Multiple sequence alignment - TraesCS3A01G128800

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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 TraesCS3A01G128800 chr3A 100.000 4218 0 0 1 4218 106400467 106404684 0.000000e+00 7790
1 TraesCS3A01G128800 chr3B 95.249 1305 57 4 2048 3347 139223312 139224616 0.000000e+00 2061
2 TraesCS3A01G128800 chr3B 95.594 1203 43 7 860 2052 139222071 139223273 0.000000e+00 1919
3 TraesCS3A01G128800 chr3B 93.981 515 26 5 3706 4217 139224896 139225408 0.000000e+00 774
4 TraesCS3A01G128800 chr3B 76.942 811 117 41 1 782 139199900 139200669 8.500000e-107 398
5 TraesCS3A01G128800 chr3D 96.087 1099 42 1 2048 3146 89802082 89803179 0.000000e+00 1790
6 TraesCS3A01G128800 chr3D 95.319 769 30 5 855 1617 89800882 89801650 0.000000e+00 1216
7 TraesCS3A01G128800 chr3D 82.477 993 142 18 1015 1978 44203344 44204333 0.000000e+00 841
8 TraesCS3A01G128800 chr3D 94.757 515 23 4 3706 4217 89803360 89803873 0.000000e+00 798
9 TraesCS3A01G128800 chr3D 96.766 402 13 0 1651 2052 89801642 89802043 0.000000e+00 671
10 TraesCS3A01G128800 chr3D 78.286 525 83 21 2090 2603 44210062 44210566 4.100000e-80 309
11 TraesCS3A01G128800 chr3D 81.389 360 58 9 16 371 89800119 89800473 6.900000e-73 285
12 TraesCS3A01G128800 chr3D 89.706 204 18 2 3322 3524 89803175 89803376 1.500000e-64 257
13 TraesCS3A01G128800 chr6B 78.138 956 162 27 1018 1961 707315782 707316702 7.920000e-157 564
14 TraesCS3A01G128800 chr6B 75.028 885 158 45 1093 1952 567844232 567845078 6.710000e-93 351
15 TraesCS3A01G128800 chr6A 76.504 881 147 44 1091 1952 522044506 522045345 3.900000e-115 425
16 TraesCS3A01G128800 chr6A 76.485 421 67 25 1123 1524 51480101 51479694 2.570000e-47 200
17 TraesCS3A01G128800 chr6D 75.740 878 160 42 1091 1952 380565587 380566427 3.950000e-105 392
18 TraesCS3A01G128800 chr6D 75.436 745 130 41 1091 1820 380495593 380496299 3.170000e-81 313
19 TraesCS3A01G128800 chr6D 76.901 342 66 11 1118 1451 39488519 39488855 9.320000e-42 182
20 TraesCS3A01G128800 chr7D 75.970 670 112 26 1093 1758 486107922 486107298 2.470000e-77 300
21 TraesCS3A01G128800 chr7D 78.756 386 59 13 1171 1547 486242827 486242456 1.960000e-58 237
22 TraesCS3A01G128800 chr7D 77.457 346 67 5 1114 1455 486307023 486307361 3.330000e-46 196
23 TraesCS3A01G128800 chr7B 73.933 867 166 38 1093 1952 513771552 513770739 1.150000e-75 294
24 TraesCS3A01G128800 chr7A 77.007 461 90 13 1091 1546 554502739 554502290 2.520000e-62 250


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 TraesCS3A01G128800 chr3A 106400467 106404684 4217 False 7790.000000 7790 100.000000 1 4218 1 chr3A.!!$F1 4217
1 TraesCS3A01G128800 chr3B 139222071 139225408 3337 False 1584.666667 2061 94.941333 860 4217 3 chr3B.!!$F2 3357
2 TraesCS3A01G128800 chr3B 139199900 139200669 769 False 398.000000 398 76.942000 1 782 1 chr3B.!!$F1 781
3 TraesCS3A01G128800 chr3D 44203344 44204333 989 False 841.000000 841 82.477000 1015 1978 1 chr3D.!!$F1 963
4 TraesCS3A01G128800 chr3D 89800119 89803873 3754 False 836.166667 1790 92.337333 16 4217 6 chr3D.!!$F3 4201
5 TraesCS3A01G128800 chr3D 44210062 44210566 504 False 309.000000 309 78.286000 2090 2603 1 chr3D.!!$F2 513
6 TraesCS3A01G128800 chr6B 707315782 707316702 920 False 564.000000 564 78.138000 1018 1961 1 chr6B.!!$F2 943
7 TraesCS3A01G128800 chr6B 567844232 567845078 846 False 351.000000 351 75.028000 1093 1952 1 chr6B.!!$F1 859
8 TraesCS3A01G128800 chr6A 522044506 522045345 839 False 425.000000 425 76.504000 1091 1952 1 chr6A.!!$F1 861
9 TraesCS3A01G128800 chr6D 380565587 380566427 840 False 392.000000 392 75.740000 1091 1952 1 chr6D.!!$F3 861
10 TraesCS3A01G128800 chr6D 380495593 380496299 706 False 313.000000 313 75.436000 1091 1820 1 chr6D.!!$F2 729
11 TraesCS3A01G128800 chr7D 486107298 486107922 624 True 300.000000 300 75.970000 1093 1758 1 chr7D.!!$R1 665
12 TraesCS3A01G128800 chr7B 513770739 513771552 813 True 294.000000 294 73.933000 1093 1952 1 chr7B.!!$R1 859

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
963 997 0.116342 TCTTACTCCTCCACCAGCCA 59.884 55.0 0.00 0.00 0.00 4.75 F
964 998 0.250513 CTTACTCCTCCACCAGCCAC 59.749 60.0 0.00 0.00 0.00 5.01 F
1089 1130 0.257039 GCCATCACCAGAATCAGGGT 59.743 55.0 0.00 0.00 38.10 4.34 F
2320 2472 0.756294 TTCCTTCAGTCAGCCGTTCA 59.244 50.0 0.00 0.00 0.00 3.18 F
2823 2985 2.027192 GCACTCCTTCAGGTACCATGAA 60.027 50.0 15.94 18.14 35.45 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 2397 0.107263 TGTGCAGCCTGTCAACTTCA 60.107 50.000 0.00 0.00 0.00 3.02 R
2284 2436 0.321919 GAATGTGCAGTGCAGGAGGA 60.322 55.000 20.42 0.30 40.08 3.71 R
3069 3231 1.547675 GGGTTGAATTGGCAGAGGTGA 60.548 52.381 0.00 0.00 0.00 4.02 R
3139 3301 0.035458 AGCAGCACAGTGGACCTAAC 59.965 55.000 1.84 0.00 0.00 2.34 R
3683 3970 0.102120 ACTCGCTCAGCTGCAGATAC 59.898 55.000 20.43 3.05 0.00 2.24 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
72 74 8.006298 TGGACACTTTTCAAATTACATGAACT 57.994 30.769 0.00 0.00 36.57 3.01
87 89 8.746922 TTACATGAACTTTCTTGAATGATTGC 57.253 30.769 0.00 0.00 36.27 3.56
92 94 4.874970 ACTTTCTTGAATGATTGCACCAC 58.125 39.130 0.00 0.00 0.00 4.16
94 96 2.170166 TCTTGAATGATTGCACCACCC 58.830 47.619 0.00 0.00 0.00 4.61
101 103 5.070981 TGAATGATTGCACCACCCTTTTAAA 59.929 36.000 0.00 0.00 0.00 1.52
