Multiple sequence alignment - TraesCS3B01G166500

Loading Multiple Alignment...

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 TraesCS3B01G166500 chr3B 100.000 3848 0 0 1 3848 166656109 166652262 0.000000e+00 7107.0
1 TraesCS3B01G166500 chr3B 97.761 134 3 0 3715 3848 166583048 166582915 8.310000e-57 231.0
2 TraesCS3B01G166500 chr3B 97.015 134 4 0 3715 3848 295044144 295044011 3.870000e-55 226.0
3 TraesCS3B01G166500 chr3B 80.153 131 20 4 3382 3512 685389141 685389017 4.090000e-15 93.5
4 TraesCS3B01G166500 chr3D 94.334 2771 120 12 756 3516 114204519 114207262 0.000000e+00 4213.0
5 TraesCS3B01G166500 chr3D 95.714 140 3 1 3570 3706 114207433 114207572 5.000000e-54 222.0
6 TraesCS3B01G166500 chr3D 80.556 108 9 7 3329 3427 63404453 63404349 5.330000e-09 73.1
7 TraesCS3B01G166500 chr3A 92.752 2249 96 26 783 3028 110069261 110071445 0.000000e+00 3188.0
8 TraesCS3B01G166500 chr5A 86.193 1702 215 16 1039 2727 472110684 472112378 0.000000e+00 1823.0
9 TraesCS3B01G166500 chr5A 94.960 754 36 1 1 754 698883703 698882952 0.000000e+00 1181.0
10 TraesCS3B01G166500 chr5A 79.037 353 62 12 1085 1431 573599537 573599883 8.310000e-57 231.0
11 TraesCS3B01G166500 chr5A 85.965 57 6 1 3379 3435 489845234 489845180 4.150000e-05 60.2
12 TraesCS3B01G166500 chr5D 85.933 1699 225 13 1039 2727 369578054 369579748 0.000000e+00 1801.0
13 TraesCS3B01G166500 chr5D 78.754 353 63 12 1085 1431 454202710 454203056 3.870000e-55 226.0
14 TraesCS3B01G166500 chr5D 80.791 177 19 6 3305 3471 415652186 415652357 1.450000e-24 124.0
15 TraesCS3B01G166500 chr5B 85.479 1701 229 14 1039 2727 438795347 438797041 0.000000e+00 1757.0
16 TraesCS3B01G166500 chr5B 88.073 109 12 1 3023 3130 665813082 665813190 1.120000e-25 128.0
17 TraesCS3B01G166500 chr4B 95.623 754 33 0 1 754 587766463 587765710 0.000000e+00 1210.0
18 TraesCS3B01G166500 chr6B 95.225 754 36 0 1 754 101197778 101198531 0.000000e+00 1194.0
19 TraesCS3B01G166500 chr6B 94.980 757 38 0 1 757 86673967 86673211 0.000000e+00 1188.0
20 TraesCS3B01G166500 chr6B 97.727 132 3 0 3717 3848 352454907 352454776 1.080000e-55 228.0
21 TraesCS3B01G166500 chr1B 95.333 750 34 1 1 750 642643610 642642862 0.000000e+00 1190.0
22 TraesCS3B01G166500 chr1B 95.093 754 37 0 1 754 508703431 508704184 0.000000e+00 1188.0
23 TraesCS3B01G166500 chr1B 94.716 757 40 0 1 757 676765608 676764852 0.000000e+00 1177.0
24 TraesCS3B01G166500 chr1B 97.015 134 4 0 3715 3848 215850503 215850370 3.870000e-55 226.0
25 TraesCS3B01G166500 chr1B 97.015 134 4 0 3715 3848 580400975 580400842 3.870000e-55 226.0
26 TraesCS3B01G166500 chr4A 94.828 754 37 1 1 754 292831843 292832594 0.000000e+00 1175.0
27 TraesCS3B01G166500 chr4A 85.556 270 30 6 1062 1324 153317501 153317768 1.360000e-69 274.0
28 TraesCS3B01G166500 chr6A 94.695 754 40 0 1 754 84055645 84054892 0.000000e+00 1171.0
29 TraesCS3B01G166500 chr2B 73.941 1723 361 76 1053 2725 639027487 639025803 7.070000e-172 614.0
30 TraesCS3B01G166500 chr2B 97.015 134 4 0 3715 3848 197732453 197732320 3.870000e-55 226.0
31 TraesCS3B01G166500 chr7B 95.745 141 5 1 3708 3848 202731101 202730962 3.870000e-55 226.0
32 TraesCS3B01G166500 chr7B 92.105 152 10 2 3699 3848 382291367 382291518 3.010000e-51 213.0
33 TraesCS3B01G166500 chr1D 93.197 147 6 4 3702 3848 154102579 154102437 3.010000e-51 213.0
34 TraesCS3B01G166500 chr2A 80.756 291 37 8 1040 1324 523848153 523847876 3.900000e-50 209.0
35 TraesCS3B01G166500 chr7A 80.402 199 23 5 1058 1252 468324998 468324812 1.860000e-28 137.0
36 TraesCS3B01G166500 chr7A 87.963 108 11 1 3025 3130 40550420 40550313 4.040000e-25 126.0
37 TraesCS3B01G166500 chr4D 89.623 106 11 0 3025 3130 386984831 386984726 6.710000e-28 135.0
38 TraesCS3B01G166500 chr4D 87.719 114 14 0 3017 3130 34661517 34661630 2.410000e-27 134.0
39 TraesCS3B01G166500 chr1A 88.679 106 12 0 3025 3130 540324069 540323964 3.120000e-26 130.0
40 TraesCS3B01G166500 chr1A 81.437 167 23 7 3017 3178 584471970 584472133 3.120000e-26 130.0
41 TraesCS3B01G166500 chr7D 88.462 104 12 0 3027 3130 376062677 376062780 4.040000e-25 126.0
42 TraesCS3B01G166500 chr2D 88.462 104 12 0 3027 3130 318256882 318256985 4.040000e-25 126.0
43 TraesCS3B01G166500 chr6D 80.769 78 14 1 1400 1476 346071261 346071184 4.150000e-05 60.2


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 TraesCS3B01G166500 chr3B 166652262 166656109 3847 True 7107.0 7107 100.000 1 3848 1 chr3B.!!$R2 3847
1 TraesCS3B01G166500 chr3D 114204519 114207572 3053 False 2217.5 4213 95.024 756 3706 2 chr3D.!!$F1 2950
2 TraesCS3B01G166500 chr3A 110069261 110071445 2184 False 3188.0 3188 92.752 783 3028 1 chr3A.!!$F1 2245
3 TraesCS3B01G166500 chr5A 472110684 472112378 1694 False 1823.0 1823 86.193 1039 2727 1 chr5A.!!$F1 1688
