Multiple sequence alignment - TraesCS3A01G252700

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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 TraesCS3A01G252700 chr3A 100.000 3114 0 0 1 3114 473218519 473215406 0.000000e+00 5751
1 TraesCS3A01G252700 chr3A 90.041 241 21 2 2400 2640 54462267 54462504 3.020000e-80 309
2 TraesCS3A01G252700 chr3A 94.495 109 4 2 2788 2894 264939940 264939832 1.920000e-37 167
3 TraesCS3A01G252700 chr3B 88.210 2061 125 54 356 2381 455067497 455065520 0.000000e+00 2351
4 TraesCS3A01G252700 chr3B 85.714 378 41 11 2 372 455131974 455131603 1.350000e-103 387
5 TraesCS3A01G252700 chr3B 75.971 412 70 21 1019 1421 749193458 749193067 5.300000e-43 185
6 TraesCS3A01G252700 chr3D 87.890 2081 132 55 326 2385 354622432 354620451 0.000000e+00 2337
7 TraesCS3A01G252700 chr3D 87.332 371 39 8 2 367 354622729 354622362 4.800000e-113 418
8 TraesCS3A01G252700 chr3D 77.017 409 71 16 1019 1421 588696316 588696707 2.430000e-51 213
9 TraesCS3A01G252700 chr2B 88.318 428 30 11 2385 2792 186942386 186942813 2.160000e-136 496
10 TraesCS3A01G252700 chr2B 91.855 221 15 1 2896 3113 186942814 186943034 3.900000e-79 305
11 TraesCS3A01G252700 chr2A 88.889 378 35 5 2385 2759 760111977 760111604 2.830000e-125 459
12 TraesCS3A01G252700 chr2A 95.872 218 9 0 2896 3113 760110587 760110370 1.370000e-93 353
13 TraesCS3A01G252700 chr2A 94.521 219 8 4 2896 3113 315766148 315765933 4.980000e-88 335
14 TraesCS3A01G252700 chr2A 94.326 141 8 0 2652 2792 315766289 315766149 1.880000e-52 217
15 TraesCS3A01G252700 chr2A 83.333 156 20 6 2791 2941 333169322 333169168 4.190000e-29 139
16 TraesCS3A01G252700 chr4D 96.094 256 10 0 2385 2640 22913944 22913689 4.800000e-113 418
17 TraesCS3A01G252700 chr4D 96.330 218 8 0 2896 3113 22913496 22913279 2.950000e-95 359
18 TraesCS3A01G252700 chr4D 95.035 141 7 0 2652 2792 22913637 22913497 4.040000e-54 222
19 TraesCS3A01G252700 chrUn 95.703 256 10 1 2385 2640 94059915 94059661 8.040000e-111 411
20 TraesCS3A01G252700 chrUn 95.872 218 8 1 2896 3113 94059469 94059253 4.940000e-93 351
21 TraesCS3A01G252700 chrUn 92.254 142 8 3 2652 2792 94059609 94059470 6.810000e-47 198
22 TraesCS3A01G252700 chr7D 94.922 256 12 1 2385 2640 488092258 488092512 1.740000e-107 399
23 TraesCS3A01G252700 chr7D 95.872 218 8 1 2896 3113 488092705 488092921 4.940000e-93 351
24 TraesCS3A01G252700 chr7D 93.617 141 9 0 2652 2792 488092564 488092704 8.750000e-51 211
25 TraesCS3A01G252700 chr2D 95.397 239 9 1 2402 2640 484364496 484364260 2.270000e-101 379
26 TraesCS3A01G252700 chr2D 95.413 218 9 1 2896 3113 484364066 484363850 2.300000e-91 346
27 TraesCS3A01G252700 chr2D 77.859 411 64 17 1019 1421 586831126 586831517 2.420000e-56 230
28 TraesCS3A01G252700 chr2D 92.958 142 9 1 2652 2792 484364208 484364067 4.070000e-49 206
29 TraesCS3A01G252700 chr2D 93.694 111 5 2 2786 2894 87030972 87031082 6.910000e-37 165
30 TraesCS3A01G252700 chr2D 93.694 111 5 2 2786 2894 87035729 87035839 6.910000e-37 165
31 TraesCS3A01G252700 chr6A 92.578 256 17 1 2385 2640 152795182 152795435 1.760000e-97 366
32 TraesCS3A01G252700 chr6A 91.866 209 15 2 2907 3113 152795658 152795866 1.090000e-74 291
33 TraesCS3A01G252700 chr6A 91.129 124 6 5 2774 2894 130415900 130415779 2.480000e-36 163
34 TraesCS3A01G252700 chr6A 92.174 115 7 1 2782 2894 484566953 484566839 8.940000e-36 161
35 TraesCS3A01G252700 chr6B 89.844 256 24 2 2385 2640 55971270 55971523 8.330000e-86 327
36 TraesCS3A01G252700 chr6B 92.237 219 13 3 2898 3113 55971734 55971951 1.080000e-79 307
37 TraesCS3A01G252700 chr6B 91.549 142 10 2 2652 2792 55971575 55971715 8.810000e-46 195
38 TraesCS3A01G252700 chr1B 77.855 429 74 17 999 1419 613415580 613415165 2.400000e-61 246
39 TraesCS3A01G252700 chr1A 77.598 433 72 20 999 1421 544048745 544048328 4.010000e-59 239
40 TraesCS3A01G252700 chr1D 77.064 436 69 19 999 1421 447925417 447925000 4.040000e-54 222
41 TraesCS3A01G252700 chr5B 76.389 432 73 22 999 1421 527733241 527733652 4.070000e-49 206
42 TraesCS3A01G252700 chr7B 76.585 410 71 17 1019 1421 97120331 97119940 5.270000e-48 202
43 TraesCS3A01G252700 chr7B 76.341 410 72 16 1019 1421 689142500 689142109 2.450000e-46 196
44 TraesCS3A01G252700 chr7B 76.341 410 70 18 1019 1421 89870217 89869828 8.810000e-46 195
45 TraesCS3A01G252700 chr5D 76.528 409 73 15 1019 1421 556578548 556578157 5.270000e-48 202
46 TraesCS3A01G252700 chr4A 94.595 111 4 2 2786 2894 537434420 537434310 1.480000e-38 171
47 TraesCS3A01G252700 chr4A 93.636 110 5 2 2787 2894 628491006 628491115 2.480000e-36 163
48 TraesCS3A01G252700 chr5A 88.976 127 8 6 2772 2894 503510588 503510712 5.380000e-33 152
49 TraesCS3A01G252700 chr7A 82.482 137 19 5 2790 2921 8939428 8939292 7.060000e-22 115


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 TraesCS3A01G252700 chr3A 473215406 473218519 3113 True 5751.000000 5751 100.000000 1 3114 1 chr3A.!!$R2 3113
