Multiple sequence alignment - TraesCS3A01G426200

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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 TraesCS3A01G426200 chr3A 100.000 4039 0 0 1 4039 669522947 669526985 0.000000e+00 7459.0
1 TraesCS3A01G426200 chr3A 89.667 571 56 2 2481 3048 669564339 669564909 0.000000e+00 725.0
2 TraesCS3A01G426200 chr3A 82.520 738 110 12 1498 2223 669563493 669564223 7.370000e-177 630.0
3 TraesCS3A01G426200 chr3A 78.095 525 89 22 2523 3030 667950741 667951256 3.920000e-80 309.0
4 TraesCS3A01G426200 chr3A 82.456 228 32 4 377 601 202823202 202823424 4.120000e-45 193.0
5 TraesCS3A01G426200 chr3A 74.686 478 93 20 1578 2032 668818155 668818627 1.920000e-43 187.0
6 TraesCS3A01G426200 chr3A 83.942 137 17 5 1578 1711 668867880 668868014 4.240000e-25 126.0
7 TraesCS3A01G426200 chr3A 83.942 137 17 5 1578 1711 669054042 669054176 4.240000e-25 126.0
8 TraesCS3A01G426200 chr3A 83.212 137 18 5 1578 1711 668924785 668924919 1.970000e-23 121.0
9 TraesCS3A01G426200 chr3B 94.045 3342 170 17 716 4039 705545945 705549275 0.000000e+00 5042.0
10 TraesCS3A01G426200 chr3B 90.909 902 75 6 2152 3048 705564240 705565139 0.000000e+00 1205.0
11 TraesCS3A01G426200 chr3B 80.707 933 160 14 1498 2418 705566540 705567464 0.000000e+00 708.0
12 TraesCS3A01G426200 chr3B 85.185 594 64 7 1 574 705545265 705545854 4.500000e-164 588.0
13 TraesCS3A01G426200 chr3B 82.581 620 95 11 1498 2108 705563625 705564240 5.940000e-148 534.0
14 TraesCS3A01G426200 chr3B 76.953 512 101 12 2551 3048 705154454 705154962 3.980000e-70 276.0
15 TraesCS3A01G426200 chr3B 85.333 75 11 0 3296 3370 74456325 74456251 1.200000e-10 78.7
16 TraesCS3A01G426200 chr3D 91.185 2144 113 38 1 2097 533667528 533669642 0.000000e+00 2843.0
17 TraesCS3A01G426200 chr3D 96.853 1144 34 2 2158 3300 533669641 533670783 0.000000e+00 1912.0
18 TraesCS3A01G426200 chr3D 93.074 592 35 2 3332 3923 533671046 533671631 0.000000e+00 861.0
19 TraesCS3A01G426200 chr3D 82.291 943 135 21 1498 2418 533673609 533674541 0.000000e+00 787.0
20 TraesCS3A01G426200 chr3D 91.594 571 44 3 2481 3048 533674538 533675107 0.000000e+00 785.0
21 TraesCS3A01G426200 chr3D 81.175 919 150 18 1498 2404 533676509 533677416 0.000000e+00 717.0
22 TraesCS3A01G426200 chr3D 78.320 512 91 13 2551 3048 532956668 532957173 3.030000e-81 313.0
23 TraesCS3A01G426200 chr3D 78.161 522 89 19 2524 3030 532776989 532777500 3.920000e-80 309.0
24 TraesCS3A01G426200 chr3D 78.780 410 75 9 1739 2142 532955972 532956375 8.610000e-67 265.0
25 TraesCS3A01G426200 chr3D 76.812 483 87 16 1578 2038 532992014 532992493 8.670000e-62 248.0
26 TraesCS3A01G426200 chr3D 75.891 477 90 16 1578 2032 533393251 533393724 1.890000e-53 220.0
27 TraesCS3A01G426200 chr3D 75.652 460 85 18 1578 2014 533375481 533375936 1.900000e-48 204.0
28 TraesCS3A01G426200 chr3D 93.939 132 8 0 3908 4039 533671644 533671775 2.460000e-47 200.0
