Multiple sequence alignment - TraesCS2A01G166700

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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 TraesCS2A01G166700 chr2A 100.000 3807 0 0 1703 5509 119083735 119079929 0.000000e+00 7031.0
1 TraesCS2A01G166700 chr2A 100.000 1092 0 0 1 1092 119085437 119084346 0.000000e+00 2017.0
2 TraesCS2A01G166700 chr2A 98.701 154 2 0 4128 4281 119081262 119081109 1.960000e-69 274.0
3 TraesCS2A01G166700 chr2A 98.701 154 2 0 4176 4329 119081310 119081157 1.960000e-69 274.0
4 TraesCS2A01G166700 chr2A 98.113 106 2 0 4128 4233 119081214 119081109 9.420000e-43 185.0
5 TraesCS2A01G166700 chr2A 98.113 106 2 0 4224 4329 119081310 119081205 9.420000e-43 185.0
6 TraesCS2A01G166700 chr2A 96.552 58 2 0 4128 4185 119081166 119081109 4.540000e-16 97.1
7 TraesCS2A01G166700 chr2A 96.552 58 2 0 4272 4329 119081310 119081253 4.540000e-16 97.1
8 TraesCS2A01G166700 chr2D 92.906 2495 130 22 1726 4185 117835458 117832976 0.000000e+00 3583.0
9 TraesCS2A01G166700 chr2D 89.938 805 40 15 4648 5434 117832626 117831845 0.000000e+00 1000.0
10 TraesCS2A01G166700 chr2D 92.007 613 26 4 5 616 117836745 117836155 0.000000e+00 839.0
11 TraesCS2A01G166700 chr2D 92.031 389 22 4 4272 4653 117833038 117832652 6.280000e-149 538.0
12 TraesCS2A01G166700 chr2D 83.878 490 39 27 616 1090 117835974 117835510 1.100000e-116 431.0
13 TraesCS2A01G166700 chr2D 88.889 63 2 1 4224 4281 117833038 117832976 7.650000e-09 73.1
14 TraesCS2A01G166700 chr2D 88.889 63 2 1 4176 4233 117833038 117832976 7.650000e-09 73.1
15 TraesCS2A01G166700 chr2B 91.923 879 52 12 2549 3416 168616341 168615471 0.000000e+00 1212.0
16 TraesCS2A01G166700 chr2B 91.755 849 55 10 1703 2550 168617259 168616425 0.000000e+00 1166.0
17 TraesCS2A01G166700 chr2B 94.484 707 35 2 3475 4177 168615327 168614621 0.000000e+00 1086.0
18 TraesCS2A01G166700 chr2B 89.786 607 40 7 16 616 168618554 168617964 0.000000e+00 758.0
19 TraesCS2A01G166700 chr2B 88.212 509 27 8 616 1092 168617793 168617286 1.330000e-160 577.0
20 TraesCS2A01G166700 chr2B 87.476 511 30 15 4928 5427 168612741 168612254 4.820000e-155 558.0
21 TraesCS2A01G166700 chr2B 96.787 249 5 2 4274 4519 168614671 168614423 3.970000e-111 412.0
22 TraesCS2A01G166700 chr2B 87.702 309 13 7 4556 4862 168614238 168613953 2.460000e-88 337.0
23 TraesCS2A01G166700 chr2B 98.182 55 1 0 4874 4928 168613917 168613863 4.540000e-16 97.1
24 TraesCS2A01G166700 chr2B 94.118 51 0 2 4226 4273 168614671 168614621 2.130000e-09 75.0
25 TraesCS2A01G166700 chr2B 94.118 51 0 2 4178 4225 168614671 168614621 2.130000e-09 75.0


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 TraesCS2A01G166700 chr2A 119079929 119085437 5508 True 1270.025000 7031 98.341500 1 5509 8 chr2A.!!$R1 5508
1 TraesCS2A01G166700 chr2D 117831845 117836745 4900 True 933.885714 3583 89.791143 5 5434 7 chr2D.!!$R1 5429
2 TraesCS2A01G166700 chr2B 168612254 168618554 6300 True 577.554545 1212 92.231182 16 5427 11 chr2B.!!$R1 5411

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
459 466 0.034756 ACGCTGTTCTGTGCCATGTA 59.965 50.0 0.00 0.00 0.00 2.29 F
1993 2227 1.195115 CCAGGTAGCTTGGCTCACTA 58.805 55.0 0.00 0.00 40.44 2.74 F
2278 2512 0.037590 TATGCGAGGCACCAAAACCT 59.962 50.0 0.00 0.00 43.04 3.50 F
2389 2623 0.245266 TATCAGTGCCGCTTCGTCAA 59.755 50.0 0.00 0.00 0.00 3.18 F
2913 3233 0.612229 CGATATCTCTGGCCTGGCAT 59.388 55.0 22.05 7.36 0.00 4.40 F
3453 3790 0.891904 TAAGAACCCCTTTGCACGCC 60.892 55.0 0.00 0.00 36.34 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2437 0.034059 CAACTGGAGTCTGAACCGCT 59.966 55.0 0.00 0.0 0.00 5.52 R
2902 3222 0.108207 CTCCTAGAATGCCAGGCCAG 59.892 60.0 9.64 0.0 0.00 4.85 R
3442 3779 0.244450 ATCATGTTGGCGTGCAAAGG 59.756 50.0 0.00 0.0 0.00 3.11 R
4006 4437 2.737252 CGCGGAGATAGGCTTTTATTCC 59.263 50.0 0.00 0.0 0.00 3.01 R
4442 4875 0.602562 TTTTGTACTGCAGCATGGGC 59.397 50.0 15.27 0.0 41.61 5.36 R
5429 7214 0.664466 GGAAAAAGCAACGCTCCTGC 60.664 55.0 0.00 0.0 38.25 4.85 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
55 56 3.871594 GGATCGTCATTTGTTCCTACAGG 59.128 47.826 0.00 0.00 35.28 4.00
78 79 4.345859 TTGACTTCCACCTTTCGTACAT 57.654 40.909 0.00 0.00 0.00 2.29
149 150 1.452110 CATGCTCACCGATGAAACCA 58.548 50.000 0.00 0.00 33.30 3.67
207 208 8.291191 TGTCAATTGTATTGATGCAGGATTTA 57.709 30.769 5.13 0.00 0.00 1.40
235 236 2.225727 GACCAGTTTTCTACCGGCTTTG 59.774 50.000 0.00 0.00 0.00 2.77
326 327 4.082665 AGTGTGGGATGATCATTGCTAG 57.917 45.455 10.14 0.00 0.00 3.42
388 389 5.988561 GCCTTGTCTTCTCTAGATGTATTGG 59.011 44.000 0.00 0.00 34.79 3.16
442 449 5.470368 TCAAGGACTCTTATTCTTGACACG 58.530 41.667 0.00 0.00 40.13 4.49
