Multiple sequence alignment - TraesCS4A01G187000

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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 TraesCS4A01G187000 chr4A 100.000 4523 0 0 1 4523 465893744 465889222 0.000000e+00 8353.0
1 TraesCS4A01G187000 chr4A 78.177 362 61 13 2750 3111 465546654 465546311 9.850000e-52 215.0
2 TraesCS4A01G187000 chr4D 92.639 4320 196 42 270 4519 111052424 111056691 0.000000e+00 6104.0
3 TraesCS4A01G187000 chr4D 82.299 548 41 21 1623 2159 345247882 345248384 1.500000e-114 424.0
4 TraesCS4A01G187000 chr4D 88.550 262 13 12 1 251 111050871 111051126 7.350000e-78 302.0
5 TraesCS4A01G187000 chr4D 75.634 513 98 16 2599 3111 111586493 111586978 3.520000e-56 230.0
6 TraesCS4A01G187000 chr4D 100.000 30 0 0 1550 1579 345247848 345247877 6.320000e-04 56.5
7 TraesCS4A01G187000 chr4B 93.200 3794 141 42 1 3734 171144931 171141195 0.000000e+00 5469.0
8 TraesCS4A01G187000 chr4B 88.348 678 62 11 3822 4492 172027247 172027914 0.000000e+00 798.0
9 TraesCS4A01G187000 chr4B 74.708 514 101 20 2599 3111 172378950 172379435 7.670000e-48 202.0
10 TraesCS4A01G187000 chrUn 80.612 98 17 2 3178 3274 313595573 313595477 1.750000e-09 75.0
11 TraesCS4A01G187000 chr6B 80.612 98 17 2 3178 3274 707426404 707426500 1.750000e-09 75.0
12 TraesCS4A01G187000 chr6B 80.612 98 17 2 3178 3274 707766095 707766191 1.750000e-09 75.0
13 TraesCS4A01G187000 chr7D 80.808 99 14 4 3177 3271 509699825 509699922 6.280000e-09 73.1
14 TraesCS4A01G187000 chr7A 79.439 107 15 6 3173 3274 580655278 580655174 8.120000e-08 69.4
15 TraesCS4A01G187000 chr5D 93.333 45 3 0 3229 3273 72902364 72902320 2.920000e-07 67.6
16 TraesCS4A01G187000 chr1A 93.182 44 1 2 3232 3274 541398915 541398873 3.780000e-06 63.9


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 TraesCS4A01G187000 chr4A 465889222 465893744 4522 True 8353.00 8353 100.0000 1 4523 1 chr4A.!!$R2 4522
1 TraesCS4A01G187000 chr4D 111050871 111056691 5820 False 3203.00 6104 90.5945 1 4519 2 chr4D.!!$F2 4518
2 TraesCS4A01G187000 chr4D 345247848 345248384 536 False 240.25 424 91.1495 1550 2159 2 chr4D.!!$F3 609
3 TraesCS4A01G187000 chr4B 171141195 171144931 3736 True 5469.00 5469 93.2000 1 3734 1 chr4B.!!$R1 3733
4 TraesCS4A01G187000 chr4B 172027247 172027914 667 False 798.00 798 88.3480 3822 4492 1 chr4B.!!$F1 670

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
651 1980 0.512952 CACTGTTAGCGCAGAACCAC 59.487 55.0 18.94 3.78 39.62 4.16 F
1062 2392 1.812235 TGAGCTTGTTGATCGCATGT 58.188 45.0 0.00 0.00 32.98 3.21 F
2589 3925 0.615331 TCATCCTCCTCACCACAAGC 59.385 55.0 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 3368 1.078848 AGTGCCATCAGCTTCGTCC 60.079 57.895 0.0 0.0 44.23 4.79 R
3055 4394 1.153489 CCAGATCACGGTCCAGCAG 60.153 63.158 0.0 0.0 0.00 4.24 R
