Multiple sequence alignment - TraesCS2A01G321600

Loading Multiple Alignment...

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 TraesCS2A01G321600 chr2A 100.000 5581 0 0 1 5581 551254233 551248653 0.000000e+00 10307.0
1 TraesCS2A01G321600 chr2A 97.059 34 0 1 5391 5424 551248699 551248667 7.810000e-04 56.5
2 TraesCS2A01G321600 chr2A 97.059 34 0 1 5535 5567 551248843 551248810 7.810000e-04 56.5
3 TraesCS2A01G321600 chr2D 94.850 4621 175 28 118 4723 437674163 437678735 0.000000e+00 7156.0
4 TraesCS2A01G321600 chr2D 92.948 553 28 7 5034 5579 437679202 437679750 0.000000e+00 795.0
5 TraesCS2A01G321600 chr2D 91.262 103 5 1 11 113 437666495 437666593 2.710000e-28 137.0
6 TraesCS2A01G321600 chr2D 97.500 40 1 0 108 147 437674127 437674166 1.000000e-07 69.4
7 TraesCS2A01G321600 chr2D 97.059 34 0 1 5535 5567 437679560 437679593 7.810000e-04 56.5
8 TraesCS2A01G321600 chr2D 97.059 34 0 1 5391 5424 437679706 437679738 7.810000e-04 56.5
9 TraesCS2A01G321600 chr2B 93.744 2014 97 14 1540 3541 514030173 514032169 0.000000e+00 2994.0
10 TraesCS2A01G321600 chr2B 93.285 2055 82 24 3538 5581 514032231 514034240 0.000000e+00 2979.0
11 TraesCS2A01G321600 chr2B 89.368 1298 76 23 11 1266 514028503 514029780 0.000000e+00 1576.0
12 TraesCS2A01G321600 chr2B 88.670 203 14 4 1268 1465 514029829 514030027 7.230000e-59 239.0
13 TraesCS2A01G321600 chr2B 97.059 34 0 1 5391 5424 514034194 514034226 7.810000e-04 56.5
14 TraesCS2A01G321600 chr1B 80.473 1014 149 27 1607 2596 8239328 8240316 0.000000e+00 730.0
15 TraesCS2A01G321600 chr7B 82.678 814 96 26 1801 2590 23080433 23081225 0.000000e+00 680.0
16 TraesCS2A01G321600 chr5A 81.128 922 110 35 2641 3526 35658854 35659747 0.000000e+00 680.0
17 TraesCS2A01G321600 chr6B 84.247 584 82 9 2018 2596 643396838 643396260 1.360000e-155 560.0
18 TraesCS2A01G321600 chr6B 83.333 294 43 3 2641 2934 643396183 643395896 3.310000e-67 267.0
19 TraesCS2A01G321600 chr6B 80.399 301 56 3 2770 3069 422650670 422650968 5.630000e-55 226.0
20 TraesCS2A01G321600 chr6B 90.435 115 11 0 1939 2053 422649382 422649496 9.680000e-33 152.0
21 TraesCS2A01G321600 chr6D 82.084 547 62 18 2065 2590 445831113 445831644 8.590000e-118 435.0
22 TraesCS2A01G321600 chr6D 91.304 115 10 0 1939 2053 270050742 270050856 2.080000e-34 158.0


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 TraesCS2A01G321600 chr2A 551248653 551254233 5580 True 10307.00 10307 100.0000 1 5581 1 chr2A.!!$R1 5580
1 TraesCS2A01G321600 chr2D 437674127 437679750 5623 False 1626.68 7156 95.8832 108 5579 5 chr2D.!!$F2 5471
