Multiple sequence alignment - TraesCS1D01G338400

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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 TraesCS1D01G338400 chr1D 100.000 5989 0 0 1 5989 427623876 427617888 0.000000e+00 11060.0
1 TraesCS1D01G338400 chr1D 85.253 929 94 24 3547 4458 476229630 476230532 0.000000e+00 917.0
2 TraesCS1D01G338400 chr1D 80.645 372 49 12 2760 3113 476227499 476227865 3.560000e-67 267.0
3 TraesCS1D01G338400 chr1D 88.811 143 11 3 3166 3303 476229254 476229396 2.870000e-38 171.0
4 TraesCS1D01G338400 chr1B 91.607 2383 92 20 3384 5692 579790319 579787971 0.000000e+00 3193.0
5 TraesCS1D01G338400 chr1B 92.445 1178 38 10 2236 3388 579791515 579790364 0.000000e+00 1635.0
6 TraesCS1D01G338400 chr1B 82.941 1231 105 40 214 1408 579793737 579792576 0.000000e+00 1013.0
7 TraesCS1D01G338400 chr1B 86.688 924 88 24 3547 4458 662545232 662546132 0.000000e+00 992.0
8 TraesCS1D01G338400 chr1B 85.694 706 63 25 3547 4240 662550591 662551270 0.000000e+00 710.0
9 TraesCS1D01G338400 chr1B 88.889 567 55 6 1677 2238 579792168 579791605 0.000000e+00 691.0
10 TraesCS1D01G338400 chr1B 96.154 312 12 0 5678 5989 579785664 579785353 1.490000e-140 510.0
11 TraesCS1D01G338400 chr1B 92.337 261 8 6 1427 1680 579792496 579792241 1.590000e-95 361.0
12 TraesCS1D01G338400 chr1B 93.793 145 9 0 2760 2904 662549435 662549579 1.010000e-52 219.0
13 TraesCS1D01G338400 chr1B 92.143 140 11 0 2765 2904 662537220 662537359 1.320000e-46 198.0
14 TraesCS1D01G338400 chr1B 77.446 368 43 19 2924 3259 662549629 662549988 3.690000e-42 183.0
15 TraesCS1D01G338400 chr1B 89.062 128 9 3 3202 3324 662545003 662545130 2.890000e-33 154.0
16 TraesCS1D01G338400 chr1A 91.349 1942 128 21 3459 5391 522956160 522954250 0.000000e+00 2619.0
17 TraesCS1D01G338400 chr1A 88.860 1167 64 17 2236 3388 522957416 522956302 0.000000e+00 1375.0
18 TraesCS1D01G338400 chr1A 91.904 877 62 6 1366 2238 522958377 522957506 0.000000e+00 1218.0
19 TraesCS1D01G338400 chr1A 85.974 1155 84 34 190 1329 522959468 522958377 0.000000e+00 1164.0
20 TraesCS1D01G338400 chr1A 85.281 924 103 19 3547 4458 572013712 572014614 0.000000e+00 922.0
21 TraesCS1D01G338400 chr1A 94.412 519 25 4 5472 5989 522953457 522952942 0.000000e+00 795.0
22 TraesCS1D01G338400 chr1A 97.581 248 6 0 1070 1317 492795273 492795026 5.550000e-115 425.0
23 TraesCS1D01G338400 chr1A 96.457 254 9 0 1064 1317 22988815 22988562 2.580000e-113 420.0
24 TraesCS1D01G338400 chr1A 95.669 254 11 0 1064 1317 22995778 22995525 5.590000e-110 409.0
25 TraesCS1D01G338400 chr1A 95.968 248 10 0 1070 1317 9898594 9898347 2.600000e-108 403.0
26 TraesCS1D01G338400 chr1A 85.673 349 46 3 4479 4823 572014788 572015136 1.230000e-96 364.0
27 TraesCS1D01G338400 chr1A 91.124 169 14 1 3118 3286 572005145 572005312 1.680000e-55 228.0
28 TraesCS1D01G338400 chr1A 92.517 147 11 0 2758 2904 572004726 572004872 1.690000e-50 211.0
29 TraesCS1D01G338400 chr1A 90.000 130 6 7 810 934 22988986 22988859 1.730000e-35 161.0
30 TraesCS1D01G338400 chr1A 88.462 130 8 7 810 934 9898771 9898644 3.740000e-32 150.0
31 TraesCS1D01G338400 chr1A 88.889 126 7 7 814 934 326572470 326572347 1.340000e-31 148.0
32 TraesCS1D01G338400 chr1A 95.833 48 1 1 5430 5476 522953516 522953469 6.440000e-10 76.8
33 TraesCS1D01G338400 chr1A 95.652 46 1 1 1882 1927 522957814 522957770 8.330000e-09 73.1
34 TraesCS1D01G338400 chr5B 91.749 1612 105 17 3509 5105 92234689 92233091 0.000000e+00 2215.0
35 TraesCS1D01G338400 chr5B 86.534 802 70 17 2236 3011 92236185 92235396 0.000000e+00 848.0
36 TraesCS1D01G338400 chr5B 90.491 326 29 1 189 512 710235644 710235969 4.290000e-116 429.0
37 TraesCS1D01G338400 chr5B 90.493 284 15 8 3116 3388 92235324 92235042 1.230000e-96 364.0
38 TraesCS1D01G338400 chr5B 83.607 366 44 12 1447 1805 92237623 92237267 4.470000e-86 329.0
39 TraesCS1D01G338400 chr5B 91.667 48 2 1 2931 2978 396068042 396067997 1.390000e-06 65.8
40 TraesCS1D01G338400 chr5D 90.860 1674 111 22 3459 5116 84901693 84900046 0.000000e+00 2206.0