459 466 0.034756 ACGCTGTTCTGTGCCATGTA 59.965 50.000 0.00 0.00 0.00 2.29
469 476 6.435591 TGTTCTGTGCCATGTATATTTTTCCA 59.564 34.615 0.00 0.00 0.00 3.53
471 478 7.041635 TCTGTGCCATGTATATTTTTCCATG 57.958 36.000 0.00 0.00 35.56 3.66
495 502 4.380867 GGAGTTGTTCATAAGGTGCAATGG 60.381 45.833 0.00 0.00 0.00 3.16
518 525 4.093514 CACAATGTGCTCGATTTGCTAAG 58.906 43.478 0.00 0.00 0.00 2.18
603 610 9.136952 GTCAGAAGGAAATTTGAAAATCATCAG 57.863 33.333 0.00 0.00 0.00 2.90
621 809 4.027572 TCAGCCAAAGTTCTCAAAAACG 57.972 40.909 0.00 0.00 34.27 3.60
624 812 2.535574 GCCAAAGTTCTCAAAAACGCTG 59.464 45.455 0.00 0.00 34.27 5.18
636 824 4.270084 TCAAAAACGCTGTCTGTACAAGAG 59.730 41.667 0.00 0.00 34.84 2.85
656 844 8.031277 ACAAGAGCTTAAAAATCATGTGGAATC 58.969 33.333 0.00 0.00 0.00 2.52
671 859 8.298854 TCATGTGGAATCTTGTCAAATGTTAAG 58.701 33.333 0.00 0.00 30.43 1.85
676 864 8.664798 TGGAATCTTGTCAAATGTTAAGTATCG 58.335 33.333 0.00 0.00 0.00 2.92
690 878 7.156000 TGTTAAGTATCGGTTCATGTTCTGAA 58.844 34.615 0.00 0.00 41.61 3.02
691 879 7.822334 TGTTAAGTATCGGTTCATGTTCTGAAT 59.178 33.333 0.00 0.00 45.36 2.57
692 880 6.668541 AAGTATCGGTTCATGTTCTGAATG 57.331 37.500 0.00 0.00 45.36 2.67
695 883 5.551760 ATCGGTTCATGTTCTGAATGTTC 57.448 39.130 0.00 0.00 45.36 3.18
700 888 5.241506 GGTTCATGTTCTGAATGTTCCAAGA 59.758 40.000 0.00 0.00 45.36 3.02
794 992 2.039216 AGTCAGAGGAGAACACGAGAGA 59.961 50.000 0.00 0.00 0.00 3.10
816 1014 1.909376 CGATCTTGACCGTACACAGG 58.091 55.000 0.00 0.00 0.00 4.00
866 1064 2.742372 CACTCCGCGTTCCCCTTG 60.742 66.667 4.92 0.00 0.00 3.61
867 1065 4.016706 ACTCCGCGTTCCCCTTGG 62.017 66.667 4.92 0.00 0.00 3.61
868 1066 3.702048 CTCCGCGTTCCCCTTGGA 61.702 66.667 4.92 0.00 39.54 3.53
869 1067 3.006728 TCCGCGTTCCCCTTGGAT 61.007 61.111 4.92 0.00 41.40 3.41
870 1068 2.513897 CCGCGTTCCCCTTGGATC 60.514 66.667 4.92 0.00 41.40 3.36
874 1072 4.542075 GTTCCCCTTGGATCGAGC 57.458 61.111 0.00 0.00 41.40 5.03
910 1125 2.646719 CCGTCGTCGACTCCCAAA 59.353 61.111 22.18 0.00 39.71 3.28
973 1204 1.526225 AGATCGTCGGAGCATCGGA 60.526 57.895 0.00 0.00 42.52 4.55
1721 1955 1.635663 ATTCTCTTCGTTTGGCCGCG 61.636 55.000 0.00 0.00 0.00 6.46
1722 1956 2.981977 TTCTCTTCGTTTGGCCGCGT 62.982 55.000 4.92 0.00 0.00 6.01
1723 1957 3.011760 CTCTTCGTTTGGCCGCGTC 62.012 63.158 4.92 0.00 0.00 5.19
1724 1958 4.084888 CTTCGTTTGGCCGCGTCC 62.085 66.667 4.92 0.42 0.00 4.79
1893 2127 5.693555 GCTTGCTTGATTAAACTCTTTGCTT 59.306 36.000 0.00 0.00 0.00 3.91
1894 2128 6.128982 GCTTGCTTGATTAAACTCTTTGCTTC 60.129 38.462 0.00 0.00 0.00 3.86
1895 2129 5.451908 TGCTTGATTAAACTCTTTGCTTCG 58.548 37.500 0.00 0.00 0.00 3.79
1951 2185 2.184579 GACGCCAGGGTCTGCTAC 59.815 66.667 7.54 0.00 34.09 3.58
1985 2219 4.885907 ACAAATCATCATCCAGGTAGCTTG 59.114 41.667 0.00 0.00 0.00 4.01
1993 2227 1.195115 CCAGGTAGCTTGGCTCACTA 58.805 55.000 0.00 0.00 40.44 2.74
1995 2229 1.827969 CAGGTAGCTTGGCTCACTAGT 59.172 52.381 0.00 0.00 40.44 2.57
2002 2236 2.416893 GCTTGGCTCACTAGTTTGCTAC 59.583 50.000 14.23 2.76 0.00 3.58
2019 2253 6.915544 TTGCTACAATCTGATGAATCTGAC 57.084 37.500 2.41 0.00 37.54 3.51
2020 2254 5.363101 TGCTACAATCTGATGAATCTGACC 58.637 41.667 2.41 0.00 37.54 4.02
2034 2268 2.248431 GACCGCGCAAACACTGAC 59.752 61.111 8.75 0.00 0.00 3.51
2067 2301 9.308000 TGGTCTGGATATAAACTGAATTTTTGT 57.692 29.630 0.00 0.00 0.00 2.83
2110 2344 1.363885 GACGCGGGGGTGTTGATAAC 61.364 60.000 12.47 0.00 0.00 1.89
2161 2395 1.818642 CAGACTCCTTTTCAGGGCTG 58.181 55.000 0.00 0.00 41.25 4.85
2203 2437 3.000815 GTTGCCCACGAGAAGTTCA 57.999 52.632 5.50 0.00 0.00 3.18
2214 2448 2.062519 GAGAAGTTCAGCGGTTCAGAC 58.937 52.381 5.50 0.00 0.00 3.51
2220 2454 0.827925 TCAGCGGTTCAGACTCCAGT 60.828 55.000 0.00 0.00 0.00 4.00
2278 2512 0.037590 TATGCGAGGCACCAAAACCT 59.962 50.000 0.00 0.00 43.04 3.50
2389 2623 0.245266 TATCAGTGCCGCTTCGTCAA 59.755 50.000 0.00 0.00 0.00 3.18
2394 2628 3.345808 GCCGCTTCGTCAACTGCA 61.346 61.111 0.00 0.00 0.00 4.41
2714 3034 3.737266 CACAAACATTTTGCCTGTAGCTG 59.263 43.478 0.00 0.00 44.23 4.24
2740 3060 4.732672 TCTCATCTCTGTGTCCTGATTG 57.267 45.455 0.00 0.00 0.00 2.67
2786 3106 0.955428 TTGGCCTGATGAGCAACGAC 60.955 55.000 3.32 0.00 0.00 4.34
2839 3159 4.957327 AGTTACTGGAGAGGTAAGCTTAGG 59.043 45.833 6.38 0.00 31.03 2.69
2840 3160 3.759815 ACTGGAGAGGTAAGCTTAGGA 57.240 47.619 6.38 0.00 0.00 2.94
2858 3178 2.568956 AGGAACAGCTCAATAGTGCTCA 59.431 45.455 0.00 0.00 42.28 4.26
2865 3185 5.123502 ACAGCTCAATAGTGCTCATTTTCTG 59.876 40.000 0.00 0.00 42.28 3.02
2871 3191 8.169977 TCAATAGTGCTCATTTTCTGTTTCTT 57.830 30.769 0.00 0.00 0.00 2.52
2872 3192 8.632679 TCAATAGTGCTCATTTTCTGTTTCTTT 58.367 29.630 0.00 0.00 0.00 2.52
2902 3222 4.489810 CCATCAGGTACTTGCGATATCTC 58.510 47.826 0.00 0.00 34.60 2.75
