Multiple sequence alignment - TraesCS4A01G410200

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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 TraesCS4A01G410200 chr4A 100.000 5251 0 0 1 5251 683489380 683484130 0.000000e+00 9697.0
1 TraesCS4A01G410200 chr4D 93.992 4311 152 45 426 4698 476306992 476302751 0.000000e+00 6427.0
2 TraesCS4A01G410200 chr4D 89.667 300 25 3 4954 5251 476302520 476302225 1.380000e-100 377.0
3 TraesCS4A01G410200 chr4D 91.111 225 14 2 219 442 476307167 476306948 3.070000e-77 300.0
4 TraesCS4A01G410200 chr4D 89.767 215 13 5 4748 4960 476302749 476302542 3.120000e-67 267.0
5 TraesCS4A01G410200 chr4D 88.298 94 9 2 1 93 476307389 476307297 1.550000e-20 111.0
6 TraesCS4A01G410200 chr4B 92.179 3516 144 47 1214 4698 600657807 600654392 0.000000e+00 4848.0
7 TraesCS4A01G410200 chr4B 87.755 735 49 20 421 1130 600658913 600658195 0.000000e+00 821.0
8 TraesCS4A01G410200 chr4B 84.387 538 37 21 4748 5251 600654390 600653866 7.910000e-133 484.0
9 TraesCS4A01G410200 chr4B 89.614 337 32 3 1 335 600659280 600658945 4.860000e-115 425.0
10 TraesCS4A01G410200 chr2D 83.464 1403 174 33 2876 4255 367503918 367502551 0.000000e+00 1253.0
11 TraesCS4A01G410200 chr2D 78.155 824 128 39 1989 2794 367504813 367504024 1.320000e-130 477.0
12 TraesCS4A01G410200 chr2D 94.372 231 13 0 1261 1491 367505464 367505234 6.470000e-94 355.0
13 TraesCS4A01G410200 chr2D 86.891 267 34 1 1608 1873 367505156 367504890 1.110000e-76 298.0
14 TraesCS4A01G410200 chr2A 83.166 1396 181 30 2876 4255 497653850 497652493 0.000000e+00 1227.0
15 TraesCS4A01G410200 chr2A 77.857 840 120 46 1989 2794 497654768 497653961 1.330000e-125 460.0
16 TraesCS4A01G410200 chr2A 89.850 266 26 1 1608 1873 497655113 497654849 1.810000e-89 340.0
17 TraesCS4A01G410200 chr2A 93.103 232 16 0 1261 1492 497655429 497655198 1.810000e-89 340.0
18 TraesCS4A01G410200 chr2A 91.071 56 4 1 4696 4751 16488899 16488845 2.030000e-09 75.0
19 TraesCS4A01G410200 chr2B 88.800 625 68 2 3237 3860 436239043 436238420 0.000000e+00 765.0
20 TraesCS4A01G410200 chr2B 78.372 823 119 40 1989 2794 436240278 436239498 3.680000e-131 479.0
21 TraesCS4A01G410200 chr2B 94.828 232 12 0 1261 1492 436240940 436240709 3.870000e-96 363.0
22 TraesCS4A01G410200 chr2B 90.977 266 24 0 2876 3141 436239392 436239127 5.000000e-95 359.0
23 TraesCS4A01G410200 chr2B 89.098 266 28 1 1608 1873 436240623 436240359 3.920000e-86 329.0
24 TraesCS4A01G410200 chr2B 83.861 316 39 5 3949 4255 436238364 436238052 1.850000e-74 291.0
25 TraesCS4A01G410200 chr2B 80.899 267 51 0 2876 3142 436960280 436960546 1.480000e-50 211.0
26 TraesCS4A01G410200 chr6A 75.593 590 130 13 3267 3849 33585023 33585605 4.000000e-71 279.0
27 TraesCS4A01G410200 chr6A 81.974 233 39 1 1261 1490 33542559 33542327 1.490000e-45 195.0
28 TraesCS4A01G410200 chr7A 96.491 57 2 0 4695 4751 538579062 538579006 1.560000e-15 95.3
29 TraesCS4A01G410200 chr7D 92.593 54 3 1 4683 4735 321247683 321247736 5.640000e-10 76.8
30 TraesCS4A01G410200 chr7D 86.111 72 3 3 4689 4754 17342037 17341967 2.620000e-08 71.3
31 TraesCS4A01G410200 chr6B 94.118 51 2 1 4686 4735 182337533 182337583 5.640000e-10 76.8
32 TraesCS4A01G410200 chr3D 90.000 60 2 1 4695 4750 422648338 422648397 2.030000e-09 75.0
33 TraesCS4A01G410200 chr3D 90.000 60 1 3 4696 4750 122572234 122572175 7.290000e-09 73.1
34 TraesCS4A01G410200 chr6D 90.909 55 4 1 4682 4735 437956068 437956014 7.290000e-09 73.1
35 TraesCS4A01G410200 chr1D 88.525 61 4 2 4675 4735 433188102 433188045 2.620000e-08 71.3


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 TraesCS4A01G410200 chr4A 683484130 683489380 5250 True 9697.00 9697 100.00000 1 5251 1 chr4A.!!$R1 5250
1 TraesCS4A01G410200 chr4D 476302225 476307389 5164 True 1496.40 6427 90.56700 1 5251 5 chr4D.!!$R1 5250
2 TraesCS4A01G410200 chr4B 600653866 600659280 5414 True 1644.50 4848 88.48375 1 5251 4 chr4B.!!$R1 5250
3 TraesCS4A01G410200 chr2D 367502551 367505464 2913 True 595.75 1253 85.72050 1261 4255 4 chr2D.!!$R1 2994
4 TraesCS4A01G410200 chr2A 497652493 497655429 2936 True 591.75 1227 85.99400 1261 4255 4 chr2A.!!$R2 2994
5 TraesCS4A01G410200 chr2B 436238052 436240940 2888 True 431.00 765 87.65600 1261 4255 6 chr2B.!!$R1 2994
6 TraesCS4A01G410200 chr6A 33585023 33585605 582 False 279.00 279 75.59300 3267 3849 1 chr6A.!!$F1 582

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
706 718 0.656785 TGTTTTACCCGCGTGAACAC 59.343 50.000 4.92 0.00 29.64 3.32 F
