Multiple sequence alignment - TraesCS3D01G217500

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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 TraesCS3D01G217500 chr3D 100.000 4926 0 0 1 4926 295154034 295149109 0.000000e+00 9097.0
1 TraesCS3D01G217500 chr3A 95.586 2560 75 14 794 3318 393106706 393104150 0.000000e+00 4067.0
2 TraesCS3D01G217500 chr3A 90.456 1205 50 25 3301 4451 393104063 393102870 0.000000e+00 1528.0
3 TraesCS3D01G217500 chr3A 92.568 296 22 0 4626 4921 393102576 393102281 4.560000e-115 425.0
4 TraesCS3D01G217500 chr3A 93.370 181 9 1 4488 4668 393102752 393102575 1.050000e-66 265.0
5 TraesCS3D01G217500 chr3B 93.887 1505 49 10 745 2219 389313226 389311735 0.000000e+00 2230.0
6 TraesCS3D01G217500 chr3B 88.332 1097 61 29 3240 4296 389310842 389309773 0.000000e+00 1254.0
7 TraesCS3D01G217500 chr3B 90.793 391 18 10 2696 3086 389311216 389310844 1.580000e-139 507.0
8 TraesCS3D01G217500 chr3B 86.567 402 30 15 2222 2613 389311687 389311300 5.900000e-114 422.0
9 TraesCS3D01G217500 chr3B 85.921 277 27 4 4547 4812 389309788 389309513 8.070000e-73 285.0
10 TraesCS3D01G217500 chr2B 87.363 546 67 2 2 545 578050008 578049463 4.190000e-175 625.0
11 TraesCS3D01G217500 chr2B 91.124 169 9 5 3083 3246 212577255 212577422 1.780000e-54 224.0
12 TraesCS3D01G217500 chr2B 95.833 48 2 0 642 689 578049312 578049265 1.470000e-10 78.7
13 TraesCS3D01G217500 chr2D 93.143 175 9 3 3073 3245 560154060 560153887 2.280000e-63 254.0
14 TraesCS3D01G217500 chr4A 90.341 176 14 3 3072 3245 75884036 75883862 1.380000e-55 228.0
15 TraesCS3D01G217500 chr6A 91.515 165 12 2 3082 3245 42179116 42178953 4.960000e-55 226.0
16 TraesCS3D01G217500 chr7D 88.764 178 19 1 3072 3248 416234244 416234067 2.990000e-52 217.0
17 TraesCS3D01G217500 chr6B 88.525 183 16 4 3080 3260 652640545 652640724 2.990000e-52 217.0
18 TraesCS3D01G217500 chr6B 89.394 132 13 1 572 703 542880479 542880609 1.100000e-36 165.0
19 TraesCS3D01G217500 chr5B 89.535 172 16 2 3074 3245 526902811 526902980 2.990000e-52 217.0
20 TraesCS3D01G217500 chr1B 89.535 172 16 2 3074 3245 555355644 555355813 2.990000e-52 217.0
21 TraesCS3D01G217500 chr6D 95.283 106 3 2 599 703 361411422 361411318 3.050000e-37 167.0
22 TraesCS3D01G217500 chr1D 84.211 114 13 4 2497 2608 337900298 337900188 6.740000e-19 106.0


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 TraesCS3D01G217500 chr3D 295149109 295154034 4925 True 9097.00 9097 100.000 1 4926 1 chr3D.!!$R1 4925
1 TraesCS3D01G217500 chr3A 393102281 393106706 4425 True 1571.25 4067 92.995 794 4921 4 chr3A.!!$R1 4127
2 TraesCS3D01G217500 chr3B 389309513 389313226 3713 True 939.60 2230 89.100 745 4812 5 chr3B.!!$R1 4067
3 TraesCS3D01G217500 chr2B 578049265 578050008 743 True 351.85 625 91.598 2 689 2 chr2B.!!$R1 687

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
740 826 0.034337 GTCCCACGAAGCACCTACAA 59.966 55.0 0.00 0.0 0.00 2.41 F
1233 1334 0.394216 CAGCCATGGATCCCACGAAA 60.394 55.0 18.40 0.0 35.80 3.46 F
2140 2273 0.243636 AAGTTGTAGCGCATTTGGCC 59.756 50.0 11.47 0.0 40.31 5.36 F
3545 3932 1.014564 GTTCTCCGGGCTTCTGTTCG 61.015 60.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1830 0.174845 TAATTCAGGCCGTCACCTCG 59.825 55.0 0.00 0.0 38.26 4.63 R
3166 3431 2.477357 CGGAGCGAAACGAGTGAATCTA 60.477 50.0 0.00 0.0 0.00 1.98 R
3748 4135 0.729116 GGAGACACGCATCACCATTG 59.271 55.0 0.00 0.0 30.29 2.82 R
4368 4816 0.110486 TCTCCCTTTGTGCACCTTCC 59.890 55.0 15.69 0.0 0.00 3.46 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
19 20 0.610232 AGATTTGGAGGCTGGTGCAC 60.610 55.000 8.80 8.80 41.91 4.57
21 22 4.641645 TTGGAGGCTGGTGCACGG 62.642 66.667 11.45 7.42 41.91 4.94
24 25 2.281484 GAGGCTGGTGCACGGAAA 60.281 61.111 11.45 0.00 41.91 3.13
28 29 2.844451 GCTGGTGCACGGAAAGCAA 61.844 57.895 20.76 0.00 44.64 3.91
38 39 1.247567 CGGAAAGCAACTCAACCCAT 58.752 50.000 0.00 0.00 0.00 4.00
41 42 2.161609 GGAAAGCAACTCAACCCATACG 59.838 50.000 0.00 0.00 0.00 3.06
42 43 1.821216 AAGCAACTCAACCCATACGG 58.179 50.000 0.00 0.00 37.81 4.02
66 68 1.005340 GACAAGATTCGCTGGCTCAG 58.995 55.000 0.00 0.00 34.12 3.35
107 109 3.859961 CACTACGAGTTCAGCATACAAGG 59.140 47.826 0.00 0.00 0.00 3.61
119 121 2.095059 GCATACAAGGTGCAGTTTCAGG 60.095 50.000 0.00 0.00 42.08 3.86
120 122 1.604604 TACAAGGTGCAGTTTCAGGC 58.395 50.000 0.00 0.00 0.00 4.85
123 125 0.538287 AAGGTGCAGTTTCAGGCCTC 60.538 55.000 0.00 0.00 0.00 4.70
140 142 2.811873 GCCTCAGAAGAAACTTGCCTCA 60.812 50.000 0.00 0.00 0.00 3.86
164 166 2.580322 TCCTGTATTTGGAAGCCATGGA 59.420 45.455 18.40 0.00 31.53 3.41
165 167 2.689983 CCTGTATTTGGAAGCCATGGAC 59.310 50.000 18.40 7.03 31.53 4.02
167 169 2.290641 TGTATTTGGAAGCCATGGACGT 60.291 45.455 18.40 5.00 31.53 4.34
170 172 2.511600 GGAAGCCATGGACGTCGG 60.512 66.667 18.40 6.54 0.00 4.79
178 180 1.302511 ATGGACGTCGGCAAAGCTT 60.303 52.632 9.92 0.00 0.00 3.74
187 189 3.364964 CGTCGGCAAAGCTTAAGATGTTT 60.365 43.478 6.67 0.00 0.00 2.83
194 196 5.985530 GCAAAGCTTAAGATGTTTTTCTGGT 59.014 36.000 6.67 0.00 0.00 4.00
205 207 4.431809 TGTTTTTCTGGTTGTTGCATCTG 58.568 39.130 0.00 0.00 0.00 2.90
209 211 0.883833 CTGGTTGTTGCATCTGGACC 59.116 55.000 0.00 0.00 0.00 4.46