1 TraesCS3A01G252700 chr3B 455065520 455067497 1977 True 2351.000000 2351 88.210000 356 2381 1 chr3B.!!$R1 2025
2 TraesCS3A01G252700 chr3D 354620451 354622729 2278 True 1377.500000 2337 87.611000 2 2385 2 chr3D.!!$R1 2383
3 TraesCS3A01G252700 chr2B 186942386 186943034 648 False 400.500000 496 90.086500 2385 3113 2 chr2B.!!$F1 728
4 TraesCS3A01G252700 chr2A 760110370 760111977 1607 True 406.000000 459 92.380500 2385 3113 2 chr2A.!!$R3 728
5 TraesCS3A01G252700 chr4D 22913279 22913944 665 True 333.000000 418 95.819667 2385 3113 3 chr4D.!!$R1 728
6 TraesCS3A01G252700 chrUn 94059253 94059915 662 True 320.000000 411 94.609667 2385 3113 3 chrUn.!!$R1 728
7 TraesCS3A01G252700 chr7D 488092258 488092921 663 False 320.333333 399 94.803667 2385 3113 3 chr7D.!!$F1 728
8 TraesCS3A01G252700 chr2D 484363850 484364496 646 True 310.333333 379 94.589333 2402 3113 3 chr2D.!!$R1 711
9 TraesCS3A01G252700 chr6A 152795182 152795866 684 False 328.500000 366 92.222000 2385 3113 2 chr6A.!!$F1 728
10 TraesCS3A01G252700 chr6B 55971270 55971951 681 False 276.333333 327 91.210000 2385 3113 3 chr6B.!!$F1 728

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
858 866 0.598419 TGTTCGTCTGCTCAGCTGTG 60.598 55.0 14.67 12.95 0.00 3.66 F
1223 1232 0.033504 TTCGTCCACTGACTGAAGGC 59.966 55.0 0.00 0.00 39.47 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1772 0.895530 TAAGGCTCAGAACAGGTCGG 59.104 55.000 0.0 0.0 0.00 4.79 R
2854 3930 1.000163 ACTCGTCGCAGAAATGAGTGT 60.000 47.619 0.0 0.0 41.82 3.55 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
23 25 1.961793 TTGGTCAAAGAACAGTCGGG 58.038 50.000 0.00 0.00 28.15 5.14
27 29 2.557317 GTCAAAGAACAGTCGGGAACA 58.443 47.619 0.00 0.00 0.00 3.18
29 31 2.169769 TCAAAGAACAGTCGGGAACAGT 59.830 45.455 0.00 0.00 0.00 3.55
30 32 2.528041 AAGAACAGTCGGGAACAGTC 57.472 50.000 0.00 0.00 0.00 3.51
101 104 6.428083 TCTTCCAATACTGACTTTGGTACA 57.572 37.500 0.00 0.00 42.47 2.90
115 118 4.425180 TTGGTACAGTTTCTTAGTGCCA 57.575 40.909 0.00 0.00 44.49 4.92
118 121 4.759693 TGGTACAGTTTCTTAGTGCCATTG 59.240 41.667 0.00 0.00 41.97 2.82
128 131 6.299805 TCTTAGTGCCATTGTAGATTCTGT 57.700 37.500 0.00 0.00 0.00 3.41
192 195 5.099042 ACAGAACTGTTGTTTCTGTACCT 57.901 39.130 14.52 0.00 41.83 3.08
195 198 6.093633 ACAGAACTGTTGTTTCTGTACCTTTC 59.906 38.462 14.52 0.00 41.83 2.62
200 203 8.209917 ACTGTTGTTTCTGTACCTTTCTTTAG 57.790 34.615 0.00 0.00 0.00 1.85
210 213 9.720769 TCTGTACCTTTCTTTAGGAGTTTAATG 57.279 33.333 0.00 0.00 38.73 1.90
214 217 8.563123 ACCTTTCTTTAGGAGTTTAATGTAGC 57.437 34.615 0.00 0.00 38.73 3.58
218 221 9.662947 TTTCTTTAGGAGTTTAATGTAGCTACC 57.337 33.333 21.01 4.51 0.00 3.18
224 227 7.110810 AGGAGTTTAATGTAGCTACCTTTTCC 58.889 38.462 21.01 18.48 0.00 3.13
225 228 6.882678 GGAGTTTAATGTAGCTACCTTTTCCA 59.117 38.462 21.01 0.72 0.00 3.53
226 229 7.556635 GGAGTTTAATGTAGCTACCTTTTCCAT 59.443 37.037 21.01 3.26 0.00 3.41
227 230 8.281212 AGTTTAATGTAGCTACCTTTTCCATG 57.719 34.615 21.01 0.00 0.00 3.66
249 253 8.800332 CCATGAATAGAATCAGATTTTTAGGGG 58.200 37.037 0.00 0.00 31.76 4.79
431 437 1.708993 AACAGCTCAGCCCACTCCAA 61.709 55.000 0.00 0.00 0.00 3.53
441 447 1.383799 CCACTCCAATCCAGCCCAA 59.616 57.895 0.00 0.00 0.00 4.12
612 618 1.529744 ACCTTTCCCTCCTTTCCACA 58.470 50.000 0.00 0.00 0.00 4.17
640 646 2.733590 CCTGCGAGGCCACTCTATA 58.266 57.895 5.01 0.00 41.71 1.31
663 669 2.743664 GCTCCCAATTGTTCAATTTGCC 59.256 45.455 4.43 0.00 0.00 4.52
730 737 3.869832 GGTTAACGGGTGAAATCTCTAGC 59.130 47.826 0.00 0.00 0.00 3.42
769 776 2.282555 CGCATCGTATATGCCATACTGC 59.717 50.000 4.50 8.55 41.71 4.40
800 807 1.727880 TGTACGGCGTAGTTGATTTGC 59.272 47.619 21.64 5.78 0.00 3.68
802 809 2.373540 ACGGCGTAGTTGATTTGCTA 57.626 45.000 12.58 0.00 0.00 3.49
815 822 3.753272 TGATTTGCTAGAAACCAGTCAGC 59.247 43.478 0.00 0.00 0.00 4.26
858 866 0.598419 TGTTCGTCTGCTCAGCTGTG 60.598 55.000 14.67 12.95 0.00 3.66
873 881 1.132643 GCTGTGTCTCGTCCGATAGTT 59.867 52.381 0.00 0.00 0.00 2.24
936 945 4.142227 GGGTCGTTGATATGGCGATAGTAT 60.142 45.833 0.00 0.00 37.00 2.12
980 989 9.112725 CTTCATATTCAGTGGTTGATATGTGAA 57.887 33.333 12.29 0.00 35.19 3.18
981 990 8.667076 TCATATTCAGTGGTTGATATGTGAAG 57.333 34.615 12.29 0.00 35.27 3.02
986 995 7.202016 TCAGTGGTTGATATGTGAAGTTTTC 57.798 36.000 0.00 0.00 0.00 2.29
1162 1171 3.059352 ACTCTGGTCAGTGGTTATTGC 57.941 47.619 5.26 0.00 0.00 3.56
1170 1179 1.076265 GTGGTTATTGCCCTCCCCC 60.076 63.158 0.00 0.00 0.00 5.40
1176 1185 1.715019 TATTGCCCTCCCCCGATTGG 61.715 60.000 0.00 0.00 0.00 3.16
1187 1196 2.088423 CCCCGATTGGTTGAATTTCGA 58.912 47.619 0.00 0.00 31.74 3.71
1196 1205 5.247507 TGGTTGAATTTCGAATGCTATGG 57.752 39.130 0.00 0.00 0.00 2.74
1197 1206 4.946772 TGGTTGAATTTCGAATGCTATGGA 59.053 37.500 0.00 0.00 0.00 3.41
1202 1211 5.239306 TGAATTTCGAATGCTATGGATGTCC 59.761 40.000 0.00 0.00 0.00 4.02
1217 1226 0.469331 TGTCCCTTCGTCCACTGACT 60.469 55.000 0.00 0.00 39.47 3.41
1220 1229 0.679505 CCCTTCGTCCACTGACTGAA 59.320 55.000 0.00 0.00 39.47 3.02
