Multiple sequence alignment - TraesCS3B01G517200

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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 TraesCS3B01G517200 chr3B 100.000 3026 0 0 1 3026 760333333 760336358 0.000000e+00 5589
1 TraesCS3B01G517200 chr3B 84.030 1052 118 24 994 2002 760304657 760305701 0.000000e+00 966
2 TraesCS3B01G517200 chr2B 94.645 1027 51 4 2003 3026 14539546 14538521 0.000000e+00 1589
3 TraesCS3B01G517200 chr2B 94.558 1029 52 4 2001 3026 14521710 14520683 0.000000e+00 1587
4 TraesCS3B01G517200 chr2B 93.611 1033 55 5 2001 3026 632159676 632160704 0.000000e+00 1531
5 TraesCS3B01G517200 chr2B 90.997 1033 77 13 2002 3026 770053445 770052421 0.000000e+00 1378
6 TraesCS3B01G517200 chr1B 93.191 1028 64 6 2003 3026 604102398 604101373 0.000000e+00 1506
7 TraesCS3B01G517200 chr1B 88.505 983 83 12 1 976 543598950 543597991 0.000000e+00 1162
8 TraesCS3B01G517200 chr5B 92.480 1024 67 8 2009 3026 277793386 277794405 0.000000e+00 1456
9 TraesCS3B01G517200 chr5A 92.278 1023 74 5 2007 3026 114933573 114932553 0.000000e+00 1447
10 TraesCS3B01G517200 chr7A 91.165 1030 80 9 2003 3026 163359453 163358429 0.000000e+00 1387
11 TraesCS3B01G517200 chrUn 89.778 1037 81 17 2003 3026 23901883 23902907 0.000000e+00 1304
12 TraesCS3B01G517200 chrUn 85.599 618 69 10 989 1597 33036972 33036366 5.510000e-177 630
13 TraesCS3B01G517200 chrUn 89.199 287 31 0 1593 1879 33034319 33034033 2.870000e-95 359
14 TraesCS3B01G517200 chr1D 86.579 991 102 17 1 976 21640172 21641146 0.000000e+00 1064
15 TraesCS3B01G517200 chr3A 85.564 762 83 7 1252 2002 705117004 705117749 0.000000e+00 773


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 TraesCS3B01G517200 chr3B 760333333 760336358 3025 False 5589.0 5589 100.000 1 3026 1 chr3B.!!$F2 3025
1 TraesCS3B01G517200 chr3B 760304657 760305701 1044 False 966.0 966 84.030 994 2002 1 chr3B.!!$F1 1008
2 TraesCS3B01G517200 chr2B 14538521 14539546 1025 True 1589.0 1589 94.645 2003 3026 1 chr2B.!!$R2 1023
3 TraesCS3B01G517200 chr2B 14520683 14521710 1027 True 1587.0 1587 94.558 2001 3026 1 chr2B.!!$R1 1025
4 TraesCS3B01G517200 chr2B 632159676 632160704 1028 False 1531.0 1531 93.611 2001 3026 1 chr2B.!!$F1 1025
5 TraesCS3B01G517200 chr2B 770052421 770053445 1024 True 1378.0 1378 90.997 2002 3026 1 chr2B.!!$R3 1024
6 TraesCS3B01G517200 chr1B 604101373 604102398 1025 True 1506.0 1506 93.191 2003 3026 1 chr1B.!!$R2 1023
7 TraesCS3B01G517200 chr1B 543597991 543598950 959 True 1162.0 1162 88.505 1 976 1 chr1B.!!$R1 975
8 TraesCS3B01G517200 chr5B 277793386 277794405 1019 False 1456.0 1456 92.480 2009 3026 1 chr5B.!!$F1 1017
