Multiple sequence alignment - TraesCS4B01G045200

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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 TraesCS4B01G045200 chr4B 100.000 2243 0 0 1 2243 32488139 32485897 0.000000e+00 4143
1 TraesCS4B01G045200 chr4B 86.013 479 47 11 1 472 394813524 394813989 1.550000e-136 496
2 TraesCS4B01G045200 chr4B 86.742 445 41 9 1 439 637162796 637163228 1.560000e-131 479
3 TraesCS4B01G045200 chr4B 87.294 425 39 9 1 423 549388915 549389326 2.610000e-129 472
4 TraesCS4B01G045200 chr4B 91.005 189 15 1 1387 1575 488893100 488893286 1.030000e-63 254
5 TraesCS4B01G045200 chr4B 83.333 282 29 9 164 439 94044222 94043953 6.190000e-61 244
6 TraesCS4B01G045200 chr4D 91.264 870 43 13 546 1410 20536175 20535334 0.000000e+00 1155
7 TraesCS4B01G045200 chr4D 94.080 473 26 2 1 472 20539236 20538765 0.000000e+00 717
8 TraesCS4B01G045200 chr4D 83.796 685 94 5 1575 2243 20535332 20534649 3.140000e-178 634
9 TraesCS4B01G045200 chr4D 93.750 176 11 0 1407 1582 477898791 477898966 4.750000e-67 265
10 TraesCS4B01G045200 chr4A 87.343 877 46 30 546 1410 581150547 581151370 0.000000e+00 944
11 TraesCS4B01G045200 chr4A 93.535 495 23 4 1 487 581149629 581150122 0.000000e+00 728
12 TraesCS4B01G045200 chr4A 96.923 65 2 0 486 550 581150238 581150302 2.360000e-20 110
13 TraesCS4B01G045200 chr6B 86.192 478 47 10 1 472 208793368 208793832 1.200000e-137 499
14 TraesCS4B01G045200 chr6B 87.191 445 39 9 1 439 177349756 177350188 7.200000e-135 490
15 TraesCS4B01G045200 chr7B 85.565 478 51 9 1 472 205798718 205799183 3.350000e-133 484
16 TraesCS4B01G045200 chr7B 78.026 537 102 6 1718 2240 483025419 483025953 7.730000e-85 324
17 TraesCS4B01G045200 chr3B 86.966 445 40 9 1 439 818951042 818951474 3.350000e-133 484
18 TraesCS4B01G045200 chr3B 78.148 540 96 13 1720 2243 12592028 12591495 7.730000e-85 324
19 TraesCS4B01G045200 chr5B 86.742 445 41 8 1 439 540795189 540794757 1.560000e-131 479
20 TraesCS4B01G045200 chr1B 87.529 425 39 9 1 423 492594354 492593942 1.560000e-131 479
21 TraesCS4B01G045200 chr1B 85.489 317 33 8 111 426 15195333 15195029 3.590000e-83 318
22 TraesCS4B01G045200 chr1B 82.979 282 30 9 164 439 603892764 603893033 2.880000e-59 239
23 TraesCS4B01G045200 chr1A 81.538 455 65 8 1800 2236 107468654 107469107 7.620000e-95 357
24 TraesCS4B01G045200 chr1A 79.065 492 87 10 1718 2193 584876728 584877219 7.730000e-85 324
25 TraesCS4B01G045200 chr3D 78.810 538 93 11 1717 2236 480679176 480679710 2.130000e-90 342
26 TraesCS4B01G045200 chr3D 79.752 484 76 10 1772 2240 522295859 522296335 4.620000e-87 331
27 TraesCS4B01G045200 chr5D 79.915 468 79 9 1737 2190 388049565 388050031 1.660000e-86 329
28 TraesCS4B01G045200 chr5D 76.181 508 80 28 1714 2194 362667901 362668394 1.730000e-56 230
29 TraesCS4B01G045200 chr5D 78.212 358 62 9 1852 2194 318053675 318054031 4.850000e-52 215
30 TraesCS4B01G045200 chr6D 80.220 455 74 9 1737 2176 427470888 427470435 5.970000e-86 327
31 TraesCS4B01G045200 chr6D 77.802 464 84 11 1791 2240 409334014 409334472 3.670000e-68 268
