Multiple sequence alignment - TraesCS3B01G467200

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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 TraesCS3B01G467200 chr3B 100.000 2276 0 0 1 2276 709519236 709516961 0.000000e+00 4204.0
1 TraesCS3B01G467200 chr3B 83.459 532 82 4 776 1307 10721487 10720962 7.310000e-135 490.0
2 TraesCS3B01G467200 chr3B 79.907 642 121 4 1642 2276 709450789 709450149 4.430000e-127 464.0
3 TraesCS3B01G467200 chr3B 76.786 504 97 14 650 1141 693750498 693750993 4.820000e-67 265.0
4 TraesCS3B01G467200 chr2B 92.006 1301 103 1 1 1300 626103981 626105281 0.000000e+00 1825.0
5 TraesCS3B01G467200 chr2D 86.729 1183 154 3 124 1304 424042709 424043890 0.000000e+00 1312.0
6 TraesCS3B01G467200 chr3A 90.224 849 75 6 1430 2276 672217268 672216426 0.000000e+00 1101.0
7 TraesCS3B01G467200 chr3A 82.003 639 107 4 1645 2276 672211480 672210843 9.250000e-149 536.0
8 TraesCS3B01G467200 chr6B 94.201 707 40 1 599 1304 711634960 711634254 0.000000e+00 1077.0
9 TraesCS3B01G467200 chr3D 88.179 829 61 18 1380 2207 537032070 537031278 0.000000e+00 953.0
10 TraesCS3B01G467200 chr3D 93.421 152 10 0 2125 2276 536989797 536989646 2.270000e-55 226.0
11 TraesCS3B01G467200 chr1A 86.523 742 98 2 564 1304 579871142 579871882 0.000000e+00 815.0
12 TraesCS3B01G467200 chr1A 85.955 178 25 0 1127 1304 579877141 579877318 8.300000e-45 191.0
13 TraesCS3B01G467200 chr5D 86.919 688 88 2 618 1304 461848537 461849223 0.000000e+00 771.0
14 TraesCS3B01G467200 chr5D 84.804 612 93 0 3 614 461660323 461660934 1.160000e-172 616.0
15 TraesCS3B01G467200 chr7A 83.677 533 75 6 772 1304 639231329 639231849 2.030000e-135 492.0
16 TraesCS3B01G467200 chr7A 95.745 47 1 1 1318 1363 717919442 717919488 8.720000e-10 75.0
17 TraesCS3B01G467200 chr2A 96.491 57 2 0 1307 1363 699381765 699381709 6.690000e-16 95.3
18 TraesCS3B01G467200 chrUn 93.103 58 4 0 1307 1364 322140920 322140977 4.030000e-13 86.1
19 TraesCS3B01G467200 chr5B 93.103 58 4 0 1307 1364 513808911 513808968 4.030000e-13 86.1
20 TraesCS3B01G467200 chr5B 90.164 61 6 0 1307 1367 2618555 2618495 1.870000e-11 80.5
21 TraesCS3B01G467200 chr7B 91.379 58 5 0 1307 1364 318416367 318416424 1.870000e-11 80.5
22 TraesCS3B01G467200 chr5A 90.164 61 6 0 1307 1367 643565336 643565276 1.870000e-11 80.5


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 TraesCS3B01G467200 chr3B 709516961 709519236 2275 True 4204 4204 100.000 1 2276 1 chr3B.!!$R3 2275
1 TraesCS3B01G467200 chr3B 10720962 10721487 525 True 490 490 83.459 776 1307 1 chr3B.!!$R1 531
2 TraesCS3B01G467200 chr3B 709450149 709450789 640 True 464 464 79.907 1642 2276 1 chr3B.!!$R2 634
3 TraesCS3B01G467200 chr2B 626103981 626105281 1300 False 1825 1825 92.006 1 1300 1 chr2B.!!$F1 1299
