Multiple sequence alignment - TraesCS7A01G040400

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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 TraesCS7A01G040400 chr7A 100.000 3317 0 0 1 3317 18737412 18740728 0.000000e+00 6126.0
1 TraesCS7A01G040400 chr7A 84.838 277 37 4 890 1164 18650059 18650332 1.170000e-69 274.0
2 TraesCS7A01G040400 chr7A 86.228 167 18 3 3 169 18649143 18649304 3.400000e-40 176.0
3 TraesCS7A01G040400 chr7A 92.063 63 1 3 2410 2468 18739761 18739823 5.900000e-13 86.1
4 TraesCS7A01G040400 chr7A 92.063 63 1 3 2350 2412 18739821 18739879 5.900000e-13 86.1
5 TraesCS7A01G040400 chr7D 92.902 1606 88 16 1724 3317 18245220 18246811 0.000000e+00 2311.0
6 TraesCS7A01G040400 chr7D 86.483 1598 141 35 1 1585 18243479 18245014 0.000000e+00 1685.0
7 TraesCS7A01G040400 chr7D 84.108 409 65 0 1054 1462 28346731 28346323 2.400000e-106 396.0
8 TraesCS7A01G040400 chr7D 81.330 391 69 4 1930 2318 28337970 28337582 6.910000e-82 315.0
9 TraesCS7A01G040400 chr7D 83.133 332 41 7 3 327 18243034 18243357 4.190000e-74 289.0
10 TraesCS7A01G040400 chr7D 91.018 167 8 3 1575 1739 18245037 18245198 5.570000e-53 219.0
11 TraesCS7A01G040400 chr7D 92.063 63 1 1 2350 2412 18245911 18245969 5.900000e-13 86.1
12 TraesCS7A01G040400 chrUn 87.549 1775 165 35 1 1737 311346334 311344578 0.000000e+00 2002.0
13 TraesCS7A01G040400 chrUn 87.437 1775 167 35 1 1737 311334637 311332881 0.000000e+00 1991.0
14 TraesCS7A01G040400 chrUn 85.579 950 95 21 1 935 446129633 446130555 0.000000e+00 957.0
15 TraesCS7A01G040400 chrUn 91.477 704 43 10 1724 2415 311332863 311332165 0.000000e+00 952.0
16 TraesCS7A01G040400 chrUn 91.477 704 43 10 1724 2415 311344560 311343862 0.000000e+00 952.0
17 TraesCS7A01G040400 chrUn 91.622 561 36 7 2410 2968 311332226 311331675 0.000000e+00 765.0
18 TraesCS7A01G040400 chrUn 91.622 561 36 7 2410 2968 311343923 311343372 0.000000e+00 765.0
19 TraesCS7A01G040400 chrUn 92.804 403 26 2 2568 2968 471061140 471060739 6.170000e-162 580.0
20 TraesCS7A01G040400 chrUn 95.726 351 11 1 2159 2509 309059625 309059279 2.230000e-156 562.0
21 TraesCS7A01G040400 chrUn 95.502 289 9 1 2221 2509 391833489 391833205 3.020000e-125 459.0
22 TraesCS7A01G040400 chrUn 84.841 409 62 0 1054 1462 81970993 81970585 2.380000e-111 412.0
23 TraesCS7A01G040400 chrUn 84.956 339 38 6 1 330 460040715 460041049 6.860000e-87 331.0
24 TraesCS7A01G040400 chrUn 80.102 392 78 0 1930 2321 81891824 81891433 3.240000e-75 292.0
