Multiple sequence alignment - TraesCS2D01G117900

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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 TraesCS2D01G117900 chr2D 100.000 5805 0 0 1 5805 67238314 67232510 0.000000e+00 10720.0
1 TraesCS2D01G117900 chr2B 91.463 4908 307 51 230 5081 104232692 104237543 0.000000e+00 6639.0
2 TraesCS2D01G117900 chr2B 91.176 238 18 2 5563 5799 104238390 104238625 2.610000e-83 320.0
3 TraesCS2D01G117900 chr2B 88.938 226 16 3 5226 5450 104237742 104237959 2.670000e-68 270.0
4 TraesCS2D01G117900 chr2B 95.556 45 2 0 5140 5184 104237585 104237629 8.070000e-09 73.1
5 TraesCS2D01G117900 chr2A 93.582 3132 147 26 2114 5207 67518964 67522079 0.000000e+00 4621.0
6 TraesCS2D01G117900 chr2A 91.384 1207 83 13 880 2079 67517771 67518963 0.000000e+00 1633.0
7 TraesCS2D01G117900 chr2A 87.785 745 54 20 112 842 67517045 67517766 0.000000e+00 837.0
8 TraesCS2D01G117900 chr2A 85.135 222 13 10 5226 5447 67522207 67522408 5.890000e-50 209.0
9 TraesCS2D01G117900 chr2A 91.150 113 9 1 3 114 67516794 67516906 1.010000e-32 152.0
10 TraesCS2D01G117900 chr2A 92.754 69 4 1 5139 5207 67521940 67522007 1.330000e-16 99.0
11 TraesCS2D01G117900 chr2A 96.226 53 2 0 5100 5152 67522045 67522097 2.880000e-13 87.9
12 TraesCS2D01G117900 chr4B 82.585 936 119 15 1103 2033 610798087 610798983 0.000000e+00 785.0
13 TraesCS2D01G117900 chr7D 82.203 944 120 19 1103 2039 205655320 205654418 0.000000e+00 769.0
14 TraesCS2D01G117900 chr7D 79.960 998 141 21 1052 2034 521640506 521641459 0.000000e+00 680.0
15 TraesCS2D01G117900 chr3D 81.463 998 131 22 1052 2039 590146642 590145689 0.000000e+00 769.0
16 TraesCS2D01G117900 chr3D 82.900 538 61 10 1507 2039 532138903 532138392 6.860000e-124 455.0
17 TraesCS2D01G117900 chr4D 81.300 1000 135 22 1047 2039 220275112 220274158 0.000000e+00 763.0
18 TraesCS2D01G117900 chr4D 81.231 991 134 18 1052 2033 30346256 30347203 0.000000e+00 752.0
19 TraesCS2D01G117900 chr4D 83.632 391 33 10 1648 2033 187468410 187468774 7.210000e-89 339.0
20 TraesCS2D01G117900 chr7A 81.760 943 127 15 1103 2039 513575301 513574398 0.000000e+00 747.0
21 TraesCS2D01G117900 chr3A 80.221 996 134 21 1055 2034 726004650 726003702 0.000000e+00 689.0
22 TraesCS2D01G117900 chr3A 85.542 83 8 3 2069 2147 696374297 696374379 3.730000e-12 84.2
23 TraesCS2D01G117900 chr5D 82.051 585 86 7 1107 1685 423850944 423850373 1.130000e-131 481.0
24 TraesCS2D01G117900 chr5D 88.158 76 7 2 2077 2150 549576651 549576576 8.010000e-14 89.8
25 TraesCS2D01G117900 chr1D 80.469 640 99 13 1055 1685 110582957 110582335 3.170000e-127 466.0
26 TraesCS2D01G117900 chr1B 82.947 475 49 8 1563 2033 417809946 417810392 3.260000e-107 399.0
27 TraesCS2D01G117900 chr3B 86.667 90 7 3 2074 2159 744906482 744906570 1.720000e-15 95.3
28 TraesCS2D01G117900 chr3B 85.106 94 9 5 2064 2155 710390503 710390413 2.230000e-14 91.6
29 TraesCS2D01G117900 chr3B 89.041 73 6 1 2077 2147 744906555 744906483 8.010000e-14 89.8
30 TraesCS2D01G117900 chr3B 89.041 73 6 1 2077 2147 746342192 746342120 8.010000e-14 89.8
31 TraesCS2D01G117900 chr5B 88.732 71 6 2 2079 2147 701152530 701152600 1.040000e-12 86.1
32 TraesCS2D01G117900 chr7B 86.842 76 7 1 2077 2149 588500564 588500639 1.340000e-11 82.4


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 TraesCS2D01G117900 chr2D 67232510 67238314 5804 True 10720.000000 10720 100.000000 1 5805 1 chr2D.!!$R1 5804
1 TraesCS2D01G117900 chr2B 104232692 104238625 5933 False 1825.525000 6639 91.783250 230 5799 4 chr2B.!!$F1 5569
2 TraesCS2D01G117900 chr2A 67516794 67522408 5614 False 1091.271429 4621 91.145143 3 5447 7 chr2A.!!$F1 5444
3 TraesCS2D01G117900 chr4B 610798087 610798983 896 False 785.000000 785 82.585000 1103 2033 1 chr4B.!!$F1 930
4 TraesCS2D01G117900 chr7D 205654418 205655320 902 True 769.000000 769 82.203000 1103 2039 1 chr7D.!!$R1 936
5 TraesCS2D01G117900 chr7D 521640506 521641459 953 False 680.000000 680 79.960000 1052 2034 1 chr7D.!!$F1 982
6 TraesCS2D01G117900 chr3D 590145689 590146642 953 True 769.000000 769 81.463000 1052 2039 1 chr3D.!!$R2 987
7 TraesCS2D01G117900 chr3D 532138392 532138903 511 True 455.000000 455 82.900000 1507 2039 1 chr3D.!!$R1 532
8 TraesCS2D01G117900 chr4D 220274158 220275112 954 True 763.000000 763 81.300000 1047 2039 1 chr4D.!!$R1 992
9 TraesCS2D01G117900 chr4D 30346256 30347203 947 False 752.000000 752 81.231000 1052 2033 1 chr4D.!!$F1 981
10 TraesCS2D01G117900 chr7A 513574398 513575301 903 True 747.000000 747 81.760000 1103 2039 1 chr7A.!!$R1 936
11 TraesCS2D01G117900 chr3A 726003702 726004650 948 True 689.000000 689 80.221000 1055 2034 1 chr3A.!!$R1 979
12 TraesCS2D01G117900 chr5D 423850373 423850944 571 True 481.000000 481 82.051000 1107 1685 1 chr5D.!!$R1 578
13 TraesCS2D01G117900 chr1D 110582335 110582957 622 True 466.000000 466 80.469000 1055 1685 1 chr1D.!!$R1 630

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
58 59 0.102300 GCCCATTGCGATAACCAACC 59.898 55.000 0.00 0.00 0.00 3.77 F
700 862 0.240411 GAGTACCGTCACTTCGCTGT 59.760 55.000 0.00 0.00 0.00 4.40 F
894 1066 0.250234 CCGAGACAAGCTGGGAATCA 59.750 55.000 0.00 0.00 44.66 2.57 F
1168 1348 1.377202 TTCTGATCTGGTTGCGCCC 60.377 57.895 4.18 0.00 36.04 6.13 F
