Multiple sequence alignment - TraesCS2B01G010100

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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 TraesCS2B01G010100 chr2B 100.000 3266 0 0 1 3266 5627353 5630618 0.000000e+00 6032.0
1 TraesCS2B01G010100 chr2B 81.434 1255 212 19 1021 2266 754928657 754927415 0.000000e+00 1007.0
2 TraesCS2B01G010100 chr2D 88.116 3164 173 90 155 3252 5746788 5749814 0.000000e+00 3572.0
3 TraesCS2B01G010100 chr2D 81.862 1246 203 20 1031 2266 618288572 618287340 0.000000e+00 1027.0
4 TraesCS2B01G010100 chr2A 91.302 2035 111 32 776 2786 4294025 4292033 0.000000e+00 2717.0
5 TraesCS2B01G010100 chr2A 81.638 1258 204 21 1021 2266 749104597 749103355 0.000000e+00 1018.0
6 TraesCS2B01G010100 chr2A 86.384 448 25 19 2845 3265 4292061 4291623 1.070000e-124 457.0
7 TraesCS2B01G010100 chr2A 81.520 487 38 29 142 590 4294587 4294115 1.440000e-93 353.0
8 TraesCS2B01G010100 chrUn 75.000 1108 211 42 1072 2160 50772329 50773389 4.970000e-123 451.0
9 TraesCS2B01G010100 chr4A 89.091 110 7 4 2520 2629 656045843 656045739 7.350000e-27 132.0
10 TraesCS2B01G010100 chr7A 75.429 175 41 2 1445 1618 32701482 32701309 2.090000e-12 84.2


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 TraesCS2B01G010100 chr2B 5627353 5630618 3265 False 6032.000000 6032 100.000 1 3266 1 chr2B.!!$F1 3265
1 TraesCS2B01G010100 chr2B 754927415 754928657 1242 True 1007.000000 1007 81.434 1021 2266 1 chr2B.!!$R1 1245
2 TraesCS2B01G010100 chr2D 5746788 5749814 3026 False 3572.000000 3572 88.116 155 3252 1 chr2D.!!$F1 3097
3 TraesCS2B01G010100 chr2D 618287340 618288572 1232 True 1027.000000 1027 81.862 1031 2266 1 chr2D.!!$R1 1235
4 TraesCS2B01G010100 chr2A 4291623 4294587 2964 True 1175.666667 2717 86.402 142 3265 3 chr2A.!!$R2 3123
5 TraesCS2B01G010100 chr2A 749103355 749104597 1242 True 1018.000000 1018 81.638 1021 2266 1 chr2A.!!$R1 1245
6 TraesCS2B01G010100 chrUn 50772329 50773389 1060 False 451.000000 451 75.000 1072 2160 1 chrUn.!!$F1 1088

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
117 118 0.032912 TATGACTAGTCGGCCCCACA 60.033 55.0 17.85 0.0 0.00 4.17 F
311 318 0.035152 GTGATGCCAGTCCCATGACA 60.035 55.0 0.00 0.0 44.33 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1832 0.253327 GGAGAGGAACACCATGACCC 59.747 60.0 0.0 0.0 0.00 4.46 R
2302 2392 0.104487 TTGGTTAGTCGTTGCCGTCA 59.896 50.0 0.0 0.0 35.01 4.35 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
22 23 5.461032 TGACATGTTTTACCCCATTGAAC 57.539 39.130 0.00 0.00 0.00 3.18
23 24 4.895889 TGACATGTTTTACCCCATTGAACA 59.104 37.500 0.00 0.00 35.04 3.18
24 25 5.363868 TGACATGTTTTACCCCATTGAACAA 59.636 36.000 0.00 0.00 34.34 2.83
25 26 6.127054 TGACATGTTTTACCCCATTGAACAAA 60.127 34.615 0.00 0.00 34.34 2.83
26 27 6.653989 ACATGTTTTACCCCATTGAACAAAA 58.346 32.000 0.00 0.00 34.34 2.44
27 28 7.112779 ACATGTTTTACCCCATTGAACAAAAA 58.887 30.769 0.00 0.00 34.34 1.94
28 29 7.281999 ACATGTTTTACCCCATTGAACAAAAAG 59.718 33.333 0.00 0.00 34.34 2.27
29 30 6.712276 TGTTTTACCCCATTGAACAAAAAGT 58.288 32.000 0.00 0.00 0.00 2.66
30 31 7.848128 TGTTTTACCCCATTGAACAAAAAGTA 58.152 30.769 0.00 0.00 0.00 2.24
31 32 8.487028 TGTTTTACCCCATTGAACAAAAAGTAT 58.513 29.630 0.00 0.00 0.00 2.12
32 33 8.984764 GTTTTACCCCATTGAACAAAAAGTATC 58.015 33.333 0.00 0.00 0.00 2.24
33 34 8.485578 TTTACCCCATTGAACAAAAAGTATCT 57.514 30.769 0.00 0.00 0.00 1.98
34 35 6.345096 ACCCCATTGAACAAAAAGTATCTG 57.655 37.500 0.00 0.00 0.00 2.90
35 36 5.838521 ACCCCATTGAACAAAAAGTATCTGT 59.161 36.000 0.00 0.00 0.00 3.41
36 37 6.326323 ACCCCATTGAACAAAAAGTATCTGTT 59.674 34.615 0.00 0.00 36.02 3.16
37 38 7.147567 ACCCCATTGAACAAAAAGTATCTGTTT 60.148 33.333 0.00 0.00 33.53 2.83
38 39 7.714813 CCCCATTGAACAAAAAGTATCTGTTTT 59.285 33.333 0.00 0.00 33.53 2.43
39 40 9.757227 CCCATTGAACAAAAAGTATCTGTTTTA 57.243 29.630 0.00 0.00 33.53 1.52
52 53 8.843885 AGTATCTGTTTTACTCAGTTTAACCC 57.156 34.615 0.00 0.00 34.86 4.11
53 54 8.434392 AGTATCTGTTTTACTCAGTTTAACCCA 58.566 33.333 0.00 0.00 34.86 4.51
54 55 9.059260 GTATCTGTTTTACTCAGTTTAACCCAA 57.941 33.333 0.00 0.00 34.86 4.12
55 56 7.324354 TCTGTTTTACTCAGTTTAACCCAAC 57.676 36.000 0.00 0.00 34.86 3.77
56 57 6.037391 TCTGTTTTACTCAGTTTAACCCAACG 59.963 38.462 0.00 0.00 34.86 4.10
57 58 5.066246 TGTTTTACTCAGTTTAACCCAACGG 59.934 40.000 0.00 0.00 0.00 4.44
58 59 1.601166 ACTCAGTTTAACCCAACGGC 58.399 50.000 0.00 0.00 0.00 5.68
59 60 1.142262 ACTCAGTTTAACCCAACGGCT 59.858 47.619 0.00 0.00 0.00 5.52
60 61 1.535462 CTCAGTTTAACCCAACGGCTG 59.465 52.381 0.00 0.00 0.00 4.85
61 62 0.039527 CAGTTTAACCCAACGGCTGC 60.040 55.000 0.00 0.00 0.00 5.25
62 63 1.176619 AGTTTAACCCAACGGCTGCC 61.177 55.000 9.11 9.11 0.00 4.85
72 73 2.046700 CGGCTGCCGTTCCCTTTA 60.047 61.111 31.72 0.00 42.73 1.85
73 74 1.451387 CGGCTGCCGTTCCCTTTAT 60.451 57.895 31.72 0.00 42.73 1.40
