Multiple sequence alignment - TraesCS2B01G295300

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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 TraesCS2B01G295300 chr2B 100.000 4394 0 0 1 4394 412398666 412403059 0.000000e+00 8115.0
1 TraesCS2B01G295300 chr2A 92.156 2078 76 33 1753 3781 460900439 460902478 0.000000e+00 2854.0
2 TraesCS2B01G295300 chr2A 87.910 1373 79 39 404 1727 460899104 460900438 0.000000e+00 1535.0
3 TraesCS2B01G295300 chr2A 97.305 334 9 0 4061 4394 460902883 460903216 6.380000e-158 568.0
4 TraesCS2B01G295300 chr2D 92.000 1700 80 11 712 2400 346574558 346576212 0.000000e+00 2335.0
5 TraesCS2B01G295300 chr2D 93.357 1385 54 21 2418 3781 346576284 346577651 0.000000e+00 2013.0
6 TraesCS2B01G295300 chr2D 88.005 742 30 28 1 713 346573822 346574533 0.000000e+00 822.0
7 TraesCS2B01G295300 chr2D 96.447 394 13 1 4002 4394 346578267 346578660 0.000000e+00 649.0
8 TraesCS2B01G295300 chr7D 89.674 1104 93 8 2406 3504 91679601 91678514 0.000000e+00 1387.0
9 TraesCS2B01G295300 chr7D 89.306 346 29 3 1960 2305 91681370 91681033 1.130000e-115 427.0
10 TraesCS2B01G295300 chr7D 90.164 61 3 2 779 837 91690492 91690433 4.710000e-10 76.8
11 TraesCS2B01G295300 chr7A 87.438 1218 113 29 2303 3506 93252478 93251287 0.000000e+00 1365.0
12 TraesCS2B01G295300 chr7A 83.072 319 34 6 1765 2071 93253161 93252851 5.600000e-69 272.0
13 TraesCS2B01G295300 chr7B 88.305 1103 108 11 2407 3504 43249060 43250146 0.000000e+00 1303.0
14 TraesCS2B01G295300 chr7B 84.679 483 55 3 1750 2221 43247524 43247998 8.610000e-127 464.0
15 TraesCS2B01G295300 chr7B 87.671 73 3 3 2230 2302 43248297 43248363 3.640000e-11 80.5
16 TraesCS2B01G295300 chr5D 86.179 738 86 8 2682 3403 543586797 543586060 0.000000e+00 784.0
17 TraesCS2B01G295300 chr5D 89.888 178 11 2 1979 2149 543587260 543587083 5.720000e-54 222.0
18 TraesCS2B01G295300 chr5A 88.933 506 53 2 2613 3118 9593706 9593204 4.830000e-174 621.0
19 TraesCS2B01G295300 chr5A 88.660 388 35 7 3122 3504 9590239 9589856 8.610000e-127 464.0
20 TraesCS2B01G295300 chr5A 86.500 400 44 8 1910 2305 9595523 9595130 8.730000e-117 431.0
21 TraesCS2B01G295300 chr5A 82.353 340 35 11 2303 2627 9594544 9594215 5.600000e-69 272.0


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 TraesCS2B01G295300 chr2B 412398666 412403059 4393 False 8115.000000 8115 100.00000 1 4394 1 chr2B.!!$F1 4393
1 TraesCS2B01G295300 chr2A 460899104 460903216 4112 False 1652.333333 2854 92.45700 404 4394 3 chr2A.!!$F1 3990
2 TraesCS2B01G295300 chr2D 346573822 346578660 4838 False 1454.750000 2335 92.45225 1 4394 4 chr2D.!!$F1 4393
3 TraesCS2B01G295300 chr7D 91678514 91681370 2856 True 907.000000 1387 89.49000 1960 3504 2 chr7D.!!$R2 1544
4 TraesCS2B01G295300 chr7A 93251287 93253161 1874 True 818.500000 1365 85.25500 1765 3506 2 chr7A.!!$R1 1741
5 TraesCS2B01G295300 chr7B 43247524 43250146 2622 False 615.833333 1303 86.88500 1750 3504 3 chr7B.!!$F1 1754
