Multiple sequence alignment - TraesCS5B01G419700

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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 TraesCS5B01G419700 chr5B 100.000 3353 0 0 3984 7336 595341040 595337688 0.000000e+00 6192.0
1 TraesCS5B01G419700 chr5B 100.000 2665 0 0 1 2665 595345023 595342359 0.000000e+00 4922.0
2 TraesCS5B01G419700 chr5B 100.000 774 0 0 2971 3744 595342053 595341280 0.000000e+00 1430.0
3 TraesCS5B01G419700 chr5B 89.919 248 22 2 2419 2664 647390116 647389870 4.270000e-82 316.0
4 TraesCS5B01G419700 chr5B 97.778 45 1 0 2360 2404 406856065 406856021 2.190000e-10 78.7
5 TraesCS5B01G419700 chr5B 97.778 45 1 0 2360 2404 598028660 598028616 2.190000e-10 78.7
6 TraesCS5B01G419700 chr5D 95.719 1495 40 7 881 2359 484294418 484292932 0.000000e+00 2385.0
7 TraesCS5B01G419700 chr5D 94.943 1404 43 7 4489 5888 484292945 484291566 0.000000e+00 2174.0
8 TraesCS5B01G419700 chr5D 91.480 669 52 2 6669 7332 484219324 484218656 0.000000e+00 915.0
9 TraesCS5B01G419700 chr5D 87.039 787 58 13 5888 6651 484291530 484290765 0.000000e+00 848.0
10 TraesCS5B01G419700 chr5D 86.722 723 59 19 5947 6646 484220155 484219447 0.000000e+00 769.0
11 TraesCS5B01G419700 chr5D 83.292 808 85 22 5888 6657 484228835 484228040 0.000000e+00 699.0
12 TraesCS5B01G419700 chr5D 90.830 458 36 5 5432 5888 484229332 484228880 6.290000e-170 608.0
13 TraesCS5B01G419700 chr5D 92.973 370 12 5 1 364 484296258 484295897 1.810000e-145 527.0
14 TraesCS5B01G419700 chr5D 95.556 45 2 0 2360 2404 499676640 499676684 1.020000e-08 73.1
15 TraesCS5B01G419700 chr5D 100.000 28 0 0 6632 6659 484219430 484219403 1.300000e-02 52.8
16 TraesCS5B01G419700 chr5A 93.145 1488 61 15 5888 7336 605768844 605767359 0.000000e+00 2145.0
17 TraesCS5B01G419700 chr5A 90.909 1353 75 20 881 2216 605771724 605770403 0.000000e+00 1773.0
18 TraesCS5B01G419700 chr5A 93.624 894 37 7 5003 5888 605769761 605768880 0.000000e+00 1317.0
19 TraesCS5B01G419700 chr5A 83.228 1270 129 43 5432 6657 605758965 605757736 0.000000e+00 1088.0
20 TraesCS5B01G419700 chr5A 94.107 560 25 2 1808 2359 605740629 605740070 0.000000e+00 845.0
21 TraesCS5B01G419700 chr5A 94.139 546 24 2 1822 2359 605716504 605715959 0.000000e+00 824.0
22 TraesCS5B01G419700 chr5A 85.451 543 46 11 4489 5006 605770321 605769787 1.080000e-147 534.0
23 TraesCS5B01G419700 chr5A 82.745 510 70 12 375 869 605783762 605783256 8.740000e-119 438.0
24 TraesCS5B01G419700 chr5A 93.684 190 10 2 185 373 605797327 605797139 4.330000e-72 283.0
25 TraesCS5B01G419700 chr5A 95.714 70 3 0 2290 2359 605770377 605770308 6.020000e-21 113.0
26 TraesCS5B01G419700 chr4A 94.961 774 39 0 2971 3744 650833442 650834215 0.000000e+00 1214.0
27 TraesCS5B01G419700 chr3B 94.703 774 40 1 2971 3744 761814407 761813635 0.000000e+00 1201.0
28 TraesCS5B01G419700 chr3B 96.647 507 16 1 3984 4489 35763781 35763275 0.000000e+00 841.0
29 TraesCS5B01G419700 chr3B 96.647 507 16 1 3984 4489 35822303 35821797 0.000000e+00 841.0
30 TraesCS5B01G419700 chr3B 96.450 507 17 1 3984 4489 35753323 35752817 0.000000e+00 835.0
31 TraesCS5B01G419700 chr3B 96.450 507 17 1 3984 4489 35833079 35832573 0.000000e+00 835.0
32 TraesCS5B01G419700 chr3B 96.450 507 15 3 3984 4489 35812208 35811704 0.000000e+00 833.0
33 TraesCS5B01G419700 chr3B 96.443 506 15 3 3984 4488 35742341 35741838 0.000000e+00 832.0
34 TraesCS5B01G419700 chr3B 95.045 222 10 1 2419 2639 466623279 466623058 1.510000e-91 348.0
35 TraesCS5B01G419700 chr3B 91.532 248 20 1 2419 2665 761814694 761814447 2.530000e-89 340.0
36 TraesCS5B01G419700 chr3A 94.444 774 42 1 2972 3744 691336367 691335594 0.000000e+00 1190.0
37 TraesCS5B01G419700 chr3A 92.946 241 15 2 2426 2665 27187394 27187155 4.210000e-92 350.0
38 TraesCS5B01G419700 chr3A 93.191 235 15 1 2419 2652 691336909 691336675 1.960000e-90 344.0
39 TraesCS5B01G419700 chr3A 92.275 233 17 1 2421 2652 27233746 27233514 5.490000e-86 329.0
40 TraesCS5B01G419700 chr3A 97.778 45 1 0 2360 2404 16369944 16369988 2.190000e-10 78.7
41 TraesCS5B01G419700 chr3A 97.778 45 1 0 2360 2404 17670595 17670639 2.190000e-10 78.7
42 TraesCS5B01G419700 chr6B 94.186 774 45 0 2971 3744 151203633 151204406 0.000000e+00 1181.0
