Multiple sequence alignment - TraesCS7A01G075100

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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 TraesCS7A01G075100 chr7A 100.000 3845 0 0 1 3845 40698155 40701999 0.000000e+00 7101
1 TraesCS7A01G075100 chr7A 82.278 1563 270 6 2286 3845 492818414 492816856 0.000000e+00 1345
2 TraesCS7A01G075100 chr6A 80.638 2381 403 38 1479 3845 181589209 181586873 0.000000e+00 1790
3 TraesCS7A01G075100 chr6A 95.106 613 30 0 3233 3845 587756638 587757250 0.000000e+00 966
4 TraesCS7A01G075100 chr5B 90.201 1296 126 1 2288 3582 251506947 251508242 0.000000e+00 1688
5 TraesCS7A01G075100 chr5B 95.556 270 12 0 3576 3845 251534429 251534698 2.120000e-117 433
6 TraesCS7A01G075100 chr6B 90.480 1250 109 3 1021 2270 436797126 436795887 0.000000e+00 1640
7 TraesCS7A01G075100 chr6B 89.675 1201 121 2 2648 3845 436784475 436783275 0.000000e+00 1528
8 TraesCS7A01G075100 chr6B 89.583 384 40 0 568 951 436797501 436797118 4.460000e-134 488
9 TraesCS7A01G075100 chr6B 88.187 364 43 0 2286 2649 436795778 436795415 5.900000e-118 435
10 TraesCS7A01G075100 chr7D 91.342 1028 88 1 920 1946 245386525 245387552 0.000000e+00 1404
11 TraesCS7A01G075100 chr7D 83.345 1477 233 9 2375 3845 245389560 245391029 0.000000e+00 1352
12 TraesCS7A01G075100 chr7D 92.844 531 32 3 1 527 41260786 41261314 0.000000e+00 765
13 TraesCS7A01G075100 chr7D 83.846 520 68 12 1 511 41348670 41348158 7.470000e-132 481
14 TraesCS7A01G075100 chr7D 85.494 324 36 4 1948 2270 245389100 245389413 1.030000e-85 327
15 TraesCS7A01G075100 chr7D 89.000 200 20 2 688 886 245386336 245386534 2.970000e-61 246
16 TraesCS7A01G075100 chr7D 87.135 171 15 4 564 733 245386169 245386333 1.820000e-43 187
17 TraesCS7A01G075100 chr4B 86.111 1188 152 5 1034 2220 469173719 469174894 0.000000e+00 1267
18 TraesCS7A01G075100 chr4B 88.945 199 20 2 689 886 469164678 469164875 1.070000e-60 244
19 TraesCS7A01G075100 chr4B 88.095 168 18 2 567 733 469164508 469164674 8.430000e-47 198
20 TraesCS7A01G075100 chr4B 88.333 120 12 2 920 1038 469164866 469164984 4.000000e-30 143
21 TraesCS7A01G075100 chr2D 81.027 1207 211 10 2644 3845 144375107 144373914 0.000000e+00 944
22 TraesCS7A01G075100 chr5A 82.927 943 150 8 2909 3845 564609706 564608769 0.000000e+00 839
23 TraesCS7A01G075100 chr7B 81.517 936 156 14 2910 3836 120359312 120360239 0.000000e+00 754
24 TraesCS7A01G075100 chr7B 80.597 201 33 5 1720 1914 504818734 504818934 2.390000e-32 150
25 TraesCS7A01G075100 chrUn 83.659 563 53 21 1 561 48812836 48813361 9.600000e-136 494
26 TraesCS7A01G075100 chr4A 92.459 305 19 2 259 560 648143895 648144198 2.120000e-117 433
27 TraesCS7A01G075100 chr4A 91.342 231 19 1 1 230 648142684 648142914 8.020000e-82 315
