Multiple sequence alignment - TraesCS7D01G432200

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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 TraesCS7D01G432200 chr7D 100.000 2754 0 0 1 2754 551929531 551926778 0.000000e+00 5086.0
1 TraesCS7D01G432200 chr7D 88.013 951 72 20 877 1808 551809226 551808299 0.000000e+00 1086.0
2 TraesCS7D01G432200 chr7D 85.124 847 91 28 967 1800 551000372 550999548 0.000000e+00 833.0
3 TraesCS7D01G432200 chr7D 86.825 463 49 5 331 790 551816124 551815671 8.800000e-140 507.0
4 TraesCS7D01G432200 chr7D 86.825 463 49 5 331 790 551834760 551834307 8.800000e-140 507.0
5 TraesCS7D01G432200 chr7D 87.073 410 43 4 381 790 551815100 551814701 3.230000e-124 455.0
6 TraesCS7D01G432200 chr7D 87.283 346 18 9 4 324 551836127 551835783 3.350000e-99 372.0
7 TraesCS7D01G432200 chr7D 86.705 346 20 9 4 324 551817491 551817147 7.250000e-96 361.0
8 TraesCS7D01G432200 chr7D 86.455 347 19 15 4 324 551115861 551115517 3.370000e-94 355.0
9 TraesCS7D01G432200 chr7D 94.505 91 5 0 444 534 551115137 551115047 1.030000e-29 141.0
10 TraesCS7D01G432200 chr7A 88.709 1913 166 26 346 2236 637337566 637335682 0.000000e+00 2290.0
11 TraesCS7D01G432200 chr7A 85.640 1156 107 19 580 1695 637037116 637035980 0.000000e+00 1160.0
12 TraesCS7D01G432200 chr7A 86.139 606 66 13 1097 1695 636919475 636918881 2.990000e-179 638.0
13 TraesCS7D01G432200 chr7A 82.776 598 65 22 891 1459 637078058 637077470 1.470000e-137 499.0
14 TraesCS7D01G432200 chr7A 88.047 343 14 10 4 321 637338729 637338389 5.570000e-102 381.0
15 TraesCS7D01G432200 chr7A 91.204 216 17 2 28 243 637037912 637037699 2.680000e-75 292.0
16 TraesCS7D01G432200 chr7A 84.722 144 17 3 330 468 722278921 722278778 3.700000e-29 139.0
17 TraesCS7D01G432200 chr7A 92.308 91 5 2 444 534 637037208 637037120 8.010000e-26 128.0
18 TraesCS7D01G432200 chr7B 83.232 1473 188 31 353 1815 596783188 596781765 0.000000e+00 1297.0
19 TraesCS7D01G432200 chr7B 85.870 920 67 25 897 1797 596680839 596679964 0.000000e+00 920.0
20 TraesCS7D01G432200 chr7B 85.150 835 86 24 891 1695 595882294 595881468 0.000000e+00 821.0
21 TraesCS7D01G432200 chr7B 83.593 835 85 28 891 1695 596539080 596538268 0.000000e+00 736.0
22 TraesCS7D01G432200 chr7B 82.994 835 90 29 891 1695 596516244 596515432 0.000000e+00 708.0
23 TraesCS7D01G432200 chr7B 89.367 442 39 7 2315 2754 596677835 596677400 1.440000e-152 549.0
24 TraesCS7D01G432200 chr7B 84.743 544 73 6 330 870 596685981 596685445 1.120000e-148 536.0
25 TraesCS7D01G432200 chr7B 82.759 522 57 18 1184 1695 595993706 595993208 4.210000e-118 435.0
26 TraesCS7D01G432200 chr7B 81.920 448 59 10 1802 2243 596678413 596677982 2.610000e-95 359.0
