Multiple sequence alignment - TraesCS2D01G558100

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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 TraesCS2D01G558100 chr2D 100.000 3788 0 0 1 3788 631240399 631236612 0.000000e+00 6996.0
1 TraesCS2D01G558100 chr2D 92.620 271 15 4 334 600 631480493 631480224 5.940000e-103 385.0
2 TraesCS2D01G558100 chr2D 87.000 300 18 5 690 968 631480168 631479869 6.110000e-83 318.0
3 TraesCS2D01G558100 chr2D 86.711 301 19 5 689 968 631805550 631805850 7.900000e-82 315.0
4 TraesCS2D01G558100 chr2D 92.386 197 10 4 334 526 631805204 631805399 3.730000e-70 276.0
5 TraesCS2D01G558100 chr2D 78.169 142 20 7 1 134 631480849 631480711 3.140000e-11 80.5
6 TraesCS2D01G558100 chr2D 78.014 141 20 7 1 133 631804848 631804985 1.130000e-10 78.7
7 TraesCS2D01G558100 chr2A 94.047 2083 60 16 841 2901 760118696 760120736 0.000000e+00 3101.0
8 TraesCS2D01G558100 chr2A 90.452 796 36 15 3014 3788 760120734 760121510 0.000000e+00 1013.0
9 TraesCS2D01G558100 chr2A 96.440 309 7 2 109 417 760118396 760118700 1.210000e-139 507.0
10 TraesCS2D01G558100 chr2A 95.833 120 5 0 2898 3017 144655750 144655631 1.070000e-45 195.0
11 TraesCS2D01G558100 chr2A 79.839 248 39 7 1821 2064 25586781 25586541 1.810000e-38 171.0
12 TraesCS2D01G558100 chr2A 97.143 70 1 1 1 70 760118322 760118390 2.390000e-22 117.0
13 TraesCS2D01G558100 chr2B 92.191 2241 72 31 692 2901 744388266 744390434 0.000000e+00 3073.0
14 TraesCS2D01G558100 chr2B 91.304 1242 39 25 692 1910 774716309 774715114 0.000000e+00 1631.0
15 TraesCS2D01G558100 chr2B 94.737 703 24 3 2212 2901 774694110 774693408 0.000000e+00 1081.0
16 TraesCS2D01G558100 chr2B 94.684 602 24 6 1 600 744387640 744388235 0.000000e+00 928.0
17 TraesCS2D01G558100 chr2B 87.060 796 54 22 3015 3788 774693405 774692637 0.000000e+00 854.0
18 TraesCS2D01G558100 chr2B 87.936 688 43 14 3122 3788 744390504 744391172 0.000000e+00 774.0
19 TraesCS2D01G558100 chr2B 91.575 273 16 5 334 600 774944801 774944530 1.660000e-98 370.0
20 TraesCS2D01G558100 chr2B 91.575 273 8 2 1942 2202 774715120 774714851 2.780000e-96 363.0
21 TraesCS2D01G558100 chr2B 94.340 212 11 1 389 600 774716549 774716339 1.310000e-84 324.0
22 TraesCS2D01G558100 chr2B 86.735 294 18 6 696 968 774944469 774944176 1.320000e-79 307.0
23 TraesCS2D01G558100 chr2B 97.143 70 2 0 3014 3083 744390432 744390501 6.650000e-23 119.0
24 TraesCS2D01G558100 chr2B 91.549 71 6 0 334 404 774716636 774716566 8.660000e-17 99.0
25 TraesCS2D01G558100 chr2B 96.078 51 2 0 1 51 774716966 774716916 2.420000e-12 84.2
26 TraesCS2D01G558100 chr2B 77.465 142 21 7 1 134 774945157 774945019 1.460000e-09 75.0
27 TraesCS2D01G558100 chr5D 87.470 1237 104 30 873 2077 518872605 518873822 0.000000e+00 1378.0
28 TraesCS2D01G558100 chr5D 81.159 759 96 14 2155 2890 518873966 518874700 1.980000e-157 566.0
29 TraesCS2D01G558100 chr5D 94.805 77 4 0 3027 3103 518874712 518874788 1.850000e-23 121.0
30 TraesCS2D01G558100 chr5B 88.723 1073 104 10 1009 2077 652520521 652521580 0.000000e+00 1295.0
31 TraesCS2D01G558100 chr5B 80.380 790 99 22 2134 2890 652521684 652522450 1.990000e-152 549.0
32 TraesCS2D01G558100 chr5B 81.618 136 19 4 3027 3157 652522462 652522596 1.440000e-19 108.0
33 TraesCS2D01G558100 chr5B 91.525 59 4 1 871 928 652520245 652520303 3.140000e-11 80.5
34 TraesCS2D01G558100 chr3B 78.678 802 140 21 1145 1929 744728706 744729493 4.370000e-139 505.0
35 TraesCS2D01G558100 chr3B 78.678 802 140 21 1145 1929 744847279 744848066 4.370000e-139 505.0
36 TraesCS2D01G558100 chr3B 74.386 285 57 11 1648 1928 746357134 746356862 1.440000e-19 108.0
37 TraesCS2D01G558100 chr3D 78.086 794 153 15 1145 1929 560640242 560641023 2.050000e-132 483.0
38 TraesCS2D01G558100 chr3D 78.217 785 146 19 1154 1927 560827016 560827786 2.650000e-131 479.0
39 TraesCS2D01G558100 chr3D 96.581 117 4 0 2900 3016 182423695 182423811 1.070000e-45 195.0
40 TraesCS2D01G558100 chr1B 96.063 127 4 1 2894 3020 451733231 451733356 4.960000e-49 206.0
41 TraesCS2D01G558100 chr1B 94.737 95 4 1 606 700 343995937 343996030 3.050000e-31 147.0
42 TraesCS2D01G558100 chr7B 96.581 117 4 0 2900 3016 290000920 290001036 1.070000e-45 195.0
43 TraesCS2D01G558100 chr7A 96.581 117 4 0 2900 3016 140983157 140983041 1.070000e-45 195.0