41 TraesCS1D01G338400 chr5D 86.713 1144 98 29 2236 3339 84903154 84902025 0.000000e+00 1221.0
42 TraesCS1D01G338400 chr5D 86.000 300 34 8 1447 1739 84904479 84904181 1.250000e-81 315.0
43 TraesCS1D01G338400 chr5D 96.429 56 1 1 3335 3389 84901901 84901846 2.300000e-14 91.6
44 TraesCS1D01G338400 chr5A 90.496 1673 119 20 3459 5116 79285872 79284225 0.000000e+00 2172.0
45 TraesCS1D01G338400 chr5A 85.892 964 85 26 2414 3339 79287160 79286210 0.000000e+00 979.0
46 TraesCS1D01G338400 chr5A 85.333 300 37 7 1447 1739 79289054 79288755 2.710000e-78 303.0
47 TraesCS1D01G338400 chr5A 90.217 184 15 3 2236 2417 79287647 79287465 2.790000e-58 237.0
48 TraesCS1D01G338400 chr5A 90.551 127 4 8 813 934 476078633 476078510 1.730000e-35 161.0
49 TraesCS1D01G338400 chr5A 94.643 56 2 1 3335 3389 79286086 79286031 1.070000e-12 86.1
50 TraesCS1D01G338400 chr7B 90.491 326 29 1 189 512 380073294 380072969 4.290000e-116 429.0
51 TraesCS1D01G338400 chr3B 90.491 326 29 1 189 512 534159644 534159319 4.290000e-116 429.0
52 TraesCS1D01G338400 chr2A 96.850 254 8 0 1064 1317 642680066 642680319 5.550000e-115 425.0
53 TraesCS1D01G338400 chr2A 90.184 326 30 1 189 512 537234073 537233748 2.000000e-114 424.0
54 TraesCS1D01G338400 chr2A 96.457 254 9 0 1064 1317 310043642 310043895 2.580000e-113 420.0
55 TraesCS1D01G338400 chr2A 96.063 254 10 0 1064 1317 713665186 713664933 1.200000e-111 414.0
56 TraesCS1D01G338400 chr2A 95.669 254 11 0 1064 1317 685276419 685276166 5.590000e-110 409.0
57 TraesCS1D01G338400 chr2A 85.859 198 16 6 1 190 204626285 204626092 3.660000e-47 200.0
58 TraesCS1D01G338400 chr2A 92.063 126 3 6 814 934 713665353 713665230 2.870000e-38 171.0
59 TraesCS1D01G338400 chr2A 87.121 132 8 9 810 934 685276592 685276463 2.250000e-29 141.0
60 TraesCS1D01G338400 chr2A 97.059 34 0 1 126 159 43154178 43154210 8.390000e-04 56.5
61 TraesCS1D01G338400 chr2B 90.184 326 30 1 189 512 795075186 795074861 2.000000e-114 424.0
62 TraesCS1D01G338400 chr7D 90.154 325 30 1 189 511 475155377 475155053 7.180000e-114 422.0
63 TraesCS1D01G338400 chr7D 80.000 195 29 7 1 189 465568626 465568436 1.050000e-27 135.0
64 TraesCS1D01G338400 chr6D 90.154 325 30 1 190 512 454064161 454064485 7.180000e-114 422.0
65 TraesCS1D01G338400 chrUn 89.877 326 31 1 189 512 136395320 136394995 9.280000e-113 418.0
66 TraesCS1D01G338400 chr6A 95.276 254 12 0 1064 1317 231643682 231643935 2.600000e-108 403.0
67 TraesCS1D01G338400 chr6A 88.095 126 8 7 814 934 574906315 574906438 6.260000e-30 143.0
68 TraesCS1D01G338400 chr4B 80.795 302 43 13 1447 1741 577022478 577022185 7.810000e-54 222.0
69 TraesCS1D01G338400 chr4D 84.264 197 18 6 1 188 491395704 491395896 4.770000e-41 180.0
70 TraesCS1D01G338400 chr3D 87.179 156 16 4 17 172 585095923 585095772 2.220000e-39 174.0
71 TraesCS1D01G338400 chr2D 79.333 150 24 4 28 171 184131267 184131119 1.370000e-16 99.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G338400 chr1D 427617888 427623876 5988 True 11060.000000 11060 100.000000 1 5989 1 chr1D.!!$R1 5988
1 TraesCS1D01G338400 chr1D 476227499 476230532 3033 False 451.666667 917 84.903000 2760 4458 3 chr1D.!!$F1 1698
2 TraesCS1D01G338400 chr1B 579785353 579793737 8384 True 1233.833333 3193 90.728833 214 5989 6 chr1B.!!$R1 5775
3 TraesCS1D01G338400 chr1B 662545003 662551270 6267 False 451.600000 992 86.536600 2760 4458 5 chr1B.!!$F2 1698
4 TraesCS1D01G338400 chr1A 522952942 522959468 6526 True 1045.842857 2619 91.997714 190 5989 7 chr1A.!!$R6 5799
5 TraesCS1D01G338400 chr1A 572013712 572015136 1424 False 643.000000 922 85.477000 3547 4823 2 chr1A.!!$F2 1276
6 TraesCS1D01G338400 chr1A 572004726 572005312 586 False 219.500000 228 91.820500 2758 3286 2 chr1A.!!$F1 528
7 TraesCS1D01G338400 chr5B 92233091 92237623 4532 True 939.000000 2215 88.095750 1447 5105 4 chr5B.!!$R2 3658
8 TraesCS1D01G338400 chr5D 84900046 84904479 4433 True 958.400000 2206 90.000500 1447 5116 4 chr5D.!!$R1 3669
9 TraesCS1D01G338400 chr5A 79284225 79289054 4829 True 755.420000 2172 89.316200 1447 5116 5 chr5A.!!$R2 3669

