Multiple sequence alignment - TraesCS1D01G083600

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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 TraesCS1D01G083600 chr1D 100.000 5227 0 0 1 5227 66554791 66560017 0.000000e+00 9653.0
1 TraesCS1D01G083600 chr1D 98.603 716 10 0 4512 5227 306679151 306679866 0.000000e+00 1267.0
2 TraesCS1D01G083600 chr1D 83.573 487 57 12 2745 3230 209522355 209522819 8.040000e-118 435.0
3 TraesCS1D01G083600 chr1A 90.003 3571 220 65 1 3513 65261319 65264810 0.000000e+00 4490.0
4 TraesCS1D01G083600 chr1A 93.452 901 53 5 3616 4513 65264808 65265705 0.000000e+00 1332.0
5 TraesCS1D01G083600 chr1A 84.810 237 33 3 2526 2762 147166543 147166776 8.750000e-58 235.0
6 TraesCS1D01G083600 chr1A 92.969 128 7 2 3505 3631 546033795 546033669 8.940000e-43 185.0
7 TraesCS1D01G083600 chr1B 95.693 1927 57 9 1562 3474 107133951 107135865 0.000000e+00 3075.0
8 TraesCS1D01G083600 chr1B 90.101 1586 84 26 17 1562 107132331 107133883 0.000000e+00 1991.0
9 TraesCS1D01G083600 chr1B 92.569 619 35 7 3900 4513 107136250 107136862 0.000000e+00 878.0
10 TraesCS1D01G083600 chr1B 84.447 733 44 27 4515 5227 39599563 39598881 0.000000e+00 658.0
11 TraesCS1D01G083600 chr1B 95.076 264 12 1 3616 3878 107135890 107136153 1.050000e-111 414.0
12 TraesCS1D01G083600 chr1B 92.891 211 14 1 4524 4733 31536013 31536223 6.580000e-79 305.0
13 TraesCS1D01G083600 chr1B 92.891 211 14 1 4524 4733 31559113 31559323 6.580000e-79 305.0
14 TraesCS1D01G083600 chr1B 83.525 261 28 3 4737 4989 31559774 31560027 4.070000e-56 230.0
15 TraesCS1D01G083600 chr1B 100.000 35 0 0 3479 3513 107135858 107135892 1.210000e-06 65.8
16 TraesCS1D01G083600 chr5B 93.046 719 41 7 4514 5227 705133845 705134559 0.000000e+00 1042.0
17 TraesCS1D01G083600 chr5B 82.213 506 71 10 2745 3249 203498605 203498118 8.100000e-113 418.0
18 TraesCS1D01G083600 chr5B 81.050 438 44 22 520 942 699073702 699073289 3.930000e-81 313.0
19 TraesCS1D01G083600 chr5B 80.909 440 45 23 517 942 555729091 555728677 1.410000e-80 311.0
20 TraesCS1D01G083600 chr3A 86.546 721 53 17 4524 5227 693592498 693593191 0.000000e+00 754.0
21 TraesCS1D01G083600 chr3A 82.586 758 110 14 2494 3249 511213071 511212334 0.000000e+00 649.0
22 TraesCS1D01G083600 chr4A 85.975 713 58 18 4529 5227 636390947 636390263 0.000000e+00 725.0
23 TraesCS1D01G083600 chr4A 84.524 756 51 25 4511 5227 603334602 603335330 0.000000e+00 688.0
24 TraesCS1D01G083600 chr4A 80.682 440 46 25 517 942 375967557 375967143 6.580000e-79 305.0
25 TraesCS1D01G083600 chr4A 93.023 129 7 1 3489 3617 550136367 550136493 2.490000e-43 187.0
26 TraesCS1D01G083600 chr6A 82.815 739 105 14 2494 3230 474882911 474882193 4.410000e-180 641.0
27 TraesCS1D01G083600 chr6A 82.345 759 110 16 2494 3249 474453069 474452332 5.710000e-179 638.0
28 TraesCS1D01G083600 chr6A 97.391 115 2 1 3510 3623 555582294 555582180 1.490000e-45 195.0
29 TraesCS1D01G083600 chr2A 81.159 759 117 18 2494 3249 603917405 603916670 2.100000e-163 586.0
30 TraesCS1D01G083600 chr2A 93.701 127 6 2 3511 3637 57865497 57865373 6.910000e-44 189.0
31 TraesCS1D01G083600 chr7A 83.361 601 79 14 2640 3238 47777161 47776580 2.140000e-148 536.0
32 TraesCS1D01G083600 chr7A 80.822 438 48 24 517 942 320366444 320366031 1.410000e-80 311.0
33 TraesCS1D01G083600 chr7A 90.141 142 10 4 3493 3631 109354944 109354804 1.160000e-41 182.0
34 TraesCS1D01G083600 chr6B 81.693 437 45 21 517 942 518611335 518611747 1.080000e-86 331.0
35 TraesCS1D01G083600 chr2B 81.549 439 44 24 517 942 42566200 42566614 1.400000e-85 327.0
36 TraesCS1D01G083600 chr2B 81.465 437 46 21 517 942 306176563 306176151 5.050000e-85 326.0
37 TraesCS1D01G083600 chr2B 81.007 437 48 19 517 942 190629180 190629592 1.090000e-81 315.0
38 TraesCS1D01G083600 chr2B 96.581 117 3 1 3508 3623 691451322 691451438 5.340000e-45 193.0
39 TraesCS1D01G083600 chr7B 92.478 226 13 4 4976 5198 509634535 509634759 2.350000e-83 320.0
40 TraesCS1D01G083600 chr7B 95.833 120 5 0 3511 3630 452155143 452155262 1.490000e-45 195.0
41 TraesCS1D01G083600 chr7B 82.828 99 2 4 4517 4615 509614891 509614974 2.020000e-09 75.0
42 TraesCS1D01G083600 chr5D 92.481 133 8 2 3492 3623 299595133 299595002 6.910000e-44 189.0
43 TraesCS1D01G083600 chr3B 90.000 140 9 5 3508 3645 593563693 593563557 5.380000e-40 176.0


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 TraesCS1D01G083600 chr1D 66554791 66560017 5226 False 9653.00 9653 100.0000 1 5227 1 chr1D.!!$F1 5226
