Multiple sequence alignment - TraesCS5A01G022600

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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 TraesCS5A01G022600 chr5A 100.000 3268 0 0 1 3268 18575050 18578317 0.000000e+00 6035.0
1 TraesCS5A01G022600 chr5A 100.000 403 0 0 3550 3952 18578599 18579001 0.000000e+00 745.0
2 TraesCS5A01G022600 chr5A 82.700 711 95 19 1037 1733 18394994 18395690 1.210000e-169 606.0
3 TraesCS5A01G022600 chr5A 94.015 401 21 3 3554 3952 680233543 680233144 4.370000e-169 604.0
4 TraesCS5A01G022600 chr5A 82.014 695 99 18 1046 1733 18572651 18571976 5.730000e-158 568.0
5 TraesCS5A01G022600 chr5A 95.833 168 7 0 3098 3265 18630282 18630449 5.030000e-69 272.0
6 TraesCS5A01G022600 chr5D 91.730 1306 49 21 479 1770 26784725 26785985 0.000000e+00 1759.0
7 TraesCS5A01G022600 chr5D 96.516 488 14 2 2376 2860 26786652 26787139 0.000000e+00 804.0
8 TraesCS5A01G022600 chr5D 83.333 684 88 18 1063 1733 26507944 26507274 3.380000e-170 608.0
9 TraesCS5A01G022600 chr5D 81.616 718 88 21 1035 1733 26523348 26522656 4.460000e-154 555.0
10 TraesCS5A01G022600 chr5D 87.312 465 27 21 46 479 26784119 26784582 1.640000e-138 503.0
11 TraesCS5A01G022600 chr5D 84.139 517 71 6 1224 1733 26682400 26681888 1.280000e-134 490.0
12 TraesCS5A01G022600 chr5D 95.492 244 8 3 2858 3099 26787198 26787440 1.720000e-103 387.0
13 TraesCS5A01G022600 chr5D 82.460 439 65 10 1301 1733 26474491 26474059 1.340000e-99 374.0
14 TraesCS5A01G022600 chr5D 88.889 279 25 3 2083 2357 26786389 26786665 4.890000e-89 339.0
15 TraesCS5A01G022600 chr5D 90.769 130 12 0 1774 1903 26786152 26786281 1.460000e-39 174.0
16 TraesCS5A01G022600 chr5D 85.124 121 9 8 1046 1166 26682536 26682425 8.970000e-22 115.0
17 TraesCS5A01G022600 chr7A 96.742 399 12 1 3554 3952 46214795 46214398 0.000000e+00 664.0
18 TraesCS5A01G022600 chr7A 87.250 400 48 3 3554 3952 521341187 521340790 1.670000e-123 453.0
19 TraesCS5A01G022600 chr7A 97.436 156 4 0 3098 3253 46210359 46210204 2.340000e-67 267.0
20 TraesCS5A01G022600 chr7A 95.918 147 6 0 3099 3245 46215149 46215003 5.100000e-59 239.0
21 TraesCS5A01G022600 chr7A 79.646 113 20 1 2151 2263 57701762 57701653 1.180000e-10 78.7
22 TraesCS5A01G022600 chr5B 82.393 727 86 25 1032 1733 18664628 18665337 2.630000e-166 595.0
23 TraesCS5A01G022600 chr5B 82.496 697 89 18 1050 1733 18775845 18776521 7.360000e-162 580.0
24 TraesCS5A01G022600 chr5B 90.380 395 38 0 3558 3952 103330793 103330399 1.630000e-143 520.0
25 TraesCS5A01G022600 chr5B 96.000 150 6 0 3098 3247 103326417 103326268 1.100000e-60 244.0
26 TraesCS5A01G022600 chr7B 90.380 395 38 0 3558 3952 744724957 744725351 1.630000e-143 520.0
27 TraesCS5A01G022600 chr7B 87.342 395 50 0 3558 3952 745929 746323 1.670000e-123 453.0
28 TraesCS5A01G022600 chr7B 95.294 170 7 1 3100 3268 677353061 677352892 6.510000e-68 268.0
29 TraesCS5A01G022600 chr7B 94.771 153 7 1 3098 3249 677348223 677348071 1.840000e-58 237.0
30 TraesCS5A01G022600 chr3D 89.873 395 40 0 3558 3952 528961404 528961798 3.520000e-140 508.0
31 TraesCS5A01G022600 chr1B 88.889 396 42 2 3558 3952 561631142 561630748 1.650000e-133 486.0
32 TraesCS5A01G022600 chr1B 88.636 44 5 0 2040 2083 24159577 24159534 2.000000e-03 54.7
33 TraesCS5A01G022600 chr3A 88.325 394 46 0 3559 3952 621149358 621149751 1.290000e-129 473.0
34 TraesCS5A01G022600 chr3A 79.755 163 33 0 2152 2314 747565886 747565724 6.940000e-23 119.0
35 TraesCS5A01G022600 chr6B 98.026 152 3 0 3100 3251 687739763 687739612 8.420000e-67 265.0
36 TraesCS5A01G022600 chr6B 98.000 150 3 0 3098 3247 687737293 687737144 1.090000e-65 261.0
37 TraesCS5A01G022600 chr6B 82.424 165 27 2 2151 2314 704954990 704954827 4.120000e-30 143.0
38 TraesCS5A01G022600 chr6B 78.947 114 18 5 2172 2283 40149589 40149480 5.480000e-09 73.1
39 TraesCS5A01G022600 chr4B 95.270 148 7 0 3098 3245 458942398 458942251 6.600000e-58 235.0
