Multiple sequence alignment - TraesCS1B01G207100

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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 TraesCS1B01G207100 chr1B 100.000 3888 0 0 1 3888 374331407 374327520 0.000000e+00 7180.0
1 TraesCS1B01G207100 chr1B 92.857 56 4 0 2556 2611 374322847 374322792 8.950000e-12 82.4
2 TraesCS1B01G207100 chr1A 93.668 2590 116 26 646 3211 347636257 347633692 0.000000e+00 3831.0
3 TraesCS1B01G207100 chr1A 86.139 606 44 4 1193 1798 239909152 239908587 5.520000e-173 617.0
4 TraesCS1B01G207100 chr1A 87.678 211 14 3 437 645 347637582 347637382 6.490000e-58 235.0
5 TraesCS1B01G207100 chr1A 84.496 129 16 2 3762 3886 347626415 347626287 1.470000e-24 124.0
6 TraesCS1B01G207100 chr1D 94.972 2307 72 15 846 3122 275139811 275137519 0.000000e+00 3578.0
7 TraesCS1B01G207100 chr1D 94.325 881 21 7 3019 3888 275137517 275136655 0.000000e+00 1323.0
8 TraesCS1B01G207100 chr1D 79.805 614 54 36 252 829 275140436 275139857 2.190000e-102 383.0
9 TraesCS1B01G207100 chrUn 89.752 605 51 7 1194 1798 239745056 239745649 0.000000e+00 763.0
10 TraesCS1B01G207100 chrUn 93.720 207 8 4 1 204 62697614 62697818 4.880000e-79 305.0
11 TraesCS1B01G207100 chr3B 89.796 392 39 1 1194 1585 426651566 426651956 5.800000e-138 501.0
12 TraesCS1B01G207100 chr3B 90.785 293 15 1 1290 1582 823473564 823473844 7.880000e-102 381.0
13 TraesCS1B01G207100 chr3B 89.493 276 29 0 1193 1468 522027735 522027460 2.220000e-92 350.0
14 TraesCS1B01G207100 chr3B 95.408 196 7 1 1 194 725369374 725369179 1.050000e-80 311.0
15 TraesCS1B01G207100 chr3B 93.333 60 4 0 1190 1249 823473511 823473570 5.350000e-14 89.8
16 TraesCS1B01G207100 chr5A 94.981 259 8 4 1 255 704588682 704588939 6.050000e-108 401.0
17 TraesCS1B01G207100 chr6A 94.466 253 9 4 1 250 457607357 457607607 6.090000e-103 385.0
18 TraesCS1B01G207100 chr6A 92.941 255 11 6 1 251 457589953 457590204 7.940000e-97 364.0
19 TraesCS1B01G207100 chr6A 94.737 57 3 0 1377 1433 478310575 478310519 5.350000e-14 89.8
20 TraesCS1B01G207100 chr3D 92.941 255 15 2 1 252 194684348 194684094 6.140000e-98 368.0
21 TraesCS1B01G207100 chr7A 90.226 266 12 9 1 253 40879390 40879654 6.220000e-88 335.0
22 TraesCS1B01G207100 chr7A 89.855 207 8 3 1 194 680599278 680599072 1.790000e-63 254.0
23 TraesCS1B01G207100 chr7A 93.878 98 5 1 1 97 697884604 697884507 3.130000e-31 147.0
24 TraesCS1B01G207100 chr5D 88.593 263 15 5 2 252 520751125 520750866 4.880000e-79 305.0
25 TraesCS1B01G207100 chr6B 94.388 196 7 3 1 194 437148767 437148960 8.170000e-77 298.0
26 TraesCS1B01G207100 chr6B 96.078 51 2 0 1489 1539 482470608 482470658 2.490000e-12 84.2
27 TraesCS1B01G207100 chr6D 96.078 51 2 0 1489 1539 337842842 337842792 2.490000e-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 TraesCS1B01G207100 chr1B 374327520 374331407 3887 True 7180.000000 7180 100.000000 1 3888 1 chr1B.!!$R2 3887
1 TraesCS1B01G207100 chr1A 347633692 347637582 3890 True 2033.000000 3831 90.673000 437 3211 2 chr1A.!!$R3 2774
2 TraesCS1B01G207100 chr1A 239908587 239909152 565 True 617.000000 617 86.139000 1193 1798 1 chr1A.!!$R1 605
3 TraesCS1B01G207100 chr1D 275136655 275140436 3781 True 1761.333333 3578 89.700667 252 3888 3 chr1D.!!$R1 3636
4 TraesCS1B01G207100 chrUn 239745056 239745649 593 False 763.000000 763 89.752000 1194 1798 1 chrUn.!!$F2 604

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
28 29 0.180406 GGCAGGGAATAGGAAGCGAA 59.820 55.000 0.00 0.00 0.00 4.70 F
123 124 0.244994 CTGAGACTTGACCGGACCAG 59.755 60.000 9.46 5.83 0.00 4.00 F
853 2026 0.324943 ACACTCTAGCACCGCCATTT 59.675 50.000 0.00 0.00 0.00 2.32 F
1046 2242 1.392710 TTCGATCGAGCCCCTTCCTC 61.393 60.000 18.54 0.00 0.00 3.71 F
1539 2765 1.979693 GTCCTCGAGCAGACCCACT 60.980 63.158 6.99 0.00 0.00 4.00 F
2345 3571 1.135575 CGCCAGAATTTGCCTGAAGTC 60.136 52.381 0.00 0.00 33.65 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1028 2224 1.828660 GAGGAAGGGGCTCGATCGA 60.829 63.158 18.32 18.32 0.00 3.59 R
2049 3275 1.202891 GGCCTTGAAGTTGTACACCCT 60.203 52.381 0.00 0.00 0.00 4.34 R
2141 3367 0.039074 GCTGGTACCGAGATCCATCG 60.039 60.000 7.57 0.00 42.36 3.84 R
2222 3448 0.321653 GGTGCCCAAGATGAGTTCGT 60.322 55.000 0.00 0.00 0.00 3.85 R
2363 3589 0.382158 TGCGTCGCCTCTTCTCATAG 59.618 55.000 15.88 0.00 0.00 2.23 R
3806 5164 1.110518 TGAGGGGCGTTGGGAAAAAC 61.111 55.000 0.00 0.00 0.00 2.43 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
17 18 4.373551 TAGCGATCAGGCAGGGAA 57.626 55.556 0.00 0.00 34.64 3.97
18 19 2.840199 TAGCGATCAGGCAGGGAAT 58.160 52.632 0.00 0.00 34.64 3.01
19 20 2.009681 TAGCGATCAGGCAGGGAATA 57.990 50.000 0.00 0.00 34.64 1.75
20 21 0.683973 AGCGATCAGGCAGGGAATAG 59.316 55.000 0.00 0.00 34.64 1.73
21 22 0.321122 GCGATCAGGCAGGGAATAGG 60.321 60.000 0.00 0.00 0.00 2.57