105 107 5.540337 TGATTGCACCACCCTTTTAAATACA 59.460 36.000 0.00 0.00 0.00 2.29
210 215 9.296400 CTACATACAATTTTTAAAATGGTCCGG 57.704 33.333 13.10 0.00 0.00 5.14
223 228 1.565067 GGTCCGGACCCTTTCTCTAA 58.435 55.000 39.24 0.00 45.68 2.10
234 239 7.041780 CGGACCCTTTCTCTAATTACATGAATG 60.042 40.741 0.00 0.00 0.00 2.67
235 240 7.775561 GGACCCTTTCTCTAATTACATGAATGT 59.224 37.037 0.00 0.95 44.48 2.71
236 241 9.832445 GACCCTTTCTCTAATTACATGAATGTA 57.168 33.333 0.00 0.00 41.97 2.29
694 716 9.803315 TTTGTAATTGCATAAACACTTTGTACA 57.197 25.926 0.00 0.00 0.00 2.90
696 718 9.973450 TGTAATTGCATAAACACTTTGTACATT 57.027 25.926 0.00 0.00 0.00 2.71
776 810 3.426525 GCTCGGCAAGAACATTCTTTTTG 59.573 43.478 4.08 0.00 44.70 2.44
782 816 7.708752 TCGGCAAGAACATTCTTTTTGTAAAAT 59.291 29.630 4.08 0.00 44.70 1.82
783 817 7.793427 CGGCAAGAACATTCTTTTTGTAAAATG 59.207 33.333 4.08 0.00 44.70 2.32
784 818 8.825745 GGCAAGAACATTCTTTTTGTAAAATGA 58.174 29.630 4.08 2.63 44.70 2.57
785 819 9.636965 GCAAGAACATTCTTTTTGTAAAATGAC 57.363 29.630 4.08 0.00 44.70 3.06
786 820 9.833894 CAAGAACATTCTTTTTGTAAAATGACG 57.166 29.630 4.08 3.86 44.70 4.35
787 821 8.574196 AGAACATTCTTTTTGTAAAATGACGG 57.426 30.769 5.49 4.40 33.50 4.79
788 822 6.763303 ACATTCTTTTTGTAAAATGACGGC 57.237 33.333 5.49 0.00 33.50 5.68
789 823 6.276847 ACATTCTTTTTGTAAAATGACGGCA 58.723 32.000 0.00 0.00 33.50 5.69
790 824 6.758886 ACATTCTTTTTGTAAAATGACGGCAA 59.241 30.769 0.00 0.00 33.50 4.52
791 825 6.820470 TTCTTTTTGTAAAATGACGGCAAG 57.180 33.333 0.00 0.00 33.50 4.01
792 826 6.137794 TCTTTTTGTAAAATGACGGCAAGA 57.862 33.333 0.00 0.00 30.17 3.02
793 827 6.565234 TCTTTTTGTAAAATGACGGCAAGAA 58.435 32.000 0.00 0.00 30.17 2.52
794 828 6.474102 TCTTTTTGTAAAATGACGGCAAGAAC 59.526 34.615 0.00 0.00 30.17 3.01
795 829 4.902443 TTGTAAAATGACGGCAAGAACA 57.098 36.364 0.00 0.00 0.00 3.18
796 830 5.446143 TTGTAAAATGACGGCAAGAACAT 57.554 34.783 0.00 0.00 0.00 2.71
797 831 5.446143 TGTAAAATGACGGCAAGAACATT 57.554 34.783 0.00 0.00 34.29 2.71
798 832 5.837437 TGTAAAATGACGGCAAGAACATTT 58.163 33.333 0.00 0.00 39.62 2.32
805 839 4.083324 TGACGGCAAGAACATTTCATCTTC 60.083 41.667 0.00 0.00 33.73 2.87
810 844 6.129009 CGGCAAGAACATTTCATCTTCTTTTG 60.129 38.462 0.00 0.00 32.96 2.44
815 849 8.585189 AGAACATTTCATCTTCTTTTGCTTTC 57.415 30.769 0.00 0.00 0.00 2.62
816 850 8.419442 AGAACATTTCATCTTCTTTTGCTTTCT 58.581 29.630 0.00 0.00 0.00 2.52
817 851 8.953368 AACATTTCATCTTCTTTTGCTTTCTT 57.047 26.923 0.00 0.00 0.00 2.52
818 852 8.953368 ACATTTCATCTTCTTTTGCTTTCTTT 57.047 26.923 0.00 0.00 0.00 2.52
819 853 9.387257 ACATTTCATCTTCTTTTGCTTTCTTTT 57.613 25.926 0.00 0.00 0.00 2.27
837 871 1.995376 TTTTTGAGGGGGTCTTCTGC 58.005 50.000 0.00 0.00 0.00 4.26
838 872 1.149101 TTTTGAGGGGGTCTTCTGCT 58.851 50.000 0.00 0.00 0.00 4.24
839 873 1.149101 TTTGAGGGGGTCTTCTGCTT 58.851 50.000 0.00 0.00 0.00 3.91
840 874 1.149101 TTGAGGGGGTCTTCTGCTTT 58.851 50.000 0.00 0.00 0.00 3.51
841 875 1.149101 TGAGGGGGTCTTCTGCTTTT 58.851 50.000 0.00 0.00 0.00 2.27
842 876 1.499007 TGAGGGGGTCTTCTGCTTTTT 59.501 47.619 0.00 0.00 0.00 1.94
894 928 3.434319 CGGCCACGAATGCAGCTT 61.434 61.111 2.24 0.00 44.60 3.74
962 996 1.276622 TTCTTACTCCTCCACCAGCC 58.723 55.000 0.00 0.00 0.00 4.85
963 997 0.116342 TCTTACTCCTCCACCAGCCA 59.884 55.000 0.00 0.00 0.00 4.75
964 998 0.250513 CTTACTCCTCCACCAGCCAC 59.749 60.000 0.00 0.00 0.00 5.01
965 999 1.198759 TTACTCCTCCACCAGCCACC 61.199 60.000 0.00 0.00 0.00 4.61
966 1000 2.106923 TACTCCTCCACCAGCCACCT 62.107 60.000 0.00 0.00 0.00 4.00
968 1002 3.721706 CCTCCACCAGCCACCTCC 61.722 72.222 0.00 0.00 0.00 4.30
969 1003 2.930019 CTCCACCAGCCACCTCCA 60.930 66.667 0.00 0.00 0.00 3.86
971 1005 3.569210 CCACCAGCCACCTCCACA 61.569 66.667 0.00 0.00 0.00 4.17
972 1006 2.281761 CACCAGCCACCTCCACAC 60.282 66.667 0.00 0.00 0.00 3.82
973 1007 3.570212 ACCAGCCACCTCCACACC 61.570 66.667 0.00 0.00 0.00 4.16
974 1008 4.704833 CCAGCCACCTCCACACCG 62.705 72.222 0.00 0.00 0.00 4.94
975 1009 4.704833 CAGCCACCTCCACACCGG 62.705 72.222 0.00 0.00 0.00 5.28
1069 1110 3.323286 TGGTTCCCCGGCATCGAA 61.323 61.111 0.00 0.00 39.00 3.71
1081 1122 0.462581 GCATCGAAGCCATCACCAGA 60.463 55.000 0.00 0.00 0.00 3.86
1089 1130 0.257039 GCCATCACCAGAATCAGGGT 59.743 55.000 0.00 0.00 38.10 4.34
1608 1683 1.004918 CACACCTCCGGGAACTCAC 60.005 63.158 0.00 0.00 36.25 3.51
1837 1936 9.142788 ATTCTGTGGAAAACCATTGATGGTGAG 62.143 40.741 15.96 4.95 45.81 3.51
1843 1942 2.401583 CCATTGATGGTGAGGACGAA 57.598 50.000 1.73 0.00 43.05 3.85
2284 2436 3.695060 ACATCGAGGTGACTTCTTCGTAT 59.305 43.478 0.00 0.00 44.43 3.06
2320 2472 0.756294 TTCCTTCAGTCAGCCGTTCA 59.244 50.000 0.00 0.00 0.00 3.18
2331 2483 4.058124 GTCAGCCGTTCAGCATTCATATA 58.942 43.478 0.00 0.00 34.23 0.86
2371 2528 6.213600 ACTGAGGTGATTAAACTACTGTCCAT 59.786 38.462 0.00 0.00 0.00 3.41
2511 2673 2.697431 TGAATTCCGCGGAAAACAAG 57.303 45.000 41.31 6.53 37.69 3.16
2823 2985 2.027192 GCACTCCTTCAGGTACCATGAA 60.027 50.000 15.94 18.14 35.45 2.57
2887 3049 3.882288 TGACATGTTATGCACTGTGTGTT 59.118 39.130 9.86 0.00 35.75 3.32
2903 3065 5.941733 TGTGTGTTATCAACATTGATCTGC 58.058 37.500 10.34 3.85 44.17 4.26
2953 3115 7.161404 ACATGCAGTTAGTTACATCTTGAGAA 58.839 34.615 0.00 0.00 0.00 2.87
3024 3186 4.572985 TTTTCTGTTTCATCCAGCACTG 57.427 40.909 0.00 0.00 0.00 3.66