1 TraesCS1D01G083600 chr1D 306679151 306679866 715 False 1267.00 1267 98.6030 4512 5227 1 chr1D.!!$F3 715
2 TraesCS1D01G083600 chr1A 65261319 65265705 4386 False 2911.00 4490 91.7275 1 4513 2 chr1A.!!$F2 4512
3 TraesCS1D01G083600 chr1B 107132331 107136862 4531 False 1284.76 3075 94.6878 17 4513 5 chr1B.!!$F3 4496
4 TraesCS1D01G083600 chr1B 39598881 39599563 682 True 658.00 658 84.4470 4515 5227 1 chr1B.!!$R1 712
5 TraesCS1D01G083600 chr1B 31559113 31560027 914 False 267.50 305 88.2080 4524 4989 2 chr1B.!!$F2 465
6 TraesCS1D01G083600 chr5B 705133845 705134559 714 False 1042.00 1042 93.0460 4514 5227 1 chr5B.!!$F1 713
7 TraesCS1D01G083600 chr3A 693592498 693593191 693 False 754.00 754 86.5460 4524 5227 1 chr3A.!!$F1 703
8 TraesCS1D01G083600 chr3A 511212334 511213071 737 True 649.00 649 82.5860 2494 3249 1 chr3A.!!$R1 755
9 TraesCS1D01G083600 chr4A 636390263 636390947 684 True 725.00 725 85.9750 4529 5227 1 chr4A.!!$R2 698
10 TraesCS1D01G083600 chr4A 603334602 603335330 728 False 688.00 688 84.5240 4511 5227 1 chr4A.!!$F2 716
11 TraesCS1D01G083600 chr6A 474882193 474882911 718 True 641.00 641 82.8150 2494 3230 1 chr6A.!!$R2 736
12 TraesCS1D01G083600 chr6A 474452332 474453069 737 True 638.00 638 82.3450 2494 3249 1 chr6A.!!$R1 755
13 TraesCS1D01G083600 chr2A 603916670 603917405 735 True 586.00 586 81.1590 2494 3249 1 chr2A.!!$R2 755
14 TraesCS1D01G083600 chr7A 47776580 47777161 581 True 536.00 536 83.3610 2640 3238 1 chr7A.!!$R1 598

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
146 147 0.037697 CCATTCGTCTCACCCGTTCA 60.038 55.000 0.00 0.00 0.00 3.18 F
960 1019 0.536233 TTGGCTAACTGCGGCTGAAA 60.536 50.000 14.07 0.33 44.05 2.69 F
1140 1201 0.668706 CCTATGAATCTCTGGCCGCG 60.669 60.000 0.00 0.00 0.00 6.46 F
1882 2014 1.221840 CCTGACATCTCCGTTGGGG 59.778 63.158 0.00 0.00 37.02 4.96 F
3541 3700 0.458889 TCGGAATTACTTGTCGCGGG 60.459 55.000 6.13 0.00 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2104 1.069973 TCGCACAAAAGAGAATGCACG 60.070 47.619 0.00 0.00 37.97 5.34 R
2249 2389 1.207488 ATACTGTTGGGCCAGCCAGA 61.207 55.000 30.61 19.16 35.83 3.86 R
3135 3283 3.002965 GTCACCACTTACCCTTTTTCACG 59.997 47.826 0.00 0.00 0.00 4.35 R
3600 3759 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55 R
4634 4907 2.801077 TTTACCCCTAAGCTCAAGGC 57.199 50.000 9.18 0.00 42.19 4.35 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
85 86 2.740714 GAGTCGCGCGCCTTCAATT 61.741 57.895 27.95 2.62 0.00 2.32
86 87 2.276680 GTCGCGCGCCTTCAATTC 60.277 61.111 27.95 3.19 0.00 2.17
87 88 2.434185 TCGCGCGCCTTCAATTCT 60.434 55.556 27.95 0.00 0.00 2.40
88 89 2.021931 CGCGCGCCTTCAATTCTC 59.978 61.111 27.72 0.00 0.00 2.87
89 90 2.405191 GCGCGCCTTCAATTCTCC 59.595 61.111 23.24 0.00 0.00 3.71
144 145 0.902531 ATCCATTCGTCTCACCCGTT 59.097 50.000 0.00 0.00 0.00 4.44
146 147 0.037697 CCATTCGTCTCACCCGTTCA 60.038 55.000 0.00 0.00 0.00 3.18
214 215 1.136984 CCGAGTGACACGTAGCTCC 59.863 63.158 1.26 0.00 0.00 4.70
215 216 1.583495 CCGAGTGACACGTAGCTCCA 61.583 60.000 1.26 0.00 0.00 3.86
219 220 2.683867 GAGTGACACGTAGCTCCATACT 59.316 50.000 0.00 0.00 0.00 2.12
231 232 0.953471 TCCATACTGCGCACGCTTTT 60.953 50.000 16.77 2.92 42.51 2.27
296 297 1.811266 CTCCCTCGTGTGATTGGCG 60.811 63.158 0.00 0.00 0.00 5.69
297 298 2.819595 CCCTCGTGTGATTGGCGG 60.820 66.667 0.00 0.00 0.00 6.13
298 299 2.819595 CCTCGTGTGATTGGCGGG 60.820 66.667 0.00 0.00 0.00 6.13
299 300 2.047274 CTCGTGTGATTGGCGGGT 60.047 61.111 0.00 0.00 0.00 5.28
300 301 2.358125 TCGTGTGATTGGCGGGTG 60.358 61.111 0.00 0.00 0.00 4.61
301 302 4.101790 CGTGTGATTGGCGGGTGC 62.102 66.667 0.00 0.00 41.71 5.01
381 385 2.355837 GCCGTCTCACTCGCAACA 60.356 61.111 0.00 0.00 0.00 3.33
423 437 1.687493 GAGGTGGGAGTGGAGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
466 487 3.344515 GCGAGGTAAGGGATTTTTCACT 58.655 45.455 0.00 0.00 0.00 3.41
501 523 6.777526 GCATCTGCTCTATTTAGTTACTGG 57.222 41.667 0.00 0.00 38.21 4.00
506 528 5.661458 TGCTCTATTTAGTTACTGGTGCTC 58.339 41.667 0.00 0.00 0.00 4.26
507 529 5.422331 TGCTCTATTTAGTTACTGGTGCTCT 59.578 40.000 0.00 0.00 0.00 4.09
526 548 7.418025 GGTGCTCTCAGTACTGGTATAAAATCT 60.418 40.741 22.48 0.00 31.18 2.40
547 569 4.680237 TCTTGCTGGCCGTCACCG 62.680 66.667 0.00 0.00 0.00 4.94
573 603 2.039216 TCGATTGGGCTGTTAGGTTCAA 59.961 45.455 0.00 0.00 0.00 2.69
580 610 3.017442 GGCTGTTAGGTTCAATCCCTTC 58.983 50.000 0.00 0.00 33.35 3.46
590 620 4.697828 GGTTCAATCCCTTCTGAGTTCTTC 59.302 45.833 0.00 0.00 0.00 2.87