29 TraesCS3A01G426200 chr3D 85.052 194 26 2 382 573 500665982 500665790 1.150000e-45 195.0
30 TraesCS3A01G426200 chr3D 87.342 79 2 5 2412 2486 533669968 533669894 2.590000e-12 84.2
31 TraesCS3A01G426200 chr6A 81.509 411 67 6 1740 2144 75906703 75907110 3.010000e-86 329.0
32 TraesCS3A01G426200 chr6A 85.281 231 26 5 375 602 262056494 262056719 8.730000e-57 231.0
33 TraesCS3A01G426200 chr2A 82.051 234 30 9 375 605 374592063 374592287 5.330000e-44 189.0
34 TraesCS3A01G426200 chr2D 85.326 184 23 4 381 563 552068323 552068143 1.920000e-43 187.0
35 TraesCS3A01G426200 chr7B 80.889 225 37 6 379 602 96806434 96806215 5.370000e-39 172.0
36 TraesCS3A01G426200 chr5D 80.435 230 40 5 375 602 277065229 277065455 1.930000e-38 171.0
37 TraesCS3A01G426200 chr4A 80.258 233 41 5 371 602 708677221 708676993 1.930000e-38 171.0
38 TraesCS3A01G426200 chr2B 86.585 82 5 4 2409 2485 6259493 6259573 7.190000e-13 86.1
39 TraesCS3A01G426200 chr2B 87.671 73 5 2 2414 2482 551568428 551568356 9.300000e-12 82.4
40 TraesCS3A01G426200 chr1B 87.013 77 7 2 2415 2491 98724197 98724124 2.590000e-12 84.2
41 TraesCS3A01G426200 chr1B 85.542 83 8 4 2411 2492 338014835 338014756 2.590000e-12 84.2
42 TraesCS3A01G426200 chr4B 83.333 72 10 1 2415 2486 640002163 640002232 9.370000e-07 65.8


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 TraesCS3A01G426200 chr3A 669522947 669526985 4038 False 7459.000000 7459 100.000000 1 4039 1 chr3A.!!$F7 4038
1 TraesCS3A01G426200 chr3A 669563493 669564909 1416 False 677.500000 725 86.093500 1498 3048 2 chr3A.!!$F8 1550
2 TraesCS3A01G426200 chr3A 667950741 667951256 515 False 309.000000 309 78.095000 2523 3030 1 chr3A.!!$F2 507
3 TraesCS3A01G426200 chr3B 705545265 705549275 4010 False 2815.000000 5042 89.615000 1 4039 2 chr3B.!!$F2 4038
4 TraesCS3A01G426200 chr3B 705563625 705567464 3839 False 815.666667 1205 84.732333 1498 3048 3 chr3B.!!$F3 1550
5 TraesCS3A01G426200 chr3B 705154454 705154962 508 False 276.000000 276 76.953000 2551 3048 1 chr3B.!!$F1 497
6 TraesCS3A01G426200 chr3D 533667528 533677416 9888 False 1157.857143 2843 90.015857 1 4039 7 chr3D.!!$F6 4038
7 TraesCS3A01G426200 chr3D 532776989 532777500 511 False 309.000000 309 78.161000 2524 3030 1 chr3D.!!$F1 506
8 TraesCS3A01G426200 chr3D 532955972 532957173 1201 False 289.000000 313 78.550000 1739 3048 2 chr3D.!!$F5 1309

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
209 214 0.392706 TATCACCCCACGCATAGCAG 59.607 55.0 0.0 0.0 0.00 4.24 F
698 787 0.675522 ATGGGGACGTTGTAAAGGCG 60.676 55.0 0.0 0.0 34.48 5.52 F
1445 1547 0.745845 GCTGATGATGCCTGACGGTT 60.746 55.0 0.0 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 1476 0.539986 GAGGATCTAAACGCACCCCA 59.460 55.0 0.00 0.0 0.0 4.96 R
2670 7397 0.242825 CCATGAGGTTGTTGCTGCTG 59.757 55.0 0.00 0.0 0.0 4.41 R