6 TraesCS2B01G295300 chr5D 543586060 543587260 1200 True 503.000000 784 88.03350 1979 3403 2 chr5D.!!$R1 1424
7 TraesCS2B01G295300 chr5A 9589856 9595523 5667 True 447.000000 621 86.61150 1910 3504 4 chr5A.!!$R1 1594

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
647 687 0.317269 CTTTTCACACACTGCTGCGG 60.317 55.0 6.98 6.98 0.00 5.69 F
1565 1653 0.033504 AATAGGTCGCGCATACCTGG 59.966 55.0 31.54 5.83 46.90 4.45 F
2514 4319 0.764890 TGGTCCTGGAGTGAAAGGTG 59.235 55.0 0.00 0.00 34.94 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1711 0.698238 TGTTTGGGATCCAGGAGTGG 59.302 55.0 15.23 0.0 46.63 4.00 R
3303 8617 0.443869 CATCGCTCAACGGGAACTTG 59.556 55.0 0.00 0.0 43.89 3.16 R
3893 9519 0.391263 GGACAAGGCGGAGTACAAGG 60.391 60.0 0.00 0.0 0.00 3.61 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
199 202 2.897972 ACGCGAGTAATCCCCACC 59.102 61.111 15.93 0.00 46.88 4.61
200 203 2.108362 CGCGAGTAATCCCCACCC 59.892 66.667 0.00 0.00 0.00 4.61
201 204 2.509422 GCGAGTAATCCCCACCCC 59.491 66.667 0.00 0.00 0.00 4.95
202 205 2.372074 GCGAGTAATCCCCACCCCA 61.372 63.158 0.00 0.00 0.00 4.96
243 246 4.484537 ACTGATGATCTGAACAGAAGGG 57.515 45.455 8.59 0.48 41.36 3.95
244 247 4.099633 ACTGATGATCTGAACAGAAGGGA 58.900 43.478 8.59 0.00 41.36 4.20
245 248 4.081198 ACTGATGATCTGAACAGAAGGGAC 60.081 45.833 8.59 1.79 41.36 4.46
246 249 3.840078 TGATGATCTGAACAGAAGGGACA 59.160 43.478 8.59 5.41 41.36 4.02
247 250 3.685139 TGATCTGAACAGAAGGGACAC 57.315 47.619 8.59 0.00 41.36 3.67
248 251 2.972021 TGATCTGAACAGAAGGGACACA 59.028 45.455 8.59 0.00 41.36 3.72
249 252 3.390967 TGATCTGAACAGAAGGGACACAA 59.609 43.478 8.59 0.00 41.36 3.33
250 253 3.924114 TCTGAACAGAAGGGACACAAA 57.076 42.857 1.79 0.00 33.91 2.83
251 254 4.437682 TCTGAACAGAAGGGACACAAAT 57.562 40.909 1.79 0.00 33.91 2.32
252 255 4.136796 TCTGAACAGAAGGGACACAAATG 58.863 43.478 1.79 0.00 33.91 2.32
253 256 4.136796 CTGAACAGAAGGGACACAAATGA 58.863 43.478 0.00 0.00 0.00 2.57
254 257 4.136796 TGAACAGAAGGGACACAAATGAG 58.863 43.478 0.00 0.00 0.00 2.90
255 258 4.141505 TGAACAGAAGGGACACAAATGAGA 60.142 41.667 0.00 0.00 0.00 3.27
261 264 2.304180 AGGGACACAAATGAGAGACCAG 59.696 50.000 0.00 0.00 0.00 4.00
312 315 2.386661 AGACCAACCGCTACATCTTG 57.613 50.000 0.00 0.00 0.00 3.02
322 325 4.631813 ACCGCTACATCTTGTCTCATTTTC 59.368 41.667 0.00 0.00 0.00 2.29
494 497 0.450583 GGAGGGCCGTTTCGAATTTC 59.549 55.000 0.00 0.00 0.00 2.17
505 508 4.026804 CGTTTCGAATTTCCCGACAGATAG 60.027 45.833 0.00 0.00 35.61 2.08
565 576 2.049156 TCGAGGTGCGCAGACAAG 60.049 61.111 12.22 5.38 40.61 3.16
570 581 2.661866 GTGCGCAGACAAGGACGT 60.662 61.111 12.22 0.00 0.00 4.34
593 604 2.754995 GGCCTTAGCTTCGCACAGC 61.755 63.158 0.00 0.00 40.44 4.40
647 687 0.317269 CTTTTCACACACTGCTGCGG 60.317 55.000 6.98 6.98 0.00 5.69
750 818 4.282703 GCCTTCTAGAACCAACCCGATATA 59.717 45.833 0.00 0.00 0.00 0.86
