Multiple sequence alignment - TraesCS5A01G361600

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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 TraesCS5A01G361600 chr5A 100.000 5602 0 0 1 5602 562895291 562889690 0.000000e+00 10346.0
1 TraesCS5A01G361600 chr5A 86.688 939 88 15 1680 2589 562992245 562991315 0.000000e+00 1007.0
2 TraesCS5A01G361600 chr5A 89.547 574 57 1 2956 3529 562977349 562976779 0.000000e+00 725.0
3 TraesCS5A01G361600 chr5A 78.116 690 147 4 2842 3529 563441172 563440485 8.620000e-118 435.0
4 TraesCS5A01G361600 chr5A 89.836 305 19 3 5132 5436 89705047 89705339 1.140000e-101 381.0
5 TraesCS5A01G361600 chr5A 95.455 154 7 0 5184 5337 631267121 631266968 4.330000e-61 246.0
6 TraesCS5A01G361600 chr5A 88.636 176 13 1 5434 5602 631266888 631266713 2.050000e-49 207.0
7 TraesCS5A01G361600 chr5A 87.931 174 14 5 5434 5600 549151013 549151186 1.230000e-46 198.0
8 TraesCS5A01G361600 chr5A 93.878 49 3 0 5390 5438 631266967 631266919 2.160000e-09 75.0
9 TraesCS5A01G361600 chr5B 96.033 2647 79 12 1 2632 542955367 542952732 0.000000e+00 4283.0
10 TraesCS5A01G361600 chr5B 97.265 914 21 2 2833 3744 542952734 542951823 0.000000e+00 1546.0
11 TraesCS5A01G361600 chr5B 84.951 1422 125 44 1193 2595 542983400 542982049 0.000000e+00 1358.0
12 TraesCS5A01G361600 chr5B 82.291 1135 153 23 2833 3961 542982005 542980913 0.000000e+00 939.0
13 TraesCS5A01G361600 chr5B 81.906 724 68 33 3742 4452 542951666 542950993 2.280000e-153 553.0
14 TraesCS5A01G361600 chr5B 89.521 334 23 5 4566 4898 542950954 542950632 4.040000e-111 412.0
15 TraesCS5A01G361600 chr5B 98.990 198 1 1 2635 2832 251568512 251568708 2.480000e-93 353.0
16 TraesCS5A01G361600 chr5B 91.515 165 13 1 674 837 542983651 542983487 5.650000e-55 226.0
17 TraesCS5A01G361600 chr5B 94.231 104 5 1 5032 5134 542950619 542950516 2.090000e-34 158.0
18 TraesCS5A01G361600 chr5B 97.222 36 1 0 207 242 542955257 542955222 1.690000e-05 62.1
19 TraesCS5A01G361600 chr5D 90.606 2342 135 42 2833 5134 445318989 445316693 0.000000e+00 3027.0
20 TraesCS5A01G361600 chr5D 96.693 1391 35 4 1252 2632 445320376 445318987 0.000000e+00 2303.0
21 TraesCS5A01G361600 chr5D 94.519 1186 47 10 1 1179 445321572 445320398 0.000000e+00 1814.0
22 TraesCS5A01G361600 chr5D 88.241 978 87 11 1680 2632 445378708 445377734 0.000000e+00 1144.0
23 TraesCS5A01G361600 chr5D 89.383 697 71 1 2833 3529 445377736 445377043 0.000000e+00 874.0
24 TraesCS5A01G361600 chr5D 83.996 956 79 23 709 1637 445379611 445378703 0.000000e+00 850.0
25 TraesCS5A01G361600 chr5D 94.426 305 16 1 5132 5436 530155930 530155627 8.500000e-128 468.0
26 TraesCS5A01G361600 chr5D 79.059 425 61 23 3610 4020 445376997 445376587 3.330000e-67 267.0
27 TraesCS5A01G361600 chr5D 90.909 176 9 5 5434 5602 530155594 530155419 4.370000e-56 230.0
28 TraesCS5A01G361600 chr5D 97.222 36 1 0 207 242 445321462 445321427 1.690000e-05 62.1
29 TraesCS5A01G361600 chr4B 94.805 308 16 0 5132 5439 584950106 584950413 1.090000e-131 481.0
30 TraesCS5A01G361600 chr4B 86.364 176 16 4 5434 5602 584950443 584950617 9.580000e-43 185.0
31 TraesCS5A01G361600 chr4D 93.871 310 12 3 5132 5438 477757849 477757544 1.420000e-125 460.0
32 TraesCS5A01G361600 chr4D 78.287 677 137 6 2842 3511 4030894 4030221 1.440000e-115 427.0
33 TraesCS5A01G361600 chr4D 90.722 194 17 1 5245 5438 488659312 488659120 2.000000e-64 257.0
34 TraesCS5A01G361600 chr4D 90.341 176 10 3 5434 5602 477757513 477757338 2.030000e-54 224.0
35 TraesCS5A01G361600 chr3A 93.811 307 18 1 5132 5438 610039967 610040272 1.420000e-125 460.0
36 TraesCS5A01G361600 chr4A 91.503 306 25 1 5132 5437 146696683 146696987 2.410000e-113 420.0
37 TraesCS5A01G361600 chr4A 98.122 213 2 2 2635 2847 76927909 76927699 2.470000e-98 370.0
38 TraesCS5A01G361600 chr2D 77.810 685 146 6 2847 3528 7587600 7586919 8.680000e-113 418.0
39 TraesCS5A01G361600 chr7B 89.474 304 29 3 5135 5438 498565142 498564842 1.140000e-101 381.0
40 TraesCS5A01G361600 chr7B 98.522 203 2 1 2635 2837 388817319 388817520 1.920000e-94 357.0
41 TraesCS5A01G361600 chr7B 98.030 203 3 1 2635 2837 388798059 388798260 8.930000e-93 351.0
42 TraesCS5A01G361600 chr6A 99.500 200 0 1 2635 2834 49403817 49403619 4.130000e-96 363.0
43 TraesCS5A01G361600 chr2A 99.000 200 0 2 2635 2833 196117774 196117972 1.920000e-94 357.0
44 TraesCS5A01G361600 chr1B 99.000 200 1 1 2635 2834 229951330 229951132 1.920000e-94 357.0
45 TraesCS5A01G361600 chr7A 98.995 199 0 2 2635 2832 142528061 142528258 6.900000e-94 355.0
46 TraesCS5A01G361600 chr7A 83.251 203 32 1 5141 5343 671744059 671744259 9.580000e-43 185.0
47 TraesCS5A01G361600 chr7A 84.302 172 25 2 722 892 7828170 7828340 3.470000e-37 167.0
48 TraesCS5A01G361600 chr2B 98.030 203 3 1 2635 2837 290527007 290527208 8.930000e-93 351.0
49 TraesCS5A01G361600 chr2B 74.625 800 167 27 1803 2590 9106431 9105656 2.520000e-83 320.0
50 TraesCS5A01G361600 chr6D 91.667 144 11 1 926 1069 12035372 12035514 1.230000e-46 198.0


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 TraesCS5A01G361600 chr5A 562889690 562895291 5601 True 10346.000000 10346 100.000000 1 5602 1 chr5A.!!$R1 5601
1 TraesCS5A01G361600 chr5A 562991315 562992245 930 True 1007.000000 1007 86.688000 1680 2589 1 chr5A.!!$R3 909
