Multiple sequence alignment - TraesCS6B01G295100

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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 TraesCS6B01G295100 chr6B 100.000 3952 0 0 1 3952 529888541 529892492 0.000000e+00 7299.0
1 TraesCS6B01G295100 chr6B 96.821 1667 50 3 1321 2985 530852208 530850543 0.000000e+00 2782.0
2 TraesCS6B01G295100 chr6B 95.212 1671 78 2 1318 2988 529774032 529775700 0.000000e+00 2641.0
3 TraesCS6B01G295100 chr6B 81.975 1620 236 35 1356 2953 52086465 52088050 0.000000e+00 1323.0
4 TraesCS6B01G295100 chr6B 97.951 244 5 0 191 434 12675688 12675931 1.310000e-114 424.0
5 TraesCS6B01G295100 chr6B 95.565 248 7 1 191 434 529883434 529883681 1.030000e-105 394.0
6 TraesCS6B01G295100 chr6B 94.186 172 10 0 3072 3243 636490647 636490818 3.030000e-66 263.0
7 TraesCS6B01G295100 chr6B 90.526 190 18 0 3061 3250 694262867 694263056 6.560000e-63 252.0
8 TraesCS6B01G295100 chr6B 96.460 113 4 0 191 303 529882865 529882977 1.880000e-43 187.0
9 TraesCS6B01G295100 chr6B 96.078 51 2 0 3244 3294 529775774 529775824 2.530000e-12 84.2
10 TraesCS6B01G295100 chr6B 97.674 43 1 0 798 840 529773279 529773321 1.520000e-09 75.0
11 TraesCS6B01G295100 chr6A 96.579 1783 54 4 1293 3071 494046956 494048735 0.000000e+00 2948.0
12 TraesCS6B01G295100 chr6A 97.032 1752 43 3 1321 3071 495154091 495152348 0.000000e+00 2939.0
13 TraesCS6B01G295100 chr6A 95.377 1709 72 6 1301 3004 493842453 493844159 0.000000e+00 2712.0
14 TraesCS6B01G295100 chr6A 95.033 1671 79 2 1318 2988 493756294 493757960 0.000000e+00 2623.0
15 TraesCS6B01G295100 chr6A 86.013 765 46 25 443 1197 494046173 494046886 0.000000e+00 763.0
16 TraesCS6B01G295100 chr6A 86.556 543 32 24 501 1040 493841820 493842324 9.590000e-156 560.0
17 TraesCS6B01G295100 chr6A 87.500 368 41 4 3293 3658 493845620 493845984 1.700000e-113 420.0
18 TraesCS6B01G295100 chr6A 86.721 369 40 6 3293 3658 493830929 493831291 6.150000e-108 401.0
19 TraesCS6B01G295100 chr6A 82.337 368 44 13 3306 3659 494048768 494049128 2.310000e-77 300.0
20 TraesCS6B01G295100 chr6A 93.902 82 4 1 3393 3473 494048893 494048974 5.360000e-24 122.0
21 TraesCS6B01G295100 chr6D 97.057 1665 48 1 1318 2982 349031407 349033070 0.000000e+00 2802.0
22 TraesCS6B01G295100 chr6D 96.611 1682 53 3 1321 3002 348861347 348863024 0.000000e+00 2787.0
23 TraesCS6B01G295100 chr6D 95.004 1341 65 2 1648 2988 350204789 350203451 0.000000e+00 2104.0
24 TraesCS6B01G295100 chr6D 89.309 767 35 23 443 1197 350084783 350084052 0.000000e+00 918.0
25 TraesCS6B01G295100 chr6D 88.340 729 54 15 3243 3949 350062872 350062153 0.000000e+00 846.0
26 TraesCS6B01G295100 chr6D 83.557 596 40 28 443 1027 349172667 349173215 4.560000e-139 505.0
27 TraesCS6B01G295100 chr6D 83.896 385 34 10 3293 3658 350136808 350136433 3.780000e-90 342.0
28 TraesCS6B01G295100 chr6D 79.715 281 38 12 3663 3927 467194753 467194476 6.740000e-43 185.0
29 TraesCS6B01G295100 chr6D 78.571 224 26 15 843 1050 349030635 349030852 1.150000e-25 128.0
30 TraesCS6B01G295100 chr6D 96.078 51 2 0 3244 3294 350203377 350203327 2.530000e-12 84.2
31 TraesCS6B01G295100 chr3B 95.812 382 15 1 52 433 44229543 44229163 2.020000e-172 616.0
32 TraesCS6B01G295100 chr3B 97.531 243 6 0 191 433 44234395 44234153 2.200000e-112 416.0
33 TraesCS6B01G295100 chr3B 97.768 224 5 0 191 414 750330684 750330907 1.720000e-103 387.0
34 TraesCS6B01G295100 chr3B 91.099 191 17 0 3059 3249 15974177 15973987 3.920000e-65 259.0
35 TraesCS6B01G295100 chr3B 90.576 191 15 3 3062 3251 809026650 809026838 2.360000e-62 250.0
36 TraesCS6B01G295100 chr3B 96.226 53 2 0 1 53 44229624 44229572 1.960000e-13 87.9
37 TraesCS6B01G295100 chr4D 94.256 383 19 3 52 433 397376539 397376919 2.050000e-162 582.0
38 TraesCS6B01G295100 chr4D 94.787 211 8 3 191 400 397369759 397369967 3.810000e-85 326.0
39 TraesCS6B01G295100 chr4D 84.752 282 26 6 3663 3927 21890203 21890484 2.340000e-67 267.0
40 TraesCS6B01G295100 chr2D 92.765 387 24 4 52 436 272136966 272137350 1.240000e-154 556.0
41 TraesCS6B01G295100 chr2D 93.033 244 14 3 191 433 272123758 272123999 1.750000e-93 353.0
42 TraesCS6B01G295100 chr2D 83.032 277 34 10 3663 3927 567787466 567787741 5.100000e-59 239.0
43 TraesCS6B01G295100 chr2D 82.745 255 21 13 3663 3895 17008988 17009241 5.180000e-49 206.0
44 TraesCS6B01G295100 chr7B 96.633 297 8 2 52 348 176210743 176210449 3.550000e-135 492.0
45 TraesCS6B01G295100 chr7B 96.930 228 6 1 191 418 176215995 176215769 8.010000e-102 381.0
46 TraesCS6B01G295100 chr7B 92.350 183 13 1 3065 3247 662001633 662001452 3.920000e-65 259.0
47 TraesCS6B01G295100 chr7B 90.000 200 15 4 3062 3257 716683387 716683189 1.820000e-63 254.0
48 TraesCS6B01G295100 chr7B 82.746 284 30 11 3663 3927 2080025 2080308 6.600000e-58 235.0
49 TraesCS6B01G295100 chr7B 98.969 97 1 0 340 436 176210181 176210085 1.460000e-39 174.0
50 TraesCS6B01G295100 chr7B 100.000 53 0 0 1 53 176210824 176210772 9.040000e-17 99.0
51 TraesCS6B01G295100 chr4A 93.714 175 11 0 3072 3246 672816726 672816900 3.030000e-66 263.0
52 TraesCS6B01G295100 chr4A 81.949 277 35 12 3663 3927 724132047 724132320 1.850000e-53 220.0
53 TraesCS6B01G295100 chr1B 91.351 185 16 0 3063 3247 198484693 198484877 1.820000e-63 254.0
54 TraesCS6B01G295100 chr4B 89.109 202 20 2 3061 3260 123497929 123497728 2.360000e-62 250.0
55 TraesCS6B01G295100 chr7A 82.578 287 30 11 3661 3927 406102062 406102348 6.600000e-58 235.0
56 TraesCS6B01G295100 chr5A 82.807 285 27 10 3663 3927 170855299 170855581 6.600000e-58 235.0