4 TraesCS3B01G166500 chr5A 698882952 698883703 751 True 1181.0 1181 94.960 1 754 1 chr5A.!!$R2 753
5 TraesCS3B01G166500 chr5D 369578054 369579748 1694 False 1801.0 1801 85.933 1039 2727 1 chr5D.!!$F1 1688
6 TraesCS3B01G166500 chr5B 438795347 438797041 1694 False 1757.0 1757 85.479 1039 2727 1 chr5B.!!$F1 1688
7 TraesCS3B01G166500 chr4B 587765710 587766463 753 True 1210.0 1210 95.623 1 754 1 chr4B.!!$R1 753
8 TraesCS3B01G166500 chr6B 101197778 101198531 753 False 1194.0 1194 95.225 1 754 1 chr6B.!!$F1 753
9 TraesCS3B01G166500 chr6B 86673211 86673967 756 True 1188.0 1188 94.980 1 757 1 chr6B.!!$R1 756
10 TraesCS3B01G166500 chr1B 642642862 642643610 748 True 1190.0 1190 95.333 1 750 1 chr1B.!!$R3 749
11 TraesCS3B01G166500 chr1B 508703431 508704184 753 False 1188.0 1188 95.093 1 754 1 chr1B.!!$F1 753
12 TraesCS3B01G166500 chr1B 676764852 676765608 756 True 1177.0 1177 94.716 1 757 1 chr1B.!!$R4 756
13 TraesCS3B01G166500 chr4A 292831843 292832594 751 False 1175.0 1175 94.828 1 754 1 chr4A.!!$F2 753
14 TraesCS3B01G166500 chr6A 84054892 84055645 753 True 1171.0 1171 94.695 1 754 1 chr6A.!!$R1 753
15 TraesCS3B01G166500 chr2B 639025803 639027487 1684 True 614.0 614 73.941 1053 2725 1 chr2B.!!$R2 1672

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
935 949 0.178861 ACCACACTCCCTCCTCCATT 60.179 55.0 0.00 0.00 0.00 3.16 F
2622 2660 0.323725 CCAACCTGTTCCTCATGGGG 60.324 60.0 4.76 4.76 35.33 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2768 2806 0.748367 CTCACCAGCAGCAGCATCAT 60.748 55.0 3.17 0.00 45.49 2.45 R
3785 3947 0.040067 CCACCTTGCAGAAGCGTTTC 60.040 55.0 3.49 3.49 46.23 2.78 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
50 51 8.754080 GGTATGTTAGTATCTTCATGCTCCTAT 58.246 37.037 0.00 0.00 0.00 2.57
58 59 6.931790 ATCTTCATGCTCCTATAGATGTGT 57.068 37.500 0.00 0.00 0.00 3.72
107 108 3.318017 GTTATGTGCGTCTCACTGTCTT 58.682 45.455 0.00 0.00 45.81 3.01
157 158 5.070847 TCCTCTGCTGTTATATCTGCATTCA 59.929 40.000 13.70 3.63 40.37 2.57
237 238 7.068716 GCTGTATTTCTGGGTCCTAATTTGATT 59.931 37.037 0.00 0.00 0.00 2.57
454 455 2.949451 TGCACGAACCAAACACATTT 57.051 40.000 0.00 0.00 0.00 2.32
521 522 8.417884 GCTACTACAGATCAAGTTTATCTCCTT 58.582 37.037 0.00 0.00 31.22 3.36
623 624 4.586421 CCTAGATGCATCAGGAGTGAGTTA 59.414 45.833 27.70 10.64 35.66 2.24
734 735 4.600062 CCTATAAAGGGTTGAGCCAGTTT 58.400 43.478 1.66 0.00 39.48 2.66
740 741 1.620822 GGTTGAGCCAGTTTCCACAT 58.379 50.000 0.00 0.00 37.17 3.21
767 768 1.946521 GTTTAACAAACGCTCGGCTC 58.053 50.000 0.00 0.00 0.00 4.70
768 769 1.262151 GTTTAACAAACGCTCGGCTCA 59.738 47.619 0.00 0.00 0.00 4.26
769 770 0.863144 TTAACAAACGCTCGGCTCAC 59.137 50.000 0.00 0.00 0.00 3.51
770 771 0.249531 TAACAAACGCTCGGCTCACA 60.250 50.000 0.00 0.00 0.00 3.58
771 772 1.772063 AACAAACGCTCGGCTCACAC 61.772 55.000 0.00 0.00 0.00 3.82
772 773 3.036084 AAACGCTCGGCTCACACG 61.036 61.111 0.00 0.00 0.00 4.49
777 778 1.959226 GCTCGGCTCACACGGAAAA 60.959 57.895 0.00 0.00 0.00 2.29
779 780 0.512952 CTCGGCTCACACGGAAAAAG 59.487 55.000 0.00 0.00 0.00 2.27
780 781 0.179067 TCGGCTCACACGGAAAAAGT 60.179 50.000 0.00 0.00 0.00 2.66
794 806 3.853671 GGAAAAAGTACATGCGATGCAAG 59.146 43.478 0.00 0.00 43.62 4.01
795 807 4.475944 GAAAAAGTACATGCGATGCAAGT 58.524 39.130 4.99 4.99 43.62 3.16
796 808 5.391523 GGAAAAAGTACATGCGATGCAAGTA 60.392 40.000 3.05 3.05 43.62 2.24
797 809 5.818136 AAAAGTACATGCGATGCAAGTAT 57.182 34.783 9.67 0.00 42.95 2.12
798 810 4.801147 AAGTACATGCGATGCAAGTATG 57.199 40.909 17.46 17.46 42.95 2.39
823 835 1.211212 TGGAGATAGGGACTCGTCGAA 59.789 52.381 0.00 0.00 41.75 3.71
836 848 0.701303 CGTCGAACGCAAGACTACAC 59.299 55.000 0.00 0.00 43.62 2.90
838 850 2.121786 GTCGAACGCAAGACTACACAA 58.878 47.619 0.00 0.00 43.62 3.33
839 851 2.097541 GTCGAACGCAAGACTACACAAC 60.098 50.000 0.00 0.00 43.62 3.32
854 866 0.179094 ACAACAAGACGTTCCGCTCA 60.179 50.000 0.00 0.00 34.86 4.26
935 949 0.178861 ACCACACTCCCTCCTCCATT 60.179 55.000 0.00 0.00 0.00 3.16
946 960 0.991920 TCCTCCATTTCCAGTCCACC 59.008 55.000 0.00 0.00 0.00 4.61
1311 1328 1.446792 CGGCATCTTCGTGCTCACT 60.447 57.895 0.00 0.00 44.45 3.41
1371 1388 1.449246 CTCCTACGTCGTCTCCGGT 60.449 63.158 0.00 0.00 33.95 5.28
1611 1631 0.867753 GCATACAGACGTCGCTCAGG 60.868 60.000 10.46 0.93 0.00 3.86
2622 2660 0.323725 CCAACCTGTTCCTCATGGGG 60.324 60.000 4.76 4.76 35.33 4.96
2758 2796 4.720090 CGAAGACGAGCTAAAAGACTACA 58.280 43.478 0.00 0.00 42.66 2.74
2768 2806 0.956633 AAAGACTACAGCGACACCGA 59.043 50.000 0.00 0.00 38.22 4.69
2796 2834 4.704833 GCTGGTGAGAAGGCGGCA 62.705 66.667 13.08 0.00 0.00 5.69
2798 2836 3.241530 TGGTGAGAAGGCGGCAGT 61.242 61.111 13.08 0.00 0.00 4.40
