Multiple sequence alignment - TraesCS2A01G469200

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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 TraesCS2A01G469200 chr2A 100.000 4599 0 0 1 4599 712790048 712794646 0.000000e+00 8493
1 TraesCS2A01G469200 chr2D 91.761 4661 187 58 1 4571 574383385 574387938 0.000000e+00 6298
2 TraesCS2A01G469200 chr2B 89.348 1887 131 36 46 1901 690584629 690586476 0.000000e+00 2307
3 TraesCS2A01G469200 chr2B 94.076 1283 35 12 2800 4076 690587521 690588768 0.000000e+00 1910
4 TraesCS2A01G469200 chr2B 91.286 964 22 17 1880 2815 690586481 690587410 0.000000e+00 1258
5 TraesCS2A01G469200 chr2B 92.216 334 15 6 4273 4599 690589072 690589401 3.240000e-126 462


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 TraesCS2A01G469200 chr2A 712790048 712794646 4598 False 8493.00 8493 100.0000 1 4599 1 chr2A.!!$F1 4598
1 TraesCS2A01G469200 chr2D 574383385 574387938 4553 False 6298.00 6298 91.7610 1 4571 1 chr2D.!!$F1 4570
2 TraesCS2A01G469200 chr2B 690584629 690589401 4772 False 1484.25 2307 91.7315 46 4599 4 chr2B.!!$F1 4553

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
248 269 0.741326 CGATGTGATGGACCGAGAGT 59.259 55.0 0.00 0.00 0.00 3.24 F
884 929 0.806868 ATTGCATTGCACGTGAGAGG 59.193 50.0 22.23 9.35 38.71 3.69 F
1269 1314 0.540365 ACCTTGCCACCACTGGATTG 60.540 55.0 0.71 0.00 40.55 2.67 F
1747 1793 0.667184 GCTTGGATGGTTGGTTTGCG 60.667 55.0 0.00 0.00 0.00 4.85 F
2948 3179 0.826062 CCCCAATGAACAAGCCCATC 59.174 55.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1288 0.107831 GTGGTGGCAAGGTGACAGTA 59.892 55.000 0.0 0.0 35.04 2.74 R
2255 2358 3.760738 TCAAGGAACAATGTGGCATGTA 58.239 40.909 0.0 0.0 0.00 2.29 R
2922 3153 0.757188 TTGTTCATTGGGGTGGCGTT 60.757 50.000 0.0 0.0 0.00 4.84 R
3003 3234 1.532868 GATGTGCAGATATGGCGTTCC 59.467 52.381 0.0 0.0 0.00 3.62 R
4268 4656 0.093026 GTTTGATGTCTTCGACGCCG 59.907 55.000 0.0 0.0 34.95 6.46 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
44 45 5.090139 TGGAACCCAAACCACAAATATCAT 58.910 37.500 0.00 0.00 0.00 2.45
52 63 7.988599 CCCAAACCACAAATATCATCAATCATT 59.011 33.333 0.00 0.00 0.00 2.57
133 147 0.803768 CCGTCCAGCGAGACATCAAG 60.804 60.000 9.41 0.00 44.77 3.02
146 160 2.742589 GACATCAAGGGAAAGAACGGAC 59.257 50.000 0.00 0.00 0.00 4.79
152 166 0.886563 GGGAAAGAACGGACGAGAGA 59.113 55.000 0.00 0.00 0.00 3.10
226 243 1.280746 CAGCACACAAGTCAAGCGG 59.719 57.895 0.00 0.00 0.00 5.52
238 255 1.061411 CAAGCGGTGCGATGTGATG 59.939 57.895 0.00 0.00 0.00 3.07
248 269 0.741326 CGATGTGATGGACCGAGAGT 59.259 55.000 0.00 0.00 0.00 3.24
