Multiple sequence alignment - TraesCS3B01G596500

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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 TraesCS3B01G596500 chr3B 100.000 6768 0 0 1 6768 819369342 819362575 0.000000e+00 12499.0
1 TraesCS3B01G596500 chr3B 88.473 2698 266 29 3133 5806 819189281 819186605 0.000000e+00 3217.0
2 TraesCS3B01G596500 chr3B 86.426 2932 321 47 3156 6061 819505493 819502613 0.000000e+00 3138.0
3 TraesCS3B01G596500 chr3B 86.784 2111 208 39 4350 6432 819280657 819278590 0.000000e+00 2287.0
4 TraesCS3B01G596500 chr3B 87.568 1826 173 32 4115 5928 819630831 819629048 0.000000e+00 2065.0
5 TraesCS3B01G596500 chr3B 87.896 1264 141 8 677 1931 819635277 819634017 0.000000e+00 1476.0
6 TraesCS3B01G596500 chr3B 85.968 1297 165 11 645 1931 819507928 819506639 0.000000e+00 1371.0
7 TraesCS3B01G596500 chr3B 84.091 1408 165 29 532 1930 819285456 819284099 0.000000e+00 1304.0
8 TraesCS3B01G596500 chr3B 91.765 935 61 9 5796 6721 819186577 819185650 0.000000e+00 1286.0
9 TraesCS3B01G596500 chr3B 92.150 879 60 3 4587 5461 818334104 818334977 0.000000e+00 1232.0
10 TraesCS3B01G596500 chr3B 83.976 1011 146 11 924 1928 819192543 819191543 0.000000e+00 955.0
11 TraesCS3B01G596500 chr3B 82.817 1001 165 5 3129 4127 819632336 819631341 0.000000e+00 889.0
12 TraesCS3B01G596500 chr3B 83.628 226 27 4 1932 2154 819191502 819191284 3.200000e-48 204.0
13 TraesCS3B01G596500 chr3B 90.816 98 6 1 6627 6721 819276793 819276696 1.980000e-25 128.0
14 TraesCS3B01G596500 chr3A 84.839 3331 363 67 3142 6432 742323246 742320018 0.000000e+00 3223.0
15 TraesCS3B01G596500 chr3A 88.707 2683 216 41 4117 6768 742239409 742236783 0.000000e+00 3195.0
16 TraesCS3B01G596500 chr3A 88.311 1942 202 14 1 1931 742328122 742326195 0.000000e+00 2305.0
17 TraesCS3B01G596500 chr3A 83.102 1438 189 20 532 1928 742229214 742227790 0.000000e+00 1260.0
18 TraesCS3B01G596500 chr3A 85.339 1180 156 10 761 1927 742243502 742242327 0.000000e+00 1205.0
19 TraesCS3B01G596500 chr3A 88.723 940 98 6 5188 6126 742212469 742211537 0.000000e+00 1142.0
20 TraesCS3B01G596500 chr3A 82.363 1117 169 18 3000 4097 742240668 742239561 0.000000e+00 946.0
21 TraesCS3B01G596500 chr3A 82.806 948 123 21 3094 4031 742226967 742226050 0.000000e+00 811.0
22 TraesCS3B01G596500 chr3A 86.547 446 31 7 6120 6564 742205020 742204603 1.330000e-126 464.0
23 TraesCS3B01G596500 chr3A 81.278 454 64 11 1940 2385 742227742 742227302 1.400000e-91 348.0
24 TraesCS3B01G596500 chr3A 94.186 172 10 0 6550 6721 742203382 742203211 5.210000e-66 263.0
25 TraesCS3B01G596500 chr3A 82.258 248 27 2 4037 4283 742224316 742224085 1.490000e-46 198.0
26 TraesCS3B01G596500 chr3D 86.946 2030 219 26 4258 6274 608925581 608923585 0.000000e+00 2239.0
27 TraesCS3B01G596500 chr3D 85.620 1363 163 11 588 1928 608932155 608930804 0.000000e+00 1400.0
28 TraesCS3B01G596500 chr3D 91.321 772 50 9 1 765 608933192 608932431 0.000000e+00 1038.0
29 TraesCS3B01G596500 chr3D 90.179 784 47 14 1 765 608971725 608970953 0.000000e+00 994.0
30 TraesCS3B01G596500 chr3D 80.546 1136 182 22 3095 4211 608926826 608925711 0.000000e+00 837.0
31 TraesCS3B01G596500 chr3D 88.618 492 52 4 769 1258 608968734 608968245 4.520000e-166 595.0
32 TraesCS3B01G596500 chr6A 83.069 945 145 13 4691 5628 39442930 39441994 0.000000e+00 845.0
33 TraesCS3B01G596500 chr2B 90.909 44 4 0 3641 3684 3208244 3208201 7.330000e-05 60.2


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 TraesCS3B01G596500 chr3B 819362575 819369342 6767 True 12499.000000 12499 100.000000 1 6768 1 chr3B.!!$R1 6767
1 TraesCS3B01G596500 chr3B 819502613 819507928 5315 True 2254.500000 3138 86.197000 645 6061 2 chr3B.!!$R4 5416
2 TraesCS3B01G596500 chr3B 819629048 819635277 6229 True 1476.666667 2065 86.093667 677 5928 3 chr3B.!!$R5 5251
3 TraesCS3B01G596500 chr3B 819185650 819192543 6893 True 1415.500000 3217 86.960500 924 6721 4 chr3B.!!$R2 5797
4 TraesCS3B01G596500 chr3B 819276696 819285456 8760 True 1239.666667 2287 87.230333 532 6721 3 chr3B.!!$R3 6189
5 TraesCS3B01G596500 chr3B 818334104 818334977 873 False 1232.000000 1232 92.150000 4587 5461 1 chr3B.!!$F1 874
6 TraesCS3B01G596500 chr3A 742320018 742328122 8104 True 2764.000000 3223 86.575000 1 6432 2 chr3A.!!$R5 6431
7 TraesCS3B01G596500 chr3A 742236783 742243502 6719 True 1782.000000 3195 85.469667 761 6768 3 chr3A.!!$R4 6007
8 TraesCS3B01G596500 chr3A 742211537 742212469 932 True 1142.000000 1142 88.723000 5188 6126 1 chr3A.!!$R1 938
9 TraesCS3B01G596500 chr3A 742224085 742229214 5129 True 654.250000 1260 82.361000 532 4283 4 chr3A.!!$R3 3751
10 TraesCS3B01G596500 chr3A 742203211 742205020 1809 True 363.500000 464 90.366500 6120 6721 2 chr3A.!!$R2 601
11 TraesCS3B01G596500 chr3D 608923585 608933192 9607 True 1378.500000 2239 86.108250 1 6274 4 chr3D.!!$R1 6273
12 TraesCS3B01G596500 chr3D 608968245 608971725 3480 True 794.500000 994 89.398500 1 1258 2 chr3D.!!$R2 1257
13 TraesCS3B01G596500 chr6A 39441994 39442930 936 True 845.000000 845 83.069000 4691 5628 1 chr6A.!!$R1 937

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
734 1259 0.034337 GGGTACACAGCCTGTTCGAA 59.966 55.0 0.00 0.0 39.38 3.71 F
966 3721 0.035152 AGCGATGCATGGTTCAGGAA 60.035 50.0 2.46 0.0 0.00 3.36 F
1018 3777 0.170116 AATGGCGCACATAACAACCG 59.830 50.0 10.83 0.0 39.40 4.44 F
1512 4282 0.179000 CCCAAGCGCTATCCACTCTT 59.821 55.0 12.05 0.0 0.00 2.85 F