3069 3231 6.165700 TGCAGATATCATATATGTGCCGAT 57.834 37.500 20.08 6.10 41.69 4.18
3139 3301 2.108776 TGAATTAGCCCCTGGATCATGG 59.891 50.000 0.00 0.00 0.00 3.66
3147 3309 1.421646 CCCTGGATCATGGTTAGGTCC 59.578 57.143 8.81 0.00 0.00 4.46
3148 3310 2.126882 CCTGGATCATGGTTAGGTCCA 58.873 52.381 0.00 0.00 42.01 4.02
3152 3314 2.505819 GGATCATGGTTAGGTCCACTGT 59.494 50.000 0.00 0.00 40.51 3.55
3190 3352 7.286775 AGTTTTAGTTTTCTTGGTTGCTCCATA 59.713 33.333 2.36 0.00 46.60 2.74
3259 3544 7.444299 AGCAAAACTATCATGGATGTTTGTTT 58.556 30.769 10.09 5.13 37.18 2.83
3260 3545 8.584157 AGCAAAACTATCATGGATGTTTGTTTA 58.416 29.630 10.09 0.00 35.76 2.01
3279 3564 7.977789 TGTTTAAGCTTATTCTGTGTGATCA 57.022 32.000 7.08 0.00 0.00 2.92
3299 3584 1.627297 GGAGGACTTGATCGGGGCTT 61.627 60.000 0.00 0.00 0.00 4.35
3314 3599 1.137675 GGGCTTGTTAGGGTAGGTACG 59.862 57.143 0.00 0.00 0.00 3.67
3347 3633 2.490991 TGATGTGCTGATGATGCTAGC 58.509 47.619 8.10 8.10 37.93 3.42
3386 3672 6.426328 AGCATATATTCGCCTCAGAAAAGAAG 59.574 38.462 0.00 0.00 33.43 2.85
3387 3673 6.203723 GCATATATTCGCCTCAGAAAAGAAGT 59.796 38.462 0.00 0.00 33.43 3.01
3406 3692 4.008074 AGTTGCAGCAGTACATAACACT 57.992 40.909 2.55 0.00 0.00 3.55
3409 3695 3.738982 TGCAGCAGTACATAACACTTGT 58.261 40.909 0.00 0.00 0.00 3.16
3412 3698 5.168569 GCAGCAGTACATAACACTTGTCTA 58.831 41.667 0.00 0.00 0.00 2.59
3421 3707 6.456501 ACATAACACTTGTCTAGACCTTGAC 58.543 40.000 20.11 4.97 36.20 3.18
3429 3715 3.181422 TGTCTAGACCTTGACCTTGAGGA 60.181 47.826 20.11 0.00 38.94 3.71
3434 3720 2.040412 GACCTTGACCTTGAGGACCATT 59.960 50.000 3.59 0.00 38.94 3.16
3438 3724 4.401925 CTTGACCTTGAGGACCATTTTCT 58.598 43.478 3.59 0.00 38.94 2.52
3476 3763 2.187946 GGGAGATGCCTGTGACGG 59.812 66.667 0.00 0.00 36.66 4.79
3481 3768 1.409064 GAGATGCCTGTGACGGTCATA 59.591 52.381 14.78 10.85 0.00 2.15
3512 3799 9.973246 CACTCAATAAATTACACACATCAGTAC 57.027 33.333 0.00 0.00 0.00 2.73
3516 3803 9.973246 CAATAAATTACACACATCAGTACTGTC 57.027 33.333 21.99 0.00 0.00 3.51
3520 3807 4.415881 ACACACATCAGTACTGTCCAAA 57.584 40.909 21.99 3.12 0.00 3.28
3522 3809 5.376625 ACACACATCAGTACTGTCCAAATT 58.623 37.500 21.99 1.55 0.00 1.82
3523 3810 5.827797 ACACACATCAGTACTGTCCAAATTT 59.172 36.000 21.99 0.00 0.00 1.82
3524 3811 6.321181 ACACACATCAGTACTGTCCAAATTTT 59.679 34.615 21.99 0.00 0.00 1.82
3525 3812 7.147915 ACACACATCAGTACTGTCCAAATTTTT 60.148 33.333 21.99 0.00 0.00 1.94
3526 3813 7.167968 CACACATCAGTACTGTCCAAATTTTTG 59.832 37.037 21.99 7.58 37.90 2.44
3527 3814 7.147915 ACACATCAGTACTGTCCAAATTTTTGT 60.148 33.333 21.99 8.11 36.45 2.83
3528 3815 7.706179 CACATCAGTACTGTCCAAATTTTTGTT 59.294 33.333 21.99 0.00 36.45 2.83
3529 3816 7.706179 ACATCAGTACTGTCCAAATTTTTGTTG 59.294 33.333 21.99 1.81 36.45 3.33
3530 3817 7.397892 TCAGTACTGTCCAAATTTTTGTTGA 57.602 32.000 21.99 0.00 36.45 3.18
3531 3818 7.831753 TCAGTACTGTCCAAATTTTTGTTGAA 58.168 30.769 21.99 0.00 36.45 2.69
3532 3819 7.757624 TCAGTACTGTCCAAATTTTTGTTGAAC 59.242 33.333 21.99 0.00 36.45 3.18
3533 3820 7.543868 CAGTACTGTCCAAATTTTTGTTGAACA 59.456 33.333 15.06 0.00 36.45 3.18
3534 3821 8.091449 AGTACTGTCCAAATTTTTGTTGAACAA 58.909 29.630 6.66 6.66 36.11 2.83
3535 3822 7.920160 ACTGTCCAAATTTTTGTTGAACAAT 57.080 28.000 11.97 0.00 38.00 2.71
3536 3823 7.973601 ACTGTCCAAATTTTTGTTGAACAATC 58.026 30.769 11.97 0.00 38.00 2.67
3537 3824 7.605691 ACTGTCCAAATTTTTGTTGAACAATCA 59.394 29.630 11.97 1.94 38.00 2.57
3538 3825 7.746929 TGTCCAAATTTTTGTTGAACAATCAC 58.253 30.769 11.97 1.50 38.00 3.06
3539 3826 7.148340 TGTCCAAATTTTTGTTGAACAATCACC 60.148 33.333 11.97 0.00 38.00 4.02
3540 3827 6.036517 TCCAAATTTTTGTTGAACAATCACCG 59.963 34.615 11.97 0.00 38.00 4.94
3541 3828 5.982465 AATTTTTGTTGAACAATCACCGG 57.018 34.783 11.97 0.00 38.00 5.28
3542 3829 3.444703 TTTTGTTGAACAATCACCGGG 57.555 42.857 11.97 0.00 38.00 5.73
3543 3830 1.323412 TTGTTGAACAATCACCGGGG 58.677 50.000 6.66 0.00 32.34 5.73
3544 3831 0.538516 TGTTGAACAATCACCGGGGG 60.539 55.000 2.42 0.00 34.61 5.40
3566 3853 4.484872 GGGGGAGGCCTGCGTTAC 62.485 72.222 19.04 8.19 0.00 2.50
3567 3854 3.712907 GGGGAGGCCTGCGTTACA 61.713 66.667 19.04 0.00 0.00 2.41
3568 3855 2.590092 GGGAGGCCTGCGTTACAT 59.410 61.111 19.04 0.00 0.00 2.29
3569 3856 1.523938 GGGAGGCCTGCGTTACATC 60.524 63.158 19.04 0.00 0.00 3.06
3570 3857 1.220749 GGAGGCCTGCGTTACATCA 59.779 57.895 12.00 0.00 0.00 3.07
3571 3858 0.811616 GGAGGCCTGCGTTACATCAG 60.812 60.000 12.00 0.00 0.00 2.90
3572 3859 0.175760 GAGGCCTGCGTTACATCAGA 59.824 55.000 12.00 0.00 32.26 3.27
3573 3860 0.176680 AGGCCTGCGTTACATCAGAG 59.823 55.000 3.11 0.00 32.26 3.35
3574 3861 0.175760 GGCCTGCGTTACATCAGAGA 59.824 55.000 0.00 0.00 32.26 3.10
3575 3862 1.565305 GCCTGCGTTACATCAGAGAG 58.435 55.000 3.70 0.00 32.26 3.20
3576 3863 1.134965 GCCTGCGTTACATCAGAGAGT 60.135 52.381 3.70 0.00 32.26 3.24
3577 3864 2.099263 GCCTGCGTTACATCAGAGAGTA 59.901 50.000 3.70 0.00 32.26 2.59
3578 3865 3.696898 CCTGCGTTACATCAGAGAGTAC 58.303 50.000 3.70 0.00 32.26 2.73
3579 3866 3.128764 CCTGCGTTACATCAGAGAGTACA 59.871 47.826 0.00 0.00 32.26 2.90
3580 3867 4.380550 CCTGCGTTACATCAGAGAGTACAA 60.381 45.833 0.00 0.00 32.26 2.41
3581 3868 5.324784 TGCGTTACATCAGAGAGTACAAT 57.675 39.130 0.00 0.00 0.00 2.71
