Multiple sequence alignment - TraesCS7A01G404400

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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 TraesCS7A01G404400 chr7A 100.000 3782 0 0 956 4737 585358810 585355029 0.000000e+00 6985.0
1 TraesCS7A01G404400 chr7A 100.000 441 0 0 1 441 585359765 585359325 0.000000e+00 815.0
2 TraesCS7A01G404400 chr7A 89.160 369 39 1 2884 3251 221267308 221266940 4.320000e-125 459.0
3 TraesCS7A01G404400 chr7B 94.534 2744 101 23 1999 4734 544481915 544479213 0.000000e+00 4191.0
4 TraesCS7A01G404400 chr7B 95.595 1067 41 2 956 2016 544482998 544481932 0.000000e+00 1705.0
5 TraesCS7A01G404400 chr7B 95.294 425 16 3 17 439 544483514 544483092 0.000000e+00 671.0
6 TraesCS7A01G404400 chr7B 89.946 368 36 1 2884 3250 193310835 193311202 1.540000e-129 473.0
7 TraesCS7A01G404400 chr7D 95.168 1966 72 13 2774 4734 512747182 512745235 0.000000e+00 3083.0
8 TraesCS7A01G404400 chr7D 93.253 1586 54 19 956 2499 512749193 512747619 0.000000e+00 2287.0
9 TraesCS7A01G404400 chr7D 93.287 432 21 5 13 439 512749715 512749287 8.650000e-177 630.0
10 TraesCS7A01G404400 chr7D 89.160 369 39 1 2884 3251 208223488 208223120 4.320000e-125 459.0
11 TraesCS7A01G404400 chr7D 96.753 154 5 0 2576 2729 512747334 512747181 1.690000e-64 257.0
12 TraesCS7A01G404400 chr5D 86.031 451 55 5 2885 3334 374391716 374392159 1.190000e-130 477.0
13 TraesCS7A01G404400 chr5B 88.060 402 46 2 2885 3285 446996505 446996905 4.290000e-130 475.0
14 TraesCS7A01G404400 chr5A 89.333 375 38 2 2885 3258 476225335 476225708 2.000000e-128 470.0
15 TraesCS7A01G404400 chr3B 84.935 385 54 4 2885 3267 638357251 638356869 2.070000e-103 387.0
16 TraesCS7A01G404400 chr4B 92.000 50 2 2 3878 3926 449297788 449297836 8.510000e-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 TraesCS7A01G404400 chr7A 585355029 585359765 4736 True 3900.00 6985 100.00000 1 4737 2 chr7A.!!$R2 4736
1 TraesCS7A01G404400 chr7B 544479213 544483514 4301 True 2189.00 4191 95.14100 17 4734 3 chr7B.!!$R1 4717
2 TraesCS7A01G404400 chr7D 512745235 512749715 4480 True 1564.25 3083 94.61525 13 4734 4 chr7D.!!$R2 4721

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
50 51 1.338973 GTGGACCAACGTGTACAGAGA 59.661 52.381 0.0 0.0 27.08 3.10 F
68 69 1.971357 AGAAACTCTTGCCTCTCGGAA 59.029 47.619 0.0 0.0 0.00 4.30 F
1505 1522 0.467290 GGCAACCACCACCAAGAAGA 60.467 55.000 0.0 0.0 0.00 2.87 F
2134 2193 0.043334 TGGGAAGAGGGAAGAGGGAG 59.957 60.000 0.0 0.0 0.00 4.30 F
2763 3044 0.043053 CACACGCAACGAACACTCTG 60.043 55.000 0.0 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1506 0.178990 GCCTCTTCTTGGTGGTGGTT 60.179 55.000 0.00 0.00 0.00 3.67 R
1515 1532 0.685785 CCTCAGCAGCTACTCCTCCA 60.686 60.000 0.00 0.00 0.00 3.86 R
2744 3025 0.043053 CAGAGTGTTCGTTGCGTGTG 60.043 55.000 0.00 0.00 0.00 3.82 R