25 TraesCS7A01G040400 chrUn 80.826 339 50 9 1 333 359895233 359894904 5.490000e-63 252.0
26 TraesCS7A01G040400 chrUn 98.507 67 1 0 2508 2574 309059120 309059054 5.810000e-23 119.0
27 TraesCS7A01G040400 chrUn 98.507 67 1 0 2508 2574 391833046 391832980 5.810000e-23 119.0
28 TraesCS7A01G040400 chrUn 98.507 67 1 0 2508 2574 436571470 436571536 5.810000e-23 119.0
29 TraesCS7A01G040400 chrUn 90.909 66 2 1 2350 2415 309059378 309059317 5.900000e-13 86.1
30 TraesCS7A01G040400 chrUn 90.909 66 2 1 2350 2415 391833304 391833243 5.900000e-13 86.1
31 TraesCS7A01G040400 chrUn 95.122 41 2 0 2830 2870 61742542 61742582 7.680000e-07 65.8
32 TraesCS7A01G040400 chr4B 80.524 611 76 24 996 1605 652414623 652415191 2.360000e-116 429.0
33 TraesCS7A01G040400 chr4B 78.442 719 104 30 927 1624 652376082 652376770 3.960000e-114 422.0
34 TraesCS7A01G040400 chr4A 84.634 410 63 0 1052 1461 702039462 702039053 3.080000e-110 409.0
35 TraesCS7A01G040400 chr4A 84.767 407 62 0 1054 1460 702046158 702045752 3.080000e-110 409.0
36 TraesCS7A01G040400 chr4A 78.406 389 84 0 1930 2318 702038715 702038327 1.530000e-63 254.0
37 TraesCS7A01G040400 chr4A 80.826 339 50 9 1 333 714260205 714259876 5.490000e-63 252.0
38 TraesCS7A01G040400 chr4D 79.254 617 85 26 996 1605 505553352 505553932 1.120000e-104 390.0
39 TraesCS7A01G040400 chr4D 82.051 390 68 2 1930 2318 505554237 505554625 6.860000e-87 331.0
40 TraesCS7A01G040400 chr4D 95.122 41 2 0 2830 2870 499897973 499897933 7.680000e-07 65.8
41 TraesCS7A01G040400 chr5A 82.776 389 65 2 1931 2318 689935210 689935597 2.450000e-91 346.0
42 TraesCS7A01G040400 chr5A 82.308 390 67 2 1930 2318 689957067 689957455 1.470000e-88 337.0
43 TraesCS7A01G040400 chr5A 97.143 35 1 0 2830 2864 487917528 487917562 3.570000e-05 60.2
44 TraesCS7A01G040400 chr3A 97.143 35 1 0 2830 2864 497657985 497658019 3.570000e-05 60.2


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 TraesCS7A01G040400 chr7A 18737412 18740728 3316 False 2099.400000 6126 94.708667 1 3317 3 chr7A.!!$F2 3316
1 TraesCS7A01G040400 chr7A 18649143 18650332 1189 False 225.000000 274 85.533000 3 1164 2 chr7A.!!$F1 1161
2 TraesCS7A01G040400 chr7D 18243034 18246811 3777 False 918.020000 2311 89.119800 1 3317 5 chr7D.!!$F1 3316
3 TraesCS7A01G040400 chrUn 311343372 311346334 2962 True 1239.666667 2002 90.216000 1 2968 3 chrUn.!!$R7 2967
4 TraesCS7A01G040400 chrUn 311331675 311334637 2962 True 1236.000000 1991 90.178667 1 2968 3 chrUn.!!$R6 2967