44 TraesCS2D01G558100 chr7A 96.581 117 4 0 2900 3016 141260327 141260211 1.070000e-45 195.0
45 TraesCS2D01G558100 chr7A 93.939 99 6 0 598 696 138960732 138960830 2.360000e-32 150.0
46 TraesCS2D01G558100 chr5A 96.581 117 4 0 2900 3016 142840428 142840312 1.070000e-45 195.0
47 TraesCS2D01G558100 chr5A 91.525 118 10 0 1811 1928 645423190 645423307 3.030000e-36 163.0
48 TraesCS2D01G558100 chr5A 92.208 77 6 0 3027 3103 645424263 645424339 4.000000e-20 110.0
49 TraesCS2D01G558100 chr3A 92.029 138 9 2 2881 3017 712959072 712958936 3.860000e-45 193.0
50 TraesCS2D01G558100 chr7D 94.400 125 6 1 2897 3021 241094120 241094243 1.390000e-44 191.0
51 TraesCS2D01G558100 chr7D 93.396 106 5 1 598 703 621487583 621487686 5.070000e-34 156.0
52 TraesCS2D01G558100 chr4A 96.774 93 3 0 602 694 680395033 680395125 5.070000e-34 156.0
53 TraesCS2D01G558100 chr4A 93.000 100 5 2 596 693 521847425 521847326 1.100000e-30 145.0
54 TraesCS2D01G558100 chr6D 92.593 108 5 3 600 706 443958511 443958616 6.550000e-33 152.0
55 TraesCS2D01G558100 chr6D 95.556 90 4 0 604 693 27308608 27308697 1.100000e-30 145.0
56 TraesCS2D01G558100 chr4B 95.699 93 4 0 602 694 21543542 21543450 2.360000e-32 150.0
57 TraesCS2D01G558100 chr6B 92.308 104 4 4 605 708 682556007 682556106 1.100000e-30 145.0
58 TraesCS2D01G558100 chrUn 97.059 34 1 0 3357 3390 62161250 62161217 1.470000e-04 58.4


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 TraesCS2D01G558100 chr2D 631236612 631240399 3787 True 6996.000000 6996 100.000000 1 3788 1 chr2D.!!$R1 3787
1 TraesCS2D01G558100 chr2D 631479869 631480849 980 True 261.166667 385 85.929667 1 968 3 chr2D.!!$R2 967
2 TraesCS2D01G558100 chr2D 631804848 631805850 1002 False 223.233333 315 85.703667 1 968 3 chr2D.!!$F1 967
3 TraesCS2D01G558100 chr2A 760118322 760121510 3188 False 1184.500000 3101 94.520500 1 3788 4 chr2A.!!$F1 3787
4 TraesCS2D01G558100 chr2B 744387640 744391172 3532 False 1223.500000 3073 92.988500 1 3788 4 chr2B.!!$F1 3787
5 TraesCS2D01G558100 chr2B 774692637 774694110 1473 True 967.500000 1081 90.898500 2212 3788 2 chr2B.!!$R1 1576
6 TraesCS2D01G558100 chr2B 774714851 774716966 2115 True 500.240000 1631 92.969200 1 2202 5 chr2B.!!$R2 2201
7 TraesCS2D01G558100 chr2B 774944176 774945157 981 True 250.666667 370 85.258333 1 968 3 chr2B.!!$R3 967
8 TraesCS2D01G558100 chr5D 518872605 518874788 2183 False 688.333333 1378 87.811333 873 3103 3 chr5D.!!$F1 2230
9 TraesCS2D01G558100 chr5B 652520245 652522596 2351 False 508.125000 1295 85.561500 871 3157 4 chr5B.!!$F1 2286
10 TraesCS2D01G558100 chr3B 744728706 744729493 787 False 505.000000 505 78.678000 1145 1929 1 chr3B.!!$F1 784
11 TraesCS2D01G558100 chr3B 744847279 744848066 787 False 505.000000 505 78.678000 1145 1929 1 chr3B.!!$F2 784
12 TraesCS2D01G558100 chr3D 560640242 560641023 781 False 483.000000 483 78.086000 1145 1929 1 chr3D.!!$F2 784
13 TraesCS2D01G558100 chr3D 560827016 560827786 770 False 479.000000 479 78.217000 1154 1927 1 chr3D.!!$F3 773

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
338 462 1.216990 ACCCTTGGAGCCCTAATCTG 58.783 55.0 0.0 0.0 0.0 2.90 F
2193 2724 0.324943 GGCTGGGACTAAGTTGAGCA 59.675 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2837 1.332195 CCTGGATATGGAGCGTCTCA 58.668 55.0 8.71 0.0 31.08 3.27 R
2995 3564 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.0 5.23 0.0 44.66 1.40 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
57 59 4.517453 TGTGAAAATGTGCTGTACCTAACC 59.483 41.667 0.00 0.00 0.00 2.85
93 99 1.751924 AGAGTCGTTGGATCTAGCACC 59.248 52.381 0.00 0.00 0.00 5.01
176 215 7.270047 TCTAACAGTTTATTAGGGGTCATTCG 58.730 38.462 0.00 0.00 31.65 3.34
226 294 1.403323 TGTTCAACAATGTTGCTCGCA 59.597 42.857 20.34 12.76 0.00 5.10
288 412 3.559238 ATCATTTGCCTCGTGTTTGAC 57.441 42.857 0.00 0.00 0.00 3.18
308 432 2.263077 CCGGAAATCTTCACTCAGTCG 58.737 52.381 0.00 0.00 0.00 4.18
309 433 2.094700 CCGGAAATCTTCACTCAGTCGA 60.095 50.000 0.00 0.00 0.00 4.20
310 434 3.429547 CCGGAAATCTTCACTCAGTCGAT 60.430 47.826 0.00 0.00 0.00 3.59
311 435 3.794028 CGGAAATCTTCACTCAGTCGATC 59.206 47.826 0.00 0.00 0.00 3.69
312 436 3.794028 GGAAATCTTCACTCAGTCGATCG 59.206 47.826 9.36 9.36 0.00 3.69
338 462 1.216990 ACCCTTGGAGCCCTAATCTG 58.783 55.000 0.00 0.00 0.00 2.90