74 75 1.029947 CGGCTGCCGTTCCCTTTATT 61.030 55.000 31.72 0.00 42.73 1.40
75 76 1.182667 GGCTGCCGTTCCCTTTATTT 58.817 50.000 1.35 0.00 0.00 1.40
76 77 1.548719 GGCTGCCGTTCCCTTTATTTT 59.451 47.619 1.35 0.00 0.00 1.82
77 78 2.028476 GGCTGCCGTTCCCTTTATTTTT 60.028 45.455 1.35 0.00 0.00 1.94
78 79 3.250744 GCTGCCGTTCCCTTTATTTTTC 58.749 45.455 0.00 0.00 0.00 2.29
79 80 3.305744 GCTGCCGTTCCCTTTATTTTTCA 60.306 43.478 0.00 0.00 0.00 2.69
80 81 4.485163 CTGCCGTTCCCTTTATTTTTCAG 58.515 43.478 0.00 0.00 0.00 3.02
81 82 3.892588 TGCCGTTCCCTTTATTTTTCAGT 59.107 39.130 0.00 0.00 0.00 3.41
82 83 4.234574 GCCGTTCCCTTTATTTTTCAGTG 58.765 43.478 0.00 0.00 0.00 3.66
83 84 4.261867 GCCGTTCCCTTTATTTTTCAGTGT 60.262 41.667 0.00 0.00 0.00 3.55
84 85 5.219633 CCGTTCCCTTTATTTTTCAGTGTG 58.780 41.667 0.00 0.00 0.00 3.82
85 86 4.679654 CGTTCCCTTTATTTTTCAGTGTGC 59.320 41.667 0.00 0.00 0.00 4.57
86 87 5.507315 CGTTCCCTTTATTTTTCAGTGTGCT 60.507 40.000 0.00 0.00 0.00 4.40
87 88 6.293735 CGTTCCCTTTATTTTTCAGTGTGCTA 60.294 38.462 0.00 0.00 0.00 3.49
88 89 7.574967 CGTTCCCTTTATTTTTCAGTGTGCTAT 60.575 37.037 0.00 0.00 0.00 2.97
89 90 8.736244 GTTCCCTTTATTTTTCAGTGTGCTATA 58.264 33.333 0.00 0.00 0.00 1.31
90 91 9.474313 TTCCCTTTATTTTTCAGTGTGCTATAT 57.526 29.630 0.00 0.00 0.00 0.86
98 99 9.632638 ATTTTTCAGTGTGCTATATATGAACCT 57.367 29.630 0.00 0.00 0.00 3.50
101 102 9.710900 TTTCAGTGTGCTATATATGAACCTATG 57.289 33.333 0.00 0.00 0.00 2.23
102 103 8.650143 TCAGTGTGCTATATATGAACCTATGA 57.350 34.615 0.00 0.00 0.00 2.15
103 104 8.523658 TCAGTGTGCTATATATGAACCTATGAC 58.476 37.037 0.00 0.00 0.00 3.06
104 105 8.526978 CAGTGTGCTATATATGAACCTATGACT 58.473 37.037 0.00 0.00 0.00 3.41
105 106 9.755122 AGTGTGCTATATATGAACCTATGACTA 57.245 33.333 0.00 0.00 0.00 2.59
107 108 9.755122 TGTGCTATATATGAACCTATGACTAGT 57.245 33.333 0.00 0.00 0.00 2.57
109 110 9.110502 TGCTATATATGAACCTATGACTAGTCG 57.889 37.037 17.85 6.20 0.00 4.18
110 111 8.561212 GCTATATATGAACCTATGACTAGTCGG 58.439 40.741 17.85 14.83 0.00 4.79
111 112 5.646577 ATATGAACCTATGACTAGTCGGC 57.353 43.478 17.85 2.85 0.00 5.54
112 113 2.029623 TGAACCTATGACTAGTCGGCC 58.970 52.381 17.85 9.16 0.00 6.13
113 114 1.340568 GAACCTATGACTAGTCGGCCC 59.659 57.143 17.85 5.35 0.00 5.80
114 115 0.469518 ACCTATGACTAGTCGGCCCC 60.470 60.000 17.85 0.00 0.00 5.80
115 116 0.469331 CCTATGACTAGTCGGCCCCA 60.469 60.000 17.85 0.09 0.00 4.96
116 117 0.674534 CTATGACTAGTCGGCCCCAC 59.325 60.000 17.85 0.00 0.00 4.61
117 118 0.032912 TATGACTAGTCGGCCCCACA 60.033 55.000 17.85 0.00 0.00 4.17
118 119 0.691078 ATGACTAGTCGGCCCCACAT 60.691 55.000 17.85 1.19 0.00 3.21
119 120 0.907704 TGACTAGTCGGCCCCACATT 60.908 55.000 17.85 0.00 0.00 2.71
120 121 0.252197 GACTAGTCGGCCCCACATTT 59.748 55.000 7.22 0.00 0.00 2.32
121 122 1.483415 GACTAGTCGGCCCCACATTTA 59.517 52.381 7.22 0.00 0.00 1.40
122 123 1.910671 ACTAGTCGGCCCCACATTTAA 59.089 47.619 0.00 0.00 0.00 1.52
123 124 2.285977 CTAGTCGGCCCCACATTTAAC 58.714 52.381 0.00 0.00 0.00 2.01
124 125 0.696501 AGTCGGCCCCACATTTAACT 59.303 50.000 0.00 0.00 0.00 2.24
125 126 1.074889 AGTCGGCCCCACATTTAACTT 59.925 47.619 0.00 0.00 0.00 2.66
126 127 1.201414 GTCGGCCCCACATTTAACTTG 59.799 52.381 0.00 0.00 0.00 3.16
127 128 0.530288 CGGCCCCACATTTAACTTGG 59.470 55.000 0.00 0.00 0.00 3.61
128 129 0.249120 GGCCCCACATTTAACTTGGC 59.751 55.000 0.00 0.00 36.68 4.52
129 130 0.972883 GCCCCACATTTAACTTGGCA 59.027 50.000 0.00 0.00 37.36 4.92
130 131 1.554617 GCCCCACATTTAACTTGGCAT 59.445 47.619 0.00 0.00 37.36 4.40
131 132 2.027285 GCCCCACATTTAACTTGGCATT 60.027 45.455 0.00 0.00 37.36 3.56
132 133 3.860641 CCCCACATTTAACTTGGCATTC 58.139 45.455 0.00 0.00 0.00 2.67
133 134 3.369366 CCCCACATTTAACTTGGCATTCC 60.369 47.826 0.00 0.00 0.00 3.01
134 135 3.260380 CCCACATTTAACTTGGCATTCCA 59.740 43.478 0.00 0.00 41.55 3.53
135 136 4.497300 CCACATTTAACTTGGCATTCCAG 58.503 43.478 0.00 0.00 44.53 3.86
136 137 3.928375 CACATTTAACTTGGCATTCCAGC 59.072 43.478 0.00 0.00 44.53 4.85
137 138 3.834231 ACATTTAACTTGGCATTCCAGCT 59.166 39.130 0.00 0.00 44.53 4.24
138 139 3.940209 TTTAACTTGGCATTCCAGCTG 57.060 42.857 6.78 6.78 44.53 4.24
139 140 1.838112 TAACTTGGCATTCCAGCTGG 58.162 50.000 27.87 27.87 44.53 4.85
140 141 0.178953 AACTTGGCATTCCAGCTGGT 60.179 50.000 31.58 11.73 44.53 4.00
146 147 0.807496 GCATTCCAGCTGGTTCAGTC 59.193 55.000 31.58 13.54 36.34 3.51
160 161 2.882137 GTTCAGTCCATTCCGGTTTTCA 59.118 45.455 0.00 0.00 35.57 2.69
193 197 0.616964 TGTCATCCTCCTCTGCTGCT 60.617 55.000 0.00 0.00 0.00 4.24
229 233 3.615056 TGGCAGTCGTAATTAATGACACG 59.385 43.478 16.96 7.32 45.20 4.49
268 274 0.584396 TTGACGTCGTGCATGGTTTC 59.416 50.000 11.62 0.61 0.00 2.78
304 311 0.535335 TTAGTCCGTGATGCCAGTCC 59.465 55.000 0.00 0.00 0.00 3.85
309 316 1.221566 CGTGATGCCAGTCCCATGA 59.778 57.895 0.00 0.00 0.00 3.07
311 318 0.035152 GTGATGCCAGTCCCATGACA 60.035 55.000 0.00 0.00 44.33 3.58
