Multiple sequence alignment - TraesCS5D01G182100

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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 TraesCS5D01G182100 chr5D 100.000 7070 0 0 1 7070 283013145 283020214 0.000000e+00 13056.0
1 TraesCS5D01G182100 chr5D 100.000 41 0 0 6320 6360 283019424 283019464 7.600000e-10 76.8
2 TraesCS5D01G182100 chr5D 100.000 41 0 0 6280 6320 283019464 283019504 7.600000e-10 76.8
3 TraesCS5D01G182100 chr5A 94.889 3913 139 35 421 4316 375370180 375374048 0.000000e+00 6061.0
4 TraesCS5D01G182100 chr5A 97.371 1826 39 4 4313 6129 375374251 375376076 0.000000e+00 3097.0
5 TraesCS5D01G182100 chr5A 90.596 638 36 3 6364 7001 375376155 375376768 0.000000e+00 824.0
6 TraesCS5D01G182100 chr5A 91.781 73 5 1 6193 6265 375376081 375376152 4.510000e-17 100.0
7 TraesCS5D01G182100 chr5B 92.236 3658 166 48 722 4322 321410947 321414543 0.000000e+00 5073.0
8 TraesCS5D01G182100 chr5B 95.174 1927 55 15 4313 6231 321414739 321416635 0.000000e+00 3009.0
9 TraesCS5D01G182100 chr5B 86.371 587 72 7 124 708 512940305 512940885 1.000000e-177 634.0
10 TraesCS5D01G182100 chr5B 90.499 421 28 8 6591 7001 321417173 321417591 4.820000e-151 545.0
11 TraesCS5D01G182100 chr5B 92.308 130 4 3 6466 6589 321416977 321417106 5.630000e-41 180.0
12 TraesCS5D01G182100 chr2D 85.139 646 87 4 65 708 616500638 616500000 0.000000e+00 652.0
13 TraesCS5D01G182100 chr2D 81.202 649 98 20 82 717 546780574 546779937 1.060000e-137 501.0
14 TraesCS5D01G182100 chr6D 83.515 643 99 5 74 714 2900634 2899997 1.700000e-165 593.0
15 TraesCS5D01G182100 chr6D 83.254 627 98 6 90 713 337846666 337847288 2.860000e-158 569.0
16 TraesCS5D01G182100 chr7D 83.028 654 98 12 73 721 5318321 5318966 1.320000e-161 580.0
17 TraesCS5D01G182100 chr6A 83.051 649 101 5 65 708 554781622 554782266 1.320000e-161 580.0
18 TraesCS5D01G182100 chr4D 83.151 641 97 9 74 711 8151991 8152623 6.150000e-160 575.0
19 TraesCS5D01G182100 chr4D 82.488 651 98 11 67 708 484063199 484062556 2.230000e-154 556.0


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 TraesCS5D01G182100 chr5D 283013145 283020214 7069 False 4403.20 13056 100.00000 1 7070 3 chr5D.!!$F1 7069
1 TraesCS5D01G182100 chr5A 375370180 375376768 6588 False 2520.50 6061 93.65925 421 7001 4 chr5A.!!$F1 6580
2 TraesCS5D01G182100 chr5B 321410947 321417591 6644 False 2201.75 5073 92.55425 722 7001 4 chr5B.!!$F2 6279
3 TraesCS5D01G182100 chr5B 512940305 512940885 580 False 634.00 634 86.37100 124 708 1 chr5B.!!$F1 584
4 TraesCS5D01G182100 chr2D 616500000 616500638 638 True 652.00 652 85.13900 65 708 1 chr2D.!!$R2 643
5 TraesCS5D01G182100 chr2D 546779937 546780574 637 True 501.00 501 81.20200 82 717 1 chr2D.!!$R1 635
6 TraesCS5D01G182100 chr6D 2899997 2900634 637 True 593.00 593 83.51500 74 714 1 chr6D.!!$R1 640
7 TraesCS5D01G182100 chr6D 337846666 337847288 622 False 569.00 569 83.25400 90 713 1 chr6D.!!$F1 623
8 TraesCS5D01G182100 chr7D 5318321 5318966 645 False 580.00 580 83.02800 73 721 1 chr7D.!!$F1 648
9 TraesCS5D01G182100 chr6A 554781622 554782266 644 False 580.00 580 83.05100 65 708 1 chr6A.!!$F1 643
10 TraesCS5D01G182100 chr4D 8151991 8152623 632 False 575.00 575 83.15100 74 711 1 chr4D.!!$F1 637
11 TraesCS5D01G182100 chr4D 484062556 484063199 643 True 556.00 556 82.48800 67 708 1 chr4D.!!$R1 641

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
389 400 1.003646 TCCTGCCACTCCTCTAGACT 58.996 55.000 0.00 0.00 0.00 3.24 F
1127 1142 0.224499 CGTTCGTTCGTTCGTTCGTT 59.776 50.000 9.89 0.00 0.00 3.85 F
1457 1498 0.904649 TCTGAACATCCGTGGAGCAT 59.095 50.000 0.00 0.00 0.00 3.79 F
1543 1594 2.230508 GTGATGGAACGTACAGACAGGA 59.769 50.000 0.00 0.00 0.00 3.86 F
1547 1598 2.894765 TGGAACGTACAGACAGGATCAA 59.105 45.455 0.00 0.00 0.00 2.57 F
2042 2103 3.054728 TCTGGTTTGGTTCACAGAAGTCA 60.055 43.478 0.00 0.00 37.06 3.41 F
3826 3899 0.319405 ACTTTGCTGGCTTGCCAATC 59.681 50.000 15.63 10.53 0.00 2.67 F
5059 5344 1.072173 TGGTGGAAGACATCACACAGG 59.928 52.381 0.00 0.00 34.61 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1315 1.080772 CTCTACGGTCGCACAGCAA 60.081 57.895 0.00 0.00 0.00 3.91 R
2678 2744 3.222603 GGGATAACTACCATGCAAAGGG 58.777 50.000 12.59 7.13 0.00 3.95 R
2703 2769 3.389329 ACAGATAGGGCTATGTGGTTCAG 59.611 47.826 0.00 0.00 40.07 3.02 R
3681 3754 2.646930 TGGAGAACGCGGATACTAGAA 58.353 47.619 12.47 0.00 0.00 2.10 R
3746 3819 8.603242 TTTTCAGGTTCTACATAGTCTGAAAC 57.397 34.615 20.59 8.73 40.57 2.78 R
