Multiple sequence alignment - TraesCS5D01G186600

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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 TraesCS5D01G186600 chr5D 100.000 5962 0 0 1 5962 288544866 288550827 0.000000e+00 11010.0
1 TraesCS5D01G186600 chr5D 92.157 51 4 0 2472 2522 277243047 277242997 8.290000e-09 73.1
2 TraesCS5D01G186600 chr5A 90.855 2537 138 49 1 2479 382067526 382070026 0.000000e+00 3314.0
3 TraesCS5D01G186600 chr5A 90.066 2285 143 22 3672 5939 382071332 382073549 0.000000e+00 2885.0
4 TraesCS5D01G186600 chr5A 91.140 1140 71 14 2473 3592 382070073 382071202 0.000000e+00 1519.0
5 TraesCS5D01G186600 chr5A 92.157 51 4 0 2472 2522 366234746 366234696 8.290000e-09 73.1
6 TraesCS5D01G186600 chr5A 81.319 91 15 2 5453 5542 536677089 536677000 8.290000e-09 73.1
7 TraesCS5D01G186600 chr5B 91.393 2463 109 46 56 2476 328103392 328105793 0.000000e+00 3278.0
8 TraesCS5D01G186600 chr5B 93.772 1991 63 21 2472 4410 328105842 328107823 0.000000e+00 2933.0
9 TraesCS5D01G186600 chr5B 88.172 1395 105 21 4558 5939 328108060 328109407 0.000000e+00 1607.0
10 TraesCS5D01G186600 chr5B 87.121 132 11 4 4395 4521 328107842 328107972 1.730000e-30 145.0
11 TraesCS5D01G186600 chr3A 87.596 911 68 26 1295 2185 512327925 512328810 0.000000e+00 1014.0
12 TraesCS5D01G186600 chr3A 78.906 128 20 7 5419 5542 8796856 8796980 4.950000e-11 80.5
13 TraesCS5D01G186600 chr3A 87.500 64 5 2 2184 2247 512329042 512329102 2.980000e-08 71.3
14 TraesCS5D01G186600 chr3D 90.909 528 43 4 1660 2186 392350340 392350863 0.000000e+00 704.0
15 TraesCS5D01G186600 chr3D 90.909 66 4 2 2418 2482 488265103 488265039 2.960000e-13 87.9
16 TraesCS5D01G186600 chr3D 97.619 42 1 0 2184 2225 392351083 392351124 8.290000e-09 73.1
17 TraesCS5D01G186600 chr7D 92.188 64 3 2 2418 2479 454079077 454079140 8.230000e-14 89.8
18 TraesCS5D01G186600 chr7D 81.395 86 16 0 5466 5551 541380881 541380796 2.980000e-08 71.3
19 TraesCS5D01G186600 chr2D 93.443 61 3 1 2418 2477 617101061 617101121 8.230000e-14 89.8
20 TraesCS5D01G186600 chr2D 92.157 51 4 0 2472 2522 46297724 46297774 8.290000e-09 73.1
21 TraesCS5D01G186600 chr2A 93.443 61 3 1 2418 2477 747272175 747272235 8.230000e-14 89.8
22 TraesCS5D01G186600 chr2A 81.250 96 16 2 5466 5560 743578076 743577982 6.410000e-10 76.8
23 TraesCS5D01G186600 chr2A 93.878 49 3 0 2472 2520 79316113 79316161 2.300000e-09 75.0
24 TraesCS5D01G186600 chr7B 92.063 63 4 1 2418 2479 369872719 369872781 2.960000e-13 87.9
25 TraesCS5D01G186600 chr7A 92.063 63 4 1 2418 2479 421785006 421785068 2.960000e-13 87.9
26 TraesCS5D01G186600 chr7A 82.474 97 14 3 5466 5560 680258170 680258075 1.380000e-11 82.4
27 TraesCS5D01G186600 chr4B 88.571 70 7 1 2411 2479 438375174 438375243 3.830000e-12 84.2
28 TraesCS5D01G186600 chr4B 95.745 47 2 0 2472 2518 316295919 316295873 6.410000e-10 76.8
29 TraesCS5D01G186600 chr4A 79.339 121 17 5 5445 5560 658069014 658069131 1.780000e-10 78.7
30 TraesCS5D01G186600 chr4A 78.814 118 23 2 5445 5560 658107994 658108111 1.780000e-10 78.7
31 TraesCS5D01G186600 chr6D 92.453 53 3 1 2472 2524 256728558 256728609 2.300000e-09 75.0
32 TraesCS5D01G186600 chr6D 92.453 53 3 1 2472 2524 256729355 256729406 2.300000e-09 75.0
33 TraesCS5D01G186600 chr2B 94.737 38 2 0 1519 1556 753640355 753640392 6.450000e-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 TraesCS5D01G186600 chr5D 288544866 288550827 5961 False 11010.000000 11010 100.0000 1 5962 1 chr5D.!!$F1 5961
1 TraesCS5D01G186600 chr5A 382067526 382073549 6023 False 2572.666667 3314 90.6870 1 5939 3 chr5A.!!$F1 5938
2 TraesCS5D01G186600 chr5B 328103392 328109407 6015 False 1990.750000 3278 90.1145 56 5939 4 chr5B.!!$F1 5883
3 TraesCS5D01G186600 chr3A 512327925 512329102 1177 False 542.650000 1014 87.5480 1295 2247 2 chr3A.!!$F2 952
4 TraesCS5D01G186600 chr3D 392350340 392351124 784 False 388.550000 704 94.2640 1660 2225 2 chr3D.!!$F1 565

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
956 1011 0.114168 TCCACCCCTGATTGGTTTGG 59.886 55.000 0.00 0.0 37.24 3.28 F
1198 1259 0.247460 GAGAGGCAATTGGTTTGGGC 59.753 55.000 7.72 0.0 35.75 5.36 F
1487 1571 1.208358 CATTGGCGGCTCATATGCG 59.792 57.895 11.43 0.0 0.00 4.73 F
2645 3033 2.031245 TGATTGGCACTTTAGCAACACG 60.031 45.455 0.00 0.0 35.83 4.49 F
3732 4196 1.153745 CACTGCGACTGGCTCTACC 60.154 63.158 0.00 0.0 44.05 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 1917 3.069872 TGGACTGAAAAACCTAGCACGTA 59.930 43.478 0.00 0.00 0.00 3.57 R
2712 3117 4.387026 TTGAAGATTGGTCCAGGAACAT 57.613 40.909 8.43 0.00 0.00 2.71 R
2850 3256 5.698832 TCTCATGGTGCTAAATGTTTTTCG 58.301 37.500 0.00 0.00 0.00 3.46 R
4193 4660 0.108585 TGGTGAACTGCAGGAAGGAC 59.891 55.000 19.93 6.85 0.00 3.85 R
5393 5996 0.521242 GGTCTTATTGCAACAGCGCG 60.521 55.000 0.00 0.00 33.35 6.86 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
22 23 2.289569 TGCAAGGCCACAAAAATCATCC 60.290 45.455 5.01 0.00 0.00 3.51
23 24 2.027837 GCAAGGCCACAAAAATCATCCT 60.028 45.455 5.01 0.00 0.00 3.24
28 29 6.432403 AGGCCACAAAAATCATCCTAAAAA 57.568 33.333 5.01 0.00 0.00 1.94