32 TraesCS4B01G045200 chr7D 78.090 534 98 9 1717 2236 74954470 74954998 9.990000e-84 320
33 TraesCS4B01G045200 chr7D 78.070 456 82 11 1799 2240 617207496 617207045 2.840000e-69 272
34 TraesCS4B01G045200 chr2A 93.820 178 10 1 1408 1584 746756986 746757163 1.320000e-67 267
35 TraesCS4B01G045200 chr1D 94.186 172 9 1 1406 1576 238940386 238940215 6.140000e-66 261
36 TraesCS4B01G045200 chr1D 91.803 183 15 0 1401 1583 206955711 206955529 2.860000e-64 255
37 TraesCS4B01G045200 chr2D 93.182 176 12 0 1404 1579 376349580 376349405 2.210000e-65 259
38 TraesCS4B01G045200 chr2D 91.892 185 12 2 1411 1594 161907016 161906834 2.860000e-64 255
39 TraesCS4B01G045200 chr2D 91.803 183 13 2 1408 1590 516708309 516708489 1.030000e-63 254
40 TraesCS4B01G045200 chr2D 77.167 473 78 23 1743 2194 290814252 290813789 4.780000e-62 248
41 TraesCS4B01G045200 chr2D 77.119 472 80 21 1743 2194 290894160 290893697 4.780000e-62 248
42 TraesCS4B01G045200 chr2D 80.243 329 52 13 1716 2039 582649511 582649831 3.720000e-58 235
43 TraesCS4B01G045200 chr5A 89.320 206 21 1 1411 1615 456897902 456897697 7.950000e-65 257
44 TraesCS4B01G045200 chr7A 79.377 257 45 6 1928 2181 459455927 459455676 8.230000e-40 174


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 TraesCS4B01G045200 chr4B 32485897 32488139 2242 True 4143.000000 4143 100.000000 1 2243 1 chr4B.!!$R1 2242
1 TraesCS4B01G045200 chr4D 20534649 20539236 4587 True 835.333333 1155 89.713333 1 2243 3 chr4D.!!$R1 2242
2 TraesCS4B01G045200 chr4A 581149629 581151370 1741 False 594.000000 944 92.600333 1 1410 3 chr4A.!!$F1 1409
3 TraesCS4B01G045200 chr7B 483025419 483025953 534 False 324.000000 324 78.026000 1718 2240 1 chr7B.!!$F2 522
4 TraesCS4B01G045200 chr3B 12591495 12592028 533 True 324.000000 324 78.148000 1720 2243 1 chr3B.!!$R1 523
5 TraesCS4B01G045200 chr3D 480679176 480679710 534 False 342.000000 342 78.810000 1717 2236 1 chr3D.!!$F1 519
6 TraesCS4B01G045200 chr7D 74954470 74954998 528 False 320.000000 320 78.090000 1717 2236 1 chr7D.!!$F1 519

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
725 3255 0.193574 TTCTTCCTCCCAGTCCCAGT 59.806 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 4105 0.174845 TTTGCGACATACTCCCTCGG 59.825 55.0 0.0 0.0 0.0 4.63 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
80 81 6.332630 ACAACATTCAGTGGAAACTTGAAAG 58.667 36.000 0.00 0.00 37.86 2.62
120 121 1.533625 CTGCCATGGTTCGGAAAAGA 58.466 50.000 14.67 0.00 0.00 2.52
127 128 6.106003 GCCATGGTTCGGAAAAGAAAATTAT 58.894 36.000 14.67 0.00 0.00 1.28
132 133 6.492087 TGGTTCGGAAAAGAAAATTATCTGGT 59.508 34.615 0.00 0.00 0.00 4.00
235 236 8.618677 TGAAATTCAGCTATGCTTCTATCTTTG 58.381 33.333 0.00 0.00 36.40 2.77
260 268 9.766277 TGTTGTTGTTTTATTTTGATTTTGCTC 57.234 25.926 0.00 0.00 0.00 4.26
283 291 3.411446 TCCAGTGGTTTGCTTAGATGTG 58.589 45.455 9.54 0.00 0.00 3.21
320 328 3.947196 ACTTGTGTGATTTGACTGCTTCA 59.053 39.130 0.00 0.00 0.00 3.02
325 333 4.214971 GTGTGATTTGACTGCTTCATGTCT 59.785 41.667 0.00 0.00 32.84 3.41
521 656 4.111375 TGATAAGAAGCTTGAGACGGTC 57.889 45.455 2.10 0.00 0.00 4.79
