Multiple sequence alignment - TraesCS2D01G529600

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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 TraesCS2D01G529600 chr2D 100.000 4981 0 0 1 4981 616638377 616633397 0.000000e+00 9199.0
1 TraesCS2D01G529600 chr2A 94.220 3149 125 22 1854 4981 746853622 746850510 0.000000e+00 4754.0
2 TraesCS2D01G529600 chr2A 88.742 453 18 10 700 1129 746855890 746855448 1.590000e-144 523.0
3 TraesCS2D01G529600 chr2A 86.918 451 41 13 1395 1837 746855260 746854820 1.610000e-134 490.0
4 TraesCS2D01G529600 chr2A 91.892 37 3 0 4153 4189 772659679 772659643 9.000000e-03 52.8
5 TraesCS2D01G529600 chr2B 88.212 3843 260 102 363 4093 751844978 751841217 0.000000e+00 4409.0
6 TraesCS2D01G529600 chr2B 94.410 322 16 2 1 321 751848684 751848364 1.250000e-135 494.0
7 TraesCS2D01G529600 chr2B 79.188 394 62 13 4128 4512 53712475 53712093 6.400000e-64 255.0
8 TraesCS2D01G529600 chr2B 96.078 51 2 0 319 369 751848085 751848035 3.200000e-12 84.2
9 TraesCS2D01G529600 chr3B 80.488 451 58 22 3084 3520 559341545 559341111 8.050000e-83 318.0
10 TraesCS2D01G529600 chr3B 83.860 285 33 7 2097 2381 191259616 191259345 4.950000e-65 259.0
11 TraesCS2D01G529600 chr3B 86.486 111 14 1 4314 4424 784913453 784913562 2.440000e-23 121.0
12 TraesCS2D01G529600 chr7A 80.446 404 60 14 4125 4520 721589110 721589502 1.750000e-74 291.0
13 TraesCS2D01G529600 chr7A 80.149 403 60 12 4128 4522 721594271 721594661 2.940000e-72 283.0
14 TraesCS2D01G529600 chr7A 82.731 249 36 7 4128 4373 148476198 148475954 1.090000e-51 215.0
15 TraesCS2D01G529600 chrUn 80.203 394 59 12 4128 4512 24925745 24925362 1.370000e-70 278.0
16 TraesCS2D01G529600 chrUn 89.474 152 16 0 3305 3456 98211670 98211519 5.090000e-45 193.0
17 TraesCS2D01G529600 chr3D 89.908 218 18 3 3303 3520 427816891 427816678 1.370000e-70 278.0
18 TraesCS2D01G529600 chr3A 89.908 218 18 3 3303 3520 557949763 557949976 1.370000e-70 278.0
19 TraesCS2D01G529600 chr1D 80.053 376 60 12 4128 4501 214268934 214268572 1.060000e-66 265.0
20 TraesCS2D01G529600 chr4A 80.464 302 49 9 4128 4425 623826809 623826514 6.490000e-54 222.0
21 TraesCS2D01G529600 chr6B 83.410 217 31 4 4208 4424 664060621 664060832 3.930000e-46 196.0
22 TraesCS2D01G529600 chr6B 89.474 152 16 0 3305 3456 107771882 107771731 5.090000e-45 193.0
23 TraesCS2D01G529600 chr6A 89.474 152 16 0 3305 3456 53156894 53156743 5.090000e-45 193.0
24 TraesCS2D01G529600 chr6A 73.460 211 39 14 72 279 466221487 466221291 4.160000e-06 63.9
25 TraesCS2D01G529600 chr5B 86.747 166 17 5 3299 3461 562048317 562048480 3.960000e-41 180.0
26 TraesCS2D01G529600 chr7D 80.682 176 25 9 26 196 460635274 460635103 1.460000e-25 128.0
27 TraesCS2D01G529600 chr1A 75.500 200 42 4 448 642 5031550 5031747 1.910000e-14 91.6
28 TraesCS2D01G529600 chr7B 92.157 51 4 0 2335 2385 39542657 39542607 6.920000e-09 73.1
29 TraesCS2D01G529600 chr7B 92.157 51 4 0 2335 2385 711498742 711498692 6.920000e-09 73.1


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 TraesCS2D01G529600 chr2D 616633397 616638377 4980 True 9199.000000 9199 100.00 1 4981 1 chr2D.!!$R1 4980
1 TraesCS2D01G529600 chr2A 746850510 746855890 5380 True 1922.333333 4754 89.96 700 4981 3 chr2A.!!$R2 4281
2 TraesCS2D01G529600 chr2B 751841217 751848684 7467 True 1662.400000 4409 92.90 1 4093 3 chr2B.!!$R2 4092

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
537 3880 0.036388 ATGGAGTTCGATGGCGTGTT 60.036 50.000 0.00 0.0 38.98 3.32 F
1179 4591 0.103937 CTCCGCATCTCTCTCCCAAC 59.896 60.000 0.00 0.0 0.00 3.77 F
1362 4795 0.321564 CCGCCACCTGACTGAATCAA 60.322 55.000 0.00 0.0 36.69 2.57 F
1611 5055 0.971386 CAGTGCCTTCCTTGCCATTT 59.029 50.000 0.00 0.0 0.00 2.32 F
1763 5225 1.003118 CTGTCCCGGTGATTCTGGAAA 59.997 52.381 0.00 0.0 45.09 3.13 F
3265 7914 0.461135 GGCGGCCATGAACAAATGAT 59.539 50.000 15.62 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 5201 0.037590 TGGTTTCCAGAATCACCGGG 59.962 55.000 6.32 0.0 31.24 5.73 R
2153 6799 0.095417 GCGTTGAGCTCGAATTGGAC 59.905 55.000 4.86 0.0 44.04 4.02 R
2479 7125 0.392863 TGCTGATCCCGTTCCACATG 60.393 55.000 0.00 0.0 0.00 3.21 R
2740 7389 1.145819 GATCTCCTCCAGCAGCACC 59.854 63.158 0.00 0.0 0.00 5.01 R
3667 8319 1.997874 ACCACCCTCTGCTGGATCC 60.998 63.158 4.20 4.2 0.00 3.36 R
4352 9025 0.679505 GAGCCCCCACCAAAGAAAAC 59.320 55.000 0.00 0.0 0.00 2.43 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
78 79 3.075134 AGAAGAGGGCTCCACAAGAAATT 59.925 43.478 0.00 0.00 0.00 1.82
111 112 3.971109 GAAACCGAGCGGGAAGGGG 62.971 68.421 14.07 0.00 39.97 4.79
117 118 2.531942 AGCGGGAAGGGGAGGTTT 60.532 61.111 0.00 0.00 0.00 3.27
118 119 1.229723 AGCGGGAAGGGGAGGTTTA 60.230 57.895 0.00 0.00 0.00 2.01
119 120 1.223763 GCGGGAAGGGGAGGTTTAG 59.776 63.158 0.00 0.00 0.00 1.85
120 121 1.559965 GCGGGAAGGGGAGGTTTAGT 61.560 60.000 0.00 0.00 0.00 2.24
129 131 3.010250 AGGGGAGGTTTAGTAGCAAAAGG 59.990 47.826 0.00 0.00 0.00 3.11
