Multiple sequence alignment - TraesCS3B01G490600

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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 TraesCS3B01G490600 chr3B 100.000 3169 0 0 1 3169 736674291 736671123 0.000000e+00 5853.0
1 TraesCS3B01G490600 chr3B 77.919 471 78 17 1722 2170 736665892 736665426 1.450000e-68 270.0
2 TraesCS3B01G490600 chr3A 86.316 1637 117 52 998 2577 690977354 690975768 0.000000e+00 1683.0
3 TraesCS3B01G490600 chr3A 99.217 383 3 0 2578 2960 12466958 12466576 0.000000e+00 691.0
4 TraesCS3B01G490600 chr3A 86.134 476 49 5 1712 2170 691063668 691063193 6.100000e-137 497.0
5 TraesCS3B01G490600 chr3A 89.637 386 35 3 1 381 690978151 690977766 1.320000e-133 486.0
6 TraesCS3B01G490600 chr3A 89.972 359 34 2 2578 2936 416164119 416164475 2.230000e-126 462.0
7 TraesCS3B01G490600 chr3A 98.883 179 2 0 2991 3169 12466575 12466397 1.420000e-83 320.0
8 TraesCS3B01G490600 chr3A 86.842 228 25 5 408 631 690977768 690977542 1.890000e-62 250.0
9 TraesCS3B01G490600 chr3A 90.854 164 14 1 1000 1163 691076848 691076686 5.320000e-53 219.0
10 TraesCS3B01G490600 chr3D 92.680 888 40 15 1710 2577 554398812 554397930 0.000000e+00 1256.0
11 TraesCS3B01G490600 chr3D 83.243 555 63 23 879 1419 554399986 554399448 1.710000e-132 483.0
12 TraesCS3B01G490600 chr3D 89.860 286 27 1 1 284 554400868 554400583 1.800000e-97 366.0
13 TraesCS3B01G490600 chr3D 78.556 471 75 17 1722 2170 554383480 554383014 1.440000e-73 287.0
14 TraesCS3B01G490600 chr3D 82.143 224 32 6 408 627 554400529 554400310 5.400000e-43 185.0
15 TraesCS3B01G490600 chr3D 79.191 173 11 15 1459 1612 554399264 554399098 2.600000e-16 97.1
16 TraesCS3B01G490600 chr7B 89.344 366 36 3 2572 2936 327256461 327256098 1.040000e-124 457.0
17 TraesCS3B01G490600 chr7B 89.344 366 36 3 2572 2936 327261686 327261323 1.040000e-124 457.0
18 TraesCS3B01G490600 chr4D 79.227 414 37 19 888 1265 187475749 187476149 3.160000e-60 243.0
19 TraesCS3B01G490600 chr6B 97.260 73 2 0 3097 3169 627449047 627449119 1.190000e-24 124.0
20 TraesCS3B01G490600 chr6B 97.260 73 2 0 3097 3169 627490057 627490129 1.190000e-24 124.0
21 TraesCS3B01G490600 chr6B 97.260 73 2 0 3097 3169 627522243 627522315 1.190000e-24 124.0
22 TraesCS3B01G490600 chr4A 97.260 73 2 0 3097 3169 727088937 727088865 1.190000e-24 124.0
23 TraesCS3B01G490600 chr2B 92.941 85 4 2 3087 3169 104014185 104014101 4.290000e-24 122.0
24 TraesCS3B01G490600 chr2B 95.000 40 2 0 2970 3009 96081658 96081619 2.640000e-06 63.9
25 TraesCS3B01G490600 chr2B 94.872 39 1 1 2975 3012 748072880 748072918 3.410000e-05 60.2
26 TraesCS3B01G490600 chr2D 95.890 73 3 0 3097 3169 113794463 113794535 5.550000e-23 119.0
27 TraesCS3B01G490600 chr1B 95.890 73 3 0 3097 3169 454750338 454750266 5.550000e-23 119.0
28 TraesCS3B01G490600 chr1A 95.890 73 3 0 3097 3169 208592283 208592355 5.550000e-23 119.0
29 TraesCS3B01G490600 chr5B 94.286 35 1 1 2975 3008 655193464 655193498 6.000000e-03 52.8


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 TraesCS3B01G490600 chr3B 736671123 736674291 3168 True 5853.000000 5853 100.000000 1 3169 1 chr3B.!!$R2 3168
1 TraesCS3B01G490600 chr3A 690975768 690978151 2383 True 806.333333 1683 87.598333 1 2577 3 chr3A.!!$R4 2576
2 TraesCS3B01G490600 chr3A 12466397 12466958 561 True 505.500000 691 99.050000 2578 3169 2 chr3A.!!$R3 591
3 TraesCS3B01G490600 chr3D 554397930 554400868 2938 True 477.420000 1256 85.423400 1 2577 5 chr3D.!!$R2 2576

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
934 1040 0.111639 AGAGAGAGCGGATAGGGGTC 59.888 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 2675 0.036732 TAGGCAAGCAACCACCTCAG 59.963 55.0 0.0 0.0 33.6 3.35 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
38 39 4.706962 ACCCATTGAGCCATAGAGAAAAAC 59.293 41.667 0.00 0.00 0.00 2.43
43 44 5.689383 TGAGCCATAGAGAAAAACACAAC 57.311 39.130 0.00 0.00 0.00 3.32
50 51 6.198216 CCATAGAGAAAAACACAACCAAAACG 59.802 38.462 0.00 0.00 0.00 3.60
84 85 8.931385 ATCAATTGTTCACATGGCTATAAAAC 57.069 30.769 5.13 0.00 0.00 2.43
166 167 2.693591 TGATAGTAGAAGTTGGGCCTCG 59.306 50.000 4.53 0.00 0.00 4.63
192 195 2.094894 GGTCATTCTGCTCAATGTGTCG 59.905 50.000 7.73 0.00 35.56 4.35
193 196 1.733912 TCATTCTGCTCAATGTGTCGC 59.266 47.619 7.73 0.00 35.56 5.19
209 212 0.179150 TCGCAGTTGTGTTGTTTGGC 60.179 50.000 0.00 0.00 0.00 4.52
259 263 2.124693 GGAGAGGGCGAGAGAGTGG 61.125 68.421 0.00 0.00 0.00 4.00
275 279 1.002403 TGGCGGGGAGTTATGGAGA 59.998 57.895 0.00 0.00 0.00 3.71
297 301 2.419297 GGCGATGGAGATGGATGGATAC 60.419 54.545 0.00 0.00 0.00 2.24
308 312 3.376636 TGGATGGATACCCTTTCGTACA 58.623 45.455 0.00 0.00 0.00 2.90
316 320 6.887545 TGGATACCCTTTCGTACAATGAAATT 59.112 34.615 0.00 0.00 36.63 1.82