458 614 2.826725 AGACTCTAGGTTCGAAACAGGG 59.173 50.000 16.95 12.83 0.00 4.45
588 779 5.182001 GGTTAGCACATTCTTGTTGATGACT 59.818 40.000 0.00 0.00 32.34 3.41
594 815 6.349611 GCACATTCTTGTTGATGACTGGTAAT 60.350 38.462 0.00 0.00 32.34 1.89
600 821 8.231692 TCTTGTTGATGACTGGTAATTGAAAA 57.768 30.769 0.00 0.00 0.00 2.29
601 822 8.690884 TCTTGTTGATGACTGGTAATTGAAAAA 58.309 29.630 0.00 0.00 0.00 1.94
624 845 5.557576 AAAAAGTACTCCCTCCGTAAACT 57.442 39.130 0.00 0.00 0.00 2.66
626 847 6.670695 AAAAGTACTCCCTCCGTAAACTAA 57.329 37.500 0.00 0.00 0.00 2.24
627 848 6.864151 AAAGTACTCCCTCCGTAAACTAAT 57.136 37.500 0.00 0.00 0.00 1.73
629 850 8.544687 AAAGTACTCCCTCCGTAAACTAATAT 57.455 34.615 0.00 0.00 0.00 1.28
631 852 9.646522 AAGTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
632 853 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
633 854 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
634 855 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
635 856 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
637 858 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
668 889 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
669 890 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
670 891 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
683 904 9.865321 ATCTAAACGCTCTTACATTAGTTTACA 57.135 29.630 0.00 0.00 34.29 2.41
684 905 9.350357 TCTAAACGCTCTTACATTAGTTTACAG 57.650 33.333 0.00 0.00 34.29 2.74
685 906 9.350357 CTAAACGCTCTTACATTAGTTTACAGA 57.650 33.333 0.00 0.00 34.29 3.41
686 907 7.813852 AACGCTCTTACATTAGTTTACAGAG 57.186 36.000 0.00 0.00 0.00 3.35
687 908 6.331061 ACGCTCTTACATTAGTTTACAGAGG 58.669 40.000 0.00 0.00 0.00 3.69
1014 1418 2.278142 GCCATGTCAAATCGCCGC 60.278 61.111 0.00 0.00 0.00 6.53
1088 1492 3.760035 GGAGAGCGACGGCCTTGA 61.760 66.667 0.00 0.00 41.24 3.02
1143 1547 1.215647 GACCGTCGTCCAATGCTCT 59.784 57.895 0.00 0.00 32.40 4.09
1758 2185 2.125350 GACCTCGCCTTCCTGCTG 60.125 66.667 0.00 0.00 0.00 4.41
1794 2221 2.302445 CCTGGAGATCCTCACCATCATC 59.698 54.545 0.00 0.00 36.55 2.92
1795 2222 2.302445 CTGGAGATCCTCACCATCATCC 59.698 54.545 0.00 0.00 36.55 3.51
1796 2223 2.090324 TGGAGATCCTCACCATCATCCT 60.090 50.000 0.00 0.00 32.13 3.24
1798 2225 2.971330 GAGATCCTCACCATCATCCTGT 59.029 50.000 0.00 0.00 0.00 4.00
1799 2226 3.390639 GAGATCCTCACCATCATCCTGTT 59.609 47.826 0.00 0.00 0.00 3.16
1800 2227 4.560739 AGATCCTCACCATCATCCTGTTA 58.439 43.478 0.00 0.00 0.00 2.41
1801 2228 5.161135 AGATCCTCACCATCATCCTGTTAT 58.839 41.667 0.00 0.00 0.00 1.89
1802 2229 5.610132 AGATCCTCACCATCATCCTGTTATT 59.390 40.000 0.00 0.00 0.00 1.40
1803 2230 5.296151 TCCTCACCATCATCCTGTTATTC 57.704 43.478 0.00 0.00 0.00 1.75
1978 2424 0.678048 GAGGTGCTGCAGGGTTAAGG 60.678 60.000 17.12 0.00 0.00 2.69
2192 2723 0.615850 AGGCTGGGACTAAGTTGAGC 59.384 55.000 0.00 0.00 0.00 4.26
2193 2724 0.324943 GGCTGGGACTAAGTTGAGCA 59.675 55.000 0.00 0.00 0.00 4.26
2194 2725 1.443802 GCTGGGACTAAGTTGAGCAC 58.556 55.000 0.00 0.00 0.00 4.40
2195 2726 1.946283 GCTGGGACTAAGTTGAGCACC 60.946 57.143 0.00 0.00 0.00 5.01
2196 2727 1.347707 CTGGGACTAAGTTGAGCACCA 59.652 52.381 0.00 0.00 0.00 4.17
2197 2728 1.347707 TGGGACTAAGTTGAGCACCAG 59.652 52.381 0.00 0.00 0.00 4.00
2306 2837 1.877443 CTCCGATGTTTTCCCAACGTT 59.123 47.619 0.00 0.00 0.00 3.99
2336 2876 5.799213 CTCCATATCCAGGTATCCAAAGAC 58.201 45.833 0.00 0.00 0.00 3.01
2608 3156 0.614697 TCGGGTGCTGGAGAAGATGA 60.615 55.000 0.00 0.00 0.00 2.92
2727 3284 6.613233 AGTATACAAGAGCATATACAGCGAC 58.387 40.000 5.50 0.00 36.93 5.19
2855 3418 4.583871 AGCATTGTTCCTCTGTTAGAAGG 58.416 43.478 0.00 0.00 0.00 3.46
2903 3472 8.534333 TGATTGTTATCAGACAACTTGTACTC 57.466 34.615 0.00 0.00 41.86 2.59
2904 3473 7.602644 TGATTGTTATCAGACAACTTGTACTCC 59.397 37.037 0.00 0.00 41.86 3.85
2905 3474 5.790593 TGTTATCAGACAACTTGTACTCCC 58.209 41.667 0.00 0.00 0.00 4.30
2906 3475 5.542635 TGTTATCAGACAACTTGTACTCCCT 59.457 40.000 0.00 0.00 0.00 4.20
2907 3476 4.810191 ATCAGACAACTTGTACTCCCTC 57.190 45.455 0.00 0.00 0.00 4.30
2908 3477 2.897969 TCAGACAACTTGTACTCCCTCC 59.102 50.000 0.00 0.00 0.00 4.30
2909 3478 1.893801 AGACAACTTGTACTCCCTCCG 59.106 52.381 0.00 0.00 0.00 4.63
2910 3479 1.617357 GACAACTTGTACTCCCTCCGT 59.383 52.381 0.00 0.00 0.00 4.69
