Multiple sequence alignment - TraesCS2A01G444900

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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 TraesCS2A01G444900 chr2A 100.000 5224 0 0 1 5224 694910368 694905145 0.000000e+00 9648.0
1 TraesCS2A01G444900 chrUn 91.134 3429 213 55 967 4344 26268330 26264942 0.000000e+00 4564.0
2 TraesCS2A01G444900 chrUn 87.135 855 31 29 61 880 26269170 26268360 0.000000e+00 896.0
3 TraesCS2A01G444900 chr2B 92.616 3169 149 39 1291 4399 661452935 661449792 0.000000e+00 4477.0
4 TraesCS2A01G444900 chr2B 92.611 785 51 6 4446 5224 661448922 661448139 0.000000e+00 1122.0
5 TraesCS2A01G444900 chr2B 84.714 857 67 26 468 1297 661453792 661452973 0.000000e+00 798.0
6 TraesCS2A01G444900 chr2B 100.000 37 0 0 270 306 661453960 661453924 9.390000e-08 69.4


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 TraesCS2A01G444900 chr2A 694905145 694910368 5223 True 9648.0 9648 100.00000 1 5224 1 chr2A.!!$R1 5223
1 TraesCS2A01G444900 chrUn 26264942 26269170 4228 True 2730.0 4564 89.13450 61 4344 2 chrUn.!!$R1 4283
2 TraesCS2A01G444900 chr2B 661448139 661453960 5821 True 1616.6 4477 92.48525 270 5224 4 chr2B.!!$R1 4954

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
727 804 0.028242 CCAGCGAGCACTACTAGTCG 59.972 60.0 0.00 0.00 35.51 4.18 F
1305 1448 0.099968 TCTACGCGCGCTTACAGATT 59.900 50.0 32.58 9.66 0.00 2.40 F
2951 3170 0.319083 CCACCAGGTACGCACTTGTA 59.681 55.0 0.00 0.00 29.97 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1768 0.528466 CGATGATGGTCTCGGTGGTG 60.528 60.0 0.0 0.0 0.00 4.17 R
2988 3209 0.533755 AGTGAGCTTGACAGGTGCAC 60.534 55.0 8.8 8.8 32.85 4.57 R
4876 5941 0.107410 AACACAGCCGAGGTCACAAA 60.107 50.0 0.0 0.0 0.00 2.83 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
20 21 2.435372 TTTGCTCCCATCCCATGTAC 57.565 50.000 0.00 0.00 0.00 2.90
21 22 0.550914 TTGCTCCCATCCCATGTACC 59.449 55.000 0.00 0.00 0.00 3.34
22 23 0.623031 TGCTCCCATCCCATGTACCA 60.623 55.000 0.00 0.00 0.00 3.25
23 24 0.773644 GCTCCCATCCCATGTACCAT 59.226 55.000 0.00 0.00 0.00 3.55
24 25 1.985159 GCTCCCATCCCATGTACCATA 59.015 52.381 0.00 0.00 0.00 2.74
25 26 2.290323 GCTCCCATCCCATGTACCATAC 60.290 54.545 0.00 0.00 0.00 2.39
26 27 3.251484 CTCCCATCCCATGTACCATACT 58.749 50.000 0.00 0.00 0.00 2.12
27 28 3.652869 CTCCCATCCCATGTACCATACTT 59.347 47.826 0.00 0.00 0.00 2.24
28 29 4.051478 TCCCATCCCATGTACCATACTTT 58.949 43.478 0.00 0.00 0.00 2.66
29 30 4.141274 TCCCATCCCATGTACCATACTTTG 60.141 45.833 0.00 0.00 0.00 2.77
42 43 4.843728 CCATACTTTGGTGTCATGTACCT 58.156 43.478 18.24 5.48 40.99 3.08
43 44 4.635765 CCATACTTTGGTGTCATGTACCTG 59.364 45.833 18.24 12.48 40.99 4.00
44 45 5.487433 CATACTTTGGTGTCATGTACCTGA 58.513 41.667 18.24 0.00 39.01 3.86
45 46 3.740115 ACTTTGGTGTCATGTACCTGAC 58.260 45.455 20.61 20.61 44.70 3.51
46 47 3.391296 ACTTTGGTGTCATGTACCTGACT 59.609 43.478 25.44 6.90 44.73 3.41
47 48 4.141482 ACTTTGGTGTCATGTACCTGACTT 60.141 41.667 25.44 5.22 44.73 3.01
48 49 3.401033 TGGTGTCATGTACCTGACTTG 57.599 47.619 25.44 0.00 44.73 3.16
49 50 2.038426 TGGTGTCATGTACCTGACTTGG 59.962 50.000 25.44 0.00 44.73 3.61
50 51 2.615493 GGTGTCATGTACCTGACTTGGG 60.615 54.545 25.44 0.00 44.73 4.12
51 52 2.038557 GTGTCATGTACCTGACTTGGGT 59.961 50.000 25.44 0.00 44.73 4.51
52 53 3.259876 GTGTCATGTACCTGACTTGGGTA 59.740 47.826 25.44 7.51 44.73 3.69
129 130 4.214758 AGCTTTGCATTTTCCATTTGAAGC 59.785 37.500 3.72 3.72 37.75 3.86
132 133 5.676532 TTGCATTTTCCATTTGAAGCAAG 57.323 34.783 0.00 0.00 36.98 4.01
133 134 4.706035 TGCATTTTCCATTTGAAGCAAGT 58.294 34.783 0.00 0.00 31.12 3.16
134 135 4.512198 TGCATTTTCCATTTGAAGCAAGTG 59.488 37.500 0.00 0.00 31.12 3.16
135 136 4.612033 GCATTTTCCATTTGAAGCAAGTGC 60.612 41.667 0.00 0.00 42.49 4.40
136 137 3.815856 TTTCCATTTGAAGCAAGTGCA 57.184 38.095 6.00 0.00 45.16 4.57
137 138 3.815856 TTCCATTTGAAGCAAGTGCAA 57.184 38.095 6.00 0.00 45.16 4.08
138 139 3.374220 TCCATTTGAAGCAAGTGCAAG 57.626 42.857 6.00 0.00 45.16 4.01
149 150 2.008268 AAGTGCAAGTGCCACACTGC 62.008 55.000 13.30 13.30 44.62 4.40
180 181 3.441163 TCGCCACGAGATTACATTACAC 58.559 45.455 0.00 0.00 0.00 2.90
187 188 6.183360 CCACGAGATTACATTACACCAGAGTA 60.183 42.308 0.00 0.00 0.00 2.59
190 191 6.481434 AGATTACATTACACCAGAGTACCC 57.519 41.667 0.00 0.00 0.00 3.69
223 224 4.060205 GCAGTGGCATTGAAAACTGATTT 58.940 39.130 14.75 0.00 42.09 2.17
232 233 6.815142 GCATTGAAAACTGATTTAGGCTTCAT 59.185 34.615 0.00 0.00 33.67 2.57
233 234 7.009907 GCATTGAAAACTGATTTAGGCTTCATC 59.990 37.037 0.00 0.00 33.67 2.92
234 235 6.182039 TGAAAACTGATTTAGGCTTCATCG 57.818 37.500 0.00 0.00 30.62 3.84
235 236 5.705441 TGAAAACTGATTTAGGCTTCATCGT 59.295 36.000 0.00 0.00 30.62 3.73
236 237 6.876789 TGAAAACTGATTTAGGCTTCATCGTA 59.123 34.615 0.00 0.00 30.62 3.43
237 238 6.910536 AAACTGATTTAGGCTTCATCGTAG 57.089 37.500 0.00 0.00 0.00 3.51
