Multiple sequence alignment - TraesCS3A01G371900

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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 TraesCS3A01G371900 chr3A 100.000 4621 0 0 1 4621 622708949 622713569 0.000000e+00 8534.0
1 TraesCS3A01G371900 chr3A 94.137 4315 204 14 1 4297 622817350 622821633 0.000000e+00 6521.0
2 TraesCS3A01G371900 chr3A 93.979 4318 215 12 1 4300 622898561 622902851 0.000000e+00 6492.0
3 TraesCS3A01G371900 chr3A 93.886 4318 214 15 1 4300 622717662 622721947 0.000000e+00 6466.0
4 TraesCS3A01G371900 chr3A 94.515 2771 143 7 1856 4621 622891720 622894486 0.000000e+00 4266.0
5 TraesCS3A01G371900 chr3A 95.075 1604 73 5 3022 4621 622811671 622813272 0.000000e+00 2519.0
6 TraesCS3A01G371900 chr3A 94.293 1174 63 3 1856 3028 622801595 622802765 0.000000e+00 1794.0
7 TraesCS3A01G371900 chr3A 83.108 1403 163 41 319 1691 622276815 622278173 0.000000e+00 1210.0
8 TraesCS3A01G371900 chr3A 94.427 323 18 0 4299 4621 622704538 622704860 8.930000e-137 497.0
9 TraesCS3A01G371900 chr3A 91.022 323 29 0 4299 4621 651903693 651903371 1.970000e-118 436.0
10 TraesCS3A01G371900 chr3D 91.538 2517 182 17 1688 4182 479914025 479911518 0.000000e+00 3439.0
11 TraesCS3A01G371900 chr3D 91.394 2510 196 13 1688 4182 479451135 479453639 0.000000e+00 3421.0
12 TraesCS3A01G371900 chr3D 91.069 2508 199 18 1688 4181 479894615 479892119 0.000000e+00 3367.0
13 TraesCS3A01G371900 chr3D 89.876 1699 150 11 1 1685 479449400 479451090 0.000000e+00 2165.0
14 TraesCS3A01G371900 chr3D 84.085 2262 270 47 1688 3890 478739261 478741491 0.000000e+00 2100.0
15 TraesCS3A01G371900 chr3D 85.944 1992 217 38 1916 3891 479213665 479215609 0.000000e+00 2069.0
16 TraesCS3A01G371900 chr3D 86.543 1828 198 25 2074 3891 479962061 479960272 0.000000e+00 1969.0
17 TraesCS3A01G371900 chr3D 86.994 1730 181 29 2490 4182 479122403 479124125 0.000000e+00 1908.0
18 TraesCS3A01G371900 chr3D 84.885 1396 158 30 321 1686 478737845 478739217 0.000000e+00 1360.0
19 TraesCS3A01G371900 chr3D 88.715 895 71 13 1 877 479919240 479918358 0.000000e+00 1066.0
20 TraesCS3A01G371900 chr3D 88.793 812 76 7 877 1688 479914863 479914067 0.000000e+00 981.0
21 TraesCS3A01G371900 chr3D 88.043 276 26 4 4348 4621 92739824 92740094 2.070000e-83 320.0
22 TraesCS3A01G371900 chr3D 93.496 123 7 1 4178 4300 479910829 479910708 1.020000e-41 182.0
