Multiple sequence alignment - TraesCS2A01G420500

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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 TraesCS2A01G420500 chr2A 100.000 3285 0 0 1 3285 676266888 676263604 0.000000e+00 6067.0
1 TraesCS2A01G420500 chr2A 85.797 866 108 8 2432 3285 384897433 384898295 0.000000e+00 904.0
2 TraesCS2A01G420500 chr2A 89.610 77 8 0 2342 2418 751532492 751532416 7.500000e-17 99.0
3 TraesCS2A01G420500 chr2D 91.798 1646 87 25 542 2180 531675728 531674124 0.000000e+00 2248.0
4 TraesCS2A01G420500 chr2D 83.371 884 96 22 2342 3208 317599472 317600321 0.000000e+00 771.0
5 TraesCS2A01G420500 chr2D 96.416 279 10 0 1 279 531676250 531675972 8.310000e-126 460.0
6 TraesCS2A01G420500 chr2D 91.096 146 4 4 277 422 531675859 531675723 4.330000e-44 189.0
7 TraesCS2A01G420500 chr2B 91.439 1063 60 20 542 1603 631440188 631439156 0.000000e+00 1430.0
8 TraesCS2A01G420500 chr2B 87.774 638 50 11 1547 2177 631439170 631438554 0.000000e+00 721.0
9 TraesCS2A01G420500 chr2B 94.550 422 20 3 1 421 631440603 631440184 0.000000e+00 649.0
10 TraesCS2A01G420500 chr2B 95.652 46 1 1 2311 2356 779099236 779099192 4.550000e-09 73.1
11 TraesCS2A01G420500 chr1D 86.260 968 110 8 2341 3285 38363686 38362719 0.000000e+00 1029.0
12 TraesCS2A01G420500 chr3B 83.904 1081 144 12 2221 3278 136811736 136812809 0.000000e+00 1005.0
13 TraesCS2A01G420500 chr3B 83.204 905 108 22 2346 3231 449295511 449296390 0.000000e+00 789.0
14 TraesCS2A01G420500 chr3B 79.088 636 90 19 2205 2799 762409275 762409908 6.600000e-107 398.0
15 TraesCS2A01G420500 chr6D 85.655 969 112 16 2342 3285 405660045 405659079 0.000000e+00 994.0
16 TraesCS2A01G420500 chr6D 92.908 141 9 1 415 555 435990507 435990646 1.550000e-48 204.0
17 TraesCS2A01G420500 chr5B 83.227 1097 151 17 2210 3278 354725061 354726152 0.000000e+00 976.0
18 TraesCS2A01G420500 chr5B 85.193 959 114 13 2342 3278 577246136 577247088 0.000000e+00 959.0
19 TraesCS2A01G420500 chr3A 84.098 1025 130 11 2236 3227 399702085 399703109 0.000000e+00 959.0
20 TraesCS2A01G420500 chr6B 85.146 956 114 13 2345 3274 686198112 686197159 0.000000e+00 953.0
21 TraesCS2A01G420500 chr6B 82.665 998 123 23 2258 3231 689279432 689278461 0.000000e+00 839.0
22 TraesCS2A01G420500 chr6B 89.759 166 12 4 410 573 67527380 67527542 1.190000e-49 207.0
23 TraesCS2A01G420500 chr7A 85.248 949 111 17 2344 3268 162599383 162600326 0.000000e+00 950.0
24 TraesCS2A01G420500 chr7A 94.776 134 7 0 415 548 442265751 442265884 3.320000e-50 209.0
25 TraesCS2A01G420500 chr1B 81.282 577 72 10 2341 2900 573759497 573758940 5.030000e-118 435.0
26 TraesCS2A01G420500 chr1B 93.525 139 7 2 410 548 252023591 252023455 4.300000e-49 206.0
27 TraesCS2A01G420500 chr7B 79.455 550 81 10 2312 2853 713670272 713669747 8.670000e-96 361.0
28 TraesCS2A01G420500 chr7B 98.425 127 2 0 419 545 529151454 529151328 1.190000e-54 224.0
29 TraesCS2A01G420500 chr6A 78.899 327 60 4 2437 2755 592208179 592208504 2.570000e-51 213.0
30 TraesCS2A01G420500 chr6A 94.245 139 6 1 409 545 542709486 542709348 9.240000e-51 211.0
31 TraesCS2A01G420500 chr5D 96.154 130 5 0 416 545 392813855 392813726 2.570000e-51 213.0
32 TraesCS2A01G420500 chr5D 92.361 144 10 1 410 552 211375759 211375616 1.550000e-48 204.0
33 TraesCS2A01G420500 chr3D 93.617 141 9 0 419 559 614251218 614251078 9.240000e-51 211.0


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 TraesCS2A01G420500 chr2A 676263604 676266888 3284 True 6067.000000 6067 100.000000 1 3285 1 chr2A.!!$R1 3284
1 TraesCS2A01G420500 chr2A 384897433 384898295 862 False 904.000000 904 85.797000 2432 3285 1 chr2A.!!$F1 853
2 TraesCS2A01G420500 chr2D 531674124 531676250 2126 True 965.666667 2248 93.103333 1 2180 3 chr2D.!!$R1 2179
3 TraesCS2A01G420500 chr2D 317599472 317600321 849 False 771.000000 771 83.371000 2342 3208 1 chr2D.!!$F1 866
4 TraesCS2A01G420500 chr2B 631438554 631440603 2049 True 933.333333 1430 91.254333 1 2177 3 chr2B.!!$R2 2176
5 TraesCS2A01G420500 chr1D 38362719 38363686 967 True 1029.000000 1029 86.260000 2341 3285 1 chr1D.!!$R1 944
6 TraesCS2A01G420500 chr3B 136811736 136812809 1073 False 1005.000000 1005 83.904000 2221 3278 1 chr3B.!!$F1 1057
7 TraesCS2A01G420500 chr3B 449295511 449296390 879 False 789.000000 789 83.204000 2346 3231 1 chr3B.!!$F2 885
8 TraesCS2A01G420500 chr3B 762409275 762409908 633 False 398.000000 398 79.088000 2205 2799 1 chr3B.!!$F3 594
9 TraesCS2A01G420500 chr6D 405659079 405660045 966 True 994.000000 994 85.655000 2342 3285 1 chr6D.!!$R1 943