316 323 0.754217 GCCAGTCCCATGACATGCAT 60.754 55.000 10.10 0.00 44.33 3.96
317 324 1.315690 CCAGTCCCATGACATGCATC 58.684 55.000 10.10 2.44 44.33 3.91
336 345 0.879400 CCACAGATCTCGATGCAGCC 60.879 60.000 0.00 0.00 0.00 4.85
385 415 2.556287 CGGCGTGCTTCTTCAACC 59.444 61.111 0.00 0.00 0.00 3.77
386 416 1.961277 CGGCGTGCTTCTTCAACCT 60.961 57.895 0.00 0.00 0.00 3.50
387 417 1.869690 GGCGTGCTTCTTCAACCTC 59.130 57.895 0.00 0.00 0.00 3.85
388 418 1.578206 GGCGTGCTTCTTCAACCTCC 61.578 60.000 0.00 0.00 0.00 4.30
389 419 1.578206 GCGTGCTTCTTCAACCTCCC 61.578 60.000 0.00 0.00 0.00 4.30
390 420 0.955919 CGTGCTTCTTCAACCTCCCC 60.956 60.000 0.00 0.00 0.00 4.81
391 421 0.955919 GTGCTTCTTCAACCTCCCCG 60.956 60.000 0.00 0.00 0.00 5.73
392 422 1.125093 TGCTTCTTCAACCTCCCCGA 61.125 55.000 0.00 0.00 0.00 5.14
393 423 0.391793 GCTTCTTCAACCTCCCCGAG 60.392 60.000 0.00 0.00 0.00 4.63
528 582 3.376078 GCACCATGCACACCCCTG 61.376 66.667 0.00 0.00 44.26 4.45
529 583 3.376078 CACCATGCACACCCCTGC 61.376 66.667 0.00 0.00 37.70 4.85
533 587 2.937689 ATGCACACCCCTGCCTCT 60.938 61.111 0.00 0.00 36.21 3.69
534 588 2.976490 ATGCACACCCCTGCCTCTC 61.976 63.158 0.00 0.00 36.21 3.20
535 589 4.416738 GCACACCCCTGCCTCTCC 62.417 72.222 0.00 0.00 0.00 3.71
548 602 2.054799 GCCTCTCCCTCTCTCTCTAGA 58.945 57.143 0.00 0.00 0.00 2.43
590 644 7.313951 ACCAAAATCGAATTTCTCTCTCATC 57.686 36.000 0.00 0.00 0.00 2.92
600 654 7.591057 CGAATTTCTCTCTCATCAGTGTATCTC 59.409 40.741 0.00 0.00 0.00 2.75
603 657 6.499106 TCTCTCTCATCAGTGTATCTCTCT 57.501 41.667 0.00 0.00 0.00 3.10
625 679 5.113446 TCTAGAGAGAAGTTCATACCGGT 57.887 43.478 13.98 13.98 0.00 5.28
626 680 6.244552 TCTAGAGAGAAGTTCATACCGGTA 57.755 41.667 18.46 18.46 0.00 4.02
627 681 6.289834 TCTAGAGAGAAGTTCATACCGGTAG 58.710 44.000 20.91 12.04 0.00 3.18
642 696 9.461312 TCATACCGGTAGTAAACTAAACTAAGA 57.539 33.333 20.91 0.00 33.70 2.10
692 746 7.992754 AAATGGCACTTAGATCCTATCAATC 57.007 36.000 0.00 0.00 0.00 2.67
726 780 1.849039 CTGTTCCCTCCCTCCATGATT 59.151 52.381 0.00 0.00 0.00 2.57
727 781 1.846439 TGTTCCCTCCCTCCATGATTC 59.154 52.381 0.00 0.00 0.00 2.52
729 783 2.105649 GTTCCCTCCCTCCATGATTCTC 59.894 54.545 0.00 0.00 0.00 2.87
730 784 1.582624 TCCCTCCCTCCATGATTCTCT 59.417 52.381 0.00 0.00 0.00 3.10
732 786 2.427593 CCCTCCCTCCATGATTCTCTCT 60.428 54.545 0.00 0.00 0.00 3.10
733 787 2.899256 CCTCCCTCCATGATTCTCTCTC 59.101 54.545 0.00 0.00 0.00 3.20
734 788 3.438372 CCTCCCTCCATGATTCTCTCTCT 60.438 52.174 0.00 0.00 0.00 3.10
735 789 3.828451 CTCCCTCCATGATTCTCTCTCTC 59.172 52.174 0.00 0.00 0.00 3.20
737 791 3.438372 CCCTCCATGATTCTCTCTCTCCT 60.438 52.174 0.00 0.00 0.00 3.69
742 796 4.763793 CCATGATTCTCTCTCTCCTCTCTC 59.236 50.000 0.00 0.00 0.00 3.20
743 797 5.457197 CCATGATTCTCTCTCTCCTCTCTCT 60.457 48.000 0.00 0.00 0.00 3.10
744 798 5.296151 TGATTCTCTCTCTCCTCTCTCTC 57.704 47.826 0.00 0.00 0.00 3.20
756 810 6.331032 TCTCCTCTCTCTCTCTACCTATCAT 58.669 44.000 0.00 0.00 0.00 2.45
757 811 6.213397 TCTCCTCTCTCTCTCTACCTATCATG 59.787 46.154 0.00 0.00 0.00 3.07
758 812 4.943705 CCTCTCTCTCTCTACCTATCATGC 59.056 50.000 0.00 0.00 0.00 4.06
759 813 5.514659 CCTCTCTCTCTCTACCTATCATGCA 60.515 48.000 0.00 0.00 0.00 3.96
760 814 6.138391 TCTCTCTCTCTACCTATCATGCAT 57.862 41.667 0.00 0.00 0.00 3.96
764 818 5.388654 TCTCTCTACCTATCATGCATCACA 58.611 41.667 0.00 0.00 0.00 3.58
767 821 4.948847 TCTACCTATCATGCATCACACAC 58.051 43.478 0.00 0.00 0.00 3.82
814 868 4.654262 TCCTCTCTCTCTCTAACCTCTCTC 59.346 50.000 0.00 0.00 0.00 3.20
815 869 4.202367 CCTCTCTCTCTCTAACCTCTCTCC 60.202 54.167 0.00 0.00 0.00 3.71
816 870 4.631234 TCTCTCTCTCTAACCTCTCTCCT 58.369 47.826 0.00 0.00 0.00 3.69
817 871 4.654262 TCTCTCTCTCTAACCTCTCTCCTC 59.346 50.000 0.00 0.00 0.00 3.71
821 880 1.856920 CTCTAACCTCTCTCCTCCCCT 59.143 57.143 0.00 0.00 0.00 4.79
826 885 2.018086 CTCTCTCCTCCCCTCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
851 910 1.541310 TAAGCACCACCACTCCCTCG 61.541 60.000 0.00 0.00 0.00 4.63
892 951 3.425577 ACACATCAGCAACAACAACAG 57.574 42.857 0.00 0.00 0.00 3.16
954 1026 0.322008 CCACCTTCTCTCAACCAGCC 60.322 60.000 0.00 0.00 0.00 4.85
955 1027 0.689623 CACCTTCTCTCAACCAGCCT 59.310 55.000 0.00 0.00 0.00 4.58
956 1028 0.980423 ACCTTCTCTCAACCAGCCTC 59.020 55.000 0.00 0.00 0.00 4.70
957 1029 0.979665 CCTTCTCTCAACCAGCCTCA 59.020 55.000 0.00 0.00 0.00 3.86
958 1030 1.338579 CCTTCTCTCAACCAGCCTCAC 60.339 57.143 0.00 0.00 0.00 3.51
959 1031 1.345741 CTTCTCTCAACCAGCCTCACA 59.654 52.381 0.00 0.00 0.00 3.58
960 1032 0.972134 TCTCTCAACCAGCCTCACAG 59.028 55.000 0.00 0.00 0.00 3.66
961 1033 0.673022 CTCTCAACCAGCCTCACAGC 60.673 60.000 0.00 0.00 0.00 4.40
962 1034 1.123861 TCTCAACCAGCCTCACAGCT 61.124 55.000 0.00 0.00 46.45 4.24
970 1042 1.451028 GCCTCACAGCTGATCACCC 60.451 63.158 23.35 0.00 0.00 4.61
975 1047 0.322277 CACAGCTGATCACCCAAGCT 60.322 55.000 23.35 0.77 36.12 3.74
