Multiple sequence alignment - TraesCS6B01G314200

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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 TraesCS6B01G314200 chr6B 100.000 4304 0 0 1 4304 561832493 561836796 0.000000e+00 7949.0
1 TraesCS6B01G314200 chr6B 84.615 390 43 4 2933 3306 561712441 561712829 5.260000e-99 372.0
2 TraesCS6B01G314200 chr6B 80.892 471 71 16 2249 2714 561711587 561712043 1.900000e-93 353.0
3 TraesCS6B01G314200 chr6B 93.778 225 14 0 2712 2936 561712140 561712364 5.330000e-89 339.0
4 TraesCS6B01G314200 chr6B 86.166 253 32 2 1767 2016 561705051 561705303 1.970000e-68 270.0
5 TraesCS6B01G314200 chr6B 91.667 48 4 0 375 422 712504400 712504353 2.780000e-07 67.6
6 TraesCS6B01G314200 chr6D 94.896 2253 63 23 2085 4304 375291712 375293945 0.000000e+00 3476.0
7 TraesCS6B01G314200 chr6D 88.719 1179 83 17 843 2012 375290577 375291714 0.000000e+00 1395.0
8 TraesCS6B01G314200 chr6D 90.196 561 50 2 1 556 375288829 375289389 0.000000e+00 726.0
9 TraesCS6B01G314200 chr6D 84.359 390 44 14 2933 3306 375096930 375097318 2.450000e-97 366.0
10 TraesCS6B01G314200 chr6D 81.184 473 64 19 2255 2714 375096071 375096531 1.470000e-94 357.0
11 TraesCS6B01G314200 chr6D 93.778 225 14 0 2712 2936 375096623 375096847 5.330000e-89 339.0
12 TraesCS6B01G314200 chr6D 85.375 253 34 2 1767 2016 375090674 375090926 4.270000e-65 259.0
13 TraesCS6B01G314200 chr6D 88.660 194 15 4 365 552 375289524 375289716 3.350000e-56 230.0
14 TraesCS6B01G314200 chr6A 94.620 2249 67 19 2085 4304 516675585 516677808 0.000000e+00 3434.0
15 TraesCS6B01G314200 chr6A 89.362 1175 92 16 843 2012 516674441 516675587 0.000000e+00 1447.0
16 TraesCS6B01G314200 chr6A 88.838 439 46 2 1 439 516611269 516611704 1.760000e-148 536.0
17 TraesCS6B01G314200 chr6A 81.345 461 61 21 2261 2714 516605755 516606197 6.850000e-93 351.0
18 TraesCS6B01G314200 chr6A 83.333 390 48 9 2933 3306 516606594 516606982 1.150000e-90 344.0
19 TraesCS6B01G314200 chr6A 92.889 225 16 0 2712 2936 516606288 516606512 1.150000e-85 327.0
20 TraesCS6B01G314200 chr6A 85.375 253 34 2 1767 2016 516583937 516584189 4.270000e-65 259.0
21 TraesCS6B01G314200 chr2D 77.434 226 35 12 2260 2480 594577763 594577549 2.100000e-23 121.0
22 TraesCS6B01G314200 chr2B 76.991 226 36 12 2260 2480 722326044 722325830 9.780000e-22 115.0
23 TraesCS6B01G314200 chr5B 75.652 230 47 7 142 367 404079718 404079942 5.890000e-19 106.0
24 TraesCS6B01G314200 chr5A 74.194 217 45 8 144 353 444845760 444845972 3.570000e-11 80.5
25 TraesCS6B01G314200 chr7D 88.889 54 2 3 509 558 39217820 39217767 3.590000e-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 TraesCS6B01G314200 chr6B 561832493 561836796 4303 False 7949.000000 7949 100.000000 1 4304 1 chr6B.!!$F2 4303
1 TraesCS6B01G314200 chr6B 561711587 561712829 1242 False 354.666667 372 86.428333 2249 3306 3 chr6B.!!$F3 1057
2 TraesCS6B01G314200 chr6D 375288829 375293945 5116 False 1456.750000 3476 90.617750 1 4304 4 chr6D.!!$F3 4303
3 TraesCS6B01G314200 chr6D 375096071 375097318 1247 False 354.000000 366 86.440333 2255 3306 3 chr6D.!!$F2 1051
4 TraesCS6B01G314200 chr6A 516674441 516677808 3367 False 2440.500000 3434 91.991000 843 4304 2 chr6A.!!$F4 3461
5 TraesCS6B01G314200 chr6A 516605755 516606982 1227 False 340.666667 351 85.855667 2261 3306 3 chr6A.!!$F3 1045

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
342 343 0.034198 GAGCCTATTCTTCCCCTCGC 59.966 60.0 0.00 0.00 0.00 5.03 F
826 1197 0.038310 GCTAGGTCCCACTGCCTTTT 59.962 55.0 0.00 0.00 36.38 2.27 F
2512 3490 0.034337 TCGGTAGGTGCAGAAACCAC 59.966 55.0 10.86 0.39 43.20 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 3310 0.594284 GCATGTAGTAGGCGTCCGAC 60.594 60.000 0.00 1.89 0.00 4.79 R
2540 3528 1.079888 ATCTCATGACACGCACGCA 60.080 52.632 0.00 0.00 0.00 5.24 R
3866 5091 0.835276 TGATCACAGCTGCTATGGCT 59.165 50.000 15.27 0.00 41.07 4.75 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
40 41 3.688272 CCATGTTCATGAAGATTGACGC 58.312 45.455 15.03 0.00 0.00 5.19
59 60 2.203209 GCGGCGGAGGGATTTGAT 60.203 61.111 9.78 0.00 0.00 2.57
69 70 2.424956 GAGGGATTTGATTGGAGCACAC 59.575 50.000 0.00 0.00 0.00 3.82
70 71 2.042162 AGGGATTTGATTGGAGCACACT 59.958 45.455 0.00 0.00 0.00 3.55
75 76 2.865119 TGATTGGAGCACACTGATGT 57.135 45.000 0.00 0.00 40.80 3.06
82 83 0.248565 AGCACACTGATGTCATCGCT 59.751 50.000 8.29 7.25 36.72 4.93
98 99 4.914420 CTAGCTCTGCGTCGGCCG 62.914 72.222 22.12 22.12 38.85 6.13
171 172 2.093658 GCGAGGAAAAGTAGACCATGGA 60.094 50.000 21.47 0.00 0.00 3.41