4050 4124 2.028748 CACAGGCCCAAGGAAATTTCTG 60.029 50.000 17.42 9.00 0.00 3.02 R
5706 5999 1.884579 AGCGTAGTCGAAAGAGGTTCA 59.115 47.619 0.00 0.00 43.49 3.18 R
6340 6718 0.249398 ATGCTTACTCACCGTGTCCC 59.751 55.000 0.00 0.00 0.00 4.46 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
63 64 9.950680 TTTTTCTTGTTAAAAATTGTTGCACAA 57.049 22.222 7.41 7.41 42.95 3.33
77 79 1.270839 TGCACAAGAGAACCCACTAGC 60.271 52.381 0.00 0.00 0.00 3.42
99 101 3.659841 GTTTCTCTCTCCCTCCCCTATT 58.340 50.000 0.00 0.00 0.00 1.73
110 116 2.203351 CCCTATTCCTTGGCGGCC 60.203 66.667 13.32 13.32 0.00 6.13
121 127 2.035155 GGCGGCCAGGGTAAACTT 59.965 61.111 15.62 0.00 0.00 2.66
133 141 2.109480 GGGTAAACTTTCCCTTCCAGGT 59.891 50.000 0.00 0.00 40.48 4.00
169 177 2.066999 GGATTCGCCTCCCCTCTGT 61.067 63.158 0.00 0.00 0.00 3.41
181 189 3.443925 CTCTGTCTGCCGCTCCGA 61.444 66.667 0.00 0.00 0.00 4.55
183 191 3.753434 CTGTCTGCCGCTCCGACT 61.753 66.667 8.68 0.00 0.00 4.18
227 235 2.922503 TGCCTCCGCTCTGGTCAA 60.923 61.111 0.00 0.00 39.52 3.18
341 351 3.242804 CCTCCTCGAGTTCGTTCATCTAC 60.243 52.174 12.31 0.00 40.80 2.59
350 360 4.453478 AGTTCGTTCATCTACACGTAGTCA 59.547 41.667 4.22 0.00 41.61 3.41
389 400 1.003646 TCCTGCCACTCCTCTAGACT 58.996 55.000 0.00 0.00 0.00 3.24
396 407 1.748493 CACTCCTCTAGACTGTGAGGC 59.252 57.143 16.88 0.00 46.90 4.70
412 425 2.488545 TGAGGCTAGAGTTTCTCGTCAC 59.511 50.000 0.00 0.00 35.36 3.67
441 455 5.448496 CGAGATTTGGTGTCAGTTGTTTCAA 60.448 40.000 0.00 0.00 0.00 2.69
512 526 2.486636 TAGAGGCACGTGCACGAAGG 62.487 60.000 42.94 30.06 44.36 3.46
679 694 4.062293 TGTACTTCCGGTGAACTTTGATG 58.938 43.478 0.00 0.00 0.00 3.07
680 695 3.485463 ACTTCCGGTGAACTTTGATGA 57.515 42.857 0.00 0.00 0.00 2.92
681 696 4.021102 ACTTCCGGTGAACTTTGATGAT 57.979 40.909 0.00 0.00 0.00 2.45
714 729 9.859427 TCTGAATCATTTTCGCAAAAGAATAAT 57.141 25.926 0.00 0.00 33.22 1.28
834 849 1.218047 CGTGAGCGAAGGAATGGGA 59.782 57.895 0.00 0.00 41.33 4.37
1065 1080 0.698818 ATTTCTTGGGGAAGAGCGGT 59.301 50.000 0.00 0.00 35.16 5.68
1094 1109 1.293498 GAGTGCCCTTCGCTTCTCA 59.707 57.895 0.00 0.00 38.28 3.27
1112 1127 1.862201 TCACCGTTCATGTGTTCGTTC 59.138 47.619 0.00 0.00 35.25 3.95
1113 1128 0.856641 ACCGTTCATGTGTTCGTTCG 59.143 50.000 0.00 0.00 0.00 3.95
1114 1129 0.856641 CCGTTCATGTGTTCGTTCGT 59.143 50.000 0.00 0.00 0.00 3.85
1115 1130 1.259507 CCGTTCATGTGTTCGTTCGTT 59.740 47.619 0.00 0.00 0.00 3.85
1116 1131 2.546665 CGTTCATGTGTTCGTTCGTTC 58.453 47.619 0.00 0.00 0.00 3.95
1117 1132 2.546665 GTTCATGTGTTCGTTCGTTCG 58.453 47.619 0.00 0.00 0.00 3.95
1118 1133 1.842720 TCATGTGTTCGTTCGTTCGT 58.157 45.000 0.00 0.00 0.00 3.85
1119 1134 2.195096 TCATGTGTTCGTTCGTTCGTT 58.805 42.857 0.00 0.00 0.00 3.85
1120 1135 2.216940 TCATGTGTTCGTTCGTTCGTTC 59.783 45.455 0.00 0.00 0.00 3.95
1121 1136 0.567051 TGTGTTCGTTCGTTCGTTCG 59.433 50.000 2.67 0.00 0.00 3.95
1122 1137 0.567509 GTGTTCGTTCGTTCGTTCGT 59.432 50.000 9.89 0.00 0.00 3.85
1123 1138 1.007114 GTGTTCGTTCGTTCGTTCGTT 60.007 47.619 9.89 0.00 0.00 3.85
1124 1139 1.252524 TGTTCGTTCGTTCGTTCGTTC 59.747 47.619 9.89 6.75 0.00 3.95
1125 1140 0.493966 TTCGTTCGTTCGTTCGTTCG 59.506 50.000 9.89 7.92 0.00 3.95
1126 1141 0.588730 TCGTTCGTTCGTTCGTTCGT 60.589 50.000 14.44 0.00 33.45 3.85
1127 1142 0.224499 CGTTCGTTCGTTCGTTCGTT 59.776 50.000 9.89 0.00 0.00 3.85
1128 1143 1.709190 CGTTCGTTCGTTCGTTCGTTC 60.709 52.381 9.89 5.85 0.00 3.95
1360 1399 3.441572 GCACTTGCTACAATGTTCTGGAT 59.558 43.478 0.00 0.00 38.21 3.41
1373 1412 6.566079 ATGTTCTGGATTGAGGATCTTGTA 57.434 37.500 0.00 0.00 35.02 2.41
1376 1415 4.033009 TCTGGATTGAGGATCTTGTAGCA 58.967 43.478 0.00 0.00 35.02 3.49
1388 1427 5.595952 GGATCTTGTAGCAAATCCTGGAATT 59.404 40.000 0.00 0.00 35.75 2.17
1390 1429 7.285401 GGATCTTGTAGCAAATCCTGGAATTAA 59.715 37.037 0.00 0.00 35.75 1.40
1392 1431 7.999679 TCTTGTAGCAAATCCTGGAATTAATG 58.000 34.615 0.00 0.00 0.00 1.90
1402 1442 7.738437 ATCCTGGAATTAATGAATTGTTGGT 57.262 32.000 0.00 0.00 35.33 3.67
1420 1460 2.152016 GGTGCTCCTGAAACCTGTAAC 58.848 52.381 0.00 0.00 0.00 2.50
1432 1473 2.490991 ACCTGTAACGGAAGCAGTTTC 58.509 47.619 0.00 0.00 33.42 2.78
1457 1498 0.904649 TCTGAACATCCGTGGAGCAT 59.095 50.000 0.00 0.00 0.00 3.79
1475 1516 5.391950 GGAGCATCACACGTTTCAACATATT 60.392 40.000 0.00 0.00 36.25 1.28
1535 1586 6.630444 TCTATTAGAGGTGATGGAACGTAC 57.370 41.667 0.00 0.00 0.00 3.67
1543 1594 2.230508 GTGATGGAACGTACAGACAGGA 59.769 50.000 0.00 0.00 0.00 3.86
1545 1596 3.130516 TGATGGAACGTACAGACAGGATC 59.869 47.826 0.00 0.00 0.00 3.36