238 239 5.599999 ACTGATTTAGGCTTCATCGTAGT 57.400 39.130 0.00 0.00 0.00 2.73
250 251 6.266323 GCTTCATCGTAGTTCTTACATCAGA 58.734 40.000 0.00 0.00 32.27 3.27
255 256 7.337184 TCATCGTAGTTCTTACATCAGAGACTT 59.663 37.037 0.00 0.00 32.27 3.01
256 257 8.613482 CATCGTAGTTCTTACATCAGAGACTTA 58.387 37.037 0.00 0.00 32.27 2.24
258 259 8.039538 TCGTAGTTCTTACATCAGAGACTTAGA 58.960 37.037 0.00 0.00 32.27 2.10
259 260 8.666573 CGTAGTTCTTACATCAGAGACTTAGAA 58.333 37.037 0.00 0.00 32.27 2.10
267 268 9.862371 TTACATCAGAGACTTAGAATTTCTGAC 57.138 33.333 9.22 0.00 44.80 3.51
317 345 3.071874 CAAAAGTGCTGGGTGGATAGA 57.928 47.619 0.00 0.00 0.00 1.98
326 354 0.105039 GGGTGGATAGAGCGGTGAAG 59.895 60.000 0.00 0.00 0.00 3.02
389 425 4.449405 GTGGAGAGCAGAGTGTAAAAACTC 59.551 45.833 0.00 0.00 45.82 3.01
400 436 6.526566 AGTGTAAAAACTCAACTAGCTTCG 57.473 37.500 0.00 0.00 0.00 3.79
403 439 5.526111 TGTAAAAACTCAACTAGCTTCGCTT 59.474 36.000 0.00 0.00 40.44 4.68
404 440 4.474226 AAAACTCAACTAGCTTCGCTTG 57.526 40.909 0.00 0.00 40.44 4.01
430 481 1.471684 CCTTGCCTTGCTGATCACTTC 59.528 52.381 0.00 0.00 0.00 3.01
433 484 1.275010 TGCCTTGCTGATCACTTCGTA 59.725 47.619 0.00 0.00 0.00 3.43
435 486 2.544685 CCTTGCTGATCACTTCGTAGG 58.455 52.381 0.00 0.00 0.00 3.18
436 487 2.093973 CCTTGCTGATCACTTCGTAGGT 60.094 50.000 0.00 0.00 0.00 3.08
437 488 3.589988 CTTGCTGATCACTTCGTAGGTT 58.410 45.455 0.00 0.00 0.00 3.50
438 489 3.232213 TGCTGATCACTTCGTAGGTTC 57.768 47.619 0.00 0.00 0.00 3.62
439 490 2.826128 TGCTGATCACTTCGTAGGTTCT 59.174 45.455 0.00 0.00 0.00 3.01
440 491 3.119459 TGCTGATCACTTCGTAGGTTCTC 60.119 47.826 0.00 0.00 0.00 2.87
530 582 3.247006 TCTTCTTGCGAATCACTACCC 57.753 47.619 0.00 0.00 0.00 3.69
535 587 0.172578 TGCGAATCACTACCCGTCTG 59.827 55.000 0.00 0.00 0.00 3.51
536 588 1.146358 GCGAATCACTACCCGTCTGC 61.146 60.000 0.00 0.00 0.00 4.26
537 589 0.527817 CGAATCACTACCCGTCTGCC 60.528 60.000 0.00 0.00 0.00 4.85
538 590 0.824759 GAATCACTACCCGTCTGCCT 59.175 55.000 0.00 0.00 0.00 4.75
539 591 2.029623 GAATCACTACCCGTCTGCCTA 58.970 52.381 0.00 0.00 0.00 3.93
578 633 4.015872 TCGATAGGATTGGGCAAATACC 57.984 45.455 0.00 0.00 27.78 2.73
579 634 3.392947 TCGATAGGATTGGGCAAATACCA 59.607 43.478 0.00 0.00 35.88 3.25
580 635 3.502211 CGATAGGATTGGGCAAATACCAC 59.498 47.826 0.00 0.00 37.82 4.16
581 636 2.917713 AGGATTGGGCAAATACCACA 57.082 45.000 0.00 0.00 37.82 4.17
584 639 2.365293 GGATTGGGCAAATACCACATCC 59.635 50.000 0.00 0.00 37.82 3.51
593 648 2.644555 ATACCACATCCCGTCTGCGC 62.645 60.000 0.00 0.00 36.67 6.09
613 670 2.287009 GCTAGTTTTATCGGCATGCACC 60.287 50.000 21.36 1.35 0.00 5.01
624 681 0.593128 GCATGCACCGAGAAAGTTGT 59.407 50.000 14.21 0.00 0.00 3.32
644 701 2.102252 GTCCTATCCTGTTCCAGCTCTG 59.898 54.545 0.00 0.00 0.00 3.35
720 797 1.257750 ATCACACCCAGCGAGCACTA 61.258 55.000 0.00 0.00 0.00 2.74
721 798 1.738099 CACACCCAGCGAGCACTAC 60.738 63.158 0.00 0.00 0.00 2.73
722 799 1.908793 ACACCCAGCGAGCACTACT 60.909 57.895 0.00 0.00 0.00 2.57
723 800 0.611062 ACACCCAGCGAGCACTACTA 60.611 55.000 0.00 0.00 0.00 1.82
724 801 0.101399 CACCCAGCGAGCACTACTAG 59.899 60.000 0.00 0.00 0.00 2.57
725 802 0.323542 ACCCAGCGAGCACTACTAGT 60.324 55.000 0.00 0.00 0.00 2.57
726 803 0.382515 CCCAGCGAGCACTACTAGTC 59.617 60.000 0.00 0.00 0.00 2.59
727 804 0.028242 CCAGCGAGCACTACTAGTCG 59.972 60.000 0.00 0.00 35.51 4.18
828 912 4.335037 GCGCCCTATCTGTACTATACTACC 59.665 50.000 0.00 0.00 0.00 3.18
832 916 5.816777 CCCTATCTGTACTATACTACCGCTC 59.183 48.000 0.00 0.00 0.00 5.03
925 1009 2.125552 TCGAGCAACTCATGGCCG 60.126 61.111 0.00 0.00 0.00 6.13
927 1011 3.512516 GAGCAACTCATGGCCGCC 61.513 66.667 1.04 1.04 0.00 6.13
942 1026 4.760047 GCCATCCACCTCGCGTGT 62.760 66.667 5.77 1.40 41.26 4.49
943 1027 2.509336 CCATCCACCTCGCGTGTC 60.509 66.667 5.77 0.00 41.26 3.67
944 1028 2.509336 CATCCACCTCGCGTGTCC 60.509 66.667 5.77 0.00 41.26 4.02
945 1029 2.994995 ATCCACCTCGCGTGTCCA 60.995 61.111 5.77 0.00 41.26 4.02
946 1030 3.296709 ATCCACCTCGCGTGTCCAC 62.297 63.158 5.77 0.00 41.26 4.02
963 1047 4.465512 CGTACCGTACGTGCGCCT 62.466 66.667 21.12 9.92 43.66 5.52
964 1048 2.126346 GTACCGTACGTGCGCCTT 60.126 61.111 21.12 9.21 0.00 4.35
965 1049 2.126385 TACCGTACGTGCGCCTTG 60.126 61.111 21.12 9.43 0.00 3.61
981 1065 2.035066 GCCTTGCCTATAAATGGTGCAG 59.965 50.000 0.00 0.00 32.88 4.41
993 1077 4.783621 GTGCAGCTCATGGCCGGA 62.784 66.667 5.05 0.00 43.05 5.14
1067 1151 5.646793 ACAGAACTAACGAGCAGTAGATACA 59.353 40.000 0.00 0.00 0.00 2.29
1269 1368 0.674581 CCATTCTCAAGAGGTGCGCA 60.675 55.000 5.66 5.66 0.00 6.09
1270 1369 1.376543 CATTCTCAAGAGGTGCGCAT 58.623 50.000 15.91 0.00 0.00 4.73
1271 1370 1.063616 CATTCTCAAGAGGTGCGCATG 59.936 52.381 15.91 7.64 0.00 4.06
1272 1371 1.300971 TTCTCAAGAGGTGCGCATGC 61.301 55.000 15.91 7.91 43.20 4.06
1303 1446 1.062047 CTCTACGCGCGCTTACAGA 59.938 57.895 32.58 21.61 0.00 3.41
