Multiple sequence alignment - TraesCS4A01G483700

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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 TraesCS4A01G483700 chr4A 100.000 4202 0 0 1 4202 738525087 738520886 0.000000e+00 7760.0
1 TraesCS4A01G483700 chr4A 85.634 2847 345 39 1087 3893 738351486 738354308 0.000000e+00 2933.0
2 TraesCS4A01G483700 chr4A 84.842 2342 305 37 1491 3800 737854198 737851875 0.000000e+00 2313.0
3 TraesCS4A01G483700 chr4A 85.429 1853 238 23 1492 3338 738391480 738389654 0.000000e+00 1897.0
4 TraesCS4A01G483700 chr4A 87.350 1336 154 13 1093 2421 737846087 737844760 0.000000e+00 1517.0
5 TraesCS4A01G483700 chr4A 85.019 267 26 6 3904 4156 737844336 737844070 4.170000e-65 259.0
6 TraesCS4A01G483700 chr4A 89.000 200 13 2 3455 3651 738384648 738384455 5.430000e-59 239.0
7 TraesCS4A01G483700 chr4A 82.727 220 22 8 3947 4151 738354315 738354533 9.280000e-42 182.0
8 TraesCS4A01G483700 chr4A 85.350 157 16 2 3927 4077 738384277 738384122 5.630000e-34 156.0
9 TraesCS4A01G483700 chr7A 87.253 2479 279 23 1087 3542 5000307 5002771 0.000000e+00 2793.0
10 TraesCS4A01G483700 chr7A 86.693 2292 284 16 1087 3372 5610752 5613028 0.000000e+00 2523.0
11 TraesCS4A01G483700 chr7A 86.455 2296 290 17 1087 3372 5353401 5351117 0.000000e+00 2497.0
12 TraesCS4A01G483700 chr7A 86.111 2268 282 17 1093 3356 5748109 5745871 0.000000e+00 2412.0
13 TraesCS4A01G483700 chr7A 87.083 1649 204 5 1722 3366 5023345 5024988 0.000000e+00 1857.0
14 TraesCS4A01G483700 chr7A 86.814 1130 128 17 1093 2210 5777193 5776073 0.000000e+00 1242.0
15 TraesCS4A01G483700 chr7A 88.610 597 64 3 1093 1689 5022763 5023355 0.000000e+00 723.0
16 TraesCS4A01G483700 chr7A 86.726 113 8 2 3540 3651 5007864 5007970 7.380000e-23 119.0
17 TraesCS4A01G483700 chr1B 89.954 1095 62 26 1 1086 16129510 16128455 0.000000e+00 1369.0
18 TraesCS4A01G483700 chr1B 86.306 1110 116 28 1 1086 57700462 57699365 0.000000e+00 1175.0
19 TraesCS4A01G483700 chr7B 87.455 1108 112 19 1 1088 596613536 596612436 0.000000e+00 1251.0
20 TraesCS4A01G483700 chr6B 86.787 1105 121 21 1 1088 713917213 713918309 0.000000e+00 1208.0
21 TraesCS4A01G483700 chr4B 86.673 1088 113 25 1 1069 613705700 613706774 0.000000e+00 1177.0
22 TraesCS4A01G483700 chr3B 85.650 1108 126 25 1 1088 68197668 68196574 0.000000e+00 1134.0
23 TraesCS4A01G483700 chr3B 85.789 950 106 22 1 929 752521953 752522894 0.000000e+00 979.0
24 TraesCS4A01G483700 chr2D 85.070 1065 151 6 2310 3372 614368090 614369148 0.000000e+00 1079.0
25 TraesCS4A01G483700 chr5A 85.774 949 109 19 1 930 32100214 32101155 0.000000e+00 981.0
26 TraesCS4A01G483700 chr5A 85.549 948 111 21 1 930 30787529 30786590 0.000000e+00 968.0
27 TraesCS4A01G483700 chr5A 92.920 113 6 1 976 1088 32101163 32101273 3.360000e-36 163.0
28 TraesCS4A01G483700 chr2B 95.601 591 23 3 499 1088 172171616 172171028 0.000000e+00 944.0
29 TraesCS4A01G483700 chr7D 85.805 472 65 2 1087 1557 5025340 5025810 2.260000e-137 499.0
30 TraesCS4A01G483700 chr5D 94.444 144 6 1 945 1088 482871357 482871216 1.970000e-53 220.0
31 TraesCS4A01G483700 chr6D 97.059 34 1 0 4169 4202 53280070 53280037 1.630000e-04 58.4
32 TraesCS4A01G483700 chr6D 97.059 34 1 0 4169 4202 109355610 109355643 1.630000e-04 58.4
33 TraesCS4A01G483700 chr6D 97.059 34 1 0 4169 4202 152387961 152387994 1.630000e-04 58.4
34 TraesCS4A01G483700 chr6D 97.059 34 1 0 4169 4202 297342334 297342367 1.630000e-04 58.4
35 TraesCS4A01G483700 chr6D 97.059 34 1 0 4169 4202 343692465 343692432 1.630000e-04 58.4
36 TraesCS4A01G483700 chr4D 94.595 37 2 0 4166 4202 377556679 377556715 1.630000e-04 58.4
37 TraesCS4A01G483700 chr4D 94.595 37 2 0 4166 4202 377563517 377563553 1.630000e-04 58.4
38 TraesCS4A01G483700 chr1D 97.059 34 1 0 4169 4202 57703046 57703079 1.630000e-04 58.4
39 TraesCS4A01G483700 chr1D 97.059 34 1 0 4169 4202 134791308 134791275 1.630000e-04 58.4


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 TraesCS4A01G483700 chr4A 738520886 738525087 4201 True 7760.0 7760 100.0000 1 4202 1 chr4A.!!$R3 4201
1 TraesCS4A01G483700 chr4A 737851875 737854198 2323 True 2313.0 2313 84.8420 1491 3800 1 chr4A.!!$R1 2309
2 TraesCS4A01G483700 chr4A 738389654 738391480 1826 True 1897.0 1897 85.4290 1492 3338 1 chr4A.!!$R2 1846
3 TraesCS4A01G483700 chr4A 738351486 738354533 3047 False 1557.5 2933 84.1805 1087 4151 2 chr4A.!!$F1 3064
4 TraesCS4A01G483700 chr4A 737844070 737846087 2017 True 888.0 1517 86.1845 1093 4156 2 chr4A.!!$R4 3063