227 229 0.464373 CCGGCTATGGTGCAATGACT 60.464 55.000 0.00 0.00 34.04 3.41
228 230 0.659427 CGGCTATGGTGCAATGACTG 59.341 55.000 0.00 0.00 34.04 3.51
232 234 2.353889 GCTATGGTGCAATGACTGTCTG 59.646 50.000 9.51 1.00 0.00 3.51
236 238 0.109873 GTGCAATGACTGTCTGCTGC 60.110 55.000 18.87 17.85 37.00 5.25
253 255 2.753043 CGCAGAGGCTGGCCAAAT 60.753 61.111 7.01 0.00 38.92 2.32
260 262 0.965363 AGGCTGGCCAAATGGTTACG 60.965 55.000 7.01 0.00 38.92 3.18
264 266 2.937873 GCTGGCCAAATGGTTACGTCTA 60.938 50.000 7.01 0.00 37.57 2.59
267 269 1.061566 GCCAAATGGTTACGTCTACGC 59.938 52.381 1.74 0.00 39.31 4.42
274 276 0.179205 GTTACGTCTACGCGCTCTGT 60.179 55.000 5.73 0.77 44.43 3.41
285 287 1.882989 GCGCTCTGTCAGAGGAACCT 61.883 60.000 27.35 0.00 42.54 3.50
289 291 1.824230 CTCTGTCAGAGGAACCTGGAG 59.176 57.143 20.50 0.00 38.67 3.86
294 296 0.248843 CAGAGGAACCTGGAGTGCTC 59.751 60.000 0.00 8.09 32.76 4.26
298 300 1.255667 GGAACCTGGAGTGCTCGGTA 61.256 60.000 0.00 0.00 0.00 4.02
301 303 0.614979 ACCTGGAGTGCTCGGTACAT 60.615 55.000 0.00 0.00 0.00 2.29
315 317 3.570125 TCGGTACATCTATTCTGGAGCTG 59.430 47.826 0.00 0.00 0.00 4.24
316 318 3.319405 CGGTACATCTATTCTGGAGCTGT 59.681 47.826 0.00 0.00 0.00 4.40
322 324 4.478206 TCTATTCTGGAGCTGTCCTTTG 57.522 45.455 0.00 0.00 44.30 2.77
338 340 1.876156 CTTTGTCCTCTCAAGTGTGGC 59.124 52.381 0.00 0.00 0.00 5.01
347 349 2.847234 AAGTGTGGCGGGAGGTCA 60.847 61.111 0.00 0.00 0.00 4.02
357 359 1.229529 GGGAGGTCACTTCCTGGGA 60.230 63.158 5.83 0.00 39.53 4.37
361 363 1.539124 GGTCACTTCCTGGGAGGGT 60.539 63.158 3.65 0.00 35.59 4.34
366 368 1.301293 CTTCCTGGGAGGGTTGCTC 59.699 63.158 0.00 0.00 35.59 4.26
367 369 1.463214 TTCCTGGGAGGGTTGCTCA 60.463 57.895 0.00 0.00 35.59 4.26
368 370 1.492133 TTCCTGGGAGGGTTGCTCAG 61.492 60.000 0.00 0.00 35.59 3.35
373 375 1.682257 GGAGGGTTGCTCAGCTCTT 59.318 57.895 0.00 0.00 0.00 2.85
383 385 1.293924 CTCAGCTCTTAATGCACGGG 58.706 55.000 0.00 0.00 0.00 5.28
385 387 1.277842 TCAGCTCTTAATGCACGGGAA 59.722 47.619 0.00 0.00 0.00 3.97
387 389 1.003118 AGCTCTTAATGCACGGGAACA 59.997 47.619 0.00 0.00 0.00 3.18
416 419 2.038952 TGGTCACCAGGACTTCAATCTG 59.961 50.000 0.00 0.00 46.16 2.90
417 420 2.039084 GGTCACCAGGACTTCAATCTGT 59.961 50.000 0.00 0.00 46.16 3.41
418 421 3.330267 GTCACCAGGACTTCAATCTGTC 58.670 50.000 0.00 0.00 43.46 3.51
430 433 2.431782 TCAATCTGTCAGGCGATCATCA 59.568 45.455 0.00 0.00 0.00 3.07
436 439 2.208431 GTCAGGCGATCATCAGGAAAG 58.792 52.381 0.00 0.00 0.00 2.62
444 447 4.676196 GCGATCATCAGGAAAGCAACAAAT 60.676 41.667 0.00 0.00 33.74 2.32
448 451 3.648339 TCAGGAAAGCAACAAATGAGC 57.352 42.857 0.00 0.00 0.00 4.26
453 456 0.314935 AAGCAACAAATGAGCACCGG 59.685 50.000 0.00 0.00 0.00 5.28
468 471 1.205460 ACCGGTGGGGCATAAAGACT 61.205 55.000 6.12 0.00 40.62 3.24
488 491 7.496346 AGACTTTGATCATTCTGGTTACCTA 57.504 36.000 2.07 0.00 0.00 3.08
497 500 3.019799 TCTGGTTACCTAGGAGCTCTG 57.980 52.381 17.98 6.63 0.00 3.35
512 515 2.114616 GCTCTGGAAGGAGAGGAATGA 58.885 52.381 0.00 0.00 40.04 2.57
515 518 3.710677 CTCTGGAAGGAGAGGAATGATGT 59.289 47.826 0.00 0.00 36.57 3.06
522 525 5.096443 AGGAGAGGAATGATGTTGTCTTC 57.904 43.478 0.00 0.00 0.00 2.87
545 548 2.622942 GGAGCAAAACACCTGATCAACA 59.377 45.455 0.00 0.00 30.72 3.33
546 549 3.304928 GGAGCAAAACACCTGATCAACAG 60.305 47.826 0.00 0.00 45.36 3.16
547 550 3.290710 AGCAAAACACCTGATCAACAGT 58.709 40.909 0.00 0.00 44.40 3.55
548 551 3.067180 AGCAAAACACCTGATCAACAGTG 59.933 43.478 15.20 15.20 44.40 3.66
549 552 3.374745 CAAAACACCTGATCAACAGTGC 58.625 45.455 16.23 0.00 44.40 4.40
550 553 1.609208 AACACCTGATCAACAGTGCC 58.391 50.000 16.23 0.00 44.40 5.01
555 639 1.642037 CTGATCAACAGTGCCCTGCG 61.642 60.000 0.00 0.00 42.81 5.18
561 645 0.613260 AACAGTGCCCTGCGAGATAA 59.387 50.000 0.00 0.00 42.81 1.75
562 646 0.833287 ACAGTGCCCTGCGAGATAAT 59.167 50.000 0.00 0.00 42.81 1.28
564 648 0.107456 AGTGCCCTGCGAGATAATGG 59.893 55.000 0.00 0.00 0.00 3.16
569 653 1.607509 CCCTGCGAGATAATGGCTGAG 60.608 57.143 0.00 0.00 34.16 3.35
570 654 1.342496 CCTGCGAGATAATGGCTGAGA 59.658 52.381 0.00 0.00 34.16 3.27
571 655 2.028294 CCTGCGAGATAATGGCTGAGAT 60.028 50.000 0.00 0.00 34.16 2.75
573 657 3.396560 TGCGAGATAATGGCTGAGATTG 58.603 45.455 0.00 0.00 33.04 2.67
574 658 3.181462 TGCGAGATAATGGCTGAGATTGT 60.181 43.478 0.00 0.00 33.04 2.71
578 662 6.197276 CGAGATAATGGCTGAGATTGTTTTG 58.803 40.000 0.00 0.00 0.00 2.44
579 663 6.037500 CGAGATAATGGCTGAGATTGTTTTGA 59.962 38.462 0.00 0.00 0.00 2.69
580 664 7.255035 CGAGATAATGGCTGAGATTGTTTTGAT 60.255 37.037 0.00 0.00 0.00 2.57
581 665 7.713750 AGATAATGGCTGAGATTGTTTTGATG 58.286 34.615 0.00 0.00 0.00 3.07
582 666 3.581024 TGGCTGAGATTGTTTTGATGC 57.419 42.857 0.00 0.00 0.00 3.91
583 667 3.159472 TGGCTGAGATTGTTTTGATGCT 58.841 40.909 0.00 0.00 0.00 3.79
585 669 4.039488 TGGCTGAGATTGTTTTGATGCTTT 59.961 37.500 0.00 0.00 0.00 3.51
586 670 4.387862 GGCTGAGATTGTTTTGATGCTTTG 59.612 41.667 0.00 0.00 0.00 2.77
587 671 4.143179 GCTGAGATTGTTTTGATGCTTTGC 60.143 41.667 0.00 0.00 0.00 3.68
597 683 4.471761 TGCTTTGCATCGTGTCCA 57.528 50.000 0.00 0.00 31.71 4.02
600 686 0.385974 GCTTTGCATCGTGTCCACAC 60.386 55.000 0.00 0.00 43.15 3.82
613 699 5.204673 GTGTCCACACGATGTTTTCTATC 57.795 43.478 0.00 0.00 37.10 2.08