313 334 6.700960 AGCATACTTTGAGATTTGAGATCTCG 59.299 38.462 17.76 2.14 45.58 4.04
338 362 6.861572 GCCAAAGCGAATTATATTCCCTTAAC 59.138 38.462 0.00 0.00 0.00 2.01
365 389 1.145119 AGAAAAAGAGAAAGCGGGGGT 59.855 47.619 0.00 0.00 0.00 4.95
611 655 3.799753 GACGGCATCGATTGTGCT 58.200 55.556 9.20 0.00 42.16 4.40
615 659 0.869880 CGGCATCGATTGTGCTACGA 60.870 55.000 9.20 0.00 42.16 3.43
669 713 4.662961 CGCTGCTGGTGACCACGA 62.663 66.667 0.00 0.00 0.00 4.35
670 714 2.280797 GCTGCTGGTGACCACGAA 60.281 61.111 0.00 0.00 0.00 3.85
671 715 2.320587 GCTGCTGGTGACCACGAAG 61.321 63.158 0.00 2.29 0.00 3.79
672 716 2.280797 TGCTGGTGACCACGAAGC 60.281 61.111 0.00 2.95 40.18 3.86
728 772 2.624316 TTCGTAGCGAATCGAACAGT 57.376 45.000 6.91 0.00 41.05 3.55
729 773 2.624316 TCGTAGCGAATCGAACAGTT 57.376 45.000 6.91 0.00 31.06 3.16
737 781 5.657474 AGCGAATCGAACAGTTAATTAGGA 58.343 37.500 6.91 0.00 0.00 2.94
783 827 1.136147 CGAGACGAGGGTTACACGG 59.864 63.158 0.00 0.00 0.00 4.94
830 875 1.795170 ATGGCCAGCAACGTCAACAC 61.795 55.000 13.05 0.00 0.00 3.32
840 885 2.342956 CGTCAACACGTAGCGGTAC 58.657 57.895 14.72 14.72 41.42 3.34
850 895 1.136557 CGTAGCGGTACCGTTTTGTTG 60.137 52.381 33.34 14.46 42.09 3.33
853 898 1.788067 GCGGTACCGTTTTGTTGCCT 61.788 55.000 33.34 0.00 42.09 4.75
861 906 1.879380 CGTTTTGTTGCCTGGAGATGA 59.121 47.619 0.00 0.00 0.00 2.92
865 910 4.365514 TTTGTTGCCTGGAGATGACTTA 57.634 40.909 0.00 0.00 0.00 2.24
868 913 4.264253 TGTTGCCTGGAGATGACTTATTG 58.736 43.478 0.00 0.00 0.00 1.90
876 921 4.096833 TGGAGATGACTTATTGCATTGCAC 59.903 41.667 11.66 0.00 38.71 4.57
877 922 4.277258 GAGATGACTTATTGCATTGCACG 58.723 43.478 11.66 3.04 38.71 5.34
880 925 2.810852 TGACTTATTGCATTGCACGTGA 59.189 40.909 22.23 0.00 38.71 4.35
884 929 0.806868 ATTGCATTGCACGTGAGAGG 59.193 50.000 22.23 9.35 38.71 3.69
893 938 1.732259 GCACGTGAGAGGGTATTGTTG 59.268 52.381 22.23 0.00 0.00 3.33
894 939 2.346803 CACGTGAGAGGGTATTGTTGG 58.653 52.381 10.90 0.00 0.00 3.77
907 952 5.242838 GGGTATTGTTGGACAATTCTGTGAA 59.757 40.000 11.11 0.00 45.80 3.18
914 959 5.063180 TGGACAATTCTGTGAAATGATGC 57.937 39.130 2.83 0.00 35.30 3.91
937 982 4.889832 ATGATTTTGCAGGAATCTCGAC 57.110 40.909 19.41 1.92 35.15 4.20
944 989 2.237143 TGCAGGAATCTCGACAAGGATT 59.763 45.455 0.00 0.00 35.23 3.01
948 993 2.474816 GAATCTCGACAAGGATTCCCG 58.525 52.381 11.99 0.00 40.84 5.14
951 996 1.621814 TCTCGACAAGGATTCCCGTTT 59.378 47.619 0.00 0.00 37.58 3.60
957 1002 4.320870 GACAAGGATTCCCGTTTCAAGTA 58.679 43.478 0.00 0.00 37.58 2.24
960 1005 4.903045 AGGATTCCCGTTTCAAGTAAGA 57.097 40.909 0.00 0.00 37.58 2.10
