Multiple sequence alignment - TraesCS1D01G391900

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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 TraesCS1D01G391900 chr1D 100.000 3064 0 0 1 3064 462299718 462302781 0.000000e+00 5659.0
1 TraesCS1D01G391900 chr1D 94.444 738 38 2 42 777 354530078 354529342 0.000000e+00 1133.0
2 TraesCS1D01G391900 chr1D 88.822 331 23 8 2743 3064 462307919 462308244 7.960000e-106 394.0
3 TraesCS1D01G391900 chr2D 95.055 728 34 2 42 769 54602806 54602081 0.000000e+00 1144.0
4 TraesCS1D01G391900 chr1A 87.586 1023 80 20 1797 2795 554085985 554086984 0.000000e+00 1142.0
5 TraesCS1D01G391900 chr1A 97.740 177 4 0 1465 1641 554085812 554085988 3.840000e-79 305.0
6 TraesCS1D01G391900 chr1A 90.000 210 16 3 779 985 554084396 554084603 1.810000e-67 267.0
7 TraesCS1D01G391900 chr5D 94.587 739 35 3 42 777 398866552 398867288 0.000000e+00 1138.0
8 TraesCS1D01G391900 chr5D 90.643 171 14 2 1637 1805 59947845 59947675 3.070000e-55 226.0
9 TraesCS1D01G391900 chr5D 100.000 39 0 0 1 39 527146723 527146761 4.240000e-09 73.1
10 TraesCS1D01G391900 chrUn 94.565 736 38 2 42 777 441810960 441811693 0.000000e+00 1136.0
11 TraesCS1D01G391900 chr7D 94.452 739 37 2 42 777 205948340 205949077 0.000000e+00 1134.0
12 TraesCS1D01G391900 chr7D 92.899 169 10 2 1639 1805 397555077 397554909 8.490000e-61 244.0
13 TraesCS1D01G391900 chr7D 88.144 194 14 6 1619 1803 525767940 525768133 3.980000e-54 222.0
14 TraesCS1D01G391900 chr4D 94.444 738 37 3 42 777 329671856 329672591 0.000000e+00 1133.0
15 TraesCS1D01G391900 chr4D 89.385 179 15 3 1639 1815 326382448 326382624 3.980000e-54 222.0
16 TraesCS1D01G391900 chr4D 89.011 182 14 6 1629 1809 508222924 508222748 1.430000e-53 220.0
17 TraesCS1D01G391900 chr1B 94.317 739 37 4 42 777 584562166 584562902 0.000000e+00 1127.0
18 TraesCS1D01G391900 chr1B 94.317 739 37 4 42 777 584600222 584600958 0.000000e+00 1127.0
19 TraesCS1D01G391900 chr1B 88.391 491 34 5 1797 2266 637370320 637370808 1.230000e-158 569.0
20 TraesCS1D01G391900 chr1B 88.745 462 24 16 779 1234 637369069 637369508 9.670000e-150 540.0
21 TraesCS1D01G391900 chr1B 89.239 381 29 4 1260 1636 637369939 637370311 1.660000e-127 466.0
22 TraesCS1D01G391900 chr1B 91.279 172 15 0 2893 3064 637370807 637370978 5.110000e-58 235.0
23 TraesCS1D01G391900 chr1B 81.513 119 18 4 2941 3058 636876778 636876893 9.040000e-16 95.3
24 TraesCS1D01G391900 chr3B 93.968 746 39 4 42 784 812702599 812703341 0.000000e+00 1123.0
25 TraesCS1D01G391900 chr3B 83.884 242 34 4 776 1013 673097589 673097349 3.070000e-55 226.0
26 TraesCS1D01G391900 chr3B 85.806 155 22 0 1917 2071 673094980 673094826 6.800000e-37 165.0
27 TraesCS1D01G391900 chr3B 90.756 119 11 0 1448 1566 673095259 673095141 3.160000e-35 159.0
28 TraesCS1D01G391900 chr3B 83.929 168 26 1 1904 2071 673140471 673140305 3.160000e-35 159.0
29 TraesCS1D01G391900 chr7B 92.899 169 10 2 1639 1805 401532722 401532554 8.490000e-61 244.0
30 TraesCS1D01G391900 chr7A 92.308 169 11 2 1639 1805 451519811 451519979 3.950000e-59 239.0
31 TraesCS1D01G391900 chr7A 92.771 166 11 1 1639 1803 494786829 494786994 3.950000e-59 239.0
32 TraesCS1D01G391900 chr3A 85.169 236 32 1 781 1013 647499167 647498932 3.950000e-59 239.0
33 TraesCS1D01G391900 chr4B 90.449 178 10 7 1626 1800 406389285 406389458 8.550000e-56 228.0
34 TraesCS1D01G391900 chr3D 91.597 119 10 0 1448 1566 511442254 511442136 6.800000e-37 165.0
35 TraesCS1D01G391900 chr3D 88.722 133 15 0 1434 1566 511447624 511447492 2.440000e-36 163.0
36 TraesCS1D01G391900 chr3D 83.929 168 26 1 1904 2071 511441987 511441821 3.160000e-35 159.0


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 TraesCS1D01G391900 chr1D 462299718 462302781 3063 False 5659.000000 5659 100.000000 1 3064 1 chr1D.!!$F1 3063
1 TraesCS1D01G391900 chr1D 354529342 354530078 736 True 1133.000000 1133 94.444000 42 777 1 chr1D.!!$R1 735
2 TraesCS1D01G391900 chr2D 54602081 54602806 725 True 1144.000000 1144 95.055000 42 769 1 chr2D.!!$R1 727
3 TraesCS1D01G391900 chr1A 554084396 554086984 2588 False 571.333333 1142 91.775333 779 2795 3 chr1A.!!$F1 2016
4 TraesCS1D01G391900 chr5D 398866552 398867288 736 False 1138.000000 1138 94.587000 42 777 1 chr5D.!!$F1 735
5 TraesCS1D01G391900 chrUn 441810960 441811693 733 False 1136.000000 1136 94.565000 42 777 1 chrUn.!!$F1 735
6 TraesCS1D01G391900 chr7D 205948340 205949077 737 False 1134.000000 1134 94.452000 42 777 1 chr7D.!!$F1 735
7 TraesCS1D01G391900 chr4D 329671856 329672591 735 False 1133.000000 1133 94.444000 42 777 1 chr4D.!!$F2 735
8 TraesCS1D01G391900 chr1B 584562166 584562902 736 False 1127.000000 1127 94.317000 42 777 1 chr1B.!!$F1 735
9 TraesCS1D01G391900 chr1B 584600222 584600958 736 False 1127.000000 1127 94.317000 42 777 1 chr1B.!!$F2 735
10 TraesCS1D01G391900 chr1B 637369069 637370978 1909 False 452.500000 569 89.413500 779 3064 4 chr1B.!!$F4 2285
11 TraesCS1D01G391900 chr3B 812702599 812703341 742 False 1123.000000 1123 93.968000 42 784 1 chr3B.!!$F1 742

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
329 331 0.322456 GGTGGTACTTGGCAGCATGA 60.322 55.0 0.00 0.0 39.69 3.07 F