9 TraesCS3B01G517200 chr5A 114932553 114933573 1020 True 1447.0 1447 92.278 2007 3026 1 chr5A.!!$R1 1019
10 TraesCS3B01G517200 chr7A 163358429 163359453 1024 True 1387.0 1387 91.165 2003 3026 1 chr7A.!!$R1 1023
11 TraesCS3B01G517200 chrUn 23901883 23902907 1024 False 1304.0 1304 89.778 2003 3026 1 chrUn.!!$F1 1023
12 TraesCS3B01G517200 chrUn 33034033 33036972 2939 True 494.5 630 87.399 989 1879 2 chrUn.!!$R1 890
13 TraesCS3B01G517200 chr1D 21640172 21641146 974 False 1064.0 1064 86.579 1 976 1 chr1D.!!$F1 975
14 TraesCS3B01G517200 chr3A 705117004 705117749 745 False 773.0 773 85.564 1252 2002 1 chr3A.!!$F1 750

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
978 993 0.10576 GGGAGAGGAGAGCCATCAGA 60.106 60.0 0.0 0.0 36.29 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 4382 0.250901 TGGCAAAGCTCCTTGAGGTC 60.251 55.0 2.23 0.0 39.62 3.85 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
30 31 1.518352 CGATCCATGGCAACGACGA 60.518 57.895 6.96 0.00 42.51 4.20
35 36 4.673298 ATGGCAACGACGACCGCA 62.673 61.111 0.00 0.00 43.32 5.69
74 75 4.880426 GGGGGAGGGGATCTGCGA 62.880 72.222 0.00 0.00 34.34 5.10
113 114 0.671251 GGGAGCGACGAAGATCTGAT 59.329 55.000 0.00 0.00 0.00 2.90
163 165 2.957060 GGGACCCTTGCTAACCAAC 58.043 57.895 2.09 0.00 0.00 3.77
177 179 0.679960 ACCAACATAAAGCCGGAGCC 60.680 55.000 5.05 0.00 41.25 4.70
289 291 4.034410 GAGGGGGAAAGTCACTAGAAGAT 58.966 47.826 0.00 0.00 0.00 2.40
344 346 1.920835 GAGGAGGCCAGAGTGGGTT 60.921 63.158 5.01 0.00 38.19 4.11
375 377 0.250234 CCACAAGCCTCTTGATCGGA 59.750 55.000 12.89 0.00 0.00 4.55
490 493 0.939106 GCAAGACAAACGCGCCAAAT 60.939 50.000 5.73 0.00 0.00 2.32
571 575 1.671054 CGGCTCCACCAACGAACAT 60.671 57.895 0.00 0.00 39.03 2.71
799 805 2.672098 GAGCCAGATCCAAGAGTAGGA 58.328 52.381 0.00 0.00 39.97 2.94
802 808 2.691241 GCCAGATCCAAGAGTAGGAGGA 60.691 54.545 0.00 0.00 38.83 3.71
821 833 4.767892 AAGGAGGGGAGCAGGGGG 62.768 72.222 0.00 0.00 0.00 5.40
838 850 1.457831 GGGTAGGGGAGCATCGAGT 60.458 63.158 0.00 0.00 34.37 4.18
842 854 1.944896 TAGGGGAGCATCGAGTGGGA 61.945 60.000 0.00 0.00 34.37 4.37
846 858 1.330655 GGAGCATCGAGTGGGAAGGA 61.331 60.000 0.00 0.00 34.37 3.36
847 859 0.755686 GAGCATCGAGTGGGAAGGAT 59.244 55.000 0.00 0.00 0.00 3.24
889 901 2.683933 GAGAGGAAGTGGGGGCGA 60.684 66.667 0.00 0.00 0.00 5.54
932 947 2.449322 CAGGGAGGATGGGGAGGG 60.449 72.222 0.00 0.00 0.00 4.30
933 948 4.523282 AGGGAGGATGGGGAGGGC 62.523 72.222 0.00 0.00 0.00 5.19
976 991 1.074926 GGGGAGAGGAGAGCCATCA 60.075 63.158 0.00 0.00 36.29 3.07