79 80 8.531530 GCAATTAAACAATACGGAATGACATTC 58.468 33.333 18.24 18.24 38.55 2.67
84 85 6.668541 ACAATACGGAATGACATTCAAGAG 57.331 37.500 25.59 16.64 41.03 2.85
87 88 7.390440 ACAATACGGAATGACATTCAAGAGAAA 59.610 33.333 25.59 7.51 41.03 2.52
88 89 8.400947 CAATACGGAATGACATTCAAGAGAAAT 58.599 33.333 25.59 9.14 41.03 2.17
146 150 2.228822 GGGAATCAGATTGCACGTGTTT 59.771 45.455 18.38 1.78 31.57 2.83
298 309 0.880718 GATCCGAGGCCATTTCCGTC 60.881 60.000 5.01 0.00 0.00 4.79
308 319 2.456577 CCATTTCCGTCCCCAGAAATT 58.543 47.619 0.00 0.00 39.97 1.82
309 320 2.166254 CCATTTCCGTCCCCAGAAATTG 59.834 50.000 0.00 0.00 39.97 2.32
335 346 2.271944 GCTAATCCGCCATTAACCCT 57.728 50.000 0.00 0.00 0.00 4.34
336 347 3.412237 GCTAATCCGCCATTAACCCTA 57.588 47.619 0.00 0.00 0.00 3.53
337 348 3.335579 GCTAATCCGCCATTAACCCTAG 58.664 50.000 0.00 0.00 0.00 3.02
339 350 1.815757 ATCCGCCATTAACCCTAGGT 58.184 50.000 8.29 0.00 37.65 3.08
366 381 0.727398 CCCGAAAGAAACCGATGCTC 59.273 55.000 0.00 0.00 0.00 4.26
698 743 2.100252 CTCCTGGTATGCAATTGCTTGG 59.900 50.000 29.37 19.65 42.66 3.61
699 744 1.472026 CCTGGTATGCAATTGCTTGGC 60.472 52.381 29.37 19.10 42.66 4.52
796 846 4.260985 TCCAGCGATTGATAGCTCAAAAA 58.739 39.130 0.00 0.00 44.29 1.94
798 848 5.357878 TCCAGCGATTGATAGCTCAAAAATT 59.642 36.000 0.00 0.00 44.29 1.82
805 855 8.054236 CGATTGATAGCTCAAAAATTTTGATGC 58.946 33.333 19.84 21.69 44.29 3.91
846 896 3.041946 GGGAGCTTGAGAGGATTCCTTA 58.958 50.000 6.68 0.00 31.76 2.69
855 905 7.232534 GCTTGAGAGGATTCCTTAATCTCTCTA 59.767 40.741 16.44 9.79 42.97 2.43
856 906 8.472007 TTGAGAGGATTCCTTAATCTCTCTAC 57.528 38.462 16.44 10.34 42.97 2.59
858 908 8.950480 TGAGAGGATTCCTTAATCTCTCTACTA 58.050 37.037 16.44 0.00 42.97 1.82
875 928 7.840931 TCTCTACTATCACTTTTCATCTTGCA 58.159 34.615 0.00 0.00 0.00 4.08
876 929 8.314021 TCTCTACTATCACTTTTCATCTTGCAA 58.686 33.333 0.00 0.00 0.00 4.08
939 994 1.228862 TTTGCTGCCTTTCCCCTCC 60.229 57.895 0.00 0.00 0.00 4.30
940 995 2.017668 TTTGCTGCCTTTCCCCTCCA 62.018 55.000 0.00 0.00 0.00 3.86
944 999 4.062032 GCCTTTCCCCTCCACCCC 62.062 72.222 0.00 0.00 0.00 4.95
946 1001 2.616458 CCTTTCCCCTCCACCCCTG 61.616 68.421 0.00 0.00 0.00 4.45
947 1002 1.541368 CTTTCCCCTCCACCCCTGA 60.541 63.158 0.00 0.00 0.00 3.86
948 1003 0.921256 CTTTCCCCTCCACCCCTGAT 60.921 60.000 0.00 0.00 0.00 2.90
949 1004 0.479589 TTTCCCCTCCACCCCTGATT 60.480 55.000 0.00 0.00 0.00 2.57
950 1005 1.214305 TTCCCCTCCACCCCTGATTG 61.214 60.000 0.00 0.00 0.00 2.67
951 1006 2.693871 CCCCTCCACCCCTGATTGG 61.694 68.421 0.00 0.00 0.00 3.16
952 1007 1.930656 CCCTCCACCCCTGATTGGT 60.931 63.158 0.00 0.00 36.21 3.67
953 1008 1.509548 CCCTCCACCCCTGATTGGTT 61.510 60.000 0.00 0.00 32.46 3.67
954 1009 0.409484 CCTCCACCCCTGATTGGTTT 59.591 55.000 0.00 0.00 32.46 3.27
955 1010 1.549203 CTCCACCCCTGATTGGTTTG 58.451 55.000 0.00 0.00 32.46 2.93
956 1011 0.114168 TCCACCCCTGATTGGTTTGG 59.886 55.000 0.00 0.00 37.24 3.28
969 1025 3.915437 TGGTTTGGAAGCGAAAAGATC 57.085 42.857 0.00 0.00 0.00 2.75
970 1026 2.556622 TGGTTTGGAAGCGAAAAGATCC 59.443 45.455 0.00 0.00 0.00 3.36
996 1057 1.205655 CCTGAGCAGAGGTTCGATTGA 59.794 52.381 0.00 0.00 0.00 2.57
1005 1066 3.009723 GAGGTTCGATTGAGAAATGGCA 58.990 45.455 0.00 0.00 0.00 4.92
1117 1178 3.516700 TCTGTGCCATCTCATCTCTCAAA 59.483 43.478 0.00 0.00 0.00 2.69
1198 1259 0.247460 GAGAGGCAATTGGTTTGGGC 59.753 55.000 7.72 0.00 35.75 5.36
1309 1376 7.289084 ACTTTCTCCCCTTTTTATGTTTGCTAA 59.711 33.333 0.00 0.00 0.00 3.09
1310 1377 7.790782 TTCTCCCCTTTTTATGTTTGCTAAT 57.209 32.000 0.00 0.00 0.00 1.73
1312 1379 6.951198 TCTCCCCTTTTTATGTTTGCTAATCA 59.049 34.615 0.00 0.00 0.00 2.57
1313 1380 7.122650 TCTCCCCTTTTTATGTTTGCTAATCAG 59.877 37.037 0.00 0.00 0.00 2.90
1415 1490 4.994852 GTGGTTCAGACACTGCTATTTGTA 59.005 41.667 0.00 0.00 35.98 2.41
1442 1526 2.724977 TAAAGACACTGCTCCAGACG 57.275 50.000 0.00 0.00 35.18 4.18
1487 1571 1.208358 CATTGGCGGCTCATATGCG 59.792 57.895 11.43 0.00 0.00 4.73
1520 1604 4.535294 CCAGTCCTCTCCATAATCCATGAT 59.465 45.833 0.00 0.00 36.69 2.45
1526 1610 5.128335 CCTCTCCATAATCCATGATCGATCA 59.872 44.000 29.09 29.09 41.70 2.92
1650 1734 2.658373 TGCAAACATCCATGTCATGC 57.342 45.000 17.38 17.38 45.73 4.06
1651 1735 2.658373 GCAAACATCCATGTCATGCA 57.342 45.000 18.53 0.00 45.28 3.96
1652 1736 3.173668 GCAAACATCCATGTCATGCAT 57.826 42.857 18.53 0.00 45.28 3.96
1653 1737 3.527533 GCAAACATCCATGTCATGCATT 58.472 40.909 18.53 0.00 45.28 3.56
1654 1738 3.936453 GCAAACATCCATGTCATGCATTT 59.064 39.130 18.53 2.39 45.28 2.32
1655 1739 4.033587 GCAAACATCCATGTCATGCATTTC 59.966 41.667 18.53 0.00 45.28 2.17
1656 1740 5.172205 CAAACATCCATGTCATGCATTTCA 58.828 37.500 7.35 0.00 40.80 2.69
1657 1741 4.649088 ACATCCATGTCATGCATTTCAG 57.351 40.909 7.35 0.00 35.87 3.02
1658 1742 4.021229 ACATCCATGTCATGCATTTCAGT 58.979 39.130 7.35 0.00 35.87 3.41
1666 1750 5.463286 TGTCATGCATTTCAGTTTCATGTC 58.537 37.500 0.00 0.00 36.73 3.06
1683 1767 6.572167 TCATGTCATGCATTTCAGTTTACA 57.428 33.333 8.03 0.00 35.19 2.41
1829 1914 7.234355 ACAAGAAACTCCCACTTCTCATTTAT 58.766 34.615 0.00 0.00 30.57 1.40