620 706 1.597663 CGATGTTTTCTATCGGCCACC 59.402 52.381 2.24 0.00 42.63 4.61
631 717 4.963878 GGCCACCGATCACTTGAT 57.036 55.556 0.00 0.00 37.51 2.57
632 718 2.695314 GGCCACCGATCACTTGATC 58.305 57.895 8.90 8.90 45.60 2.92
691 777 8.669946 AAAGCCAGTATAAAGCTAGATCTTTC 57.330 34.615 0.00 0.00 37.46 2.62
692 778 7.366847 AGCCAGTATAAAGCTAGATCTTTCA 57.633 36.000 0.00 0.00 37.46 2.69
693 779 7.796054 AGCCAGTATAAAGCTAGATCTTTCAA 58.204 34.615 0.00 0.00 37.46 2.69
694 780 8.267894 AGCCAGTATAAAGCTAGATCTTTCAAA 58.732 33.333 0.00 0.00 37.46 2.69
695 781 8.893727 GCCAGTATAAAGCTAGATCTTTCAAAA 58.106 33.333 0.00 0.00 37.46 2.44
717 803 2.839486 AAAATCTCCGTCACTCAGCA 57.161 45.000 0.00 0.00 0.00 4.41
718 804 2.086054 AAATCTCCGTCACTCAGCAC 57.914 50.000 0.00 0.00 0.00 4.40
719 805 0.969149 AATCTCCGTCACTCAGCACA 59.031 50.000 0.00 0.00 0.00 4.57
720 806 0.529833 ATCTCCGTCACTCAGCACAG 59.470 55.000 0.00 0.00 0.00 3.66
721 807 1.080230 CTCCGTCACTCAGCACAGG 60.080 63.158 0.00 0.00 0.00 4.00
722 808 1.810606 CTCCGTCACTCAGCACAGGT 61.811 60.000 0.00 0.00 0.00 4.00
723 809 1.373497 CCGTCACTCAGCACAGGTC 60.373 63.158 0.00 0.00 0.00 3.85
724 810 1.373497 CGTCACTCAGCACAGGTCC 60.373 63.158 0.00 0.00 0.00 4.46
725 811 1.004440 GTCACTCAGCACAGGTCCC 60.004 63.158 0.00 0.00 0.00 4.46
726 812 1.459348 TCACTCAGCACAGGTCCCA 60.459 57.895 0.00 0.00 0.00 4.37
727 813 1.302033 CACTCAGCACAGGTCCCAC 60.302 63.158 0.00 0.00 0.00 4.61
728 814 2.047844 CTCAGCACAGGTCCCACG 60.048 66.667 0.00 0.00 0.00 4.94
729 815 2.523168 TCAGCACAGGTCCCACGA 60.523 61.111 0.00 0.00 0.00 4.35
730 816 2.099652 CTCAGCACAGGTCCCACGAA 62.100 60.000 0.00 0.00 0.00 3.85
731 817 1.669115 CAGCACAGGTCCCACGAAG 60.669 63.158 0.00 0.00 0.00 3.79
732 818 3.050275 GCACAGGTCCCACGAAGC 61.050 66.667 0.00 0.00 0.00 3.86
733 819 2.425592 CACAGGTCCCACGAAGCA 59.574 61.111 0.00 0.00 0.00 3.91
734 820 1.961277 CACAGGTCCCACGAAGCAC 60.961 63.158 0.00 0.00 0.00 4.40
735 821 2.358737 CAGGTCCCACGAAGCACC 60.359 66.667 0.00 0.00 0.00 5.01
736 822 2.526873 AGGTCCCACGAAGCACCT 60.527 61.111 0.00 0.00 34.18 4.00
737 823 1.229082 AGGTCCCACGAAGCACCTA 60.229 57.895 0.00 0.00 37.50 3.08
738 824 1.079336 GGTCCCACGAAGCACCTAC 60.079 63.158 0.00 0.00 0.00 3.18
739 825 1.669440 GTCCCACGAAGCACCTACA 59.331 57.895 0.00 0.00 0.00 2.74
740 826 0.034337 GTCCCACGAAGCACCTACAA 59.966 55.000 0.00 0.00 0.00 2.41
741 827 0.759959 TCCCACGAAGCACCTACAAA 59.240 50.000 0.00 0.00 0.00 2.83
742 828 1.156736 CCCACGAAGCACCTACAAAG 58.843 55.000 0.00 0.00 0.00 2.77
743 829 1.270625 CCCACGAAGCACCTACAAAGA 60.271 52.381 0.00 0.00 0.00 2.52
771 857 5.049954 GTCGTAGCTAGTCATACAGAAGGAG 60.050 48.000 0.00 0.00 0.00 3.69
848 934 4.363990 CCTCTGACACGCGTGCCT 62.364 66.667 37.35 20.95 0.00 4.75
921 1013 1.338674 CCCACATAACCGCTGACAAGA 60.339 52.381 0.00 0.00 0.00 3.02
1054 1152 3.606886 GGCAACGTCAGGAAAGAGA 57.393 52.632 0.00 0.00 0.00 3.10
1191 1289 3.554960 CCAATCTCTCACGGAACAACTCA 60.555 47.826 0.00 0.00 0.00 3.41
1233 1334 0.394216 CAGCCATGGATCCCACGAAA 60.394 55.000 18.40 0.00 35.80 3.46
1245 1346 1.677820 CCCACGAAACTACCCATCACC 60.678 57.143 0.00 0.00 0.00 4.02
1263 1364 1.512156 CCAAGTTGGGGGACGTTTCG 61.512 60.000 14.64 0.00 32.67 3.46
1274 1375 3.606886 ACGTTTCGTCTCAAGGCAT 57.393 47.368 0.00 0.00 33.69 4.40
1409 1526 4.228567 GCCGGAGAGCTACTGGGC 62.229 72.222 5.05 10.55 37.55 5.36
1413 1530 4.577246 GAGAGCTACTGGGCGCCG 62.577 72.222 22.54 10.51 37.29 6.46
1760 1883 6.867519 TTCTTTGTGTACCATCTCCATCTA 57.132 37.500 0.00 0.00 0.00 1.98
1781 1914 7.333528 TCTAGTGGACAAAATAATTCATGGC 57.666 36.000 0.00 0.00 0.00 4.40
1782 1915 4.997565 AGTGGACAAAATAATTCATGGCG 58.002 39.130 0.00 0.00 0.00 5.69
1783 1916 4.704540 AGTGGACAAAATAATTCATGGCGA 59.295 37.500 0.00 0.00 0.00 5.54
1784 1917 5.360714 AGTGGACAAAATAATTCATGGCGAT 59.639 36.000 0.00 0.00 0.00 4.58
1785 1918 5.687285 GTGGACAAAATAATTCATGGCGATC 59.313 40.000 0.00 0.00 0.00 3.69
1786 1919 5.221224 TGGACAAAATAATTCATGGCGATCC 60.221 40.000 0.00 0.00 0.00 3.36
1818 1951 1.745489 CCCCGTTAGAGTTGCAGGC 60.745 63.158 0.00 0.00 0.00 4.85
1920 2053 4.378046 GCATGGCAAGCTCAAAATTTTCTG 60.378 41.667 7.57 0.00 0.00 3.02
2140 2273 0.243636 AAGTTGTAGCGCATTTGGCC 59.756 50.000 11.47 0.00 40.31 5.36
2387 2579 3.771479 ACAGTATGAGCATGTTCAGGAGA 59.229 43.478 17.57 0.86 39.69 3.71
2651 2900 2.517166 GCCGATTTGAGGGCTCCC 60.517 66.667 0.00 0.00 45.93 4.30
2687 2936 1.581447 GTTTGCTTTGAGGAGCGGG 59.419 57.895 0.00 0.00 45.64 6.13
2775 3024 6.865726 GCAACCAAACACACACATAATGAATA 59.134 34.615 0.00 0.00 0.00 1.75
2776 3025 7.545265 GCAACCAAACACACACATAATGAATAT 59.455 33.333 0.00 0.00 0.00 1.28
3078 3339 6.040209 TGTGGGATCTGATTGGAATTTTTG 57.960 37.500 0.00 0.00 0.00 2.44
3084 3345 8.406297 GGGATCTGATTGGAATTTTTGTACTAC 58.594 37.037 0.00 0.00 0.00 2.73
3091 3352 5.812286 TGGAATTTTTGTACTACTCCCTCC 58.188 41.667 0.00 0.00 0.00 4.30
3092 3353 5.311121 TGGAATTTTTGTACTACTCCCTCCA 59.689 40.000 0.00 0.00 0.00 3.86
3102 3363 8.019656 TGTACTACTCCCTCCATTTCTAAATC 57.980 38.462 0.00 0.00 0.00 2.17
3139 3404 8.678593 AGAGATTTCGATACAGACTACATACA 57.321 34.615 0.00 0.00 0.00 2.29
3185 3450 3.301116 GTGTAGATTCACTCGTTTCGCTC 59.699 47.826 0.00 0.00 35.68 5.03
