Multiple sequence alignment - TraesCS3D01G452000

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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 TraesCS3D01G452000 chr3D 100.000 2288 0 0 1 2288 559917204 559914917 0.000000e+00 4226
1 TraesCS3D01G452000 chr3D 92.777 886 51 7 462 1342 559937542 559936665 0.000000e+00 1269
2 TraesCS3D01G452000 chr3D 93.893 655 32 3 1635 2288 49539755 49539108 0.000000e+00 981
3 TraesCS3D01G452000 chr3D 93.041 661 38 6 1633 2288 464248080 464248737 0.000000e+00 959
4 TraesCS3D01G452000 chr3D 86.610 351 21 5 4 353 559937904 559937579 4.650000e-97 364
5 TraesCS3D01G452000 chr3B 91.311 1266 74 12 55 1310 743814435 743813196 0.000000e+00 1696
6 TraesCS3D01G452000 chr3A 91.736 956 62 9 394 1342 696168338 696167393 0.000000e+00 1312
7 TraesCS3D01G452000 chr3A 92.966 654 38 7 1635 2286 706196476 706197123 0.000000e+00 946
8 TraesCS3D01G452000 chr3A 89.708 651 41 8 815 1440 628874576 628873927 0.000000e+00 808
9 TraesCS3D01G452000 chr3A 89.216 408 29 2 4 396 628875951 628875544 1.580000e-136 496
10 TraesCS3D01G452000 chr3A 89.216 408 29 2 4 396 696169001 696168594 1.580000e-136 496
11 TraesCS3D01G452000 chr3A 87.298 433 38 9 394 819 628875287 628874865 1.590000e-131 479
12 TraesCS3D01G452000 chr1B 93.930 659 30 7 1632 2288 669063766 669064416 0.000000e+00 987
13 TraesCS3D01G452000 chr5D 93.778 659 31 5 1632 2288 561560314 561560964 0.000000e+00 981
14 TraesCS3D01G452000 chr6D 93.750 656 35 5 1635 2288 312196176 312196827 0.000000e+00 979
15 TraesCS3D01G452000 chr7D 93.465 658 33 9 1633 2288 213759927 213759278 0.000000e+00 968
16 TraesCS3D01G452000 chr7D 93.435 655 29 9 1635 2288 169807073 169807714 0.000000e+00 959
17 TraesCS3D01G452000 chr7D 93.119 654 33 7 1635 2288 631356611 631355970 0.000000e+00 948
18 TraesCS3D01G452000 chr4B 76.211 681 125 30 609 1276 552028425 552027769 2.190000e-85 326
19 TraesCS3D01G452000 chr4B 90.909 165 15 0 1472 1636 426774499 426774335 2.960000e-54 222
20 TraesCS3D01G452000 chr2A 91.925 161 13 0 1472 1632 28828251 28828411 2.290000e-55 226
21 TraesCS3D01G452000 chr2A 90.798 163 15 0 1472 1634 133674268 133674430 3.830000e-53 219
22 TraesCS3D01G452000 chr7A 90.909 165 15 0 1472 1636 224311197 224311361 2.960000e-54 222
23 TraesCS3D01G452000 chrUn 90.798 163 15 0 1472 1634 359680916 359680754 3.830000e-53 219
24 TraesCS3D01G452000 chr5B 90.798 163 15 0 1472 1634 253884876 253884714 3.830000e-53 219
25 TraesCS3D01G452000 chr6A 90.683 161 15 0 1472 1632 607984403 607984243 4.950000e-52 215
26 TraesCS3D01G452000 chr4D 90.683 161 15 0 1472 1632 403022918 403023078 4.950000e-52 215
27 TraesCS3D01G452000 chr6B 89.759 166 17 0 1472 1637 276304497 276304662 1.780000e-51 213