1832 1917 7.694093 AGAAACTCCCACTTCTCATTTATCTT 58.306 34.615 0.00 0.00 0.00 2.40
1856 1942 3.502211 CGTGCTAGGTTTTTCAGTCCAAT 59.498 43.478 0.00 0.00 0.00 3.16
1902 1988 9.143155 TGGCTTATGTCAGAATCTTAGTGTATA 57.857 33.333 0.00 0.00 0.00 1.47
2100 2197 3.053693 CCCATCAGTTTGAATAGTGGGGA 60.054 47.826 7.34 0.00 38.63 4.81
2373 2707 9.204570 GTTTAGCTCTACTCACTTTGATGTTTA 57.795 33.333 0.00 0.00 0.00 2.01
2445 2779 6.099125 TCCCTCCGTTCACAAATATAAGATGA 59.901 38.462 0.00 0.00 0.00 2.92
2568 2956 5.278022 GCCTACCTTGCTAGTTTGATAATGC 60.278 44.000 0.00 0.00 0.00 3.56
2645 3033 2.031245 TGATTGGCACTTTAGCAACACG 60.031 45.455 0.00 0.00 35.83 4.49
2692 3080 9.471084 TGTTACATATGGTACGTAAGATGAATG 57.529 33.333 7.80 5.86 43.62 2.67
2694 3082 9.908152 TTACATATGGTACGTAAGATGAATGAG 57.092 33.333 7.80 0.00 43.62 2.90
2695 3083 8.178313 ACATATGGTACGTAAGATGAATGAGA 57.822 34.615 7.80 0.00 43.62 3.27
2698 3086 6.525578 TGGTACGTAAGATGAATGAGAAGT 57.474 37.500 0.00 0.00 43.62 3.01
2699 3087 6.330278 TGGTACGTAAGATGAATGAGAAGTG 58.670 40.000 0.00 0.00 43.62 3.16
2700 3088 5.749109 GGTACGTAAGATGAATGAGAAGTGG 59.251 44.000 0.00 0.00 43.62 4.00
2701 3089 4.759782 ACGTAAGATGAATGAGAAGTGGG 58.240 43.478 0.00 0.00 43.62 4.61
2702 3090 4.466370 ACGTAAGATGAATGAGAAGTGGGA 59.534 41.667 0.00 0.00 43.62 4.37
2703 3091 5.046529 CGTAAGATGAATGAGAAGTGGGAG 58.953 45.833 0.00 0.00 43.02 4.30
2707 3112 5.495640 AGATGAATGAGAAGTGGGAGTTTC 58.504 41.667 0.00 0.00 0.00 2.78
2712 3117 7.287061 TGAATGAGAAGTGGGAGTTTCTAAAA 58.713 34.615 0.00 0.00 33.97 1.52
2842 3248 5.163713 CCATACTCTGTTAGCTTGCCTTTTC 60.164 44.000 0.00 0.00 0.00 2.29
2850 3256 5.221244 TGTTAGCTTGCCTTTTCTTTTCTCC 60.221 40.000 0.00 0.00 0.00 3.71
2880 3286 6.742109 ACATTTAGCACCATGAGATTTATGC 58.258 36.000 0.00 0.00 0.00 3.14
3204 3610 4.220602 GGCTTCCACACCACTTATTCATTT 59.779 41.667 0.00 0.00 0.00 2.32
3205 3611 5.402398 GCTTCCACACCACTTATTCATTTC 58.598 41.667 0.00 0.00 0.00 2.17
3206 3612 5.622233 GCTTCCACACCACTTATTCATTTCC 60.622 44.000 0.00 0.00 0.00 3.13
3207 3613 4.991776 TCCACACCACTTATTCATTTCCA 58.008 39.130 0.00 0.00 0.00 3.53
3208 3614 4.764823 TCCACACCACTTATTCATTTCCAC 59.235 41.667 0.00 0.00 0.00 4.02
3209 3615 4.522405 CCACACCACTTATTCATTTCCACA 59.478 41.667 0.00 0.00 0.00 4.17
3219 3625 9.071276 ACTTATTCATTTCCACATCCATATGAC 57.929 33.333 3.65 0.00 36.54 3.06
3352 3763 5.047943 GTGATGGTGTCGCTAATAGAGGTAT 60.048 44.000 0.00 0.00 34.46 2.73
3356 3767 5.048013 TGGTGTCGCTAATAGAGGTATCATG 60.048 44.000 0.00 0.00 0.00 3.07
3732 4196 1.153745 CACTGCGACTGGCTCTACC 60.154 63.158 0.00 0.00 44.05 3.18
3788 4253 3.489355 AGATTGTTCTGTTGTGGCATGA 58.511 40.909 0.00 0.00 0.00 3.07
3795 4260 5.411361 TGTTCTGTTGTGGCATGACTAATAC 59.589 40.000 0.00 0.00 0.00 1.89
3796 4261 4.513442 TCTGTTGTGGCATGACTAATACC 58.487 43.478 0.00 0.00 0.00 2.73
3799 4264 5.260424 TGTTGTGGCATGACTAATACCATT 58.740 37.500 0.00 0.00 34.05 3.16
3844 4309 4.103153 AGTGAGAATGTTGGTCTTCTTGGA 59.897 41.667 0.00 0.00 31.99 3.53
3952 4417 3.173853 GCCACGAGCACGCATTTA 58.826 55.556 2.62 0.00 43.96 1.40
4003 4468 4.628333 GTCGATGTTGTAGGAAAATTCGGA 59.372 41.667 0.00 0.00 0.00 4.55
4106 4571 5.129320 AGCAGGAAAAGTGGAAGATGTTTTT 59.871 36.000 0.00 0.00 0.00 1.94
4141 4606 5.596361 TCCTGAGTTCTCTAGCTAGATTTGG 59.404 44.000 23.48 16.80 0.00 3.28
4149 4614 5.129320 TCTCTAGCTAGATTTGGATTGCACA 59.871 40.000 23.48 0.00 0.00 4.57
4184 4651 2.280797 GTTGTGTCTCCAGCGGCA 60.281 61.111 1.45 0.00 0.00 5.69
4220 4687 2.559668 CCTGCAGTTCACCAACATGAAT 59.440 45.455 13.81 0.00 40.60 2.57
4268 4735 4.805719 GGTTTTTCACTCTTTCTTGGCTTG 59.194 41.667 0.00 0.00 0.00 4.01
4350 4817 0.035820 GGCTGGATGGGTTCGTAACA 60.036 55.000 0.00 0.00 0.00 2.41
4361 4828 3.387050 GGGTTCGTAACATCACTATCCCT 59.613 47.826 0.00 0.00 0.00 4.20
4396 4868 3.548770 TGTACTAGTATGGACTCCCACG 58.451 50.000 5.75 0.00 46.98 4.94
4437 4943 4.263139 TGAATTCGAAATGACATCTGCG 57.737 40.909 0.00 0.00 0.00 5.18
4451 4957 3.758023 ACATCTGCGAAAATGTCCAATCA 59.242 39.130 0.00 0.00 30.35 2.57
4456 4965 5.879777 TCTGCGAAAATGTCCAATCAATCTA 59.120 36.000 0.00 0.00 0.00 1.98
4469 4978 9.241317 GTCCAATCAATCTAGCACAAAATAATG 57.759 33.333 0.00 0.00 0.00 1.90
4475 4984 9.624697 TCAATCTAGCACAAAATAATGACAAAC 57.375 29.630 0.00 0.00 0.00 2.93
4476 4985 9.630098 CAATCTAGCACAAAATAATGACAAACT 57.370 29.630 0.00 0.00 0.00 2.66
4482 4991 9.248291 AGCACAAAATAATGACAAACTTTACTG 57.752 29.630 0.00 0.00 0.00 2.74
4483 4992 9.243637 GCACAAAATAATGACAAACTTTACTGA 57.756 29.630 0.00 0.00 0.00 3.41
4500 5009 8.512138 ACTTTACTGATAGTAAAATGTTGTGGC 58.488 33.333 13.32 0.00 46.41 5.01
4501 5010 7.987750 TTACTGATAGTAAAATGTTGTGGCA 57.012 32.000 0.00 0.00 37.71 4.92
4502 5011 8.574251 TTACTGATAGTAAAATGTTGTGGCAT 57.426 30.769 0.00 0.00 37.71 4.40
4503 5012 6.855836 ACTGATAGTAAAATGTTGTGGCATG 58.144 36.000 0.00 0.00 0.00 4.06
4547 5143 8.768955 GGAAGTTAATATGCAGTCTGAAGTATG 58.231 37.037 3.32 0.00 0.00 2.39
4579 5175 7.801716 ACACTAATTTAGCACAGAAAAGACA 57.198 32.000 3.28 0.00 0.00 3.41
4693 5289 5.244851 GTCATCTCCATGCAAGAGTCCTATA 59.755 44.000 14.73 0.00 32.93 1.31