43 TraesCS5B01G419700 chr6B 92.987 770 54 0 2971 3740 700856290 700857059 0.000000e+00 1123.0
44 TraesCS5B01G419700 chrUn 93.798 774 48 0 2971 3744 463438305 463437532 0.000000e+00 1164.0
45 TraesCS5B01G419700 chrUn 93.152 774 52 1 2971 3744 265769535 265768763 0.000000e+00 1134.0
46 TraesCS5B01G419700 chrUn 93.023 774 53 1 2971 3744 335747687 335746915 0.000000e+00 1129.0
47 TraesCS5B01G419700 chrUn 93.145 671 43 3 6669 7336 244093544 244092874 0.000000e+00 981.0
48 TraesCS5B01G419700 chrUn 93.145 671 43 3 6669 7336 244106187 244105517 0.000000e+00 981.0
49 TraesCS5B01G419700 chrUn 93.145 671 43 3 6669 7336 262358776 262359446 0.000000e+00 981.0
50 TraesCS5B01G419700 chrUn 97.239 507 13 1 3984 4489 168710720 168711226 0.000000e+00 857.0
51 TraesCS5B01G419700 chrUn 97.239 507 13 1 3984 4489 168712714 168713220 0.000000e+00 857.0
52 TraesCS5B01G419700 chrUn 97.041 507 14 1 3984 4489 340152080 340151574 0.000000e+00 852.0
53 TraesCS5B01G419700 chrUn 86.295 664 59 18 5947 6588 244094330 244093677 0.000000e+00 693.0
54 TraesCS5B01G419700 chrUn 86.295 664 59 18 5947 6588 244106973 244106320 0.000000e+00 693.0
55 TraesCS5B01G419700 chrUn 86.295 664 59 18 5947 6588 262357990 262358643 0.000000e+00 693.0
56 TraesCS5B01G419700 chrUn 95.556 45 2 0 2360 2404 314912403 314912447 1.020000e-08 73.1
57 TraesCS5B01G419700 chrUn 95.556 45 2 0 2360 2404 350109067 350109023 1.020000e-08 73.1
58 TraesCS5B01G419700 chr2B 93.677 775 48 1 2971 3744 583384134 583384908 0.000000e+00 1158.0
59 TraesCS5B01G419700 chr2B 94.690 226 11 1 2419 2643 583383473 583383698 4.210000e-92 350.0
60 TraesCS5B01G419700 chr2B 94.737 209 10 1 2419 2627 404159567 404159774 2.550000e-84 324.0
61 TraesCS5B01G419700 chr1A 90.612 245 22 1 2421 2664 276642324 276642080 2.550000e-84 324.0
62 TraesCS5B01G419700 chr4B 83.200 250 37 4 495 741 62974581 62974334 2.660000e-54 224.0
63 TraesCS5B01G419700 chr4B 95.652 46 2 0 2360 2405 661733038 661732993 2.840000e-09 75.0
64 TraesCS5B01G419700 chr3D 80.498 241 35 9 495 733 175556920 175556690 2.720000e-39 174.0
65 TraesCS5B01G419700 chr4D 95.556 45 2 0 2360 2404 419447136 419447180 1.020000e-08 73.1


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 TraesCS5B01G419700 chr5B 595337688 595345023 7335 True 4181.333333 6192 100.0000 1 7336 3 chr5B.!!$R4 7335
1 TraesCS5B01G419700 chr5D 484290765 484296258 5493 True 1483.500000 2385 92.6685 1 6651 4 chr5D.!!$R3 6650
2 TraesCS5B01G419700 chr5D 484228040 484229332 1292 True 653.500000 699 87.0610 5432 6657 2 chr5D.!!$R2 1225
3 TraesCS5B01G419700 chr5D 484218656 484220155 1499 True 578.933333 915 92.7340 5947 7332 3 chr5D.!!$R1 1385
4 TraesCS5B01G419700 chr5A 605767359 605771724 4365 True 1176.400000 2145 91.7686 881 7336 5 chr5A.!!$R6 6455
5 TraesCS5B01G419700 chr5A 605757736 605758965 1229 True 1088.000000 1088 83.2280 5432 6657 1 chr5A.!!$R3 1225
6 TraesCS5B01G419700 chr5A 605740070 605740629 559 True 845.000000 845 94.1070 1808 2359 1 chr5A.!!$R2 551
7 TraesCS5B01G419700 chr5A 605715959 605716504 545 True 824.000000 824 94.1390 1822 2359 1 chr5A.!!$R1 537
8 TraesCS5B01G419700 chr5A 605783256 605783762 506 True 438.000000 438 82.7450 375 869 1 chr5A.!!$R4 494
9 TraesCS5B01G419700 chr4A 650833442 650834215 773 False 1214.000000 1214 94.9610 2971 3744 1 chr4A.!!$F1 773
10 TraesCS5B01G419700 chr3B 35763275 35763781 506 True 841.000000 841 96.6470 3984 4489 1 chr3B.!!$R3 505
11 TraesCS5B01G419700 chr3B 35821797 35822303 506 True 841.000000 841 96.6470 3984 4489 1 chr3B.!!$R5 505
12 TraesCS5B01G419700 chr3B 35752817 35753323 506 True 835.000000 835 96.4500 3984 4489 1 chr3B.!!$R2 505
13 TraesCS5B01G419700 chr3B 35832573 35833079 506 True 835.000000 835 96.4500 3984 4489 1 chr3B.!!$R6 505
14 TraesCS5B01G419700 chr3B 35811704 35812208 504 True 833.000000 833 96.4500 3984 4489 1 chr3B.!!$R4 505
15 TraesCS5B01G419700 chr3B 35741838 35742341 503 True 832.000000 832 96.4430 3984 4488 1 chr3B.!!$R1 504
16 TraesCS5B01G419700 chr3B 761813635 761814694 1059 True 770.500000 1201 93.1175 2419 3744 2 chr3B.!!$R8 1325
17 TraesCS5B01G419700 chr3A 691335594 691336909 1315 True 767.000000 1190 93.8175 2419 3744 2 chr3A.!!$R3 1325