971 1016 5.751243 TTTCAAGTAAGAAACTGCCAGTC 57.249 39.130 0.00 0.00 38.88 3.51
974 1019 5.057149 TCAAGTAAGAAACTGCCAGTCTTC 58.943 41.667 0.00 4.86 38.88 2.87
982 1027 2.292103 CTGCCAGTCTTCTAGCAGTC 57.708 55.000 7.31 0.00 46.13 3.51
988 1033 2.747989 CAGTCTTCTAGCAGTCGGTACA 59.252 50.000 0.00 0.00 0.00 2.90
1103 1148 8.749354 TCGGCTGTTTACATATCAGTATATCAT 58.251 33.333 0.00 0.00 0.00 2.45
1104 1149 8.811378 CGGCTGTTTACATATCAGTATATCATG 58.189 37.037 0.00 0.00 0.00 3.07
1105 1150 9.102757 GGCTGTTTACATATCAGTATATCATGG 57.897 37.037 0.00 0.00 0.00 3.66
1106 1151 9.875691 GCTGTTTACATATCAGTATATCATGGA 57.124 33.333 0.00 0.00 0.00 3.41
1136 1181 2.679837 GCTGTTGACCATATCCAGTGTG 59.320 50.000 0.00 0.00 0.00 3.82
1174 1219 6.997655 AGAAGAATTATCATCACTATGCCGA 58.002 36.000 0.00 0.00 32.76 5.54
1189 1234 3.706600 TGCCGATTATATAACCCCACC 57.293 47.619 0.00 0.00 0.00 4.61
1225 1270 7.756395 AACTTGCTGGATGATTCTATTATGG 57.244 36.000 0.00 0.00 0.00 2.74
1243 1288 3.057969 TGGTCATTTGCAACTCGAGAT 57.942 42.857 21.68 3.75 0.00 2.75
1247 1292 4.033358 GGTCATTTGCAACTCGAGATACTG 59.967 45.833 21.68 11.34 0.00 2.74
1252 1297 2.094700 TGCAACTCGAGATACTGTCACC 60.095 50.000 21.68 0.00 0.00 4.02
1253 1298 2.164624 GCAACTCGAGATACTGTCACCT 59.835 50.000 21.68 0.00 0.00 4.00
1269 1314 0.540365 ACCTTGCCACCACTGGATTG 60.540 55.000 0.71 0.00 40.55 2.67
1279 1324 1.815003 CCACTGGATTGTTTGCCTCTC 59.185 52.381 0.00 0.00 0.00 3.20
1328 1374 5.128919 AGATGTATCATCTTTTCCTGCACC 58.871 41.667 6.45 0.00 0.00 5.01
1357 1403 5.123820 TCACCATTTTGCACTAAGTAGCATC 59.876 40.000 0.00 0.00 40.94 3.91
1358 1404 5.009631 ACCATTTTGCACTAAGTAGCATCA 58.990 37.500 0.00 0.00 40.94 3.07
1416 1462 7.852945 GGAACAGATAATAGCAAAAAGTCGATG 59.147 37.037 0.00 0.00 0.00 3.84
1495 1541 1.081242 GTTGCTGGCGTGTGGATTG 60.081 57.895 0.00 0.00 0.00 2.67
1496 1542 2.267351 TTGCTGGCGTGTGGATTGG 61.267 57.895 0.00 0.00 0.00 3.16
1747 1793 0.667184 GCTTGGATGGTTGGTTTGCG 60.667 55.000 0.00 0.00 0.00 4.85
2019 2095 9.793259 TTGAAACTATCTGACAACTTTATCCTT 57.207 29.630 0.00 0.00 0.00 3.36
2253 2356 7.426743 GCTCAAAGCACTTCGATCTTAATTTAC 59.573 37.037 0.00 0.00 41.89 2.01
2255 2358 8.999431 TCAAAGCACTTCGATCTTAATTTACTT 58.001 29.630 0.00 0.00 0.00 2.24
2405 2508 2.419673 TCAATTTGTACAGCTCATGCCG 59.580 45.455 0.00 0.00 40.80 5.69
2453 2556 9.022884 GTAGGTACCTAATCCTGTATCTAAAGG 57.977 40.741 23.40 0.00 33.64 3.11
2472 2575 5.665916 AAGGCACCAAAAGGAAGATAATG 57.334 39.130 0.00 0.00 0.00 1.90
2534 2637 5.948758 TGTGATGGTTTTATGGTGCATAGAA 59.051 36.000 0.00 0.00 0.00 2.10
2539 2642 8.947055 ATGGTTTTATGGTGCATAGAATTTTC 57.053 30.769 0.00 0.00 0.00 2.29