3073 7868 0.396139 ATCTGATTTGCGGCACCCAT 60.396 50.0 0.05 0.0 0.0 4.00 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
162 167 1.479709 ACCCTTGAGACGAGATCCAG 58.520 55.000 0.00 0.00 0.00 3.86
166 171 3.133721 CCCTTGAGACGAGATCCAGAAAT 59.866 47.826 0.00 0.00 0.00 2.17
167 172 4.383552 CCCTTGAGACGAGATCCAGAAATT 60.384 45.833 0.00 0.00 0.00 1.82
201 206 3.337694 TGGTTAAAGTATCACCCCACG 57.662 47.619 0.00 0.00 0.00 4.94
206 211 2.910688 AAGTATCACCCCACGCATAG 57.089 50.000 0.00 0.00 0.00 2.23
209 214 0.392706 TATCACCCCACGCATAGCAG 59.607 55.000 0.00 0.00 0.00 4.24
270 275 1.363443 CACCATGCCACACAACACC 59.637 57.895 0.00 0.00 0.00 4.16
274 279 0.947960 CATGCCACACAACACCGTTA 59.052 50.000 0.00 0.00 0.00 3.18
363 369 8.474025 TCTTTAAAAGACACACCATGAAACAAT 58.526 29.630 0.00 0.00 31.20 2.71
367 373 7.581213 AAAGACACACCATGAAACAATCTTA 57.419 32.000 0.00 0.00 0.00 2.10
368 374 6.560253 AGACACACCATGAAACAATCTTAC 57.440 37.500 0.00 0.00 0.00 2.34
371 377 4.766891 CACACCATGAAACAATCTTACCCT 59.233 41.667 0.00 0.00 0.00 4.34
372 378 5.243730 CACACCATGAAACAATCTTACCCTT 59.756 40.000 0.00 0.00 0.00 3.95
403 426 1.202806 GGCCAATGCATAGCTACAGGA 60.203 52.381 18.16 0.00 40.13 3.86
408 431 5.737860 CCAATGCATAGCTACAGGATGATA 58.262 41.667 0.00 0.00 39.69 2.15
409 432 5.583854 CCAATGCATAGCTACAGGATGATAC 59.416 44.000 0.00 0.00 39.69 2.24
429 452 1.544093 CCTCGCATGCCATGTAGGATT 60.544 52.381 18.19 0.00 41.22 3.01
430 453 2.289631 CCTCGCATGCCATGTAGGATTA 60.290 50.000 18.19 0.00 41.22 1.75
443 466 7.041508 GCCATGTAGGATTAGATGTCAGAAAAG 60.042 40.741 0.00 0.00 41.22 2.27
447 470 9.042450 TGTAGGATTAGATGTCAGAAAAGGTAA 57.958 33.333 0.00 0.00 0.00 2.85
455 478 7.931275 AGATGTCAGAAAAGGTAAGTTCAAAC 58.069 34.615 0.00 0.00 0.00 2.93
462 485 3.581265 AGGTAAGTTCAAACGGGGAAA 57.419 42.857 0.00 0.00 0.00 3.13
530 553 4.035909 GTCCGGTGTAAAAAGCTGAAAAGA 59.964 41.667 0.00 0.00 0.00 2.52
543 566 5.002516 AGCTGAAAAGATTGAAGTGGAGAG 58.997 41.667 0.00 0.00 0.00 3.20
606 695 5.006386 CCTTAATGAGACCCATTAGATGCC 58.994 45.833 0.00 0.00 45.46 4.40
637 726 6.515272 TTTTTCTCAAAGGGCATCTGTATC 57.485 37.500 0.00 0.00 0.00 2.24
638 727 3.845781 TCTCAAAGGGCATCTGTATCC 57.154 47.619 0.00 0.00 0.00 2.59
639 728 3.114606 TCTCAAAGGGCATCTGTATCCA 58.885 45.455 0.00 0.00 0.00 3.41
640 729 3.118261 TCTCAAAGGGCATCTGTATCCAC 60.118 47.826 0.00 0.00 0.00 4.02
641 730 2.575735 TCAAAGGGCATCTGTATCCACA 59.424 45.455 0.00 0.00 0.00 4.17
642 731 3.202818 TCAAAGGGCATCTGTATCCACAT 59.797 43.478 0.00 0.00 33.14 3.21
643 732 3.956199 CAAAGGGCATCTGTATCCACATT 59.044 43.478 0.00 0.00 33.14 2.71
644 733 3.219176 AGGGCATCTGTATCCACATTG 57.781 47.619 0.00 0.00 33.14 2.82
645 734 1.610522 GGGCATCTGTATCCACATTGC 59.389 52.381 4.96 4.96 40.41 3.56
647 736 2.300433 GCATCTGTATCCACATTGCCA 58.700 47.619 0.00 0.00 37.56 4.92
648 737 2.033801 GCATCTGTATCCACATTGCCAC 59.966 50.000 0.00 0.00 37.56 5.01
