Multiple sequence alignment - TraesCS3D01G220900

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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 TraesCS3D01G220900 chr3D 100.000 6964 0 0 1 6964 301446553 301439590 0.000000e+00 12861.0
1 TraesCS3D01G220900 chr3D 83.154 558 71 15 2 539 604298919 604299473 8.120000e-134 488.0
2 TraesCS3D01G220900 chr3D 93.069 303 21 0 6660 6962 25538709 25538407 1.780000e-120 444.0
3 TraesCS3D01G220900 chr3D 92.739 303 20 1 6660 6962 41141429 41141129 2.980000e-118 436.0
4 TraesCS3D01G220900 chr3D 87.912 91 6 4 6158 6245 557459100 557459188 1.240000e-17 102.0
5 TraesCS3D01G220900 chr3B 95.342 5560 191 25 557 6093 419761421 419766935 0.000000e+00 8770.0
6 TraesCS3D01G220900 chr3B 94.590 573 17 3 6077 6635 419766950 419767522 0.000000e+00 874.0
7 TraesCS3D01G220900 chr3B 92.500 40 2 1 537 575 253893203 253893164 1.000000e-03 56.5
8 TraesCS3D01G220900 chr3A 96.336 3384 105 9 2523 5896 433997287 434000661 0.000000e+00 5544.0
9 TraesCS3D01G220900 chr3A 93.493 1967 94 17 566 2530 433994436 433996370 0.000000e+00 2892.0
10 TraesCS3D01G220900 chr3A 94.954 753 20 6 5923 6659 434000658 434001408 0.000000e+00 1164.0
11 TraesCS3D01G220900 chr3A 93.031 287 19 1 6661 6947 514268109 514267824 1.080000e-112 418.0
12 TraesCS3D01G220900 chr3A 80.470 553 77 21 5 542 409490152 409489616 1.820000e-105 394.0
13 TraesCS3D01G220900 chr3A 85.542 83 5 6 6158 6233 713309480 713309398 5.790000e-11 80.5
14 TraesCS3D01G220900 chr3A 97.222 36 1 0 540 575 19686777 19686742 2.100000e-05 62.1
15 TraesCS3D01G220900 chr5B 87.844 2468 292 8 3071 5535 675080220 675082682 0.000000e+00 2889.0
16 TraesCS3D01G220900 chr5B 87.637 2467 297 8 3071 5534 674892251 674894712 0.000000e+00 2859.0
17 TraesCS3D01G220900 chr5B 82.686 566 66 13 1 542 377132568 377132011 2.270000e-129 473.0
18 TraesCS3D01G220900 chr7B 87.857 2454 292 6 3071 5521 624351128 624353578 0.000000e+00 2876.0
19 TraesCS3D01G220900 chr7B 96.875 32 1 0 508 539 244663264 244663295 4.000000e-03 54.7
20 TraesCS3D01G220900 chr5D 87.652 2470 293 11 3071 5535 534637034 534639496 0.000000e+00 2861.0
21 TraesCS3D01G220900 chr5D 87.520 2452 300 6 3071 5519 534865051 534867499 0.000000e+00 2828.0
22 TraesCS3D01G220900 chr5D 83.214 560 63 16 5 539 133375364 133375917 1.050000e-132 484.0
23 TraesCS3D01G220900 chr7D 87.607 2453 300 4 3071 5521 568598504 568600954 0.000000e+00 2843.0
24 TraesCS3D01G220900 chr7D 93.069 303 21 0 6660 6962 496105656 496105354 1.780000e-120 444.0
25 TraesCS3D01G220900 chr7D 82.004 489 51 16 81 539 39185849 39185368 1.420000e-101 381.0
26 TraesCS3D01G220900 chr7D 97.619 42 0 1 540 580 602852556 602852597 3.480000e-08 71.3
27 TraesCS3D01G220900 chr4A 87.394 2467 299 12 3071 5532 636687164 636684705 0.000000e+00 2822.0
28 TraesCS3D01G220900 chr4A 83.673 147 21 3 2086 2231 636687839 636687695 1.220000e-27 135.0
29 TraesCS3D01G220900 chr1D 73.937 2398 537 72 3071 5412 10025406 10027771 0.000000e+00 885.0
30 TraesCS3D01G220900 chr1D 94.059 303 18 0 6660 6962 456923922 456923620 1.770000e-125 460.0
31 TraesCS3D01G220900 chr1D 92.409 303 23 0 6660 6962 470880757 470880455 3.860000e-117 433.0
32 TraesCS3D01G220900 chr1D 82.979 94 6 7 6154 6240 106956552 106956462 7.490000e-10 76.8
33 TraesCS3D01G220900 chr1D 94.737 38 1 1 540 577 470941562 470941598 2.710000e-04 58.4
34 TraesCS3D01G220900 chr1A 76.379 1613 310 49 3071 4641 11719838 11721421 0.000000e+00 802.0
35 TraesCS3D01G220900 chr1A 82.979 94 6 7 6154 6240 105905172 105905262 7.490000e-10 76.8
36 TraesCS3D01G220900 chr4D 84.258 559 61 15 4 539 506102194 506101640 2.880000e-143 520.0
37 TraesCS3D01G220900 chr4D 83.769 536 55 18 27 539 310011263 310011789 4.890000e-131 479.0
38 TraesCS3D01G220900 chr4D 82.819 518 62 9 45 539 437152813 437152300 8.290000e-119 438.0
39 TraesCS3D01G220900 chr4D 83.610 482 48 13 4 462 43306023 43306496 2.320000e-114 424.0
40 TraesCS3D01G220900 chr2A 84.050 558 61 15 4 539 620257511 620256960 4.820000e-141 512.0
41 TraesCS3D01G220900 chr2A 76.761 284 37 17 6397 6653 504546816 504546535 1.580000e-26 132.0
42 TraesCS3D01G220900 chr6D 84.107 560 56 17 5 539 157160628 157160077 1.730000e-140 510.0
43 TraesCS3D01G220900 chr6D 91.089 303 24 3 6660 6962 38577389 38577688 2.340000e-109 407.0
44 TraesCS3D01G220900 chr6A 83.519 540 73 13 6 539 57096621 57097150 2.260000e-134 490.0
45 TraesCS3D01G220900 chr1B 83.304 563 63 12 1 539 25840777 25840222 2.260000e-134 490.0
46 TraesCS3D01G220900 chr1B 82.440 541 71 19 6 539 689386188 689386711 1.070000e-122 451.0
47 TraesCS3D01G220900 chr1B 88.372 86 4 5 6158 6238 491083484 491083400 1.600000e-16 99.0
48 TraesCS3D01G220900 chr1B 85.106 94 6 5 6158 6245 491083400 491083491 9.620000e-14 89.8
49 TraesCS3D01G220900 chr2D 83.394 554 62 15 9 539 563023191 563023737 2.920000e-133 486.0
50 TraesCS3D01G220900 chr2D 75.610 287 41 17 6394 6653 372813173 372813457 1.590000e-21 115.0
51 TraesCS3D01G220900 chr2D 87.778 90 5 4 6154 6238 101695509 101695421 4.440000e-17 100.0
52 TraesCS3D01G220900 chr7A 83.184 559 64 17 4 539 224832394 224831843 1.050000e-132 484.0
53 TraesCS3D01G220900 chr4B 92.739 303 22 0 6660 6962 625982940 625983242 8.290000e-119 438.0
