Multiple sequence alignment - TraesCS3D01G376600

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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 TraesCS3D01G376600 chr3D 100.000 3647 0 0 1 3647 490306542 490302896 0.000000e+00 6735.0
1 TraesCS3D01G376600 chr3D 90.566 53 5 0 551 603 163116445 163116497 1.820000e-08 71.3
2 TraesCS3D01G376600 chr3A 95.437 2279 80 13 763 3028 632778071 632775804 0.000000e+00 3611.0
3 TraesCS3D01G376600 chr3A 90.602 415 26 9 1 403 632779058 632778645 4.140000e-149 538.0
4 TraesCS3D01G376600 chr3A 81.429 350 32 12 3250 3585 632775274 632774944 4.670000e-64 255.0
5 TraesCS3D01G376600 chr3A 95.349 86 4 0 3105 3190 632775388 632775303 1.770000e-28 137.0
6 TraesCS3D01G376600 chr3B 94.143 2305 104 12 671 2956 652497916 652495624 0.000000e+00 3480.0
7 TraesCS3D01G376600 chr3B 86.166 506 59 8 1 502 652499166 652498668 1.490000e-148 536.0
8 TraesCS3D01G376600 chr3B 92.437 238 10 5 3020 3249 652495609 652495372 2.100000e-87 333.0
9 TraesCS3D01G376600 chr3B 85.965 285 29 4 3250 3523 652495330 652495046 9.900000e-76 294.0
10 TraesCS3D01G376600 chr1B 85.622 1398 183 17 1209 2597 488393676 488395064 0.000000e+00 1452.0
11 TraesCS3D01G376600 chr1B 96.970 33 0 1 492 524 8913114 8913145 2.000000e-03 54.7
12 TraesCS3D01G376600 chr1D 85.408 1398 186 17 1209 2597 365040884 365042272 0.000000e+00 1435.0
13 TraesCS3D01G376600 chr1A 85.204 1399 187 19 1209 2597 463921495 463922883 0.000000e+00 1419.0
14 TraesCS3D01G376600 chr4D 84.459 296 37 2 1369 1664 207778634 207778348 2.140000e-72 283.0
15 TraesCS3D01G376600 chr4D 84.091 264 39 3 1391 1654 163254810 163254550 6.050000e-63 252.0
16 TraesCS3D01G376600 chr2D 84.122 296 38 2 1369 1664 632273932 632274218 9.970000e-71 278.0
17 TraesCS3D01G376600 chr2D 94.340 53 3 0 551 603 621477777 621477829 8.390000e-12 82.4
18 TraesCS3D01G376600 chr2D 93.023 43 0 2 493 534 423558736 423558776 3.930000e-05 60.2
19 TraesCS3D01G376600 chr2B 89.333 75 7 1 551 624 2763724 2763650 3.880000e-15 93.5
20 TraesCS3D01G376600 chr2B 88.406 69 7 1 548 615 721297628 721297696 8.390000e-12 82.4
21 TraesCS3D01G376600 chr4A 85.714 84 11 1 551 633 677992280 677992363 1.800000e-13 87.9
22 TraesCS3D01G376600 chrUn 94.340 53 3 0 562 614 91511568 91511620 8.390000e-12 82.4
23 TraesCS3D01G376600 chr5A 92.453 53 4 0 551 603 66592745 66592693 3.910000e-10 76.8
24 TraesCS3D01G376600 chr6D 90.566 53 5 0 551 603 277162208 277162156 1.820000e-08 71.3
25 TraesCS3D01G376600 chr5D 89.286 56 4 1 548 601 510128041 510127986 6.530000e-08 69.4


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 TraesCS3D01G376600 chr3D 490302896 490306542 3646 True 6735.00 6735 100.00000 1 3647 1 chr3D.!!$R1 3646
1 TraesCS3D01G376600 chr3A 632774944 632779058 4114 True 1135.25 3611 90.70425 1 3585 4 chr3A.!!$R1 3584
2 TraesCS3D01G376600 chr3B 652495046 652499166 4120 True 1160.75 3480 89.67775 1 3523 4 chr3B.!!$R1 3522