330 334 3.451141 TGAAATTGTTTGTGTGAGGGC 57.549 42.857 0.00 0.00 0.00 5.19
339 343 1.968540 GTGTGAGGGCTTGCTCCAC 60.969 63.158 7.01 7.01 0.00 4.02
355 363 2.038269 CACGCAAACGGGTGGCTAT 61.038 57.895 2.00 0.00 46.04 2.97
375 383 1.966451 CCTGACGTGGCAAACCTCC 60.966 63.158 0.00 0.00 36.63 4.30
376 384 1.966451 CTGACGTGGCAAACCTCCC 60.966 63.158 0.00 0.00 36.63 4.30
377 385 3.047877 GACGTGGCAAACCTCCCG 61.048 66.667 0.00 0.00 36.63 5.14
378 386 3.819877 GACGTGGCAAACCTCCCGT 62.820 63.158 0.00 0.00 37.90 5.28
379 387 3.353836 CGTGGCAAACCTCCCGTG 61.354 66.667 0.00 0.00 36.63 4.94
380 388 3.670377 GTGGCAAACCTCCCGTGC 61.670 66.667 0.00 0.00 36.63 5.34
381 389 3.884774 TGGCAAACCTCCCGTGCT 61.885 61.111 0.00 0.00 38.36 4.40
382 390 2.597510 GGCAAACCTCCCGTGCTT 60.598 61.111 0.00 0.00 38.36 3.91
383 391 2.626780 GGCAAACCTCCCGTGCTTC 61.627 63.158 0.00 0.00 38.36 3.86
384 392 1.896660 GCAAACCTCCCGTGCTTCA 60.897 57.895 0.00 0.00 35.36 3.02
385 393 1.452145 GCAAACCTCCCGTGCTTCAA 61.452 55.000 0.00 0.00 35.36 2.69
386 394 0.593128 CAAACCTCCCGTGCTTCAAG 59.407 55.000 0.00 0.00 0.00 3.02
387 395 0.472471 AAACCTCCCGTGCTTCAAGA 59.528 50.000 0.00 0.00 0.00 3.02
388 396 0.693049 AACCTCCCGTGCTTCAAGAT 59.307 50.000 0.00 0.00 0.00 2.40
389 397 0.250513 ACCTCCCGTGCTTCAAGATC 59.749 55.000 0.00 0.00 0.00 2.75
390 398 0.462759 CCTCCCGTGCTTCAAGATCC 60.463 60.000 0.00 0.00 0.00 3.36
391 399 0.250234 CTCCCGTGCTTCAAGATCCA 59.750 55.000 0.00 0.00 0.00 3.41
392 400 0.911769 TCCCGTGCTTCAAGATCCAT 59.088 50.000 0.00 0.00 0.00 3.41
393 401 1.019673 CCCGTGCTTCAAGATCCATG 58.980 55.000 0.00 0.00 0.00 3.66
394 402 1.679944 CCCGTGCTTCAAGATCCATGT 60.680 52.381 0.00 0.00 0.00 3.21
395 403 2.086869 CCGTGCTTCAAGATCCATGTT 58.913 47.619 0.00 0.00 0.00 2.71
396 404 2.096496 CCGTGCTTCAAGATCCATGTTC 59.904 50.000 0.00 0.00 0.00 3.18
397 405 3.005554 CGTGCTTCAAGATCCATGTTCT 58.994 45.455 0.00 0.00 0.00 3.01
398 406 3.438087 CGTGCTTCAAGATCCATGTTCTT 59.562 43.478 0.00 3.04 33.75 2.52
399 407 4.436584 CGTGCTTCAAGATCCATGTTCTTC 60.437 45.833 5.43 0.00 31.11 2.87
400 408 4.456911 GTGCTTCAAGATCCATGTTCTTCA 59.543 41.667 5.43 0.03 31.11 3.02
401 409 5.125097 GTGCTTCAAGATCCATGTTCTTCAT 59.875 40.000 5.43 0.00 37.22 2.57
402 410 5.356190 TGCTTCAAGATCCATGTTCTTCATC 59.644 40.000 5.43 0.00 34.09 2.92
403 411 5.589452 GCTTCAAGATCCATGTTCTTCATCT 59.411 40.000 5.43 0.00 34.09 2.90
406 414 6.111382 TCAAGATCCATGTTCTTCATCTGAC 58.889 40.000 5.43 0.00 34.09 3.51
429 437 1.841556 AGAAGGGTGTTCGCTGGGA 60.842 57.895 0.00 0.00 36.95 4.37
453 462 1.996292 CGGAGTTTTCTGATCGCTCA 58.004 50.000 0.00 0.00 0.00 4.26
455 464 1.656095 GGAGTTTTCTGATCGCTCACG 59.344 52.381 0.00 0.00 42.01 4.35
474 483 5.132502 TCACGATGCATCATTTCCCTAAAT 58.867 37.500 25.70 0.00 35.65 1.40
478 487 7.920151 CACGATGCATCATTTCCCTAAATTTTA 59.080 33.333 25.70 0.00 32.87 1.52
479 488 7.920682 ACGATGCATCATTTCCCTAAATTTTAC 59.079 33.333 25.70 0.00 32.87 2.01
480 489 8.137437 CGATGCATCATTTCCCTAAATTTTACT 58.863 33.333 25.70 0.00 32.87 2.24
483 492 9.034800 TGCATCATTTCCCTAAATTTTACTCTT 57.965 29.630 0.00 0.00 32.87 2.85
517 529 2.963548 CGAAAGGGTAGAGGAGAACC 57.036 55.000 0.00 0.00 34.85 3.62
628 642 8.750298 CAGGTGTATCCCGTATAATCTATTCTT 58.250 37.037 0.00 0.00 36.75 2.52
701 715 3.836151 TCGATTGCGATCTCCGGA 58.164 55.556 12.19 2.93 42.51 5.14
705 719 3.708210 TTGCGATCTCCGGAACCT 58.292 55.556 5.23 0.00 43.60 3.50
706 720 1.515954 TTGCGATCTCCGGAACCTC 59.484 57.895 5.23 1.27 43.60 3.85
707 721 1.254975 TTGCGATCTCCGGAACCTCA 61.255 55.000 5.23 0.00 43.60 3.86
708 722 1.227002 GCGATCTCCGGAACCTCAC 60.227 63.158 5.23 0.00 39.04 3.51
709 723 1.668101 GCGATCTCCGGAACCTCACT 61.668 60.000 5.23 0.00 39.04 3.41
710 724 1.676746 CGATCTCCGGAACCTCACTA 58.323 55.000 5.23 0.00 33.91 2.74
711 725 1.604755 CGATCTCCGGAACCTCACTAG 59.395 57.143 5.23 0.00 33.91 2.57
713 727 5.875182 CGATCTCCGGAACCTCACTAGGA 62.875 56.522 5.23 0.00 38.85 2.94
748 813 0.688749 GGTACCCCCACCACGTAGAT 60.689 60.000 0.00 0.00 38.55 1.98
758 823 3.822192 ACGTAGATGCAGCCGCGA 61.822 61.111 19.85 0.00 42.97 5.87
825 894 0.463204 CGATGGCCATCACTCTCACT 59.537 55.000 38.08 7.24 37.69 3.41
869 939 3.625745 GGTGTGAAACCTCGTGGAT 57.374 52.632 11.17 0.00 46.55 3.41
874 944 1.459592 GTGAAACCTCGTGGATTGACG 59.540 52.381 11.17 0.00 40.83 4.35
875 945 0.442699 GAAACCTCGTGGATTGACGC 59.557 55.000 11.17 0.00 39.27 5.19
876 946 0.953960 AAACCTCGTGGATTGACGCC 60.954 55.000 11.17 0.00 39.27 5.68
877 947 1.827399 AACCTCGTGGATTGACGCCT 61.827 55.000 11.17 0.00 39.27 5.52
924 1030 1.165907 ATCGAGAGGCAGAGAGAGCG 61.166 60.000 0.00 0.00 0.00 5.03
933 1039 0.178975 CAGAGAGAGCGGATAGGGGT 60.179 60.000 0.00 0.00 0.00 4.95