5 TraesCS4A01G483700 chr7A 5000307 5002771 2464 False 2793.0 2793 87.2530 1087 3542 1 chr7A.!!$F1 2455
6 TraesCS4A01G483700 chr7A 5610752 5613028 2276 False 2523.0 2523 86.6930 1087 3372 1 chr7A.!!$F3 2285
7 TraesCS4A01G483700 chr7A 5351117 5353401 2284 True 2497.0 2497 86.4550 1087 3372 1 chr7A.!!$R1 2285
8 TraesCS4A01G483700 chr7A 5745871 5748109 2238 True 2412.0 2412 86.1110 1093 3356 1 chr7A.!!$R2 2263
9 TraesCS4A01G483700 chr7A 5022763 5024988 2225 False 1290.0 1857 87.8465 1093 3366 2 chr7A.!!$F4 2273
10 TraesCS4A01G483700 chr7A 5776073 5777193 1120 True 1242.0 1242 86.8140 1093 2210 1 chr7A.!!$R3 1117
11 TraesCS4A01G483700 chr1B 16128455 16129510 1055 True 1369.0 1369 89.9540 1 1086 1 chr1B.!!$R1 1085
12 TraesCS4A01G483700 chr1B 57699365 57700462 1097 True 1175.0 1175 86.3060 1 1086 1 chr1B.!!$R2 1085
13 TraesCS4A01G483700 chr7B 596612436 596613536 1100 True 1251.0 1251 87.4550 1 1088 1 chr7B.!!$R1 1087
14 TraesCS4A01G483700 chr6B 713917213 713918309 1096 False 1208.0 1208 86.7870 1 1088 1 chr6B.!!$F1 1087
15 TraesCS4A01G483700 chr4B 613705700 613706774 1074 False 1177.0 1177 86.6730 1 1069 1 chr4B.!!$F1 1068
16 TraesCS4A01G483700 chr3B 68196574 68197668 1094 True 1134.0 1134 85.6500 1 1088 1 chr3B.!!$R1 1087
17 TraesCS4A01G483700 chr3B 752521953 752522894 941 False 979.0 979 85.7890 1 929 1 chr3B.!!$F1 928
18 TraesCS4A01G483700 chr2D 614368090 614369148 1058 False 1079.0 1079 85.0700 2310 3372 1 chr2D.!!$F1 1062
19 TraesCS4A01G483700 chr5A 30786590 30787529 939 True 968.0 968 85.5490 1 930 1 chr5A.!!$R1 929
20 TraesCS4A01G483700 chr5A 32100214 32101273 1059 False 572.0 981 89.3470 1 1088 2 chr5A.!!$F1 1087
21 TraesCS4A01G483700 chr2B 172171028 172171616 588 True 944.0 944 95.6010 499 1088 1 chr2B.!!$R1 589

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
917 957 0.251653 ACCCAAGCGAGGTCACTCTA 60.252 55.0 0.0 0.0 41.71 2.43 F
2472 2589 0.035881 ATGCGACAGCCATGATAGGG 59.964 55.0 0.0 0.0 44.33 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2655 2778 0.245266 TCAACGCATCAAGAGCCGTA 59.755 50.0 0.0 0.0 0.00 4.02 R
3444 3576 0.036294 AGAGTCCCAAAAGGCTACGC 60.036 55.0 0.0 0.0 34.51 4.42 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
357 372 7.388437 TCCCAAAATGATTGAGATTTTTCCAG 58.612 34.615 0.00 0.00 31.96 3.86
358 373 7.235193 TCCCAAAATGATTGAGATTTTTCCAGA 59.765 33.333 0.00 0.00 31.96 3.86
621 643 8.024285 TGTCCGCGTTTCTTCATAAAATATTTT 58.976 29.630 17.18 17.18 0.00 1.82
794 834 3.278574 CATAAACTTCCCGGATTCTGCA 58.721 45.455 0.73 0.00 0.00 4.41
895 935 0.617413 AAGGTGGAGGTGCAGAGATG 59.383 55.000 0.00 0.00 0.00 2.90
899 939 2.079925 GTGGAGGTGCAGAGATGAAAC 58.920 52.381 0.00 0.00 0.00 2.78
917 957 0.251653 ACCCAAGCGAGGTCACTCTA 60.252 55.000 0.00 0.00 41.71 2.43
918 958 0.895530 CCCAAGCGAGGTCACTCTAA 59.104 55.000 0.00 0.00 41.71 2.10
919 959 1.275291 CCCAAGCGAGGTCACTCTAAA 59.725 52.381 0.00 0.00 41.71 1.85
920 960 2.093447 CCCAAGCGAGGTCACTCTAAAT 60.093 50.000 0.00 0.00 41.71 1.40
921 961 3.600388 CCAAGCGAGGTCACTCTAAATT 58.400 45.455 0.00 0.00 41.71 1.82
922 962 3.619038 CCAAGCGAGGTCACTCTAAATTC 59.381 47.826 0.00 0.00 41.71 2.17
923 963 4.499183 CAAGCGAGGTCACTCTAAATTCT 58.501 43.478 0.00 0.00 41.71 2.40
924 964 4.810191 AGCGAGGTCACTCTAAATTCTT 57.190 40.909 0.00 0.00 41.71 2.52
925 965 5.153950 AGCGAGGTCACTCTAAATTCTTT 57.846 39.130 0.00 0.00 41.71 2.52
926 966 5.552178 AGCGAGGTCACTCTAAATTCTTTT 58.448 37.500 0.00 0.00 41.71 2.27
927 967 5.998363 AGCGAGGTCACTCTAAATTCTTTTT 59.002 36.000 0.00 0.00 41.71 1.94
1116 1180 3.776969 TCCAACATCTCTACCTTGCTGAT 59.223 43.478 0.00 0.00 0.00 2.90
1127 1191 7.561722 TCTCTACCTTGCTGATACTCAACTATT 59.438 37.037 0.00 0.00 0.00 1.73
1170 1234 1.539065 GCACATATGACGTCCCTCCAG 60.539 57.143 14.12 0.34 0.00 3.86
1199 1263 8.184192 CCTTGATTTGTCATGTAATCCTAACAC 58.816 37.037 12.22 0.00 31.29 3.32
1203 1270 5.607939 TGTCATGTAATCCTAACACGGAT 57.392 39.130 0.00 0.00 45.59 4.18
1259 1326 5.342017 TCTGAGAATCCTGGACCTTTCTTA 58.658 41.667 11.31 7.42 0.00 2.10
1269 1336 6.434028 TCCTGGACCTTTCTTATTGTCAAATG 59.566 38.462 0.00 0.00 0.00 2.32
1330 1397 2.297701 GTCCCTTGAACAAACTGCAGA 58.702 47.619 23.35 0.00 0.00 4.26
1350 1417 3.834231 AGAAGTTGCATTTGGGCTACAAT 59.166 39.130 0.00 0.00 41.09 2.71
1371 1438 2.865119 ATATCAGCGGAATCATGCCA 57.135 45.000 0.00 0.00 0.00 4.92
1404 1471 1.816835 CACTTGACCAGCCTAGTCGTA 59.183 52.381 0.00 0.00 37.04 3.43
1430 1497 5.784177 TGACATCTCTCAGAACAACCTAAC 58.216 41.667 0.00 0.00 0.00 2.34
1434 1501 3.578716 TCTCTCAGAACAACCTAACTGGG 59.421 47.826 0.00 0.00 41.11 4.45