2911 3480 1.617357 ACAACTTGTACTCCCTCCGTC 59.383 52.381 0.00 0.00 0.00 4.79
2912 3481 1.067071 CAACTTGTACTCCCTCCGTCC 60.067 57.143 0.00 0.00 0.00 4.79
2913 3482 0.964358 ACTTGTACTCCCTCCGTCCG 60.964 60.000 0.00 0.00 0.00 4.79
2914 3483 1.664321 CTTGTACTCCCTCCGTCCGG 61.664 65.000 0.00 0.00 0.00 5.14
2915 3484 2.141011 TTGTACTCCCTCCGTCCGGA 62.141 60.000 0.00 0.00 42.90 5.14
2916 3485 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2917 3486 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2918 3487 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2919 3488 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2920 3489 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2921 3490 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2922 3491 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2923 3492 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2924 3493 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2925 3494 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2926 3495 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
2927 3496 1.066716 CCGTCCGGAAATACTTGTCCA 60.067 52.381 5.23 0.00 37.50 4.02
2928 3497 2.613474 CCGTCCGGAAATACTTGTCCAA 60.613 50.000 5.23 0.00 37.50 3.53
2929 3498 2.671396 CGTCCGGAAATACTTGTCCAAG 59.329 50.000 5.23 5.51 43.79 3.61
2930 3499 3.007635 GTCCGGAAATACTTGTCCAAGG 58.992 50.000 5.23 0.00 42.53 3.61
2931 3500 2.907696 TCCGGAAATACTTGTCCAAGGA 59.092 45.455 0.00 3.13 42.53 3.36
2932 3501 3.328343 TCCGGAAATACTTGTCCAAGGAA 59.672 43.478 0.00 0.16 42.53 3.36
2933 3502 4.018779 TCCGGAAATACTTGTCCAAGGAAT 60.019 41.667 0.00 2.40 42.53 3.01
2934 3503 4.096382 CCGGAAATACTTGTCCAAGGAATG 59.904 45.833 11.45 0.00 42.53 2.67
2935 3504 4.941263 CGGAAATACTTGTCCAAGGAATGA 59.059 41.667 11.45 0.00 42.53 2.57
2936 3505 5.414454 CGGAAATACTTGTCCAAGGAATGAA 59.586 40.000 11.45 0.00 42.53 2.57
2937 3506 6.095440 CGGAAATACTTGTCCAAGGAATGAAT 59.905 38.462 11.45 0.00 42.53 2.57
2938 3507 7.260603 GGAAATACTTGTCCAAGGAATGAATG 58.739 38.462 11.45 0.00 42.53 2.67
2939 3508 7.093771 GGAAATACTTGTCCAAGGAATGAATGT 60.094 37.037 11.45 0.00 42.53 2.71
2940 3509 8.877864 AAATACTTGTCCAAGGAATGAATGTA 57.122 30.769 11.45 0.00 42.53 2.29
2941 3510 9.479549 AAATACTTGTCCAAGGAATGAATGTAT 57.520 29.630 11.45 0.00 42.53 2.29
2942 3511 8.682936 ATACTTGTCCAAGGAATGAATGTATC 57.317 34.615 11.45 0.00 42.53 2.24
2943 3512 6.725364 ACTTGTCCAAGGAATGAATGTATCT 58.275 36.000 11.45 0.00 42.53 1.98
2944 3513 7.861629 ACTTGTCCAAGGAATGAATGTATCTA 58.138 34.615 11.45 0.00 42.53 1.98
2945 3514 7.989741 ACTTGTCCAAGGAATGAATGTATCTAG 59.010 37.037 11.45 0.00 42.53 2.43
2946 3515 7.675161 TGTCCAAGGAATGAATGTATCTAGA 57.325 36.000 0.00 0.00 0.00 2.43
2947 3516 8.267620 TGTCCAAGGAATGAATGTATCTAGAT 57.732 34.615 10.73 10.73 0.00 1.98
2948 3517 8.152898 TGTCCAAGGAATGAATGTATCTAGATG 58.847 37.037 15.79 0.00 0.00 2.90
2949 3518 8.153550 GTCCAAGGAATGAATGTATCTAGATGT 58.846 37.037 15.79 0.00 0.00 3.06
2950 3519 9.379770 TCCAAGGAATGAATGTATCTAGATGTA 57.620 33.333 15.79 4.44 0.00 2.29
2993 3562 9.685276 ACTCATTTGTATCCATTTCTATGACAA 57.315 29.630 0.00 0.00 33.37 3.18
2995 3564 9.685276 TCATTTGTATCCATTTCTATGACAAGT 57.315 29.630 0.00 0.00 31.59 3.16
3002 3571 7.786178 TCCATTTCTATGACAAGTATTTCCG 57.214 36.000 0.00 0.00 33.37 4.30
3003 3572 6.765989 TCCATTTCTATGACAAGTATTTCCGG 59.234 38.462 0.00 0.00 33.37 5.14
3004 3573 6.765989 CCATTTCTATGACAAGTATTTCCGGA 59.234 38.462 0.00 0.00 33.37 5.14
3005 3574 7.254795 CCATTTCTATGACAAGTATTTCCGGAC 60.255 40.741 1.83 0.00 33.37 4.79
3006 3575 4.928601 TCTATGACAAGTATTTCCGGACG 58.071 43.478 1.83 0.00 0.00 4.79
3007 3576 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3008 3577 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3009 3578 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3010 3579 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3011 3580 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3012 3581 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3025 3594 5.629600 CGGACGGAGGGAGTATCTATCTATT 60.630 48.000 0.00 0.00 33.73 1.73
3124 3703 3.118261 ACCAGTATCATGCTACAAGGTGG 60.118 47.826 17.71 13.87 33.60 4.61
3237 3823 9.826574 TTAGAGTTAAACTAGTTGTTGTGTCAT 57.173 29.630 9.34 0.00 39.13 3.06