2 TraesCS2A01G321600 chr2B 514028503 514034240 5737 False 1568.90 2994 92.4252 11 5581 5 chr2B.!!$F1 5570
3 TraesCS2A01G321600 chr1B 8239328 8240316 988 False 730.00 730 80.4730 1607 2596 1 chr1B.!!$F1 989
4 TraesCS2A01G321600 chr7B 23080433 23081225 792 False 680.00 680 82.6780 1801 2590 1 chr7B.!!$F1 789
5 TraesCS2A01G321600 chr5A 35658854 35659747 893 False 680.00 680 81.1280 2641 3526 1 chr5A.!!$F1 885
6 TraesCS2A01G321600 chr6B 643395896 643396838 942 True 413.50 560 83.7900 2018 2934 2 chr6B.!!$R1 916
7 TraesCS2A01G321600 chr6D 445831113 445831644 531 False 435.00 435 82.0840 2065 2590 1 chr6D.!!$F2 525

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
202 252 0.460109 CACGACGCAATCTCCATCCA 60.460 55.0 0.00 0.00 0.00 3.41 F
449 499 0.474660 ACCCCAGCCATCTATCTCCC 60.475 60.0 0.00 0.00 0.00 4.30 F
504 561 0.537371 AACTCCAACCAGGCTTTCCG 60.537 55.0 0.00 0.00 37.29 4.30 F
1957 2166 0.035152 CAGGTGTTCTGCTATGCCCA 60.035 55.0 0.00 0.00 36.60 5.36 F
2878 3207 0.607489 ACAAGTGCCCTGTGATGCTC 60.607 55.0 0.00 0.00 0.00 4.26 F
4471 4889 0.533085 GGATCCCAAGCGCTAAGGTC 60.533 60.0 22.76 18.14 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1193 1262 0.033781 GCAAGGAAATGCACAGCCAA 59.966 50.000 0.00 0.00 45.70 4.52 R
1753 1951 1.578583 GCAAATCCATGGCTTGCATC 58.421 50.000 31.05 13.28 43.89 3.91 R
2273 2488 2.553602 TGCATCGAATGTGGCCATTATC 59.446 45.455 9.72 6.63 41.37 1.75 R
2995 3326 2.054453 GGATGCAAGAACAGCCCCC 61.054 63.158 0.00 0.00 40.32 5.40 R
4481 4899 1.656441 GCTAAGCATCCGGGCAATG 59.344 57.895 0.00 0.00 35.83 2.82 R
5452 6169 0.031721 GTAGCCGTCTTGTATCCCCG 59.968 60.000 0.00 0.00 0.00 5.73 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
69 70 3.519930 GCCTCCCGTCGGTCTCTC 61.520 72.222 11.06 0.00 0.00 3.20
70 71 2.272797 CCTCCCGTCGGTCTCTCT 59.727 66.667 11.06 0.00 0.00 3.10
71 72 1.820481 CCTCCCGTCGGTCTCTCTC 60.820 68.421 11.06 0.00 0.00 3.20
202 252 0.460109 CACGACGCAATCTCCATCCA 60.460 55.000 0.00 0.00 0.00 3.41
435 485 2.929477 GTAACCACCCCGACCCCA 60.929 66.667 0.00 0.00 0.00 4.96
443 493 2.445845 CCCGACCCCAGCCATCTA 60.446 66.667 0.00 0.00 0.00 1.98
444 494 1.843376 CCCGACCCCAGCCATCTAT 60.843 63.158 0.00 0.00 0.00 1.98
445 495 1.674057 CCGACCCCAGCCATCTATC 59.326 63.158 0.00 0.00 0.00 2.08
448 498 0.980423 GACCCCAGCCATCTATCTCC 59.020 60.000 0.00 0.00 0.00 3.71
449 499 0.474660 ACCCCAGCCATCTATCTCCC 60.475 60.000 0.00 0.00 0.00 4.30
451 501 0.982704 CCCAGCCATCTATCTCCCTG 59.017 60.000 0.00 0.00 0.00 4.45
496 552 1.277557 CTCTCCTCCAACTCCAACCAG 59.722 57.143 0.00 0.00 0.00 4.00
