Multiple sequence alignment - TraesCS3A01G468200

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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 TraesCS3A01G468200 chr3A 100.000 3277 0 0 1001 4277 701138833 701142109 0.000000e+00 6052.0
1 TraesCS3A01G468200 chr3A 98.289 760 11 1 3424 4181 696202406 696203165 0.000000e+00 1330.0
2 TraesCS3A01G468200 chr3A 100.000 469 0 0 1 469 701137833 701138301 0.000000e+00 867.0
3 TraesCS3A01G468200 chr3A 82.662 894 106 29 1563 2418 700960319 700961201 0.000000e+00 747.0
4 TraesCS3A01G468200 chr3A 85.924 682 62 8 3528 4177 733264917 733264238 0.000000e+00 697.0
5 TraesCS3A01G468200 chr3A 80.905 707 102 17 1949 2639 700953249 700953938 1.050000e-145 527.0
6 TraesCS3A01G468200 chr3A 82.261 637 80 9 2645 3270 700953979 700954593 1.760000e-143 520.0
7 TraesCS3A01G468200 chr3A 83.598 567 67 9 2645 3209 701123957 701124499 3.820000e-140 508.0
8 TraesCS3A01G468200 chr3A 80.702 627 90 18 1820 2439 700944711 700945313 3.900000e-125 459.0
9 TraesCS3A01G468200 chr3A 82.342 538 74 13 2131 2649 700908738 700909273 8.440000e-122 448.0
10 TraesCS3A01G468200 chr3A 82.828 495 65 13 1892 2378 701123303 701123785 3.950000e-115 425.0
11 TraesCS3A01G468200 chr3A 78.450 645 80 30 2052 2645 700893085 700893721 2.430000e-97 366.0
12 TraesCS3A01G468200 chr3A 85.886 333 25 15 143 469 701122091 701122407 6.850000e-88 335.0
13 TraesCS3A01G468200 chr3A 83.333 396 28 27 91 469 700891002 700891376 8.860000e-87 331.0
14 TraesCS3A01G468200 chr3A 85.091 275 26 12 198 469 700959237 700959499 2.540000e-67 267.0
15 TraesCS3A01G468200 chr3A 79.357 373 39 19 1455 1821 700944031 700944371 1.200000e-55 228.0
16 TraesCS3A01G468200 chr3A 89.831 177 16 2 1824 1998 700908503 700908679 4.300000e-55 226.0
17 TraesCS3A01G468200 chr3A 82.000 250 24 13 2419 2648 700945397 700945645 4.360000e-45 193.0
18 TraesCS3A01G468200 chr3A 98.851 87 0 1 1 87 700907468 700907553 2.060000e-33 154.0
19 TraesCS3A01G468200 chr3A 87.500 112 9 4 1060 1167 700959573 700959683 1.610000e-24 124.0
20 TraesCS3A01G468200 chr3A 89.000 100 10 1 4178 4277 700894529 700894627 5.810000e-24 122.0
21 TraesCS3A01G468200 chr3A 85.714 119 14 2 1342 1460 700959794 700959909 5.810000e-24 122.0
22 TraesCS3A01G468200 chr3A 82.963 135 13 9 140 268 700943329 700943459 3.500000e-21 113.0
23 TraesCS3A01G468200 chr3A 97.727 44 1 0 1394 1437 701122772 701122815 4.590000e-10 76.8
24 TraesCS3A01G468200 chr3A 100.000 28 0 0 1718 1745 701139496 701139523 8.000000e-03 52.8
25 TraesCS3A01G468200 chr3A 100.000 28 0 0 1664 1691 701139550 701139577 8.000000e-03 52.8
26 TraesCS3A01G468200 chr3B 91.912 1051 67 7 2390 3430 756082366 756081324 0.000000e+00 1454.0
27 TraesCS3A01G468200 chr3B 81.726 788 93 22 2657 3431 755575905 755576654 1.020000e-170 610.0
28 TraesCS3A01G468200 chr3B 83.308 671 71 25 1742 2388 755659286 755659939 7.970000e-162 580.0
29 TraesCS3A01G468200 chr3B 85.887 496 63 2 2655 3143 755660338 755660833 4.900000e-144 521.0
30 TraesCS3A01G468200 chr3B 85.714 497 63 2 2655 3143 754771830 754772326 6.340000e-143 518.0
31 TraesCS3A01G468200 chr3B 81.308 642 79 13 2645 3270 755606058 755606674 2.310000e-132 483.0
32 TraesCS3A01G468200 chr3B 81.210 628 87 19 1939 2554 755605178 755605786 1.080000e-130 477.0
33 TraesCS3A01G468200 chr3B 80.945 635 84 10 2645 3266 754722213 754722823 6.480000e-128 468.0
34 TraesCS3A01G468200 chr3B 80.892 628 82 21 1818 2439 755709894 755710489 1.080000e-125 460.0
35 TraesCS3A01G468200 chr3B 82.214 551 69 21 2019 2551 755575233 755575772 8.440000e-122 448.0
36 TraesCS3A01G468200 chr3B 84.487 419 55 4 2645 3055 755771442 755771858 5.150000e-109 405.0
37 TraesCS3A01G468200 chr3B 84.755 387 42 10 91 469 755573540 755573917 5.220000e-99 372.0
38 TraesCS3A01G468200 chr3B 83.558 371 40 14 1457 1822 754719128 754719482 1.150000e-85 327.0
39 TraesCS3A01G468200 chr3B 87.500 280 22 9 198 469 754718145 754718419 1.150000e-80 311.0
40 TraesCS3A01G468200 chr3B 87.004 277 29 7 198 469 755604071 755604345 5.370000e-79 305.0
41 TraesCS3A01G468200 chr3B 85.666 293 29 8 189 469 755769535 755769826 3.230000e-76 296.0
42 TraesCS3A01G468200 chr3B 85.106 282 40 2 2097 2378 755770991 755771270 1.950000e-73 287.0
43 TraesCS3A01G468200 chr3B 82.759 319 34 15 140 451 755707931 755708235 9.120000e-67 265.0
44 TraesCS3A01G468200 chr3B 81.041 269 23 10 1455 1720 755708699 755708942 5.650000e-44 189.0