1547 1598 2.894765 TGGAACGTACAGACAGGATCAA 59.105 45.455 0.00 0.00 0.00 2.57
1549 1600 3.056749 GGAACGTACAGACAGGATCAAGT 60.057 47.826 0.00 0.00 0.00 3.16
1555 1613 4.543590 ACAGACAGGATCAAGTAGTTGG 57.456 45.455 10.39 0.00 34.09 3.77
1564 1622 4.096984 GGATCAAGTAGTTGGCAAGAATGG 59.903 45.833 10.39 0.00 34.09 3.16
1601 1659 4.602340 TCTGTAAGAAGTTGACCACCTC 57.398 45.455 0.00 0.00 42.31 3.85
1603 1661 4.039245 TCTGTAAGAAGTTGACCACCTCTG 59.961 45.833 0.00 0.00 42.31 3.35
1634 1695 4.449068 CACTGTCCTGTTGATTGTGTAGAC 59.551 45.833 0.00 0.00 0.00 2.59
1744 1805 8.874816 GGTCAGTAGATAGTTTGAAGTGAATTC 58.125 37.037 0.00 0.00 38.50 2.17
1747 1808 7.063426 CAGTAGATAGTTTGAAGTGAATTCGCA 59.937 37.037 20.55 4.13 41.14 5.10
1756 1817 9.305110 GTTTGAAGTGAATTCGCAATAAATTTG 57.695 29.630 20.55 0.00 41.14 2.32
1766 1827 6.825284 TCGCAATAAATTTGGCATAATGTG 57.175 33.333 0.00 0.00 0.00 3.21
2042 2103 3.054728 TCTGGTTTGGTTCACAGAAGTCA 60.055 43.478 0.00 0.00 37.06 3.41
2536 2598 5.507149 CCATCTGAAGAGATTGAGTAGACCG 60.507 48.000 0.00 0.00 36.75 4.79
2676 2742 4.020307 TCACAAGTCATGTTATCTCTGGCA 60.020 41.667 0.00 0.00 41.46 4.92
2678 2744 3.191078 AGTCATGTTATCTCTGGCAGC 57.809 47.619 10.34 0.00 0.00 5.25
2703 2769 5.010012 CCTTTGCATGGTAGTTATCCCAATC 59.990 44.000 0.00 0.00 33.66 2.67
2973 3039 4.385825 ACGAGCAGGTAAAAGTTCATCAA 58.614 39.130 0.00 0.00 0.00 2.57
3076 3145 7.964604 AAACTCTGTAACTTTCACCATAGTC 57.035 36.000 0.00 0.00 0.00 2.59
3681 3754 4.689612 ATACTCCATATCAACAAGCGGT 57.310 40.909 0.00 0.00 0.00 5.68
3746 3819 8.970859 ATTACCTTCTCTAATGAAACCTCATG 57.029 34.615 0.00 0.00 41.66 3.07
3826 3899 0.319405 ACTTTGCTGGCTTGCCAATC 59.681 50.000 15.63 10.53 0.00 2.67
4050 4124 6.146510 TCGGTGTGTTGTACATTCTTTCATAC 59.853 38.462 0.00 0.00 42.24 2.39
4110 4185 2.365586 CCTGCCTCTGGAGTCTGGG 61.366 68.421 0.00 0.00 0.00 4.45
4113 4188 2.596851 GCCTCTGGAGTCTGGGCAA 61.597 63.158 0.00 0.00 42.08 4.52
4307 4382 5.607119 TTAGGAAAGATGCGTCAGTTTTC 57.393 39.130 8.99 9.32 0.00 2.29
4308 4383 3.476552 AGGAAAGATGCGTCAGTTTTCA 58.523 40.909 16.53 0.00 31.19 2.69
4429 4711 6.873605 TCGTCAAAACAATACTGTGATCTCAT 59.126 34.615 0.00 0.00 35.37 2.90
5030 5315 9.333724 ACCAAATTTTGACTATAATACCCTACG 57.666 33.333 10.72 0.00 0.00 3.51
5059 5344 1.072173 TGGTGGAAGACATCACACAGG 59.928 52.381 0.00 0.00 34.61 4.00
5076 5362 8.073467 TCACACAGGTTTTATTTCTCCTTTTT 57.927 30.769 0.00 0.00 0.00 1.94
5478 5770 7.665559 TGCTTATGTGAATTCTACCTGAACTTT 59.334 33.333 7.05 0.00 37.52 2.66
5515 5807 4.399004 TTGCAACTTGCTTATTGTGGTT 57.601 36.364 14.78 0.00 45.31 3.67
5672 5964 6.427853 CAGTCCAAAGTACATCATTGTCTTGA 59.572 38.462 0.00 0.00 37.28 3.02
5673 5965 6.652481 AGTCCAAAGTACATCATTGTCTTGAG 59.348 38.462 0.00 0.00 37.28 3.02
5784 6077 3.785486 CGAGCATATTGAGACACTGGAA 58.215 45.455 0.00 0.00 0.00 3.53
5883 6176 2.035632 ACCTCATCCTTCATCTCGGAC 58.964 52.381 0.00 0.00 30.90 4.79
5889 6182 1.066587 CTTCATCTCGGACCTCGCC 59.933 63.158 0.00 0.00 39.05 5.54
5930 6223 3.842923 CTCTGCCTCCGCGATGGT 61.843 66.667 8.23 0.00 39.52 3.55
6030 6323 2.293170 GCCTTCTTCCTGCTGTTATCC 58.707 52.381 0.00 0.00 0.00 2.59
6131 6424 7.447374 TTGGTGATTGTAACTAGAAACCATG 57.553 36.000 0.00 0.00 36.41 3.66
6223 6516 2.057922 TCTGGGTGAGAAAGAAAGGCT 58.942 47.619 0.00 0.00 0.00 4.58
6283 6661 6.273071 TCGACAATGTCATAGGTACTTCATG 58.727 40.000 14.24 0.00 34.10 3.07
6303 6681 5.729229 TCATGTTTCTATAAGAACTGGGGGA 59.271 40.000 0.00 0.00 33.26 4.81
6304 6682 5.431179 TGTTTCTATAAGAACTGGGGGAC 57.569 43.478 0.00 0.00 33.26 4.46
6305 6683 4.847512 TGTTTCTATAAGAACTGGGGGACA 59.152 41.667 0.00 0.00 33.26 4.02
6306 6684 5.183969 GTTTCTATAAGAACTGGGGGACAC 58.816 45.833 0.00 0.00 33.26 3.67
6307 6685 3.028850 TCTATAAGAACTGGGGGACACG 58.971 50.000 0.00 0.00 0.00 4.49
6308 6686 0.909623 ATAAGAACTGGGGGACACGG 59.090 55.000 0.00 0.00 0.00 4.94
6309 6687 0.472352 TAAGAACTGGGGGACACGGT 60.472 55.000 0.00 0.00 0.00 4.83
6310 6688 2.032071 GAACTGGGGGACACGGTG 59.968 66.667 6.58 6.58 0.00 4.94
6311 6689 2.446994 AACTGGGGGACACGGTGA 60.447 61.111 16.29 0.00 0.00 4.02
6312 6690 2.450479 GAACTGGGGGACACGGTGAG 62.450 65.000 16.29 2.84 0.00 3.51
6313 6691 2.923035 CTGGGGGACACGGTGAGT 60.923 66.667 16.29 0.00 0.00 3.41
6314 6692 1.608336 CTGGGGGACACGGTGAGTA 60.608 63.158 16.29 0.00 0.00 2.59
6315 6693 1.152290 TGGGGGACACGGTGAGTAA 60.152 57.895 16.29 0.00 0.00 2.24
6316 6694 1.189524 TGGGGGACACGGTGAGTAAG 61.190 60.000 16.29 0.00 0.00 2.34
6317 6695 1.079336 GGGGACACGGTGAGTAAGC 60.079 63.158 16.29 0.00 0.00 3.09