18 TraesCS5B01G419700 chr6B 151203633 151204406 773 False 1181.000000 1181 94.1860 2971 3744 1 chr6B.!!$F1 773
19 TraesCS5B01G419700 chr6B 700856290 700857059 769 False 1123.000000 1123 92.9870 2971 3740 1 chr6B.!!$F2 769
20 TraesCS5B01G419700 chrUn 463437532 463438305 773 True 1164.000000 1164 93.7980 2971 3744 1 chrUn.!!$R5 773
21 TraesCS5B01G419700 chrUn 265768763 265769535 772 True 1134.000000 1134 93.1520 2971 3744 1 chrUn.!!$R1 773
22 TraesCS5B01G419700 chrUn 335746915 335747687 772 True 1129.000000 1129 93.0230 2971 3744 1 chrUn.!!$R2 773
23 TraesCS5B01G419700 chrUn 168710720 168713220 2500 False 857.000000 857 97.2390 3984 4489 2 chrUn.!!$F2 505
24 TraesCS5B01G419700 chrUn 340151574 340152080 506 True 852.000000 852 97.0410 3984 4489 1 chrUn.!!$R3 505
25 TraesCS5B01G419700 chrUn 244092874 244094330 1456 True 837.000000 981 89.7200 5947 7336 2 chrUn.!!$R6 1389
26 TraesCS5B01G419700 chrUn 244105517 244106973 1456 True 837.000000 981 89.7200 5947 7336 2 chrUn.!!$R7 1389
27 TraesCS5B01G419700 chrUn 262357990 262359446 1456 False 837.000000 981 89.7200 5947 7336 2 chrUn.!!$F3 1389
28 TraesCS5B01G419700 chr2B 583383473 583384908 1435 False 754.000000 1158 94.1835 2419 3744 2 chr2B.!!$F2 1325

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
944 2060 0.184933 CAGGTTCCCCAAACAGACCA 59.815 55.00 0.0 0.0 39.81 4.02 F
1647 2763 1.238439 CAAAGTTCATGCCGTCCTGT 58.762 50.00 0.0 0.0 0.00 4.00 F
2406 3550 3.508793 ACAGCAATAGCAACATTTCAGCT 59.491 39.13 0.0 0.0 45.49 4.24 F
3339 4862 0.539051 CAACCCCTCTTCTCGATGCT 59.461 55.00 0.0 0.0 0.00 3.79 F
4353 7872 0.235665 CGGTTGCTTGTGTAGTGCTG 59.764 55.00 0.0 0.0 0.00 4.41 F
4420 7939 0.248990 GTGCATGTGTTGTGGTGGTG 60.249 55.00 0.0 0.0 0.00 4.17 F
5840 9424 0.329931 AACCGTTGCCCATCATACCA 59.670 50.00 0.0 0.0 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2962 0.738389 AATTCAACCAATAGGCGCGG 59.262 50.000 8.83 0.0 39.06 6.46 R
3321 4844 0.827368 GAGCATCGAGAAGAGGGGTT 59.173 55.000 0.00 0.0 0.00 4.11 R
4337 7856 0.537143 CCCCAGCACTACACAAGCAA 60.537 55.000 0.00 0.0 0.00 3.91 R
4420 7939 0.246635 ACATCCAGGTACAGACGCAC 59.753 55.000 0.00 0.0 0.00 5.34 R
5840 9424 0.729116 GCATGTGCGCAATCACTAGT 59.271 50.000 14.00 0.0 37.81 2.57 R
6197 9842 2.106511 AGGCCAGTAACAGCAGAGAAAA 59.893 45.455 5.01 0.0 0.00 2.29 R
6855 10629 0.250513 CCTACAGAGAAGGCCACCAC 59.749 60.000 5.01 0.0 0.00 4.16 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
30 31 6.824305 ACTCACTCAAATACAATTTCCTGG 57.176 37.500 0.00 0.00 0.00 4.45
39 40 9.396022 TCAAATACAATTTCCTGGATTACTCTC 57.604 33.333 0.00 0.00 29.27 3.20
47 48 3.706594 TCCTGGATTACTCTCAGCGAAAT 59.293 43.478 0.00 0.00 0.00 2.17
48 49 3.806521 CCTGGATTACTCTCAGCGAAATG 59.193 47.826 0.00 0.00 0.00 2.32
49 50 4.442052 CCTGGATTACTCTCAGCGAAATGA 60.442 45.833 0.00 0.00 0.00 2.57
50 51 4.433615 TGGATTACTCTCAGCGAAATGAC 58.566 43.478 0.00 0.00 0.00 3.06
51 52 4.081697 TGGATTACTCTCAGCGAAATGACA 60.082 41.667 0.00 0.00 0.00 3.58
52 53 5.053145 GGATTACTCTCAGCGAAATGACAT 58.947 41.667 0.00 0.00 0.00 3.06
53 54 5.050499 GGATTACTCTCAGCGAAATGACATG 60.050 44.000 0.00 0.00 0.00 3.21
54 55 3.325293 ACTCTCAGCGAAATGACATGT 57.675 42.857 0.00 0.00 0.00 3.21
157 163 5.675538 AGGTGTTTCTATCTCCATGCTTAC 58.324 41.667 0.00 0.00 0.00 2.34
183 189 1.211709 GCGTGTTTACCCATGTGCC 59.788 57.895 0.00 0.00 0.00 5.01
256 262 5.222631 GTTGTTTTCTTTCTCCGATGCATT 58.777 37.500 0.00 0.00 0.00 3.56
286 292 5.018539 AGTTGTATGCTCGCTACCATAAA 57.981 39.130 0.00 0.00 0.00 1.40
312 318 9.665719 AAAAGGGTAAAATTAGTATGCAATTGG 57.334 29.630 7.72 0.00 0.00 3.16
358 364 4.836825 CTGTCTAATCAAGGCTTCTTCCA 58.163 43.478 0.00 0.00 0.00 3.53
359 365 5.435291 CTGTCTAATCAAGGCTTCTTCCAT 58.565 41.667 0.00 0.00 0.00 3.41
360 366 5.431765 TGTCTAATCAAGGCTTCTTCCATC 58.568 41.667 0.00 0.00 0.00 3.51
361 367 5.190528 TGTCTAATCAAGGCTTCTTCCATCT 59.809 40.000 0.00 0.00 0.00 2.90
363 369 6.259829 GTCTAATCAAGGCTTCTTCCATCTTC 59.740 42.308 0.00 0.00 0.00 2.87
364 370 4.581309 ATCAAGGCTTCTTCCATCTTCA 57.419 40.909 0.00 0.00 0.00 3.02
365 371 4.581309 TCAAGGCTTCTTCCATCTTCAT 57.419 40.909 0.00 0.00 0.00 2.57
366 372 5.698741 TCAAGGCTTCTTCCATCTTCATA 57.301 39.130 0.00 0.00 0.00 2.15
368 374 6.060136 TCAAGGCTTCTTCCATCTTCATATG 58.940 40.000 0.00 0.00 0.00 1.78