57 TraesCS6B01G295100 chr2B 82.734 278 35 9 3663 3927 550830247 550829970 6.600000e-58 235.0
58 TraesCS6B01G295100 chr5B 79.863 293 39 13 3651 3927 621298933 621298645 3.120000e-46 196.0
59 TraesCS6B01G295100 chr3D 84.865 185 17 5 3754 3927 595863461 595863277 4.060000e-40 176.0
60 TraesCS6B01G295100 chr3D 83.708 178 11 7 3663 3822 130020617 130020440 6.840000e-33 152.0
61 TraesCS6B01G295100 chr1D 100.000 29 0 0 1077 1105 265745311 265745283 2.000000e-03 54.7


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 TraesCS6B01G295100 chr6B 529888541 529892492 3951 False 7299.000000 7299 100.000000 1 3952 1 chr6B.!!$F3 3951
1 TraesCS6B01G295100 chr6B 530850543 530852208 1665 True 2782.000000 2782 96.821000 1321 2985 1 chr6B.!!$R1 1664
2 TraesCS6B01G295100 chr6B 52086465 52088050 1585 False 1323.000000 1323 81.975000 1356 2953 1 chr6B.!!$F2 1597
3 TraesCS6B01G295100 chr6B 529773279 529775824 2545 False 933.400000 2641 96.321333 798 3294 3 chr6B.!!$F6 2496
4 TraesCS6B01G295100 chr6B 529882865 529883681 816 False 290.500000 394 96.012500 191 434 2 chr6B.!!$F7 243
5 TraesCS6B01G295100 chr6A 495152348 495154091 1743 True 2939.000000 2939 97.032000 1321 3071 1 chr6A.!!$R1 1750
6 TraesCS6B01G295100 chr6A 493756294 493757960 1666 False 2623.000000 2623 95.033000 1318 2988 1 chr6A.!!$F1 1670
7 TraesCS6B01G295100 chr6A 493841820 493845984 4164 False 1230.666667 2712 89.811000 501 3658 3 chr6A.!!$F3 3157
8 TraesCS6B01G295100 chr6A 494046173 494049128 2955 False 1033.250000 2948 89.707750 443 3659 4 chr6A.!!$F4 3216
9 TraesCS6B01G295100 chr6D 348861347 348863024 1677 False 2787.000000 2787 96.611000 1321 3002 1 chr6D.!!$F1 1681
10 TraesCS6B01G295100 chr6D 349030635 349033070 2435 False 1465.000000 2802 87.814000 843 2982 2 chr6D.!!$F3 2139
11 TraesCS6B01G295100 chr6D 350203327 350204789 1462 True 1094.100000 2104 95.541000 1648 3294 2 chr6D.!!$R5 1646
12 TraesCS6B01G295100 chr6D 350084052 350084783 731 True 918.000000 918 89.309000 443 1197 1 chr6D.!!$R2 754
13 TraesCS6B01G295100 chr6D 350062153 350062872 719 True 846.000000 846 88.340000 3243 3949 1 chr6D.!!$R1 706
14 TraesCS6B01G295100 chr6D 349172667 349173215 548 False 505.000000 505 83.557000 443 1027 1 chr6D.!!$F2 584
15 TraesCS6B01G295100 chr7B 176210085 176210824 739 True 255.000000 492 98.534000 1 436 3 chr7B.!!$R4 435

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
878 1548 0.040336 CAGCAGAACACAGCAGCAAG 60.040 55.0 0.00 0.00 0.0 4.01 F
1086 1809 0.105964 CTCCCTCCGATCTTCCTCCA 60.106 60.0 0.00 0.00 0.0 3.86 F
1277 2391 0.524816 CGATGAAATGCCAGCAGTGC 60.525 55.0 7.13 7.13 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 3355 1.202330 CTTGAGCTCCTCCACCTGAT 58.798 55.000 12.15 0.0 0.00 2.90 R
2900 4034 1.445410 GACGATGCCGCTGTACACA 60.445 57.895 0.00 0.0 39.95 3.72 R
3144 4295 0.592637 ATGTGTGTGCGTTGACATGG 59.407 50.000 0.00 0.0 0.00 3.66 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
215 595 5.306532 TGAGTACTGTAAATCTCACCGTC 57.693 43.478 0.00 0.00 32.95 4.79
259 639 8.952278 CAAGGGCTATAAGTACACATTTACAAA 58.048 33.333 0.00 0.00 0.00 2.83
376 1035 0.445436 CGTGTAGTTAGACGCCGAGT 59.555 55.000 0.00 0.00 36.20 4.18
436 1095 2.752354 CGTGGGCATATTCCAACAAGAA 59.248 45.455 0.00 0.00 35.86 2.52
437 1096 3.427503 CGTGGGCATATTCCAACAAGAAC 60.428 47.826 0.00 0.00 35.86 3.01
438 1097 3.509575 GTGGGCATATTCCAACAAGAACA 59.490 43.478 0.00 0.00 35.86 3.18
439 1098 4.021544 GTGGGCATATTCCAACAAGAACAA 60.022 41.667 0.00 0.00 35.86 2.83
440 1099 4.021544 TGGGCATATTCCAACAAGAACAAC 60.022 41.667 0.00 0.00 0.00 3.32
441 1100 4.220602 GGGCATATTCCAACAAGAACAACT 59.779 41.667 0.00 0.00 0.00 3.16
478 1138 3.537388 GCCTCTGCTCCTCTCCTC 58.463 66.667 0.00 0.00 33.53 3.71
479 1139 1.076044 GCCTCTGCTCCTCTCCTCT 60.076 63.158 0.00 0.00 33.53 3.69
493 1153 2.662596 CTCTTGGCACCTACCGCA 59.337 61.111 0.00 0.00 0.00 5.69
534 1203 2.758423 ACTCTTTTCCAACGCCAAGTTT 59.242 40.909 0.00 0.00 42.02 2.66
535 1204 3.194755 ACTCTTTTCCAACGCCAAGTTTT 59.805 39.130 0.00 0.00 42.02 2.43
589 1258 2.288458 GCAAAGCAAACTACCACGTGTA 59.712 45.455 15.65 6.27 0.00 2.90
724 1393 1.908066 GCTGCGTCGAAATTTCCGGT 61.908 55.000 12.54 0.00 0.00 5.28
756 1425 1.482593 GTGGACTAGTATGCACAGGCT 59.517 52.381 0.00 0.00 40.41 4.58
840 1509 8.548721 CGTCCAAGTTAAACCTGCTATATAAAG 58.451 37.037 0.00 0.00 0.00 1.85
841 1510 9.392259 GTCCAAGTTAAACCTGCTATATAAAGT 57.608 33.333 0.00 0.00 0.00 2.66
852 1521 9.924650 ACCTGCTATATAAAGTTATAAACCTCG 57.075 33.333 0.00 0.00 0.00 4.63
853 1522 9.924650 CCTGCTATATAAAGTTATAAACCTCGT 57.075 33.333 0.00 0.00 0.00 4.18
874 1544 2.554775 CGCAGCAGAACACAGCAG 59.445 61.111 0.00 0.00 0.00 4.24
875 1545 2.254651 GCAGCAGAACACAGCAGC 59.745 61.111 0.00 0.00 36.15 5.25
876 1546 2.549198 GCAGCAGAACACAGCAGCA 61.549 57.895 0.00 0.00 42.04 4.41
877 1547 2.027325 CAGCAGAACACAGCAGCAA 58.973 52.632 0.00 0.00 0.00 3.91
878 1548 0.040336 CAGCAGAACACAGCAGCAAG 60.040 55.000 0.00 0.00 0.00 4.01
879 1549 1.371389 GCAGAACACAGCAGCAAGC 60.371 57.895 0.00 0.00 46.19 4.01
902 1591 3.756727 GAGCAGCAGCCAAAGCCC 61.757 66.667 0.00 0.00 43.56 5.19
935 1624 6.287525 CAAAGAAAGAGTTCAGAGAGGAAGT 58.712 40.000 0.00 0.00 36.09 3.01
965 1660 7.883492 AGCCTAGCTAGGTGATTCCTTCACT 62.883 48.000 34.85 18.89 45.15 3.41
973 1676 0.620556 GATTCCTTCACTGGCCTCCA 59.379 55.000 3.32 0.00 0.00 3.86
1084 1807 1.468506 GCCTCCCTCCGATCTTCCTC 61.469 65.000 0.00 0.00 0.00 3.71