2911 3231 1.375268 GCGATATCTCTGGCCTGGC 60.375 63.158 11.05 11.05 0.00 4.85
2913 3233 0.612229 CGATATCTCTGGCCTGGCAT 59.388 55.000 22.05 7.36 0.00 4.40
3021 3341 6.174049 GTGAAGAAACTTCTTAGCCAGGTAT 58.826 40.000 4.71 0.00 46.84 2.73
3030 3350 7.331791 ACTTCTTAGCCAGGTATTGTTTCTAG 58.668 38.462 0.00 0.00 0.00 2.43
3089 3420 1.668419 ATTACATTGCGCAGGGAGTC 58.332 50.000 11.31 0.00 0.00 3.36
3145 3476 5.384063 TTGCTACATTTGGTATGTGGTTG 57.616 39.130 0.00 0.00 33.74 3.77
3152 3483 6.517605 ACATTTGGTATGTGGTTGTTTTACC 58.482 36.000 0.00 0.00 38.73 2.85
3204 3535 6.527722 GCACATCATTGTACCATTTTGTGTAG 59.472 38.462 15.14 0.00 36.49 2.74
3205 3536 6.527722 CACATCATTGTACCATTTTGTGTAGC 59.472 38.462 9.33 0.00 33.76 3.58
3238 3569 1.946984 ATGTTCGGTCCTACAAGGGA 58.053 50.000 0.00 0.00 35.59 4.20
3243 3574 1.345415 TCGGTCCTACAAGGGAAACAC 59.655 52.381 0.00 0.00 37.10 3.32
3264 3595 2.480073 CCATTTGCGATGTAAAGGCCAG 60.480 50.000 5.01 0.00 0.00 4.85
3320 3651 5.348724 ACGTGTGCACTAATACTGAAATGAG 59.651 40.000 19.41 0.00 0.00 2.90
3371 3702 6.430925 CCAAAGATTCACTTGACCAGATTACA 59.569 38.462 1.27 0.00 38.98 2.41
3375 3706 5.627499 TTCACTTGACCAGATTACATTGC 57.373 39.130 0.00 0.00 0.00 3.56
3411 3742 4.764308 TGTTGCTTCTGTATGTGCCAAATA 59.236 37.500 0.00 0.00 0.00 1.40
3422 3753 8.552083 TGTATGTGCCAAATACAGATGATATC 57.448 34.615 3.51 0.00 35.97 1.63
3423 3754 7.607607 TGTATGTGCCAAATACAGATGATATCC 59.392 37.037 3.51 0.00 35.97 2.59
3424 3755 5.316167 TGTGCCAAATACAGATGATATCCC 58.684 41.667 0.00 0.00 0.00 3.85
3425 3756 4.702131 GTGCCAAATACAGATGATATCCCC 59.298 45.833 0.00 0.00 0.00 4.81
3426 3757 4.263905 TGCCAAATACAGATGATATCCCCC 60.264 45.833 0.00 0.00 0.00 5.40
3453 3790 0.891904 TAAGAACCCCTTTGCACGCC 60.892 55.000 0.00 0.00 36.34 5.68
3467 3804 3.339141 TGCACGCCAACATGATTACTTA 58.661 40.909 0.00 0.00 0.00 2.24
3531 3947 4.488126 TTGTGCTACAGAAGATTGTTGC 57.512 40.909 5.79 5.79 45.72 4.17
3536 3952 3.908382 GCTACAGAAGATTGTTGCGTTTG 59.092 43.478 0.00 0.00 39.31 2.93
3599 4016 6.047511 ACATCTATCTGCCTATGGACAATC 57.952 41.667 0.00 0.00 0.00 2.67
3657 4074 5.247110 TCTTATTCTCATGGATAGTGGAGCC 59.753 44.000 0.00 0.00 0.00 4.70
3706 4124 5.123979 GGTTGGTTGCTTTTACTATCTGAGG 59.876 44.000 0.00 0.00 0.00 3.86
3837 4260 4.081972 CCTATCCGATCTACCAATCCACTG 60.082 50.000 0.00 0.00 0.00 3.66
3839 4262 3.371034 TCCGATCTACCAATCCACTGAA 58.629 45.455 0.00 0.00 0.00 3.02
3845 4268 8.094548 CCGATCTACCAATCCACTGAATTAATA 58.905 37.037 0.00 0.00 0.00 0.98
3923 4346 3.350833 AGCTAGCATGGACAAAAGGAAG 58.649 45.455 18.83 0.00 0.00 3.46
3926 4349 3.515602 AGCATGGACAAAAGGAAGAGT 57.484 42.857 0.00 0.00 0.00 3.24
3947 4370 4.774200 AGTTTAATTGGATTGCAAGGCTCT 59.226 37.500 4.94 0.00 0.00 4.09
4370 4803 2.042686 TCATCAATAGTGCTGTGCCC 57.957 50.000 0.00 0.00 0.00 5.36
4378 4811 1.081242 GTGCTGTGCCCAAATGACG 60.081 57.895 0.00 0.00 0.00 4.35
4442 4875 1.304052 TCCTTTGGATTGTGCCCCG 60.304 57.895 0.00 0.00 0.00 5.73
4525 4958 2.630889 TGAGGGAGATGGTCTCTGTT 57.369 50.000 6.89 0.00 42.95 3.16
4548 4981 2.759114 CTTTCTGCTGGCCTCCCA 59.241 61.111 3.32 0.00 39.32 4.37
4550 4983 0.750911 CTTTCTGCTGGCCTCCCATC 60.751 60.000 3.32 0.00 41.21 3.51
4554 4987 0.750911 CTGCTGGCCTCCCATCTTTC 60.751 60.000 3.32 0.00 41.21 2.62
4628 5210 2.578940 AGGGGGTTCGGTGATTCATTTA 59.421 45.455 0.00 0.00 0.00 1.40
4638 5220 6.280643 TCGGTGATTCATTTAGGTATCACAG 58.719 40.000 13.48 10.51 45.38 3.66
4643 5257 6.424812 TGATTCATTTAGGTATCACAGCATCG 59.575 38.462 0.00 0.00 0.00 3.84
4646 5260 3.349488 TTAGGTATCACAGCATCGTCG 57.651 47.619 0.00 0.00 0.00 5.12
4673 5287 1.588239 ATGCTGGAATCTCACAGGGA 58.412 50.000 0.00 0.00 35.30 4.20
4685 5299 0.954452 CACAGGGAGTGGTCTTTTGC 59.046 55.000 0.00 0.00 44.69 3.68
4701 5315 7.121168 TGGTCTTTTGCTCCTGAATAAGTTATG 59.879 37.037 0.00 0.00 0.00 1.90
4714 5328 6.039717 TGAATAAGTTATGCTGCCCAATCTTC 59.960 38.462 2.48 0.00 0.00 2.87
4716 5330 3.907221 AGTTATGCTGCCCAATCTTCAT 58.093 40.909 0.00 0.00 0.00 2.57
4780 5394 5.780282 TCCCCAGATCCATTGTATACTACTG 59.220 44.000 4.17 0.35 0.00 2.74
4781 5395 5.544176 CCCCAGATCCATTGTATACTACTGT 59.456 44.000 4.17 0.00 0.00 3.55
4782 5396 6.724441 CCCCAGATCCATTGTATACTACTGTA 59.276 42.308 4.17 0.00 0.00 2.74
4783 5397 7.309867 CCCCAGATCCATTGTATACTACTGTAC 60.310 44.444 4.17 0.00 0.00 2.90
4784 5398 7.451877 CCCAGATCCATTGTATACTACTGTACT 59.548 40.741 4.17 0.00 0.00 2.73
4785 5399 9.516546 CCAGATCCATTGTATACTACTGTACTA 57.483 37.037 4.17 0.00 0.00 1.82
4803 5417 6.302269 TGTACTACTAATACTACTCCCTGGC 58.698 44.000 0.00 0.00 0.00 4.85
4818 5432 0.033228 CTGGCGCCCATGTTGAAAAA 59.967 50.000 26.77 0.00 30.82 1.94
4885 5526 8.925700 CAACAAAGTTTTAGCCAATATTTCCTC 58.074 33.333 0.00 0.00 0.00 3.71