3179 3506 0.674895 GCTTGAAGTCAGACCCGCAT 60.675 55.000 0.00 0.00 0.00 4.73 R
3786 4116 1.073763 AGTAAGTCTGTGGCCATTGCA 59.926 47.619 9.72 0.32 40.13 4.08 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 4.928661 CCGAACAGGACTCAAAAGTATG 57.071 45.455 0.00 0.00 45.00 2.39
22 23 3.684788 CCGAACAGGACTCAAAAGTATGG 59.315 47.826 0.00 0.00 45.00 2.74
23 24 4.315803 CGAACAGGACTCAAAAGTATGGT 58.684 43.478 0.00 0.00 35.28 3.55
29 30 7.690256 ACAGGACTCAAAAGTATGGTTAGATT 58.310 34.615 0.00 0.00 35.28 2.40
38 39 5.772393 AGTATGGTTAGATTGTGGACCAA 57.228 39.130 0.00 0.00 44.60 3.67
45 46 2.762745 AGATTGTGGACCAACGTGTAC 58.237 47.619 0.00 0.00 35.44 2.90
50 51 1.338973 GTGGACCAACGTGTACAGAGA 59.661 52.381 0.00 0.00 27.08 3.10
65 66 2.029470 ACAGAGAAACTCTTGCCTCTCG 60.029 50.000 0.00 0.00 38.99 4.04
68 69 1.971357 AGAAACTCTTGCCTCTCGGAA 59.029 47.619 0.00 0.00 0.00 4.30
79 80 2.223994 GCCTCTCGGAATGTAACCCTAC 60.224 54.545 0.00 0.00 0.00 3.18
87 88 6.072649 TCGGAATGTAACCCTACTCATATGA 58.927 40.000 5.07 5.07 0.00 2.15
137 138 4.285260 ACCGAGTCATAGGGTAACTGTTTT 59.715 41.667 0.00 0.00 30.76 2.43
279 280 8.891501 GGGAATAATAAGGGAAGGAGAGAATTA 58.108 37.037 0.00 0.00 0.00 1.40
439 444 2.628178 CACCAAAACTTTTCCCCTCTCC 59.372 50.000 0.00 0.00 0.00 3.71
1001 1006 4.389374 CACACACAACACCTTTATCTCCT 58.611 43.478 0.00 0.00 0.00 3.69
1013 1018 6.550854 CACCTTTATCTCCTTCTCTCTCATCT 59.449 42.308 0.00 0.00 0.00 2.90
1017 1022 4.437682 TCTCCTTCTCTCTCATCTCTCC 57.562 50.000 0.00 0.00 0.00 3.71
1019 1024 2.855599 TCCTTCTCTCTCATCTCTCCCA 59.144 50.000 0.00 0.00 0.00 4.37
1089 1103 9.672673 TCTCTATTTATATTAGCTGCCATTTCC 57.327 33.333 0.00 0.00 0.00 3.13
1218 1232 2.267324 GCAGCGGCTTCTTCCTCT 59.733 61.111 0.00 0.00 36.96 3.69
1306 1320 4.465446 TCCCCCTCCTCAGCCTCG 62.465 72.222 0.00 0.00 0.00 4.63
1505 1522 0.467290 GGCAACCACCACCAAGAAGA 60.467 55.000 0.00 0.00 0.00 2.87
1506 1523 0.954452 GCAACCACCACCAAGAAGAG 59.046 55.000 0.00 0.00 0.00 2.85
1515 1532 2.046507 CAAGAAGAGGCAGCGGCT 60.047 61.111 9.17 6.56 42.48 5.52
1524 1541 3.461773 GCAGCGGCTGGAGGAGTA 61.462 66.667 29.44 0.00 36.96 2.59
1581 1598 2.684499 GCAGGAGGAAGGGGAAGGG 61.684 68.421 0.00 0.00 0.00 3.95
1882 1899 6.325919 TGGATGTTTATGTTGTGAACTTCC 57.674 37.500 11.32 11.32 44.37 3.46
1887 1904 8.871686 ATGTTTATGTTGTGAACTTCCTTTTC 57.128 30.769 0.00 0.00 0.00 2.29
1972 1989 1.043673 AGTGGCGGTGGATCTAGGAC 61.044 60.000 0.00 0.00 0.00 3.85
1973 1990 2.125326 TGGCGGTGGATCTAGGACG 61.125 63.158 0.00 0.00 0.00 4.79
1991 2008 1.014044 CGAAGTGCCGCTGCTTCTTA 61.014 55.000 18.91 0.00 39.01 2.10
1993 2010 1.328986 GAAGTGCCGCTGCTTCTTATC 59.671 52.381 16.01 0.00 38.36 1.75
1995 2012 0.744414 GTGCCGCTGCTTCTTATCCA 60.744 55.000 0.70 0.00 38.71 3.41
2026 2078 4.052608 CTCTCTCTCGCTGACGTATCTTA 58.947 47.826 0.00 0.00 41.18 2.10
2131 2190 2.112190 GTAGTGGGAAGAGGGAAGAGG 58.888 57.143 0.00 0.00 0.00 3.69