3 TraesCS3D01G376600 chr1B 488393676 488395064 1388 False 1452.00 1452 85.62200 1209 2597 1 chr1B.!!$F2 1388
4 TraesCS3D01G376600 chr1D 365040884 365042272 1388 False 1435.00 1435 85.40800 1209 2597 1 chr1D.!!$F1 1388
5 TraesCS3D01G376600 chr1A 463921495 463922883 1388 False 1419.00 1419 85.20400 1209 2597 1 chr1A.!!$F1 1388

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
200 201 1.139058 TCTTCTTCTATCTTGGCGGCC 59.861 52.381 13.32 13.32 0.00 6.13 F
1107 1753 1.569030 ATCCACAGCTCAGGTGCCAT 61.569 55.000 3.01 0.00 34.04 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1187 1833 2.325082 CCGAAGTTGAAGGGCGTGG 61.325 63.158 0.0 0.0 0.0 4.94 R
2673 3319 0.807667 CATGCGGAGTACAGAGCCAC 60.808 60.000 0.0 0.0 0.0 5.01 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
21 22 2.203139 CACACCACTTGACCCGCA 60.203 61.111 0.00 0.00 0.00 5.69
60 61 4.265056 GTGGGCCCTTGTGTCGGT 62.265 66.667 25.70 0.00 0.00 4.69
61 62 3.948719 TGGGCCCTTGTGTCGGTC 61.949 66.667 25.70 0.00 0.00 4.79
120 121 4.786425 ACTAGCCAGGGAAGAATTGAATC 58.214 43.478 0.00 0.00 0.00 2.52
179 180 1.202698 AGTCAAAAGACGGCTTCAGCT 60.203 47.619 2.63 0.00 41.70 4.24
190 191 3.196685 ACGGCTTCAGCTTCTTCTTCTAT 59.803 43.478 0.00 0.00 41.70 1.98
200 201 1.139058 TCTTCTTCTATCTTGGCGGCC 59.861 52.381 13.32 13.32 0.00 6.13
297 316 7.155328 GCTCCTCGAATCCAGAAGATTAATTA 58.845 38.462 0.00 0.00 45.52 1.40
330 349 4.282957 TCAATTCTTGCCCACAAATAGCAA 59.717 37.500 0.00 0.00 43.83 3.91
403 434 9.597681 AGAATTGGGAGCAAATGATTATATTCT 57.402 29.630 0.00 0.00 0.00 2.40
462 500 9.751542 ATTTAAACGTTTGTAATTGATTGGACA 57.248 25.926 23.46 0.00 0.00 4.02
463 501 8.789881 TTAAACGTTTGTAATTGATTGGACAG 57.210 30.769 23.46 0.00 0.00 3.51
482 520 5.351948 ACAGGTGGTTTAGCAACAAAATT 57.648 34.783 0.00 0.00 34.15 1.82
489 527 7.203218 GTGGTTTAGCAACAAAATTCTCTCTT 58.797 34.615 0.00 0.00 34.15 2.85
490 528 7.706607 GTGGTTTAGCAACAAAATTCTCTCTTT 59.293 33.333 0.00 0.00 34.15 2.52
491 529 8.257306 TGGTTTAGCAACAAAATTCTCTCTTTT 58.743 29.630 0.00 0.00 34.15 2.27
520 576 6.604735 AAGATTTCAATGCGGACTACATAC 57.395 37.500 0.00 0.00 0.00 2.39
522 578 2.502213 TCAATGCGGACTACATACGG 57.498 50.000 0.00 0.00 0.00 4.02
524 580 2.124903 CAATGCGGACTACATACGGAC 58.875 52.381 0.00 0.00 0.00 4.79
532 588 5.235186 GCGGACTACATACGGACGTATATAT 59.765 44.000 15.98 8.38 39.07 0.86
615 1207 8.533569 TCTGTATGTAGTCTGTATTGGAATCA 57.466 34.615 0.00 0.00 0.00 2.57
616 1208 9.147732 TCTGTATGTAGTCTGTATTGGAATCAT 57.852 33.333 0.00 0.00 0.00 2.45
745 1368 6.305693 AGATATCGCTGGTGAATTTAAAGC 57.694 37.500 0.00 0.00 0.00 3.51
762 1389 9.571816 AATTTAAAGCAAAAATCCTGGATTTCA 57.428 25.926 29.44 10.46 40.77 2.69
764 1391 6.423776 AAAGCAAAAATCCTGGATTTCAGA 57.576 33.333 29.44 0.00 46.18 3.27
839 1479 7.696992 TCATTTTACCCAAAATCCAGAGTAC 57.303 36.000 0.00 0.00 41.41 2.73
850 1490 6.481954 AAATCCAGAGTACAAAATGACGAC 57.518 37.500 0.00 0.00 0.00 4.34
871 1511 3.134081 ACGGGAGTCAAAATATCGTGGAT 59.866 43.478 0.00 0.00 40.62 3.41