5 TraesCS7A01G040400 chrUn 446129633 446130555 922 False 957.000000 957 85.579000 1 935 1 chrUn.!!$F3 934
6 TraesCS7A01G040400 chrUn 309059054 309059625 571 True 255.700000 562 95.047333 2159 2574 3 chrUn.!!$R5 415
7 TraesCS7A01G040400 chrUn 391832980 391833489 509 True 221.366667 459 94.972667 2221 2574 3 chrUn.!!$R8 353
8 TraesCS7A01G040400 chr4B 652414623 652415191 568 False 429.000000 429 80.524000 996 1605 1 chr4B.!!$F2 609
9 TraesCS7A01G040400 chr4B 652376082 652376770 688 False 422.000000 422 78.442000 927 1624 1 chr4B.!!$F1 697
10 TraesCS7A01G040400 chr4A 702038327 702039462 1135 True 331.500000 409 81.520000 1052 2318 2 chr4A.!!$R3 1266
11 TraesCS7A01G040400 chr4D 505553352 505554625 1273 False 360.500000 390 80.652500 996 2318 2 chr4D.!!$F1 1322

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
783 1220 0.179018 ACACCAACCACCTCTTCTGC 60.179 55.0 0.0 0.0 0.00 4.26 F
1323 2259 0.108992 GTCACTACCGCCGTGATTCA 60.109 55.0 0.0 0.0 42.68 2.57 F
2200 3511 0.108898 CGGTGAGAGACAGAAGCTGG 60.109 60.0 0.0 0.0 35.51 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 2818 0.032130 GCCGTCTCTGTGACTGTGAA 59.968 55.000 8.09 0.0 43.25 3.18 R
2289 3600 0.041535 TGTAGTACATGGGGTCGGGT 59.958 55.000 0.00 0.0 0.00 5.28 R
3181 4711 1.337260 GGCGCCGTAGATGATGAAGAT 60.337 52.381 12.58 0.0 0.00 2.40 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
37 38 3.831323 TCAACAATGACATCAACACCCT 58.169 40.909 0.00 0.00 0.00 4.34
71 72 7.093771 ACTCTTAATTTTGTGAATGGATGGGTC 60.094 37.037 0.00 0.00 0.00 4.46
163 164 2.043411 CACGGTGAAGCACGAAAAATG 58.957 47.619 0.74 0.00 34.83 2.32
248 256 3.576861 TGGATAACTCAGATGTCCGGAT 58.423 45.455 7.81 0.00 0.00 4.18
251 259 5.104527 TGGATAACTCAGATGTCCGGATTTT 60.105 40.000 7.81 0.00 0.00 1.82
299 307 1.408822 CCGCCCCTATCAGAAAAAGCT 60.409 52.381 0.00 0.00 0.00 3.74
398 835 2.360350 CCTGACCGCATGCCAACT 60.360 61.111 13.15 0.00 0.00 3.16
399 836 2.693762 CCTGACCGCATGCCAACTG 61.694 63.158 13.15 7.25 0.00 3.16
431 868 5.355596 TGTTGCCCTGTTAAATCTTTTGTG 58.644 37.500 0.00 0.00 0.00 3.33
473 910 1.405526 CCAACACATCTACCACCTCCG 60.406 57.143 0.00 0.00 0.00 4.63
485 922 0.806102 CACCTCCGAACATAGCCACG 60.806 60.000 0.00 0.00 0.00 4.94
486 923 0.968901 ACCTCCGAACATAGCCACGA 60.969 55.000 0.00 0.00 0.00 4.35
493 930 3.183754 CGAACATAGCCACGAACATGTA 58.816 45.455 0.00 0.00 31.55 2.29
514 951 7.639113 TGTAAATCCTTCCACAAATATCACC 57.361 36.000 0.00 0.00 0.00 4.02
518 955 8.525290 AAATCCTTCCACAAATATCACCTAAG 57.475 34.615 0.00 0.00 0.00 2.18
