Multiple sequence alignment - TraesCS7A01G141000

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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 TraesCS7A01G141000 chr7A 100.000 3341 0 0 1 3341 92800847 92797507 0.000000e+00 6170.0
1 TraesCS7A01G141000 chr7A 84.044 727 82 20 7 703 92394867 92394145 0.000000e+00 669.0
2 TraesCS7A01G141000 chr7A 83.357 709 76 19 7 687 91924458 91925152 4.740000e-173 617.0
3 TraesCS7A01G141000 chr7A 78.204 991 189 22 938 1921 91946463 91947433 2.850000e-170 608.0
4 TraesCS7A01G141000 chr7A 82.125 593 61 26 1453 2032 92393750 92393190 1.820000e-127 466.0
5 TraesCS7A01G141000 chr7A 84.326 319 46 4 1056 1371 92394096 92393779 3.240000e-80 309.0
6 TraesCS7A01G141000 chr7A 78.681 455 82 12 1919 2365 91947596 91948043 4.220000e-74 289.0
7 TraesCS7A01G141000 chr7A 81.159 345 52 8 165 498 91919544 91919886 7.110000e-67 265.0
8 TraesCS7A01G141000 chr7A 82.609 138 10 13 7 134 91919315 91919448 3.520000e-20 110.0
9 TraesCS7A01G141000 chr7A 90.123 81 3 4 2577 2654 78670891 78670969 2.120000e-17 100.0
10 TraesCS7A01G141000 chr7D 92.733 1789 118 9 746 2527 90626014 90624231 0.000000e+00 2573.0
11 TraesCS7A01G141000 chr7D 92.722 742 31 15 1 729 90629163 90628432 0.000000e+00 1050.0
12 TraesCS7A01G141000 chr7D 84.254 724 82 19 7 703 90620705 90619987 0.000000e+00 676.0
13 TraesCS7A01G141000 chr7D 83.045 578 53 21 1458 2032 90619587 90619052 1.800000e-132 483.0
14 TraesCS7A01G141000 chr7D 81.884 414 53 16 2653 3054 90623906 90623503 2.480000e-86 329.0
15 TraesCS7A01G141000 chr7D 81.686 344 50 8 166 498 90586379 90586720 1.180000e-69 274.0
16 TraesCS7A01G141000 chr7D 93.333 75 4 1 7 80 90596416 90596490 3.520000e-20 110.0
17 TraesCS7A01G141000 chr7D 80.255 157 18 5 176 332 90596669 90596812 4.560000e-19 106.0
18 TraesCS7A01G141000 chr7D 82.171 129 11 11 7 125 90586148 90586274 2.120000e-17 100.0
19 TraesCS7A01G141000 chr7B 94.217 1591 75 10 2 1581 41543089 41541505 0.000000e+00 2412.0
20 TraesCS7A01G141000 chr7B 89.432 1003 101 4 1578 2577 41541224 41540224 0.000000e+00 1260.0
21 TraesCS7A01G141000 chr7B 79.503 1449 261 29 938 2369 41523398 41521969 0.000000e+00 998.0
22 TraesCS7A01G141000 chr7B 80.747 1018 129 37 7 997 41532854 41531877 0.000000e+00 732.0
23 TraesCS7A01G141000 chr7B 87.640 89 7 3 2569 2654 1759391 1759304 2.120000e-17 100.0
24 TraesCS7A01G141000 chr2D 94.444 72 4 0 2583 2654 564921762 564921691 9.800000e-21 111.0
25 TraesCS7A01G141000 chr4A 89.655 87 8 1 2568 2654 663651228 663651313 3.520000e-20 110.0
26 TraesCS7A01G141000 chr3A 88.372 86 9 1 2565 2650 231001830 231001914 5.900000e-18 102.0
27 TraesCS7A01G141000 chr3B 89.873 79 7 1 2577 2654 99020238 99020316 2.120000e-17 100.0
28 TraesCS7A01G141000 chr3B 89.873 79 7 1 2577 2654 809833121 809833043 2.120000e-17 100.0
29 TraesCS7A01G141000 chr4D 88.608 79 8 1 2577 2654 11573372 11573294 9.870000e-16 95.3
30 TraesCS7A01G141000 chr2B 85.393 89 12 1 2577 2664 787980605 787980693 1.280000e-14 91.6


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 TraesCS7A01G141000 chr7A 92797507 92800847 3340 True 6170.000000 6170 100.000000 1 3341 1 chr7A.!!$R1 3340
1 TraesCS7A01G141000 chr7A 91924458 91925152 694 False 617.000000 617 83.357000 7 687 1 chr7A.!!$F2 680
2 TraesCS7A01G141000 chr7A 92393190 92394867 1677 True 481.333333 669 83.498333 7 2032 3 chr7A.!!$R2 2025
3 TraesCS7A01G141000 chr7A 91946463 91948043 1580 False 448.500000 608 78.442500 938 2365 2 chr7A.!!$F4 1427
4 TraesCS7A01G141000 chr7D 90619052 90629163 10111 True 1022.200000 2573 86.927600 1 3054 5 chr7D.!!$R1 3053
5 TraesCS7A01G141000 chr7B 41540224 41543089 2865 True 1836.000000 2412 91.824500 2 2577 2 chr7B.!!$R4 2575
6 TraesCS7A01G141000 chr7B 41521969 41523398 1429 True 998.000000 998 79.503000 938 2369 1 chr7B.!!$R2 1431
7 TraesCS7A01G141000 chr7B 41531877 41532854 977 True 732.000000 732 80.747000 7 997 1 chr7B.!!$R3 990

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
84 85 2.093306 TAGAAACCTGGTCACGCATG 57.907 50.000 0.00 0.0 0.00 4.06 F
1127 3577 1.302949 GCCCAGACATGGCCTGTTA 59.697 57.895 3.32 0.0 46.19 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 3675 0.476611 AGGAAGAGGCCCCAGTTCTT 60.477 55.0 0.0 0.34 34.06 2.52 R
2644 5861 0.032017 ATAGGAAGTGCTCCCTCCGT 60.032 55.0 0.0 0.00 46.81 4.69 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
84 85 2.093306 TAGAAACCTGGTCACGCATG 57.907 50.000 0.00 0.00 0.00 4.06
136 156 4.679654 CCGAAAATGCAAAGACCAAAGTAC 59.320 41.667 0.00 0.00 0.00 2.73
143 163 6.761099 TGCAAAGACCAAAGTACAACTTAA 57.239 33.333 0.00 0.00 37.47 1.85
729 773 4.188247 ACTCTGTATTTTGCTACGCAGA 57.812 40.909 0.00 0.00 40.61 4.26
733 777 2.410392 TGTATTTTGCTACGCAGACACG 59.590 45.455 0.00 0.00 40.61 4.49
822 3266 5.351465 ACATCCTAAACTAATCACTTGTGCG 59.649 40.000 0.00 0.00 0.00 5.34
835 3279 3.123284 CACTTGTGCGCATAAAAATTGGG 59.877 43.478 20.34 9.43 0.00 4.12
840 3284 4.102649 GTGCGCATAAAAATTGGGTCTAC 58.897 43.478 15.91 0.00 0.00 2.59
932 3376 3.455619 ACAAACTATTCGCTTTCGCAG 57.544 42.857 0.00 0.00 35.30 5.18
1127 3577 1.302949 GCCCAGACATGGCCTGTTA 59.697 57.895 3.32 0.00 46.19 2.41
1155 3605 1.406069 CCCGATCCGATCCCAATCATC 60.406 57.143 2.69 0.00 31.76 2.92
