Multiple sequence alignment - TraesCS5B01G414300

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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 TraesCS5B01G414300 chr5B 100.000 3989 0 0 1 3989 588777612 588781600 0.000000e+00 7367
1 TraesCS5B01G414300 chr5B 87.155 1448 146 20 2010 3447 588833735 588835152 0.000000e+00 1607
2 TraesCS5B01G414300 chr5B 84.972 905 87 18 996 1893 588832799 588833661 0.000000e+00 872
3 TraesCS5B01G414300 chr5B 85.435 817 76 27 1 797 588831913 588832706 0.000000e+00 809
4 TraesCS5B01G414300 chr5A 87.701 1992 202 26 2016 3989 599452368 599454334 0.000000e+00 2281
5 TraesCS5B01G414300 chr5A 91.615 1455 69 19 1 1440 599389839 599391255 0.000000e+00 1962
6 TraesCS5B01G414300 chr5A 93.799 758 39 4 2312 3068 599392200 599392950 0.000000e+00 1133
7 TraesCS5B01G414300 chr5A 89.750 839 58 12 1495 2311 599391261 599392093 0.000000e+00 1048
8 TraesCS5B01G414300 chr5A 87.797 926 70 9 975 1893 599451217 599452106 0.000000e+00 1044
9 TraesCS5B01G414300 chr5A 86.323 892 98 11 3114 3987 599393241 599394126 0.000000e+00 950
10 TraesCS5B01G414300 chr5A 91.058 671 50 8 1 663 599448379 599449047 0.000000e+00 898
11 TraesCS5B01G414300 chr2B 82.843 612 85 15 61 661 3906788 3906186 7.590000e-147 531
12 TraesCS5B01G414300 chr2B 82.680 612 86 15 61 661 4185793 4185191 3.530000e-145 525
13 TraesCS5B01G414300 chr2B 81.672 622 86 22 61 660 3788174 3787559 3.580000e-135 492
14 TraesCS5B01G414300 chr2B 81.488 605 84 22 52 634 1317387 1317985 4.670000e-129 472
15 TraesCS5B01G414300 chr7A 80.389 719 98 20 3203 3895 208526356 208527057 1.280000e-139 507
16 TraesCS5B01G414300 chrUn 81.458 631 89 22 52 660 177132281 177132905 3.580000e-135 492
17 TraesCS5B01G414300 chrUn 81.458 631 89 22 52 660 306187226 306187850 3.580000e-135 492
18 TraesCS5B01G414300 chr7D 79.861 720 100 18 3203 3895 199129942 199130643 5.990000e-133 484
19 TraesCS5B01G414300 chr5D 84.881 463 56 9 3121 3580 480493829 480494280 4.700000e-124 455
20 TraesCS5B01G414300 chr7B 83.059 425 69 3 3200 3622 163010965 163011388 2.250000e-102 383
21 TraesCS5B01G414300 chr6D 83.123 397 43 8 3510 3885 132306045 132305652 1.370000e-89 340
22 TraesCS5B01G414300 chr6D 87.156 109 14 0 1037 1145 456251650 456251758 1.510000e-24 124
23 TraesCS5B01G414300 chr2A 80.590 407 51 6 3510 3889 734968240 734968645 5.040000e-74 289


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 TraesCS5B01G414300 chr5B 588777612 588781600 3988 False 7367.000000 7367 100.00000 1 3989 1 chr5B.!!$F1 3988
1 TraesCS5B01G414300 chr5B 588831913 588835152 3239 False 1096.000000 1607 85.85400 1 3447 3 chr5B.!!$F2 3446
2 TraesCS5B01G414300 chr5A 599448379 599454334 5955 False 1407.666667 2281 88.85200 1 3989 3 chr5A.!!$F2 3988
3 TraesCS5B01G414300 chr5A 599389839 599394126 4287 False 1273.250000 1962 90.37175 1 3987 4 chr5A.!!$F1 3986
4 TraesCS5B01G414300 chr2B 3906186 3906788 602 True 531.000000 531 82.84300 61 661 1 chr2B.!!$R2 600
5 TraesCS5B01G414300 chr2B 4185191 4185793 602 True 525.000000 525 82.68000 61 661 1 chr2B.!!$R3 600