2134 2193 0.043334 TGGGAAGAGGGAAGAGGGAG 59.957 60.000 0.00 0.00 0.00 4.30
2258 2317 4.730324 GCGCTTGTTTTGCCTTTTCAATTT 60.730 37.500 0.00 0.00 0.00 1.82
2296 2355 0.248843 AGCGCAGAGAGAGAAAAGGG 59.751 55.000 11.47 0.00 0.00 3.95
2423 2484 1.152546 GGCTCCTCCTCCTCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
2435 2496 0.823460 CTCTCTCCCCTTCTCTGCAC 59.177 60.000 0.00 0.00 0.00 4.57
2436 2497 0.411452 TCTCTCCCCTTCTCTGCACT 59.589 55.000 0.00 0.00 0.00 4.40
2437 2498 0.823460 CTCTCCCCTTCTCTGCACTC 59.177 60.000 0.00 0.00 0.00 3.51
2438 2499 0.411452 TCTCCCCTTCTCTGCACTCT 59.589 55.000 0.00 0.00 0.00 3.24
2439 2500 0.823460 CTCCCCTTCTCTGCACTCTC 59.177 60.000 0.00 0.00 0.00 3.20
2440 2501 0.411452 TCCCCTTCTCTGCACTCTCT 59.589 55.000 0.00 0.00 0.00 3.10
2441 2502 0.823460 CCCCTTCTCTGCACTCTCTC 59.177 60.000 0.00 0.00 0.00 3.20
2442 2503 1.619432 CCCCTTCTCTGCACTCTCTCT 60.619 57.143 0.00 0.00 0.00 3.10
2443 2504 1.477700 CCCTTCTCTGCACTCTCTCTG 59.522 57.143 0.00 0.00 0.00 3.35
2444 2505 1.135024 CCTTCTCTGCACTCTCTCTGC 60.135 57.143 0.00 0.00 35.03 4.26
2445 2506 1.545136 CTTCTCTGCACTCTCTCTGCA 59.455 52.381 0.00 0.00 42.42 4.41
2446 2507 1.625511 TCTCTGCACTCTCTCTGCAA 58.374 50.000 0.00 0.00 43.96 4.08
2447 2508 1.545136 TCTCTGCACTCTCTCTGCAAG 59.455 52.381 0.00 0.00 43.96 4.01
2480 2544 0.761187 AGCAGTGCCTTTCAGTCTCA 59.239 50.000 12.58 0.00 0.00 3.27
2568 2849 6.082031 AGATACTGGTAGCTAGAGAGAGAGA 58.918 44.000 0.00 0.00 28.84 3.10
2569 2850 4.689612 ACTGGTAGCTAGAGAGAGAGAG 57.310 50.000 0.00 0.00 0.00 3.20
2570 2851 4.295201 ACTGGTAGCTAGAGAGAGAGAGA 58.705 47.826 0.00 0.00 0.00 3.10
2571 2852 4.719773 ACTGGTAGCTAGAGAGAGAGAGAA 59.280 45.833 0.00 0.00 0.00 2.87
2572 2853 5.163301 ACTGGTAGCTAGAGAGAGAGAGAAG 60.163 48.000 0.00 0.00 0.00 2.85
2573 2854 4.966168 TGGTAGCTAGAGAGAGAGAGAAGA 59.034 45.833 0.00 0.00 0.00 2.87
2574 2855 5.070446 TGGTAGCTAGAGAGAGAGAGAAGAG 59.930 48.000 0.00 0.00 0.00 2.85
2575 2856 5.304614 GGTAGCTAGAGAGAGAGAGAAGAGA 59.695 48.000 0.00 0.00 0.00 3.10
2576 2857 5.543507 AGCTAGAGAGAGAGAGAAGAGAG 57.456 47.826 0.00 0.00 0.00 3.20
2588 2869 3.272020 AGAGAAGAGAGAGATGGTCCCTT 59.728 47.826 0.00 0.00 0.00 3.95
2593 2874 1.280421 AGAGAGATGGTCCCTTTGCAC 59.720 52.381 0.00 0.00 0.00 4.57
2606 2887 4.959839 TCCCTTTGCACCTTAAATTATCCC 59.040 41.667 0.00 0.00 0.00 3.85
2700 2981 1.446792 CCTGACTAGCCACAGTGCG 60.447 63.158 0.00 0.00 36.02 5.34
2733 3014 4.755546 GCTCGATAGCTCCGATCG 57.244 61.111 8.51 8.51 45.85 3.69
2742 3023 3.893763 CTCCGATCGAGCCGCTGT 61.894 66.667 18.66 0.00 0.00 4.40
2743 3024 4.193334 TCCGATCGAGCCGCTGTG 62.193 66.667 18.66 0.00 0.00 3.66
2746 3027 3.558411 GATCGAGCCGCTGTGCAC 61.558 66.667 10.75 10.75 0.00 4.57
2747 3028 4.377708 ATCGAGCCGCTGTGCACA 62.378 61.111 20.37 20.37 0.00 4.57
2760 3041 2.707039 GCACACGCAACGAACACT 59.293 55.556 0.00 0.00 38.36 3.55