1165 3615 2.323599 TCCCAATCATCGATCTCAGCT 58.676 47.619 0.00 0.00 0.00 4.24
1215 3668 3.785486 TGAGGTTGATAAGATGCAGTCG 58.215 45.455 0.00 0.00 0.00 4.18
1222 3675 0.901827 TAAGATGCAGTCGGCCTTGA 59.098 50.000 0.00 0.00 43.89 3.02
1265 3718 0.034670 AGCTTGCCCTGATGAACTCC 60.035 55.000 0.00 0.00 0.00 3.85
1393 3848 5.468746 CGAGAGAATTTTACAAACTCCCACA 59.531 40.000 0.00 0.00 0.00 4.17
1394 3849 6.017440 CGAGAGAATTTTACAAACTCCCACAA 60.017 38.462 0.00 0.00 0.00 3.33
1780 4520 6.043411 GCTCGATTTACATGAGGACTACTTT 58.957 40.000 0.00 0.00 0.00 2.66
1805 4555 3.303593 CGAAATGATTGAAGAGGATGCCG 60.304 47.826 0.00 0.00 0.00 5.69
1816 4566 0.601046 AGGATGCCGTCACATATGCG 60.601 55.000 1.58 0.00 0.00 4.73
1836 4586 3.243468 GCGAGATTCAACTACTACCCTCC 60.243 52.174 0.00 0.00 0.00 4.30
1894 4652 0.901827 ACACTGATGCCACGGTGATA 59.098 50.000 20.70 0.00 46.40 2.15
1909 4667 5.179368 CACGGTGATAACAGTTGTCTTCATT 59.821 40.000 11.01 0.00 0.00 2.57
1912 4670 6.603095 GGTGATAACAGTTGTCTTCATTGAC 58.397 40.000 11.01 0.00 37.47 3.18
1937 4860 2.930019 TCAGTGGGCTCCAGGTGG 60.930 66.667 0.00 0.00 32.34 4.61
1951 4874 1.613437 CAGGTGGAGAAAAATGGCGTT 59.387 47.619 0.00 0.00 0.00 4.84
2064 4987 0.807496 GATCTTGCCCTGTGAACAGC 59.193 55.000 4.87 0.00 42.47 4.40
2155 5088 3.044059 GCCGTGACCAATGCAGAGC 62.044 63.158 0.00 0.00 0.00 4.09
2166 5099 0.179062 ATGCAGAGCAAGATCGGGTC 60.179 55.000 10.46 10.46 43.62 4.46
2169 5102 0.248825 CAGAGCAAGATCGGGTCTCG 60.249 60.000 16.09 10.15 40.86 4.04
2184 5117 4.179298 GGGTCTCGTTGGTTATGTTCTAC 58.821 47.826 0.00 0.00 0.00 2.59
2188 5121 3.577667 TCGTTGGTTATGTTCTACACGG 58.422 45.455 0.00 0.00 0.00 4.94
2205 5138 3.760035 GCGGACCCAGAGAGCGAA 61.760 66.667 0.00 0.00 0.00 4.70
2206 5139 2.182030 CGGACCCAGAGAGCGAAC 59.818 66.667 0.00 0.00 0.00 3.95
2220 5153 2.671177 CGAACTTGAGCCAGTGCCG 61.671 63.158 0.00 0.00 38.69 5.69
2233 5166 2.364973 TGCCGGAGCTGGTGGATA 60.365 61.111 5.05 0.00 40.80 2.59
2241 5174 2.103941 GGAGCTGGTGGATAAGAAGAGG 59.896 54.545 0.00 0.00 0.00 3.69
2245 5178 1.839994 TGGTGGATAAGAAGAGGCCAG 59.160 52.381 5.01 0.00 0.00 4.85
2246 5179 1.475930 GGTGGATAAGAAGAGGCCAGC 60.476 57.143 5.01 0.00 39.54 4.85
2372 5305 4.797471 TGAAGTGCAAAAGATTGATTCGG 58.203 39.130 0.00 0.00 38.94 4.30
2383 5316 3.198635 AGATTGATTCGGAGTGTGGTGAT 59.801 43.478 0.00 0.00 0.00 3.06
2384 5317 3.417069 TTGATTCGGAGTGTGGTGATT 57.583 42.857 0.00 0.00 0.00 2.57
2484 5421 5.984926 CACTTTTGTGTGATTGTATGCCTTT 59.015 36.000 0.00 0.00 44.94 3.11
2501 5438 2.094545 CCTTTTGCAGGCCACTTCATAC 60.095 50.000 5.01 0.00 35.13 2.39
2518 5455 9.057089 CACTTCATACCTCTTTTAGTTCAAGTT 57.943 33.333 0.00 0.00 0.00 2.66
2530 5747 8.770010 TTTTAGTTCAAGTTTTATCCCCTTGA 57.230 30.769 0.00 0.00 41.95 3.02
2568 5785 4.973168 ACTGTATCAGGTTTCTGCTTCAA 58.027 39.130 1.90 0.00 40.69 2.69
2577 5794 4.944317 AGGTTTCTGCTTCAAATAGCTACC 59.056 41.667 0.00 0.00 41.76 3.18
2578 5795 4.096532 GGTTTCTGCTTCAAATAGCTACCC 59.903 45.833 0.00 0.00 41.76 3.69
2579 5796 3.560636 TCTGCTTCAAATAGCTACCCC 57.439 47.619 0.00 0.00 41.76 4.95
2580 5797 3.115390 TCTGCTTCAAATAGCTACCCCT 58.885 45.455 0.00 0.00 41.76 4.79
2581 5798 4.295201 TCTGCTTCAAATAGCTACCCCTA 58.705 43.478 0.00 0.00 41.76 3.53
2582 5799 4.907875 TCTGCTTCAAATAGCTACCCCTAT 59.092 41.667 0.00 0.00 41.76 2.57
2583 5800 6.082031 TCTGCTTCAAATAGCTACCCCTATA 58.918 40.000 0.00 0.00 41.76 1.31
2584 5801 6.557253 TCTGCTTCAAATAGCTACCCCTATAA 59.443 38.462 0.00 0.00 41.76 0.98
2585 5802 7.071950 TCTGCTTCAAATAGCTACCCCTATAAA 59.928 37.037 0.00 0.00 41.76 1.40
2586 5803 7.224297 TGCTTCAAATAGCTACCCCTATAAAG 58.776 38.462 0.00 0.00 41.76 1.85
2587 5804 7.071950 TGCTTCAAATAGCTACCCCTATAAAGA 59.928 37.037 0.00 0.00 41.76 2.52
2588 5805 7.937394 GCTTCAAATAGCTACCCCTATAAAGAA 59.063 37.037 0.00 0.00 38.15 2.52
2589 5806 9.847224 CTTCAAATAGCTACCCCTATAAAGAAA 57.153 33.333 0.00 0.00 0.00 2.52
2609 5826 8.819643 AAGAAATATAGGAGCGTTTAGATCAC 57.180 34.615 0.00 0.00 36.90 3.06
2610 5827 8.184304 AGAAATATAGGAGCGTTTAGATCACT 57.816 34.615 0.00 0.00 36.90 3.41
2611 5828 9.298250 AGAAATATAGGAGCGTTTAGATCACTA 57.702 33.333 0.00 0.00 36.90 2.74
2612 5829 9.344309 GAAATATAGGAGCGTTTAGATCACTAC 57.656 37.037 0.00 0.00 36.90 2.73
2613 5830 8.638629 AATATAGGAGCGTTTAGATCACTACT 57.361 34.615 0.00 0.00 36.90 2.57
2614 5831 6.963083 ATAGGAGCGTTTAGATCACTACTT 57.037 37.500 0.00 0.00 36.90 2.24
2615 5832 5.662674 AGGAGCGTTTAGATCACTACTTT 57.337 39.130 0.00 0.00 36.90 2.66
2616 5833 6.770746 AGGAGCGTTTAGATCACTACTTTA 57.229 37.500 0.00 0.00 36.90 1.85
2617 5834 6.797454 AGGAGCGTTTAGATCACTACTTTAG 58.203 40.000 0.00 0.00 36.90 1.85
2618 5835 6.377712 AGGAGCGTTTAGATCACTACTTTAGT 59.622 38.462 0.00 0.00 40.28 2.24
2648 5865 6.811253 AACATGCTTACATTTCTTTACGGA 57.189 33.333 0.00 0.00 32.87 4.69
2649 5866 6.422776 ACATGCTTACATTTCTTTACGGAG 57.577 37.500 0.00 0.00 32.87 4.63
2650 5867 5.354234 ACATGCTTACATTTCTTTACGGAGG 59.646 40.000 0.00 0.00 32.87 4.30
2651 5868 4.258543 TGCTTACATTTCTTTACGGAGGG 58.741 43.478 0.00 0.00 0.00 4.30
2652 5869 4.020039 TGCTTACATTTCTTTACGGAGGGA 60.020 41.667 0.00 0.00 0.00 4.20
2653 5870 4.571176 GCTTACATTTCTTTACGGAGGGAG 59.429 45.833 0.00 0.00 0.00 4.30
2654 5871 2.987232 ACATTTCTTTACGGAGGGAGC 58.013 47.619 0.00 0.00 0.00 4.70