1091 1737 4.832608 GCCGTCCACCGTCCATCC 62.833 72.222 0.00 0.00 33.66 3.51
1107 1753 1.569030 ATCCACAGCTCAGGTGCCAT 61.569 55.000 3.01 0.00 34.04 4.40
1209 1855 2.677979 GCCCTTCAACTTCGGCGAC 61.678 63.158 10.16 0.00 0.00 5.19
2007 2653 4.314440 TTCGCGCTGCCCAACTCT 62.314 61.111 5.56 0.00 0.00 3.24
2394 3040 4.575973 ATGCGCATCTCCAGCCCC 62.576 66.667 19.28 0.00 0.00 5.80
2671 3317 0.325296 ATGTGCGACTAGGGAAGGGA 60.325 55.000 0.00 0.00 0.00 4.20
2673 3319 0.175989 GTGCGACTAGGGAAGGGAAG 59.824 60.000 0.00 0.00 0.00 3.46
2720 3367 1.510844 GATTTTGGGCGTGGCGAAT 59.489 52.632 0.00 0.00 0.00 3.34
2746 3393 1.193644 CGTGGCAATTGCATTCATCG 58.806 50.000 30.32 19.20 44.36 3.84
2748 3395 2.609350 GTGGCAATTGCATTCATCGTT 58.391 42.857 30.32 0.00 44.36 3.85
2775 3422 7.277539 TGAATTTTTGCAGGTCTTAAGTTTGTG 59.722 33.333 1.63 0.00 0.00 3.33
2778 3425 3.211045 TGCAGGTCTTAAGTTTGTGTCC 58.789 45.455 1.63 0.00 0.00 4.02
2810 3457 0.875059 CGTTCCTTGGCCTCTCAAAC 59.125 55.000 3.32 1.41 0.00 2.93
2912 3560 2.152699 CGCCGACGTGAACTGCTAG 61.153 63.158 0.00 0.00 33.53 3.42
2940 3589 3.575256 TGCATTTTTCAAGCTCCTGTGAT 59.425 39.130 0.00 0.00 0.00 3.06
2975 3628 7.553881 TTCTATTAGTTACATCTGCAAAGCC 57.446 36.000 0.00 0.00 0.00 4.35
3014 3667 5.221303 TGTGGAGGTAGTGTTAGTTGTGTAC 60.221 44.000 0.00 0.00 0.00 2.90
3022 3675 3.488310 GTGTTAGTTGTGTACTGACGGTG 59.512 47.826 0.00 0.00 44.15 4.94
3056 3709 4.786507 CATTGCTGATTTTGAGTCAACGA 58.213 39.130 4.68 0.00 0.00 3.85
3060 3713 4.994217 TGCTGATTTTGAGTCAACGATGTA 59.006 37.500 4.68 0.00 0.00 2.29
3079 3732 6.851837 CGATGTAACTAGATAGAAGTCAACCG 59.148 42.308 0.00 0.00 0.00 4.44
3107 4113 3.975168 TCCTAGCTTGGACACTAAACC 57.025 47.619 13.28 0.00 0.00 3.27
3162 4169 5.750067 TGACATTGACATGTATCATGAGTCG 59.250 40.000 15.25 3.98 44.22 4.18
3185 4192 4.890088 AGTGTAATCTTGGCTACAACGAA 58.110 39.130 0.00 0.00 32.14 3.85
3188 4195 7.272978 AGTGTAATCTTGGCTACAACGAATAT 58.727 34.615 0.00 0.00 32.14 1.28
3189 4196 7.224753 AGTGTAATCTTGGCTACAACGAATATG 59.775 37.037 0.00 0.00 32.14 1.78
3190 4197 7.011109 GTGTAATCTTGGCTACAACGAATATGT 59.989 37.037 0.00 0.00 32.14 2.29
3251 4265 3.950869 TGATGCTTCTGCTTCAGCT 57.049 47.368 0.00 0.00 44.77 4.24
3252 4266 1.735386 TGATGCTTCTGCTTCAGCTC 58.265 50.000 0.00 0.00 44.77 4.09
3255 4269 0.683412 TGCTTCTGCTTCAGCTCTCA 59.317 50.000 0.00 0.00 42.66 3.27
3257 4271 1.338011 GCTTCTGCTTCAGCTCTCAGT 60.338 52.381 0.00 0.00 42.66 3.41
3259 4273 3.616076 GCTTCTGCTTCAGCTCTCAGTTA 60.616 47.826 0.00 0.00 42.66 2.24
3261 4275 4.815533 TCTGCTTCAGCTCTCAGTTATT 57.184 40.909 0.00 0.00 42.66 1.40
3262 4276 5.157940 TCTGCTTCAGCTCTCAGTTATTT 57.842 39.130 0.00 0.00 42.66 1.40
3279 4334 9.844790 TCAGTTATTTGCTTTGACATATTCAAG 57.155 29.630 0.00 0.00 45.22 3.02
3280 4335 8.589629 CAGTTATTTGCTTTGACATATTCAAGC 58.410 33.333 2.47 2.47 45.22 4.01
3282 4337 3.135414 TGCTTTGACATATTCAAGCGC 57.865 42.857 0.00 0.00 45.22 5.92