174 175 4.081642 CGAGGAAAAGTAGACCATGGAAGA 60.082 45.833 21.47 0.00 0.00 2.87
176 177 4.846940 AGGAAAAGTAGACCATGGAAGACT 59.153 41.667 21.47 14.53 0.00 3.24
244 245 3.560251 ACAGTCGGTGGCTTGCCT 61.560 61.111 13.18 0.00 0.00 4.75
250 251 2.598394 GGTGGCTTGCCTGCTTCA 60.598 61.111 13.18 0.00 0.00 3.02
274 275 3.873781 GCATAGGCCACCACAACTA 57.126 52.632 5.01 0.00 0.00 2.24
276 277 2.222027 GCATAGGCCACCACAACTATC 58.778 52.381 5.01 0.00 0.00 2.08
296 297 0.397254 TTCCCTCGCCCAAAAACCAA 60.397 50.000 0.00 0.00 0.00 3.67
314 315 0.250124 AACCGTTCATCCGTGCTTCA 60.250 50.000 0.00 0.00 0.00 3.02
326 327 2.817396 GCTTCACGGAGGCAGAGC 60.817 66.667 3.69 0.00 34.72 4.09
341 342 1.342819 CAGAGCCTATTCTTCCCCTCG 59.657 57.143 0.00 0.00 0.00 4.63
342 343 0.034198 GAGCCTATTCTTCCCCTCGC 59.966 60.000 0.00 0.00 0.00 5.03
369 370 1.105759 CATTTAGCTCTGGGGCTGGC 61.106 60.000 5.09 0.00 43.01 4.85
399 400 1.195448 GTGAGCTTGTTGTCGGACATG 59.805 52.381 12.26 4.40 0.00 3.21
417 749 1.745489 GGGGAAGACATGTCGTGGC 60.745 63.158 19.32 9.90 35.41 5.01
432 764 0.447801 GTGGCAAACAGGCTATGTCG 59.552 55.000 0.00 0.00 43.00 4.35
433 765 1.305219 TGGCAAACAGGCTATGTCGC 61.305 55.000 0.00 7.81 43.00 5.19
484 817 9.841295 TCCGCCATAGTTTAGTTAAAATATTCT 57.159 29.630 2.77 0.00 35.15 2.40
505 838 6.236017 TCTGAAATGTAAATGTGTTCGTCC 57.764 37.500 0.00 0.00 0.00 4.79
512 845 0.309612 AATGTGTTCGTCCGGTTTGC 59.690 50.000 0.00 0.00 0.00 3.68
537 874 7.468357 GCATGAATTTTGGTTTGTTGAAATCCA 60.468 33.333 0.00 0.00 0.00 3.41
538 875 8.569641 CATGAATTTTGGTTTGTTGAAATCCAT 58.430 29.630 0.00 0.00 0.00 3.41
552 889 8.719648 TGTTGAAATCCATTTTGAAATGTATGC 58.280 29.630 13.64 3.27 43.24 3.14
554 891 6.534436 TGAAATCCATTTTGAAATGTATGCGG 59.466 34.615 13.64 0.32 43.24 5.69
556 893 4.992688 TCCATTTTGAAATGTATGCGGAC 58.007 39.130 13.64 0.00 43.24 4.79
560 897 5.697473 TTTTGAAATGTATGCGGACAAGA 57.303 34.783 0.00 0.00 31.83 3.02
561 898 5.697473 TTTGAAATGTATGCGGACAAGAA 57.303 34.783 0.00 0.00 31.83 2.52
562 899 4.678509 TGAAATGTATGCGGACAAGAAC 57.321 40.909 0.00 0.00 31.83 3.01
563 900 4.323417 TGAAATGTATGCGGACAAGAACT 58.677 39.130 0.00 0.00 31.83 3.01
564 901 4.154015 TGAAATGTATGCGGACAAGAACTG 59.846 41.667 0.00 0.00 31.83 3.16
567 904 3.521560 TGTATGCGGACAAGAACTGATC 58.478 45.455 0.00 0.00 0.00 2.92
572 943 2.677902 GCGGACAAGAACTGATCCATCA 60.678 50.000 0.00 0.00 35.16 3.07
578 949 5.763355 ACAAGAACTGATCCATCAATCCAT 58.237 37.500 0.00 0.00 36.18 3.41
595 966 0.606401 CATGGATGGATACGGTGCCC 60.606 60.000 0.00 0.00 42.51 5.36
611 982 3.545724 CCCGGTTTAGAGGGTCAAC 57.454 57.895 0.00 0.00 42.67 3.18
612 983 0.390735 CCCGGTTTAGAGGGTCAACG 60.391 60.000 0.00 0.00 42.67 4.10
613 984 0.390735 CCGGTTTAGAGGGTCAACGG 60.391 60.000 0.00 0.00 0.00 4.44
614 985 0.390735 CGGTTTAGAGGGTCAACGGG 60.391 60.000 0.00 0.00 0.00 5.28
615 986 0.978907 GGTTTAGAGGGTCAACGGGA 59.021 55.000 0.00 0.00 0.00 5.14
616 987 1.066358 GGTTTAGAGGGTCAACGGGAG 60.066 57.143 0.00 0.00 0.00 4.30
617 988 1.897802 GTTTAGAGGGTCAACGGGAGA 59.102 52.381 0.00 0.00 0.00 3.71
618 989 2.500504 GTTTAGAGGGTCAACGGGAGAT 59.499 50.000 0.00 0.00 0.00 2.75
619 990 1.776662 TAGAGGGTCAACGGGAGATG 58.223 55.000 0.00 0.00 0.00 2.90
620 991 1.153349 GAGGGTCAACGGGAGATGC 60.153 63.158 0.00 0.00 32.05 3.91
621 992 2.124695 GGGTCAACGGGAGATGCC 60.125 66.667 0.00 0.00 32.05 4.40
673 1044 2.027192 ACCAAGCTCGCTCTTCCAAATA 60.027 45.455 0.00 0.00 0.00 1.40
681 1052 4.060900 TCGCTCTTCCAAATAGATGATGC 58.939 43.478 0.00 0.00 0.00 3.91
692 1063 7.605309 TCCAAATAGATGATGCATGAGTGATAC 59.395 37.037 2.46 0.00 0.00 2.24
707 1078 3.570975 AGTGATACGTTGGTGACTGTACA 59.429 43.478 0.00 0.00 0.00 2.90
712 1083 2.429610 ACGTTGGTGACTGTACAGAGTT 59.570 45.455 29.30 7.06 0.00 3.01
714 1085 3.243434 CGTTGGTGACTGTACAGAGTTCT 60.243 47.826 29.30 6.23 0.00 3.01
715 1086 4.694339 GTTGGTGACTGTACAGAGTTCTT 58.306 43.478 29.30 5.42 0.00 2.52
716 1087 4.585955 TGGTGACTGTACAGAGTTCTTC 57.414 45.455 29.30 14.98 0.00 2.87
717 1088 4.215908 TGGTGACTGTACAGAGTTCTTCT 58.784 43.478 29.30 3.81 36.25 2.85
718 1089 4.649674 TGGTGACTGTACAGAGTTCTTCTT 59.350 41.667 29.30 3.01 32.41 2.52
719 1090 5.128827 TGGTGACTGTACAGAGTTCTTCTTT 59.871 40.000 29.30 2.21 32.41 2.52
720 1091 6.049790 GGTGACTGTACAGAGTTCTTCTTTT 58.950 40.000 29.30 1.64 32.41 2.27
722 1093 7.873505 GGTGACTGTACAGAGTTCTTCTTTTAT 59.126 37.037 29.30 0.94 32.41 1.40
723 1094 8.917655 GTGACTGTACAGAGTTCTTCTTTTATC 58.082 37.037 29.30 11.07 32.41 1.75
724 1095 8.861086 TGACTGTACAGAGTTCTTCTTTTATCT 58.139 33.333 29.30 0.00 32.41 1.98