2660 5877 0.611714 TTTACGGAGGGAGCACTTCC 59.388 55.000 0.20 0.20 46.00 3.46
2665 5882 0.676736 GGAGGGAGCACTTCCTATCG 59.323 60.000 0.00 0.00 45.98 2.92
2673 5890 4.320641 GGAGCACTTCCTATCGTGTCTATC 60.321 50.000 0.00 0.00 43.16 2.08
2674 5891 4.465886 AGCACTTCCTATCGTGTCTATCT 58.534 43.478 0.00 0.00 33.78 1.98
2706 5923 6.910536 ATTTTTCTCCTATTGTCGCTAGTG 57.089 37.500 0.00 0.00 0.00 2.74
2710 5927 4.270834 TCTCCTATTGTCGCTAGTGACTT 58.729 43.478 30.82 22.00 39.64 3.01
2712 5929 5.296283 TCTCCTATTGTCGCTAGTGACTTAC 59.704 44.000 30.82 11.24 39.64 2.34
2725 5942 5.331876 AGTGACTTACAGCTGGTCTATTC 57.668 43.478 19.93 6.99 0.00 1.75
2727 5944 3.130516 TGACTTACAGCTGGTCTATTCGG 59.869 47.826 19.93 0.20 0.00 4.30
2733 5950 1.414181 AGCTGGTCTATTCGGTGATGG 59.586 52.381 0.00 0.00 0.00 3.51
2737 5954 1.583054 GTCTATTCGGTGATGGCCAC 58.417 55.000 8.16 2.36 44.95 5.01
2738 5955 1.139058 GTCTATTCGGTGATGGCCACT 59.861 52.381 8.16 0.00 45.03 4.00
2747 5964 3.620488 GGTGATGGCCACTCTGATTAAA 58.380 45.455 8.16 0.00 45.03 1.52
2761 5978 8.559536 CACTCTGATTAAAACAAAGTCAGCTTA 58.440 33.333 0.00 0.00 36.97 3.09
2806 6024 5.519206 CCTCGGCAACAATAGTCTAAACTAC 59.481 44.000 0.00 0.00 40.74 2.73
2807 6025 5.413499 TCGGCAACAATAGTCTAAACTACC 58.587 41.667 0.00 0.00 40.74 3.18
2835 6053 5.841810 CCTGACAAAGGCACATTCTTTTAA 58.158 37.500 0.00 0.00 39.93 1.52
2836 6054 5.922544 CCTGACAAAGGCACATTCTTTTAAG 59.077 40.000 0.00 0.00 39.93 1.85
2837 6055 6.239008 CCTGACAAAGGCACATTCTTTTAAGA 60.239 38.462 0.00 0.00 39.93 2.10
2840 6058 7.068103 TGACAAAGGCACATTCTTTTAAGAGAA 59.932 33.333 10.57 10.57 39.76 2.87
2852 6070 7.979444 TCTTTTAAGAGAATGAAATGACCGT 57.021 32.000 0.00 0.00 0.00 4.83
2862 6080 2.167662 GAAATGACCGTGGGGACAAAT 58.832 47.619 0.00 0.00 46.06 2.32
2867 6085 2.040545 TGACCGTGGGGACAAATTACAT 59.959 45.455 0.00 0.00 46.06 2.29
2871 6089 3.605634 CGTGGGGACAAATTACATCAGA 58.394 45.455 0.00 0.00 46.06 3.27
2872 6090 4.006989 CGTGGGGACAAATTACATCAGAA 58.993 43.478 0.00 0.00 46.06 3.02
2876 6094 7.467267 CGTGGGGACAAATTACATCAGAATAAG 60.467 40.741 0.00 0.00 46.06 1.73
2877 6095 7.339466 GTGGGGACAAATTACATCAGAATAAGT 59.661 37.037 0.00 0.00 46.06 2.24
2878 6096 8.553153 TGGGGACAAATTACATCAGAATAAGTA 58.447 33.333 0.00 0.00 37.44 2.24
2879 6097 9.403583 GGGGACAAATTACATCAGAATAAGTAA 57.596 33.333 0.00 0.00 0.00 2.24
2896 6114 8.975663 AATAAGTAATTTCCAACTAGTAGGGC 57.024 34.615 8.33 0.00 0.00 5.19
2906 6124 2.482494 ACTAGTAGGGCAAATGAGGCT 58.518 47.619 1.45 0.00 0.00 4.58
2907 6125 3.654273 ACTAGTAGGGCAAATGAGGCTA 58.346 45.455 1.45 0.00 0.00 3.93
2908 6126 4.235372 ACTAGTAGGGCAAATGAGGCTAT 58.765 43.478 1.45 0.00 0.00 2.97
2909 6127 4.660771 ACTAGTAGGGCAAATGAGGCTATT 59.339 41.667 1.45 0.00 0.00 1.73
2911 6129 4.974399 AGTAGGGCAAATGAGGCTATTAC 58.026 43.478 0.00 0.00 0.00 1.89
2912 6130 3.951563 AGGGCAAATGAGGCTATTACA 57.048 42.857 0.00 0.00 0.00 2.41
2914 6132 4.808042 AGGGCAAATGAGGCTATTACAAT 58.192 39.130 0.00 0.00 0.00 2.71
2915 6133 4.586001 AGGGCAAATGAGGCTATTACAATG 59.414 41.667 0.00 0.00 0.00 2.82
2916 6134 4.262164 GGGCAAATGAGGCTATTACAATGG 60.262 45.833 0.00 0.00 0.00 3.16
2917 6135 4.584325 GGCAAATGAGGCTATTACAATGGA 59.416 41.667 0.00 0.00 0.00 3.41
2926 6149 5.006386 GGCTATTACAATGGAAGGATGAGG 58.994 45.833 0.00 0.00 0.00 3.86
2932 6155 3.294214 CAATGGAAGGATGAGGGAAAGG 58.706 50.000 0.00 0.00 0.00 3.11
2960 6183 1.593006 CAGGACCATACATCGAAACGC 59.407 52.381 0.00 0.00 0.00 4.84
2961 6184 1.480954 AGGACCATACATCGAAACGCT 59.519 47.619 0.00 0.00 0.00 5.07
2964 6187 3.242316 GGACCATACATCGAAACGCTTTC 60.242 47.826 0.00 0.00 36.32 2.62
2965 6188 3.331150 ACCATACATCGAAACGCTTTCA 58.669 40.909 0.00 0.83 39.63 2.69
2968 6191 2.969443 ACATCGAAACGCTTTCAAGG 57.031 45.000 0.00 0.00 39.63 3.61
2976 6199 5.346822 TCGAAACGCTTTCAAGGTAATCTAC 59.653 40.000 9.90 0.00 39.63 2.59
2977 6200 5.445540 CGAAACGCTTTCAAGGTAATCTACC 60.446 44.000 9.90 0.00 43.23 3.18
2978 6201 5.410439 GAAACGCTTTCAAGGTAATCTACCA 59.590 40.000 5.67 0.00 43.92 3.25
2980 6203 8.694124 GAAACGCTTTCAAGGTAATCTACCAGT 61.694 40.741 5.67 0.00 43.92 4.00
2990 6213 5.456548 GTAATCTACCAGTAAGAGGCCTC 57.543 47.826 26.22 26.22 0.00 4.70
2991 6214 3.689872 ATCTACCAGTAAGAGGCCTCA 57.310 47.619 33.90 12.52 0.00 3.86
2992 6215 3.689872 TCTACCAGTAAGAGGCCTCAT 57.310 47.619 33.90 25.32 0.00 2.90
2993 6216 3.995636 TCTACCAGTAAGAGGCCTCATT 58.004 45.455 33.90 24.66 0.00 2.57
2994 6217 3.706594 TCTACCAGTAAGAGGCCTCATTG 59.293 47.826 33.90 23.03 0.00 2.82
2995 6218 2.269940 ACCAGTAAGAGGCCTCATTGT 58.730 47.619 33.90 18.02 0.00 2.71
2996 6219 2.237392 ACCAGTAAGAGGCCTCATTGTC 59.763 50.000 33.90 18.11 0.00 3.18
2997 6220 2.544685 CAGTAAGAGGCCTCATTGTCG 58.455 52.381 33.90 13.93 0.00 4.35
3000 6223 2.125512 GAGGCCTCATTGTCGCGT 60.126 61.111 28.43 0.00 0.00 6.01
3038 6261 5.181748 AGAGTTCACTGGCTTATTCATGTC 58.818 41.667 0.00 0.00 0.00 3.06
3048 6271 5.529800 TGGCTTATTCATGTCATGAGTGATG 59.470 40.000 18.39 10.39 40.94 3.07
3050 6273 6.707608 GGCTTATTCATGTCATGAGTGATGTA 59.292 38.462 18.39 2.80 40.94 2.29
3054 6277 3.708121 TCATGTCATGAGTGATGTAGCCT 59.292 43.478 11.62 0.00 36.60 4.58
3055 6278 3.531934 TGTCATGAGTGATGTAGCCTG 57.468 47.619 0.00 0.00 36.60 4.85