3196 3461 1.844357 CGTTTCGCTCCGTATGTAGTG 59.156 52.381 0.00 0.00 0.00 2.74
3318 3592 8.445275 TTGTGGGTATGCTAACAAGTAATATG 57.555 34.615 0.00 0.00 0.00 1.78
3319 3593 7.797062 TGTGGGTATGCTAACAAGTAATATGA 58.203 34.615 0.00 0.00 0.00 2.15
3320 3594 7.713507 TGTGGGTATGCTAACAAGTAATATGAC 59.286 37.037 0.00 0.00 0.00 3.06
3322 3596 7.931407 TGGGTATGCTAACAAGTAATATGACTG 59.069 37.037 0.00 0.00 0.00 3.51
3409 3796 2.483714 GGATAAGAGCCTTCGCATCACA 60.484 50.000 0.00 0.00 37.52 3.58
3545 3932 1.014564 GTTCTCCGGGCTTCTGTTCG 61.015 60.000 0.00 0.00 0.00 3.95
3548 3935 2.154798 CTCCGGGCTTCTGTTCGTGA 62.155 60.000 0.00 0.00 0.00 4.35
3748 4135 4.219070 AGAGCAGCTGATCTCATCTATGAC 59.781 45.833 28.29 0.00 35.67 3.06
3884 4283 0.040958 CGAAGCAAAGTGTGAGCCAC 60.041 55.000 0.00 0.00 44.89 5.01
3971 4370 2.553904 CCATCCACCAGACTTTCAGCTT 60.554 50.000 0.00 0.00 0.00 3.74
4102 4503 4.319249 GCGTGTTGCACCCTTTTC 57.681 55.556 0.00 0.00 45.45 2.29
4103 4504 1.435515 GCGTGTTGCACCCTTTTCA 59.564 52.632 0.00 0.00 45.45 2.69
4104 4505 0.594796 GCGTGTTGCACCCTTTTCAG 60.595 55.000 0.00 0.00 45.45 3.02
4166 4577 2.848887 CGTCGCATCTCTGTAAAGTCTG 59.151 50.000 0.00 0.00 0.00 3.51
4179 4590 2.080286 AAGTCTGCGTGTATGTGGTC 57.920 50.000 0.00 0.00 0.00 4.02
4251 4674 1.440893 CCAGAGCCCTCGATGTGAG 59.559 63.158 0.00 0.00 44.83 3.51
4281 4704 5.437289 TTTACTTTCACATGGACAGCAAG 57.563 39.130 0.00 0.00 0.00 4.01
4291 4716 3.672295 GACAGCAAGAGGGAGGCCG 62.672 68.421 0.00 0.00 0.00 6.13
4317 4742 4.717233 TTTTTCTTGTGCATGCGGATAT 57.283 36.364 14.09 0.00 0.00 1.63
4318 4743 3.969117 TTTCTTGTGCATGCGGATATC 57.031 42.857 14.09 0.00 0.00 1.63
4319 4744 2.916702 TCTTGTGCATGCGGATATCT 57.083 45.000 14.09 0.00 0.00 1.98
4321 4746 4.335400 TCTTGTGCATGCGGATATCTTA 57.665 40.909 14.09 0.00 0.00 2.10
4359 4807 5.066375 TCAAAACAAAGTCTGACATCCAGTG 59.934 40.000 10.88 0.00 43.38 3.66
4361 4809 2.158769 ACAAAGTCTGACATCCAGTGCA 60.159 45.455 10.88 0.00 43.38 4.57
4363 4811 0.036577 AGTCTGACATCCAGTGCAGC 60.037 55.000 10.88 0.00 43.38 5.25
4368 4816 0.805322 GACATCCAGTGCAGCTCTCG 60.805 60.000 0.00 0.00 0.00 4.04
4372 4820 1.447489 CCAGTGCAGCTCTCGGAAG 60.447 63.158 0.00 0.00 0.00 3.46
4374 4822 1.910772 AGTGCAGCTCTCGGAAGGT 60.911 57.895 0.00 0.00 0.00 3.50
4439 5004 9.965902 ACAAGACAAGATGACTAAATTCCTATT 57.034 29.630 0.00 0.00 0.00 1.73
4465 5030 9.788960 TCTATTATTGGATCGTCATCTAAATCG 57.211 33.333 0.00 0.00 33.55 3.34
4466 5031 7.834068 ATTATTGGATCGTCATCTAAATCGG 57.166 36.000 0.00 0.00 33.55 4.18
4467 5032 4.665833 TTGGATCGTCATCTAAATCGGT 57.334 40.909 0.00 0.00 0.00 4.69
4468 5033 4.665833 TGGATCGTCATCTAAATCGGTT 57.334 40.909 0.00 0.00 0.00 4.44
4469 5034 4.368315 TGGATCGTCATCTAAATCGGTTG 58.632 43.478 0.00 0.00 0.00 3.77
4470 5035 4.142026 TGGATCGTCATCTAAATCGGTTGT 60.142 41.667 0.00 0.00 0.00 3.32
4471 5036 5.068067 TGGATCGTCATCTAAATCGGTTGTA 59.932 40.000 0.00 0.00 0.00 2.41
4472 5037 6.157211 GGATCGTCATCTAAATCGGTTGTAT 58.843 40.000 0.00 0.00 0.00 2.29
4473 5038 7.040271 TGGATCGTCATCTAAATCGGTTGTATA 60.040 37.037 0.00 0.00 0.00 1.47
4474 5039 7.974501 GGATCGTCATCTAAATCGGTTGTATAT 59.025 37.037 0.00 0.00 0.00 0.86
4475 5040 9.999009 GATCGTCATCTAAATCGGTTGTATATA 57.001 33.333 0.00 0.00 0.00 0.86
4477 5042 9.999009 TCGTCATCTAAATCGGTTGTATATATC 57.001 33.333 0.00 0.00 0.00 1.63
4478 5043 9.234384 CGTCATCTAAATCGGTTGTATATATCC 57.766 37.037 0.00 0.00 0.00 2.59
4479 5044 9.530633 GTCATCTAAATCGGTTGTATATATCCC 57.469 37.037 0.00 0.00 0.00 3.85
4480 5045 9.262240 TCATCTAAATCGGTTGTATATATCCCA 57.738 33.333 0.00 0.00 0.00 4.37
4483 5048 7.985184 TCTAAATCGGTTGTATATATCCCATGC 59.015 37.037 0.00 0.00 0.00 4.06
4484 5049 5.957771 ATCGGTTGTATATATCCCATGCT 57.042 39.130 0.00 0.00 0.00 3.79
4485 5050 7.432148 AATCGGTTGTATATATCCCATGCTA 57.568 36.000 0.00 0.00 0.00 3.49
4486 5051 6.216801 TCGGTTGTATATATCCCATGCTAC 57.783 41.667 0.00 0.00 0.00 3.58
4487 5052 5.128171 TCGGTTGTATATATCCCATGCTACC 59.872 44.000 0.00 0.00 33.09 3.18
4488 5053 5.357257 GGTTGTATATATCCCATGCTACCG 58.643 45.833 0.00 0.00 28.30 4.02
4489 5054 5.105064 GGTTGTATATATCCCATGCTACCGT 60.105 44.000 0.00 0.00 28.30 4.83
4490 5055 5.847111 TGTATATATCCCATGCTACCGTC 57.153 43.478 0.00 0.00 0.00 4.79
4491 5056 5.516044 TGTATATATCCCATGCTACCGTCT 58.484 41.667 0.00 0.00 0.00 4.18
4492 5057 5.593095 TGTATATATCCCATGCTACCGTCTC 59.407 44.000 0.00 0.00 0.00 3.36
4493 5058 1.629043 TATCCCATGCTACCGTCTCC 58.371 55.000 0.00 0.00 0.00 3.71
4494 5059 1.122019 ATCCCATGCTACCGTCTCCC 61.122 60.000 0.00 0.00 0.00 4.30
4495 5060 2.063979 CCCATGCTACCGTCTCCCA 61.064 63.158 0.00 0.00 0.00 4.37
4496 5061 1.443407 CCATGCTACCGTCTCCCAG 59.557 63.158 0.00 0.00 0.00 4.45
4499 5064 1.330655 ATGCTACCGTCTCCCAGTGG 61.331 60.000 0.63 0.63 0.00 4.00
4506 5071 1.451936 GTCTCCCAGTGGTTGCACT 59.548 57.895 8.74 0.00 35.49 4.40
4533 5098 2.290960 ACCAAAAGCTCCATGTAGTCCC 60.291 50.000 0.00 0.00 0.00 4.46
4537 5102 2.089600 AGCTCCATGTAGTCCCTACC 57.910 55.000 0.00 0.00 36.24 3.18
4542 5107 1.955080 CCATGTAGTCCCTACCGTCTC 59.045 57.143 0.00 0.00 36.24 3.36
4549 5114 0.901580 TCCCTACCGTCTCCCAACAC 60.902 60.000 0.00 0.00 0.00 3.32
4636 5201 6.719829 TCTCTATAGTGTTTGTGGAGTCAGAA 59.280 38.462 0.00 0.00 0.00 3.02