1726 1927 2.174639 TCTTGTGTTTCAGGTCCATGGT 59.825 45.455 12.58 0.00 0.00 3.55 F
3391 3610 1.549203 ATGACTGGGATGTTGCAACC 58.451 50.000 26.14 11.86 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1825 0.036294 AAGGCCAGTTCTTCGTAGCC 60.036 55.000 5.01 0.00 40.79 3.93 R
1632 1831 0.322906 CCTCCCAAGGCCAGTTCTTC 60.323 60.000 5.01 0.00 35.37 2.87 R
2825 3040 2.604046 CTGGAAGGGGATACAAGTCG 57.396 55.000 0.00 0.00 39.74 4.18 R
2969 3185 7.339466 ACACCAAGTAGAAAGACAATCAAAAGT 59.661 33.333 0.00 0.00 0.00 2.66 R
3665 3895 2.097629 GGATTTAGGCGAGCAAGAAACC 59.902 50.000 0.00 0.00 0.00 3.27 R
5023 5265 0.179000 AGACCGATGAACATCTGGGC 59.821 55.000 20.34 18.87 38.74 5.36 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
58 59 0.102300 GCCCATTGCGATAACCAACC 59.898 55.000 0.00 0.00 0.00 3.77
59 60 0.380378 CCCATTGCGATAACCAACCG 59.620 55.000 0.00 0.00 0.00 4.44
62 63 2.286833 CCATTGCGATAACCAACCGTAG 59.713 50.000 0.00 0.00 0.00 3.51
79 80 1.460273 TAGGCCGTCGCATGCTCATA 61.460 55.000 17.13 0.00 36.38 2.15
176 319 5.125356 ACAATTTGCTTTTTCTTTGAGGGG 58.875 37.500 0.00 0.00 0.00 4.79
177 320 3.836365 TTTGCTTTTTCTTTGAGGGGG 57.164 42.857 0.00 0.00 0.00 5.40
179 322 2.597455 TGCTTTTTCTTTGAGGGGGAG 58.403 47.619 0.00 0.00 0.00 4.30
180 323 2.176798 TGCTTTTTCTTTGAGGGGGAGA 59.823 45.455 0.00 0.00 0.00 3.71
181 324 3.181418 TGCTTTTTCTTTGAGGGGGAGAT 60.181 43.478 0.00 0.00 0.00 2.75
182 325 4.044065 TGCTTTTTCTTTGAGGGGGAGATA 59.956 41.667 0.00 0.00 0.00 1.98
388 543 0.665068 CGCCGCCGCACTATATAACA 60.665 55.000 0.00 0.00 34.03 2.41
392 547 2.131972 CGCCGCACTATATAACAAGCA 58.868 47.619 0.00 0.00 0.00 3.91
443 598 5.395546 CCTCCTCTGATCTGAAGGAGAAAAG 60.396 48.000 29.14 18.30 46.61 2.27
444 599 5.336945 TCCTCTGATCTGAAGGAGAAAAGA 58.663 41.667 13.20 0.00 33.12 2.52
445 600 5.782331 TCCTCTGATCTGAAGGAGAAAAGAA 59.218 40.000 13.20 0.00 33.12 2.52
482 638 1.272554 CCCTAATCCCTATCCGGCCC 61.273 65.000 0.00 0.00 0.00 5.80
492 648 1.412453 TATCCGGCCCGCTTAACCAT 61.412 55.000 0.00 0.00 0.00 3.55
568 730 2.095252 GCACCTCCGTCTTCTTCGC 61.095 63.158 0.00 0.00 0.00 4.70
571 733 2.184579 CTCCGTCTTCTTCGCCCC 59.815 66.667 0.00 0.00 0.00 5.80
591 753 1.627297 ATGCTTCCTCCTCCGTTCCC 61.627 60.000 0.00 0.00 0.00 3.97
677 839 1.226491 CGACGTCGTGGGGTATCAC 60.226 63.158 29.08 0.00 34.11 3.06
679 841 1.382522 GACGTCGTGGGGTATCACTA 58.617 55.000 0.63 0.00 35.63 2.74
680 842 1.952296 GACGTCGTGGGGTATCACTAT 59.048 52.381 0.63 0.00 35.63 2.12
681 843 1.679680 ACGTCGTGGGGTATCACTATG 59.320 52.381 0.00 0.00 35.63 2.23
682 844 1.951602 CGTCGTGGGGTATCACTATGA 59.048 52.381 0.00 0.00 35.63 2.15
683 845 2.031069 CGTCGTGGGGTATCACTATGAG 60.031 54.545 0.00 0.00 35.63 2.90
684 846 2.957006 GTCGTGGGGTATCACTATGAGT 59.043 50.000 0.00 0.00 35.63 3.41
685 847 4.139786 GTCGTGGGGTATCACTATGAGTA 58.860 47.826 0.00 0.00 35.63 2.59
700 862 0.240411 GAGTACCGTCACTTCGCTGT 59.760 55.000 0.00 0.00 0.00 4.40
729 891 3.614092 TCCCATCTGAATTCTTGCTCAC 58.386 45.455 7.05 0.00 0.00 3.51
800 967 1.817447 AGTACCGGCAGTGTTCTAGTC 59.183 52.381 0.00 0.00 0.00 2.59
824 996 7.844653 GTCCTAGAAGCGATTTTATTTGTAACG 59.155 37.037 0.00 0.00 0.00 3.18
847 1019 2.292267 CAAGATTGGGGATTCAGTCGG 58.708 52.381 0.00 0.00 0.00 4.79
852 1024 4.547367 GGGATTCAGTCGGGCCCG 62.547 72.222 39.13 39.13 41.35 6.13
894 1066 0.250234 CCGAGACAAGCTGGGAATCA 59.750 55.000 0.00 0.00 44.66 2.57
957 1129 4.537135 GGATTGGATCCTCGTATTGCTA 57.463 45.455 14.23 0.00 46.19 3.49
997 1173 2.595124 TCAGTTGCAGAGACGTTTCA 57.405 45.000 8.98 0.00 0.00 2.69
1118 1298 3.315880 TGAATGATTGATGCCCATGGA 57.684 42.857 15.22 0.00 0.00 3.41
1168 1348 1.377202 TTCTGATCTGGTTGCGCCC 60.377 57.895 4.18 0.00 36.04 6.13
1319 1503 4.265073 ACCCTGAACTGAACAGATTATGC 58.735 43.478 8.87 0.00 37.54 3.14
1359 1543 7.870445 TGCTTTCAGTTTTATAACATTTGTCCC 59.130 33.333 0.00 0.00 36.70 4.46
1478 1668 8.627403 AGTATGATTTGATTTGCAGAACTATGG 58.373 33.333 0.00 0.00 0.00 2.74
1482 1672 4.970662 TGATTTGCAGAACTATGGCTTC 57.029 40.909 0.00 0.00 0.00 3.86
1492 1684 5.587844 CAGAACTATGGCTTCTTGTTAGCAT 59.412 40.000 0.00 0.00 40.42 3.79
1496 1688 6.234177 ACTATGGCTTCTTGTTAGCATATCC 58.766 40.000 0.00 0.00 40.42 2.59
1500 1692 4.276926 GGCTTCTTGTTAGCATATCCCTTG 59.723 45.833 0.00 0.00 40.42 3.61
1504 1696 5.611374 TCTTGTTAGCATATCCCTTGTAGC 58.389 41.667 0.00 0.00 0.00 3.58
1505 1697 3.990092 TGTTAGCATATCCCTTGTAGCG 58.010 45.455 0.00 0.00 0.00 4.26
1517 1709 5.172934 TCCCTTGTAGCGTACTTTTACATG 58.827 41.667 0.00 0.00 0.00 3.21
1522 1714 7.490079 CCTTGTAGCGTACTTTTACATGATGTA 59.510 37.037 0.23 0.23 0.00 2.29
1530 1722 8.795341 CGTACTTTTACATGATGTACTACAGTG 58.205 37.037 4.50 0.00 31.69 3.66
1531 1723 9.850628 GTACTTTTACATGATGTACTACAGTGA 57.149 33.333 4.50 0.00 31.69 3.41
1535 1727 9.586435 TTTTACATGATGTACTACAGTGAGATG 57.414 33.333 4.50 0.00 31.69 2.90
1548 1742 9.900710 ACTACAGTGAGATGATATATTCGTTTC 57.099 33.333 0.00 0.00 0.00 2.78
1549 1743 9.899226 CTACAGTGAGATGATATATTCGTTTCA 57.101 33.333 0.00 0.00 33.36 2.69
1552 1746 9.415544 CAGTGAGATGATATATTCGTTTCATGA 57.584 33.333 0.00 0.00 36.98 3.07
1564 1758 4.883083 TCGTTTCATGATATAGGACTGGC 58.117 43.478 0.00 0.00 0.00 4.85
1584 1779 3.645975 CGGTTCAGCGTGGCGTTT 61.646 61.111 0.00 0.00 0.00 3.60
1632 1831 2.686816 CCCTTTTGGTGCGGCTACG 61.687 63.158 0.00 0.00 39.84 3.51