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 TraesCS3D01G452000 chr3D 559914917 559917204 2287 True 4226.000000 4226 100.000000 1 2288 1 chr3D.!!$R2 2287
1 TraesCS3D01G452000 chr3D 49539108 49539755 647 True 981.000000 981 93.893000 1635 2288 1 chr3D.!!$R1 653
2 TraesCS3D01G452000 chr3D 464248080 464248737 657 False 959.000000 959 93.041000 1633 2288 1 chr3D.!!$F1 655
3 TraesCS3D01G452000 chr3D 559936665 559937904 1239 True 816.500000 1269 89.693500 4 1342 2 chr3D.!!$R3 1338
4 TraesCS3D01G452000 chr3B 743813196 743814435 1239 True 1696.000000 1696 91.311000 55 1310 1 chr3B.!!$R1 1255
5 TraesCS3D01G452000 chr3A 706196476 706197123 647 False 946.000000 946 92.966000 1635 2286 1 chr3A.!!$F1 651
6 TraesCS3D01G452000 chr3A 696167393 696169001 1608 True 904.000000 1312 90.476000 4 1342 2 chr3A.!!$R2 1338
7 TraesCS3D01G452000 chr3A 628873927 628875951 2024 True 594.333333 808 88.740667 4 1440 3 chr3A.!!$R1 1436
8 TraesCS3D01G452000 chr1B 669063766 669064416 650 False 987.000000 987 93.930000 1632 2288 1 chr1B.!!$F1 656
9 TraesCS3D01G452000 chr5D 561560314 561560964 650 False 981.000000 981 93.778000 1632 2288 1 chr5D.!!$F1 656
10 TraesCS3D01G452000 chr6D 312196176 312196827 651 False 979.000000 979 93.750000 1635 2288 1 chr6D.!!$F1 653
11 TraesCS3D01G452000 chr7D 213759278 213759927 649 True 968.000000 968 93.465000 1633 2288 1 chr7D.!!$R1 655
12 TraesCS3D01G452000 chr7D 169807073 169807714 641 False 959.000000 959 93.435000 1635 2288 1 chr7D.!!$F1 653
13 TraesCS3D01G452000 chr7D 631355970 631356611 641 True 948.000000 948 93.119000 1635 2288 1 chr7D.!!$R2 653
14 TraesCS3D01G452000 chr4B 552027769 552028425 656 True 326.000000 326 76.211000 609 1276 1 chr4B.!!$R2 667

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
234 243 0.111061 AAGACATGCAGGCAGTTGGA 59.889 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1945 0.250684 TGAGCGACTTTGATTGGCCA 60.251 50.0 0.0 0.0 0.0 5.36 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
76 77 2.028778 GCTCAGCCGCTCGATGAT 59.971 61.111 0.00 0.00 0.00 2.45
88 89 2.547430 GCTCGATGATGCCAGATCTGAA 60.547 50.000 24.62 12.14 0.00 3.02
167 168 7.946776 ACTATTGATGCTTAGGCTTTATGGATT 59.053 33.333 0.00 0.00 39.59 3.01
170 171 6.128486 TGATGCTTAGGCTTTATGGATTGAA 58.872 36.000 0.00 0.00 39.59 2.69
176 177 7.201947 GCTTAGGCTTTATGGATTGAAAAGGAT 60.202 37.037 0.00 0.00 32.14 3.24
206 207 4.618912 CGTCATGTCAGAGAGTGTTTACAG 59.381 45.833 0.00 0.00 0.00 2.74
231 240 0.178981 ACCAAGACATGCAGGCAGTT 60.179 50.000 0.00 0.00 0.00 3.16
234 243 0.111061 AAGACATGCAGGCAGTTGGA 59.889 50.000 0.00 0.00 0.00 3.53
235 244 0.607489 AGACATGCAGGCAGTTGGAC 60.607 55.000 0.00 0.00 0.00 4.02
264 273 0.784778 GAGCAAGACAACGAGAACCG 59.215 55.000 0.00 0.00 45.44 4.44
266 275 1.860078 CAAGACAACGAGAACCGGC 59.140 57.895 0.00 0.00 43.93 6.13