6318 6696 1.669440 GGGACACGGTGAGTAAGCA 59.331 57.895 16.29 0.00 0.00 3.91
6319 6697 0.249398 GGGACACGGTGAGTAAGCAT 59.751 55.000 16.29 0.00 0.00 3.79
6320 6698 1.641577 GGACACGGTGAGTAAGCATC 58.358 55.000 16.29 0.00 0.00 3.91
6321 6699 1.067142 GGACACGGTGAGTAAGCATCA 60.067 52.381 16.29 0.00 0.00 3.07
6322 6700 2.418746 GGACACGGTGAGTAAGCATCAT 60.419 50.000 16.29 0.00 0.00 2.45
6323 6701 2.604914 GACACGGTGAGTAAGCATCATG 59.395 50.000 16.29 0.00 0.00 3.07
6324 6702 2.028112 ACACGGTGAGTAAGCATCATGT 60.028 45.455 16.29 0.00 0.00 3.21
6325 6703 3.002791 CACGGTGAGTAAGCATCATGTT 58.997 45.455 0.74 0.00 0.00 2.71
6326 6704 3.436704 CACGGTGAGTAAGCATCATGTTT 59.563 43.478 0.74 0.00 0.00 2.83
6327 6705 3.684788 ACGGTGAGTAAGCATCATGTTTC 59.315 43.478 0.00 0.00 0.00 2.78
6328 6706 3.935203 CGGTGAGTAAGCATCATGTTTCT 59.065 43.478 0.00 0.00 0.00 2.52
6329 6707 5.109210 CGGTGAGTAAGCATCATGTTTCTA 58.891 41.667 0.00 0.00 0.00 2.10
6330 6708 5.755375 CGGTGAGTAAGCATCATGTTTCTAT 59.245 40.000 0.00 0.00 0.00 1.98
6331 6709 6.923508 CGGTGAGTAAGCATCATGTTTCTATA 59.076 38.462 0.00 0.00 0.00 1.31
6332 6710 7.438160 CGGTGAGTAAGCATCATGTTTCTATAA 59.562 37.037 0.00 0.00 0.00 0.98
6333 6711 8.768955 GGTGAGTAAGCATCATGTTTCTATAAG 58.231 37.037 0.00 0.00 0.00 1.73
6334 6712 9.534565 GTGAGTAAGCATCATGTTTCTATAAGA 57.465 33.333 0.00 0.00 0.00 2.10
6339 6717 7.798596 AGCATCATGTTTCTATAAGAACTGG 57.201 36.000 0.00 0.00 33.26 4.00
6340 6718 6.769822 AGCATCATGTTTCTATAAGAACTGGG 59.230 38.462 0.00 0.00 33.26 4.45
6341 6719 6.016777 GCATCATGTTTCTATAAGAACTGGGG 60.017 42.308 0.00 0.00 33.26 4.96
6342 6720 6.001449 TCATGTTTCTATAAGAACTGGGGG 57.999 41.667 0.00 0.00 33.26 5.40
6346 6724 5.183969 GTTTCTATAAGAACTGGGGGACAC 58.816 45.833 0.00 0.00 33.26 3.67
6366 6744 2.303600 ACGGTGAGTAAGCATTTACCCA 59.696 45.455 0.00 0.00 40.03 4.51
6408 6786 2.294233 CCACCAGCATGTATAATGGCAC 59.706 50.000 0.00 0.00 36.21 5.01
6675 7185 1.781429 CGTTCTGACAGTCTGACGTTG 59.219 52.381 6.91 0.00 0.00 4.10
6716 7227 7.489113 ACGTCATCAAGGCATTTTATTCATTTC 59.511 33.333 0.00 0.00 0.00 2.17
6718 7229 6.476380 TCATCAAGGCATTTTATTCATTTCGC 59.524 34.615 0.00 0.00 0.00 4.70
6719 7230 5.964758 TCAAGGCATTTTATTCATTTCGCT 58.035 33.333 0.00 0.00 0.00 4.93
6720 7231 6.397272 TCAAGGCATTTTATTCATTTCGCTT 58.603 32.000 0.00 0.00 0.00 4.68
6820 7340 3.001939 AGAAAAGAAACGTAGCGTGTTGG 59.998 43.478 0.00 0.00 39.99 3.77
6878 7398 8.939929 CCAGCATTTTGGTATCTGTATATGTAG 58.060 37.037 0.00 0.00 33.38 2.74
6889 7409 6.635030 TCTGTATATGTAGACGCACTGATT 57.365 37.500 0.00 0.00 0.00 2.57
6903 7423 0.723414 CTGATTGATGTCAAGCGCGT 59.277 50.000 8.43 0.00 44.49 6.01
6936 7456 2.549282 CGACACGCCGGACAAAAG 59.451 61.111 5.05 0.00 0.00 2.27
6946 7466 3.911964 CGCCGGACAAAAGTTTAATTGAG 59.088 43.478 5.05 0.00 0.00 3.02
6973 7493 6.669977 GCATAACGATCCATGCGTATTTCTAC 60.670 42.308 5.99 0.00 41.75 2.59
6974 7494 4.316205 ACGATCCATGCGTATTTCTACA 57.684 40.909 0.00 0.00 40.65 2.74
6981 7501 4.201812 CCATGCGTATTTCTACACAGGTTG 60.202 45.833 0.00 0.00 0.00 3.77
6997 7517 5.534654 CACAGGTTGACCTCCTTTTCATTAA 59.465 40.000 0.00 0.00 46.65 1.40
6998 7518 5.770162 ACAGGTTGACCTCCTTTTCATTAAG 59.230 40.000 0.00 0.00 46.65 1.85
6999 7519 5.770162 CAGGTTGACCTCCTTTTCATTAAGT 59.230 40.000 0.00 0.00 46.65 2.24
7000 7520 6.940298 CAGGTTGACCTCCTTTTCATTAAGTA 59.060 38.462 0.00 0.00 46.65 2.24
7001 7521 7.611855 CAGGTTGACCTCCTTTTCATTAAGTAT 59.388 37.037 0.00 0.00 46.65 2.12
7002 7522 7.611855 AGGTTGACCTCCTTTTCATTAAGTATG 59.388 37.037 0.00 0.00 44.77 2.39
7003 7523 7.610305 GGTTGACCTCCTTTTCATTAAGTATGA 59.390 37.037 0.00 0.00 41.50 2.15
7004 7524 8.669243 GTTGACCTCCTTTTCATTAAGTATGAG 58.331 37.037 0.00 0.00 43.87 2.90
7005 7525 7.918076 TGACCTCCTTTTCATTAAGTATGAGT 58.082 34.615 0.00 0.00 43.87 3.41
7006 7526 9.042450 TGACCTCCTTTTCATTAAGTATGAGTA 57.958 33.333 0.00 0.00 43.87 2.59
7020 7540 9.529325 TTAAGTATGAGTATTTCGAATGGACTG 57.471 33.333 10.75 0.00 0.00 3.51
7021 7541 7.348080 AGTATGAGTATTTCGAATGGACTGA 57.652 36.000 10.75 4.55 0.00 3.41
7022 7542 7.782049 AGTATGAGTATTTCGAATGGACTGAA 58.218 34.615 10.75 2.09 0.00 3.02
7023 7543 8.258007 AGTATGAGTATTTCGAATGGACTGAAA 58.742 33.333 10.75 0.00 36.19 2.69
7024 7544 6.968131 TGAGTATTTCGAATGGACTGAAAG 57.032 37.500 10.75 0.00 42.29 2.62
7025 7545 6.697395 TGAGTATTTCGAATGGACTGAAAGA 58.303 36.000 10.75 0.00 37.43 2.52
7026 7546 6.590292 TGAGTATTTCGAATGGACTGAAAGAC 59.410 38.462 10.75 4.12 41.61 3.01
7027 7547 6.464222 AGTATTTCGAATGGACTGAAAGACA 58.536 36.000 12.40 0.00 42.94 3.41
