 3.69
2207 3939 5.614308 CATGGAAGATGCAACATACTCCTA 58.386 41.667 0.00 0.00 0.00 2.94
2208 3940 5.894298 TGGAAGATGCAACATACTCCTAT 57.106 39.130 0.00 0.00 0.00 2.57
2286 4056 4.617223 GCCTTCAAGTTTATTTGCTCGTTC 59.383 41.667 0.00 0.00 0.00 3.95
2438 4209 3.896888 ACATCACTCTCTCCATCCATCTC 59.103 47.826 0.00 0.00 0.00 2.75
2450 4223 4.074259 CCATCCATCTCACACAGTTTCAA 58.926 43.478 0.00 0.00 0.00 2.69
2451 4224 4.083110 CCATCCATCTCACACAGTTTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2452 4225 3.476552 TCCATCTCACACAGTTTCAACC 58.523 45.455 0.00 0.00 0.00 3.77
2459 4232 3.442273 TCACACAGTTTCAACCACCTTTC 59.558 43.478 0.00 0.00 0.00 2.62
2485 4258 0.042448 CATCACGCTGCACATCATCG 60.042 55.000 0.00 0.00 39.92 3.84
2491 4277 1.019673 GCTGCACATCATCGGTTCAT 58.980 50.000 0.00 0.00 0.00 2.57
2492 4278 1.268386 GCTGCACATCATCGGTTCATG 60.268 52.381 0.00 0.00 0.00 3.07
2493 4279 2.011947 CTGCACATCATCGGTTCATGT 58.988 47.619 0.00 0.00 0.00 3.21
2494 4280 2.421073 CTGCACATCATCGGTTCATGTT 59.579 45.455 0.00 0.00 0.00 2.71
2495 4281 2.419673 TGCACATCATCGGTTCATGTTC 59.580 45.455 0.00 0.00 0.00 3.18
2496 4282 2.419673 GCACATCATCGGTTCATGTTCA 59.580 45.455 0.00 0.00 0.00 3.18
2497 4283 3.065786 GCACATCATCGGTTCATGTTCAT 59.934 43.478 0.00 0.00 0.00 2.57
2498 4284 4.594136 CACATCATCGGTTCATGTTCATG 58.406 43.478 6.46 6.46 0.00 3.07
2499 4285 3.628942 ACATCATCGGTTCATGTTCATGG 59.371 43.478 12.02 0.00 0.00 3.66
2500 4286 2.016318 TCATCGGTTCATGTTCATGGC 58.984 47.619 12.02 6.40 0.00 4.40
2501 4287 1.744522 CATCGGTTCATGTTCATGGCA 59.255 47.619 12.02 0.00 0.00 4.92
2502 4288 1.452110 TCGGTTCATGTTCATGGCAG 58.548 50.000 12.02 7.27 0.00 4.85
2503 4289 0.452987 CGGTTCATGTTCATGGCAGG 59.547 55.000 12.02 0.00 0.00 4.85
2504 4290 0.174162 GGTTCATGTTCATGGCAGGC 59.826 55.000 12.02 0.00 0.00 4.85
2505 4291 0.889994 GTTCATGTTCATGGCAGGCA 59.110 50.000 12.02 0.00 0.00 4.75
2506 4292 1.479323 GTTCATGTTCATGGCAGGCAT 59.521 47.619 2.93 2.93 0.00 4.40
2507 4293 1.107945 TCATGTTCATGGCAGGCATG 58.892 50.000 27.38 27.38 38.49 4.06
2508 4294 1.107945 CATGTTCATGGCAGGCATGA 58.892 50.000 30.75 30.75 39.21 3.07
2509 4295 1.067060 CATGTTCATGGCAGGCATGAG 59.933 52.381 31.83 20.45 39.80 2.90
2564 4350 5.235186 CAGGAATGATACGAACATCCTGAAC 59.765 44.000 13.05 0.00 40.76 3.18
2594 4380 2.425592 TGGAACAGTGGCACCTCG 59.574 61.111 15.27 5.86 0.00 4.63
2794 4592 0.764369 TGAGACCAAGGTGGCTGAGT 60.764 55.000 0.00 0.00 42.67 3.41
2892 4699 4.977963 CCACTGAAACAATTTGTACTGCAG 59.022 41.667 13.48 13.48 0.00 4.41