1304 1447 0.317103 CTCTACGCGCGCTTACAGAT 60.317 55.000 32.58 10.51 0.00 2.90
1305 1448 0.099968 TCTACGCGCGCTTACAGATT 59.900 50.000 32.58 9.66 0.00 2.40
1306 1449 0.921347 CTACGCGCGCTTACAGATTT 59.079 50.000 32.58 8.80 0.00 2.17
1422 1573 0.388649 AGTACAAGCACGGCTTCTCG 60.389 55.000 7.99 1.68 46.77 4.04
1557 1708 2.807045 CTGCAGCAGACGGACGTC 60.807 66.667 18.42 16.39 44.86 4.34
1644 1795 1.118356 AGACCATCATCGGCCTCCTC 61.118 60.000 0.00 0.00 0.00 3.71
1849 2011 1.591059 CAGGAAGCTGATCGGAGCG 60.591 63.158 5.48 0.00 44.24 5.03
1852 2014 1.299773 GAAGCTGATCGGAGCGAGG 60.300 63.158 5.48 0.00 44.24 4.63
1861 2023 0.807667 TCGGAGCGAGGTACTACGAC 60.808 60.000 14.12 8.15 45.30 4.34
2134 2296 0.938008 TCGACATCATCTCGGTCTCG 59.062 55.000 0.00 0.00 37.82 4.04
2164 2326 2.433146 GCCCTACTTCTCCCCGGAC 61.433 68.421 0.73 0.00 0.00 4.79
2236 2398 4.722700 ATGGTGGTGTGCTCGGCC 62.723 66.667 0.00 0.00 0.00 6.13
2336 2498 1.134281 GACTTCGAGTCGGACGTCC 59.866 63.158 25.28 25.28 35.28 4.79
2341 2503 2.104859 CGAGTCGGACGTCCTGCTA 61.105 63.158 30.92 11.92 0.00 3.49
2373 2535 2.540515 CACCGCTGTCAAGGTACTATG 58.459 52.381 0.00 0.00 38.49 2.23
2375 2537 1.200483 CGCTGTCAAGGTACTATGCG 58.800 55.000 0.00 0.00 38.49 4.73
2376 2538 1.469251 CGCTGTCAAGGTACTATGCGT 60.469 52.381 0.00 0.00 38.49 5.24
2383 2545 3.196039 TCAAGGTACTATGCGTTGCCTTA 59.804 43.478 0.26 0.00 38.49 2.69
2392 2554 0.715551 GCGTTGCCTTAATTTGCTGC 59.284 50.000 0.00 0.00 0.00 5.25
2393 2555 1.934399 GCGTTGCCTTAATTTGCTGCA 60.934 47.619 0.00 0.00 0.00 4.41
2409 2571 2.417933 GCTGCATCCTGACACTTGTTAG 59.582 50.000 0.00 0.00 0.00 2.34
2413 2575 4.515191 TGCATCCTGACACTTGTTAGTTTC 59.485 41.667 0.99 0.00 32.78 2.78
2415 2577 5.308825 CATCCTGACACTTGTTAGTTTCCT 58.691 41.667 0.99 0.00 31.43 3.36
2416 2578 6.464222 CATCCTGACACTTGTTAGTTTCCTA 58.536 40.000 0.99 0.00 31.43 2.94
2417 2579 6.097915 TCCTGACACTTGTTAGTTTCCTAG 57.902 41.667 0.99 0.00 31.43 3.02
2418 2580 5.601313 TCCTGACACTTGTTAGTTTCCTAGT 59.399 40.000 0.99 0.00 31.43 2.57
2419 2581 6.099269 TCCTGACACTTGTTAGTTTCCTAGTT 59.901 38.462 0.99 0.00 31.43 2.24
2422 2584 8.570068 TGACACTTGTTAGTTTCCTAGTTTTT 57.430 30.769 0.00 0.00 31.43 1.94
2535 2715 0.968901 AGTACCCGTTGATCGCAGGA 60.969 55.000 2.20 0.00 38.35 3.86
2577 2757 4.944930 TCAGCTTCTAGTACTTCTGACTCC 59.055 45.833 0.00 0.00 0.00 3.85
2605 2798 7.781548 AGGTAACACATATACGAACCAATTC 57.218 36.000 0.00 0.00 41.41 2.17
2613 2807 8.559536 CACATATACGAACCAATTCAATAAGCT 58.440 33.333 0.00 0.00 34.14 3.74
2614 2808 9.772973 ACATATACGAACCAATTCAATAAGCTA 57.227 29.630 0.00 0.00 34.14 3.32
2653 2850 2.279741 ACCCGTGATGTGATTTCATCG 58.720 47.619 0.00 0.00 44.82 3.84
2656 2853 2.537529 CCGTGATGTGATTTCATCGTGC 60.538 50.000 0.00 0.00 44.82 5.34
2666 2885 5.291858 GTGATTTCATCGTGCTTCTCATGTA 59.708 40.000 0.00 0.00 33.44 2.29
2667 2886 6.018425 GTGATTTCATCGTGCTTCTCATGTAT 60.018 38.462 0.00 0.00 33.44 2.29
2668 2887 6.539826 TGATTTCATCGTGCTTCTCATGTATT 59.460 34.615 0.00 0.00 33.44 1.89
2680 2899 2.998670 CTCATGTATTATGCCCTGCTCG 59.001 50.000 0.00 0.00 0.00 5.03
2735 2954 1.676529 CTGGATGCCAGCAAGATCAAG 59.323 52.381 0.00 0.00 45.13 3.02
2792 3011 3.254060 CACGTCTAAGATGGTGAAGGTG 58.746 50.000 0.00 0.00 0.00 4.00
2936 3155 1.812571 CACAAGTACATTGCCTCCACC 59.187 52.381 0.00 0.00 43.15 4.61
2947 3166 2.283529 CCTCCACCAGGTACGCACT 61.284 63.158 0.00 0.00 37.53 4.40
2948 3167 1.671742 CTCCACCAGGTACGCACTT 59.328 57.895 0.00 0.00 35.89 3.16
2949 3168 0.670546 CTCCACCAGGTACGCACTTG 60.671 60.000 0.00 0.00 35.89 3.16
2951 3170 0.319083 CCACCAGGTACGCACTTGTA 59.681 55.000 0.00 0.00 29.97 2.41
2952 3171 1.425412 CACCAGGTACGCACTTGTAC 58.575 55.000 0.00 0.00 43.15 2.90
2953 3172 1.042229 ACCAGGTACGCACTTGTACA 58.958 50.000 0.00 0.00 45.16 2.90
2954 3173 1.413445 ACCAGGTACGCACTTGTACAA 59.587 47.619 8.28 8.28 45.16 2.41
2955 3174 2.038033 ACCAGGTACGCACTTGTACAAT 59.962 45.455 9.13 0.00 45.16 2.71
2956 3175 2.415168 CCAGGTACGCACTTGTACAATG 59.585 50.000 9.13 10.58 45.16 2.82
2957 3176 2.073816 AGGTACGCACTTGTACAATGC 58.926 47.619 22.51 22.51 45.16 3.56
2958 3177 1.801771 GGTACGCACTTGTACAATGCA 59.198 47.619 27.32 15.51 45.16 3.96
2959 3178 2.412325 GGTACGCACTTGTACAATGCAC 60.412 50.000 27.32 21.76 45.16 4.57
2961 3180 0.590682 CGCACTTGTACAATGCACCA 59.409 50.000 27.32 3.25 39.39 4.17
2963 3182 2.351641 CGCACTTGTACAATGCACCAAT 60.352 45.455 27.32 3.32 39.39 3.16
2972 3193 5.589855 TGTACAATGCACCAATATCTTCCAG 59.410 40.000 0.00 0.00 0.00 3.86
2982 3203 6.769822 CACCAATATCTTCCAGTTAAGCTCAT 59.230 38.462 0.00 0.00 0.00 2.90
2985 3206 7.040823 CCAATATCTTCCAGTTAAGCTCATTCC 60.041 40.741 0.00 0.00 0.00 3.01
2988 3209 3.634397 TCCAGTTAAGCTCATTCCCAG 57.366 47.619 0.00 0.00 0.00 4.45
2994 3215 0.610232 AAGCTCATTCCCAGTGCACC 60.610 55.000 14.63 0.00 0.00 5.01
2995 3216 1.001641 GCTCATTCCCAGTGCACCT 60.002 57.895 14.63 0.00 0.00 4.00