2808 2846 3.959975 GCGGCAGTGAAAACGGCA 61.960 61.111 0.00 0.00 32.53 5.69
3005 3044 8.716646 ACACACGATTGTAATCTTCATATTCA 57.283 30.769 0.00 0.00 33.30 2.57
3006 3045 8.820933 ACACACGATTGTAATCTTCATATTCAG 58.179 33.333 0.00 0.00 33.30 3.02
3031 3070 7.442666 AGAGTCTTGATCTTTGTTTTGTACTCC 59.557 37.037 0.00 0.00 31.14 3.85
3052 3091 7.677892 ACTCCCTCCGTTCCTAAATATAAATC 58.322 38.462 0.00 0.00 0.00 2.17
3130 3170 3.822167 TGCAGATTCACTCATTTTGCTCA 59.178 39.130 0.00 0.00 0.00 4.26
3137 3177 2.098607 CACTCATTTTGCTCATCCGCAT 59.901 45.455 0.00 0.00 40.04 4.73
3138 3178 2.098607 ACTCATTTTGCTCATCCGCATG 59.901 45.455 0.00 0.00 40.04 4.06
3190 3230 3.582647 TGGAGGAAGTGATGTACATGTGT 59.417 43.478 14.43 0.00 0.00 3.72
3191 3231 3.935203 GGAGGAAGTGATGTACATGTGTG 59.065 47.826 14.43 0.00 0.00 3.82
3235 3275 8.611654 TCAATACATTGACATCACCATATGAG 57.388 34.615 3.65 0.00 40.25 2.90
3254 3294 8.853345 CATATGAGAACTTGTTATTTGTGCAAC 58.147 33.333 0.00 0.00 37.35 4.17
3301 3342 8.538856 GCAGAAAAATTGCGTGCAATATATTTA 58.461 29.630 19.43 0.00 44.86 1.40
3309 3350 6.058833 TGCGTGCAATATATTTAAAGGGAGA 58.941 36.000 0.00 0.00 0.00 3.71
3365 3406 7.392953 TGCATCAGTCACTTTTTATATGAACCA 59.607 33.333 0.00 0.00 0.00 3.67
3385 3427 7.227314 TGAACCATCGGATCTTGATCAAAATAG 59.773 37.037 9.88 0.00 0.00 1.73
3390 3432 5.635280 TCGGATCTTGATCAAAATAGATCGC 59.365 40.000 20.95 15.42 45.81 4.58
3392 3434 4.715520 TCTTGATCAAAATAGATCGCGC 57.284 40.909 9.88 0.00 45.81 6.86
3412 3454 3.440228 GCTACTGTTCATCGTCTTCCTC 58.560 50.000 0.00 0.00 0.00 3.71
3440 3482 0.747255 CTCATCCTCATCCCGAACGT 59.253 55.000 0.00 0.00 0.00 3.99
3461 3503 2.767073 AGCCTACCCCGCCCTAAC 60.767 66.667 0.00 0.00 0.00 2.34
3532 3574 3.339093 CCCCACCCTCCCCTCAAC 61.339 72.222 0.00 0.00 0.00 3.18
3533 3575 3.339093 CCCACCCTCCCCTCAACC 61.339 72.222 0.00 0.00 0.00 3.77
3534 3576 2.204151 CCACCCTCCCCTCAACCT 60.204 66.667 0.00 0.00 0.00 3.50
3535 3577 2.301738 CCACCCTCCCCTCAACCTC 61.302 68.421 0.00 0.00 0.00 3.85
3536 3578 2.125225 ACCCTCCCCTCAACCTCC 59.875 66.667 0.00 0.00 0.00 4.30
3537 3579 2.692741 CCCTCCCCTCAACCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
3538 3580 2.692741 CCTCCCCTCAACCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
3539 3581 2.692741 CTCCCCTCAACCTCCCCC 60.693 72.222 0.00 0.00 0.00 5.40
3540 3582 3.216371 TCCCCTCAACCTCCCCCT 61.216 66.667 0.00 0.00 0.00 4.79
3541 3583 2.692741 CCCCTCAACCTCCCCCTC 60.693 72.222 0.00 0.00 0.00 4.30
3542 3584 2.692741 CCCTCAACCTCCCCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
3543 3585 2.124996 CCTCAACCTCCCCCTCCA 59.875 66.667 0.00 0.00 0.00 3.86
3544 3586 2.301738 CCTCAACCTCCCCCTCCAC 61.302 68.421 0.00 0.00 0.00 4.02
3545 3587 2.204090 TCAACCTCCCCCTCCACC 60.204 66.667 0.00 0.00 0.00 4.61
3546 3588 3.339093 CAACCTCCCCCTCCACCC 61.339 72.222 0.00 0.00 0.00 4.61
3547 3589 3.882670 AACCTCCCCCTCCACCCA 61.883 66.667 0.00 0.00 0.00 4.51
3548 3590 4.677151 ACCTCCCCCTCCACCCAC 62.677 72.222 0.00 0.00 0.00 4.61
3553 3595 4.344865 CCCCTCCACCCACCGTTG 62.345 72.222 0.00 0.00 0.00 4.10
3554 3596 3.566210 CCCTCCACCCACCGTTGT 61.566 66.667 0.00 0.00 0.00 3.32
3555 3597 2.513895 CCTCCACCCACCGTTGTT 59.486 61.111 0.00 0.00 0.00 2.83
3556 3598 1.896660 CCTCCACCCACCGTTGTTG 60.897 63.158 0.00 0.00 0.00 3.33
3557 3599 1.153046 CTCCACCCACCGTTGTTGT 60.153 57.895 0.00 0.00 0.00 3.32
3558 3600 0.750182 CTCCACCCACCGTTGTTGTT 60.750 55.000 0.00 0.00 0.00 2.83
3559 3601 0.545171 TCCACCCACCGTTGTTGTTA 59.455 50.000 0.00 0.00 0.00 2.41
3560 3602 0.948678 CCACCCACCGTTGTTGTTAG 59.051 55.000 0.00 0.00 0.00 2.34
3561 3603 0.309612 CACCCACCGTTGTTGTTAGC 59.690 55.000 0.00 0.00 0.00 3.09
3562 3604 0.820482 ACCCACCGTTGTTGTTAGCC 60.820 55.000 0.00 0.00 0.00 3.93
3563 3605 0.820074 CCCACCGTTGTTGTTAGCCA 60.820 55.000 0.00 0.00 0.00 4.75
3564 3606 0.309612 CCACCGTTGTTGTTAGCCAC 59.690 55.000 0.00 0.00 0.00 5.01
3565 3607 1.305201 CACCGTTGTTGTTAGCCACT 58.695 50.000 0.00 0.00 0.00 4.00
3566 3608 1.002900 CACCGTTGTTGTTAGCCACTG 60.003 52.381 0.00 0.00 0.00 3.66
3567 3609 0.040425 CCGTTGTTGTTAGCCACTGC 60.040 55.000 0.00 0.00 37.95 4.40
3568 3610 0.040425 CGTTGTTGTTAGCCACTGCC 60.040 55.000 0.00 0.00 38.69 4.85
3591 3750 2.427753 CATCCCTCTAAGCCCGGC 59.572 66.667 0.00 0.00 0.00 6.13
3628 3787 1.586154 CCGGTGATCCCTTGCAACAC 61.586 60.000 8.26 8.26 0.00 3.32
3706 3868 0.687354 TCTTCTCCGGCAAGCTTCTT 59.313 50.000 0.00 0.00 0.00 2.52
3707 3869 0.801251 CTTCTCCGGCAAGCTTCTTG 59.199 55.000 0.00 2.40 0.00 3.02
3708 3870 0.396435 TTCTCCGGCAAGCTTCTTGA 59.604 50.000 10.44 0.00 0.00 3.02
3709 3871 0.615331 TCTCCGGCAAGCTTCTTGAT 59.385 50.000 10.44 0.00 0.00 2.57
3710 3872 1.831106 TCTCCGGCAAGCTTCTTGATA 59.169 47.619 10.44 0.00 0.00 2.15
