Multiple sequence alignment - TraesCS3A01G474200

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 TraesCS3A01G474200 chr3A 100.000 4760 0 0 1 4760 705312853 705308094 0.000000e+00 8791.0
1 TraesCS3A01G474200 chr3A 82.431 1349 192 26 2299 3621 706335436 706336765 0.000000e+00 1136.0
2 TraesCS3A01G474200 chr3A 81.951 1302 192 24 2304 3581 706018178 706019460 0.000000e+00 1062.0
3 TraesCS3A01G474200 chr3A 81.295 1374 171 48 2527 3854 705949656 705950989 0.000000e+00 1035.0
4 TraesCS3A01G474200 chr3A 78.755 1012 134 42 1334 2289 705370181 705369195 1.900000e-168 603.0
5 TraesCS3A01G474200 chr3A 85.892 241 19 9 1102 1331 705370473 705370237 4.760000e-60 243.0
6 TraesCS3A01G474200 chr3A 83.684 190 15 9 1033 1217 706257245 706257423 1.060000e-36 165.0
7 TraesCS3A01G474200 chr3A 94.872 78 4 0 6 83 705312063 705311986 6.470000e-24 122.0
8 TraesCS3A01G474200 chr3A 94.872 78 4 0 791 868 705312848 705312771 6.470000e-24 122.0
9 TraesCS3A01G474200 chrUn 94.022 2710 105 23 1399 4066 132057518 132060212 0.000000e+00 4054.0
10 TraesCS3A01G474200 chrUn 78.550 1021 120 56 1329 2280 131949399 131950389 8.880000e-162 580.0
11 TraesCS3A01G474200 chrUn 84.492 561 51 21 791 1319 132056835 132057391 5.460000e-144 521.0
12 TraesCS3A01G474200 chrUn 90.678 236 16 4 1102 1331 131949121 131949356 4.630000e-80 309.0
13 TraesCS3A01G474200 chrUn 84.896 192 20 4 3875 4066 132132270 132132452 8.130000e-43 185.0
14 TraesCS3A01G474200 chr3B 91.765 2465 142 20 1399 3833 760481793 760479360 0.000000e+00 3371.0
15 TraesCS3A01G474200 chr3B 82.688 1369 187 28 2299 3640 761369810 761371155 0.000000e+00 1170.0
16 TraesCS3A01G474200 chr3B 82.410 1336 170 32 2537 3841 761004691 761005992 0.000000e+00 1105.0
17 TraesCS3A01G474200 chr3B 84.055 1016 123 19 2554 3547 761195160 761196158 0.000000e+00 942.0
18 TraesCS3A01G474200 chr3B 80.015 1321 170 59 1037 2289 760493007 760491713 0.000000e+00 891.0
19 TraesCS3A01G474200 chr3B 90.385 520 34 7 83 602 268966775 268966272 0.000000e+00 669.0
20 TraesCS3A01G474200 chr3B 81.870 706 95 21 3162 3854 761061922 761062607 8.940000e-157 564.0
21 TraesCS3A01G474200 chr3B 78.089 785 120 34 1550 2299 761368957 761369724 2.610000e-122 449.0
22 TraesCS3A01G474200 chr3B 84.395 314 35 11 1990 2299 761393512 761393815 3.600000e-76 296.0
23 TraesCS3A01G474200 chr3B 78.431 408 34 22 840 1233 760482636 760482269 2.880000e-52 217.0
24 TraesCS3A01G474200 chr3B 87.500 168 19 2 2585 2751 760491205 760491039 4.860000e-45 193.0
25 TraesCS3A01G474200 chr3B 93.966 116 7 0 1102 1217 761368405 761368520 4.900000e-40 176.0
26 TraesCS3A01G474200 chr3B 74.298 463 95 18 3174 3621 760818776 760819229 1.760000e-39 174.0
27 TraesCS3A01G474200 chr3D 82.772 1306 183 23 2304 3581 572508987 572507696 0.000000e+00 1127.0
28 TraesCS3A01G474200 chr3D 75.467 750 100 39 1580 2299 572489479 572488784 6.030000e-74 289.0
29 TraesCS3A01G474200 chr3D 94.828 116 6 0 1102 1217 572510393 572510278 1.050000e-41 182.0
30 TraesCS3A01G474200 chr3D 88.430 121 9 3 1102 1217 572490049 572489929 1.790000e-29 141.0
31 TraesCS3A01G474200 chr7B 94.509 692 30 7 4076 4760 735316485 735315795 0.000000e+00 1061.0
32 TraesCS3A01G474200 chr1B 92.199 705 35 14 4057 4749 152312899 152313595 0.000000e+00 979.0
33 TraesCS3A01G474200 chr1B 88.100 521 44 12 83 602 299259336 299259839 1.900000e-168 603.0
34 TraesCS3A01G474200 chr1B 88.356 146 17 0 631 776 299260235 299260380 4.900000e-40 176.0
35 TraesCS3A01G474200 chr1B 84.536 97 15 0 4658 4754 64237654 64237750 3.920000e-16 97.1
36 TraesCS3A01G474200 chr2D 92.068 706 39 12 4066 4760 522899209 522899908 0.000000e+00 977.0
37 TraesCS3A01G474200 chr2D 88.846 520 39 9 83 602 460753505 460753005 5.230000e-174 621.0
38 TraesCS3A01G474200 chr2D 90.210 143 14 0 637 779 460752603 460752461 2.260000e-43 187.0
39 TraesCS3A01G474200 chr4B 92.230 695 36 12 4066 4749 593353488 593354175 0.000000e+00 968.0
40 TraesCS3A01G474200 chr4B 91.275 298 19 5 4464 4760 250725641 250725932 2.670000e-107 399.0
41 TraesCS3A01G474200 chr4B 98.551 69 0 1 1991 2059 120058445 120058378 2.330000e-23 121.0
42 TraesCS3A01G474200 chr6B 91.114 709 42 12 4066 4760 139427957 139427256 0.000000e+00 941.0
43 TraesCS3A01G474200 chr5A 91.163 679 38 7 1399 2059 69514960 69515634 0.000000e+00 902.0
44 TraesCS3A01G474200 chr5A 88.840 681 51 11 1399 2059 259314447 259315122 0.000000e+00 813.0
45 TraesCS3A01G474200 chr5A 93.156 263 17 1 1475 1736 507145733 507145471 7.470000e-103 385.0
46 TraesCS3A01G474200 chr5A 92.593 270 13 5 4068 4330 150020038 150019769 9.670000e-102 381.0
47 TraesCS3A01G474200 chr5A 92.593 270 13 5 4068 4330 344345717 344345986 9.670000e-102 381.0