369 375 5.643421 AGGCTTCTTCCATCTTCATATGT 57.357 39.130 1.90 0.00 0.00 2.29
370 376 6.753913 AGGCTTCTTCCATCTTCATATGTA 57.246 37.500 1.90 0.00 0.00 2.29
371 377 6.529220 AGGCTTCTTCCATCTTCATATGTAC 58.471 40.000 1.90 0.00 0.00 2.90
372 378 6.100279 AGGCTTCTTCCATCTTCATATGTACA 59.900 38.462 0.00 0.00 0.00 2.90
373 379 6.426328 GGCTTCTTCCATCTTCATATGTACAG 59.574 42.308 0.33 0.00 0.00 2.74
386 396 9.823647 CTTCATATGTACAGAATTTGGAGTAGT 57.176 33.333 0.33 0.00 0.00 2.73
406 416 4.770795 AGTTAACTATGCTGGTGACCATC 58.229 43.478 4.03 0.24 30.82 3.51
419 429 2.615912 GTGACCATCAGCAAATAGGAGC 59.384 50.000 0.00 0.00 0.00 4.70
513 527 8.531146 CCAAATATTTTTGACCCTGATAAGTGT 58.469 33.333 9.87 0.00 44.11 3.55
520 534 1.421410 CCCTGATAAGTGTCGCACGC 61.421 60.000 4.69 0.00 39.64 5.34
521 535 1.625870 CTGATAAGTGTCGCACGCG 59.374 57.895 3.53 3.53 39.64 6.01
537 551 2.555782 CGTGGCACGAACACATGG 59.444 61.111 34.85 1.03 46.05 3.66
538 552 2.250939 CGTGGCACGAACACATGGT 61.251 57.895 34.85 0.00 46.05 3.55
549 563 3.121279 CGAACACATGGTAACTCTGAACG 59.879 47.826 0.00 0.00 37.61 3.95
550 564 3.746045 ACACATGGTAACTCTGAACGT 57.254 42.857 0.00 0.00 37.61 3.99
560 574 5.163884 GGTAACTCTGAACGTTTTCTATGGC 60.164 44.000 0.46 0.00 32.36 4.40
572 586 7.081976 ACGTTTTCTATGGCAAGTTTAATGAC 58.918 34.615 0.00 0.00 0.00 3.06
591 680 5.356882 TGACGCAAGGATGAAAACTTTAG 57.643 39.130 0.00 0.00 46.39 1.85
594 683 6.483974 TGACGCAAGGATGAAAACTTTAGTTA 59.516 34.615 0.00 0.00 46.39 2.24
623 713 7.373493 AGTATGGCAACTTTCTTTTTGATGAG 58.627 34.615 0.00 0.00 37.61 2.90
630 720 8.323854 GCAACTTTCTTTTTGATGAGAAGTTTC 58.676 33.333 0.00 0.00 33.77 2.78
667 760 9.949174 GTTTGTTTTTAATTTTCAGATGGCAAT 57.051 25.926 0.00 0.00 0.00 3.56
713 806 1.948834 CGGATTGCTTCATGCCACATA 59.051 47.619 0.00 0.00 42.00 2.29
718 811 2.725637 TGCTTCATGCCACATATGTGT 58.274 42.857 29.25 12.55 44.21 3.72
721 814 3.317149 GCTTCATGCCACATATGTGTCAT 59.683 43.478 29.25 26.28 44.32 3.06
790 884 1.375013 GGACGCGGCTTCCTAAACA 60.375 57.895 13.91 0.00 0.00 2.83
797 891 1.405661 CGGCTTCCTAAACAGGTCCTC 60.406 57.143 0.00 0.00 0.00 3.71
900 2008 2.863401 AAAAACGTGCAAGGGAAGTC 57.137 45.000 4.26 0.00 0.00 3.01
944 2060 0.184933 CAGGTTCCCCAAACAGACCA 59.815 55.000 0.00 0.00 39.81 4.02
953 2069 2.301346 CCAAACAGACCAAGCAGACTT 58.699 47.619 0.00 0.00 36.19 3.01
1345 2461 2.446036 GATCCCCCGCCTACCAGT 60.446 66.667 0.00 0.00 0.00 4.00
1497 2613 2.261671 CTCGTAGCTGCGGGTGTT 59.738 61.111 24.11 0.00 0.00 3.32
1647 2763 1.238439 CAAAGTTCATGCCGTCCTGT 58.762 50.000 0.00 0.00 0.00 4.00
1679 2795 6.060136 GGGATTACATCAGGGTAGGTAAAAC 58.940 44.000 0.00 0.00 30.41 2.43
1708 2824 6.426937 GTGACCTGACAACTAAATTAGCTTCA 59.573 38.462 0.00 0.08 0.00 3.02
1820 2937 5.646577 ATTACTACCTGCGGCTCTATAAG 57.353 43.478 0.00 0.00 0.00 1.73
1872 3000 6.165577 GCCTATTGGTTGAATTGTTGAATGT 58.834 36.000 0.00 0.00 35.27 2.71
1948 3077 3.887716 TCGGTGTAAGCTCCTTAGGATAC 59.112 47.826 0.00 2.40 0.00 2.24
2216 3360 6.419710 TCACATTTGTATTCGCTAATACTCCG 59.580 38.462 18.66 9.48 45.22 4.63
2223 3367 8.098220 TGTATTCGCTAATACTCCGTATGTTA 57.902 34.615 18.66 0.00 45.22 2.41
2359 3503 6.957920 TTGACAACAAAGATTCTTGGATGA 57.042 33.333 15.73 0.00 32.73 2.92
2360 3504 7.528996 TTGACAACAAAGATTCTTGGATGAT 57.471 32.000 15.73 3.02 32.73 2.45
2361 3505 8.634335 TTGACAACAAAGATTCTTGGATGATA 57.366 30.769 15.73 3.88 32.73 2.15
2362 3506 8.812513 TGACAACAAAGATTCTTGGATGATAT 57.187 30.769 15.73 0.00 0.00 1.63
2363 3507 8.680001 TGACAACAAAGATTCTTGGATGATATG 58.320 33.333 15.73 4.05 0.00 1.78
2364 3508 8.812513 ACAACAAAGATTCTTGGATGATATGA 57.187 30.769 15.73 0.00 0.00 2.15
2365 3509 9.246670 ACAACAAAGATTCTTGGATGATATGAA 57.753 29.630 15.73 0.00 0.00 2.57
2366 3510 9.512435 CAACAAAGATTCTTGGATGATATGAAC 57.488 33.333 7.82 0.00 0.00 3.18
2367 3511 8.812513 ACAAAGATTCTTGGATGATATGAACA 57.187 30.769 7.82 0.00 0.00 3.18
2368 3512 9.246670 ACAAAGATTCTTGGATGATATGAACAA 57.753 29.630 7.82 0.00 0.00 2.83
2372 3516 9.246670 AGATTCTTGGATGATATGAACAAAACA 57.753 29.630 0.00 0.00 0.00 2.83
2373 3517 9.859427 GATTCTTGGATGATATGAACAAAACAA 57.141 29.630 0.00 0.00 0.00 2.83
2374 3518 9.643693 ATTCTTGGATGATATGAACAAAACAAC 57.356 29.630 0.00 0.00 0.00 3.32