3056 6279 3.099141 TGTCATGAGTGATGTAGCCTGA 58.901 45.455 0.00 0.00 36.60 3.86
3058 6281 4.202192 TGTCATGAGTGATGTAGCCTGATC 60.202 45.833 0.00 0.00 36.60 2.92
3059 6282 4.039004 GTCATGAGTGATGTAGCCTGATCT 59.961 45.833 0.00 0.00 36.60 2.75
3061 6284 2.697229 TGAGTGATGTAGCCTGATCTGG 59.303 50.000 14.07 14.07 0.00 3.86
3062 6285 2.961741 GAGTGATGTAGCCTGATCTGGA 59.038 50.000 21.91 1.54 0.00 3.86
3063 6286 2.964464 AGTGATGTAGCCTGATCTGGAG 59.036 50.000 21.91 0.00 0.00 3.86
3064 6287 2.697751 GTGATGTAGCCTGATCTGGAGT 59.302 50.000 21.91 10.44 0.00 3.85
3065 6288 3.891977 GTGATGTAGCCTGATCTGGAGTA 59.108 47.826 21.91 9.49 0.00 2.59
3066 6289 4.022416 GTGATGTAGCCTGATCTGGAGTAG 60.022 50.000 21.91 0.00 0.00 2.57
3067 6290 2.311463 TGTAGCCTGATCTGGAGTAGC 58.689 52.381 21.91 6.28 0.00 3.58
3069 6292 2.173126 AGCCTGATCTGGAGTAGCTT 57.827 50.000 21.91 0.00 0.00 3.74
3070 6293 1.761784 AGCCTGATCTGGAGTAGCTTG 59.238 52.381 21.91 0.00 0.00 4.01
3071 6294 1.809651 GCCTGATCTGGAGTAGCTTGC 60.810 57.143 21.91 0.00 0.00 4.01
3072 6295 1.537776 CCTGATCTGGAGTAGCTTGCG 60.538 57.143 13.18 0.00 0.00 4.85
3076 6299 3.118629 TGATCTGGAGTAGCTTGCGAAAT 60.119 43.478 0.00 0.00 0.00 2.17
3079 6302 4.433615 TCTGGAGTAGCTTGCGAAATAAG 58.566 43.478 0.00 0.00 0.00 1.73
3080 6303 4.081642 TCTGGAGTAGCTTGCGAAATAAGT 60.082 41.667 0.00 0.00 0.00 2.24
3081 6304 4.575885 TGGAGTAGCTTGCGAAATAAGTT 58.424 39.130 0.00 0.00 0.00 2.66
3082 6305 4.391830 TGGAGTAGCTTGCGAAATAAGTTG 59.608 41.667 0.00 0.00 0.00 3.16
3083 6306 4.201822 GGAGTAGCTTGCGAAATAAGTTGG 60.202 45.833 0.00 0.00 0.00 3.77
3084 6307 4.324267 AGTAGCTTGCGAAATAAGTTGGT 58.676 39.130 0.00 0.00 0.00 3.67
3085 6308 5.484715 AGTAGCTTGCGAAATAAGTTGGTA 58.515 37.500 0.00 0.00 0.00 3.25
3086 6309 5.935789 AGTAGCTTGCGAAATAAGTTGGTAA 59.064 36.000 0.00 0.00 0.00 2.85
3087 6310 5.699097 AGCTTGCGAAATAAGTTGGTAAA 57.301 34.783 0.00 0.00 0.00 2.01
3088 6311 6.079424 AGCTTGCGAAATAAGTTGGTAAAA 57.921 33.333 0.00 0.00 0.00 1.52
3089 6312 6.687604 AGCTTGCGAAATAAGTTGGTAAAAT 58.312 32.000 0.00 0.00 0.00 1.82
3090 6313 7.822658 AGCTTGCGAAATAAGTTGGTAAAATA 58.177 30.769 0.00 0.00 0.00 1.40
3091 6314 8.301002 AGCTTGCGAAATAAGTTGGTAAAATAA 58.699 29.630 0.00 0.00 0.00 1.40
3092 6315 8.583765 GCTTGCGAAATAAGTTGGTAAAATAAG 58.416 33.333 0.00 0.00 0.00 1.73
3093 6316 9.620660 CTTGCGAAATAAGTTGGTAAAATAAGT 57.379 29.630 0.00 0.00 0.00 2.24
3094 6317 9.968870 TTGCGAAATAAGTTGGTAAAATAAGTT 57.031 25.926 0.00 0.00 0.00 2.66
3115 6338 8.519799 AAGTTATTTGTCCTCTGAAAGAAACA 57.480 30.769 0.00 0.00 46.34 2.83
3116 6339 7.931275 AGTTATTTGTCCTCTGAAAGAAACAC 58.069 34.615 0.00 0.00 46.34 3.32
3117 6340 7.556275 AGTTATTTGTCCTCTGAAAGAAACACA 59.444 33.333 0.00 0.00 46.34 3.72
3118 6341 6.773976 ATTTGTCCTCTGAAAGAAACACAA 57.226 33.333 0.00 0.00 46.34 3.33
3119 6342 6.582677 TTTGTCCTCTGAAAGAAACACAAA 57.417 33.333 0.00 0.00 46.34 2.83
3120 6343 6.773976 TTGTCCTCTGAAAGAAACACAAAT 57.226 33.333 0.00 0.00 46.34 2.32
3121 6344 6.773976 TGTCCTCTGAAAGAAACACAAATT 57.226 33.333 0.00 0.00 46.34 1.82
3122 6345 7.873719 TGTCCTCTGAAAGAAACACAAATTA 57.126 32.000 0.00 0.00 46.34 1.40
3123 6346 7.703328 TGTCCTCTGAAAGAAACACAAATTAC 58.297 34.615 0.00 0.00 46.34 1.89
3124 6347 7.556275 TGTCCTCTGAAAGAAACACAAATTACT 59.444 33.333 0.00 0.00 46.34 2.24
3125 6348 7.857885 GTCCTCTGAAAGAAACACAAATTACTG 59.142 37.037 0.00 0.00 46.34 2.74
3126 6349 6.638468 CCTCTGAAAGAAACACAAATTACTGC 59.362 38.462 0.00 0.00 46.34 4.40
3127 6350 7.333528 TCTGAAAGAAACACAAATTACTGCT 57.666 32.000 0.00 0.00 42.31 4.24
3128 6351 7.417612 TCTGAAAGAAACACAAATTACTGCTC 58.582 34.615 0.00 0.00 42.31 4.26
3141 6364 2.632987 ACTGCTCTGTAAAACCGGTT 57.367 45.000 15.86 15.86 0.00 4.44
3147 6370 4.060205 GCTCTGTAAAACCGGTTTCAGTA 58.940 43.478 31.88 21.27 31.60 2.74
3159 6382 5.479375 ACCGGTTTCAGTAGTCTAATCTTGA 59.521 40.000 0.00 0.00 0.00 3.02
3176 6399 5.661056 TCTTGATTCATCTGAACTACCGT 57.339 39.130 0.00 0.00 36.80 4.83
3177 6400 6.769134 TCTTGATTCATCTGAACTACCGTA 57.231 37.500 0.00 0.00 36.80 4.02
3178 6401 6.796426 TCTTGATTCATCTGAACTACCGTAG 58.204 40.000 3.88 3.88 36.80 3.51
3181 6404 4.634184 TTCATCTGAACTACCGTAGAGC 57.366 45.455 12.66 4.35 0.00 4.09
3183 6406 5.032327 TCATCTGAACTACCGTAGAGCTA 57.968 43.478 12.66 0.00 0.00 3.32
3226 6449 2.143876 TTTTTCTATCAGCCAGGGCC 57.856 50.000 6.70 0.00 43.17 5.80
3227 6450 0.258774 TTTTCTATCAGCCAGGGCCC 59.741 55.000 16.46 16.46 43.17 5.80
3228 6451 0.624500 TTTCTATCAGCCAGGGCCCT 60.625 55.000 22.28 22.28 43.17 5.19
3229 6452 1.056700 TTCTATCAGCCAGGGCCCTC 61.057 60.000 25.77 12.80 43.17 4.30
3230 6453 2.844362 TATCAGCCAGGGCCCTCG 60.844 66.667 25.77 18.97 43.17 4.63
3246 6469 1.002624 TCGCCGGCAGGAGAAAAAT 60.003 52.632 28.98 0.00 43.46 1.82
3247 6470 1.137404 CGCCGGCAGGAGAAAAATG 59.863 57.895 28.98 0.37 39.96 2.32
3250 6473 0.171903 CCGGCAGGAGAAAAATGCAG 59.828 55.000 0.00 0.00 41.78 4.41
3251 6474 0.883833 CGGCAGGAGAAAAATGCAGT 59.116 50.000 0.00 0.00 41.78 4.40
3252 6475 1.270550 CGGCAGGAGAAAAATGCAGTT 59.729 47.619 0.00 0.00 41.78 3.16
3253 6476 2.680577 GGCAGGAGAAAAATGCAGTTG 58.319 47.619 0.00 0.00 41.78 3.16
3254 6477 2.064014 GCAGGAGAAAAATGCAGTTGC 58.936 47.619 0.00 0.00 39.75 4.17