6 TraesCS5B01G414300 chr2B 3787559 3788174 615 True 492.000000 492 81.67200 61 660 1 chr2B.!!$R1 599
7 TraesCS5B01G414300 chr2B 1317387 1317985 598 False 472.000000 472 81.48800 52 634 1 chr2B.!!$F1 582
8 TraesCS5B01G414300 chr7A 208526356 208527057 701 False 507.000000 507 80.38900 3203 3895 1 chr7A.!!$F1 692
9 TraesCS5B01G414300 chrUn 177132281 177132905 624 False 492.000000 492 81.45800 52 660 1 chrUn.!!$F1 608
10 TraesCS5B01G414300 chrUn 306187226 306187850 624 False 492.000000 492 81.45800 52 660 1 chrUn.!!$F2 608
11 TraesCS5B01G414300 chr7D 199129942 199130643 701 False 484.000000 484 79.86100 3203 3895 1 chr7D.!!$F1 692

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
894 2853 0.327576 ACCCAGGCCAGGTATAAGCT 60.328 55.0 15.53 0.00 35.24 3.74 F
2824 5080 0.457851 CCTCTACAGGTGCGAAGAGG 59.542 60.0 3.02 3.02 46.73 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2834 5090 0.250945 TTTGTACGGGCTTGCCATGA 60.251 50.000 14.04 0.0 0.0 3.07 R
3786 6328 4.354662 AGCCTTTCTTAGTAGTGCCTAGT 58.645 43.478 0.00 0.0 0.0 2.57 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
123 132 4.717629 CGGCGTCGCTTCCAGTCA 62.718 66.667 18.11 0.00 0.00 3.41
249 258 3.769739 AGCTCCATGTCAGTACAACAA 57.230 42.857 5.35 0.00 39.58 2.83
288 297 5.074115 CCCAACCAGTACAGGAATGTTTTA 58.926 41.667 11.86 0.00 0.00 1.52
368 398 3.069158 CCGATTAGGTAGGTGGTTACAGG 59.931 52.174 0.00 0.00 34.51 4.00
376 409 3.237268 AGGTGGTTACAGGCATTCAAA 57.763 42.857 0.00 0.00 0.00 2.69
430 463 3.670377 GAAGGGTTGCACGGTGGC 61.670 66.667 10.60 3.04 0.00 5.01
443 476 1.450134 GGTGGCGATGCAGTCATGA 60.450 57.895 0.00 0.00 31.96 3.07
515 548 2.583441 CGGCAGAGACCCAACCAGA 61.583 63.158 0.00 0.00 0.00 3.86
567 600 2.203280 CGAACCACCTGGCCACAA 60.203 61.111 0.00 0.00 39.32 3.33
597 630 3.181451 CCTCCAAAGCAGATACCATAGCA 60.181 47.826 0.00 0.00 0.00 3.49
711 744 8.951243 GCTTAATTAACTTCTGATTGTTCTCCT 58.049 33.333 0.00 0.00 0.00 3.69
725 758 4.507710 TGTTCTCCTGTTGCTGATGTATC 58.492 43.478 0.00 0.00 0.00 2.24
749 782 8.591114 TCTAGGTATTTATATAGCACTGGTCC 57.409 38.462 5.39 0.00 37.23 4.46
750 783 8.399529 TCTAGGTATTTATATAGCACTGGTCCT 58.600 37.037 5.39 0.00 37.23 3.85
751 784 9.696572 CTAGGTATTTATATAGCACTGGTCCTA 57.303 37.037 5.39 0.00 37.23 2.94
752 785 8.596781 AGGTATTTATATAGCACTGGTCCTAG 57.403 38.462 5.39 0.00 37.23 3.02
753 786 7.124448 AGGTATTTATATAGCACTGGTCCTAGC 59.876 40.741 5.39 0.00 37.23 3.42
754 787 5.740290 TTTATATAGCACTGGTCCTAGCC 57.260 43.478 0.00 0.00 0.00 3.93
755 788 2.767644 TATAGCACTGGTCCTAGCCA 57.232 50.000 0.00 0.00 36.97 4.75
817 2724 5.891451 AGAGTTTTGTTTTCCGAAAAGAGG 58.109 37.500 6.54 0.00 0.00 3.69
850 2757 3.070429 GCTATGCACACAGCCATAAAC 57.930 47.619 5.66 0.00 44.83 2.01
852 2759 3.242870 GCTATGCACACAGCCATAAACTC 60.243 47.826 5.66 0.00 44.83 3.01
855 2762 4.014569 TGCACACAGCCATAAACTCTTA 57.985 40.909 0.00 0.00 44.83 2.10
858 2765 5.300539 TGCACACAGCCATAAACTCTTAAAA 59.699 36.000 0.00 0.00 44.83 1.52
861 2768 7.425606 CACACAGCCATAAACTCTTAAAAAGT 58.574 34.615 0.00 0.00 0.00 2.66
