Multiple sequence alignment - TraesCS1A01G060800

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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 TraesCS1A01G060800 chr1A 100.000 3211 0 0 1 3211 41760420 41757210 0.000000e+00 5930.0
1 TraesCS1A01G060800 chr1A 91.647 431 32 4 2142 2569 514878413 514877984 7.670000e-166 593.0
2 TraesCS1A01G060800 chr1A 90.951 431 35 4 2142 2569 515134603 515134174 7.720000e-161 577.0
3 TraesCS1A01G060800 chr1B 93.319 1362 86 4 785 2143 61943947 61942588 0.000000e+00 2006.0
4 TraesCS1A01G060800 chr1B 86.408 618 33 12 180 761 61944732 61944130 2.100000e-176 628.0
5 TraesCS1A01G060800 chr1B 91.860 430 31 4 2142 2567 11980723 11981152 5.930000e-167 597.0
6 TraesCS1A01G060800 chr1D 93.673 1296 61 9 849 2143 41758078 41756803 0.000000e+00 1919.0
7 TraesCS1A01G060800 chr1D 89.744 819 32 12 7 786 41758919 41758114 0.000000e+00 1000.0
8 TraesCS1A01G060800 chr1D 89.412 170 18 0 1 170 488539993 488540162 6.980000e-52 215.0
9 TraesCS1A01G060800 chr1D 92.857 56 4 0 3115 3170 401137841 401137896 7.380000e-12 82.4
10 TraesCS1A01G060800 chr6B 91.248 1074 83 8 2142 3211 391075969 391077035 0.000000e+00 1452.0
11 TraesCS1A01G060800 chr6B 92.754 69 5 0 18 86 537459590 537459658 2.040000e-17 100.0
12 TraesCS1A01G060800 chr3D 80.763 1206 180 37 933 2122 10660497 10661666 0.000000e+00 894.0
13 TraesCS1A01G060800 chr3D 87.500 464 56 2 1681 2143 10647252 10647714 4.710000e-148 534.0
14 TraesCS1A01G060800 chr3A 80.114 1232 191 41 929 2143 17606880 17605686 0.000000e+00 869.0
15 TraesCS1A01G060800 chr3A 91.395 430 30 6 2142 2568 737647457 737647032 1.660000e-162 582.0
16 TraesCS1A01G060800 chr3B 83.243 734 111 8 1413 2143 26532060 26531336 0.000000e+00 664.0
17 TraesCS1A01G060800 chr3B 87.313 536 66 2 1609 2143 26578115 26577581 2.120000e-171 612.0
18 TraesCS1A01G060800 chr3B 82.678 687 109 7 1410 2094 14402186 14401508 4.580000e-168 601.0
19 TraesCS1A01G060800 chr3B 81.957 327 49 7 1474 1793 26688842 26688519 5.280000e-68 268.0
20 TraesCS1A01G060800 chr2B 86.745 596 64 15 2138 2728 38619592 38620177 0.000000e+00 649.0
21 TraesCS1A01G060800 chr2B 90.826 436 33 7 2143 2573 103846606 103847039 7.720000e-161 577.0
22 TraesCS1A01G060800 chr6A 86.458 576 68 8 2139 2710 559747727 559748296 9.780000e-175 623.0
23 TraesCS1A01G060800 chr6A 90.888 428 35 4 2142 2567 558173667 558173242 3.590000e-159 571.0