760 828 4.278956 CCGATATAACGGCCCAGC 57.721 61.111 8.63 0.00 46.20 4.85
879 947 1.555533 GTACCCCAAGAACCAGAGAGG 59.444 57.143 0.00 0.00 45.67 3.69
918 986 3.469970 ATCTCCGGCCACGCATCA 61.470 61.111 2.24 0.00 39.22 3.07
1011 1079 4.900704 CATCCCATGGCCACCCCG 62.901 72.222 8.16 0.00 35.87 5.73
1095 1163 5.417811 GGCCTCAAGGTAAAGAGTTACTAC 58.582 45.833 0.00 0.00 39.73 2.73
1096 1164 5.187381 GGCCTCAAGGTAAAGAGTTACTACT 59.813 44.000 0.00 0.00 39.73 2.57
1097 1165 6.379417 GGCCTCAAGGTAAAGAGTTACTACTA 59.621 42.308 0.00 0.00 39.73 1.82
1111 1179 0.243095 CTACTATTCGGGGTAGCGGC 59.757 60.000 0.00 0.00 30.80 6.53
1132 1200 3.803555 CTCGAAGCTTGTTAGTTTGCTG 58.196 45.455 2.10 0.00 35.79 4.41
1150 1218 4.228567 TGTGTTCTGGTCGGCGCA 62.229 61.111 10.83 0.00 0.00 6.09
1163 1231 1.934463 GGCGCACGAGATTGGTATG 59.066 57.895 10.83 0.00 0.00 2.39
1388 1472 1.911293 TTGCTCTAGCGGCTTTTGCG 61.911 55.000 8.26 0.00 45.83 4.85
1415 1499 4.515404 GTGATGGGCACTCGGTAC 57.485 61.111 0.00 0.00 44.27 3.34
1429 1513 6.087522 GCACTCGGTACTTGTATGATCTATC 58.912 44.000 0.00 0.00 0.00 2.08
1435 1519 8.039538 TCGGTACTTGTATGATCTATCGAGTAT 58.960 37.037 11.70 0.00 0.00 2.12
1436 1520 8.329583 CGGTACTTGTATGATCTATCGAGTATC 58.670 40.741 11.70 10.77 0.00 2.24
1446 1530 5.769484 TCTATCGAGTATCTTGGTGGTTC 57.231 43.478 0.00 0.00 0.00 3.62
1447 1531 5.446860 TCTATCGAGTATCTTGGTGGTTCT 58.553 41.667 0.00 0.00 0.00 3.01
1480 1568 6.145209 GTGATGTGTTGCACTAGCTAGATATG 59.855 42.308 27.45 15.71 42.74 1.78
1517 1605 3.263261 GTCTACTTGGCTTTAGGAGTGC 58.737 50.000 0.00 0.00 0.00 4.40
1536 1624 5.853936 AGTGCTTAAGATGTGTTACAGTGA 58.146 37.500 6.67 0.00 0.00 3.41
1565 1653 0.033504 AATAGGTCGCGCATACCTGG 59.966 55.000 31.54 5.83 46.90 4.45
1591 1679 2.174349 GCTCGGAAAAGCACTGCG 59.826 61.111 0.00 0.00 42.05 5.18
1627 1715 3.164024 TGACCCATGAGTCACCACT 57.836 52.632 5.87 0.00 41.78 4.00
1731 1820 2.937149 GGAAAAGCACCGGAGATACTTC 59.063 50.000 9.46 5.88 0.00 3.01
1740 1829 5.234543 GCACCGGAGATACTTCTTGTAAATC 59.765 44.000 9.46 0.00 34.45 2.17
1741 1830 5.753921 CACCGGAGATACTTCTTGTAAATCC 59.246 44.000 9.46 0.00 36.90 3.01
1872 1971 4.773510 GCTTGATGCTTATACCGCTTAAC 58.226 43.478 0.00 0.00 38.95 2.01
1999 2111 7.673641 ACCTGTGATTCTGAAATCTCTCTAT 57.326 36.000 0.00 0.00 41.63 1.98
2204 2326 7.226325 GGATGCTAGCCATTATCTATCAATCAC 59.774 40.741 13.29 0.00 33.29 3.06
2212 2334 7.981789 GCCATTATCTATCAATCACGGATTCTA 59.018 37.037 0.00 0.00 28.87 2.10
2228 2350 5.454755 CGGATTCTATTTGGAGGCTTCCTAA 60.455 44.000 16.82 15.18 44.36 2.69
2297 2709 8.099364 ACGTTATTTGATCATGTCTGTCTTTT 57.901 30.769 0.00 0.00 0.00 2.27
2298 2710 8.230486 ACGTTATTTGATCATGTCTGTCTTTTC 58.770 33.333 0.00 0.00 0.00 2.29
2514 4319 0.764890 TGGTCCTGGAGTGAAAGGTG 59.235 55.000 0.00 0.00 34.94 4.00
3104 5451 2.029073 CGGTGTCAGCTGGTCGTT 59.971 61.111 15.13 0.00 0.00 3.85
3303 8617 0.809385 TGAAGACGGTGATCGACTCC 59.191 55.000 0.00 0.00 42.45 3.85