977 1049 1.209019 ACAGCTGATCACCCAAGCTAG 59.791 52.381 23.35 4.57 34.16 3.42
985 1057 0.539438 CACCCAAGCTAGCCACCAAA 60.539 55.000 12.13 0.00 0.00 3.28
986 1058 0.251341 ACCCAAGCTAGCCACCAAAG 60.251 55.000 12.13 0.00 0.00 2.77
987 1059 0.251341 CCCAAGCTAGCCACCAAAGT 60.251 55.000 12.13 0.00 0.00 2.66
988 1060 1.168714 CCAAGCTAGCCACCAAAGTC 58.831 55.000 12.13 0.00 0.00 3.01
989 1061 1.545428 CCAAGCTAGCCACCAAAGTCA 60.545 52.381 12.13 0.00 0.00 3.41
990 1062 2.440409 CAAGCTAGCCACCAAAGTCAT 58.560 47.619 12.13 0.00 0.00 3.06
991 1063 2.409948 AGCTAGCCACCAAAGTCATC 57.590 50.000 12.13 0.00 0.00 2.92
992 1064 1.065126 AGCTAGCCACCAAAGTCATCC 60.065 52.381 12.13 0.00 0.00 3.51
993 1065 1.340017 GCTAGCCACCAAAGTCATCCA 60.340 52.381 2.29 0.00 0.00 3.41
994 1066 2.684927 GCTAGCCACCAAAGTCATCCAT 60.685 50.000 2.29 0.00 0.00 3.41
997 1069 2.170166 GCCACCAAAGTCATCCATCAA 58.830 47.619 0.00 0.00 0.00 2.57
1017 1089 0.692419 CCATGGTGCTCCTCCCTAGT 60.692 60.000 2.57 0.00 34.23 2.57
1751 1832 1.734477 CGCTCTGGTTCGTGGACAG 60.734 63.158 0.00 0.00 0.00 3.51
1791 1872 1.817099 GCTCATCCTCGGCAACCTG 60.817 63.158 0.00 0.00 0.00 4.00
1896 1980 1.941734 GCTCGCGAAGATCAGGTCG 60.942 63.158 11.33 8.60 40.24 4.79
1907 1991 2.021068 ATCAGGTCGGGCGACATCAG 62.021 60.000 0.00 0.00 46.20 2.90
1942 2026 2.359975 CCCGGTTCACCAAGAGCC 60.360 66.667 0.00 0.00 43.64 4.70
1947 2031 4.697756 TTCACCAAGAGCCGGGCG 62.698 66.667 14.39 0.78 0.00 6.13
2100 2184 4.410400 GGGTGGAAGGGGCAGTCG 62.410 72.222 0.00 0.00 0.00 4.18
2269 2353 4.505922 GCATCTCCGTCATCTTCTAAACAG 59.494 45.833 0.00 0.00 0.00 3.16
2273 2357 3.197766 TCCGTCATCTTCTAAACAGCCAT 59.802 43.478 0.00 0.00 0.00 4.40
2274 2358 3.941483 CCGTCATCTTCTAAACAGCCATT 59.059 43.478 0.00 0.00 0.00 3.16
2275 2359 4.396166 CCGTCATCTTCTAAACAGCCATTT 59.604 41.667 0.00 0.00 0.00 2.32
2276 2360 5.584649 CCGTCATCTTCTAAACAGCCATTTA 59.415 40.000 0.00 0.00 0.00 1.40
2289 2379 0.324943 CCATTTATCCCTCCGGCGAT 59.675 55.000 9.30 0.00 0.00 4.58
2290 2380 1.676014 CCATTTATCCCTCCGGCGATC 60.676 57.143 9.30 0.00 0.00 3.69
2291 2381 0.246635 ATTTATCCCTCCGGCGATCG 59.753 55.000 11.69 11.69 38.88 3.69
2292 2382 0.824595 TTTATCCCTCCGGCGATCGA 60.825 55.000 21.57 0.00 42.43 3.59
2350 2440 7.093814 CCCCTTGATTACTTTGTTGATGATGAA 60.094 37.037 0.00 0.00 0.00 2.57
2351 2441 7.972277 CCCTTGATTACTTTGTTGATGATGAAG 59.028 37.037 0.00 0.00 0.00 3.02
2352 2442 8.733458 CCTTGATTACTTTGTTGATGATGAAGA 58.267 33.333 0.00 0.00 0.00 2.87
2355 2445 9.506018 TGATTACTTTGTTGATGATGAAGAAGA 57.494 29.630 0.00 0.00 0.00 2.87
2397 2489 6.503589 TTGTAAGAGTAAGAGTGAGAGAGC 57.496 41.667 0.00 0.00 0.00 4.09
2515 2616 3.672295 GAAGCGGAGTGAGCCCCTG 62.672 68.421 0.00 0.00 34.64 4.45
2614 2715 3.071874 TGGCTTTACCCAGTGATGAAG 57.928 47.619 0.00 0.00 37.83 3.02
2629 2730 4.275443 GTGATGAAGGATGAGGCTCATTTC 59.725 45.833 29.35 26.82 37.20 2.17
2635 2736 2.883386 GGATGAGGCTCATTTCACCATC 59.117 50.000 29.35 15.52 37.20 3.51
2642 2743 4.702131 AGGCTCATTTCACCATCTTGTAAC 59.298 41.667 0.00 0.00 0.00 2.50
2648 2749 8.862325 TCATTTCACCATCTTGTAACAATACT 57.138 30.769 0.00 0.00 32.98 2.12
2650 2751 9.559958 CATTTCACCATCTTGTAACAATACTTC 57.440 33.333 0.00 0.00 32.98 3.01
2651 2752 8.918202 TTTCACCATCTTGTAACAATACTTCT 57.082 30.769 0.00 0.00 32.98 2.85
2652 2753 8.918202 TTCACCATCTTGTAACAATACTTCTT 57.082 30.769 0.00 0.00 32.98 2.52
2653 2754 8.322906 TCACCATCTTGTAACAATACTTCTTG 57.677 34.615 0.00 0.00 32.98 3.02
2654 2755 7.936847 TCACCATCTTGTAACAATACTTCTTGT 59.063 33.333 0.00 0.00 41.01 3.16
2656 2757 9.131791 ACCATCTTGTAACAATACTTCTTGTTT 57.868 29.630 7.42 0.00 44.76 2.83
2657 2758 9.965824 CCATCTTGTAACAATACTTCTTGTTTT 57.034 29.630 7.42 0.00 44.76 2.43
2691 2792 8.357402 TCTTCCAATTTTTACTTTACTGCCTTC 58.643 33.333 0.00 0.00 0.00 3.46
2723 2827 5.512060 CCCCTCAGTGAATATACATGACCAG 60.512 48.000 0.00 0.00 0.00 4.00
2725 2829 6.219473 CCTCAGTGAATATACATGACCAGTC 58.781 44.000 0.00 0.00 0.00 3.51
2870 2976 9.758651 AATTTACAGTTCCTTTTCACCAATAAC 57.241 29.630 0.00 0.00 0.00 1.89
2871 2977 8.528044 TTTACAGTTCCTTTTCACCAATAACT 57.472 30.769 0.00 0.00 0.00 2.24
2872 2978 9.629878 TTTACAGTTCCTTTTCACCAATAACTA 57.370 29.630 0.00 0.00 0.00 2.24
2873 2979 9.802039 TTACAGTTCCTTTTCACCAATAACTAT 57.198 29.630 0.00 0.00 0.00 2.12
2874 2980 8.110860 ACAGTTCCTTTTCACCAATAACTATG 57.889 34.615 0.00 0.00 0.00 2.23
2875 2981 7.724061 ACAGTTCCTTTTCACCAATAACTATGT 59.276 33.333 0.00 0.00 0.00 2.29
2876 2982 8.576442 CAGTTCCTTTTCACCAATAACTATGTT 58.424 33.333 0.00 0.00 0.00 2.71
2877 2983 9.143155 AGTTCCTTTTCACCAATAACTATGTTT 57.857 29.630 0.00 0.00 0.00 2.83
2878 2984 9.758651 GTTCCTTTTCACCAATAACTATGTTTT 57.241 29.630 0.00 0.00 0.00 2.43
2929 3035 7.554118 CCATTTTTACAGCTCCTTCTCATTCTA 59.446 37.037 0.00 0.00 0.00 2.10
2977 3107 6.738832 AGTAGCATTATTAGCATCAGCATG 57.261 37.500 0.00 0.00 45.49 4.06