534 971 1.497309 TAAGGTGTTCCAGGCCCCAG 61.497 60.000 0.00 0.00 35.89 4.45
617 1054 4.250464 ACATACACCAACCACATACTTCG 58.750 43.478 0.00 0.00 0.00 3.79
681 1118 1.681264 CCAAGTTCCCAACTGACCAAC 59.319 52.381 0.00 0.00 41.91 3.77
701 1138 6.183360 ACCAACCGAAATTGTCTGTTGTAATT 60.183 34.615 9.45 0.00 45.22 1.40
780 1217 1.141053 ACTGACACCAACCACCTCTTC 59.859 52.381 0.00 0.00 0.00 2.87
783 1220 0.179018 ACACCAACCACCTCTTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
829 1266 4.996758 CGGTCATTGTCATTGATGGCTATA 59.003 41.667 0.98 0.00 32.56 1.31
831 1268 6.183360 CGGTCATTGTCATTGATGGCTATATC 60.183 42.308 0.98 0.00 32.56 1.63
958 1872 2.045926 GCTAGCCACCCCACACTG 60.046 66.667 2.29 0.00 0.00 3.66
967 1881 0.324943 ACCCCACACTGTCTGCATAC 59.675 55.000 0.00 0.00 0.00 2.39
1023 1952 2.483876 GCAATGGCTACGAAGATGCTA 58.516 47.619 0.00 0.00 36.96 3.49
1032 1961 1.827969 ACGAAGATGCTACTCCTGCTT 59.172 47.619 0.00 0.00 0.00 3.91
1104 2037 4.704833 ATGCCGGCGTCAGTTGCT 62.705 61.111 23.90 0.00 0.00 3.91
1108 2041 1.666553 CCGGCGTCAGTTGCTACAA 60.667 57.895 6.01 0.00 0.00 2.41
1323 2259 0.108992 GTCACTACCGCCGTGATTCA 60.109 55.000 0.00 0.00 42.68 2.57
1332 2268 0.517316 GCCGTGATTCAAAGCTCGTT 59.483 50.000 0.00 0.00 30.40 3.85
1486 2423 8.235230 ACCTGCCTGCCTATATATAGTATACAT 58.765 37.037 16.78 0.00 0.00 2.29
1518 2465 3.861113 ACGTACGTGCACATTATACTTGG 59.139 43.478 22.14 0.00 0.00 3.61
1519 2466 4.106909 CGTACGTGCACATTATACTTGGA 58.893 43.478 18.64 0.00 0.00 3.53
1571 2527 2.135139 TGCACTCATCTTGTCGTTCAC 58.865 47.619 0.00 0.00 0.00 3.18
1585 2541 7.441157 TCTTGTCGTTCACATGAAGTAGAAATT 59.559 33.333 0.00 0.00 36.48 1.82
1626 2616 3.068024 AGCATCAACTCACTAGCTAGCTC 59.932 47.826 23.26 1.39 0.00 4.09
1627 2617 3.798548 GCATCAACTCACTAGCTAGCTCC 60.799 52.174 23.26 0.00 0.00 4.70
1628 2618 2.379972 TCAACTCACTAGCTAGCTCCC 58.620 52.381 23.26 0.00 0.00 4.30
1629 2619 1.410882 CAACTCACTAGCTAGCTCCCC 59.589 57.143 23.26 0.00 0.00 4.81
1721 2732 7.414436 TGAGACCAGAAGTTGAAATAAAAACG 58.586 34.615 0.00 0.00 0.00 3.60
1722 2733 7.281324 TGAGACCAGAAGTTGAAATAAAAACGA 59.719 33.333 0.00 0.00 0.00 3.85
1745 2793 5.560966 AATTATTGGACGTGTTGGACATC 57.439 39.130 0.00 0.00 0.00 3.06
1758 2806 1.098050 GGACATCATTGCTGGTCACC 58.902 55.000 0.00 0.00 32.00 4.02
1759 2807 1.340405 GGACATCATTGCTGGTCACCT 60.340 52.381 0.00 0.00 32.00 4.00
1766 2817 4.767255 GCTGGTCACCTGCCTCCG 62.767 72.222 14.77 0.00 41.62 4.63
1767 2818 3.314331 CTGGTCACCTGCCTCCGT 61.314 66.667 0.00 0.00 0.00 4.69