48 TraesCS3A01G474200 chr5A 88.976 254 11 8 1804 2040 541262715 541262968 1.000000e-76 298.0
49 TraesCS3A01G474200 chr4A 90.294 680 43 10 1399 2059 18937342 18938017 0.000000e+00 869.0
50 TraesCS3A01G474200 chr4A 91.169 385 16 6 1673 2040 379642147 379642530 1.530000e-139 507.0
51 TraesCS3A01G474200 chr4A 90.649 385 18 5 1673 2040 379662886 379663269 3.310000e-136 496.0
52 TraesCS3A01G474200 chr4A 88.432 389 34 8 4373 4760 336063372 336063750 4.340000e-125 459.0
53 TraesCS3A01G474200 chr4A 94.677 263 13 1 1475 1736 579991983 579991721 1.590000e-109 407.0
54 TraesCS3A01G474200 chr4A 77.222 360 61 16 1615 1965 623982170 623981823 1.750000e-44 191.0
55 TraesCS3A01G474200 chr4A 90.714 140 11 2 637 776 502353502 502353365 8.130000e-43 185.0
56 TraesCS3A01G474200 chr6D 88.326 711 52 15 4066 4760 158226760 158226065 0.000000e+00 824.0
57 TraesCS3A01G474200 chr4D 90.019 521 34 9 83 602 283083135 283082632 0.000000e+00 658.0
58 TraesCS3A01G474200 chr5D 89.695 524 35 9 80 602 451604788 451605293 0.000000e+00 651.0
59 TraesCS3A01G474200 chr5D 89.484 523 36 9 81 602 451611990 451611486 1.120000e-180 643.0
60 TraesCS3A01G474200 chr5D 88.007 542 37 14 4055 4580 390511557 390512086 2.430000e-172 616.0
61 TraesCS3A01G474200 chr5D 90.634 363 27 6 222 578 44564405 44564044 4.310000e-130 475.0
62 TraesCS3A01G474200 chr5D 90.351 114 11 0 663 776 44549090 44548977 2.970000e-32 150.0
63 TraesCS3A01G474200 chr7D 89.655 522 34 10 83 602 193936850 193937353 0.000000e+00 647.0
64 TraesCS3A01G474200 chr1D 89.635 521 36 9 83 602 258912713 258912210 0.000000e+00 647.0
65 TraesCS3A01G474200 chr1D 88.868 530 42 7 74 602 385608420 385608933 1.870000e-178 636.0
66 TraesCS3A01G474200 chr1D 89.041 146 16 0 631 776 239625298 239625443 1.050000e-41 182.0
67 TraesCS3A01G474200 chr6A 93.031 287 20 0 1496 1782 174385014 174384728 2.050000e-113 420.0
68 TraesCS3A01G474200 chr1A 93.704 270 10 5 4068 4330 303740672 303740941 9.600000e-107 398.0
69 TraesCS3A01G474200 chr1A 86.316 95 13 0 658 752 292584291 292584385 2.340000e-18 104.0
70 TraesCS3A01G474200 chr5B 91.756 279 13 7 4062 4330 203382365 203382643 3.480000e-101 379.0
71 TraesCS3A01G474200 chr5B 86.301 146 20 0 631 776 46637506 46637651 4.930000e-35 159.0
72 TraesCS3A01G474200 chr5B 84.158 101 8 5 678 773 377628545 377628642 1.820000e-14 91.6
73 TraesCS3A01G474200 chr2A 92.776 263 18 1 1475 1736 161022270 161022008 3.480000e-101 379.0
74 TraesCS3A01G474200 chr2A 90.551 254 7 2 1804 2040 347120947 347120694 2.140000e-83 320.0
75 TraesCS3A01G474200 chr7A 76.796 362 62 15 1615 1967 633799996 633800344 2.930000e-42 183.0
76 TraesCS3A01G474200 chr7A 88.652 141 13 2 636 776 323707513 323707650 8.190000e-38 169.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G474200 chr3A 705308094 705312853 4759 True 3011.666667 8791 96.581333 1 4760 3 chr3A.!!$R1 4759
1 TraesCS3A01G474200 chr3A 706335436 706336765 1329 False 1136.000000 1136 82.431000 2299 3621 1 chr3A.!!$F4 1322
2 TraesCS3A01G474200 chr3A 706018178 706019460 1282 False 1062.000000 1062 81.951000 2304 3581 1 chr3A.!!$F2 1277
3 TraesCS3A01G474200 chr3A 705949656 705950989 1333 False 1035.000000 1035 81.295000 2527 3854 1 chr3A.!!$F1 1327
4 TraesCS3A01G474200 chr3A 705369195 705370473 1278 True 423.000000 603 82.323500 1102 2289 2 chr3A.!!$R2 1187
5 TraesCS3A01G474200 chrUn 132056835 132060212 3377 False 2287.500000 4054 89.257000 791 4066 2 chrUn.!!$F3 3275
6 TraesCS3A01G474200 chrUn 131949121 131950389 1268 False 444.500000 580 84.614000 1102 2280 2 chrUn.!!$F2 1178
7 TraesCS3A01G474200 chr3B 760479360 760482636 3276 True 1794.000000 3371 85.098000 840 3833 2 chr3B.!!$R2 2993
8 TraesCS3A01G474200 chr3B 761004691 761005992 1301 False 1105.000000 1105 82.410000 2537 3841 1 chr3B.!!$F2 1304
9 TraesCS3A01G474200 chr3B 761195160 761196158 998 False 942.000000 942 84.055000 2554 3547 1 chr3B.!!$F4 993
10 TraesCS3A01G474200 chr3B 268966272 268966775 503 True 669.000000 669 90.385000 83 602 1 chr3B.!!$R1 519
11 TraesCS3A01G474200 chr3B 761368405 761371155 2750 False 598.333333 1170 84.914333 1102 3640 3 chr3B.!!$F6 2538
12 TraesCS3A01G474200 chr3B 761061922 761062607 685 False 564.000000 564 81.870000 3162 3854 1 chr3B.!!$F3 692
13 TraesCS3A01G474200 chr3B 760491039 760493007 1968 True 542.000000 891 83.757500 1037 2751 2 chr3B.!!$R3 1714
14 TraesCS3A01G474200 chr3D 572507696 572510393 2697 True 654.500000 1127 88.800000 1102 3581 2 chr3D.!!$R2 2479
15 TraesCS3A01G474200 chr3D 572488784 572490049 1265 True 215.000000 289 81.948500 1102 2299 2 chr3D.!!$R1 1197
16 TraesCS3A01G474200 chr7B 735315795 735316485 690 True 1061.000000 1061 94.509000 4076 4760 1 chr7B.!!$R1 684