23 TraesCS3A01G371900 chr3D 91.538 130 9 2 4178 4306 479854070 479853942 1.320000e-40 178.0
24 TraesCS3A01G371900 chr3D 90.769 130 10 2 4178 4306 479150302 479150430 6.150000e-39 172.0
25 TraesCS3A01G371900 chr3D 91.870 123 9 1 4178 4300 479891429 479891308 2.210000e-38 171.0
26 TraesCS3A01G371900 chr3D 84.848 66 10 0 1619 1684 478751511 478751576 2.980000e-07 67.6
27 TraesCS3A01G371900 chr3B 85.207 1379 153 29 335 1686 639753499 639754853 0.000000e+00 1369.0
28 TraesCS3A01G371900 chr3B 83.799 1395 171 32 321 1686 639148634 639150002 0.000000e+00 1273.0
29 TraesCS3A01G371900 chr3B 83.202 1393 183 29 321 1686 639552861 639554229 0.000000e+00 1229.0
30 TraesCS3A01G371900 chr3B 82.749 1397 166 35 324 1686 639398409 639399764 0.000000e+00 1175.0
31 TraesCS3A01G371900 chr3B 83.133 1162 130 35 2747 3890 639756000 639757113 0.000000e+00 1000.0
32 TraesCS3A01G371900 chr3B 80.503 159 31 0 1533 1691 639007335 639007493 6.280000e-24 122.0
33 TraesCS3A01G371900 chr4A 92.593 324 23 1 4299 4621 408059977 408060300 9.060000e-127 464.0
34 TraesCS3A01G371900 chr2D 90.110 273 25 2 4348 4618 201436400 201436672 2.050000e-93 353.0
35 TraesCS3A01G371900 chr7A 89.209 278 26 4 4348 4621 693024600 693024323 1.230000e-90 344.0
36 TraesCS3A01G371900 chrUn 84.838 277 38 4 4348 4621 424516799 424516524 4.550000e-70 276.0


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 TraesCS3A01G371900 chr3A 622708949 622713569 4620 False 8534.0 8534 100.0000 1 4621 1 chr3A.!!$F3 4620
1 TraesCS3A01G371900 chr3A 622817350 622821633 4283 False 6521.0 6521 94.1370 1 4297 1 chr3A.!!$F7 4296
2 TraesCS3A01G371900 chr3A 622898561 622902851 4290 False 6492.0 6492 93.9790 1 4300 1 chr3A.!!$F9 4299
3 TraesCS3A01G371900 chr3A 622717662 622721947 4285 False 6466.0 6466 93.8860 1 4300 1 chr3A.!!$F4 4299
4 TraesCS3A01G371900 chr3A 622891720 622894486 2766 False 4266.0 4266 94.5150 1856 4621 1 chr3A.!!$F8 2765
5 TraesCS3A01G371900 chr3A 622811671 622813272 1601 False 2519.0 2519 95.0750 3022 4621 1 chr3A.!!$F6 1599
6 TraesCS3A01G371900 chr3A 622801595 622802765 1170 False 1794.0 1794 94.2930 1856 3028 1 chr3A.!!$F5 1172
7 TraesCS3A01G371900 chr3A 622276815 622278173 1358 False 1210.0 1210 83.1080 319 1691 1 chr3A.!!$F1 1372
8 TraesCS3A01G371900 chr3D 479449400 479453639 4239 False 2793.0 3421 90.6350 1 4182 2 chr3D.!!$F7 4181