3711 3873 1.936547 CTCCGGCAAGCTTCTTGATAC 59.063 52.381 10.44 0.00 0.00 2.24
3712 3874 0.652592 CCGGCAAGCTTCTTGATACG 59.347 55.000 10.44 10.10 0.00 3.06
3713 3875 1.359848 CGGCAAGCTTCTTGATACGT 58.640 50.000 10.44 0.00 0.00 3.57
3714 3876 1.324736 CGGCAAGCTTCTTGATACGTC 59.675 52.381 10.44 0.00 0.00 4.34
3715 3877 2.622436 GGCAAGCTTCTTGATACGTCT 58.378 47.619 10.44 0.00 0.00 4.18
3716 3878 3.003480 GGCAAGCTTCTTGATACGTCTT 58.997 45.455 10.44 0.00 0.00 3.01
3717 3879 3.181516 GGCAAGCTTCTTGATACGTCTTG 60.182 47.826 10.44 0.00 34.32 3.02
3718 3880 3.433615 GCAAGCTTCTTGATACGTCTTGT 59.566 43.478 10.44 0.00 33.88 3.16
3719 3881 4.434857 GCAAGCTTCTTGATACGTCTTGTC 60.435 45.833 10.44 0.00 33.88 3.18
3720 3882 4.521130 AGCTTCTTGATACGTCTTGTCA 57.479 40.909 0.00 0.00 0.00 3.58
3721 3883 4.238514 AGCTTCTTGATACGTCTTGTCAC 58.761 43.478 0.00 0.00 0.00 3.67
3722 3884 3.059570 GCTTCTTGATACGTCTTGTCACG 59.940 47.826 0.00 0.00 45.65 4.35
3723 3885 2.592194 TCTTGATACGTCTTGTCACGC 58.408 47.619 0.00 0.00 43.93 5.34
3724 3886 1.654105 CTTGATACGTCTTGTCACGCC 59.346 52.381 0.00 0.00 43.93 5.68
3725 3887 0.108992 TGATACGTCTTGTCACGCCC 60.109 55.000 0.00 0.00 43.93 6.13
3726 3888 0.108992 GATACGTCTTGTCACGCCCA 60.109 55.000 0.00 0.00 43.93 5.36
3727 3889 0.319083 ATACGTCTTGTCACGCCCAA 59.681 50.000 0.00 0.00 43.93 4.12
3728 3890 0.319083 TACGTCTTGTCACGCCCAAT 59.681 50.000 0.00 0.00 43.93 3.16
3729 3891 0.319083 ACGTCTTGTCACGCCCAATA 59.681 50.000 0.00 0.00 43.93 1.90
3730 3892 1.066430 ACGTCTTGTCACGCCCAATAT 60.066 47.619 0.00 0.00 43.93 1.28
3731 3893 1.327460 CGTCTTGTCACGCCCAATATG 59.673 52.381 0.00 0.00 31.96 1.78
3732 3894 2.356135 GTCTTGTCACGCCCAATATGT 58.644 47.619 0.00 0.00 0.00 2.29
3733 3895 2.095853 GTCTTGTCACGCCCAATATGTG 59.904 50.000 0.00 0.00 34.96 3.21
3734 3896 2.027653 TCTTGTCACGCCCAATATGTGA 60.028 45.455 0.00 0.00 40.12 3.58
3736 3898 3.469564 TCACGCCCAATATGTGACC 57.530 52.632 0.00 0.00 37.69 4.02
3737 3899 0.107410 TCACGCCCAATATGTGACCC 60.107 55.000 0.00 0.00 37.69 4.46
3738 3900 0.107214 CACGCCCAATATGTGACCCT 60.107 55.000 0.00 0.00 35.66 4.34
3739 3901 1.140052 CACGCCCAATATGTGACCCTA 59.860 52.381 0.00 0.00 35.66 3.53
3740 3902 2.054799 ACGCCCAATATGTGACCCTAT 58.945 47.619 0.00 0.00 0.00 2.57
3741 3903 2.038557 ACGCCCAATATGTGACCCTATC 59.961 50.000 0.00 0.00 0.00 2.08
3742 3904 2.615493 CGCCCAATATGTGACCCTATCC 60.615 54.545 0.00 0.00 0.00 2.59
3743 3905 2.375174 GCCCAATATGTGACCCTATCCA 59.625 50.000 0.00 0.00 0.00 3.41
3744 3906 3.181434 GCCCAATATGTGACCCTATCCAA 60.181 47.826 0.00 0.00 0.00 3.53
3745 3907 4.655963 CCCAATATGTGACCCTATCCAAG 58.344 47.826 0.00 0.00 0.00 3.61
3746 3908 4.350816 CCCAATATGTGACCCTATCCAAGA 59.649 45.833 0.00 0.00 0.00 3.02
3747 3909 5.513788 CCCAATATGTGACCCTATCCAAGAG 60.514 48.000 0.00 0.00 0.00 2.85
3748 3910 5.513788 CCAATATGTGACCCTATCCAAGAGG 60.514 48.000 0.00 0.00 0.00 3.69
3764 3926 4.353383 AAGAGGAACTTGAAGGTACCAC 57.647 45.455 15.94 8.42 41.55 4.16
3765 3927 2.638363 AGAGGAACTTGAAGGTACCACC 59.362 50.000 15.94 5.61 41.55 4.61
3766 3928 2.370849 GAGGAACTTGAAGGTACCACCA 59.629 50.000 15.94 8.45 41.55 4.17
3767 3929 2.781174 AGGAACTTGAAGGTACCACCAA 59.219 45.455 15.94 15.58 36.09 3.67
3768 3930 3.146847 GGAACTTGAAGGTACCACCAAG 58.853 50.000 29.42 29.42 41.95 3.61
3769 3931 2.951229 ACTTGAAGGTACCACCAAGG 57.049 50.000 31.87 21.33 41.95 3.61
3770 3932 2.414612 ACTTGAAGGTACCACCAAGGA 58.585 47.619 31.87 11.46 41.95 3.36
3771 3933 2.986728 ACTTGAAGGTACCACCAAGGAT 59.013 45.455 31.87 19.37 41.95 3.24
3772 3934 4.172807 ACTTGAAGGTACCACCAAGGATA 58.827 43.478 31.87 10.93 41.95 2.59
3773 3935 4.225267 ACTTGAAGGTACCACCAAGGATAG 59.775 45.833 31.87 18.61 41.95 2.08
3774 3936 4.069312 TGAAGGTACCACCAAGGATAGA 57.931 45.455 15.94 0.00 41.95 1.98
3775 3937 3.773119 TGAAGGTACCACCAAGGATAGAC 59.227 47.826 15.94 0.00 41.95 2.59
3776 3938 2.760581 AGGTACCACCAAGGATAGACC 58.239 52.381 15.94 0.00 41.95 3.85
3777 3939 1.767088 GGTACCACCAAGGATAGACCC 59.233 57.143 7.15 0.00 41.22 4.46
3778 3940 1.411612 GTACCACCAAGGATAGACCCG 59.588 57.143 0.00 0.00 41.22 5.28
3779 3941 1.146263 CCACCAAGGATAGACCCGC 59.854 63.158 0.00 0.00 41.22 6.13
3780 3942 1.622607 CCACCAAGGATAGACCCGCA 61.623 60.000 0.00 0.00 41.22 5.69
3781 3943 0.469917 CACCAAGGATAGACCCGCAT 59.530 55.000 0.00 0.00 40.05 4.73
3782 3944 1.691976 CACCAAGGATAGACCCGCATA 59.308 52.381 0.00 0.00 40.05 3.14
3783 3945 2.303022 CACCAAGGATAGACCCGCATAT 59.697 50.000 0.00 0.00 40.05 1.78
3784 3946 2.979678 ACCAAGGATAGACCCGCATATT 59.020 45.455 0.00 0.00 40.05 1.28
3785 3947 3.244561 ACCAAGGATAGACCCGCATATTG 60.245 47.826 0.00 0.00 40.05 1.90
3786 3948 3.007940 CCAAGGATAGACCCGCATATTGA 59.992 47.826 0.00 0.00 40.05 2.57