17 TraesCS3A01G474200 chr1B 152312899 152313595 696 False 979.000000 979 92.199000 4057 4749 1 chr1B.!!$F2 692
18 TraesCS3A01G474200 chr1B 299259336 299260380 1044 False 389.500000 603 88.228000 83 776 2 chr1B.!!$F3 693
19 TraesCS3A01G474200 chr2D 522899209 522899908 699 False 977.000000 977 92.068000 4066 4760 1 chr2D.!!$F1 694
20 TraesCS3A01G474200 chr2D 460752461 460753505 1044 True 404.000000 621 89.528000 83 779 2 chr2D.!!$R1 696
21 TraesCS3A01G474200 chr4B 593353488 593354175 687 False 968.000000 968 92.230000 4066 4749 1 chr4B.!!$F2 683
22 TraesCS3A01G474200 chr6B 139427256 139427957 701 True 941.000000 941 91.114000 4066 4760 1 chr6B.!!$R1 694
23 TraesCS3A01G474200 chr5A 69514960 69515634 674 False 902.000000 902 91.163000 1399 2059 1 chr5A.!!$F1 660
24 TraesCS3A01G474200 chr5A 259314447 259315122 675 False 813.000000 813 88.840000 1399 2059 1 chr5A.!!$F2 660
25 TraesCS3A01G474200 chr4A 18937342 18938017 675 False 869.000000 869 90.294000 1399 2059 1 chr4A.!!$F1 660
26 TraesCS3A01G474200 chr6D 158226065 158226760 695 True 824.000000 824 88.326000 4066 4760 1 chr6D.!!$R1 694
27 TraesCS3A01G474200 chr4D 283082632 283083135 503 True 658.000000 658 90.019000 83 602 1 chr4D.!!$R1 519
28 TraesCS3A01G474200 chr5D 451604788 451605293 505 False 651.000000 651 89.695000 80 602 1 chr5D.!!$F2 522
29 TraesCS3A01G474200 chr5D 451611486 451611990 504 True 643.000000 643 89.484000 81 602 1 chr5D.!!$R3 521
30 TraesCS3A01G474200 chr5D 390511557 390512086 529 False 616.000000 616 88.007000 4055 4580 1 chr5D.!!$F1 525
31 TraesCS3A01G474200 chr7D 193936850 193937353 503 False 647.000000 647 89.655000 83 602 1 chr7D.!!$F1 519
32 TraesCS3A01G474200 chr1D 258912210 258912713 503 True 647.000000 647 89.635000 83 602 1 chr1D.!!$R1 519
33 TraesCS3A01G474200 chr1D 385608420 385608933 513 False 636.000000 636 88.868000 74 602 1 chr1D.!!$F2 528

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
971 1383 1.273324 ACCCAAGTCCACAAAAACCCA 60.273 47.619 0.0 0.0 0.0 4.51 F
1412 2402 0.038599 TTGTGATGCCTGCTGTCCAT 59.961 50.000 0.0 0.0 0.0 3.41 F
3184 4541 0.106967 TGCTGGTGGTTGTTGCACTA 60.107 50.000 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2745 4068 3.205338 CCTTTTGTTTTGCCTCTTTGGG 58.795 45.455 0.0 0.0 36.0 4.12 R
3227 4591 2.161211 GCTCTTGAACACATCTGGCTTC 59.839 50.000 0.0 0.0 0.0 3.86 R
4395 5791 3.371285 GGGAGTTGCGAGTTCTATGAAAC 59.629 47.826 0.0 0.0 0.0 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
26 27 8.642908 TCCATAGTTCTTGTCGTATGTAATTG 57.357 34.615 0.00 0.00 0.00 2.32
27 28 7.223971 TCCATAGTTCTTGTCGTATGTAATTGC 59.776 37.037 0.00 0.00 0.00 3.56
28 29 7.224753 CCATAGTTCTTGTCGTATGTAATTGCT 59.775 37.037 0.00 0.00 0.00 3.91
29 30 9.244799 CATAGTTCTTGTCGTATGTAATTGCTA 57.755 33.333 0.00 0.00 0.00 3.49
30 31 9.811995 ATAGTTCTTGTCGTATGTAATTGCTAA 57.188 29.630 0.00 0.00 0.00 3.09
31 32 8.718102 AGTTCTTGTCGTATGTAATTGCTAAT 57.282 30.769 0.00 0.00 0.00 1.73
32 33 9.162764 AGTTCTTGTCGTATGTAATTGCTAATT 57.837 29.630 0.00 0.00 34.90 1.40
33 34 9.210426 GTTCTTGTCGTATGTAATTGCTAATTG 57.790 33.333 0.00 0.00 32.38 2.32
34 35 7.915508 TCTTGTCGTATGTAATTGCTAATTGG 58.084 34.615 0.00 0.00 32.38 3.16
35 36 7.766738 TCTTGTCGTATGTAATTGCTAATTGGA 59.233 33.333 0.00 0.00 32.38 3.53
36 37 7.851387 TGTCGTATGTAATTGCTAATTGGAA 57.149 32.000 0.00 0.00 32.38 3.53
37 38 8.445275 TGTCGTATGTAATTGCTAATTGGAAT 57.555 30.769 0.00 0.00 38.38 3.01
38 39 9.549078 TGTCGTATGTAATTGCTAATTGGAATA 57.451 29.630 0.00 0.00 35.62 1.75
39 40 9.807386 GTCGTATGTAATTGCTAATTGGAATAC 57.193 33.333 0.00 7.87 35.62 1.89
40 41 9.549078 TCGTATGTAATTGCTAATTGGAATACA 57.451 29.630 0.00 0.00 35.62 2.29
63 64 7.785033 ACATTCCATAATTCCATTTCAAGTCC 58.215 34.615 0.00 0.00 0.00 3.85
64 65 6.449635 TTCCATAATTCCATTTCAAGTCCG 57.550 37.500 0.00 0.00 0.00 4.79
65 66 5.750524 TCCATAATTCCATTTCAAGTCCGA 58.249 37.500 0.00 0.00 0.00 4.55
66 67 5.822519 TCCATAATTCCATTTCAAGTCCGAG 59.177 40.000 0.00 0.00 0.00 4.63
67 68 5.590259 CCATAATTCCATTTCAAGTCCGAGT 59.410 40.000 0.00 0.00 0.00 4.18
68 69 6.238484 CCATAATTCCATTTCAAGTCCGAGTC 60.238 42.308 0.00 0.00 0.00 3.36
69 70 4.559862 ATTCCATTTCAAGTCCGAGTCT 57.440 40.909 0.00 0.00 0.00 3.24
70 71 3.319137 TCCATTTCAAGTCCGAGTCTG 57.681 47.619 0.00 0.00 0.00 3.51
71 72 2.897326 TCCATTTCAAGTCCGAGTCTGA 59.103 45.455 0.00 0.00 0.00 3.27
72 73 3.323691 TCCATTTCAAGTCCGAGTCTGAA 59.676 43.478 0.00 0.00 0.00 3.02
95 96 7.438757 TGAAATTACAAACACTAGTAGAACGCA 59.561 33.333 3.59 0.00 0.00 5.24
96 97 7.900782 AATTACAAACACTAGTAGAACGCAT 57.099 32.000 3.59 0.00 0.00 4.73
155 156 4.868171 TGCTACTCACGGTGCTAAAATAAG 59.132 41.667 2.51 0.00 0.00 1.73