1221 1230 1.337260 CCCTTCGTCCACTGACTGAAG 60.337 57.143 14.55 14.55 43.64 3.02
1223 1232 0.033504 TTCGTCCACTGACTGAAGGC 59.966 55.000 0.00 0.00 39.47 4.35
1224 1233 0.827925 TCGTCCACTGACTGAAGGCT 60.828 55.000 0.00 0.00 39.47 4.58
1225 1234 0.034059 CGTCCACTGACTGAAGGCTT 59.966 55.000 0.00 0.00 39.47 4.35
1226 1235 1.517242 GTCCACTGACTGAAGGCTTG 58.483 55.000 3.46 0.00 38.53 4.01
1227 1236 0.397941 TCCACTGACTGAAGGCTTGG 59.602 55.000 3.46 0.00 0.00 3.61
1228 1237 0.109342 CCACTGACTGAAGGCTTGGT 59.891 55.000 3.46 2.96 0.00 3.67
1229 1238 1.233019 CACTGACTGAAGGCTTGGTG 58.767 55.000 3.46 0.43 0.00 4.17
1230 1239 0.839946 ACTGACTGAAGGCTTGGTGT 59.160 50.000 3.46 0.00 0.00 4.16
1231 1240 1.212935 ACTGACTGAAGGCTTGGTGTT 59.787 47.619 3.46 0.00 0.00 3.32
1232 1241 2.301346 CTGACTGAAGGCTTGGTGTTT 58.699 47.619 3.46 0.00 0.00 2.83
1233 1242 2.023673 TGACTGAAGGCTTGGTGTTTG 58.976 47.619 3.46 0.00 0.00 2.93
1234 1243 1.338020 GACTGAAGGCTTGGTGTTTGG 59.662 52.381 3.46 0.00 0.00 3.28
1235 1244 1.341976 ACTGAAGGCTTGGTGTTTGGT 60.342 47.619 3.46 0.00 0.00 3.67
1236 1245 1.067516 CTGAAGGCTTGGTGTTTGGTG 59.932 52.381 3.46 0.00 0.00 4.17
1237 1246 1.111277 GAAGGCTTGGTGTTTGGTGT 58.889 50.000 3.46 0.00 0.00 4.16
1238 1247 0.823460 AAGGCTTGGTGTTTGGTGTG 59.177 50.000 0.00 0.00 0.00 3.82
1239 1248 0.033601 AGGCTTGGTGTTTGGTGTGA 60.034 50.000 0.00 0.00 0.00 3.58
1240 1249 1.039856 GGCTTGGTGTTTGGTGTGAT 58.960 50.000 0.00 0.00 0.00 3.06
1273 1282 2.945668 GGCAAACAAGAAGACTGTGACT 59.054 45.455 0.00 0.00 0.00 3.41
1303 1312 2.368221 AGCTGCTGATAAGGAGATGACC 59.632 50.000 2.00 0.00 0.00 4.02
1351 1360 2.960170 CAGAACAAGCCTGCTGCC 59.040 61.111 0.00 0.00 42.71 4.85
1403 1412 1.451927 CGCAAGATGGCCAAGGCTA 60.452 57.895 10.96 5.12 40.03 3.93
1439 1448 7.880195 AGGTATTAGCATCAGAACAACCATATC 59.120 37.037 0.00 0.00 0.00 1.63
1453 1463 9.438291 GAACAACCATATCGTTCTTTTATGATG 57.562 33.333 0.00 0.00 36.84 3.07
1473 1483 2.821378 TGAAAGTTGTGATGCTGGATGG 59.179 45.455 0.00 0.00 0.00 3.51
1492 1502 9.226606 CTGGATGGTCTAGATTAAGTACTCTAG 57.773 40.741 9.55 9.55 41.47 2.43
1533 1543 9.315363 TGGAAATATAACCTGTAACAACCATTT 57.685 29.630 0.00 0.00 0.00 2.32
1547 1557 2.227194 ACCATTTCAGTGTTTCGGTCC 58.773 47.619 0.00 0.00 0.00 4.46
1548 1558 2.158667 ACCATTTCAGTGTTTCGGTCCT 60.159 45.455 0.00 0.00 0.00 3.85
1549 1559 2.484264 CCATTTCAGTGTTTCGGTCCTC 59.516 50.000 0.00 0.00 0.00 3.71
1550 1560 1.860676 TTTCAGTGTTTCGGTCCTCG 58.139 50.000 0.00 0.00 40.90 4.63
1561 1571 1.475280 TCGGTCCTCGTAGGTGAAATG 59.525 52.381 1.60 0.00 40.32 2.32
1570 1580 5.120208 CCTCGTAGGTGAAATGTAACTGTTG 59.880 44.000 2.69 0.00 0.00 3.33
1573 1583 5.464057 CGTAGGTGAAATGTAACTGTTGTGA 59.536 40.000 2.69 0.00 0.00 3.58
1577 1587 5.920273 GGTGAAATGTAACTGTTGTGATTGG 59.080 40.000 2.69 0.00 0.00 3.16
1580 1590 5.789643 AATGTAACTGTTGTGATTGGCTT 57.210 34.783 2.69 0.00 0.00 4.35
1583 1593 4.887071 TGTAACTGTTGTGATTGGCTTCTT 59.113 37.500 2.69 0.00 0.00 2.52
1593 1607 6.769512 TGTGATTGGCTTCTTAGTTTAGTCT 58.230 36.000 0.00 0.00 0.00 3.24
1594 1608 6.650807 TGTGATTGGCTTCTTAGTTTAGTCTG 59.349 38.462 0.00 0.00 0.00 3.51
1597 1611 8.103305 TGATTGGCTTCTTAGTTTAGTCTGATT 58.897 33.333 0.00 0.00 0.00 2.57
1643 1657 9.612066 TGTGTTATGAAATCTGCAGATGTAATA 57.388 29.630 29.34 22.73 34.49 0.98
1719 1762 9.952030 TCAATTTGGTTGTATCTAGTATGTGAA 57.048 29.630 0.00 0.00 38.95 3.18
1720 1763 9.988350 CAATTTGGTTGTATCTAGTATGTGAAC 57.012 33.333 0.00 0.00 33.01 3.18
1736 1779 2.833794 TGAACTTTCACTTCCGACCTG 58.166 47.619 0.00 0.00 31.01 4.00
1737 1780 2.169769 TGAACTTTCACTTCCGACCTGT 59.830 45.455 0.00 0.00 31.01 4.00
1739 1782 2.835027 ACTTTCACTTCCGACCTGTTC 58.165 47.619 0.00 0.00 0.00 3.18
1761 1804 4.766891 TCTGAGCCTTAATGTGGAAAAAGG 59.233 41.667 0.00 0.00 0.00 3.11
1765 1808 6.126911 TGAGCCTTAATGTGGAAAAAGGTTTT 60.127 34.615 0.00 0.00 0.00 2.43
1768 1811 9.095700 AGCCTTAATGTGGAAAAAGGTTTTATA 57.904 29.630 0.00 0.00 0.00 0.98
1769 1812 9.884636 GCCTTAATGTGGAAAAAGGTTTTATAT 57.115 29.630 0.00 0.00 0.00 0.86
1793 1836 8.884124 ATCCAGTAAAGATTGGAATTTTCTGA 57.116 30.769 6.04 0.00 44.04 3.27
1794 1837 8.340618 TCCAGTAAAGATTGGAATTTTCTGAG 57.659 34.615 6.04 0.00 38.46 3.35
1795 1838 7.031975 CCAGTAAAGATTGGAATTTTCTGAGC 58.968 38.462 6.04 0.00 36.48 4.26
1796 1839 7.309377 CCAGTAAAGATTGGAATTTTCTGAGCA 60.309 37.037 6.04 0.00 36.48 4.26
1797 1840 7.754027 CAGTAAAGATTGGAATTTTCTGAGCAG 59.246 37.037 0.00 0.00 36.48 4.24
1798 1841 6.661304 AAAGATTGGAATTTTCTGAGCAGT 57.339 33.333 0.00 0.00 0.00 4.40
1829 1872 0.960861 GTAAACTGCCCCTGCCTGTC 60.961 60.000 0.00 0.00 36.33 3.51
1833 1876 2.203922 TGCCCCTGCCTGTCTGTA 60.204 61.111 0.00 0.00 36.33 2.74
1858 1901 7.970102 ACTTGGTTTTCTATGGTACTAGTTGA 58.030 34.615 0.00 0.00 0.00 3.18
1859 1902 8.603304 ACTTGGTTTTCTATGGTACTAGTTGAT 58.397 33.333 0.00 0.00 0.00 2.57
1904 1949 5.327737 TCCTACCTTTGGTGGTTACAAAT 57.672 39.130 0.00 0.00 41.22 2.32