4940 6703 7.125792 AGGAAGCATATAATATTACGAGGGG 57.874 40.000 0.00 0.00 0.00 4.79
4953 6716 8.732746 ATATTACGAGGGGATTTGTATATTGC 57.267 34.615 0.00 0.00 0.00 3.56
4998 6762 8.911918 TTGGTACTAGTACATTGTTTCACATT 57.088 30.769 29.38 0.00 37.78 2.71
4999 6763 8.542497 TGGTACTAGTACATTGTTTCACATTC 57.458 34.615 29.38 11.08 37.78 2.67
5000 6764 8.151596 TGGTACTAGTACATTGTTTCACATTCA 58.848 33.333 29.38 13.20 37.78 2.57
5001 6765 8.440833 GGTACTAGTACATTGTTTCACATTCAC 58.559 37.037 29.38 6.77 37.78 3.18
5002 6766 8.984764 GTACTAGTACATTGTTTCACATTCACA 58.015 33.333 25.02 0.00 36.15 3.58
5003 6767 8.621532 ACTAGTACATTGTTTCACATTCACAT 57.378 30.769 0.00 0.00 0.00 3.21
5024 6788 5.997129 ACATGGGTGATTGAAATGGTTTTTC 59.003 36.000 0.00 0.00 0.00 2.29
5045 6809 3.578716 TCCTTAGAGGTGGTTGAGTCTTG 59.421 47.826 0.00 0.00 36.53 3.02
5119 6892 3.842126 CGCGCTGTCCATGTCACG 61.842 66.667 5.56 0.01 0.00 4.35
5244 7019 1.566018 CCGGCGAAAATATCTCGGGC 61.566 60.000 9.30 2.80 38.23 6.13
5250 7025 2.353406 CGAAAATATCTCGGGCCCGTAT 60.353 50.000 41.57 34.26 40.74 3.06
5384 7168 4.790765 TCATGGATAGAACTGGATAGCG 57.209 45.455 0.00 0.00 0.00 4.26
5392 7176 0.311165 AACTGGATAGCGGTCGATCG 59.689 55.000 15.15 15.15 0.00 3.69
5393 7177 0.534427 ACTGGATAGCGGTCGATCGA 60.534 55.000 24.71 15.15 0.00 3.59
5394 7178 0.805614 CTGGATAGCGGTCGATCGAT 59.194 55.000 24.71 20.03 0.00 3.59
5396 7180 1.088306 GGATAGCGGTCGATCGATCT 58.912 55.000 24.71 20.55 0.00 2.75
5397 7181 1.469308 GGATAGCGGTCGATCGATCTT 59.531 52.381 24.71 15.54 0.00 2.40
5398 7182 2.476519 GGATAGCGGTCGATCGATCTTC 60.477 54.545 24.71 15.96 0.00 2.87
5424 7209 7.377662 CCAGTAAAAATAGTCACCGAAACAAAC 59.622 37.037 0.00 0.00 0.00 2.93
5426 7211 5.838531 AAAATAGTCACCGAAACAAACCA 57.161 34.783 0.00 0.00 0.00 3.67
5427 7212 5.432885 AAATAGTCACCGAAACAAACCAG 57.567 39.130 0.00 0.00 0.00 4.00
5428 7213 1.021968 AGTCACCGAAACAAACCAGC 58.978 50.000 0.00 0.00 0.00 4.85
5429 7214 0.316689 GTCACCGAAACAAACCAGCG 60.317 55.000 0.00 0.00 0.00 5.18
5430 7215 1.657181 CACCGAAACAAACCAGCGC 60.657 57.895 0.00 0.00 0.00 5.92
5431 7216 2.115911 ACCGAAACAAACCAGCGCA 61.116 52.632 11.47 0.00 0.00 6.09
5432 7217 1.370414 CCGAAACAAACCAGCGCAG 60.370 57.895 11.47 0.00 0.00 5.18
5434 7219 1.781025 CGAAACAAACCAGCGCAGGA 61.781 55.000 27.14 0.00 0.00 3.86
5435 7220 0.040067 GAAACAAACCAGCGCAGGAG 60.040 55.000 27.14 16.32 0.00 3.69
5436 7221 2.075426 AAACAAACCAGCGCAGGAGC 62.075 55.000 27.14 0.00 37.42 4.70
5447 7232 2.801388 GCAGGAGCGTTGCTTTTTC 58.199 52.632 0.00 0.00 39.88 2.29
5448 7233 0.664466 GCAGGAGCGTTGCTTTTTCC 60.664 55.000 0.00 0.00 39.88 3.13
5449 7234 0.667993 CAGGAGCGTTGCTTTTTCCA 59.332 50.000 0.00 0.00 39.88 3.53
5450 7235 1.066908 CAGGAGCGTTGCTTTTTCCAA 59.933 47.619 0.00 0.00 39.88 3.53
5451 7236 1.754226 AGGAGCGTTGCTTTTTCCAAA 59.246 42.857 0.00 0.00 39.88 3.28
5452 7237 2.167487 AGGAGCGTTGCTTTTTCCAAAA 59.833 40.909 0.00 0.00 39.88 2.44
5453 7238 2.539688 GGAGCGTTGCTTTTTCCAAAAG 59.460 45.455 4.84 4.84 39.88 2.27
5454 7239 2.539688 GAGCGTTGCTTTTTCCAAAAGG 59.460 45.455 10.27 0.00 39.88 3.11
5461 7246 3.059884 GCTTTTTCCAAAAGGCACTAGC 58.940 45.455 12.58 2.07 46.44 3.42
5462 7247 3.243873 GCTTTTTCCAAAAGGCACTAGCT 60.244 43.478 12.58 0.00 46.44 3.32
5463 7248 4.740634 GCTTTTTCCAAAAGGCACTAGCTT 60.741 41.667 12.58 0.00 46.44 3.74
5464 7249 4.320608 TTTTCCAAAAGGCACTAGCTTG 57.679 40.909 0.00 0.00 38.49 4.01
5465 7250 1.247567 TCCAAAAGGCACTAGCTTGC 58.752 50.000 1.52 1.52 38.49 4.01
5466 7251 1.202927 TCCAAAAGGCACTAGCTTGCT 60.203 47.619 10.12 0.00 42.56 3.91
5467 7252 1.615392 CCAAAAGGCACTAGCTTGCTT 59.385 47.619 10.12 0.00 42.56 3.91
5468 7253 2.819608 CCAAAAGGCACTAGCTTGCTTA 59.180 45.455 10.12 0.00 42.56 3.09
5469 7254 3.255642 CCAAAAGGCACTAGCTTGCTTAA 59.744 43.478 10.12 0.00 42.56 1.85
5470 7255 4.261994 CCAAAAGGCACTAGCTTGCTTAAA 60.262 41.667 10.12 0.00 42.56 1.52
5471 7256 4.505313 AAAGGCACTAGCTTGCTTAAAC 57.495 40.909 10.12 0.00 42.56 2.01
5472 7257 3.140325 AGGCACTAGCTTGCTTAAACA 57.860 42.857 10.12 0.00 42.56 2.83
5473 7258 3.690460 AGGCACTAGCTTGCTTAAACAT 58.310 40.909 10.12 0.00 42.56 2.71
5474 7259 3.691609 AGGCACTAGCTTGCTTAAACATC 59.308 43.478 10.12 0.00 42.56 3.06
5475 7260 3.691609 GGCACTAGCTTGCTTAAACATCT 59.308 43.478 10.12 0.00 42.56 2.90
5476 7261 4.156739 GGCACTAGCTTGCTTAAACATCTT 59.843 41.667 10.12 0.00 42.56 2.40
5477 7262 5.091431 GCACTAGCTTGCTTAAACATCTTG 58.909 41.667 3.04 0.00 39.59 3.02
5478 7263 5.335191 GCACTAGCTTGCTTAAACATCTTGT 60.335 40.000 3.04 0.00 39.59 3.16
5479 7264 6.310197 CACTAGCTTGCTTAAACATCTTGTC 58.690 40.000 0.00 0.00 0.00 3.18
5480 7265 6.148480 CACTAGCTTGCTTAAACATCTTGTCT 59.852 38.462 0.00 0.00 0.00 3.41