583 585 0.539518 TGTTAGGCTTGGCTGCGATA 59.460 50.0 6.97 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 2694 0.259938 GGATCTTGTTCTGGGCCCAT 59.740 55.0 28.82 7.65 0.00 4.00 R
2422 3663 0.029300 TTTGCTCTTTGTGTGCGCTC 59.971 50.0 9.73 5.51 37.94 5.03 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
19 20 4.296265 GGTGAAAACCGAGCCGAT 57.704 55.556 0.00 0.00 0.00 4.18
20 21 1.794222 GGTGAAAACCGAGCCGATG 59.206 57.895 0.00 0.00 0.00 3.84
21 22 1.644786 GGTGAAAACCGAGCCGATGG 61.645 60.000 0.00 0.00 0.00 3.51
40 41 4.778143 GGGTGATGGCGGCGTTCT 62.778 66.667 9.37 0.00 0.00 3.01
55 56 2.159338 GCGTTCTGACCCACTCGTATTA 60.159 50.000 0.00 0.00 0.00 0.98
60 61 3.021695 CTGACCCACTCGTATTACTCCA 58.978 50.000 0.00 0.00 0.00 3.86
83 84 1.134068 GGAAACCCTAGGATCTGGTGC 60.134 57.143 11.48 0.00 31.32 5.01
129 130 1.000607 CGGTGTCGTTTCTCTCTTGGA 60.001 52.381 0.00 0.00 0.00 3.53
152 154 0.602638 ATCGTTTTGTGGAGCAGCGA 60.603 50.000 0.00 0.00 34.27 4.93
329 331 0.322456 GGTGGTACTTGGCAGCATGA 60.322 55.000 0.00 0.00 39.69 3.07
359 361 1.022982 TATCAGTGACGACCGCGACT 61.023 55.000 8.23 0.00 41.64 4.18
524 526 2.436646 GGATCAGTGTGTGCCCCG 60.437 66.667 0.00 0.00 0.00 5.73
583 585 0.539518 TGTTAGGCTTGGCTGCGATA 59.460 50.000 6.97 0.00 0.00 2.92
605 607 5.957771 ATCTGTTTGGTATTAGGCTCAGA 57.042 39.130 0.00 0.00 35.65 3.27
616 618 2.350057 AGGCTCAGACTATCTACGCA 57.650 50.000 0.00 0.00 0.00 5.24
627 629 5.303078 AGACTATCTACGCACCTTCATCAAT 59.697 40.000 0.00 0.00 0.00 2.57
630 632 4.200838 TCTACGCACCTTCATCAATTGA 57.799 40.909 11.26 11.26 0.00 2.57
653 655 3.738830 AGGTGTAGCGACAGTTTGTTA 57.261 42.857 0.00 0.00 35.82 2.41
663 665 4.293415 CGACAGTTTGTTACTTAGACGGT 58.707 43.478 0.00 0.00 33.85 4.83
756 758 4.804420 AGATGCAGAGGCCGGGGA 62.804 66.667 2.18 0.00 40.13 4.81
758 760 2.122413 ATGCAGAGGCCGGGGATA 60.122 61.111 2.18 0.00 40.13 2.59
808 810 3.593551 AACAACGCGGCGCAGATTG 62.594 57.895 32.61 29.94 0.00 2.67
818 820 1.959085 CGCAGATTGTTGCCAAGGT 59.041 52.632 0.00 0.00 41.01 3.50
865 870 1.003355 CACCTGATGGCGACCAACT 60.003 57.895 2.68 0.00 36.95 3.16
1012 1017 4.679639 CGCTCTACAGTATGGCAAAAGGTA 60.680 45.833 0.00 0.00 43.62 3.08
1049 1124 7.923344 TCTTTTTCAATTTTCGGTGATTGCTTA 59.077 29.630 0.00 0.00 34.15 3.09
1092 1167 3.308188 GGTGTACCCTATTGCCTCTGTTT 60.308 47.826 0.00 0.00 0.00 2.83
1110 1185 8.390354 CCTCTGTTTTCCAAACTTTTGAATTTC 58.610 33.333 3.17 0.00 40.55 2.17
1122 1198 8.593492 AACTTTTGAATTTCATAAGTCCAAGC 57.407 30.769 25.49 0.00 44.13 4.01
1123 1199 7.725251 ACTTTTGAATTTCATAAGTCCAAGCA 58.275 30.769 22.00 0.00 42.28 3.91
1161 1237 9.256477 CTACTTTTGGATACTAATTCATACGCA 57.744 33.333 0.00 0.00 37.61 5.24
1162 1238 8.677148 ACTTTTGGATACTAATTCATACGCAT 57.323 30.769 0.00 0.00 37.61 4.73
1163 1239 8.559536 ACTTTTGGATACTAATTCATACGCATG 58.440 33.333 0.00 0.00 37.61 4.06
1164 1240 8.669946 TTTTGGATACTAATTCATACGCATGA 57.330 30.769 0.00 0.00 37.07 3.07
1165 1241 8.669946 TTTGGATACTAATTCATACGCATGAA 57.330 30.769 13.28 13.28 45.91 2.57
1183 1259 9.764363 ACGCATGAATCTAAGTATTCAATCTAA 57.236 29.630 0.00 0.00 46.12 2.10
1238 1315 8.239038 TGAAATTAGACTCTATCCTTGACGAT 57.761 34.615 0.00 0.00 0.00 3.73
1239 1316 9.350951 TGAAATTAGACTCTATCCTTGACGATA 57.649 33.333 0.00 0.00 0.00 2.92
1248 1367 9.747898 ACTCTATCCTTGACGATATTCTTAGAT 57.252 33.333 0.00 0.00 0.00 1.98
1255 1374 8.246871 CCTTGACGATATTCTTAGATGCTATCA 58.753 37.037 0.00 0.00 0.00 2.15
1256 1375 9.631452 CTTGACGATATTCTTAGATGCTATCAA 57.369 33.333 0.00 0.00 0.00 2.57
1329 1811 6.604171 AGATTGTGCTCATTGGGATATACAA 58.396 36.000 0.00 0.00 31.52 2.41
1395 1879 7.469594 GCAGCTCAATCCATATTTCAATTCAGA 60.470 37.037 0.00 0.00 0.00 3.27
1487 2694 2.479566 CAAGGAGCCTTGCTACAGAA 57.520 50.000 15.66 0.00 42.99 3.02
1571 2778 0.037326 ACAGTGTACGCACCATCAGG 60.037 55.000 9.48 0.00 46.35 3.86
1647 2865 8.653036 AAGTAGTTATATGATGTACTCCCTCC 57.347 38.462 0.00 0.00 0.00 4.30
1648 2866 7.766628 AGTAGTTATATGATGTACTCCCTCCA 58.233 38.462 0.00 0.00 0.00 3.86
1649 2867 8.402683 AGTAGTTATATGATGTACTCCCTCCAT 58.597 37.037 0.00 0.00 0.00 3.41
1650 2868 9.036980 GTAGTTATATGATGTACTCCCTCCATT 57.963 37.037 0.00 0.00 0.00 3.16
1651 2869 8.511748 AGTTATATGATGTACTCCCTCCATTT 57.488 34.615 0.00 0.00 0.00 2.32
1652 2870 8.949421 AGTTATATGATGTACTCCCTCCATTTT 58.051 33.333 0.00 0.00 0.00 1.82
1653 2871 9.574516 GTTATATGATGTACTCCCTCCATTTTT 57.425 33.333 0.00 0.00 0.00 1.94
1709 2927 9.020731 TGAACTACATATGGATGTATATGACGT 57.979 33.333 7.80 0.00 45.42 4.34
1712 2930 9.682465 ACTACATATGGATGTATATGACGTAGT 57.318 33.333 7.80 0.00 45.77 2.73
1732 2950 8.737175 ACGTAGTTTAGAGTGTAGATTCATTCA 58.263 33.333 0.00 0.00 37.78 2.57
1733 2951 9.737427 CGTAGTTTAGAGTGTAGATTCATTCAT 57.263 33.333 0.00 0.00 0.00 2.57
1739 2957 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
1740 2958 7.983307 AGAGTGTAGATTCATTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
1741 2959 7.066766 AGAGTGTAGATTCATTCATTTTGCTCC 59.933 37.037 0.00 0.00 0.00 4.70
1742 2960 6.660521 AGTGTAGATTCATTCATTTTGCTCCA 59.339 34.615 0.00 0.00 0.00 3.86
1743 2961 7.341256 AGTGTAGATTCATTCATTTTGCTCCAT 59.659 33.333 0.00 0.00 0.00 3.41