27 TraesCS7D01G432200 chr7B 85.000 320 21 10 30 324 596785367 596785050 1.600000e-77 300.0
28 TraesCS7D01G432200 chr7B 86.007 293 15 10 57 324 596688733 596688442 9.650000e-75 291.0
29 TraesCS7D01G432200 chr7B 83.673 98 12 3 2060 2157 304137919 304137826 3.780000e-14 89.8
30 TraesCS7D01G432200 chr1D 88.703 239 23 3 4 242 254578945 254579179 3.470000e-74 289.0
31 TraesCS7D01G432200 chr6A 88.655 238 22 4 4 240 578707226 578706993 4.490000e-73 285.0
32 TraesCS7D01G432200 chr6A 78.740 127 20 4 2045 2171 46736338 46736457 8.180000e-11 78.7
33 TraesCS7D01G432200 chr6D 85.271 258 15 10 330 569 432676298 432676046 7.620000e-61 244.0
34 TraesCS7D01G432200 chr6D 97.059 34 0 1 610 642 418157710 418157743 3.830000e-04 56.5
35 TraesCS7D01G432200 chr3D 80.800 125 17 4 2045 2169 442798921 442799038 1.050000e-14 91.6
36 TraesCS7D01G432200 chr3B 82.243 107 15 2 2044 2150 512741904 512742006 3.780000e-14 89.8
37 TraesCS7D01G432200 chr5B 79.845 129 18 4 2044 2171 413048758 413048879 1.360000e-13 87.9
38 TraesCS7D01G432200 chr6B 91.803 61 5 0 585 645 5066822 5066762 4.890000e-13 86.1
39 TraesCS7D01G432200 chr6B 80.342 117 15 3 2059 2175 689172805 689172697 6.320000e-12 82.4
40 TraesCS7D01G432200 chr2A 78.986 138 20 7 2035 2171 611025401 611025272 4.890000e-13 86.1
41 TraesCS7D01G432200 chr2B 100.000 36 0 0 607 642 69555901 69555866 1.770000e-07 67.6


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 TraesCS7D01G432200 chr7D 551926778 551929531 2753 True 5086.000000 5086 100.000000 1 2754 1 chr7D.!!$R3 2753
1 TraesCS7D01G432200 chr7D 551808299 551809226 927 True 1086.000000 1086 88.013000 877 1808 1 chr7D.!!$R2 931
2 TraesCS7D01G432200 chr7D 550999548 551000372 824 True 833.000000 833 85.124000 967 1800 1 chr7D.!!$R1 833
3 TraesCS7D01G432200 chr7D 551814701 551817491 2790 True 441.000000 507 86.867667 4 790 3 chr7D.!!$R5 786
4 TraesCS7D01G432200 chr7D 551834307 551836127 1820 True 439.500000 507 87.054000 4 790 2 chr7D.!!$R6 786
5 TraesCS7D01G432200 chr7D 551115047 551115861 814 True 248.000000 355 90.480000 4 534 2 chr7D.!!$R4 530
6 TraesCS7D01G432200 chr7A 637335682 637338729 3047 True 1335.500000 2290 88.378000 4 2236 2 chr7A.!!$R5 2232
7 TraesCS7D01G432200 chr7A 636918881 636919475 594 True 638.000000 638 86.139000 1097 1695 1 chr7A.!!$R1 598
8 TraesCS7D01G432200 chr7A 637035980 637037912 1932 True 526.666667 1160 89.717333 28 1695 3 chr7A.!!$R4 1667
9 TraesCS7D01G432200 chr7A 637077470 637078058 588 True 499.000000 499 82.776000 891 1459 1 chr7A.!!$R2 568
10 TraesCS7D01G432200 chr7B 595881468 595882294 826 True 821.000000 821 85.150000 891 1695 1 chr7B.!!$R2 804