3360 4423 3.194968 GGGACGGTCTGTTTCTCTGAATA 59.805 47.826 8.23 0.00 0.00 1.75
3414 4480 4.320546 AAGTGATGAAACCCATGATCCA 57.679 40.909 0.00 0.00 35.17 3.41
3436 4505 4.510167 ATGCTGCTCTACCCTGTTAAAT 57.490 40.909 0.00 0.00 0.00 1.40
3440 4509 5.130311 TGCTGCTCTACCCTGTTAAATCATA 59.870 40.000 0.00 0.00 0.00 2.15
3450 4519 6.204688 ACCCTGTTAAATCATATACATGCACG 59.795 38.462 0.00 0.00 31.73 5.34
3451 4520 6.204688 CCCTGTTAAATCATATACATGCACGT 59.795 38.462 0.00 0.00 31.73 4.49
3455 4524 9.099454 TGTTAAATCATATACATGCACGTACAA 57.901 29.630 0.00 0.00 31.73 2.41
3471 4540 4.038763 ACGTACAACAAATCTGACCTCTCA 59.961 41.667 0.00 0.00 0.00 3.27
3474 4543 6.147821 CGTACAACAAATCTGACCTCTCAAAT 59.852 38.462 0.00 0.00 0.00 2.32
3477 4546 3.438087 ACAAATCTGACCTCTCAAATGCG 59.562 43.478 0.00 0.00 0.00 4.73
3478 4547 3.340814 AATCTGACCTCTCAAATGCGT 57.659 42.857 0.00 0.00 0.00 5.24
3479 4548 2.084610 TCTGACCTCTCAAATGCGTG 57.915 50.000 0.00 0.00 0.00 5.34
3480 4549 0.445436 CTGACCTCTCAAATGCGTGC 59.555 55.000 0.00 0.00 0.00 5.34
3483 4552 1.741401 CCTCTCAAATGCGTGCGGA 60.741 57.895 0.00 0.00 0.00 5.54
3524 4596 1.269958 GGCAGCCCTCAAATTTCCTT 58.730 50.000 0.00 0.00 0.00 3.36
3525 4597 2.456577 GGCAGCCCTCAAATTTCCTTA 58.543 47.619 0.00 0.00 0.00 2.69
3529 4601 4.202090 GCAGCCCTCAAATTTCCTTATCTG 60.202 45.833 0.00 0.00 0.00 2.90
3530 4602 3.956848 AGCCCTCAAATTTCCTTATCTGC 59.043 43.478 0.00 0.00 0.00 4.26
3540 4612 7.992754 AATTTCCTTATCTGCATCTGGATAC 57.007 36.000 0.00 0.00 0.00 2.24
3546 4618 6.382282 CCTTATCTGCATCTGGATACCTCATA 59.618 42.308 0.00 0.00 0.00 2.15
3585 4657 5.702865 TCATACAGAGCATGCAAAAGAAAC 58.297 37.500 21.98 0.67 0.00 2.78
3586 4658 3.004024 ACAGAGCATGCAAAAGAAACG 57.996 42.857 21.98 0.00 0.00 3.60
3587 4659 1.717645 CAGAGCATGCAAAAGAAACGC 59.282 47.619 21.98 0.00 0.00 4.84
3588 4660 1.063031 GAGCATGCAAAAGAAACGCC 58.937 50.000 21.98 0.00 0.00 5.68
3589 4661 0.675633 AGCATGCAAAAGAAACGCCT 59.324 45.000 21.98 0.00 0.00 5.52
3590 4662 1.885887 AGCATGCAAAAGAAACGCCTA 59.114 42.857 21.98 0.00 0.00 3.93
3591 4663 1.985684 GCATGCAAAAGAAACGCCTAC 59.014 47.619 14.21 0.00 0.00 3.18
3592 4664 2.606795 GCATGCAAAAGAAACGCCTACA 60.607 45.455 14.21 0.00 0.00 2.74
3593 4665 3.836949 CATGCAAAAGAAACGCCTACAT 58.163 40.909 0.00 0.00 0.00 2.29
3594 4666 4.674101 GCATGCAAAAGAAACGCCTACATA 60.674 41.667 14.21 0.00 0.00 2.29
3595 4667 4.413495 TGCAAAAGAAACGCCTACATAC 57.587 40.909 0.00 0.00 0.00 2.39
3596 4668 4.069304 TGCAAAAGAAACGCCTACATACT 58.931 39.130 0.00 0.00 0.00 2.12
3597 4669 4.083537 TGCAAAAGAAACGCCTACATACTG 60.084 41.667 0.00 0.00 0.00 2.74
3598 4670 4.083484 GCAAAAGAAACGCCTACATACTGT 60.083 41.667 0.00 0.00 0.00 3.55
3599 4671 5.121142 GCAAAAGAAACGCCTACATACTGTA 59.879 40.000 0.00 0.00 0.00 2.74
3600 4672 6.531439 CAAAAGAAACGCCTACATACTGTAC 58.469 40.000 0.00 0.00 0.00 2.90
3601 4673 5.395682 AAGAAACGCCTACATACTGTACA 57.604 39.130 0.00 0.00 0.00 2.90