2 TraesCS5A01G361600 chr5A 562976779 562977349 570 True 725.000000 725 89.547000 2956 3529 1 chr5A.!!$R2 573
3 TraesCS5A01G361600 chr5A 563440485 563441172 687 True 435.000000 435 78.116000 2842 3529 1 chr5A.!!$R4 687
4 TraesCS5A01G361600 chr5B 542950516 542955367 4851 True 1169.016667 4283 92.696333 1 5134 6 chr5B.!!$R1 5133
5 TraesCS5A01G361600 chr5B 542980913 542983651 2738 True 841.000000 1358 86.252333 674 3961 3 chr5B.!!$R2 3287
6 TraesCS5A01G361600 chr5D 445316693 445321572 4879 True 1801.525000 3027 94.760000 1 5134 4 chr5D.!!$R1 5133
7 TraesCS5A01G361600 chr5D 445376587 445379611 3024 True 783.750000 1144 85.169750 709 4020 4 chr5D.!!$R2 3311
8 TraesCS5A01G361600 chr5D 530155419 530155930 511 True 349.000000 468 92.667500 5132 5602 2 chr5D.!!$R3 470
9 TraesCS5A01G361600 chr4B 584950106 584950617 511 False 333.000000 481 90.584500 5132 5602 2 chr4B.!!$F1 470
10 TraesCS5A01G361600 chr4D 4030221 4030894 673 True 427.000000 427 78.287000 2842 3511 1 chr4D.!!$R1 669
11 TraesCS5A01G361600 chr4D 477757338 477757849 511 True 342.000000 460 92.106000 5132 5602 2 chr4D.!!$R3 470
12 TraesCS5A01G361600 chr2D 7586919 7587600 681 True 418.000000 418 77.810000 2847 3528 1 chr2D.!!$R1 681
13 TraesCS5A01G361600 chr2B 9105656 9106431 775 True 320.000000 320 74.625000 1803 2590 1 chr2B.!!$R1 787

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
86 87 1.405121 GCGGGTCTACTTTCAATCGGT 60.405 52.381 0.00 0.00 0.00 4.69 F
1083 1093 1.143684 ACTTTGCTTCCTCTGCTGGAA 59.856 47.619 6.32 6.32 43.16 3.53 F
2047 2147 0.748005 CCGGGATGCGGTTCTTCATT 60.748 55.000 0.00 0.00 0.00 2.57 F
2672 2790 0.121197 TCTCCCAGAATTGACCCCCT 59.879 55.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1729 0.037326 TAGCAGCAGCCACTACACAC 60.037 55.000 0.00 0.00 43.56 3.82 R
2357 2457 0.108585 ACGCCAAAGACTGTCATGGT 59.891 50.000 24.46 10.53 35.34 3.55 R
3013 3131 1.137404 CATGGGCTACTTTGTGCGC 59.863 57.895 0.00 0.00 41.57 6.09 R
4649 5021 0.257905 ATCTGCTGATGTGCCCATGT 59.742 50.000 5.15 0.00 0.00 3.21 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
52 53 6.647334 TGTCCAAAGCATGTAAAATCTGAA 57.353 33.333 0.00 0.00 0.00 3.02
69 70 3.850098 AACAAGTCCTGCCCAGCGG 62.850 63.158 0.00 0.00 34.23 5.52
86 87 1.405121 GCGGGTCTACTTTCAATCGGT 60.405 52.381 0.00 0.00 0.00 4.69
87 88 2.159198 GCGGGTCTACTTTCAATCGGTA 60.159 50.000 0.00 0.00 0.00 4.02
88 89 3.492137 GCGGGTCTACTTTCAATCGGTAT 60.492 47.826 0.00 0.00 0.00 2.73
139 140 5.647658 ACTAGGTCATTCGATGCAAATCAAA 59.352 36.000 0.00 0.00 0.00 2.69
163 164 6.621737 TTAAGACGTGCTTCTGTAAATACG 57.378 37.500 0.00 0.00 38.05 3.06
192 193 2.676750 CGTTGCTGCCTAGGTACATGAA 60.677 50.000 11.31 0.00 0.00 2.57
584 586 4.688879 CCACGCAATGTCTGTACTTTTCTA 59.311 41.667 0.00 0.00 0.00 2.10
911 915 5.187186 CGTATATCCTGGCCTATGGTAAGTT 59.813 44.000 3.32 0.00 0.00 2.66
919 923 3.432326 GGCCTATGGTAAGTTCTCAGGTG 60.432 52.174 0.00 0.00 0.00 4.00
1035 1045 2.042297 TCCTCGATCTAGCAGGATGGAT 59.958 50.000 4.68 0.00 35.86 3.41
1083 1093 1.143684 ACTTTGCTTCCTCTGCTGGAA 59.856 47.619 6.32 6.32 43.16 3.53
1124 1134 4.471904 TTCTGCATCTGGTTAGTCGATT 57.528 40.909 0.00 0.00 0.00 3.34
1207 1227 2.811431 TGTCTGCATTTTAGTGGAACCG 59.189 45.455 0.00 0.00 37.80 4.44
1228 1248 4.035091 CCGTCGGCTTTATTCATTCATTCA 59.965 41.667 0.00 0.00 0.00 2.57
1231 1251 5.743872 GTCGGCTTTATTCATTCATTCAACC 59.256 40.000 0.00 0.00 0.00 3.77
1234 1284 7.012327 TCGGCTTTATTCATTCATTCAACCTAG 59.988 37.037 0.00 0.00 0.00 3.02
1245 1295 9.784531 CATTCATTCAACCTAGTATTATCTGGT 57.215 33.333 0.00 0.00 0.00 4.00
1246 1296 9.784531 ATTCATTCAACCTAGTATTATCTGGTG 57.215 33.333 0.00 0.00 0.00 4.17
1247 1297 8.547481 TCATTCAACCTAGTATTATCTGGTGA 57.453 34.615 0.00 0.00 0.00 4.02
1248 1298 8.988060 TCATTCAACCTAGTATTATCTGGTGAA 58.012 33.333 0.00 0.00 0.00 3.18
1249 1299 9.613428 CATTCAACCTAGTATTATCTGGTGAAA 57.387 33.333 0.00 0.00 0.00 2.69
1362 1421 2.046023 TTGAGCTGGATGCCCGTG 60.046 61.111 0.00 0.00 44.23 4.94
1497 1568 1.411246 GGAGGTACCATACGCATGACA 59.589 52.381 15.94 0.00 38.79 3.58
1636 1709 3.547601 GTGCACCAAAACGTATGTGTAC 58.452 45.455 5.22 10.38 37.21 2.90
1777 1863 2.196595 CATCCAAGTAGTCCTCCCCAA 58.803 52.381 0.00 0.00 0.00 4.12
2047 2147 0.748005 CCGGGATGCGGTTCTTCATT 60.748 55.000 0.00 0.00 0.00 2.57
2357 2457 4.454161 CGAGGTTAATGTTTGACATCACCA 59.546 41.667 17.78 0.00 41.16 4.17
2600 2718 0.322546 GAAGACCAACGGAGGCCAAT 60.323 55.000 5.01 0.00 0.00 3.16
2632 2750 4.251103 AGAGGTTGTGGGGGATATTTTC 57.749 45.455 0.00 0.00 0.00 2.29
2633 2751 3.596046 AGAGGTTGTGGGGGATATTTTCA 59.404 43.478 0.00 0.00 0.00 2.69
2634 2752 3.954258 GAGGTTGTGGGGGATATTTTCAG 59.046 47.826 0.00 0.00 0.00 3.02
2635 2753 2.430694 GGTTGTGGGGGATATTTTCAGC 59.569 50.000 0.00 0.00 0.00 4.26
2636 2754 2.430694 GTTGTGGGGGATATTTTCAGCC 59.569 50.000 0.00 0.00 0.00 4.85
2637 2755 1.643286 TGTGGGGGATATTTTCAGCCA 59.357 47.619 0.00 0.00 0.00 4.75
2638 2756 2.310538 GTGGGGGATATTTTCAGCCAG 58.689 52.381 0.00 0.00 0.00 4.85
2639 2757 1.929494 TGGGGGATATTTTCAGCCAGT 59.071 47.619 0.00 0.00 0.00 4.00
2640 2758 2.314549 TGGGGGATATTTTCAGCCAGTT 59.685 45.455 0.00 0.00 0.00 3.16
2641 2759 2.959030 GGGGGATATTTTCAGCCAGTTC 59.041 50.000 0.00 0.00 0.00 3.01
2642 2760 3.373110 GGGGGATATTTTCAGCCAGTTCT 60.373 47.826 0.00 0.00 0.00 3.01