146 148 1.518367 AGGAAAGGGTGAGTTGTGGA 58.482 50.000 0.00 0.00 0.00 4.02
152 154 1.705997 GGGTGAGTTGTGGAGTGGGT 61.706 60.000 0.00 0.00 0.00 4.51
156 158 2.357952 GTGAGTTGTGGAGTGGGTTTTC 59.642 50.000 0.00 0.00 0.00 2.29
167 169 3.756963 GAGTGGGTTTTCTATGTTGGGAC 59.243 47.826 0.00 0.00 0.00 4.46
213 215 7.644157 GGCGAATAGTTTGGAAGAACATATTTC 59.356 37.037 0.00 0.00 31.94 2.17
281 283 1.089123 TTGGGTTTTGGGGAGCCTAT 58.911 50.000 0.00 0.00 35.71 2.57
299 301 3.448301 CCTATTGGGTGCATGTTTGATGT 59.552 43.478 0.00 0.00 0.00 3.06
313 315 4.083749 TGTTTGATGTCCGAACATAAACGG 60.084 41.667 11.87 0.00 46.20 4.44
322 324 4.863391 CGAACATAAACGGAGCGTATAG 57.137 45.455 0.00 0.00 39.99 1.31
323 325 4.285292 CGAACATAAACGGAGCGTATAGT 58.715 43.478 0.00 0.00 39.99 2.12
325 327 4.644103 ACATAAACGGAGCGTATAGTGT 57.356 40.909 0.00 0.00 39.99 3.55
424 3767 2.051345 GTTTGCGTCGGTGCCAAG 60.051 61.111 0.00 0.00 0.00 3.61
492 3835 1.480954 GTATGCTTTCCTCCTCCGACA 59.519 52.381 0.00 0.00 0.00 4.35
537 3880 0.036388 ATGGAGTTCGATGGCGTGTT 60.036 50.000 0.00 0.00 38.98 3.32
542 3885 3.943479 TTCGATGGCGTGTTCGGGG 62.943 63.158 0.00 0.00 38.98 5.73
544 3887 2.580276 GATGGCGTGTTCGGGGTA 59.420 61.111 0.00 0.00 37.56 3.69
548 3891 2.341176 GCGTGTTCGGGGTACTGT 59.659 61.111 0.00 0.00 37.56 3.55
553 3896 0.250858 TGTTCGGGGTACTGTCTCGA 60.251 55.000 0.00 0.00 0.00 4.04
557 3900 1.487976 TCGGGGTACTGTCTCGACTAT 59.512 52.381 0.00 0.00 0.00 2.12
563 3906 6.214399 GGGGTACTGTCTCGACTATATTTTG 58.786 44.000 0.00 0.00 0.00 2.44
568 3911 7.813852 ACTGTCTCGACTATATTTTGTCAAC 57.186 36.000 0.00 0.00 33.18 3.18
588 3931 2.347452 ACGACAATAACTTCGCATTCGG 59.653 45.455 0.00 0.00 38.88 4.30
601 3944 4.357142 TCGCATTCGGTAAGCTACTTTAG 58.643 43.478 0.00 0.00 36.13 1.85
618 3961 5.238583 ACTTTAGAGATCCGGAAAGTTGTG 58.761 41.667 9.01 0.00 38.63 3.33
627 3970 1.393539 CGGAAAGTTGTGTATCAGCGG 59.606 52.381 0.00 0.00 32.51 5.52
630 3973 1.808411 AAGTTGTGTATCAGCGGTGG 58.192 50.000 15.67 0.00 32.51 4.61
658 4001 2.342948 GTCGAGCTAAGCGAACTCTTTG 59.657 50.000 0.00 0.00 39.73 2.77
670 4013 4.461405 CGAACTCTTTGTCTTGATTGCAG 58.539 43.478 0.00 0.00 0.00 4.41
674 4018 5.585390 ACTCTTTGTCTTGATTGCAGTTTG 58.415 37.500 0.00 0.00 0.00 2.93
679 4023 3.132646 TGTCTTGATTGCAGTTTGCCTTT 59.867 39.130 0.00 0.00 44.23 3.11
690 4034 4.747810 CAGTTTGCCTTTTTGTCTTGTCT 58.252 39.130 0.00 0.00 0.00 3.41
696 4040 4.280677 TGCCTTTTTGTCTTGTCTTATGGG 59.719 41.667 0.00 0.00 0.00 4.00
697 4041 4.280929 GCCTTTTTGTCTTGTCTTATGGGT 59.719 41.667 0.00 0.00 0.00 4.51
720 4064 6.321717 GTTTTTGTGAGTTGTGTCTGATTGA 58.678 36.000 0.00 0.00 0.00 2.57
748 4092 1.305201 GCGAAGGTGTCAAAGTGGAA 58.695 50.000 0.00 0.00 0.00 3.53
750 4094 2.833794 CGAAGGTGTCAAAGTGGAAGA 58.166 47.619 0.00 0.00 0.00 2.87
751 4095 3.403038 CGAAGGTGTCAAAGTGGAAGAT 58.597 45.455 0.00 0.00 0.00 2.40
752 4096 3.187227 CGAAGGTGTCAAAGTGGAAGATG 59.813 47.826 0.00 0.00 0.00 2.90
753 4097 3.864789 AGGTGTCAAAGTGGAAGATGT 57.135 42.857 0.00 0.00 0.00 3.06
755 4099 3.392616 AGGTGTCAAAGTGGAAGATGTCT 59.607 43.478 0.00 0.00 0.00 3.41
769 4124 2.012673 GATGTCTAAGCAGCTTGGGTG 58.987 52.381 18.54 5.54 0.00 4.61
946 4320 3.465588 TCCTTTTCCTTTCCCTTTCTCCA 59.534 43.478 0.00 0.00 0.00 3.86
1081 4464 1.892391 GGATCCAAATCGCCCGACC 60.892 63.158 6.95 0.00 32.24 4.79
1118 4501 2.321296 ACCCTAATTCCTGGTACCTCCT 59.679 50.000 14.36 0.00 37.07 3.69
1119 4502 2.973406 CCCTAATTCCTGGTACCTCCTC 59.027 54.545 14.36 0.00 37.07 3.71
1120 4503 2.973406 CCTAATTCCTGGTACCTCCTCC 59.027 54.545 14.36 0.00 37.07 4.30
1121 4504 2.972153 AATTCCTGGTACCTCCTCCT 57.028 50.000 14.36 0.00 37.07 3.69
1122 4505 2.480642 ATTCCTGGTACCTCCTCCTC 57.519 55.000 14.36 0.00 37.07 3.71
1132 4515 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1133 4516 2.520741 CCTCCTCCTCCTCCTCGC 60.521 72.222 0.00 0.00 0.00 5.03
1135 4518 4.507916 TCCTCCTCCTCCTCGCCG 62.508 72.222 0.00 0.00 0.00 6.46
1151 4543 3.197790 CGCCTCACCTTGCCGATG 61.198 66.667 0.00 0.00 0.00 3.84
1163 4555 1.228276 GCCGATGGATTTCCCCTCC 60.228 63.158 0.00 0.00 34.29 4.30
1164 4556 1.071471 CCGATGGATTTCCCCTCCG 59.929 63.158 0.00 0.00 35.41 4.63
1177 4589 1.456518 CCTCCGCATCTCTCTCCCA 60.457 63.158 0.00 0.00 0.00 4.37
1178 4590 1.045350 CCTCCGCATCTCTCTCCCAA 61.045 60.000 0.00 0.00 0.00 4.12
1179 4591 0.103937 CTCCGCATCTCTCTCCCAAC 59.896 60.000 0.00 0.00 0.00 3.77
1180 4592 0.324738 TCCGCATCTCTCTCCCAACT 60.325 55.000 0.00 0.00 0.00 3.16
1181 4593 0.539051 CCGCATCTCTCTCCCAACTT 59.461 55.000 0.00 0.00 0.00 2.66
1183 4595 1.480137 CGCATCTCTCTCCCAACTTCT 59.520 52.381 0.00 0.00 0.00 2.85
1184 4596 2.690497 CGCATCTCTCTCCCAACTTCTA 59.310 50.000 0.00 0.00 0.00 2.10
1187 4599 4.161377 GCATCTCTCTCCCAACTTCTACTT 59.839 45.833 0.00 0.00 0.00 2.24
1188 4600 5.361285 GCATCTCTCTCCCAACTTCTACTTA 59.639 44.000 0.00 0.00 0.00 2.24
1189 4601 6.041523 GCATCTCTCTCCCAACTTCTACTTAT 59.958 42.308 0.00 0.00 0.00 1.73