726 1097 7.600752 ACTGTACAGAGTTCTTCTTTTATCTGC 59.399 37.037 29.30 0.00 38.14 4.26
728 1099 8.150945 TGTACAGAGTTCTTCTTTTATCTGCTT 58.849 33.333 0.00 0.00 38.14 3.91
729 1100 7.665561 ACAGAGTTCTTCTTTTATCTGCTTC 57.334 36.000 0.00 0.00 38.14 3.86
730 1101 7.449247 ACAGAGTTCTTCTTTTATCTGCTTCT 58.551 34.615 0.00 0.00 38.14 2.85
731 1102 7.602265 ACAGAGTTCTTCTTTTATCTGCTTCTC 59.398 37.037 0.00 0.00 38.14 2.87
732 1103 6.811170 AGAGTTCTTCTTTTATCTGCTTCTCG 59.189 38.462 0.00 0.00 29.61 4.04
733 1104 5.872070 AGTTCTTCTTTTATCTGCTTCTCGG 59.128 40.000 0.00 0.00 0.00 4.63
734 1105 4.184629 TCTTCTTTTATCTGCTTCTCGGC 58.815 43.478 0.00 0.00 0.00 5.54
735 1106 2.906354 TCTTTTATCTGCTTCTCGGCC 58.094 47.619 0.00 0.00 0.00 6.13
736 1107 1.594862 CTTTTATCTGCTTCTCGGCCG 59.405 52.381 22.12 22.12 0.00 6.13
737 1108 0.810031 TTTATCTGCTTCTCGGCCGC 60.810 55.000 23.51 6.41 0.00 6.53
738 1109 1.955495 TTATCTGCTTCTCGGCCGCA 61.955 55.000 23.51 11.62 0.00 5.69
739 1110 2.629050 TATCTGCTTCTCGGCCGCAC 62.629 60.000 23.51 8.05 0.00 5.34
743 1114 2.736995 CTTCTCGGCCGCACGAAA 60.737 61.111 23.51 8.71 42.98 3.46
744 1115 2.280254 TTCTCGGCCGCACGAAAA 60.280 55.556 23.51 0.00 42.98 2.29
745 1116 2.227968 CTTCTCGGCCGCACGAAAAG 62.228 60.000 23.51 11.25 42.98 2.27
746 1117 3.788766 CTCGGCCGCACGAAAAGG 61.789 66.667 23.51 0.00 42.98 3.11
747 1118 4.612412 TCGGCCGCACGAAAAGGT 62.612 61.111 23.51 0.00 40.34 3.50
748 1119 3.656045 CGGCCGCACGAAAAGGTT 61.656 61.111 14.67 0.00 35.47 3.50
749 1120 2.050442 GGCCGCACGAAAAGGTTG 60.050 61.111 0.00 0.00 0.00 3.77
750 1121 2.719354 GCCGCACGAAAAGGTTGT 59.281 55.556 0.00 0.00 0.00 3.32
795 1166 1.269361 ACCGGTTTTTCATCAAACGGC 60.269 47.619 0.00 0.00 37.50 5.68
802 1173 2.787473 TTCATCAAACGGCAGAGGAT 57.213 45.000 0.00 0.00 0.00 3.24
826 1197 0.038310 GCTAGGTCCCACTGCCTTTT 59.962 55.000 0.00 0.00 36.38 2.27
827 1198 1.547901 GCTAGGTCCCACTGCCTTTTT 60.548 52.381 0.00 0.00 36.38 1.94
828 1199 2.290705 GCTAGGTCCCACTGCCTTTTTA 60.291 50.000 0.00 0.00 36.38 1.52
829 1200 3.624959 GCTAGGTCCCACTGCCTTTTTAT 60.625 47.826 0.00 0.00 36.38 1.40
830 1201 2.807676 AGGTCCCACTGCCTTTTTATG 58.192 47.619 0.00 0.00 0.00 1.90
831 1202 2.378547 AGGTCCCACTGCCTTTTTATGA 59.621 45.455 0.00 0.00 0.00 2.15
832 1203 3.161866 GGTCCCACTGCCTTTTTATGAA 58.838 45.455 0.00 0.00 0.00 2.57
833 1204 3.576550 GGTCCCACTGCCTTTTTATGAAA 59.423 43.478 0.00 0.00 0.00 2.69
834 1205 4.039852 GGTCCCACTGCCTTTTTATGAAAA 59.960 41.667 0.00 0.00 33.86 2.29
835 1206 5.454045 GGTCCCACTGCCTTTTTATGAAAAA 60.454 40.000 0.00 0.00 37.99 1.94
870 1821 1.153349 GACTCCGGATTGGGACAGC 60.153 63.158 3.57 0.00 42.39 4.40
914 1865 4.932200 ACACTACTACTGACGTACTGTACC 59.068 45.833 12.08 0.29 33.04 3.34
928 1879 5.107607 CGTACTGTACCATTCTGTGTTGTTC 60.108 44.000 12.08 0.00 0.00 3.18
967 1918 0.991920 ACCCACCAGTACAAGGGATG 59.008 55.000 15.98 4.17 44.30 3.51
1027 1978 3.064900 AGCCAAGTCTCTTGGACAATC 57.935 47.619 26.37 12.03 46.72 2.67
1030 1981 3.403038 CCAAGTCTCTTGGACAATCGTT 58.597 45.455 19.98 0.00 46.72 3.85
1041 1992 4.963373 TGGACAATCGTTACAAAGAGGAA 58.037 39.130 0.00 0.00 0.00 3.36
1043 1994 5.468746 TGGACAATCGTTACAAAGAGGAAAG 59.531 40.000 0.00 0.00 0.00 2.62
1054 2005 6.048732 ACAAAGAGGAAAGAGGAGAAGATC 57.951 41.667 0.00 0.00 0.00 2.75
1073 2024 1.903877 CGTGAAGCCATGGGAGGAGT 61.904 60.000 15.13 0.00 0.00 3.85
1074 2025 0.329596 GTGAAGCCATGGGAGGAGTT 59.670 55.000 15.13 0.00 0.00 3.01
1077 2028 1.867595 AAGCCATGGGAGGAGTTGGG 61.868 60.000 15.13 0.00 0.00 4.12
1082 2033 2.692741 GGGAGGAGTTGGGGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
1083 2034 2.454941 GGAGGAGTTGGGGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
1084 2035 1.690985 GGAGGAGTTGGGGGAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
1085 2036 1.690985 GAGGAGTTGGGGGAGGAGG 60.691 68.421 0.00 0.00 0.00 4.30
1086 2037 2.182858 GAGGAGTTGGGGGAGGAGGA 62.183 65.000 0.00 0.00 0.00 3.71
1087 2038 1.229853 GGAGTTGGGGGAGGAGGAA 60.230 63.158 0.00 0.00 0.00 3.36
1088 2039 1.563577 GGAGTTGGGGGAGGAGGAAC 61.564 65.000 0.00 0.00 0.00 3.62
1089 2040 0.840722 GAGTTGGGGGAGGAGGAACA 60.841 60.000 0.00 0.00 0.00 3.18
1090 2041 0.842467 AGTTGGGGGAGGAGGAACAG 60.842 60.000 0.00 0.00 0.00 3.16
1091 2042 1.541368 TTGGGGGAGGAGGAACAGG 60.541 63.158 0.00 0.00 0.00 4.00
1092 2043 2.125225 GGGGGAGGAGGAACAGGT 59.875 66.667 0.00 0.00 0.00 4.00
1093 2044 1.394963 GGGGGAGGAGGAACAGGTA 59.605 63.158 0.00 0.00 0.00 3.08
1094 2045 0.691413 GGGGGAGGAGGAACAGGTAG 60.691 65.000 0.00 0.00 0.00 3.18