3321 8635 0.673644 CCAAGTTCCCGTTGAGCGAT 60.674 55.000 0.00 0.00 44.77 4.58
3409 8723 3.845178 AGCTGATCGTCGTCAATGTTTA 58.155 40.909 0.00 0.00 0.00 2.01
3410 8724 4.433615 AGCTGATCGTCGTCAATGTTTAT 58.566 39.130 0.00 0.00 0.00 1.40
3411 8725 4.870426 AGCTGATCGTCGTCAATGTTTATT 59.130 37.500 0.00 0.00 0.00 1.40
3412 8726 6.040247 AGCTGATCGTCGTCAATGTTTATTA 58.960 36.000 0.00 0.00 0.00 0.98
3413 8727 6.019801 AGCTGATCGTCGTCAATGTTTATTAC 60.020 38.462 0.00 0.00 0.00 1.89
3415 8729 7.166970 GCTGATCGTCGTCAATGTTTATTACTA 59.833 37.037 0.00 0.00 0.00 1.82
3454 8771 3.071580 GCATACAGACAGTGGAGGC 57.928 57.895 0.00 0.00 40.26 4.70
3531 8852 6.456988 GGGTGATGTTCGTTTATTCAGCTTAG 60.457 42.308 0.00 0.00 0.00 2.18
3535 8856 8.817100 TGATGTTCGTTTATTCAGCTTAGTATG 58.183 33.333 0.00 0.00 0.00 2.39
3551 8898 8.200792 AGCTTAGTATGTTTATTGGACAGAGAG 58.799 37.037 0.00 0.00 0.00 3.20
3636 8983 0.800631 TCGCTCTTTGCTGATGCTTG 59.199 50.000 0.00 0.00 40.48 4.01
3673 9020 3.431415 AGTACTGCAGTGGTCATCTGTA 58.569 45.455 29.57 1.60 35.60 2.74
3674 9021 3.832490 AGTACTGCAGTGGTCATCTGTAA 59.168 43.478 29.57 1.01 35.60 2.41
3675 9022 3.325293 ACTGCAGTGGTCATCTGTAAG 57.675 47.619 20.97 0.00 35.60 2.34
3676 9023 2.634940 ACTGCAGTGGTCATCTGTAAGT 59.365 45.455 20.97 0.00 35.60 2.24
3677 9024 2.998670 CTGCAGTGGTCATCTGTAAGTG 59.001 50.000 5.25 0.00 35.60 3.16
3678 9025 2.632512 TGCAGTGGTCATCTGTAAGTGA 59.367 45.455 0.00 0.00 35.60 3.41
3679 9026 3.261643 TGCAGTGGTCATCTGTAAGTGAT 59.738 43.478 0.00 0.00 35.60 3.06
3680 9027 3.868077 GCAGTGGTCATCTGTAAGTGATC 59.132 47.826 0.00 0.00 35.60 2.92
3681 9028 4.382470 GCAGTGGTCATCTGTAAGTGATCT 60.382 45.833 0.00 0.00 35.60 2.75
3686 9033 4.383552 GGTCATCTGTAAGTGATCTTGGCT 60.384 45.833 0.00 0.00 35.36 4.75
3697 9044 5.669477 AGTGATCTTGGCTAGAATTCAGAC 58.331 41.667 8.44 6.05 36.22 3.51
3758 9106 4.363991 ACCTCTGCAGAAGAACAAATCT 57.636 40.909 19.22 0.00 41.32 2.40
3790 9175 4.017126 ACCCTAAAGCAGACCAAATTAGC 58.983 43.478 0.00 0.00 0.00 3.09
3813 9198 5.507985 GCAAGTTCAATTCTAAAGCACAGGT 60.508 40.000 0.00 0.00 0.00 4.00
3845 9232 5.240844 CCATTTAGTCGTTCCCAGAAAAAGT 59.759 40.000 0.00 0.00 0.00 2.66
3852 9239 3.129638 CGTTCCCAGAAAAAGTGGTTTGA 59.870 43.478 0.00 0.00 32.62 2.69
3857 9244 4.503643 CCCAGAAAAAGTGGTTTGATGCAT 60.504 41.667 0.00 0.00 32.62 3.96
3865 9252 9.949174 AAAAAGTGGTTTGATGCATTAATTTTC 57.051 25.926 4.56 0.00 0.00 2.29
3873 9498 8.924691 GTTTGATGCATTAATTTTCAGCAACTA 58.075 29.630 4.56 0.77 38.85 2.24
3888 9514 7.624360 TCAGCAACTATAAACAATTACCCAG 57.376 36.000 0.00 0.00 0.00 4.45
3893 9519 4.887655 ACTATAAACAATTACCCAGCCAGC 59.112 41.667 0.00 0.00 0.00 4.85
3905 9592 2.820037 GCCAGCCTTGTACTCCGC 60.820 66.667 0.00 0.00 0.00 5.54
3911 9598 1.019805 GCCTTGTACTCCGCCTTGTC 61.020 60.000 0.00 0.00 0.00 3.18
3913 9600 0.320374 CTTGTACTCCGCCTTGTCCA 59.680 55.000 0.00 0.00 0.00 4.02
3921 9608 0.322456 CCGCCTTGTCCAAATCAGGA 60.322 55.000 0.00 0.00 34.64 3.86