4999 5595 1.016130 CGGGTACTGCAAGCAGAGTG 61.016 60.000 27.17 9.08 46.30 3.51
5023 5619 4.386652 CCAAATGAAGAAACCTTTGCATCG 59.613 41.667 0.00 0.00 0.00 3.84
5056 5652 6.292973 GCATGCTTCTGAATTCTGATAGAGTG 60.293 42.308 11.37 15.00 0.00 3.51
5070 5666 5.832221 TGATAGAGTGGAAGAGGAGAAGAA 58.168 41.667 0.00 0.00 0.00 2.52
5103 5699 2.126502 GACCCGCATGCCGTTTTG 60.127 61.111 13.15 0.00 34.38 2.44
5109 5705 1.212490 GCATGCCGTTTTGCTAGCA 59.788 52.632 14.93 14.93 40.00 3.49
5132 5728 3.201363 AGGATGGAGGAATTTCCCTTCA 58.799 45.455 11.92 8.34 45.44 3.02
5161 5757 9.908152 CTGTCCGATTGTACATAGATATTTGTA 57.092 33.333 0.00 0.00 0.00 2.41
5201 5797 8.761575 ATGAATTAATGGTAGTTTTTGCTGTG 57.238 30.769 0.00 0.00 0.00 3.66
5202 5798 7.721402 TGAATTAATGGTAGTTTTTGCTGTGT 58.279 30.769 0.00 0.00 0.00 3.72
5203 5799 7.651304 TGAATTAATGGTAGTTTTTGCTGTGTG 59.349 33.333 0.00 0.00 0.00 3.82
5204 5800 2.861462 TGGTAGTTTTTGCTGTGTGC 57.139 45.000 0.00 0.00 43.25 4.57
5205 5801 1.064803 TGGTAGTTTTTGCTGTGTGCG 59.935 47.619 0.00 0.00 46.63 5.34
5206 5802 1.120437 GTAGTTTTTGCTGTGTGCGC 58.880 50.000 0.00 0.00 46.63 6.09
5239 5842 4.025015 AGATCTCATGAAACATTTGCGC 57.975 40.909 0.00 0.00 0.00 6.09
5240 5843 2.634982 TCTCATGAAACATTTGCGCC 57.365 45.000 4.18 0.00 0.00 6.53
5263 5866 4.983538 CACAAATGAAGCACATTGTTAGCA 59.016 37.500 9.30 0.00 46.90 3.49
5318 5921 8.845413 TCCAAACAAGCAAAAATTATAGCATT 57.155 26.923 0.00 0.00 0.00 3.56
5321 5924 7.670009 AACAAGCAAAAATTATAGCATTGCA 57.330 28.000 11.91 0.00 46.59 4.08
5356 5959 2.643551 CCATTAATCCTTGTCGGCACT 58.356 47.619 0.00 0.00 0.00 4.40
5358 5961 2.004583 TTAATCCTTGTCGGCACTCG 57.995 50.000 0.00 0.00 40.90 4.18
5359 5962 0.174845 TAATCCTTGTCGGCACTCGG 59.825 55.000 0.00 0.00 39.77 4.63
5393 5996 2.257691 ATGCTGCTCAGATCATGTCC 57.742 50.000 0.00 0.00 0.00 4.02
5410 6013 0.672091 TCCGCGCTGTTGCAATAAGA 60.672 50.000 14.41 0.00 39.64 2.10
5411 6014 0.521242 CCGCGCTGTTGCAATAAGAC 60.521 55.000 14.41 6.07 39.64 3.01
5412 6015 0.521242 CGCGCTGTTGCAATAAGACC 60.521 55.000 14.41 4.93 39.64 3.85
5413 6016 0.179163 GCGCTGTTGCAATAAGACCC 60.179 55.000 14.41 0.00 39.64 4.46
5414 6017 1.453155 CGCTGTTGCAATAAGACCCT 58.547 50.000 14.41 0.00 39.64 4.34
5415 6018 1.812571 CGCTGTTGCAATAAGACCCTT 59.187 47.619 14.41 0.00 39.64 3.95
5416 6019 2.414559 CGCTGTTGCAATAAGACCCTTG 60.415 50.000 14.41 0.00 39.64 3.61
5417 6020 2.558359 GCTGTTGCAATAAGACCCTTGT 59.442 45.455 14.41 0.00 39.41 3.16
5418 6021 3.756434 GCTGTTGCAATAAGACCCTTGTA 59.244 43.478 14.41 0.00 39.41 2.41
5419 6022 4.217550 GCTGTTGCAATAAGACCCTTGTAA 59.782 41.667 14.41 0.00 39.41 2.41
5420 6023 5.619981 GCTGTTGCAATAAGACCCTTGTAAG 60.620 44.000 14.41 0.00 39.41 2.34
5421 6024 5.626142 TGTTGCAATAAGACCCTTGTAAGA 58.374 37.500 0.59 0.00 29.51 2.10
5448 6051 6.449698 CCTTGTAAGAGTTAGTCGGTTTACA 58.550 40.000 0.00 0.00 31.39 2.41
5498 6101 1.780309 ACATGGTCAGGTTTTCCCTCA 59.220 47.619 0.00 0.00 43.86 3.86
5562 6165 4.964593 TGACCTAACTTTGACCACTTACC 58.035 43.478 0.00 0.00 0.00 2.85
5620 6236 4.789012 AATTGTGCAATCGGATTGAGTT 57.211 36.364 29.70 12.34 42.83 3.01
5645 6261 4.728772 TGGACCAATGACTCATTTCACTT 58.271 39.130 1.17 0.00 31.05 3.16
5662 6278 2.027377 CACTTCATTGCTCCTGAGACCT 60.027 50.000 0.00 0.00 0.00 3.85
5665 6281 0.179936 CATTGCTCCTGAGACCTCCC 59.820 60.000 0.00 0.00 0.00 4.30
5672 6288 0.618680 CCTGAGACCTCCCCACATCA 60.619 60.000 0.00 0.00 0.00 3.07
5677 6293 0.693049 GACCTCCCCACATCAGTTGT 59.307 55.000 0.00 0.00 39.91 3.32
5678 6294 1.906574 GACCTCCCCACATCAGTTGTA 59.093 52.381 0.00 0.00 36.57 2.41
5679 6295 2.505819 GACCTCCCCACATCAGTTGTAT 59.494 50.000 0.00 0.00 36.57 2.29
5680 6296 3.709653 GACCTCCCCACATCAGTTGTATA 59.290 47.826 0.00 0.00 36.57 1.47
5681 6297 3.454812 ACCTCCCCACATCAGTTGTATAC 59.545 47.826 0.00 0.00 36.57 1.47
5682 6298 3.454447 CCTCCCCACATCAGTTGTATACA 59.546 47.826 0.08 0.08 36.57 2.29
5688 6310 6.057533 CCCACATCAGTTGTATACATCATGT 58.942 40.000 14.76 12.90 36.57 3.21
5689 6311 6.017687 CCCACATCAGTTGTATACATCATGTG 60.018 42.308 24.24 24.24 36.57 3.21
5718 6340 7.953158 TTTGATGAAGAAACAACAACACAAA 57.047 28.000 0.00 0.00 33.61 2.83
5791 6419 5.104277 TGGGTTTTCATCCGGATAGTATGTT 60.104 40.000 18.63 0.00 0.00 2.71
5795 6423 7.228706 GGTTTTCATCCGGATAGTATGTTTGAT 59.771 37.037 18.63 0.00 0.00 2.57
5829 6457 5.862924 ACAATATCTTCAACAAGGACACG 57.137 39.130 0.00 0.00 0.00 4.49
5832 6460 2.971660 TCTTCAACAAGGACACGACA 57.028 45.000 0.00 0.00 0.00 4.35
5833 6461 3.254470 TCTTCAACAAGGACACGACAA 57.746 42.857 0.00 0.00 0.00 3.18
5840 6468 5.411977 TCAACAAGGACACGACAAGTAAAAA 59.588 36.000 0.00 0.00 0.00 1.94
5841 6469 5.225899 ACAAGGACACGACAAGTAAAAAC 57.774 39.130 0.00 0.00 0.00 2.43
5843 6471 3.876341 AGGACACGACAAGTAAAAACCA 58.124 40.909 0.00 0.00 0.00 3.67
5889 6518 4.510038 GGTCGTACCTAGAGTTTTCACA 57.490 45.455 0.00 0.00 34.73 3.58
5904 6533 3.946308 TTCACACTAGAGCTCGATACG 57.054 47.619 8.37 0.00 0.00 3.06
5914 6543 1.655654 CTCGATACGCGGTGCTCAG 60.656 63.158 12.47 0.00 41.33 3.35
5919 6548 0.747255 ATACGCGGTGCTCAGAAGAT 59.253 50.000 12.47 0.00 0.00 2.40