3602 4674 5.593679 AGAAACGCCTACATACTGTACAT 57.406 39.130 0.00 0.00 0.00 2.29
3603 4675 6.704289 AGAAACGCCTACATACTGTACATA 57.296 37.500 0.00 0.00 0.00 2.29
3604 4676 6.736123 AGAAACGCCTACATACTGTACATAG 58.264 40.000 0.00 0.00 0.00 2.23
3605 4677 6.544931 AGAAACGCCTACATACTGTACATAGA 59.455 38.462 0.00 0.00 0.00 1.98
3606 4678 6.896021 AACGCCTACATACTGTACATAGAT 57.104 37.500 0.00 0.00 0.00 1.98
3607 4679 6.497785 ACGCCTACATACTGTACATAGATC 57.502 41.667 0.00 0.00 0.00 2.75
3608 4680 6.002082 ACGCCTACATACTGTACATAGATCA 58.998 40.000 0.00 0.00 0.00 2.92
3609 4681 6.489022 ACGCCTACATACTGTACATAGATCAA 59.511 38.462 0.00 0.00 0.00 2.57
3610 4682 6.802348 CGCCTACATACTGTACATAGATCAAC 59.198 42.308 0.00 0.00 0.00 3.18
3611 4683 7.308649 CGCCTACATACTGTACATAGATCAACT 60.309 40.741 0.00 0.00 0.00 3.16
3612 4684 9.011095 GCCTACATACTGTACATAGATCAACTA 57.989 37.037 0.00 0.00 35.42 2.24
3616 4688 9.409918 ACATACTGTACATAGATCAACTACACT 57.590 33.333 0.00 0.00 33.62 3.55
3624 4696 8.367943 ACATAGATCAACTACACTACTAGTCG 57.632 38.462 0.00 0.00 33.62 4.18
3625 4697 7.986320 ACATAGATCAACTACACTACTAGTCGT 59.014 37.037 0.00 0.00 33.62 4.34
3626 4698 6.907206 AGATCAACTACACTACTAGTCGTC 57.093 41.667 0.00 0.00 0.00 4.20
3627 4699 5.816777 AGATCAACTACACTACTAGTCGTCC 59.183 44.000 0.00 0.00 0.00 4.79
3628 4700 5.157940 TCAACTACACTACTAGTCGTCCT 57.842 43.478 0.00 0.00 0.00 3.85
3629 4701 5.555017 TCAACTACACTACTAGTCGTCCTT 58.445 41.667 0.00 0.00 0.00 3.36
3630 4702 5.410746 TCAACTACACTACTAGTCGTCCTTG 59.589 44.000 0.00 1.79 0.00 3.61
3631 4703 4.260170 ACTACACTACTAGTCGTCCTTGG 58.740 47.826 0.00 0.00 0.00 3.61
3632 4704 3.430042 ACACTACTAGTCGTCCTTGGA 57.570 47.619 0.00 0.00 0.00 3.53
3633 4705 3.345414 ACACTACTAGTCGTCCTTGGAG 58.655 50.000 0.00 0.00 33.51 3.86
3634 4706 3.008813 ACACTACTAGTCGTCCTTGGAGA 59.991 47.826 0.00 0.00 31.89 3.71
3635 4707 4.200874 CACTACTAGTCGTCCTTGGAGAT 58.799 47.826 0.00 0.00 31.89 2.75
3636 4708 4.035792 CACTACTAGTCGTCCTTGGAGATG 59.964 50.000 0.00 0.00 31.89 2.90
3637 4709 3.088789 ACTAGTCGTCCTTGGAGATGT 57.911 47.619 0.00 0.00 0.00 3.06
3638 4710 3.018149 ACTAGTCGTCCTTGGAGATGTC 58.982 50.000 0.00 0.00 0.00 3.06
3639 4711 1.187087 AGTCGTCCTTGGAGATGTCC 58.813 55.000 0.83 0.83 44.24 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 4.684485 CGATTCAATTCTTCCCTGGCTAGT 60.684 45.833 0.00 0.00 0.00 2.57
120 121 0.863538 CAAGCAGATCTCGACCGTCG 60.864 60.000 14.94 14.94 42.10 5.12
179 180 2.420129 GGCCGCCAAGATAGAAGAAGAA 60.420 50.000 3.91 0.00 0.00 2.52
190 191 3.303761 TTTCGATCGGCCGCCAAGA 62.304 57.895 23.51 14.22 0.00 3.02
200 201 2.628106 CGCCATGGCTTTCGATCG 59.372 61.111 33.07 9.36 39.32 3.69
210 211 1.524621 CCTTCCTAGTGCGCCATGG 60.525 63.158 7.63 7.63 0.00 3.66
239 258 5.067273 ACCACTTATGACGGTTCATGAAAA 58.933 37.500 10.35 0.00 42.79 2.29
345 364 7.391833 GGATAAGCCCCTAATCTTATGTTCTTG 59.608 40.741 0.00 0.00 36.09 3.02
348 367 6.881602 CAGGATAAGCCCCTAATCTTATGTTC 59.118 42.308 0.00 0.00 36.09 3.18