977 992 1.120795 GGGGAGAGGAGAGCCATCAG 61.121 65.000 0.00 0.00 36.29 2.90
978 993 0.105760 GGGAGAGGAGAGCCATCAGA 60.106 60.000 0.00 0.00 36.29 3.27
979 994 1.482930 GGGAGAGGAGAGCCATCAGAT 60.483 57.143 0.00 0.00 36.29 2.90
980 995 2.225242 GGGAGAGGAGAGCCATCAGATA 60.225 54.545 0.00 0.00 36.29 1.98
981 996 3.091545 GGAGAGGAGAGCCATCAGATAG 58.908 54.545 0.00 0.00 36.29 2.08
982 997 2.493278 GAGAGGAGAGCCATCAGATAGC 59.507 54.545 0.00 0.00 36.29 2.97
983 998 1.202114 GAGGAGAGCCATCAGATAGCG 59.798 57.143 0.00 0.00 36.29 4.26
984 999 0.965439 GGAGAGCCATCAGATAGCGT 59.035 55.000 0.00 0.00 0.00 5.07
985 1000 1.067915 GGAGAGCCATCAGATAGCGTC 60.068 57.143 0.00 0.00 0.00 5.19
986 1001 0.965439 AGAGCCATCAGATAGCGTCC 59.035 55.000 0.00 0.00 0.00 4.79
987 1002 0.965439 GAGCCATCAGATAGCGTCCT 59.035 55.000 0.00 0.00 0.00 3.85
988 1003 1.342819 GAGCCATCAGATAGCGTCCTT 59.657 52.381 0.00 0.00 0.00 3.36
989 1004 1.342819 AGCCATCAGATAGCGTCCTTC 59.657 52.381 0.00 0.00 0.00 3.46
990 1005 1.606737 GCCATCAGATAGCGTCCTTCC 60.607 57.143 0.00 0.00 0.00 3.46
991 1006 1.967066 CCATCAGATAGCGTCCTTCCT 59.033 52.381 0.00 0.00 0.00 3.36
992 1007 3.157881 CCATCAGATAGCGTCCTTCCTA 58.842 50.000 0.00 0.00 0.00 2.94
1034 1049 7.103641 AGTCACTTGTTCGTGGAAACATATAT 58.896 34.615 0.00 0.00 46.14 0.86
1035 1050 8.255206 AGTCACTTGTTCGTGGAAACATATATA 58.745 33.333 0.00 0.00 46.14 0.86
1036 1051 8.540492 GTCACTTGTTCGTGGAAACATATATAG 58.460 37.037 0.00 0.00 46.14 1.31
1037 1052 8.255206 TCACTTGTTCGTGGAAACATATATAGT 58.745 33.333 0.00 0.00 46.14 2.12
1038 1053 9.524106 CACTTGTTCGTGGAAACATATATAGTA 57.476 33.333 0.00 0.00 46.14 1.82
1045 1060 9.293404 TCGTGGAAACATATATAGTAAGTAGCT 57.707 33.333 0.00 0.00 46.14 3.32
1063 1095 3.287222 AGCTACAAACAAGAAACCAGCA 58.713 40.909 0.00 0.00 0.00 4.41
1064 1096 3.316308 AGCTACAAACAAGAAACCAGCAG 59.684 43.478 0.00 0.00 0.00 4.24
1103 1135 6.358178 TCCATGCATGCCAAATTAATCAATT 58.642 32.000 21.69 0.00 35.84 2.32
1106 1138 7.040755 CCATGCATGCCAAATTAATCAATTCAT 60.041 33.333 21.69 0.00 33.09 2.57
1107 1139 7.252965 TGCATGCCAAATTAATCAATTCATG 57.747 32.000 16.68 10.64 37.16 3.07
1108 1140 6.140110 GCATGCCAAATTAATCAATTCATGC 58.860 36.000 6.36 18.19 44.20 4.06
1109 1141 6.238511 GCATGCCAAATTAATCAATTCATGCA 60.239 34.615 23.09 7.74 46.49 3.96
1116 1148 6.645790 ATTAATCAATTCATGCAGGAGGAC 57.354 37.500 0.00 0.00 0.00 3.85
1140 1172 2.954989 AGACGATCTGATCAGCAAGCTA 59.045 45.455 18.36 0.00 0.00 3.32
1162 1194 4.410492 CCTGACGAGGTTCTTTTCAATG 57.590 45.455 0.00 0.00 34.16 2.82
1250 1282 1.352622 ATCCCCGCTATGCTCCCAAA 61.353 55.000 0.00 0.00 0.00 3.28