3582 3869 5.102313 TGCGTTACATCAGAGAGTACAATG 58.898 41.667 0.00 0.00 0.00 2.82
3583 3870 5.105917 TGCGTTACATCAGAGAGTACAATGA 60.106 40.000 0.00 0.00 0.00 2.57
3584 3871 5.457148 GCGTTACATCAGAGAGTACAATGAG 59.543 44.000 0.00 0.00 0.00 2.90
3585 3872 6.678164 GCGTTACATCAGAGAGTACAATGAGA 60.678 42.308 0.00 0.00 0.00 3.27
3586 3873 6.909895 CGTTACATCAGAGAGTACAATGAGAG 59.090 42.308 0.00 0.00 0.00 3.20
3587 3874 5.850557 ACATCAGAGAGTACAATGAGAGG 57.149 43.478 0.00 0.00 0.00 3.69
3588 3875 5.514169 ACATCAGAGAGTACAATGAGAGGA 58.486 41.667 0.00 0.00 0.00 3.71
3589 3876 5.593909 ACATCAGAGAGTACAATGAGAGGAG 59.406 44.000 0.00 0.00 0.00 3.69
3590 3877 5.443230 TCAGAGAGTACAATGAGAGGAGA 57.557 43.478 0.00 0.00 0.00 3.71
3591 3878 5.436175 TCAGAGAGTACAATGAGAGGAGAG 58.564 45.833 0.00 0.00 0.00 3.20
3592 3879 4.580167 CAGAGAGTACAATGAGAGGAGAGG 59.420 50.000 0.00 0.00 0.00 3.69
3593 3880 4.476846 AGAGAGTACAATGAGAGGAGAGGA 59.523 45.833 0.00 0.00 0.00 3.71
3594 3881 5.044476 AGAGAGTACAATGAGAGGAGAGGAA 60.044 44.000 0.00 0.00 0.00 3.36
3595 3882 5.776358 AGAGTACAATGAGAGGAGAGGAAT 58.224 41.667 0.00 0.00 0.00 3.01
3596 3883 6.916909 AGAGTACAATGAGAGGAGAGGAATA 58.083 40.000 0.00 0.00 0.00 1.75
3597 3884 7.004086 AGAGTACAATGAGAGGAGAGGAATAG 58.996 42.308 0.00 0.00 0.00 1.73
3598 3885 6.074648 AGTACAATGAGAGGAGAGGAATAGG 58.925 44.000 0.00 0.00 0.00 2.57
3599 3886 4.889780 ACAATGAGAGGAGAGGAATAGGT 58.110 43.478 0.00 0.00 0.00 3.08
3600 3887 4.653341 ACAATGAGAGGAGAGGAATAGGTG 59.347 45.833 0.00 0.00 0.00 4.00
3601 3888 2.672098 TGAGAGGAGAGGAATAGGTGC 58.328 52.381 0.00 0.00 0.00 5.01
3602 3889 1.967779 GAGAGGAGAGGAATAGGTGCC 59.032 57.143 0.00 0.00 0.00 5.01
3603 3890 1.292242 AGAGGAGAGGAATAGGTGCCA 59.708 52.381 0.00 0.00 0.00 4.92
3604 3891 2.119495 GAGGAGAGGAATAGGTGCCAA 58.881 52.381 0.00 0.00 0.00 4.52
3605 3892 2.103941 GAGGAGAGGAATAGGTGCCAAG 59.896 54.545 0.00 0.00 0.00 3.61
3606 3893 2.119495 GGAGAGGAATAGGTGCCAAGA 58.881 52.381 0.00 0.00 0.00 3.02
3607 3894 2.158885 GGAGAGGAATAGGTGCCAAGAC 60.159 54.545 0.00 0.00 0.00 3.01
3608 3895 2.501723 GAGAGGAATAGGTGCCAAGACA 59.498 50.000 0.00 0.00 0.00 3.41
3609 3896 3.118531 AGAGGAATAGGTGCCAAGACAT 58.881 45.455 0.00 0.00 0.00 3.06
3610 3897 3.118112 AGAGGAATAGGTGCCAAGACATG 60.118 47.826 0.00 0.00 0.00 3.21
3618 3905 3.499737 CCAAGACATGGCGGCGTC 61.500 66.667 3.62 3.62 43.80 5.19
3619 3906 3.499737 CAAGACATGGCGGCGTCC 61.500 66.667 9.84 11.43 32.33 4.79
3620 3907 4.778143 AAGACATGGCGGCGTCCC 62.778 66.667 9.84 2.09 32.33 4.46
3622 3909 3.845259 GACATGGCGGCGTCCCTA 61.845 66.667 9.84 0.00 0.00 3.53
3623 3910 4.157120 ACATGGCGGCGTCCCTAC 62.157 66.667 9.84 0.00 0.00 3.18
3624 3911 3.849951 CATGGCGGCGTCCCTACT 61.850 66.667 9.84 0.00 0.00 2.57
3625 3912 2.123597 ATGGCGGCGTCCCTACTA 60.124 61.111 9.84 0.00 0.00 1.82
3626 3913 1.759299 ATGGCGGCGTCCCTACTAA 60.759 57.895 9.84 0.00 0.00 2.24
3627 3914 2.024590 ATGGCGGCGTCCCTACTAAC 62.025 60.000 9.84 0.00 0.00 2.34
3628 3915 2.713967 GGCGGCGTCCCTACTAACA 61.714 63.158 9.37 0.00 0.00 2.41
3629 3916 1.226888 GCGGCGTCCCTACTAACAG 60.227 63.158 9.37 0.00 0.00 3.16
3630 3917 1.436336 CGGCGTCCCTACTAACAGG 59.564 63.158 0.00 0.00 35.26 4.00
3641 3928 4.576879 CCTACTAACAGGGTCTTTGAACC 58.423 47.826 0.00 0.00 40.27 3.62
3651 3938 4.828829 GGGTCTTTGAACCTAAAGATCGA 58.171 43.478 4.49 0.00 44.80 3.59
3652 3939 5.243207 GGGTCTTTGAACCTAAAGATCGAA 58.757 41.667 4.49 0.00 44.80 3.71
3653 3940 5.704053 GGGTCTTTGAACCTAAAGATCGAAA 59.296 40.000 4.49 0.00 44.80 3.46
3654 3941 6.128254 GGGTCTTTGAACCTAAAGATCGAAAG 60.128 42.308 4.49 0.00 44.80 2.62
3655 3942 6.307915 GTCTTTGAACCTAAAGATCGAAAGC 58.692 40.000 4.49 0.00 45.40 3.51
3656 3943 5.995282 TCTTTGAACCTAAAGATCGAAAGCA 59.005 36.000 0.00 0.00 40.66 3.91
3657 3944 6.655003 TCTTTGAACCTAAAGATCGAAAGCAT 59.345 34.615 0.00 0.00 40.66 3.79
3658 3945 5.801350 TGAACCTAAAGATCGAAAGCATG 57.199 39.130 0.00 0.00 0.00 4.06
3659 3946 5.487433 TGAACCTAAAGATCGAAAGCATGA 58.513 37.500 0.00 0.00 0.00 3.07
3660 3947 5.937540 TGAACCTAAAGATCGAAAGCATGAA 59.062 36.000 0.00 0.00 0.00 2.57
3661 3948 6.429692 TGAACCTAAAGATCGAAAGCATGAAA 59.570 34.615 0.00 0.00 0.00 2.69
3662 3949 7.121168 TGAACCTAAAGATCGAAAGCATGAAAT 59.879 33.333 0.00 0.00 0.00 2.17
3663 3950 7.020914 ACCTAAAGATCGAAAGCATGAAATC 57.979 36.000 0.00 0.00 0.00 2.17
3664 3951 6.599244 ACCTAAAGATCGAAAGCATGAAATCA 59.401 34.615 0.00 0.00 0.00 2.57
3665 3952 7.130917 CCTAAAGATCGAAAGCATGAAATCAG 58.869 38.462 0.00 0.00 0.00 2.90
3666 3953 6.748333 AAAGATCGAAAGCATGAAATCAGA 57.252 33.333 0.00 0.00 0.00 3.27
3667 3954 5.987777 AGATCGAAAGCATGAAATCAGAG 57.012 39.130 0.00 0.00 0.00 3.35
3668 3955 5.668471 AGATCGAAAGCATGAAATCAGAGA 58.332 37.500 0.00 0.00 0.00 3.10
3669 3956 6.289834 AGATCGAAAGCATGAAATCAGAGAT 58.710 36.000 0.00 0.00 0.00 2.75
3670 3957 6.766944 AGATCGAAAGCATGAAATCAGAGATT 59.233 34.615 0.00 0.00 0.00 2.40
3671 3958 7.930325 AGATCGAAAGCATGAAATCAGAGATTA 59.070 33.333 0.00 0.00 0.00 1.75
3672 3959 7.239166 TCGAAAGCATGAAATCAGAGATTAC 57.761 36.000 0.00 0.00 0.00 1.89
3673 3960 6.818142 TCGAAAGCATGAAATCAGAGATTACA 59.182 34.615 0.00 0.00 0.00 2.41
3674 3961 7.496920 TCGAAAGCATGAAATCAGAGATTACAT 59.503 33.333 0.00 0.00 0.00 2.29
3675 3962 8.127327 CGAAAGCATGAAATCAGAGATTACATT 58.873 33.333 0.00 0.00 0.00 2.71