11 TraesCS7D01G432200 chr7B 596781765 596785367 3602 True 798.500000 1297 84.116000 30 1815 2 chr7B.!!$R8 1785
12 TraesCS7D01G432200 chr7B 596538268 596539080 812 True 736.000000 736 83.593000 891 1695 1 chr7B.!!$R5 804
13 TraesCS7D01G432200 chr7B 596515432 596516244 812 True 708.000000 708 82.994000 891 1695 1 chr7B.!!$R4 804
14 TraesCS7D01G432200 chr7B 596677400 596680839 3439 True 609.333333 920 85.719000 897 2754 3 chr7B.!!$R6 1857
15 TraesCS7D01G432200 chr7B 596685445 596688733 3288 True 413.500000 536 85.375000 57 870 2 chr7B.!!$R7 813

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
467 4849 0.107214 AGGACCTGCGAGAGAGAGAG 60.107 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 8346 0.30776 GACAACTCGCCCACACTTTG 59.692 55.0 0.0 0.0 0.0 2.77 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
26 27 8.894768 AAGTTCCGGAGAAGAAAATCATATAG 57.105 34.615 3.34 0.00 30.91 1.31
63 64 5.365021 TTTGGCAAGAATCCCAAGAAAAA 57.635 34.783 0.00 0.00 41.71 1.94
71 72 9.822185 GCAAGAATCCCAAGAAAAATGTAATAT 57.178 29.630 0.00 0.00 0.00 1.28
324 355 4.545678 AGATTGCAAATGCTACCCCAATA 58.454 39.130 1.71 0.00 42.66 1.90
326 357 4.669206 TTGCAAATGCTACCCCAATATG 57.331 40.909 6.97 0.00 42.66 1.78
327 358 2.964464 TGCAAATGCTACCCCAATATGG 59.036 45.455 6.97 0.00 42.66 2.74
328 359 2.289010 GCAAATGCTACCCCAATATGGC 60.289 50.000 0.00 0.00 35.46 4.40
333 3735 0.606401 CTACCCCAATATGGCGGCTG 60.606 60.000 11.43 0.00 35.79 4.85
466 4848 0.329931 AAGGACCTGCGAGAGAGAGA 59.670 55.000 0.00 0.00 0.00 3.10
467 4849 0.107214 AGGACCTGCGAGAGAGAGAG 60.107 60.000 0.00 0.00 0.00 3.20
534 4916 4.796231 GCGTCGGCGACATCACCT 62.796 66.667 35.62 0.00 41.33 4.00
546 4928 2.525124 ATCACCTGCCACCGGACAA 61.525 57.895 9.46 0.00 0.00 3.18
574 4956 1.016627 CACCGTCGCCATGATCAATT 58.983 50.000 0.00 0.00 0.00 2.32
647 5029 1.080501 CTTTCTCTCGCAGCGACCA 60.081 57.895 15.11 2.07 0.00 4.02
668 5050 2.991250 AGCAGTTCTGTGTGTTGAAGT 58.009 42.857 1.78 0.00 0.00 3.01
670 5052 4.708177 AGCAGTTCTGTGTGTTGAAGTAT 58.292 39.130 1.78 0.00 0.00 2.12
671 5053 5.126067 AGCAGTTCTGTGTGTTGAAGTATT 58.874 37.500 1.78 0.00 0.00 1.89
695 5078 3.581265 TTTTTCTTCGGGTGGGTTAGT 57.419 42.857 0.00 0.00 0.00 2.24
709 5092 0.179119 GTTAGTGACCGGGTGGATCG 60.179 60.000 3.30 0.00 39.21 3.69
770 5153 4.436998 GACAGTCGGCCCAGGTCG 62.437 72.222 3.81 3.81 45.47 4.79
804 5187 2.927014 GCTGAAACGAAGATCTGACGGT 60.927 50.000 20.93 14.85 0.00 4.83
842 5225 4.574828 ACGCATAATCTAACAGCCGAAAAT 59.425 37.500 0.00 0.00 0.00 1.82
870 5253 1.610038 TCGTGAGACAGCTCGGTTTAA 59.390 47.619 0.00 0.00 44.33 1.52
959 5363 2.283966 CCCTGTCCTCTCCCGTGT 60.284 66.667 0.00 0.00 0.00 4.49