934 1040 0.111639 AGAGAGAGCGGATAGGGGTC 59.888 60.000 0.00 0.00 0.00 4.46
935 1041 0.178987 GAGAGAGCGGATAGGGGTCA 60.179 60.000 0.00 0.00 34.46 4.02
936 1042 0.178975 AGAGAGCGGATAGGGGTCAG 60.179 60.000 0.00 0.00 34.46 3.51
937 1043 0.468400 GAGAGCGGATAGGGGTCAGT 60.468 60.000 0.00 0.00 34.46 3.41
938 1044 0.851469 AGAGCGGATAGGGGTCAGTA 59.149 55.000 0.00 0.00 34.46 2.74
941 1047 1.217183 AGCGGATAGGGGTCAGTAGAA 59.783 52.381 0.00 0.00 0.00 2.10
942 1048 1.614413 GCGGATAGGGGTCAGTAGAAG 59.386 57.143 0.00 0.00 0.00 2.85
943 1049 1.614413 CGGATAGGGGTCAGTAGAAGC 59.386 57.143 0.00 0.00 0.00 3.86
944 1050 2.679082 GGATAGGGGTCAGTAGAAGCA 58.321 52.381 0.00 0.00 0.00 3.91
947 1053 2.031495 AGGGGTCAGTAGAAGCAAGT 57.969 50.000 0.00 0.00 0.00 3.16
948 1054 1.903183 AGGGGTCAGTAGAAGCAAGTC 59.097 52.381 0.00 0.00 0.00 3.01
949 1055 1.404315 GGGGTCAGTAGAAGCAAGTCG 60.404 57.143 0.00 0.00 0.00 4.18
952 1058 2.255316 GTCAGTAGAAGCAAGTCGAGC 58.745 52.381 0.00 0.00 0.00 5.03
953 1059 1.135660 TCAGTAGAAGCAAGTCGAGCG 60.136 52.381 0.00 0.00 37.01 5.03
954 1060 1.135660 CAGTAGAAGCAAGTCGAGCGA 60.136 52.381 0.00 0.00 37.01 4.93
955 1061 1.131504 AGTAGAAGCAAGTCGAGCGAG 59.868 52.381 0.00 0.00 37.01 5.03
956 1062 0.179161 TAGAAGCAAGTCGAGCGAGC 60.179 55.000 0.00 0.00 37.01 5.03
986 1099 1.340502 GCAGGAAGGAAGGAAGGAAGG 60.341 57.143 0.00 0.00 0.00 3.46
990 1103 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
1036 1149 1.067416 TACGGGATGATGCTGTCGC 59.933 57.895 0.38 0.00 0.00 5.19
1068 1181 3.058160 GTGGCCACGCTGCTCAAT 61.058 61.111 22.49 0.00 0.00 2.57
1160 1284 2.502692 AAGCTCAACGTACGCTCCCC 62.503 60.000 16.72 1.24 32.70 4.81
1161 1285 2.183555 CTCAACGTACGCTCCCCC 59.816 66.667 16.72 0.00 0.00 5.40
1162 1286 2.283388 TCAACGTACGCTCCCCCT 60.283 61.111 16.72 0.00 0.00 4.79
1163 1287 2.125673 CAACGTACGCTCCCCCTG 60.126 66.667 16.72 0.00 0.00 4.45
1164 1288 4.078516 AACGTACGCTCCCCCTGC 62.079 66.667 16.72 0.00 0.00 4.85
1166 1290 3.771160 CGTACGCTCCCCCTGCTT 61.771 66.667 0.52 0.00 0.00 3.91
1167 1291 2.187163 GTACGCTCCCCCTGCTTC 59.813 66.667 0.00 0.00 0.00 3.86
1168 1292 3.081409 TACGCTCCCCCTGCTTCC 61.081 66.667 0.00 0.00 0.00 3.46
1172 1296 3.415087 CTCCCCCTGCTTCCCCTG 61.415 72.222 0.00 0.00 0.00 4.45
1186 1310 3.333219 CCTGCTTCCCCTGCTCCA 61.333 66.667 0.00 0.00 0.00 3.86
1192 1316 0.830648 CTTCCCCTGCTCCATCGTTA 59.169 55.000 0.00 0.00 0.00 3.18
1204 1331 7.108841 TGCTCCATCGTTAATTACTAGTTCT 57.891 36.000 0.00 0.00 0.00 3.01
1210 1337 5.953183 TCGTTAATTACTAGTTCTTCGCCA 58.047 37.500 0.00 0.00 0.00 5.69
1217 1344 2.159226 ACTAGTTCTTCGCCAAGATCCG 60.159 50.000 0.00 0.00 38.50 4.18
1219 1346 1.090052 GTTCTTCGCCAAGATCCGGG 61.090 60.000 0.00 0.00 38.50 5.73
1220 1347 1.261938 TTCTTCGCCAAGATCCGGGA 61.262 55.000 0.00 0.00 38.50 5.14
1221 1348 1.521681 CTTCGCCAAGATCCGGGAC 60.522 63.158 0.00 0.00 0.00 4.46
1222 1349 1.961180 CTTCGCCAAGATCCGGGACT 61.961 60.000 0.00 0.00 0.00 3.85
1223 1350 0.685131 TTCGCCAAGATCCGGGACTA 60.685 55.000 0.00 0.00 0.00 2.59
1225 1352 0.393077 CGCCAAGATCCGGGACTAAT 59.607 55.000 0.00 0.00 0.00 1.73
1228 1355 3.493699 CGCCAAGATCCGGGACTAATTTA 60.494 47.826 0.00 0.00 0.00 1.40
1230 1357 4.444449 GCCAAGATCCGGGACTAATTTACT 60.444 45.833 0.00 0.00 0.00 2.24
1232 1359 5.527582 CCAAGATCCGGGACTAATTTACTTG 59.472 44.000 0.00 0.00 0.00 3.16
1233 1360 4.704965 AGATCCGGGACTAATTTACTTGC 58.295 43.478 0.00 0.00 0.00 4.01
1234 1361 3.271055 TCCGGGACTAATTTACTTGCC 57.729 47.619 0.00 0.00 0.00 4.52
1235 1362 2.841881 TCCGGGACTAATTTACTTGCCT 59.158 45.455 0.00 0.00 0.00 4.75
1236 1363 3.118519 TCCGGGACTAATTTACTTGCCTC 60.119 47.826 0.00 0.00 0.00 4.70
1237 1364 3.370103 CCGGGACTAATTTACTTGCCTCA 60.370 47.826 0.00 0.00 0.00 3.86
1240 1367 4.636206 GGGACTAATTTACTTGCCTCACTG 59.364 45.833 0.00 0.00 0.00 3.66
1250 1377 1.673665 GCCTCACTGCTCTGGTTGG 60.674 63.158 0.00 0.00 0.00 3.77
1254 1381 0.546122 TCACTGCTCTGGTTGGTTGT 59.454 50.000 0.00 0.00 0.00 3.32
1269 1396 0.597377 GTTGTTTGCAGCCTTTCGGG 60.597 55.000 0.00 0.00 38.36 5.14
1321 1448 5.924475 AGTTGTCTTCGGTAACAATTCTG 57.076 39.130 0.00 0.00 37.67 3.02
1322 1449 4.213482 AGTTGTCTTCGGTAACAATTCTGC 59.787 41.667 0.00 0.00 37.67 4.26
1323 1450 3.071479 TGTCTTCGGTAACAATTCTGCC 58.929 45.455 0.00 0.00 0.00 4.85
1324 1451 2.093783 GTCTTCGGTAACAATTCTGCCG 59.906 50.000 7.13 7.13 43.32 5.69
1325 1452 0.800012 TTCGGTAACAATTCTGCCGC 59.200 50.000 8.28 0.00 41.89 6.53
1326 1453 0.036765 TCGGTAACAATTCTGCCGCT 60.037 50.000 8.28 0.00 41.89 5.52
1327 1454 0.373716 CGGTAACAATTCTGCCGCTC 59.626 55.000 1.39 0.00 35.90 5.03
1328 1455 0.733150 GGTAACAATTCTGCCGCTCC 59.267 55.000 0.00 0.00 0.00 4.70
1331 1458 1.168714 AACAATTCTGCCGCTCCTTC 58.831 50.000 0.00 0.00 0.00 3.46