28 TraesCS7A01G075100 chr4A 85.906 298 34 5 43 340 648658424 648658713 1.040000e-80 311
29 TraesCS7A01G075100 chr3A 76.966 725 152 14 3128 3845 526883102 526883818 2.150000e-107 399


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 TraesCS7A01G075100 chr7A 40698155 40701999 3844 False 7101.000000 7101 100.000000 1 3845 1 chr7A.!!$F1 3844
1 TraesCS7A01G075100 chr7A 492816856 492818414 1558 True 1345.000000 1345 82.278000 2286 3845 1 chr7A.!!$R1 1559
2 TraesCS7A01G075100 chr6A 181586873 181589209 2336 True 1790.000000 1790 80.638000 1479 3845 1 chr6A.!!$R1 2366
3 TraesCS7A01G075100 chr6A 587756638 587757250 612 False 966.000000 966 95.106000 3233 3845 1 chr6A.!!$F1 612
4 TraesCS7A01G075100 chr5B 251506947 251508242 1295 False 1688.000000 1688 90.201000 2288 3582 1 chr5B.!!$F1 1294
5 TraesCS7A01G075100 chr6B 436783275 436784475 1200 True 1528.000000 1528 89.675000 2648 3845 1 chr6B.!!$R1 1197
6 TraesCS7A01G075100 chr6B 436795415 436797501 2086 True 854.333333 1640 89.416667 568 2649 3 chr6B.!!$R2 2081
7 TraesCS7A01G075100 chr7D 41260786 41261314 528 False 765.000000 765 92.844000 1 527 1 chr7D.!!$F1 526
8 TraesCS7A01G075100 chr7D 245386169 245391029 4860 False 703.200000 1404 87.263200 564 3845 5 chr7D.!!$F2 3281
9 TraesCS7A01G075100 chr7D 41348158 41348670 512 True 481.000000 481 83.846000 1 511 1 chr7D.!!$R1 510
10 TraesCS7A01G075100 chr4B 469173719 469174894 1175 False 1267.000000 1267 86.111000 1034 2220 1 chr4B.!!$F1 1186
11 TraesCS7A01G075100 chr2D 144373914 144375107 1193 True 944.000000 944 81.027000 2644 3845 1 chr2D.!!$R1 1201
12 TraesCS7A01G075100 chr5A 564608769 564609706 937 True 839.000000 839 82.927000 2909 3845 1 chr5A.!!$R1 936
13 TraesCS7A01G075100 chr7B 120359312 120360239 927 False 754.000000 754 81.517000 2910 3836 1 chr7B.!!$F1 926
14 TraesCS7A01G075100 chrUn 48812836 48813361 525 False 494.000000 494 83.659000 1 561 1 chrUn.!!$F1 560
15 TraesCS7A01G075100 chr4A 648142684 648144198 1514 False 374.000000 433 91.900500 1 560 2 chr4A.!!$F2 559
16 TraesCS7A01G075100 chr3A 526883102 526883818 716 False 399.000000 399 76.966000 3128 3845 1 chr3A.!!$F1 717

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
810 1820 0.814010 GTCAATCCGGCTGCCGTAAT 60.814 55.0 35.82 26.09 46.8 1.89 F
2027 4584 0.034059 GATGGTAGGCGTGATGGAGG 59.966 60.0 0.00 0.00 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2631 5281 0.460284 CGGTAAGCTGTTCGCCATCT 60.460 55.0 0.00 0.0 40.39 2.90 R
3084 5746 0.112995 AGCAGCAATTGGGAGGAACA 59.887 50.0 7.72 0.0 0.00 3.18 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
57 59 9.040939 GCAACATTGATAAATATGGGTAAAACC 57.959 33.333 0.00 0.00 37.60 3.27