40 TraesCS5A01G022600 chr3B 80.000 135 27 0 2151 2285 715145261 715145395 2.510000e-17 100.0
41 TraesCS5A01G022600 chr2D 83.186 113 15 4 2189 2300 605437790 605437681 2.510000e-17 100.0
42 TraesCS5A01G022600 chrUn 91.379 58 2 3 132 187 287771879 287771823 4.230000e-10 76.8
43 TraesCS5A01G022600 chrUn 91.379 58 2 3 132 187 297961004 297960948 4.230000e-10 76.8
44 TraesCS5A01G022600 chr4A 91.837 49 4 0 2268 2316 673787692 673787740 7.090000e-08 69.4
45 TraesCS5A01G022600 chr7D 87.500 48 4 2 43 90 5409992 5409947 2.000000e-03 54.7


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 TraesCS5A01G022600 chr5A 18575050 18579001 3951 False 3390.0 6035 100.000000 1 3952 2 chr5A.!!$F3 3951
1 TraesCS5A01G022600 chr5A 18394994 18395690 696 False 606.0 606 82.700000 1037 1733 1 chr5A.!!$F1 696
2 TraesCS5A01G022600 chr5A 18571976 18572651 675 True 568.0 568 82.014000 1046 1733 1 chr5A.!!$R1 687
3 TraesCS5A01G022600 chr5D 26784119 26787440 3321 False 661.0 1759 91.784667 46 3099 6 chr5D.!!$F1 3053
4 TraesCS5A01G022600 chr5D 26507274 26507944 670 True 608.0 608 83.333000 1063 1733 1 chr5D.!!$R2 670
5 TraesCS5A01G022600 chr5D 26522656 26523348 692 True 555.0 555 81.616000 1035 1733 1 chr5D.!!$R3 698
6 TraesCS5A01G022600 chr5D 26681888 26682536 648 True 302.5 490 84.631500 1046 1733 2 chr5D.!!$R4 687
7 TraesCS5A01G022600 chr7A 46214398 46215149 751 True 451.5 664 96.330000 3099 3952 2 chr7A.!!$R4 853
8 TraesCS5A01G022600 chr5B 18664628 18665337 709 False 595.0 595 82.393000 1032 1733 1 chr5B.!!$F1 701
9 TraesCS5A01G022600 chr5B 18775845 18776521 676 False 580.0 580 82.496000 1050 1733 1 chr5B.!!$F2 683
10 TraesCS5A01G022600 chr5B 103326268 103330793 4525 True 382.0 520 93.190000 3098 3952 2 chr5B.!!$R1 854
11 TraesCS5A01G022600 chr6B 687737144 687739763 2619 True 263.0 265 98.013000 3098 3251 2 chr6B.!!$R3 153

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
858 1046 1.649815 GTCGATCGCTCTCGGACAT 59.350 57.895 11.09 0.0 39.13 3.06 F
1462 1680 0.179181 GTACGTCTCATCGCCGACAA 60.179 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2699 0.252197 GATGGTCGGTTAGGCTGGTT 59.748 55.0 0.0 0.0 0.0 3.67 R
3044 3505 0.032515 CCAGGGGGTTTTGGGGTATC 60.033 60.0 0.0 0.0 0.0 2.24 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
94 96 9.701355 AAAATGCGAACACTTTTTAAAAATGAG 57.299 25.926 13.55 5.33 0.00 2.90
97 99 8.467402 TGCGAACACTTTTTAAAAATGAGAAA 57.533 26.923 13.55 0.00 0.00 2.52
168 196 6.425417 GGAACAAAGTTTGAAACCTGACAAAA 59.575 34.615 22.23 0.00 37.66 2.44
179 207 7.158021 TGAAACCTGACAAAATTTTGAAGTGT 58.842 30.769 32.20 22.59 40.55 3.55
184 212 6.589523 CCTGACAAAATTTTGAAGTGTGAACA 59.410 34.615 32.20 16.61 40.55 3.18
261 290 8.726988 TGTAAGAAAAATGTTAGTGGCATCTAC 58.273 33.333 0.00 0.00 0.00 2.59
270 299 5.186198 GTTAGTGGCATCTACAAAGGTCAT 58.814 41.667 0.00 0.00 0.00 3.06
304 333 3.266541 TGTGCGTGAAATGTGTGATTC 57.733 42.857 0.00 0.00 0.00 2.52
394 423 7.293745 TGTGTTTGCAACATTTACAAAAAGTG 58.706 30.769 0.00 0.00 44.35 3.16
397 426 5.462034 TGCAACATTTACAAAAAGTGTGC 57.538 34.783 0.00 0.00 41.89 4.57
401 430 6.420588 CAACATTTACAAAAAGTGTGCATGG 58.579 36.000 0.00 0.00 41.89 3.66
520 695 2.911120 TGAAAAATGTCGCAAGCGTAC 58.089 42.857 14.57 11.37 40.74 3.67
530 705 3.004171 TCGCAAGCGTACCAAAATATGT 58.996 40.909 14.57 0.00 40.74 2.29
560 735 6.079763 GTGTGTGCTAGAAATGTACATTGTG 58.920 40.000 21.46 12.44 33.11 3.33
619 795 9.474920 AAATCGATTAAAATCAGCAAAGAAACA 57.525 25.926 11.83 0.00 35.11 2.83
669 845 6.877611 ACAAATGAAAACCGAGAGTACAAT 57.122 33.333 0.00 0.00 0.00 2.71
672 848 9.010029 ACAAATGAAAACCGAGAGTACAATAAT 57.990 29.630 0.00 0.00 0.00 1.28
673 849 9.840427 CAAATGAAAACCGAGAGTACAATAATT 57.160 29.630 0.00 0.00 0.00 1.40
704 880 9.660180 TTTAAAAATAAAGCACCAGTGAAAAGT 57.340 25.926 0.99 0.00 0.00 2.66
712 888 8.685838 AAAGCACCAGTGAAAAGTAAAGTATA 57.314 30.769 0.99 0.00 0.00 1.47