1332 1459 0.326264 ACAATTCTGCCGCTCCTTCT 59.674 50.000 0.00 0.00 0.00 2.85
1333 1460 1.012841 CAATTCTGCCGCTCCTTCTC 58.987 55.000 0.00 0.00 0.00 2.87
1334 1461 0.107459 AATTCTGCCGCTCCTTCTCC 60.107 55.000 0.00 0.00 0.00 3.71
1335 1462 0.980231 ATTCTGCCGCTCCTTCTCCT 60.980 55.000 0.00 0.00 0.00 3.69
1336 1463 1.194781 TTCTGCCGCTCCTTCTCCTT 61.195 55.000 0.00 0.00 0.00 3.36
1337 1464 1.153469 CTGCCGCTCCTTCTCCTTC 60.153 63.158 0.00 0.00 0.00 3.46
1338 1465 1.610673 TGCCGCTCCTTCTCCTTCT 60.611 57.895 0.00 0.00 0.00 2.85
1339 1466 1.194781 TGCCGCTCCTTCTCCTTCTT 61.195 55.000 0.00 0.00 0.00 2.52
1340 1467 0.824759 GCCGCTCCTTCTCCTTCTTA 59.175 55.000 0.00 0.00 0.00 2.10
1341 1468 1.471851 GCCGCTCCTTCTCCTTCTTAC 60.472 57.143 0.00 0.00 0.00 2.34
1343 1470 2.159170 CCGCTCCTTCTCCTTCTTACAG 60.159 54.545 0.00 0.00 0.00 2.74
1344 1471 2.755655 CGCTCCTTCTCCTTCTTACAGA 59.244 50.000 0.00 0.00 0.00 3.41
1345 1472 3.193691 CGCTCCTTCTCCTTCTTACAGAA 59.806 47.826 0.00 0.00 32.50 3.02
1346 1473 4.142049 CGCTCCTTCTCCTTCTTACAGAAT 60.142 45.833 0.00 0.00 33.13 2.40
1347 1474 5.625656 CGCTCCTTCTCCTTCTTACAGAATT 60.626 44.000 0.00 0.00 33.13 2.17
1374 1501 3.133721 AGATCTGTTCTGGTAGATGCACC 59.866 47.826 0.00 0.00 39.20 5.01
1383 1510 2.291865 TGGTAGATGCACCTCAGTCTCT 60.292 50.000 0.00 0.00 39.50 3.10
1384 1511 2.360801 GGTAGATGCACCTCAGTCTCTC 59.639 54.545 0.00 0.00 35.55 3.20
1386 1513 2.378038 AGATGCACCTCAGTCTCTCTC 58.622 52.381 0.00 0.00 0.00 3.20
1389 1518 0.173255 GCACCTCAGTCTCTCTCAGC 59.827 60.000 0.00 0.00 0.00 4.26
1399 1530 3.704061 AGTCTCTCTCAGCAGGATTTACC 59.296 47.826 0.00 0.00 39.35 2.85
1429 1561 2.134287 ACTGACCACACACGGCTCT 61.134 57.895 0.00 0.00 0.00 4.09
1433 1565 2.088674 GACCACACACGGCTCTCTGT 62.089 60.000 0.00 0.00 0.00 3.41
1449 1581 5.808030 GCTCTCTGTAACTGTATCTTGTTCC 59.192 44.000 0.00 0.00 0.00 3.62
1495 1790 2.224066 CCGCCGATCTATCCAAACTTCT 60.224 50.000 0.00 0.00 0.00 2.85
1497 1792 4.230657 CGCCGATCTATCCAAACTTCTAG 58.769 47.826 0.00 0.00 0.00 2.43
1498 1793 4.561105 GCCGATCTATCCAAACTTCTAGG 58.439 47.826 0.00 0.00 0.00 3.02
1500 1795 5.046950 GCCGATCTATCCAAACTTCTAGGAT 60.047 44.000 0.00 0.00 44.09 3.24
1501 1796 6.153000 GCCGATCTATCCAAACTTCTAGGATA 59.847 42.308 0.00 0.00 42.03 2.59
1502 1797 7.540299 CCGATCTATCCAAACTTCTAGGATAC 58.460 42.308 0.00 0.00 42.03 2.24
1534 1843 7.818997 TTCTCGAGAAGGTAGAATATGCTTA 57.181 36.000 23.74 0.00 0.00 3.09
1555 1864 9.842775 TGCTTATAATTTGTCTGATCTGAGATT 57.157 29.630 2.02 6.75 0.00 2.40
1601 1910 8.515414 GGTCAATAACAAAGCAAGTAAGAATCT 58.485 33.333 0.00 0.00 0.00 2.40
1602 1911 9.899226 GTCAATAACAAAGCAAGTAAGAATCTT 57.101 29.630 0.00 0.00 0.00 2.40
1606 1915 7.817418 AACAAAGCAAGTAAGAATCTTACCA 57.183 32.000 24.72 0.00 0.00 3.25
1609 1918 7.284489 ACAAAGCAAGTAAGAATCTTACCAACA 59.716 33.333 24.72 0.00 0.00 3.33
1628 1937 4.647424 ACAGAGCAGATCTACTAGCAAC 57.353 45.455 0.00 0.00 36.10 4.17
1649 1958 0.036022 AACCAGTCCAGCAGAGCTTC 59.964 55.000 0.00 0.00 36.40 3.86
1675 1984 4.167554 TCTTTGTTCTTGTTTTGCGTGT 57.832 36.364 0.00 0.00 0.00 4.49
1689 1998 1.585002 CGTGTAGCAGAGCTCGAGC 60.585 63.158 30.01 30.01 40.44 5.03
1720 2222 4.322650 CCCCAAATCATCAACGAATTTGGT 60.323 41.667 19.31 0.00 45.80 3.67
1866 2368 3.181967 CGCTGGTGTACGAGCTGC 61.182 66.667 15.34 12.74 44.12 5.25
2102 2604 2.971598 CGTCAAGGCCTGGTGGGAT 61.972 63.158 5.69 0.00 37.23 3.85
2179 2681 2.347322 GCGTCTGAGCCTCTGAGGT 61.347 63.158 23.92 11.50 37.80 3.85
2180 2682 1.510383 CGTCTGAGCCTCTGAGGTG 59.490 63.158 23.92 12.34 37.80 4.00
2182 2684 0.902516 GTCTGAGCCTCTGAGGTGGT 60.903 60.000 23.92 10.00 37.80 4.16
2183 2685 0.178921 TCTGAGCCTCTGAGGTGGTT 60.179 55.000 23.92 8.47 37.80 3.67
2186 2688 1.835927 GAGCCTCTGAGGTGGTTGCT 61.836 60.000 23.92 13.72 37.80 3.91
2187 2689 1.073897 GCCTCTGAGGTGGTTGCTT 59.926 57.895 23.92 0.00 37.80 3.91
2188 2690 1.239968 GCCTCTGAGGTGGTTGCTTG 61.240 60.000 23.92 0.00 37.80 4.01
2189 2691 1.239968 CCTCTGAGGTGGTTGCTTGC 61.240 60.000 15.76 0.00 0.00 4.01
2190 2692 1.228245 TCTGAGGTGGTTGCTTGCC 60.228 57.895 0.00 0.00 0.00 4.52
2235 2760 6.377327 AAAATCGCGATGATGGAATAAACT 57.623 33.333 24.47 0.00 37.39 2.66
2269 2794 2.485814 AGAAGCTTCGAATTCTTGGTGC 59.514 45.455 20.43 5.74 31.76 5.01
2276 2804 0.886563 GAATTCTTGGTGCTGCTGCT 59.113 50.000 17.00 0.00 40.48 4.24
2277 2805 0.601558 AATTCTTGGTGCTGCTGCTG 59.398 50.000 17.00 0.77 40.48 4.41
2278 2806 0.538977 ATTCTTGGTGCTGCTGCTGT 60.539 50.000 17.00 0.00 40.48 4.40
2330 2858 6.000840 TGTTTATGGCGCATCTATTTATCCA 58.999 36.000 10.83 0.00 0.00 3.41
2431 2960 0.747255 ATGATTACGCGCCTCTGTCT 59.253 50.000 5.73 0.00 0.00 3.41
2447 2976 1.603171 TCTACCACACCGTGCCGTA 60.603 57.895 0.00 0.00 31.34 4.02