2761 3042 1.367665 GCACACGCAACGAACACTC 60.368 57.895 0.00 0.00 38.36 3.51
2762 3043 1.762222 GCACACGCAACGAACACTCT 61.762 55.000 0.00 0.00 38.36 3.24
2763 3044 0.043053 CACACGCAACGAACACTCTG 60.043 55.000 0.00 0.00 0.00 3.35
2764 3045 1.083401 CACGCAACGAACACTCTGC 60.083 57.895 0.00 0.00 0.00 4.26
2765 3046 2.168621 CGCAACGAACACTCTGCG 59.831 61.111 0.55 0.55 39.33 5.18
2766 3047 2.551270 GCAACGAACACTCTGCGG 59.449 61.111 0.00 0.00 0.00 5.69
2767 3048 2.244651 GCAACGAACACTCTGCGGT 61.245 57.895 0.00 0.00 0.00 5.68
2768 3049 1.853319 CAACGAACACTCTGCGGTC 59.147 57.895 0.00 0.00 0.00 4.79
2769 3050 1.300697 AACGAACACTCTGCGGTCC 60.301 57.895 0.00 0.00 0.00 4.46
2770 3051 2.805353 CGAACACTCTGCGGTCCG 60.805 66.667 6.99 6.99 0.00 4.79
2903 3230 3.072486 GCAGATGCACATGTGGGGC 62.072 63.158 26.55 13.52 41.59 5.80
3059 3386 4.329545 TTCCGCACCCTGCAGACC 62.330 66.667 17.39 0.00 45.36 3.85
3179 3506 1.374631 CAAGCTCTGGTACTGCGCA 60.375 57.895 10.98 10.98 40.45 6.09
3320 3647 1.227438 CGAGGTTGACCACACCGTT 60.227 57.895 2.56 0.00 38.89 4.44
3499 3829 5.702670 TGGCAGTACGTACTATCTGTATACC 59.297 44.000 26.95 16.08 34.13 2.73
3561 3891 4.098807 ACAGTGAAGGGTGCGTTTTAATTT 59.901 37.500 0.00 0.00 0.00 1.82
3800 4130 1.478916 CATGAATGCAATGGCCACAGA 59.521 47.619 8.16 0.00 40.13 3.41
3802 4132 1.180029 GAATGCAATGGCCACAGACT 58.820 50.000 8.16 0.00 40.13 3.24
3825 4155 6.380274 ACTTACTGGCTTATTACTGCTACTCA 59.620 38.462 0.00 0.00 0.00 3.41
3830 4160 4.099573 GGCTTATTACTGCTACTCACTCCA 59.900 45.833 0.00 0.00 0.00 3.86
3840 4170 3.879892 GCTACTCACTCCATCCCAAAATC 59.120 47.826 0.00 0.00 0.00 2.17
3861 4191 3.493129 TCAGTGTCGTTGATTTAGCACAC 59.507 43.478 0.00 0.00 35.42 3.82
3862 4192 3.247411 CAGTGTCGTTGATTTAGCACACA 59.753 43.478 0.00 0.00 37.25 3.72
3868 4198 7.377397 GTGTCGTTGATTTAGCACACAAATTTA 59.623 33.333 0.00 0.00 35.31 1.40
3893 4223 7.803724 AGTACAAAGTTGTTCTAAATTAGCGG 58.196 34.615 1.35 0.00 42.35 5.52
4233 4563 3.837355 ACATGGGATATTTCCAGCTTCC 58.163 45.455 4.48 0.00 44.60 3.46
4332 4663 5.245751 TCCTCAATAGAAAATGGCTGCAAAA 59.754 36.000 0.50 0.00 0.00 2.44
4336 4667 7.090173 TCAATAGAAAATGGCTGCAAAACTAC 58.910 34.615 0.50 0.00 0.00 2.73
4350 4681 0.749049 AACTACTATTCGCCCCGTCC 59.251 55.000 0.00 0.00 0.00 4.79
4351 4682 1.285023 CTACTATTCGCCCCGTCCG 59.715 63.158 0.00 0.00 0.00 4.79
4484 4815 2.191375 CGCATGCCTGGTCATCCT 59.809 61.111 13.15 0.00 34.23 3.24
4553 4884 9.408648 AGTAGTCAAGAAAAGGAAGAATCAAAA 57.591 29.630 0.00 0.00 0.00 2.44
4612 4943 9.468532 GCAATGGACATAATTATTTCTTCTTCC 57.531 33.333 10.62 3.19 0.00 3.46
4644 4977 5.011090 AGAACTTCATAATCTAGCACGCA 57.989 39.130 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.315803 ACCATACTTTTGAGTCCTGTTCG 58.684 43.478 0.00 0.00 0.00 3.95
2 3 7.159372 TCTAACCATACTTTTGAGTCCTGTTC 58.841 38.462 0.00 0.00 0.00 3.18