777 964 9.516314 AAGACCAAATAAAACGAAAAAGAGAAG 57.484 29.630 0.00 0.00 0.00 2.85
856 1044 2.328639 GGTCGATCGCTCTCGGAC 59.671 66.667 11.09 0.82 39.13 4.79
858 1046 1.649815 GTCGATCGCTCTCGGACAT 59.350 57.895 11.09 0.00 39.13 3.06
902 1090 3.096791 GACTCGTCGACCTACCCG 58.903 66.667 10.58 0.00 0.00 5.28
922 1110 4.814294 GTGCGTGGACCGGGCTAG 62.814 72.222 7.57 0.00 36.94 3.42
925 1113 4.208686 CGTGGACCGGGCTAGCTC 62.209 72.222 15.72 10.26 0.00 4.09
926 1114 3.851128 GTGGACCGGGCTAGCTCC 61.851 72.222 15.72 13.97 0.00 4.70
933 1121 4.273257 GGGCTAGCTCCGAGTCGC 62.273 72.222 15.72 0.00 0.00 5.19
934 1122 4.615834 GGCTAGCTCCGAGTCGCG 62.616 72.222 15.72 0.00 40.47 5.87
935 1123 3.574445 GCTAGCTCCGAGTCGCGA 61.574 66.667 3.71 3.71 44.57 5.87
936 1124 2.325166 CTAGCTCCGAGTCGCGAC 59.675 66.667 31.30 31.30 44.57 5.19
937 1125 2.435410 TAGCTCCGAGTCGCGACA 60.435 61.111 37.85 18.65 44.57 4.35
938 1126 2.368131 CTAGCTCCGAGTCGCGACAG 62.368 65.000 37.85 29.49 44.57 3.51
939 1127 4.838486 GCTCCGAGTCGCGACAGG 62.838 72.222 37.85 35.58 44.57 4.00
940 1128 4.838486 CTCCGAGTCGCGACAGGC 62.838 72.222 37.85 25.20 44.57 4.85
946 1134 4.681978 GTCGCGACAGGCCACCTT 62.682 66.667 33.09 0.00 38.94 3.50
947 1135 3.936203 TCGCGACAGGCCACCTTT 61.936 61.111 3.71 0.00 38.94 3.11
948 1136 2.047655 CGCGACAGGCCACCTTTA 60.048 61.111 5.01 0.00 38.94 1.85
949 1137 2.100631 CGCGACAGGCCACCTTTAG 61.101 63.158 5.01 0.00 38.94 1.85
965 1153 8.979534 GCCACCTTTAGTAGCCTATTATATACT 58.020 37.037 0.00 0.00 33.27 2.12
1085 1273 3.695606 TGGTGCTCGCTCTCCCAC 61.696 66.667 0.00 0.00 0.00 4.61
1187 1387 1.162698 CTCTACTCCGTCGTTGTCCA 58.837 55.000 0.00 0.00 0.00 4.02
1216 1425 1.901948 TGTCGAGGCCACTTCGTCT 60.902 57.895 5.01 0.00 0.00 4.18
1217 1426 0.607217 TGTCGAGGCCACTTCGTCTA 60.607 55.000 5.01 0.00 0.00 2.59
1367 1582 3.591254 GAAGGAGCGCGACCTTGGT 62.591 63.158 33.89 18.71 46.14 3.67
1380 1595 1.780309 ACCTTGGTGAGTCCCATTTCA 59.220 47.619 1.70 0.00 33.60 2.69
1462 1680 0.179181 GTACGTCTCATCGCCGACAA 60.179 55.000 0.00 0.00 0.00 3.18
1646 1875 3.140225 GATCGGAGCCACGTCCTCC 62.140 68.421 17.84 17.84 44.35 4.30
1770 1999 1.541588 GCAGGGTTTCATGTTCAGGTC 59.458 52.381 0.00 0.00 0.00 3.85
1772 2001 1.165270 GGGTTTCATGTTCAGGTCCG 58.835 55.000 0.00 0.00 0.00 4.79
1777 2169 2.967599 TCATGTTCAGGTCCGATCTG 57.032 50.000 1.83 1.83 0.00 2.90
1811 2203 6.090358 CGTTGCTTTCGGTTATTTTCTCTAGA 59.910 38.462 0.00 0.00 0.00 2.43
1837 2229 1.042003 ACCACATTGCAAGGCACACA 61.042 50.000 11.69 0.00 38.71 3.72
1851 2243 1.481240 CACACAGCGGATATCACGAG 58.519 55.000 15.11 9.88 0.00 4.18
1853 2245 2.032924 CACACAGCGGATATCACGAGTA 59.967 50.000 15.11 0.00 0.00 2.59
1855 2247 2.548480 CACAGCGGATATCACGAGTAGA 59.452 50.000 15.11 0.00 0.00 2.59
1860 2252 4.278669 AGCGGATATCACGAGTAGATTGTT 59.721 41.667 15.11 0.00 0.00 2.83
1868 2260 2.751259 ACGAGTAGATTGTTGCTACCGA 59.249 45.455 1.78 0.00 39.17 4.69
1869 2261 3.192001 ACGAGTAGATTGTTGCTACCGAA 59.808 43.478 1.78 0.00 39.17 4.30
1870 2262 4.171005 CGAGTAGATTGTTGCTACCGAAA 58.829 43.478 0.00 0.00 39.17 3.46
1889 2281 0.988832 ATTCCTACGCCCAACCTTCA 59.011 50.000 0.00 0.00 0.00 3.02
1903 2295 4.178540 CAACCTTCATACGACGGTACATT 58.821 43.478 0.00 0.00 42.73 2.71
1904 2296 4.460948 ACCTTCATACGACGGTACATTT 57.539 40.909 0.00 0.00 41.79 2.32
1905 2297 4.824289 ACCTTCATACGACGGTACATTTT 58.176 39.130 0.00 0.00 41.79 1.82
1906 2298 5.240121 ACCTTCATACGACGGTACATTTTT 58.760 37.500 0.00 0.00 41.79 1.94
1946 2338 8.029522 ACATACTATATACAATGACCGCTTCAG 58.970 37.037 6.58 0.00 37.77 3.02
1952 2344 4.071961 ACAATGACCGCTTCAGCATATA 57.928 40.909 0.00 0.00 42.21 0.86
1953 2345 4.645535 ACAATGACCGCTTCAGCATATAT 58.354 39.130 0.00 0.00 42.21 0.86
1957 2349 7.391554 ACAATGACCGCTTCAGCATATATATTT 59.608 33.333 0.00 0.00 42.21 1.40
1960 2352 7.105588 TGACCGCTTCAGCATATATATTTCAT 58.894 34.615 0.00 0.00 42.21 2.57
