Multiple sequence alignment - TraesCS6D01G258600

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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 TraesCS6D01G258600 chr6D 100.000 4703 0 0 1 4703 364497919 364493217 0.000000e+00 8685.0
1 TraesCS6D01G258600 chr6D 89.286 168 13 4 4185 4350 392273063 392273227 6.170000e-49 206.0
2 TraesCS6D01G258600 chr6B 92.274 3430 144 59 837 4226 549625440 549622092 0.000000e+00 4754.0
3 TraesCS6D01G258600 chr6B 91.429 175 14 1 4226 4400 549621400 549621227 6.080000e-59 239.0
4 TraesCS6D01G258600 chr6B 78.610 187 13 6 657 836 549653006 549652840 1.080000e-16 99.0
5 TraesCS6D01G258600 chr6B 97.778 45 1 0 4608 4652 549621166 549621122 1.400000e-10 78.7
6 TraesCS6D01G258600 chr6B 100.000 29 0 0 4570 4598 549621225 549621197 2.000000e-03 54.7
7 TraesCS6D01G258600 chr6A 96.522 2070 52 4 2203 4271 506099349 506097299 0.000000e+00 3406.0
8 TraesCS6D01G258600 chr6A 94.581 1347 33 12 629 1953 506100833 506099505 0.000000e+00 2047.0
9 TraesCS6D01G258600 chr6A 89.634 656 40 11 3 647 506102122 506101484 0.000000e+00 809.0
10 TraesCS6D01G258600 chr6A 97.419 155 2 2 4303 4456 506097302 506097149 3.610000e-66 263.0
11 TraesCS6D01G258600 chr6A 96.610 59 2 0 2110 2168 506099407 506099349 1.080000e-16 99.0
12 TraesCS6D01G258600 chr6A 96.364 55 1 1 4650 4703 506097152 506097098 6.480000e-14 89.8
13 TraesCS6D01G258600 chr7B 85.567 970 132 6 968 1936 333963302 333962340 0.000000e+00 1009.0
14 TraesCS6D01G258600 chr7B 87.778 180 12 7 4191 4368 477814818 477814989 7.980000e-48 202.0
15 TraesCS6D01G258600 chr7A 85.358 963 134 5 970 1932 194791335 194792290 0.000000e+00 990.0
16 TraesCS6D01G258600 chr7D 84.735 963 140 5 970 1932 189250894 189249939 0.000000e+00 957.0
17 TraesCS6D01G258600 chr7D 91.195 159 12 1 4191 4349 454079074 454079230 1.020000e-51 215.0
18 TraesCS6D01G258600 chr3D 92.903 155 8 2 4196 4350 441388669 441388820 6.130000e-54 222.0
19 TraesCS6D01G258600 chr3D 92.258 155 7 4 4196 4348 315480427 315480578 1.020000e-51 215.0
20 TraesCS6D01G258600 chr3A 92.258 155 9 2 4196 4350 582283217 582283368 2.850000e-52 217.0
21 TraesCS6D01G258600 chr4A 90.244 164 12 3 4187 4349 450791498 450791658 1.330000e-50 211.0
22 TraesCS6D01G258600 chr4A 78.723 94 18 2 75 167 603660065 603660157 1.410000e-05 62.1


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 TraesCS6D01G258600 chr6D 364493217 364497919 4702 True 8685.000000 8685 100.000000 1 4703 1 chr6D.!!$R1 4702
1 TraesCS6D01G258600 chr6B 549621122 549625440 4318 True 1281.600000 4754 95.370250 837 4652 4 chr6B.!!$R2 3815
2 TraesCS6D01G258600 chr6A 506097098 506102122 5024 True 1118.966667 3406 95.188333 3 4703 6 chr6A.!!$R1 4700
3 TraesCS6D01G258600 chr7B 333962340 333963302 962 True 1009.000000 1009 85.567000 968 1936 1 chr7B.!!$R1 968
4 TraesCS6D01G258600 chr7A 194791335 194792290 955 False 990.000000 990 85.358000 970 1932 1 chr7A.!!$F1 962
5 TraesCS6D01G258600 chr7D 189249939 189250894 955 True 957.000000 957 84.735000 970 1932 1 chr7D.!!$R1 962

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
130 132 0.175760 TTTTCTCGGCTGGATCCTCG 59.824 55.0 14.23 13.96 0.00 4.63 F
354 357 0.179156 CAAGCCGTTGATGCACCATC 60.179 55.0 0.00 0.00 40.88 3.51 F
906 1595 0.179234 TTGGCTCACACGGAGTTGAA 59.821 50.0 0.00 0.00 45.88 2.69 F
2091 2806 0.110328 CAGCTGCTTCTTTGCTCGTG 60.110 55.0 0.00 0.00 34.51 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2543 0.324923 TGGTATGTGTAGAGCCCGGT 60.325 55.000 0.0 0.0 0.00 5.28 R
2074 2789 1.148310 TACACGAGCAAAGAAGCAGC 58.852 50.000 0.0 0.0 36.85 5.25 R
2505 3226 1.303561 GTGGCAAGAGCACCCATGA 60.304 57.895 0.0 0.0 44.61 3.07 R
3738 4468 0.536006 AAGCTCAGAGTGCGGCTTTT 60.536 50.000 0.0 0.0 41.44 2.27 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
67 69 4.659115 ACGTTATATTTAGGGGATTGGCC 58.341 43.478 0.00 0.00 0.00 5.36
68 70 4.105057 ACGTTATATTTAGGGGATTGGCCA 59.895 41.667 0.00 0.00 38.95 5.36
69 71 5.222254 ACGTTATATTTAGGGGATTGGCCAT 60.222 40.000 6.09 0.00 38.95 4.40
75 77 2.595095 GGGATTGGCCATGTCCGA 59.405 61.111 23.96 3.44 38.95 4.55
76 78 1.823899 GGGATTGGCCATGTCCGAC 60.824 63.158 23.96 12.56 38.95 4.79
86 88 2.161609 GCCATGTCCGACCAAAACTTAG 59.838 50.000 0.00 0.00 0.00 2.18
97 99 6.427547 CCGACCAAAACTTAGTGTGGTAAATA 59.572 38.462 17.59 0.00 44.42 1.40
114 116 9.676861 GTGGTAAATATACTCCACTAAGGTTTT 57.323 33.333 12.77 0.00 44.57 2.43
121 123 1.975680 TCCACTAAGGTTTTCTCGGCT 59.024 47.619 0.00 0.00 39.02 5.52
130 132 0.175760 TTTTCTCGGCTGGATCCTCG 59.824 55.000 14.23 13.96 0.00 4.63
165 168 3.493524 GGATCAGCTAGAGTTGGCCTTAC 60.494 52.174 3.32 1.81 0.00 2.34
167 170 2.903784 TCAGCTAGAGTTGGCCTTACAA 59.096 45.455 3.32 0.00 0.00 2.41