176 177 2.160219 GCGAGAACAATGCATGTCTCAA 59.840 45.455 24.19 0.00 42.99 3.02
183 184 4.397420 ACAATGCATGTCTCAACTACCAA 58.603 39.130 0.00 0.00 37.96 3.67
200 201 2.834549 ACCAAACATCTCAGATCCTCGT 59.165 45.455 0.00 0.00 0.00 4.18
213 214 2.631418 TCCTCGTTTCTCAGCTAACG 57.369 50.000 12.25 12.25 46.16 3.18
222 223 1.471287 TCTCAGCTAACGCGCTTCTTA 59.529 47.619 5.73 0.00 42.32 2.10
360 362 7.769044 ACAGATTAAGTTATTGTGACCGCTATT 59.231 33.333 8.45 0.00 0.00 1.73
415 417 3.431626 CCCAGTTATTGTGACGGCTATCA 60.432 47.826 0.00 0.00 0.00 2.15
458 460 6.804295 CAGATACTTATATGCGGAAGAGACAC 59.196 42.308 0.00 0.00 0.00 3.67
502 504 3.747529 TGGCAAAACCTACGTTAAGCTAC 59.252 43.478 0.00 0.00 40.22 3.58
511 514 9.927668 AAACCTACGTTAAGCTACAATAAGTAA 57.072 29.630 0.00 0.00 30.92 2.24
513 516 9.578439 ACCTACGTTAAGCTACAATAAGTAAAG 57.422 33.333 0.00 0.00 30.92 1.85
552 555 2.284754 TGGGCATAGCACAACAAAGA 57.715 45.000 0.00 0.00 39.83 2.52
553 556 2.806434 TGGGCATAGCACAACAAAGAT 58.194 42.857 0.00 0.00 39.83 2.40
554 557 2.492881 TGGGCATAGCACAACAAAGATG 59.507 45.455 0.00 0.00 39.83 2.90
555 558 2.493278 GGGCATAGCACAACAAAGATGT 59.507 45.455 0.00 0.00 43.14 3.06
556 559 3.694072 GGGCATAGCACAACAAAGATGTA 59.306 43.478 0.00 0.00 39.40 2.29
557 560 4.201950 GGGCATAGCACAACAAAGATGTAG 60.202 45.833 0.00 0.00 39.40 2.74
558 561 4.635765 GGCATAGCACAACAAAGATGTAGA 59.364 41.667 0.00 0.00 39.40 2.59
582 585 1.811359 CAGCTTGCCTCCTTTTCAGAG 59.189 52.381 0.00 0.00 0.00 3.35
609 612 7.432350 AAAAACAACTTGATTGCACAGAAAA 57.568 28.000 0.00 0.00 42.62 2.29
610 613 7.432350 AAAACAACTTGATTGCACAGAAAAA 57.568 28.000 0.00 0.00 42.62 1.94
635 638 5.643777 ACAACTTGATTGATCCTACTTTCGG 59.356 40.000 0.00 0.00 41.23 4.30
670 1062 3.677963 CCAATTTGGCCTCACCTCT 57.322 52.632 3.32 0.00 40.22 3.69
703 1095 1.862827 CACTTTTGAAAGCCTGCAAGC 59.137 47.619 0.00 0.00 39.63 4.01
704 1096 1.481772 ACTTTTGAAAGCCTGCAAGCA 59.518 42.857 10.50 0.00 39.63 3.91
705 1097 2.093553 ACTTTTGAAAGCCTGCAAGCAA 60.094 40.909 10.50 0.00 39.63 3.91
708 1100 1.364901 GAAAGCCTGCAAGCAAGCA 59.635 52.632 16.97 3.03 43.35 3.91
715 1107 2.362736 CCTGCAAGCAAGCAAGAGATA 58.637 47.619 4.63 0.00 45.13 1.98
718 1110 2.290514 TGCAAGCAAGCAAGAGATAGGT 60.291 45.455 0.17 0.00 42.46 3.08
721 1113 2.983229 AGCAAGCAAGAGATAGGTGTG 58.017 47.619 0.00 0.00 0.00 3.82
747 1139 7.970384 AGCACAATATTTTGCAATCAAATGAG 58.030 30.769 24.44 0.00 41.37 2.90
757 1149 4.934001 TGCAATCAAATGAGAGAGAGTCAC 59.066 41.667 0.00 0.00 0.00 3.67
762 1154 2.051334 ATGAGAGAGAGTCACGGAGG 57.949 55.000 0.00 0.00 0.00 4.30
798 1190 8.817092 TTTTCCCCAATATAAGGTAGTTCTTG 57.183 34.615 0.00 0.00 0.00 3.02
799 1191 7.519347 TTCCCCAATATAAGGTAGTTCTTGT 57.481 36.000 0.00 0.00 0.00 3.16
816 1208 3.930229 TCTTGTCGTGCGTAATTGCTAAT 59.070 39.130 0.00 0.00 35.36 1.73
830 1222 7.011950 CGTAATTGCTAATTGGACTACATTCCA 59.988 37.037 0.00 0.00 44.39 3.53
831 1223 7.902920 AATTGCTAATTGGACTACATTCCAT 57.097 32.000 0.00 0.00 45.42 3.41
832 1224 8.995027 AATTGCTAATTGGACTACATTCCATA 57.005 30.769 0.00 0.00 45.42 2.74
833 1225 8.995027 ATTGCTAATTGGACTACATTCCATAA 57.005 30.769 0.00 0.00 45.42 1.90
834 1226 8.995027 TTGCTAATTGGACTACATTCCATAAT 57.005 30.769 0.00 0.00 45.42 1.28
836 1228 9.066892 TGCTAATTGGACTACATTCCATAATTC 57.933 33.333 0.00 0.00 45.42 2.17
837 1229 8.515414 GCTAATTGGACTACATTCCATAATTCC 58.485 37.037 0.00 0.00 45.42 3.01
858 1263 3.681897 CCATTTCAAGTCCGAGTCTGAAG 59.318 47.826 0.00 0.00 0.00 3.02
936 1348 4.858942 GGATGCCCCGGCCCAAAT 62.859 66.667 2.62 0.00 41.09 2.32
971 1383 1.273324 ACCCAAGTCCACAAAAACCCA 60.273 47.619 0.00 0.00 0.00 4.51
1011 1423 1.079057 GCGTCTCTTCCCCACTTCC 60.079 63.158 0.00 0.00 0.00 3.46
1016 1428 1.612442 TCTTCCCCACTTCCCCTCG 60.612 63.158 0.00 0.00 0.00 4.63
1017 1429 1.918800 CTTCCCCACTTCCCCTCGT 60.919 63.158 0.00 0.00 0.00 4.18
1018 1430 1.900545 CTTCCCCACTTCCCCTCGTC 61.901 65.000 0.00 0.00 0.00 4.20
1019 1431 3.400054 CCCCACTTCCCCTCGTCC 61.400 72.222 0.00 0.00 0.00 4.79
1021 1433 2.284699 CCACTTCCCCTCGTCCCT 60.285 66.667 0.00 0.00 0.00 4.20
1024 1436 2.364961 CTTCCCCTCGTCCCTCCT 59.635 66.667 0.00 0.00 0.00 3.69
1025 1437 1.219824 ACTTCCCCTCGTCCCTCCTA 61.220 60.000 0.00 0.00 0.00 2.94
1026 1438 0.468400 CTTCCCCTCGTCCCTCCTAG 60.468 65.000 0.00 0.00 0.00 3.02
1027 1439 2.522193 CCCCTCGTCCCTCCTAGC 60.522 72.222 0.00 0.00 0.00 3.42
1028 1440 2.604152 CCCTCGTCCCTCCTAGCT 59.396 66.667 0.00 0.00 0.00 3.32
1030 1442 1.395826 CCCTCGTCCCTCCTAGCTTG 61.396 65.000 0.00 0.00 0.00 4.01
1031 1443 0.395862 CCTCGTCCCTCCTAGCTTGA 60.396 60.000 0.00 0.00 0.00 3.02
1032 1444 0.741915 CTCGTCCCTCCTAGCTTGAC 59.258 60.000 0.00 0.00 0.00 3.18