3693 5032 0.037975 GGGCAAAGACTACGTTCGGA 60.038 55.000 0.0 0.0 0.00 4.55 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
38 39 2.026262 AGGTTTGGTGCCAATCGTATCT 60.026 45.455 4.32 0.00 35.70 1.98
49 50 4.271291 GCCAATCGTATCTCAAAACCTCTC 59.729 45.833 0.00 0.00 0.00 3.20
51 52 5.521735 CCAATCGTATCTCAAAACCTCTCTG 59.478 44.000 0.00 0.00 0.00 3.35
52 53 5.923733 ATCGTATCTCAAAACCTCTCTGT 57.076 39.130 0.00 0.00 0.00 3.41
54 55 5.470368 TCGTATCTCAAAACCTCTCTGTTG 58.530 41.667 0.00 0.00 0.00 3.33
56 57 2.851195 TCTCAAAACCTCTCTGTTGCC 58.149 47.619 0.00 0.00 0.00 4.52
59 60 3.631250 TCAAAACCTCTCTGTTGCCTTT 58.369 40.909 0.00 0.00 0.00 3.11
61 62 4.466015 TCAAAACCTCTCTGTTGCCTTTTT 59.534 37.500 0.00 0.00 0.00 1.94
62 63 4.391405 AAACCTCTCTGTTGCCTTTTTG 57.609 40.909 0.00 0.00 0.00 2.44
64 65 2.689983 ACCTCTCTGTTGCCTTTTTGTG 59.310 45.455 0.00 0.00 0.00 3.33
69 70 4.584325 TCTCTGTTGCCTTTTTGTGCTATT 59.416 37.500 0.00 0.00 0.00 1.73
70 71 5.068987 TCTCTGTTGCCTTTTTGTGCTATTT 59.931 36.000 0.00 0.00 0.00 1.40
71 72 5.049167 TCTGTTGCCTTTTTGTGCTATTTG 58.951 37.500 0.00 0.00 0.00 2.32
72 73 4.764172 TGTTGCCTTTTTGTGCTATTTGT 58.236 34.783 0.00 0.00 0.00 2.83
75 76 4.870363 TGCCTTTTTGTGCTATTTGTCTC 58.130 39.130 0.00 0.00 0.00 3.36
85 86 9.554724 TTTGTGCTATTTGTCTCGATTTTATTC 57.445 29.630 0.00 0.00 0.00 1.75
124 125 5.443185 TCCTTTTCTTGATTCAGTTGCTG 57.557 39.130 0.00 0.00 0.00 4.41
210 211 5.399858 CGTGACTACACAGTAAAGCATACT 58.600 41.667 0.00 0.00 46.20 2.12
211 212 5.512082 CGTGACTACACAGTAAAGCATACTC 59.488 44.000 0.00 0.00 46.20 2.59
308 1606 7.025365 TGTGTAGACATTTTACTGTAGCGTAG 58.975 38.462 0.00 0.00 0.00 3.51
355 1654 1.915141 CAAGATGCCTGAGGTGGTTT 58.085 50.000 0.00 0.00 0.00 3.27
370 1669 3.584834 GTGGTTTCCATTGCATTACACC 58.415 45.455 0.00 0.00 35.28 4.16
443 1742 2.094026 TGACGATCCATTGACTCACTGG 60.094 50.000 8.80 8.80 35.83 4.00
499 1798 3.116079 CAGCTTTTCCATTGGCTGTTT 57.884 42.857 0.00 0.00 44.69 2.83
500 1799 4.255833 CAGCTTTTCCATTGGCTGTTTA 57.744 40.909 0.00 0.00 44.69 2.01
501 1800 4.824289 CAGCTTTTCCATTGGCTGTTTAT 58.176 39.130 0.00 0.00 44.69 1.40
502 1801 4.628333 CAGCTTTTCCATTGGCTGTTTATG 59.372 41.667 0.00 0.00 44.69 1.90
503 1802 4.284234 AGCTTTTCCATTGGCTGTTTATGT 59.716 37.500 0.00 0.00 33.50 2.29
504 1803 5.480073 AGCTTTTCCATTGGCTGTTTATGTA 59.520 36.000 0.00 0.00 33.50 2.29
510 1835 6.629128 TCCATTGGCTGTTTATGTAATTGTG 58.371 36.000 0.00 0.00 0.00 3.33
543 1868 8.811017 CCATACAGTGAGATTATCTAGACCATT 58.189 37.037 0.00 0.00 0.00 3.16
550 1876 9.039870 GTGAGATTATCTAGACCATTTTGTCTG 57.960 37.037 0.00 0.00 45.03 3.51
584 1910 5.181748 GCTACAGATCATCAAACCAAGAGT 58.818 41.667 0.00 0.00 0.00 3.24
651 1980 0.512952 CACTGTTAGCGCAGAACCAC 59.487 55.000 18.94 3.78 39.62 4.16
722 2051 4.691860 GCTTTCTTTGAGCTCAAGCATA 57.308 40.909 27.02 13.20 45.16 3.14