233 236 9.667107 TTTCTACAAAAGTTCGGATTCAGATAT 57.333 29.630 0.00 0.00 0.00 1.63
312 315 1.766494 TGAAACCTCTATACCGCCGA 58.234 50.000 0.00 0.00 0.00 5.54
328 331 1.361668 CCGAAAGATCACCACCGCTG 61.362 60.000 0.00 0.00 0.00 5.18
343 346 1.227234 GCTGCCAAAACAAGCCGTT 60.227 52.632 0.00 0.00 40.50 4.44
354 357 0.179156 CAAGCCGTTGATGCACCATC 60.179 55.000 0.00 0.00 40.88 3.51
385 388 1.041437 GCTACCGGAGCCAGTCTAAT 58.959 55.000 9.46 0.00 46.41 1.73
394 397 4.681781 CGGAGCCAGTCTAATCTTGTCAAT 60.682 45.833 0.00 0.00 0.00 2.57
397 400 5.181748 AGCCAGTCTAATCTTGTCAATGAC 58.818 41.667 6.41 6.41 0.00 3.06
399 402 5.064452 GCCAGTCTAATCTTGTCAATGACAG 59.936 44.000 16.10 10.64 43.69 3.51
401 404 6.652481 CCAGTCTAATCTTGTCAATGACAGTT 59.348 38.462 16.10 14.07 43.69 3.16
402 405 7.173907 CCAGTCTAATCTTGTCAATGACAGTTT 59.826 37.037 16.10 12.86 43.69 2.66
403 406 8.562892 CAGTCTAATCTTGTCAATGACAGTTTT 58.437 33.333 16.10 12.55 43.69 2.43
404 407 9.778741 AGTCTAATCTTGTCAATGACAGTTTTA 57.221 29.630 16.10 12.95 43.69 1.52
447 450 6.287589 ACCTTCAACCACTAGTATCTCTTG 57.712 41.667 0.00 0.00 0.00 3.02
448 451 5.112686 CCTTCAACCACTAGTATCTCTTGC 58.887 45.833 0.00 0.00 0.00 4.01
468 471 2.736400 GCATGATTTTGCTGGCTACACC 60.736 50.000 0.00 0.00 39.57 4.16
470 473 1.885887 TGATTTTGCTGGCTACACCAC 59.114 47.619 0.00 0.00 46.36 4.16
502 505 6.757897 TGGCACTCTCTATTTTTATGTTGG 57.242 37.500 0.00 0.00 0.00 3.77
559 570 8.330466 TCATTTAGTAAATGCCATATTACCCG 57.670 34.615 24.82 3.38 46.09 5.28
578 589 1.732405 CGCTCTGAACGTGCTCATACA 60.732 52.381 0.00 0.00 0.00 2.29
585 596 7.609760 TCTGAACGTGCTCATACAAATAAAT 57.390 32.000 0.00 0.00 0.00 1.40
586 597 7.463544 TCTGAACGTGCTCATACAAATAAATG 58.536 34.615 0.00 0.00 0.00 2.32
587 598 7.119116 TCTGAACGTGCTCATACAAATAAATGT 59.881 33.333 0.00 0.00 37.32 2.71
618 630 6.250819 GTGTGTTCATAGGATCGAATGTTTG 58.749 40.000 0.00 0.00 0.00 2.93
622 634 4.512484 TCATAGGATCGAATGTTTGTGCA 58.488 39.130 0.00 0.00 0.00 4.57
641 1321 8.631676 TTGTGCATGTATGTAAATATTTGCAG 57.368 30.769 21.12 10.47 39.29 4.41
671 1351 7.981142 ACTCGTTTCTCAAAAACAAACTATGA 58.019 30.769 2.05 0.00 0.00 2.15
689 1369 6.636705 ACTATGAGTTGTTCTATACGGCAAA 58.363 36.000 0.00 0.00 0.00 3.68
701 1381 9.615295 GTTCTATACGGCAAATTTTAAGAACAA 57.385 29.630 0.00 0.00 39.85 2.83
732 1412 8.946085 TCGCATATATAGAACCATGGAAAAATC 58.054 33.333 21.47 8.32 0.00 2.17
733 1413 8.729756 CGCATATATAGAACCATGGAAAAATCA 58.270 33.333 21.47 0.00 0.00 2.57
742 1422 4.822685 CATGGAAAAATCACATGGGGAA 57.177 40.909 0.00 0.00 38.58 3.97
743 1423 5.163281 CATGGAAAAATCACATGGGGAAA 57.837 39.130 0.00 0.00 38.58 3.13
744 1424 5.747342 CATGGAAAAATCACATGGGGAAAT 58.253 37.500 0.00 0.00 38.58 2.17
745 1425 5.839517 TGGAAAAATCACATGGGGAAATT 57.160 34.783 0.00 0.00 0.00 1.82
746 1426 6.198237 TGGAAAAATCACATGGGGAAATTT 57.802 33.333 0.00 0.00 0.00 1.82
747 1427 6.237154 TGGAAAAATCACATGGGGAAATTTC 58.763 36.000 9.83 9.83 0.00 2.17
748 1428 6.183361 TGGAAAAATCACATGGGGAAATTTCA 60.183 34.615 19.49 0.42 30.66 2.69
749 1429 6.372381 GGAAAAATCACATGGGGAAATTTCAG 59.628 38.462 19.49 6.43 30.66 3.02
750 1430 6.438186 AAAATCACATGGGGAAATTTCAGT 57.562 33.333 19.49 7.00 0.00 3.41
751 1431 7.552050 AAAATCACATGGGGAAATTTCAGTA 57.448 32.000 19.49 5.38 0.00 2.74
752 1432 6.530019 AATCACATGGGGAAATTTCAGTAC 57.470 37.500 19.49 7.03 0.00 2.73
770 1450 5.952347 TCAGTACTAGTGTGAATCACAGGAT 59.048 40.000 17.28 8.47 45.43 3.24
805 1494 4.127171 ACAAGTCATAGAAACTGCAACGT 58.873 39.130 0.00 0.00 0.00 3.99
831 1520 2.509052 TCACAGACCAGTCACGAAAG 57.491 50.000 0.00 0.00 0.00 2.62
838 1527 1.376037 CAGTCACGAAAGGAGGGCC 60.376 63.158 0.00 0.00 0.00 5.80
839 1528 2.434359 GTCACGAAAGGAGGGCCG 60.434 66.667 0.00 0.00 39.96 6.13
857 1546 1.550065 CGTCACGATTGCTGGTCTAG 58.450 55.000 0.00 0.00 0.00 2.43
903 1592 1.227853 GGTTGGCTCACACGGAGTT 60.228 57.895 0.00 0.00 45.88 3.01
904 1593 1.507141 GGTTGGCTCACACGGAGTTG 61.507 60.000 0.00 0.00 45.88 3.16
906 1595 0.179234 TTGGCTCACACGGAGTTGAA 59.821 50.000 0.00 0.00 45.88 2.69
907 1596 0.179234 TGGCTCACACGGAGTTGAAA 59.821 50.000 0.00 0.00 45.88 2.69
908 1597 0.868406 GGCTCACACGGAGTTGAAAG 59.132 55.000 0.00 0.00 45.88 2.62
927 1625 1.132643 AGATTGACCTACGACACGAGC 59.867 52.381 0.00 0.00 0.00 5.03
944 1642 2.681976 CGAGCAGTCATTTCAATCCCCT 60.682 50.000 0.00 0.00 0.00 4.79
959 1657 1.002502 CCCTCCGAAACCCTGAACC 60.003 63.158 0.00 0.00 0.00 3.62
960 1658 1.375523 CCTCCGAAACCCTGAACCG 60.376 63.158 0.00 0.00 0.00 4.44
961 1659 2.031465 TCCGAAACCCTGAACCGC 59.969 61.111 0.00 0.00 0.00 5.68
962 1660 2.281208 CCGAAACCCTGAACCGCA 60.281 61.111 0.00 0.00 0.00 5.69
963 1661 2.325082 CCGAAACCCTGAACCGCAG 61.325 63.158 0.00 0.00 44.49 5.18
964 1662 2.954611 GAAACCCTGAACCGCAGC 59.045 61.111 0.00 0.00 43.50 5.25
1569 2279 1.143183 GTACATCATCCACCGGCGT 59.857 57.895 6.01 0.00 0.00 5.68