2490 3021 3.512516 GAGCTGGGCAATGGCGTC 61.513 66.667 0.00 0.00 42.47 5.19
2509 3040 0.094216 CGCAGCTGTCGAACAGATTG 59.906 55.000 21.01 13.59 43.03 2.67
2556 3091 1.300931 ACGTTCAGAGCGCACACAT 60.301 52.632 11.47 0.00 0.00 3.21
2559 3094 2.327343 TTCAGAGCGCACACATGGC 61.327 57.895 11.47 0.00 0.00 4.40
2561 3096 4.334118 AGAGCGCACACATGGCCA 62.334 61.111 8.56 8.56 0.00 5.36
2565 3100 3.751246 CGCACACATGGCCAAGGG 61.751 66.667 10.96 9.94 0.00 3.95
2698 3233 9.875708 TGATAAATTTACATATAGCCCCTTGTT 57.124 29.630 0.00 0.00 0.00 2.83
2882 3417 8.506168 TGGATTAATCAGACTAACACCAAATC 57.494 34.615 17.07 0.00 0.00 2.17
2960 3495 5.722021 TGCTATAATGCGACCAAGAGATA 57.278 39.130 0.00 0.00 35.36 1.98
2961 3496 5.470368 TGCTATAATGCGACCAAGAGATAC 58.530 41.667 0.00 0.00 35.36 2.24
2962 3497 5.243954 TGCTATAATGCGACCAAGAGATACT 59.756 40.000 0.00 0.00 35.36 2.12
2963 3498 5.574830 GCTATAATGCGACCAAGAGATACTG 59.425 44.000 0.00 0.00 0.00 2.74
2964 3499 3.895232 AATGCGACCAAGAGATACTGT 57.105 42.857 0.00 0.00 0.00 3.55
2965 3500 3.895232 ATGCGACCAAGAGATACTGTT 57.105 42.857 0.00 0.00 0.00 3.16
2966 3501 2.959516 TGCGACCAAGAGATACTGTTG 58.040 47.619 0.00 0.00 35.01 3.33
2967 3502 2.560981 TGCGACCAAGAGATACTGTTGA 59.439 45.455 9.61 0.00 36.97 3.18
2968 3503 3.195610 TGCGACCAAGAGATACTGTTGAT 59.804 43.478 9.61 0.00 36.97 2.57
2969 3504 3.553511 GCGACCAAGAGATACTGTTGATG 59.446 47.826 9.61 1.93 36.97 3.07
2970 3505 3.553511 CGACCAAGAGATACTGTTGATGC 59.446 47.826 9.61 0.04 36.97 3.91
2971 3506 4.679106 CGACCAAGAGATACTGTTGATGCT 60.679 45.833 9.61 0.00 36.97 3.79
2972 3507 4.511527 ACCAAGAGATACTGTTGATGCTG 58.488 43.478 9.61 0.00 36.97 4.41
2973 3508 4.223700 ACCAAGAGATACTGTTGATGCTGA 59.776 41.667 9.61 0.00 36.97 4.26
2974 3509 5.104610 ACCAAGAGATACTGTTGATGCTGAT 60.105 40.000 9.61 0.00 36.97 2.90
2975 3510 5.236695 CCAAGAGATACTGTTGATGCTGATG 59.763 44.000 9.61 0.00 36.97 3.07
2976 3511 4.378774 AGAGATACTGTTGATGCTGATGC 58.621 43.478 0.00 0.00 40.20 3.91
2977 3512 4.101274 AGAGATACTGTTGATGCTGATGCT 59.899 41.667 0.00 0.00 40.48 3.79
2978 3513 5.303845 AGAGATACTGTTGATGCTGATGCTA 59.696 40.000 0.00 0.00 40.48 3.49
2979 3514 6.014413 AGAGATACTGTTGATGCTGATGCTAT 60.014 38.462 0.00 0.00 40.48 2.97
2980 3515 7.178097 AGAGATACTGTTGATGCTGATGCTATA 59.822 37.037 0.00 0.00 40.48 1.31
2981 3516 7.849160 AGATACTGTTGATGCTGATGCTATAT 58.151 34.615 0.00 0.00 40.48 0.86
2982 3517 7.980662 AGATACTGTTGATGCTGATGCTATATC 59.019 37.037 0.00 0.00 40.48 1.63
2983 3518 6.111669 ACTGTTGATGCTGATGCTATATCT 57.888 37.500 0.00 0.00 40.48 1.98
2984 3519 7.237209 ACTGTTGATGCTGATGCTATATCTA 57.763 36.000 0.00 0.00 40.48 1.98
2985 3520 7.849160 ACTGTTGATGCTGATGCTATATCTAT 58.151 34.615 0.00 0.00 40.48 1.98
2986 3521 8.975295 ACTGTTGATGCTGATGCTATATCTATA 58.025 33.333 0.00 0.00 40.48 1.31
2987 3522 9.984190 CTGTTGATGCTGATGCTATATCTATAT 57.016 33.333 0.00 0.00 40.48 0.86
3037 3572 5.757850 TCTTTCCAAAAACTGAGCTTCTC 57.242 39.130 0.00 0.00 0.00 2.87
3101 3636 2.050144 TGCTCACTTTCTCCAACTCCT 58.950 47.619 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.258230 TGTGTTTTTCTCTATGGCTCAATG 57.742 37.500 0.00 0.00 0.00 2.82
38 39 7.922505 TGATTAATTTCTCGTTTTGGTTGTG 57.077 32.000 0.00 0.00 0.00 3.33
50 51 8.598075 GCCATGTGAACAATTGATTAATTTCTC 58.402 33.333 13.59 5.97 34.34 2.87
132 133 7.671302 ACTTCTACTATCACACAACATTGTCT 58.329 34.615 0.00 0.00 39.91 3.41
166 167 4.036027 CACATTGAGCAGAATGACCCATAC 59.964 45.833 13.09 0.00 39.69 2.39
192 195 1.145162 CCGCCAAACAACACAACTGC 61.145 55.000 0.00 0.00 0.00 4.40
193 196 0.172352 ACCGCCAAACAACACAACTG 59.828 50.000 0.00 0.00 0.00 3.16
209 212 4.527564 GATTTAGATCATTTGCCGAACCG 58.472 43.478 0.00 0.00 32.33 4.44
259 263 1.749033 CCTCTCCATAACTCCCCGC 59.251 63.158 0.00 0.00 0.00 6.13
275 279 0.472543 TCCATCCATCTCCATCGCCT 60.473 55.000 0.00 0.00 0.00 5.52
308 312 4.101430 AGCCCTCACACAAACAATTTCATT 59.899 37.500 0.00 0.00 0.00 2.57
316 320 0.395586 AGCAAGCCCTCACACAAACA 60.396 50.000 0.00 0.00 0.00 2.83
322 326 2.431683 GTGGAGCAAGCCCTCACA 59.568 61.111 0.00 0.00 33.47 3.58
339 343 2.791256 CATAGCCACCCGTTTGCG 59.209 61.111 0.00 0.00 37.95 4.85
367 375 0.593128 CTTGAAGCACGGGAGGTTTG 59.407 55.000 0.00 0.00 0.00 2.93
375 383 1.742761 ACATGGATCTTGAAGCACGG 58.257 50.000 0.00 0.00 0.00 4.94
376 384 3.005554 AGAACATGGATCTTGAAGCACG 58.994 45.455 0.00 0.00 0.00 5.34
377 385 4.456911 TGAAGAACATGGATCTTGAAGCAC 59.543 41.667 17.61 5.96 37.26 4.40
378 386 4.654915 TGAAGAACATGGATCTTGAAGCA 58.345 39.130 17.61 8.81 37.26 3.91
379 387 5.589452 AGATGAAGAACATGGATCTTGAAGC 59.411 40.000 17.61 10.25 39.56 3.86
380 388 6.822170 TCAGATGAAGAACATGGATCTTGAAG 59.178 38.462 17.61 7.17 39.56 3.02