996 5415 3.150949 CACTCCCACAGTGCCTCA 58.849 61.111 0.00 0.00 46.30 3.86
1396 5870 1.819632 CCCTACCCAGTGCATTCGC 60.820 63.158 0.00 0.00 39.24 4.70
1399 5873 1.078497 TACCCAGTGCATTCGCCAG 60.078 57.895 0.00 0.00 37.32 4.85
1409 5886 3.185188 GTGCATTCGCCAGACACATATAG 59.815 47.826 0.00 0.00 37.32 1.31
1584 6063 0.460311 GAGGTGGTATACTGCGTGCT 59.540 55.000 2.25 0.00 0.00 4.40
1716 6203 2.109126 GCGAGGAGGAAATTGCGCT 61.109 57.895 9.73 0.00 41.09 5.92
1732 6219 3.972227 CTGGTTTCCAGCCTCACG 58.028 61.111 2.77 0.00 45.13 4.35
1733 6220 1.371183 CTGGTTTCCAGCCTCACGA 59.629 57.895 2.77 0.00 45.13 4.35
1734 6221 0.671781 CTGGTTTCCAGCCTCACGAG 60.672 60.000 2.77 0.00 45.13 4.18
1735 6222 1.371558 GGTTTCCAGCCTCACGAGT 59.628 57.895 0.00 0.00 0.00 4.18
1736 6223 0.670854 GGTTTCCAGCCTCACGAGTC 60.671 60.000 0.00 0.00 0.00 3.36
1737 6224 0.033504 GTTTCCAGCCTCACGAGTCA 59.966 55.000 0.00 0.00 0.00 3.41
1738 6225 0.033504 TTTCCAGCCTCACGAGTCAC 59.966 55.000 0.00 0.00 0.00 3.67
1798 6291 6.394345 AAGGTATATCCCCCTGAATTCATC 57.606 41.667 8.96 0.00 36.75 2.92
1811 7852 9.268268 CCCCTGAATTCATCAATCAAATAATTG 57.732 33.333 8.96 0.00 37.67 2.32
1846 7888 1.467920 CTGTTTGGATTGGAGCCCTC 58.532 55.000 0.00 0.00 0.00 4.30
1959 8002 9.490379 TCTCAGTTCCTTTAGTTCAATTCTAAC 57.510 33.333 0.00 0.00 0.00 2.34
1960 8003 9.495572 CTCAGTTCCTTTAGTTCAATTCTAACT 57.504 33.333 7.63 7.63 40.25 2.24
1972 8015 9.041354 AGTTCAATTCTAACTAGTGAAGATCCT 57.959 33.333 8.58 0.00 35.44 3.24
2012 8057 0.899019 GGGCCGGCTTTAAAATCCAA 59.101 50.000 28.56 0.00 0.00 3.53
2059 8109 3.008375 AGCATGCTACTTCCTTTGTCTGA 59.992 43.478 21.21 0.00 0.00 3.27
2143 8193 6.264970 TCATTTTCATCCATGTCTGTGACAAA 59.735 34.615 4.46 0.00 45.96 2.83
2151 8201 7.757941 TCCATGTCTGTGACAAATAATTTCA 57.242 32.000 4.46 0.00 45.96 2.69
2158 8209 6.947733 TCTGTGACAAATAATTTCAGATGGGT 59.052 34.615 0.00 0.00 0.00 4.51
2159 8210 8.106462 TCTGTGACAAATAATTTCAGATGGGTA 58.894 33.333 0.00 0.00 0.00 3.69
2197 8249 6.754209 GCACTATAGCATGCTATTAACGAGAT 59.246 38.462 37.80 19.69 39.65 2.75
2199 8251 9.227490 CACTATAGCATGCTATTAACGAGATAC 57.773 37.037 37.80 0.00 39.65 2.24
2243 8295 6.592994 GTGATCTATTGCTCAGCATGCTATAA 59.407 38.462 22.19 13.10 38.76 0.98
2245 8297 4.925646 TCTATTGCTCAGCATGCTATAACG 59.074 41.667 22.19 7.86 38.76 3.18
2246 8298 1.220529 TGCTCAGCATGCTATAACGC 58.779 50.000 22.19 17.55 34.76 4.84
2255 8344 6.073602 TCAGCATGCTATAACGCAATTCTAAG 60.074 38.462 22.19 1.34 44.06 2.18
2257 8346 5.385617 CATGCTATAACGCAATTCTAAGCC 58.614 41.667 0.00 0.00 44.06 4.35
2261 8350 5.909610 GCTATAACGCAATTCTAAGCCAAAG 59.090 40.000 0.00 0.00 0.00 2.77
2265 8354 3.236816 CGCAATTCTAAGCCAAAGTGTG 58.763 45.455 0.00 0.00 0.00 3.82