2375 3519 8.175925 TCTTGGATGATATGAACAAAACAACA 57.824 30.769 0.00 0.00 0.00 3.33
2376 3520 8.081633 TCTTGGATGATATGAACAAAACAACAC 58.918 33.333 0.00 0.00 0.00 3.32
2377 3521 7.523293 TGGATGATATGAACAAAACAACACT 57.477 32.000 0.00 0.00 0.00 3.55
2378 3522 8.628630 TGGATGATATGAACAAAACAACACTA 57.371 30.769 0.00 0.00 0.00 2.74
2379 3523 8.729756 TGGATGATATGAACAAAACAACACTAG 58.270 33.333 0.00 0.00 0.00 2.57
2380 3524 7.698130 GGATGATATGAACAAAACAACACTAGC 59.302 37.037 0.00 0.00 0.00 3.42
2381 3525 7.503521 TGATATGAACAAAACAACACTAGCA 57.496 32.000 0.00 0.00 0.00 3.49
2382 3526 8.109705 TGATATGAACAAAACAACACTAGCAT 57.890 30.769 0.00 0.00 0.00 3.79
2383 3527 9.225436 TGATATGAACAAAACAACACTAGCATA 57.775 29.630 0.00 0.00 0.00 3.14
2385 3529 9.840427 ATATGAACAAAACAACACTAGCATAAC 57.160 29.630 0.00 0.00 0.00 1.89
2386 3530 7.089770 TGAACAAAACAACACTAGCATAACA 57.910 32.000 0.00 0.00 0.00 2.41
2387 3531 7.192913 TGAACAAAACAACACTAGCATAACAG 58.807 34.615 0.00 0.00 0.00 3.16
2388 3532 5.519722 ACAAAACAACACTAGCATAACAGC 58.480 37.500 0.00 0.00 0.00 4.40
2389 3533 5.067153 ACAAAACAACACTAGCATAACAGCA 59.933 36.000 0.00 0.00 36.85 4.41
2390 3534 5.766150 AAACAACACTAGCATAACAGCAA 57.234 34.783 0.00 0.00 36.85 3.91
2391 3535 5.964958 AACAACACTAGCATAACAGCAAT 57.035 34.783 0.00 0.00 36.85 3.56
2392 3536 7.447374 AAACAACACTAGCATAACAGCAATA 57.553 32.000 0.00 0.00 36.85 1.90
2393 3537 6.668541 ACAACACTAGCATAACAGCAATAG 57.331 37.500 0.00 0.00 36.85 1.73
2394 3538 5.065218 ACAACACTAGCATAACAGCAATAGC 59.935 40.000 0.00 0.00 42.56 2.97
2395 3539 4.769688 ACACTAGCATAACAGCAATAGCA 58.230 39.130 0.00 0.00 45.49 3.49
2396 3540 5.185454 ACACTAGCATAACAGCAATAGCAA 58.815 37.500 0.00 0.00 45.49 3.91
2397 3541 5.065218 ACACTAGCATAACAGCAATAGCAAC 59.935 40.000 0.00 0.00 45.49 4.17
2398 3542 5.065090 CACTAGCATAACAGCAATAGCAACA 59.935 40.000 0.00 0.00 45.49 3.33
2399 3543 5.824624 ACTAGCATAACAGCAATAGCAACAT 59.175 36.000 0.00 0.00 45.49 2.71
2400 3544 5.587388 AGCATAACAGCAATAGCAACATT 57.413 34.783 0.00 0.00 45.49 2.71
2401 3545 5.969423 AGCATAACAGCAATAGCAACATTT 58.031 33.333 0.00 0.00 45.49 2.32
2402 3546 6.038356 AGCATAACAGCAATAGCAACATTTC 58.962 36.000 0.00 0.00 45.49 2.17
2403 3547 5.806502 GCATAACAGCAATAGCAACATTTCA 59.193 36.000 0.00 0.00 45.49 2.69
2404 3548 6.020121 GCATAACAGCAATAGCAACATTTCAG 60.020 38.462 0.00 0.00 45.49 3.02
2405 3549 3.841643 ACAGCAATAGCAACATTTCAGC 58.158 40.909 0.00 0.00 45.49 4.26
2406 3550 3.508793 ACAGCAATAGCAACATTTCAGCT 59.491 39.130 0.00 0.00 45.49 4.24
2407 3551 4.701651 ACAGCAATAGCAACATTTCAGCTA 59.298 37.500 0.00 0.00 45.49 3.32
2408 3552 5.183713 ACAGCAATAGCAACATTTCAGCTAA 59.816 36.000 0.00 0.00 43.32 3.09
2409 3553 6.127535 ACAGCAATAGCAACATTTCAGCTAAT 60.128 34.615 0.00 0.00 43.32 1.73
2410 3554 6.417044 CAGCAATAGCAACATTTCAGCTAATC 59.583 38.462 0.00 0.00 43.32 1.75
2411 3555 6.320672 AGCAATAGCAACATTTCAGCTAATCT 59.679 34.615 0.00 0.00 43.32 2.40
2412 3556 7.500227 AGCAATAGCAACATTTCAGCTAATCTA 59.500 33.333 0.00 0.00 43.32 1.98
2413 3557 7.802251 GCAATAGCAACATTTCAGCTAATCTAG 59.198 37.037 0.00 0.00 43.32 2.43
2478 3623 4.091939 GAAACCCTAGCCCGCGGT 62.092 66.667 26.12 9.29 0.00 5.68
3312 4835 4.641645 TTGGTGAGCGGCCTGTGG 62.642 66.667 0.00 0.00 0.00 4.17
3321 4844 2.947532 CGGCCTGTGGAGAGCTTCA 61.948 63.158 0.00 0.00 0.00 3.02
3339 4862 0.539051 CAACCCCTCTTCTCGATGCT 59.461 55.000 0.00 0.00 0.00 3.79
3592 5116 2.933287 TTGTGTGCCCCGGGATCT 60.933 61.111 26.32 0.00 0.00 2.75
3602 5126 1.576920 CCGGGATCTGATCGTCTCG 59.423 63.158 11.28 11.42 38.05 4.04
3657 5181 3.116174 GGTTCCTAGGTCTTGGATTCCT 58.884 50.000 9.08 0.00 34.62 3.36
3683 5207 4.912395 GCCCTGGTGGTGGTTGCA 62.912 66.667 0.00 0.00 36.04 4.08
3684 5208 2.912025 CCCTGGTGGTGGTTGCAC 60.912 66.667 0.00 0.00 0.00 4.57
3685 5209 3.286751 CCTGGTGGTGGTTGCACG 61.287 66.667 0.00 0.00 0.00 5.34
3686 5210 3.286751 CTGGTGGTGGTTGCACGG 61.287 66.667 0.00 0.00 0.00 4.94
3687 5211 4.116585 TGGTGGTGGTTGCACGGT 62.117 61.111 0.00 0.00 0.00 4.83
3688 5212 3.591835 GGTGGTGGTTGCACGGTG 61.592 66.667 3.15 3.15 0.00 4.94
3689 5213 4.264638 GTGGTGGTTGCACGGTGC 62.265 66.667 25.55 25.55 45.29 5.01
3690 5214 4.497984 TGGTGGTTGCACGGTGCT 62.498 61.111 30.81 0.00 45.31 4.40
3691 5215 3.660111 GGTGGTTGCACGGTGCTC 61.660 66.667 30.81 22.73 45.31 4.26