1726 1927 2.174639 TCTTGTGTTTCAGGTCCATGGT 59.825 45.455 12.58 0.00 0.00 3.55
1985 2188 9.185192 GCAGTTTGATTATGATTATTTACAGGC 57.815 33.333 0.00 0.00 0.00 4.85
1988 2191 8.564574 GTTTGATTATGATTATTTACAGGCGGA 58.435 33.333 0.00 0.00 0.00 5.54
1989 2192 7.667043 TGATTATGATTATTTACAGGCGGAC 57.333 36.000 0.00 0.00 0.00 4.79
1990 2193 7.220740 TGATTATGATTATTTACAGGCGGACA 58.779 34.615 0.00 0.00 0.00 4.02
1991 2194 6.854496 TTATGATTATTTACAGGCGGACAC 57.146 37.500 0.00 0.00 0.00 3.67
2075 2289 5.010012 ACTTGCCCTGTGACTAAAAAGAATG 59.990 40.000 0.00 0.00 0.00 2.67
2083 2297 4.396478 GTGACTAAAAAGAATGCTCCCTCC 59.604 45.833 0.00 0.00 0.00 4.30
2084 2298 4.042809 TGACTAAAAAGAATGCTCCCTCCA 59.957 41.667 0.00 0.00 0.00 3.86
2088 2302 4.328118 AAAAGAATGCTCCCTCCAATCT 57.672 40.909 0.00 0.00 0.00 2.40
2095 2309 8.454859 AGAATGCTCCCTCCAATCTATATTAA 57.545 34.615 0.00 0.00 0.00 1.40
2100 2314 8.448008 TGCTCCCTCCAATCTATATTAATTGTT 58.552 33.333 0.00 0.00 32.20 2.83
2197 2412 5.235186 CACAATAGAACCGAACTGATCATCC 59.765 44.000 0.00 0.00 0.00 3.51
2676 2891 5.522456 TCACTGCATTTGTGAATTTGAGTC 58.478 37.500 4.89 0.00 40.89 3.36
2798 3013 7.990886 TGGGTTGTGTCTAAATATCATAGGAAC 59.009 37.037 0.00 0.00 0.00 3.62
2825 3040 7.041303 CCTTCCTTCTGGTTAGTTGTTTAACTC 60.041 40.741 0.00 0.00 39.98 3.01
2828 3043 6.073927 CCTTCTGGTTAGTTGTTTAACTCGAC 60.074 42.308 0.00 0.00 43.53 4.20
2952 3167 7.227156 AGAGAGAACTTGAACATTTGGTATGT 58.773 34.615 0.00 0.00 0.00 2.29
2956 3171 7.202526 AGAACTTGAACATTTGGTATGTGTTG 58.797 34.615 0.00 0.00 36.30 3.33
2976 3192 7.335673 TGTGTTGACATACTTCTTGACTTTTGA 59.664 33.333 0.00 0.00 0.00 2.69
2977 3193 8.345565 GTGTTGACATACTTCTTGACTTTTGAT 58.654 33.333 0.00 0.00 0.00 2.57
3176 3392 3.146847 GGTTCGAGTCTCCCAAATTTGT 58.853 45.455 16.73 0.00 0.00 2.83
3190 3406 9.626045 CTCCCAAATTTGTCAGTAAATAGTTTC 57.374 33.333 16.73 0.00 30.47 2.78
3223 3439 7.959651 CCGCTTTATGATAATTGAAGATACTGC 59.040 37.037 0.00 0.00 0.00 4.40
3233 3449 4.456280 TGAAGATACTGCGTGTCTGAAT 57.544 40.909 8.26 0.00 34.39 2.57
3234 3450 4.424626 TGAAGATACTGCGTGTCTGAATC 58.575 43.478 8.26 4.57 34.39 2.52
3324 3543 8.674607 GTTTGTCGTCTGGAAAATATAGGAAAT 58.325 33.333 0.00 0.00 0.00 2.17
3326 3545 9.893634 TTGTCGTCTGGAAAATATAGGAAATTA 57.106 29.630 0.00 0.00 0.00 1.40
3352 3571 9.628500 ATTAACAGGACTGGAAAGAATAATACC 57.372 33.333 4.14 0.00 34.19 2.73
3391 3610 1.549203 ATGACTGGGATGTTGCAACC 58.451 50.000 26.14 11.86 0.00 3.77
3444 3663 7.942341 TCTTACAGGTAATCTTTGAAATGTGGT 59.058 33.333 0.00 0.00 0.00 4.16
3553 3774 7.454380 TGGAATTTAACCATGTTTTCCTGAGAT 59.546 33.333 9.22 0.00 34.93 2.75
3564 3787 9.829507 CATGTTTTCCTGAGATATCTTAGAACT 57.170 33.333 22.65 8.84 31.92 3.01
3665 3895 3.237268 ACTCTCTCTGGGCATAGGTAG 57.763 52.381 0.00 0.00 0.00 3.18
3693 3923 2.698274 TGCTCGCCTAAATCCAGTCATA 59.302 45.455 0.00 0.00 0.00 2.15
3706 3936 6.992063 ATCCAGTCATAACAGCTTAAAGTG 57.008 37.500 0.00 0.00 0.00 3.16
3772 4002 2.420269 CCATCATGAGCTTGAGACTGCT 60.420 50.000 0.09 0.00 42.82 4.24
3793 4023 5.181811 TGCTCGCATTAATGATATTCTTGGG 59.818 40.000 19.73 0.00 0.00 4.12
3817 4047 3.243501 ACATTGATGCAAACACTGGTGAC 60.244 43.478 7.78 0.00 0.00 3.67
3848 4078 9.778741 AAGTTGGTATGTGTATAGTTCATATGG 57.221 33.333 2.13 0.00 0.00 2.74
3861 4091 3.719268 TCATATGGTGGCTGTGACTTT 57.281 42.857 2.13 0.00 0.00 2.66
3864 4094 4.218200 TCATATGGTGGCTGTGACTTTTTG 59.782 41.667 2.13 0.00 0.00 2.44
3880 4110 6.378564 TGACTTTTTGAAATCCCTGTTACACA 59.621 34.615 0.00 0.00 0.00 3.72
3895 4125 6.307318 CCTGTTACACACTTAGTAGCTTAACG 59.693 42.308 0.00 0.00 0.00 3.18
3962 4192 6.211584 TCCTTACAGACATTTCAGAAGCTACT 59.788 38.462 0.00 0.00 0.00 2.57
4067 4298 8.871629 ACAGTATCATGTTTGGTTACCATTTA 57.128 30.769 4.38 0.00 31.53 1.40
4077 4308 9.315363 TGTTTGGTTACCATTTAATTCAGGTAT 57.685 29.630 4.38 0.00 36.57 2.73
4079 4310 7.795482 TGGTTACCATTTAATTCAGGTATCG 57.205 36.000 0.00 0.00 36.57 2.92
4099 4330 4.323417 TCGGTGCTCATAATTTGTTCTGT 58.677 39.130 0.00 0.00 0.00 3.41
4176 4407 8.886719 CAAATTGTTAGCTCTCACTATCATTGA 58.113 33.333 0.00 0.00 0.00 2.57
4201 4432 4.836125 TCTGTGAATTGAGCTTTGGTTC 57.164 40.909 0.00 0.00 0.00 3.62
4215 4447 4.438200 GCTTTGGTTCGACAGAAACTTTGA 60.438 41.667 0.00 0.00 44.20 2.69
4250 4482 1.691195 TTTGTGGTGACAGGCGGAGA 61.691 55.000 0.00 0.00 44.46 3.71
4396 4628 4.126437 GGTAAAGTTTGCATGTGCCTTTT 58.874 39.130 11.19 5.98 41.18 2.27
4447 4679 1.985622 AGGATGGTTCCCTGGATGAA 58.014 50.000 0.00 0.00 43.76 2.57
4453 4685 2.983192 TGGTTCCCTGGATGAACTTGTA 59.017 45.455 13.28 0.00 41.42 2.41
4526 4758 5.590530 ACACAAATTAGCAAGTTTGGACA 57.409 34.783 10.92 0.00 39.12 4.02
4665 4898 2.099405 CCATCCGGCAAACAGGTAAAT 58.901 47.619 0.00 0.00 0.00 1.40
4670 4903 1.135402 CGGCAAACAGGTAAATGGAGC 60.135 52.381 0.00 0.00 0.00 4.70
4678 4911 5.099042 ACAGGTAAATGGAGCGATAAACT 57.901 39.130 0.00 0.00 0.00 2.66
4689 4922 4.369182 GAGCGATAAACTTAGGCAGCTTA 58.631 43.478 0.00 0.00 33.51 3.09
4706 4939 6.915544 CAGCTTATCTTTCACTGCTCAATA 57.084 37.500 0.00 0.00 0.00 1.90
4833 5072 4.011698 GCCCACGGTTCTAGGAATAAAAA 58.988 43.478 0.00 0.00 0.00 1.94
4982 5221 5.173131 CAGAATTAAACTTGTTCGCCAACAC 59.827 40.000 0.00 0.00 42.46 3.32
5007 5247 2.749621 GTTGGGCTGAACTATGTTCCAG 59.250 50.000 7.81 6.72 0.00 3.86
5009 5249 2.290260 TGGGCTGAACTATGTTCCAGTG 60.290 50.000 7.81 0.00 0.00 3.66