142 149 5.588648 TGACGGAGAAAAACAATCTTGAACT 59.411 36.000 0.00 0.00 0.00 3.01
158 165 5.311121 TCTTGAACTGGAACCCCATTACTTA 59.689 40.000 0.00 0.00 42.59 2.24
161 168 4.296621 ACTGGAACCCCATTACTTACAC 57.703 45.455 0.00 0.00 42.59 2.90
169 176 3.331150 CCCATTACTTACACGTGCAAGA 58.669 45.455 30.43 13.04 0.00 3.02
204 258 2.130426 GCATGGCGAGGGAGAGAGA 61.130 63.158 0.00 0.00 0.00 3.10
205 259 2.040330 CATGGCGAGGGAGAGAGAG 58.960 63.158 0.00 0.00 0.00 3.20
216 270 0.823460 GAGAGAGAGGAGTGGCAAGG 59.177 60.000 0.00 0.00 0.00 3.61
238 292 4.825634 GGCCATTGATCATGATCTCTCAAA 59.174 41.667 30.65 19.16 38.60 2.69
240 294 5.048643 GCCATTGATCATGATCTCTCAAAGG 60.049 44.000 30.65 24.63 38.73 3.11
269 1230 2.589540 CAATGGAGGGCTACGGCA 59.410 61.111 0.00 0.00 40.87 5.69
379 1341 4.997395 CACCAATCTAACAGCACTGTAGTT 59.003 41.667 3.26 0.00 44.13 2.24
396 1358 9.273016 CACTGTAGTTTTCTTCTTTCCTGATTA 57.727 33.333 0.00 0.00 0.00 1.75
433 1398 1.202639 ACGCATCCACAGTCAGTTGAA 60.203 47.619 0.00 0.00 0.00 2.69
561 1526 1.181098 AAGCCCAGAACACATGCACC 61.181 55.000 0.00 0.00 0.00 5.01
562 1527 2.981560 GCCCAGAACACATGCACCG 61.982 63.158 0.00 0.00 0.00 4.94
563 1528 2.562912 CCAGAACACATGCACCGC 59.437 61.111 0.00 0.00 0.00 5.68
564 1529 2.174107 CAGAACACATGCACCGCG 59.826 61.111 0.00 0.00 0.00 6.46
565 1530 3.726517 AGAACACATGCACCGCGC 61.727 61.111 0.00 0.00 42.89 6.86
617 1582 2.033911 TGATGGCTCAAGCGGCAA 59.966 55.556 1.45 0.00 43.02 4.52
645 1610 2.813908 GAATGGCGCCTCGTTCGT 60.814 61.111 29.70 4.28 0.00 3.85
682 1647 4.767255 CTGAGCGCTCCACCCACC 62.767 72.222 33.23 8.30 0.00 4.61
684 1649 4.767255 GAGCGCTCCACCCACCAG 62.767 72.222 27.22 0.00 0.00 4.00
690 1655 2.531428 TCCACCCACCAGCCATCA 60.531 61.111 0.00 0.00 0.00 3.07
697 1707 1.376424 CACCAGCCATCAAGACGCT 60.376 57.895 0.00 0.00 0.00 5.07
699 1709 1.817099 CCAGCCATCAAGACGCTCC 60.817 63.158 0.00 0.00 0.00 4.70
718 1728 3.385115 TCCTCTGGGTCTTCTTATTCCC 58.615 50.000 0.00 0.00 40.26 3.97
807 1817 3.958147 CTGTCAATCCGGCTGCCGT 62.958 63.158 35.82 18.99 46.80 5.68
810 1820 0.814010 GTCAATCCGGCTGCCGTAAT 60.814 55.000 35.82 26.09 46.80 1.89
954 1964 4.115199 GCGGCCCCTCTCCAACAT 62.115 66.667 0.00 0.00 0.00 2.71
957 1967 1.048724 CGGCCCCTCTCCAACATCTA 61.049 60.000 0.00 0.00 0.00 1.98
968 1978 2.676265 AACATCTACCGCCCCCACC 61.676 63.158 0.00 0.00 0.00 4.61
1003 2013 4.387343 CCTTGGCTGGCCCCATGT 62.387 66.667 9.28 0.00 34.21 3.21
1005 2015 4.738998 TTGGCTGGCCCCATGTCG 62.739 66.667 9.28 0.00 34.21 4.35
1075 2085 3.839589 AGGGCCATGTGGTCATCA 58.160 55.556 6.18 0.00 42.93 3.07
1096 2106 3.147595 CCACGCCGGAGATGGAGA 61.148 66.667 13.83 0.00 36.56 3.71
1104 2114 0.178767 CGGAGATGGAGACCAATGCA 59.821 55.000 0.00 0.00 36.95 3.96
1192 2202 1.918262 AGATCAAGGAGGCCATCAACA 59.082 47.619 5.01 0.00 0.00 3.33