1156 1192 0.322456 CGTCCTTCCCCTGCAATTCA 60.322 55.000 0.00 0.00 0.00 2.57 F
1161 1197 0.332632 TTCCCCTGCAATTCAGAGGG 59.667 55.000 16.51 16.51 46.35 4.30 F
1175 1521 0.749454 AGAGGGCCATGTCAATTCGC 60.749 55.000 6.18 0.00 0.00 4.70 F
1181 1527 1.063006 CATGTCAATTCGCCGGCAG 59.937 57.895 28.98 19.33 0.00 4.85 F
1580 1933 1.093159 CTGGATTGCTGAAGCTGGAC 58.907 55.000 3.61 0.00 42.66 4.02 F
3167 3641 1.538047 CACCACTCCCACTTCAATGG 58.462 55.000 0.00 0.00 39.71 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1903 0.453390 GCAATCCAGCAAGCAGGTAC 59.547 55.000 3.34 0.0 0.00 3.34 R
3146 3620 0.405585 ATTGAAGTGGGAGTGGTGGG 59.594 55.000 0.00 0.0 0.00 4.61 R
3156 3630 4.753233 TCAAACACAAACCATTGAAGTGG 58.247 39.130 0.00 0.0 45.04 4.00 R
3157 3631 6.041511 TCATCAAACACAAACCATTGAAGTG 58.958 36.000 0.00 0.0 38.94 3.16 R
3167 3641 6.756074 TGTTGAAAGGATCATCAAACACAAAC 59.244 34.615 8.77 0.0 38.03 2.93 R
3407 3881 0.390860 CGAAGCAGATGGGGAGGTAG 59.609 60.000 0.00 0.0 0.00 3.18 R
4271 4758 0.033504 GCACATCCCCGATCATACGT 59.966 55.000 0.00 0.0 0.00 3.57 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.512435 GTGTATATGAACGTCTATGTTTGTACT 57.488 33.333 0.00 0.00 30.75 2.73
79 80 8.241497 TCTAAACCAAGTATATCACACCGTAT 57.759 34.615 0.00 0.00 0.00 3.06
95 96 1.806623 CGTATGTGCTCCTGCCTTACC 60.807 57.143 0.00 0.00 38.71 2.85
113 114 3.799281 ACCGCAATTATCACCCAAATG 57.201 42.857 0.00 0.00 0.00 2.32
123 124 2.633692 TCACCCAAATGTAGTACCCCA 58.366 47.619 0.00 0.00 0.00 4.96
198 199 7.592439 AGTTTTACTAGATGCCGAGTTTTAC 57.408 36.000 0.00 0.00 30.77 2.01
233 238 5.812127 CAGGCAAGCATATTTTACCCTTTTC 59.188 40.000 0.00 0.00 0.00 2.29
235 240 6.213397 AGGCAAGCATATTTTACCCTTTTCTT 59.787 34.615 0.00 0.00 0.00 2.52
239 244 7.085052 AGCATATTTTACCCTTTTCTTCGAC 57.915 36.000 0.00 0.00 0.00 4.20
240 245 6.095021 AGCATATTTTACCCTTTTCTTCGACC 59.905 38.462 0.00 0.00 0.00 4.79
292 298 2.263077 CAGGTCATACGAGCAGTGAAC 58.737 52.381 0.00 0.00 42.32 3.18
309 315 1.089481 AACTCACACCGGCATATGCG 61.089 55.000 21.04 15.52 43.26 4.73
342 348 6.588204 ACTGAGGTCACATGTACAAGTAAAA 58.412 36.000 2.97 0.00 0.00 1.52
343 349 7.051623 ACTGAGGTCACATGTACAAGTAAAAA 58.948 34.615 2.97 0.00 0.00 1.94
379 385 1.366854 GCCAAAACGATCCGGAGACC 61.367 60.000 11.34 0.22 0.00 3.85
401 407 1.387756 CACCGTCGCGTTAAGTAAAGG 59.612 52.381 5.77 0.00 0.00 3.11
420 426 6.431198 AAAGGCATTATTTGTCGACGTAAT 57.569 33.333 11.62 14.75 34.17 1.89
422 428 7.542534 AAGGCATTATTTGTCGACGTAATTA 57.457 32.000 17.43 11.16 34.17 1.40
423 429 7.542534 AGGCATTATTTGTCGACGTAATTAA 57.457 32.000 17.43 11.32 34.17 1.40
424 430 7.976826 AGGCATTATTTGTCGACGTAATTAAA 58.023 30.769 17.43 9.37 34.17 1.52
425 431 8.452534 AGGCATTATTTGTCGACGTAATTAAAA 58.547 29.630 17.43 8.74 34.17 1.52
426 432 9.063739 GGCATTATTTGTCGACGTAATTAAAAA 57.936 29.630 17.43 8.11 0.00 1.94
483 489 6.816640 GCATTATTTGTCGCCTACTCCATATA 59.183 38.462 0.00 0.00 0.00 0.86
492 498 4.705507 CGCCTACTCCATATATACACACCT 59.294 45.833 0.00 0.00 0.00 4.00
496 502 7.396623 GCCTACTCCATATATACACACCTAAGT 59.603 40.741 0.00 0.00 0.00 2.24
497 503 9.970553 CCTACTCCATATATACACACCTAAGTA 57.029 37.037 0.00 0.00 0.00 2.24
531 537 5.941555 AGTAACCTACCTTGGAGAAGATG 57.058 43.478 0.00 0.00 0.00 2.90
546 552 5.835257 GAGAAGATGAGTTCTCTGATCTGG 58.165 45.833 6.40 0.00 46.18 3.86
584 590 5.596836 TGATTGGGATTTGTTTATCTGGC 57.403 39.130 0.00 0.00 0.00 4.85
586 592 2.374184 TGGGATTTGTTTATCTGGCGG 58.626 47.619 0.00 0.00 0.00 6.13
587 593 1.067060 GGGATTTGTTTATCTGGCGGC 59.933 52.381 0.00 0.00 0.00 6.53
588 594 2.024414 GGATTTGTTTATCTGGCGGCT 58.976 47.619 11.43 0.00 0.00 5.52
590 596 3.630312 GGATTTGTTTATCTGGCGGCTAA 59.370 43.478 11.43 0.00 0.00 3.09
617 623 2.301902 GACGCAAGCAATCTCGGCAG 62.302 60.000 0.00 0.00 45.62 4.85
644 655 1.303309 CCGAGGCCTCATTTGCTAAG 58.697 55.000 31.67 12.17 0.00 2.18
645 656 1.407437 CCGAGGCCTCATTTGCTAAGT 60.407 52.381 31.67 0.00 0.00 2.24
646 657 2.158957 CCGAGGCCTCATTTGCTAAGTA 60.159 50.000 31.67 0.00 0.00 2.24
647 658 3.531538 CGAGGCCTCATTTGCTAAGTAA 58.468 45.455 31.67 0.00 0.00 2.24
688 699 3.792956 GTGGCAGCATTCGTTTGAATATG 59.207 43.478 0.00 0.00 42.94 1.78
695 707 7.462724 GCAGCATTCGTTTGAATATGTTTTACC 60.463 37.037 0.00 0.00 42.94 2.85
706 718 0.656785 TGTTTTACCCGCGTGAACAC 59.343 50.000 4.92 0.00 29.64 3.32
746 758 4.217118 ACTTTTAAGTGCTCATGAGGCTTG 59.783 41.667 23.89 0.00 37.98 4.01
793 805 4.287067 CCCAGGTATGATAATGTACCAGCT 59.713 45.833 4.57 0.00 42.25 4.24