4 5 6.681729 TCTAACCATACTTTTGAGTCCTGT 57.318 37.500 0.00 0.00 0.00 4.00
5 6 7.607991 ACAATCTAACCATACTTTTGAGTCCTG 59.392 37.037 0.00 0.00 0.00 3.86
6 7 7.607991 CACAATCTAACCATACTTTTGAGTCCT 59.392 37.037 0.00 0.00 0.00 3.85
7 8 7.148239 CCACAATCTAACCATACTTTTGAGTCC 60.148 40.741 0.00 0.00 0.00 3.85
8 9 7.606456 TCCACAATCTAACCATACTTTTGAGTC 59.394 37.037 0.00 0.00 0.00 3.36
9 10 7.390718 GTCCACAATCTAACCATACTTTTGAGT 59.609 37.037 0.00 0.00 0.00 3.41
10 11 7.148239 GGTCCACAATCTAACCATACTTTTGAG 60.148 40.741 0.00 0.00 0.00 3.02
11 12 6.657541 GGTCCACAATCTAACCATACTTTTGA 59.342 38.462 0.00 0.00 0.00 2.69
13 14 6.548321 TGGTCCACAATCTAACCATACTTTT 58.452 36.000 0.00 0.00 36.88 2.27
14 15 6.134535 TGGTCCACAATCTAACCATACTTT 57.865 37.500 0.00 0.00 36.88 2.66
15 16 5.772393 TGGTCCACAATCTAACCATACTT 57.228 39.130 0.00 0.00 36.88 2.24
16 17 5.497474 GTTGGTCCACAATCTAACCATACT 58.503 41.667 0.00 0.00 41.23 2.12
17 18 4.331717 CGTTGGTCCACAATCTAACCATAC 59.668 45.833 0.00 0.00 41.23 2.39
18 19 4.020039 ACGTTGGTCCACAATCTAACCATA 60.020 41.667 0.00 0.00 41.23 2.74
19 20 3.244770 ACGTTGGTCCACAATCTAACCAT 60.245 43.478 0.00 0.00 41.23 3.55
20 21 2.105134 ACGTTGGTCCACAATCTAACCA 59.895 45.455 0.00 0.00 41.95 3.67
21 22 2.482721 CACGTTGGTCCACAATCTAACC 59.517 50.000 0.00 0.00 41.95 2.85
22 23 3.135994 ACACGTTGGTCCACAATCTAAC 58.864 45.455 0.00 0.00 41.95 2.34
23 24 3.478857 ACACGTTGGTCCACAATCTAA 57.521 42.857 0.00 0.00 41.95 2.10
29 30 1.067974 CTCTGTACACGTTGGTCCACA 59.932 52.381 0.00 0.00 0.00 4.17
38 39 3.381949 GCAAGAGTTTCTCTGTACACGT 58.618 45.455 0.00 0.00 40.28 4.49
45 46 2.605030 CGAGAGGCAAGAGTTTCTCTG 58.395 52.381 0.00 0.00 40.28 3.35
112 113 3.288964 CAGTTACCCTATGACTCGGTCT 58.711 50.000 5.77 0.00 33.15 3.85
137 138 8.043113 AGCAAGAAAATCAGTGACAGTATATCA 58.957 33.333 0.00 0.00 0.00 2.15
279 280 1.217942 ACCTTGGGACTTGGAAGCTTT 59.782 47.619 0.00 0.00 0.00 3.51
1001 1006 3.527253 AGAGTGGGAGAGATGAGAGAGAA 59.473 47.826 0.00 0.00 0.00 2.87
1013 1018 4.396357 AGAGAAGAAGAAGAGTGGGAGA 57.604 45.455 0.00 0.00 0.00 3.71
1017 1022 4.039730 TCACCAAGAGAAGAAGAAGAGTGG 59.960 45.833 0.00 0.00 0.00 4.00
1019 1024 5.046663 GGATCACCAAGAGAAGAAGAAGAGT 60.047 44.000 0.00 0.00 35.97 3.24
1089 1103 0.539051 GAGAGACAGGGTGTGGATGG 59.461 60.000 0.00 0.00 0.00 3.51
1218 1232 1.618447 GTAGCTGGGGAAGGGGGAA 60.618 63.158 0.00 0.00 0.00 3.97
1306 1320 1.614241 TAGGTTGAGGAGGAAGGCGC 61.614 60.000 0.00 0.00 0.00 6.53
1311 1325 1.652947 GGTGGTAGGTTGAGGAGGAA 58.347 55.000 0.00 0.00 0.00 3.36
1489 1506 0.178990 GCCTCTTCTTGGTGGTGGTT 60.179 55.000 0.00 0.00 0.00 3.67
1515 1532 0.685785 CCTCAGCAGCTACTCCTCCA 60.686 60.000 0.00 0.00 0.00 3.86
1524 1541 1.616091 GGCTTCTCTCCTCAGCAGCT 61.616 60.000 0.00 0.00 35.05 4.24
1550 1567 1.845627 CTCCTGCCCTTCTTCCTGCA 61.846 60.000 0.00 0.00 0.00 4.41
1581 1598 2.817056 GCTGCCATCCTCCTCCTCC 61.817 68.421 0.00 0.00 0.00 4.30