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
349 352 0.390860 CCGGGCAAACATTGTTGGAA 59.609 50.000 8.14 0.0 0.00 3.53 F
492 495 0.462047 AACGAAGACCGGATCCATGC 60.462 55.000 9.46 0.0 43.93 4.06 F
1414 1464 0.237498 TCAGTGTACTGTCTGTCGCG 59.763 55.000 11.44 0.0 44.12 5.87 F
1440 1551 0.671781 ACTGCTGGAGATTGCACGTC 60.672 55.000 2.24 0.0 35.20 4.34 F
1736 1930 1.065491 ACAAGCTATGCGGATTGTCCA 60.065 47.619 0.00 0.0 41.11 4.02 F
2537 3940 1.815003 GCACTTGCTAGGAATGCACTT 59.185 47.619 19.10 0.0 40.40 3.16 F
3891 7882 1.352083 TAGCTGAAGGTGCTCCTGTT 58.648 50.000 8.37 0.0 44.35 3.16 F
4583 8747 0.251077 CAAAGGGCACAGAGAAGGCT 60.251 55.000 0.00 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 1464 0.250513 AATCTCCAGCAGTCGGAACC 59.749 55.000 0.00 0.00 30.33 3.62 R
2251 3344 2.093306 TATGCCCACACAGAAAGTCG 57.907 50.000 0.00 0.00 0.00 4.18 R
2854 4528 1.478105 CGTGGACATCTGTCATCCTCA 59.522 52.381 12.10 0.00 46.47 3.86 R
3108 4855 5.915196 GCACAAGAGCTTAAAACCTTGTAAG 59.085 40.000 13.92 6.38 44.97 2.34 R
3742 7726 1.738030 GCTTCATGCTGGTTCATTGCC 60.738 52.381 0.00 0.00 38.95 4.52 R
4176 8169 0.336737 ACCCTGAGGACTCCCTGTAG 59.663 60.000 0.00 0.00 44.53 2.74 R
4712 8876 0.519077 CCACTTTCTCGCCTTTGCTC 59.481 55.000 0.00 0.00 34.43 4.26 R
5564 10486 1.077716 GCGGTTGGACCCTAGCATT 60.078 57.895 0.00 0.00 33.75 3.56 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
42 43 4.664150 TTTCTTTGCCACACCTTTTAGG 57.336 40.909 0.00 0.00 42.49 2.69
43 44 3.586470 TCTTTGCCACACCTTTTAGGA 57.414 42.857 0.00 0.00 37.67 2.94
44 45 3.904717 TCTTTGCCACACCTTTTAGGAA 58.095 40.909 0.00 0.00 37.67 3.36
46 47 4.280677 TCTTTGCCACACCTTTTAGGAATG 59.719 41.667 0.00 0.00 37.67 2.67
48 49 2.890311 TGCCACACCTTTTAGGAATGTG 59.110 45.455 8.67 8.67 40.26 3.21
49 50 3.153919 GCCACACCTTTTAGGAATGTGA 58.846 45.455 14.60 0.00 42.02 3.58
53 54 6.389906 CCACACCTTTTAGGAATGTGATTTC 58.610 40.000 14.60 0.00 42.02 2.17
54 55 6.015519 CCACACCTTTTAGGAATGTGATTTCA 60.016 38.462 14.60 0.00 42.02 2.69
58 59 7.756722 CACCTTTTAGGAATGTGATTTCATGAC 59.243 37.037 0.00 0.00 37.67 3.06
59 60 6.968904 CCTTTTAGGAATGTGATTTCATGACG 59.031 38.462 0.00 0.00 37.67 4.35
60 61 7.148255 CCTTTTAGGAATGTGATTTCATGACGA 60.148 37.037 0.00 0.00 37.67 4.20
62 63 7.864108 TTAGGAATGTGATTTCATGACGATT 57.136 32.000 0.00 0.00 0.00 3.34
63 64 6.764308 AGGAATGTGATTTCATGACGATTT 57.236 33.333 0.00 0.00 0.00 2.17
64 65 7.161773 AGGAATGTGATTTCATGACGATTTT 57.838 32.000 0.00 0.00 0.00 1.82
65 66 7.605449 AGGAATGTGATTTCATGACGATTTTT 58.395 30.769 0.00 0.00 0.00 1.94
101 102 8.710835 TTAAAACTTTTGTCAATGTTTCTCCC 57.289 30.769 13.86 0.00 38.61 4.30
103 104 5.930837 ACTTTTGTCAATGTTTCTCCCAA 57.069 34.783 0.00 0.00 0.00 4.12
104 105 6.293004 ACTTTTGTCAATGTTTCTCCCAAA 57.707 33.333 0.00 0.00 0.00 3.28
105 106 6.706295 ACTTTTGTCAATGTTTCTCCCAAAA 58.294 32.000 0.00 0.00 0.00 2.44
106 107 7.164803 ACTTTTGTCAATGTTTCTCCCAAAAA 58.835 30.769 0.00 0.00 32.07 1.94
152 153 7.470289 TTGTTTTGATTTTATTGTTCACCCG 57.530 32.000 0.00 0.00 0.00 5.28
153 154 6.806751 TGTTTTGATTTTATTGTTCACCCGA 58.193 32.000 0.00 0.00 0.00 5.14
155 156 4.695217 TGATTTTATTGTTCACCCGAGC 57.305 40.909 0.00 0.00 0.00 5.03
157 158 4.394920 TGATTTTATTGTTCACCCGAGCTC 59.605 41.667 2.73 2.73 0.00 4.09
161 162 2.270352 TTGTTCACCCGAGCTCATTT 57.730 45.000 15.40 0.00 0.00 2.32
163 164 1.202758 TGTTCACCCGAGCTCATTTGT 60.203 47.619 15.40 1.46 0.00 2.83
164 165 1.197721 GTTCACCCGAGCTCATTTGTG 59.802 52.381 15.40 13.93 0.00 3.33
165 166 0.955428 TCACCCGAGCTCATTTGTGC 60.955 55.000 15.40 0.00 35.00 4.57
166 167 0.957395 CACCCGAGCTCATTTGTGCT 60.957 55.000 15.40 6.82 46.17 4.40
172 173 0.613260 AGCTCATTTGTGCTCGGGTA 59.387 50.000 1.46 0.00 40.42 3.69
173 174 1.210478 AGCTCATTTGTGCTCGGGTAT 59.790 47.619 1.46 0.00 40.42 2.73
175 176 2.802816 GCTCATTTGTGCTCGGGTATAG 59.197 50.000 0.00 0.00 0.00 1.31
176 177 3.492656 GCTCATTTGTGCTCGGGTATAGA 60.493 47.826 0.00 0.00 0.00 1.98
178 179 5.092554 TCATTTGTGCTCGGGTATAGAAA 57.907 39.130 0.00 0.00 0.00 2.52