5921 6550 1.140589 CGCGGTGCTCAGAAGATCT 59.859 57.895 0.00 0.00 0.00 2.75
5939 6568 2.436646 CCACGAAGCCGAAGCCAT 60.437 61.111 0.00 0.00 41.25 4.40
5940 6569 2.464459 CCACGAAGCCGAAGCCATC 61.464 63.158 0.00 0.00 41.25 3.51
5941 6570 1.741401 CACGAAGCCGAAGCCATCA 60.741 57.895 0.00 0.00 41.25 3.07
5942 6571 1.741770 ACGAAGCCGAAGCCATCAC 60.742 57.895 0.00 0.00 41.25 3.06
5943 6572 2.464459 CGAAGCCGAAGCCATCACC 61.464 63.158 0.00 0.00 41.25 4.02
5944 6573 2.044946 AAGCCGAAGCCATCACCC 60.045 61.111 0.00 0.00 41.25 4.61
5945 6574 3.645268 AAGCCGAAGCCATCACCCC 62.645 63.158 0.00 0.00 41.25 4.95
5947 6576 3.411517 CCGAAGCCATCACCCCCT 61.412 66.667 0.00 0.00 0.00 4.79
5948 6577 2.677228 CGAAGCCATCACCCCCTT 59.323 61.111 0.00 0.00 0.00 3.95
5949 6578 1.000896 CGAAGCCATCACCCCCTTT 60.001 57.895 0.00 0.00 0.00 3.11
5950 6579 0.611896 CGAAGCCATCACCCCCTTTT 60.612 55.000 0.00 0.00 0.00 2.27
5951 6580 0.897621 GAAGCCATCACCCCCTTTTG 59.102 55.000 0.00 0.00 0.00 2.44
5952 6581 1.194121 AAGCCATCACCCCCTTTTGC 61.194 55.000 0.00 0.00 0.00 3.68
5953 6582 1.912763 GCCATCACCCCCTTTTGCA 60.913 57.895 0.00 0.00 0.00 4.08
5954 6583 1.891722 GCCATCACCCCCTTTTGCAG 61.892 60.000 0.00 0.00 0.00 4.41
5955 6584 0.251742 CCATCACCCCCTTTTGCAGA 60.252 55.000 0.00 0.00 0.00 4.26
5956 6585 1.631405 CATCACCCCCTTTTGCAGAA 58.369 50.000 0.00 0.00 0.00 3.02
5957 6586 1.547372 CATCACCCCCTTTTGCAGAAG 59.453 52.381 9.98 9.98 0.00 2.85
5958 6587 0.850100 TCACCCCCTTTTGCAGAAGA 59.150 50.000 18.08 0.00 0.00 2.87
5959 6588 1.216678 TCACCCCCTTTTGCAGAAGAA 59.783 47.619 18.08 0.00 0.00 2.52
5960 6589 1.615392 CACCCCCTTTTGCAGAAGAAG 59.385 52.381 18.08 8.91 0.00 2.85
5961 6590 1.260544 CCCCCTTTTGCAGAAGAAGG 58.739 55.000 18.08 16.39 39.69 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.432403 TTTTAGGATGATTTTTGTGGCCTT 57.568 33.333 3.32 0.00 0.00 4.35
28 29 2.235898 TCTTGCTGTTTTTGTGGCCTTT 59.764 40.909 3.32 0.00 0.00 3.11
29 30 1.830477 TCTTGCTGTTTTTGTGGCCTT 59.170 42.857 3.32 0.00 0.00 4.35
30 31 1.484038 TCTTGCTGTTTTTGTGGCCT 58.516 45.000 3.32 0.00 0.00 5.19
31 32 2.159114 TCTTCTTGCTGTTTTTGTGGCC 60.159 45.455 0.00 0.00 0.00 5.36
32 33 3.118542 CTCTTCTTGCTGTTTTTGTGGC 58.881 45.455 0.00 0.00 0.00 5.01
34 35 3.772932 TGCTCTTCTTGCTGTTTTTGTG 58.227 40.909 0.00 0.00 0.00 3.33
35 36 4.454728 TTGCTCTTCTTGCTGTTTTTGT 57.545 36.364 0.00 0.00 0.00 2.83
36 37 5.978934 AATTGCTCTTCTTGCTGTTTTTG 57.021 34.783 0.00 0.00 0.00 2.44
37 38 7.548780 TGTTTAATTGCTCTTCTTGCTGTTTTT 59.451 29.630 0.00 0.00 0.00 1.94
38 39 7.041107 TGTTTAATTGCTCTTCTTGCTGTTTT 58.959 30.769 0.00 0.00 0.00 2.43
44 45 6.251376 CCGTATTGTTTAATTGCTCTTCTTGC 59.749 38.462 0.00 0.00 0.00 4.01
87 88 9.632638 AGGATGCTCTTTTATGTTGTACATAAT 57.367 29.630 11.74 0.00 46.69 1.28
88 89 9.109393 GAGGATGCTCTTTTATGTTGTACATAA 57.891 33.333 7.03 7.89 46.07 1.90
124 128 0.374758 CACGTGCAATCTGATTCCCG 59.625 55.000 0.82 5.75 0.00 5.14
146 150 2.094182 GGTGTGGCGTTATCTTCAGAGA 60.094 50.000 0.00 0.00 36.09 3.10
298 309 1.591183 CCCGTTGCAATTTCTGGGG 59.409 57.895 0.59 3.42 32.85 4.96
332 343 3.793888 GGGGCGTTCCACCTAGGG 61.794 72.222 14.81 1.73 38.24 3.53
335 346 2.175035 CTTTCGGGGCGTTCCACCTA 62.175 60.000 0.00 0.00 37.22 3.08
336 347 3.546714 CTTTCGGGGCGTTCCACCT 62.547 63.158 0.00 0.00 37.22 4.00
337 348 3.053896 CTTTCGGGGCGTTCCACC 61.054 66.667 0.00 0.00 37.22 4.61
339 350 1.148723 TTTCTTTCGGGGCGTTCCA 59.851 52.632 0.00 0.00 37.22 3.53
366 381 2.541120 CCCTCTCGCTACGGTACCG 61.541 68.421 32.22 32.22 46.03 4.02
371 386 3.111939 CACTCCCTCTCGCTACGG 58.888 66.667 0.00 0.00 0.00 4.02
698 743 0.039708 GCAAGCTTTGAGTGACAGGC 60.040 55.000 0.00 0.00 0.00 4.85
699 744 1.602311 AGCAAGCTTTGAGTGACAGG 58.398 50.000 0.00 0.00 0.00 4.00
732 778 6.942886 GACTGAAGAAATAGTCTGTCACTG 57.057 41.667 0.00 0.00 40.06 3.66
805 855 3.998341 CCCAAACCAATCTGCAAAATGAG 59.002 43.478 0.00 0.00 0.00 2.90
855 905 8.114331 TCAATTGCAAGATGAAAAGTGATAGT 57.886 30.769 13.60 0.00 0.00 2.12
856 906 9.582431 AATCAATTGCAAGATGAAAAGTGATAG 57.418 29.630 18.30 0.00 28.95 2.08
858 908 8.842358 AAATCAATTGCAAGATGAAAAGTGAT 57.158 26.923 18.30 5.09 29.73 3.06
939 994 1.895131 CTTCCAAACCAATCAGGGGTG 59.105 52.381 0.00 0.00 43.89 4.61
940 995 1.827245 GCTTCCAAACCAATCAGGGGT 60.827 52.381 0.00 0.00 43.89 4.95
944 999 3.641437 TTTCGCTTCCAAACCAATCAG 57.359 42.857 0.00 0.00 0.00 2.90
946 1001 4.237349 TCTTTTCGCTTCCAAACCAATC 57.763 40.909 0.00 0.00 0.00 2.67
947 1002 4.321974 GGATCTTTTCGCTTCCAAACCAAT 60.322 41.667 0.00 0.00 0.00 3.16
948 1003 3.005367 GGATCTTTTCGCTTCCAAACCAA 59.995 43.478 0.00 0.00 0.00 3.67
949 1004 2.556622 GGATCTTTTCGCTTCCAAACCA 59.443 45.455 0.00 0.00 0.00 3.67
950 1005 2.820197 AGGATCTTTTCGCTTCCAAACC 59.180 45.455 0.00 0.00 0.00 3.27
951 1006 4.023193 TGAAGGATCTTTTCGCTTCCAAAC 60.023 41.667 0.00 0.00 33.85 2.93
952 1007 4.141287 TGAAGGATCTTTTCGCTTCCAAA 58.859 39.130 0.00 0.00 33.85 3.28
953 1008 3.750371 TGAAGGATCTTTTCGCTTCCAA 58.250 40.909 0.00 0.00 33.85 3.53
954 1009 3.417069 TGAAGGATCTTTTCGCTTCCA 57.583 42.857 0.00 0.00 33.85 3.53
955 1010 3.313803 GGATGAAGGATCTTTTCGCTTCC 59.686 47.826 0.00 2.49 33.85 3.46