22 23 1.342074 CGATCAGGCAGGGAATAGGA 58.658 55.000 0.00 0.00 0.00 2.94
23 24 1.694150 CGATCAGGCAGGGAATAGGAA 59.306 52.381 0.00 0.00 0.00 3.36
24 25 2.289320 CGATCAGGCAGGGAATAGGAAG 60.289 54.545 0.00 0.00 0.00 3.46
25 26 0.839946 TCAGGCAGGGAATAGGAAGC 59.160 55.000 0.00 0.00 0.00 3.86
26 27 0.533755 CAGGCAGGGAATAGGAAGCG 60.534 60.000 0.00 0.00 0.00 4.68
27 28 0.691078 AGGCAGGGAATAGGAAGCGA 60.691 55.000 0.00 0.00 0.00 4.93
28 29 0.180406 GGCAGGGAATAGGAAGCGAA 59.820 55.000 0.00 0.00 0.00 4.70
29 30 1.408266 GGCAGGGAATAGGAAGCGAAA 60.408 52.381 0.00 0.00 0.00 3.46
30 31 1.943340 GCAGGGAATAGGAAGCGAAAG 59.057 52.381 0.00 0.00 0.00 2.62
31 32 2.681097 GCAGGGAATAGGAAGCGAAAGT 60.681 50.000 0.00 0.00 0.00 2.66
32 33 3.610911 CAGGGAATAGGAAGCGAAAGTT 58.389 45.455 0.00 0.00 0.00 2.66
33 34 4.766375 CAGGGAATAGGAAGCGAAAGTTA 58.234 43.478 0.00 0.00 0.00 2.24
34 35 4.571176 CAGGGAATAGGAAGCGAAAGTTAC 59.429 45.833 0.00 0.00 0.00 2.50
35 36 3.554731 GGGAATAGGAAGCGAAAGTTACG 59.445 47.826 0.00 0.00 0.00 3.18
36 37 3.554731 GGAATAGGAAGCGAAAGTTACGG 59.445 47.826 0.00 0.00 0.00 4.02
37 38 4.427312 GAATAGGAAGCGAAAGTTACGGA 58.573 43.478 0.00 0.00 0.00 4.69
38 39 2.825861 AGGAAGCGAAAGTTACGGAA 57.174 45.000 0.00 0.00 0.00 4.30
39 40 2.410939 AGGAAGCGAAAGTTACGGAAC 58.589 47.619 0.95 0.95 35.64 3.62
56 57 3.118454 CGTACTGCGTTGGGGCTG 61.118 66.667 0.00 0.00 37.80 4.85
57 58 2.032071 GTACTGCGTTGGGGCTGT 59.968 61.111 2.78 2.78 45.37 4.40
58 59 2.033194 GTACTGCGTTGGGGCTGTC 61.033 63.158 0.33 0.00 42.94 3.51
59 60 3.583276 TACTGCGTTGGGGCTGTCG 62.583 63.158 0.33 0.00 42.94 4.35
60 61 4.988598 CTGCGTTGGGGCTGTCGT 62.989 66.667 0.00 0.00 0.00 4.34
61 62 4.555709 TGCGTTGGGGCTGTCGTT 62.556 61.111 0.00 0.00 0.00 3.85
62 63 3.284449 GCGTTGGGGCTGTCGTTT 61.284 61.111 0.00 0.00 0.00 3.60
63 64 2.943653 CGTTGGGGCTGTCGTTTC 59.056 61.111 0.00 0.00 0.00 2.78
64 65 1.890041 CGTTGGGGCTGTCGTTTCA 60.890 57.895 0.00 0.00 0.00 2.69
65 66 1.234615 CGTTGGGGCTGTCGTTTCAT 61.235 55.000 0.00 0.00 0.00 2.57
66 67 0.521735 GTTGGGGCTGTCGTTTCATC 59.478 55.000 0.00 0.00 0.00 2.92
67 68 0.400213 TTGGGGCTGTCGTTTCATCT 59.600 50.000 0.00 0.00 0.00 2.90
68 69 1.271856 TGGGGCTGTCGTTTCATCTA 58.728 50.000 0.00 0.00 0.00 1.98
69 70 1.066430 TGGGGCTGTCGTTTCATCTAC 60.066 52.381 0.00 0.00 0.00 2.59
70 71 1.278238 GGGCTGTCGTTTCATCTACG 58.722 55.000 0.00 0.00 40.23 3.51
71 72 1.135199 GGGCTGTCGTTTCATCTACGA 60.135 52.381 0.00 0.00 44.88 3.43
78 79 4.806342 TCGTTTCATCTACGATCGATCA 57.194 40.909 24.34 5.92 42.51 2.92
79 80 5.164606 TCGTTTCATCTACGATCGATCAA 57.835 39.130 24.34 11.24 42.51 2.57
80 81 5.758924 TCGTTTCATCTACGATCGATCAAT 58.241 37.500 24.34 14.32 42.51 2.57
81 82 5.851703 TCGTTTCATCTACGATCGATCAATC 59.148 40.000 24.34 7.98 42.51 2.67
82 83 5.059832 CGTTTCATCTACGATCGATCAATCC 59.940 44.000 24.34 0.00 41.33 3.01
83 84 5.705609 TTCATCTACGATCGATCAATCCA 57.294 39.130 24.34 5.01 0.00 3.41
84 85 5.048153 TCATCTACGATCGATCAATCCAC 57.952 43.478 24.34 0.00 0.00 4.02
85 86 3.537793 TCTACGATCGATCAATCCACG 57.462 47.619 24.34 12.01 0.00 4.94
86 87 1.979469 CTACGATCGATCAATCCACGC 59.021 52.381 24.34 0.00 0.00 5.34
87 88 0.934901 ACGATCGATCAATCCACGCG 60.935 55.000 24.34 3.53 0.00 6.01
88 89 0.660300 CGATCGATCAATCCACGCGA 60.660 55.000 24.40 0.00 35.32 5.87
89 90 0.778815 GATCGATCAATCCACGCGAC 59.221 55.000 20.52 0.00 33.52 5.19
90 91 0.934901 ATCGATCAATCCACGCGACG 60.935 55.000 15.93 2.53 33.52 5.12
91 92 2.576893 CGATCAATCCACGCGACGG 61.577 63.158 15.93 13.67 0.00 4.79
92 93 2.202878 ATCAATCCACGCGACGGG 60.203 61.111 15.93 11.82 0.00 5.28
93 94 2.622903 GATCAATCCACGCGACGGGA 62.623 60.000 15.93 17.34 37.64 5.14
94 95 2.233605 ATCAATCCACGCGACGGGAA 62.234 55.000 15.93 2.24 36.62 3.97
95 96 2.030401 CAATCCACGCGACGGGAAA 61.030 57.895 15.93 3.65 36.62 3.13
96 97 1.740296 AATCCACGCGACGGGAAAG 60.740 57.895 15.93 7.73 36.62 2.62
102 103 3.306634 GCGACGGGAAAGCGTATC 58.693 61.111 0.00 0.00 0.00 2.24
103 104 2.574222 GCGACGGGAAAGCGTATCG 61.574 63.158 0.00 0.00 0.00 2.92
116 117 1.828832 CGTATCGCTGAGACTTGACC 58.171 55.000 0.00 0.00 0.00 4.02
117 118 1.828832 GTATCGCTGAGACTTGACCG 58.171 55.000 0.00 0.00 0.00 4.79
118 119 0.738975 TATCGCTGAGACTTGACCGG 59.261 55.000 0.00 0.00 0.00 5.28
119 120 0.965866 ATCGCTGAGACTTGACCGGA 60.966 55.000 9.46 0.00 0.00 5.14
120 121 1.444553 CGCTGAGACTTGACCGGAC 60.445 63.158 9.46 1.07 0.00 4.79
121 122 1.079750 GCTGAGACTTGACCGGACC 60.080 63.158 9.46 0.00 0.00 4.46
122 123 1.816863 GCTGAGACTTGACCGGACCA 61.817 60.000 9.46 2.07 0.00 4.02
123 124 0.244994 CTGAGACTTGACCGGACCAG 59.755 60.000 9.46 5.83 0.00 4.00
124 125 1.185618 TGAGACTTGACCGGACCAGG 61.186 60.000 9.46 8.89 37.30 4.45
125 126 2.047179 GACTTGACCGGACCAGGC 60.047 66.667 9.46 0.16 33.69 4.85
