Multiple sequence alignment - TraesCS6B01G166200

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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 TraesCS6B01G166200 chr6B 100.000 3845 0 0 1 3845 173390680 173394524 0.000000e+00 7101.0
1 TraesCS6B01G166200 chr6B 74.263 373 78 17 2443 2806 42004962 42004599 1.440000e-29 141.0
2 TraesCS6B01G166200 chr6A 92.506 2829 102 55 740 3493 109135368 109138161 0.000000e+00 3949.0
3 TraesCS6B01G166200 chr6A 91.924 681 26 14 1 659 109134522 109135195 0.000000e+00 926.0
4 TraesCS6B01G166200 chr6A 88.532 218 18 3 3635 3845 109138486 109138703 1.370000e-64 257.0
5 TraesCS6B01G166200 chr6D 94.532 1591 42 22 1908 3479 90923578 90925142 0.000000e+00 2414.0
6 TraesCS6B01G166200 chr6D 92.626 1207 43 20 740 1907 90922352 90923551 0.000000e+00 1694.0
7 TraesCS6B01G166200 chr6D 93.675 664 31 6 1 659 90921527 90922184 0.000000e+00 983.0
8 TraesCS6B01G166200 chr6D 74.531 373 77 17 2443 2806 25804292 25803929 3.100000e-31 147.0
9 TraesCS6B01G166200 chr1A 85.714 364 46 4 3486 3845 554911490 554911129 2.800000e-101 379.0
10 TraesCS6B01G166200 chr5D 80.114 352 52 12 3501 3841 80193955 80194299 2.970000e-61 246.0
11 TraesCS6B01G166200 chr7A 74.205 566 116 26 2283 2833 670946630 670946080 3.890000e-50 209.0
12 TraesCS6B01G166200 chr7A 76.289 388 76 13 1126 1504 517414678 517414298 3.920000e-45 193.0
13 TraesCS6B01G166200 chr7A 84.264 197 29 2 1309 1504 516997902 516997707 1.410000e-44 191.0
14 TraesCS6B01G166200 chr7A 73.930 514 100 27 2283 2782 516997596 516997103 3.950000e-40 176.0
15 TraesCS6B01G166200 chr7A 73.786 515 101 27 2282 2782 517414199 517413705 5.110000e-39 172.0
16 TraesCS6B01G166200 chr7A 86.667 105 14 0 1126 1230 516998099 516997995 2.430000e-22 117.0
17 TraesCS6B01G166200 chr7A 81.333 75 14 0 2756 2830 497778459 497778533 1.150000e-05 62.1
18 TraesCS6B01G166200 chr3A 78.286 350 55 14 1160 1504 113922401 113922068 5.040000e-49 206.0
19 TraesCS6B01G166200 chr7D 84.925 199 28 2 1307 1504 478327891 478328088 2.340000e-47 200.0
20 TraesCS6B01G166200 chr7D 75.940 399 69 20 1126 1504 478572480 478572089 3.050000e-41 180.0
21 TraesCS6B01G166200 chr7D 73.896 521 102 28 2275 2782 478328201 478328700 1.100000e-40 178.0
22 TraesCS6B01G166200 chr7D 81.633 147 25 2 1085 1230 478333349 478333494 1.880000e-23 121.0
23 TraesCS6B01G166200 chr7D 83.594 128 17 4 1102 1227 478370370 478370495 2.430000e-22 117.0
24 TraesCS6B01G166200 chr7B 73.628 565 121 25 2283 2833 643295732 643295182 3.920000e-45 193.0
25 TraesCS6B01G166200 chr7B 83.920 199 30 2 1307 1504 503472874 503473071 5.070000e-44 189.0
26 TraesCS6B01G166200 chr7B 83.333 198 33 0 1307 1504 504244323 504244126 2.360000e-42 183.0
27 TraesCS6B01G166200 chr7B 81.633 147 25 2 1085 1230 503496245 503496390 1.880000e-23 121.0
28 TraesCS6B01G166200 chr7B 86.667 105 14 0 1126 1230 504244555 504244451 2.430000e-22 117.0
29 TraesCS6B01G166200 chr3D 75.000 428 78 23 1084 1504 95840333 95839928 1.840000e-38 171.0
30 TraesCS6B01G166200 chr3B 80.519 154 25 5 1083 1234 146707048 146706898 3.140000e-21 113.0


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 TraesCS6B01G166200 chr6B 173390680 173394524 3844 False 7101.000000 7101 100.000000 1 3845 1 chr6B.!!$F1 3844
1 TraesCS6B01G166200 chr6A 109134522 109138703 4181 False 1710.666667 3949 90.987333 1 3845 3 chr6A.!!$F1 3844
2 TraesCS6B01G166200 chr6D 90921527 90925142 3615 False 1697.000000 2414 93.611000 1 3479 3 chr6D.!!$F1 3478
3 TraesCS6B01G166200 chr7A 670946080 670946630 550 True 209.000000 209 74.205000 2283 2833 1 chr7A.!!$R1 550

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
910 1028 0.105401 TGGTACCACTCCACTGACCA 60.105 55.000 11.60 0.0 34.63 4.02 F
1242 1374 1.005137 GTCAACGTACGTCGCCAAAAA 60.005 47.619 23.05 0.0 44.19 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1942 0.608640 TGCCAACATCATGCATGCAA 59.391 45.0 26.68 9.94 35.65 4.08 R
3211 3435 1.369091 AATCATCGTTGGAGCCACGC 61.369 55.0 6.62 0.00 0.00 5.34 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
61 63 2.875296 TGGATTTGTTTGGTGAGAGGG 58.125 47.619 0.00 0.00 0.00 4.30
137 143 2.677524 GCCTCAAGCCACATGCCA 60.678 61.111 0.00 0.00 42.71 4.92
138 144 2.998279 GCCTCAAGCCACATGCCAC 61.998 63.158 0.00 0.00 42.71 5.01
139 145 1.604308 CCTCAAGCCACATGCCACA 60.604 57.895 0.00 0.00 42.71 4.17
205 215 6.690194 AGAGAAGAATGCAATACAATCACC 57.310 37.500 0.00 0.00 29.89 4.02
515 534 1.020861 CCAAACGCCCCGTACTAACC 61.021 60.000 0.00 0.00 39.99 2.85
522 541 1.405121 GCCCCGTACTAACCAACTCTG 60.405 57.143 0.00 0.00 0.00 3.35
564 585 8.466798 GGCAAAGATAGTTACACCAAAATACAT 58.533 33.333 0.00 0.00 0.00 2.29
579 600 2.127271 TACATACTTCCACCGTCCGA 57.873 50.000 0.00 0.00 0.00 4.55
583 604 3.448301 ACATACTTCCACCGTCCGAAATA 59.552 43.478 0.00 0.00 0.00 1.40
584 605 2.667473 ACTTCCACCGTCCGAAATAG 57.333 50.000 0.00 0.00 0.00 1.73
599 624 7.065923 CGTCCGAAATAGATCTAGATACATCCA 59.934 40.741 4.89 0.00 0.00 3.41
623 648 2.289195 TGAGCGTCAACTAATTTCGGGT 60.289 45.455 0.00 0.00 0.00 5.28
633 658 1.208165 AATTTCGGGTGGAGGGAGCT 61.208 55.000 0.00 0.00 0.00 4.09
634 659 1.915078 ATTTCGGGTGGAGGGAGCTG 61.915 60.000 0.00 0.00 0.00 4.24