1262 2272 0.239082 TTCTTCGCGCTGTTCGAGTA 59.761 50.000 5.56 0.00 41.67 2.59
1363 2373 3.986006 GTGACGCCCACTCCGACA 61.986 66.667 1.75 0.00 42.44 4.35
1454 2465 4.560743 TGCGCAAGTGCTGGGACA 62.561 61.111 8.16 0.00 40.40 4.02
1503 2514 1.512310 CACGCTCCGTCGAGAAGAC 60.512 63.158 0.00 0.00 46.16 3.01
1631 2642 2.484062 CCGCTGCCATTGGTCATCC 61.484 63.158 4.26 0.00 0.00 3.51
1850 2861 1.541588 TGATGACCGCGATAGAGATGG 59.458 52.381 8.23 0.00 38.63 3.51
1905 2916 1.616628 TTCCTGGAGGGGCCTCTTC 60.617 63.158 6.58 4.65 42.38 2.87
1949 4506 3.157252 GAGGGCGGATGAGGAGCA 61.157 66.667 0.00 0.00 0.00 4.26
1956 4513 2.419198 GATGAGGAGCATCGCGGT 59.581 61.111 6.13 0.00 43.57 5.68
1959 4516 1.752358 ATGAGGAGCATCGCGGTGAT 61.752 55.000 26.37 19.61 38.01 3.06
2020 4577 2.890474 GGCGTGATGGTAGGCGTG 60.890 66.667 0.00 0.00 32.53 5.34
2021 4578 2.183300 GCGTGATGGTAGGCGTGA 59.817 61.111 0.00 0.00 0.00 4.35
2022 4579 1.227263 GCGTGATGGTAGGCGTGAT 60.227 57.895 0.00 0.00 0.00 3.06
2023 4580 1.490693 GCGTGATGGTAGGCGTGATG 61.491 60.000 0.00 0.00 0.00 3.07
2024 4581 0.875908 CGTGATGGTAGGCGTGATGG 60.876 60.000 0.00 0.00 0.00 3.51
2025 4582 0.464036 GTGATGGTAGGCGTGATGGA 59.536 55.000 0.00 0.00 0.00 3.41
2026 4583 0.752658 TGATGGTAGGCGTGATGGAG 59.247 55.000 0.00 0.00 0.00 3.86
2027 4584 0.034059 GATGGTAGGCGTGATGGAGG 59.966 60.000 0.00 0.00 0.00 4.30
2028 4585 1.410850 ATGGTAGGCGTGATGGAGGG 61.411 60.000 0.00 0.00 0.00 4.30
2030 4587 2.364973 TAGGCGTGATGGAGGGCA 60.365 61.111 0.00 0.00 37.47 5.36
2066 4623 2.584391 GGCCACGACAGAGGGACTT 61.584 63.158 0.00 0.00 41.55 3.01
2154 4711 1.739562 GTCTTCCTCTGCTGCCGTG 60.740 63.158 0.00 0.00 0.00 4.94
2227 4784 1.878069 CTCAACATCGATGCGGCGA 60.878 57.895 25.11 14.43 45.22 5.54
2228 4785 2.082437 CTCAACATCGATGCGGCGAC 62.082 60.000 25.11 2.02 43.79 5.19
2229 4786 2.125713 AACATCGATGCGGCGACA 60.126 55.556 25.11 9.05 43.79 4.35
2250 4807 3.756082 ACCATCTCTCCTCTTCAGTCT 57.244 47.619 0.00 0.00 0.00 3.24
2252 4809 4.792068 ACCATCTCTCCTCTTCAGTCTAG 58.208 47.826 0.00 0.00 0.00 2.43
2279 4929 0.612229 CACTCACTGGCACCTGAGAT 59.388 55.000 19.57 5.87 36.14 2.75
2283 4933 1.922369 ACTGGCACCTGAGATGGCT 60.922 57.895 0.83 0.00 42.86 4.75
2284 4934 1.302285 CTGGCACCTGAGATGGCTT 59.698 57.895 0.83 0.00 42.86 4.35
2295 4945 2.436646 ATGGCTTTGGACTCGGCG 60.437 61.111 0.00 0.00 0.00 6.46
2306 4956 4.200283 CTCGGCGTCCTCTCCAGC 62.200 72.222 6.85 0.00 0.00 4.85
2316 4966 1.580845 CCTCTCCAGCGCCAAGTTTG 61.581 60.000 2.29 0.00 0.00 2.93
2326 4976 2.336088 CAAGTTTGGTGCTGGCCG 59.664 61.111 0.00 0.00 0.00 6.13
2365 5015 1.002888 CTGATCTGCACCACCTTGTCT 59.997 52.381 0.00 0.00 0.00 3.41
2373 5023 0.178990 ACCACCTTGTCTTGGAAGCC 60.179 55.000 0.00 0.00 36.28 4.35