1744 2962 8.623903 GTGTAGATTCATTCATTTTGCTCCATA 58.376 33.333 0.00 0.00 0.00 2.74
1745 2963 9.358406 TGTAGATTCATTCATTTTGCTCCATAT 57.642 29.630 0.00 0.00 0.00 1.78
1746 2964 9.622004 GTAGATTCATTCATTTTGCTCCATATG 57.378 33.333 0.00 0.00 0.00 1.78
1747 2965 8.246430 AGATTCATTCATTTTGCTCCATATGT 57.754 30.769 1.24 0.00 0.00 2.29
1748 2966 9.358406 AGATTCATTCATTTTGCTCCATATGTA 57.642 29.630 1.24 0.00 0.00 2.29
1749 2967 9.622004 GATTCATTCATTTTGCTCCATATGTAG 57.378 33.333 1.24 0.00 0.00 2.74
1750 2968 8.523915 TTCATTCATTTTGCTCCATATGTAGT 57.476 30.769 1.24 0.00 0.00 2.73
1751 2969 8.158169 TCATTCATTTTGCTCCATATGTAGTC 57.842 34.615 1.24 0.00 0.00 2.59
1752 2970 6.942532 TTCATTTTGCTCCATATGTAGTCC 57.057 37.500 1.24 0.00 0.00 3.85
1753 2971 6.000246 TCATTTTGCTCCATATGTAGTCCA 58.000 37.500 1.24 0.00 0.00 4.02
1754 2972 6.604171 TCATTTTGCTCCATATGTAGTCCAT 58.396 36.000 1.24 0.00 37.58 3.41
1755 2973 7.744733 TCATTTTGCTCCATATGTAGTCCATA 58.255 34.615 1.24 0.00 40.27 2.74
1756 2974 8.385491 TCATTTTGCTCCATATGTAGTCCATAT 58.615 33.333 1.24 0.00 45.67 1.78
1757 2975 9.017509 CATTTTGCTCCATATGTAGTCCATATT 57.982 33.333 1.24 0.00 42.87 1.28
1758 2976 7.984422 TTTGCTCCATATGTAGTCCATATTG 57.016 36.000 1.24 0.00 42.87 1.90
1759 2977 6.053632 TGCTCCATATGTAGTCCATATTGG 57.946 41.667 1.24 0.00 42.87 3.16
1760 2978 5.784906 TGCTCCATATGTAGTCCATATTGGA 59.215 40.000 1.24 0.00 45.98 3.53
1793 3011 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
1794 3012 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1795 3013 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1796 3014 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1797 3015 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
1798 3016 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
1799 3017 7.954620 ACTTATATTTAGGAACGGAGGGAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
1889 3108 0.109781 ACGCATGGCAAAATGTCGAC 60.110 50.000 9.11 9.11 33.90 4.20
1994 3232 4.094887 GCGATTGTGGTGTCATTTCTATGT 59.905 41.667 0.00 0.00 33.34 2.29
2093 3331 4.756502 AGAGTACCTTGCGAATAAACTCC 58.243 43.478 0.00 0.00 33.91 3.85
2131 3369 4.142271 ACAAAGAGCGACAAAATCCAACAA 60.142 37.500 0.00 0.00 0.00 2.83
2148 3386 4.681025 CCAACAATCCAAAGACATTTCGTG 59.319 41.667 0.00 0.00 0.00 4.35
2161 3399 1.246649 TTTCGTGGTACGTAGGCAGA 58.753 50.000 0.00 0.00 43.14 4.26
2197 3435 5.220719 GTGTAACAGCGTGAGGTAACTTTTT 60.221 40.000 0.00 0.00 43.62 1.94
2230 3468 7.339466 AGTGAAAGAAAGGCAATCCGTATAAAT 59.661 33.333 0.00 0.00 37.47 1.40
2234 3472 9.965824 AAAGAAAGGCAATCCGTATAAATAATG 57.034 29.630 0.00 0.00 37.47 1.90
2265 3503 8.889717 CATGGGTGTTAATTAGTTGTTACTAGG 58.110 37.037 0.00 0.00 38.09 3.02
2268 3506 9.676861 GGGTGTTAATTAGTTGTTACTAGGATT 57.323 33.333 0.00 0.00 38.09 3.01
2311 3550 7.093902 GCTTTGCCCTTTTCTATTAGTTAACCT 60.094 37.037 0.88 0.00 0.00 3.50
2346 3587 6.850752 TGCATATATCTCTAATCGTTGGGA 57.149 37.500 0.00 0.00 0.00 4.37
2356 3597 6.984474 TCTCTAATCGTTGGGATGAAATACAC 59.016 38.462 0.00 0.00 34.93 2.90
2363 3604 5.331902 GTTGGGATGAAATACACGAACATG 58.668 41.667 0.00 0.00 0.00 3.21
2368 3609 7.093988 TGGGATGAAATACACGAACATGATTTT 60.094 33.333 0.00 0.00 0.00 1.82
2426 3667 8.728088 AAATAAAATCACAACAAAGTAGAGCG 57.272 30.769 0.00 0.00 0.00 5.03
2429 3670 1.864711 TCACAACAAAGTAGAGCGCAC 59.135 47.619 11.47 2.25 0.00 5.34
2437 3678 2.071688 AGTAGAGCGCACACAAAGAG 57.928 50.000 11.47 0.00 0.00 2.85
2453 3694 6.088824 CACAAAGAGCAAAGATCATTGGTAC 58.911 40.000 14.71 9.08 40.82 3.34
2454 3695 5.769662 ACAAAGAGCAAAGATCATTGGTACA 59.230 36.000 14.71 0.00 40.82 2.90
2496 3737 4.950205 TTTCGAAGTGAAGTCCTTACCT 57.050 40.909 0.00 0.00 37.99 3.08
2508 3749 1.524482 CTTACCTCTGGCCTGGCTC 59.476 63.158 19.68 9.39 0.00 4.70
2516 3757 0.543277 CTGGCCTGGCTCTATGAACA 59.457 55.000 19.68 4.21 0.00 3.18
2519 3760 1.474143 GGCCTGGCTCTATGAACACTC 60.474 57.143 19.68 0.00 0.00 3.51
2521 3762 1.139853 CCTGGCTCTATGAACACTCCC 59.860 57.143 0.00 0.00 0.00 4.30
2524 3765 1.471676 GGCTCTATGAACACTCCCACG 60.472 57.143 0.00 0.00 0.00 4.94
2530 3771 1.292541 GAACACTCCCACGAGGTCC 59.707 63.158 0.00 0.00 40.77 4.46
2531 3772 1.458777 AACACTCCCACGAGGTCCA 60.459 57.895 0.00 0.00 40.77 4.02
2532 3773 1.755393 AACACTCCCACGAGGTCCAC 61.755 60.000 0.00 0.00 40.77 4.02
2533 3774 2.989824 ACTCCCACGAGGTCCACG 60.990 66.667 7.20 7.20 40.77 4.94
2534 3775 2.675423 CTCCCACGAGGTCCACGA 60.675 66.667 16.05 0.00 36.75 4.35
2535 3776 2.987547 TCCCACGAGGTCCACGAC 60.988 66.667 16.05 0.00 36.75 4.34
2536 3777 3.299977 CCCACGAGGTCCACGACA 61.300 66.667 16.05 0.00 33.68 4.35
2537 3778 2.049433 CCACGAGGTCCACGACAC 60.049 66.667 16.05 0.00 33.68 3.67
2538 3779 2.428569 CACGAGGTCCACGACACG 60.429 66.667 16.05 1.91 38.76 4.49
2539 3780 2.592574 ACGAGGTCCACGACACGA 60.593 61.111 16.05 0.00 37.34 4.35
2550 3791 4.295119 GACACGACACGCCACCCT 62.295 66.667 0.00 0.00 0.00 4.34
2551 3792 4.602259 ACACGACACGCCACCCTG 62.602 66.667 0.00 0.00 0.00 4.45
2560 3801 1.823899 CGCCACCCTGCCTAATTCC 60.824 63.158 0.00 0.00 0.00 3.01
2563 3804 1.823899 CACCCTGCCTAATTCCGCC 60.824 63.158 0.00 0.00 0.00 6.13
2564 3805 2.305607 ACCCTGCCTAATTCCGCCA 61.306 57.895 0.00 0.00 0.00 5.69