1085 1808 0.830023 CCTCCCTCCGATCTTCCTCC 60.830 65.000 0.00 0.00 0.00 4.30
1086 1809 0.105964 CTCCCTCCGATCTTCCTCCA 60.106 60.000 0.00 0.00 0.00 3.86
1222 2336 4.503741 TGTAAGCAAAGCTCAATGTTCC 57.496 40.909 0.00 0.00 38.25 3.62
1237 2351 5.013495 TCAATGTTCCTCTCATTGTCCTTCT 59.987 40.000 15.09 0.00 46.76 2.85
1238 2352 4.982241 TGTTCCTCTCATTGTCCTTCTT 57.018 40.909 0.00 0.00 0.00 2.52
1239 2353 4.899502 TGTTCCTCTCATTGTCCTTCTTC 58.100 43.478 0.00 0.00 0.00 2.87
1242 2356 5.413309 TCCTCTCATTGTCCTTCTTCTTC 57.587 43.478 0.00 0.00 0.00 2.87
1243 2357 5.090139 TCCTCTCATTGTCCTTCTTCTTCT 58.910 41.667 0.00 0.00 0.00 2.85
1244 2358 5.186797 TCCTCTCATTGTCCTTCTTCTTCTC 59.813 44.000 0.00 0.00 0.00 2.87
1245 2359 5.187576 CCTCTCATTGTCCTTCTTCTTCTCT 59.812 44.000 0.00 0.00 0.00 3.10
1248 2362 8.372877 TCTCATTGTCCTTCTTCTTCTCTATT 57.627 34.615 0.00 0.00 0.00 1.73
1249 2363 8.474025 TCTCATTGTCCTTCTTCTTCTCTATTC 58.526 37.037 0.00 0.00 0.00 1.75
1250 2364 8.372877 TCATTGTCCTTCTTCTTCTCTATTCT 57.627 34.615 0.00 0.00 0.00 2.40
1251 2365 8.256605 TCATTGTCCTTCTTCTTCTCTATTCTG 58.743 37.037 0.00 0.00 0.00 3.02
1252 2366 5.971763 TGTCCTTCTTCTTCTCTATTCTGC 58.028 41.667 0.00 0.00 0.00 4.26
1253 2367 5.719085 TGTCCTTCTTCTTCTCTATTCTGCT 59.281 40.000 0.00 0.00 0.00 4.24
1254 2368 6.892456 TGTCCTTCTTCTTCTCTATTCTGCTA 59.108 38.462 0.00 0.00 0.00 3.49
1255 2369 7.563188 TGTCCTTCTTCTTCTCTATTCTGCTAT 59.437 37.037 0.00 0.00 0.00 2.97
1256 2370 9.073475 GTCCTTCTTCTTCTCTATTCTGCTATA 57.927 37.037 0.00 0.00 0.00 1.31
1257 2371 9.821240 TCCTTCTTCTTCTCTATTCTGCTATAT 57.179 33.333 0.00 0.00 0.00 0.86
1259 2373 9.773328 CTTCTTCTTCTCTATTCTGCTATATCG 57.227 37.037 0.00 0.00 0.00 2.92
1261 2375 9.679661 TCTTCTTCTCTATTCTGCTATATCGAT 57.320 33.333 2.16 2.16 0.00 3.59
1262 2376 9.720667 CTTCTTCTCTATTCTGCTATATCGATG 57.279 37.037 8.54 0.00 0.00 3.84
1263 2377 9.454859 TTCTTCTCTATTCTGCTATATCGATGA 57.545 33.333 8.54 0.00 0.00 2.92
1264 2378 9.454859 TCTTCTCTATTCTGCTATATCGATGAA 57.545 33.333 8.54 1.91 0.00 2.57
1268 2382 8.640091 TCTATTCTGCTATATCGATGAAATGC 57.360 34.615 8.54 6.02 0.00 3.56
1269 2383 6.674694 ATTCTGCTATATCGATGAAATGCC 57.325 37.500 8.54 0.00 0.00 4.40
1270 2384 5.151297 TCTGCTATATCGATGAAATGCCA 57.849 39.130 8.54 0.00 0.00 4.92
1271 2385 5.173664 TCTGCTATATCGATGAAATGCCAG 58.826 41.667 8.54 5.66 0.00 4.85
1272 2386 3.686241 TGCTATATCGATGAAATGCCAGC 59.314 43.478 8.54 0.89 0.00 4.85
1273 2387 3.686241 GCTATATCGATGAAATGCCAGCA 59.314 43.478 8.54 0.00 0.00 4.41
1274 2388 4.201792 GCTATATCGATGAAATGCCAGCAG 60.202 45.833 8.54 0.00 0.00 4.24
1275 2389 2.048444 ATCGATGAAATGCCAGCAGT 57.952 45.000 0.00 0.00 0.00 4.40
1276 2390 1.089112 TCGATGAAATGCCAGCAGTG 58.911 50.000 0.00 0.00 0.00 3.66
1277 2391 0.524816 CGATGAAATGCCAGCAGTGC 60.525 55.000 7.13 7.13 0.00 4.40
1278 2392 0.815734 GATGAAATGCCAGCAGTGCT 59.184 50.000 13.14 13.14 40.77 4.40
1289 2403 2.574006 AGCAGTGCTGGATCTTTCAA 57.426 45.000 18.98 0.00 37.57 2.69
1290 2404 2.867624 AGCAGTGCTGGATCTTTCAAA 58.132 42.857 18.98 0.00 37.57 2.69
1291 2405 3.225104 AGCAGTGCTGGATCTTTCAAAA 58.775 40.909 18.98 0.00 37.57 2.44
1292 2406 3.638160 AGCAGTGCTGGATCTTTCAAAAA 59.362 39.130 18.98 0.00 37.57 1.94
1293 2407 4.282703 AGCAGTGCTGGATCTTTCAAAAAT 59.717 37.500 18.98 0.00 37.57 1.82
1294 2408 4.992951 GCAGTGCTGGATCTTTCAAAAATT 59.007 37.500 8.18 0.00 0.00 1.82
1295 2409 5.107220 GCAGTGCTGGATCTTTCAAAAATTG 60.107 40.000 8.18 0.00 0.00 2.32
1296 2410 5.987347 CAGTGCTGGATCTTTCAAAAATTGT 59.013 36.000 0.00 0.00 0.00 2.71
1297 2411 6.145048 CAGTGCTGGATCTTTCAAAAATTGTC 59.855 38.462 0.00 0.00 0.00 3.18
1298 2412 6.041296 AGTGCTGGATCTTTCAAAAATTGTCT 59.959 34.615 0.00 0.00 0.00 3.41
1299 2413 6.703165 GTGCTGGATCTTTCAAAAATTGTCTT 59.297 34.615 0.00 0.00 0.00 3.01
1300 2414 7.225341 GTGCTGGATCTTTCAAAAATTGTCTTT 59.775 33.333 0.00 0.00 0.00 2.52
1301 2415 7.439056 TGCTGGATCTTTCAAAAATTGTCTTTC 59.561 33.333 0.00 0.00 0.00 2.62
2230 3355 1.891919 GGAAGCTGTGCACCGTGAA 60.892 57.895 15.69 0.00 0.00 3.18
2609 3743 1.688735 CGTGGGGAAGAGATCAGCATA 59.311 52.381 0.00 0.00 0.00 3.14
2669 3803 1.135139 GAGGTCTTCTGCTACATCGCA 59.865 52.381 0.00 0.00 38.40 5.10
2900 4034 1.087202 TGTGCACGCTCAACTTCGTT 61.087 50.000 13.13 0.00 36.73 3.85
2947 4081 1.066573 CAGGCTCAAGACGGTCATCTT 60.067 52.381 11.27 0.00 39.60 2.40
2988 4132 6.973460 ATCTTCAAGATTCCATTCCATTCC 57.027 37.500 0.00 0.00 28.69 3.01
2989 4133 5.829986 TCTTCAAGATTCCATTCCATTCCA 58.170 37.500 0.00 0.00 0.00 3.53
2990 4134 6.437755 TCTTCAAGATTCCATTCCATTCCAT 58.562 36.000 0.00 0.00 0.00 3.41
3046 4197 6.920758 GTGATGGATGAACAGTAACTAGCTAG 59.079 42.308 19.44 19.44 0.00 3.42
3047 4198 6.607600 TGATGGATGAACAGTAACTAGCTAGT 59.392 38.462 20.95 20.95 38.39 2.57
3048 4199 7.778382 TGATGGATGAACAGTAACTAGCTAGTA 59.222 37.037 26.29 12.08 34.99 1.82
3068 4219 9.054922 GCTAGTAGTAGCCAGGTACATATATAC 57.945 40.741 17.43 3.33 45.37 1.47
3070 4221 8.804912 AGTAGTAGCCAGGTACATATATACAC 57.195 38.462 9.48 0.00 0.00 2.90
3071 4222 6.754702 AGTAGCCAGGTACATATATACACG 57.245 41.667 9.48 0.00 0.00 4.49
3072 4223 5.651139 AGTAGCCAGGTACATATATACACGG 59.349 44.000 9.48 0.00 0.00 4.94
3073 4224 3.767673 AGCCAGGTACATATATACACGGG 59.232 47.826 0.00 0.00 0.00 5.28
3074 4225 3.765511 GCCAGGTACATATATACACGGGA 59.234 47.826 0.00 0.00 0.00 5.14
3075 4226 4.142227 GCCAGGTACATATATACACGGGAG 60.142 50.000 0.00 0.00 0.00 4.30
3077 4228 6.182627 CCAGGTACATATATACACGGGAGTA 58.817 44.000 0.00 0.00 44.67 2.59