3924 9611 2.681976 CGCCTTGTCCAAATCAGGAGAT 60.682 50.000 0.00 0.00 38.64 2.75
3927 9614 4.853007 CCTTGTCCAAATCAGGAGATCTT 58.147 43.478 0.00 0.00 38.64 2.40
3928 9615 5.259632 CCTTGTCCAAATCAGGAGATCTTT 58.740 41.667 0.00 0.00 38.64 2.52
3929 9616 5.356470 CCTTGTCCAAATCAGGAGATCTTTC 59.644 44.000 0.00 0.00 38.64 2.62
3934 9623 8.163408 TGTCCAAATCAGGAGATCTTTCTTAAA 58.837 33.333 0.00 0.00 38.64 1.52
3935 9624 9.183368 GTCCAAATCAGGAGATCTTTCTTAAAT 57.817 33.333 0.00 0.00 38.64 1.40
3936 9625 9.759473 TCCAAATCAGGAGATCTTTCTTAAATT 57.241 29.630 0.00 0.00 31.90 1.82
3985 9674 7.854557 CTGACATCAGATTTTAGATTGTGGA 57.145 36.000 2.51 0.00 46.59 4.02
3987 9676 8.044060 TGACATCAGATTTTAGATTGTGGAAC 57.956 34.615 0.00 0.00 37.35 3.62
4049 9802 3.115554 GCGACAACATAATTTGCCATCC 58.884 45.455 0.00 0.00 0.00 3.51
4058 9811 2.028561 ATTTGCCATCCCAGGTGTTT 57.971 45.000 0.00 0.00 0.00 2.83
4075 9828 4.389687 GGTGTTTGATTTGCCATGCTAAAG 59.610 41.667 0.00 0.00 0.00 1.85
4088 9841 5.346822 GCCATGCTAAAGAAAACTGATGTTG 59.653 40.000 0.00 0.00 36.39 3.33
4091 9844 6.899393 TGCTAAAGAAAACTGATGTTGGAT 57.101 33.333 0.00 0.00 36.39 3.41
4210 9963 9.826574 TCTACAATTAGTAACCAATATCACCAC 57.173 33.333 0.00 0.00 30.92 4.16
4241 9994 1.269257 GCCACAAAACAAGGAGAGCAC 60.269 52.381 0.00 0.00 0.00 4.40
4279 10032 2.943345 GCTGACAACGACCGCACAG 61.943 63.158 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 157 5.576774 TCATATGAGTAGCAGTTTCAACACG 59.423 40.000 0.00 0.00 0.00 4.49
157 160 5.582269 TGCTCATATGAGTAGCAGTTTCAAC 59.418 40.000 28.92 11.59 41.15 3.18
198 201 1.212935 CCTCTGGTACAAAGGATGGGG 59.787 57.143 0.00 0.00 38.70 4.96
199 202 1.916181 ACCTCTGGTACAAAGGATGGG 59.084 52.381 12.79 5.47 38.70 4.00
200 203 2.571653 TGACCTCTGGTACAAAGGATGG 59.428 50.000 12.79 7.33 38.70 3.51
201 204 3.981071 TGACCTCTGGTACAAAGGATG 57.019 47.619 12.79 0.00 38.70 3.51
202 205 3.910627 AGTTGACCTCTGGTACAAAGGAT 59.089 43.478 12.79 0.26 38.70 3.24
243 246 5.106396 CCATTTCTGGTCTCTCATTTGTGTC 60.106 44.000 0.00 0.00 37.79 3.67
244 247 4.763793 CCATTTCTGGTCTCTCATTTGTGT 59.236 41.667 0.00 0.00 37.79 3.72
245 248 5.005740 TCCATTTCTGGTCTCTCATTTGTG 58.994 41.667 0.00 0.00 43.61 3.33
246 249 5.006386 GTCCATTTCTGGTCTCTCATTTGT 58.994 41.667 0.00 0.00 43.61 2.83
247 250 5.251764 AGTCCATTTCTGGTCTCTCATTTG 58.748 41.667 0.00 0.00 43.61 2.32
248 251 5.511386 AGTCCATTTCTGGTCTCTCATTT 57.489 39.130 0.00 0.00 43.61 2.32
249 252 5.222007 ACAAGTCCATTTCTGGTCTCTCATT 60.222 40.000 0.00 0.00 39.61 2.57
250 253 4.288105 ACAAGTCCATTTCTGGTCTCTCAT 59.712 41.667 0.00 0.00 39.61 2.90
251 254 3.648067 ACAAGTCCATTTCTGGTCTCTCA 59.352 43.478 0.00 0.00 39.61 3.27
252 255 4.278975 ACAAGTCCATTTCTGGTCTCTC 57.721 45.455 0.00 0.00 39.61 3.20
253 256 4.322049 CGTACAAGTCCATTTCTGGTCTCT 60.322 45.833 0.00 0.00 39.61 3.10
254 257 3.927142 CGTACAAGTCCATTTCTGGTCTC 59.073 47.826 0.00 0.00 39.61 3.36