1905 1950 6.451292 TCCTACCTTTGGTGGTTACAAATA 57.549 37.500 0.00 0.00 41.22 1.40
1906 1951 6.478129 TCCTACCTTTGGTGGTTACAAATAG 58.522 40.000 0.00 0.00 41.22 1.73
1907 1952 6.272792 TCCTACCTTTGGTGGTTACAAATAGA 59.727 38.462 0.00 0.00 41.22 1.98
1949 1994 5.042463 TGTCTTCCTGTTAAACCATGTCA 57.958 39.130 0.00 0.00 0.00 3.58
1967 2012 7.069331 ACCATGTCACCTTCATTTGTTTTCTTA 59.931 33.333 0.00 0.00 0.00 2.10
2056 2102 0.669932 CTCTTGCAAGACTGAGCGCT 60.670 55.000 25.16 11.27 0.00 5.92
2148 2194 4.021719 CCAATGAGCTTGTTTTGTGGATCT 60.022 41.667 0.00 0.00 32.61 2.75
2221 2267 4.823442 TGAATATGATGAATGGTGTGCTCC 59.177 41.667 0.00 0.00 0.00 4.70
2299 2345 6.409524 TGTGAAGCCTCTTGAAATCATTTT 57.590 33.333 0.00 0.00 0.00 1.82
2338 2384 8.498054 TTTCCACATTAATTGTTTTTGCTGAA 57.502 26.923 0.00 0.00 36.00 3.02
2351 2397 4.405116 TTTGCTGAATTGCTTGGAGTTT 57.595 36.364 0.00 0.00 0.00 2.66
2471 2519 7.301054 GGTATTTCTATTATGAGCATGTGCAC 58.699 38.462 10.75 10.75 45.16 4.57
2522 2570 4.749245 AACGTCCTTGCATTCTGTTAAG 57.251 40.909 0.00 0.00 0.00 1.85
2588 2636 8.806177 AAAATTTAGGAAAATCACACGGTTAC 57.194 30.769 0.00 0.00 34.12 2.50
2674 2764 3.507233 TCGGAACAACGTGTATAAGGACT 59.493 43.478 0.00 0.00 34.94 3.85
2682 2772 5.916661 ACGTGTATAAGGACTGAGTCAAT 57.083 39.130 15.33 7.18 33.68 2.57
2711 2802 6.015434 GCCTTTCCCTTGAAGTTTTCTTATCA 60.015 38.462 0.00 0.00 40.61 2.15
2746 2839 6.804677 ACATTTTTCAAGTGCAACATGTCTA 58.195 32.000 0.00 0.00 41.43 2.59
2747 2840 7.264221 ACATTTTTCAAGTGCAACATGTCTAA 58.736 30.769 0.00 0.00 41.43 2.10
2792 3868 9.881529 GCATCAGTACTACATCTACTAAACTAC 57.118 37.037 0.00 0.00 0.00 2.73
2795 3871 9.829507 TCAGTACTACATCTACTAAACTACTCC 57.170 37.037 0.00 0.00 0.00 3.85
2796 3872 9.054922 CAGTACTACATCTACTAAACTACTCCC 57.945 40.741 0.00 0.00 0.00 4.30
2797 3873 8.217111 AGTACTACATCTACTAAACTACTCCCC 58.783 40.741 0.00 0.00 0.00 4.81
2798 3874 6.060788 ACTACATCTACTAAACTACTCCCCG 58.939 44.000 0.00 0.00 0.00 5.73
2799 3875 4.864726 ACATCTACTAAACTACTCCCCGT 58.135 43.478 0.00 0.00 0.00 5.28
2800 3876 5.267587 ACATCTACTAAACTACTCCCCGTT 58.732 41.667 0.00 0.00 0.00 4.44
2801 3877 5.359292 ACATCTACTAAACTACTCCCCGTTC 59.641 44.000 0.00 0.00 0.00 3.95
2802 3878 4.273318 TCTACTAAACTACTCCCCGTTCC 58.727 47.826 0.00 0.00 0.00 3.62
2803 3879 1.821136 ACTAAACTACTCCCCGTTCCG 59.179 52.381 0.00 0.00 0.00 4.30
2804 3880 2.094675 CTAAACTACTCCCCGTTCCGA 58.905 52.381 0.00 0.00 0.00 4.55
2805 3881 1.341080 AAACTACTCCCCGTTCCGAA 58.659 50.000 0.00 0.00 0.00 4.30
2806 3882 1.565067 AACTACTCCCCGTTCCGAAT 58.435 50.000 0.00 0.00 0.00 3.34
2807 3883 1.565067 ACTACTCCCCGTTCCGAATT 58.435 50.000 0.00 0.00 0.00 2.17
2808 3884 2.738743 ACTACTCCCCGTTCCGAATTA 58.261 47.619 0.00 0.00 0.00 1.40
2809 3885 2.428530 ACTACTCCCCGTTCCGAATTAC 59.571 50.000 0.00 0.00 0.00 1.89
2810 3886 1.565067 ACTCCCCGTTCCGAATTACT 58.435 50.000 0.00 0.00 0.00 2.24
2811 3887 1.904537 ACTCCCCGTTCCGAATTACTT 59.095 47.619 0.00 0.00 0.00 2.24
2812 3888 2.277084 CTCCCCGTTCCGAATTACTTG 58.723 52.381 0.00 0.00 0.00 3.16
2813 3889 1.624813 TCCCCGTTCCGAATTACTTGT 59.375 47.619 0.00 0.00 0.00 3.16
2814 3890 2.004733 CCCCGTTCCGAATTACTTGTC 58.995 52.381 0.00 0.00 0.00 3.18
2815 3891 1.657094 CCCGTTCCGAATTACTTGTCG 59.343 52.381 0.00 0.00 37.01 4.35
2816 3892 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2817 3893 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2818 3894 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
2819 3895 1.355971 TCCGAATTACTTGTCGCAGC 58.644 50.000 0.00 0.00 35.93 5.25
2820 3896 1.067142 TCCGAATTACTTGTCGCAGCT 60.067 47.619 0.00 0.00 35.93 4.24
2821 3897 2.164827 TCCGAATTACTTGTCGCAGCTA 59.835 45.455 0.00 0.00 35.93 3.32
2822 3898 3.123804 CCGAATTACTTGTCGCAGCTAT 58.876 45.455 0.00 0.00 35.93 2.97
2823 3899 3.060272 CCGAATTACTTGTCGCAGCTATG 60.060 47.826 0.00 0.00 35.93 2.23
2824 3900 3.060272 CGAATTACTTGTCGCAGCTATGG 60.060 47.826 0.00 0.00 0.00 2.74
2825 3901 3.819564 ATTACTTGTCGCAGCTATGGA 57.180 42.857 0.00 0.00 0.00 3.41
2826 3902 3.819564 TTACTTGTCGCAGCTATGGAT 57.180 42.857 0.00 0.00 0.00 3.41
2827 3903 1.945387 ACTTGTCGCAGCTATGGATG 58.055 50.000 0.00 0.00 0.00 3.51
2828 3904 1.208052 ACTTGTCGCAGCTATGGATGT 59.792 47.619 0.00 0.00 0.00 3.06
2829 3905 2.430694 ACTTGTCGCAGCTATGGATGTA 59.569 45.455 0.00 0.00 0.00 2.29
2830 3906 3.070159 ACTTGTCGCAGCTATGGATGTAT 59.930 43.478 0.00 0.00 0.00 2.29
2831 3907 3.303881 TGTCGCAGCTATGGATGTATC 57.696 47.619 0.00 0.00 0.00 2.24
2832 3908 2.893489 TGTCGCAGCTATGGATGTATCT 59.107 45.455 0.00 0.00 0.00 1.98
2833 3909 4.079253 TGTCGCAGCTATGGATGTATCTA 58.921 43.478 0.00 0.00 0.00 1.98
2834 3910 4.156739 TGTCGCAGCTATGGATGTATCTAG 59.843 45.833 0.00 0.00 0.00 2.43
2835 3911 4.396478 GTCGCAGCTATGGATGTATCTAGA 59.604 45.833 0.00 0.00 0.00 2.43
2836 3912 5.067153 GTCGCAGCTATGGATGTATCTAGAT 59.933 44.000 10.73 10.73 0.00 1.98
2837 3913 5.067023 TCGCAGCTATGGATGTATCTAGATG 59.933 44.000 15.79 0.00 32.27 2.90