833 847 1.600413 CCACCTCAAGCAAACGAAAGC 60.600 52.381 0.00 0.00 0.00 3.51
921 948 1.338200 CCTCACCTTCTTCCTCCAACG 60.338 57.143 0.00 0.00 0.00 4.10
1007 1043 1.144936 CCCTGAAGGAGATGTCGGC 59.855 63.158 0.00 0.00 38.24 5.54
1137 1173 4.464951 TCCCGGGTATGTATATCATGTGTC 59.535 45.833 22.86 0.00 37.91 3.67
1138 1174 4.421058 CCGGGTATGTATATCATGTGTCG 58.579 47.826 0.00 0.00 37.91 4.35
1139 1175 4.082408 CCGGGTATGTATATCATGTGTCGT 60.082 45.833 0.00 0.00 37.91 4.34
1140 1176 5.093457 CGGGTATGTATATCATGTGTCGTC 58.907 45.833 0.00 0.00 37.91 4.20
1143 1179 6.295123 GGGTATGTATATCATGTGTCGTCCTT 60.295 42.308 0.00 0.00 37.91 3.36
1153 1189 1.299976 GTCGTCCTTCCCCTGCAAT 59.700 57.895 0.00 0.00 0.00 3.56
1156 1192 0.322456 CGTCCTTCCCCTGCAATTCA 60.322 55.000 0.00 0.00 0.00 2.57
1157 1193 1.467920 GTCCTTCCCCTGCAATTCAG 58.532 55.000 0.00 0.00 42.49 3.02
1158 1194 1.004745 GTCCTTCCCCTGCAATTCAGA 59.995 52.381 6.50 0.00 45.72 3.27
1159 1195 1.283029 TCCTTCCCCTGCAATTCAGAG 59.717 52.381 6.50 0.00 45.72 3.35
1160 1196 1.684248 CCTTCCCCTGCAATTCAGAGG 60.684 57.143 6.50 3.66 45.72 3.69
1161 1197 0.332632 TTCCCCTGCAATTCAGAGGG 59.667 55.000 16.51 16.51 46.35 4.30
1162 1198 1.755783 CCCCTGCAATTCAGAGGGC 60.756 63.158 7.27 0.00 44.74 5.19
1173 1519 2.425143 TCAGAGGGCCATGTCAATTC 57.575 50.000 6.18 0.00 0.00 2.17
1174 1520 1.019673 CAGAGGGCCATGTCAATTCG 58.980 55.000 6.18 0.00 0.00 3.34
1175 1521 0.749454 AGAGGGCCATGTCAATTCGC 60.749 55.000 6.18 0.00 0.00 4.70
1176 1522 1.728490 GAGGGCCATGTCAATTCGCC 61.728 60.000 6.18 0.00 38.96 5.54
1178 1524 2.408835 GCCATGTCAATTCGCCGG 59.591 61.111 0.00 0.00 0.00 6.13
1179 1525 2.408835 CCATGTCAATTCGCCGGC 59.591 61.111 19.07 19.07 0.00 6.13
1180 1526 2.405805 CCATGTCAATTCGCCGGCA 61.406 57.895 28.98 8.41 0.00 5.69
1181 1527 1.063006 CATGTCAATTCGCCGGCAG 59.937 57.895 28.98 19.33 0.00 4.85
1182 1528 2.764314 ATGTCAATTCGCCGGCAGC 61.764 57.895 28.98 8.01 38.52 5.25
1183 1529 3.430862 GTCAATTCGCCGGCAGCA 61.431 61.111 28.98 9.78 44.04 4.41
1184 1530 2.671276 TCAATTCGCCGGCAGCAA 60.671 55.556 28.98 16.15 44.04 3.91
1185 1531 2.045708 TCAATTCGCCGGCAGCAAT 61.046 52.632 28.98 17.78 44.04 3.56
1186 1532 1.874915 CAATTCGCCGGCAGCAATG 60.875 57.895 28.98 14.29 44.04 2.82
1187 1533 3.067480 AATTCGCCGGCAGCAATGG 62.067 57.895 28.98 8.23 44.04 3.16
1205 1551 2.107366 TGGTGCAATCTATCTGACGGA 58.893 47.619 0.00 0.00 0.00 4.69
1208 1554 1.756538 TGCAATCTATCTGACGGAGCA 59.243 47.619 0.00 0.00 0.00 4.26
1210 1556 2.223923 GCAATCTATCTGACGGAGCAGT 60.224 50.000 0.00 0.00 37.20 4.40
1211 1557 3.379240 CAATCTATCTGACGGAGCAGTG 58.621 50.000 0.00 0.00 37.20 3.66
1212 1558 2.130272 TCTATCTGACGGAGCAGTGT 57.870 50.000 0.00 0.00 37.20 3.55
1234 1587 5.713861 TGTGAGTACCCTACTTAACTTCCTC 59.286 44.000 0.00 0.00 39.59 3.71
1250 1603 4.471908 TCTGGGCGACGCATGCAT 62.472 61.111 23.09 0.36 0.00 3.96
1251 1604 4.246206 CTGGGCGACGCATGCATG 62.246 66.667 22.70 22.70 0.00 4.06
1252 1605 4.774503 TGGGCGACGCATGCATGA 62.775 61.111 30.64 3.39 0.00 3.07
1253 1606 3.282157 GGGCGACGCATGCATGAT 61.282 61.111 30.64 16.97 0.00 2.45
1503 1856 6.073327 ACGGAGATGGTATATATGCATACG 57.927 41.667 8.99 6.02 33.04 3.06
1521 1874 7.395645 TGCATACGCATTTACGCATATATAAC 58.604 34.615 0.00 0.00 45.36 1.89
1546 1899 6.098124 CCCCAATTAGTTCCATCAAATTAGCA 59.902 38.462 0.00 0.00 0.00 3.49
1550 1903 9.385902 CAATTAGTTCCATCAAATTAGCATACG 57.614 33.333 0.00 0.00 0.00 3.06
1580 1933 1.093159 CTGGATTGCTGAAGCTGGAC 58.907 55.000 3.61 0.00 42.66 4.02
1586 1939 2.675056 GCTGAAGCTGGACTGCACG 61.675 63.158 4.05 0.00 38.21 5.34
2054 2440 4.333926 GCCTGACTCAAAGTATGTGAATCC 59.666 45.833 0.00 0.00 27.24 3.01
2426 2823 6.040054 GTCACAGGTAACCAACAATTTAACCT 59.960 38.462 0.00 0.00 37.17 3.50
2588 2997 2.054799 AGGGCTGTTCAGGTACTTCAA 58.945 47.619 1.97 0.00 34.60 2.69
2594 3003 5.472137 GGCTGTTCAGGTACTTCAATGTTTA 59.528 40.000 1.97 0.00 34.60 2.01
2802 3233 5.375956 AGATCTATCCCAGGTAGGTACAAGA 59.624 44.000 0.00 0.00 34.66 3.02
2884 3358 2.360475 GTTCCTCCTGCAGCACCC 60.360 66.667 8.66 0.00 0.00 4.61
3124 3598 2.463589 GAACCACCACCAGCATCGGA 62.464 60.000 0.00 0.00 0.00 4.55
3146 3620 5.296035 GGACATGCTTATGGTAAGTTGGTAC 59.704 44.000 0.00 0.00 0.00 3.34
3167 3641 1.538047 CACCACTCCCACTTCAATGG 58.462 55.000 0.00 0.00 39.71 3.16
3209 3683 2.564062 CAACAGCCTGATGGGTCAAAAT 59.436 45.455 0.00 0.00 43.07 1.82
3213 3687 3.258872 CAGCCTGATGGGTCAAAATTTGA 59.741 43.478 4.03 4.03 43.07 2.69