45 TraesCS3A01G468200 chr3B 83.412 211 23 5 2453 2652 754771541 754771750 7.300000e-43 185.0
46 TraesCS3A01G468200 chr3B 84.239 184 13 6 1357 1540 754770464 754770631 9.510000e-37 165.0
47 TraesCS3A01G468200 chr3B 85.526 152 10 5 1363 1514 755657326 755657465 9.580000e-32 148.0
48 TraesCS3A01G468200 chr3B 90.196 102 8 2 4178 4277 756081330 756081229 9.650000e-27 132.0
49 TraesCS3A01G468200 chr3B 84.615 91 9 1 1192 1282 754769880 754769965 7.620000e-13 86.1
50 TraesCS3A01G468200 chr3B 97.727 44 1 0 1394 1437 755770167 755770210 4.590000e-10 76.8
51 TraesCS3A01G468200 chr3B 100.000 28 0 0 1718 1745 755708886 755708913 8.000000e-03 52.8
52 TraesCS3A01G468200 chrUn 91.944 993 65 6 2445 3427 408040540 408041527 0.000000e+00 1376.0
53 TraesCS3A01G468200 chrUn 94.281 577 25 6 2390 2962 40792162 40792734 0.000000e+00 876.0
54 TraesCS3A01G468200 chrUn 94.107 577 26 4 2390 2962 310420579 310420007 0.000000e+00 870.0
55 TraesCS3A01G468200 chrUn 94.107 577 26 4 2390 2962 338101842 338102414 0.000000e+00 870.0
56 TraesCS3A01G468200 chrUn 90.196 102 8 2 4178 4277 408041524 408041625 9.650000e-27 132.0
57 TraesCS3A01G468200 chr6A 96.410 752 21 2 3432 4177 502924782 502924031 0.000000e+00 1234.0
58 TraesCS3A01G468200 chr5D 92.369 747 32 10 3432 4178 482763351 482762630 0.000000e+00 1040.0
59 TraesCS3A01G468200 chr3D 89.023 829 54 12 2176 3004 566101600 566100809 0.000000e+00 992.0
60 TraesCS3A01G468200 chr3D 77.490 1235 166 64 1457 2645 566301190 566300022 4.660000e-179 638.0
61 TraesCS3A01G468200 chr3D 83.358 673 81 21 1895 2554 566131961 566131307 1.020000e-165 593.0
62 TraesCS3A01G468200 chr3D 81.748 652 83 19 2020 2645 566423138 566422497 2.950000e-141 512.0
63 TraesCS3A01G468200 chr3D 82.919 603 67 17 2648 3239 566422443 566421866 1.060000e-140 510.0
64 TraesCS3A01G468200 chr3D 90.933 375 23 6 3059 3431 566100808 566100443 1.070000e-135 494.0
65 TraesCS3A01G468200 chr3D 86.689 293 26 9 189 469 566302068 566301777 3.210000e-81 313.0
66 TraesCS3A01G468200 chr3D 85.409 281 26 12 198 469 566138681 566138407 1.170000e-70 278.0
67 TraesCS3A01G468200 chr3D 84.507 284 26 11 198 469 566394941 566394664 9.120000e-67 265.0
68 TraesCS3A01G468200 chr3D 83.784 296 24 14 186 469 566103766 566103483 4.240000e-65 259.0
69 TraesCS3A01G468200 chr3D 85.787 197 10 9 1403 1597 566394319 566394139 4.360000e-45 193.0
70 TraesCS3A01G468200 chr3D 89.781 137 10 2 1457 1593 566137701 566137569 5.690000e-39 172.0
71 TraesCS3A01G468200 chr3D 80.000 245 22 13 1060 1292 566394587 566394358 5.730000e-34 156.0
72 TraesCS3A01G468200 chr3D 90.244 82 7 1 4197 4277 566095268 566095187 5.850000e-19 106.0
73 TraesCS3A01G468200 chr3D 95.455 44 2 0 1394 1437 566301491 566301448 2.130000e-08 71.3
74 TraesCS3A01G468200 chr5B 87.726 774 67 7 3432 4177 510534717 510535490 0.000000e+00 878.0
75 TraesCS3A01G468200 chr5B 87.597 774 68 7 3432 4177 9080107 9079334 0.000000e+00 872.0
76 TraesCS3A01G468200 chr1B 82.648 778 77 24 3432 4179 59540108 59539359 1.680000e-178 636.0
77 TraesCS3A01G468200 chr4B 82.278 790 78 22 3432 4187 643652316 643651555 1.010000e-175 627.0
78 TraesCS3A01G468200 chr4B 93.478 46 2 1 1466 1511 649491004 649491048 2.760000e-07 67.6
79 TraesCS3A01G468200 chr2D 82.005 778 67 22 3432 4175 498531761 498531023 1.020000e-165 593.0
80 TraesCS3A01G468200 chr2D 84.946 93 14 0 3432 3524 109129693 109129601 1.270000e-15 95.3
81 TraesCS3A01G468200 chr4D 81.491 778 73 28 3432 4177 366977085 366976347 1.330000e-159 573.0
82 TraesCS3A01G468200 chr7D 83.562 73 10 2 3427 3498 549259552 549259623 2.760000e-07 67.6
83 TraesCS3A01G468200 chr2A 82.192 73 11 2 3428 3499 776476627 776476556 1.280000e-05 62.1
84 TraesCS3A01G468200 chr7A 82.353 68 10 2 3432 3498 690643119 690643053 1.660000e-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 TraesCS3A01G468200 chr3A 701137833 701142109 4276 False 1756.150000 6052 100.000000 1 4277 4 chr3A.!!$F8 4276
1 TraesCS3A01G468200 chr3A 696202406 696203165 759 False 1330.000000 1330 98.289000 3424 4181 1 chr3A.!!$F1 757
2 TraesCS3A01G468200 chr3A 733264238 733264917 679 True 697.000000 697 85.924000 3528 4177 1 chr3A.!!$R1 649
3 TraesCS3A01G468200 chr3A 700953249 700954593 1344 False 523.500000 527 81.583000 1949 3270 2 chr3A.!!$F5 1321
4 TraesCS3A01G468200 chr3A 701122091 701124499 2408 False 336.200000 508 87.509750 143 3209 4 chr3A.!!$F7 3066
5 TraesCS3A01G468200 chr3A 700959237 700961201 1964 False 315.000000 747 85.241750 198 2418 4 chr3A.!!$F6 2220