1641 1658 1.133809 ACTGCCCCTTTGTGAGCCTA 61.134 55.000 0.00 0.00 0.00 3.93
1868 1885 7.410120 AAAGAGAAAAGGAAGTTCACAACAT 57.590 32.000 5.01 0.00 0.00 2.71
1882 1899 2.872245 TCACGCACAGGAAAGAGAAAAG 59.128 45.455 0.00 0.00 0.00 2.27
1887 1904 2.095567 CCAATTCACGCACAGGAAAGAG 60.096 50.000 0.00 0.00 0.00 2.85
1955 1972 2.125326 CGTCCTAGATCCACCGCCA 61.125 63.158 0.00 0.00 0.00 5.69
1972 1989 1.014044 TAAGAAGCAGCGGCACTTCG 61.014 55.000 22.10 0.88 45.56 3.79
1973 1990 1.328986 GATAAGAAGCAGCGGCACTTC 59.671 52.381 21.33 21.33 44.61 3.01
1991 2008 3.433598 CGAGAGAGAGAGAGAGGTTGGAT 60.434 52.174 0.00 0.00 0.00 3.41
1993 2010 2.288666 CGAGAGAGAGAGAGAGGTTGG 58.711 57.143 0.00 0.00 0.00 3.77
1995 2012 1.559682 AGCGAGAGAGAGAGAGAGGTT 59.440 52.381 0.00 0.00 0.00 3.50
2026 2078 3.347216 CTCCCGGTTCAGTCAAATCAAT 58.653 45.455 0.00 0.00 0.00 2.57
2131 2190 0.825010 CCATTACTGCATGCCCCTCC 60.825 60.000 16.68 0.00 0.00 4.30
2134 2193 1.456331 AGCCATTACTGCATGCCCC 60.456 57.895 16.68 0.00 0.00 5.80
2214 2273 2.996621 CAAACTCCAAGATCGGTCAGTC 59.003 50.000 0.00 0.00 0.00 3.51
2296 2355 5.213891 GATCTTTCTTCCCAGATCTCTCC 57.786 47.826 0.00 0.00 41.56 3.71
2406 2467 1.152546 GGGAGAGAGGAGGAGGAGC 60.153 68.421 0.00 0.00 0.00 4.70
2408 2469 0.556380 AAGGGGAGAGAGGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
2409 2470 0.105709 GAAGGGGAGAGAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
2423 2484 1.477700 CAGAGAGAGTGCAGAGAAGGG 59.522 57.143 0.00 0.00 0.00 3.95
2435 2496 1.349026 TGGGGTTTCTTGCAGAGAGAG 59.651 52.381 0.00 0.00 35.37 3.20
2436 2497 1.072331 GTGGGGTTTCTTGCAGAGAGA 59.928 52.381 0.00 0.00 35.37 3.10
2437 2498 1.528129 GTGGGGTTTCTTGCAGAGAG 58.472 55.000 0.00 0.00 35.37 3.20
2438 2499 0.110486 GGTGGGGTTTCTTGCAGAGA 59.890 55.000 0.00 0.00 0.00 3.10
2439 2500 0.178992 TGGTGGGGTTTCTTGCAGAG 60.179 55.000 0.00 0.00 0.00 3.35
2440 2501 0.467290 GTGGTGGGGTTTCTTGCAGA 60.467 55.000 0.00 0.00 0.00 4.26
2441 2502 1.795170 CGTGGTGGGGTTTCTTGCAG 61.795 60.000 0.00 0.00 0.00 4.41
2442 2503 1.826054 CGTGGTGGGGTTTCTTGCA 60.826 57.895 0.00 0.00 0.00 4.08
2443 2504 1.515521 CTCGTGGTGGGGTTTCTTGC 61.516 60.000 0.00 0.00 0.00 4.01
2444 2505 1.515521 GCTCGTGGTGGGGTTTCTTG 61.516 60.000 0.00 0.00 0.00 3.02
2445 2506 1.228154 GCTCGTGGTGGGGTTTCTT 60.228 57.895 0.00 0.00 0.00 2.52
2446 2507 2.397413 CTGCTCGTGGTGGGGTTTCT 62.397 60.000 0.00 0.00 0.00 2.52
2447 2508 1.966451 CTGCTCGTGGTGGGGTTTC 60.966 63.158 0.00 0.00 0.00 2.78
2470 2534 4.129380 CAATGGACTGTGTGAGACTGAAA 58.871 43.478 0.00 0.00 0.00 2.69
2480 2544 2.346766 TGTTGAGCAATGGACTGTGT 57.653 45.000 0.00 0.00 0.00 3.72
2541 2605 6.045072 TCTCTCTAGCTACCAGTATCTAGC 57.955 45.833 9.75 0.00 33.93 3.42
2568 2849 3.774216 CAAAGGGACCATCTCTCTCTTCT 59.226 47.826 0.00 0.00 0.00 2.85