3078 4229 6.094603 CCAGGTACATATATACACGGGAGTAC 59.905 46.154 0.00 0.00 44.67 2.73
3079 4230 6.094603 CAGGTACATATATACACGGGAGTACC 59.905 46.154 13.21 13.21 46.50 3.34
3080 4231 6.183347 GGTACATATATACACGGGAGTACCT 58.817 44.000 13.58 0.00 44.12 3.08
3081 4232 7.338710 GGTACATATATACACGGGAGTACCTA 58.661 42.308 13.58 0.00 44.12 3.08
3082 4233 7.829211 GGTACATATATACACGGGAGTACCTAA 59.171 40.741 13.58 0.00 44.12 2.69
3083 4234 9.231297 GTACATATATACACGGGAGTACCTAAA 57.769 37.037 0.00 0.00 44.67 1.85
3084 4235 8.710749 ACATATATACACGGGAGTACCTAAAA 57.289 34.615 0.00 0.00 44.67 1.52
3085 4236 8.579863 ACATATATACACGGGAGTACCTAAAAC 58.420 37.037 0.00 0.00 44.67 2.43
3086 4237 8.800332 CATATATACACGGGAGTACCTAAAACT 58.200 37.037 0.00 0.00 44.67 2.66
3087 4238 3.949842 ACACGGGAGTACCTAAAACTC 57.050 47.619 0.00 0.00 44.67 3.01
3088 4239 3.233507 ACACGGGAGTACCTAAAACTCA 58.766 45.455 0.00 0.00 44.25 3.41
3089 4240 3.836562 ACACGGGAGTACCTAAAACTCAT 59.163 43.478 0.00 0.00 44.25 2.90
3090 4241 4.081807 ACACGGGAGTACCTAAAACTCATC 60.082 45.833 0.00 0.00 44.25 2.92
3091 4242 4.159879 CACGGGAGTACCTAAAACTCATCT 59.840 45.833 5.67 0.00 44.25 2.90
3092 4243 5.359009 CACGGGAGTACCTAAAACTCATCTA 59.641 44.000 5.67 0.00 44.25 1.98
3093 4244 5.593502 ACGGGAGTACCTAAAACTCATCTAG 59.406 44.000 5.67 0.00 44.25 2.43
3094 4245 5.826737 CGGGAGTACCTAAAACTCATCTAGA 59.173 44.000 0.00 0.00 44.25 2.43
3095 4246 6.490721 CGGGAGTACCTAAAACTCATCTAGAT 59.509 42.308 0.00 0.00 44.25 1.98
3096 4247 7.522399 CGGGAGTACCTAAAACTCATCTAGATG 60.522 44.444 24.32 24.32 44.25 2.90
3097 4248 7.506261 GGGAGTACCTAAAACTCATCTAGATGA 59.494 40.741 29.17 29.17 44.25 2.92
3154 4305 6.677781 AAACAGATATAACCCATGTCAACG 57.322 37.500 0.00 0.00 0.00 4.10
3155 4306 4.127171 ACAGATATAACCCATGTCAACGC 58.873 43.478 0.00 0.00 0.00 4.84
3156 4307 4.126437 CAGATATAACCCATGTCAACGCA 58.874 43.478 0.00 0.00 0.00 5.24
3157 4308 4.024893 CAGATATAACCCATGTCAACGCAC 60.025 45.833 0.00 0.00 0.00 5.34
3158 4309 2.192664 ATAACCCATGTCAACGCACA 57.807 45.000 0.00 0.00 0.00 4.57
3159 4310 1.231221 TAACCCATGTCAACGCACAC 58.769 50.000 0.00 0.00 0.00 3.82
3160 4311 0.749818 AACCCATGTCAACGCACACA 60.750 50.000 0.00 0.00 0.00 3.72
3161 4312 1.282570 CCCATGTCAACGCACACAC 59.717 57.895 0.00 0.00 0.00 3.82
3162 4313 1.443322 CCCATGTCAACGCACACACA 61.443 55.000 0.00 0.00 0.00 3.72
3163 4314 0.592637 CCATGTCAACGCACACACAT 59.407 50.000 0.00 0.00 0.00 3.21
3164 4315 1.400113 CCATGTCAACGCACACACATC 60.400 52.381 0.00 0.00 0.00 3.06
3165 4316 1.532437 CATGTCAACGCACACACATCT 59.468 47.619 0.00 0.00 0.00 2.90
3166 4317 1.662517 TGTCAACGCACACACATCTT 58.337 45.000 0.00 0.00 0.00 2.40
3167 4318 2.827652 TGTCAACGCACACACATCTTA 58.172 42.857 0.00 0.00 0.00 2.10
3168 4319 3.398406 TGTCAACGCACACACATCTTAT 58.602 40.909 0.00 0.00 0.00 1.73
3169 4320 4.561105 TGTCAACGCACACACATCTTATA 58.439 39.130 0.00 0.00 0.00 0.98
3170 4321 4.625311 TGTCAACGCACACACATCTTATAG 59.375 41.667 0.00 0.00 0.00 1.31
3171 4322 3.616821 TCAACGCACACACATCTTATAGC 59.383 43.478 0.00 0.00 0.00 2.97
3172 4323 3.245518 ACGCACACACATCTTATAGCA 57.754 42.857 0.00 0.00 0.00 3.49
3173 4324 3.797039 ACGCACACACATCTTATAGCAT 58.203 40.909 0.00 0.00 0.00 3.79
3174 4325 3.804325 ACGCACACACATCTTATAGCATC 59.196 43.478 0.00 0.00 0.00 3.91
3175 4326 3.803778 CGCACACACATCTTATAGCATCA 59.196 43.478 0.00 0.00 0.00 3.07
3176 4327 4.450080 CGCACACACATCTTATAGCATCAT 59.550 41.667 0.00 0.00 0.00 2.45
3177 4328 5.634859 CGCACACACATCTTATAGCATCATA 59.365 40.000 0.00 0.00 0.00 2.15
3178 4329 6.312180 CGCACACACATCTTATAGCATCATAT 59.688 38.462 0.00 0.00 0.00 1.78
3179 4330 7.148523 CGCACACACATCTTATAGCATCATATT 60.149 37.037 0.00 0.00 0.00 1.28
3180 4331 8.173775 GCACACACATCTTATAGCATCATATTC 58.826 37.037 0.00 0.00 0.00 1.75
3181 4332 9.211485 CACACACATCTTATAGCATCATATTCA 57.789 33.333 0.00 0.00 0.00 2.57
3182 4333 9.783081 ACACACATCTTATAGCATCATATTCAA 57.217 29.630 0.00 0.00 0.00 2.69
3186 4337 8.900781 ACATCTTATAGCATCATATTCAATGGC 58.099 33.333 0.00 0.00 0.00 4.40
3187 4338 9.121658 CATCTTATAGCATCATATTCAATGGCT 57.878 33.333 0.00 0.00 0.00 4.75
3195 4346 8.746530 AGCATCATATTCAATGGCTATAAAAGG 58.253 33.333 0.00 0.00 0.00 3.11
3196 4347 8.526147 GCATCATATTCAATGGCTATAAAAGGT 58.474 33.333 0.00 0.00 0.00 3.50
3197 4348 9.850628 CATCATATTCAATGGCTATAAAAGGTG 57.149 33.333 0.00 0.00 0.00 4.00
3198 4349 9.812347 ATCATATTCAATGGCTATAAAAGGTGA 57.188 29.630 0.00 0.00 0.00 4.02
3199 4350 9.639563 TCATATTCAATGGCTATAAAAGGTGAA 57.360 29.630 0.00 0.00 0.00 3.18
3202 4353 7.953005 TTCAATGGCTATAAAAGGTGAATGA 57.047 32.000 0.00 0.00 0.00 2.57
3203 4354 7.572523 TCAATGGCTATAAAAGGTGAATGAG 57.427 36.000 0.00 0.00 0.00 2.90
3204 4355 7.345691 TCAATGGCTATAAAAGGTGAATGAGA 58.654 34.615 0.00 0.00 0.00 3.27
3205 4356 7.283127 TCAATGGCTATAAAAGGTGAATGAGAC 59.717 37.037 0.00 0.00 0.00 3.36
3206 4357 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
3207 4358 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
3208 4359 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
3209 4360 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
3210 4361 7.068716 GGCTATAAAAGGTGAATGAGACCAAAT 59.931 37.037 0.00 0.00 35.76 2.32
3211 4362 8.470002 GCTATAAAAGGTGAATGAGACCAAATT 58.530 33.333 0.00 0.00 35.76 1.82
3219 4370 9.699410 AGGTGAATGAGACCAAATTATATTTCA 57.301 29.630 0.00 0.00 35.76 2.69
3394 5896 6.927381 TCCGCCCGTTTTTAAATTAAATGAAA 59.073 30.769 0.00 0.00 0.00 2.69
3473 6042 2.413310 AATGATAAGGGCCGAACGTT 57.587 45.000 0.00 0.00 0.00 3.99