1961 2353 7.064966 TGACCGCTTCAGCATATATATTTCATG 59.935 37.037 0.00 0.00 42.21 3.07
1964 2356 8.239314 CCGCTTCAGCATATATATTTCATGTTT 58.761 33.333 0.00 0.00 42.21 2.83
2061 2453 9.410556 TGTTTAGAAAGTACTCCATACGTAAAC 57.589 33.333 0.00 5.23 38.97 2.01
2062 2454 9.631452 GTTTAGAAAGTACTCCATACGTAAACT 57.369 33.333 0.00 0.00 38.97 2.66
2074 2466 9.275231 CTCCATACGTAAACTAATATAAGAGCG 57.725 37.037 0.00 0.00 0.00 5.03
2075 2467 8.786898 TCCATACGTAAACTAATATAAGAGCGT 58.213 33.333 0.00 0.00 0.00 5.07
2076 2468 9.403110 CCATACGTAAACTAATATAAGAGCGTT 57.597 33.333 0.00 0.00 0.00 4.84
2080 2472 9.787532 ACGTAAACTAATATAAGAGCGTTTACA 57.212 29.630 17.54 0.00 43.00 2.41
2120 2512 3.402628 GAGGTAGTCTCTTTGTTGCCA 57.597 47.619 0.00 0.00 39.38 4.92
2127 2519 3.823304 AGTCTCTTTGTTGCCAATCCTTC 59.177 43.478 0.00 0.00 0.00 3.46
2129 2521 4.074970 TCTCTTTGTTGCCAATCCTTCTC 58.925 43.478 0.00 0.00 0.00 2.87
2136 2528 1.005924 TGCCAATCCTTCTCCCCTTTC 59.994 52.381 0.00 0.00 0.00 2.62
2137 2529 1.005924 GCCAATCCTTCTCCCCTTTCA 59.994 52.381 0.00 0.00 0.00 2.69
2197 2589 5.373222 AGCTTTGGAGTGTGTTATGTTACA 58.627 37.500 0.00 0.00 0.00 2.41
2199 2591 6.320164 AGCTTTGGAGTGTGTTATGTTACAAA 59.680 34.615 0.00 0.00 0.00 2.83
2218 2612 8.561212 GTTACAAAAACATACTATGTCACCACA 58.439 33.333 2.05 0.00 44.07 4.17
2219 2613 7.575414 ACAAAAACATACTATGTCACCACAA 57.425 32.000 2.05 0.00 44.07 3.33
2230 2624 2.238646 TGTCACCACAAACACCTCTCTT 59.761 45.455 0.00 0.00 0.00 2.85
2242 2636 7.873505 ACAAACACCTCTCTTCTCATTAACTAC 59.126 37.037 0.00 0.00 0.00 2.73
2244 2638 8.880991 AACACCTCTCTTCTCATTAACTACTA 57.119 34.615 0.00 0.00 0.00 1.82
2259 2653 8.840321 CATTAACTACTAGCCACATAAGCAAAT 58.160 33.333 0.00 0.00 0.00 2.32
2277 2671 7.759489 AGCAAATTTGTCTAGGAATGTGTTA 57.241 32.000 19.03 0.00 0.00 2.41
2278 2672 8.353423 AGCAAATTTGTCTAGGAATGTGTTAT 57.647 30.769 19.03 0.00 0.00 1.89
2279 2673 8.246180 AGCAAATTTGTCTAGGAATGTGTTATG 58.754 33.333 19.03 0.00 0.00 1.90
2310 2704 7.907389 TGCTATGTTAATCCCTCTATAACCAG 58.093 38.462 0.00 0.00 0.00 4.00
2313 2707 5.224441 TGTTAATCCCTCTATAACCAGCCT 58.776 41.667 0.00 0.00 0.00 4.58
2332 2728 1.138266 CTAACCGACCATCACCCGATT 59.862 52.381 0.00 0.00 0.00 3.34
2341 2737 2.436417 CATCACCCGATTGAACTTGGT 58.564 47.619 0.00 0.00 0.00 3.67
2357 2753 5.505173 ACTTGGTGAGTTCAGTCAAATTG 57.495 39.130 0.00 0.00 33.92 2.32
2358 2754 4.339247 ACTTGGTGAGTTCAGTCAAATTGG 59.661 41.667 0.00 0.00 33.92 3.16
2359 2755 3.897239 TGGTGAGTTCAGTCAAATTGGT 58.103 40.909 0.00 0.00 0.00 3.67
2360 2756 3.882888 TGGTGAGTTCAGTCAAATTGGTC 59.117 43.478 0.00 0.00 0.00 4.02
2361 2757 3.058914 GGTGAGTTCAGTCAAATTGGTCG 60.059 47.826 0.00 0.00 0.00 4.79
2362 2758 3.058914 GTGAGTTCAGTCAAATTGGTCGG 60.059 47.826 0.00 0.00 0.00 4.79
2363 2759 1.880027 AGTTCAGTCAAATTGGTCGGC 59.120 47.619 0.00 0.00 0.00 5.54
2364 2760 1.880027 GTTCAGTCAAATTGGTCGGCT 59.120 47.619 0.00 0.00 0.00 5.52
2365 2761 1.808411 TCAGTCAAATTGGTCGGCTC 58.192 50.000 0.00 0.00 0.00 4.70
2366 2762 1.071542 TCAGTCAAATTGGTCGGCTCA 59.928 47.619 0.00 0.00 0.00 4.26
2367 2763 1.879380 CAGTCAAATTGGTCGGCTCAA 59.121 47.619 0.00 0.00 0.00 3.02
2368 2764 2.293122 CAGTCAAATTGGTCGGCTCAAA 59.707 45.455 0.00 0.00 0.00 2.69
2369 2765 2.955660 AGTCAAATTGGTCGGCTCAAAA 59.044 40.909 0.00 0.00 0.00 2.44
2370 2766 3.383185 AGTCAAATTGGTCGGCTCAAAAA 59.617 39.130 0.00 0.00 0.00 1.94
2394 2790 6.625873 AGAAAGTTCAGTCAAATTCCAGTC 57.374 37.500 0.00 0.00 0.00 3.51
2406 2802 8.157476 AGTCAAATTCCAGTCACTATGTAACTT 58.843 33.333 0.00 0.00 0.00 2.66
2465 2863 1.269012 AATGTTCAATGTGCCCCCTG 58.731 50.000 0.00 0.00 0.00 4.45
2468 2867 0.039035 GTTCAATGTGCCCCCTGGTA 59.961 55.000 0.00 0.00 0.00 3.25
2471 2870 0.331278 CAATGTGCCCCCTGGTAGAA 59.669 55.000 0.00 0.00 0.00 2.10
2481 2880 2.556782 CCCCTGGTAGAAACCCTTTTCC 60.557 54.545 0.00 0.00 46.16 3.13
2526 2925 6.266558 TGTTTAGTATGAAACCCATGCAAGTT 59.733 34.615 0.00 0.00 39.89 2.66