729 2058 5.410746 TCTTTGAGCTCAAGCATAAGAGTTG 59.589 40.000 27.02 2.63 45.16 3.16
789 2118 7.600375 CCTCGTGATGCTTATACAATAATCAGT 59.400 37.037 0.00 0.00 0.00 3.41
801 2130 4.754618 ACAATAATCAGTTCACAGCAACGA 59.245 37.500 0.00 0.00 0.00 3.85
803 2132 3.609103 AATCAGTTCACAGCAACGAAC 57.391 42.857 0.00 4.50 41.48 3.95
813 2142 2.617274 GCAACGAACCCTCCAGTGC 61.617 63.158 0.00 0.00 0.00 4.40
896 2225 5.391950 GGATCGCCGTTGATGCATAAAATAT 60.392 40.000 0.00 0.00 36.77 1.28
898 2227 6.164408 TCGCCGTTGATGCATAAAATATAG 57.836 37.500 0.00 0.00 0.00 1.31
921 2251 5.246203 AGCTGTTGACTTGACCTGATTACTA 59.754 40.000 0.00 0.00 0.00 1.82
923 2253 6.665992 TGTTGACTTGACCTGATTACTACT 57.334 37.500 0.00 0.00 0.00 2.57
924 2254 6.688578 TGTTGACTTGACCTGATTACTACTC 58.311 40.000 0.00 0.00 0.00 2.59
927 2257 5.652891 TGACTTGACCTGATTACTACTCCTC 59.347 44.000 0.00 0.00 0.00 3.71
968 2298 3.407424 TCACTGACCTGTCCAAATCAG 57.593 47.619 0.00 0.00 43.47 2.90
983 2313 4.081862 CCAAATCAGCAACATTCCAGTGAT 60.082 41.667 0.00 0.00 0.00 3.06
984 2314 4.713824 AATCAGCAACATTCCAGTGATG 57.286 40.909 0.00 0.00 0.00 3.07
985 2315 1.814394 TCAGCAACATTCCAGTGATGC 59.186 47.619 0.00 1.53 45.07 3.91
988 2318 3.687572 GCAACATTCCAGTGATGCTAG 57.312 47.619 0.00 0.00 42.50 3.42
1054 2384 2.682856 GTCTGTGGTTTGAGCTTGTTGA 59.317 45.455 0.00 0.00 0.00 3.18
1057 2387 2.290367 TGTGGTTTGAGCTTGTTGATCG 59.710 45.455 0.00 0.00 32.98 3.69
1062 2392 1.812235 TGAGCTTGTTGATCGCATGT 58.188 45.000 0.00 0.00 32.98 3.21
2101 3437 1.586564 CTCAACGACGGCGAGATCC 60.587 63.158 22.49 0.00 41.64 3.36
2296 3632 1.250154 CCACGTCCACCAATGGCAAT 61.250 55.000 0.00 0.00 46.80 3.56
2342 3678 3.643237 TCCTTGAGGAGAATATCACCGT 58.357 45.455 0.00 0.00 39.78 4.83
2371 3707 4.445545 GCGCCGCTCAAAAGGTCG 62.446 66.667 0.00 0.00 0.00 4.79
2589 3925 0.615331 TCATCCTCCTCACCACAAGC 59.385 55.000 0.00 0.00 0.00 4.01
2691 4027 1.139095 GTACAGGGGCGTTCTCGAG 59.861 63.158 5.93 5.93 39.71 4.04
2897 4233 0.716108 CTCGCCACGATGTTGTTCTC 59.284 55.000 0.00 0.00 34.61 2.87
3055 4394 2.866762 GACATGAAGCCGGAGAACATAC 59.133 50.000 5.05 0.00 0.00 2.39
3543 4882 0.324943 CCCAAAGGTGGTCGATCAGT 59.675 55.000 0.00 0.00 44.30 3.41
3544 4883 1.553248 CCCAAAGGTGGTCGATCAGTA 59.447 52.381 0.00 0.00 44.30 2.74
3545 4884 2.027561 CCCAAAGGTGGTCGATCAGTAA 60.028 50.000 0.00 0.00 44.30 2.24
3546 4885 3.370527 CCCAAAGGTGGTCGATCAGTAAT 60.371 47.826 0.00 0.00 44.30 1.89
3550 4889 3.375699 AGGTGGTCGATCAGTAATTCCT 58.624 45.455 0.00 0.00 0.00 3.36
3562 4901 5.313712 TCAGTAATTCCTTTGGAACAGACC 58.686 41.667 0.71 0.00 45.07 3.85
3609 4948 5.999205 TTTGGCCAATCAGTAATTCATGT 57.001 34.783 21.26 0.00 0.00 3.21
3610 4949 7.473735 TTTTGGCCAATCAGTAATTCATGTA 57.526 32.000 21.26 0.00 0.00 2.29
3611 4950 6.449635 TTGGCCAATCAGTAATTCATGTAC 57.550 37.500 16.05 0.00 0.00 2.90
3612 4951 4.574421 TGGCCAATCAGTAATTCATGTACG 59.426 41.667 0.61 0.00 0.00 3.67
