Multiple sequence alignment - TraesCS2D01G325200

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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 TraesCS2D01G325200 chr2D 100.000 4848 0 0 1 4848 418778248 418773401 0.000000e+00 8953
1 TraesCS2D01G325200 chr2B 92.919 4152 179 38 114 4227 490870223 490866149 0.000000e+00 5932
2 TraesCS2D01G325200 chr2B 88.697 522 42 11 4340 4848 490865000 490864483 5.330000e-174 621
3 TraesCS2D01G325200 chr2B 89.600 125 5 7 4244 4367 490865141 490865024 8.400000e-33 152
4 TraesCS2D01G325200 chr2B 92.079 101 8 0 15 115 680200486 680200586 5.060000e-30 143
5 TraesCS2D01G325200 chr2B 90.566 106 10 0 15 120 72818589 72818484 1.820000e-29 141
6 TraesCS2D01G325200 chr2A 93.249 3807 168 39 246 4024 571462992 571466737 0.000000e+00 5524
7 TraesCS2D01G325200 chr2A 91.648 443 24 10 4011 4451 571466895 571467326 6.940000e-168 601
8 TraesCS2D01G325200 chr2A 94.839 155 7 1 114 268 571462077 571462230 1.740000e-59 241
9 TraesCS2D01G325200 chr4B 94.393 107 6 0 9 115 673201569 673201675 1.080000e-36 165
10 TraesCS2D01G325200 chr3B 90.991 111 10 0 9 119 829125029 829125139 3.020000e-32 150
11 TraesCS2D01G325200 chr6B 90.654 107 10 0 9 115 421004981 421004875 5.060000e-30 143
12 TraesCS2D01G325200 chr6A 90.000 110 11 0 6 115 537685420 537685529 5.060000e-30 143
13 TraesCS2D01G325200 chr5B 90.000 110 11 0 15 124 331547458 331547349 5.060000e-30 143
14 TraesCS2D01G325200 chr5B 92.079 101 8 0 15 115 571209366 571209266 5.060000e-30 143
15 TraesCS2D01G325200 chr5B 88.136 118 11 3 15 130 653800262 653800146 2.350000e-28 137


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 TraesCS2D01G325200 chr2D 418773401 418778248 4847 True 8953 8953 100.000000 1 4848 1 chr2D.!!$R1 4847
1 TraesCS2D01G325200 chr2B 490864483 490870223 5740 True 2235 5932 90.405333 114 4848 3 chr2B.!!$R2 4734
2 TraesCS2D01G325200 chr2A 571462077 571467326 5249 False 2122 5524 93.245333 114 4451 3 chr2A.!!$F1 4337

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
401 1195 0.108992 ACCTGGCATGTGTACGTACG 60.109 55.0 20.18 15.01 0.00 3.67 F
1524 2353 0.033504 TCCTCACGTGCAGGAAGTTC 59.966 55.0 25.12 0.00 37.09 3.01 F
3083 3923 0.038166 TTGGCCACATCAGGAAGTCC 59.962 55.0 3.88 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2872 0.767375 TCTGCACTCCTGGAAAGCTT 59.233 50.0 17.56 0.0 0.00 3.74 R
3128 3968 0.391661 CGGCTGCAACAGTACAGGAT 60.392 55.0 0.50 0.0 34.38 3.24 R
4723 6792 0.108662 AGCACATTCGACGCTCATGA 60.109 50.0 0.00 0.0 0.00 3.07 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 8.196802 TCTATTTGTCTGAAAATACATGTCGG 57.803 34.615 0.00 0.00 32.16 4.79
27 28 8.038351 TCTATTTGTCTGAAAATACATGTCGGA 58.962 33.333 0.00 0.00 32.16 4.55
28 29 6.480524 TTTGTCTGAAAATACATGTCGGAG 57.519 37.500 0.00 0.00 0.00 4.63
29 30 5.400066 TGTCTGAAAATACATGTCGGAGA 57.600 39.130 0.00 0.00 0.00 3.71
30 31 5.789521 TGTCTGAAAATACATGTCGGAGAA 58.210 37.500 0.00 0.00 39.69 2.87
31 32 6.227522 TGTCTGAAAATACATGTCGGAGAAA 58.772 36.000 0.00 0.00 39.69 2.52
32 33 6.878923 TGTCTGAAAATACATGTCGGAGAAAT 59.121 34.615 0.00 0.00 39.69 2.17
43 44 6.683974 ATGTCGGAGAAATGGATAAAAGTG 57.316 37.500 0.00 0.00 39.69 3.16
44 45 4.941263 TGTCGGAGAAATGGATAAAAGTGG 59.059 41.667 0.00 0.00 39.69 4.00
45 46 5.183228 GTCGGAGAAATGGATAAAAGTGGA 58.817 41.667 0.00 0.00 39.69 4.02
46 47 5.823045 GTCGGAGAAATGGATAAAAGTGGAT 59.177 40.000 0.00 0.00 39.69 3.41
47 48 5.822519 TCGGAGAAATGGATAAAAGTGGATG 59.177 40.000 0.00 0.00 0.00 3.51
48 49 5.590259 CGGAGAAATGGATAAAAGTGGATGT 59.410 40.000 0.00 0.00 0.00 3.06
49 50 6.765989 CGGAGAAATGGATAAAAGTGGATGTA 59.234 38.462 0.00 0.00 0.00 2.29
50 51 7.445402 CGGAGAAATGGATAAAAGTGGATGTAT 59.555 37.037 0.00 0.00 0.00 2.29
51 52 8.787852 GGAGAAATGGATAAAAGTGGATGTATC 58.212 37.037 0.00 0.00 0.00 2.24
52 53 9.566432 GAGAAATGGATAAAAGTGGATGTATCT 57.434 33.333 0.00 0.00 0.00 1.98
66 67 8.993121 AGTGGATGTATCTAGAATTAAAATGCG 58.007 33.333 0.00 0.00 0.00 4.73
67 68 8.774586 GTGGATGTATCTAGAATTAAAATGCGT 58.225 33.333 0.00 0.00 0.00 5.24
68 69 8.988934 TGGATGTATCTAGAATTAAAATGCGTC 58.011 33.333 0.00 0.00 0.00 5.19
69 70 9.209175 GGATGTATCTAGAATTAAAATGCGTCT 57.791 33.333 0.00 0.00 0.00 4.18