420 702 1.604604 GCAGGCTACCAAAGTTGACA 58.395 50.000 0.00 0.00 0.00 3.58
428 710 4.558095 GCTACCAAAGTTGACAGTCGACTA 60.558 45.833 21.91 6.98 40.12 2.59
429 711 4.602340 ACCAAAGTTGACAGTCGACTAT 57.398 40.909 21.91 7.01 40.12 2.12
509 792 3.688185 GCCATGTGCACTCATATGATAGG 59.312 47.826 19.41 6.76 42.32 2.57
559 847 0.598680 GTGACTTGTGAGCTCGCTGT 60.599 55.000 26.56 23.19 0.00 4.40
574 862 1.738350 CGCTGTAGAAACGAGAGGAGA 59.262 52.381 0.00 0.00 0.00 3.71
592 880 2.041366 GAAAAGATGAGCGAGCCGGC 62.041 60.000 21.89 21.89 0.00 6.13
669 957 3.015145 TAGGGCTGAAGGGGGTGC 61.015 66.667 0.00 0.00 0.00 5.01
811 1102 1.424240 GAGTCGCTCGTCATCGTCA 59.576 57.895 0.00 0.00 38.33 4.35
924 1511 3.444805 AGGTGCTCGAGGACGCTC 61.445 66.667 27.67 15.91 37.24 5.03
1060 1647 2.028190 CCATAGGGCTGCTCGACG 59.972 66.667 0.00 0.00 0.00 5.12
1342 1936 3.054287 TGGTGAGTTGTGACCCAAAACTA 60.054 43.478 2.78 0.00 41.42 2.24
1344 1938 5.163184 TGGTGAGTTGTGACCCAAAACTATA 60.163 40.000 2.78 0.00 41.42 1.31
1345 1939 5.944007 GGTGAGTTGTGACCCAAAACTATAT 59.056 40.000 2.78 0.00 41.42 0.86
1348 1942 9.826574 GTGAGTTGTGACCCAAAACTATATATA 57.173 33.333 2.78 0.00 41.42 0.86
1354 1969 9.073475 TGTGACCCAAAACTATATATATTTGGC 57.927 33.333 22.18 14.74 46.64 4.52
1382 1997 6.734137 TCAAAGTCGCTCACAATGTAAAAAT 58.266 32.000 0.00 0.00 0.00 1.82
1392 2007 9.533253 GCTCACAATGTAAAAATATATTTGGCT 57.467 29.630 11.42 2.85 0.00 4.75
1400 2015 9.664332 TGTAAAAATATATTTGGCTGTTGCAAT 57.336 25.926 11.42 0.00 41.91 3.56
1406 2021 9.889128 AATATATTTGGCTGTTGCAATAACTTT 57.111 25.926 0.59 0.00 41.91 2.66
1417 2032 5.446143 TGCAATAACTTTGACCAACGATT 57.554 34.783 0.00 0.00 0.00 3.34
1418 2033 5.837437 TGCAATAACTTTGACCAACGATTT 58.163 33.333 0.00 0.00 0.00 2.17
1421 2036 3.619233 AACTTTGACCAACGATTTCCG 57.381 42.857 0.00 0.00 45.44 4.30
1440 2055 4.984205 TCCGTAACAAAAACTTTGACCAC 58.016 39.130 6.15 0.88 0.00 4.16
1441 2056 3.787105 CCGTAACAAAAACTTTGACCACG 59.213 43.478 6.15 10.48 0.00 4.94
1442 2057 4.437121 CCGTAACAAAAACTTTGACCACGA 60.437 41.667 17.68 0.00 0.00 4.35
1443 2058 5.087397 CGTAACAAAAACTTTGACCACGAA 58.913 37.500 6.15 0.00 0.00 3.85
1444 2059 5.740099 CGTAACAAAAACTTTGACCACGAAT 59.260 36.000 6.15 0.00 0.00 3.34
1445 2060 6.251801 CGTAACAAAAACTTTGACCACGAATT 59.748 34.615 6.15 0.00 0.00 2.17
1446 2061 7.428761 CGTAACAAAAACTTTGACCACGAATTA 59.571 33.333 6.15 0.00 0.00 1.40
1447 2062 7.514573 AACAAAAACTTTGACCACGAATTAC 57.485 32.000 6.15 0.00 0.00 1.89
1448 2063 6.859017 ACAAAAACTTTGACCACGAATTACT 58.141 32.000 6.15 0.00 0.00 2.24
1449 2064 7.987649 ACAAAAACTTTGACCACGAATTACTA 58.012 30.769 6.15 0.00 0.00 1.82
1450 2065 8.626526 ACAAAAACTTTGACCACGAATTACTAT 58.373 29.630 6.15 0.00 0.00 2.12
1455 2070 8.836268 ACTTTGACCACGAATTACTATAAACA 57.164 30.769 0.00 0.00 0.00 2.83