678 3208 3.820557 GGAACCATAAAGCTATCAGGCA 58.179 45.455 0.00 0.00 34.17 4.75
680 3210 4.444876 GGAACCATAAAGCTATCAGGCAGA 60.445 45.833 0.00 0.00 34.17 4.26
688 3218 1.538634 GCTATCAGGCAGAGCAGAGTG 60.539 57.143 0.00 0.00 36.20 3.51
690 3220 1.857965 ATCAGGCAGAGCAGAGTGTA 58.142 50.000 0.00 0.00 0.00 2.90
694 3224 0.390472 GGCAGAGCAGAGTGTACACC 60.390 60.000 22.28 13.56 0.00 4.16
720 3250 2.239681 TCCTCTTCTTCCTCCCAGTC 57.760 55.000 0.00 0.00 0.00 3.51
721 3251 1.199615 CCTCTTCTTCCTCCCAGTCC 58.800 60.000 0.00 0.00 0.00 3.85
722 3252 1.199615 CTCTTCTTCCTCCCAGTCCC 58.800 60.000 0.00 0.00 0.00 4.46
723 3253 0.491823 TCTTCTTCCTCCCAGTCCCA 59.508 55.000 0.00 0.00 0.00 4.37
724 3254 0.908198 CTTCTTCCTCCCAGTCCCAG 59.092 60.000 0.00 0.00 0.00 4.45
725 3255 0.193574 TTCTTCCTCCCAGTCCCAGT 59.806 55.000 0.00 0.00 0.00 4.00
726 3256 0.252284 TCTTCCTCCCAGTCCCAGTC 60.252 60.000 0.00 0.00 0.00 3.51
727 3257 1.229529 TTCCTCCCAGTCCCAGTCC 60.230 63.158 0.00 0.00 0.00 3.85
728 3258 2.689034 CCTCCCAGTCCCAGTCCC 60.689 72.222 0.00 0.00 0.00 4.46
729 3259 2.122729 CTCCCAGTCCCAGTCCCA 59.877 66.667 0.00 0.00 0.00 4.37
730 3260 1.992277 CTCCCAGTCCCAGTCCCAG 60.992 68.421 0.00 0.00 0.00 4.45
731 3261 2.203998 CCCAGTCCCAGTCCCAGT 60.204 66.667 0.00 0.00 0.00 4.00
773 3303 1.861542 CGTTTCATGGCCCGAAAGCA 61.862 55.000 15.71 0.00 33.20 3.91
780 3310 0.316841 TGGCCCGAAAGCAAAATGAC 59.683 50.000 0.00 0.00 0.00 3.06
858 3388 2.866028 CACGAGAAAGCAGCAGCC 59.134 61.111 0.00 0.00 43.56 4.85
905 3436 4.904466 CGCCCCTATATACGCACC 57.096 61.111 0.00 0.00 0.00 5.01
927 3458 1.138883 CTGCATGATGCCTGCACAC 59.861 57.895 15.70 0.00 44.30 3.82
972 3503 2.583593 GTTCGGAGCTAGCAGGCG 60.584 66.667 18.83 3.15 37.29 5.52
1200 3731 4.129737 CTCGTCGATGGTGCCGGT 62.130 66.667 1.90 0.00 0.00 5.28
1282 3820 4.489795 CACGCACGCGCATGTCTC 62.490 66.667 12.02 0.00 44.19 3.36
1305 3843 1.154016 ATTCTCGTCGGCTCGTGTG 60.154 57.895 0.00 0.00 0.00 3.82
1365 3903 3.022287 CAACTTGCAAGCGTCGGT 58.978 55.556 26.27 3.43 0.00 4.69
1367 3905 0.657368 CAACTTGCAAGCGTCGGTTC 60.657 55.000 26.27 3.46 0.00 3.62
1371 3909 1.495584 TTGCAAGCGTCGGTTCTCAC 61.496 55.000 6.72 0.00 0.00 3.51
1377 3918 0.527817 GCGTCGGTTCTCACCCTATG 60.528 60.000 0.00 0.00 40.52 2.23
1416 3957 8.910351 ACTGATAGCAGATAAATTTTACTCCC 57.090 34.615 16.32 0.00 45.17 4.30
1417 3958 8.718656 ACTGATAGCAGATAAATTTTACTCCCT 58.281 33.333 16.32 0.00 45.17 4.20
1418 3959 9.213799 CTGATAGCAGATAAATTTTACTCCCTC 57.786 37.037 0.40 0.00 45.17 4.30
1419 3960 8.157476 TGATAGCAGATAAATTTTACTCCCTCC 58.843 37.037 0.00 0.00 0.00 4.30
1420 3961 5.368989 AGCAGATAAATTTTACTCCCTCCG 58.631 41.667 0.00 0.00 0.00 4.63
1421 3962 5.104485 AGCAGATAAATTTTACTCCCTCCGT 60.104 40.000 0.00 0.00 0.00 4.69
1422 3963 5.589050 GCAGATAAATTTTACTCCCTCCGTT 59.411 40.000 0.00 0.00 0.00 4.44
1423 3964 6.238402 GCAGATAAATTTTACTCCCTCCGTTC 60.238 42.308 0.00 0.00 0.00 3.95
1424 3965 7.048512 CAGATAAATTTTACTCCCTCCGTTCT 58.951 38.462 0.00 0.00 0.00 3.01
1425 3966 7.553044 CAGATAAATTTTACTCCCTCCGTTCTT 59.447 37.037 0.00 0.00 0.00 2.52
1426 3967 8.765517 AGATAAATTTTACTCCCTCCGTTCTTA 58.234 33.333 0.00 0.00 0.00 2.10