9 TraesCS3A01G371900 chr3D 479213665 479215609 1944 False 2069.0 2069 85.9440 1916 3891 1 chr3D.!!$F5 1975
10 TraesCS3A01G371900 chr3D 479960272 479962061 1789 True 1969.0 1969 86.5430 2074 3891 1 chr3D.!!$R2 1817
11 TraesCS3A01G371900 chr3D 479122403 479124125 1722 False 1908.0 1908 86.9940 2490 4182 1 chr3D.!!$F3 1692
12 TraesCS3A01G371900 chr3D 479891308 479894615 3307 True 1769.0 3367 91.4695 1688 4300 2 chr3D.!!$R3 2612
13 TraesCS3A01G371900 chr3D 478737845 478741491 3646 False 1730.0 2100 84.4850 321 3890 2 chr3D.!!$F6 3569
14 TraesCS3A01G371900 chr3D 479910708 479919240 8532 True 1417.0 3439 90.6355 1 4300 4 chr3D.!!$R4 4299
15 TraesCS3A01G371900 chr3B 639148634 639150002 1368 False 1273.0 1273 83.7990 321 1686 1 chr3B.!!$F2 1365
16 TraesCS3A01G371900 chr3B 639552861 639554229 1368 False 1229.0 1229 83.2020 321 1686 1 chr3B.!!$F4 1365
17 TraesCS3A01G371900 chr3B 639753499 639757113 3614 False 1184.5 1369 84.1700 335 3890 2 chr3B.!!$F5 3555
18 TraesCS3A01G371900 chr3B 639398409 639399764 1355 False 1175.0 1175 82.7490 324 1686 1 chr3B.!!$F3 1362

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
765 824 1.303317 GAATGGAACCGGCACACCT 60.303 57.895 0.00 0.0 0.0 4.00 F
1014 4597 0.039035 ACACACCACAACCCACAAGT 59.961 50.000 0.00 0.0 0.0 3.16 F
1519 5107 0.461870 CTCGCCATTGATTCCCGTCA 60.462 55.000 0.00 0.0 0.0 4.35 F
2623 6262 0.463474 GCTGGCAGGAGGATGAGAAC 60.463 60.000 17.64 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 6072 3.005791 AGCCACAAGGTGTTTTCATTAGC 59.994 43.478 0.0 0.0 37.19 3.09 R
2438 6075 3.457610 CAGCCACAAGGTGTTTTCATT 57.542 42.857 0.0 0.0 39.23 2.57 R
3464 7309 0.178891 AAGTCCTCTTCCTCCTGCCA 60.179 55.000 0.0 0.0 0.00 4.92 R
4529 9109 0.038526 GTTTCTCCTCGCCGTTCTCA 60.039 55.000 0.0 0.0 0.00 3.27 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
39 40 5.344743 AGTGGAACATGATACACGAGATT 57.655 39.130 12.24 0.00 44.52 2.40
93 94 2.414594 GCGGGCAGAAATGCATCC 59.585 61.111 0.00 0.00 36.33 3.51
101 102 2.225019 GCAGAAATGCATCCTGGTATCG 59.775 50.000 22.64 4.98 34.41 2.92
195 197 2.675658 TTTTCCACTCCTTGAAGGGG 57.324 50.000 10.16 10.16 43.27 4.79
210 212 5.596836 TGAAGGGGCAATATGACATTTTC 57.403 39.130 0.00 0.00 0.00 2.29
261 264 5.712217 TTTTGTAGAACACACAAGAGTCG 57.288 39.130 0.00 0.00 37.22 4.18
268 271 9.587192 TGTAGAACACACAAGAGTCGGTATGAC 62.587 44.444 3.71 0.00 39.06 3.06