2838 3914 5.163571 CGCAGCTATGGATGTATCTAGATGT 60.164 44.000 15.79 1.25 31.86 3.06
2839 3915 6.038714 CGCAGCTATGGATGTATCTAGATGTA 59.961 42.308 15.79 4.44 31.86 2.29
2840 3916 7.255416 CGCAGCTATGGATGTATCTAGATGTAT 60.255 40.741 15.79 9.11 31.86 2.29
2841 3917 8.420222 GCAGCTATGGATGTATCTAGATGTATT 58.580 37.037 15.79 0.00 31.86 1.89
2867 3943 9.587772 TTTAGTTCTAGATACACTCATTTCTGC 57.412 33.333 0.00 0.00 0.00 4.26
2868 3944 6.269315 AGTTCTAGATACACTCATTTCTGCG 58.731 40.000 0.00 0.00 0.00 5.18
2869 3945 6.095580 AGTTCTAGATACACTCATTTCTGCGA 59.904 38.462 0.00 0.00 0.00 5.10
2870 3946 5.822278 TCTAGATACACTCATTTCTGCGAC 58.178 41.667 0.00 0.00 0.00 5.19
2871 3947 3.439293 AGATACACTCATTTCTGCGACG 58.561 45.455 0.00 0.00 0.00 5.12
2872 3948 3.128764 AGATACACTCATTTCTGCGACGA 59.871 43.478 0.00 0.00 0.00 4.20
2873 3949 1.702886 ACACTCATTTCTGCGACGAG 58.297 50.000 0.00 0.00 0.00 4.18
2874 3950 1.000163 ACACTCATTTCTGCGACGAGT 60.000 47.619 0.00 0.00 37.42 4.18
2875 3951 2.228103 ACACTCATTTCTGCGACGAGTA 59.772 45.455 0.00 0.00 35.24 2.59
2876 3952 3.242518 CACTCATTTCTGCGACGAGTAA 58.757 45.455 0.00 0.00 35.24 2.24
2877 3953 3.859961 CACTCATTTCTGCGACGAGTAAT 59.140 43.478 0.00 0.00 35.24 1.89
2878 3954 4.327357 CACTCATTTCTGCGACGAGTAATT 59.673 41.667 0.00 0.00 35.24 1.40
2879 3955 4.929808 ACTCATTTCTGCGACGAGTAATTT 59.070 37.500 0.00 0.00 35.24 1.82
2880 3956 5.163953 ACTCATTTCTGCGACGAGTAATTTG 60.164 40.000 0.00 0.00 35.24 2.32
2881 3957 4.092821 TCATTTCTGCGACGAGTAATTTGG 59.907 41.667 0.00 0.00 0.00 3.28
2882 3958 2.736144 TCTGCGACGAGTAATTTGGT 57.264 45.000 0.00 0.00 0.00 3.67
2883 3959 3.853831 TCTGCGACGAGTAATTTGGTA 57.146 42.857 0.00 0.00 0.00 3.25
2884 3960 3.504863 TCTGCGACGAGTAATTTGGTAC 58.495 45.455 0.00 0.00 0.00 3.34
2885 3961 2.601763 CTGCGACGAGTAATTTGGTACC 59.398 50.000 4.43 4.43 0.00 3.34
2886 3962 1.585214 GCGACGAGTAATTTGGTACCG 59.415 52.381 7.57 0.00 0.00 4.02
2887 3963 2.731968 GCGACGAGTAATTTGGTACCGA 60.732 50.000 7.57 1.50 0.00 4.69
2888 3964 3.103738 CGACGAGTAATTTGGTACCGAG 58.896 50.000 7.57 0.00 0.00 4.63
2889 3965 3.442100 GACGAGTAATTTGGTACCGAGG 58.558 50.000 7.57 0.00 0.00 4.63
2890 3966 2.167075 ACGAGTAATTTGGTACCGAGGG 59.833 50.000 7.57 0.00 0.00 4.30
2891 3967 2.428171 CGAGTAATTTGGTACCGAGGGA 59.572 50.000 7.57 0.00 0.00 4.20
2892 3968 3.490419 CGAGTAATTTGGTACCGAGGGAG 60.490 52.174 7.57 0.00 0.00 4.30
2893 3969 3.447950 AGTAATTTGGTACCGAGGGAGT 58.552 45.455 7.57 0.00 0.00 3.85
2894 3970 3.450096 AGTAATTTGGTACCGAGGGAGTC 59.550 47.826 7.57 0.00 0.00 3.36
3113 4213 6.551227 AGGGAGCTAAAAATAACAATCCCATC 59.449 38.462 9.46 0.00 46.32 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.517453 CCCGACTGTTCTTTGACCAAATAA 59.483 41.667 0.00 0.00 0.00 1.40
89 92 5.526111 GCACTAAGAAACTGTACCAAAGTCA 59.474 40.000 0.00 0.00 0.00 3.41
101 104 7.335422 CAGAATCTACAATGGCACTAAGAAACT 59.665 37.037 0.00 0.00 0.00 2.66
180 183 7.133133 ACTCCTAAAGAAAGGTACAGAAACA 57.867 36.000 0.00 0.00 37.91 2.83
181 184 8.447924 AAACTCCTAAAGAAAGGTACAGAAAC 57.552 34.615 0.00 0.00 37.91 2.78
192 195 9.662947 GGTAGCTACATTAAACTCCTAAAGAAA 57.337 33.333 24.75 0.00 0.00 2.52
195 198 9.668497 AAAGGTAGCTACATTAAACTCCTAAAG 57.332 33.333 22.87 0.00 29.18 1.85
200 203 6.882678 TGGAAAAGGTAGCTACATTAAACTCC 59.117 38.462 22.87 22.46 29.18 3.85
208 211 8.034313 TCTATTCATGGAAAAGGTAGCTACAT 57.966 34.615 24.75 16.12 0.00 2.29
210 213 8.910351 ATTCTATTCATGGAAAAGGTAGCTAC 57.090 34.615 15.88 15.88 30.96 3.58
214 217 9.790344 ATCTGATTCTATTCATGGAAAAGGTAG 57.210 33.333 0.00 0.00 30.96 3.18
224 227 8.800332 CCCCCTAAAAATCTGATTCTATTCATG 58.200 37.037 2.92 0.00 0.00 3.07
225 228 8.736675 TCCCCCTAAAAATCTGATTCTATTCAT 58.263 33.333 2.92 0.00 0.00 2.57
226 229 8.113114 TCCCCCTAAAAATCTGATTCTATTCA 57.887 34.615 2.92 0.00 0.00 2.57
227 230 8.440771 TCTCCCCCTAAAAATCTGATTCTATTC 58.559 37.037 2.92 0.00 0.00 1.75
263 267 9.746457 GAGGGCCTAAAATAAATCTGAATCTAT 57.254 33.333 5.73 0.00 0.00 1.98
268 272 8.664669 AAAAGAGGGCCTAAAATAAATCTGAA 57.335 30.769 5.73 0.00 0.00 3.02
269 273 9.936329 ATAAAAGAGGGCCTAAAATAAATCTGA 57.064 29.630 5.73 0.00 0.00 3.27
277 281 9.579932 CTGATTCTATAAAAGAGGGCCTAAAAT 57.420 33.333 5.73 0.00 35.05 1.82
381 385 6.370166 GGGCATACAGCTGATTCTATACTTTC 59.630 42.308 23.35 0.00 44.79 2.62
385 391 5.152623 TGGGCATACAGCTGATTCTATAC 57.847 43.478 23.35 2.16 44.79 1.47
400 406 0.833287 GAGCTGTTCTCCTGGGCATA 59.167 55.000 0.00 0.00 35.77 3.14
431 437 1.547472 GGCTGCTTTTTGGGCTGGAT 61.547 55.000 0.00 0.00 0.00 3.41
625 631 0.676736 AGCTTATAGAGTGGCCTCGC 59.323 55.000 3.32 1.25 42.86 5.03
640 646 4.067192 GCAAATTGAACAATTGGGAGCTT 58.933 39.130 10.83 0.00 40.57 3.74
730 737 1.560923 CGAGAGCATACCAAGGAACG 58.439 55.000 0.00 0.00 0.00 3.95
858 866 4.619973 TCTAGAGAACTATCGGACGAGAC 58.380 47.826 0.00 0.00 0.00 3.36
873 881 5.696030 TCTTGCACCTAGCTAATCTAGAGA 58.304 41.667 0.00 0.00 46.12 3.10
949 958 3.845781 ACCACTGAATATGAAGCCGAT 57.154 42.857 0.00 0.00 0.00 4.18