1190 4602 7.432869 CATCTCTCTCCCAACTTCTACTTATG 58.567 42.308 0.00 0.00 0.00 1.90
1193 4605 6.936279 TCTCTCCCAACTTCTACTTATGTTG 58.064 40.000 0.00 0.00 39.35 3.33
1194 4606 6.724441 TCTCTCCCAACTTCTACTTATGTTGA 59.276 38.462 0.00 0.00 41.35 3.18
1195 4607 7.400339 TCTCTCCCAACTTCTACTTATGTTGAT 59.600 37.037 0.00 0.00 41.35 2.57
1196 4608 7.556844 TCTCCCAACTTCTACTTATGTTGATC 58.443 38.462 0.00 0.00 41.35 2.92
1197 4609 6.338146 TCCCAACTTCTACTTATGTTGATCG 58.662 40.000 0.00 0.00 41.35 3.69
1198 4610 6.153851 TCCCAACTTCTACTTATGTTGATCGA 59.846 38.462 0.00 0.00 41.35 3.59
1199 4611 6.986817 CCCAACTTCTACTTATGTTGATCGAT 59.013 38.462 0.00 0.00 41.35 3.59
1200 4612 7.169982 CCCAACTTCTACTTATGTTGATCGATC 59.830 40.741 18.72 18.72 41.35 3.69
1201 4613 7.096436 CCAACTTCTACTTATGTTGATCGATCG 60.096 40.741 20.03 9.36 41.35 3.69
1202 4614 7.260558 ACTTCTACTTATGTTGATCGATCGA 57.739 36.000 21.86 21.86 0.00 3.59
1203 4615 7.133513 ACTTCTACTTATGTTGATCGATCGAC 58.866 38.462 30.96 30.96 40.79 4.20
1204 4616 5.998553 TCTACTTATGTTGATCGATCGACC 58.001 41.667 33.10 12.29 39.88 4.79
1205 4617 3.629058 ACTTATGTTGATCGATCGACCG 58.371 45.455 33.10 23.10 39.88 4.79
1206 4618 3.314357 ACTTATGTTGATCGATCGACCGA 59.686 43.478 33.10 22.17 39.88 4.69
1226 4638 2.370281 TGTCGACATCAGCCTCTTTC 57.630 50.000 15.76 0.00 0.00 2.62
1227 4639 1.272781 GTCGACATCAGCCTCTTTCG 58.727 55.000 11.55 0.00 0.00 3.46
1228 4640 1.135373 GTCGACATCAGCCTCTTTCGA 60.135 52.381 11.55 0.00 33.34 3.71
1229 4641 1.544246 TCGACATCAGCCTCTTTCGAA 59.456 47.619 0.00 0.00 32.86 3.71
1230 4642 2.166459 TCGACATCAGCCTCTTTCGAAT 59.834 45.455 0.00 0.00 32.86 3.34
1231 4643 2.537625 CGACATCAGCCTCTTTCGAATC 59.462 50.000 0.00 0.00 0.00 2.52
1232 4644 3.525537 GACATCAGCCTCTTTCGAATCA 58.474 45.455 0.00 0.00 0.00 2.57
1233 4645 3.265791 ACATCAGCCTCTTTCGAATCAC 58.734 45.455 0.00 0.00 0.00 3.06
1252 4664 1.148157 CGTCTTCCTACGCATGCAGG 61.148 60.000 19.57 17.72 35.87 4.85
1275 4687 5.117135 GGACTGCGCTTTTCATTTTAGAAAC 59.883 40.000 9.73 0.00 37.24 2.78
1276 4688 5.831997 ACTGCGCTTTTCATTTTAGAAACT 58.168 33.333 9.73 0.00 37.24 2.66
1277 4689 6.966021 ACTGCGCTTTTCATTTTAGAAACTA 58.034 32.000 9.73 0.00 37.24 2.24
1278 4690 6.856426 ACTGCGCTTTTCATTTTAGAAACTAC 59.144 34.615 9.73 0.00 37.24 2.73
1279 4691 6.730175 TGCGCTTTTCATTTTAGAAACTACA 58.270 32.000 9.73 0.00 37.24 2.74
1292 4708 4.081406 AGAAACTACAATCCAATGCTGCA 58.919 39.130 4.13 4.13 0.00 4.41
1293 4709 3.855689 AACTACAATCCAATGCTGCAC 57.144 42.857 3.57 0.00 0.00 4.57
1294 4710 3.077484 ACTACAATCCAATGCTGCACT 57.923 42.857 3.57 0.00 0.00 4.40
1295 4711 3.424703 ACTACAATCCAATGCTGCACTT 58.575 40.909 3.57 0.00 0.00 3.16
1296 4712 4.588899 ACTACAATCCAATGCTGCACTTA 58.411 39.130 3.57 0.00 0.00 2.24
1306 4722 3.921119 TGCTGCACTTAATTTGGTGAG 57.079 42.857 0.00 8.84 35.69 3.51
1330 4746 3.485633 GAATTTGTTCCTTCGCGGTAAC 58.514 45.455 6.13 6.56 0.00 2.50
1332 4748 1.950828 TTGTTCCTTCGCGGTAACAA 58.049 45.000 18.38 18.38 38.89 2.83
1336 4769 0.947180 TCCTTCGCGGTAACAACTGC 60.947 55.000 6.13 0.00 38.56 4.40
1355 4788 2.665000 CATGTCCGCCACCTGACT 59.335 61.111 0.00 0.00 32.67 3.41
1361 4794 1.191489 TCCGCCACCTGACTGAATCA 61.191 55.000 0.00 0.00 35.45 2.57
1362 4795 0.321564 CCGCCACCTGACTGAATCAA 60.322 55.000 0.00 0.00 36.69 2.57
1366 4799 3.674997 GCCACCTGACTGAATCAAAGTA 58.325 45.455 0.00 0.00 36.69 2.24
1368 4801 4.083271 GCCACCTGACTGAATCAAAGTAAC 60.083 45.833 0.00 0.00 36.69 2.50
1369 4802 4.152402 CCACCTGACTGAATCAAAGTAACG 59.848 45.833 0.00 0.00 36.69 3.18
1370 4803 3.746492 ACCTGACTGAATCAAAGTAACGC 59.254 43.478 0.00 0.00 36.69 4.84
1371 4804 3.181530 CCTGACTGAATCAAAGTAACGCG 60.182 47.826 3.53 3.53 36.69 6.01
1373 4806 2.139917 ACTGAATCAAAGTAACGCGCA 58.860 42.857 5.73 0.00 0.00 6.09
1374 4807 2.546368 ACTGAATCAAAGTAACGCGCAA 59.454 40.909 5.73 0.00 0.00 4.85
1375 4808 3.002862 ACTGAATCAAAGTAACGCGCAAA 59.997 39.130 5.73 0.00 0.00 3.68
1376 4809 4.153958 TGAATCAAAGTAACGCGCAAAT 57.846 36.364 5.73 0.00 0.00 2.32
1378 4811 5.690816 TGAATCAAAGTAACGCGCAAATAA 58.309 33.333 5.73 0.00 0.00 1.40
1379 4812 5.792962 TGAATCAAAGTAACGCGCAAATAAG 59.207 36.000 5.73 0.00 0.00 1.73
1380 4813 4.073169 TCAAAGTAACGCGCAAATAAGG 57.927 40.909 5.73 0.00 0.00 2.69
1381 4814 3.499157 TCAAAGTAACGCGCAAATAAGGT 59.501 39.130 5.73 0.00 0.00 3.50
1384 4817 2.809696 AGTAACGCGCAAATAAGGTTGT 59.190 40.909 5.73 0.00 0.00 3.32
1385 4818 3.995705 AGTAACGCGCAAATAAGGTTGTA 59.004 39.130 5.73 0.00 0.00 2.41
1386 4819 2.886587 ACGCGCAAATAAGGTTGTAC 57.113 45.000 5.73 0.00 0.00 2.90
1389 4822 3.368843 ACGCGCAAATAAGGTTGTACTAC 59.631 43.478 5.73 0.00 0.00 2.73
1391 4824 3.368843 GCGCAAATAAGGTTGTACTACGT 59.631 43.478 0.30 0.00 0.00 3.57
1392 4825 4.562394 GCGCAAATAAGGTTGTACTACGTA 59.438 41.667 0.30 0.00 0.00 3.57
1393 4826 5.499176 GCGCAAATAAGGTTGTACTACGTAC 60.499 44.000 0.30 0.00 39.24 3.67