1427 3968 9.387257 GATAAATTTTACTCCCTCCGTTCTTAA 57.613 33.333 0.00 0.00 0.00 1.85
1428 3969 9.743581 ATAAATTTTACTCCCTCCGTTCTTAAA 57.256 29.630 0.00 0.00 0.00 1.52
1429 3970 8.645814 AAATTTTACTCCCTCCGTTCTTAAAT 57.354 30.769 0.00 0.00 0.00 1.40
1430 3971 9.743581 AAATTTTACTCCCTCCGTTCTTAAATA 57.256 29.630 0.00 0.00 0.00 1.40
1431 3972 9.916360 AATTTTACTCCCTCCGTTCTTAAATAT 57.084 29.630 0.00 0.00 0.00 1.28
1432 3973 9.916360 ATTTTACTCCCTCCGTTCTTAAATATT 57.084 29.630 0.00 0.00 0.00 1.28
1433 3974 9.743581 TTTTACTCCCTCCGTTCTTAAATATTT 57.256 29.630 5.89 5.89 0.00 1.40
1434 3975 8.726870 TTACTCCCTCCGTTCTTAAATATTTG 57.273 34.615 11.05 0.00 0.00 2.32
1435 3976 6.718294 ACTCCCTCCGTTCTTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
1436 3977 6.822170 ACTCCCTCCGTTCTTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
1437 3978 6.954232 TCCCTCCGTTCTTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
1438 3979 7.399634 TCCCTCCGTTCTTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
1439 3980 7.886446 TCCCTCCGTTCTTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
1440 3981 8.182227 CCCTCCGTTCTTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
1441 3982 8.947115 CCTCCGTTCTTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
1468 4009 9.737427 AGAGATTTCAATAAGTGACTACATACG 57.263 33.333 0.00 0.00 35.39 3.06
1469 4010 8.873215 AGATTTCAATAAGTGACTACATACGG 57.127 34.615 0.00 0.00 35.39 4.02
1470 4011 8.692710 AGATTTCAATAAGTGACTACATACGGA 58.307 33.333 0.00 0.00 35.39 4.69
1471 4012 8.873215 ATTTCAATAAGTGACTACATACGGAG 57.127 34.615 0.00 0.00 35.39 4.63
1472 4013 5.828747 TCAATAAGTGACTACATACGGAGC 58.171 41.667 0.00 0.00 0.00 4.70
1473 4014 5.358725 TCAATAAGTGACTACATACGGAGCA 59.641 40.000 0.00 0.00 0.00 4.26
1474 4015 5.847111 ATAAGTGACTACATACGGAGCAA 57.153 39.130 0.00 0.00 0.00 3.91
1475 4016 4.530710 AAGTGACTACATACGGAGCAAA 57.469 40.909 0.00 0.00 0.00 3.68
1476 4017 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
1477 4018 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
1478 4019 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
1479 4020 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
1480 4021 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
1481 4022 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1482 4023 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1483 4024 3.674997 ACATACGGAGCAAAATGAGTGT 58.325 40.909 0.00 0.00 0.00 3.55
1484 4025 4.827692 ACATACGGAGCAAAATGAGTGTA 58.172 39.130 0.00 0.00 0.00 2.90
1485 4026 4.630069 ACATACGGAGCAAAATGAGTGTAC 59.370 41.667 0.00 0.00 0.00 2.90
1486 4027 2.423577 ACGGAGCAAAATGAGTGTACC 58.576 47.619 0.00 0.00 0.00 3.34
1487 4028 2.038557 ACGGAGCAAAATGAGTGTACCT 59.961 45.455 0.00 0.00 0.00 3.08
1488 4029 3.259876 ACGGAGCAAAATGAGTGTACCTA 59.740 43.478 0.00 0.00 0.00 3.08
1489 4030 3.617263 CGGAGCAAAATGAGTGTACCTAC 59.383 47.826 0.00 0.00 0.00 3.18
1490 4031 4.575885 GGAGCAAAATGAGTGTACCTACA 58.424 43.478 0.00 0.00 0.00 2.74
1569 4110 7.625828 AAAGACAAATATTTAGGAACCGAGG 57.374 36.000 0.00 0.00 0.00 4.63