54 TraesCS3D01G220900 chrUn 93.515 293 17 1 6660 6952 96240641 96240351 1.070000e-117 435.0
55 TraesCS3D01G220900 chr2B 77.003 287 37 17 6394 6653 442337633 442337917 3.390000e-28 137.0
56 TraesCS3D01G220900 chr2B 97.222 36 1 0 540 575 548017584 548017549 2.100000e-05 62.1
57 TraesCS3D01G220900 chr2B 94.872 39 0 2 537 574 772348728 772348765 7.540000e-05 60.2
58 TraesCS3D01G220900 chr2B 90.698 43 2 2 540 582 141154228 141154268 1.000000e-03 56.5
59 TraesCS3D01G220900 chr6B 100.000 34 0 0 540 573 696354048 696354015 5.830000e-06 63.9


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 TraesCS3D01G220900 chr3D 301439590 301446553 6963 True 12861.0 12861 100.000000 1 6964 1 chr3D.!!$R3 6963
1 TraesCS3D01G220900 chr3D 604298919 604299473 554 False 488.0 488 83.154000 2 539 1 chr3D.!!$F2 537
2 TraesCS3D01G220900 chr3B 419761421 419767522 6101 False 4822.0 8770 94.966000 557 6635 2 chr3B.!!$F1 6078
3 TraesCS3D01G220900 chr3A 433994436 434001408 6972 False 3200.0 5544 94.927667 566 6659 3 chr3A.!!$F1 6093
4 TraesCS3D01G220900 chr3A 409489616 409490152 536 True 394.0 394 80.470000 5 542 1 chr3A.!!$R2 537
5 TraesCS3D01G220900 chr5B 675080220 675082682 2462 False 2889.0 2889 87.844000 3071 5535 1 chr5B.!!$F2 2464
6 TraesCS3D01G220900 chr5B 674892251 674894712 2461 False 2859.0 2859 87.637000 3071 5534 1 chr5B.!!$F1 2463
7 TraesCS3D01G220900 chr5B 377132011 377132568 557 True 473.0 473 82.686000 1 542 1 chr5B.!!$R1 541
8 TraesCS3D01G220900 chr7B 624351128 624353578 2450 False 2876.0 2876 87.857000 3071 5521 1 chr7B.!!$F2 2450
9 TraesCS3D01G220900 chr5D 534637034 534639496 2462 False 2861.0 2861 87.652000 3071 5535 1 chr5D.!!$F2 2464
10 TraesCS3D01G220900 chr5D 534865051 534867499 2448 False 2828.0 2828 87.520000 3071 5519 1 chr5D.!!$F3 2448
11 TraesCS3D01G220900 chr5D 133375364 133375917 553 False 484.0 484 83.214000 5 539 1 chr5D.!!$F1 534
12 TraesCS3D01G220900 chr7D 568598504 568600954 2450 False 2843.0 2843 87.607000 3071 5521 1 chr7D.!!$F1 2450
13 TraesCS3D01G220900 chr4A 636684705 636687839 3134 True 1478.5 2822 85.533500 2086 5532 2 chr4A.!!$R1 3446
14 TraesCS3D01G220900 chr1D 10025406 10027771 2365 False 885.0 885 73.937000 3071 5412 1 chr1D.!!$F1 2341
15 TraesCS3D01G220900 chr1A 11719838 11721421 1583 False 802.0 802 76.379000 3071 4641 1 chr1A.!!$F1 1570
16 TraesCS3D01G220900 chr4D 506101640 506102194 554 True 520.0 520 84.258000 4 539 1 chr4D.!!$R2 535
17 TraesCS3D01G220900 chr4D 310011263 310011789 526 False 479.0 479 83.769000 27 539 1 chr4D.!!$F2 512
18 TraesCS3D01G220900 chr4D 437152300 437152813 513 True 438.0 438 82.819000 45 539 1 chr4D.!!$R1 494
19 TraesCS3D01G220900 chr2A 620256960 620257511 551 True 512.0 512 84.050000 4 539 1 chr2A.!!$R2 535
20 TraesCS3D01G220900 chr6D 157160077 157160628 551 True 510.0 510 84.107000 5 539 1 chr6D.!!$R1 534
21 TraesCS3D01G220900 chr6A 57096621 57097150 529 False 490.0 490 83.519000 6 539 1 chr6A.!!$F1 533
22 TraesCS3D01G220900 chr1B 25840222 25840777 555 True 490.0 490 83.304000 1 539 1 chr1B.!!$R1 538
23 TraesCS3D01G220900 chr1B 689386188 689386711 523 False 451.0 451 82.440000 6 539 1 chr1B.!!$F2 533
24 TraesCS3D01G220900 chr2D 563023191 563023737 546 False 486.0 486 83.394000 9 539 1 chr2D.!!$F2 530
25 TraesCS3D01G220900 chr7A 224831843 224832394 551 True 484.0 484 83.184000 4 539 1 chr7A.!!$R1 535


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
402 438 0.107410 AATCTCGCGGGCCAAACATA 60.107 50.000 6.13 0.0 0.00 2.29 F
403 439 0.532862 ATCTCGCGGGCCAAACATAG 60.533 55.000 6.13 0.0 0.00 2.23 F
881 922 0.911769 TTCCTTGGTGCAGATCGGAT 59.088 50.000 0.00 0.0 0.00 4.18 F
1173 1219 1.065928 CCCTGTAGATCGTCCGTGC 59.934 63.158 0.00 0.0 0.00 5.34 F
1926 1980 1.067635 ACCATGTCTGCCGAATTTTGC 60.068 47.619 0.00 0.0 0.00 3.68 F
2000 2055 2.496070 CCGAATCTGGTTAGGACTGTCA 59.504 50.000 10.38 0.0 34.78 3.58 F
3173 4552 1.783711 GATACTCGTGCAGATGAAGCG 59.216 52.381 0.00 0.0 33.85 4.68 F
4172 5578 0.239879 GATTCTTTGCGTTTGGCCGA 59.760 50.000 0.00 0.0 42.61 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2368 1.209128 AGAGACAACACGAACAAGCG 58.791 50.000 0.00 0.00 37.29 4.68 R
2320 2379 7.016361 ACTGTTCATACAAACAAGAGACAAC 57.984 36.000 0.00 0.00 38.60 3.32 R
2607 3598 4.795278 GTGCACAATCATGTTTAAGCTAGC 59.205 41.667 13.17 6.62 37.82 3.42 R
3065 4060 1.202582 AGCGTAGACTTGCCTGTAGTG 59.797 52.381 0.00 0.00 0.00 2.74 R
3069 4064 1.893801 AGTAAGCGTAGACTTGCCTGT 59.106 47.619 0.00 0.00 33.23 4.00 R
3694 5100 4.098501 CCCAAAGCCTCTCCATCATTTTAC 59.901 45.833 0.00 0.00 0.00 2.01 R
5069 6475 1.072965 CCTCCCCTGTGAATAGCATCC 59.927 57.143 0.00 0.00 0.00 3.51 R
6051 7462 1.067916 GCCCAGGTTGCACTTTGTG 59.932 57.895 0.00 0.00 36.51 3.33 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
76 77 8.291888 TCACAAATTCAAAATAATGTTCGTGG 57.708 30.769 0.00 0.00 0.00 4.94
179 183 8.062065 TGATGTTTCTTTATCCGCCTTAAAAT 57.938 30.769 0.00 0.00 0.00 1.82
180 184 7.973388 TGATGTTTCTTTATCCGCCTTAAAATG 59.027 33.333 0.00 0.00 0.00 2.32
381 417 3.117016 TCCGACCAACCCCACTACTATAT 60.117 47.826 0.00 0.00 0.00 0.86
382 418 3.644738 CCGACCAACCCCACTACTATATT 59.355 47.826 0.00 0.00 0.00 1.28