2570 3811 0.533085 GCCTAATTCCGCCAGTCCTC 60.533 60.000 0.00 0.00 0.00 3.71
2573 3814 0.326238 TAATTCCGCCAGTCCTCCCT 60.326 55.000 0.00 0.00 0.00 4.20
2575 3816 3.846405 TTCCGCCAGTCCTCCCTGT 62.846 63.158 0.00 0.00 0.00 4.00
2587 3828 3.707102 GTCCTCCCTGTCTACTTATGCTT 59.293 47.826 0.00 0.00 0.00 3.91
2589 3830 3.706594 CCTCCCTGTCTACTTATGCTTGA 59.293 47.826 0.00 0.00 0.00 3.02
2596 3837 6.332735 TGTCTACTTATGCTTGATATCGCT 57.667 37.500 0.00 0.00 0.00 4.93
2597 3838 6.382608 TGTCTACTTATGCTTGATATCGCTC 58.617 40.000 0.00 0.00 0.00 5.03
2607 3848 4.711721 CTTGATATCGCTCTCTTCTCTCG 58.288 47.826 0.00 0.00 0.00 4.04
2612 3853 2.791868 GCTCTCTTCTCTCGGCCCC 61.792 68.421 0.00 0.00 0.00 5.80
2620 3861 0.909610 TCTCTCGGCCCCTTCATTGT 60.910 55.000 0.00 0.00 0.00 2.71
2623 3864 1.304052 TCGGCCCCTTCATTGTTGG 60.304 57.895 0.00 0.00 0.00 3.77
2626 3867 3.005540 GCCCCTTCATTGTTGGCCG 62.006 63.158 0.00 0.00 36.07 6.13
2643 3884 1.347707 GCCGGGATGATCCAGTTATCA 59.652 52.381 14.36 0.00 38.64 2.15
2647 3888 3.744660 GGGATGATCCAGTTATCACACC 58.255 50.000 14.36 0.00 38.65 4.16
2658 3899 1.195442 TATCACACCACTCCCGCCAA 61.195 55.000 0.00 0.00 0.00 4.52
2660 3901 4.265056 ACACCACTCCCGCCAACC 62.265 66.667 0.00 0.00 0.00 3.77
2673 3914 2.602676 CCAACCGGACCACTCCCAT 61.603 63.158 9.46 0.00 31.93 4.00
2676 3917 4.838152 CCGGACCACTCCCATGCG 62.838 72.222 0.00 0.00 31.93 4.73
2683 3924 1.746615 CACTCCCATGCGTTCCCAG 60.747 63.158 0.00 0.00 0.00 4.45
2688 3929 3.803082 CATGCGTTCCCAGCCACG 61.803 66.667 0.00 0.00 39.49 4.94
2702 3943 2.765807 CACGCCATCCCTCCTCCT 60.766 66.667 0.00 0.00 0.00 3.69
2710 3951 1.069823 CATCCCTCCTCCTCATGAACG 59.930 57.143 0.00 0.00 0.00 3.95
2724 3965 0.858583 TGAACGTGAACATGCTGTCG 59.141 50.000 0.00 0.00 0.00 4.35
2737 3978 4.742649 TGTCGCGCCTCCTCTCCT 62.743 66.667 0.00 0.00 0.00 3.69
2755 3996 2.590007 CCGCACATAGCTCTGGCC 60.590 66.667 3.94 0.00 42.61 5.36
2771 4012 2.867472 CCGGTTGACGCCATTGAC 59.133 61.111 0.00 0.00 42.52 3.18
2786 4027 2.025589 TTGACGCACACAAGGTGTTA 57.974 45.000 0.00 0.00 45.08 2.41
2827 4068 9.740710 AGATAGTATGCTACCTCTTTTTGTTTT 57.259 29.630 0.00 0.00 0.00 2.43
2828 4069 9.989869 GATAGTATGCTACCTCTTTTTGTTTTC 57.010 33.333 0.00 0.00 0.00 2.29
2829 4070 9.740710 ATAGTATGCTACCTCTTTTTGTTTTCT 57.259 29.630 0.00 0.00 0.00 2.52
2830 4071 8.465273 AGTATGCTACCTCTTTTTGTTTTCTT 57.535 30.769 0.00 0.00 0.00 2.52
2831 4072 8.914011 AGTATGCTACCTCTTTTTGTTTTCTTT 58.086 29.630 0.00 0.00 0.00 2.52
2832 4073 9.529325 GTATGCTACCTCTTTTTGTTTTCTTTT 57.471 29.630 0.00 0.00 0.00 2.27
2834 4075 8.474006 TGCTACCTCTTTTTGTTTTCTTTTTC 57.526 30.769 0.00 0.00 0.00 2.29
2835 4076 7.547722 TGCTACCTCTTTTTGTTTTCTTTTTCC 59.452 33.333 0.00 0.00 0.00 3.13
2836 4077 7.011109 GCTACCTCTTTTTGTTTTCTTTTTCCC 59.989 37.037 0.00 0.00 0.00 3.97
2837 4078 6.177610 ACCTCTTTTTGTTTTCTTTTTCCCC 58.822 36.000 0.00 0.00 0.00 4.81
2838 4079 6.176896 CCTCTTTTTGTTTTCTTTTTCCCCA 58.823 36.000 0.00 0.00 0.00 4.96
2839 4080 6.316140 CCTCTTTTTGTTTTCTTTTTCCCCAG 59.684 38.462 0.00 0.00 0.00 4.45
2840 4081 5.645929 TCTTTTTGTTTTCTTTTTCCCCAGC 59.354 36.000 0.00 0.00 0.00 4.85
2841 4082 4.559862 TTTGTTTTCTTTTTCCCCAGCA 57.440 36.364 0.00 0.00 0.00 4.41
2842 4083 4.559862 TTGTTTTCTTTTTCCCCAGCAA 57.440 36.364 0.00 0.00 0.00 3.91
2843 4084 4.769345 TGTTTTCTTTTTCCCCAGCAAT 57.231 36.364 0.00 0.00 0.00 3.56
2844 4085 5.109500 TGTTTTCTTTTTCCCCAGCAATT 57.891 34.783 0.00 0.00 0.00 2.32
2845 4086 6.240549 TGTTTTCTTTTTCCCCAGCAATTA 57.759 33.333 0.00 0.00 0.00 1.40
2846 4087 6.287525 TGTTTTCTTTTTCCCCAGCAATTAG 58.712 36.000 0.00 0.00 0.00 1.73
2847 4088 6.098982 TGTTTTCTTTTTCCCCAGCAATTAGA 59.901 34.615 0.00 0.00 0.00 2.10
2848 4089 6.933514 TTTCTTTTTCCCCAGCAATTAGAT 57.066 33.333 0.00 0.00 0.00 1.98
2849 4090 6.530019 TTCTTTTTCCCCAGCAATTAGATC 57.470 37.500 0.00 0.00 0.00 2.75
2850 4091 5.579047 TCTTTTTCCCCAGCAATTAGATCA 58.421 37.500 0.00 0.00 0.00 2.92
2851 4092 6.197168 TCTTTTTCCCCAGCAATTAGATCAT 58.803 36.000 0.00 0.00 0.00 2.45
2852 4093 5.857471 TTTTCCCCAGCAATTAGATCATG 57.143 39.130 0.00 0.00 0.00 3.07
2853 4094 4.524802 TTCCCCAGCAATTAGATCATGT 57.475 40.909 0.00 0.00 0.00 3.21
2854 4095 4.524802 TCCCCAGCAATTAGATCATGTT 57.475 40.909 0.00 0.00 0.00 2.71
2855 4096 4.870636 TCCCCAGCAATTAGATCATGTTT 58.129 39.130 0.00 0.00 0.00 2.83
2856 4097 6.012337 TCCCCAGCAATTAGATCATGTTTA 57.988 37.500 0.00 0.00 0.00 2.01
2857 4098 6.430864 TCCCCAGCAATTAGATCATGTTTAA 58.569 36.000 0.00 0.00 0.00 1.52
2858 4099 6.894654 TCCCCAGCAATTAGATCATGTTTAAA 59.105 34.615 0.00 0.00 0.00 1.52
2859 4100 7.564660 TCCCCAGCAATTAGATCATGTTTAAAT 59.435 33.333 0.00 0.00 0.00 1.40
2860 4101 7.654520 CCCCAGCAATTAGATCATGTTTAAATG 59.345 37.037 0.00 0.00 0.00 2.32
2861 4102 8.415553 CCCAGCAATTAGATCATGTTTAAATGA 58.584 33.333 0.00 0.00 40.73 2.57
2862 4103 9.459640 CCAGCAATTAGATCATGTTTAAATGAG 57.540 33.333 0.00 0.00 39.84 2.90
2870 4111 8.425577 AGATCATGTTTAAATGAGTAAGGACG 57.574 34.615 0.00 0.00 39.84 4.79
2871 4112 8.041323 AGATCATGTTTAAATGAGTAAGGACGT 58.959 33.333 0.00 0.00 39.84 4.34
2872 4113 7.972832 TCATGTTTAAATGAGTAAGGACGTT 57.027 32.000 0.00 0.00 32.75 3.99