623 653 6.940739 AGCTTGGTCCTTATATATGCTAGTG 58.059 40.000 0.00 0.00 0.00 2.74
668 706 1.032014 GTGTGTTGTGTGATTGGCCT 58.968 50.000 3.32 0.00 0.00 5.19
669 707 1.031235 TGTGTTGTGTGATTGGCCTG 58.969 50.000 3.32 0.00 0.00 4.85
678 718 4.164030 TGTGTGATTGGCCTGTATATGTCT 59.836 41.667 3.32 0.00 0.00 3.41
707 747 5.069516 GGTTGGTGCAAATCCTGATGATATT 59.930 40.000 0.00 0.00 31.83 1.28
708 748 6.407299 GGTTGGTGCAAATCCTGATGATATTT 60.407 38.462 0.00 0.00 31.83 1.40
709 749 7.201902 GGTTGGTGCAAATCCTGATGATATTTA 60.202 37.037 0.00 0.00 31.83 1.40
710 750 8.362639 GTTGGTGCAAATCCTGATGATATTTAT 58.637 33.333 0.00 0.00 31.83 1.40
770 810 5.948162 ACTGAATCTGCAATAAACCTGATGT 59.052 36.000 0.00 0.00 0.00 3.06
771 811 7.112122 ACTGAATCTGCAATAAACCTGATGTA 58.888 34.615 0.00 0.00 0.00 2.29
772 812 7.066284 ACTGAATCTGCAATAAACCTGATGTAC 59.934 37.037 0.00 0.00 0.00 2.90
773 813 5.991328 ATCTGCAATAAACCTGATGTACG 57.009 39.130 0.00 0.00 0.00 3.67
774 814 3.621268 TCTGCAATAAACCTGATGTACGC 59.379 43.478 0.00 0.00 0.00 4.42
775 815 3.605634 TGCAATAAACCTGATGTACGCT 58.394 40.909 0.00 0.00 0.00 5.07
777 817 4.808895 TGCAATAAACCTGATGTACGCTAG 59.191 41.667 0.00 0.00 0.00 3.42
778 818 4.809426 GCAATAAACCTGATGTACGCTAGT 59.191 41.667 0.00 0.00 0.00 2.57
813 871 4.606210 TGTTTTAGGGGAAATTAGGAGCC 58.394 43.478 0.00 0.00 0.00 4.70
877 936 4.272748 GGTTCTATGTCCTGAAATAACGGC 59.727 45.833 0.00 0.00 0.00 5.68
882 941 2.746904 TGTCCTGAAATAACGGCACATG 59.253 45.455 0.00 0.00 0.00 3.21
932 991 1.334960 GGCTTCAACCACACATGAACG 60.335 52.381 0.00 0.00 32.46 3.95
934 993 2.602217 GCTTCAACCACACATGAACGAC 60.602 50.000 0.00 0.00 32.46 4.34
960 1019 0.536233 TTGGCTAACTGCGGCTGAAA 60.536 50.000 14.07 0.33 44.05 2.69
962 1021 1.065782 TGGCTAACTGCGGCTGAAATA 60.066 47.619 14.07 3.37 44.05 1.40
990 1050 5.261216 TCACCAGGTTCTTTTGAGTTTCTT 58.739 37.500 0.00 0.00 0.00 2.52
991 1051 5.714806 TCACCAGGTTCTTTTGAGTTTCTTT 59.285 36.000 0.00 0.00 0.00 2.52
992 1052 6.036470 CACCAGGTTCTTTTGAGTTTCTTTC 58.964 40.000 0.00 0.00 0.00 2.62
993 1053 5.952347 ACCAGGTTCTTTTGAGTTTCTTTCT 59.048 36.000 0.00 0.00 0.00 2.52
996 1056 7.201857 CCAGGTTCTTTTGAGTTTCTTTCTGAT 60.202 37.037 0.00 0.00 0.00 2.90
1079 1140 2.437359 GCACCATGCTTCCTCGCT 60.437 61.111 0.00 0.00 40.96 4.93
1140 1201 0.668706 CCTATGAATCTCTGGCCGCG 60.669 60.000 0.00 0.00 0.00 6.46
1349 1410 2.599082 GCTATTTCTCGGTCAGTGTTCG 59.401 50.000 0.00 0.00 0.00 3.95
1350 1411 1.429463 ATTTCTCGGTCAGTGTTCGC 58.571 50.000 0.00 0.00 0.00 4.70
1352 1413 2.050351 CTCGGTCAGTGTTCGCGT 60.050 61.111 5.77 0.00 0.00 6.01
1355 1416 2.354305 GGTCAGTGTTCGCGTCGT 60.354 61.111 5.77 0.00 0.00 4.34
1464 1526 1.615883 AGATAGCATGCTACCTCCACG 59.384 52.381 29.11 0.00 0.00 4.94
1512 1574 4.201950 GCACTTACAAAGCAGATGGTATGG 60.202 45.833 0.00 0.00 0.00 2.74
1514 1576 5.065218 CACTTACAAAGCAGATGGTATGGTC 59.935 44.000 0.00 0.00 0.00 4.02
1516 1578 6.156256 ACTTACAAAGCAGATGGTATGGTCTA 59.844 38.462 0.00 0.00 0.00 2.59
1528 1590 5.338632 TGGTATGGTCTACCTTTCTGAAGA 58.661 41.667 0.02 0.00 38.39 2.87
1554 1616 4.214971 GGATCTCATGTTTGCGCTATTCAT 59.785 41.667 9.73 6.59 0.00 2.57
1571 1701 7.692705 CGCTATTCATGAGATTATTGCTGAATG 59.307 37.037 9.00 0.00 35.56 2.67
1627 1757 6.473455 GTGAGACTTGCAAAATTACATATGGC 59.527 38.462 7.80 0.00 0.00 4.40
1678 1808 4.329638 TGATAATGTGTTGGTTGGGGAT 57.670 40.909 0.00 0.00 0.00 3.85
1701 1831 8.306761 GGATCTTGTTGTGAAAAATCAGGTAAT 58.693 33.333 0.00 0.00 0.00 1.89
1749 1879 6.235231 TCCTCATGTTAACCTTCACCTATC 57.765 41.667 2.48 0.00 0.00 2.08
1751 1881 6.386927 TCCTCATGTTAACCTTCACCTATCAT 59.613 38.462 2.48 0.00 0.00 2.45
1882 2014 1.221840 CCTGACATCTCCGTTGGGG 59.778 63.158 0.00 0.00 37.02 4.96
1959 2099 5.540911 CCACATTTGCCAGTTTATCAAGTT 58.459 37.500 0.00 0.00 0.00 2.66
1964 2104 7.651704 ACATTTGCCAGTTTATCAAGTTAACAC 59.348 33.333 8.61 0.00 0.00 3.32
1967 2107 5.144359 GCCAGTTTATCAAGTTAACACGTG 58.856 41.667 15.48 15.48 33.96 4.49
2087 2227 1.490490 TCTGGTGGTGAGCTTGTCTTT 59.510 47.619 0.00 0.00 0.00 2.52
2102 2242 1.228831 CTTTGGTGGCATGGACCCA 60.229 57.895 0.00 0.00 31.84 4.51
2116 2256 4.552883 TGGACCCAGATCACTATAAGGA 57.447 45.455 0.00 0.00 0.00 3.36
2135 2275 2.443416 GAAAACCACACCTATGTCCCC 58.557 52.381 0.00 0.00 36.72 4.81
2616 2756 1.335496 GTGAGCCAGTACGGAGAGATC 59.665 57.143 7.77 0.00 36.56 2.75
3096 3244 4.938226 CCAGGTTACTTCCTTTGTGATCTC 59.062 45.833 0.00 0.00 35.37 2.75
3104 3252 2.108075 TCCTTTGTGATCTCCTTTGCCA 59.892 45.455 0.00 0.00 0.00 4.92