1059 1505 1.074405 GGGTTTTACTTTCCCCTCCGT 59.926 52.381 0.00 0.00 35.52 4.69
1209 1680 0.179032 ATTTGGTGCCGTGTCAGACA 60.179 50.000 0.00 0.00 0.00 3.41
1234 1738 5.774498 AAAATGATTATTTCGCCTCTCCC 57.226 39.130 0.00 0.00 35.50 4.30
1247 2052 1.831652 CTCTCCCTGCTTGTTCGGGT 61.832 60.000 0.00 0.00 39.10 5.28
1309 2130 3.975670 CGGTAGATCTCGTCTGTTTATGC 59.024 47.826 0.00 0.00 37.83 3.14
1361 2272 3.111098 CTGCGCTTATCCTGCAATTTTC 58.889 45.455 9.73 0.00 38.30 2.29
1412 2402 0.038599 TTGTGATGCCTGCTGTCCAT 59.961 50.000 0.00 0.00 0.00 3.41
1447 2437 8.585881 TCAGTTTCAGAGTTTGCTAATACTACT 58.414 33.333 0.00 0.00 0.00 2.57
1448 2438 9.856488 CAGTTTCAGAGTTTGCTAATACTACTA 57.144 33.333 0.00 0.00 0.00 1.82
1469 2460 3.366052 TCCTTTGGTATTTCTGGAGCC 57.634 47.619 0.00 0.00 0.00 4.70
1481 2472 2.023673 TCTGGAGCCAACTTTGTTGTG 58.976 47.619 9.20 3.10 0.00 3.33
1484 2475 2.361757 TGGAGCCAACTTTGTTGTGATG 59.638 45.455 9.20 0.00 0.00 3.07
1555 2573 0.457851 TGTGGTTCCCTTTTGTTGCG 59.542 50.000 0.00 0.00 0.00 4.85
1576 2594 4.201685 GCGTATTGAAATGCTACTGTCGTT 60.202 41.667 0.00 0.00 0.00 3.85
1632 2658 6.257994 AGGGAGCATAGAGAAATCATTCAA 57.742 37.500 0.00 0.00 38.06 2.69
1710 2736 7.664758 TGGAAGTCTGTTAGAAACCTAACTAC 58.335 38.462 14.14 12.14 43.86 2.73
2230 3321 7.470563 GCCTATTTCTTATTGTAATGCTGCCTT 60.471 37.037 0.00 0.00 0.00 4.35
2322 3519 4.700213 CCGTATTGACCTCTTTTGGTTCAT 59.300 41.667 0.00 0.00 41.00 2.57
2354 3551 7.361713 CCTGTTTTCTATTTGCCGATTAGACAA 60.362 37.037 0.00 0.00 0.00 3.18
2396 3595 9.197694 CTCTAATATTCTGTTCTTTCCATACCG 57.802 37.037 0.00 0.00 0.00 4.02
2668 3984 7.913674 GCTTTTGCTATTATAGTCCTGCTAT 57.086 36.000 0.94 0.00 41.70 2.97
2710 4026 2.893637 AGTATGACGTGATGCTGGAAC 58.106 47.619 4.60 0.00 0.00 3.62
2745 4068 5.978322 CGAGTAGCTAATCCTTTGTACCTTC 59.022 44.000 15.14 0.00 0.00 3.46
2748 4071 3.850173 AGCTAATCCTTTGTACCTTCCCA 59.150 43.478 0.00 0.00 0.00 4.37
2901 4236 3.320541 CACTTGCCATTTCCAGTGGTTAA 59.679 43.478 9.54 5.51 39.01 2.01
2968 4307 9.912634 TTCTGGTCTTATGCAAAATTTAGAAAG 57.087 29.630 0.00 0.00 0.00 2.62
2971 4310 9.077885 TGGTCTTATGCAAAATTTAGAAAGTCT 57.922 29.630 0.00 0.00 0.00 3.24
3182 4539 0.958091 TATGCTGGTGGTTGTTGCAC 59.042 50.000 0.00 0.00 36.44 4.57
3184 4541 0.106967 TGCTGGTGGTTGTTGCACTA 60.107 50.000 0.00 0.00 0.00 2.74
3194 4551 6.238925 GGTGGTTGTTGCACTATCTTAACTTT 60.239 38.462 0.00 0.00 0.00 2.66
3227 4591 3.068165 TGCAGGTTATGTATGTCCTCTCG 59.932 47.826 0.00 0.00 0.00 4.04
3591 4959 2.916269 TGATAACAGGGTGTGGGATTGA 59.084 45.455 0.00 0.00 0.00 2.57
3651 5020 1.350684 TGCAGTTGCTGGATTGGTAGA 59.649 47.619 5.62 0.00 42.66 2.59
3854 5233 6.730507 AGATTTTATTCCCAAACTCCAACCAT 59.269 34.615 0.00 0.00 0.00 3.55
3867 5246 3.295093 TCCAACCATTGTGACATTGTGT 58.705 40.909 6.71 2.31 0.00 3.72
3890 5269 9.490663 GTGTGATTTAGAAACAATTAAGATCGG 57.509 33.333 0.00 0.00 0.00 4.18
3906 5285 3.325135 AGATCGGACTCCTTCAGTTTTGT 59.675 43.478 0.00 0.00 34.41 2.83
3907 5286 2.833794 TCGGACTCCTTCAGTTTTGTG 58.166 47.619 0.00 0.00 34.41 3.33
3917 5296 2.560504 TCAGTTTTGTGTGACGAGCAT 58.439 42.857 0.00 0.00 0.00 3.79
3920 5299 4.104776 CAGTTTTGTGTGACGAGCATTTT 58.895 39.130 0.00 0.00 0.00 1.82
3957 5336 6.060788 AGATGAACAGCTTTGAAGAGTCTTT 58.939 36.000 6.88 0.00 0.00 2.52
4017 5396 6.092533 CCAAATTTGTTGCTTTGACCATATCC 59.907 38.462 16.73 0.00 34.93 2.59
4020 5399 5.999205 TTGTTGCTTTGACCATATCCATT 57.001 34.783 0.00 0.00 0.00 3.16
4049 5428 4.223923 TGTTTTTGTTTGGAGGATGGTTGT 59.776 37.500 0.00 0.00 0.00 3.32
4053 5432 2.955660 TGTTTGGAGGATGGTTGTCAAC 59.044 45.455 7.20 7.20 0.00 3.18
4056 5435 3.140325 TGGAGGATGGTTGTCAACTTC 57.860 47.619 15.17 11.86 0.00 3.01
4100 5481 2.793268 GTGCAACGGACGTATAAACC 57.207 50.000 0.00 0.00 0.00 3.27
4101 5482 2.067766 GTGCAACGGACGTATAAACCA 58.932 47.619 0.00 0.00 0.00 3.67
4102 5483 2.093152 GTGCAACGGACGTATAAACCAG 59.907 50.000 0.00 0.00 0.00 4.00
4103 5484 2.029200 TGCAACGGACGTATAAACCAGA 60.029 45.455 0.00 0.00 0.00 3.86
4139 5523 6.408548 CCTCATTCATCCTAGTTAAGAGGCAA 60.409 42.308 0.00 0.00 34.40 4.52
4287 5680 5.125356 TGTTCATGTCTCTGACACACAAAT 58.875 37.500 2.31 0.00 45.65 2.32
4353 5746 6.128007 CCACTAGGCGTAAATTTCAAAGTCAT 60.128 38.462 0.00 0.00 0.00 3.06
4394 5790 8.893563 ATGTTCAATAAACCTTTCTATCCCAA 57.106 30.769 0.00 0.00 37.03 4.12
4395 5791 8.348285 TGTTCAATAAACCTTTCTATCCCAAG 57.652 34.615 0.00 0.00 37.03 3.61
4409 5805 6.806751 TCTATCCCAAGTTTCATAGAACTCG 58.193 40.000 0.00 0.00 38.86 4.18
4462 5858 4.236935 AGCCGCAAATTACAAAGTCAATG 58.763 39.130 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.224753 AGCAATTACATACGACAAGAACTATGG 59.775 37.037 0.00 0.00 0.00 2.74
3 4 8.131455 AGCAATTACATACGACAAGAACTATG 57.869 34.615 0.00 0.00 0.00 2.23