383 419 4.834496 CCGACCAACCCCACTACTATATTA 59.166 45.833 0.00 0.00 0.00 0.98
402 438 0.107410 AATCTCGCGGGCCAAACATA 60.107 50.000 6.13 0.00 0.00 2.29
403 439 0.532862 ATCTCGCGGGCCAAACATAG 60.533 55.000 6.13 0.00 0.00 2.23
433 470 6.183360 CGAGAACACTACAACTCTCTACTCTC 60.183 46.154 0.00 0.00 33.58 3.20
558 599 6.370593 TGCTAATGCAGACTAAAAAGAAACG 58.629 36.000 0.00 0.00 45.31 3.60
559 600 5.795441 GCTAATGCAGACTAAAAAGAAACGG 59.205 40.000 0.00 0.00 39.41 4.44
560 601 6.348213 GCTAATGCAGACTAAAAAGAAACGGA 60.348 38.462 0.00 0.00 39.41 4.69
561 602 5.613358 ATGCAGACTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
562 603 3.813166 TGCAGACTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
563 604 3.188667 GCAGACTAAAAAGAAACGGAGGG 59.811 47.826 0.00 0.00 0.00 4.30
564 605 4.638304 CAGACTAAAAAGAAACGGAGGGA 58.362 43.478 0.00 0.00 0.00 4.20
585 626 6.385467 AGGGAGTATCATTTAGAGCTTCTGTT 59.615 38.462 0.00 0.00 36.25 3.16
614 655 7.834068 TGTTCATAGTAGAGCAGATTTGTTC 57.166 36.000 0.00 0.00 35.03 3.18
672 713 1.269413 ACGACTTGTCCACACTAACCG 60.269 52.381 0.00 0.00 0.00 4.44
788 829 4.569564 CACTATACGTAAGGGCCAAGTTTC 59.430 45.833 6.18 0.00 46.39 2.78
860 901 2.910688 GGGCATTCTCCGAACTATCA 57.089 50.000 0.00 0.00 0.00 2.15
881 922 0.911769 TTCCTTGGTGCAGATCGGAT 59.088 50.000 0.00 0.00 0.00 4.18
920 961 2.183300 GCACGGACAGCCACGATA 59.817 61.111 0.00 0.00 0.00 2.92
955 996 2.509336 GCGCCGTCACTATGCAGT 60.509 61.111 0.00 0.00 34.42 4.40
1101 1147 3.069443 GTCCTCATCTCATTCCTCCTGAC 59.931 52.174 0.00 0.00 0.00 3.51
1110 1156 2.363018 CCTCCTGACAGCGAGGGA 60.363 66.667 22.79 6.24 41.79 4.20
1173 1219 1.065928 CCCTGTAGATCGTCCGTGC 59.934 63.158 0.00 0.00 0.00 5.34
1175 1221 1.939785 CTGTAGATCGTCCGTGCGC 60.940 63.158 0.00 0.00 0.00 6.09
1178 1224 2.110352 TAGATCGTCCGTGCGCTGA 61.110 57.895 9.73 0.00 0.00 4.26
1179 1225 2.319011 TAGATCGTCCGTGCGCTGAC 62.319 60.000 9.73 11.38 0.00 3.51
1180 1226 4.796231 ATCGTCCGTGCGCTGACC 62.796 66.667 15.05 0.00 0.00 4.02
1304 1350 6.071896 TGCCGATCTAATTCTGGTAGATGTAG 60.072 42.308 0.00 0.00 38.22 2.74
1313 1359 8.494016 AATTCTGGTAGATGTAGCTTTTGTAC 57.506 34.615 0.00 0.00 0.00 2.90
1323 1369 4.884744 TGTAGCTTTTGTACCACACAACAT 59.115 37.500 0.00 0.00 46.80 2.71
1511 1561 2.736682 CGCAGGGCCGTAAGTTTCG 61.737 63.158 0.00 0.00 0.00 3.46
1779 1831 5.673337 TGTGTTGCAGTCTAAAGTTCATC 57.327 39.130 0.00 0.00 0.00 2.92
1798 1850 7.538678 AGTTCATCATTCTGCGAAATGTTTAAC 59.461 33.333 9.81 9.39 37.77 2.01
1816 1868 9.667989 ATGTTTAACGTTACAACATTTACCTTC 57.332 29.630 25.98 4.28 37.79 3.46
1880 1932 7.003482 TGGCTTGCATTATATTGATGTCCTTA 58.997 34.615 0.00 0.00 0.00 2.69
1926 1980 1.067635 ACCATGTCTGCCGAATTTTGC 60.068 47.619 0.00 0.00 0.00 3.68
1964 2019 6.159988 GCTTACCTCTGGCACTTATGTATAG 58.840 44.000 0.00 0.00 0.00 1.31
1981 2036 6.570672 TGTATAGAAACATAGGAGCTACCG 57.429 41.667 0.00 0.00 44.74 4.02
1998 2053 2.537143 ACCGAATCTGGTTAGGACTGT 58.463 47.619 6.82 0.00 39.99 3.55
1999 2054 2.496470 ACCGAATCTGGTTAGGACTGTC 59.504 50.000 6.82 0.00 39.99 3.51
2000 2055 2.496070 CCGAATCTGGTTAGGACTGTCA 59.504 50.000 10.38 0.00 34.78 3.58
2001 2056 3.056107 CCGAATCTGGTTAGGACTGTCAA 60.056 47.826 10.38 0.00 34.78 3.18
2013 2072 5.762179 AGGACTGTCAATCATTTCTACCA 57.238 39.130 10.38 0.00 0.00 3.25
2309 2368 4.867086 TCTATGGGGGTTGATCCTTTTTC 58.133 43.478 0.00 0.00 36.25 2.29
2320 2379 2.748461 TCCTTTTTCGCTTGTTCGTG 57.252 45.000 0.00 0.00 0.00 4.35
2403 2462 8.615211 CACAGCATAGCTTGTTTATATTTCTGA 58.385 33.333 0.00 0.00 36.40 3.27
2642 3633 7.362662 ACATGATTGTGCACAGTAAAGTAAAG 58.637 34.615 20.59 6.37 33.85 1.85
2706 3697 7.805163 TCTGATCATCCAGGATTTAAAGCTAA 58.195 34.615 0.00 0.00 34.99 3.09
2742 3733 9.403583 GTCCTGAAGTAAATGGGTGATTATTTA 57.596 33.333 0.00 0.00 0.00 1.40
2861 3852 9.364989 TCTCTCCTGTTTGTTTTTGTTTTAATG 57.635 29.630 0.00 0.00 0.00 1.90
2930 3921 6.206634 TCTGAATTCCAACATTTGTGTACTCC 59.793 38.462 2.27 0.00 0.00 3.85
2937 3928 5.163353 CCAACATTTGTGTACTCCCCTTTTT 60.163 40.000 0.00 0.00 0.00 1.94
2983 3974 5.236478 GCTCTATCTTTATGGCGTTTTAGCA 59.764 40.000 0.00 0.00 39.27 3.49
3019 4010 8.251750 TGTTCAATATTAAGAGTGTGCACTAC 57.748 34.615 19.41 14.16 42.66 2.73
3020 4011 8.094548 TGTTCAATATTAAGAGTGTGCACTACT 58.905 33.333 19.41 18.59 42.66 2.57
3021 4012 8.383619 GTTCAATATTAAGAGTGTGCACTACTG 58.616 37.037 21.48 4.13 42.66 2.74
3032 4023 5.874810 AGTGTGCACTACTGGTAATTACATG 59.125 40.000 19.41 10.91 40.43 3.21
3041 4036 8.946085 ACTACTGGTAATTACATGTCATGTTTG 58.054 33.333 23.05 6.17 41.63 2.93
3047 4042 4.740741 TTACATGTCATGTTTGTGACCG 57.259 40.909 23.05 0.00 46.17 4.79
3065 4060 4.273969 TGACCGTGTTCATGGTTTTAACTC 59.726 41.667 16.42 4.52 38.99 3.01
3068 4063 4.274950 CCGTGTTCATGGTTTTAACTCACT 59.725 41.667 3.13 0.00 0.00 3.41
3069 4064 5.467399 CCGTGTTCATGGTTTTAACTCACTA 59.533 40.000 3.13 0.00 0.00 2.74
3173 4552 1.783711 GATACTCGTGCAGATGAAGCG 59.216 52.381 0.00 0.00 33.85 4.68
4172 5578 0.239879 GATTCTTTGCGTTTGGCCGA 59.760 50.000 0.00 0.00 42.61 5.54
4355 5761 1.202348 GTTGCTATGGTTGGCTTGGAC 59.798 52.381 0.00 0.00 0.00 4.02
4685 6091 0.596577 TCTCTTTCCGTGAGACCGTG 59.403 55.000 0.00 0.00 35.86 4.94
4955 6361 4.081642 TGCAAGGGAGTACAGTATCTGAAC 60.082 45.833 3.70 0.00 35.18 3.18