2996 3126 5.059161 GCATGAGCATCTGATAAACCACTA 58.941 41.667 0.00 0.00 41.58 2.74
2997 3127 5.178996 GCATGAGCATCTGATAAACCACTAG 59.821 44.000 0.00 0.00 41.58 2.57
2998 3128 5.282055 TGAGCATCTGATAAACCACTAGG 57.718 43.478 0.00 0.00 37.09 3.02
2999 3129 4.101585 TGAGCATCTGATAAACCACTAGGG 59.898 45.833 0.00 0.00 38.46 3.53
3000 3130 6.344204 TGAGCATCTGATAAACCACTAGGGT 61.344 44.000 0.00 0.00 45.62 4.34
3184 3333 6.038050 GCTCTGGGAAGTTAAATCAGAATCAG 59.962 42.308 0.00 0.00 34.58 2.90
3204 3353 1.134848 GCCAGATCTCACTCACTCACC 60.135 57.143 0.00 0.00 0.00 4.02
3207 3356 2.166050 CAGATCTCACTCACTCACCCAG 59.834 54.545 0.00 0.00 0.00 4.45
3208 3357 0.901124 ATCTCACTCACTCACCCAGC 59.099 55.000 0.00 0.00 0.00 4.85
3209 3358 0.178950 TCTCACTCACTCACCCAGCT 60.179 55.000 0.00 0.00 0.00 4.24
3210 3359 0.037512 CTCACTCACTCACCCAGCTG 60.038 60.000 6.78 6.78 0.00 4.24
3259 3416 1.538876 ACCTGCTGCCTCCAAGGTA 60.539 57.895 6.81 0.00 37.80 3.08
3261 3418 1.222936 CTGCTGCCTCCAAGGTAGG 59.777 63.158 12.22 3.93 46.63 3.18
3265 3422 1.915078 CTGCCTCCAAGGTAGGGGTG 61.915 65.000 3.39 0.00 43.39 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.895889 TGTTCAATGGGGTAAAACATGTCA 59.104 37.500 0.00 0.00 0.00 3.58
1 2 5.461032 TGTTCAATGGGGTAAAACATGTC 57.539 39.130 0.00 0.00 0.00 3.06
2 3 5.878406 TTGTTCAATGGGGTAAAACATGT 57.122 34.783 0.00 0.00 30.62 3.21
3 4 7.281999 ACTTTTTGTTCAATGGGGTAAAACATG 59.718 33.333 0.00 0.00 30.62 3.21
4 5 7.342581 ACTTTTTGTTCAATGGGGTAAAACAT 58.657 30.769 0.00 0.00 30.62 2.71
5 6 6.712276 ACTTTTTGTTCAATGGGGTAAAACA 58.288 32.000 0.00 0.00 0.00 2.83
6 7 8.896320 ATACTTTTTGTTCAATGGGGTAAAAC 57.104 30.769 0.00 0.00 0.00 2.43
7 8 8.929487 AGATACTTTTTGTTCAATGGGGTAAAA 58.071 29.630 0.00 0.00 0.00 1.52
8 9 8.364142 CAGATACTTTTTGTTCAATGGGGTAAA 58.636 33.333 0.00 0.00 0.00 2.01
9 10 7.507616 ACAGATACTTTTTGTTCAATGGGGTAA 59.492 33.333 0.00 0.00 0.00 2.85
10 11 7.007723 ACAGATACTTTTTGTTCAATGGGGTA 58.992 34.615 0.00 0.00 0.00 3.69
11 12 5.838521 ACAGATACTTTTTGTTCAATGGGGT 59.161 36.000 0.00 0.00 0.00 4.95
12 13 6.345096 ACAGATACTTTTTGTTCAATGGGG 57.655 37.500 0.00 0.00 0.00 4.96
13 14 8.661352 AAAACAGATACTTTTTGTTCAATGGG 57.339 30.769 0.00 0.00 34.18 4.00
26 27 9.281371 GGGTTAAACTGAGTAAAACAGATACTT 57.719 33.333 10.80 0.00 38.55 2.24
27 28 8.434392 TGGGTTAAACTGAGTAAAACAGATACT 58.566 33.333 10.80 0.00 38.55 2.12
28 29 8.611654 TGGGTTAAACTGAGTAAAACAGATAC 57.388 34.615 10.80 0.00 38.55 2.24
29 30 9.059260 GTTGGGTTAAACTGAGTAAAACAGATA 57.941 33.333 10.80 0.00 38.55 1.98
30 31 7.255001 CGTTGGGTTAAACTGAGTAAAACAGAT 60.255 37.037 10.80 0.00 38.55 2.90
31 32 6.037391 CGTTGGGTTAAACTGAGTAAAACAGA 59.963 38.462 10.80 0.00 38.55 3.41
32 33 6.196571 CGTTGGGTTAAACTGAGTAAAACAG 58.803 40.000 10.80 0.00 40.68 3.16
33 34 5.066246 CCGTTGGGTTAAACTGAGTAAAACA 59.934 40.000 10.80 0.00 0.00 2.83
34 35 5.513376 CCGTTGGGTTAAACTGAGTAAAAC 58.487 41.667 0.00 0.00 0.00 2.43
35 36 4.036616 GCCGTTGGGTTAAACTGAGTAAAA 59.963 41.667 0.00 0.00 34.97 1.52
36 37 3.565063 GCCGTTGGGTTAAACTGAGTAAA 59.435 43.478 0.00 0.00 34.97 2.01
37 38 3.140623 GCCGTTGGGTTAAACTGAGTAA 58.859 45.455 0.00 0.00 34.97 2.24
38 39 2.369532 AGCCGTTGGGTTAAACTGAGTA 59.630 45.455 0.00 0.00 34.97 2.59
39 40 1.142262 AGCCGTTGGGTTAAACTGAGT 59.858 47.619 0.00 0.00 34.97 3.41
40 41 1.535462 CAGCCGTTGGGTTAAACTGAG 59.465 52.381 0.00 0.00 34.97 3.35
41 42 1.600023 CAGCCGTTGGGTTAAACTGA 58.400 50.000 0.00 0.00 34.97 3.41
42 43 0.039527 GCAGCCGTTGGGTTAAACTG 60.040 55.000 0.00 0.00 34.97 3.16
43 44 1.176619 GGCAGCCGTTGGGTTAAACT 61.177 55.000 0.00 0.00 34.97 2.66
44 45 1.287815 GGCAGCCGTTGGGTTAAAC 59.712 57.895 0.00 0.00 34.97 2.01
45 46 2.262303 CGGCAGCCGTTGGGTTAAA 61.262 57.895 26.69 0.00 42.73 1.52
46 47 2.670251 CGGCAGCCGTTGGGTTAA 60.670 61.111 26.69 0.00 42.73 2.01
56 57 1.182667 AAATAAAGGGAACGGCAGCC 58.817 50.000 0.00 0.00 0.00 4.85
57 58 3.250744 GAAAAATAAAGGGAACGGCAGC 58.749 45.455 0.00 0.00 0.00 5.25
58 59 4.022329 ACTGAAAAATAAAGGGAACGGCAG 60.022 41.667 0.00 0.00 0.00 4.85
59 60 3.892588 ACTGAAAAATAAAGGGAACGGCA 59.107 39.130 0.00 0.00 0.00 5.69
60 61 4.234574 CACTGAAAAATAAAGGGAACGGC 58.765 43.478 0.00 0.00 0.00 5.68
61 62 5.219633 CACACTGAAAAATAAAGGGAACGG 58.780 41.667 0.00 0.00 0.00 4.44
62 63 4.679654 GCACACTGAAAAATAAAGGGAACG 59.320 41.667 0.00 0.00 0.00 3.95
63 64 5.842907 AGCACACTGAAAAATAAAGGGAAC 58.157 37.500 0.00 0.00 0.00 3.62
64 65 7.775053 ATAGCACACTGAAAAATAAAGGGAA 57.225 32.000 0.00 0.00 0.00 3.97
72 73 9.632638 AGGTTCATATATAGCACACTGAAAAAT 57.367 29.630 0.00 0.00 0.00 1.82
75 76 9.710900 CATAGGTTCATATATAGCACACTGAAA 57.289 33.333 0.00 0.00 0.00 2.69
76 77 9.088987 TCATAGGTTCATATATAGCACACTGAA 57.911 33.333 0.00 0.00 0.00 3.02
77 78 8.523658 GTCATAGGTTCATATATAGCACACTGA 58.476 37.037 0.00 0.00 0.00 3.41
78 79 8.526978 AGTCATAGGTTCATATATAGCACACTG 58.473 37.037 0.00 0.00 0.00 3.66