3474 6043 3.547054 AATGATAAGGGCCGAACGTTA 57.453 42.857 0.00 0.00 0.00 3.18
3475 6044 2.589798 TGATAAGGGCCGAACGTTAG 57.410 50.000 0.00 0.00 0.00 2.34
3476 6045 1.137479 TGATAAGGGCCGAACGTTAGG 59.863 52.381 21.73 21.73 0.00 2.69
3477 6046 1.410153 GATAAGGGCCGAACGTTAGGA 59.590 52.381 28.90 9.72 0.00 2.94
3478 6047 1.265236 TAAGGGCCGAACGTTAGGAA 58.735 50.000 28.90 7.11 0.00 3.36
3479 6048 0.616891 AAGGGCCGAACGTTAGGAAT 59.383 50.000 28.90 11.85 0.00 3.01
3480 6049 0.616891 AGGGCCGAACGTTAGGAATT 59.383 50.000 28.90 11.16 0.00 2.17
3481 6050 1.003928 AGGGCCGAACGTTAGGAATTT 59.996 47.619 28.90 9.50 0.00 1.82
3482 6051 1.814394 GGGCCGAACGTTAGGAATTTT 59.186 47.619 28.90 0.00 0.00 1.82
3483 6052 2.414957 GGGCCGAACGTTAGGAATTTTG 60.415 50.000 28.90 3.16 0.00 2.44
3484 6053 2.227149 GGCCGAACGTTAGGAATTTTGT 59.773 45.455 28.90 0.00 0.00 2.83
3485 6054 3.304861 GGCCGAACGTTAGGAATTTTGTT 60.305 43.478 28.90 0.00 0.00 2.83
3486 6055 3.666797 GCCGAACGTTAGGAATTTTGTTG 59.333 43.478 28.90 1.06 0.00 3.33
3487 6056 4.790444 GCCGAACGTTAGGAATTTTGTTGT 60.790 41.667 28.90 0.00 0.00 3.32
3488 6057 5.275494 CCGAACGTTAGGAATTTTGTTGTT 58.725 37.500 21.55 0.00 0.00 2.83
3489 6058 5.397240 CCGAACGTTAGGAATTTTGTTGTTC 59.603 40.000 21.55 0.00 0.00 3.18
3490 6059 5.112937 CGAACGTTAGGAATTTTGTTGTTCG 59.887 40.000 0.00 8.90 46.31 3.95
3491 6060 4.851010 ACGTTAGGAATTTTGTTGTTCGG 58.149 39.130 0.00 0.00 0.00 4.30
3492 6061 3.666797 CGTTAGGAATTTTGTTGTTCGGC 59.333 43.478 0.00 0.00 0.00 5.54
3493 6062 2.812358 AGGAATTTTGTTGTTCGGCC 57.188 45.000 0.00 0.00 0.00 6.13
3494 6063 1.343142 AGGAATTTTGTTGTTCGGCCC 59.657 47.619 0.00 0.00 0.00 5.80
3495 6064 1.414378 GAATTTTGTTGTTCGGCCCG 58.586 50.000 0.00 0.00 0.00 6.13
3496 6065 1.001158 GAATTTTGTTGTTCGGCCCGA 60.001 47.619 0.00 0.00 0.00 5.14
3497 6066 1.033574 ATTTTGTTGTTCGGCCCGAA 58.966 45.000 15.93 15.93 43.75 4.30
3659 6228 7.139392 TCTATCTTATCCATTTTCACTCGTCG 58.861 38.462 0.00 0.00 0.00 5.12
3692 6262 0.731514 TAGTACACACGCAAGCGCTC 60.732 55.000 12.06 0.00 44.19 5.03
3701 6271 1.208259 CGCAAGCGCTCATATACACA 58.792 50.000 12.06 0.00 35.30 3.72
3703 6273 1.933181 GCAAGCGCTCATATACACACA 59.067 47.619 12.06 0.00 34.30 3.72
3705 6275 2.225068 AGCGCTCATATACACACACC 57.775 50.000 2.64 0.00 0.00 4.16
3706 6276 1.202533 AGCGCTCATATACACACACCC 60.203 52.381 2.64 0.00 0.00 4.61
3707 6277 1.202533 GCGCTCATATACACACACCCT 60.203 52.381 0.00 0.00 0.00 4.34
3708 6278 2.035449 GCGCTCATATACACACACCCTA 59.965 50.000 0.00 0.00 0.00 3.53
3709 6279 3.639538 CGCTCATATACACACACCCTAC 58.360 50.000 0.00 0.00 0.00 3.18
3713 6283 3.051650 TCATATACACACACCCTACCCCT 60.052 47.826 0.00 0.00 0.00 4.79
3714 6284 4.170449 TCATATACACACACCCTACCCCTA 59.830 45.833 0.00 0.00 0.00 3.53
3715 6285 3.719368 ATACACACACCCTACCCCTAT 57.281 47.619 0.00 0.00 0.00 2.57
3716 6286 1.580059 ACACACACCCTACCCCTATG 58.420 55.000 0.00 0.00 0.00 2.23
3717 6287 1.079825 ACACACACCCTACCCCTATGA 59.920 52.381 0.00 0.00 0.00 2.15
3727 6303 1.789523 ACCCCTATGAGCACATACGT 58.210 50.000 0.00 0.00 37.87 3.57
3730 6306 2.626266 CCCCTATGAGCACATACGTACA 59.374 50.000 0.00 0.00 37.87 2.90
3731 6307 3.258372 CCCCTATGAGCACATACGTACAT 59.742 47.826 0.00 0.00 37.87 2.29
3736 6312 4.563337 TGAGCACATACGTACATCCTAC 57.437 45.455 0.00 0.00 0.00 3.18
3750 6327 0.487772 TCCTACCCCTATGAGCCCTC 59.512 60.000 0.00 0.00 0.00 4.30
3756 6333 1.059913 CCCTATGAGCCCTCCGAAAT 58.940 55.000 0.00 0.00 0.00 2.17
3766 6343 0.249489 CCTCCGAAATACTGAGCCGG 60.249 60.000 0.00 0.00 41.36 6.13
3784 6361 5.316167 AGCCGGCATATCATCTTGAAATTA 58.684 37.500 31.54 0.00 0.00 1.40
3785 6362 5.182001 AGCCGGCATATCATCTTGAAATTAC 59.818 40.000 31.54 0.00 0.00 1.89
3786 6363 5.621422 CCGGCATATCATCTTGAAATTACG 58.379 41.667 0.00 0.00 0.00 3.18
3787 6364 5.408299 CCGGCATATCATCTTGAAATTACGA 59.592 40.000 0.00 0.00 0.00 3.43
3789 6366 7.361201 CCGGCATATCATCTTGAAATTACGAAT 60.361 37.037 0.00 0.00 0.00 3.34
3830 6418 1.325640 CGTCTCCTCACATTGAATGCG 59.674 52.381 4.84 0.00 0.00 4.73
3836 6424 1.063027 CTCACATTGAATGCGCATCGT 59.937 47.619 25.53 9.22 0.00 3.73
3839 6427 0.301388 CATTGAATGCGCATCGTCGA 59.699 50.000 25.53 18.40 0.00 4.20
3842 6430 0.094558 TGAATGCGCATCGTCGAAAC 59.905 50.000 25.53 8.31 0.00 2.78
3844 6432 0.796312 AATGCGCATCGTCGAAACTT 59.204 45.000 25.53 0.76 0.00 2.66
3847 6435 1.265568 GCGCATCGTCGAAACTTCTA 58.734 50.000 0.30 0.00 0.00 2.10
3860 6448 8.653338 CGTCGAAACTTCTAAAATAAATCCAGA 58.347 33.333 0.00 0.00 0.00 3.86
3877 6465 3.119531 TCCAGAAATAAATGCAAGCACCG 60.120 43.478 0.00 0.00 0.00 4.94
3889 6477 1.705997 AAGCACCGGGACTTGAACCT 61.706 55.000 6.32 0.00 0.00 3.50
3895 6483 0.107831 CGGGACTTGAACCTTGGTGA 59.892 55.000 0.00 0.00 0.00 4.02
3896 6484 1.476110 CGGGACTTGAACCTTGGTGAA 60.476 52.381 0.00 0.00 0.00 3.18
3898 6486 3.230976 GGGACTTGAACCTTGGTGAATT 58.769 45.455 0.00 0.00 0.00 2.17
3902 6490 3.230134 CTTGAACCTTGGTGAATTGGGA 58.770 45.455 0.00 0.00 0.00 4.37
3906 6494 4.770010 TGAACCTTGGTGAATTGGGAATAC 59.230 41.667 0.00 0.00 0.00 1.89
3907 6495 4.675063 ACCTTGGTGAATTGGGAATACT 57.325 40.909 0.00 0.00 0.00 2.12
3911 6499 5.590259 CCTTGGTGAATTGGGAATACTACAG 59.410 44.000 0.00 0.00 0.00 2.74
3949 6537 5.278266 CCTCTCTTCTATCTCATTCCACGTC 60.278 48.000 0.00 0.00 0.00 4.34
3950 6538 5.193679 TCTCTTCTATCTCATTCCACGTCA 58.806 41.667 0.00 0.00 0.00 4.35
3951 6539 5.066634 TCTCTTCTATCTCATTCCACGTCAC 59.933 44.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 595 4.277672 CCCTTGAGGCAGATCAATACAATG 59.722 45.833 0.00 0.00 38.47 2.82