3238 3824 8.732746 AGAGTTAAACTAGTTGTTGTGTCATT 57.267 30.769 9.34 0.00 39.13 2.57
3250 3836 8.632679 AGTTGTTGTGTCATTGAGTTGAATAAT 58.367 29.630 0.00 0.00 0.00 1.28
3251 3837 8.905702 GTTGTTGTGTCATTGAGTTGAATAATC 58.094 33.333 0.00 0.00 0.00 1.75
3252 3838 7.592938 TGTTGTGTCATTGAGTTGAATAATCC 58.407 34.615 0.00 0.00 0.00 3.01
3254 3840 7.381766 TGTGTCATTGAGTTGAATAATCCTG 57.618 36.000 0.00 0.00 0.00 3.86
3255 3841 7.167535 TGTGTCATTGAGTTGAATAATCCTGA 58.832 34.615 0.00 0.00 0.00 3.86
3256 3842 7.830697 TGTGTCATTGAGTTGAATAATCCTGAT 59.169 33.333 0.00 0.00 0.00 2.90
3257 3843 8.680903 GTGTCATTGAGTTGAATAATCCTGATT 58.319 33.333 0.00 0.00 34.93 2.57
3258 3844 9.904198 TGTCATTGAGTTGAATAATCCTGATTA 57.096 29.630 2.29 2.29 37.64 1.75
3262 3848 7.658179 TGAGTTGAATAATCCTGATTATCGC 57.342 36.000 11.69 8.52 41.66 4.58
3263 3849 7.216494 TGAGTTGAATAATCCTGATTATCGCA 58.784 34.615 11.69 10.45 41.66 5.10
3264 3850 7.714813 TGAGTTGAATAATCCTGATTATCGCAA 59.285 33.333 11.69 14.39 41.66 4.85
3265 3851 8.450578 AGTTGAATAATCCTGATTATCGCAAA 57.549 30.769 19.08 9.17 41.66 3.68
3266 3852 9.071276 AGTTGAATAATCCTGATTATCGCAAAT 57.929 29.630 19.08 17.13 41.66 2.32
3267 3853 9.121517 GTTGAATAATCCTGATTATCGCAAATG 57.878 33.333 19.08 0.00 41.66 2.32
3269 3855 9.065798 TGAATAATCCTGATTATCGCAAATGAA 57.934 29.630 11.69 0.00 41.66 2.57
3272 3858 5.947228 TCCTGATTATCGCAAATGAATCC 57.053 39.130 0.00 0.00 0.00 3.01
3273 3859 5.624159 TCCTGATTATCGCAAATGAATCCT 58.376 37.500 0.00 0.00 0.00 3.24
3274 3860 5.471116 TCCTGATTATCGCAAATGAATCCTG 59.529 40.000 0.00 0.00 0.00 3.86
3275 3861 5.471116 CCTGATTATCGCAAATGAATCCTGA 59.529 40.000 0.00 0.00 0.00 3.86
3276 3862 6.150641 CCTGATTATCGCAAATGAATCCTGAT 59.849 38.462 0.00 0.00 0.00 2.90
3277 3863 7.309012 CCTGATTATCGCAAATGAATCCTGATT 60.309 37.037 0.00 0.00 0.00 2.57
3278 3864 8.620116 TGATTATCGCAAATGAATCCTGATTA 57.380 30.769 0.00 0.00 0.00 1.75
3279 3865 9.234827 TGATTATCGCAAATGAATCCTGATTAT 57.765 29.630 0.00 0.00 0.00 1.28
3280 3866 9.713740 GATTATCGCAAATGAATCCTGATTATC 57.286 33.333 0.00 0.00 0.00 1.75
3281 3867 8.853077 TTATCGCAAATGAATCCTGATTATCT 57.147 30.769 0.00 0.00 0.00 1.98
3285 3871 7.386025 TCGCAAATGAATCCTGATTATCTAGTG 59.614 37.037 0.00 0.00 0.00 2.74
3291 3877 9.722184 ATGAATCCTGATTATCTAGTGTGAATG 57.278 33.333 0.00 0.00 0.00 2.67
3307 3893 2.110213 TGGCACAACTCCGTGGTC 59.890 61.111 0.00 0.00 37.37 4.02
3308 3894 2.668550 GGCACAACTCCGTGGTCC 60.669 66.667 0.00 0.00 37.37 4.46
3315 3904 2.432628 CTCCGTGGTCCGAAGTGC 60.433 66.667 0.00 0.00 39.56 4.40
3329 3918 4.962122 GTGCAGCGGCGTGTTGTG 62.962 66.667 9.37 0.00 45.35 3.33
3342 3932 0.829333 TGTTGTGGTTTGCCTGCAAT 59.171 45.000 5.25 0.00 35.70 3.56
3358 3948 1.528161 GCAATTGAAGCCAACTTGCAC 59.472 47.619 10.34 0.00 41.25 4.57
3397 3987 1.140852 CTGTCCTGGTGAGTTGAACCA 59.859 52.381 0.00 0.00 45.49 3.67
3441 4031 4.748102 TCAGTGTTTAAGTCAGTTTAGGCG 59.252 41.667 0.00 0.00 0.00 5.52
3444 4034 5.693555 AGTGTTTAAGTCAGTTTAGGCGTAC 59.306 40.000 0.00 0.00 0.00 3.67
3496 4099 3.299503 AGAAGAAAAGGGCATGTGTTGT 58.700 40.909 0.00 0.00 0.00 3.32
3510 4113 2.879646 TGTGTTGTCCGGAACCAAATAC 59.120 45.455 5.23 10.59 0.00 1.89
3764 4367 2.989422 ATTCCTTTTGCGTTTCTCCG 57.011 45.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.404391 CCAAATCCTCTCAGCATGCAC 59.596 52.381 21.98 0.00 34.76 4.57
57 59 9.291664 CCAACGACTCTAGAGTTAGATTTTAAG 57.708 37.037 25.86 9.98 42.66 1.85
76 78 2.380084 TTGGTGCTAGATCCAACGAC 57.620 50.000 12.85 0.00 38.57 4.34
93 99 7.170320 GCAAATATTCAACAGATAGGGCATTTG 59.830 37.037 0.00 0.00 0.00 2.32
176 215 2.462456 TGCATGTTCAGAGAGTGACC 57.538 50.000 0.00 0.00 33.71 4.02
288 412 2.094700 TCGACTGAGTGAAGATTTCCGG 60.095 50.000 0.00 0.00 0.00 5.14
308 432 0.608035 TCCAAGGGTTTGCACCGATC 60.608 55.000 0.00 0.00 45.39 3.69
309 433 0.609131 CTCCAAGGGTTTGCACCGAT 60.609 55.000 0.00 0.00 45.39 4.18
310 434 1.228124 CTCCAAGGGTTTGCACCGA 60.228 57.895 0.00 0.00 45.39 4.69
311 435 2.919494 GCTCCAAGGGTTTGCACCG 61.919 63.158 0.00 0.00 45.39 4.94
312 436 2.574018 GGCTCCAAGGGTTTGCACC 61.574 63.158 0.00 0.00 43.37 5.01
338 462 3.631250 TCCATTTTCATACAAGGCCTCC 58.369 45.455 5.23 0.00 0.00 4.30
458 614 4.430908 ACAGTAATAAGCGACTTAGGCAC 58.569 43.478 5.72 3.98 29.02 5.01
