Multiple sequence alignment - TraesCS6A01G245700

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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 TraesCS6A01G245700 chr6A 100.000 3339 0 0 1 3339 457071249 457074587 0.000000e+00 6167.0
1 TraesCS6A01G245700 chr6A 94.118 51 1 2 3289 3339 122740815 122740767 3.570000e-10 76.8
2 TraesCS6A01G245700 chr6A 100.000 28 0 0 3312 3339 199998738 199998711 6.000000e-03 52.8
3 TraesCS6A01G245700 chr6D 92.596 2215 105 22 963 3151 319244075 319246256 0.000000e+00 3127.0
4 TraesCS6A01G245700 chr6D 91.971 137 8 3 3163 3299 319246389 319246522 4.400000e-44 189.0
5 TraesCS6A01G245700 chr6D 91.304 46 4 0 3294 3339 354363152 354363197 2.780000e-06 63.9
6 TraesCS6A01G245700 chr6B 90.553 1916 87 33 1414 3295 504074425 504072570 0.000000e+00 2449.0
7 TraesCS6A01G245700 chr6B 90.154 518 30 9 7 504 504107332 504106816 0.000000e+00 654.0
8 TraesCS6A01G245700 chr6B 94.762 420 19 1 963 1382 504074837 504074421 0.000000e+00 651.0
9 TraesCS6A01G245700 chr6B 89.062 256 17 3 562 806 504075085 504074830 1.160000e-79 307.0
10 TraesCS6A01G245700 chr6B 95.349 43 2 0 3291 3333 513979142 513979184 5.980000e-08 69.4
11 TraesCS6A01G245700 chr1D 90.057 523 31 6 2 504 458392361 458391840 0.000000e+00 658.0
12 TraesCS6A01G245700 chr1D 89.655 522 33 9 1 501 75673953 75674474 0.000000e+00 645.0
13 TraesCS6A01G245700 chr1D 73.074 1311 288 41 1276 2557 18243167 18241893 4.010000e-109 405.0
14 TraesCS6A01G245700 chr1D 84.644 267 36 4 1222 1487 474877403 474877141 9.190000e-66 261.0
15 TraesCS6A01G245700 chr1D 82.022 267 37 9 1225 1487 474883657 474883398 2.020000e-52 217.0
16 TraesCS6A01G245700 chr4D 89.695 524 34 7 1 504 5249808 5249285 0.000000e+00 651.0
17 TraesCS6A01G245700 chr3B 89.122 524 37 4 1 504 692129791 692130314 4.700000e-178 634.0
18 TraesCS6A01G245700 chr3B 100.000 30 0 0 540 569 757287149 757287120 4.650000e-04 56.5
19 TraesCS6A01G245700 chr1B 88.889 522 36 10 1 502 23035967 23036486 1.020000e-174 623.0
20 TraesCS6A01G245700 chr1B 88.506 522 38 10 1 502 23057707 23058226 2.200000e-171 612.0
21 TraesCS6A01G245700 chr1B 91.935 124 10 0 810 933 22976044 22975921 1.230000e-39 174.0
22 TraesCS6A01G245700 chr1B 91.406 128 10 1 810 936 311679108 311678981 1.230000e-39 174.0
23 TraesCS6A01G245700 chr1B 87.302 63 6 2 1012 1073 134435160 134435221 1.660000e-08 71.3
24 TraesCS6A01G245700 chr5B 88.740 524 36 6 1 504 230773290 230772770 1.320000e-173 619.0
25 TraesCS6A01G245700 chr5B 86.689 293 19 8 232 504 357930569 357930277 1.160000e-79 307.0
26 TraesCS6A01G245700 chr5B 91.339 127 11 0 807 933 244611970 244612096 1.230000e-39 174.0
27 TraesCS6A01G245700 chr5B 91.339 127 11 0 807 933 670699422 670699548 1.230000e-39 174.0
28 TraesCS6A01G245700 chr5B 96.000 50 1 1 3290 3339 15661766 15661814 2.760000e-11 80.5
29 TraesCS6A01G245700 chr2D 88.359 524 41 5 1 504 651564633 651564110 2.200000e-171 612.0
30 TraesCS6A01G245700 chr2D 95.000 40 2 0 3299 3338 577751098 577751059 2.780000e-06 63.9
31 TraesCS6A01G245700 chr3D 88.212 509 56 4 1 505 565263340 565263848 3.680000e-169 604.0
32 TraesCS6A01G245700 chr3D 91.339 127 11 0 807 933 563962939 563963065 1.230000e-39 174.0
33 TraesCS6A01G245700 chr5D 87.954 523 38 10 2 504 513458273 513457756 7.980000e-166 593.0
34 TraesCS6A01G245700 chr5D 87.115 520 45 8 5 504 136941231 136940714 1.340000e-158 569.0
35 TraesCS6A01G245700 chr5D 92.742 124 9 0 810 933 36212470 36212347 2.650000e-41 180.0
36 TraesCS6A01G245700 chr5D 81.279 219 22 6 301 500 207991111 207991329 3.450000e-35 159.0
37 TraesCS6A01G245700 chr2B 86.004 493 66 3 12 501 97428081 97428573 2.950000e-145 525.0
38 TraesCS6A01G245700 chr2B 90.840 131 12 0 803 933 751321020 751321150 3.420000e-40 176.0
39 TraesCS6A01G245700 chr2B 91.935 124 10 0 810 933 58834622 58834499 1.230000e-39 174.0
40 TraesCS6A01G245700 chr1A 73.511 1310 288 37 1276 2557 20245856 20244578 3.060000e-120 442.0
41 TraesCS6A01G245700 chr1A 72.881 1357 306 41 1278 2604 20237667 20236343 8.620000e-111 411.0
42 TraesCS6A01G245700 chr1A 85.019 267 35 4 1222 1487 570388640 570388378 1.970000e-67 267.0
43 TraesCS6A01G245700 chr1A 83.700 227 34 2 1261 1487 570374464 570374241 9.390000e-51 211.0
44 TraesCS6A01G245700 chr1A 94.118 51 1 2 3289 3339 590638248 590638200 3.570000e-10 76.8
45 TraesCS6A01G245700 chr1A 93.878 49 3 0 3291 3339 319311959 319312007 1.280000e-09 75.0
46 TraesCS6A01G245700 chr1A 93.617 47 1 2 3293 3339 588758848 588758892 5.980000e-08 69.4
47 TraesCS6A01G245700 chr1A 84.127 63 8 2 1012 1073 99903720 99903781 3.600000e-05 60.2
48 TraesCS6A01G245700 chr4B 91.339 127 11 0 807 933 200795061 200794935 1.230000e-39 174.0
49 TraesCS6A01G245700 chr5A 96.154 52 0 2 3288 3339 19081069 19081020 2.130000e-12 84.2
50 TraesCS6A01G245700 chr5A 100.000 43 0 0 3297 3339 567573048 567573006 2.760000e-11 80.5