1424 4861 2.102252 AGTGGCGAATGAGAGGAAGATC 59.898 50.000 0.00 0.00 0.00 2.75
1425 4862 2.110578 TGGCGAATGAGAGGAAGATCA 58.889 47.619 0.00 0.00 0.00 2.92
1426 4863 2.702478 TGGCGAATGAGAGGAAGATCAT 59.298 45.455 0.00 0.00 37.77 2.45
1427 4864 3.135348 TGGCGAATGAGAGGAAGATCATT 59.865 43.478 0.00 0.29 46.21 2.57
1428 4865 4.133078 GGCGAATGAGAGGAAGATCATTT 58.867 43.478 0.00 0.00 44.18 2.32
1430 4867 5.277731 GGCGAATGAGAGGAAGATCATTTTC 60.278 44.000 0.00 0.00 44.18 2.29
1432 4869 5.750547 CGAATGAGAGGAAGATCATTTTCGA 59.249 40.000 0.00 0.00 44.18 3.71
1433 4870 6.074409 CGAATGAGAGGAAGATCATTTTCGAG 60.074 42.308 0.00 0.00 44.18 4.04
1434 4871 5.921962 TGAGAGGAAGATCATTTTCGAGA 57.078 39.130 0.00 0.00 0.00 4.04
1435 4872 5.900425 TGAGAGGAAGATCATTTTCGAGAG 58.100 41.667 0.00 0.00 0.00 3.20
1436 4873 4.692228 AGAGGAAGATCATTTTCGAGAGC 58.308 43.478 0.00 0.00 0.00 4.09
1437 4874 3.802866 AGGAAGATCATTTTCGAGAGCC 58.197 45.455 0.00 0.00 0.00 4.70
1438 4875 3.198635 AGGAAGATCATTTTCGAGAGCCA 59.801 43.478 0.00 0.00 0.00 4.75
1439 4876 4.133078 GGAAGATCATTTTCGAGAGCCAT 58.867 43.478 0.00 0.00 0.00 4.40
1440 4877 4.578105 GGAAGATCATTTTCGAGAGCCATT 59.422 41.667 0.00 0.00 0.00 3.16
1459 4898 6.071728 AGCCATTATTTGTCAGGAGAAACTTG 60.072 38.462 0.00 0.00 0.00 3.16
1484 4923 4.872691 AGATTATTCAGGAGCGAAACAGTG 59.127 41.667 0.00 0.00 0.00 3.66
1517 4956 5.248477 TCAGTAGATACCTTTCCTGCACTTT 59.752 40.000 0.00 0.00 0.00 2.66
1535 4974 3.622612 ACTTTTGCAATTGGAAACACAGC 59.377 39.130 22.82 0.00 42.67 4.40
1536 4975 1.850377 TTGCAATTGGAAACACAGCG 58.150 45.000 10.24 0.00 42.67 5.18
1578 5022 5.423610 AGAGTACTGCTATGTTGATCTTGGT 59.576 40.000 0.00 0.00 0.00 3.67
1580 5024 6.476378 AGTACTGCTATGTTGATCTTGGTTT 58.524 36.000 0.00 0.00 0.00 3.27
1585 5029 7.230510 ACTGCTATGTTGATCTTGGTTTACAAA 59.769 33.333 0.00 0.00 38.91 2.83
1586 5030 8.121305 TGCTATGTTGATCTTGGTTTACAAAT 57.879 30.769 0.00 0.00 38.91 2.32
1587 5031 8.243426 TGCTATGTTGATCTTGGTTTACAAATC 58.757 33.333 0.00 0.00 38.91 2.17
1611 5055 0.971386 CAGTGCCTTCCTTGCCATTT 59.029 50.000 0.00 0.00 0.00 2.32
1681 5125 2.438021 CGGGGACATTTCCTTCCATCTA 59.562 50.000 0.00 0.00 42.38 1.98
1706 5160 4.167268 CAAGGTACGTACTTTGCTCTCTC 58.833 47.826 29.92 9.76 36.66 3.20
1717 5171 4.644685 ACTTTGCTCTCTCTATCTCTGTCC 59.355 45.833 0.00 0.00 0.00 4.02
1724 5178 9.052365 TGCTCTCTCTATCTCTGTCCTATATTA 57.948 37.037 0.00 0.00 0.00 0.98
1726 5180 9.832445 CTCTCTCTATCTCTGTCCTATATTACC 57.168 40.741 0.00 0.00 0.00 2.85
1727 5181 9.569074 TCTCTCTATCTCTGTCCTATATTACCT 57.431 37.037 0.00 0.00 0.00 3.08
1728 5182 9.613428 CTCTCTATCTCTGTCCTATATTACCTG 57.387 40.741 0.00 0.00 0.00 4.00
1730 5184 9.967451 CTCTATCTCTGTCCTATATTACCTGAA 57.033 37.037 0.00 0.00 0.00 3.02
1731 5185 9.967451 TCTATCTCTGTCCTATATTACCTGAAG 57.033 37.037 0.00 0.00 0.00 3.02
1763 5225 1.003118 CTGTCCCGGTGATTCTGGAAA 59.997 52.381 0.00 0.00 45.09 3.13
1791 5253 4.082625 TGTCAAATTGTCACATCATGCTCC 60.083 41.667 0.00 0.00 0.00 4.70
1808 5270 7.370383 TCATGCTCCAAGTTTGAAAATTCTAC 58.630 34.615 0.00 0.00 0.00 2.59
1830 5292 8.314021 TCTACCCATCTACATGCAGTAATTATG 58.686 37.037 0.00 0.61 30.92 1.90
1837 5299 8.193953 TCTACATGCAGTAATTATGATCCTCA 57.806 34.615 0.00 0.00 30.92 3.86
1839 5301 7.502120 ACATGCAGTAATTATGATCCTCAAC 57.498 36.000 0.00 0.00 0.00 3.18
1840 5302 7.056006 ACATGCAGTAATTATGATCCTCAACA 58.944 34.615 0.00 0.00 0.00 3.33
1842 5304 7.558161 TGCAGTAATTATGATCCTCAACAAG 57.442 36.000 0.00 0.00 0.00 3.16
1847 6490 8.336235 AGTAATTATGATCCTCAACAAGGGAAA 58.664 33.333 0.00 0.00 46.23 3.13
1848 6491 7.410120 AATTATGATCCTCAACAAGGGAAAC 57.590 36.000 0.00 0.00 46.23 2.78
1850 6493 4.453480 TGATCCTCAACAAGGGAAACTT 57.547 40.909 0.00 0.00 46.23 2.66
1852 6495 5.208121 TGATCCTCAACAAGGGAAACTTTT 58.792 37.500 0.00 0.00 46.23 2.27
1861 6504 6.002653 ACAAGGGAAACTTTTCTACTCACT 57.997 37.500 1.88 0.00 37.29 3.41
1881 6525 4.574013 CACTACTGAAATTGGCCATCTCTC 59.426 45.833 6.09 1.60 0.00 3.20
1887 6531 4.263639 TGAAATTGGCCATCTCTCTCACTT 60.264 41.667 6.09 0.00 0.00 3.16
1890 6534 2.111384 TGGCCATCTCTCTCACTTACC 58.889 52.381 0.00 0.00 0.00 2.85
1893 6537 2.763448 GCCATCTCTCTCACTTACCTGT 59.237 50.000 0.00 0.00 0.00 4.00
1894 6538 3.954904 GCCATCTCTCTCACTTACCTGTA 59.045 47.826 0.00 0.00 0.00 2.74
1895 6539 4.037446 GCCATCTCTCTCACTTACCTGTAG 59.963 50.000 0.00 0.00 0.00 2.74
1921 6565 2.882742 GCTTGCTGCACTTGTAGTAC 57.117 50.000 0.00 0.00 42.31 2.73
1929 6573 4.613622 GCTGCACTTGTAGTACATTGTTGG 60.614 45.833 3.28 0.00 0.00 3.77
1967 6613 6.659254 CTGTACTGACAGCATGCAGCAAAG 62.659 50.000 21.98 12.46 46.41 2.77
2007 6653 3.855599 TCCATCCAGTTCCCCTTAATCAA 59.144 43.478 0.00 0.00 0.00 2.57
2016 6662 1.668419 CCCTTAATCAACCGGAGCAG 58.332 55.000 9.46 0.00 0.00 4.24
2104 6750 2.875485 GTGCAGCTCGACGACCTA 59.125 61.111 0.00 0.00 0.00 3.08
2153 6799 1.009829 GGCCAAGTTCTGCTACGATG 58.990 55.000 0.00 0.00 0.00 3.84
2719 7368 4.223514 GACACCACGTCGTCTGAC 57.776 61.111 0.00 0.00 41.91 3.51