403 434 5.860941 TTCTTAGGATGCAACCAAACAAA 57.139 34.783 16.21 0.15 0.00 2.83
443 481 5.153513 CACCTGTCCAATCAATTACAAACG 58.846 41.667 0.00 0.00 0.00 3.60
448 486 5.722021 AAACCACCTGTCCAATCAATTAC 57.278 39.130 0.00 0.00 0.00 1.89
455 493 2.890945 GTTGCTAAACCACCTGTCCAAT 59.109 45.455 0.00 0.00 0.00 3.16
462 500 5.598417 AGAGAATTTTGTTGCTAAACCACCT 59.402 36.000 0.00 0.00 35.25 4.00
463 501 5.842907 AGAGAATTTTGTTGCTAAACCACC 58.157 37.500 0.00 0.00 35.25 4.61
489 527 7.657336 AGTCCGCATTGAAATCTTTAGAAAAA 58.343 30.769 0.00 0.00 0.00 1.94
490 528 7.214467 AGTCCGCATTGAAATCTTTAGAAAA 57.786 32.000 0.00 0.00 0.00 2.29
491 529 6.817765 AGTCCGCATTGAAATCTTTAGAAA 57.182 33.333 0.00 0.00 0.00 2.52
497 552 5.234329 CGTATGTAGTCCGCATTGAAATCTT 59.766 40.000 0.00 0.00 0.00 2.40
499 555 4.084537 CCGTATGTAGTCCGCATTGAAATC 60.085 45.833 0.00 0.00 0.00 2.17
508 564 0.937304 TACGTCCGTATGTAGTCCGC 59.063 55.000 0.00 0.00 0.00 5.54
588 1180 8.768501 ATTCCAATACAGACTACATACAGAGA 57.231 34.615 0.00 0.00 0.00 3.10
745 1368 8.891671 TTTTTCTCTGAAATCCAGGATTTTTG 57.108 30.769 25.57 20.23 41.56 2.44
839 1479 1.790755 TGACTCCCGTCGTCATTTTG 58.209 50.000 0.00 0.00 43.21 2.44
850 1490 3.173668 TCCACGATATTTTGACTCCCG 57.826 47.619 0.00 0.00 0.00 5.14
871 1511 2.260434 GCCCTACGCACGAGTGAA 59.740 61.111 7.50 0.00 37.47 3.18
1091 1737 2.697761 GCATGGCACCTGAGCTGTG 61.698 63.158 0.00 0.00 36.79 3.66
1187 1833 2.325082 CCGAAGTTGAAGGGCGTGG 61.325 63.158 0.00 0.00 0.00 4.94
2082 2728 4.735132 ATGACCACGTCGGCGGTG 62.735 66.667 16.39 9.76 43.45 4.94
2634 3280 3.615937 CACATTCTGGTCAGTCTTCATCG 59.384 47.826 0.00 0.00 0.00 3.84
2671 3317 1.185618 TGCGGAGTACAGAGCCACTT 61.186 55.000 0.00 0.00 0.00 3.16
2673 3319 0.807667 CATGCGGAGTACAGAGCCAC 60.808 60.000 0.00 0.00 0.00 5.01
2720 3367 0.817229 TGCAATTGCCACGACACAGA 60.817 50.000 26.94 1.64 41.18 3.41
2746 3393 7.770801 ACTTAAGACCTGCAAAAATTCAAAC 57.229 32.000 10.09 0.00 0.00 2.93
2748 3395 7.821846 ACAAACTTAAGACCTGCAAAAATTCAA 59.178 29.630 10.09 0.00 0.00 2.69
2775 3422 4.577246 CGCTAGCCGCTCAGGGAC 62.577 72.222 9.66 0.00 41.48 4.46
2778 3425 2.583593 GAACGCTAGCCGCTCAGG 60.584 66.667 9.66 0.00 41.76 3.86
2818 3466 4.287238 TGACTCAAGAAAAAGGTTTCGC 57.713 40.909 0.00 0.00 46.56 4.70
2852 3500 5.938125 GCCTGACTTGTCAACCTTTCTTATA 59.062 40.000 4.95 0.00 0.00 0.98
2853 3501 4.762251 GCCTGACTTGTCAACCTTTCTTAT 59.238 41.667 4.95 0.00 0.00 1.73
2906 3554 6.400727 GCTTGAAAAATGCAATTCACTAGCAG 60.401 38.462 20.57 13.43 42.14 4.24
2912 3560 4.992951 AGGAGCTTGAAAAATGCAATTCAC 59.007 37.500 11.18 3.65 33.67 3.18
2940 3589 6.880484 TGTAACTAATAGAAATGCTCCCGAA 58.120 36.000 0.00 0.00 0.00 4.30
2986 3639 5.071250 ACAACTAACACTACCTCCACATGAA 59.929 40.000 0.00 0.00 0.00 2.57
2987 3640 4.591498 ACAACTAACACTACCTCCACATGA 59.409 41.667 0.00 0.00 0.00 3.07
2988 3641 4.690748 CACAACTAACACTACCTCCACATG 59.309 45.833 0.00 0.00 0.00 3.21
2989 3642 4.347000 ACACAACTAACACTACCTCCACAT 59.653 41.667 0.00 0.00 0.00 3.21