1456 2071 8.932791 ACTTTGACCACGAATTACTATAAACAG 58.067 33.333 0.00 0.00 0.00 3.16
1457 2072 8.836268 TTTGACCACGAATTACTATAAACAGT 57.164 30.769 0.00 0.00 0.00 3.55
1458 2073 8.836268 TTGACCACGAATTACTATAAACAGTT 57.164 30.769 0.00 0.00 0.00 3.16
1459 2074 8.836268 TGACCACGAATTACTATAAACAGTTT 57.164 30.769 3.49 3.49 0.00 2.66
1460 2075 9.275398 TGACCACGAATTACTATAAACAGTTTT 57.725 29.630 3.25 0.00 0.00 2.43
1486 2101 8.740123 ACTCTATCACACTATAATATAGCGCT 57.260 34.615 17.26 17.26 0.00 5.92
1487 2102 9.179909 ACTCTATCACACTATAATATAGCGCTT 57.820 33.333 18.68 6.25 0.00 4.68
1488 2103 9.658475 CTCTATCACACTATAATATAGCGCTTC 57.342 37.037 18.68 0.00 0.00 3.86
1489 2104 9.397280 TCTATCACACTATAATATAGCGCTTCT 57.603 33.333 18.68 6.28 0.00 2.85
1502 2117 4.425577 AGCGCTTCTTAAAACAAGATGG 57.574 40.909 2.64 0.00 0.00 3.51
1503 2118 3.191371 AGCGCTTCTTAAAACAAGATGGG 59.809 43.478 2.64 10.63 37.40 4.00
1504 2119 3.057526 GCGCTTCTTAAAACAAGATGGGT 60.058 43.478 0.00 0.00 37.00 4.51
1505 2120 4.723248 CGCTTCTTAAAACAAGATGGGTC 58.277 43.478 8.08 0.00 33.04 4.46
1506 2121 4.455877 CGCTTCTTAAAACAAGATGGGTCT 59.544 41.667 8.08 0.00 35.82 3.85
1507 2122 5.642063 CGCTTCTTAAAACAAGATGGGTCTA 59.358 40.000 8.08 0.00 33.30 2.59
1508 2123 6.402226 CGCTTCTTAAAACAAGATGGGTCTAC 60.402 42.308 8.08 0.00 33.30 2.59
1509 2124 6.430000 GCTTCTTAAAACAAGATGGGTCTACA 59.570 38.462 0.00 0.00 33.30 2.74
1510 2125 7.040686 GCTTCTTAAAACAAGATGGGTCTACAA 60.041 37.037 0.00 0.00 33.30 2.41
1511 2126 8.754991 TTCTTAAAACAAGATGGGTCTACAAA 57.245 30.769 0.00 0.00 33.30 2.83
1512 2127 8.161699 TCTTAAAACAAGATGGGTCTACAAAC 57.838 34.615 0.00 0.00 33.30 2.93
1513 2128 7.996644 TCTTAAAACAAGATGGGTCTACAAACT 59.003 33.333 0.00 0.00 33.30 2.66
1514 2129 9.280174 CTTAAAACAAGATGGGTCTACAAACTA 57.720 33.333 0.00 0.00 33.30 2.24
1515 2130 9.629878 TTAAAACAAGATGGGTCTACAAACTAA 57.370 29.630 0.00 0.00 33.30 2.24
1516 2131 8.706322 AAAACAAGATGGGTCTACAAACTAAT 57.294 30.769 0.00 0.00 33.30 1.73
1517 2132 9.802039 AAAACAAGATGGGTCTACAAACTAATA 57.198 29.630 0.00 0.00 33.30 0.98
1518 2133 9.802039 AAACAAGATGGGTCTACAAACTAATAA 57.198 29.630 0.00 0.00 33.30 1.40
1519 2134 9.802039 AACAAGATGGGTCTACAAACTAATAAA 57.198 29.630 0.00 0.00 33.30 1.40
1520 2135 9.975218 ACAAGATGGGTCTACAAACTAATAAAT 57.025 29.630 0.00 0.00 33.30 1.40
1525 2140 9.975218 ATGGGTCTACAAACTAATAAATGAAGT 57.025 29.630 0.00 0.00 0.00 3.01
1526 2141 9.444600 TGGGTCTACAAACTAATAAATGAAGTC 57.555 33.333 0.00 0.00 0.00 3.01
1527 2142 8.890718 GGGTCTACAAACTAATAAATGAAGTCC 58.109 37.037 0.00 0.00 0.00 3.85
1528 2143 9.668497 GGTCTACAAACTAATAAATGAAGTCCT 57.332 33.333 0.00 0.00 0.00 3.85
1541 2156 7.906199 AAATGAAGTCCTCTATAGCACTACT 57.094 36.000 0.00 0.00 0.00 2.57
1542 2157 8.998277 AAATGAAGTCCTCTATAGCACTACTA 57.002 34.615 0.00 0.00 34.64 1.82
