Multiple sequence alignment - TraesCS2A01G479900

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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 TraesCS2A01G479900 chr2A 100.000 7376 0 0 1 7376 717947423 717940048 0.000000e+00 13622.0
1 TraesCS2A01G479900 chr2A 97.541 122 3 0 3478 3599 717943768 717943647 7.500000e-50 209.0
2 TraesCS2A01G479900 chr2A 97.541 122 3 0 3656 3777 717943946 717943825 7.500000e-50 209.0
3 TraesCS2A01G479900 chr2A 98.889 90 1 0 3387 3476 71560836 71560747 2.130000e-35 161.0
4 TraesCS2A01G479900 chr2A 97.368 38 1 0 3335 3372 717943827 717943790 1.720000e-06 65.8
5 TraesCS2A01G479900 chr2D 94.030 3434 131 41 1 3410 580017293 580013910 0.000000e+00 5138.0
6 TraesCS2A01G479900 chr2D 95.851 2796 68 16 3791 6578 580013476 580010721 0.000000e+00 4477.0
7 TraesCS2A01G479900 chr2D 87.594 532 27 9 6555 7048 580010669 580010139 1.380000e-161 580.0
8 TraesCS2A01G479900 chr2D 86.071 280 35 2 1793 2072 428579141 428578866 1.560000e-76 298.0
9 TraesCS2A01G479900 chr2D 87.578 161 6 7 3656 3802 580013765 580013605 2.740000e-39 174.0
10 TraesCS2A01G479900 chr2D 98.851 87 1 0 3389 3475 30458019 30457933 9.910000e-34 156.0
11 TraesCS2A01G479900 chr2D 82.716 162 11 9 3452 3599 580013788 580013630 2.160000e-25 128.0
12 TraesCS2A01G479900 chr2B 94.464 3179 90 32 3949 7055 698966165 698963001 0.000000e+00 4817.0
13 TraesCS2A01G479900 chr2B 92.477 3230 122 58 205 3392 698969648 698966498 0.000000e+00 4506.0
14 TraesCS2A01G479900 chr2B 95.226 398 12 5 3597 3991 698966555 698966162 2.260000e-174 623.0
15 TraesCS2A01G479900 chr2B 84.894 331 30 6 7053 7376 698962906 698962589 4.300000e-82 316.0
16 TraesCS2A01G479900 chr2B 81.587 315 55 3 7059 7371 684756896 684756583 2.640000e-64 257.0
17 TraesCS2A01G479900 chr2B 97.656 128 3 0 3472 3599 698966501 698966374 3.460000e-53 220.0
18 TraesCS2A01G479900 chr1D 85.948 306 35 2 7053 7350 354721117 354721422 3.320000e-83 320.0
19 TraesCS2A01G479900 chr1D 93.269 104 5 2 3372 3473 446424987 446425090 1.280000e-32 152.0
20 TraesCS2A01G479900 chr1D 90.351 114 9 2 3361 3473 201754066 201753954 1.660000e-31 148.0
21 TraesCS2A01G479900 chr5D 83.587 329 45 4 7054 7374 329425527 329425854 4.330000e-77 300.0
22 TraesCS2A01G479900 chr5A 86.071 280 35 2 1793 2072 707718864 707719139 1.560000e-76 298.0
23 TraesCS2A01G479900 chr5B 82.985 335 38 10 7059 7376 621601477 621601145 1.210000e-72 285.0
24 TraesCS2A01G479900 chr1B 83.129 326 29 17 7053 7376 476344580 476344881 2.620000e-69 274.0
25 TraesCS2A01G479900 chr1B 87.255 102 13 0 1831 1932 646208826 646208725 4.680000e-22 117.0
26 TraesCS2A01G479900 chr3A 87.963 216 22 4 7049 7262 128080977 128080764 1.230000e-62 252.0
27 TraesCS2A01G479900 chr7D 97.826 92 2 0 3388 3479 540399159 540399250 7.660000e-35 159.0
28 TraesCS2A01G479900 chr6B 95.000 100 5 0 3380 3479 720985494 720985395 2.750000e-34 158.0
29 TraesCS2A01G479900 chr1A 95.833 96 4 0 3382 3477 486046070 486046165 9.910000e-34 156.0
30 TraesCS2A01G479900 chr1A 94.949 99 4 1 3381 3479 583302744 583302841 3.560000e-33 154.0
31 TraesCS2A01G479900 chr1A 86.275 102 14 0 1831 1932 560965650 560965549 2.180000e-20 111.0
32 TraesCS2A01G479900 chr4B 95.789 95 4 0 3380 3474 500839959 500840053 3.560000e-33 154.0
33 TraesCS2A01G479900 chr7A 78.146 151 29 4 1297 1445 448444 448592 7.880000e-15 93.5


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 TraesCS2A01G479900 chr2A 717940048 717947423 7375 True 3526.45 13622 98.1125 1 7376 4 chr2A.!!$R2 7375
1 TraesCS2A01G479900 chr2D 580010139 580017293 7154 True 2099.40 5138 89.5538 1 7048 5 chr2D.!!$R3 7047
2 TraesCS2A01G479900 chr2B 698962589 698969648 7059 True 2096.40 4817 92.9434 205 7376 5 chr2B.!!$R2 7171

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
967 1024 0.096976 CCGTTGCGCAAGATAGTTGG 59.903 55.000 25.78 12.54 43.02 3.77 F
1075 1132 0.806868 AGGCAAAGACATCACGCATG 59.193 50.000 0.00 0.00 38.64 4.06 F
1129 1186 2.618053 CTATTGACGGTGTTGACTCCC 58.382 52.381 0.00 0.00 0.00 4.30 F
1995 2064 4.372656 GGGTGACTTTGATCGGATTCTAG 58.627 47.826 0.00 0.00 0.00 2.43 F
3403 3475 3.271225 TGTTATCTACTCCCTCTGTCCCA 59.729 47.826 0.00 0.00 0.00 4.37 F
3508 3660 0.040781 CGTAAACCCACACGCCTTTG 60.041 55.000 0.00 0.00 0.00 2.77 F
3514 3666 0.107410 CCCACACGCCTTTGCCTATA 60.107 55.000 0.00 0.00 0.00 1.31 F
5451 5802 1.063174 GCAGGAAATAGTTCTGCAGCG 59.937 52.381 9.47 0.00 37.61 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1919 2.811101 CGTTTGGTTGGCCTTGCA 59.189 55.556 3.32 0.00 35.27 4.08 R
1973 2042 3.268023 AGAATCCGATCAAAGTCACCC 57.732 47.619 0.00 0.00 0.00 4.61 R
2023 2092 3.851458 TTCCTGACTGATATGCTGCAT 57.149 42.857 20.18 20.18 0.00 3.96 R