3233 3707 4.438148 TGATGTGATACGTATGTTGGTGG 58.562 43.478 13.97 0.00 0.00 4.61
3363 3837 1.899814 TCGTGTTTGGCTCCATAGAGT 59.100 47.619 0.00 0.00 42.59 3.24
3407 3881 1.649267 GAAATTCATCGAGGGCGGC 59.351 57.895 0.00 0.00 38.28 6.53
4015 4501 1.287503 GGAGGATCGCTAGCTTCCG 59.712 63.158 21.28 4.75 34.37 4.30
4052 4538 2.481104 CGAGGAGGAGAAGCAACTGATC 60.481 54.545 0.00 0.00 0.00 2.92
4091 4577 2.057922 GGGATGGTGTATCTGATGGGT 58.942 52.381 0.00 0.00 36.03 4.51
4121 4607 2.978010 ACCGCCAAAGCCAACTCG 60.978 61.111 0.00 0.00 34.57 4.18
4257 4743 9.509855 GGATCACATACGAGATATAGTGATTTC 57.490 37.037 7.22 0.00 39.51 2.17
4271 4758 1.072489 TGATTTCACCCCAAGCGTGTA 59.928 47.619 0.00 0.00 32.86 2.90
4282 4769 1.779157 CAAGCGTGTACGTATGATCGG 59.221 52.381 0.00 0.00 42.22 4.18
4331 4821 6.490381 TGATTCTGGCTGTATGGTAGTACTAG 59.510 42.308 1.87 0.00 0.00 2.57
4354 4844 1.070758 TGAAGGGCGAAGAGGATATGC 59.929 52.381 0.00 0.00 0.00 3.14
4415 4907 4.885413 TGATGGTTTTCTTCATGCTTTGG 58.115 39.130 0.00 0.00 0.00 3.28
4498 4991 7.693969 AAGTTATAGGGATGATATTGCAAGC 57.306 36.000 4.94 0.00 0.00 4.01
4526 5019 1.056700 AACTGGTGAGTGTGCTCCCT 61.057 55.000 0.00 0.00 40.95 4.20
4575 5068 0.396435 TGACTGGTCGGAATGCAGTT 59.604 50.000 0.00 0.00 0.00 3.16
4590 5083 1.457346 CAGTTGTGGAGCCAGGATTC 58.543 55.000 0.00 0.00 0.00 2.52
4680 5173 8.678510 CACAATTAACGACAATGAAAGTACAAC 58.321 33.333 0.00 0.00 0.00 3.32
4681 5174 8.399425 ACAATTAACGACAATGAAAGTACAACA 58.601 29.630 0.00 0.00 0.00 3.33
4682 5175 9.227490 CAATTAACGACAATGAAAGTACAACAA 57.773 29.630 0.00 0.00 0.00 2.83
4690 5183 8.905103 ACAATGAAAGTACAACAAACTGTTAC 57.095 30.769 0.00 0.00 38.77 2.50
4704 5197 3.314541 CTGTTACACAGTACACCCTCC 57.685 52.381 0.00 0.00 41.19 4.30
4705 5198 1.614903 TGTTACACAGTACACCCTCCG 59.385 52.381 0.00 0.00 0.00 4.63
4706 5199 1.615392 GTTACACAGTACACCCTCCGT 59.385 52.381 0.00 0.00 0.00 4.69
4707 5200 1.538047 TACACAGTACACCCTCCGTC 58.462 55.000 0.00 0.00 0.00 4.79
4708 5201 1.183676 ACACAGTACACCCTCCGTCC 61.184 60.000 0.00 0.00 0.00 4.79
4709 5202 1.608627 ACAGTACACCCTCCGTCCC 60.609 63.158 0.00 0.00 0.00 4.46
4710 5203 1.608336 CAGTACACCCTCCGTCCCA 60.608 63.158 0.00 0.00 0.00 4.37
4711 5204 1.156803 AGTACACCCTCCGTCCCAA 59.843 57.895 0.00 0.00 0.00 4.12
4712 5205 0.472352 AGTACACCCTCCGTCCCAAA 60.472 55.000 0.00 0.00 0.00 3.28
4713 5206 0.397564 GTACACCCTCCGTCCCAAAA 59.602 55.000 0.00 0.00 0.00 2.44
4714 5207 1.003928 GTACACCCTCCGTCCCAAAAT 59.996 52.381 0.00 0.00 0.00 1.82
4715 5208 1.364269 ACACCCTCCGTCCCAAAATA 58.636 50.000 0.00 0.00 0.00 1.40
4716 5209 1.706305 ACACCCTCCGTCCCAAAATAA 59.294 47.619 0.00 0.00 0.00 1.40
4717 5210 2.290705 ACACCCTCCGTCCCAAAATAAG 60.291 50.000 0.00 0.00 0.00 1.73
4718 5211 1.990327 ACCCTCCGTCCCAAAATAAGT 59.010 47.619 0.00 0.00 0.00 2.24
4719 5212 2.290705 ACCCTCCGTCCCAAAATAAGTG 60.291 50.000 0.00 0.00 0.00 3.16
4720 5213 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
4721 5214 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
4722 5215 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
4723 5216 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
4724 5217 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
4725 5218 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4726 5219 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
4727 5220 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
4728 5221 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
4729 5222 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
4730 5223 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
4731 5224 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
4732 5225 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
4733 5226 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
4734 5227 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
4735 5228 9.438291 CAAAATAAGTGACTCAACTTTGTACTG 57.562 33.333 0.00 0.00 40.77 2.74
4736 5229 7.730364 AATAAGTGACTCAACTTTGTACTGG 57.270 36.000 0.00 0.00 40.77 4.00
4737 5230 4.073293 AGTGACTCAACTTTGTACTGGG 57.927 45.455 0.00 0.00 0.00 4.45
4738 5231 3.709653 AGTGACTCAACTTTGTACTGGGA 59.290 43.478 0.00 0.00 0.00 4.37
4739 5232 3.808174 GTGACTCAACTTTGTACTGGGAC 59.192 47.826 0.00 0.00 0.00 4.46
4740 5233 3.057734 GACTCAACTTTGTACTGGGACG 58.942 50.000 0.00 0.00 0.00 4.79
4741 5234 2.224209 ACTCAACTTTGTACTGGGACGG 60.224 50.000 0.00 0.00 42.99 4.79
4742 5235 2.036733 CTCAACTTTGTACTGGGACGGA 59.963 50.000 0.00 0.00 38.67 4.69