10 TraesCS2A01G420500 chr5B 354725061 354726152 1091 False 976.000000 976 83.227000 2210 3278 1 chr5B.!!$F1 1068
11 TraesCS2A01G420500 chr5B 577246136 577247088 952 False 959.000000 959 85.193000 2342 3278 1 chr5B.!!$F2 936
12 TraesCS2A01G420500 chr3A 399702085 399703109 1024 False 959.000000 959 84.098000 2236 3227 1 chr3A.!!$F1 991
13 TraesCS2A01G420500 chr6B 686197159 686198112 953 True 953.000000 953 85.146000 2345 3274 1 chr6B.!!$R1 929
14 TraesCS2A01G420500 chr6B 689278461 689279432 971 True 839.000000 839 82.665000 2258 3231 1 chr6B.!!$R2 973
15 TraesCS2A01G420500 chr7A 162599383 162600326 943 False 950.000000 950 85.248000 2344 3268 1 chr7A.!!$F1 924
16 TraesCS2A01G420500 chr1B 573758940 573759497 557 True 435.000000 435 81.282000 2341 2900 1 chr1B.!!$R2 559
17 TraesCS2A01G420500 chr7B 713669747 713670272 525 True 361.000000 361 79.455000 2312 2853 1 chr7B.!!$R2 541

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
435 551 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.0 0.0 3.28 F
1103 1224 0.174162 GTGCTTGATTGTGGATGGGC 59.826 55.000 0.00 0.0 0.0 5.36 F
1862 2030 1.153208 GTGGCAGCCTCCTCATCAG 60.153 63.158 14.15 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1850 0.037605 GGTAGTAGTTGTGGTGCGCT 60.038 55.0 9.73 0.0 0.00 5.92 R
2187 2358 0.038166 GGGGTGTGATTGGAGAAGCA 59.962 55.0 0.00 0.0 0.00 3.91 R
2695 2945 0.321122 CGCTTGAGGAGAACAAGGCT 60.321 55.0 0.00 0.0 43.12 4.58 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.221466 CCGGTGCGGCTACATGTATG 61.221 60.000 5.91 2.21 41.17 2.39
120 121 5.050490 GTGCTGTATACTCTGTAACATGGG 58.950 45.833 4.17 0.00 0.00 4.00
149 150 6.699575 AAGCTGTATCAAATGGATGGTTAC 57.300 37.500 0.00 0.00 36.72 2.50
184 185 9.485206 GAAGTGGACTTAGTGTATTTGTTTCTA 57.515 33.333 0.00 0.00 36.11 2.10
202 203 5.692115 TTCTAAAGGATGTATGACAGGCA 57.308 39.130 0.00 0.00 0.00 4.75
286 402 4.119136 ACCATTTGCAGTTACAACTTTGC 58.881 39.130 0.00 0.00 37.08 3.68
428 544 9.458727 TGAAGTAATATTATAGTACTCCCTCCG 57.541 37.037 11.93 0.00 38.48 4.63
429 545 9.460019 GAAGTAATATTATAGTACTCCCTCCGT 57.540 37.037 11.93 0.00 38.48 4.69
430 546 9.460019 AAGTAATATTATAGTACTCCCTCCGTC 57.540 37.037 11.93 0.00 38.48 4.79
431 547 8.052141 AGTAATATTATAGTACTCCCTCCGTCC 58.948 40.741 6.54 0.00 34.84 4.79
432 548 3.515602 TTATAGTACTCCCTCCGTCCC 57.484 52.381 0.00 0.00 0.00 4.46
433 549 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
434 550 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
435 551 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
436 552 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
437 553 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
438 554 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
439 555 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
440 556 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
441 557 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
442 558 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
443 559 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
444 560 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
445 561 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
446 562 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
447 563 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
448 564 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
449 565 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
450 566 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
451 567 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
452 568 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
453 569 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
454 570 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
455 571 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
456 572 7.814587 CCCAAAATTCTTGTCTTAGATTTGTCC 59.185 37.037 0.00 0.00 28.79 4.02
457 573 8.359642 CCAAAATTCTTGTCTTAGATTTGTCCA 58.640 33.333 0.00 0.00 28.79 4.02
458 574 9.748708 CAAAATTCTTGTCTTAGATTTGTCCAA 57.251 29.630 0.00 0.00 0.00 3.53
459 575 9.971922 AAAATTCTTGTCTTAGATTTGTCCAAG 57.028 29.630 2.76 2.76 0.00 3.61
460 576 8.697507 AATTCTTGTCTTAGATTTGTCCAAGT 57.302 30.769 7.54 0.00 31.97 3.16
461 577 9.793259 AATTCTTGTCTTAGATTTGTCCAAGTA 57.207 29.630 7.54 0.81 31.97 2.24
462 578 8.603242 TTCTTGTCTTAGATTTGTCCAAGTAC 57.397 34.615 7.54 0.00 31.97 2.73
463 579 6.866770 TCTTGTCTTAGATTTGTCCAAGTACG 59.133 38.462 7.54 0.00 31.97 3.67
464 580 5.475719 TGTCTTAGATTTGTCCAAGTACGG 58.524 41.667 0.00 0.00 0.00 4.02
465 581 5.244402 TGTCTTAGATTTGTCCAAGTACGGA 59.756 40.000 0.00 0.00 0.00 4.69