3158 7807 1.467920 CTCCCAGTTCCAGCAAATCC 58.532 55.000 0.00 0.00 0.00 3.01
3265 7914 0.461135 GGCGGCCATGAACAAATGAT 59.539 50.000 15.62 0.00 0.00 2.45
3292 7941 2.346803 TGAGCTTGCGTTTGATACCTC 58.653 47.619 0.00 0.00 0.00 3.85
3917 8575 1.069227 GGTCGCATGTGGTTTTCAGAC 60.069 52.381 6.39 0.00 0.00 3.51
3971 8636 5.993748 TTTCCCCGCTGAAATAAGAATTT 57.006 34.783 0.00 0.00 38.03 1.82
3977 8642 6.202226 CCCGCTGAAATAAGAATTTTAGAGC 58.798 40.000 6.77 0.00 39.75 4.09
3981 8646 8.276325 CGCTGAAATAAGAATTTTAGAGCGTAT 58.724 33.333 16.47 0.00 42.79 3.06
4072 8745 6.207691 TCCTAGCATAATTTTGGCAAGAAC 57.792 37.500 0.00 0.00 0.00 3.01
4126 8799 6.286758 CAGCTAGCTTTGATAATTCTCCTCA 58.713 40.000 16.46 0.00 0.00 3.86
4146 8819 3.199946 TCAAGACAGGACTTTCAACACCT 59.800 43.478 0.00 0.00 0.00 4.00
4149 8822 1.609208 CAGGACTTTCAACACCTGGG 58.391 55.000 0.00 0.00 44.04 4.45
4150 8823 1.133792 CAGGACTTTCAACACCTGGGT 60.134 52.381 0.00 0.00 44.04 4.51
4246 8919 5.665916 GGGACCAAAGATGATCAAACATT 57.334 39.130 0.00 0.00 0.00 2.71
4264 8937 4.787598 ACATTCGATGTTCTTGCAAAGTC 58.212 39.130 0.00 0.00 41.63 3.01
4272 8945 1.597742 TCTTGCAAAGTCTCAGCCAC 58.402 50.000 0.00 0.00 46.34 5.01
4315 8988 6.599638 ACCTCACCTAAAGAAATAACATCAGC 59.400 38.462 0.00 0.00 0.00 4.26
4352 9025 4.026310 GTGCACTTTTGAGCAGTGATTTTG 60.026 41.667 10.32 0.00 46.01 2.44
4357 9030 7.175410 CACTTTTGAGCAGTGATTTTGTTTTC 58.825 34.615 0.00 0.00 43.90 2.29
4419 9092 6.533185 ACTTTGCAAGAACGTCAAAATTTTG 58.467 32.000 22.40 22.40 39.48 2.44
4440 9119 3.760151 TGATCATGCCTCCAAAGTTTCAG 59.240 43.478 0.00 0.00 0.00 3.02
4441 9120 3.507162 TCATGCCTCCAAAGTTTCAGA 57.493 42.857 0.00 0.00 0.00 3.27
4524 9203 2.952310 GGGGCTGTCATACATTTTCCTC 59.048 50.000 0.00 0.00 0.00 3.71
4550 9229 9.025020 CATCCTAAATAATCATATCGTTCTCCG 57.975 37.037 0.00 0.00 38.13 4.63
4586 9265 6.405278 AAATTTACAGGTTCCAAGTTGAGG 57.595 37.500 3.87 0.00 0.00 3.86
4607 9286 6.002062 AGGAATTGCACGAAGAGTTAAAAG 57.998 37.500 0.00 0.00 0.00 2.27
4706 9385 3.706086 ACTTTCACCCTGCATTTTCTGTT 59.294 39.130 0.00 0.00 0.00 3.16
4754 9434 3.300388 TGTTGATTTTGTGCCCCTTGTA 58.700 40.909 0.00 0.00 0.00 2.41
4766 9446 4.947388 GTGCCCCTTGTACAAAATGATCTA 59.053 41.667 10.03 0.00 0.00 1.98
4777 9457 7.942341 TGTACAAAATGATCTACTCCCTGTTTT 59.058 33.333 0.00 0.00 0.00 2.43
4942 9622 2.417933 CGAACAGCCCAAAAGAGATCAG 59.582 50.000 0.00 0.00 0.00 2.90
4966 9646 9.388506 CAGTCATCCATTAGTAAAAGAACATCT 57.611 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 4.029809 CCCCTTCCCGCTCGGTTT 62.030 66.667 7.59 0.00 0.00 3.27
111 112 5.183331 CCCTTTCCTTTTGCTACTAAACCTC 59.817 44.000 0.00 0.00 0.00 3.85
117 118 4.349930 ACTCACCCTTTCCTTTTGCTACTA 59.650 41.667 0.00 0.00 0.00 1.82
118 119 3.138468 ACTCACCCTTTCCTTTTGCTACT 59.862 43.478 0.00 0.00 0.00 2.57
119 120 3.487372 ACTCACCCTTTCCTTTTGCTAC 58.513 45.455 0.00 0.00 0.00 3.58
120 121 3.876309 ACTCACCCTTTCCTTTTGCTA 57.124 42.857 0.00 0.00 0.00 3.49
129 131 2.222027 CACTCCACAACTCACCCTTTC 58.778 52.381 0.00 0.00 0.00 2.62
146 148 3.499745 GGTCCCAACATAGAAAACCCACT 60.500 47.826 0.00 0.00 0.00 4.00
152 154 1.706305 ACGGGGTCCCAACATAGAAAA 59.294 47.619 10.98 0.00 35.37 2.29
156 158 0.326927 AACACGGGGTCCCAACATAG 59.673 55.000 10.98 0.00 35.37 2.23
186 188 2.739913 TGTTCTTCCAAACTATTCGCCG 59.260 45.455 0.00 0.00 0.00 6.46
187 189 4.965119 ATGTTCTTCCAAACTATTCGCC 57.035 40.909 0.00 0.00 0.00 5.54
226 228 5.032846 TCAGGACTCCATCAAATCTAACCT 58.967 41.667 0.00 0.00 0.00 3.50
281 283 1.617850 GGACATCAAACATGCACCCAA 59.382 47.619 0.00 0.00 0.00 4.12
313 315 6.263344 TGACACTATTCAACACTATACGCTC 58.737 40.000 0.00 0.00 0.00 5.03
318 320 9.971922 CATGAGATGACACTATTCAACACTATA 57.028 33.333 0.00 0.00 0.00 1.31
321 323 6.111382 CCATGAGATGACACTATTCAACACT 58.889 40.000 0.00 0.00 0.00 3.55
322 324 5.877012 ACCATGAGATGACACTATTCAACAC 59.123 40.000 0.00 0.00 0.00 3.32
323 325 6.053632 ACCATGAGATGACACTATTCAACA 57.946 37.500 0.00 0.00 0.00 3.33
325 327 7.093333 ACTGTACCATGAGATGACACTATTCAA 60.093 37.037 0.00 0.00 0.00 2.69
389 3732 5.163893 CGCAAACAACGTCATAGTTAGGATT 60.164 40.000 0.00 0.00 32.35 3.01
424 3767 4.067896 ACACATGATCCACAGTCTTTCAC 58.932 43.478 0.00 0.00 0.00 3.18
470 3813 0.106894 CGGAGGAGGAAAGCATACCC 59.893 60.000 0.00 0.00 0.00 3.69
526 3869 3.359515 TACCCCGAACACGCCATCG 62.360 63.158 0.00 0.00 42.43 3.84
537 3880 0.904649 TAGTCGAGACAGTACCCCGA 59.095 55.000 5.99 0.00 0.00 5.14
542 3885 8.796278 GTTGACAAAATATAGTCGAGACAGTAC 58.204 37.037 5.99 0.00 37.58 2.73
544 3887 6.527023 CGTTGACAAAATATAGTCGAGACAGT 59.473 38.462 5.99 0.00 37.58 3.55
548 3891 6.614160 TGTCGTTGACAAAATATAGTCGAGA 58.386 36.000 0.00 0.00 39.78 4.04
563 3906 3.781341 TGCGAAGTTATTGTCGTTGAC 57.219 42.857 0.00 0.00 39.46 3.18
568 3911 2.347452 ACCGAATGCGAAGTTATTGTCG 59.653 45.455 0.00 0.00 40.82 4.35
588 3931 6.388435 TTCCGGATCTCTAAAGTAGCTTAC 57.612 41.667 4.15 0.00 0.00 2.34