24 TraesCS1A01G060800 chr5D 91.686 433 31 4 2140 2570 400401336 400401765 2.130000e-166 595.0
25 TraesCS1A01G060800 chr7A 87.261 157 16 4 23 177 650673617 650673771 3.290000e-40 176.0
26 TraesCS1A01G060800 chr7A 85.987 157 18 4 23 177 650687882 650688036 7.130000e-37 165.0
27 TraesCS1A01G060800 chr2A 83.974 156 25 0 16 171 542758983 542758828 2.000000e-32 150.0
28 TraesCS1A01G060800 chr6D 90.476 63 6 0 1 63 356233091 356233153 2.050000e-12 84.2


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 TraesCS1A01G060800 chr1A 41757210 41760420 3210 True 5930.0 5930 100.0000 1 3211 1 chr1A.!!$R1 3210
1 TraesCS1A01G060800 chr1B 61942588 61944732 2144 True 1317.0 2006 89.8635 180 2143 2 chr1B.!!$R1 1963
2 TraesCS1A01G060800 chr1D 41756803 41758919 2116 True 1459.5 1919 91.7085 7 2143 2 chr1D.!!$R1 2136
3 TraesCS1A01G060800 chr6B 391075969 391077035 1066 False 1452.0 1452 91.2480 2142 3211 1 chr6B.!!$F1 1069
4 TraesCS1A01G060800 chr3D 10660497 10661666 1169 False 894.0 894 80.7630 933 2122 1 chr3D.!!$F2 1189
5 TraesCS1A01G060800 chr3A 17605686 17606880 1194 True 869.0 869 80.1140 929 2143 1 chr3A.!!$R1 1214
6 TraesCS1A01G060800 chr3B 26531336 26532060 724 True 664.0 664 83.2430 1413 2143 1 chr3B.!!$R2 730
7 TraesCS1A01G060800 chr3B 26577581 26578115 534 True 612.0 612 87.3130 1609 2143 1 chr3B.!!$R3 534
8 TraesCS1A01G060800 chr3B 14401508 14402186 678 True 601.0 601 82.6780 1410 2094 1 chr3B.!!$R1 684
9 TraesCS1A01G060800 chr2B 38619592 38620177 585 False 649.0 649 86.7450 2138 2728 1 chr2B.!!$F1 590
10 TraesCS1A01G060800 chr6A 559747727 559748296 569 False 623.0 623 86.4580 2139 2710 1 chr6A.!!$F1 571

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
172 173 0.179004 TCAGCCGGGTGAACACAAAT 60.179 50.0 33.02 0.0 0.00 2.32 F
484 517 0.752376 CTCGGAGTAGGAGGTCACCC 60.752 65.0 0.00 0.0 0.00 4.61 F
1505 1745 0.034896 AACTGGACTACAAGTGCCCG 59.965 55.0 0.00 0.0 35.52 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 1734 0.391130 GAGCATGTCGGGCACTTGTA 60.391 55.0 0.0 0.0 33.52 2.41 R
1601 1841 0.526662 AGTAGGTGAACTTCTCCGCG 59.473 55.0 0.0 0.0 35.32 6.46 R
2532 2776 0.320374 TCACGGCCTCAAATCGAACT 59.680 50.0 0.0 0.0 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.897239 TCTGAAACATGGGTGAAGTTGT 58.103 40.909 0.00 0.00 0.00 3.32
69 70 7.560368 TGAAACATGGGTGAAGTTGTAAAAAT 58.440 30.769 0.00 0.00 0.00 1.82
70 71 7.493971 TGAAACATGGGTGAAGTTGTAAAAATG 59.506 33.333 0.00 0.00 0.00 2.32