126 127 3.607370 GACTTGACCGGACCAGGCC 62.607 68.421 9.46 0.00 33.69 5.19
127 128 4.410400 CTTGACCGGACCAGGCCC 62.410 72.222 9.46 0.00 33.69 5.80
130 131 4.410400 GACCGGACCAGGCCCAAG 62.410 72.222 9.46 0.00 33.69 3.61
131 132 4.974438 ACCGGACCAGGCCCAAGA 62.974 66.667 9.46 0.00 33.69 3.02
132 133 3.646715 CCGGACCAGGCCCAAGAA 61.647 66.667 0.00 0.00 0.00 2.52
133 134 2.045926 CGGACCAGGCCCAAGAAG 60.046 66.667 0.00 0.00 0.00 2.85
134 135 2.356667 GGACCAGGCCCAAGAAGG 59.643 66.667 0.00 0.00 37.03 3.46
145 146 3.154827 CCCAAGAAGGCCTAAAACTGA 57.845 47.619 5.16 0.00 35.39 3.41
146 147 3.496331 CCCAAGAAGGCCTAAAACTGAA 58.504 45.455 5.16 0.00 35.39 3.02
147 148 4.089361 CCCAAGAAGGCCTAAAACTGAAT 58.911 43.478 5.16 0.00 35.39 2.57
148 149 4.528206 CCCAAGAAGGCCTAAAACTGAATT 59.472 41.667 5.16 0.00 35.39 2.17
149 150 5.012046 CCCAAGAAGGCCTAAAACTGAATTT 59.988 40.000 5.16 0.00 35.39 1.82
150 151 6.464322 CCCAAGAAGGCCTAAAACTGAATTTT 60.464 38.462 5.16 0.00 39.01 1.82
151 152 6.992123 CCAAGAAGGCCTAAAACTGAATTTTT 59.008 34.615 5.16 0.00 40.99 1.94
179 180 9.642343 TCCAGACTACATATATGTATATGGACC 57.358 37.037 28.79 16.23 46.13 4.46
180 181 8.861086 CCAGACTACATATATGTATATGGACCC 58.139 40.741 27.61 13.74 46.13 4.46
181 182 9.647918 CAGACTACATATATGTATATGGACCCT 57.352 37.037 22.72 10.22 46.13 4.34
187 188 9.213777 ACATATATGTATATGGACCCTAGTTGG 57.786 37.037 16.85 0.00 46.13 3.77
203 204 2.365502 GGGGGCCCCAGGATTTTG 60.366 66.667 41.80 0.00 44.65 2.44
204 205 2.365502 GGGGCCCCAGGATTTTGG 60.366 66.667 37.61 0.00 38.00 3.28
210 211 2.365502 CCAGGATTTTGGGGCCCC 60.366 66.667 36.14 36.14 34.46 5.80
211 212 2.779981 CAGGATTTTGGGGCCCCT 59.220 61.111 40.66 22.40 36.94 4.79
212 213 1.686800 CAGGATTTTGGGGCCCCTG 60.687 63.158 40.66 25.03 38.48 4.45
213 214 2.176812 AGGATTTTGGGGCCCCTGT 61.177 57.895 40.66 23.46 36.94 4.00
214 215 1.989508 GGATTTTGGGGCCCCTGTG 60.990 63.158 40.66 0.00 36.94 3.66
215 216 2.607442 ATTTTGGGGCCCCTGTGC 60.607 61.111 40.66 15.68 36.94 4.57
236 237 4.806481 CGCACAGCTCGCACATGC 62.806 66.667 5.55 0.00 37.78 4.06
237 238 4.471726 GCACAGCTCGCACATGCC 62.472 66.667 0.00 0.00 37.91 4.40
238 239 3.807538 CACAGCTCGCACATGCCC 61.808 66.667 0.00 0.00 37.91 5.36
239 240 4.025858 ACAGCTCGCACATGCCCT 62.026 61.111 0.00 0.00 37.91 5.19
240 241 2.749044 CAGCTCGCACATGCCCTT 60.749 61.111 0.00 0.00 37.91 3.95
241 242 2.749044 AGCTCGCACATGCCCTTG 60.749 61.111 0.00 0.00 37.91 3.61
242 243 2.747460 GCTCGCACATGCCCTTGA 60.747 61.111 0.00 0.00 37.91 3.02
243 244 2.334946 GCTCGCACATGCCCTTGAA 61.335 57.895 0.00 0.00 37.91 2.69
244 245 1.503542 CTCGCACATGCCCTTGAAC 59.496 57.895 0.00 0.00 37.91 3.18
245 246 2.176546 CGCACATGCCCTTGAACG 59.823 61.111 0.00 0.00 37.91 3.95
246 247 2.568090 GCACATGCCCTTGAACGG 59.432 61.111 0.00 0.00 34.31 4.44
248 249 2.676471 ACATGCCCTTGAACGGCC 60.676 61.111 2.79 0.00 46.48 6.13
249 250 3.451894 CATGCCCTTGAACGGCCC 61.452 66.667 0.00 0.00 46.48 5.80
250 251 3.661648 ATGCCCTTGAACGGCCCT 61.662 61.111 0.00 0.00 46.48 5.19
251 252 3.944250 ATGCCCTTGAACGGCCCTG 62.944 63.158 0.00 0.00 46.48 4.45
253 254 4.659172 CCCTTGAACGGCCCTGCA 62.659 66.667 0.00 0.00 0.00 4.41
254 255 2.361610 CCTTGAACGGCCCTGCAT 60.362 61.111 0.00 0.00 0.00 3.96
255 256 2.703798 CCTTGAACGGCCCTGCATG 61.704 63.158 0.00 0.00 0.00 4.06
256 257 1.675310 CTTGAACGGCCCTGCATGA 60.675 57.895 0.00 0.00 0.00 3.07
257 258 1.926511 CTTGAACGGCCCTGCATGAC 61.927 60.000 0.00 0.00 0.00 3.06
258 259 3.499737 GAACGGCCCTGCATGACG 61.500 66.667 9.85 9.85 0.00 4.35
302 303 3.692690 TGGGCCCATTACTTGAGTTTAC 58.307 45.455 24.45 0.00 0.00 2.01
310 317 6.071391 CCCATTACTTGAGTTTACTGCCATTT 60.071 38.462 0.00 0.00 0.00 2.32
336 343 9.833917 TTTTTATTATTGGTTTCTTCCGGTTTT 57.166 25.926 0.00 0.00 0.00 2.43
338 345 3.744238 ATTGGTTTCTTCCGGTTTTGG 57.256 42.857 0.00 0.00 0.00 3.28
339 346 2.438800 TGGTTTCTTCCGGTTTTGGA 57.561 45.000 0.00 0.00 35.83 3.53
340 347 2.025898 TGGTTTCTTCCGGTTTTGGAC 58.974 47.619 0.00 0.00 37.89 4.02
341 348 2.304092 GGTTTCTTCCGGTTTTGGACT 58.696 47.619 0.00 0.00 37.89 3.85
342 349 3.117963 TGGTTTCTTCCGGTTTTGGACTA 60.118 43.478 0.00 0.00 37.89 2.59
343 350 3.501062 GGTTTCTTCCGGTTTTGGACTAG 59.499 47.826 0.00 0.00 37.89 2.57
362 369 6.590677 GGACTAGCTATGTTCTTTCGTTTTCT 59.409 38.462 0.00 0.00 0.00 2.52
393 400 8.130469 ACATTTCTTCATGTTTTCCAATTTTGC 58.870 29.630 0.00 0.00 33.29 3.68
394 401 7.621428 TTTCTTCATGTTTTCCAATTTTGCA 57.379 28.000 0.00 0.00 0.00 4.08
395 402 7.804843 TTCTTCATGTTTTCCAATTTTGCAT 57.195 28.000 0.00 0.00 0.00 3.96
396 403 7.804843 TCTTCATGTTTTCCAATTTTGCATT 57.195 28.000 0.00 0.00 0.00 3.56
397 404 8.223177 TCTTCATGTTTTCCAATTTTGCATTT 57.777 26.923 0.00 0.00 0.00 2.32
398 405 8.684520 TCTTCATGTTTTCCAATTTTGCATTTT 58.315 25.926 0.00 0.00 0.00 1.82