601 3944 4.755411 TGATACACAACTTTCCGGATCTC 58.245 43.478 4.15 0.00 0.00 2.75
630 3973 2.652496 CTTAGCTCGACGCGGCTC 60.652 66.667 11.76 0.00 45.59 4.70
645 3988 4.555511 GCAATCAAGACAAAGAGTTCGCTT 60.556 41.667 0.00 0.00 0.00 4.68
670 4013 6.200854 CCATAAGACAAGACAAAAAGGCAAAC 59.799 38.462 0.00 0.00 0.00 2.93
674 4018 4.280929 ACCCATAAGACAAGACAAAAAGGC 59.719 41.667 0.00 0.00 0.00 4.35
679 4023 7.038659 CACAAAAACCCATAAGACAAGACAAA 58.961 34.615 0.00 0.00 0.00 2.83
690 4034 5.654650 AGACACAACTCACAAAAACCCATAA 59.345 36.000 0.00 0.00 0.00 1.90
696 4040 6.251376 GTCAATCAGACACAACTCACAAAAAC 59.749 38.462 0.00 0.00 46.77 2.43
697 4041 6.321717 GTCAATCAGACACAACTCACAAAAA 58.678 36.000 0.00 0.00 46.77 1.94
748 4092 1.912043 ACCCAAGCTGCTTAGACATCT 59.088 47.619 15.51 0.00 0.00 2.90
750 4094 1.352352 ACACCCAAGCTGCTTAGACAT 59.648 47.619 15.51 0.00 0.00 3.06
751 4095 0.764890 ACACCCAAGCTGCTTAGACA 59.235 50.000 15.51 0.00 0.00 3.41
752 4096 1.160137 CACACCCAAGCTGCTTAGAC 58.840 55.000 15.51 0.00 0.00 2.59
753 4097 0.036732 CCACACCCAAGCTGCTTAGA 59.963 55.000 15.51 0.00 0.00 2.10
755 4099 1.074775 CCCACACCCAAGCTGCTTA 59.925 57.895 15.51 0.00 0.00 3.09
769 4124 1.908066 CTACTTCCGCGCAAACCCAC 61.908 60.000 8.75 0.00 0.00 4.61
852 4223 4.754667 GAACCCGTGGAGGTCGCC 62.755 72.222 0.00 0.00 40.05 5.54
874 4245 2.577644 GAACGGCATGCATGTGCG 60.578 61.111 26.79 15.60 45.97 5.34
946 4320 3.736482 GAGACGCCGCGACGAGATT 62.736 63.158 24.48 0.00 36.70 2.40
977 4351 1.900545 CGTGGGAAGGGAGGAAGGAC 61.901 65.000 0.00 0.00 0.00 3.85
1118 4501 4.507916 CGGCGAGGAGGAGGAGGA 62.508 72.222 0.00 0.00 0.00 3.71
1135 4518 2.615227 ATCCATCGGCAAGGTGAGGC 62.615 60.000 0.00 0.00 30.86 4.70
1137 4520 1.672881 GAAATCCATCGGCAAGGTGAG 59.327 52.381 0.00 0.00 30.86 3.51
1146 4529 1.071471 CGGAGGGGAAATCCATCGG 59.929 63.158 1.22 0.23 46.66 4.18
1147 4539 1.598130 GCGGAGGGGAAATCCATCG 60.598 63.158 1.22 0.96 46.66 3.84
1151 4543 0.250510 GAGATGCGGAGGGGAAATCC 60.251 60.000 0.00 0.00 0.00 3.01
1163 4555 1.480137 AGAAGTTGGGAGAGAGATGCG 59.520 52.381 0.00 0.00 0.00 4.73
1164 4556 3.704061 AGTAGAAGTTGGGAGAGAGATGC 59.296 47.826 0.00 0.00 0.00 3.91
1177 4589 7.644551 GTCGATCGATCAACATAAGTAGAAGTT 59.355 37.037 22.50 0.00 0.00 2.66
1178 4590 7.133513 GTCGATCGATCAACATAAGTAGAAGT 58.866 38.462 22.50 0.00 0.00 3.01
1179 4591 6.579292 GGTCGATCGATCAACATAAGTAGAAG 59.421 42.308 23.20 3.79 0.00 2.85
1180 4592 6.436261 GGTCGATCGATCAACATAAGTAGAA 58.564 40.000 23.20 0.00 0.00 2.10
1181 4593 5.333875 CGGTCGATCGATCAACATAAGTAGA 60.334 44.000 26.79 7.16 0.00 2.59
1183 4595 4.512571 TCGGTCGATCGATCAACATAAGTA 59.487 41.667 26.79 0.00 33.92 2.24
1184 4596 3.314357 TCGGTCGATCGATCAACATAAGT 59.686 43.478 26.79 0.00 33.92 2.24
1187 4599 3.252458 ACATCGGTCGATCGATCAACATA 59.748 43.478 29.73 9.09 46.59 2.29
1188 4600 2.034685 ACATCGGTCGATCGATCAACAT 59.965 45.455 29.73 12.97 46.59 2.71
1189 4601 1.404035 ACATCGGTCGATCGATCAACA 59.596 47.619 29.73 11.23 46.59 3.33
1190 4602 2.044860 GACATCGGTCGATCGATCAAC 58.955 52.381 29.73 18.99 46.59 3.18
1205 4617 6.737044 TCGAAAGAGGCTGATGTCGACATC 62.737 50.000 39.40 39.40 43.30 3.06
1206 4618 2.736719 CGAAAGAGGCTGATGTCGACAT 60.737 50.000 30.37 30.37 39.70 3.06
1207 4619 1.402852 CGAAAGAGGCTGATGTCGACA 60.403 52.381 22.48 22.48 0.00 4.35
1208 4620 1.135373 TCGAAAGAGGCTGATGTCGAC 60.135 52.381 9.11 9.11 32.98 4.20
1209 4621 1.173913 TCGAAAGAGGCTGATGTCGA 58.826 50.000 7.35 7.35 35.34 4.20
1210 4622 1.996292 TTCGAAAGAGGCTGATGTCG 58.004 50.000 0.00 0.00 43.69 4.35
1211 4623 3.308323 GTGATTCGAAAGAGGCTGATGTC 59.692 47.826 0.00 0.00 43.69 3.06
1212 4624 3.265791 GTGATTCGAAAGAGGCTGATGT 58.734 45.455 0.00 0.00 43.69 3.06
1213 4625 2.283617 CGTGATTCGAAAGAGGCTGATG 59.716 50.000 0.00 0.00 43.69 3.07
1214 4626 2.093973 ACGTGATTCGAAAGAGGCTGAT 60.094 45.455 0.00 0.00 43.69 2.90
1215 4627 1.272490 ACGTGATTCGAAAGAGGCTGA 59.728 47.619 0.00 0.00 43.69 4.26
1216 4628 1.656095 GACGTGATTCGAAAGAGGCTG 59.344 52.381 0.00 0.00 43.69 4.85
1217 4629 1.546476 AGACGTGATTCGAAAGAGGCT 59.454 47.619 0.00 0.00 43.69 4.58
1218 4630 1.997669 AGACGTGATTCGAAAGAGGC 58.002 50.000 0.00 0.00 43.69 4.70
1219 4631 2.924290 GGAAGACGTGATTCGAAAGAGG 59.076 50.000 0.00 0.00 43.69 3.69
1220 4632 3.839293 AGGAAGACGTGATTCGAAAGAG 58.161 45.455 0.00 0.00 43.69 2.85
1221 4633 3.936372 AGGAAGACGTGATTCGAAAGA 57.064 42.857 0.00 0.00 42.86 2.52
1222 4634 3.542704 CGTAGGAAGACGTGATTCGAAAG 59.457 47.826 0.00 0.00 42.86 2.62
1223 4635 3.495193 CGTAGGAAGACGTGATTCGAAA 58.505 45.455 0.00 0.00 42.86 3.46
1224 4636 2.730090 GCGTAGGAAGACGTGATTCGAA 60.730 50.000 0.00 0.00 44.74 3.71
1225 4637 1.202110 GCGTAGGAAGACGTGATTCGA 60.202 52.381 0.00 0.00 44.74 3.71
1226 4638 1.189403 GCGTAGGAAGACGTGATTCG 58.811 55.000 0.00 0.00 44.74 3.34
1227 4639 2.273370 TGCGTAGGAAGACGTGATTC 57.727 50.000 0.00 0.00 44.74 2.52
1228 4640 2.540515 CATGCGTAGGAAGACGTGATT 58.459 47.619 0.00 0.00 44.74 2.57