2908 3139 5.772672 TGTGGGTTTTAACAGCTTGATACAT 59.227 36.000 0.00 0.00 0.00 2.29
2922 3153 8.829612 CAGCTTGATACATGACATATTTGTGTA 58.170 33.333 0.00 0.00 35.79 2.90
2948 3179 0.826062 CCCCAATGAACAAGCCCATC 59.174 55.000 0.00 0.00 0.00 3.51
2949 3180 1.559368 CCCAATGAACAAGCCCATCA 58.441 50.000 0.00 0.00 0.00 3.07
3058 3289 5.787953 TTCCATCTTCTCACATGCAAAAA 57.212 34.783 0.00 0.00 0.00 1.94
3380 3611 5.875359 CACATGATCATATATGCAGAGCTGT 59.125 40.000 8.15 0.00 0.00 4.40
3381 3612 6.371825 CACATGATCATATATGCAGAGCTGTT 59.628 38.462 8.15 0.00 0.00 3.16
3382 3613 6.940867 ACATGATCATATATGCAGAGCTGTTT 59.059 34.615 8.15 0.00 0.00 2.83
3429 3662 1.605710 ACTCATGTGCTTGTGTTCTGC 59.394 47.619 0.00 0.00 0.00 4.26
3536 3770 4.260985 TGCGACATTCATGTACATTTCCT 58.739 39.130 5.37 0.00 41.95 3.36
3655 3889 6.215845 GCGGGCATATTCAAGAAAAACATAT 58.784 36.000 0.00 0.00 0.00 1.78
3923 4158 2.621998 CCAGAAATGATGATGGTGCCTC 59.378 50.000 0.00 0.00 0.00 4.70
3965 4200 4.519540 ACATGCCAACATTTACTTGGTC 57.480 40.909 0.00 0.00 40.46 4.02
3983 4218 3.506455 TGGTCGTTTTCTTTGTGGTTTCA 59.494 39.130 0.00 0.00 0.00 2.69
4103 4358 6.147864 TGCATGCCTAGTTTCCATTTATTC 57.852 37.500 16.68 0.00 0.00 1.75
4104 4359 5.655974 TGCATGCCTAGTTTCCATTTATTCA 59.344 36.000 16.68 0.00 0.00 2.57
4151 4539 1.744320 AAACAAAGCCCTGCCCGTTC 61.744 55.000 0.00 0.00 0.00 3.95
4152 4540 2.597217 CAAAGCCCTGCCCGTTCA 60.597 61.111 0.00 0.00 0.00 3.18
4153 4541 2.197324 AAAGCCCTGCCCGTTCAA 59.803 55.556 0.00 0.00 0.00 2.69
4161 4549 1.845809 CTGCCCGTTCAACAGCTCAC 61.846 60.000 1.55 0.00 0.00 3.51
4171 4559 2.882876 CAGCTCACTGGCAATGGC 59.117 61.111 0.00 0.00 40.48 4.40
4220 4608 1.070105 TTGTTCCGTTCAGGGGACG 59.930 57.895 0.00 0.00 41.52 4.79
4268 4656 5.961843 CACATGAATTTAGTCGATTGCACTC 59.038 40.000 0.00 0.00 0.00 3.51
4295 4683 1.327764 GAAGACATCAAACGGATCGCC 59.672 52.381 0.00 0.00 32.57 5.54
4308 4696 0.652592 GATCGCCGTCACATGAAAGG 59.347 55.000 0.00 0.00 0.00 3.11
4314 4702 1.006086 CGTCACATGAAAGGCGCATA 58.994 50.000 10.83 0.00 0.00 3.14
4315 4703 1.004610 CGTCACATGAAAGGCGCATAG 60.005 52.381 10.83 0.00 0.00 2.23
4319 4707 2.938451 CACATGAAAGGCGCATAGAGAA 59.062 45.455 10.83 0.00 0.00 2.87
4324 4712 6.318648 ACATGAAAGGCGCATAGAGAAAATTA 59.681 34.615 10.83 0.00 0.00 1.40
4325 4713 6.751514 TGAAAGGCGCATAGAGAAAATTAA 57.248 33.333 10.83 0.00 0.00 1.40
4326 4714 6.551736 TGAAAGGCGCATAGAGAAAATTAAC 58.448 36.000 10.83 0.00 0.00 2.01
4351 4739 3.057386 CACATCAAAAGTGCAGCACCATA 60.057 43.478 22.41 4.09 34.49 2.74
4352 4740 3.765511 ACATCAAAAGTGCAGCACCATAT 59.234 39.130 22.41 6.30 34.49 1.78