3275 6498 4.935885 CAGTCTTGCAGATAACTGGAAC 57.064 45.455 2.73 0.00 46.43 3.62
3284 6507 6.864342 TGCAGATAACTGGAACTAGTCTAAC 58.136 40.000 0.00 0.00 41.25 2.34
3293 6516 5.012239 TGGAACTAGTCTAACACGGTGTAT 58.988 41.667 15.11 7.60 0.00 2.29
3294 6517 6.179756 TGGAACTAGTCTAACACGGTGTATA 58.820 40.000 15.11 8.32 0.00 1.47
3295 6518 6.094048 TGGAACTAGTCTAACACGGTGTATAC 59.906 42.308 15.11 12.45 0.00 1.47
3296 6519 6.094048 GGAACTAGTCTAACACGGTGTATACA 59.906 42.308 15.11 0.08 0.00 2.29
3297 6520 6.674694 ACTAGTCTAACACGGTGTATACAG 57.325 41.667 15.11 9.53 0.00 2.74
3298 6521 6.176183 ACTAGTCTAACACGGTGTATACAGT 58.824 40.000 15.11 13.93 35.55 3.55
3299 6522 7.331026 ACTAGTCTAACACGGTGTATACAGTA 58.669 38.462 15.11 1.11 33.35 2.74
3303 6526 9.347240 AGTCTAACACGGTGTATACAGTATATT 57.653 33.333 15.11 1.68 33.35 1.28
3304 6527 9.390795 GTCTAACACGGTGTATACAGTATATTG 57.609 37.037 15.11 1.08 33.35 1.90
3305 6528 9.123902 TCTAACACGGTGTATACAGTATATTGT 57.876 33.333 15.11 6.13 33.35 2.71
3308 6531 8.681486 ACACGGTGTATACAGTATATTGTCTA 57.319 34.615 12.96 0.00 33.35 2.59
3320 6543 9.838339 ACAGTATATTGTCTATTTTAGCAAGCT 57.162 29.630 0.00 0.00 0.00 3.74
3328 6551 9.938280 TTGTCTATTTTAGCAAGCTAAGACTAA 57.062 29.630 22.30 13.05 39.36 2.24
3334 6557 9.681062 ATTTTAGCAAGCTAAGACTAAACCATA 57.319 29.630 13.56 0.00 39.36 2.74
3336 6559 8.662781 TTAGCAAGCTAAGACTAAACCATATG 57.337 34.615 10.29 0.00 34.02 1.78
3338 6561 7.792032 AGCAAGCTAAGACTAAACCATATGTA 58.208 34.615 1.24 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.776417 TCTGATGGATTCTGTGATGACCA 59.224 43.478 0.00 0.00 0.00 4.02
80 81 5.567138 ACTTGCTATTTCTGTAACCATGC 57.433 39.130 0.00 0.00 0.00 4.06
84 85 6.649557 ACAGTGTACTTGCTATTTCTGTAACC 59.350 38.462 0.00 0.00 33.96 2.85
136 156 6.598753 TTCGAGTTTCCTGTTCTTAAGTTG 57.401 37.500 1.63 0.00 0.00 3.16
729 773 7.604927 ACCGGTGAAATATATATATTTGCGTGT 59.395 33.333 27.67 17.28 41.59 4.49
811 3255 4.626604 CCAATTTTTATGCGCACAAGTGAT 59.373 37.500 14.90 0.00 0.00 3.06
822 3266 7.029563 CACTTCTGTAGACCCAATTTTTATGC 58.970 38.462 0.00 0.00 0.00 3.14
835 3279 4.039366 ACTCCTTTGTCCACTTCTGTAGAC 59.961 45.833 0.00 0.00 35.80 2.59
840 3284 4.962155 ACTAACTCCTTTGTCCACTTCTG 58.038 43.478 0.00 0.00 0.00 3.02
932 3376 4.144297 TGGCAGTTTTATGGGCATAGATC 58.856 43.478 0.00 0.00 31.66 2.75
1127 3577 1.867919 GATCGGATCGGGCATCTCGT 61.868 60.000 1.62 0.00 31.06 4.18
1155 3605 0.528033 CAGGCAGACAGCTGAGATCG 60.528 60.000 23.35 4.88 45.17 3.69
1165 3615 3.863114 TACCAGGGGCAGGCAGACA 62.863 63.158 0.00 0.00 0.00 3.41
1202 3655 1.486310 TCAAGGCCGACTGCATCTTAT 59.514 47.619 0.00 0.00 43.89 1.73
1203 3656 0.901827 TCAAGGCCGACTGCATCTTA 59.098 50.000 0.00 0.00 43.89 2.10
1215 3668 1.979155 GCCCCAGTTCTTCAAGGCC 60.979 63.158 0.00 0.00 34.23 5.19
1222 3675 0.476611 AGGAAGAGGCCCCAGTTCTT 60.477 55.000 0.00 0.34 34.06 2.52
1393 3848 6.412362 TTGAGTACTTCTGCTTCTCTTCTT 57.588 37.500 0.00 0.00 0.00 2.52
1394 3849 6.041523 AGTTTGAGTACTTCTGCTTCTCTTCT 59.958 38.462 0.00 0.00 0.00 2.85
1780 4520 4.333649 GCATCCTCTTCAATCATTTCGACA 59.666 41.667 0.00 0.00 0.00 4.35
1805 4555 5.980116 AGTAGTTGAATCTCGCATATGTGAC 59.020 40.000 14.94 6.29 0.00 3.67
1816 4566 4.342665 CAGGGAGGGTAGTAGTTGAATCTC 59.657 50.000 0.00 0.00 0.00 2.75
1894 4652 6.346598 CGTTATCGTCAATGAAGACAACTGTT 60.347 38.462 15.82 0.00 38.43 3.16
1912 4670 0.527817 GGAGCCCACTGACGTTATCG 60.528 60.000 0.00 0.00 43.34 2.92
1937 4860 4.231718 TGTACCAAACGCCATTTTTCTC 57.768 40.909 0.00 0.00 0.00 2.87
1951 4874 5.470777 CGGAACTATTGGAACTTTGTACCAA 59.529 40.000 0.00 0.00 45.64 3.67
1963 4886 5.680619 AGTAATGCATTCGGAACTATTGGA 58.319 37.500 16.86 0.00 0.00 3.53
2064 4987 5.300539 TCAGGTGTAATAGAGCTCAGCTTAG 59.699 44.000 17.77 0.00 39.88 2.18
2081 5014 5.620738 AAGTATCTGCATGTATCAGGTGT 57.379 39.130 0.00 0.00 32.63 4.16
2084 5017 5.787380 TGCTAAGTATCTGCATGTATCAGG 58.213 41.667 0.00 0.00 32.63 3.86
2139 5072 0.167470 CTTGCTCTGCATTGGTCACG 59.833 55.000 0.00 0.00 38.76 4.35
2155 5088 0.246635 ACCAACGAGACCCGATCTTG 59.753 55.000 0.00 3.11 43.81 3.02
2166 5099 3.611113 CCGTGTAGAACATAACCAACGAG 59.389 47.826 0.00 0.00 0.00 4.18
2169 5102 2.093152 CGCCGTGTAGAACATAACCAAC 59.907 50.000 0.00 0.00 0.00 3.77
2184 5117 4.135153 CTCTCTGGGTCCGCCGTG 62.135 72.222 0.00 0.00 34.97 4.94
2188 5121 3.760035 TTCGCTCTCTGGGTCCGC 61.760 66.667 0.00 0.00 0.00 5.54
2202 5135 2.671177 CGGCACTGGCTCAAGTTCG 61.671 63.158 0.52 0.00 40.87 3.95
2205 5138 3.241530 TCCGGCACTGGCTCAAGT 61.242 61.111 0.00 0.00 40.87 3.16
2206 5139 2.435586 CTCCGGCACTGGCTCAAG 60.436 66.667 0.00 0.00 40.87 3.02
2220 5153 2.103941 CCTCTTCTTATCCACCAGCTCC 59.896 54.545 0.00 0.00 0.00 4.70
2233 5166 4.767255 CCGCGCTGGCCTCTTCTT 62.767 66.667 5.56 0.00 35.02 2.52
2241 5174 4.752879 TTCCTGTACCGCGCTGGC 62.753 66.667 16.48 3.77 43.94 4.85
2245 5178 1.859080 CTTTATCTTCCTGTACCGCGC 59.141 52.381 0.00 0.00 0.00 6.86
2246 5179 3.114065 GTCTTTATCTTCCTGTACCGCG 58.886 50.000 0.00 0.00 0.00 6.46
2388 5321 2.957402 AGAGGACAGATTGTTGGCAA 57.043 45.000 0.00 0.00 39.16 4.52
2390 5323 5.918608 TCTATAAGAGGACAGATTGTTGGC 58.081 41.667 0.00 0.00 0.00 4.52
2433 5368 9.210228 TCCATATATAGCACATTCTGATCAGAT 57.790 33.333 25.64 12.40 37.29 2.90
2440 5375 8.613060 AAAGTGTCCATATATAGCACATTCTG 57.387 34.615 12.80 0.00 32.99 3.02