3137 3285 9.935241 ATTCTCTGATGCTATGTAATAATTCGT 57.065 29.630 0.00 0.00 0.00 3.85
3138 3286 8.748380 TCTCTGATGCTATGTAATAATTCGTG 57.252 34.615 0.00 0.00 0.00 4.35
3274 3423 2.557924 TCTTGCTTTCACCATCGCAAAT 59.442 40.909 0.00 0.00 41.26 2.32
3435 3588 9.891828 TTTTTAGCATACTGTGAACAAGTTATG 57.108 29.630 0.00 0.00 0.00 1.90
3442 3595 6.851222 ACTGTGAACAAGTTATGAGTGAAG 57.149 37.500 0.00 0.00 0.00 3.02
3455 3614 2.033675 TGAGTGAAGCATTTGTGCAGTG 59.966 45.455 3.03 0.00 37.25 3.66
3516 3675 9.713713 GACATTTTCTAGGAATCTTATACTCCC 57.286 37.037 0.00 0.00 0.00 4.30
3517 3676 9.453830 ACATTTTCTAGGAATCTTATACTCCCT 57.546 33.333 0.00 0.00 0.00 4.20
3518 3677 9.936759 CATTTTCTAGGAATCTTATACTCCCTC 57.063 37.037 0.00 0.00 0.00 4.30
3519 3678 8.493787 TTTTCTAGGAATCTTATACTCCCTCC 57.506 38.462 0.00 0.00 0.00 4.30
3520 3679 5.817784 TCTAGGAATCTTATACTCCCTCCG 58.182 45.833 0.00 0.00 0.00 4.63
3521 3680 4.472690 AGGAATCTTATACTCCCTCCGT 57.527 45.455 0.00 0.00 0.00 4.69
3522 3681 4.817286 AGGAATCTTATACTCCCTCCGTT 58.183 43.478 0.00 0.00 0.00 4.44
3523 3682 4.833938 AGGAATCTTATACTCCCTCCGTTC 59.166 45.833 0.00 0.00 0.00 3.95
3524 3683 4.321082 GGAATCTTATACTCCCTCCGTTCG 60.321 50.000 0.00 0.00 0.00 3.95
3525 3684 2.579873 TCTTATACTCCCTCCGTTCGG 58.420 52.381 4.74 4.74 0.00 4.30
3526 3685 2.173356 TCTTATACTCCCTCCGTTCGGA 59.827 50.000 13.34 13.34 0.00 4.55
3527 3686 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
3528 3687 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
3529 3688 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
3530 3689 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3531 3690 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3532 3691 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3533 3692 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3534 3693 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3535 3694 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3536 3695 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3537 3696 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3538 3697 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3539 3698 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
3540 3699 1.060122 GTTCGGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 0.00 6.46
3541 3700 0.458889 TCGGAATTACTTGTCGCGGG 60.459 55.000 6.13 0.00 0.00 6.13
3542 3701 0.458889 CGGAATTACTTGTCGCGGGA 60.459 55.000 6.13 0.00 0.00 5.14
3543 3702 1.729284 GGAATTACTTGTCGCGGGAA 58.271 50.000 6.13 0.00 0.00 3.97
3544 3703 2.285977 GGAATTACTTGTCGCGGGAAT 58.714 47.619 6.13 0.00 0.00 3.01
3545 3704 2.031683 GGAATTACTTGTCGCGGGAATG 59.968 50.000 6.13 0.00 0.00 2.67
3546 3705 1.663695 ATTACTTGTCGCGGGAATGG 58.336 50.000 6.13 0.00 0.00 3.16
3547 3706 0.609151 TTACTTGTCGCGGGAATGGA 59.391 50.000 6.13 0.00 0.00 3.41
3548 3707 0.828022 TACTTGTCGCGGGAATGGAT 59.172 50.000 6.13 0.00 0.00 3.41
3549 3708 0.744414 ACTTGTCGCGGGAATGGATG 60.744 55.000 6.13 0.00 0.00 3.51
3550 3709 0.744414 CTTGTCGCGGGAATGGATGT 60.744 55.000 6.13 0.00 0.00 3.06
3551 3710 0.537653 TTGTCGCGGGAATGGATGTA 59.462 50.000 6.13 0.00 0.00 2.29
3552 3711 0.756294 TGTCGCGGGAATGGATGTAT 59.244 50.000 6.13 0.00 0.00 2.29
3553 3712 1.270094 TGTCGCGGGAATGGATGTATC 60.270 52.381 6.13 0.00 0.00 2.24
3554 3713 1.000955 GTCGCGGGAATGGATGTATCT 59.999 52.381 6.13 0.00 0.00 1.98
3555 3714 2.230508 GTCGCGGGAATGGATGTATCTA 59.769 50.000 6.13 0.00 0.00 1.98
3556 3715 2.492088 TCGCGGGAATGGATGTATCTAG 59.508 50.000 6.13 0.00 0.00 2.43
3557 3716 2.492088 CGCGGGAATGGATGTATCTAGA 59.508 50.000 0.00 0.00 0.00 2.43
3558 3717 3.673594 CGCGGGAATGGATGTATCTAGAC 60.674 52.174 0.00 0.00 0.00 2.59
3559 3718 3.673594 GCGGGAATGGATGTATCTAGACG 60.674 52.174 0.00 0.00 0.00 4.18
3560 3719 3.506455 CGGGAATGGATGTATCTAGACGT 59.494 47.826 0.00 0.00 0.00 4.34
3561 3720 4.698780 CGGGAATGGATGTATCTAGACGTA 59.301 45.833 0.00 0.00 0.00 3.57
3562 3721 5.357314 CGGGAATGGATGTATCTAGACGTAT 59.643 44.000 0.00 0.00 0.00 3.06
3563 3722 6.127703 CGGGAATGGATGTATCTAGACGTATT 60.128 42.308 0.00 0.00 0.00 1.89
3564 3723 7.577046 CGGGAATGGATGTATCTAGACGTATTT 60.577 40.741 0.00 0.00 0.00 1.40
3565 3724 8.095169 GGGAATGGATGTATCTAGACGTATTTT 58.905 37.037 0.00 0.00 0.00 1.82
3588 3747 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
3589 3748 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
3590 3749 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
3591 3750 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