3495 3647 0.107410 TATAGGCAAAGGCGTGTGGG 60.107 55.000 0.00 0.00 42.47 4.61 R
4767 5113 0.108804 CAGCAGCAGCAAATTCCTGG 60.109 55.000 3.17 0.00 45.49 4.45 R
5451 5802 0.866427 CCGATGATGCTGATGCTGAC 59.134 55.000 0.00 0.00 40.48 3.51 R
5520 5910 2.671963 CCTGCTGCTGCTGCTGAA 60.672 61.111 30.01 13.93 40.01 3.02 R
7175 7799 0.175531 TCGCCAGCGATGAGAAATCA 59.824 50.000 11.27 0.00 44.01 2.57 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
80 82 3.338126 GACGACCACGACCATCGCT 62.338 63.158 0.00 0.00 45.12 4.93
83 85 4.796231 ACCACGACCATCGCTCGC 62.796 66.667 0.00 0.00 45.12 5.03
123 125 4.767255 CCACCCTGCTCGGTCTGC 62.767 72.222 0.00 0.00 32.17 4.26
127 129 4.463879 CCTGCTCGGTCTGCCTGG 62.464 72.222 0.00 0.00 0.00 4.45
198 207 3.640000 CCACGATCCGATTGGCGC 61.640 66.667 0.00 0.00 39.11 6.53
224 233 4.653888 AGGTTTCCGTTGGCCCCG 62.654 66.667 0.00 1.83 0.00 5.73
338 359 3.788766 CCCGCCGTCGCTTTCTTG 61.789 66.667 0.00 0.00 0.00 3.02
360 383 3.006859 GGGGGTGAGTTTTTGAATCTTGG 59.993 47.826 0.00 0.00 0.00 3.61
375 398 1.644786 CTTGGTTCGGACGGAATGGC 61.645 60.000 0.00 0.00 36.92 4.40
378 401 2.125832 TTCGGACGGAATGGCGTC 60.126 61.111 0.00 0.00 34.71 5.19
379 402 3.975083 TTCGGACGGAATGGCGTCG 62.975 63.158 0.00 0.00 36.14 5.12
384 407 3.554692 CGGAATGGCGTCGTGAGC 61.555 66.667 0.00 0.00 0.00 4.26
410 433 7.023575 CGTTCTTGAATTCTTTTCGATGGAAT 58.976 34.615 7.05 0.00 30.88 3.01
423 446 4.339748 TCGATGGAATGGTTTGATTGGAA 58.660 39.130 0.00 0.00 0.00 3.53
464 500 1.308998 ATTGAATCCGCGGCCTTTAG 58.691 50.000 23.51 0.00 0.00 1.85
502 542 4.812476 CGCTGGGAATCGGTCGCA 62.812 66.667 6.60 6.60 46.26 5.10
554 595 2.514824 GAGGCCGACTGGGATTGC 60.515 66.667 0.00 0.00 38.47 3.56
606 647 4.326826 TCTCTTGATTGCTCCATCGTTTT 58.673 39.130 0.00 0.00 0.00 2.43
607 648 4.393062 TCTCTTGATTGCTCCATCGTTTTC 59.607 41.667 0.00 0.00 0.00 2.29
610 651 5.241506 TCTTGATTGCTCCATCGTTTTCTTT 59.758 36.000 0.00 0.00 0.00 2.52
612 653 6.757897 TGATTGCTCCATCGTTTTCTTTAT 57.242 33.333 0.00 0.00 0.00 1.40
613 654 7.857734 TGATTGCTCCATCGTTTTCTTTATA 57.142 32.000 0.00 0.00 0.00 0.98
614 655 8.450578 TGATTGCTCCATCGTTTTCTTTATAT 57.549 30.769 0.00 0.00 0.00 0.86
615 656 9.554395 TGATTGCTCCATCGTTTTCTTTATATA 57.446 29.630 0.00 0.00 0.00 0.86
636 677 8.943909 ATATAAATTATAAGTCGGCTGCTACC 57.056 34.615 0.00 0.00 0.00 3.18
637 678 4.957684 AATTATAAGTCGGCTGCTACCT 57.042 40.909 0.00 0.00 0.00 3.08
638 679 3.728076 TTATAAGTCGGCTGCTACCTG 57.272 47.619 0.00 0.00 0.00 4.00
648 704 2.028020 GGCTGCTACCTGTAGTTTCAGT 60.028 50.000 0.00 0.00 35.65 3.41
651 707 2.230508 TGCTACCTGTAGTTTCAGTCGG 59.769 50.000 6.22 0.00 35.65 4.79
683 739 2.691526 ACGACACTGTTCTGTTCCTGTA 59.308 45.455 0.00 0.00 0.00 2.74
684 740 3.050619 CGACACTGTTCTGTTCCTGTAC 58.949 50.000 0.00 0.00 0.00 2.90
727 784 7.949690 AAAAAGGTTAAGGTTTCAGTGTACT 57.050 32.000 0.00 0.00 0.00 2.73
732 789 6.990939 AGGTTAAGGTTTCAGTGTACTTCTTC 59.009 38.462 0.00 0.00 0.00 2.87
745 802 3.268013 ACTTCTTCGTTGAATTTGCGG 57.732 42.857 0.00 0.00 0.00 5.69
760 817 1.649267 GCGGCTGCAATTACCTAGC 59.351 57.895 14.08 0.00 42.15 3.42
761 818 0.815615 GCGGCTGCAATTACCTAGCT 60.816 55.000 14.08 0.00 42.15 3.32
762 819 0.940126 CGGCTGCAATTACCTAGCTG 59.060 55.000 0.50 0.00 36.45 4.24
767 824 4.220533 CTGCAATTACCTAGCTGCAATC 57.779 45.455 1.02 0.00 43.74 2.67
768 825 2.951642 TGCAATTACCTAGCTGCAATCC 59.048 45.455 1.02 0.00 41.61 3.01
769 826 3.217626 GCAATTACCTAGCTGCAATCCT 58.782 45.455 1.02 0.00 34.87 3.24
770 827 3.004106 GCAATTACCTAGCTGCAATCCTG 59.996 47.826 1.02 0.00 34.87 3.86
771 828 3.498774 ATTACCTAGCTGCAATCCTGG 57.501 47.619 1.02 0.00 0.00 4.45
772 829 1.879575 TACCTAGCTGCAATCCTGGT 58.120 50.000 1.02 3.22 0.00 4.00
773 830 0.543749 ACCTAGCTGCAATCCTGGTC 59.456 55.000 1.02 0.00 0.00 4.02
774 831 0.531532 CCTAGCTGCAATCCTGGTCG 60.532 60.000 1.02 0.00 0.00 4.79
775 832 1.153369 TAGCTGCAATCCTGGTCGC 60.153 57.895 1.02 0.00 0.00 5.19
776 833 2.593468 TAGCTGCAATCCTGGTCGCC 62.593 60.000 1.02 0.00 0.00 5.54
777 834 3.197790 CTGCAATCCTGGTCGCCG 61.198 66.667 0.00 0.00 0.00 6.46
778 835 3.958147 CTGCAATCCTGGTCGCCGT 62.958 63.158 0.00 0.00 0.00 5.68
779 836 2.746277 GCAATCCTGGTCGCCGTT 60.746 61.111 0.00 0.00 0.00 4.44
783 840 4.980805 TCCTGGTCGCCGTTGTGC 62.981 66.667 0.00 0.00 0.00 4.57
827 884 2.808906 AGGTTTATCCACCTGCTTCC 57.191 50.000 0.00 0.00 46.22 3.46
846 903 2.754552 TCCTGCACATGTTTATCTTGCC 59.245 45.455 0.00 0.00 31.94 4.52
863 920 5.923204 TCTTGCCCACATTTGTTTGTTATT 58.077 33.333 0.00 0.00 0.00 1.40
866 923 7.439655 TCTTGCCCACATTTGTTTGTTATTTAC 59.560 33.333 0.00 0.00 0.00 2.01
868 925 6.926272 TGCCCACATTTGTTTGTTATTTACTC 59.074 34.615 0.00 0.00 0.00 2.59