79 80 8.657387 AGTCATAGGTTCATATATAGCACACT 57.343 34.615 0.00 0.00 0.00 3.55
81 82 9.755122 ACTAGTCATAGGTTCATATATAGCACA 57.245 33.333 0.00 0.00 32.90 4.57
83 84 9.110502 CGACTAGTCATAGGTTCATATATAGCA 57.889 37.037 22.37 0.00 32.90 3.49
84 85 8.561212 CCGACTAGTCATAGGTTCATATATAGC 58.439 40.741 22.37 0.00 32.90 2.97
85 86 8.561212 GCCGACTAGTCATAGGTTCATATATAG 58.439 40.741 22.37 0.15 32.90 1.31
86 87 7.501559 GGCCGACTAGTCATAGGTTCATATATA 59.498 40.741 22.37 0.00 32.90 0.86
87 88 6.321690 GGCCGACTAGTCATAGGTTCATATAT 59.678 42.308 22.37 0.00 32.90 0.86
88 89 5.651139 GGCCGACTAGTCATAGGTTCATATA 59.349 44.000 22.37 0.00 32.90 0.86
89 90 4.463186 GGCCGACTAGTCATAGGTTCATAT 59.537 45.833 22.37 0.00 32.90 1.78
90 91 3.825014 GGCCGACTAGTCATAGGTTCATA 59.175 47.826 22.37 0.00 32.90 2.15
91 92 2.628657 GGCCGACTAGTCATAGGTTCAT 59.371 50.000 22.37 0.00 32.90 2.57
92 93 2.029623 GGCCGACTAGTCATAGGTTCA 58.970 52.381 22.37 0.00 32.90 3.18
93 94 1.340568 GGGCCGACTAGTCATAGGTTC 59.659 57.143 22.37 11.39 32.90 3.62
94 95 1.411041 GGGCCGACTAGTCATAGGTT 58.589 55.000 22.37 0.00 32.90 3.50
95 96 0.469518 GGGGCCGACTAGTCATAGGT 60.470 60.000 22.37 0.00 32.90 3.08
96 97 0.469331 TGGGGCCGACTAGTCATAGG 60.469 60.000 22.37 15.87 32.90 2.57
97 98 0.674534 GTGGGGCCGACTAGTCATAG 59.325 60.000 22.37 11.31 34.96 2.23
98 99 0.032912 TGTGGGGCCGACTAGTCATA 60.033 55.000 22.37 0.00 0.00 2.15
99 100 0.691078 ATGTGGGGCCGACTAGTCAT 60.691 55.000 22.37 3.80 0.00 3.06
100 101 0.907704 AATGTGGGGCCGACTAGTCA 60.908 55.000 22.37 1.37 0.00 3.41
101 102 0.252197 AAATGTGGGGCCGACTAGTC 59.748 55.000 19.81 13.18 0.00 2.59
102 103 1.575419 TAAATGTGGGGCCGACTAGT 58.425 50.000 19.81 0.00 0.00 2.57
103 104 2.093128 AGTTAAATGTGGGGCCGACTAG 60.093 50.000 19.81 0.00 0.00 2.57
104 105 1.910671 AGTTAAATGTGGGGCCGACTA 59.089 47.619 19.81 6.75 0.00 2.59
105 106 0.696501 AGTTAAATGTGGGGCCGACT 59.303 50.000 19.81 2.11 0.00 4.18
106 107 1.201414 CAAGTTAAATGTGGGGCCGAC 59.799 52.381 12.27 12.27 0.00 4.79
107 108 1.540267 CAAGTTAAATGTGGGGCCGA 58.460 50.000 0.00 0.00 0.00 5.54
108 109 0.530288 CCAAGTTAAATGTGGGGCCG 59.470 55.000 0.00 0.00 0.00 6.13
109 110 0.249120 GCCAAGTTAAATGTGGGGCC 59.751 55.000 0.00 0.00 33.93 5.80
110 111 0.972883 TGCCAAGTTAAATGTGGGGC 59.027 50.000 0.00 0.00 40.29 5.80
111 112 3.369366 GGAATGCCAAGTTAAATGTGGGG 60.369 47.826 6.36 0.00 32.71 4.96
112 113 3.260380 TGGAATGCCAAGTTAAATGTGGG 59.740 43.478 0.00 0.00 42.49 4.61
113 114 4.497300 CTGGAATGCCAAGTTAAATGTGG 58.503 43.478 0.00 0.00 45.41 4.17
114 115 3.928375 GCTGGAATGCCAAGTTAAATGTG 59.072 43.478 0.00 0.00 45.41 3.21
115 116 3.834231 AGCTGGAATGCCAAGTTAAATGT 59.166 39.130 0.00 0.00 45.41 2.71
116 117 4.178540 CAGCTGGAATGCCAAGTTAAATG 58.821 43.478 5.57 0.00 45.41 2.32
117 118 3.196254 CCAGCTGGAATGCCAAGTTAAAT 59.804 43.478 29.88 0.00 45.41 1.40
118 119 2.562298 CCAGCTGGAATGCCAAGTTAAA 59.438 45.455 29.88 0.00 45.41 1.52
119 120 2.170166 CCAGCTGGAATGCCAAGTTAA 58.830 47.619 29.88 0.00 45.41 2.01
120 121 1.075374 ACCAGCTGGAATGCCAAGTTA 59.925 47.619 39.19 0.00 45.41 2.24
121 122 0.178953 ACCAGCTGGAATGCCAAGTT 60.179 50.000 39.19 9.77 45.41 2.66
122 123 0.178953 AACCAGCTGGAATGCCAAGT 60.179 50.000 39.19 10.61 45.41 3.16
123 124 0.529378 GAACCAGCTGGAATGCCAAG 59.471 55.000 39.19 9.60 45.41 3.61
124 125 0.178967 TGAACCAGCTGGAATGCCAA 60.179 50.000 39.19 13.61 45.41 4.52
125 126 0.609957 CTGAACCAGCTGGAATGCCA 60.610 55.000 39.19 23.60 43.47 4.92
126 127 0.610232 ACTGAACCAGCTGGAATGCC 60.610 55.000 39.19 20.64 38.94 4.40
127 128 0.807496 GACTGAACCAGCTGGAATGC 59.193 55.000 39.19 22.65 38.94 3.56
128 129 1.271543 TGGACTGAACCAGCTGGAATG 60.272 52.381 39.19 24.71 38.94 2.67
129 130 1.067295 TGGACTGAACCAGCTGGAAT 58.933 50.000 39.19 25.99 38.94 3.01
130 131 1.067295 ATGGACTGAACCAGCTGGAA 58.933 50.000 39.19 21.56 43.49 3.53
131 132 1.003580 GAATGGACTGAACCAGCTGGA 59.996 52.381 39.19 16.40 43.49 3.86
132 133 1.457346 GAATGGACTGAACCAGCTGG 58.543 55.000 31.60 31.60 43.49 4.85
133 134 1.457346 GGAATGGACTGAACCAGCTG 58.543 55.000 6.78 6.78 43.49 4.24
134 135 0.036010 CGGAATGGACTGAACCAGCT 60.036 55.000 0.00 0.00 43.49 4.24
135 136 1.026718 CCGGAATGGACTGAACCAGC 61.027 60.000 0.00 0.00 43.49 4.85
136 137 0.324943 ACCGGAATGGACTGAACCAG 59.675 55.000 9.46 0.00 43.49 4.00
137 138 0.768622 AACCGGAATGGACTGAACCA 59.231 50.000 9.46 0.00 44.41 3.67
138 139 1.905637 AAACCGGAATGGACTGAACC 58.094 50.000 9.46 0.00 42.00 3.62
139 140 2.882137 TGAAAACCGGAATGGACTGAAC 59.118 45.455 9.46 0.00 42.00 3.18
140 141 3.216187 TGAAAACCGGAATGGACTGAA 57.784 42.857 9.46 0.00 42.00 3.02
146 147 1.670811 CCTCGATGAAAACCGGAATGG 59.329 52.381 9.46 0.00 46.41 3.16
160 161 1.274703 ATGACAAGTGGGGCCTCGAT 61.275 55.000 0.84 0.00 0.00 3.59
193 197 1.915489 ACTGCCATCTTACATGTGGGA 59.085 47.619 9.11 6.82 33.58 4.37
229 233 7.281999 ACGTCAAGGGTTAAGTATACTAGTCTC 59.718 40.741 5.65 0.00 0.00 3.36