83 84 8.514330 AGTTGTAAAAATGTGAAGTAGGTGAA 57.486 30.769 0.00 0.00 0.00 3.18
101 102 1.988406 AGGTGGCTCCTAACCGTCC 60.988 63.158 6.27 0.00 46.10 4.79
172 173 0.179004 TCAGCCGGGTGAACACAAAT 60.179 50.000 33.02 0.00 0.00 2.32
401 434 2.041115 CAGGCTCAGGTCGACGAGA 61.041 63.158 20.50 14.53 0.00 4.04
484 517 0.752376 CTCGGAGTAGGAGGTCACCC 60.752 65.000 0.00 0.00 0.00 4.61
539 576 2.808321 GGAAACGGCGACCTCGAC 60.808 66.667 16.62 0.00 45.58 4.20
613 650 1.725557 CGGCTAGCTGCGTCCTTCTA 61.726 60.000 15.72 0.00 44.05 2.10
615 652 1.025812 GCTAGCTGCGTCCTTCTAGA 58.974 55.000 7.70 0.00 32.41 2.43
627 664 5.272397 CGTCCTTCTAGATTCGTAACCTTC 58.728 45.833 0.00 0.00 0.00 3.46
782 847 8.434661 CCAACATATGTGTTAAATTGCAGTTTC 58.565 33.333 10.79 0.00 46.49 2.78
786 851 9.206870 CATATGTGTTAAATTGCAGTTTCCTTT 57.793 29.630 10.79 0.00 0.00 3.11
787 852 6.900568 TGTGTTAAATTGCAGTTTCCTTTG 57.099 33.333 10.79 0.00 0.00 2.77
788 853 5.814705 TGTGTTAAATTGCAGTTTCCTTTGG 59.185 36.000 10.79 0.00 0.00 3.28
829 1036 2.923121 CCTTTCTAGCTTATGCCTGCA 58.077 47.619 0.00 0.00 40.80 4.41
860 1068 4.003648 CCAACTACCAGTTCCATGACTTC 58.996 47.826 0.00 0.00 36.03 3.01
870 1078 2.959516 TCCATGACTTCTGTTAGTGCG 58.040 47.619 0.00 0.00 0.00 5.34
897 1105 1.528129 GAACAGGTGAAAGGAGCAGG 58.472 55.000 0.00 0.00 0.00 4.85
978 1186 1.906574 ACCAAGAAAGATAGTGCGGGA 59.093 47.619 0.00 0.00 0.00 5.14
1125 1333 3.356290 TGACTGTACTATCTGCTCTGCA 58.644 45.455 0.00 0.00 36.92 4.41
1203 1411 9.750125 GTCTTTGAACTCAACCTTTTATTTCAT 57.250 29.630 0.00 0.00 35.28 2.57
1244 1452 8.870075 AGTTAAAAGTAGAGCTTGGATGAATT 57.130 30.769 0.00 0.00 37.52 2.17
1293 1501 5.930837 TGGAAAGGAATTGTTTCTTGTGT 57.069 34.783 8.91 0.00 34.81 3.72
1294 1502 7.411486 TTGGAAAGGAATTGTTTCTTGTGTA 57.589 32.000 8.91 0.00 34.81 2.90
1295 1503 7.038154 TGGAAAGGAATTGTTTCTTGTGTAG 57.962 36.000 8.91 0.00 34.81 2.74
1308 1519 9.419297 TGTTTCTTGTGTAGACATAACATAGTC 57.581 33.333 10.05 0.00 29.98 2.59
1336 1550 6.441093 TGTTAGCTCAAATGATGGAATGTC 57.559 37.500 0.00 0.00 0.00 3.06
1343 1557 4.460034 TCAAATGATGGAATGTCTGTGGTG 59.540 41.667 0.00 0.00 0.00 4.17
1362 1576 3.869246 GGTGGTTACCTATCATGTTGTCG 59.131 47.826 2.07 0.00 43.97 4.35
1363 1577 4.501071 GTGGTTACCTATCATGTTGTCGT 58.499 43.478 2.07 0.00 0.00 4.34
1364 1578 4.328983 GTGGTTACCTATCATGTTGTCGTG 59.671 45.833 2.07 0.00 0.00 4.35
1365 1579 4.020928 TGGTTACCTATCATGTTGTCGTGT 60.021 41.667 2.07 0.00 32.85 4.49