649 738 2.418368 TCTGTATCCACATTGCCACC 57.582 50.000 0.00 0.00 33.14 4.61
650 739 1.915489 TCTGTATCCACATTGCCACCT 59.085 47.619 0.00 0.00 33.14 4.00
651 740 2.308570 TCTGTATCCACATTGCCACCTT 59.691 45.455 0.00 0.00 33.14 3.50
652 741 3.521531 TCTGTATCCACATTGCCACCTTA 59.478 43.478 0.00 0.00 33.14 2.69
653 742 3.879295 CTGTATCCACATTGCCACCTTAG 59.121 47.826 0.00 0.00 33.14 2.18
654 743 3.265737 TGTATCCACATTGCCACCTTAGT 59.734 43.478 0.00 0.00 0.00 2.24
655 744 2.969821 TCCACATTGCCACCTTAGTT 57.030 45.000 0.00 0.00 0.00 2.24
656 745 3.237268 TCCACATTGCCACCTTAGTTT 57.763 42.857 0.00 0.00 0.00 2.66
657 746 3.571590 TCCACATTGCCACCTTAGTTTT 58.428 40.909 0.00 0.00 0.00 2.43
658 747 3.572255 TCCACATTGCCACCTTAGTTTTC 59.428 43.478 0.00 0.00 0.00 2.29
659 748 3.320541 CCACATTGCCACCTTAGTTTTCA 59.679 43.478 0.00 0.00 0.00 2.69
660 749 4.021192 CCACATTGCCACCTTAGTTTTCAT 60.021 41.667 0.00 0.00 0.00 2.57
661 750 4.925054 CACATTGCCACCTTAGTTTTCATG 59.075 41.667 0.00 0.00 0.00 3.07
662 751 3.658757 TTGCCACCTTAGTTTTCATGC 57.341 42.857 0.00 0.00 0.00 4.06
663 752 1.892474 TGCCACCTTAGTTTTCATGCC 59.108 47.619 0.00 0.00 0.00 4.40
698 787 0.675522 ATGGGGACGTTGTAAAGGCG 60.676 55.000 0.00 0.00 34.48 5.52
699 788 1.004679 GGGGACGTTGTAAAGGCGA 60.005 57.895 0.00 0.00 34.48 5.54
700 789 1.293963 GGGGACGTTGTAAAGGCGAC 61.294 60.000 0.00 0.00 34.48 5.19
711 806 1.797025 AAAGGCGACGGAGAAAGAAG 58.203 50.000 0.00 0.00 0.00 2.85
754 854 4.134563 TCGTCAAAAAGAGAGAAAAGGGG 58.865 43.478 0.00 0.00 0.00 4.79
781 881 3.902112 CTGGCCCACCACCCAGTT 61.902 66.667 0.00 0.00 42.67 3.16
826 926 2.214235 GGGTAGTCCGCCATTGGTA 58.786 57.895 4.26 0.00 33.83 3.25
828 928 1.474498 GGGTAGTCCGCCATTGGTAAG 60.474 57.143 4.26 0.00 33.83 2.34
829 929 1.208776 GGTAGTCCGCCATTGGTAAGT 59.791 52.381 4.26 0.00 0.00 2.24
830 930 2.547826 GTAGTCCGCCATTGGTAAGTC 58.452 52.381 4.26 0.00 0.00 3.01
835 935 1.694856 GCCATTGGTAAGTCCCCCA 59.305 57.895 4.26 0.00 34.77 4.96
920 1021 1.705873 CTCCTACTATTGGGTCGGCT 58.294 55.000 0.00 0.00 0.00 5.52
1104 1206 1.595357 GGTCGATCCCCAGTTCGTT 59.405 57.895 0.00 0.00 36.72 3.85
1114 1216 1.006086 CCAGTTCGTTATGATGCGCA 58.994 50.000 14.96 14.96 0.00 6.09
1251 1353 2.336945 TCAGGCATCATGCTTACTGG 57.663 50.000 10.11 0.00 44.28 4.00
1252 1354 1.839354 TCAGGCATCATGCTTACTGGA 59.161 47.619 10.11 0.00 44.28 3.86
1295 1397 8.755696 TCACAAAATTATAAGCAAAAGCGATT 57.244 26.923 0.00 0.00 0.00 3.34
1296 1398 8.646356 TCACAAAATTATAAGCAAAAGCGATTG 58.354 29.630 0.00 0.71 0.00 2.67
1311 1413 2.158449 GCGATTGTAGATATGGTGCTGC 59.842 50.000 0.00 0.00 0.00 5.25
1320 1422 4.202441 AGATATGGTGCTGCTCGAAATTT 58.798 39.130 0.00 0.00 0.00 1.82
1321 1423 4.641989 AGATATGGTGCTGCTCGAAATTTT 59.358 37.500 0.00 0.00 0.00 1.82
1322 1424 5.822519 AGATATGGTGCTGCTCGAAATTTTA 59.177 36.000 0.00 0.00 0.00 1.52
1323 1425 3.829886 TGGTGCTGCTCGAAATTTTAG 57.170 42.857 0.00 0.00 0.00 1.85