4377 4782 4.537135 AATAGACATCACAAGTCCACGT 57.463 40.909 0.00 0.00 36.68 4.49
4573 4988 0.105760 ATCTCCATCCTGCGGTCTCT 60.106 55.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.992442 TTGGGTTCCAACATTAAAATAGGTATA 57.008 29.630 0.00 0.00 38.75 1.47
6 7 8.586744 GTTTGGGTTCCAACATTAAAATAGGTA 58.413 33.333 0.00 0.00 43.82 3.08
8 9 6.876789 GGTTTGGGTTCCAACATTAAAATAGG 59.123 38.462 0.00 0.00 43.82 2.57
18 19 1.938585 TTGTGGTTTGGGTTCCAACA 58.061 45.000 0.00 0.00 43.82 3.33
21 22 4.483950 TGATATTTGTGGTTTGGGTTCCA 58.516 39.130 0.00 0.00 0.00 3.53
44 45 9.676861 ATGTCTTAATGAAGTCTGAATGATTGA 57.323 29.630 0.00 0.00 34.03 2.57
66 80 9.562583 TTGTGTTTTGTTGTAGACTTTTATGTC 57.437 29.630 0.00 0.00 37.23 3.06
126 140 2.779506 GTCCGTTCTTTCCCTTGATGT 58.220 47.619 0.00 0.00 0.00 3.06
133 147 0.886563 TCTCTCGTCCGTTCTTTCCC 59.113 55.000 0.00 0.00 0.00 3.97
146 160 2.202544 GCGTGTGGAGCTCTCTCG 60.203 66.667 14.64 18.40 40.26 4.04
216 233 1.301716 ACATCGCACCGCTTGACTT 60.302 52.632 0.00 0.00 0.00 3.01
226 243 1.148157 CTCGGTCCATCACATCGCAC 61.148 60.000 0.00 0.00 0.00 5.34
238 255 1.401539 GCAAATTGCAACTCTCGGTCC 60.402 52.381 13.73 0.00 44.26 4.46
313 334 5.453567 AAGGGAATATAATTCGCTTTGGC 57.546 39.130 20.09 0.00 45.48 4.52
338 362 5.460091 CCCGCTTTCTCTTTTTCTTTTTCTG 59.540 40.000 0.00 0.00 0.00 3.02
351 375 0.476771 TTTTGACCCCCGCTTTCTCT 59.523 50.000 0.00 0.00 0.00 3.10
352 376 1.324383 TTTTTGACCCCCGCTTTCTC 58.676 50.000 0.00 0.00 0.00 2.87
353 377 3.524346 TTTTTGACCCCCGCTTTCT 57.476 47.368 0.00 0.00 0.00 2.52
608 652 2.986979 TGGAGCACCGTCGTAGCA 60.987 61.111 8.56 0.00 39.42 3.49
610 654 2.202623 GCTGGAGCACCGTCGTAG 60.203 66.667 0.00 0.00 41.59 3.51
611 655 4.111016 CGCTGGAGCACCGTCGTA 62.111 66.667 0.00 0.00 42.21 3.43
728 772 0.391597 CGGGGCTCGCTCCTAATTAA 59.608 55.000 6.21 0.00 33.46 1.40
729 773 0.468585 TCGGGGCTCGCTCCTAATTA 60.469 55.000 0.00 0.00 39.05 1.40
737 781 4.841617 TCCAGATCGGGGCTCGCT 62.842 66.667 12.28 0.00 39.05 4.93
763 807 0.179205 CGTGTAACCCTCGTCTCGTC 60.179 60.000 0.00 0.00 0.00 4.20
764 808 1.580845 CCGTGTAACCCTCGTCTCGT 61.581 60.000 0.00 0.00 0.00 4.18
791 836 5.791681 GCCATAGCTACCTACGTAATTCGTT 60.792 44.000 0.00 0.00 42.68 3.85
794 839 4.021719 TGGCCATAGCTACCTACGTAATTC 60.022 45.833 0.00 0.00 39.73 2.17
830 875 1.136557 CAACAAAACGGTACCGCTACG 60.137 52.381 33.62 21.38 44.19 3.51
833 878 1.650363 GCAACAAAACGGTACCGCT 59.350 52.632 33.62 20.42 44.19 5.52
840 885 1.068333 CATCTCCAGGCAACAAAACGG 60.068 52.381 0.00 0.00 41.41 4.44
850 895 2.923121 TGCAATAAGTCATCTCCAGGC 58.077 47.619 0.00 0.00 0.00 4.85