1366 1580 4.328983 GGTTACCTATCATGTTGTCGTGTG 59.671 45.833 0.00 0.00 32.85 3.82
1367 1581 2.972625 ACCTATCATGTTGTCGTGTGG 58.027 47.619 0.00 0.00 32.85 4.17
1384 1616 6.577427 GTCGTGTGGTATTTCAATTCTTTGTC 59.423 38.462 0.00 0.00 34.32 3.18
1385 1617 5.563751 CGTGTGGTATTTCAATTCTTTGTCG 59.436 40.000 0.00 0.00 34.32 4.35
1399 1639 6.476243 TTCTTTGTCGCTGGTAAGATTTAC 57.524 37.500 0.00 0.00 0.00 2.01
1476 1716 3.112709 GCTCCTCGTGCCGTGAAC 61.113 66.667 0.00 0.00 0.00 3.18
1505 1745 0.034896 AACTGGACTACAAGTGCCCG 59.965 55.000 0.00 0.00 35.52 6.13
1516 1756 3.503363 GTGCCCGACATGCTCTGC 61.503 66.667 0.00 0.00 0.00 4.26
1601 1841 2.609459 CTCCAATGACAAGTACGGATGC 59.391 50.000 0.00 0.00 0.00 3.91
1728 1968 1.372087 GCTCCTGGACCATTTCGCTG 61.372 60.000 0.00 0.00 0.00 5.18
1829 2069 0.253044 AATGCACCGACACCAGCTAT 59.747 50.000 0.00 0.00 0.00 2.97
1851 2091 1.330234 TTTCTTGCTCAGCATGGCAA 58.670 45.000 12.39 6.87 45.42 4.52
1919 2159 1.060122 GTTACGGAATTCAGGTTCGCG 59.940 52.381 10.43 0.00 0.00 5.87
2062 2302 6.293955 GGAAAGGTTTCTGATGATGAAAACGA 60.294 38.462 2.60 0.00 43.55 3.85
2122 2362 3.438434 GGTCTCAGCAGATCTTGTTTTCC 59.562 47.826 0.00 0.00 0.00 3.13
2202 2442 2.800544 CAGTTGGACTTGGAGTTGTACG 59.199 50.000 0.00 0.00 0.00 3.67
2211 2451 1.614903 TGGAGTTGTACGGTGTGTAGG 59.385 52.381 0.00 0.00 32.51 3.18
2233 2473 2.311463 AGGATATGGAGTCGTGTCCTG 58.689 52.381 10.41 0.00 45.20 3.86
2274 2514 1.069358 GCCTCTCATATATAGCGGGGC 59.931 57.143 4.43 4.43 0.00 5.80
2289 2529 0.249398 GGGGCTAGACACACGATGTT 59.751 55.000 0.00 0.00 43.56 2.71
2291 2531 2.102588 GGGGCTAGACACACGATGTTAT 59.897 50.000 0.00 0.00 43.56 1.89
2293 2533 3.181479 GGGCTAGACACACGATGTTATCA 60.181 47.826 0.00 0.00 43.56 2.15
2315 2555 3.364460 TGCCAACATAATAGCACAGGT 57.636 42.857 0.00 0.00 0.00 4.00
2376 2618 1.079681 GGTGCGGTATTGTGACGGA 60.080 57.895 0.00 0.00 0.00 4.69
2446 2688 4.128643 TCGGTGAACCTCGTTAACAAATT 58.871 39.130 6.39 0.00 28.88 1.82
2454 2696 4.336153 ACCTCGTTAACAAATTTCGGTGTT 59.664 37.500 6.39 0.00 40.88 3.32
2460 2703 2.808244 ACAAATTTCGGTGTTGTGCTG 58.192 42.857 0.00 0.00 34.28 4.41
2474 2717 0.953727 GTGCTGGTGTGATTGCTTGA 59.046 50.000 0.00 0.00 0.00 3.02
2477 2720 1.814394 GCTGGTGTGATTGCTTGATCA 59.186 47.619 0.00 0.00 33.81 2.92
2516 2760 4.020039 TGGCCTCGGACTTATTCTAACAAA 60.020 41.667 3.32 0.00 0.00 2.83
2532 2776 7.936496 TCTAACAAATGGTATCATGAGCAAA 57.064 32.000 0.09 0.00 33.18 3.68
2553 2797 1.737793 GTTCGATTTGAGGCCGTGATT 59.262 47.619 0.00 0.00 0.00 2.57