79 80 9.262358 AGAATTAAAATGCGTCTAGATACTTCC 57.738 33.333 0.00 0.00 0.00 3.46
80 81 8.958119 AATTAAAATGCGTCTAGATACTTCCA 57.042 30.769 0.00 0.00 0.00 3.53
81 82 9.561069 AATTAAAATGCGTCTAGATACTTCCAT 57.439 29.630 0.00 0.00 0.00 3.41
82 83 8.958119 TTAAAATGCGTCTAGATACTTCCATT 57.042 30.769 0.00 0.00 0.00 3.16
83 84 7.865706 AAAATGCGTCTAGATACTTCCATTT 57.134 32.000 0.00 3.17 0.00 2.32
84 85 7.484035 AAATGCGTCTAGATACTTCCATTTC 57.516 36.000 0.00 0.00 0.00 2.17
85 86 5.854010 TGCGTCTAGATACTTCCATTTCT 57.146 39.130 0.00 0.00 0.00 2.52
86 87 5.833082 TGCGTCTAGATACTTCCATTTCTC 58.167 41.667 0.00 0.00 0.00 2.87
87 88 5.221263 TGCGTCTAGATACTTCCATTTCTCC 60.221 44.000 0.00 0.00 0.00 3.71
88 89 5.453648 CGTCTAGATACTTCCATTTCTCCG 58.546 45.833 0.00 0.00 0.00 4.63
89 90 5.238868 CGTCTAGATACTTCCATTTCTCCGA 59.761 44.000 0.00 0.00 0.00 4.55
90 91 6.440436 GTCTAGATACTTCCATTTCTCCGAC 58.560 44.000 0.00 0.00 0.00 4.79
91 92 6.039493 GTCTAGATACTTCCATTTCTCCGACA 59.961 42.308 0.00 0.00 0.00 4.35
92 93 5.677319 AGATACTTCCATTTCTCCGACAA 57.323 39.130 0.00 0.00 0.00 3.18
93 94 5.665459 AGATACTTCCATTTCTCCGACAAG 58.335 41.667 0.00 0.00 0.00 3.16
94 95 3.771577 ACTTCCATTTCTCCGACAAGT 57.228 42.857 0.00 0.00 0.00 3.16
95 96 4.884668 ACTTCCATTTCTCCGACAAGTA 57.115 40.909 0.00 0.00 0.00 2.24
96 97 5.422214 ACTTCCATTTCTCCGACAAGTAT 57.578 39.130 0.00 0.00 0.00 2.12
97 98 5.805728 ACTTCCATTTCTCCGACAAGTATT 58.194 37.500 0.00 0.00 0.00 1.89
98 99 6.238648 ACTTCCATTTCTCCGACAAGTATTT 58.761 36.000 0.00 0.00 0.00 1.40
99 100 6.371825 ACTTCCATTTCTCCGACAAGTATTTC 59.628 38.462 0.00 0.00 0.00 2.17
100 101 4.868171 TCCATTTCTCCGACAAGTATTTCG 59.132 41.667 0.00 0.00 34.93 3.46
151 152 1.000283 CAGGCGCTAGATCTTACCTGG 60.000 57.143 18.38 0.00 40.80 4.45
176 177 2.753043 CCAGTCTGCCACATGCCC 60.753 66.667 0.00 0.00 40.16 5.36
285 1069 0.779997 AGGGCACTCAATTCCCAACT 59.220 50.000 2.24 0.00 42.52 3.16
367 1161 1.673923 GGGTACGGTGCCTTACAGTTC 60.674 57.143 15.02 0.00 38.65 3.01
401 1195 0.108992 ACCTGGCATGTGTACGTACG 60.109 55.000 20.18 15.01 0.00 3.67
402 1196 0.108992 CCTGGCATGTGTACGTACGT 60.109 55.000 25.98 25.98 0.00 3.57
443 1237 0.955428 TGAGACCAGCGGCATTGAAC 60.955 55.000 1.45 0.00 0.00 3.18
532 1326 1.795768 TTGTTGTCTGACGCCTGATC 58.204 50.000 2.98 0.00 0.00 2.92
751 1554 1.202580 AGTGCCATTGACGCCTATCTC 60.203 52.381 0.00 0.00 0.00 2.75
760 1563 2.432146 TGACGCCTATCTCAGCTGATTT 59.568 45.455 18.63 10.26 0.00 2.17
762 1565 3.462021 ACGCCTATCTCAGCTGATTTTC 58.538 45.455 18.63 4.00 0.00 2.29
763 1566 3.133721 ACGCCTATCTCAGCTGATTTTCT 59.866 43.478 18.63 3.03 0.00 2.52
764 1567 3.740321 CGCCTATCTCAGCTGATTTTCTC 59.260 47.826 18.63 5.06 0.00 2.87
765 1568 4.501229 CGCCTATCTCAGCTGATTTTCTCT 60.501 45.833 18.63 0.00 0.00 3.10
766 1569 4.990426 GCCTATCTCAGCTGATTTTCTCTC 59.010 45.833 18.63 0.00 0.00 3.20
768 1571 6.686126 GCCTATCTCAGCTGATTTTCTCTCTT 60.686 42.308 18.63 0.00 0.00 2.85
770 1573 5.999205 TCTCAGCTGATTTTCTCTCTTCT 57.001 39.130 18.63 0.00 0.00 2.85
772 1575 6.397272 TCTCAGCTGATTTTCTCTCTTCTTC 58.603 40.000 18.63 0.00 0.00 2.87
773 1576 6.211184 TCTCAGCTGATTTTCTCTCTTCTTCT 59.789 38.462 18.63 0.00 0.00 2.85
774 1577 6.767456 TCAGCTGATTTTCTCTCTTCTTCTT 58.233 36.000 13.74 0.00 0.00 2.52
971 1788 2.863137 GCTCTTCTACCAAATCAGAGCG 59.137 50.000 3.85 0.00 45.17 5.03
1003 1820 0.039618 TCCTCCCCACCTTGAAATGC 59.960 55.000 0.00 0.00 0.00 3.56
1134 1951 1.178534 GCGAGGAGAGGGGAGATCAG 61.179 65.000 0.00 0.00 0.00 2.90
1151 1971 2.361610 GGCTGATGGTGGTGGTGG 60.362 66.667 0.00 0.00 0.00 4.61
1152 1972 3.064324 GCTGATGGTGGTGGTGGC 61.064 66.667 0.00 0.00 0.00 5.01
1153 1973 2.747460 CTGATGGTGGTGGTGGCG 60.747 66.667 0.00 0.00 0.00 5.69
1165 1985 4.410743 GTGGCGCTGGCAGCTTTC 62.411 66.667 34.17 23.09 39.60 2.62
1314 2143 2.749044 CACTTGCCGCTGCTCCAT 60.749 61.111 0.70 0.00 38.71 3.41
1365 2194 1.671742 GAAAGTCGCCCACAGGAGA 59.328 57.895 0.00 0.00 40.03 3.71
1524 2353 0.033504 TCCTCACGTGCAGGAAGTTC 59.966 55.000 25.12 0.00 37.09 3.01
1587 2416 2.584391 GGTGAGCTTCGACCCTGGT 61.584 63.158 0.00 0.00 0.00 4.00
1590 2419 3.003763 AGCTTCGACCCTGGTCCC 61.004 66.667 10.65 0.00 41.76 4.46
1592 2421 2.982130 CTTCGACCCTGGTCCCAG 59.018 66.667 10.65 6.35 41.76 4.45