853 898 4.096833 GTGCAATGCAATAAGTCATCTCCA 59.903 41.667 10.44 0.00 41.47 3.86
861 906 3.073678 TCTCACGTGCAATGCAATAAGT 58.926 40.909 10.44 5.27 41.47 2.24
865 910 0.806868 CCTCTCACGTGCAATGCAAT 59.193 50.000 10.44 0.00 41.47 3.56
868 913 0.391130 TACCCTCTCACGTGCAATGC 60.391 55.000 11.67 0.00 0.00 3.56
876 921 2.028476 TGTCCAACAATACCCTCTCACG 60.028 50.000 0.00 0.00 0.00 4.35
877 922 3.695830 TGTCCAACAATACCCTCTCAC 57.304 47.619 0.00 0.00 0.00 3.51
893 938 5.063180 TGCATCATTTCACAGAATTGTCC 57.937 39.130 0.00 0.00 34.62 4.02
894 939 6.809689 TCATTGCATCATTTCACAGAATTGTC 59.190 34.615 0.00 0.00 34.62 3.18
914 959 5.032863 GTCGAGATTCCTGCAAAATCATTG 58.967 41.667 18.64 10.60 35.92 2.82
937 982 5.001232 TCTTACTTGAAACGGGAATCCTTG 58.999 41.667 0.00 0.00 0.00 3.61
951 996 4.689612 AGACTGGCAGTTTCTTACTTGA 57.310 40.909 22.98 0.00 33.85 3.02
970 1015 3.628032 CAGATGTACCGACTGCTAGAAGA 59.372 47.826 4.16 0.00 0.00 2.87
971 1016 3.628032 TCAGATGTACCGACTGCTAGAAG 59.372 47.826 0.00 0.00 0.00 2.85
974 1019 2.033550 GGTCAGATGTACCGACTGCTAG 59.966 54.545 0.00 0.00 0.00 3.42
982 1027 3.198068 CCATTGAAGGTCAGATGTACCG 58.802 50.000 0.00 0.00 42.15 4.02
988 1033 0.035152 TGCGCCATTGAAGGTCAGAT 60.035 50.000 4.18 0.00 0.00 2.90
1103 1148 0.764271 TCAACAGCACCATGAGTCCA 59.236 50.000 0.00 0.00 0.00 4.02
1104 1149 1.160137 GTCAACAGCACCATGAGTCC 58.840 55.000 0.00 0.00 0.00 3.85
1105 1150 1.160137 GGTCAACAGCACCATGAGTC 58.840 55.000 0.00 0.00 33.63 3.36
1106 1151 0.473755 TGGTCAACAGCACCATGAGT 59.526 50.000 0.00 0.00 39.11 3.41
1107 1152 3.327600 TGGTCAACAGCACCATGAG 57.672 52.632 0.00 0.00 39.11 2.90
1112 1157 2.292267 CTGGATATGGTCAACAGCACC 58.708 52.381 0.00 0.00 31.21 5.01
1174 1219 4.979039 TGTGGACTGGTGGGGTTATATAAT 59.021 41.667 0.00 0.00 0.00 1.28
1184 1229 3.154827 AGTTAAATGTGGACTGGTGGG 57.845 47.619 0.00 0.00 0.00 4.61
1189 1234 3.820467 TCCAGCAAGTTAAATGTGGACTG 59.180 43.478 0.00 0.00 0.00 3.51
1225 1270 4.627467 ACAGTATCTCGAGTTGCAAATGAC 59.373 41.667 13.13 0.00 0.00 3.06
1243 1288 0.107831 GTGGTGGCAAGGTGACAGTA 59.892 55.000 0.00 0.00 35.04 2.74
1247 1292 1.898574 CCAGTGGTGGCAAGGTGAC 60.899 63.158 0.00 0.00 36.89 3.67
1252 1297 1.331214 AACAATCCAGTGGTGGCAAG 58.669 50.000 9.54 0.00 44.60 4.01
1253 1298 1.411977 CAAACAATCCAGTGGTGGCAA 59.588 47.619 9.54 0.00 44.60 4.52
1316 1362 1.000938 GTGAAGCTGGTGCAGGAAAAG 60.001 52.381 0.00 0.00 42.74 2.27
1328 1374 2.806608 AGTGCAAAATGGTGAAGCTG 57.193 45.000 0.00 0.00 0.00 4.24
1435 1481 3.904800 TGCACTCTTCCGAATATTCCA 57.095 42.857 9.87 0.00 0.00 3.53
1706 1752 4.443457 GCCATCACAGAAGAAGCTGGTATA 60.443 45.833 0.00 0.00 40.20 1.47