1374 1476 4.701765 TGCATACACATTTGGCAACTTTT 58.298 34.783 0.00 0.00 37.61 2.27
1398 1500 3.335579 GGTGCGTTTAGATCCTCTGTTT 58.664 45.455 0.00 0.00 0.00 2.83
1399 1501 3.125316 GGTGCGTTTAGATCCTCTGTTTG 59.875 47.826 0.00 0.00 0.00 2.93
1401 1503 2.096013 GCGTTTAGATCCTCTGTTTGGC 59.904 50.000 0.00 0.00 0.00 4.52
1445 1547 0.745845 GCTGATGATGCCTGACGGTT 60.746 55.000 0.00 0.00 0.00 4.44
1446 1548 1.293924 CTGATGATGCCTGACGGTTC 58.706 55.000 0.00 0.00 0.00 3.62
1463 1565 4.092968 ACGGTTCGAGTTTGATATGAAAGC 59.907 41.667 0.00 0.00 0.00 3.51
1574 1679 1.632965 ATTGGCGGAGGAGGTTACCC 61.633 60.000 0.00 0.00 0.00 3.69
1900 2031 3.837731 TGATTCTGACACCTGGTATCACA 59.162 43.478 3.12 0.00 0.00 3.58
2440 2592 6.214412 ACTCCCTCTGTCTCAAAATGTAAGAT 59.786 38.462 0.00 0.00 0.00 2.40
2586 7313 6.518208 ACTAACTTGGTTTGTGTTGCTTTA 57.482 33.333 0.00 0.00 31.24 1.85
2660 7387 5.396772 GGATGAACCCTACACATCAAGATCA 60.397 44.000 0.00 0.00 41.17 2.92
2670 7397 0.842635 ATCAAGATCACCCCAGAGCC 59.157 55.000 0.00 0.00 0.00 4.70
2671 7398 0.547471 TCAAGATCACCCCAGAGCCA 60.547 55.000 0.00 0.00 0.00 4.75
2675 7402 2.605854 GATCACCCCAGAGCCAGCAG 62.606 65.000 0.00 0.00 0.00 4.24
2686 7413 2.195567 GCCAGCAGCAACAACCTCA 61.196 57.895 0.00 0.00 42.97 3.86
2689 7416 0.242825 CAGCAGCAACAACCTCATGG 59.757 55.000 0.00 0.00 39.83 3.66
3073 7868 7.565768 ACCCTGTTTTATTTTCTCTTTTACCCA 59.434 33.333 0.00 0.00 0.00 4.51
3074 7869 8.593679 CCCTGTTTTATTTTCTCTTTTACCCAT 58.406 33.333 0.00 0.00 0.00 4.00
3127 7922 5.649395 CAGAAGCAGGTTTGATTAAGGATGA 59.351 40.000 0.00 0.00 32.04 2.92
3146 7941 6.506770 AGGATGACATTAACAGGGATATGGAT 59.493 38.462 0.00 0.00 0.00 3.41
3238 8033 3.067106 CGCTGTGAGTTGTATCTTGGTT 58.933 45.455 0.00 0.00 0.00 3.67
3305 8100 7.864686 TCAGAGTTGTTGCATATATATGTTGC 58.135 34.615 21.10 11.33 36.11 4.17
3348 8143 3.243877 GTGTTGTGATATCTACTGCTGCG 59.756 47.826 3.98 0.00 0.00 5.18
3387 8182 7.958974 ATGTTGTCATGTGCACATTGTGTGG 62.959 44.000 29.48 16.92 39.55 4.17
3448 8243 3.948473 GAGGTGCTAGATCTGTACAGTGA 59.052 47.826 21.99 4.97 0.00 3.41
3449 8244 3.697045 AGGTGCTAGATCTGTACAGTGAC 59.303 47.826 21.99 13.94 0.00 3.67
3455 8250 0.818296 ATCTGTACAGTGACGCTCCC 59.182 55.000 21.99 0.00 0.00 4.30
3546 8347 2.027192 GTGGTCATTGCTTAGTCCCTCA 60.027 50.000 0.00 0.00 0.00 3.86
3598 8399 6.636562 TTTTTCTTTTACGGCCATGACTTA 57.363 33.333 2.24 0.00 0.00 2.24
3618 8419 3.090765 CCCTTTGGACCTCCTGGG 58.909 66.667 0.00 0.00 41.89 4.45
3703 8504 3.597255 CATTTATGTTGCAATGGTGGCA 58.403 40.909 0.59 0.00 40.00 4.92
3735 8536 1.322442 TGAGATGCTCGATGATCGGT 58.678 50.000 15.48 0.00 40.88 4.69
3822 9678 0.032615 TTCTTTGGTTGTGCCCCTGT 60.033 50.000 0.00 0.00 36.04 4.00
3912 9768 2.373169 TCTTGAAGATGGCACCAAGAGT 59.627 45.455 15.05 0.00 39.76 3.24
3946 9803 2.550978 GATGGGTCGAACATGGTGTAG 58.449 52.381 1.31 0.00 0.00 2.74
3989 9846 1.553706 AGCCTCAAGCCTTGGATTTG 58.446 50.000 4.30 0.00 45.47 2.32