869 926 6.367695 GCCCACATTTGTTTGTTATTTACTCC 59.632 38.462 0.00 0.00 0.00 3.85
895 952 5.499047 GTGTTATTATTGCCAGCTAACGTC 58.501 41.667 0.00 0.00 0.00 4.34
926 983 5.618640 GCTTCTTGCAGGATTTAGACACTTG 60.619 44.000 0.00 0.00 42.31 3.16
946 1003 0.905357 AATCGACAAGACCCCTCTGG 59.095 55.000 0.00 0.00 41.37 3.86
955 1012 4.760047 CCCCTCTGGACCGTTGCG 62.760 72.222 0.00 0.00 35.39 4.85
964 1021 0.739813 GGACCGTTGCGCAAGATAGT 60.740 55.000 25.78 17.85 43.02 2.12
967 1024 0.096976 CCGTTGCGCAAGATAGTTGG 59.903 55.000 25.78 12.54 43.02 3.77
1045 1102 7.348080 TCAGATAGTGAGGACGATGTTAAAT 57.652 36.000 0.00 0.00 0.00 1.40
1071 1128 3.624326 TCAAAAGGCAAAGACATCACG 57.376 42.857 0.00 0.00 0.00 4.35
1075 1132 0.806868 AGGCAAAGACATCACGCATG 59.193 50.000 0.00 0.00 38.64 4.06
1100 1157 3.134623 TGCTCAGAGGACAGAAAAGACAA 59.865 43.478 0.00 0.00 0.00 3.18
1119 1176 4.906618 ACAATCTTGTTCCTATTGACGGT 58.093 39.130 0.00 0.00 38.47 4.83
1129 1186 2.618053 CTATTGACGGTGTTGACTCCC 58.382 52.381 0.00 0.00 0.00 4.30
1242 1299 5.336293 CGCTTCATGCTCTTATAGATCTCCA 60.336 44.000 0.00 0.00 40.11 3.86
1597 1666 4.766891 ACATCGTCAATGGATTGGAAACTT 59.233 37.500 0.00 0.00 39.90 2.66
1917 1986 8.827832 ATGAGAGAGCTATATATGAAGAAGCT 57.172 34.615 6.65 6.65 45.82 3.74
1973 2042 7.066163 TGGAGATCATATATGCTTTAATTGCCG 59.934 37.037 7.92 0.00 0.00 5.69
1995 2064 4.372656 GGGTGACTTTGATCGGATTCTAG 58.627 47.826 0.00 0.00 0.00 2.43
1999 2068 6.476053 GGTGACTTTGATCGGATTCTAGTTAC 59.524 42.308 10.78 10.78 0.00 2.50
2000 2069 7.259161 GTGACTTTGATCGGATTCTAGTTACT 58.741 38.462 11.44 0.00 0.00 2.24
2124 2193 9.292195 CAGGTAAACTTTATCTTCCAAAACCTA 57.708 33.333 0.00 0.00 31.48 3.08
2303 2372 4.635765 CCTAGCTTATTGCACTTGCTGTTA 59.364 41.667 12.27 0.00 45.94 2.41
2414 2483 3.953542 AAAGGAGAGGGTTCAACAGTT 57.046 42.857 0.00 0.00 0.00 3.16
2586 2655 6.183360 GGAGTGCTTTTAATAGAATGGCCAAT 60.183 38.462 10.96 0.00 0.00 3.16
2896 2965 5.245977 TCTGATGACGATATGGAGCCAAATA 59.754 40.000 0.00 0.00 0.00 1.40
2950 3019 3.625764 TGCTGCTCGTAAAAGAAAACTGT 59.374 39.130 0.00 0.00 0.00 3.55
3003 3072 6.603599 AGAAAAAGAAGGTTAACAGTTCAGCT 59.396 34.615 17.55 0.00 0.00 4.24
3397 3469 6.599638 GCAATTGTTTGTTATCTACTCCCTCT 59.400 38.462 7.40 0.00 35.17 3.69
3400 3472 6.282199 TGTTTGTTATCTACTCCCTCTGTC 57.718 41.667 0.00 0.00 0.00 3.51
3403 3475 3.271225 TGTTATCTACTCCCTCTGTCCCA 59.729 47.826 0.00 0.00 0.00 4.37
3410 3482 6.689561 TCTACTCCCTCTGTCCCAAAATATA 58.310 40.000 0.00 0.00 0.00 0.86
3411 3483 7.136885 TCTACTCCCTCTGTCCCAAAATATAA 58.863 38.462 0.00 0.00 0.00 0.98
3413 3485 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
3414 3486 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
3415 3487 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
3416 3488 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
3420 3492 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
3421 3493 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
3435 3507 8.707938 AAGAACGTTTTTAACACTACACTAGT 57.292 30.769 0.46 0.00 40.28 2.57
3448 3520 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
3449 3521 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
3460 3612 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3468 3620 5.184479 CGTTCTTATATTATGGGACGGAGGA 59.816 44.000 0.00 0.00 0.00 3.71
3471 3623 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
3472 3624 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
3473 3625 5.997384 ATATTATGGGACGGAGGAAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
3498 3650 3.230115 CCGTAAAGGCGTAAACCCA 57.770 52.632 0.00 0.00 0.00 4.51
3499 3651 0.798159 CCGTAAAGGCGTAAACCCAC 59.202 55.000 0.00 0.00 0.00 4.61
3500 3652 1.510776 CGTAAAGGCGTAAACCCACA 58.489 50.000 0.00 0.00 0.00 4.17
3501 3653 1.195222 CGTAAAGGCGTAAACCCACAC 59.805 52.381 0.00 0.00 0.00 3.82
3502 3654 1.195222 GTAAAGGCGTAAACCCACACG 59.805 52.381 0.00 0.00 41.04 4.49
3506 3658 4.052519 CGTAAACCCACACGCCTT 57.947 55.556 0.00 0.00 0.00 4.35
3507 3659 2.323213 CGTAAACCCACACGCCTTT 58.677 52.632 0.00 0.00 0.00 3.11
3508 3660 0.040781 CGTAAACCCACACGCCTTTG 60.041 55.000 0.00 0.00 0.00 2.77
3509 3661 0.318360 GTAAACCCACACGCCTTTGC 60.318 55.000 0.00 0.00 0.00 3.68
3510 3662 1.457009 TAAACCCACACGCCTTTGCC 61.457 55.000 0.00 0.00 0.00 4.52
3511 3663 3.731766 AACCCACACGCCTTTGCCT 62.732 57.895 0.00 0.00 0.00 4.75
3512 3664 2.033448 CCCACACGCCTTTGCCTA 59.967 61.111 0.00 0.00 0.00 3.93
3513 3665 1.378514 CCCACACGCCTTTGCCTAT 60.379 57.895 0.00 0.00 0.00 2.57
3514 3666 0.107410 CCCACACGCCTTTGCCTATA 60.107 55.000 0.00 0.00 0.00 1.31
3515 3667 1.299541 CCACACGCCTTTGCCTATAG 58.700 55.000 0.00 0.00 0.00 1.31
3516 3668 1.134521 CCACACGCCTTTGCCTATAGA 60.135 52.381 0.00 0.00 0.00 1.98