2044 4884 0.317479 GGGTACGCTAGGTGCTATGG 59.683 60.0 2.05 0.0 40.11 2.74 F
3111 11017 0.399091 CATGCTGTCCTAGGGGGAGA 60.399 60.0 9.46 0.0 46.10 3.71 F
3402 12573 0.401356 TGCATGTCCTCTCCAGCAAA 59.599 50.0 0.00 0.0 0.00 3.68 F
3926 13103 0.462581 GACATGAAGGCGCATCCAGA 60.463 55.0 10.83 0.0 37.29 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2695 7213 0.107410 TGGTCGCTTGGTTTGTCACT 60.107 50.000 0.00 0.00 0.00 3.41 R
2696 7214 0.951558 ATGGTCGCTTGGTTTGTCAC 59.048 50.000 0.00 0.00 0.00 3.67 R
2919 10292 1.078709 GTTCTCGCATTACTGCTGCA 58.921 50.000 0.88 0.88 46.65 4.41 R
3248 12409 0.322546 GTTGAACCCTGGCCAGTAGG 60.323 60.000 30.63 26.29 38.23 3.18 R
3394 12565 0.332293 TCCATGATGGCTTTGCTGGA 59.668 50.000 6.59 0.00 37.47 3.86 R
4498 16095 0.179100 TCAGCAGCAGGAGTAATCGC 60.179 55.000 0.00 0.00 0.00 4.58 R
4499 16096 1.135915 ACTCAGCAGCAGGAGTAATCG 59.864 52.381 15.89 0.00 42.30 3.34 R
5836 17490 2.224378 ACAGACAAGGGATATGGATGCG 60.224 50.000 0.00 0.00 0.00 4.73 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
34 35 3.449349 AAAAATGGTTCGGGCGCA 58.551 50.000 10.83 0.00 0.00 6.09
94 95 2.092968 TGGAGATGTCCTTGCCATACAC 60.093 50.000 10.72 0.00 44.30 2.90
100 101 2.406616 CCTTGCCATACACACCGCC 61.407 63.158 0.00 0.00 0.00 6.13
101 102 2.744318 TTGCCATACACACCGCCG 60.744 61.111 0.00 0.00 0.00 6.46
120 121 1.175983 GGTTTGGGTCCGTGCATTGA 61.176 55.000 0.00 0.00 0.00 2.57
161 162 2.406002 ATCGGCGGACAGTTTGGGTT 62.406 55.000 7.21 0.00 0.00 4.11
245 246 0.457443 TGTGACTGGAGAGCGCATAG 59.543 55.000 11.47 2.30 0.00 2.23
269 270 2.995283 TCGACTATTCGGTCTGGAGAA 58.005 47.619 2.41 0.00 45.90 2.87
413 427 1.686110 CCGGCCCCTAACTGTCTCT 60.686 63.158 0.00 0.00 0.00 3.10
414 428 1.677637 CCGGCCCCTAACTGTCTCTC 61.678 65.000 0.00 0.00 0.00 3.20
415 429 0.684805 CGGCCCCTAACTGTCTCTCT 60.685 60.000 0.00 0.00 0.00 3.10
416 430 1.574263 GGCCCCTAACTGTCTCTCTT 58.426 55.000 0.00 0.00 0.00 2.85
425 459 6.180472 CCTAACTGTCTCTCTTTCTCTCTCT 58.820 44.000 0.00 0.00 0.00 3.10
437 471 0.926293 CTCTCTCTCTCCCTGGTCCT 59.074 60.000 0.00 0.00 0.00 3.85
449 483 0.177604 CTGGTCCTAAGCTCTGCAGG 59.822 60.000 15.13 5.82 0.00 4.85
455 489 1.761784 CCTAAGCTCTGCAGGTCATCT 59.238 52.381 15.13 1.21 0.00 2.90
467 501 2.038952 CAGGTCATCTTGGTCACCTTCA 59.961 50.000 0.00 0.00 37.13 3.02
483 517 0.319555 TTCAACCTCAAGTCTCGCCG 60.320 55.000 0.00 0.00 0.00 6.46
487 521 2.049156 CTCAAGTCTCGCCGCACA 60.049 61.111 0.00 0.00 0.00 4.57
643 677 1.643292 GCATCATGCGTATGTGCGT 59.357 52.632 18.98 2.72 37.81 5.24
653 687 1.205657 GTATGTGCGTATGTGGTCGG 58.794 55.000 0.00 0.00 0.00 4.79
718 780 1.147600 GTTTCACACTCCACGGGGT 59.852 57.895 2.12 0.00 34.93 4.95
734 1259 0.034337 GGGTACACAGCCTGTTCGAA 59.966 55.000 0.00 0.00 39.38 3.71
813 3556 0.991920 GGAGAGGACATTTGACCCCA 59.008 55.000 0.00 0.00 0.00 4.96
848 3591 2.289694 CCCTTGGTTCTCACTTGTCGAT 60.290 50.000 0.00 0.00 0.00 3.59
935 3690 1.508632 GCGCCATCTTTATAAGCCGA 58.491 50.000 0.00 0.00 0.00 5.54
939 3694 2.486548 GCCATCTTTATAAGCCGACCCA 60.487 50.000 0.00 0.00 0.00 4.51
941 3696 3.403038 CATCTTTATAAGCCGACCCAGG 58.597 50.000 0.00 0.00 0.00 4.45
966 3721 0.035152 AGCGATGCATGGTTCAGGAA 60.035 50.000 2.46 0.00 0.00 3.36
976 3731 1.831736 TGGTTCAGGAACTAGCTAGCC 59.168 52.381 20.91 14.35 40.94 3.93
1018 3777 0.170116 AATGGCGCACATAACAACCG 59.830 50.000 10.83 0.00 39.40 4.44
1092 3852 1.024579 TCGCCGGAGCAGAAATTTCC 61.025 55.000 14.61 0.00 39.83 3.13
1211 3971 0.890996 GGGTTCAACCTCACCTGCAG 60.891 60.000 6.78 6.78 38.64 4.41
1224 3984 2.906388 TGCAGCCGCTCAAGCAAA 60.906 55.556 1.56 0.00 42.21 3.68
1227 3987 2.203337 AGCCGCTCAAGCAAACCA 60.203 55.556 2.50 0.00 42.21 3.67
1248 4008 3.434319 CGGTTGCTGCTTGGCGAT 61.434 61.111 0.00 0.00 34.52 4.58
1281 4045 1.552792 GTCCAAGAGTTCTCCCTCAGG 59.447 57.143 0.00 0.00 33.75 3.86
1282 4046 1.150135 TCCAAGAGTTCTCCCTCAGGT 59.850 52.381 0.00 0.00 33.75 4.00
1283 4047 1.277557 CCAAGAGTTCTCCCTCAGGTG 59.722 57.143 0.00 0.00 33.75 4.00
1284 4048 1.277557 CAAGAGTTCTCCCTCAGGTGG 59.722 57.143 0.00 0.00 33.75 4.61
1296 4066 2.816087 CCTCAGGTGGTCATTTGTGAAG 59.184 50.000 0.00 0.00 0.00 3.02
1314 4084 1.009222 GGTCATACGTACGGGCGAG 60.009 63.158 21.06 4.74 35.59 5.03
1381 4151 2.359478 CCAACGGGCCCTACACAC 60.359 66.667 22.43 0.00 0.00 3.82
1404 4174 2.763039 TCATCCAACCAGCTCATCCTA 58.237 47.619 0.00 0.00 0.00 2.94
1453 4223 3.605749 AACGGCGAGGTGACCATGG 62.606 63.158 16.62 11.19 0.00 3.66
1478 4248 2.861360 GCTGTTCTTCTGGCTGCAAAAG 60.861 50.000 0.50 1.81 0.00 2.27
1497 4267 2.721167 CGGCGATGGACTCTCCCAA 61.721 63.158 0.00 0.00 40.04 4.12
1509 4279 0.687757 TCTCCCAAGCGCTATCCACT 60.688 55.000 12.05 0.00 0.00 4.00
1512 4282 0.179000 CCCAAGCGCTATCCACTCTT 59.821 55.000 12.05 0.00 0.00 2.85
1590 4360 1.304962 TGCGGAGGTAGCAGGAAGA 60.305 57.895 0.00 0.00 40.01 2.87
1597 4367 1.546476 AGGTAGCAGGAAGACTTGTCG 59.454 52.381 0.00 0.00 0.00 4.35
1599 4369 2.166664 GGTAGCAGGAAGACTTGTCGAT 59.833 50.000 0.00 0.00 0.00 3.59
1603 4373 3.119316 AGCAGGAAGACTTGTCGATAGTG 60.119 47.826 7.76 0.00 37.40 2.74
1607 4377 3.243336 GAAGACTTGTCGATAGTGCGTT 58.757 45.455 7.76 0.27 37.40 4.84
1684 4454 1.343821 GCACACGTCTTTATCGCGG 59.656 57.895 6.13 0.00 0.00 6.46
1733 4503 2.034939 TCTTCCACGAGCTGTTACGAAA 59.965 45.455 0.00 0.00 0.00 3.46
1736 4506 1.136336 CCACGAGCTGTTACGAAAAGC 60.136 52.381 0.00 0.00 37.20 3.51
1773 4543 2.417787 GGATGCAATGCAAGTTCCCTTC 60.418 50.000 13.45 1.97 43.62 3.46
1798 4576 1.456287 GACTGGGAGGTTGTTGGCT 59.544 57.895 0.00 0.00 0.00 4.75