466 582 6.070995 TGTCTTAGATTTGTCCAAGTACGGAT 60.071 38.462 0.00 0.00 37.41 4.18
467 583 6.255887 GTCTTAGATTTGTCCAAGTACGGATG 59.744 42.308 0.00 0.00 37.41 3.51
468 584 4.553330 AGATTTGTCCAAGTACGGATGT 57.447 40.909 0.00 0.00 37.41 3.06
469 585 5.670792 AGATTTGTCCAAGTACGGATGTA 57.329 39.130 0.00 0.00 37.41 2.29
479 595 2.523015 GTACGGATGTACCAAGTCACG 58.477 52.381 0.00 0.00 44.25 4.35
480 596 0.963962 ACGGATGTACCAAGTCACGT 59.036 50.000 0.00 0.00 38.90 4.49
481 597 1.342174 ACGGATGTACCAAGTCACGTT 59.658 47.619 0.00 0.00 38.90 3.99
482 598 2.224113 ACGGATGTACCAAGTCACGTTT 60.224 45.455 0.00 0.00 38.90 3.60
483 599 2.803956 CGGATGTACCAAGTCACGTTTT 59.196 45.455 0.00 0.00 38.90 2.43
484 600 3.989167 CGGATGTACCAAGTCACGTTTTA 59.011 43.478 0.00 0.00 38.90 1.52
485 601 4.090930 CGGATGTACCAAGTCACGTTTTAG 59.909 45.833 0.00 0.00 38.90 1.85
486 602 4.992951 GGATGTACCAAGTCACGTTTTAGT 59.007 41.667 0.00 0.00 38.79 2.24
487 603 6.158598 GGATGTACCAAGTCACGTTTTAGTA 58.841 40.000 0.00 0.00 38.79 1.82
488 604 6.815142 GGATGTACCAAGTCACGTTTTAGTAT 59.185 38.462 0.00 0.00 38.79 2.12
489 605 7.332678 GGATGTACCAAGTCACGTTTTAGTATT 59.667 37.037 0.00 0.00 38.79 1.89
490 606 9.357652 GATGTACCAAGTCACGTTTTAGTATTA 57.642 33.333 0.00 0.00 0.00 0.98
491 607 8.746922 TGTACCAAGTCACGTTTTAGTATTAG 57.253 34.615 0.00 0.00 0.00 1.73
492 608 8.359642 TGTACCAAGTCACGTTTTAGTATTAGT 58.640 33.333 0.00 0.00 0.00 2.24
493 609 9.196552 GTACCAAGTCACGTTTTAGTATTAGTT 57.803 33.333 0.00 0.00 0.00 2.24
495 611 9.196552 ACCAAGTCACGTTTTAGTATTAGTTAC 57.803 33.333 0.00 0.00 0.00 2.50
496 612 9.195411 CCAAGTCACGTTTTAGTATTAGTTACA 57.805 33.333 0.00 0.00 32.87 2.41
532 648 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
533 649 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
534 650 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
535 651 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
536 652 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
537 653 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
538 654 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
539 655 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
540 656 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
541 657 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
542 658 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
543 659 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
544 660 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
545 661 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
546 662 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
626 744 1.624479 ATGTCTCTGCCCTGCTCTGG 61.624 60.000 0.00 0.00 0.00 3.86
646 764 1.669115 GCTGGCGCAAGAACAGAGA 60.669 57.895 18.24 0.00 43.68 3.10
676 794 3.057548 CGGCTGCCATGCAACTGA 61.058 61.111 20.29 0.00 38.41 3.41
727 847 0.452987 CATCATTGAGTTGTGCCCGG 59.547 55.000 0.00 0.00 0.00 5.73
807 928 0.949105 AATCAACAGACGGACCGTGC 60.949 55.000 27.26 15.80 41.37 5.34
830 951 2.680577 GTATGGCCGGGTATCTAAACG 58.319 52.381 2.18 0.00 0.00 3.60
899 1020 7.116662 GTGTTCGTTCACTGGTGTATAAATACA 59.883 37.037 0.00 0.00 36.91 2.29
1029 1150 3.118445 AGGAAGAAGAGCTCAAGGTATGC 60.118 47.826 17.77 2.19 0.00 3.14
1030 1151 3.369892 GGAAGAAGAGCTCAAGGTATGCA 60.370 47.826 17.77 0.00 0.00 3.96
1033 1154 5.212532 AGAAGAGCTCAAGGTATGCATAG 57.787 43.478 17.77 0.00 0.00 2.23
1048 1169 3.790091 TGCATAGCATTCAGTCAGAGAC 58.210 45.455 0.00 0.00 31.71 3.36
1049 1170 3.450096 TGCATAGCATTCAGTCAGAGACT 59.550 43.478 0.00 0.00 37.17 3.24
1050 1171 4.050553 GCATAGCATTCAGTCAGAGACTC 58.949 47.826 0.00 0.00 41.37 3.36
1051 1172 4.441217 GCATAGCATTCAGTCAGAGACTCA 60.441 45.833 5.02 0.00 41.37 3.41
1052 1173 3.872511 AGCATTCAGTCAGAGACTCAG 57.127 47.619 5.02 0.00 41.37 3.35
1053 1174 3.429492 AGCATTCAGTCAGAGACTCAGA 58.571 45.455 5.02 0.00 41.37 3.27
1054 1175 3.444742 AGCATTCAGTCAGAGACTCAGAG 59.555 47.826 5.02 0.00 41.37 3.35
1055 1176 3.772932 CATTCAGTCAGAGACTCAGAGC 58.227 50.000 5.02 0.00 41.37 4.09
1056 1177 2.877097 TCAGTCAGAGACTCAGAGCT 57.123 50.000 5.02 0.00 41.37 4.09
1057 1178 2.710377 TCAGTCAGAGACTCAGAGCTC 58.290 52.381 5.27 5.27 41.37 4.09
1058 1179 2.039613 TCAGTCAGAGACTCAGAGCTCA 59.960 50.000 17.77 0.00 41.37 4.26
1059 1180 2.421073 CAGTCAGAGACTCAGAGCTCAG 59.579 54.545 17.77 8.39 41.37 3.35
1060 1181 2.040278 AGTCAGAGACTCAGAGCTCAGT 59.960 50.000 17.77 11.69 38.71 3.41
1061 1182 2.819608 GTCAGAGACTCAGAGCTCAGTT 59.180 50.000 17.77 0.00 33.62 3.16
1062 1183 2.819019 TCAGAGACTCAGAGCTCAGTTG 59.181 50.000 17.77 5.75 33.62 3.16