635 660 3.846405 TTCGGGTGGAGGGAGCTGT 62.846 63.158 0.00 0.00 0.00 4.40
661 732 8.644216 TGTATACAGAAGAGTTGGTTCTTGTTA 58.356 33.333 0.08 0.00 37.53 2.41
673 744 7.778382 AGTTGGTTCTTGTTACTTGTAAGGATT 59.222 33.333 0.00 0.00 0.00 3.01
688 759 9.813446 CTTGTAAGGATTATTTTCTAGGTACGT 57.187 33.333 0.00 0.00 30.46 3.57
691 762 7.998753 AAGGATTATTTTCTAGGTACGTTCG 57.001 36.000 0.00 0.00 0.00 3.95
692 763 5.981915 AGGATTATTTTCTAGGTACGTTCGC 59.018 40.000 0.00 0.00 0.00 4.70
722 793 2.493030 CGCCCGTAAGACCGTGAT 59.507 61.111 0.00 0.00 43.02 3.06
833 951 0.781278 ATTTTTCCTTCGGGTCCCCA 59.219 50.000 1.00 0.00 36.28 4.96
848 966 4.347453 CCAGGCAACAACCGCAGC 62.347 66.667 0.00 0.00 41.41 5.25
878 996 5.595542 ACACTATATAGTTCACGGGTTAGCA 59.404 40.000 12.87 0.00 33.46 3.49
910 1028 0.105401 TGGTACCACTCCACTGACCA 60.105 55.000 11.60 0.00 34.63 4.02
918 1036 2.666190 CCACTGACCACTGCCACG 60.666 66.667 0.00 0.00 0.00 4.94
919 1037 3.349006 CACTGACCACTGCCACGC 61.349 66.667 0.00 0.00 0.00 5.34
921 1039 4.624364 CTGACCACTGCCACGCCA 62.624 66.667 0.00 0.00 0.00 5.69
922 1040 4.927782 TGACCACTGCCACGCCAC 62.928 66.667 0.00 0.00 0.00 5.01
923 1041 4.626081 GACCACTGCCACGCCACT 62.626 66.667 0.00 0.00 0.00 4.00
924 1042 4.935495 ACCACTGCCACGCCACTG 62.935 66.667 0.00 0.00 0.00 3.66
927 1045 3.625897 ACTGCCACGCCACTGCTA 61.626 61.111 0.00 0.00 34.43 3.49
948 1066 4.254402 ACTCCAAGTCGTAAAGGAACTC 57.746 45.455 0.00 0.00 38.49 3.01
953 1083 2.242043 AGTCGTAAAGGAACTCGGGAA 58.758 47.619 0.00 0.00 38.49 3.97
995 1127 2.690173 ACTGCTATACTAAGCTCGCG 57.310 50.000 0.00 0.00 43.19 5.87
1242 1374 1.005137 GTCAACGTACGTCGCCAAAAA 60.005 47.619 23.05 0.00 44.19 1.94
1244 1376 2.096811 TCAACGTACGTCGCCAAAAATC 60.097 45.455 23.05 0.00 44.19 2.17
1256 1392 3.681594 CGCCAAAAATCCCTGCTACTCTA 60.682 47.826 0.00 0.00 0.00 2.43
1260 1396 6.546034 GCCAAAAATCCCTGCTACTCTATTAA 59.454 38.462 0.00 0.00 0.00 1.40
1262 1401 7.013369 CCAAAAATCCCTGCTACTCTATTAACC 59.987 40.741 0.00 0.00 0.00 2.85
1266 1405 3.256136 CCCTGCTACTCTATTAACCTCCG 59.744 52.174 0.00 0.00 0.00 4.63
1269 1408 5.711036 CCTGCTACTCTATTAACCTCCGTAT 59.289 44.000 0.00 0.00 0.00 3.06
1271 1410 6.066690 TGCTACTCTATTAACCTCCGTATGT 58.933 40.000 0.00 0.00 0.00 2.29
1286 1425 3.426159 CCGTATGTTGCAAATGGTCTCAC 60.426 47.826 0.00 0.00 0.00 3.51
1432 1577 1.686325 CCATCAAGTCCCGGGTCGAT 61.686 60.000 22.86 14.90 0.00 3.59
1517 1662 6.091169 CGTTAACCTGGTAATTTAAGCTCGAA 59.909 38.462 0.00 0.00 0.00 3.71
1620 1775 2.287427 GCGAACTAGCTGTCGCCTTATA 60.287 50.000 23.10 0.00 44.62 0.98
1750 1908 2.687200 ATGTGGGCTACCCTCGCA 60.687 61.111 3.93 1.30 45.70 5.10
1751 1909 2.735772 ATGTGGGCTACCCTCGCAG 61.736 63.158 3.93 0.00 45.70 5.18
1779 1942 2.590575 CGGTGAGGTTGTTGCCGT 60.591 61.111 0.00 0.00 37.87 5.68
2006 2204 2.867287 TTTCACCACGACGTACTTGA 57.133 45.000 0.00 0.41 0.00 3.02
2036 2239 7.268586 ACATTGTCTCGATCTAGCTAAACAAT 58.731 34.615 0.00 6.33 36.75 2.71
2037 2240 8.414003 ACATTGTCTCGATCTAGCTAAACAATA 58.586 33.333 10.04 0.00 35.11 1.90
2111 2318 9.862371 AGTCTATAACTTAAACATGAGTGACTG 57.138 33.333 0.00 0.00 33.03 3.51
2112 2319 9.088512 GTCTATAACTTAAACATGAGTGACTGG 57.911 37.037 0.00 0.00 0.00 4.00
2113 2320 8.812972 TCTATAACTTAAACATGAGTGACTGGT 58.187 33.333 0.00 0.00 0.00 4.00
2114 2321 9.436957 CTATAACTTAAACATGAGTGACTGGTT 57.563 33.333 0.00 0.00 0.00 3.67
2115 2322 6.619801 AACTTAAACATGAGTGACTGGTTC 57.380 37.500 0.00 0.00 0.00 3.62
2116 2323 5.063880 ACTTAAACATGAGTGACTGGTTCC 58.936 41.667 0.00 0.00 0.00 3.62
2117 2324 3.576078 AAACATGAGTGACTGGTTCCA 57.424 42.857 0.00 0.00 0.00 3.53
2118 2325 2.550830 ACATGAGTGACTGGTTCCAC 57.449 50.000 0.00 0.00 0.00 4.02
2119 2326 1.072331 ACATGAGTGACTGGTTCCACC 59.928 52.381 0.00 0.00 39.22 4.61
2121 2328 0.468226 TGAGTGACTGGTTCCACCAC 59.532 55.000 0.00 9.92 44.79 4.16
2145 2352 3.314357 AGGAAACAAACTAAGTTCACCGC 59.686 43.478 0.00 0.00 33.59 5.68
2257 2468 6.887002 TGATTACCACATGTGCCTATTTGTTA 59.113 34.615 20.81 5.41 0.00 2.41
2451 2666 3.490759 GACATGGTGGCGCTGTCG 61.491 66.667 7.64 0.00 39.07 4.35
2883 3098 3.935024 CCTCGAGATTCGTGGGGA 58.065 61.111 15.71 0.00 46.33 4.81
2953 3171 0.402861 TTCTGGTGGGGGAGAAGGTT 60.403 55.000 0.00 0.00 0.00 3.50
2954 3172 1.133809 TCTGGTGGGGGAGAAGGTTG 61.134 60.000 0.00 0.00 0.00 3.77
2955 3173 1.073319 TGGTGGGGGAGAAGGTTGA 60.073 57.895 0.00 0.00 0.00 3.18
2956 3174 1.133809 TGGTGGGGGAGAAGGTTGAG 61.134 60.000 0.00 0.00 0.00 3.02
2957 3175 1.134438 GGTGGGGGAGAAGGTTGAGT 61.134 60.000 0.00 0.00 0.00 3.41
2958 3176 0.325272 GTGGGGGAGAAGGTTGAGTC 59.675 60.000 0.00 0.00 0.00 3.36
2959 3177 0.193574 TGGGGGAGAAGGTTGAGTCT 59.806 55.000 0.00 0.00 0.00 3.24
2960 3178 1.363246 GGGGGAGAAGGTTGAGTCTT 58.637 55.000 0.00 0.00 0.00 3.01
3033 3251 0.612174 TCAGGTGAGGAGAGGAACGG 60.612 60.000 0.00 0.00 0.00 4.44
3034 3252 1.305381 AGGTGAGGAGAGGAACGGG 60.305 63.158 0.00 0.00 0.00 5.28
3035 3253 1.305046 GGTGAGGAGAGGAACGGGA 60.305 63.158 0.00 0.00 0.00 5.14
3036 3254 1.605971 GGTGAGGAGAGGAACGGGAC 61.606 65.000 0.00 0.00 0.00 4.46
3037 3255 1.305046 TGAGGAGAGGAACGGGACC 60.305 63.158 0.00 0.00 0.00 4.46
3211 3435 7.303261 TCAGATGTAAGTCTTGTAAGTACGTG 58.697 38.462 0.00 0.00 0.00 4.49
3318 3545 1.303724 TGTACCAAACCCGGGCATG 60.304 57.895 24.08 19.98 0.00 4.06