4 TraesCS3B01G467200 chr2D 424042709 424043890 1181 False 1312 1312 86.729 124 1304 1 chr2D.!!$F1 1180
5 TraesCS3B01G467200 chr3A 672216426 672217268 842 True 1101 1101 90.224 1430 2276 1 chr3A.!!$R2 846
6 TraesCS3B01G467200 chr3A 672210843 672211480 637 True 536 536 82.003 1645 2276 1 chr3A.!!$R1 631
7 TraesCS3B01G467200 chr6B 711634254 711634960 706 True 1077 1077 94.201 599 1304 1 chr6B.!!$R1 705
8 TraesCS3B01G467200 chr3D 537031278 537032070 792 True 953 953 88.179 1380 2207 1 chr3D.!!$R2 827
9 TraesCS3B01G467200 chr1A 579871142 579871882 740 False 815 815 86.523 564 1304 1 chr1A.!!$F1 740
10 TraesCS3B01G467200 chr5D 461848537 461849223 686 False 771 771 86.919 618 1304 1 chr5D.!!$F2 686
11 TraesCS3B01G467200 chr5D 461660323 461660934 611 False 616 616 84.804 3 614 1 chr5D.!!$F1 611
12 TraesCS3B01G467200 chr7A 639231329 639231849 520 False 492 492 83.677 772 1304 1 chr7A.!!$F1 532

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
309 310 0.108615 GGACCATCATCGCCGGATAG 60.109 60.0 5.05 0.0 0.0 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2133 0.036952 CCAAGGATGTGCTCGTGTCT 60.037 55.0 0.0 0.0 0.0 3.41 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
82 83 4.836125 TTCAGATTTGTTTGAGCAGGAC 57.164 40.909 0.00 0.00 0.00 3.85
109 110 3.329386 CGCATGGGATATAGAAGTGGTG 58.671 50.000 3.11 0.00 0.00 4.17
136 137 1.386533 ATTTCCTTGCTCCTGATGCG 58.613 50.000 0.00 0.00 0.00 4.73
154 155 1.086696 CGGACGCCATTCTCAACATT 58.913 50.000 0.00 0.00 0.00 2.71
157 158 1.062587 GACGCCATTCTCAACATTCCG 59.937 52.381 0.00 0.00 0.00 4.30
167 168 2.946947 AACATTCCGTTGAGGGCAG 58.053 52.632 0.00 0.00 41.52 4.85
175 176 2.530151 TTGAGGGCAGCTGGAGGT 60.530 61.111 17.12 0.00 0.00 3.85
242 243 2.032924 GTCAAAACAGCTTACCGTGCTT 59.967 45.455 0.00 0.00 38.92 3.91
309 310 0.108615 GGACCATCATCGCCGGATAG 60.109 60.000 5.05 0.00 0.00 2.08
310 311 0.888619 GACCATCATCGCCGGATAGA 59.111 55.000 5.05 0.25 0.00 1.98
316 317 2.578786 TCATCGCCGGATAGACACTTA 58.421 47.619 5.05 0.00 0.00 2.24
322 323 2.891580 GCCGGATAGACACTTATGGAGA 59.108 50.000 5.05 0.00 0.00 3.71
355 356 7.236019 TGGAAACTCAAGGTTATACCAAGAGTA 59.764 37.037 17.68 5.69 46.68 2.59
406 407 3.073650 GGATTCTCCCTGATTATGCCACT 59.926 47.826 0.00 0.00 0.00 4.00
409 410 2.702478 TCTCCCTGATTATGCCACTCTG 59.298 50.000 0.00 0.00 0.00 3.35
431 432 2.930040 CAGCACCGTCATATTCGAACTT 59.070 45.455 0.00 0.00 0.00 2.66
448 449 1.294659 CTTTGGCTCGCTGTGACCTC 61.295 60.000 9.93 0.00 0.00 3.85
451 452 2.653702 GCTCGCTGTGACCTCTGT 59.346 61.111 0.00 0.00 0.00 3.41
472 473 3.300388 TCAAGCTATGACGGAGGATCTT 58.700 45.455 0.00 0.00 31.50 2.40
482 483 2.303022 ACGGAGGATCTTCAACATGTGT 59.697 45.455 7.20 0.00 33.73 3.72
504 505 0.450583 ATGTTCTGCTCGCATGCAAG 59.549 50.000 19.57 10.47 42.83 4.01
520 521 2.031097 GCAAGGCAATATTGGAGGGCT 61.031 52.381 17.02 5.73 37.82 5.19