51 TraesCS6A01G245700 chrUn 90.323 62 6 0 1010 1071 9922305 9922366 7.680000e-12 82.4
52 TraesCS6A01G245700 chr7B 95.918 49 2 0 3291 3339 547734498 547734546 2.760000e-11 80.5
53 TraesCS6A01G245700 chr4A 100.000 43 0 0 3297 3339 162077725 162077683 2.760000e-11 80.5
54 TraesCS6A01G245700 chr4A 92.593 54 3 1 3287 3339 681182796 681182849 3.570000e-10 76.8
55 TraesCS6A01G245700 chr3A 94.340 53 2 1 3287 3339 665992747 665992798 2.760000e-11 80.5
56 TraesCS6A01G245700 chr7A 94.118 51 1 2 3289 3339 483967087 483967135 3.570000e-10 76.8
57 TraesCS6A01G245700 chr7A 93.878 49 3 0 3291 3339 427289665 427289713 1.280000e-09 75.0


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 TraesCS6A01G245700 chr6A 457071249 457074587 3338 False 6167.000000 6167 100.0000 1 3339 1 chr6A.!!$F1 3338
1 TraesCS6A01G245700 chr6D 319244075 319246522 2447 False 1658.000000 3127 92.2835 963 3299 2 chr6D.!!$F2 2336
2 TraesCS6A01G245700 chr6B 504072570 504075085 2515 True 1135.666667 2449 91.4590 562 3295 3 chr6B.!!$R2 2733
3 TraesCS6A01G245700 chr6B 504106816 504107332 516 True 654.000000 654 90.1540 7 504 1 chr6B.!!$R1 497
4 TraesCS6A01G245700 chr1D 458391840 458392361 521 True 658.000000 658 90.0570 2 504 1 chr1D.!!$R2 502
5 TraesCS6A01G245700 chr1D 75673953 75674474 521 False 645.000000 645 89.6550 1 501 1 chr1D.!!$F1 500
6 TraesCS6A01G245700 chr1D 18241893 18243167 1274 True 405.000000 405 73.0740 1276 2557 1 chr1D.!!$R1 1281
7 TraesCS6A01G245700 chr4D 5249285 5249808 523 True 651.000000 651 89.6950 1 504 1 chr4D.!!$R1 503
8 TraesCS6A01G245700 chr3B 692129791 692130314 523 False 634.000000 634 89.1220 1 504 1 chr3B.!!$F1 503
9 TraesCS6A01G245700 chr1B 23035967 23036486 519 False 623.000000 623 88.8890 1 502 1 chr1B.!!$F1 501
10 TraesCS6A01G245700 chr1B 23057707 23058226 519 False 612.000000 612 88.5060 1 502 1 chr1B.!!$F2 501
11 TraesCS6A01G245700 chr5B 230772770 230773290 520 True 619.000000 619 88.7400 1 504 1 chr5B.!!$R1 503
12 TraesCS6A01G245700 chr2D 651564110 651564633 523 True 612.000000 612 88.3590 1 504 1 chr2D.!!$R2 503
13 TraesCS6A01G245700 chr3D 565263340 565263848 508 False 604.000000 604 88.2120 1 505 1 chr3D.!!$F2 504
14 TraesCS6A01G245700 chr5D 513457756 513458273 517 True 593.000000 593 87.9540 2 504 1 chr5D.!!$R3 502
15 TraesCS6A01G245700 chr5D 136940714 136941231 517 True 569.000000 569 87.1150 5 504 1 chr5D.!!$R2 499
16 TraesCS6A01G245700 chr1A 20244578 20245856 1278 True 442.000000 442 73.5110 1276 2557 1 chr1A.!!$R2 1281
17 TraesCS6A01G245700 chr1A 20236343 20237667 1324 True 411.000000 411 72.8810 1278 2604 1 chr1A.!!$R1 1326

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
535 558 0.028770 TTTTCTCCAGCGCGTTGTTG 59.971 50.0 21.64 13.27 0.0 3.33 F
830 864 0.037232 GCGGCGCTAGGGATATTCTT 60.037 55.0 26.86 0.00 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2041 0.103208 CTCACGGTACTCCTCCATGC 59.897 60.0 0.0 0.0 0.00 4.06 R
2562 2671 0.834261 TGACCCATCAGACGGTTCCA 60.834 55.0 0.0 0.0 30.56 3.53 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
23 24 1.652563 GAACCCGCGAGCTTTGTTT 59.347 52.632 8.23 0.00 0.00 2.83
103 105 1.603802 CACTTGCACAATTCCGACTGT 59.396 47.619 0.00 0.00 0.00 3.55
178 180 3.958147 TCAACTAGATCAGCCGGAATACA 59.042 43.478 5.05 0.00 0.00 2.29
453 476 5.049398 TCGGCTTTTTATTAACGTGCATT 57.951 34.783 0.00 0.00 0.00 3.56
488 511 1.945580 AGGTCCTCCTCCTCTTGAAC 58.054 55.000 0.00 0.00 40.58 3.18
505 528 7.258022 TCTTGAACATCAAATTCTTCGTCAA 57.742 32.000 0.00 0.00 35.73 3.18
506 529 7.874940 TCTTGAACATCAAATTCTTCGTCAAT 58.125 30.769 0.00 0.00 35.73 2.57
507 530 8.998377 TCTTGAACATCAAATTCTTCGTCAATA 58.002 29.630 0.00 0.00 35.73 1.90
508 531 9.611284 CTTGAACATCAAATTCTTCGTCAATAA 57.389 29.630 0.00 0.00 35.73 1.40
509 532 9.958234 TTGAACATCAAATTCTTCGTCAATAAA 57.042 25.926 0.00 0.00 32.71 1.40
510 533 9.958234 TGAACATCAAATTCTTCGTCAATAAAA 57.042 25.926 0.00 0.00 0.00 1.52
513 536 8.915654 ACATCAAATTCTTCGTCAATAAAAAGC 58.084 29.630 0.00 0.00 0.00 3.51
514 537 7.867445 TCAAATTCTTCGTCAATAAAAAGCC 57.133 32.000 0.00 0.00 0.00 4.35
515 538 6.580791 TCAAATTCTTCGTCAATAAAAAGCCG 59.419 34.615 0.00 0.00 0.00 5.52
516 539 5.622770 ATTCTTCGTCAATAAAAAGCCGT 57.377 34.783 0.00 0.00 0.00 5.68
517 540 5.427036 TTCTTCGTCAATAAAAAGCCGTT 57.573 34.783 0.00 0.00 0.00 4.44
518 541 5.427036 TCTTCGTCAATAAAAAGCCGTTT 57.573 34.783 0.00 0.00 0.00 3.60
519 542 5.823353 TCTTCGTCAATAAAAAGCCGTTTT 58.177 33.333 1.75 1.75 42.24 2.43
520 543 5.910723 TCTTCGTCAATAAAAAGCCGTTTTC 59.089 36.000 0.00 0.00 40.07 2.29
521 544 5.427036 TCGTCAATAAAAAGCCGTTTTCT 57.573 34.783 0.00 0.00 40.07 2.52
522 545 5.445845 TCGTCAATAAAAAGCCGTTTTCTC 58.554 37.500 0.00 0.00 40.07 2.87
523 546 4.615541 CGTCAATAAAAAGCCGTTTTCTCC 59.384 41.667 0.00 0.00 40.07 3.71