504 561 0.537371 AACTCCAACCAGGCTTTCCG 60.537 55.000 0.00 0.00 37.29 4.30
641 698 0.811915 ATCTTCAGTCAGGTCCGTCG 59.188 55.000 0.00 0.00 0.00 5.12
643 700 2.214181 CTTCAGTCAGGTCCGTCGGG 62.214 65.000 12.29 0.00 0.00 5.14
669 726 6.339587 TCGCCTGGTTCTTGATTTATTTTT 57.660 33.333 0.00 0.00 0.00 1.94
710 767 1.651138 GAGATGTCGTTGTTGCTCTCG 59.349 52.381 0.00 0.00 0.00 4.04
740 797 1.511254 GAAATTCGTCGCCGGTTGC 60.511 57.895 1.90 0.00 33.95 4.17
874 937 0.681243 GGTGACCAAGGATTCCTGGC 60.681 60.000 5.84 0.00 32.13 4.85
941 1004 0.969149 GGGGTTTTGGAGGAAAGCTG 59.031 55.000 0.00 0.00 37.23 4.24
993 1062 1.157585 GACCAAGGCCGAAGAAGAAC 58.842 55.000 0.00 0.00 0.00 3.01
1032 1101 3.465403 AGTAGCAGGCTCTGGGCG 61.465 66.667 0.00 0.00 42.94 6.13
1124 1193 4.134563 GACATCCTGGTCTCTCTACTCTC 58.865 52.174 0.00 0.00 34.92 3.20
1130 1199 3.616219 TGGTCTCTCTACTCTCTTGCTC 58.384 50.000 0.00 0.00 0.00 4.26
1139 1208 5.084519 TCTACTCTCTTGCTCCTTTTGGTA 58.915 41.667 0.00 0.00 41.38 3.25
1155 1224 4.558226 TTGGTATGCAAGTCTGATCTGT 57.442 40.909 0.00 0.00 0.00 3.41
1156 1225 4.128925 TGGTATGCAAGTCTGATCTGTC 57.871 45.455 0.00 0.00 0.00 3.51
1157 1226 3.515104 TGGTATGCAAGTCTGATCTGTCA 59.485 43.478 0.00 0.00 0.00 3.58
1158 1227 4.162888 TGGTATGCAAGTCTGATCTGTCAT 59.837 41.667 0.00 0.00 32.98 3.06
1159 1228 4.749099 GGTATGCAAGTCTGATCTGTCATC 59.251 45.833 0.00 0.00 32.98 2.92
1160 1229 4.757019 ATGCAAGTCTGATCTGTCATCT 57.243 40.909 0.00 0.00 32.98 2.90
1161 1230 5.866159 ATGCAAGTCTGATCTGTCATCTA 57.134 39.130 0.00 0.00 32.98 1.98
1162 1231 5.003692 TGCAAGTCTGATCTGTCATCTAC 57.996 43.478 0.00 0.00 32.98 2.59
1193 1262 7.336931 GTGTGAGTAAAATGGAGTGGTCATATT 59.663 37.037 0.00 0.00 0.00 1.28
1308 1426 6.889177 TCCAGCTTTTGTTATGATATGACCAA 59.111 34.615 0.00 0.00 0.00 3.67
1340 1458 4.333926 CACCTGGCTTGAGTTATTAGCTTC 59.666 45.833 0.00 0.00 35.30 3.86
1455 1576 4.927267 ATAACCCTTTGTGGACAGATGA 57.073 40.909 0.00 0.00 38.35 2.92
1465 1586 5.612725 TGTGGACAGATGATATGCACTTA 57.387 39.130 0.00 0.00 0.00 2.24
1467 1588 4.445718 GTGGACAGATGATATGCACTTACG 59.554 45.833 0.00 0.00 0.00 3.18
1484 1651 2.851263 ACGCACTTTCACCCATAAGA 57.149 45.000 0.00 0.00 0.00 2.10
1515 1696 5.010617 GGGCTTCAACCTGAAAAATCTTGTA 59.989 40.000 0.00 0.00 35.73 2.41
1533 1714 7.072177 TCTTGTAGTTTCTCACACACAAAAG 57.928 36.000 0.00 0.00 34.14 2.27
1690 1888 6.211785 TGTTAGGTACATATGTGACCTTGTGA 59.788 38.462 27.45 15.55 40.85 3.58
1733 1931 3.342269 CTTTCGGTTGAATTATGTCGCG 58.658 45.455 0.00 0.00 33.20 5.87
1753 1951 2.286359 CGTGTTGTCTGTTGATGTGTGG 60.286 50.000 0.00 0.00 0.00 4.17