863 2770 9.127277 ACACAGCCATAAACTCTTAAAAAGTTA 57.873 29.630 3.94 0.00 35.96 2.24
864 2771 9.612620 CACAGCCATAAACTCTTAAAAAGTTAG 57.387 33.333 3.94 0.00 35.96 2.34
865 2772 9.569122 ACAGCCATAAACTCTTAAAAAGTTAGA 57.431 29.630 3.94 0.00 35.96 2.10
894 2853 0.327576 ACCCAGGCCAGGTATAAGCT 60.328 55.000 15.53 0.00 35.24 3.74
918 2877 6.625873 TGCATTGCATTATAAATACACGGA 57.374 33.333 7.38 0.00 31.71 4.69
993 2960 4.229876 GTTGCAAGTTACAGCCAGAAATC 58.770 43.478 0.00 0.00 0.00 2.17
1017 2984 1.005805 TCCATGGCCAATAACAGCAGT 59.994 47.619 10.96 0.00 0.00 4.40
1053 3020 1.071605 CGCAGGAGCTAGTTTGTGTC 58.928 55.000 0.00 0.00 39.10 3.67
1113 3080 2.435693 GCTCCTCCACCGTGGCTAT 61.436 63.158 13.19 0.00 37.47 2.97
1216 3194 1.546923 CCATCACTTGCTTCAATGGCA 59.453 47.619 0.00 0.00 37.97 4.92
1257 3235 1.289109 CGGACCGCAAGAACGTTCAT 61.289 55.000 28.78 15.87 43.02 2.57
1287 3265 1.152652 GGAGGGAGCCGATGAGAGA 60.153 63.158 0.00 0.00 0.00 3.10
1288 3266 0.541764 GGAGGGAGCCGATGAGAGAT 60.542 60.000 0.00 0.00 0.00 2.75
1297 3275 3.900601 AGCCGATGAGAGATTATCCTTGT 59.099 43.478 0.00 0.00 0.00 3.16
1444 3422 9.534565 AGCATATATACTTAATTACCATCTGCG 57.465 33.333 0.00 0.00 0.00 5.18
1445 3423 8.765219 GCATATATACTTAATTACCATCTGCGG 58.235 37.037 0.00 0.00 0.00 5.69
1446 3424 9.817809 CATATATACTTAATTACCATCTGCGGT 57.182 33.333 0.00 0.00 43.46 5.68
1447 3425 9.817809 ATATATACTTAATTACCATCTGCGGTG 57.182 33.333 0.00 0.00 40.39 4.94
1448 3426 4.216411 ACTTAATTACCATCTGCGGTGT 57.784 40.909 0.00 0.00 40.39 4.16
1449 3427 5.347620 ACTTAATTACCATCTGCGGTGTA 57.652 39.130 0.00 0.00 40.39 2.90
1450 3428 5.925509 ACTTAATTACCATCTGCGGTGTAT 58.074 37.500 0.00 0.00 40.39 2.29
1451 3429 7.058023 ACTTAATTACCATCTGCGGTGTATA 57.942 36.000 0.00 0.00 40.39 1.47
1452 3430 6.927381 ACTTAATTACCATCTGCGGTGTATAC 59.073 38.462 0.00 0.00 40.39 1.47
1453 3431 5.546621 AATTACCATCTGCGGTGTATACT 57.453 39.130 4.17 0.00 40.39 2.12
1454 3432 5.546621 ATTACCATCTGCGGTGTATACTT 57.453 39.130 4.17 0.00 40.39 2.24
1455 3433 6.659745 ATTACCATCTGCGGTGTATACTTA 57.340 37.500 4.17 0.00 40.39 2.24
1456 3434 6.468333 TTACCATCTGCGGTGTATACTTAA 57.532 37.500 4.17 0.00 40.39 1.85
1457 3435 5.546621 ACCATCTGCGGTGTATACTTAAT 57.453 39.130 4.17 0.00 38.07 1.40
1458 3436 5.925509 ACCATCTGCGGTGTATACTTAATT 58.074 37.500 4.17 0.00 38.07 1.40
1459 3437 7.058023 ACCATCTGCGGTGTATACTTAATTA 57.942 36.000 4.17 0.00 38.07 1.40
1460 3438 6.927381 ACCATCTGCGGTGTATACTTAATTAC 59.073 38.462 4.17 0.00 38.07 1.89
1461 3439 6.367969 CCATCTGCGGTGTATACTTAATTACC 59.632 42.308 4.17 1.23 0.00 2.85
1462 3440 6.468333 TCTGCGGTGTATACTTAATTACCA 57.532 37.500 4.17 0.00 0.00 3.25
1463 3441 7.058023 TCTGCGGTGTATACTTAATTACCAT 57.942 36.000 4.17 0.00 0.00 3.55
1464 3442 7.149973 TCTGCGGTGTATACTTAATTACCATC 58.850 38.462 4.17 0.00 0.00 3.51
1547 3529 4.417437 GGGGCTCTATGTAGGAACTCATA 58.583 47.826 0.00 0.00 41.75 2.15
1622 3604 2.426752 CGCCGCCTTGTTTTCACG 60.427 61.111 0.00 0.00 0.00 4.35
1679 3661 2.072487 CCCCGACACCATCCTGGAT 61.072 63.158 2.57 2.57 40.96 3.41