524 547 5.525199 GTCAATAAAAAGCCGTTTTCTCCA 58.475 37.500 0.00 0.00 40.07 3.86
525 548 5.629435 GTCAATAAAAAGCCGTTTTCTCCAG 59.371 40.000 0.00 0.00 40.07 3.86
526 549 2.509052 AAAAAGCCGTTTTCTCCAGC 57.491 45.000 0.00 0.00 34.11 4.85
527 550 0.310854 AAAAGCCGTTTTCTCCAGCG 59.689 50.000 0.00 0.00 29.29 5.18
528 551 2.130073 AAAGCCGTTTTCTCCAGCGC 62.130 55.000 0.00 0.00 0.00 5.92
529 552 4.445545 GCCGTTTTCTCCAGCGCG 62.446 66.667 0.00 0.00 0.00 6.86
530 553 3.041940 CCGTTTTCTCCAGCGCGT 61.042 61.111 8.43 0.00 0.00 6.01
531 554 2.604174 CCGTTTTCTCCAGCGCGTT 61.604 57.895 8.43 0.00 0.00 4.84
532 555 1.438710 CGTTTTCTCCAGCGCGTTG 60.439 57.895 16.72 16.72 0.00 4.10
533 556 1.647084 GTTTTCTCCAGCGCGTTGT 59.353 52.632 21.64 0.00 0.00 3.32
534 557 0.028902 GTTTTCTCCAGCGCGTTGTT 59.971 50.000 21.64 0.00 0.00 2.83
535 558 0.028770 TTTTCTCCAGCGCGTTGTTG 59.971 50.000 21.64 13.27 0.00 3.33
536 559 0.812014 TTTCTCCAGCGCGTTGTTGA 60.812 50.000 21.64 15.29 0.00 3.18
537 560 1.221466 TTCTCCAGCGCGTTGTTGAG 61.221 55.000 21.64 19.82 0.00 3.02
538 561 1.664649 CTCCAGCGCGTTGTTGAGA 60.665 57.895 21.64 10.46 0.00 3.27
539 562 1.005037 TCCAGCGCGTTGTTGAGAT 60.005 52.632 21.64 0.00 0.00 2.75
540 563 0.602638 TCCAGCGCGTTGTTGAGATT 60.603 50.000 21.64 0.00 0.00 2.40
541 564 0.453282 CCAGCGCGTTGTTGAGATTG 60.453 55.000 21.64 0.00 0.00 2.67
542 565 1.061799 CAGCGCGTTGTTGAGATTGC 61.062 55.000 15.40 0.00 0.00 3.56
543 566 4.026156 CGCGTTGTTGAGATTGCG 57.974 55.556 0.00 0.00 39.57 4.85
544 567 2.139811 CGCGTTGTTGAGATTGCGC 61.140 57.895 0.00 0.00 39.06 6.09
545 568 2.139811 GCGTTGTTGAGATTGCGCG 61.140 57.895 0.00 0.00 35.71 6.86
546 569 1.204062 CGTTGTTGAGATTGCGCGT 59.796 52.632 8.43 0.00 0.00 6.01
547 570 0.785708 CGTTGTTGAGATTGCGCGTC 60.786 55.000 8.43 3.30 0.00 5.19
548 571 0.512952 GTTGTTGAGATTGCGCGTCT 59.487 50.000 14.10 14.10 0.00 4.18
549 572 0.512518 TTGTTGAGATTGCGCGTCTG 59.487 50.000 18.35 0.00 0.00 3.51
550 573 0.599991 TGTTGAGATTGCGCGTCTGT 60.600 50.000 18.35 0.00 0.00 3.41
551 574 0.512952 GTTGAGATTGCGCGTCTGTT 59.487 50.000 18.35 0.00 0.00 3.16
552 575 0.512518 TTGAGATTGCGCGTCTGTTG 59.487 50.000 18.35 0.00 0.00 3.33
553 576 0.319469 TGAGATTGCGCGTCTGTTGA 60.319 50.000 18.35 0.00 0.00 3.18
554 577 0.790207 GAGATTGCGCGTCTGTTGAA 59.210 50.000 18.35 0.00 0.00 2.69
555 578 0.792640 AGATTGCGCGTCTGTTGAAG 59.207 50.000 13.53 0.00 0.00 3.02
556 579 0.790207 GATTGCGCGTCTGTTGAAGA 59.210 50.000 8.43 0.00 0.00 2.87
557 580 1.394917 GATTGCGCGTCTGTTGAAGAT 59.605 47.619 8.43 0.00 37.23 2.40
558 581 0.512518 TTGCGCGTCTGTTGAAGATG 59.487 50.000 8.43 0.00 43.79 2.90
594 617 2.496470 ACCACGGACCAGAATTCTCTAC 59.504 50.000 4.57 0.00 0.00 2.59
595 618 2.159085 CCACGGACCAGAATTCTCTACC 60.159 54.545 4.57 7.97 0.00 3.18
639 670 1.640670 ACTGACATATGGGCCAGGTTT 59.359 47.619 13.78 0.00 0.00 3.27
651 682 0.039618 CCAGGTTTAGGCCCACATGT 59.960 55.000 0.00 0.00 0.00 3.21
670 701 1.964373 CAGTGGCCCAACGGTACAC 60.964 63.158 0.00 0.00 38.61 2.90
674 705 2.111460 GCCCAACGGTACACACCA 59.889 61.111 0.00 0.00 46.14 4.17
690 721 1.066303 CACCATACGTCAGAGGAGCTC 59.934 57.143 4.71 4.71 0.00 4.09
702 733 2.596411 AGGAGCTCCTTCCCCTTATT 57.404 50.000 30.40 3.41 46.09 1.40
718 749 4.445735 CCCTTATTACGGGGTCACATTCAT 60.446 45.833 0.00 0.00 38.08 2.57
736 767 0.744414 ATGCAAACGATACAGCCGCT 60.744 50.000 0.00 0.00 0.00 5.52
803 837 4.194720 GACGGCTGTCGATCGGCT 62.195 66.667 21.85 0.00 46.74 5.52
804 838 4.194720 ACGGCTGTCGATCGGCTC 62.195 66.667 21.85 12.26 46.74 4.70
805 839 4.193334 CGGCTGTCGATCGGCTCA 62.193 66.667 21.85 13.63 46.74 4.26
806 840 2.583593 GGCTGTCGATCGGCTCAC 60.584 66.667 21.85 9.49 46.74 3.51
807 841 2.181777 GCTGTCGATCGGCTCACA 59.818 61.111 21.85 13.74 44.39 3.58
808 842 1.446099 GCTGTCGATCGGCTCACAA 60.446 57.895 21.85 0.00 44.39 3.33
809 843 1.416813 GCTGTCGATCGGCTCACAAG 61.417 60.000 21.85 10.42 44.39 3.16
810 844 0.803768 CTGTCGATCGGCTCACAAGG 60.804 60.000 21.85 0.73 0.00 3.61
811 845 1.519455 GTCGATCGGCTCACAAGGG 60.519 63.158 13.54 0.00 0.00 3.95
812 846 2.892425 CGATCGGCTCACAAGGGC 60.892 66.667 7.38 0.00 0.00 5.19
819 853 4.451150 CTCACAAGGGCGGCGCTA 62.451 66.667 32.30 3.49 0.00 4.26
820 854 4.451150 TCACAAGGGCGGCGCTAG 62.451 66.667 32.30 19.97 0.00 3.42
825 859 4.615795 AGGGCGGCGCTAGGGATA 62.616 66.667 32.30 0.00 0.00 2.59
826 860 3.391382 GGGCGGCGCTAGGGATAT 61.391 66.667 32.30 0.00 0.00 1.63
827 861 2.663196 GGCGGCGCTAGGGATATT 59.337 61.111 32.30 0.00 0.00 1.28
828 862 1.448013 GGCGGCGCTAGGGATATTC 60.448 63.158 32.30 6.78 0.00 1.75
829 863 1.592223 GCGGCGCTAGGGATATTCT 59.408 57.895 26.86 0.00 0.00 2.40
830 864 0.037232 GCGGCGCTAGGGATATTCTT 60.037 55.000 26.86 0.00 0.00 2.52
831 865 1.714794 CGGCGCTAGGGATATTCTTG 58.285 55.000 11.61 0.00 0.00 3.02
832 866 1.673033 CGGCGCTAGGGATATTCTTGG 60.673 57.143 11.61 0.00 0.00 3.61