268 274 5.377478 GGACTAATCTGGTCAATTAAGGGG 58.623 45.833 0.00 0.00 35.61 4.79
304 311 2.047002 TCTGTGGATGCATGTCATGG 57.953 50.000 14.64 0.32 35.05 3.66
309 316 1.758862 TCGAGATCTGTGGATGCATGT 59.241 47.619 2.46 0.00 31.46 3.21
311 318 3.041508 CATCGAGATCTGTGGATGCAT 57.958 47.619 0.00 0.00 31.01 3.96
316 323 0.103755 GCTGCATCGAGATCTGTGGA 59.896 55.000 0.00 0.00 0.00 4.02
317 324 0.879400 GGCTGCATCGAGATCTGTGG 60.879 60.000 0.00 0.00 0.00 4.17
392 422 4.722535 TTCCAGCTCGGGGAGGCT 62.723 66.667 0.00 0.00 39.60 4.58
393 423 3.717294 TTTCCAGCTCGGGGAGGC 61.717 66.667 2.86 0.00 35.46 4.70
432 462 2.769652 GAACATGCAGGAGGCCACCA 62.770 60.000 22.29 0.39 43.89 4.17
522 576 3.288381 AGAGGGAGAGGCAGGGGT 61.288 66.667 0.00 0.00 0.00 4.95
528 582 2.054799 TCTAGAGAGAGAGGGAGAGGC 58.945 57.143 0.00 0.00 0.00 4.70
529 583 4.788925 TTTCTAGAGAGAGAGGGAGAGG 57.211 50.000 0.00 0.00 31.77 3.69
603 657 5.113446 ACCGGTATGAACTTCTCTCTAGA 57.887 43.478 4.49 0.00 0.00 2.43
641 695 7.722363 TCAAAAACCCCAACTTCTTCTTATTC 58.278 34.615 0.00 0.00 0.00 1.75
642 696 7.669089 TCAAAAACCCCAACTTCTTCTTATT 57.331 32.000 0.00 0.00 0.00 1.40
643 697 7.669089 TTCAAAAACCCCAACTTCTTCTTAT 57.331 32.000 0.00 0.00 0.00 1.73
706 760 1.516110 ATCATGGAGGGAGGGAACAG 58.484 55.000 0.00 0.00 0.00 3.16
709 763 2.021639 AGAGAATCATGGAGGGAGGGAA 60.022 50.000 0.00 0.00 37.82 3.97
726 780 4.271807 AGAGAGAGAGAGGAGAGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
727 781 4.282195 GGTAGAGAGAGAGAGGAGAGAGAG 59.718 54.167 0.00 0.00 0.00 3.20
729 783 4.227197 AGGTAGAGAGAGAGAGGAGAGAG 58.773 52.174 0.00 0.00 0.00 3.20
730 784 4.280789 AGGTAGAGAGAGAGAGGAGAGA 57.719 50.000 0.00 0.00 0.00 3.10
732 786 5.722290 TGATAGGTAGAGAGAGAGAGGAGA 58.278 45.833 0.00 0.00 0.00 3.71
733 787 6.409704 CATGATAGGTAGAGAGAGAGAGGAG 58.590 48.000 0.00 0.00 0.00 3.69
734 788 5.280470 GCATGATAGGTAGAGAGAGAGAGGA 60.280 48.000 0.00 0.00 0.00 3.71
735 789 4.943705 GCATGATAGGTAGAGAGAGAGAGG 59.056 50.000 0.00 0.00 0.00 3.69
737 791 5.574970 TGCATGATAGGTAGAGAGAGAGA 57.425 43.478 0.00 0.00 0.00 3.10
742 796 5.010415 TGTGTGATGCATGATAGGTAGAGAG 59.990 44.000 2.46 0.00 0.00 3.20
743 797 4.895297 TGTGTGATGCATGATAGGTAGAGA 59.105 41.667 2.46 0.00 0.00 3.10
744 798 4.987285 GTGTGTGATGCATGATAGGTAGAG 59.013 45.833 2.46 0.00 0.00 2.43
756 810 0.467844 AAAGCAGGGTGTGTGATGCA 60.468 50.000 0.00 0.00 41.14 3.96
757 811 0.242017 GAAAGCAGGGTGTGTGATGC 59.758 55.000 0.00 0.00 38.97 3.91
758 812 1.808945 GAGAAAGCAGGGTGTGTGATG 59.191 52.381 0.00 0.00 0.00 3.07
759 813 1.701847 AGAGAAAGCAGGGTGTGTGAT 59.298 47.619 0.00 0.00 0.00 3.06
760 814 1.070758 GAGAGAAAGCAGGGTGTGTGA 59.929 52.381 0.00 0.00 0.00 3.58
764 818 0.980423 GGAGAGAGAAAGCAGGGTGT 59.020 55.000 0.00 0.00 0.00 4.16
767 821 1.206849 GTGAGGAGAGAGAAAGCAGGG 59.793 57.143 0.00 0.00 0.00 4.45
814 868 3.252351 CTTAAATAGAGGGGAGGGGAGG 58.748 54.545 0.00 0.00 0.00 4.30
815 869 2.640332 GCTTAAATAGAGGGGAGGGGAG 59.360 54.545 0.00 0.00 0.00 4.30
816 870 2.021441 TGCTTAAATAGAGGGGAGGGGA 60.021 50.000 0.00 0.00 0.00 4.81
817 871 2.106684 GTGCTTAAATAGAGGGGAGGGG 59.893 54.545 0.00 0.00 0.00 4.79
821 880 2.508300 GGTGGTGCTTAAATAGAGGGGA 59.492 50.000 0.00 0.00 0.00 4.81
826 885 3.054655 GGGAGTGGTGGTGCTTAAATAGA 60.055 47.826 0.00 0.00 0.00 1.98
851 910 0.458260 GTGTGTTGGTGGTTTGGGAC 59.542 55.000 0.00 0.00 0.00 4.46
892 951 1.227031 TGTTTGTTGCTGCTGCTGC 60.227 52.632 22.51 22.51 40.48 5.25
954 1026 1.735386 CTTGGGTGATCAGCTGTGAG 58.265 55.000 23.24 12.36 35.66 3.51
955 1027 0.321919 GCTTGGGTGATCAGCTGTGA 60.322 55.000 23.24 7.24 37.02 3.58
956 1028 0.322277 AGCTTGGGTGATCAGCTGTG 60.322 55.000 23.24 14.08 34.25 3.66
957 1029 1.209019 CTAGCTTGGGTGATCAGCTGT 59.791 52.381 23.24 0.42 37.08 4.40
958 1030 1.950828 CTAGCTTGGGTGATCAGCTG 58.049 55.000 23.24 7.63 37.08 4.24
959 1031 0.179936 GCTAGCTTGGGTGATCAGCT 59.820 55.000 23.24 16.73 39.36 4.24
960 1032 0.817229 GGCTAGCTTGGGTGATCAGC 60.817 60.000 16.65 16.65 0.00 4.26
961 1033 0.543277 TGGCTAGCTTGGGTGATCAG 59.457 55.000 15.72 0.00 0.00 2.90
962 1034 0.253044 GTGGCTAGCTTGGGTGATCA 59.747 55.000 15.72 0.00 0.00 2.92
963 1035 0.464554 GGTGGCTAGCTTGGGTGATC 60.465 60.000 15.72 0.00 0.00 2.92
964 1036 1.207488 TGGTGGCTAGCTTGGGTGAT 61.207 55.000 15.72 0.00 0.00 3.06
965 1037 1.422977 TTGGTGGCTAGCTTGGGTGA 61.423 55.000 15.72 0.00 0.00 4.02
970 1042 1.896220 TGACTTTGGTGGCTAGCTTG 58.104 50.000 15.72 0.00 0.00 4.01
975 1047 2.575735 TGATGGATGACTTTGGTGGCTA 59.424 45.455 0.00 0.00 0.00 3.93
977 1049 1.838112 TGATGGATGACTTTGGTGGC 58.162 50.000 0.00 0.00 0.00 5.01
992 1064 1.386533 GAGGAGCACCATGGTTGATG 58.613 55.000 16.84 5.00 38.94 3.07
993 1065 0.257039 GGAGGAGCACCATGGTTGAT 59.743 55.000 16.84 9.86 38.94 2.57
994 1066 1.685224 GGAGGAGCACCATGGTTGA 59.315 57.895 16.84 0.00 38.94 3.18
997 1069 0.692419 CTAGGGAGGAGCACCATGGT 60.692 60.000 13.00 13.00 38.94 3.55