3383 3611 2.586293 CGTCCTACCAAACCCGGGT 61.586 63.158 24.16 24.16 42.48 5.28
3487 3715 7.159437 GTTGATCAAACTATCACTCGATCAG 57.841 40.000 10.35 0.00 40.06 2.90
3493 3721 3.417101 ACTATCACTCGATCAGCTAGGG 58.583 50.000 0.00 0.00 32.73 3.53
3494 3722 0.965439 ATCACTCGATCAGCTAGGGC 59.035 55.000 0.00 0.00 39.06 5.19
3495 3723 1.007964 CACTCGATCAGCTAGGGCG 60.008 63.158 0.00 0.00 44.37 6.13
3496 3724 2.196925 ACTCGATCAGCTAGGGCGG 61.197 63.158 0.00 0.00 44.37 6.13
3497 3725 2.912542 TCGATCAGCTAGGGCGGG 60.913 66.667 0.00 0.00 44.37 6.13
3498 3726 3.227276 CGATCAGCTAGGGCGGGT 61.227 66.667 0.00 0.00 44.37 5.28
3499 3727 2.797278 CGATCAGCTAGGGCGGGTT 61.797 63.158 0.00 0.00 44.37 4.11
3500 3728 1.227674 GATCAGCTAGGGCGGGTTG 60.228 63.158 0.00 0.00 44.37 3.77
3501 3729 1.686325 GATCAGCTAGGGCGGGTTGA 61.686 60.000 0.00 0.00 44.37 3.18
3502 3730 1.056700 ATCAGCTAGGGCGGGTTGAT 61.057 55.000 0.00 0.00 44.37 2.57
3503 3731 1.524621 CAGCTAGGGCGGGTTGATG 60.525 63.158 0.00 0.00 44.37 3.07
3504 3732 1.689233 AGCTAGGGCGGGTTGATGA 60.689 57.895 0.00 0.00 44.37 2.92
3505 3733 1.056700 AGCTAGGGCGGGTTGATGAT 61.057 55.000 0.00 0.00 44.37 2.45
3506 3734 0.886490 GCTAGGGCGGGTTGATGATG 60.886 60.000 0.00 0.00 0.00 3.07
3507 3735 0.250467 CTAGGGCGGGTTGATGATGG 60.250 60.000 0.00 0.00 0.00 3.51
3508 3736 1.705002 TAGGGCGGGTTGATGATGGG 61.705 60.000 0.00 0.00 0.00 4.00
3509 3737 3.219198 GGCGGGTTGATGATGGGC 61.219 66.667 0.00 0.00 0.00 5.36
3510 3738 2.440065 GCGGGTTGATGATGGGCA 60.440 61.111 0.00 0.00 0.00 5.36
3511 3739 2.051518 GCGGGTTGATGATGGGCAA 61.052 57.895 0.00 0.00 0.00 4.52
3512 3740 1.603236 GCGGGTTGATGATGGGCAAA 61.603 55.000 0.00 0.00 0.00 3.68
3513 3741 0.173255 CGGGTTGATGATGGGCAAAC 59.827 55.000 0.00 0.00 0.00 2.93
3514 3742 0.536724 GGGTTGATGATGGGCAAACC 59.463 55.000 0.00 0.00 43.83 3.27
3523 3751 3.549730 GGGCAAACCAAGGTTGCT 58.450 55.556 16.23 0.00 38.47 3.91
3524 3752 2.740121 GGGCAAACCAAGGTTGCTA 58.260 52.632 16.23 0.00 38.47 3.49
3525 3753 1.044611 GGGCAAACCAAGGTTGCTAA 58.955 50.000 16.23 0.00 38.47 3.09
3526 3754 1.414550 GGGCAAACCAAGGTTGCTAAA 59.585 47.619 16.23 0.00 38.47 1.85
3527 3755 2.038426 GGGCAAACCAAGGTTGCTAAAT 59.962 45.455 16.23 0.00 38.47 1.40
3528 3756 3.066380 GGCAAACCAAGGTTGCTAAATG 58.934 45.455 16.23 5.10 38.47 2.32
3529 3757 3.066380 GCAAACCAAGGTTGCTAAATGG 58.934 45.455 10.03 0.00 38.47 3.16
3530 3758 3.244044 GCAAACCAAGGTTGCTAAATGGA 60.244 43.478 10.03 0.00 38.47 3.41
3531 3759 4.306600 CAAACCAAGGTTGCTAAATGGAC 58.693 43.478 5.06 0.00 38.47 4.02
3532 3760 2.525368 ACCAAGGTTGCTAAATGGACC 58.475 47.619 0.00 0.00 35.16 4.46
3533 3761 2.158385 ACCAAGGTTGCTAAATGGACCA 60.158 45.455 0.00 0.00 34.60 4.02
3534 3762 2.896685 CCAAGGTTGCTAAATGGACCAA 59.103 45.455 0.00 0.00 34.60 3.67
3535 3763 3.323403 CCAAGGTTGCTAAATGGACCAAA 59.677 43.478 0.00 0.00 34.60 3.28
3536 3764 4.202305 CCAAGGTTGCTAAATGGACCAAAA 60.202 41.667 0.00 0.00 34.60 2.44
3537 3765 4.600692 AGGTTGCTAAATGGACCAAAAC 57.399 40.909 0.00 0.00 34.60 2.43
3538 3766 3.964031 AGGTTGCTAAATGGACCAAAACA 59.036 39.130 0.00 0.00 34.60 2.83
3539 3767 4.039124 AGGTTGCTAAATGGACCAAAACAG 59.961 41.667 0.00 0.00 34.60 3.16
3540 3768 4.038642 GGTTGCTAAATGGACCAAAACAGA 59.961 41.667 0.00 0.00 32.41 3.41
3541 3769 5.222631 GTTGCTAAATGGACCAAAACAGAG 58.777 41.667 0.00 0.00 0.00 3.35
3542 3770 3.255642 TGCTAAATGGACCAAAACAGAGC 59.744 43.478 0.00 2.88 0.00 4.09
3543 3771 3.507622 GCTAAATGGACCAAAACAGAGCT 59.492 43.478 0.00 0.00 0.00 4.09
3544 3772 4.700213 GCTAAATGGACCAAAACAGAGCTA 59.300 41.667 0.00 0.00 0.00 3.32
3545 3773 5.183140 GCTAAATGGACCAAAACAGAGCTAA 59.817 40.000 0.00 0.00 0.00 3.09
3546 3774 6.294508 GCTAAATGGACCAAAACAGAGCTAAA 60.295 38.462 0.00 0.00 0.00 1.85
3547 3775 6.670695 AAATGGACCAAAACAGAGCTAAAT 57.329 33.333 0.00 0.00 0.00 1.40
3548 3776 5.649782 ATGGACCAAAACAGAGCTAAATG 57.350 39.130 0.00 0.00 0.00 2.32
3549 3777 4.469657 TGGACCAAAACAGAGCTAAATGT 58.530 39.130 0.00 0.00 0.00 2.71
3550 3778 4.278170 TGGACCAAAACAGAGCTAAATGTG 59.722 41.667 0.00 0.00 0.00 3.21
3551 3779 4.278419 GGACCAAAACAGAGCTAAATGTGT 59.722 41.667 0.00 0.00 0.00 3.72
3552 3780 5.472137 GGACCAAAACAGAGCTAAATGTGTA 59.528 40.000 0.00 0.00 0.00 2.90
3553 3781 6.151144 GGACCAAAACAGAGCTAAATGTGTAT 59.849 38.462 0.00 0.00 0.00 2.29
3554 3782 7.335924 GGACCAAAACAGAGCTAAATGTGTATA 59.664 37.037 0.00 0.00 0.00 1.47
3555 3783 8.630054 ACCAAAACAGAGCTAAATGTGTATAA 57.370 30.769 0.00 0.00 0.00 0.98
3556 3784 9.073475 ACCAAAACAGAGCTAAATGTGTATAAA 57.927 29.630 0.00 0.00 0.00 1.40
3557 3785 9.906660 CCAAAACAGAGCTAAATGTGTATAAAA 57.093 29.630 0.00 0.00 0.00 1.52
3561 3789 8.807948 ACAGAGCTAAATGTGTATAAAATGGT 57.192 30.769 0.00 0.00 0.00 3.55
3562 3790 9.243105 ACAGAGCTAAATGTGTATAAAATGGTT 57.757 29.630 0.00 0.00 0.00 3.67
3563 3791 9.507280 CAGAGCTAAATGTGTATAAAATGGTTG 57.493 33.333 0.00 0.00 0.00 3.77
3564 3792 9.461312 AGAGCTAAATGTGTATAAAATGGTTGA 57.539 29.630 0.00 0.00 0.00 3.18
3567 3795 8.755018 GCTAAATGTGTATAAAATGGTTGATGC 58.245 33.333 0.00 0.00 0.00 3.91
3568 3796 9.800433 CTAAATGTGTATAAAATGGTTGATGCA 57.200 29.630 0.00 0.00 0.00 3.96
3570 3798 9.669887 AAATGTGTATAAAATGGTTGATGCAAT 57.330 25.926 0.00 0.00 0.00 3.56