2484 5421 0.698238 AGGTATGAAGTGGCCTGCAA 59.302 50.000 3.32 0.00 27.14 4.08
2501 5438 7.670140 AGGGGATAAAACTTGAACTAAAAGAGG 59.330 37.037 0.00 0.00 0.00 3.69
2551 5768 5.259632 AGCTATTTGAAGCAGAAACCTGAT 58.740 37.500 0.00 0.00 45.30 2.90
2553 5770 5.163713 GGTAGCTATTTGAAGCAGAAACCTG 60.164 44.000 0.00 0.00 45.30 4.00
2555 5772 4.096532 GGGTAGCTATTTGAAGCAGAAACC 59.903 45.833 0.00 0.00 45.30 3.27
2583 5800 9.262358 GTGATCTAAACGCTCCTATATTTCTTT 57.738 33.333 0.00 0.00 0.00 2.52
2584 5801 8.643324 AGTGATCTAAACGCTCCTATATTTCTT 58.357 33.333 0.00 0.00 0.00 2.52
2585 5802 8.184304 AGTGATCTAAACGCTCCTATATTTCT 57.816 34.615 0.00 0.00 0.00 2.52
2586 5803 9.344309 GTAGTGATCTAAACGCTCCTATATTTC 57.656 37.037 0.00 0.00 0.00 2.17
2587 5804 9.080097 AGTAGTGATCTAAACGCTCCTATATTT 57.920 33.333 0.00 0.00 0.00 1.40
2588 5805 8.638629 AGTAGTGATCTAAACGCTCCTATATT 57.361 34.615 0.00 0.00 0.00 1.28
2589 5806 8.638629 AAGTAGTGATCTAAACGCTCCTATAT 57.361 34.615 0.00 0.00 0.00 0.86
2590 5807 8.461249 AAAGTAGTGATCTAAACGCTCCTATA 57.539 34.615 0.00 0.00 0.00 1.31
2591 5808 6.963083 AAGTAGTGATCTAAACGCTCCTAT 57.037 37.500 0.00 0.00 0.00 2.57
2592 5809 6.770746 AAAGTAGTGATCTAAACGCTCCTA 57.229 37.500 0.00 0.00 0.00 2.94
2593 5810 5.662674 AAAGTAGTGATCTAAACGCTCCT 57.337 39.130 0.00 0.00 0.00 3.69
2594 5811 6.562518 ACTAAAGTAGTGATCTAAACGCTCC 58.437 40.000 0.00 0.00 37.69 4.70
2622 5839 8.952278 TCCGTAAAGAAATGTAAGCATGTTTAT 58.048 29.630 5.24 0.00 35.15 1.40
2623 5840 8.325421 TCCGTAAAGAAATGTAAGCATGTTTA 57.675 30.769 0.00 0.00 35.15 2.01
2624 5841 7.209471 TCCGTAAAGAAATGTAAGCATGTTT 57.791 32.000 0.00 0.00 35.15 2.83
2625 5842 6.128007 CCTCCGTAAAGAAATGTAAGCATGTT 60.128 38.462 0.00 0.00 35.15 2.71
2626 5843 5.354234 CCTCCGTAAAGAAATGTAAGCATGT 59.646 40.000 0.00 0.00 35.15 3.21
2627 5844 5.220854 CCCTCCGTAAAGAAATGTAAGCATG 60.221 44.000 0.00 0.00 35.15 4.06
2628 5845 4.881850 CCCTCCGTAAAGAAATGTAAGCAT 59.118 41.667 0.00 0.00 36.80 3.79
2629 5846 4.020039 TCCCTCCGTAAAGAAATGTAAGCA 60.020 41.667 0.00 0.00 0.00 3.91
2630 5847 4.510571 TCCCTCCGTAAAGAAATGTAAGC 58.489 43.478 0.00 0.00 0.00 3.09
2631 5848 4.571176 GCTCCCTCCGTAAAGAAATGTAAG 59.429 45.833 0.00 0.00 0.00 2.34
2632 5849 4.020039 TGCTCCCTCCGTAAAGAAATGTAA 60.020 41.667 0.00 0.00 0.00 2.41
2633 5850 3.516300 TGCTCCCTCCGTAAAGAAATGTA 59.484 43.478 0.00 0.00 0.00 2.29
2634 5851 2.304761 TGCTCCCTCCGTAAAGAAATGT 59.695 45.455 0.00 0.00 0.00 2.71
2635 5852 2.678336 GTGCTCCCTCCGTAAAGAAATG 59.322 50.000 0.00 0.00 0.00 2.32
2636 5853 2.572104 AGTGCTCCCTCCGTAAAGAAAT 59.428 45.455 0.00 0.00 0.00 2.17
2637 5854 1.975680 AGTGCTCCCTCCGTAAAGAAA 59.024 47.619 0.00 0.00 0.00 2.52
2638 5855 1.640917 AGTGCTCCCTCCGTAAAGAA 58.359 50.000 0.00 0.00 0.00 2.52
2639 5856 1.549170 GAAGTGCTCCCTCCGTAAAGA 59.451 52.381 0.00 0.00 0.00 2.52
2640 5857 1.405661 GGAAGTGCTCCCTCCGTAAAG 60.406 57.143 0.00 0.00 38.44 1.85
2641 5858 0.611714 GGAAGTGCTCCCTCCGTAAA 59.388 55.000 0.00 0.00 38.44 2.01
2642 5859 0.252103 AGGAAGTGCTCCCTCCGTAA 60.252 55.000 0.00 0.00 46.81 3.18
2643 5860 0.627451 TAGGAAGTGCTCCCTCCGTA 59.373 55.000 0.00 0.00 46.81 4.02
2644 5861 0.032017 ATAGGAAGTGCTCCCTCCGT 60.032 55.000 0.00 0.00 46.81 4.69
2645 5862 0.676736 GATAGGAAGTGCTCCCTCCG 59.323 60.000 0.00 0.00 46.81 4.63
2646 5863 0.676736 CGATAGGAAGTGCTCCCTCC 59.323 60.000 0.00 0.00 46.81 4.30
2647 5864 1.067821 CACGATAGGAAGTGCTCCCTC 59.932 57.143 0.00 0.00 46.81 4.30
2648 5865 1.115467 CACGATAGGAAGTGCTCCCT 58.885 55.000 0.00 0.00 46.81 4.20
2649 5866 0.824759 ACACGATAGGAAGTGCTCCC 59.175 55.000 0.00 0.00 46.81 4.30
2650 5867 1.751924 AGACACGATAGGAAGTGCTCC 59.248 52.381 0.00 0.00 45.81 4.70
2651 5868 4.517453 AGATAGACACGATAGGAAGTGCTC 59.483 45.833 0.00 0.00 41.72 4.26
2652 5869 4.465886 AGATAGACACGATAGGAAGTGCT 58.534 43.478 0.00 0.00 41.72 4.40
2653 5870 4.839668 AGATAGACACGATAGGAAGTGC 57.160 45.455 0.00 0.00 41.72 4.40
2654 5871 6.627395 AGAAGATAGACACGATAGGAAGTG 57.373 41.667 0.00 0.00 43.46 3.16
2674 5891 9.162764 CGACAATAGGAGAAAAATAAGGAAGAA 57.837 33.333 0.00 0.00 0.00 2.52
2706 5923 3.130693 ACCGAATAGACCAGCTGTAAGTC 59.869 47.826 13.81 12.88 35.30 3.01
2710 5927 2.730382 TCACCGAATAGACCAGCTGTA 58.270 47.619 13.81 0.00 0.00 2.74
2712 5929 2.477825 CATCACCGAATAGACCAGCTG 58.522 52.381 6.78 6.78 0.00 4.24
2727 5944 4.458989 TGTTTTAATCAGAGTGGCCATCAC 59.541 41.667 9.72 3.39 46.39 3.06
2733 5950 6.072112 TGACTTTGTTTTAATCAGAGTGGC 57.928 37.500 4.31 0.00 31.91 5.01
2737 5954 8.778358 AGTAAGCTGACTTTGTTTTAATCAGAG 58.222 33.333 0.00 1.95 39.33 3.35
2738 5955 8.677148 AGTAAGCTGACTTTGTTTTAATCAGA 57.323 30.769 0.00 0.00 39.33 3.27
2747 5964 8.677148 TTCTTGATTAGTAAGCTGACTTTGTT 57.323 30.769 9.63 0.00 37.33 2.83
2761 5978 3.763897 GGCACACCCAATTCTTGATTAGT 59.236 43.478 0.00 0.00 0.00 2.24
2766 5983 1.881925 CGAGGCACACCCAATTCTTGA 60.882 52.381 0.00 0.00 36.11 3.02
2767 5984 0.523072 CGAGGCACACCCAATTCTTG 59.477 55.000 0.00 0.00 36.11 3.02
2798 6016 3.928727 TGTCAGGTCACGGTAGTTTAG 57.071 47.619 0.00 0.00 0.00 1.85
2806 6024 1.227823 TGCCTTTGTCAGGTCACGG 60.228 57.895 0.00 0.00 46.07 4.94
2807 6025 0.813610 TGTGCCTTTGTCAGGTCACG 60.814 55.000 9.45 0.00 45.58 4.35