1869 4647 2.467566 AGGGTAACAAAGGCTACACG 57.532 50.000 0.00 0.00 39.74 4.49
1938 4761 0.796927 GCAAAGGTCTGGCGAGTAAC 59.203 55.000 0.00 0.00 0.00 2.50
1967 4790 5.168647 TCGGGGTTTCTCTTTGCTTAATA 57.831 39.130 0.00 0.00 0.00 0.98
1985 4812 7.661027 TGCTTAATACTAGCATGCATGTATTGA 59.339 33.333 33.83 29.14 43.30 2.57
2018 4849 8.719560 ATATATGTGTAGATATCGACGAGTGT 57.280 34.615 10.83 0.00 0.00 3.55
2019 4850 4.790810 TGTGTAGATATCGACGAGTGTC 57.209 45.455 10.83 1.34 41.91 3.67
2035 4872 2.427453 AGTGTCATGAAGGGTACGCTAG 59.573 50.000 13.46 4.31 31.26 3.42
2042 4882 1.962100 GAAGGGTACGCTAGGTGCTAT 59.038 52.381 13.46 0.00 40.11 2.97
2043 4883 1.329256 AGGGTACGCTAGGTGCTATG 58.671 55.000 11.28 0.00 40.11 2.23
2044 4884 0.317479 GGGTACGCTAGGTGCTATGG 59.683 60.000 2.05 0.00 40.11 2.74
2050 4890 0.815615 GCTAGGTGCTATGGTGGTGC 60.816 60.000 0.00 0.00 38.95 5.01
2125 4968 2.285368 CCCTACCCTGCCTGGTGA 60.285 66.667 4.58 0.00 39.53 4.02
2126 4969 1.694169 CCCTACCCTGCCTGGTGAT 60.694 63.158 4.58 0.00 39.53 3.06
2159 5009 4.161565 TCCGTCTCAGGTAAGCAATATTGT 59.838 41.667 16.61 0.70 0.00 2.71
2160 5010 4.271049 CCGTCTCAGGTAAGCAATATTGTG 59.729 45.833 16.61 6.27 0.00 3.33
2161 5011 4.271049 CGTCTCAGGTAAGCAATATTGTGG 59.729 45.833 16.61 1.75 0.00 4.17
2162 5012 5.186198 GTCTCAGGTAAGCAATATTGTGGT 58.814 41.667 16.61 5.31 0.00 4.16
2163 5013 5.065218 GTCTCAGGTAAGCAATATTGTGGTG 59.935 44.000 16.61 6.66 0.00 4.17
2164 5014 4.917385 TCAGGTAAGCAATATTGTGGTGT 58.083 39.130 16.61 1.43 0.00 4.16
2172 5022 1.173043 ATATTGTGGTGTGGCAACCG 58.827 50.000 12.19 0.00 43.73 4.44
2176 5026 2.983030 TGGTGTGGCAACCGCATC 60.983 61.111 2.77 3.12 46.11 3.91
2196 5047 8.446273 CCGCATCTATTTTTACTATCAAGATGG 58.554 37.037 10.45 0.00 39.34 3.51
2236 5192 8.675705 TGAACAAGAAAGAACAGATCATAACA 57.324 30.769 0.00 0.00 0.00 2.41
2243 5199 8.112183 AGAAAGAACAGATCATAACAATCCCTT 58.888 33.333 0.00 0.00 0.00 3.95
2249 5205 8.877864 ACAGATCATAACAATCCCTTAACAAA 57.122 30.769 0.00 0.00 0.00 2.83
2250 5206 8.960591 ACAGATCATAACAATCCCTTAACAAAG 58.039 33.333 0.00 0.00 0.00 2.77
2251 5207 8.960591 CAGATCATAACAATCCCTTAACAAAGT 58.039 33.333 0.00 0.00 0.00 2.66
2283 5251 8.806177 AAATTTTAACACCGGATAAACTCAAC 57.194 30.769 9.46 0.00 0.00 3.18
2307 5275 4.623932 AGTGTGCAGTTAAAGGATCAGA 57.376 40.909 0.00 0.00 0.00 3.27
2368 5388 7.568349 AGTGCCATCATCTTAGAGAACAAATA 58.432 34.615 0.00 0.00 0.00 1.40
2386 5406 9.394477 GAACAAATACAGGACTAAAAATGACAC 57.606 33.333 0.00 0.00 0.00 3.67
2394 5418 8.095169 ACAGGACTAAAAATGACACTAACCTAG 58.905 37.037 0.00 0.00 0.00 3.02
2406 5430 8.018537 TGACACTAACCTAGTATATTGCACAT 57.981 34.615 0.00 0.00 37.23 3.21
2429 5454 9.877178 ACATAAACAAACAAAAGGTCACATTAA 57.123 25.926 0.00 0.00 0.00 1.40
2468 6511 6.763610 CGGATTAGTTAGCAAGAGGAAGAAAT 59.236 38.462 0.00 0.00 0.00 2.17
2486 6529 7.039714 GGAAGAAATCACAGGTGGACTAAAATT 60.040 37.037 0.00 0.00 0.00 1.82
2494 6537 7.227910 TCACAGGTGGACTAAAATTAAGAACAC 59.772 37.037 0.00 0.00 0.00 3.32
2499 6542 9.758651 GGTGGACTAAAATTAAGAACACAAATT 57.241 29.630 14.79 0.00 0.00 1.82
2533 6578 6.219417 TCACATTGTTCACTCCAATTTTGT 57.781 33.333 0.00 0.00 30.28 2.83
2534 6579 6.638610 TCACATTGTTCACTCCAATTTTGTT 58.361 32.000 0.00 0.00 30.28 2.83
2546 6592 9.357652 CACTCCAATTTTGTTAATTACTCATGG 57.642 33.333 0.00 0.00 0.00 3.66
2591 6648 4.645588 ACTATCAGTTTAGACTTCCCTCCG 59.354 45.833 0.00 0.00 32.54 4.63
2605 6666 2.907696 TCCCTCCGGAACATCAAAAGTA 59.092 45.455 5.23 0.00 34.19 2.24
2608 6669 4.705023 CCCTCCGGAACATCAAAAGTAAAT 59.295 41.667 5.23 0.00 0.00 1.40
2623 6684 3.535561 AGTAAATGTTCGCATCAGAGGG 58.464 45.455 0.00 0.00 36.70 4.30
2632 6695 0.883814 GCATCAGAGGGCGAAGATGG 60.884 60.000 0.00 0.00 38.57 3.51
2639 6702 2.975489 AGAGGGCGAAGATGGATATTGT 59.025 45.455 0.00 0.00 0.00 2.71
2640 6703 3.070018 GAGGGCGAAGATGGATATTGTG 58.930 50.000 0.00 0.00 0.00 3.33
2647 7162 5.334414 GCGAAGATGGATATTGTGATGTTCC 60.334 44.000 0.00 0.00 0.00 3.62
2675 7191 5.163963 CCCAACTTAAAAATGAGCGCAAATC 60.164 40.000 11.47 0.00 0.00 2.17
2689 7207 4.082571 AGCGCAAATCATTTTAACAGCTCT 60.083 37.500 11.47 0.00 0.00 4.09
2695 7213 4.365514 TCATTTTAACAGCTCTCCACCA 57.634 40.909 0.00 0.00 0.00 4.17
2696 7214 4.326826 TCATTTTAACAGCTCTCCACCAG 58.673 43.478 0.00 0.00 0.00 4.00
2708 7226 1.949525 CTCCACCAGTGACAAACCAAG 59.050 52.381 0.00 0.00 0.00 3.61
2720 7238 4.279671 TGACAAACCAAGCGACCATAAAAT 59.720 37.500 0.00 0.00 0.00 1.82
2726 7245 4.522789 ACCAAGCGACCATAAAATCTTTGT 59.477 37.500 0.00 0.00 0.00 2.83
2744 7899 6.035843 TCTTTGTCAGCAAATCTGTGAAAAC 58.964 36.000 0.00 0.00 42.88 2.43
2745 7900 3.951306 TGTCAGCAAATCTGTGAAAACG 58.049 40.909 0.00 0.00 43.32 3.60
2751 7906 7.378461 GTCAGCAAATCTGTGAAAACGATTTTA 59.622 33.333 0.00 0.00 43.32 1.52
2762 7917 8.242053 TGTGAAAACGATTTTACAGGTAAAACA 58.758 29.630 16.95 8.11 44.68 2.83
2808 7983 7.379529 CAGCAAAATATTCATCCGATAAACCAC 59.620 37.037 0.00 0.00 0.00 4.16
2823 7998 7.411372 CCGATAAACCACATACAAATTTTGCAC 60.411 37.037 9.04 0.00 0.00 4.57
2830 9320 7.978975 ACCACATACAAATTTTGCACCATATAC 59.021 33.333 9.04 0.00 0.00 1.47
2897 10199 2.751166 ACAAACTCCACTGGATCTCG 57.249 50.000 0.00 0.00 0.00 4.04
2919 10292 1.270465 GCAAAGCTCCATTTGGCAACT 60.270 47.619 0.00 0.00 39.94 3.16
2931 10304 0.883153 TGGCAACTGCAGCAGTAATG 59.117 50.000 28.48 23.26 44.62 1.90
2956 10329 5.067153 CGAGAACATGAGATCTACCACTCTT 59.933 44.000 0.00 0.00 34.65 2.85
2957 10330 6.405286 CGAGAACATGAGATCTACCACTCTTT 60.405 42.308 0.00 0.00 34.65 2.52