1749 2459 2.599216 CCTTAAGGTGTCCGGGCTA 58.401 57.895 13.83 0.00 0.00 3.93
1833 2543 0.411452 ATGGGTATGTGGCCACCAAA 59.589 50.000 32.62 15.49 36.48 3.28
1908 2618 4.038042 CAGGATAAGAAGTATCGTCAGGCA 59.962 45.833 0.00 0.00 39.78 4.75
1935 2645 1.134491 GCCGCTGGTTCAGGTATTACT 60.134 52.381 0.00 0.00 31.21 2.24
1936 2646 2.101917 GCCGCTGGTTCAGGTATTACTA 59.898 50.000 0.00 0.00 31.21 1.82
1937 2647 3.244112 GCCGCTGGTTCAGGTATTACTAT 60.244 47.826 0.00 0.00 31.21 2.12
1938 2648 4.021719 GCCGCTGGTTCAGGTATTACTATA 60.022 45.833 0.00 0.00 31.21 1.31
1939 2649 5.710984 CCGCTGGTTCAGGTATTACTATAG 58.289 45.833 0.00 0.00 31.21 1.31
1940 2650 5.162075 CGCTGGTTCAGGTATTACTATAGC 58.838 45.833 0.00 0.00 35.44 2.97
1941 2651 5.278808 CGCTGGTTCAGGTATTACTATAGCA 60.279 44.000 0.00 0.00 37.23 3.49
1942 2652 5.927115 GCTGGTTCAGGTATTACTATAGCAC 59.073 44.000 0.00 0.00 37.23 4.40
1943 2653 6.239345 GCTGGTTCAGGTATTACTATAGCACT 60.239 42.308 0.00 0.00 37.23 4.40
1944 2654 7.039923 GCTGGTTCAGGTATTACTATAGCACTA 60.040 40.741 0.00 0.00 37.23 2.74
1945 2655 8.951614 TGGTTCAGGTATTACTATAGCACTAT 57.048 34.615 0.00 0.00 37.23 2.12
1946 2656 8.803235 TGGTTCAGGTATTACTATAGCACTATG 58.197 37.037 0.00 0.00 37.23 2.23
1947 2657 8.804204 GGTTCAGGTATTACTATAGCACTATGT 58.196 37.037 0.00 0.52 37.23 2.29
1948 2658 9.627395 GTTCAGGTATTACTATAGCACTATGTG 57.373 37.037 0.00 0.00 37.23 3.21
1949 2659 9.582648 TTCAGGTATTACTATAGCACTATGTGA 57.417 33.333 0.00 0.00 37.23 3.58
1950 2660 9.755122 TCAGGTATTACTATAGCACTATGTGAT 57.245 33.333 0.00 0.00 37.23 3.06
2008 2723 7.552458 TTGATTGTATATGTGTTGCTAGTGG 57.448 36.000 0.00 0.00 0.00 4.00
2025 2740 8.657074 TGCTAGTGGTCAATTTGTATACATAC 57.343 34.615 6.36 1.02 0.00 2.39
2074 2789 6.944290 TCCATTTTCATATGCTTAGGGATCAG 59.056 38.462 0.00 0.00 0.00 2.90
2075 2790 6.349944 CCATTTTCATATGCTTAGGGATCAGC 60.350 42.308 0.00 0.00 36.49 4.26
2086 2801 0.455005 GGGATCAGCTGCTTCTTTGC 59.545 55.000 9.47 0.00 0.00 3.68
2087 2802 1.461559 GGATCAGCTGCTTCTTTGCT 58.538 50.000 9.47 0.00 37.56 3.91
2088 2803 1.401199 GGATCAGCTGCTTCTTTGCTC 59.599 52.381 9.47 0.00 34.51 4.26
2089 2804 1.062294 GATCAGCTGCTTCTTTGCTCG 59.938 52.381 9.47 0.00 34.51 5.03
2090 2805 0.250038 TCAGCTGCTTCTTTGCTCGT 60.250 50.000 9.47 0.00 34.51 4.18
2091 2806 0.110328 CAGCTGCTTCTTTGCTCGTG 60.110 55.000 0.00 0.00 34.51 4.35
2092 2807 0.533755 AGCTGCTTCTTTGCTCGTGT 60.534 50.000 0.00 0.00 30.41 4.49
2093 2808 1.148310 GCTGCTTCTTTGCTCGTGTA 58.852 50.000 0.00 0.00 0.00 2.90
2094 2809 1.734465 GCTGCTTCTTTGCTCGTGTAT 59.266 47.619 0.00 0.00 0.00 2.29
2095 2810 2.930040 GCTGCTTCTTTGCTCGTGTATA 59.070 45.455 0.00 0.00 0.00 1.47
2096 2811 3.557595 GCTGCTTCTTTGCTCGTGTATAT 59.442 43.478 0.00 0.00 0.00 0.86
2097 2812 4.745125 GCTGCTTCTTTGCTCGTGTATATA 59.255 41.667 0.00 0.00 0.00 0.86
2098 2813 5.107683 GCTGCTTCTTTGCTCGTGTATATAG 60.108 44.000 0.00 0.00 0.00 1.31
2099 2814 5.902681 TGCTTCTTTGCTCGTGTATATAGT 58.097 37.500 0.00 0.00 0.00 2.12
2100 2815 7.034685 TGCTTCTTTGCTCGTGTATATAGTA 57.965 36.000 0.00 0.00 0.00 1.82
2101 2816 7.485810 TGCTTCTTTGCTCGTGTATATAGTAA 58.514 34.615 0.00 0.00 0.00 2.24
2102 2817 8.141909 TGCTTCTTTGCTCGTGTATATAGTAAT 58.858 33.333 0.00 0.00 0.00 1.89
2103 2818 8.979574 GCTTCTTTGCTCGTGTATATAGTAATT 58.020 33.333 0.00 0.00 0.00 1.40
2169 2886 4.035208 TGAGCTTTGGAAAGAAACGAGTTC 59.965 41.667 3.23 0.00 38.28 3.01
2247 2965 0.755327 GGACTGTTGGTGCCCAAACT 60.755 55.000 8.06 0.00 45.73 2.66
2255 2973 1.109323 GGTGCCCAAACTTGCTGACT 61.109 55.000 0.00 0.00 0.00 3.41
2292 3010 4.993028 ACTGTTTCCAAGCAAGGGTAATA 58.007 39.130 0.00 0.00 0.00 0.98
2422 3142 6.055231 TGTACCAGAACGAATGAAAACTTG 57.945 37.500 0.00 0.00 0.00 3.16
2615 3336 1.925455 AGCACATACCCCTGCAGGT 60.925 57.895 30.63 17.19 44.37 4.00
2744 3465 1.542492 CTCAAAGCATGCCCTGTTCT 58.458 50.000 15.66 0.00 0.00 3.01
2802 3523 2.171448 AGTGTCCAATCATAGCTGACCC 59.829 50.000 0.00 0.00 33.22 4.46
3026 3749 5.121105 TGCAGAATGTTATGGTCATCTCAG 58.879 41.667 0.00 0.00 39.31 3.35
3183 3906 9.236498 TGTATGCCCTGAATAATACCCATATAT 57.764 33.333 0.00 0.00 0.00 0.86
3223 3946 6.830873 AAATATCATAGATGCTCCTTTGCC 57.169 37.500 0.00 0.00 0.00 4.52
3228 3951 1.542492 AGATGCTCCTTTGCCAAGTG 58.458 50.000 0.00 0.00 0.00 3.16
3288 4011 5.189928 TGTCACTGGAAACACATGTTACTT 58.810 37.500 0.00 0.00 37.25 2.24
3337 4060 2.192861 TGGGCAGAAAACCAGCACG 61.193 57.895 0.00 0.00 32.77 5.34
3738 4468 1.591703 GACGACCATCAGCTCACCA 59.408 57.895 0.00 0.00 0.00 4.17
3840 4581 4.020662 GTCATTAGGAGGCCCTAGATCAAG 60.021 50.000 0.00 0.00 45.26 3.02
3977 4719 6.946340 TCCACCAGGTATGTATGCTATTATG 58.054 40.000 0.00 0.00 35.89 1.90
4024 4766 4.154195 GCGTATTCTGAAAACATGTCTGGT 59.846 41.667 0.00 0.00 0.00 4.00