3676 3963 9.448294 GAAAGCATGAAATCAGAGATTACATTC 57.552 33.333 0.00 0.00 0.00 2.67
3677 3964 8.749026 AAGCATGAAATCAGAGATTACATTCT 57.251 30.769 0.00 0.00 0.00 2.40
3678 3965 8.155821 AGCATGAAATCAGAGATTACATTCTG 57.844 34.615 0.00 0.00 41.67 3.02
3679 3966 7.774157 AGCATGAAATCAGAGATTACATTCTGT 59.226 33.333 0.00 0.00 41.21 3.41
3680 3967 9.049523 GCATGAAATCAGAGATTACATTCTGTA 57.950 33.333 0.00 0.00 41.21 2.74
3683 3970 9.605275 TGAAATCAGAGATTACATTCTGTAAGG 57.395 33.333 5.99 0.00 44.89 2.69
3684 3971 9.606631 GAAATCAGAGATTACATTCTGTAAGGT 57.393 33.333 5.99 0.00 44.89 3.50
3688 3975 9.647918 TCAGAGATTACATTCTGTAAGGTATCT 57.352 33.333 5.99 3.97 44.89 1.98
3689 3976 9.689976 CAGAGATTACATTCTGTAAGGTATCTG 57.310 37.037 9.23 9.23 44.89 2.90
3690 3977 8.364142 AGAGATTACATTCTGTAAGGTATCTGC 58.636 37.037 5.99 0.00 44.89 4.26
3691 3978 8.023021 AGATTACATTCTGTAAGGTATCTGCA 57.977 34.615 5.99 0.00 44.89 4.41
3692 3979 8.147058 AGATTACATTCTGTAAGGTATCTGCAG 58.853 37.037 7.63 7.63 44.89 4.41
3693 3980 4.446371 ACATTCTGTAAGGTATCTGCAGC 58.554 43.478 9.47 0.00 31.34 5.25
3694 3981 4.163078 ACATTCTGTAAGGTATCTGCAGCT 59.837 41.667 9.47 0.82 31.34 4.24
3695 3982 3.808466 TCTGTAAGGTATCTGCAGCTG 57.192 47.619 10.11 10.11 31.34 4.24
3696 3983 3.365472 TCTGTAAGGTATCTGCAGCTGA 58.635 45.455 20.43 4.21 31.34 4.26
3697 3984 3.382865 TCTGTAAGGTATCTGCAGCTGAG 59.617 47.826 20.43 12.20 31.34 3.35
3698 3985 2.159043 TGTAAGGTATCTGCAGCTGAGC 60.159 50.000 20.43 5.58 0.00 4.26
3699 3986 0.179089 AAGGTATCTGCAGCTGAGCG 60.179 55.000 20.43 4.31 37.31 5.03
3700 3987 1.039785 AGGTATCTGCAGCTGAGCGA 61.040 55.000 20.43 10.22 37.31 4.93
3701 3988 0.597118 GGTATCTGCAGCTGAGCGAG 60.597 60.000 20.43 7.02 37.31 5.03
3702 3989 0.102120 GTATCTGCAGCTGAGCGAGT 59.898 55.000 20.43 0.00 37.31 4.18
3703 3990 0.383590 TATCTGCAGCTGAGCGAGTC 59.616 55.000 20.43 0.00 37.31 3.36
3704 3991 2.610700 ATCTGCAGCTGAGCGAGTCG 62.611 60.000 20.43 8.54 37.31 4.18
3718 4005 3.040990 CGAGTCGCAGTAGTGTTCTAG 57.959 52.381 0.00 0.00 0.00 2.43
3721 4008 4.613167 CGAGTCGCAGTAGTGTTCTAGTTT 60.613 45.833 0.00 0.00 0.00 2.66
3808 4095 4.030452 GTGTGCAGCCACGCCTTC 62.030 66.667 0.00 0.00 44.65 3.46
3836 4123 5.568423 GCATCCTAATCCTCACCAGTATCTG 60.568 48.000 0.00 0.00 0.00 2.90
3874 4161 2.241281 TCGTCTGACCCTTATCCCAA 57.759 50.000 1.55 0.00 0.00 4.12
3875 4162 1.829222 TCGTCTGACCCTTATCCCAAC 59.171 52.381 1.55 0.00 0.00 3.77
3897 4185 3.775261 ATTTGCTGCATTTTCCAACCT 57.225 38.095 1.84 0.00 0.00 3.50
3912 4200 1.338973 CAACCTGTGGATATGCATGCC 59.661 52.381 16.68 11.38 0.00 4.40
3920 4208 2.827322 TGGATATGCATGCCATTTAGCC 59.173 45.455 16.68 13.72 35.34 3.93
3922 4210 3.119245 GGATATGCATGCCATTTAGCCTG 60.119 47.826 16.68 0.00 35.34 4.85
3923 4211 1.784358 ATGCATGCCATTTAGCCTGT 58.216 45.000 16.68 0.00 31.74 4.00
3924 4212 0.818938 TGCATGCCATTTAGCCTGTG 59.181 50.000 16.68 0.00 31.74 3.66
3932 4220 4.141413 TGCCATTTAGCCTGTGACATATCT 60.141 41.667 0.00 0.00 0.00 1.98
3939 4227 7.603180 TTAGCCTGTGACATATCTATCACTT 57.397 36.000 10.93 1.15 44.59 3.16
3946 4234 5.698545 GTGACATATCTATCACTTTCCTGCC 59.301 44.000 0.00 0.00 41.69 4.85
3951 4239 1.566231 CTATCACTTTCCTGCCCCCTT 59.434 52.381 0.00 0.00 0.00 3.95
3986 4274 5.694995 CACATCCATAAAACCCACCTAGAT 58.305 41.667 0.00 0.00 0.00 1.98
4047 4335 1.739562 GGCTGCAGAGGTCTTCACG 60.740 63.158 20.43 0.00 0.00 4.35
4108 4396 1.000385 GAGAGGCTCATGTCGGATGAG 60.000 57.143 18.26 16.69 46.12 2.90
4126 4414 1.227380 GCATAGCCAGTGGACCTCG 60.227 63.158 15.20 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 49 8.006298 AGTTCATGTAATTTGAAAAGTGTCCA 57.994 30.769 0.00 0.00 35.03 4.02
72 74 3.006752 GGGTGGTGCAATCATTCAAGAAA 59.993 43.478 0.00 0.00 0.00 2.52
78 80 3.683365 AAAAGGGTGGTGCAATCATTC 57.317 42.857 0.00 0.00 0.00 2.67
86 88 5.652994 TCATGTATTTAAAAGGGTGGTGC 57.347 39.130 0.00 0.00 0.00 5.01
154 158 8.449251 AAAAATCAAGGCATTAAAAAGAAGCA 57.551 26.923 0.00 0.00 0.00 3.91
184 189 9.296400 CCGGACCATTTTAAAAATTGTATGTAG 57.704 33.333 4.44 0.00 0.00 2.74
205 210 3.908643 AATTAGAGAAAGGGTCCGGAC 57.091 47.619 27.04 27.04 0.00 4.79
210 215 8.738645 ACATTCATGTAATTAGAGAAAGGGTC 57.261 34.615 0.00 0.00 39.68 4.46
332 338 7.595819 AGTGTTCCAACCATTTAAGAAATCA 57.404 32.000 0.00 0.00 0.00 2.57
529 541 9.603921 AGAACTGTTTGATGAATTTCAAAATGT 57.396 25.926 2.68 6.46 44.71 2.71
725 747 8.831550 GCTGGGTTTCATGTAATTTTAAAACAA 58.168 29.630 1.97 0.00 0.00 2.83
726 748 7.987458 TGCTGGGTTTCATGTAATTTTAAAACA 59.013 29.630 1.97 0.00 0.00 2.83
727 749 8.371770 TGCTGGGTTTCATGTAATTTTAAAAC 57.628 30.769 1.97 0.00 0.00 2.43
747 781 2.042259 TTCTTGCCGAGCATGCTGG 61.042 57.895 28.27 24.57 38.76 4.85
776 810 5.918011 TGAAATGTTCTTGCCGTCATTTTAC 59.082 36.000 0.00 0.00 39.52 2.01
782 816 3.411446 AGATGAAATGTTCTTGCCGTCA 58.589 40.909 0.00 0.00 0.00 4.35
783 817 4.406943 GAAGATGAAATGTTCTTGCCGTC 58.593 43.478 0.00 0.00 42.78 4.79
784 818 4.425577 GAAGATGAAATGTTCTTGCCGT 57.574 40.909 0.00 0.00 42.78 5.68
791 825 8.585189 AGAAAGCAAAAGAAGATGAAATGTTC 57.415 30.769 0.00 0.00 46.11 3.18
792 826 8.953368 AAGAAAGCAAAAGAAGATGAAATGTT 57.047 26.923 0.00 0.00 29.44 2.71
793 827 8.953368 AAAGAAAGCAAAAGAAGATGAAATGT 57.047 26.923 0.00 0.00 0.00 2.71
818 852 1.499007 AGCAGAAGACCCCCTCAAAAA 59.501 47.619 0.00 0.00 0.00 1.94