4743 5236 2.036733 TCAACTTTGTACTGGGACGGAG 59.963 50.000 0.00 0.00 38.67 4.63
4744 5237 0.974383 ACTTTGTACTGGGACGGAGG 59.026 55.000 0.00 0.00 38.67 4.30
4745 5238 0.249398 CTTTGTACTGGGACGGAGGG 59.751 60.000 0.00 0.00 38.67 4.30
4746 5239 0.178926 TTTGTACTGGGACGGAGGGA 60.179 55.000 0.00 0.00 38.67 4.20
4758 5251 3.387050 GGACGGAGGGAGTATGTAACAAT 59.613 47.826 0.00 0.00 0.00 2.71
4794 5287 5.689819 AGTTGAGTTACATCGCAAAATCAC 58.310 37.500 0.00 0.00 30.24 3.06
4824 5318 9.220767 GAAATCACAAGTTAACTCTACAATCCT 57.779 33.333 8.95 0.00 0.00 3.24
4850 5344 2.443416 AGAAAAGGGGAATAACGGCAC 58.557 47.619 0.00 0.00 0.00 5.01
4870 5364 5.413499 GCACCATCTTTTACTTGCATGAAT 58.587 37.500 6.60 0.00 0.00 2.57
4902 5398 5.281727 GTTCAAGAAAAGTAACCAGGCAAG 58.718 41.667 0.00 0.00 0.00 4.01
4903 5399 3.888930 TCAAGAAAAGTAACCAGGCAAGG 59.111 43.478 0.00 0.00 0.00 3.61
4904 5400 2.239400 AGAAAAGTAACCAGGCAAGGC 58.761 47.619 0.00 0.00 0.00 4.35
4905 5401 1.960689 GAAAAGTAACCAGGCAAGGCA 59.039 47.619 0.00 0.00 0.00 4.75
4906 5402 2.080654 AAAGTAACCAGGCAAGGCAA 57.919 45.000 0.00 0.00 0.00 4.52
4907 5403 2.080654 AAGTAACCAGGCAAGGCAAA 57.919 45.000 0.00 0.00 0.00 3.68
4908 5404 1.328279 AGTAACCAGGCAAGGCAAAC 58.672 50.000 0.00 0.00 0.00 2.93
4926 5422 1.210931 CCATGGAAGCACGCACAAG 59.789 57.895 5.56 0.00 0.00 3.16
4927 5423 1.236616 CCATGGAAGCACGCACAAGA 61.237 55.000 5.56 0.00 0.00 3.02
4928 5424 0.592637 CATGGAAGCACGCACAAGAA 59.407 50.000 0.00 0.00 0.00 2.52
4929 5425 1.001487 CATGGAAGCACGCACAAGAAA 60.001 47.619 0.00 0.00 0.00 2.52
4930 5426 1.098869 TGGAAGCACGCACAAGAAAA 58.901 45.000 0.00 0.00 0.00 2.29
4941 5437 5.509272 CACGCACAAGAAAAGTAATGCATAG 59.491 40.000 0.00 0.00 33.27 2.23
5013 5537 1.806542 TGCTGAAACTCGATTGGCTTC 59.193 47.619 0.00 0.00 0.00 3.86
5067 5597 1.143073 GGTCACCCTCTGTTCTTGGTT 59.857 52.381 0.00 0.00 0.00 3.67
5071 5601 1.421646 ACCCTCTGTTCTTGGTTGGAG 59.578 52.381 0.00 0.00 0.00 3.86
5076 5606 5.514834 CCCTCTGTTCTTGGTTGGAGAAATA 60.515 44.000 0.00 0.00 35.11 1.40
5099 5629 9.936759 AATACAGAAACCTAGAAGAAGAAGAAG 57.063 33.333 0.00 0.00 0.00 2.85
5100 5630 7.604657 ACAGAAACCTAGAAGAAGAAGAAGA 57.395 36.000 0.00 0.00 0.00 2.87
5115 5645 8.865090 AGAAGAAGAAGATTAGAGAACTCACAA 58.135 33.333 4.64 0.00 0.00 3.33
5126 5656 0.874607 AACTCACAACAGACGCCGAC 60.875 55.000 0.00 0.00 0.00 4.79
5189 5719 1.332997 GGATAACGTGACGAGGACGAT 59.667 52.381 13.70 0.00 42.66 3.73
5225 5755 0.109226 GCCGTGGTGACAGAGAGTAC 60.109 60.000 0.00 0.00 44.46 2.73
5229 5759 2.515854 GTGGTGACAGAGAGTACTGGA 58.484 52.381 0.00 0.00 44.46 3.86
5235 5765 1.711375 ACAGAGAGTACTGGAGTGGGA 59.289 52.381 0.00 0.00 41.59 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.752101 AGATTTCCTTGTGAAAGTGAGTCG 59.248 41.667 0.00 0.00 45.74 4.18
34 35 7.730364 TTAGATTTCCTTGTGAAAGTGAGTC 57.270 36.000 0.00 0.00 45.74 3.36
36 37 7.013274 TGGTTTAGATTTCCTTGTGAAAGTGAG 59.987 37.037 0.00 0.00 45.74 3.51
79 80 2.662596 CGGTAAGGCAGGAGCACA 59.337 61.111 0.00 0.00 44.61 4.57
95 96 5.499139 ACTACATTTGGGTGATAATTGCG 57.501 39.130 0.00 0.00 0.00 4.85
113 114 4.546829 TTCACTTCATGTGGGGTACTAC 57.453 45.455 0.00 0.00 46.20 2.73
217 222 6.093082 ACGGTCGAAGAAAAGGGTAAAATATG 59.907 38.462 0.00 0.00 39.69 1.78
292 298 0.249280 TACGCATATGCCGGTGTGAG 60.249 55.000 21.77 7.69 37.91 3.51
309 315 5.178797 ACATGTGACCTCAGTTATGCTTAC 58.821 41.667 0.00 0.00 0.00 2.34
342 348 1.601914 GGCATCGCGTTTCACCTTTTT 60.602 47.619 5.77 0.00 0.00 1.94
343 349 0.039527 GGCATCGCGTTTCACCTTTT 60.040 50.000 5.77 0.00 0.00 2.27
344 350 1.169661 TGGCATCGCGTTTCACCTTT 61.170 50.000 5.77 0.00 0.00 3.11
345 351 1.169661 TTGGCATCGCGTTTCACCTT 61.170 50.000 5.77 0.00 0.00 3.50
346 352 1.169661 TTTGGCATCGCGTTTCACCT 61.170 50.000 5.77 0.00 0.00 4.00
356 362 1.087202 TCCGGATCGTTTTGGCATCG 61.087 55.000 0.00 0.00 0.00 3.84
379 385 1.407434 TTACTTAACGCGACGGTGTG 58.593 50.000 15.93 0.00 36.89 3.82
483 489 5.009410 GCCGATGTAGTACTTAGGTGTGTAT 59.991 44.000 0.00 0.00 0.00 2.29
492 498 5.653769 AGGTTACTTGCCGATGTAGTACTTA 59.346 40.000 0.00 0.00 0.00 2.24
496 502 4.339247 GGTAGGTTACTTGCCGATGTAGTA 59.661 45.833 0.00 0.00 0.00 1.82
497 503 3.131755 GGTAGGTTACTTGCCGATGTAGT 59.868 47.826 0.00 0.00 0.00 2.73
498 504 3.383825 AGGTAGGTTACTTGCCGATGTAG 59.616 47.826 0.00 0.00 0.00 2.74
531 537 7.766278 TGCTATTTTAACCAGATCAGAGAACTC 59.234 37.037 0.00 0.00 0.00 3.01
583 589 2.006772 CGTCCATTGACTTAGCCGC 58.993 57.895 0.00 0.00 39.47 6.53