1570 4111 5.681639 AGACAAATATTTAGGAACCGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1571 4112 5.427481 AGACAAATATTTAGGAACCGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1572 4113 5.681639 ACAAATATTTAGGAACCGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1573 4114 5.191124 ACAAATATTTAGGAACCGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
1586 4127 1.599542 GAGGGAGTATGTCGCAAATGC 59.400 52.381 0.00 0.00 40.67 3.56
1587 4128 1.210478 AGGGAGTATGTCGCAAATGCT 59.790 47.619 3.63 0.00 40.67 3.79
1618 4159 5.241285 TCATGTTGCAAATGTTAAGCAGAGA 59.759 36.000 0.00 0.00 39.72 3.10
1620 4161 5.522456 TGTTGCAAATGTTAAGCAGAGAAG 58.478 37.500 0.00 0.00 39.72 2.85
1625 4166 5.340667 GCAAATGTTAAGCAGAGAAGTTTCG 59.659 40.000 0.00 0.00 0.00 3.46
1656 4197 1.677052 TGTTGCCGTTGTTAAAGGTCC 59.323 47.619 0.00 0.00 0.00 4.46
1666 4207 7.182089 CCGTTGTTAAAGGTCCGTAATTTATC 58.818 38.462 0.00 0.00 0.00 1.75
1678 4219 5.650266 TCCGTAATTTATCATGGCTGTTGTT 59.350 36.000 0.00 0.00 0.00 2.83
1751 4293 3.611530 CGGTTGAACTTGGCAAATTCGAT 60.612 43.478 13.86 0.00 0.00 3.59
1797 4339 4.640855 CACGTCCGCCGACAGTGT 62.641 66.667 15.94 0.00 39.11 3.55
1954 4497 1.060698 GTTGCGCTCCGTAGAATGTTC 59.939 52.381 9.73 0.00 0.00 3.18
2041 4584 0.689623 CATCTCCCATGCCCTACTCC 59.310 60.000 0.00 0.00 0.00 3.85
2042 4585 0.474660 ATCTCCCATGCCCTACTCCC 60.475 60.000 0.00 0.00 0.00 4.30
2054 4610 1.150986 CCTACTCCCTGGATCCCTGAT 59.849 57.143 9.90 0.00 0.00 2.90
2064 4620 2.270874 GATCCCTGATGGTGCCGGTT 62.271 60.000 1.90 0.00 34.77 4.44
2181 4738 0.976641 AAGAATGTGACTCCGCCTCA 59.023 50.000 0.00 0.00 0.00 3.86
2194 4751 2.825982 CCTCACCAACGTCCACCA 59.174 61.111 0.00 0.00 0.00 4.17
2195 4752 1.374947 CCTCACCAACGTCCACCAT 59.625 57.895 0.00 0.00 0.00 3.55
2197 4754 1.604604 CTCACCAACGTCCACCATTT 58.395 50.000 0.00 0.00 0.00 2.32
2199 4756 1.142060 TCACCAACGTCCACCATTTCT 59.858 47.619 0.00 0.00 0.00 2.52
2207 4764 2.290071 CGTCCACCATTTCTAGGGTTGT 60.290 50.000 0.00 0.00 35.97 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 5.343249 CAGCCAATTTCCTTAACACTATGC 58.657 41.667 0.00 0.00 0.00 3.14
127 128 7.423844 AATTCAGTACATAGTGATCACCAGA 57.576 36.000 22.21 8.62 35.72 3.86
170 171 7.957002 ACCATTTACATATTCTGATCTCGACT 58.043 34.615 0.00 0.00 0.00 4.18
235 236 9.220635 GGAGCAAAATCAAAATAAAACAACAAC 57.779 29.630 0.00 0.00 0.00 3.32
258 266 2.303022 TCTAAGCAAACCACTGGAGGAG 59.697 50.000 0.71 0.00 0.00 3.69
260 268 2.859165 TCTAAGCAAACCACTGGAGG 57.141 50.000 0.71 0.00 0.00 4.30
283 291 4.793216 CACACAAGTTTGCTTCTTACACAC 59.207 41.667 0.00 0.00 31.49 3.82
440 449 7.581213 TGGTTGAATTGAATCACAACTAACT 57.419 32.000 19.43 0.00 41.52 2.24
506 641 3.851976 TCTAAGACCGTCTCAAGCTTC 57.148 47.619 0.35 0.00 0.00 3.86
521 656 5.700373 GGAATAGGAGCAAGCTGAATCTAAG 59.300 44.000 0.00 0.00 0.00 2.18
571 3096 4.704833 TTGAGCCCGCTCCACAGC 62.705 66.667 13.93 0.00 42.09 4.40
670 3200 1.857965 ACACTCTGCTCTGCCTGATA 58.142 50.000 0.00 0.00 0.00 2.15
672 3202 0.891373 GTACACTCTGCTCTGCCTGA 59.109 55.000 0.00 0.00 0.00 3.86
676 3206 0.318441 TGGTGTACACTCTGCTCTGC 59.682 55.000 24.55 6.10 0.00 4.26