3613 4952 4.814234 GGCCAATCAGTAATTCATGTACGA 59.186 41.667 0.00 0.00 0.00 3.43
3614 4953 5.050091 GGCCAATCAGTAATTCATGTACGAG 60.050 44.000 0.00 0.00 0.00 4.18
3615 4954 5.559035 GCCAATCAGTAATTCATGTACGAGC 60.559 44.000 0.00 0.00 0.00 5.03
3616 4955 5.332581 CCAATCAGTAATTCATGTACGAGCG 60.333 44.000 0.00 0.00 0.00 5.03
3617 4956 3.113322 TCAGTAATTCATGTACGAGCGC 58.887 45.455 0.00 0.00 0.00 5.92
3618 4957 3.116300 CAGTAATTCATGTACGAGCGCT 58.884 45.455 11.27 11.27 0.00 5.92
3619 4958 3.180584 CAGTAATTCATGTACGAGCGCTC 59.819 47.826 27.64 27.64 0.00 5.03
3620 4959 2.586258 AATTCATGTACGAGCGCTCT 57.414 45.000 32.88 22.11 0.00 4.09
3621 4960 2.586258 ATTCATGTACGAGCGCTCTT 57.414 45.000 32.88 27.06 0.00 2.85
3622 4961 1.909376 TTCATGTACGAGCGCTCTTC 58.091 50.000 32.88 22.18 0.00 2.87
3623 4962 0.808755 TCATGTACGAGCGCTCTTCA 59.191 50.000 32.88 26.32 0.00 3.02
3679 5018 2.093869 CCGTATCCTCCGAAAACTCCAA 60.094 50.000 0.00 0.00 0.00 3.53
3681 5020 3.370061 CGTATCCTCCGAAAACTCCAAAC 59.630 47.826 0.00 0.00 0.00 2.93
3693 5032 5.852282 AAACTCCAAACAATACTGTGCTT 57.148 34.783 0.00 0.00 35.37 3.91
3696 5035 2.811431 TCCAAACAATACTGTGCTTCCG 59.189 45.455 0.00 0.00 35.37 4.30
3745 5091 9.002600 TGCACATCACTTAGCTATAATTATTGG 57.997 33.333 2.68 0.00 0.00 3.16
3756 5102 8.863872 AGCTATAATTATTGGCCGAAAGTAAT 57.136 30.769 2.68 0.00 0.00 1.89
3769 5115 6.856426 GGCCGAAAGTAATTGTAGCAAATATC 59.144 38.462 0.00 0.00 0.00 1.63
3770 5116 7.414436 GCCGAAAGTAATTGTAGCAAATATCA 58.586 34.615 0.00 0.00 0.00 2.15
3807 5153 5.690464 ACTCTCTCCATCTGCAAATACTT 57.310 39.130 0.00 0.00 0.00 2.24
3811 5157 5.046376 TCTCTCCATCTGCAAATACTTGTCA 60.046 40.000 0.00 0.00 34.79 3.58
3812 5158 5.559770 TCTCCATCTGCAAATACTTGTCAA 58.440 37.500 0.00 0.00 34.79 3.18
3813 5159 6.003326 TCTCCATCTGCAAATACTTGTCAAA 58.997 36.000 0.00 0.00 34.79 2.69
3832 5178 8.408043 TGTCAAAGAAATGGATTTGTCTATGT 57.592 30.769 0.00 0.00 37.60 2.29
3833 5179 8.514594 TGTCAAAGAAATGGATTTGTCTATGTC 58.485 33.333 0.00 0.00 37.60 3.06
3850 5200 9.952030 TGTCTATGTCATAAGTTGGTGAAAATA 57.048 29.630 0.00 0.00 0.00 1.40
3876 5227 1.155889 TGGACACACATGCATTCGAC 58.844 50.000 0.00 0.00 0.00 4.20
3891 5242 5.239306 TGCATTCGACTGAACAGAAAAATCT 59.761 36.000 6.99 0.00 36.81 2.40
3982 5333 6.586751 CATGTGTTTTCATGAAGAAACATGC 58.413 36.000 32.85 20.07 45.48 4.06
3998 5349 3.900941 ACATGCTGTTTTAGGCGAAAAG 58.099 40.909 5.73 0.00 37.70 2.27
4055 5406 4.214332 AGCATCGGTTCTGTCTTTTCTTTC 59.786 41.667 0.00 0.00 0.00 2.62
4056 5407 4.613850 GCATCGGTTCTGTCTTTTCTTTCC 60.614 45.833 0.00 0.00 0.00 3.13
4060 5411 3.570125 GGTTCTGTCTTTTCTTTCCCCAG 59.430 47.826 0.00 0.00 0.00 4.45
4106 5463 4.881850 ACGAAAATTCATACATGGGACTCC 59.118 41.667 0.00 0.00 0.00 3.85
4192 5550 1.590147 CTAGGAGCCAAACGTCCGT 59.410 57.895 0.00 0.00 37.97 4.69