1778 2829 1.069090 GCCTCCGTTCACAGTCACA 59.931 57.895 0.00 0.00 0.00 3.58
1802 2854 2.567615 GACGGCCAGAAGGACCATATAT 59.432 50.000 2.24 0.00 41.31 0.86
1827 2879 2.262915 CCCTGTGAGTGACGAGCC 59.737 66.667 0.00 0.00 0.00 4.70
1828 2880 2.279069 CCCTGTGAGTGACGAGCCT 61.279 63.158 0.00 0.00 0.00 4.58
1831 2883 1.402984 CCTGTGAGTGACGAGCCTAAC 60.403 57.143 0.00 0.00 0.00 2.34
1844 2896 0.615850 GCCTAACCAAGAGGACTGCT 59.384 55.000 0.00 0.00 35.99 4.24
1901 3048 6.534793 TGGATTTATTTCGTAACCGTCCTTAC 59.465 38.462 0.00 0.00 35.01 2.34
1952 3263 0.179119 GCTACGCCGTACAACTGGAT 60.179 55.000 0.00 0.00 0.00 3.41
2017 3328 2.430921 AGACGAAGCGGCTGTTCG 60.431 61.111 19.37 19.37 46.62 3.95
2104 3415 2.280524 CCGTCACAAACCTCCGCA 60.281 61.111 0.00 0.00 0.00 5.69
2134 3445 1.229051 TCTGGGTGGATGACGGTGA 60.229 57.895 0.00 0.00 0.00 4.02
2200 3511 0.108898 CGGTGAGAGACAGAAGCTGG 60.109 60.000 0.00 0.00 35.51 4.85
2289 3600 0.675522 GTGCCCGCACCTTTAAGCTA 60.676 55.000 8.68 0.00 40.79 3.32
2415 3726 2.572191 CAATGCATGCTTGGTCGATT 57.428 45.000 20.33 5.27 0.00 3.34
2443 3754 5.464722 CGAATAAGTTACATGCATGCTCTCT 59.535 40.000 26.53 15.84 0.00 3.10
2455 3766 4.012319 CATGCTCTCTGTTACATGCAAC 57.988 45.455 1.56 1.56 34.11 4.17
2614 4141 4.162888 TCTGCAATTCAGAGATGAGCCTAA 59.837 41.667 4.18 0.00 46.34 2.69
2699 4227 2.449464 CATCCAAGATTCTTGGGTGCA 58.551 47.619 34.55 21.50 42.97 4.57
2706 4234 2.503356 AGATTCTTGGGTGCACTAGGAG 59.497 50.000 17.98 9.88 0.00 3.69
2766 4294 5.775686 CTCATGGCAGAAGAACAAAATTGA 58.224 37.500 0.00 0.00 0.00 2.57
2889 4417 0.747255 ACCTAGCGCACCTGAGTATG 59.253 55.000 11.47 0.00 0.00 2.39
2958 4488 8.988064 TTTTAATTTATTGTTTATCGGCAGCA 57.012 26.923 0.00 0.00 0.00 4.41
2988 4518 1.099879 ATGGGCTCTGAAATCGCTGC 61.100 55.000 0.00 0.00 0.00 5.25
2994 4524 1.136695 CTCTGAAATCGCTGCTCTCCT 59.863 52.381 0.00 0.00 0.00 3.69
3004 4534 2.546584 CGCTGCTCTCCTATTGTATGCA 60.547 50.000 0.00 0.00 0.00 3.96
3010 4540 6.925211 TGCTCTCCTATTGTATGCACTATAC 58.075 40.000 0.00 0.00 41.68 1.47
3057 4587 7.431084 ACTCACACGTTAATTCATTGTTGAAAC 59.569 33.333 0.00 0.00 44.70 2.78
3076 4606 5.488919 TGAAACATATTTCCCACCTCTCTCT 59.511 40.000 0.00 0.00 43.18 3.10
3094 4624 8.840321 CCTCTCTCTGTCAATTTTTACTTTTGA 58.160 33.333 0.00 0.00 0.00 2.69
3157 4687 7.620491 AGAGTCAATCTGCCATATCTCATCTAT 59.380 37.037 0.00 0.00 36.69 1.98
3181 4711 7.257790 TCTTTCCAATCTACCTTCAATCTCA 57.742 36.000 0.00 0.00 0.00 3.27
3222 4752 1.216678 TGCCCTCTTCTCCAACCAAAA 59.783 47.619 0.00 0.00 0.00 2.44