4025 4767 5.334879 GCGTATTCTGAAAACATGTCTGGTT 60.335 40.000 0.00 0.00 32.19 3.67
4026 4768 6.668323 CGTATTCTGAAAACATGTCTGGTTT 58.332 36.000 0.00 0.00 44.95 3.27
4065 4807 8.474025 ACATTTCAAAAACATGTCTGGTCTTTA 58.526 29.630 0.00 0.00 0.00 1.85
4066 4808 9.480053 CATTTCAAAAACATGTCTGGTCTTTAT 57.520 29.630 0.00 0.00 0.00 1.40
4181 4926 7.927048 ACTAAATAAAGCCTAAGCCATAAACG 58.073 34.615 0.00 0.00 41.25 3.60
4223 4968 7.713507 CCCTCCGTTCACAAATATAAGATGTTA 59.286 37.037 0.00 0.00 0.00 2.41
4267 5703 9.692749 CGGATGTATATAGACATGTTTTAGTGT 57.307 33.333 17.40 0.00 40.18 3.55
4285 5721 9.658475 TTTTAGTGTATTTGTTCACTCATTTCG 57.342 29.630 1.08 0.00 42.77 3.46
4288 5724 6.073222 AGTGTATTTGTTCACTCATTTCGGTC 60.073 38.462 0.00 0.00 40.28 4.79
4289 5725 5.995282 TGTATTTGTTCACTCATTTCGGTCT 59.005 36.000 0.00 0.00 0.00 3.85
4294 5730 6.275494 TGTTCACTCATTTCGGTCTGTATA 57.725 37.500 0.00 0.00 0.00 1.47
4300 5736 7.040617 TCACTCATTTCGGTCTGTATATAGTCC 60.041 40.741 3.21 3.21 0.00 3.85
4406 5842 0.250553 TCGGCTCATCCAAAAACGGT 60.251 50.000 0.00 0.00 34.01 4.83
4415 5851 1.407258 TCCAAAAACGGTGCCTTCAAG 59.593 47.619 0.00 0.00 0.00 3.02
4416 5852 1.136110 CCAAAAACGGTGCCTTCAAGT 59.864 47.619 0.00 0.00 0.00 3.16
4417 5853 2.359531 CCAAAAACGGTGCCTTCAAGTA 59.640 45.455 0.00 0.00 0.00 2.24
4418 5854 3.368495 CAAAAACGGTGCCTTCAAGTAC 58.632 45.455 0.00 0.00 0.00 2.73
4419 5855 2.335316 AAACGGTGCCTTCAAGTACA 57.665 45.000 0.00 0.00 0.00 2.90
4420 5856 2.561478 AACGGTGCCTTCAAGTACAT 57.439 45.000 0.00 0.00 0.00 2.29
4421 5857 2.094762 ACGGTGCCTTCAAGTACATC 57.905 50.000 0.00 0.00 0.00 3.06
4456 5892 3.641436 GGAAAACAAGTTCAAGGGTGGAT 59.359 43.478 0.00 0.00 0.00 3.41
4457 5893 4.100963 GGAAAACAAGTTCAAGGGTGGATT 59.899 41.667 0.00 0.00 0.00 3.01
4458 5894 4.670896 AAACAAGTTCAAGGGTGGATTG 57.329 40.909 0.00 0.00 0.00 2.67
4459 5895 3.593442 ACAAGTTCAAGGGTGGATTGA 57.407 42.857 0.00 0.00 34.93 2.57
4460 5896 3.490348 ACAAGTTCAAGGGTGGATTGAG 58.510 45.455 0.00 0.00 37.91 3.02
4461 5897 3.138283 ACAAGTTCAAGGGTGGATTGAGA 59.862 43.478 0.00 0.00 37.91 3.27
4462 5898 4.144297 CAAGTTCAAGGGTGGATTGAGAA 58.856 43.478 0.00 0.00 37.91 2.87
4463 5899 4.453480 AGTTCAAGGGTGGATTGAGAAA 57.547 40.909 0.00 0.00 37.91 2.52
4464 5900 4.803452 AGTTCAAGGGTGGATTGAGAAAA 58.197 39.130 0.00 0.00 37.91 2.29
4465 5901 4.584743 AGTTCAAGGGTGGATTGAGAAAAC 59.415 41.667 0.00 0.00 37.91 2.43
4466 5902 3.496331 TCAAGGGTGGATTGAGAAAACC 58.504 45.455 0.00 0.00 32.96 3.27
4467 5903 3.117322 TCAAGGGTGGATTGAGAAAACCA 60.117 43.478 0.00 0.00 32.96 3.67
4468 5904 3.833559 AGGGTGGATTGAGAAAACCAT 57.166 42.857 0.00 0.00 34.87 3.55
4469 5905 3.434309 AGGGTGGATTGAGAAAACCATG 58.566 45.455 0.00 0.00 34.87 3.66
4470 5906 3.165071 GGGTGGATTGAGAAAACCATGT 58.835 45.455 0.00 0.00 34.87 3.21
4471 5907 3.193479 GGGTGGATTGAGAAAACCATGTC 59.807 47.826 0.00 0.00 34.87 3.06
4472 5908 4.082125 GGTGGATTGAGAAAACCATGTCT 58.918 43.478 0.00 0.00 34.87 3.41
4473 5909 4.082571 GGTGGATTGAGAAAACCATGTCTG 60.083 45.833 0.00 0.00 34.87 3.51
4474 5910 4.520492 GTGGATTGAGAAAACCATGTCTGT 59.480 41.667 0.00 0.00 34.87 3.41
4475 5911 5.010012 GTGGATTGAGAAAACCATGTCTGTT 59.990 40.000 0.00 0.00 34.87 3.16
4476 5912 5.598005 TGGATTGAGAAAACCATGTCTGTTT 59.402 36.000 0.00 0.00 37.52 2.83
4477 5913 6.152379 GGATTGAGAAAACCATGTCTGTTTC 58.848 40.000 0.00 0.78 34.97 2.78
4478 5914 6.239008 GGATTGAGAAAACCATGTCTGTTTCA 60.239 38.462 0.00 0.00 34.97 2.69
4479 5915 5.756195 TGAGAAAACCATGTCTGTTTCAG 57.244 39.130 0.00 0.00 34.97 3.02
4480 5916 4.580167 TGAGAAAACCATGTCTGTTTCAGG 59.420 41.667 0.00 0.00 34.97 3.86
4481 5917 4.536765 AGAAAACCATGTCTGTTTCAGGT 58.463 39.130 0.00 0.00 34.97 4.00
4482 5918 4.339247 AGAAAACCATGTCTGTTTCAGGTG 59.661 41.667 0.00 0.00 34.97 4.00
4483 5919 3.576078 AACCATGTCTGTTTCAGGTGA 57.424 42.857 0.00 0.00 31.51 4.02
4484 5920 3.576078 ACCATGTCTGTTTCAGGTGAA 57.424 42.857 0.00 0.00 31.51 3.18
4485 5921 3.897239 ACCATGTCTGTTTCAGGTGAAA 58.103 40.909 0.87 0.87 41.29 2.69
4505 5941 7.280769 GTGAAACCGTTTTTAATCAAATCAGC 58.719 34.615 0.00 0.00 0.00 4.26
4506 5942 6.422400 TGAAACCGTTTTTAATCAAATCAGCC 59.578 34.615 0.00 0.00 0.00 4.85
4507 5943 4.481463 ACCGTTTTTAATCAAATCAGCCG 58.519 39.130 0.00 0.00 0.00 5.52
4508 5944 3.303229 CCGTTTTTAATCAAATCAGCCGC 59.697 43.478 0.00 0.00 0.00 6.53
4509 5945 3.917380 CGTTTTTAATCAAATCAGCCGCA 59.083 39.130 0.00 0.00 0.00 5.69
4510 5946 4.201485 CGTTTTTAATCAAATCAGCCGCAC 60.201 41.667 0.00 0.00 0.00 5.34
4511 5947 3.502191 TTTAATCAAATCAGCCGCACC 57.498 42.857 0.00 0.00 0.00 5.01
4512 5948 2.418368 TAATCAAATCAGCCGCACCT 57.582 45.000 0.00 0.00 0.00 4.00
4513 5949 0.813184 AATCAAATCAGCCGCACCTG 59.187 50.000 0.00 0.00 0.00 4.00
4514 5950 1.660560 ATCAAATCAGCCGCACCTGC 61.661 55.000 0.00 0.00 32.87 4.85