3571 3799 8.651391 ATGTGTATAAAATGGTTGATGCAATG 57.349 30.769 0.00 0.00 0.00 2.82
3572 3800 6.534436 TGTGTATAAAATGGTTGATGCAATGC 59.466 34.615 0.00 0.00 0.00 3.56
3573 3801 6.757947 GTGTATAAAATGGTTGATGCAATGCT 59.242 34.615 6.82 0.00 0.00 3.79
3574 3802 7.920151 GTGTATAAAATGGTTGATGCAATGCTA 59.080 33.333 6.82 0.00 0.00 3.49
3575 3803 8.640651 TGTATAAAATGGTTGATGCAATGCTAT 58.359 29.630 6.82 0.00 0.00 2.97
3578 3806 7.956420 AAAATGGTTGATGCAATGCTATATG 57.044 32.000 6.82 0.00 0.00 1.78
3579 3807 5.654603 ATGGTTGATGCAATGCTATATGG 57.345 39.130 6.82 0.00 0.00 2.74
3580 3808 4.727677 TGGTTGATGCAATGCTATATGGA 58.272 39.130 6.82 0.00 0.00 3.41
3581 3809 5.326900 TGGTTGATGCAATGCTATATGGAT 58.673 37.500 6.82 0.00 0.00 3.41
3582 3810 5.184287 TGGTTGATGCAATGCTATATGGATG 59.816 40.000 6.82 0.00 0.00 3.51
3583 3811 5.416639 GGTTGATGCAATGCTATATGGATGA 59.583 40.000 6.82 0.00 0.00 2.92
3584 3812 6.096423 GGTTGATGCAATGCTATATGGATGAT 59.904 38.462 6.82 0.00 0.00 2.45
3585 3813 6.693315 TGATGCAATGCTATATGGATGATG 57.307 37.500 6.82 0.00 0.00 3.07
3586 3814 5.592688 TGATGCAATGCTATATGGATGATGG 59.407 40.000 6.82 0.00 0.00 3.51
3587 3815 5.182169 TGCAATGCTATATGGATGATGGA 57.818 39.130 6.82 0.00 0.00 3.41
3588 3816 5.572252 TGCAATGCTATATGGATGATGGAA 58.428 37.500 6.82 0.00 0.00 3.53
3589 3817 5.650703 TGCAATGCTATATGGATGATGGAAG 59.349 40.000 6.82 0.00 0.00 3.46
3590 3818 5.067413 GCAATGCTATATGGATGATGGAAGG 59.933 44.000 0.00 0.00 0.00 3.46
3591 3819 4.849813 TGCTATATGGATGATGGAAGGG 57.150 45.455 0.00 0.00 0.00 3.95
3592 3820 3.524789 TGCTATATGGATGATGGAAGGGG 59.475 47.826 0.00 0.00 0.00 4.79
3593 3821 3.782523 GCTATATGGATGATGGAAGGGGA 59.217 47.826 0.00 0.00 0.00 4.81
3594 3822 4.141528 GCTATATGGATGATGGAAGGGGAG 60.142 50.000 0.00 0.00 0.00 4.30
3595 3823 0.776176 ATGGATGATGGAAGGGGAGC 59.224 55.000 0.00 0.00 0.00 4.70
3596 3824 0.327867 TGGATGATGGAAGGGGAGCT 60.328 55.000 0.00 0.00 0.00 4.09
3597 3825 1.061424 TGGATGATGGAAGGGGAGCTA 60.061 52.381 0.00 0.00 0.00 3.32
3598 3826 1.349357 GGATGATGGAAGGGGAGCTAC 59.651 57.143 0.00 0.00 0.00 3.58
3599 3827 2.050144 GATGATGGAAGGGGAGCTACA 58.950 52.381 0.00 0.00 0.00 2.74
3600 3828 1.965414 TGATGGAAGGGGAGCTACAA 58.035 50.000 0.00 0.00 0.00 2.41
3601 3829 1.559682 TGATGGAAGGGGAGCTACAAC 59.440 52.381 0.00 0.00 0.00 3.32
3602 3830 1.559682 GATGGAAGGGGAGCTACAACA 59.440 52.381 0.00 0.00 0.00 3.33
3603 3831 0.984230 TGGAAGGGGAGCTACAACAG 59.016 55.000 0.00 0.00 0.00 3.16
3604 3832 0.984995 GGAAGGGGAGCTACAACAGT 59.015 55.000 0.00 0.00 0.00 3.55
3605 3833 1.351350 GGAAGGGGAGCTACAACAGTT 59.649 52.381 0.00 0.00 0.00 3.16
3606 3834 2.427506 GAAGGGGAGCTACAACAGTTG 58.572 52.381 12.03 12.03 0.00 3.16
3608 3836 2.616524 AGGGGAGCTACAACAGTTGTA 58.383 47.619 22.27 22.27 43.27 2.41
3609 3837 2.302157 AGGGGAGCTACAACAGTTGTAC 59.698 50.000 20.32 16.52 43.27 2.90
3610 3838 2.302157 GGGGAGCTACAACAGTTGTACT 59.698 50.000 20.32 20.08 43.27 2.73
3611 3839 3.244457 GGGGAGCTACAACAGTTGTACTT 60.244 47.826 20.32 12.12 43.27 2.24
3612 3840 3.995048 GGGAGCTACAACAGTTGTACTTC 59.005 47.826 20.32 18.74 43.27 3.01
3613 3841 3.673809 GGAGCTACAACAGTTGTACTTCG 59.326 47.826 20.32 12.65 43.27 3.79
3614 3842 4.296690 GAGCTACAACAGTTGTACTTCGT 58.703 43.478 20.32 5.30 43.27 3.85
3615 3843 5.443185 AGCTACAACAGTTGTACTTCGTA 57.557 39.130 20.32 2.67 43.27 3.43
3616 3844 5.835257 AGCTACAACAGTTGTACTTCGTAA 58.165 37.500 20.32 1.97 43.27 3.18
3617 3845 6.453092 AGCTACAACAGTTGTACTTCGTAAT 58.547 36.000 20.32 0.00 43.27 1.89
3618 3846 6.585322 AGCTACAACAGTTGTACTTCGTAATC 59.415 38.462 20.32 0.00 43.27 1.75
3619 3847 6.364165 GCTACAACAGTTGTACTTCGTAATCA 59.636 38.462 20.32 0.10 43.27 2.57
3620 3848 7.063074 GCTACAACAGTTGTACTTCGTAATCAT 59.937 37.037 20.32 0.00 43.27 2.45
3621 3849 7.347508 ACAACAGTTGTACTTCGTAATCATC 57.652 36.000 17.74 0.00 43.27 2.92
3622 3850 6.089016 ACAACAGTTGTACTTCGTAATCATCG 59.911 38.462 17.74 0.00 43.27 3.84
3623 3851 5.946298 ACAGTTGTACTTCGTAATCATCGA 58.054 37.500 0.00 0.00 35.50 3.59
3624 3852 6.028368 ACAGTTGTACTTCGTAATCATCGAG 58.972 40.000 0.00 0.00 38.52 4.04
3625 3853 5.455849 CAGTTGTACTTCGTAATCATCGAGG 59.544 44.000 0.00 0.00 39.60 4.63
3626 3854 4.563337 TGTACTTCGTAATCATCGAGGG 57.437 45.455 0.00 0.00 38.40 4.30
3627 3855 3.317149 TGTACTTCGTAATCATCGAGGGG 59.683 47.826 0.00 0.00 38.40 4.79
3628 3856 2.662866 ACTTCGTAATCATCGAGGGGA 58.337 47.619 0.00 0.00 38.40 4.81
3629 3857 2.623889 ACTTCGTAATCATCGAGGGGAG 59.376 50.000 0.00 0.00 38.40 4.30
3630 3858 1.617322 TCGTAATCATCGAGGGGAGG 58.383 55.000 0.00 0.00 33.38 4.30
3631 3859 0.038159 CGTAATCATCGAGGGGAGGC 60.038 60.000 0.00 0.00 0.00 4.70
3632 3860 0.038159 GTAATCATCGAGGGGAGGCG 60.038 60.000 0.00 0.00 0.00 5.52
3633 3861 0.178973 TAATCATCGAGGGGAGGCGA 60.179 55.000 0.00 0.00 41.14 5.54
3639 4050 2.501610 GAGGGGAGGCGATGTCAC 59.498 66.667 0.00 0.00 0.00 3.67
3664 4075 6.183360 CGTGGCTCTTTCTTATTTGATCATGT 60.183 38.462 0.00 0.00 0.00 3.21
3665 4076 6.971184 GTGGCTCTTTCTTATTTGATCATGTG 59.029 38.462 0.00 0.00 0.00 3.21
3666 4077 6.660521 TGGCTCTTTCTTATTTGATCATGTGT 59.339 34.615 0.00 0.00 0.00 3.72
3667 4078 7.177216 TGGCTCTTTCTTATTTGATCATGTGTT 59.823 33.333 0.00 0.00 0.00 3.32
3668 4079 7.699812 GGCTCTTTCTTATTTGATCATGTGTTC 59.300 37.037 0.00 0.00 0.00 3.18