2096 2925 2.224042 GCCAACCAAAGGAGACAAAAGG 60.224 50.000 0.00 0.00 0.00 3.11
2108 2937 2.039613 AGACAAAAGGAGAGGCAGGAAG 59.960 50.000 0.00 0.00 0.00 3.46
2163 2992 2.122729 CCACCACCTCCTCCTCCA 59.877 66.667 0.00 0.00 0.00 3.86
2347 3182 1.678635 CTGGGGAAGAATGGCGCAA 60.679 57.895 10.83 0.00 0.00 4.85
2465 3300 3.064900 AGCCTGGATCAGTTTGACTTC 57.935 47.619 0.00 0.00 0.00 3.01
2497 3332 0.235665 CACGCACGCACTCATCTTTT 59.764 50.000 0.00 0.00 0.00 2.27
2498 3333 0.944386 ACGCACGCACTCATCTTTTT 59.056 45.000 0.00 0.00 0.00 1.94
2499 3334 1.321016 CGCACGCACTCATCTTTTTG 58.679 50.000 0.00 0.00 0.00 2.44
2500 3335 1.069973 CGCACGCACTCATCTTTTTGA 60.070 47.619 0.00 0.00 0.00 2.69
2501 3336 2.601979 CGCACGCACTCATCTTTTTGAA 60.602 45.455 0.00 0.00 0.00 2.69
2502 3337 3.568538 GCACGCACTCATCTTTTTGAAT 58.431 40.909 0.00 0.00 0.00 2.57
2503 3338 3.605486 GCACGCACTCATCTTTTTGAATC 59.395 43.478 0.00 0.00 0.00 2.52
2504 3339 4.614535 GCACGCACTCATCTTTTTGAATCT 60.615 41.667 0.00 0.00 0.00 2.40
2505 3340 4.849926 CACGCACTCATCTTTTTGAATCTG 59.150 41.667 0.00 0.00 0.00 2.90
2506 3341 4.756642 ACGCACTCATCTTTTTGAATCTGA 59.243 37.500 0.00 0.00 0.00 3.27
2507 3342 5.239306 ACGCACTCATCTTTTTGAATCTGAA 59.761 36.000 0.00 0.00 0.00 3.02
2529 3364 5.741388 ACTGAAGCAGTACAACTTTTGAG 57.259 39.130 0.00 0.00 43.46 3.02
2530 3365 5.186198 ACTGAAGCAGTACAACTTTTGAGT 58.814 37.500 0.00 0.08 43.46 3.41
2531 3366 5.648092 ACTGAAGCAGTACAACTTTTGAGTT 59.352 36.000 0.00 0.00 43.46 3.01
2532 3367 6.119144 TGAAGCAGTACAACTTTTGAGTTC 57.881 37.500 0.00 0.00 0.00 3.01
2534 3369 5.741388 AGCAGTACAACTTTTGAGTTCTG 57.259 39.130 0.00 0.00 0.00 3.02
2535 3370 5.428253 AGCAGTACAACTTTTGAGTTCTGA 58.572 37.500 9.37 0.00 0.00 3.27
2536 3371 5.294552 AGCAGTACAACTTTTGAGTTCTGAC 59.705 40.000 9.37 0.97 0.00 3.51
2537 3372 5.064707 GCAGTACAACTTTTGAGTTCTGACA 59.935 40.000 9.37 0.00 0.00 3.58
2538 3373 6.403200 GCAGTACAACTTTTGAGTTCTGACAA 60.403 38.462 9.37 0.00 0.00 3.18
2539 3374 7.182761 CAGTACAACTTTTGAGTTCTGACAAG 58.817 38.462 0.00 0.00 0.00 3.16
2540 3375 6.879458 AGTACAACTTTTGAGTTCTGACAAGT 59.121 34.615 0.00 0.00 0.00 3.16
2541 3376 5.942872 ACAACTTTTGAGTTCTGACAAGTG 58.057 37.500 0.00 0.00 0.00 3.16
2542 3377 4.622701 ACTTTTGAGTTCTGACAAGTGC 57.377 40.909 0.00 0.00 0.00 4.40
2543 3378 4.265073 ACTTTTGAGTTCTGACAAGTGCT 58.735 39.130 0.00 0.00 0.00 4.40
2544 3379 5.428253 ACTTTTGAGTTCTGACAAGTGCTA 58.572 37.500 0.00 0.00 0.00 3.49
2545 3380 5.294552 ACTTTTGAGTTCTGACAAGTGCTAC 59.705 40.000 0.00 0.00 0.00 3.58
2546 3381 4.672587 TTGAGTTCTGACAAGTGCTACT 57.327 40.909 0.00 0.00 0.00 2.57
2547 3382 4.244425 TGAGTTCTGACAAGTGCTACTC 57.756 45.455 0.00 0.00 0.00 2.59
2548 3383 3.005897 TGAGTTCTGACAAGTGCTACTCC 59.994 47.826 0.00 0.00 31.81 3.85
2664 3499 1.903877 CTCCCTCGGCAACCATGTCT 61.904 60.000 0.00 0.00 0.00 3.41
2771 3606 2.314647 TAACTCAACGGCTGCACGC 61.315 57.895 0.50 0.00 37.37 5.34
2795 3635 2.714480 CACGTATCTATCAACACGCTCG 59.286 50.000 0.00 0.00 37.92 5.03
2809 3649 1.336887 ACGCTCGTATCATATGGTGGC 60.337 52.381 2.13 0.00 0.00 5.01
2824 3664 1.407437 GGTGGCGATCCTTGATTGACT 60.407 52.381 0.00 0.00 32.82 3.41
2830 3670 2.611292 CGATCCTTGATTGACTTGGAGC 59.389 50.000 0.00 0.00 0.00 4.70
2852 3692 2.676748 TCTTGGTTTGGTTGCTGGATT 58.323 42.857 0.00 0.00 0.00 3.01
2891 3731 0.393132 TGTCGGTGCAACAACTGGAA 60.393 50.000 0.98 0.00 39.98 3.53
3002 3842 2.031012 CTCAAGGCGGTGCTCACA 59.969 61.111 2.21 0.00 0.00 3.58
3083 3923 0.038166 TTGGCCACATCAGGAAGTCC 59.962 55.000 3.88 0.00 0.00 3.85
3128 3968 1.742880 GCAGAGCTCGACATGCCAA 60.743 57.895 13.28 0.00 32.49 4.52
3144 3984 1.470098 GCCAATCCTGTACTGTTGCAG 59.530 52.381 0.00 5.45 37.52 4.41
3172 4015 7.460120 CGCGATAGTTCATTGACATTTTGTTTC 60.460 37.037 0.00 0.00 39.35 2.78
3173 4016 7.538678 GCGATAGTTCATTGACATTTTGTTTCT 59.461 33.333 0.00 0.00 39.35 2.52
3181 4024 5.447478 TGACATTTTGTTTCTTTTGCGTG 57.553 34.783 0.00 0.00 0.00 5.34
3230 4073 1.802960 CGAGCAAGCTGTTCATGAAGT 59.197 47.619 8.80 0.00 0.00 3.01
3367 4210 2.033141 AAGACCACGCTGCTGCAT 59.967 55.556 16.29 0.00 39.64 3.96
3376 4219 1.634757 CGCTGCTGCATTTCGTGGTA 61.635 55.000 16.29 0.00 39.64 3.25