6 TraesCS3A01G468200 chr3A 700907468 700909273 1805 False 276.000000 448 90.341333 1 2649 3 chr3A.!!$F3 2648
7 TraesCS3A01G468200 chr3A 700891002 700894627 3625 False 273.000000 366 83.594333 91 4277 3 chr3A.!!$F2 4186
8 TraesCS3A01G468200 chr3A 700943329 700945645 2316 False 248.250000 459 81.255500 140 2648 4 chr3A.!!$F4 2508
9 TraesCS3A01G468200 chr3B 756081229 756082366 1137 True 793.000000 1454 91.054000 2390 4277 2 chr3B.!!$R1 1887
10 TraesCS3A01G468200 chr3B 755573540 755576654 3114 False 476.666667 610 82.898333 91 3431 3 chr3B.!!$F3 3340
11 TraesCS3A01G468200 chr3B 755604071 755606674 2603 False 421.666667 483 83.174000 198 3270 3 chr3B.!!$F4 3072
12 TraesCS3A01G468200 chr3B 755657326 755660833 3507 False 416.333333 580 84.907000 1363 3143 3 chr3B.!!$F5 1780
13 TraesCS3A01G468200 chr3B 754718145 754722823 4678 False 368.666667 468 84.001000 198 3266 3 chr3B.!!$F1 3068
14 TraesCS3A01G468200 chr3B 755769535 755771858 2323 False 266.200000 405 88.246500 189 3055 4 chr3B.!!$F7 2866
15 TraesCS3A01G468200 chr3B 755707931 755710489 2558 False 241.700000 460 86.173000 140 2439 4 chr3B.!!$F6 2299
16 TraesCS3A01G468200 chr3B 754769880 754772326 2446 False 238.525000 518 84.495000 1192 3143 4 chr3B.!!$F2 1951
17 TraesCS3A01G468200 chrUn 40792162 40792734 572 False 876.000000 876 94.281000 2390 2962 1 chrUn.!!$F1 572
18 TraesCS3A01G468200 chrUn 310420007 310420579 572 True 870.000000 870 94.107000 2390 2962 1 chrUn.!!$R1 572
19 TraesCS3A01G468200 chrUn 338101842 338102414 572 False 870.000000 870 94.107000 2390 2962 1 chrUn.!!$F2 572
20 TraesCS3A01G468200 chrUn 408040540 408041625 1085 False 754.000000 1376 91.070000 2445 4277 2 chrUn.!!$F3 1832
21 TraesCS3A01G468200 chr6A 502924031 502924782 751 True 1234.000000 1234 96.410000 3432 4177 1 chr6A.!!$R1 745
22 TraesCS3A01G468200 chr5D 482762630 482763351 721 True 1040.000000 1040 92.369000 3432 4178 1 chr5D.!!$R1 746
23 TraesCS3A01G468200 chr3D 566131307 566131961 654 True 593.000000 593 83.358000 1895 2554 1 chr3D.!!$R2 659
24 TraesCS3A01G468200 chr3D 566100443 566103766 3323 True 581.666667 992 87.913333 186 3431 3 chr3D.!!$R3 3245
25 TraesCS3A01G468200 chr3D 566421866 566423138 1272 True 511.000000 512 82.333500 2020 3239 2 chr3D.!!$R7 1219
26 TraesCS3A01G468200 chr3D 566300022 566302068 2046 True 340.766667 638 86.544667 189 2645 3 chr3D.!!$R5 2456
27 TraesCS3A01G468200 chr3D 566137569 566138681 1112 True 225.000000 278 87.595000 198 1593 2 chr3D.!!$R4 1395
28 TraesCS3A01G468200 chr3D 566394139 566394941 802 True 204.666667 265 83.431333 198 1597 3 chr3D.!!$R6 1399
29 TraesCS3A01G468200 chr5B 510534717 510535490 773 False 878.000000 878 87.726000 3432 4177 1 chr5B.!!$F1 745
30 TraesCS3A01G468200 chr5B 9079334 9080107 773 True 872.000000 872 87.597000 3432 4177 1 chr5B.!!$R1 745
31 TraesCS3A01G468200 chr1B 59539359 59540108 749 True 636.000000 636 82.648000 3432 4179 1 chr1B.!!$R1 747
32 TraesCS3A01G468200 chr4B 643651555 643652316 761 True 627.000000 627 82.278000 3432 4187 1 chr4B.!!$R1 755
33 TraesCS3A01G468200 chr2D 498531023 498531761 738 True 593.000000 593 82.005000 3432 4175 1 chr2D.!!$R2 743
34 TraesCS3A01G468200 chr4D 366976347 366977085 738 True 573.000000 573 81.491000 3432 4177 1 chr4D.!!$R1 745

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
122 123 0.249447 TCTCGTCACACACAAGCCAG 60.249 55.0 0.0 0.0 0.0 4.85 F
1553 2978 0.106719 CTGTCACCCACCCAACTTGT 60.107 55.0 0.0 0.0 0.0 3.16 F
2213 8867 0.673437 ACATGGGTTTTGCGTTGGAG 59.327 50.0 0.0 0.0 0.0 3.86 F
3030 11337 0.028902 GGGTAAATCGGTCGCAATGC 59.971 55.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 3828 0.030235 GGAACGAAACCCACTGCAAC 59.970 55.000 0.0 0.0 0.00 4.17 R
2380 9060 0.756442 TTGCTCCAGTGCTTGCCTTT 60.756 50.000 0.0 0.0 0.00 3.11 R
3144 11451 2.045536 CTGCTCCACCTCAAGGCC 60.046 66.667 0.0 0.0 39.32 5.19 R
4232 12634 0.600255 CTCGTATTCGATGGGTGGCC 60.600 60.000 0.0 0.0 45.21 5.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.062122 TGCATTTCACTCTGCATCTCA 57.938 42.857 0.00 0.00 43.11 3.27
87 88 2.404559 GTACCCCACCACCATCTCATA 58.595 52.381 0.00 0.00 0.00 2.15
88 89 1.511613 ACCCCACCACCATCTCATAG 58.488 55.000 0.00 0.00 0.00 2.23
90 91 2.022428 ACCCCACCACCATCTCATAGTA 60.022 50.000 0.00 0.00 0.00 1.82
91 92 3.251484 CCCCACCACCATCTCATAGTAT 58.749 50.000 0.00 0.00 0.00 2.12
92 93 3.261897 CCCCACCACCATCTCATAGTATC 59.738 52.174 0.00 0.00 0.00 2.24