2873 4114 7.802738 TCATGTTTAAATGAGTAAGGACGTTG 58.197 34.615 0.00 0.00 32.75 4.10
2874 4115 6.548441 TGTTTAAATGAGTAAGGACGTTGG 57.452 37.500 0.00 0.00 0.00 3.77
2875 4116 5.049267 TGTTTAAATGAGTAAGGACGTTGGC 60.049 40.000 0.00 0.00 0.00 4.52
2876 4117 1.722011 AATGAGTAAGGACGTTGGCG 58.278 50.000 0.00 0.00 44.93 5.69
2887 4128 3.835686 CGTTGGCGTTGTTCAATGA 57.164 47.368 8.68 0.00 33.14 2.57
2888 4129 1.394697 CGTTGGCGTTGTTCAATGAC 58.605 50.000 8.68 6.33 33.14 3.06
2889 4130 1.268285 CGTTGGCGTTGTTCAATGACA 60.268 47.619 8.96 8.96 33.14 3.58
2890 4131 2.604373 CGTTGGCGTTGTTCAATGACAT 60.604 45.455 13.10 0.00 33.14 3.06
2891 4132 3.380142 GTTGGCGTTGTTCAATGACATT 58.620 40.909 13.10 0.00 0.00 2.71
2913 4154 5.058149 TGGTGTCAATGAAAAATCATCCG 57.942 39.130 0.00 0.00 0.00 4.18
2937 4178 7.161404 CGAGGAGGAATGTTTATGATCCATTA 58.839 38.462 0.00 0.00 34.30 1.90
2942 4183 6.001460 GGAATGTTTATGATCCATTACCCGA 58.999 40.000 0.00 0.00 32.08 5.14
2967 4208 6.589648 AGGATGGTCATGAAATCCTTGAGGA 61.590 44.000 25.56 1.54 46.49 3.71
3013 4254 0.881118 TTTTGCTTGCGGAGATGGAC 59.119 50.000 0.00 0.00 0.00 4.02
3026 4267 1.303317 ATGGACGAGGGCAACAACC 60.303 57.895 0.00 0.00 39.74 3.77
3034 4275 0.827507 AGGGCAACAACCGAAAGCAT 60.828 50.000 0.00 0.00 39.74 3.79
3035 4276 0.667184 GGGCAACAACCGAAAGCATG 60.667 55.000 0.00 0.00 39.74 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.644786 CCATCGGCTCGGTTTTCACC 61.645 60.000 0.00 0.00 40.16 4.02
3 4 1.794222 CCATCGGCTCGGTTTTCAC 59.206 57.895 0.00 0.00 0.00 3.18
4 5 2.038269 GCCATCGGCTCGGTTTTCA 61.038 57.895 0.00 0.00 46.69 2.69
5 6 2.791927 GCCATCGGCTCGGTTTTC 59.208 61.111 0.00 0.00 46.69 2.29
23 24 4.778143 AGAACGCCGCCATCACCC 62.778 66.667 0.00 0.00 0.00 4.61
24 25 3.499737 CAGAACGCCGCCATCACC 61.500 66.667 0.00 0.00 0.00 4.02
25 26 2.434185 TCAGAACGCCGCCATCAC 60.434 61.111 0.00 0.00 0.00 3.06
26 27 2.434185 GTCAGAACGCCGCCATCA 60.434 61.111 0.00 0.00 0.00 3.07
27 28 3.195698 GGTCAGAACGCCGCCATC 61.196 66.667 0.00 0.00 0.00 3.51
28 29 4.778143 GGGTCAGAACGCCGCCAT 62.778 66.667 0.00 0.00 32.40 4.40
31 32 4.681978 AGTGGGTCAGAACGCCGC 62.682 66.667 0.00 0.00 37.53 6.53
32 33 2.432628 GAGTGGGTCAGAACGCCG 60.433 66.667 0.00 0.00 37.53 6.46
33 34 1.870055 TACGAGTGGGTCAGAACGCC 61.870 60.000 0.00 0.00 37.53 5.68
34 35 0.172803 ATACGAGTGGGTCAGAACGC 59.827 55.000 0.00 0.00 38.75 4.84
35 36 2.649331 AATACGAGTGGGTCAGAACG 57.351 50.000 0.00 0.00 0.00 3.95
36 37 4.439837 GGAGTAATACGAGTGGGTCAGAAC 60.440 50.000 0.00 0.00 0.00 3.01
37 38 3.698040 GGAGTAATACGAGTGGGTCAGAA 59.302 47.826 0.00 0.00 0.00 3.02
38 39 3.285484 GGAGTAATACGAGTGGGTCAGA 58.715 50.000 0.00 0.00 0.00 3.27
39 40 3.021695 TGGAGTAATACGAGTGGGTCAG 58.978 50.000 0.00 0.00 0.00 3.51
40 41 3.021695 CTGGAGTAATACGAGTGGGTCA 58.978 50.000 0.00 0.00 0.00 4.02
129 130 1.267806 CTGCTCCACAAAACGATGCTT 59.732 47.619 0.00 0.00 0.00 3.91
152 154 1.202330 CTCCTGCCTCTGACTTCCAT 58.798 55.000 0.00 0.00 0.00 3.41
329 331 1.202582 GTCACTGATACACCTCAGCGT 59.797 52.381 1.14 0.00 45.37 5.07
348 350 2.354305 GAACACAGTCGCGGTCGT 60.354 61.111 6.13 0.00 36.96 4.34
359 361 0.522286 CGCGCAAACAACTGAACACA 60.522 50.000 8.75 0.00 0.00 3.72
368 370 3.659092 CTCCCTGCGCGCAAACAA 61.659 61.111 35.50 18.84 0.00 2.83
407 409 1.008424 CAGCTATCGTCGACGCCAT 60.008 57.895 32.19 23.00 39.60 4.40
497 499 4.148825 ACTGATCCGGCGTGCTCC 62.149 66.667 6.01 0.00 0.00 4.70
510 512 3.936203 GTCCGGGGCACACACTGA 61.936 66.667 0.00 0.00 0.00 3.41
524 526 1.823899 CTAGCCATTTGCCGGGTCC 60.824 63.158 2.18 0.00 42.71 4.46
535 537 0.253160 TGAGACCCCAACCTAGCCAT 60.253 55.000 0.00 0.00 0.00 4.40
583 585 5.426833 AGTCTGAGCCTAATACCAAACAGAT 59.573 40.000 0.00 0.00 35.99 2.90
605 607 5.537300 ATTGATGAAGGTGCGTAGATAGT 57.463 39.130 0.00 0.00 0.00 2.12
627 629 4.530710 AACTGTCGCTACACCTATTCAA 57.469 40.909 0.00 0.00 0.00 2.69
630 632 4.267349 ACAAACTGTCGCTACACCTATT 57.733 40.909 0.00 0.00 0.00 1.73
653 655 3.163467 AGACTAAAGCCACCGTCTAAGT 58.837 45.455 0.00 0.00 35.15 2.24
663 665 8.978472 AGTCATATAACAGTAAGACTAAAGCCA 58.022 33.333 0.00 0.00 34.83 4.75
777 779 1.155889 CGTTGTTCACCTGCATAGCA 58.844 50.000 0.00 0.00 36.92 3.49
808 810 2.639286 CACGCTCACCTTGGCAAC 59.361 61.111 0.00 0.00 0.00 4.17
813 815 1.669115 CCACTCCACGCTCACCTTG 60.669 63.158 0.00 0.00 0.00 3.61
818 820 1.591703 GATGTCCACTCCACGCTCA 59.408 57.895 0.00 0.00 0.00 4.26
865 870 4.008330 CTGAGGTGGAAGTACGACTCTTA 58.992 47.826 0.00 0.00 0.00 2.10
903 908 1.677552 GGAGGCGTTGAGGAGGAAA 59.322 57.895 0.00 0.00 0.00 3.13
932 937 3.990469 GGATATGTTGACGATGCTACCTG 59.010 47.826 0.00 0.00 0.00 4.00
1012 1017 6.686484 AAATTGAAAAAGAGGCAATAGGGT 57.314 33.333 0.00 0.00 32.39 4.34
1049 1124 2.730094 CGGCTTGCTTTGCTTGGT 59.270 55.556 0.00 0.00 0.00 3.67
1059 1134 2.561373 GTACACCAAGCGGCTTGC 59.439 61.111 32.00 17.25 46.98 4.01
1092 1167 9.541143 GGACTTATGAAATTCAAAAGTTTGGAA 57.459 29.630 7.88 7.88 38.66 3.53
1110 1185 9.643693 AGATTTTACATTTTGCTTGGACTTATG 57.356 29.630 0.00 0.00 0.00 1.90
1153 1229 9.710900 ATTGAATACTTAGATTCATGCGTATGA 57.289 29.630 12.50 12.50 43.56 2.15
1155 1231 9.935241 AGATTGAATACTTAGATTCATGCGTAT 57.065 29.630 0.00 0.00 43.56 3.06