525 526 1.481772 GCAATATTGGAGGGCTGCAAA 59.518 47.619 17.02 0.00 43.87 3.68
567 568 0.958091 CCAAACCTGCATCCGTCAAA 59.042 50.000 0.00 0.00 0.00 2.69
614 615 6.536582 GGATGGTATTATTCTGGATCATGACG 59.463 42.308 0.00 0.00 0.00 4.35
615 616 6.664428 TGGTATTATTCTGGATCATGACGA 57.336 37.500 0.00 0.00 0.00 4.20
616 617 6.691508 TGGTATTATTCTGGATCATGACGAG 58.308 40.000 0.00 0.00 0.00 4.18
633 635 6.105397 TGACGAGGGAAACTTATTACAGTT 57.895 37.500 0.00 0.00 38.74 3.16
699 701 3.292460 ACCTGTTTTTGATCCGGTTCAA 58.708 40.909 21.41 21.41 33.89 2.69
751 753 2.195727 TGCTTGAGATACCCATGTGGA 58.804 47.619 0.00 0.00 37.39 4.02
786 788 4.416738 GGACAGTGCTGGAGGCCC 62.417 72.222 0.00 0.00 40.92 5.80
802 804 2.043652 CCCCTGATGTTGGCTGGG 60.044 66.667 0.00 0.00 42.39 4.45
804 806 1.077265 CCCTGATGTTGGCTGGGTT 59.923 57.895 0.00 0.00 39.08 4.11
825 827 6.239487 GGGTTAAAATAAATACTGATGGGGCC 60.239 42.308 0.00 0.00 0.00 5.80
990 992 2.031870 GCACAACTCTGGGGTTTTTCT 58.968 47.619 0.00 0.00 0.00 2.52
1026 1028 0.758734 TGGACTGTCTGGAGGTTGTG 59.241 55.000 7.85 0.00 0.00 3.33
1143 1145 1.150081 GCATGTCCTGAGGGATGGG 59.850 63.158 11.73 0.00 44.33 4.00
1237 1239 3.585862 CCGAGTTTTCTAGTTAGCAGCA 58.414 45.455 0.00 0.00 0.00 4.41
1321 1323 1.408969 AAAAAGCACCAATGGTCGGT 58.591 45.000 0.00 1.03 34.76 4.69
1322 1324 0.958822 AAAAGCACCAATGGTCGGTC 59.041 50.000 0.00 0.00 34.76 4.79
1323 1325 0.179004 AAAGCACCAATGGTCGGTCA 60.179 50.000 0.00 0.00 34.76 4.02
1324 1326 0.606401 AAGCACCAATGGTCGGTCAG 60.606 55.000 0.00 0.00 34.76 3.51
1325 1327 2.040544 GCACCAATGGTCGGTCAGG 61.041 63.158 0.00 0.00 33.25 3.86
1326 1328 1.676968 CACCAATGGTCGGTCAGGA 59.323 57.895 0.00 0.00 33.25 3.86
1327 1329 0.253044 CACCAATGGTCGGTCAGGAT 59.747 55.000 0.00 0.00 33.25 3.24
1328 1330 1.484653 CACCAATGGTCGGTCAGGATA 59.515 52.381 0.00 0.00 33.25 2.59
1329 1331 2.093181 CACCAATGGTCGGTCAGGATAA 60.093 50.000 0.00 0.00 33.25 1.75
1330 1332 2.093128 ACCAATGGTCGGTCAGGATAAC 60.093 50.000 0.00 0.00 27.30 1.89
1331 1333 2.093181 CCAATGGTCGGTCAGGATAACA 60.093 50.000 0.00 0.00 0.00 2.41
1332 1334 3.433598 CCAATGGTCGGTCAGGATAACAT 60.434 47.826 0.00 0.00 0.00 2.71
1333 1335 3.753294 ATGGTCGGTCAGGATAACATC 57.247 47.619 0.00 0.00 0.00 3.06
1342 1344 2.900528 GGATAACATCCTCGCGTGG 58.099 57.895 20.92 20.92 46.19 4.94
1343 1345 0.104304 GGATAACATCCTCGCGTGGT 59.896 55.000 25.10 8.69 46.19 4.16
1344 1346 1.338973 GGATAACATCCTCGCGTGGTA 59.661 52.381 25.10 10.78 46.19 3.25
1345 1347 2.029290 GGATAACATCCTCGCGTGGTAT 60.029 50.000 25.10 15.14 46.19 2.73
1346 1348 2.787601 TAACATCCTCGCGTGGTATC 57.212 50.000 25.10 0.00 0.00 2.24
1347 1349 0.821517 AACATCCTCGCGTGGTATCA 59.178 50.000 25.10 7.91 0.00 2.15
1348 1350 1.040646 ACATCCTCGCGTGGTATCAT 58.959 50.000 25.10 9.92 0.00 2.45