399 406 9.947669 CTTCATGTTTTCCAATTTTGCATTTTA 57.052 25.926 0.00 0.00 0.00 1.52
812 1949 0.651031 GCGTTTCACCTCCTATTCGC 59.349 55.000 0.00 0.00 36.06 4.70
840 2012 3.460857 AGCGTCAGAAAAGAACACTCT 57.539 42.857 0.00 0.00 0.00 3.24
853 2026 0.324943 ACACTCTAGCACCGCCATTT 59.675 50.000 0.00 0.00 0.00 2.32
884 2061 1.821136 GGGCTGCTTTGCTTGTAGAAT 59.179 47.619 0.00 0.00 0.00 2.40
934 2124 2.841160 AAAAGCCCACGCGGTGTTC 61.841 57.895 12.47 0.64 41.18 3.18
1015 2211 3.153919 CAAAGGCTACAAAACCCTAGCA 58.846 45.455 0.00 0.00 37.67 3.49
1023 2219 6.461092 GGCTACAAAACCCTAGCAAAATATCC 60.461 42.308 0.00 0.00 37.67 2.59
1028 2224 4.832560 ACCCTAGCAAAATATCCCCATT 57.167 40.909 0.00 0.00 0.00 3.16
1041 2237 2.511452 CCCATTCGATCGAGCCCCT 61.511 63.158 18.54 0.00 0.00 4.79
1046 2242 1.392710 TTCGATCGAGCCCCTTCCTC 61.393 60.000 18.54 0.00 0.00 3.71
1047 2243 2.862223 CGATCGAGCCCCTTCCTCC 61.862 68.421 10.26 0.00 0.00 4.30
1048 2244 2.446802 ATCGAGCCCCTTCCTCCC 60.447 66.667 0.00 0.00 0.00 4.30
1049 2245 4.798682 TCGAGCCCCTTCCTCCCC 62.799 72.222 0.00 0.00 0.00 4.81
1539 2765 1.979693 GTCCTCGAGCAGACCCACT 60.980 63.158 6.99 0.00 0.00 4.00
2009 3235 3.434319 ATTGCGCTGCTTGACCCG 61.434 61.111 9.73 0.00 0.00 5.28
2049 3275 4.026744 CCATCTGGAGGAGAAGAAGTACA 58.973 47.826 0.00 0.00 37.39 2.90
2141 3367 3.030291 AGAGTCACCTGAGATCACCATC 58.970 50.000 0.00 0.00 0.00 3.51
2255 3481 4.087892 CACCGTCTGAGCCCTGGG 62.088 72.222 8.86 8.86 0.00 4.45
2258 3484 2.765807 CGTCTGAGCCCTGGGGAT 60.766 66.667 16.03 2.12 37.50 3.85
2285 3511 3.054802 CCCTTGGGTATGATCTCTATGGC 60.055 52.174 0.00 0.00 0.00 4.40
2345 3571 1.135575 CGCCAGAATTTGCCTGAAGTC 60.136 52.381 0.00 0.00 33.65 3.01
2346 3572 1.888512 GCCAGAATTTGCCTGAAGTCA 59.111 47.619 0.00 0.00 33.65 3.41
2377 3603 2.622942 AGAAGAGCTATGAGAAGAGGCG 59.377 50.000 0.00 0.00 0.00 5.52
2444 3670 1.623625 TGGGAACAAGGCCAAAGGT 59.376 52.632 5.01 0.00 37.44 3.50
2454 3680 0.962855 GGCCAAAGGTGAGGAAGAGC 60.963 60.000 0.00 0.00 0.00 4.09
2463 3689 0.972983 TGAGGAAGAGCGGAGGGAAG 60.973 60.000 0.00 0.00 0.00 3.46
2472 3698 3.074687 AGAGCGGAGGGAAGATGAGTATA 59.925 47.826 0.00 0.00 0.00 1.47
2473 3699 3.158676 AGCGGAGGGAAGATGAGTATAC 58.841 50.000 0.00 0.00 0.00 1.47
2474 3700 2.891580 GCGGAGGGAAGATGAGTATACA 59.108 50.000 5.50 0.00 0.00 2.29
2476 3702 4.202223 GCGGAGGGAAGATGAGTATACAAA 60.202 45.833 5.50 0.00 0.00 2.83
2477 3703 5.511545 GCGGAGGGAAGATGAGTATACAAAT 60.512 44.000 5.50 0.00 0.00 2.32
2480 3706 7.171678 CGGAGGGAAGATGAGTATACAAATTTC 59.828 40.741 5.50 2.73 0.00 2.17
2481 3707 7.445707 GGAGGGAAGATGAGTATACAAATTTCC 59.554 40.741 5.50 10.66 32.30 3.13
2484 3710 8.624776 GGGAAGATGAGTATACAAATTTCCTTG 58.375 37.037 17.83 0.00 32.96 3.61
2485 3711 9.396022 GGAAGATGAGTATACAAATTTCCTTGA 57.604 33.333 5.50 0.00 31.39 3.02
2496 3722 5.166398 CAAATTTCCTTGATGAGTTGGAGC 58.834 41.667 0.00 0.00 0.00 4.70
2497 3723 2.099141 TTCCTTGATGAGTTGGAGCG 57.901 50.000 0.00 0.00 0.00 5.03
2498 3724 0.976641 TCCTTGATGAGTTGGAGCGT 59.023 50.000 0.00 0.00 0.00 5.07
2517 3743 5.741011 AGCGTGATCCAGAAATAAGGTTTA 58.259 37.500 0.00 0.00 0.00 2.01
2518 3744 5.585047 AGCGTGATCCAGAAATAAGGTTTAC 59.415 40.000 0.00 0.00 0.00 2.01
2540 3766 6.866179 ACGATAAATCTGTACAAGAACGAC 57.134 37.500 0.00 0.00 38.79 4.34
2645 3889 2.768527 TGGTGATGATGAGGAGGAAGAC 59.231 50.000 0.00 0.00 0.00 3.01
2690 3934 1.676529 TGAGCGAGCATGTCTACCTAC 59.323 52.381 0.00 0.00 0.00 3.18
2821 4065 5.533528 GGAGGTGTTGCTTAAAAGGTCTAAA 59.466 40.000 0.00 0.00 0.00 1.85
2859 4103 6.786207 TGTTTGTTGATGTCGACATTGTTTA 58.214 32.000 30.46 14.48 39.77 2.01
2897 4141 8.540492 CGTATCTTGGTGTAACAATAATGTCTC 58.460 37.037 0.00 0.00 39.40 3.36
2936 4180 7.135591 TCCTATCATGTCATATGTTTGTGGA 57.864 36.000 1.90 6.51 0.00 4.02
3049 4399 9.553064 GAGTGATTACTGATTATTGGATGTCTT 57.447 33.333 0.00 0.00 37.25 3.01
3068 4418 4.578105 GTCTTTCAGGGATTAGCTGAATGG 59.422 45.833 0.00 0.00 37.03 3.16
3087 4437 5.779241 ATGGTCTTTCCTAGAATGGTCAA 57.221 39.130 0.00 0.00 33.81 3.18
3132 4482 5.931146 GCTCTGTCCCAATTGTATCTATGAG 59.069 44.000 4.43 4.63 0.00 2.90
3292 4643 5.897377 ACAACTTGGTAAGATGGTTATGC 57.103 39.130 4.29 0.00 35.79 3.14
3293 4644 4.394920 ACAACTTGGTAAGATGGTTATGCG 59.605 41.667 4.29 0.00 35.79 4.73
3406 4761 1.336795 TGCACCACACTATGTCTCGTG 60.337 52.381 0.00 0.00 37.18 4.35
3480 4835 1.593933 GTTGCATTGCTTGTGTGTTGG 59.406 47.619 10.49 0.00 0.00 3.77
3549 4907 8.823220 ATTATTCAACATAGGTGGCTACTTTT 57.177 30.769 0.00 0.00 0.00 2.27
3614 4972 2.159198 CCAATTCCTTCCATTTCTGCGG 60.159 50.000 0.00 0.00 0.00 5.69
3630 4988 1.681825 GCGGAAAGCTTTTTGTACCG 58.318 50.000 24.41 24.41 44.04 4.02
3631 4989 1.264826 GCGGAAAGCTTTTTGTACCGA 59.735 47.619 29.88 0.00 44.04 4.69
3632 4990 2.095415 GCGGAAAGCTTTTTGTACCGAT 60.095 45.455 29.88 0.30 44.04 4.18