2380 8507 1.823899 GCCATGGCCCCGTTTCTAG 60.824 63.158 27.24 0.00 34.56 2.43
2386 8513 0.686769 GGCCCCGTTTCTAGAGGAGA 60.687 60.000 0.00 0.00 0.00 3.71
2392 8519 3.207778 CCGTTTCTAGAGGAGAGATCGT 58.792 50.000 0.00 0.00 34.93 3.73
2410 8537 1.103398 GTGCCTGGTTGCAGACAAGT 61.103 55.000 0.00 0.00 43.02 3.16
2411 8538 0.472044 TGCCTGGTTGCAGACAAGTA 59.528 50.000 0.00 0.00 36.16 2.24
2427 8554 7.685641 GCAGACAAGTATATATATGCCTCTCCC 60.686 44.444 5.44 0.00 0.00 4.30
2432 8559 2.349167 ATATATGCCTCTCCCCAGCA 57.651 50.000 0.00 0.00 41.50 4.41
2444 8571 1.305623 CCCAGCATCTTTCTGCCCT 59.694 57.895 0.00 0.00 43.33 5.19
2450 8577 2.782341 AGCATCTTTCTGCCCTATTCCT 59.218 45.455 0.00 0.00 43.33 3.36
2461 8588 4.307259 TGCCCTATTCCTGACCTAGAAAT 58.693 43.478 0.00 0.00 0.00 2.17
2467 8594 6.553100 CCTATTCCTGACCTAGAAATGAGTCT 59.447 42.308 0.00 0.00 0.00 3.24
2475 8602 4.790790 ACCTAGAAATGAGTCTTCCCCATT 59.209 41.667 0.00 0.00 32.46 3.16
2476 8603 5.104318 ACCTAGAAATGAGTCTTCCCCATTC 60.104 44.000 0.00 0.00 30.93 2.67
2478 8605 4.853007 AGAAATGAGTCTTCCCCATTCTG 58.147 43.478 0.00 0.00 30.93 3.02
2498 8626 1.469335 GGTGACGTCTCCAACTCCCA 61.469 60.000 27.42 0.00 0.00 4.37
2499 8627 0.391597 GTGACGTCTCCAACTCCCAA 59.608 55.000 17.92 0.00 0.00 4.12
2502 8630 1.070289 GACGTCTCCAACTCCCAAACT 59.930 52.381 8.70 0.00 0.00 2.66
2529 8657 0.251297 TCACCCATCTTTGCCTGGTG 60.251 55.000 0.00 0.00 46.19 4.17
2564 8692 6.657541 GGTTAGAGGTGATCCACATTTGTTTA 59.342 38.462 0.00 0.00 35.86 2.01
2566 8694 5.010282 AGAGGTGATCCACATTTGTTTACC 58.990 41.667 0.00 0.00 35.86 2.85
2582 8710 2.226962 TACCGAAGTAGTTGCCTCCT 57.773 50.000 0.00 0.00 0.00 3.69
2583 8711 0.896226 ACCGAAGTAGTTGCCTCCTC 59.104 55.000 0.00 0.00 0.00 3.71
2589 8717 0.099082 GTAGTTGCCTCCTCGTCTCG 59.901 60.000 0.00 0.00 0.00 4.04
2591 8719 1.444553 GTTGCCTCCTCGTCTCGTG 60.445 63.158 0.00 0.00 0.00 4.35
2610 8738 4.082679 TCGTGCTCCTACTTTTCTTCTCTC 60.083 45.833 0.00 0.00 0.00 3.20
2618 8746 2.039613 ACTTTTCTTCTCTCTGGCCCAG 59.960 50.000 3.69 3.69 0.00 4.45
2655 8783 1.874562 CTGCAAGAGAGGCAACTGC 59.125 57.895 0.00 0.00 44.12 4.40
2687 8815 1.003839 GTGTTGGGCGACAGGATCA 60.004 57.895 0.00 0.00 0.00 2.92
2689 8817 2.100631 GTTGGGCGACAGGATCACG 61.101 63.158 0.00 0.00 0.00 4.35
2703 8831 2.599645 ATCACGATGCTGGCAGGTCC 62.600 60.000 17.64 0.00 0.00 4.46
2715 8843 0.179108 GCAGGTCCGACTATGGTCAC 60.179 60.000 10.08 0.71 42.21 3.67
2744 8872 8.716646 CACTATATGTGGTAGTGTGATGAAAA 57.283 34.615 5.38 0.00 42.47 2.29
2745 8873 9.330063 CACTATATGTGGTAGTGTGATGAAAAT 57.670 33.333 5.38 0.00 42.47 1.82
2746 8874 9.905713 ACTATATGTGGTAGTGTGATGAAAATT 57.094 29.630 0.00 0.00 31.47 1.82