93 94 3.903714 CCCACCACCATCTCATAGTATCA 59.096 47.826 0.00 0.00 0.00 2.15
94 95 4.020751 CCCACCACCATCTCATAGTATCAG 60.021 50.000 0.00 0.00 0.00 2.90
95 96 4.590647 CCACCACCATCTCATAGTATCAGT 59.409 45.833 0.00 0.00 0.00 3.41
97 98 6.408548 CCACCACCATCTCATAGTATCAGTTT 60.409 42.308 0.00 0.00 0.00 2.66
99 100 8.204160 CACCACCATCTCATAGTATCAGTTTTA 58.796 37.037 0.00 0.00 0.00 1.52
100 101 8.204836 ACCACCATCTCATAGTATCAGTTTTAC 58.795 37.037 0.00 0.00 0.00 2.01
101 102 7.657761 CCACCATCTCATAGTATCAGTTTTACC 59.342 40.741 0.00 0.00 0.00 2.85
102 103 8.204160 CACCATCTCATAGTATCAGTTTTACCA 58.796 37.037 0.00 0.00 0.00 3.25
103 104 8.938883 ACCATCTCATAGTATCAGTTTTACCAT 58.061 33.333 0.00 0.00 0.00 3.55
104 105 9.429359 CCATCTCATAGTATCAGTTTTACCATC 57.571 37.037 0.00 0.00 0.00 3.51
107 108 8.568794 TCTCATAGTATCAGTTTTACCATCTCG 58.431 37.037 0.00 0.00 0.00 4.04
108 109 8.234136 TCATAGTATCAGTTTTACCATCTCGT 57.766 34.615 0.00 0.00 0.00 4.18
109 110 8.350722 TCATAGTATCAGTTTTACCATCTCGTC 58.649 37.037 0.00 0.00 0.00 4.20
110 111 6.525578 AGTATCAGTTTTACCATCTCGTCA 57.474 37.500 0.00 0.00 0.00 4.35
111 112 6.331061 AGTATCAGTTTTACCATCTCGTCAC 58.669 40.000 0.00 0.00 0.00 3.67
112 113 4.594123 TCAGTTTTACCATCTCGTCACA 57.406 40.909 0.00 0.00 0.00 3.58
113 114 4.304110 TCAGTTTTACCATCTCGTCACAC 58.696 43.478 0.00 0.00 0.00 3.82
114 115 4.055360 CAGTTTTACCATCTCGTCACACA 58.945 43.478 0.00 0.00 0.00 3.72
115 116 4.056050 AGTTTTACCATCTCGTCACACAC 58.944 43.478 0.00 0.00 0.00 3.82
116 117 3.737032 TTTACCATCTCGTCACACACA 57.263 42.857 0.00 0.00 0.00 3.72
117 118 3.737032 TTACCATCTCGTCACACACAA 57.263 42.857 0.00 0.00 0.00 3.33
118 119 2.154854 ACCATCTCGTCACACACAAG 57.845 50.000 0.00 0.00 0.00 3.16
119 120 0.792640 CCATCTCGTCACACACAAGC 59.207 55.000 0.00 0.00 0.00 4.01
120 121 0.792640 CATCTCGTCACACACAAGCC 59.207 55.000 0.00 0.00 0.00 4.35
121 122 0.392706 ATCTCGTCACACACAAGCCA 59.607 50.000 0.00 0.00 0.00 4.75
122 123 0.249447 TCTCGTCACACACAAGCCAG 60.249 55.000 0.00 0.00 0.00 4.85
123 124 1.224069 CTCGTCACACACAAGCCAGG 61.224 60.000 0.00 0.00 0.00 4.45
124 125 2.896801 CGTCACACACAAGCCAGGC 61.897 63.158 1.84 1.84 0.00 4.85
125 126 2.591429 TCACACACAAGCCAGGCG 60.591 61.111 5.55 0.00 0.00 5.52
126 127 4.332637 CACACACAAGCCAGGCGC 62.333 66.667 5.55 0.00 37.98 6.53
299 391 4.593864 GCGAGGACTCCATCGGCC 62.594 72.222 14.80 0.00 39.31 6.13
324 431 1.376166 CAGCAAGCAGAGCAGAGCT 60.376 57.895 0.00 0.00 43.88 4.09
443 565 0.733223 GTCTTCTCGTTGGTCTCCGC 60.733 60.000 0.00 0.00 0.00 5.54
1020 1148 0.108898 TTTCATTCCGCCGCAAATGG 60.109 50.000 12.96 0.00 34.37 3.16
1027 1155 0.179094 CCGCCGCAAATGGTACTCTA 60.179 55.000 0.00 0.00 0.00 2.43
1041 1190 4.776308 TGGTACTCTACTTCTTTCTTCCCC 59.224 45.833 0.00 0.00 0.00 4.81
1042 1191 4.142204 GGTACTCTACTTCTTTCTTCCCCG 60.142 50.000 0.00 0.00 0.00 5.73
1043 1192 2.234168 ACTCTACTTCTTTCTTCCCCGC 59.766 50.000 0.00 0.00 0.00 6.13
1044 1193 2.498078 CTCTACTTCTTTCTTCCCCGCT 59.502 50.000 0.00 0.00 0.00 5.52
1045 1194 3.700038 CTCTACTTCTTTCTTCCCCGCTA 59.300 47.826 0.00 0.00 0.00 4.26
1046 1195 2.764439 ACTTCTTTCTTCCCCGCTAC 57.236 50.000 0.00 0.00 0.00 3.58
1047 1196 2.258109 ACTTCTTTCTTCCCCGCTACT 58.742 47.619 0.00 0.00 0.00 2.57
1048 1197 3.438183 ACTTCTTTCTTCCCCGCTACTA 58.562 45.455 0.00 0.00 0.00 1.82
1049 1198 3.836562 ACTTCTTTCTTCCCCGCTACTAA 59.163 43.478 0.00 0.00 0.00 2.24
1050 1199 4.470304 ACTTCTTTCTTCCCCGCTACTAAT 59.530 41.667 0.00 0.00 0.00 1.73
1051 1200 4.667519 TCTTTCTTCCCCGCTACTAATC 57.332 45.455 0.00 0.00 0.00 1.75
1052 1201 3.387050 TCTTTCTTCCCCGCTACTAATCC 59.613 47.826 0.00 0.00 0.00 3.01
1053 1202 2.769602 TCTTCCCCGCTACTAATCCT 57.230 50.000 0.00 0.00 0.00 3.24
1054 1203 3.042059 TCTTCCCCGCTACTAATCCTT 57.958 47.619 0.00 0.00 0.00 3.36
1055 1204 2.963782 TCTTCCCCGCTACTAATCCTTC 59.036 50.000 0.00 0.00 0.00 3.46
1056 1205 1.713297 TCCCCGCTACTAATCCTTCC 58.287 55.000 0.00 0.00 0.00 3.46
1058 1207 2.047830 CCCCGCTACTAATCCTTCCTT 58.952 52.381 0.00 0.00 0.00 3.36
1066 1215 3.545703 ACTAATCCTTCCTTGAATGCCG 58.454 45.455 0.00 0.00 0.00 5.69
1074 1223 1.452108 CTTGAATGCCGTCCCCCTC 60.452 63.158 0.00 0.00 0.00 4.30
1100 1249 4.141756 TGTGTTTTCTTGCAAATCCATGGT 60.142 37.500 12.58 0.00 0.00 3.55
1138 1313 5.714047 CAAGCTATGTGAGTGTCTCTGTTA 58.286 41.667 0.00 0.00 0.00 2.41
1173 1356 1.603739 GGAGGACAAGGCCGCTTTT 60.604 57.895 0.00 0.00 0.00 2.27
1198 1384 4.244862 GTTGGAATCGTTGAAATGGCATT 58.755 39.130 6.96 6.96 0.00 3.56
1215 1401 0.326238 ATTCCTCCCCTACGGCTCAA 60.326 55.000 0.00 0.00 0.00 3.02