3670 4081 8.546597 TCTTTCTTATTTGATCATGTGTTCGA 57.453 30.769 0.00 0.00 0.00 3.71
3671 4082 9.166173 TCTTTCTTATTTGATCATGTGTTCGAT 57.834 29.630 0.00 0.00 0.00 3.59
3672 4083 9.218359 CTTTCTTATTTGATCATGTGTTCGATG 57.782 33.333 0.00 0.00 0.00 3.84
3673 4084 6.718388 TCTTATTTGATCATGTGTTCGATGC 58.282 36.000 0.00 0.00 0.00 3.91
3674 4085 6.539826 TCTTATTTGATCATGTGTTCGATGCT 59.460 34.615 0.00 0.00 0.00 3.79
3675 4086 4.604843 TTTGATCATGTGTTCGATGCTC 57.395 40.909 0.00 0.00 0.00 4.26
3676 4087 2.554142 TGATCATGTGTTCGATGCTCC 58.446 47.619 0.00 0.00 0.00 4.70
3677 4088 2.169144 TGATCATGTGTTCGATGCTCCT 59.831 45.455 0.00 0.00 0.00 3.69
3678 4089 2.768253 TCATGTGTTCGATGCTCCTT 57.232 45.000 0.00 0.00 0.00 3.36
3725 4142 3.130633 CGGAATGATACTTGCGGATGAA 58.869 45.455 0.00 0.00 36.47 2.57
3735 4152 1.123077 TGCGGATGAACTAGGATGCT 58.877 50.000 0.00 0.00 0.00 3.79
3736 4153 1.202568 TGCGGATGAACTAGGATGCTG 60.203 52.381 0.00 0.00 0.00 4.41
3740 4157 2.546795 GGATGAACTAGGATGCTGACGG 60.547 54.545 0.00 0.00 0.00 4.79
3762 4179 5.299949 GGGTTGTTTTTGAATCTGATTGCT 58.700 37.500 7.78 0.00 0.00 3.91
3763 4180 6.454795 GGGTTGTTTTTGAATCTGATTGCTA 58.545 36.000 7.78 0.00 0.00 3.49
3764 4181 6.587608 GGGTTGTTTTTGAATCTGATTGCTAG 59.412 38.462 7.78 0.00 0.00 3.42
3765 4182 7.370383 GGTTGTTTTTGAATCTGATTGCTAGA 58.630 34.615 7.78 0.00 0.00 2.43
3766 4183 7.867403 GGTTGTTTTTGAATCTGATTGCTAGAA 59.133 33.333 7.78 0.00 0.00 2.10
3781 4199 7.337689 TGATTGCTAGAACTTATGAATGCTTGT 59.662 33.333 0.00 0.00 0.00 3.16
3791 4209 2.455557 TGAATGCTTGTAATGGGGTGG 58.544 47.619 0.00 0.00 0.00 4.61
3824 4242 8.478775 ACTCAGCACATATACAGTTATCCTTA 57.521 34.615 0.00 0.00 0.00 2.69
3825 4243 9.094578 ACTCAGCACATATACAGTTATCCTTAT 57.905 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 3.775654 CCAGCTCACGTCCCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
179 185 6.904011 GTGATTGTATTGCATTCTTCTCTTCG 59.096 38.462 0.00 0.00 0.00 3.79
205 215 1.746239 TGTCGGCTCACATGCATGG 60.746 57.895 29.41 18.30 34.04 3.66
515 534 1.523758 GTGTGCCCTTACCAGAGTTG 58.476 55.000 0.00 0.00 0.00 3.16
522 541 1.977009 GCCTTGGTGTGCCCTTACC 60.977 63.158 0.00 0.00 37.48 2.85
564 585 3.355378 TCTATTTCGGACGGTGGAAGTA 58.645 45.455 0.00 0.00 0.00 2.24
583 604 5.589855 CGCTCAGATGGATGTATCTAGATCT 59.410 44.000 8.95 0.00 35.70 2.75
584 605 5.356751 ACGCTCAGATGGATGTATCTAGATC 59.643 44.000 8.95 2.00 35.70 2.75
599 624 3.865745 CCGAAATTAGTTGACGCTCAGAT 59.134 43.478 0.00 0.00 0.00 2.90
623 648 2.388735 CTGTATACACAGCTCCCTCCA 58.611 52.381 0.08 0.00 45.44 3.86
633 658 6.665992 AGAACCAACTCTTCTGTATACACA 57.334 37.500 0.08 0.00 0.00 3.72
634 659 6.929606 ACAAGAACCAACTCTTCTGTATACAC 59.070 38.462 0.08 0.00 33.25 2.90
635 660 7.062749 ACAAGAACCAACTCTTCTGTATACA 57.937 36.000 5.25 5.25 33.25 2.29
661 732 9.813446 CGTACCTAGAAAATAATCCTTACAAGT 57.187 33.333 0.00 0.00 0.00 3.16
673 744 6.529125 CAGAAAGCGAACGTACCTAGAAAATA 59.471 38.462 0.00 0.00 0.00 1.40
692 763 4.404654 GGGCGCGCCAACAGAAAG 62.405 66.667 46.88 0.00 37.98 2.62
722 793 5.693961 TCGTGACCCTAGTACCACATTATA 58.306 41.667 0.00 0.00 0.00 0.98
833 951 2.202395 ATTGCTGCGGTTGTTGCCT 61.202 52.632 0.00 0.00 0.00 4.75
848 966 5.926542 CCCGTGAACTATATAGTGTCCATTG 59.073 44.000 16.11 10.57 36.50 2.82
878 996 1.196012 GGTACCACCTCTAAGCTGCT 58.804 55.000 7.15 0.00 34.73 4.24
918 1036 0.737715 CGACTTGGAGTAGCAGTGGC 60.738 60.000 0.00 0.00 41.61 5.01
919 1037 0.603569 ACGACTTGGAGTAGCAGTGG 59.396 55.000 0.00 0.00 0.00 4.00
921 1039 3.056749 CCTTTACGACTTGGAGTAGCAGT 60.057 47.826 0.00 0.00 0.00 4.40
922 1040 3.192844 TCCTTTACGACTTGGAGTAGCAG 59.807 47.826 0.00 0.00 0.00 4.24
923 1041 3.159472 TCCTTTACGACTTGGAGTAGCA 58.841 45.455 0.00 0.00 0.00 3.49
924 1042 3.863142 TCCTTTACGACTTGGAGTAGC 57.137 47.619 0.00 0.00 0.00 3.58
926 1044 4.083110 CGAGTTCCTTTACGACTTGGAGTA 60.083 45.833 0.00 0.00 0.00 2.59
927 1045 3.305199 CGAGTTCCTTTACGACTTGGAGT 60.305 47.826 0.00 0.00 0.00 3.85
953 1083 3.336088 ACTATAGTATAGTTCCCCGGCCT 59.664 47.826 15.79 0.00 0.00 5.19
986 1118 2.135139 CTGCCATTAATCGCGAGCTTA 58.865 47.619 16.66 6.51 0.00 3.09
1242 1374 5.088026 GGAGGTTAATAGAGTAGCAGGGAT 58.912 45.833 0.00 0.00 0.00 3.85
1244 1376 3.256136 CGGAGGTTAATAGAGTAGCAGGG 59.744 52.174 0.00 0.00 0.00 4.45
1256 1392 5.163561 CCATTTGCAACATACGGAGGTTAAT 60.164 40.000 0.00 0.00 0.00 1.40
1260 1396 2.091541 CCATTTGCAACATACGGAGGT 58.908 47.619 0.00 0.00 0.00 3.85
1262 1401 3.009723 AGACCATTTGCAACATACGGAG 58.990 45.455 0.00 0.00 0.00 4.63
1266 1405 3.188460 ACGTGAGACCATTTGCAACATAC 59.812 43.478 0.00 0.00 0.00 2.39
1269 1408 1.601903 GACGTGAGACCATTTGCAACA 59.398 47.619 0.00 0.00 0.00 3.33
1271 1410 1.960417 TGACGTGAGACCATTTGCAA 58.040 45.000 0.00 0.00 0.00 4.08
1286 1425 2.408835 GCGGCCATGGATTTGACG 59.591 61.111 18.40 10.21 0.00 4.35
1517 1662 2.418628 GTGCATGCATGGTAAGTAACGT 59.581 45.455 25.64 0.00 0.00 3.99
1620 1775 2.558359 CGGTGCCTTTTCCTCTGAAATT 59.442 45.455 0.00 0.00 40.08 1.82
1743 1901 3.014085 TAAAGCGGGTCTGCGAGGG 62.014 63.158 0.00 0.00 40.67 4.30
1779 1942 0.608640 TGCCAACATCATGCATGCAA 59.391 45.000 26.68 9.94 35.65 4.08
1830 1998 5.992829 ACATCTGTACCATGTTCGTTACAAA 59.007 36.000 2.40 0.00 40.89 2.83