381 389 6.596888 GTCAGATGAAGAACATGGATCTTGAA 59.403 38.462 17.61 8.59 39.56 2.69
382 390 6.070366 AGTCAGATGAAGAACATGGATCTTGA 60.070 38.462 17.61 11.60 39.56 3.02
383 391 6.037281 CAGTCAGATGAAGAACATGGATCTTG 59.963 42.308 17.61 6.84 39.56 3.02
384 392 6.114089 CAGTCAGATGAAGAACATGGATCTT 58.886 40.000 13.88 13.88 39.56 2.40
385 393 5.672503 CAGTCAGATGAAGAACATGGATCT 58.327 41.667 0.00 0.00 39.56 2.75
386 394 4.272991 GCAGTCAGATGAAGAACATGGATC 59.727 45.833 0.00 0.00 39.56 3.36
387 395 4.197750 GCAGTCAGATGAAGAACATGGAT 58.802 43.478 0.00 0.00 39.56 3.41
388 396 3.603532 GCAGTCAGATGAAGAACATGGA 58.396 45.455 0.00 0.00 39.56 3.41
389 397 2.681848 GGCAGTCAGATGAAGAACATGG 59.318 50.000 0.00 0.00 39.56 3.66
390 398 3.340928 TGGCAGTCAGATGAAGAACATG 58.659 45.455 0.00 0.00 39.56 3.21
391 399 3.262660 TCTGGCAGTCAGATGAAGAACAT 59.737 43.478 15.27 0.00 46.71 2.71
392 400 2.634453 TCTGGCAGTCAGATGAAGAACA 59.366 45.455 15.27 0.00 46.71 3.18
393 401 3.325293 TCTGGCAGTCAGATGAAGAAC 57.675 47.619 15.27 0.00 46.71 3.01
402 410 0.109342 AACACCCTTCTGGCAGTCAG 59.891 55.000 15.27 11.51 44.68 3.51
403 411 0.108585 GAACACCCTTCTGGCAGTCA 59.891 55.000 15.27 1.53 37.83 3.41
406 414 2.328099 GCGAACACCCTTCTGGCAG 61.328 63.158 8.58 8.58 37.83 4.85
429 437 2.544685 CGATCAGAAAACTCCGCTCAT 58.455 47.619 0.00 0.00 0.00 2.90
436 445 2.596452 TCGTGAGCGATCAGAAAACTC 58.404 47.619 2.20 0.00 42.81 3.01
453 462 6.469782 AAATTTAGGGAAATGATGCATCGT 57.530 33.333 21.34 18.72 35.38 3.73
455 464 9.468532 GAGTAAAATTTAGGGAAATGATGCATC 57.531 33.333 20.14 20.14 35.38 3.91
457 466 8.593945 AGAGTAAAATTTAGGGAAATGATGCA 57.406 30.769 0.00 0.00 35.38 3.96
504 516 9.682465 AACAAAATATTTAGGTTCTCCTCTACC 57.318 33.333 0.01 0.00 43.94 3.18
527 539 7.990886 AGGCGATAAGTATGAAAAGGAATAACA 59.009 33.333 0.00 0.00 0.00 2.41
685 699 1.215655 GGTTCCGGAGATCGCAATCG 61.216 60.000 3.34 0.00 36.97 3.34
686 700 0.105039 AGGTTCCGGAGATCGCAATC 59.895 55.000 3.34 0.00 37.59 2.67
687 701 0.105039 GAGGTTCCGGAGATCGCAAT 59.895 55.000 3.34 0.00 37.59 3.56
688 702 1.254975 TGAGGTTCCGGAGATCGCAA 61.255 55.000 3.34 0.00 37.59 4.85
689 703 1.680989 TGAGGTTCCGGAGATCGCA 60.681 57.895 3.34 3.65 37.59 5.10
690 704 1.227002 GTGAGGTTCCGGAGATCGC 60.227 63.158 3.34 7.33 37.59 4.58
692 706 1.957877 CCTAGTGAGGTTCCGGAGATC 59.042 57.143 3.34 4.92 38.16 2.75
693 707 1.569548 TCCTAGTGAGGTTCCGGAGAT 59.430 52.381 3.34 0.00 44.19 2.75
694 708 0.997363 TCCTAGTGAGGTTCCGGAGA 59.003 55.000 3.34 0.00 44.19 3.71
695 709 1.104630 GTCCTAGTGAGGTTCCGGAG 58.895 60.000 3.34 0.00 44.19 4.63
696 710 0.324091 GGTCCTAGTGAGGTTCCGGA 60.324 60.000 0.00 0.00 44.19 5.14
697 711 1.328430 GGGTCCTAGTGAGGTTCCGG 61.328 65.000 0.00 0.00 44.19 5.14
698 712 1.664321 CGGGTCCTAGTGAGGTTCCG 61.664 65.000 11.20 11.20 45.50 4.30
700 714 1.777941 ATCGGGTCCTAGTGAGGTTC 58.222 55.000 0.00 0.00 44.19 3.62
701 715 2.108970 GAATCGGGTCCTAGTGAGGTT 58.891 52.381 0.00 0.00 44.19 3.50
702 716 1.688627 GGAATCGGGTCCTAGTGAGGT 60.689 57.143 0.00 0.00 44.19 3.85
703 717 1.041437 GGAATCGGGTCCTAGTGAGG 58.959 60.000 0.00 0.00 45.35 3.86
704 718 2.074729 AGGAATCGGGTCCTAGTGAG 57.925 55.000 6.06 0.00 46.69 3.51
709 723 0.178981 CGGGTAGGAATCGGGTCCTA 60.179 60.000 10.06 10.06 46.69 2.94
711 725 2.505167 CCGGGTAGGAATCGGGTCC 61.505 68.421 0.00 0.00 45.00 4.46
715 729 1.466851 GGTACCCGGGTAGGAATCGG 61.467 65.000 34.01 0.00 45.00 4.18
716 730 2.044452 GGTACCCGGGTAGGAATCG 58.956 63.158 34.01 0.00 45.00 3.34
730 784 0.462789 CATCTACGTGGTGGGGGTAC 59.537 60.000 0.00 0.00 0.00 3.34
773 838 3.701604 CCGTAGGCGACCAGCTGTC 62.702 68.421 13.81 9.39 46.14 3.51
774 839 3.760035 CCGTAGGCGACCAGCTGT 61.760 66.667 13.81 0.11 46.14 4.40
811 876 1.142748 CCCGAGTGAGAGTGATGGC 59.857 63.158 0.00 0.00 0.00 4.40
814 883 2.060980 GGGCCCGAGTGAGAGTGAT 61.061 63.158 5.69 0.00 0.00 3.06
844 913 4.072088 GGTTTCACACCGAGCGCG 62.072 66.667 0.00 0.00 35.12 6.86
868 938 1.671054 CGGTGGTGAAGGCGTCAAT 60.671 57.895 4.28 0.00 38.23 2.57
869 939 2.280524 CGGTGGTGAAGGCGTCAA 60.281 61.111 4.28 0.00 38.23 3.18
875 945 2.558554 CTACGGAGCGGTGGTGAAGG 62.559 65.000 0.00 0.00 0.00 3.46
876 946 1.153823 CTACGGAGCGGTGGTGAAG 60.154 63.158 0.00 0.00 0.00 3.02
877 947 2.967397 CTACGGAGCGGTGGTGAA 59.033 61.111 0.00 0.00 0.00 3.18
919 1025 0.851469 TACTGACCCCTATCCGCTCT 59.149 55.000 0.00 0.00 0.00 4.09
924 1030 2.679082 TGCTTCTACTGACCCCTATCC 58.321 52.381 0.00 0.00 0.00 2.59
933 1039 1.135660 CGCTCGACTTGCTTCTACTGA 60.136 52.381 0.00 0.00 0.00 3.41
934 1040 1.135660 TCGCTCGACTTGCTTCTACTG 60.136 52.381 0.00 0.00 0.00 2.74
935 1041 1.131504 CTCGCTCGACTTGCTTCTACT 59.868 52.381 0.00 0.00 0.00 2.57
936 1042 1.540407 CTCGCTCGACTTGCTTCTAC 58.460 55.000 0.00 0.00 0.00 2.59