2990 3643 3.707611 ACACAACTAACACTACCTCCACA 59.292 43.478 0.00 0.00 0.00 4.17
2991 3644 4.332428 ACACAACTAACACTACCTCCAC 57.668 45.455 0.00 0.00 0.00 4.02
2992 3645 5.010314 CAGTACACAACTAACACTACCTCCA 59.990 44.000 0.00 0.00 35.76 3.86
2993 3646 5.242393 TCAGTACACAACTAACACTACCTCC 59.758 44.000 0.00 0.00 35.76 4.30
2995 3648 5.278169 CGTCAGTACACAACTAACACTACCT 60.278 44.000 0.00 0.00 35.76 3.08
2996 3649 4.913924 CGTCAGTACACAACTAACACTACC 59.086 45.833 0.00 0.00 35.76 3.18
3002 3655 3.488310 CACACCGTCAGTACACAACTAAC 59.512 47.826 0.00 0.00 35.76 2.34
3022 3675 2.126346 GCAATGCGCAGGTTCCAC 60.126 61.111 18.32 0.00 41.79 4.02
3035 3688 5.048504 ACATCGTTGACTCAAAATCAGCAAT 60.049 36.000 0.00 0.00 0.00 3.56
3056 3709 6.461231 GCCGGTTGACTTCTATCTAGTTACAT 60.461 42.308 1.90 0.00 0.00 2.29
3060 3713 3.767673 TGCCGGTTGACTTCTATCTAGTT 59.232 43.478 1.90 0.00 0.00 2.24
3079 3732 1.745653 GTCCAAGCTAGGAATGTTGCC 59.254 52.381 0.00 0.00 39.92 4.52
3107 4113 2.624838 ACTTGGTTCCAGATGCAAGTTG 59.375 45.455 0.00 0.00 29.82 3.16
3162 4169 4.491676 TCGTTGTAGCCAAGATTACACTC 58.508 43.478 0.00 0.00 30.03 3.51
3185 4192 4.558898 GCAGCTAGCTACCGTACAACATAT 60.559 45.833 18.86 0.00 41.15 1.78
3188 4195 1.135199 GCAGCTAGCTACCGTACAACA 60.135 52.381 18.86 0.00 41.15 3.33
3189 4196 1.557651 GCAGCTAGCTACCGTACAAC 58.442 55.000 18.86 0.00 41.15 3.32
3217 4231 3.453717 AGCATCAGACTAGCAAATCCTGA 59.546 43.478 0.00 0.00 38.12 3.86
3249 4263 5.362556 TGTCAAAGCAAATAACTGAGAGC 57.637 39.130 0.00 0.00 0.00 4.09
3250 4264 9.713740 GAATATGTCAAAGCAAATAACTGAGAG 57.286 33.333 0.00 0.00 0.00 3.20
3251 4265 9.230122 TGAATATGTCAAAGCAAATAACTGAGA 57.770 29.630 0.00 0.00 31.51 3.27
3252 4266 9.844790 TTGAATATGTCAAAGCAAATAACTGAG 57.155 29.630 0.00 0.00 43.43 3.35
3255 4269 7.485913 CGCTTGAATATGTCAAAGCAAATAACT 59.514 33.333 7.00 0.00 45.67 2.24
3257 4271 6.253298 GCGCTTGAATATGTCAAAGCAAATAA 59.747 34.615 0.00 0.00 45.67 1.40
3259 4273 4.563976 GCGCTTGAATATGTCAAAGCAAAT 59.436 37.500 0.00 0.00 45.67 2.32
3261 4275 3.191162 AGCGCTTGAATATGTCAAAGCAA 59.809 39.130 2.64 0.00 45.67 3.91
3262 4276 2.749076 AGCGCTTGAATATGTCAAAGCA 59.251 40.909 2.64 0.00 45.67 3.91
3279 4334 0.919981 CGAGATTTCAGAGACAGCGC 59.080 55.000 0.00 0.00 0.00 5.92
3280 4335 1.135257 ACCGAGATTTCAGAGACAGCG 60.135 52.381 0.00 0.00 0.00 5.18
3282 4337 3.948473 TCCTACCGAGATTTCAGAGACAG 59.052 47.826 0.00 0.00 0.00 3.51
3360 4423 6.152831 GTCAGGGAAGCCATAACACTAAAAAT 59.847 38.462 0.00 0.00 0.00 1.82
3414 4480 4.301072 TTTAACAGGGTAGAGCAGCATT 57.699 40.909 0.00 0.00 0.00 3.56
3436 4505 6.969828 TTTGTTGTACGTGCATGTATATGA 57.030 33.333 21.19 6.19 36.36 2.15
3440 4509 5.641636 TCAGATTTGTTGTACGTGCATGTAT 59.358 36.000 21.19 5.02 0.00 2.29
3450 4519 6.861065 TTTGAGAGGTCAGATTTGTTGTAC 57.139 37.500 0.00 0.00 32.98 2.90
3451 4520 6.072508 GCATTTGAGAGGTCAGATTTGTTGTA 60.073 38.462 0.00 0.00 32.98 2.41