1799 2007 2.859165 TGACAGAGTTTCATGGGGAC 57.141 50.000 0.00 0.00 0.00 4.46
1837 2045 1.523934 GAAATTGCAGCTGTGTTGTGC 59.476 47.619 16.64 0.00 37.73 4.57
1838 2046 0.249573 AATTGCAGCTGTGTTGTGCC 60.250 50.000 16.64 0.00 36.31 5.01
1918 2127 8.660295 TTAAACTATGTATCGTATCCCCTCAT 57.340 34.615 0.00 0.00 0.00 2.90
1957 2166 0.035152 CAGGTGTTCTGCTATGCCCA 60.035 55.000 0.00 0.00 36.60 5.36
2090 2304 2.821969 CAGTTTCACCCTTAGCAAGCAT 59.178 45.455 0.00 0.00 0.00 3.79
2199 2413 1.102809 TCTTGTTGCTGCCACTGTGG 61.103 55.000 22.46 22.46 41.55 4.17
2238 2452 3.656280 TTGGCATCCCGGGAAGCA 61.656 61.111 42.08 28.84 40.18 3.91
2343 2559 7.475771 TTTGTTCATTGCTTTGTGGTAAATC 57.524 32.000 0.00 0.00 0.00 2.17
2382 2613 3.317711 TGCCATTCCTTGTATTTATGCCG 59.682 43.478 0.00 0.00 0.00 5.69
2635 2950 6.971726 ATGACCTTCATCACATATGCAAAT 57.028 33.333 1.58 0.00 29.59 2.32
2878 3207 0.607489 ACAAGTGCCCTGTGATGCTC 60.607 55.000 0.00 0.00 0.00 4.26
2995 3326 0.676466 TCTGGCCATTTGCGGTACTG 60.676 55.000 5.51 0.00 42.61 2.74
3022 3358 2.842496 TGTTCTTGCATCCATCCTCTCT 59.158 45.455 0.00 0.00 0.00 3.10
3084 3420 6.377327 CCAGGTATGGCAATTTGTACTTAG 57.623 41.667 0.00 0.00 40.52 2.18
3283 3630 4.616181 CTTGCTTTCCAAGGTATAACCG 57.384 45.455 0.00 0.00 45.78 4.44
3534 3883 8.879759 TCAAGGTTATCTTTTCTTGCTAATACG 58.120 33.333 0.00 0.00 37.21 3.06
3560 3974 3.251479 AGATCACAATGCTTCTGCGTA 57.749 42.857 0.00 0.00 43.34 4.42
3586 4000 3.311322 TGACCAGCTTCACTTTTTGTACG 59.689 43.478 0.00 0.00 0.00 3.67
3612 4026 4.889409 CCAATAGGAATAGCACATGTTGGT 59.111 41.667 0.00 0.13 36.25 3.67
3685 4102 9.958180 TCCTTGATAATTGAACTTACAGAATCA 57.042 29.630 0.00 0.00 0.00 2.57
3701 4118 6.692486 ACAGAATCAGGACATATAACCGATC 58.308 40.000 0.00 0.00 0.00 3.69
3958 4375 5.147330 TCATGTTACACCACTACCAGAAG 57.853 43.478 0.00 0.00 0.00 2.85
3959 4376 4.020573 TCATGTTACACCACTACCAGAAGG 60.021 45.833 0.00 0.00 42.21 3.46
4166 4583 0.842030 TCCTGATGGTTGGTGAGCCT 60.842 55.000 0.00 0.00 33.22 4.58
4217 4634 2.569059 CCATCACTGAATGAGCGGAAT 58.431 47.619 0.00 0.00 41.91 3.01
4272 4689 2.223433 CGCCCTGCTCATTCTTTCATTC 60.223 50.000 0.00 0.00 0.00 2.67
4275 4692 3.181489 CCCTGCTCATTCTTTCATTCTGC 60.181 47.826 0.00 0.00 0.00 4.26
4315 4732 2.109126 GCTAAACCGCCTGCTCCTG 61.109 63.158 0.00 0.00 0.00 3.86
4318 4735 2.124507 TAAACCGCCTGCTCCTGCTT 62.125 55.000 0.00 0.00 40.48 3.91
4322 4739 2.960170 GCCTGCTCCTGCTTTGTG 59.040 61.111 0.00 0.00 40.48 3.33
4325 4742 1.572085 CCTGCTCCTGCTTTGTGTCG 61.572 60.000 0.00 0.00 40.48 4.35
4346 4764 3.438087 CGTCAAGATTGCAAGGAATCACT 59.562 43.478 15.19 1.13 35.16 3.41