1157 1233 9.764363 TTAGATTGAATACTTAGATTCATGCGT 57.236 29.630 0.00 0.00 43.56 5.24
1295 1777 7.147312 CCAATGAGCACAATCTAACTTTTGAA 58.853 34.615 0.00 0.00 0.00 2.69
1299 1781 5.324409 TCCCAATGAGCACAATCTAACTTT 58.676 37.500 0.00 0.00 0.00 2.66
1308 1790 8.938801 ATATTTGTATATCCCAATGAGCACAA 57.061 30.769 0.00 0.00 0.00 3.33
1348 1830 7.368833 GCTGCAGCTATGAATATCTTCAATTT 58.631 34.615 31.33 0.00 40.30 1.82
1426 1910 4.709250 TGCATGCCAGACGGTATTTATTA 58.291 39.130 16.68 0.00 35.02 0.98
1427 1911 3.550820 TGCATGCCAGACGGTATTTATT 58.449 40.909 16.68 0.00 35.02 1.40
1428 1912 3.141398 CTGCATGCCAGACGGTATTTAT 58.859 45.455 16.68 0.00 44.64 1.40
1429 1913 2.560504 CTGCATGCCAGACGGTATTTA 58.439 47.619 16.68 0.00 44.64 1.40
1430 1914 1.382522 CTGCATGCCAGACGGTATTT 58.617 50.000 16.68 0.00 44.64 1.40
1431 1915 0.464373 CCTGCATGCCAGACGGTATT 60.464 55.000 16.68 0.00 44.64 1.89
1441 1925 0.743097 GTTGATTCCTCCTGCATGCC 59.257 55.000 16.68 0.00 0.00 4.40
1487 2694 0.259938 GGATCTTGTTCTGGGCCCAT 59.740 55.000 28.82 7.65 0.00 4.00
1693 2911 9.298250 ACTCTAAACTACGTCATATACATCCAT 57.702 33.333 0.00 0.00 0.00 3.41
1694 2912 8.565416 CACTCTAAACTACGTCATATACATCCA 58.435 37.037 0.00 0.00 0.00 3.41
1695 2913 8.566260 ACACTCTAAACTACGTCATATACATCC 58.434 37.037 0.00 0.00 0.00 3.51
1698 2916 9.822185 TCTACACTCTAAACTACGTCATATACA 57.178 33.333 0.00 0.00 0.00 2.29
1702 2920 9.387257 TGAATCTACACTCTAAACTACGTCATA 57.613 33.333 0.00 0.00 0.00 2.15
1703 2921 8.277490 TGAATCTACACTCTAAACTACGTCAT 57.723 34.615 0.00 0.00 0.00 3.06
1704 2922 7.677454 TGAATCTACACTCTAAACTACGTCA 57.323 36.000 0.00 0.00 0.00 4.35
1705 2923 9.224058 GAATGAATCTACACTCTAAACTACGTC 57.776 37.037 0.00 0.00 0.00 4.34
1706 2924 8.737175 TGAATGAATCTACACTCTAAACTACGT 58.263 33.333 0.00 0.00 0.00 3.57
1707 2925 9.737427 ATGAATGAATCTACACTCTAAACTACG 57.263 33.333 0.00 0.00 0.00 3.51
1713 2931 9.453572 AGCAAAATGAATGAATCTACACTCTAA 57.546 29.630 0.00 0.00 0.00 2.10
1714 2932 9.102757 GAGCAAAATGAATGAATCTACACTCTA 57.897 33.333 0.00 0.00 0.00 2.43
1715 2933 7.066766 GGAGCAAAATGAATGAATCTACACTCT 59.933 37.037 0.00 0.00 0.00 3.24
1716 2934 7.148188 TGGAGCAAAATGAATGAATCTACACTC 60.148 37.037 0.00 0.00 0.00 3.51
1717 2935 6.660521 TGGAGCAAAATGAATGAATCTACACT 59.339 34.615 0.00 0.00 0.00 3.55
1718 2936 6.855836 TGGAGCAAAATGAATGAATCTACAC 58.144 36.000 0.00 0.00 0.00 2.90
1719 2937 7.649533 ATGGAGCAAAATGAATGAATCTACA 57.350 32.000 0.00 0.00 0.00 2.74
1720 2938 9.622004 CATATGGAGCAAAATGAATGAATCTAC 57.378 33.333 0.00 0.00 0.00 2.59
1721 2939 9.358406 ACATATGGAGCAAAATGAATGAATCTA 57.642 29.630 7.80 0.00 0.00 1.98
1722 2940 8.246430 ACATATGGAGCAAAATGAATGAATCT 57.754 30.769 7.80 0.00 0.00 2.40
1723 2941 9.622004 CTACATATGGAGCAAAATGAATGAATC 57.378 33.333 0.89 0.00 0.00 2.52
1724 2942 9.139734 ACTACATATGGAGCAAAATGAATGAAT 57.860 29.630 15.30 0.00 0.00 2.57
1725 2943 8.523915 ACTACATATGGAGCAAAATGAATGAA 57.476 30.769 15.30 0.00 0.00 2.57
1726 2944 7.229306 GGACTACATATGGAGCAAAATGAATGA 59.771 37.037 15.30 0.00 0.00 2.57
1727 2945 7.013559 TGGACTACATATGGAGCAAAATGAATG 59.986 37.037 15.30 0.00 0.00 2.67
1728 2946 7.062322 TGGACTACATATGGAGCAAAATGAAT 58.938 34.615 15.30 0.00 0.00 2.57
1729 2947 6.422333 TGGACTACATATGGAGCAAAATGAA 58.578 36.000 15.30 0.00 0.00 2.57
1730 2948 6.000246 TGGACTACATATGGAGCAAAATGA 58.000 37.500 15.30 0.00 0.00 2.57
1731 2949 6.889301 ATGGACTACATATGGAGCAAAATG 57.111 37.500 15.30 0.00 38.26 2.32
1768 2986 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1769 2987 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1770 2988 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1771 2989 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1772 2990 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1773 2991 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1774 2992 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1776 2994 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
1777 2995 7.147707 GCATATACTCCCTCCGTTCCTAAATAT 60.148 40.741 0.00 0.00 0.00 1.28
1778 2996 6.154021 GCATATACTCCCTCCGTTCCTAAATA 59.846 42.308 0.00 0.00 0.00 1.40
1779 2997 5.046520 GCATATACTCCCTCCGTTCCTAAAT 60.047 44.000 0.00 0.00 0.00 1.40
1780 2998 4.282703 GCATATACTCCCTCCGTTCCTAAA 59.717 45.833 0.00 0.00 0.00 1.85
1781 2999 3.830755 GCATATACTCCCTCCGTTCCTAA 59.169 47.826 0.00 0.00 0.00 2.69
1782 3000 3.181426 TGCATATACTCCCTCCGTTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
1783 3001 2.249139 GCATATACTCCCTCCGTTCCT 58.751 52.381 0.00 0.00 0.00 3.36
1784 3002 1.968493 TGCATATACTCCCTCCGTTCC 59.032 52.381 0.00 0.00 0.00 3.62
1785 3003 3.746045 TTGCATATACTCCCTCCGTTC 57.254 47.619 0.00 0.00 0.00 3.95
1786 3004 5.084519 TCTATTGCATATACTCCCTCCGTT 58.915 41.667 0.00 0.00 0.00 4.44
1787 3005 4.673968 TCTATTGCATATACTCCCTCCGT 58.326 43.478 0.00 0.00 0.00 4.69
1788 3006 5.661056 TTCTATTGCATATACTCCCTCCG 57.339 43.478 0.00 0.00 0.00 4.63
1789 3007 8.312669 AGTATTCTATTGCATATACTCCCTCC 57.687 38.462 0.00 0.00 30.11 4.30
1790 3008 9.196139 AGAGTATTCTATTGCATATACTCCCTC 57.804 37.037 19.12 8.67 45.32 4.30
1791 3009 9.554053 AAGAGTATTCTATTGCATATACTCCCT 57.446 33.333 19.12 11.06 45.32 4.20