2749 8877 4.522405 TGTGGTAGTGTGATGAAAATTGGG 59.478 41.667 0.00 0.00 0.00 4.12
2750 8878 4.082245 GTGGTAGTGTGATGAAAATTGGGG 60.082 45.833 0.00 0.00 0.00 4.96
2751 8879 4.202620 TGGTAGTGTGATGAAAATTGGGGA 60.203 41.667 0.00 0.00 0.00 4.81
2752 8880 4.770010 GGTAGTGTGATGAAAATTGGGGAA 59.230 41.667 0.00 0.00 0.00 3.97
2753 8881 5.422012 GGTAGTGTGATGAAAATTGGGGAAT 59.578 40.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.982651 CTATATGATTTTCTTCTCCGGAACTTA 57.017 33.333 5.23 0.00 0.00 2.24
26 27 5.824624 TCTTGCCAAATGAATCATCCTACTC 59.175 40.000 0.00 0.00 0.00 2.59
230 232 8.121305 ACTTTGCAGTACAATGATTTGGAATA 57.879 30.769 0.00 0.00 38.31 1.75
231 233 6.996509 ACTTTGCAGTACAATGATTTGGAAT 58.003 32.000 0.00 0.00 38.31 3.01
233 235 6.403866 AACTTTGCAGTACAATGATTTGGA 57.596 33.333 0.00 0.00 38.31 3.53
235 237 9.013490 GCTATAACTTTGCAGTACAATGATTTG 57.987 33.333 0.00 0.00 38.31 2.32
324 355 3.645268 GAAGAACCCCAGCCGCCAT 62.645 63.158 0.00 0.00 0.00 4.40
326 357 4.035102 AGAAGAACCCCAGCCGCC 62.035 66.667 0.00 0.00 0.00 6.13
327 358 2.747855 CAGAAGAACCCCAGCCGC 60.748 66.667 0.00 0.00 0.00 6.53
328 359 2.747855 GCAGAAGAACCCCAGCCG 60.748 66.667 0.00 0.00 0.00 5.52
333 3735 1.743252 CTCGCAGCAGAAGAACCCC 60.743 63.158 0.00 0.00 0.00 4.95
466 4848 0.482887 CACCTCAAACCCTTTCCCCT 59.517 55.000 0.00 0.00 0.00 4.79
467 4849 0.481128 TCACCTCAAACCCTTTCCCC 59.519 55.000 0.00 0.00 0.00 4.81
534 4916 1.301623 CCCTATTTGTCCGGTGGCA 59.698 57.895 0.00 0.00 0.00 4.92
546 4928 2.125269 GCGACGGTGCACCCTATT 60.125 61.111 29.95 11.93 34.15 1.73
574 4956 3.984471 TGATGCGGGGATGGATCA 58.016 55.556 0.00 0.00 43.30 2.92
647 5029 3.347216 ACTTCAACACACAGAACTGCTT 58.653 40.909 1.46 0.00 0.00 3.91
687 5070 2.218454 CCACCCGGTCACTAACCCA 61.218 63.158 0.00 0.00 46.27 4.51
695 5078 3.072468 GGTCGATCCACCCGGTCA 61.072 66.667 0.00 0.00 35.97 4.02
729 5112 2.437895 GGCCGCTACTTTGGGGAC 60.438 66.667 1.74 0.00 41.89 4.46
736 5119 0.468648 GTCCTAATGGGCCGCTACTT 59.531 55.000 0.00 0.00 34.39 2.24
770 5153 0.878416 TTTCAGCCACAATGTACCGC 59.122 50.000 0.00 0.00 0.00 5.68
813 5196 6.092396 TCGGCTGTTAGATTATGCGTTTAAAA 59.908 34.615 0.00 0.00 0.00 1.52
833 5216 0.729116 CGACATCAGCATTTTCGGCT 59.271 50.000 0.00 0.00 43.77 5.52
849 5232 0.318784 AAACCGAGCTGTCTCACGAC 60.319 55.000 0.00 0.00 39.30 4.34
955 5359 2.046285 GCTGGGGGATTTGGACACG 61.046 63.158 0.00 0.00 0.00 4.49
959 5363 4.440829 GGCGCTGGGGGATTTGGA 62.441 66.667 7.64 0.00 0.00 3.53
996 5415 1.234821 TTTGCGAGTTCGGCATTTCT 58.765 45.000 3.50 0.00 40.23 2.52
1396 5870 8.178313 TCCTACAACATACTATATGTGTCTGG 57.822 38.462 2.33 8.60 30.04 3.86
1584 6063 1.757118 GATCTTGGATCGGTGACTCCA 59.243 52.381 0.00 0.00 39.78 3.86