1441 1508 1.997040 ACAACCTAACTGGGGGCATAA 59.003 47.619 0.00 0.00 41.11 1.90
1485 1552 6.054860 TCTAGTTTAAGCAGCCTTGATCTT 57.945 37.500 0.00 0.00 32.47 2.40
1512 1579 2.567169 CAACCATCTCAGTGGACCTGTA 59.433 50.000 0.00 0.00 42.02 2.74
1515 1582 2.461695 CATCTCAGTGGACCTGTACCT 58.538 52.381 0.00 0.00 42.19 3.08
1526 1593 3.280295 GACCTGTACCTTCTGAGATCGA 58.720 50.000 0.00 0.00 0.00 3.59
1545 1612 2.095853 CGACATGCTCGGCAATTTAACT 59.904 45.455 9.07 0.00 43.62 2.24
1549 1616 4.640201 ACATGCTCGGCAATTTAACTATGT 59.360 37.500 2.68 0.00 43.62 2.29
1560 1627 7.067494 GGCAATTTAACTATGTTGGATCTCAGT 59.933 37.037 0.00 0.00 0.00 3.41
1638 1705 6.113411 GCTAAAGAGGCTGTATTTAAGTGGA 58.887 40.000 0.00 0.00 0.00 4.02
1655 1722 9.768215 TTTAAGTGGAAATTCCTTGAGGATTAT 57.232 29.630 13.78 0.00 44.98 1.28
1755 1866 2.224744 TGCATGGCTTCAGTTCCAAGTA 60.225 45.455 0.00 0.00 35.75 2.24
1762 1873 5.012664 TGGCTTCAGTTCCAAGTAGACATTA 59.987 40.000 0.00 0.00 0.00 1.90
1847 1959 2.959516 TGCAAAGGTCACAGATCTACG 58.040 47.619 0.00 0.00 0.00 3.51
1969 2081 7.660030 ATCCCCAACTTACCAAGAAATATTG 57.340 36.000 0.00 0.00 0.00 1.90
2016 2128 6.135290 TCTTTATCTGGAAATTTGCCATCG 57.865 37.500 7.27 0.00 34.33 3.84
2024 2136 4.021632 TGGAAATTTGCCATCGAACATTGA 60.022 37.500 7.27 0.00 0.00 2.57
2028 2140 4.621068 TTTGCCATCGAACATTGAGATC 57.379 40.909 0.00 0.00 0.00 2.75
2039 2151 6.091305 TCGAACATTGAGATCACAGATTTGAC 59.909 38.462 0.00 0.00 0.00 3.18
2046 2158 7.991084 TGAGATCACAGATTTGACTTCATTT 57.009 32.000 0.00 0.00 0.00 2.32
2050 2162 6.713762 TCACAGATTTGACTTCATTTTGGT 57.286 33.333 0.00 0.00 0.00 3.67
2088 2200 3.992943 ACTGGTTGTATTCCCGAATCA 57.007 42.857 0.00 0.00 32.50 2.57
2121 2233 5.014123 AGTGGAATCCTTGTATGTCTTGGAA 59.986 40.000 0.00 0.00 0.00 3.53
2194 2309 3.947910 ACATTGGCTTTCTCATGTTGG 57.052 42.857 0.00 0.00 0.00 3.77
2225 2340 2.978156 TTCTCTGGCAACTTCCCATT 57.022 45.000 0.00 0.00 37.61 3.16
2243 2358 5.010617 TCCCATTGTTTCTAAAAAGCTGGAC 59.989 40.000 0.00 0.00 0.00 4.02
2252 2367 6.899393 TCTAAAAAGCTGGACACAATTGAT 57.101 33.333 13.59 0.00 0.00 2.57
2331 2446 7.910683 GGAGATTTGGTTGAATTACGATTTCTC 59.089 37.037 0.00 0.00 0.00 2.87
2338 2453 4.617959 TGAATTACGATTTCTCCGGCTAG 58.382 43.478 0.00 0.00 0.00 3.42
2389 2504 7.056635 CCCATGTACCATCTCAAATCTTAGTT 58.943 38.462 0.00 0.00 0.00 2.24
2390 2505 7.227512 CCCATGTACCATCTCAAATCTTAGTTC 59.772 40.741 0.00 0.00 0.00 3.01
2397 2512 6.541641 CCATCTCAAATCTTAGTTCCCTTCAG 59.458 42.308 0.00 0.00 0.00 3.02
2401 2516 6.957631 TCAAATCTTAGTTCCCTTCAGCATA 58.042 36.000 0.00 0.00 0.00 3.14
2456 2573 1.584483 CGCGGCATCTGTCAAATGC 60.584 57.895 2.26 2.26 46.98 3.56
2472 2589 0.035881 ATGCGACAGCCATGATAGGG 59.964 55.000 0.00 0.00 44.33 3.53
2480 2597 3.389329 ACAGCCATGATAGGGAAGTACAG 59.611 47.826 0.00 0.00 0.00 2.74
2486 2603 5.131142 CCATGATAGGGAAGTACAGAAAGGT 59.869 44.000 0.00 0.00 0.00 3.50
2492 2609 6.361768 AGGGAAGTACAGAAAGGTTTCTAG 57.638 41.667 4.66 3.28 45.23 2.43
2500 2617 5.094387 ACAGAAAGGTTTCTAGGGATGAGA 58.906 41.667 4.66 0.00 45.23 3.27
2503 2620 5.188751 AGAAAGGTTTCTAGGGATGAGACAG 59.811 44.000 3.04 0.00 45.17 3.51
2511 2634 8.424918 GTTTCTAGGGATGAGACAGATTATGAA 58.575 37.037 0.00 0.00 0.00 2.57
2513 2636 7.301420 TCTAGGGATGAGACAGATTATGAAGT 58.699 38.462 0.00 0.00 0.00 3.01
2514 2637 8.448816 TCTAGGGATGAGACAGATTATGAAGTA 58.551 37.037 0.00 0.00 0.00 2.24
2518 2641 8.807118 GGGATGAGACAGATTATGAAGTATACA 58.193 37.037 5.50 0.00 0.00 2.29
2596 2719 9.914834 AACTTAATTATAGTACTGGCATTTGGA 57.085 29.630 5.39 0.00 0.00 3.53
2604 2727 4.592778 AGTACTGGCATTTGGAATTTGGTT 59.407 37.500 0.00 0.00 0.00 3.67
2655 2778 4.965283 TGGGGGAATACCAGAAGAAATT 57.035 40.909 0.00 0.00 42.91 1.82
2658 2781 4.820173 GGGGGAATACCAGAAGAAATTACG 59.180 45.833 0.00 0.00 42.91 3.18
2693 2816 8.551205 TGCGTTGATAAACTTGAATCTATCATC 58.449 33.333 0.00 0.00 38.03 2.92
2694 2817 8.551205 GCGTTGATAAACTTGAATCTATCATCA 58.449 33.333 0.00 0.00 38.03 3.07
2699 2822 9.869844 GATAAACTTGAATCTATCATCAAACCG 57.130 33.333 0.00 0.00 38.03 4.44
2732 2855 5.547666 AGAAATTTCCAAATAAGCTTGGGGT 59.452 36.000 14.61 0.00 45.16 4.95
2739 2862 2.603075 ATAAGCTTGGGGTCTTGCAA 57.397 45.000 9.86 0.00 0.00 4.08
2845 2968 7.119846 GCTACTTGGACTTGTCTGATAACAATT 59.880 37.037 0.61 0.00 38.41 2.32
2871 2994 1.270358 GGGAGAATACCATCAGGACGC 60.270 57.143 0.00 0.00 38.69 5.19
2883 3006 0.320683 CAGGACGCCATCTTGACACA 60.321 55.000 0.00 0.00 36.51 3.72
2956 3079 2.487986 CCTCCTCTTCCAAACAGTTGCT 60.488 50.000 0.00 0.00 33.01 3.91
2961 3084 0.821711 TTCCAAACAGTTGCTCCGGG 60.822 55.000 0.00 0.00 33.01 5.73