3787 3949 4.504864 CCAAGGATAGACCCGCATATTGAA 60.505 45.833 0.00 0.00 40.05 2.69
3788 3950 4.974645 AGGATAGACCCGCATATTGAAA 57.025 40.909 0.00 0.00 40.05 2.69
3789 3951 4.642429 AGGATAGACCCGCATATTGAAAC 58.358 43.478 0.00 0.00 40.05 2.78
3790 3952 3.432252 GGATAGACCCGCATATTGAAACG 59.568 47.826 0.00 0.00 0.00 3.60
3791 3953 1.014352 AGACCCGCATATTGAAACGC 58.986 50.000 0.00 0.00 0.00 4.84
3792 3954 1.014352 GACCCGCATATTGAAACGCT 58.986 50.000 0.00 0.00 0.00 5.07
3793 3955 1.400494 GACCCGCATATTGAAACGCTT 59.600 47.619 0.00 0.00 0.00 4.68
3794 3956 1.400494 ACCCGCATATTGAAACGCTTC 59.600 47.619 0.00 0.00 0.00 3.86
3795 3957 1.670811 CCCGCATATTGAAACGCTTCT 59.329 47.619 0.00 0.00 32.33 2.85
3796 3958 2.539547 CCCGCATATTGAAACGCTTCTG 60.540 50.000 0.00 0.00 32.33 3.02
3797 3959 2.104144 CGCATATTGAAACGCTTCTGC 58.896 47.619 0.00 0.73 32.33 4.26
3798 3960 2.476018 CGCATATTGAAACGCTTCTGCA 60.476 45.455 10.05 0.00 39.64 4.41
3799 3961 3.500982 GCATATTGAAACGCTTCTGCAA 58.499 40.909 5.84 0.00 39.64 4.08
3800 3962 3.545078 GCATATTGAAACGCTTCTGCAAG 59.455 43.478 5.84 0.00 39.64 4.01
3801 3963 2.712057 ATTGAAACGCTTCTGCAAGG 57.288 45.000 0.00 0.00 39.64 3.61
3802 3964 1.388547 TTGAAACGCTTCTGCAAGGT 58.611 45.000 0.00 0.00 39.64 3.50
3803 3965 0.662619 TGAAACGCTTCTGCAAGGTG 59.337 50.000 0.00 0.00 39.64 4.00
3804 3966 0.040067 GAAACGCTTCTGCAAGGTGG 60.040 55.000 0.00 0.00 39.64 4.61
3805 3967 0.465460 AAACGCTTCTGCAAGGTGGA 60.465 50.000 0.00 0.00 39.64 4.02
3806 3968 0.250901 AACGCTTCTGCAAGGTGGAT 60.251 50.000 0.00 0.00 39.64 3.41
3807 3969 0.613260 ACGCTTCTGCAAGGTGGATA 59.387 50.000 0.00 0.00 39.64 2.59
3808 3970 1.210478 ACGCTTCTGCAAGGTGGATAT 59.790 47.619 0.00 0.00 39.64 1.63
3809 3971 1.869767 CGCTTCTGCAAGGTGGATATC 59.130 52.381 0.00 0.00 39.64 1.63
3810 3972 2.742856 CGCTTCTGCAAGGTGGATATCA 60.743 50.000 4.83 0.00 39.64 2.15
3811 3973 3.484407 GCTTCTGCAAGGTGGATATCAT 58.516 45.455 4.83 0.00 39.41 2.45
3812 3974 3.887716 GCTTCTGCAAGGTGGATATCATT 59.112 43.478 4.83 0.00 39.41 2.57
3813 3975 5.065914 GCTTCTGCAAGGTGGATATCATTA 58.934 41.667 4.83 0.00 39.41 1.90
3814 3976 5.049129 GCTTCTGCAAGGTGGATATCATTAC 60.049 44.000 4.83 0.54 39.41 1.89
3815 3977 5.628797 TCTGCAAGGTGGATATCATTACA 57.371 39.130 4.83 0.00 0.00 2.41
3816 3978 6.191657 TCTGCAAGGTGGATATCATTACAT 57.808 37.500 4.83 0.00 0.00 2.29
3817 3979 6.233434 TCTGCAAGGTGGATATCATTACATC 58.767 40.000 4.83 0.00 0.00 3.06
3818 3980 5.939447 TGCAAGGTGGATATCATTACATCA 58.061 37.500 4.83 0.00 0.00 3.07
3819 3981 6.363882 TGCAAGGTGGATATCATTACATCAA 58.636 36.000 4.83 0.00 0.00 2.57
3820 3982 7.005902 TGCAAGGTGGATATCATTACATCAAT 58.994 34.615 4.83 0.00 0.00 2.57
3821 3983 8.162746 TGCAAGGTGGATATCATTACATCAATA 58.837 33.333 4.83 0.00 0.00 1.90
3822 3984 9.182214 GCAAGGTGGATATCATTACATCAATAT 57.818 33.333 4.83 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.846040 ACATACCCTGTTAACCGCAAATA 58.154 39.130 2.48 0.00 32.90 1.40
31 32 9.183368 CACATCTATAGGAGCATGAAGATACTA 57.817 37.037 0.00 0.00 0.00 1.82
50 51 3.193479 CACAGCAGACCAGTACACATCTA 59.807 47.826 0.00 0.00 0.00 1.98
58 59 3.914984 GCTTCACAGCAGACCAGTA 57.085 52.632 0.00 0.00 46.49 2.74
107 108 3.717400 GTCGCAGATGAAGACCATAGA 57.283 47.619 0.00 0.00 40.67 1.98
157 158 0.395311 CCAGCCCAATCAGCATCTGT 60.395 55.000 0.00 0.00 32.61 3.41
432 433 1.383523 TGTGTTTGGTTCGTGCATGA 58.616 45.000 3.97 3.97 0.00 3.07
474 475 0.107410 TCTGTGCAACACGTTCCCTT 60.107 50.000 0.00 0.00 45.67 3.95
521 522 3.410631 TGTCGGCAAGTTGATCCTTTA 57.589 42.857 7.16 0.00 0.00 1.85
623 624 3.519913 GTCTAACACCCTCCCTCAATCTT 59.480 47.826 0.00 0.00 0.00 2.40
701 702 6.847567 TCAACCCTTTATAGGTAGCCTATCAA 59.152 38.462 10.63 6.35 42.60 2.57
710 711 4.368067 ACTGGCTCAACCCTTTATAGGTA 58.632 43.478 0.00 0.00 40.19 3.08
714 715 4.043561 TGGAAACTGGCTCAACCCTTTATA 59.956 41.667 0.00 0.00 37.83 0.98
715 716 3.181423 TGGAAACTGGCTCAACCCTTTAT 60.181 43.478 0.00 0.00 37.83 1.40
734 735 7.599630 GTTTGTTAAACGTAGGATATGTGGA 57.400 36.000 0.00 0.00 40.60 4.02
766 767 2.222213 CGCATGTACTTTTTCCGTGTGA 59.778 45.455 0.00 0.00 0.00 3.58
767 768 2.222213 TCGCATGTACTTTTTCCGTGTG 59.778 45.455 0.00 0.00 0.00 3.82
768 769 2.485903 TCGCATGTACTTTTTCCGTGT 58.514 42.857 0.00 0.00 0.00 4.49
769 770 3.416277 CATCGCATGTACTTTTTCCGTG 58.584 45.455 0.00 0.00 0.00 4.94
770 771 2.159572 GCATCGCATGTACTTTTTCCGT 60.160 45.455 0.00 0.00 0.00 4.69
771 772 2.159585 TGCATCGCATGTACTTTTTCCG 60.160 45.455 0.00 0.00 31.71 4.30
772 773 3.485947 TGCATCGCATGTACTTTTTCC 57.514 42.857 0.00 0.00 31.71 3.13
773 774 4.475944 ACTTGCATCGCATGTACTTTTTC 58.524 39.130 5.77 0.00 43.37 2.29
774 775 4.503741 ACTTGCATCGCATGTACTTTTT 57.496 36.364 5.77 0.00 43.37 1.94