7028 7548 5.613358 ATTTCGAATGGACTGAAAGACAC 57.387 39.130 0.00 0.00 37.43 3.67
7029 7549 2.672714 TCGAATGGACTGAAAGACACG 58.327 47.619 0.00 0.00 37.43 4.49
7030 7550 2.295070 TCGAATGGACTGAAAGACACGA 59.705 45.455 0.00 0.00 37.43 4.35
7031 7551 3.057019 CGAATGGACTGAAAGACACGAA 58.943 45.455 0.00 0.00 37.43 3.85
7032 7552 3.493129 CGAATGGACTGAAAGACACGAAA 59.507 43.478 0.00 0.00 37.43 3.46
7033 7553 4.608445 CGAATGGACTGAAAGACACGAAAC 60.608 45.833 0.00 0.00 37.43 2.78
7034 7554 3.254470 TGGACTGAAAGACACGAAACA 57.746 42.857 0.00 0.00 37.43 2.83
7035 7555 2.933906 TGGACTGAAAGACACGAAACAC 59.066 45.455 0.00 0.00 37.43 3.32
7036 7556 2.034001 GGACTGAAAGACACGAAACACG 60.034 50.000 0.00 0.00 42.72 4.49
7038 7558 2.997986 ACTGAAAGACACGAAACACGTT 59.002 40.909 0.00 0.00 46.07 3.99
7039 7559 3.434299 ACTGAAAGACACGAAACACGTTT 59.566 39.130 0.00 0.00 46.07 3.60
7040 7560 4.083696 ACTGAAAGACACGAAACACGTTTT 60.084 37.500 0.00 0.00 46.07 2.43
7041 7561 4.259734 CTGAAAGACACGAAACACGTTTTG 59.740 41.667 8.11 8.11 46.21 2.44
7042 7562 6.117390 CTGAAAGACACGAAACACGTTTTGT 61.117 40.000 9.31 9.31 46.21 2.83
7043 7563 7.533324 CTGAAAGACACGAAACACGTTTTGTT 61.533 38.462 11.95 5.47 46.21 2.83
7044 7564 9.210119 CTGAAAGACACGAAACACGTTTTGTTC 62.210 40.741 11.95 12.27 46.21 3.18
7052 7572 3.757745 ACACGTTTTGTTCCTTGTCAG 57.242 42.857 0.00 0.00 33.09 3.51
7053 7573 3.340034 ACACGTTTTGTTCCTTGTCAGA 58.660 40.909 0.00 0.00 33.09 3.27
7054 7574 3.754323 ACACGTTTTGTTCCTTGTCAGAA 59.246 39.130 0.00 0.00 33.09 3.02
7055 7575 4.142687 ACACGTTTTGTTCCTTGTCAGAAG 60.143 41.667 0.00 0.00 33.09 2.85
7056 7576 3.377172 ACGTTTTGTTCCTTGTCAGAAGG 59.623 43.478 0.00 0.00 38.78 3.46
7057 7577 3.706698 GTTTTGTTCCTTGTCAGAAGGC 58.293 45.455 0.00 0.00 37.34 4.35
7058 7578 1.593196 TTGTTCCTTGTCAGAAGGCG 58.407 50.000 0.00 0.00 37.34 5.52
7059 7579 0.756294 TGTTCCTTGTCAGAAGGCGA 59.244 50.000 0.00 0.00 37.34 5.54
7060 7580 1.140052 TGTTCCTTGTCAGAAGGCGAA 59.860 47.619 0.00 0.00 37.34 4.70
7061 7581 2.218603 GTTCCTTGTCAGAAGGCGAAA 58.781 47.619 0.00 0.00 37.34 3.46
7062 7582 2.169832 TCCTTGTCAGAAGGCGAAAG 57.830 50.000 0.00 0.00 37.34 2.62
7063 7583 1.691976 TCCTTGTCAGAAGGCGAAAGA 59.308 47.619 0.00 0.00 37.34 2.52
7064 7584 2.072298 CCTTGTCAGAAGGCGAAAGAG 58.928 52.381 0.00 0.00 0.00 2.85
7065 7585 2.289072 CCTTGTCAGAAGGCGAAAGAGA 60.289 50.000 0.00 0.00 0.00 3.10
7066 7586 3.594134 CTTGTCAGAAGGCGAAAGAGAT 58.406 45.455 0.00 0.00 0.00 2.75
7067 7587 3.685139 TGTCAGAAGGCGAAAGAGATT 57.315 42.857 0.00 0.00 0.00 2.40
7068 7588 4.008074 TGTCAGAAGGCGAAAGAGATTT 57.992 40.909 0.00 0.00 0.00 2.17
7069 7589 5.147330 TGTCAGAAGGCGAAAGAGATTTA 57.853 39.130 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.680338 AGTGGGTTCTCTTGTGCAAC 58.320 50.000 0.00 0.00 37.35 4.17
56 57 2.810400 GCTAGTGGGTTCTCTTGTGCAA 60.810 50.000 0.00 0.00 0.00 4.08
57 58 1.270839 GCTAGTGGGTTCTCTTGTGCA 60.271 52.381 0.00 0.00 0.00 4.57
58 59 1.443802 GCTAGTGGGTTCTCTTGTGC 58.556 55.000 0.00 0.00 0.00 4.57
59 60 1.000955 ACGCTAGTGGGTTCTCTTGTG 59.999 52.381 8.42 0.00 35.78 3.33
60 61 1.339097 ACGCTAGTGGGTTCTCTTGT 58.661 50.000 8.42 0.00 35.78 3.16
61 62 2.457366 AACGCTAGTGGGTTCTCTTG 57.543 50.000 8.42 0.00 44.42 3.02
62 63 2.633481 AGAAACGCTAGTGGGTTCTCTT 59.367 45.455 15.16 0.00 46.47 2.85
63 64 2.231721 GAGAAACGCTAGTGGGTTCTCT 59.768 50.000 27.91 17.53 46.47 3.10
77 79 0.324830 AGGGGAGGGAGAGAGAAACG 60.325 60.000 0.00 0.00 0.00 3.60
181 189 3.319198 CTACCCACCACCGGCAGT 61.319 66.667 0.00 0.00 0.00 4.40
367 377 2.769095 GTCTAGAGGAGTGGCAGGAATT 59.231 50.000 0.00 0.00 0.00 2.17
389 400 2.488545 GACGAGAAACTCTAGCCTCACA 59.511 50.000 0.00 0.00 0.00 3.58
396 407 3.480894 GTCACGTGACGAGAAACTCTAG 58.519 50.000 31.03 0.00 35.12 2.43
412 425 1.721389 CTGACACCAAATCTCGTCACG 59.279 52.381 0.00 0.00 34.78 4.35
441 455 4.019681 TGTCGTTGAACCCCTGAATAGATT 60.020 41.667 0.00 0.00 0.00 2.40
512 526 2.892425 CGATGACAGCCGGGAAGC 60.892 66.667 2.18 0.00 0.00 3.86
551 565 0.531090 TCGTTGTTGTCGTTCCCCTG 60.531 55.000 0.00 0.00 0.00 4.45
598 612 1.604604 AGACCACCGAACAACCATTG 58.395 50.000 0.00 0.00 0.00 2.82
834 849 0.325765 GGCAACTACCCTCTCCCTCT 60.326 60.000 0.00 0.00 0.00 3.69
1065 1080 2.028484 GGCACTCACGTCGTGGAA 59.972 61.111 24.33 6.07 33.87 3.53
1094 1109 0.856641 CGAACGAACACATGAACGGT 59.143 50.000 0.00 0.00 0.00 4.83
1112 1127 0.224499 AACGAACGAACGAACGAACG 59.776 50.000 18.31 15.65 39.31 3.95
1113 1128 2.336185 AAACGAACGAACGAACGAAC 57.664 45.000 18.31 5.51 37.03 3.95