1832 2000 4.926832 CACATCTGTACCATGTTCGTTACA 59.073 41.667 5.07 0.00 41.97 2.41
2006 2204 6.398234 AGCTAGATCGAGACAATGTTATGT 57.602 37.500 7.06 0.00 35.90 2.29
2036 2239 8.771920 TCAATTTATTTCAGACTTTCGAGCTA 57.228 30.769 0.00 0.00 0.00 3.32
2037 2240 7.604164 TCTCAATTTATTTCAGACTTTCGAGCT 59.396 33.333 0.00 0.00 0.00 4.09
2068 2274 2.903784 AGACTTAGCATGGGTGTGTGTA 59.096 45.455 0.00 0.00 0.00 2.90
2069 2275 1.699634 AGACTTAGCATGGGTGTGTGT 59.300 47.619 0.00 0.00 0.00 3.72
2070 2276 2.479566 AGACTTAGCATGGGTGTGTG 57.520 50.000 0.00 0.00 0.00 3.82
2071 2277 5.425539 AGTTATAGACTTAGCATGGGTGTGT 59.574 40.000 0.00 0.00 33.92 3.72
2112 2319 3.194755 AGTTTGTTTCCTTGTGGTGGAAC 59.805 43.478 0.00 0.00 42.57 3.62
2113 2320 3.436243 AGTTTGTTTCCTTGTGGTGGAA 58.564 40.909 0.00 0.00 41.33 3.53
2114 2321 3.094484 AGTTTGTTTCCTTGTGGTGGA 57.906 42.857 0.00 0.00 34.23 4.02
2115 2322 4.401202 ACTTAGTTTGTTTCCTTGTGGTGG 59.599 41.667 0.00 0.00 34.23 4.61
2116 2323 5.576447 ACTTAGTTTGTTTCCTTGTGGTG 57.424 39.130 0.00 0.00 34.23 4.17
2117 2324 5.712917 TGAACTTAGTTTGTTTCCTTGTGGT 59.287 36.000 0.00 0.00 34.23 4.16
2118 2325 6.033966 GTGAACTTAGTTTGTTTCCTTGTGG 58.966 40.000 0.00 0.00 0.00 4.17
2119 2326 6.033966 GGTGAACTTAGTTTGTTTCCTTGTG 58.966 40.000 0.00 0.00 0.00 3.33
2120 2327 5.163693 CGGTGAACTTAGTTTGTTTCCTTGT 60.164 40.000 0.00 0.00 0.00 3.16
2121 2328 5.270853 CGGTGAACTTAGTTTGTTTCCTTG 58.729 41.667 0.00 0.00 0.00 3.61
2145 2352 8.498054 TTTGATAGATCAACTAGCTCAAAAGG 57.502 34.615 4.42 0.00 45.63 3.11
2170 2377 7.984391 TGAGCAATTATTCATACACGACAAAT 58.016 30.769 0.00 0.00 0.00 2.32
2202 2409 3.631227 ACGGGTAGTAACTACATGCTCTC 59.369 47.826 0.00 0.00 38.58 3.20
2203 2410 3.629087 ACGGGTAGTAACTACATGCTCT 58.371 45.455 0.00 0.00 38.58 4.09
2220 2431 2.676342 GTGGTAATCAAGCAAGTACGGG 59.324 50.000 0.00 0.00 37.33 5.28
2257 2468 2.603110 GCACGTACGTCATCATCATGTT 59.397 45.455 19.94 0.00 0.00 2.71
2894 3109 2.548920 GCCTAATGGTACTAGCTGGCAG 60.549 54.545 10.94 10.94 38.99 4.85
2907 3122 2.203015 CACCGTCCGGCCTAATGG 60.203 66.667 5.47 6.03 39.32 3.16
2949 3167 3.181461 CCTTCACACTCAAGACTCAACCT 60.181 47.826 0.00 0.00 0.00 3.50
2953 3171 3.070159 CCTTCCTTCACACTCAAGACTCA 59.930 47.826 0.00 0.00 0.00 3.41
2954 3172 3.322254 TCCTTCCTTCACACTCAAGACTC 59.678 47.826 0.00 0.00 0.00 3.36
2955 3173 3.309296 TCCTTCCTTCACACTCAAGACT 58.691 45.455 0.00 0.00 0.00 3.24
2956 3174 3.753294 TCCTTCCTTCACACTCAAGAC 57.247 47.619 0.00 0.00 0.00 3.01
2957 3175 3.071602 CCTTCCTTCCTTCACACTCAAGA 59.928 47.826 0.00 0.00 0.00 3.02
2958 3176 3.406764 CCTTCCTTCCTTCACACTCAAG 58.593 50.000 0.00 0.00 0.00 3.02
2959 3177 2.106511 CCCTTCCTTCCTTCACACTCAA 59.893 50.000 0.00 0.00 0.00 3.02
2960 3178 1.699634 CCCTTCCTTCCTTCACACTCA 59.300 52.381 0.00 0.00 0.00 3.41
3034 3252 4.760047 ACATGCACGAGCCCGGTC 62.760 66.667 0.00 0.00 41.13 4.79
3035 3253 4.760047 GACATGCACGAGCCCGGT 62.760 66.667 0.00 0.00 41.13 5.28
3036 3254 3.958147 AAGACATGCACGAGCCCGG 62.958 63.158 1.39 0.00 41.13 5.73
3037 3255 1.577328 AAAAGACATGCACGAGCCCG 61.577 55.000 1.39 0.00 41.13 6.13
3060 3283 4.672413 GTGAGCAATCAAAACTTGACGAAG 59.328 41.667 0.00 0.00 43.48 3.79
3061 3284 4.497340 GGTGAGCAATCAAAACTTGACGAA 60.497 41.667 0.00 0.00 43.48 3.85
3211 3435 1.369091 AATCATCGTTGGAGCCACGC 61.369 55.000 6.62 0.00 0.00 5.34
3318 3545 2.682352 GAGAACTGTACTCCTACCCGTC 59.318 54.545 0.00 0.00 0.00 4.79
3383 3611 2.678470 GGCCCAACCCGGTCAATA 59.322 61.111 0.00 0.00 0.00 1.90
3416 3644 1.069049 GTGCTTGGCATTTTGTGGTCT 59.931 47.619 0.00 0.00 41.91 3.85
3482 3710 1.227674 CAACCCGCCCTAGCTGATC 60.228 63.158 0.00 0.00 36.60 2.92
3487 3715 0.886490 CATCATCAACCCGCCCTAGC 60.886 60.000 0.00 0.00 0.00 3.42
3493 3721 1.603236 TTTGCCCATCATCAACCCGC 61.603 55.000 0.00 0.00 0.00 6.13
3494 3722 0.173255 GTTTGCCCATCATCAACCCG 59.827 55.000 0.00 0.00 0.00 5.28
3495 3723 0.536724 GGTTTGCCCATCATCAACCC 59.463 55.000 0.00 0.00 0.00 4.11
3496 3724 1.265236 TGGTTTGCCCATCATCAACC 58.735 50.000 0.00 0.00 38.72 3.77
3497 3725 2.354003 CCTTGGTTTGCCCATCATCAAC 60.354 50.000 0.00 0.00 44.74 3.18
3498 3726 1.901159 CCTTGGTTTGCCCATCATCAA 59.099 47.619 0.00 0.00 44.74 2.57
3499 3727 1.203162 ACCTTGGTTTGCCCATCATCA 60.203 47.619 0.00 0.00 44.74 3.07
3500 3728 1.560505 ACCTTGGTTTGCCCATCATC 58.439 50.000 0.00 0.00 44.74 2.92
3501 3729 1.624813 CAACCTTGGTTTGCCCATCAT 59.375 47.619 1.76 0.00 44.74 2.45
3502 3730 1.047002 CAACCTTGGTTTGCCCATCA 58.953 50.000 1.76 0.00 44.74 3.07
3503 3731 0.320683 GCAACCTTGGTTTGCCCATC 60.321 55.000 1.76 0.00 44.74 3.51
3504 3732 1.754107 GCAACCTTGGTTTGCCCAT 59.246 52.632 1.76 0.00 44.74 4.00
3505 3733 3.225235 GCAACCTTGGTTTGCCCA 58.775 55.556 1.76 0.00 43.02 5.36
3509 3737 4.306600 GTCCATTTAGCAACCTTGGTTTG 58.693 43.478 1.76 0.00 39.88 2.93
3510 3738 3.323691 GGTCCATTTAGCAACCTTGGTTT 59.676 43.478 1.76 0.00 39.88 3.27
3511 3739 2.897326 GGTCCATTTAGCAACCTTGGTT 59.103 45.455 0.00 0.00 39.88 3.67
3512 3740 2.158385 TGGTCCATTTAGCAACCTTGGT 60.158 45.455 0.00 0.00 42.29 3.67
3513 3741 2.524306 TGGTCCATTTAGCAACCTTGG 58.476 47.619 0.00 0.00 32.82 3.61
3514 3742 4.599047 TTTGGTCCATTTAGCAACCTTG 57.401 40.909 0.00 0.00 32.82 3.61
3515 3743 4.407296 TGTTTTGGTCCATTTAGCAACCTT 59.593 37.500 0.00 0.00 32.82 3.50