4230 5588 7.659390 TGGGATCAAAATGTTTGGTTGTTTATC 59.341 33.333 0.00 0.00 0.00 1.75
4249 5607 9.921637 TGTTTATCCAAAGGTTTACATGATTTC 57.078 29.630 0.00 0.00 0.00 2.17
4253 5611 7.696992 TCCAAAGGTTTACATGATTTCTACC 57.303 36.000 0.00 0.00 0.00 3.18
4272 5630 3.959943 ACCGAGTTGCATGTTTTGTTAC 58.040 40.909 0.00 0.00 0.00 2.50
4293 5654 4.407365 ACCCTTGTAGGATTTTCACCTTG 58.593 43.478 0.00 0.00 37.67 3.61
4301 5662 5.262588 AGGATTTTCACCTTGTTGACAAC 57.737 39.130 11.54 11.54 33.55 3.32
4350 5711 0.038744 CCCTTCTCCACCAAGCATGT 59.961 55.000 0.00 0.00 0.00 3.21
4456 5819 8.037166 AGAAAATCTTTGCATGGTTTCTATTCC 58.963 33.333 13.07 0.00 34.45 3.01
4472 5835 8.456471 GTTTCTATTCCGCAATAGGTTAAACTT 58.544 33.333 6.27 0.00 41.39 2.66
4492 5855 2.933573 TCAAAGCAAACCTTTCCCGTA 58.066 42.857 0.00 0.00 41.75 4.02
4519 5882 4.698780 ACATACTGCGTCTACAAGTGAGTA 59.301 41.667 0.00 0.00 0.00 2.59
4520 5883 5.357314 ACATACTGCGTCTACAAGTGAGTAT 59.643 40.000 0.00 0.00 0.00 2.12
4521 5884 4.358494 ACTGCGTCTACAAGTGAGTATC 57.642 45.455 0.00 0.00 0.00 2.24
4522 5885 3.181509 ACTGCGTCTACAAGTGAGTATCG 60.182 47.826 0.00 0.00 38.61 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.297134 AAGGCAACAGAGAGGTTTTGA 57.703 42.857 0.00 0.00 41.41 2.69
49 50 4.810491 ACAAATAGCACAAAAAGGCAACAG 59.190 37.500 0.00 0.00 41.41 3.16
51 52 5.049828 AGACAAATAGCACAAAAAGGCAAC 58.950 37.500 0.00 0.00 0.00 4.17
52 53 5.275067 AGACAAATAGCACAAAAAGGCAA 57.725 34.783 0.00 0.00 0.00 4.52
54 55 3.914364 CGAGACAAATAGCACAAAAAGGC 59.086 43.478 0.00 0.00 0.00 4.35
56 57 7.858052 AAATCGAGACAAATAGCACAAAAAG 57.142 32.000 0.00 0.00 0.00 2.27
59 60 9.554724 GAATAAAATCGAGACAAATAGCACAAA 57.445 29.630 0.00 0.00 0.00 2.83
61 62 8.175069 GTGAATAAAATCGAGACAAATAGCACA 58.825 33.333 0.00 0.00 0.00 4.57
62 63 7.640240 GGTGAATAAAATCGAGACAAATAGCAC 59.360 37.037 0.00 0.00 0.00 4.40
64 65 6.846283 CGGTGAATAAAATCGAGACAAATAGC 59.154 38.462 0.00 0.00 0.00 2.97
69 70 4.325204 CGTCGGTGAATAAAATCGAGACAA 59.675 41.667 0.00 0.00 0.00 3.18
70 71 3.855379 CGTCGGTGAATAAAATCGAGACA 59.145 43.478 0.00 0.00 0.00 3.41
71 72 4.100529 TCGTCGGTGAATAAAATCGAGAC 58.899 43.478 0.00 0.00 0.00 3.36
72 73 4.348656 CTCGTCGGTGAATAAAATCGAGA 58.651 43.478 0.00 0.00 43.69 4.04
75 76 2.858344 AGCTCGTCGGTGAATAAAATCG 59.142 45.455 0.00 0.00 0.00 3.34
85 86 0.721718 GGAAATGAAGCTCGTCGGTG 59.278 55.000 0.00 0.00 0.00 4.94
124 125 3.532542 GAGAACAGTAAGGTGGTATGCC 58.467 50.000 0.00 0.00 0.00 4.40
223 234 5.006844 TCGTTTACTTTGTATGTGTGTGTGG 59.993 40.000 0.00 0.00 0.00 4.17
355 1654 2.192664 ACACGGTGTAATGCAATGGA 57.807 45.000 12.96 0.00 0.00 3.41
443 1742 1.045911 TGGGACACCTTGCAAAACCC 61.046 55.000 0.00 9.49 37.76 4.11
497 1796 9.945904 TGTATGGACACTACACAATTACATAAA 57.054 29.630 0.00 0.00 0.00 1.40
499 1798 8.755028 ACTGTATGGACACTACACAATTACATA 58.245 33.333 0.00 0.00 0.00 2.29