400 409 5.352700 AGATTCCCTCTAGATGATCCAGT 57.647 43.478 0.00 0.00 30.26 4.00
555 602 7.336679 CACCACATTTGTCACCTCTATGAATTA 59.663 37.037 0.00 0.00 0.00 1.40
565 612 7.712639 GTCACCTCTATGAATTAAAGAGCATCA 59.287 37.037 5.91 0.00 37.82 3.07
576 623 3.482156 AAGAGCATCATGCCGTAAGAT 57.518 42.857 5.84 0.00 46.52 2.40
577 624 2.763933 AGAGCATCATGCCGTAAGATG 58.236 47.619 5.84 0.00 46.52 2.90
678 735 4.000928 ACTCATATCCTTGTCTCCCACT 57.999 45.455 0.00 0.00 0.00 4.00
757 815 2.808543 GGCTAGCTATTGAATGGAACCG 59.191 50.000 15.72 0.00 0.00 4.44
765 824 1.303317 GAATGGAACCGGCACACCT 60.303 57.895 0.00 0.00 0.00 4.00
786 845 4.585162 CCTCCCGAGTTTGTCTCATATACT 59.415 45.833 0.00 0.00 42.88 2.12
913 4487 8.995220 ACCTTTTTCATCAATGACATGAATTTG 58.005 29.630 0.00 0.00 39.46 2.32
1014 4597 0.039035 ACACACCACAACCCACAAGT 59.961 50.000 0.00 0.00 0.00 3.16
1081 4666 0.820871 GTCGGAGATGAGCAAGGACT 59.179 55.000 0.00 0.00 40.67 3.85
1116 4701 1.407656 AAGAAGTCACCTCGCACCCA 61.408 55.000 0.00 0.00 0.00 4.51
1125 4710 2.031919 TCGCACCCACGCATTCTT 59.968 55.556 0.00 0.00 0.00 2.52
1262 4850 1.461127 GGACGAGTTCATGAGCAACAC 59.539 52.381 12.41 0.00 0.00 3.32
1370 4958 1.219124 GTGGCGAAGATGCAGGAGA 59.781 57.895 0.00 0.00 36.28 3.71
1488 5076 1.304381 GGTGCATTCCCAGCCTCAA 60.304 57.895 0.00 0.00 0.00 3.02
1519 5107 0.461870 CTCGCCATTGATTCCCGTCA 60.462 55.000 0.00 0.00 0.00 4.35
1528 5116 1.133761 TGATTCCCGTCAAACCACCAA 60.134 47.619 0.00 0.00 0.00 3.67
1531 5119 1.524165 CCCGTCAAACCACCAACGA 60.524 57.895 0.00 0.00 37.31 3.85
1551 5139 1.532794 GAATGGTGGTGGGGTTGCA 60.533 57.895 0.00 0.00 0.00 4.08
1617 5205 4.082245 CAGTTTCTTGTCAAGGTTGGTGTT 60.082 41.667 12.66 0.00 0.00 3.32
1980 5610 2.684374 CCGCATGATCAAGAACCATGAA 59.316 45.455 0.00 0.00 39.86 2.57
2031 5661 5.497474 CAGGTACTTACTTGGCTACCAAAT 58.503 41.667 0.03 0.00 39.26 2.32
2434 6071 3.755905 TCAAACAGTCAATGTGTGTGTGT 59.244 39.130 0.00 0.00 45.95 3.72
2435 6072 3.763097 AACAGTCAATGTGTGTGTGTG 57.237 42.857 0.00 0.00 43.00 3.82
2438 6075 2.871633 CAGTCAATGTGTGTGTGTGCTA 59.128 45.455 0.00 0.00 0.00 3.49
2623 6262 0.463474 GCTGGCAGGAGGATGAGAAC 60.463 60.000 17.64 0.00 0.00 3.01
2670 6321 1.069668 AGCGGGGTGGTATCGTAATTC 59.930 52.381 0.00 0.00 0.00 2.17
2919 6683 6.710278 TCTGAAGATTTGGATATGACACACA 58.290 36.000 0.00 0.00 0.00 3.72
2943 6707 2.153645 TGAGTTTAGTCACGTAGGCGA 58.846 47.619 0.00 0.00 42.00 5.54