3592 3751 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
3593 3752 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
3594 3753 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
3595 3754 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
3596 3755 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
3597 3756 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
3598 3757 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
3599 3758 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
3600 3759 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
3601 3760 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
3602 3761 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
3603 3762 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
3604 3763 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
3605 3764 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
3606 3765 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
3607 3766 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
3608 3767 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
3609 3768 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
3610 3769 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
3611 3770 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3612 3771 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3613 3772 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3614 3773 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3615 3774 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
3616 3775 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3617 3776 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
3669 3828 9.533253 CAGACAAATAGGTTGAATCAAAACTTT 57.467 29.630 0.00 0.00 39.87 2.66
3846 4006 9.329913 CTTGATGTTTCCTTCTAATACAAAACG 57.670 33.333 0.00 0.00 31.06 3.60
3850 4010 7.632721 TGTTTCCTTCTAATACAAAACGACAC 58.367 34.615 0.00 0.00 31.06 3.67
3851 4011 7.280428 TGTTTCCTTCTAATACAAAACGACACA 59.720 33.333 0.00 0.00 31.06 3.72
4077 4322 3.247648 GGTATGCAGCATAACACCTTACG 59.752 47.826 23.41 0.00 34.48 3.18
4090 4335 3.078837 CACCTTACGCCACCTACATTTT 58.921 45.455 0.00 0.00 0.00 1.82
4096 4341 1.839424 GCCACCTACATTTTGCCTCT 58.161 50.000 0.00 0.00 0.00 3.69
4145 4393 1.396653 CCATGAACCCTTGCAGGATC 58.603 55.000 0.00 0.00 37.67 3.36
4167 4415 1.614711 GGGGATGTCTTCATGGGCA 59.385 57.895 0.00 0.00 34.06 5.36
4220 4468 1.207089 AGAATCGGGTTCGCAGAATCA 59.793 47.619 0.00 0.00 45.90 2.57
4246 4494 2.946329 GAGGAGTCGAGAGCACTATGAA 59.054 50.000 0.00 0.00 0.00 2.57
4298 4546 7.728981 TCCTAGAATAGTTTGGGTATCTTCGAT 59.271 37.037 0.00 0.00 36.82 3.59
4302 4550 9.090103 AGAATAGTTTGGGTATCTTCGATCATA 57.910 33.333 0.00 0.00 0.00 2.15
4320 4568 0.909623 TAGGAGCCCTGCTGTAAACC 59.090 55.000 4.16 0.00 39.88 3.27
4354 4603 7.973944 GGTAAAAAGCTGAAACAAAAGAGAGAA 59.026 33.333 0.00 0.00 0.00 2.87
4356 4605 6.765915 AAAGCTGAAACAAAAGAGAGAACT 57.234 33.333 0.00 0.00 0.00 3.01
4439 4690 6.716628 AGTACATTTGTATCCATTATGGCTGG 59.283 38.462 6.33 0.00 37.47 4.85
4444 4695 3.650461 TGTATCCATTATGGCTGGTGCTA 59.350 43.478 6.33 0.00 37.47 3.49
4678 4951 7.859325 AACGTATTCATTTAGGCAGTTATGT 57.141 32.000 0.00 0.00 0.00 2.29
4810 5535 3.741029 GCGATCAGCCTGTTCTACA 57.259 52.632 1.60 0.00 40.81 2.74
5027 5769 5.079689 TGAATTGCTTCCACGTATAGACA 57.920 39.130 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.599171 CCCCCGCGATATTTTTAGAATTTTAT 58.401 34.615 8.23 0.00 0.00 1.40
13 14 1.886886 GCCCCCGCGATATTTTTAGA 58.113 50.000 8.23 0.00 0.00 2.10
85 86 1.518367 GGAGAGGAGAGGAGAGGAGA 58.482 60.000 0.00 0.00 0.00 3.71
86 87 0.108585 CGGAGAGGAGAGGAGAGGAG 59.891 65.000 0.00 0.00 0.00 3.69
87 88 1.349542 CCGGAGAGGAGAGGAGAGGA 61.350 65.000 0.00 0.00 45.00 3.71
88 89 1.150536 CCGGAGAGGAGAGGAGAGG 59.849 68.421 0.00 0.00 45.00 3.69
89 90 1.528309 GCCGGAGAGGAGAGGAGAG 60.528 68.421 5.05 0.00 45.00 3.20
144 145 2.220586 TCGGTGGCTGGATTGGTGA 61.221 57.895 0.00 0.00 0.00 4.02
146 147 1.852157 ATGTCGGTGGCTGGATTGGT 61.852 55.000 0.00 0.00 0.00 3.67
201 202 1.134367 GCAGTATGGAGCTACGTGTCA 59.866 52.381 0.00 0.00 35.86 3.58
214 215 2.030335 TCATAAAAGCGTGCGCAGTATG 59.970 45.455 12.22 18.92 44.88 2.39
215 216 2.276201 TCATAAAAGCGTGCGCAGTAT 58.724 42.857 12.22 9.51 44.88 2.12
219 220 0.871722 AGTTCATAAAAGCGTGCGCA 59.128 45.000 18.87 5.66 44.88 6.09
231 232 0.461548 CGGAGGCAGCTGAGTTCATA 59.538 55.000 20.43 0.00 0.00 2.15
297 298 4.681978 AAGAGACGCACCCGCACC 62.682 66.667 0.00 0.00 38.40 5.01