3692 5216 2.899838 GTGGTTGCACGGTGCTCA 60.900 61.111 30.81 22.58 45.31 4.26
3693 5217 2.899838 TGGTTGCACGGTGCTCAC 60.900 61.111 30.81 25.30 45.31 3.51
3694 5218 4.012895 GGTTGCACGGTGCTCACG 62.013 66.667 30.81 0.00 45.31 4.35
3695 5219 4.012895 GTTGCACGGTGCTCACGG 62.013 66.667 30.81 6.10 45.31 4.94
3730 5254 4.722700 GTGCTGCCCGGTGGTCAT 62.723 66.667 0.00 0.00 0.00 3.06
3731 5255 4.720902 TGCTGCCCGGTGGTCATG 62.721 66.667 0.00 0.00 0.00 3.07
3738 5262 4.697756 CGGTGGTCATGGCCGTGT 62.698 66.667 24.24 0.00 40.53 4.49
3739 5263 3.055719 GGTGGTCATGGCCGTGTG 61.056 66.667 24.24 10.44 0.00 3.82
3740 5264 3.055719 GTGGTCATGGCCGTGTGG 61.056 66.667 24.24 0.00 38.77 4.17
3741 5265 4.343323 TGGTCATGGCCGTGTGGG 62.343 66.667 24.24 0.00 39.58 4.61
4222 7740 6.811810 GGAGAAACCTTGATCCTCGGATCG 62.812 54.167 18.35 8.96 43.21 3.69
4337 7856 2.923035 CACTGGTGGAGTCCCGGT 60.923 66.667 6.74 0.00 42.41 5.28
4342 7861 2.430367 GTGGAGTCCCGGTTGCTT 59.570 61.111 6.74 0.00 34.29 3.91
4344 7863 2.430367 GGAGTCCCGGTTGCTTGT 59.570 61.111 0.00 0.00 0.00 3.16
4353 7872 0.235665 CGGTTGCTTGTGTAGTGCTG 59.764 55.000 0.00 0.00 0.00 4.41
4420 7939 0.248990 GTGCATGTGTTGTGGTGGTG 60.249 55.000 0.00 0.00 0.00 4.17
4456 7975 3.742369 GGATGTTGTTGGTCATTGCTTTG 59.258 43.478 0.00 0.00 0.00 2.77
4458 7977 4.199432 TGTTGTTGGTCATTGCTTTGTT 57.801 36.364 0.00 0.00 0.00 2.83
4492 8011 4.680171 CGAAAGCCTTTTTCGGTAAGAT 57.320 40.909 12.72 0.00 45.17 2.40
4493 8012 5.043189 CGAAAGCCTTTTTCGGTAAGATT 57.957 39.130 12.72 0.00 45.17 2.40
4494 8013 5.086727 CGAAAGCCTTTTTCGGTAAGATTC 58.913 41.667 12.72 0.00 45.17 2.52
4495 8014 5.106673 CGAAAGCCTTTTTCGGTAAGATTCT 60.107 40.000 12.72 0.00 45.17 2.40
4496 8015 6.567891 CGAAAGCCTTTTTCGGTAAGATTCTT 60.568 38.462 12.72 4.03 45.17 2.52
4497 8016 5.629079 AGCCTTTTTCGGTAAGATTCTTG 57.371 39.130 9.22 0.00 0.00 3.02
4649 8185 3.244911 ACCCACTGGTAAGGTCTCATTTG 60.245 47.826 0.00 0.00 45.45 2.32
4686 8223 8.267183 ACCTCATCAGTTATCATTATCACACAA 58.733 33.333 0.00 0.00 0.00 3.33
4764 8301 6.201517 CAATACCATGCGTCAATTCTTTAGG 58.798 40.000 0.00 0.00 0.00 2.69
4768 8305 3.552604 TGCGTCAATTCTTTAGGCAAC 57.447 42.857 0.00 0.00 0.00 4.17
4813 8350 6.114089 TGACACGATACTCCTATATCTAGGC 58.886 44.000 0.00 0.00 43.82 3.93
4898 8439 9.653287 AATTAAGAGAGACAACGACATAAATCA 57.347 29.630 0.00 0.00 0.00 2.57
4996 8540 7.322699 CACAGAACCAAAACGTTACATCATAAC 59.677 37.037 0.00 0.00 0.00 1.89
5049 8622 1.326245 TGTCGAAACGTTCAAGTGCAG 59.674 47.619 0.00 0.00 0.00 4.41
5133 8706 2.778299 TCTTGCTGTAATTCCGTTGCT 58.222 42.857 0.00 0.00 0.00 3.91
5173 8746 8.851541 AAGTTTTGGAAATCAAATGCATACAT 57.148 26.923 0.00 0.00 43.95 2.29
5404 8983 3.713858 TGTTCAATGGAAGCACACAAG 57.286 42.857 0.00 0.00 32.62 3.16
5555 9138 2.083774 CCATTAGAACTTGGCTTGCGA 58.916 47.619 0.00 0.00 0.00 5.10
5669 9252 3.717392 TGGGGGATACATCGGAATTAACA 59.283 43.478 0.00 0.00 39.74 2.41
5840 9424 0.329931 AACCGTTGCCCATCATACCA 59.670 50.000 0.00 0.00 0.00 3.25
6003 9634 9.944663 TTACATCAAATATTCACTTAAATCGGC 57.055 29.630 0.00 0.00 0.00 5.54
6008 9639 8.519526 TCAAATATTCACTTAAATCGGCAAGTT 58.480 29.630 0.00 0.00 32.72 2.66
6049 9681 6.998074 TCTTCTGTGGAAATAATTCACTGTGT 59.002 34.615 7.79 0.00 37.29 3.72
6057 9689 7.277760 TGGAAATAATTCACTGTGTATGAGTCG 59.722 37.037 7.79 0.00 37.29 4.18
6100 9740 6.423905 TCCTTTTCTGTCTGATAAACAAGACG 59.576 38.462 0.00 0.00 33.03 4.18
6102 9742 6.764877 TTTCTGTCTGATAAACAAGACGAC 57.235 37.500 0.00 0.00 33.03 4.34
6104 9744 3.571571 TGTCTGATAAACAAGACGACGG 58.428 45.455 0.00 0.00 33.03 4.79
6197 9842 5.407407 TCTCGAAGCCATCTAAAGAAAGT 57.593 39.130 0.00 0.00 0.00 2.66
6223 9869 1.270550 CTGCTGTTACTGGCCTTTTGG 59.729 52.381 3.32 0.00 44.18 3.28
6249 9896 6.853490 ACCTCTGAGGAACCTTTTTCTATTT 58.147 36.000 29.71 0.00 37.67 1.40
6383 10037 3.542704 CACGTAAGAAATTCCGACTCTCG 59.457 47.826 0.00 0.00 43.62 4.04
6410 10064 5.443301 CGTGTCTGTCTTGACATTGATAACG 60.443 44.000 3.79 9.29 46.77 3.18
6452 10106 2.839486 TCCTAAAGTCTGCAGTGTGG 57.161 50.000 14.67 8.79 0.00 4.17
6567 10240 7.847166 GTGCAACCAAACAACTATTACTAAC 57.153 36.000 0.00 0.00 0.00 2.34
6659 10364 7.453126 TCCTGCAAATGAAAAGGACCTAAATAA 59.547 33.333 0.00 0.00 33.85 1.40