3517 3669 2.627945 CACACGCCTTTGCCTATAGAA 58.372 47.619 0.00 0.00 0.00 2.10
3518 3670 3.206150 CACACGCCTTTGCCTATAGAAT 58.794 45.455 0.00 0.00 0.00 2.40
3519 3671 3.627577 CACACGCCTTTGCCTATAGAATT 59.372 43.478 0.00 0.00 0.00 2.17
3520 3672 3.627577 ACACGCCTTTGCCTATAGAATTG 59.372 43.478 0.00 0.00 0.00 2.32
3521 3673 3.627577 CACGCCTTTGCCTATAGAATTGT 59.372 43.478 0.00 0.00 0.00 2.71
3522 3674 4.096382 CACGCCTTTGCCTATAGAATTGTT 59.904 41.667 0.00 0.00 0.00 2.83
3523 3675 4.705023 ACGCCTTTGCCTATAGAATTGTTT 59.295 37.500 0.00 0.00 0.00 2.83
3524 3676 5.036737 CGCCTTTGCCTATAGAATTGTTTG 58.963 41.667 0.00 0.00 0.00 2.93
3525 3677 5.393027 CGCCTTTGCCTATAGAATTGTTTGT 60.393 40.000 0.00 0.00 0.00 2.83
3526 3678 6.398095 GCCTTTGCCTATAGAATTGTTTGTT 58.602 36.000 0.00 0.00 0.00 2.83
3527 3679 7.543756 GCCTTTGCCTATAGAATTGTTTGTTA 58.456 34.615 0.00 0.00 0.00 2.41
3528 3680 8.197439 GCCTTTGCCTATAGAATTGTTTGTTAT 58.803 33.333 0.00 0.00 0.00 1.89
3529 3681 9.736023 CCTTTGCCTATAGAATTGTTTGTTATC 57.264 33.333 0.00 0.00 0.00 1.75
3659 3811 8.839310 ATCTATCTGTATTTGACTTACATGCC 57.161 34.615 0.00 0.00 0.00 4.40
3660 3812 5.991328 ATCTGTATTTGACTTACATGCCG 57.009 39.130 0.00 0.00 0.00 5.69
3661 3813 4.827692 TCTGTATTTGACTTACATGCCGT 58.172 39.130 0.00 0.00 0.00 5.68
3662 3814 5.968254 TCTGTATTTGACTTACATGCCGTA 58.032 37.500 0.00 0.00 0.00 4.02
3663 3815 6.399743 TCTGTATTTGACTTACATGCCGTAA 58.600 36.000 0.00 0.00 37.76 3.18
3664 3816 6.874664 TCTGTATTTGACTTACATGCCGTAAA 59.125 34.615 0.00 0.00 39.59 2.01
3665 3817 7.064134 TCTGTATTTGACTTACATGCCGTAAAG 59.936 37.037 0.00 0.00 39.59 1.85
3666 3818 5.560966 ATTTGACTTACATGCCGTAAAGG 57.439 39.130 0.00 0.00 39.59 3.11
3679 3831 2.940410 CCGTAAAGGCGTAAATCCACAT 59.060 45.455 0.00 0.00 0.00 3.21
3900 4206 9.273016 CATAACAAAACTAGAAACTGAAGGAGA 57.727 33.333 0.00 0.00 0.00 3.71
3901 4207 7.793927 AACAAAACTAGAAACTGAAGGAGAG 57.206 36.000 0.00 0.00 0.00 3.20
4042 4387 4.661993 TTGTGTCTTAAAGTGCGCATAG 57.338 40.909 15.91 6.73 0.00 2.23
4162 4507 7.654022 AAAAGTACCTCCAAAGACAATTGAA 57.346 32.000 13.59 0.00 31.84 2.69
4357 4702 5.636965 GCAATTGTGGTGCATTAATGTTGTA 59.363 36.000 16.61 0.00 41.80 2.41
4527 4872 9.902684 TTTGTTATCCCGGTTGTCTTATATTAA 57.097 29.630 0.00 0.00 0.00 1.40
4561 4906 6.378280 ACCTTTTGATCCGATGAGCTTTTTAT 59.622 34.615 0.00 0.00 0.00 1.40
4608 4953 3.511856 CGATGCCTTCGCTATTTTCTC 57.488 47.619 0.00 0.00 41.69 2.87
4767 5113 8.220755 TGCTCATATGTTTCCTGTTTATAACC 57.779 34.615 1.90 0.00 0.00 2.85
4933 5279 3.586470 TGGCAAAACAACTTCCTAGGA 57.414 42.857 7.62 7.62 0.00 2.94
5247 5595 2.027192 GGAACCACCTGAGAATGCTGTA 60.027 50.000 0.00 0.00 35.41 2.74
5437 5788 2.671963 CAGCAGCAGCAGCAGGAA 60.672 61.111 12.92 0.00 45.49 3.36
5451 5802 1.063174 GCAGGAAATAGTTCTGCAGCG 59.937 52.381 9.47 0.00 37.61 5.18
5787 6195 2.648059 CTTGATGGGTCAATGTCCCTC 58.352 52.381 16.12 11.27 43.08 4.30
5863 6271 4.292977 ACTCCTTTCTTTTTCAGCGTTG 57.707 40.909 0.00 0.00 0.00 4.10
6131 6539 2.364002 TCACTCGGTTCACAGTCAATGA 59.636 45.455 0.00 0.00 0.00 2.57
6267 6676 4.571580 ACAAAATGTGCATGTTTCTGTTGG 59.428 37.500 0.00 0.00 0.00 3.77
6273 6682 0.675083 CATGTTTCTGTTGGCAGGCA 59.325 50.000 0.00 0.00 42.78 4.75
6318 6727 1.334599 GCATTTGGCGACGAGAAAACA 60.335 47.619 0.00 0.00 0.00 2.83
6321 6730 0.105224 TTGGCGACGAGAAAACAGGA 59.895 50.000 0.00 0.00 0.00 3.86
6370 6779 6.015856 GGAAGATCTCGGATATCTCTTCAACA 60.016 42.308 22.94 0.00 42.20 3.33
6549 6959 6.655003 CCGGTTGGCTCATGTAATTATCTTAT 59.345 38.462 0.00 0.00 0.00 1.73
6717 7207 7.047460 ACCTTTAGTCGAACTTGAGAACTTA 57.953 36.000 0.00 0.00 0.00 2.24
6803 7327 7.148103 TGCTATGATGCTGCACTTTTTATTGTA 60.148 33.333 3.57 0.00 0.00 2.41
6937 7461 2.370189 CCACTCACTCCCTCAAACTTCT 59.630 50.000 0.00 0.00 0.00 2.85
6947 7471 0.250684 TCAAACTTCTGGCGCCATCA 60.251 50.000 32.87 17.62 0.00 3.07
6967 7491 1.453669 GGGTCTCCTGGCCATGATC 59.546 63.158 5.51 5.52 0.00 2.92
7018 7545 4.038763 AGAATGTGTCAACGAGGTGAACTA 59.961 41.667 0.00 0.00 0.00 2.24
7030 7557 4.760204 CGAGGTGAACTATTTCAAGGGTTT 59.240 41.667 0.00 0.00 43.52 3.27
7052 7579 7.224362 GGTTTATGTGTCTTGAGATCATCTCTG 59.776 40.741 15.89 8.74 43.73 3.35
7055 7582 2.433604 TGTCTTGAGATCATCTCTGGCC 59.566 50.000 15.89 0.00 43.73 5.36
7056 7583 2.433604 GTCTTGAGATCATCTCTGGCCA 59.566 50.000 15.89 4.71 43.73 5.36
7058 7585 3.715315 TCTTGAGATCATCTCTGGCCAAT 59.285 43.478 15.89 0.00 43.73 3.16
7060 7587 5.367644 TCTTGAGATCATCTCTGGCCAATAA 59.632 40.000 15.89 0.00 43.73 1.40
7061 7588 5.635278 TGAGATCATCTCTGGCCAATAAA 57.365 39.130 15.89 0.00 43.73 1.40
7062 7589 6.196918 TGAGATCATCTCTGGCCAATAAAT 57.803 37.500 15.89 0.00 43.73 1.40
7063 7590 6.236409 TGAGATCATCTCTGGCCAATAAATC 58.764 40.000 15.89 5.68 43.73 2.17