1095 2046 0.338814 GGGGAGGAGGAACAGGTAGA 59.661 60.000 0.00 0.00 0.00 2.59
1096 2047 1.689892 GGGGAGGAGGAACAGGTAGAG 60.690 61.905 0.00 0.00 0.00 2.43
1155 2106 3.701040 AGCTCTCTGAATCCTCTTCTGAC 59.299 47.826 0.00 0.00 0.00 3.51
1161 2112 6.440010 TCTCTGAATCCTCTTCTGACAATTCT 59.560 38.462 0.00 0.00 0.00 2.40
1164 2115 5.871524 TGAATCCTCTTCTGACAATTCTTCG 59.128 40.000 0.00 0.00 0.00 3.79
1175 2126 2.503356 ACAATTCTTCGGAGGAGCATCT 59.497 45.455 0.00 0.00 33.73 2.90
1176 2127 3.706594 ACAATTCTTCGGAGGAGCATCTA 59.293 43.478 0.00 0.00 33.73 1.98
1206 2157 0.179073 CCGGTAAGTCCCTGCATCAG 60.179 60.000 0.00 0.00 0.00 2.90
1284 2235 1.063266 AGCTTCCAAGTTCCAAACCCA 60.063 47.619 0.00 0.00 0.00 4.51
1322 2273 6.136541 ACTTCTGGTTTTGATGTGTTCTTC 57.863 37.500 0.00 0.00 0.00 2.87
1325 2276 2.286713 TGGTTTTGATGTGTTCTTCGCG 60.287 45.455 0.00 0.00 0.00 5.87
1326 2277 2.307049 GTTTTGATGTGTTCTTCGCGG 58.693 47.619 6.13 0.00 0.00 6.46
1331 2282 1.389106 GATGTGTTCTTCGCGGTGTAC 59.611 52.381 6.13 4.19 0.00 2.90
1332 2283 0.102663 TGTGTTCTTCGCGGTGTACA 59.897 50.000 6.13 6.94 0.00 2.90
1333 2284 1.269883 TGTGTTCTTCGCGGTGTACAT 60.270 47.619 6.13 0.00 0.00 2.29
1334 2285 1.389106 GTGTTCTTCGCGGTGTACATC 59.611 52.381 6.13 0.00 0.00 3.06
1337 2288 0.172578 TCTTCGCGGTGTACATCCAG 59.827 55.000 6.13 0.00 0.00 3.86
1362 2313 1.610522 CCAGCCAGCCATATAGTTTGC 59.389 52.381 0.00 0.00 0.00 3.68
1364 2315 2.954318 CAGCCAGCCATATAGTTTGCTT 59.046 45.455 0.00 0.00 30.08 3.91
1373 2324 6.833416 AGCCATATAGTTTGCTTTTCCACATA 59.167 34.615 0.00 0.00 0.00 2.29
1413 2364 9.387257 CTTGATCTATATGCATGTAAATAGCCA 57.613 33.333 10.16 7.13 0.00 4.75
1414 2365 9.737844 TTGATCTATATGCATGTAAATAGCCAA 57.262 29.630 10.16 11.89 0.00 4.52
1415 2366 9.737844 TGATCTATATGCATGTAAATAGCCAAA 57.262 29.630 10.16 0.00 0.00 3.28
1433 2384 4.099881 GCCAAAATAAGAATCTGCCATGGA 59.900 41.667 18.40 0.00 0.00 3.41
1434 2385 5.395546 GCCAAAATAAGAATCTGCCATGGAA 60.396 40.000 18.40 3.09 0.00 3.53
1444 2395 5.841957 ATCTGCCATGGAAATACTCAAAC 57.158 39.130 18.40 0.00 0.00 2.93
1455 2406 7.235079 TGGAAATACTCAAACCATGTAAAGGA 58.765 34.615 0.00 0.00 0.00 3.36
1456 2407 7.726291 TGGAAATACTCAAACCATGTAAAGGAA 59.274 33.333 0.00 0.00 0.00 3.36
1458 2409 9.974980 GAAATACTCAAACCATGTAAAGGAAAA 57.025 29.630 0.00 0.00 0.00 2.29
1467 2418 8.606040 AACCATGTAAAGGAAAAACATTCATG 57.394 30.769 0.00 0.00 31.60 3.07
1473 2424 9.829507 TGTAAAGGAAAAACATTCATGTCATTT 57.170 25.926 0.00 0.00 40.80 2.32
1484 2440 5.565592 TTCATGTCATTTACACATCCAGC 57.434 39.130 0.00 0.00 42.09 4.85
1489 2445 4.122776 GTCATTTACACATCCAGCTCGAT 58.877 43.478 0.00 0.00 0.00 3.59
1500 2456 1.220206 AGCTCGATGGTGCTGAAGG 59.780 57.895 3.32 0.00 41.18 3.46
1501 2457 1.078848 GCTCGATGGTGCTGAAGGT 60.079 57.895 0.00 0.00 0.00 3.50
1504 2460 0.389817 TCGATGGTGCTGAAGGTTCG 60.390 55.000 0.00 0.00 0.00 3.95
1523 2483 0.673644 GGCGAGAAACTAAGCTGCCA 60.674 55.000 0.00 0.00 40.66 4.92
1534 2494 0.181114 AAGCTGCCAGTCACTGTCAA 59.819 50.000 3.56 0.00 0.00 3.18
1625 2585 2.175878 ACACATCACAACTGCTCCTC 57.824 50.000 0.00 0.00 0.00 3.71
1666 2626 1.956629 CTTCATACCCCGGCGTGAGT 61.957 60.000 6.01 2.24 0.00 3.41
1731 2691 7.312657 AGTAATTGTCTATGTGTGCATTCTG 57.687 36.000 0.00 0.00 36.58 3.02
1756 2716 4.537015 GACGGAAAAGTTTTGATCTGTGG 58.463 43.478 5.36 0.00 31.78 4.17
1757 2717 4.204012 ACGGAAAAGTTTTGATCTGTGGA 58.796 39.130 5.36 0.00 30.49 4.02
2020 2980 3.501349 GGCTCTACCTAGGTGATCATCA 58.499 50.000 25.33 0.91 34.51 3.07
2021 2981 4.093011 GGCTCTACCTAGGTGATCATCAT 58.907 47.826 25.33 0.00 34.51 2.45
2022 2982 5.265191 GGCTCTACCTAGGTGATCATCATA 58.735 45.833 25.33 0.00 34.51 2.15
2023 2983 5.896678 GGCTCTACCTAGGTGATCATCATAT 59.103 44.000 25.33 0.00 34.51 1.78
2024 2984 6.040391 GGCTCTACCTAGGTGATCATCATATC 59.960 46.154 25.33 1.19 34.51 1.63
2025 2985 6.605194 GCTCTACCTAGGTGATCATCATATCA 59.395 42.308 25.33 0.00 33.48 2.15
2026 2986 7.287466 GCTCTACCTAGGTGATCATCATATCAT 59.713 40.741 25.33 0.00 38.13 2.45
2027 2987 9.199645 CTCTACCTAGGTGATCATCATATCATT 57.800 37.037 25.33 0.00 38.13 2.57
2056 3016 9.762933 ATTCGTACCTTAGTACTGTTTACAAAA 57.237 29.630 5.39 0.74 45.68 2.44
2057 3017 9.593134 TTCGTACCTTAGTACTGTTTACAAAAA 57.407 29.630 5.39 0.00 45.68 1.94
2080 3040 1.616620 CATTTTAATGTGCGTGCGCT 58.383 45.000 17.49 0.00 42.51 5.92
2081 3041 1.984990 CATTTTAATGTGCGTGCGCTT 59.015 42.857 17.49 6.47 42.51 4.68
2082 3042 1.403493 TTTTAATGTGCGTGCGCTTG 58.597 45.000 17.49 1.22 42.51 4.01
2083 3043 1.001240 TTTAATGTGCGTGCGCTTGC 61.001 50.000 17.49 13.53 42.51 4.01