2643 2761 4.281657 GGGGATATTTTCAGCCAGTTCTT 58.718 43.478 0.00 0.00 0.00 2.52
2644 2762 4.711846 GGGGATATTTTCAGCCAGTTCTTT 59.288 41.667 0.00 0.00 0.00 2.52
2645 2763 5.187772 GGGGATATTTTCAGCCAGTTCTTTT 59.812 40.000 0.00 0.00 0.00 2.27
2646 2764 6.101997 GGGATATTTTCAGCCAGTTCTTTTG 58.898 40.000 0.00 0.00 0.00 2.44
2647 2765 6.101997 GGATATTTTCAGCCAGTTCTTTTGG 58.898 40.000 0.00 0.00 38.78 3.28
2648 2766 3.817709 TTTTCAGCCAGTTCTTTTGGG 57.182 42.857 0.00 0.00 36.19 4.12
2649 2767 1.039856 TTCAGCCAGTTCTTTTGGGC 58.960 50.000 0.00 0.00 46.77 5.36
2653 2771 2.549064 GCCAGTTCTTTTGGGCAATT 57.451 45.000 0.00 0.00 45.70 2.32
2654 2772 2.416747 GCCAGTTCTTTTGGGCAATTC 58.583 47.619 0.00 0.00 45.70 2.17
2655 2773 2.037641 GCCAGTTCTTTTGGGCAATTCT 59.962 45.455 0.00 0.00 45.70 2.40
2656 2774 3.862264 GCCAGTTCTTTTGGGCAATTCTC 60.862 47.826 0.00 0.00 45.70 2.87
2657 2775 3.306294 CCAGTTCTTTTGGGCAATTCTCC 60.306 47.826 0.00 0.00 31.87 3.71
2658 2776 2.899900 AGTTCTTTTGGGCAATTCTCCC 59.100 45.455 5.52 5.52 44.17 4.30
2671 2789 0.999712 TTCTCCCAGAATTGACCCCC 59.000 55.000 0.00 0.00 0.00 5.40
2672 2790 0.121197 TCTCCCAGAATTGACCCCCT 59.879 55.000 0.00 0.00 0.00 4.79
2673 2791 0.548510 CTCCCAGAATTGACCCCCTC 59.451 60.000 0.00 0.00 0.00 4.30
2674 2792 0.919289 TCCCAGAATTGACCCCCTCC 60.919 60.000 0.00 0.00 0.00 4.30
2675 2793 1.615262 CCAGAATTGACCCCCTCCC 59.385 63.158 0.00 0.00 0.00 4.30
2676 2794 1.615262 CAGAATTGACCCCCTCCCC 59.385 63.158 0.00 0.00 0.00 4.81
2677 2795 1.165782 AGAATTGACCCCCTCCCCA 59.834 57.895 0.00 0.00 0.00 4.96
2678 2796 0.921256 AGAATTGACCCCCTCCCCAG 60.921 60.000 0.00 0.00 0.00 4.45
2679 2797 2.573893 GAATTGACCCCCTCCCCAGC 62.574 65.000 0.00 0.00 0.00 4.85
2680 2798 3.603330 ATTGACCCCCTCCCCAGCT 62.603 63.158 0.00 0.00 0.00 4.24
2681 2799 3.829311 TTGACCCCCTCCCCAGCTT 62.829 63.158 0.00 0.00 0.00 3.74
2682 2800 3.412408 GACCCCCTCCCCAGCTTC 61.412 72.222 0.00 0.00 0.00 3.86
2683 2801 3.952799 GACCCCCTCCCCAGCTTCT 62.953 68.421 0.00 0.00 0.00 2.85
2684 2802 3.093172 CCCCCTCCCCAGCTTCTC 61.093 72.222 0.00 0.00 0.00 2.87
2685 2803 3.093172 CCCCTCCCCAGCTTCTCC 61.093 72.222 0.00 0.00 0.00 3.71
2686 2804 3.093172 CCCTCCCCAGCTTCTCCC 61.093 72.222 0.00 0.00 0.00 4.30
2687 2805 2.285668 CCTCCCCAGCTTCTCCCA 60.286 66.667 0.00 0.00 0.00 4.37
2688 2806 2.373707 CCTCCCCAGCTTCTCCCAG 61.374 68.421 0.00 0.00 0.00 4.45
2689 2807 1.306482 CTCCCCAGCTTCTCCCAGA 60.306 63.158 0.00 0.00 0.00 3.86
2690 2808 0.911525 CTCCCCAGCTTCTCCCAGAA 60.912 60.000 0.00 0.00 32.50 3.02
2691 2809 0.253347 TCCCCAGCTTCTCCCAGAAT 60.253 55.000 0.00 0.00 33.13 2.40
2692 2810 0.627986 CCCCAGCTTCTCCCAGAATT 59.372 55.000 0.00 0.00 33.13 2.17
2693 2811 1.684248 CCCCAGCTTCTCCCAGAATTG 60.684 57.143 0.00 0.00 33.13 2.32
2694 2812 1.101331 CCAGCTTCTCCCAGAATTGC 58.899 55.000 0.00 0.00 33.13 3.56
2695 2813 1.101331 CAGCTTCTCCCAGAATTGCC 58.899 55.000 0.00 0.00 33.13 4.52
2696 2814 0.700564 AGCTTCTCCCAGAATTGCCA 59.299 50.000 0.00 0.00 33.13 4.92
2697 2815 0.813821 GCTTCTCCCAGAATTGCCAC 59.186 55.000 0.00 0.00 33.13 5.01
2698 2816 1.615384 GCTTCTCCCAGAATTGCCACT 60.615 52.381 0.00 0.00 33.13 4.00
2699 2817 2.800250 CTTCTCCCAGAATTGCCACTT 58.200 47.619 0.00 0.00 33.13 3.16
2700 2818 3.873801 GCTTCTCCCAGAATTGCCACTTA 60.874 47.826 0.00 0.00 33.13 2.24
2701 2819 4.335416 CTTCTCCCAGAATTGCCACTTAA 58.665 43.478 0.00 0.00 33.13 1.85
2702 2820 4.591321 TCTCCCAGAATTGCCACTTAAT 57.409 40.909 0.00 0.00 0.00 1.40
2703 2821 5.708736 TCTCCCAGAATTGCCACTTAATA 57.291 39.130 0.00 0.00 0.00 0.98
2704 2822 6.266131 TCTCCCAGAATTGCCACTTAATAT 57.734 37.500 0.00 0.00 0.00 1.28
2705 2823 6.672593 TCTCCCAGAATTGCCACTTAATATT 58.327 36.000 0.00 0.00 0.00 1.28
2706 2824 7.125391 TCTCCCAGAATTGCCACTTAATATTT 58.875 34.615 0.00 0.00 0.00 1.40
2707 2825 7.619302 TCTCCCAGAATTGCCACTTAATATTTT 59.381 33.333 0.00 0.00 0.00 1.82
2708 2826 8.144862 TCCCAGAATTGCCACTTAATATTTTT 57.855 30.769 0.00 0.00 0.00 1.94
2733 2851 9.662947 TTTTACAATTCCTAGCTAGTTAAGGTC 57.337 33.333 19.31 0.00 37.13 3.85
2734 2852 8.605325 TTACAATTCCTAGCTAGTTAAGGTCT 57.395 34.615 19.31 0.00 37.13 3.85
2735 2853 9.705103 TTACAATTCCTAGCTAGTTAAGGTCTA 57.295 33.333 19.31 5.95 37.13 2.59
2736 2854 8.605325 ACAATTCCTAGCTAGTTAAGGTCTAA 57.395 34.615 19.31 0.00 37.13 2.10
2737 2855 9.214962 ACAATTCCTAGCTAGTTAAGGTCTAAT 57.785 33.333 19.31 0.19 37.13 1.73
2741 2859 8.406730 TCCTAGCTAGTTAAGGTCTAATTAGC 57.593 38.462 19.31 9.70 40.67 3.09
2743 2861 9.517868 CCTAGCTAGTTAAGGTCTAATTAGCTA 57.482 37.037 19.31 19.29 45.18 3.32
2745 2863 8.411991 AGCTAGTTAAGGTCTAATTAGCTAGG 57.588 38.462 15.72 0.00 45.18 3.02
2746 2864 8.226112 AGCTAGTTAAGGTCTAATTAGCTAGGA 58.774 37.037 15.72 0.00 45.18 2.94
2747 2865 8.858094 GCTAGTTAAGGTCTAATTAGCTAGGAA 58.142 37.037 7.67 0.00 41.05 3.36
2751 2869 9.833917 GTTAAGGTCTAATTAGCTAGGAATTGT 57.166 33.333 7.67 0.00 0.00 2.71
2779 2897 7.732222 AAAATATTAAGTGGCAATTCTGGGA 57.268 32.000 2.32 0.00 0.00 4.37
2780 2898 6.966534 AATATTAAGTGGCAATTCTGGGAG 57.033 37.500 2.32 0.00 0.00 4.30
2781 2899 4.591321 ATTAAGTGGCAATTCTGGGAGA 57.409 40.909 2.32 0.00 0.00 3.71
2782 2900 2.978156 AAGTGGCAATTCTGGGAGAA 57.022 45.000 0.00 0.00 38.78 2.87
2783 2901 2.503895 AGTGGCAATTCTGGGAGAAG 57.496 50.000 0.00 0.00 37.69 2.85