4005 9862 5.891198 TGGATTTGAGGAGGAAATGAAAGA 58.109 37.500 0.00 0.00 0.00 2.52
4006 9863 6.496743 TGGATTTGAGGAGGAAATGAAAGAT 58.503 36.000 0.00 0.00 0.00 2.40
4016 9873 6.892456 GGAGGAAATGAAAGATTAGGAGGTTT 59.108 38.462 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.406539 GCGTACAATCGAAGGAGGGTA 59.593 52.381 0.00 0.00 0.00 3.69
21 22 0.175073 GCGTACAATCGAAGGAGGGT 59.825 55.000 0.00 0.00 0.00 4.34
181 186 2.616001 GCGTGGGGTGATACTTTAACCA 60.616 50.000 0.00 0.00 35.56 3.67
209 214 3.081061 TGGTGGTGATGTATTGCAAGAC 58.919 45.455 17.19 17.19 0.00 3.01
217 222 2.433604 CTCTGAGCTGGTGGTGATGTAT 59.566 50.000 0.00 0.00 0.00 2.29
270 275 6.018588 TGGCTATTGGTATGACGATTTTAACG 60.019 38.462 0.00 0.00 0.00 3.18
274 279 4.275936 GCTGGCTATTGGTATGACGATTTT 59.724 41.667 0.00 0.00 0.00 1.82
397 420 2.029020 GCATGCGAGGTATCATCCTGTA 60.029 50.000 0.00 0.00 38.02 2.74
403 426 1.072806 ACATGGCATGCGAGGTATCAT 59.927 47.619 26.70 7.83 0.00 2.45
408 431 1.146930 CCTACATGGCATGCGAGGT 59.853 57.895 28.59 23.05 33.92 3.85
409 432 0.035881 ATCCTACATGGCATGCGAGG 59.964 55.000 30.04 30.04 37.80 4.63
429 452 9.052759 GTTTGAACTTACCTTTTCTGACATCTA 57.947 33.333 0.00 0.00 0.00 1.98
430 453 7.254795 CGTTTGAACTTACCTTTTCTGACATCT 60.255 37.037 0.00 0.00 0.00 2.90
443 466 2.031769 CGTTTCCCCGTTTGAACTTACC 60.032 50.000 0.00 0.00 0.00 2.85
447 470 0.820482 CCCGTTTCCCCGTTTGAACT 60.820 55.000 0.00 0.00 0.00 3.01
455 478 2.064581 AGAGGATCCCGTTTCCCCG 61.065 63.158 8.55 0.00 33.66 5.73
462 485 2.364560 TCCTGCAGAGGATCCCGT 59.635 61.111 17.39 0.00 44.13 5.28
501 524 1.605232 CTTTTTACACCGGACCACACC 59.395 52.381 9.46 0.00 0.00 4.16
530 553 4.713814 TGCATCTCTACTCTCCACTTCAAT 59.286 41.667 0.00 0.00 0.00 2.57
543 566 6.627395 AGACTAGTACACATGCATCTCTAC 57.373 41.667 0.00 0.00 0.00 2.59
584 639 5.624159 TGGCATCTAATGGGTCTCATTAAG 58.376 41.667 6.61 2.07 44.82 1.85
633 722 3.886123 ACTAAGGTGGCAATGTGGATAC 58.114 45.455 0.00 0.00 0.00 2.24
634 723 4.584638 AACTAAGGTGGCAATGTGGATA 57.415 40.909 0.00 0.00 0.00 2.59
635 724 3.456380 AACTAAGGTGGCAATGTGGAT 57.544 42.857 0.00 0.00 0.00 3.41
636 725 2.969821 AACTAAGGTGGCAATGTGGA 57.030 45.000 0.00 0.00 0.00 4.02
637 726 3.320541 TGAAAACTAAGGTGGCAATGTGG 59.679 43.478 0.00 0.00 0.00 4.17
638 727 4.582701 TGAAAACTAAGGTGGCAATGTG 57.417 40.909 0.00 0.00 0.00 3.21
639 728 4.561326 GCATGAAAACTAAGGTGGCAATGT 60.561 41.667 0.00 0.00 0.00 2.71
640 729 3.928375 GCATGAAAACTAAGGTGGCAATG 59.072 43.478 0.00 0.00 0.00 2.82
641 730 3.055891 GGCATGAAAACTAAGGTGGCAAT 60.056 43.478 0.00 0.00 33.04 3.56
642 731 2.298729 GGCATGAAAACTAAGGTGGCAA 59.701 45.455 0.00 0.00 33.04 4.52
643 732 1.892474 GGCATGAAAACTAAGGTGGCA 59.108 47.619 0.00 0.00 33.04 4.92
644 733 2.171003 AGGCATGAAAACTAAGGTGGC 58.829 47.619 0.00 0.00 0.00 5.01
645 734 5.975693 TTTAGGCATGAAAACTAAGGTGG 57.024 39.130 0.00 0.00 0.00 4.61