1254 1286 1.392589 CCGCTATGCTCCCAAACATT 58.607 50.000 0.00 0.00 0.00 2.71
1289 1321 1.172180 TCCTTCAAGCCAAAGCACCG 61.172 55.000 0.00 0.00 43.56 4.94
1297 1335 1.449601 CCAAAGCACCGCCGTAGAT 60.450 57.895 0.00 0.00 0.00 1.98
1318 1356 1.254954 GGAGTTGGGACACGAGTACT 58.745 55.000 0.00 0.00 39.29 2.73
1319 1357 1.617357 GGAGTTGGGACACGAGTACTT 59.383 52.381 0.00 0.00 39.29 2.24
1388 1426 1.043116 ATGATCGGAGCAACTCGGGA 61.043 55.000 0.00 0.00 32.74 5.14
1391 1429 1.949847 ATCGGAGCAACTCGGGACAG 61.950 60.000 0.00 0.00 32.74 3.51
1396 1434 2.425592 CAACTCGGGACAGTGCCA 59.574 61.111 12.28 0.00 0.00 4.92
1402 1448 1.820906 CGGGACAGTGCCATCATGG 60.821 63.158 12.28 0.00 41.55 3.66
1413 1459 1.145598 CATCATGGTCGGAGCAGCT 59.854 57.895 15.69 0.00 0.00 4.24
1422 1476 1.300775 CGGAGCAGCTAGGAGCATG 60.301 63.158 0.00 0.00 45.56 4.06
1428 1482 2.030262 GCTAGGAGCATGCTCGGG 59.970 66.667 34.96 27.27 43.59 5.14
1429 1483 2.502492 GCTAGGAGCATGCTCGGGA 61.502 63.158 34.96 23.27 43.59 5.14
1430 1484 1.825281 GCTAGGAGCATGCTCGGGAT 61.825 60.000 34.96 24.21 43.59 3.85
1437 1491 2.481952 GAGCATGCTCGGGATGAATAAC 59.518 50.000 30.64 5.18 33.06 1.89
1465 1519 0.179145 CCTTTACGCCATCGACGTCT 60.179 55.000 14.70 0.00 43.88 4.18
1469 1523 2.202703 TACGCCATCGACGTCTTGCA 62.203 55.000 14.70 0.00 43.88 4.08
1473 1527 0.172578 CCATCGACGTCTTGCACCTA 59.827 55.000 14.70 0.00 0.00 3.08
1477 1531 0.803117 CGACGTCTTGCACCTAGAGA 59.197 55.000 14.70 0.00 0.00 3.10
1489 1543 2.148702 ACCTAGAGATCTACCTGGGCT 58.851 52.381 12.26 0.00 34.78 5.19
1506 1560 1.270358 GGCTACCATTCCGTCTCCATC 60.270 57.143 0.00 0.00 0.00 3.51
1511 1565 2.808206 ATTCCGTCTCCATCGGCCC 61.808 63.158 0.00 0.00 46.49 5.80
1543 1597 1.971167 GCCATGGCAACGGACAAGA 60.971 57.895 32.08 0.00 41.49 3.02
1545 1599 1.176527 CCATGGCAACGGACAAGATT 58.823 50.000 0.00 0.00 34.11 2.40
1651 3756 1.666553 TCATTCGTCGGCGCTTGTT 60.667 52.632 3.52 0.00 38.14 2.83
1686 3799 1.591703 CCTCGTGCACCTCAAGCTA 59.408 57.895 12.15 0.00 0.00 3.32
1688 3801 1.073216 CTCGTGCACCTCAAGCTACG 61.073 60.000 12.15 0.00 37.63 3.51
1741 3860 0.671781 GATCCTGAGCACGTGCAAGT 60.672 55.000 39.21 21.79 45.16 3.16
1747 3866 4.988486 GCACGTGCAAGTGGCTGC 62.988 66.667 34.52 14.86 45.15 5.25
1759 3878 1.072806 AGTGGCTGCAGTTTCTCATGA 59.927 47.619 16.64 0.00 0.00 3.07
1851 3975 0.668401 TCGACTGCGACTACGACAGA 60.668 55.000 15.91 0.00 42.51 3.41
1854 3978 0.797542 ACTGCGACTACGACAGAGTC 59.202 55.000 15.91 0.00 41.93 3.36
1872 3996 2.033141 GAGCTCAAGTGGCTGCCA 59.967 61.111 19.30 19.30 40.40 4.92
1905 4029 1.674322 CACCGTTTCCCGCTGGATT 60.674 57.895 0.00 0.00 41.40 3.01