2377 5027 1.580845 CCTTGTCTTGGAAGCCGCTG 61.581 60.000 0.00 0.00 0.00 5.18
2389 5039 1.742880 GCCGCTGCACAAGAGATGA 60.743 57.895 0.00 0.00 37.47 2.92
2404 5054 2.765699 GAGATGACTGAAGAAGAGGCCT 59.234 50.000 3.86 3.86 0.00 5.19
2411 5061 1.905215 TGAAGAAGAGGCCTCTGAAGG 59.095 52.381 35.77 0.00 46.44 3.46
2421 5071 0.976641 CCTCTGAAGGTGCTACCACA 59.023 55.000 7.86 6.58 43.88 4.17
2451 5101 2.762459 CCCTGTAGGCCGGCACTA 60.762 66.667 30.85 23.09 0.00 2.74
2454 5104 0.754217 CCTGTAGGCCGGCACTACTA 60.754 60.000 34.80 25.84 41.03 1.82
2463 5113 0.683504 CGGCACTACTACCCTCACCT 60.684 60.000 0.00 0.00 0.00 4.00
2531 5181 1.734477 CGGGTGTCACGAGCTTCAG 60.734 63.158 0.00 0.00 0.00 3.02
2561 5211 4.227134 CAGCCCGAGGATCCGTGG 62.227 72.222 16.16 16.16 0.00 4.94
2631 5281 2.929903 GCGCTTGGGCATTGTGGAA 61.930 57.895 0.00 0.00 38.60 3.53
2653 5303 4.883026 GCGAACAGCTTACCGAGA 57.117 55.556 2.97 0.00 44.04 4.04
2654 5304 3.347411 GCGAACAGCTTACCGAGAT 57.653 52.632 2.97 0.00 44.04 2.75
2691 5341 3.312828 TGTGCAAATGTTTAATGGTCGC 58.687 40.909 0.00 0.00 0.00 5.19
2710 5360 1.490490 GCCTCCCTGACATCACCATTA 59.510 52.381 0.00 0.00 0.00 1.90
2720 5370 0.833287 ATCACCATTACGGCTCTGCT 59.167 50.000 0.00 0.00 39.03 4.24
2721 5371 0.613260 TCACCATTACGGCTCTGCTT 59.387 50.000 0.00 0.00 39.03 3.91
2725 5375 1.089920 CATTACGGCTCTGCTTGCTT 58.910 50.000 0.00 0.00 0.00 3.91
2823 5482 2.817056 GGGCTCTCAGGAGGATGCC 61.817 68.421 15.38 15.38 39.80 4.40
2845 5504 3.730761 CGGCTGCTGCAACCTGAC 61.731 66.667 18.96 1.38 41.91 3.51
2847 5506 3.368571 GCTGCTGCAACCTGACCC 61.369 66.667 11.11 0.00 39.41 4.46
2891 5552 6.533730 CCCTGATGTACCTGCTTTATTATGA 58.466 40.000 0.00 0.00 0.00 2.15
2902 5563 8.945193 ACCTGCTTTATTATGATAGGAACCTTA 58.055 33.333 0.00 0.00 0.00 2.69
2921 5582 7.453141 ACCTTATTTAGCTTTAGAGATGGGT 57.547 36.000 0.00 0.00 0.00 4.51
2988 5650 0.670546 GGCTGCTGCTTTGTAGTCGA 60.671 55.000 15.64 0.00 39.59 4.20
3061 5723 2.792542 GCGAGGCACAATAATCTGTTGC 60.793 50.000 0.00 0.00 0.00 4.17
3064 5726 2.756760 AGGCACAATAATCTGTTGCTGG 59.243 45.455 0.00 0.00 0.00 4.85
3069 5731 4.395854 CACAATAATCTGTTGCTGGTGCTA 59.604 41.667 0.00 0.00 40.48 3.49
3084 5746 2.171448 GGTGCTAATGATCACTGTCCCT 59.829 50.000 0.00 0.00 33.91 4.20
3095 5757 0.401395 ACTGTCCCTGTTCCTCCCAA 60.401 55.000 0.00 0.00 0.00 4.12
3110 5775 1.761784 TCCCAATTGCTGCTGTTGTTT 59.238 42.857 0.00 0.00 0.00 2.83
3157 5822 0.036952 CAGATGACAGACCGCAACCT 60.037 55.000 0.00 0.00 0.00 3.50
3279 5944 2.042842 TGCCTCCAGGAATCCAAAATGA 59.957 45.455 0.61 0.00 37.39 2.57
3345 6010 0.034337 TAAGAGTTTCGCCCAACGCT 59.966 50.000 0.00 0.00 43.23 5.07
3398 6063 2.885554 GCTTTGGGATGATGAGGTGGTT 60.886 50.000 0.00 0.00 0.00 3.67