5051 6457 2.819608 TGGTATTTGCTTTGAGGTCTGC 59.180 45.455 0.00 0.00 0.00 4.26
5069 6475 1.844003 CGACGTTGTTCTCCACACG 59.156 57.895 0.00 0.00 33.98 4.49
5087 6493 0.758734 CGGATGCTATTCACAGGGGA 59.241 55.000 0.00 0.00 0.00 4.81
5524 6933 5.772169 AGGACAAGCTCTAAATTTTTGCTCT 59.228 36.000 11.00 4.02 33.10 4.09
5543 6952 6.442112 TGCTCTCATGTTATCTGTTATCTCG 58.558 40.000 0.00 0.00 0.00 4.04
5561 6970 6.966534 ATCTCGGCCAATTTTTGATCTATT 57.033 33.333 2.24 0.00 0.00 1.73
5621 7030 2.099405 AGTTCCTTGGGTTGTGTTGTG 58.901 47.619 0.00 0.00 0.00 3.33
5759 7170 4.985538 TCTTATGTTTGAGAACCTTGGCT 58.014 39.130 0.00 0.00 34.80 4.75
5767 7178 5.767816 TTGAGAACCTTGGCTAGTTTTTC 57.232 39.130 0.00 0.00 0.00 2.29
5791 7202 5.327091 CAATGTTTCCTTGCGTCTGATAAG 58.673 41.667 0.00 0.00 0.00 1.73
5792 7203 4.265904 TGTTTCCTTGCGTCTGATAAGA 57.734 40.909 0.00 0.00 0.00 2.10
5793 7204 3.994392 TGTTTCCTTGCGTCTGATAAGAC 59.006 43.478 0.00 0.00 35.59 3.01
5912 7323 5.931532 ACGCTCATTGATTCTGTTTGTAAG 58.068 37.500 0.00 0.00 0.00 2.34
5977 7388 5.606505 TGCAATGAGAAACACTGTACACTA 58.393 37.500 0.00 0.00 0.00 2.74
6051 7462 9.199982 CCATAAAATACATCAGCATTCCAATTC 57.800 33.333 0.00 0.00 0.00 2.17
6120 7563 1.352017 ACATTGTCCATGTGCTCTGGA 59.648 47.619 0.00 3.71 45.12 3.86
6322 7779 7.781548 ATGCAATTGAAATAGCAAATCTTCC 57.218 32.000 10.34 0.00 40.76 3.46
6378 7835 6.542005 TGATTTTAAACTCTTGACTGCACTCA 59.458 34.615 7.05 0.00 0.00 3.41
6437 7894 7.065563 GTCTGACAGAAGCATAAGAAATGTGAT 59.934 37.037 6.76 0.00 0.00 3.06
6523 7980 5.353678 GTCAAGATGAAAGGGAGAGTGATTG 59.646 44.000 0.00 0.00 0.00 2.67
6631 8089 2.044551 CCCTGCTCCCTTTCTGCC 60.045 66.667 0.00 0.00 0.00 4.85
6659 8117 8.565896 TGTGCATGAACTTGACTCTTATTATT 57.434 30.769 5.18 0.00 0.00 1.40
6660 8118 8.453320 TGTGCATGAACTTGACTCTTATTATTG 58.547 33.333 5.18 0.00 0.00 1.90
6661 8119 8.454106 GTGCATGAACTTGACTCTTATTATTGT 58.546 33.333 0.00 0.00 0.00 2.71
6662 8120 9.013229 TGCATGAACTTGACTCTTATTATTGTT 57.987 29.630 0.00 0.00 0.00 2.83
6692 8150 8.630917 TGTATATAGTCTCTCTTGCACTTTACC 58.369 37.037 0.00 0.00 0.00 2.85
6693 8151 7.661536 ATATAGTCTCTCTTGCACTTTACCA 57.338 36.000 0.00 0.00 0.00 3.25
6694 8152 4.899352 AGTCTCTCTTGCACTTTACCAT 57.101 40.909 0.00 0.00 0.00 3.55
6695 8153 7.661536 ATAGTCTCTCTTGCACTTTACCATA 57.338 36.000 0.00 0.00 0.00 2.74
6696 8154 5.725362 AGTCTCTCTTGCACTTTACCATAC 58.275 41.667 0.00 0.00 0.00 2.39
6697 8155 5.246203 AGTCTCTCTTGCACTTTACCATACA 59.754 40.000 0.00 0.00 0.00 2.29
6698 8156 6.070538 AGTCTCTCTTGCACTTTACCATACAT 60.071 38.462 0.00 0.00 0.00 2.29
6699 8157 7.124298 AGTCTCTCTTGCACTTTACCATACATA 59.876 37.037 0.00 0.00 0.00 2.29
6700 8158 7.928706 GTCTCTCTTGCACTTTACCATACATAT 59.071 37.037 0.00 0.00 0.00 1.78
6701 8159 7.928167 TCTCTCTTGCACTTTACCATACATATG 59.072 37.037 0.00 0.00 0.00 1.78
6702 8160 6.483307 TCTCTTGCACTTTACCATACATATGC 59.517 38.462 1.58 0.00 32.40 3.14
6703 8161 6.118852 TCTTGCACTTTACCATACATATGCA 58.881 36.000 1.58 0.00 39.90 3.96
6704 8162 6.772233 TCTTGCACTTTACCATACATATGCAT 59.228 34.615 3.79 3.79 41.13 3.96
6705 8163 7.936301 TCTTGCACTTTACCATACATATGCATA 59.064 33.333 9.27 9.27 41.13 3.14
6706 8164 8.634335 TTGCACTTTACCATACATATGCATAT 57.366 30.769 13.63 13.63 41.13 1.78
6707 8165 8.042944 TGCACTTTACCATACATATGCATATG 57.957 34.615 34.80 34.80 44.37 1.78
6717 8175 4.226427 CATATGCATATGTACTGGCCCT 57.774 45.455 30.55 0.76 36.31 5.19
6718 8176 4.592942 CATATGCATATGTACTGGCCCTT 58.407 43.478 30.55 0.57 36.31 3.95
6719 8177 2.346766 TGCATATGTACTGGCCCTTG 57.653 50.000 0.00 0.00 0.00 3.61
6720 8178 1.133823 TGCATATGTACTGGCCCTTGG 60.134 52.381 0.00 0.00 0.00 3.61
6730 8188 4.748144 GCCCTTGGCCCTCCTGTG 62.748 72.222 0.00 0.00 44.06 3.66
6731 8189 2.935481 CCCTTGGCCCTCCTGTGA 60.935 66.667 0.00 0.00 0.00 3.58
6732 8190 2.538141 CCCTTGGCCCTCCTGTGAA 61.538 63.158 0.00 0.00 0.00 3.18
6733 8191 1.693640 CCTTGGCCCTCCTGTGAAT 59.306 57.895 0.00 0.00 0.00 2.57
6734 8192 0.682209 CCTTGGCCCTCCTGTGAATG 60.682 60.000 0.00 0.00 0.00 2.67
6735 8193 1.304381 TTGGCCCTCCTGTGAATGC 60.304 57.895 0.00 0.00 0.00 3.56
6736 8194 2.079088 TTGGCCCTCCTGTGAATGCA 62.079 55.000 0.00 0.00 0.00 3.96
6737 8195 1.751927 GGCCCTCCTGTGAATGCAG 60.752 63.158 0.00 0.00 36.31 4.41
6738 8196 1.001641 GCCCTCCTGTGAATGCAGT 60.002 57.895 0.00 0.00 34.84 4.40
6739 8197 0.610232 GCCCTCCTGTGAATGCAGTT 60.610 55.000 0.00 0.00 34.84 3.16
6740 8198 1.171308 CCCTCCTGTGAATGCAGTTG 58.829 55.000 0.00 0.00 34.84 3.16
6741 8199 0.524862 CCTCCTGTGAATGCAGTTGC 59.475 55.000 0.00 0.00 42.50 4.17
6742 8200 0.524862 CTCCTGTGAATGCAGTTGCC 59.475 55.000 1.06 0.00 41.18 4.52
6743 8201 0.895100 TCCTGTGAATGCAGTTGCCC 60.895 55.000 1.06 0.00 41.18 5.36
6744 8202 1.180456 CCTGTGAATGCAGTTGCCCA 61.180 55.000 1.06 0.00 41.18 5.36
6745 8203 0.892755 CTGTGAATGCAGTTGCCCAT 59.107 50.000 1.06 0.00 41.18 4.00
6746 8204 1.274167 CTGTGAATGCAGTTGCCCATT 59.726 47.619 1.06 0.00 41.18 3.16
6747 8205 1.273048 TGTGAATGCAGTTGCCCATTC 59.727 47.619 1.06 6.03 44.64 2.67
6748 8206 0.896923 TGAATGCAGTTGCCCATTCC 59.103 50.000 12.06 0.36 44.08 3.01
6749 8207 1.188863 GAATGCAGTTGCCCATTCCT 58.811 50.000 1.06 0.00 40.73 3.36
6750 8208 2.291475 TGAATGCAGTTGCCCATTCCTA 60.291 45.455 12.06 0.00 44.08 2.94