4515 5951 3.064324 AAATCAGCCGCACCTGCC 61.064 61.111 0.00 0.00 37.91 4.85
4516 5952 3.866379 AAATCAGCCGCACCTGCCA 62.866 57.895 0.00 0.00 37.91 4.92
4517 5953 3.866379 AATCAGCCGCACCTGCCAA 62.866 57.895 0.00 0.00 37.91 4.52
4518 5954 3.650298 ATCAGCCGCACCTGCCAAT 62.650 57.895 0.00 0.00 37.91 3.16
4519 5955 2.269520 ATCAGCCGCACCTGCCAATA 62.270 55.000 0.00 0.00 37.91 1.90
4520 5956 2.438434 AGCCGCACCTGCCAATAC 60.438 61.111 0.00 0.00 37.91 1.89
4521 5957 3.518068 GCCGCACCTGCCAATACC 61.518 66.667 0.00 0.00 37.91 2.73
4522 5958 2.272146 CCGCACCTGCCAATACCT 59.728 61.111 0.00 0.00 37.91 3.08
4523 5959 1.378514 CCGCACCTGCCAATACCTT 60.379 57.895 0.00 0.00 37.91 3.50
4524 5960 0.965363 CCGCACCTGCCAATACCTTT 60.965 55.000 0.00 0.00 37.91 3.11
4525 5961 0.887933 CGCACCTGCCAATACCTTTT 59.112 50.000 0.00 0.00 37.91 2.27
4526 5962 1.272212 CGCACCTGCCAATACCTTTTT 59.728 47.619 0.00 0.00 37.91 1.94
4546 5982 6.579666 TTTTTGATGATCAGGAGTTTCTGG 57.420 37.500 0.09 0.00 35.58 3.86
4547 5983 4.916041 TTGATGATCAGGAGTTTCTGGT 57.084 40.909 0.09 0.00 35.58 4.00
4548 5984 4.212143 TGATGATCAGGAGTTTCTGGTG 57.788 45.455 0.09 0.00 35.58 4.17
4549 5985 3.054875 TGATGATCAGGAGTTTCTGGTGG 60.055 47.826 0.09 0.00 35.58 4.61
4550 5986 1.630369 TGATCAGGAGTTTCTGGTGGG 59.370 52.381 0.00 0.00 35.58 4.61
4551 5987 0.995024 ATCAGGAGTTTCTGGTGGGG 59.005 55.000 0.00 0.00 35.58 4.96
4552 5988 1.133809 TCAGGAGTTTCTGGTGGGGG 61.134 60.000 0.00 0.00 35.58 5.40
4553 5989 1.133809 CAGGAGTTTCTGGTGGGGGA 61.134 60.000 0.00 0.00 0.00 4.81
4554 5990 0.842467 AGGAGTTTCTGGTGGGGGAG 60.842 60.000 0.00 0.00 0.00 4.30
4555 5991 1.002011 GAGTTTCTGGTGGGGGAGC 60.002 63.158 0.00 0.00 0.00 4.70
4556 5992 1.774217 AGTTTCTGGTGGGGGAGCA 60.774 57.895 0.00 0.00 0.00 4.26
4557 5993 1.152830 GTTTCTGGTGGGGGAGCAA 59.847 57.895 0.00 0.00 0.00 3.91
4558 5994 0.469144 GTTTCTGGTGGGGGAGCAAA 60.469 55.000 0.00 0.00 0.00 3.68
4559 5995 0.486879 TTTCTGGTGGGGGAGCAAAT 59.513 50.000 0.00 0.00 0.00 2.32
4560 5996 1.377690 TTCTGGTGGGGGAGCAAATA 58.622 50.000 0.00 0.00 0.00 1.40
4561 5997 0.918983 TCTGGTGGGGGAGCAAATAG 59.081 55.000 0.00 0.00 0.00 1.73
4562 5998 0.106519 CTGGTGGGGGAGCAAATAGG 60.107 60.000 0.00 0.00 0.00 2.57
4563 5999 1.230212 GGTGGGGGAGCAAATAGGG 59.770 63.158 0.00 0.00 0.00 3.53
4564 6000 1.580994 GGTGGGGGAGCAAATAGGGT 61.581 60.000 0.00 0.00 0.00 4.34
4565 6001 1.218844 GTGGGGGAGCAAATAGGGTA 58.781 55.000 0.00 0.00 0.00 3.69
4566 6002 1.567175 GTGGGGGAGCAAATAGGGTAA 59.433 52.381 0.00 0.00 0.00 2.85
4567 6003 2.024751 GTGGGGGAGCAAATAGGGTAAA 60.025 50.000 0.00 0.00 0.00 2.01
4568 6004 2.024751 TGGGGGAGCAAATAGGGTAAAC 60.025 50.000 0.00 0.00 0.00 2.01
4598 6034 0.392193 GTGAGTCTGGTGGGATGCTG 60.392 60.000 0.00 0.00 0.00 4.41
4599 6035 1.451028 GAGTCTGGTGGGATGCTGC 60.451 63.158 0.00 0.00 0.00 5.25
4600 6036 2.439156 GTCTGGTGGGATGCTGCC 60.439 66.667 0.00 0.00 0.00 4.85
4603 6039 4.100084 TGGTGGGATGCTGCCTCG 62.100 66.667 0.00 0.00 0.00 4.63
4604 6040 3.785859 GGTGGGATGCTGCCTCGA 61.786 66.667 0.00 0.00 0.00 4.04
4605 6041 2.507944 GTGGGATGCTGCCTCGAT 59.492 61.111 0.00 0.00 0.00 3.59
4606 6042 1.153086 GTGGGATGCTGCCTCGATT 60.153 57.895 0.00 0.00 0.00 3.34
4616 6073 2.636830 CTGCCTCGATTGGTTTCAGAT 58.363 47.619 0.00 0.00 0.00 2.90
4652 6109 8.246180 TCTTTAATCTTTCTTTGATGACATGGC 58.754 33.333 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.523154 TTTCGGCCGCTGAAGCAAAT 61.523 50.000 23.51 0.00 42.21 2.32
1 2 1.729470 TTTTCGGCCGCTGAAGCAAA 61.729 50.000 23.51 11.33 42.21 3.68
43 44 5.878669 GGCCAATCCCCTAAATATAACGTAG 59.121 44.000 0.00 0.00 0.00 3.51
44 45 5.310068 TGGCCAATCCCCTAAATATAACGTA 59.690 40.000 0.61 0.00 0.00 3.57
45 46 4.105057 TGGCCAATCCCCTAAATATAACGT 59.895 41.667 0.61 0.00 0.00 3.99
46 47 4.658063 TGGCCAATCCCCTAAATATAACG 58.342 43.478 0.61 0.00 0.00 3.18
60 62 0.679640 TTGGTCGGACATGGCCAATC 60.680 55.000 20.22 11.10 36.23 2.67
63 65 1.151679 TTTTGGTCGGACATGGCCA 59.848 52.632 20.22 8.56 0.00 5.36
67 69 3.813166 ACACTAAGTTTTGGTCGGACATG 59.187 43.478 10.76 0.00 0.00 3.21
68 70 3.813166 CACACTAAGTTTTGGTCGGACAT 59.187 43.478 10.76 0.00 0.00 3.06
69 71 3.199677 CACACTAAGTTTTGGTCGGACA 58.800 45.455 10.76 0.00 0.00 4.02
97 99 4.382793 GCCGAGAAAACCTTAGTGGAGTAT 60.383 45.833 0.00 0.00 39.71 2.12
114 116 1.824329 GACGAGGATCCAGCCGAGA 60.824 63.158 22.31 0.00 0.00 4.04
121 123 4.347000 CCCCTAAAAATAGACGAGGATCCA 59.653 45.833 15.82 0.00 0.00 3.41
130 132 7.015779 ACTCTAGCTGATCCCCTAAAAATAGAC 59.984 40.741 0.00 0.00 0.00 2.59
210 213 9.751542 AGTATATCTGAATCCGAACTTTTGTAG 57.248 33.333 0.00 0.00 0.00 2.74
291 294 2.159198 TCGGCGGTATAGAGGTTTCAAC 60.159 50.000 7.21 0.00 0.00 3.18
298 301 2.557056 TGATCTTTCGGCGGTATAGAGG 59.443 50.000 7.21 0.00 0.00 3.69