4 5 9.811995 TTAGCAATTACATACGACAAGAACTAT 57.188 29.630 0.00 0.00 0.00 2.12
5 6 9.811995 ATTAGCAATTACATACGACAAGAACTA 57.188 29.630 0.00 0.00 0.00 2.24
7 8 9.210426 CAATTAGCAATTACATACGACAAGAAC 57.790 33.333 0.00 0.00 0.00 3.01
8 9 8.394877 CCAATTAGCAATTACATACGACAAGAA 58.605 33.333 0.00 0.00 0.00 2.52
9 10 7.766738 TCCAATTAGCAATTACATACGACAAGA 59.233 33.333 0.00 0.00 0.00 3.02
10 11 7.915508 TCCAATTAGCAATTACATACGACAAG 58.084 34.615 0.00 0.00 0.00 3.16
11 12 7.851387 TCCAATTAGCAATTACATACGACAA 57.149 32.000 0.00 0.00 0.00 3.18
12 13 7.851387 TTCCAATTAGCAATTACATACGACA 57.149 32.000 0.00 0.00 0.00 4.35
13 14 9.807386 GTATTCCAATTAGCAATTACATACGAC 57.193 33.333 0.00 0.00 0.00 4.34
14 15 9.549078 TGTATTCCAATTAGCAATTACATACGA 57.451 29.630 0.00 0.00 0.00 3.43
37 38 8.912988 GGACTTGAAATGGAATTATGGAATGTA 58.087 33.333 0.00 0.00 33.67 2.29
38 39 7.416664 CGGACTTGAAATGGAATTATGGAATGT 60.417 37.037 0.00 0.00 33.67 2.71
39 40 6.919662 CGGACTTGAAATGGAATTATGGAATG 59.080 38.462 0.00 0.00 33.67 2.67
40 41 6.833416 TCGGACTTGAAATGGAATTATGGAAT 59.167 34.615 0.00 0.00 33.67 3.01
41 42 6.184068 TCGGACTTGAAATGGAATTATGGAA 58.816 36.000 0.00 0.00 33.67 3.53
42 43 5.750524 TCGGACTTGAAATGGAATTATGGA 58.249 37.500 0.00 0.00 33.67 3.41
43 44 5.590259 ACTCGGACTTGAAATGGAATTATGG 59.410 40.000 0.00 0.00 33.67 2.74
44 45 6.540189 AGACTCGGACTTGAAATGGAATTATG 59.460 38.462 0.00 0.00 33.67 1.90
45 46 6.540189 CAGACTCGGACTTGAAATGGAATTAT 59.460 38.462 0.00 0.00 33.67 1.28
46 47 5.874810 CAGACTCGGACTTGAAATGGAATTA 59.125 40.000 0.00 0.00 33.67 1.40
47 48 4.697352 CAGACTCGGACTTGAAATGGAATT 59.303 41.667 0.00 0.00 38.98 2.17
48 49 4.020218 TCAGACTCGGACTTGAAATGGAAT 60.020 41.667 0.00 0.00 0.00 3.01
49 50 3.323691 TCAGACTCGGACTTGAAATGGAA 59.676 43.478 0.00 0.00 0.00 3.53
50 51 2.897326 TCAGACTCGGACTTGAAATGGA 59.103 45.455 0.00 0.00 0.00 3.41
51 52 3.319137 TCAGACTCGGACTTGAAATGG 57.681 47.619 0.00 0.00 0.00 3.16
52 53 5.869753 ATTTCAGACTCGGACTTGAAATG 57.130 39.130 14.07 0.00 35.50 2.32
53 54 6.934645 TGTAATTTCAGACTCGGACTTGAAAT 59.065 34.615 11.08 11.08 37.52 2.17
54 55 6.285224 TGTAATTTCAGACTCGGACTTGAAA 58.715 36.000 8.40 8.40 0.00 2.69
55 56 5.849510 TGTAATTTCAGACTCGGACTTGAA 58.150 37.500 0.00 0.00 0.00 2.69
56 57 5.462530 TGTAATTTCAGACTCGGACTTGA 57.537 39.130 0.00 0.00 0.00 3.02
57 58 6.018262 TGTTTGTAATTTCAGACTCGGACTTG 60.018 38.462 7.17 0.00 0.00 3.16
58 59 6.018180 GTGTTTGTAATTTCAGACTCGGACTT 60.018 38.462 7.17 0.00 0.00 3.01
59 60 5.465724 GTGTTTGTAATTTCAGACTCGGACT 59.534 40.000 7.17 0.00 0.00 3.85
60 61 5.465724 AGTGTTTGTAATTTCAGACTCGGAC 59.534 40.000 7.17 0.00 0.00 4.79
61 62 5.607477 AGTGTTTGTAATTTCAGACTCGGA 58.393 37.500 7.17 0.00 0.00 4.55
62 63 5.924475 AGTGTTTGTAATTTCAGACTCGG 57.076 39.130 7.17 0.00 0.00 4.63
63 64 7.639162 ACTAGTGTTTGTAATTTCAGACTCG 57.361 36.000 0.00 1.20 0.00 4.18
64 65 9.909644 TCTACTAGTGTTTGTAATTTCAGACTC 57.090 33.333 5.39 4.13 0.00 3.36
67 68 9.188588 CGTTCTACTAGTGTTTGTAATTTCAGA 57.811 33.333 5.39 0.00 0.00 3.27
68 69 7.950496 GCGTTCTACTAGTGTTTGTAATTTCAG 59.050 37.037 5.39 0.00 0.00 3.02
69 70 7.438757 TGCGTTCTACTAGTGTTTGTAATTTCA 59.561 33.333 5.39 0.00 0.00 2.69
70 71 7.790000 TGCGTTCTACTAGTGTTTGTAATTTC 58.210 34.615 5.39 0.00 0.00 2.17
71 72 7.718272 TGCGTTCTACTAGTGTTTGTAATTT 57.282 32.000 5.39 0.00 0.00 1.82
72 73 7.386848 ACATGCGTTCTACTAGTGTTTGTAATT 59.613 33.333 5.39 0.00 0.00 1.40
129 130 1.470051 TAGCACCGTGAGTAGCATCA 58.530 50.000 1.65 0.00 0.00 3.07
130 131 2.579207 TTAGCACCGTGAGTAGCATC 57.421 50.000 1.65 0.00 0.00 3.91
155 156 1.733912 TGAGACATGCATTGTTCTCGC 59.266 47.619 18.39 4.47 39.18 5.03
176 177 4.098654 CGAGGATCTGAGATGTTTGGTAGT 59.901 45.833 0.00 0.00 0.00 2.73
183 184 4.464244 TGAGAAACGAGGATCTGAGATGTT 59.536 41.667 0.00 0.00 0.00 2.71
213 214 9.159470 GATAGTTGTAATTGATTTAAGAAGCGC 57.841 33.333 0.00 0.00 0.00 5.92
332 334 6.092259 AGCGGTCACAATAACTTAATCTGTTC 59.908 38.462 0.00 0.00 0.00 3.18
392 394 0.676782 AGCCGTCACAATAACTGGGC 60.677 55.000 0.00 0.00 39.33 5.36
446 448 1.400242 GCAAATGTGTGTCTCTTCCGC 60.400 52.381 0.00 0.00 0.00 5.54
451 453 3.282021 ACACTTGCAAATGTGTGTCTCT 58.718 40.909 20.12 0.00 44.52 3.10
452 454 3.698029 ACACTTGCAAATGTGTGTCTC 57.302 42.857 20.12 0.00 44.52 3.36
482 484 4.996062 TGTAGCTTAACGTAGGTTTTGC 57.004 40.909 6.07 10.79 37.58 3.68
511 514 7.631377 GCCCATCTCAAATTTTATGCTACACTT 60.631 37.037 0.00 0.00 0.00 3.16
513 516 5.979517 GCCCATCTCAAATTTTATGCTACAC 59.020 40.000 0.00 0.00 0.00 2.90
535 538 3.855689 ACATCTTTGTTGTGCTATGCC 57.144 42.857 0.00 0.00 29.55 4.40
550 553 0.179936 GCAAGCTGGCCTCTACATCT 59.820 55.000 0.00 0.00 0.00 2.90
551 554 2.700329 GCAAGCTGGCCTCTACATC 58.300 57.895 0.00 0.00 0.00 3.06