4385 4803 2.073816 CCTACATCCAAGCGTCGTTTT 58.926 47.619 0.00 0.00 0.00 2.43
4464 4882 3.122850 CCAATGGATCCCAAGCGC 58.877 61.111 9.90 0.00 36.95 5.92
4471 4889 0.533085 GGATCCCAAGCGCTAAGGTC 60.533 60.000 22.76 18.14 0.00 3.85
4481 4899 2.413765 CTAAGGTCGAGAGGCGGC 59.586 66.667 0.00 0.00 45.73 6.53
4509 4927 2.746142 CGGATGCTTAGCCAGAAATCCA 60.746 50.000 17.02 0.00 37.22 3.41
4780 5206 8.797350 TTTATGAGAAATCTTGCAAGATCTCA 57.203 30.769 39.25 39.25 46.70 3.27
4815 5241 4.390603 GCATTTGAACTACCACGTGACATA 59.609 41.667 19.30 5.56 0.00 2.29
4816 5242 5.064707 GCATTTGAACTACCACGTGACATAT 59.935 40.000 19.30 0.00 0.00 1.78
4840 5266 5.554437 TGGTACACAATCCAAACTACTCA 57.446 39.130 0.00 0.00 0.00 3.41
4844 5270 7.012894 TGGTACACAATCCAAACTACTCAAAAG 59.987 37.037 0.00 0.00 0.00 2.27
4847 5273 8.062065 ACACAATCCAAACTACTCAAAAGAAA 57.938 30.769 0.00 0.00 0.00 2.52
4848 5274 8.527810 ACACAATCCAAACTACTCAAAAGAAAA 58.472 29.630 0.00 0.00 0.00 2.29
4849 5275 9.364989 CACAATCCAAACTACTCAAAAGAAAAA 57.635 29.630 0.00 0.00 0.00 1.94
4873 5299 8.621532 AATGTTAGCATTTGAACTTGTCTCTA 57.378 30.769 0.00 0.00 42.19 2.43
4880 5306 9.624373 AGCATTTGAACTTGTCTCTAATATCAT 57.376 29.630 0.00 0.00 0.00 2.45
4908 5334 6.128472 GGAGAAATTGGCATTAAACAAAGCTG 60.128 38.462 0.00 0.00 0.00 4.24
4914 5340 2.989166 GCATTAAACAAAGCTGGACTGC 59.011 45.455 0.00 0.00 0.00 4.40
4921 5347 2.030805 ACAAAGCTGGACTGCGAATTTC 60.031 45.455 0.00 0.00 38.13 2.17
4989 5701 4.037446 GCAACAACAGGACACCAAAATAGA 59.963 41.667 0.00 0.00 0.00 1.98
4995 5707 1.467342 GGACACCAAAATAGACACGGC 59.533 52.381 0.00 0.00 0.00 5.68
5005 5717 2.623878 TAGACACGGCAAAAAGGACA 57.376 45.000 0.00 0.00 0.00 4.02
5006 5718 1.757682 AGACACGGCAAAAAGGACAA 58.242 45.000 0.00 0.00 0.00 3.18
5058 5770 4.318332 CACAAACTCAATACAGCTGGAGA 58.682 43.478 19.93 2.84 0.00 3.71
5102 5818 0.321919 TCCAGACATGTTCAGCAGCC 60.322 55.000 0.00 0.00 0.00 4.85
5117 5833 1.608542 GCAGCCAAATCCACAAATGCA 60.609 47.619 0.00 0.00 32.79 3.96
5289 6005 0.178975 CTACTGGAGCCTCGGAGGAT 60.179 60.000 27.95 22.46 37.67 3.24
5425 6142 5.948992 AGTCAAGCAGTTCTATCCAAAAC 57.051 39.130 0.00 0.00 0.00 2.43
5445 6162 2.135139 CGTTACCGTGCATGCATCTAT 58.865 47.619 25.64 12.41 0.00 1.98
5485 6202 2.159142 ACGGCTACAACATAGCTACCAC 60.159 50.000 0.00 0.00 40.25 4.16
5490 6207 5.221461 GGCTACAACATAGCTACCACAGTAT 60.221 44.000 0.00 0.00 40.25 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.118775 CGGTTCATCAGGTTCATCAGGTA 60.119 47.826 0.00 0.00 0.00 3.08
2 3 2.283298 CGGTTCATCAGGTTCATCAGG 58.717 52.381 0.00 0.00 0.00 3.86
5 6 2.673368 GACACGGTTCATCAGGTTCATC 59.327 50.000 0.00 0.00 0.00 2.92