1703 3685 1.068281 ACATGCTGGAGCGACTATGAG 59.932 52.381 0.00 0.00 45.83 2.90
1734 3716 4.632153 ACAGACAGGCGTATGATATTTCC 58.368 43.478 10.21 0.00 36.41 3.13
1736 3718 3.572682 AGACAGGCGTATGATATTTCCGA 59.427 43.478 0.00 0.00 0.00 4.55
1841 3840 5.518812 TGTTTGGAACTCAATCACAAATCG 58.481 37.500 0.00 0.00 34.98 3.34
1879 3878 3.995636 TCAGCTGGGATAGGTTCTTACT 58.004 45.455 15.13 0.00 34.17 2.24
1893 3892 1.921869 CTTACTGGCCACCCCCGATT 61.922 60.000 0.00 0.00 0.00 3.34
1930 3941 6.840527 AGAAACACCAAAATGGATGGATTTT 58.159 32.000 2.85 0.00 40.96 1.82
1954 3965 4.149922 GGCGAAAGTCAAGCATTTTTAACC 59.850 41.667 0.00 0.00 34.40 2.85
1957 3968 5.339611 CGAAAGTCAAGCATTTTTAACCGAG 59.660 40.000 0.00 0.00 0.00 4.63
2046 4184 0.853530 AGTGAGACCAAAAGGCCCTT 59.146 50.000 0.00 0.00 0.00 3.95
2051 4189 3.850173 TGAGACCAAAAGGCCCTTATAGT 59.150 43.478 0.00 0.00 0.00 2.12
2116 4254 8.919145 AGTGTTTGTTCCCAATTCAATAGTTTA 58.081 29.630 0.00 0.00 0.00 2.01
2156 4294 1.540267 TTAATTTGTGGCACCCGGAG 58.460 50.000 16.26 0.00 0.00 4.63
2271 4417 7.448420 TCATCAAGGATATAAGGAGCTCAAAG 58.552 38.462 17.19 0.00 0.00 2.77
2278 4424 2.592102 AAGGAGCTCAAAGGCAATGA 57.408 45.000 17.19 0.00 34.17 2.57
2281 4427 1.615384 GGAGCTCAAAGGCAATGACCT 60.615 52.381 17.19 0.00 43.91 3.85
2287 4433 1.614903 CAAAGGCAATGACCTGAAGCA 59.385 47.619 0.00 0.00 39.93 3.91
2346 4598 5.124138 AGTGTGTGTCGTCTTAGGAATCTAG 59.876 44.000 0.00 0.00 0.00 2.43
2368 4621 9.151471 TCTAGTAATTTCATTGTGCAGAACTAC 57.849 33.333 0.00 0.00 0.00 2.73
2418 4671 2.037136 CAGCAACGGAGGAGGCAAG 61.037 63.158 0.00 0.00 0.00 4.01
2426 4679 3.695747 GAGGAGGCAAGCAGGAGGC 62.696 68.421 0.00 0.00 45.30 4.70
2581 4834 1.733041 CACAGATGTCCGCGACGTT 60.733 57.895 8.23 0.00 34.95 3.99
2681 4934 0.620556 TTGCCTCCTCCAGTTGATCC 59.379 55.000 0.00 0.00 0.00 3.36
2723 4977 7.950684 ACTATCCTATCACTTCCAAGTATGCTA 59.049 37.037 0.00 0.00 37.08 3.49
2779 5035 8.515414 GCATATGCGTGTCCATATCTATATCTA 58.485 37.037 12.82 0.00 36.52 1.98
2824 5080 0.457851 CCTCTACAGGTGCGAAGAGG 59.542 60.000 3.02 3.02 46.73 3.69
2834 5090 1.080434 GCGAAGAGGACGACAAGCT 60.080 57.895 0.00 0.00 0.00 3.74
2852 5108 0.676466 CTCATGGCAAGCCCGTACAA 60.676 55.000 8.89 0.00 35.87 2.41
2994 5262 3.815962 AGCGTTCGAGCTTATAGATCAGA 59.184 43.478 0.00 0.00 46.80 3.27
3010 5278 2.959516 TCAGAATGTAGTGCGACCAAG 58.040 47.619 0.00 0.00 37.40 3.61
3032 5300 3.791953 TCCACATACCCGGAAGAAAAA 57.208 42.857 0.73 0.00 0.00 1.94
3075 5343 6.930068 AGTAATAGTGTGGACTTGTAAGGT 57.070 37.500 0.00 0.00 33.21 3.50
3076 5344 8.426569 AAGTAATAGTGTGGACTTGTAAGGTA 57.573 34.615 0.00 0.00 33.21 3.08
3083 5351 6.766467 AGTGTGGACTTGTAAGGTAGAAAAAG 59.234 38.462 0.00 0.00 0.00 2.27
3084 5352 6.764560 GTGTGGACTTGTAAGGTAGAAAAAGA 59.235 38.462 0.00 0.00 0.00 2.52
3085 5353 7.281549 GTGTGGACTTGTAAGGTAGAAAAAGAA 59.718 37.037 0.00 0.00 0.00 2.52
3086 5354 7.996644 TGTGGACTTGTAAGGTAGAAAAAGAAT 59.003 33.333 0.00 0.00 0.00 2.40
3087 5355 8.504815 GTGGACTTGTAAGGTAGAAAAAGAATC 58.495 37.037 0.00 0.00 0.00 2.52