833 867 1.623811 GGCGCTAGGGATATTCTTGGA 59.376 52.381 11.61 0.00 0.00 3.53
834 868 2.237392 GGCGCTAGGGATATTCTTGGAT 59.763 50.000 11.61 0.00 0.00 3.41
835 869 3.307762 GGCGCTAGGGATATTCTTGGATT 60.308 47.826 11.61 0.00 0.00 3.01
836 870 4.327680 GCGCTAGGGATATTCTTGGATTT 58.672 43.478 11.61 0.00 0.00 2.17
837 871 4.762251 GCGCTAGGGATATTCTTGGATTTT 59.238 41.667 11.61 0.00 0.00 1.82
838 872 5.106515 GCGCTAGGGATATTCTTGGATTTTC 60.107 44.000 11.61 0.00 0.00 2.29
839 873 5.997746 CGCTAGGGATATTCTTGGATTTTCA 59.002 40.000 0.00 0.00 0.00 2.69
840 874 6.656693 CGCTAGGGATATTCTTGGATTTTCAT 59.343 38.462 0.00 0.00 0.00 2.57
841 875 7.361542 CGCTAGGGATATTCTTGGATTTTCATG 60.362 40.741 0.00 0.00 0.00 3.07
842 876 7.449704 GCTAGGGATATTCTTGGATTTTCATGT 59.550 37.037 0.00 0.00 0.00 3.21
843 877 7.592885 AGGGATATTCTTGGATTTTCATGTG 57.407 36.000 0.00 0.00 0.00 3.21
844 878 7.356680 AGGGATATTCTTGGATTTTCATGTGA 58.643 34.615 0.00 0.00 0.00 3.58
845 879 7.840716 AGGGATATTCTTGGATTTTCATGTGAA 59.159 33.333 0.00 0.00 0.00 3.18
846 880 8.645110 GGGATATTCTTGGATTTTCATGTGAAT 58.355 33.333 0.00 0.00 33.54 2.57
872 906 8.770438 ACACATGATTTTTACAAAACAGTGTT 57.230 26.923 1.64 1.64 35.72 3.32
873 907 8.655092 ACACATGATTTTTACAAAACAGTGTTG 58.345 29.630 9.79 1.46 35.72 3.33
874 908 8.867935 CACATGATTTTTACAAAACAGTGTTGA 58.132 29.630 9.79 0.00 29.06 3.18
875 909 9.598517 ACATGATTTTTACAAAACAGTGTTGAT 57.401 25.926 9.79 0.00 29.06 2.57
889 923 9.651913 AAACAGTGTTGATTTTGATAAAACAGT 57.348 25.926 9.79 0.00 32.37 3.55
890 924 8.633075 ACAGTGTTGATTTTGATAAAACAGTG 57.367 30.769 16.20 16.20 38.12 3.66
891 925 8.465999 ACAGTGTTGATTTTGATAAAACAGTGA 58.534 29.630 21.91 0.00 36.21 3.41
892 926 8.745837 CAGTGTTGATTTTGATAAAACAGTGAC 58.254 33.333 13.72 0.00 36.21 3.67
893 927 8.465999 AGTGTTGATTTTGATAAAACAGTGACA 58.534 29.630 0.00 0.00 32.37 3.58
894 928 9.081997 GTGTTGATTTTGATAAAACAGTGACAA 57.918 29.630 0.00 0.00 32.37 3.18
895 929 9.814899 TGTTGATTTTGATAAAACAGTGACAAT 57.185 25.926 0.00 0.00 32.37 2.71
934 968 9.382275 ACAATGATTTTAGCAAAATGAATACCC 57.618 29.630 10.33 0.00 40.97 3.69
935 969 9.603921 CAATGATTTTAGCAAAATGAATACCCT 57.396 29.630 10.33 0.00 40.97 4.34
936 970 9.603921 AATGATTTTAGCAAAATGAATACCCTG 57.396 29.630 10.33 0.00 40.97 4.45
937 971 8.133024 TGATTTTAGCAAAATGAATACCCTGT 57.867 30.769 10.33 0.00 40.97 4.00
938 972 8.592809 TGATTTTAGCAAAATGAATACCCTGTT 58.407 29.630 10.33 0.00 40.97 3.16
939 973 8.776376 ATTTTAGCAAAATGAATACCCTGTTG 57.224 30.769 6.19 0.00 39.50 3.33
940 974 4.192429 AGCAAAATGAATACCCTGTTGC 57.808 40.909 0.00 0.00 40.05 4.17
941 975 3.577848 AGCAAAATGAATACCCTGTTGCA 59.422 39.130 8.05 0.00 41.73 4.08
942 976 4.040217 AGCAAAATGAATACCCTGTTGCAA 59.960 37.500 0.00 0.00 41.73 4.08
943 977 4.754114 GCAAAATGAATACCCTGTTGCAAA 59.246 37.500 0.00 0.00 39.65 3.68
944 978 5.412286 GCAAAATGAATACCCTGTTGCAAAT 59.588 36.000 0.00 0.00 39.65 2.32
945 979 6.072563 GCAAAATGAATACCCTGTTGCAAATT 60.073 34.615 0.00 0.00 39.65 1.82
946 980 7.521910 GCAAAATGAATACCCTGTTGCAAATTT 60.522 33.333 0.00 0.00 39.65 1.82
947 981 7.671495 AAATGAATACCCTGTTGCAAATTTC 57.329 32.000 0.00 0.00 0.00 2.17
948 982 6.610075 ATGAATACCCTGTTGCAAATTTCT 57.390 33.333 0.00 0.00 0.00 2.52
949 983 5.782047 TGAATACCCTGTTGCAAATTTCTG 58.218 37.500 0.00 0.00 0.00 3.02
950 984 4.806640 ATACCCTGTTGCAAATTTCTGG 57.193 40.909 0.00 2.03 0.00 3.86
951 985 2.676748 ACCCTGTTGCAAATTTCTGGA 58.323 42.857 0.00 0.00 0.00 3.86
952 986 2.629617 ACCCTGTTGCAAATTTCTGGAG 59.370 45.455 0.00 0.00 0.00 3.86
953 987 2.611224 CCCTGTTGCAAATTTCTGGAGC 60.611 50.000 0.00 0.00 0.00 4.70
954 988 2.611224 CCTGTTGCAAATTTCTGGAGCC 60.611 50.000 0.00 0.00 0.00 4.70
955 989 1.000385 TGTTGCAAATTTCTGGAGCCG 60.000 47.619 0.00 0.00 0.00 5.52
956 990 0.038343 TTGCAAATTTCTGGAGCCGC 60.038 50.000 0.00 0.00 0.00 6.53
957 991 1.153765 GCAAATTTCTGGAGCCGCC 60.154 57.895 0.00 0.00 37.10 6.13
958 992 1.137404 CAAATTTCTGGAGCCGCCG 59.863 57.895 0.00 0.00 40.66 6.46
959 993 2.700773 AAATTTCTGGAGCCGCCGC 61.701 57.895 0.00 0.00 40.66 6.53
1009 1043 3.300857 CCTTAGTATGCGATGACGTCAG 58.699 50.000 24.41 12.34 41.98 3.51
1120 1160 4.489771 CGCCGCCATTCCCCTTCT 62.490 66.667 0.00 0.00 0.00 2.85
1158 1198 1.840635 GTATGTGCCCCTCCTCTTTCT 59.159 52.381 0.00 0.00 0.00 2.52
1159 1199 1.376649 ATGTGCCCCTCCTCTTTCTT 58.623 50.000 0.00 0.00 0.00 2.52
1170 1210 4.522114 CTCCTCTTTCTTTCCTCCAATCC 58.478 47.826 0.00 0.00 0.00 3.01
1273 1313 2.105128 GAGATCCCCGACAGTGCG 59.895 66.667 0.00 0.00 0.00 5.34
1354 1394 3.790437 CCATGGCTCGCCCTCTGT 61.790 66.667 0.00 0.00 34.56 3.41
1407 1483 0.252103 ACCCTGTCCGGCTTCTTCTA 60.252 55.000 0.00 0.00 0.00 2.10
1412 1488 1.001633 TGTCCGGCTTCTTCTACAACC 59.998 52.381 0.00 0.00 0.00 3.77
1413 1489 0.245539 TCCGGCTTCTTCTACAACCG 59.754 55.000 0.00 0.00 40.30 4.44