3472 4315 1.795286 GAGCTCACCAACGTCAAGAAG 59.205 52.381 9.40 0.00 0.00 2.85
3779 4622 0.984961 CTTCCTGGGGATGCTGGAGA 60.985 60.000 0.00 0.00 0.00 3.71
3834 4677 1.753073 CCATGCTTGGAATCCTGTTCC 59.247 52.381 13.33 0.00 46.92 3.62
3850 4693 7.061566 TCCTGTTCCGAATAATGTATGATGA 57.938 36.000 0.00 0.00 0.00 2.92
3933 4780 8.160765 TGATGATTTTGGTTTGGTAGACTAGAA 58.839 33.333 0.00 0.00 0.00 2.10
3934 4781 7.979444 TGATTTTGGTTTGGTAGACTAGAAG 57.021 36.000 0.00 0.00 0.00 2.85
3935 4782 7.741785 TGATTTTGGTTTGGTAGACTAGAAGA 58.258 34.615 0.00 0.00 0.00 2.87
4059 5076 3.898741 TGTTTGTCCCCTTGTTTATTCCC 59.101 43.478 0.00 0.00 0.00 3.97
4159 5176 1.575922 CCACGTGCAGAACCATGTG 59.424 57.895 10.91 7.37 46.98 3.21
4163 5180 2.096268 CACGTGCAGAACCATGTGTTAG 60.096 50.000 0.82 0.00 44.04 2.34
4180 5197 3.006430 TGTTAGTTTCTCTGCCACGATGA 59.994 43.478 0.00 0.00 0.00 2.92
4205 5222 0.034896 TCGTGCTCTTTCAGAACCCC 59.965 55.000 0.00 0.00 0.00 4.95
4244 5261 2.261671 CGGCGGTTAGTCTGCTGT 59.738 61.111 0.00 0.00 46.53 4.40
4245 5262 1.509463 CGGCGGTTAGTCTGCTGTA 59.491 57.895 0.00 0.00 46.53 2.74
4246 5263 0.525668 CGGCGGTTAGTCTGCTGTAG 60.526 60.000 0.00 0.00 46.53 2.74
4250 5267 3.181478 GGCGGTTAGTCTGCTGTAGTAAT 60.181 47.826 0.00 0.00 46.74 1.89
4251 5268 4.037208 GGCGGTTAGTCTGCTGTAGTAATA 59.963 45.833 0.00 0.00 46.74 0.98
4258 6264 9.032420 GTTAGTCTGCTGTAGTAATAAATGGAC 57.968 37.037 0.00 0.00 0.00 4.02
4263 6269 9.764363 TCTGCTGTAGTAATAAATGGACATAAG 57.236 33.333 0.00 0.00 0.00 1.73
4295 6301 7.863666 ACACTGATAAGCGTAGTAGTAAGATC 58.136 38.462 0.00 0.00 0.00 2.75
4405 6462 8.664211 AAGTTACATAATACTAGCTCCTTTGC 57.336 34.615 0.00 0.00 0.00 3.68
4474 6531 2.589540 CCCGAACATAGGGCAGCA 59.410 61.111 0.00 0.00 42.77 4.41
4476 6533 1.376609 CCCGAACATAGGGCAGCAAC 61.377 60.000 0.00 0.00 42.77 4.17
4477 6534 0.676466 CCGAACATAGGGCAGCAACA 60.676 55.000 0.00 0.00 0.00 3.33
4478 6535 1.382522 CGAACATAGGGCAGCAACAT 58.617 50.000 0.00 0.00 0.00 2.71
4481 6538 3.242739 CGAACATAGGGCAGCAACATAAC 60.243 47.826 0.00 0.00 0.00 1.89
4482 6539 3.364460 ACATAGGGCAGCAACATAACA 57.636 42.857 0.00 0.00 0.00 2.41
4485 6542 4.082245 ACATAGGGCAGCAACATAACAAAC 60.082 41.667 0.00 0.00 0.00 2.93
4486 6543 1.269448 AGGGCAGCAACATAACAAACG 59.731 47.619 0.00 0.00 0.00 3.60
4489 6546 2.979813 GGCAGCAACATAACAAACGAAG 59.020 45.455 0.00 0.00 0.00 3.79
4555 6621 3.387962 TCCATTACAAGATCAGAGGCCT 58.612 45.455 3.86 3.86 0.00 5.19
4568 6634 2.962253 GGCCTGATACGAGCACGC 60.962 66.667 2.62 0.00 43.96 5.34
4569 6635 3.323136 GCCTGATACGAGCACGCG 61.323 66.667 3.53 3.53 43.96 6.01
4632 6698 6.585702 TGAATAAAGACAATGCAATCAAACCG 59.414 34.615 0.00 0.00 0.00 4.44
4654 6720 0.461516 GTAGAGGCACCCGCTAAACC 60.462 60.000 0.00 0.00 37.63 3.27
4656 6722 0.616679 AGAGGCACCCGCTAAACCTA 60.617 55.000 0.00 0.00 38.60 3.08
4665 6731 2.159198 CCCGCTAAACCTAAACGAGCTA 60.159 50.000 0.00 0.00 0.00 3.32
4669 6735 4.678742 CGCTAAACCTAAACGAGCTATACC 59.321 45.833 0.00 0.00 0.00 2.73
4671 6737 2.789491 ACCTAAACGAGCTATACCGC 57.211 50.000 0.00 0.00 0.00 5.68
4677 6743 0.248377 ACGAGCTATACCGCGTCAAC 60.248 55.000 4.92 0.00 36.54 3.18
4679 6745 1.478137 GAGCTATACCGCGTCAACTG 58.522 55.000 4.92 0.00 34.40 3.16
4681 6747 1.197910 GCTATACCGCGTCAACTGTC 58.802 55.000 4.92 0.00 0.00 3.51
4703 6769 4.097892 TCTTCAAAAGCCTCAAAAGTCACC 59.902 41.667 0.00 0.00 0.00 4.02
4705 6771 2.430332 CAAAAGCCTCAAAAGTCACCCA 59.570 45.455 0.00 0.00 0.00 4.51
4706 6772 2.683211 AAGCCTCAAAAGTCACCCAT 57.317 45.000 0.00 0.00 0.00 4.00
4707 6773 2.206576 AGCCTCAAAAGTCACCCATC 57.793 50.000 0.00 0.00 0.00 3.51
4723 6792 4.760204 CACCCATCTAAAAAGACGGAAAGT 59.240 41.667 0.00 0.00 0.00 2.66
4733 6802 3.123674 ACGGAAAGTCATGAGCGTC 57.876 52.632 0.00 0.00 0.00 5.19
4742 6811 0.108662 TCATGAGCGTCGAATGTGCT 60.109 50.000 0.00 2.78 42.73 4.40
4766 6835 2.526432 GCCGGGTATGATCTCCTAGAA 58.474 52.381 2.18 0.00 0.00 2.10
4773 6842 6.544650 GGGTATGATCTCCTAGAAGTACAGA 58.455 44.000 0.00 0.00 0.00 3.41
4780 6849 8.224025 TGATCTCCTAGAAGTACAGATTCTCAT 58.776 37.037 0.00 0.00 38.05 2.90
4785 6854 8.904834 TCCTAGAAGTACAGATTCTCATACAAC 58.095 37.037 0.00 2.38 38.05 3.32
4817 6886 6.704310 TCACTAAAATAGTAAAGAAGCCGGT 58.296 36.000 1.90 0.00 37.23 5.28