3253 7056 8.218488 AGAAAAATTCTCCTACACTTACCAACT 58.782 33.333 0.00 0.00 34.07 3.16
3278 7081 2.680577 CCAATTGCTTGCAAGAACCTC 58.319 47.619 30.39 12.13 0.00 3.85
3460 7305 3.624777 CACCATTCAACTTCCATAGCCT 58.375 45.455 0.00 0.00 0.00 4.58
3461 7306 4.019174 CACCATTCAACTTCCATAGCCTT 58.981 43.478 0.00 0.00 0.00 4.35
3462 7307 4.019174 ACCATTCAACTTCCATAGCCTTG 58.981 43.478 0.00 0.00 0.00 3.61
3463 7308 3.181483 CCATTCAACTTCCATAGCCTTGC 60.181 47.826 0.00 0.00 0.00 4.01
3464 7309 3.439857 TTCAACTTCCATAGCCTTGCT 57.560 42.857 0.00 0.00 43.41 3.91
3465 7310 2.715046 TCAACTTCCATAGCCTTGCTG 58.285 47.619 0.00 0.00 40.10 4.41
3466 7311 1.747355 CAACTTCCATAGCCTTGCTGG 59.253 52.381 0.00 0.00 40.10 4.85
3475 7320 2.759114 CCTTGCTGGCAGGAGGAA 59.241 61.111 19.57 0.00 0.00 3.36
3476 7321 1.378250 CCTTGCTGGCAGGAGGAAG 60.378 63.158 19.57 9.35 40.21 3.46
3477 7322 1.681666 CTTGCTGGCAGGAGGAAGA 59.318 57.895 17.64 0.00 42.42 2.87
3478 7323 0.392729 CTTGCTGGCAGGAGGAAGAG 60.393 60.000 17.64 3.24 42.42 2.85
3479 7324 1.845627 TTGCTGGCAGGAGGAAGAGG 61.846 60.000 17.64 0.00 0.00 3.69
3480 7325 1.992277 GCTGGCAGGAGGAAGAGGA 60.992 63.158 17.64 0.00 0.00 3.71
3481 7326 1.904032 CTGGCAGGAGGAAGAGGAC 59.096 63.158 6.61 0.00 0.00 3.85
3499 7345 5.544176 AGAGGACTTGAATCTGGTTGTCTTA 59.456 40.000 0.00 0.00 0.00 2.10
3511 7357 6.061441 TCTGGTTGTCTTATGTGTTTGATGT 58.939 36.000 0.00 0.00 0.00 3.06
3708 7558 6.593382 TGTGAGAAAAACTTCAAACAAATGGG 59.407 34.615 0.00 0.00 0.00 4.00
3756 7615 2.427812 CTCCGAAAGTCCCCTTCTACTC 59.572 54.545 0.00 0.00 0.00 2.59
4029 7910 6.324770 TGTTCATTAGAGAGCATATGAGGTCA 59.675 38.462 6.97 0.00 38.44 4.02
4091 7977 3.941573 TGATGTGATGCTATGTGTGTGT 58.058 40.909 0.00 0.00 0.00 3.72
4099 7985 5.243507 TGATGCTATGTGTGTGTTCCATTTT 59.756 36.000 0.00 0.00 0.00 1.82
4101 7987 4.826733 TGCTATGTGTGTGTTCCATTTTCT 59.173 37.500 0.00 0.00 0.00 2.52
4120 8006 7.639113 TTTTCTGTTTATGTTGGAGTCTTGT 57.361 32.000 0.00 0.00 0.00 3.16
4126 8012 6.605594 TGTTTATGTTGGAGTCTTGTCCTTTT 59.394 34.615 0.00 0.00 37.52 2.27
4414 8994 5.298026 TGGATTTTCTGTCACGAACAAATCA 59.702 36.000 14.51 5.06 35.61 2.57
4416 8996 6.695278 GGATTTTCTGTCACGAACAAATCAAA 59.305 34.615 14.51 6.15 35.61 2.69
4423 9003 3.002862 TCACGAACAAATCAAAGAACCGG 59.997 43.478 0.00 0.00 0.00 5.28
4426 9006 1.314730 ACAAATCAAAGAACCGGCGT 58.685 45.000 6.01 0.00 0.00 5.68