2103 3063 3.716585 GCGAGAAGAGCCAGATGC 58.283 61.111 0.00 0.00 41.71 3.91
2197 3157 6.823689 AGCATGAGGTAGTAATAAACTTGTGG 59.176 38.462 0.00 0.00 39.80 4.17
2269 3235 2.945668 ACTCTTATTTTGCAGGGCGATC 59.054 45.455 0.00 0.00 0.00 3.69
2302 3274 1.299976 CTACCACAGGGAAGGCCAC 59.700 63.158 5.01 0.00 38.05 5.01
2499 3471 1.429148 GCCGCCAAAGTGATCGGTAG 61.429 60.000 0.00 0.00 43.45 3.18
2512 3490 0.034337 TCGGTAGGTGCAGAAACCAC 59.966 55.000 10.86 0.39 43.20 4.16
2517 3495 0.178981 AGGTGCAGAAACCACAGCAT 60.179 50.000 0.00 0.00 43.20 3.79
2534 3522 1.152963 ATAATGCTCCCGCCCACAC 60.153 57.895 0.00 0.00 34.43 3.82
2551 3539 4.099585 CGTACGTGCGTGCGTGTC 62.100 66.667 22.72 8.13 46.22 3.67
2559 3547 1.346197 GCGTGCGTGTCATGAGATG 59.654 57.895 7.70 7.70 33.49 2.90
2563 3551 1.020861 TGCGTGTCATGAGATGTGCC 61.021 55.000 13.16 0.00 0.00 5.01
2564 3552 0.742281 GCGTGTCATGAGATGTGCCT 60.742 55.000 13.16 0.00 0.00 4.75
2565 3553 1.284657 CGTGTCATGAGATGTGCCTC 58.715 55.000 3.91 0.00 0.00 4.70
2566 3554 1.661341 GTGTCATGAGATGTGCCTCC 58.339 55.000 0.00 0.00 32.32 4.30
2567 3555 1.065926 GTGTCATGAGATGTGCCTCCA 60.066 52.381 0.00 0.00 32.32 3.86
2568 3556 1.841919 TGTCATGAGATGTGCCTCCAT 59.158 47.619 0.00 0.00 32.32 3.41
2724 3843 0.393132 AGATCGAGGACACGCTGAGA 60.393 55.000 0.00 0.00 0.00 3.27
3308 4533 1.670949 CCCGAGAGAAGCTAGCTGCA 61.671 60.000 25.01 0.00 45.94 4.41
3331 4556 6.311200 GCAACCAACTGAGCCAAAATTAATAG 59.689 38.462 0.00 0.00 0.00 1.73
3336 4561 7.337942 CCAACTGAGCCAAAATTAATAGTCTCT 59.662 37.037 0.00 0.00 0.00 3.10
3337 4562 9.383519 CAACTGAGCCAAAATTAATAGTCTCTA 57.616 33.333 0.00 0.00 0.00 2.43
3570 4795 3.342377 TTACACATTTCGGCCATGAGA 57.658 42.857 2.24 0.00 0.00 3.27
3866 5091 2.356553 CGCGACGGGTCTCCAAAA 60.357 61.111 0.00 0.00 0.00 2.44
4210 5435 3.691575 TGGACACAAAGTTTTCCAGTCA 58.308 40.909 3.78 0.00 33.02 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.012374 TCATGAACATGGCTTCTTTCTCC 58.988 43.478 13.67 0.00 39.24 3.71
47 48 2.027385 GTGCTCCAATCAAATCCCTCC 58.973 52.381 0.00 0.00 0.00 4.30
52 53 4.157289 ACATCAGTGTGCTCCAATCAAATC 59.843 41.667 0.00 0.00 37.14 2.17
59 60 2.703416 GATGACATCAGTGTGCTCCAA 58.297 47.619 10.67 0.00 39.09 3.53
69 70 2.663808 CAGAGCTAGCGATGACATCAG 58.336 52.381 15.58 9.12 0.00 2.90
70 71 1.269465 GCAGAGCTAGCGATGACATCA 60.269 52.381 21.82 0.00 0.00 3.07
112 113 1.815003 CATGCCGGCTTCATCGTCA 60.815 57.895 29.70 3.35 0.00 4.35
114 115 1.815421 GACATGCCGGCTTCATCGT 60.815 57.895 29.70 15.26 0.00 3.73
140 141 2.213499 CTTTTCCTCGCTATCGGCAAT 58.787 47.619 0.00 0.00 41.91 3.56
141 142 1.066430 ACTTTTCCTCGCTATCGGCAA 60.066 47.619 0.00 0.00 41.91 4.52
152 153 5.046231 AGTCTTCCATGGTCTACTTTTCCTC 60.046 44.000 12.58 0.00 0.00 3.71
171 172 2.474816 GACACAAGAAGCGACAGTCTT 58.525 47.619 0.00 0.00 34.37 3.01
174 175 0.753262 AGGACACAAGAAGCGACAGT 59.247 50.000 0.00 0.00 0.00 3.55
176 177 1.272490 CCTAGGACACAAGAAGCGACA 59.728 52.381 1.05 0.00 0.00 4.35
211 212 3.103911 GTGACGCCCGACAAGACG 61.104 66.667 0.00 0.00 0.00 4.18
237 238 3.741476 CCCGTGAAGCAGGCAAGC 61.741 66.667 0.00 0.00 0.00 4.01
244 245 2.589540 CTATGCCCCCGTGAAGCA 59.410 61.111 0.00 0.00 41.50 3.91
258 259 3.136626 GGAAGATAGTTGTGGTGGCCTAT 59.863 47.826 3.32 0.00 0.00 2.57
270 271 1.580059 TTGGGCGAGGGAAGATAGTT 58.420 50.000 0.00 0.00 0.00 2.24
274 275 1.545841 GTTTTTGGGCGAGGGAAGAT 58.454 50.000 0.00 0.00 0.00 2.40
276 277 0.825840 TGGTTTTTGGGCGAGGGAAG 60.826 55.000 0.00 0.00 0.00 3.46
296 297 0.949105 GTGAAGCACGGATGAACGGT 60.949 55.000 0.00 0.00 38.39 4.83
321 322 1.342819 CGAGGGGAAGAATAGGCTCTG 59.657 57.143 0.00 0.00 0.00 3.35
326 327 1.301009 GCGCGAGGGGAAGAATAGG 60.301 63.158 12.10 0.00 0.00 2.57
369 370 1.734477 CAAGCTCACTGGACCGTCG 60.734 63.158 0.00 0.00 0.00 5.12
399 400 1.745489 GCCACGACATGTCTTCCCC 60.745 63.158 22.95 4.71 0.00 4.81
417 749 1.715585 CCGCGACATAGCCTGTTTG 59.284 57.895 8.23 0.00 38.54 2.93
432 764 1.207085 CTAGTCTATCGTCGGCCGC 59.793 63.158 23.51 15.21 36.19 6.53
433 765 0.883814 ACCTAGTCTATCGTCGGCCG 60.884 60.000 22.12 22.12 38.13 6.13
440 772 4.142643 GGCGGATTCTAACCTAGTCTATCG 60.143 50.000 0.00 0.00 0.00 2.92
484 817 4.083749 CCGGACGAACACATTTACATTTCA 60.084 41.667 0.00 0.00 0.00 2.69
501 834 2.346099 AAATTCATGCAAACCGGACG 57.654 45.000 9.46 0.00 0.00 4.79
505 838 4.034975 ACAAACCAAAATTCATGCAAACCG 59.965 37.500 0.00 0.00 0.00 4.44
512 845 7.928103 TGGATTTCAACAAACCAAAATTCATG 58.072 30.769 0.00 0.00 0.00 3.07
537 874 6.266168 TCTTGTCCGCATACATTTCAAAAT 57.734 33.333 0.00 0.00 0.00 1.82