3223 4753 2.316108 GCCCTCTTCTCCAACCAAAAA 58.684 47.619 0.00 0.00 0.00 1.94
3276 4806 4.949856 TCCTATGGAAATGAAAGGCTCAAC 59.050 41.667 0.00 0.00 37.67 3.18
3292 4822 3.265791 CTCAACTTCTTCCCCAGATTCG 58.734 50.000 0.00 0.00 0.00 3.34
3306 4836 0.744771 GATTCGTGGGCCTGGACTTC 60.745 60.000 4.53 0.00 0.00 3.01
3308 4838 2.358737 CGTGGGCCTGGACTTCAC 60.359 66.667 4.53 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.305398 AACAGAGAGTTGGTCTAAGCG 57.695 47.619 0.00 0.00 39.49 4.68
137 138 1.701545 CGTGCTTCACCGTGTGTTGT 61.702 55.000 0.00 0.00 34.79 3.32
217 218 9.565213 GACATCTGAGTTATCCAAAAGAATTTG 57.435 33.333 0.00 0.00 44.50 2.32
272 280 2.408565 TCTGATAGGGGCGGAAAATCT 58.591 47.619 0.00 0.00 0.00 2.40
322 759 7.672983 ATTACGAATTGATTGTGACTCTGTT 57.327 32.000 0.00 0.00 0.00 3.16
371 808 2.508928 CGGTCAGGTTGGTGTGGT 59.491 61.111 0.00 0.00 0.00 4.16
398 835 3.222173 ACAGGGCAACAATACTCAACA 57.778 42.857 0.00 0.00 39.74 3.33
399 836 5.699097 TTAACAGGGCAACAATACTCAAC 57.301 39.130 0.00 0.00 39.74 3.18
431 868 5.105392 TGGATATGTGAGCAAATTTCAACCC 60.105 40.000 0.00 0.00 0.00 4.11
473 910 5.539582 TTTACATGTTCGTGGCTATGTTC 57.460 39.130 2.30 0.00 35.55 3.18
485 922 9.736023 GATATTTGTGGAAGGATTTACATGTTC 57.264 33.333 2.30 0.00 0.00 3.18
486 923 9.253832 TGATATTTGTGGAAGGATTTACATGTT 57.746 29.630 2.30 0.00 0.00 2.71
493 930 7.561356 CCTTAGGTGATATTTGTGGAAGGATTT 59.439 37.037 0.00 0.00 34.14 2.17
514 951 1.303282 GGGGCCTGGAACACCTTAG 59.697 63.158 0.84 0.00 0.00 2.18
534 971 1.169661 TGGTCGGTTGGTGTCATTGC 61.170 55.000 0.00 0.00 0.00 3.56
589 1026 2.556189 TGTGGTTGGTGTATGTCATTGC 59.444 45.455 0.00 0.00 0.00 3.56
590 1027 5.647658 AGTATGTGGTTGGTGTATGTCATTG 59.352 40.000 0.00 0.00 0.00 2.82
591 1028 5.815581 AGTATGTGGTTGGTGTATGTCATT 58.184 37.500 0.00 0.00 0.00 2.57
593 1030 4.901197 AGTATGTGGTTGGTGTATGTCA 57.099 40.909 0.00 0.00 0.00 3.58
594 1031 4.328983 CGAAGTATGTGGTTGGTGTATGTC 59.671 45.833 0.00 0.00 0.00 3.06
595 1032 4.250464 CGAAGTATGTGGTTGGTGTATGT 58.750 43.478 0.00 0.00 0.00 2.29
596 1033 4.250464 ACGAAGTATGTGGTTGGTGTATG 58.750 43.478 0.00 0.00 41.94 2.39
597 1034 4.546829 ACGAAGTATGTGGTTGGTGTAT 57.453 40.909 0.00 0.00 41.94 2.29
681 1118 7.802738 TGTAGAATTACAACAGACAATTTCGG 58.197 34.615 0.00 0.00 36.86 4.30
761 1198 1.417890 AGAAGAGGTGGTTGGTGTCAG 59.582 52.381 0.00 0.00 0.00 3.51
780 1217 5.776744 AGCTTGAAAGAAATTAAGTGGCAG 58.223 37.500 0.00 0.00 0.00 4.85
783 1220 5.853282 CGTGAGCTTGAAAGAAATTAAGTGG 59.147 40.000 0.00 0.00 0.00 4.00