306 309 2.106683 GGTGGTGATCTTTCGGCGG 61.107 63.158 7.21 0.00 0.00 6.13
312 315 1.675641 GGCAGCGGTGGTGATCTTT 60.676 57.895 17.54 0.00 32.22 2.52
328 331 1.139163 CATCAACGGCTTGTTTTGGC 58.861 50.000 0.00 0.00 39.29 4.52
343 346 3.521560 GAGTAGAAACGATGGTGCATCA 58.478 45.455 0.00 0.00 40.54 3.07
354 357 0.248377 CCGGTAGCGGAGTAGAAACG 60.248 60.000 29.00 0.00 0.00 3.60
378 381 8.682936 AAAACTGTCATTGACAAGATTAGACT 57.317 30.769 19.44 0.00 42.26 3.24
385 388 9.959749 GGTTTAATAAAACTGTCATTGACAAGA 57.040 29.630 19.44 4.93 42.26 3.02
399 402 9.575702 GTTGAGAAAAATGCGGTTTAATAAAAC 57.424 29.630 0.00 0.00 43.58 2.43
401 404 8.145122 AGGTTGAGAAAAATGCGGTTTAATAAA 58.855 29.630 0.00 0.00 0.00 1.40
402 405 7.662897 AGGTTGAGAAAAATGCGGTTTAATAA 58.337 30.769 0.00 0.00 0.00 1.40
403 406 7.222000 AGGTTGAGAAAAATGCGGTTTAATA 57.778 32.000 0.00 0.00 0.00 0.98
404 407 6.096673 AGGTTGAGAAAAATGCGGTTTAAT 57.903 33.333 0.00 0.00 0.00 1.40
405 408 5.523438 AGGTTGAGAAAAATGCGGTTTAA 57.477 34.783 0.00 0.00 0.00 1.52
406 409 5.067936 TGAAGGTTGAGAAAAATGCGGTTTA 59.932 36.000 0.00 0.00 0.00 2.01
407 410 4.142049 TGAAGGTTGAGAAAAATGCGGTTT 60.142 37.500 0.00 0.00 0.00 3.27
447 450 2.533266 GTGTAGCCAGCAAAATCATGC 58.467 47.619 0.00 0.00 46.78 4.06
448 451 2.492881 TGGTGTAGCCAGCAAAATCATG 59.507 45.455 0.00 0.00 45.54 3.07
502 505 8.813643 AGTAAAGTTGTAGTGTGTAATCACTC 57.186 34.615 2.59 0.00 45.79 3.51
541 552 4.154195 CAGAGCGGGTAATATGGCATTTAC 59.846 45.833 4.78 13.39 0.00 2.01
555 566 3.575351 GAGCACGTTCAGAGCGGGT 62.575 63.158 10.89 5.29 41.46 5.28
559 570 1.996292 TGTATGAGCACGTTCAGAGC 58.004 50.000 0.00 0.00 36.67 4.09
578 589 7.499321 TGAACACACGTAGGAACATTTATTT 57.501 32.000 0.00 0.00 0.00 1.40
585 596 4.182693 CCTATGAACACACGTAGGAACA 57.817 45.455 0.00 0.00 46.62 3.18
618 630 8.633075 AACTGCAAATATTTACATACATGCAC 57.367 30.769 0.00 0.00 35.98 4.57
641 1321 9.712359 AGTTTGTTTTTGAGAAACGAGTATAAC 57.288 29.630 0.00 0.00 44.00 1.89
671 1351 9.005777 TCTTAAAATTTGCCGTATAGAACAACT 57.994 29.630 0.00 0.00 0.00 3.16
701 1381 6.890268 TCCATGGTTCTATATATGCGAGTAGT 59.110 38.462 12.58 0.00 0.00 2.73
732 1412 6.094048 CACTAGTACTGAAATTTCCCCATGTG 59.906 42.308 15.48 11.13 0.00 3.21
733 1413 6.180472 CACTAGTACTGAAATTTCCCCATGT 58.820 40.000 15.48 8.81 0.00 3.21
735 1415 6.012858 TCACACTAGTACTGAAATTTCCCCAT 60.013 38.462 15.48 1.37 0.00 4.00
736 1416 5.308497 TCACACTAGTACTGAAATTTCCCCA 59.692 40.000 15.48 0.00 0.00 4.96
737 1417 5.801380 TCACACTAGTACTGAAATTTCCCC 58.199 41.667 15.48 1.19 0.00 4.81
738 1418 7.606456 TGATTCACACTAGTACTGAAATTTCCC 59.394 37.037 15.48 1.53 0.00 3.97
739 1419 8.443937 GTGATTCACACTAGTACTGAAATTTCC 58.556 37.037 15.48 0.07 45.13 3.13
805 1494 3.004419 CGTGACTGGTCTGTGAAGAACTA 59.996 47.826 2.38 0.00 0.00 2.24
819 1508 1.376037 GCCCTCCTTTCGTGACTGG 60.376 63.158 0.00 0.00 0.00 4.00
831 1520 2.511600 CAATCGTGACGGCCCTCC 60.512 66.667 4.70 0.00 0.00 4.30
838 1527 1.550065 CTAGACCAGCAATCGTGACG 58.450 55.000 0.00 0.00 0.00 4.35
903 1592 3.253921 TCGTGTCGTAGGTCAATCTTTCA 59.746 43.478 0.00 0.00 0.00 2.69
904 1593 3.829948 TCGTGTCGTAGGTCAATCTTTC 58.170 45.455 0.00 0.00 0.00 2.62
906 1595 2.415625 GCTCGTGTCGTAGGTCAATCTT 60.416 50.000 0.00 0.00 0.00 2.40
907 1596 1.132643 GCTCGTGTCGTAGGTCAATCT 59.867 52.381 0.00 0.00 0.00 2.40
908 1597 1.135489 TGCTCGTGTCGTAGGTCAATC 60.135 52.381 0.00 0.00 0.00 2.67
927 1625 2.092968 TCGGAGGGGATTGAAATGACTG 60.093 50.000 0.00 0.00 0.00 3.51
944 1642 2.031465 GCGGTTCAGGGTTTCGGA 59.969 61.111 0.00 0.00 0.00 4.55
1467 2177 2.435938 GCGATGGGCTTGTTCCGA 60.436 61.111 0.00 0.00 39.11 4.55
1569 2279 2.263540 GAGGCGCGGAAGGTGTTA 59.736 61.111 8.83 0.00 0.00 2.41
1833 2543 0.324923 TGGTATGTGTAGAGCCCGGT 60.325 55.000 0.00 0.00 0.00 5.28
1908 2618 1.453155 CTGAACCAGCGGCAGTAATT 58.547 50.000 1.45 0.00 0.00 1.40
1956 2666 8.518702 TCACATAGTGCTATATGTTTGCAAAAA 58.481 29.630 14.67 9.42 42.40 1.94
1957 2667 8.049655 TCACATAGTGCTATATGTTTGCAAAA 57.950 30.769 14.67 5.00 42.40 2.44
1958 2668 7.622893 TCACATAGTGCTATATGTTTGCAAA 57.377 32.000 8.05 8.05 42.40 3.68
1959 2669 7.622893 TTCACATAGTGCTATATGTTTGCAA 57.377 32.000 10.52 0.00 42.40 4.08
1960 2670 7.806409 ATTCACATAGTGCTATATGTTTGCA 57.194 32.000 10.52 0.00 42.40 4.08
1961 2671 8.344831 TCAATTCACATAGTGCTATATGTTTGC 58.655 33.333 10.52 0.00 42.40 3.68
1965 2675 9.565090 ACAATCAATTCACATAGTGCTATATGT 57.435 29.630 8.14 8.14 45.17 2.29
1995 2710 3.951037 ACAAATTGACCACTAGCAACACA 59.049 39.130 0.00 0.00 0.00 3.72
2050 2765 6.349944 GCTGATCCCTAAGCATATGAAAATGG 60.350 42.308 6.97 0.83 39.31 3.16
2051 2766 6.433404 AGCTGATCCCTAAGCATATGAAAATG 59.567 38.462 6.97 0.00 42.06 2.32
2054 2769 5.311265 CAGCTGATCCCTAAGCATATGAAA 58.689 41.667 8.42 0.00 42.06 2.69
2074 2789 1.148310 TACACGAGCAAAGAAGCAGC 58.852 50.000 0.00 0.00 36.85 5.25