552 555 4.972875 GCAAGCTGGCCTCTACAT 57.027 55.556 0.00 0.00 0.00 2.29
607 610 9.750125 GAAAGTAGGATCAATCAAGTTGTTTTT 57.250 29.630 2.11 0.00 38.95 1.94
608 611 8.076178 CGAAAGTAGGATCAATCAAGTTGTTTT 58.924 33.333 2.11 0.00 38.95 2.43
609 612 7.308589 CCGAAAGTAGGATCAATCAAGTTGTTT 60.309 37.037 2.11 0.00 38.95 2.83
610 613 6.149474 CCGAAAGTAGGATCAATCAAGTTGTT 59.851 38.462 2.11 0.00 38.95 2.83
611 614 5.643777 CCGAAAGTAGGATCAATCAAGTTGT 59.356 40.000 2.11 0.00 38.95 3.32
612 615 5.643777 ACCGAAAGTAGGATCAATCAAGTTG 59.356 40.000 0.00 0.00 39.25 3.16
613 616 5.805728 ACCGAAAGTAGGATCAATCAAGTT 58.194 37.500 0.00 0.00 0.00 2.66
614 617 5.420409 GACCGAAAGTAGGATCAATCAAGT 58.580 41.667 0.00 0.00 0.00 3.16
615 618 4.811557 GGACCGAAAGTAGGATCAATCAAG 59.188 45.833 0.00 0.00 0.00 3.02
616 619 4.469945 AGGACCGAAAGTAGGATCAATCAA 59.530 41.667 0.00 0.00 0.00 2.57
617 620 4.030913 AGGACCGAAAGTAGGATCAATCA 58.969 43.478 0.00 0.00 0.00 2.57
618 621 4.674281 AGGACCGAAAGTAGGATCAATC 57.326 45.455 0.00 0.00 0.00 2.67
619 622 5.424252 TGTAAGGACCGAAAGTAGGATCAAT 59.576 40.000 0.00 0.00 0.00 2.57
620 623 4.773674 TGTAAGGACCGAAAGTAGGATCAA 59.226 41.667 0.00 0.00 0.00 2.57
621 624 4.346730 TGTAAGGACCGAAAGTAGGATCA 58.653 43.478 0.00 0.00 0.00 2.92
622 625 4.996788 TGTAAGGACCGAAAGTAGGATC 57.003 45.455 0.00 0.00 0.00 3.36
623 626 5.424252 TGAATGTAAGGACCGAAAGTAGGAT 59.576 40.000 0.00 0.00 0.00 3.24
635 638 1.803334 TGGCGTGTGAATGTAAGGAC 58.197 50.000 0.00 0.00 0.00 3.85
670 1062 2.680974 AAAAGTGAGGCTGAGGCGCA 62.681 55.000 10.83 8.60 39.81 6.09
676 1068 1.956477 GGCTTTCAAAAGTGAGGCTGA 59.044 47.619 0.00 0.00 38.28 4.26
703 1095 2.935201 GCTCACACCTATCTCTTGCTTG 59.065 50.000 0.00 0.00 0.00 4.01
704 1096 2.568956 TGCTCACACCTATCTCTTGCTT 59.431 45.455 0.00 0.00 0.00 3.91
705 1097 2.093764 GTGCTCACACCTATCTCTTGCT 60.094 50.000 0.00 0.00 41.21 3.91
708 1100 4.833478 ATTGTGCTCACACCTATCTCTT 57.167 40.909 1.67 0.00 46.86 2.85
715 1107 3.573538 TGCAAAATATTGTGCTCACACCT 59.426 39.130 26.90 0.00 46.86 4.00
718 1110 5.780984 TGATTGCAAAATATTGTGCTCACA 58.219 33.333 26.90 20.19 41.48 3.58
721 1113 7.966111 TCATTTGATTGCAAAATATTGTGCTC 58.034 30.769 26.90 18.81 46.19 4.26
747 1139 3.243267 GCTAATTCCTCCGTGACTCTCTC 60.243 52.174 0.00 0.00 0.00 3.20
776 1168 6.183360 CGACAAGAACTACCTTATATTGGGGA 60.183 42.308 0.00 0.00 0.00 4.81
779 1171 6.018994 GCACGACAAGAACTACCTTATATTGG 60.019 42.308 0.00 0.00 0.00 3.16
780 1172 6.291637 CGCACGACAAGAACTACCTTATATTG 60.292 42.308 0.00 0.00 0.00 1.90
781 1173 5.747197 CGCACGACAAGAACTACCTTATATT 59.253 40.000 0.00 0.00 0.00 1.28
782 1174 5.163581 ACGCACGACAAGAACTACCTTATAT 60.164 40.000 0.00 0.00 0.00 0.86
783 1175 4.156556 ACGCACGACAAGAACTACCTTATA 59.843 41.667 0.00 0.00 0.00 0.98
784 1176 3.057033 ACGCACGACAAGAACTACCTTAT 60.057 43.478 0.00 0.00 0.00 1.73
785 1177 2.294233 ACGCACGACAAGAACTACCTTA 59.706 45.455 0.00 0.00 0.00 2.69
786 1178 1.068127 ACGCACGACAAGAACTACCTT 59.932 47.619 0.00 0.00 0.00 3.50
787 1179 0.672342 ACGCACGACAAGAACTACCT 59.328 50.000 0.00 0.00 0.00 3.08
788 1180 2.336554 TACGCACGACAAGAACTACC 57.663 50.000 0.00 0.00 0.00 3.18
789 1181 4.625135 CAATTACGCACGACAAGAACTAC 58.375 43.478 0.00 0.00 0.00 2.73
792 1184 2.096417 AGCAATTACGCACGACAAGAAC 60.096 45.455 0.00 0.00 0.00 3.01
798 1190 3.062909 TCCAATTAGCAATTACGCACGAC 59.937 43.478 0.00 0.00 0.00 4.34
799 1191 3.062909 GTCCAATTAGCAATTACGCACGA 59.937 43.478 0.00 0.00 0.00 4.35
816 1208 8.837099 AAATGGAATTATGGAATGTAGTCCAA 57.163 30.769 5.06 0.00 43.45 3.53
830 1222 6.540189 CAGACTCGGACTTGAAATGGAATTAT 59.460 38.462 0.00 0.00 33.67 1.28
831 1223 5.874810 CAGACTCGGACTTGAAATGGAATTA 59.125 40.000 0.00 0.00 33.67 1.40
832 1224 4.697352 CAGACTCGGACTTGAAATGGAATT 59.303 41.667 0.00 0.00 38.98 2.17
833 1225 4.020218 TCAGACTCGGACTTGAAATGGAAT 60.020 41.667 0.00 0.00 0.00 3.01
834 1226 3.323691 TCAGACTCGGACTTGAAATGGAA 59.676 43.478 0.00 0.00 0.00 3.53
836 1228 3.319137 TCAGACTCGGACTTGAAATGG 57.681 47.619 0.00 0.00 0.00 3.16
837 1229 4.310769 ACTTCAGACTCGGACTTGAAATG 58.689 43.478 0.00 0.00 0.00 2.32
888 1294 5.471456 CAGTTTATCTTGGATGGGCTCATAC 59.529 44.000 0.12 0.12 34.78 2.39
891 1297 3.523157 TCAGTTTATCTTGGATGGGCTCA 59.477 43.478 0.00 0.00 0.00 4.26
936 1348 4.028490 GGTCGGTGGGATGTGCCA 62.028 66.667 0.00 0.00 38.95 4.92
943 1355 2.926242 GGACTTGGGTCGGTGGGA 60.926 66.667 0.00 0.00 42.97 4.37
971 1383 0.099259 TTGACTCGTGTCGTCGTGTT 59.901 50.000 12.54 0.00 45.70 3.32
1011 1423 1.075896 AAGCTAGGAGGGACGAGGG 60.076 63.158 0.00 0.00 0.00 4.30
1027 1439 6.594547 GGAAAGTAAAACCCTAGCTAGTCAAG 59.405 42.308 19.31 7.73 0.00 3.02