5481 7266 5.368256 AGCTTGCTTAAACATCTTGTCTG 57.632 39.130 0.00 0.00 0.00 3.51
5482 7267 3.916776 GCTTGCTTAAACATCTTGTCTGC 59.083 43.478 0.00 0.00 0.00 4.26
5483 7268 4.320788 GCTTGCTTAAACATCTTGTCTGCT 60.321 41.667 0.00 0.00 0.00 4.24
5484 7269 4.754372 TGCTTAAACATCTTGTCTGCTG 57.246 40.909 0.00 0.00 0.00 4.41
5485 7270 4.136796 TGCTTAAACATCTTGTCTGCTGT 58.863 39.130 0.00 0.00 0.00 4.40
5486 7271 4.214119 TGCTTAAACATCTTGTCTGCTGTC 59.786 41.667 0.00 0.00 0.00 3.51
5487 7272 4.378874 GCTTAAACATCTTGTCTGCTGTCC 60.379 45.833 0.00 0.00 0.00 4.02
5488 7273 2.191128 AACATCTTGTCTGCTGTCCC 57.809 50.000 0.00 0.00 0.00 4.46
5489 7274 0.326264 ACATCTTGTCTGCTGTCCCC 59.674 55.000 0.00 0.00 0.00 4.81
5490 7275 0.393537 CATCTTGTCTGCTGTCCCCC 60.394 60.000 0.00 0.00 0.00 5.40
5491 7276 0.548682 ATCTTGTCTGCTGTCCCCCT 60.549 55.000 0.00 0.00 0.00 4.79
5492 7277 1.002868 CTTGTCTGCTGTCCCCCTG 60.003 63.158 0.00 0.00 0.00 4.45
5493 7278 2.475371 CTTGTCTGCTGTCCCCCTGG 62.475 65.000 0.00 0.00 0.00 4.45
5494 7279 2.607750 GTCTGCTGTCCCCCTGGA 60.608 66.667 0.00 0.00 38.75 3.86
5495 7280 2.284921 TCTGCTGTCCCCCTGGAG 60.285 66.667 0.00 0.00 42.85 3.86
5496 7281 4.106925 CTGCTGTCCCCCTGGAGC 62.107 72.222 0.00 0.00 42.85 4.70
5497 7282 4.664267 TGCTGTCCCCCTGGAGCT 62.664 66.667 0.00 0.00 42.85 4.09
5498 7283 2.365635 GCTGTCCCCCTGGAGCTA 60.366 66.667 0.00 0.00 42.85 3.32
5499 7284 1.995626 GCTGTCCCCCTGGAGCTAA 60.996 63.158 0.00 0.00 42.85 3.09
5500 7285 1.562672 GCTGTCCCCCTGGAGCTAAA 61.563 60.000 0.00 0.00 42.85 1.85
5501 7286 0.543749 CTGTCCCCCTGGAGCTAAAG 59.456 60.000 0.00 0.00 42.85 1.85
5502 7287 0.178873 TGTCCCCCTGGAGCTAAAGT 60.179 55.000 0.00 0.00 42.85 2.66
5503 7288 0.542333 GTCCCCCTGGAGCTAAAGTC 59.458 60.000 0.00 0.00 42.85 3.01
5504 7289 0.976073 TCCCCCTGGAGCTAAAGTCG 60.976 60.000 0.00 0.00 35.03 4.18
5505 7290 0.976073 CCCCCTGGAGCTAAAGTCGA 60.976 60.000 0.00 0.00 0.00 4.20
5506 7291 0.461961 CCCCTGGAGCTAAAGTCGAG 59.538 60.000 0.00 0.00 0.00 4.04
5507 7292 0.461961 CCCTGGAGCTAAAGTCGAGG 59.538 60.000 0.00 0.00 39.12 4.63
5508 7293 1.187087 CCTGGAGCTAAAGTCGAGGT 58.813 55.000 0.00 0.00 35.69 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.312443 TGTACGAAAGGTGGAAGTCAATC 58.688 43.478 0.00 0.00 0.00 2.67
78 79 8.783093 CACCTATGGATATTCAAAAGCGAAATA 58.217 33.333 0.00 0.00 0.00 1.40
207 208 3.313249 CGGTAGAAAACTGGTCGGTTTTT 59.687 43.478 18.19 12.14 45.62 1.94
326 327 4.335416 TGAATCACTGATTGGGTTTCCTC 58.665 43.478 9.08 0.00 31.89 3.71
459 466 7.738437 ATGAACAACTCCCATGGAAAAATAT 57.262 32.000 15.22 0.00 0.00 1.28
469 476 3.245229 TGCACCTTATGAACAACTCCCAT 60.245 43.478 0.00 0.00 0.00 4.00
471 478 2.790433 TGCACCTTATGAACAACTCCC 58.210 47.619 0.00 0.00 0.00 4.30
518 525 2.297315 CAGGGAAGGAAAACAAAGCCTC 59.703 50.000 0.00 0.00 0.00 4.70
603 610 2.535574 CAGCGTTTTTGAGAACTTTGGC 59.464 45.455 0.00 0.00 0.00 4.52
621 809 5.924475 TTTTAAGCTCTTGTACAGACAGC 57.076 39.130 12.57 12.57 36.76 4.40
624 812 8.507249 ACATGATTTTTAAGCTCTTGTACAGAC 58.493 33.333 0.00 0.00 0.00 3.51
636 824 7.814107 TGACAAGATTCCACATGATTTTTAAGC 59.186 33.333 0.00 0.00 0.00 3.09
656 844 7.802738 TGAACCGATACTTAACATTTGACAAG 58.197 34.615 0.00 0.00 0.00 3.16
690 878 3.093057 AGTAGACGAGCTCTTGGAACAT 58.907 45.455 12.85 0.00 39.30 2.71
691 879 2.229062 CAGTAGACGAGCTCTTGGAACA 59.771 50.000 12.85 0.00 0.00 3.18
692 880 2.488545 TCAGTAGACGAGCTCTTGGAAC 59.511 50.000 12.85 3.74 0.00 3.62
695 883 3.577649 TTTCAGTAGACGAGCTCTTGG 57.422 47.619 12.85 0.00 0.00 3.61
700 888 4.806247 GCACATAATTTCAGTAGACGAGCT 59.194 41.667 0.00 0.00 0.00 4.09
794 992 1.203758 TGTGTACGGTCAAGATCGCAT 59.796 47.619 2.12 0.00 38.78 4.73
866 1064 4.636249 AGGATTATTGTCTTGCTCGATCC 58.364 43.478 0.00 0.00 33.63 3.36
867 1065 5.537188 AGAGGATTATTGTCTTGCTCGATC 58.463 41.667 0.00 0.00 0.00 3.69
868 1066 5.537188 GAGAGGATTATTGTCTTGCTCGAT 58.463 41.667 0.00 0.00 0.00 3.59
869 1067 4.498177 CGAGAGGATTATTGTCTTGCTCGA 60.498 45.833 0.00 0.00 43.65 4.04
870 1068 3.733224 CGAGAGGATTATTGTCTTGCTCG 59.267 47.826 0.00 0.00 37.09 5.03
871 1069 3.492756 GCGAGAGGATTATTGTCTTGCTC 59.507 47.826 8.78 0.00 42.34 4.26
872 1070 3.462021 GCGAGAGGATTATTGTCTTGCT 58.538 45.455 8.78 0.00 42.34 3.91
873 1071 2.545946 GGCGAGAGGATTATTGTCTTGC 59.454 50.000 7.91 7.91 44.12 4.01
874 1072 2.797156 CGGCGAGAGGATTATTGTCTTG 59.203 50.000 0.00 0.00 0.00 3.02
910 1125 1.286305 ATTGGGGGCGAGGTGGTAAT 61.286 55.000 0.00 0.00 0.00 1.89
1718 1952 1.064946 GTCAGAGATCAGGGACGCG 59.935 63.158 3.53 3.53 0.00 6.01
1721 1955 4.161189 TCAAATCAGTCAGAGATCAGGGAC 59.839 45.833 0.00 0.00 0.00 4.46
1722 1956 4.161189 GTCAAATCAGTCAGAGATCAGGGA 59.839 45.833 0.00 0.00 0.00 4.20