2958 10331 7.251321 AGAACATGAGATCTACCACTCTTTT 57.749 36.000 0.00 0.00 34.65 2.27
2959 10332 7.684529 AGAACATGAGATCTACCACTCTTTTT 58.315 34.615 0.00 0.00 34.65 1.94
2960 10333 7.821846 AGAACATGAGATCTACCACTCTTTTTC 59.178 37.037 0.00 0.00 34.65 2.29
2961 10334 6.102663 ACATGAGATCTACCACTCTTTTTCG 58.897 40.000 0.00 0.00 34.65 3.46
2962 10335 4.495422 TGAGATCTACCACTCTTTTTCGC 58.505 43.478 0.00 0.00 34.65 4.70
2963 10336 3.512680 AGATCTACCACTCTTTTTCGCG 58.487 45.455 0.00 0.00 0.00 5.87
2965 10338 3.374220 TCTACCACTCTTTTTCGCGAA 57.626 42.857 19.38 19.38 0.00 4.70
2966 10339 3.921677 TCTACCACTCTTTTTCGCGAAT 58.078 40.909 24.05 6.71 0.00 3.34
2969 10342 3.139077 ACCACTCTTTTTCGCGAATCTT 58.861 40.909 24.05 1.19 0.00 2.40
2970 10343 3.564225 ACCACTCTTTTTCGCGAATCTTT 59.436 39.130 24.05 2.33 0.00 2.52
2972 10345 4.613031 CCACTCTTTTTCGCGAATCTTTTC 59.387 41.667 24.05 0.00 0.00 2.29
2974 10347 5.853282 CACTCTTTTTCGCGAATCTTTTCAT 59.147 36.000 24.05 1.80 0.00 2.57
2975 10348 6.360681 CACTCTTTTTCGCGAATCTTTTCATT 59.639 34.615 24.05 0.00 0.00 2.57
2980 10353 4.857871 TCGCGAATCTTTTCATTGGTAG 57.142 40.909 6.20 0.00 0.00 3.18
2982 10355 4.932799 TCGCGAATCTTTTCATTGGTAGAA 59.067 37.500 6.20 0.00 0.00 2.10
2983 10356 5.063438 TCGCGAATCTTTTCATTGGTAGAAG 59.937 40.000 6.20 0.00 0.00 2.85
2984 10357 5.573146 GCGAATCTTTTCATTGGTAGAAGG 58.427 41.667 0.00 0.00 0.00 3.46
2985 10358 5.354234 GCGAATCTTTTCATTGGTAGAAGGA 59.646 40.000 0.00 0.00 0.00 3.36
2986 10359 6.128007 GCGAATCTTTTCATTGGTAGAAGGAA 60.128 38.462 0.00 0.00 0.00 3.36
2987 10360 7.244192 CGAATCTTTTCATTGGTAGAAGGAAC 58.756 38.462 0.00 0.00 0.00 3.62
2990 10363 9.454859 AATCTTTTCATTGGTAGAAGGAACTAG 57.545 33.333 0.00 0.00 38.49 2.57
3111 11017 0.399091 CATGCTGTCCTAGGGGGAGA 60.399 60.000 9.46 0.00 46.10 3.71
3117 11023 2.502130 CTGTCCTAGGGGGAGAAAGAAC 59.498 54.545 9.46 0.00 46.10 3.01
3133 11039 1.937546 GAACAGGCAGCCCAAATCCG 61.938 60.000 8.22 0.00 0.00 4.18
3149 12299 5.182001 CCAAATCCGACAGAAATTGAAGTCT 59.818 40.000 0.00 0.00 30.66 3.24
3186 12347 9.243105 ACATTGCTACTTTATCAAACAGGTAAT 57.757 29.630 0.00 0.00 0.00 1.89
3187 12348 9.507280 CATTGCTACTTTATCAAACAGGTAATG 57.493 33.333 0.00 0.00 0.00 1.90
3306 12467 3.146066 CCAACAACCAGCAAAGCTACTA 58.854 45.455 0.00 0.00 36.40 1.82
3339 12509 4.498520 CTCGTCGATGGCGTGGCT 62.499 66.667 4.48 0.00 38.98 4.75
3394 12565 1.141657 ACAACACAGTGCATGTCCTCT 59.858 47.619 0.00 0.00 41.41 3.69
3395 12566 1.802960 CAACACAGTGCATGTCCTCTC 59.197 52.381 0.00 0.00 41.41 3.20
3402 12573 0.401356 TGCATGTCCTCTCCAGCAAA 59.599 50.000 0.00 0.00 0.00 3.68
3412 12583 0.744874 CTCCAGCAAAGCCATCATGG 59.255 55.000 0.00 0.00 41.55 3.66
3419 12590 5.421056 CCAGCAAAGCCATCATGGATATTAT 59.579 40.000 8.30 0.00 40.96 1.28
3437 12608 8.594881 GATATTATCCACACGAACTTCTCATT 57.405 34.615 0.00 0.00 0.00 2.57
3438 12609 6.910536 ATTATCCACACGAACTTCTCATTC 57.089 37.500 0.00 0.00 0.00 2.67
3448 12619 5.981174 CGAACTTCTCATTCGGTGTTTTAA 58.019 37.500 0.00 0.00 44.07 1.52
3449 12620 6.423862 CGAACTTCTCATTCGGTGTTTTAAA 58.576 36.000 0.00 0.00 44.07 1.52
3450 12621 6.356190 CGAACTTCTCATTCGGTGTTTTAAAC 59.644 38.462 0.20 0.20 44.07 2.01
3489 12660 1.306148 CGCCCTACTCACTATCGACA 58.694 55.000 0.00 0.00 0.00 4.35
3553 12724 0.464036 GCTGATCGGTGATGGTACCA 59.536 55.000 18.99 18.99 40.89 3.25
3561 12732 2.682856 CGGTGATGGTACCAAGGATTTG 59.317 50.000 20.76 2.10 40.89 2.32
3579 12750 1.078848 GATCAGCGGTTGTGCCTCT 60.079 57.895 0.00 0.00 34.65 3.69
3730 12907 6.147864 TGAAGTTCCAAAATCTCAACAAGG 57.852 37.500 0.00 0.00 0.00 3.61
3736 12913 2.270352 AAATCTCAACAAGGACGGCA 57.730 45.000 0.00 0.00 0.00 5.69
3740 12917 0.535102 CTCAACAAGGACGGCAACCT 60.535 55.000 0.00 0.00 39.69 3.50
3828 13005 3.099170 AAGGAGATGGCGGGGCAT 61.099 61.111 7.51 7.51 0.00 4.40
3841 13018 1.114627 GGGGCATGAGGAATCCAAAC 58.885 55.000 0.61 0.00 0.00 2.93
3906 13083 2.502692 AAGACTTACCGCGACCAGCC 62.503 60.000 8.23 0.00 44.76 4.85
3926 13103 0.462581 GACATGAAGGCGCATCCAGA 60.463 55.000 10.83 0.00 37.29 3.86
3936 13113 1.451028 GCATCCAGACTGTCCAGCC 60.451 63.158 3.76 0.00 0.00 4.85
3951 13128 4.770874 GCCGAGGTAGCCCGCAAA 62.771 66.667 0.00 0.00 35.12 3.68
3954 13131 2.100631 CGAGGTAGCCCGCAAACTG 61.101 63.158 0.00 0.00 35.12 3.16
4081 14986 6.481976 CGGATGCAAAGGTTAGAACATGTATA 59.518 38.462 0.00 0.00 0.00 1.47
4233 15722 7.452880 TTCCTCCTGTTTAATTTCACATCAG 57.547 36.000 0.00 0.00 0.00 2.90
4280 15834 9.800433 TGGTATTTGTTTCAAGCAATACATATG 57.200 29.630 0.00 0.00 0.00 1.78
4282 15836 7.775397 ATTTGTTTCAAGCAATACATATGGC 57.225 32.000 7.80 0.38 32.69 4.40
4337 15907 6.178607 AGCTTCTTCCCATGAAAATGTTTT 57.821 33.333 0.00 0.00 0.00 2.43
4388 15965 5.862924 ACTTGATGTATGTTTCTTGGTCG 57.137 39.130 0.00 0.00 0.00 4.79
4393 15970 5.637810 TGATGTATGTTTCTTGGTCGAACTC 59.362 40.000 0.33 0.00 0.00 3.01
4445 16030 3.490348 ACCCTGAACATTCTGAAACCAG 58.510 45.455 0.00 0.20 0.00 4.00
4485 16080 5.891451 ACTCACAAAGCCAAAAAGTTACTC 58.109 37.500 0.00 0.00 0.00 2.59
4499 16096 5.405331 AAGTTACTCGAGTGAACTTTTGC 57.595 39.130 28.37 12.70 39.75 3.68
4540 16137 8.048534 TGAGTAACTGTAGACCAAGTGTATAC 57.951 38.462 0.00 0.00 41.13 1.47
4654 16259 4.693283 TCATACTATTTGTTCTCGCTGGG 58.307 43.478 0.00 0.00 0.00 4.45
4665 16270 2.738521 CGCTGGGTCCTTCACACG 60.739 66.667 0.00 0.00 0.00 4.49
4690 16295 6.769608 AAGAAATTCAAACATCGAAAAGCC 57.230 33.333 0.00 0.00 0.00 4.35
4691 16296 5.841810 AGAAATTCAAACATCGAAAAGCCA 58.158 33.333 0.00 0.00 0.00 4.75