2949 4767 4.347000 GCTTACCTGAACACCCATATCCTA 59.653 45.833 0.00 0.00 0.00 2.94
2979 4797 2.584492 TGATCAGCATCCTGTACGTG 57.416 50.000 0.00 0.00 40.09 4.49
3042 4860 4.023450 AGCACATCACTGTCAATGTCAAAG 60.023 41.667 3.09 0.00 33.92 2.77
3045 4863 3.969117 TCACTGTCAATGTCAAAGCAC 57.031 42.857 0.00 0.00 0.00 4.40
3070 4896 5.394553 CCCCTGCTTGTTAATCTTCAATTCC 60.395 44.000 0.00 0.00 0.00 3.01
3114 4949 6.917217 ACAGAGAAGAAAGTTTGTCTGAAG 57.083 37.500 16.63 5.00 46.02 3.02
3153 4998 3.208922 TCCATCTGTAGGGGATCCTTGTA 59.791 47.826 12.58 0.00 41.56 2.41
3159 5004 5.491078 TCTGTAGGGGATCCTTGTAATGTTT 59.509 40.000 12.58 0.00 41.56 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.964310 ATGAGCAAGGCGCCAGAGT 61.964 57.895 31.54 10.57 44.04 3.24
143 144 0.401356 ATGTCATCCCACACAGCACA 59.599 50.000 0.00 0.00 0.00 4.57
197 198 1.452108 GCTTGGGGGAGGACGAATG 60.452 63.158 0.00 0.00 0.00 2.67
198 199 1.497309 TTGCTTGGGGGAGGACGAAT 61.497 55.000 0.00 0.00 0.00 3.34
201 202 1.750399 CATTGCTTGGGGGAGGACG 60.750 63.158 0.00 0.00 0.00 4.79
202 203 1.380380 CCATTGCTTGGGGGAGGAC 60.380 63.158 0.00 0.00 42.33 3.85
239 240 1.680651 CCTCTCAGTCCGAGCACCT 60.681 63.158 0.00 0.00 41.98 4.00
251 252 3.026630 CGTAAGAACAGTTGCCTCTCA 57.973 47.619 0.00 0.00 43.02 3.27
293 294 0.240945 CTCGCCAAATTCCGTGCTTT 59.759 50.000 0.00 0.00 0.00 3.51
305 306 1.382522 GCAGATTCATTCCTCGCCAA 58.617 50.000 0.00 0.00 0.00 4.52
435 436 2.815647 GCGGAGACCAAAGGCGAG 60.816 66.667 0.00 0.00 0.00 5.03
460 461 1.228154 GAAAGCCACCACCGAACCT 60.228 57.895 0.00 0.00 0.00 3.50
497 498 1.584380 GCAGACTTGCCCAGCTCTTG 61.584 60.000 0.00 0.00 44.74 3.02
592 593 4.645809 GCCTCAGCCAACTTAGGG 57.354 61.111 0.00 0.00 37.71 3.53
683 684 2.587194 GCGCTGCATCACCGAGAT 60.587 61.111 0.00 0.00 37.48 2.75
801 802 4.708177 AGCTAGAACATTACAATGCCGAT 58.292 39.130 0.00 0.00 40.04 4.18
894 895 3.978687 ACAAACTTACACAGAGTCTCCG 58.021 45.455 0.00 0.00 0.00 4.63
924 925 3.698040 AGAGAGAACGTCGGCCTTTATTA 59.302 43.478 0.00 0.00 0.00 0.98
1042 1048 3.016474 GCTGCCGTCTTTCGTCTGC 62.016 63.158 0.00 0.00 35.60 4.26
1075 1105 2.162338 TTACTTGCCTGGACGGACGG 62.162 60.000 0.00 0.00 33.16 4.79
1077 1107 1.012486 CGTTACTTGCCTGGACGGAC 61.012 60.000 0.00 0.00 33.16 4.79
1096 1144 1.116536 GGGGATCGAAGGGAGGAGAC 61.117 65.000 0.00 0.00 0.00 3.36
1122 1177 3.304794 GCGGCGACTAAACAGAGATAGAT 60.305 47.826 12.98 0.00 0.00 1.98
1123 1178 2.033049 GCGGCGACTAAACAGAGATAGA 59.967 50.000 12.98 0.00 0.00 1.98
1124 1179 2.386249 GCGGCGACTAAACAGAGATAG 58.614 52.381 12.98 0.00 0.00 2.08