7071 7695 7.630242 TCTCTGGCCAATAAATCTTTTACAG 57.370 36.000 7.01 0.00 0.00 2.74
7078 7702 5.186797 CCAATAAATCTTTTACAGTGGCCCA 59.813 40.000 0.00 0.00 0.00 5.36
7095 7719 1.679898 CAGAAACCGCCCCTCTCTT 59.320 57.895 0.00 0.00 0.00 2.85
7104 7728 1.412710 CGCCCCTCTCTTGCAGTATAA 59.587 52.381 0.00 0.00 0.00 0.98
7106 7730 2.436173 GCCCCTCTCTTGCAGTATAACT 59.564 50.000 0.00 0.00 0.00 2.24
7107 7731 3.641906 GCCCCTCTCTTGCAGTATAACTA 59.358 47.826 0.00 0.00 0.00 2.24
7108 7732 4.101119 GCCCCTCTCTTGCAGTATAACTAA 59.899 45.833 0.00 0.00 0.00 2.24
7109 7733 5.740513 GCCCCTCTCTTGCAGTATAACTAAG 60.741 48.000 0.00 0.00 0.00 2.18
7110 7734 5.221541 CCCCTCTCTTGCAGTATAACTAAGG 60.222 48.000 0.00 0.00 0.00 2.69
7111 7735 5.364157 CCCTCTCTTGCAGTATAACTAAGGT 59.636 44.000 0.00 0.00 0.00 3.50
7112 7736 6.127026 CCCTCTCTTGCAGTATAACTAAGGTT 60.127 42.308 0.00 0.00 39.26 3.50
7113 7737 6.981559 CCTCTCTTGCAGTATAACTAAGGTTC 59.018 42.308 0.00 0.00 36.92 3.62
7116 7740 4.459390 TGCAGTATAACTAAGGTTCGCA 57.541 40.909 0.00 0.00 36.92 5.10
7119 7743 4.683832 CAGTATAACTAAGGTTCGCAGCT 58.316 43.478 0.00 0.00 36.92 4.24
7138 7762 2.253610 CTGATATACGGGGCCTAACCA 58.746 52.381 0.84 0.00 42.05 3.67
7144 7768 0.104620 ACGGGGCCTAACCATATCCT 60.105 55.000 0.84 0.00 42.05 3.24
7151 7775 0.317160 CTAACCATATCCTCGCGCCA 59.683 55.000 0.00 0.00 0.00 5.69
7175 7799 1.031112 AATCCCTCCTCTCCCCTCTT 58.969 55.000 0.00 0.00 0.00 2.85
7184 7808 3.110705 CCTCTCCCCTCTTGATTTCTCA 58.889 50.000 0.00 0.00 0.00 3.27
7185 7809 3.715834 CCTCTCCCCTCTTGATTTCTCAT 59.284 47.826 0.00 0.00 0.00 2.90
7189 7813 2.158842 CCCCTCTTGATTTCTCATCGCT 60.159 50.000 0.00 0.00 0.00 4.93
7192 7816 2.283298 TCTTGATTTCTCATCGCTGGC 58.717 47.619 0.00 0.00 0.00 4.85
7202 7826 3.610976 TCGCTGGCGACTCCAATA 58.389 55.556 13.78 0.00 46.01 1.90
7315 7946 1.004440 GTGAGGAAACAGAGCGCCT 60.004 57.895 2.29 0.00 0.00 5.52
7339 7970 1.613520 GGTACCTCAACCAAGGCCTTC 60.614 57.143 17.29 0.00 40.34 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 82 3.072468 CCTGGGACTTACGGGCGA 61.072 66.667 0.00 0.00 0.00 5.54
83 85 4.157120 CGGCCTGGGACTTACGGG 62.157 72.222 0.00 0.00 37.43 5.28
84 86 4.832608 GCGGCCTGGGACTTACGG 62.833 72.222 0.00 0.00 0.00 4.02
107 109 4.767255 GGCAGACCGAGCAGGGTG 62.767 72.222 3.13 1.54 46.96 4.61
198 207 3.121030 CGGAAACCTGGCGAGCTG 61.121 66.667 0.00 0.00 0.00 4.24
338 359 3.006859 CCAAGATTCAAAAACTCACCCCC 59.993 47.826 0.00 0.00 0.00 5.40
360 383 2.433664 ACGCCATTCCGTCCGAAC 60.434 61.111 0.00 0.00 36.61 3.95
379 402 4.489679 AAAGAATTCAAGAACGGCTCAC 57.510 40.909 8.44 0.00 0.00 3.51
384 407 5.088739 CCATCGAAAAGAATTCAAGAACGG 58.911 41.667 8.44 1.83 0.00 4.44
389 412 6.624423 ACCATTCCATCGAAAAGAATTCAAG 58.376 36.000 8.44 0.00 0.00 3.02
410 433 2.560542 CGGACCAATTCCAATCAAACCA 59.439 45.455 0.00 0.00 46.29 3.67
423 446 2.795175 CGCTCTACATACGGACCAAT 57.205 50.000 0.00 0.00 0.00 3.16
519 559 2.435938 GCCCACGATCGCCAAGAA 60.436 61.111 16.60 0.00 0.00 2.52
557 598 1.713830 GCGCACAAATCTACGGGAC 59.286 57.895 0.30 0.00 0.00 4.46
612 653 8.033038 CAGGTAGCAGCCGACTTATAATTTATA 58.967 37.037 0.00 0.00 0.00 0.98
613 654 6.874134 CAGGTAGCAGCCGACTTATAATTTAT 59.126 38.462 0.00 0.00 0.00 1.40
614 655 6.183360 ACAGGTAGCAGCCGACTTATAATTTA 60.183 38.462 0.00 0.00 0.00 1.40
615 656 5.057149 CAGGTAGCAGCCGACTTATAATTT 58.943 41.667 0.00 0.00 0.00 1.82
616 657 4.101119 ACAGGTAGCAGCCGACTTATAATT 59.899 41.667 0.00 0.00 0.00 1.40
617 658 3.641906 ACAGGTAGCAGCCGACTTATAAT 59.358 43.478 0.00 0.00 0.00 1.28
618 659 3.028850 ACAGGTAGCAGCCGACTTATAA 58.971 45.455 0.00 0.00 0.00 0.98
619 660 2.662866 ACAGGTAGCAGCCGACTTATA 58.337 47.619 0.00 0.00 0.00 0.98
620 661 1.486211 ACAGGTAGCAGCCGACTTAT 58.514 50.000 0.00 0.00 0.00 1.73
621 662 2.022195 CTACAGGTAGCAGCCGACTTA 58.978 52.381 0.00 0.00 0.00 2.24
622 663 0.818296 CTACAGGTAGCAGCCGACTT 59.182 55.000 0.00 0.00 0.00 3.01
623 664 0.323542 ACTACAGGTAGCAGCCGACT 60.324 55.000 6.38 0.00 36.66 4.18
624 665 0.531200 AACTACAGGTAGCAGCCGAC 59.469 55.000 6.38 0.00 36.66 4.79
625 666 1.203994 GAAACTACAGGTAGCAGCCGA 59.796 52.381 6.38 0.00 36.66 5.54
626 667 1.067142 TGAAACTACAGGTAGCAGCCG 60.067 52.381 6.38 0.00 36.66 5.52
627 668 2.028020 ACTGAAACTACAGGTAGCAGCC 60.028 50.000 6.38 0.00 41.59 4.85
628 669 3.254892 GACTGAAACTACAGGTAGCAGC 58.745 50.000 6.38 0.00 41.59 5.25
629 670 3.502920 CGACTGAAACTACAGGTAGCAG 58.497 50.000 6.38 8.27 41.59 4.24
630 671 2.230508 CCGACTGAAACTACAGGTAGCA 59.769 50.000 6.38 0.00 41.59 3.49
631 672 2.230750 ACCGACTGAAACTACAGGTAGC 59.769 50.000 6.38 0.00 41.59 3.58
632 673 3.834610 CACCGACTGAAACTACAGGTAG 58.165 50.000 4.95 4.95 41.59 3.18
633 674 2.029649 GCACCGACTGAAACTACAGGTA 60.030 50.000 0.00 0.00 41.59 3.08