4673 5279 0.323087 CCTCAAAACCGGGTAAGGGG 60.323 60.000 6.32 0.00 35.02 4.79
4727 5333 1.947456 CTAGCCAAACCTTAATCCGGC 59.053 52.381 0.00 0.00 39.90 6.13
4734 5340 4.142469 CCAAACCTTAATCCGGCTTAACTG 60.142 45.833 6.39 4.16 0.00 3.16
4735 5341 2.640184 ACCTTAATCCGGCTTAACTGC 58.360 47.619 6.39 0.00 0.00 4.40
4777 5383 1.751351 TCTACCGTGGCTCAATCTCAG 59.249 52.381 0.00 0.00 0.00 3.35
4808 5415 1.514087 CTTCCCCGCGCTTGTACTA 59.486 57.895 5.56 0.00 0.00 1.82
4836 5443 4.834892 CGCGCCGCCAAAATCCAG 62.835 66.667 2.28 0.00 0.00 3.86
4846 5453 2.223665 GCCAAAATCCAGCATAGCACTC 60.224 50.000 0.00 0.00 0.00 3.51
4855 5462 2.041922 ATAGCACTCGCCCTCCCA 60.042 61.111 0.00 0.00 39.83 4.37
4856 5463 1.460305 ATAGCACTCGCCCTCCCAT 60.460 57.895 0.00 0.00 39.83 4.00
4873 5480 0.899720 CATGCCTGGCACTTCCAATT 59.100 50.000 25.99 1.71 46.01 2.32
4906 5513 2.513897 CGACTCCCCCGAAATGGC 60.514 66.667 0.00 0.00 35.87 4.40
4921 5528 4.954933 GGCAGGATTTAGCCGTCA 57.045 55.556 0.00 0.00 41.70 4.35
4922 5529 2.695314 GGCAGGATTTAGCCGTCAG 58.305 57.895 0.00 0.00 41.70 3.51
4923 5530 0.178068 GGCAGGATTTAGCCGTCAGA 59.822 55.000 0.00 0.00 41.70 3.27
4924 5531 1.576356 GCAGGATTTAGCCGTCAGAG 58.424 55.000 0.00 0.00 0.00 3.35
4925 5532 1.808133 GCAGGATTTAGCCGTCAGAGG 60.808 57.143 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.610232 GTGCACCAGCCTCCAAATCT 60.610 55.000 5.22 0.00 41.13 2.40
19 20 1.247567 ATGGGTTGAGTTGCTTTCCG 58.752 50.000 0.00 0.00 0.00 4.30
21 22 2.161609 CCGTATGGGTTGAGTTGCTTTC 59.838 50.000 0.00 0.00 0.00 2.62
22 23 2.159382 CCGTATGGGTTGAGTTGCTTT 58.841 47.619 0.00 0.00 0.00 3.51
24 25 3.551259 CCGTATGGGTTGAGTTGCT 57.449 52.632 0.00 0.00 0.00 3.91
38 39 2.004583 CGAATCTTGTCTTGCCCGTA 57.995 50.000 0.00 0.00 0.00 4.02
41 42 0.449388 CAGCGAATCTTGTCTTGCCC 59.551 55.000 0.00 0.00 0.00 5.36
42 43 0.449388 CCAGCGAATCTTGTCTTGCC 59.551 55.000 0.00 0.00 0.00 4.52
66 68 1.633945 TGTAAGCCCCCTCCTTTTCTC 59.366 52.381 0.00 0.00 0.00 2.87
107 109 0.250467 TCTGAGGCCTGAAACTGCAC 60.250 55.000 12.00 0.00 0.00 4.57
119 121 1.809547 GAGGCAAGTTTCTTCTGAGGC 59.190 52.381 0.00 0.00 0.00 4.70
120 122 3.072944 CTGAGGCAAGTTTCTTCTGAGG 58.927 50.000 0.00 0.00 0.00 3.86
123 125 3.688673 GGATCTGAGGCAAGTTTCTTCTG 59.311 47.826 0.00 0.00 0.00 3.02
140 142 4.467769 CATGGCTTCCAAATACAGGATCT 58.532 43.478 0.00 0.00 36.95 2.75
164 166 1.732259 CATCTTAAGCTTTGCCGACGT 59.268 47.619 3.20 0.00 0.00 4.34
165 167 1.732259 ACATCTTAAGCTTTGCCGACG 59.268 47.619 3.20 0.00 0.00 5.12
167 169 4.846779 AAAACATCTTAAGCTTTGCCGA 57.153 36.364 3.20 0.00 0.00 5.54
170 172 5.985530 ACCAGAAAAACATCTTAAGCTTTGC 59.014 36.000 3.20 0.00 0.00 3.68
178 180 6.214191 TGCAACAACCAGAAAAACATCTTA 57.786 33.333 0.00 0.00 0.00 2.10
187 189 2.622942 GTCCAGATGCAACAACCAGAAA 59.377 45.455 0.00 0.00 0.00 2.52
194 196 1.971167 GCCGGTCCAGATGCAACAA 60.971 57.895 1.90 0.00 0.00 2.83
205 207 1.152963 ATTGCACCATAGCCGGTCC 60.153 57.895 1.90 0.00 37.07 4.46
209 211 0.659427 CAGTCATTGCACCATAGCCG 59.341 55.000 0.00 0.00 0.00 5.52
236 238 2.753043 ATTTGGCCAGCCTCTGCG 60.753 61.111 5.11 0.00 44.33 5.18
253 255 1.135315 GAGCGCGTAGACGTAACCA 59.865 57.895 8.43 0.00 42.22 3.67
260 262 0.247894 CTCTGACAGAGCGCGTAGAC 60.248 60.000 19.25 0.00 35.30 2.59
264 266 2.268802 TTCCTCTGACAGAGCGCGT 61.269 57.895 24.62 0.00 40.98 6.01
267 269 0.108898 CAGGTTCCTCTGACAGAGCG 60.109 60.000 24.62 17.82 40.98 5.03
274 276 0.178921 AGCACTCCAGGTTCCTCTGA 60.179 55.000 0.00 0.00 36.93 3.27
285 287 2.430248 TAGATGTACCGAGCACTCCA 57.570 50.000 0.00 0.00 0.00 3.86
289 291 3.318275 TCCAGAATAGATGTACCGAGCAC 59.682 47.826 0.00 0.00 0.00 4.40
294 296 3.319405 ACAGCTCCAGAATAGATGTACCG 59.681 47.826 0.00 0.00 41.53 4.02
298 300 3.652055 AGGACAGCTCCAGAATAGATGT 58.348 45.455 0.00 0.00 45.69 3.06
301 303 3.840666 ACAAAGGACAGCTCCAGAATAGA 59.159 43.478 0.00 0.00 39.39 1.98
315 317 3.134458 CACACTTGAGAGGACAAAGGAC 58.866 50.000 0.00 0.00 0.00 3.85
316 318 2.104792 CCACACTTGAGAGGACAAAGGA 59.895 50.000 0.00 0.00 0.00 3.36
322 324 1.374758 CCGCCACACTTGAGAGGAC 60.375 63.158 0.00 0.00 0.00 3.85
338 340 2.660064 CCCAGGAAGTGACCTCCCG 61.660 68.421 0.00 0.00 38.32 5.14
347 349 1.464198 AGCAACCCTCCCAGGAAGT 60.464 57.895 0.00 0.00 37.67 3.01
357 359 2.943199 GCATTAAGAGCTGAGCAACCCT 60.943 50.000 7.39 0.00 0.00 4.34
361 363 1.733912 CGTGCATTAAGAGCTGAGCAA 59.266 47.619 7.39 0.00 33.37 3.91
366 368 1.398390 GTTCCCGTGCATTAAGAGCTG 59.602 52.381 0.00 0.00 0.00 4.24
367 369 1.003118 TGTTCCCGTGCATTAAGAGCT 59.997 47.619 0.00 0.00 0.00 4.09
368 370 1.130561 GTGTTCCCGTGCATTAAGAGC 59.869 52.381 0.00 0.00 0.00 4.09
373 375 0.390603 CGGAGTGTTCCCGTGCATTA 60.391 55.000 0.00 0.00 40.67 1.90
404 407 1.066858 TCGCCTGACAGATTGAAGTCC 60.067 52.381 3.32 0.00 33.89 3.85
416 419 2.208431 CTTTCCTGATGATCGCCTGAC 58.792 52.381 0.00 0.00 0.00 3.51
417 420 1.473965 GCTTTCCTGATGATCGCCTGA 60.474 52.381 0.00 0.00 0.00 3.86
418 421 0.942962 GCTTTCCTGATGATCGCCTG 59.057 55.000 0.00 0.00 0.00 4.85
430 433 2.036346 GGTGCTCATTTGTTGCTTTCCT 59.964 45.455 0.00 0.00 0.00 3.36
436 439 0.664166 CACCGGTGCTCATTTGTTGC 60.664 55.000 24.02 0.00 0.00 4.17
448 451 1.029947 GTCTTTATGCCCCACCGGTG 61.030 60.000 28.26 28.26 0.00 4.94