3010 3231 1.938926 GCACCTGTCAAGCTCACTCTC 60.939 57.143 0.00 0.00 0.00 3.20
3015 3236 2.415857 CTGTCAAGCTCACTCTCAATGC 59.584 50.000 0.00 0.00 0.00 3.56
3023 3244 4.335874 AGCTCACTCTCAATGCATGAAATC 59.664 41.667 0.00 0.00 37.67 2.17
3026 3247 5.250982 TCACTCTCAATGCATGAAATCAGT 58.749 37.500 0.00 0.00 37.67 3.41
3029 3250 5.123502 ACTCTCAATGCATGAAATCAGTGAC 59.876 40.000 0.00 0.00 37.67 3.67
3032 3253 2.885135 TGCATGAAATCAGTGACCCT 57.115 45.000 0.00 0.00 0.00 4.34
3035 3256 2.421424 GCATGAAATCAGTGACCCTGTC 59.579 50.000 0.00 0.00 42.19 3.51
3047 3268 2.485582 CCTGTCGCGACGATCACT 59.514 61.111 31.88 0.00 38.42 3.41
3101 3322 1.592400 CCGTCGTGGCCTACTTCTCA 61.592 60.000 3.32 0.00 0.00 3.27
3178 3399 4.002797 GCCCTTAGCCAGGTGTTG 57.997 61.111 0.00 0.00 42.02 3.33
3179 3400 1.074951 GCCCTTAGCCAGGTGTTGT 59.925 57.895 0.00 0.00 42.02 3.32
3180 3401 1.244019 GCCCTTAGCCAGGTGTTGTG 61.244 60.000 0.00 0.00 42.02 3.33
3182 3403 1.523758 CCTTAGCCAGGTGTTGTGTC 58.476 55.000 0.00 0.00 37.99 3.67
3183 3404 1.148310 CTTAGCCAGGTGTTGTGTCG 58.852 55.000 0.00 0.00 0.00 4.35
3217 3444 3.466836 ACTAACGCATCCATGTGGTATG 58.533 45.455 5.16 3.57 39.47 2.39
3290 3517 4.047059 GACGTCACTTCCGGCCGA 62.047 66.667 30.73 10.38 0.00 5.54
3390 3618 2.852075 AAGGCCTGGAACCCGACA 60.852 61.111 5.69 0.00 0.00 4.35
3444 3672 5.450592 TGACAACAGGTACGTACATAACA 57.549 39.130 26.02 13.21 0.00 2.41
3451 3679 7.181143 ACAGGTACGTACATAACAAAACAAG 57.819 36.000 26.02 6.74 0.00 3.16
3473 3701 4.122776 GCTGACAGATTAATCGTGTCCAT 58.877 43.478 27.17 5.75 39.96 3.41
3476 3704 3.871006 GACAGATTAATCGTGTCCATGCA 59.129 43.478 23.57 0.00 35.54 3.96
3477 3705 4.454678 ACAGATTAATCGTGTCCATGCAT 58.545 39.130 9.78 0.00 0.00 3.96
3478 3706 5.610398 ACAGATTAATCGTGTCCATGCATA 58.390 37.500 9.78 0.00 0.00 3.14
3479 3707 5.466728 ACAGATTAATCGTGTCCATGCATAC 59.533 40.000 9.78 0.00 0.00 2.39
3481 3709 2.708216 AATCGTGTCCATGCATACCA 57.292 45.000 0.00 0.00 0.00 3.25
3517 3752 0.457337 ATTTCGACCGTGTCTACCGC 60.457 55.000 0.00 0.00 0.00 5.68
3557 3792 0.179234 TGAACAACGACAAGGCTCCA 59.821 50.000 0.00 0.00 0.00 3.86
3566 3801 0.321653 ACAAGGCTCCAATGACGACC 60.322 55.000 0.00 0.00 0.00 4.79
3572 3807 2.431771 CCAATGACGACCGACGCA 60.432 61.111 0.00 2.78 46.94 5.24
3875 4110 2.261671 GTCGGAGCGCAGGAAGAA 59.738 61.111 11.47 0.00 0.00 2.52
3881 4116 2.669569 GCGCAGGAAGAAGCCACA 60.670 61.111 0.30 0.00 0.00 4.17
3928 4163 0.741221 GGTCTGGATGTGAAGGTCGC 60.741 60.000 0.00 0.00 0.00 5.19
4003 4238 1.534595 CTTCTCTGGCAAGAACACAGC 59.465 52.381 0.00 0.00 32.03 4.40
4106 4341 8.834465 AGCTGATGAAATGTGAAATCTATGTAC 58.166 33.333 0.00 0.00 0.00 2.90
4122 4360 4.650754 ATGTACGTACAAGATGGGACTC 57.349 45.455 30.46 0.00 39.99 3.36
4140 4378 3.719924 ACTCGTATGTCTCTCGTCTAGG 58.280 50.000 0.00 0.00 0.00 3.02
4196 4434 5.807011 GGCATTTTGGTCATGTAGTTTCATC 59.193 40.000 0.00 0.00 0.00 2.92
4240 4478 1.006571 GCACACTCGGAAGTCGGAA 60.007 57.895 0.00 0.00 39.77 4.30
4247 4485 2.206750 CTCGGAAGTCGGAACAACAAA 58.793 47.619 0.00 0.00 39.77 2.83
4280 4518 9.800433 TTGTGTAGCATAATCCATAAATGTTTG 57.200 29.630 0.00 0.00 0.00 2.93
4411 4666 8.933807 CCAAACACAATGTTAATAAATGCATCA 58.066 29.630 0.00 0.00 40.14 3.07
4425 4680 6.702716 AAATGCATCATCATGTGATACACA 57.297 33.333 0.00 7.03 45.76 3.72
4469 5530 3.914364 CGATAGTTTCTGCTTTTGTTGCC 59.086 43.478 0.00 0.00 0.00 4.52
4471 5532 3.893326 AGTTTCTGCTTTTGTTGCCTT 57.107 38.095 0.00 0.00 0.00 4.35
4473 5534 2.600470 TTCTGCTTTTGTTGCCTTGG 57.400 45.000 0.00 0.00 0.00 3.61
4505 5566 2.371841 TGATTTGTGGTGCTACAGTCCT 59.628 45.455 0.00 0.00 0.00 3.85
4516 5577 2.449031 TACAGTCCTTGGCGGCACAG 62.449 60.000 12.92 12.43 0.00 3.66
4524 5585 3.286751 GGCGGCACAGTCAAGCAA 61.287 61.111 3.07 0.00 0.00 3.91
4540 5601 0.947180 GCAACTTGCATGGTTGGCTG 60.947 55.000 24.51 9.16 44.26 4.85
4542 5603 0.760189 AACTTGCATGGTTGGCTGGT 60.760 50.000 4.44 0.00 0.00 4.00
4557 5618 0.911769 CTGGTGTGGATTGGGAGCTA 59.088 55.000 0.00 0.00 0.00 3.32
4568 5629 3.686045 GGAGCTATCCGGGGCGAG 61.686 72.222 0.00 0.00 35.37 5.03
4601 5662 1.134580 TGAGCAGGCTATCTCTTGTGC 60.135 52.381 14.48 0.29 0.00 4.57
4613 5674 2.125065 TTGTGCGGGTCGTGTTGT 60.125 55.556 0.00 0.00 0.00 3.32
4628 5691 0.038159 GTTGTAGAGCGCTCCTGTGT 60.038 55.000 32.94 17.22 0.00 3.72
4656 5719 1.202639 TCTTCGTGATGCCAGTGTTGT 60.203 47.619 0.00 0.00 0.00 3.32
4690 5754 6.340962 ACATTGAAATGGAGCCATATGATG 57.659 37.500 14.00 12.23 40.70 3.07
4718 5783 3.800826 CCCGTGCTAGGGCTAATTT 57.199 52.632 4.16 0.00 45.72 1.82
4720 5785 0.663153 CCGTGCTAGGGCTAATTTGC 59.337 55.000 3.03 3.03 39.59 3.68
4762 5827 6.072175 GCCCTCTATGTAGTCACTCTCTAATG 60.072 46.154 0.00 0.00 0.00 1.90
4824 5889 2.742116 GCCCGGGATTCAGGTGCTA 61.742 63.158 29.31 0.00 0.00 3.49
4837 5902 1.571773 GGTGCTATGTGGGACCCCTT 61.572 60.000 8.45 0.44 41.03 3.95
4850 5915 2.289133 GGACCCCTTCTTCGCATCTATC 60.289 54.545 0.00 0.00 0.00 2.08