1063 1184 2.557924 CAGAGACTCAGAGCTCAGTTGT 59.442 50.000 17.77 11.39 33.62 3.32
1064 1185 2.819608 AGAGACTCAGAGCTCAGTTGTC 59.180 50.000 17.77 18.58 33.62 3.18
1065 1186 1.892474 AGACTCAGAGCTCAGTTGTCC 59.108 52.381 17.77 0.00 0.00 4.02
1066 1187 0.600557 ACTCAGAGCTCAGTTGTCCG 59.399 55.000 17.77 2.23 0.00 4.79
1067 1188 0.600557 CTCAGAGCTCAGTTGTCCGT 59.399 55.000 17.77 0.00 0.00 4.69
1068 1189 1.000283 CTCAGAGCTCAGTTGTCCGTT 60.000 52.381 17.77 0.00 0.00 4.44
1069 1190 1.143305 CAGAGCTCAGTTGTCCGTTG 58.857 55.000 17.77 0.00 0.00 4.10
1070 1191 1.040646 AGAGCTCAGTTGTCCGTTGA 58.959 50.000 17.77 0.00 0.00 3.18
1071 1192 1.620819 AGAGCTCAGTTGTCCGTTGAT 59.379 47.619 17.77 0.00 0.00 2.57
1072 1193 1.728971 GAGCTCAGTTGTCCGTTGATG 59.271 52.381 9.40 0.00 0.00 3.07
1073 1194 1.070758 AGCTCAGTTGTCCGTTGATGT 59.929 47.619 0.00 0.00 0.00 3.06
1077 1198 2.102420 TCAGTTGTCCGTTGATGTGTCT 59.898 45.455 0.00 0.00 0.00 3.41
1087 1208 1.825090 TGATGTGTCTTCCATGGTGC 58.175 50.000 12.58 1.30 0.00 5.01
1091 1212 1.142667 TGTGTCTTCCATGGTGCTTGA 59.857 47.619 12.58 1.47 0.00 3.02
1093 1214 2.821969 GTGTCTTCCATGGTGCTTGATT 59.178 45.455 12.58 0.00 0.00 2.57
1094 1215 2.821378 TGTCTTCCATGGTGCTTGATTG 59.179 45.455 12.58 0.00 0.00 2.67
1095 1216 2.821969 GTCTTCCATGGTGCTTGATTGT 59.178 45.455 12.58 0.00 0.00 2.71
1096 1217 2.821378 TCTTCCATGGTGCTTGATTGTG 59.179 45.455 12.58 0.00 0.00 3.33
1097 1218 1.548081 TCCATGGTGCTTGATTGTGG 58.452 50.000 12.58 0.00 0.00 4.17
1100 1221 2.159156 CCATGGTGCTTGATTGTGGATG 60.159 50.000 2.57 0.00 0.00 3.51
1101 1222 1.548081 TGGTGCTTGATTGTGGATGG 58.452 50.000 0.00 0.00 0.00 3.51
1102 1223 0.819582 GGTGCTTGATTGTGGATGGG 59.180 55.000 0.00 0.00 0.00 4.00
1103 1224 0.174162 GTGCTTGATTGTGGATGGGC 59.826 55.000 0.00 0.00 0.00 5.36
1373 1499 3.191539 CAGAAGAAGCGCGAGGGC 61.192 66.667 12.10 3.83 0.00 5.19
1470 1596 2.047274 AGGACGGCATGGACAACG 60.047 61.111 0.00 0.00 0.00 4.10
1631 1799 1.541588 GCCTTCAAACAAGAAGCCGAT 59.458 47.619 0.00 0.00 42.84 4.18
1860 2028 2.202987 CGTGGCAGCCTCCTCATC 60.203 66.667 14.15 0.00 0.00 2.92
1861 2029 2.993008 GTGGCAGCCTCCTCATCA 59.007 61.111 14.15 0.00 0.00 3.07
1862 2030 1.153208 GTGGCAGCCTCCTCATCAG 60.153 63.158 14.15 0.00 0.00 2.90
1987 2158 3.088941 GCCACGTCCCATGGATCGA 62.089 63.158 26.51 9.80 39.87 3.59
2010 2181 3.192633 GGACAACGCTAATCCACCATTTT 59.807 43.478 0.00 0.00 32.35 1.82
2029 2200 4.750833 TTTTTCCCTTCTCCCACCATTA 57.249 40.909 0.00 0.00 0.00 1.90
2087 2258 8.134895 TCGCCATGAATTATTCAGTTTATTTCC 58.865 33.333 13.29 0.00 43.98 3.13
2159 2330 1.737196 CTCGCGACGCAACATCTCAG 61.737 60.000 21.35 0.00 0.00 3.35
2173 2344 7.010830 CGCAACATCTCAGAGAAATTTATCAGA 59.989 37.037 14.83 11.04 0.00 3.27
2180 2351 5.582269 TCAGAGAAATTTATCAGACCGCAAG 59.418 40.000 14.83 0.00 0.00 4.01
2181 2352 5.582269 CAGAGAAATTTATCAGACCGCAAGA 59.418 40.000 14.83 0.00 43.02 3.02
2182 2353 5.814705 AGAGAAATTTATCAGACCGCAAGAG 59.185 40.000 14.83 0.00 43.02 2.85
2183 2354 5.491982 AGAAATTTATCAGACCGCAAGAGT 58.508 37.500 0.00 0.00 43.02 3.24
2184 2355 5.940470 AGAAATTTATCAGACCGCAAGAGTT 59.060 36.000 0.00 0.00 43.02 3.01
2185 2356 7.103641 AGAAATTTATCAGACCGCAAGAGTTA 58.896 34.615 0.00 0.00 43.02 2.24
2186 2357 6.910536 AATTTATCAGACCGCAAGAGTTAG 57.089 37.500 0.00 0.00 43.02 2.34
2187 2358 5.401531 TTTATCAGACCGCAAGAGTTAGT 57.598 39.130 0.00 0.00 43.02 2.24
2188 2359 2.724977 TCAGACCGCAAGAGTTAGTG 57.275 50.000 0.00 0.00 43.02 2.74
2189 2360 1.071605 CAGACCGCAAGAGTTAGTGC 58.928 55.000 0.00 0.00 43.02 4.40
2190 2361 0.969894 AGACCGCAAGAGTTAGTGCT 59.030 50.000 0.00 0.00 38.66 4.40
2191 2362 1.344763 AGACCGCAAGAGTTAGTGCTT 59.655 47.619 0.00 0.00 38.66 3.91
2192 2363 1.727335 GACCGCAAGAGTTAGTGCTTC 59.273 52.381 0.00 0.00 38.66 3.86
2193 2364 1.344763 ACCGCAAGAGTTAGTGCTTCT 59.655 47.619 0.00 0.00 38.66 2.85
2194 2365 1.996191 CCGCAAGAGTTAGTGCTTCTC 59.004 52.381 0.00 0.00 38.66 2.87
2195 2366 1.996191 CGCAAGAGTTAGTGCTTCTCC 59.004 52.381 0.00 0.00 38.66 3.71
2196 2367 2.610479 CGCAAGAGTTAGTGCTTCTCCA 60.610 50.000 0.00 0.00 38.66 3.86
2197 2368 3.403038 GCAAGAGTTAGTGCTTCTCCAA 58.597 45.455 0.00 0.00 37.78 3.53
2198 2369 4.006319 GCAAGAGTTAGTGCTTCTCCAAT 58.994 43.478 0.00 0.00 37.78 3.16
2199 2370 4.094146 GCAAGAGTTAGTGCTTCTCCAATC 59.906 45.833 0.00 0.00 37.78 2.67
2200 2371 5.240891 CAAGAGTTAGTGCTTCTCCAATCA 58.759 41.667 0.00 0.00 0.00 2.57
2201 2372 4.826556 AGAGTTAGTGCTTCTCCAATCAC 58.173 43.478 0.00 0.00 0.00 3.06
2202 2373 4.284490 AGAGTTAGTGCTTCTCCAATCACA 59.716 41.667 0.00 0.00 32.03 3.58