3026 3155 3.321682 TCCTTTGAGCCAATGACCTTTTG 59.678 43.478 0.00 0.00 0.00 2.44
3079 3208 0.962356 CTGGGTGGTGTTCTGCATCC 60.962 60.000 0.00 0.00 0.00 3.51
3087 3216 2.030805 GGTGTTCTGCATCCTGTTGTTC 60.031 50.000 0.00 0.00 0.00 3.18
3095 3224 3.953612 TGCATCCTGTTGTTCAAGAAAGT 59.046 39.130 0.00 0.00 0.00 2.66
3170 3299 4.513692 TGTGTTTTCCGTTCTTACATGGAG 59.486 41.667 0.00 0.00 0.00 3.86
3188 3317 1.136329 AGAAGCTGGGCCAGAAAGGA 61.136 55.000 37.07 0.00 41.22 3.36
3206 3335 8.567948 CAGAAAGGAAGCTACAAATTGAGTAAA 58.432 33.333 0.00 0.00 0.00 2.01
3208 3337 9.399403 GAAAGGAAGCTACAAATTGAGTAAAAG 57.601 33.333 0.00 0.00 0.00 2.27
3333 3465 8.548721 CGTGTATGATAATACTTTTGAACTCCC 58.451 37.037 1.81 0.00 0.00 4.30
3356 3488 6.036083 CCCGTATTTTCTACTGTTCAGATGTG 59.964 42.308 6.83 0.00 0.00 3.21
3366 3498 3.076621 TGTTCAGATGTGGTGCTGATTC 58.923 45.455 0.00 0.00 40.51 2.52
3374 3506 2.358582 TGTGGTGCTGATTCTTTGTGTG 59.641 45.455 0.00 0.00 0.00 3.82
3379 3511 4.224433 GTGCTGATTCTTTGTGTGTGATG 58.776 43.478 0.00 0.00 0.00 3.07
3416 3548 8.164070 ACTCCTGTATTTCCTACTGTTCATTTT 58.836 33.333 0.00 0.00 0.00 1.82
3443 3575 9.912634 ATTGTTTGTTCCATAGTTTCATAGTTG 57.087 29.630 0.00 0.00 0.00 3.16
3444 3576 7.881142 TGTTTGTTCCATAGTTTCATAGTTGG 58.119 34.615 0.00 0.00 0.00 3.77
3446 3578 4.634004 TGTTCCATAGTTTCATAGTTGGCG 59.366 41.667 0.00 0.00 0.00 5.69
3447 3579 4.481368 TCCATAGTTTCATAGTTGGCGT 57.519 40.909 0.00 0.00 0.00 5.68
3448 3580 5.601583 TCCATAGTTTCATAGTTGGCGTA 57.398 39.130 0.00 0.00 0.00 4.42
3449 3581 5.597806 TCCATAGTTTCATAGTTGGCGTAG 58.402 41.667 0.00 0.00 0.00 3.51
3564 3716 3.871006 CAGGCTGATGCTCGTTGTATTTA 59.129 43.478 9.42 0.00 39.59 1.40
3565 3717 4.512944 CAGGCTGATGCTCGTTGTATTTAT 59.487 41.667 9.42 0.00 39.59 1.40
3566 3718 5.008019 CAGGCTGATGCTCGTTGTATTTATT 59.992 40.000 9.42 0.00 39.59 1.40
3567 3719 5.590259 AGGCTGATGCTCGTTGTATTTATTT 59.410 36.000 0.00 0.00 39.59 1.40
3568 3720 6.765989 AGGCTGATGCTCGTTGTATTTATTTA 59.234 34.615 0.00 0.00 39.59 1.40
3569 3721 7.445402 AGGCTGATGCTCGTTGTATTTATTTAT 59.555 33.333 0.00 0.00 39.59 1.40
3623 3775 7.180766 TGGTGCATATGAATATAGGATGACTCA 59.819 37.037 6.97 0.00 0.00 3.41
3650 3802 9.678260 ATTGTGTAAATTTTGAGATAGAGCTCT 57.322 29.630 22.17 22.17 35.91 4.09
3662 3814 8.160521 TGAGATAGAGCTCTAAGTACAACATC 57.839 38.462 26.62 16.64 35.91 3.06
3667 3819 3.510360 AGCTCTAAGTACAACATCGTGGT 59.490 43.478 0.00 0.00 0.00 4.16
3670 3822 5.456548 TCTAAGTACAACATCGTGGTCAA 57.543 39.130 0.00 0.00 0.00 3.18
3677 3829 1.338107 ACATCGTGGTCAACTCTGGA 58.662 50.000 0.00 0.00 0.00 3.86
3678 3830 1.691976 ACATCGTGGTCAACTCTGGAA 59.308 47.619 0.00 0.00 0.00 3.53
3681 3833 4.020573 ACATCGTGGTCAACTCTGGAATTA 60.021 41.667 0.00 0.00 0.00 1.40
3685 3837 6.001460 TCGTGGTCAACTCTGGAATTATTTT 58.999 36.000 0.00 0.00 0.00 1.82
3688 3840 7.521423 CGTGGTCAACTCTGGAATTATTTTTCA 60.521 37.037 0.00 0.00 0.00 2.69
3694 3850 7.979444 ACTCTGGAATTATTTTTCAGAACGA 57.021 32.000 0.00 0.00 0.00 3.85
3698 3854 9.624697 TCTGGAATTATTTTTCAGAACGATTTG 57.375 29.630 0.00 0.00 0.00 2.32
3718 3874 1.678101 GCTGTCCTATTGATGGTTGCC 59.322 52.381 0.00 0.00 0.00 4.52
3720 3876 2.947652 CTGTCCTATTGATGGTTGCCAG 59.052 50.000 0.00 0.00 36.75 4.85
3721 3877 2.308570 TGTCCTATTGATGGTTGCCAGT 59.691 45.455 0.00 0.00 36.75 4.00
3722 3878 2.945668 GTCCTATTGATGGTTGCCAGTC 59.054 50.000 0.00 0.00 36.75 3.51
3723 3879 1.942657 CCTATTGATGGTTGCCAGTCG 59.057 52.381 0.00 0.00 36.75 4.18
3724 3880 2.632377 CTATTGATGGTTGCCAGTCGT 58.368 47.619 0.00 0.00 36.75 4.34
3725 3881 1.453155 ATTGATGGTTGCCAGTCGTC 58.547 50.000 0.00 0.00 36.75 4.20
3726 3882 0.107643 TTGATGGTTGCCAGTCGTCA 59.892 50.000 0.00 0.00 36.75 4.35
3733 3890 4.580868 TGGTTGCCAGTCGTCAAATATTA 58.419 39.130 0.00 0.00 0.00 0.98
3760 3917 2.425312 AGTAGTGTTCATCTCTGCGGAG 59.575 50.000 16.98 16.98 40.73 4.63
3775 3932 2.531206 GCGGAGTTCTGCTAGTACTTG 58.469 52.381 0.00 0.00 44.58 3.16
3776 3933 2.531206 CGGAGTTCTGCTAGTACTTGC 58.469 52.381 20.53 20.53 0.00 4.01
3777 3934 2.164624 CGGAGTTCTGCTAGTACTTGCT 59.835 50.000 25.89 8.97 32.65 3.91
3780 3937 4.627900 GGAGTTCTGCTAGTACTTGCTTTC 59.372 45.833 25.89 16.23 32.65 2.62
3781 3938 5.474825 GAGTTCTGCTAGTACTTGCTTTCT 58.525 41.667 25.89 18.52 32.65 2.52
3783 3940 5.698545 AGTTCTGCTAGTACTTGCTTTCTTG 59.301 40.000 25.89 11.68 32.65 3.02
3787 3948 5.364778 TGCTAGTACTTGCTTTCTTGTTCA 58.635 37.500 25.89 3.18 32.65 3.18
3797 3958 4.699735 TGCTTTCTTGTTCAGAGTTGTTGA 59.300 37.500 0.00 0.00 31.12 3.18