4851 5916 1.694696 ACCCCTTCTTCGCATCTATCC 59.305 52.381 0.00 0.00 0.00 2.59
4887 5952 0.679505 TGGACTCCTTTGTGACCTCG 59.320 55.000 0.00 0.00 0.00 4.63
4891 5956 0.671781 CTCCTTTGTGACCTCGGCTG 60.672 60.000 0.00 0.00 0.00 4.85
4905 5970 1.903860 TCGGCTGTGTTTATGGTACCT 59.096 47.619 14.36 1.08 0.00 3.08
4910 5975 3.937079 GCTGTGTTTATGGTACCTACACC 59.063 47.826 24.21 13.93 38.59 4.16
4925 5990 4.675303 ACCACCCCCTAGCCAGCA 62.675 66.667 0.00 0.00 0.00 4.41
4945 6010 1.592400 CCCGCTTACGAGGAGTGTGA 61.592 60.000 0.00 0.00 43.93 3.58
4954 6019 2.760650 ACGAGGAGTGTGATGCTTATGA 59.239 45.455 0.00 0.00 0.00 2.15
4955 6020 3.386078 ACGAGGAGTGTGATGCTTATGAT 59.614 43.478 0.00 0.00 0.00 2.45
5011 6076 2.368439 TGTGGCTTCTATGGTTGATGC 58.632 47.619 0.00 0.00 34.95 3.91
5059 6124 2.061578 TTCTCGGGGCCGCTTCATA 61.062 57.895 18.79 0.00 39.59 2.15
5073 6138 6.426937 GGCCGCTTCATATCTAAGATTTACAA 59.573 38.462 0.00 0.00 0.00 2.41
5117 6183 1.285078 GCTAACCCTGGATCCTTTGGT 59.715 52.381 14.23 13.41 0.00 3.67
5148 6214 2.560105 AGAAGAAAGCAAATCAGGGCAC 59.440 45.455 0.00 0.00 0.00 5.01
5179 6246 2.363975 GCCACTACCACCCGATCCA 61.364 63.158 0.00 0.00 0.00 3.41
5191 6258 1.382522 CCGATCCAACCACATGAAGG 58.617 55.000 0.00 3.24 0.00 3.46
5197 6264 4.387026 TCCAACCACATGAAGGAGAAAT 57.613 40.909 14.40 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.622977 GGTACATGGGATGGGAGCAAAA 60.623 50.000 0.00 0.00 33.60 2.44
1 2 1.064017 GGTACATGGGATGGGAGCAAA 60.064 52.381 0.00 0.00 33.60 3.68
2 3 0.550914 GGTACATGGGATGGGAGCAA 59.449 55.000 0.00 0.00 33.60 3.91
3 4 0.623031 TGGTACATGGGATGGGAGCA 60.623 55.000 0.00 0.00 33.60 4.26
4 5 2.230664 TGGTACATGGGATGGGAGC 58.769 57.895 0.00 0.00 33.60 4.70
21 22 5.487433 TCAGGTACATGACACCAAAGTATG 58.513 41.667 19.04 10.18 38.62 2.39
22 23 5.755409 TCAGGTACATGACACCAAAGTAT 57.245 39.130 19.04 0.13 38.62 2.12
38 39 1.259840 GCCGGTACCCAAGTCAGGTA 61.260 60.000 6.25 0.00 38.89 3.08
39 40 2.590114 GCCGGTACCCAAGTCAGGT 61.590 63.158 6.25 0.00 41.64 4.00
40 41 2.267961 GCCGGTACCCAAGTCAGG 59.732 66.667 6.25 0.36 0.00 3.86
41 42 0.974010 TAGGCCGGTACCCAAGTCAG 60.974 60.000 6.25 0.00 0.00 3.51
42 43 1.078891 TAGGCCGGTACCCAAGTCA 59.921 57.895 6.25 0.00 0.00 3.41
43 44 1.259840 TGTAGGCCGGTACCCAAGTC 61.260 60.000 6.25 0.00 0.00 3.01
44 45 0.837260 TTGTAGGCCGGTACCCAAGT 60.837 55.000 6.25 0.00 0.00 3.16
45 46 0.392060 GTTGTAGGCCGGTACCCAAG 60.392 60.000 6.25 0.00 0.00 3.61
46 47 1.126329 TGTTGTAGGCCGGTACCCAA 61.126 55.000 6.25 0.23 0.00 4.12
47 48 1.535930 TGTTGTAGGCCGGTACCCA 60.536 57.895 6.25 0.00 0.00 4.51
48 49 1.078918 GTGTTGTAGGCCGGTACCC 60.079 63.158 6.25 0.00 0.00 3.69
49 50 0.671472 GTGTGTTGTAGGCCGGTACC 60.671 60.000 1.90 0.16 0.00 3.34
50 51 0.033781 TGTGTGTTGTAGGCCGGTAC 59.966 55.000 1.90 0.00 0.00 3.34
51 52 0.978151 ATGTGTGTTGTAGGCCGGTA 59.022 50.000 1.90 0.00 0.00 4.02
52 53 0.978151 TATGTGTGTTGTAGGCCGGT 59.022 50.000 1.90 0.00 0.00 5.28
53 54 2.102070 TTATGTGTGTTGTAGGCCGG 57.898 50.000 0.00 0.00 0.00 6.13
54 55 3.242284 CGATTTATGTGTGTTGTAGGCCG 60.242 47.826 0.00 0.00 0.00 6.13
55 56 3.486875 GCGATTTATGTGTGTTGTAGGCC 60.487 47.826 0.00 0.00 0.00 5.19
56 57 3.126171 TGCGATTTATGTGTGTTGTAGGC 59.874 43.478 0.00 0.00 0.00 3.93
57 58 4.937696 TGCGATTTATGTGTGTTGTAGG 57.062 40.909 0.00 0.00 0.00 3.18
58 59 6.105657 TGATGCGATTTATGTGTGTTGTAG 57.894 37.500 0.00 0.00 0.00 2.74
59 60 6.487689 TTGATGCGATTTATGTGTGTTGTA 57.512 33.333 0.00 0.00 0.00 2.41
64 65 6.728200 AGGTATTTGATGCGATTTATGTGTG 58.272 36.000 0.00 0.00 0.00 3.82
129 130 0.248743 CAGTGTGGCACTTGCACTTG 60.249 55.000 19.83 5.35 42.59 3.16
132 133 2.026590 GCAGTGTGGCACTTGCAC 59.973 61.111 29.59 17.17 42.59 4.57
133 134 2.439883 TGCAGTGTGGCACTTGCA 60.440 55.556 31.80 31.80 42.59 4.08
149 150 3.122150 TCGTGGCGAGTTGAGAATG 57.878 52.632 0.00 0.00 0.00 2.67
180 181 1.135083 CACTAACTGCGGGTACTCTGG 60.135 57.143 0.00 0.00 0.00 3.86
187 188 2.347490 CTGCCACTAACTGCGGGT 59.653 61.111 0.00 0.00 0.00 5.28
190 191 2.680913 GCCACTGCCACTAACTGCG 61.681 63.158 0.00 0.00 0.00 5.18
223 224 6.320418 TGATGTAAGAACTACGATGAAGCCTA 59.680 38.462 0.00 0.00 32.65 3.93
232 233 8.039538 TCTAAGTCTCTGATGTAAGAACTACGA 58.960 37.037 0.00 0.00 32.65 3.43
233 234 8.199176 TCTAAGTCTCTGATGTAAGAACTACG 57.801 38.462 0.00 0.00 32.65 3.51
250 251 8.951243 GCCTAAATTGTCAGAAATTCTAAGTCT 58.049 33.333 0.00 0.00 0.00 3.24
255 256 7.362920 GGCTTGCCTAAATTGTCAGAAATTCTA 60.363 37.037 4.11 0.00 0.00 2.10
256 257 6.393171 GCTTGCCTAAATTGTCAGAAATTCT 58.607 36.000 0.00 0.00 0.00 2.40
258 259 5.011943 TGGCTTGCCTAAATTGTCAGAAATT 59.988 36.000 13.18 0.00 0.00 1.82
259 260 4.527816 TGGCTTGCCTAAATTGTCAGAAAT 59.472 37.500 13.18 0.00 0.00 2.17
260 261 3.894427 TGGCTTGCCTAAATTGTCAGAAA 59.106 39.130 13.18 0.00 0.00 2.52
261 262 3.495331 TGGCTTGCCTAAATTGTCAGAA 58.505 40.909 13.18 0.00 0.00 3.02