678 3208 2.039418 TGTTGGTGTACACTCTGCTCT 58.961 47.619 24.55 0.00 0.00 4.09
680 3210 3.275617 TTTGTTGGTGTACACTCTGCT 57.724 42.857 24.55 0.00 0.00 4.24
688 3218 5.181433 GGAAGAAGAGGATTTGTTGGTGTAC 59.819 44.000 0.00 0.00 0.00 2.90
690 3220 4.141158 AGGAAGAAGAGGATTTGTTGGTGT 60.141 41.667 0.00 0.00 0.00 4.16
694 3224 4.013050 GGGAGGAAGAAGAGGATTTGTTG 58.987 47.826 0.00 0.00 0.00 3.33
720 3250 1.645710 AGAACTGTACTGGGACTGGG 58.354 55.000 4.66 0.00 0.00 4.45
721 3251 2.028020 GGAAGAACTGTACTGGGACTGG 60.028 54.545 4.66 0.00 0.00 4.00
722 3252 2.352814 CGGAAGAACTGTACTGGGACTG 60.353 54.545 4.66 0.00 0.00 3.51
723 3253 1.893801 CGGAAGAACTGTACTGGGACT 59.106 52.381 4.66 0.00 0.00 3.85
724 3254 1.617357 ACGGAAGAACTGTACTGGGAC 59.383 52.381 4.66 0.00 36.20 4.46
725 3255 2.005370 ACGGAAGAACTGTACTGGGA 57.995 50.000 4.66 0.00 36.20 4.37
726 3256 2.416972 GCTACGGAAGAACTGTACTGGG 60.417 54.545 4.66 0.00 39.10 4.45
727 3257 2.492484 AGCTACGGAAGAACTGTACTGG 59.508 50.000 4.66 0.00 39.10 4.00
728 3258 3.851976 AGCTACGGAAGAACTGTACTG 57.148 47.619 0.00 0.00 39.10 2.74
729 3259 4.868314 AAAGCTACGGAAGAACTGTACT 57.132 40.909 0.00 0.00 39.10 2.73
730 3260 5.061933 GCTTAAAGCTACGGAAGAACTGTAC 59.938 44.000 0.00 0.00 38.45 2.90
731 3261 5.166398 GCTTAAAGCTACGGAAGAACTGTA 58.834 41.667 0.00 0.00 38.45 2.74
773 3303 0.698818 AAGGCCTCGGAGGTCATTTT 59.301 50.000 29.01 13.10 44.17 1.82
780 3310 4.394712 ACGCAAAGGCCTCGGAGG 62.395 66.667 19.95 19.95 38.80 4.30
948 3479 0.737219 GCTAGCTCCGAACGAACCTA 59.263 55.000 7.70 0.00 0.00 3.08
1230 3761 3.009115 GGCCACTAGCTCACCCCA 61.009 66.667 0.00 0.00 43.05 4.96
1234 3765 2.815647 GCACGGCCACTAGCTCAC 60.816 66.667 2.24 0.00 43.05 3.51
1279 3817 1.384989 GCCGACGAGAATGGAGGAGA 61.385 60.000 0.00 0.00 0.00 3.71
1282 3820 1.066587 GAGCCGACGAGAATGGAGG 59.933 63.158 0.00 0.00 0.00 4.30
1305 3843 2.388232 CCGTACTGTTTGGCCTCGC 61.388 63.158 3.32 0.00 0.00 5.03
1365 3903 4.098914 AGCAACAAACATAGGGTGAGAA 57.901 40.909 0.00 0.00 0.00 2.87
1367 3905 6.515272 AATTAGCAACAAACATAGGGTGAG 57.485 37.500 0.00 0.00 0.00 3.51
1371 3909 7.624360 TCAGTAATTAGCAACAAACATAGGG 57.376 36.000 0.00 0.00 0.00 3.53
1377 3918 7.974675 TCTGCTATCAGTAATTAGCAACAAAC 58.025 34.615 6.16 0.00 43.81 2.93
1410 3951 7.854337 ACAAATATTTAAGAACGGAGGGAGTA 58.146 34.615 0.00 0.00 0.00 2.59
1411 3952 6.718294 ACAAATATTTAAGAACGGAGGGAGT 58.282 36.000 0.00 0.00 0.00 3.85
1412 3953 7.048512 AGACAAATATTTAAGAACGGAGGGAG 58.951 38.462 0.00 0.00 0.00 4.30
1413 3954 6.954232 AGACAAATATTTAAGAACGGAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
1414 3955 7.625828 AAGACAAATATTTAAGAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
1415 3956 8.947115 AGAAAGACAAATATTTAAGAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
1442 3983 9.737427 CGTATGTAGTCACTTATTGAAATCTCT 57.263 33.333 0.00 0.00 35.39 3.10
1443 3984 8.969267 CCGTATGTAGTCACTTATTGAAATCTC 58.031 37.037 0.00 0.00 35.39 2.75
1444 3985 8.692710 TCCGTATGTAGTCACTTATTGAAATCT 58.307 33.333 0.00 0.00 35.39 2.40
1445 3986 8.867112 TCCGTATGTAGTCACTTATTGAAATC 57.133 34.615 0.00 0.00 35.39 2.17