777 778 3.002656 GCATACTTGCATCGCATGTACTT 59.997 43.478 14.57 1.01 46.46 2.24
779 780 2.908634 GCATACTTGCATCGCATGTAC 58.091 47.619 14.57 3.00 46.46 2.90
794 806 5.234466 AGTCCCTATCTCCATTTGCATAC 57.766 43.478 0.00 0.00 0.00 2.39
795 807 4.021104 CGAGTCCCTATCTCCATTTGCATA 60.021 45.833 0.00 0.00 0.00 3.14
796 808 3.244353 CGAGTCCCTATCTCCATTTGCAT 60.244 47.826 0.00 0.00 0.00 3.96
797 809 2.103094 CGAGTCCCTATCTCCATTTGCA 59.897 50.000 0.00 0.00 0.00 4.08
798 810 2.103263 ACGAGTCCCTATCTCCATTTGC 59.897 50.000 0.00 0.00 0.00 3.68
823 835 2.864343 GTCTTGTTGTGTAGTCTTGCGT 59.136 45.455 0.00 0.00 0.00 5.24
854 866 1.445942 CGTGGGTTGGTCAGTGAGT 59.554 57.895 0.00 0.00 0.00 3.41
935 949 2.531685 CCCTGGGGTGGACTGGAA 60.532 66.667 4.27 0.00 0.00 3.53
1019 1033 2.432628 GCGCGTACTGTTCCTGCT 60.433 61.111 8.43 0.00 0.00 4.24
1371 1388 2.484928 CGAGAGCATGGCGGAGAGA 61.485 63.158 0.00 0.00 0.00 3.10
1497 1514 3.438434 CGATGATGCTCTCGAGGATAAGA 59.562 47.826 13.56 0.00 39.68 2.10
1611 1631 1.012486 CAAGCTCGTTGTACCCGTCC 61.012 60.000 0.00 0.00 0.00 4.79
1734 1754 1.121240 CGATGACGAACGCTATCACC 58.879 55.000 0.00 0.00 42.66 4.02
2280 2306 1.145819 GATGGAGAGCAGGCTGGAC 59.854 63.158 17.64 0.00 0.00 4.02
2346 2372 1.750399 GCCCCTCACGTAGTACCGA 60.750 63.158 0.00 0.00 41.61 4.69
2655 2693 1.446516 GCATGATGGCGGTGCATACA 61.447 55.000 0.00 0.00 38.68 2.29
2658 2696 2.124024 AGCATGATGGCGGTGCAT 60.124 55.556 0.00 0.00 41.19 3.96
2758 2796 1.520120 CAGCATCATCGGTGTCGCT 60.520 57.895 8.48 8.48 35.38 4.93
2768 2806 0.748367 CTCACCAGCAGCAGCATCAT 60.748 55.000 3.17 0.00 45.49 2.45
2774 2812 2.039405 GCCTTCTCACCAGCAGCAG 61.039 63.158 0.00 0.00 0.00 4.24
2808 2846 1.707239 CGCTAGCCTTCTCGACGTCT 61.707 60.000 14.70 0.00 0.00 4.18
2956 2995 9.436957 TGTAGATAAAAAGTCTTCTCACATTCC 57.563 33.333 0.00 0.00 0.00 3.01
2962 3001 7.654568 TCGTGTGTAGATAAAAAGTCTTCTCA 58.345 34.615 0.00 0.00 0.00 3.27
2997 3036 9.730705 AAACAAAGATCAAGACTCTGAATATGA 57.269 29.630 0.00 0.00 0.00 2.15
3000 3039 9.342308 ACAAAACAAAGATCAAGACTCTGAATA 57.658 29.630 0.00 0.00 0.00 1.75
3005 3044 7.442666 GGAGTACAAAACAAAGATCAAGACTCT 59.557 37.037 0.00 0.00 31.34 3.24
3006 3045 7.308049 GGGAGTACAAAACAAAGATCAAGACTC 60.308 40.741 0.00 0.00 0.00 3.36
3094 3133 9.875675 GAGTGAATCTGCATTTTAGAATATGTC 57.124 33.333 0.00 0.00 0.00 3.06
3105 3144 5.790593 AGCAAAATGAGTGAATCTGCATTT 58.209 33.333 0.00 0.00 41.27 2.32
3112 3151 4.595116 CGGATGAGCAAAATGAGTGAATC 58.405 43.478 0.00 0.00 0.00 2.52
3130 3170 2.579873 CTTCAGGATTTCCATGCGGAT 58.420 47.619 0.00 0.00 42.41 4.18
3147 3187 8.947115 CCTCCATTCGTAAATATAAATCCCTTC 58.053 37.037 0.00 0.00 0.00 3.46
3164 3204 4.123497 TGTACATCACTTCCTCCATTCG 57.877 45.455 0.00 0.00 0.00 3.34
3168 3208 3.582647 ACACATGTACATCACTTCCTCCA 59.417 43.478 5.07 0.00 0.00 3.86
3190 3230 3.195002 GCTCATTACCAGCGCGCA 61.195 61.111 35.10 13.06 0.00 6.09
3191 3231 2.051804 ATTGCTCATTACCAGCGCGC 62.052 55.000 26.66 26.66 40.01 6.86
3228 3268 8.853345 GTTGCACAAATAACAAGTTCTCATATG 58.147 33.333 0.00 0.00 0.00 1.78
3231 3271 6.804677 TGTTGCACAAATAACAAGTTCTCAT 58.195 32.000 0.00 0.00 34.17 2.90
3235 3275 6.265577 AGTCTGTTGCACAAATAACAAGTTC 58.734 36.000 0.00 0.00 36.47 3.01
3272 3312 1.793532 TGCACGCAATTTTTCTGCATG 59.206 42.857 0.00 0.00 39.91 4.06
3301 3342 5.029474 AGCTCAGAAATAGAGTCTCCCTTT 58.971 41.667 0.00 0.00 35.55 3.11
3309 3350 8.563732 GTTTCTTTTTCAGCTCAGAAATAGAGT 58.436 33.333 14.75 0.00 42.39 3.24
3318 3359 4.501921 GCAACTGTTTCTTTTTCAGCTCAG 59.498 41.667 0.00 0.00 33.12 3.35
3365 3406 6.312426 GCGATCTATTTTGATCAAGATCCGAT 59.688 38.462 21.43 19.05 42.01 4.18
3385 3427 0.772926 CGATGAACAGTAGCGCGATC 59.227 55.000 12.10 0.00 0.00 3.69
3390 3432 2.159366 AGGAAGACGATGAACAGTAGCG 60.159 50.000 0.00 0.00 0.00 4.26
3392 3434 3.181485 GGGAGGAAGACGATGAACAGTAG 60.181 52.174 0.00 0.00 0.00 2.57
3412 3454 2.371510 GGATGAGGATGAGGAAGAAGGG 59.628 54.545 0.00 0.00 0.00 3.95
3516 3558 3.339093 GGTTGAGGGGAGGGTGGG 61.339 72.222 0.00 0.00 0.00 4.61
3517 3559 2.204151 AGGTTGAGGGGAGGGTGG 60.204 66.667 0.00 0.00 0.00 4.61
3518 3560 2.301738 GGAGGTTGAGGGGAGGGTG 61.302 68.421 0.00 0.00 0.00 4.61
3519 3561 2.125225 GGAGGTTGAGGGGAGGGT 59.875 66.667 0.00 0.00 0.00 4.34
3520 3562 2.692741 GGGAGGTTGAGGGGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
3521 3563 2.692741 GGGGAGGTTGAGGGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
3522 3564 2.692741 GGGGGAGGTTGAGGGGAG 60.693 72.222 0.00 0.00 0.00 4.30
3523 3565 3.216371 AGGGGGAGGTTGAGGGGA 61.216 66.667 0.00 0.00 0.00 4.81
3524 3566 2.692741 GAGGGGGAGGTTGAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
3525 3567 2.692741 GGAGGGGGAGGTTGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