634 675 1.270147 GCACCGACTGAAACTACAGGT 60.270 52.381 0.00 0.00 41.59 4.00
635 676 1.000955 AGCACCGACTGAAACTACAGG 59.999 52.381 0.00 0.00 41.59 4.00
636 677 2.440539 AGCACCGACTGAAACTACAG 57.559 50.000 0.00 0.00 42.78 2.74
637 678 2.159014 ACAAGCACCGACTGAAACTACA 60.159 45.455 0.00 0.00 0.00 2.74
638 679 2.475487 GACAAGCACCGACTGAAACTAC 59.525 50.000 0.00 0.00 0.00 2.73
648 704 1.007734 GTCGTCAGACAAGCACCGA 60.008 57.895 0.41 0.00 46.32 4.69
672 728 2.224523 CCAAAGGCAGTACAGGAACAGA 60.225 50.000 0.00 0.00 0.00 3.41
708 764 6.073927 CGAAGAAGTACACTGAAACCTTAACC 60.074 42.308 0.00 0.00 0.00 2.85
709 765 6.478016 ACGAAGAAGTACACTGAAACCTTAAC 59.522 38.462 0.00 0.00 0.00 2.01
710 766 6.576185 ACGAAGAAGTACACTGAAACCTTAA 58.424 36.000 0.00 0.00 0.00 1.85
726 783 1.978782 GCCGCAAATTCAACGAAGAAG 59.021 47.619 0.00 0.00 0.00 2.85
727 784 1.606668 AGCCGCAAATTCAACGAAGAA 59.393 42.857 0.00 0.00 0.00 2.52
732 789 3.451250 GCAGCCGCAAATTCAACG 58.549 55.556 0.00 0.00 38.36 4.10
745 802 1.382522 TGCAGCTAGGTAATTGCAGC 58.617 50.000 0.00 0.00 41.23 5.25
754 811 0.543749 GACCAGGATTGCAGCTAGGT 59.456 55.000 0.00 0.00 0.00 3.08
757 814 1.153369 GCGACCAGGATTGCAGCTA 60.153 57.895 0.00 0.00 0.00 3.32
758 815 2.437359 GCGACCAGGATTGCAGCT 60.437 61.111 0.00 0.00 0.00 4.24
759 816 3.512516 GGCGACCAGGATTGCAGC 61.513 66.667 0.00 0.00 0.00 5.25
760 817 3.197790 CGGCGACCAGGATTGCAG 61.198 66.667 0.00 0.00 0.00 4.41
761 818 3.545124 AACGGCGACCAGGATTGCA 62.545 57.895 16.62 0.00 0.00 4.08
762 819 2.746277 AACGGCGACCAGGATTGC 60.746 61.111 16.62 0.00 0.00 3.56
763 820 1.671054 ACAACGGCGACCAGGATTG 60.671 57.895 16.62 8.37 0.00 2.67
764 821 1.671054 CACAACGGCGACCAGGATT 60.671 57.895 16.62 0.00 0.00 3.01
765 822 2.047274 CACAACGGCGACCAGGAT 60.047 61.111 16.62 0.00 0.00 3.24
766 823 4.980805 GCACAACGGCGACCAGGA 62.981 66.667 16.62 0.00 0.00 3.86
774 831 0.110373 CGTTCTAAAGGCACAACGGC 60.110 55.000 0.00 0.00 38.34 5.68
775 832 0.110373 GCGTTCTAAAGGCACAACGG 60.110 55.000 5.33 0.00 41.49 4.44
776 833 0.584396 TGCGTTCTAAAGGCACAACG 59.416 50.000 3.17 0.00 46.15 4.10
783 840 3.980775 CCAACAACAATGCGTTCTAAAGG 59.019 43.478 0.00 0.00 34.86 3.11
827 884 2.492881 TGGGCAAGATAAACATGTGCAG 59.507 45.455 0.00 0.00 36.93 4.41
841 898 6.616774 AAATAACAAACAAATGTGGGCAAG 57.383 33.333 0.00 0.00 32.81 4.01
846 903 7.598493 CCTGGAGTAAATAACAAACAAATGTGG 59.402 37.037 0.00 0.00 32.81 4.17
863 920 6.068461 TGGCAATAATAACACCTGGAGTAA 57.932 37.500 0.00 0.00 0.00 2.24
866 923 3.316308 GCTGGCAATAATAACACCTGGAG 59.684 47.826 0.00 0.00 0.00 3.86
868 925 3.290710 AGCTGGCAATAATAACACCTGG 58.709 45.455 0.00 0.00 0.00 4.45
869 926 5.504010 CGTTAGCTGGCAATAATAACACCTG 60.504 44.000 0.00 0.00 0.00 4.00
926 983 1.134670 CCAGAGGGGTCTTGTCGATTC 60.135 57.143 0.00 0.00 0.00 2.52
946 1003 1.076332 AACTATCTTGCGCAACGGTC 58.924 50.000 21.02 0.00 0.00 4.79
985 1042 0.605319 TCCATGTTGGTGGCGAACTC 60.605 55.000 0.00 0.00 39.03 3.01
1045 1102 4.527509 TGTCTTTGCCTTTTGAACACAA 57.472 36.364 0.00 0.00 0.00 3.33
1075 1132 2.533266 TTTCTGTCCTCTGAGCACAC 57.467 50.000 0.00 0.00 0.00 3.82
1100 1157 4.553330 ACACCGTCAATAGGAACAAGAT 57.447 40.909 0.00 0.00 0.00 2.40
1119 1176 4.658901 AGTAAAAGAAGAGGGGAGTCAACA 59.341 41.667 0.00 0.00 0.00 3.33
1129 1186 3.186613 GGCGTGTTGAGTAAAAGAAGAGG 59.813 47.826 0.00 0.00 0.00 3.69
1242 1299 1.059098 TCCTGTGTGATGAACCAGCT 58.941 50.000 0.00 0.00 0.00 4.24
1404 1473 8.725148 AGTGAAGAAACATTAATCTTGCTACTG 58.275 33.333 0.00 0.00 36.08 2.74
1544 1613 1.283029 CATCCCAGTTCCACCATCAGT 59.717 52.381 0.00 0.00 0.00 3.41
1597 1666 1.440618 TCTGGCTGGTACCAAAAGGA 58.559 50.000 17.11 9.35 39.86 3.36
1850 1919 2.811101 CGTTTGGTTGGCCTTGCA 59.189 55.556 3.32 0.00 35.27 4.08
1886 1955 9.791820 CTTCATATATAGCTCTCTCATCACAAG 57.208 37.037 0.00 0.00 0.00 3.16
1973 2042 3.268023 AGAATCCGATCAAAGTCACCC 57.732 47.619 0.00 0.00 0.00 4.61
2023 2092 3.851458 TTCCTGACTGATATGCTGCAT 57.149 42.857 20.18 20.18 0.00 3.96
2124 2193 8.404107 AGTAAACATACCAATAACAACAGCTT 57.596 30.769 0.00 0.00 0.00 3.74
2221 2290 4.437239 CTGGACAATGCGAACTATTCTCT 58.563 43.478 0.00 0.00 0.00 3.10
2331 2400 4.806892 ACATCATGGGAAATTATCTGGCA 58.193 39.130 0.00 0.00 0.00 4.92
2414 2483 4.631377 CGGAATCAGCAGACATGAAGTTAA 59.369 41.667 0.00 0.00 0.00 2.01
2586 2655 5.298989 TCTTGGGCTCAACTTTAACAGTA 57.701 39.130 0.00 0.00 32.94 2.74
2896 2965 6.317893 GGACATAACCCATACTTTTCATCGTT 59.682 38.462 0.00 0.00 0.00 3.85
2950 3019 4.221703 TGCCTTTTTCTTGGTCTGTTTTGA 59.778 37.500 0.00 0.00 0.00 2.69
3410 3482 8.707938 ACTAGTGTAGTGTTAAAAACGTTCTT 57.292 30.769 0.00 0.00 37.69 2.52
3425 3497 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