2540 2939 7.501892 ACCCATGCAAGTTTTTCATGTTAATTT 59.498 29.630 0.00 0.00 36.70 1.82
2591 2990 8.354711 TGTATGTAAATAGGGCTGAGATAGAG 57.645 38.462 0.00 0.00 0.00 2.43
2600 2999 1.402720 GCTGAGATAGAGGCAGATCGC 60.403 57.143 0.00 1.55 41.28 4.58
2735 3134 1.879575 TTACTCATCCCCACCCTGAG 58.120 55.000 0.00 0.00 41.69 3.35
2886 3346 2.562298 TGGGTGAATTCCATGCAAAGTC 59.438 45.455 2.27 0.00 0.00 3.01
2895 3355 1.352114 CATGCAAAGTCGGGCAAATG 58.648 50.000 0.00 0.00 44.20 2.32
2907 3367 7.648039 AGTCGGGCAAATGGTATTTTAATTA 57.352 32.000 0.00 0.00 0.00 1.40
2908 3368 8.245195 AGTCGGGCAAATGGTATTTTAATTAT 57.755 30.769 0.00 0.00 0.00 1.28
2970 3430 0.972883 ATGGCCTTAGATCTCTCCGC 59.027 55.000 3.32 0.00 0.00 5.54
3032 3493 9.186837 CCAGTAAGATTAACTCTCCTAGTAACA 57.813 37.037 0.00 0.00 37.50 2.41
3044 3505 8.578151 ACTCTCCTAGTAACAAAGACTAAACTG 58.422 37.037 0.00 0.00 36.36 3.16
3102 3563 5.940470 GTGGAACTTGAGGATTGTAGATGTT 59.060 40.000 0.00 0.00 0.00 2.71
3134 3595 4.765813 TTGTTAGGGTATAGGAGGTTGC 57.234 45.455 0.00 0.00 0.00 4.17
3251 3712 4.971282 TCCAATCTCTCTCTCTCTCTCTCT 59.029 45.833 0.00 0.00 0.00 3.10
3252 3713 5.070981 TCCAATCTCTCTCTCTCTCTCTCTC 59.929 48.000 0.00 0.00 0.00 3.20
3254 3715 6.222389 CAATCTCTCTCTCTCTCTCTCTCTC 58.778 48.000 0.00 0.00 0.00 3.20
3255 3716 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3256 3717 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3257 3718 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3258 3719 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3260 3721 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3261 3722 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3262 3723 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3263 3724 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3264 3725 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3265 3726 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3266 3727 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3267 3728 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3578 4039 2.357517 GCGTATAGCTGGCGCCAT 60.358 61.111 32.87 19.78 44.67 4.40
3601 4062 1.076533 CTACGTCGATGGCACGCTTT 61.077 55.000 9.90 0.00 41.10 3.51
3677 4138 1.004277 GGAGTATGCCACCTGGTTTCA 59.996 52.381 0.00 0.00 37.57 2.69
3709 4170 1.856259 TCATCCTCAGCTACCTCCTCT 59.144 52.381 0.00 0.00 0.00 3.69
3899 4395 3.118454 CAAGATCCGCGCCAACGT 61.118 61.111 0.00 0.00 42.83 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 9.601217 TTTAAAAATGTCTCGGGATTTCAAAAA 57.399 25.926 0.00 0.00 0.00 1.94
57 58 7.623268 AGTGTTCGCATTTTAAAAATGTCTC 57.377 32.000 4.44 0.00 0.00 3.36
149 177 8.614469 TCAAAATTTTGTCAGGTTTCAAACTT 57.386 26.923 25.98 0.00 39.18 2.66
205 233 5.216566 TCAGGTTTCATAATTTCTTCGCG 57.783 39.130 0.00 0.00 0.00 5.87
206 234 6.378582 TGTTCAGGTTTCATAATTTCTTCGC 58.621 36.000 0.00 0.00 0.00 4.70
250 279 3.264193 TCATGACCTTTGTAGATGCCACT 59.736 43.478 0.00 0.00 0.00 4.00
254 283 5.886960 AAACTCATGACCTTTGTAGATGC 57.113 39.130 0.00 0.00 0.00 3.91
313 342 9.659830 GTTACTGTTTCTTTTGAATGTACGATT 57.340 29.630 0.00 0.00 38.37 3.34
317 346 9.783256 AAGTGTTACTGTTTCTTTTGAATGTAC 57.217 29.630 0.00 0.00 38.37 2.90
334 363 8.686334 ACTCATGAACATTTTTGAAGTGTTACT 58.314 29.630 0.00 0.00 36.30 2.24
520 695 5.927689 AGCACACACATGAAACATATTTTGG 59.072 36.000 0.00 0.00 0.00 3.28
530 705 6.484977 TGTACATTTCTAGCACACACATGAAA 59.515 34.615 0.00 0.00 0.00 2.69
596 772 8.864069 TTTGTTTCTTTGCTGATTTTAATCGA 57.136 26.923 0.00 0.00 38.26 3.59
643 819 6.721321 TGTACTCTCGGTTTTCATTTGTTTC 58.279 36.000 0.00 0.00 0.00 2.78
678 854 9.660180 ACTTTTCACTGGTGCTTTATTTTTAAA 57.340 25.926 0.00 0.00 0.00 1.52
681 857 9.660180 TTTACTTTTCACTGGTGCTTTATTTTT 57.340 25.926 0.00 0.00 0.00 1.94
682 858 9.313118 CTTTACTTTTCACTGGTGCTTTATTTT 57.687 29.630 0.00 0.00 0.00 1.82
686 862 8.685838 ATACTTTACTTTTCACTGGTGCTTTA 57.314 30.769 0.00 0.00 0.00 1.85