8 9 1.798813 GTGACACGGTTCATCAGGTTC 59.201 52.381 0.00 0.00 0.00 3.62
9 10 1.542547 GGTGACACGGTTCATCAGGTT 60.543 52.381 0.00 0.00 0.00 3.50
202 252 1.151810 TGCAGGAGGAAGAAGGGGT 60.152 57.895 0.00 0.00 0.00 4.95
269 319 1.341913 GGAGGAGGGAGAAAGGAGGC 61.342 65.000 0.00 0.00 0.00 4.70
430 480 0.474660 GGGAGATAGATGGCTGGGGT 60.475 60.000 0.00 0.00 0.00 4.95
435 485 0.839853 GGGCAGGGAGATAGATGGCT 60.840 60.000 0.00 0.00 38.23 4.75
439 489 1.190833 CGCAGGGCAGGGAGATAGAT 61.191 60.000 0.00 0.00 0.00 1.98
440 490 1.834378 CGCAGGGCAGGGAGATAGA 60.834 63.158 0.00 0.00 0.00 1.98
441 491 2.739784 CGCAGGGCAGGGAGATAG 59.260 66.667 0.00 0.00 0.00 2.08
442 492 3.550431 GCGCAGGGCAGGGAGATA 61.550 66.667 0.30 0.00 42.87 1.98
504 561 4.681978 AGACAAGCCCGTGCCGTC 62.682 66.667 2.41 2.41 39.52 4.79
641 698 4.035102 AAGAACCAGGCGAGCCCC 62.035 66.667 10.95 0.00 36.58 5.80
643 700 0.678048 AATCAAGAACCAGGCGAGCC 60.678 55.000 5.89 5.89 0.00 4.70
669 726 2.290071 CGGCAGAAAAGGAAGGGAGTAA 60.290 50.000 0.00 0.00 0.00 2.24
710 767 4.403453 CGACGAATTTCTCATTCAAACCC 58.597 43.478 0.00 0.00 0.00 4.11
788 850 1.521450 CCCAGACACAAGCAAGGCTG 61.521 60.000 0.00 0.00 39.62 4.85
833 895 0.836606 AACTTGGCAAAACCTTGGGG 59.163 50.000 0.00 0.00 40.22 4.96
834 896 2.287769 CAAACTTGGCAAAACCTTGGG 58.712 47.619 0.00 0.00 40.22 4.12
941 1004 0.615850 AGCAGGAGGCCAAGACTTAC 59.384 55.000 5.01 0.00 46.50 2.34
993 1062 2.891941 TAGGCGGCTCCATTGGCAAG 62.892 60.000 17.67 0.00 37.29 4.01
1032 1101 3.513515 ACTTGATGAAGGTCCAGAGAGAC 59.486 47.826 0.00 0.00 32.95 3.36
1124 1193 3.940209 TTGCATACCAAAAGGAGCAAG 57.060 42.857 0.00 0.00 37.10 4.01
1130 1199 4.946157 AGATCAGACTTGCATACCAAAAGG 59.054 41.667 0.00 0.00 31.94 3.11
1139 1208 4.757019 AGATGACAGATCAGACTTGCAT 57.243 40.909 0.00 0.00 38.57 3.96
1193 1262 0.033781 GCAAGGAAATGCACAGCCAA 59.966 50.000 0.00 0.00 45.70 4.52
1308 1426 2.298163 CTCAAGCCAGGTGAAAGCAATT 59.702 45.455 0.00 0.00 36.26 2.32
1340 1458 8.030106 TCAGTTAAAACCAACAACTACTTTTGG 58.970 33.333 0.00 0.00 44.66 3.28
1465 1586 2.038557 AGTCTTATGGGTGAAAGTGCGT 59.961 45.455 0.00 0.00 0.00 5.24
1467 1588 4.575885 TGTAGTCTTATGGGTGAAAGTGC 58.424 43.478 0.00 0.00 0.00 4.40
1484 1651 1.985159 TCAGGTTGAAGCCCATGTAGT 59.015 47.619 0.00 0.00 0.00 2.73
1515 1696 5.590259 AGCATACTTTTGTGTGTGAGAAACT 59.410 36.000 0.00 0.00 42.50 2.66
1652 1850 6.870971 TGTACCTAACAAACTTCATGGTTC 57.129 37.500 0.00 0.00 34.29 3.62
1690 1888 5.237048 AGCATTCAAACGGCACAATAAATT 58.763 33.333 0.00 0.00 0.00 1.82
1733 1931 2.942376 TCCACACATCAACAGACAACAC 59.058 45.455 0.00 0.00 0.00 3.32