2784 2902 0.813821 GTGGCAATTCTGGGAGAAGC 59.186 55.000 0.00 0.00 37.69 3.86
2785 2903 0.700564 TGGCAATTCTGGGAGAAGCT 59.299 50.000 0.00 0.00 37.69 3.74
2786 2904 1.101331 GGCAATTCTGGGAGAAGCTG 58.899 55.000 0.00 0.00 37.69 4.24
2787 2905 1.101331 GCAATTCTGGGAGAAGCTGG 58.899 55.000 0.00 0.00 37.69 4.85
2788 2906 1.760192 CAATTCTGGGAGAAGCTGGG 58.240 55.000 0.00 0.00 37.69 4.45
2789 2907 0.627986 AATTCTGGGAGAAGCTGGGG 59.372 55.000 0.00 0.00 37.69 4.96
2790 2908 0.253347 ATTCTGGGAGAAGCTGGGGA 60.253 55.000 0.00 0.00 37.69 4.81
2791 2909 0.911525 TTCTGGGAGAAGCTGGGGAG 60.912 60.000 0.00 0.00 29.50 4.30
2792 2910 2.285668 TGGGAGAAGCTGGGGAGG 60.286 66.667 0.00 0.00 0.00 4.30
2793 2911 3.093172 GGGAGAAGCTGGGGAGGG 61.093 72.222 0.00 0.00 0.00 4.30
2794 2912 3.093172 GGAGAAGCTGGGGAGGGG 61.093 72.222 0.00 0.00 0.00 4.79
2795 2913 3.093172 GAGAAGCTGGGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
2810 2928 2.709992 GGGGGTCAATTCTGGGAGA 58.290 57.895 0.00 0.00 0.00 3.71
2811 2929 0.999712 GGGGGTCAATTCTGGGAGAA 59.000 55.000 0.00 0.00 38.78 2.87
2812 2930 1.570979 GGGGGTCAATTCTGGGAGAAT 59.429 52.381 0.00 0.00 46.22 2.40
2825 2943 3.319137 GGGAGAATTGCCCAAAAGAAC 57.681 47.619 7.89 0.00 45.31 3.01
2826 2944 2.899900 GGGAGAATTGCCCAAAAGAACT 59.100 45.455 7.89 0.00 45.31 3.01
2827 2945 3.306294 GGGAGAATTGCCCAAAAGAACTG 60.306 47.826 7.89 0.00 45.31 3.16
2828 2946 3.306294 GGAGAATTGCCCAAAAGAACTGG 60.306 47.826 0.00 0.00 0.00 4.00
2829 2947 2.037641 AGAATTGCCCAAAAGAACTGGC 59.962 45.455 0.00 0.00 44.27 4.85
2830 2948 0.686789 ATTGCCCAAAAGAACTGGCC 59.313 50.000 0.00 0.00 43.35 5.36
2831 2949 1.406860 TTGCCCAAAAGAACTGGCCC 61.407 55.000 0.00 0.00 43.35 5.80
2832 2950 1.533994 GCCCAAAAGAACTGGCCCT 60.534 57.895 0.00 0.00 37.94 5.19
2833 2951 1.121407 GCCCAAAAGAACTGGCCCTT 61.121 55.000 0.00 0.00 37.94 3.95
2834 2952 1.423584 CCCAAAAGAACTGGCCCTTT 58.576 50.000 0.00 0.00 34.39 3.11
3013 3131 5.233050 CGTAATGAACTCTCACCTATTGCAG 59.767 44.000 0.00 0.00 33.30 4.41
3058 3176 0.684535 TGCCACGGTCATCTTTGAGA 59.315 50.000 0.00 0.00 30.85 3.27
3425 3548 0.317020 GCAGTCGTGTGGAACTTTGC 60.317 55.000 0.00 0.00 38.04 3.68
3441 3564 4.106925 GCCCTGGAGCTGGTGGAG 62.107 72.222 0.00 0.00 0.00 3.86
3459 3582 1.817099 GAGCCAGAGCATCCAACCG 60.817 63.158 0.00 0.00 43.56 4.44
3632 3804 7.766738 ACGTGTGTGTCCATATACATATTTTCA 59.233 33.333 0.00 0.00 0.00 2.69
3732 3908 1.811965 TGGATGGTGCAAATGTTCTCG 59.188 47.619 0.00 0.00 0.00 4.04
3806 4143 9.408648 AGATTATCCAAGTAAATGACCGAAAAT 57.591 29.630 0.00 0.00 0.00 1.82
3893 4237 3.648009 GAGACGATGCCTCCTTATTGAG 58.352 50.000 0.00 0.00 0.00 3.02
3940 4288 4.887748 TGAACTGTTTGTTTTTCTTGCCA 58.112 34.783 0.00 0.00 39.30 4.92
3941 4289 4.928615 TGAACTGTTTGTTTTTCTTGCCAG 59.071 37.500 0.00 0.00 39.30 4.85
3966 4319 5.678483 GCACACAGACATATATTTTTCAGCG 59.322 40.000 0.00 0.00 0.00 5.18
4093 4454 7.118101 GCAAATCTCAAGCACCAAATTCAATTA 59.882 33.333 0.00 0.00 0.00 1.40
4125 4486 4.081531 ACAAGGATGTTTTGGTGGCATATG 60.082 41.667 0.00 0.00 35.91 1.78
4138 4499 6.486056 TGGTGGCATATGTAAGGAGTTTTTA 58.514 36.000 4.29 0.00 0.00 1.52
4140 4501 7.617723 TGGTGGCATATGTAAGGAGTTTTTAAT 59.382 33.333 4.29 0.00 0.00 1.40
4141 4502 8.474831 GGTGGCATATGTAAGGAGTTTTTAATT 58.525 33.333 4.29 0.00 0.00 1.40
4172 4533 4.481112 CAGTCAATTGCCCGCGCC 62.481 66.667 0.00 0.00 0.00 6.53
4273 4635 1.831580 GCTTCTGGCTGGAATTGACT 58.168 50.000 0.00 0.00 38.06 3.41
4282 4644 0.040058 TGGAATTGACTGGCCATGCT 59.960 50.000 5.51 0.00 0.00 3.79
4308 4674 2.159085 GCCTACTGAGAGCGTATTTGGT 60.159 50.000 0.00 0.00 0.00 3.67
4361 4727 2.911928 TGGCACAACCGGAAGACA 59.088 55.556 9.46 0.00 43.94 3.41
4365 4731 1.497278 CACAACCGGAAGACATGCG 59.503 57.895 9.46 0.00 43.28 4.73
4432 4804 2.646930 CATGAAGCCCTGCAACTCATA 58.353 47.619 0.00 0.00 0.00 2.15
4433 4805 3.220110 CATGAAGCCCTGCAACTCATAT 58.780 45.455 0.00 0.00 0.00 1.78
4499 4871 2.945668 GGAAGATCAAATCAAGGACCCG 59.054 50.000 0.00 0.00 0.00 5.28
4561 4933 2.488952 TGCTTCATACGAACAAGTGCA 58.511 42.857 0.00 0.00 0.00 4.57
4648 5020 6.769822 CCATGGATTTCTGCTTCTACTACATT 59.230 38.462 5.56 0.00 0.00 2.71
4649 5021 7.933577 CCATGGATTTCTGCTTCTACTACATTA 59.066 37.037 5.56 0.00 0.00 1.90
4650 5022 8.768955 CATGGATTTCTGCTTCTACTACATTAC 58.231 37.037 0.00 0.00 0.00 1.89
4651 5023 7.847096 TGGATTTCTGCTTCTACTACATTACA 58.153 34.615 0.00 0.00 0.00 2.41
4652 5024 8.486210 TGGATTTCTGCTTCTACTACATTACAT 58.514 33.333 0.00 0.00 0.00 2.29
4657 5029 4.163268 TGCTTCTACTACATTACATGGGCA 59.837 41.667 0.00 0.00 33.60 5.36
4670 5042 0.534427 ATGGGCACATCAGCAGATCG 60.534 55.000 0.00 0.00 35.83 3.69
4681 5056 1.067416 GCAGATCGCCGATGTACCA 59.933 57.895 3.34 0.00 32.94 3.25
4685 5060 0.102481 GATCGCCGATGTACCACTGT 59.898 55.000 3.34 0.00 0.00 3.55
4693 5068 2.066262 GATGTACCACTGTTCGGTGTG 58.934 52.381 10.31 5.26 37.33 3.82
4699 5074 1.364721 CACTGTTCGGTGTGTTCACA 58.635 50.000 1.23 1.23 45.45 3.58
4737 5115 2.980233 GGGTGTGCTGTCTGGTGC 60.980 66.667 0.00 0.00 0.00 5.01
4756 5134 1.186200 CGGAAGATCTCCTCACCACA 58.814 55.000 0.00 0.00 42.85 4.17
4766 5144 3.011821 TCTCCTCACCACAGTAGATCCTT 59.988 47.826 0.00 0.00 0.00 3.36
4803 5181 1.064463 TCCATGGAAGGTGATTGAGGC 60.064 52.381 13.46 0.00 0.00 4.70