956 1011 4.034975 CAGGATGAAGGATCTTTTCGCTTC 59.965 45.833 0.00 0.00 39.69 3.86
996 1057 2.554032 CGGTTTCACTTCTGCCATTTCT 59.446 45.455 0.00 0.00 0.00 2.52
1005 1066 3.307059 CCATCTCTTCCGGTTTCACTTCT 60.307 47.826 0.00 0.00 0.00 2.85
1117 1178 3.181484 CGATTGATCCAACATGCCAACAT 60.181 43.478 0.00 0.00 36.79 2.71
1310 1377 9.899661 AATAGTATGTTGTACCAAATTAGCTGA 57.100 29.630 0.00 0.00 0.00 4.26
1342 1414 6.481644 ACACACAAACAAACAACATTTTCAGT 59.518 30.769 0.00 0.00 0.00 3.41
1343 1415 6.886307 ACACACAAACAAACAACATTTTCAG 58.114 32.000 0.00 0.00 0.00 3.02
1344 1416 6.851222 ACACACAAACAAACAACATTTTCA 57.149 29.167 0.00 0.00 0.00 2.69
1345 1417 9.097672 GTAAACACACAAACAAACAACATTTTC 57.902 29.630 0.00 0.00 0.00 2.29
1415 1490 3.307762 GGAGCAGTGTCTTTATCCCAGTT 60.308 47.826 0.00 0.00 0.00 3.16
1487 1571 3.260884 TGGAGAGGACTGGAACAACATAC 59.739 47.826 0.00 0.00 38.70 2.39
1520 1604 2.193447 GCTATTTGTGCGAGTGATCGA 58.807 47.619 1.17 0.00 34.64 3.59
1526 1610 1.290203 CATCGGCTATTTGTGCGAGT 58.710 50.000 0.00 0.00 0.00 4.18
1584 1668 5.316167 TGCCATGATTCTTGTTACAAGACT 58.684 37.500 25.19 20.52 0.00 3.24
1639 1723 4.523558 TGAAACTGAAATGCATGACATGGA 59.476 37.500 17.03 14.81 39.60 3.41
1640 1724 4.811908 TGAAACTGAAATGCATGACATGG 58.188 39.130 17.03 1.19 39.60 3.66
1641 1725 5.867174 ACATGAAACTGAAATGCATGACATG 59.133 36.000 11.27 11.27 39.60 3.21
1642 1726 6.032956 ACATGAAACTGAAATGCATGACAT 57.967 33.333 0.00 0.00 42.30 3.06
1643 1727 5.009811 TGACATGAAACTGAAATGCATGACA 59.990 36.000 0.00 2.75 38.82 3.58
1644 1728 5.463286 TGACATGAAACTGAAATGCATGAC 58.537 37.500 0.00 0.00 38.82 3.06
1645 1729 5.708877 TGACATGAAACTGAAATGCATGA 57.291 34.783 0.00 0.00 38.82 3.07
1646 1730 5.220397 GCATGACATGAAACTGAAATGCATG 60.220 40.000 19.76 0.00 41.44 4.06
1647 1731 4.868171 GCATGACATGAAACTGAAATGCAT 59.132 37.500 19.76 0.00 37.87 3.96
1648 1732 4.239304 GCATGACATGAAACTGAAATGCA 58.761 39.130 19.76 0.00 37.87 3.96
1649 1733 4.239304 TGCATGACATGAAACTGAAATGC 58.761 39.130 19.76 0.92 38.16 3.56
1650 1734 6.961359 AATGCATGACATGAAACTGAAATG 57.039 33.333 19.76 0.00 39.60 2.32
1651 1735 7.156000 TGAAATGCATGACATGAAACTGAAAT 58.844 30.769 19.76 0.00 39.60 2.17
1652 1736 6.514063 TGAAATGCATGACATGAAACTGAAA 58.486 32.000 19.76 0.00 39.60 2.69
1653 1737 6.086785 TGAAATGCATGACATGAAACTGAA 57.913 33.333 19.76 0.00 39.60 3.02
1654 1738 5.242171 ACTGAAATGCATGACATGAAACTGA 59.758 36.000 19.76 0.00 39.60 3.41
1655 1739 5.466819 ACTGAAATGCATGACATGAAACTG 58.533 37.500 19.76 10.63 39.60 3.16
1656 1740 5.717078 ACTGAAATGCATGACATGAAACT 57.283 34.783 19.76 0.00 39.60 2.66
1657 1741 6.774354 AAACTGAAATGCATGACATGAAAC 57.226 33.333 19.76 5.76 39.60 2.78
1658 1742 7.432059 TGTAAACTGAAATGCATGACATGAAA 58.568 30.769 19.76 6.66 39.60 2.69
1666 1750 8.767085 AGAACAAAATGTAAACTGAAATGCATG 58.233 29.630 0.00 0.00 0.00 4.06
1683 1767 5.649831 GGAACCTCTGCAGATAGAACAAAAT 59.350 40.000 18.63 0.00 0.00 1.82
1829 1914 4.952460 ACTGAAAAACCTAGCACGTAAGA 58.048 39.130 0.00 0.00 43.62 2.10
1832 1917 3.069872 TGGACTGAAAAACCTAGCACGTA 59.930 43.478 0.00 0.00 0.00 3.57
2373 2707 5.243981 CCATTCTTCAGTGTGATGAGTTCT 58.756 41.667 0.00 0.00 33.06 3.01
2680 3068 5.011090 TCCCACTTCTCATTCATCTTACG 57.989 43.478 0.00 0.00 0.00 3.18
2683 3071 5.511386 AACTCCCACTTCTCATTCATCTT 57.489 39.130 0.00 0.00 0.00 2.40
2684 3072 5.250313 AGAAACTCCCACTTCTCATTCATCT 59.750 40.000 0.00 0.00 0.00 2.90
2685 3073 5.495640 AGAAACTCCCACTTCTCATTCATC 58.504 41.667 0.00 0.00 0.00 2.92
2687 3075 4.982241 AGAAACTCCCACTTCTCATTCA 57.018 40.909 0.00 0.00 0.00 2.57
2688 3076 7.745620 TTTTAGAAACTCCCACTTCTCATTC 57.254 36.000 0.00 0.00 33.89 2.67
2689 3077 7.725844 ACATTTTAGAAACTCCCACTTCTCATT 59.274 33.333 0.00 0.00 33.89 2.57
2691 3079 6.601332 ACATTTTAGAAACTCCCACTTCTCA 58.399 36.000 0.00 0.00 33.89 3.27
2692 3080 7.308649 GGAACATTTTAGAAACTCCCACTTCTC 60.309 40.741 0.00 0.00 33.89 2.87
2694 3082 6.490381 AGGAACATTTTAGAAACTCCCACTTC 59.510 38.462 0.00 0.00 0.00 3.01
2695 3083 6.265422 CAGGAACATTTTAGAAACTCCCACTT 59.735 38.462 0.00 0.00 0.00 3.16
2698 3086 5.076873 CCAGGAACATTTTAGAAACTCCCA 58.923 41.667 0.00 0.00 0.00 4.37
2699 3087 5.183331 GTCCAGGAACATTTTAGAAACTCCC 59.817 44.000 0.00 0.00 0.00 4.30
2700 3088 5.183331 GGTCCAGGAACATTTTAGAAACTCC 59.817 44.000 0.00 0.00 0.00 3.85
2701 3089 5.768164 TGGTCCAGGAACATTTTAGAAACTC 59.232 40.000 1.73 0.00 0.00 3.01
2702 3090 5.701224 TGGTCCAGGAACATTTTAGAAACT 58.299 37.500 1.73 0.00 0.00 2.66
2703 3091 6.399639 TTGGTCCAGGAACATTTTAGAAAC 57.600 37.500 8.43 0.00 0.00 2.78
2707 3112 6.434028 TGAAGATTGGTCCAGGAACATTTTAG 59.566 38.462 8.43 0.00 0.00 1.85
2712 3117 4.387026 TTGAAGATTGGTCCAGGAACAT 57.613 40.909 8.43 0.00 0.00 2.71
2842 3248 6.143919 GGTGCTAAATGTTTTTCGGAGAAAAG 59.856 38.462 7.80 0.00 45.90 2.27
2850 3256 5.698832 TCTCATGGTGCTAAATGTTTTTCG 58.301 37.500 0.00 0.00 0.00 3.46
2901 3307 5.885912 GCAACCTGACAAAATATCCTTCCTA 59.114 40.000 0.00 0.00 0.00 2.94
3204 3610 6.727697 ACTGAGATATGTCATATGGATGTGGA 59.272 38.462 10.15 0.00 34.41 4.02