1349 1351 1.269778 ACATCCTCGCGTGGTATCATG 60.270 52.381 25.10 21.77 0.00 3.07
1350 1352 1.040646 ATCCTCGCGTGGTATCATGT 58.959 50.000 25.10 3.37 32.65 3.21
1351 1353 0.384309 TCCTCGCGTGGTATCATGTC 59.616 55.000 25.10 0.00 32.65 3.06
1352 1354 0.597637 CCTCGCGTGGTATCATGTCC 60.598 60.000 18.86 0.00 32.65 4.02
1353 1355 0.597637 CTCGCGTGGTATCATGTCCC 60.598 60.000 5.77 0.00 32.65 4.46
1354 1356 1.142965 CGCGTGGTATCATGTCCCA 59.857 57.895 0.00 0.00 32.65 4.37
1355 1357 0.461163 CGCGTGGTATCATGTCCCAA 60.461 55.000 0.00 0.00 32.65 4.12
1356 1358 1.745232 GCGTGGTATCATGTCCCAAA 58.255 50.000 0.00 0.00 32.65 3.28
1357 1359 2.088423 GCGTGGTATCATGTCCCAAAA 58.912 47.619 0.00 0.00 32.65 2.44
1358 1360 2.490115 GCGTGGTATCATGTCCCAAAAA 59.510 45.455 0.00 0.00 32.65 1.94
1359 1361 3.130340 GCGTGGTATCATGTCCCAAAAAT 59.870 43.478 0.00 0.00 32.65 1.82
1360 1362 4.381505 GCGTGGTATCATGTCCCAAAAATT 60.382 41.667 0.00 0.00 32.65 1.82
1361 1363 5.339990 CGTGGTATCATGTCCCAAAAATTC 58.660 41.667 0.00 0.00 0.00 2.17
1362 1364 5.339990 GTGGTATCATGTCCCAAAAATTCG 58.660 41.667 0.00 0.00 0.00 3.34
1363 1365 4.142271 TGGTATCATGTCCCAAAAATTCGC 60.142 41.667 0.00 0.00 0.00 4.70
1364 1366 4.142271 GGTATCATGTCCCAAAAATTCGCA 60.142 41.667 0.00 0.00 0.00 5.10
1365 1367 4.741321 ATCATGTCCCAAAAATTCGCAT 57.259 36.364 0.00 0.00 0.00 4.73
1366 1368 4.108699 TCATGTCCCAAAAATTCGCATC 57.891 40.909 0.00 0.00 0.00 3.91
1367 1369 3.763360 TCATGTCCCAAAAATTCGCATCT 59.237 39.130 0.00 0.00 0.00 2.90
1368 1370 4.946772 TCATGTCCCAAAAATTCGCATCTA 59.053 37.500 0.00 0.00 0.00 1.98
1369 1371 5.417266 TCATGTCCCAAAAATTCGCATCTAA 59.583 36.000 0.00 0.00 0.00 2.10
1370 1372 5.309323 TGTCCCAAAAATTCGCATCTAAG 57.691 39.130 0.00 0.00 0.00 2.18
1371 1373 4.764823 TGTCCCAAAAATTCGCATCTAAGT 59.235 37.500 0.00 0.00 0.00 2.24
1372 1374 5.941058 TGTCCCAAAAATTCGCATCTAAGTA 59.059 36.000 0.00 0.00 0.00 2.24
1373 1375 6.601613 TGTCCCAAAAATTCGCATCTAAGTAT 59.398 34.615 0.00 0.00 0.00 2.12
1374 1376 7.122055 TGTCCCAAAAATTCGCATCTAAGTATT 59.878 33.333 0.00 0.00 0.00 1.89
1375 1377 8.617809 GTCCCAAAAATTCGCATCTAAGTATTA 58.382 33.333 0.00 0.00 0.00 0.98
1376 1378 8.617809 TCCCAAAAATTCGCATCTAAGTATTAC 58.382 33.333 0.00 0.00 0.00 1.89
1377 1379 8.621286 CCCAAAAATTCGCATCTAAGTATTACT 58.379 33.333 0.00 0.00 0.00 2.24
1420 1422 8.588290 ACAAATATTGTAGTTGCCTTCCAATA 57.412 30.769 0.00 0.00 43.27 1.90
1440 1442 9.187996 TCCAATAATTGCTCATATCTCAAAACA 57.812 29.630 0.00 0.00 0.00 2.83
1446 1448 5.808042 GCTCATATCTCAAAACAAGAGCA 57.192 39.130 0.00 0.00 44.77 4.26
1447 1449 5.808403 GCTCATATCTCAAAACAAGAGCAG 58.192 41.667 0.00 0.00 44.77 4.24
1448 1450 5.730010 GCTCATATCTCAAAACAAGAGCAGC 60.730 44.000 0.00 0.00 44.77 5.25
1458 1460 1.802960 ACAAGAGCAGCGTCAATGAAG 59.197 47.619 0.00 0.00 0.00 3.02
1474 1476 8.555166 GTCAATGAAGACGAAACAAAATGTTA 57.445 30.769 0.00 0.00 40.14 2.41