980 989 6.766467 CGCCATTTATCCTAACCTAGAAAACT 59.234 38.462 0.00 0.00 0.00 2.66
981 990 6.764560 TCGCCATTTATCCTAACCTAGAAAAC 59.235 38.462 0.00 0.00 0.00 2.43
986 995 4.235360 CGTCGCCATTTATCCTAACCTAG 58.765 47.826 0.00 0.00 0.00 3.02
1162 1171 1.858739 TTCAACCAATCGGGGGAGGG 61.859 60.000 0.00 0.00 42.91 4.30
1170 1179 4.414852 AGCATTCGAAATTCAACCAATCG 58.585 39.130 0.00 0.00 34.98 3.34
1176 1185 6.498304 ACATCCATAGCATTCGAAATTCAAC 58.502 36.000 0.00 0.00 0.00 3.18
1187 1196 2.439507 ACGAAGGGACATCCATAGCATT 59.560 45.455 0.00 0.00 38.24 3.56
1196 1205 0.895530 TCAGTGGACGAAGGGACATC 59.104 55.000 0.00 0.00 0.00 3.06
1197 1206 0.608640 GTCAGTGGACGAAGGGACAT 59.391 55.000 0.00 0.00 33.68 3.06
1217 1226 1.110442 CACCAAACACCAAGCCTTCA 58.890 50.000 0.00 0.00 0.00 3.02
1220 1229 0.033601 TCACACCAAACACCAAGCCT 60.034 50.000 0.00 0.00 0.00 4.58
1221 1230 1.039856 ATCACACCAAACACCAAGCC 58.960 50.000 0.00 0.00 0.00 4.35
1223 1232 5.174395 TGAAAAATCACACCAAACACCAAG 58.826 37.500 0.00 0.00 0.00 3.61
1224 1233 5.152623 TGAAAAATCACACCAAACACCAA 57.847 34.783 0.00 0.00 0.00 3.67
1225 1234 4.382470 CCTGAAAAATCACACCAAACACCA 60.382 41.667 0.00 0.00 0.00 4.17
1226 1235 4.119136 CCTGAAAAATCACACCAAACACC 58.881 43.478 0.00 0.00 0.00 4.16
1227 1236 3.555547 GCCTGAAAAATCACACCAAACAC 59.444 43.478 0.00 0.00 0.00 3.32
1228 1237 3.431486 GGCCTGAAAAATCACACCAAACA 60.431 43.478 0.00 0.00 0.00 2.83
1229 1238 3.130633 GGCCTGAAAAATCACACCAAAC 58.869 45.455 0.00 0.00 0.00 2.93
1230 1239 3.037549 AGGCCTGAAAAATCACACCAAA 58.962 40.909 3.11 0.00 0.00 3.28
1231 1240 2.364970 CAGGCCTGAAAAATCACACCAA 59.635 45.455 29.88 0.00 0.00 3.67
1232 1241 1.962807 CAGGCCTGAAAAATCACACCA 59.037 47.619 29.88 0.00 0.00 4.17
1233 1242 1.273327 CCAGGCCTGAAAAATCACACC 59.727 52.381 34.91 0.00 0.00 4.16
1234 1243 1.337167 GCCAGGCCTGAAAAATCACAC 60.337 52.381 34.91 6.00 0.00 3.82
1235 1244 0.968405 GCCAGGCCTGAAAAATCACA 59.032 50.000 34.91 0.00 0.00 3.58
1236 1245 0.968405 TGCCAGGCCTGAAAAATCAC 59.032 50.000 34.91 12.30 0.00 3.06
1237 1246 1.714541 TTGCCAGGCCTGAAAAATCA 58.285 45.000 34.91 17.11 0.00 2.57
1238 1247 2.224257 TGTTTGCCAGGCCTGAAAAATC 60.224 45.455 34.91 22.78 0.00 2.17
1239 1248 1.767681 TGTTTGCCAGGCCTGAAAAAT 59.232 42.857 34.91 0.00 0.00 1.82
1240 1249 1.198713 TGTTTGCCAGGCCTGAAAAA 58.801 45.000 34.91 27.22 0.00 1.94
1291 1300 1.006758 AGGACCACGGTCATCTCCTTA 59.993 52.381 17.72 0.00 46.20 2.69
1321 1330 4.286101 GCTTGTTCTGCTTCTTTGACTTC 58.714 43.478 0.00 0.00 0.00 3.01
1351 1360 2.620251 TGACAGTCTTGTGGGTGAAG 57.380 50.000 1.31 0.00 37.76 3.02
1403 1412 6.100279 TCTGATGCTAATACCTGGTTCTTGAT 59.900 38.462 3.84 0.00 0.00 2.57
1439 1448 8.843733 CATCACAACTTTCATCATAAAAGAACG 58.156 33.333 2.84 0.00 37.22 3.95
1453 1463 2.821969 ACCATCCAGCATCACAACTTTC 59.178 45.455 0.00 0.00 0.00 2.62
1456 1466 1.632409 AGACCATCCAGCATCACAACT 59.368 47.619 0.00 0.00 0.00 3.16
1524 1534 3.020984 ACCGAAACACTGAAATGGTTGT 58.979 40.909 0.00 0.00 26.57 3.32
1533 1543 1.538512 CTACGAGGACCGAAACACTGA 59.461 52.381 0.00 0.00 41.76 3.41
1547 1557 5.694910 ACAACAGTTACATTTCACCTACGAG 59.305 40.000 0.00 0.00 0.00 4.18
1548 1558 5.464057 CACAACAGTTACATTTCACCTACGA 59.536 40.000 0.00 0.00 0.00 3.43
1549 1559 5.464057 TCACAACAGTTACATTTCACCTACG 59.536 40.000 0.00 0.00 0.00 3.51
1550 1560 6.854496 TCACAACAGTTACATTTCACCTAC 57.146 37.500 0.00 0.00 0.00 3.18
1561 1571 5.438761 AAGAAGCCAATCACAACAGTTAC 57.561 39.130 0.00 0.00 0.00 2.50
1570 1580 6.874134 TCAGACTAAACTAAGAAGCCAATCAC 59.126 38.462 0.00 0.00 0.00 3.06
1573 1583 8.870075 AAATCAGACTAAACTAAGAAGCCAAT 57.130 30.769 0.00 0.00 0.00 3.16
1593 1607 7.345653 ACAGTCCCTACAGATGATTAGAAATCA 59.654 37.037 4.90 4.90 0.00 2.57
1594 1608 7.655328 CACAGTCCCTACAGATGATTAGAAATC 59.345 40.741 0.00 0.00 0.00 2.17
1597 1611 5.958380 ACACAGTCCCTACAGATGATTAGAA 59.042 40.000 0.00 0.00 0.00 2.10
1605 1619 6.620877 TTTCATAACACAGTCCCTACAGAT 57.379 37.500 0.00 0.00 0.00 2.90
1692 1723 9.599866 TCACATACTAGATACAACCAAATTGAG 57.400 33.333 0.00 0.00 41.23 3.02
1695 1726 9.959721 AGTTCACATACTAGATACAACCAAATT 57.040 29.630 0.00 0.00 0.00 1.82
1719 1762 2.434702 AGAACAGGTCGGAAGTGAAAGT 59.565 45.455 0.00 0.00 0.00 2.66
1720 1763 2.802816 CAGAACAGGTCGGAAGTGAAAG 59.197 50.000 0.00 0.00 0.00 2.62
1729 1772 0.895530 TAAGGCTCAGAACAGGTCGG 59.104 55.000 0.00 0.00 0.00 4.79
1730 1773 2.743636 TTAAGGCTCAGAACAGGTCG 57.256 50.000 0.00 0.00 0.00 4.79
1734 1777 3.942829 TCCACATTAAGGCTCAGAACAG 58.057 45.455 0.00 0.00 0.00 3.16
1735 1778 4.365514 TTCCACATTAAGGCTCAGAACA 57.634 40.909 0.00 0.00 0.00 3.18
1736 1779 5.705609 TTTTCCACATTAAGGCTCAGAAC 57.294 39.130 0.00 0.00 0.00 3.01
1737 1780 5.243730 CCTTTTTCCACATTAAGGCTCAGAA 59.756 40.000 0.00 0.00 31.59 3.02
1739 1782 4.524328 ACCTTTTTCCACATTAAGGCTCAG 59.476 41.667 0.00 0.00 40.63 3.35
1768 1811 8.884124 TCAGAAAATTCCAATCTTTACTGGAT 57.116 30.769 0.00 0.00 41.36 3.41