3526 3568 2.124996 TGGAGGGGGAGGTTGAGG 59.875 66.667 0.00 0.00 0.00 3.86
3527 3569 2.301738 GGTGGAGGGGGAGGTTGAG 61.302 68.421 0.00 0.00 0.00 3.02
3528 3570 2.204090 GGTGGAGGGGGAGGTTGA 60.204 66.667 0.00 0.00 0.00 3.18
3529 3571 3.339093 GGGTGGAGGGGGAGGTTG 61.339 72.222 0.00 0.00 0.00 3.77
3530 3572 3.882670 TGGGTGGAGGGGGAGGTT 61.883 66.667 0.00 0.00 0.00 3.50
3531 3573 4.677151 GTGGGTGGAGGGGGAGGT 62.677 72.222 0.00 0.00 0.00 3.85
3536 3578 4.344865 CAACGGTGGGTGGAGGGG 62.345 72.222 0.00 0.00 0.00 4.79
3537 3579 3.128032 AACAACGGTGGGTGGAGGG 62.128 63.158 4.97 0.00 0.00 4.30
3538 3580 1.896660 CAACAACGGTGGGTGGAGG 60.897 63.158 4.97 0.00 0.00 4.30
3539 3581 0.750182 AACAACAACGGTGGGTGGAG 60.750 55.000 4.97 0.00 0.00 3.86
3540 3582 0.545171 TAACAACAACGGTGGGTGGA 59.455 50.000 4.97 0.00 0.00 4.02
3541 3583 0.948678 CTAACAACAACGGTGGGTGG 59.051 55.000 4.97 0.00 0.00 4.61
3542 3584 0.309612 GCTAACAACAACGGTGGGTG 59.690 55.000 4.97 4.97 0.00 4.61
3543 3585 0.820482 GGCTAACAACAACGGTGGGT 60.820 55.000 4.97 0.00 0.00 4.51
3544 3586 0.820074 TGGCTAACAACAACGGTGGG 60.820 55.000 4.97 0.00 0.00 4.61
3545 3587 0.309612 GTGGCTAACAACAACGGTGG 59.690 55.000 4.97 0.00 0.00 4.61
3546 3588 1.002900 CAGTGGCTAACAACAACGGTG 60.003 52.381 0.00 0.00 0.00 4.94
3547 3589 1.305201 CAGTGGCTAACAACAACGGT 58.695 50.000 0.00 0.00 0.00 4.83
3548 3590 0.040425 GCAGTGGCTAACAACAACGG 60.040 55.000 0.00 0.00 36.96 4.44
3549 3591 0.040425 GGCAGTGGCTAACAACAACG 60.040 55.000 9.90 0.00 40.87 4.10
3550 3592 0.313987 GGGCAGTGGCTAACAACAAC 59.686 55.000 17.16 0.00 40.87 3.32
3551 3593 0.825840 GGGGCAGTGGCTAACAACAA 60.826 55.000 17.16 0.00 40.87 2.83
3552 3594 1.228429 GGGGCAGTGGCTAACAACA 60.228 57.895 17.16 0.00 40.87 3.33
3553 3595 1.228429 TGGGGCAGTGGCTAACAAC 60.228 57.895 17.16 0.00 40.87 3.32
3554 3596 1.228429 GTGGGGCAGTGGCTAACAA 60.228 57.895 17.16 0.00 40.87 2.83
3555 3597 2.434331 GTGGGGCAGTGGCTAACA 59.566 61.111 17.16 10.52 40.87 2.41
3556 3598 2.361230 GGTGGGGCAGTGGCTAAC 60.361 66.667 17.16 14.13 40.87 2.34
3557 3599 3.657350 GGGTGGGGCAGTGGCTAA 61.657 66.667 17.16 2.06 40.87 3.09
3558 3600 4.992982 TGGGTGGGGCAGTGGCTA 62.993 66.667 17.16 3.32 40.87 3.93
3561 3603 4.447342 GGATGGGTGGGGCAGTGG 62.447 72.222 0.00 0.00 0.00 4.00
3562 3604 4.447342 GGGATGGGTGGGGCAGTG 62.447 72.222 0.00 0.00 0.00 3.66
3563 3605 4.701437 AGGGATGGGTGGGGCAGT 62.701 66.667 0.00 0.00 0.00 4.40
3564 3606 2.914734 TAGAGGGATGGGTGGGGCAG 62.915 65.000 0.00 0.00 0.00 4.85
3565 3607 2.500381 TTAGAGGGATGGGTGGGGCA 62.500 60.000 0.00 0.00 0.00 5.36
3566 3608 1.696314 TTAGAGGGATGGGTGGGGC 60.696 63.158 0.00 0.00 0.00 5.80
3567 3609 1.709994 GCTTAGAGGGATGGGTGGGG 61.710 65.000 0.00 0.00 0.00 4.96
3568 3610 1.709994 GGCTTAGAGGGATGGGTGGG 61.710 65.000 0.00 0.00 0.00 4.61
3591 3750 0.740737 GGAGATTTTCATGGGTGCCG 59.259 55.000 0.00 0.00 0.00 5.69
3593 3752 0.740737 CCGGAGATTTTCATGGGTGC 59.259 55.000 0.00 0.00 0.00 5.01
3628 3787 2.269940 CCCATCTATCTTAGGGGTGGG 58.730 57.143 0.00 0.00 37.66 4.61
3706 3868 0.108992 GGGCGTGACAAGACGTATCA 60.109 55.000 0.00 0.00 41.54 2.15
3707 3869 0.108992 TGGGCGTGACAAGACGTATC 60.109 55.000 0.00 0.00 41.54 2.24
3708 3870 0.319083 TTGGGCGTGACAAGACGTAT 59.681 50.000 0.00 0.00 41.54 3.06
3709 3871 0.319083 ATTGGGCGTGACAAGACGTA 59.681 50.000 0.00 0.00 41.54 3.57
3710 3872 0.319083 TATTGGGCGTGACAAGACGT 59.681 50.000 0.00 0.00 41.54 4.34
3711 3873 1.327460 CATATTGGGCGTGACAAGACG 59.673 52.381 0.00 0.00 42.42 4.18
3712 3874 2.095853 CACATATTGGGCGTGACAAGAC 59.904 50.000 0.00 0.00 32.23 3.01
3713 3875 2.027653 TCACATATTGGGCGTGACAAGA 60.028 45.455 0.00 0.00 34.83 3.02
3714 3876 2.355197 TCACATATTGGGCGTGACAAG 58.645 47.619 0.00 0.00 34.83 3.16
3715 3877 2.481289 TCACATATTGGGCGTGACAA 57.519 45.000 0.00 0.00 34.83 3.18
3718 3880 0.107410 GGGTCACATATTGGGCGTGA 60.107 55.000 0.00 0.00 37.33 4.35
3719 3881 0.107214 AGGGTCACATATTGGGCGTG 60.107 55.000 0.00 0.00 0.00 5.34
3720 3882 1.502690 TAGGGTCACATATTGGGCGT 58.497 50.000 0.00 0.00 0.00 5.68
3721 3883 2.615493 GGATAGGGTCACATATTGGGCG 60.615 54.545 0.00 0.00 0.00 6.13
3722 3884 2.375174 TGGATAGGGTCACATATTGGGC 59.625 50.000 0.00 0.00 0.00 5.36
3723 3885 4.350816 TCTTGGATAGGGTCACATATTGGG 59.649 45.833 0.00 0.00 0.00 4.12
3724 3886 5.513788 CCTCTTGGATAGGGTCACATATTGG 60.514 48.000 0.00 0.00 34.57 3.16
3725 3887 5.307976 TCCTCTTGGATAGGGTCACATATTG 59.692 44.000 0.00 0.00 37.46 1.90
3726 3888 5.476983 TCCTCTTGGATAGGGTCACATATT 58.523 41.667 0.00 0.00 37.46 1.28
3727 3889 5.093236 TCCTCTTGGATAGGGTCACATAT 57.907 43.478 0.00 0.00 37.46 1.78
3728 3890 4.552883 TCCTCTTGGATAGGGTCACATA 57.447 45.455 0.00 0.00 37.46 2.29
3729 3891 3.421394 TCCTCTTGGATAGGGTCACAT 57.579 47.619 0.00 0.00 37.46 3.21