1510 1512 8.488651 AAAGTACGTAGTCTTTCCCATTATTG 57.511 34.615 2.79 0.00 43.93 1.90
1513 1515 8.752187 AGTACGTAGTCTTTCCCATTATTGTTA 58.248 33.333 0.00 0.00 43.93 2.41
1519 1521 7.699878 AGTCTTTCCCATTATTGTTAAGGACT 58.300 34.615 0.00 0.00 32.21 3.85
1529 1531 9.301153 CATTATTGTTAAGGACTTACATTTGGC 57.699 33.333 0.00 0.00 0.00 4.52
1556 1560 7.498070 GCACAAGCAAATACATACTTCTTTC 57.502 36.000 0.00 0.00 41.58 2.62
1557 1561 7.308435 GCACAAGCAAATACATACTTCTTTCT 58.692 34.615 0.00 0.00 41.58 2.52
1574 1578 4.166144 TCTTTCTGAAAAGAGGGGAACACT 59.834 41.667 4.18 0.00 44.63 3.55
1576 1580 3.318313 TCTGAAAAGAGGGGAACACTCT 58.682 45.455 0.00 0.00 46.77 3.24
1579 1583 2.011122 AAAGAGGGGAACACTCTCGA 57.989 50.000 0.91 0.00 44.17 4.04
1583 1587 0.969894 AGGGGAACACTCTCGACTTG 59.030 55.000 0.00 0.00 0.00 3.16
1584 1588 0.670854 GGGGAACACTCTCGACTTGC 60.671 60.000 0.00 0.00 0.00 4.01
1613 1617 2.289002 GTGATGCACATAGCCTTAGCAC 59.711 50.000 0.00 0.00 44.83 4.40
1614 1618 2.093021 TGATGCACATAGCCTTAGCACA 60.093 45.455 0.00 0.00 44.83 4.57
1618 1622 1.660607 CACATAGCCTTAGCACACACG 59.339 52.381 0.00 0.00 43.56 4.49
1619 1623 1.275291 ACATAGCCTTAGCACACACGT 59.725 47.619 0.00 0.00 43.56 4.49
1620 1624 2.494471 ACATAGCCTTAGCACACACGTA 59.506 45.455 0.00 0.00 43.56 3.57
1621 1625 2.642139 TAGCCTTAGCACACACGTAC 57.358 50.000 0.00 0.00 43.56 3.67
1664 1668 8.939929 TCAAGATGTCAAAATGTAAGATCTGAC 58.060 33.333 2.87 2.87 34.99 3.51
1667 1671 4.935205 TGTCAAAATGTAAGATCTGACCCG 59.065 41.667 7.81 0.00 33.78 5.28
1696 1700 2.041485 TCTCCTCAACAATGCCATCCAA 59.959 45.455 0.00 0.00 0.00 3.53
1723 1727 4.890158 TTGCCATCTCTTCAGTCAAGTA 57.110 40.909 0.00 0.00 33.27 2.24
1724 1728 4.890158 TGCCATCTCTTCAGTCAAGTAA 57.110 40.909 0.00 0.00 33.27 2.24
1779 1783 4.017683 AGAAGGAAGAATTCTCCATTGGCT 60.018 41.667 19.67 1.76 46.56 4.75
1802 1806 2.567169 CCCGCCAATCCTATCAGATACA 59.433 50.000 0.00 0.00 0.00 2.29
1817 1821 2.431057 AGATACACCGGATGAGTTGACC 59.569 50.000 9.46 0.00 0.00 4.02
1858 1862 2.069273 GAAGCTACACAAGTGCACGAT 58.931 47.619 12.01 1.15 0.00 3.73
1859 1863 1.714794 AGCTACACAAGTGCACGATC 58.285 50.000 12.01 0.00 0.00 3.69
2051 2055 2.696526 TAGGCCCATACGAGGATTCT 57.303 50.000 0.00 0.00 0.00 2.40
2123 2133 5.815581 ACCTTGTAGATGAAGTGCCATAAA 58.184 37.500 0.00 0.00 0.00 1.40
2150 2160 1.296392 CACATCCTTGGGACTGCGA 59.704 57.895 0.00 0.00 32.98 5.10
2181 2191 1.990160 AACTCGGCAACCAAGGGTCA 61.990 55.000 0.00 0.00 33.12 4.02
2212 2222 2.664851 CAGCAGCGTGACCGGAAA 60.665 61.111 9.46 0.00 33.68 3.13
2257 2267 0.820074 GGGAGCTTCTCGAGATCGGA 60.820 60.000 17.44 0.00 41.75 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 5.914085 AACAAATCTGAAACTCTGTCGAG 57.086 39.130 0.00 0.00 43.10 4.04
52 53 6.048073 TCAAACAAATCTGAAACTCTGTCG 57.952 37.500 0.00 0.00 0.00 4.35