829 1266 3.900601 GGCCTCCAGATATATCGATGGAT 59.099 47.826 19.04 0.39 40.91 3.41
831 1268 2.035193 CGGCCTCCAGATATATCGATGG 59.965 54.545 8.54 12.73 0.00 3.51
882 1322 0.458260 TACAGTGTGTGTGTGACGCT 59.542 50.000 5.88 0.00 40.69 5.07
883 1323 0.575390 GTACAGTGTGTGTGTGACGC 59.425 55.000 5.88 0.00 40.69 5.19
884 1324 1.852280 CAGTACAGTGTGTGTGTGACG 59.148 52.381 5.88 0.00 40.69 4.35
967 1881 1.673665 GCTTCCTGAGGTGCAGTGG 60.674 63.158 12.65 0.00 43.33 4.00
1104 2037 1.632920 TCATCCATGGCAGTGGTTGTA 59.367 47.619 6.96 9.09 39.13 2.41
1108 2041 1.611419 CCTCATCCATGGCAGTGGT 59.389 57.895 6.96 0.00 40.27 4.16
1194 2130 2.669229 CTGTCACATGCCACGCCA 60.669 61.111 0.00 0.00 0.00 5.69
1332 2268 2.088104 AGGAGATGGCCTCGTCAATA 57.912 50.000 3.32 0.00 42.89 1.90
1498 2435 6.598753 AATCCAAGTATAATGTGCACGTAC 57.401 37.500 12.96 11.93 0.00 3.67
1518 2465 7.226325 GCTCAGATATATCCACCTGCAATAATC 59.774 40.741 9.18 0.00 0.00 1.75
1519 2466 7.052873 GCTCAGATATATCCACCTGCAATAAT 58.947 38.462 9.18 0.00 0.00 1.28
1605 2594 3.380142 GAGCTAGCTAGTGAGTTGATGC 58.620 50.000 19.38 4.48 0.00 3.91
1626 2616 2.751357 TTTACCGGCGGTTTCTGGGG 62.751 60.000 38.73 4.41 37.09 4.96
1627 2617 0.890090 TTTTACCGGCGGTTTCTGGG 60.890 55.000 38.73 5.27 37.09 4.45
1628 2618 0.239082 GTTTTACCGGCGGTTTCTGG 59.761 55.000 38.73 6.14 37.09 3.86
1629 2619 0.239082 GGTTTTACCGGCGGTTTCTG 59.761 55.000 38.73 7.02 37.09 3.02
1709 2720 9.680315 ACGTCCAATAATTTCGTTTTTATTTCA 57.320 25.926 0.00 0.00 0.00 2.69
1719 2730 4.066490 TCCAACACGTCCAATAATTTCGT 58.934 39.130 0.00 0.00 35.12 3.85
1721 2732 5.365403 TGTCCAACACGTCCAATAATTTC 57.635 39.130 0.00 0.00 0.00 2.17
1722 2733 5.475220 TGATGTCCAACACGTCCAATAATTT 59.525 36.000 0.00 0.00 40.01 1.82
1745 2793 1.303888 AGGCAGGTGACCAGCAATG 60.304 57.895 20.76 2.20 33.87 2.82
1758 2806 0.946221 GTGACTGTGAACGGAGGCAG 60.946 60.000 0.00 0.00 35.31 4.85
1759 2807 1.069090 GTGACTGTGAACGGAGGCA 59.931 57.895 0.00 0.00 0.00 4.75
1766 2817 1.772182 CCGTCTCTGTGACTGTGAAC 58.228 55.000 8.09 0.00 43.25 3.18
1767 2818 0.032130 GCCGTCTCTGTGACTGTGAA 59.968 55.000 8.09 0.00 43.25 3.18
1778 2829 1.985116 GGTCCTTCTGGCCGTCTCT 60.985 63.158 0.00 0.00 0.00 3.10
1802 2854 0.911053 TCACTCACAGGGCATGCATA 59.089 50.000 21.36 0.00 0.00 3.14
1827 2879 1.134965 CCGAGCAGTCCTCTTGGTTAG 60.135 57.143 0.00 0.00 38.49 2.34
1828 2880 0.895530 CCGAGCAGTCCTCTTGGTTA 59.104 55.000 0.00 0.00 38.49 2.85
1831 2883 0.967887 TCTCCGAGCAGTCCTCTTGG 60.968 60.000 0.00 0.00 38.49 3.61
1844 2896 4.657013 AGCTATCACATCACTATCTCCGA 58.343 43.478 0.00 0.00 0.00 4.55