182 183 5.864418 TTGTGCTCGGGTATAGAAACTAT 57.136 39.130 0.00 0.00 0.00 2.12
183 184 5.196341 TGTGCTCGGGTATAGAAACTATG 57.804 43.478 0.00 0.00 0.00 2.23
184 185 3.988517 GTGCTCGGGTATAGAAACTATGC 59.011 47.826 0.00 0.00 0.00 3.14
185 186 3.243336 GCTCGGGTATAGAAACTATGCG 58.757 50.000 0.00 0.00 0.00 4.73
186 187 3.305199 GCTCGGGTATAGAAACTATGCGT 60.305 47.826 0.00 0.00 0.00 5.24
188 189 3.254166 TCGGGTATAGAAACTATGCGTCC 59.746 47.826 0.00 0.00 0.00 4.79
193 194 2.981859 AGAAACTATGCGTCCCGATT 57.018 45.000 0.00 0.00 0.00 3.34
195 196 4.395959 AGAAACTATGCGTCCCGATTTA 57.604 40.909 0.00 0.00 0.00 1.40
209 210 5.584649 GTCCCGATTTATTCATCAACTGTCA 59.415 40.000 0.00 0.00 0.00 3.58
211 212 6.316140 TCCCGATTTATTCATCAACTGTCAAG 59.684 38.462 0.00 0.00 0.00 3.02
212 213 6.458751 CCCGATTTATTCATCAACTGTCAAGG 60.459 42.308 0.00 0.00 0.00 3.61
218 219 8.997621 TTATTCATCAACTGTCAAGGTAGTAC 57.002 34.615 0.00 0.00 0.00 2.73
227 228 6.827727 ACTGTCAAGGTAGTACAAAGAACAT 58.172 36.000 2.06 0.00 0.00 2.71
279 280 1.404391 CCACCTAGCGACGACTACAAT 59.596 52.381 0.00 0.00 0.00 2.71
347 350 1.667510 GCCGGGCAAACATTGTTGG 60.668 57.895 15.62 0.54 0.00 3.77
349 352 0.390860 CCGGGCAAACATTGTTGGAA 59.609 50.000 8.14 0.00 0.00 3.53
358 361 6.215845 GCAAACATTGTTGGAATAGACAGTT 58.784 36.000 8.14 0.00 0.00 3.16
360 363 7.424803 CAAACATTGTTGGAATAGACAGTTGA 58.575 34.615 2.13 0.00 0.00 3.18
370 373 5.694910 GGAATAGACAGTTGAAAAGTCGTCA 59.305 40.000 0.00 0.00 37.36 4.35
389 392 2.106511 TCATGCTAAGGCCCCATAAGAC 59.893 50.000 0.00 0.00 37.74 3.01
392 395 1.202818 GCTAAGGCCCCATAAGACCAG 60.203 57.143 0.00 0.00 0.00 4.00
405 408 1.891919 GACCAGCGCACCAGAACAA 60.892 57.895 11.47 0.00 0.00 2.83
492 495 0.462047 AACGAAGACCGGATCCATGC 60.462 55.000 9.46 0.00 43.93 4.06
493 496 1.951130 CGAAGACCGGATCCATGCG 60.951 63.158 9.46 0.72 41.50 4.73
552 560 7.596494 TGATTGATTCATCTTCACAGGAAAAC 58.404 34.615 0.00 0.00 31.35 2.43
556 564 9.958180 TTGATTCATCTTCACAGGAAAACTATA 57.042 29.630 0.00 0.00 31.35 1.31
557 565 9.958180 TGATTCATCTTCACAGGAAAACTATAA 57.042 29.630 0.00 0.00 31.35 0.98
628 640 6.877668 TTTCTTTAGGGGAAAACAAACCTT 57.122 33.333 0.00 0.00 34.59 3.50
629 641 6.877668 TTCTTTAGGGGAAAACAAACCTTT 57.122 33.333 0.00 0.00 34.59 3.11
630 642 6.877668 TCTTTAGGGGAAAACAAACCTTTT 57.122 33.333 0.00 0.00 34.59 2.27
652 664 4.922471 TTTTTACGGAAGGGGAAAACAG 57.078 40.909 0.00 0.00 0.00 3.16
657 669 1.202891 CGGAAGGGGAAAACAGACCTT 60.203 52.381 0.00 0.00 45.50 3.50
658 670 2.751816 CGGAAGGGGAAAACAGACCTTT 60.752 50.000 0.00 0.00 43.03 3.11
724 736 4.022464 ACAAAAACGTTTCGCTTGATGA 57.978 36.364 23.72 0.00 0.00 2.92
728 740 1.429463 ACGTTTCGCTTGATGACTCC 58.571 50.000 0.00 0.00 0.00 3.85
837 850 2.047151 CTCTCTCTCACGCTCGCTCC 62.047 65.000 0.00 0.00 0.00 4.70
839 852 2.101965 CTCTCACGCTCGCTCCTG 59.898 66.667 0.00 0.00 0.00 3.86
843 856 4.803426 CACGCTCGCTCCTGTCCC 62.803 72.222 0.00 0.00 0.00 4.46
911 924 3.636231 CCTCCAACTCCGCCCACA 61.636 66.667 0.00 0.00 0.00 4.17
1040 1066 1.027255 TGAGTTCCTCGGCTCTCTCG 61.027 60.000 0.00 0.00 32.35 4.04
1041 1067 2.103340 GTTCCTCGGCTCTCTCGC 59.897 66.667 0.00 0.00 0.00 5.03
1110 1137 3.982058 GTGTGTACTGCTCTAGTGTGAAC 59.018 47.826 0.00 0.00 40.65 3.18
1156 1183 5.177327 GCCAGTGAAACAATTTTGTATGGTG 59.823 40.000 0.00 0.00 41.31 4.17
1163 1190 3.070734 ACAATTTTGTATGGTGCTGGCAA 59.929 39.130 0.00 0.00 40.16 4.52
1165 1192 3.316071 TTTTGTATGGTGCTGGCAATG 57.684 42.857 0.00 0.00 0.00 2.82
1166 1193 1.921982 TTGTATGGTGCTGGCAATGT 58.078 45.000 0.00 0.00 0.00 2.71
1167 1194 1.921982 TGTATGGTGCTGGCAATGTT 58.078 45.000 0.00 0.00 0.00 2.71
1168 1195 1.545136 TGTATGGTGCTGGCAATGTTG 59.455 47.619 0.00 0.00 0.00 3.33
1169 1196 1.545582 GTATGGTGCTGGCAATGTTGT 59.454 47.619 0.00 0.00 0.00 3.32
1170 1197 1.050204 ATGGTGCTGGCAATGTTGTT 58.950 45.000 0.00 0.00 0.00 2.83
1172 1199 0.600782 GGTGCTGGCAATGTTGTTGG 60.601 55.000 0.00 0.00 0.00 3.77
1174 1201 1.339610 GTGCTGGCAATGTTGTTGGTA 59.660 47.619 0.00 0.00 0.00 3.25
1190 1217 4.754618 TGTTGGTACTGTCAATGCTTAGTG 59.245 41.667 0.00 0.00 0.00 2.74