3455 4524 3.438087 CGCATTTGAGAGGTCAGATTTGT 59.562 43.478 0.00 0.00 32.98 2.83
3483 4552 1.544691 GGTCACTGTCTATGGACACGT 59.455 52.381 7.97 7.97 46.19 4.49
3491 4563 1.961180 GCTGCCCGGTCACTGTCTAT 61.961 60.000 0.00 0.00 0.00 1.98
3493 4565 4.008933 GCTGCCCGGTCACTGTCT 62.009 66.667 0.00 0.00 0.00 3.41
3524 4596 6.497640 ACTATGAGGTATCCAGATGCAGATA 58.502 40.000 0.00 0.00 0.00 1.98
3525 4597 5.340322 ACTATGAGGTATCCAGATGCAGAT 58.660 41.667 0.00 0.00 0.00 2.90
3529 4601 5.474578 TGAACTATGAGGTATCCAGATGC 57.525 43.478 0.00 0.00 0.00 3.91
3530 4602 7.038445 AGGATTGAACTATGAGGTATCCAGATG 60.038 40.741 0.00 0.00 34.02 2.90
3546 4618 8.897752 GCTCTGTATGATTTTAAGGATTGAACT 58.102 33.333 0.00 0.00 0.00 3.01
3562 4634 5.617529 CGTTTCTTTTGCATGCTCTGTATGA 60.618 40.000 20.33 5.33 0.00 2.15
3569 4641 1.063031 GGCGTTTCTTTTGCATGCTC 58.937 50.000 20.33 0.00 0.00 4.26
3598 4670 9.473640 CGACTAGTAGTGTAGTTGATCTATGTA 57.526 37.037 7.76 0.00 36.77 2.29
3599 4671 7.986320 ACGACTAGTAGTGTAGTTGATCTATGT 59.014 37.037 7.76 0.00 37.71 2.29
3600 4672 8.367943 ACGACTAGTAGTGTAGTTGATCTATG 57.632 38.462 7.76 0.00 37.71 2.23
3601 4673 7.656948 GGACGACTAGTAGTGTAGTTGATCTAT 59.343 40.741 13.78 0.00 37.71 1.98
3602 4674 6.983307 GGACGACTAGTAGTGTAGTTGATCTA 59.017 42.308 13.78 0.00 37.71 1.98
3603 4675 5.816777 GGACGACTAGTAGTGTAGTTGATCT 59.183 44.000 13.78 0.00 37.71 2.75
3604 4676 5.816777 AGGACGACTAGTAGTGTAGTTGATC 59.183 44.000 13.78 0.00 37.71 2.92
3605 4677 5.743117 AGGACGACTAGTAGTGTAGTTGAT 58.257 41.667 13.78 0.00 37.71 2.57
3606 4678 5.157940 AGGACGACTAGTAGTGTAGTTGA 57.842 43.478 13.78 0.00 37.71 3.18
3607 4679 5.391736 CCAAGGACGACTAGTAGTGTAGTTG 60.392 48.000 13.78 10.30 39.49 3.16
3608 4680 4.699257 CCAAGGACGACTAGTAGTGTAGTT 59.301 45.833 13.78 0.00 33.18 2.24
3609 4681 4.019860 TCCAAGGACGACTAGTAGTGTAGT 60.020 45.833 13.78 5.01 35.88 2.73
3610 4682 4.511527 TCCAAGGACGACTAGTAGTGTAG 58.488 47.826 13.78 1.65 0.00 2.74
3611 4683 4.223700 TCTCCAAGGACGACTAGTAGTGTA 59.776 45.833 13.78 0.00 0.00 2.90
3612 4684 3.008813 TCTCCAAGGACGACTAGTAGTGT 59.991 47.826 13.78 6.33 0.00 3.55
3613 4685 3.607741 TCTCCAAGGACGACTAGTAGTG 58.392 50.000 13.78 3.03 0.00 2.74
3614 4686 3.996921 TCTCCAAGGACGACTAGTAGT 57.003 47.619 8.51 8.51 0.00 2.73
3615 4687 4.200874 ACATCTCCAAGGACGACTAGTAG 58.799 47.826 0.00 0.00 0.00 2.57
3616 4688 4.197750 GACATCTCCAAGGACGACTAGTA 58.802 47.826 0.00 0.00 0.00 1.82
3617 4689 3.018149 GACATCTCCAAGGACGACTAGT 58.982 50.000 0.00 0.00 0.00 2.57
3618 4690 2.359531 GGACATCTCCAAGGACGACTAG 59.640 54.545 0.00 0.00 36.42 2.57
3619 4691 2.291346 TGGACATCTCCAAGGACGACTA 60.291 50.000 0.00 0.00 44.26 2.59
3620 4692 1.187087 GGACATCTCCAAGGACGACT 58.813 55.000 0.00 0.00 36.42 4.18
3621 4693 0.895530 TGGACATCTCCAAGGACGAC 59.104 55.000 0.00 0.00 44.26 4.34
3622 4694 3.374318 TGGACATCTCCAAGGACGA 57.626 52.632 0.00 0.00 44.26 4.20


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

AutoCloner maintained by Alex Coulton.