453 456 4.016444 TGATCAAAGTCTTTATGCCCCAC 58.984 43.478 0.00 0.00 0.00 4.61
462 465 7.234355 AGGTAACCAGAATGATCAAAGTCTTT 58.766 34.615 0.00 0.00 39.69 2.52
468 471 6.632672 GCTCCTAGGTAACCAGAATGATCAAA 60.633 42.308 9.08 0.00 39.69 2.69
488 491 0.032217 CCTCTCCTTCCAGAGCTCCT 60.032 60.000 10.93 0.00 38.98 3.69
497 500 4.080638 AGACAACATCATTCCTCTCCTTCC 60.081 45.833 0.00 0.00 0.00 3.46
512 515 3.953612 TGTTTTGCTCCTGAAGACAACAT 59.046 39.130 0.00 0.00 0.00 2.71
515 518 2.687935 GGTGTTTTGCTCCTGAAGACAA 59.312 45.455 0.00 0.00 0.00 3.18
545 548 0.107456 CCATTATCTCGCAGGGCACT 59.893 55.000 0.00 0.00 0.00 4.40
546 549 1.510480 GCCATTATCTCGCAGGGCAC 61.510 60.000 0.00 0.00 41.02 5.01
547 550 1.227943 GCCATTATCTCGCAGGGCA 60.228 57.895 0.00 0.00 41.02 5.36
548 551 1.072159 AGCCATTATCTCGCAGGGC 59.928 57.895 0.00 0.00 41.65 5.19
549 552 0.394192 TCAGCCATTATCTCGCAGGG 59.606 55.000 0.00 0.00 0.00 4.45
550 553 1.342496 TCTCAGCCATTATCTCGCAGG 59.658 52.381 0.00 0.00 0.00 4.85
555 639 7.325660 TCAAAACAATCTCAGCCATTATCTC 57.674 36.000 0.00 0.00 0.00 2.75
561 645 3.767673 AGCATCAAAACAATCTCAGCCAT 59.232 39.130 0.00 0.00 0.00 4.40
562 646 3.159472 AGCATCAAAACAATCTCAGCCA 58.841 40.909 0.00 0.00 0.00 4.75
564 648 4.143179 GCAAAGCATCAAAACAATCTCAGC 60.143 41.667 0.00 0.00 0.00 4.26
579 663 4.270230 GTGTGGACACGATGCAAAGCAT 62.270 50.000 3.85 3.85 43.69 3.79
580 664 0.817229 TGTGGACACGATGCAAAGCA 60.817 50.000 0.00 0.00 44.86 3.91
581 665 0.385974 GTGTGGACACGATGCAAAGC 60.386 55.000 0.00 0.00 37.10 3.51
582 666 3.753774 GTGTGGACACGATGCAAAG 57.246 52.632 0.00 0.00 37.10 2.77
597 683 2.277084 GGCCGATAGAAAACATCGTGT 58.723 47.619 4.28 0.00 42.89 4.49
600 686 1.597663 GGTGGCCGATAGAAAACATCG 59.402 52.381 0.00 0.00 43.80 3.84
614 700 2.695314 GATCAAGTGATCGGTGGCC 58.305 57.895 5.57 0.00 41.15 5.36
622 708 5.334879 GCGGTACAAAGTTTGATCAAGTGAT 60.335 40.000 22.23 0.00 37.51 3.06
623 709 4.024387 GCGGTACAAAGTTTGATCAAGTGA 60.024 41.667 22.23 0.00 0.00 3.41
624 710 4.024048 AGCGGTACAAAGTTTGATCAAGTG 60.024 41.667 22.23 8.30 0.00 3.16
625 711 4.134563 AGCGGTACAAAGTTTGATCAAGT 58.865 39.130 22.23 5.44 0.00 3.16
626 712 4.378459 GGAGCGGTACAAAGTTTGATCAAG 60.378 45.833 22.23 9.81 0.00 3.02
627 713 3.500680 GGAGCGGTACAAAGTTTGATCAA 59.499 43.478 22.23 3.38 0.00 2.57
628 714 3.071479 GGAGCGGTACAAAGTTTGATCA 58.929 45.455 22.23 4.13 0.00 2.92
629 715 2.418976 GGGAGCGGTACAAAGTTTGATC 59.581 50.000 22.23 13.02 0.00 2.92
630 716 2.039879 AGGGAGCGGTACAAAGTTTGAT 59.960 45.455 22.23 8.93 0.00 2.57
631 717 1.418637 AGGGAGCGGTACAAAGTTTGA 59.581 47.619 22.23 3.32 0.00 2.69
632 718 1.892209 AGGGAGCGGTACAAAGTTTG 58.108 50.000 14.13 14.13 0.00 2.93
633 719 2.105993 AGAAGGGAGCGGTACAAAGTTT 59.894 45.455 0.00 0.00 0.00 2.66
634 720 1.697982 AGAAGGGAGCGGTACAAAGTT 59.302 47.619 0.00 0.00 0.00 2.66
635 721 1.002087 CAGAAGGGAGCGGTACAAAGT 59.998 52.381 0.00 0.00 0.00 2.66
636 722 1.726853 CAGAAGGGAGCGGTACAAAG 58.273 55.000 0.00 0.00 0.00 2.77
637 723 0.321298 GCAGAAGGGAGCGGTACAAA 60.321 55.000 0.00 0.00 0.00 2.83
638 724 1.192146 AGCAGAAGGGAGCGGTACAA 61.192 55.000 0.00 0.00 35.48 2.41
639 725 0.323999 TAGCAGAAGGGAGCGGTACA 60.324 55.000 0.00 0.00 35.48 2.90
640 726 0.822164 TTAGCAGAAGGGAGCGGTAC 59.178 55.000 0.00 0.00 35.48 3.34
641 727 1.563924 TTTAGCAGAAGGGAGCGGTA 58.436 50.000 0.00 0.00 35.48 4.02
642 728 0.912486 ATTTAGCAGAAGGGAGCGGT 59.088 50.000 0.00 0.00 35.48 5.68
643 729 1.139853 AGATTTAGCAGAAGGGAGCGG 59.860 52.381 0.00 0.00 35.48 5.52
644 730 2.611225 AGATTTAGCAGAAGGGAGCG 57.389 50.000 0.00 0.00 35.48 5.03
697 783 2.808543 GTGCTGAGTGACGGAGATTTTT 59.191 45.455 0.00 0.00 0.00 1.94
698 784 2.224281 TGTGCTGAGTGACGGAGATTTT 60.224 45.455 0.00 0.00 0.00 1.82
699 785 1.344438 TGTGCTGAGTGACGGAGATTT 59.656 47.619 0.00 0.00 0.00 2.17
700 786 0.969149 TGTGCTGAGTGACGGAGATT 59.031 50.000 0.00 0.00 0.00 2.40
701 787 0.529833 CTGTGCTGAGTGACGGAGAT 59.470 55.000 0.00 0.00 0.00 2.75
702 788 1.527433 CCTGTGCTGAGTGACGGAGA 61.527 60.000 0.00 0.00 0.00 3.71
703 789 1.080230 CCTGTGCTGAGTGACGGAG 60.080 63.158 0.00 0.00 0.00 4.63
704 790 1.806461 GACCTGTGCTGAGTGACGGA 61.806 60.000 0.00 0.00 0.00 4.69
705 791 1.373497 GACCTGTGCTGAGTGACGG 60.373 63.158 0.00 0.00 0.00 4.79
706 792 1.373497 GGACCTGTGCTGAGTGACG 60.373 63.158 0.00 0.00 0.00 4.35
707 793 1.004440 GGGACCTGTGCTGAGTGAC 60.004 63.158 0.00 0.00 0.00 3.67
708 794 1.459348 TGGGACCTGTGCTGAGTGA 60.459 57.895 0.00 0.00 0.00 3.41
709 795 1.302033 GTGGGACCTGTGCTGAGTG 60.302 63.158 0.00 0.00 0.00 3.51
710 796 2.872388 CGTGGGACCTGTGCTGAGT 61.872 63.158 0.00 0.00 0.00 3.41
711 797 2.047844 CGTGGGACCTGTGCTGAG 60.048 66.667 0.00 0.00 0.00 3.35
712 798 2.099652 CTTCGTGGGACCTGTGCTGA 62.100 60.000 0.00 0.00 0.00 4.26
713 799 1.669115 CTTCGTGGGACCTGTGCTG 60.669 63.158 0.00 0.00 0.00 4.41
714 800 2.743718 CTTCGTGGGACCTGTGCT 59.256 61.111 0.00 0.00 0.00 4.40
715 801 3.050275 GCTTCGTGGGACCTGTGC 61.050 66.667 0.00 0.00 0.00 4.57
716 802 1.961277 GTGCTTCGTGGGACCTGTG 60.961 63.158 0.00 0.00 0.00 3.66
717 803 2.426023 GTGCTTCGTGGGACCTGT 59.574 61.111 0.00 0.00 0.00 4.00
718 804 2.358737 GGTGCTTCGTGGGACCTG 60.359 66.667 11.98 0.00 43.09 4.00
720 806 1.079336 GTAGGTGCTTCGTGGGACC 60.079 63.158 11.49 11.49 46.08 4.46