6660 10365 7.761249 CCTGCAAATGAAAAGGACCTAAATAAG 59.239 37.037 0.00 0.00 30.92 1.73
6661 10366 8.415950 TGCAAATGAAAAGGACCTAAATAAGA 57.584 30.769 0.00 0.00 0.00 2.10
6664 10369 9.358872 CAAATGAAAAGGACCTAAATAAGAAGC 57.641 33.333 0.00 0.00 0.00 3.86
6665 10370 8.650143 AATGAAAAGGACCTAAATAAGAAGCA 57.350 30.769 0.00 0.00 0.00 3.91
6667 10372 8.110860 TGAAAAGGACCTAAATAAGAAGCAAG 57.889 34.615 0.00 0.00 0.00 4.01
6748 10522 3.111853 TGCTGGCTTTATGTCGGATAG 57.888 47.619 0.00 0.00 0.00 2.08
6788 10562 7.175990 ACGCTGGGTTTAATATTTTCTTTCTGA 59.824 33.333 0.00 0.00 0.00 3.27
6855 10629 1.131126 GAATTCGTGCCATGGTGACTG 59.869 52.381 14.67 7.42 0.00 3.51
6889 10663 0.543174 GTAGGAGGGGCGATCCAGAT 60.543 60.000 9.04 0.00 39.47 2.90
6949 10723 5.313712 CCCCTAGACAAACACATTTACACT 58.686 41.667 0.00 0.00 0.00 3.55
7048 10822 1.152631 TCGCTCCCACCGATATCCA 60.153 57.895 0.00 0.00 0.00 3.41
7086 10860 3.838565 TGGCATTTTCAGGACCAACTTA 58.161 40.909 0.00 0.00 0.00 2.24
7096 10870 3.374058 CAGGACCAACTTATTGCCTTACG 59.626 47.826 0.00 0.00 34.17 3.18
7138 10912 3.008704 TGGCTTACCCTTTTAGGACTGTC 59.991 47.826 0.00 0.00 37.67 3.51
7241 11023 7.633789 ACTACCACTGTATTTGGATTTCTCAT 58.366 34.615 0.00 0.00 37.58 2.90
7305 11094 6.774673 TGGTGTACAATACTTTCATGGAGAA 58.225 36.000 0.00 0.00 0.00 2.87
7311 11100 7.076842 ACAATACTTTCATGGAGAATCAACG 57.923 36.000 0.00 0.00 35.83 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.272018 CGCTGAGAGTAATCCAGGAAATTG 59.728 45.833 0.00 0.00 0.00 2.32
30 31 5.521735 ACATGTCATTTCGCTGAGAGTAATC 59.478 40.000 0.00 0.00 0.00 1.75
39 40 2.095617 TGAGCAACATGTCATTTCGCTG 60.096 45.455 0.00 0.00 0.00 5.18
157 163 1.339247 TGGGTAAACACGCCACATAGG 60.339 52.381 0.00 0.00 41.84 2.57
183 189 7.305474 AGTAATCCTTTTGTTGAATAGTTGCG 58.695 34.615 0.00 0.00 0.00 4.85
229 235 2.946990 TCGGAGAAAGAAAACAACCACC 59.053 45.455 0.00 0.00 0.00 4.61
256 262 2.156891 GCGAGCATACAACTTTTCACGA 59.843 45.455 0.00 0.00 0.00 4.35
286 292 9.665719 CCAATTGCATACTAATTTTACCCTTTT 57.334 29.630 0.00 0.00 0.00 2.27
315 321 3.435186 GCAAGGGCGAACTCCAGC 61.435 66.667 0.00 0.00 0.00 4.85
320 326 2.034687 AGCATGCAAGGGCGAACT 59.965 55.556 21.98 0.00 45.35 3.01
360 366 9.823647 ACTACTCCAAATTCTGTACATATGAAG 57.176 33.333 10.38 4.23 0.00 3.02
369 375 9.595823 GCATAGTTAACTACTCCAAATTCTGTA 57.404 33.333 17.45 0.00 38.33 2.74
370 376 8.322091 AGCATAGTTAACTACTCCAAATTCTGT 58.678 33.333 17.45 0.00 38.33 3.41
371 377 8.607459 CAGCATAGTTAACTACTCCAAATTCTG 58.393 37.037 17.45 7.38 38.33 3.02
372 378 7.770897 CCAGCATAGTTAACTACTCCAAATTCT 59.229 37.037 17.45 0.00 38.33 2.40
373 379 7.553044 ACCAGCATAGTTAACTACTCCAAATTC 59.447 37.037 17.45 0.00 38.33 2.17
386 396 4.835284 TGATGGTCACCAGCATAGTTAA 57.165 40.909 11.81 0.00 45.45 2.01
406 416 1.456296 TGCAGTGCTCCTATTTGCTG 58.544 50.000 17.60 0.00 35.85 4.41
409 419 4.978083 AGAAATGCAGTGCTCCTATTTG 57.022 40.909 17.60 0.00 0.00 2.32
419 429 7.558161 TCTAATCCACATTAGAAATGCAGTG 57.442 36.000 0.00 0.00 45.09 3.66
500 513 0.108804 CGTGCGACACTTATCAGGGT 60.109 55.000 8.07 0.00 40.51 4.34
501 514 1.421410 GCGTGCGACACTTATCAGGG 61.421 60.000 8.07 0.00 31.34 4.45
520 534 0.946700 TACCATGTGTTCGTGCCACG 60.947 55.000 11.80 11.80 44.19 4.94
521 535 1.069500 GTTACCATGTGTTCGTGCCAC 60.069 52.381 0.00 0.00 0.00 5.01
537 551 5.407387 TGCCATAGAAAACGTTCAGAGTTAC 59.593 40.000 0.00 0.00 36.09 2.50
538 552 5.543714 TGCCATAGAAAACGTTCAGAGTTA 58.456 37.500 0.00 0.00 36.09 2.24
549 563 6.033513 GCGTCATTAAACTTGCCATAGAAAAC 59.966 38.462 0.00 0.00 0.00 2.43
550 564 6.090129 GCGTCATTAAACTTGCCATAGAAAA 58.910 36.000 0.00 0.00 0.00 2.29
560 574 5.295431 TCATCCTTGCGTCATTAAACTTG 57.705 39.130 0.00 0.00 0.00 3.16
572 586 7.526608 TCATAACTAAAGTTTTCATCCTTGCG 58.473 34.615 0.00 0.00 39.31 4.85
591 680 9.476202 AAAAAGAAAGTTGCCATACTTCATAAC 57.524 29.630 0.00 0.00 37.37 1.89
594 683 7.725251 TCAAAAAGAAAGTTGCCATACTTCAT 58.275 30.769 0.00 0.00 37.37 2.57
604 693 7.761651 AACTTCTCATCAAAAAGAAAGTTGC 57.238 32.000 0.00 0.00 31.45 4.17
651 744 8.907222 ACAACTAAAATTGCCATCTGAAAATT 57.093 26.923 0.00 0.00 32.47 1.82
652 745 9.995003 TTACAACTAAAATTGCCATCTGAAAAT 57.005 25.926 0.00 0.00 32.47 1.82
684 777 2.897436 TGAAGCAATCCGACTCTGATG 58.103 47.619 0.00 0.00 0.00 3.07