4815 5194 1.217057 ATTGAGGCCTGTGGGTGGAT 61.217 55.000 12.00 0.00 34.45 3.41
4819 5198 0.624500 AGGCCTGTGGGTGGATATGT 60.625 55.000 3.11 0.00 34.45 2.29
4842 5221 1.439644 CTTCTCCTCGGCCAGTAGC 59.560 63.158 2.24 0.00 42.60 3.58
4843 5222 1.304962 TTCTCCTCGGCCAGTAGCA 60.305 57.895 2.24 0.00 46.50 3.49
4845 5224 2.037367 TCCTCGGCCAGTAGCAGT 59.963 61.111 2.24 0.00 46.50 4.40
4846 5225 0.752009 CTCCTCGGCCAGTAGCAGTA 60.752 60.000 2.24 0.00 46.50 2.74
4847 5226 0.752009 TCCTCGGCCAGTAGCAGTAG 60.752 60.000 2.24 0.00 46.50 2.57
4848 5227 1.736586 CTCGGCCAGTAGCAGTAGG 59.263 63.158 2.24 0.00 46.50 3.18
4849 5228 1.000019 TCGGCCAGTAGCAGTAGGT 60.000 57.895 2.24 0.00 46.50 3.08
4850 5229 1.141881 CGGCCAGTAGCAGTAGGTG 59.858 63.158 2.24 0.00 46.50 4.00
4851 5230 1.605058 CGGCCAGTAGCAGTAGGTGT 61.605 60.000 2.24 0.00 46.50 4.16
4852 5231 0.175989 GGCCAGTAGCAGTAGGTGTC 59.824 60.000 0.00 0.00 46.50 3.67
4901 5280 4.154347 CACGGAGGGGAGCTGCTC 62.154 72.222 21.17 21.17 0.00 4.26
4902 5281 4.704103 ACGGAGGGGAGCTGCTCA 62.704 66.667 28.95 0.00 31.08 4.26
4905 5284 2.373707 GGAGGGGAGCTGCTCACAT 61.374 63.158 30.98 26.16 35.24 3.21
4906 5285 1.050988 GGAGGGGAGCTGCTCACATA 61.051 60.000 30.98 0.00 35.24 2.29
4907 5286 1.055040 GAGGGGAGCTGCTCACATAT 58.945 55.000 30.98 17.42 35.24 1.78
4908 5287 2.251818 GAGGGGAGCTGCTCACATATA 58.748 52.381 30.98 0.00 35.24 0.86
4909 5288 1.974236 AGGGGAGCTGCTCACATATAC 59.026 52.381 30.98 14.74 35.24 1.47
4910 5289 1.974236 GGGGAGCTGCTCACATATACT 59.026 52.381 30.98 0.00 35.24 2.12
4912 5291 2.028567 GGGAGCTGCTCACATATACTCC 60.029 54.545 28.95 14.68 41.21 3.85
4913 5292 2.896685 GGAGCTGCTCACATATACTCCT 59.103 50.000 28.95 0.00 39.30 3.69
4914 5293 4.082845 GGAGCTGCTCACATATACTCCTA 58.917 47.826 28.95 0.00 39.30 2.94
4928 5307 1.482593 ACTCCTATTTGGCTCCTGTCG 59.517 52.381 0.00 0.00 35.26 4.35
4933 5312 0.254178 ATTTGGCTCCTGTCGCTCAT 59.746 50.000 0.00 0.00 0.00 2.90
4934 5313 0.674581 TTTGGCTCCTGTCGCTCATG 60.675 55.000 0.00 0.00 0.00 3.07
4935 5314 2.202987 GGCTCCTGTCGCTCATGG 60.203 66.667 0.00 0.00 0.00 3.66
4936 5315 2.202987 GCTCCTGTCGCTCATGGG 60.203 66.667 0.00 0.00 0.00 4.00
4937 5316 2.503061 CTCCTGTCGCTCATGGGG 59.497 66.667 0.00 0.00 0.00 4.96
4939 5318 1.383109 TCCTGTCGCTCATGGGGAT 60.383 57.895 0.00 0.00 39.09 3.85
4943 5322 1.271127 TGTCGCTCATGGGGATGGAA 61.271 55.000 0.00 0.00 39.09 3.53
4944 5323 0.107214 GTCGCTCATGGGGATGGAAA 60.107 55.000 0.00 0.00 39.09 3.13
4970 5353 1.514553 CGAGAGGCTGCAGATGACA 59.485 57.895 20.43 0.00 0.00 3.58
4987 5370 1.000163 GACAGAGCTTTCGAGTGGACA 60.000 52.381 0.00 0.00 0.00 4.02
5024 5407 0.622665 CTCCATCAACTTCCCAGGCT 59.377 55.000 0.00 0.00 0.00 4.58
5027 5410 1.561542 CCATCAACTTCCCAGGCTAGT 59.438 52.381 0.00 0.00 0.00 2.57
5028 5411 2.771943 CCATCAACTTCCCAGGCTAGTA 59.228 50.000 0.00 0.00 0.00 1.82
5030 5413 2.185387 TCAACTTCCCAGGCTAGTACC 58.815 52.381 0.00 0.00 0.00 3.34
5033 5416 2.351336 CTTCCCAGGCTAGTACCGCG 62.351 65.000 0.00 0.00 33.69 6.46
5035 5418 2.420568 CCCAGGCTAGTACCGCGAA 61.421 63.158 8.23 0.00 33.69 4.70
5036 5419 1.065928 CCAGGCTAGTACCGCGAAG 59.934 63.158 8.23 0.00 33.69 3.79
5189 5589 2.673368 GTGTCGCGATCTTTCCTGAAAT 59.327 45.455 14.06 0.00 0.00 2.17
5194 5594 3.557185 CGCGATCTTTCCTGAAATCATCA 59.443 43.478 0.00 0.00 36.38 3.07
5424 5827 0.038166 GCCAAGATGAGTTGGGGTCA 59.962 55.000 4.85 0.00 46.31 4.02
5441 5879 2.688666 ATGGCTCGGGCTCTTCCA 60.689 61.111 7.48 0.00 38.73 3.53
5452 5890 1.538047 GCTCTTCCATGGTTGCTTGA 58.462 50.000 12.58 1.81 0.00 3.02
5487 5925 1.672356 GCTGCGGTGGATTGTGTCT 60.672 57.895 0.00 0.00 0.00 3.41
5529 5974 3.119096 GTTCGCGGAGGTCTTGGC 61.119 66.667 6.13 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.335647 CCGCTGGGCAGGACTTGT 62.336 66.667 0.00 0.00 0.00 3.16
69 70 8.033038 TGCATATATACCGATTGAAAGTAGACC 58.967 37.037 0.00 0.00 0.00 3.85
71 72 8.581578 TGTGCATATATACCGATTGAAAGTAGA 58.418 33.333 0.00 0.00 0.00 2.59
88 89 9.606631 TGTCTATGTTGTTTACATGTGCATATA 57.393 29.630 9.11 6.45 46.81 0.86
113 114 4.944962 TTTGCATCGAATGACCTAGTTG 57.055 40.909 0.00 0.00 0.00 3.16
139 140 6.255020 CCGTATTTACAGAAGCACGTCTTAAT 59.745 38.462 0.00 0.00 34.56 1.40
163 164 2.298158 TAGGCAGCAACGCTCTAGCC 62.298 60.000 7.53 7.53 42.96 3.93
192 193 4.100963 TGACCTAGTTGCATCGAATATGGT 59.899 41.667 0.00 0.00 0.00 3.55
336 337 1.283029 AGCAGAGCAGGCATTTCCTTA 59.717 47.619 0.00 0.00 44.75 2.69
440 441 4.307432 AGCACCGATTAAGATGGAATACG 58.693 43.478 0.00 0.00 0.00 3.06
584 586 4.294347 TCCCCACAAAAGAGGAACAAAAT 58.706 39.130 0.00 0.00 0.00 1.82
911 915 3.701205 AATGCATGTACACACCTGAGA 57.299 42.857 0.00 0.00 0.00 3.27
1035 1045 7.847096 TGATTTGAATCAAGTAGGTAGCTACA 58.153 34.615 28.68 12.81 42.11 2.74
1083 1093 0.996762 TCCCAACTTCAACCCCAGGT 60.997 55.000 0.00 0.00 37.65 4.00
1124 1134 9.137459 TCAAAACTAAAAATAGATGTTGGTCCA 57.863 29.630 0.00 0.00 0.00 4.02
1207 1227 5.743872 GGTTGAATGAATGAATAAAGCCGAC 59.256 40.000 0.00 0.00 0.00 4.79
1242 1292 9.941325 AGCATTATTTGTATTTCATTTTCACCA 57.059 25.926 0.00 0.00 0.00 4.17
1362 1421 1.735920 CAGGAGACTCGTGCACTGC 60.736 63.158 16.19 0.26 40.21 4.40
1653 1726 0.870393 CAGCAGCCACTACACACAAG 59.130 55.000 0.00 0.00 0.00 3.16
1656 1729 0.037326 TAGCAGCAGCCACTACACAC 60.037 55.000 0.00 0.00 43.56 3.82