937 1043 0.179161 GCTCGCTCGACTTGCTTCTA 60.179 55.000 0.00 0.00 0.00 2.10
938 1044 1.445238 GCTCGCTCGACTTGCTTCT 60.445 57.895 0.00 0.00 0.00 2.85
941 1047 3.675482 CTCGCTCGCTCGACTTGCT 62.675 63.158 0.00 0.00 34.46 3.91
942 1048 3.243892 CTCGCTCGCTCGACTTGC 61.244 66.667 0.00 0.00 34.46 4.01
943 1049 3.243892 GCTCGCTCGCTCGACTTG 61.244 66.667 0.00 0.00 34.46 3.16
944 1050 3.675482 CTGCTCGCTCGCTCGACTT 62.675 63.158 0.00 0.00 34.46 3.01
956 1062 2.818714 CTTCCTGCTGCCTGCTCG 60.819 66.667 0.00 0.00 43.37 5.03
966 1079 1.340502 CCTTCCTTCCTTCCTTCCTGC 60.341 57.143 0.00 0.00 0.00 4.85
971 1084 1.996291 CCCTTCCTTCCTTCCTTCCTT 59.004 52.381 0.00 0.00 0.00 3.36
972 1085 1.154434 TCCCTTCCTTCCTTCCTTCCT 59.846 52.381 0.00 0.00 0.00 3.36
973 1086 1.562008 CTCCCTTCCTTCCTTCCTTCC 59.438 57.143 0.00 0.00 0.00 3.46
975 1088 1.132036 ACCTCCCTTCCTTCCTTCCTT 60.132 52.381 0.00 0.00 0.00 3.36
986 1099 1.529309 GCCATCTCCACCTCCCTTC 59.471 63.158 0.00 0.00 0.00 3.46
990 1103 4.554036 GGCGCCATCTCCACCTCC 62.554 72.222 24.80 0.00 0.00 4.30
1054 1167 2.789917 CTCATTGAGCAGCGTGGC 59.210 61.111 0.00 0.00 0.00 5.01
1068 1181 2.676822 AAGTCGAGGCCGAGCTCA 60.677 61.111 15.40 0.00 46.52 4.26
1128 1241 1.448717 GAGCTTGAGGAAGTCGGGC 60.449 63.158 0.00 0.00 0.00 6.13
1160 1284 2.044551 GGAAGCAGGGGAAGCAGG 60.045 66.667 0.00 0.00 0.00 4.85
1161 1285 2.044551 GGGAAGCAGGGGAAGCAG 60.045 66.667 0.00 0.00 0.00 4.24
1162 1286 3.661648 GGGGAAGCAGGGGAAGCA 61.662 66.667 0.00 0.00 0.00 3.91
1163 1287 3.342477 AGGGGAAGCAGGGGAAGC 61.342 66.667 0.00 0.00 0.00 3.86
1164 1288 2.679716 CAGGGGAAGCAGGGGAAG 59.320 66.667 0.00 0.00 0.00 3.46
1165 1289 3.661648 GCAGGGGAAGCAGGGGAA 61.662 66.667 0.00 0.00 0.00 3.97
1166 1290 4.682714 AGCAGGGGAAGCAGGGGA 62.683 66.667 0.00 0.00 0.00 4.81
1167 1291 4.120755 GAGCAGGGGAAGCAGGGG 62.121 72.222 0.00 0.00 0.00 4.79
1168 1292 4.120755 GGAGCAGGGGAAGCAGGG 62.121 72.222 0.00 0.00 0.00 4.45
1169 1293 2.621517 GATGGAGCAGGGGAAGCAGG 62.622 65.000 0.00 0.00 0.00 4.85
1170 1294 1.153005 GATGGAGCAGGGGAAGCAG 60.153 63.158 0.00 0.00 0.00 4.24
1171 1295 3.001514 GATGGAGCAGGGGAAGCA 58.998 61.111 0.00 0.00 0.00 3.91
1172 1296 2.203126 CGATGGAGCAGGGGAAGC 60.203 66.667 0.00 0.00 0.00 3.86
1173 1297 0.830648 TAACGATGGAGCAGGGGAAG 59.169 55.000 0.00 0.00 0.00 3.46
1174 1298 1.281419 TTAACGATGGAGCAGGGGAA 58.719 50.000 0.00 0.00 0.00 3.97
1186 1310 6.567050 TGGCGAAGAACTAGTAATTAACGAT 58.433 36.000 0.00 0.00 0.00 3.73
1192 1316 6.049790 GGATCTTGGCGAAGAACTAGTAATT 58.950 40.000 15.48 0.00 41.64 1.40
1204 1331 0.685131 TAGTCCCGGATCTTGGCGAA 60.685 55.000 0.73 0.00 0.00 4.70
1210 1337 5.123936 GCAAGTAAATTAGTCCCGGATCTT 58.876 41.667 0.73 0.00 0.00 2.40
1217 1344 4.636206 CAGTGAGGCAAGTAAATTAGTCCC 59.364 45.833 0.00 0.00 0.00 4.46
1219 1346 4.938226 AGCAGTGAGGCAAGTAAATTAGTC 59.062 41.667 0.00 0.00 35.83 2.59
1220 1347 4.911390 AGCAGTGAGGCAAGTAAATTAGT 58.089 39.130 0.00 0.00 35.83 2.24
1221 1348 5.064452 CAGAGCAGTGAGGCAAGTAAATTAG 59.936 44.000 0.00 0.00 35.83 1.73
1222 1349 4.937620 CAGAGCAGTGAGGCAAGTAAATTA 59.062 41.667 0.00 0.00 35.83 1.40
1223 1350 3.755378 CAGAGCAGTGAGGCAAGTAAATT 59.245 43.478 0.00 0.00 35.83 1.82
1225 1352 2.550855 CCAGAGCAGTGAGGCAAGTAAA 60.551 50.000 0.00 0.00 35.83 2.01
1228 1355 1.374190 CCAGAGCAGTGAGGCAAGT 59.626 57.895 0.00 0.00 35.83 3.16
1230 1357 0.535780 CAACCAGAGCAGTGAGGCAA 60.536 55.000 0.00 0.00 35.83 4.52
1232 1359 1.673665 CCAACCAGAGCAGTGAGGC 60.674 63.158 0.00 0.00 0.00 4.70
1233 1360 0.109342 AACCAACCAGAGCAGTGAGG 59.891 55.000 0.00 0.00 0.00 3.86
1234 1361 1.233019 CAACCAACCAGAGCAGTGAG 58.767 55.000 0.00 0.00 0.00 3.51
1235 1362 0.546122 ACAACCAACCAGAGCAGTGA 59.454 50.000 0.00 0.00 0.00 3.41
1236 1363 1.392589 AACAACCAACCAGAGCAGTG 58.607 50.000 0.00 0.00 0.00 3.66
1237 1364 1.750778 CAAACAACCAACCAGAGCAGT 59.249 47.619 0.00 0.00 0.00 4.40
1240 1367 0.459489 TGCAAACAACCAACCAGAGC 59.541 50.000 0.00 0.00 0.00 4.09
1284 1411 2.580601 AACTTCGTCCCCGTCCTGG 61.581 63.158 0.00 0.00 35.01 4.45
1315 1442 0.107459 GGAGAAGGAGCGGCAGAATT 60.107 55.000 1.45 0.00 0.00 2.17
1321 1448 0.824759 TAAGAAGGAGAAGGAGCGGC 59.175 55.000 0.00 0.00 0.00 6.53
1322 1449 1.825474 TGTAAGAAGGAGAAGGAGCGG 59.175 52.381 0.00 0.00 0.00 5.52
1323 1450 2.755655 TCTGTAAGAAGGAGAAGGAGCG 59.244 50.000 0.00 0.00 42.31 5.03
1336 1463 9.249053 AGAACAGATCTGAGTAATTCTGTAAGA 57.751 33.333 29.27 0.00 45.98 2.10
1359 1486 2.497675 GACTGAGGTGCATCTACCAGAA 59.502 50.000 19.58 0.00 43.37 3.02
1361 1488 2.100584 GAGACTGAGGTGCATCTACCAG 59.899 54.545 12.85 12.85 43.37 4.00
1374 1501 2.127271 TCCTGCTGAGAGAGACTGAG 57.873 55.000 0.00 0.00 33.08 3.35
1383 1510 2.027192 GTGTGGGTAAATCCTGCTGAGA 60.027 50.000 0.00 0.00 36.25 3.27