1251 1437 2.859165 TAGCTTTCCAGTGTCTTGGG 57.141 50.000 0.00 0.00 38.81 4.12
1295 1801 5.500645 AAGTTTCAGTTTGTGTCTTAGGC 57.499 39.130 0.00 0.00 0.00 3.93
1336 1844 9.942850 TCTTTCTTTCAAGAGAAAATTTTGGTT 57.057 25.926 8.47 0.00 43.06 3.67
1338 1846 8.716646 TTCTTTCAAGAGAAAATTTTGGTTCC 57.283 30.769 8.47 0.00 42.78 3.62
1339 1847 7.846066 TCTTTCAAGAGAAAATTTTGGTTCCA 58.154 30.769 8.47 0.00 42.78 3.53
1340 1848 8.317679 TCTTTCAAGAGAAAATTTTGGTTCCAA 58.682 29.630 8.47 0.00 42.78 3.53
1358 1866 8.041323 TGGTTCCAAGAATAAGATAAGAGACAC 58.959 37.037 0.00 0.00 0.00 3.67
1363 2030 6.701145 AGAATAAGATAAGAGACACGCAGA 57.299 37.500 0.00 0.00 0.00 4.26
1372 2039 1.080434 GACACGCAGAGGACTGGTC 60.080 63.158 0.00 0.00 43.62 4.02
1519 2944 8.734386 CCTTCAATGCTCTCAAAATTAGTACTT 58.266 33.333 0.00 0.00 0.00 2.24
1551 2976 0.991355 TCCTGTCACCCACCCAACTT 60.991 55.000 0.00 0.00 0.00 2.66
1553 2978 0.106719 CTGTCACCCACCCAACTTGT 60.107 55.000 0.00 0.00 0.00 3.16
1554 2979 1.142060 CTGTCACCCACCCAACTTGTA 59.858 52.381 0.00 0.00 0.00 2.41
1555 2980 1.134037 TGTCACCCACCCAACTTGTAC 60.134 52.381 0.00 0.00 0.00 2.90
1567 3741 9.538508 CCACCCAACTTGTACTAGTAAATATAC 57.461 37.037 10.43 0.00 0.00 1.47
1599 3775 4.937620 CGGAACAGAGGAAATGAAATGAGA 59.062 41.667 0.00 0.00 0.00 3.27
1600 3776 5.163814 CGGAACAGAGGAAATGAAATGAGAC 60.164 44.000 0.00 0.00 0.00 3.36
1619 3800 5.010719 TGAGACTTCATTACGTCACTTCCTT 59.989 40.000 0.00 0.00 32.68 3.36
1620 3801 6.208007 TGAGACTTCATTACGTCACTTCCTTA 59.792 38.462 0.00 0.00 32.68 2.69
1642 3828 9.277783 CCTTATATTGGAGTTCTAAGATGGTTG 57.722 37.037 0.00 0.00 0.00 3.77
1643 3829 9.838339 CTTATATTGGAGTTCTAAGATGGTTGT 57.162 33.333 0.00 0.00 0.00 3.32
1705 3893 3.327757 TGCAGGAGGACTACAAACTTGAT 59.672 43.478 0.00 0.00 0.00 2.57
1731 5268 7.694388 TCGTACATATTTACAGAGTTCATGC 57.306 36.000 0.28 0.00 0.00 4.06
1734 5271 8.058328 CGTACATATTTACAGAGTTCATGCTTG 58.942 37.037 0.28 0.00 0.00 4.01
1738 5275 9.069078 CATATTTACAGAGTTCATGCTTGTTTG 57.931 33.333 0.00 0.00 0.00 2.93
1739 5276 3.360249 ACAGAGTTCATGCTTGTTTGC 57.640 42.857 0.00 0.00 0.00 3.68
1751 6454 3.315191 TGCTTGTTTGCAGGAGTTTACTC 59.685 43.478 1.18 1.18 38.92 2.59
1776 6481 6.636850 CGAACTTGGGTGTTCTTTTTCATAAG 59.363 38.462 0.00 0.00 42.82 1.73
1804 6524 4.221703 ACTGGAGTGTTCTGTTATCCTCTG 59.778 45.833 0.00 0.00 0.00 3.35
1858 7775 9.487790 TTTGTTCAAAAATGGAACTGGAATATC 57.512 29.630 6.80 0.00 43.84 1.63
1908 7826 2.067766 GCGTGGGTATGTGTAACGAAA 58.932 47.619 0.00 0.00 42.39 3.46
1944 7865 2.859165 TACCTGCAGTTTTCCTCCAG 57.141 50.000 13.81 0.00 0.00 3.86
2017 7947 3.430218 GTGACATGTCTTGACTGCTGTAC 59.570 47.826 25.55 7.95 0.00 2.90
2070 8685 4.707030 TTCACATCAAGTTCATGCCATC 57.293 40.909 0.00 0.00 0.00 3.51
2085 8701 3.023832 TGCCATCGAGACTATGAACTGA 58.976 45.455 0.00 0.00 0.00 3.41
2089 8705 5.861251 GCCATCGAGACTATGAACTGAATAG 59.139 44.000 0.00 0.00 34.40 1.73
2090 8706 6.385843 CCATCGAGACTATGAACTGAATAGG 58.614 44.000 0.00 0.00 32.81 2.57
2092 8708 6.621316 TCGAGACTATGAACTGAATAGGTC 57.379 41.667 0.00 0.00 41.20 3.85
2093 8709 5.531659 TCGAGACTATGAACTGAATAGGTCC 59.468 44.000 0.00 0.00 40.04 4.46
2094 8710 5.533154 CGAGACTATGAACTGAATAGGTCCT 59.467 44.000 0.00 0.00 40.04 3.85
2095 8711 6.039941 CGAGACTATGAACTGAATAGGTCCTT 59.960 42.308 0.00 0.00 40.04 3.36
2112 8742 7.176589 AGGTCCTTATTTCTTGACTACTCTG 57.823 40.000 0.00 0.00 0.00 3.35
2120 8757 7.992754 ATTTCTTGACTACTCTGCAGAATTT 57.007 32.000 18.85 7.60 0.00 1.82
2180 8834 7.501225 TCATCTAACGAGTGTATTATGGTCTCA 59.499 37.037 0.00 0.00 0.00 3.27
2202 8856 6.548321 TCACTTTATTTCAGGTACATGGGTT 58.452 36.000 7.81 0.00 0.00 4.11
2204 8858 7.507616 TCACTTTATTTCAGGTACATGGGTTTT 59.492 33.333 7.81 0.00 0.00 2.43
2211 8865 1.336424 GGTACATGGGTTTTGCGTTGG 60.336 52.381 0.00 0.00 0.00 3.77
2212 8866 1.609555 GTACATGGGTTTTGCGTTGGA 59.390 47.619 0.00 0.00 0.00 3.53
2213 8867 0.673437 ACATGGGTTTTGCGTTGGAG 59.327 50.000 0.00 0.00 0.00 3.86
2220 8874 2.074230 TTTTGCGTTGGAGCTGCAGG 62.074 55.000 17.12 6.00 40.15 4.85
2347 9027 2.528041 AGTCGTTCACTTTGTCTCCC 57.472 50.000 0.00 0.00 26.56 4.30
2352 9032 3.194968 TCGTTCACTTTGTCTCCCCTATC 59.805 47.826 0.00 0.00 0.00 2.08
2356 9036 3.447586 TCACTTTGTCTCCCCTATCTTCG 59.552 47.826 0.00 0.00 0.00 3.79
2360 9040 1.964223 TGTCTCCCCTATCTTCGATGC 59.036 52.381 0.00 0.00 0.00 3.91
2365 9045 1.071385 CCCCTATCTTCGATGCAGCTT 59.929 52.381 0.00 0.00 0.00 3.74
2367 9047 2.411904 CCTATCTTCGATGCAGCTTCC 58.588 52.381 0.00 0.00 0.00 3.46