1551 1627 0.470833 GGCCTCCTCCTCTGCAGATA 60.471 60.000 18.63 7.82 0.00 1.98
1553 1629 1.337118 CCTCCTCCTCTGCAGATACC 58.663 60.000 18.63 0.00 0.00 2.73
1621 1697 2.938798 AATCCTGCCACCGGGGAA 60.939 61.111 4.41 0.00 40.01 3.97
1682 1758 0.172578 CGGCGTTCCTGTGATCTACA 59.827 55.000 0.00 0.00 37.78 2.74
1811 1890 3.528370 CGGAGACTAGGCGGTGGG 61.528 72.222 0.00 0.00 0.00 4.61
1861 1940 1.269936 ACCGTTCTTCTTGGTGGTACG 60.270 52.381 0.00 0.00 33.91 3.67
1904 1983 4.707105 CACAATGCATCTGACTACCCATA 58.293 43.478 0.00 0.00 0.00 2.74
1905 1984 4.753610 CACAATGCATCTGACTACCCATAG 59.246 45.833 0.00 0.00 34.25 2.23
1920 1999 5.871396 ACCCATAGTGGTACAATAGTCAG 57.129 43.478 0.00 0.00 43.88 3.51
1962 2041 3.294214 CTTGGAGGGAAATTGAGGATGG 58.706 50.000 0.00 0.00 0.00 3.51
1973 2052 0.326904 TGAGGATGGCATGGAGGAGT 60.327 55.000 3.81 0.00 0.00 3.85
2002 2087 4.677182 AGGTTGTTTCTATTGGGCATTCT 58.323 39.130 0.00 0.00 0.00 2.40
2158 2243 1.213094 CGGACAAAGACGAAGCGTGT 61.213 55.000 0.00 0.00 41.37 4.49
2365 2458 2.485426 GCTGCTGCTTTCATGTACTTGA 59.515 45.455 8.53 7.33 36.03 3.02
2437 2537 1.754226 GTTTTGTGGACTGGCTTGGAA 59.246 47.619 0.00 0.00 0.00 3.53
2491 2596 6.931840 ACTTCAGTTTGTTCTTCCTATCTGTC 59.068 38.462 0.00 0.00 0.00 3.51
2496 2601 5.808366 TTGTTCTTCCTATCTGTCTGTGT 57.192 39.130 0.00 0.00 0.00 3.72
2497 2602 5.808366 TGTTCTTCCTATCTGTCTGTGTT 57.192 39.130 0.00 0.00 0.00 3.32
2498 2603 5.784177 TGTTCTTCCTATCTGTCTGTGTTC 58.216 41.667 0.00 0.00 0.00 3.18
2499 2604 5.304357 TGTTCTTCCTATCTGTCTGTGTTCA 59.696 40.000 0.00 0.00 0.00 3.18
2500 2605 5.651387 TCTTCCTATCTGTCTGTGTTCAG 57.349 43.478 0.00 0.00 42.54 3.02
2501 2606 5.325239 TCTTCCTATCTGTCTGTGTTCAGA 58.675 41.667 0.00 0.00 46.85 3.27
2551 2660 4.513442 TGAACATCACTGGTTAGCCATAC 58.487 43.478 0.00 0.00 45.05 2.39
2557 2666 5.435686 TCACTGGTTAGCCATACAGAATT 57.564 39.130 0.00 0.00 45.05 2.17
2604 2713 3.963428 ATCGAGGTCACTTTGTTAGCT 57.037 42.857 0.00 0.00 0.00 3.32
2628 2737 3.417101 TCACGTGGGCTAAATTTGACAT 58.583 40.909 17.00 0.00 0.00 3.06
2629 2738 3.438781 TCACGTGGGCTAAATTTGACATC 59.561 43.478 17.00 0.00 0.00 3.06
2722 2832 5.998454 AAGGTCATGATATTTCTTCTGCG 57.002 39.130 0.00 0.00 0.00 5.18
2728 2838 4.963276 TGATATTTCTTCTGCGTTTGGG 57.037 40.909 0.00 0.00 0.00 4.12
2730 2840 5.007034 TGATATTTCTTCTGCGTTTGGGAA 58.993 37.500 0.00 0.00 0.00 3.97
2752 2865 6.038714 GGAACATCACTCTCTTGTCTGTTTTT 59.961 38.462 0.00 0.00 0.00 1.94
2796 2911 6.866010 TTATCAGTGATGTGATATTGTGCC 57.134 37.500 16.15 0.00 38.83 5.01
2822 2937 7.933577 CCTGACCTTTCTGTATTATGCATAGAA 59.066 37.037 6.50 5.66 0.00 2.10
2823 2938 8.893219 TGACCTTTCTGTATTATGCATAGAAG 57.107 34.615 6.50 3.98 0.00 2.85
2824 2939 7.933577 TGACCTTTCTGTATTATGCATAGAAGG 59.066 37.037 6.50 12.63 0.00 3.46
2825 2940 7.806180 ACCTTTCTGTATTATGCATAGAAGGT 58.194 34.615 16.45 16.45 30.86 3.50
2826 2941 8.934697 ACCTTTCTGTATTATGCATAGAAGGTA 58.065 33.333 18.63 3.32 32.40 3.08
2827 2942 9.778741 CCTTTCTGTATTATGCATAGAAGGTAA 57.221 33.333 13.92 0.00 0.00 2.85
3072 3208 9.661954 ACTTAATATCCTTCTGTAATCCTCTGA 57.338 33.333 0.00 0.00 0.00 3.27
3074 3210 9.661954 TTAATATCCTTCTGTAATCCTCTGAGT 57.338 33.333 3.66 0.00 0.00 3.41
3093 3229 5.784177 TGAGTCACTGTAACTTCAAGATCC 58.216 41.667 0.00 0.00 0.00 3.36
3161 3297 6.290294 AGCACCGGTACTATCTTCTTTTTA 57.710 37.500 6.87 0.00 0.00 1.52
3279 3536 9.528018 TTCAAAATGAAAAAGATAGAAAAGCGT 57.472 25.926 0.00 0.00 32.71 5.07
3287 3544 7.923414 AAAAGATAGAAAAGCGTCCTACAAT 57.077 32.000 0.00 0.00 0.00 2.71
3289 3546 9.444600 AAAAGATAGAAAAGCGTCCTACAATTA 57.555 29.630 0.00 0.00 0.00 1.40
3291 3548 9.614792 AAGATAGAAAAGCGTCCTACAATTATT 57.385 29.630 0.00 0.00 0.00 1.40
3317 3574 8.922931 ATTATTTTGAAACCAGGCAAAAGATT 57.077 26.923 8.79 0.63 44.30 2.40
3318 3575 8.744568 TTATTTTGAAACCAGGCAAAAGATTT 57.255 26.923 8.79 0.00 44.30 2.17
3319 3576 6.434018 TTTTGAAACCAGGCAAAAGATTTG 57.566 33.333 0.00 0.00 38.60 2.32
3320 3577 3.465871 TGAAACCAGGCAAAAGATTTGC 58.534 40.909 17.18 17.18 44.22 3.68
3334 3591 9.628746 GCAAAAGATTTGCCATTTTCATTAAAT 57.371 25.926 15.12 0.00 39.38 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.469657 ACACCACAAAGCTTTTGGAGATA 58.530 39.130 30.50 0.00 34.24 1.98
103 105 0.587768 CATGTGTGTCAAGCGCTTCA 59.412 50.000 22.21 13.97 0.00 3.02
453 476 1.069204 GACCTCGCAATGATCCTAGCA 59.931 52.381 0.00 0.00 0.00 3.49
488 511 8.375465 GGCTTTTTATTGACGAAGAATTTGATG 58.625 33.333 0.00 0.00 32.44 3.07
505 528 3.365969 CGCTGGAGAAAACGGCTTTTTAT 60.366 43.478 1.33 0.00 37.54 1.40
506 529 2.031508 CGCTGGAGAAAACGGCTTTTTA 60.032 45.455 1.33 0.00 37.54 1.52
507 530 1.269051 CGCTGGAGAAAACGGCTTTTT 60.269 47.619 0.87 0.87 40.30 1.94
508 531 0.310854 CGCTGGAGAAAACGGCTTTT 59.689 50.000 0.00 0.00 38.07 2.27
509 532 1.949257 CGCTGGAGAAAACGGCTTT 59.051 52.632 0.00 0.00 38.07 3.51
510 533 2.617274 GCGCTGGAGAAAACGGCTT 61.617 57.895 0.00 0.00 38.07 4.35