4829 6898 0.182775 AAGCCGGTATAAGCCCCAAG 59.817 55.000 1.90 0.00 0.00 3.61
4830 6899 0.693092 AGCCGGTATAAGCCCCAAGA 60.693 55.000 1.90 0.00 0.00 3.02
4834 6903 3.146847 CCGGTATAAGCCCCAAGAAATC 58.853 50.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.664798 CCGACATGTATTTTCAGACAAATAGAA 58.335 33.333 0.00 0.00 30.77 2.10
1 2 8.038351 TCCGACATGTATTTTCAGACAAATAGA 58.962 33.333 0.00 0.00 30.77 1.98
2 3 8.196802 TCCGACATGTATTTTCAGACAAATAG 57.803 34.615 0.00 0.00 30.77 1.73
3 4 8.038351 TCTCCGACATGTATTTTCAGACAAATA 58.962 33.333 0.00 0.00 0.00 1.40
4 5 6.878923 TCTCCGACATGTATTTTCAGACAAAT 59.121 34.615 0.00 0.00 0.00 2.32
5 6 6.227522 TCTCCGACATGTATTTTCAGACAAA 58.772 36.000 0.00 0.00 0.00 2.83
6 7 5.789521 TCTCCGACATGTATTTTCAGACAA 58.210 37.500 0.00 0.00 0.00 3.18
7 8 5.400066 TCTCCGACATGTATTTTCAGACA 57.600 39.130 0.00 0.00 0.00 3.41
8 9 6.721571 TTTCTCCGACATGTATTTTCAGAC 57.278 37.500 0.00 0.00 0.00 3.51
9 10 6.316140 CCATTTCTCCGACATGTATTTTCAGA 59.684 38.462 0.00 0.00 0.00 3.27
10 11 6.316140 TCCATTTCTCCGACATGTATTTTCAG 59.684 38.462 0.00 0.00 0.00 3.02
11 12 6.176896 TCCATTTCTCCGACATGTATTTTCA 58.823 36.000 0.00 0.00 0.00 2.69
12 13 6.677781 TCCATTTCTCCGACATGTATTTTC 57.322 37.500 0.00 0.00 0.00 2.29
13 14 8.746052 TTATCCATTTCTCCGACATGTATTTT 57.254 30.769 0.00 0.00 0.00 1.82
14 15 8.746052 TTTATCCATTTCTCCGACATGTATTT 57.254 30.769 0.00 0.00 0.00 1.40
15 16 8.746052 TTTTATCCATTTCTCCGACATGTATT 57.254 30.769 0.00 0.00 0.00 1.89
16 17 7.993183 ACTTTTATCCATTTCTCCGACATGTAT 59.007 33.333 0.00 0.00 0.00 2.29
17 18 7.279981 CACTTTTATCCATTTCTCCGACATGTA 59.720 37.037 0.00 0.00 0.00 2.29
18 19 6.094048 CACTTTTATCCATTTCTCCGACATGT 59.906 38.462 0.00 0.00 0.00 3.21
19 20 6.458751 CCACTTTTATCCATTTCTCCGACATG 60.459 42.308 0.00 0.00 0.00 3.21
20 21 5.590259 CCACTTTTATCCATTTCTCCGACAT 59.410 40.000 0.00 0.00 0.00 3.06
21 22 4.941263 CCACTTTTATCCATTTCTCCGACA 59.059 41.667 0.00 0.00 0.00 4.35
22 23 5.183228 TCCACTTTTATCCATTTCTCCGAC 58.817 41.667 0.00 0.00 0.00 4.79
23 24 5.429681 TCCACTTTTATCCATTTCTCCGA 57.570 39.130 0.00 0.00 0.00 4.55
24 25 5.590259 ACATCCACTTTTATCCATTTCTCCG 59.410 40.000 0.00 0.00 0.00 4.63
25 26 8.697507 ATACATCCACTTTTATCCATTTCTCC 57.302 34.615 0.00 0.00 0.00 3.71
26 27 9.566432 AGATACATCCACTTTTATCCATTTCTC 57.434 33.333 0.00 0.00 0.00 2.87
40 41 8.993121 CGCATTTTAATTCTAGATACATCCACT 58.007 33.333 0.00 0.00 0.00 4.00
41 42 8.774586 ACGCATTTTAATTCTAGATACATCCAC 58.225 33.333 0.00 0.00 0.00 4.02
42 43 8.902540 ACGCATTTTAATTCTAGATACATCCA 57.097 30.769 0.00 0.00 0.00 3.41
43 44 9.209175 AGACGCATTTTAATTCTAGATACATCC 57.791 33.333 0.00 0.00 0.00 3.51
53 54 9.262358 GGAAGTATCTAGACGCATTTTAATTCT 57.738 33.333 0.00 0.00 0.00 2.40
54 55 9.042008 TGGAAGTATCTAGACGCATTTTAATTC 57.958 33.333 0.00 0.00 0.00 2.17
55 56 8.958119 TGGAAGTATCTAGACGCATTTTAATT 57.042 30.769 0.00 0.00 0.00 1.40
56 57 9.561069 AATGGAAGTATCTAGACGCATTTTAAT 57.439 29.630 0.00 0.00 0.00 1.40
57 58 8.958119 AATGGAAGTATCTAGACGCATTTTAA 57.042 30.769 0.00 0.00 0.00 1.52
58 59 8.958119 AAATGGAAGTATCTAGACGCATTTTA 57.042 30.769 0.00 0.00 0.00 1.52
59 60 7.770897 AGAAATGGAAGTATCTAGACGCATTTT 59.229 33.333 0.00 0.00 0.00 1.82
60 61 7.275920 AGAAATGGAAGTATCTAGACGCATTT 58.724 34.615 0.00 0.00 0.00 2.32
61 62 6.821388 AGAAATGGAAGTATCTAGACGCATT 58.179 36.000 0.00 0.00 0.00 3.56
62 63 6.412362 AGAAATGGAAGTATCTAGACGCAT 57.588 37.500 0.00 0.00 0.00 4.73
63 64 5.221263 GGAGAAATGGAAGTATCTAGACGCA 60.221 44.000 0.00 0.00 0.00 5.24
64 65 5.224135 GGAGAAATGGAAGTATCTAGACGC 58.776 45.833 0.00 0.00 0.00 5.19
65 66 5.238868 TCGGAGAAATGGAAGTATCTAGACG 59.761 44.000 0.00 0.00 0.00 4.18
66 67 6.039493 TGTCGGAGAAATGGAAGTATCTAGAC 59.961 42.308 0.00 0.00 39.69 2.59
67 68 6.127101 TGTCGGAGAAATGGAAGTATCTAGA 58.873 40.000 0.00 0.00 39.69 2.43
68 69 6.392625 TGTCGGAGAAATGGAAGTATCTAG 57.607 41.667 0.00 0.00 39.69 2.43
69 70 6.380274 ACTTGTCGGAGAAATGGAAGTATCTA 59.620 38.462 0.00 0.00 39.69 1.98
70 71 5.187967 ACTTGTCGGAGAAATGGAAGTATCT 59.812 40.000 0.00 0.00 39.69 1.98
71 72 5.420409 ACTTGTCGGAGAAATGGAAGTATC 58.580 41.667 0.00 0.00 39.69 2.24
72 73 5.422214 ACTTGTCGGAGAAATGGAAGTAT 57.578 39.130 0.00 0.00 39.69 2.12