6751 8209 2.530460 ATGCAGTTGCCCATTCCTAA 57.470 45.000 1.06 0.00 41.18 2.69
6752 8210 1.544724 TGCAGTTGCCCATTCCTAAC 58.455 50.000 1.06 0.00 41.18 2.34
6753 8211 1.202989 TGCAGTTGCCCATTCCTAACA 60.203 47.619 1.06 0.00 41.18 2.41
6754 8212 2.102578 GCAGTTGCCCATTCCTAACAT 58.897 47.619 0.00 0.00 34.31 2.71
6755 8213 2.159198 GCAGTTGCCCATTCCTAACATG 60.159 50.000 0.00 0.00 34.31 3.21
6756 8214 2.428171 CAGTTGCCCATTCCTAACATGG 59.572 50.000 0.00 0.00 41.02 3.66
6757 8215 2.042979 AGTTGCCCATTCCTAACATGGT 59.957 45.455 0.00 0.00 39.86 3.55
6758 8216 3.268334 AGTTGCCCATTCCTAACATGGTA 59.732 43.478 0.00 0.00 39.86 3.25
6759 8217 4.079212 AGTTGCCCATTCCTAACATGGTAT 60.079 41.667 0.00 0.00 39.86 2.73
6760 8218 4.098914 TGCCCATTCCTAACATGGTATC 57.901 45.455 0.00 0.00 39.86 2.24
6761 8219 3.461458 TGCCCATTCCTAACATGGTATCA 59.539 43.478 0.00 0.00 39.86 2.15
6762 8220 4.074970 GCCCATTCCTAACATGGTATCAG 58.925 47.826 0.00 0.00 39.86 2.90
6763 8221 4.202461 GCCCATTCCTAACATGGTATCAGA 60.202 45.833 0.00 0.00 39.86 3.27
6764 8222 5.515534 GCCCATTCCTAACATGGTATCAGAT 60.516 44.000 0.00 0.00 39.86 2.90
6765 8223 5.942236 CCCATTCCTAACATGGTATCAGATG 59.058 44.000 0.00 0.00 39.86 2.90
6766 8224 5.413833 CCATTCCTAACATGGTATCAGATGC 59.586 44.000 0.00 0.00 37.07 3.91
6767 8225 5.894298 TTCCTAACATGGTATCAGATGCT 57.106 39.130 0.00 0.00 0.00 3.79
6768 8226 5.894298 TCCTAACATGGTATCAGATGCTT 57.106 39.130 0.00 0.00 0.00 3.91
6769 8227 6.994421 TCCTAACATGGTATCAGATGCTTA 57.006 37.500 0.00 0.00 0.00 3.09
6770 8228 6.997655 TCCTAACATGGTATCAGATGCTTAG 58.002 40.000 0.00 0.00 0.00 2.18
6771 8229 6.014242 TCCTAACATGGTATCAGATGCTTAGG 60.014 42.308 13.79 13.79 36.25 2.69
6772 8230 5.636903 AACATGGTATCAGATGCTTAGGT 57.363 39.130 0.00 0.00 0.00 3.08
6773 8231 5.636903 ACATGGTATCAGATGCTTAGGTT 57.363 39.130 0.00 0.00 0.00 3.50
6774 8232 5.615289 ACATGGTATCAGATGCTTAGGTTC 58.385 41.667 0.00 0.00 0.00 3.62
6775 8233 4.689612 TGGTATCAGATGCTTAGGTTCC 57.310 45.455 0.00 0.00 0.00 3.62
6776 8234 4.298626 TGGTATCAGATGCTTAGGTTCCT 58.701 43.478 0.00 0.00 0.00 3.36
6777 8235 4.345257 TGGTATCAGATGCTTAGGTTCCTC 59.655 45.833 0.00 0.00 0.00 3.71
6778 8236 4.591072 GGTATCAGATGCTTAGGTTCCTCT 59.409 45.833 0.00 0.00 0.00 3.69
6779 8237 4.953940 ATCAGATGCTTAGGTTCCTCTC 57.046 45.455 0.00 0.00 0.00 3.20
6780 8238 3.034635 TCAGATGCTTAGGTTCCTCTCC 58.965 50.000 0.00 0.00 0.00 3.71
6781 8239 3.037549 CAGATGCTTAGGTTCCTCTCCT 58.962 50.000 0.00 0.00 38.91 3.69
6782 8240 3.037549 AGATGCTTAGGTTCCTCTCCTG 58.962 50.000 0.00 0.00 36.60 3.86
6783 8241 0.905357 TGCTTAGGTTCCTCTCCTGC 59.095 55.000 0.00 0.00 36.60 4.85
6784 8242 1.199615 GCTTAGGTTCCTCTCCTGCT 58.800 55.000 0.00 0.00 36.60 4.24
6785 8243 1.138069 GCTTAGGTTCCTCTCCTGCTC 59.862 57.143 0.00 0.00 36.60 4.26
6786 8244 1.760029 CTTAGGTTCCTCTCCTGCTCC 59.240 57.143 0.00 0.00 36.60 4.70
6787 8245 0.032017 TAGGTTCCTCTCCTGCTCCC 60.032 60.000 0.00 0.00 36.60 4.30
6788 8246 2.726351 GGTTCCTCTCCTGCTCCCG 61.726 68.421 0.00 0.00 0.00 5.14
6789 8247 3.077556 TTCCTCTCCTGCTCCCGC 61.078 66.667 0.00 0.00 0.00 6.13
6790 8248 3.905153 TTCCTCTCCTGCTCCCGCA 62.905 63.158 0.00 0.00 45.60 5.69
6791 8249 3.160047 CCTCTCCTGCTCCCGCAT 61.160 66.667 0.00 0.00 46.74 4.73
6792 8250 2.108566 CTCTCCTGCTCCCGCATG 59.891 66.667 0.00 0.00 46.74 4.06
6793 8251 4.166888 TCTCCTGCTCCCGCATGC 62.167 66.667 7.91 7.91 46.74 4.06
6794 8252 4.172512 CTCCTGCTCCCGCATGCT 62.173 66.667 17.13 0.00 46.74 3.79
6795 8253 4.166888 TCCTGCTCCCGCATGCTC 62.167 66.667 17.13 0.17 46.74 4.26
6839 8297 4.862823 GCCGGCCTCCCTCTACCT 62.863 72.222 18.11 0.00 0.00 3.08
6840 8298 2.522193 CCGGCCTCCCTCTACCTC 60.522 72.222 0.00 0.00 0.00 3.85
6841 8299 2.907917 CGGCCTCCCTCTACCTCG 60.908 72.222 0.00 0.00 0.00 4.63
6842 8300 2.279408 GGCCTCCCTCTACCTCGT 59.721 66.667 0.00 0.00 0.00 4.18
6843 8301 1.829096 GGCCTCCCTCTACCTCGTC 60.829 68.421 0.00 0.00 0.00 4.20
6844 8302 2.188161 GCCTCCCTCTACCTCGTCG 61.188 68.421 0.00 0.00 0.00 5.12
6845 8303 2.188161 CCTCCCTCTACCTCGTCGC 61.188 68.421 0.00 0.00 0.00 5.19
6846 8304 2.124403 TCCCTCTACCTCGTCGCC 60.124 66.667 0.00 0.00 0.00 5.54
6847 8305 3.584052 CCCTCTACCTCGTCGCCG 61.584 72.222 0.00 0.00 0.00 6.46
6848 8306 3.584052 CCTCTACCTCGTCGCCGG 61.584 72.222 0.00 0.00 33.95 6.13
6849 8307 4.253257 CTCTACCTCGTCGCCGGC 62.253 72.222 19.07 19.07 33.95 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 156 7.455641 TTTTAAGGCGGATAAAGAAACATCA 57.544 32.000 0.00 0.00 0.00 3.07
155 157 7.973944 ACATTTTAAGGCGGATAAAGAAACATC 59.026 33.333 0.00 0.00 0.00 3.06
162 165 6.751888 CAGGAAACATTTTAAGGCGGATAAAG 59.248 38.462 0.00 0.00 0.00 1.85
166 169 4.086457 ACAGGAAACATTTTAAGGCGGAT 58.914 39.130 0.00 0.00 0.00 4.18
179 183 7.513968 CAAACATTTTTCGAAAACAGGAAACA 58.486 30.769 22.41 6.35 32.30 2.83
180 184 6.464519 GCAAACATTTTTCGAAAACAGGAAAC 59.535 34.615 22.41 7.54 32.30 2.78
273 306 3.008594 TGGCGACCTCCTGATTTTTCTTA 59.991 43.478 0.00 0.00 0.00 2.10
292 325 0.951040 CTCCTTGTCGAGGTTGTGGC 60.951 60.000 6.00 0.00 46.39 5.01
320 353 5.163652 CCAACTCGTGTCTTTTCTTTCCTTT 60.164 40.000 0.00 0.00 0.00 3.11
328 364 3.493503 CACTACCCAACTCGTGTCTTTTC 59.506 47.826 0.00 0.00 0.00 2.29