1193 1220 4.039852 TGGTACTGTCAATGCTTAGTGTGA 59.960 41.667 0.00 0.00 0.00 3.58
1333 1383 6.059787 AGCAATTCATCTTTGAGTCCTACT 57.940 37.500 0.00 0.00 32.27 2.57
1334 1384 7.187824 AGCAATTCATCTTTGAGTCCTACTA 57.812 36.000 0.00 0.00 32.27 1.82
1335 1385 7.271511 AGCAATTCATCTTTGAGTCCTACTAG 58.728 38.462 0.00 0.00 32.27 2.57
1336 1386 6.481644 GCAATTCATCTTTGAGTCCTACTAGG 59.518 42.308 0.00 0.00 32.55 3.02
1357 1407 2.301870 GTTGGATGGTGTAGAGTGGACA 59.698 50.000 0.00 0.00 0.00 4.02
1411 1461 4.521130 TTGGATCAGTGTACTGTCTGTC 57.479 45.455 11.44 6.47 44.12 3.51
1414 1464 0.237498 TCAGTGTACTGTCTGTCGCG 59.763 55.000 11.44 0.00 44.12 5.87
1440 1551 0.671781 ACTGCTGGAGATTGCACGTC 60.672 55.000 2.24 0.00 35.20 4.34
1467 1578 2.673775 TCCCTGCAATTGGTCTTTGA 57.326 45.000 7.72 0.00 0.00 2.69
1476 1587 5.239306 TGCAATTGGTCTTTGAGTAAGTGAG 59.761 40.000 7.72 0.00 35.28 3.51
1496 1607 3.235200 AGCAGGAGTAGAAGACACAAGT 58.765 45.455 0.00 0.00 0.00 3.16
1503 1618 5.695363 GGAGTAGAAGACACAAGTTGTAACC 59.305 44.000 8.49 0.95 39.17 2.85
1726 1920 5.354234 AGGTGTACAACATTACAAGCTATGC 59.646 40.000 14.58 0.00 33.73 3.14
1736 1930 1.065491 ACAAGCTATGCGGATTGTCCA 60.065 47.619 0.00 0.00 41.11 4.02
1873 2098 6.645790 AGAGTTTCTTTTGCATGATGTTCT 57.354 33.333 0.00 0.00 0.00 3.01
1953 2180 6.942532 ACATAAATAGTTGCATGTCGGAAT 57.057 33.333 0.00 0.00 0.00 3.01
1957 2184 5.679734 AATAGTTGCATGTCGGAATCATC 57.320 39.130 0.00 0.00 0.00 2.92
1993 2220 3.485394 TGCATCTGTTTAAGCCTTGACA 58.515 40.909 0.00 0.00 0.00 3.58
1997 2224 4.164843 TCTGTTTAAGCCTTGACAACCT 57.835 40.909 0.00 0.00 0.00 3.50
2015 2244 5.104485 ACAACCTTACTGAAGTCTGACCTTT 60.104 40.000 3.76 0.00 0.00 3.11
2016 2245 5.632034 ACCTTACTGAAGTCTGACCTTTT 57.368 39.130 3.76 0.00 0.00 2.27
2017 2246 5.368989 ACCTTACTGAAGTCTGACCTTTTG 58.631 41.667 3.76 0.00 0.00 2.44
2018 2247 4.214332 CCTTACTGAAGTCTGACCTTTTGC 59.786 45.833 3.76 0.00 0.00 3.68
2261 3354 5.305585 TCTGAATTTTAGGCGACTTTCTGT 58.694 37.500 0.00 0.00 43.67 3.41
2263 3356 4.819630 TGAATTTTAGGCGACTTTCTGTGT 59.180 37.500 0.00 0.00 43.67 3.72
2401 3494 7.127032 TGGTGGCCATATTTTCTTTCCAATATT 59.873 33.333 9.72 0.00 0.00 1.28
2537 3940 1.815003 GCACTTGCTAGGAATGCACTT 59.185 47.619 19.10 0.00 40.40 3.16
2673 4091 9.620259 TTTGCCTTGGTTTCTTACAATAATTTT 57.380 25.926 0.00 0.00 0.00 1.82
2700 4121 8.873215 AGAATGATTAGTAACTAATGGACGTG 57.127 34.615 0.00 0.00 36.87 4.49
2729 4150 8.210265 TGTGCACATTCTGTTCCATATAGAATA 58.790 33.333 17.42 0.00 41.23 1.75
2967 4694 8.082242 GCCTCTTTACAATTTAGAGCAAAGAAA 58.918 33.333 0.00 0.00 35.24 2.52
2968 4695 9.965824 CCTCTTTACAATTTAGAGCAAAGAAAA 57.034 29.630 0.00 0.00 35.24 2.29
2974 4701 8.862550 ACAATTTAGAGCAAAGAAAACTTCAG 57.137 30.769 0.00 0.00 0.00 3.02
3142 4913 7.452880 TTTAAGCTCTTGTGCACTATTTGAT 57.547 32.000 19.41 2.55 34.99 2.57
3742 7726 3.797039 TGATCTTATCCAGGAAAGTGCG 58.203 45.455 0.00 0.00 0.00 5.34
3795 7779 6.620877 ATTTATCCAGGTCACTACTGTTCA 57.379 37.500 0.00 0.00 34.16 3.18
3891 7882 1.352083 TAGCTGAAGGTGCTCCTGTT 58.648 50.000 8.37 0.00 44.35 3.16
4310 8303 5.840715 CTCTATGCTGAGCAGAATGAACTA 58.159 41.667 14.36 0.00 43.65 2.24
4460 8466 5.470098 GCTTGAGGTTTGTCAGATCTTTGTA 59.530 40.000 0.00 0.00 0.00 2.41
4470 8627 4.808364 GTCAGATCTTTGTAGCCTCATGAC 59.192 45.833 0.00 0.00 0.00 3.06
4473 8630 6.381133 TCAGATCTTTGTAGCCTCATGACTTA 59.619 38.462 0.00 0.00 0.00 2.24
4475 8632 7.010923 CAGATCTTTGTAGCCTCATGACTTAAC 59.989 40.741 0.00 0.00 0.00 2.01
4583 8747 0.251077 CAAAGGGCACAGAGAAGGCT 60.251 55.000 0.00 0.00 0.00 4.58
4736 8900 2.436824 GGCGAGAAAGTGGCCCTC 60.437 66.667 0.00 0.00 44.24 4.30
4772 8936 2.537560 GCATTGGCGTCTCATCGGG 61.538 63.158 0.00 0.00 0.00 5.14
4844 9009 0.257039 GAAGCACACCCCCATCTGAT 59.743 55.000 0.00 0.00 0.00 2.90
4851 9016 3.194116 CACACCCCCATCTGATTGAAAAG 59.806 47.826 0.00 0.00 0.00 2.27
4985 9160 7.326547 GGATTTATCTACGCTACTAGTTTGCTC 59.673 40.741 0.00 0.00 0.00 4.26
4991 9166 2.599082 CGCTACTAGTTTGCTCCTTTCG 59.401 50.000 0.00 0.00 0.00 3.46
5004 9179 2.415512 CTCCTTTCGGTTTGTCGGAATC 59.584 50.000 0.00 0.00 35.79 2.52