3408 6073 1.890876 TGAGGTGGTTCATTTGTCCG 58.109 50.000 0.00 0.00 0.00 4.79
3425 6090 1.071542 TCCGATGTCCACTTTCAAGCA 59.928 47.619 0.00 0.00 0.00 3.91
3497 6162 3.071874 TCCTTCAAGCTAACCATGGTG 57.928 47.619 20.60 8.15 0.00 4.17
3549 6214 0.389166 CTTCTTCGCCGAGCTTGTCT 60.389 55.000 0.00 0.00 0.00 3.41
3594 6259 1.762858 TGGTTGGTCACGGGAGACA 60.763 57.895 0.00 0.00 40.29 3.41
3704 6369 6.822676 CCTGTGAGCTTAAAGAGATTCATCTT 59.177 38.462 0.00 0.00 41.31 2.40
3738 6403 3.334583 TCACTTGGAGTAATGGACAGC 57.665 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 165 1.411246 TCCTTGTAGTCTTGCACGTGT 59.589 47.619 18.38 0.00 0.00 4.49
161 168 1.272490 TCCTCCTTGTAGTCTTGCACG 59.728 52.381 0.00 0.00 0.00 5.34
169 176 0.253160 TGCCCCATCCTCCTTGTAGT 60.253 55.000 0.00 0.00 0.00 2.73
216 270 5.048643 CCTTTGAGAGATCATGATCAATGGC 60.049 44.000 31.99 18.42 38.99 4.40
219 273 5.942961 AGCCTTTGAGAGATCATGATCAAT 58.057 37.500 31.99 21.75 40.22 2.57
230 284 3.931578 GCTTTGACTAGCCTTTGAGAGA 58.068 45.455 0.00 0.00 35.06 3.10
240 294 2.019984 CCTCCATTGGCTTTGACTAGC 58.980 52.381 0.00 0.00 40.48 3.42
305 1267 7.155328 GGTCTCACTTGATAAGAGAAAAGACA 58.845 38.462 0.00 0.00 39.85 3.41
367 1329 5.529060 AGGAAAGAAGAAAACTACAGTGCTG 59.471 40.000 0.00 0.00 0.00 4.41
396 1358 7.386299 GTGGATGCGTGATAATAGAAGAAAGAT 59.614 37.037 0.00 0.00 0.00 2.40
433 1398 0.888619 TTCGAGAACGATGGTGCTCT 59.111 50.000 13.44 0.00 45.37 4.09
587 1552 0.873054 GCCATCAGATCGCCATGAAG 59.127 55.000 0.00 0.00 0.00 3.02
617 1582 2.919043 GCCATTCATCCTCCGGGT 59.081 61.111 0.00 0.00 0.00 5.28
645 1610 4.823419 CGCCACCAATACGCGGGA 62.823 66.667 12.47 0.00 42.14 5.14
682 1647 0.809241 GAGGAGCGTCTTGATGGCTG 60.809 60.000 4.35 0.00 37.10 4.85
684 1649 0.809241 CAGAGGAGCGTCTTGATGGC 60.809 60.000 0.00 0.00 0.00 4.40
690 1655 0.543174 AAGACCCAGAGGAGCGTCTT 60.543 55.000 0.00 0.00 40.00 3.01
697 1707 3.385115 GGGAATAAGAAGACCCAGAGGA 58.615 50.000 0.00 0.00 41.72 3.71
699 1709 3.388913 AGGGGAATAAGAAGACCCAGAG 58.611 50.000 0.00 0.00 43.96 3.35
734 1744 1.493311 CGAAGCTTGACGAACTGCC 59.507 57.895 2.10 0.00 0.00 4.85
807 1817 2.055633 TCGGCAGGTCAGCGGATTA 61.056 57.895 0.00 0.00 38.68 1.75
862 1872 2.204244 GGGGAAGGGAGGGTTGGA 60.204 66.667 0.00 0.00 0.00 3.53
1015 2025 4.899239 GATGCGGAGAGGGCGTGG 62.899 72.222 0.00 0.00 0.00 4.94
1075 2085 4.592192 CATCTCCGGCGTGGCGAT 62.592 66.667 17.90 0.00 43.05 4.58
1096 2106 2.437359 GAGGCTCGCTGCATTGGT 60.437 61.111 0.00 0.00 45.15 3.67
1104 2114 4.434354 AGGGACTCGAGGCTCGCT 62.434 66.667 31.01 18.93 40.21 4.93
1171 2181 2.309755 TGTTGATGGCCTCCTTGATCTT 59.690 45.455 3.32 0.00 0.00 2.40
1192 2202 1.234615 CGGTCGATGCCAAACTGGTT 61.235 55.000 0.00 0.00 40.46 3.67
1363 2373 3.451178 ACATGGTAGTTAGCTTGGACGAT 59.549 43.478 0.00 0.00 34.40 3.73