381 417 0.321741 TGTTTGGCCCGCGAGATTAA 60.322 50.000 8.23 0.00 0.00 1.40
382 418 0.107410 ATGTTTGGCCCGCGAGATTA 60.107 50.000 8.23 0.00 0.00 1.75
383 419 0.107410 TATGTTTGGCCCGCGAGATT 60.107 50.000 8.23 0.00 0.00 2.40
402 438 0.956633 TTGTAGTGTTCTCGCGGACT 59.043 50.000 6.13 3.63 0.00 3.85
403 439 1.058404 GTTGTAGTGTTCTCGCGGAC 58.942 55.000 6.13 3.57 0.00 4.79
539 580 4.455877 CCTCCGTTTCTTTTTAGTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
542 583 4.638304 TCCCTCCGTTTCTTTTTAGTCTG 58.362 43.478 0.00 0.00 0.00 3.51
543 584 4.347292 ACTCCCTCCGTTTCTTTTTAGTCT 59.653 41.667 0.00 0.00 0.00 3.24
544 585 4.639334 ACTCCCTCCGTTTCTTTTTAGTC 58.361 43.478 0.00 0.00 0.00 2.59
545 586 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
546 587 6.403878 TGATACTCCCTCCGTTTCTTTTTAG 58.596 40.000 0.00 0.00 0.00 1.85
547 588 6.363167 TGATACTCCCTCCGTTTCTTTTTA 57.637 37.500 0.00 0.00 0.00 1.52
548 589 5.237236 TGATACTCCCTCCGTTTCTTTTT 57.763 39.130 0.00 0.00 0.00 1.94
549 590 4.903045 TGATACTCCCTCCGTTTCTTTT 57.097 40.909 0.00 0.00 0.00 2.27
550 591 5.437191 AATGATACTCCCTCCGTTTCTTT 57.563 39.130 0.00 0.00 0.00 2.52
551 592 5.437191 AAATGATACTCCCTCCGTTTCTT 57.563 39.130 0.00 0.00 0.00 2.52
552 593 5.897824 TCTAAATGATACTCCCTCCGTTTCT 59.102 40.000 0.00 0.00 0.00 2.52
553 594 6.158023 TCTAAATGATACTCCCTCCGTTTC 57.842 41.667 0.00 0.00 0.00 2.78
554 595 5.453480 GCTCTAAATGATACTCCCTCCGTTT 60.453 44.000 0.00 0.00 0.00 3.60
555 596 4.039366 GCTCTAAATGATACTCCCTCCGTT 59.961 45.833 0.00 0.00 0.00 4.44
556 597 3.574826 GCTCTAAATGATACTCCCTCCGT 59.425 47.826 0.00 0.00 0.00 4.69
557 598 3.829601 AGCTCTAAATGATACTCCCTCCG 59.170 47.826 0.00 0.00 0.00 4.63
558 599 5.542251 AGAAGCTCTAAATGATACTCCCTCC 59.458 44.000 0.00 0.00 0.00 4.30
559 600 6.041523 ACAGAAGCTCTAAATGATACTCCCTC 59.958 42.308 0.00 0.00 0.00 4.30
560 601 5.902431 ACAGAAGCTCTAAATGATACTCCCT 59.098 40.000 0.00 0.00 0.00 4.20
561 602 6.168270 ACAGAAGCTCTAAATGATACTCCC 57.832 41.667 0.00 0.00 0.00 4.30
562 603 8.634444 TCTAACAGAAGCTCTAAATGATACTCC 58.366 37.037 0.00 0.00 0.00 3.85
585 626 9.755804 CAAATCTGCTCTACTATGAACATTCTA 57.244 33.333 0.00 0.00 0.00 2.10
614 655 7.285401 AGCCAAAATACCAATGTGAATACTAGG 59.715 37.037 0.00 0.00 0.00 3.02
672 713 0.106708 TATGCAGCCTCCGGTCAATC 59.893 55.000 0.00 0.00 0.00 2.67
721 762 5.125578 GCCCTTACTCTTCCATTTTTACCTG 59.874 44.000 0.00 0.00 0.00 4.00
722 763 5.262009 GCCCTTACTCTTCCATTTTTACCT 58.738 41.667 0.00 0.00 0.00 3.08
723 764 4.401519 GGCCCTTACTCTTCCATTTTTACC 59.598 45.833 0.00 0.00 0.00 2.85
788 829 5.526846 GCCACTCTTCCATCTCTCAAATAAG 59.473 44.000 0.00 0.00 0.00 1.73
842 883 3.460857 AGTGATAGTTCGGAGAATGCC 57.539 47.619 0.00 0.00 45.90 4.40
860 901 0.036010 CCGATCTGCACCAAGGAAGT 60.036 55.000 0.00 0.00 0.00 3.01
1110 1156 3.242867 TGTTGTCTCACCTTGAGGATCT 58.757 45.455 3.59 0.00 44.39 2.75
1175 1221 0.588252 CAAAACCACTCAGCGGTCAG 59.412 55.000 0.00 0.00 34.99 3.51
1178 1224 0.818040 GACCAAAACCACTCAGCGGT 60.818 55.000 0.00 0.00 38.85 5.68
1179 1225 1.515521 GGACCAAAACCACTCAGCGG 61.516 60.000 0.00 0.00 0.00 5.52
1180 1226 0.817634 TGGACCAAAACCACTCAGCG 60.818 55.000 0.00 0.00 32.03 5.18
1181 1227 0.954452 CTGGACCAAAACCACTCAGC 59.046 55.000 0.00 0.00 33.57 4.26
1182 1228 0.954452 GCTGGACCAAAACCACTCAG 59.046 55.000 0.00 0.00 33.57 3.35
1211 1257 2.543777 TTCCACGGGAAGAACAAGAG 57.456 50.000 1.68 0.00 36.71 2.85
1313 1359 2.425143 ATCTAGGGCATGTTGTGTGG 57.575 50.000 0.00 0.00 0.00 4.17
1323 1369 3.189606 TCAGGGAGAAAAATCTAGGGCA 58.810 45.455 0.00 0.00 0.00 5.36
1477 1527 4.202111 GCCCTGCGGAAACAATACATTTAT 60.202 41.667 0.00 0.00 0.00 1.40
1502 1552 2.750948 TGTCACTCTGCCGAAACTTAC 58.249 47.619 0.00 0.00 0.00 2.34
1511 1561 3.136763 CACATATCCATGTCACTCTGCC 58.863 50.000 0.00 0.00 43.73 4.85
1571 1621 5.602458 TCGCATGAATCAGAAGCATAATC 57.398 39.130 0.00 0.00 0.00 1.75
1580 1630 5.520376 TCTAGTGAATCGCATGAATCAGA 57.480 39.130 0.00 0.00 34.76 3.27
1779 1831 6.575572 TGTAACGTTAAACATTTCGCAGAATG 59.424 34.615 10.11 7.32 45.90 2.67
1816 1868 8.642885 GTCTATATTAGATTCTGCATGACAACG 58.357 37.037 0.00 0.00 37.13 4.10
1880 1932 7.628769 AAAAATCAAAGCACAGGTTGAAAAT 57.371 28.000 0.00 0.00 37.31 1.82
1917 1971 2.925563 GAGCATGGAAAGGCAAAATTCG 59.074 45.455 0.00 0.00 0.00 3.34
1926 1980 2.019984 GGTAAGCAGAGCATGGAAAGG 58.980 52.381 0.00 0.00 0.00 3.11
1964 2019 4.985409 CAGATTCGGTAGCTCCTATGTTTC 59.015 45.833 0.00 0.00 0.00 2.78
1981 2036 5.734720 TGATTGACAGTCCTAACCAGATTC 58.265 41.667 0.00 0.00 0.00 2.52
1998 2053 4.229353 TCACCCCATGGTAGAAATGATTGA 59.771 41.667 11.73 0.00 45.57 2.57
1999 2054 4.535781 TCACCCCATGGTAGAAATGATTG 58.464 43.478 11.73 0.00 45.57 2.67
2000 2055 4.879295 TCACCCCATGGTAGAAATGATT 57.121 40.909 11.73 0.00 45.57 2.57
2001 2056 5.103558 TGAATCACCCCATGGTAGAAATGAT 60.104 40.000 11.73 7.31 45.57 2.45
2013 2072 5.983333 AGAAGATTACTGAATCACCCCAT 57.017 39.130 0.87 0.00 43.51 4.00
2050 2109 9.265901 CCAAGTTAGAATCCATGTAATCACTAG 57.734 37.037 0.00 0.00 0.00 2.57
2055 2114 9.614792 AGTAACCAAGTTAGAATCCATGTAATC 57.385 33.333 0.00 0.00 0.00 1.75
2309 2368 1.209128 AGAGACAACACGAACAAGCG 58.791 50.000 0.00 0.00 37.29 4.68
2320 2379 7.016361 ACTGTTCATACAAACAAGAGACAAC 57.984 36.000 0.00 0.00 38.60 3.32