1543 2158 9.594936 AAATGAAGTCCTCTATAGCACTACTAT 57.405 33.333 0.00 0.00 44.12 2.12
1544 2159 9.594936 AATGAAGTCCTCTATAGCACTACTATT 57.405 33.333 0.00 0.00 41.91 1.73
1580 2195 9.409918 TGCACTATGAAGATAGTAACTTAGACT 57.590 33.333 0.00 0.00 42.55 3.24
1587 2202 9.955102 TGAAGATAGTAACTTAGACTAGTGTCA 57.045 33.333 0.00 0.00 45.20 3.58
1593 2208 8.521170 AGTAACTTAGACTAGTGTCATATGCA 57.479 34.615 0.00 0.00 45.20 3.96
1594 2209 9.137459 AGTAACTTAGACTAGTGTCATATGCAT 57.863 33.333 3.79 3.79 45.20 3.96
1595 2210 9.186323 GTAACTTAGACTAGTGTCATATGCATG 57.814 37.037 10.16 0.00 45.20 4.06
1596 2211 7.588497 ACTTAGACTAGTGTCATATGCATGA 57.412 36.000 10.16 0.00 45.20 3.07
1616 2231 9.542462 TGCATGACACTAGTATAAATTACTTCC 57.458 33.333 0.00 0.00 0.00 3.46
1617 2232 8.989980 GCATGACACTAGTATAAATTACTTCCC 58.010 37.037 0.00 0.00 0.00 3.97
1620 2235 9.263446 TGACACTAGTATAAATTACTTCCCACT 57.737 33.333 0.00 0.00 0.00 4.00
1627 2242 9.220906 AGTATAAATTACTTCCCACTATGACCA 57.779 33.333 0.00 0.00 0.00 4.02
1628 2243 9.490379 GTATAAATTACTTCCCACTATGACCAG 57.510 37.037 0.00 0.00 0.00 4.00
1629 2244 3.906720 TTACTTCCCACTATGACCAGC 57.093 47.619 0.00 0.00 0.00 4.85
1630 2245 0.912486 ACTTCCCACTATGACCAGCC 59.088 55.000 0.00 0.00 0.00 4.85
1631 2246 1.207791 CTTCCCACTATGACCAGCCT 58.792 55.000 0.00 0.00 0.00 4.58
1738 2353 1.291877 ATCCGTGTTCTGTTGCGCTC 61.292 55.000 9.73 2.14 0.00 5.03
1762 2378 8.330466 TCATGTATTTCTTGTCCAAAACGTAT 57.670 30.769 0.00 0.00 0.00 3.06
1786 2402 0.036732 CTTTGTCCCAGCAGGCACTA 59.963 55.000 0.00 0.00 36.02 2.74
1820 2436 2.026641 TGCATTGCTTTCCTATCTGGC 58.973 47.619 10.49 0.00 35.26 4.85
1998 2620 8.746530 TGTATTCACGTCTACTTTTATCCTTCT 58.253 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 0.907704 AGGGGCGTGGTATGAAGACA 60.908 55.000 0.00 0.00 0.00 3.41
167 168 5.063204 ACATGACGTCTGAAATCCTTTTCA 58.937 37.500 17.92 1.63 46.88 2.69
170 171 4.641396 TGACATGACGTCTGAAATCCTTT 58.359 39.130 17.92 0.00 45.60 3.11
198 199 6.459024 GCATGTCTTGGTTTGTACTGTAAACA 60.459 38.462 8.91 0.89 39.24 2.83
206 207 2.351738 GCCTGCATGTCTTGGTTTGTAC 60.352 50.000 0.00 0.00 0.00 2.90
231 240 2.170397 TCTTGCTCAAGTCTGTTGTCCA 59.830 45.455 9.20 0.00 39.38 4.02
234 243 3.266510 TGTCTTGCTCAAGTCTGTTGT 57.733 42.857 9.20 0.00 39.38 3.32
235 244 3.544834 CGTTGTCTTGCTCAAGTCTGTTG 60.545 47.826 9.20 0.00 39.38 3.33
264 273 1.065551 GATGCCAAAGGTAATGTCGCC 59.934 52.381 0.00 0.00 0.00 5.54
266 275 2.223340 GCTGATGCCAAAGGTAATGTCG 60.223 50.000 0.00 0.00 0.00 4.35
355 365 1.135698 TGGCGATGGGATCATGGGAT 61.136 55.000 0.00 0.00 36.13 3.85
428 710 5.872617 TCAATTTTCTACCGACGACATCAAT 59.127 36.000 0.00 0.00 0.00 2.57
429 711 5.231702 TCAATTTTCTACCGACGACATCAA 58.768 37.500 0.00 0.00 0.00 2.57