262 263 3.084039 CTGGCTTGCCTAAATTGTCAGA 58.916 45.455 13.18 0.00 0.00 3.27
263 264 2.416431 GCTGGCTTGCCTAAATTGTCAG 60.416 50.000 13.18 0.00 0.00 3.51
264 265 1.545582 GCTGGCTTGCCTAAATTGTCA 59.454 47.619 13.18 0.00 0.00 3.58
265 266 2.284263 GCTGGCTTGCCTAAATTGTC 57.716 50.000 13.18 0.00 0.00 3.18
307 335 0.105039 CTTCACCGCTCTATCCACCC 59.895 60.000 0.00 0.00 0.00 4.61
398 434 3.673484 GCAAGGCAAGGCAAGCGA 61.673 61.111 0.00 0.00 0.00 4.93
400 436 2.875804 AAGGCAAGGCAAGGCAAGC 61.876 57.895 5.62 0.00 0.00 4.01
403 439 3.618750 GCAAGGCAAGGCAAGGCA 61.619 61.111 5.62 0.00 0.00 4.75
404 440 3.308705 AGCAAGGCAAGGCAAGGC 61.309 61.111 0.00 0.00 0.00 4.35
530 582 1.323412 ACATCTAGGCTAGGCAGACG 58.677 55.000 20.92 13.44 33.60 4.18
535 587 1.269998 CGTGGTACATCTAGGCTAGGC 59.730 57.143 20.92 8.55 44.52 3.93
536 588 2.860009 TCGTGGTACATCTAGGCTAGG 58.140 52.381 20.92 8.81 44.52 3.02
537 589 3.125487 CGATCGTGGTACATCTAGGCTAG 59.875 52.174 15.56 15.56 44.52 3.42
538 590 3.072211 CGATCGTGGTACATCTAGGCTA 58.928 50.000 7.03 0.00 44.52 3.93
539 591 1.880675 CGATCGTGGTACATCTAGGCT 59.119 52.381 7.03 0.00 44.52 4.58
578 633 1.589993 CTAGCGCAGACGGGATGTG 60.590 63.158 11.47 0.00 40.57 3.21
579 634 1.605058 AACTAGCGCAGACGGGATGT 61.605 55.000 11.47 0.00 40.57 3.06
580 635 0.460284 AAACTAGCGCAGACGGGATG 60.460 55.000 11.47 0.00 40.57 3.51
581 636 0.249398 AAAACTAGCGCAGACGGGAT 59.751 50.000 11.47 0.00 40.57 3.85
584 639 1.517276 CGATAAAACTAGCGCAGACGG 59.483 52.381 11.47 0.00 40.57 4.79
593 648 3.609103 GGTGCATGCCGATAAAACTAG 57.391 47.619 16.68 0.00 0.00 2.57
613 670 4.457834 ACAGGATAGGACAACTTTCTCG 57.542 45.455 0.00 0.00 0.00 4.04
614 671 5.179533 GGAACAGGATAGGACAACTTTCTC 58.820 45.833 0.00 0.00 0.00 2.87
615 672 4.597507 TGGAACAGGATAGGACAACTTTCT 59.402 41.667 0.00 0.00 0.00 2.52
644 701 2.568090 CAATGCGTGGTTCAGGCC 59.432 61.111 0.00 0.00 43.45 5.19
720 797 1.836802 GGAGTGGAAGGTCGACTAGT 58.163 55.000 16.46 0.00 35.54 2.57
721 798 0.733729 CGGAGTGGAAGGTCGACTAG 59.266 60.000 16.46 0.00 35.54 2.57
722 799 0.679002 CCGGAGTGGAAGGTCGACTA 60.679 60.000 16.46 0.00 42.00 2.59
723 800 1.977544 CCGGAGTGGAAGGTCGACT 60.978 63.158 16.46 0.00 42.00 4.18
724 801 1.813728 AACCGGAGTGGAAGGTCGAC 61.814 60.000 9.46 7.13 42.00 4.20
725 802 0.251297 TAACCGGAGTGGAAGGTCGA 60.251 55.000 9.46 0.00 42.00 4.20
726 803 0.604578 TTAACCGGAGTGGAAGGTCG 59.395 55.000 9.46 0.00 42.00 4.79
727 804 1.670967 CGTTAACCGGAGTGGAAGGTC 60.671 57.143 9.46 0.00 42.00 3.85
779 856 4.520846 CTGATTTCCCACGCGCGC 62.521 66.667 32.58 23.91 0.00 6.86
780 857 1.906994 TTTCTGATTTCCCACGCGCG 61.907 55.000 30.96 30.96 0.00 6.86
828 912 4.265630 CGCGTGCATTACCGAGCG 62.266 66.667 0.00 0.71 41.56 5.03
907 991 2.456119 CGGCCATGAGTTGCTCGAC 61.456 63.158 2.24 0.00 32.35 4.20
908 992 2.125552 CGGCCATGAGTTGCTCGA 60.126 61.111 2.24 0.00 32.35 4.04
947 1031 2.126346 AAGGCGCACGTACGGTAC 60.126 61.111 21.06 8.25 0.00 3.34
948 1032 2.126385 CAAGGCGCACGTACGGTA 60.126 61.111 21.06 0.00 0.00 4.02
951 1035 3.848256 TATAGGCAAGGCGCACGTACG 62.848 57.143 15.01 15.01 45.17 3.67
952 1036 0.249155 TATAGGCAAGGCGCACGTAC 60.249 55.000 10.83 0.00 45.17 3.67
953 1037 0.460722 TTATAGGCAAGGCGCACGTA 59.539 50.000 10.83 1.63 45.17 3.57
954 1038 0.391927 TTTATAGGCAAGGCGCACGT 60.392 50.000 10.83 0.00 45.17 4.49
955 1039 0.944386 ATTTATAGGCAAGGCGCACG 59.056 50.000 10.83 0.00 45.17 5.34
956 1040 1.001378 CCATTTATAGGCAAGGCGCAC 60.001 52.381 10.83 0.00 45.17 5.34
957 1041 1.317613 CCATTTATAGGCAAGGCGCA 58.682 50.000 10.83 0.00 45.17 6.09
958 1042 1.001378 CACCATTTATAGGCAAGGCGC 60.001 52.381 0.00 0.00 41.28 6.53
959 1043 1.001378 GCACCATTTATAGGCAAGGCG 60.001 52.381 0.00 0.00 0.00 5.52
960 1044 2.031120 TGCACCATTTATAGGCAAGGC 58.969 47.619 0.00 0.00 0.00 4.35
961 1045 2.035066 GCTGCACCATTTATAGGCAAGG 59.965 50.000 0.00 0.00 33.58 3.61
962 1046 2.954318 AGCTGCACCATTTATAGGCAAG 59.046 45.455 1.02 0.00 33.58 4.01
963 1047 2.951642 GAGCTGCACCATTTATAGGCAA 59.048 45.455 1.02 0.00 33.58 4.52
964 1048 2.092484 TGAGCTGCACCATTTATAGGCA 60.092 45.455 1.02 0.00 0.00 4.75
965 1049 2.575532 TGAGCTGCACCATTTATAGGC 58.424 47.619 1.02 0.00 0.00 3.93
981 1065 2.821366 CACTGTCCGGCCATGAGC 60.821 66.667 2.24 0.00 42.60 4.26
1024 1108 2.863740 TGTCAGTTGAACGCTGTGTAAG 59.136 45.455 0.00 0.00 35.60 2.34
1037 1121 3.381045 TGCTCGTTAGTTCTGTCAGTTG 58.619 45.455 0.00 0.00 0.00 3.16
1067 1151 0.905357 GGCCGTGCCCTATCTATGAT 59.095 55.000 3.73 0.00 44.06 2.45
1157 1256 4.814294 CGTACACCTGGCTCCCGC 62.814 72.222 0.00 0.00 0.00 6.13
1158 1257 3.379445 ACGTACACCTGGCTCCCG 61.379 66.667 0.00 0.00 0.00 5.14
1325 1468 7.186804 CCGTGCGATTTACTTTCTGAATATTT 58.813 34.615 0.00 0.00 0.00 1.40
1557 1708 1.482278 GCTTAGCCGAGTCGATCTTG 58.518 55.000 15.64 8.22 0.00 3.02
1617 1768 0.528466 CGATGATGGTCTCGGTGGTG 60.528 60.000 0.00 0.00 0.00 4.17
1623 1774 3.133014 AGGCCGATGATGGTCTCG 58.867 61.111 0.00 0.00 40.97 4.04