4493 9073 7.962964 TCTAGAAAATATAGTTTGATGGCCG 57.037 36.000 2.34 0.00 0.00 6.13
4497 9077 4.431416 AATATAGTTTGATGGCCGTGGA 57.569 40.909 0.00 0.00 0.00 4.02
4529 9109 4.332819 GCGACATAAAGTGCTTTGTATCCT 59.667 41.667 7.38 0.00 34.23 3.24
4537 9117 2.673368 GTGCTTTGTATCCTGAGAACGG 59.327 50.000 0.00 0.00 0.00 4.44
4594 9174 3.937706 CACTTCAAGCAATAGGGAGACTG 59.062 47.826 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.891451 TCTCGTGTATCATGTTCCACTAAG 58.109 41.667 0.00 0.00 0.00 2.18
29 30 5.447144 GCACAAACATGCATAATCTCGTGTA 60.447 40.000 0.00 0.00 45.39 2.90
39 40 0.525311 CCACCGCACAAACATGCATA 59.475 50.000 0.00 0.00 46.47 3.14
93 94 6.692486 AGAAATAATGGCTAGACGATACCAG 58.308 40.000 0.00 0.00 35.20 4.00
101 102 7.604545 GGGTTCAGATAGAAATAATGGCTAGAC 59.395 40.741 0.00 0.00 38.13 2.59
195 197 6.907212 CGTGTTCTAGGAAAATGTCATATTGC 59.093 38.462 0.00 0.00 0.00 3.56
210 212 4.175787 ACTAACTCTTGCGTGTTCTAGG 57.824 45.455 0.00 0.00 0.00 3.02
261 264 4.678509 TTTTTGCGAGACATGTCATACC 57.321 40.909 27.02 12.63 0.00 2.73
555 602 3.266510 TCTTACGGCATGATGCTCTTT 57.733 42.857 17.84 1.90 44.28 2.52
565 612 2.170607 AGTACAAGGCATCTTACGGCAT 59.829 45.455 0.00 0.00 0.00 4.40
576 623 2.441750 GGGGATGGATTAGTACAAGGCA 59.558 50.000 0.00 0.00 0.00 4.75
577 624 2.224793 GGGGGATGGATTAGTACAAGGC 60.225 54.545 0.00 0.00 0.00 4.35
650 697 5.277857 AGACAAGGATATGAGTAAACCGG 57.722 43.478 0.00 0.00 0.00 5.28
678 735 4.112634 GACTGAGCATTACGCACATTAGA 58.887 43.478 0.00 0.00 46.13 2.10
757 815 1.966451 CAAACTCGGGAGGTGTGCC 60.966 63.158 0.00 0.00 0.00 5.01
786 845 0.248289 GTGGCCACGAGTTAAGCCTA 59.752 55.000 22.49 0.00 45.94 3.93
878 4452 5.404466 TTGATGAAAAAGGTGGGCAATAG 57.596 39.130 0.00 0.00 0.00 1.73
879 4453 5.483231 TCATTGATGAAAAAGGTGGGCAATA 59.517 36.000 0.00 0.00 33.08 1.90
880 4454 4.286549 TCATTGATGAAAAAGGTGGGCAAT 59.713 37.500 0.00 0.00 33.08 3.56
881 4455 3.645212 TCATTGATGAAAAAGGTGGGCAA 59.355 39.130 0.00 0.00 33.08 4.52
882 4456 3.006752 GTCATTGATGAAAAAGGTGGGCA 59.993 43.478 0.00 0.00 38.75 5.36
1014 4597 3.453717 TGGTCTCGCTCTACCTACTCTTA 59.546 47.826 0.00 0.00 36.67 2.10
1081 4666 5.221641 TGACTTCTTCCTCGGAGAAATTCAA 60.222 40.000 6.58 0.00 34.09 2.69
1116 4701 1.347707 TCCTCACCTTCAAGAATGCGT 59.652 47.619 0.00 0.00 0.00 5.24
1125 4710 1.536073 CCGTCTGCTCCTCACCTTCA 61.536 60.000 0.00 0.00 0.00 3.02