584 590 0.739462 TGCGTCCATTGACTTAGCCG 60.739 55.000 0.00 0.00 39.47 5.52
586 592 1.202076 GCTTGCGTCCATTGACTTAGC 60.202 52.381 0.00 0.00 39.47 3.09
587 593 2.076100 TGCTTGCGTCCATTGACTTAG 58.924 47.619 0.00 0.00 39.47 2.18
588 594 2.177394 TGCTTGCGTCCATTGACTTA 57.823 45.000 0.00 0.00 39.47 2.24
590 596 1.470098 GATTGCTTGCGTCCATTGACT 59.530 47.619 0.00 0.00 39.47 3.41
644 655 5.292101 CACCAGATCGAAGAAGATTGGTTAC 59.708 44.000 0.00 0.00 43.58 2.50
645 656 5.419542 CACCAGATCGAAGAAGATTGGTTA 58.580 41.667 0.00 0.00 43.58 2.85
646 657 4.256920 CACCAGATCGAAGAAGATTGGTT 58.743 43.478 0.00 0.00 43.58 3.67
647 658 3.369892 CCACCAGATCGAAGAAGATTGGT 60.370 47.826 0.00 7.50 43.58 3.67
688 699 0.383368 CGTGTTCACGCGGGTAAAAC 60.383 55.000 8.89 17.78 45.14 2.43
706 718 3.584406 AAGTCATTGGTGTCTCTCTCG 57.416 47.619 0.00 0.00 0.00 4.04
716 728 5.769662 TCATGAGCACTTAAAAGTCATTGGT 59.230 36.000 0.00 0.00 37.08 3.67
746 758 8.088365 GGGTGATAATTGGTGCTATTTTAATCC 58.912 37.037 0.00 0.00 0.00 3.01
793 805 1.835267 ACTGACCGTACACCCAGCA 60.835 57.895 0.00 0.00 0.00 4.41
833 847 3.260740 GCTCCTGAGAGTTGACATGAAG 58.739 50.000 0.00 0.00 42.59 3.02
921 948 1.745264 CTGCAGGTAGCTAGCTCCC 59.255 63.158 23.26 20.57 45.94 4.30
1137 1173 0.322456 TGAATTGCAGGGGAAGGACG 60.322 55.000 0.00 0.00 0.00 4.79
1138 1174 1.004745 TCTGAATTGCAGGGGAAGGAC 59.995 52.381 0.00 0.00 44.98 3.85
1139 1175 1.283029 CTCTGAATTGCAGGGGAAGGA 59.717 52.381 0.00 0.00 44.98 3.36
1140 1176 1.760192 CTCTGAATTGCAGGGGAAGG 58.240 55.000 0.00 0.00 44.98 3.46
1153 1189 2.726821 GAATTGACATGGCCCTCTGAA 58.273 47.619 0.00 0.00 0.00 3.02
1156 1192 0.749454 GCGAATTGACATGGCCCTCT 60.749 55.000 0.00 0.00 0.00 3.69
1157 1193 1.728490 GGCGAATTGACATGGCCCTC 61.728 60.000 0.00 0.00 37.82 4.30
1158 1194 1.754234 GGCGAATTGACATGGCCCT 60.754 57.895 0.00 0.00 37.82 5.19
1159 1195 2.807622 GGCGAATTGACATGGCCC 59.192 61.111 0.00 0.00 37.82 5.80
1160 1196 2.408835 CGGCGAATTGACATGGCC 59.591 61.111 0.00 0.00 40.36 5.36
1161 1197 2.408835 CCGGCGAATTGACATGGC 59.591 61.111 9.30 0.00 0.00 4.40
1162 1198 2.327002 CTGCCGGCGAATTGACATGG 62.327 60.000 23.90 0.00 0.00 3.66
1182 1528 3.249320 CCGTCAGATAGATTGCACCATTG 59.751 47.826 0.00 0.00 0.00 2.82
1183 1529 3.134623 TCCGTCAGATAGATTGCACCATT 59.865 43.478 0.00 0.00 0.00 3.16
1184 1530 2.700371 TCCGTCAGATAGATTGCACCAT 59.300 45.455 0.00 0.00 0.00 3.55
1185 1531 2.101415 CTCCGTCAGATAGATTGCACCA 59.899 50.000 0.00 0.00 0.00 4.17
1186 1532 2.748605 CTCCGTCAGATAGATTGCACC 58.251 52.381 0.00 0.00 0.00 5.01
1187 1533 2.131183 GCTCCGTCAGATAGATTGCAC 58.869 52.381 0.00 0.00 0.00 4.57
1188 1534 1.756538 TGCTCCGTCAGATAGATTGCA 59.243 47.619 0.00 0.00 0.00 4.08
1189 1535 2.223923 ACTGCTCCGTCAGATAGATTGC 60.224 50.000 3.99 0.00 37.51 3.56
1190 1536 3.181482 ACACTGCTCCGTCAGATAGATTG 60.181 47.826 3.99 0.00 37.51 2.67
1191 1537 3.027412 ACACTGCTCCGTCAGATAGATT 58.973 45.455 3.99 0.00 37.51 2.40
1194 1540 1.745653 TCACACTGCTCCGTCAGATAG 59.254 52.381 3.99 0.00 37.51 2.08
1205 1551 2.606751 AGTAGGGTACTCACACTGCT 57.393 50.000 0.00 0.00 45.28 4.24
1208 1554 5.479724 GGAAGTTAAGTAGGGTACTCACACT 59.520 44.000 0.00 0.00 42.59 3.55
1210 1556 5.648247 AGGAAGTTAAGTAGGGTACTCACA 58.352 41.667 0.00 0.00 38.26 3.58
1211 1557 5.951148 AGAGGAAGTTAAGTAGGGTACTCAC 59.049 44.000 0.00 0.00 38.26 3.51
1212 1558 5.950549 CAGAGGAAGTTAAGTAGGGTACTCA 59.049 44.000 0.00 0.00 38.26 3.41
1234 1587 4.246206 CATGCATGCGTCGCCCAG 62.246 66.667 14.93 5.52 0.00 4.45
1248 1601 7.603024 CCAGCTCACCTGCATATATATATCATG 59.397 40.741 2.03 3.74 40.36 3.07
1250 1603 6.042437 CCCAGCTCACCTGCATATATATATCA 59.958 42.308 2.03 4.11 40.36 2.15
1251 1604 6.042552 ACCCAGCTCACCTGCATATATATATC 59.957 42.308 2.03 0.00 40.36 1.63
1252 1605 5.907662 ACCCAGCTCACCTGCATATATATAT 59.092 40.000 0.00 0.00 40.36 0.86
1253 1606 5.280499 ACCCAGCTCACCTGCATATATATA 58.720 41.667 0.00 0.00 40.36 0.86
1295 1648 2.125512 ATGCCGACGCTCTGGAAC 60.126 61.111 0.00 0.00 35.36 3.62
1503 1856 6.503589 TTGGGGTTATATATGCGTAAATGC 57.496 37.500 0.00 0.00 0.00 3.56
1508 1861 8.042515 GGAACTAATTGGGGTTATATATGCGTA 58.957 37.037 0.00 0.00 0.00 4.42
1509 1862 6.882678 GGAACTAATTGGGGTTATATATGCGT 59.117 38.462 0.00 0.00 0.00 5.24
1511 1864 8.823220 ATGGAACTAATTGGGGTTATATATGC 57.177 34.615 0.00 0.00 0.00 3.14
1521 1874 6.098124 TGCTAATTTGATGGAACTAATTGGGG 59.902 38.462 0.00 0.00 29.93 4.96
1530 1883 6.482308 AGGTACGTATGCTAATTTGATGGAAC 59.518 38.462 0.00 0.00 0.00 3.62