5022 5264 3.689161 TGTTCCAGTGTTCTCTGTGTTTG 59.311 43.478 0.00 0.00 34.02 2.93
5023 5265 2.917933 TCCAGTGTTCTCTGTGTTTGG 58.082 47.619 0.00 0.00 34.02 3.28
5032 5274 0.478072 TCTGTGTTTGGCCCAGATGT 59.522 50.000 0.00 0.00 30.58 3.06
5180 5437 4.625607 TTTTGGTCAAGGTTTTGGTTGT 57.374 36.364 0.00 0.00 34.97 3.32
5203 5460 2.643551 AGTATCGGCAACCATCCAAAG 58.356 47.619 0.00 0.00 0.00 2.77
5204 5461 1.065551 GTATCGGCAACCATCCAAAGC 59.934 52.381 0.00 0.00 0.00 3.51
5206 5463 0.825425 TCGGCAACCATCCAAAGCAA 60.825 50.000 0.00 0.00 0.00 3.91
5208 5465 1.539929 CGGCAACCATCCAAAGCAAAA 60.540 47.619 0.00 0.00 0.00 2.44
5209 5466 2.570135 GGCAACCATCCAAAGCAAAAA 58.430 42.857 0.00 0.00 0.00 1.94
5210 5467 3.148412 GGCAACCATCCAAAGCAAAAAT 58.852 40.909 0.00 0.00 0.00 1.82
5211 5468 4.322567 GGCAACCATCCAAAGCAAAAATA 58.677 39.130 0.00 0.00 0.00 1.40
5296 5663 8.426489 ACTTCCCGTGTAAGCAAATATAAGATA 58.574 33.333 0.00 0.00 0.00 1.98
5441 5808 5.425539 AGCCAGAGTCTAAATAGGTAGCAAA 59.574 40.000 0.00 0.00 0.00 3.68
5442 5809 5.755861 GCCAGAGTCTAAATAGGTAGCAAAG 59.244 44.000 0.00 0.00 0.00 2.77
5443 5810 5.755861 CCAGAGTCTAAATAGGTAGCAAAGC 59.244 44.000 0.00 0.00 0.00 3.51
5446 5826 6.381420 AGAGTCTAAATAGGTAGCAAAGCTCA 59.619 38.462 0.00 0.00 40.44 4.26
5448 5828 7.213678 AGTCTAAATAGGTAGCAAAGCTCATC 58.786 38.462 0.00 0.00 40.44 2.92
5453 5833 3.276857 AGGTAGCAAAGCTCATCATGTG 58.723 45.455 0.00 0.00 40.44 3.21
5469 5849 4.321718 TCATGTGAGAAAGCAAGAAGAGG 58.678 43.478 0.00 0.00 0.00 3.69
5470 5850 3.131709 TGTGAGAAAGCAAGAAGAGGG 57.868 47.619 0.00 0.00 0.00 4.30
5471 5851 2.705658 TGTGAGAAAGCAAGAAGAGGGA 59.294 45.455 0.00 0.00 0.00 4.20
5472 5852 3.136443 TGTGAGAAAGCAAGAAGAGGGAA 59.864 43.478 0.00 0.00 0.00 3.97
5473 5853 4.137543 GTGAGAAAGCAAGAAGAGGGAAA 58.862 43.478 0.00 0.00 0.00 3.13
5476 5856 5.222007 TGAGAAAGCAAGAAGAGGGAAATCT 60.222 40.000 0.00 0.00 0.00 2.40
5477 5857 5.008980 AGAAAGCAAGAAGAGGGAAATCTG 58.991 41.667 0.00 0.00 0.00 2.90
5478 5858 3.362870 AGCAAGAAGAGGGAAATCTGG 57.637 47.619 0.00 0.00 0.00 3.86
5479 5859 2.646798 AGCAAGAAGAGGGAAATCTGGT 59.353 45.455 0.00 0.00 0.00 4.00
5480 5860 3.013219 GCAAGAAGAGGGAAATCTGGTC 58.987 50.000 0.00 0.00 0.00 4.02
5481 5861 3.560025 GCAAGAAGAGGGAAATCTGGTCA 60.560 47.826 0.00 0.00 0.00 4.02
5482 5862 4.655963 CAAGAAGAGGGAAATCTGGTCAA 58.344 43.478 0.00 0.00 0.00 3.18
5485 5865 3.990959 AGAGGGAAATCTGGTCAACTC 57.009 47.619 0.00 0.00 0.00 3.01
5486 5866 3.525862 AGAGGGAAATCTGGTCAACTCT 58.474 45.455 0.00 0.00 0.00 3.24
5487 5867 3.262915 AGAGGGAAATCTGGTCAACTCTG 59.737 47.826 0.00 0.00 32.75 3.35
5488 5868 2.982488 AGGGAAATCTGGTCAACTCTGT 59.018 45.455 0.00 0.00 0.00 3.41
5489 5869 3.395941 AGGGAAATCTGGTCAACTCTGTT 59.604 43.478 0.00 0.00 0.00 3.16
5490 5870 4.141158 AGGGAAATCTGGTCAACTCTGTTT 60.141 41.667 0.00 0.00 0.00 2.83
5491 5871 4.216472 GGGAAATCTGGTCAACTCTGTTTC 59.784 45.833 0.00 0.00 0.00 2.78
5492 5872 4.216472 GGAAATCTGGTCAACTCTGTTTCC 59.784 45.833 0.00 0.00 37.34 3.13
5493 5873 4.437682 AATCTGGTCAACTCTGTTTCCA 57.562 40.909 0.00 0.00 0.00 3.53
5494 5874 3.475566 TCTGGTCAACTCTGTTTCCAG 57.524 47.619 17.41 17.41 42.36 3.86
5495 5875 3.038280 TCTGGTCAACTCTGTTTCCAGA 58.962 45.455 19.96 19.96 45.76 3.86
5496 5876 3.648067 TCTGGTCAACTCTGTTTCCAGAT 59.352 43.478 19.96 0.00 46.38 2.90
5497 5877 4.103153 TCTGGTCAACTCTGTTTCCAGATT 59.897 41.667 19.96 0.00 46.38 2.40
5498 5878 4.389374 TGGTCAACTCTGTTTCCAGATTC 58.611 43.478 0.00 0.00 46.38 2.52
5499 5879 4.103153 TGGTCAACTCTGTTTCCAGATTCT 59.897 41.667 0.00 0.00 46.38 2.40
5500 5880 4.693095 GGTCAACTCTGTTTCCAGATTCTC 59.307 45.833 0.00 0.00 46.38 2.87
5501 5881 4.693095 GTCAACTCTGTTTCCAGATTCTCC 59.307 45.833 0.00 0.00 46.38 3.71
5502 5882 4.347876 TCAACTCTGTTTCCAGATTCTCCA 59.652 41.667 0.00 0.00 46.38 3.86
5503 5883 4.550076 ACTCTGTTTCCAGATTCTCCAG 57.450 45.455 0.00 0.00 46.38 3.86
5504 5884 3.262915 ACTCTGTTTCCAGATTCTCCAGG 59.737 47.826 0.00 0.00 46.38 4.45
5505 5885 2.026822 TCTGTTTCCAGATTCTCCAGGC 60.027 50.000 0.00 0.00 42.80 4.85
5506 5886 1.704628 TGTTTCCAGATTCTCCAGGCA 59.295 47.619 0.00 0.00 0.00 4.75
5507 5887 2.290514 TGTTTCCAGATTCTCCAGGCAG 60.291 50.000 0.00 0.00 0.00 4.85
5508 5888 0.254178 TTCCAGATTCTCCAGGCAGC 59.746 55.000 0.00 0.00 0.00 5.25
5509 5889 0.911045 TCCAGATTCTCCAGGCAGCA 60.911 55.000 0.00 0.00 0.00 4.41
5510 5890 0.464013 CCAGATTCTCCAGGCAGCAG 60.464 60.000 0.00 0.00 0.00 4.24
5511 5891 1.096386 CAGATTCTCCAGGCAGCAGC 61.096 60.000 0.00 0.00 41.10 5.25
5521 5901 4.347453 GCAGCAGCCGTTGGGTTG 62.347 66.667 0.00 0.00 46.45 3.77
5522 5902 3.673484 CAGCAGCCGTTGGGTTGG 61.673 66.667 0.00 0.00 44.11 3.77
5523 5903 4.974721 AGCAGCCGTTGGGTTGGG 62.975 66.667 0.00 0.00 44.11 4.12
5524 5904 4.966787 GCAGCCGTTGGGTTGGGA 62.967 66.667 0.00 0.00 44.11 4.37
5525 5905 2.983592 CAGCCGTTGGGTTGGGAC 60.984 66.667 0.00 0.00 40.57 4.46
5526 5906 3.175710 AGCCGTTGGGTTGGGACT 61.176 61.111 0.00 0.00 34.97 3.85
5527 5907 2.203437 GCCGTTGGGTTGGGACTT 60.203 61.111 0.00 0.00 34.97 3.01
5528 5908 2.265904 GCCGTTGGGTTGGGACTTC 61.266 63.158 0.00 0.00 34.97 3.01
5529 5909 1.149627 CCGTTGGGTTGGGACTTCA 59.850 57.895 0.00 0.00 0.00 3.02
5530 5910 0.466555 CCGTTGGGTTGGGACTTCAA 60.467 55.000 0.00 0.00 0.00 2.69