3426 3498 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
3435 3507 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3436 3508 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3438 3510 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
3439 3511 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
3440 3512 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
3442 3514 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3444 3516 5.184479 TCCTCCGTCCCATAATATAAGAACG 59.816 44.000 0.00 0.00 0.00 3.95
3445 3517 6.600882 TCCTCCGTCCCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
3446 3518 6.785963 ACTTCCTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
3447 3519 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
3448 3520 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
3449 3521 7.243824 AGTACTTCCTCCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
3456 3608 3.614568 ATAGTACTTCCTCCGTCCCAT 57.385 47.619 0.00 0.00 0.00 4.00
3457 3609 4.404640 CATATAGTACTTCCTCCGTCCCA 58.595 47.826 0.00 0.00 0.00 4.37
3460 3612 3.119919 CGGCATATAGTACTTCCTCCGTC 60.120 52.174 0.00 0.00 0.00 4.79
3495 3647 0.107410 TATAGGCAAAGGCGTGTGGG 60.107 55.000 0.00 0.00 42.47 4.61
3496 3648 1.134521 TCTATAGGCAAAGGCGTGTGG 60.135 52.381 0.00 0.00 42.47 4.17
3497 3649 2.309528 TCTATAGGCAAAGGCGTGTG 57.690 50.000 0.00 0.00 42.47 3.82
3498 3650 3.560636 ATTCTATAGGCAAAGGCGTGT 57.439 42.857 0.00 0.00 42.47 4.49
3499 3651 3.627577 ACAATTCTATAGGCAAAGGCGTG 59.372 43.478 0.00 0.00 42.47 5.34
3500 3652 3.886123 ACAATTCTATAGGCAAAGGCGT 58.114 40.909 0.00 0.00 42.47 5.68
3501 3653 4.900635 AACAATTCTATAGGCAAAGGCG 57.099 40.909 0.00 0.00 42.47 5.52
3502 3654 5.965922 ACAAACAATTCTATAGGCAAAGGC 58.034 37.500 0.00 0.00 40.13 4.35
3503 3655 9.736023 GATAACAAACAATTCTATAGGCAAAGG 57.264 33.333 0.00 0.00 0.00 3.11
3633 3785 9.929180 GGCATGTAAGTCAAATACAGATAGATA 57.071 33.333 0.00 0.00 36.75 1.98
3634 3786 7.600375 CGGCATGTAAGTCAAATACAGATAGAT 59.400 37.037 0.00 0.00 36.75 1.98
3635 3787 6.923508 CGGCATGTAAGTCAAATACAGATAGA 59.076 38.462 0.00 0.00 36.75 1.98
3636 3788 6.701841 ACGGCATGTAAGTCAAATACAGATAG 59.298 38.462 0.00 0.00 36.75 2.08
3637 3789 6.578944 ACGGCATGTAAGTCAAATACAGATA 58.421 36.000 0.00 0.00 36.75 1.98
3638 3790 5.428253 ACGGCATGTAAGTCAAATACAGAT 58.572 37.500 0.00 0.00 36.75 2.90
3639 3791 4.827692 ACGGCATGTAAGTCAAATACAGA 58.172 39.130 0.00 0.00 36.75 3.41
3640 3792 6.656314 TTACGGCATGTAAGTCAAATACAG 57.344 37.500 0.00 0.00 38.12 2.74
3641 3793 6.092944 CCTTTACGGCATGTAAGTCAAATACA 59.907 38.462 0.00 0.00 43.63 2.29
3642 3794 6.483687 CCTTTACGGCATGTAAGTCAAATAC 58.516 40.000 0.00 0.00 43.63 1.89
3643 3795 6.671614 CCTTTACGGCATGTAAGTCAAATA 57.328 37.500 0.00 0.00 43.63 1.40
3644 3796 5.560966 CCTTTACGGCATGTAAGTCAAAT 57.439 39.130 0.00 0.00 43.63 2.32
3658 3810 2.348660 TGTGGATTTACGCCTTTACGG 58.651 47.619 0.00 0.00 37.37 4.02
3659 3811 3.787476 GCATGTGGATTTACGCCTTTACG 60.787 47.826 0.00 0.00 39.50 3.18
3660 3812 3.488553 GGCATGTGGATTTACGCCTTTAC 60.489 47.826 0.00 0.00 36.58 2.01
3661 3813 2.685897 GGCATGTGGATTTACGCCTTTA 59.314 45.455 0.00 0.00 36.58 1.85
3662 3814 1.476488 GGCATGTGGATTTACGCCTTT 59.524 47.619 0.00 0.00 36.58 3.11
3663 3815 1.102978 GGCATGTGGATTTACGCCTT 58.897 50.000 0.00 0.00 36.58 4.35
3664 3816 0.255890 AGGCATGTGGATTTACGCCT 59.744 50.000 0.00 0.00 44.89 5.52
3665 3817 1.102978 AAGGCATGTGGATTTACGCC 58.897 50.000 0.00 0.00 39.90 5.68
3666 3818 2.529151 CAAAGGCATGTGGATTTACGC 58.471 47.619 0.00 0.00 0.00 4.42
3667 3819 2.529151 GCAAAGGCATGTGGATTTACG 58.471 47.619 0.00 0.00 40.72 3.18
3668 3820 2.497273 AGGCAAAGGCATGTGGATTTAC 59.503 45.455 0.00 0.00 43.71 2.01
3669 3821 2.818921 AGGCAAAGGCATGTGGATTTA 58.181 42.857 0.00 0.00 43.71 1.40
3670 3822 1.648116 AGGCAAAGGCATGTGGATTT 58.352 45.000 0.00 0.00 43.71 2.17
3671 3823 2.530460 TAGGCAAAGGCATGTGGATT 57.470 45.000 0.00 0.00 43.71 3.01
3679 3831 5.480073 ACAAACAATTCTATAGGCAAAGGCA 59.520 36.000 0.00 0.00 43.71 4.75
3900 4206 7.618117 CCTATATTTTTGTACTTTGTTCCCCCT 59.382 37.037 0.00 0.00 0.00 4.79
3901 4207 7.147794 CCCTATATTTTTGTACTTTGTTCCCCC 60.148 40.741 0.00 0.00 0.00 5.40
4042 4387 4.278419 ACCAATGAAGAACCAAGTTACAGC 59.722 41.667 0.00 0.00 0.00 4.40
4280 4625 3.907474 TCCAACTGAGTGACCAAGGATAA 59.093 43.478 0.00 0.00 0.00 1.75
4382 4727 3.918258 TTTTCGACTTCAACGAGTGTG 57.082 42.857 0.00 0.00 40.72 3.82
4383 4728 3.680937 TGTTTTTCGACTTCAACGAGTGT 59.319 39.130 0.00 0.00 40.72 3.55
4527 4872 5.677319 TCGGATCAAAAGGTTCTATCAGT 57.323 39.130 0.00 0.00 0.00 3.41
4547 4892 5.911280 CCAATACAGCATAAAAAGCTCATCG 59.089 40.000 0.00 0.00 41.14 3.84
4561 4906 1.833630 CCCTCTGAGACCAATACAGCA 59.166 52.381 6.17 0.00 0.00 4.41