1919 4043 0.911769 TGGATTTCTCCGCATGACCT 59.088 50.000 0.00 0.00 45.37 3.85
1953 4077 1.194781 ATGTCCCGTTGCTCAGGAGT 61.195 55.000 0.00 0.00 0.00 3.85
2058 4183 4.587262 TCTCGGGCCGCATGTATATATTAT 59.413 41.667 23.83 0.00 0.00 1.28
2240 4382 2.171448 CCAACACTCCCCCTCAATCTAG 59.829 54.545 0.00 0.00 0.00 2.43
2274 4416 5.538433 AGCTTTGCCAAGGTTAAGATTGTAA 59.462 36.000 0.00 0.00 37.46 2.41
2338 4480 3.254657 CCCATCTACGAGTTGATCTCCTC 59.745 52.174 0.00 0.00 39.84 3.71
2342 4485 1.479709 ACGAGTTGATCTCCTCTGGG 58.520 55.000 9.53 0.00 39.84 4.45
2374 4517 2.826128 TCTCCAGAAGCTTTCGAGCTAA 59.174 45.455 0.00 0.00 45.54 3.09
2408 4551 8.961294 TGACAAAATGGAAATCAACTTCAATT 57.039 26.923 0.00 0.00 31.45 2.32
2431 4574 8.983307 ATTTGTTTTGTTTGTGCATGAAAAAT 57.017 23.077 0.00 0.00 0.00 1.82
2499 4642 0.798776 CGCAGCCTGTGGAGTTTTAG 59.201 55.000 0.00 0.00 0.00 1.85
2539 4682 8.635765 AGTAATGTTTGTATCCACATCACTTT 57.364 30.769 0.00 0.00 28.84 2.66
2616 4759 0.040067 GGCCTGTTTTCTTGCACTCG 60.040 55.000 0.00 0.00 0.00 4.18
2646 4789 4.513406 AGGTTAGTTCCCAGAAACACAA 57.487 40.909 0.00 0.00 0.00 3.33
2757 4900 5.825593 AATGTTGAGACCAAGACCTTCTA 57.174 39.130 0.00 0.00 32.06 2.10
2811 4954 5.073311 TGCAGTCCAATGAGTAGTTCTAC 57.927 43.478 2.14 2.14 0.00 2.59
2992 5136 1.001378 GGTGTGTTAACTGGCTTGCAG 60.001 52.381 7.22 0.00 0.00 4.41
3000 5144 1.708341 ACTGGCTTGCAGTTTTCCAT 58.292 45.000 0.00 0.00 0.00 3.41
3021 5165 7.309091 TCCATTCCTACTCTCCTGAGAATATT 58.691 38.462 0.00 0.00 42.73 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.971357 TCTTTCTCTCTCCTTTGCGGT 59.029 47.619 0.00 0.00 0.00 5.68
35 36 3.837731 CTCCACCTCTTTCTCTCTCCTTT 59.162 47.826 0.00 0.00 0.00 3.11
74 75 2.737180 CACCGCATCCCGCTCTAT 59.263 61.111 0.00 0.00 39.08 1.98
113 114 1.825474 CTAGGGTTTCCTGCTTCTCGA 59.175 52.381 0.00 0.00 44.61 4.04
147 149 4.380550 GCTTTATGTTGGTTAGCAAGGGTC 60.381 45.833 0.00 0.00 0.00 4.46
156 158 2.361789 GCTCCGGCTTTATGTTGGTTA 58.638 47.619 0.00 0.00 35.22 2.85
161 163 1.451387 CGGGCTCCGGCTTTATGTT 60.451 57.895 0.00 0.00 44.15 2.71
253 255 1.221781 CCCCCTCTCTCTATTCTGGGT 59.778 57.143 0.00 0.00 33.13 4.51
375 377 2.093447 CGTCCAACCCTAGCTCTTGATT 60.093 50.000 0.00 0.00 0.00 2.57
380 382 2.711922 CGCGTCCAACCCTAGCTCT 61.712 63.158 0.00 0.00 0.00 4.09
465 468 2.966309 GCGTTTGTCTTGCTCCCCG 61.966 63.158 0.00 0.00 0.00 5.73
544 548 4.754667 GTGGAGCCGTTCGGGGAC 62.755 72.222 13.16 0.00 35.78 4.46
560 564 1.964373 GTCGGGCATGTTCGTTGGT 60.964 57.895 9.04 0.00 0.00 3.67
563 567 1.671054 CAGGTCGGGCATGTTCGTT 60.671 57.895 9.04 0.00 0.00 3.85