1668 1741 3.181455 CCATTGGTACCATACTAGCAGCA 60.181 47.826 17.17 0.00 0.00 4.41
2047 2147 2.925706 TTGGCAGGGTCGCAGGTA 60.926 61.111 0.00 0.00 0.00 3.08
2357 2457 0.108585 ACGCCAAAGACTGTCATGGT 59.891 50.000 24.46 10.53 35.34 3.55
2579 2679 2.046217 GCCTCCGTTGGTCTTCCC 60.046 66.667 0.00 0.00 0.00 3.97
2600 2718 3.455910 CCCACAACCTCTTCATCCTCATA 59.544 47.826 0.00 0.00 0.00 2.15
2632 2750 0.752054 TTGCCCAAAAGAACTGGCTG 59.248 50.000 0.00 0.00 44.32 4.85
2633 2751 1.720781 ATTGCCCAAAAGAACTGGCT 58.279 45.000 0.00 0.00 44.32 4.75
2634 2752 2.037641 AGAATTGCCCAAAAGAACTGGC 59.962 45.455 0.00 0.00 44.27 4.85
2635 2753 3.306294 GGAGAATTGCCCAAAAGAACTGG 60.306 47.826 0.00 0.00 0.00 4.00
2636 2754 3.306294 GGGAGAATTGCCCAAAAGAACTG 60.306 47.826 7.89 0.00 45.31 3.16
2637 2755 2.899900 GGGAGAATTGCCCAAAAGAACT 59.100 45.455 7.89 0.00 45.31 3.01
2638 2756 3.319137 GGGAGAATTGCCCAAAAGAAC 57.681 47.619 7.89 0.00 45.31 3.01
2651 2769 1.570979 GGGGGTCAATTCTGGGAGAAT 59.429 52.381 0.00 0.00 46.22 2.40
2652 2770 0.999712 GGGGGTCAATTCTGGGAGAA 59.000 55.000 0.00 0.00 38.78 2.87
2653 2771 0.121197 AGGGGGTCAATTCTGGGAGA 59.879 55.000 0.00 0.00 0.00 3.71
2654 2772 0.548510 GAGGGGGTCAATTCTGGGAG 59.451 60.000 0.00 0.00 0.00 4.30
2655 2773 0.919289 GGAGGGGGTCAATTCTGGGA 60.919 60.000 0.00 0.00 0.00 4.37
2656 2774 1.615262 GGAGGGGGTCAATTCTGGG 59.385 63.158 0.00 0.00 0.00 4.45
2657 2775 1.615262 GGGAGGGGGTCAATTCTGG 59.385 63.158 0.00 0.00 0.00 3.86
2658 2776 1.214305 TGGGGAGGGGGTCAATTCTG 61.214 60.000 0.00 0.00 0.00 3.02
2659 2777 0.921256 CTGGGGAGGGGGTCAATTCT 60.921 60.000 0.00 0.00 0.00 2.40
2660 2778 1.615262 CTGGGGAGGGGGTCAATTC 59.385 63.158 0.00 0.00 0.00 2.17
2661 2779 2.626467 GCTGGGGAGGGGGTCAATT 61.626 63.158 0.00 0.00 0.00 2.32
2662 2780 3.023735 GCTGGGGAGGGGGTCAAT 61.024 66.667 0.00 0.00 0.00 2.57
2663 2781 3.829311 AAGCTGGGGAGGGGGTCAA 62.829 63.158 0.00 0.00 0.00 3.18
2664 2782 4.285790 AAGCTGGGGAGGGGGTCA 62.286 66.667 0.00 0.00 0.00 4.02
2665 2783 3.412408 GAAGCTGGGGAGGGGGTC 61.412 72.222 0.00 0.00 0.00 4.46
2666 2784 3.952799 GAGAAGCTGGGGAGGGGGT 62.953 68.421 0.00 0.00 0.00 4.95
2667 2785 3.093172 GAGAAGCTGGGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
2668 2786 3.093172 GGAGAAGCTGGGGAGGGG 61.093 72.222 0.00 0.00 0.00 4.79
2669 2787 3.093172 GGGAGAAGCTGGGGAGGG 61.093 72.222 0.00 0.00 0.00 4.30
2670 2788 2.285668 TGGGAGAAGCTGGGGAGG 60.286 66.667 0.00 0.00 0.00 4.30
2671 2789 0.911525 TTCTGGGAGAAGCTGGGGAG 60.912 60.000 0.00 0.00 29.50 4.30
2672 2790 0.253347 ATTCTGGGAGAAGCTGGGGA 60.253 55.000 0.00 0.00 37.69 4.81
2673 2791 0.627986 AATTCTGGGAGAAGCTGGGG 59.372 55.000 0.00 0.00 37.69 4.96
2674 2792 1.760192 CAATTCTGGGAGAAGCTGGG 58.240 55.000 0.00 0.00 37.69 4.45
2675 2793 1.101331 GCAATTCTGGGAGAAGCTGG 58.899 55.000 0.00 0.00 37.69 4.85
2676 2794 1.101331 GGCAATTCTGGGAGAAGCTG 58.899 55.000 0.00 0.00 37.69 4.24
2677 2795 0.700564 TGGCAATTCTGGGAGAAGCT 59.299 50.000 0.00 0.00 37.69 3.74
2678 2796 0.813821 GTGGCAATTCTGGGAGAAGC 59.186 55.000 0.00 0.00 37.69 3.86
2679 2797 2.503895 AGTGGCAATTCTGGGAGAAG 57.496 50.000 0.00 0.00 37.69 2.85
2680 2798 2.978156 AAGTGGCAATTCTGGGAGAA 57.022 45.000 0.00 0.00 38.78 2.87
2681 2799 4.591321 ATTAAGTGGCAATTCTGGGAGA 57.409 40.909 2.32 0.00 0.00 3.71
2682 2800 6.966534 AATATTAAGTGGCAATTCTGGGAG 57.033 37.500 2.32 0.00 0.00 4.30
2683 2801 7.732222 AAAATATTAAGTGGCAATTCTGGGA 57.268 32.000 2.32 0.00 0.00 4.37
2707 2825 9.662947 GACCTTAACTAGCTAGGAATTGTAAAA 57.337 33.333 24.35 1.45 33.21 1.52
2708 2826 9.043548 AGACCTTAACTAGCTAGGAATTGTAAA 57.956 33.333 24.35 6.07 33.21 2.01
2709 2827 8.605325 AGACCTTAACTAGCTAGGAATTGTAA 57.395 34.615 24.35 10.98 33.21 2.41
2710 2828 9.705103 TTAGACCTTAACTAGCTAGGAATTGTA 57.295 33.333 24.35 8.34 33.21 2.41
2711 2829 8.605325 TTAGACCTTAACTAGCTAGGAATTGT 57.395 34.615 24.35 14.92 33.21 2.71
2715 2833 8.858094 GCTAATTAGACCTTAACTAGCTAGGAA 58.142 37.037 24.35 16.07 33.21 3.36
2716 2834 8.226112 AGCTAATTAGACCTTAACTAGCTAGGA 58.774 37.037 24.35 9.48 33.21 2.94
2717 2835 8.411991 AGCTAATTAGACCTTAACTAGCTAGG 57.588 38.462 24.35 11.75 35.14 3.02
2719 2837 9.517868 CCTAGCTAATTAGACCTTAACTAGCTA 57.482 37.037 16.85 13.29 29.48 3.32
2720 2838 8.226112 TCCTAGCTAATTAGACCTTAACTAGCT 58.774 37.037 16.85 12.62 29.48 3.32
2721 2839 8.406730 TCCTAGCTAATTAGACCTTAACTAGC 57.593 38.462 16.85 0.00 29.48 3.42
2725 2843 9.833917 ACAATTCCTAGCTAATTAGACCTTAAC 57.166 33.333 16.85 0.00 0.00 2.01
2754 2872 8.144862 TCCCAGAATTGCCACTTAATATTTTT 57.855 30.769 0.00 0.00 0.00 1.94
2755 2873 7.619302 TCTCCCAGAATTGCCACTTAATATTTT 59.381 33.333 0.00 0.00 0.00 1.82
2756 2874 7.125391 TCTCCCAGAATTGCCACTTAATATTT 58.875 34.615 0.00 0.00 0.00 1.40
2757 2875 6.672593 TCTCCCAGAATTGCCACTTAATATT 58.327 36.000 0.00 0.00 0.00 1.28
2758 2876 6.266131 TCTCCCAGAATTGCCACTTAATAT 57.734 37.500 0.00 0.00 0.00 1.28
2759 2877 5.708736 TCTCCCAGAATTGCCACTTAATA 57.291 39.130 0.00 0.00 0.00 0.98
2760 2878 4.591321 TCTCCCAGAATTGCCACTTAAT 57.409 40.909 0.00 0.00 0.00 1.40
2761 2879 4.335416 CTTCTCCCAGAATTGCCACTTAA 58.665 43.478 0.00 0.00 33.13 1.85
2762 2880 3.873801 GCTTCTCCCAGAATTGCCACTTA 60.874 47.826 0.00 0.00 33.13 2.24
2763 2881 2.800250 CTTCTCCCAGAATTGCCACTT 58.200 47.619 0.00 0.00 33.13 3.16
2764 2882 1.615384 GCTTCTCCCAGAATTGCCACT 60.615 52.381 0.00 0.00 33.13 4.00