1747 1793 4.906618 TGTTACCTTGATTGAACCTCCTC 58.093 43.478 0.00 0.00 0.00 3.71
1911 1987 8.579850 TCAAACAGGACATAAGCAGATATTTT 57.420 30.769 0.00 0.00 0.00 1.82
1915 1991 7.394016 TCTTTCAAACAGGACATAAGCAGATA 58.606 34.615 0.00 0.00 0.00 1.98
2019 2095 5.585820 ATGTTGATGCTGATACATGCAAA 57.414 34.783 0.00 0.00 42.74 3.68
2253 2356 4.218200 TCAAGGAACAATGTGGCATGTAAG 59.782 41.667 0.00 0.00 0.00 2.34
2255 2358 3.760738 TCAAGGAACAATGTGGCATGTA 58.239 40.909 0.00 0.00 0.00 2.29
2405 2508 7.766738 CCTACTAGGAGAACAAAAGAGAAATCC 59.233 40.741 2.52 0.00 37.67 3.01
2534 2637 4.479619 GCTCTTGAACAATGAGCGAAAAT 58.520 39.130 16.43 0.00 42.70 1.82
2560 2663 9.167311 AGAGACAGAAAACGAAATATAGCAAAT 57.833 29.630 0.00 0.00 0.00 2.32
2908 3139 3.437395 GGTGGCGTTACACAAATATGTCA 59.563 43.478 8.77 0.00 43.08 3.58
2922 3153 0.757188 TTGTTCATTGGGGTGGCGTT 60.757 50.000 0.00 0.00 0.00 4.84
3003 3234 1.532868 GATGTGCAGATATGGCGTTCC 59.467 52.381 0.00 0.00 0.00 3.62
3058 3289 8.691661 AATGTACAGAACCTGTAAGTTGAAAT 57.308 30.769 8.23 0.00 46.55 2.17
3144 3375 9.191995 GCTTGATTAGAGAAGAAAGCTATAGAC 57.808 37.037 3.21 0.00 35.52 2.59
3154 3385 8.618677 CATGCTAATTGCTTGATTAGAGAAGAA 58.381 33.333 14.91 0.00 46.07 2.52
3166 3397 3.242284 GCAACATGCATGCTAATTGCTTG 60.242 43.478 30.55 23.13 44.26 4.01
3394 3625 4.395854 CACATGAGTGTTAGCCTAATTGCA 59.604 41.667 0.00 0.00 40.92 4.08
3429 3662 6.866480 ACATATGCCTAAAACTTGACCATTG 58.134 36.000 1.58 0.00 0.00 2.82
3536 3770 3.708890 CAGCTGTTTTCATCTGCAAACA 58.291 40.909 5.25 7.68 38.46 2.83
3689 3923 4.965814 ACATCAAGGAGCTACCATATGTG 58.034 43.478 6.80 0.00 42.04 3.21
3690 3924 6.728164 AGATACATCAAGGAGCTACCATATGT 59.272 38.462 11.24 11.24 42.04 2.29
3691 3925 7.180322 AGATACATCAAGGAGCTACCATATG 57.820 40.000 0.00 0.00 42.04 1.78
3692 3926 7.805083 AAGATACATCAAGGAGCTACCATAT 57.195 36.000 0.00 0.00 42.04 1.78
3693 3927 7.618019 AAAGATACATCAAGGAGCTACCATA 57.382 36.000 0.00 0.00 42.04 2.74
3694 3928 6.506538 AAAGATACATCAAGGAGCTACCAT 57.493 37.500 0.00 0.00 42.04 3.55
3695 3929 5.957771 AAAGATACATCAAGGAGCTACCA 57.042 39.130 0.00 0.00 42.04 3.25
3696 3930 7.769044 TGTTAAAAGATACATCAAGGAGCTACC 59.231 37.037 0.00 0.00 39.35 3.18
3697 3931 8.718102 TGTTAAAAGATACATCAAGGAGCTAC 57.282 34.615 0.00 0.00 0.00 3.58
3923 4158 1.916777 ACTGGTACAACGGGAGGGG 60.917 63.158 0.00 0.00 38.70 4.79
3965 4200 6.248210 GCAAATTTGAAACCACAAAGAAAACG 59.752 34.615 22.31 0.00 41.87 3.60
4103 4358 5.181811 TCTGGTGCAAATGATACTTTCTGTG 59.818 40.000 0.00 0.00 0.00 3.66
4104 4359 5.316167 TCTGGTGCAAATGATACTTTCTGT 58.684 37.500 0.00 0.00 0.00 3.41