1521 2532 0.323725 GGTTGTCAGACCATGCCCAT 60.324 55.000 0.00 0.00 39.57 4.00
1713 2724 5.491070 CATGTAAAAGGATCAGTGTGAGGA 58.509 41.667 0.00 0.00 0.00 3.71
1850 2861 4.742201 TGTCGCGGCCTCTTCTGC 62.742 66.667 8.89 0.00 35.08 4.26
1956 4513 3.017771 ATGGTCACCGCTGCGATCA 62.018 57.895 25.45 10.86 0.00 2.92
1959 4516 4.758251 CCATGGTCACCGCTGCGA 62.758 66.667 25.45 1.78 0.00 5.10
2020 4577 1.076485 AACTGGCATGCCCTCCATC 60.076 57.895 33.44 7.62 34.56 3.51
2021 4578 1.076485 GAACTGGCATGCCCTCCAT 60.076 57.895 33.44 15.25 34.56 3.41
2022 4579 2.356278 GAACTGGCATGCCCTCCA 59.644 61.111 33.44 14.41 34.56 3.86
2023 4580 2.440980 GGAACTGGCATGCCCTCC 60.441 66.667 33.44 28.82 34.56 4.30
2024 4581 2.440980 GGGAACTGGCATGCCCTC 60.441 66.667 33.44 24.63 37.59 4.30
2025 4582 2.943265 AGGGAACTGGCATGCCCT 60.943 61.111 33.44 19.01 45.97 5.19
2055 4612 1.613630 ATCCGCCAAGTCCCTCTGT 60.614 57.895 0.00 0.00 0.00 3.41
2109 4666 2.101415 CTGAATGATGTCGCAGGAGGTA 59.899 50.000 0.00 0.00 0.00 3.08
2227 4784 3.513515 GACTGAAGAGGAGAGATGGTTGT 59.486 47.826 0.00 0.00 0.00 3.32
2228 4785 3.768757 AGACTGAAGAGGAGAGATGGTTG 59.231 47.826 0.00 0.00 0.00 3.77
2229 4786 4.059773 AGACTGAAGAGGAGAGATGGTT 57.940 45.455 0.00 0.00 0.00 3.67
2250 4807 2.122729 AGTGAGTGGGCAGGCCTA 59.877 61.111 15.38 3.17 36.10 3.93
2252 4809 4.729918 CCAGTGAGTGGGCAGGCC 62.730 72.222 5.91 5.91 43.63 5.19
2270 4827 1.004044 AGTCCAAAGCCATCTCAGGTG 59.996 52.381 0.00 0.00 0.00 4.00
2271 4828 1.280421 GAGTCCAAAGCCATCTCAGGT 59.720 52.381 0.00 0.00 0.00 4.00
2272 4829 1.741732 CGAGTCCAAAGCCATCTCAGG 60.742 57.143 0.00 0.00 0.00 3.86
2279 4929 3.876589 GACGCCGAGTCCAAAGCCA 62.877 63.158 0.00 0.00 43.95 4.75
2295 4945 2.125350 CTTGGCGCTGGAGAGGAC 60.125 66.667 7.64 0.00 0.00 3.85
2365 5015 2.518112 TTGTGCAGCGGCTTCCAA 60.518 55.556 10.92 7.64 41.91 3.53
2373 5023 0.720027 CAGTCATCTCTTGTGCAGCG 59.280 55.000 0.00 0.00 0.00 5.18
2377 5027 4.564041 TCTTCTTCAGTCATCTCTTGTGC 58.436 43.478 0.00 0.00 0.00 4.57
2389 5039 2.317371 TCAGAGGCCTCTTCTTCAGT 57.683 50.000 33.33 6.82 37.98 3.41
2411 5061 1.812571 CAAAGATGGGTGTGGTAGCAC 59.187 52.381 18.10 18.10 38.56 4.40
2421 5071 1.916181 CTACAGGGGACAAAGATGGGT 59.084 52.381 0.00 0.00 0.00 4.51
2451 5101 0.492276 AGGTTGGAGGTGAGGGTAGT 59.508 55.000 0.00 0.00 0.00 2.73
2454 5104 1.847968 CCAGGTTGGAGGTGAGGGT 60.848 63.158 0.00 0.00 40.96 4.34
2463 5113 1.694525 TGGTGGTGTCCAGGTTGGA 60.695 57.895 0.00 0.00 45.98 3.53
2561 5211 1.377856 GGCAGCCTCTGGTTCTTCC 60.378 63.158 3.29 0.00 31.21 3.46
2562 5212 1.377856 GGGCAGCCTCTGGTTCTTC 60.378 63.158 12.43 0.00 31.21 2.87
2617 5267 1.559368 CCATCTTCCACAATGCCCAA 58.441 50.000 0.00 0.00 0.00 4.12