2380 9060 5.420725 TGCAGCTTCCTCTGAATTAACTA 57.579 39.130 0.00 0.00 36.19 2.24
2387 9067 6.151144 GCTTCCTCTGAATTAACTAAAGGCAA 59.849 38.462 0.00 0.00 0.00 4.52
2609 10826 4.864704 TGCCTGACTTTTTGGTTAATCC 57.135 40.909 0.00 0.00 0.00 3.01
2850 11150 3.371097 CTGCGGGGCATACTCACGT 62.371 63.158 0.00 0.00 38.13 4.49
2934 11234 3.349927 TGCATCATCTTTCTCTGGGTTG 58.650 45.455 0.00 0.00 0.00 3.77
3030 11337 0.028902 GGGTAAATCGGTCGCAATGC 59.971 55.000 0.00 0.00 0.00 3.56
3068 11375 2.017049 GATTTCAGTTATGGGCGTGCT 58.983 47.619 0.00 0.00 0.00 4.40
3300 11621 4.446719 GCTTTGCATCCATAGCTAATTTGC 59.553 41.667 3.49 3.49 41.17 3.68
3340 11665 6.670695 AAACAAGTCATCCTTTTATTGCCT 57.329 33.333 0.00 0.00 0.00 4.75
3361 11686 5.685075 GCCTAGCAATGTAGGTATGTTGTCT 60.685 44.000 9.49 0.00 41.69 3.41
3383 11708 8.816894 TGTCTTTCTCATCATAGTTAGGAAGTT 58.183 33.333 0.00 0.00 0.00 2.66
3384 11709 9.308318 GTCTTTCTCATCATAGTTAGGAAGTTC 57.692 37.037 0.00 0.00 0.00 3.01
3385 11710 9.261035 TCTTTCTCATCATAGTTAGGAAGTTCT 57.739 33.333 2.25 0.00 0.00 3.01
3386 11711 9.528018 CTTTCTCATCATAGTTAGGAAGTTCTC 57.472 37.037 2.25 0.00 0.00 2.87
3387 11712 8.830915 TTCTCATCATAGTTAGGAAGTTCTCT 57.169 34.615 2.25 1.22 0.00 3.10
3430 11755 3.365820 GCGTCTTGAGGCATGAAAAATTG 59.634 43.478 9.98 0.00 0.00 2.32
3722 12099 1.269309 CCCTCGATGTCTCCGTTGATC 60.269 57.143 0.00 0.00 0.00 2.92
4202 12604 3.662759 TGTTTGACCTTGTCCTCCTTT 57.337 42.857 0.00 0.00 0.00 3.11
4231 12633 7.787904 AGTATGGGTGTCATGGTCTATTAAGTA 59.212 37.037 0.00 0.00 37.30 2.24
4232 12634 6.479972 TGGGTGTCATGGTCTATTAAGTAG 57.520 41.667 0.00 0.00 0.00 2.57
4266 12668 5.390145 CGAATACGAGATTTTGTCGGGTTTT 60.390 40.000 0.00 0.00 41.88 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 6.071560 TGTGACGAGATGGTAAAACTGATACT 60.072 38.462 0.00 0.00 0.00 2.12
88 89 6.034683 GTGTGACGAGATGGTAAAACTGATAC 59.965 42.308 0.00 0.00 0.00 2.24
90 91 4.929808 GTGTGACGAGATGGTAAAACTGAT 59.070 41.667 0.00 0.00 0.00 2.90
91 92 4.202172 TGTGTGACGAGATGGTAAAACTGA 60.202 41.667 0.00 0.00 0.00 3.41
92 93 4.055360 TGTGTGACGAGATGGTAAAACTG 58.945 43.478 0.00 0.00 0.00 3.16
93 94 4.056050 GTGTGTGACGAGATGGTAAAACT 58.944 43.478 0.00 0.00 0.00 2.66
94 95 3.805422 TGTGTGTGACGAGATGGTAAAAC 59.195 43.478 0.00 0.00 0.00 2.43
95 96 4.061357 TGTGTGTGACGAGATGGTAAAA 57.939 40.909 0.00 0.00 0.00 1.52
97 98 3.649073 CTTGTGTGTGACGAGATGGTAA 58.351 45.455 0.00 0.00 38.26 2.85
99 100 1.873903 GCTTGTGTGTGACGAGATGGT 60.874 52.381 0.00 0.00 38.26 3.55
100 101 0.792640 GCTTGTGTGTGACGAGATGG 59.207 55.000 0.00 0.00 38.26 3.51
101 102 0.792640 GGCTTGTGTGTGACGAGATG 59.207 55.000 0.00 0.00 38.26 2.90
102 103 0.392706 TGGCTTGTGTGTGACGAGAT 59.607 50.000 0.00 0.00 38.26 2.75
103 104 0.249447 CTGGCTTGTGTGTGACGAGA 60.249 55.000 0.00 0.00 38.26 4.04
104 105 1.224069 CCTGGCTTGTGTGTGACGAG 61.224 60.000 0.00 0.00 38.96 4.18
105 106 1.227527 CCTGGCTTGTGTGTGACGA 60.228 57.895 0.00 0.00 0.00 4.20
106 107 2.896801 GCCTGGCTTGTGTGTGACG 61.897 63.158 12.43 0.00 0.00 4.35
107 108 2.896801 CGCCTGGCTTGTGTGTGAC 61.897 63.158 17.92 0.00 0.00 3.67
108 109 2.591429 CGCCTGGCTTGTGTGTGA 60.591 61.111 17.92 0.00 0.00 3.58
109 110 4.332637 GCGCCTGGCTTGTGTGTG 62.333 66.667 17.92 0.00 39.11 3.82
126 127 4.825679 GGGGACTGGGAGAGGGGG 62.826 77.778 0.00 0.00 0.00 5.40
127 128 3.353689 ATGGGGACTGGGAGAGGGG 62.354 68.421 0.00 0.00 0.00 4.79
128 129 1.768077 GATGGGGACTGGGAGAGGG 60.768 68.421 0.00 0.00 0.00 4.30
129 130 1.003442 TGATGGGGACTGGGAGAGG 59.997 63.158 0.00 0.00 0.00 3.69
130 131 1.341156 GGTGATGGGGACTGGGAGAG 61.341 65.000 0.00 0.00 0.00 3.20
131 132 1.306997 GGTGATGGGGACTGGGAGA 60.307 63.158 0.00 0.00 0.00 3.71
132 133 0.916358 AAGGTGATGGGGACTGGGAG 60.916 60.000 0.00 0.00 0.00 4.30
133 134 0.477597 AAAGGTGATGGGGACTGGGA 60.478 55.000 0.00 0.00 0.00 4.37
134 135 0.034089 GAAAGGTGATGGGGACTGGG 60.034 60.000 0.00 0.00 0.00 4.45
135 136 0.034089 GGAAAGGTGATGGGGACTGG 60.034 60.000 0.00 0.00 0.00 4.00
136 137 0.034089 GGGAAAGGTGATGGGGACTG 60.034 60.000 0.00 0.00 0.00 3.51
137 138 0.477597 TGGGAAAGGTGATGGGGACT 60.478 55.000 0.00 0.00 0.00 3.85
138 139 0.631212 ATGGGAAAGGTGATGGGGAC 59.369 55.000 0.00 0.00 0.00 4.46
192 245 4.463879 CTGTGAGCAGGAGCCGGG 62.464 72.222 2.18 0.00 43.56 5.73
284 376 1.456705 AGAGGCCGATGGAGTCCTC 60.457 63.158 11.33 4.73 44.09 3.71
1010 1138 2.311124 AGTAGAGTACCATTTGCGGC 57.689 50.000 0.00 0.00 0.00 6.53
1020 1148 4.677514 GCGGGGAAGAAAGAAGTAGAGTAC 60.678 50.000 0.00 0.00 0.00 2.73