819 853 1.149101 AGCAGAAGACCCCCTCAAAA 58.851 50.000 0.00 0.00 0.00 2.44
820 854 1.149101 AAGCAGAAGACCCCCTCAAA 58.851 50.000 0.00 0.00 0.00 2.69
821 855 1.149101 AAAGCAGAAGACCCCCTCAA 58.851 50.000 0.00 0.00 0.00 3.02
822 856 1.149101 AAAAGCAGAAGACCCCCTCA 58.851 50.000 0.00 0.00 0.00 3.86
823 857 2.294449 AAAAAGCAGAAGACCCCCTC 57.706 50.000 0.00 0.00 0.00 4.30
841 875 6.061441 TGGAGTGTTCTTGCTCATCTAAAAA 58.939 36.000 0.00 0.00 33.66 1.94
842 876 5.620206 TGGAGTGTTCTTGCTCATCTAAAA 58.380 37.500 0.00 0.00 33.66 1.52
843 877 5.227569 TGGAGTGTTCTTGCTCATCTAAA 57.772 39.130 0.00 0.00 33.66 1.85
844 878 4.890158 TGGAGTGTTCTTGCTCATCTAA 57.110 40.909 0.00 0.00 33.66 2.10
845 879 4.713814 AGATGGAGTGTTCTTGCTCATCTA 59.286 41.667 0.00 0.00 32.88 1.98
846 880 3.518705 AGATGGAGTGTTCTTGCTCATCT 59.481 43.478 0.00 0.00 33.66 2.90
847 881 3.870419 GAGATGGAGTGTTCTTGCTCATC 59.130 47.826 0.00 0.00 33.66 2.92
848 882 3.678252 CGAGATGGAGTGTTCTTGCTCAT 60.678 47.826 0.00 0.00 33.66 2.90
849 883 2.353109 CGAGATGGAGTGTTCTTGCTCA 60.353 50.000 0.00 0.00 33.66 4.26
850 884 2.266554 CGAGATGGAGTGTTCTTGCTC 58.733 52.381 0.00 0.00 0.00 4.26
851 885 1.066573 CCGAGATGGAGTGTTCTTGCT 60.067 52.381 0.00 0.00 42.00 3.91
852 886 1.338200 ACCGAGATGGAGTGTTCTTGC 60.338 52.381 0.00 0.00 42.00 4.01
853 887 2.341257 CACCGAGATGGAGTGTTCTTG 58.659 52.381 0.00 0.00 42.00 3.02
881 915 0.099968 CCCATGAAGCTGCATTCGTG 59.900 55.000 3.72 18.74 43.07 4.35
885 919 2.420568 CGGCCCATGAAGCTGCATT 61.421 57.895 3.72 0.00 0.00 3.56
972 1006 4.888325 ATGGAGGGGGAGCTCCGG 62.888 72.222 26.36 0.00 42.42 5.14
973 1007 2.770048 AATGGAGGGGGAGCTCCG 60.770 66.667 26.36 0.00 42.42 4.63
974 1008 2.456443 GGAATGGAGGGGGAGCTCC 61.456 68.421 25.59 25.59 40.05 4.70
975 1009 2.812619 CGGAATGGAGGGGGAGCTC 61.813 68.421 4.71 4.71 0.00 4.09
977 1011 3.878667 CCGGAATGGAGGGGGAGC 61.879 72.222 0.00 0.00 42.00 4.70
983 1024 1.604147 GGTTTTGGCCGGAATGGAGG 61.604 60.000 5.05 0.00 42.00 4.30
1069 1110 0.549950 CCCTGATTCTGGTGATGGCT 59.450 55.000 8.58 0.00 0.00 4.75
1076 1117 1.613630 AGGCGACCCTGATTCTGGT 60.614 57.895 8.58 3.82 40.94 4.00
1526 1588 1.683441 GGAACGTCCAGAACCCCAT 59.317 57.895 0.00 0.00 36.28 4.00
1837 1936 4.309950 ACAGCCACCGGTTCGTCC 62.310 66.667 2.97 0.00 0.00 4.79
2022 2129 2.115337 AGAGGCCATGCTCCTTCTAT 57.885 50.000 5.01 0.00 33.24 1.98
2245 2397 0.107263 TGTGCAGCCTGTCAACTTCA 60.107 50.000 0.00 0.00 0.00 3.02
2284 2436 0.321919 GAATGTGCAGTGCAGGAGGA 60.322 55.000 20.42 0.30 40.08 3.71
2348 2500 6.620877 ATGGACAGTAGTTTAATCACCTCA 57.379 37.500 0.00 0.00 0.00 3.86
2371 2528 6.039616 GTGACAGACTGCAAAATGGTAAAAA 58.960 36.000 1.25 0.00 0.00 1.94
2511 2673 2.225727 ACTTGAGGAATTCGTTTTCGCC 59.774 45.455 1.57 0.00 43.73 5.54
2752 2914 2.307686 GGGTCCTTAACACAGGGATCAA 59.692 50.000 0.00 0.00 34.24 2.57
2823 2985 1.755179 ACTTGAACACTTGCAGCTGT 58.245 45.000 16.64 0.00 0.00 4.40
2903 3065 8.394121 GTCTTTTACTTCTATCAGCATCAAAGG 58.606 37.037 0.00 0.00 0.00 3.11
3069 3231 1.547675 GGGTTGAATTGGCAGAGGTGA 60.548 52.381 0.00 0.00 0.00 4.02
3109 3271 2.582636 AGGGGCTAATTCATCAACCTGT 59.417 45.455 0.00 0.00 0.00 4.00
3139 3301 0.035458 AGCAGCACAGTGGACCTAAC 59.965 55.000 1.84 0.00 0.00 2.34
3259 3544 6.407412 CCTCCTGATCACACAGAATAAGCTTA 60.407 42.308 8.99 8.99 39.94 3.09
3260 3545 5.426504 CTCCTGATCACACAGAATAAGCTT 58.573 41.667 3.48 3.48 39.94 3.74
3268 3553 2.564504 CAAGTCCTCCTGATCACACAGA 59.435 50.000 0.00 0.00 39.94 3.41
3279 3564 2.066999 GCCCCGATCAAGTCCTCCT 61.067 63.158 0.00 0.00 0.00 3.69
3293 3578 1.487976 GTACCTACCCTAACAAGCCCC 59.512 57.143 0.00 0.00 0.00 5.80
3299 3584 6.342906 CAATTGATTCGTACCTACCCTAACA 58.657 40.000 0.00 0.00 0.00 2.41
3347 3633 2.428888 TATGCTGCTACTGCTCATCG 57.571 50.000 0.00 0.00 40.48 3.84
3356 3642 3.849911 TGAGGCGAATATATGCTGCTAC 58.150 45.455 0.00 3.95 0.00 3.58
3386 3672 4.024048 ACAAGTGTTATGTACTGCTGCAAC 60.024 41.667 3.02 0.00 0.00 4.17
3387 3673 4.133820 ACAAGTGTTATGTACTGCTGCAA 58.866 39.130 3.02 0.00 0.00 4.08
3406 3692 3.578716 CCTCAAGGTCAAGGTCTAGACAA 59.421 47.826 23.91 3.99 36.50 3.18
3409 3695 3.432378 GTCCTCAAGGTCAAGGTCTAGA 58.568 50.000 0.00 0.00 36.34 2.43
3412 3698 1.353091 GGTCCTCAAGGTCAAGGTCT 58.647 55.000 0.00 0.00 36.34 3.85
3421 3707 4.655963 TCTTCAGAAAATGGTCCTCAAGG 58.344 43.478 0.00 0.00 0.00 3.61
3450 3736 0.779997 AGGCATCTCCCCAACTTGTT 59.220 50.000 0.00 0.00 34.51 2.83
3451 3737 0.038744 CAGGCATCTCCCCAACTTGT 59.961 55.000 0.00 0.00 34.51 3.16
3459 3746 2.187946 CCGTCACAGGCATCTCCC 59.812 66.667 0.00 0.00 34.51 4.30
3512 3799 7.904461 GTGATTGTTCAACAAAAATTTGGACAG 59.096 33.333 7.14 0.00 42.23 3.51
3516 3803 6.190962 CGGTGATTGTTCAACAAAAATTTGG 58.809 36.000 7.14 0.00 41.96 3.28
3520 3807 4.376146 CCCGGTGATTGTTCAACAAAAAT 58.624 39.130 7.14 0.00 41.96 1.82
3522 3809 2.101582 CCCCGGTGATTGTTCAACAAAA 59.898 45.455 7.14 0.00 41.96 2.44
3523 3810 1.683917 CCCCGGTGATTGTTCAACAAA 59.316 47.619 7.14 0.00 41.96 2.83
3524 3811 1.323412 CCCCGGTGATTGTTCAACAA 58.677 50.000 5.18 5.18 39.72 2.83
3525 3812 0.538516 CCCCCGGTGATTGTTCAACA 60.539 55.000 0.00 0.00 39.72 3.33
3526 3813 2.263153 CCCCCGGTGATTGTTCAAC 58.737 57.895 0.00 0.00 36.14 3.18
3527 3814 4.832741 CCCCCGGTGATTGTTCAA 57.167 55.556 0.00 0.00 32.48 2.69
3549 3836 4.484872 GTAACGCAGGCCTCCCCC 62.485 72.222 0.00 0.00 0.00 5.40