1723 1957 4.440880 GTCAAATCAGTCAGAGATCAGGG 58.559 47.826 0.00 0.00 0.00 4.45
1724 1958 4.111198 CGTCAAATCAGTCAGAGATCAGG 58.889 47.826 0.00 0.00 0.00 3.86
1840 2074 2.248248 CCTTGACTCCCTACACTCACA 58.752 52.381 0.00 0.00 0.00 3.58
1893 2127 1.923395 AGGGCCTGGAACCAATCGA 60.923 57.895 4.50 0.00 0.00 3.59
1894 2128 1.750399 CAGGGCCTGGAACCAATCG 60.750 63.158 26.34 0.00 0.00 3.34
1895 2129 2.054453 GCAGGGCCTGGAACCAATC 61.054 63.158 33.43 11.56 31.21 2.67
1951 2185 4.408993 TGATGATTTGTTGAAGCACTCG 57.591 40.909 0.00 0.00 36.31 4.18
1985 2219 4.331168 CAGATTGTAGCAAACTAGTGAGCC 59.669 45.833 14.25 3.52 0.00 4.70
1993 2227 7.065563 GTCAGATTCATCAGATTGTAGCAAACT 59.934 37.037 0.00 0.00 0.00 2.66
1995 2229 6.317140 GGTCAGATTCATCAGATTGTAGCAAA 59.683 38.462 0.00 0.00 0.00 3.68
2002 2236 2.220363 CGCGGTCAGATTCATCAGATTG 59.780 50.000 0.00 0.00 0.00 2.67
2019 2253 0.095245 CATAGTCAGTGTTTGCGCGG 59.905 55.000 8.83 0.00 0.00 6.46
2020 2254 0.790207 ACATAGTCAGTGTTTGCGCG 59.210 50.000 0.00 0.00 0.00 6.86
2034 2268 9.613428 TTCAGTTTATATCCAGACCAAACATAG 57.387 33.333 0.00 0.00 32.75 2.23
2067 2301 1.399714 ACATCGCACGGGAAGATAGA 58.600 50.000 0.00 0.00 0.00 1.98
2161 2395 9.956720 AACGAATCATCATCTTTATCCAAATTC 57.043 29.630 0.00 0.00 0.00 2.17
2196 2430 2.062519 GAGTCTGAACCGCTGAACTTC 58.937 52.381 0.00 0.00 0.00 3.01
2203 2437 0.034059 CAACTGGAGTCTGAACCGCT 59.966 55.000 0.00 0.00 0.00 5.52
2214 2448 1.135083 ACTCGATAACGGCAACTGGAG 60.135 52.381 0.00 0.00 40.21 3.86
2220 2454 1.514003 TTTGCACTCGATAACGGCAA 58.486 45.000 4.01 4.01 40.33 4.52
2278 2512 0.605319 CCTTTACAGGCGCAGGTTCA 60.605 55.000 10.83 0.00 31.53 3.18
2364 2598 1.869767 GAAGCGGCACTGATATTCTGG 59.130 52.381 1.45 0.00 0.00 3.86
2389 2623 2.483538 GCTTTGGGTTTGATTGTGCAGT 60.484 45.455 0.00 0.00 0.00 4.40
2394 2628 5.622346 TTTTAGGCTTTGGGTTTGATTGT 57.378 34.783 0.00 0.00 0.00 2.71
2593 2913 5.928264 GCAATAGATCTTGCCAAACAAAGTT 59.072 36.000 8.01 0.00 44.56 2.66
2637 2957 5.653255 AGAATGTATAGGTCCTGGCATTT 57.347 39.130 0.00 0.00 0.00 2.32
2694 3014 3.983344 GTCAGCTACAGGCAAAATGTTTG 59.017 43.478 0.00 0.00 44.79 2.93
2703 3023 0.898320 GAGAAGGTCAGCTACAGGCA 59.102 55.000 0.00 0.00 44.79 4.75
2714 3034 3.096092 AGGACACAGAGATGAGAAGGTC 58.904 50.000 0.00 0.00 0.00 3.85
2740 3060 9.508567 GATTTAAGAATGAGCTGGAATAACAAC 57.491 33.333 0.00 0.00 0.00 3.32
2839 3159 5.557891 AAATGAGCACTATTGAGCTGTTC 57.442 39.130 3.59 0.00 40.10 3.18
2840 3160 5.709164 AGAAAATGAGCACTATTGAGCTGTT 59.291 36.000 3.59 0.00 40.10 3.16
2858 3178 9.710900 GATGGGTTGAATAAAGAAACAGAAAAT 57.289 29.630 0.00 0.00 0.00 1.82
2891 3211 0.394192 CCAGGCCAGAGATATCGCAA 59.606 55.000 5.01 0.00 0.00 4.85
2902 3222 0.108207 CTCCTAGAATGCCAGGCCAG 59.892 60.000 9.64 0.00 0.00 4.85
2913 3233 9.635404 TGGATTTTTAACAGAAAACTCCTAGAA 57.365 29.630 15.79 0.00 32.93 2.10
3021 3341 6.920569 AAACGAGAGAAAAGCTAGAAACAA 57.079 33.333 0.00 0.00 0.00 2.83
3069 3390 2.017049 GACTCCCTGCGCAATGTAATT 58.983 47.619 13.05 0.00 36.63 1.40
3079 3410 1.405821 AGTTAGAATCGACTCCCTGCG 59.594 52.381 0.00 0.00 0.00 5.18
3089 3420 3.240861 GCTTGTCGCAGTAGTTAGAATCG 59.759 47.826 0.00 0.00 38.92 3.34
3119 3450 5.048083 ACCACATACCAAATGTAGCAAAGTG 60.048 40.000 0.00 0.00 31.61 3.16
3145 3476 2.148768 CCACGAGGGAGTTGGTAAAAC 58.851 52.381 0.00 0.00 40.01 2.43
3152 3483 0.393077 AGTTGACCACGAGGGAGTTG 59.607 55.000 3.29 0.00 41.15 3.16
3204 3535 3.789224 CCGAACATTTATAAGCAAACGGC 59.211 43.478 0.00 0.00 45.30 5.68
3205 3536 4.976987 ACCGAACATTTATAAGCAAACGG 58.023 39.130 15.53 15.53 41.85 4.44
3224 3555 1.609841 GGTGTTTCCCTTGTAGGACCG 60.610 57.143 0.00 0.00 37.67 4.79
3238 3569 4.555262 CCTTTACATCGCAAATGGTGTTT 58.445 39.130 1.58 0.00 0.00 2.83
3243 3574 1.476085 TGGCCTTTACATCGCAAATGG 59.524 47.619 3.32 0.00 0.00 3.16
3264 3595 0.393402 TCAGATGCATGGGTGTGCTC 60.393 55.000 2.46 0.00 45.27 4.26
3342 3673 6.173339 TCTGGTCAAGTGAATCTTTGGATAC 58.827 40.000 0.00 0.00 33.63 2.24
3354 3685 4.009675 GGCAATGTAATCTGGTCAAGTGA 58.990 43.478 0.00 0.00 0.00 3.41
3371 3702 3.152341 CAACAGTTCCAGAGAAGGCAAT 58.848 45.455 0.00 0.00 30.91 3.56
3375 3706 2.557920 AGCAACAGTTCCAGAGAAGG 57.442 50.000 0.00 0.00 30.91 3.46
3424 3755 1.361197 AGGGGTTCTTAATTGTGGGGG 59.639 52.381 0.00 0.00 0.00 5.40
3425 3756 2.919772 AGGGGTTCTTAATTGTGGGG 57.080 50.000 0.00 0.00 0.00 4.96
3426 3757 3.306710 GCAAAGGGGTTCTTAATTGTGGG 60.307 47.826 0.00 0.00 34.78 4.61
3427 3758 3.323403 TGCAAAGGGGTTCTTAATTGTGG 59.677 43.478 0.00 0.00 34.78 4.17
3428 3759 4.306600 GTGCAAAGGGGTTCTTAATTGTG 58.693 43.478 0.00 0.00 34.78 3.33
3442 3779 0.244450 ATCATGTTGGCGTGCAAAGG 59.756 50.000 0.00 0.00 0.00 3.11
3483 3899 7.403312 AAGCATGTGCACCACTAAATTATTA 57.597 32.000 15.69 0.00 45.16 0.98