1901 3048 5.406175 ACCATGCATGTCAAAAATCTTTTCG 59.594 36.000 24.58 6.44 0.00 3.46
1952 3263 0.109272 CGCGTACTCTTGGAAGCTCA 60.109 55.000 0.00 0.00 0.00 4.26
2015 3326 0.039437 GACCGAGAGCAACTTGTCGA 60.039 55.000 2.67 0.00 34.28 4.20
2017 3328 1.009389 CCGACCGAGAGCAACTTGTC 61.009 60.000 0.00 0.00 0.00 3.18
2104 3415 2.612115 CCCAGAGAACCCCTGCCT 60.612 66.667 0.00 0.00 0.00 4.75
2164 3475 2.027625 CGGACTTGAAGGTCACCGC 61.028 63.158 0.00 0.00 37.91 5.68
2200 3511 2.202837 GACATACCCGGCGTCCAC 60.203 66.667 6.01 0.00 0.00 4.02
2271 3582 0.675522 GTAGCTTAAAGGTGCGGGCA 60.676 55.000 0.00 0.00 0.00 5.36
2289 3600 0.041535 TGTAGTACATGGGGTCGGGT 59.958 55.000 0.00 0.00 0.00 5.28
2415 3726 4.260743 GCATGCATGTAACTTATTCGAGCA 60.261 41.667 26.79 0.00 0.00 4.26
2455 3766 2.287788 GGGATTATTGACCAAGCATGCG 60.288 50.000 13.01 0.00 0.00 4.73
2614 4141 7.838079 ACTATTCAATGAGAGTAGATGAGCT 57.162 36.000 0.00 0.00 38.47 4.09
2664 4192 8.788238 AATCTTGGATGCCCTAAGAATTTAAT 57.212 30.769 6.20 0.00 35.11 1.40
2666 4194 7.586349 AGAATCTTGGATGCCCTAAGAATTTA 58.414 34.615 6.20 0.00 35.11 1.40
2699 4227 4.098914 TGAAAATTGGCACACTCCTAGT 57.901 40.909 0.00 0.00 39.29 2.57
2706 4234 3.383620 TGACCATGAAAATTGGCACAC 57.616 42.857 0.00 0.00 39.29 3.82
2814 4342 6.650807 CGAGGAGCTCTTGGCAAAATAATATA 59.349 38.462 14.64 0.00 44.79 0.86
2943 4473 3.603158 TCTACTGCTGCCGATAAACAA 57.397 42.857 0.00 0.00 0.00 2.83
2984 4514 2.805099 GTGCATACAATAGGAGAGCAGC 59.195 50.000 0.00 0.00 0.00 5.25
3025 4555 8.779303 ACAATGAATTAACGTGTGAGTTCATAA 58.221 29.630 13.11 0.00 35.82 1.90
3034 4564 7.443218 TGTTTCAACAATGAATTAACGTGTG 57.557 32.000 0.00 0.00 44.70 3.82
3057 4587 4.406972 TGACAGAGAGAGGTGGGAAATATG 59.593 45.833 0.00 0.00 0.00 1.78
3076 4606 8.770438 AGTTGCTTCAAAAGTAAAAATTGACA 57.230 26.923 0.00 0.00 34.88 3.58
3094 4624 7.839907 TGAATTTATGCTCCAATTAGTTGCTT 58.160 30.769 0.00 0.00 33.90 3.91
3157 4687 7.257790 TGAGATTGAAGGTAGATTGGAAAGA 57.742 36.000 0.00 0.00 0.00 2.52
3181 4711 1.337260 GGCGCCGTAGATGATGAAGAT 60.337 52.381 12.58 0.00 0.00 2.40
3222 4752 6.591750 TTCTCTCGTAAGTTCCTCAGATTT 57.408 37.500 0.00 0.00 39.48 2.17
3223 4753 6.591750 TTTCTCTCGTAAGTTCCTCAGATT 57.408 37.500 0.00 0.00 39.48 2.40
3224 4754 6.209788 AGTTTTCTCTCGTAAGTTCCTCAGAT 59.790 38.462 0.00 0.00 39.48 2.90
3276 4806 1.407437 CCCACGAATCTGGGGAAGAAG 60.407 57.143 9.14 0.00 46.76 2.85
3292 4822 2.358737 CGTGAAGTCCAGGCCCAC 60.359 66.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.