500 1799 7.549134 CACTGTATGGACACTACACAATTACAT 59.451 37.037 0.00 0.00 0.00 2.29
501 1800 6.871492 CACTGTATGGACACTACACAATTACA 59.129 38.462 0.00 0.00 0.00 2.41
502 1801 7.094631 TCACTGTATGGACACTACACAATTAC 58.905 38.462 0.00 0.00 0.00 1.89
503 1802 7.177744 TCTCACTGTATGGACACTACACAATTA 59.822 37.037 0.00 0.00 0.00 1.40
504 1803 6.014584 TCTCACTGTATGGACACTACACAATT 60.015 38.462 0.00 0.00 0.00 2.32
510 1835 8.172352 AGATAATCTCACTGTATGGACACTAC 57.828 38.462 0.00 0.00 0.00 2.73
543 1868 0.319900 GCGCTGACTCTCCAGACAAA 60.320 55.000 0.00 0.00 36.29 2.83
550 1876 1.001815 GATCTGTAGCGCTGACTCTCC 60.002 57.143 22.90 0.00 0.00 3.71
584 1910 9.995003 ATATTGGCAAAAGTTAATTTCAGTCAA 57.005 25.926 3.01 5.35 35.92 3.18
639 1968 3.865929 CTGTCCGTGGTTCTGCGCT 62.866 63.158 9.73 0.00 0.00 5.92
640 1969 3.414700 CTGTCCGTGGTTCTGCGC 61.415 66.667 0.00 0.00 0.00 6.09
651 1980 0.105964 TTGTCCAGTTGTCCTGTCCG 59.894 55.000 0.00 0.00 39.74 4.79
722 2051 3.817647 GGTTGAATCTGACTGCAACTCTT 59.182 43.478 14.58 0.00 40.21 2.85
729 2058 2.350772 CGGTTTGGTTGAATCTGACTGC 60.351 50.000 0.00 0.00 0.00 4.40
789 2118 0.534203 GGAGGGTTCGTTGCTGTGAA 60.534 55.000 0.00 0.00 0.00 3.18
801 2130 0.687354 CTAGTGTGCACTGGAGGGTT 59.313 55.000 19.41 0.00 41.75 4.11
803 2132 0.687354 AACTAGTGTGCACTGGAGGG 59.313 55.000 19.41 6.04 41.75 4.30
813 2142 6.887376 AGCATCGTGTAATAAACTAGTGTG 57.113 37.500 0.00 0.00 0.00 3.82
896 2225 4.623932 AATCAGGTCAAGTCAACAGCTA 57.376 40.909 0.00 0.00 0.00 3.32
898 2227 4.319177 AGTAATCAGGTCAAGTCAACAGC 58.681 43.478 0.00 0.00 0.00 4.40
921 2251 5.519808 TCACTGTTCATATGTAGGAGGAGT 58.480 41.667 1.90 0.00 0.00 3.85
923 2253 6.377080 AGATCACTGTTCATATGTAGGAGGA 58.623 40.000 1.90 0.00 0.00 3.71
924 2254 6.662865 AGATCACTGTTCATATGTAGGAGG 57.337 41.667 1.90 0.00 0.00 4.30
927 2257 7.706281 GTGAAGATCACTGTTCATATGTAGG 57.294 40.000 1.90 0.00 43.73 3.18
968 2298 3.012518 ACTAGCATCACTGGAATGTTGC 58.987 45.455 0.00 1.45 42.94 4.17
983 2313 2.218603 TCATCGATCGTAGCACTAGCA 58.781 47.619 15.94 0.00 45.49 3.49
984 2314 2.480802 TCTCATCGATCGTAGCACTAGC 59.519 50.000 15.94 0.00 42.56 3.42
985 2315 3.120477 GGTCTCATCGATCGTAGCACTAG 60.120 52.174 15.94 4.77 0.00 2.57
986 2316 2.806818 GGTCTCATCGATCGTAGCACTA 59.193 50.000 15.94 0.00 0.00 2.74
987 2317 1.604755 GGTCTCATCGATCGTAGCACT 59.395 52.381 15.94 0.00 0.00 4.40
988 2318 1.335142 GGGTCTCATCGATCGTAGCAC 60.335 57.143 15.94 6.70 0.00 4.40
1266 2596 2.034687 CCCTTGCTGTGGACAGGG 59.965 66.667 8.82 1.83 43.94 4.45
1440 2770 2.970974 GAAACTCTGCCACAGCGCC 61.971 63.158 2.29 0.00 44.31 6.53
1455 2785 1.346479 TGTCCGTGGGGAAGTGGAAA 61.346 55.000 0.00 0.00 46.08 3.13
2036 3368 1.078848 AGTGCCATCAGCTTCGTCC 60.079 57.895 0.00 0.00 44.23 4.79
2240 3576 2.511600 CGACCGGGACCTTGATGC 60.512 66.667 6.32 0.00 0.00 3.91