4741 16347 0.383949 ACCGTGGACAATTGTTGCAC 59.616 50.000 13.36 15.58 0.00 4.57
5020 16626 2.908688 ATGGTTGTTGCCTTGAAACC 57.091 45.000 0.00 0.00 42.03 3.27
5174 16780 4.707105 TCATCTTCACTCAACAGCTTCAA 58.293 39.130 0.00 0.00 0.00 2.69
5245 16855 2.143925 ACTCTAACAGCAAAAGTCGCC 58.856 47.619 0.00 0.00 0.00 5.54
5690 17300 3.973206 AATGTCCACCGACTGTTGATA 57.027 42.857 0.00 0.00 39.94 2.15
5756 17366 7.911651 AGAAGAGTTCATGTTATCTTCAAGGA 58.088 34.615 24.69 0.00 46.51 3.36
5767 17377 6.155565 TGTTATCTTCAAGGAATCCTCGGTAA 59.844 38.462 0.56 0.00 30.89 2.85
5810 17461 6.671190 TCATCACTGCATTAGTTTTCAACAG 58.329 36.000 0.00 0.00 37.60 3.16
5813 17464 5.009911 TCACTGCATTAGTTTTCAACAGCAT 59.990 36.000 0.00 0.00 37.60 3.79
5838 17492 2.398803 GGAGATTCTCCTTTGCCGC 58.601 57.895 23.09 0.00 46.41 6.53
5845 17499 0.836606 TCTCCTTTGCCGCATCCATA 59.163 50.000 0.00 0.00 0.00 2.74
5854 17508 1.813513 CCGCATCCATATCCCTTGTC 58.186 55.000 0.00 0.00 0.00 3.18
5855 17509 1.349026 CCGCATCCATATCCCTTGTCT 59.651 52.381 0.00 0.00 0.00 3.41
5889 17547 1.683011 GCTTCCATGGCAGCTCCTTTA 60.683 52.381 26.79 0.00 35.26 1.85
5897 17555 2.573462 TGGCAGCTCCTTTACTTCATCT 59.427 45.455 0.00 0.00 35.26 2.90
5987 17659 2.036475 ACCAGGTGCTTAGCTATCATCG 59.964 50.000 5.60 0.00 0.00 3.84
6011 17683 9.382275 TCGATGAATCAAAAGAATGTAATGAGA 57.618 29.630 0.00 0.00 0.00 3.27
6048 17720 6.678663 CGATCGATTGTTCTTTATGTGTGTTC 59.321 38.462 10.26 0.00 0.00 3.18
6066 17738 4.160626 GTGTTCTTCCTGGAGCTACACTAT 59.839 45.833 20.61 0.00 33.23 2.12
6067 17739 5.360144 GTGTTCTTCCTGGAGCTACACTATA 59.640 44.000 20.61 0.00 33.23 1.31
6084 17762 9.745880 CTACACTATACGTTGAGTTATCCAAAT 57.254 33.333 0.00 0.00 0.00 2.32
6123 17801 7.630242 AACACCACAATTATGTCTATTCCAG 57.370 36.000 0.00 0.00 37.82 3.86
6137 17815 1.098712 TTCCAGGTGCGTGTGTTTCC 61.099 55.000 0.00 0.00 0.00 3.13
6140 17818 1.594293 AGGTGCGTGTGTTTCCTCG 60.594 57.895 0.00 0.00 0.00 4.63
6197 17877 3.121929 ACACCCACTACAGATGGATCT 57.878 47.619 0.00 0.00 39.87 2.75
6212 17892 2.568956 TGGATCTACTCAAACAGCAGCT 59.431 45.455 0.00 0.00 0.00 4.24
6406 18092 1.601903 AGCGAAAAATTGTCTGCACGA 59.398 42.857 0.00 0.00 0.00 4.35
6535 18221 7.962441 AGTACCATTTGTCTAGCCAAAAATTT 58.038 30.769 2.63 0.00 37.81 1.82
6559 19481 6.308371 AGAAATGTTAGTACGGTTTGGTTG 57.692 37.500 0.00 0.00 0.00 3.77
6625 19547 5.882040 TGATCCTTGGTTTGTGGTTGTATA 58.118 37.500 0.00 0.00 0.00 1.47
6644 21264 9.277783 GTTGTATAATGGAGAGCAATTCACTAT 57.722 33.333 0.00 0.00 0.00 2.12
6703 21323 4.054780 TCACTACCATTTATCGTCAGGC 57.945 45.455 0.00 0.00 0.00 4.85
6726 21349 2.435372 TTTGCTGTCCAAGAACCTGT 57.565 45.000 0.00 0.00 34.34 4.00
6727 21350 3.569194 TTTGCTGTCCAAGAACCTGTA 57.431 42.857 0.00 0.00 34.34 2.74
6728 21351 3.569194 TTGCTGTCCAAGAACCTGTAA 57.431 42.857 0.00 0.00 0.00 2.41
6729 21352 3.126001 TGCTGTCCAAGAACCTGTAAG 57.874 47.619 0.00 0.00 0.00 2.34
6730 21353 2.438021 TGCTGTCCAAGAACCTGTAAGT 59.562 45.455 0.00 0.00 0.00 2.24
6731 21354 2.808543 GCTGTCCAAGAACCTGTAAGTG 59.191 50.000 0.00 0.00 0.00 3.16
6732 21355 2.808543 CTGTCCAAGAACCTGTAAGTGC 59.191 50.000 0.00 0.00 0.00 4.40
6733 21356 2.152016 GTCCAAGAACCTGTAAGTGCC 58.848 52.381 0.00 0.00 0.00 5.01
6734 21357 2.054799 TCCAAGAACCTGTAAGTGCCT 58.945 47.619 0.00 0.00 0.00 4.75
6735 21358 3.007614 GTCCAAGAACCTGTAAGTGCCTA 59.992 47.826 0.00 0.00 0.00 3.93
6736 21359 3.007614 TCCAAGAACCTGTAAGTGCCTAC 59.992 47.826 0.00 0.00 0.00 3.18
6737 21360 3.335579 CAAGAACCTGTAAGTGCCTACC 58.664 50.000 0.00 0.00 0.00 3.18
6738 21361 2.616524 AGAACCTGTAAGTGCCTACCA 58.383 47.619 0.00 0.00 0.00 3.25
6741 21364 4.042934 AGAACCTGTAAGTGCCTACCATTT 59.957 41.667 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.187599 AAACGTCTTGGCAGATGCGC 62.188 55.000 0.00 0.00 39.43 6.09
34 35 1.577328 CCGCAAACGTCTTGGCAGAT 61.577 55.000 10.89 0.00 37.70 2.90
101 102 1.175983 TCAATGCACGGACCCAAACC 61.176 55.000 0.00 0.00 0.00 3.27
178 179 6.810182 GTCTAATCATGGTACGTGTTGTAAGT 59.190 38.462 0.00 0.00 34.07 2.24
223 224 1.253593 TGCGCTCTCCAGTCACAGAT 61.254 55.000 9.73 0.00 0.00 2.90
413 427 2.652348 ACCAGGGAGAGAGAGAGAAAGA 59.348 50.000 0.00 0.00 0.00 2.52
414 428 3.023832 GACCAGGGAGAGAGAGAGAAAG 58.976 54.545 0.00 0.00 0.00 2.62
415 429 2.291930 GGACCAGGGAGAGAGAGAGAAA 60.292 54.545 0.00 0.00 0.00 2.52
416 430 1.286553 GGACCAGGGAGAGAGAGAGAA 59.713 57.143 0.00 0.00 0.00 2.87
425 459 1.011595 AGAGCTTAGGACCAGGGAGA 58.988 55.000 0.00 0.00 0.00 3.71
437 471 2.093288 CCAAGATGACCTGCAGAGCTTA 60.093 50.000 17.39 0.00 0.00 3.09
449 483 2.814336 GGTTGAAGGTGACCAAGATGAC 59.186 50.000 3.63 0.00 35.95 3.06
455 489 2.241176 ACTTGAGGTTGAAGGTGACCAA 59.759 45.455 3.63 0.00 38.42 3.67
467 501 2.048127 GCGGCGAGACTTGAGGTT 60.048 61.111 12.98 0.00 0.00 3.50
483 517 4.741781 GTGTGCGCCATCGTGTGC 62.742 66.667 4.18 0.00 42.05 4.57
487 521 3.353836 GGTTGTGTGCGCCATCGT 61.354 61.111 4.18 0.00 38.14 3.73
538 572 1.092348 ACAGCACATGTAGCATGCAG 58.908 50.000 21.98 6.52 41.60 4.41
574 608 1.449601 AGCGCAATAGAACCCGGTG 60.450 57.895 11.47 0.00 0.00 4.94
643 677 2.574929 GTCCGTGCCGACCACATA 59.425 61.111 6.91 0.00 44.91 2.29
718 780 3.462483 TTCTTTCGAACAGGCTGTGTA 57.538 42.857 22.83 6.83 39.03 2.90
734 1259 1.066143 CCCAGCTGTCCACGTATTCTT 60.066 52.381 13.81 0.00 0.00 2.52
780 3522 4.141505 TGTCCTCTCCATCTGTCAAAAACA 60.142 41.667 0.00 0.00 36.18 2.83
813 3556 1.544917 AAGGGCATCTCCAAGGGGT 60.545 57.895 0.00 0.00 36.21 4.95