3802 3963 8.506168 TTTCTTGTTCAGAGTTGTTGATAGTT 57.494 30.769 0.00 0.00 31.12 2.24
3803 3964 8.506168 TTCTTGTTCAGAGTTGTTGATAGTTT 57.494 30.769 0.00 0.00 31.12 2.66
3831 3995 9.626045 TCAACTAGCACTTCATATATAACATCG 57.374 33.333 0.00 0.00 0.00 3.84
3832 3996 9.411801 CAACTAGCACTTCATATATAACATCGT 57.588 33.333 0.00 0.00 0.00 3.73
3836 4000 8.349568 AGCACTTCATATATAACATCGTCCTA 57.650 34.615 0.00 0.00 0.00 2.94
3847 4011 5.687166 AACATCGTCCTAGGGATTGTTAA 57.313 39.130 9.46 0.00 33.59 2.01
3853 4017 7.385778 TCGTCCTAGGGATTGTTAAATTTTG 57.614 36.000 9.46 0.00 32.73 2.44
3854 4018 6.943718 TCGTCCTAGGGATTGTTAAATTTTGT 59.056 34.615 9.46 0.00 32.73 2.83
3857 4021 9.239551 GTCCTAGGGATTGTTAAATTTTGTAGT 57.760 33.333 9.46 0.00 32.73 2.73
3862 4026 8.576442 AGGGATTGTTAAATTTTGTAGTGTCAG 58.424 33.333 0.00 0.00 0.00 3.51
3893 4057 0.915364 GTTCCCCTTCTCCAGCTGAT 59.085 55.000 17.39 0.00 0.00 2.90
3894 4058 1.283321 GTTCCCCTTCTCCAGCTGATT 59.717 52.381 17.39 0.00 0.00 2.57
3896 4060 0.179062 CCCCTTCTCCAGCTGATTCG 60.179 60.000 17.39 0.00 0.00 3.34
3898 4062 1.202510 CCCTTCTCCAGCTGATTCGAG 60.203 57.143 17.39 13.22 0.00 4.04
3899 4063 1.569708 CTTCTCCAGCTGATTCGAGC 58.430 55.000 17.39 0.00 39.46 5.03
3909 4073 1.346538 GATTCGAGCTGCGCTGAAC 59.653 57.895 19.32 9.48 39.88 3.18
3942 4106 3.057969 TGTACTGAACCAAGGCATCTG 57.942 47.619 0.00 0.00 0.00 2.90
4003 4167 3.691118 TGATTCTGCAAGCCTACACATTC 59.309 43.478 0.00 0.00 0.00 2.67
4006 4170 1.394917 CTGCAAGCCTACACATTCGAC 59.605 52.381 0.00 0.00 0.00 4.20
4019 4189 3.675225 CACATTCGACTGTCTACAACCAG 59.325 47.826 5.30 0.00 34.82 4.00
4030 4200 0.472044 TACAACCAGCAGCAGTTCCA 59.528 50.000 0.00 0.00 0.00 3.53
4058 4228 4.183101 GACACCATATCGAACCCGTTTTA 58.817 43.478 0.00 0.00 37.05 1.52
4073 4243 4.034394 CCCGTTTTAAGGGTCGCTATAAAC 59.966 45.833 12.85 12.85 43.89 2.01
4075 4245 5.122082 CCGTTTTAAGGGTCGCTATAAACAA 59.878 40.000 18.54 2.38 0.00 2.83
4077 4247 7.245604 CGTTTTAAGGGTCGCTATAAACAAAT 58.754 34.615 18.54 0.00 0.00 2.32
4078 4248 7.217447 CGTTTTAAGGGTCGCTATAAACAAATG 59.783 37.037 18.54 6.43 0.00 2.32
4079 4249 4.632538 AAGGGTCGCTATAAACAAATGC 57.367 40.909 0.00 0.00 0.00 3.56
4081 4251 4.270008 AGGGTCGCTATAAACAAATGCTT 58.730 39.130 0.00 0.00 0.00 3.91
4082 4252 4.096382 AGGGTCGCTATAAACAAATGCTTG 59.904 41.667 0.00 0.00 38.61 4.01
4084 4254 4.142469 GGTCGCTATAAACAAATGCTTGGT 60.142 41.667 0.00 0.00 36.82 3.67
4110 4288 8.840833 TTGAACAATAGCAGTCATAAGTGTTA 57.159 30.769 0.00 0.00 0.00 2.41
4112 4290 9.098355 TGAACAATAGCAGTCATAAGTGTTATC 57.902 33.333 0.00 0.00 32.80 1.75
4127 4305 5.020132 AGTGTTATCAGCTAGGTTCAGTCT 58.980 41.667 0.00 0.00 0.00 3.24
4129 4307 5.578727 GTGTTATCAGCTAGGTTCAGTCTTG 59.421 44.000 0.00 0.00 0.00 3.02
4130 4308 5.246203 TGTTATCAGCTAGGTTCAGTCTTGT 59.754 40.000 0.00 0.00 0.00 3.16
4134 4312 4.100963 TCAGCTAGGTTCAGTCTTGTTTCA 59.899 41.667 0.00 0.00 0.00 2.69
4140 4318 4.339247 AGGTTCAGTCTTGTTTCAATGGTG 59.661 41.667 0.00 0.00 0.00 4.17
4145 4323 7.397892 TCAGTCTTGTTTCAATGGTGTTTTA 57.602 32.000 0.00 0.00 0.00 1.52
4156 4334 8.954950 TTCAATGGTGTTTTATTTGTTGTGAT 57.045 26.923 0.00 0.00 0.00 3.06
4157 4335 8.954950 TCAATGGTGTTTTATTTGTTGTGATT 57.045 26.923 0.00 0.00 0.00 2.57
4158 4336 9.388506 TCAATGGTGTTTTATTTGTTGTGATTT 57.611 25.926 0.00 0.00 0.00 2.17
4187 4365 8.367660 TCTGTTCATACCTCTATTCTTTGAGT 57.632 34.615 0.00 0.00 0.00 3.41
4188 4366 8.470805 TCTGTTCATACCTCTATTCTTTGAGTC 58.529 37.037 0.00 0.00 0.00 3.36
4189 4367 8.134202 TGTTCATACCTCTATTCTTTGAGTCA 57.866 34.615 0.00 0.00 0.00 3.41
4190 4368 8.035394 TGTTCATACCTCTATTCTTTGAGTCAC 58.965 37.037 0.00 0.00 0.00 3.67
4191 4369 7.962995 TCATACCTCTATTCTTTGAGTCACT 57.037 36.000 0.00 0.00 0.00 3.41
4192 4370 8.367660 TCATACCTCTATTCTTTGAGTCACTT 57.632 34.615 0.00 0.00 0.00 3.16
4193 4371 9.475620 TCATACCTCTATTCTTTGAGTCACTTA 57.524 33.333 0.00 0.00 0.00 2.24
4194 4372 9.743057 CATACCTCTATTCTTTGAGTCACTTAG 57.257 37.037 0.00 0.00 0.00 2.18
4195 4373 7.176589 ACCTCTATTCTTTGAGTCACTTAGG 57.823 40.000 0.00 0.00 0.00 2.69
4196 4374 6.954684 ACCTCTATTCTTTGAGTCACTTAGGA 59.045 38.462 0.00 0.00 0.00 2.94
4197 4375 7.621683 ACCTCTATTCTTTGAGTCACTTAGGAT 59.378 37.037 0.00 0.00 0.00 3.24
4198 4376 8.482128 CCTCTATTCTTTGAGTCACTTAGGATT 58.518 37.037 0.00 0.00 0.00 3.01
4199 4377 9.883142 CTCTATTCTTTGAGTCACTTAGGATTT 57.117 33.333 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 286 6.452494 TTTGAAAGTTCCAAACATTACGGA 57.548 33.333 0.00 0.00 0.00 4.69
313 327 5.337219 GGGAAACCGCAAACAATTTTTAG 57.663 39.130 0.00 0.00 43.64 1.85