1229 4641 1.802880 GCATGCGTAGGAAGACGTGAT 60.803 52.381 0.00 0.00 44.74 3.06
1230 4642 0.457853 GCATGCGTAGGAAGACGTGA 60.458 55.000 0.00 0.00 44.74 4.35
1231 4643 0.735978 TGCATGCGTAGGAAGACGTG 60.736 55.000 14.09 0.00 44.74 4.49
1232 4644 0.458543 CTGCATGCGTAGGAAGACGT 60.459 55.000 14.09 0.00 44.74 4.34
1233 4645 2.291843 CTGCATGCGTAGGAAGACG 58.708 57.895 14.09 0.00 45.70 4.18
1252 4664 5.915196 AGTTTCTAAAATGAAAAGCGCAGTC 59.085 36.000 11.47 3.83 37.63 3.51
1275 4687 5.565592 TTAAGTGCAGCATTGGATTGTAG 57.434 39.130 0.00 0.00 0.00 2.74
1276 4688 6.528537 AATTAAGTGCAGCATTGGATTGTA 57.471 33.333 0.00 0.00 0.00 2.41
1277 4689 5.410355 AATTAAGTGCAGCATTGGATTGT 57.590 34.783 0.00 0.00 0.00 2.71
1278 4690 5.064198 CCAAATTAAGTGCAGCATTGGATTG 59.936 40.000 15.49 9.25 38.44 2.67
1279 4691 5.180271 CCAAATTAAGTGCAGCATTGGATT 58.820 37.500 15.49 5.51 38.44 3.01
1285 4701 4.081406 TCTCACCAAATTAAGTGCAGCAT 58.919 39.130 0.00 0.00 33.90 3.79
1292 4708 7.839680 ACAAATTCCTCTCACCAAATTAAGT 57.160 32.000 0.00 0.00 0.00 2.24
1293 4709 8.748380 GAACAAATTCCTCTCACCAAATTAAG 57.252 34.615 0.00 0.00 0.00 1.85
1322 4738 2.038269 ATGGGCAGTTGTTACCGCG 61.038 57.895 0.00 0.00 0.00 6.46
1330 4746 3.443045 GGCGGACATGGGCAGTTG 61.443 66.667 0.00 0.00 0.00 3.16
1332 4748 4.722700 GTGGCGGACATGGGCAGT 62.723 66.667 0.00 0.00 40.91 4.40
1336 4769 3.716195 TCAGGTGGCGGACATGGG 61.716 66.667 0.00 0.00 36.97 4.00
1355 4788 3.610786 TTTGCGCGTTACTTTGATTCA 57.389 38.095 8.43 0.00 0.00 2.57
1361 4794 4.223659 CAACCTTATTTGCGCGTTACTTT 58.776 39.130 8.43 0.00 0.00 2.66
1362 4795 3.251487 ACAACCTTATTTGCGCGTTACTT 59.749 39.130 8.43 0.00 0.00 2.24
1366 4799 2.809696 AGTACAACCTTATTTGCGCGTT 59.190 40.909 8.43 0.00 0.00 4.84
1368 4801 3.540744 CGTAGTACAACCTTATTTGCGCG 60.541 47.826 0.00 0.00 0.00 6.86
1369 4802 3.368843 ACGTAGTACAACCTTATTTGCGC 59.631 43.478 0.00 0.00 41.94 6.09
1384 4817 4.868171 CCACTACCTTGTACGTACGTAGTA 59.132 45.833 28.76 22.12 45.11 1.82
1386 4819 3.485877 GCCACTACCTTGTACGTACGTAG 60.486 52.174 27.48 25.21 34.03 3.51
1389 4822 1.791555 CGCCACTACCTTGTACGTACG 60.792 57.143 20.18 15.01 0.00 3.67
1391 4824 1.819928 TCGCCACTACCTTGTACGTA 58.180 50.000 0.00 0.00 0.00 3.57
1392 4825 0.961019 TTCGCCACTACCTTGTACGT 59.039 50.000 0.00 0.00 0.00 3.57
1393 4826 1.924524 CATTCGCCACTACCTTGTACG 59.075 52.381 0.00 0.00 0.00 3.67
1424 4861 6.554419 TGACAAATAATGGCTCTCGAAAATG 58.446 36.000 0.00 0.00 38.19 2.32
1425 4862 6.183360 CCTGACAAATAATGGCTCTCGAAAAT 60.183 38.462 0.00 0.00 38.19 1.82
1426 4863 5.123820 CCTGACAAATAATGGCTCTCGAAAA 59.876 40.000 0.00 0.00 38.19 2.29
1427 4864 4.635765 CCTGACAAATAATGGCTCTCGAAA 59.364 41.667 0.00 0.00 38.19 3.46
1428 4865 4.081142 TCCTGACAAATAATGGCTCTCGAA 60.081 41.667 0.00 0.00 38.19 3.71
1430 4867 3.797039 TCCTGACAAATAATGGCTCTCG 58.203 45.455 0.00 0.00 38.19 4.04
1432 4869 5.441718 TTCTCCTGACAAATAATGGCTCT 57.558 39.130 0.00 0.00 38.19 4.09
1433 4870 5.649831 AGTTTCTCCTGACAAATAATGGCTC 59.350 40.000 0.00 0.00 38.19 4.70
1434 4871 5.574188 AGTTTCTCCTGACAAATAATGGCT 58.426 37.500 0.00 0.00 38.19 4.75
1435 4872 5.904362 AGTTTCTCCTGACAAATAATGGC 57.096 39.130 0.00 0.00 37.68 4.40
1436 4873 6.095377 GCAAGTTTCTCCTGACAAATAATGG 58.905 40.000 0.00 0.00 0.00 3.16
1437 4874 6.680810 TGCAAGTTTCTCCTGACAAATAATG 58.319 36.000 0.00 0.00 0.00 1.90
1438 4875 6.716628 TCTGCAAGTTTCTCCTGACAAATAAT 59.283 34.615 0.00 0.00 33.76 1.28
1439 4876 6.061441 TCTGCAAGTTTCTCCTGACAAATAA 58.939 36.000 0.00 0.00 33.76 1.40
1440 4877 5.620206 TCTGCAAGTTTCTCCTGACAAATA 58.380 37.500 0.00 0.00 33.76 1.40
1459 4898 3.623060 TGTTTCGCTCCTGAATAATCTGC 59.377 43.478 0.00 0.00 0.00 4.26
1484 4923 6.706716 GGAAAGGTATCTACTGAAGGTTATGC 59.293 42.308 0.00 0.00 0.00 3.14
1517 4956 1.850377 CGCTGTGTTTCCAATTGCAA 58.150 45.000 0.00 0.00 0.00 4.08
1535 4974 1.980844 CTGTAATGCTGCTGTTTTGCG 59.019 47.619 0.00 0.00 35.36 4.85
1536 4975 3.240069 CTCTGTAATGCTGCTGTTTTGC 58.760 45.455 0.00 0.00 0.00 3.68
1562 5001 8.243426 TGATTTGTAAACCAAGATCAACATAGC 58.757 33.333 0.00 0.00 32.55 2.97
1578 5022 5.048083 GGAAGGCACTGTGATGATTTGTAAA 60.048 40.000 12.86 0.00 40.86 2.01
1580 5024 4.009675 GGAAGGCACTGTGATGATTTGTA 58.990 43.478 12.86 0.00 40.86 2.41
1585 5029 2.719739 CAAGGAAGGCACTGTGATGAT 58.280 47.619 12.86 0.00 40.86 2.45
1586 5030 1.883638 GCAAGGAAGGCACTGTGATGA 60.884 52.381 12.86 0.00 40.86 2.92
1587 5031 0.524862 GCAAGGAAGGCACTGTGATG 59.475 55.000 12.86 0.00 40.86 3.07
1629 5073 2.882777 CATCGCTCGCAAGCTCGT 60.883 61.111 0.00 0.00 46.91 4.18
1681 5125 3.069158 AGAGCAAAGTACGTACCTTGTGT 59.931 43.478 28.66 20.16 31.85 3.72
1706 5160 9.184523 CCTTCAGGTAATATAGGACAGAGATAG 57.815 40.741 0.00 0.00 0.00 2.08
1717 5171 9.974980 GAGAAGTTTCTCCTTCAGGTAATATAG 57.025 37.037 10.15 0.00 46.20 1.31
1747 5201 0.037590 TGGTTTCCAGAATCACCGGG 59.962 55.000 6.32 0.00 31.24 5.73