848 3591 9.832445 CCAGCTATCAAGAGGTAAAAGTAATTA 57.168 33.333 0.00 0.00 0.00 1.40
935 3690 2.039624 ATCGCTCTCCACCTGGGT 59.960 61.111 0.00 0.00 38.11 4.51
939 3694 1.145598 CATGCATCGCTCTCCACCT 59.854 57.895 0.00 0.00 0.00 4.00
941 3696 0.745845 AACCATGCATCGCTCTCCAC 60.746 55.000 0.00 0.00 0.00 4.02
966 3721 0.324738 TGTCTGCCTGGCTAGCTAGT 60.325 55.000 24.56 0.00 0.00 2.57
976 3731 0.535780 TGGTTGAGCTTGTCTGCCTG 60.536 55.000 0.00 0.00 0.00 4.85
1018 3777 1.000896 CCATCACCACCCCCAAGAC 60.001 63.158 0.00 0.00 0.00 3.01
1111 3871 0.593128 GTGATGTCACAGTTGGGCAC 59.407 55.000 8.22 0.00 45.75 5.01
1211 3971 2.050077 GTGGTTTGCTTGAGCGGC 60.050 61.111 0.00 0.00 45.83 6.53
1248 4008 2.067932 CTTGGACTTGGAGGGTGCCA 62.068 60.000 0.00 0.00 35.78 4.92
1281 4045 4.142902 CGTATGACCTTCACAAATGACCAC 60.143 45.833 0.00 0.00 33.38 4.16
1282 4046 4.000325 CGTATGACCTTCACAAATGACCA 59.000 43.478 0.00 0.00 33.38 4.02
1283 4047 4.000988 ACGTATGACCTTCACAAATGACC 58.999 43.478 0.00 0.00 33.38 4.02
1284 4048 5.220154 CGTACGTATGACCTTCACAAATGAC 60.220 44.000 9.25 0.00 33.38 3.06
1296 4066 1.009222 CTCGCCCGTACGTATGACC 60.009 63.158 16.44 5.60 0.00 4.02
1314 4084 2.676342 ACCGTTGCCATCGACTTTTATC 59.324 45.455 0.00 0.00 0.00 1.75
1381 4151 2.686915 GGATGAGCTGGTTGGATGAAAG 59.313 50.000 0.00 0.00 0.00 2.62
1404 4174 0.540365 CCTGGACATTGCAACCCACT 60.540 55.000 0.00 0.00 0.00 4.00
1443 4213 2.753043 CAGCTGGCCATGGTCACC 60.753 66.667 17.02 9.69 0.00 4.02
1497 4267 1.472376 GCTTCAAGAGTGGATAGCGCT 60.472 52.381 17.26 17.26 0.00 5.92
1548 4318 1.883926 TCGAAGACAATGTCCGACTGA 59.116 47.619 10.12 0.00 32.18 3.41
1590 4360 3.189910 TGTAGAACGCACTATCGACAAGT 59.810 43.478 0.00 0.00 29.93 3.16
1607 4377 3.249799 CCATTTGAGTTGCACGTTGTAGA 59.750 43.478 0.00 0.00 0.00 2.59
1620 4390 0.400213 TCCAGCCGAACCATTTGAGT 59.600 50.000 0.00 0.00 0.00 3.41
1643 4413 3.933722 ACTGCTGGTCTGCGCTGT 61.934 61.111 9.73 0.00 35.36 4.40
1773 4543 2.227036 AACCTCCCAGTCCAGCCAG 61.227 63.158 0.00 0.00 0.00 4.85
1836 4614 0.970640 TACCCTTTGTGCAGTCGCTA 59.029 50.000 0.00 0.00 39.64 4.26
1938 4761 4.211164 GCAAAGAGAAACCCCGAAAATTTG 59.789 41.667 0.00 0.00 0.00 2.32
1967 4790 4.453478 CCGAATCAATACATGCATGCTAGT 59.547 41.667 26.53 18.59 0.00 2.57
1976 4799 9.317936 ACACATATATAGCCGAATCAATACATG 57.682 33.333 0.00 0.00 0.00 3.21
1985 4812 9.503399 TCGATATCTACACATATATAGCCGAAT 57.497 33.333 0.34 0.00 0.00 3.34
2018 4849 1.754803 CACCTAGCGTACCCTTCATGA 59.245 52.381 0.00 0.00 0.00 3.07
2019 4850 1.806623 GCACCTAGCGTACCCTTCATG 60.807 57.143 0.00 0.00 0.00 3.07
2035 4872 0.609131 ACAAGCACCACCATAGCACC 60.609 55.000 0.00 0.00 0.00 5.01
2066 4906 4.565652 GGACACCGGCAATAATATGATCCT 60.566 45.833 0.00 0.00 0.00 3.24
2100 4940 3.043999 GCAGGGTAGGGTCGCCATT 62.044 63.158 0.00 0.00 0.00 3.16
2125 4968 0.976641 TGAGACGGAACTGAGGCAAT 59.023 50.000 0.00 0.00 0.00 3.56
2126 4969 0.318441 CTGAGACGGAACTGAGGCAA 59.682 55.000 0.00 0.00 0.00 4.52
2159 5009 2.118233 TAGATGCGGTTGCCACACCA 62.118 55.000 0.00 0.00 41.78 4.17
2160 5010 0.748005 ATAGATGCGGTTGCCACACC 60.748 55.000 0.00 0.00 41.78 4.16
2161 5011 1.094785 AATAGATGCGGTTGCCACAC 58.905 50.000 0.00 0.00 41.78 3.82
2162 5012 1.832883 AAATAGATGCGGTTGCCACA 58.167 45.000 0.00 0.00 41.78 4.17
2163 5013 2.939460 AAAATAGATGCGGTTGCCAC 57.061 45.000 0.00 0.00 41.78 5.01
2164 5014 4.013728 AGTAAAAATAGATGCGGTTGCCA 58.986 39.130 0.00 0.00 41.78 4.92
2196 5047 5.957798 TCTTGTTCATTCCTCATTTGCATC 58.042 37.500 0.00 0.00 0.00 3.91
2198 5049 5.787953 TTCTTGTTCATTCCTCATTTGCA 57.212 34.783 0.00 0.00 0.00 4.08
2264 5220 6.869913 CACTTAGTTGAGTTTATCCGGTGTTA 59.130 38.462 0.00 0.00 0.00 2.41
2276 5244 6.038271 CCTTTAACTGCACACTTAGTTGAGTT 59.962 38.462 0.00 0.00 37.66 3.01
2278 5246 5.758296 TCCTTTAACTGCACACTTAGTTGAG 59.242 40.000 0.00 0.00 37.66 3.02
2283 5251 6.166279 TCTGATCCTTTAACTGCACACTTAG 58.834 40.000 0.00 0.00 0.00 2.18
2341 5361 6.154203 TGTTCTCTAAGATGATGGCACTAG 57.846 41.667 0.00 0.00 0.00 2.57
2368 5388 6.838382 AGGTTAGTGTCATTTTTAGTCCTGT 58.162 36.000 0.00 0.00 0.00 4.00
2397 5421 7.981789 TGACCTTTTGTTTGTTTATGTGCAATA 59.018 29.630 0.00 0.00 0.00 1.90
2429 5454 8.351461 GCTAACTAATCCGTAAAGTCTCACTAT 58.649 37.037 0.00 0.00 0.00 2.12
2468 6511 7.227910 GTGTTCTTAATTTTAGTCCACCTGTGA 59.772 37.037 0.00 0.00 0.00 3.58
2486 6529 9.527157 TGAATCCCTTCATAATTTGTGTTCTTA 57.473 29.630 0.00 0.00 36.46 2.10
2494 6537 9.090692 GAACAATGTGAATCCCTTCATAATTTG 57.909 33.333 0.00 0.00 43.08 2.32
2499 6542 6.484288 AGTGAACAATGTGAATCCCTTCATA 58.516 36.000 0.00 0.00 43.08 2.15
2502 6545 4.156739 GGAGTGAACAATGTGAATCCCTTC 59.843 45.833 1.87 0.00 0.00 3.46
2511 6555 6.907206 AACAAAATTGGAGTGAACAATGTG 57.093 33.333 0.00 0.00 38.47 3.21
2533 6578 5.079689 TGACGCTGTCCATGAGTAATTAA 57.920 39.130 0.00 0.00 0.00 1.40
2534 6579 4.729227 TGACGCTGTCCATGAGTAATTA 57.271 40.909 0.00 0.00 0.00 1.40
2546 6592 7.061752 AGTTCTATAACAAAATGACGCTGTC 57.938 36.000 2.32 2.32 38.12 3.51
2605 6666 1.098050 GCCCTCTGATGCGAACATTT 58.902 50.000 0.00 0.00 36.35 2.32
2623 6684 5.334414 GGAACATCACAATATCCATCTTCGC 60.334 44.000 0.00 0.00 0.00 4.70
2632 6695 2.887152 GGGGCAGGAACATCACAATATC 59.113 50.000 0.00 0.00 0.00 1.63
2639 6702 0.482446 AAGTTGGGGCAGGAACATCA 59.518 50.000 0.00 0.00 0.00 3.07
2640 6703 2.507407 TAAGTTGGGGCAGGAACATC 57.493 50.000 0.00 0.00 0.00 3.06
2647 7162 3.588955 GCTCATTTTTAAGTTGGGGCAG 58.411 45.455 0.00 0.00 0.00 4.85
2675 7191 4.074970 ACTGGTGGAGAGCTGTTAAAATG 58.925 43.478 0.00 0.00 0.00 2.32