1114 1129 2.091899 ACAAAACGAACGAACGAACGAA 59.908 40.909 18.31 0.00 37.03 3.85
1115 1130 1.653114 ACAAAACGAACGAACGAACGA 59.347 42.857 18.31 0.00 37.03 3.85
1116 1131 2.061956 ACAAAACGAACGAACGAACG 57.938 45.000 11.97 8.41 37.03 3.95
1117 1132 3.662863 AGAACAAAACGAACGAACGAAC 58.337 40.909 11.97 0.00 37.03 3.95
1118 1133 3.995412 AGAACAAAACGAACGAACGAA 57.005 38.095 11.97 0.00 37.03 3.85
1119 1134 3.995412 AAGAACAAAACGAACGAACGA 57.005 38.095 11.97 0.00 37.03 3.85
1120 1135 5.410371 AAAAAGAACAAAACGAACGAACG 57.590 34.783 0.14 0.00 39.31 3.95
1121 1136 7.775358 CGATTAAAAAGAACAAAACGAACGAAC 59.225 33.333 0.14 0.00 0.00 3.95
1122 1137 7.511812 GCGATTAAAAAGAACAAAACGAACGAA 60.512 33.333 0.14 0.00 0.00 3.85
1123 1138 6.075988 GCGATTAAAAAGAACAAAACGAACGA 60.076 34.615 0.14 0.00 0.00 3.85
1124 1139 6.047816 GCGATTAAAAAGAACAAAACGAACG 58.952 36.000 0.00 0.00 0.00 3.95
1125 1140 7.044576 TCAGCGATTAAAAAGAACAAAACGAAC 60.045 33.333 0.00 0.00 0.00 3.95
1126 1141 6.967767 TCAGCGATTAAAAAGAACAAAACGAA 59.032 30.769 0.00 0.00 0.00 3.85
1127 1142 6.487960 TCAGCGATTAAAAAGAACAAAACGA 58.512 32.000 0.00 0.00 0.00 3.85
1128 1143 6.726035 TCAGCGATTAAAAAGAACAAAACG 57.274 33.333 0.00 0.00 0.00 3.60
1293 1315 1.080772 CTCTACGGTCGCACAGCAA 60.081 57.895 0.00 0.00 0.00 3.91
1328 1359 3.471680 TGTAGCAAGTGCACACATGTTA 58.528 40.909 21.04 13.69 45.16 2.41
1360 1399 5.188434 CAGGATTTGCTACAAGATCCTCAA 58.812 41.667 15.23 0.00 44.96 3.02
1373 1412 7.854337 ACAATTCATTAATTCCAGGATTTGCT 58.146 30.769 6.82 0.00 32.87 3.91
1376 1415 8.605065 ACCAACAATTCATTAATTCCAGGATTT 58.395 29.630 2.17 2.17 32.87 2.17
1388 1427 4.661222 TCAGGAGCACCAACAATTCATTA 58.339 39.130 2.07 0.00 38.94 1.90
1390 1429 3.159213 TCAGGAGCACCAACAATTCAT 57.841 42.857 2.07 0.00 38.94 2.57
1392 1431 3.552890 GGTTTCAGGAGCACCAACAATTC 60.553 47.826 2.07 0.00 38.94 2.17
1402 1442 1.270625 CCGTTACAGGTTTCAGGAGCA 60.271 52.381 0.00 0.00 0.00 4.26
1432 1473 1.745087 CCACGGATGTTCAGAAATGGG 59.255 52.381 0.00 0.00 0.00 4.00
1433 1474 2.679837 CTCCACGGATGTTCAGAAATGG 59.320 50.000 0.00 0.00 0.00 3.16
1457 1498 6.876789 ACTCCATAATATGTTGAAACGTGTGA 59.123 34.615 0.00 0.00 0.00 3.58
1503 1544 8.651389 TCCATCACCTCTAATAGATTTTGGTAG 58.349 37.037 0.00 0.00 0.00 3.18
1526 1577 2.521126 TGATCCTGTCTGTACGTTCCA 58.479 47.619 0.00 0.00 0.00 3.53
1535 1586 3.265791 GCCAACTACTTGATCCTGTCTG 58.734 50.000 0.00 0.00 0.00 3.51
1543 1594 3.445096 GCCATTCTTGCCAACTACTTGAT 59.555 43.478 0.00 0.00 0.00 2.57
1545 1596 2.821969 AGCCATTCTTGCCAACTACTTG 59.178 45.455 0.00 0.00 0.00 3.16
1547 1598 2.887151 AGCCATTCTTGCCAACTACT 57.113 45.000 0.00 0.00 0.00 2.57
1549 1600 3.519510 ACTCTAGCCATTCTTGCCAACTA 59.480 43.478 0.00 0.00 0.00 2.24
1555 1613 2.998316 AGGACTCTAGCCATTCTTGC 57.002 50.000 0.00 0.00 0.00 4.01
1564 1622 5.828859 TCTTACAGACCATTAGGACTCTAGC 59.171 44.000 0.00 0.00 37.85 3.42
1590 1648 4.009675 TGCATATTTCAGAGGTGGTCAAC 58.990 43.478 0.00 0.00 0.00 3.18
1591 1649 4.009675 GTGCATATTTCAGAGGTGGTCAA 58.990 43.478 0.00 0.00 0.00 3.18
1593 1651 3.624861 CAGTGCATATTTCAGAGGTGGTC 59.375 47.826 0.00 0.00 0.00 4.02
1595 1653 3.614092 ACAGTGCATATTTCAGAGGTGG 58.386 45.455 0.00 0.00 0.00 4.61
1596 1654 3.624861 GGACAGTGCATATTTCAGAGGTG 59.375 47.826 0.00 0.00 0.00 4.00
1597 1655 3.521126 AGGACAGTGCATATTTCAGAGGT 59.479 43.478 0.00 0.00 0.00 3.85
1598 1656 3.875727 CAGGACAGTGCATATTTCAGAGG 59.124 47.826 0.00 0.00 0.00 3.69
1599 1657 4.511527 ACAGGACAGTGCATATTTCAGAG 58.488 43.478 0.00 0.00 0.00 3.35
1600 1658 4.558226 ACAGGACAGTGCATATTTCAGA 57.442 40.909 0.00 0.00 0.00 3.27
1601 1659 4.696877 TCAACAGGACAGTGCATATTTCAG 59.303 41.667 0.00 0.00 0.00 3.02
1603 1661 5.824904 ATCAACAGGACAGTGCATATTTC 57.175 39.130 0.00 0.00 0.00 2.17
1634 1695 7.277539 GTCTTCTAAACTCATGATCTTCTGTGG 59.722 40.741 0.00 0.00 0.00 4.17
1639 1700 8.939201 TCATGTCTTCTAAACTCATGATCTTC 57.061 34.615 0.00 0.00 39.53 2.87
1744 1805 5.752472 TCCACATTATGCCAAATTTATTGCG 59.248 36.000 0.00 0.00 0.00 4.85
1756 1817 7.226325 GCTAGATCAATCTATCCACATTATGCC 59.774 40.741 0.00 0.00 38.60 4.40
1766 1827 7.278424 GCAATCAGAAGCTAGATCAATCTATCC 59.722 40.741 0.00 0.00 38.60 2.59
1877 1938 3.058914 GTCAATGGTAGCACAGTCAACAC 60.059 47.826 0.00 0.00 0.00 3.32
2042 2103 6.476378 AGATGGTGCTGATGTTTAAGTACTT 58.524 36.000 13.68 13.68 30.66 2.24
2676 2742 3.555966 GATAACTACCATGCAAAGGGCT 58.444 45.455 12.59 0.00 45.15 5.19
2678 2744 3.222603 GGGATAACTACCATGCAAAGGG 58.777 50.000 12.59 7.13 0.00 3.95
2703 2769 3.389329 ACAGATAGGGCTATGTGGTTCAG 59.611 47.826 0.00 0.00 40.07 3.02