1763 5225 4.206375 TGATGTGACAATTTGACACTGGT 58.794 39.130 24.91 15.00 42.09 4.00
1791 5253 8.792633 TGTAGATGGGTAGAATTTTCAAACTTG 58.207 33.333 0.00 0.00 0.00 3.16
1808 5270 7.281774 GGATCATAATTACTGCATGTAGATGGG 59.718 40.741 18.40 0.76 32.08 4.00
1830 5292 5.536538 AGAAAAGTTTCCCTTGTTGAGGATC 59.463 40.000 0.13 0.00 45.92 3.36
1837 5299 6.424032 AGTGAGTAGAAAAGTTTCCCTTGTT 58.576 36.000 0.13 0.00 37.92 2.83
1839 5301 7.171678 CAGTAGTGAGTAGAAAAGTTTCCCTTG 59.828 40.741 0.13 0.00 37.92 3.61
1840 5302 7.070821 TCAGTAGTGAGTAGAAAAGTTTCCCTT 59.929 37.037 0.00 0.00 37.92 3.95
1842 5304 6.756221 TCAGTAGTGAGTAGAAAAGTTTCCC 58.244 40.000 0.00 0.00 37.92 3.97
1843 5305 8.658499 TTTCAGTAGTGAGTAGAAAAGTTTCC 57.342 34.615 0.00 0.00 34.24 3.13
1847 6490 7.173390 GCCAATTTCAGTAGTGAGTAGAAAAGT 59.827 37.037 0.00 0.00 32.98 2.66
1848 6491 7.361286 GGCCAATTTCAGTAGTGAGTAGAAAAG 60.361 40.741 0.00 0.00 32.98 2.27
1850 6493 5.938125 GGCCAATTTCAGTAGTGAGTAGAAA 59.062 40.000 0.00 0.00 32.98 2.52
1852 6495 4.530553 TGGCCAATTTCAGTAGTGAGTAGA 59.469 41.667 0.61 0.00 32.98 2.59
1861 6504 4.471025 TGAGAGAGATGGCCAATTTCAGTA 59.529 41.667 10.96 0.00 0.00 2.74
1881 6525 7.624344 GCAAGCAAATTACTACAGGTAAGTGAG 60.624 40.741 0.00 0.00 42.74 3.51
1887 6531 4.394920 GCAGCAAGCAAATTACTACAGGTA 59.605 41.667 0.00 0.00 44.79 3.08
1920 6564 9.912634 CAGTAAATATGAAAGAACCAACAATGT 57.087 29.630 0.00 0.00 0.00 2.71
1921 6565 9.912634 ACAGTAAATATGAAAGAACCAACAATG 57.087 29.630 0.00 0.00 0.00 2.82
1955 6601 2.599659 GGAAGTTACTTTGCTGCATGC 58.400 47.619 11.82 11.82 43.25 4.06
1967 6613 6.056236 GGATGGAAATACAGAGGGAAGTTAC 58.944 44.000 0.00 0.00 0.00 2.50
2153 6799 0.095417 GCGTTGAGCTCGAATTGGAC 59.905 55.000 4.86 0.00 44.04 4.02
2371 7017 3.260483 GCCAGCGACTCGATGCAG 61.260 66.667 11.24 0.10 42.12 4.41
2471 7117 3.799755 GTTCCACATGACGGGCGC 61.800 66.667 0.00 0.00 0.00 6.53
2479 7125 0.392863 TGCTGATCCCGTTCCACATG 60.393 55.000 0.00 0.00 0.00 3.21
2698 7347 1.950007 AGACGACGTGGTGTCTGAG 59.050 57.895 8.32 0.00 45.87 3.35
2701 7350 1.653115 GTCAGACGACGTGGTGTCT 59.347 57.895 8.32 8.41 45.87 3.41
2740 7389 1.145819 GATCTCCTCCAGCAGCACC 59.854 63.158 0.00 0.00 0.00 5.01
3079 7728 2.733218 TCGACGAGCTTGGCAACG 60.733 61.111 7.80 7.12 42.51 4.10
3158 7807 4.803426 GTCAGGGACGAGCGCCAG 62.803 72.222 2.29 0.00 0.00 4.85
3258 7907 4.089493 CGCAAGCTCAAGAACAATCATTTG 59.911 41.667 0.00 0.00 38.86 2.32
3259 7908 4.232221 CGCAAGCTCAAGAACAATCATTT 58.768 39.130 0.00 0.00 0.00 2.32
3265 7914 2.421775 TCAAACGCAAGCTCAAGAACAA 59.578 40.909 0.00 0.00 45.62 2.83
3292 7941 3.200593 GCGCCTGCCATGACAGAG 61.201 66.667 11.02 5.43 40.25 3.35
3667 8319 1.997874 ACCACCCTCTGCTGGATCC 60.998 63.158 4.20 4.20 0.00 3.36
3673 8325 2.930562 GGTCCACCACCCTCTGCT 60.931 66.667 0.00 0.00 39.69 4.24
3842 8500 2.359230 AACCTGCTGCGCTTCTCC 60.359 61.111 9.73 0.00 0.00 3.71
3917 8575 5.105310 ACCAGTGTGCTAACCTATTCTACAG 60.105 44.000 0.00 0.00 0.00 2.74
3952 8617 6.693315 TCTAAAATTCTTATTTCAGCGGGG 57.307 37.500 0.00 0.00 32.85 5.73
4126 8799 3.545703 CAGGTGTTGAAAGTCCTGTCTT 58.454 45.455 0.00 0.00 41.51 3.01
4149 8822 3.055385 TGTTCATAGAAGGTGTAGGGCAC 60.055 47.826 0.00 0.00 46.97 5.01
4150 8823 3.178046 TGTTCATAGAAGGTGTAGGGCA 58.822 45.455 0.00 0.00 0.00 5.36
4151 8824 3.197983 ACTGTTCATAGAAGGTGTAGGGC 59.802 47.826 0.00 0.00 0.00 5.19
4152 8825 6.540438 TTACTGTTCATAGAAGGTGTAGGG 57.460 41.667 0.00 0.00 0.00 3.53
4214 8887 1.856920 TCTTTGGTCCCCCAGAGTTTT 59.143 47.619 0.00 0.00 42.33 2.43
4221 8894 1.679981 TGATCATCTTTGGTCCCCCA 58.320 50.000 0.00 0.00 39.65 4.96
4246 8919 3.727726 TGAGACTTTGCAAGAACATCGA 58.272 40.909 0.00 0.00 0.00 3.59
4264 8937 4.201851 CCTCGAATGTTATTTGTGGCTGAG 60.202 45.833 0.00 0.00 0.00 3.35
4272 8945 5.975410 GAGGTCTCCTCGAATGTTATTTG 57.025 43.478 0.00 0.00 41.08 2.32
4315 8988 6.252441 TCAAAAGTGCACATAAACTTTGAACG 59.748 34.615 21.04 0.64 43.92 3.95
4352 9025 0.679505 GAGCCCCCACCAAAGAAAAC 59.320 55.000 0.00 0.00 0.00 2.43
4357 9030 2.356667 GAGGAGCCCCCACCAAAG 59.643 66.667 0.00 0.00 37.41 2.77
4419 9092 4.012374 TCTGAAACTTTGGAGGCATGATC 58.988 43.478 0.00 0.00 0.00 2.92
4469 9148 7.768582 CACTACACCCTCATGAACAATACATTA 59.231 37.037 0.00 0.00 0.00 1.90
4470 9149 6.599244 CACTACACCCTCATGAACAATACATT 59.401 38.462 0.00 0.00 0.00 2.71
4476 9155 2.708861 ACCACTACACCCTCATGAACAA 59.291 45.455 0.00 0.00 0.00 2.83
4550 9229 9.447040 GAACCTGTAAATTTAACAGTGTTCTTC 57.553 33.333 25.77 16.31 43.14 2.87
4586 9265 5.212194 TGCTTTTAACTCTTCGTGCAATTC 58.788 37.500 0.00 0.00 0.00 2.17
4607 9286 2.032377 TCTTTTCGGTGTTCGTGAATGC 60.032 45.455 0.00 0.00 40.32 3.56
4754 9434 7.505585 TCAAAAACAGGGAGTAGATCATTTTGT 59.494 33.333 0.00 0.00 36.87 2.83
4766 9446 2.108952 AGGAGCATCAAAAACAGGGAGT 59.891 45.455 0.00 0.00 36.25 3.85
4777 9457 2.799017 AGCACAATGAAGGAGCATCAA 58.201 42.857 0.00 0.00 36.25 2.57


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

AutoCloner maintained by Alex Coulton.