646 735 5.863935 GCTTTTAGGCATGAAAACTAAGGTG 59.136 40.000 0.00 0.00 0.00 4.00
647 736 5.775195 AGCTTTTAGGCATGAAAACTAAGGT 59.225 36.000 0.00 0.00 34.17 3.50
648 737 6.272822 AGCTTTTAGGCATGAAAACTAAGG 57.727 37.500 0.00 0.00 34.17 2.69
649 738 9.691362 TTTAAGCTTTTAGGCATGAAAACTAAG 57.309 29.630 3.20 0.00 34.17 2.18
652 741 8.956533 TTTTTAAGCTTTTAGGCATGAAAACT 57.043 26.923 3.20 0.00 34.17 2.66
681 770 1.004679 TCGCCTTTACAACGTCCCC 60.005 57.895 0.00 0.00 0.00 4.81
698 787 3.669588 GTCTCGTTTCTTCTTTCTCCGTC 59.330 47.826 0.00 0.00 0.00 4.79
699 788 3.640592 GTCTCGTTTCTTCTTTCTCCGT 58.359 45.455 0.00 0.00 0.00 4.69
700 789 2.657372 CGTCTCGTTTCTTCTTTCTCCG 59.343 50.000 0.00 0.00 0.00 4.63
701 790 2.987821 CCGTCTCGTTTCTTCTTTCTCC 59.012 50.000 0.00 0.00 0.00 3.71
711 806 1.342796 GGAAGCGTCCGTCTCGTTTC 61.343 60.000 1.94 10.36 43.76 2.78
781 881 4.243008 TGCACGAGCGGGGTCAAA 62.243 61.111 0.00 0.00 46.23 2.69
826 926 1.641192 GGAGAAAGGAATGGGGGACTT 59.359 52.381 0.00 0.00 0.00 3.01
828 928 0.259065 GGGAGAAAGGAATGGGGGAC 59.741 60.000 0.00 0.00 0.00 4.46
829 929 0.924226 GGGGAGAAAGGAATGGGGGA 60.924 60.000 0.00 0.00 0.00 4.81
830 930 0.926220 AGGGGAGAAAGGAATGGGGG 60.926 60.000 0.00 0.00 0.00 5.40
835 935 1.371415 AGGGAGAGGGGAGAAAGGAAT 59.629 52.381 0.00 0.00 0.00 3.01
920 1021 3.326385 ATGCCGTGGGGGTAGGAGA 62.326 63.158 0.00 0.00 38.44 3.71
955 1056 3.799672 CCGGCCCGGTAAATCCCA 61.800 66.667 15.86 0.00 42.73 4.37
1114 1216 0.829333 ATCTTGTCTCGGATGCTGCT 59.171 50.000 0.00 0.00 0.00 4.24
1121 1223 1.816835 ACGCTTACATCTTGTCTCGGA 59.183 47.619 0.00 0.00 0.00 4.55
1251 1353 6.758593 TGTGAATGAAACAACGTAGTACTC 57.241 37.500 0.00 0.00 45.00 2.59
1252 1354 7.542534 TTTGTGAATGAAACAACGTAGTACT 57.457 32.000 0.00 0.00 45.00 2.73
1289 1391 3.657634 CAGCACCATATCTACAATCGCT 58.342 45.455 0.00 0.00 0.00 4.93
1295 1397 2.306847 TCGAGCAGCACCATATCTACA 58.693 47.619 0.00 0.00 0.00 2.74
1296 1398 3.371102 TTCGAGCAGCACCATATCTAC 57.629 47.619 0.00 0.00 0.00 2.59
1304 1406 3.492313 CACTAAAATTTCGAGCAGCACC 58.508 45.455 0.00 0.00 0.00 5.01
1311 1413 4.010349 AGGGAAGCCACTAAAATTTCGAG 58.990 43.478 0.00 0.00 0.00 4.04
1349 1451 3.740631 TTGCCAAATGTGTATGCAACA 57.259 38.095 0.00 0.00 37.04 3.33
1374 1476 0.539986 GAGGATCTAAACGCACCCCA 59.460 55.000 0.00 0.00 0.00 4.96
1398 1500 2.172717 GCCTAAATAACCCTCAGAGCCA 59.827 50.000 0.00 0.00 0.00 4.75
1399 1501 2.439880 AGCCTAAATAACCCTCAGAGCC 59.560 50.000 0.00 0.00 0.00 4.70
1401 1503 7.616313 CCTTATAGCCTAAATAACCCTCAGAG 58.384 42.308 0.00 0.00 0.00 3.35
1441 1543 4.092821 TGCTTTCATATCAAACTCGAACCG 59.907 41.667 0.00 0.00 0.00 4.44
1445 1547 5.487433 TCCTTGCTTTCATATCAAACTCGA 58.513 37.500 0.00 0.00 0.00 4.04
1446 1548 5.220739 CCTCCTTGCTTTCATATCAAACTCG 60.221 44.000 0.00 0.00 0.00 4.18
1494 1599 9.407380 TCTGCCAATTCAATAACAAGTATATGT 57.593 29.630 0.00 0.00 34.24 2.29