255 258 3.323979 ACGTACAAGTCCATTTCTGGTCT 59.676 43.478 0.00 0.00 41.91 3.85
261 264 5.178809 AGCTGTTTACGTACAAGTCCATTTC 59.821 40.000 0.00 0.00 0.00 2.17
312 315 4.412207 GCCGGTGTATTTGAAAATGAGAC 58.588 43.478 1.90 0.00 0.00 3.36
322 325 1.433837 GCGTAGGGCCGGTGTATTTG 61.434 60.000 1.90 0.00 34.80 2.32
357 360 7.171508 CGCTTCATAATCAGAATTGGCTAACTA 59.828 37.037 0.00 0.00 0.00 2.24
494 497 3.751698 TGATCGTGTATCTATCTGTCGGG 59.248 47.826 0.00 0.00 35.45 5.14
505 508 0.527600 TGCGTGCCTGATCGTGTATC 60.528 55.000 0.00 0.00 34.93 2.24
548 551 2.049156 CTTGTCTGCGCACCTCGA 60.049 61.111 5.66 0.00 41.67 4.04
549 552 3.114616 CCTTGTCTGCGCACCTCG 61.115 66.667 5.66 0.00 42.12 4.63
551 554 2.031163 GTCCTTGTCTGCGCACCT 59.969 61.111 5.66 0.00 0.00 4.00
553 556 0.736325 ATACGTCCTTGTCTGCGCAC 60.736 55.000 5.66 0.00 0.00 5.34
554 557 0.735978 CATACGTCCTTGTCTGCGCA 60.736 55.000 10.98 10.98 0.00 6.09
555 558 1.999051 CATACGTCCTTGTCTGCGC 59.001 57.895 0.00 0.00 0.00 6.09
556 559 1.999051 GCATACGTCCTTGTCTGCG 59.001 57.895 0.00 0.00 33.22 5.18
565 576 1.954651 GCTAAGGCCGCATACGTCC 60.955 63.158 0.00 0.00 37.67 4.79
570 581 4.750460 CGAAGCTAAGGCCGCATA 57.250 55.556 0.00 0.00 39.73 3.14
611 651 4.424566 GCGGTCGTAGCGTTCCCA 62.425 66.667 7.94 0.00 41.74 4.37
624 664 0.748005 AGCAGTGTGTGAAAAGCGGT 60.748 50.000 0.00 0.00 0.00 5.68
783 851 1.423921 AGGAATCCTGGGTTTTGACGT 59.576 47.619 0.00 0.00 29.57 4.34
879 947 2.123033 AGGGGTTGGGTTGGTTGC 60.123 61.111 0.00 0.00 0.00 4.17
918 986 0.588252 CTGTTTGCGTGTGCTTAGCT 59.412 50.000 5.60 0.00 43.34 3.32
1095 1163 1.289380 GAGCCGCTACCCCGAATAG 59.711 63.158 0.00 0.00 0.00 1.73
1096 1164 2.558286 CGAGCCGCTACCCCGAATA 61.558 63.158 0.00 0.00 0.00 1.75
1097 1165 3.912907 CGAGCCGCTACCCCGAAT 61.913 66.667 0.00 0.00 0.00 3.34
1111 1179 3.248602 ACAGCAAACTAACAAGCTTCGAG 59.751 43.478 0.00 0.00 34.61 4.04
1132 1200 3.712881 GCGCCGACCAGAACACAC 61.713 66.667 0.00 0.00 0.00 3.82
1150 1218 2.939640 GCACCAACCATACCAATCTCGT 60.940 50.000 0.00 0.00 0.00 4.18
1163 1231 3.131046 CCAAATCATCCTTAGCACCAACC 59.869 47.826 0.00 0.00 0.00 3.77
1245 1326 2.292587 ACCAAGGTGTTCCCAGGAAAAA 60.293 45.455 0.00 0.00 35.75 1.94
1246 1327 1.289530 ACCAAGGTGTTCCCAGGAAAA 59.710 47.619 0.00 0.00 35.75 2.29
1247 1328 0.930726 ACCAAGGTGTTCCCAGGAAA 59.069 50.000 0.00 0.00 35.75 3.13
1248 1329 0.184933 CACCAAGGTGTTCCCAGGAA 59.815 55.000 11.08 0.00 40.91 3.36
1249 1330 1.715019 CCACCAAGGTGTTCCCAGGA 61.715 60.000 17.36 0.00 44.02 3.86
1250 1331 1.228552 CCACCAAGGTGTTCCCAGG 60.229 63.158 17.36 0.00 44.02 4.45
1251 1332 0.250901 CTCCACCAAGGTGTTCCCAG 60.251 60.000 17.36 1.97 44.02 4.45
1252 1333 0.696143 TCTCCACCAAGGTGTTCCCA 60.696 55.000 17.36 0.00 44.02 4.37
1253 1334 0.698818 ATCTCCACCAAGGTGTTCCC 59.301 55.000 17.36 0.00 44.02 3.97
1254 1335 1.676014 CGATCTCCACCAAGGTGTTCC 60.676 57.143 17.36 2.31 44.02 3.62