250 630 6.586463 TCTGCGTAGTCTCTCTTTTGTAAATG 59.414 38.462 0.00 0.00 0.00 2.32
251 631 6.688578 TCTGCGTAGTCTCTCTTTTGTAAAT 58.311 36.000 0.00 0.00 0.00 1.40
259 639 2.361789 GGACTCTGCGTAGTCTCTCTT 58.638 52.381 15.47 0.00 44.42 2.85
376 1035 1.269012 AACTTCCCACGACCGGATAA 58.731 50.000 9.46 0.00 0.00 1.75
436 1095 6.325919 TCAGTTTCAAAGTTGTTCAGTTGT 57.674 33.333 0.00 0.00 0.00 3.32
437 1096 6.183360 GCTTCAGTTTCAAAGTTGTTCAGTTG 60.183 38.462 0.00 0.00 0.00 3.16
438 1097 5.863935 GCTTCAGTTTCAAAGTTGTTCAGTT 59.136 36.000 0.00 0.00 0.00 3.16
439 1098 5.402398 GCTTCAGTTTCAAAGTTGTTCAGT 58.598 37.500 0.00 0.00 0.00 3.41
440 1099 4.800471 GGCTTCAGTTTCAAAGTTGTTCAG 59.200 41.667 0.00 0.00 0.00 3.02
441 1100 4.462483 AGGCTTCAGTTTCAAAGTTGTTCA 59.538 37.500 0.00 0.00 0.00 3.18
475 1135 2.125106 GCGGTAGGTGCCAAGAGG 60.125 66.667 0.00 0.00 38.23 3.69
476 1136 1.741770 GTGCGGTAGGTGCCAAGAG 60.742 63.158 0.00 0.00 0.00 2.85
477 1137 2.345991 GTGCGGTAGGTGCCAAGA 59.654 61.111 0.00 0.00 0.00 3.02
478 1138 2.746277 GGTGCGGTAGGTGCCAAG 60.746 66.667 0.00 0.00 0.00 3.61
479 1139 3.561241 TGGTGCGGTAGGTGCCAA 61.561 61.111 0.00 0.00 0.00 4.52
493 1153 0.250234 CCATGTCATCGTCCTGTGGT 59.750 55.000 0.00 0.00 0.00 4.16
534 1203 0.250467 GAGACTGAACTGCCCAGCAA 60.250 55.000 0.00 0.00 38.41 3.91
535 1204 1.372683 GAGACTGAACTGCCCAGCA 59.627 57.895 0.00 0.00 35.14 4.41
618 1287 2.602257 TGTCGGATCATTGCACCTAG 57.398 50.000 0.00 0.00 0.00 3.02
619 1288 2.485302 CCATGTCGGATCATTGCACCTA 60.485 50.000 0.00 0.00 36.56 3.08
620 1289 1.671979 CATGTCGGATCATTGCACCT 58.328 50.000 0.00 0.00 0.00 4.00
621 1290 0.664761 CCATGTCGGATCATTGCACC 59.335 55.000 0.00 0.00 36.56 5.01
622 1291 0.029834 GCCATGTCGGATCATTGCAC 59.970 55.000 0.00 0.00 36.76 4.57
623 1292 0.394080 TGCCATGTCGGATCATTGCA 60.394 50.000 12.08 12.08 41.74 4.08
724 1393 1.813178 CTAGTCCACGACTCTGCAAGA 59.187 52.381 0.00 0.00 42.40 3.02
840 1509 1.655099 TGCGCGAACGAGGTTTATAAC 59.345 47.619 12.10 0.00 43.93 1.89
841 1510 1.921887 CTGCGCGAACGAGGTTTATAA 59.078 47.619 12.10 0.00 43.93 0.98
843 1512 1.693083 GCTGCGCGAACGAGGTTTAT 61.693 55.000 12.10 0.00 43.93 1.40
844 1513 2.377310 GCTGCGCGAACGAGGTTTA 61.377 57.895 12.10 0.00 43.93 2.01
846 1515 4.961511 TGCTGCGCGAACGAGGTT 62.962 61.111 12.10 0.00 43.93 3.50
852 1521 2.127609 GTGTTCTGCTGCGCGAAC 60.128 61.111 12.10 20.72 39.99 3.95
853 1522 2.587473 TGTGTTCTGCTGCGCGAA 60.587 55.556 12.10 0.00 0.00 4.70
856 1525 3.590443 CTGCTGTGTTCTGCTGCGC 62.590 63.158 0.00 0.00 38.91 6.09
870 1540 2.047465 CTCCGTCTGCTTGCTGCT 60.047 61.111 0.00 0.00 43.37 4.24
871 1541 3.797546 GCTCCGTCTGCTTGCTGC 61.798 66.667 0.00 0.00 43.25 5.25
872 1542 2.357881 TGCTCCGTCTGCTTGCTG 60.358 61.111 0.00 0.00 0.00 4.41
873 1543 2.047465 CTGCTCCGTCTGCTTGCT 60.047 61.111 0.00 0.00 0.00 3.91
874 1544 3.797546 GCTGCTCCGTCTGCTTGC 61.798 66.667 0.00 0.00 0.00 4.01
875 1545 2.357881 TGCTGCTCCGTCTGCTTG 60.358 61.111 0.00 0.00 32.95 4.01
876 1546 2.047465 CTGCTGCTCCGTCTGCTT 60.047 61.111 0.00 0.00 32.95 3.91
877 1547 4.756458 GCTGCTGCTCCGTCTGCT 62.756 66.667 8.53 0.00 36.03 4.24
879 1549 3.889134 TTGGCTGCTGCTCCGTCTG 62.889 63.158 15.64 0.00 39.59 3.51
880 1550 3.182590 TTTGGCTGCTGCTCCGTCT 62.183 57.895 15.64 0.00 39.59 4.18
881 1551 2.669569 TTTGGCTGCTGCTCCGTC 60.670 61.111 15.64 0.00 39.59 4.79
882 1552 2.670934 CTTTGGCTGCTGCTCCGT 60.671 61.111 15.64 0.00 39.59 4.69
883 1553 4.112341 GCTTTGGCTGCTGCTCCG 62.112 66.667 15.64 3.37 39.59 4.63
884 1554 3.756727 GGCTTTGGCTGCTGCTCC 61.757 66.667 15.64 2.78 39.59 4.70
885 1555 3.756727 GGGCTTTGGCTGCTGCTC 61.757 66.667 15.64 6.34 39.59 4.26
902 1591 0.718343 CTCTTTCTTTGCTCGCCTCG 59.282 55.000 0.00 0.00 0.00 4.63
965 1660 3.006752 GTGATGAATTTGTTTGGAGGCCA 59.993 43.478 5.01 0.00 0.00 5.36
971 1674 4.475944 GACGAGGTGATGAATTTGTTTGG 58.524 43.478 0.00 0.00 0.00 3.28
973 1676 3.188460 CCGACGAGGTGATGAATTTGTTT 59.812 43.478 0.00 0.00 34.51 2.83
1042 1765 2.467566 AAATCGGCGACAGTTACCTT 57.532 45.000 13.76 0.00 0.00 3.50
1061 1784 1.971357 GAAGATCGGAGGGAGGCAATA 59.029 52.381 0.00 0.00 0.00 1.90
1084 1807 0.252467 ACCAGAAGAGGAGGAGGTGG 60.252 60.000 0.00 0.00 0.00 4.61
1085 1808 1.277557 CAACCAGAAGAGGAGGAGGTG 59.722 57.143 0.00 0.00 0.00 4.00
1086 1809 1.650528 CAACCAGAAGAGGAGGAGGT 58.349 55.000 0.00 0.00 0.00 3.85
1222 2336 6.284891 AGAGAAGAAGAAGGACAATGAGAG 57.715 41.667 0.00 0.00 0.00 3.20
1237 2351 9.454859 TCATCGATATAGCAGAATAGAGAAGAA 57.545 33.333 0.00 0.00 0.00 2.52
1238 2352 9.454859 TTCATCGATATAGCAGAATAGAGAAGA 57.545 33.333 0.00 0.00 0.00 2.87
1242 2356 8.754096 GCATTTCATCGATATAGCAGAATAGAG 58.246 37.037 0.00 0.00 0.00 2.43
1243 2357 7.708322 GGCATTTCATCGATATAGCAGAATAGA 59.292 37.037 0.00 0.00 0.00 1.98
1244 2358 7.493645 TGGCATTTCATCGATATAGCAGAATAG 59.506 37.037 0.00 0.00 0.00 1.73
1245 2359 7.330262 TGGCATTTCATCGATATAGCAGAATA 58.670 34.615 0.00 0.00 0.00 1.75
1248 2362 5.151297 TGGCATTTCATCGATATAGCAGA 57.849 39.130 0.00 0.00 0.00 4.26
1249 2363 4.201792 GCTGGCATTTCATCGATATAGCAG 60.202 45.833 0.00 1.27 0.00 4.24
1250 2364 3.686241 GCTGGCATTTCATCGATATAGCA 59.314 43.478 0.00 0.00 0.00 3.49
1251 2365 3.686241 TGCTGGCATTTCATCGATATAGC 59.314 43.478 0.00 0.00 0.00 2.97
1252 2366 4.934001 ACTGCTGGCATTTCATCGATATAG 59.066 41.667 0.00 0.00 0.00 1.31
1253 2367 4.692155 CACTGCTGGCATTTCATCGATATA 59.308 41.667 0.00 0.00 0.00 0.86
1254 2368 3.501062 CACTGCTGGCATTTCATCGATAT 59.499 43.478 0.00 0.00 0.00 1.63
1255 2369 2.874086 CACTGCTGGCATTTCATCGATA 59.126 45.455 0.00 0.00 0.00 2.92