721 807 0.034337 TTGTAGGTGCTTCGTGGGAC 59.966 55.000 0.00 0.00 0.00 4.46
722 808 0.759959 TTTGTAGGTGCTTCGTGGGA 59.240 50.000 0.00 0.00 0.00 4.37
723 809 1.156736 CTTTGTAGGTGCTTCGTGGG 58.843 55.000 0.00 0.00 0.00 4.61
724 810 2.163818 TCTTTGTAGGTGCTTCGTGG 57.836 50.000 0.00 0.00 0.00 4.94
725 811 2.869801 TGTTCTTTGTAGGTGCTTCGTG 59.130 45.455 0.00 0.00 0.00 4.35
726 812 3.131396 CTGTTCTTTGTAGGTGCTTCGT 58.869 45.455 0.00 0.00 0.00 3.85
727 813 3.131396 ACTGTTCTTTGTAGGTGCTTCG 58.869 45.455 0.00 0.00 0.00 3.79
728 814 3.184581 CGACTGTTCTTTGTAGGTGCTTC 59.815 47.826 0.00 0.00 0.00 3.86
729 815 3.131396 CGACTGTTCTTTGTAGGTGCTT 58.869 45.455 0.00 0.00 0.00 3.91
730 816 2.102588 ACGACTGTTCTTTGTAGGTGCT 59.897 45.455 0.00 0.00 0.00 4.40
731 817 2.480845 ACGACTGTTCTTTGTAGGTGC 58.519 47.619 0.00 0.00 0.00 5.01
732 818 3.673809 GCTACGACTGTTCTTTGTAGGTG 59.326 47.826 0.00 0.00 34.51 4.00
733 819 3.573110 AGCTACGACTGTTCTTTGTAGGT 59.427 43.478 0.00 0.00 38.59 3.08
734 820 4.175787 AGCTACGACTGTTCTTTGTAGG 57.824 45.455 0.00 0.00 34.51 3.18
735 821 5.940595 ACTAGCTACGACTGTTCTTTGTAG 58.059 41.667 0.00 0.00 36.47 2.74
736 822 5.471116 TGACTAGCTACGACTGTTCTTTGTA 59.529 40.000 0.00 0.00 0.00 2.41
737 823 4.277672 TGACTAGCTACGACTGTTCTTTGT 59.722 41.667 0.00 0.00 0.00 2.83
738 824 4.795268 TGACTAGCTACGACTGTTCTTTG 58.205 43.478 0.00 0.00 0.00 2.77
739 825 5.646577 ATGACTAGCTACGACTGTTCTTT 57.353 39.130 0.00 0.00 0.00 2.52
740 826 5.646793 TGTATGACTAGCTACGACTGTTCTT 59.353 40.000 0.00 0.00 0.00 2.52
741 827 5.183969 TGTATGACTAGCTACGACTGTTCT 58.816 41.667 0.00 0.00 0.00 3.01
742 828 5.293814 TCTGTATGACTAGCTACGACTGTTC 59.706 44.000 0.00 0.00 0.00 3.18
743 829 5.183969 TCTGTATGACTAGCTACGACTGTT 58.816 41.667 0.00 0.00 0.00 3.16
848 934 2.623878 TCTACTTTTTGGGCGTGTCA 57.376 45.000 0.00 0.00 0.00 3.58
895 981 2.822255 CGGTTATGTGGGGGCGTG 60.822 66.667 0.00 0.00 0.00 5.34
896 982 4.789123 GCGGTTATGTGGGGGCGT 62.789 66.667 0.00 0.00 0.00 5.68
897 983 4.483243 AGCGGTTATGTGGGGGCG 62.483 66.667 0.00 0.00 0.00 6.13
973 1065 3.800863 CAGCAGCAGCAGAAGCCG 61.801 66.667 3.17 0.00 45.49 5.52
1054 1152 0.463295 CTGCCGAGGCTGTGAATGAT 60.463 55.000 15.75 0.00 42.51 2.45
1191 1289 3.627395 TGGTCTTTGGAGTATTGCGAT 57.373 42.857 0.00 0.00 0.00 4.58
1233 1334 2.879103 CCAACTTGGTGATGGGTAGT 57.121 50.000 0.00 0.00 35.26 2.73
1245 1346 0.816421 ACGAAACGTCCCCCAACTTG 60.816 55.000 0.00 0.00 33.69 3.16
1263 1364 2.887152 ACCAAGAAACATGCCTTGAGAC 59.113 45.455 18.83 0.00 41.56 3.36
1274 1375 5.982516 CGAAATGGAATCAAACCAAGAAACA 59.017 36.000 0.00 0.00 40.93 2.83
1371 1488 4.060038 GCCTTGCCGTGCTTGCAT 62.060 61.111 0.00 0.00 38.76 3.96
1413 1530 1.551452 CTATCCTCCTCCACCCGATC 58.449 60.000 0.00 0.00 0.00 3.69
1482 1599 3.419580 TCCATGAGGCCGCCCATT 61.420 61.111 5.55 0.00 33.74 3.16
1713 1830 0.174845 TAATTCAGGCCGTCACCTCG 59.825 55.000 0.00 0.00 38.26 4.63
1760 1883 4.704540 TCGCCATGAATTATTTTGTCCACT 59.295 37.500 0.00 0.00 0.00 4.00
1780 1913 2.088674 ACCTGAGCGGTATGGATCGC 62.089 60.000 11.60 0.00 46.73 4.58
1781 1914 2.041976 ACCTGAGCGGTATGGATCG 58.958 57.895 11.60 0.00 46.73 3.69
1803 1936 2.740714 GCCGCCTGCAACTCTAACG 61.741 63.158 0.00 0.00 40.77 3.18
1920 2053 4.337763 CTTTCACATGAAGCGCTGTTATC 58.662 43.478 12.58 5.01 35.21 1.75
2140 2273 2.587194 CATCGAGCAAGGCGGGAG 60.587 66.667 0.00 0.00 0.00 4.30
2387 2579 5.474876 CAGCAGGTTTAGGTCTTCTTGATTT 59.525 40.000 0.00 0.00 0.00 2.17
2687 2936 2.608752 CCACAAAGAGAAACATGCCTGC 60.609 50.000 0.00 0.00 0.00 4.85
3078 3339 8.252624 AGATTTAGAAATGGAGGGAGTAGTAC 57.747 38.462 0.00 0.00 0.00 2.73
3084 3345 8.028652 AGACTTAGATTTAGAAATGGAGGGAG 57.971 38.462 0.00 0.00 0.00 4.30
3165 3430 2.853003 GGAGCGAAACGAGTGAATCTAC 59.147 50.000 0.00 0.00 0.00 2.59
3166 3431 2.477357 CGGAGCGAAACGAGTGAATCTA 60.477 50.000 0.00 0.00 0.00 1.98
3177 3442 2.850647 GACACTACATACGGAGCGAAAC 59.149 50.000 0.00 0.00 0.00 2.78
3181 3446 4.024302 TCAATAGACACTACATACGGAGCG 60.024 45.833 0.00 0.00 0.00 5.03
3185 3450 8.353684 AGAGATTTCAATAGACACTACATACGG 58.646 37.037 0.00 0.00 0.00 4.02
3318 3592 5.086104 TCATAGAAAAGGTACAGGCAGTC 57.914 43.478 0.00 0.00 0.00 3.51
3319 3593 5.700402 ATCATAGAAAAGGTACAGGCAGT 57.300 39.130 0.00 0.00 0.00 4.40
3320 3594 9.376075 CATATATCATAGAAAAGGTACAGGCAG 57.624 37.037 0.00 0.00 0.00 4.85
3322 3596 8.540388 TCCATATATCATAGAAAAGGTACAGGC 58.460 37.037 0.00 0.00 0.00 4.85
3409 3796 4.283212 CCACCAAAAATGGTCAGGTTATGT 59.717 41.667 0.00 0.00 40.85 2.29
3748 4135 0.729116 GGAGACACGCATCACCATTG 59.271 55.000 0.00 0.00 30.29 2.82
3860 4259 0.934496 TCACACTTTGCTTCGAACGG 59.066 50.000 0.00 0.00 0.00 4.44
3884 4283 1.535462 CAAGTGGTAACCTTGAAGCGG 59.465 52.381 3.63 0.00 43.42 5.52
3971 4370 2.815503 CAATGTCACTCTGCATGGTGAA 59.184 45.455 18.97 12.10 42.88 3.18
4096 4497 1.971695 GTGCCGTCCCCTGAAAAGG 60.972 63.158 0.00 0.00 0.00 3.11
4097 4498 1.228124 TGTGCCGTCCCCTGAAAAG 60.228 57.895 0.00 0.00 0.00 2.27
4098 4499 1.527380 GTGTGCCGTCCCCTGAAAA 60.527 57.895 0.00 0.00 0.00 2.29
4099 4500 2.112297 GTGTGCCGTCCCCTGAAA 59.888 61.111 0.00 0.00 0.00 2.69
4100 4501 4.308458 CGTGTGCCGTCCCCTGAA 62.308 66.667 0.00 0.00 0.00 3.02