1446 3987 7.438459 GCTCCGTATGTAGTCACTTATTGAAAT 59.562 37.037 0.00 0.00 35.39 2.17
1447 3988 6.755141 GCTCCGTATGTAGTCACTTATTGAAA 59.245 38.462 0.00 0.00 35.39 2.69
1448 3989 6.127563 TGCTCCGTATGTAGTCACTTATTGAA 60.128 38.462 0.00 0.00 35.39 2.69
1449 3990 5.358725 TGCTCCGTATGTAGTCACTTATTGA 59.641 40.000 0.00 0.00 0.00 2.57
1450 3991 5.588240 TGCTCCGTATGTAGTCACTTATTG 58.412 41.667 0.00 0.00 0.00 1.90
1451 3992 5.847111 TGCTCCGTATGTAGTCACTTATT 57.153 39.130 0.00 0.00 0.00 1.40
1452 3993 5.847111 TTGCTCCGTATGTAGTCACTTAT 57.153 39.130 0.00 0.00 0.00 1.73
1453 3994 5.648178 TTTGCTCCGTATGTAGTCACTTA 57.352 39.130 0.00 0.00 0.00 2.24
1454 3995 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
1455 3996 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
1456 3997 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
1457 3998 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1458 3999 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1459 4000 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1460 4001 4.870426 ACACTCATTTTGCTCCGTATGTAG 59.130 41.667 0.00 0.00 0.00 2.74
1461 4002 4.827692 ACACTCATTTTGCTCCGTATGTA 58.172 39.130 0.00 0.00 0.00 2.29
1462 4003 3.674997 ACACTCATTTTGCTCCGTATGT 58.325 40.909 0.00 0.00 0.00 2.29
1463 4004 4.034048 GGTACACTCATTTTGCTCCGTATG 59.966 45.833 0.00 0.00 0.00 2.39
1464 4005 4.081087 AGGTACACTCATTTTGCTCCGTAT 60.081 41.667 0.00 0.00 0.00 3.06
1465 4006 3.259876 AGGTACACTCATTTTGCTCCGTA 59.740 43.478 0.00 0.00 0.00 4.02
1466 4007 2.038557 AGGTACACTCATTTTGCTCCGT 59.961 45.455 0.00 0.00 0.00 4.69
1467 4008 2.699954 AGGTACACTCATTTTGCTCCG 58.300 47.619 0.00 0.00 0.00 4.63
1468 4009 4.575885 TGTAGGTACACTCATTTTGCTCC 58.424 43.478 0.00 0.00 0.00 4.70
1543 4084 8.520351 CCTCGGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
1544 4085 7.122204 CCCTCGGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
1545 4086 6.602009 CCCTCGGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1546 4087 6.069847 TCCCTCGGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1547 4088 5.427481 TCCCTCGGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1548 4089 5.677567 TCCCTCGGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1549 4090 5.191124 ACTCCCTCGGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1550 4091 5.681639 ACTCCCTCGGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1551 4092 5.970501 ACTCCCTCGGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1552 4093 6.557633 ACATACTCCCTCGGTTCCTAAATATT 59.442 38.462 0.00 0.00 0.00 1.28
1553 4094 6.082707 ACATACTCCCTCGGTTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
1554 4095 5.461327 ACATACTCCCTCGGTTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
1555 4096 4.296056 ACATACTCCCTCGGTTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
1556 4097 3.703052 GACATACTCCCTCGGTTCCTAAA 59.297 47.826 0.00 0.00 0.00 1.85
1557 4098 3.294214 GACATACTCCCTCGGTTCCTAA 58.706 50.000 0.00 0.00 0.00 2.69
1558 4099 2.747467 CGACATACTCCCTCGGTTCCTA 60.747 54.545 0.00 0.00 0.00 2.94