1546 1899 1.191535 TCCAGCAAGCAGGTACGTAT 58.808 50.000 0.00 0.00 0.00 3.06
1550 1903 0.453390 GCAATCCAGCAAGCAGGTAC 59.547 55.000 3.34 0.00 0.00 3.34
1586 1939 1.674980 AGCCAGCAAGAAGAGCAGC 60.675 57.895 0.00 0.00 34.82 5.25
2054 2440 7.731054 ACATCTTAGCTACTAATCCTTCCTTG 58.269 38.462 0.00 0.00 0.00 3.61
2131 2528 2.645730 TGTGCTGTTCAAACAACCAC 57.354 45.000 14.54 14.54 39.59 4.16
2426 2823 5.745227 AGGTCTTTTCAGTGAGTCAGAAAA 58.255 37.500 15.58 15.58 38.54 2.29
2612 3022 5.428184 AGGGAAAGATAGTTGACTTCCAG 57.572 43.478 0.00 0.00 0.00 3.86
2802 3233 6.543430 TTGCTGGGAATATGCTTATTTGTT 57.457 33.333 6.33 0.00 0.00 2.83
2850 3304 6.488006 AGGAGGAACATGCACACATATTTATC 59.512 38.462 0.00 0.00 33.67 1.75
2884 3358 1.619654 TGAAGGTTGGCCAGAACATG 58.380 50.000 5.11 0.00 37.19 3.21
3124 3598 5.190677 GGTACCAACTTACCATAAGCATGT 58.809 41.667 7.15 0.00 41.27 3.21
3146 3620 0.405585 ATTGAAGTGGGAGTGGTGGG 59.594 55.000 0.00 0.00 0.00 4.61
3156 3630 4.753233 TCAAACACAAACCATTGAAGTGG 58.247 39.130 0.00 0.00 45.04 4.00
3157 3631 6.041511 TCATCAAACACAAACCATTGAAGTG 58.958 36.000 0.00 0.00 38.94 3.16
3167 3641 6.756074 TGTTGAAAGGATCATCAAACACAAAC 59.244 34.615 8.77 0.00 38.03 2.93
3209 3683 5.352846 CCACCAACATACGTATCACATCAAA 59.647 40.000 4.74 0.00 0.00 2.69
3213 3687 3.118408 AGCCACCAACATACGTATCACAT 60.118 43.478 4.74 0.00 0.00 3.21
3233 3707 1.078848 AACACAGATCCCTGCGAGC 60.079 57.895 0.00 0.00 44.16 5.03
3363 3837 6.436027 ACAGTATGGAAGAGAGGTAGATCAA 58.564 40.000 0.00 0.00 43.62 2.57
3407 3881 0.390860 CGAAGCAGATGGGGAGGTAG 59.609 60.000 0.00 0.00 0.00 3.18
3560 4034 1.615424 GTAGAGGAGGCCAACCCCA 60.615 63.158 5.01 0.00 36.11 4.96
4006 4492 2.750815 CGGTTGGAACGGAAGCTAG 58.249 57.895 0.00 0.00 0.00 3.42
4052 4538 0.387367 CGTGTTCCACCTCTCTGTCG 60.387 60.000 0.00 0.00 0.00 4.35
4091 4577 2.359850 GCGGTGACATTGGCCTCA 60.360 61.111 3.32 0.00 0.00 3.86
4121 4607 2.480419 CACCATCTTCTTGAACACCGAC 59.520 50.000 0.00 0.00 0.00 4.79
4271 4758 0.033504 GCACATCCCCGATCATACGT 59.966 55.000 0.00 0.00 0.00 3.57
4282 4769 0.727398 GTTTAGCTCACGCACATCCC 59.273 55.000 0.00 0.00 39.10 3.85
4331 4821 2.115343 ATCCTCTTCGCCCTTCAAAC 57.885 50.000 0.00 0.00 0.00 2.93
4373 4865 6.716173 CCATCAAATCCAAACCCAAAGAAAAT 59.284 34.615 0.00 0.00 0.00 1.82
4415 4907 8.186821 AGATAACGGTACACTGTACATAGAAAC 58.813 37.037 18.91 6.57 34.49 2.78
4476 4969 6.430925 TGTGCTTGCAATATCATCCCTATAAC 59.569 38.462 0.00 0.00 0.00 1.89
4498 4991 3.009723 ACACTCACCAGTTGAAGTTGTG 58.990 45.455 0.00 0.00 34.39 3.33
4526 5019 6.660521 AGAATCATGAACCTTGCTTATGACAA 59.339 34.615 0.00 0.00 31.34 3.18
4575 5068 1.003580 GTTGAGAATCCTGGCTCCACA 59.996 52.381 0.00 0.00 29.87 4.17
4590 5083 3.077484 ACTCCCCACATTCATGTTGAG 57.923 47.619 5.59 8.39 39.39 3.02
4648 5141 8.948853 TTTCATTGTCGTTAATTGTGAATCTC 57.051 30.769 0.00 0.00 0.00 2.75
4690 5183 1.590147 GGACGGAGGGTGTACTGTG 59.410 63.158 0.00 0.00 0.00 3.66
4698 5191 1.990327 ACTTATTTTGGGACGGAGGGT 59.010 47.619 0.00 0.00 0.00 4.34
4699 5192 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
4700 5193 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4701 5194 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
4702 5195 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
4703 5196 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
4704 5197 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
4705 5198 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
4706 5199 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
4707 5200 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
4708 5201 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
4709 5202 9.438291 CAGTACAAAGTTGAGTCACTTATTTTG 57.562 33.333 8.80 8.80 35.87 2.44
4710 5203 8.621286 CCAGTACAAAGTTGAGTCACTTATTTT 58.379 33.333 0.00 0.00 35.87 1.82
4711 5204 7.228706 CCCAGTACAAAGTTGAGTCACTTATTT 59.771 37.037 0.00 0.00 35.87 1.40
4712 5205 6.710744 CCCAGTACAAAGTTGAGTCACTTATT 59.289 38.462 0.00 0.00 35.87 1.40
4713 5206 6.042781 TCCCAGTACAAAGTTGAGTCACTTAT 59.957 38.462 0.00 0.00 35.87 1.73
4714 5207 5.364446 TCCCAGTACAAAGTTGAGTCACTTA 59.636 40.000 0.00 0.00 35.87 2.24
4715 5208 4.163458 TCCCAGTACAAAGTTGAGTCACTT 59.837 41.667 0.00 0.00 38.74 3.16
4716 5209 3.709653 TCCCAGTACAAAGTTGAGTCACT 59.290 43.478 0.00 0.00 0.00 3.41
4717 5210 3.808174 GTCCCAGTACAAAGTTGAGTCAC 59.192 47.826 0.00 0.00 0.00 3.67
4718 5211 3.491964 CGTCCCAGTACAAAGTTGAGTCA 60.492 47.826 0.00 0.00 0.00 3.41