82 83 3.657448 TATATCCCATGCGCGCCGG 62.657 63.158 30.77 27.64 0.00 6.13
89 90 3.077359 GCACCACTTCTATATCCCATGC 58.923 50.000 0.00 0.00 0.00 4.06
136 137 1.401905 GGAATGTTGAGAATGGCGTCC 59.598 52.381 0.00 0.00 0.00 4.79
154 155 4.020617 CCAGCTGCCCTCAACGGA 62.021 66.667 8.66 0.00 33.16 4.69
157 158 2.045536 CCTCCAGCTGCCCTCAAC 60.046 66.667 8.66 0.00 0.00 3.18
166 167 4.530875 CATAAAAATCCTCACCTCCAGCT 58.469 43.478 0.00 0.00 0.00 4.24
167 168 3.067320 GCATAAAAATCCTCACCTCCAGC 59.933 47.826 0.00 0.00 0.00 4.85
175 176 3.701040 GAGCCCAAGCATAAAAATCCTCA 59.299 43.478 0.00 0.00 43.56 3.86
242 243 2.192664 TGCCCTTTGCGAGTCATTAA 57.807 45.000 0.00 0.00 45.60 1.40
309 310 3.257393 CACACAGCTCTCCATAAGTGTC 58.743 50.000 0.00 0.00 38.05 3.67
310 311 2.027745 CCACACAGCTCTCCATAAGTGT 60.028 50.000 0.00 0.00 40.48 3.55
316 317 1.701847 AGTTTCCACACAGCTCTCCAT 59.298 47.619 0.00 0.00 0.00 3.41
322 323 1.212935 ACCTTGAGTTTCCACACAGCT 59.787 47.619 0.00 0.00 0.00 4.24
355 356 0.669318 CACGCCACCAGAATACACGT 60.669 55.000 0.00 0.00 0.00 4.49
385 386 4.041444 AGAGTGGCATAATCAGGGAGAATC 59.959 45.833 0.00 0.00 0.00 2.52
397 398 0.677731 GGTGCTGCAGAGTGGCATAA 60.678 55.000 20.43 0.00 43.97 1.90
406 407 1.802508 CGAATATGACGGTGCTGCAGA 60.803 52.381 20.43 0.00 0.00 4.26
409 410 1.004927 GTTCGAATATGACGGTGCTGC 60.005 52.381 0.00 0.00 0.00 5.25
431 432 2.210013 AGAGGTCACAGCGAGCCAA 61.210 57.895 0.00 0.00 43.50 4.52
451 452 2.950781 AGATCCTCCGTCATAGCTTGA 58.049 47.619 0.00 0.00 0.00 3.02
472 473 5.334028 CGAGCAGAACATTAACACATGTTGA 60.334 40.000 7.53 0.00 45.55 3.18
482 483 2.083002 TGCATGCGAGCAGAACATTAA 58.917 42.857 14.09 0.00 40.11 1.40
504 505 0.756442 TGCAGCCCTCCAATATTGCC 60.756 55.000 10.11 0.00 0.00 4.52
520 521 4.654915 TGATGTCCAGAATCTCTTTTGCA 58.345 39.130 0.00 0.00 0.00 4.08
525 526 5.126707 GGCAATTTGATGTCCAGAATCTCTT 59.873 40.000 0.00 0.00 0.00 2.85
567 568 0.329931 TACAATGTCCCGTGCCCAAT 59.670 50.000 0.00 0.00 0.00 3.16
614 615 7.465513 CGTGCATAACTGTAATAAGTTTCCCTC 60.466 40.741 0.00 0.00 40.77 4.30
615 616 6.315393 CGTGCATAACTGTAATAAGTTTCCCT 59.685 38.462 0.00 0.00 40.77 4.20
616 617 6.483687 CGTGCATAACTGTAATAAGTTTCCC 58.516 40.000 0.00 0.00 40.77 3.97
633 635 2.606108 GATGTCCATATCGCGTGCATA 58.394 47.619 5.77 0.00 0.00 3.14
699 701 1.633432 TCCCTGACCATTTTCACCGAT 59.367 47.619 0.00 0.00 0.00 4.18
751 753 2.747177 TCCATCAGGAATACCACGTCT 58.253 47.619 0.00 0.00 42.23 4.18
786 788 0.331278 TAACCCAGCCAACATCAGGG 59.669 55.000 0.00 0.00 45.20 4.45
802 804 7.354751 TGGCCCCATCAGTATTTATTTTAAC 57.645 36.000 0.00 0.00 0.00 2.01
804 806 9.308000 CTAATGGCCCCATCAGTATTTATTTTA 57.692 33.333 0.00 0.00 35.31 1.52
825 827 8.303156 CCTCCAGAGTGATTATCAGTACTAATG 58.697 40.741 2.13 0.00 28.50 1.90
933 935 1.078426 GAGGGCTAAAGCTTCGGCA 60.078 57.895 20.15 0.00 44.74 5.69