2835 6053 2.356125 CCCCACGGTCATTTCATTCTCT 60.356 50.000 0.00 0.00 0.00 3.10
2836 6054 2.017049 CCCCACGGTCATTTCATTCTC 58.983 52.381 0.00 0.00 0.00 2.87
2837 6055 1.633432 TCCCCACGGTCATTTCATTCT 59.367 47.619 0.00 0.00 0.00 2.40
2840 6058 0.695924 TGTCCCCACGGTCATTTCAT 59.304 50.000 0.00 0.00 0.00 2.57
2847 6065 2.188062 TGTAATTTGTCCCCACGGTC 57.812 50.000 0.00 0.00 0.00 4.79
2852 6070 7.410174 ACTTATTCTGATGTAATTTGTCCCCA 58.590 34.615 0.00 0.00 0.00 4.96
2871 6089 8.554011 TGCCCTACTAGTTGGAAATTACTTATT 58.446 33.333 23.03 0.00 0.00 1.40
2872 6090 8.097791 TGCCCTACTAGTTGGAAATTACTTAT 57.902 34.615 23.03 0.00 0.00 1.73
2876 6094 7.338449 TCATTTGCCCTACTAGTTGGAAATTAC 59.662 37.037 23.03 7.09 0.00 1.89
2877 6095 7.406916 TCATTTGCCCTACTAGTTGGAAATTA 58.593 34.615 23.03 11.20 0.00 1.40
2878 6096 6.252995 TCATTTGCCCTACTAGTTGGAAATT 58.747 36.000 23.03 11.10 0.00 1.82
2879 6097 5.826643 TCATTTGCCCTACTAGTTGGAAAT 58.173 37.500 23.03 17.62 0.00 2.17
2886 6104 2.482494 AGCCTCATTTGCCCTACTAGT 58.518 47.619 0.00 0.00 0.00 2.57
2896 6114 6.547141 TCCTTCCATTGTAATAGCCTCATTTG 59.453 38.462 0.00 0.00 0.00 2.32
2906 6124 6.840090 TTCCCTCATCCTTCCATTGTAATA 57.160 37.500 0.00 0.00 0.00 0.98
2907 6125 5.732331 TTCCCTCATCCTTCCATTGTAAT 57.268 39.130 0.00 0.00 0.00 1.89
2908 6126 5.509498 CTTTCCCTCATCCTTCCATTGTAA 58.491 41.667 0.00 0.00 0.00 2.41
2909 6127 4.079787 CCTTTCCCTCATCCTTCCATTGTA 60.080 45.833 0.00 0.00 0.00 2.41
2911 6129 3.294214 CCTTTCCCTCATCCTTCCATTG 58.706 50.000 0.00 0.00 0.00 2.82
2912 6130 2.929043 ACCTTTCCCTCATCCTTCCATT 59.071 45.455 0.00 0.00 0.00 3.16
2914 6132 2.059756 ACCTTTCCCTCATCCTTCCA 57.940 50.000 0.00 0.00 0.00 3.53
2915 6133 2.357257 GGAACCTTTCCCTCATCCTTCC 60.357 54.545 0.00 0.00 44.30 3.46
2916 6134 3.006112 GGAACCTTTCCCTCATCCTTC 57.994 52.381 0.00 0.00 44.30 3.46
2926 6149 1.818131 GGTCCTGTGTGGAACCTTTCC 60.818 57.143 0.00 0.00 46.80 3.13
2939 6162 2.888594 CGTTTCGATGTATGGTCCTGT 58.111 47.619 0.00 0.00 0.00 4.00
2940 6163 1.593006 GCGTTTCGATGTATGGTCCTG 59.407 52.381 0.00 0.00 0.00 3.86
2941 6164 1.480954 AGCGTTTCGATGTATGGTCCT 59.519 47.619 0.00 0.00 0.00 3.85
2968 6191 4.894114 TGAGGCCTCTTACTGGTAGATTAC 59.106 45.833 32.28 1.55 0.00 1.89
2976 6199 2.739932 CGACAATGAGGCCTCTTACTGG 60.740 54.545 32.28 17.95 0.00 4.00
2977 6200 2.544685 CGACAATGAGGCCTCTTACTG 58.455 52.381 32.28 22.85 0.00 2.74
2978 6201 1.134670 GCGACAATGAGGCCTCTTACT 60.135 52.381 32.28 14.92 0.00 2.24
2980 6203 0.179111 CGCGACAATGAGGCCTCTTA 60.179 55.000 32.28 15.01 0.00 2.10
2981 6204 1.448540 CGCGACAATGAGGCCTCTT 60.449 57.895 32.28 24.06 0.00 2.85
2992 6215 9.697250 CTCTATTTAATAAAATTGACGCGACAA 57.303 29.630 24.84 24.84 36.67 3.18
2993 6216 8.875803 ACTCTATTTAATAAAATTGACGCGACA 58.124 29.630 15.93 11.23 36.67 4.35
2994 6217 9.698617 AACTCTATTTAATAAAATTGACGCGAC 57.301 29.630 15.93 7.62 36.67 5.19
2995 6218 9.910511 GAACTCTATTTAATAAAATTGACGCGA 57.089 29.630 15.93 0.00 36.67 5.87
2996 6219 9.697250 TGAACTCTATTTAATAAAATTGACGCG 57.303 29.630 3.53 3.53 36.67 6.01
3016 6239 4.937620 TGACATGAATAAGCCAGTGAACTC 59.062 41.667 0.00 0.00 0.00 3.01
3023 6246 5.121105 TCACTCATGACATGAATAAGCCAG 58.879 41.667 18.49 7.42 39.11 4.85
3024 6247 5.101648 TCACTCATGACATGAATAAGCCA 57.898 39.130 18.49 0.00 39.11 4.75
3025 6248 5.530171 ACATCACTCATGACATGAATAAGCC 59.470 40.000 18.49 0.00 39.11 4.35
3026 6249 6.615264 ACATCACTCATGACATGAATAAGC 57.385 37.500 18.49 0.00 39.11 3.09
3038 6261 4.308265 CAGATCAGGCTACATCACTCATG 58.692 47.826 8.03 0.00 38.64 3.07
3048 6271 2.593026 AGCTACTCCAGATCAGGCTAC 58.407 52.381 0.00 0.00 0.00 3.58
3050 6273 1.761784 CAAGCTACTCCAGATCAGGCT 59.238 52.381 0.00 0.00 0.00 4.58
3054 6277 1.474330 TCGCAAGCTACTCCAGATCA 58.526 50.000 0.00 0.00 37.18 2.92
3055 6278 2.586258 TTCGCAAGCTACTCCAGATC 57.414 50.000 0.00 0.00 37.18 2.75
3056 6279 3.550437 ATTTCGCAAGCTACTCCAGAT 57.450 42.857 0.00 0.00 37.18 2.90
3058 6281 4.184629 ACTTATTTCGCAAGCTACTCCAG 58.815 43.478 0.00 0.00 37.18 3.86
3059 6282 4.202245 ACTTATTTCGCAAGCTACTCCA 57.798 40.909 0.00 0.00 37.18 3.86
3061 6284 4.392138 ACCAACTTATTTCGCAAGCTACTC 59.608 41.667 0.00 0.00 37.18 2.59
3062 6285 4.324267 ACCAACTTATTTCGCAAGCTACT 58.676 39.130 0.00 0.00 37.18 2.57
3063 6286 4.680171 ACCAACTTATTTCGCAAGCTAC 57.320 40.909 0.00 0.00 37.18 3.58
3064 6287 6.804770 TTTACCAACTTATTTCGCAAGCTA 57.195 33.333 0.00 0.00 37.18 3.32
3065 6288 5.699097 TTTACCAACTTATTTCGCAAGCT 57.301 34.783 0.00 0.00 37.18 3.74
3066 6289 6.944557 ATTTTACCAACTTATTTCGCAAGC 57.055 33.333 0.00 0.00 37.18 4.01
3067 6290 9.620660 ACTTATTTTACCAACTTATTTCGCAAG 57.379 29.630 0.00 0.00 0.00 4.01
3089 6312 9.621629 TGTTTCTTTCAGAGGACAAATAACTTA 57.378 29.630 0.00 0.00 0.00 2.24
3090 6313 8.406297 GTGTTTCTTTCAGAGGACAAATAACTT 58.594 33.333 0.00 0.00 0.00 2.66
3091 6314 7.556275 TGTGTTTCTTTCAGAGGACAAATAACT 59.444 33.333 0.00 0.00 0.00 2.24
3092 6315 7.703328 TGTGTTTCTTTCAGAGGACAAATAAC 58.297 34.615 0.00 0.00 0.00 1.89
3093 6316 7.873719 TGTGTTTCTTTCAGAGGACAAATAA 57.126 32.000 0.00 0.00 0.00 1.40
3094 6317 7.873719 TTGTGTTTCTTTCAGAGGACAAATA 57.126 32.000 0.00 0.00 0.00 1.40
3095 6318 6.773976 TTGTGTTTCTTTCAGAGGACAAAT 57.226 33.333 0.00 0.00 0.00 2.32
3096 6319 6.582677 TTTGTGTTTCTTTCAGAGGACAAA 57.417 33.333 0.00 0.00 31.68 2.83