4719 5212 3.057734 CGTCCCAGTACAAAGTTGAGTC 58.942 50.000 0.00 0.00 0.00 3.36
4720 5213 2.224209 CCGTCCCAGTACAAAGTTGAGT 60.224 50.000 0.00 0.00 0.00 3.41
4721 5214 2.036733 TCCGTCCCAGTACAAAGTTGAG 59.963 50.000 0.00 0.00 0.00 3.02
4722 5215 2.036733 CTCCGTCCCAGTACAAAGTTGA 59.963 50.000 0.00 0.00 0.00 3.18
4723 5216 2.413837 CTCCGTCCCAGTACAAAGTTG 58.586 52.381 0.00 0.00 0.00 3.16
4724 5217 1.346722 CCTCCGTCCCAGTACAAAGTT 59.653 52.381 0.00 0.00 0.00 2.66
4725 5218 0.974383 CCTCCGTCCCAGTACAAAGT 59.026 55.000 0.00 0.00 0.00 2.66
4726 5219 0.249398 CCCTCCGTCCCAGTACAAAG 59.751 60.000 0.00 0.00 0.00 2.77
4727 5220 0.178926 TCCCTCCGTCCCAGTACAAA 60.179 55.000 0.00 0.00 0.00 2.83
4728 5221 0.613853 CTCCCTCCGTCCCAGTACAA 60.614 60.000 0.00 0.00 0.00 2.41
4729 5222 1.000019 CTCCCTCCGTCCCAGTACA 60.000 63.158 0.00 0.00 0.00 2.90
4730 5223 0.257039 TACTCCCTCCGTCCCAGTAC 59.743 60.000 0.00 0.00 0.00 2.73
4731 5224 1.133575 CATACTCCCTCCGTCCCAGTA 60.134 57.143 0.00 0.00 0.00 2.74
4732 5225 0.397254 CATACTCCCTCCGTCCCAGT 60.397 60.000 0.00 0.00 0.00 4.00
4733 5226 0.397254 ACATACTCCCTCCGTCCCAG 60.397 60.000 0.00 0.00 0.00 4.45
4734 5227 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
4735 5228 1.685517 GTTACATACTCCCTCCGTCCC 59.314 57.143 0.00 0.00 0.00 4.46
4736 5229 2.381911 TGTTACATACTCCCTCCGTCC 58.618 52.381 0.00 0.00 0.00 4.79
4737 5230 4.667519 ATTGTTACATACTCCCTCCGTC 57.332 45.455 0.00 0.00 0.00 4.79
4738 5231 5.422970 TGTTATTGTTACATACTCCCTCCGT 59.577 40.000 0.00 0.00 0.00 4.69
4739 5232 5.909477 TGTTATTGTTACATACTCCCTCCG 58.091 41.667 0.00 0.00 0.00 4.63
4740 5233 7.736893 AGATGTTATTGTTACATACTCCCTCC 58.263 38.462 0.00 0.00 36.41 4.30
4741 5234 7.873505 GGAGATGTTATTGTTACATACTCCCTC 59.126 40.741 15.73 7.56 40.19 4.30
4742 5235 7.569111 AGGAGATGTTATTGTTACATACTCCCT 59.431 37.037 19.35 9.47 42.92 4.20
4743 5236 7.657761 CAGGAGATGTTATTGTTACATACTCCC 59.342 40.741 19.35 8.08 42.92 4.30
4744 5237 8.204836 ACAGGAGATGTTATTGTTACATACTCC 58.795 37.037 17.34 17.34 39.96 3.85
4758 5251 7.770366 TGTAACTCAACTACAGGAGATGTTA 57.230 36.000 0.00 0.00 39.96 2.41
4794 5287 6.866770 TGTAGAGTTAACTTGTGATTTCTCCG 59.133 38.462 10.02 0.00 0.00 4.63
4824 5318 5.416639 GCCGTTATTCCCCTTTTCTAAAAGA 59.583 40.000 15.16 0.00 46.39 2.52
4845 5339 1.539388 TGCAAGTAAAAGATGGTGCCG 59.461 47.619 0.00 0.00 0.00 5.69
4902 5398 1.080569 CGTGCTTCCATGGTTTGCC 60.081 57.895 12.58 7.88 0.00 4.52
4903 5399 1.734117 GCGTGCTTCCATGGTTTGC 60.734 57.895 12.58 14.52 0.00 3.68
4904 5400 0.664166 GTGCGTGCTTCCATGGTTTG 60.664 55.000 12.58 4.38 0.00 2.93
4905 5401 1.106351 TGTGCGTGCTTCCATGGTTT 61.106 50.000 12.58 0.00 0.00 3.27
4906 5402 1.106351 TTGTGCGTGCTTCCATGGTT 61.106 50.000 12.58 0.00 0.00 3.67
4907 5403 1.518056 CTTGTGCGTGCTTCCATGGT 61.518 55.000 12.58 0.00 0.00 3.55
4908 5404 1.210931 CTTGTGCGTGCTTCCATGG 59.789 57.895 4.97 4.97 0.00 3.66
4926 5422 9.294030 CAAGGTGAAATCTATGCATTACTTTTC 57.706 33.333 3.54 10.26 0.00 2.29
4927 5423 7.761249 GCAAGGTGAAATCTATGCATTACTTTT 59.239 33.333 3.54 0.27 34.10 2.27
4928 5424 7.123247 AGCAAGGTGAAATCTATGCATTACTTT 59.877 33.333 3.54 2.00 36.30 2.66
4929 5425 6.604795 AGCAAGGTGAAATCTATGCATTACTT 59.395 34.615 3.54 0.00 36.30 2.24
4930 5426 6.125029 AGCAAGGTGAAATCTATGCATTACT 58.875 36.000 3.54 0.00 36.30 2.24
4941 5437 3.013219 GAGGAAGGAGCAAGGTGAAATC 58.987 50.000 0.00 0.00 0.00 2.17
4987 5511 3.365364 CCAATCGAGTTTCAGCAACCTTC 60.365 47.826 0.00 0.00 35.77 3.46
5022 5552 1.135046 CTATTGATCTGTCTGCCGCG 58.865 55.000 0.00 0.00 0.00 6.46
5023 5553 2.515926 TCTATTGATCTGTCTGCCGC 57.484 50.000 0.00 0.00 0.00 6.53
5067 5597 7.792364 TCTTCTAGGTTTCTGTATTTCTCCA 57.208 36.000 0.00 0.00 0.00 3.86
5071 5601 9.930693 TCTTCTTCTTCTAGGTTTCTGTATTTC 57.069 33.333 0.00 0.00 0.00 2.17
5076 5606 7.604657 TCTTCTTCTTCTTCTAGGTTTCTGT 57.395 36.000 0.00 0.00 0.00 3.41
5098 5628 5.704888 CGTCTGTTGTGAGTTCTCTAATCT 58.295 41.667 1.53 0.00 0.00 2.40
5099 5629 4.324936 GCGTCTGTTGTGAGTTCTCTAATC 59.675 45.833 1.53 0.00 0.00 1.75
5100 5630 4.238514 GCGTCTGTTGTGAGTTCTCTAAT 58.761 43.478 1.53 0.00 0.00 1.73
5106 5636 0.596600 TCGGCGTCTGTTGTGAGTTC 60.597 55.000 6.85 0.00 0.00 3.01
5168 5698 0.248377 CGTCCTCGTCACGTTATCCC 60.248 60.000 0.00 0.00 32.41 3.85
5172 5702 0.179181 GCATCGTCCTCGTCACGTTA 60.179 55.000 0.00 0.00 38.45 3.18
5225 5755 0.979709 TGCCTGATCTCCCACTCCAG 60.980 60.000 0.00 0.00 0.00 3.86
5229 5759 1.326213 CGTCTGCCTGATCTCCCACT 61.326 60.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.