2689 7207 2.021723 GCTTGGTTTGTCACTGGTGGA 61.022 52.381 0.70 0.00 0.00 4.02
2695 7213 0.107410 TGGTCGCTTGGTTTGTCACT 60.107 50.000 0.00 0.00 0.00 3.41
2696 7214 0.951558 ATGGTCGCTTGGTTTGTCAC 59.048 50.000 0.00 0.00 0.00 3.67
2708 7226 4.098416 GCTGACAAAGATTTTATGGTCGC 58.902 43.478 0.00 0.00 0.00 5.19
2726 7245 7.378461 GTAAAATCGTTTTCACAGATTTGCTGA 59.622 33.333 0.00 0.00 41.89 4.26
2744 7899 6.027749 GGCAGATGTTTTACCTGTAAAATCG 58.972 40.000 15.89 9.41 44.01 3.34
2745 7900 6.919721 TGGCAGATGTTTTACCTGTAAAATC 58.080 36.000 15.89 11.38 44.01 2.17
2751 7906 5.606348 TTTTTGGCAGATGTTTTACCTGT 57.394 34.783 0.00 0.00 0.00 4.00
2775 7934 6.262944 TCGGATGAATATTTTGCTGCTAATGT 59.737 34.615 0.00 0.00 0.00 2.71
2776 7935 6.671190 TCGGATGAATATTTTGCTGCTAATG 58.329 36.000 0.00 0.00 0.00 1.90
2808 7983 9.585099 ACTTGTATATGGTGCAAAATTTGTATG 57.415 29.630 7.60 0.00 31.83 2.39
2873 10172 6.153851 TCGAGATCCAGTGGAGTTTGTTTATA 59.846 38.462 18.69 0.00 34.05 0.98
2875 10174 4.282449 TCGAGATCCAGTGGAGTTTGTTTA 59.718 41.667 18.69 0.00 34.05 2.01
2919 10292 1.078709 GTTCTCGCATTACTGCTGCA 58.921 50.000 0.88 0.88 46.65 4.41
2931 10304 3.067461 AGTGGTAGATCTCATGTTCTCGC 59.933 47.826 0.00 0.00 0.00 5.03
2956 10329 4.865776 ACCAATGAAAAGATTCGCGAAAA 58.134 34.783 27.23 3.73 38.46 2.29
2957 10330 4.497473 ACCAATGAAAAGATTCGCGAAA 57.503 36.364 27.23 7.71 38.46 3.46
2958 10331 4.932799 TCTACCAATGAAAAGATTCGCGAA 59.067 37.500 25.66 25.66 38.46 4.70
2959 10332 4.500127 TCTACCAATGAAAAGATTCGCGA 58.500 39.130 3.71 3.71 38.46 5.87
2960 10333 4.857871 TCTACCAATGAAAAGATTCGCG 57.142 40.909 0.00 0.00 38.46 5.87
2961 10334 5.354234 TCCTTCTACCAATGAAAAGATTCGC 59.646 40.000 0.00 0.00 38.46 4.70
2962 10335 6.985188 TCCTTCTACCAATGAAAAGATTCG 57.015 37.500 0.00 0.00 38.46 3.34
2963 10336 8.341892 AGTTCCTTCTACCAATGAAAAGATTC 57.658 34.615 0.00 0.00 36.04 2.52
2965 10338 8.826765 TCTAGTTCCTTCTACCAATGAAAAGAT 58.173 33.333 0.00 0.00 0.00 2.40
2966 10339 8.202461 TCTAGTTCCTTCTACCAATGAAAAGA 57.798 34.615 0.00 0.00 0.00 2.52
2969 10342 8.602424 TCATTCTAGTTCCTTCTACCAATGAAA 58.398 33.333 0.00 0.00 29.99 2.69
2970 10343 8.146053 TCATTCTAGTTCCTTCTACCAATGAA 57.854 34.615 0.00 0.00 29.99 2.57
2972 10345 7.493971 CACTCATTCTAGTTCCTTCTACCAATG 59.506 40.741 0.00 0.00 0.00 2.82
2974 10347 6.724441 TCACTCATTCTAGTTCCTTCTACCAA 59.276 38.462 0.00 0.00 0.00 3.67
2975 10348 6.253758 TCACTCATTCTAGTTCCTTCTACCA 58.746 40.000 0.00 0.00 0.00 3.25
2980 10353 8.608844 TTTTTCTCACTCATTCTAGTTCCTTC 57.391 34.615 0.00 0.00 0.00 3.46
3033 10936 6.228273 AGTGAACGTCATACAGTTTGATTG 57.772 37.500 0.00 0.00 0.00 2.67
3047 10950 6.810182 TGTAATTAGGCTCTAAAGTGAACGTC 59.190 38.462 0.00 0.00 0.00 4.34
3049 10952 6.035758 GGTGTAATTAGGCTCTAAAGTGAACG 59.964 42.308 0.00 0.00 0.00 3.95
3093 10999 0.343372 TTCTCCCCCTAGGACAGCAT 59.657 55.000 11.48 0.00 40.93 3.79
3111 11017 1.620323 GATTTGGGCTGCCTGTTCTTT 59.380 47.619 19.68 0.00 0.00 2.52
3117 11023 2.045045 TCGGATTTGGGCTGCCTG 60.045 61.111 19.68 0.00 0.00 4.85
3162 12319 8.686334 CCATTACCTGTTTGATAAAGTAGCAAT 58.314 33.333 0.00 0.00 33.67 3.56
3248 12409 0.322546 GTTGAACCCTGGCCAGTAGG 60.323 60.000 30.63 26.29 38.23 3.18
3334 12504 1.215647 CGTGGTAGGAGTCAGCCAC 59.784 63.158 15.71 15.71 45.64 5.01
3338 12508 1.202582 CCTTGACGTGGTAGGAGTCAG 59.797 57.143 0.00 0.00 44.37 3.51
3339 12509 1.202964 TCCTTGACGTGGTAGGAGTCA 60.203 52.381 0.00 0.00 42.36 3.41
3370 12540 2.031682 GGACATGCACTGTGTTGTTCTC 60.032 50.000 16.03 7.09 38.54 2.87
3394 12565 0.332293 TCCATGATGGCTTTGCTGGA 59.668 50.000 6.59 0.00 37.47 3.86
3395 12566 1.410004 ATCCATGATGGCTTTGCTGG 58.590 50.000 6.59 0.00 37.47 4.85
3412 12583 8.594881 AATGAGAAGTTCGTGTGGATAATATC 57.405 34.615 0.00 0.00 0.00 1.63
3419 12590 2.609491 CCGAATGAGAAGTTCGTGTGGA 60.609 50.000 7.38 0.00 45.05 4.02
3422 12593 2.223971 ACACCGAATGAGAAGTTCGTGT 60.224 45.455 7.38 5.07 45.05 4.49
3426 12597 6.635641 GGTTTAAAACACCGAATGAGAAGTTC 59.364 38.462 0.00 0.00 0.00 3.01
3431 12602 5.009210 CCAAGGTTTAAAACACCGAATGAGA 59.991 40.000 5.94 0.00 39.56 3.27
3432 12603 5.219633 CCAAGGTTTAAAACACCGAATGAG 58.780 41.667 5.94 0.00 39.56 2.90
3433 12604 4.500035 GCCAAGGTTTAAAACACCGAATGA 60.500 41.667 5.94 0.00 39.56 2.57
3436 12607 2.758979 TGCCAAGGTTTAAAACACCGAA 59.241 40.909 5.94 0.00 39.56 4.30
3437 12608 2.376109 TGCCAAGGTTTAAAACACCGA 58.624 42.857 5.94 0.00 39.56 4.69
3438 12609 2.861335 GTTGCCAAGGTTTAAAACACCG 59.139 45.455 5.94 0.00 39.56 4.94
3440 12611 5.898174 AGTAGTTGCCAAGGTTTAAAACAC 58.102 37.500 5.94 0.00 0.00 3.32
3442 12613 6.038936 TCTGAGTAGTTGCCAAGGTTTAAAAC 59.961 38.462 0.00 0.00 0.00 2.43
3448 12619 2.039084 CCTCTGAGTAGTTGCCAAGGTT 59.961 50.000 3.66 0.00 0.00 3.50
3449 12620 1.625818 CCTCTGAGTAGTTGCCAAGGT 59.374 52.381 3.66 0.00 0.00 3.50
3450 12621 1.677217 GCCTCTGAGTAGTTGCCAAGG 60.677 57.143 3.66 0.00 0.00 3.61
3489 12660 2.223829 CGATAGGATGAACTCGTTGCCT 60.224 50.000 0.00 0.00 0.00 4.75
3543 12714 5.439721 CTGATCAAATCCTTGGTACCATCA 58.560 41.667 17.17 11.85 33.01 3.07
3553 12724 2.489329 CACAACCGCTGATCAAATCCTT 59.511 45.455 0.00 0.00 0.00 3.36
3561 12732 3.490890 GAGGCACAACCGCTGATC 58.509 61.111 0.00 0.00 46.52 2.92
3579 12750 1.072505 GACGTTGGAGGGGCAGAAA 59.927 57.895 0.00 0.00 0.00 2.52
3730 12907 3.655481 CAACTCCAGGTTGCCGTC 58.345 61.111 0.00 0.00 46.89 4.79
3736 12913 1.052124 TGGGACGTCAACTCCAGGTT 61.052 55.000 18.91 0.00 38.93 3.50
3740 12917 2.741092 GCTGGGACGTCAACTCCA 59.259 61.111 18.91 14.05 0.00 3.86