3097 6320 6.773976 ATTTGTGTTTCTTTCAGAGGACAA 57.226 33.333 0.00 0.00 0.00 3.18
3098 6321 6.773976 AATTTGTGTTTCTTTCAGAGGACA 57.226 33.333 0.00 0.00 0.00 4.02
3099 6322 7.857885 CAGTAATTTGTGTTTCTTTCAGAGGAC 59.142 37.037 0.00 0.00 0.00 3.85
3100 6323 7.468631 GCAGTAATTTGTGTTTCTTTCAGAGGA 60.469 37.037 0.00 0.00 0.00 3.71
3101 6324 6.638468 GCAGTAATTTGTGTTTCTTTCAGAGG 59.362 38.462 0.00 0.00 0.00 3.69
3102 6325 7.420800 AGCAGTAATTTGTGTTTCTTTCAGAG 58.579 34.615 0.00 0.00 0.00 3.35
3103 6326 7.283127 AGAGCAGTAATTTGTGTTTCTTTCAGA 59.717 33.333 0.00 0.00 0.00 3.27
3104 6327 7.377928 CAGAGCAGTAATTTGTGTTTCTTTCAG 59.622 37.037 0.00 0.00 0.00 3.02
3105 6328 7.148086 ACAGAGCAGTAATTTGTGTTTCTTTCA 60.148 33.333 0.00 0.00 0.00 2.69
3106 6329 7.196331 ACAGAGCAGTAATTTGTGTTTCTTTC 58.804 34.615 0.00 0.00 0.00 2.62
3107 6330 7.100458 ACAGAGCAGTAATTTGTGTTTCTTT 57.900 32.000 0.00 0.00 0.00 2.52
3108 6331 6.699575 ACAGAGCAGTAATTTGTGTTTCTT 57.300 33.333 0.00 0.00 0.00 2.52
3109 6332 7.801716 TTACAGAGCAGTAATTTGTGTTTCT 57.198 32.000 0.00 0.00 0.00 2.52
3110 6333 8.743099 GTTTTACAGAGCAGTAATTTGTGTTTC 58.257 33.333 0.00 0.00 34.25 2.78
3111 6334 7.704899 GGTTTTACAGAGCAGTAATTTGTGTTT 59.295 33.333 0.00 0.00 34.25 2.83
3112 6335 7.200455 GGTTTTACAGAGCAGTAATTTGTGTT 58.800 34.615 0.00 0.00 34.25 3.32
3113 6336 6.512741 CGGTTTTACAGAGCAGTAATTTGTGT 60.513 38.462 0.00 0.00 34.25 3.72
3114 6337 5.851177 CGGTTTTACAGAGCAGTAATTTGTG 59.149 40.000 0.00 0.00 34.25 3.33
3115 6338 5.048991 CCGGTTTTACAGAGCAGTAATTTGT 60.049 40.000 0.00 0.00 34.25 2.83
3116 6339 5.048991 ACCGGTTTTACAGAGCAGTAATTTG 60.049 40.000 0.00 0.00 34.25 2.32
3117 6340 5.067954 ACCGGTTTTACAGAGCAGTAATTT 58.932 37.500 0.00 0.00 34.25 1.82
3118 6341 4.648651 ACCGGTTTTACAGAGCAGTAATT 58.351 39.130 0.00 0.00 34.25 1.40
3119 6342 4.281898 ACCGGTTTTACAGAGCAGTAAT 57.718 40.909 0.00 0.00 34.25 1.89
3120 6343 3.756933 ACCGGTTTTACAGAGCAGTAA 57.243 42.857 0.00 0.00 32.46 2.24
3121 6344 3.756933 AACCGGTTTTACAGAGCAGTA 57.243 42.857 15.86 0.00 0.00 2.74
3122 6345 2.632987 AACCGGTTTTACAGAGCAGT 57.367 45.000 15.86 0.00 0.00 4.40
3123 6346 2.875933 TGAAACCGGTTTTACAGAGCAG 59.124 45.455 32.06 0.00 32.11 4.24
3124 6347 2.875933 CTGAAACCGGTTTTACAGAGCA 59.124 45.455 30.92 22.39 32.11 4.26
3125 6348 2.876550 ACTGAAACCGGTTTTACAGAGC 59.123 45.455 36.61 23.51 32.11 4.09
3126 6349 5.295152 ACTACTGAAACCGGTTTTACAGAG 58.705 41.667 36.61 30.53 32.11 3.35
3127 6350 5.069516 AGACTACTGAAACCGGTTTTACAGA 59.930 40.000 36.61 24.93 32.11 3.41
3128 6351 5.295152 AGACTACTGAAACCGGTTTTACAG 58.705 41.667 31.91 31.91 32.11 2.74
3159 6382 4.890581 AGCTCTACGGTAGTTCAGATGAAT 59.109 41.667 14.45 0.00 36.33 2.57
3210 6433 1.004758 AGGGCCCTGGCTGATAGAA 59.995 57.895 28.05 0.00 41.60 2.10
3211 6434 1.460305 GAGGGCCCTGGCTGATAGA 60.460 63.158 34.59 0.00 41.60 1.98
3212 6435 2.876945 CGAGGGCCCTGGCTGATAG 61.877 68.421 34.59 5.86 41.60 2.08
3213 6436 2.844362 CGAGGGCCCTGGCTGATA 60.844 66.667 34.59 0.00 41.60 2.15
3226 6449 3.605749 TTTTCTCCTGCCGGCGAGG 62.606 63.158 28.82 28.82 44.97 4.63
3227 6450 1.026718 ATTTTTCTCCTGCCGGCGAG 61.027 55.000 23.90 22.50 0.00 5.03
3228 6451 1.002624 ATTTTTCTCCTGCCGGCGA 60.003 52.632 23.90 13.24 0.00 5.54
3229 6452 1.137404 CATTTTTCTCCTGCCGGCG 59.863 57.895 23.90 16.52 0.00 6.46
3230 6453 1.153765 GCATTTTTCTCCTGCCGGC 60.154 57.895 22.73 22.73 0.00 6.13
3258 6481 5.971763 AGACTAGTTCCAGTTATCTGCAAG 58.028 41.667 0.00 0.00 40.09 4.01
3259 6482 7.039293 TGTTAGACTAGTTCCAGTTATCTGCAA 60.039 37.037 0.00 0.00 40.09 4.08
3260 6483 6.436218 TGTTAGACTAGTTCCAGTTATCTGCA 59.564 38.462 0.00 0.00 40.09 4.41
3261 6484 6.752815 GTGTTAGACTAGTTCCAGTTATCTGC 59.247 42.308 0.00 0.00 40.09 4.26
3264 6487 6.127786 ACCGTGTTAGACTAGTTCCAGTTATC 60.128 42.308 0.00 0.00 0.00 1.75
3265 6488 5.713861 ACCGTGTTAGACTAGTTCCAGTTAT 59.286 40.000 0.00 0.00 0.00 1.89
3266 6489 5.048504 CACCGTGTTAGACTAGTTCCAGTTA 60.049 44.000 0.00 0.00 0.00 2.24
3267 6490 3.893813 ACCGTGTTAGACTAGTTCCAGTT 59.106 43.478 0.00 0.00 0.00 3.16
3268 6491 3.255149 CACCGTGTTAGACTAGTTCCAGT 59.745 47.826 0.00 0.00 0.00 4.00
3269 6492 3.255149 ACACCGTGTTAGACTAGTTCCAG 59.745 47.826 0.00 0.00 0.00 3.86
3270 6493 3.225104 ACACCGTGTTAGACTAGTTCCA 58.775 45.455 0.00 0.00 0.00 3.53
3271 6494 3.930634 ACACCGTGTTAGACTAGTTCC 57.069 47.619 0.00 0.00 0.00 3.62
3272 6495 7.076842 TGTATACACCGTGTTAGACTAGTTC 57.923 40.000 9.98 0.00 0.00 3.01
3275 6498 6.674694 ACTGTATACACCGTGTTAGACTAG 57.325 41.667 9.98 8.23 0.00 2.57
3294 6517 9.838339 AGCTTGCTAAAATAGACAATATACTGT 57.162 29.630 0.00 0.00 0.00 3.55
3303 6526 9.938280 TTTAGTCTTAGCTTGCTAAAATAGACA 57.062 29.630 23.02 12.93 32.55 3.41
3305 6528 9.379791 GGTTTAGTCTTAGCTTGCTAAAATAGA 57.620 33.333 14.81 7.01 35.87 1.98
3308 6531 7.996098 TGGTTTAGTCTTAGCTTGCTAAAAT 57.004 32.000 14.81 8.76 35.87 1.82
3310 6533 9.109393 CATATGGTTTAGTCTTAGCTTGCTAAA 57.891 33.333 14.81 0.00 32.90 1.85
3311 6534 8.265055 ACATATGGTTTAGTCTTAGCTTGCTAA 58.735 33.333 13.52 13.52 0.00 3.09
3313 6536 6.653989 ACATATGGTTTAGTCTTAGCTTGCT 58.346 36.000 7.80 0.00 0.00 3.91
3314 6537 6.927294 ACATATGGTTTAGTCTTAGCTTGC 57.073 37.500 7.80 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.