3550 3837 2.942648 GATGTAACGCAGGCCTCCCC 62.943 65.000 0.00 0.00 0.00 4.81
3551 3838 1.523938 GATGTAACGCAGGCCTCCC 60.524 63.158 0.00 0.00 0.00 4.30
3552 3839 0.811616 CTGATGTAACGCAGGCCTCC 60.812 60.000 0.00 0.00 0.00 4.30
3553 3840 0.175760 TCTGATGTAACGCAGGCCTC 59.824 55.000 0.00 0.00 33.05 4.70
3554 3841 0.176680 CTCTGATGTAACGCAGGCCT 59.823 55.000 0.00 0.00 33.05 5.19
3555 3842 0.175760 TCTCTGATGTAACGCAGGCC 59.824 55.000 0.00 0.00 33.05 5.19
3556 3843 1.134965 ACTCTCTGATGTAACGCAGGC 60.135 52.381 0.00 0.00 33.05 4.85
3557 3844 2.949451 ACTCTCTGATGTAACGCAGG 57.051 50.000 0.00 0.00 33.05 4.85
3558 3845 4.357018 TGTACTCTCTGATGTAACGCAG 57.643 45.455 0.00 0.00 0.00 5.18
3559 3846 4.776795 TTGTACTCTCTGATGTAACGCA 57.223 40.909 0.00 0.00 0.00 5.24
3560 3847 5.340803 TCATTGTACTCTCTGATGTAACGC 58.659 41.667 0.00 0.00 0.00 4.84
3561 3848 6.786207 TCTCATTGTACTCTCTGATGTAACG 58.214 40.000 0.00 0.00 0.00 3.18
3562 3849 7.067615 TCCTCTCATTGTACTCTCTGATGTAAC 59.932 40.741 0.00 0.00 0.00 2.50
3563 3850 7.119387 TCCTCTCATTGTACTCTCTGATGTAA 58.881 38.462 0.00 0.00 0.00 2.41
3564 3851 6.663734 TCCTCTCATTGTACTCTCTGATGTA 58.336 40.000 0.00 0.00 0.00 2.29
3565 3852 5.514169 TCCTCTCATTGTACTCTCTGATGT 58.486 41.667 0.00 0.00 0.00 3.06
3566 3853 5.827267 TCTCCTCTCATTGTACTCTCTGATG 59.173 44.000 0.00 0.00 0.00 3.07
3567 3854 6.012337 TCTCCTCTCATTGTACTCTCTGAT 57.988 41.667 0.00 0.00 0.00 2.90
3568 3855 5.436175 CTCTCCTCTCATTGTACTCTCTGA 58.564 45.833 0.00 0.00 0.00 3.27
3569 3856 4.580167 CCTCTCCTCTCATTGTACTCTCTG 59.420 50.000 0.00 0.00 0.00 3.35
3570 3857 4.476846 TCCTCTCCTCTCATTGTACTCTCT 59.523 45.833 0.00 0.00 0.00 3.10
3571 3858 4.787551 TCCTCTCCTCTCATTGTACTCTC 58.212 47.826 0.00 0.00 0.00 3.20
3572 3859 4.871871 TCCTCTCCTCTCATTGTACTCT 57.128 45.455 0.00 0.00 0.00 3.24
3573 3860 6.208599 CCTATTCCTCTCCTCTCATTGTACTC 59.791 46.154 0.00 0.00 0.00 2.59
3574 3861 6.074648 CCTATTCCTCTCCTCTCATTGTACT 58.925 44.000 0.00 0.00 0.00 2.73
3575 3862 5.836358 ACCTATTCCTCTCCTCTCATTGTAC 59.164 44.000 0.00 0.00 0.00 2.90
3576 3863 5.835819 CACCTATTCCTCTCCTCTCATTGTA 59.164 44.000 0.00 0.00 0.00 2.41
3577 3864 4.653341 CACCTATTCCTCTCCTCTCATTGT 59.347 45.833 0.00 0.00 0.00 2.71
3578 3865 4.502950 GCACCTATTCCTCTCCTCTCATTG 60.503 50.000 0.00 0.00 0.00 2.82
3579 3866 3.645687 GCACCTATTCCTCTCCTCTCATT 59.354 47.826 0.00 0.00 0.00 2.57
3580 3867 3.238597 GCACCTATTCCTCTCCTCTCAT 58.761 50.000 0.00 0.00 0.00 2.90
3581 3868 2.672098 GCACCTATTCCTCTCCTCTCA 58.328 52.381 0.00 0.00 0.00 3.27
3582 3869 1.967779 GGCACCTATTCCTCTCCTCTC 59.032 57.143 0.00 0.00 0.00 3.20
3583 3870 1.292242 TGGCACCTATTCCTCTCCTCT 59.708 52.381 0.00 0.00 0.00 3.69
3584 3871 1.794714 TGGCACCTATTCCTCTCCTC 58.205 55.000 0.00 0.00 0.00 3.71
3585 3872 2.122768 CTTGGCACCTATTCCTCTCCT 58.877 52.381 0.00 0.00 0.00 3.69
3586 3873 2.119495 TCTTGGCACCTATTCCTCTCC 58.881 52.381 0.00 0.00 0.00 3.71
3587 3874 2.501723 TGTCTTGGCACCTATTCCTCTC 59.498 50.000 0.00 0.00 0.00 3.20
3588 3875 2.551270 TGTCTTGGCACCTATTCCTCT 58.449 47.619 0.00 0.00 0.00 3.69
3589 3876 3.209410 CATGTCTTGGCACCTATTCCTC 58.791 50.000 0.00 0.00 0.00 3.71
3590 3877 2.092212 CCATGTCTTGGCACCTATTCCT 60.092 50.000 0.00 0.00 39.09 3.36
3591 3878 2.301346 CCATGTCTTGGCACCTATTCC 58.699 52.381 0.00 0.00 39.09 3.01
3602 3889 3.499737 GGACGCCGCCATGTCTTG 61.500 66.667 0.00 0.00 35.45 3.02
3603 3890 4.778143 GGGACGCCGCCATGTCTT 62.778 66.667 0.00 0.00 35.45 3.01
3605 3892 3.845259 TAGGGACGCCGCCATGTC 61.845 66.667 0.00 0.00 0.00 3.06
3606 3893 4.157120 GTAGGGACGCCGCCATGT 62.157 66.667 0.00 0.00 0.00 3.21
3607 3894 2.023414 TTAGTAGGGACGCCGCCATG 62.023 60.000 0.33 0.00 0.00 3.66
3608 3895 1.759299 TTAGTAGGGACGCCGCCAT 60.759 57.895 0.33 0.00 0.00 4.40
3609 3896 2.362760 TTAGTAGGGACGCCGCCA 60.363 61.111 0.33 0.00 0.00 5.69
3610 3897 2.105729 GTTAGTAGGGACGCCGCC 59.894 66.667 0.00 0.00 0.00 6.13
3611 3898 1.226888 CTGTTAGTAGGGACGCCGC 60.227 63.158 0.00 0.00 0.00 6.53
3612 3899 1.436336 CCTGTTAGTAGGGACGCCG 59.564 63.158 0.00 0.00 34.06 6.46
3619 3906 4.286291 AGGTTCAAAGACCCTGTTAGTAGG 59.714 45.833 0.00 0.00 40.73 3.18
3620 3907 5.485209 AGGTTCAAAGACCCTGTTAGTAG 57.515 43.478 0.00 0.00 40.73 2.57
3621 3908 6.999705 TTAGGTTCAAAGACCCTGTTAGTA 57.000 37.500 0.00 0.00 40.73 1.82
3622 3909 5.899631 TTAGGTTCAAAGACCCTGTTAGT 57.100 39.130 0.00 0.00 40.73 2.24
3623 3910 6.531021 TCTTTAGGTTCAAAGACCCTGTTAG 58.469 40.000 0.00 0.00 39.13 2.34
3624 3911 6.503560 TCTTTAGGTTCAAAGACCCTGTTA 57.496 37.500 0.00 0.00 39.13 2.41
3625 3912 5.382664 TCTTTAGGTTCAAAGACCCTGTT 57.617 39.130 0.00 0.00 39.13 3.16
3626 3913 5.561679 GATCTTTAGGTTCAAAGACCCTGT 58.438 41.667 0.67 0.00 44.92 4.00
3627 3914 4.631813 CGATCTTTAGGTTCAAAGACCCTG 59.368 45.833 0.67 0.00 44.92 4.45
3628 3915 4.530946 TCGATCTTTAGGTTCAAAGACCCT 59.469 41.667 0.67 0.00 44.92 4.34
3629 3916 4.828829 TCGATCTTTAGGTTCAAAGACCC 58.171 43.478 0.67 0.00 44.92 4.46
3630 3917 6.620949 GCTTTCGATCTTTAGGTTCAAAGACC 60.621 42.308 0.67 0.00 44.92 3.85
3631 3918 6.073222 TGCTTTCGATCTTTAGGTTCAAAGAC 60.073 38.462 0.67 0.00 44.92 3.01
3632 3919 5.995282 TGCTTTCGATCTTTAGGTTCAAAGA 59.005 36.000 1.14 1.14 45.86 2.52
3633 3920 6.241207 TGCTTTCGATCTTTAGGTTCAAAG 57.759 37.500 0.00 0.00 36.95 2.77