2203 2374 4.319177 AGTTAGTGCTTCTCCAATCACAC 58.681 43.478 0.00 0.00 32.03 3.82
2262 2435 1.005037 GTCCACAGACACGGATGCA 60.005 57.895 0.00 0.00 42.99 3.96
2271 2444 1.267574 ACACGGATGCAGGAGGATGT 61.268 55.000 0.00 0.00 0.00 3.06
2293 2466 4.508124 GTCATCCAATCGTAGTCACATTCC 59.492 45.833 0.00 0.00 0.00 3.01
2294 2467 4.161377 TCATCCAATCGTAGTCACATTCCA 59.839 41.667 0.00 0.00 0.00 3.53
2296 2469 5.097742 TCCAATCGTAGTCACATTCCATT 57.902 39.130 0.00 0.00 0.00 3.16
2298 2471 4.875536 CCAATCGTAGTCACATTCCATTCA 59.124 41.667 0.00 0.00 0.00 2.57
2301 2474 2.603110 CGTAGTCACATTCCATTCACCG 59.397 50.000 0.00 0.00 0.00 4.94
2303 2476 1.351017 AGTCACATTCCATTCACCGGT 59.649 47.619 0.00 0.00 0.00 5.28
2308 2481 4.638421 TCACATTCCATTCACCGGTAAATC 59.362 41.667 6.87 0.00 0.00 2.17
2309 2482 4.640201 CACATTCCATTCACCGGTAAATCT 59.360 41.667 6.87 0.00 0.00 2.40
2339 2528 3.737032 TCTACGTTGATCCACACAACA 57.263 42.857 0.00 0.00 45.09 3.33
2366 2555 3.118112 GGATCACATCCCTGATCACAACT 60.118 47.826 10.52 0.00 45.89 3.16
2426 2619 6.824305 AACCCAAAAGAACATCAGTCTATG 57.176 37.500 0.00 0.00 0.00 2.23
2427 2620 4.702131 ACCCAAAAGAACATCAGTCTATGC 59.298 41.667 0.00 0.00 0.00 3.14
2472 2678 1.745087 GCAAGATGCTTCCGGATCAAA 59.255 47.619 4.15 0.00 40.13 2.69
2562 2808 1.542472 TCGCCGCCGATGATATTTCTA 59.458 47.619 0.00 0.00 38.82 2.10
2588 2834 0.108804 CAACATCTGGTAGCGGACGT 60.109 55.000 5.39 0.06 0.00 4.34
2607 2853 6.586463 CGGACGTATTGCATGATAATTCTAGT 59.414 38.462 0.00 0.00 0.00 2.57
2643 2889 5.411781 AGAGTCGATATTCAAGGTCAACAC 58.588 41.667 0.00 0.00 0.00 3.32
2680 2930 1.450312 GGCGGTCATCTTCACCCTG 60.450 63.158 0.00 0.00 0.00 4.45
2695 2945 1.667830 CCTGTTTTCCTCGAGCGCA 60.668 57.895 11.47 0.00 0.00 6.09
2710 2981 1.004560 CGCAGCCTTGTTCTCCTCA 60.005 57.895 0.00 0.00 0.00 3.86
2786 3061 0.371301 CGTCGCATCCATCAACTGTG 59.629 55.000 0.00 0.00 0.00 3.66
2805 3081 1.535444 TGAACCTCTCCGCCTTCCA 60.535 57.895 0.00 0.00 0.00 3.53
2853 3129 1.406069 GCATGCCTCTTCCTTCTTCGA 60.406 52.381 6.36 0.00 0.00 3.71
2866 3142 3.699038 CCTTCTTCGACAAGATCTCCTCT 59.301 47.826 0.00 0.00 38.50 3.69
2977 3254 1.149627 CGGTTCTTGGGTTGGGTCA 59.850 57.895 0.00 0.00 0.00 4.02
3007 3284 1.821136 CTGGTTTCTTCCTCATTGGCC 59.179 52.381 0.00 0.00 35.26 5.36
3086 3363 4.068599 TCAACAATGCATAACGGTGAAGA 58.931 39.130 0.00 0.00 0.00 2.87
3130 3410 0.317160 CCACACAAGCACGAGTAGGA 59.683 55.000 0.00 0.00 0.00 2.94
3135 3415 3.119459 ACACAAGCACGAGTAGGATACAG 60.119 47.826 0.00 0.00 46.26 2.74
3144 3426 6.565234 CACGAGTAGGATACAGAAGTGAAAT 58.435 40.000 0.00 0.00 46.26 2.17
3212 3494 6.183360 GCTAGTGATCAACAAAACTAGAGCAG 60.183 42.308 16.11 0.00 43.08 4.24
3238 3520 6.931838 TCCGACTAGTGATCAACAAAACTAT 58.068 36.000 0.00 0.00 0.00 2.12
3260 3542 4.775058 AGCATATCCGACTAGTGATCAC 57.225 45.455 18.47 18.47 0.00 3.06
3274 3556 4.573900 AGTGATCACCAAAACTAGAGCAG 58.426 43.478 22.21 0.00 0.00 4.24
3278 3560 5.188555 TGATCACCAAAACTAGAGCAGATCT 59.811 40.000 0.00 0.00 42.47 2.75
3280 3562 4.528206 TCACCAAAACTAGAGCAGATCTGA 59.472 41.667 27.04 4.19 39.20 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 7.849804 ACATTATACCGATAAATCTGATGGC 57.150 36.000 0.00 0.00 31.28 4.40
120 121 5.290158 CATCCATTTGATACAGCTTTTGCAC 59.710 40.000 0.00 0.00 39.10 4.57
184 185 5.263599 TGAATTGCCTGTCATACATCCTTT 58.736 37.500 0.00 0.00 0.00 3.11
202 203 2.519771 TTGATCAGGCTGGCTGAATT 57.480 45.000 33.27 20.67 34.26 2.17
286 402 3.091545 ACTTGCTGGGACATGGTTTATG 58.908 45.455 0.00 0.00 42.68 1.90
414 530 1.229131 TGGGACGGAGGGAGTACTAT 58.771 55.000 0.00 0.00 0.00 2.12
422 538 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
423 539 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
424 540 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
425 541 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
426 542 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
427 543 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
428 544 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
429 545 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
430 546 7.814587 GGACAAATCTAAGACAAGAATTTTGGG 59.185 37.037 0.00 0.00 33.04 4.12
431 547 8.359642 TGGACAAATCTAAGACAAGAATTTTGG 58.640 33.333 0.00 0.00 33.04 3.28
432 548 9.748708 TTGGACAAATCTAAGACAAGAATTTTG 57.251 29.630 0.00 0.00 34.13 2.44
433 549 9.971922 CTTGGACAAATCTAAGACAAGAATTTT 57.028 29.630 0.00 0.00 44.19 1.82
434 550 9.136323 ACTTGGACAAATCTAAGACAAGAATTT 57.864 29.630 7.33 0.00 44.19 1.82
435 551 8.697507 ACTTGGACAAATCTAAGACAAGAATT 57.302 30.769 7.33 0.00 44.19 2.17