518 539 9.798885 CTGAACAATTTTTAAAAACGTGAACAA 57.201 25.926 23.31 11.10 0.00 2.83
698 728 5.616488 ATGTTTGAAAATCCAGCAATTGC 57.384 34.783 23.05 23.05 42.49 3.56
794 834 9.415544 CGTACCACTTTAAGAACTAACTACAAT 57.584 33.333 0.00 0.00 0.00 2.71
895 935 0.250338 AGTGACCTCGCTTGGGTTTC 60.250 55.000 0.00 0.00 37.17 2.78
899 939 0.895530 TTAGAGTGACCTCGCTTGGG 59.104 55.000 0.00 0.00 42.86 4.12
932 972 3.914916 CACCTACTGTGCCGATATGATCG 60.915 52.174 1.86 1.86 43.28 3.69
933 973 3.579709 CACCTACTGTGCCGATATGATC 58.420 50.000 0.00 0.00 38.34 2.92
934 974 3.667497 CACCTACTGTGCCGATATGAT 57.333 47.619 0.00 0.00 38.34 2.45
955 1017 1.283029 AGGTACCCGTAGTAGTGCTCA 59.717 52.381 8.74 0.00 0.00 4.26
960 1022 2.357569 CCAGGAAGGTACCCGTAGTAGT 60.358 54.545 8.74 0.00 0.00 2.73
1091 1155 2.501723 GCAAGGTAGAGATGTTGGAGGA 59.498 50.000 0.00 0.00 0.00 3.71
1116 1180 5.248477 AGGAGCTTGACCAAATAGTTGAGTA 59.752 40.000 4.10 0.00 36.83 2.59
1127 1191 0.401356 TGCATCAGGAGCTTGACCAA 59.599 50.000 0.00 0.00 0.00 3.67
1170 1234 5.888161 AGGATTACATGACAAATCAAGGACC 59.112 40.000 0.00 0.00 38.69 4.46
1199 1263 5.532557 TGAAGCTTGTAGTCATCATATCCG 58.467 41.667 2.10 0.00 0.00 4.18
1203 1270 6.818644 GGTTTCTGAAGCTTGTAGTCATCATA 59.181 38.462 2.10 0.00 0.00 2.15
1259 1326 9.889128 CCTTTATATTTCCAACCATTTGACAAT 57.111 29.630 0.00 0.00 34.24 2.71
1290 1357 0.769776 ACTGGGGCATCCTCCCTATG 60.770 60.000 0.00 0.00 45.80 2.23
1330 1397 5.736951 TTATTGTAGCCCAAATGCAACTT 57.263 34.783 0.00 0.00 36.44 2.66
1350 1417 4.020307 TCTGGCATGATTCCGCTGATATTA 60.020 41.667 0.00 0.00 0.00 0.98
1371 1438 1.000955 GTCAAGTGTGGTGTCCGATCT 59.999 52.381 0.00 0.00 0.00 2.75
1404 1471 4.346418 AGGTTGTTCTGAGAGATGTCAAGT 59.654 41.667 0.00 0.00 0.00 3.16
1430 1497 0.819259 CCATCGTGTTATGCCCCCAG 60.819 60.000 0.00 0.00 0.00 4.45
1434 1501 1.101049 CCACCCATCGTGTTATGCCC 61.101 60.000 0.00 0.00 41.26 5.36
1441 1508 2.032528 CAGCACCACCCATCGTGT 59.967 61.111 0.00 0.00 41.26 4.49
1454 1521 3.961480 TGCTTAAACTAGAGAGCAGCA 57.039 42.857 0.00 0.42 39.97 4.41
1485 1552 4.262894 GGTCCACTGAGATGGTTGTAAGAA 60.263 45.833 0.00 0.00 40.95 2.52
1512 1579 2.100584 GAGCATGTCGATCTCAGAAGGT 59.899 50.000 0.00 0.00 0.00 3.50
1526 1593 4.640201 ACATAGTTAAATTGCCGAGCATGT 59.360 37.500 0.00 0.00 38.76 3.21
1545 1612 5.675684 TGTTGCTACTGAGATCCAACATA 57.324 39.130 7.18 0.00 40.32 2.29
1549 1616 4.623932 AGTTGTTGCTACTGAGATCCAA 57.376 40.909 0.00 0.00 0.00 3.53
1560 1627 3.568007 GGTCACCATTCAAGTTGTTGCTA 59.432 43.478 2.11 0.00 33.23 3.49
1610 1677 4.844349 AAATACAGCCTCTTTAGCCTCA 57.156 40.909 0.00 0.00 0.00 3.86
1755 1866 9.211410 CTTGATATATCCATCTCCCTAATGTCT 57.789 37.037 10.25 0.00 0.00 3.41
1762 1873 5.096521 TGTGCTTGATATATCCATCTCCCT 58.903 41.667 10.25 0.00 0.00 4.20
1847 1959 5.100259 CACTGATTTCATTGTTGGAGATGC 58.900 41.667 0.00 0.00 0.00 3.91
1969 2081 2.408271 TCAGACATGTCCAAGATGGC 57.592 50.000 22.21 0.00 37.47 4.40
2016 2128 7.375106 AGTCAAATCTGTGATCTCAATGTTC 57.625 36.000 0.00 0.00 0.00 3.18
2024 2136 7.232127 ACCAAAATGAAGTCAAATCTGTGATCT 59.768 33.333 0.00 0.00 0.00 2.75
2028 2140 6.292488 GCAACCAAAATGAAGTCAAATCTGTG 60.292 38.462 0.00 0.00 0.00 3.66
2039 2151 1.000385 TGGAGCGCAACCAAAATGAAG 60.000 47.619 20.84 0.00 34.25 3.02
2050 2162 3.119531 CCAGTTATTTGATTGGAGCGCAA 60.120 43.478 11.47 0.00 32.34 4.85
2088 2200 5.568620 ACAAGGATTCCACTTTACAGAGT 57.431 39.130 5.29 0.00 0.00 3.24
2121 2233 6.151817 GTCCCTCAAGAAGATTGTTGCTTAAT 59.848 38.462 0.00 0.00 32.09 1.40
2225 2340 5.906113 TTGTGTCCAGCTTTTTAGAAACA 57.094 34.783 0.00 0.00 0.00 2.83
2243 2358 9.409312 GTGATAGATCTAGAGACATCAATTGTG 57.591 37.037 8.70 5.96 39.18 3.33
2295 2410 4.898265 TCAACCAAATCTCCAATCCACAAA 59.102 37.500 0.00 0.00 0.00 2.83
2368 2483 6.443849 AGGGAACTAAGATTTGAGATGGTACA 59.556 38.462 0.00 0.00 42.10 2.90
2389 2504 3.071602 GCTAGGTTCATATGCTGAAGGGA 59.928 47.826 0.00 0.00 44.44 4.20
2390 2505 3.181451 TGCTAGGTTCATATGCTGAAGGG 60.181 47.826 0.00 0.00 44.44 3.95
2397 2512 2.260844 TGCCTGCTAGGTTCATATGC 57.739 50.000 0.00 0.00 37.80 3.14
2401 2516 2.025863 GCCATTGCCTGCTAGGTTCAT 61.026 52.381 4.45 0.00 37.80 2.57
2456 2573 1.414181 ACTTCCCTATCATGGCTGTCG 59.586 52.381 0.00 0.00 0.00 4.35
2472 2589 6.356186 TCCCTAGAAACCTTTCTGTACTTC 57.644 41.667 10.07 0.00 46.34 3.01
2480 2597 5.187967 TCTGTCTCATCCCTAGAAACCTTTC 59.812 44.000 0.00 0.00 37.45 2.62
2486 2603 8.553085 TTCATAATCTGTCTCATCCCTAGAAA 57.447 34.615 0.00 0.00 0.00 2.52
2492 2609 8.807118 TGTATACTTCATAATCTGTCTCATCCC 58.193 37.037 4.17 0.00 0.00 3.85