2479 3815 2.892425 GCCGAGCCCGATGACAAG 60.892 66.667 0.00 0.00 38.22 3.16
2589 3925 2.853731 CGTAGCTGTACCTCTGGAAG 57.146 55.000 0.00 0.00 0.00 3.46
2916 4252 4.923710 TGATCATCGCCGCCGTCG 62.924 66.667 0.00 0.00 35.54 5.12
3055 4394 1.153489 CCAGATCACGGTCCAGCAG 60.153 63.158 0.00 0.00 0.00 4.24
3336 4675 1.091771 AATGCATCTTCTCGCCCACG 61.092 55.000 0.00 0.00 42.01 4.94
3411 4750 0.106719 CAACCACCACCTTCACCTGT 60.107 55.000 0.00 0.00 0.00 4.00
3534 4873 5.642063 TGTTCCAAAGGAATTACTGATCGAC 59.358 40.000 1.30 0.00 44.04 4.20
3537 4876 6.094186 GGTCTGTTCCAAAGGAATTACTGATC 59.906 42.308 1.30 0.00 44.04 2.92
3538 4877 5.946377 GGTCTGTTCCAAAGGAATTACTGAT 59.054 40.000 1.30 0.00 44.04 2.90
3539 4878 5.163141 TGGTCTGTTCCAAAGGAATTACTGA 60.163 40.000 1.30 0.00 44.04 3.41
3541 4880 5.070685 GTGGTCTGTTCCAAAGGAATTACT 58.929 41.667 1.30 0.00 44.04 2.24
3543 4882 4.069304 CGTGGTCTGTTCCAAAGGAATTA 58.931 43.478 1.30 0.00 44.04 1.40
3544 4883 2.884639 CGTGGTCTGTTCCAAAGGAATT 59.115 45.455 1.30 0.00 44.04 2.17
3545 4884 2.158667 ACGTGGTCTGTTCCAAAGGAAT 60.159 45.455 1.30 0.00 44.04 3.01
3546 4885 1.210967 ACGTGGTCTGTTCCAAAGGAA 59.789 47.619 0.00 0.00 39.66 3.36
3550 4889 3.876341 AGTAAACGTGGTCTGTTCCAAA 58.124 40.909 0.00 0.00 39.34 3.28
3583 4922 8.707449 ACATGAATTACTGATTGGCCAAAATAT 58.293 29.630 24.71 5.43 0.00 1.28
3594 4933 4.209288 GCGCTCGTACATGAATTACTGATT 59.791 41.667 0.00 0.00 0.00 2.57
3607 4946 0.526211 ACATGAAGAGCGCTCGTACA 59.474 50.000 30.39 27.92 34.09 2.90
3608 4947 2.110226 GTACATGAAGAGCGCTCGTAC 58.890 52.381 30.39 27.77 34.09 3.67
3609 4948 2.014857 AGTACATGAAGAGCGCTCGTA 58.985 47.619 30.39 22.09 34.09 3.43
3610 4949 0.811915 AGTACATGAAGAGCGCTCGT 59.188 50.000 30.39 28.28 34.09 4.18
3611 4950 1.202188 TGAGTACATGAAGAGCGCTCG 60.202 52.381 30.39 18.63 34.09 5.03
3612 4951 2.568696 TGAGTACATGAAGAGCGCTC 57.431 50.000 30.01 30.01 0.00 5.03
3613 4952 2.029020 TGTTGAGTACATGAAGAGCGCT 60.029 45.455 11.27 11.27 0.00 5.92
3614 4953 2.092838 GTGTTGAGTACATGAAGAGCGC 59.907 50.000 0.00 0.00 39.39 5.92
3615 4954 3.579709 AGTGTTGAGTACATGAAGAGCG 58.420 45.455 0.00 0.00 39.39 5.03
3616 4955 5.931441 AAAGTGTTGAGTACATGAAGAGC 57.069 39.130 0.00 0.00 39.39 4.09
3617 4956 6.017605 AGCAAAAGTGTTGAGTACATGAAGAG 60.018 38.462 0.00 0.00 39.39 2.85
3618 4957 5.822519 AGCAAAAGTGTTGAGTACATGAAGA 59.177 36.000 0.00 0.00 39.39 2.87
3619 4958 6.064846 AGCAAAAGTGTTGAGTACATGAAG 57.935 37.500 0.00 0.00 39.39 3.02
3620 4959 5.588246 TGAGCAAAAGTGTTGAGTACATGAA 59.412 36.000 0.00 0.00 39.39 2.57
3621 4960 5.007626 GTGAGCAAAAGTGTTGAGTACATGA 59.992 40.000 0.00 0.00 39.39 3.07
3622 4961 5.008019 AGTGAGCAAAAGTGTTGAGTACATG 59.992 40.000 0.00 0.00 39.39 3.21
3623 4962 5.126067 AGTGAGCAAAAGTGTTGAGTACAT 58.874 37.500 0.00 0.00 39.39 2.29
3664 5003 4.760204 AGTATTGTTTGGAGTTTTCGGAGG 59.240 41.667 0.00 0.00 0.00 4.30