538 875 5.697473 TCTTGTCCGCATACATTTCAAAA 57.303 34.783 0.00 0.00 0.00 2.44
552 889 3.251479 TGATGGATCAGTTCTTGTCCG 57.749 47.619 0.00 0.00 32.74 4.79
554 891 5.188434 TGGATTGATGGATCAGTTCTTGTC 58.812 41.667 0.00 0.00 38.19 3.18
556 893 5.009710 CCATGGATTGATGGATCAGTTCTTG 59.990 44.000 5.56 0.00 45.24 3.02
560 897 4.801521 TCCATGGATTGATGGATCAGTT 57.198 40.909 11.44 0.00 45.85 3.16
578 949 3.236391 GGGCACCGTATCCATCCA 58.764 61.111 0.00 0.00 40.86 3.41
593 964 0.390735 CGTTGACCCTCTAAACCGGG 60.391 60.000 6.32 0.00 46.26 5.73
595 966 0.390735 CCCGTTGACCCTCTAAACCG 60.391 60.000 0.00 0.00 0.00 4.44
596 967 0.978907 TCCCGTTGACCCTCTAAACC 59.021 55.000 0.00 0.00 0.00 3.27
598 969 2.314071 TCTCCCGTTGACCCTCTAAA 57.686 50.000 0.00 0.00 0.00 1.85
599 970 2.108168 CATCTCCCGTTGACCCTCTAA 58.892 52.381 0.00 0.00 0.00 2.10
602 973 1.153349 GCATCTCCCGTTGACCCTC 60.153 63.158 0.00 0.00 0.00 4.30
603 974 2.670148 GGCATCTCCCGTTGACCCT 61.670 63.158 0.00 0.00 0.00 4.34
619 990 1.185315 TTCCAATGCTTGCTTAGGGC 58.815 50.000 0.00 0.00 42.22 5.19
620 991 2.762327 ACATTCCAATGCTTGCTTAGGG 59.238 45.455 0.00 0.00 40.04 3.53
621 992 4.460948 AACATTCCAATGCTTGCTTAGG 57.539 40.909 0.00 0.00 40.04 2.69
622 993 4.628333 CCAAACATTCCAATGCTTGCTTAG 59.372 41.667 9.13 0.00 39.78 2.18
623 994 4.040217 ACCAAACATTCCAATGCTTGCTTA 59.960 37.500 9.13 0.00 39.78 3.09
624 995 3.181452 ACCAAACATTCCAATGCTTGCTT 60.181 39.130 9.13 0.00 39.78 3.91
625 996 2.369532 ACCAAACATTCCAATGCTTGCT 59.630 40.909 9.13 0.00 39.78 3.91
626 997 2.769893 ACCAAACATTCCAATGCTTGC 58.230 42.857 9.13 0.00 39.78 4.01
627 998 4.021192 AGGTACCAAACATTCCAATGCTTG 60.021 41.667 15.94 8.01 40.42 4.01
628 999 4.021192 CAGGTACCAAACATTCCAATGCTT 60.021 41.667 15.94 0.00 40.04 3.91
645 1016 0.458716 GAGCGAGCTTGGTCAGGTAC 60.459 60.000 25.13 0.07 36.41 3.34
673 1044 4.597404 ACGTATCACTCATGCATCATCT 57.403 40.909 0.00 0.00 0.00 2.90
681 1052 3.614176 CAGTCACCAACGTATCACTCATG 59.386 47.826 0.00 0.00 0.00 3.07
692 1063 2.795175 ACTCTGTACAGTCACCAACG 57.205 50.000 21.99 5.09 0.00 4.10
707 1078 6.811170 CGAGAAGCAGATAAAAGAAGAACTCT 59.189 38.462 0.00 0.00 35.13 3.24
712 1083 4.184629 GCCGAGAAGCAGATAAAAGAAGA 58.815 43.478 0.00 0.00 0.00 2.87
714 1085 3.270877 GGCCGAGAAGCAGATAAAAGAA 58.729 45.455 0.00 0.00 0.00 2.52
715 1086 2.738643 CGGCCGAGAAGCAGATAAAAGA 60.739 50.000 24.07 0.00 0.00 2.52
716 1087 1.594862 CGGCCGAGAAGCAGATAAAAG 59.405 52.381 24.07 0.00 0.00 2.27
717 1088 1.651987 CGGCCGAGAAGCAGATAAAA 58.348 50.000 24.07 0.00 0.00 1.52
718 1089 0.810031 GCGGCCGAGAAGCAGATAAA 60.810 55.000 33.48 0.00 0.00 1.40
719 1090 1.227263 GCGGCCGAGAAGCAGATAA 60.227 57.895 33.48 0.00 0.00 1.75
720 1091 2.417516 GCGGCCGAGAAGCAGATA 59.582 61.111 33.48 0.00 0.00 1.98
722 1093 4.742201 GTGCGGCCGAGAAGCAGA 62.742 66.667 33.48 0.00 41.93 4.26
726 1097 2.227968 CTTTTCGTGCGGCCGAGAAG 62.228 60.000 33.48 16.83 40.93 2.85
728 1099 2.736995 CTTTTCGTGCGGCCGAGA 60.737 61.111 33.48 21.66 38.23 4.04
729 1100 3.788766 CCTTTTCGTGCGGCCGAG 61.789 66.667 33.48 19.49 38.23 4.63
730 1101 4.612412 ACCTTTTCGTGCGGCCGA 62.612 61.111 33.48 11.82 34.52 5.54
731 1102 3.656045 AACCTTTTCGTGCGGCCG 61.656 61.111 24.05 24.05 0.00 6.13
732 1103 2.050442 CAACCTTTTCGTGCGGCC 60.050 61.111 0.00 0.00 0.00 6.13
733 1104 0.526739 AAACAACCTTTTCGTGCGGC 60.527 50.000 0.00 0.00 0.00 6.53
734 1105 1.915952 AAAACAACCTTTTCGTGCGG 58.084 45.000 0.00 0.00 0.00 5.69
760 1131 1.825474 ACCGGTCTAATGGACTCTGTG 59.175 52.381 0.00 0.00 43.97 3.66
764 1135 4.320870 TGAAAAACCGGTCTAATGGACTC 58.679 43.478 8.04 0.00 43.97 3.36
771 1142 4.023878 CCGTTTGATGAAAAACCGGTCTAA 60.024 41.667 8.04 0.00 36.83 2.10
779 1150 3.004315 TCCTCTGCCGTTTGATGAAAAAC 59.996 43.478 0.00 0.00 36.81 2.43
795 1166 0.313672 GACCTAGCGAGCATCCTCTG 59.686 60.000 0.00 0.00 35.90 3.35
802 1173 2.037367 AGTGGGACCTAGCGAGCA 59.963 61.111 0.00 0.00 0.00 4.26
832 1203 6.879458 GGAGTCTACCACATCAGTATGTTTTT 59.121 38.462 0.00 0.00 44.07 1.94
833 1204 6.407202 GGAGTCTACCACATCAGTATGTTTT 58.593 40.000 0.00 0.00 44.07 2.43
834 1205 5.394224 CGGAGTCTACCACATCAGTATGTTT 60.394 44.000 0.00 0.00 44.07 2.83
835 1206 4.098044 CGGAGTCTACCACATCAGTATGTT 59.902 45.833 0.00 0.00 44.07 2.71
838 1209 3.117625 TCCGGAGTCTACCACATCAGTAT 60.118 47.826 0.00 0.00 0.00 2.12
841 1212 1.763968 TCCGGAGTCTACCACATCAG 58.236 55.000 0.00 0.00 0.00 2.90
844 1795 1.762957 CCAATCCGGAGTCTACCACAT 59.237 52.381 11.34 0.00 36.56 3.21
851 1802 1.617947 GCTGTCCCAATCCGGAGTCT 61.618 60.000 11.34 0.00 36.56 3.24