1889 3108 6.266330 TGATCTCCAGGTATAGTGATCAGTTG 59.734 42.308 8.68 0.14 37.82 3.16
1975 3213 5.356751 GGCATACATAGAAATGACACCACAA 59.643 40.000 0.00 0.00 36.54 3.33
2131 3369 3.682858 CGTACCACGAAATGTCTTTGGAT 59.317 43.478 7.29 0.00 46.05 3.41
2148 3386 2.857592 TTTCGATCTGCCTACGTACC 57.142 50.000 0.00 0.00 0.00 3.34
2161 3399 3.424829 CGCTGTTACACATGCTTTTCGAT 60.425 43.478 0.00 0.00 0.00 3.59
2197 3435 7.378181 GGATTGCCTTTCTTTCACTTCAATAA 58.622 34.615 0.00 0.00 0.00 1.40
2230 3468 7.579105 ACTAATTAACACCCATGTAGCCATTA 58.421 34.615 0.00 0.00 38.45 1.90
2234 3472 5.650703 ACAACTAATTAACACCCATGTAGCC 59.349 40.000 0.00 0.00 38.45 3.93
2270 3508 2.536393 GCAAAGCCGCGTTTAAGAAAAA 59.464 40.909 4.92 0.00 0.00 1.94
2285 3523 7.033791 GGTTAACTAATAGAAAAGGGCAAAGC 58.966 38.462 5.42 0.00 0.00 3.51
2286 3524 8.349568 AGGTTAACTAATAGAAAAGGGCAAAG 57.650 34.615 5.42 0.00 0.00 2.77
2325 3564 9.875691 TTTCATCCCAACGATTAGAGATATATG 57.124 33.333 0.00 0.00 0.00 1.78
2343 3584 6.377327 AATCATGTTCGTGTATTTCATCCC 57.623 37.500 0.00 0.00 0.00 3.85
2414 3655 1.948104 TTGTGTGCGCTCTACTTTGT 58.052 45.000 9.73 0.00 0.00 2.83
2418 3659 1.937108 GCTCTTTGTGTGCGCTCTACT 60.937 52.381 9.73 0.00 0.00 2.57
2419 3660 0.440371 GCTCTTTGTGTGCGCTCTAC 59.560 55.000 9.73 5.60 0.00 2.59
2422 3663 0.029300 TTTGCTCTTTGTGTGCGCTC 59.971 50.000 9.73 5.51 37.94 5.03
2426 3667 3.631145 TGATCTTTGCTCTTTGTGTGC 57.369 42.857 0.00 0.00 35.88 4.57
2429 3670 5.130292 ACCAATGATCTTTGCTCTTTGTG 57.870 39.130 14.34 3.06 0.00 3.33
2475 3716 4.587684 AGAGGTAAGGACTTCACTTCGAAA 59.412 41.667 0.00 0.00 34.15 3.46
2476 3717 4.022242 CAGAGGTAAGGACTTCACTTCGAA 60.022 45.833 0.00 0.00 34.15 3.71
2496 3737 0.833287 GTTCATAGAGCCAGGCCAGA 59.167 55.000 8.22 0.00 0.00 3.86
2508 3749 1.825474 ACCTCGTGGGAGTGTTCATAG 59.175 52.381 8.63 0.00 38.70 2.23
2516 3757 2.989824 CGTGGACCTCGTGGGAGT 60.990 66.667 8.63 0.00 38.70 3.85
2519 3760 3.299977 TGTCGTGGACCTCGTGGG 61.300 66.667 15.10 2.00 41.89 4.61
2521 3762 2.428569 CGTGTCGTGGACCTCGTG 60.429 66.667 15.10 1.75 0.00 4.35
2524 3765 1.371389 GTGTCGTGTCGTGGACCTC 60.371 63.158 0.00 0.00 32.19 3.85
2530 3771 3.688330 GTGGCGTGTCGTGTCGTG 61.688 66.667 0.00 0.00 0.00 4.35
2531 3772 4.936823 GGTGGCGTGTCGTGTCGT 62.937 66.667 0.00 0.00 0.00 4.34
2533 3774 4.295119 AGGGTGGCGTGTCGTGTC 62.295 66.667 0.00 0.00 0.00 3.67
2534 3775 4.602259 CAGGGTGGCGTGTCGTGT 62.602 66.667 0.00 0.00 0.00 4.49
2550 3791 1.223487 GGACTGGCGGAATTAGGCA 59.777 57.895 0.00 8.89 42.00 4.75
2551 3792 0.533085 GAGGACTGGCGGAATTAGGC 60.533 60.000 0.00 0.73 0.00 3.93
2563 3804 3.068873 GCATAAGTAGACAGGGAGGACTG 59.931 52.174 0.00 0.00 44.03 3.51
2564 3805 3.052490 AGCATAAGTAGACAGGGAGGACT 60.052 47.826 0.00 0.00 0.00 3.85
2570 3811 6.096036 CGATATCAAGCATAAGTAGACAGGG 58.904 44.000 3.12 0.00 0.00 4.45
2573 3814 6.207614 AGAGCGATATCAAGCATAAGTAGACA 59.792 38.462 3.12 0.00 35.48 3.41
2575 3816 6.657117 AGAGAGCGATATCAAGCATAAGTAGA 59.343 38.462 3.12 0.00 35.48 2.59
2587 3828 3.070748 CCGAGAGAAGAGAGCGATATCA 58.929 50.000 3.12 0.00 0.00 2.15
2589 3830 1.810151 GCCGAGAGAAGAGAGCGATAT 59.190 52.381 0.00 0.00 0.00 1.63
2596 3837 0.684805 GAAGGGGCCGAGAGAAGAGA 60.685 60.000 0.00 0.00 0.00 3.10
2597 3838 0.972983 TGAAGGGGCCGAGAGAAGAG 60.973 60.000 0.00 0.00 0.00 2.85
2607 3848 2.981302 GCCAACAATGAAGGGGCC 59.019 61.111 0.00 0.00 38.70 5.80
2612 3853 0.457035 CATCCCGGCCAACAATGAAG 59.543 55.000 2.24 0.00 0.00 3.02
2620 3861 1.570857 AACTGGATCATCCCGGCCAA 61.571 55.000 2.24 0.00 35.03 4.52
2623 3864 1.347707 TGATAACTGGATCATCCCGGC 59.652 52.381 0.00 0.00 35.03 6.13
2626 3867 3.136443 TGGTGTGATAACTGGATCATCCC 59.864 47.826 0.00 9.21 38.11 3.85
2643 3884 4.265056 GGTTGGCGGGAGTGGTGT 62.265 66.667 0.00 0.00 0.00 4.16
2658 3899 3.717294 GCATGGGAGTGGTCCGGT 61.717 66.667 0.00 0.00 45.05 5.28
2660 3901 3.605749 AACGCATGGGAGTGGTCCG 62.606 63.158 17.76 0.00 45.05 4.79
2661 3902 1.745489 GAACGCATGGGAGTGGTCC 60.745 63.158 17.76 0.00 43.05 4.46
2662 3903 1.745489 GGAACGCATGGGAGTGGTC 60.745 63.158 17.76 5.39 35.03 4.02
2676 3917 3.134127 GATGGCGTGGCTGGGAAC 61.134 66.667 0.00 0.00 0.00 3.62
2683 3924 4.554036 GAGGAGGGATGGCGTGGC 62.554 72.222 0.00 0.00 0.00 5.01
2688 3929 0.765903 TCATGAGGAGGAGGGATGGC 60.766 60.000 0.00 0.00 0.00 4.40
2755 3996 2.474266 CGTCAATGGCGTCAACCG 59.526 61.111 0.00 0.00 40.40 4.44
2801 4042 9.740710 AAAACAAAAAGAGGTAGCATACTATCT 57.259 29.630 0.00 0.00 42.80 1.98
2802 4043 9.989869 GAAAACAAAAAGAGGTAGCATACTATC 57.010 33.333 0.00 0.00 42.51 2.08
2803 4044 9.740710 AGAAAACAAAAAGAGGTAGCATACTAT 57.259 29.630 0.00 0.00 42.51 2.12
2804 4045 9.569122 AAGAAAACAAAAAGAGGTAGCATACTA 57.431 29.630 0.00 0.00 42.51 1.82
2805 4046 8.465273 AAGAAAACAAAAAGAGGTAGCATACT 57.535 30.769 0.00 0.00 42.51 2.12
2806 4047 9.529325 AAAAGAAAACAAAAAGAGGTAGCATAC 57.471 29.630 0.00 0.00 42.04 2.39
2808 4049 9.098355 GAAAAAGAAAACAAAAAGAGGTAGCAT 57.902 29.630 0.00 0.00 0.00 3.79
2809 4050 7.547722 GGAAAAAGAAAACAAAAAGAGGTAGCA 59.452 33.333 0.00 0.00 0.00 3.49
2810 4051 7.011109 GGGAAAAAGAAAACAAAAAGAGGTAGC 59.989 37.037 0.00 0.00 0.00 3.58
2811 4052 7.494625 GGGGAAAAAGAAAACAAAAAGAGGTAG 59.505 37.037 0.00 0.00 0.00 3.18