1256 2370 1.674441 CACTGCTGGCATTTCATCGAT 59.326 47.619 0.00 0.00 0.00 3.59
1257 2371 1.089112 CACTGCTGGCATTTCATCGA 58.911 50.000 0.00 0.00 0.00 3.59
1258 2372 0.524816 GCACTGCTGGCATTTCATCG 60.525 55.000 0.00 0.00 0.00 3.84
1259 2373 0.815734 AGCACTGCTGGCATTTCATC 59.184 50.000 1.67 0.00 37.57 2.92
1261 2375 4.506039 AGCACTGCTGGCATTTCA 57.494 50.000 1.67 0.00 37.57 2.69
1270 2384 2.574006 TTGAAAGATCCAGCACTGCT 57.426 45.000 0.00 0.00 40.77 4.24
1271 2385 3.648339 TTTTGAAAGATCCAGCACTGC 57.352 42.857 0.00 0.00 0.00 4.40
1272 2386 5.987347 ACAATTTTTGAAAGATCCAGCACTG 59.013 36.000 0.00 0.00 0.00 3.66
1273 2387 6.041296 AGACAATTTTTGAAAGATCCAGCACT 59.959 34.615 0.00 0.00 0.00 4.40
1274 2388 6.218746 AGACAATTTTTGAAAGATCCAGCAC 58.781 36.000 0.00 0.00 0.00 4.40
1275 2389 6.409524 AGACAATTTTTGAAAGATCCAGCA 57.590 33.333 0.00 0.00 0.00 4.41
1276 2390 7.654923 AGAAAGACAATTTTTGAAAGATCCAGC 59.345 33.333 0.00 0.00 0.00 4.85
1277 2391 9.538508 AAGAAAGACAATTTTTGAAAGATCCAG 57.461 29.630 0.00 0.00 0.00 3.86
1278 2392 9.533253 GAAGAAAGACAATTTTTGAAAGATCCA 57.467 29.630 0.00 0.00 0.00 3.41
1279 2393 9.755804 AGAAGAAAGACAATTTTTGAAAGATCC 57.244 29.630 0.00 0.00 0.00 3.36
1293 2407 9.613428 TCTTCAAGACAATAAGAAGAAAGACAA 57.387 29.630 0.00 0.00 42.33 3.18
1314 2430 6.169557 TCAGTTAAACCACTAGCTTCTTCA 57.830 37.500 0.00 0.00 0.00 3.02
1413 2532 2.588620 GAGGACGGTCTCCAGATACAT 58.411 52.381 8.23 0.00 42.46 2.29
2230 3355 1.202330 CTTGAGCTCCTCCACCTGAT 58.798 55.000 12.15 0.00 0.00 2.90
2669 3803 3.471680 GTCAAAGAAGAACTCCAGCTGT 58.528 45.455 13.81 0.00 0.00 4.40
2900 4034 1.445410 GACGATGCCGCTGTACACA 60.445 57.895 0.00 0.00 39.95 3.72
2947 4081 4.226427 AGATTTAGAGCAAGCCATCACA 57.774 40.909 0.00 0.00 0.00 3.58
2988 4132 8.843733 GCGATTTGCAATGTAATCTATGTAATG 58.156 33.333 0.00 0.00 45.45 1.90
2989 4133 8.955061 GCGATTTGCAATGTAATCTATGTAAT 57.045 30.769 0.00 0.00 45.45 1.89
3046 4197 7.201679 CCGTGTATATATGTACCTGGCTACTAC 60.202 44.444 7.12 0.00 0.00 2.73
3047 4198 6.825213 CCGTGTATATATGTACCTGGCTACTA 59.175 42.308 7.12 0.00 0.00 1.82
3048 4199 5.651139 CCGTGTATATATGTACCTGGCTACT 59.349 44.000 7.12 0.00 0.00 2.57
3068 4219 3.947910 TGAGTTTTAGGTACTCCCGTG 57.052 47.619 0.00 0.00 41.02 4.94
3069 4220 4.351127 AGATGAGTTTTAGGTACTCCCGT 58.649 43.478 0.00 0.00 41.02 5.28
3070 4221 5.826737 TCTAGATGAGTTTTAGGTACTCCCG 59.173 44.000 0.00 0.00 41.02 5.14
3071 4222 7.506261 TCATCTAGATGAGTTTTAGGTACTCCC 59.494 40.741 27.93 0.00 42.42 4.30
3072 4223 8.466617 TCATCTAGATGAGTTTTAGGTACTCC 57.533 38.462 27.93 0.00 42.42 3.85
3128 4279 8.670135 CGTTGACATGGGTTATATCTGTTTTTA 58.330 33.333 0.00 0.00 0.00 1.52
3129 4280 7.535139 CGTTGACATGGGTTATATCTGTTTTT 58.465 34.615 0.00 0.00 0.00 1.94
3130 4281 6.404293 GCGTTGACATGGGTTATATCTGTTTT 60.404 38.462 0.00 0.00 0.00 2.43
3131 4282 5.065988 GCGTTGACATGGGTTATATCTGTTT 59.934 40.000 0.00 0.00 0.00 2.83
3132 4283 4.574828 GCGTTGACATGGGTTATATCTGTT 59.425 41.667 0.00 0.00 0.00 3.16
3133 4284 4.127171 GCGTTGACATGGGTTATATCTGT 58.873 43.478 0.00 0.00 0.00 3.41
3134 4285 4.024893 GTGCGTTGACATGGGTTATATCTG 60.025 45.833 0.00 0.00 0.00 2.90
3135 4286 4.127171 GTGCGTTGACATGGGTTATATCT 58.873 43.478 0.00 0.00 0.00 1.98
3136 4287 3.874543 TGTGCGTTGACATGGGTTATATC 59.125 43.478 0.00 0.00 0.00 1.63
3137 4288 3.625764 GTGTGCGTTGACATGGGTTATAT 59.374 43.478 0.00 0.00 0.00 0.86
3138 4289 3.004171 GTGTGCGTTGACATGGGTTATA 58.996 45.455 0.00 0.00 0.00 0.98
3139 4290 1.810151 GTGTGCGTTGACATGGGTTAT 59.190 47.619 0.00 0.00 0.00 1.89
3140 4291 1.231221 GTGTGCGTTGACATGGGTTA 58.769 50.000 0.00 0.00 0.00 2.85
3141 4292 0.749818 TGTGTGCGTTGACATGGGTT 60.750 50.000 0.00 0.00 0.00 4.11
3142 4293 1.153066 TGTGTGCGTTGACATGGGT 60.153 52.632 0.00 0.00 0.00 4.51
3143 4294 1.282570 GTGTGTGCGTTGACATGGG 59.717 57.895 0.00 0.00 0.00 4.00
3144 4295 0.592637 ATGTGTGTGCGTTGACATGG 59.407 50.000 0.00 0.00 0.00 3.66
3145 4296 1.532437 AGATGTGTGTGCGTTGACATG 59.468 47.619 0.00 0.00 0.00 3.21
3146 4297 1.882912 AGATGTGTGTGCGTTGACAT 58.117 45.000 0.00 0.00 0.00 3.06
3147 4298 1.662517 AAGATGTGTGTGCGTTGACA 58.337 45.000 0.00 0.00 0.00 3.58
3148 4299 4.492570 GCTATAAGATGTGTGTGCGTTGAC 60.493 45.833 0.00 0.00 0.00 3.18
3149 4300 3.616821 GCTATAAGATGTGTGTGCGTTGA 59.383 43.478 0.00 0.00 0.00 3.18
3150 4301 3.370672 TGCTATAAGATGTGTGTGCGTTG 59.629 43.478 0.00 0.00 0.00 4.10
3151 4302 3.595173 TGCTATAAGATGTGTGTGCGTT 58.405 40.909 0.00 0.00 0.00 4.84
3152 4303 3.245518 TGCTATAAGATGTGTGTGCGT 57.754 42.857 0.00 0.00 0.00 5.24
3153 4304 3.803778 TGATGCTATAAGATGTGTGTGCG 59.196 43.478 0.00 0.00 0.00 5.34
3154 4305 5.936686 ATGATGCTATAAGATGTGTGTGC 57.063 39.130 0.00 0.00 0.00 4.57
3155 4306 9.211485 TGAATATGATGCTATAAGATGTGTGTG 57.789 33.333 0.00 0.00 0.00 3.82
3156 4307 9.783081 TTGAATATGATGCTATAAGATGTGTGT 57.217 29.630 0.00 0.00 0.00 3.72
3160 4311 8.900781 GCCATTGAATATGATGCTATAAGATGT 58.099 33.333 0.00 0.00 0.00 3.06
3161 4312 9.121658 AGCCATTGAATATGATGCTATAAGATG 57.878 33.333 0.00 0.00 0.00 2.90
3169 4320 8.746530 CCTTTTATAGCCATTGAATATGATGCT 58.253 33.333 0.00 0.00 0.00 3.79
3170 4321 8.526147 ACCTTTTATAGCCATTGAATATGATGC 58.474 33.333 0.00 0.00 0.00 3.91
3171 4322 9.850628 CACCTTTTATAGCCATTGAATATGATG 57.149 33.333 0.00 0.00 0.00 3.07
3172 4323 9.812347 TCACCTTTTATAGCCATTGAATATGAT 57.188 29.630 0.00 0.00 0.00 2.45
3173 4324 9.639563 TTCACCTTTTATAGCCATTGAATATGA 57.360 29.630 0.00 0.00 0.00 2.15
3176 4327 9.639563 TCATTCACCTTTTATAGCCATTGAATA 57.360 29.630 0.00 0.00 32.53 1.75