511 534 3.050275 GCGCTGGAGAAAACGGCT 61.050 61.111 0.00 0.00 38.07 5.52
512 535 4.445545 CGCGCTGGAGAAAACGGC 62.446 66.667 5.56 0.00 36.88 5.68
513 536 2.604174 AACGCGCTGGAGAAAACGG 61.604 57.895 5.73 0.00 0.00 4.44
514 537 1.438710 CAACGCGCTGGAGAAAACG 60.439 57.895 5.73 0.00 0.00 3.60
515 538 0.028902 AACAACGCGCTGGAGAAAAC 59.971 50.000 14.82 0.00 0.00 2.43
516 539 0.028770 CAACAACGCGCTGGAGAAAA 59.971 50.000 14.82 0.00 0.00 2.29
517 540 0.812014 TCAACAACGCGCTGGAGAAA 60.812 50.000 14.82 0.00 0.00 2.52
518 541 1.221466 CTCAACAACGCGCTGGAGAA 61.221 55.000 14.82 0.00 0.00 2.87
519 542 1.664649 CTCAACAACGCGCTGGAGA 60.665 57.895 14.82 9.88 0.00 3.71
520 543 1.016130 ATCTCAACAACGCGCTGGAG 61.016 55.000 14.82 11.40 0.00 3.86
521 544 0.602638 AATCTCAACAACGCGCTGGA 60.603 50.000 14.82 1.46 0.00 3.86
522 545 0.453282 CAATCTCAACAACGCGCTGG 60.453 55.000 14.82 2.34 0.00 4.85
523 546 1.061799 GCAATCTCAACAACGCGCTG 61.062 55.000 5.73 7.11 0.00 5.18
524 547 1.207593 GCAATCTCAACAACGCGCT 59.792 52.632 5.73 0.00 0.00 5.92
525 548 2.139811 CGCAATCTCAACAACGCGC 61.140 57.895 5.73 0.00 35.97 6.86
526 549 2.139811 GCGCAATCTCAACAACGCG 61.140 57.895 3.53 3.53 45.13 6.01
527 550 2.139811 CGCGCAATCTCAACAACGC 61.140 57.895 8.75 0.00 42.69 4.84
528 551 0.785708 GACGCGCAATCTCAACAACG 60.786 55.000 5.73 0.00 0.00 4.10
529 552 0.512952 AGACGCGCAATCTCAACAAC 59.487 50.000 5.73 0.00 0.00 3.32
530 553 0.512518 CAGACGCGCAATCTCAACAA 59.487 50.000 5.73 0.00 0.00 2.83
531 554 0.599991 ACAGACGCGCAATCTCAACA 60.600 50.000 5.73 0.00 0.00 3.33
532 555 0.512952 AACAGACGCGCAATCTCAAC 59.487 50.000 5.73 0.00 0.00 3.18
533 556 0.512518 CAACAGACGCGCAATCTCAA 59.487 50.000 5.73 0.00 0.00 3.02
534 557 0.319469 TCAACAGACGCGCAATCTCA 60.319 50.000 5.73 0.00 0.00 3.27
535 558 0.790207 TTCAACAGACGCGCAATCTC 59.210 50.000 5.73 0.00 0.00 2.75
536 559 0.792640 CTTCAACAGACGCGCAATCT 59.207 50.000 5.73 6.80 0.00 2.40
537 560 0.790207 TCTTCAACAGACGCGCAATC 59.210 50.000 5.73 4.01 0.00 2.67
538 561 1.129251 CATCTTCAACAGACGCGCAAT 59.871 47.619 5.73 0.00 32.83 3.56
539 562 0.512518 CATCTTCAACAGACGCGCAA 59.487 50.000 5.73 0.00 32.83 4.85
540 563 1.900585 GCATCTTCAACAGACGCGCA 61.901 55.000 5.73 0.00 29.35 6.09
541 564 1.225854 GCATCTTCAACAGACGCGC 60.226 57.895 5.73 0.00 29.35 6.86
542 565 0.368227 GAGCATCTTCAACAGACGCG 59.632 55.000 3.53 3.53 45.88 6.01
555 578 3.939592 GTGGTAAGGTGGTTTAGAGCATC 59.060 47.826 0.00 0.00 35.44 3.91
556 579 3.618997 CGTGGTAAGGTGGTTTAGAGCAT 60.619 47.826 0.00 0.00 35.44 3.79
557 580 2.289195 CGTGGTAAGGTGGTTTAGAGCA 60.289 50.000 0.00 0.00 0.00 4.26
558 581 2.344025 CGTGGTAAGGTGGTTTAGAGC 58.656 52.381 0.00 0.00 0.00 4.09
559 582 2.564062 TCCGTGGTAAGGTGGTTTAGAG 59.436 50.000 0.00 0.00 0.00 2.43
560 583 2.299867 GTCCGTGGTAAGGTGGTTTAGA 59.700 50.000 0.00 0.00 0.00 2.10
601 624 3.195698 GGTCGAACGGCATCCTGC 61.196 66.667 0.61 0.00 44.08 4.85
606 629 1.374252 GTCAGTGGTCGAACGGCAT 60.374 57.895 0.00 0.00 0.00 4.40
609 632 2.193447 CATATGTCAGTGGTCGAACGG 58.807 52.381 0.00 0.00 0.00 4.44
651 682 2.141448 TGTACCGTTGGGCCACTGA 61.141 57.895 5.23 0.00 36.48 3.41
670 701 1.066303 GAGCTCCTCTGACGTATGGTG 59.934 57.143 0.87 0.00 0.00 4.17
702 733 0.615850 TGCATGAATGTGACCCCGTA 59.384 50.000 0.00 0.00 0.00 4.02
718 749 1.375396 AGCGGCTGTATCGTTTGCA 60.375 52.632 0.00 0.00 0.00 4.08
736 767 0.112412 GTTTGGGAAGAAGGAGGGCA 59.888 55.000 0.00 0.00 0.00 5.36
802 836 4.451150 TAGCGCCGCCCTTGTGAG 62.451 66.667 4.98 0.00 0.00 3.51
803 837 4.451150 CTAGCGCCGCCCTTGTGA 62.451 66.667 4.98 0.00 0.00 3.58
808 842 3.907027 ATATCCCTAGCGCCGCCCT 62.907 63.158 4.98 0.00 0.00 5.19
809 843 2.854187 GAATATCCCTAGCGCCGCCC 62.854 65.000 4.98 0.00 0.00 6.13
810 844 1.448013 GAATATCCCTAGCGCCGCC 60.448 63.158 4.98 0.00 0.00 6.13
811 845 0.037232 AAGAATATCCCTAGCGCCGC 60.037 55.000 2.29 0.00 0.00 6.53
812 846 1.673033 CCAAGAATATCCCTAGCGCCG 60.673 57.143 2.29 0.00 0.00 6.46
813 847 1.623811 TCCAAGAATATCCCTAGCGCC 59.376 52.381 2.29 0.00 0.00 6.53
814 848 3.618690 ATCCAAGAATATCCCTAGCGC 57.381 47.619 0.00 0.00 0.00 5.92
815 849 5.997746 TGAAAATCCAAGAATATCCCTAGCG 59.002 40.000 0.00 0.00 0.00 4.26
816 850 7.449704 ACATGAAAATCCAAGAATATCCCTAGC 59.550 37.037 0.00 0.00 0.00 3.42
817 851 8.790718 CACATGAAAATCCAAGAATATCCCTAG 58.209 37.037 0.00 0.00 0.00 3.02
818 852 8.501904 TCACATGAAAATCCAAGAATATCCCTA 58.498 33.333 0.00 0.00 0.00 3.53
819 853 7.356680 TCACATGAAAATCCAAGAATATCCCT 58.643 34.615 0.00 0.00 0.00 4.20
820 854 7.587037 TCACATGAAAATCCAAGAATATCCC 57.413 36.000 0.00 0.00 0.00 3.85
846 880 9.862371 AACACTGTTTTGTAAAAATCATGTGTA 57.138 25.926 16.53 0.00 31.54 2.90
847 881 8.655092 CAACACTGTTTTGTAAAAATCATGTGT 58.345 29.630 13.37 13.37 32.20 3.72
848 882 8.867935 TCAACACTGTTTTGTAAAAATCATGTG 58.132 29.630 6.58 12.59 0.00 3.21