436 552 9.220767 GTACTTGGACAAATCTAAGACAAGAAT 57.779 33.333 7.33 0.00 44.19 2.40
437 553 7.384115 CGTACTTGGACAAATCTAAGACAAGAA 59.616 37.037 7.33 0.00 44.19 2.52
438 554 6.866770 CGTACTTGGACAAATCTAAGACAAGA 59.133 38.462 7.33 0.00 44.19 3.02
439 555 6.090898 CCGTACTTGGACAAATCTAAGACAAG 59.909 42.308 7.33 0.00 44.19 3.16
440 556 5.929992 CCGTACTTGGACAAATCTAAGACAA 59.070 40.000 7.33 0.00 44.19 3.18
441 557 5.244402 TCCGTACTTGGACAAATCTAAGACA 59.756 40.000 7.33 0.00 44.19 3.41
442 558 5.717119 TCCGTACTTGGACAAATCTAAGAC 58.283 41.667 7.33 1.75 44.19 3.01
443 559 5.988310 TCCGTACTTGGACAAATCTAAGA 57.012 39.130 7.33 0.00 44.19 2.10
444 560 6.106673 ACATCCGTACTTGGACAAATCTAAG 58.893 40.000 0.00 0.00 46.22 2.18
445 561 6.045072 ACATCCGTACTTGGACAAATCTAA 57.955 37.500 0.00 0.00 41.85 2.10
446 562 5.670792 ACATCCGTACTTGGACAAATCTA 57.329 39.130 0.00 0.00 41.85 1.98
447 563 4.553330 ACATCCGTACTTGGACAAATCT 57.447 40.909 0.00 0.00 41.85 2.40
448 564 4.569564 GGTACATCCGTACTTGGACAAATC 59.430 45.833 0.00 0.00 46.15 2.17
449 565 4.020039 TGGTACATCCGTACTTGGACAAAT 60.020 41.667 0.00 0.00 46.15 2.32
450 566 3.324268 TGGTACATCCGTACTTGGACAAA 59.676 43.478 0.00 0.00 46.15 2.83
451 567 2.898612 TGGTACATCCGTACTTGGACAA 59.101 45.455 0.00 0.00 46.15 3.18
452 568 2.527497 TGGTACATCCGTACTTGGACA 58.473 47.619 0.00 0.00 46.15 4.02
453 569 3.056322 ACTTGGTACATCCGTACTTGGAC 60.056 47.826 0.00 0.00 46.15 4.02
454 570 3.167485 ACTTGGTACATCCGTACTTGGA 58.833 45.455 0.00 0.00 46.15 3.53
455 571 3.056393 TGACTTGGTACATCCGTACTTGG 60.056 47.826 0.00 0.00 46.15 3.61
456 572 3.924686 GTGACTTGGTACATCCGTACTTG 59.075 47.826 0.00 0.00 46.15 3.16
457 573 3.366679 CGTGACTTGGTACATCCGTACTT 60.367 47.826 0.00 0.00 46.15 2.24
458 574 2.163010 CGTGACTTGGTACATCCGTACT 59.837 50.000 0.00 0.00 46.15 2.73
459 575 2.095059 ACGTGACTTGGTACATCCGTAC 60.095 50.000 0.00 0.00 46.18 3.67
460 576 2.161855 ACGTGACTTGGTACATCCGTA 58.838 47.619 0.00 0.00 39.30 4.02
461 577 0.963962 ACGTGACTTGGTACATCCGT 59.036 50.000 0.00 0.00 39.30 4.69
462 578 2.074547 AACGTGACTTGGTACATCCG 57.925 50.000 0.00 0.00 39.30 4.18
463 579 4.992951 ACTAAAACGTGACTTGGTACATCC 59.007 41.667 0.00 0.00 39.30 3.51
464 580 7.823149 ATACTAAAACGTGACTTGGTACATC 57.177 36.000 0.00 0.00 39.30 3.06
465 581 9.362539 CTAATACTAAAACGTGACTTGGTACAT 57.637 33.333 0.00 0.00 39.30 2.29
466 582 8.359642 ACTAATACTAAAACGTGACTTGGTACA 58.640 33.333 0.00 0.00 0.00 2.90
467 583 8.748380 ACTAATACTAAAACGTGACTTGGTAC 57.252 34.615 0.00 0.00 0.00 3.34
469 585 9.196552 GTAACTAATACTAAAACGTGACTTGGT 57.803 33.333 0.00 0.00 0.00 3.67
470 586 9.195411 TGTAACTAATACTAAAACGTGACTTGG 57.805 33.333 0.00 0.00 35.42 3.61
506 622 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
507 623 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
508 624 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
509 625 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
510 626 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
511 627 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
512 628 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
513 629 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
514 630 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
515 631 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
516 632 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
517 633 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
518 634 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
519 635 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
520 636 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
521 637 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
522 638 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
523 639 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
524 640 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
525 641 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
526 642 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
527 643 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
528 644 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
529 645 0.549950 CTAGTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
530 646 0.822944 GCTAGTACTCCCTCCGTCCC 60.823 65.000 0.00 0.00 0.00 4.46
531 647 0.183252 AGCTAGTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.00 4.79
532 648 2.926778 TAGCTAGTACTCCCTCCGTC 57.073 55.000 0.00 0.00 0.00 4.79
533 649 3.201708 TCTTTAGCTAGTACTCCCTCCGT 59.798 47.826 0.00 0.00 0.00 4.69
534 650 3.818180 TCTTTAGCTAGTACTCCCTCCG 58.182 50.000 0.00 0.00 0.00 4.63