440 722 6.417930 GCTTGTCAAACACTCAATTTTCTACC 59.582 38.462 0.00 0.00 0.00 3.18
496 779 3.071602 GGTGTGGTGCCTATCATATGAGT 59.928 47.826 11.78 2.62 0.00 3.41
502 785 0.107017 GCTGGTGTGGTGCCTATCAT 60.107 55.000 0.00 0.00 0.00 2.45
505 788 1.574526 ATGGCTGGTGTGGTGCCTAT 61.575 55.000 0.00 0.00 46.23 2.57
509 792 1.185315 AATAATGGCTGGTGTGGTGC 58.815 50.000 0.00 0.00 0.00 5.01
559 847 6.626181 GCTCATCTTTTCTCCTCTCGTTTCTA 60.626 42.308 0.00 0.00 0.00 2.10
574 862 2.109126 GCCGGCTCGCTCATCTTTT 61.109 57.895 22.15 0.00 0.00 2.27
669 957 0.753262 CCTGGATGAACTCGTAGGGG 59.247 60.000 0.00 0.00 0.00 4.79
811 1102 1.183676 AAGGCCTCGTCCACGTACTT 61.184 55.000 5.23 0.00 40.80 2.24
924 1511 2.671177 CGTCCACAGCGCCTTGAAG 61.671 63.158 2.29 0.00 0.00 3.02
957 1544 2.522436 TCCACGAACCCACTCCGT 60.522 61.111 0.00 0.00 36.95 4.69
963 1550 3.319198 GCCTCCTCCACGAACCCA 61.319 66.667 0.00 0.00 0.00 4.51
1087 1677 2.680352 GACCTCCTCCAGCACCGA 60.680 66.667 0.00 0.00 0.00 4.69
1187 1777 1.221466 CGGCAAGCACTTCTTCACGA 61.221 55.000 0.00 0.00 34.66 4.35
1342 1936 7.394359 AGCGACTTTGATTGGCCAAATATATAT 59.606 33.333 24.71 3.14 35.72 0.86
1344 1938 5.536161 AGCGACTTTGATTGGCCAAATATAT 59.464 36.000 24.71 4.96 35.72 0.86
1345 1939 4.887071 AGCGACTTTGATTGGCCAAATATA 59.113 37.500 24.71 8.65 35.72 0.86
1348 1942 1.895131 AGCGACTTTGATTGGCCAAAT 59.105 42.857 24.71 11.29 35.72 2.32
1350 1944 0.881118 GAGCGACTTTGATTGGCCAA 59.119 50.000 23.00 23.00 0.00 4.52
1351 1945 0.250684 TGAGCGACTTTGATTGGCCA 60.251 50.000 0.00 0.00 0.00 5.36
1354 1969 3.058016 ACATTGTGAGCGACTTTGATTGG 60.058 43.478 0.00 0.00 0.00 3.16
1382 1997 8.526978 TCAAAGTTATTGCAACAGCCAAATATA 58.473 29.630 0.00 0.00 0.00 0.86
1389 2004 3.243704 TGGTCAAAGTTATTGCAACAGCC 60.244 43.478 0.00 0.00 0.00 4.85
1392 2007 4.096532 TCGTTGGTCAAAGTTATTGCAACA 59.903 37.500 0.00 0.00 0.00 3.33
1396 2011 5.344933 GGAAATCGTTGGTCAAAGTTATTGC 59.655 40.000 0.00 0.00 0.00 3.56
1400 2015 4.735662 CGGAAATCGTTGGTCAAAGTTA 57.264 40.909 0.00 0.00 0.00 2.24
1417 2032 5.400703 GTGGTCAAAGTTTTTGTTACGGAA 58.599 37.500 1.92 0.00 0.00 4.30
1418 2033 4.437121 CGTGGTCAAAGTTTTTGTTACGGA 60.437 41.667 14.02 0.00 0.00 4.69
1421 2036 7.514573 AATTCGTGGTCAAAGTTTTTGTTAC 57.485 32.000 1.92 0.00 0.00 2.50
1422 2037 8.460428 AGTAATTCGTGGTCAAAGTTTTTGTTA 58.540 29.630 1.92 0.00 0.00 2.41
1460 2075 9.833917 AGCGCTATATTATAGTGTGATAGAGTA 57.166 33.333 8.99 0.00 0.00 2.59
1461 2076 8.740123 AGCGCTATATTATAGTGTGATAGAGT 57.260 34.615 8.99 0.38 0.00 3.24
1462 2077 9.658475 GAAGCGCTATATTATAGTGTGATAGAG 57.342 37.037 12.05 0.00 0.00 2.43
1463 2078 9.397280 AGAAGCGCTATATTATAGTGTGATAGA 57.603 33.333 12.05 0.00 0.00 1.98
1476 2091 8.345565 CCATCTTGTTTTAAGAAGCGCTATATT 58.654 33.333 12.05 8.72 0.00 1.28
1477 2092 7.041098 CCCATCTTGTTTTAAGAAGCGCTATAT 60.041 37.037 12.05 1.48 0.00 0.86