4767 5113 0.108804 CAGCAGCAGCAAATTCCTGG 60.109 55.000 3.17 0.00 45.49 4.45
4933 5279 9.132521 CTTTTCGAGCAAATTCATCACTATTTT 57.867 29.630 0.00 0.00 0.00 1.82
5206 5554 2.490903 CCTGCAAAATGAGGGAACAGAG 59.509 50.000 0.00 0.00 0.00 3.35
5247 5595 7.493320 CAGAAAATATGGCAGCATGTTGTTATT 59.507 33.333 11.44 9.30 39.31 1.40
5437 5788 1.338105 TGCTGACGCTGCAGAACTATT 60.338 47.619 20.43 0.00 38.14 1.73
5451 5802 0.866427 CCGATGATGCTGATGCTGAC 59.134 55.000 0.00 0.00 40.48 3.51
5520 5910 2.671963 CCTGCTGCTGCTGCTGAA 60.672 61.111 30.01 13.93 40.01 3.02
5521 5911 3.607370 CTCCTGCTGCTGCTGCTGA 62.607 63.158 30.01 23.60 40.01 4.26
5787 6195 3.358775 CACTGCTTCTTCTCTATCGTCG 58.641 50.000 0.00 0.00 0.00 5.12
6072 6480 1.364626 GGCCGATTCTGTGTGCTCTG 61.365 60.000 0.00 0.00 0.00 3.35
6117 6525 3.002656 CCACTGTGTCATTGACTGTGAAC 59.997 47.826 25.02 14.52 34.16 3.18
6131 6539 1.552337 AGATGCGATCTTCCACTGTGT 59.448 47.619 7.08 0.00 35.76 3.72
6318 6727 2.185350 CGAGTTGCGATGCCTCCT 59.815 61.111 0.00 0.00 44.57 3.69
6321 6730 4.087892 AGCCGAGTTGCGATGCCT 62.088 61.111 0.00 0.00 44.57 4.75
6597 7084 0.608130 CACATGGGAAGAGACACGGA 59.392 55.000 0.00 0.00 0.00 4.69
6599 7086 3.143675 CCACATGGGAAGAGACACG 57.856 57.895 0.00 0.00 40.01 4.49
6717 7207 4.215827 ACGAGTTTCGAGACACAAGTATCT 59.784 41.667 8.98 0.00 43.74 1.98
6803 7327 8.836413 TCAACATCTTACGAGTTTTCAAAATCT 58.164 29.630 0.00 0.00 31.33 2.40
6848 7372 6.012508 TGTTCCCTGAGGATTCTTGTTATCTT 60.013 38.462 0.00 0.00 43.54 2.40
6852 7376 5.779241 ATGTTCCCTGAGGATTCTTGTTA 57.221 39.130 0.00 0.00 43.54 2.41
6947 7471 3.402681 CATGGCCAGGAGACCCGT 61.403 66.667 13.35 0.00 37.58 5.28
7018 7545 7.004086 TCTCAAGACACATAAACCCTTGAAAT 58.996 34.615 0.00 0.00 41.51 2.17
7030 7557 5.221402 GCCAGAGATGATCTCAAGACACATA 60.221 44.000 23.17 0.00 45.73 2.29
7052 7579 5.109210 GCCACTGTAAAAGATTTATTGGCC 58.891 41.667 15.35 0.00 40.97 5.36
7055 7582 6.152661 TCTGGGCCACTGTAAAAGATTTATTG 59.847 38.462 0.00 0.00 0.00 1.90
7056 7583 6.252995 TCTGGGCCACTGTAAAAGATTTATT 58.747 36.000 0.00 0.00 0.00 1.40
7058 7585 5.249780 TCTGGGCCACTGTAAAAGATTTA 57.750 39.130 0.00 0.00 0.00 1.40
7060 7587 3.806949 TCTGGGCCACTGTAAAAGATT 57.193 42.857 0.00 0.00 0.00 2.40
7061 7588 3.806949 TTCTGGGCCACTGTAAAAGAT 57.193 42.857 0.00 0.00 0.00 2.40
7062 7589 3.219281 GTTTCTGGGCCACTGTAAAAGA 58.781 45.455 0.00 0.00 0.00 2.52
7063 7590 2.296190 GGTTTCTGGGCCACTGTAAAAG 59.704 50.000 0.00 0.00 0.00 2.27
7078 7702 1.679898 CAAGAGAGGGGCGGTTTCT 59.320 57.895 0.00 0.00 0.00 2.52
7090 7714 6.561614 CGAACCTTAGTTATACTGCAAGAGA 58.438 40.000 0.00 0.00 35.94 3.10
7095 7719 4.430007 CTGCGAACCTTAGTTATACTGCA 58.570 43.478 0.00 0.00 35.94 4.41
7104 7728 4.556898 CGTATATCAGCTGCGAACCTTAGT 60.557 45.833 9.47 0.00 0.00 2.24
7106 7730 3.305131 CCGTATATCAGCTGCGAACCTTA 60.305 47.826 9.47 0.00 0.00 2.69
7107 7731 2.545952 CCGTATATCAGCTGCGAACCTT 60.546 50.000 9.47 0.00 0.00 3.50
7108 7732 1.000163 CCGTATATCAGCTGCGAACCT 60.000 52.381 9.47 0.00 0.00 3.50
7109 7733 1.419374 CCGTATATCAGCTGCGAACC 58.581 55.000 9.47 0.00 0.00 3.62
7110 7734 1.419374 CCCGTATATCAGCTGCGAAC 58.581 55.000 9.47 3.62 0.00 3.95
7111 7735 0.317160 CCCCGTATATCAGCTGCGAA 59.683 55.000 9.47 0.00 0.00 4.70
7112 7736 1.964448 CCCCGTATATCAGCTGCGA 59.036 57.895 9.47 0.00 0.00 5.10
7113 7737 1.738099 GCCCCGTATATCAGCTGCG 60.738 63.158 9.47 6.25 0.00 5.18
7116 7740 1.900486 GTTAGGCCCCGTATATCAGCT 59.100 52.381 0.00 0.00 0.00 4.24
7119 7743 2.402182 TGGTTAGGCCCCGTATATCA 57.598 50.000 0.00 0.00 36.04 2.15
7138 7762 4.664677 GCGGTGGCGCGAGGATAT 62.665 66.667 12.10 0.00 0.00 1.63
7151 7775 2.066999 GGAGAGGAGGGATTGCGGT 61.067 63.158 0.00 0.00 0.00 5.68
7175 7799 0.175531 TCGCCAGCGATGAGAAATCA 59.824 50.000 11.27 0.00 44.01 2.57
7192 7816 2.960129 GGCGGCGTATTGGAGTCG 60.960 66.667 9.37 0.00 38.64 4.18
7287 7918 4.717629 TTCCTCACGGCGTCAGCG 62.718 66.667 10.85 0.50 46.35 5.18
7288 7919 2.357034 TTTCCTCACGGCGTCAGC 60.357 61.111 10.85 0.00 44.18 4.26
7289 7920 1.284982 CTGTTTCCTCACGGCGTCAG 61.285 60.000 10.85 6.81 0.00 3.51
7290 7921 1.300620 CTGTTTCCTCACGGCGTCA 60.301 57.895 10.85 0.00 0.00 4.35
7291 7922 1.006571 TCTGTTTCCTCACGGCGTC 60.007 57.895 10.85 0.00 0.00 5.19
7292 7923 1.006102 CTCTGTTTCCTCACGGCGT 60.006 57.895 6.77 6.77 0.00 5.68
7293 7924 2.383527 GCTCTGTTTCCTCACGGCG 61.384 63.158 4.80 4.80 0.00 6.46
7294 7925 2.383527 CGCTCTGTTTCCTCACGGC 61.384 63.158 0.00 0.00 0.00 5.68
7307 7938 2.760385 GGTACCTCCAGGCGCTCT 60.760 66.667 7.64 0.00 39.32 4.09
7315 7946 1.358152 CCTTGGTTGAGGTACCTCCA 58.642 55.000 34.05 24.76 42.09 3.86


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

AutoCloner maintained by Alex Coulton.