1384 1511 2.359900 GTGTGGGTAAATCCTGCTGAG 58.640 52.381 0.00 0.00 36.25 3.35
1386 1513 1.463674 GGTGTGGGTAAATCCTGCTG 58.536 55.000 0.00 0.00 36.25 4.41
1389 1518 1.278127 ACTCGGTGTGGGTAAATCCTG 59.722 52.381 0.00 0.00 36.25 3.86
1399 1530 1.006102 GGTCAGTGACTCGGTGTGG 60.006 63.158 22.18 0.00 32.47 4.17
1429 1561 6.948886 AGAGAGGAACAAGATACAGTTACAGA 59.051 38.462 0.00 0.00 30.86 3.41
1507 1802 7.556844 AGCATATTCTACCTTCTCGAGAAAAA 58.443 34.615 26.87 16.17 33.15 1.94
1558 1867 3.976015 TGACCAAACCCTCACTCTTTTT 58.024 40.909 0.00 0.00 0.00 1.94
1559 1868 3.662759 TGACCAAACCCTCACTCTTTT 57.337 42.857 0.00 0.00 0.00 2.27
1561 1870 3.884037 ATTGACCAAACCCTCACTCTT 57.116 42.857 0.00 0.00 0.00 2.85
1564 1873 4.447138 TGTTATTGACCAAACCCTCACT 57.553 40.909 0.00 0.00 0.00 3.41
1571 1880 7.918562 TCTTACTTGCTTTGTTATTGACCAAAC 59.081 33.333 0.00 0.00 0.00 2.93
1593 1902 6.605471 TCTGCTCTGTTGGTAAGATTCTTA 57.395 37.500 1.90 1.90 0.00 2.10
1601 1910 5.067936 GCTAGTAGATCTGCTCTGTTGGTAA 59.932 44.000 17.28 0.00 35.28 2.85
1602 1911 4.580995 GCTAGTAGATCTGCTCTGTTGGTA 59.419 45.833 17.28 0.00 35.28 3.25
1606 1915 4.709397 AGTTGCTAGTAGATCTGCTCTGTT 59.291 41.667 17.28 0.00 35.28 3.16
1609 1918 5.300792 GGTTAGTTGCTAGTAGATCTGCTCT 59.699 44.000 17.28 10.03 38.06 4.09
1628 1937 0.901124 AGCTCTGCTGGACTGGTTAG 59.099 55.000 0.00 0.00 37.57 2.34
1649 1958 5.516339 ACGCAAAACAAGAACAAAGAATCTG 59.484 36.000 0.00 0.00 0.00 2.90
1708 2210 3.300009 GACTCTGCAACCAAATTCGTTG 58.700 45.455 12.00 12.00 42.83 4.10
2170 2672 1.239968 GCAAGCAACCACCTCAGAGG 61.240 60.000 15.72 15.72 42.49 3.69
2173 2675 0.036732 TAGGCAAGCAACCACCTCAG 59.963 55.000 0.00 0.00 33.60 3.35
2174 2676 0.036732 CTAGGCAAGCAACCACCTCA 59.963 55.000 0.00 0.00 33.60 3.86
2189 2691 1.953138 CATTCTCGCCGCAGCTAGG 60.953 63.158 3.19 3.19 36.60 3.02
2190 2692 1.953138 CCATTCTCGCCGCAGCTAG 60.953 63.158 0.00 0.00 36.60 3.42
2198 2723 3.555518 GCGATTTTATTCCATTCTCGCC 58.444 45.455 2.86 0.00 42.90 5.54
2235 2760 9.490379 AATTCGAAGCTTCTTCTCTAAAAAGTA 57.510 29.630 23.50 0.00 0.00 2.24
2256 2781 0.455633 GCAGCAGCACCAAGAATTCG 60.456 55.000 0.00 0.00 41.58 3.34
2269 2794 2.787601 ACATTCAACAACAGCAGCAG 57.212 45.000 0.00 0.00 0.00 4.24
2276 2804 6.041511 CACCAAGATTCAACATTCAACAACA 58.958 36.000 0.00 0.00 0.00 3.33
2277 2805 6.042143 ACACCAAGATTCAACATTCAACAAC 58.958 36.000 0.00 0.00 0.00 3.32
2278 2806 6.219417 ACACCAAGATTCAACATTCAACAA 57.781 33.333 0.00 0.00 0.00 2.83
2330 2858 4.694982 CCAACAAAGTTCAAGCCAAAAACT 59.305 37.500 0.00 0.00 34.81 2.66
2412 2941 0.747255 AGACAGAGGCGCGTAATCAT 59.253 50.000 8.43 0.00 0.00 2.45
2447 2976 1.138266 ACAGCAAACACTCGGTACTGT 59.862 47.619 0.64 0.00 34.98 3.55
2490 3021 0.094216 CAATCTGTTCGACAGCTGCG 59.906 55.000 15.27 18.19 45.54 5.18
2506 3037 2.579201 CCTGTCGTCGCCCTCAAT 59.421 61.111 0.00 0.00 0.00 2.57
2565 3100 3.706315 TATTTTCCCCCTGCCTGGTGC 62.706 57.143 0.00 0.00 41.77 5.01
2569 3104 1.217689 TGGATATTTTCCCCCTGCCTG 59.782 52.381 0.00 0.00 44.77 4.85
2698 3233 2.429971 TGCTGTGATTTTGCAAGGACAA 59.570 40.909 0.00 0.00 33.48 3.18
2882 3417 2.688507 ACTTGCAGTGTCGTCCTAATG 58.311 47.619 0.00 0.00 0.00 1.90
2924 3459 9.267084 TCGCATTATAGCAAGTAAATATGTCAA 57.733 29.630 0.00 0.00 0.00 3.18
2960 3495 6.111669 AGATATAGCATCAGCATCAACAGT 57.888 37.500 0.00 0.00 45.49 3.55
2961 3496 9.984190 ATATAGATATAGCATCAGCATCAACAG 57.016 33.333 0.00 0.00 45.49 3.16
2976 3511 7.299586 GCTTTCGTCCCGCTATATAGATATAG 58.700 42.308 14.16 10.90 43.16 1.31
2977 3512 6.206243 GGCTTTCGTCCCGCTATATAGATATA 59.794 42.308 14.16 0.00 0.00 0.86
2978 3513 5.009811 GGCTTTCGTCCCGCTATATAGATAT 59.990 44.000 14.16 0.00 0.00 1.63
2979 3514 4.337555 GGCTTTCGTCCCGCTATATAGATA 59.662 45.833 14.16 0.00 0.00 1.98
2980 3515 3.130693 GGCTTTCGTCCCGCTATATAGAT 59.869 47.826 14.16 0.00 0.00 1.98
2981 3516 2.490903 GGCTTTCGTCCCGCTATATAGA 59.509 50.000 14.16 0.00 0.00 1.98
2982 3517 2.492484 AGGCTTTCGTCCCGCTATATAG 59.508 50.000 5.30 5.30 0.00 1.31
2983 3518 2.522185 AGGCTTTCGTCCCGCTATATA 58.478 47.619 0.00 0.00 0.00 0.86
2984 3519 1.339097 AGGCTTTCGTCCCGCTATAT 58.661 50.000 0.00 0.00 0.00 0.86
2985 3520 1.117150 AAGGCTTTCGTCCCGCTATA 58.883 50.000 0.00 0.00 0.00 1.31
2986 3521 0.252197 AAAGGCTTTCGTCCCGCTAT 59.748 50.000 6.68 0.00 0.00 2.97
2987 3522 0.035739 AAAAGGCTTTCGTCCCGCTA 59.964 50.000 13.76 0.00 0.00 4.26
2988 3523 0.822121 AAAAAGGCTTTCGTCCCGCT 60.822 50.000 13.76 0.00 0.00 5.52
2989 3524 0.386858 GAAAAAGGCTTTCGTCCCGC 60.387 55.000 13.76 0.00 0.00 6.13
3037 3572 5.403897 TTTTCTTCTGCTTGTACTTGTCG 57.596 39.130 0.00 0.00 0.00 4.35
3101 3636 8.568676 TTGATGATAAGTATTTTTGGACGGAA 57.431 30.769 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.