2596 2840 1.257936 CGGGATGTCGCAGTAAAATCG 59.742 52.381 0.00 0.00 0.00 3.34
2600 2844 3.242316 GGATGTCGCAGTAAAATCGGTTC 60.242 47.826 0.00 0.00 0.00 3.62
2623 2867 1.733041 CGTGGTGTGTCGAGCGATT 60.733 57.895 0.00 0.00 0.00 3.34
2659 2903 2.995283 TCTCGGGAGATTAAGTCGACA 58.005 47.619 19.50 0.00 38.80 4.35
2719 2964 0.537188 AGATCGGAAGCAACACGGAT 59.463 50.000 0.00 0.00 0.00 4.18
2745 2990 2.860628 GCGTGATCGATCGTGCACC 61.861 63.158 27.15 18.48 39.71 5.01
2746 2991 2.568031 CGTGATCGATCGTGCACCG 61.568 63.158 25.56 19.64 39.71 4.94
2767 3012 2.713894 GGCACGCGTACGAGTTGTC 61.714 63.158 22.31 14.83 43.93 3.18
2772 3017 1.063951 CGCGTACGAGTTGTCAGGAC 61.064 60.000 21.65 0.00 43.93 3.85
2777 3022 0.962489 ACGAGTTGTCAGGACTCAGG 59.038 55.000 5.69 0.00 42.85 3.86
2802 3047 3.304257 CAGCCTGTAGAAGATCGATTCG 58.696 50.000 0.00 0.00 34.27 3.34
2807 3052 4.276183 CCTGTAGAAGATCGATTCGGAAGA 59.724 45.833 6.18 0.00 34.27 2.87
2817 3062 2.597305 CGATTCGGAAGACGTAAAGGTG 59.403 50.000 0.00 0.00 44.69 4.00
2834 3079 2.110213 GGAGTGCACGTGGTTCCA 59.890 61.111 18.88 3.30 0.00 3.53
2844 3089 1.294459 GTGGTTCCACGTAGGGGTC 59.706 63.158 6.22 0.00 38.24 4.46
2853 3098 1.143183 CGTAGGGGTCGGTTCCATG 59.857 63.158 0.00 0.00 0.00 3.66
3054 3299 2.364579 CCACATGGGCTGGGCATT 60.365 61.111 0.00 0.00 0.00 3.56
3055 3300 2.428925 CCACATGGGCTGGGCATTC 61.429 63.158 0.00 0.00 0.00 2.67
3098 3343 4.735132 GTGCACGCGGCTGGAGTA 62.735 66.667 12.47 0.00 45.15 2.59
3113 3358 1.226686 GAGTAGCAGCATGGCGATGG 61.227 60.000 10.93 0.00 39.27 3.51
3152 3397 3.560896 GGAGGTCATGTACGTAGAGAGAC 59.439 52.174 15.50 15.50 0.00 3.36
3158 3403 6.380190 GTCATGTACGTAGAGAGACTTGTTT 58.620 40.000 16.16 0.00 0.00 2.83
3159 3404 7.361542 GGTCATGTACGTAGAGAGACTTGTTTA 60.362 40.741 20.16 0.00 0.00 2.01
3192 3437 0.179225 CGTCAGGTATTTGTGCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.114882 GCACTTGCTGTAGATAGACAATATG 57.885 40.000 0.00 0.00 38.21 1.78
51 52 6.153680 ACTTCACATTTTTACAACTTCACCCA 59.846 34.615 0.00 0.00 0.00 4.51
63 64 6.488683 CCACCTTCACCTACTTCACATTTTTA 59.511 38.462 0.00 0.00 0.00 1.52
69 70 1.071699 GCCACCTTCACCTACTTCACA 59.928 52.381 0.00 0.00 0.00 3.58
70 71 1.348036 AGCCACCTTCACCTACTTCAC 59.652 52.381 0.00 0.00 0.00 3.18
139 140 1.480219 GGCTGATCTTTCCGTACGCG 61.480 60.000 10.49 3.53 37.95 6.01
147 148 1.087501 GTTCACCCGGCTGATCTTTC 58.912 55.000 0.00 0.00 0.00 2.62