990 992 1.984424 TCCACTTCCATCACCACATGA 59.016 47.619 0.00 0.00 43.13 3.07
1143 1145 2.898705 CAGAGGTCTGCCACACTATTC 58.101 52.381 0.00 0.00 37.15 1.75
1237 1239 3.684788 GTCCTGTTACAATCAGCACGAAT 59.315 43.478 0.00 0.00 0.00 3.34
1307 1309 2.040544 CCTGACCGACCATTGGTGC 61.041 63.158 14.44 4.22 40.63 5.01
1308 1310 0.253044 ATCCTGACCGACCATTGGTG 59.747 55.000 14.44 1.96 40.63 4.17
1309 1311 1.874129 TATCCTGACCGACCATTGGT 58.126 50.000 8.42 8.42 44.10 3.67
1310 1312 2.093181 TGTTATCCTGACCGACCATTGG 60.093 50.000 0.00 0.00 0.00 3.16
1311 1313 3.260475 TGTTATCCTGACCGACCATTG 57.740 47.619 0.00 0.00 0.00 2.82
1312 1314 3.181454 GGATGTTATCCTGACCGACCATT 60.181 47.826 0.61 0.00 46.19 3.16
1313 1315 2.368875 GGATGTTATCCTGACCGACCAT 59.631 50.000 0.61 0.00 46.19 3.55
1314 1316 1.760613 GGATGTTATCCTGACCGACCA 59.239 52.381 0.61 0.00 46.19 4.02
1315 1317 2.528041 GGATGTTATCCTGACCGACC 57.472 55.000 0.61 0.00 46.19 4.79
1325 1327 2.787601 TACCACGCGAGGATGTTATC 57.212 50.000 29.67 0.00 0.00 1.75
1326 1328 2.626266 TGATACCACGCGAGGATGTTAT 59.374 45.455 29.67 15.60 0.00 1.89
1327 1329 2.025898 TGATACCACGCGAGGATGTTA 58.974 47.619 29.67 11.24 0.00 2.41
1328 1330 0.821517 TGATACCACGCGAGGATGTT 59.178 50.000 29.67 9.17 0.00 2.71
1329 1331 1.040646 ATGATACCACGCGAGGATGT 58.959 50.000 29.67 13.63 0.00 3.06
1330 1332 1.269778 ACATGATACCACGCGAGGATG 60.270 52.381 29.67 22.14 0.00 3.51
1331 1333 1.000163 GACATGATACCACGCGAGGAT 60.000 52.381 29.67 17.09 0.00 3.24
1332 1334 0.384309 GACATGATACCACGCGAGGA 59.616 55.000 29.67 12.99 0.00 3.71
1333 1335 0.597637 GGACATGATACCACGCGAGG 60.598 60.000 21.59 21.59 0.00 4.63
1334 1336 0.597637 GGGACATGATACCACGCGAG 60.598 60.000 15.93 4.16 0.00 5.03
1335 1337 1.324005 TGGGACATGATACCACGCGA 61.324 55.000 15.93 0.00 0.00 5.87
1336 1338 0.461163 TTGGGACATGATACCACGCG 60.461 55.000 3.53 3.53 39.30 6.01
1337 1339 1.745232 TTTGGGACATGATACCACGC 58.255 50.000 0.00 0.00 39.30 5.34
1338 1340 4.981806 ATTTTTGGGACATGATACCACG 57.018 40.909 0.00 0.00 39.30 4.94
1339 1341 5.339990 CGAATTTTTGGGACATGATACCAC 58.660 41.667 0.00 0.00 39.30 4.16
1340 1342 4.142271 GCGAATTTTTGGGACATGATACCA 60.142 41.667 0.00 1.24 39.30 3.25
1341 1343 4.142271 TGCGAATTTTTGGGACATGATACC 60.142 41.667 0.00 0.00 39.30 2.73
1342 1344 4.992688 TGCGAATTTTTGGGACATGATAC 58.007 39.130 0.00 0.00 39.30 2.24
1343 1345 5.593909 AGATGCGAATTTTTGGGACATGATA 59.406 36.000 0.00 0.00 39.30 2.15
1344 1346 4.403432 AGATGCGAATTTTTGGGACATGAT 59.597 37.500 0.00 0.00 39.30 2.45
1345 1347 3.763360 AGATGCGAATTTTTGGGACATGA 59.237 39.130 0.00 0.00 39.30 3.07
1346 1348 4.114058 AGATGCGAATTTTTGGGACATG 57.886 40.909 0.00 0.00 39.30 3.21
1347 1349 5.418840 ACTTAGATGCGAATTTTTGGGACAT 59.581 36.000 0.00 0.00 39.30 3.06
1348 1350 4.764823 ACTTAGATGCGAATTTTTGGGACA 59.235 37.500 0.00 0.00 0.00 4.02