2765 2883 0.813821 GCTTCTCCCAGAATTGCCAC 59.186 55.000 0.00 0.00 33.13 5.01
2766 2884 0.700564 AGCTTCTCCCAGAATTGCCA 59.299 50.000 0.00 0.00 33.13 4.92
2767 2885 1.101331 CAGCTTCTCCCAGAATTGCC 58.899 55.000 0.00 0.00 33.13 4.52
2768 2886 1.101331 CCAGCTTCTCCCAGAATTGC 58.899 55.000 0.00 0.00 33.13 3.56
2769 2887 1.684248 CCCCAGCTTCTCCCAGAATTG 60.684 57.143 0.00 0.00 33.13 2.32
2770 2888 0.627986 CCCCAGCTTCTCCCAGAATT 59.372 55.000 0.00 0.00 33.13 2.17
2771 2889 0.253347 TCCCCAGCTTCTCCCAGAAT 60.253 55.000 0.00 0.00 33.13 2.40
2772 2890 0.911525 CTCCCCAGCTTCTCCCAGAA 60.912 60.000 0.00 0.00 32.50 3.02
2773 2891 1.306482 CTCCCCAGCTTCTCCCAGA 60.306 63.158 0.00 0.00 0.00 3.86
2774 2892 2.373707 CCTCCCCAGCTTCTCCCAG 61.374 68.421 0.00 0.00 0.00 4.45
2775 2893 2.285668 CCTCCCCAGCTTCTCCCA 60.286 66.667 0.00 0.00 0.00 4.37
2776 2894 3.093172 CCCTCCCCAGCTTCTCCC 61.093 72.222 0.00 0.00 0.00 4.30
2777 2895 3.093172 CCCCTCCCCAGCTTCTCC 61.093 72.222 0.00 0.00 0.00 3.71
2778 2896 3.093172 CCCCCTCCCCAGCTTCTC 61.093 72.222 0.00 0.00 0.00 2.87
2792 2910 0.999712 TTCTCCCAGAATTGACCCCC 59.000 55.000 0.00 0.00 0.00 5.40
2805 2923 2.899900 AGTTCTTTTGGGCAATTCTCCC 59.100 45.455 5.52 5.52 44.17 4.30
2806 2924 3.306294 CCAGTTCTTTTGGGCAATTCTCC 60.306 47.826 0.00 0.00 31.87 3.71
2807 2925 3.862264 GCCAGTTCTTTTGGGCAATTCTC 60.862 47.826 0.00 0.00 45.70 2.87
2808 2926 2.037641 GCCAGTTCTTTTGGGCAATTCT 59.962 45.455 0.00 0.00 45.70 2.40
2809 2927 2.416747 GCCAGTTCTTTTGGGCAATTC 58.583 47.619 0.00 0.00 45.70 2.17
2810 2928 2.549064 GCCAGTTCTTTTGGGCAATT 57.451 45.000 0.00 0.00 45.70 2.32
2815 2933 1.423584 AAAGGGCCAGTTCTTTTGGG 58.576 50.000 6.18 0.00 36.19 4.12
2816 2934 4.089361 AGATAAAGGGCCAGTTCTTTTGG 58.911 43.478 6.18 0.00 38.78 3.28
2817 2935 5.012893 AGAGATAAAGGGCCAGTTCTTTTG 58.987 41.667 6.18 0.00 35.22 2.44
2818 2936 5.014649 AGAGAGATAAAGGGCCAGTTCTTTT 59.985 40.000 6.18 0.00 35.22 2.27
2819 2937 4.538089 AGAGAGATAAAGGGCCAGTTCTTT 59.462 41.667 6.18 7.55 37.09 2.52
2820 2938 4.107820 AGAGAGATAAAGGGCCAGTTCTT 58.892 43.478 6.18 0.00 0.00 2.52
2821 2939 3.730269 AGAGAGATAAAGGGCCAGTTCT 58.270 45.455 6.18 1.71 0.00 3.01
2822 2940 4.406003 TGTAGAGAGATAAAGGGCCAGTTC 59.594 45.833 6.18 0.00 0.00 3.01
2823 2941 4.362677 TGTAGAGAGATAAAGGGCCAGTT 58.637 43.478 6.18 1.31 0.00 3.16
2824 2942 3.995636 TGTAGAGAGATAAAGGGCCAGT 58.004 45.455 6.18 0.00 0.00 4.00
2825 2943 4.590647 TGATGTAGAGAGATAAAGGGCCAG 59.409 45.833 6.18 0.00 0.00 4.85
2826 2944 4.556697 TGATGTAGAGAGATAAAGGGCCA 58.443 43.478 6.18 0.00 0.00 5.36
2827 2945 5.552870 TTGATGTAGAGAGATAAAGGGCC 57.447 43.478 0.00 0.00 0.00 5.80
2828 2946 6.648725 GTCATTGATGTAGAGAGATAAAGGGC 59.351 42.308 0.00 0.00 0.00 5.19
2829 2947 7.158021 GGTCATTGATGTAGAGAGATAAAGGG 58.842 42.308 0.00 0.00 0.00 3.95
2830 2948 7.158021 GGGTCATTGATGTAGAGAGATAAAGG 58.842 42.308 0.00 0.00 0.00 3.11
2831 2949 7.730084 TGGGTCATTGATGTAGAGAGATAAAG 58.270 38.462 0.00 0.00 0.00 1.85
2832 2950 7.565029 TCTGGGTCATTGATGTAGAGAGATAAA 59.435 37.037 0.00 0.00 0.00 1.40
2833 2951 7.014711 GTCTGGGTCATTGATGTAGAGAGATAA 59.985 40.741 0.00 0.00 0.00 1.75
2834 2952 6.491745 GTCTGGGTCATTGATGTAGAGAGATA 59.508 42.308 0.00 0.00 0.00 1.98
3013 3131 1.137404 CATGGGCTACTTTGTGCGC 59.863 57.895 0.00 0.00 41.57 6.09
3265 3388 1.915141 AGCCATCTGTTTGGGTTGAG 58.085 50.000 0.00 0.00 44.96 3.02
3425 3548 2.284921 TCTCCACCAGCTCCAGGG 60.285 66.667 0.00 0.00 0.00 4.45
3441 3564 1.817099 CGGTTGGATGCTCTGGCTC 60.817 63.158 0.00 0.00 39.59 4.70
3459 3582 6.536582 TCATCTGCAGTAAACAAGATAGCTTC 59.463 38.462 14.67 0.00 30.14 3.86
3632 3804 6.485313 TGAATAAAGTTGTCCGACATGAAAGT 59.515 34.615 1.09 0.00 0.00 2.66
3793 4130 9.423061 CTGAATTCCTTAAATTTTCGGTCATTT 57.577 29.630 2.27 0.00 37.70 2.32
3940 4288 6.183360 GCTGAAAAATATATGTCTGTGTGCCT 60.183 38.462 0.00 0.00 0.00 4.75
3941 4289 5.973565 GCTGAAAAATATATGTCTGTGTGCC 59.026 40.000 0.00 0.00 0.00 5.01
4062 4423 5.465532 TTGGTGCTTGAGATTTGCAAATA 57.534 34.783 24.15 6.84 38.50 1.40
4093 4454 4.575645 CCAAAACATCCTTGTGCAATTGTT 59.424 37.500 7.40 0.00 35.83 2.83
4147 4508 2.744202 CGGGCAATTGACTGATATAGCC 59.256 50.000 15.62 0.47 40.08 3.93
4149 4510 2.413112 CGCGGGCAATTGACTGATATAG 59.587 50.000 24.86 5.07 0.00 1.31
4159 4520 3.969642 GACAAGGCGCGGGCAATTG 62.970 63.158 28.27 28.27 42.47 2.32
4282 4644 0.612174 ACGCTCTCAGTAGGCTTCCA 60.612 55.000 0.00 0.00 0.00 3.53
4308 4674 3.256704 AGAATCCCACCAGGTAAACAGA 58.743 45.455 0.00 0.00 36.75 3.41
4360 4726 6.669032 GCAATTGAAGAAAATCAAGACGCATG 60.669 38.462 10.34 0.00 42.21 4.06
4361 4727 5.346822 GCAATTGAAGAAAATCAAGACGCAT 59.653 36.000 10.34 0.00 42.21 4.73
4365 4731 9.213819 GTTTTTGCAATTGAAGAAAATCAAGAC 57.786 29.630 10.34 2.62 42.21 3.01
4394 4760 6.416631 TTCATGGACCAAATTTGATCAACA 57.583 33.333 19.86 6.84 0.00 3.33
4432 4804 5.655532 AGAATCAGCTCTGTAATGGCAAAAT 59.344 36.000 0.00 0.00 0.00 1.82
4433 4805 5.012239 AGAATCAGCTCTGTAATGGCAAAA 58.988 37.500 0.00 0.00 0.00 2.44
4499 4871 2.561478 TGAACTTCCAGTAACTGCCC 57.439 50.000 0.00 0.00 0.00 5.36
4541 4913 2.488952 TGCACTTGTTCGTATGAAGCA 58.511 42.857 0.00 1.08 33.98 3.91
4551 4923 3.304928 CCAGATCTTGGTTGCACTTGTTC 60.305 47.826 0.00 0.00 42.41 3.18