2569 2850 3.681313 GCAAAGGGACCATCTCTCTCTTC 60.681 52.174 0.00 0.00 0.00 2.87
2570 2851 2.238395 GCAAAGGGACCATCTCTCTCTT 59.762 50.000 0.00 0.00 0.00 2.85
2571 2852 1.836802 GCAAAGGGACCATCTCTCTCT 59.163 52.381 0.00 0.00 0.00 3.10
2572 2853 1.556911 TGCAAAGGGACCATCTCTCTC 59.443 52.381 0.00 0.00 0.00 3.20
2573 2854 1.280421 GTGCAAAGGGACCATCTCTCT 59.720 52.381 0.00 0.00 0.00 3.10
2574 2855 1.743996 GTGCAAAGGGACCATCTCTC 58.256 55.000 0.00 0.00 0.00 3.20
2575 2856 3.965888 GTGCAAAGGGACCATCTCT 57.034 52.632 0.00 0.00 0.00 3.10
2729 3010 3.558411 GTGCACAGCGGCTCGATC 61.558 66.667 13.17 0.00 34.04 3.69
2730 3011 4.377708 TGTGCACAGCGGCTCGAT 62.378 61.111 17.42 0.00 34.04 3.59
2743 3024 1.367665 GAGTGTTCGTTGCGTGTGC 60.368 57.895 0.00 0.00 43.20 4.57
2744 3025 0.043053 CAGAGTGTTCGTTGCGTGTG 60.043 55.000 0.00 0.00 0.00 3.82
2745 3026 1.762222 GCAGAGTGTTCGTTGCGTGT 61.762 55.000 0.00 0.00 0.00 4.49
2746 3027 1.083401 GCAGAGTGTTCGTTGCGTG 60.083 57.895 0.00 0.00 0.00 5.34
2747 3028 3.319904 GCAGAGTGTTCGTTGCGT 58.680 55.556 0.00 0.00 0.00 5.24
2749 3030 2.159272 GACCGCAGAGTGTTCGTTGC 62.159 60.000 0.00 0.00 0.00 4.17
2750 3031 1.557443 GGACCGCAGAGTGTTCGTTG 61.557 60.000 0.00 0.00 0.00 4.10
2751 3032 1.300697 GGACCGCAGAGTGTTCGTT 60.301 57.895 0.00 0.00 0.00 3.85
2752 3033 2.338984 GGACCGCAGAGTGTTCGT 59.661 61.111 0.00 0.00 0.00 3.85
2753 3034 2.805353 CGGACCGCAGAGTGTTCG 60.805 66.667 0.00 0.00 0.00 3.95
2766 3047 4.030452 GTGCTTGCTGGTGCGGAC 62.030 66.667 0.00 0.00 43.34 4.79
2769 3050 4.332637 GTGGTGCTTGCTGGTGCG 62.333 66.667 0.00 0.00 43.34 5.34
2770 3051 2.908940 AGTGGTGCTTGCTGGTGC 60.909 61.111 0.00 0.00 40.20 5.01
2771 3052 2.263741 GGAGTGGTGCTTGCTGGTG 61.264 63.158 0.00 0.00 0.00 4.17
2772 3053 2.113986 GGAGTGGTGCTTGCTGGT 59.886 61.111 0.00 0.00 0.00 4.00
2903 3230 4.789075 CGGTACTGCGACCCGTGG 62.789 72.222 0.00 0.00 35.95 4.94
3059 3386 1.207593 GTGCTTGCGCTTGTAGTGG 59.792 57.895 9.73 0.00 36.97 4.00
3179 3506 0.674895 GCTTGAAGTCAGACCCGCAT 60.675 55.000 0.00 0.00 0.00 4.73
3185 3512 1.070309 CGCTTGTGCTTGAAGTCAGAC 60.070 52.381 0.00 0.00 36.97 3.51
3188 3515 0.815213 AGCGCTTGTGCTTGAAGTCA 60.815 50.000 2.64 0.00 44.46 3.41
3499 3829 2.991076 GCCTGCCTGCAAGCTTCAG 61.991 63.158 9.08 15.09 31.23 3.02
3588 3918 3.999663 CGATCCCTTGATTAATCCAGCTC 59.000 47.826 12.90 7.26 0.00 4.09
3674 4004 2.445905 TGAAGCTAGCTAGGGTAGGCTA 59.554 50.000 19.70 0.00 39.65 3.93
3675 4005 1.218196 TGAAGCTAGCTAGGGTAGGCT 59.782 52.381 19.70 9.85 41.92 4.58
3784 4114 1.636148 AAGTCTGTGGCCATTGCATT 58.364 45.000 9.72 0.00 40.13 3.56
3785 4115 2.094675 GTAAGTCTGTGGCCATTGCAT 58.905 47.619 9.72 0.00 40.13 3.96
3786 4116 1.073763 AGTAAGTCTGTGGCCATTGCA 59.926 47.619 9.72 0.32 40.13 4.08
3787 4117 1.470098 CAGTAAGTCTGTGGCCATTGC 59.530 52.381 9.72 1.65 39.17 3.56
3798 4128 5.941555 AGCAGTAATAAGCCAGTAAGTCT 57.058 39.130 0.00 0.00 0.00 3.24