5531 5911 1.394618 CGTTGGGTTGGGACTTCAAA 58.605 50.000 0.00 0.00 0.00 2.69
5532 5912 1.336755 CGTTGGGTTGGGACTTCAAAG 59.663 52.381 0.00 0.00 0.00 2.77
5533 5913 2.384828 GTTGGGTTGGGACTTCAAAGT 58.615 47.619 0.00 0.00 43.16 2.66
5534 5914 2.764010 GTTGGGTTGGGACTTCAAAGTT 59.236 45.455 0.00 0.00 39.88 2.66
5535 5915 3.108847 TGGGTTGGGACTTCAAAGTTT 57.891 42.857 0.00 0.00 39.88 2.66
5536 5916 3.028130 TGGGTTGGGACTTCAAAGTTTC 58.972 45.455 0.00 0.00 39.88 2.78
5537 5917 3.296854 GGGTTGGGACTTCAAAGTTTCT 58.703 45.455 0.00 0.00 39.88 2.52
5538 5918 3.318275 GGGTTGGGACTTCAAAGTTTCTC 59.682 47.826 0.00 0.00 39.88 2.87
5539 5919 3.951680 GGTTGGGACTTCAAAGTTTCTCA 59.048 43.478 0.00 0.00 39.88 3.27
5540 5920 4.584743 GGTTGGGACTTCAAAGTTTCTCAT 59.415 41.667 0.00 0.00 39.88 2.90
5541 5921 5.278512 GGTTGGGACTTCAAAGTTTCTCATC 60.279 44.000 0.00 0.00 39.88 2.92
5542 5922 5.310409 TGGGACTTCAAAGTTTCTCATCT 57.690 39.130 0.00 0.00 39.88 2.90
5543 5923 5.694995 TGGGACTTCAAAGTTTCTCATCTT 58.305 37.500 0.00 0.00 39.88 2.40
5544 5924 5.532406 TGGGACTTCAAAGTTTCTCATCTTG 59.468 40.000 0.00 0.00 39.88 3.02
5545 5925 5.765182 GGGACTTCAAAGTTTCTCATCTTGA 59.235 40.000 0.00 0.00 39.88 3.02
5546 5926 6.432472 GGGACTTCAAAGTTTCTCATCTTGAT 59.568 38.462 0.00 0.00 39.88 2.57
5547 5927 7.361628 GGGACTTCAAAGTTTCTCATCTTGATC 60.362 40.741 0.00 0.00 39.88 2.92
5548 5928 7.126726 ACTTCAAAGTTTCTCATCTTGATCG 57.873 36.000 0.00 0.00 35.21 3.69
5549 5929 5.536554 TCAAAGTTTCTCATCTTGATCGC 57.463 39.130 0.00 0.00 0.00 4.58
5550 5930 4.996758 TCAAAGTTTCTCATCTTGATCGCA 59.003 37.500 0.00 0.00 0.00 5.10
5551 5931 5.469760 TCAAAGTTTCTCATCTTGATCGCAA 59.530 36.000 0.00 0.00 0.00 4.85
5567 6252 1.177401 GCAAGCTTTAGGAAGGTGGG 58.823 55.000 0.00 0.00 42.47 4.61
5577 6262 0.694444 GGAAGGTGGGAGCCTGGATA 60.694 60.000 0.00 0.00 39.17 2.59
5583 6268 0.918983 TGGGAGCCTGGATACTTTGG 59.081 55.000 0.00 0.00 37.61 3.28
5628 6313 4.444876 GCAGCTGAGAAAATATGACCCCTA 60.445 45.833 20.43 0.00 0.00 3.53
5660 6345 5.932303 CCTGAGAAAATAGGACGAAAAGACA 59.068 40.000 0.00 0.00 36.11 3.41
5664 6349 8.846211 TGAGAAAATAGGACGAAAAGACAAAAT 58.154 29.630 0.00 0.00 0.00 1.82
5680 6365 3.780902 CAAAATATCTTTTGCCCGGTCC 58.219 45.455 0.00 0.00 43.33 4.46
5698 6383 4.568359 CGGTCCTTGATAGATTCAACAGTG 59.432 45.833 0.00 0.00 39.44 3.66
5701 6386 6.758886 GGTCCTTGATAGATTCAACAGTGTAG 59.241 42.308 0.00 0.00 39.44 2.74
5707 6392 6.663523 TGATAGATTCAACAGTGTAGGTCTGA 59.336 38.462 0.00 0.00 36.81 3.27
5708 6393 5.808366 AGATTCAACAGTGTAGGTCTGAA 57.192 39.130 9.21 9.21 36.81 3.02
5769 6455 9.630098 GTCAAAATCAAGCATGAAGAGATTTAA 57.370 29.630 0.00 0.00 39.49 1.52
5799 6485 0.249155 TTTGCTCGTCGTCGGTCTTT 60.249 50.000 1.55 0.00 37.69 2.52
5800 6486 0.937699 TTGCTCGTCGTCGGTCTTTG 60.938 55.000 1.55 0.00 37.69 2.77
5801 6487 2.087009 GCTCGTCGTCGGTCTTTGG 61.087 63.158 1.55 0.00 37.69 3.28
5802 6488 1.285023 CTCGTCGTCGGTCTTTGGT 59.715 57.895 1.55 0.00 37.69 3.67
5803 6489 1.002250 CTCGTCGTCGGTCTTTGGTG 61.002 60.000 1.55 0.00 37.69 4.17
5804 6490 2.654912 CGTCGTCGGTCTTTGGTGC 61.655 63.158 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.328819 AGATGCTCTGATCCAACTGC 57.671 50.000 0.00 0.00 0.00 4.40
2 3 5.176741 AGAAAAGATGCTCTGATCCAACT 57.823 39.130 0.00 0.00 0.00 3.16
5 6 3.431346 CGGAGAAAAGATGCTCTGATCCA 60.431 47.826 0.00 0.00 39.36 3.41
12 13 2.609916 GCCTAACGGAGAAAAGATGCTC 59.390 50.000 0.00 0.00 0.00 4.26
45 46 0.460635 GCCTACGGTTGGTTATCGCA 60.461 55.000 10.26 0.00 0.00 5.10
47 48 0.872881 CGGCCTACGGTTGGTTATCG 60.873 60.000 10.26 6.09 39.42 2.92
59 60 2.962253 GAGCATGCGACGGCCTAC 60.962 66.667 13.01 0.00 38.85 3.18
62 63 2.280119 TATGAGCATGCGACGGCC 60.280 61.111 13.01 0.00 38.85 6.13
79 80 4.699257 GTCTGCTCTTGGATTTGATCTTGT 59.301 41.667 0.00 0.00 0.00 3.16
160 303 2.876581 TCTCCCCCTCAAAGAAAAAGC 58.123 47.619 0.00 0.00 0.00 3.51
163 306 5.592587 TGTTATCTCCCCCTCAAAGAAAA 57.407 39.130 0.00 0.00 0.00 2.29
165 308 5.592587 TTTGTTATCTCCCCCTCAAAGAA 57.407 39.130 0.00 0.00 0.00 2.52
167 310 6.404734 CGAAATTTGTTATCTCCCCCTCAAAG 60.405 42.308 0.00 0.00 0.00 2.77
171 314 4.777463 TCGAAATTTGTTATCTCCCCCTC 58.223 43.478 0.00 0.00 0.00 4.30
172 315 4.855298 TCGAAATTTGTTATCTCCCCCT 57.145 40.909 0.00 0.00 0.00 4.79
220 363 7.562454 TCGTTTTACCAGACTTTGATTTCTT 57.438 32.000 0.00 0.00 0.00 2.52
221 364 7.255139 CCTTCGTTTTACCAGACTTTGATTTCT 60.255 37.037 0.00 0.00 0.00 2.52
225 368 4.215613 GCCTTCGTTTTACCAGACTTTGAT 59.784 41.667 0.00 0.00 0.00 2.57
226 369 3.562557 GCCTTCGTTTTACCAGACTTTGA 59.437 43.478 0.00 0.00 0.00 2.69
227 370 3.304458 GGCCTTCGTTTTACCAGACTTTG 60.304 47.826 0.00 0.00 0.00 2.77
228 371 2.882761 GGCCTTCGTTTTACCAGACTTT 59.117 45.455 0.00 0.00 0.00 2.66
378 529 5.835819 TGCTCCTCTCTGCTTGTTATATAGT 59.164 40.000 0.00 0.00 0.00 2.12
388 543 0.543883 TCCACTGCTCCTCTCTGCTT 60.544 55.000 0.00 0.00 0.00 3.91
392 547 2.974623 CAGTCCACTGCTCCTCTCT 58.025 57.895 0.00 0.00 37.15 3.10
443 598 2.550180 GGAGAGTGGCTGAAGTGTTTTC 59.450 50.000 0.00 0.00 0.00 2.29
444 599 2.576615 GGAGAGTGGCTGAAGTGTTTT 58.423 47.619 0.00 0.00 0.00 2.43
445 600 1.202818 GGGAGAGTGGCTGAAGTGTTT 60.203 52.381 0.00 0.00 0.00 2.83
482 638 2.124901 TGCGGGGATGGTTAAGCG 60.125 61.111 0.00 0.00 0.00 4.68
552 714 2.647158 GGGCGAAGAAGACGGAGGT 61.647 63.158 0.00 0.00 0.00 3.85