3828 13005 3.308402 CCTTGGCTAGTTTGGATTCCTCA 60.308 47.826 3.95 0.00 0.00 3.86
3841 13018 0.678048 GGAACCTGCACCTTGGCTAG 60.678 60.000 0.00 0.00 34.04 3.42
3906 13083 1.769098 CTGGATGCGCCTTCATGTCG 61.769 60.000 4.18 0.00 37.63 4.35
3926 13103 2.352032 GCTACCTCGGCTGGACAGT 61.352 63.158 0.82 0.00 0.00 3.55
3936 13113 2.100631 CAGTTTGCGGGCTACCTCG 61.101 63.158 0.00 0.00 33.28 4.63
4233 15722 7.916914 ACCAAGTGTAATACAATACTTGTCC 57.083 36.000 16.09 0.00 45.16 4.02
4280 15834 7.120873 TCGATTAGTATCTACACTAGAATGGCC 59.879 40.741 0.00 0.00 38.50 5.36
4282 15836 9.221933 AGTCGATTAGTATCTACACTAGAATGG 57.778 37.037 0.00 0.00 38.50 3.16
4311 15881 6.272822 ACATTTTCATGGGAAGAAGCTAAC 57.727 37.500 0.00 0.00 34.27 2.34
4314 15884 5.813513 AAACATTTTCATGGGAAGAAGCT 57.186 34.783 0.00 0.00 34.27 3.74
4453 16038 3.141398 TGGCTTTGTGAGTTCAGATGAC 58.859 45.455 0.00 0.00 0.00 3.06
4458 16053 4.747810 ACTTTTTGGCTTTGTGAGTTCAG 58.252 39.130 0.00 0.00 0.00 3.02
4468 16063 4.879545 TCACTCGAGTAACTTTTTGGCTTT 59.120 37.500 19.57 0.00 0.00 3.51
4485 16080 4.434330 GGAGTAATCGCAAAAGTTCACTCG 60.434 45.833 0.00 0.00 33.58 4.18
4498 16095 0.179100 TCAGCAGCAGGAGTAATCGC 60.179 55.000 0.00 0.00 0.00 4.58
4499 16096 1.135915 ACTCAGCAGCAGGAGTAATCG 59.864 52.381 15.89 0.00 42.30 3.34
4654 16259 5.917541 TGAATTTCTTACGTGTGAAGGAC 57.082 39.130 0.00 0.00 0.00 3.85
4665 16270 7.381139 TGGCTTTTCGATGTTTGAATTTCTTAC 59.619 33.333 0.00 0.00 0.00 2.34
4690 16295 5.424121 AGAACTTCCGTTTCAACATCTTG 57.576 39.130 0.00 0.00 32.39 3.02
4691 16296 5.277345 CGAAGAACTTCCGTTTCAACATCTT 60.277 40.000 8.66 0.00 36.27 2.40
4741 16347 6.757897 TTAGCTCTTTGTGATACCAATTGG 57.242 37.500 23.31 23.31 42.17 3.16
4787 16393 3.465871 CCTTCTCAAGCTCATCTAAGGC 58.534 50.000 0.00 0.00 0.00 4.35
5174 16780 9.156940 CTTGATATCTCTATGGATGATGGGTAT 57.843 37.037 3.98 0.00 0.00 2.73
5245 16855 4.872691 ACATATCTTGAAGCTCCAAAGTCG 59.127 41.667 0.00 0.00 0.00 4.18
5528 17138 3.748568 GCGACTTCTTCCATTTCTCTGTT 59.251 43.478 0.00 0.00 0.00 3.16
5529 17139 3.244215 TGCGACTTCTTCCATTTCTCTGT 60.244 43.478 0.00 0.00 0.00 3.41
5690 17300 5.598830 TGGATAATTCTTCGCTCCTACTTCT 59.401 40.000 0.00 0.00 0.00 2.85
5756 17366 4.816925 GCTTAAGCAGAATTACCGAGGATT 59.183 41.667 22.59 0.00 41.59 3.01
5767 17377 3.086733 GCTCGGGCTTAAGCAGAAT 57.913 52.632 27.83 0.00 44.36 2.40
5836 17490 2.224378 ACAGACAAGGGATATGGATGCG 60.224 50.000 0.00 0.00 0.00 4.73
5837 17491 3.498774 ACAGACAAGGGATATGGATGC 57.501 47.619 0.00 0.00 0.00 3.91
5838 17492 4.581824 CCAAACAGACAAGGGATATGGATG 59.418 45.833 0.00 0.00 0.00 3.51
5845 17499 5.520748 AATAGACCAAACAGACAAGGGAT 57.479 39.130 0.00 0.00 0.00 3.85
5854 17508 5.404946 CATGGAAGCAAATAGACCAAACAG 58.595 41.667 0.00 0.00 34.28 3.16
5855 17509 4.220382 CCATGGAAGCAAATAGACCAAACA 59.780 41.667 5.56 0.00 34.28 2.83
6011 17683 4.253685 ACAATCGATCGGAACAAAGTGAT 58.746 39.130 16.41 0.00 0.00 3.06
6048 17720 3.884091 ACGTATAGTGTAGCTCCAGGAAG 59.116 47.826 0.00 0.00 0.00 3.46
6066 17738 5.795972 TGACCATTTGGATAACTCAACGTA 58.204 37.500 3.01 0.00 38.94 3.57
6067 17739 4.647611 TGACCATTTGGATAACTCAACGT 58.352 39.130 3.01 0.00 38.94 3.99
6084 17762 2.441375 TGGTGTTTGATTCTCCTGACCA 59.559 45.455 0.00 0.00 0.00 4.02
6123 17801 2.604174 CCGAGGAAACACACGCACC 61.604 63.158 0.00 0.00 0.00 5.01
6137 17815 4.332819 GTCCATAACATTTTGGAGTCCGAG 59.667 45.833 4.30 0.00 42.55 4.63
6140 17818 4.142381 GCTGTCCATAACATTTTGGAGTCC 60.142 45.833 0.73 0.73 42.55 3.85
6197 17877 3.067106 GTGCTTAGCTGCTGTTTGAGTA 58.933 45.455 13.43 0.00 0.00 2.59
6212 17892 7.254761 CCGAATGTGCAAATCTATAAGTGCTTA 60.255 37.037 0.00 0.00 37.87 3.09
6505 18191 7.670605 TTGGCTAGACAAATGGTACTAGTAT 57.329 36.000 9.08 0.00 35.96 2.12
6535 18221 7.215789 TCAACCAAACCGTACTAACATTTCTA 58.784 34.615 0.00 0.00 0.00 2.10
6575 19497 5.819825 AGTCTCTTGAACACCAGTTTTTC 57.180 39.130 0.00 0.00 38.30 2.29
6625 19547 5.378230 TCCATAGTGAATTGCTCTCCATT 57.622 39.130 0.00 0.00 0.00 3.16
6644 21264 6.068010 ACCATTCTGTCATTTACAAGTTCCA 58.932 36.000 0.00 0.00 37.74 3.53
6721 21344 5.710409 ATAAATGGTAGGCACTTACAGGT 57.290 39.130 0.00 0.00 41.75 4.00
6722 21345 5.885912 ACAATAAATGGTAGGCACTTACAGG 59.114 40.000 0.00 0.00 41.75 4.00
6723 21346 6.823689 AGACAATAAATGGTAGGCACTTACAG 59.176 38.462 0.00 0.00 41.75 2.74
6724 21347 6.717289 AGACAATAAATGGTAGGCACTTACA 58.283 36.000 0.00 0.00 41.75 2.41
6726 21349 9.914834 AATAAGACAATAAATGGTAGGCACTTA 57.085 29.630 0.00 0.00 41.75 2.24
6727 21350 8.823220 AATAAGACAATAAATGGTAGGCACTT 57.177 30.769 0.00 0.00 41.75 3.16
6728 21351 8.686334 CAAATAAGACAATAAATGGTAGGCACT 58.314 33.333 0.00 0.00 46.37 4.40
6729 21352 8.682710 TCAAATAAGACAATAAATGGTAGGCAC 58.317 33.333 0.00 0.00 0.00 5.01
6730 21353 8.682710 GTCAAATAAGACAATAAATGGTAGGCA 58.317 33.333 0.00 0.00 38.40 4.75
6731 21354 8.682710 TGTCAAATAAGACAATAAATGGTAGGC 58.317 33.333 0.00 0.00 44.92 3.93
6733 21356 9.722056 GCTGTCAAATAAGACAATAAATGGTAG 57.278 33.333 0.00 0.00 46.90 3.18
6734 21357 9.237187 TGCTGTCAAATAAGACAATAAATGGTA 57.763 29.630 0.00 0.00 46.90 3.25
6735 21358 8.121305 TGCTGTCAAATAAGACAATAAATGGT 57.879 30.769 0.00 0.00 46.90 3.55
6736 21359 9.027129 CATGCTGTCAAATAAGACAATAAATGG 57.973 33.333 0.00 0.00 46.90 3.16
6737 21360 9.577110 ACATGCTGTCAAATAAGACAATAAATG 57.423 29.630 0.00 0.00 46.90 2.32
6738 21361 9.793252 GACATGCTGTCAAATAAGACAATAAAT 57.207 29.630 10.30 0.00 46.90 1.40


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

AutoCloner maintained by Alex Coulton.