3633 4991 3.743886 CGGAAAGCTTTTTGTACCGATC 58.256 45.455 24.44 4.91 41.09 3.69
3634 4992 3.435671 CGGAAAGCTTTTTGTACCGATCT 59.564 43.478 24.44 0.00 41.09 2.75
3635 4993 4.435651 CGGAAAGCTTTTTGTACCGATCTC 60.436 45.833 24.44 4.25 41.09 2.75
3636 4994 4.695928 GGAAAGCTTTTTGTACCGATCTCT 59.304 41.667 14.05 0.00 0.00 3.10
3637 4995 5.390991 GGAAAGCTTTTTGTACCGATCTCTG 60.391 44.000 14.05 0.00 0.00 3.35
3638 4996 4.273148 AGCTTTTTGTACCGATCTCTGT 57.727 40.909 0.00 0.00 0.00 3.41
3639 4997 4.642429 AGCTTTTTGTACCGATCTCTGTT 58.358 39.130 0.00 0.00 0.00 3.16
3640 4998 5.063880 AGCTTTTTGTACCGATCTCTGTTT 58.936 37.500 0.00 0.00 0.00 2.83
3641 4999 5.531287 AGCTTTTTGTACCGATCTCTGTTTT 59.469 36.000 0.00 0.00 0.00 2.43
3642 5000 5.851703 GCTTTTTGTACCGATCTCTGTTTTC 59.148 40.000 0.00 0.00 0.00 2.29
3643 5001 6.293462 GCTTTTTGTACCGATCTCTGTTTTCT 60.293 38.462 0.00 0.00 0.00 2.52
3644 5002 7.562454 TTTTTGTACCGATCTCTGTTTTCTT 57.438 32.000 0.00 0.00 0.00 2.52
3645 5003 8.665643 TTTTTGTACCGATCTCTGTTTTCTTA 57.334 30.769 0.00 0.00 0.00 2.10
3646 5004 7.647907 TTTGTACCGATCTCTGTTTTCTTAC 57.352 36.000 0.00 0.00 0.00 2.34
3647 5005 5.717119 TGTACCGATCTCTGTTTTCTTACC 58.283 41.667 0.00 0.00 0.00 2.85
3656 5014 5.477291 TCTCTGTTTTCTTACCGATCTCTGT 59.523 40.000 0.00 0.00 0.00 3.41
3683 5041 1.071071 CCCGTGAGAAAACCCACTACA 59.929 52.381 0.00 0.00 0.00 2.74
3723 5081 1.869767 CAACAGAGTCTCACCTGCAAC 59.130 52.381 1.94 0.00 33.90 4.17
3819 5177 2.570442 TGAGTTGTTTTTCCCAACGC 57.430 45.000 0.00 0.00 45.31 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.895798 CTATTCCCTGCCTGATCGCTA 59.104 52.381 0.00 0.00 0.00 4.26
1 2 0.683973 CTATTCCCTGCCTGATCGCT 59.316 55.000 0.00 0.00 0.00 4.93
2 3 0.321122 CCTATTCCCTGCCTGATCGC 60.321 60.000 0.00 0.00 0.00 4.58
3 4 1.342074 TCCTATTCCCTGCCTGATCG 58.658 55.000 0.00 0.00 0.00 3.69
5 6 1.423161 GCTTCCTATTCCCTGCCTGAT 59.577 52.381 0.00 0.00 0.00 2.90
6 7 0.839946 GCTTCCTATTCCCTGCCTGA 59.160 55.000 0.00 0.00 0.00 3.86
7 8 0.533755 CGCTTCCTATTCCCTGCCTG 60.534 60.000 0.00 0.00 0.00 4.85
8 9 0.691078 TCGCTTCCTATTCCCTGCCT 60.691 55.000 0.00 0.00 0.00 4.75
9 10 0.180406 TTCGCTTCCTATTCCCTGCC 59.820 55.000 0.00 0.00 0.00 4.85
10 11 1.943340 CTTTCGCTTCCTATTCCCTGC 59.057 52.381 0.00 0.00 0.00 4.85
11 12 3.268023 ACTTTCGCTTCCTATTCCCTG 57.732 47.619 0.00 0.00 0.00 4.45
12 13 4.679905 CGTAACTTTCGCTTCCTATTCCCT 60.680 45.833 0.00 0.00 0.00 4.20
13 14 3.554731 CGTAACTTTCGCTTCCTATTCCC 59.445 47.826 0.00 0.00 0.00 3.97
14 15 3.554731 CCGTAACTTTCGCTTCCTATTCC 59.445 47.826 0.00 0.00 0.00 3.01
15 16 4.427312 TCCGTAACTTTCGCTTCCTATTC 58.573 43.478 0.00 0.00 0.00 1.75
16 17 4.460948 TCCGTAACTTTCGCTTCCTATT 57.539 40.909 0.00 0.00 0.00 1.73
17 18 4.179298 GTTCCGTAACTTTCGCTTCCTAT 58.821 43.478 0.00 0.00 32.54 2.57
18 19 3.578688 GTTCCGTAACTTTCGCTTCCTA 58.421 45.455 0.00 0.00 32.54 2.94
19 20 2.410939 GTTCCGTAACTTTCGCTTCCT 58.589 47.619 0.00 0.00 32.54 3.36
20 21 1.125566 CGTTCCGTAACTTTCGCTTCC 59.874 52.381 0.00 0.00 33.15 3.46
21 22 1.788886 ACGTTCCGTAACTTTCGCTTC 59.211 47.619 0.00 0.00 38.73 3.86
22 23 1.856802 ACGTTCCGTAACTTTCGCTT 58.143 45.000 0.00 0.00 38.73 4.68
23 24 2.030805 AGTACGTTCCGTAACTTTCGCT 60.031 45.455 0.00 0.00 43.95 4.93
24 25 2.089581 CAGTACGTTCCGTAACTTTCGC 59.910 50.000 0.00 0.00 43.95 4.70
25 26 2.089581 GCAGTACGTTCCGTAACTTTCG 59.910 50.000 0.00 0.00 43.95 3.46
26 27 2.089581 CGCAGTACGTTCCGTAACTTTC 59.910 50.000 0.00 0.00 43.95 2.62
27 28 2.053627 CGCAGTACGTTCCGTAACTTT 58.946 47.619 0.00 0.00 43.95 2.66
28 29 1.689959 CGCAGTACGTTCCGTAACTT 58.310 50.000 0.00 0.00 43.95 2.66
29 30 3.389741 CGCAGTACGTTCCGTAACT 57.610 52.632 0.00 0.00 43.95 2.24
39 40 3.118454 CAGCCCCAACGCAGTACG 61.118 66.667 0.00 0.00 45.00 3.67
40 41 2.032071 ACAGCCCCAACGCAGTAC 59.968 61.111 0.00 0.00 45.00 2.73
41 42 2.345991 GACAGCCCCAACGCAGTA 59.654 61.111 0.00 0.00 45.00 2.74
43 44 4.988598 ACGACAGCCCCAACGCAG 62.989 66.667 0.00 0.00 0.00 5.18
44 45 4.555709 AACGACAGCCCCAACGCA 62.556 61.111 0.00 0.00 0.00 5.24
45 46 3.249973 GAAACGACAGCCCCAACGC 62.250 63.158 0.00 0.00 0.00 4.84
46 47 1.234615 ATGAAACGACAGCCCCAACG 61.235 55.000 0.00 0.00 0.00 4.10
47 48 0.521735 GATGAAACGACAGCCCCAAC 59.478 55.000 0.00 0.00 0.00 3.77
48 49 0.400213 AGATGAAACGACAGCCCCAA 59.600 50.000 0.00 0.00 0.00 4.12
49 50 1.066430 GTAGATGAAACGACAGCCCCA 60.066 52.381 0.00 0.00 0.00 4.96
50 51 1.653151 GTAGATGAAACGACAGCCCC 58.347 55.000 0.00 0.00 0.00 5.80
51 52 1.135199 TCGTAGATGAAACGACAGCCC 60.135 52.381 0.00 0.00 43.90 5.19
52 53 2.273370 TCGTAGATGAAACGACAGCC 57.727 50.000 0.00 0.00 43.90 4.85
58 59 5.059832 GGATTGATCGATCGTAGATGAAACG 59.940 44.000 20.03 0.00 45.12 3.60
59 60 5.920840 TGGATTGATCGATCGTAGATGAAAC 59.079 40.000 20.03 6.10 45.12 2.78