3531 3947 6.019398 TCGTTTCTATATGTATGTGCCAAACG 60.019 38.462 6.75 6.75 42.93 3.60
3536 3952 4.988540 TGCTCGTTTCTATATGTATGTGCC 59.011 41.667 0.00 0.00 0.00 5.01
3657 4074 4.391216 TGCCCATTTTTGCGTTGAATATTG 59.609 37.500 0.00 0.00 0.00 1.90
3691 4108 9.383519 TGATAAAACTGCCTCAGATAGTAAAAG 57.616 33.333 0.29 0.00 35.18 2.27
3750 4173 9.932207 TTATAAATCAACTTTAGGAACTCGACA 57.068 29.630 0.00 0.00 41.75 4.35
3839 4262 9.706691 AGAACATTCGACGGTATCAATATTAAT 57.293 29.630 0.00 0.00 0.00 1.40
3845 4268 6.814644 TGTAAAGAACATTCGACGGTATCAAT 59.185 34.615 0.00 0.00 31.43 2.57
3853 4276 4.702247 TGTGTGTAAAGAACATTCGACG 57.298 40.909 0.00 0.00 41.10 5.12
3923 4346 5.077134 AGCCTTGCAATCCAATTAAACTC 57.923 39.130 0.00 0.00 31.91 3.01
3926 4349 5.743636 AAGAGCCTTGCAATCCAATTAAA 57.256 34.783 0.00 0.00 31.91 1.52
4006 4437 2.737252 CGCGGAGATAGGCTTTTATTCC 59.263 50.000 0.00 0.00 0.00 3.01
4025 4456 2.982744 GCTGTCTGGAAAAGCCCGC 61.983 63.158 0.00 0.00 34.97 6.13
4370 4803 2.993220 TCGATTCTGTCACCGTCATTTG 59.007 45.455 0.00 0.00 0.00 2.32
4378 4811 6.535150 TCATCAAAGTTATCGATTCTGTCACC 59.465 38.462 1.71 0.00 0.00 4.02
4442 4875 0.602562 TTTTGTACTGCAGCATGGGC 59.397 50.000 15.27 0.00 41.61 5.36
4496 4929 3.310954 ACCATCTCCCTCATACAGGTCTT 60.311 47.826 0.00 0.00 41.51 3.01
4525 4958 2.601367 GCCAGCAGAAAGGCCCAA 60.601 61.111 0.00 0.00 45.18 4.12
4576 5157 2.275134 TTTGCAATCACTCAGGAGCA 57.725 45.000 0.00 0.00 0.00 4.26
4628 5210 1.103803 ACGACGATGCTGTGATACCT 58.896 50.000 0.00 0.00 0.00 3.08
4638 5220 3.362986 CCAGCATTAATACACGACGATGC 60.363 47.826 0.00 4.48 39.97 3.91
4643 5257 5.753438 TGAGATTCCAGCATTAATACACGAC 59.247 40.000 0.00 0.00 0.00 4.34
4646 5260 6.017605 CCTGTGAGATTCCAGCATTAATACAC 60.018 42.308 0.00 0.00 0.00 2.90
4673 5287 3.515602 ATTCAGGAGCAAAAGACCACT 57.484 42.857 0.00 0.00 0.00 4.00
4685 5299 3.817647 GGGCAGCATAACTTATTCAGGAG 59.182 47.826 0.00 0.00 0.00 3.69
4701 5315 5.526506 AGAAATTATGAAGATTGGGCAGC 57.473 39.130 0.00 0.00 0.00 5.25
4780 5394 5.411053 CGCCAGGGAGTAGTATTAGTAGTAC 59.589 48.000 2.75 2.75 37.11 2.73
4781 5395 5.555017 CGCCAGGGAGTAGTATTAGTAGTA 58.445 45.833 0.00 0.00 0.00 1.82
4782 5396 4.396522 CGCCAGGGAGTAGTATTAGTAGT 58.603 47.826 0.00 0.00 0.00 2.73
4783 5397 3.190953 GCGCCAGGGAGTAGTATTAGTAG 59.809 52.174 0.00 0.00 0.00 2.57
4784 5398 3.152341 GCGCCAGGGAGTAGTATTAGTA 58.848 50.000 0.00 0.00 0.00 1.82
4785 5399 1.962100 GCGCCAGGGAGTAGTATTAGT 59.038 52.381 0.00 0.00 0.00 2.24
4786 5400 1.272769 GGCGCCAGGGAGTAGTATTAG 59.727 57.143 24.80 0.00 0.00 1.73
4787 5401 1.335145 GGCGCCAGGGAGTAGTATTA 58.665 55.000 24.80 0.00 0.00 0.98
4803 5417 5.118510 GTCATTTACTTTTTCAACATGGGCG 59.881 40.000 0.00 0.00 0.00 6.13
4818 5432 7.120579 TCAATAATGCCAGAAACGTCATTTACT 59.879 33.333 3.60 0.00 32.20 2.24
4859 5473 8.831715 AGGAAATATTGGCTAAAACTTTGTTG 57.168 30.769 0.00 0.00 0.00 3.33
4860 5474 8.870116 AGAGGAAATATTGGCTAAAACTTTGTT 58.130 29.630 0.00 0.00 0.00 2.83
4861 5475 8.422577 AGAGGAAATATTGGCTAAAACTTTGT 57.577 30.769 0.00 0.00 0.00 2.83
4885 5526 2.279582 ACAAAGTACCATCTCGCGAG 57.720 50.000 30.03 30.03 0.00 5.03
4950 6713 9.970395 CCAAATATCATTAGCTTTTCATAGCAA 57.030 29.630 0.00 0.00 43.68 3.91
4951 6714 9.135189 ACCAAATATCATTAGCTTTTCATAGCA 57.865 29.630 0.00 0.00 43.68 3.49
4999 6763 4.540359 AACCATTTCAATCACCCATGTG 57.460 40.909 0.00 0.00 44.18 3.21
5000 6764 5.565455 AAAACCATTTCAATCACCCATGT 57.435 34.783 0.00 0.00 0.00 3.21
5001 6765 5.412286 GGAAAAACCATTTCAATCACCCATG 59.588 40.000 3.63 0.00 38.79 3.66
5002 6766 5.310331 AGGAAAAACCATTTCAATCACCCAT 59.690 36.000 3.63 0.00 42.04 4.00
5003 6767 4.657969 AGGAAAAACCATTTCAATCACCCA 59.342 37.500 3.63 0.00 42.04 4.51
5024 6788 3.307059 CCAAGACTCAACCACCTCTAAGG 60.307 52.174 0.00 0.00 42.49 2.69
5045 6809 9.730420 CACCTAGTATAATGCAAAACAAATACC 57.270 33.333 0.00 0.00 34.22 2.73
5068 6835 4.946784 ACACTCTTTTAATCGATGCACC 57.053 40.909 0.00 0.00 0.00 5.01
5244 7019 5.622460 CGAGGAAGATGGATAAGAATACGGG 60.622 48.000 0.00 0.00 0.00 5.28
5250 7025 2.035961 CGGCGAGGAAGATGGATAAGAA 59.964 50.000 0.00 0.00 0.00 2.52
5384 7168 3.984508 TTACTGGAAGATCGATCGACC 57.015 47.619 22.06 25.84 37.43 4.79
5392 7176 7.039882 TCGGTGACTATTTTTACTGGAAGATC 58.960 38.462 0.00 0.00 37.43 2.75
5393 7177 6.942976 TCGGTGACTATTTTTACTGGAAGAT 58.057 36.000 0.00 0.00 37.43 2.40
5394 7178 6.349243 TCGGTGACTATTTTTACTGGAAGA 57.651 37.500 0.00 0.00 37.43 2.87
5396 7180 6.766944 TGTTTCGGTGACTATTTTTACTGGAA 59.233 34.615 0.00 0.00 0.00 3.53
5397 7181 6.289834 TGTTTCGGTGACTATTTTTACTGGA 58.710 36.000 0.00 0.00 0.00 3.86
5398 7182 6.548441 TGTTTCGGTGACTATTTTTACTGG 57.452 37.500 0.00 0.00 0.00 4.00