294 298 1.601419 CCTGGGCGTCTTCTCGGTTA 61.601 60.000 0.00 0.00 0.00 2.85
484 517 1.299773 GAGGAGATCGCTTGCCTCG 60.300 63.158 0.00 0.00 37.75 4.63
539 576 4.680237 TGCAAGACCTGGTCGGCG 62.680 66.667 28.64 19.55 39.35 6.46
613 650 5.589050 GCAATTAAGGGAAGGTTACGAATCT 59.411 40.000 0.00 0.00 0.00 2.40
615 652 4.643334 GGCAATTAAGGGAAGGTTACGAAT 59.357 41.667 0.00 0.00 0.00 3.34
656 693 8.970859 AACAAGAGATTTATTCCGATTCAGAT 57.029 30.769 0.00 0.00 0.00 2.90
786 851 4.276926 GCAATTGTTTTGGGCAAAATACCA 59.723 37.500 7.40 0.00 41.64 3.25
787 852 4.320861 GGCAATTGTTTTGGGCAAAATACC 60.321 41.667 7.40 0.00 41.64 2.73
788 853 4.518590 AGGCAATTGTTTTGGGCAAAATAC 59.481 37.500 7.40 0.00 41.64 1.89
829 1036 0.687354 CTGGTAGTTGGTCTGGTGCT 59.313 55.000 0.00 0.00 0.00 4.40
860 1068 0.240145 TCCACGAGACGCACTAACAG 59.760 55.000 0.00 0.00 0.00 3.16
870 1078 2.135933 CTTTCACCTGTTCCACGAGAC 58.864 52.381 0.00 0.00 0.00 3.36
897 1105 7.253422 CAAACCTATTGATCAACACAATCTCC 58.747 38.462 11.07 0.00 38.61 3.71
978 1186 2.035632 TGCCAACGAAATTCCAAGGTT 58.964 42.857 0.00 0.00 0.00 3.50
991 1199 0.109365 TTGATCGCCATTTGCCAACG 60.109 50.000 0.00 0.00 36.24 4.10
1125 1333 2.037304 ATATCGGAGGCCTGAGGGGT 62.037 60.000 12.00 0.00 37.43 4.95
1228 1436 9.253832 TCCAAAAATAAATTCATCCAAGCTCTA 57.746 29.630 0.00 0.00 0.00 2.43
1326 1537 2.496899 ACCACCACAGACATTCCATC 57.503 50.000 0.00 0.00 0.00 3.51
1343 1557 4.328983 CACACGACAACATGATAGGTAACC 59.671 45.833 0.00 0.00 37.17 2.85
1350 1564 6.166982 TGAAATACCACACGACAACATGATA 58.833 36.000 0.00 0.00 0.00 2.15
1351 1565 5.000591 TGAAATACCACACGACAACATGAT 58.999 37.500 0.00 0.00 0.00 2.45
1352 1566 4.381411 TGAAATACCACACGACAACATGA 58.619 39.130 0.00 0.00 0.00 3.07
1353 1567 4.740741 TGAAATACCACACGACAACATG 57.259 40.909 0.00 0.00 0.00 3.21
1354 1568 5.957842 ATTGAAATACCACACGACAACAT 57.042 34.783 0.00 0.00 0.00 2.71
1355 1569 5.529430 AGAATTGAAATACCACACGACAACA 59.471 36.000 0.00 0.00 0.00 3.33
1356 1570 5.997385 AGAATTGAAATACCACACGACAAC 58.003 37.500 0.00 0.00 0.00 3.32
1357 1571 6.627395 AAGAATTGAAATACCACACGACAA 57.373 33.333 0.00 0.00 0.00 3.18
1358 1572 6.038825 ACAAAGAATTGAAATACCACACGACA 59.961 34.615 0.00 0.00 38.94 4.35
1359 1573 6.435428 ACAAAGAATTGAAATACCACACGAC 58.565 36.000 0.00 0.00 38.94 4.34
1360 1574 6.565060 CGACAAAGAATTGAAATACCACACGA 60.565 38.462 0.00 0.00 38.94 4.35
1361 1575 5.563751 CGACAAAGAATTGAAATACCACACG 59.436 40.000 0.00 0.00 38.94 4.49