712 888 4.820173 CAGGGTTTTCTTCTTACCTTCGTT 59.180 41.667 0.00 0.00 32.46 3.85
754 941 9.863845 TTTCTTCTCTTTTTCGTTTTATTTGGT 57.136 25.926 0.00 0.00 0.00 3.67
838 1026 2.124860 TCCGAGAGCGATCGACCA 60.125 61.111 21.57 0.00 45.56 4.02
839 1027 1.787057 ATGTCCGAGAGCGATCGACC 61.787 60.000 21.57 9.26 45.56 4.79
840 1028 0.658829 CATGTCCGAGAGCGATCGAC 60.659 60.000 21.57 11.92 45.56 4.20
916 1104 4.273257 GCGACTCGGAGCTAGCCC 62.273 72.222 12.13 11.54 0.00 5.19
917 1105 4.615834 CGCGACTCGGAGCTAGCC 62.616 72.222 12.13 2.59 33.78 3.93
918 1106 3.574445 TCGCGACTCGGAGCTAGC 61.574 66.667 3.71 6.62 39.05 3.42
919 1107 2.325166 GTCGCGACTCGGAGCTAG 59.675 66.667 31.12 0.00 39.05 3.42
921 1109 3.805307 CTGTCGCGACTCGGAGCT 61.805 66.667 36.27 0.00 39.05 4.09
922 1110 4.838486 CCTGTCGCGACTCGGAGC 62.838 72.222 36.27 12.16 39.05 4.70
923 1111 4.838486 GCCTGTCGCGACTCGGAG 62.838 72.222 35.76 26.75 39.05 4.63
929 1117 2.775032 TAAAGGTGGCCTGTCGCGAC 62.775 60.000 31.66 31.66 44.87 5.19
930 1118 2.501223 CTAAAGGTGGCCTGTCGCGA 62.501 60.000 3.71 3.71 38.94 5.87
931 1119 2.047655 TAAAGGTGGCCTGTCGCG 60.048 61.111 3.32 0.00 38.94 5.87
932 1120 0.248289 TACTAAAGGTGGCCTGTCGC 59.752 55.000 3.32 0.00 32.13 5.19
933 1121 1.739371 GCTACTAAAGGTGGCCTGTCG 60.739 57.143 3.32 0.00 45.00 4.35
934 1122 2.025589 GCTACTAAAGGTGGCCTGTC 57.974 55.000 3.32 0.00 45.00 3.51
1367 1582 1.348064 ACTCGGTGAAATGGGACTCA 58.652 50.000 0.00 0.00 0.00 3.41
1380 1595 2.299013 TGTAGATGTGCTTCAACTCGGT 59.701 45.455 0.00 0.00 31.70 4.69
1462 1680 1.677300 TTGGCGGCGTGGATGATTT 60.677 52.632 9.37 0.00 0.00 2.17
1646 1875 0.751643 CTAAAATCCTGCCACCGGGG 60.752 60.000 6.32 0.00 38.11 5.73
1748 1977 0.523072 CTGAACATGAAACCCTGCGG 59.477 55.000 0.00 0.00 0.00 5.69
1749 1978 0.523072 CCTGAACATGAAACCCTGCG 59.477 55.000 0.00 0.00 0.00 5.18
1750 1979 1.541588 GACCTGAACATGAAACCCTGC 59.458 52.381 0.00 0.00 0.00 4.85
1761 1990 0.526211 CGTCAGATCGGACCTGAACA 59.474 55.000 18.61 0.00 41.72 3.18
1765 1994 1.062685 CGTCGTCAGATCGGACCTG 59.937 63.158 18.61 7.37 34.24 4.00
1770 1999 2.944557 CGCACGTCGTCAGATCGG 60.945 66.667 0.00 0.00 0.00 4.18
1793 2185 5.820947 GCCCAATCTAGAGAAAATAACCGAA 59.179 40.000 0.00 0.00 0.00 4.30
1811 2203 0.322322 CTTGCAATGTGGTGCCCAAT 59.678 50.000 0.00 0.00 44.26 3.16
1837 2229 3.821600 ACAATCTACTCGTGATATCCGCT 59.178 43.478 0.00 0.00 0.00 5.52
1851 2243 5.585047 AGGAATTTCGGTAGCAACAATCTAC 59.415 40.000 0.00 0.00 36.55 2.59
1853 2245 4.589908 AGGAATTTCGGTAGCAACAATCT 58.410 39.130 0.00 0.00 0.00 2.40
1855 2247 4.331717 CGTAGGAATTTCGGTAGCAACAAT 59.668 41.667 0.00 0.00 0.00 2.71
1860 2252 1.472026 GGCGTAGGAATTTCGGTAGCA 60.472 52.381 0.00 0.00 0.00 3.49
1868 2260 2.224917 TGAAGGTTGGGCGTAGGAATTT 60.225 45.455 0.00 0.00 0.00 1.82
1869 2261 1.353022 TGAAGGTTGGGCGTAGGAATT 59.647 47.619 0.00 0.00 0.00 2.17
1870 2262 0.988832 TGAAGGTTGGGCGTAGGAAT 59.011 50.000 0.00 0.00 0.00 3.01
1913 2305 9.770503 GGTCATTGTATATAGTATGTACTGTCG 57.229 37.037 15.56 5.00 37.10 4.35
1914 2306 9.770503 CGGTCATTGTATATAGTATGTACTGTC 57.229 37.037 15.56 6.74 37.10 3.51
1915 2307 8.242053 GCGGTCATTGTATATAGTATGTACTGT 58.758 37.037 15.56 0.00 37.10 3.55
1916 2308 8.459635 AGCGGTCATTGTATATAGTATGTACTG 58.540 37.037 15.56 8.55 37.10 2.74
1917 2309 8.577048 AGCGGTCATTGTATATAGTATGTACT 57.423 34.615 15.56 0.00 40.24 2.73
1918 2310 9.286946 GAAGCGGTCATTGTATATAGTATGTAC 57.713 37.037 9.49 9.49 0.00 2.90
1919 2311 9.016438 TGAAGCGGTCATTGTATATAGTATGTA 57.984 33.333 0.00 0.00 0.00 2.29
1920 2312 7.892609 TGAAGCGGTCATTGTATATAGTATGT 58.107 34.615 0.00 0.00 0.00 2.29
1921 2313 7.009631 GCTGAAGCGGTCATTGTATATAGTATG 59.990 40.741 0.00 0.00 35.07 2.39
1922 2314 7.036220 GCTGAAGCGGTCATTGTATATAGTAT 58.964 38.462 0.00 0.00 35.07 2.12
1923 2315 6.015772 TGCTGAAGCGGTCATTGTATATAGTA 60.016 38.462 0.00 0.00 45.83 1.82
1924 2316 5.221441 TGCTGAAGCGGTCATTGTATATAGT 60.221 40.000 0.00 0.00 45.83 2.12