535 651 5.010213 CACATCTTTAGCTAGTACTCCCTCC 59.990 48.000 0.00 0.00 0.00 4.30
536 652 5.010213 CCACATCTTTAGCTAGTACTCCCTC 59.990 48.000 0.00 0.00 0.00 4.30
537 653 4.896482 CCACATCTTTAGCTAGTACTCCCT 59.104 45.833 0.00 0.00 0.00 4.20
538 654 4.650131 ACCACATCTTTAGCTAGTACTCCC 59.350 45.833 0.00 0.00 0.00 4.30
539 655 5.360144 TGACCACATCTTTAGCTAGTACTCC 59.640 44.000 0.00 0.00 0.00 3.85
540 656 6.452494 TGACCACATCTTTAGCTAGTACTC 57.548 41.667 0.00 0.00 0.00 2.59
541 657 7.045126 GATGACCACATCTTTAGCTAGTACT 57.955 40.000 0.00 0.00 46.47 2.73
609 727 2.289532 ACCAGAGCAGGGCAGAGAC 61.290 63.158 0.00 0.00 0.00 3.36
646 764 1.959085 CAGCCGCTCACCATGTTTT 59.041 52.632 0.00 0.00 0.00 2.43
666 784 5.978919 ACAATTGTGTACTTTCAGTTGCATG 59.021 36.000 11.07 0.00 35.72 4.06
676 794 8.764524 TGCAGTTAAAAACAATTGTGTACTTT 57.235 26.923 12.82 11.60 36.80 2.66
694 813 6.230472 ACTCAATGATGTGTACTTGCAGTTA 58.770 36.000 0.00 0.00 31.80 2.24
711 830 1.750193 ATACCGGGCACAACTCAATG 58.250 50.000 6.32 0.00 0.00 2.82
727 847 5.599242 GCATAAGGGAGGAGAGGGTATATAC 59.401 48.000 4.14 4.14 0.00 1.47
807 928 1.250328 TAGATACCCGGCCATACGTG 58.750 55.000 2.24 0.00 0.00 4.49
830 951 3.272031 GCTCTTGCAACTGGAGCC 58.728 61.111 22.27 9.34 44.46 4.70
899 1020 3.771160 CTAGACCGTTGCCGCCCT 61.771 66.667 0.00 0.00 0.00 5.19
1029 1150 5.067544 TCTGAGTCTCTGACTGAATGCTATG 59.932 44.000 4.85 0.00 43.53 2.23
1030 1151 5.199723 TCTGAGTCTCTGACTGAATGCTAT 58.800 41.667 4.85 0.00 43.53 2.97
1033 1154 3.772932 CTCTGAGTCTCTGACTGAATGC 58.227 50.000 4.85 0.00 43.53 3.56
1041 1162 2.819019 CAACTGAGCTCTGAGTCTCTGA 59.181 50.000 25.49 8.92 33.98 3.27
1042 1163 2.557924 ACAACTGAGCTCTGAGTCTCTG 59.442 50.000 25.49 22.00 35.33 3.35
1043 1164 2.819608 GACAACTGAGCTCTGAGTCTCT 59.180 50.000 25.49 6.78 0.00 3.10
1044 1165 2.094752 GGACAACTGAGCTCTGAGTCTC 60.095 54.545 29.62 22.29 0.00 3.36
1045 1166 1.892474 GGACAACTGAGCTCTGAGTCT 59.108 52.381 29.62 13.60 0.00 3.24
1047 1168 0.600557 CGGACAACTGAGCTCTGAGT 59.399 55.000 25.49 21.17 0.00 3.41
1048 1169 0.600557 ACGGACAACTGAGCTCTGAG 59.399 55.000 25.49 18.52 0.00 3.35
1049 1170 1.040646 AACGGACAACTGAGCTCTGA 58.959 50.000 25.49 0.11 0.00 3.27
1050 1171 1.143305 CAACGGACAACTGAGCTCTG 58.857 55.000 18.15 18.15 0.00 3.35
1051 1172 1.040646 TCAACGGACAACTGAGCTCT 58.959 50.000 16.19 0.00 0.00 4.09
1052 1173 1.728971 CATCAACGGACAACTGAGCTC 59.271 52.381 6.82 6.82 0.00 4.09
1053 1174 1.070758 ACATCAACGGACAACTGAGCT 59.929 47.619 0.00 0.00 0.00 4.09
1054 1175 1.195448 CACATCAACGGACAACTGAGC 59.805 52.381 0.00 0.00 0.00 4.26
1055 1176 2.476619 GACACATCAACGGACAACTGAG 59.523 50.000 0.00 0.00 0.00 3.35
1056 1177 2.102420 AGACACATCAACGGACAACTGA 59.898 45.455 0.00 0.00 0.00 3.41
1057 1178 2.483876 AGACACATCAACGGACAACTG 58.516 47.619 0.00 0.00 0.00 3.16
1058 1179 2.910688 AGACACATCAACGGACAACT 57.089 45.000 0.00 0.00 0.00 3.16
1059 1180 2.223377 GGAAGACACATCAACGGACAAC 59.777 50.000 0.00 0.00 0.00 3.32
1060 1181 2.158885 TGGAAGACACATCAACGGACAA 60.159 45.455 0.00 0.00 0.00 3.18
1061 1182 1.414550 TGGAAGACACATCAACGGACA 59.585 47.619 0.00 0.00 0.00 4.02
1062 1183 2.163818 TGGAAGACACATCAACGGAC 57.836 50.000 0.00 0.00 0.00 4.79
1063 1184 2.615240 CCATGGAAGACACATCAACGGA 60.615 50.000 5.56 0.00 0.00 4.69
1064 1185 1.739466 CCATGGAAGACACATCAACGG 59.261 52.381 5.56 0.00 0.00 4.44
1065 1186 2.160219 CACCATGGAAGACACATCAACG 59.840 50.000 21.47 0.00 0.00 4.10
1066 1187 2.095059 GCACCATGGAAGACACATCAAC 60.095 50.000 21.47 0.00 0.00 3.18
1067 1188 2.161855 GCACCATGGAAGACACATCAA 58.838 47.619 21.47 0.00 0.00 2.57
1068 1189 1.352017 AGCACCATGGAAGACACATCA 59.648 47.619 21.47 0.00 0.00 3.07
1069 1190 2.119801 AGCACCATGGAAGACACATC 57.880 50.000 21.47 0.00 0.00 3.06
1070 1191 2.165167 CAAGCACCATGGAAGACACAT 58.835 47.619 21.47 0.00 0.00 3.21
1071 1192 1.142667 TCAAGCACCATGGAAGACACA 59.857 47.619 21.47 0.00 0.00 3.72
1072 1193 1.896220 TCAAGCACCATGGAAGACAC 58.104 50.000 21.47 0.41 0.00 3.67
1073 1194 2.821378 CAATCAAGCACCATGGAAGACA 59.179 45.455 21.47 0.00 0.00 3.41
1077 1198 1.894466 CCACAATCAAGCACCATGGAA 59.106 47.619 21.47 0.00 0.00 3.53
1087 1208 1.205417 GGTTGCCCATCCACAATCAAG 59.795 52.381 0.00 0.00 0.00 3.02
1091 1212 0.706433 AGAGGTTGCCCATCCACAAT 59.294 50.000 0.00 0.00 0.00 2.71
1093 1214 1.133181 TCAGAGGTTGCCCATCCACA 61.133 55.000 0.00 0.00 0.00 4.17
1094 1215 0.678048 GTCAGAGGTTGCCCATCCAC 60.678 60.000 0.00 0.00 0.00 4.02
1095 1216 1.685224 GTCAGAGGTTGCCCATCCA 59.315 57.895 0.00 0.00 0.00 3.41
1096 1217 1.077429 GGTCAGAGGTTGCCCATCC 60.077 63.158 0.00 0.00 0.00 3.51