914 1865 4.637483 AACCACAGAACAACACAGAATG 57.363 40.909 0.00 0.00 46.00 2.67
980 1931 9.166173 TGTGCATATCAGCTTCATTATATAACC 57.834 33.333 0.00 0.00 34.99 2.85
1027 1978 5.135508 TCTCCTCTTTCCTCTTTGTAACG 57.864 43.478 0.00 0.00 0.00 3.18
1030 1981 6.127591 CGATCTTCTCCTCTTTCCTCTTTGTA 60.128 42.308 0.00 0.00 0.00 2.41
1041 1992 2.167487 GGCTTCACGATCTTCTCCTCTT 59.833 50.000 0.00 0.00 0.00 2.85
1043 1994 1.478510 TGGCTTCACGATCTTCTCCTC 59.521 52.381 0.00 0.00 0.00 3.71
1054 2005 1.153289 CTCCTCCCATGGCTTCACG 60.153 63.158 6.09 0.00 0.00 4.35
1073 2024 1.541368 CCTGTTCCTCCTCCCCCAA 60.541 63.158 0.00 0.00 0.00 4.12
1074 2025 1.457380 TACCTGTTCCTCCTCCCCCA 61.457 60.000 0.00 0.00 0.00 4.96
1077 2028 1.689892 CCTCTACCTGTTCCTCCTCCC 60.690 61.905 0.00 0.00 0.00 4.30
1082 2033 3.028130 CCTCTTCCTCTACCTGTTCCTC 58.972 54.545 0.00 0.00 0.00 3.71
1083 2034 2.890602 GCCTCTTCCTCTACCTGTTCCT 60.891 54.545 0.00 0.00 0.00 3.36
1084 2035 1.483004 GCCTCTTCCTCTACCTGTTCC 59.517 57.143 0.00 0.00 0.00 3.62
1085 2036 1.135333 CGCCTCTTCCTCTACCTGTTC 59.865 57.143 0.00 0.00 0.00 3.18
1086 2037 1.187087 CGCCTCTTCCTCTACCTGTT 58.813 55.000 0.00 0.00 0.00 3.16
1087 2038 0.331954 TCGCCTCTTCCTCTACCTGT 59.668 55.000 0.00 0.00 0.00 4.00
1088 2039 1.611491 GATCGCCTCTTCCTCTACCTG 59.389 57.143 0.00 0.00 0.00 4.00
1089 2040 1.816183 CGATCGCCTCTTCCTCTACCT 60.816 57.143 0.26 0.00 0.00 3.08
1090 2041 0.594110 CGATCGCCTCTTCCTCTACC 59.406 60.000 0.26 0.00 0.00 3.18
1091 2042 0.039888 GCGATCGCCTCTTCCTCTAC 60.040 60.000 29.48 0.00 34.56 2.59
1092 2043 2.332277 GCGATCGCCTCTTCCTCTA 58.668 57.895 29.48 0.00 34.56 2.43
1093 2044 3.124686 GCGATCGCCTCTTCCTCT 58.875 61.111 29.48 0.00 34.56 3.69
1140 2091 5.871524 CGAAGAATTGTCAGAAGAGGATTCA 59.128 40.000 0.00 0.00 32.63 2.57
1155 2106 3.191078 AGATGCTCCTCCGAAGAATTG 57.809 47.619 0.00 0.00 0.00 2.32
1161 2112 2.437085 TCACTAGATGCTCCTCCGAA 57.563 50.000 0.00 0.00 0.00 4.30
1164 2115 4.744795 TCTTTTCACTAGATGCTCCTCC 57.255 45.455 0.00 0.00 0.00 4.30
1175 2126 4.262592 GGGACTTACCGGTTCTTTTCACTA 60.263 45.833 15.04 0.00 40.11 2.74
1176 2127 3.495629 GGGACTTACCGGTTCTTTTCACT 60.496 47.826 15.04 0.00 40.11 3.41
1236 2187 4.100035 ACATAGCTTCTGACGAATCATCCA 59.900 41.667 0.00 0.00 33.22 3.41
1237 2188 4.626042 ACATAGCTTCTGACGAATCATCC 58.374 43.478 0.00 0.00 33.22 3.51
1284 2235 1.707427 AGAAGTTTCAGACATGGGGCT 59.293 47.619 0.00 0.00 0.00 5.19
1322 2273 2.890474 GGCTGGATGTACACCGCG 60.890 66.667 0.00 0.00 0.00 6.46
1325 2276 1.452108 GGCTGGCTGGATGTACACC 60.452 63.158 0.00 2.40 0.00 4.16
1326 2277 0.745845 CTGGCTGGCTGGATGTACAC 60.746 60.000 0.00 0.00 0.00 2.90
1331 2282 4.435970 TGGCTGGCTGGCTGGATG 62.436 66.667 18.27 0.00 42.34 3.51
1332 2283 4.124943 CTGGCTGGCTGGCTGGAT 62.125 66.667 18.27 0.00 42.34 3.41
1337 2288 2.416107 TATATGGCTGGCTGGCTGGC 62.416 60.000 23.48 23.48 42.34 4.85
1401 2352 9.971922 GCAGATTCTTATTTTGGCTATTTACAT 57.028 29.630 0.00 0.00 0.00 2.29
1402 2353 8.413229 GGCAGATTCTTATTTTGGCTATTTACA 58.587 33.333 0.00 0.00 0.00 2.41
1408 2359 5.302568 CCATGGCAGATTCTTATTTTGGCTA 59.697 40.000 0.00 0.00 35.59 3.93
1410 2361 4.099881 TCCATGGCAGATTCTTATTTTGGC 59.900 41.667 6.96 0.00 35.19 4.52
1413 2364 9.205513 AGTATTTCCATGGCAGATTCTTATTTT 57.794 29.630 6.96 0.00 0.00 1.82
1414 2365 8.773033 AGTATTTCCATGGCAGATTCTTATTT 57.227 30.769 6.96 0.00 0.00 1.40
1415 2366 8.000709 TGAGTATTTCCATGGCAGATTCTTATT 58.999 33.333 6.96 0.00 0.00 1.40
1416 2367 7.520798 TGAGTATTTCCATGGCAGATTCTTAT 58.479 34.615 6.96 0.00 0.00 1.73
1417 2368 6.899089 TGAGTATTTCCATGGCAGATTCTTA 58.101 36.000 6.96 0.00 0.00 2.10
1420 2371 6.268566 GTTTGAGTATTTCCATGGCAGATTC 58.731 40.000 6.96 0.46 0.00 2.52
1434 2385 9.758651 GTTTTTCCTTTACATGGTTTGAGTATT 57.241 29.630 0.00 0.00 0.00 1.89
1444 2395 7.871973 TGACATGAATGTTTTTCCTTTACATGG 59.128 33.333 0.00 0.00 41.95 3.66
1451 2402 9.260002 GTGTAAATGACATGAATGTTTTTCCTT 57.740 29.630 0.00 0.00 41.95 3.36
1455 2406 9.206870 GGATGTGTAAATGACATGAATGTTTTT 57.793 29.630 0.00 4.46 41.95 1.94
1456 2407 8.366401 TGGATGTGTAAATGACATGAATGTTTT 58.634 29.630 0.00 0.00 41.95 2.43
1458 2409 7.465353 TGGATGTGTAAATGACATGAATGTT 57.535 32.000 0.00 0.00 41.95 2.71
1459 2410 6.405065 GCTGGATGTGTAAATGACATGAATGT 60.405 38.462 0.00 0.00 45.16 2.71
1467 2418 3.521560 TCGAGCTGGATGTGTAAATGAC 58.478 45.455 0.00 0.00 0.00 3.06
1472 2423 1.831106 ACCATCGAGCTGGATGTGTAA 59.169 47.619 29.67 0.00 41.76 2.41
1473 2424 1.136891 CACCATCGAGCTGGATGTGTA 59.863 52.381 29.67 0.00 41.76 2.90