4166 4577 2.163815 ACTAGTGAGACCACATACACGC 59.836 50.000 0.00 0.00 45.54 5.34
4179 4590 2.229062 TGCTCGAGGAAACACTAGTGAG 59.771 50.000 29.30 13.90 0.00 3.51
4251 4674 6.426937 TGTCCATGTGAAAGTAAAGCTAAGAC 59.573 38.462 0.00 0.00 0.00 3.01
4281 4704 3.266240 AAAAACATCGGCCTCCCTC 57.734 52.632 0.00 0.00 0.00 4.30
4301 4726 5.618056 AATAAGATATCCGCATGCACAAG 57.382 39.130 19.57 2.96 0.00 3.16
4304 4729 7.535258 CACTTTTAATAAGATATCCGCATGCAC 59.465 37.037 19.57 1.43 0.00 4.57
4306 4731 6.524586 GCACTTTTAATAAGATATCCGCATGC 59.475 38.462 7.91 7.91 0.00 4.06
4307 4732 7.023575 GGCACTTTTAATAAGATATCCGCATG 58.976 38.462 0.00 0.00 0.00 4.06
4309 4734 6.058833 TGGCACTTTTAATAAGATATCCGCA 58.941 36.000 0.00 0.00 0.00 5.69
4310 4735 6.554334 TGGCACTTTTAATAAGATATCCGC 57.446 37.500 0.00 0.00 0.00 5.54
4311 4736 8.783093 TGATTGGCACTTTTAATAAGATATCCG 58.217 33.333 0.00 0.00 0.00 4.18
4316 4741 9.995003 TGTTTTGATTGGCACTTTTAATAAGAT 57.005 25.926 0.00 0.00 0.00 2.40
4317 4742 9.823647 TTGTTTTGATTGGCACTTTTAATAAGA 57.176 25.926 0.00 0.00 0.00 2.10
4321 4746 8.504812 ACTTTGTTTTGATTGGCACTTTTAAT 57.495 26.923 0.00 0.00 0.00 1.40
4359 4807 2.817396 GCACCTTCCGAGAGCTGC 60.817 66.667 0.00 0.00 0.00 5.25
4361 4809 1.758440 TTGTGCACCTTCCGAGAGCT 61.758 55.000 15.69 0.00 0.00 4.09
4363 4811 1.151668 CTTTGTGCACCTTCCGAGAG 58.848 55.000 15.69 0.00 0.00 3.20
4368 4816 0.110486 TCTCCCTTTGTGCACCTTCC 59.890 55.000 15.69 0.00 0.00 3.46
4413 4978 9.965902 AATAGGAATTTAGTCATCTTGTCTTGT 57.034 29.630 0.00 0.00 0.00 3.16
4439 5004 9.788960 CGATTTAGATGACGATCCAATAATAGA 57.211 33.333 0.00 0.00 0.00 1.98
4449 5014 8.912787 ATATACAACCGATTTAGATGACGATC 57.087 34.615 0.00 0.00 0.00 3.69
4451 5016 9.999009 GATATATACAACCGATTTAGATGACGA 57.001 33.333 0.00 0.00 0.00 4.20
4457 5022 7.985184 GCATGGGATATATACAACCGATTTAGA 59.015 37.037 0.00 0.00 0.00 2.10
4462 5027 5.957771 AGCATGGGATATATACAACCGAT 57.042 39.130 0.00 0.00 0.00 4.18
4463 5028 5.128171 GGTAGCATGGGATATATACAACCGA 59.872 44.000 0.00 0.00 0.00 4.69
4464 5029 5.357257 GGTAGCATGGGATATATACAACCG 58.643 45.833 0.00 0.00 0.00 4.44
4465 5030 5.105064 ACGGTAGCATGGGATATATACAACC 60.105 44.000 0.00 0.00 0.00 3.77
4466 5031 5.974108 ACGGTAGCATGGGATATATACAAC 58.026 41.667 0.00 0.00 0.00 3.32
4467 5032 5.955959 AGACGGTAGCATGGGATATATACAA 59.044 40.000 0.00 0.00 0.00 2.41
4468 5033 5.516044 AGACGGTAGCATGGGATATATACA 58.484 41.667 0.00 0.00 0.00 2.29
4469 5034 5.009811 GGAGACGGTAGCATGGGATATATAC 59.990 48.000 0.00 0.00 0.00 1.47
4470 5035 5.138276 GGAGACGGTAGCATGGGATATATA 58.862 45.833 0.00 0.00 0.00 0.86
4471 5036 3.961408 GGAGACGGTAGCATGGGATATAT 59.039 47.826 0.00 0.00 0.00 0.86
4472 5037 3.362706 GGAGACGGTAGCATGGGATATA 58.637 50.000 0.00 0.00 0.00 0.86
4473 5038 2.180276 GGAGACGGTAGCATGGGATAT 58.820 52.381 0.00 0.00 0.00 1.63
4474 5039 1.629043 GGAGACGGTAGCATGGGATA 58.371 55.000 0.00 0.00 0.00 2.59
4475 5040 1.122019 GGGAGACGGTAGCATGGGAT 61.122 60.000 0.00 0.00 0.00 3.85
4476 5041 1.760875 GGGAGACGGTAGCATGGGA 60.761 63.158 0.00 0.00 0.00 4.37
4477 5042 2.032860 CTGGGAGACGGTAGCATGGG 62.033 65.000 0.00 0.00 0.00 4.00
4478 5043 1.330655 ACTGGGAGACGGTAGCATGG 61.331 60.000 0.00 0.00 36.76 3.66
4479 5044 0.179100 CACTGGGAGACGGTAGCATG 60.179 60.000 0.00 0.00 36.76 4.06
4480 5045 1.330655 CCACTGGGAGACGGTAGCAT 61.331 60.000 0.00 0.00 36.76 3.79
4481 5046 1.982395 CCACTGGGAGACGGTAGCA 60.982 63.158 0.00 0.00 36.76 3.49
4482 5047 1.542187 AACCACTGGGAGACGGTAGC 61.542 60.000 0.00 0.00 36.76 3.58
4483 5048 0.246635 CAACCACTGGGAGACGGTAG 59.753 60.000 0.00 0.00 36.76 3.18
4484 5049 1.823169 GCAACCACTGGGAGACGGTA 61.823 60.000 0.00 0.00 36.76 4.02
4485 5050 3.148084 CAACCACTGGGAGACGGT 58.852 61.111 0.00 0.00 40.00 4.83
4486 5051 2.358737 GCAACCACTGGGAGACGG 60.359 66.667 0.00 0.00 38.05 4.79
4487 5052 1.961277 GTGCAACCACTGGGAGACG 60.961 63.158 0.00 0.00 38.93 4.18
4488 5053 4.065110 GTGCAACCACTGGGAGAC 57.935 61.111 0.00 0.00 38.93 3.36
4499 5064 4.620982 AGCTTTTGGTTATTGAGTGCAAC 58.379 39.130 0.00 0.00 36.72 4.17
4506 5071 6.245408 ACTACATGGAGCTTTTGGTTATTGA 58.755 36.000 4.32 0.00 0.00 2.57
4533 5098 1.202582 CTCAGTGTTGGGAGACGGTAG 59.797 57.143 0.00 0.00 32.87 3.18
4537 5102 1.374758 GCCTCAGTGTTGGGAGACG 60.375 63.158 6.97 0.00 32.87 4.18
4542 5107 1.746615 CATCGGCCTCAGTGTTGGG 60.747 63.158 0.00 2.19 0.00 4.12
4549 5114 1.593750 GCAGCTACATCGGCCTCAG 60.594 63.158 0.00 0.00 0.00 3.35
4636 5201 6.808321 TTGAGGGACTATTGCTATAGTTGT 57.192 37.500 19.62 9.25 45.43 3.32
4673 5279 7.980742 AACTCTTGAAAACGAATTTTGTACC 57.019 32.000 0.00 0.00 38.17 3.34
4727 5333 6.424207 AGGAGTAAAAGTTTCGAGCAGTTAAG 59.576 38.462 0.00 0.00 0.00 1.85
4734 5340 4.496360 AGCTAGGAGTAAAAGTTTCGAGC 58.504 43.478 0.00 0.00 0.00 5.03
4735 5341 6.391537 AGAAGCTAGGAGTAAAAGTTTCGAG 58.608 40.000 0.00 0.00 36.10 4.04
4777 5383 1.838077 CGGGGAAGGGGTGATATATCC 59.162 57.143 10.25 1.94 0.00 2.59
4804 5411 1.637934 CGCGGACGTCGATGTAGTA 59.362 57.895 10.95 0.00 42.43 1.82
4836 5443 2.280457 GGAGGGCGAGTGCTATGC 60.280 66.667 0.00 0.00 42.25 3.14
4897 5504 2.781945 GCTAAATCCTGCCATTTCGG 57.218 50.000 0.00 0.00 38.11 4.30
4906 5513 2.231215 CCTCTGACGGCTAAATCCTG 57.769 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.