3177 4328 8.537728 TCATTCACCTTTTATAGCCATTGAAT 57.462 30.769 0.00 0.00 33.72 2.57
3178 4329 7.833682 TCTCATTCACCTTTTATAGCCATTGAA 59.166 33.333 0.00 0.00 0.00 2.69
3179 4330 7.283127 GTCTCATTCACCTTTTATAGCCATTGA 59.717 37.037 0.00 0.00 0.00 2.57
3180 4331 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
3181 4332 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
3182 4333 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
3183 4334 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
3184 4335 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
3185 4336 7.391148 TTTGGTCTCATTCACCTTTTATAGC 57.609 36.000 0.00 0.00 34.66 2.97
3193 4344 9.699410 TGAAATATAATTTGGTCTCATTCACCT 57.301 29.630 0.00 0.00 34.66 4.00
3356 5858 0.395724 GGGCGGAGGAAATGAATGGT 60.396 55.000 0.00 0.00 0.00 3.55
3473 6042 2.559231 GGGCCGAACAACAAAATTCCTA 59.441 45.455 0.00 0.00 0.00 2.94
3474 6043 1.343142 GGGCCGAACAACAAAATTCCT 59.657 47.619 0.00 0.00 0.00 3.36
3475 6044 1.790755 GGGCCGAACAACAAAATTCC 58.209 50.000 0.00 0.00 0.00 3.01
3476 6045 1.001158 TCGGGCCGAACAACAAAATTC 60.001 47.619 29.11 0.00 31.06 2.17
3477 6046 1.033574 TCGGGCCGAACAACAAAATT 58.966 45.000 29.11 0.00 31.06 1.82
3478 6047 1.033574 TTCGGGCCGAACAACAAAAT 58.966 45.000 35.71 0.00 41.05 1.82
3479 6048 2.490165 TTCGGGCCGAACAACAAAA 58.510 47.368 35.71 13.23 41.05 2.44
3480 6049 4.237445 TTCGGGCCGAACAACAAA 57.763 50.000 35.71 14.06 41.05 2.83
3487 6056 3.636313 CTAGCACGTTCGGGCCGAA 62.636 63.158 35.71 35.71 43.75 4.30
3488 6057 4.124351 CTAGCACGTTCGGGCCGA 62.124 66.667 27.46 27.46 0.00 5.54
3492 6061 4.430765 ACCGCTAGCACGTTCGGG 62.431 66.667 16.45 8.28 45.58 5.14
3493 6062 2.879462 GACCGCTAGCACGTTCGG 60.879 66.667 16.45 9.04 46.61 4.30
3494 6063 1.076533 AATGACCGCTAGCACGTTCG 61.077 55.000 16.45 0.00 0.00 3.95
3495 6064 0.370273 CAATGACCGCTAGCACGTTC 59.630 55.000 16.45 5.28 0.00 3.95
3496 6065 1.019278 CCAATGACCGCTAGCACGTT 61.019 55.000 16.45 9.95 0.00 3.99
3497 6066 1.447838 CCAATGACCGCTAGCACGT 60.448 57.895 16.45 9.98 0.00 4.49
3498 6067 0.530650 ATCCAATGACCGCTAGCACG 60.531 55.000 16.45 6.38 0.00 5.34
3499 6068 0.940126 CATCCAATGACCGCTAGCAC 59.060 55.000 16.45 6.08 0.00 4.40
3500 6069 0.829990 TCATCCAATGACCGCTAGCA 59.170 50.000 16.45 0.00 33.59 3.49
3503 6072 2.548707 GCTCATCATCCAATGACCGCTA 60.549 50.000 0.00 0.00 43.01 4.26
3507 6076 2.646930 TGTGCTCATCATCCAATGACC 58.353 47.619 0.00 0.00 43.01 4.02
3609 6178 2.764547 AGGGCGGTAGAGGGCTTC 60.765 66.667 0.00 0.00 0.00 3.86
3628 6197 7.936301 AGTGAAAATGGATAAGATAGAAGGAGC 59.064 37.037 0.00 0.00 0.00 4.70
3672 6242 0.108804 AGCGCTTGCGTGTGTACTAT 60.109 50.000 16.38 0.00 45.69 2.12
3673 6243 0.731514 GAGCGCTTGCGTGTGTACTA 60.732 55.000 13.26 0.00 45.69 1.82
3680 6250 1.071239 GTGTATATGAGCGCTTGCGTG 60.071 52.381 13.26 0.00 45.69 5.34
3683 6253 1.933181 TGTGTGTATATGAGCGCTTGC 59.067 47.619 13.26 0.00 39.58 4.01
3692 6262 3.314693 AGGGGTAGGGTGTGTGTATATG 58.685 50.000 0.00 0.00 0.00 1.78
3701 6271 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
3703 6273 0.341961 TGTGCTCATAGGGGTAGGGT 59.658 55.000 0.00 0.00 0.00 4.34
3705 6275 2.231478 CGTATGTGCTCATAGGGGTAGG 59.769 54.545 16.83 0.00 38.19 3.18
3706 6276 2.891580 ACGTATGTGCTCATAGGGGTAG 59.108 50.000 24.34 9.89 42.89 3.18
3707 6277 2.953453 ACGTATGTGCTCATAGGGGTA 58.047 47.619 24.34 0.00 42.89 3.69
3708 6278 1.789523 ACGTATGTGCTCATAGGGGT 58.210 50.000 24.34 13.94 42.89 4.95
3709 6279 2.626266 TGTACGTATGTGCTCATAGGGG 59.374 50.000 24.34 13.46 42.89 4.79
3713 6283 5.182570 GGTAGGATGTACGTATGTGCTCATA 59.817 44.000 4.38 4.38 35.70 2.15
3714 6284 4.022242 GGTAGGATGTACGTATGTGCTCAT 60.022 45.833 6.50 6.50 38.00 2.90
3715 6285 3.317149 GGTAGGATGTACGTATGTGCTCA 59.683 47.826 0.00 0.00 0.00 4.26
3716 6286 3.305199 GGGTAGGATGTACGTATGTGCTC 60.305 52.174 0.00 0.48 0.00 4.26
3717 6287 2.626743 GGGTAGGATGTACGTATGTGCT 59.373 50.000 0.00 4.04 0.00 4.40
3727 6303 2.225547 GGGCTCATAGGGGTAGGATGTA 60.226 54.545 0.00 0.00 0.00 2.29
3730 6306 1.079658 GAGGGCTCATAGGGGTAGGAT 59.920 57.143 0.00 0.00 0.00 3.24
3731 6307 0.487772 GAGGGCTCATAGGGGTAGGA 59.512 60.000 0.00 0.00 0.00 2.94
3736 6312 1.054406 TTTCGGAGGGCTCATAGGGG 61.054 60.000 0.00 0.00 0.00 4.79
3750 6327 0.532862 ATGCCGGCTCAGTATTTCGG 60.533 55.000 29.70 0.00 43.13 4.30
3756 6333 2.529632 AGATGATATGCCGGCTCAGTA 58.470 47.619 29.70 15.24 0.00 2.74
3766 6343 9.322776 GTGATTCGTAATTTCAAGATGATATGC 57.677 33.333 0.00 0.00 0.00 3.14
3785 6362 1.422662 TCGACGACGAGGTGATTCG 59.577 57.895 5.75 0.00 43.81 3.34
3819 6407 0.026674 CGACGATGCGCATTCAATGT 59.973 50.000 26.12 17.22 0.00 2.71
3822 6410 0.793250 TTTCGACGATGCGCATTCAA 59.207 45.000 26.12 12.44 0.00 2.69
3830 6418 8.822105 ATTTATTTTAGAAGTTTCGACGATGC 57.178 30.769 0.00 0.00 0.00 3.91
3860 6448 2.094234 GTCCCGGTGCTTGCATTTATTT 60.094 45.455 0.00 0.00 0.00 1.40
3877 6465 2.358322 TTCACCAAGGTTCAAGTCCC 57.642 50.000 0.00 0.00 0.00 4.46
3889 6477 6.134535 ACTGTAGTATTCCCAATTCACCAA 57.865 37.500 0.00 0.00 0.00 3.67
3902 6490 7.540183 AGGATGATTAGAGGGACTGTAGTATT 58.460 38.462 0.00 0.00 41.55 1.89
3906 6494 5.640147 AGAGGATGATTAGAGGGACTGTAG 58.360 45.833 0.00 0.00 41.55 2.74
3907 6495 5.374154 AGAGAGGATGATTAGAGGGACTGTA 59.626 44.000 0.00 0.00 41.55 2.74
3911 6499 5.393866 AGAAGAGAGGATGATTAGAGGGAC 58.606 45.833 0.00 0.00 0.00 4.46
3921 6509 6.493115 GTGGAATGAGATAGAAGAGAGGATGA 59.507 42.308 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.