3800 4130 6.380274 TGAGTAGCAGTAATAAGCCAGTAAGT 59.620 38.462 0.00 0.00 0.00 2.24
3802 4132 6.380274 AGTGAGTAGCAGTAATAAGCCAGTAA 59.620 38.462 0.00 0.00 0.00 2.24
3818 4148 3.350219 TTTTGGGATGGAGTGAGTAGC 57.650 47.619 0.00 0.00 0.00 3.58
3825 4155 3.690460 GACACTGATTTTGGGATGGAGT 58.310 45.455 0.00 0.00 0.00 3.85
3830 4160 3.750371 TCAACGACACTGATTTTGGGAT 58.250 40.909 0.00 0.00 0.00 3.85
3840 4170 3.247411 TGTGTGCTAAATCAACGACACTG 59.753 43.478 0.00 0.00 35.74 3.66
3856 4186 7.749539 ACAACTTTGTACTAAATTTGTGTGC 57.250 32.000 17.36 4.37 40.16 4.57
3868 4198 7.572539 GCCGCTAATTTAGAACAACTTTGTACT 60.573 37.037 7.63 0.00 41.31 2.73
3893 4223 4.706962 ACTCCTTCATCCCAAAATAAGTGC 59.293 41.667 0.00 0.00 0.00 4.40
3984 4314 6.070481 TGCAAGACTCCAATATACCACAACTA 60.070 38.462 0.00 0.00 0.00 2.24
4032 4362 9.617523 ACTTTCAACTTCCAATCATTTCAAATT 57.382 25.926 0.00 0.00 0.00 1.82
4033 4363 9.264719 GACTTTCAACTTCCAATCATTTCAAAT 57.735 29.630 0.00 0.00 0.00 2.32
4034 4364 8.477256 AGACTTTCAACTTCCAATCATTTCAAA 58.523 29.630 0.00 0.00 0.00 2.69
4035 4365 8.010733 AGACTTTCAACTTCCAATCATTTCAA 57.989 30.769 0.00 0.00 0.00 2.69
4036 4366 7.587037 AGACTTTCAACTTCCAATCATTTCA 57.413 32.000 0.00 0.00 0.00 2.69
4037 4367 8.787852 ACTAGACTTTCAACTTCCAATCATTTC 58.212 33.333 0.00 0.00 0.00 2.17
4038 4368 8.697507 ACTAGACTTTCAACTTCCAATCATTT 57.302 30.769 0.00 0.00 0.00 2.32
4039 4369 8.697507 AACTAGACTTTCAACTTCCAATCATT 57.302 30.769 0.00 0.00 0.00 2.57
4081 4411 8.487028 AGTAAATCACTTCTTGTATCTAAGGGG 58.513 37.037 0.00 0.00 31.59 4.79
4150 4480 7.906160 ACACAAAGTACGCATATCAGTTTATC 58.094 34.615 0.00 0.00 0.00 1.75
4162 4492 2.039818 TGGGAAACACAAAGTACGCA 57.960 45.000 0.00 0.00 0.00 5.24
4165 4495 7.506328 ACTAGAAATGGGAAACACAAAGTAC 57.494 36.000 0.00 0.00 0.00 2.73
4214 4544 3.723681 TCAGGAAGCTGGAAATATCCCAT 59.276 43.478 0.00 0.00 45.95 4.00
4233 4563 7.439157 TCCGCATGGAAATTAGAAATATCAG 57.561 36.000 0.00 0.00 42.85 2.90
4302 4632 7.335171 GCAGCCATTTTCTATTGAGGAAATTTT 59.665 33.333 0.00 0.00 38.63 1.82
4332 4663 1.450531 CGGACGGGGCGAATAGTAGT 61.451 60.000 0.00 0.00 0.00 2.73
4336 4667 2.279252 CACGGACGGGGCGAATAG 60.279 66.667 0.00 0.00 0.00 1.73
4350 4681 8.341903 TGAAATATAAATCTTGGTACATGCACG 58.658 33.333 0.00 0.00 39.30 5.34
4351 4682 9.450807 GTGAAATATAAATCTTGGTACATGCAC 57.549 33.333 0.00 0.00 39.30 4.57
4407 4738 4.716784 TCTCCAGCAATACCAGAGTTGTAT 59.283 41.667 0.00 0.00 0.00 2.29
4408 4739 4.093743 TCTCCAGCAATACCAGAGTTGTA 58.906 43.478 0.00 0.00 0.00 2.41
4418 4749 7.426929 ACAAAATCGATATCTCCAGCAATAC 57.573 36.000 0.00 0.00 0.00 1.89
4484 4815 6.484308 ACATCAAGTGAATGCATGATAATCGA 59.516 34.615 0.00 0.00 31.59 3.59
4624 4955 3.551890 CGTGCGTGCTAGATTATGAAGTT 59.448 43.478 0.00 0.00 0.00 2.66
4657 4990 9.921637 TTGTTAGTTTTCAAAAGAAATCACAGT 57.078 25.926 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.