612 616 4.675029 CGTGGACGGCCGGTCTTT 62.675 66.667 31.76 7.71 45.35 2.52
799 805 1.614824 CTGCTCCCCTCCTTGTCCT 60.615 63.158 0.00 0.00 0.00 3.85
802 808 2.612115 CCCTGCTCCCCTCCTTGT 60.612 66.667 0.00 0.00 0.00 3.16
821 833 1.742768 CACTCGATGCTCCCCTACC 59.257 63.158 0.00 0.00 0.00 3.18
842 854 3.854669 CTCTCCGGCGCCATCCTT 61.855 66.667 28.98 0.00 0.00 3.36
846 858 3.854669 CTTCCTCTCCGGCGCCAT 61.855 66.667 28.98 0.00 0.00 4.40
916 931 4.523282 GCCCTCCCCATCCTCCCT 62.523 72.222 0.00 0.00 0.00 4.20
932 947 4.200283 CTCTCCCGTGCTCCTCGC 62.200 72.222 0.00 0.00 39.77 5.03
933 948 3.522731 CCTCTCCCGTGCTCCTCG 61.523 72.222 0.00 0.00 0.00 4.63
934 949 3.151022 CCCTCTCCCGTGCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
976 991 3.811454 GCTAGGTAGGAAGGACGCTATCT 60.811 52.174 0.00 0.00 0.00 1.98
977 992 2.488937 GCTAGGTAGGAAGGACGCTATC 59.511 54.545 0.00 0.00 0.00 2.08
978 993 2.516906 GCTAGGTAGGAAGGACGCTAT 58.483 52.381 0.00 0.00 0.00 2.97
979 994 1.478288 GGCTAGGTAGGAAGGACGCTA 60.478 57.143 0.00 0.00 0.00 4.26
980 995 0.756070 GGCTAGGTAGGAAGGACGCT 60.756 60.000 0.00 0.00 0.00 5.07
981 996 1.041447 TGGCTAGGTAGGAAGGACGC 61.041 60.000 0.00 0.00 0.00 5.19
982 997 1.341531 CATGGCTAGGTAGGAAGGACG 59.658 57.143 0.00 0.00 0.00 4.79
983 998 1.070914 GCATGGCTAGGTAGGAAGGAC 59.929 57.143 0.00 0.00 0.00 3.85
984 999 1.062121 AGCATGGCTAGGTAGGAAGGA 60.062 52.381 0.00 0.00 36.99 3.36
985 1000 1.071385 CAGCATGGCTAGGTAGGAAGG 59.929 57.143 0.00 0.00 36.40 3.46
986 1001 2.540265 CAGCATGGCTAGGTAGGAAG 57.460 55.000 0.00 0.00 36.40 3.46
1034 1049 8.423349 TGGTTTCTTGTTTGTAGCTACTTACTA 58.577 33.333 23.84 16.05 0.00 1.82
1035 1050 7.277396 TGGTTTCTTGTTTGTAGCTACTTACT 58.723 34.615 23.84 0.00 0.00 2.24
1036 1051 7.486802 TGGTTTCTTGTTTGTAGCTACTTAC 57.513 36.000 23.84 19.89 0.00 2.34
1037 1052 6.204108 GCTGGTTTCTTGTTTGTAGCTACTTA 59.796 38.462 23.84 9.97 0.00 2.24
1038 1053 5.008712 GCTGGTTTCTTGTTTGTAGCTACTT 59.991 40.000 23.84 0.00 0.00 2.24
1039 1054 4.515567 GCTGGTTTCTTGTTTGTAGCTACT 59.484 41.667 23.84 0.00 0.00 2.57
1045 1060 4.265893 TCACTGCTGGTTTCTTGTTTGTA 58.734 39.130 0.00 0.00 0.00 2.41
1048 1063 6.463995 TTAATCACTGCTGGTTTCTTGTTT 57.536 33.333 0.00 0.00 0.00 2.83
1063 1095 7.148373 GCATGCATGGAAAACAAATTAATCACT 60.148 33.333 27.34 0.00 0.00 3.41
1064 1096 6.962678 GCATGCATGGAAAACAAATTAATCAC 59.037 34.615 27.34 0.87 0.00 3.06
1103 1135 1.000359 TCTCCGTCCTCCTGCATGA 60.000 57.895 0.00 0.00 0.00 3.07
1106 1138 2.838748 ATCGTCTCCGTCCTCCTGCA 62.839 60.000 0.00 0.00 35.01 4.41
1107 1139 2.065906 GATCGTCTCCGTCCTCCTGC 62.066 65.000 0.00 0.00 35.01 4.85