1349 1351 5.310720 ACTTAGATGCGAATTTTTGGGAC 57.689 39.130 0.00 0.00 0.00 4.46
1350 1352 7.639113 AATACTTAGATGCGAATTTTTGGGA 57.361 32.000 0.00 0.00 0.00 4.37
1351 1353 8.621286 AGTAATACTTAGATGCGAATTTTTGGG 58.379 33.333 0.00 0.00 0.00 4.12
1420 1422 7.256286 GCTCTTGTTTTGAGATATGAGCAATT 58.744 34.615 0.00 0.00 43.33 2.32
1440 1442 2.072298 GTCTTCATTGACGCTGCTCTT 58.928 47.619 0.00 0.00 0.00 2.85
1447 1449 9.077531 AACATTTTGTTTCGTCTTCATTGACGC 62.078 37.037 11.52 0.32 44.15 5.19
1448 1450 6.196353 AACATTTTGTTTCGTCTTCATTGACG 59.804 34.615 10.30 10.30 44.42 4.35
1484 1486 8.601476 CAATAATGGGAAAGACTACGTACTTTC 58.399 37.037 21.68 21.68 46.16 2.62
1502 1504 9.801873 CCAAATGTAAGTCCTTAACAATAATGG 57.198 33.333 0.00 0.00 0.00 3.16
1510 1512 5.161358 GCAAGCCAAATGTAAGTCCTTAAC 58.839 41.667 0.00 0.00 0.00 2.01
1513 1515 3.005791 GTGCAAGCCAAATGTAAGTCCTT 59.994 43.478 0.00 0.00 0.00 3.36
1552 1556 4.464947 AGTGTTCCCCTCTTTTCAGAAAG 58.535 43.478 0.00 0.00 42.92 2.62
1556 1560 3.669536 GAGAGTGTTCCCCTCTTTTCAG 58.330 50.000 0.00 0.00 39.36 3.02
1557 1561 2.037251 CGAGAGTGTTCCCCTCTTTTCA 59.963 50.000 0.00 0.00 39.36 2.69
1574 1578 2.874751 TCGATGCGCAAGTCGAGA 59.125 55.556 27.11 10.71 41.44 4.04
1576 1580 1.801512 CACTCGATGCGCAAGTCGA 60.802 57.895 28.34 28.34 43.79 4.20
1579 1583 2.377004 CATCACTCGATGCGCAAGT 58.623 52.632 17.11 11.47 42.54 3.16
1613 1617 9.849607 GATTATTGTCATGATTAAGTACGTGTG 57.150 33.333 0.00 0.00 0.00 3.82
1614 1618 9.594478 TGATTATTGTCATGATTAAGTACGTGT 57.406 29.630 0.00 0.00 0.00 4.49
1661 1665 0.832135 AGGAGAAGTTGAGCGGGTCA 60.832 55.000 5.66 5.66 0.00 4.02
1664 1668 0.321671 TTGAGGAGAAGTTGAGCGGG 59.678 55.000 0.00 0.00 0.00 6.13
1667 1671 3.365767 GCATTGTTGAGGAGAAGTTGAGC 60.366 47.826 0.00 0.00 0.00 4.26
1696 1700 4.202398 TGACTGAAGAGATGGCAAAGAAGT 60.202 41.667 0.00 0.00 0.00 3.01
1723 1727 1.047801 GGTTGGTGACTGGGCAAATT 58.952 50.000 0.00 0.00 0.00 1.82
1724 1728 0.188342 AGGTTGGTGACTGGGCAAAT 59.812 50.000 0.00 0.00 0.00 2.32
1779 1783 0.105194 TCTGATAGGATTGGCGGGGA 60.105 55.000 0.00 0.00 0.00 4.81
1858 1862 1.902508 GATGTGGAGTTGTGGAGGAGA 59.097 52.381 0.00 0.00 0.00 3.71
1859 1863 1.905215 AGATGTGGAGTTGTGGAGGAG 59.095 52.381 0.00 0.00 0.00 3.69
1943 1947 2.881111 ATGATGAGATGATGGCCCAG 57.119 50.000 0.00 0.00 0.00 4.45
2051 2055 4.442753 GCATTTGAGTTGTTTTCCAAGGGA 60.443 41.667 0.00 0.00 32.51 4.20
2123 2133 0.036952 CCAAGGATGTGCTCGTGTCT 60.037 55.000 0.00 0.00 0.00 3.41
2150 2160 3.671008 TGCCGAGTTGTGTACTTATGT 57.329 42.857 0.00 0.00 37.17 2.29
2210 2220 0.332972 GGCTCCTCTCCACCCATTTT 59.667 55.000 0.00 0.00 0.00 1.82
2212 2222 0.551131 AAGGCTCCTCTCCACCCATT 60.551 55.000 0.00 0.00 0.00 3.16
2257 2267 1.680651 CGTCAGCTCCACCCTCTCT 60.681 63.158 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.