1027 1155 2.258109 AGTAGCGGGGAAGAAAGAAGT 58.742 47.619 0.00 0.00 0.00 3.01
1041 1190 4.212214 GCATTCAAGGAAGGATTAGTAGCG 59.788 45.833 0.00 0.00 0.00 4.26
1042 1191 4.517075 GGCATTCAAGGAAGGATTAGTAGC 59.483 45.833 0.00 0.00 0.00 3.58
1043 1192 4.752101 CGGCATTCAAGGAAGGATTAGTAG 59.248 45.833 0.00 0.00 0.00 2.57
1044 1193 4.163458 ACGGCATTCAAGGAAGGATTAGTA 59.837 41.667 0.00 0.00 0.00 1.82
1045 1194 3.054361 ACGGCATTCAAGGAAGGATTAGT 60.054 43.478 0.00 0.00 0.00 2.24
1046 1195 3.545703 ACGGCATTCAAGGAAGGATTAG 58.454 45.455 0.00 0.00 0.00 1.73
1047 1196 3.541632 GACGGCATTCAAGGAAGGATTA 58.458 45.455 0.00 0.00 0.00 1.75
1048 1197 2.369394 GACGGCATTCAAGGAAGGATT 58.631 47.619 0.00 0.00 0.00 3.01
1049 1198 1.408822 GGACGGCATTCAAGGAAGGAT 60.409 52.381 0.00 0.00 0.00 3.24
1050 1199 0.035439 GGACGGCATTCAAGGAAGGA 60.035 55.000 0.00 0.00 0.00 3.36
1051 1200 1.032114 GGGACGGCATTCAAGGAAGG 61.032 60.000 0.00 0.00 0.00 3.46
1052 1201 1.032114 GGGGACGGCATTCAAGGAAG 61.032 60.000 0.00 0.00 0.00 3.46
1053 1202 1.001393 GGGGACGGCATTCAAGGAA 60.001 57.895 0.00 0.00 0.00 3.36
1054 1203 2.674754 GGGGACGGCATTCAAGGA 59.325 61.111 0.00 0.00 0.00 3.36
1055 1204 2.440247 GGGGGACGGCATTCAAGG 60.440 66.667 0.00 0.00 0.00 3.61
1056 1205 1.452108 GAGGGGGACGGCATTCAAG 60.452 63.158 0.00 0.00 0.00 3.02
1058 1207 2.285368 AGAGGGGGACGGCATTCA 60.285 61.111 0.00 0.00 0.00 2.57
1066 1215 1.700186 AGAAAACACAGAGAGGGGGAC 59.300 52.381 0.00 0.00 0.00 4.46
1074 1223 4.935702 TGGATTTGCAAGAAAACACAGAG 58.064 39.130 0.00 0.00 0.00 3.35
1100 1249 2.191400 AGCTTGCTACTTGAGGGATGA 58.809 47.619 0.00 0.00 0.00 2.92
1138 1313 3.075882 TCCTCCAAACCCAGATCAAACAT 59.924 43.478 0.00 0.00 0.00 2.71
1173 1356 4.054671 GCCATTTCAACGATTCCAACAAA 58.945 39.130 0.00 0.00 0.00 2.83
1176 1359 3.296322 TGCCATTTCAACGATTCCAAC 57.704 42.857 0.00 0.00 0.00 3.77
1178 1361 3.119173 GGAATGCCATTTCAACGATTCCA 60.119 43.478 0.00 0.00 39.04 3.53
1183 1366 2.091541 GGAGGAATGCCATTTCAACGA 58.908 47.619 0.00 0.00 36.29 3.85
1251 1437 0.861837 CTAATGCTCGACCGGCAATC 59.138 55.000 0.00 0.00 43.14 2.67
1286 1776 1.729586 AACTCACCCAGCCTAAGACA 58.270 50.000 0.00 0.00 0.00 3.41
1335 1843 6.757010 GCGTGTCTCTTATCTTATTCTTGGAA 59.243 38.462 0.00 0.00 0.00 3.53
1336 1844 6.127451 TGCGTGTCTCTTATCTTATTCTTGGA 60.127 38.462 0.00 0.00 0.00 3.53
1337 1845 6.042777 TGCGTGTCTCTTATCTTATTCTTGG 58.957 40.000 0.00 0.00 0.00 3.61
1338 1846 6.975197 TCTGCGTGTCTCTTATCTTATTCTTG 59.025 38.462 0.00 0.00 0.00 3.02
1339 1847 7.101652 TCTGCGTGTCTCTTATCTTATTCTT 57.898 36.000 0.00 0.00 0.00 2.52
1340 1848 6.238897 CCTCTGCGTGTCTCTTATCTTATTCT 60.239 42.308 0.00 0.00 0.00 2.40
1372 2039 5.587388 ATGTGAATCCTTGTAAGCAATGG 57.413 39.130 0.00 0.00 33.65 3.16
1463 2799 9.045223 TCATGGAGATATGTTTCGAAGTTTATG 57.955 33.333 0.00 0.00 0.00 1.90
1519 2944 4.263156 GGGTGACAGGACAAATACCAGTTA 60.263 45.833 0.00 0.00 0.00 2.24
1551 2976 6.207417 GGTGAGGCCGTATATTTACTAGTACA 59.793 42.308 0.91 0.00 0.00 2.90
1553 2978 6.824305 GGTGAGGCCGTATATTTACTAGTA 57.176 41.667 0.00 0.00 0.00 1.82
1554 2979 5.718724 GGTGAGGCCGTATATTTACTAGT 57.281 43.478 0.00 0.00 0.00 2.57
1599 3775 9.314321 CAATATAAGGAAGTGACGTAATGAAGT 57.686 33.333 0.00 0.00 0.00 3.01
1600 3776 8.765219 CCAATATAAGGAAGTGACGTAATGAAG 58.235 37.037 0.00 0.00 0.00 3.02
1619 3800 9.613428 CAACAACCATCTTAGAACTCCAATATA 57.387 33.333 0.00 0.00 0.00 0.86
1620 3801 7.067494 GCAACAACCATCTTAGAACTCCAATAT 59.933 37.037 0.00 0.00 0.00 1.28
1642 3828 0.030235 GGAACGAAACCCACTGCAAC 59.970 55.000 0.00 0.00 0.00 4.17
1643 3829 0.394488 TGGAACGAAACCCACTGCAA 60.394 50.000 0.00 0.00 0.00 4.08
1705 3893 9.406828 GCATGAACTCTGTAAATATGTACGATA 57.593 33.333 0.00 0.00 0.00 2.92
1729 5266 3.287222 AGTAAACTCCTGCAAACAAGCA 58.713 40.909 0.00 0.00 43.35 3.91
1731 5268 3.807622 TCGAGTAAACTCCTGCAAACAAG 59.192 43.478 4.58 0.00 39.79 3.16
1734 5271 3.808174 AGTTCGAGTAAACTCCTGCAAAC 59.192 43.478 4.58 2.85 39.79 2.93
1738 5275 2.737252 CCAAGTTCGAGTAAACTCCTGC 59.263 50.000 4.58 0.00 38.52 4.85
1739 5276 3.244112 ACCCAAGTTCGAGTAAACTCCTG 60.244 47.826 4.58 0.00 38.52 3.86
1740 5277 2.970640 ACCCAAGTTCGAGTAAACTCCT 59.029 45.455 4.58 0.00 38.52 3.69
1776 6481 6.486993 AGGATAACAGAACACTCCAGTTTTTC 59.513 38.462 0.00 0.00 0.00 2.29
1858 7775 5.624900 CACATACACAAAGAAAACATGTCCG 59.375 40.000 0.00 0.00 0.00 4.79
1889 7807 2.412770 GGTTTCGTTACACATACCCACG 59.587 50.000 0.00 0.00 0.00 4.94