5032 9207 6.038936 GGGTTTGTTATACTCGCCATGTTATT 59.961 38.462 0.00 0.00 0.00 1.40
5125 9307 4.517285 ACTCCATTATGTCTTGCGTTGAT 58.483 39.130 0.00 0.00 0.00 2.57
5303 9498 3.303881 TTCTTCCAGTGTGAGACATCG 57.696 47.619 0.00 0.00 0.00 3.84
5321 9516 2.227194 TCGCCAGAAGGGAAAAAGAAC 58.773 47.619 0.00 0.00 40.01 3.01
5351 9553 3.402110 CAGTGACCAGAACATGCTAACA 58.598 45.455 0.00 0.00 0.00 2.41
5371 9573 9.988350 GCTAACATTTATTTCTTTCGATCAGAA 57.012 29.630 3.92 3.92 37.01 3.02
5497 10411 5.989477 TCATACGAATCCTCAACCATTCTT 58.011 37.500 0.00 0.00 0.00 2.52
5564 10486 3.071874 ACTGAATTTGCGAATCCTCCA 57.928 42.857 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.187967 TCCTAAAAGGTGTGGCAAAGAAAAA 59.812 36.000 0.00 0.00 36.53 1.94
20 21 4.712337 TCCTAAAAGGTGTGGCAAAGAAAA 59.288 37.500 0.00 0.00 36.53 2.29
21 22 4.282496 TCCTAAAAGGTGTGGCAAAGAAA 58.718 39.130 0.00 0.00 36.53 2.52
23 24 3.586470 TCCTAAAAGGTGTGGCAAAGA 57.414 42.857 0.00 0.00 36.53 2.52
24 25 4.039124 ACATTCCTAAAAGGTGTGGCAAAG 59.961 41.667 0.00 0.00 36.53 2.77
25 26 3.964031 ACATTCCTAAAAGGTGTGGCAAA 59.036 39.130 0.00 0.00 36.53 3.68
26 27 3.320541 CACATTCCTAAAAGGTGTGGCAA 59.679 43.478 8.22 0.00 38.19 4.52
29 30 5.982890 AATCACATTCCTAAAAGGTGTGG 57.017 39.130 13.65 0.00 40.68 4.17
30 31 6.980593 TGAAATCACATTCCTAAAAGGTGTG 58.019 36.000 9.37 9.37 41.28 3.82
31 32 7.451255 TCATGAAATCACATTCCTAAAAGGTGT 59.549 33.333 0.00 0.00 36.53 4.16
33 34 7.362056 CGTCATGAAATCACATTCCTAAAAGGT 60.362 37.037 0.00 0.00 36.53 3.50
34 35 6.968904 CGTCATGAAATCACATTCCTAAAAGG 59.031 38.462 0.00 0.00 36.46 3.11
35 36 7.751732 TCGTCATGAAATCACATTCCTAAAAG 58.248 34.615 0.00 0.00 0.00 2.27
37 38 7.864108 ATCGTCATGAAATCACATTCCTAAA 57.136 32.000 0.00 0.00 0.00 1.85
38 39 7.864108 AATCGTCATGAAATCACATTCCTAA 57.136 32.000 0.00 0.00 0.00 2.69
39 40 7.864108 AAATCGTCATGAAATCACATTCCTA 57.136 32.000 0.00 0.00 0.00 2.94
41 42 7.816945 AAAAATCGTCATGAAATCACATTCC 57.183 32.000 0.00 0.00 0.00 3.01
68 69 9.665719 ACATTGACAAAAGTTTTAATTCCTTGT 57.334 25.926 0.00 0.00 0.00 3.16
75 76 9.325198 GGGAGAAACATTGACAAAAGTTTTAAT 57.675 29.630 17.76 10.63 37.33 1.40
76 77 8.314751 TGGGAGAAACATTGACAAAAGTTTTAA 58.685 29.630 17.76 0.00 37.33 1.52
77 78 7.841956 TGGGAGAAACATTGACAAAAGTTTTA 58.158 30.769 17.76 5.91 37.33 1.52
78 79 6.706295 TGGGAGAAACATTGACAAAAGTTTT 58.294 32.000 17.76 0.00 37.33 2.43
79 80 6.293004 TGGGAGAAACATTGACAAAAGTTT 57.707 33.333 17.09 17.09 39.28 2.66
80 81 5.930837 TGGGAGAAACATTGACAAAAGTT 57.069 34.783 0.00 0.00 0.00 2.66
81 82 5.930837 TTGGGAGAAACATTGACAAAAGT 57.069 34.783 0.00 0.00 0.00 2.66
126 127 8.391106 CGGGTGAACAATAAAATCAAAACAAAA 58.609 29.630 0.00 0.00 0.00 2.44
127 128 7.764443 TCGGGTGAACAATAAAATCAAAACAAA 59.236 29.630 0.00 0.00 0.00 2.83
128 129 7.265673 TCGGGTGAACAATAAAATCAAAACAA 58.734 30.769 0.00 0.00 0.00 2.83
130 131 6.128929 GCTCGGGTGAACAATAAAATCAAAAC 60.129 38.462 0.00 0.00 0.00 2.43
131 132 5.923684 GCTCGGGTGAACAATAAAATCAAAA 59.076 36.000 0.00 0.00 0.00 2.44
132 133 5.242838 AGCTCGGGTGAACAATAAAATCAAA 59.757 36.000 0.00 0.00 0.00 2.69
133 134 4.764823 AGCTCGGGTGAACAATAAAATCAA 59.235 37.500 0.00 0.00 0.00 2.57
135 136 4.394920 TGAGCTCGGGTGAACAATAAAATC 59.605 41.667 9.64 0.00 0.00 2.17
136 137 4.331968 TGAGCTCGGGTGAACAATAAAAT 58.668 39.130 9.64 0.00 0.00 1.82
139 140 3.627395 ATGAGCTCGGGTGAACAATAA 57.373 42.857 9.64 0.00 0.00 1.40
140 141 3.627395 AATGAGCTCGGGTGAACAATA 57.373 42.857 9.64 0.00 0.00 1.90
146 147 0.955428 GCACAAATGAGCTCGGGTGA 60.955 55.000 22.84 2.53 0.00 4.02
148 149 0.674895 GAGCACAAATGAGCTCGGGT 60.675 55.000 15.29 1.30 45.72 5.28
149 150 2.093216 GAGCACAAATGAGCTCGGG 58.907 57.895 15.29 0.00 45.72 5.14
153 154 0.613260 TACCCGAGCACAAATGAGCT 59.387 50.000 5.00 5.00 44.44 4.09
155 156 4.322080 TCTATACCCGAGCACAAATGAG 57.678 45.455 0.00 0.00 0.00 2.90
157 158 4.876107 AGTTTCTATACCCGAGCACAAATG 59.124 41.667 0.00 0.00 0.00 2.32
161 162 4.500887 GCATAGTTTCTATACCCGAGCACA 60.501 45.833 0.00 0.00 0.00 4.57