3205 3611 6.944096 ACTGAGATATGTCATATGGATGTGG 58.056 40.000 10.15 0.00 34.41 4.17
3206 3612 8.092687 TGAACTGAGATATGTCATATGGATGTG 58.907 37.037 10.15 0.00 34.41 3.21
3207 3613 8.198807 TGAACTGAGATATGTCATATGGATGT 57.801 34.615 10.15 2.11 34.41 3.06
3208 3614 9.668497 AATGAACTGAGATATGTCATATGGATG 57.332 33.333 10.15 1.56 0.00 3.51
3356 3767 9.478019 CGAGAAATCATGTATTTGACAAGTAAC 57.522 33.333 7.55 0.00 42.78 2.50
3732 4196 2.096565 CAGATGCACTCACACAGAAACG 60.097 50.000 0.00 0.00 0.00 3.60
3795 4260 6.147164 GCATTGCATCCAAATATTCTGAATGG 59.853 38.462 13.01 7.24 34.05 3.16
3796 4261 6.704050 TGCATTGCATCCAAATATTCTGAATG 59.296 34.615 7.38 0.00 34.05 2.67
3799 4264 5.361571 ACTGCATTGCATCCAAATATTCTGA 59.638 36.000 12.53 0.00 38.13 3.27
3844 4309 2.422519 CCTGCTGCCAATCCTTGTAGAT 60.423 50.000 0.00 0.00 0.00 1.98
3952 4417 5.147032 TCAGAACCCTGAAAAATCCAATGT 58.853 37.500 0.00 0.00 45.74 2.71
4106 4571 6.732896 AGAGAACTCAGGAAACTACAAAGA 57.267 37.500 4.64 0.00 40.21 2.52
4141 4606 6.393720 ACGAGCAAAATTATTTGTGCAATC 57.606 33.333 18.99 11.89 46.19 2.67
4149 4614 7.491048 AGACACAACAAACGAGCAAAATTATTT 59.509 29.630 0.00 0.00 0.00 1.40
4184 4651 2.208349 AGGAAGGACAGCCCCACT 59.792 61.111 0.00 0.00 34.66 4.00
4193 4660 0.108585 TGGTGAACTGCAGGAAGGAC 59.891 55.000 19.93 6.85 0.00 3.85
4220 4687 2.760634 TGAAGAGGTTGCGCATAGAA 57.239 45.000 12.75 0.00 0.00 2.10
4268 4735 5.264712 CGAGAAAAGTACTCTGGTATCGAC 58.735 45.833 0.00 0.00 32.87 4.20
4350 4817 2.877154 AGGGTGTGAGGGATAGTGAT 57.123 50.000 0.00 0.00 0.00 3.06
4361 4828 8.262227 CCATACTAGTACAAATTAAGGGTGTGA 58.738 37.037 4.31 0.00 0.00 3.58
4396 4868 3.191581 TCAAATCTCGAGACAGTGGACTC 59.808 47.826 19.30 8.81 33.32 3.36
4437 4943 6.855836 TGTGCTAGATTGATTGGACATTTTC 58.144 36.000 0.00 0.00 0.00 2.29
4456 4965 9.248291 CAGTAAAGTTTGTCATTATTTTGTGCT 57.752 29.630 0.00 0.00 0.00 4.40
4476 4985 8.397575 TGCCACAACATTTTACTATCAGTAAA 57.602 30.769 7.29 7.29 45.78 2.01
4477 4986 7.987750 TGCCACAACATTTTACTATCAGTAA 57.012 32.000 0.00 0.00 38.79 2.24
4479 4988 6.625740 GCATGCCACAACATTTTACTATCAGT 60.626 38.462 6.36 0.00 0.00 3.41
4480 4989 5.745294 GCATGCCACAACATTTTACTATCAG 59.255 40.000 6.36 0.00 0.00 2.90
4481 4990 5.418524 AGCATGCCACAACATTTTACTATCA 59.581 36.000 15.66 0.00 0.00 2.15
4482 4991 5.745294 CAGCATGCCACAACATTTTACTATC 59.255 40.000 15.66 0.00 0.00 2.08
4483 4992 5.418524 TCAGCATGCCACAACATTTTACTAT 59.581 36.000 15.66 0.00 34.76 2.12
4484 4993 4.764308 TCAGCATGCCACAACATTTTACTA 59.236 37.500 15.66 0.00 34.76 1.82
4485 4994 3.573538 TCAGCATGCCACAACATTTTACT 59.426 39.130 15.66 0.00 34.76 2.24
4486 4995 3.911868 TCAGCATGCCACAACATTTTAC 58.088 40.909 15.66 0.00 34.76 2.01
4487 4996 4.496360 CATCAGCATGCCACAACATTTTA 58.504 39.130 15.66 0.00 34.76 1.52
4488 4997 3.331150 CATCAGCATGCCACAACATTTT 58.669 40.909 15.66 0.00 34.76 1.82
4489 4998 2.354303 CCATCAGCATGCCACAACATTT 60.354 45.455 15.66 0.00 34.76 2.32
4490 4999 1.206132 CCATCAGCATGCCACAACATT 59.794 47.619 15.66 0.00 34.76 2.71
4491 5000 0.821517 CCATCAGCATGCCACAACAT 59.178 50.000 15.66 0.00 34.76 2.71
4492 5001 0.540133 ACCATCAGCATGCCACAACA 60.540 50.000 15.66 0.00 34.76 3.33
4493 5002 1.462616 TACCATCAGCATGCCACAAC 58.537 50.000 15.66 0.00 34.76 3.32
4494 5003 2.212812 TTACCATCAGCATGCCACAA 57.787 45.000 15.66 0.00 34.76 3.33
4495 5004 2.212812 TTTACCATCAGCATGCCACA 57.787 45.000 15.66 0.00 34.76 4.17
4496 5005 3.119029 ACATTTTACCATCAGCATGCCAC 60.119 43.478 15.66 0.00 34.76 5.01
4497 5006 3.098377 ACATTTTACCATCAGCATGCCA 58.902 40.909 15.66 0.78 34.76 4.92
4498 5007 3.806625 ACATTTTACCATCAGCATGCC 57.193 42.857 15.66 0.00 34.76 4.40
4499 5008 5.067674 TCCTAACATTTTACCATCAGCATGC 59.932 40.000 10.51 10.51 34.76 4.06
4500 5009 6.698008 TCCTAACATTTTACCATCAGCATG 57.302 37.500 0.00 0.00 37.54 4.06
4501 5010 6.891908 ACTTCCTAACATTTTACCATCAGCAT 59.108 34.615 0.00 0.00 0.00 3.79
4502 5011 6.245408 ACTTCCTAACATTTTACCATCAGCA 58.755 36.000 0.00 0.00 0.00 4.41
4503 5012 6.759497 ACTTCCTAACATTTTACCATCAGC 57.241 37.500 0.00 0.00 0.00 4.26
4547 5143 8.703604 TCTGTGCTAAATTAGTGTATGAGTTC 57.296 34.615 1.68 0.00 0.00 3.01
4567 5163 3.047796 GCTGTGCATTGTCTTTTCTGTG 58.952 45.455 0.00 0.00 0.00 3.66
4579 5175 1.608590 GTGGTGTACAAGCTGTGCATT 59.391 47.619 0.00 0.00 44.34 3.56
4693 5289 8.339714 CAAACTCAACTTCAAAATGATGCAAAT 58.660 29.630 0.00 0.00 0.00 2.32
4999 5595 3.465871 TGCAAAGGTTTCTTCATTTGGC 58.534 40.909 6.09 0.00 38.81 4.52
5023 5619 1.016627 TCAGAAGCATGCCGTATTGC 58.983 50.000 15.66 0.00 0.00 3.56
5056 5652 6.844097 TCTCTACTTTTCTTCTCCTCTTCC 57.156 41.667 0.00 0.00 0.00 3.46
5070 5666 4.649674 TGCGGGTCTTATCATCTCTACTTT 59.350 41.667 0.00 0.00 0.00 2.66
5103 5699 2.717639 TTCCTCCATCCTTTGCTAGC 57.282 50.000 8.10 8.10 0.00 3.42
5109 5705 4.045846 TGAAGGGAAATTCCTCCATCCTTT 59.954 41.667 12.28 0.00 37.20 3.11
5132 5728 5.537300 ATCTATGTACAATCGGACAGCTT 57.463 39.130 0.00 0.00 0.00 3.74
5175 5771 9.206870 CACAGCAAAAACTACCATTAATTCATT 57.793 29.630 0.00 0.00 0.00 2.57
5176 5772 8.367156 ACACAGCAAAAACTACCATTAATTCAT 58.633 29.630 0.00 0.00 0.00 2.57
5177 5773 7.651304 CACACAGCAAAAACTACCATTAATTCA 59.349 33.333 0.00 0.00 0.00 2.57