1362 1576 5.342259 GCGACAAAGAATTGAAATACCACAC 59.658 40.000 0.00 0.00 38.94 3.82
1363 1577 5.240623 AGCGACAAAGAATTGAAATACCACA 59.759 36.000 0.00 0.00 38.94 4.17
1364 1578 5.569059 CAGCGACAAAGAATTGAAATACCAC 59.431 40.000 0.00 0.00 38.94 4.16
1365 1579 5.335583 CCAGCGACAAAGAATTGAAATACCA 60.336 40.000 0.00 0.00 38.94 3.25
1366 1580 5.095490 CCAGCGACAAAGAATTGAAATACC 58.905 41.667 0.00 0.00 38.94 2.73
1367 1581 5.699839 ACCAGCGACAAAGAATTGAAATAC 58.300 37.500 0.00 0.00 38.94 1.89
1426 1666 2.005451 CCACAGAGCACTGCAGAATAC 58.995 52.381 23.35 9.04 46.95 1.89
1432 1672 4.648626 GCCCCACAGAGCACTGCA 62.649 66.667 11.37 0.00 46.95 4.41
1476 1716 2.492088 TGTAGTCCAGTTGATCCTCACG 59.508 50.000 0.00 0.00 0.00 4.35
1494 1734 0.391130 GAGCATGTCGGGCACTTGTA 60.391 55.000 0.00 0.00 33.52 2.41
1505 1745 2.352127 GGAAGTTTTGGCAGAGCATGTC 60.352 50.000 0.00 0.00 0.00 3.06
1516 1756 1.338020 AGCGCTTGAAGGAAGTTTTGG 59.662 47.619 2.64 0.00 33.73 3.28
1601 1841 0.526662 AGTAGGTGAACTTCTCCGCG 59.473 55.000 0.00 0.00 35.32 6.46
1728 1968 3.357079 CGGACACTTGTGCTGGGC 61.357 66.667 0.10 0.00 33.97 5.36
1851 2091 0.598065 GCATGTCCAAAAGGCTTCGT 59.402 50.000 0.00 0.00 0.00 3.85
1919 2159 3.548415 GGCAGTCGTAGCTCATAGTACAC 60.548 52.174 0.00 0.00 0.00 2.90
2062 2302 1.180029 GGTGGCTTTGAGCATGATGT 58.820 50.000 0.00 0.00 44.75 3.06
2122 2362 0.905357 AGGAGTCGGACCCATTTCTG 59.095 55.000 15.16 0.00 0.00 3.02
2202 2442 2.037772 CTCCATATCCTGCCTACACACC 59.962 54.545 0.00 0.00 0.00 4.16
2211 2451 1.269831 GGACACGACTCCATATCCTGC 60.270 57.143 0.00 0.00 0.00 4.85
2240 2480 4.808767 TGAGAGGCCTAGGATACAAGTA 57.191 45.455 14.75 0.00 41.41 2.24
2274 2514 5.050769 GGCATTGATAACATCGTGTGTCTAG 60.051 44.000 0.00 0.00 41.14 2.43
2289 2529 6.207221 CCTGTGCTATTATGTTGGCATTGATA 59.793 38.462 0.00 0.00 37.05 2.15
2291 2531 4.338964 CCTGTGCTATTATGTTGGCATTGA 59.661 41.667 0.00 0.00 37.05 2.57
2293 2533 4.280819 ACCTGTGCTATTATGTTGGCATT 58.719 39.130 0.00 0.00 37.05 3.56
2376 2618 3.474570 GCGCTCCTCCCCATGACT 61.475 66.667 0.00 0.00 0.00 3.41
2446 2688 1.078072 ACACCAGCACAACACCGAA 60.078 52.632 0.00 0.00 0.00 4.30
2454 2696 0.669619 CAAGCAATCACACCAGCACA 59.330 50.000 0.00 0.00 0.00 4.57
2460 2703 2.032550 CCGATGATCAAGCAATCACACC 59.967 50.000 0.00 0.00 38.43 4.16
2474 2717 1.535896 CACCGTCGATCTACCGATGAT 59.464 52.381 7.04 0.00 45.52 2.45
2477 2720 1.793134 GCCACCGTCGATCTACCGAT 61.793 60.000 0.00 0.00 40.91 4.18