1639 1744 4.864806 GCCAAAGCTACAAAATAAGAAGGC 59.135 41.667 0.00 0.00 35.50 4.35
1725 1831 6.229936 TGTAGTACTCCGCCTGAATATTTT 57.770 37.500 0.00 0.00 0.00 1.82
1727 1833 5.864418 TTGTAGTACTCCGCCTGAATATT 57.136 39.130 0.00 0.00 0.00 1.28
1900 2031 1.065551 GAAGTTTCACTTGCGCCTTGT 59.934 47.619 4.18 0.00 38.80 3.16
2586 7313 0.627986 CAGGAGCTTCCCCTGGAAAT 59.372 55.000 11.34 0.00 45.66 2.17
2652 7379 0.547471 TGGCTCTGGGGTGATCTTGA 60.547 55.000 0.00 0.00 0.00 3.02
2655 7382 2.373707 GCTGGCTCTGGGGTGATCT 61.374 63.158 0.00 0.00 0.00 2.75
2670 7397 0.242825 CCATGAGGTTGTTGCTGCTG 59.757 55.000 0.00 0.00 0.00 4.41
2671 7398 2.649831 CCATGAGGTTGTTGCTGCT 58.350 52.632 0.00 0.00 0.00 4.24
2686 7413 2.037251 GTGTGTCCACTGTGTCTACCAT 59.963 50.000 7.08 0.00 38.61 3.55
2689 7416 1.687123 AGGTGTGTCCACTGTGTCTAC 59.313 52.381 7.08 2.97 41.53 2.59
2996 7740 1.270412 ACGCGGTGGAAACTGTTCATA 60.270 47.619 12.47 0.00 35.25 2.15
3073 7868 0.396139 ATCTGATTTGCGGCACCCAT 60.396 50.000 0.05 0.00 0.00 4.00
3074 7869 1.001020 ATCTGATTTGCGGCACCCA 60.001 52.632 0.05 0.00 0.00 4.51
3081 7876 5.639757 TGAAATGTTACCATCTGATTTGCG 58.360 37.500 0.00 0.00 0.00 4.85
3127 7922 6.514012 TGACATCCATATCCCTGTTAATGT 57.486 37.500 0.00 0.00 0.00 2.71
3146 7941 7.807977 AGACTCTAAAGAAAAGCAAATGACA 57.192 32.000 0.00 0.00 0.00 3.58
3238 8033 4.523083 GGATACAATACAAGGGTCTTGCA 58.477 43.478 7.48 0.00 35.23 4.08
3305 8100 5.649395 ACACAATTCCATAACAGATCCACAG 59.351 40.000 0.00 0.00 0.00 3.66
3387 8182 2.124695 GACCCGAAGATGCCACCC 60.125 66.667 0.00 0.00 0.00 4.61
3455 8250 1.210155 GCAAAAGTGTAGCGCCCTG 59.790 57.895 2.29 0.00 0.00 4.45
3465 8260 3.184094 CCTCGCAAAGGCAAAAGTG 57.816 52.632 0.00 0.00 38.67 3.16
3536 8337 3.792114 TCCTCCTATCAGTGAGGGACTAA 59.208 47.826 12.05 1.25 46.71 2.24
3577 8378 5.335348 GCTTAAGTCATGGCCGTAAAAGAAA 60.335 40.000 0.00 0.00 0.00 2.52
3596 8397 1.354368 CAGGAGGTCCAAAGGGCTTAA 59.646 52.381 0.00 0.00 38.89 1.85
3598 8399 1.770324 CAGGAGGTCCAAAGGGCTT 59.230 57.895 0.00 0.00 38.89 4.35
3618 8419 2.663879 CGTGAGCAATCACAAGCTTGTC 60.664 50.000 28.97 17.16 42.04 3.18
3735 8536 2.114411 GTTGGAACCGGAAGCCCA 59.886 61.111 9.46 6.62 0.00 5.36
3822 9678 8.809066 TCTGAACAACTAGTATAAAGTAAGCCA 58.191 33.333 0.00 0.00 0.00 4.75
3833 9689 5.187186 ACCGACCAATCTGAACAACTAGTAT 59.813 40.000 0.00 0.00 0.00 2.12
3852 9708 4.150098 CGCCTTTATAGATAAAGCACCGAC 59.850 45.833 14.15 2.05 44.85 4.79
3912 9768 1.302431 CCATCCGCAGTTCCACACA 60.302 57.895 0.00 0.00 0.00 3.72
3913 9769 2.040544 CCCATCCGCAGTTCCACAC 61.041 63.158 0.00 0.00 0.00 3.82
3946 9803 5.560966 TCTTTTCGCCCAAATGTATTCTC 57.439 39.130 0.00 0.00 0.00 2.87
3989 9846 6.126623 ACCTCCTAATCTTTCATTTCCTCCTC 60.127 42.308 0.00 0.00 0.00 3.71
4005 9862 0.394352 CGCCTGCCAAACCTCCTAAT 60.394 55.000 0.00 0.00 0.00 1.73
4006 9863 1.002624 CGCCTGCCAAACCTCCTAA 60.003 57.895 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.