5187 5783 1.120437 GCGCACACAGCAAAAACTAC 58.880 50.000 0.30 0.00 46.13 2.73
5203 5799 1.667724 AGATCTTACATTGCACAGCGC 59.332 47.619 0.00 0.00 42.89 5.92
5204 5800 2.931969 TGAGATCTTACATTGCACAGCG 59.068 45.455 0.00 0.00 0.00 5.18
5205 5801 4.573607 TCATGAGATCTTACATTGCACAGC 59.426 41.667 0.00 0.00 0.00 4.40
5206 5802 6.673154 TTCATGAGATCTTACATTGCACAG 57.327 37.500 0.00 0.00 0.00 3.66
5239 5842 4.386652 GCTAACAATGTGCTTCATTTGTGG 59.613 41.667 5.27 1.59 43.33 4.17
5240 5843 4.983538 TGCTAACAATGTGCTTCATTTGTG 59.016 37.500 5.27 0.08 43.33 3.33
5249 5852 4.641396 TCAACTACTGCTAACAATGTGCT 58.359 39.130 0.00 0.00 0.00 4.40
5263 5866 2.880443 TCTACGGTGGGTTCAACTACT 58.120 47.619 0.00 0.00 0.00 2.57
5358 5961 1.586042 CATATTGCGGTTGTGCGCC 60.586 57.895 4.18 0.00 37.81 6.53
5359 5962 2.223549 GCATATTGCGGTTGTGCGC 61.224 57.895 0.00 0.00 37.81 6.09
5369 5972 3.502595 ACATGATCTGAGCAGCATATTGC 59.497 43.478 0.00 0.00 45.46 3.56
5370 5973 4.154375 GGACATGATCTGAGCAGCATATTG 59.846 45.833 0.00 0.00 0.00 1.90
5371 5974 4.325119 GGACATGATCTGAGCAGCATATT 58.675 43.478 0.00 0.00 0.00 1.28
5393 5996 0.521242 GGTCTTATTGCAACAGCGCG 60.521 55.000 0.00 0.00 33.35 6.86
5410 6013 4.661709 TCTTACAAGGGTTCTTACAAGGGT 59.338 41.667 0.00 0.00 0.00 4.34
5411 6014 5.221864 ACTCTTACAAGGGTTCTTACAAGGG 60.222 44.000 0.00 0.00 35.90 3.95
5412 6015 5.866207 ACTCTTACAAGGGTTCTTACAAGG 58.134 41.667 0.00 0.00 35.90 3.61
5413 6016 8.148999 ACTAACTCTTACAAGGGTTCTTACAAG 58.851 37.037 10.44 4.77 46.42 3.16
5414 6017 8.026396 ACTAACTCTTACAAGGGTTCTTACAA 57.974 34.615 10.44 0.00 46.42 2.41
5415 6018 7.522725 CGACTAACTCTTACAAGGGTTCTTACA 60.523 40.741 10.44 0.00 46.42 2.41
5416 6019 6.805760 CGACTAACTCTTACAAGGGTTCTTAC 59.194 42.308 10.44 2.00 46.42 2.34
5417 6020 6.071728 CCGACTAACTCTTACAAGGGTTCTTA 60.072 42.308 10.44 0.00 46.42 2.10
5418 6021 5.279356 CCGACTAACTCTTACAAGGGTTCTT 60.279 44.000 10.44 0.00 46.42 2.52
5419 6022 4.220163 CCGACTAACTCTTACAAGGGTTCT 59.780 45.833 10.44 0.00 46.42 3.01
5420 6023 4.021632 ACCGACTAACTCTTACAAGGGTTC 60.022 45.833 10.44 0.00 46.42 3.62
5448 6051 1.053424 TCAACCTACCTTGACCGCTT 58.947 50.000 0.00 0.00 0.00 4.68
5498 6101 6.068010 TCAAATAAGGCCATAACCGATTCAT 58.932 36.000 5.01 0.00 33.69 2.57
5562 6165 6.592798 AACTCAATTTGATTGCACACTTTG 57.407 33.333 0.00 0.00 40.05 2.77
5596 6212 5.540911 ACTCAATCCGATTGCACAATTTTT 58.459 33.333 15.21 0.00 40.05 1.94
5601 6217 5.392919 CCATTAACTCAATCCGATTGCACAA 60.393 40.000 15.21 7.65 40.05 3.33
5620 6236 6.484288 AGTGAAATGAGTCATTGGTCCATTA 58.516 36.000 18.94 0.00 34.04 1.90
5645 6261 1.198713 GGAGGTCTCAGGAGCAATGA 58.801 55.000 0.14 0.00 41.89 2.57
5662 6278 4.719273 TGATGTATACAACTGATGTGGGGA 59.281 41.667 10.14 0.00 43.77 4.81
5665 6281 6.512253 GCACATGATGTATACAACTGATGTGG 60.512 42.308 28.42 18.78 43.77 4.17
5672 6288 7.174772 TCAAAAGTGCACATGATGTATACAACT 59.825 33.333 21.04 3.24 0.00 3.16
5677 6293 7.862512 TCATCAAAAGTGCACATGATGTATA 57.137 32.000 34.43 24.02 45.83 1.47
5678 6294 6.762702 TCATCAAAAGTGCACATGATGTAT 57.237 33.333 34.43 16.73 45.83 2.29
5679 6295 6.430616 TCTTCATCAAAAGTGCACATGATGTA 59.569 34.615 34.43 29.41 45.83 2.29
5680 6296 5.242171 TCTTCATCAAAAGTGCACATGATGT 59.758 36.000 34.43 17.47 45.83 3.06
5681 6297 5.705902 TCTTCATCAAAAGTGCACATGATG 58.294 37.500 32.70 32.70 46.62 3.07
5682 6298 5.970317 TCTTCATCAAAAGTGCACATGAT 57.030 34.783 21.04 20.71 32.94 2.45
5688 6310 5.718146 TGTTGTTTCTTCATCAAAAGTGCA 58.282 33.333 0.00 0.00 0.00 4.57
5689 6311 6.090628 TGTTGTTGTTTCTTCATCAAAAGTGC 59.909 34.615 0.00 0.00 31.68 4.40
5718 6340 1.736696 CGACGGGGCGTACACTTTTAT 60.737 52.381 0.00 0.00 41.37 1.40
5740 6368 0.837272 ACCTATGGTGGTTGGATCCG 59.163 55.000 7.39 0.00 36.89 4.18
5795 6423 9.119418 TGTTGAAGATATTGTTTTGAAGTCTGA 57.881 29.630 0.00 0.00 0.00 3.27
5812 6440 3.469008 TGTCGTGTCCTTGTTGAAGAT 57.531 42.857 0.00 0.00 0.00 2.40
5813 6441 2.971660 TGTCGTGTCCTTGTTGAAGA 57.028 45.000 0.00 0.00 0.00 2.87
5829 6457 5.537188 TGGCAATGATGGTTTTTACTTGTC 58.463 37.500 0.00 0.00 0.00 3.18
5832 6460 4.996758 GCTTGGCAATGATGGTTTTTACTT 59.003 37.500 0.00 0.00 0.00 2.24
5833 6461 4.568956 GCTTGGCAATGATGGTTTTTACT 58.431 39.130 0.00 0.00 0.00 2.24
5840 6468 2.887360 GCGCTTGGCAATGATGGT 59.113 55.556 0.00 0.00 42.87 3.55
5889 6518 0.532417 ACCGCGTATCGAGCTCTAGT 60.532 55.000 12.85 0.00 41.67 2.57
5904 6533 0.529555 GGAGATCTTCTGAGCACCGC 60.530 60.000 0.00 0.00 30.48 5.68
5914 6543 0.456221 TCGGCTTCGTGGAGATCTTC 59.544 55.000 0.00 0.00 35.06 2.87
5919 6548 2.261671 GCTTCGGCTTCGTGGAGA 59.738 61.111 0.00 0.00 38.08 3.71
5921 6550 2.852495 GATGGCTTCGGCTTCGTGGA 62.852 60.000 0.00 0.00 41.44 4.02
5939 6568 0.850100 TCTTCTGCAAAAGGGGGTGA 59.150 50.000 0.00 0.00 0.00 4.02
5940 6569 1.615392 CTTCTTCTGCAAAAGGGGGTG 59.385 52.381 0.00 0.00 0.00 4.61
5941 6570 1.481242 CCTTCTTCTGCAAAAGGGGGT 60.481 52.381 0.00 0.00 36.68 4.95
5942 6571 1.260544 CCTTCTTCTGCAAAAGGGGG 58.739 55.000 0.00 0.00 36.68 5.40


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

AutoCloner maintained by Alex Coulton.