849 883 8.994429 TCAACACTGTTTTGTAAAAATCATGT 57.006 26.923 6.58 0.00 0.00 3.21
863 897 9.651913 ACTGTTTTATCAAAATCAACACTGTTT 57.348 25.926 0.00 0.00 32.22 2.83
864 898 9.086336 CACTGTTTTATCAAAATCAACACTGTT 57.914 29.630 0.00 0.00 32.22 3.16
865 899 8.465999 TCACTGTTTTATCAAAATCAACACTGT 58.534 29.630 0.00 0.00 32.22 3.55
866 900 8.745837 GTCACTGTTTTATCAAAATCAACACTG 58.254 33.333 0.00 0.00 32.22 3.66
867 901 8.465999 TGTCACTGTTTTATCAAAATCAACACT 58.534 29.630 0.00 0.00 32.22 3.55
868 902 8.627487 TGTCACTGTTTTATCAAAATCAACAC 57.373 30.769 0.00 0.00 32.22 3.32
869 903 9.814899 ATTGTCACTGTTTTATCAAAATCAACA 57.185 25.926 0.00 0.00 32.22 3.33
908 942 9.382275 GGGTATTCATTTTGCTAAAATCATTGT 57.618 29.630 0.00 0.00 38.97 2.71
909 943 9.603921 AGGGTATTCATTTTGCTAAAATCATTG 57.396 29.630 0.00 0.00 38.97 2.82
910 944 9.603921 CAGGGTATTCATTTTGCTAAAATCATT 57.396 29.630 0.00 0.00 38.97 2.57
911 945 8.761689 ACAGGGTATTCATTTTGCTAAAATCAT 58.238 29.630 0.00 0.83 38.97 2.45
912 946 8.133024 ACAGGGTATTCATTTTGCTAAAATCA 57.867 30.769 0.00 0.00 38.97 2.57
913 947 8.872845 CAACAGGGTATTCATTTTGCTAAAATC 58.127 33.333 0.00 0.00 38.97 2.17
914 948 7.334171 GCAACAGGGTATTCATTTTGCTAAAAT 59.666 33.333 0.00 0.00 41.57 1.82
915 949 6.648725 GCAACAGGGTATTCATTTTGCTAAAA 59.351 34.615 0.00 0.00 35.95 1.52
916 950 6.162777 GCAACAGGGTATTCATTTTGCTAAA 58.837 36.000 0.00 0.00 35.95 1.85
917 951 5.244851 TGCAACAGGGTATTCATTTTGCTAA 59.755 36.000 0.00 0.00 38.89 3.09
918 952 4.769488 TGCAACAGGGTATTCATTTTGCTA 59.231 37.500 0.00 0.00 38.89 3.49
919 953 3.577848 TGCAACAGGGTATTCATTTTGCT 59.422 39.130 0.00 0.00 38.89 3.91
920 954 3.924144 TGCAACAGGGTATTCATTTTGC 58.076 40.909 0.00 0.00 38.65 3.68
921 955 7.437793 AATTTGCAACAGGGTATTCATTTTG 57.562 32.000 0.00 0.00 0.00 2.44
922 956 7.938490 AGAAATTTGCAACAGGGTATTCATTTT 59.062 29.630 0.00 0.00 0.00 1.82
923 957 7.388500 CAGAAATTTGCAACAGGGTATTCATTT 59.612 33.333 0.00 0.00 0.00 2.32
924 958 6.875195 CAGAAATTTGCAACAGGGTATTCATT 59.125 34.615 0.00 0.00 0.00 2.57
925 959 6.400568 CAGAAATTTGCAACAGGGTATTCAT 58.599 36.000 0.00 0.00 0.00 2.57
926 960 5.279406 CCAGAAATTTGCAACAGGGTATTCA 60.279 40.000 0.00 0.00 0.00 2.57
927 961 5.047377 TCCAGAAATTTGCAACAGGGTATTC 60.047 40.000 0.00 0.00 0.00 1.75
928 962 4.837860 TCCAGAAATTTGCAACAGGGTATT 59.162 37.500 0.00 0.00 0.00 1.89
929 963 4.415596 TCCAGAAATTTGCAACAGGGTAT 58.584 39.130 0.00 0.00 0.00 2.73
930 964 3.826157 CTCCAGAAATTTGCAACAGGGTA 59.174 43.478 0.00 0.00 0.00 3.69
931 965 2.629617 CTCCAGAAATTTGCAACAGGGT 59.370 45.455 0.00 0.00 0.00 4.34
932 966 2.611224 GCTCCAGAAATTTGCAACAGGG 60.611 50.000 0.00 0.00 0.00 4.45
933 967 2.611224 GGCTCCAGAAATTTGCAACAGG 60.611 50.000 0.00 0.00 0.00 4.00
934 968 2.680577 GGCTCCAGAAATTTGCAACAG 58.319 47.619 0.00 0.00 0.00 3.16
935 969 1.000385 CGGCTCCAGAAATTTGCAACA 60.000 47.619 0.00 0.00 0.00 3.33
936 970 1.701704 CGGCTCCAGAAATTTGCAAC 58.298 50.000 0.00 0.00 0.00 4.17
937 971 0.038343 GCGGCTCCAGAAATTTGCAA 60.038 50.000 0.00 0.00 0.00 4.08
938 972 1.586028 GCGGCTCCAGAAATTTGCA 59.414 52.632 0.00 0.00 0.00 4.08
939 973 1.153765 GGCGGCTCCAGAAATTTGC 60.154 57.895 0.00 0.00 34.01 3.68
940 974 1.137404 CGGCGGCTCCAGAAATTTG 59.863 57.895 7.61 0.00 34.01 2.32
941 975 2.700773 GCGGCGGCTCCAGAAATTT 61.701 57.895 9.78 0.00 35.83 1.82
942 976 3.134127 GCGGCGGCTCCAGAAATT 61.134 61.111 9.78 0.00 35.83 1.82
991 1025 2.548480 CTCCTGACGTCATCGCATACTA 59.452 50.000 20.40 0.00 41.18 1.82
1009 1043 2.520741 CTCGCCTCCTCCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
1120 1160 4.482684 CTCGAGCGCTGCTTCGGA 62.483 66.667 18.48 0.86 39.88 4.55
1170 1210 0.955919 GCTCCCTTTGTTGGACTCCG 60.956 60.000 0.00 0.00 0.00 4.63
1269 1309 2.652496 GGATCTCGACGAGCGCAC 60.652 66.667 20.11 0.96 40.61 5.34
1273 1313 1.010574 CGACAGGATCTCGACGAGC 60.011 63.158 20.11 6.96 32.65 5.03
1551 1627 1.538687 CCCTTTGTACGAGTCCCGGT 61.539 60.000 0.00 0.00 43.93 5.28
1553 1629 1.447314 GCCCTTTGTACGAGTCCCG 60.447 63.158 0.00 0.00 45.44 5.14
1621 1697 0.837691 TGAGGGTCAGCACAGTCCAT 60.838 55.000 0.00 0.00 0.00 3.41
1682 1758 3.369892 CCCAGGAAGAGATCGTTCACATT 60.370 47.826 11.56 0.00 0.00 2.71
1811 1890 2.202676 CTCGCTCTCCACGGAAGC 60.203 66.667 9.08 9.08 0.00 3.86
1885 1964 4.202398 CCACTATGGGTAGTCAGATGCATT 60.202 45.833 0.00 0.00 39.12 3.56
1904 1983 4.077108 TCGACACTGACTATTGTACCACT 58.923 43.478 0.00 0.00 0.00 4.00
1905 1984 4.164294 GTCGACACTGACTATTGTACCAC 58.836 47.826 11.55 0.00 35.95 4.16
1937 2016 3.264450 TCCTCAATTTCCCTCCAAGTCTC 59.736 47.826 0.00 0.00 0.00 3.36
1962 2041 0.103208 CTCACGGTACTCCTCCATGC 59.897 60.000 0.00 0.00 0.00 4.06
1973 2052 4.563993 CCCAATAGAAACAACCTCACGGTA 60.564 45.833 0.00 0.00 44.73 4.02
1990 2075 0.925558 TGCCCTGAGAATGCCCAATA 59.074 50.000 0.00 0.00 0.00 1.90
2002 2087 3.066190 GCATGCAAGCTGCCCTGA 61.066 61.111 14.21 0.00 44.23 3.86