3681 3754 2.646930 TGGAGAACGCGGATACTAGAA 58.353 47.619 12.47 0.00 0.00 2.10
3746 3819 8.603242 TTTTCAGGTTCTACATAGTCTGAAAC 57.397 34.615 20.59 8.73 40.57 2.78
3826 3899 6.016777 GCTGGTACCAAGATTCAATAATGGAG 60.017 42.308 17.11 0.00 35.16 3.86
4050 4124 2.028748 CACAGGCCCAAGGAAATTTCTG 60.029 50.000 17.42 9.00 0.00 3.02
4307 4382 8.629986 CATACTTCAGTATTCGCAAAAAGTTTG 58.370 33.333 0.00 0.00 39.06 2.93
4308 4383 7.326063 GCATACTTCAGTATTCGCAAAAAGTTT 59.674 33.333 0.00 0.00 39.06 2.66
4429 4711 7.744087 ACAACATCTGCTAAGAATGTTACAA 57.256 32.000 0.00 0.00 34.85 2.41
4916 5198 8.665685 CATAACCCTTAACAGTGATTACAAGAC 58.334 37.037 0.00 0.00 0.00 3.01
5017 5302 8.963725 CACCATGTAGATTCGTAGGGTATTATA 58.036 37.037 0.00 0.00 0.00 0.98
5030 5315 5.525378 GTGATGTCTTCCACCATGTAGATTC 59.475 44.000 0.00 0.00 0.00 2.52
5059 5344 9.955208 TCGGTAAAGAAAAAGGAGAAATAAAAC 57.045 29.630 0.00 0.00 0.00 2.43
5076 5362 8.044908 AGAAAGGTTAATAGCATTCGGTAAAGA 58.955 33.333 0.00 0.00 35.33 2.52
5478 5770 3.431673 TGCAAACAGGTACATGATGGA 57.568 42.857 15.54 10.92 0.00 3.41
5515 5807 4.929808 ACCAACGCAATAAACACAAACAAA 59.070 33.333 0.00 0.00 0.00 2.83
5706 5999 1.884579 AGCGTAGTCGAAAGAGGTTCA 59.115 47.619 0.00 0.00 43.49 3.18
5709 6002 2.816087 TGTAAGCGTAGTCGAAAGAGGT 59.184 45.455 0.00 0.00 43.49 3.85
5784 6077 3.133003 CCCTGTACTCCATGTCGATTTCT 59.867 47.826 0.00 0.00 0.00 2.52
5865 6158 2.295909 GAGGTCCGAGATGAAGGATGAG 59.704 54.545 0.00 0.00 38.97 2.90
6030 6323 2.202892 GCGGAAACTAGCCTCGGG 60.203 66.667 0.00 0.00 0.00 5.14
6169 6462 3.838244 TTATCATGGCAGTCTACCACC 57.162 47.619 0.00 0.00 40.82 4.61
6200 6493 3.004839 GCCTTTCTTTCTCACCCAGAAAC 59.995 47.826 0.00 0.00 44.78 2.78
6209 6502 5.930135 ACAAACTCTAGCCTTTCTTTCTCA 58.070 37.500 0.00 0.00 0.00 3.27
6223 6516 7.041372 GGCAAGACATAAGTGAAACAAACTCTA 60.041 37.037 0.00 0.00 41.43 2.43
6283 6661 5.183969 GTGTCCCCCAGTTCTTATAGAAAC 58.816 45.833 0.00 0.00 35.75 2.78
6293 6671 2.032071 CACCGTGTCCCCCAGTTC 59.968 66.667 0.00 0.00 0.00 3.01
6303 6681 2.028112 ACATGATGCTTACTCACCGTGT 60.028 45.455 0.00 0.00 0.00 4.49
6304 6682 2.621338 ACATGATGCTTACTCACCGTG 58.379 47.619 0.00 0.00 0.00 4.94
6305 6683 3.334583 AACATGATGCTTACTCACCGT 57.665 42.857 0.00 0.00 0.00 4.83
6306 6684 3.935203 AGAAACATGATGCTTACTCACCG 59.065 43.478 0.00 0.00 0.00 4.94
6307 6685 8.662781 TTATAGAAACATGATGCTTACTCACC 57.337 34.615 0.00 0.00 0.00 4.02
6308 6686 9.534565 TCTTATAGAAACATGATGCTTACTCAC 57.465 33.333 0.00 0.00 0.00 3.51
6313 6691 9.330063 CCAGTTCTTATAGAAACATGATGCTTA 57.670 33.333 0.00 0.00 35.75 3.09
6314 6692 7.284034 CCCAGTTCTTATAGAAACATGATGCTT 59.716 37.037 0.00 0.00 35.75 3.91
6315 6693 6.769822 CCCAGTTCTTATAGAAACATGATGCT 59.230 38.462 0.00 0.00 35.75 3.79
6316 6694 6.016777 CCCCAGTTCTTATAGAAACATGATGC 60.017 42.308 0.00 0.00 35.75 3.91
6317 6695 6.488006 CCCCCAGTTCTTATAGAAACATGATG 59.512 42.308 0.00 0.00 35.75 3.07
6318 6696 6.389869 TCCCCCAGTTCTTATAGAAACATGAT 59.610 38.462 0.00 0.00 35.75 2.45
6319 6697 5.729229 TCCCCCAGTTCTTATAGAAACATGA 59.271 40.000 0.00 0.00 35.75 3.07
6320 6698 5.823045 GTCCCCCAGTTCTTATAGAAACATG 59.177 44.000 0.00 0.00 35.75 3.21
6321 6699 5.491078 TGTCCCCCAGTTCTTATAGAAACAT 59.509 40.000 0.00 0.00 35.75 2.71
6322 6700 4.847512 TGTCCCCCAGTTCTTATAGAAACA 59.152 41.667 0.00 0.00 35.75 2.83
6323 6701 5.183969 GTGTCCCCCAGTTCTTATAGAAAC 58.816 45.833 0.00 0.00 35.75 2.78
6324 6702 4.081309 CGTGTCCCCCAGTTCTTATAGAAA 60.081 45.833 0.00 0.00 35.75 2.52
6325 6703 3.449737 CGTGTCCCCCAGTTCTTATAGAA 59.550 47.826 0.00 0.00 0.00 2.10
6326 6704 3.028850 CGTGTCCCCCAGTTCTTATAGA 58.971 50.000 0.00 0.00 0.00 1.98
6327 6705 2.102588 CCGTGTCCCCCAGTTCTTATAG 59.897 54.545 0.00 0.00 0.00 1.31
6328 6706 2.112998 CCGTGTCCCCCAGTTCTTATA 58.887 52.381 0.00 0.00 0.00 0.98
6329 6707 0.909623 CCGTGTCCCCCAGTTCTTAT 59.090 55.000 0.00 0.00 0.00 1.73
6330 6708 0.472352 ACCGTGTCCCCCAGTTCTTA 60.472 55.000 0.00 0.00 0.00 2.10
6331 6709 1.768888 ACCGTGTCCCCCAGTTCTT 60.769 57.895 0.00 0.00 0.00 2.52
6332 6710 2.122547 ACCGTGTCCCCCAGTTCT 60.123 61.111 0.00 0.00 0.00 3.01
6333 6711 2.032071 CACCGTGTCCCCCAGTTC 59.968 66.667 0.00 0.00 0.00 3.01
6334 6712 2.446994 TCACCGTGTCCCCCAGTT 60.447 61.111 0.00 0.00 0.00 3.16
6335 6713 2.376225 TACTCACCGTGTCCCCCAGT 62.376 60.000 0.00 0.00 0.00 4.00
6336 6714 1.189524 TTACTCACCGTGTCCCCCAG 61.190 60.000 0.00 0.00 0.00 4.45
6337 6715 1.152290 TTACTCACCGTGTCCCCCA 60.152 57.895 0.00 0.00 0.00 4.96