1125 1180 1.268386 CGCGGCGACTAAACAGAGATA 60.268 52.381 19.16 0.00 0.00 1.98
1235 1290 4.612939 GCAAGGATAACCACGAAAACAGAC 60.613 45.833 0.00 0.00 38.94 3.51
1238 1293 3.482436 AGCAAGGATAACCACGAAAACA 58.518 40.909 0.00 0.00 38.94 2.83
1346 1433 7.490840 AGTCAGATCTTGATGACAACTATGAG 58.509 38.462 13.49 0.00 46.63 2.90
1382 1469 0.673437 AAGGTTCAATTGTGCACCGG 59.327 50.000 15.69 0.00 0.00 5.28
1383 1470 1.602668 CCAAGGTTCAATTGTGCACCG 60.603 52.381 15.69 0.00 0.00 4.94
1385 1472 1.069049 AGCCAAGGTTCAATTGTGCAC 59.931 47.619 10.75 10.75 0.00 4.57
1387 1474 2.531522 AAGCCAAGGTTCAATTGTGC 57.468 45.000 5.13 0.00 0.00 4.57
1392 1479 4.922206 TCTCATGTAAGCCAAGGTTCAAT 58.078 39.130 0.00 0.00 0.00 2.57
1486 1576 3.366052 ACAGATAGGTTTTCCCGCAAT 57.634 42.857 0.00 0.00 41.86 3.56
1504 1594 6.369340 TCTGAACTTACTGACGAACAAAAACA 59.631 34.615 0.00 0.00 0.00 2.83
1539 1629 2.354821 GACAAGCGGATATTGGAACACC 59.645 50.000 0.00 0.00 39.29 4.16
1573 1663 9.175312 TCTTTGATTACAATCTACTCGAGTAGT 57.825 33.333 38.45 27.66 46.08 2.73
1575 1665 9.784680 GTTCTTTGATTACAATCTACTCGAGTA 57.215 33.333 23.34 23.34 36.39 2.59
1576 1666 7.485277 CGTTCTTTGATTACAATCTACTCGAGT 59.515 37.037 23.66 23.66 36.39 4.18
1577 1667 7.696872 TCGTTCTTTGATTACAATCTACTCGAG 59.303 37.037 11.84 11.84 36.39 4.04
1578 1668 7.484007 GTCGTTCTTTGATTACAATCTACTCGA 59.516 37.037 3.76 0.00 36.39 4.04
1579 1669 7.272731 TGTCGTTCTTTGATTACAATCTACTCG 59.727 37.037 3.76 2.52 36.39 4.18
1580 1670 8.462143 TGTCGTTCTTTGATTACAATCTACTC 57.538 34.615 3.76 0.00 36.39 2.59
1621 1820 4.996758 TGATATATCTGCACATTCAACGGG 59.003 41.667 13.79 0.00 0.00 5.28
1757 3436 0.671472 CAATCGAGCACACAGGAGCA 60.671 55.000 0.00 0.00 32.55 4.26
1760 3439 0.678950 TCACAATCGAGCACACAGGA 59.321 50.000 0.00 0.00 0.00 3.86
1857 3572 2.478539 CGACGATGCACTCATCTCTGAA 60.479 50.000 0.00 0.00 45.32 3.02
1904 3619 0.179062 GCCTGTGAGCTTCGATCCAT 60.179 55.000 0.00 0.00 0.00 3.41
2019 3734 5.682659 AGGCGACTACTCTAACTGAATCTA 58.317 41.667 0.00 0.00 40.61 1.98
2038 3753 1.932511 ACAACATTGCAAAACAAGGCG 59.067 42.857 1.71 0.00 43.87 5.52
2049 3764 1.877443 ACCGTACAGGAACAACATTGC 59.123 47.619 10.17 0.00 45.00 3.56
2066 3781 1.607713 CATATCGAGCTCGCTAACCG 58.392 55.000 30.97 14.32 39.60 4.44
2085 3808 7.944554 TCAGTAATTTATCTCCCATGGAAATCC 59.055 37.037 15.22 5.52 0.00 3.01
2086 3809 8.924511 TCAGTAATTTATCTCCCATGGAAATC 57.075 34.615 15.22 0.29 0.00 2.17
2114 3837 3.438781 TCAAATGACCCATAAAGTCGCAC 59.561 43.478 0.00 0.00 37.04 5.34