3088 5356 8.215050 TGGACTTGTAAGGTAGAAAAAGAATCA 58.785 33.333 0.00 0.00 0.00 2.57
3089 5357 8.722394 GGACTTGTAAGGTAGAAAAAGAATCAG 58.278 37.037 0.00 0.00 0.00 2.90
3090 5358 9.490379 GACTTGTAAGGTAGAAAAAGAATCAGA 57.510 33.333 0.00 0.00 0.00 3.27
3112 5625 9.799106 TCAGATATCAGATATCGGATATGCTAA 57.201 33.333 30.90 17.17 44.92 3.09
3195 5717 9.362539 GCAAGATGTTATGAAAATTGAAGACAT 57.637 29.630 0.00 0.00 0.00 3.06
3269 5794 9.606631 AAAACCAATTAGCAACAATAAGTCAAA 57.393 25.926 0.00 0.00 0.00 2.69
3270 5795 8.587952 AACCAATTAGCAACAATAAGTCAAAC 57.412 30.769 0.00 0.00 0.00 2.93
3305 5831 6.619801 AGTCACCTTGTAAATGTTTCTCAC 57.380 37.500 0.00 0.00 0.00 3.51
3315 5841 6.601613 TGTAAATGTTTCTCACCATATCCACC 59.398 38.462 0.00 0.00 0.00 4.61
3316 5842 4.860802 ATGTTTCTCACCATATCCACCA 57.139 40.909 0.00 0.00 0.00 4.17
3318 5844 4.331968 TGTTTCTCACCATATCCACCAAC 58.668 43.478 0.00 0.00 0.00 3.77
3338 5864 1.425448 CCTTCCCAACAAGAACCTCCT 59.575 52.381 0.00 0.00 0.00 3.69
3343 5869 2.821969 CCCAACAAGAACCTCCTCAATG 59.178 50.000 0.00 0.00 0.00 2.82
3368 5894 3.883489 GGGCCTGAACATCAATAACCTAC 59.117 47.826 0.84 0.00 0.00 3.18
3378 5904 6.415573 ACATCAATAACCTACAGGAAACCTC 58.584 40.000 1.29 0.00 38.94 3.85
3400 5926 4.141041 TCTCCAAGATGGGGAAAACAAAGA 60.141 41.667 0.00 0.00 45.82 2.52
3457 5983 6.210078 CCTCAGATTACGAGGTCATAAACTC 58.790 44.000 0.00 0.00 44.35 3.01
3485 6011 5.690857 ACTAACAGTAACGTCAGAAGAAAGC 59.309 40.000 0.00 0.00 0.00 3.51
3546 6072 4.512944 AGTCATTCAACACAAGTAGCACAG 59.487 41.667 0.00 0.00 0.00 3.66
3602 6128 6.264067 AGGCAGAGAAATAATCAGCATTAACC 59.736 38.462 0.00 0.00 0.00 2.85
3604 6130 7.137426 GCAGAGAAATAATCAGCATTAACCTG 58.863 38.462 0.00 0.00 0.00 4.00
3652 6178 8.036273 ACACCAAATAGTCGGTTAAATAAGTG 57.964 34.615 0.00 0.00 31.41 3.16
3664 6190 6.530181 CGGTTAAATAAGTGAAAATTGAGGGC 59.470 38.462 0.00 0.00 0.00 5.19
3703 6229 8.447833 TCAAAACTGTAGTTGTTTAACACTGAG 58.552 33.333 0.00 3.10 39.30 3.35
3786 6328 9.337396 GTTCTATGTACCCACATCAATCAAATA 57.663 33.333 0.00 0.00 44.42 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.846248 GACGATCAAGGTTACTACTTACTAAAA 57.154 33.333 0.00 0.00 0.00 1.52
123 132 3.632145 GGGTCATATTTGCAAACGGAGAT 59.368 43.478 15.41 0.00 0.00 2.75
288 297 2.158559 TGTGCGTGCAATTAATCAGGT 58.841 42.857 0.00 0.00 0.00 4.00
330 347 2.963548 TCGGTCGTTATGGCATGTAA 57.036 45.000 10.98 0.00 0.00 2.41
335 352 1.758280 ACCTAATCGGTCGTTATGGCA 59.242 47.619 0.00 0.00 44.93 4.92
336 353 2.521105 ACCTAATCGGTCGTTATGGC 57.479 50.000 0.00 0.00 44.93 4.40
346 373 3.069158 CCTGTAACCACCTACCTAATCGG 59.931 52.174 0.00 0.00 39.35 4.18
430 463 1.209998 CAGCTCTCATGACTGCATCG 58.790 55.000 15.03 2.81 30.68 3.84
503 536 1.222567 ACAGGTTTCTGGTTGGGTCT 58.777 50.000 0.00 0.00 44.99 3.85
567 600 0.392998 CTGCTTTGGAGGCCGTATGT 60.393 55.000 0.00 0.00 0.00 2.29
725 758 8.596781 AGGACCAGTGCTATATAAATACCTAG 57.403 38.462 0.00 0.00 0.00 3.02
745 778 1.540707 GCGTACTATCTGGCTAGGACC 59.459 57.143 0.00 0.00 29.97 4.46
748 781 0.889306 GGGCGTACTATCTGGCTAGG 59.111 60.000 0.00 0.00 0.00 3.02