1925 2317 5.230182 TGCTGAAGCGGTCATTGTATATAG 58.770 41.667 0.00 0.00 45.83 1.31
1926 2318 5.208463 TGCTGAAGCGGTCATTGTATATA 57.792 39.130 0.00 0.00 45.83 0.86
1927 2319 4.071961 TGCTGAAGCGGTCATTGTATAT 57.928 40.909 0.00 0.00 45.83 0.86
1928 2320 3.535280 TGCTGAAGCGGTCATTGTATA 57.465 42.857 0.00 0.00 45.83 1.47
1929 2321 2.401583 TGCTGAAGCGGTCATTGTAT 57.598 45.000 0.00 0.00 45.83 2.29
1930 2322 2.401583 ATGCTGAAGCGGTCATTGTA 57.598 45.000 0.00 0.00 45.83 2.41
1931 2323 2.401583 TATGCTGAAGCGGTCATTGT 57.598 45.000 0.00 0.00 45.83 2.71
1932 2324 6.915544 ATATATATGCTGAAGCGGTCATTG 57.084 37.500 0.00 0.00 45.83 2.82
1936 2328 6.968131 TGAAATATATATGCTGAAGCGGTC 57.032 37.500 0.00 0.00 45.83 4.79
1975 2367 6.399204 ACCAGTACGAACGAACAATTATTC 57.601 37.500 0.14 0.00 0.00 1.75
1976 2368 6.790285 AACCAGTACGAACGAACAATTATT 57.210 33.333 0.14 0.00 0.00 1.40
1979 2371 6.790285 AATAACCAGTACGAACGAACAATT 57.210 33.333 0.14 0.00 0.00 2.32
1981 2373 5.523188 ACAAATAACCAGTACGAACGAACAA 59.477 36.000 0.14 0.00 0.00 2.83
1982 2374 5.049167 ACAAATAACCAGTACGAACGAACA 58.951 37.500 0.14 0.00 0.00 3.18
1983 2375 5.050837 ACACAAATAACCAGTACGAACGAAC 60.051 40.000 0.14 0.00 0.00 3.95
1984 2376 5.049167 ACACAAATAACCAGTACGAACGAA 58.951 37.500 0.14 0.00 0.00 3.85
1985 2377 4.619973 ACACAAATAACCAGTACGAACGA 58.380 39.130 0.14 0.00 0.00 3.85
1986 2378 4.977741 ACACAAATAACCAGTACGAACG 57.022 40.909 0.00 0.00 0.00 3.95
1991 2383 7.707774 AATGCAAAACACAAATAACCAGTAC 57.292 32.000 0.00 0.00 0.00 2.73
2048 2440 9.275231 CGCTCTTATATTAGTTTACGTATGGAG 57.725 37.037 0.00 0.00 0.00 3.86
2049 2441 8.786898 ACGCTCTTATATTAGTTTACGTATGGA 58.213 33.333 0.00 0.00 0.00 3.41
2050 2442 8.961294 ACGCTCTTATATTAGTTTACGTATGG 57.039 34.615 0.00 0.00 0.00 2.74
2068 2460 9.269453 ACTAATACTTTCTTTGTAAACGCTCTT 57.731 29.630 0.00 0.00 0.00 2.85
2069 2461 8.709646 CACTAATACTTTCTTTGTAAACGCTCT 58.290 33.333 0.00 0.00 0.00 4.09
2070 2462 8.493547 ACACTAATACTTTCTTTGTAAACGCTC 58.506 33.333 0.00 0.00 0.00 5.03
2071 2463 8.280497 CACACTAATACTTTCTTTGTAAACGCT 58.720 33.333 0.00 0.00 0.00 5.07
2072 2464 8.066000 ACACACTAATACTTTCTTTGTAAACGC 58.934 33.333 0.00 0.00 0.00 4.84
2078 2470 8.648693 ACCTCTACACACTAATACTTTCTTTGT 58.351 33.333 0.00 0.00 0.00 2.83
2081 2473 9.531158 ACTACCTCTACACACTAATACTTTCTT 57.469 33.333 0.00 0.00 0.00 2.52
2082 2474 9.176460 GACTACCTCTACACACTAATACTTTCT 57.824 37.037 0.00 0.00 0.00 2.52
2083 2475 9.176460 AGACTACCTCTACACACTAATACTTTC 57.824 37.037 0.00 0.00 0.00 2.62
2084 2476 9.176460 GAGACTACCTCTACACACTAATACTTT 57.824 37.037 0.00 0.00 38.86 2.66
2085 2477 8.735692 GAGACTACCTCTACACACTAATACTT 57.264 38.462 0.00 0.00 38.86 2.24
2120 2512 8.685257 AATTATTTTGAAAGGGGAGAAGGATT 57.315 30.769 0.00 0.00 0.00 3.01
2165 2557 7.582667 AACACACTCCAAAGCTAAATAAGTT 57.417 32.000 0.00 0.00 0.00 2.66
2197 2589 7.918562 GTGTTTGTGGTGACATAGTATGTTTTT 59.081 33.333 16.80 0.00 45.03 1.94
2199 2591 6.016610 GGTGTTTGTGGTGACATAGTATGTTT 60.017 38.462 16.80 0.00 45.03 2.83
2210 2602 2.622064 AGAGAGGTGTTTGTGGTGAC 57.378 50.000 0.00 0.00 0.00 3.67
2212 2604 3.134458 GAGAAGAGAGGTGTTTGTGGTG 58.866 50.000 0.00 0.00 0.00 4.17
2213 2605 2.771943 TGAGAAGAGAGGTGTTTGTGGT 59.228 45.455 0.00 0.00 0.00 4.16
2218 2612 8.196378 AGTAGTTAATGAGAAGAGAGGTGTTT 57.804 34.615 0.00 0.00 0.00 2.83
2219 2613 7.784470 AGTAGTTAATGAGAAGAGAGGTGTT 57.216 36.000 0.00 0.00 0.00 3.32
2230 2624 7.069455 TGCTTATGTGGCTAGTAGTTAATGAGA 59.931 37.037 0.00 0.00 0.00 3.27
2242 2636 6.199937 AGACAAATTTGCTTATGTGGCTAG 57.800 37.500 18.12 0.00 28.89 3.42
2244 2638 5.126061 CCTAGACAAATTTGCTTATGTGGCT 59.874 40.000 18.12 0.39 35.27 4.75
2259 2653 9.787435 AAGTAACATAACACATTCCTAGACAAA 57.213 29.630 0.00 0.00 0.00 2.83
2277 2671 7.806180 AGAGGGATTAACATAGCAAGTAACAT 58.194 34.615 0.00 0.00 0.00 2.71
2278 2672 7.195374 AGAGGGATTAACATAGCAAGTAACA 57.805 36.000 0.00 0.00 0.00 2.41