1478 2093 6.260050 CCCATCTTGTTTTAAGAAGCGCTATA 59.740 38.462 12.05 1.18 0.00 1.31
1479 2094 5.066505 CCCATCTTGTTTTAAGAAGCGCTAT 59.933 40.000 12.05 2.35 0.00 2.97
1480 2095 4.394920 CCCATCTTGTTTTAAGAAGCGCTA 59.605 41.667 12.05 0.00 0.00 4.26
1481 2096 3.191371 CCCATCTTGTTTTAAGAAGCGCT 59.809 43.478 2.64 2.64 0.00 5.92
1482 2097 3.057526 ACCCATCTTGTTTTAAGAAGCGC 60.058 43.478 0.00 0.00 0.00 5.92
1483 2098 4.455877 AGACCCATCTTGTTTTAAGAAGCG 59.544 41.667 0.00 0.00 0.00 4.68
1484 2099 5.966742 AGACCCATCTTGTTTTAAGAAGC 57.033 39.130 0.00 0.00 0.00 3.86
1485 2100 7.979444 TGTAGACCCATCTTGTTTTAAGAAG 57.021 36.000 0.00 0.00 36.29 2.85
1486 2101 8.626526 GTTTGTAGACCCATCTTGTTTTAAGAA 58.373 33.333 0.00 0.00 36.29 2.52
1487 2102 7.996644 AGTTTGTAGACCCATCTTGTTTTAAGA 59.003 33.333 0.00 0.00 36.29 2.10
1488 2103 8.166422 AGTTTGTAGACCCATCTTGTTTTAAG 57.834 34.615 0.00 0.00 36.29 1.85
1489 2104 9.629878 TTAGTTTGTAGACCCATCTTGTTTTAA 57.370 29.630 0.00 0.00 36.29 1.52
1490 2105 9.802039 ATTAGTTTGTAGACCCATCTTGTTTTA 57.198 29.630 0.00 0.00 36.29 1.52
1491 2106 8.706322 ATTAGTTTGTAGACCCATCTTGTTTT 57.294 30.769 0.00 0.00 36.29 2.43
1492 2107 9.802039 TTATTAGTTTGTAGACCCATCTTGTTT 57.198 29.630 0.00 0.00 36.29 2.83
1493 2108 9.802039 TTTATTAGTTTGTAGACCCATCTTGTT 57.198 29.630 0.00 0.00 36.29 2.83
1494 2109 9.975218 ATTTATTAGTTTGTAGACCCATCTTGT 57.025 29.630 0.00 0.00 36.29 3.16
1499 2114 9.975218 ACTTCATTTATTAGTTTGTAGACCCAT 57.025 29.630 0.00 0.00 0.00 4.00
1500 2115 9.444600 GACTTCATTTATTAGTTTGTAGACCCA 57.555 33.333 0.00 0.00 0.00 4.51
1501 2116 8.890718 GGACTTCATTTATTAGTTTGTAGACCC 58.109 37.037 0.00 0.00 0.00 4.46
1502 2117 9.668497 AGGACTTCATTTATTAGTTTGTAGACC 57.332 33.333 0.00 0.00 0.00 3.85
1554 2169 9.409918 AGTCTAAGTTACTATCTTCATAGTGCA 57.590 33.333 5.12 0.00 44.33 4.57
1561 2176 9.955102 TGACACTAGTCTAAGTTACTATCTTCA 57.045 33.333 0.00 0.00 45.20 3.02
1567 2182 9.623000 TGCATATGACACTAGTCTAAGTTACTA 57.377 33.333 6.97 0.00 45.20 1.82
1568 2183 8.521170 TGCATATGACACTAGTCTAAGTTACT 57.479 34.615 6.97 0.00 45.20 2.24
1569 2184 9.186323 CATGCATATGACACTAGTCTAAGTTAC 57.814 37.037 6.97 0.00 45.20 2.50
1570 2185 9.131791 TCATGCATATGACACTAGTCTAAGTTA 57.868 33.333 6.97 0.00 45.20 2.24
1571 2186 8.011844 TCATGCATATGACACTAGTCTAAGTT 57.988 34.615 6.97 0.00 45.20 2.66
1572 2187 7.588497 TCATGCATATGACACTAGTCTAAGT 57.412 36.000 6.97 0.00 45.20 2.24
1590 2205 9.542462 GGAAGTAATTTATACTAGTGTCATGCA 57.458 33.333 5.39 0.00 0.00 3.96
1591 2206 8.989980 GGGAAGTAATTTATACTAGTGTCATGC 58.010 37.037 5.39 0.00 0.00 4.06
1594 2209 9.263446 AGTGGGAAGTAATTTATACTAGTGTCA 57.737 33.333 5.39 0.00 0.00 3.58
1601 2216 9.220906 TGGTCATAGTGGGAAGTAATTTATACT 57.779 33.333 0.00 0.00 0.00 2.12
1602 2217 9.490379 CTGGTCATAGTGGGAAGTAATTTATAC 57.510 37.037 0.00 0.00 0.00 1.47