568 730 2.922234 GGAGGAGGAAGCATGGGG 59.078 66.667 0.00 0.00 0.00 4.96
571 733 0.462759 GGAACGGAGGAGGAAGCATG 60.463 60.000 0.00 0.00 0.00 4.06
658 820 2.409055 TGATACCCCACGACGTCGG 61.409 63.158 37.89 26.50 44.95 4.79
677 839 2.355132 AGCGAAGTGACGGTACTCATAG 59.645 50.000 0.00 0.00 42.05 2.23
679 841 1.135373 CAGCGAAGTGACGGTACTCAT 60.135 52.381 0.00 0.00 41.95 2.90
680 842 0.240145 CAGCGAAGTGACGGTACTCA 59.760 55.000 0.00 0.00 41.95 3.41
681 843 0.240411 ACAGCGAAGTGACGGTACTC 59.760 55.000 0.00 0.00 41.95 2.59
682 844 0.240411 GACAGCGAAGTGACGGTACT 59.760 55.000 0.00 0.00 41.95 2.73
683 845 1.063951 CGACAGCGAAGTGACGGTAC 61.064 60.000 0.00 0.00 41.95 3.34
684 846 1.208358 CGACAGCGAAGTGACGGTA 59.792 57.895 0.00 0.00 41.95 4.02
685 847 2.050351 CGACAGCGAAGTGACGGT 60.050 61.111 0.00 0.00 44.63 4.83
700 862 4.272489 AGAATTCAGATGGGATTTTGCGA 58.728 39.130 8.44 0.00 0.00 5.10
729 891 4.770874 AACCGGACGGATTGGCGG 62.771 66.667 18.80 0.00 38.96 6.13
785 952 2.366533 TCTAGGACTAGAACACTGCCG 58.633 52.381 6.59 0.00 39.08 5.69
788 955 3.690139 TCGCTTCTAGGACTAGAACACTG 59.310 47.826 15.79 8.96 44.58 3.66
791 958 5.916661 AAATCGCTTCTAGGACTAGAACA 57.083 39.130 15.79 5.69 44.58 3.18
800 967 7.902032 TCGTTACAAATAAAATCGCTTCTAGG 58.098 34.615 0.00 0.00 0.00 3.02
824 996 3.375299 CGACTGAATCCCCAATCTTGTTC 59.625 47.826 0.00 0.00 0.00 3.18
857 1029 1.445582 GTACGAACCGCTGGACCTG 60.446 63.158 1.50 0.00 0.00 4.00
894 1066 0.697079 TCTATCTATCCGCGGGTCCT 59.303 55.000 27.83 9.03 0.00 3.85
951 1123 9.638239 AACAAAACAAATGTATCGATTAGCAAT 57.362 25.926 1.71 0.00 0.00 3.56
953 1125 9.123709 GAAACAAAACAAATGTATCGATTAGCA 57.876 29.630 1.71 1.05 0.00 3.49
954 1126 9.123709 TGAAACAAAACAAATGTATCGATTAGC 57.876 29.630 1.71 0.00 0.00 3.09
957 1129 9.528018 AACTGAAACAAAACAAATGTATCGATT 57.472 25.926 1.71 0.00 0.00 3.34
997 1173 2.797278 CCGCGCCCTTCCTCATACT 61.797 63.158 0.00 0.00 0.00 2.12
1078 1258 5.255710 TCAAATCAAAGAAGACCGCAAAA 57.744 34.783 0.00 0.00 0.00 2.44
1319 1503 2.030363 TGAAAGCAACCCATTAACAGCG 60.030 45.455 0.00 0.00 0.00 5.18
1328 1512 6.716934 TGTTATAAAACTGAAAGCAACCCA 57.283 33.333 0.00 0.00 37.60 4.51
1359 1543 1.000060 CCCTGCCACACAATTGTTCAG 60.000 52.381 8.77 12.85 35.20 3.02
1463 1653 4.768968 ACAAGAAGCCATAGTTCTGCAAAT 59.231 37.500 0.00 0.00 34.40 2.32
1464 1654 4.144297 ACAAGAAGCCATAGTTCTGCAAA 58.856 39.130 0.00 0.00 34.40 3.68
1465 1655 3.754965 ACAAGAAGCCATAGTTCTGCAA 58.245 40.909 0.00 0.00 34.40 4.08
1466 1656 3.423539 ACAAGAAGCCATAGTTCTGCA 57.576 42.857 0.00 0.00 34.40 4.41
1467 1657 4.201861 GCTAACAAGAAGCCATAGTTCTGC 60.202 45.833 0.00 0.00 34.40 4.26
1478 1668 4.884164 ACAAGGGATATGCTAACAAGAAGC 59.116 41.667 0.00 0.00 40.50 3.86
1482 1672 4.449068 CGCTACAAGGGATATGCTAACAAG 59.551 45.833 0.00 0.00 0.00 3.16
1492 1684 6.528537 TGTAAAAGTACGCTACAAGGGATA 57.471 37.500 0.00 0.00 32.40 2.59
1496 1688 6.312918 ACATCATGTAAAAGTACGCTACAAGG 59.687 38.462 0.00 5.40 32.40 3.61
1500 1692 7.982371 AGTACATCATGTAAAAGTACGCTAC 57.018 36.000 0.00 0.00 39.84 3.58
1504 1696 8.795341 CACTGTAGTACATCATGTAAAAGTACG 58.205 37.037 2.82 0.00 39.84 3.67
1505 1697 9.850628 TCACTGTAGTACATCATGTAAAAGTAC 57.149 33.333 2.82 0.00 34.21 2.73
1522 1714 9.900710 GAAACGAATATATCATCTCACTGTAGT 57.099 33.333 0.00 0.00 0.00 2.73
1548 1742 2.614779 CGCAGCCAGTCCTATATCATG 58.385 52.381 0.00 0.00 0.00 3.07
1549 1743 1.552337 CCGCAGCCAGTCCTATATCAT 59.448 52.381 0.00 0.00 0.00 2.45
1552 1746 1.344763 GAACCGCAGCCAGTCCTATAT 59.655 52.381 0.00 0.00 0.00 0.86
1584 1779 1.706995 TACCCCGGAAAGTGTGCCAA 61.707 55.000 0.73 0.00 0.00 4.52
1626 1825 0.036294 AAGGCCAGTTCTTCGTAGCC 60.036 55.000 5.01 0.00 40.79 3.93
1632 1831 0.322906 CCTCCCAAGGCCAGTTCTTC 60.323 60.000 5.01 0.00 35.37 2.87
1701 1900 4.371624 TGGACCTGAAACACAAGATCAT 57.628 40.909 0.00 0.00 0.00 2.45
1715 1914 5.653507 CAATTTCATAACACCATGGACCTG 58.346 41.667 21.47 9.24 0.00 4.00
1726 1927 9.716531 TTCCAACAAATATGCAATTTCATAACA 57.283 25.926 1.85 0.00 33.19 2.41
1838 2040 4.530857 GGGGCGATGTCCCTGTCG 62.531 72.222 0.00 0.00 45.53 4.35
1985 2188 4.450757 TGAAAACATAGTCATGTGTGTCCG 59.549 41.667 0.00 0.00 44.83 4.79
2075 2289 8.734386 CAACAATTAATATAGATTGGAGGGAGC 58.266 37.037 12.82 0.00 37.53 4.70
2109 2323 7.792925 TCCATATTAATTGTCGCTGATTTACG 58.207 34.615 0.00 0.00 0.00 3.18
2239 2454 7.755591 TGCTATTTTAGACAGAAGCAATCTTG 58.244 34.615 0.00 0.00 37.05 3.02
2333 2548 5.104259 AGGAGCCAAGGTAGTCAAATTAG 57.896 43.478 0.00 0.00 0.00 1.73
2381 2596 3.576982 TGTGAACAGAAGACCCGTAAGAT 59.423 43.478 0.00 0.00 43.02 2.40
2676 2891 4.866486 GGCCTTGCTTAATTTCAAGTCATG 59.134 41.667 0.00 0.00 38.33 3.07
2798 3013 3.790089 ACAACTAACCAGAAGGAAGGG 57.210 47.619 0.00 0.00 38.69 3.95
2825 3040 2.604046 CTGGAAGGGGATACAAGTCG 57.396 55.000 0.00 0.00 39.74 4.18
2952 3167 7.857734 TCAAAAGTCAAGAAGTATGTCAACA 57.142 32.000 0.00 0.00 0.00 3.33
2956 3171 8.778358 AGACAATCAAAAGTCAAGAAGTATGTC 58.222 33.333 0.00 0.00 37.23 3.06
2968 3184 7.857885 CACCAAGTAGAAAGACAATCAAAAGTC 59.142 37.037 0.00 0.00 35.02 3.01
2969 3185 7.339466 ACACCAAGTAGAAAGACAATCAAAAGT 59.661 33.333 0.00 0.00 0.00 2.66
3176 3392 6.653320 AGCGGAACAATGAAACTATTTACTGA 59.347 34.615 0.00 0.00 0.00 3.41
3190 3406 8.854979 TTCAATTATCATAAAGCGGAACAATG 57.145 30.769 0.00 0.00 0.00 2.82