1559 4100 1.777941 GACATACTCCCTCGGTTCCT 58.222 55.000 0.00 0.00 0.00 3.36
1560 4101 0.384669 CGACATACTCCCTCGGTTCC 59.615 60.000 0.00 0.00 0.00 3.62
1561 4102 0.248949 GCGACATACTCCCTCGGTTC 60.249 60.000 0.00 0.00 0.00 3.62
1562 4103 0.968901 TGCGACATACTCCCTCGGTT 60.969 55.000 0.00 0.00 0.00 4.44
1563 4104 0.968901 TTGCGACATACTCCCTCGGT 60.969 55.000 0.00 0.00 0.00 4.69
1564 4105 0.174845 TTTGCGACATACTCCCTCGG 59.825 55.000 0.00 0.00 0.00 4.63
1565 4106 1.860950 CATTTGCGACATACTCCCTCG 59.139 52.381 0.00 0.00 0.00 4.63
1566 4107 1.599542 GCATTTGCGACATACTCCCTC 59.400 52.381 0.00 0.00 0.00 4.30
1567 4108 1.668419 GCATTTGCGACATACTCCCT 58.332 50.000 0.00 0.00 0.00 4.20
1592 4133 6.279123 TCTGCTTAACATTTGCAACATGAAA 58.721 32.000 20.96 15.05 36.22 2.69
1618 4159 3.569250 ACACTTGCAACAACGAAACTT 57.431 38.095 0.00 0.00 0.00 2.66
1620 4161 3.616444 CAACACTTGCAACAACGAAAC 57.384 42.857 0.00 0.00 0.00 2.78
1645 4186 7.201750 GCCATGATAAATTACGGACCTTTAACA 60.202 37.037 0.00 0.00 0.00 2.41
1652 4193 4.134563 ACAGCCATGATAAATTACGGACC 58.865 43.478 0.00 0.00 0.00 4.46
1656 4197 7.639850 CAGTAACAACAGCCATGATAAATTACG 59.360 37.037 0.00 0.00 0.00 3.18
1666 4207 2.877786 TGTGACAGTAACAACAGCCATG 59.122 45.455 0.00 0.00 0.00 3.66
1691 4232 5.703592 ACCGCACACAAACTATTTATCTTCA 59.296 36.000 0.00 0.00 0.00 3.02
1695 4236 5.796350 AGACCGCACACAAACTATTTATC 57.204 39.130 0.00 0.00 0.00 1.75
1697 4238 6.457355 TCTAAGACCGCACACAAACTATTTA 58.543 36.000 0.00 0.00 0.00 1.40
1735 4277 3.826157 TGAAGGATCGAATTTGCCAAGTT 59.174 39.130 0.00 0.00 0.00 2.66
1751 4293 3.811118 TTCGCGGGCGTTTGAAGGA 62.811 57.895 13.21 0.00 40.74 3.36
1789 4331 1.078759 GGCTTGATCGGACACTGTCG 61.079 60.000 3.04 0.00 32.65 4.35
1797 4339 4.141505 TGGATTATTTGAGGCTTGATCGGA 60.142 41.667 0.00 0.00 0.00 4.55
1886 4428 1.779724 CGAACGAGCTCCGCTTAATAC 59.220 52.381 8.47 0.00 39.88 1.89
1935 4478 1.355971 GAACATTCTACGGAGCGCAA 58.644 50.000 11.47 0.00 0.00 4.85
1944 4487 1.135575 ACGACCGGACGAACATTCTAC 60.136 52.381 31.92 0.00 37.03 2.59
1954 4497 4.495939 CTCGTCGACGACCGGACG 62.496 72.222 34.97 24.38 44.22 4.79
1997 4540 2.583441 CCTTGAGTCCCGTGAGCCA 61.583 63.158 0.00 0.00 0.00 4.75
2023 4566 0.474660 GGGAGTAGGGCATGGGAGAT 60.475 60.000 0.00 0.00 0.00 2.75
2041 4584 1.150081 GCACCATCAGGGATCCAGG 59.850 63.158 15.23 9.28 41.15 4.45
2042 4585 1.150081 GGCACCATCAGGGATCCAG 59.850 63.158 15.23 5.52 41.15 3.86
2054 4610 3.800685 CTGTCGTCAACCGGCACCA 62.801 63.158 0.00 0.00 45.60 4.17
2069 4625 3.191581 GGACGTATCCATCATCGATCTGT 59.808 47.826 0.00 0.00 45.47 3.41
2086 4643 3.374402 CGGCTCCTCACAGGACGT 61.374 66.667 0.00 0.00 40.06 4.34
2169 4726 2.741092 GTTGGTGAGGCGGAGTCA 59.259 61.111 0.00 0.00 0.00 3.41
2181 4738 2.290071 CCTAGAAATGGTGGACGTTGGT 60.290 50.000 0.00 0.00 0.00 3.67
2194 4751 0.743345 GCGGCGACAACCCTAGAAAT 60.743 55.000 12.98 0.00 0.00 2.17
2195 4752 1.375013 GCGGCGACAACCCTAGAAA 60.375 57.895 12.98 0.00 0.00 2.52
2197 4754 3.766691 GGCGGCGACAACCCTAGA 61.767 66.667 12.98 0.00 0.00 2.43
2199 4756 3.766691 GAGGCGGCGACAACCCTA 61.767 66.667 18.30 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.