2295 2689 4.168883 GGTTAGGCTGGTTATAGAGGGAT 58.831 47.826 0.00 0.00 0.00 3.85
2305 2699 0.252197 GATGGTCGGTTAGGCTGGTT 59.748 55.000 0.00 0.00 0.00 3.67
2310 2704 1.153229 GGGTGATGGTCGGTTAGGC 60.153 63.158 0.00 0.00 0.00 3.93
2313 2707 1.134640 CAATCGGGTGATGGTCGGTTA 60.135 52.381 0.00 0.00 34.24 2.85
2341 2737 3.138304 CCGACCAATTTGACTGAACTCA 58.862 45.455 0.00 0.00 0.00 3.41
2367 2763 8.314021 ACTGGAATTTGACTGAACTTTCTTTTT 58.686 29.630 0.00 0.00 0.00 1.94
2368 2764 7.840931 ACTGGAATTTGACTGAACTTTCTTTT 58.159 30.769 0.00 0.00 0.00 2.27
2369 2765 7.122650 TGACTGGAATTTGACTGAACTTTCTTT 59.877 33.333 0.00 0.00 0.00 2.52
2370 2766 6.603201 TGACTGGAATTTGACTGAACTTTCTT 59.397 34.615 0.00 0.00 0.00 2.52
2371 2767 6.038714 GTGACTGGAATTTGACTGAACTTTCT 59.961 38.462 0.00 0.00 0.00 2.52
2372 2768 6.038714 AGTGACTGGAATTTGACTGAACTTTC 59.961 38.462 0.00 0.00 0.00 2.62
2373 2769 5.888161 AGTGACTGGAATTTGACTGAACTTT 59.112 36.000 0.00 0.00 0.00 2.66
2374 2770 5.440610 AGTGACTGGAATTTGACTGAACTT 58.559 37.500 0.00 0.00 0.00 2.66
2375 2771 5.041191 AGTGACTGGAATTTGACTGAACT 57.959 39.130 0.00 0.00 0.00 3.01
2376 2772 6.428159 ACATAGTGACTGGAATTTGACTGAAC 59.572 38.462 0.00 0.00 0.00 3.18
2377 2773 6.533730 ACATAGTGACTGGAATTTGACTGAA 58.466 36.000 0.00 0.00 0.00 3.02
2378 2774 6.114187 ACATAGTGACTGGAATTTGACTGA 57.886 37.500 0.00 0.00 0.00 3.41
2379 2775 7.604164 AGTTACATAGTGACTGGAATTTGACTG 59.396 37.037 0.00 0.00 31.25 3.51
2380 2776 7.680730 AGTTACATAGTGACTGGAATTTGACT 58.319 34.615 0.00 0.00 31.25 3.41
2381 2777 7.907214 AGTTACATAGTGACTGGAATTTGAC 57.093 36.000 0.00 0.00 31.25 3.18
2382 2778 7.094805 GCAAGTTACATAGTGACTGGAATTTGA 60.095 37.037 8.54 0.00 36.68 2.69
2383 2779 7.023575 GCAAGTTACATAGTGACTGGAATTTG 58.976 38.462 0.00 0.00 37.27 2.32
2465 2863 4.368565 AGTCTGGAAAAGGGTTTCTACC 57.631 45.455 0.00 0.00 42.45 3.18
2468 2867 5.906772 TCTAAGTCTGGAAAAGGGTTTCT 57.093 39.130 0.00 0.00 42.45 2.52
2471 2870 4.767409 GCAATCTAAGTCTGGAAAAGGGTT 59.233 41.667 0.00 0.00 0.00 4.11
2526 2925 8.084073 CAGGAGAGCTTCAAATTAACATGAAAA 58.916 33.333 0.00 0.00 35.31 2.29
2540 2939 4.194640 GCAACATTATCAGGAGAGCTTCA 58.805 43.478 0.00 0.00 0.00 3.02
2544 2943 3.205784 AGGCAACATTATCAGGAGAGC 57.794 47.619 0.00 0.00 41.41 4.09
2591 2990 1.602311 AGATTCCAATGCGATCTGCC 58.398 50.000 7.00 0.00 45.60 4.85
2600 2999 2.470196 CGAGCAGCAAGATTCCAATG 57.530 50.000 0.00 0.00 0.00 2.82
2735 3134 0.739813 ATAAACGCGCCAGTCTGTCC 60.740 55.000 5.73 0.00 0.00 4.02
2913 3373 3.890756 TGTCTTTACGGACACACCTCTTA 59.109 43.478 0.00 0.00 40.72 2.10
2914 3374 2.696707 TGTCTTTACGGACACACCTCTT 59.303 45.455 0.00 0.00 40.72 2.85
2916 3376 2.806608 TGTCTTTACGGACACACCTC 57.193 50.000 0.00 0.00 40.72 3.85
2959 3419 4.346418 ACCATTATCTTTGCGGAGAGATCT 59.654 41.667 13.32 0.00 34.60 2.75
3032 3493 6.492429 GGTTTTGGGGTATCAGTTTAGTCTTT 59.508 38.462 0.00 0.00 0.00 2.52
3044 3505 0.032515 CCAGGGGGTTTTGGGGTATC 60.033 60.000 0.00 0.00 0.00 2.24
3549 4010 3.433274 CAGCTATACGCAGAGAGAGAGAG 59.567 52.174 0.00 0.00 42.61 3.20
3550 4011 3.398406 CAGCTATACGCAGAGAGAGAGA 58.602 50.000 0.00 0.00 42.61 3.10
3551 4012 2.483877 CCAGCTATACGCAGAGAGAGAG 59.516 54.545 0.00 0.00 42.61 3.20
3552 4013 2.499197 CCAGCTATACGCAGAGAGAGA 58.501 52.381 0.00 0.00 42.61 3.10
3553 4014 1.068610 GCCAGCTATACGCAGAGAGAG 60.069 57.143 0.00 0.00 42.61 3.20
3554 4015 0.955178 GCCAGCTATACGCAGAGAGA 59.045 55.000 0.00 0.00 42.61 3.10
3555 4016 0.386605 CGCCAGCTATACGCAGAGAG 60.387 60.000 0.00 0.00 42.61 3.20
3556 4017 1.654774 CGCCAGCTATACGCAGAGA 59.345 57.895 0.00 0.00 42.61 3.10
3578 4039 3.071837 TGCCATCGACGTAGCCCA 61.072 61.111 0.00 0.00 0.00 5.36
3812 4273 3.299503 TCCATCTTGATCTGGACGATGA 58.700 45.455 0.00 0.00 36.63 2.92
3924 4420 2.038813 TCCTCCTCACGCATGGGA 59.961 61.111 17.76 1.86 0.00 4.37


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

AutoCloner maintained by Alex Coulton.