1028 1440 6.470278 GGAAAGTAAAACCCTAGCTAGTCAA 58.530 40.000 19.31 0.00 0.00 3.18
1030 1442 5.426504 GGGAAAGTAAAACCCTAGCTAGTC 58.573 45.833 19.31 6.13 40.39 2.59
1031 1443 4.226846 GGGGAAAGTAAAACCCTAGCTAGT 59.773 45.833 19.31 3.10 42.86 2.57
1032 1444 4.778579 GGGGAAAGTAAAACCCTAGCTAG 58.221 47.826 14.20 14.20 42.86 3.42
1071 1517 4.745751 CGGGTGCGCCGGTAAGAA 62.746 66.667 15.33 0.00 34.97 2.52
1209 1680 6.039829 GGGAGAGGCGAAATAATCATTTTTCT 59.960 38.462 0.00 0.00 34.44 2.52
1234 1738 0.736325 CGTAGGACCCGAACAAGCAG 60.736 60.000 0.00 0.00 0.00 4.24
1247 2052 3.598019 ACAAAATAAGCCGACGTAGGA 57.402 42.857 19.84 0.00 0.00 2.94
1309 2130 2.512515 GCTCTGCAACCTAGGCGG 60.513 66.667 9.30 1.73 39.01 6.13
1412 2402 6.516718 CAAACTCTGAAACTGAACTCCTAGA 58.483 40.000 0.00 0.00 0.00 2.43
1447 2437 4.476846 TGGCTCCAGAAATACCAAAGGATA 59.523 41.667 0.00 0.00 0.00 2.59
1448 2438 3.269381 TGGCTCCAGAAATACCAAAGGAT 59.731 43.478 0.00 0.00 0.00 3.24
1449 2439 2.647299 TGGCTCCAGAAATACCAAAGGA 59.353 45.455 0.00 0.00 0.00 3.36
1458 2449 3.706086 ACAACAAAGTTGGCTCCAGAAAT 59.294 39.130 13.71 0.00 0.00 2.17
1469 2460 1.270252 GGGCCCATCACAACAAAGTTG 60.270 52.381 19.95 8.24 0.00 3.16
1481 2472 1.039233 CACCAATCACAGGGCCCATC 61.039 60.000 27.56 0.00 0.00 3.51
1484 2475 1.678970 GTCACCAATCACAGGGCCC 60.679 63.158 16.46 16.46 0.00 5.80
1603 2628 7.865706 TGATTTCTCTATGCTCCCTTAAAAC 57.134 36.000 0.00 0.00 0.00 2.43
1710 2736 5.240183 ACAGCATATAAGCATAAGCACAAGG 59.760 40.000 2.37 0.00 45.49 3.61
1761 2795 5.410746 ACAGAAAGTTATGCTCACACATCTG 59.589 40.000 0.00 0.00 34.91 2.90
2046 3121 5.905331 TCAAGGATAGGCTCATCTTCCTTAA 59.095 40.000 12.39 0.70 43.27 1.85
2285 3376 8.488651 AGGTCAATACGGATAAGTAAAGTTTG 57.511 34.615 0.00 0.00 0.00 2.93
2322 3519 5.067936 TCGGCAAATAGAAAACAGGTCAAAA 59.932 36.000 0.00 0.00 0.00 2.44
2354 3551 7.873699 ATATTAGAGGGTACAAACTGGCTAT 57.126 36.000 0.00 0.00 0.00 2.97
2396 3595 3.385193 AAACCACAAAGGCATAGCAAC 57.615 42.857 0.00 0.00 43.14 4.17
2668 3984 6.757237 ACTAAATGCATTGAAATGGTTCACA 58.243 32.000 13.82 0.00 43.52 3.58
2745 4068 3.205338 CCTTTTGTTTTGCCTCTTTGGG 58.795 45.455 0.00 0.00 36.00 4.12
2748 4071 6.498303 AGATATCCCTTTTGTTTTGCCTCTTT 59.502 34.615 0.00 0.00 0.00 2.52
2968 4307 8.333908 CAGAAAGCACAGATATATTGTCAAGAC 58.666 37.037 0.00 0.00 0.00 3.01
2971 4310 6.543465 CCCAGAAAGCACAGATATATTGTCAA 59.457 38.462 0.00 0.00 0.00 3.18
3184 4541 8.253113 CCTGCAATTATGTGGAAAAGTTAAGAT 58.747 33.333 0.00 0.00 0.00 2.40
3227 4591 2.161211 GCTCTTGAACACATCTGGCTTC 59.839 50.000 0.00 0.00 0.00 3.86
3591 4959 3.953612 TGACATGACCAGAAACTGCTTTT 59.046 39.130 0.00 0.00 0.00 2.27
3651 5020 6.530019 AGTTTGGTGAACAGAAAAACAGAT 57.470 33.333 0.00 0.00 40.84 2.90
3854 5233 7.766283 TGTTTCTAAATCACACAATGTCACAA 58.234 30.769 0.00 0.00 0.00 3.33
3867 5246 9.667107 AGTCCGATCTTAATTGTTTCTAAATCA 57.333 29.630 0.00 0.00 0.00 2.57
3890 5269 3.001330 CGTCACACAAAACTGAAGGAGTC 59.999 47.826 0.00 0.00 31.73 3.36
3917 5296 5.125257 TGTTCATCTTGTCAACAGCAGAAAA 59.875 36.000 0.00 0.00 0.00 2.29
3920 5299 3.807553 TGTTCATCTTGTCAACAGCAGA 58.192 40.909 0.00 0.00 0.00 4.26
3925 5304 4.639755 TCAAAGCTGTTCATCTTGTCAACA 59.360 37.500 0.00 0.00 0.00 3.33
3957 5336 4.944619 TGTCAAAATGCAAACATACCCA 57.055 36.364 0.00 0.00 34.62 4.51
4017 5396 8.885494 TCCTCCAAACAAAAACAGATTAAATG 57.115 30.769 0.00 0.00 0.00 2.32
4020 5399 7.070571 ACCATCCTCCAAACAAAAACAGATTAA 59.929 33.333 0.00 0.00 0.00 1.40
4049 5428 9.297586 CGTTTACTAGTATATGCAAGAAGTTGA 57.702 33.333 2.79 0.00 35.46 3.18
4053 5432 7.222031 TGCACGTTTACTAGTATATGCAAGAAG 59.778 37.037 20.03 4.96 38.78 2.85
4056 5435 6.559703 CGTGCACGTTTACTAGTATATGCAAG 60.560 42.308 30.50 20.75 42.92 4.01
4089 5468 9.070149 GGAAATATATCGTCTGGTTTATACGTC 57.930 37.037 0.00 0.00 37.83 4.34
4100 5481 8.256605 AGGATGAATGAGGAAATATATCGTCTG 58.743 37.037 0.00 0.00 35.71 3.51
4101 5482 8.372877 AGGATGAATGAGGAAATATATCGTCT 57.627 34.615 0.00 0.00 35.71 4.18
4102 5483 9.743057 CTAGGATGAATGAGGAAATATATCGTC 57.257 37.037 0.00 0.00 35.36 4.20
4103 5484 9.261035 ACTAGGATGAATGAGGAAATATATCGT 57.739 33.333 0.00 0.00 0.00 3.73
4251 5644 6.427853 AGAGACATGAACATTCATCGTTTCAA 59.572 34.615 18.61 0.00 45.62 2.69
4287 5680 5.487488 AGGGAGTTGTCCAGTTTCATGTATA 59.513 40.000 0.00 0.00 46.07 1.47
4331 5724 9.834628 TTTAATGACTTTGAAATTTACGCCTAG 57.165 29.630 0.00 0.00 0.00 3.02
4394 5790 4.246458 GGAGTTGCGAGTTCTATGAAACT 58.754 43.478 0.00 0.00 42.10 2.66
4395 5791 3.371285 GGGAGTTGCGAGTTCTATGAAAC 59.629 47.826 0.00 0.00 0.00 2.78
4409 5805 9.000486 GTAATTCCATATTAGTTAGGGAGTTGC 58.000 37.037 4.86 0.82 41.57 4.17
4485 5881 9.216117 TCTAAAAATTAAGGTGCTCACTAGAAC 57.784 33.333 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.