2115 3838 3.680490 TCAAATGACCCATAAAGTCGCA 58.320 40.909 0.00 0.00 37.04 5.10
2116 3839 3.938963 TCTCAAATGACCCATAAAGTCGC 59.061 43.478 0.00 0.00 37.04 5.19
2117 3840 6.494893 TTTCTCAAATGACCCATAAAGTCG 57.505 37.500 0.00 0.00 37.04 4.18
2133 3861 9.883142 AAAATAAACACCAAGAACATTTCTCAA 57.117 25.926 0.00 0.00 39.61 3.02
2142 3870 6.256975 GGGACAACAAAATAAACACCAAGAAC 59.743 38.462 0.00 0.00 0.00 3.01
2154 3882 4.640771 AGCAGAGAGGGACAACAAAATA 57.359 40.909 0.00 0.00 0.00 1.40
2160 3889 2.262423 ACAAAGCAGAGAGGGACAAC 57.738 50.000 0.00 0.00 0.00 3.32
2167 3896 2.352421 CCATGCCAAACAAAGCAGAGAG 60.352 50.000 0.00 0.00 43.38 3.20
2198 3930 9.956720 GAAATTTCCACATCAAATAGGAGTATG 57.043 33.333 6.95 0.00 0.00 2.39
2201 3933 8.599624 ATGAAATTTCCACATCAAATAGGAGT 57.400 30.769 15.48 0.00 0.00 3.85
2203 3935 9.699410 ACTATGAAATTTCCACATCAAATAGGA 57.301 29.630 15.48 0.00 0.00 2.94
2204 3936 9.740239 CACTATGAAATTTCCACATCAAATAGG 57.260 33.333 15.48 4.62 0.00 2.57
2286 4056 0.325602 AAACCATGGGCATTTGCAGG 59.674 50.000 18.09 3.36 44.36 4.85
2314 4084 6.709846 GGATGAGAAGAGAATAAGGGTGATTG 59.290 42.308 0.00 0.00 0.00 2.67
2438 4209 3.730662 CGAAAGGTGGTTGAAACTGTGTG 60.731 47.826 0.00 0.00 0.00 3.82
2450 4223 0.107654 GATGCCTAGCGAAAGGTGGT 60.108 55.000 5.50 0.00 44.53 4.16
2451 4224 0.107703 TGATGCCTAGCGAAAGGTGG 60.108 55.000 5.50 0.00 44.53 4.61
2452 4225 1.009829 GTGATGCCTAGCGAAAGGTG 58.990 55.000 5.50 0.00 44.53 4.00
2485 4258 0.174162 GCCTGCCATGAACATGAACC 59.826 55.000 15.21 5.16 41.20 3.62
2503 4289 1.407979 CCAAATCCTGAAGGCTCATGC 59.592 52.381 0.00 0.00 38.76 4.06
2504 4290 2.029623 CCCAAATCCTGAAGGCTCATG 58.970 52.381 0.00 0.00 34.44 3.07
2505 4291 1.687368 GCCCAAATCCTGAAGGCTCAT 60.687 52.381 0.00 0.00 40.57 2.90
2506 4292 0.323725 GCCCAAATCCTGAAGGCTCA 60.324 55.000 0.00 0.00 40.57 4.26
2507 4293 0.323725 TGCCCAAATCCTGAAGGCTC 60.324 55.000 0.00 0.00 44.19 4.70
2508 4294 0.114954 TTGCCCAAATCCTGAAGGCT 59.885 50.000 0.00 0.00 44.19 4.58
2509 4295 1.134610 CATTGCCCAAATCCTGAAGGC 60.135 52.381 0.00 0.00 44.13 4.35
2794 4592 0.103390 TGACAGCGACGAGGTTTTCA 59.897 50.000 0.00 0.00 0.00 2.69
2892 4699 3.801114 ACAGGCAAAGTTTTCCTTCAC 57.199 42.857 3.82 0.00 31.27 3.18
2949 4767 0.627451 TGCTGATCAAGGCTGGGATT 59.373 50.000 8.27 0.00 0.00 3.01
2979 4797 3.490890 GAGTTGTCGATGCTGCCC 58.509 61.111 0.00 0.00 0.00 5.36
3045 4863 3.085952 TGAAGATTAACAAGCAGGGGG 57.914 47.619 0.00 0.00 0.00 5.40
3070 4896 3.003394 TCTTGTTATGGCTGGGTCATG 57.997 47.619 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.