1769 1812 7.094205 GCTCAGAAAATTCCAATCTTTACTGGA 60.094 37.037 0.00 0.00 40.03 3.86
1770 1813 7.031975 GCTCAGAAAATTCCAATCTTTACTGG 58.968 38.462 0.00 0.00 0.00 4.00
1785 1828 5.191426 AGACATGCATACTGCTCAGAAAAT 58.809 37.500 0.00 0.00 45.31 1.82
1786 1829 4.582869 AGACATGCATACTGCTCAGAAAA 58.417 39.130 0.00 0.00 45.31 2.29
1787 1830 4.212143 AGACATGCATACTGCTCAGAAA 57.788 40.909 0.00 0.00 45.31 2.52
1788 1831 3.900966 AGACATGCATACTGCTCAGAA 57.099 42.857 0.00 0.00 45.31 3.02
1789 1832 3.055602 ACAAGACATGCATACTGCTCAGA 60.056 43.478 0.00 0.00 45.31 3.27
1790 1833 3.268330 ACAAGACATGCATACTGCTCAG 58.732 45.455 0.00 0.00 45.31 3.35
1791 1834 3.339253 ACAAGACATGCATACTGCTCA 57.661 42.857 0.00 0.00 45.31 4.26
1792 1835 5.352569 AGTTTACAAGACATGCATACTGCTC 59.647 40.000 0.00 0.00 45.31 4.26
1793 1836 5.122869 CAGTTTACAAGACATGCATACTGCT 59.877 40.000 0.00 0.00 45.31 4.24
1794 1837 5.327091 CAGTTTACAAGACATGCATACTGC 58.673 41.667 0.00 0.00 45.29 4.40
1795 1838 5.327091 GCAGTTTACAAGACATGCATACTG 58.673 41.667 13.60 13.60 37.07 2.74
1796 1839 4.396166 GGCAGTTTACAAGACATGCATACT 59.604 41.667 0.00 0.00 35.40 2.12
1797 1840 4.438744 GGGCAGTTTACAAGACATGCATAC 60.439 45.833 0.00 0.00 35.40 2.39
1798 1841 3.694072 GGGCAGTTTACAAGACATGCATA 59.306 43.478 0.00 0.00 35.40 3.14
1803 1846 2.795329 CAGGGGCAGTTTACAAGACAT 58.205 47.619 0.00 0.00 0.00 3.06
1829 1872 8.529476 ACTAGTACCATAGAAAACCAAGTACAG 58.471 37.037 0.00 0.00 32.88 2.74
1833 1876 7.970102 TCAACTAGTACCATAGAAAACCAAGT 58.030 34.615 0.00 0.00 0.00 3.16
1858 1901 9.754382 GGAAGCATTGATGTTTATGTTCATTAT 57.246 29.630 0.00 0.00 31.18 1.28
1859 1902 8.970020 AGGAAGCATTGATGTTTATGTTCATTA 58.030 29.630 0.00 0.00 31.18 1.90
1864 1907 6.891908 AGGTAGGAAGCATTGATGTTTATGTT 59.108 34.615 0.00 0.00 31.18 2.71
1865 1908 6.426587 AGGTAGGAAGCATTGATGTTTATGT 58.573 36.000 0.00 0.00 31.18 2.29
1866 1909 6.949352 AGGTAGGAAGCATTGATGTTTATG 57.051 37.500 0.00 0.00 31.18 1.90
1867 1910 7.147846 CCAAAGGTAGGAAGCATTGATGTTTAT 60.148 37.037 0.00 0.00 34.57 1.40
1868 1911 6.152661 CCAAAGGTAGGAAGCATTGATGTTTA 59.847 38.462 0.00 0.00 34.57 2.01
1869 1912 5.047092 CCAAAGGTAGGAAGCATTGATGTTT 60.047 40.000 0.00 0.00 34.57 2.83
1870 1913 4.463891 CCAAAGGTAGGAAGCATTGATGTT 59.536 41.667 0.00 0.00 34.57 2.71
1871 1914 4.019174 CCAAAGGTAGGAAGCATTGATGT 58.981 43.478 0.00 0.00 34.57 3.06
1872 1915 4.019174 ACCAAAGGTAGGAAGCATTGATG 58.981 43.478 0.00 0.00 34.57 3.07
1873 1916 4.019174 CACCAAAGGTAGGAAGCATTGAT 58.981 43.478 0.00 0.00 34.57 2.57
1874 1917 3.420893 CACCAAAGGTAGGAAGCATTGA 58.579 45.455 0.00 0.00 34.57 2.57
1875 1918 2.493278 CCACCAAAGGTAGGAAGCATTG 59.507 50.000 0.00 0.00 32.11 2.82
1876 1919 2.110011 ACCACCAAAGGTAGGAAGCATT 59.890 45.455 10.33 0.00 40.98 3.56
1877 1920 1.710809 ACCACCAAAGGTAGGAAGCAT 59.289 47.619 10.33 0.00 40.98 3.79
1878 1921 1.145571 ACCACCAAAGGTAGGAAGCA 58.854 50.000 10.33 0.00 40.98 3.91
1879 1922 2.287977 AACCACCAAAGGTAGGAAGC 57.712 50.000 10.33 0.00 42.25 3.86
1880 1923 4.360951 TGTAACCACCAAAGGTAGGAAG 57.639 45.455 10.33 0.00 42.25 3.46
1881 1924 4.792513 TTGTAACCACCAAAGGTAGGAA 57.207 40.909 10.33 0.00 42.25 3.36
1904 1949 5.939764 TCTTAAGCAGCATTTCTCCTCTA 57.060 39.130 0.00 0.00 0.00 2.43
1905 1950 4.833478 TCTTAAGCAGCATTTCTCCTCT 57.167 40.909 0.00 0.00 0.00 3.69
1906 1951 4.880696 ACATCTTAAGCAGCATTTCTCCTC 59.119 41.667 0.00 0.00 0.00 3.71
1907 1952 4.853007 ACATCTTAAGCAGCATTTCTCCT 58.147 39.130 0.00 0.00 0.00 3.69
1975 2020 5.385198 ACCTGGAAAGCAAGAAGAATAACA 58.615 37.500 0.00 0.00 0.00 2.41
2056 2102 1.003839 CTGGAGGCTGCGGTAAACA 60.004 57.895 6.69 0.00 0.00 2.83
2148 2194 5.606348 AAAGCTGGAAACATAAACCAACA 57.394 34.783 0.00 0.00 41.51 3.33
2196 2242 6.015688 GGAGCACACCATTCATCATATTCAAT 60.016 38.462 0.00 0.00 0.00 2.57
2221 2267 2.226437 AGAAAACTTGTGCCAGTATGCG 59.774 45.455 0.00 0.00 31.97 4.73
2338 2384 2.295349 CAGCACTCAAACTCCAAGCAAT 59.705 45.455 0.00 0.00 0.00 3.56
2351 2397 2.030958 CACGCATCAGCAGCACTCA 61.031 57.895 0.00 0.00 42.27 3.41
2445 2493 6.147656 TGCACATGCTCATAATAGAAATACCG 59.852 38.462 5.31 0.00 42.66 4.02
2471 2519 7.293745 GTGATATGATAAACCGATCAGCTTTG 58.706 38.462 0.00 0.00 39.18 2.77
2522 2570 9.665264 GTGTCTTAGTAAATAAAATAGGCATGC 57.335 33.333 9.90 9.90 0.00 4.06
2674 2764 1.004745 GGGAAAGGCCTGATTGACTCA 59.995 52.381 5.69 0.00 36.66 3.41
2682 2772 1.149101 ACTTCAAGGGAAAGGCCTGA 58.851 50.000 5.69 0.00 36.66 3.86
2711 2802 8.629158 TGCACTTGAAAAATGTAAAGTATCAGT 58.371 29.630 0.00 0.00 31.80 3.41
2724 2815 6.421801 GCTTAGACATGTTGCACTTGAAAAAT 59.578 34.615 0.00 0.00 0.00 1.82
2747 2840 2.892852 TGCAACAAAAGCCTAAGATGCT 59.107 40.909 0.00 0.00 41.89 3.79
2798 3874 2.474032 GCTGCGACAAGTAATTCGGAAC 60.474 50.000 0.00 0.00 35.02 3.62
2799 3875 1.730064 GCTGCGACAAGTAATTCGGAA 59.270 47.619 0.00 0.00 35.02 4.30
2800 3876 1.067142 AGCTGCGACAAGTAATTCGGA 60.067 47.619 0.00 0.00 35.73 4.55
2801 3877 1.359848 AGCTGCGACAAGTAATTCGG 58.640 50.000 0.00 0.00 35.73 4.30