2173 2258 7.738437 AACCAAATTACAATCTGGATGGATT 57.262 32.000 1.29 0.00 36.49 3.01
2365 2458 6.597562 TGGTATTTGTGAAGTACTTCCACTT 58.402 36.000 28.43 17.58 41.44 3.16
2437 2537 2.433970 GGAGCTAAGAGCCTGAGACATT 59.566 50.000 0.00 0.00 43.77 2.71
2491 2596 4.813161 ACACATCTGAAGTTCTGAACACAG 59.187 41.667 26.46 26.46 38.47 3.66
2496 2601 3.141398 GGCACACATCTGAAGTTCTGAA 58.859 45.455 15.40 1.39 0.00 3.02
2497 2602 2.104622 TGGCACACATCTGAAGTTCTGA 59.895 45.455 14.02 14.02 0.00 3.27
2498 2603 2.497138 TGGCACACATCTGAAGTTCTG 58.503 47.619 4.17 3.79 0.00 3.02
2499 2604 2.936919 TGGCACACATCTGAAGTTCT 57.063 45.000 4.17 0.00 0.00 3.01
2557 2666 1.001974 CCATCAGACGGTTCCACAGAA 59.998 52.381 0.00 0.00 0.00 3.02
2562 2671 0.834261 TGACCCATCAGACGGTTCCA 60.834 55.000 0.00 0.00 30.56 3.53
2569 2678 3.322254 ACCTCGATAATGACCCATCAGAC 59.678 47.826 0.00 0.00 38.57 3.51
2604 2713 2.039216 TCAAATTTAGCCCACGTGAGGA 59.961 45.455 19.30 0.93 0.00 3.71
2702 2812 5.741388 AACGCAGAAGAAATATCATGACC 57.259 39.130 0.00 0.00 0.00 4.02
2706 2816 5.192927 TCCCAAACGCAGAAGAAATATCAT 58.807 37.500 0.00 0.00 0.00 2.45
2720 2830 1.464997 GAGAGTGATGTTCCCAAACGC 59.535 52.381 0.00 0.00 38.28 4.84
2722 2832 4.137543 ACAAGAGAGTGATGTTCCCAAAC 58.862 43.478 0.00 0.00 35.85 2.93
2728 2838 6.610741 AAAACAGACAAGAGAGTGATGTTC 57.389 37.500 0.00 0.00 33.73 3.18
2796 2911 7.445121 TCTATGCATAATACAGAAAGGTCAGG 58.555 38.462 8.00 0.00 0.00 3.86
2822 2937 4.838904 AGCGGATTTCTTTACCTTACCT 57.161 40.909 0.00 0.00 0.00 3.08
2823 2938 4.095932 CCAAGCGGATTTCTTTACCTTACC 59.904 45.833 0.00 0.00 0.00 2.85
2824 2939 4.698780 ACCAAGCGGATTTCTTTACCTTAC 59.301 41.667 0.00 0.00 35.59 2.34
2825 2940 4.698304 CACCAAGCGGATTTCTTTACCTTA 59.302 41.667 0.00 0.00 35.59 2.69
2826 2941 3.506067 CACCAAGCGGATTTCTTTACCTT 59.494 43.478 0.00 0.00 35.59 3.50
2827 2942 3.081804 CACCAAGCGGATTTCTTTACCT 58.918 45.455 0.00 0.00 35.59 3.08
2912 3027 4.272489 TCTCTGCCCCAACAATTATTCTG 58.728 43.478 0.00 0.00 0.00 3.02
2914 3029 4.462483 TGTTCTCTGCCCCAACAATTATTC 59.538 41.667 0.00 0.00 0.00 1.75
2915 3030 4.415596 TGTTCTCTGCCCCAACAATTATT 58.584 39.130 0.00 0.00 0.00 1.40
2916 3031 4.019174 CTGTTCTCTGCCCCAACAATTAT 58.981 43.478 0.00 0.00 29.78 1.28
2918 3033 2.158475 TCTGTTCTCTGCCCCAACAATT 60.158 45.455 0.00 0.00 29.78 2.32
2919 3034 1.425066 TCTGTTCTCTGCCCCAACAAT 59.575 47.619 0.00 0.00 29.78 2.71
2988 3120 9.707957 TTATAATACCATCTGTCAAAACCCAAT 57.292 29.630 0.00 0.00 0.00 3.16
3056 3192 5.184864 ACAGTGACTCAGAGGATTACAGAAG 59.815 44.000 1.53 0.00 0.00 2.85
3058 3194 4.667573 ACAGTGACTCAGAGGATTACAGA 58.332 43.478 1.53 0.00 0.00 3.41
3059 3195 6.151985 AGTTACAGTGACTCAGAGGATTACAG 59.848 42.308 1.53 0.00 0.00 2.74
3060 3196 6.010850 AGTTACAGTGACTCAGAGGATTACA 58.989 40.000 1.53 0.00 0.00 2.41
3061 3197 6.518208 AGTTACAGTGACTCAGAGGATTAC 57.482 41.667 1.53 0.00 0.00 1.89
3062 3198 6.719829 TGAAGTTACAGTGACTCAGAGGATTA 59.280 38.462 1.53 0.00 0.00 1.75
3063 3199 5.540337 TGAAGTTACAGTGACTCAGAGGATT 59.460 40.000 1.53 0.00 0.00 3.01
3064 3200 5.080337 TGAAGTTACAGTGACTCAGAGGAT 58.920 41.667 1.53 0.00 0.00 3.24
3065 3201 4.470602 TGAAGTTACAGTGACTCAGAGGA 58.529 43.478 1.53 0.00 0.00 3.71
3066 3202 4.855715 TGAAGTTACAGTGACTCAGAGG 57.144 45.455 1.53 0.00 0.00 3.69
3067 3203 6.078202 TCTTGAAGTTACAGTGACTCAGAG 57.922 41.667 0.00 0.00 0.00 3.35
3068 3204 6.294787 GGATCTTGAAGTTACAGTGACTCAGA 60.295 42.308 0.00 2.09 0.00 3.27
3069 3205 5.866633 GGATCTTGAAGTTACAGTGACTCAG 59.133 44.000 0.00 0.00 0.00 3.35
3070 3206 5.279506 GGGATCTTGAAGTTACAGTGACTCA 60.280 44.000 0.00 0.00 0.00 3.41
3071 3207 5.172205 GGGATCTTGAAGTTACAGTGACTC 58.828 45.833 0.00 0.00 0.00 3.36
3072 3208 4.593206 TGGGATCTTGAAGTTACAGTGACT 59.407 41.667 0.00 0.00 0.00 3.41
3073 3209 4.894784 TGGGATCTTGAAGTTACAGTGAC 58.105 43.478 0.00 0.00 0.00 3.67
3074 3210 4.563580 GCTGGGATCTTGAAGTTACAGTGA 60.564 45.833 0.00 0.00 0.00 3.41
3093 3229 6.314896 CCAAGAAGAGATAGTTAACTTGCTGG 59.685 42.308 14.49 5.33 34.09 4.85
3161 3297 3.137728 AGGTAGTAAAGGTGTGTTTGCCT 59.862 43.478 0.00 0.00 36.51 4.75
3226 3483 7.774157 TGACAATAAACACCAGGTTACAACTTA 59.226 33.333 0.00 0.00 39.29 2.24
3230 3487 7.285629 TGAATGACAATAAACACCAGGTTACAA 59.714 33.333 0.00 0.00 39.29 2.41
3292 3549 8.922931 AATCTTTTGCCTGGTTTCAAAATAAT 57.077 26.923 9.97 6.00 40.19 1.28
3295 3552 6.459985 GCAAATCTTTTGCCTGGTTTCAAAAT 60.460 34.615 12.74 0.00 40.19 1.82
3297 3554 4.335037 GCAAATCTTTTGCCTGGTTTCAAA 59.665 37.500 12.74 0.00 39.38 2.69
3298 3555 3.876320 GCAAATCTTTTGCCTGGTTTCAA 59.124 39.130 12.74 0.00 39.38 2.69
3299 3556 3.465871 GCAAATCTTTTGCCTGGTTTCA 58.534 40.909 12.74 0.00 39.38 2.69
3308 3565 9.628746 ATTTAATGAAAATGGCAAATCTTTTGC 57.371 25.926 14.88 14.88 36.41 3.68


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

AutoCloner maintained by Alex Coulton.