60 61 5.920840 GTGGATTGATCGATCGTAGATGAAA 59.079 40.000 20.03 6.93 45.12 2.69
61 62 5.461526 GTGGATTGATCGATCGTAGATGAA 58.538 41.667 20.03 7.64 45.12 2.57
62 63 4.378459 CGTGGATTGATCGATCGTAGATGA 60.378 45.833 20.03 0.00 45.12 2.92
63 64 3.848582 CGTGGATTGATCGATCGTAGATG 59.151 47.826 20.03 5.24 45.12 2.90
64 65 3.670895 GCGTGGATTGATCGATCGTAGAT 60.671 47.826 20.03 11.18 45.12 1.98
65 66 2.350484 GCGTGGATTGATCGATCGTAGA 60.350 50.000 20.03 6.95 45.75 2.59
66 67 1.979469 GCGTGGATTGATCGATCGTAG 59.021 52.381 20.03 10.24 0.00 3.51
67 68 1.662026 CGCGTGGATTGATCGATCGTA 60.662 52.381 20.03 11.27 0.00 3.43
68 69 0.934901 CGCGTGGATTGATCGATCGT 60.935 55.000 20.03 11.53 0.00 3.73
69 70 0.660300 TCGCGTGGATTGATCGATCG 60.660 55.000 20.03 9.36 0.00 3.69
70 71 0.778815 GTCGCGTGGATTGATCGATC 59.221 55.000 18.72 18.72 0.00 3.69
71 72 0.934901 CGTCGCGTGGATTGATCGAT 60.935 55.000 5.77 0.00 0.00 3.59
72 73 1.585261 CGTCGCGTGGATTGATCGA 60.585 57.895 5.77 0.00 0.00 3.59
73 74 2.576893 CCGTCGCGTGGATTGATCG 61.577 63.158 13.71 3.23 0.00 3.69
74 75 2.237751 CCCGTCGCGTGGATTGATC 61.238 63.158 19.30 0.00 0.00 2.92
75 76 2.202878 CCCGTCGCGTGGATTGAT 60.203 61.111 19.30 0.00 0.00 2.57
76 77 2.437518 TTTCCCGTCGCGTGGATTGA 62.438 55.000 19.30 7.42 0.00 2.57
77 78 1.966493 CTTTCCCGTCGCGTGGATTG 61.966 60.000 19.30 9.86 0.00 2.67
78 79 1.740296 CTTTCCCGTCGCGTGGATT 60.740 57.895 19.30 0.00 0.00 3.01
79 80 2.125673 CTTTCCCGTCGCGTGGAT 60.126 61.111 19.30 0.00 0.00 3.41
85 86 2.574222 CGATACGCTTTCCCGTCGC 61.574 63.158 0.00 0.00 42.20 5.19
86 87 3.597162 CGATACGCTTTCCCGTCG 58.403 61.111 0.00 0.00 42.20 5.12
97 98 1.828832 GGTCAAGTCTCAGCGATACG 58.171 55.000 0.00 0.00 0.00 3.06
98 99 1.534175 CCGGTCAAGTCTCAGCGATAC 60.534 57.143 0.00 0.00 35.53 2.24
99 100 0.738975 CCGGTCAAGTCTCAGCGATA 59.261 55.000 0.00 0.00 35.53 2.92
100 101 0.965866 TCCGGTCAAGTCTCAGCGAT 60.966 55.000 0.00 0.00 35.53 4.58
101 102 1.602605 TCCGGTCAAGTCTCAGCGA 60.603 57.895 0.00 0.00 35.53 4.93
102 103 1.444553 GTCCGGTCAAGTCTCAGCG 60.445 63.158 0.00 0.00 0.00 5.18
103 104 1.079750 GGTCCGGTCAAGTCTCAGC 60.080 63.158 0.00 0.00 0.00 4.26
104 105 0.244994 CTGGTCCGGTCAAGTCTCAG 59.755 60.000 0.00 0.00 0.00 3.35
105 106 1.185618 CCTGGTCCGGTCAAGTCTCA 61.186 60.000 0.00 0.00 0.00 3.27
106 107 1.592223 CCTGGTCCGGTCAAGTCTC 59.408 63.158 0.00 0.00 0.00 3.36
107 108 2.584391 GCCTGGTCCGGTCAAGTCT 61.584 63.158 0.00 0.00 0.00 3.24
108 109 2.047179 GCCTGGTCCGGTCAAGTC 60.047 66.667 0.00 0.00 0.00 3.01
109 110 3.637273 GGCCTGGTCCGGTCAAGT 61.637 66.667 0.00 0.00 0.00 3.16
110 111 4.410400 GGGCCTGGTCCGGTCAAG 62.410 72.222 0.00 0.00 0.00 3.02
113 114 4.410400 CTTGGGCCTGGTCCGGTC 62.410 72.222 13.62 0.00 0.00 4.79
114 115 4.974438 TCTTGGGCCTGGTCCGGT 62.974 66.667 13.62 0.00 0.00 5.28
115 116 3.628646 CTTCTTGGGCCTGGTCCGG 62.629 68.421 13.62 8.31 0.00 5.14
116 117 2.045926 CTTCTTGGGCCTGGTCCG 60.046 66.667 13.62 0.00 0.00 4.79
117 118 2.356667 CCTTCTTGGGCCTGGTCC 59.643 66.667 11.32 11.32 0.00 4.46
118 119 2.361737 GCCTTCTTGGGCCTGGTC 60.362 66.667 4.53 0.00 45.92 4.02
124 125 9.789759 AAAATTCAGTTTTAGGCCTTCTTGGGC 62.790 40.741 12.58 0.00 45.25 5.36
125 126 3.154827 TCAGTTTTAGGCCTTCTTGGG 57.845 47.619 12.58 0.00 36.00 4.12
126 127 5.728637 AATTCAGTTTTAGGCCTTCTTGG 57.271 39.130 12.58 0.00 39.35 3.61
153 154 9.642343 GGTCCATATACATATATGTAGTCTGGA 57.358 37.037 28.79 28.79 45.46 3.86
154 155 8.861086 GGGTCCATATACATATATGTAGTCTGG 58.139 40.741 26.70 26.70 45.46 3.86
155 156 9.647918 AGGGTCCATATACATATATGTAGTCTG 57.352 37.037 25.52 20.83 45.46 3.51
161 162 9.213777 CCAACTAGGGTCCATATACATATATGT 57.786 37.037 21.57 21.57 42.40 2.29
186 187 2.365502 CAAAATCCTGGGGCCCCC 60.366 66.667 38.81 20.71 45.71 5.40
187 188 2.365502 CCAAAATCCTGGGGCCCC 60.366 66.667 36.14 36.14 32.32 5.80
193 194 2.365502 GGGGCCCCAAAATCCTGG 60.366 66.667 37.61 0.00 36.10 4.45
194 195 1.686800 CAGGGGCCCCAAAATCCTG 60.687 63.158 42.48 25.78 38.96 3.86
195 196 2.176812 ACAGGGGCCCCAAAATCCT 61.177 57.895 42.48 18.12 38.92 3.24
196 197 1.989508 CACAGGGGCCCCAAAATCC 60.990 63.158 42.48 14.27 38.92 3.01
197 198 2.659063 GCACAGGGGCCCCAAAATC 61.659 63.158 42.48 22.46 38.92 2.17
198 199 2.607442 GCACAGGGGCCCCAAAAT 60.607 61.111 42.48 20.31 38.92 1.82
219 220 4.806481 GCATGTGCGAGCTGTGCG 62.806 66.667 0.00 0.00 34.24 5.34
220 221 4.471726 GGCATGTGCGAGCTGTGC 62.472 66.667 0.00 0.00 43.26 4.57
221 222 3.807538 GGGCATGTGCGAGCTGTG 61.808 66.667 0.00 0.00 43.26 3.66
222 223 3.557903 AAGGGCATGTGCGAGCTGT 62.558 57.895 0.00 0.00 43.26 4.40
223 224 2.749044 AAGGGCATGTGCGAGCTG 60.749 61.111 0.00 0.00 43.26 4.24
224 225 2.749044 CAAGGGCATGTGCGAGCT 60.749 61.111 0.00 0.00 43.26 4.09
225 226 2.334946 TTCAAGGGCATGTGCGAGC 61.335 57.895 0.00 0.00 43.26 5.03