4151 4539 0.242825 CCATTGCCAGTGAGCTGTTG 59.757 55.000 0.00 0.00 41.02 3.33
4152 4540 1.530013 GCCATTGCCAGTGAGCTGTT 61.530 55.000 0.00 0.00 41.02 3.16
4153 4541 1.975407 GCCATTGCCAGTGAGCTGT 60.975 57.895 0.00 0.00 41.02 4.40
4164 4552 0.461135 CAGTACCATTGGGCCATTGC 59.539 55.000 20.40 9.12 37.90 3.56
4165 4553 1.851304 ACAGTACCATTGGGCCATTG 58.149 50.000 19.18 19.18 37.90 2.82
4166 4554 2.310349 TGTACAGTACCATTGGGCCATT 59.690 45.455 7.26 0.00 37.90 3.16
4167 4555 1.919654 TGTACAGTACCATTGGGCCAT 59.080 47.619 7.26 0.00 37.90 4.40
4168 4556 1.003812 GTGTACAGTACCATTGGGCCA 59.996 52.381 0.00 0.00 37.90 5.36
4169 4557 1.680860 GGTGTACAGTACCATTGGGCC 60.681 57.143 7.78 0.00 38.12 5.80
4170 4558 1.280998 AGGTGTACAGTACCATTGGGC 59.719 52.381 7.78 0.00 40.74 5.36
4171 4559 3.263425 AGAAGGTGTACAGTACCATTGGG 59.737 47.826 7.78 0.00 40.74 4.12
4172 4560 4.253685 CAGAAGGTGTACAGTACCATTGG 58.746 47.826 8.30 0.00 40.74 3.16
4173 4561 4.690748 CACAGAAGGTGTACAGTACCATTG 59.309 45.833 8.30 0.00 42.75 2.82
4203 4591 2.738480 CGTCCCCTGAACGGAACA 59.262 61.111 0.00 0.00 36.51 3.18
4220 4608 1.096416 TTGTTGTGTTGTTCCGGACC 58.904 50.000 1.83 0.00 0.00 4.46
4221 4609 2.923605 TTTGTTGTGTTGTTCCGGAC 57.076 45.000 1.83 0.00 0.00 4.79
4223 4611 4.032331 GTGAAATTTGTTGTGTTGTTCCGG 59.968 41.667 0.00 0.00 0.00 5.14
4224 4612 4.623167 TGTGAAATTTGTTGTGTTGTTCCG 59.377 37.500 0.00 0.00 0.00 4.30
4256 4644 2.789203 GACGCCGAGTGCAATCGAC 61.789 63.158 35.37 24.82 45.56 4.20
4268 4656 0.093026 GTTTGATGTCTTCGACGCCG 59.907 55.000 0.00 0.00 34.95 6.46
4295 4683 1.004610 CTATGCGCCTTTCATGTGACG 60.005 52.381 4.18 0.00 0.00 4.35
4308 4696 4.956184 GTGACGTTAATTTTCTCTATGCGC 59.044 41.667 0.00 0.00 0.00 6.09
4314 4702 8.621286 ACTTTTGATGTGACGTTAATTTTCTCT 58.379 29.630 0.00 0.00 0.00 3.10
4315 4703 8.682016 CACTTTTGATGTGACGTTAATTTTCTC 58.318 33.333 0.00 0.00 37.60 2.87
4319 4707 6.269315 TGCACTTTTGATGTGACGTTAATTT 58.731 32.000 0.00 0.00 37.60 1.82
4324 4712 2.541588 GCTGCACTTTTGATGTGACGTT 60.542 45.455 0.00 0.00 37.60 3.99
4325 4713 1.002468 GCTGCACTTTTGATGTGACGT 60.002 47.619 0.00 0.00 37.60 4.34
4326 4714 1.002576 TGCTGCACTTTTGATGTGACG 60.003 47.619 0.00 0.00 37.60 4.35
4351 4739 5.882557 GTGGACTTGTGATGTCTATTTCCAT 59.117 40.000 0.00 0.00 33.34 3.41
4352 4740 5.245531 GTGGACTTGTGATGTCTATTTCCA 58.754 41.667 0.00 0.00 35.04 3.53
4377 4782 4.895854 GCCGTGCGTTTCTACCTA 57.104 55.556 0.00 0.00 0.00 3.08
4395 4801 5.388225 AATTCGTGTGAAATTTGTTGTGC 57.612 34.783 0.00 0.00 37.71 4.57


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

AutoCloner maintained by Alex Coulton.