3326 3545 9.628500 GGTATTATTCTTTCCAGTCCTGTTAAT 57.372 33.333 0.00 0.00 0.00 1.40
3361 3580 5.030147 ACATCCCAGTCATACCTGTAAAGA 58.970 41.667 0.00 0.00 0.00 2.52
3366 3585 2.356125 GCAACATCCCAGTCATACCTGT 60.356 50.000 0.00 0.00 0.00 4.00
3391 3610 7.308229 CCAAACTTCTGTAGGAAAGAGAATGTG 60.308 40.741 0.00 0.00 36.92 3.21
3480 3700 8.787852 TGTTGCAAATCTACACATAAACATACA 58.212 29.630 0.00 0.00 0.00 2.29
3604 3834 8.543774 CGACATTTATCTTGAATTCTCCTGTAC 58.456 37.037 7.05 0.00 0.00 2.90
3665 3895 2.097629 GGATTTAGGCGAGCAAGAAACC 59.902 50.000 0.00 0.00 0.00 3.27
3693 3923 8.130671 TGGTACTAGTATCACTTTAAGCTGTT 57.869 34.615 11.96 0.00 0.00 3.16
3717 3947 7.023575 GGACACAAGTTTTAGATGCAGTTATG 58.976 38.462 0.00 0.00 0.00 1.90
3772 4002 6.770303 TGTTCCCAAGAATATCATTAATGCGA 59.230 34.615 10.76 1.24 33.67 5.10
3793 4023 3.737266 CACCAGTGTTTGCATCAATGTTC 59.263 43.478 15.08 0.00 0.00 3.18
3847 4077 3.518634 TTTCAAAAAGTCACAGCCACC 57.481 42.857 0.00 0.00 0.00 4.61
3848 4078 4.051237 GGATTTCAAAAAGTCACAGCCAC 58.949 43.478 0.00 0.00 0.00 5.01
3880 4110 7.432059 AGAGTTGAAACGTTAAGCTACTAAGT 58.568 34.615 0.00 0.00 0.00 2.24
3895 4125 5.181690 TGCCAACATGTAAGAGTTGAAAC 57.818 39.130 0.00 0.00 46.01 2.78
3962 4192 8.684386 TCTTAACCACACTTGACATAATCAAA 57.316 30.769 0.00 0.00 46.80 2.69
4067 4298 3.845781 ATGAGCACCGATACCTGAATT 57.154 42.857 0.00 0.00 0.00 2.17
4077 4308 4.323417 ACAGAACAAATTATGAGCACCGA 58.677 39.130 0.00 0.00 31.23 4.69
4079 4310 6.446318 TCAAACAGAACAAATTATGAGCACC 58.554 36.000 0.00 0.00 31.23 5.01
4099 4330 2.026729 TCCATCCTGCAACCGTATCAAA 60.027 45.455 0.00 0.00 0.00 2.69
4176 4407 4.586001 ACCAAAGCTCAATTCACAGAACAT 59.414 37.500 0.00 0.00 0.00 2.71
4201 4432 4.319046 CCATGTCAGTCAAAGTTTCTGTCG 60.319 45.833 4.70 0.00 0.00 4.35
4215 4447 4.405358 ACCACAAAACAATTCCATGTCAGT 59.595 37.500 0.00 0.00 31.81 3.41
4250 4482 4.020543 GGTCCTCAACATCAGTACTCTCT 58.979 47.826 0.00 0.00 0.00 3.10
4356 4588 7.633789 ACTTTACCAGGTCATGAACTAATGAT 58.366 34.615 14.23 0.00 38.76 2.45
4357 4589 7.016153 ACTTTACCAGGTCATGAACTAATGA 57.984 36.000 14.23 0.00 34.16 2.57
4358 4590 7.687941 AACTTTACCAGGTCATGAACTAATG 57.312 36.000 14.23 9.24 0.00 1.90
4453 4685 2.125912 CTCTGGTAGCGCTTGCGT 60.126 61.111 18.68 0.00 45.69 5.24
4526 4758 9.472361 CACAATTCAATCTCTTTGAGAAAACAT 57.528 29.630 1.20 0.00 44.90 2.71
4568 4801 0.389025 CCCAGCCTGTTTCAAACCAC 59.611 55.000 0.00 0.00 0.00 4.16
4665 4898 2.741878 GCTGCCTAAGTTTATCGCTCCA 60.742 50.000 0.00 0.00 0.00 3.86
4678 4911 3.941483 GCAGTGAAAGATAAGCTGCCTAA 59.059 43.478 0.00 0.00 44.61 2.69
4701 4934 7.378181 TCAGCGCAGAGATATATTTGTATTGA 58.622 34.615 11.47 0.00 0.00 2.57
4706 4939 5.459536 TCTCAGCGCAGAGATATATTTGT 57.540 39.130 26.48 0.00 39.62 2.83
4833 5072 4.749310 CGAGGGCGTGCTCTTGCT 62.749 66.667 0.00 0.00 40.48 3.91
4982 5221 1.066143 ACATAGTTCAGCCCAACTCCG 60.066 52.381 1.20 0.00 37.75 4.63
5007 5247 0.668535 GGGCCAAACACAGAGAACAC 59.331 55.000 4.39 0.00 0.00 3.32
5009 5249 0.954452 CTGGGCCAAACACAGAGAAC 59.046 55.000 8.04 0.00 34.21 3.01
5022 5264 0.815615 GACCGATGAACATCTGGGCC 60.816 60.000 20.34 0.00 35.16 5.80
5023 5265 0.179000 AGACCGATGAACATCTGGGC 59.821 55.000 20.34 18.87 38.74 5.36
5032 5274 2.635915 ACACACCCTTAAGACCGATGAA 59.364 45.455 3.36 0.00 0.00 2.57
5072 5315 4.906618 TGCTAGCCAAATATTAGTAGGCC 58.093 43.478 13.29 0.00 46.35 5.19
5073 5316 6.877611 TTTGCTAGCCAAATATTAGTAGGC 57.122 37.500 13.29 11.21 45.54 3.93
5180 5437 1.557371 TGGATGGTTGCCGATACTTGA 59.443 47.619 0.00 0.00 0.00 3.02
5208 5465 7.773224 GCTGGGGCCTACATTTTTATTTTTATT 59.227 33.333 0.84 0.00 0.00 1.40
5209 5466 7.279615 GCTGGGGCCTACATTTTTATTTTTAT 58.720 34.615 0.84 0.00 0.00 1.40
5210 5467 6.645306 GCTGGGGCCTACATTTTTATTTTTA 58.355 36.000 0.84 0.00 0.00 1.52
5211 5468 5.496556 GCTGGGGCCTACATTTTTATTTTT 58.503 37.500 0.84 0.00 0.00 1.94
5228 5485 2.745255 TTTGTTGATGGGGGCTGGGG 62.745 60.000 0.00 0.00 0.00 4.96
5229 5486 0.618393 ATTTGTTGATGGGGGCTGGG 60.618 55.000 0.00 0.00 0.00 4.45
5230 5487 1.278537 AATTTGTTGATGGGGGCTGG 58.721 50.000 0.00 0.00 0.00 4.85
5231 5488 3.421919 AAAATTTGTTGATGGGGGCTG 57.578 42.857 0.00 0.00 0.00 4.85
5296 5663 8.890410 TTGTACTACCTCTACTGACCTAAAAT 57.110 34.615 0.00 0.00 0.00 1.82
5307 5674 9.781633 TGATATTCTCTCTTGTACTACCTCTAC 57.218 37.037 0.00 0.00 0.00 2.59
5332 5699 2.451132 CCACGCTCTTGTCGTATACTG 58.549 52.381 0.56 0.00 38.19 2.74
5340 5707 1.827399 TTCTCCCCCACGCTCTTGTC 61.827 60.000 0.00 0.00 0.00 3.18
5398 5765 2.555757 GCTTTGACCAGTTTGATGAGCT 59.444 45.455 0.00 0.00 0.00 4.09
5446 5826 4.942483 CCTCTTCTTGCTTTCTCACATGAT 59.058 41.667 0.00 0.00 0.00 2.45
5448 5828 3.439476 CCCTCTTCTTGCTTTCTCACATG 59.561 47.826 0.00 0.00 0.00 3.21
5453 5833 5.123661 CAGATTTCCCTCTTCTTGCTTTCTC 59.876 44.000 0.00 0.00 0.00 2.87
5457 5837 3.075134 ACCAGATTTCCCTCTTCTTGCTT 59.925 43.478 0.00 0.00 0.00 3.91
5469 5849 4.216472 GGAAACAGAGTTGACCAGATTTCC 59.784 45.833 0.00 0.00 37.69 3.13
5470 5850 4.821805 TGGAAACAGAGTTGACCAGATTTC 59.178 41.667 5.42 0.00 35.01 2.17
5471 5851 4.792068 TGGAAACAGAGTTGACCAGATTT 58.208 39.130 5.42 0.00 35.01 2.17
5472 5852 4.437682 TGGAAACAGAGTTGACCAGATT 57.562 40.909 5.42 0.00 35.01 2.40
5486 5866 1.704628 TGCCTGGAGAATCTGGAAACA 59.295 47.619 0.00 0.00 39.59 2.83