1259 1340 1.194781 ACTGCGATCTCCACCAAGGT 61.195 55.000 0.00 0.00 39.02 3.50
1321 1405 4.399934 AGCTAGCTACTTGACTACTTGTCC 59.600 45.833 17.69 0.00 44.75 4.02
1429 1513 5.050490 CCATAAGAACCACCAAGATACTCG 58.950 45.833 0.00 0.00 0.00 4.18
1435 1519 2.714250 ACCACCATAAGAACCACCAAGA 59.286 45.455 0.00 0.00 0.00 3.02
1436 1520 2.819608 CACCACCATAAGAACCACCAAG 59.180 50.000 0.00 0.00 0.00 3.61
1439 1523 2.871096 TCACCACCATAAGAACCACC 57.129 50.000 0.00 0.00 0.00 4.61
1446 1530 2.819019 TGCAACACATCACCACCATAAG 59.181 45.455 0.00 0.00 0.00 1.73
1447 1531 2.556189 GTGCAACACATCACCACCATAA 59.444 45.455 0.00 0.00 36.32 1.90
1480 1568 5.616488 AGTAGACACGAGAAAGAGAGAAC 57.384 43.478 0.00 0.00 0.00 3.01
1536 1624 6.613755 ATGCGCGACCTATTTAACTAATTT 57.386 33.333 12.10 0.00 0.00 1.82
1565 1653 1.401539 GCTTTTCCGAGCATCCAACAC 60.402 52.381 0.00 0.00 42.25 3.32
1591 1679 6.451393 TGGGTCACAATACAAAAACTATTGC 58.549 36.000 0.00 0.00 35.72 3.56
1623 1711 0.698238 TGTTTGGGATCCAGGAGTGG 59.302 55.000 15.23 0.00 46.63 4.00
1627 1715 3.181445 CGGAATATGTTTGGGATCCAGGA 60.181 47.826 15.23 0.00 33.81 3.86
1696 1784 5.183904 GGTGCTTTTCCAATCATCTAACACT 59.816 40.000 0.00 0.00 0.00 3.55
1747 1836 6.774656 ACTGACTTGGTCATCTCAATCTTTTT 59.225 34.615 0.71 0.00 41.94 1.94
1748 1837 6.302269 ACTGACTTGGTCATCTCAATCTTTT 58.698 36.000 0.71 0.00 41.94 2.27
1999 2111 1.340017 GGGGACTTCTACATGCTGCAA 60.340 52.381 6.36 0.00 0.00 4.08
2204 2326 3.142174 GGAAGCCTCCAAATAGAATCCG 58.858 50.000 0.00 0.00 41.96 4.18
2212 2334 4.888626 AGGAATTAGGAAGCCTCCAAAT 57.111 40.909 3.68 0.00 45.24 2.32
2228 2350 7.659390 GTGCTATTTTGCTCTCTACATAGGAAT 59.341 37.037 0.00 0.00 0.00 3.01
2297 2709 8.621532 AGAACAAAATAACATAGCAAGACTGA 57.378 30.769 0.00 0.00 0.00 3.41
2298 2710 9.334693 GAAGAACAAAATAACATAGCAAGACTG 57.665 33.333 0.00 0.00 0.00 3.51
2519 4324 0.736325 CGACGACTTGATCACCCACC 60.736 60.000 0.00 0.00 0.00 4.61
2664 5001 6.441274 AGACATTGTCACATTAACAAGCTTG 58.559 36.000 24.84 24.84 39.78 4.01
2670 5007 6.183360 ACAGCAAAGACATTGTCACATTAACA 60.183 34.615 18.57 0.00 41.32 2.41
3303 8617 0.443869 CATCGCTCAACGGGAACTTG 59.556 55.000 0.00 0.00 43.89 3.16
3412 8726 8.591072 TGCAAGTTCTTTGGTAATACTAGTAGT 58.409 33.333 8.85 8.47 37.26 2.73
3413 8727 8.997621 TGCAAGTTCTTTGGTAATACTAGTAG 57.002 34.615 8.85 0.00 37.26 2.57
3415 8729 9.379791 GTATGCAAGTTCTTTGGTAATACTAGT 57.620 33.333 0.00 0.00 37.26 2.57
3431 8745 3.557898 CCTCCACTGTCTGTATGCAAGTT 60.558 47.826 0.00 0.00 0.00 2.66
3535 8856 7.334421 TGCAACTTATCTCTCTGTCCAATAAAC 59.666 37.037 0.00 0.00 0.00 2.01
3539 8860 5.426689 TGCAACTTATCTCTCTGTCCAAT 57.573 39.130 0.00 0.00 0.00 3.16
3540 8861 4.890158 TGCAACTTATCTCTCTGTCCAA 57.110 40.909 0.00 0.00 0.00 3.53
3542 8863 6.560253 TTTTTGCAACTTATCTCTCTGTCC 57.440 37.500 0.00 0.00 0.00 4.02
3598 8945 3.669557 GCGAACCGTATTTTTGACAGCAT 60.670 43.478 0.00 0.00 0.00 3.79
3636 8983 2.148768 GTACTTGGTAGTGGTTGCACC 58.851 52.381 0.00 0.00 39.22 5.01