2531 2654 9.958180 TGACCACAGAAGAAAAATCATATCTAA 57.042 29.630 0.00 0.00 0.00 2.10
2534 2657 8.896744 TGATGACCACAGAAGAAAAATCATATC 58.103 33.333 0.00 0.00 0.00 1.63
2547 2670 1.001974 CGTCCCTTGATGACCACAGAA 59.998 52.381 0.00 0.00 0.00 3.02
2596 2719 9.860898 GAAAGATAAGTCAATGCTAACCAAATT 57.139 29.630 0.00 0.00 0.00 1.82
2604 2727 7.994425 TTGGTTGAAAGATAAGTCAATGCTA 57.006 32.000 0.00 0.00 36.23 3.49
2655 2778 0.245266 TCAACGCATCAAGAGCCGTA 59.755 50.000 0.00 0.00 0.00 4.02
2658 2781 3.375299 AGTTTATCAACGCATCAAGAGCC 59.625 43.478 0.00 0.00 38.03 4.70
2693 2816 5.858581 GGAAATTTCTCACTCAATCGGTTTG 59.141 40.000 17.42 0.00 36.61 2.93
2694 2817 5.534654 TGGAAATTTCTCACTCAATCGGTTT 59.465 36.000 17.42 0.00 0.00 3.27
2699 2822 9.080915 GCTTATTTGGAAATTTCTCACTCAATC 57.919 33.333 17.42 0.00 0.00 2.67
2732 2855 3.159472 AGTGATTCCAATGCTTGCAAGA 58.841 40.909 30.39 15.09 0.00 3.02
2739 2862 3.009916 AGAGGTCAAGTGATTCCAATGCT 59.990 43.478 0.00 0.00 0.00 3.79
2845 2968 5.130477 GTCCTGATGGTATTCTCCCTGTTAA 59.870 44.000 0.00 0.00 34.23 2.01
2871 2994 4.021981 TCTGTGTAGAGTGTGTCAAGATGG 60.022 45.833 0.00 0.00 0.00 3.51
2956 3079 2.617021 GCCTTGTTACATTCTTCCCGGA 60.617 50.000 0.73 0.00 0.00 5.14
2961 3084 6.500684 TCATCTTGCCTTGTTACATTCTTC 57.499 37.500 0.00 0.00 0.00 2.87
3026 3155 0.034896 TCCCAGAGCGAGTCCAAAAC 59.965 55.000 0.00 0.00 0.00 2.43
3079 3208 5.997746 TCCTCCATACTTTCTTGAACAACAG 59.002 40.000 0.00 0.00 0.00 3.16
3087 3216 7.814264 ATAAGCAATCCTCCATACTTTCTTG 57.186 36.000 0.00 0.00 0.00 3.02
3095 3224 5.063204 CACGGAAATAAGCAATCCTCCATA 58.937 41.667 0.00 0.00 0.00 2.74
3170 3299 0.251341 TTCCTTTCTGGCCCAGCTTC 60.251 55.000 5.66 0.00 35.26 3.86
3188 3317 6.717084 AGCTCCTTTTACTCAATTTGTAGCTT 59.283 34.615 0.00 0.00 0.00 3.74
3206 3335 0.908198 ATGCTTCTTCGGAGCTCCTT 59.092 50.000 29.73 0.00 0.00 3.36
3208 3337 0.176680 TCATGCTTCTTCGGAGCTCC 59.823 55.000 23.79 23.79 0.00 4.70
3256 3388 8.458573 TCCTTTACAATAACTTCAAGCAAGAA 57.541 30.769 0.00 0.00 35.82 2.52
3257 3389 8.635765 ATCCTTTACAATAACTTCAAGCAAGA 57.364 30.769 0.00 0.00 35.82 3.02
3333 3465 6.590292 ACCACATCTGAACAGTAGAAAATACG 59.410 38.462 1.73 0.00 0.00 3.06
3340 3472 2.899900 AGCACCACATCTGAACAGTAGA 59.100 45.455 1.73 0.00 0.00 2.59
3356 3488 2.618241 TCACACACAAAGAATCAGCACC 59.382 45.455 0.00 0.00 0.00 5.01
3366 3498 8.131100 AGTTCAAAAGTATCATCACACACAAAG 58.869 33.333 0.00 0.00 0.00 2.77
3374 3506 8.723942 ATACAGGAGTTCAAAAGTATCATCAC 57.276 34.615 0.00 0.00 0.00 3.06
3379 3511 8.794335 AGGAAATACAGGAGTTCAAAAGTATC 57.206 34.615 0.00 0.00 33.68 2.24
3402 3534 9.191995 GGAACAAACAATAAAATGAACAGTAGG 57.808 33.333 0.00 0.00 0.00 3.18
3444 3576 0.036294 AGAGTCCCAAAAGGCTACGC 60.036 55.000 0.00 0.00 34.51 4.42
3446 3578 2.861147 ACAGAGTCCCAAAAGGCTAC 57.139 50.000 0.00 0.00 34.51 3.58
3447 3579 3.876309 AAACAGAGTCCCAAAAGGCTA 57.124 42.857 0.00 0.00 34.51 3.93
3448 3580 2.755952 AAACAGAGTCCCAAAAGGCT 57.244 45.000 0.00 0.00 34.51 4.58
3449 3581 3.819564 AAAAACAGAGTCCCAAAAGGC 57.180 42.857 0.00 0.00 34.51 4.35
3642 3794 5.066117 CCACGATGTTGTACTTAGAGCTCTA 59.934 44.000 19.72 19.72 0.00 2.43
3650 3802 5.010314 AGAGTTGACCACGATGTTGTACTTA 59.990 40.000 0.00 0.00 0.00 2.24
3662 3814 5.880054 AAATAATTCCAGAGTTGACCACG 57.120 39.130 0.00 0.00 0.00 4.94
3667 3819 8.289618 CGTTCTGAAAAATAATTCCAGAGTTGA 58.710 33.333 0.00 0.00 0.00 3.18
3670 3822 7.979444 TCGTTCTGAAAAATAATTCCAGAGT 57.021 32.000 0.00 0.00 0.00 3.24
3677 3829 8.816640 ACAGCAAATCGTTCTGAAAAATAATT 57.183 26.923 0.00 0.00 0.00 1.40
3678 3830 7.542130 GGACAGCAAATCGTTCTGAAAAATAAT 59.458 33.333 0.00 0.00 0.00 1.28
3681 3833 5.010012 AGGACAGCAAATCGTTCTGAAAAAT 59.990 36.000 0.00 0.00 0.00 1.82
3685 3837 3.126001 AGGACAGCAAATCGTTCTGAA 57.874 42.857 0.00 0.00 0.00 3.02
3688 3840 4.832248 TCAATAGGACAGCAAATCGTTCT 58.168 39.130 0.00 0.00 0.00 3.01
3694 3850 4.142093 GCAACCATCAATAGGACAGCAAAT 60.142 41.667 0.00 0.00 0.00 2.32
3698 3854 1.678101 GGCAACCATCAATAGGACAGC 59.322 52.381 0.00 0.00 0.00 4.40
3733 3890 5.807520 CGCAGAGATGAACACTACTAACAAT 59.192 40.000 0.00 0.00 0.00 2.71
3744 3901 1.895798 AGAACTCCGCAGAGATGAACA 59.104 47.619 3.36 0.00 43.39 3.18
3750 3907 1.098869 CTAGCAGAACTCCGCAGAGA 58.901 55.000 3.36 0.00 43.39 3.10
3760 3917 5.467063 ACAAGAAAGCAAGTACTAGCAGAAC 59.533 40.000 0.00 0.00 0.00 3.01
3769 3926 5.993106 ACTCTGAACAAGAAAGCAAGTAC 57.007 39.130 0.00 0.00 33.37 2.73
3770 3927 5.880332 ACAACTCTGAACAAGAAAGCAAGTA 59.120 36.000 0.00 0.00 33.37 2.24
3771 3928 4.702131 ACAACTCTGAACAAGAAAGCAAGT 59.298 37.500 0.00 0.00 33.37 3.16