1753 1951 1.578583 GCAAATCCATGGCTTGCATC 58.421 50.000 31.05 13.28 43.89 3.91
1799 2007 7.331440 TGCAATTTCAGCTTTTACATACATTGG 59.669 33.333 0.00 0.00 0.00 3.16
1829 2037 5.959618 AGAAGTATTTAAGGGCACAACAC 57.040 39.130 0.00 0.00 0.00 3.32
1891 2100 8.362639 TGAGGGGATACGATACATAGTTTAAAC 58.637 37.037 10.47 10.47 37.60 2.01
1918 2127 8.262227 ACACCTGTTAGACGGAATAATATGAAA 58.738 33.333 0.00 0.00 0.00 2.69
2199 2413 7.308229 GCCAACTATCAACCATAAGATCATGAC 60.308 40.741 0.00 0.00 0.00 3.06
2238 2452 8.439964 AAGCCATATAATAATCCAGCCAAAAT 57.560 30.769 0.00 0.00 0.00 1.82
2273 2488 2.553602 TGCATCGAATGTGGCCATTATC 59.446 45.455 9.72 6.63 41.37 1.75
2343 2559 3.963665 TGGCATGTTTCACGAAAAGAAG 58.036 40.909 0.00 0.00 31.33 2.85
2878 3207 2.290641 CAGTCGTTTCCACCCTTTGAAG 59.709 50.000 0.00 0.00 0.00 3.02
2995 3326 2.054453 GGATGCAAGAACAGCCCCC 61.054 63.158 0.00 0.00 40.32 5.40
3022 3358 5.252164 ACCAAACAGGCCTAAAGGAATACTA 59.748 40.000 3.98 0.00 43.14 1.82
3084 3420 9.903682 AGCATTTGTCACTATATGATAATTTGC 57.096 29.630 10.89 10.89 42.26 3.68
3096 3436 6.656693 GGATATTGCCTAGCATTTGTCACTAT 59.343 38.462 0.00 0.00 38.76 2.12
3283 3630 4.810491 CCAAAGGCATGCAATATGGTTTAC 59.190 41.667 21.36 0.00 0.00 2.01
3534 3883 4.033817 GCAGAAGCATTGTGATCTACTGAC 59.966 45.833 0.00 0.00 42.84 3.51
3586 4000 4.718961 ACATGTGCTATTCCTATTGGACC 58.281 43.478 0.00 0.00 43.06 4.46
3685 4102 4.156190 CAGCTACGATCGGTTATATGTCCT 59.844 45.833 20.98 0.00 0.00 3.85
3701 4118 2.220363 CAGCATCTGCATAACAGCTACG 59.780 50.000 4.79 0.00 46.76 3.51
3938 4355 3.263425 CCCTTCTGGTAGTGGTGTAACAT 59.737 47.826 0.00 0.00 39.98 2.71
3958 4375 4.395625 GCTAAGGTAATCATAACACCCCC 58.604 47.826 0.00 0.00 32.43 5.40
3959 4376 4.104261 AGGCTAAGGTAATCATAACACCCC 59.896 45.833 0.00 0.00 32.43 4.95
4166 4583 3.185880 AGAGTGCCCTTGAGGTTACTA 57.814 47.619 4.13 0.00 35.93 1.82
4217 4634 4.402583 CAAATGCGTCGATTTCTGCTTTA 58.597 39.130 0.00 0.00 0.00 1.85
4272 4689 7.628235 CAAATATCAGTGATAGTGTTGAGCAG 58.372 38.462 17.52 0.00 0.00 4.24
4275 4692 7.783090 AGCAAATATCAGTGATAGTGTTGAG 57.217 36.000 24.47 12.13 0.00 3.02
4315 4732 2.286950 TGCAATCTTGACGACACAAAGC 60.287 45.455 0.00 0.00 0.00 3.51
4318 4735 2.290367 CCTTGCAATCTTGACGACACAA 59.710 45.455 0.00 0.00 0.00 3.33
4322 4739 3.436704 TGATTCCTTGCAATCTTGACGAC 59.563 43.478 0.00 0.00 34.35 4.34
4325 4742 6.150140 ACTTAGTGATTCCTTGCAATCTTGAC 59.850 38.462 0.00 0.00 34.35 3.18
4346 4764 9.478768 GATGTAGGATATCTCGATATCGACTTA 57.521 37.037 23.48 16.94 46.61 2.24
4385 4803 5.798125 AGAGAGACTTCACAAGAACATCA 57.202 39.130 0.00 0.00 0.00 3.07