298 299 3.112709 GAAGAGACGCACCCGCAC 61.113 66.667 0.00 0.00 38.40 5.34
299 300 4.373116 GGAAGAGACGCACCCGCA 62.373 66.667 0.00 0.00 38.40 5.69
300 301 3.591254 AAGGAAGAGACGCACCCGC 62.591 63.158 0.00 0.00 38.22 6.13
301 302 1.004918 AAAGGAAGAGACGCACCCG 60.005 57.895 0.00 0.00 41.14 5.28
381 385 0.032017 AAGAGATAGCAGACGGGGGT 60.032 55.000 0.00 0.00 0.00 4.95
408 422 1.001760 TAGCCTCCTCCACTCCCAC 59.998 63.158 0.00 0.00 0.00 4.61
491 513 5.183331 CAGTACTGAGAGCACCAGTAACTAA 59.817 44.000 18.45 0.00 45.38 2.24
501 523 7.493367 AGATTTTATACCAGTACTGAGAGCAC 58.507 38.462 24.68 7.00 0.00 4.40
526 548 0.175760 GTGACGGCCAGCAAGAGATA 59.824 55.000 2.24 0.00 0.00 1.98
547 569 1.331756 CTAACAGCCCAATCGATGTGC 59.668 52.381 0.00 2.00 31.84 4.57
554 576 3.381590 GGATTGAACCTAACAGCCCAATC 59.618 47.826 0.00 0.00 39.17 2.67
555 577 3.365472 GGATTGAACCTAACAGCCCAAT 58.635 45.455 0.00 0.00 0.00 3.16
573 603 2.763448 CTCCGAAGAACTCAGAAGGGAT 59.237 50.000 0.00 0.00 0.00 3.85
580 610 2.928731 GCTTGGACTCCGAAGAACTCAG 60.929 54.545 10.01 0.00 0.00 3.35
609 639 6.992123 ACAACAGCAAGCACTAGCATATATAA 59.008 34.615 0.00 0.00 45.49 0.98
623 653 2.608752 CCATCCAAGAACAACAGCAAGC 60.609 50.000 0.00 0.00 0.00 4.01
668 706 4.457603 GCACCAACCAAACAGACATATACA 59.542 41.667 0.00 0.00 0.00 2.29
669 707 4.457603 TGCACCAACCAAACAGACATATAC 59.542 41.667 0.00 0.00 0.00 1.47
678 718 2.114616 AGGATTTGCACCAACCAAACA 58.885 42.857 0.00 0.00 35.27 2.83
707 747 5.642063 GCAGTAGAAACCACAGCAGTTATAA 59.358 40.000 0.00 0.00 0.00 0.98
708 748 5.175859 GCAGTAGAAACCACAGCAGTTATA 58.824 41.667 0.00 0.00 0.00 0.98
709 749 4.003648 GCAGTAGAAACCACAGCAGTTAT 58.996 43.478 0.00 0.00 0.00 1.89
710 750 3.181459 TGCAGTAGAAACCACAGCAGTTA 60.181 43.478 0.00 0.00 34.04 2.24
770 810 5.302360 ACAAGGAATTGACAAACTAGCGTA 58.698 37.500 0.00 0.00 0.00 4.42
771 811 4.134563 ACAAGGAATTGACAAACTAGCGT 58.865 39.130 0.00 0.00 0.00 5.07
772 812 4.749245 ACAAGGAATTGACAAACTAGCG 57.251 40.909 0.00 0.00 0.00 4.26
773 813 7.595130 CCTAAAACAAGGAATTGACAAACTAGC 59.405 37.037 0.00 0.00 39.15 3.42
774 814 8.082242 CCCTAAAACAAGGAATTGACAAACTAG 58.918 37.037 0.00 0.00 39.15 2.57
775 815 7.014808 CCCCTAAAACAAGGAATTGACAAACTA 59.985 37.037 0.00 0.00 39.15 2.24
777 817 5.989168 CCCCTAAAACAAGGAATTGACAAAC 59.011 40.000 0.00 0.00 39.15 2.93
778 818 5.900123 TCCCCTAAAACAAGGAATTGACAAA 59.100 36.000 0.00 0.00 39.15 2.83
813 871 8.419076 ACAGCAAATTTTACAACTTTGGTAAG 57.581 30.769 4.36 0.00 38.22 2.34
877 936 6.798476 GTCAAACAGTGATATGTTGACATGTG 59.202 38.462 1.15 0.00 42.49 3.21
882 941 6.204688 TGGAAGTCAAACAGTGATATGTTGAC 59.795 38.462 0.00 8.40 42.49 3.18
932 991 2.285834 CGCAGTTAGCCAATTCATCGTC 60.286 50.000 0.00 0.00 41.38 4.20
934 993 1.003545 CCGCAGTTAGCCAATTCATCG 60.004 52.381 0.00 0.00 41.38 3.84
960 1019 8.250143 ACTCAAAAGAACCTGGTGAAAAATAT 57.750 30.769 0.00 0.00 0.00 1.28
962 1021 6.544928 ACTCAAAAGAACCTGGTGAAAAAT 57.455 33.333 0.00 0.00 0.00 1.82
990 1050 1.770658 CTCTGCCCCATGGTATCAGAA 59.229 52.381 20.98 10.65 33.93 3.02
991 1051 1.427809 CTCTGCCCCATGGTATCAGA 58.572 55.000 20.02 20.02 33.35 3.27
992 1052 0.399454 CCTCTGCCCCATGGTATCAG 59.601 60.000 11.73 13.90 0.00 2.90
993 1053 1.708993 GCCTCTGCCCCATGGTATCA 61.709 60.000 11.73 4.38 0.00 2.15
996 1056 2.042762 AGCCTCTGCCCCATGGTA 59.957 61.111 11.73 0.00 38.69 3.25
1079 1140 4.517285 GTTGATCCTAAGCAGTCCATCAA 58.483 43.478 0.00 0.00 0.00 2.57
1112 1173 4.502950 CCAGAGATTCATAGGTCAAGCTCC 60.503 50.000 0.00 0.00 35.96 4.70
1190 1251 1.138883 GGCACGATGTCGCTGTCTA 59.861 57.895 1.77 0.00 44.43 2.59
1349 1410 6.525280 ACATGAATTTGGTAAATTTACGACGC 59.475 34.615 19.48 8.41 40.97 5.19
1350 1411 7.535940 ACACATGAATTTGGTAAATTTACGACG 59.464 33.333 19.48 0.00 40.97 5.12
1352 1413 7.327275 GCACACATGAATTTGGTAAATTTACGA 59.673 33.333 19.48 14.44 40.97 3.43
1355 1416 9.553064 AAAGCACACATGAATTTGGTAAATTTA 57.447 25.926 0.00 0.00 40.97 1.40
1464 1526 2.484264 ACTTGCTCGACTTGTATTTGGC 59.516 45.455 0.00 0.00 0.00 4.52
1512 1574 2.824341 TCCCGTCTTCAGAAAGGTAGAC 59.176 50.000 0.00 0.00 34.96 2.59
1514 1576 3.702045 AGATCCCGTCTTCAGAAAGGTAG 59.298 47.826 0.00 0.00 31.47 3.18
1516 1578 2.498078 GAGATCCCGTCTTCAGAAAGGT 59.502 50.000 0.00 0.00 37.29 3.50
1528 1590 1.369091 GCGCAAACATGAGATCCCGT 61.369 55.000 0.30 0.00 0.00 5.28
1554 1616 8.780249 CACATATGACATTCAGCAATAATCTCA 58.220 33.333 10.38 0.00 0.00 3.27
1627 1757 3.278668 AATCCAGAGATTGCACCAGAG 57.721 47.619 0.00 0.00 41.30 3.35