163 164 3.305131 CGCATAGTTTCTATACCCGAGCA 60.305 47.826 0.00 0.00 0.00 4.26
164 165 3.243336 CGCATAGTTTCTATACCCGAGC 58.757 50.000 0.00 0.00 0.00 5.03
165 166 4.474113 GACGCATAGTTTCTATACCCGAG 58.526 47.826 0.00 0.00 0.00 4.63
166 167 3.254166 GGACGCATAGTTTCTATACCCGA 59.746 47.826 0.00 0.00 0.00 5.14
167 168 3.572584 GGACGCATAGTTTCTATACCCG 58.427 50.000 0.00 0.00 0.00 5.28
168 169 3.922910 GGGACGCATAGTTTCTATACCC 58.077 50.000 0.00 0.00 0.00 3.69
185 186 5.584649 TGACAGTTGATGAATAAATCGGGAC 59.415 40.000 0.00 0.00 0.00 4.46
186 187 5.739959 TGACAGTTGATGAATAAATCGGGA 58.260 37.500 0.00 0.00 0.00 5.14
188 189 6.094048 ACCTTGACAGTTGATGAATAAATCGG 59.906 38.462 0.00 0.00 0.00 4.18
193 194 8.590204 TGTACTACCTTGACAGTTGATGAATAA 58.410 33.333 0.00 0.00 0.00 1.40
195 196 7.004555 TGTACTACCTTGACAGTTGATGAAT 57.995 36.000 0.00 0.00 0.00 2.57
279 280 2.989253 TTCGGCTCGCTCCAGTGA 60.989 61.111 0.00 0.00 0.00 3.41
347 350 6.764877 TGACGACTTTTCAACTGTCTATTC 57.235 37.500 0.00 0.00 0.00 1.75
349 352 5.120830 GCATGACGACTTTTCAACTGTCTAT 59.879 40.000 0.00 0.00 0.00 1.98
358 361 2.742053 GCCTTAGCATGACGACTTTTCA 59.258 45.455 0.00 0.00 39.53 2.69
360 363 2.084546 GGCCTTAGCATGACGACTTTT 58.915 47.619 0.00 0.00 42.56 2.27
370 373 1.425448 GGTCTTATGGGGCCTTAGCAT 59.575 52.381 0.84 0.14 42.56 3.79
389 392 1.723608 TTGTTGTTCTGGTGCGCTGG 61.724 55.000 9.73 0.00 0.00 4.85
392 395 1.299089 GGTTGTTGTTCTGGTGCGC 60.299 57.895 0.00 0.00 0.00 6.09
492 495 2.616960 TGTTTGTCTTCGATGGATCCG 58.383 47.619 7.39 0.00 0.00 4.18
493 496 3.751175 TGTTGTTTGTCTTCGATGGATCC 59.249 43.478 4.20 4.20 0.00 3.36
494 497 5.356882 TTGTTGTTTGTCTTCGATGGATC 57.643 39.130 0.00 0.00 0.00 3.36
500 503 6.616947 AGTCAAAATTGTTGTTTGTCTTCGA 58.383 32.000 0.00 0.00 37.28 3.71
502 505 8.375465 CAAGAGTCAAAATTGTTGTTTGTCTTC 58.625 33.333 0.00 0.00 35.45 2.87
556 564 7.710907 GGCTCTGTTTGTTCTTTCCTTTTTATT 59.289 33.333 0.00 0.00 0.00 1.40
557 565 7.069950 AGGCTCTGTTTGTTCTTTCCTTTTTAT 59.930 33.333 0.00 0.00 0.00 1.40
559 567 5.187772 AGGCTCTGTTTGTTCTTTCCTTTTT 59.812 36.000 0.00 0.00 0.00 1.94
560 568 4.711846 AGGCTCTGTTTGTTCTTTCCTTTT 59.288 37.500 0.00 0.00 0.00 2.27
633 645 3.479489 GTCTGTTTTCCCCTTCCGTAAA 58.521 45.455 0.00 0.00 0.00 2.01
637 649 0.400594 AGGTCTGTTTTCCCCTTCCG 59.599 55.000 0.00 0.00 0.00 4.30
639 651 3.501062 CGTAAAGGTCTGTTTTCCCCTTC 59.499 47.826 0.00 0.00 36.30 3.46
640 652 3.483421 CGTAAAGGTCTGTTTTCCCCTT 58.517 45.455 0.00 0.00 38.94 3.95
641 653 2.812983 GCGTAAAGGTCTGTTTTCCCCT 60.813 50.000 0.00 0.00 0.00 4.79
642 654 1.538512 GCGTAAAGGTCTGTTTTCCCC 59.461 52.381 0.00 0.00 0.00 4.81
644 656 3.562557 TCAAGCGTAAAGGTCTGTTTTCC 59.437 43.478 0.00 0.00 0.00 3.13
647 659 4.067972 TCTCAAGCGTAAAGGTCTGTTT 57.932 40.909 0.00 0.00 0.00 2.83
649 661 3.746045 TTCTCAAGCGTAAAGGTCTGT 57.254 42.857 0.00 0.00 0.00 3.41
650 662 5.292101 CCTATTTCTCAAGCGTAAAGGTCTG 59.708 44.000 0.00 0.00 0.00 3.51
651 663 5.046520 ACCTATTTCTCAAGCGTAAAGGTCT 60.047 40.000 0.00 0.00 0.00 3.85
652 664 5.176592 ACCTATTTCTCAAGCGTAAAGGTC 58.823 41.667 0.00 0.00 0.00 3.85
657 669 4.357142 CGCTACCTATTTCTCAAGCGTAA 58.643 43.478 6.38 0.00 45.60 3.18
658 670 3.961182 CGCTACCTATTTCTCAAGCGTA 58.039 45.455 6.38 0.00 45.60 4.42
724 736 2.132352 GTTCGGATAGGGGCGGAGT 61.132 63.158 0.00 0.00 0.00 3.85
728 740 2.260088 TTTGGGTTCGGATAGGGGCG 62.260 60.000 0.00 0.00 0.00 6.13
815 828 2.013807 CGAGCGTGAGAGAGAGAGG 58.986 63.158 0.00 0.00 0.00 3.69
837 850 2.554564 GGGAAAACCTAACAGGGGACAG 60.555 54.545 0.00 0.00 40.58 3.51
839 852 1.272313 GGGGAAAACCTAACAGGGGAC 60.272 57.143 0.00 0.00 40.58 4.46
843 856 1.549265 GGTGGGGGAAAACCTAACAGG 60.549 57.143 0.00 0.00 42.49 4.00
1110 1137 1.474077 GCCACCAATCCAAACTAGCAG 59.526 52.381 0.00 0.00 0.00 4.24
1156 1183 1.613437 AGTACCAACAACATTGCCAGC 59.387 47.619 0.00 0.00 0.00 4.85
1163 1190 4.144297 AGCATTGACAGTACCAACAACAT 58.856 39.130 0.00 0.00 0.00 2.71
1165 1192 4.568152 AAGCATTGACAGTACCAACAAC 57.432 40.909 0.00 0.00 0.00 3.32
1166 1193 5.238432 CACTAAGCATTGACAGTACCAACAA 59.762 40.000 0.00 0.00 0.00 2.83