4464 4882 1.739338 ATGCCGCCTCTCGACCTTAG 61.739 60.000 0.00 0.00 41.67 2.18
4481 4899 1.656441 GCTAAGCATCCGGGCAATG 59.344 57.895 0.00 0.00 35.83 2.82
4490 4908 4.261909 CCAATGGATTTCTGGCTAAGCATC 60.262 45.833 0.00 0.00 0.00 3.91
4509 4927 3.499338 TGATGTTTGCAGTCTTCCCAAT 58.501 40.909 0.00 0.00 0.00 3.16
4520 4938 5.509716 GATCTTCATCCATGATGTTTGCA 57.490 39.130 0.00 0.00 40.55 4.08
4550 4968 2.767505 CGAGCCTTCCTTGTTACTTGT 58.232 47.619 0.00 0.00 0.00 3.16
4675 5098 5.648572 AGCTACACCTAAGAACGTTCATAC 58.351 41.667 28.78 8.67 0.00 2.39
4780 5206 8.537016 TGGTAGTTCAAATGCTAACATAGTAGT 58.463 33.333 0.00 0.00 34.62 2.73
4815 5241 5.876357 AGTAGTTTGGATTGTGTACCACAT 58.124 37.500 0.00 0.00 44.16 3.21
4816 5242 5.163290 TGAGTAGTTTGGATTGTGTACCACA 60.163 40.000 0.00 0.00 43.02 4.17
4820 5246 8.149973 TCTTTTGAGTAGTTTGGATTGTGTAC 57.850 34.615 0.00 0.00 0.00 2.90
4823 5249 8.925161 TTTTCTTTTGAGTAGTTTGGATTGTG 57.075 30.769 0.00 0.00 0.00 3.33
4849 5275 8.621532 TTAGAGACAAGTTCAAATGCTAACAT 57.378 30.769 0.00 0.00 38.49 2.71
4850 5276 8.621532 ATTAGAGACAAGTTCAAATGCTAACA 57.378 30.769 0.00 0.00 0.00 2.41
4854 5280 9.624373 ATGATATTAGAGACAAGTTCAAATGCT 57.376 29.630 0.00 0.00 0.00 3.79
4880 5306 7.602265 GCTTTGTTTAATGCCAATTTCTCCTTA 59.398 33.333 0.00 0.00 32.47 2.69
4881 5307 6.427853 GCTTTGTTTAATGCCAATTTCTCCTT 59.572 34.615 0.00 0.00 32.47 3.36
4908 5334 1.664151 CCGGTAAGAAATTCGCAGTCC 59.336 52.381 0.00 0.00 0.00 3.85
4914 5340 5.875930 ACAAATTAGCCGGTAAGAAATTCG 58.124 37.500 1.90 0.00 0.00 3.34
4921 5347 4.351131 GTGGAACAAATTAGCCGGTAAG 57.649 45.455 1.90 0.00 44.16 2.34
4989 5701 3.535280 ATTTTGTCCTTTTTGCCGTGT 57.465 38.095 0.00 0.00 0.00 4.49
5006 5718 6.039270 TGACAGTCCTCAAAATTCGTCAATTT 59.961 34.615 0.00 0.00 42.95 1.82
5027 5739 2.388310 TTGAGTTTGTGGTCGTGACA 57.612 45.000 2.00 0.00 0.00 3.58
5076 5788 5.061179 TGCTGAACATGTCTGGATATCATG 58.939 41.667 0.00 2.58 42.86 3.07
5078 5790 4.700700 CTGCTGAACATGTCTGGATATCA 58.299 43.478 0.00 0.00 0.00 2.15
5079 5791 3.497640 GCTGCTGAACATGTCTGGATATC 59.502 47.826 0.00 0.00 0.00 1.63
5082 5794 1.681166 GGCTGCTGAACATGTCTGGAT 60.681 52.381 0.00 0.00 0.00 3.41
5128 5844 1.880027 GAGTTTCACGCAATTCCCAGT 59.120 47.619 0.00 0.00 0.00 4.00
5154 5870 1.737793 GACGGACCTGGTGCTTAAATG 59.262 52.381 16.57 2.08 0.00 2.32
5452 6169 0.031721 GTAGCCGTCTTGTATCCCCG 59.968 60.000 0.00 0.00 0.00 5.73
5485 6202 5.362556 GCAGGGTGCACATTAATATACTG 57.637 43.478 20.43 12.01 44.26 2.74


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

AutoCloner maintained by Alex Coulton.