73 74 4.884668 ACTTGTCGGAGAAATGGAAGTA 57.115 40.909 0.00 0.00 39.69 2.24
74 75 3.771577 ACTTGTCGGAGAAATGGAAGT 57.228 42.857 0.00 0.00 39.69 3.01
75 76 6.455646 CGAAATACTTGTCGGAGAAATGGAAG 60.456 42.308 0.00 0.00 39.69 3.46
76 77 5.350365 CGAAATACTTGTCGGAGAAATGGAA 59.650 40.000 0.00 0.00 39.69 3.53
77 78 4.868171 CGAAATACTTGTCGGAGAAATGGA 59.132 41.667 0.00 0.00 39.69 3.41
78 79 5.143916 CGAAATACTTGTCGGAGAAATGG 57.856 43.478 0.00 0.00 39.69 3.16
87 88 1.135315 TCCGTCCCGAAATACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
88 89 2.537401 CTCCGTCCCGAAATACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
89 90 1.206371 CCTCCGTCCCGAAATACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
90 91 1.472728 CCCTCCGTCCCGAAATACTTG 60.473 57.143 0.00 0.00 0.00 3.16
91 92 0.828677 CCCTCCGTCCCGAAATACTT 59.171 55.000 0.00 0.00 0.00 2.24
92 93 0.032813 TCCCTCCGTCCCGAAATACT 60.033 55.000 0.00 0.00 0.00 2.12
93 94 0.388294 CTCCCTCCGTCCCGAAATAC 59.612 60.000 0.00 0.00 0.00 1.89
94 95 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
95 96 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
96 97 0.251742 TTACTCCCTCCGTCCCGAAA 60.252 55.000 0.00 0.00 0.00 3.46
97 98 0.032813 ATTACTCCCTCCGTCCCGAA 60.033 55.000 0.00 0.00 0.00 4.30
98 99 0.846015 TATTACTCCCTCCGTCCCGA 59.154 55.000 0.00 0.00 0.00 5.14
99 100 1.920610 ATATTACTCCCTCCGTCCCG 58.079 55.000 0.00 0.00 0.00 5.14
100 101 3.806157 GCAAATATTACTCCCTCCGTCCC 60.806 52.174 0.00 0.00 0.00 4.46
101 102 3.071167 AGCAAATATTACTCCCTCCGTCC 59.929 47.826 0.00 0.00 0.00 4.79
102 103 4.058817 CAGCAAATATTACTCCCTCCGTC 58.941 47.826 0.00 0.00 0.00 4.79
103 104 3.181454 CCAGCAAATATTACTCCCTCCGT 60.181 47.826 0.00 0.00 0.00 4.69
104 105 3.071023 TCCAGCAAATATTACTCCCTCCG 59.929 47.826 0.00 0.00 0.00 4.63
105 106 4.706842 TCCAGCAAATATTACTCCCTCC 57.293 45.455 0.00 0.00 0.00 4.30
106 107 8.103305 TGAATATCCAGCAAATATTACTCCCTC 58.897 37.037 0.00 0.00 31.15 4.30
107 108 7.988937 TGAATATCCAGCAAATATTACTCCCT 58.011 34.615 0.00 0.00 31.15 4.20
108 109 7.337942 CCTGAATATCCAGCAAATATTACTCCC 59.662 40.741 0.00 0.00 31.15 4.30
109 110 7.148171 GCCTGAATATCCAGCAAATATTACTCC 60.148 40.741 0.00 0.00 31.15 3.85
110 111 7.413438 CGCCTGAATATCCAGCAAATATTACTC 60.413 40.741 0.00 0.00 31.15 2.59
111 112 6.372659 CGCCTGAATATCCAGCAAATATTACT 59.627 38.462 0.00 0.00 31.15 2.24
112 113 6.546395 CGCCTGAATATCCAGCAAATATTAC 58.454 40.000 0.00 0.00 31.15 1.89
151 152 2.217038 TGGCAGACTGGACCAGGTC 61.217 63.158 25.34 18.47 35.51 3.85
285 1069 0.615850 TGCGTGGACCCATGAATGTA 59.384 50.000 12.19 0.00 35.09 2.29
367 1161 2.796735 GCCAGGTGGTGTGTTTAAAACG 60.797 50.000 0.00 0.00 37.57 3.60
401 1195 1.129811 CGTTTGAATTGGCCGGAGTAC 59.870 52.381 5.05 0.00 0.00 2.73
402 1196 1.444836 CGTTTGAATTGGCCGGAGTA 58.555 50.000 5.05 0.00 0.00 2.59
443 1237 3.343941 TGATTCTCCCCTGTAAAACGG 57.656 47.619 0.00 0.00 0.00 4.44
751 1554 6.621164 GCAAGAAGAAGAGAGAAAATCAGCTG 60.621 42.308 7.63 7.63 0.00 4.24
760 1563 5.440610 AGTTTTGGCAAGAAGAAGAGAGAA 58.559 37.500 0.00 0.00 0.00 2.87
762 1565 5.506982 CCAAGTTTTGGCAAGAAGAAGAGAG 60.507 44.000 0.00 0.00 45.17 3.20
763 1566 4.339247 CCAAGTTTTGGCAAGAAGAAGAGA 59.661 41.667 0.00 0.00 45.17 3.10
764 1567 4.614946 CCAAGTTTTGGCAAGAAGAAGAG 58.385 43.478 0.00 0.00 45.17 2.85
765 1568 4.654091 CCAAGTTTTGGCAAGAAGAAGA 57.346 40.909 0.00 0.00 45.17 2.87
970 1787 0.464554 GGAGGAAGGAGGAAATGCCG 60.465 60.000 0.00 0.00 43.43 5.69
971 1788 0.106469 GGGAGGAAGGAGGAAATGCC 60.106 60.000 0.00 0.00 0.00 4.40
1003 1820 1.511305 CAGGCTTGCAGGCATCAAG 59.489 57.895 23.28 12.52 44.19 3.02
1134 1951 2.361610 CCACCACCACCATCAGCC 60.362 66.667 0.00 0.00 0.00 4.85
1153 1973 1.515736 GCAATCGAAAGCTGCCAGC 60.516 57.895 9.13 9.13 42.84 4.85
1154 1974 2.177950 AGCAATCGAAAGCTGCCAG 58.822 52.632 13.37 0.00 40.13 4.85
1164 1984 1.708193 CGATGCCAAGCAGCAATCGA 61.708 55.000 5.61 0.00 45.92 3.59
1165 1985 1.298116 CGATGCCAAGCAGCAATCG 60.298 57.895 5.61 1.01 45.92 3.34
1195 2015 4.161295 CCTCCGCAATGGCCTCGA 62.161 66.667 3.32 0.00 37.80 4.04
1314 2143 4.807039 GGGAGGCGCGCGTTCTTA 62.807 66.667 32.35 0.00 0.00 2.10
1587 2416 1.687146 CAGGTAGAGCAGGCTGGGA 60.687 63.158 17.64 0.00 0.00 4.37