1097 1218 0.393537 CAGGTCAGAGGTTGCCCATC 60.394 60.000 0.00 0.00 0.00 3.51
1100 1221 2.069165 AACCAGGTCAGAGGTTGCCC 62.069 60.000 0.00 0.00 45.91 5.36
1101 1222 0.178990 AAACCAGGTCAGAGGTTGCC 60.179 55.000 0.00 0.00 46.92 4.52
1102 1223 1.692411 AAAACCAGGTCAGAGGTTGC 58.308 50.000 0.00 0.00 46.92 4.17
1103 1224 3.023832 ACAAAAACCAGGTCAGAGGTTG 58.976 45.455 0.00 0.00 46.92 3.77
1115 1238 1.276421 CACCACCACCAACAAAAACCA 59.724 47.619 0.00 0.00 0.00 3.67
1344 1470 3.123620 CTTCTGCTGCTCGGGCAC 61.124 66.667 5.44 4.06 44.28 5.01
1346 1472 2.046892 TTCTTCTGCTGCTCGGGC 60.047 61.111 0.00 0.00 39.26 6.13
1373 1499 2.186903 CGGTCCTTCCCACCATCG 59.813 66.667 0.00 0.00 32.89 3.84
1423 1549 3.798954 CTCTTCTCGCCCGCCATCC 62.799 68.421 0.00 0.00 0.00 3.51
1598 1766 3.055905 GAAGGCGCTCGTTTCGTCG 62.056 63.158 7.64 0.00 36.56 5.12
1606 1774 0.586319 TTCTTGTTTGAAGGCGCTCG 59.414 50.000 7.64 0.00 0.00 5.03
1682 1850 0.037605 GGTAGTAGTTGTGGTGCGCT 60.038 55.000 9.73 0.00 0.00 5.92
1903 2071 2.589720 TGTCCTCGTTGAAGTAGTCCA 58.410 47.619 0.00 0.00 0.00 4.02
1987 2158 0.981183 TGGTGGATTAGCGTTGTCCT 59.019 50.000 6.98 0.00 33.15 3.85
2010 2181 2.310647 GGTAATGGTGGGAGAAGGGAAA 59.689 50.000 0.00 0.00 0.00 3.13
2012 2183 1.082194 AGGTAATGGTGGGAGAAGGGA 59.918 52.381 0.00 0.00 0.00 4.20
2029 2200 3.007506 TGGATGTTGTACATGAACGAGGT 59.992 43.478 0.00 0.00 39.27 3.85
2087 2258 5.939883 TCAACAGTTCAACATAGGATTCCAG 59.060 40.000 5.29 0.00 0.00 3.86
2159 2330 5.582665 ACTCTTGCGGTCTGATAAATTTCTC 59.417 40.000 0.00 0.00 0.00 2.87
2173 2344 1.344763 AGAAGCACTAACTCTTGCGGT 59.655 47.619 0.00 0.00 43.87 5.68
2180 2351 4.390297 GTGTGATTGGAGAAGCACTAACTC 59.610 45.833 4.96 0.00 46.60 3.01
2181 2352 4.319177 GTGTGATTGGAGAAGCACTAACT 58.681 43.478 4.96 0.00 46.60 2.24
2182 2353 3.437049 GGTGTGATTGGAGAAGCACTAAC 59.563 47.826 4.96 0.00 46.60 2.34
2183 2354 3.559171 GGGTGTGATTGGAGAAGCACTAA 60.559 47.826 4.96 0.00 46.60 2.24
2184 2355 2.027192 GGGTGTGATTGGAGAAGCACTA 60.027 50.000 4.96 0.00 46.60 2.74
2185 2356 1.271597 GGGTGTGATTGGAGAAGCACT 60.272 52.381 4.96 0.00 46.60 4.40
2186 2357 1.168714 GGGTGTGATTGGAGAAGCAC 58.831 55.000 0.00 0.00 46.64 4.40
2187 2358 0.038166 GGGGTGTGATTGGAGAAGCA 59.962 55.000 0.00 0.00 0.00 3.91
2188 2359 1.026718 CGGGGTGTGATTGGAGAAGC 61.027 60.000 0.00 0.00 0.00 3.86
2189 2360 1.026718 GCGGGGTGTGATTGGAGAAG 61.027 60.000 0.00 0.00 0.00 2.85
2190 2361 1.002624 GCGGGGTGTGATTGGAGAA 60.003 57.895 0.00 0.00 0.00 2.87
2191 2362 1.773856 TTGCGGGGTGTGATTGGAGA 61.774 55.000 0.00 0.00 0.00 3.71
2192 2363 0.893270 TTTGCGGGGTGTGATTGGAG 60.893 55.000 0.00 0.00 0.00 3.86
2193 2364 0.468214 TTTTGCGGGGTGTGATTGGA 60.468 50.000 0.00 0.00 0.00 3.53
2194 2365 0.390860 TTTTTGCGGGGTGTGATTGG 59.609 50.000 0.00 0.00 0.00 3.16
2195 2366 3.976339 TTTTTGCGGGGTGTGATTG 57.024 47.368 0.00 0.00 0.00 2.67
2271 2444 4.161377 TGGAATGTGACTACGATTGGATGA 59.839 41.667 0.00 0.00 0.00 2.92
2279 2452 3.674955 CGGTGAATGGAATGTGACTACGA 60.675 47.826 0.00 0.00 0.00 3.43
2465 2671 1.363744 CGACAGCACCTCTTTGATCC 58.636 55.000 0.00 0.00 0.00 3.36
2550 2795 5.297547 TGTTGGAGCGGTAGAAATATCATC 58.702 41.667 0.00 0.00 0.00 2.92
2588 2834 8.141268 TGTCGACACTAGAATTATCATGCAATA 58.859 33.333 15.76 0.00 0.00 1.90
2643 2889 2.430465 CCAATGCGGAGGATATCAAGG 58.570 52.381 4.83 0.00 37.86 3.61
2668 2918 2.744202 CGAGGAAAACAGGGTGAAGATG 59.256 50.000 0.00 0.00 0.00 2.90
2680 2930 2.476499 GCTGCGCTCGAGGAAAAC 59.524 61.111 15.58 0.00 0.00 2.43
2695 2945 0.321122 CGCTTGAGGAGAACAAGGCT 60.321 55.000 0.00 0.00 43.12 4.58
2701 2972 3.491652 GCGGCGCTTGAGGAGAAC 61.492 66.667 26.86 0.00 0.00 3.01
2710 2981 4.459089 GAGAGGAAGGCGGCGCTT 62.459 66.667 32.30 23.33 0.00 4.68
2786 3061 1.079057 GGAAGGCGGAGAGGTTCAC 60.079 63.158 0.00 0.00 0.00 3.18
2805 3081 1.479709 CTCGGACATCAAGGAGGAGT 58.520 55.000 0.00 0.00 0.00 3.85
2853 3129 4.542697 GGAGAGGTTAGAGGAGATCTTGT 58.457 47.826 0.00 0.00 39.64 3.16
2866 3142 0.895530 CCAAGCTGACGGAGAGGTTA 59.104 55.000 0.00 0.00 30.10 2.85
2977 3254 2.638363 GGAAGAAACCAGTGACCCTACT 59.362 50.000 0.00 0.00 0.00 2.57
3086 3363 6.539103 GTGTACAAGAAGTTGGAGAAGAAGTT 59.461 38.462 0.00 0.00 38.07 2.66
3144 3426 6.084326 TGCTCACTAGACGAATATGCATTA 57.916 37.500 3.54 0.00 0.00 1.90
3212 3494 5.869888 AGTTTTGTTGATCACTAGTCGGATC 59.130 40.000 13.71 13.71 40.22 3.36
3238 3520 4.700692 GGTGATCACTAGTCGGATATGCTA 59.299 45.833 24.50 0.00 0.00 3.49
3260 3542 5.083533 AGTCAGATCTGCTCTAGTTTTGG 57.916 43.478 18.36 0.00 31.13 3.28


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

AutoCloner maintained by Alex Coulton.