1678 1808 9.959749 GTTATTACCTGATTTTTCACAACAAGA 57.040 29.630 0.00 0.00 0.00 3.02
1882 2014 1.416772 GTACCATACTGGAGGGGCTTC 59.583 57.143 0.00 0.00 40.96 3.86
1959 2099 4.788201 GCACAAAAGAGAATGCACGTGTTA 60.788 41.667 18.38 7.28 38.00 2.41
1964 2104 1.069973 TCGCACAAAAGAGAATGCACG 60.070 47.619 0.00 0.00 37.97 5.34
1967 2107 2.686558 TGTCGCACAAAAGAGAATGC 57.313 45.000 0.00 0.00 34.66 3.56
2087 2227 1.925285 GATCTGGGTCCATGCCACCA 61.925 60.000 12.75 7.21 35.35 4.17
2102 2242 6.215636 AGGTGTGGTTTTCCTTATAGTGATCT 59.784 38.462 0.00 0.00 41.38 2.75
2116 2256 1.271707 CGGGGACATAGGTGTGGTTTT 60.272 52.381 0.00 0.00 39.09 2.43
2249 2389 1.207488 ATACTGTTGGGCCAGCCAGA 61.207 55.000 30.61 19.16 35.83 3.86
2411 2551 8.824756 TTGAAAGATACCAGACACTATCTAGT 57.175 34.615 0.00 0.00 35.15 2.57
2432 2572 5.708736 TCTAGGCCTTCACCATATTTGAA 57.291 39.130 12.58 0.00 0.00 2.69
2616 2756 6.293081 CCTGTGCTATTAACAATTCGAGGATG 60.293 42.308 0.00 0.00 0.00 3.51
3096 3244 4.221262 TCAGAGAATGGAAAATGGCAAAGG 59.779 41.667 0.00 0.00 0.00 3.11
3104 3252 8.985315 TTACATAGCATCAGAGAATGGAAAAT 57.015 30.769 0.00 0.00 0.00 1.82
3131 3279 4.891168 ACCACTTACCCTTTTTCACGAATT 59.109 37.500 0.00 0.00 0.00 2.17
3132 3280 4.277423 CACCACTTACCCTTTTTCACGAAT 59.723 41.667 0.00 0.00 0.00 3.34
3133 3281 3.628487 CACCACTTACCCTTTTTCACGAA 59.372 43.478 0.00 0.00 0.00 3.85
3135 3283 3.002965 GTCACCACTTACCCTTTTTCACG 59.997 47.826 0.00 0.00 0.00 4.35
3136 3284 3.949113 TGTCACCACTTACCCTTTTTCAC 59.051 43.478 0.00 0.00 0.00 3.18
3137 3285 4.237976 TGTCACCACTTACCCTTTTTCA 57.762 40.909 0.00 0.00 0.00 2.69
3138 3286 4.885325 TCTTGTCACCACTTACCCTTTTTC 59.115 41.667 0.00 0.00 0.00 2.29
3143 3291 4.724279 AAATCTTGTCACCACTTACCCT 57.276 40.909 0.00 0.00 0.00 4.34
3411 3564 8.840833 TCATAACTTGTTCACAGTATGCTAAA 57.159 30.769 0.00 0.00 42.53 1.85
3455 3614 6.673154 ATAACCTTCAAAAGTACGGTATGC 57.327 37.500 0.00 0.00 0.00 3.14
3513 3672 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3514 3673 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3515 3674 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3516 3675 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3517 3676 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3518 3677 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3519 3678 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
3520 3679 1.060122 CCGCGACAAGTAATTCCGAAC 59.940 52.381 8.23 0.00 0.00 3.95
3521 3680 1.352114 CCGCGACAAGTAATTCCGAA 58.648 50.000 8.23 0.00 0.00 4.30
3522 3681 0.458889 CCCGCGACAAGTAATTCCGA 60.459 55.000 8.23 0.00 0.00 4.55
3523 3682 0.458889 TCCCGCGACAAGTAATTCCG 60.459 55.000 8.23 0.00 0.00 4.30
3524 3683 1.729284 TTCCCGCGACAAGTAATTCC 58.271 50.000 8.23 0.00 0.00 3.01
3525 3684 2.031683 CCATTCCCGCGACAAGTAATTC 59.968 50.000 8.23 0.00 0.00 2.17
3526 3685 2.014128 CCATTCCCGCGACAAGTAATT 58.986 47.619 8.23 0.00 0.00 1.40
3527 3686 1.208535 TCCATTCCCGCGACAAGTAAT 59.791 47.619 8.23 0.00 0.00 1.89
3528 3687 0.609151 TCCATTCCCGCGACAAGTAA 59.391 50.000 8.23 0.00 0.00 2.24
3529 3688 0.828022 ATCCATTCCCGCGACAAGTA 59.172 50.000 8.23 0.00 0.00 2.24
3530 3689 0.744414 CATCCATTCCCGCGACAAGT 60.744 55.000 8.23 0.00 0.00 3.16
3531 3690 0.744414 ACATCCATTCCCGCGACAAG 60.744 55.000 8.23 0.00 0.00 3.16
3532 3691 0.537653 TACATCCATTCCCGCGACAA 59.462 50.000 8.23 0.00 0.00 3.18
3533 3692 0.756294 ATACATCCATTCCCGCGACA 59.244 50.000 8.23 0.00 0.00 4.35
3534 3693 1.000955 AGATACATCCATTCCCGCGAC 59.999 52.381 8.23 0.00 0.00 5.19
3535 3694 1.338107 AGATACATCCATTCCCGCGA 58.662 50.000 8.23 0.00 0.00 5.87
3536 3695 2.492088 TCTAGATACATCCATTCCCGCG 59.508 50.000 0.00 0.00 0.00 6.46
3537 3696 3.673594 CGTCTAGATACATCCATTCCCGC 60.674 52.174 0.00 0.00 0.00 6.13
3538 3697 3.506455 ACGTCTAGATACATCCATTCCCG 59.494 47.826 0.00 0.00 0.00 5.14
3539 3698 6.777213 ATACGTCTAGATACATCCATTCCC 57.223 41.667 0.00 0.00 0.00 3.97
3562 3721 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
3563 3722 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
3564 3723 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
3565 3724 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
3566 3725 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
3567 3726 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
3568 3727 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
3569 3728 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
3570 3729 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