2075 2790 5.980116 ACTATATACACGAGCAAAGAAGCAG 59.020 40.000 0.00 0.00 36.85 4.24
2125 2840 6.349611 GCTCAAACACCACATTCTATTGTCAT 60.350 38.462 0.00 0.00 0.00 3.06
2183 2900 8.318167 GCGAACTAATTTTAATACAATGTTGGC 58.682 33.333 0.00 0.00 31.92 4.52
2247 2965 3.450904 AGGTGTCCCTAATAGTCAGCAA 58.549 45.455 0.00 0.00 40.19 3.91
2255 2973 5.786457 TGGAAACAGTAAGGTGTCCCTAATA 59.214 40.000 0.30 0.00 43.43 0.98
2451 3172 3.826524 TCATGCAGTTTGAACCTTGGTA 58.173 40.909 0.00 0.00 0.00 3.25
2505 3226 1.303561 GTGGCAAGAGCACCCATGA 60.304 57.895 0.00 0.00 44.61 3.07
2551 3272 2.805099 GCTAATCAGAATCAAGCCCGAG 59.195 50.000 0.00 0.00 0.00 4.63
2802 3523 3.352648 ACACCCAGTTCAATAATTCCCG 58.647 45.455 0.00 0.00 0.00 5.14
3026 3749 6.543831 ACTTGATTGATTGAGTGCTAATACCC 59.456 38.462 0.00 0.00 0.00 3.69
3073 3796 8.630037 ACAAATACTTTTGGAACAGAACCTTAG 58.370 33.333 3.76 0.00 45.34 2.18
3288 4011 3.535280 TTGGAAGTGACGCATAGCATA 57.465 42.857 0.00 0.00 0.00 3.14
3337 4060 3.931578 ACAGATGAGTTCCACAGTAAGC 58.068 45.455 0.00 0.00 0.00 3.09
3559 4289 3.308473 GGAGCCACTAAAGGTCAATTCCT 60.308 47.826 0.00 0.00 39.84 3.36
3738 4468 0.536006 AAGCTCAGAGTGCGGCTTTT 60.536 50.000 0.00 0.00 41.44 2.27
3840 4581 6.012658 TCATTTCCAGCACACTAATGAAAC 57.987 37.500 0.00 0.00 33.61 2.78
3977 4719 4.982295 GGTGCTCCAAACATGTAGAAAAAC 59.018 41.667 0.00 0.00 0.00 2.43
4083 4825 1.542915 CATGAGCCAACAAAGACCAGG 59.457 52.381 0.00 0.00 0.00 4.45
4181 4926 5.485620 ACGGAGGGAGAAGTAATTAACAAC 58.514 41.667 0.00 0.00 0.00 3.32
4194 4939 5.659525 TCTTATATTTGTGAACGGAGGGAGA 59.340 40.000 0.00 0.00 0.00 3.71
4267 5703 5.995282 ACAGACCGAAATGAGTGAACAAATA 59.005 36.000 0.00 0.00 0.00 1.40
4284 5720 8.740906 ACTTCAATATGGACTATATACAGACCG 58.259 37.037 0.00 0.00 33.65 4.79
4406 5842 6.544928 TCTATCTTGATGTACTTGAAGGCA 57.455 37.500 7.86 0.00 0.00 4.75
4456 5892 5.067674 CCTGAAACAGACATGGTTTTCTCAA 59.932 40.000 0.00 0.00 36.13 3.02
4457 5893 4.580167 CCTGAAACAGACATGGTTTTCTCA 59.420 41.667 0.00 0.00 36.13 3.27
4458 5894 4.580580 ACCTGAAACAGACATGGTTTTCTC 59.419 41.667 0.00 0.00 36.13 2.87
4459 5895 4.339247 CACCTGAAACAGACATGGTTTTCT 59.661 41.667 0.00 0.00 36.13 2.52
4460 5896 4.338118 TCACCTGAAACAGACATGGTTTTC 59.662 41.667 0.00 0.99 36.13 2.29
4461 5897 4.277476 TCACCTGAAACAGACATGGTTTT 58.723 39.130 0.00 0.00 36.13 2.43
4462 5898 3.897239 TCACCTGAAACAGACATGGTTT 58.103 40.909 0.00 0.00 36.13 3.27
4463 5899 3.576078 TCACCTGAAACAGACATGGTT 57.424 42.857 0.00 0.00 39.73 3.67
4464 5900 3.576078 TTCACCTGAAACAGACATGGT 57.424 42.857 0.00 0.00 32.44 3.55
4474 5910 6.864342 TGATTAAAAACGGTTTCACCTGAAA 58.136 32.000 6.57 0.00 41.29 2.69
4475 5911 6.452494 TGATTAAAAACGGTTTCACCTGAA 57.548 33.333 6.57 0.00 35.66 3.02
4476 5912 6.452494 TTGATTAAAAACGGTTTCACCTGA 57.548 33.333 6.57 0.00 35.66 3.86
4477 5913 7.436673 TGATTTGATTAAAAACGGTTTCACCTG 59.563 33.333 6.57 0.00 35.66 4.00
4478 5914 7.493367 TGATTTGATTAAAAACGGTTTCACCT 58.507 30.769 6.57 0.00 35.66 4.00
4479 5915 7.568679 GCTGATTTGATTAAAAACGGTTTCACC 60.569 37.037 6.57 0.00 31.31 4.02
4480 5916 7.280769 GCTGATTTGATTAAAAACGGTTTCAC 58.719 34.615 6.57 0.00 31.31 3.18
4481 5917 6.422400 GGCTGATTTGATTAAAAACGGTTTCA 59.578 34.615 6.57 0.00 31.31 2.69
4482 5918 6.399564 CGGCTGATTTGATTAAAAACGGTTTC 60.400 38.462 6.57 0.00 31.31 2.78
4483 5919 5.404066 CGGCTGATTTGATTAAAAACGGTTT 59.596 36.000 0.00 0.00 31.31 3.27
4484 5920 4.920927 CGGCTGATTTGATTAAAAACGGTT 59.079 37.500 0.00 0.00 31.31 4.44
4485 5921 4.481463 CGGCTGATTTGATTAAAAACGGT 58.519 39.130 0.00 0.00 31.31 4.83
4486 5922 3.303229 GCGGCTGATTTGATTAAAAACGG 59.697 43.478 0.00 0.00 31.71 4.44
4487 5923 3.917380 TGCGGCTGATTTGATTAAAAACG 59.083 39.130 0.00 0.00 0.00 3.60
4488 5924 4.091365 GGTGCGGCTGATTTGATTAAAAAC 59.909 41.667 0.00 0.00 0.00 2.43
4489 5925 4.021544 AGGTGCGGCTGATTTGATTAAAAA 60.022 37.500 0.00 0.00 0.00 1.94
4490 5926 3.509575 AGGTGCGGCTGATTTGATTAAAA 59.490 39.130 0.00 0.00 0.00 1.52
4491 5927 3.088532 AGGTGCGGCTGATTTGATTAAA 58.911 40.909 0.00 0.00 0.00 1.52
4492 5928 2.423185 CAGGTGCGGCTGATTTGATTAA 59.577 45.455 0.00 0.00 0.00 1.40
4493 5929 2.016318 CAGGTGCGGCTGATTTGATTA 58.984 47.619 0.00 0.00 0.00 1.75
4494 5930 0.813184 CAGGTGCGGCTGATTTGATT 59.187 50.000 0.00 0.00 0.00 2.57
4495 5931 1.660560 GCAGGTGCGGCTGATTTGAT 61.661 55.000 0.00 0.00 0.00 2.57
4496 5932 2.334946 GCAGGTGCGGCTGATTTGA 61.335 57.895 0.00 0.00 0.00 2.69
4497 5933 2.180017 GCAGGTGCGGCTGATTTG 59.820 61.111 0.00 0.00 0.00 2.32
4498 5934 3.064324 GGCAGGTGCGGCTGATTT 61.064 61.111 0.00 0.00 43.26 2.17
4499 5935 3.744330 TATTGGCAGGTGCGGCTGATT 62.744 52.381 0.00 0.00 43.26 2.57
4500 5936 2.269520 TATTGGCAGGTGCGGCTGAT 62.270 55.000 0.00 0.00 43.26 2.90
4501 5937 2.965520 TATTGGCAGGTGCGGCTGA 61.966 57.895 0.00 0.00 43.26 4.26