3634 3921 6.429692 TCATGCTTTCGATCTTTAGGTTCAAA 59.570 34.615 0.00 0.00 0.00 2.69
3635 3922 5.937540 TCATGCTTTCGATCTTTAGGTTCAA 59.062 36.000 0.00 0.00 0.00 2.69
3636 3923 5.487433 TCATGCTTTCGATCTTTAGGTTCA 58.513 37.500 0.00 0.00 0.00 3.18
3637 3924 6.422776 TTCATGCTTTCGATCTTTAGGTTC 57.577 37.500 0.00 0.00 0.00 3.62
3638 3925 6.817765 TTTCATGCTTTCGATCTTTAGGTT 57.182 33.333 0.00 0.00 0.00 3.50
3639 3926 6.599244 TGATTTCATGCTTTCGATCTTTAGGT 59.401 34.615 0.00 0.00 0.00 3.08
3640 3927 7.011763 TCTGATTTCATGCTTTCGATCTTTAGG 59.988 37.037 0.00 0.00 0.00 2.69
3641 3928 7.913423 TCTGATTTCATGCTTTCGATCTTTAG 58.087 34.615 0.00 0.00 0.00 1.85
3642 3929 7.765819 TCTCTGATTTCATGCTTTCGATCTTTA 59.234 33.333 0.00 0.00 0.00 1.85
3643 3930 6.596888 TCTCTGATTTCATGCTTTCGATCTTT 59.403 34.615 0.00 0.00 0.00 2.52
3644 3931 6.111382 TCTCTGATTTCATGCTTTCGATCTT 58.889 36.000 0.00 0.00 0.00 2.40
3645 3932 5.668471 TCTCTGATTTCATGCTTTCGATCT 58.332 37.500 0.00 0.00 0.00 2.75
3646 3933 5.980698 TCTCTGATTTCATGCTTTCGATC 57.019 39.130 0.00 0.00 0.00 3.69
3647 3934 6.939132 AATCTCTGATTTCATGCTTTCGAT 57.061 33.333 0.00 0.00 0.00 3.59
3648 3935 6.818142 TGTAATCTCTGATTTCATGCTTTCGA 59.182 34.615 0.00 0.00 0.00 3.71
3649 3936 7.008440 TGTAATCTCTGATTTCATGCTTTCG 57.992 36.000 0.00 0.00 0.00 3.46
3650 3937 9.448294 GAATGTAATCTCTGATTTCATGCTTTC 57.552 33.333 11.28 5.01 0.00 2.62
3651 3938 9.186837 AGAATGTAATCTCTGATTTCATGCTTT 57.813 29.630 11.95 1.19 0.00 3.51
3652 3939 8.622157 CAGAATGTAATCTCTGATTTCATGCTT 58.378 33.333 13.97 2.55 41.38 3.91
3653 3940 8.155821 CAGAATGTAATCTCTGATTTCATGCT 57.844 34.615 11.95 11.95 41.38 3.79
3672 3959 4.510711 CAGCTGCAGATACCTTACAGAATG 59.489 45.833 20.43 0.00 46.00 2.67
3673 3960 4.406972 TCAGCTGCAGATACCTTACAGAAT 59.593 41.667 20.43 0.00 0.00 2.40
3674 3961 3.769300 TCAGCTGCAGATACCTTACAGAA 59.231 43.478 20.43 0.00 0.00 3.02
3675 3962 3.365472 TCAGCTGCAGATACCTTACAGA 58.635 45.455 20.43 0.00 0.00 3.41
3676 3963 3.715495 CTCAGCTGCAGATACCTTACAG 58.285 50.000 20.43 0.00 0.00 2.74
3677 3964 2.159043 GCTCAGCTGCAGATACCTTACA 60.159 50.000 20.43 0.00 0.00 2.41
3678 3965 2.478831 GCTCAGCTGCAGATACCTTAC 58.521 52.381 20.43 0.00 0.00 2.34
3679 3966 1.067669 CGCTCAGCTGCAGATACCTTA 59.932 52.381 20.43 0.00 0.00 2.69
3680 3967 0.179089 CGCTCAGCTGCAGATACCTT 60.179 55.000 20.43 0.00 0.00 3.50
3681 3968 1.039785 TCGCTCAGCTGCAGATACCT 61.040 55.000 20.43 0.98 0.00 3.08
3682 3969 0.597118 CTCGCTCAGCTGCAGATACC 60.597 60.000 20.43 0.00 0.00 2.73
3683 3970 0.102120 ACTCGCTCAGCTGCAGATAC 59.898 55.000 20.43 3.05 0.00 2.24
3684 3971 0.383590 GACTCGCTCAGCTGCAGATA 59.616 55.000 20.43 0.00 0.00 1.98
3685 3972 1.141449 GACTCGCTCAGCTGCAGAT 59.859 57.895 20.43 8.90 0.00 2.90
3686 3973 2.570706 GACTCGCTCAGCTGCAGA 59.429 61.111 20.43 7.12 0.00 4.26
3687 3974 2.879933 CGACTCGCTCAGCTGCAG 60.880 66.667 10.11 10.11 0.00 4.41
3698 3985 2.415857 ACTAGAACACTACTGCGACTCG 59.584 50.000 0.00 0.00 0.00 4.18
3699 3986 4.422546 AACTAGAACACTACTGCGACTC 57.577 45.455 0.00 0.00 0.00 3.36
3700 3987 4.850347 AAACTAGAACACTACTGCGACT 57.150 40.909 0.00 0.00 0.00 4.18
3701 3988 6.998258 TTTAAACTAGAACACTACTGCGAC 57.002 37.500 0.00 0.00 0.00 5.19
3702 3989 8.086522 AGAATTTAAACTAGAACACTACTGCGA 58.913 33.333 0.00 0.00 0.00 5.10
3703 3990 8.240883 AGAATTTAAACTAGAACACTACTGCG 57.759 34.615 0.00 0.00 0.00 5.18
3706 3993 9.852091 CGGTAGAATTTAAACTAGAACACTACT 57.148 33.333 0.00 0.00 0.00 2.57
3707 3994 9.846248 TCGGTAGAATTTAAACTAGAACACTAC 57.154 33.333 0.00 0.00 0.00 2.73
3709 3996 9.367444 CATCGGTAGAATTTAAACTAGAACACT 57.633 33.333 0.00 0.00 0.00 3.55
3710 3997 9.148104 ACATCGGTAGAATTTAAACTAGAACAC 57.852 33.333 0.00 0.00 0.00 3.32
3711 3998 9.715121 AACATCGGTAGAATTTAAACTAGAACA 57.285 29.630 0.00 0.00 0.00 3.18
3712 3999 9.968743 CAACATCGGTAGAATTTAAACTAGAAC 57.031 33.333 0.00 0.00 0.00 3.01
3713 4000 9.715121 ACAACATCGGTAGAATTTAAACTAGAA 57.285 29.630 0.00 0.00 0.00 2.10
3808 4095 2.173356 TGGTGAGGATTAGGATGCTTGG 59.827 50.000 0.00 0.00 33.67 3.61
3809 4096 3.118112 ACTGGTGAGGATTAGGATGCTTG 60.118 47.826 0.00 0.00 33.67 4.01
3874 4161 3.565063 GGTTGGAAAATGCAGCAAATTGT 59.435 39.130 0.00 0.00 0.00 2.71
3875 4162 3.816523 AGGTTGGAAAATGCAGCAAATTG 59.183 39.130 0.00 0.00 0.00 2.32
3897 4185 3.256383 GCTAAATGGCATGCATATCCACA 59.744 43.478 21.36 6.51 31.94 4.17
3912 4200 8.093307 AGTGATAGATATGTCACAGGCTAAATG 58.907 37.037 17.88 0.00 45.47 2.32
3920 4208 6.423302 GCAGGAAAGTGATAGATATGTCACAG 59.577 42.308 17.88 3.64 45.47 3.66
3922 4210 5.698545 GGCAGGAAAGTGATAGATATGTCAC 59.301 44.000 9.00 9.00 43.85 3.67
3923 4211 5.221722 GGGCAGGAAAGTGATAGATATGTCA 60.222 44.000 0.00 0.00 0.00 3.58
3924 4212 5.241662 GGGCAGGAAAGTGATAGATATGTC 58.758 45.833 0.00 0.00 0.00 3.06
3932 4220 1.681229 AAGGGGGCAGGAAAGTGATA 58.319 50.000 0.00 0.00 0.00 2.15
3939 4227 3.021263 GGGCTAAGGGGGCAGGAA 61.021 66.667 0.00 0.00 0.00 3.36
3946 4234 0.753111 GTGCAATGAGGGCTAAGGGG 60.753 60.000 0.00 0.00 0.00 4.79
3951 4239 0.918258 TGGATGTGCAATGAGGGCTA 59.082 50.000 0.00 0.00 0.00 3.93
3986 4274 1.777878 TGCCCTTCTTCTGGGTTTGTA 59.222 47.619 0.00 0.00 46.22 2.41
4047 4335 1.573108 TCCTGACCTCCTGAATGTCC 58.427 55.000 0.00 0.00 0.00 4.02
4108 4396 1.227380 CGAGGTCCACTGGCTATGC 60.227 63.158 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.