749 782 0.889306 GGGGCGTACTATCTGGCTAG 59.111 60.000 0.00 0.00 0.00 3.42
750 783 0.186630 TGGGGCGTACTATCTGGCTA 59.813 55.000 0.00 0.00 0.00 3.93
751 784 1.075525 TGGGGCGTACTATCTGGCT 60.076 57.895 0.00 0.00 0.00 4.75
752 785 1.069258 GTGGGGCGTACTATCTGGC 59.931 63.158 0.00 0.00 0.00 4.85
753 786 1.120530 AAGTGGGGCGTACTATCTGG 58.879 55.000 0.00 0.00 0.00 3.86
754 787 1.806623 GCAAGTGGGGCGTACTATCTG 60.807 57.143 0.00 0.00 0.00 2.90
755 788 0.464452 GCAAGTGGGGCGTACTATCT 59.536 55.000 0.00 0.00 0.00 1.98
756 789 0.532196 GGCAAGTGGGGCGTACTATC 60.532 60.000 0.00 0.00 0.00 2.08
757 790 0.981277 AGGCAAGTGGGGCGTACTAT 60.981 55.000 0.00 0.00 38.57 2.12
758 791 0.324552 TAGGCAAGTGGGGCGTACTA 60.325 55.000 0.00 0.00 38.57 1.82
759 792 1.611261 TAGGCAAGTGGGGCGTACT 60.611 57.895 0.00 0.00 38.57 2.73
760 793 1.153429 CTAGGCAAGTGGGGCGTAC 60.153 63.158 0.00 0.00 38.57 3.67
761 794 3.026431 GCTAGGCAAGTGGGGCGTA 62.026 63.158 0.00 0.00 38.57 4.42
762 795 4.410400 GCTAGGCAAGTGGGGCGT 62.410 66.667 0.00 0.00 38.57 5.68
763 796 3.628646 AAGCTAGGCAAGTGGGGCG 62.629 63.158 0.00 0.00 38.57 6.13
855 2762 8.929487 CCTGGGTCTCTATCTATCTAACTTTTT 58.071 37.037 0.00 0.00 0.00 1.94
858 2765 6.014012 GCCTGGGTCTCTATCTATCTAACTT 58.986 44.000 0.00 0.00 0.00 2.66
861 2768 4.357097 TGGCCTGGGTCTCTATCTATCTAA 59.643 45.833 3.32 0.00 0.00 2.10
863 2770 2.724672 TGGCCTGGGTCTCTATCTATCT 59.275 50.000 3.32 0.00 0.00 1.98
864 2771 3.096092 CTGGCCTGGGTCTCTATCTATC 58.904 54.545 3.32 0.00 0.00 2.08
865 2772 2.225496 CCTGGCCTGGGTCTCTATCTAT 60.225 54.545 20.77 0.00 0.00 1.98
894 2853 7.032377 TCCGTGTATTTATAATGCAATGCAA 57.968 32.000 13.45 0.00 43.62 4.08
918 2877 1.905894 ACAAACTTGCCTTGTGGGTTT 59.094 42.857 0.00 0.00 35.70 3.27
993 2960 2.287788 GCTGTTATTGGCCATGGAATCG 60.288 50.000 18.40 0.00 0.00 3.34
1113 3080 3.998672 GCGGTTCCCCTGACACGA 61.999 66.667 0.00 0.00 0.00 4.35
1216 3194 2.112380 TCACATGATTGGTGCACGAT 57.888 45.000 11.45 7.43 36.22 3.73
1224 3202 0.734889 GGTCCGCTTCACATGATTGG 59.265 55.000 0.00 0.00 0.00 3.16
1254 3232 2.580322 TCCCTCCAAGGTATGCAAATGA 59.420 45.455 0.00 0.00 31.93 2.57
1257 3235 1.340991 GCTCCCTCCAAGGTATGCAAA 60.341 52.381 0.00 0.00 31.93 3.68
1287 3265 2.186826 GGCGCGGCACAAGGATAAT 61.187 57.895 29.32 0.00 0.00 1.28
1288 3266 2.822255 GGCGCGGCACAAGGATAA 60.822 61.111 29.32 0.00 0.00 1.75
1440 3418 7.116376 CAGATGGTAATTAAGTATACACCGCAG 59.884 40.741 5.50 0.00 0.00 5.18
1442 3420 6.128634 GCAGATGGTAATTAAGTATACACCGC 60.129 42.308 5.50 0.00 0.00 5.68
1443 3421 6.089016 CGCAGATGGTAATTAAGTATACACCG 59.911 42.308 5.50 0.00 0.00 4.94
1444 3422 6.367969 CCGCAGATGGTAATTAAGTATACACC 59.632 42.308 5.50 3.33 0.00 4.16
1445 3423 6.927381 ACCGCAGATGGTAATTAAGTATACAC 59.073 38.462 5.50 0.00 41.55 2.90
1446 3424 6.926826 CACCGCAGATGGTAATTAAGTATACA 59.073 38.462 5.50 0.00 41.38 2.29
1447 3425 6.128634 GCACCGCAGATGGTAATTAAGTATAC 60.129 42.308 0.00 0.00 41.38 1.47
1448 3426 5.929992 GCACCGCAGATGGTAATTAAGTATA 59.070 40.000 0.00 0.00 41.38 1.47
1449 3427 4.755123 GCACCGCAGATGGTAATTAAGTAT 59.245 41.667 0.00 0.00 41.38 2.12