1908 7826 7.342799 ACTGCAGGTAAATGAAAATCATATGGT 59.657 33.333 19.93 0.00 35.76 3.55
2017 7947 3.289834 GCCACACACCAGCACAGG 61.290 66.667 0.00 0.00 0.00 4.00
2070 8685 5.533154 AGGACCTATTCAGTTCATAGTCTCG 59.467 44.000 0.00 0.00 0.00 4.04
2085 8701 9.495382 AGAGTAGTCAAGAAATAAGGACCTATT 57.505 33.333 0.00 0.00 0.00 1.73
2089 8705 5.813157 GCAGAGTAGTCAAGAAATAAGGACC 59.187 44.000 0.00 0.00 0.00 4.46
2090 8706 6.398918 TGCAGAGTAGTCAAGAAATAAGGAC 58.601 40.000 0.00 0.00 0.00 3.85
2092 8708 6.634805 TCTGCAGAGTAGTCAAGAAATAAGG 58.365 40.000 13.74 0.00 0.00 2.69
2093 8709 8.715191 ATTCTGCAGAGTAGTCAAGAAATAAG 57.285 34.615 17.43 0.00 0.00 1.73
2094 8710 9.507329 AAATTCTGCAGAGTAGTCAAGAAATAA 57.493 29.630 17.43 0.00 0.00 1.40
2095 8711 9.155975 GAAATTCTGCAGAGTAGTCAAGAAATA 57.844 33.333 17.43 0.00 0.00 1.40
2112 8742 0.965363 TCCGGCCCAAGAAATTCTGC 60.965 55.000 0.00 0.00 0.00 4.26
2120 8757 0.404040 AATTGAGTTCCGGCCCAAGA 59.596 50.000 0.00 0.00 0.00 3.02
2180 8834 7.666623 CAAAACCCATGTACCTGAAATAAAGT 58.333 34.615 0.00 0.00 0.00 2.66
2202 8856 2.554636 CCTGCAGCTCCAACGCAAA 61.555 57.895 8.66 0.00 34.75 3.68
2204 8858 3.772853 AACCTGCAGCTCCAACGCA 62.773 57.895 8.66 0.00 0.00 5.24
2211 8865 1.227943 TCCACACAACCTGCAGCTC 60.228 57.895 8.66 0.00 0.00 4.09
2212 8866 1.228063 CTCCACACAACCTGCAGCT 60.228 57.895 8.66 0.00 0.00 4.24
2213 8867 1.103398 AACTCCACACAACCTGCAGC 61.103 55.000 8.66 0.00 0.00 5.25
2220 8874 1.102978 AGGCACAAACTCCACACAAC 58.897 50.000 0.00 0.00 0.00 3.32
2347 9027 2.036992 AGGAAGCTGCATCGAAGATAGG 59.963 50.000 1.02 0.00 45.12 2.57
2352 9032 1.134877 TCAGAGGAAGCTGCATCGAAG 60.135 52.381 0.00 0.00 35.86 3.79
2356 9036 4.880696 AGTTAATTCAGAGGAAGCTGCATC 59.119 41.667 0.00 0.00 36.25 3.91
2360 9040 6.183360 GCCTTTAGTTAATTCAGAGGAAGCTG 60.183 42.308 0.00 0.00 36.25 4.24
2365 9045 5.648092 GCTTGCCTTTAGTTAATTCAGAGGA 59.352 40.000 0.00 0.00 0.00 3.71
2367 9047 6.150140 AGTGCTTGCCTTTAGTTAATTCAGAG 59.850 38.462 0.00 0.00 0.00 3.35
2380 9060 0.756442 TTGCTCCAGTGCTTGCCTTT 60.756 50.000 0.00 0.00 0.00 3.11
2387 9067 1.251251 GGTTCAATTGCTCCAGTGCT 58.749 50.000 0.00 0.00 0.00 4.40
2451 9258 7.002879 AGCCAATAGAGAATTATGAGTTGCAT 58.997 34.615 0.00 0.00 41.08 3.96
2462 9269 8.870075 AACAAGAACTTAGCCAATAGAGAATT 57.130 30.769 0.00 0.00 0.00 2.17
2609 10826 7.772332 ATAAGCTTTGATAAACTCTACCGTG 57.228 36.000 3.20 0.00 0.00 4.94
2802 11102 5.636121 CACATCCCACATGAAGAAAATTGTG 59.364 40.000 0.00 1.21 39.29 3.33
2934 11234 4.327680 AGAAGAATGAAACCAGTAGCCAC 58.672 43.478 0.00 0.00 0.00 5.01
2976 11276 1.311859 AGCATAATGCCACACCGATG 58.688 50.000 0.00 0.00 46.52 3.84
3030 11337 3.724508 ATCTAGCAAGTGTCCTGATCG 57.275 47.619 0.00 0.00 0.00 3.69
3068 11375 6.928348 TCTATCTAACAAGTGGTGAAGGAA 57.072 37.500 0.00 0.00 0.00 3.36
3125 11432 3.200165 GGCCTTCATAACCAACTCCTAGT 59.800 47.826 0.00 0.00 0.00 2.57
3144 11451 2.045536 CTGCTCCACCTCAAGGCC 60.046 66.667 0.00 0.00 39.32 5.19
3201 11510 7.066781 TCGATGGCCACTTATCTCCATATATA 58.933 38.462 8.16 0.00 39.25 0.86
3252 11568 9.120538 GCCACACTAAGAGATAAAATTCCATTA 57.879 33.333 0.00 0.00 0.00 1.90
3271 11592 2.372264 CTATGGATGCAAAGCCACACT 58.628 47.619 8.28 0.00 36.92 3.55
3311 11632 7.759489 ATAAAAGGATGACTTGTTTACTGCA 57.241 32.000 0.00 0.00 39.96 4.41
3312 11633 7.062255 GCAATAAAAGGATGACTTGTTTACTGC 59.938 37.037 0.00 0.00 39.96 4.40
3317 11638 6.670695 AGGCAATAAAAGGATGACTTGTTT 57.329 33.333 0.00 0.00 39.96 2.83
3340 11665 7.620880 AGAAAGACAACATACCTACATTGCTA 58.379 34.615 0.00 0.00 0.00 3.49
3361 11686 9.261035 AGAGAACTTCCTAACTATGATGAGAAA 57.739 33.333 0.00 0.00 0.00 2.52
3383 11708 9.019656 GCAGAAGATATCCTTAGTATTCAGAGA 57.980 37.037 0.00 0.00 34.68 3.10
3384 11709 7.967854 CGCAGAAGATATCCTTAGTATTCAGAG 59.032 40.741 0.00 0.00 34.68 3.35
3385 11710 7.448777 ACGCAGAAGATATCCTTAGTATTCAGA 59.551 37.037 0.00 0.00 34.68 3.27
3386 11711 7.598278 ACGCAGAAGATATCCTTAGTATTCAG 58.402 38.462 0.00 0.00 34.68 3.02
3387 11712 7.448777 AGACGCAGAAGATATCCTTAGTATTCA 59.551 37.037 0.00 0.00 34.68 2.57
3430 11755 2.306341 GGGTACCGTAAAAGAGCTCC 57.694 55.000 10.93 0.00 40.86 4.70
4160 12561 7.100458 ACAATTTTGAGCTCTTTTACAGTGT 57.900 32.000 16.19 0.00 0.00 3.55
4202 12604 3.181329 AGACCATGACACCCATACTTGA 58.819 45.455 0.00 0.00 33.31 3.02
4231 12633 1.046472 TCGTATTCGATGGGTGGCCT 61.046 55.000 3.32 0.00 41.35 5.19
4232 12634 0.600255 CTCGTATTCGATGGGTGGCC 60.600 60.000 0.00 0.00 45.21 5.36


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

AutoCloner maintained by Alex Coulton.