602 823 5.557576 AGTTTACGGAGGGAGTACTTTTT 57.442 39.130 0.00 0.00 0.00 1.94
603 824 6.670695 TTAGTTTACGGAGGGAGTACTTTT 57.329 37.500 0.00 0.00 0.00 2.27
604 825 6.864151 ATTAGTTTACGGAGGGAGTACTTT 57.136 37.500 0.00 0.00 0.00 2.66
606 827 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
607 828 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
609 830 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
610 831 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
612 833 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
613 834 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
642 863 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
644 865 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
657 878 9.865321 TGTAAACTAATGTAAGAGCGTTTAGAT 57.135 29.630 0.00 0.00 30.36 1.98
658 879 9.350357 CTGTAAACTAATGTAAGAGCGTTTAGA 57.650 33.333 0.00 0.00 30.36 2.10
659 880 9.350357 TCTGTAAACTAATGTAAGAGCGTTTAG 57.650 33.333 0.00 0.00 30.36 1.85
660 881 9.350357 CTCTGTAAACTAATGTAAGAGCGTTTA 57.650 33.333 0.00 0.00 0.00 2.01
661 882 7.331193 CCTCTGTAAACTAATGTAAGAGCGTTT 59.669 37.037 0.00 0.00 0.00 3.60
662 883 6.812160 CCTCTGTAAACTAATGTAAGAGCGTT 59.188 38.462 0.00 0.00 0.00 4.84
663 884 6.331061 CCTCTGTAAACTAATGTAAGAGCGT 58.669 40.000 0.00 0.00 0.00 5.07
664 885 5.749109 CCCTCTGTAAACTAATGTAAGAGCG 59.251 44.000 0.00 0.00 0.00 5.03
665 886 6.875076 TCCCTCTGTAAACTAATGTAAGAGC 58.125 40.000 0.00 0.00 0.00 4.09
666 887 8.068892 ACTCCCTCTGTAAACTAATGTAAGAG 57.931 38.462 0.00 0.00 0.00 2.85
667 888 9.186837 CTACTCCCTCTGTAAACTAATGTAAGA 57.813 37.037 0.00 0.00 0.00 2.10
668 889 7.921745 GCTACTCCCTCTGTAAACTAATGTAAG 59.078 40.741 0.00 0.00 0.00 2.34
669 890 7.618512 AGCTACTCCCTCTGTAAACTAATGTAA 59.381 37.037 0.00 0.00 0.00 2.41
670 891 7.068348 CAGCTACTCCCTCTGTAAACTAATGTA 59.932 40.741 0.00 0.00 0.00 2.29
671 892 5.958987 AGCTACTCCCTCTGTAAACTAATGT 59.041 40.000 0.00 0.00 0.00 2.71
672 893 6.096987 TCAGCTACTCCCTCTGTAAACTAATG 59.903 42.308 0.00 0.00 0.00 1.90
673 894 6.195700 TCAGCTACTCCCTCTGTAAACTAAT 58.804 40.000 0.00 0.00 0.00 1.73
674 895 5.577100 TCAGCTACTCCCTCTGTAAACTAA 58.423 41.667 0.00 0.00 0.00 2.24
675 896 5.188988 TCAGCTACTCCCTCTGTAAACTA 57.811 43.478 0.00 0.00 0.00 2.24
676 897 4.048970 TCAGCTACTCCCTCTGTAAACT 57.951 45.455 0.00 0.00 0.00 2.66
677 898 4.221041 ACTTCAGCTACTCCCTCTGTAAAC 59.779 45.833 0.00 0.00 0.00 2.01
678 899 4.417437 ACTTCAGCTACTCCCTCTGTAAA 58.583 43.478 0.00 0.00 0.00 2.01
679 900 4.048970 ACTTCAGCTACTCCCTCTGTAA 57.951 45.455 0.00 0.00 0.00 2.41
680 901 3.741245 ACTTCAGCTACTCCCTCTGTA 57.259 47.619 0.00 0.00 0.00 2.74
681 902 2.614134 ACTTCAGCTACTCCCTCTGT 57.386 50.000 0.00 0.00 0.00 3.41
682 903 5.606348 ATTTACTTCAGCTACTCCCTCTG 57.394 43.478 0.00 0.00 0.00 3.35
683 904 7.302184 AGATATTTACTTCAGCTACTCCCTCT 58.698 38.462 0.00 0.00 0.00 3.69
684 905 7.533289 AGATATTTACTTCAGCTACTCCCTC 57.467 40.000 0.00 0.00 0.00 4.30
685 906 7.922699 AAGATATTTACTTCAGCTACTCCCT 57.077 36.000 0.00 0.00 0.00 4.20
686 907 8.204836 TGAAAGATATTTACTTCAGCTACTCCC 58.795 37.037 0.00 0.00 0.00 4.30
687 908 9.771534 ATGAAAGATATTTACTTCAGCTACTCC 57.228 33.333 0.00 0.00 0.00 3.85
761 985 4.081198 AGGAAACACATCAACCTTTGCAAA 60.081 37.500 12.14 12.14 0.00 3.68
1354 1764 2.035783 GTTGGGGAGGAAGTGGGC 59.964 66.667 0.00 0.00 0.00 5.36
1625 2052 3.672295 CTGAGGAAGAGGCGGGTGC 62.672 68.421 0.00 0.00 41.71 5.01
1720 2147 2.202756 GTCCTCCATGGCGACGAC 60.203 66.667 6.96 5.76 35.26 4.34
2192 2723 3.797507 AAGGGTGCTGGTGCTGGTG 62.798 63.158 0.00 0.00 40.48 4.17
2193 2724 3.501911 AAGGGTGCTGGTGCTGGT 61.502 61.111 0.00 0.00 40.48 4.00
2194 2725 2.987547 CAAGGGTGCTGGTGCTGG 60.988 66.667 0.00 0.00 40.48 4.85
2195 2726 2.203394 ACAAGGGTGCTGGTGCTG 60.203 61.111 0.00 0.00 40.48 4.41
2196 2727 2.113986 GACAAGGGTGCTGGTGCT 59.886 61.111 0.00 0.00 40.48 4.40
2197 2728 2.985847 GGACAAGGGTGCTGGTGC 60.986 66.667 0.00 0.00 40.20 5.01
2306 2837 1.332195 CCTGGATATGGAGCGTCTCA 58.668 55.000 8.71 0.00 31.08 3.27
2360 2900 2.098607 TCTAGCAAAGCACGCTACGTAT 59.901 45.455 0.00 0.00 38.32 3.06
2490 3031 1.682323 TGCTGCCGGATACACGTTATA 59.318 47.619 5.05 0.00 0.00 0.98
2493 3034 0.392461 ATTGCTGCCGGATACACGTT 60.392 50.000 5.05 0.00 0.00 3.99