5429 7214 0.664466 GGAAAAAGCAACGCTCCTGC 60.664 55.000 0.00 0.00 38.25 4.85
5430 7215 0.667993 TGGAAAAAGCAACGCTCCTG 59.332 50.000 0.00 0.00 38.25 3.86
5431 7216 1.398692 TTGGAAAAAGCAACGCTCCT 58.601 45.000 0.00 0.00 38.25 3.69
5432 7217 2.217429 TTTGGAAAAAGCAACGCTCC 57.783 45.000 0.00 0.00 38.25 4.70
5434 7219 2.549926 CCTTTTGGAAAAAGCAACGCT 58.450 42.857 6.90 0.00 44.07 5.07
5435 7220 1.003972 GCCTTTTGGAAAAAGCAACGC 60.004 47.619 6.90 2.41 44.07 4.84
5436 7221 2.030335 GTGCCTTTTGGAAAAAGCAACG 59.970 45.455 9.20 0.00 44.24 4.10
5437 7222 3.270027 AGTGCCTTTTGGAAAAAGCAAC 58.730 40.909 9.20 7.28 44.24 4.17
5438 7223 3.625649 AGTGCCTTTTGGAAAAAGCAA 57.374 38.095 9.20 0.00 44.24 3.91
5439 7224 3.492482 GCTAGTGCCTTTTGGAAAAAGCA 60.492 43.478 4.39 4.39 41.54 3.91
5440 7225 3.059884 GCTAGTGCCTTTTGGAAAAAGC 58.940 45.455 6.90 2.24 44.07 3.51
5441 7226 4.590850 AGCTAGTGCCTTTTGGAAAAAG 57.409 40.909 5.65 5.65 44.07 2.27
5442 7227 4.692228 CAAGCTAGTGCCTTTTGGAAAAA 58.308 39.130 0.00 0.00 44.07 1.94
5443 7228 3.492482 GCAAGCTAGTGCCTTTTGGAAAA 60.492 43.478 0.00 0.00 44.07 2.29
5444 7229 2.035832 GCAAGCTAGTGCCTTTTGGAAA 59.964 45.455 0.00 0.00 44.07 3.13
5445 7230 1.613437 GCAAGCTAGTGCCTTTTGGAA 59.387 47.619 0.00 0.00 44.07 3.53
5446 7231 1.202927 AGCAAGCTAGTGCCTTTTGGA 60.203 47.619 6.77 0.00 46.14 3.53
5447 7232 1.251251 AGCAAGCTAGTGCCTTTTGG 58.749 50.000 6.77 0.00 46.14 3.28
5448 7233 4.503741 TTAAGCAAGCTAGTGCCTTTTG 57.496 40.909 6.77 0.00 46.14 2.44
5449 7234 4.340950 TGTTTAAGCAAGCTAGTGCCTTTT 59.659 37.500 6.77 0.00 46.14 2.27
5450 7235 3.888930 TGTTTAAGCAAGCTAGTGCCTTT 59.111 39.130 6.77 0.00 46.14 3.11
5451 7236 3.486383 TGTTTAAGCAAGCTAGTGCCTT 58.514 40.909 6.77 4.09 46.14 4.35
5452 7237 3.140325 TGTTTAAGCAAGCTAGTGCCT 57.860 42.857 6.77 0.00 46.14 4.75
5453 7238 3.691609 AGATGTTTAAGCAAGCTAGTGCC 59.308 43.478 6.77 0.00 46.14 5.01
5454 7239 4.954092 AGATGTTTAAGCAAGCTAGTGC 57.046 40.909 1.95 1.95 45.28 4.40
5455 7240 6.148480 AGACAAGATGTTTAAGCAAGCTAGTG 59.852 38.462 0.00 0.00 0.00 2.74
5456 7241 6.148480 CAGACAAGATGTTTAAGCAAGCTAGT 59.852 38.462 0.00 0.00 0.00 2.57
5457 7242 6.541086 CAGACAAGATGTTTAAGCAAGCTAG 58.459 40.000 0.00 0.00 0.00 3.42
5458 7243 5.106555 GCAGACAAGATGTTTAAGCAAGCTA 60.107 40.000 0.00 0.00 0.00 3.32
5459 7244 4.320788 GCAGACAAGATGTTTAAGCAAGCT 60.321 41.667 0.00 0.00 0.00 3.74
5460 7245 3.916776 GCAGACAAGATGTTTAAGCAAGC 59.083 43.478 0.00 0.00 0.00 4.01
5461 7246 5.152097 CAGCAGACAAGATGTTTAAGCAAG 58.848 41.667 0.00 0.00 0.00 4.01
5462 7247 4.580167 ACAGCAGACAAGATGTTTAAGCAA 59.420 37.500 0.00 0.00 33.80 3.91
5463 7248 4.136796 ACAGCAGACAAGATGTTTAAGCA 58.863 39.130 0.00 0.00 33.80 3.91
5464 7249 4.378874 GGACAGCAGACAAGATGTTTAAGC 60.379 45.833 0.00 0.00 38.41 3.09
5465 7250 4.154918 GGGACAGCAGACAAGATGTTTAAG 59.845 45.833 0.00 0.00 38.41 1.85
5466 7251 4.072131 GGGACAGCAGACAAGATGTTTAA 58.928 43.478 0.00 0.00 38.41 1.52
5467 7252 3.559171 GGGGACAGCAGACAAGATGTTTA 60.559 47.826 0.00 0.00 38.41 2.01
5468 7253 2.508526 GGGACAGCAGACAAGATGTTT 58.491 47.619 0.00 0.00 38.41 2.83
5469 7254 1.271597 GGGGACAGCAGACAAGATGTT 60.272 52.381 0.00 0.00 38.41 2.71
5470 7255 0.326264 GGGGACAGCAGACAAGATGT 59.674 55.000 0.00 0.00 41.46 3.06
5471 7256 0.393537 GGGGGACAGCAGACAAGATG 60.394 60.000 0.00 0.00 0.00 2.90
5472 7257 0.548682 AGGGGGACAGCAGACAAGAT 60.549 55.000 0.00 0.00 0.00 2.40
5473 7258 1.152030 AGGGGGACAGCAGACAAGA 60.152 57.895 0.00 0.00 0.00 3.02
5474 7259 1.002868 CAGGGGGACAGCAGACAAG 60.003 63.158 0.00 0.00 0.00 3.16
5475 7260 2.528818 CCAGGGGGACAGCAGACAA 61.529 63.158 0.00 0.00 35.59 3.18
5476 7261 2.930019 CCAGGGGGACAGCAGACA 60.930 66.667 0.00 0.00 35.59 3.41
5477 7262 2.607750 TCCAGGGGGACAGCAGAC 60.608 66.667 0.00 0.00 38.64 3.51
5478 7263 2.284921 CTCCAGGGGGACAGCAGA 60.285 66.667 0.00 0.00 38.64 4.26
5479 7264 4.106925 GCTCCAGGGGGACAGCAG 62.107 72.222 0.00 0.00 38.64 4.24
5480 7265 2.763988 TTAGCTCCAGGGGGACAGCA 62.764 60.000 0.00 0.00 38.64 4.41
5481 7266 1.562672 TTTAGCTCCAGGGGGACAGC 61.563 60.000 0.00 0.00 38.64 4.40
5482 7267 0.543749 CTTTAGCTCCAGGGGGACAG 59.456 60.000 0.00 0.00 38.64 3.51
5483 7268 0.178873 ACTTTAGCTCCAGGGGGACA 60.179 55.000 0.00 0.00 38.64 4.02
5484 7269 0.542333 GACTTTAGCTCCAGGGGGAC 59.458 60.000 0.00 0.00 38.64 4.46
5485 7270 0.976073 CGACTTTAGCTCCAGGGGGA 60.976 60.000 0.00 0.00 42.29 4.81
5486 7271 0.976073 TCGACTTTAGCTCCAGGGGG 60.976 60.000 0.00 0.00 0.00 5.40
5487 7272 0.461961 CTCGACTTTAGCTCCAGGGG 59.538 60.000 0.00 0.00 0.00 4.79
5488 7273 0.461961 CCTCGACTTTAGCTCCAGGG 59.538 60.000 0.00 0.00 0.00 4.45
5489 7274 1.187087 ACCTCGACTTTAGCTCCAGG 58.813 55.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.