3730 3892 2.838202 GTTCCTCTTGGATAGGGTCACA 59.162 50.000 0.00 0.00 42.81 3.58
3731 3893 3.108376 AGTTCCTCTTGGATAGGGTCAC 58.892 50.000 0.00 0.00 42.81 3.67
3732 3894 3.491766 AGTTCCTCTTGGATAGGGTCA 57.508 47.619 0.00 0.00 42.81 4.02
3733 3895 4.143986 CAAGTTCCTCTTGGATAGGGTC 57.856 50.000 0.00 0.00 46.85 4.46
3742 3904 5.042905 GGTGGTACCTTCAAGTTCCTCTTG 61.043 50.000 14.36 1.71 43.58 3.02
3743 3905 3.072622 GGTGGTACCTTCAAGTTCCTCTT 59.927 47.826 14.36 0.00 34.73 2.85
3744 3906 2.638363 GGTGGTACCTTCAAGTTCCTCT 59.362 50.000 14.36 0.00 34.73 3.69
3745 3907 2.370849 TGGTGGTACCTTCAAGTTCCTC 59.629 50.000 14.36 0.00 39.58 3.71
3746 3908 2.414612 TGGTGGTACCTTCAAGTTCCT 58.585 47.619 14.36 0.00 39.58 3.36
3747 3909 2.943036 TGGTGGTACCTTCAAGTTCC 57.057 50.000 14.36 3.72 39.58 3.62
3748 3910 3.146847 CCTTGGTGGTACCTTCAAGTTC 58.853 50.000 28.89 9.33 39.58 3.01
3749 3911 2.781174 TCCTTGGTGGTACCTTCAAGTT 59.219 45.455 28.89 0.00 39.58 2.66
3750 3912 2.414612 TCCTTGGTGGTACCTTCAAGT 58.585 47.619 28.89 0.00 39.58 3.16
3751 3913 3.721087 ATCCTTGGTGGTACCTTCAAG 57.279 47.619 26.69 26.69 39.58 3.02
3752 3914 4.224370 GTCTATCCTTGGTGGTACCTTCAA 59.776 45.833 14.36 15.36 39.58 2.69
3753 3915 3.773119 GTCTATCCTTGGTGGTACCTTCA 59.227 47.826 14.36 8.51 39.58 3.02
3754 3916 3.134262 GGTCTATCCTTGGTGGTACCTTC 59.866 52.174 14.36 6.30 39.58 3.46
3755 3917 3.113043 GGTCTATCCTTGGTGGTACCTT 58.887 50.000 14.36 0.00 39.58 3.50
3756 3918 2.628829 GGGTCTATCCTTGGTGGTACCT 60.629 54.545 14.36 0.00 36.33 3.08
3757 3919 1.767088 GGGTCTATCCTTGGTGGTACC 59.233 57.143 4.43 4.43 36.07 3.34
3758 3920 1.411612 CGGGTCTATCCTTGGTGGTAC 59.588 57.143 0.00 0.00 37.07 3.34
3759 3921 1.784358 CGGGTCTATCCTTGGTGGTA 58.216 55.000 0.00 0.00 37.07 3.25
3760 3922 1.623542 GCGGGTCTATCCTTGGTGGT 61.624 60.000 0.00 0.00 37.07 4.16
3761 3923 1.146263 GCGGGTCTATCCTTGGTGG 59.854 63.158 0.00 0.00 36.25 4.61
3762 3924 0.469917 ATGCGGGTCTATCCTTGGTG 59.530 55.000 0.00 0.00 36.25 4.17
3763 3925 2.097110 TATGCGGGTCTATCCTTGGT 57.903 50.000 0.00 0.00 36.25 3.67
3764 3926 3.007940 TCAATATGCGGGTCTATCCTTGG 59.992 47.826 0.00 0.00 36.25 3.61
3765 3927 4.271696 TCAATATGCGGGTCTATCCTTG 57.728 45.455 0.00 0.00 36.25 3.61
3766 3928 4.974645 TTCAATATGCGGGTCTATCCTT 57.025 40.909 0.00 0.00 36.25 3.36
3767 3929 4.642429 GTTTCAATATGCGGGTCTATCCT 58.358 43.478 0.00 0.00 36.25 3.24
3768 3930 3.432252 CGTTTCAATATGCGGGTCTATCC 59.568 47.826 0.00 0.00 0.00 2.59
3769 3931 3.120649 GCGTTTCAATATGCGGGTCTATC 60.121 47.826 0.00 0.00 0.00 2.08
3770 3932 2.806244 GCGTTTCAATATGCGGGTCTAT 59.194 45.455 0.00 0.00 0.00 1.98
3771 3933 2.159014 AGCGTTTCAATATGCGGGTCTA 60.159 45.455 0.00 0.00 35.20 2.59
3772 3934 1.014352 GCGTTTCAATATGCGGGTCT 58.986 50.000 0.00 0.00 0.00 3.85
3773 3935 1.014352 AGCGTTTCAATATGCGGGTC 58.986 50.000 0.00 0.00 35.20 4.46
3774 3936 1.400494 GAAGCGTTTCAATATGCGGGT 59.600 47.619 7.17 0.00 35.20 5.28
3775 3937 1.670811 AGAAGCGTTTCAATATGCGGG 59.329 47.619 14.70 0.00 35.70 6.13
3776 3938 2.708514 CAGAAGCGTTTCAATATGCGG 58.291 47.619 14.70 0.00 35.70 5.69
3777 3939 2.104144 GCAGAAGCGTTTCAATATGCG 58.896 47.619 14.70 0.00 35.70 4.73
3778 3940 3.135414 TGCAGAAGCGTTTCAATATGC 57.865 42.857 14.70 14.49 46.23 3.14
3779 3941 4.100529 CCTTGCAGAAGCGTTTCAATATG 58.899 43.478 14.70 4.82 46.23 1.78
3780 3942 3.758554 ACCTTGCAGAAGCGTTTCAATAT 59.241 39.130 14.70 0.00 46.23 1.28
3781 3943 3.058293 CACCTTGCAGAAGCGTTTCAATA 60.058 43.478 14.70 0.00 46.23 1.90
3782 3944 1.956477 ACCTTGCAGAAGCGTTTCAAT 59.044 42.857 14.70 0.00 46.23 2.57
3783 3945 1.065401 CACCTTGCAGAAGCGTTTCAA 59.935 47.619 14.70 0.00 46.23 2.69
3784 3946 0.662619 CACCTTGCAGAAGCGTTTCA 59.337 50.000 14.70 0.00 46.23 2.69
3785 3947 0.040067 CCACCTTGCAGAAGCGTTTC 60.040 55.000 3.49 3.49 46.23 2.78
3786 3948 0.465460 TCCACCTTGCAGAAGCGTTT 60.465 50.000 0.00 0.00 46.23 3.60
3787 3949 0.250901 ATCCACCTTGCAGAAGCGTT 60.251 50.000 0.00 0.00 46.23 4.84
3788 3950 0.613260 TATCCACCTTGCAGAAGCGT 59.387 50.000 0.00 0.00 46.23 5.07
3789 3951 1.869767 GATATCCACCTTGCAGAAGCG 59.130 52.381 0.00 0.00 46.23 4.68
3790 3952 2.923121 TGATATCCACCTTGCAGAAGC 58.077 47.619 0.00 0.00 42.57 3.86
3791 3953 6.057533 TGTAATGATATCCACCTTGCAGAAG 58.942 40.000 0.00 0.00 0.00 2.85
3792 3954 6.000246 TGTAATGATATCCACCTTGCAGAA 58.000 37.500 0.00 0.00 0.00 3.02
3793 3955 5.628797 TGTAATGATATCCACCTTGCAGA 57.371 39.130 0.00 0.00 0.00 4.26
3794 3956 5.999600 TGATGTAATGATATCCACCTTGCAG 59.000 40.000 0.00 0.00 0.00 4.41
3795 3957 5.939447 TGATGTAATGATATCCACCTTGCA 58.061 37.500 0.00 0.00 0.00 4.08
3796 3958 6.882610 TTGATGTAATGATATCCACCTTGC 57.117 37.500 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.