2608 3156 4.642429 GAAGACAAGTAGACCACAACCAT 58.358 43.478 0.00 0.00 0.00 3.55
2727 3284 1.079875 CATAAACCGGACGTGACCCG 61.080 60.000 9.46 7.17 46.10 5.28
2855 3418 3.543680 TCTAAGTACCTGCCAGAATGC 57.456 47.619 0.00 0.00 31.97 3.56
2901 3470 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2902 3471 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2903 3472 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2904 3473 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2905 3474 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2906 3475 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
2907 3476 1.066716 TGGACAAGTATTTCCGGACGG 60.067 52.381 1.83 3.96 34.24 4.79
2908 3477 2.373540 TGGACAAGTATTTCCGGACG 57.626 50.000 1.83 0.00 34.24 4.79
2909 3478 3.007635 CCTTGGACAAGTATTTCCGGAC 58.992 50.000 1.83 0.00 36.72 4.79
2910 3479 2.907696 TCCTTGGACAAGTATTTCCGGA 59.092 45.455 0.00 0.00 36.72 5.14
2911 3480 3.343941 TCCTTGGACAAGTATTTCCGG 57.656 47.619 10.81 0.00 36.72 5.14
2912 3481 4.941263 TCATTCCTTGGACAAGTATTTCCG 59.059 41.667 10.81 0.00 36.72 4.30
2913 3482 6.834168 TTCATTCCTTGGACAAGTATTTCC 57.166 37.500 10.81 0.00 36.72 3.13
2914 3483 7.830739 ACATTCATTCCTTGGACAAGTATTTC 58.169 34.615 10.81 0.00 36.72 2.17
2915 3484 7.781324 ACATTCATTCCTTGGACAAGTATTT 57.219 32.000 10.81 0.00 36.72 1.40
2916 3485 9.125026 GATACATTCATTCCTTGGACAAGTATT 57.875 33.333 10.81 0.00 36.72 1.89
2917 3486 8.497745 AGATACATTCATTCCTTGGACAAGTAT 58.502 33.333 10.81 2.07 36.72 2.12
2918 3487 7.861629 AGATACATTCATTCCTTGGACAAGTA 58.138 34.615 10.81 0.00 36.72 2.24
2919 3488 6.725364 AGATACATTCATTCCTTGGACAAGT 58.275 36.000 10.81 0.00 36.72 3.16
2920 3489 8.206867 TCTAGATACATTCATTCCTTGGACAAG 58.793 37.037 5.09 5.09 38.14 3.16
2921 3490 8.089625 TCTAGATACATTCATTCCTTGGACAA 57.910 34.615 0.00 0.00 0.00 3.18
2922 3491 7.675161 TCTAGATACATTCATTCCTTGGACA 57.325 36.000 0.00 0.00 0.00 4.02
2923 3492 8.153550 ACATCTAGATACATTCATTCCTTGGAC 58.846 37.037 4.54 0.00 0.00 4.02
2924 3493 8.267620 ACATCTAGATACATTCATTCCTTGGA 57.732 34.615 4.54 0.00 0.00 3.53
2976 3545 9.489084 CGGAAATACTTGTCATAGAAATGGATA 57.511 33.333 0.00 0.00 33.61 2.59
2977 3546 7.445402 CCGGAAATACTTGTCATAGAAATGGAT 59.555 37.037 0.00 0.00 33.61 3.41
2978 3547 6.765989 CCGGAAATACTTGTCATAGAAATGGA 59.234 38.462 0.00 0.00 33.61 3.41
2979 3548 6.765989 TCCGGAAATACTTGTCATAGAAATGG 59.234 38.462 0.00 0.00 33.61 3.16
2980 3549 7.516785 CGTCCGGAAATACTTGTCATAGAAATG 60.517 40.741 5.23 0.00 0.00 2.32
2981 3550 6.479001 CGTCCGGAAATACTTGTCATAGAAAT 59.521 38.462 5.23 0.00 0.00 2.17
2982 3551 5.808540 CGTCCGGAAATACTTGTCATAGAAA 59.191 40.000 5.23 0.00 0.00 2.52
2983 3552 5.345702 CGTCCGGAAATACTTGTCATAGAA 58.654 41.667 5.23 0.00 0.00 2.10
2984 3553 4.202080 CCGTCCGGAAATACTTGTCATAGA 60.202 45.833 5.23 0.00 37.50 1.98
2985 3554 4.049186 CCGTCCGGAAATACTTGTCATAG 58.951 47.826 5.23 0.00 37.50 2.23
2986 3555 3.700539 TCCGTCCGGAAATACTTGTCATA 59.299 43.478 5.23 0.00 42.05 2.15
2987 3556 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2988 3557 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2989 3558 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2990 3559 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2991 3560 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2992 3561 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2993 3562 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2994 3563 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2995 3564 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2996 3565 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2997 3566 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2998 3567 0.466922 GATACTCCCTCCGTCCGGAA 60.467 60.000 5.23 0.00 44.66 4.30
2999 3568 1.150081 GATACTCCCTCCGTCCGGA 59.850 63.158 0.00 0.00 42.90 5.14
3000 3569 0.399454 TAGATACTCCCTCCGTCCGG 59.601 60.000 0.00 0.00 0.00 5.14
3001 3570 2.027007 AGATAGATACTCCCTCCGTCCG 60.027 54.545 0.00 0.00 0.00 4.79
3002 3571 3.724732 AGATAGATACTCCCTCCGTCC 57.275 52.381 0.00 0.00 0.00 4.79
3003 3572 6.404954 GCAAATAGATAGATACTCCCTCCGTC 60.405 46.154 0.00 0.00 0.00 4.79
3004 3573 5.419471 GCAAATAGATAGATACTCCCTCCGT 59.581 44.000 0.00 0.00 0.00 4.69
3005 3574 5.419155 TGCAAATAGATAGATACTCCCTCCG 59.581 44.000 0.00 0.00 0.00 4.63