1450 3428 4.124238 GCACCGCAGATGGTAATTAAGTA 58.876 43.478 0.00 0.00 41.38 2.24
1451 3429 2.943033 GCACCGCAGATGGTAATTAAGT 59.057 45.455 0.00 0.00 41.38 2.24
1452 3430 2.942376 TGCACCGCAGATGGTAATTAAG 59.058 45.455 0.00 0.00 41.38 1.85
1453 3431 2.992593 TGCACCGCAGATGGTAATTAA 58.007 42.857 0.00 0.00 41.38 1.40
1454 3432 2.700722 TGCACCGCAGATGGTAATTA 57.299 45.000 0.00 0.00 41.38 1.40
1455 3433 1.745087 CTTGCACCGCAGATGGTAATT 59.255 47.619 0.00 0.00 41.38 1.40
1456 3434 1.382522 CTTGCACCGCAGATGGTAAT 58.617 50.000 0.00 0.00 41.38 1.89
1457 3435 0.676466 CCTTGCACCGCAGATGGTAA 60.676 55.000 0.00 0.00 41.38 2.85
1458 3436 1.078497 CCTTGCACCGCAGATGGTA 60.078 57.895 0.00 0.00 41.38 3.25
1459 3437 2.360350 CCTTGCACCGCAGATGGT 60.360 61.111 0.00 0.00 45.21 3.55
1460 3438 1.651240 CTTCCTTGCACCGCAGATGG 61.651 60.000 0.00 0.00 40.61 3.51
1461 3439 0.674581 TCTTCCTTGCACCGCAGATG 60.675 55.000 0.00 0.00 40.61 2.90
1462 3440 0.036732 TTCTTCCTTGCACCGCAGAT 59.963 50.000 0.00 0.00 40.61 2.90
1463 3441 0.179032 TTTCTTCCTTGCACCGCAGA 60.179 50.000 0.00 0.00 40.61 4.26
1464 3442 0.883833 ATTTCTTCCTTGCACCGCAG 59.116 50.000 0.00 0.00 40.61 5.18
1533 3515 2.621998 CGACCGGTATGAGTTCCTACAT 59.378 50.000 7.34 0.00 0.00 2.29
1679 3661 1.216444 GTCGCTCCAGCATGTCTCA 59.784 57.895 0.00 0.00 42.21 3.27
1734 3716 3.780801 GCAATGAATGTTAAGTCGCTTCG 59.219 43.478 0.00 0.00 0.00 3.79
1736 3718 4.764679 TGCAATGAATGTTAAGTCGCTT 57.235 36.364 0.00 0.00 0.00 4.68
1871 3870 1.001269 GGGGGTGGCCAGTAAGAAC 60.001 63.158 5.11 0.00 0.00 3.01
1879 3878 2.528708 AAAAATCGGGGGTGGCCA 59.471 55.556 0.00 0.00 0.00 5.36
1898 3897 6.882656 TCCATTTTGGTGTTTCTCAAAATCA 58.117 32.000 10.02 0.50 45.88 2.57
1899 3898 7.095102 CCATCCATTTTGGTGTTTCTCAAAATC 60.095 37.037 10.02 0.00 45.88 2.17
1905 3906 5.665916 ATCCATCCATTTTGGTGTTTCTC 57.334 39.130 0.00 0.00 39.03 2.87
1907 3908 6.901265 CAAAATCCATCCATTTTGGTGTTTC 58.099 36.000 9.76 0.00 44.73 2.78
1930 3941 3.451141 AAAAATGCTTGACTTTCGCCA 57.549 38.095 0.00 0.00 0.00 5.69
1943 3954 3.926821 TTGGGACTCGGTTAAAAATGC 57.073 42.857 0.00 0.00 0.00 3.56
1957 3968 4.440940 AACGTCAAGTTTTCCATTTGGGAC 60.441 41.667 0.00 0.00 39.66 4.46
1971 3982 5.064198 TCAGACAATTTCGAAAACGTCAAGT 59.936 36.000 29.54 16.10 0.00 3.16
2014 4152 6.985188 TTGGTCTCACTTGCATTTAGATAC 57.015 37.500 0.00 0.00 0.00 2.24
2032 4170 3.945921 GACACTATAAGGGCCTTTTGGTC 59.054 47.826 26.29 19.64 45.31 4.02
2046 4184 8.474831 TGCATAGCAAGTTTCTAAGACACTATA 58.525 33.333 0.00 0.00 34.76 1.31
2051 4189 8.206867 AGATATGCATAGCAAGTTTCTAAGACA 58.793 33.333 23.03 0.00 43.62 3.41
2186 4324 3.055675 TGACCCGACCACCTGTATTTTAG 60.056 47.826 0.00 0.00 0.00 1.85
2241 4387 7.982252 AGCTCCTTATATCCTTGATGAATTGA 58.018 34.615 0.00 0.00 0.00 2.57
2271 4417 1.760192 ATCTGCTTCAGGTCATTGCC 58.240 50.000 0.00 0.00 31.51 4.52
2278 4424 3.565307 TGTTTGGAAATCTGCTTCAGGT 58.435 40.909 0.00 0.00 31.51 4.00
2281 4427 7.471721 CGTATTATGTTTGGAAATCTGCTTCA 58.528 34.615 0.00 0.00 0.00 3.02
2287 4433 7.566760 TCATGCGTATTATGTTTGGAAATCT 57.433 32.000 0.00 0.00 0.00 2.40