2812 4053 7.038231 TGGGGAAAAAGAAAACAAAAAGAGGTA 60.038 33.333 0.00 0.00 0.00 3.08
2813 4054 6.177610 GGGGAAAAAGAAAACAAAAAGAGGT 58.822 36.000 0.00 0.00 0.00 3.85
2814 4055 6.176896 TGGGGAAAAAGAAAACAAAAAGAGG 58.823 36.000 0.00 0.00 0.00 3.69
2815 4056 6.183360 GCTGGGGAAAAAGAAAACAAAAAGAG 60.183 38.462 0.00 0.00 0.00 2.85
2816 4057 5.645929 GCTGGGGAAAAAGAAAACAAAAAGA 59.354 36.000 0.00 0.00 0.00 2.52
2817 4058 5.414144 TGCTGGGGAAAAAGAAAACAAAAAG 59.586 36.000 0.00 0.00 0.00 2.27
2818 4059 5.316987 TGCTGGGGAAAAAGAAAACAAAAA 58.683 33.333 0.00 0.00 0.00 1.94
2819 4060 4.911390 TGCTGGGGAAAAAGAAAACAAAA 58.089 34.783 0.00 0.00 0.00 2.44
2820 4061 4.559862 TGCTGGGGAAAAAGAAAACAAA 57.440 36.364 0.00 0.00 0.00 2.83
2821 4062 4.559862 TTGCTGGGGAAAAAGAAAACAA 57.440 36.364 0.00 0.00 0.00 2.83
2822 4063 4.769345 ATTGCTGGGGAAAAAGAAAACA 57.231 36.364 0.00 0.00 0.00 2.83
2823 4064 6.521162 TCTAATTGCTGGGGAAAAAGAAAAC 58.479 36.000 0.00 0.00 0.00 2.43
2824 4065 6.739331 TCTAATTGCTGGGGAAAAAGAAAA 57.261 33.333 0.00 0.00 0.00 2.29
2825 4066 6.496565 TGATCTAATTGCTGGGGAAAAAGAAA 59.503 34.615 0.00 0.00 0.00 2.52
2826 4067 6.015918 TGATCTAATTGCTGGGGAAAAAGAA 58.984 36.000 0.00 0.00 0.00 2.52
2827 4068 5.579047 TGATCTAATTGCTGGGGAAAAAGA 58.421 37.500 0.00 0.00 0.00 2.52
2828 4069 5.920193 TGATCTAATTGCTGGGGAAAAAG 57.080 39.130 0.00 0.00 0.00 2.27
2829 4070 5.721000 ACATGATCTAATTGCTGGGGAAAAA 59.279 36.000 0.00 0.00 0.00 1.94
2830 4071 5.271598 ACATGATCTAATTGCTGGGGAAAA 58.728 37.500 0.00 0.00 0.00 2.29
2831 4072 4.870636 ACATGATCTAATTGCTGGGGAAA 58.129 39.130 0.00 0.00 0.00 3.13
2832 4073 4.524802 ACATGATCTAATTGCTGGGGAA 57.475 40.909 0.00 0.00 0.00 3.97
2833 4074 4.524802 AACATGATCTAATTGCTGGGGA 57.475 40.909 0.00 0.00 0.00 4.81
2834 4075 6.713762 TTAAACATGATCTAATTGCTGGGG 57.286 37.500 0.00 0.00 0.00 4.96
2835 4076 8.415553 TCATTTAAACATGATCTAATTGCTGGG 58.584 33.333 0.00 0.00 0.00 4.45
2836 4077 9.459640 CTCATTTAAACATGATCTAATTGCTGG 57.540 33.333 0.00 0.00 32.59 4.85
2844 4085 9.529325 CGTCCTTACTCATTTAAACATGATCTA 57.471 33.333 0.00 0.00 32.59 1.98
2845 4086 8.041323 ACGTCCTTACTCATTTAAACATGATCT 58.959 33.333 0.00 0.00 32.59 2.75
2846 4087 8.197988 ACGTCCTTACTCATTTAAACATGATC 57.802 34.615 0.00 0.00 32.59 2.92
2847 4088 8.450964 CAACGTCCTTACTCATTTAAACATGAT 58.549 33.333 0.00 0.00 32.59 2.45
2848 4089 7.094975 CCAACGTCCTTACTCATTTAAACATGA 60.095 37.037 0.00 0.00 0.00 3.07
2849 4090 7.021196 CCAACGTCCTTACTCATTTAAACATG 58.979 38.462 0.00 0.00 0.00 3.21
2850 4091 6.349033 GCCAACGTCCTTACTCATTTAAACAT 60.349 38.462 0.00 0.00 0.00 2.71
2851 4092 5.049267 GCCAACGTCCTTACTCATTTAAACA 60.049 40.000 0.00 0.00 0.00 2.83
2852 4093 5.388111 GCCAACGTCCTTACTCATTTAAAC 58.612 41.667 0.00 0.00 0.00 2.01
2853 4094 4.152759 CGCCAACGTCCTTACTCATTTAAA 59.847 41.667 0.00 0.00 33.53 1.52
2854 4095 3.680937 CGCCAACGTCCTTACTCATTTAA 59.319 43.478 0.00 0.00 33.53 1.52
2855 4096 3.255725 CGCCAACGTCCTTACTCATTTA 58.744 45.455 0.00 0.00 33.53 1.40
2856 4097 2.073816 CGCCAACGTCCTTACTCATTT 58.926 47.619 0.00 0.00 33.53 2.32
2857 4098 1.722011 CGCCAACGTCCTTACTCATT 58.278 50.000 0.00 0.00 33.53 2.57
2858 4099 3.436001 CGCCAACGTCCTTACTCAT 57.564 52.632 0.00 0.00 33.53 2.90
2859 4100 4.979204 CGCCAACGTCCTTACTCA 57.021 55.556 0.00 0.00 33.53 3.41
2869 4110 6.105304 CAATGTCATTGAACAACGCCAACG 62.105 45.833 19.06 0.00 42.83 4.10
2870 4111 2.483583 TGTCATTGAACAACGCCAAC 57.516 45.000 0.00 0.00 0.00 3.77
2871 4112 3.379240 CAATGTCATTGAACAACGCCAA 58.621 40.909 19.06 0.00 42.83 4.52
2872 4113 2.288091 CCAATGTCATTGAACAACGCCA 60.288 45.455 24.31 0.00 42.83 5.69
2873 4114 2.288152 ACCAATGTCATTGAACAACGCC 60.288 45.455 24.31 0.00 42.83 5.68
2874 4115 2.725723 CACCAATGTCATTGAACAACGC 59.274 45.455 24.31 0.00 42.83 4.84
2875 4116 3.963665 ACACCAATGTCATTGAACAACG 58.036 40.909 24.31 10.57 42.83 4.10
2889 4130 6.071447 TCGGATGATTTTTCATTGACACCAAT 60.071 34.615 0.00 0.00 43.37 3.16
2890 4131 5.242615 TCGGATGATTTTTCATTGACACCAA 59.757 36.000 0.00 0.00 36.61 3.67
2891 4132 4.764308 TCGGATGATTTTTCATTGACACCA 59.236 37.500 0.00 0.00 0.00 4.17
2902 4143 4.860022 ACATTCCTCCTCGGATGATTTTT 58.140 39.130 0.00 0.00 42.70 1.94
2912 4153 4.960938 TGGATCATAAACATTCCTCCTCG 58.039 43.478 0.00 0.00 0.00 4.63
2913 4154 7.391833 GGTAATGGATCATAAACATTCCTCCTC 59.608 40.741 0.00 0.00 36.36 3.71
2928 4169 2.371841 CCATCCTTCGGGTAATGGATCA 59.628 50.000 0.00 0.00 40.17 2.92
2932 4173 1.488812 TGACCATCCTTCGGGTAATGG 59.511 52.381 0.00 0.00 42.19 3.16
2937 4178 1.285280 TTCATGACCATCCTTCGGGT 58.715 50.000 0.00 0.00 40.96 5.28
2959 4200 4.523173 CCCAAATCATCATCATCCTCAAGG 59.477 45.833 0.00 0.00 0.00 3.61
2967 4208 3.323691 CACCATGCCCAAATCATCATCAT 59.676 43.478 0.00 0.00 0.00 2.45
2969 4210 2.036733 CCACCATGCCCAAATCATCATC 59.963 50.000 0.00 0.00 0.00 2.92
3013 4254 1.574428 CTTTCGGTTGTTGCCCTCG 59.426 57.895 0.00 0.00 0.00 4.63
3026 4267 2.905959 TGAGAACATGCATGCTTTCG 57.094 45.000 26.53 6.95 0.00 3.46
3034 4275 1.303236 CCCCGGTTGAGAACATGCA 60.303 57.895 0.00 0.00 0.00 3.96
3035 4276 1.303317 ACCCCGGTTGAGAACATGC 60.303 57.895 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.