1262 4850 1.753073 GGAACTCCTTGGCATTCCATG 59.247 52.381 11.08 0.00 43.05 3.66
1370 4958 2.361230 GCCGGGCTAGGTTGCTTT 60.361 61.111 12.87 0.00 0.00 3.51
1420 5008 0.119155 ACCTCCTCCACCATCTTCCA 59.881 55.000 0.00 0.00 0.00 3.53
1519 5107 1.133606 ACCATTCCTCGTTGGTGGTTT 60.134 47.619 6.66 0.00 44.49 3.27
1528 5116 2.602676 CCCCACCACCATTCCTCGT 61.603 63.158 0.00 0.00 0.00 4.18
1531 5119 1.464722 CAACCCCACCACCATTCCT 59.535 57.895 0.00 0.00 0.00 3.36
1551 5139 2.357517 CCCTGCTGTTCGTTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
1617 5205 3.399181 GTGCCAGATCCCCGGACA 61.399 66.667 0.73 0.00 0.00 4.02
2031 5661 3.072944 GGCATTGCATAAAGCCAACAAA 58.927 40.909 11.39 0.00 46.26 2.83
2434 6071 3.243704 GCCACAAGGTGTTTTCATTAGCA 60.244 43.478 0.00 0.00 37.19 3.49
2435 6072 3.005791 AGCCACAAGGTGTTTTCATTAGC 59.994 43.478 0.00 0.00 37.19 3.09
2438 6075 3.457610 CAGCCACAAGGTGTTTTCATT 57.542 42.857 0.00 0.00 39.23 2.57
2507 6146 5.396213 CCCTTCTTGGTGTTCAAATTTTCCA 60.396 40.000 0.00 0.00 34.56 3.53
2623 6262 7.625828 AGAAAGGAAAGGTAACCATTATTCG 57.374 36.000 0.00 0.00 37.17 3.34
2670 6321 8.419442 CCTTATGGGTTTTAGGTACTACTAGTG 58.581 40.741 5.39 0.00 42.67 2.74
2777 6515 8.839310 TTTCTTTTGTTCCATTTGTTTGAAGA 57.161 26.923 0.00 0.00 0.00 2.87
2919 6683 4.304939 GCCTACGTGACTAAACTCAACTT 58.695 43.478 0.00 0.00 0.00 2.66
3253 7056 2.915349 TCTTGCAAGCAATTGGCAAAA 58.085 38.095 21.99 6.07 45.78 2.44
3371 7183 3.760151 TCTTGGCATTGATGTTCTCCTTG 59.240 43.478 0.00 0.00 0.00 3.61
3460 7305 1.681666 CTCTTCCTCCTGCCAGCAA 59.318 57.895 0.00 0.00 0.00 3.91
3461 7306 2.296365 CCTCTTCCTCCTGCCAGCA 61.296 63.158 0.00 0.00 0.00 4.41
3462 7307 1.992277 TCCTCTTCCTCCTGCCAGC 60.992 63.158 0.00 0.00 0.00 4.85
3463 7308 0.617249 AGTCCTCTTCCTCCTGCCAG 60.617 60.000 0.00 0.00 0.00 4.85
3464 7309 0.178891 AAGTCCTCTTCCTCCTGCCA 60.179 55.000 0.00 0.00 0.00 4.92
3465 7310 0.251634 CAAGTCCTCTTCCTCCTGCC 59.748 60.000 0.00 0.00 0.00 4.85
3466 7311 1.270907 TCAAGTCCTCTTCCTCCTGC 58.729 55.000 0.00 0.00 0.00 4.85
3467 7312 3.774216 AGATTCAAGTCCTCTTCCTCCTG 59.226 47.826 0.00 0.00 0.00 3.86
3468 7313 3.774216 CAGATTCAAGTCCTCTTCCTCCT 59.226 47.826 0.00 0.00 0.00 3.69
3469 7314 3.118445 CCAGATTCAAGTCCTCTTCCTCC 60.118 52.174 0.00 0.00 0.00 4.30
3470 7315 3.517500 ACCAGATTCAAGTCCTCTTCCTC 59.482 47.826 0.00 0.00 0.00 3.71