1108 1140 0.464735 AGATCGTCTCCGTCCTCCTG 60.465 60.000 0.00 0.00 35.01 3.86
1109 1141 0.464735 CAGATCGTCTCCGTCCTCCT 60.465 60.000 0.00 0.00 35.01 3.69
1116 1148 0.665298 TGCTGATCAGATCGTCTCCG 59.335 55.000 27.04 0.00 0.00 4.63
1127 1159 1.134995 CGTCAGGTAGCTTGCTGATCA 60.135 52.381 5.26 0.00 0.00 2.92
1219 1251 2.286121 GGGGATCCACCTCCACCA 60.286 66.667 15.23 0.00 37.01 4.17
1228 1260 2.217038 GGAGCATAGCGGGGATCCA 61.217 63.158 15.23 0.00 39.36 3.41
1254 1286 1.182667 AGGAATCGACCGACATGACA 58.817 50.000 0.00 0.00 34.73 3.58
1289 1321 1.146263 CCCAACTCCCATCTACGGC 59.854 63.158 0.00 0.00 0.00 5.68
1293 1331 1.191535 CGTGTCCCAACTCCCATCTA 58.808 55.000 0.00 0.00 0.00 1.98
1297 1335 0.178955 TACTCGTGTCCCAACTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
1381 1419 1.267574 ATGATGGCACTGTCCCGAGT 61.268 55.000 0.00 0.00 0.00 4.18
1388 1426 1.078214 CCGACCATGATGGCACTGT 60.078 57.895 12.25 0.00 42.67 3.55
1391 1429 2.182842 GCTCCGACCATGATGGCAC 61.183 63.158 12.25 5.28 42.67 5.01
1396 1434 0.678395 CTAGCTGCTCCGACCATGAT 59.322 55.000 4.91 0.00 0.00 2.45
1402 1448 1.743321 ATGCTCCTAGCTGCTCCGAC 61.743 60.000 4.91 0.00 42.97 4.79
1413 1459 0.469892 TCATCCCGAGCATGCTCCTA 60.470 55.000 35.77 23.69 39.77 2.94
1422 1476 2.158957 TCTGGTGTTATTCATCCCGAGC 60.159 50.000 0.00 0.00 0.00 5.03
1428 1482 5.904362 AAAGGCTTCTGGTGTTATTCATC 57.096 39.130 0.00 0.00 0.00 2.92
1429 1483 5.354234 CGTAAAGGCTTCTGGTGTTATTCAT 59.646 40.000 0.00 0.00 0.00 2.57
1430 1484 4.693566 CGTAAAGGCTTCTGGTGTTATTCA 59.306 41.667 0.00 0.00 0.00 2.57
1437 1491 0.605319 TGGCGTAAAGGCTTCTGGTG 60.605 55.000 0.00 0.00 46.88 4.17
1465 1519 3.300388 CCAGGTAGATCTCTAGGTGCAA 58.700 50.000 0.00 0.00 0.00 4.08
1469 1523 2.148702 AGCCCAGGTAGATCTCTAGGT 58.851 52.381 0.00 0.00 0.00 3.08
1473 1527 1.860240 TGGTAGCCCAGGTAGATCTCT 59.140 52.381 0.00 0.00 35.17 3.10
1477 1531 2.339769 GGAATGGTAGCCCAGGTAGAT 58.660 52.381 0.00 0.00 46.15 1.98
1533 1587 1.882352 GCCAGACCAATCTTGTCCGTT 60.882 52.381 0.00 0.00 30.42 4.44
1555 1609 0.322546 GGGGCCAAGATCGTGAACTT 60.323 55.000 10.47 0.00 0.00 2.66
1570 1624 2.825264 CCAGATCTCCTTCGGGGC 59.175 66.667 0.00 0.00 35.37 5.80
1626 3731 2.882876 CCGACGAATGACCGGAGT 59.117 61.111 9.46 0.00 45.58 3.85
1635 3740 2.677003 CCAACAAGCGCCGACGAAT 61.677 57.895 2.29 0.00 43.93 3.34
1673 3786 2.028112 AGATTTCGTAGCTTGAGGTGCA 60.028 45.455 0.00 0.00 0.00 4.57
1676 3789 3.118956 CCTCAGATTTCGTAGCTTGAGGT 60.119 47.826 15.72 0.00 37.50 3.85
1686 3799 2.457598 TCTGGTAGCCTCAGATTTCGT 58.542 47.619 0.00 0.00 36.46 3.85
1688 3801 4.376146 GTCATCTGGTAGCCTCAGATTTC 58.624 47.826 10.23 4.93 46.33 2.17