1626 1777 1.369321 GAGGAGGCCGATGATGGTC 59.631 63.158 0.00 0.00 0.00 4.02
1706 1857 1.672356 CAGACGCCCTTCCACTTGG 60.672 63.158 0.00 0.00 0.00 3.61
1747 1898 1.211703 TCACTTGTTGCAGTTGGAGGA 59.788 47.619 0.00 0.00 0.00 3.71
1852 2014 1.640604 CTCGCCGAGGTCGTAGTAC 59.359 63.158 6.13 0.00 37.74 2.73
2120 2282 1.511318 CCGAGCGAGACCGAGATGAT 61.511 60.000 0.00 0.00 38.22 2.45
2164 2326 1.739338 CGATGGGGTCCTCGGAGAAG 61.739 65.000 6.58 0.00 34.09 2.85
2215 2377 2.382746 CGAGCACACCACCATGACG 61.383 63.158 0.00 0.00 0.00 4.35
2355 2517 1.571919 GCATAGTACCTTGACAGCGG 58.428 55.000 0.00 0.00 0.00 5.52
2373 2535 0.715551 GCAGCAAATTAAGGCAACGC 59.284 50.000 0.00 0.00 46.39 4.84
2375 2537 2.931969 GGATGCAGCAAATTAAGGCAAC 59.068 45.455 3.51 0.00 38.08 4.17
2376 2538 2.833338 AGGATGCAGCAAATTAAGGCAA 59.167 40.909 3.51 0.00 38.08 4.52
2383 2545 2.522185 AGTGTCAGGATGCAGCAAATT 58.478 42.857 3.51 0.00 34.76 1.82
2392 2554 5.308825 AGGAAACTAACAAGTGTCAGGATG 58.691 41.667 0.00 0.00 40.61 3.51
2393 2555 5.568620 AGGAAACTAACAAGTGTCAGGAT 57.431 39.130 0.00 0.00 40.61 3.24
2461 2641 0.677731 CCACCCTGCATTGACACGAT 60.678 55.000 0.00 0.00 0.00 3.73
2535 2715 4.252073 CTGAACTAGACTTTGCTGATGCT 58.748 43.478 0.00 0.00 40.48 3.79
2577 2757 4.026310 GGTTCGTATATGTGTTACCTTGCG 60.026 45.833 0.00 0.00 0.00 4.85
2595 2776 6.747280 CCTTTGTAGCTTATTGAATTGGTTCG 59.253 38.462 0.00 0.00 37.15 3.95
2605 2798 6.262944 TGCATATGGTCCTTTGTAGCTTATTG 59.737 38.462 4.56 0.00 0.00 1.90
2613 2807 5.381757 GGGTATTGCATATGGTCCTTTGTA 58.618 41.667 4.56 0.00 0.00 2.41
2614 2808 4.215109 GGGTATTGCATATGGTCCTTTGT 58.785 43.478 4.56 0.00 0.00 2.83
2653 2850 4.214971 CAGGGCATAATACATGAGAAGCAC 59.785 45.833 0.00 0.00 0.00 4.40
2656 2853 4.649692 AGCAGGGCATAATACATGAGAAG 58.350 43.478 0.00 0.00 0.00 2.85
2666 2885 2.645838 ACATTCGAGCAGGGCATAAT 57.354 45.000 0.00 0.00 0.00 1.28
2667 2886 2.418368 AACATTCGAGCAGGGCATAA 57.582 45.000 0.00 0.00 0.00 1.90
2668 2887 2.418368 AAACATTCGAGCAGGGCATA 57.582 45.000 0.00 0.00 0.00 3.14
2680 2899 3.374745 CAGTGACTGCACCAAAACATTC 58.625 45.455 0.00 0.00 46.32 2.67
2745 2964 2.833533 GCGAGTGGTTGCACAGCAA 61.834 57.895 0.00 0.00 46.80 3.91
2777 2996 2.496070 CTCGTCCACCTTCACCATCTTA 59.504 50.000 0.00 0.00 0.00 2.10
2936 3155 2.159707 GCATTGTACAAGTGCGTACCTG 60.160 50.000 19.88 0.00 40.91 4.00
2947 3166 5.948758 TGGAAGATATTGGTGCATTGTACAA 59.051 36.000 11.41 11.41 0.00 2.41
2948 3167 5.504853 TGGAAGATATTGGTGCATTGTACA 58.495 37.500 7.21 0.00 0.00 2.90
2949 3168 5.590259 ACTGGAAGATATTGGTGCATTGTAC 59.410 40.000 0.00 0.00 37.43 2.90
2951 3170 4.603131 ACTGGAAGATATTGGTGCATTGT 58.397 39.130 0.00 0.00 37.43 2.71
2952 3171 5.587388 AACTGGAAGATATTGGTGCATTG 57.413 39.130 0.00 0.00 37.43 2.82
2953 3172 6.183360 GCTTAACTGGAAGATATTGGTGCATT 60.183 38.462 0.00 0.00 37.43 3.56
2954 3173 5.300286 GCTTAACTGGAAGATATTGGTGCAT 59.700 40.000 0.00 0.00 37.43 3.96
2955 3174 4.640201 GCTTAACTGGAAGATATTGGTGCA 59.360 41.667 0.00 0.00 37.43 4.57
2956 3175 4.884164 AGCTTAACTGGAAGATATTGGTGC 59.116 41.667 0.00 0.00 37.43 5.01
2957 3176 6.115446 TGAGCTTAACTGGAAGATATTGGTG 58.885 40.000 0.00 0.00 37.43 4.17
2958 3177 6.313519 TGAGCTTAACTGGAAGATATTGGT 57.686 37.500 0.00 0.00 37.43 3.67
2959 3178 7.040823 GGAATGAGCTTAACTGGAAGATATTGG 60.041 40.741 0.00 0.00 37.43 3.16
2961 3180 7.001073 GGGAATGAGCTTAACTGGAAGATATT 58.999 38.462 0.00 0.00 37.43 1.28
2963 3182 5.428457 TGGGAATGAGCTTAACTGGAAGATA 59.572 40.000 0.00 0.00 37.43 1.98
2972 3193 2.162408 GTGCACTGGGAATGAGCTTAAC 59.838 50.000 10.32 0.00 0.00 2.01
2988 3209 0.533755 AGTGAGCTTGACAGGTGCAC 60.534 55.000 8.80 8.80 32.85 4.57
2994 3215 2.415857 GCATTGAGAGTGAGCTTGACAG 59.584 50.000 0.00 0.00 0.00 3.51
2995 3216 2.224354 TGCATTGAGAGTGAGCTTGACA 60.224 45.455 0.00 0.00 0.00 3.58
3010 3231 3.446161 AGGGTCACTGATTTCATGCATTG 59.554 43.478 0.00 0.00 0.00 2.82
3026 3247 3.047718 GATCGTCGCGACAGGGTCA 62.048 63.158 35.71 14.14 39.18 4.02
3029 3250 2.579787 GTGATCGTCGCGACAGGG 60.580 66.667 35.71 21.39 39.18 4.45
3032 3253 2.483745 GGAGTGATCGTCGCGACA 59.516 61.111 35.71 23.77 39.18 4.35
3035 3256 2.648102 GTCGGAGTGATCGTCGCG 60.648 66.667 0.00 0.00 30.95 5.87
3176 3397 1.954927 TTGCATACACACCGACACAA 58.045 45.000 0.00 0.00 0.00 3.33
3178 3399 1.871039 AGTTTGCATACACACCGACAC 59.129 47.619 10.02 0.00 0.00 3.67
3179 3400 2.248280 AGTTTGCATACACACCGACA 57.752 45.000 10.02 0.00 0.00 4.35
3180 3401 3.422603 CGTTAGTTTGCATACACACCGAC 60.423 47.826 10.02 0.00 0.00 4.79
3182 3403 2.723618 GCGTTAGTTTGCATACACACCG 60.724 50.000 10.02 7.08 0.00 4.94
3183 3404 2.224549 TGCGTTAGTTTGCATACACACC 59.775 45.455 10.02 1.70 35.90 4.16
3237 3464 2.612493 AAGGATGTTCACCCCCGGG 61.612 63.158 15.80 15.80 42.03 5.73
3402 3630 4.552365 ATGGCTGACCGGATGGCG 62.552 66.667 9.46 0.00 39.70 5.69
3444 3672 6.017109 ACACGATTAATCTGTCAGCTTGTTTT 60.017 34.615 13.45 0.00 0.00 2.43