3006 3575 6.439058 ACTGCAAATAGATAGATACTCCCTCC 59.561 42.308 0.00 0.00 0.00 4.30
3007 3576 7.475137 ACTGCAAATAGATAGATACTCCCTC 57.525 40.000 0.00 0.00 0.00 4.30
3008 3577 7.510685 TGAACTGCAAATAGATAGATACTCCCT 59.489 37.037 0.00 0.00 0.00 4.20
3009 3578 7.671302 TGAACTGCAAATAGATAGATACTCCC 58.329 38.462 0.00 0.00 0.00 4.30
3010 3579 9.149225 CATGAACTGCAAATAGATAGATACTCC 57.851 37.037 0.00 0.00 0.00 3.85
3011 3580 9.703892 ACATGAACTGCAAATAGATAGATACTC 57.296 33.333 0.00 0.00 0.00 2.59
3012 3581 9.703892 GACATGAACTGCAAATAGATAGATACT 57.296 33.333 0.00 0.00 0.00 2.12
3025 3594 5.122869 GCTAGAGAAATGACATGAACTGCAA 59.877 40.000 0.00 0.00 0.00 4.08
3124 3703 0.951558 ACAGCCAACATTCCAACGAC 59.048 50.000 0.00 0.00 0.00 4.34
3219 3805 7.120579 TCAACTCAATGACACAACAACTAGTTT 59.879 33.333 5.07 0.00 38.74 2.66
3224 3810 5.895636 TTCAACTCAATGACACAACAACT 57.104 34.783 0.00 0.00 0.00 3.16
3231 3817 7.615582 TCAGGATTATTCAACTCAATGACAC 57.384 36.000 0.00 0.00 0.00 3.67
3237 3823 7.714813 TGCGATAATCAGGATTATTCAACTCAA 59.285 33.333 14.01 0.00 42.32 3.02
3238 3824 7.216494 TGCGATAATCAGGATTATTCAACTCA 58.784 34.615 14.01 2.82 42.32 3.41
3250 3836 5.471116 CAGGATTCATTTGCGATAATCAGGA 59.529 40.000 0.00 0.00 31.38 3.86
3251 3837 5.471116 TCAGGATTCATTTGCGATAATCAGG 59.529 40.000 0.00 0.00 31.38 3.86
3252 3838 6.549912 TCAGGATTCATTTGCGATAATCAG 57.450 37.500 0.00 0.00 31.38 2.90
3254 3840 9.713740 GATAATCAGGATTCATTTGCGATAATC 57.286 33.333 0.00 0.00 32.50 1.75
3255 3841 9.458727 AGATAATCAGGATTCATTTGCGATAAT 57.541 29.630 0.00 0.00 32.50 1.28
3256 3842 8.853077 AGATAATCAGGATTCATTTGCGATAA 57.147 30.769 0.00 0.00 32.50 1.75
3257 3843 9.591792 CTAGATAATCAGGATTCATTTGCGATA 57.408 33.333 0.00 0.00 32.50 2.92
3258 3844 8.099537 ACTAGATAATCAGGATTCATTTGCGAT 58.900 33.333 0.00 0.00 32.50 4.58
3260 3846 7.172190 ACACTAGATAATCAGGATTCATTTGCG 59.828 37.037 0.00 0.00 32.50 4.85
3261 3847 8.288208 CACACTAGATAATCAGGATTCATTTGC 58.712 37.037 0.00 0.00 32.50 3.68
3262 3848 9.551734 TCACACTAGATAATCAGGATTCATTTG 57.448 33.333 0.00 0.00 32.50 2.32
3265 3851 9.722184 CATTCACACTAGATAATCAGGATTCAT 57.278 33.333 0.00 0.00 32.50 2.57
3266 3852 8.152898 CCATTCACACTAGATAATCAGGATTCA 58.847 37.037 0.00 0.00 32.50 2.57
3267 3853 7.118971 GCCATTCACACTAGATAATCAGGATTC 59.881 40.741 0.00 0.00 32.50 2.52
3269 3855 6.043590 TGCCATTCACACTAGATAATCAGGAT 59.956 38.462 0.00 0.00 0.00 3.24
3270 3856 5.366477 TGCCATTCACACTAGATAATCAGGA 59.634 40.000 0.00 0.00 0.00 3.86
3271 3857 5.468072 GTGCCATTCACACTAGATAATCAGG 59.532 44.000 0.00 0.00 44.98 3.86
3272 3858 6.536731 GTGCCATTCACACTAGATAATCAG 57.463 41.667 0.00 0.00 44.98 2.90
3285 3871 0.238289 CACGGAGTTGTGCCATTCAC 59.762 55.000 0.00 0.00 41.61 3.18
3290 3876 2.110213 GACCACGGAGTTGTGCCA 59.890 61.111 0.00 0.00 41.61 4.92
3291 3877 2.668550 GGACCACGGAGTTGTGCC 60.669 66.667 0.00 0.00 41.61 5.01
3300 3886 2.738521 CTGCACTTCGGACCACGG 60.739 66.667 0.00 0.00 44.45 4.94
3301 3887 3.414700 GCTGCACTTCGGACCACG 61.415 66.667 0.00 0.00 46.11 4.94
3315 3904 3.119709 AAACCACAACACGCCGCTG 62.120 57.895 0.00 0.00 0.00 5.18
3322 3911 0.108424 TTGCAGGCAAACCACAACAC 60.108 50.000 3.86 0.00 39.06 3.32
3328 3917 1.540797 GCTTCAATTGCAGGCAAACCA 60.541 47.619 11.10 0.00 39.55 3.67
3329 3918 1.150827 GCTTCAATTGCAGGCAAACC 58.849 50.000 11.10 0.00 39.55 3.27
3342 3932 0.746063 CCTGTGCAAGTTGGCTTCAA 59.254 50.000 4.75 0.00 31.49 2.69
3410 4000 5.585047 ACTGACTTAAACACTGAACTGAACC 59.415 40.000 0.00 0.00 0.00 3.62
3411 4001 6.663944 ACTGACTTAAACACTGAACTGAAC 57.336 37.500 0.00 0.00 0.00 3.18
3412 4002 7.681939 AAACTGACTTAAACACTGAACTGAA 57.318 32.000 0.00 0.00 0.00 3.02
3413 4003 7.494625 CCTAAACTGACTTAAACACTGAACTGA 59.505 37.037 0.00 0.00 0.00 3.41
3414 4004 7.630924 CCTAAACTGACTTAAACACTGAACTG 58.369 38.462 0.00 0.00 0.00 3.16
3441 4031 6.897259 TTAGCCGAATGACTAAACATGTAC 57.103 37.500 0.00 0.00 0.00 2.90
3444 4034 7.015226 TCAATTAGCCGAATGACTAAACATG 57.985 36.000 0.00 0.00 32.43 3.21
3496 4099 4.091549 AGACAGTAGTATTTGGTTCCGGA 58.908 43.478 0.00 0.00 0.00 5.14
3621 4224 3.731264 GCAGCTCAACAGATCAGAAATGC 60.731 47.826 0.00 0.00 0.00 3.56
3764 4367 2.968574 TCCAGAGGCCTTGTATGAGATC 59.031 50.000 6.77 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.