2516 2760 4.769688 TCGAACTTTGCTCATGATACCAT 58.230 39.130 0.00 0.00 0.00 3.55
2532 2776 0.320374 TCACGGCCTCAAATCGAACT 59.680 50.000 0.00 0.00 0.00 3.01
2553 2797 4.141846 GGCTCATCACCTCTAGATCAACAA 60.142 45.833 0.00 0.00 0.00 2.83
2596 2840 1.005394 ACACACCACGGATCGAACC 60.005 57.895 0.70 0.70 0.00 3.62
2600 2844 1.514228 CTCGACACACCACGGATCG 60.514 63.158 0.00 0.00 0.00 3.69
2623 2867 1.404181 CGAGATTGCTCCCGAGTTTCA 60.404 52.381 0.00 0.00 37.91 2.69
2659 2903 5.052693 TCCCATCGATCCAATGAATTTCT 57.947 39.130 0.00 0.00 0.00 2.52
2745 2990 3.238241 CTCGTACGCGTGCCTTCG 61.238 66.667 24.59 17.38 39.49 3.79
2746 2991 1.731969 AACTCGTACGCGTGCCTTC 60.732 57.895 24.59 6.10 39.49 3.46
2747 2992 2.019951 CAACTCGTACGCGTGCCTT 61.020 57.895 24.59 7.88 39.49 4.35
2748 2993 2.430244 CAACTCGTACGCGTGCCT 60.430 61.111 24.59 0.96 39.49 4.75
2749 2994 2.713894 GACAACTCGTACGCGTGCC 61.714 63.158 24.59 11.52 39.49 5.01
2755 3000 1.534163 TGAGTCCTGACAACTCGTACG 59.466 52.381 9.53 9.53 44.96 3.67
2767 3012 2.436292 GCTGCTGCCTGAGTCCTG 60.436 66.667 3.85 0.00 0.00 3.86
2777 3022 1.580815 GATCTTCTACAGGCTGCTGC 58.419 55.000 15.89 7.10 38.76 5.25
2791 3036 4.627611 TTACGTCTTCCGAATCGATCTT 57.372 40.909 3.36 0.00 40.70 2.40
2802 3047 2.685100 CACTCCACCTTTACGTCTTCC 58.315 52.381 0.00 0.00 0.00 3.46
2807 3052 0.599204 CGTGCACTCCACCTTTACGT 60.599 55.000 16.19 0.00 41.53 3.57
2817 3062 2.110213 TGGAACCACGTGCACTCC 59.890 61.111 16.19 14.78 0.00 3.85
2834 3079 1.305549 ATGGAACCGACCCCTACGT 60.306 57.895 0.00 0.00 0.00 3.57
2842 3087 1.745489 GCCTCACCATGGAACCGAC 60.745 63.158 21.47 0.00 0.00 4.79
2844 3089 1.746615 CTGCCTCACCATGGAACCG 60.747 63.158 21.47 3.71 0.00 4.44
2853 3098 3.745803 GCTGCTTGCTGCCTCACC 61.746 66.667 12.43 0.00 42.00 4.02
2915 3160 2.749865 CCCACTATTGCCACGTGCG 61.750 63.158 10.91 4.74 45.60 5.34
2926 3171 2.025321 CCCAACCAACTTAGCCCACTAT 60.025 50.000 0.00 0.00 0.00 2.12
2927 3172 1.353022 CCCAACCAACTTAGCCCACTA 59.647 52.381 0.00 0.00 0.00 2.74
2979 3224 2.754375 CCTGGTAAACCCCGCTGT 59.246 61.111 0.00 0.00 34.29 4.40
2990 3235 3.923864 CTATGCCGCCGCCTGGTA 61.924 66.667 0.00 0.00 37.67 3.25
3054 3299 2.032376 TGCACGCCTCATTGCAGA 59.968 55.556 0.00 0.00 43.79 4.26
3098 3343 2.203167 CTCCATCGCCATGCTGCT 60.203 61.111 0.00 0.00 0.00 4.24
3105 3350 1.153309 CATCACAGCTCCATCGCCA 60.153 57.895 0.00 0.00 0.00 5.69
3113 3358 1.448540 CCACGTCCCATCACAGCTC 60.449 63.158 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.