3647 8994 2.321719 TGACCACTGCAGTACTTGGTA 58.678 47.619 22.71 11.25 42.60 3.25
3650 8997 2.998670 CAGATGACCACTGCAGTACTTG 59.001 50.000 21.20 10.93 0.00 3.16
3655 9002 2.634940 ACTTACAGATGACCACTGCAGT 59.365 45.455 15.25 15.25 38.74 4.40
3673 9020 6.070309 AGTCTGAATTCTAGCCAAGATCACTT 60.070 38.462 7.05 0.00 33.05 3.16
3674 9021 5.424895 AGTCTGAATTCTAGCCAAGATCACT 59.575 40.000 7.05 0.00 33.05 3.41
3675 9022 5.669477 AGTCTGAATTCTAGCCAAGATCAC 58.331 41.667 7.05 0.00 33.05 3.06
3676 9023 5.423290 TGAGTCTGAATTCTAGCCAAGATCA 59.577 40.000 7.05 3.92 33.05 2.92
3677 9024 5.752955 GTGAGTCTGAATTCTAGCCAAGATC 59.247 44.000 7.05 0.00 33.05 2.75
3678 9025 5.396213 GGTGAGTCTGAATTCTAGCCAAGAT 60.396 44.000 7.05 0.00 33.05 2.40
3679 9026 4.081420 GGTGAGTCTGAATTCTAGCCAAGA 60.081 45.833 7.05 0.00 0.00 3.02
3680 9027 4.081198 AGGTGAGTCTGAATTCTAGCCAAG 60.081 45.833 7.05 0.00 0.00 3.61
3681 9028 3.840666 AGGTGAGTCTGAATTCTAGCCAA 59.159 43.478 7.05 0.00 0.00 4.52
3686 9033 6.672266 AACTGAAGGTGAGTCTGAATTCTA 57.328 37.500 7.05 0.00 0.00 2.10
3697 9044 4.390297 GGATCGAGAAAAACTGAAGGTGAG 59.610 45.833 0.00 0.00 0.00 3.51
3758 9106 6.385759 TGGTCTGCTTTAGGGTCTCAATATAA 59.614 38.462 0.00 0.00 0.00 0.98
3763 9111 2.334977 TGGTCTGCTTTAGGGTCTCAA 58.665 47.619 0.00 0.00 0.00 3.02
3769 9117 4.016444 TGCTAATTTGGTCTGCTTTAGGG 58.984 43.478 0.00 0.00 0.00 3.53
3772 9120 6.264292 TGAACTTGCTAATTTGGTCTGCTTTA 59.736 34.615 0.00 0.00 0.00 1.85
3790 9175 6.076981 ACCTGTGCTTTAGAATTGAACTTG 57.923 37.500 0.00 0.00 0.00 3.16
3813 9198 4.439057 GGAACGACTAAATGGCATCAGTA 58.561 43.478 13.01 1.12 0.00 2.74
3845 9232 6.228995 TGCTGAAAATTAATGCATCAAACCA 58.771 32.000 0.00 0.00 0.00 3.67
3865 9252 6.265577 GCTGGGTAATTGTTTATAGTTGCTG 58.734 40.000 0.00 0.00 0.00 4.41
3873 9498 3.031013 GGCTGGCTGGGTAATTGTTTAT 58.969 45.455 0.00 0.00 0.00 1.40
3888 9514 2.820037 GCGGAGTACAAGGCTGGC 60.820 66.667 0.00 0.00 0.00 4.85
3893 9519 0.391263 GGACAAGGCGGAGTACAAGG 60.391 60.000 0.00 0.00 0.00 3.61
3905 9592 4.500499 AGATCTCCTGATTTGGACAAGG 57.500 45.455 0.00 0.00 32.19 3.61
3961 9650 7.854557 TCCACAATCTAAAATCTGATGTCAG 57.145 36.000 3.61 3.61 45.08 3.51
4024 9777 2.413502 GGCAAATTATGTTGTCGCGTGA 60.414 45.455 5.77 0.00 0.00 4.35
4028 9781 3.115554 GGATGGCAAATTATGTTGTCGC 58.884 45.455 0.00 0.00 35.83 5.19
4030 9783 4.441913 CCTGGGATGGCAAATTATGTTGTC 60.442 45.833 0.00 0.00 33.59 3.18
4049 9802 2.690786 CATGGCAAATCAAACACCTGG 58.309 47.619 0.00 0.00 0.00 4.45
4058 9811 5.927689 CAGTTTTCTTTAGCATGGCAAATCA 59.072 36.000 0.00 0.00 0.00 2.57
4075 9828 8.816640 ATGTTACAAATCCAACATCAGTTTTC 57.183 30.769 0.00 0.00 40.47 2.29
4210 9963 2.204237 GTTTTGTGGCAAGGAAAGCAG 58.796 47.619 0.00 0.00 0.00 4.24
4241 9994 5.527214 TCAGCGTATTCAGGTCATAAATTGG 59.473 40.000 0.00 0.00 0.00 3.16
4279 10032 1.668151 GTGTCGTGAGCTGGGTTCC 60.668 63.158 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.