1674 6161 4.025858 GGGCTGCCTGCTGAGACA 62.026 66.667 19.68 0.00 42.39 3.41
1704 6191 0.603065 GGAAACCAGCGCAATTTCCT 59.397 50.000 28.74 0.45 45.31 3.36
1716 6203 1.371183 CTCGTGAGGCTGGAAACCA 59.629 57.895 0.00 0.00 0.00 3.67
1739 6226 2.750712 AGACAAGCTACTCGAGGAGTTC 59.249 50.000 25.43 15.94 40.28 3.01
1811 7852 4.479619 CAAACAGCCTCAATCTTGTAAGC 58.520 43.478 0.00 0.00 0.00 3.09
1820 7861 3.094572 CTCCAATCCAAACAGCCTCAAT 58.905 45.455 0.00 0.00 0.00 2.57
1824 7865 0.613012 GGCTCCAATCCAAACAGCCT 60.613 55.000 0.84 0.00 45.40 4.58
1982 8025 0.323087 AGCCGGCCCGTTAGATTTTT 60.323 50.000 26.15 0.00 0.00 1.94
1983 8026 0.323087 AAGCCGGCCCGTTAGATTTT 60.323 50.000 26.15 3.11 0.00 1.82
1985 8028 0.542805 TAAAGCCGGCCCGTTAGATT 59.457 50.000 26.15 4.89 0.00 2.40
1987 8030 0.324285 TTTAAAGCCGGCCCGTTAGA 59.676 50.000 26.15 11.82 0.00 2.10
1988 8031 1.166989 TTTTAAAGCCGGCCCGTTAG 58.833 50.000 26.15 0.00 0.00 2.34
1989 8032 1.744522 GATTTTAAAGCCGGCCCGTTA 59.255 47.619 26.15 16.57 0.00 3.18
1992 8035 1.316706 TGGATTTTAAAGCCGGCCCG 61.317 55.000 26.15 0.00 40.70 6.13
1993 8036 0.899019 TTGGATTTTAAAGCCGGCCC 59.101 50.000 26.15 15.36 40.70 5.80
1994 8037 2.979814 ATTGGATTTTAAAGCCGGCC 57.020 45.000 26.15 4.35 40.70 6.13
1997 8040 7.167468 GCACACTAATATTGGATTTTAAAGCCG 59.833 37.037 7.50 0.00 40.70 5.52
2118 8168 5.315348 TGTCACAGACATGGATGAAAATGA 58.685 37.500 6.44 0.00 37.67 2.57
2125 8175 8.245491 TGAAATTATTTGTCACAGACATGGATG 58.755 33.333 0.12 0.00 42.40 3.51
2132 8182 7.094205 ACCCATCTGAAATTATTTGTCACAGAC 60.094 37.037 8.36 0.00 36.11 3.51
2143 8193 6.848562 ACTCCCTTACCCATCTGAAATTAT 57.151 37.500 0.00 0.00 0.00 1.28
2151 8201 4.024670 GCGATATACTCCCTTACCCATCT 58.975 47.826 0.00 0.00 0.00 2.90
2158 8209 6.420638 TGCTATAGTGCGATATACTCCCTTA 58.579 40.000 0.84 0.00 35.36 2.69
2159 8210 5.262009 TGCTATAGTGCGATATACTCCCTT 58.738 41.667 0.84 0.00 35.36 3.95
2219 8271 3.487120 AGCATGCTGAGCAATAGATCA 57.513 42.857 21.98 0.00 43.62 2.92
2236 8288 4.447290 TGGCTTAGAATTGCGTTATAGCA 58.553 39.130 0.00 0.00 46.54 3.49
2243 8295 2.884639 ACACTTTGGCTTAGAATTGCGT 59.115 40.909 0.00 0.00 0.00 5.24
2245 8297 3.578688 CCACACTTTGGCTTAGAATTGC 58.421 45.455 0.00 0.00 39.07 3.56
2246 8298 3.614870 GCCCACACTTTGGCTTAGAATTG 60.615 47.826 0.00 0.00 45.37 2.32
2255 8344 2.193536 AACTCGCCCACACTTTGGC 61.194 57.895 0.00 0.00 45.37 4.52
2257 8346 0.307760 GACAACTCGCCCACACTTTG 59.692 55.000 0.00 0.00 0.00 2.77
2261 8350 2.022129 CTCGACAACTCGCCCACAC 61.022 63.158 0.00 0.00 39.96 3.82
2265 8354 0.601841 TTTTCCTCGACAACTCGCCC 60.602 55.000 0.00 0.00 39.96 6.13
2268 8357 4.468095 ACAATTTTTCCTCGACAACTCG 57.532 40.909 0.00 0.00 41.65 4.18