5487 5867 2.363683 CTGCCTGGAGAATCTGGAAAC 58.636 52.381 0.00 0.00 32.13 2.78
5488 5868 1.340405 GCTGCCTGGAGAATCTGGAAA 60.340 52.381 0.00 0.00 32.13 3.13
5489 5869 0.254178 GCTGCCTGGAGAATCTGGAA 59.746 55.000 0.00 0.00 32.13 3.53
5490 5870 0.911045 TGCTGCCTGGAGAATCTGGA 60.911 55.000 0.00 0.00 32.13 3.86
5491 5871 0.464013 CTGCTGCCTGGAGAATCTGG 60.464 60.000 0.00 0.00 36.08 3.86
5492 5872 1.096386 GCTGCTGCCTGGAGAATCTG 61.096 60.000 3.85 0.00 36.08 2.90
5493 5873 1.224039 GCTGCTGCCTGGAGAATCT 59.776 57.895 3.85 0.00 36.08 2.40
5494 5874 3.824810 GCTGCTGCCTGGAGAATC 58.175 61.111 3.85 0.00 36.08 2.52
5504 5884 4.347453 CAACCCAACGGCTGCTGC 62.347 66.667 8.71 7.10 38.76 5.25
5505 5885 3.673484 CCAACCCAACGGCTGCTG 61.673 66.667 6.98 6.98 0.00 4.41
5506 5886 4.974721 CCCAACCCAACGGCTGCT 62.975 66.667 0.00 0.00 0.00 4.24
5507 5887 4.966787 TCCCAACCCAACGGCTGC 62.967 66.667 0.00 0.00 0.00 5.25
5508 5888 2.976494 AAGTCCCAACCCAACGGCTG 62.976 60.000 0.00 0.00 0.00 4.85
5509 5889 2.692273 GAAGTCCCAACCCAACGGCT 62.692 60.000 0.00 0.00 0.00 5.52
5510 5890 2.203437 AAGTCCCAACCCAACGGC 60.203 61.111 0.00 0.00 0.00 5.68
5511 5891 0.466555 TTGAAGTCCCAACCCAACGG 60.467 55.000 0.00 0.00 0.00 4.44
5512 5892 1.336755 CTTTGAAGTCCCAACCCAACG 59.663 52.381 0.00 0.00 0.00 4.10
5513 5893 2.384828 ACTTTGAAGTCCCAACCCAAC 58.615 47.619 0.00 0.00 32.86 3.77
5514 5894 2.838637 ACTTTGAAGTCCCAACCCAA 57.161 45.000 0.00 0.00 32.86 4.12
5515 5895 2.838637 AACTTTGAAGTCCCAACCCA 57.161 45.000 0.00 0.00 38.57 4.51
5516 5896 3.296854 AGAAACTTTGAAGTCCCAACCC 58.703 45.455 0.00 0.00 38.57 4.11
5517 5897 3.951680 TGAGAAACTTTGAAGTCCCAACC 59.048 43.478 0.00 0.00 38.57 3.77
5518 5898 5.532779 AGATGAGAAACTTTGAAGTCCCAAC 59.467 40.000 0.00 0.00 38.57 3.77
5519 5899 5.694995 AGATGAGAAACTTTGAAGTCCCAA 58.305 37.500 0.00 0.00 38.57 4.12
5520 5900 5.310409 AGATGAGAAACTTTGAAGTCCCA 57.690 39.130 0.00 0.00 38.57 4.37
5521 5901 5.765182 TCAAGATGAGAAACTTTGAAGTCCC 59.235 40.000 0.00 0.00 38.57 4.46
5522 5902 6.867662 TCAAGATGAGAAACTTTGAAGTCC 57.132 37.500 0.00 0.00 38.57 3.85
5523 5903 7.232994 CGATCAAGATGAGAAACTTTGAAGTC 58.767 38.462 0.00 0.00 38.57 3.01
5524 5904 6.348050 GCGATCAAGATGAGAAACTTTGAAGT 60.348 38.462 0.00 0.00 42.04 3.01
5525 5905 6.020372 GCGATCAAGATGAGAAACTTTGAAG 58.980 40.000 0.00 0.00 0.00 3.02
5526 5906 5.469760 TGCGATCAAGATGAGAAACTTTGAA 59.530 36.000 0.00 0.00 0.00 2.69
5527 5907 4.996758 TGCGATCAAGATGAGAAACTTTGA 59.003 37.500 0.00 0.00 0.00 2.69
5528 5908 5.287170 TGCGATCAAGATGAGAAACTTTG 57.713 39.130 0.00 0.00 0.00 2.77
5529 5909 5.947228 TTGCGATCAAGATGAGAAACTTT 57.053 34.783 0.00 0.00 0.00 2.66
5542 5922 3.009723 CCTTCCTAAAGCTTGCGATCAA 58.990 45.455 0.00 0.00 0.00 2.57
5543 5923 2.027192 ACCTTCCTAAAGCTTGCGATCA 60.027 45.455 0.00 0.00 0.00 2.92
5544 5924 2.352960 CACCTTCCTAAAGCTTGCGATC 59.647 50.000 0.00 0.00 0.00 3.69
5545 5925 2.359900 CACCTTCCTAAAGCTTGCGAT 58.640 47.619 0.00 0.00 0.00 4.58
5546 5926 1.610624 CCACCTTCCTAAAGCTTGCGA 60.611 52.381 0.00 0.00 0.00 5.10
5547 5927 0.804989 CCACCTTCCTAAAGCTTGCG 59.195 55.000 0.00 0.00 0.00 4.85
5548 5928 1.177401 CCCACCTTCCTAAAGCTTGC 58.823 55.000 0.00 0.00 0.00 4.01
5549 5929 2.716217 CTCCCACCTTCCTAAAGCTTG 58.284 52.381 0.00 0.00 0.00 4.01
5550 5930 1.004862 GCTCCCACCTTCCTAAAGCTT 59.995 52.381 0.00 0.00 0.00 3.74
5551 5931 0.621082 GCTCCCACCTTCCTAAAGCT 59.379 55.000 0.00 0.00 0.00 3.74
5552 5932 0.394488 GGCTCCCACCTTCCTAAAGC 60.394 60.000 0.00 0.00 0.00 3.51
5553 5933 1.065126 CAGGCTCCCACCTTCCTAAAG 60.065 57.143 0.00 0.00 38.26 1.85
5554 5934 0.991920 CAGGCTCCCACCTTCCTAAA 59.008 55.000 0.00 0.00 38.26 1.85
5555 5935 0.914417 CCAGGCTCCCACCTTCCTAA 60.914 60.000 0.00 0.00 38.26 2.69
5556 5936 1.306997 CCAGGCTCCCACCTTCCTA 60.307 63.158 0.00 0.00 38.26 2.94
5557 5937 2.498820 ATCCAGGCTCCCACCTTCCT 62.499 60.000 0.00 0.00 38.26 3.36
5558 5938 0.694444 TATCCAGGCTCCCACCTTCC 60.694 60.000 0.00 0.00 38.26 3.46
5559 5939 0.470341 GTATCCAGGCTCCCACCTTC 59.530 60.000 0.00 0.00 38.26 3.46
5560 5940 0.044855 AGTATCCAGGCTCCCACCTT 59.955 55.000 0.00 0.00 38.26 3.50
5561 5941 0.044855 AAGTATCCAGGCTCCCACCT 59.955 55.000 0.00 0.00 42.30 4.00
5567 6252 3.633986 CCAATTCCAAAGTATCCAGGCTC 59.366 47.826 0.00 0.00 0.00 4.70
5577 6262 6.782494 AGTTTGATAAGACCCAATTCCAAAGT 59.218 34.615 0.00 0.00 0.00 2.66
5583 6268 5.047377 TGCCAAGTTTGATAAGACCCAATTC 60.047 40.000 0.00 0.00 0.00 2.17
5635 6320 5.932883 GTCTTTTCGTCCTATTTTCTCAGGT 59.067 40.000 0.00 0.00 33.37 4.00
5660 6345 3.708451 AGGACCGGGCAAAAGATATTTT 58.292 40.909 11.00 0.00 0.00 1.82
5664 6349 1.631388 TCAAGGACCGGGCAAAAGATA 59.369 47.619 11.00 0.00 0.00 1.98
5673 6358 3.838244 TTGAATCTATCAAGGACCGGG 57.162 47.619 6.32 0.00 43.08 5.73
5698 6383 8.200792 AGATCATGTGTTATCTTTCAGACCTAC 58.799 37.037 0.00 0.00 0.00 3.18
5701 6386 6.238320 GCAGATCATGTGTTATCTTTCAGACC 60.238 42.308 0.00 0.00 29.93 3.85
5737 6423 7.211573 TCTTCATGCTTGATTTTGACAATTGT 58.788 30.769 11.78 11.78 0.00 2.71
5740 6426 7.223260 TCTCTTCATGCTTGATTTTGACAAT 57.777 32.000 2.75 0.00 0.00 2.71
5778 6464 0.938168 AGACCGACGACGAGCAAAAC 60.938 55.000 9.28 0.00 42.66 2.43
5786 6472 2.654912 GCACCAAAGACCGACGACG 61.655 63.158 0.00 0.00 39.43 5.12


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

AutoCloner maintained by Alex Coulton.