1484 2440 1.363744 GAACCTTCAGCACCATCGAG 58.636 55.000 0.00 0.00 0.00 4.04
1489 2445 2.281484 GCCGAACCTTCAGCACCA 60.281 61.111 0.00 0.00 31.08 4.17
1496 2452 2.358939 TAGTTTCTCGCCGAACCTTC 57.641 50.000 0.00 0.00 0.00 3.46
1498 2454 1.672145 GCTTAGTTTCTCGCCGAACCT 60.672 52.381 0.00 0.00 0.00 3.50
1500 2456 1.390463 CAGCTTAGTTTCTCGCCGAAC 59.610 52.381 0.00 0.00 0.00 3.95
1501 2457 1.710013 CAGCTTAGTTTCTCGCCGAA 58.290 50.000 0.00 0.00 0.00 4.30
1504 2460 0.673644 TGGCAGCTTAGTTTCTCGCC 60.674 55.000 0.00 0.00 38.56 5.54
1584 2544 5.757320 TGTTTGGAATTGTGGTTATGCTTTG 59.243 36.000 0.00 0.00 0.00 2.77
1641 2601 0.759346 GCCGGGGTATGAAGTCATCT 59.241 55.000 2.18 0.00 37.76 2.90
1666 2626 2.243957 CCGTGCAAGCAAGTGACGA 61.244 57.895 7.19 0.00 31.71 4.20
1671 2631 0.951040 GTCTAGCCGTGCAAGCAAGT 60.951 55.000 12.15 0.00 0.00 3.16
1707 2667 7.312657 CAGAATGCACACATAGACAATTACT 57.687 36.000 0.00 0.00 34.62 2.24
1731 2691 2.225727 AGATCAAAACTTTTCCGTCGGC 59.774 45.455 6.34 0.00 0.00 5.54
1910 2870 3.386237 GCGAGCAGGGAGGACTGT 61.386 66.667 0.00 0.00 40.59 3.55
2056 3016 4.756444 CGCACGCACATTAAAATGTTTTT 58.244 34.783 5.60 0.00 46.95 1.94
2057 3017 3.362499 GCGCACGCACATTAAAATGTTTT 60.362 39.130 10.65 0.00 46.95 2.43
2058 3018 2.154772 GCGCACGCACATTAAAATGTTT 59.845 40.909 10.65 0.00 46.95 2.83
2059 3019 1.718711 GCGCACGCACATTAAAATGTT 59.281 42.857 10.65 0.00 46.95 2.71
2061 3021 1.616620 AGCGCACGCACATTAAAATG 58.383 45.000 18.24 1.13 44.88 2.32
2062 3022 1.984990 CAAGCGCACGCACATTAAAAT 59.015 42.857 18.24 0.00 44.88 1.82
2063 3023 1.403493 CAAGCGCACGCACATTAAAA 58.597 45.000 18.24 0.00 44.88 1.52
2064 3024 1.001240 GCAAGCGCACGCACATTAAA 61.001 50.000 18.24 0.00 44.88 1.52
2065 3025 1.441849 GCAAGCGCACGCACATTAA 60.442 52.632 18.24 0.00 44.88 1.40
2066 3026 2.175566 GCAAGCGCACGCACATTA 59.824 55.556 18.24 0.00 44.88 1.90
2067 3027 3.884581 CTGCAAGCGCACGCACATT 62.885 57.895 18.43 0.00 45.36 2.71
2068 3028 4.394078 CTGCAAGCGCACGCACAT 62.394 61.111 18.43 0.00 45.36 3.21
2078 3038 2.748843 GCTCTTCTCGCCTGCAAGC 61.749 63.158 0.00 0.00 0.00 4.01
2079 3039 2.105466 GGCTCTTCTCGCCTGCAAG 61.105 63.158 0.00 0.00 44.17 4.01
2080 3040 2.046892 GGCTCTTCTCGCCTGCAA 60.047 61.111 0.00 0.00 44.17 4.08
2086 3046 3.716585 GCATCTGGCTCTTCTCGC 58.283 61.111 0.00 0.00 40.25 5.03
2103 3063 1.298859 CCGAGGAAAAACCCGCTGAG 61.299 60.000 0.00 0.00 40.05 3.35
2105 3065 2.978018 GCCGAGGAAAAACCCGCTG 61.978 63.158 0.00 0.00 40.05 5.18
2228 3194 4.584327 GTTGGCCAACTAATCACAACTT 57.416 40.909 36.26 0.00 38.25 2.66
2338 3310 0.594284 GCATGTAGTAGGCGTCCGAC 60.594 60.000 0.00 1.89 0.00 4.79
2439 3411 3.039252 AGGAGTAGGAGAAGGACATGG 57.961 52.381 0.00 0.00 0.00 3.66
2499 3471 1.533625 TATGCTGTGGTTTCTGCACC 58.466 50.000 0.00 0.00 42.91 5.01
2534 3522 4.099585 GACACGCACGCACGTACG 62.100 66.667 15.01 15.01 46.34 3.67
2536 3524 2.049894 ATGACACGCACGCACGTA 60.050 55.556 2.78 0.00 46.34 3.57
2540 3528 1.079888 ATCTCATGACACGCACGCA 60.080 52.632 0.00 0.00 0.00 5.24
2541 3529 1.346197 CATCTCATGACACGCACGC 59.654 57.895 0.00 0.00 0.00 5.34
2549 3537 2.634815 ATGGAGGCACATCTCATGAC 57.365 50.000 0.00 0.00 35.58 3.06
2550 3538 3.657398 AAATGGAGGCACATCTCATGA 57.343 42.857 0.00 0.00 35.58 3.07
2551 3539 3.952323 AGAAAATGGAGGCACATCTCATG 59.048 43.478 0.00 0.00 35.58 3.07
2559 3547 4.074970 TCTCTGAAAGAAAATGGAGGCAC 58.925 43.478 0.00 0.00 46.34 5.01
2564 3552 6.546484 ACTCCATTCTCTGAAAGAAAATGGA 58.454 36.000 19.18 19.18 46.34 3.41
2565 3553 6.432162 TGACTCCATTCTCTGAAAGAAAATGG 59.568 38.462 13.84 13.84 46.34 3.16
2566 3554 7.444629 TGACTCCATTCTCTGAAAGAAAATG 57.555 36.000 0.00 0.00 46.34 2.32
2567 3555 7.886970 TGATGACTCCATTCTCTGAAAGAAAAT 59.113 33.333 0.00 0.00 46.85 1.82
2568 3556 7.226441 TGATGACTCCATTCTCTGAAAGAAAA 58.774 34.615 0.00 0.00 46.85 2.29
3308 4533 7.451566 AGACTATTAATTTTGGCTCAGTTGGTT 59.548 33.333 0.00 0.00 0.00 3.67
3331 4556 9.649167 CCTAGCTAAGTACTAGAGAATAGAGAC 57.351 40.741 8.55 0.00 39.64 3.36
3382 4607 3.127030 GCGTGTTCCCCTTTGAATTAGAG 59.873 47.826 0.00 0.00 0.00 2.43
3383 4608 3.078837 GCGTGTTCCCCTTTGAATTAGA 58.921 45.455 0.00 0.00 0.00 2.10
3384 4609 2.163613 GGCGTGTTCCCCTTTGAATTAG 59.836 50.000 0.00 0.00 0.00 1.73
3385 4610 2.164338 GGCGTGTTCCCCTTTGAATTA 58.836 47.619 0.00 0.00 0.00 1.40
3386 4611 0.966179 GGCGTGTTCCCCTTTGAATT 59.034 50.000 0.00 0.00 0.00 2.17
3866 5091 0.835276 TGATCACAGCTGCTATGGCT 59.165 50.000 15.27 0.00 41.07 4.75
4210 5435 5.701290 GCATTTAACTGTAGTCCACTTGTCT 59.299 40.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.