3772 3929 5.240713 ACAACTCTGAACAAGAAAGCAAG 57.759 39.130 0.00 0.00 33.37 4.01
3775 3932 5.235305 TCAACAACTCTGAACAAGAAAGC 57.765 39.130 0.00 0.00 33.37 3.51
3776 3933 8.147642 ACTATCAACAACTCTGAACAAGAAAG 57.852 34.615 0.00 0.00 33.37 2.62
3777 3934 8.506168 AACTATCAACAACTCTGAACAAGAAA 57.494 30.769 0.00 0.00 33.37 2.52
3780 3937 8.147642 AGAAACTATCAACAACTCTGAACAAG 57.852 34.615 0.00 0.00 0.00 3.16
3781 3938 7.768582 TGAGAAACTATCAACAACTCTGAACAA 59.231 33.333 0.00 0.00 0.00 2.83
3783 3940 7.715265 TGAGAAACTATCAACAACTCTGAAC 57.285 36.000 0.00 0.00 0.00 3.18
3818 3982 8.696374 ACAATCCCTAGGACGATGTTATATATG 58.304 37.037 11.48 0.98 32.98 1.78
3826 3990 5.687166 TTTAACAATCCCTAGGACGATGT 57.313 39.130 11.48 6.98 32.98 3.06
3831 3995 9.239551 ACTACAAAATTTAACAATCCCTAGGAC 57.760 33.333 11.48 0.00 32.98 3.85
3832 3996 9.238368 CACTACAAAATTTAACAATCCCTAGGA 57.762 33.333 11.48 0.00 35.55 2.94
3836 4000 8.472007 TGACACTACAAAATTTAACAATCCCT 57.528 30.769 0.00 0.00 0.00 4.20
3853 4017 8.448615 GGGAACACATATAAAAACTGACACTAC 58.551 37.037 0.00 0.00 0.00 2.73
3854 4018 7.608761 GGGGAACACATATAAAAACTGACACTA 59.391 37.037 0.00 0.00 0.00 2.74
3857 4021 6.548321 AGGGGAACACATATAAAAACTGACA 58.452 36.000 0.00 0.00 0.00 3.58
3862 4026 6.661805 TGGAGAAGGGGAACACATATAAAAAC 59.338 38.462 0.00 0.00 0.00 2.43
3876 4040 1.207791 GAATCAGCTGGAGAAGGGGA 58.792 55.000 15.13 0.00 0.00 4.81
3899 4063 0.735978 TACATGGTCGTTCAGCGCAG 60.736 55.000 11.47 0.00 41.07 5.18
3900 4064 0.735978 CTACATGGTCGTTCAGCGCA 60.736 55.000 11.47 0.00 41.07 6.09
3901 4065 1.999051 CTACATGGTCGTTCAGCGC 59.001 57.895 0.00 0.00 41.07 5.92
3902 4066 0.735978 TGCTACATGGTCGTTCAGCG 60.736 55.000 0.00 0.00 43.01 5.18
3909 4073 3.436700 TCAGTACATGCTACATGGTCG 57.563 47.619 11.91 0.00 0.00 4.79
4003 4167 1.702886 CTGCTGGTTGTAGACAGTCG 58.297 55.000 0.00 0.00 37.07 4.18
4006 4170 1.270518 ACTGCTGCTGGTTGTAGACAG 60.271 52.381 11.29 0.00 37.95 3.51
4019 4189 1.814394 TGTCATCATTGGAACTGCTGC 59.186 47.619 0.00 0.00 0.00 5.25
4030 4200 4.389374 GGGTTCGATATGGTGTCATCATT 58.611 43.478 3.37 0.00 34.96 2.57
4058 4228 4.270008 AGCATTTGTTTATAGCGACCCTT 58.730 39.130 0.00 0.00 0.00 3.95
4063 4233 5.637006 AACCAAGCATTTGTTTATAGCGA 57.363 34.783 0.00 0.00 32.21 4.93
4065 4235 7.170658 TGTTCAAACCAAGCATTTGTTTATAGC 59.829 33.333 0.00 0.00 38.08 2.97
4073 4243 5.466058 TGCTATTGTTCAAACCAAGCATTTG 59.534 36.000 8.80 0.00 38.21 2.32
4075 4245 5.212532 TGCTATTGTTCAAACCAAGCATT 57.787 34.783 8.80 0.00 34.29 3.56
4077 4247 3.636300 ACTGCTATTGTTCAAACCAAGCA 59.364 39.130 11.15 11.15 36.31 3.91
4078 4248 4.229876 GACTGCTATTGTTCAAACCAAGC 58.770 43.478 0.00 0.00 0.00 4.01
4079 4249 5.437289 TGACTGCTATTGTTCAAACCAAG 57.563 39.130 0.00 0.00 0.00 3.61
4081 4251 6.714810 ACTTATGACTGCTATTGTTCAAACCA 59.285 34.615 0.00 0.00 0.00 3.67
4082 4252 7.023575 CACTTATGACTGCTATTGTTCAAACC 58.976 38.462 0.00 0.00 0.00 3.27
4084 4254 7.744087 ACACTTATGACTGCTATTGTTCAAA 57.256 32.000 0.00 0.00 0.00 2.69
4110 4288 4.899352 AACAAGACTGAACCTAGCTGAT 57.101 40.909 0.00 0.00 0.00 2.90
4112 4290 4.380531 TGAAACAAGACTGAACCTAGCTG 58.619 43.478 0.00 0.00 0.00 4.24
4127 4305 9.003658 ACAACAAATAAAACACCATTGAAACAA 57.996 25.926 0.00 0.00 0.00 2.83
4129 4307 8.660373 TCACAACAAATAAAACACCATTGAAAC 58.340 29.630 0.00 0.00 0.00 2.78
4130 4308 8.777865 TCACAACAAATAAAACACCATTGAAA 57.222 26.923 0.00 0.00 0.00 2.69
4161 4339 8.986991 ACTCAAAGAATAGAGGTATGAACAGAT 58.013 33.333 0.00 0.00 36.20 2.90
4162 4340 8.367660 ACTCAAAGAATAGAGGTATGAACAGA 57.632 34.615 0.00 0.00 36.20 3.41
4163 4341 8.253810 TGACTCAAAGAATAGAGGTATGAACAG 58.746 37.037 0.00 0.00 36.20 3.16
4164 4342 8.035394 GTGACTCAAAGAATAGAGGTATGAACA 58.965 37.037 0.00 0.00 36.20 3.18
4165 4343 8.254508 AGTGACTCAAAGAATAGAGGTATGAAC 58.745 37.037 0.00 0.00 36.20 3.18
4166 4344 8.367660 AGTGACTCAAAGAATAGAGGTATGAA 57.632 34.615 0.00 0.00 36.20 2.57
4167 4345 7.962995 AGTGACTCAAAGAATAGAGGTATGA 57.037 36.000 0.00 0.00 36.20 2.15
4168 4346 9.743057 CTAAGTGACTCAAAGAATAGAGGTATG 57.257 37.037 0.00 0.00 36.20 2.39
4169 4347 8.919145 CCTAAGTGACTCAAAGAATAGAGGTAT 58.081 37.037 0.00 0.00 36.20 2.73
4170 4348 8.114102 TCCTAAGTGACTCAAAGAATAGAGGTA 58.886 37.037 0.00 0.00 36.20 3.08
4171 4349 6.954684 TCCTAAGTGACTCAAAGAATAGAGGT 59.045 38.462 0.00 0.00 36.20 3.85
4172 4350 7.411486 TCCTAAGTGACTCAAAGAATAGAGG 57.589 40.000 0.00 0.00 36.20 3.69
4173 4351 9.883142 AAATCCTAAGTGACTCAAAGAATAGAG 57.117 33.333 0.00 0.00 37.87 2.43


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

AutoCloner maintained by Alex Coulton.