226 227 1.503542 GTTCAAGGGCATGTGCGAG 59.496 57.895 0.00 0.00 43.26 5.03
227 228 2.324330 CGTTCAAGGGCATGTGCGA 61.324 57.895 0.00 0.00 43.26 5.10
228 229 2.176546 CGTTCAAGGGCATGTGCG 59.823 61.111 0.00 0.00 43.26 5.34
229 230 2.568090 CCGTTCAAGGGCATGTGC 59.432 61.111 0.00 0.00 41.14 4.57
236 237 3.944250 ATGCAGGGCCGTTCAAGGG 62.944 63.158 0.97 0.00 0.00 3.95
237 238 2.361610 ATGCAGGGCCGTTCAAGG 60.362 61.111 0.97 0.00 0.00 3.61
238 239 1.675310 TCATGCAGGGCCGTTCAAG 60.675 57.895 0.97 0.00 0.00 3.02
239 240 1.971167 GTCATGCAGGGCCGTTCAA 60.971 57.895 0.97 0.00 0.00 2.69
240 241 2.359850 GTCATGCAGGGCCGTTCA 60.360 61.111 0.00 0.00 0.00 3.18
241 242 3.499737 CGTCATGCAGGGCCGTTC 61.500 66.667 0.00 0.00 0.00 3.95
245 246 4.830765 TACGCGTCATGCAGGGCC 62.831 66.667 18.63 0.00 46.97 5.80
246 247 3.264897 CTACGCGTCATGCAGGGC 61.265 66.667 18.63 0.00 46.97 5.19
247 248 2.572095 TTCCTACGCGTCATGCAGGG 62.572 60.000 18.63 8.03 46.97 4.45
248 249 0.530650 ATTCCTACGCGTCATGCAGG 60.531 55.000 18.63 17.71 46.97 4.85
249 250 1.004610 CAATTCCTACGCGTCATGCAG 60.005 52.381 18.63 7.09 46.97 4.41
250 251 1.006086 CAATTCCTACGCGTCATGCA 58.994 50.000 18.63 0.00 46.97 3.96
251 252 0.316196 GCAATTCCTACGCGTCATGC 60.316 55.000 18.63 14.59 41.47 4.06
252 253 1.290203 AGCAATTCCTACGCGTCATG 58.710 50.000 18.63 7.51 0.00 3.07
253 254 1.933853 GAAGCAATTCCTACGCGTCAT 59.066 47.619 18.63 0.36 34.78 3.06
254 255 1.355971 GAAGCAATTCCTACGCGTCA 58.644 50.000 18.63 0.96 34.78 4.35
255 256 0.651031 GGAAGCAATTCCTACGCGTC 59.349 55.000 18.63 0.00 38.09 5.19
256 257 0.036765 TGGAAGCAATTCCTACGCGT 60.037 50.000 19.17 19.17 41.65 6.01
257 258 0.373716 GTGGAAGCAATTCCTACGCG 59.626 55.000 3.53 3.53 41.65 6.01
258 259 0.373716 CGTGGAAGCAATTCCTACGC 59.626 55.000 14.41 0.00 41.65 4.42
259 260 1.006832 CCGTGGAAGCAATTCCTACG 58.993 55.000 17.42 17.42 41.65 3.51
260 261 2.007608 GTCCGTGGAAGCAATTCCTAC 58.992 52.381 8.40 4.62 41.65 3.18
281 282 2.990740 AAACTCAAGTAATGGGCCCA 57.009 45.000 30.92 30.92 30.00 5.36
310 317 9.833917 AAAACCGGAAGAAACCAATAATAAAAA 57.166 25.926 9.46 0.00 0.00 1.94
313 320 7.232941 TCCAAAACCGGAAGAAACCAATAATAA 59.767 33.333 9.46 0.00 29.93 1.40
315 322 5.540719 TCCAAAACCGGAAGAAACCAATAAT 59.459 36.000 9.46 0.00 29.93 1.28
318 325 3.069016 GTCCAAAACCGGAAGAAACCAAT 59.931 43.478 9.46 0.00 36.62 3.16
320 327 2.025898 GTCCAAAACCGGAAGAAACCA 58.974 47.619 9.46 0.00 36.62 3.67
331 338 6.402226 CGAAAGAACATAGCTAGTCCAAAACC 60.402 42.308 0.00 0.00 0.00 3.27
332 339 6.147328 ACGAAAGAACATAGCTAGTCCAAAAC 59.853 38.462 0.00 0.00 0.00 2.43
336 343 5.401531 AACGAAAGAACATAGCTAGTCCA 57.598 39.130 0.00 0.00 0.00 4.02
338 345 7.583860 AGAAAACGAAAGAACATAGCTAGTC 57.416 36.000 0.00 0.00 0.00 2.59
339 346 7.964604 AAGAAAACGAAAGAACATAGCTAGT 57.035 32.000 0.00 0.00 0.00 2.57
342 349 9.447040 GTTAAAAGAAAACGAAAGAACATAGCT 57.553 29.630 0.00 0.00 0.00 3.32
343 350 9.228636 TGTTAAAAGAAAACGAAAGAACATAGC 57.771 29.630 0.00 0.00 0.00 2.97
614 624 9.709495 TCCTGAATTTTAAAGAATGTTCATTGG 57.291 29.630 2.63 0.00 0.00 3.16
630 640 7.898918 TCATTCATGTGTTCATCCTGAATTTT 58.101 30.769 0.00 0.00 38.79 1.82
750 1886 9.838339 TGGGCTGTCAAAAGAAATAAAATTTTA 57.162 25.926 12.85 12.85 0.00 1.52
829 2001 1.608283 GGCGGTGCTAGAGTGTTCTTT 60.608 52.381 0.00 0.00 34.79 2.52
831 2003 1.185618 TGGCGGTGCTAGAGTGTTCT 61.186 55.000 0.00 0.00 37.46 3.01
834 2006 0.324943 AAATGGCGGTGCTAGAGTGT 59.675 50.000 0.00 0.00 0.00 3.55
840 2012 1.448893 GACGGAAATGGCGGTGCTA 60.449 57.895 0.00 0.00 0.00 3.49
884 2061 1.826720 GATGCTGAATGGGCCTTTTGA 59.173 47.619 4.53 0.00 0.00 2.69
934 2124 0.293723 CGAAGGCGATTACGTTGTCG 59.706 55.000 15.31 15.31 40.82 4.35
983 2179 1.209747 GTAGCCTTTGTAGGTGGGGAG 59.790 57.143 0.00 0.00 44.00 4.30
999 2195 6.461092 GGGATATTTTGCTAGGGTTTTGTAGC 60.461 42.308 0.00 0.00 41.81 3.58
1015 2211 4.003648 GCTCGATCGAATGGGGATATTTT 58.996 43.478 19.92 0.00 0.00 1.82
1023 2219 2.031163 GGGGCTCGATCGAATGGG 59.969 66.667 19.92 8.50 0.00 4.00
1028 2224 1.828660 GAGGAAGGGGCTCGATCGA 60.829 63.158 18.32 18.32 0.00 3.59
1075 2272 3.909137 GAATCGAATCGAATCGGCG 57.091 52.632 21.78 0.00 42.92 6.46
2049 3275 1.202891 GGCCTTGAAGTTGTACACCCT 60.203 52.381 0.00 0.00 0.00 4.34
2141 3367 0.039074 GCTGGTACCGAGATCCATCG 60.039 60.000 7.57 0.00 42.36 3.84
2183 3409 9.090692 GTATCATTTTTCCCAAAATCAGACATG 57.909 33.333 0.00 0.00 40.09 3.21
2222 3448 0.321653 GGTGCCCAAGATGAGTTCGT 60.322 55.000 0.00 0.00 0.00 3.85
2248 3474 4.529731 GGGCAAGATCCCCAGGGC 62.530 72.222 0.00 0.00 42.36 5.19
2255 3481 1.494721 TCATACCCAAGGGCAAGATCC 59.505 52.381 4.70 0.00 39.32 3.36
2258 3484 2.439507 GAGATCATACCCAAGGGCAAGA 59.560 50.000 4.70 0.64 39.32 3.02
2285 3511 7.227910 TCCATATCATCATCATTCATATTGGCG 59.772 37.037 0.00 0.00 0.00 5.69