2298 8388 3.625764 GCAACCATAAGACGAGCCAAATA 59.374 43.478 0.00 0.00 0.00 1.40
2301 8391 1.448985 GCAACCATAAGACGAGCCAA 58.551 50.000 0.00 0.00 0.00 4.52
2305 8395 2.854777 CTCTTCGCAACCATAAGACGAG 59.145 50.000 0.00 0.00 33.84 4.18
2308 8398 1.324736 CGCTCTTCGCAACCATAAGAC 59.675 52.381 0.00 0.00 39.08 3.01
2331 8458 0.543277 TCTCCATCCATGTGTCAGCC 59.457 55.000 0.00 0.00 0.00 4.85
2359 8486 2.044352 AAACGGGGCCATGGCTAC 60.044 61.111 34.70 26.39 41.60 3.58
2380 8507 1.040339 ACCAGGCACGATCTCTCCTC 61.040 60.000 0.00 0.00 0.00 3.71
2386 8513 1.376424 CTGCAACCAGGCACGATCT 60.376 57.895 0.00 0.00 39.25 2.75
2410 8537 5.156401 TGCTGGGGAGAGGCATATATATA 57.844 43.478 0.00 0.00 0.00 0.86
2411 8538 4.012931 TGCTGGGGAGAGGCATATATAT 57.987 45.455 0.00 0.00 0.00 0.86
2427 8554 2.653234 ATAGGGCAGAAAGATGCTGG 57.347 50.000 0.00 0.00 45.75 4.85
2432 8559 3.137360 GGTCAGGAATAGGGCAGAAAGAT 59.863 47.826 0.00 0.00 0.00 2.40
2444 8571 7.070074 GGAAGACTCATTTCTAGGTCAGGAATA 59.930 40.741 0.00 0.00 29.91 1.75
2450 8577 3.775316 GGGGAAGACTCATTTCTAGGTCA 59.225 47.826 0.00 0.00 0.00 4.02
2475 8602 0.469331 AGTTGGAGACGTCACCCAGA 60.469 55.000 26.35 15.31 0.00 3.86
2476 8603 0.038159 GAGTTGGAGACGTCACCCAG 60.038 60.000 26.35 0.00 0.00 4.45
2478 8605 1.292541 GGAGTTGGAGACGTCACCC 59.707 63.158 26.35 21.49 0.00 4.61
2481 8608 1.124780 TTTGGGAGTTGGAGACGTCA 58.875 50.000 19.50 0.00 0.00 4.35
2482 8609 1.070289 AGTTTGGGAGTTGGAGACGTC 59.930 52.381 7.70 7.70 0.00 4.34
2483 8610 1.129058 AGTTTGGGAGTTGGAGACGT 58.871 50.000 0.00 0.00 0.00 4.34
2518 8646 1.593196 TTCGTTCTCACCAGGCAAAG 58.407 50.000 0.00 0.00 0.00 2.77
2524 8652 4.238514 CTCTAACCTTTCGTTCTCACCAG 58.761 47.826 0.00 0.00 35.79 4.00
2529 8657 4.516365 TCACCTCTAACCTTTCGTTCTC 57.484 45.455 0.00 0.00 35.79 2.87
2582 8710 1.531423 AAAGTAGGAGCACGAGACGA 58.469 50.000 0.00 0.00 0.00 4.20
2583 8711 2.095161 AGAAAAGTAGGAGCACGAGACG 60.095 50.000 0.00 0.00 0.00 4.18
2589 8717 5.167845 CAGAGAGAAGAAAAGTAGGAGCAC 58.832 45.833 0.00 0.00 0.00 4.40
2591 8719 4.754322 CCAGAGAGAAGAAAAGTAGGAGC 58.246 47.826 0.00 0.00 0.00 4.70
2610 8738 1.550072 CCCAAATAACAACTGGGCCAG 59.450 52.381 31.62 31.62 43.35 4.85
2618 8746 4.217550 TGCAGCTAGAACCCAAATAACAAC 59.782 41.667 0.00 0.00 0.00 3.32
2633 8761 1.066286 AGTTGCCTCTCTTGCAGCTAG 60.066 52.381 0.00 0.00 46.51 3.42
2687 8815 4.457496 CGGACCTGCCAGCATCGT 62.457 66.667 0.00 0.00 35.94 3.73
2689 8817 1.676678 TAGTCGGACCTGCCAGCATC 61.677 60.000 4.14 0.00 35.94 3.91
2697 8825 0.100682 CGTGACCATAGTCGGACCTG 59.899 60.000 4.14 3.03 46.74 4.00


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

AutoCloner maintained by Alex Coulton.