2457 2516 6.643770 GCAAAACAAGAGACATCATGAACAAT 59.356 34.615 0.00 0.00 0.00 2.71
2607 3598 4.795278 GTGCACAATCATGTTTAAGCTAGC 59.205 41.667 13.17 6.62 37.82 3.42
2642 3633 6.015434 AGGAACAAACAGGTTATCCATTGAAC 60.015 38.462 5.27 0.00 35.89 3.18
2706 3697 8.531146 CCCATTTACTTCAGGACAATACAAAAT 58.469 33.333 0.00 0.00 0.00 1.82
2742 3733 7.259161 ACACAAAATACAACCAACACGTATTT 58.741 30.769 0.00 0.00 43.94 1.40
2747 3738 6.195613 CAGTAACACAAAATACAACCAACACG 59.804 38.462 0.00 0.00 0.00 4.49
2832 3823 5.567138 ACAAAAACAAACAGGAGAGACAG 57.433 39.130 0.00 0.00 0.00 3.51
2905 3896 6.206634 GGAGTACACAAATGTTGGAATTCAGA 59.793 38.462 7.93 0.00 40.48 3.27
2937 3928 2.217750 CAGTCGAAACATTGACCCACA 58.782 47.619 0.00 0.00 35.71 4.17
3019 4010 7.750458 GTCACAAACATGACATGTAATTACCAG 59.250 37.037 21.10 7.83 46.89 4.00
3020 4011 7.589395 GTCACAAACATGACATGTAATTACCA 58.411 34.615 21.10 4.15 46.89 3.25
3032 4023 2.353269 TGAACACGGTCACAAACATGAC 59.647 45.455 0.00 0.00 46.95 3.06
3041 4036 4.035909 AGTTAAAACCATGAACACGGTCAC 59.964 41.667 0.00 0.00 33.17 3.67
3047 4042 7.254227 TGTAGTGAGTTAAAACCATGAACAC 57.746 36.000 0.00 0.00 0.00 3.32
3065 4060 1.202582 AGCGTAGACTTGCCTGTAGTG 59.797 52.381 0.00 0.00 0.00 2.74
3068 4063 3.087031 AGTAAGCGTAGACTTGCCTGTA 58.913 45.455 0.00 0.00 33.23 2.74
3069 4064 1.893801 AGTAAGCGTAGACTTGCCTGT 59.106 47.619 0.00 0.00 33.23 4.00
3173 4552 5.448632 GGATTTGATTGTGATACCACGTTCC 60.449 44.000 0.00 0.00 46.06 3.62
3551 4951 6.529125 CACCAAGTTTTGCATCTTCATATGTC 59.471 38.462 1.90 0.00 0.00 3.06
3694 5100 4.098501 CCCAAAGCCTCTCCATCATTTTAC 59.901 45.833 0.00 0.00 0.00 2.01
4145 5551 2.489938 ACGCAAAGAATCTGCCCTTA 57.510 45.000 0.00 0.00 36.40 2.69
4355 5761 4.778534 AGCATTCTTTGTGATGAACTGG 57.221 40.909 0.00 0.00 0.00 4.00
4478 5884 2.778299 TCCACAAGTTTGGGAAGATCG 58.222 47.619 0.00 0.00 37.24 3.69
4685 6091 2.394563 GCGGCAGGACTTCTCAAGC 61.395 63.158 0.00 0.00 0.00 4.01
4955 6361 2.157668 CACAACGGAGTCCTTGATTTCG 59.842 50.000 21.20 4.46 45.00 3.46
5051 6457 1.545614 CCGTGTGGAGAACAACGTCG 61.546 60.000 0.00 0.00 41.57 5.12
5069 6475 1.072965 CCTCCCCTGTGAATAGCATCC 59.927 57.143 0.00 0.00 0.00 3.51
5087 6493 1.990060 CGGGATGACCTGACCACCT 60.990 63.158 0.00 0.00 44.87 4.00
5524 6933 4.343814 TGGCCGAGATAACAGATAACATGA 59.656 41.667 0.00 0.00 0.00 3.07
5543 6952 6.643388 ACCAAGAATAGATCAAAAATTGGCC 58.357 36.000 15.09 0.00 39.62 5.36
5561 6970 3.643320 ACATCTCTTGACACAGACCAAGA 59.357 43.478 0.00 0.00 44.38 3.02
5591 7000 2.640826 ACCCAAGGAACTGGAATACGAA 59.359 45.455 0.00 0.00 40.86 3.85
5592 7001 2.262637 ACCCAAGGAACTGGAATACGA 58.737 47.619 0.00 0.00 40.86 3.43
5621 7030 3.528597 AGAGACCGAAATAGGTTCAGC 57.471 47.619 0.00 0.00 46.09 4.26
5669 7078 7.443272 TCAACCACTCAATCAAGCATATCATAG 59.557 37.037 0.00 0.00 0.00 2.23
5759 7170 5.163499 ACGCAAGGAAACATTGGAAAAACTA 60.163 36.000 0.00 0.00 46.39 2.24
5767 7178 1.879380 TCAGACGCAAGGAAACATTGG 59.121 47.619 0.00 0.00 46.39 3.16
5791 7202 1.541379 ATAAAACCAGTTGGGGCGTC 58.459 50.000 2.79 0.00 42.91 5.19
5792 7203 1.616374 CAATAAAACCAGTTGGGGCGT 59.384 47.619 2.79 0.00 42.91 5.68
5793 7204 1.889829 TCAATAAAACCAGTTGGGGCG 59.110 47.619 2.79 0.00 42.91 6.13
5887 7298 5.940192 ACAAACAGAATCAATGAGCGTAA 57.060 34.783 0.00 0.00 0.00 3.18
5999 7410 7.492994 GGGTGTTTCTTAAGTTAAATGCAACAA 59.507 33.333 1.63 0.00 0.00 2.83
6051 7462 1.067916 GCCCAGGTTGCACTTTGTG 59.932 57.895 0.00 0.00 36.51 3.33
6120 7563 9.739276 TTCAAGAGTGAACTTCCATTTATATGT 57.261 29.630 0.00 0.00 38.88 2.29
6322 7779 9.074576 AGTAAAAACAGAAATTACCAGGGTTAG 57.925 33.333 0.00 0.00 31.43 2.34
6523 7980 4.285851 GCATCTATACGCCAGCCC 57.714 61.111 0.00 0.00 0.00 5.19
6631 8089 2.545526 AGAGTCAAGTTCATGCACAACG 59.454 45.455 0.00 0.00 0.00 4.10
6666 8124 8.630917 GGTAAAGTGCAAGAGAGACTATATACA 58.369 37.037 0.00 0.00 0.00 2.29
6667 8125 8.630917 TGGTAAAGTGCAAGAGAGACTATATAC 58.369 37.037 0.00 0.00 0.00 1.47
6668 8126 8.762481 TGGTAAAGTGCAAGAGAGACTATATA 57.238 34.615 0.00 0.00 0.00 0.86
6669 8127 7.661536 TGGTAAAGTGCAAGAGAGACTATAT 57.338 36.000 0.00 0.00 0.00 0.86
6670 8128 7.661536 ATGGTAAAGTGCAAGAGAGACTATA 57.338 36.000 0.00 0.00 0.00 1.31
6671 8129 6.552445 ATGGTAAAGTGCAAGAGAGACTAT 57.448 37.500 0.00 0.00 0.00 2.12
6672 8130 6.436218 TGTATGGTAAAGTGCAAGAGAGACTA 59.564 38.462 0.00 0.00 0.00 2.59
6673 8131 4.899352 ATGGTAAAGTGCAAGAGAGACT 57.101 40.909 0.00 0.00 0.00 3.24
6674 8132 5.479306 TGTATGGTAAAGTGCAAGAGAGAC 58.521 41.667 0.00 0.00 0.00 3.36
6675 8133 5.738619 TGTATGGTAAAGTGCAAGAGAGA 57.261 39.130 0.00 0.00 0.00 3.10
6676 8134 7.307632 GCATATGTATGGTAAAGTGCAAGAGAG 60.308 40.741 4.29 0.00 34.32 3.20
6677 8135 6.483307 GCATATGTATGGTAAAGTGCAAGAGA 59.517 38.462 4.29 0.00 34.32 3.10
6678 8136 6.260714 TGCATATGTATGGTAAAGTGCAAGAG 59.739 38.462 4.29 0.00 38.27 2.85
6679 8137 6.118852 TGCATATGTATGGTAAAGTGCAAGA 58.881 36.000 4.29 0.00 38.27 3.02
6680 8138 6.375945 TGCATATGTATGGTAAAGTGCAAG 57.624 37.500 4.29 0.00 38.27 4.01
6681 8139 6.957920 ATGCATATGTATGGTAAAGTGCAA 57.042 33.333 5.40 0.00 43.48 4.08
6682 8140 8.042944 CATATGCATATGTATGGTAAAGTGCA 57.957 34.615 30.55 0.00 44.24 4.57
6696 8154 4.226427 AGGGCCAGTACATATGCATATG 57.774 45.455 34.80 34.80 44.37 1.78