3471 7316 3.525862 ACCAGATTCAAGTCCTCTTCCT 58.474 45.455 0.00 0.00 0.00 3.36
3472 7317 3.990959 ACCAGATTCAAGTCCTCTTCC 57.009 47.619 0.00 0.00 0.00 3.46
3473 7318 4.646572 ACAACCAGATTCAAGTCCTCTTC 58.353 43.478 0.00 0.00 0.00 2.87
3474 7319 4.349342 AGACAACCAGATTCAAGTCCTCTT 59.651 41.667 0.00 0.00 0.00 2.85
3475 7320 3.906846 AGACAACCAGATTCAAGTCCTCT 59.093 43.478 0.00 0.00 0.00 3.69
3476 7321 4.278975 AGACAACCAGATTCAAGTCCTC 57.721 45.455 0.00 0.00 0.00 3.71
3477 7322 4.713792 AAGACAACCAGATTCAAGTCCT 57.286 40.909 0.00 0.00 0.00 3.85
3478 7323 5.940470 ACATAAGACAACCAGATTCAAGTCC 59.060 40.000 0.00 0.00 0.00 3.85
3479 7324 6.428159 ACACATAAGACAACCAGATTCAAGTC 59.572 38.462 0.00 0.00 0.00 3.01
3480 7325 6.299141 ACACATAAGACAACCAGATTCAAGT 58.701 36.000 0.00 0.00 0.00 3.16
3481 7326 6.808008 ACACATAAGACAACCAGATTCAAG 57.192 37.500 0.00 0.00 0.00 3.02
3499 7345 7.990917 TGTTGTTGTAGTTACATCAAACACAT 58.009 30.769 14.17 0.00 43.44 3.21
3511 7357 5.437946 TCACCACCATTGTTGTTGTAGTTA 58.562 37.500 0.00 0.00 0.00 2.24
3725 7584 3.512680 GGACTTTCGGAGTACACATCAG 58.487 50.000 0.00 0.00 39.20 2.90
4091 7977 7.505585 AGACTCCAACATAAACAGAAAATGGAA 59.494 33.333 0.00 0.00 35.46 3.53
4099 7985 5.071788 AGGACAAGACTCCAACATAAACAGA 59.928 40.000 0.00 0.00 31.94 3.41
4101 7987 5.304686 AGGACAAGACTCCAACATAAACA 57.695 39.130 0.00 0.00 31.94 2.83
4147 8033 5.357257 ACTAAACTCAACTCGTGTGTCATT 58.643 37.500 0.00 0.00 32.80 2.57
4398 8978 4.970003 GGTTCTTTGATTTGTTCGTGACAG 59.030 41.667 0.00 0.00 39.94 3.51
4423 9003 1.356938 GCTGTACCTAGTTGGAACGC 58.643 55.000 0.00 0.00 39.71 4.84
4426 9006 0.248289 GCGGCTGTACCTAGTTGGAA 59.752 55.000 0.00 0.00 39.71 3.53
4433 9013 2.574929 CCGTTGCGGCTGTACCTA 59.425 61.111 0.00 0.00 41.17 3.08
4467 9047 8.836413 CGGCCATCAAACTATATTTTCTAGAAA 58.164 33.333 13.99 13.99 0.00 2.52
4493 9073 0.389948 ATGTCGCGTTCTTCCTCCAC 60.390 55.000 5.77 0.00 0.00 4.02
4497 9077 2.993899 CACTTTATGTCGCGTTCTTCCT 59.006 45.455 5.77 0.00 0.00 3.36
4529 9109 0.038526 GTTTCTCCTCGCCGTTCTCA 60.039 55.000 0.00 0.00 0.00 3.27
4537 9117 1.807573 CCTGCTCGTTTCTCCTCGC 60.808 63.158 0.00 0.00 0.00 5.03
4570 9150 2.019984 CTCCCTATTGCTTGAAGTGCC 58.980 52.381 0.00 0.00 0.00 5.01
4571 9151 2.680339 GTCTCCCTATTGCTTGAAGTGC 59.320 50.000 0.00 0.00 0.00 4.40
4594 9174 2.043227 CACTTCCTCTCCCTATGGTCC 58.957 57.143 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.