2802 3878 3.060272 CCATAGCTGCGACAAGTAATTCG 60.060 47.826 0.00 0.00 38.31 3.34
2803 3879 4.119862 TCCATAGCTGCGACAAGTAATTC 58.880 43.478 0.00 0.00 0.00 2.17
2804 3880 4.137116 TCCATAGCTGCGACAAGTAATT 57.863 40.909 0.00 0.00 0.00 1.40
2805 3881 3.819564 TCCATAGCTGCGACAAGTAAT 57.180 42.857 0.00 0.00 0.00 1.89
2806 3882 3.118775 ACATCCATAGCTGCGACAAGTAA 60.119 43.478 0.00 0.00 0.00 2.24
2807 3883 2.430694 ACATCCATAGCTGCGACAAGTA 59.569 45.455 0.00 0.00 0.00 2.24
2808 3884 1.208052 ACATCCATAGCTGCGACAAGT 59.792 47.619 0.00 0.00 0.00 3.16
2809 3885 1.945387 ACATCCATAGCTGCGACAAG 58.055 50.000 0.00 0.00 0.00 3.16
2810 3886 3.321968 AGATACATCCATAGCTGCGACAA 59.678 43.478 0.00 0.00 0.00 3.18
2811 3887 2.893489 AGATACATCCATAGCTGCGACA 59.107 45.455 0.00 0.00 0.00 4.35
2812 3888 3.584406 AGATACATCCATAGCTGCGAC 57.416 47.619 0.00 0.00 0.00 5.19
2813 3889 4.589908 TCTAGATACATCCATAGCTGCGA 58.410 43.478 0.00 0.00 0.00 5.10
2814 3890 4.972514 TCTAGATACATCCATAGCTGCG 57.027 45.455 0.00 0.00 0.00 5.18
2815 3891 6.219417 ACATCTAGATACATCCATAGCTGC 57.781 41.667 4.54 0.00 0.00 5.25
2841 3917 9.587772 GCAGAAATGAGTGTATCTAGAACTAAA 57.412 33.333 0.00 0.00 0.00 1.85
2842 3918 7.915923 CGCAGAAATGAGTGTATCTAGAACTAA 59.084 37.037 0.00 0.00 0.00 2.24
2843 3919 7.282450 TCGCAGAAATGAGTGTATCTAGAACTA 59.718 37.037 0.00 0.00 0.00 2.24
2844 3920 6.095580 TCGCAGAAATGAGTGTATCTAGAACT 59.904 38.462 0.00 0.00 0.00 3.01
2845 3921 6.197468 GTCGCAGAAATGAGTGTATCTAGAAC 59.803 42.308 0.00 0.00 39.69 3.01
2846 3922 6.266323 GTCGCAGAAATGAGTGTATCTAGAA 58.734 40.000 0.00 0.00 39.69 2.10
2847 3923 5.504173 CGTCGCAGAAATGAGTGTATCTAGA 60.504 44.000 0.00 0.00 39.69 2.43
2848 3924 4.672862 CGTCGCAGAAATGAGTGTATCTAG 59.327 45.833 0.00 0.00 39.69 2.43
2849 3925 4.334481 TCGTCGCAGAAATGAGTGTATCTA 59.666 41.667 0.00 0.00 39.69 1.98
2850 3926 3.128764 TCGTCGCAGAAATGAGTGTATCT 59.871 43.478 0.00 0.00 39.69 1.98
2851 3927 3.435566 TCGTCGCAGAAATGAGTGTATC 58.564 45.455 0.00 0.00 39.69 2.24
2852 3928 3.119459 ACTCGTCGCAGAAATGAGTGTAT 60.119 43.478 0.00 0.00 41.82 2.29
2853 3929 2.228103 ACTCGTCGCAGAAATGAGTGTA 59.772 45.455 0.00 0.00 41.82 2.90
2854 3930 1.000163 ACTCGTCGCAGAAATGAGTGT 60.000 47.619 0.00 0.00 41.82 3.55
2855 3931 1.702886 ACTCGTCGCAGAAATGAGTG 58.297 50.000 0.00 0.00 41.82 3.51
2856 3932 3.570926 TTACTCGTCGCAGAAATGAGT 57.429 42.857 3.72 3.72 44.25 3.41
2857 3933 5.251081 CAAATTACTCGTCGCAGAAATGAG 58.749 41.667 0.00 0.00 39.69 2.90
2858 3934 4.092821 CCAAATTACTCGTCGCAGAAATGA 59.907 41.667 0.00 0.00 39.69 2.57
2859 3935 4.142902 ACCAAATTACTCGTCGCAGAAATG 60.143 41.667 0.00 0.00 39.69 2.32
2860 3936 4.000988 ACCAAATTACTCGTCGCAGAAAT 58.999 39.130 0.00 0.00 39.69 2.17
2861 3937 3.395639 ACCAAATTACTCGTCGCAGAAA 58.604 40.909 0.00 0.00 39.69 2.52
2862 3938 3.034721 ACCAAATTACTCGTCGCAGAA 57.965 42.857 0.00 0.00 39.69 3.02
2863 3939 2.736144 ACCAAATTACTCGTCGCAGA 57.264 45.000 0.00 0.00 0.00 4.26
2864 3940 2.601763 GGTACCAAATTACTCGTCGCAG 59.398 50.000 7.15 0.00 0.00 5.18
2865 3941 2.609350 GGTACCAAATTACTCGTCGCA 58.391 47.619 7.15 0.00 0.00 5.10
2866 3942 1.585214 CGGTACCAAATTACTCGTCGC 59.415 52.381 13.54 0.00 0.00 5.19
2867 3943 3.103738 CTCGGTACCAAATTACTCGTCG 58.896 50.000 13.54 0.00 0.00 5.12
2868 3944 3.442100 CCTCGGTACCAAATTACTCGTC 58.558 50.000 13.54 0.00 0.00 4.20
2869 3945 2.167075 CCCTCGGTACCAAATTACTCGT 59.833 50.000 13.54 0.00 0.00 4.18
2870 3946 2.428171 TCCCTCGGTACCAAATTACTCG 59.572 50.000 13.54 0.00 0.00 4.18
2871 3947 3.450096 ACTCCCTCGGTACCAAATTACTC 59.550 47.826 13.54 0.00 0.00 2.59
2872 3948 3.447950 ACTCCCTCGGTACCAAATTACT 58.552 45.455 13.54 0.00 0.00 2.24
2873 3949 3.450096 AGACTCCCTCGGTACCAAATTAC 59.550 47.826 13.54 0.00 0.00 1.89
2874 3950 3.716431 AGACTCCCTCGGTACCAAATTA 58.284 45.455 13.54 0.00 0.00 1.40
2875 3951 2.547990 AGACTCCCTCGGTACCAAATT 58.452 47.619 13.54 0.00 0.00 1.82
2876 3952 2.249309 AGACTCCCTCGGTACCAAAT 57.751 50.000 13.54 0.00 0.00 2.32
2877 3953 2.905415 TAGACTCCCTCGGTACCAAA 57.095 50.000 13.54 0.00 0.00 3.28
2878 3954 2.905415 TTAGACTCCCTCGGTACCAA 57.095 50.000 13.54 0.00 0.00 3.67
2879 3955 2.024655 ACATTAGACTCCCTCGGTACCA 60.025 50.000 13.54 0.00 0.00 3.25
2880 3956 2.664015 ACATTAGACTCCCTCGGTACC 58.336 52.381 0.16 0.16 0.00 3.34
2881 3957 4.081807 ACAAACATTAGACTCCCTCGGTAC 60.082 45.833 0.00 0.00 0.00 3.34
2882 3958 4.091549 ACAAACATTAGACTCCCTCGGTA 58.908 43.478 0.00 0.00 0.00 4.02
2883 3959 2.904434 ACAAACATTAGACTCCCTCGGT 59.096 45.455 0.00 0.00 0.00 4.69
2884 3960 3.611766 ACAAACATTAGACTCCCTCGG 57.388 47.619 0.00 0.00 0.00 4.63
2885 3961 4.994852 TGAAACAAACATTAGACTCCCTCG 59.005 41.667 0.00 0.00 0.00 4.63
2886 3962 6.431234 ACATGAAACAAACATTAGACTCCCTC 59.569 38.462 0.00 0.00 0.00 4.30
2887 3963 6.306987 ACATGAAACAAACATTAGACTCCCT 58.693 36.000 0.00 0.00 0.00 4.20
2888 3964 6.575162 ACATGAAACAAACATTAGACTCCC 57.425 37.500 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.