3516 3744 3.964031 TGTTTTGGTCCATTTAGCAACCT 59.036 39.130 0.00 0.00 32.82 3.50
3517 3745 4.038642 TCTGTTTTGGTCCATTTAGCAACC 59.961 41.667 0.00 0.00 31.69 3.77
3518 3746 5.195001 TCTGTTTTGGTCCATTTAGCAAC 57.805 39.130 0.00 0.00 31.69 4.17
3519 3747 4.261994 GCTCTGTTTTGGTCCATTTAGCAA 60.262 41.667 0.00 0.00 31.69 3.91
3520 3748 3.255642 GCTCTGTTTTGGTCCATTTAGCA 59.744 43.478 0.00 0.00 0.00 3.49
3521 3749 3.507622 AGCTCTGTTTTGGTCCATTTAGC 59.492 43.478 0.00 0.00 0.00 3.09
3522 3750 6.817765 TTAGCTCTGTTTTGGTCCATTTAG 57.182 37.500 0.00 0.00 0.00 1.85
3523 3751 7.232534 ACATTTAGCTCTGTTTTGGTCCATTTA 59.767 33.333 0.00 0.00 0.00 1.40
3524 3752 6.041979 ACATTTAGCTCTGTTTTGGTCCATTT 59.958 34.615 0.00 0.00 0.00 2.32
3525 3753 5.539955 ACATTTAGCTCTGTTTTGGTCCATT 59.460 36.000 0.00 0.00 0.00 3.16
3526 3754 5.047802 CACATTTAGCTCTGTTTTGGTCCAT 60.048 40.000 0.00 0.00 0.00 3.41
3527 3755 4.278170 CACATTTAGCTCTGTTTTGGTCCA 59.722 41.667 0.00 0.00 0.00 4.02
3528 3756 4.278419 ACACATTTAGCTCTGTTTTGGTCC 59.722 41.667 0.00 0.00 0.00 4.46
3529 3757 5.438761 ACACATTTAGCTCTGTTTTGGTC 57.561 39.130 0.00 0.00 0.00 4.02
3530 3758 8.630054 TTATACACATTTAGCTCTGTTTTGGT 57.370 30.769 0.00 0.00 0.00 3.67
3531 3759 9.906660 TTTTATACACATTTAGCTCTGTTTTGG 57.093 29.630 0.00 0.00 0.00 3.28
3535 3763 9.243105 ACCATTTTATACACATTTAGCTCTGTT 57.757 29.630 0.00 0.00 0.00 3.16
3536 3764 8.807948 ACCATTTTATACACATTTAGCTCTGT 57.192 30.769 0.00 0.00 0.00 3.41
3537 3765 9.507280 CAACCATTTTATACACATTTAGCTCTG 57.493 33.333 0.00 0.00 0.00 3.35
3538 3766 9.461312 TCAACCATTTTATACACATTTAGCTCT 57.539 29.630 0.00 0.00 0.00 4.09
3541 3769 8.755018 GCATCAACCATTTTATACACATTTAGC 58.245 33.333 0.00 0.00 0.00 3.09
3542 3770 9.800433 TGCATCAACCATTTTATACACATTTAG 57.200 29.630 0.00 0.00 0.00 1.85
3544 3772 9.669887 ATTGCATCAACCATTTTATACACATTT 57.330 25.926 0.00 0.00 0.00 2.32
3545 3773 9.100554 CATTGCATCAACCATTTTATACACATT 57.899 29.630 0.00 0.00 0.00 2.71
3546 3774 7.225145 GCATTGCATCAACCATTTTATACACAT 59.775 33.333 3.15 0.00 0.00 3.21
3547 3775 6.534436 GCATTGCATCAACCATTTTATACACA 59.466 34.615 3.15 0.00 0.00 3.72
3548 3776 6.757947 AGCATTGCATCAACCATTTTATACAC 59.242 34.615 11.91 0.00 0.00 2.90
3549 3777 6.876155 AGCATTGCATCAACCATTTTATACA 58.124 32.000 11.91 0.00 0.00 2.29
3552 3780 9.647797 CATATAGCATTGCATCAACCATTTTAT 57.352 29.630 11.91 0.00 0.00 1.40
3553 3781 8.089597 CCATATAGCATTGCATCAACCATTTTA 58.910 33.333 11.91 0.00 0.00 1.52
3554 3782 6.932400 CCATATAGCATTGCATCAACCATTTT 59.068 34.615 11.91 0.00 0.00 1.82
3555 3783 6.268158 TCCATATAGCATTGCATCAACCATTT 59.732 34.615 11.91 0.00 0.00 2.32
3556 3784 5.776208 TCCATATAGCATTGCATCAACCATT 59.224 36.000 11.91 0.00 0.00 3.16
3557 3785 5.326900 TCCATATAGCATTGCATCAACCAT 58.673 37.500 11.91 0.00 0.00 3.55
3558 3786 4.727677 TCCATATAGCATTGCATCAACCA 58.272 39.130 11.91 0.00 0.00 3.67
3559 3787 5.416639 TCATCCATATAGCATTGCATCAACC 59.583 40.000 11.91 0.00 0.00 3.77
3560 3788 6.505044 TCATCCATATAGCATTGCATCAAC 57.495 37.500 11.91 0.00 0.00 3.18
3561 3789 6.096282 CCATCATCCATATAGCATTGCATCAA 59.904 38.462 11.91 0.00 0.00 2.57
3562 3790 5.592688 CCATCATCCATATAGCATTGCATCA 59.407 40.000 11.91 0.00 0.00 3.07
3563 3791 5.826208 TCCATCATCCATATAGCATTGCATC 59.174 40.000 11.91 0.00 0.00 3.91
3564 3792 5.762279 TCCATCATCCATATAGCATTGCAT 58.238 37.500 11.91 5.24 0.00 3.96
3565 3793 5.182169 TCCATCATCCATATAGCATTGCA 57.818 39.130 11.91 0.00 0.00 4.08
3566 3794 5.067413 CCTTCCATCATCCATATAGCATTGC 59.933 44.000 0.00 0.00 0.00 3.56
3567 3795 5.593095 CCCTTCCATCATCCATATAGCATTG 59.407 44.000 0.00 0.00 0.00 2.82
3568 3796 5.340611 CCCCTTCCATCATCCATATAGCATT 60.341 44.000 0.00 0.00 0.00 3.56
3569 3797 4.167502 CCCCTTCCATCATCCATATAGCAT 59.832 45.833 0.00 0.00 0.00 3.79
3570 3798 3.524789 CCCCTTCCATCATCCATATAGCA 59.475 47.826 0.00 0.00 0.00 3.49
3571 3799 3.782523 TCCCCTTCCATCATCCATATAGC 59.217 47.826 0.00 0.00 0.00 2.97
3572 3800 4.141528 GCTCCCCTTCCATCATCCATATAG 60.142 50.000 0.00 0.00 0.00 1.31
3573 3801 3.782523 GCTCCCCTTCCATCATCCATATA 59.217 47.826 0.00 0.00 0.00 0.86
3574 3802 2.579860 GCTCCCCTTCCATCATCCATAT 59.420 50.000 0.00 0.00 0.00 1.78
3575 3803 1.988107 GCTCCCCTTCCATCATCCATA 59.012 52.381 0.00 0.00 0.00 2.74
3576 3804 0.776176 GCTCCCCTTCCATCATCCAT 59.224 55.000 0.00 0.00 0.00 3.41
3577 3805 0.327867 AGCTCCCCTTCCATCATCCA 60.328 55.000 0.00 0.00 0.00 3.41
3578 3806 1.349357 GTAGCTCCCCTTCCATCATCC 59.651 57.143 0.00 0.00 0.00 3.51
3579 3807 2.050144 TGTAGCTCCCCTTCCATCATC 58.950 52.381 0.00 0.00 0.00 2.92
3580 3808 2.173569 GTTGTAGCTCCCCTTCCATCAT 59.826 50.000 0.00 0.00 0.00 2.45
3581 3809 1.559682 GTTGTAGCTCCCCTTCCATCA 59.440 52.381 0.00 0.00 0.00 3.07
3582 3810 1.559682 TGTTGTAGCTCCCCTTCCATC 59.440 52.381 0.00 0.00 0.00 3.51
3583 3811 1.561542 CTGTTGTAGCTCCCCTTCCAT 59.438 52.381 0.00 0.00 0.00 3.41
3584 3812 0.984230 CTGTTGTAGCTCCCCTTCCA 59.016 55.000 0.00 0.00 0.00 3.53
3585 3813 0.984995 ACTGTTGTAGCTCCCCTTCC 59.015 55.000 0.00 0.00 0.00 3.46
3586 3814 2.224548 ACAACTGTTGTAGCTCCCCTTC 60.225 50.000 23.62 0.00 43.27 3.46
3587 3815 1.774856 ACAACTGTTGTAGCTCCCCTT 59.225 47.619 23.62 0.00 43.27 3.95
3588 3816 1.435256 ACAACTGTTGTAGCTCCCCT 58.565 50.000 23.62 0.00 43.27 4.79