1741 3860 2.089201 CATCATGAGAAACTGCAGCCA 58.911 47.619 15.27 4.73 0.00 4.75
1747 3866 5.625251 GCAGTTGTACATCATGAGAAACTG 58.375 41.667 22.02 22.02 43.60 3.16
1759 3878 2.092291 CCGCGTCGCAGTTGTACAT 61.092 57.895 18.75 0.00 0.00 2.29
1848 3972 0.735632 GCCACTTGAGCTCGACTCTG 60.736 60.000 9.64 0.00 46.41 3.35
1851 3975 1.291588 CAGCCACTTGAGCTCGACT 59.708 57.895 9.64 0.00 38.95 4.18
1854 3978 3.123620 GGCAGCCACTTGAGCTCG 61.124 66.667 6.55 0.00 38.95 5.03
1905 4029 1.296392 CACCAGGTCATGCGGAGAA 59.704 57.895 0.00 0.00 0.00 2.87
1919 4043 0.605319 GACATGGCCGAAAGACACCA 60.605 55.000 0.00 0.00 36.43 4.17
1953 4077 4.080919 AGACAAGTATTAGCCATGCTCACA 60.081 41.667 0.00 0.00 40.44 3.58
1994 4118 7.979444 TCCCAAATACTTTTACAAGACTGAG 57.021 36.000 0.00 0.00 33.72 3.35
1995 4119 7.040686 GCTTCCCAAATACTTTTACAAGACTGA 60.041 37.037 0.00 0.00 33.72 3.41
1996 4120 7.084486 GCTTCCCAAATACTTTTACAAGACTG 58.916 38.462 0.00 0.00 33.72 3.51
1997 4121 6.072673 CGCTTCCCAAATACTTTTACAAGACT 60.073 38.462 0.00 0.00 33.72 3.24
1998 4122 6.084277 CGCTTCCCAAATACTTTTACAAGAC 58.916 40.000 0.00 0.00 33.72 3.01
1999 4123 5.766174 ACGCTTCCCAAATACTTTTACAAGA 59.234 36.000 0.00 0.00 33.72 3.02
2058 4183 1.273048 CTTGTATGCCAAGGCTTTGCA 59.727 47.619 25.68 25.68 45.70 4.08
2196 4328 8.701908 TGGAATAGACGTATAGGAGTTGTATT 57.298 34.615 0.00 0.00 0.00 1.89
2240 4382 0.250901 TGGCAAAGCTCCTTGAGGTC 60.251 55.000 2.23 0.00 39.62 3.85
2274 4416 9.525826 ACAGAGAGAAGGTTGAATGAATTTAAT 57.474 29.630 0.00 0.00 0.00 1.40
2323 4465 1.006043 TCCCAGAGGAGATCAACTCGT 59.994 52.381 10.00 0.00 45.76 4.18
2338 4480 3.388024 TCTGGAGATTCGGTTTATCCCAG 59.612 47.826 0.00 0.00 39.39 4.45
2342 4485 4.698575 AGCTTCTGGAGATTCGGTTTATC 58.301 43.478 0.00 0.00 0.00 1.75
2374 4517 8.413309 TGATTTCCATTTTGTCAGAGAAAGAT 57.587 30.769 0.00 0.00 0.00 2.40
2408 4551 8.180267 CCTATTTTTCATGCACAAACAAAACAA 58.820 29.630 0.00 0.00 0.00 2.83
2431 4574 5.592054 CAACGTATCTCTCAGCAAATCCTA 58.408 41.667 0.00 0.00 0.00 2.94
2499 4642 8.082242 ACAAACATTACTTTATGAACTTGGAGC 58.918 33.333 0.00 0.00 0.00 4.70
2539 4682 1.694150 CCCTGGCTAATGCTACAGCTA 59.306 52.381 2.44 0.00 42.66 3.32
2616 4759 4.003648 CTGGGAACTAACCTTGTGTCATC 58.996 47.826 0.00 0.00 0.00 2.92
2646 4789 5.568620 AGAAGATCTACAGGTGGTTTTGT 57.431 39.130 0.00 0.00 0.00 2.83
2811 4954 5.048782 AGGTATGCCAATATTTACATGCACG 60.049 40.000 1.54 0.00 37.19 5.34
2992 5136 5.187967 TCTCAGGAGAGTAGGAATGGAAAAC 59.812 44.000 0.00 0.00 42.66 2.43


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

AutoCloner maintained by Alex Coulton.