1603 2218 8.154856 GCTGGTCATAGTGGGAAGTAATTTATA 58.845 37.037 0.00 0.00 0.00 0.98
1604 2219 6.998673 GCTGGTCATAGTGGGAAGTAATTTAT 59.001 38.462 0.00 0.00 0.00 1.40
1605 2220 6.354130 GCTGGTCATAGTGGGAAGTAATTTA 58.646 40.000 0.00 0.00 0.00 1.40
1606 2221 5.193679 GCTGGTCATAGTGGGAAGTAATTT 58.806 41.667 0.00 0.00 0.00 1.82
1607 2222 4.385310 GGCTGGTCATAGTGGGAAGTAATT 60.385 45.833 0.00 0.00 0.00 1.40
1608 2223 3.136626 GGCTGGTCATAGTGGGAAGTAAT 59.863 47.826 0.00 0.00 0.00 1.89
1609 2224 2.504175 GGCTGGTCATAGTGGGAAGTAA 59.496 50.000 0.00 0.00 0.00 2.24
1610 2225 2.116238 GGCTGGTCATAGTGGGAAGTA 58.884 52.381 0.00 0.00 0.00 2.24
1611 2226 0.912486 GGCTGGTCATAGTGGGAAGT 59.088 55.000 0.00 0.00 0.00 3.01
1612 2227 1.207791 AGGCTGGTCATAGTGGGAAG 58.792 55.000 0.00 0.00 0.00 3.46
1613 2228 2.561209 TAGGCTGGTCATAGTGGGAA 57.439 50.000 0.00 0.00 0.00 3.97
1614 2229 2.398588 CTTAGGCTGGTCATAGTGGGA 58.601 52.381 0.00 0.00 0.00 4.37
1615 2230 1.417890 CCTTAGGCTGGTCATAGTGGG 59.582 57.143 0.00 0.00 0.00 4.61
1616 2231 1.417890 CCCTTAGGCTGGTCATAGTGG 59.582 57.143 0.00 0.00 0.00 4.00
1617 2232 1.417890 CCCCTTAGGCTGGTCATAGTG 59.582 57.143 0.00 0.00 0.00 2.74
1618 2233 1.009675 ACCCCTTAGGCTGGTCATAGT 59.990 52.381 0.00 0.00 40.58 2.12
1619 2234 1.807814 ACCCCTTAGGCTGGTCATAG 58.192 55.000 0.00 0.00 40.58 2.23
1620 2235 2.241176 CAAACCCCTTAGGCTGGTCATA 59.759 50.000 0.00 0.00 40.58 2.15
1621 2236 1.005924 CAAACCCCTTAGGCTGGTCAT 59.994 52.381 0.00 0.00 40.58 3.06
1622 2237 0.404040 CAAACCCCTTAGGCTGGTCA 59.596 55.000 0.00 0.00 40.58 4.02
1623 2238 0.965866 GCAAACCCCTTAGGCTGGTC 60.966 60.000 0.00 0.00 40.58 4.02
1624 2239 1.076727 GCAAACCCCTTAGGCTGGT 59.923 57.895 0.00 0.00 40.58 4.00
1625 2240 0.623723 TAGCAAACCCCTTAGGCTGG 59.376 55.000 0.00 0.00 40.58 4.85
1626 2241 2.736670 ATAGCAAACCCCTTAGGCTG 57.263 50.000 0.00 0.00 40.58 4.85
1627 2242 4.243643 AGATATAGCAAACCCCTTAGGCT 58.756 43.478 0.00 0.00 40.58 4.58
1628 2243 4.041691 TGAGATATAGCAAACCCCTTAGGC 59.958 45.833 0.00 0.00 40.58 3.93
1629 2244 5.308237 ACTGAGATATAGCAAACCCCTTAGG 59.692 44.000 0.00 0.00 43.78 2.69
1630 2245 6.426646 ACTGAGATATAGCAAACCCCTTAG 57.573 41.667 0.00 0.00 0.00 2.18
1631 2246 5.010719 CGACTGAGATATAGCAAACCCCTTA 59.989 44.000 0.00 0.00 0.00 2.69
1722 2337 0.451628 CATGAGCGCAACAGAACACG 60.452 55.000 11.47 0.00 0.00 4.49
1738 2353 8.849490 CAATACGTTTTGGACAAGAAATACATG 58.151 33.333 10.50 0.00 0.00 3.21
1820 2436 2.993471 GCAAGCGACAACCCATGGG 61.993 63.158 30.23 30.23 42.03 4.00
1924 2546 1.675552 ACTGTGCACACTTACCCAAC 58.324 50.000 17.42 0.00 0.00 3.77
1930 2552 4.202212 TGAGCTTCTTACTGTGCACACTTA 60.202 41.667 17.42 7.41 0.00 2.24


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

AutoCloner maintained by Alex Coulton.