1590 2419 1.519719 GTCCAGGTAGAGCAGGCTG 59.480 63.158 10.94 10.94 0.00 4.85
1592 2421 2.496817 CGTCCAGGTAGAGCAGGC 59.503 66.667 0.00 0.00 0.00 4.85
2037 2866 3.758554 GCACTCCTGGAAAGCTTAATGAA 59.241 43.478 0.00 0.00 0.00 2.57
2043 2872 0.767375 TCTGCACTCCTGGAAAGCTT 59.233 50.000 17.56 0.00 0.00 3.74
2080 2909 3.416156 CCTCTCCTTTTGTCTCCTTTGG 58.584 50.000 0.00 0.00 0.00 3.28
2096 2925 2.817396 GCACGCTTCCTGCCTCTC 60.817 66.667 0.00 0.00 38.78 3.20
2145 2974 3.403558 GGAGGAGGAGGTGGTGGC 61.404 72.222 0.00 0.00 0.00 5.01
2232 3067 3.185246 TGCTCCTTCAGTATTAGCAGC 57.815 47.619 0.00 0.00 38.22 5.25
2465 3300 0.719465 GTGCGTGACAGATAAACGGG 59.281 55.000 0.00 0.00 37.77 5.28
2497 3332 5.610398 TGTACTGCTTCAGTTCAGATTCAA 58.390 37.500 4.70 0.00 42.59 2.69
2498 3333 5.213891 TGTACTGCTTCAGTTCAGATTCA 57.786 39.130 4.70 0.00 42.59 2.57
2499 3334 5.698545 AGTTGTACTGCTTCAGTTCAGATTC 59.301 40.000 4.70 0.43 42.59 2.52
2500 3335 5.615289 AGTTGTACTGCTTCAGTTCAGATT 58.385 37.500 4.70 0.00 42.59 2.40
2501 3336 5.220710 AGTTGTACTGCTTCAGTTCAGAT 57.779 39.130 4.70 0.00 42.59 2.90
2502 3337 4.672587 AGTTGTACTGCTTCAGTTCAGA 57.327 40.909 4.70 0.00 42.59 3.27
2503 3338 5.741388 AAAGTTGTACTGCTTCAGTTCAG 57.259 39.130 4.70 0.00 42.59 3.02
2504 3339 5.645929 TCAAAAGTTGTACTGCTTCAGTTCA 59.354 36.000 4.70 3.66 42.59 3.18
2505 3340 6.119144 TCAAAAGTTGTACTGCTTCAGTTC 57.881 37.500 4.70 0.98 42.59 3.01
2506 3341 5.648092 ACTCAAAAGTTGTACTGCTTCAGTT 59.352 36.000 4.70 0.00 37.97 3.16
2507 3342 5.186198 ACTCAAAAGTTGTACTGCTTCAGT 58.814 37.500 4.78 4.78 39.47 3.41
2529 3364 3.669251 AGGAGTAGCACTTGTCAGAAC 57.331 47.619 0.00 0.00 0.00 3.01
2530 3365 4.380531 CAAAGGAGTAGCACTTGTCAGAA 58.619 43.478 0.00 0.00 0.00 3.02
2531 3366 3.244215 CCAAAGGAGTAGCACTTGTCAGA 60.244 47.826 0.00 0.00 0.00 3.27
2532 3367 3.070018 CCAAAGGAGTAGCACTTGTCAG 58.930 50.000 0.00 0.00 0.00 3.51
2534 3369 3.127425 ACCAAAGGAGTAGCACTTGTC 57.873 47.619 0.00 0.00 0.00 3.18
2535 3370 3.577805 AACCAAAGGAGTAGCACTTGT 57.422 42.857 0.00 0.00 0.00 3.16
2536 3371 3.550842 GCAAACCAAAGGAGTAGCACTTG 60.551 47.826 0.00 0.00 0.00 3.16
2537 3372 2.623416 GCAAACCAAAGGAGTAGCACTT 59.377 45.455 0.00 0.00 0.00 3.16
2538 3373 2.230660 GCAAACCAAAGGAGTAGCACT 58.769 47.619 0.00 0.00 0.00 4.40
2539 3374 1.953686 TGCAAACCAAAGGAGTAGCAC 59.046 47.619 0.00 0.00 0.00 4.40
2540 3375 2.158682 TCTGCAAACCAAAGGAGTAGCA 60.159 45.455 0.00 0.00 0.00 3.49
2541 3376 2.504367 TCTGCAAACCAAAGGAGTAGC 58.496 47.619 0.00 0.00 0.00 3.58
2542 3377 4.082571 CCAATCTGCAAACCAAAGGAGTAG 60.083 45.833 0.00 0.00 0.00 2.57
2543 3378 3.826157 CCAATCTGCAAACCAAAGGAGTA 59.174 43.478 0.00 0.00 0.00 2.59
2544 3379 2.629617 CCAATCTGCAAACCAAAGGAGT 59.370 45.455 0.00 0.00 0.00 3.85
2545 3380 2.892852 TCCAATCTGCAAACCAAAGGAG 59.107 45.455 0.00 0.00 0.00 3.69
2546 3381 2.627699 GTCCAATCTGCAAACCAAAGGA 59.372 45.455 0.00 0.00 0.00 3.36
2547 3382 2.607771 CGTCCAATCTGCAAACCAAAGG 60.608 50.000 0.00 0.00 0.00 3.11
2548 3383 2.293122 TCGTCCAATCTGCAAACCAAAG 59.707 45.455 0.00 0.00 0.00 2.77
2664 3499 4.659172 CAGCCGCTTGGGGTCCAA 62.659 66.667 5.63 0.00 45.54 3.53
2771 3606 1.779157 CGTGTTGATAGATACGTGCGG 59.221 52.381 0.00 0.00 30.79 5.69
2795 3635 3.895232 AGGATCGCCACCATATGATAC 57.105 47.619 3.65 0.00 36.29 2.24
2809 3649 2.611292 GCTCCAAGTCAATCAAGGATCG 59.389 50.000 0.00 0.00 0.00 3.69
2824 3664 2.430332 CAACCAAACCAAGAAGCTCCAA 59.570 45.455 0.00 0.00 0.00 3.53
2830 3670 2.031120 TCCAGCAACCAAACCAAGAAG 58.969 47.619 0.00 0.00 0.00 2.85
2852 3692 0.537828 GGCCGTTCCCTGTACCAAAA 60.538 55.000 0.00 0.00 0.00 2.44
2891 3731 1.886313 CGCCATCTTGATGAGCGCT 60.886 57.895 11.27 11.27 40.35 5.92
3065 3905 0.842030 AGGACTTCCTGATGTGGCCA 60.842 55.000 0.00 0.00 46.55 5.36
3083 3923 2.169789 CACCTCGAGCATGGCGAAG 61.170 63.158 6.99 0.00 37.32 3.79
3128 3968 0.391661 CGGCTGCAACAGTACAGGAT 60.392 55.000 0.50 0.00 34.38 3.24
3144 3984 1.286501 TGTCAATGAACTATCGCGGC 58.713 50.000 6.13 0.00 0.00 6.53
3172 4015 1.741993 CGTCCTTTCACACGCAAAAG 58.258 50.000 0.00 0.00 33.26 2.27
3173 4016 3.907927 CGTCCTTTCACACGCAAAA 57.092 47.368 0.00 0.00 0.00 2.44
3181 4024 2.551270 CTGCACGCGTCCTTTCAC 59.449 61.111 9.86 0.00 0.00 3.18