3679 5018 2.478894 CGTTCGGAAGCACAGTATTGTT 59.521 45.455 0.00 0.00 34.62 2.83
3681 5020 2.066262 ACGTTCGGAAGCACAGTATTG 58.934 47.619 0.00 0.00 0.00 1.90
3693 5032 0.037975 GGGCAAAGACTACGTTCGGA 60.038 55.000 0.00 0.00 0.00 4.55
3696 5035 1.886886 TTGGGGCAAAGACTACGTTC 58.113 50.000 0.00 0.00 0.00 3.95
3736 5080 8.347035 GCTACAATTACTTTCGGCCAATAATTA 58.653 33.333 2.24 0.00 0.00 1.40
3737 5081 7.147983 TGCTACAATTACTTTCGGCCAATAATT 60.148 33.333 2.24 2.40 0.00 1.40
3739 5083 5.648526 TGCTACAATTACTTTCGGCCAATAA 59.351 36.000 2.24 0.00 0.00 1.40
3745 5091 7.414436 TGATATTTGCTACAATTACTTTCGGC 58.586 34.615 0.00 0.00 0.00 5.54
3782 5128 8.363390 CAAGTATTTGCAGATGGAGAGAGTATA 58.637 37.037 0.00 0.00 0.00 1.47
3783 5129 6.992664 AGTATTTGCAGATGGAGAGAGTAT 57.007 37.500 0.00 0.00 0.00 2.12
3784 5130 6.155221 ACAAGTATTTGCAGATGGAGAGAGTA 59.845 38.462 0.00 0.00 37.85 2.59
3789 5135 5.164620 TGACAAGTATTTGCAGATGGAGA 57.835 39.130 0.00 0.00 37.85 3.71
3794 5140 7.816031 CCATTTCTTTGACAAGTATTTGCAGAT 59.184 33.333 0.00 0.00 37.85 2.90
3804 5150 7.352079 AGACAAATCCATTTCTTTGACAAGT 57.648 32.000 2.33 0.00 36.19 3.16
3807 5153 8.408043 ACATAGACAAATCCATTTCTTTGACA 57.592 30.769 2.33 0.00 36.19 3.58
3813 5159 9.911788 ACTTATGACATAGACAAATCCATTTCT 57.088 29.630 0.00 0.00 0.00 2.52
3833 5179 9.787532 CCATTGTAGTATTTTCACCAACTTATG 57.212 33.333 0.00 0.00 0.00 1.90
3850 5200 3.138884 TGCATGTGTGTCCATTGTAGT 57.861 42.857 0.00 0.00 0.00 2.73
3932 5283 1.333619 ACAACACTCGACCATGTTTGC 59.666 47.619 2.91 0.00 36.92 3.68
3982 5333 7.218204 CGATTTTATCCTTTTCGCCTAAAACAG 59.782 37.037 0.00 0.00 33.49 3.16
3998 5349 5.359860 ACATTTTGGAGGTCCGATTTTATCC 59.640 40.000 0.00 0.00 39.43 2.59
4055 5406 0.038744 AAATCTGTGGTGCTCTGGGG 59.961 55.000 0.00 0.00 0.00 4.96
4056 5407 1.271543 TGAAATCTGTGGTGCTCTGGG 60.272 52.381 0.00 0.00 0.00 4.45
4060 5411 5.403466 GTGAAAAATGAAATCTGTGGTGCTC 59.597 40.000 0.00 0.00 0.00 4.26
4192 5550 3.304911 TTGATCCCAAACTCACCAACA 57.695 42.857 0.00 0.00 0.00 3.33
4230 5588 6.373216 TCGGTAGAAATCATGTAAACCTTTGG 59.627 38.462 0.00 0.00 0.00 3.28
4249 5607 3.896648 ACAAAACATGCAACTCGGTAG 57.103 42.857 0.00 0.00 0.00 3.18
4250 5608 4.023878 GGTAACAAAACATGCAACTCGGTA 60.024 41.667 0.00 0.00 0.00 4.02
4252 5610 3.305110 GGTAACAAAACATGCAACTCGG 58.695 45.455 0.00 0.00 0.00 4.63
4253 5611 3.004315 AGGGTAACAAAACATGCAACTCG 59.996 43.478 0.00 0.00 39.74 4.18
4272 5630 4.407365 ACAAGGTGAAAATCCTACAAGGG 58.593 43.478 0.00 0.00 35.59 3.95
4293 5654 2.095567 AGCGCTCATCATTGTTGTCAAC 60.096 45.455 2.64 8.86 36.33 3.18
4301 5662 0.580578 CGAGGAAGCGCTCATCATTG 59.419 55.000 12.06 3.03 34.38 2.82
4456 5819 5.457140 TGCTTTGAAGTTTAACCTATTGCG 58.543 37.500 0.00 0.00 0.00 4.85
4472 5835 1.770294 ACGGGAAAGGTTTGCTTTGA 58.230 45.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.