3571 3730 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
3572 3731 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
3573 3732 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
3574 3733 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
3575 3734 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
3576 3735 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
3577 3736 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
3578 3737 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
3579 3738 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
3580 3739 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
3581 3740 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
3582 3741 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
3583 3742 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
3584 3743 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
3585 3744 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
3586 3745 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
3587 3746 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
3588 3747 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
3589 3748 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
3590 3749 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3591 3750 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3592 3751 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3593 3752 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3594 3753 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3595 3754 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3596 3755 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3597 3756 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
3598 3757 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
3599 3758 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
3600 3759 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
3601 3760 0.822164 AATGTACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
3602 3761 1.475280 TGAATGTACTCCCTCCGTTCG 59.525 52.381 0.00 0.00 0.00 3.95
3603 3762 2.758979 TCTGAATGTACTCCCTCCGTTC 59.241 50.000 0.00 0.00 0.00 3.95
3604 3763 2.761208 CTCTGAATGTACTCCCTCCGTT 59.239 50.000 0.00 0.00 0.00 4.44
3605 3764 2.291670 ACTCTGAATGTACTCCCTCCGT 60.292 50.000 0.00 0.00 0.00 4.69
3606 3765 2.099921 CACTCTGAATGTACTCCCTCCG 59.900 54.545 0.00 0.00 0.00 4.63
3607 3766 3.366396 TCACTCTGAATGTACTCCCTCC 58.634 50.000 0.00 0.00 0.00 4.30
3608 3767 4.274147 TCTCACTCTGAATGTACTCCCTC 58.726 47.826 0.00 0.00 0.00 4.30
3609 3768 4.323569 TCTCACTCTGAATGTACTCCCT 57.676 45.455 0.00 0.00 0.00 4.20
3610 3769 6.065374 TCTATCTCACTCTGAATGTACTCCC 58.935 44.000 0.00 0.00 0.00 4.30
3611 3770 7.759489 ATCTATCTCACTCTGAATGTACTCC 57.241 40.000 0.00 0.00 0.00 3.85
3679 3838 9.311916 AGAGATTCTCTTTTATGAACTTGATCG 57.688 33.333 10.50 0.00 37.60 3.69
3712 3871 6.426646 ACTAATCGCCTCATCCTAAATCTT 57.573 37.500 0.00 0.00 0.00 2.40
3842 4002 2.946329 TGCACCTAAATGTGTGTCGTTT 59.054 40.909 0.00 0.00 38.52 3.60
3846 4006 4.475944 GAACATGCACCTAAATGTGTGTC 58.524 43.478 0.00 0.00 37.11 3.67
3850 4010 3.684305 TCTCGAACATGCACCTAAATGTG 59.316 43.478 0.00 0.00 37.11 3.21
3851 4011 3.937814 TCTCGAACATGCACCTAAATGT 58.062 40.909 0.00 0.00 38.66 2.71
3898 4059 6.915300 GCAGCGATGAATATAGATAGGTACTG 59.085 42.308 4.02 0.00 41.52 2.74
4077 4322 1.839424 AGAGGCAAAATGTAGGTGGC 58.161 50.000 0.00 0.00 38.06 5.01
4145 4393 0.107456 CCATGAAGACATCCCCGAGG 59.893 60.000 0.00 0.00 34.15 4.63
4167 4415 0.746063 TCGAACACGGTGTGGTAAGT 59.254 50.000 15.53 0.00 37.94 2.24
4220 4468 0.610509 TGCTCTCGACTCCTCAAGCT 60.611 55.000 0.00 0.00 0.00 3.74
4246 4494 0.317479 CGTGGAGACCTTCGGAAACT 59.683 55.000 0.00 0.00 0.00 2.66
4298 4546 2.170607 GTTTACAGCAGGGCTCCTATGA 59.829 50.000 10.61 0.00 36.40 2.15
4302 4550 1.133809 TGGTTTACAGCAGGGCTCCT 61.134 55.000 0.00 0.00 36.40 3.69
4320 4568 9.474920 TTTGTTTCAGCTTTTTACCTATCAATG 57.525 29.630 0.00 0.00 0.00 2.82
4374 4623 9.423061 GTTGAAGCATCCAGTTATTATTTGTTT 57.577 29.630 0.00 0.00 0.00 2.83
4381 4630 6.946340 TCAGAGTTGAAGCATCCAGTTATTA 58.054 36.000 0.00 0.00 0.00 0.98
4439 4690 6.512415 GCACTCCATTCTTCATTACATAGCAC 60.512 42.308 0.00 0.00 0.00 4.40
4444 4695 5.163581 GCAAGCACTCCATTCTTCATTACAT 60.164 40.000 0.00 0.00 0.00 2.29
4634 4907 2.801077 TTTACCCCTAAGCTCAAGGC 57.199 50.000 9.18 0.00 42.19 4.35
5027 5769 3.833732 TCAGTTAGAGTGAGGTGAGTGT 58.166 45.455 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.