4561 4933 1.915141 CTGCAACCCAGATCTTGGTT 58.085 50.000 22.44 22.44 46.25 3.67
4648 5020 0.911053 TCTGCTGATGTGCCCATGTA 59.089 50.000 0.00 0.00 0.00 2.29
4649 5021 0.257905 ATCTGCTGATGTGCCCATGT 59.742 50.000 5.15 0.00 0.00 3.21
4650 5022 0.952280 GATCTGCTGATGTGCCCATG 59.048 55.000 11.21 0.00 32.19 3.66
4651 5023 0.534427 CGATCTGCTGATGTGCCCAT 60.534 55.000 11.21 0.00 32.19 4.00
4652 5024 1.153309 CGATCTGCTGATGTGCCCA 60.153 57.895 11.21 0.00 32.19 5.36
4670 5042 1.082117 CCGAACAGTGGTACATCGGC 61.082 60.000 9.52 0.00 45.41 5.54
4681 5056 2.102070 TTGTGAACACACCGAACAGT 57.898 45.000 7.16 0.00 41.67 3.55
4685 5060 0.665835 GGCATTGTGAACACACCGAA 59.334 50.000 7.16 0.00 41.67 4.30
4693 5068 1.896220 TCACCAGAGGCATTGTGAAC 58.104 50.000 0.00 0.00 34.98 3.18
4766 5144 7.631510 TCCATGGATTGTCTTATCATCCTTA 57.368 36.000 11.44 0.00 32.83 2.69
4775 5153 5.715439 ATCACCTTCCATGGATTGTCTTA 57.285 39.130 17.06 0.00 0.00 2.10
4803 5181 2.923121 CAGAACATATCCACCCACAGG 58.077 52.381 0.00 0.00 40.04 4.00
4815 5194 1.137086 GCCGAGGAGAAGCAGAACATA 59.863 52.381 0.00 0.00 0.00 2.29
4819 5198 1.892819 CTGGCCGAGGAGAAGCAGAA 61.893 60.000 0.00 0.00 0.00 3.02
4842 5221 1.101331 GGTACCCTCGACACCTACTG 58.899 60.000 0.00 0.00 0.00 2.74
4843 5222 0.998145 AGGTACCCTCGACACCTACT 59.002 55.000 8.74 0.00 40.93 2.57
4845 5224 1.915489 TGTAGGTACCCTCGACACCTA 59.085 52.381 8.74 6.44 42.65 3.08
4846 5225 0.700564 TGTAGGTACCCTCGACACCT 59.299 55.000 8.74 8.01 44.79 4.00
4847 5226 0.813821 GTGTAGGTACCCTCGACACC 59.186 60.000 19.17 7.64 37.22 4.16
4848 5227 0.449388 CGTGTAGGTACCCTCGACAC 59.551 60.000 19.63 19.63 38.83 3.67
4849 5228 0.677731 CCGTGTAGGTACCCTCGACA 60.678 60.000 8.74 5.36 34.61 4.35
4850 5229 1.997928 GCCGTGTAGGTACCCTCGAC 61.998 65.000 8.74 2.53 43.70 4.20
4851 5230 1.750399 GCCGTGTAGGTACCCTCGA 60.750 63.158 8.74 0.00 43.70 4.04
4852 5231 1.597797 TTGCCGTGTAGGTACCCTCG 61.598 60.000 8.74 6.95 43.70 4.63
4868 5247 1.363807 GTGGTGCCCAAACTCTTGC 59.636 57.895 0.00 0.00 34.18 4.01
4898 5277 5.799213 AGCCAAATAGGAGTATATGTGAGC 58.201 41.667 0.00 0.00 41.22 4.26
4899 5278 6.212388 AGGAGCCAAATAGGAGTATATGTGAG 59.788 42.308 0.00 0.00 41.22 3.51
4900 5279 6.014242 CAGGAGCCAAATAGGAGTATATGTGA 60.014 42.308 0.00 0.00 41.22 3.58
4901 5280 6.169094 CAGGAGCCAAATAGGAGTATATGTG 58.831 44.000 0.00 0.00 41.22 3.21
4902 5281 5.846714 ACAGGAGCCAAATAGGAGTATATGT 59.153 40.000 0.00 0.00 41.22 2.29
4905 5284 4.523173 CGACAGGAGCCAAATAGGAGTATA 59.477 45.833 0.00 0.00 41.22 1.47
4906 5285 3.322254 CGACAGGAGCCAAATAGGAGTAT 59.678 47.826 0.00 0.00 41.22 2.12
4907 5286 2.693591 CGACAGGAGCCAAATAGGAGTA 59.306 50.000 0.00 0.00 41.22 2.59
4908 5287 1.482593 CGACAGGAGCCAAATAGGAGT 59.517 52.381 0.00 0.00 41.22 3.85
4909 5288 1.808133 GCGACAGGAGCCAAATAGGAG 60.808 57.143 0.00 0.00 41.22 3.69
4910 5289 0.178068 GCGACAGGAGCCAAATAGGA 59.822 55.000 0.00 0.00 41.22 2.94
4912 5291 1.134699 TGAGCGACAGGAGCCAAATAG 60.135 52.381 0.00 0.00 34.64 1.73
4913 5292 0.901827 TGAGCGACAGGAGCCAAATA 59.098 50.000 0.00 0.00 34.64 1.40
4914 5293 0.254178 ATGAGCGACAGGAGCCAAAT 59.746 50.000 0.00 0.00 34.64 2.32
4928 5307 0.259938 AGGTTTCCATCCCCATGAGC 59.740 55.000 0.00 0.00 30.57 4.26
4933 5312 1.078347 GGCAAGGTTTCCATCCCCA 59.922 57.895 0.00 0.00 0.00 4.96
4934 5313 1.685765 GGGCAAGGTTTCCATCCCC 60.686 63.158 0.00 0.00 0.00 4.81
4935 5314 2.052104 CGGGCAAGGTTTCCATCCC 61.052 63.158 0.00 0.00 0.00 3.85
4936 5315 1.001393 TCGGGCAAGGTTTCCATCC 60.001 57.895 0.00 0.00 0.00 3.51
4937 5316 0.035439 TCTCGGGCAAGGTTTCCATC 60.035 55.000 0.00 0.00 0.00 3.51
4939 5318 1.374947 CTCTCGGGCAAGGTTTCCA 59.625 57.895 0.00 0.00 0.00 3.53
4966 5349 1.000163 GTCCACTCGAAAGCTCTGTCA 60.000 52.381 0.00 0.00 0.00 3.58
4970 5353 1.001406 CCTTGTCCACTCGAAAGCTCT 59.999 52.381 0.00 0.00 0.00 4.09
4987 5370 3.443045 CAGCGCCGGCATTTCCTT 61.443 61.111 28.98 0.00 43.41 3.36
5024 5407 0.038343 AAAACGGCTTCGCGGTACTA 60.038 50.000 6.13 0.00 41.05 1.82
5027 5410 0.879400 TCAAAAACGGCTTCGCGGTA 60.879 50.000 6.13 0.00 41.05 4.02
5028 5411 1.716826 TTCAAAAACGGCTTCGCGGT 61.717 50.000 6.13 0.00 43.64 5.68
5030 5413 1.192793 TTTTCAAAAACGGCTTCGCG 58.807 45.000 0.00 0.00 37.41 5.87
5033 5416 6.285790 ACATCAATTTTCAAAAACGGCTTC 57.714 33.333 0.00 0.00 0.00 3.86
5035 5418 6.676237 AAACATCAATTTTCAAAAACGGCT 57.324 29.167 0.00 0.00 0.00 5.52
5036 5419 7.696035 AGAAAAACATCAATTTTCAAAAACGGC 59.304 29.630 12.60 0.00 45.06 5.68
5064 5455 6.073112 GCTTCCAAAAATAAGCAAATGCAGAA 60.073 34.615 8.28 0.00 45.89 3.02
5082 5482 7.575414 TGTATGAACTACAAAAAGCTTCCAA 57.425 32.000 0.00 0.00 37.40 3.53
5189 5589 1.704628 ACCACACCTCCACAATGATGA 59.295 47.619 0.00 0.00 0.00 2.92
5194 5594 3.725754 GTGACCACACCTCCACAAT 57.274 52.632 0.00 0.00 40.74 2.71
5267 5667 2.490148 CGCTAGGACGCCTCCATCA 61.490 63.158 4.47 0.00 39.39 3.07
5424 5827 2.074948 ATGGAAGAGCCCGAGCCAT 61.075 57.895 0.00 0.00 41.25 4.40
5441 5879 2.964464 TCCACAACAATCAAGCAACCAT 59.036 40.909 0.00 0.00 0.00 3.55
5452 5890 2.146342 CAGCTTCGACTCCACAACAAT 58.854 47.619 0.00 0.00 0.00 2.71
5487 5925 2.632544 CGAGTGCCGTCACCACCTA 61.633 63.158 0.00 0.00 44.16 3.08
5546 5991 3.922240 CGACAATCTTTGCAAGGGAAATG 59.078 43.478 8.88 12.01 0.00 2.32


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

AutoCloner maintained by Alex Coulton.