3451 3679 3.521560 TGGACACGATTAATCTGTCAGC 58.478 45.455 29.07 20.71 37.03 4.26
3473 3701 0.034186 CTTTGAGCCCCTGGTATGCA 60.034 55.000 0.00 0.00 0.00 3.96
3476 3704 1.561542 CAGACTTTGAGCCCCTGGTAT 59.438 52.381 0.00 0.00 0.00 2.73
3477 3705 0.984230 CAGACTTTGAGCCCCTGGTA 59.016 55.000 0.00 0.00 0.00 3.25
3478 3706 0.768221 TCAGACTTTGAGCCCCTGGT 60.768 55.000 0.00 0.00 0.00 4.00
3479 3707 0.401738 TTCAGACTTTGAGCCCCTGG 59.598 55.000 0.00 0.00 37.07 4.45
3481 3709 3.425659 GAAATTCAGACTTTGAGCCCCT 58.574 45.455 0.00 0.00 37.07 4.79
3517 3752 2.177531 GAGTTGCTGCATGCCACG 59.822 61.111 16.68 4.74 41.58 4.94
3557 3792 2.126071 CCTGCGTCGGTCGTCATT 60.126 61.111 0.00 0.00 42.13 2.57
3605 3840 3.637273 GTCGGGTTCACCTGCCCT 61.637 66.667 0.00 0.00 42.67 5.19
3761 3996 0.179089 CGGAGATGAGGTCCTTGCTG 60.179 60.000 0.00 0.00 31.14 4.41
3875 4110 1.366366 GGCGACGGTATATGTGGCT 59.634 57.895 12.45 0.00 40.40 4.75
3928 4163 4.711949 ACTGGAGCTTGCTGGGCG 62.712 66.667 0.00 0.00 34.52 6.13
4106 4341 3.066342 ACATACGAGTCCCATCTTGTACG 59.934 47.826 0.00 0.00 37.20 3.67
4122 4360 5.285845 CGTATACCTAGACGAGAGACATACG 59.714 48.000 0.00 0.00 42.92 3.06
4140 4378 6.728200 TGGTGCTACTACATTGTACGTATAC 58.272 40.000 0.00 0.00 0.00 1.47
4323 4562 8.301002 ACACATTTATGGGTTATGTTACACAAC 58.699 33.333 0.00 0.00 42.97 3.32
4383 4622 8.081208 TGCATTTATTAACATTGTGTTTGGTG 57.919 30.769 0.20 0.00 41.45 4.17
4432 5493 9.261180 CAGAAACTATCGTCACCAAATATACAT 57.739 33.333 0.00 0.00 0.00 2.29
4435 5496 7.497595 AGCAGAAACTATCGTCACCAAATATA 58.502 34.615 0.00 0.00 0.00 0.86
4437 5498 5.730550 AGCAGAAACTATCGTCACCAAATA 58.269 37.500 0.00 0.00 0.00 1.40
4438 5499 4.579869 AGCAGAAACTATCGTCACCAAAT 58.420 39.130 0.00 0.00 0.00 2.32
4441 5502 3.678056 AAGCAGAAACTATCGTCACCA 57.322 42.857 0.00 0.00 0.00 4.17
4444 5505 5.747565 CAACAAAAGCAGAAACTATCGTCA 58.252 37.500 0.00 0.00 0.00 4.35
4505 5566 3.286751 GCTTGACTGTGCCGCCAA 61.287 61.111 0.00 0.00 0.00 4.52
4524 5585 1.152483 ACCAGCCAACCATGCAAGT 60.152 52.632 0.00 0.00 0.00 3.16
4533 5594 1.535204 CCCAATCCACACCAGCCAAC 61.535 60.000 0.00 0.00 0.00 3.77
4537 5598 2.048603 GCTCCCAATCCACACCAGC 61.049 63.158 0.00 0.00 0.00 4.85
4540 5601 1.202818 GGATAGCTCCCAATCCACACC 60.203 57.143 8.17 0.00 41.21 4.16
4542 5603 0.758734 CGGATAGCTCCCAATCCACA 59.241 55.000 12.66 0.00 41.57 4.17
4587 5648 0.530870 GACCCGCACAAGAGATAGCC 60.531 60.000 0.00 0.00 0.00 3.93
4601 5662 1.800315 CGCTCTACAACACGACCCG 60.800 63.158 0.00 0.00 0.00 5.28
4613 5674 0.741326 GATGACACAGGAGCGCTCTA 59.259 55.000 34.46 13.95 0.00 2.43
4628 5691 1.410517 GGCATCACGAAGAGGAGATGA 59.589 52.381 0.00 0.00 38.16 2.92
4656 5719 3.561960 CCATTTCAATGTCCTCTGTGGGA 60.562 47.826 0.00 0.00 34.60 4.37
4673 5737 8.370182 GGATTAAAACATCATATGGCTCCATTT 58.630 33.333 6.73 0.00 37.82 2.32
4690 5754 2.294979 CCTAGCACGGGGGATTAAAAC 58.705 52.381 0.00 0.00 0.00 2.43
4720 5785 4.514577 CAGGGTAGGCAGCGACGG 62.515 72.222 0.00 0.00 0.00 4.79
4722 5787 4.840005 GGCAGGGTAGGCAGCGAC 62.840 72.222 0.00 0.00 0.00 5.19
4762 5827 0.251341 ACCATGGAGTTGGCTTCACC 60.251 55.000 21.47 0.00 40.68 4.02
4772 5837 1.903877 CGGAGCCAAGACCATGGAGT 61.904 60.000 21.47 0.94 43.54 3.85
4810 5875 1.477558 CCCACATAGCACCTGAATCCC 60.478 57.143 0.00 0.00 0.00 3.85
4824 5889 1.991230 CGAAGAAGGGGTCCCACAT 59.009 57.895 10.98 0.00 38.92 3.21
4837 5902 1.609072 CTCCACGGATAGATGCGAAGA 59.391 52.381 10.54 5.41 44.78 2.87
4850 5915 1.381872 ACCTCCAGATCCTCCACGG 60.382 63.158 0.00 0.00 0.00 4.94
4851 5916 1.680522 CCACCTCCAGATCCTCCACG 61.681 65.000 0.00 0.00 0.00 4.94
4875 5940 0.532862 ACACAGCCGAGGTCACAAAG 60.533 55.000 0.00 0.00 0.00 2.77
4876 5941 0.107410 AACACAGCCGAGGTCACAAA 60.107 50.000 0.00 0.00 0.00 2.83
4887 5952 3.937079 GTGTAGGTACCATAAACACAGCC 59.063 47.826 23.77 6.96 40.08 4.85
4905 5970 1.306654 CTGGCTAGGGGGTGGTGTA 60.307 63.158 0.00 0.00 0.00 2.90
4910 5975 4.115199 GGTGCTGGCTAGGGGGTG 62.115 72.222 0.00 0.00 0.00 4.61
4925 5990 1.605738 ACACTCCTCGTAAGCGGGT 60.606 57.895 0.00 0.00 44.13 5.28
4929 5994 1.134965 AGCATCACACTCCTCGTAAGC 60.135 52.381 0.00 0.00 37.18 3.09
5011 6076 4.034258 CACAAGCCGTGGCAGCAG 62.034 66.667 14.29 2.17 44.88 4.24
5059 6124 8.818057 CGACGAGGAAAATTGTAAATCTTAGAT 58.182 33.333 0.00 0.00 0.00 1.98
5073 6138 0.323629 TCCAAGCCGACGAGGAAAAT 59.676 50.000 0.00 0.00 45.00 1.82
5080 6146 0.605319 AGCAAAATCCAAGCCGACGA 60.605 50.000 0.00 0.00 0.00 4.20
5117 6183 3.213206 TGCTTTCTTCTTCAAGAGGCA 57.787 42.857 9.09 9.09 42.11 4.75
5148 6214 2.420129 GGTAGTGGCACCCATCTTACTG 60.420 54.545 15.27 0.00 35.28 2.74
5162 6229 0.107848 GTTGGATCGGGTGGTAGTGG 60.108 60.000 0.00 0.00 0.00 4.00
5179 6246 7.595819 TGTTTTATTTCTCCTTCATGTGGTT 57.404 32.000 7.23 0.00 0.00 3.67
5197 6264 7.950512 TCCTTCATGATTTTGCTCTTGTTTTA 58.049 30.769 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.