2581 4834 0.752658 CGAGGAGATGGGCATGTACA 59.247 55.000 0.00 0.00 0.00 2.90
2624 4877 2.896443 GAAGCAGAGGTAGCGGCT 59.104 61.111 7.98 7.98 41.05 5.52
2646 4899 4.308458 AACTGCGGTGTAGCGCCA 62.308 61.111 23.23 11.86 40.67 5.69
2681 4934 2.554370 TAGTGTGGAAAAAGACCCCG 57.446 50.000 0.00 0.00 0.00 5.73
2723 4977 9.965902 AGGTTGATATTTCATTCAGAGTAAACT 57.034 29.630 0.00 0.00 0.00 2.66
2779 5035 3.498774 ATCGGTAGTCGGTACAGGTAT 57.501 47.619 0.00 0.00 39.77 2.73
2824 5080 0.445436 CTTGCCATGAGCTTGTCGTC 59.555 55.000 0.00 0.00 44.23 4.20
2834 5090 0.250945 TTTGTACGGGCTTGCCATGA 60.251 50.000 14.04 0.00 0.00 3.07
2852 5108 4.319177 CTCGAGTCTTTGGTTGGAGAATT 58.681 43.478 3.62 0.00 0.00 2.17
2994 5262 2.224426 TGGAACTTGGTCGCACTACATT 60.224 45.455 0.00 0.00 0.00 2.71
3010 5278 2.773993 TTCTTCCGGGTATGTGGAAC 57.226 50.000 0.00 0.00 39.29 3.62
3048 5316 9.063615 CCTTACAAGTCCACACTATTACTTTTT 57.936 33.333 0.00 0.00 29.93 1.94
3058 5326 5.881923 TTTCTACCTTACAAGTCCACACT 57.118 39.130 0.00 0.00 0.00 3.55
3083 5351 9.571810 GCATATCCGATATCTGATATCTGATTC 57.428 37.037 31.55 22.47 40.83 2.52
3084 5352 9.311676 AGCATATCCGATATCTGATATCTGATT 57.688 33.333 31.55 22.21 40.83 2.57
3085 5353 8.882557 AGCATATCCGATATCTGATATCTGAT 57.117 34.615 30.30 30.30 43.77 2.90
3086 5354 9.799106 TTAGCATATCCGATATCTGATATCTGA 57.201 33.333 26.63 25.57 39.55 3.27
3195 5717 8.710835 TGAATTCATGCGTACTTTTAGTATCA 57.289 30.769 3.38 0.00 32.65 2.15
3261 5786 9.997482 GTGACTTGTTATTTTCTGTTTGACTTA 57.003 29.630 0.00 0.00 0.00 2.24
3296 5822 4.331968 GTTGGTGGATATGGTGAGAAACA 58.668 43.478 0.00 0.00 0.00 2.83
3297 5823 3.694566 GGTTGGTGGATATGGTGAGAAAC 59.305 47.826 0.00 0.00 0.00 2.78
3298 5824 3.591527 AGGTTGGTGGATATGGTGAGAAA 59.408 43.478 0.00 0.00 0.00 2.52
3305 5831 1.568597 TGGGAAGGTTGGTGGATATGG 59.431 52.381 0.00 0.00 0.00 2.74
3315 5841 2.623416 GAGGTTCTTGTTGGGAAGGTTG 59.377 50.000 0.00 0.00 0.00 3.77
3316 5842 2.424379 GGAGGTTCTTGTTGGGAAGGTT 60.424 50.000 0.00 0.00 0.00 3.50
3318 5844 1.425448 AGGAGGTTCTTGTTGGGAAGG 59.575 52.381 0.00 0.00 0.00 3.46
3338 5864 2.041485 TGATGTTCAGGCCCTTCATTGA 59.959 45.455 0.00 0.00 0.00 2.57
3343 5869 3.381590 GGTTATTGATGTTCAGGCCCTTC 59.618 47.826 0.00 0.00 0.00 3.46
3368 5894 2.356535 CCCATCTTGGAGAGGTTTCCTG 60.357 54.545 0.00 0.00 40.96 3.86
3378 5904 4.151883 TCTTTGTTTTCCCCATCTTGGAG 58.848 43.478 0.00 0.00 40.96 3.86
3469 5995 2.143008 TGCGCTTTCTTCTGACGTTA 57.857 45.000 9.73 0.00 0.00 3.18
3485 6011 1.153353 AAACTTGTACCGTGGATGCG 58.847 50.000 0.00 0.00 0.00 4.73
3533 6059 1.998315 CTAGCTGCTGTGCTACTTGTG 59.002 52.381 13.43 0.00 43.74 3.33
3546 6072 1.470494 GTCTTGCCTTTTCCTAGCTGC 59.530 52.381 0.00 0.00 0.00 5.25
3602 6128 1.006571 CCAGTTTGCCTTGCTGCAG 60.007 57.895 10.11 10.11 43.21 4.41
3604 6130 0.108945 GATCCAGTTTGCCTTGCTGC 60.109 55.000 0.00 0.00 0.00 5.25
3697 6223 7.804614 GACACTTAACTGTCTAATCTCAGTG 57.195 40.000 7.71 0.00 42.95 3.66
3786 6328 4.354662 AGCCTTTCTTAGTAGTGCCTAGT 58.645 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.