1134 1206 1.880340 GCGCTCCAGGACGATGAAG 60.880 63.158 13.67 0.00 0.00 3.02
1410 1482 1.359475 GTACTCCATCTCGCCGGAC 59.641 63.158 5.05 0.00 0.00 4.79
1751 1832 0.253327 GGAGAGGAACACCATGACCC 59.747 60.000 0.00 0.00 0.00 4.46
1830 1911 1.719780 CCGTACTTGTTCTTGAGCGTC 59.280 52.381 0.00 0.00 0.00 5.19
1875 1956 3.326210 CTGATCTTCGCGAGCGCC 61.326 66.667 9.59 1.10 39.59 6.53
2094 2178 2.787567 GGAGTAGAGCCCCGACTGC 61.788 68.421 0.00 0.00 32.55 4.40
2100 2184 3.155167 CCCACGGAGTAGAGCCCC 61.155 72.222 0.00 0.00 41.61 5.80
2247 2331 4.505922 GCTGTTTAGAAGATGACGGAGATG 59.494 45.833 0.00 0.00 0.00 2.90
2290 2380 3.024609 CCGTCATCATCGCCGTCG 61.025 66.667 0.00 0.00 0.00 5.12
2291 2381 3.330853 GCCGTCATCATCGCCGTC 61.331 66.667 0.00 0.00 0.00 4.79
2292 2382 3.657448 TTGCCGTCATCATCGCCGT 62.657 57.895 0.00 0.00 0.00 5.68
2295 2385 2.164663 TCGTTGCCGTCATCATCGC 61.165 57.895 0.00 0.00 35.01 4.58
2296 2386 0.802222 AGTCGTTGCCGTCATCATCG 60.802 55.000 0.00 0.00 35.01 3.84
2297 2387 2.203800 TAGTCGTTGCCGTCATCATC 57.796 50.000 0.00 0.00 35.01 2.92
2299 2389 1.670674 GGTTAGTCGTTGCCGTCATCA 60.671 52.381 0.00 0.00 35.01 3.07
2300 2390 0.997196 GGTTAGTCGTTGCCGTCATC 59.003 55.000 0.00 0.00 35.01 2.92
2301 2391 0.319083 TGGTTAGTCGTTGCCGTCAT 59.681 50.000 0.00 0.00 35.01 3.06
2302 2392 0.104487 TTGGTTAGTCGTTGCCGTCA 59.896 50.000 0.00 0.00 35.01 4.35
2303 2393 1.219646 TTTGGTTAGTCGTTGCCGTC 58.780 50.000 0.00 0.00 35.01 4.79
2304 2394 1.802365 GATTTGGTTAGTCGTTGCCGT 59.198 47.619 0.00 0.00 35.01 5.68
2305 2395 1.129811 GGATTTGGTTAGTCGTTGCCG 59.870 52.381 0.00 0.00 0.00 5.69
2306 2396 1.471287 GGGATTTGGTTAGTCGTTGCC 59.529 52.381 0.00 0.00 0.00 4.52
2307 2397 1.471287 GGGGATTTGGTTAGTCGTTGC 59.529 52.381 0.00 0.00 0.00 4.17
2308 2398 3.067684 AGGGGATTTGGTTAGTCGTTG 57.932 47.619 0.00 0.00 0.00 4.10
2309 2399 3.073356 TCAAGGGGATTTGGTTAGTCGTT 59.927 43.478 0.00 0.00 0.00 3.85
2350 2440 7.678947 ATGAACGAAATCAACATCTTCTTCT 57.321 32.000 0.00 0.00 32.06 2.85
2351 2441 7.805071 ACAATGAACGAAATCAACATCTTCTTC 59.195 33.333 0.00 0.00 32.06 2.87
2352 2442 7.651808 ACAATGAACGAAATCAACATCTTCTT 58.348 30.769 0.00 0.00 32.06 2.52
2353 2443 7.206981 ACAATGAACGAAATCAACATCTTCT 57.793 32.000 0.00 0.00 32.06 2.85
2354 2444 8.948853 TTACAATGAACGAAATCAACATCTTC 57.051 30.769 0.00 0.00 32.06 2.87
2355 2445 8.783093 TCTTACAATGAACGAAATCAACATCTT 58.217 29.630 0.00 0.00 32.06 2.40
2397 2489 2.030805 TCACATCACACTCACTCACTCG 60.031 50.000 0.00 0.00 0.00 4.18
2469 2570 0.179097 CAAGAGGGCTCCGCTTCTAC 60.179 60.000 7.14 0.00 41.50 2.59
2472 2573 1.448717 GACAAGAGGGCTCCGCTTC 60.449 63.158 7.14 0.00 41.50 3.86
2515 2616 2.626266 CAGTAATAAAAATCCCGGCCCC 59.374 50.000 0.00 0.00 0.00 5.80
2595 2696 2.026262 TCCTTCATCACTGGGTAAAGCC 60.026 50.000 0.00 0.00 0.00 4.35
2614 2715 2.425143 TGGTGAAATGAGCCTCATCC 57.575 50.000 7.84 5.46 35.76 3.51
2629 2730 8.099364 ACAAGAAGTATTGTTACAAGATGGTG 57.901 34.615 3.63 0.00 40.47 4.17
2664 2765 7.886338 AGGCAGTAAAGTAAAAATTGGAAGAG 58.114 34.615 0.00 0.00 0.00 2.85
2691 2792 3.703001 ATTCACTGAGGGGTTACACAG 57.297 47.619 0.00 0.00 36.58 3.66
2723 2827 7.171678 ACAAGAAGAGCATGTTACTAACAAGAC 59.828 37.037 5.73 0.00 45.86 3.01
2725 2829 7.386299 AGACAAGAAGAGCATGTTACTAACAAG 59.614 37.037 5.73 3.02 45.86 3.16
2876 2982 7.554118 TGTTGCCAGAAAATTATTGGTGAAAAA 59.446 29.630 5.12 0.00 34.43 1.94
2877 2983 7.011857 GTGTTGCCAGAAAATTATTGGTGAAAA 59.988 33.333 5.12 0.00 34.43 2.29
2878 2984 6.481644 GTGTTGCCAGAAAATTATTGGTGAAA 59.518 34.615 5.12 0.00 34.43 2.69
2879 2985 5.988561 GTGTTGCCAGAAAATTATTGGTGAA 59.011 36.000 5.12 0.00 34.43 3.18
2880 2986 5.510520 GGTGTTGCCAGAAAATTATTGGTGA 60.511 40.000 5.12 0.00 37.17 4.02
2881 2987 4.690280 GGTGTTGCCAGAAAATTATTGGTG 59.310 41.667 5.12 0.00 37.17 4.17
2882 2988 4.346418 TGGTGTTGCCAGAAAATTATTGGT 59.654 37.500 5.12 0.00 43.61 3.67
2883 2989 4.892433 TGGTGTTGCCAGAAAATTATTGG 58.108 39.130 0.00 0.00 43.61 3.16
2931 3037 8.984112 ACTAGTAACCCTAGAGAGATCTAGAT 57.016 38.462 4.47 4.47 45.21 1.98
2964 3094 3.139077 CAGATGCTCATGCTGATGCTAA 58.861 45.455 0.00 0.00 40.48 3.09
2965 3095 2.367567 TCAGATGCTCATGCTGATGCTA 59.632 45.455 0.00 0.00 40.48 3.49
2966 3096 1.141053 TCAGATGCTCATGCTGATGCT 59.859 47.619 0.00 0.00 40.48 3.79
2977 3107 4.636249 CCCTAGTGGTTTATCAGATGCTC 58.364 47.826 0.00 0.00 0.00 4.26
2996 3126 2.031495 ACTGCTTCCTCAGTAACCCT 57.969 50.000 0.00 0.00 44.77 4.34
2997 3127 2.832733 ACTACTGCTTCCTCAGTAACCC 59.167 50.000 5.33 0.00 45.64 4.11
2998 3128 3.368531 CCACTACTGCTTCCTCAGTAACC 60.369 52.174 5.33 0.00 45.64 2.85
2999 3129 3.258622 ACCACTACTGCTTCCTCAGTAAC 59.741 47.826 5.33 0.00 45.64 2.50
3000 3130 3.258372 CACCACTACTGCTTCCTCAGTAA 59.742 47.826 5.33 0.00 45.64 2.24
3184 3333 1.134848 GGTGAGTGAGTGAGATCTGGC 60.135 57.143 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.