6697 8155 4.568380 CCAAGGGCCAGTACATATGCATAT 60.568 45.833 13.63 13.63 0.00 1.78
6698 8156 3.244875 CCAAGGGCCAGTACATATGCATA 60.245 47.826 9.27 9.27 0.00 3.14
6699 8157 2.489619 CCAAGGGCCAGTACATATGCAT 60.490 50.000 6.18 3.79 0.00 3.96
6700 8158 1.133823 CCAAGGGCCAGTACATATGCA 60.134 52.381 6.18 0.00 0.00 3.96
6701 8159 1.609208 CCAAGGGCCAGTACATATGC 58.391 55.000 6.18 0.00 0.00 3.14
6702 8160 1.609208 GCCAAGGGCCAGTACATATG 58.391 55.000 6.18 0.00 44.06 1.78
6714 8172 1.867595 ATTCACAGGAGGGCCAAGGG 61.868 60.000 6.18 0.00 36.29 3.95
6715 8173 0.682209 CATTCACAGGAGGGCCAAGG 60.682 60.000 6.18 0.00 36.29 3.61
6716 8174 1.318158 GCATTCACAGGAGGGCCAAG 61.318 60.000 6.18 0.00 36.29 3.61
6717 8175 1.304381 GCATTCACAGGAGGGCCAA 60.304 57.895 6.18 0.00 36.29 4.52
6718 8176 2.356278 GCATTCACAGGAGGGCCA 59.644 61.111 6.18 0.00 36.29 5.36
6719 8177 1.751927 CTGCATTCACAGGAGGGCC 60.752 63.158 0.00 0.00 33.85 5.80
6720 8178 0.610232 AACTGCATTCACAGGAGGGC 60.610 55.000 0.00 0.00 42.21 5.19
6721 8179 1.171308 CAACTGCATTCACAGGAGGG 58.829 55.000 0.00 0.00 42.21 4.30
6722 8180 0.524862 GCAACTGCATTCACAGGAGG 59.475 55.000 0.00 0.00 42.21 4.30
6723 8181 0.524862 GGCAACTGCATTCACAGGAG 59.475 55.000 3.76 0.00 44.36 3.69
6724 8182 0.895100 GGGCAACTGCATTCACAGGA 60.895 55.000 3.76 0.00 44.36 3.86
6725 8183 1.180456 TGGGCAACTGCATTCACAGG 61.180 55.000 3.76 0.00 44.36 4.00
6726 8184 0.892755 ATGGGCAACTGCATTCACAG 59.107 50.000 3.76 0.00 44.36 3.66
6727 8185 1.273048 GAATGGGCAACTGCATTCACA 59.727 47.619 3.76 0.00 41.87 3.58
6728 8186 1.404583 GGAATGGGCAACTGCATTCAC 60.405 52.381 13.60 3.77 43.18 3.18
6729 8187 0.896923 GGAATGGGCAACTGCATTCA 59.103 50.000 13.60 5.85 43.18 2.57
6730 8188 1.188863 AGGAATGGGCAACTGCATTC 58.811 50.000 3.76 5.29 41.67 2.67
6731 8189 2.497273 GTTAGGAATGGGCAACTGCATT 59.503 45.455 3.76 0.00 44.36 3.56
6732 8190 2.102578 GTTAGGAATGGGCAACTGCAT 58.897 47.619 3.76 0.00 44.36 3.96
6733 8191 1.202989 TGTTAGGAATGGGCAACTGCA 60.203 47.619 3.76 0.00 44.36 4.41
6734 8192 1.544724 TGTTAGGAATGGGCAACTGC 58.455 50.000 0.00 0.00 41.14 4.40
6735 8193 2.428171 CCATGTTAGGAATGGGCAACTG 59.572 50.000 0.00 0.00 40.86 3.16
6736 8194 2.738743 CCATGTTAGGAATGGGCAACT 58.261 47.619 0.00 0.00 40.86 3.16
6743 8201 6.236409 AGCATCTGATACCATGTTAGGAATG 58.764 40.000 0.00 0.00 0.00 2.67
6744 8202 6.445451 AGCATCTGATACCATGTTAGGAAT 57.555 37.500 0.00 0.00 0.00 3.01
6745 8203 5.894298 AGCATCTGATACCATGTTAGGAA 57.106 39.130 0.00 0.00 0.00 3.36
6746 8204 5.894298 AAGCATCTGATACCATGTTAGGA 57.106 39.130 0.00 0.00 0.00 2.94
6747 8205 6.169094 CCTAAGCATCTGATACCATGTTAGG 58.831 44.000 0.00 0.00 32.99 2.69
6748 8206 6.763355 ACCTAAGCATCTGATACCATGTTAG 58.237 40.000 0.00 0.00 0.00 2.34
6749 8207 6.747414 ACCTAAGCATCTGATACCATGTTA 57.253 37.500 0.00 0.00 0.00 2.41
6750 8208 5.636903 ACCTAAGCATCTGATACCATGTT 57.363 39.130 0.00 0.00 0.00 2.71
6751 8209 5.455326 GGAACCTAAGCATCTGATACCATGT 60.455 44.000 0.00 0.00 0.00 3.21
6752 8210 4.999950 GGAACCTAAGCATCTGATACCATG 59.000 45.833 0.00 0.00 0.00 3.66
6753 8211 4.910304 AGGAACCTAAGCATCTGATACCAT 59.090 41.667 0.00 0.00 0.00 3.55
6754 8212 4.298626 AGGAACCTAAGCATCTGATACCA 58.701 43.478 0.00 0.00 0.00 3.25
6755 8213 4.591072 AGAGGAACCTAAGCATCTGATACC 59.409 45.833 0.00 0.00 0.00 2.73
6756 8214 5.279256 GGAGAGGAACCTAAGCATCTGATAC 60.279 48.000 0.00 0.00 0.00 2.24
6757 8215 4.835615 GGAGAGGAACCTAAGCATCTGATA 59.164 45.833 0.00 0.00 0.00 2.15
6758 8216 3.645687 GGAGAGGAACCTAAGCATCTGAT 59.354 47.826 0.00 0.00 0.00 2.90
6759 8217 3.034635 GGAGAGGAACCTAAGCATCTGA 58.965 50.000 0.00 0.00 0.00 3.27
6760 8218 3.037549 AGGAGAGGAACCTAAGCATCTG 58.962 50.000 0.00 0.00 35.84 2.90
6761 8219 3.037549 CAGGAGAGGAACCTAAGCATCT 58.962 50.000 0.00 0.00 35.84 2.90
6762 8220 2.484594 GCAGGAGAGGAACCTAAGCATC 60.485 54.545 0.00 0.00 35.84 3.91
6763 8221 1.488393 GCAGGAGAGGAACCTAAGCAT 59.512 52.381 0.00 0.00 35.84 3.79
6764 8222 0.905357 GCAGGAGAGGAACCTAAGCA 59.095 55.000 0.00 0.00 35.84 3.91
6765 8223 1.138069 GAGCAGGAGAGGAACCTAAGC 59.862 57.143 0.00 0.00 35.84 3.09
6766 8224 1.760029 GGAGCAGGAGAGGAACCTAAG 59.240 57.143 0.00 0.00 35.84 2.18
6767 8225 1.622725 GGGAGCAGGAGAGGAACCTAA 60.623 57.143 0.00 0.00 35.84 2.69
6768 8226 0.032017 GGGAGCAGGAGAGGAACCTA 60.032 60.000 0.00 0.00 35.84 3.08
6769 8227 1.306568 GGGAGCAGGAGAGGAACCT 60.307 63.158 0.00 0.00 38.40 3.50
6770 8228 2.726351 CGGGAGCAGGAGAGGAACC 61.726 68.421 0.00 0.00 0.00 3.62
6771 8229 2.896443 CGGGAGCAGGAGAGGAAC 59.104 66.667 0.00 0.00 0.00 3.62
6822 8280 4.862823 AGGTAGAGGGAGGCCGGC 62.863 72.222 21.18 21.18 0.00 6.13
6823 8281 2.522193 GAGGTAGAGGGAGGCCGG 60.522 72.222 0.00 0.00 0.00 6.13
6824 8282 2.907917 CGAGGTAGAGGGAGGCCG 60.908 72.222 0.00 0.00 0.00 6.13
6825 8283 1.829096 GACGAGGTAGAGGGAGGCC 60.829 68.421 0.00 0.00 0.00 5.19
6826 8284 2.188161 CGACGAGGTAGAGGGAGGC 61.188 68.421 0.00 0.00 0.00 4.70
6827 8285 2.188161 GCGACGAGGTAGAGGGAGG 61.188 68.421 0.00 0.00 0.00 4.30
6828 8286 2.188161 GGCGACGAGGTAGAGGGAG 61.188 68.421 0.00 0.00 0.00 4.30
6829 8287 2.124403 GGCGACGAGGTAGAGGGA 60.124 66.667 0.00 0.00 0.00 4.20



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

AutoCloner maintained by Alex Coulton.