2345 3571 5.668471 TCATAGCTCTTCTTGACCAGAATG 58.332 41.667 0.00 0.00 40.95 2.67
2346 3572 5.660417 TCTCATAGCTCTTCTTGACCAGAAT 59.340 40.000 0.00 0.00 40.95 2.40
2363 3589 0.382158 TGCGTCGCCTCTTCTCATAG 59.618 55.000 15.88 0.00 0.00 2.23
2366 3592 2.258591 GTGCGTCGCCTCTTCTCA 59.741 61.111 15.88 0.00 0.00 3.27
2444 3670 0.972983 CTTCCCTCCGCTCTTCCTCA 60.973 60.000 0.00 0.00 0.00 3.86
2454 3680 5.531122 TTTGTATACTCATCTTCCCTCCG 57.469 43.478 4.17 0.00 0.00 4.63
2472 3698 5.279156 GCTCCAACTCATCAAGGAAATTTGT 60.279 40.000 0.00 0.00 0.00 2.83
2473 3699 5.166398 GCTCCAACTCATCAAGGAAATTTG 58.834 41.667 0.00 0.00 0.00 2.32
2474 3700 4.082571 CGCTCCAACTCATCAAGGAAATTT 60.083 41.667 0.00 0.00 0.00 1.82
2476 3702 3.012518 CGCTCCAACTCATCAAGGAAAT 58.987 45.455 0.00 0.00 0.00 2.17
2477 3703 2.224523 ACGCTCCAACTCATCAAGGAAA 60.225 45.455 0.00 0.00 0.00 3.13
2480 3706 1.081892 CACGCTCCAACTCATCAAGG 58.918 55.000 0.00 0.00 0.00 3.61
2481 3707 2.084610 TCACGCTCCAACTCATCAAG 57.915 50.000 0.00 0.00 0.00 3.02
2484 3710 1.134699 TGGATCACGCTCCAACTCATC 60.135 52.381 0.00 0.00 42.36 2.92
2485 3711 0.904649 TGGATCACGCTCCAACTCAT 59.095 50.000 0.00 0.00 42.36 2.90
2489 3715 1.808411 TTTCTGGATCACGCTCCAAC 58.192 50.000 0.00 0.00 44.59 3.77
2496 3722 5.808540 TCGTAAACCTTATTTCTGGATCACG 59.191 40.000 0.00 0.00 0.00 4.35
2497 3723 7.787725 ATCGTAAACCTTATTTCTGGATCAC 57.212 36.000 0.00 0.00 0.00 3.06
2498 3724 9.893634 TTTATCGTAAACCTTATTTCTGGATCA 57.106 29.630 0.00 0.00 0.00 2.92
2517 3743 5.510674 CGTCGTTCTTGTACAGATTTATCGT 59.489 40.000 0.00 0.00 0.00 3.73
2518 3744 5.735892 TCGTCGTTCTTGTACAGATTTATCG 59.264 40.000 0.00 0.00 0.00 2.92
2526 3752 4.137849 TGTAGTCGTCGTTCTTGTACAG 57.862 45.455 0.00 0.00 0.00 2.74
2645 3889 1.162181 CCATACCAGCATCTGCACCG 61.162 60.000 4.79 0.00 45.16 4.94
2690 3934 3.148412 TGAACAGTCATGACCAATGGTG 58.852 45.455 22.21 14.64 35.25 4.17
2821 4065 8.206189 ACATCAACAAACAGAGAAATCCAAAAT 58.794 29.630 0.00 0.00 0.00 1.82
2859 4103 6.650120 ACACCAAGATACGAGATATGGTTTT 58.350 36.000 0.00 0.00 39.05 2.43
2936 4180 8.735692 ATCAAAAATGACAACTGAAAACCATT 57.264 26.923 0.00 0.00 0.00 3.16
3017 4262 7.280876 TCCAATAATCAGTAATCACTCAGCAAC 59.719 37.037 0.00 0.00 30.46 4.17
3024 4374 9.911788 AAAGACATCCAATAATCAGTAATCACT 57.088 29.630 0.00 0.00 34.42 3.41
3068 4418 5.794894 TCAGTTGACCATTCTAGGAAAGAC 58.205 41.667 0.00 0.00 32.51 3.01
3087 4437 2.037385 AGAGGGGAAAAGCTCTCAGT 57.963 50.000 0.00 0.00 0.00 3.41
3147 4497 3.737663 GCAGCCTCAACAAAATCACAACA 60.738 43.478 0.00 0.00 0.00 3.33
3148 4498 2.796593 GCAGCCTCAACAAAATCACAAC 59.203 45.455 0.00 0.00 0.00 3.32
3292 4643 2.031037 AAGCAAACATGCGTTGTACG 57.969 45.000 10.48 0.00 45.88 3.67
3293 4644 2.724174 GGAAAGCAAACATGCGTTGTAC 59.276 45.455 6.71 0.00 37.68 2.90
3549 4907 2.217038 AGAGGCCACGAGCTTGGAA 61.217 57.895 5.01 0.00 43.05 3.53
3614 4972 5.179555 ACAGAGATCGGTACAAAAAGCTTTC 59.820 40.000 13.10 0.00 0.00 2.62
3630 4988 6.695278 CAGAGATCGGTAAGAAAACAGAGATC 59.305 42.308 0.00 0.00 34.98 2.75
3631 4989 6.153680 ACAGAGATCGGTAAGAAAACAGAGAT 59.846 38.462 0.00 0.00 0.00 2.75
3632 4990 5.477291 ACAGAGATCGGTAAGAAAACAGAGA 59.523 40.000 0.00 0.00 0.00 3.10
3633 4991 5.715070 ACAGAGATCGGTAAGAAAACAGAG 58.285 41.667 0.00 0.00 0.00 3.35
3634 4992 5.723672 ACAGAGATCGGTAAGAAAACAGA 57.276 39.130 0.00 0.00 0.00 3.41
3635 4993 6.787085 AAACAGAGATCGGTAAGAAAACAG 57.213 37.500 0.00 0.00 0.00 3.16
3636 4994 6.990349 AGAAAACAGAGATCGGTAAGAAAACA 59.010 34.615 0.00 0.00 0.00 2.83
3637 4995 7.360185 GGAGAAAACAGAGATCGGTAAGAAAAC 60.360 40.741 0.00 0.00 0.00 2.43
3638 4996 6.649557 GGAGAAAACAGAGATCGGTAAGAAAA 59.350 38.462 0.00 0.00 0.00 2.29
3639 4997 6.164176 GGAGAAAACAGAGATCGGTAAGAAA 58.836 40.000 0.00 0.00 0.00 2.52
3640 4998 5.337330 GGGAGAAAACAGAGATCGGTAAGAA 60.337 44.000 0.00 0.00 0.00 2.52
3641 4999 4.159879 GGGAGAAAACAGAGATCGGTAAGA 59.840 45.833 0.00 0.00 0.00 2.10
3642 5000 4.434520 GGGAGAAAACAGAGATCGGTAAG 58.565 47.826 0.00 0.00 0.00 2.34
3643 5001 3.197116 GGGGAGAAAACAGAGATCGGTAA 59.803 47.826 0.00 0.00 0.00 2.85
3644 5002 2.764572 GGGGAGAAAACAGAGATCGGTA 59.235 50.000 0.00 0.00 0.00 4.02
3645 5003 1.555533 GGGGAGAAAACAGAGATCGGT 59.444 52.381 0.00 0.00 0.00 4.69
3646 5004 1.471676 CGGGGAGAAAACAGAGATCGG 60.472 57.143 0.00 0.00 0.00 4.18
3647 5005 1.204941 ACGGGGAGAAAACAGAGATCG 59.795 52.381 0.00 0.00 0.00 3.69
3683 5041 6.106003 TGTTGCTAACATGACTGTAATCGAT 58.894 36.000 0.00 0.00 36.25 3.59
3723 5081 1.463831 AGTCCGTAGCGCTATATGACG 59.536 52.381 21.96 20.79 0.00 4.35
3806 5164 1.110518 TGAGGGGCGTTGGGAAAAAC 61.111 55.000 0.00 0.00 0.00 2.43
3819 5177 3.023116 TGCCTTGGGGATGAGGGG 61.023 66.667 0.00 0.00 33.58 4.79


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

AutoCloner maintained by Alex Coulton.