2631 5281 0.460284 CGGTAAGCTGTTCGCCATCT 60.460 55.000 0.00 0.00 40.39 2.90
2646 5296 1.048160 TGCTGATGGCCATCTCGGTA 61.048 55.000 38.59 26.22 40.92 4.02
2653 5303 1.274167 CACAAACTTGCTGATGGCCAT 59.726 47.619 20.96 20.96 40.92 4.40
2654 5304 0.675083 CACAAACTTGCTGATGGCCA 59.325 50.000 8.56 8.56 40.92 5.36
2691 5341 2.483714 CGTAATGGTGATGTCAGGGAGG 60.484 54.545 0.00 0.00 0.00 4.30
2710 5360 1.103398 AACAAAGCAAGCAGAGCCGT 61.103 50.000 0.00 0.00 0.00 5.68
2720 5370 3.675775 GCAGTCAAGGTTGAACAAAGCAA 60.676 43.478 0.00 0.00 39.21 3.91
2721 5371 2.159254 GCAGTCAAGGTTGAACAAAGCA 60.159 45.455 0.00 0.00 39.21 3.91
2725 5375 2.031258 TCGCAGTCAAGGTTGAACAA 57.969 45.000 0.00 0.00 39.21 2.83
2812 5471 4.598894 CGCCTCGGCATCCTCCTG 62.599 72.222 8.87 0.00 42.06 3.86
2845 5504 1.028905 TCACAAAGAAAACCAGCGGG 58.971 50.000 0.00 0.00 41.29 6.13
2847 5506 2.053627 GCATCACAAAGAAAACCAGCG 58.946 47.619 0.00 0.00 0.00 5.18
2902 5563 4.381411 GCGACCCATCTCTAAAGCTAAAT 58.619 43.478 0.00 0.00 0.00 1.40
2921 5582 1.725641 CTGCAGATACAAACAGGCGA 58.274 50.000 8.42 0.00 0.00 5.54
2974 5636 2.279136 GCGTACATCGACTACAAAGCAG 59.721 50.000 0.00 0.00 42.86 4.24
2988 5650 0.606401 AGCAGCAAACAGGCGTACAT 60.606 50.000 0.00 0.00 39.27 2.29
3048 5710 5.565592 TTAGCACCAGCAACAGATTATTG 57.434 39.130 0.00 0.00 45.49 1.90
3050 5712 5.439721 TCATTAGCACCAGCAACAGATTAT 58.560 37.500 0.00 0.00 45.49 1.28
3061 5723 3.201290 GGACAGTGATCATTAGCACCAG 58.799 50.000 0.00 0.00 43.16 4.00
3064 5726 3.201290 CAGGGACAGTGATCATTAGCAC 58.799 50.000 0.00 0.00 42.46 4.40
3069 5731 2.915604 AGGAACAGGGACAGTGATCATT 59.084 45.455 0.00 0.00 0.00 2.57
3084 5746 0.112995 AGCAGCAATTGGGAGGAACA 59.887 50.000 7.72 0.00 0.00 3.18
3095 5757 1.935199 GCACAAAACAACAGCAGCAAT 59.065 42.857 0.00 0.00 0.00 3.56
3110 5775 0.233590 GCATACGTCGTTGTGCACAA 59.766 50.000 27.96 27.96 37.52 3.33
3157 5822 5.258841 TCTAGTTTAGGATCGTGAGGTTGA 58.741 41.667 0.00 0.00 0.00 3.18
3368 6033 4.413189 TCATCATCCCAAAGCAGAAGGATA 59.587 41.667 0.00 0.00 36.99 2.59
3398 6063 3.417069 AAGTGGACATCGGACAAATGA 57.583 42.857 0.00 0.00 0.00 2.57
3408 6073 4.479619 GTGAATGCTTGAAAGTGGACATC 58.520 43.478 0.00 0.00 0.00 3.06
3425 6090 0.617413 CTGTGGCTGAGAGGGTGAAT 59.383 55.000 0.00 0.00 0.00 2.57
3497 6162 4.886489 AGGTTACTTCTAGTCGGTCCATAC 59.114 45.833 0.00 0.00 0.00 2.39
3549 6214 0.821711 CCTTGTGGTGGCTTTTCGGA 60.822 55.000 0.00 0.00 0.00 4.55
3594 6259 2.223711 GCGCCCGATAAATTTGGTTGAT 60.224 45.455 0.00 0.00 0.00 2.57
3704 6369 5.960811 ACTCCAAGTGAATCTCCTATTCTGA 59.039 40.000 0.00 0.00 0.00 3.27
3738 6403 0.609957 TTGCTCAAGGTGGGCTCATG 60.610 55.000 1.21 0.00 46.08 3.07
3784 6449 2.632512 GAGCCAAATTCCAAGTCCCAAA 59.367 45.455 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.