6338 6716 1.595357 CTTACTCACCGTGTCCCCC 59.405 63.158 0.00 0.00 0.00 5.40
6339 6717 1.079336 GCTTACTCACCGTGTCCCC 60.079 63.158 0.00 0.00 0.00 4.81
6340 6718 0.249398 ATGCTTACTCACCGTGTCCC 59.751 55.000 0.00 0.00 0.00 4.46
6341 6719 2.094762 AATGCTTACTCACCGTGTCC 57.905 50.000 0.00 0.00 0.00 4.02
6342 6720 3.370061 GGTAAATGCTTACTCACCGTGTC 59.630 47.826 0.00 0.00 38.01 3.67
6346 6724 2.980568 TGGGTAAATGCTTACTCACCG 58.019 47.619 0.00 0.00 42.45 4.94
6366 6744 4.968719 TGGTACATGACTCCTCCATACAAT 59.031 41.667 0.00 0.00 0.00 2.71
6374 6752 1.134670 GCTGGTGGTACATGACTCCTC 60.135 57.143 0.00 0.00 44.52 3.71
6408 6786 6.480524 TTTAAGCGCCAGTATATAAGCATG 57.519 37.500 2.29 0.00 0.00 4.06
6550 6991 3.988379 TTGGTGCTCAACAAGTCATTC 57.012 42.857 0.00 0.00 32.22 2.67
6690 7200 5.895636 TGAATAAAATGCCTTGATGACGT 57.104 34.783 0.00 0.00 0.00 4.34
6716 7227 4.320667 TGACGTTTCACAATATCAAGCG 57.679 40.909 0.00 0.00 0.00 4.68
6718 7229 6.999241 CGATTGACGTTTCACAATATCAAG 57.001 37.500 0.65 0.00 36.94 3.02
6820 7340 5.981174 TGACGTGAACTAAACTGCATTAAC 58.019 37.500 0.00 0.00 0.00 2.01
6878 7398 2.475187 GCTTGACATCAATCAGTGCGTC 60.475 50.000 0.00 0.00 35.02 5.19
6889 7409 2.809174 CGGACGCGCTTGACATCA 60.809 61.111 5.73 0.00 0.00 3.07
6903 7423 1.002201 TGTCGGCTAAATTTGTCCGGA 59.998 47.619 23.60 0.00 41.98 5.14
6929 7449 8.840867 CGTTATGCTCTCAATTAAACTTTTGTC 58.159 33.333 0.00 0.00 0.00 3.18
6930 7450 8.564574 TCGTTATGCTCTCAATTAAACTTTTGT 58.435 29.630 0.00 0.00 0.00 2.83
6936 7456 7.246674 TGGATCGTTATGCTCTCAATTAAAC 57.753 36.000 0.00 0.00 0.00 2.01
6946 7466 1.502231 ACGCATGGATCGTTATGCTC 58.498 50.000 19.40 1.13 45.64 4.26
6997 7517 7.348080 TCAGTCCATTCGAAATACTCATACT 57.652 36.000 0.00 0.00 0.00 2.12
6998 7518 8.420374 TTTCAGTCCATTCGAAATACTCATAC 57.580 34.615 0.00 0.00 0.00 2.39
6999 7519 8.474831 TCTTTCAGTCCATTCGAAATACTCATA 58.525 33.333 0.00 0.00 0.00 2.15
7000 7520 7.278868 GTCTTTCAGTCCATTCGAAATACTCAT 59.721 37.037 0.00 0.00 0.00 2.90
7001 7521 6.590292 GTCTTTCAGTCCATTCGAAATACTCA 59.410 38.462 0.00 0.00 0.00 3.41
7002 7522 6.590292 TGTCTTTCAGTCCATTCGAAATACTC 59.410 38.462 0.00 0.00 31.01 2.59
7003 7523 6.369065 GTGTCTTTCAGTCCATTCGAAATACT 59.631 38.462 0.00 3.17 31.01 2.12
7004 7524 6.534934 GTGTCTTTCAGTCCATTCGAAATAC 58.465 40.000 0.00 0.57 0.00 1.89
7005 7525 5.347635 CGTGTCTTTCAGTCCATTCGAAATA 59.652 40.000 0.00 0.00 0.00 1.40
7006 7526 4.152402 CGTGTCTTTCAGTCCATTCGAAAT 59.848 41.667 0.00 0.00 0.00 2.17
7007 7527 3.493129 CGTGTCTTTCAGTCCATTCGAAA 59.507 43.478 0.00 0.00 0.00 3.46
7008 7528 3.057019 CGTGTCTTTCAGTCCATTCGAA 58.943 45.455 0.00 0.00 0.00 3.71
7009 7529 2.295070 TCGTGTCTTTCAGTCCATTCGA 59.705 45.455 0.00 0.00 0.00 3.71
7010 7530 2.672714 TCGTGTCTTTCAGTCCATTCG 58.327 47.619 0.00 0.00 0.00 3.34
7011 7531 4.272504 TGTTTCGTGTCTTTCAGTCCATTC 59.727 41.667 0.00 0.00 0.00 2.67
7012 7532 4.035208 GTGTTTCGTGTCTTTCAGTCCATT 59.965 41.667 0.00 0.00 0.00 3.16
7013 7533 3.560068 GTGTTTCGTGTCTTTCAGTCCAT 59.440 43.478 0.00 0.00 0.00 3.41
7014 7534 2.933906 GTGTTTCGTGTCTTTCAGTCCA 59.066 45.455 0.00 0.00 0.00 4.02
7015 7535 2.034001 CGTGTTTCGTGTCTTTCAGTCC 60.034 50.000 0.00 0.00 34.52 3.85
7016 7536 3.220350 CGTGTTTCGTGTCTTTCAGTC 57.780 47.619 0.00 0.00 34.52 3.51
7032 7552 3.340034 TCTGACAAGGAACAAAACGTGT 58.660 40.909 0.00 0.00 44.64 4.49
7033 7553 4.342772 CTTCTGACAAGGAACAAAACGTG 58.657 43.478 0.00 0.00 0.00 4.49
7034 7554 3.377172 CCTTCTGACAAGGAACAAAACGT 59.623 43.478 0.00 0.00 39.81 3.99
7035 7555 3.792124 GCCTTCTGACAAGGAACAAAACG 60.792 47.826 4.49 0.00 39.81 3.60
7036 7556 3.706698 GCCTTCTGACAAGGAACAAAAC 58.293 45.455 4.49 0.00 39.81 2.43
7037 7557 2.357637 CGCCTTCTGACAAGGAACAAAA 59.642 45.455 4.49 0.00 39.81 2.44
7038 7558 1.946768 CGCCTTCTGACAAGGAACAAA 59.053 47.619 4.49 0.00 39.81 2.83
7039 7559 1.140052 TCGCCTTCTGACAAGGAACAA 59.860 47.619 4.49 0.00 39.81 2.83
7040 7560 0.756294 TCGCCTTCTGACAAGGAACA 59.244 50.000 4.49 0.00 39.81 3.18
7041 7561 1.878953 TTCGCCTTCTGACAAGGAAC 58.121 50.000 4.49 0.00 39.81 3.62
7042 7562 2.104111 TCTTTCGCCTTCTGACAAGGAA 59.896 45.455 4.49 0.00 39.81 3.36
7043 7563 1.691976 TCTTTCGCCTTCTGACAAGGA 59.308 47.619 4.49 0.00 39.81 3.36
7044 7564 2.072298 CTCTTTCGCCTTCTGACAAGG 58.928 52.381 0.00 0.00 40.39 3.61
7045 7565 3.032017 TCTCTTTCGCCTTCTGACAAG 57.968 47.619 0.00 0.00 0.00 3.16
7046 7566 3.685139 ATCTCTTTCGCCTTCTGACAA 57.315 42.857 0.00 0.00 0.00 3.18
7047 7567 3.685139 AATCTCTTTCGCCTTCTGACA 57.315 42.857 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.