3589 3817 2.302157 AGTACAACTGTTGTAGCTCCCC 59.698 50.000 28.37 17.56 45.99 4.81
3590 3818 3.679824 AGTACAACTGTTGTAGCTCCC 57.320 47.619 28.37 18.15 45.99 4.30
3591 3819 3.673809 CGAAGTACAACTGTTGTAGCTCC 59.326 47.826 28.37 18.46 45.99 4.70
3592 3820 4.296690 ACGAAGTACAACTGTTGTAGCTC 58.703 43.478 28.37 24.19 45.99 4.09
3593 3821 4.317671 ACGAAGTACAACTGTTGTAGCT 57.682 40.909 28.37 23.66 45.99 3.32
3594 3822 6.364165 TGATTACGAAGTACAACTGTTGTAGC 59.636 38.462 28.37 22.25 45.76 3.58
3595 3823 7.862741 TGATTACGAAGTACAACTGTTGTAG 57.137 36.000 28.37 20.12 45.76 2.74
3596 3824 7.271868 CGATGATTACGAAGTACAACTGTTGTA 59.728 37.037 25.14 25.14 45.76 2.41
3597 3825 6.089016 CGATGATTACGAAGTACAACTGTTGT 59.911 38.462 27.14 27.14 45.76 3.32
3598 3826 6.307077 TCGATGATTACGAAGTACAACTGTTG 59.693 38.462 18.44 18.44 45.76 3.33
3599 3827 6.384224 TCGATGATTACGAAGTACAACTGTT 58.616 36.000 0.00 0.00 45.76 3.16
3600 3828 5.946298 TCGATGATTACGAAGTACAACTGT 58.054 37.500 0.00 0.00 45.76 3.55
3601 3829 5.455849 CCTCGATGATTACGAAGTACAACTG 59.544 44.000 0.00 0.00 45.76 3.16
3602 3830 5.450137 CCCTCGATGATTACGAAGTACAACT 60.450 44.000 0.00 0.00 45.76 3.16
3603 3831 4.738740 CCCTCGATGATTACGAAGTACAAC 59.261 45.833 0.00 0.00 45.76 3.32
3604 3832 4.202080 CCCCTCGATGATTACGAAGTACAA 60.202 45.833 0.00 0.00 45.76 2.41
3605 3833 3.317149 CCCCTCGATGATTACGAAGTACA 59.683 47.826 0.00 0.00 45.76 2.90
3606 3834 3.567164 TCCCCTCGATGATTACGAAGTAC 59.433 47.826 0.00 0.00 45.76 2.73
3607 3835 3.819337 CTCCCCTCGATGATTACGAAGTA 59.181 47.826 0.00 0.00 45.11 2.24
3609 3837 2.029828 CCTCCCCTCGATGATTACGAAG 60.030 54.545 0.00 0.00 39.23 3.79
3610 3838 1.961394 CCTCCCCTCGATGATTACGAA 59.039 52.381 0.00 0.00 39.23 3.85
3611 3839 1.617322 CCTCCCCTCGATGATTACGA 58.383 55.000 0.00 0.00 38.11 3.43
3612 3840 0.038159 GCCTCCCCTCGATGATTACG 60.038 60.000 0.00 0.00 0.00 3.18
3613 3841 0.038159 CGCCTCCCCTCGATGATTAC 60.038 60.000 0.00 0.00 0.00 1.89
3614 3842 0.178973 TCGCCTCCCCTCGATGATTA 60.179 55.000 0.00 0.00 0.00 1.75
3615 3843 0.833834 ATCGCCTCCCCTCGATGATT 60.834 55.000 0.00 0.00 42.95 2.57
3616 3844 1.229019 ATCGCCTCCCCTCGATGAT 60.229 57.895 0.00 0.00 42.95 2.45
3617 3845 2.198703 ATCGCCTCCCCTCGATGA 59.801 61.111 0.00 0.00 42.95 2.92
3619 3847 2.123251 ACATCGCCTCCCCTCGAT 60.123 61.111 0.00 0.00 45.11 3.59
3620 3848 2.833582 GACATCGCCTCCCCTCGA 60.834 66.667 0.00 0.00 39.17 4.04
3621 3849 3.147595 TGACATCGCCTCCCCTCG 61.148 66.667 0.00 0.00 0.00 4.63
3622 3850 2.501610 GTGACATCGCCTCCCCTC 59.498 66.667 0.00 0.00 0.00 4.30
3623 3851 3.461773 CGTGACATCGCCTCCCCT 61.462 66.667 0.00 0.00 0.00 4.79
3624 3852 3.771160 ACGTGACATCGCCTCCCC 61.771 66.667 0.00 0.00 0.00 4.81
3625 3853 2.509336 CACGTGACATCGCCTCCC 60.509 66.667 10.90 0.00 0.00 4.30
3626 3854 2.509336 CCACGTGACATCGCCTCC 60.509 66.667 19.30 0.00 0.00 4.30
3627 3855 3.188786 GCCACGTGACATCGCCTC 61.189 66.667 19.30 0.00 0.00 4.70
3628 3856 3.649277 GAGCCACGTGACATCGCCT 62.649 63.158 19.30 1.45 0.00 5.52
3629 3857 3.188786 GAGCCACGTGACATCGCC 61.189 66.667 19.30 2.04 0.00 5.54
3630 3858 1.291877 AAAGAGCCACGTGACATCGC 61.292 55.000 19.30 11.60 0.00 4.58
3631 3859 0.716108 GAAAGAGCCACGTGACATCG 59.284 55.000 19.30 0.00 0.00 3.84
3632 3860 2.086054 AGAAAGAGCCACGTGACATC 57.914 50.000 19.30 11.60 0.00 3.06
3633 3861 2.550830 AAGAAAGAGCCACGTGACAT 57.449 45.000 19.30 1.35 0.00 3.06
3639 4050 5.801350 TGATCAAATAAGAAAGAGCCACG 57.199 39.130 0.00 0.00 0.00 4.94
3664 4075 1.447838 GCGGAAGGAGCATCGAACA 60.448 57.895 0.00 0.00 34.37 3.18
3665 4076 2.517450 CGCGGAAGGAGCATCGAAC 61.517 63.158 0.00 0.00 34.37 3.95
3666 4077 2.202743 CGCGGAAGGAGCATCGAA 60.203 61.111 0.00 0.00 34.37 3.71
3667 4078 4.207281 CCGCGGAAGGAGCATCGA 62.207 66.667 24.07 0.00 34.37 3.59
3668 4079 4.207281 TCCGCGGAAGGAGCATCG 62.207 66.667 28.99 0.00 34.92 3.84
3674 4085 3.605412 TAACCCCTCCGCGGAAGGA 62.605 63.158 38.78 20.24 38.80 3.36
3675 4086 3.078836 TAACCCCTCCGCGGAAGG 61.079 66.667 32.22 32.22 33.16 3.46
3676 4087 2.499685 CTAACCCCTCCGCGGAAG 59.500 66.667 30.53 23.77 33.16 3.46
3677 4088 3.777910 GCTAACCCCTCCGCGGAA 61.778 66.667 30.53 12.41 33.16 4.30
3678 4089 4.772231 AGCTAACCCCTCCGCGGA 62.772 66.667 29.03 29.03 33.16 5.54
3725 4142 0.537188 CAACCCGTCAGCATCCTAGT 59.463 55.000 0.00 0.00 0.00 2.57
3735 4152 3.948473 TCAGATTCAAAAACAACCCGTCA 59.052 39.130 0.00 0.00 0.00 4.35
3736 4153 4.561735 TCAGATTCAAAAACAACCCGTC 57.438 40.909 0.00 0.00 0.00 4.79
3740 4157 7.370383 TCTAGCAATCAGATTCAAAAACAACC 58.630 34.615 0.00 0.00 0.00 3.77
3762 4179 7.502226 CCCCATTACAAGCATTCATAAGTTCTA 59.498 37.037 0.00 0.00 0.00 2.10
3763 4180 6.322201 CCCCATTACAAGCATTCATAAGTTCT 59.678 38.462 0.00 0.00 0.00 3.01
3764 4181 6.096846 ACCCCATTACAAGCATTCATAAGTTC 59.903 38.462 0.00 0.00 0.00 3.01
3765 4182 5.957774 ACCCCATTACAAGCATTCATAAGTT 59.042 36.000 0.00 0.00 0.00 2.66
3766 4183 5.360714 CACCCCATTACAAGCATTCATAAGT 59.639 40.000 0.00 0.00 0.00 2.24
3776 4194 0.323360 TCAGCCACCCCATTACAAGC 60.323 55.000 0.00 0.00 0.00 4.01
3781 4199 3.525609 TGAGTATTTCAGCCACCCCATTA 59.474 43.478 0.00 0.00 0.00 1.90
3824 4242 3.928727 CGCCATATGGAAGCAATCAAT 57.071 42.857 26.47 0.00 37.39 2.57


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

AutoCloner maintained by Alex Coulton.