1167 1194 4.754618 CACTAAGCATTGACAGTACCAACA 59.245 41.667 0.00 0.00 0.00 3.33
1168 1195 4.755123 ACACTAAGCATTGACAGTACCAAC 59.245 41.667 0.00 0.00 0.00 3.77
1169 1196 4.754618 CACACTAAGCATTGACAGTACCAA 59.245 41.667 0.00 0.00 0.00 3.67
1170 1197 4.039852 TCACACTAAGCATTGACAGTACCA 59.960 41.667 0.00 0.00 0.00 3.25
1172 1199 6.727824 AATCACACTAAGCATTGACAGTAC 57.272 37.500 0.00 0.00 0.00 2.73
1174 1201 6.039717 ACAAAATCACACTAAGCATTGACAGT 59.960 34.615 0.00 0.00 0.00 3.55
1333 1383 3.104512 CCACTCTACACCATCCAACCTA 58.895 50.000 0.00 0.00 0.00 3.08
1334 1384 1.909302 CCACTCTACACCATCCAACCT 59.091 52.381 0.00 0.00 0.00 3.50
1335 1385 1.906574 TCCACTCTACACCATCCAACC 59.093 52.381 0.00 0.00 0.00 3.77
1336 1386 2.301870 TGTCCACTCTACACCATCCAAC 59.698 50.000 0.00 0.00 0.00 3.77
1357 1407 5.486526 CAGAGTCTAAAATCTGCCTGAGTT 58.513 41.667 0.00 0.00 36.80 3.01
1414 1464 0.250513 AATCTCCAGCAGTCGGAACC 59.749 55.000 0.00 0.00 30.33 3.62
1440 1551 4.952335 AGACCAATTGCAGGGAAATAGAAG 59.048 41.667 0.00 0.00 0.00 2.85
1467 1578 4.703093 GTCTTCTACTCCTGCTCACTTACT 59.297 45.833 0.00 0.00 0.00 2.24
1476 1587 3.669251 ACTTGTGTCTTCTACTCCTGC 57.331 47.619 0.00 0.00 0.00 4.85
1726 1920 5.527214 TCATTAGCTAACAATGGACAATCCG 59.473 40.000 8.70 0.00 40.17 4.18
1736 1930 4.034510 GCGCAGAACTCATTAGCTAACAAT 59.965 41.667 8.70 0.00 0.00 2.71
1850 2072 6.645790 AGAACATCATGCAAAAGAAACTCT 57.354 33.333 0.00 0.00 0.00 3.24
1935 2162 5.125356 TGATGATTCCGACATGCAACTATT 58.875 37.500 0.00 0.00 0.00 1.73
1942 2169 4.825546 AAAGATGATGATTCCGACATGC 57.174 40.909 0.00 0.00 0.00 4.06
1953 2180 8.837389 CAGATGCATAAAGAGAAAAGATGATGA 58.163 33.333 0.00 0.00 0.00 2.92
1976 2203 4.164843 AGGTTGTCAAGGCTTAAACAGA 57.835 40.909 16.63 1.96 0.00 3.41
1993 2220 5.632034 AAAGGTCAGACTTCAGTAAGGTT 57.368 39.130 0.00 0.00 37.01 3.50
1997 2224 5.036117 AGCAAAAGGTCAGACTTCAGTAA 57.964 39.130 0.00 0.00 0.00 2.24
2251 3344 2.093306 TATGCCCACACAGAAAGTCG 57.907 50.000 0.00 0.00 0.00 4.18
2261 3354 7.838079 AAAGATAGCAAATATTATGCCCACA 57.162 32.000 14.85 4.05 44.91 4.17
2263 3356 9.532494 ACATAAAGATAGCAAATATTATGCCCA 57.468 29.630 14.85 7.51 44.91 5.36
2697 4118 3.982213 CAGAATGTGCACATCCACG 57.018 52.632 31.45 16.66 38.55 4.94
2854 4528 1.478105 CGTGGACATCTGTCATCCTCA 59.522 52.381 12.10 0.00 46.47 3.86
3108 4855 5.915196 GCACAAGAGCTTAAAACCTTGTAAG 59.085 40.000 13.92 6.38 44.97 2.34
3742 7726 1.738030 GCTTCATGCTGGTTCATTGCC 60.738 52.381 0.00 0.00 38.95 4.52
3827 7816 7.150783 AGTAAAAGAGATCAAGCCATGAAAC 57.849 36.000 0.00 0.00 42.54 2.78
4176 8169 0.336737 ACCCTGAGGACTCCCTGTAG 59.663 60.000 0.00 0.00 44.53 2.74
4388 8386 0.902531 TTTCTCCTAAGACCTGGCCG 59.097 55.000 0.00 0.00 0.00 6.13
4398 8396 1.407979 GAGCGACCCGATTTCTCCTAA 59.592 52.381 0.00 0.00 0.00 2.69
4460 8466 3.181434 TGTTTGGGTTAAGTCATGAGGCT 60.181 43.478 0.00 0.00 0.00 4.58
4470 8627 5.551760 CAGCTATCACTGTTTGGGTTAAG 57.448 43.478 0.00 0.00 32.78 1.85
4583 8747 0.473694 TGAGCTTGGAGACCTTCCCA 60.474 55.000 0.00 0.00 46.19 4.37
4712 8876 0.519077 CCACTTTCTCGCCTTTGCTC 59.481 55.000 0.00 0.00 34.43 4.26
4742 8906 1.291877 GCCAATGCTTCTCGACACGT 61.292 55.000 0.00 0.00 33.53 4.49
4763 8927 4.731853 TGGCCCCACCCGATGAGA 62.732 66.667 0.00 0.00 37.83 3.27
4772 8936 2.440980 GCTTGGATCTGGCCCCAC 60.441 66.667 0.00 0.00 31.11 4.61
4851 9016 1.065600 TTGTTTCACAAGCTGCGGC 59.934 52.632 10.33 10.33 32.34 6.53
4991 9166 3.345508 AACCCTAGATTCCGACAAACC 57.654 47.619 0.00 0.00 0.00 3.27
5004 9179 4.395959 TGGCGAGTATAACAAACCCTAG 57.604 45.455 0.00 0.00 0.00 3.02
5032 9207 0.892755 CTCGCCTACTAACCACCACA 59.107 55.000 0.00 0.00 0.00 4.17
5269 9463 7.387673 CACACTGGAAGAATACAGTATTGTTCA 59.612 37.037 30.27 20.50 45.21 3.18
5303 9498 3.222603 TCTGTTCTTTTTCCCTTCTGGC 58.777 45.455 0.00 0.00 0.00 4.85
5321 9516 4.136796 TGTTCTGGTCACTGGAATTTCTG 58.863 43.478 0.00 0.00 0.00 3.02
5564 10486 1.077716 GCGGTTGGACCCTAGCATT 60.078 57.895 0.00 0.00 33.75 3.56
5710 12953 1.455383 CGTGGCCCTGCAGTTTTTCT 61.455 55.000 13.81 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.