4502 5938 2.438254 TATTGGCAGGTGCGGCTG 60.438 61.111 0.00 0.00 43.26 4.85
4503 5939 2.438434 GTATTGGCAGGTGCGGCT 60.438 61.111 0.00 0.00 43.26 5.52
4504 5940 3.518068 GGTATTGGCAGGTGCGGC 61.518 66.667 0.00 0.00 43.26 6.53
4505 5941 0.965363 AAAGGTATTGGCAGGTGCGG 60.965 55.000 0.00 0.00 43.26 5.69
4506 5942 0.887933 AAAAGGTATTGGCAGGTGCG 59.112 50.000 0.00 0.00 43.26 5.34
4523 5959 6.016024 CACCAGAAACTCCTGATCATCAAAAA 60.016 38.462 0.00 0.00 36.29 1.94
4524 5960 5.474532 CACCAGAAACTCCTGATCATCAAAA 59.525 40.000 0.00 0.00 36.29 2.44
4525 5961 5.005740 CACCAGAAACTCCTGATCATCAAA 58.994 41.667 0.00 0.00 36.29 2.69
4526 5962 4.566278 CCACCAGAAACTCCTGATCATCAA 60.566 45.833 0.00 0.00 36.29 2.57
4527 5963 3.054875 CCACCAGAAACTCCTGATCATCA 60.055 47.826 0.00 0.00 36.29 3.07
4528 5964 3.539604 CCACCAGAAACTCCTGATCATC 58.460 50.000 0.00 0.00 36.29 2.92
4529 5965 2.240667 CCCACCAGAAACTCCTGATCAT 59.759 50.000 0.00 0.00 36.29 2.45
4530 5966 1.630369 CCCACCAGAAACTCCTGATCA 59.370 52.381 0.00 0.00 36.29 2.92
4531 5967 1.065126 CCCCACCAGAAACTCCTGATC 60.065 57.143 0.00 0.00 36.29 2.92
4532 5968 0.995024 CCCCACCAGAAACTCCTGAT 59.005 55.000 0.00 0.00 36.29 2.90
4533 5969 1.133809 CCCCCACCAGAAACTCCTGA 61.134 60.000 0.00 0.00 36.29 3.86
4534 5970 1.133809 TCCCCCACCAGAAACTCCTG 61.134 60.000 0.00 0.00 0.00 3.86
4535 5971 0.842467 CTCCCCCACCAGAAACTCCT 60.842 60.000 0.00 0.00 0.00 3.69
4536 5972 1.685820 CTCCCCCACCAGAAACTCC 59.314 63.158 0.00 0.00 0.00 3.85
4537 5973 1.002011 GCTCCCCCACCAGAAACTC 60.002 63.158 0.00 0.00 0.00 3.01
4538 5974 1.360393 TTGCTCCCCCACCAGAAACT 61.360 55.000 0.00 0.00 0.00 2.66
4539 5975 0.469144 TTTGCTCCCCCACCAGAAAC 60.469 55.000 0.00 0.00 0.00 2.78
4540 5976 0.486879 ATTTGCTCCCCCACCAGAAA 59.513 50.000 0.00 0.00 0.00 2.52
4541 5977 1.284785 CTATTTGCTCCCCCACCAGAA 59.715 52.381 0.00 0.00 0.00 3.02
4542 5978 0.918983 CTATTTGCTCCCCCACCAGA 59.081 55.000 0.00 0.00 0.00 3.86
4543 5979 0.106519 CCTATTTGCTCCCCCACCAG 60.107 60.000 0.00 0.00 0.00 4.00
4544 5980 1.580066 CCCTATTTGCTCCCCCACCA 61.580 60.000 0.00 0.00 0.00 4.17
4545 5981 1.230212 CCCTATTTGCTCCCCCACC 59.770 63.158 0.00 0.00 0.00 4.61
4546 5982 1.218844 TACCCTATTTGCTCCCCCAC 58.781 55.000 0.00 0.00 0.00 4.61
4547 5983 1.988539 TTACCCTATTTGCTCCCCCA 58.011 50.000 0.00 0.00 0.00 4.96
4548 5984 2.662866 GTTTACCCTATTTGCTCCCCC 58.337 52.381 0.00 0.00 0.00 5.40
4549 5985 2.092807 TCGTTTACCCTATTTGCTCCCC 60.093 50.000 0.00 0.00 0.00 4.81
4550 5986 3.271055 TCGTTTACCCTATTTGCTCCC 57.729 47.619 0.00 0.00 0.00 4.30
4551 5987 5.396484 GTTTTCGTTTACCCTATTTGCTCC 58.604 41.667 0.00 0.00 0.00 4.70
4552 5988 5.182570 AGGTTTTCGTTTACCCTATTTGCTC 59.817 40.000 0.00 0.00 34.90 4.26
4553 5989 5.048294 CAGGTTTTCGTTTACCCTATTTGCT 60.048 40.000 0.00 0.00 34.90 3.91
4554 5990 5.158494 CAGGTTTTCGTTTACCCTATTTGC 58.842 41.667 0.00 0.00 34.90 3.68
4555 5991 6.146898 CACAGGTTTTCGTTTACCCTATTTG 58.853 40.000 0.00 0.00 34.90 2.32
4556 5992 5.829391 ACACAGGTTTTCGTTTACCCTATTT 59.171 36.000 0.00 0.00 34.90 1.40
4557 5993 5.239963 CACACAGGTTTTCGTTTACCCTATT 59.760 40.000 0.00 0.00 34.90 1.73
4558 5994 4.758165 CACACAGGTTTTCGTTTACCCTAT 59.242 41.667 0.00 0.00 34.90 2.57
4559 5995 4.128643 CACACAGGTTTTCGTTTACCCTA 58.871 43.478 0.00 0.00 34.90 3.53
4560 5996 2.946990 CACACAGGTTTTCGTTTACCCT 59.053 45.455 0.00 0.00 34.90 4.34
4561 5997 2.944349 TCACACAGGTTTTCGTTTACCC 59.056 45.455 0.00 0.00 34.90 3.69
4562 5998 3.624410 ACTCACACAGGTTTTCGTTTACC 59.376 43.478 0.00 0.00 34.54 2.85
4563 5999 4.569564 AGACTCACACAGGTTTTCGTTTAC 59.430 41.667 0.00 0.00 0.00 2.01
4564 6000 4.569162 CAGACTCACACAGGTTTTCGTTTA 59.431 41.667 0.00 0.00 0.00 2.01
4565 6001 3.374058 CAGACTCACACAGGTTTTCGTTT 59.626 43.478 0.00 0.00 0.00 3.60
4566 6002 2.936498 CAGACTCACACAGGTTTTCGTT 59.064 45.455 0.00 0.00 0.00 3.85
4567 6003 2.550978 CAGACTCACACAGGTTTTCGT 58.449 47.619 0.00 0.00 0.00 3.85
4568 6004 1.867233 CCAGACTCACACAGGTTTTCG 59.133 52.381 0.00 0.00 0.00 3.46
4598 6034 5.757850 AAATATCTGAAACCAATCGAGGC 57.242 39.130 0.00 0.00 0.00 4.70
4599 6035 7.320443 TCAAAATATCTGAAACCAATCGAGG 57.680 36.000 0.00 0.00 0.00 4.63
4600 6036 6.909357 GCTCAAAATATCTGAAACCAATCGAG 59.091 38.462 0.00 0.00 0.00 4.04
4603 6039 7.994194 AGAGCTCAAAATATCTGAAACCAATC 58.006 34.615 17.77 0.00 0.00 2.67
4604 6040 7.951347 AGAGCTCAAAATATCTGAAACCAAT 57.049 32.000 17.77 0.00 0.00 3.16
4605 6041 7.765695 AAGAGCTCAAAATATCTGAAACCAA 57.234 32.000 17.77 0.00 0.00 3.67
4606 6042 7.765695 AAAGAGCTCAAAATATCTGAAACCA 57.234 32.000 17.77 0.00 0.00 3.67
4652 6109 4.032445 CGATTGCAAAATTCTCCATGCTTG 59.968 41.667 1.71 0.00 39.49 4.01


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

AutoCloner maintained by Alex Coulton.