3230 4073 4.704833 GAGCACGGCCTCCAGCAA 62.705 66.667 0.00 0.00 46.50 3.91
3367 4210 3.061322 CGTCATTTCCTGTACCACGAAA 58.939 45.455 0.00 0.00 0.00 3.46
3376 4219 1.736645 CGACCGCGTCATTTCCTGT 60.737 57.895 4.92 0.00 32.09 4.00
3586 4429 2.509336 ATGAAGGCGACGAAGCGG 60.509 61.111 0.00 0.00 38.18 5.52
3587 4430 2.697425 CATGAAGGCGACGAAGCG 59.303 61.111 0.00 0.00 38.18 4.68
3779 4622 1.770110 TGACCTCCTTGCACACCCT 60.770 57.895 0.00 0.00 0.00 4.34
3834 4677 9.949174 TCAAAACCAATCATCATACATTATTCG 57.051 29.630 0.00 0.00 0.00 3.34
3850 4693 3.181466 GCCAAGAACCACTCAAAACCAAT 60.181 43.478 0.00 0.00 0.00 3.16
3984 4831 5.390251 CCAGTTCAAACATCATCTTGTCTCG 60.390 44.000 0.00 0.00 0.00 4.04
4059 5076 1.928868 ATGGGCAAGGAGACAAAAGG 58.071 50.000 0.00 0.00 0.00 3.11
4159 5176 3.368236 GTCATCGTGGCAGAGAAACTAAC 59.632 47.826 0.00 0.00 0.00 2.34
4163 5180 1.728971 CAGTCATCGTGGCAGAGAAAC 59.271 52.381 0.00 0.00 0.00 2.78
4230 5247 7.169308 CCATTTATTACTACAGCAGACTAACCG 59.831 40.741 0.00 0.00 0.00 4.44
4382 6439 7.217906 AGGCAAAGGAGCTAGTATTATGTAAC 58.782 38.462 0.00 0.00 34.17 2.50
4458 6515 0.676466 TGTTGCTGCCCTATGTTCGG 60.676 55.000 0.00 0.00 0.00 4.30
4460 6517 3.694072 TGTTATGTTGCTGCCCTATGTTC 59.306 43.478 0.00 0.00 0.00 3.18
4467 6524 1.268352 TCGTTTGTTATGTTGCTGCCC 59.732 47.619 0.00 0.00 0.00 5.36
4469 6526 2.979813 CCTTCGTTTGTTATGTTGCTGC 59.020 45.455 0.00 0.00 0.00 5.25
4470 6527 2.979813 GCCTTCGTTTGTTATGTTGCTG 59.020 45.455 0.00 0.00 0.00 4.41
4472 6529 2.324860 GGCCTTCGTTTGTTATGTTGC 58.675 47.619 0.00 0.00 0.00 4.17
4473 6530 2.352323 GGGGCCTTCGTTTGTTATGTTG 60.352 50.000 0.84 0.00 0.00 3.33
4474 6531 1.890489 GGGGCCTTCGTTTGTTATGTT 59.110 47.619 0.84 0.00 0.00 2.71
4476 6533 1.540267 TGGGGCCTTCGTTTGTTATG 58.460 50.000 0.84 0.00 0.00 1.90
4477 6534 2.296073 TTGGGGCCTTCGTTTGTTAT 57.704 45.000 0.84 0.00 0.00 1.89
4478 6535 1.957877 CTTTGGGGCCTTCGTTTGTTA 59.042 47.619 0.84 0.00 0.00 2.41
4481 6538 1.665442 CCTTTGGGGCCTTCGTTTG 59.335 57.895 0.84 0.00 0.00 2.93
4482 6539 4.191243 CCTTTGGGGCCTTCGTTT 57.809 55.556 0.84 0.00 0.00 3.60
4555 6621 4.865761 GCCCGCGTGCTCGTATCA 62.866 66.667 6.24 0.00 39.49 2.15
4568 6634 1.667724 CTTAGTTTGCATCTGAGCCCG 59.332 52.381 0.00 0.00 0.00 6.13
4569 6635 2.991250 TCTTAGTTTGCATCTGAGCCC 58.009 47.619 0.00 0.00 0.00 5.19
4619 6685 3.535561 CTCTACTCCGGTTTGATTGCAT 58.464 45.455 0.00 0.00 0.00 3.96
4632 6698 1.041447 TTAGCGGGTGCCTCTACTCC 61.041 60.000 0.00 0.00 44.31 3.85
4654 6720 2.286595 TGACGCGGTATAGCTCGTTTAG 60.287 50.000 19.59 0.00 35.12 1.85
4656 6722 0.452987 TGACGCGGTATAGCTCGTTT 59.547 50.000 19.59 0.00 35.12 3.60
4665 6731 1.271379 TGAAGACAGTTGACGCGGTAT 59.729 47.619 12.47 0.00 0.00 2.73
4669 6735 2.629022 CTTTTGAAGACAGTTGACGCG 58.371 47.619 3.53 3.53 0.00 6.01
4671 6737 2.614057 AGGCTTTTGAAGACAGTTGACG 59.386 45.455 0.00 0.00 39.74 4.35
4677 6743 5.163622 TGACTTTTGAGGCTTTTGAAGACAG 60.164 40.000 0.00 0.00 39.74 3.51
4679 6745 5.037385 GTGACTTTTGAGGCTTTTGAAGAC 58.963 41.667 0.00 0.00 36.52 3.01
4681 6747 4.363138 GGTGACTTTTGAGGCTTTTGAAG 58.637 43.478 0.00 0.00 0.00 3.02
4703 6769 6.371548 TCATGACTTTCCGTCTTTTTAGATGG 59.628 38.462 7.02 7.02 44.31 3.51
4705 6771 6.092807 GCTCATGACTTTCCGTCTTTTTAGAT 59.907 38.462 0.00 0.00 43.25 1.98
4706 6772 5.408604 GCTCATGACTTTCCGTCTTTTTAGA 59.591 40.000 0.00 0.00 43.25 2.10
4707 6773 5.622378 GCTCATGACTTTCCGTCTTTTTAG 58.378 41.667 0.00 0.00 43.25 1.85
4723 6792 0.108662 AGCACATTCGACGCTCATGA 60.109 50.000 0.00 0.00 0.00 3.07
4724 6793 0.723414 AAGCACATTCGACGCTCATG 59.277 50.000 0.00 0.00 34.11 3.07
4725 6794 0.723414 CAAGCACATTCGACGCTCAT 59.277 50.000 0.00 0.00 34.11 2.90
4733 6802 3.814268 CCGGCCCAAGCACATTCG 61.814 66.667 0.00 0.00 42.56 3.34
4742 6811 1.415672 GGAGATCATACCCGGCCCAA 61.416 60.000 0.00 0.00 0.00 4.12
4766 6835 9.950496 AGATTTTGTTGTATGAGAATCTGTACT 57.050 29.630 0.00 0.00 33.83 2.73
4805 6874 2.105306 GGGGCTTATACCGGCTTCTTTA 59.895 50.000 0.00 0.00 0.00 1.85
4814 6883 3.815401 CTGATTTCTTGGGGCTTATACCG 59.185 47.826 0.00 0.00 0.00 4.02
4817 6886 4.476846 TGGTCTGATTTCTTGGGGCTTATA 59.523 41.667 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.