687 780 1.329906 GCATGAAGCAATCCGACTCTG 59.670 52.381 0.00 0.00 44.79 3.35
751 845 0.458669 CTCCCTAGCGCTTCGGTAAA 59.541 55.000 18.68 3.93 39.29 2.01
752 846 2.012902 GCTCCCTAGCGCTTCGGTAA 62.013 60.000 18.68 6.42 39.29 2.85
753 847 2.487532 GCTCCCTAGCGCTTCGGTA 61.488 63.158 18.68 2.43 39.39 4.02
754 848 3.839432 GCTCCCTAGCGCTTCGGT 61.839 66.667 18.68 0.00 39.39 4.69
772 866 1.359459 CTGTTTAGGAAGCCGCGTCC 61.359 60.000 16.80 16.80 35.17 4.79
774 868 4.278956 CTGTTTAGGAAGCCGCGT 57.721 55.556 4.92 0.00 0.00 6.01
944 2060 1.071385 CTGGTGGACTGAAGTCTGCTT 59.929 52.381 10.17 0.00 44.20 3.91
953 2069 1.663379 CGTATCGGCTGGTGGACTGA 61.663 60.000 0.00 0.00 0.00 3.41
1281 2397 1.511768 GAAGAAGACGAGGTCCGGG 59.488 63.158 0.00 0.00 43.93 5.73
1410 2526 3.642778 GAAGCCGCCGTAGCTGACA 62.643 63.158 0.00 0.00 40.49 3.58
1485 2601 4.586235 AGGCAAACACCCGCAGCT 62.586 61.111 0.00 0.00 0.00 4.24
1647 2763 4.478317 ACCCTGATGTAATCCCTGATGAAA 59.522 41.667 0.00 0.00 44.73 2.69
1708 2824 2.796031 CAACAATGCAGCACAACGAAAT 59.204 40.909 0.00 0.00 0.00 2.17
1844 2962 0.738389 AATTCAACCAATAGGCGCGG 59.262 50.000 8.83 0.00 39.06 6.46
1872 3000 6.544928 TTGCAACTAATAGAGATCACCTGA 57.455 37.500 0.00 0.00 0.00 3.86
1969 3111 6.718454 GGGGAGAATCATTTGATGTCATATGT 59.282 38.462 1.90 0.00 36.88 2.29
2355 3499 8.236586 TGCTAGTGTTGTTTTGTTCATATCATC 58.763 33.333 0.00 0.00 0.00 2.92
2356 3500 8.109705 TGCTAGTGTTGTTTTGTTCATATCAT 57.890 30.769 0.00 0.00 0.00 2.45
2357 3501 7.503521 TGCTAGTGTTGTTTTGTTCATATCA 57.496 32.000 0.00 0.00 0.00 2.15
2359 3503 9.840427 GTTATGCTAGTGTTGTTTTGTTCATAT 57.160 29.630 0.00 0.00 0.00 1.78
2360 3504 8.841300 TGTTATGCTAGTGTTGTTTTGTTCATA 58.159 29.630 0.00 0.00 0.00 2.15
2361 3505 7.711846 TGTTATGCTAGTGTTGTTTTGTTCAT 58.288 30.769 0.00 0.00 0.00 2.57
2362 3506 7.089770 TGTTATGCTAGTGTTGTTTTGTTCA 57.910 32.000 0.00 0.00 0.00 3.18
2363 3507 6.142320 GCTGTTATGCTAGTGTTGTTTTGTTC 59.858 38.462 0.00 0.00 0.00 3.18
2364 3508 5.977129 GCTGTTATGCTAGTGTTGTTTTGTT 59.023 36.000 0.00 0.00 0.00 2.83
2365 3509 5.067153 TGCTGTTATGCTAGTGTTGTTTTGT 59.933 36.000 0.00 0.00 0.00 2.83
2366 3510 5.518812 TGCTGTTATGCTAGTGTTGTTTTG 58.481 37.500 0.00 0.00 0.00 2.44
2367 3511 5.766150 TGCTGTTATGCTAGTGTTGTTTT 57.234 34.783 0.00 0.00 0.00 2.43
2368 3512 5.766150 TTGCTGTTATGCTAGTGTTGTTT 57.234 34.783 0.00 0.00 0.00 2.83
2369 3513 5.964958 ATTGCTGTTATGCTAGTGTTGTT 57.035 34.783 0.00 0.00 0.00 2.83
2370 3514 5.065218 GCTATTGCTGTTATGCTAGTGTTGT 59.935 40.000 0.00 0.00 36.03 3.32
2371 3515 5.065090 TGCTATTGCTGTTATGCTAGTGTTG 59.935 40.000 0.00 0.00 40.48 3.33
2372 3516 5.185454 TGCTATTGCTGTTATGCTAGTGTT 58.815 37.500 0.00 0.00 40.48 3.32
2373 3517 4.769688 TGCTATTGCTGTTATGCTAGTGT 58.230 39.130 0.00 0.00 40.48 3.55
2374 3518 5.065090 TGTTGCTATTGCTGTTATGCTAGTG 59.935 40.000 0.00 0.00 40.48 2.74
2375 3519 5.185454 TGTTGCTATTGCTGTTATGCTAGT 58.815 37.500 0.00 0.00 40.48 2.57
2376 3520 5.739752 TGTTGCTATTGCTGTTATGCTAG 57.260 39.130 0.00 0.00 40.48 3.42
2377 3521 6.698008 AATGTTGCTATTGCTGTTATGCTA 57.302 33.333 0.00 0.00 40.48 3.49
2378 3522 5.587388 AATGTTGCTATTGCTGTTATGCT 57.413 34.783 0.00 0.00 40.48 3.79
2379 3523 5.806502 TGAAATGTTGCTATTGCTGTTATGC 59.193 36.000 0.00 0.00 40.48 3.14
2380 3524 6.020121 GCTGAAATGTTGCTATTGCTGTTATG 60.020 38.462 0.00 0.00 40.48 1.90
2381 3525 6.038356 GCTGAAATGTTGCTATTGCTGTTAT 58.962 36.000 0.00 0.00 40.48 1.89
2382 3526 5.183713 AGCTGAAATGTTGCTATTGCTGTTA 59.816 36.000 0.00 0.00 40.48 2.41
2383 3527 4.021719 AGCTGAAATGTTGCTATTGCTGTT 60.022 37.500 0.00 0.00 40.48 3.16
2384 3528 3.508793 AGCTGAAATGTTGCTATTGCTGT 59.491 39.130 0.00 0.00 40.48 4.40
2385 3529 4.106029 AGCTGAAATGTTGCTATTGCTG 57.894 40.909 0.00 0.00 40.48 4.41
2386 3530 5.902613 TTAGCTGAAATGTTGCTATTGCT 57.097 34.783 0.00 0.00 38.80 3.91
2387 3531 6.501781 AGATTAGCTGAAATGTTGCTATTGC 58.498 36.000 0.00 0.00 38.80 3.56
2405 3549 1.899142 GAGGGGAGCCAGCTAGATTAG 59.101 57.143 0.00 0.00 0.00 1.73
2406 3550 1.483307 GGAGGGGAGCCAGCTAGATTA 60.483 57.143 0.00 0.00 0.00 1.75
2407 3551 0.766288 GGAGGGGAGCCAGCTAGATT 60.766 60.000 0.00 0.00 0.00 2.40
2408 3552 1.152139 GGAGGGGAGCCAGCTAGAT 60.152 63.158 0.00 0.00 0.00 1.98
2409 3553 2.283809 GGAGGGGAGCCAGCTAGA 59.716 66.667 0.00 0.00 0.00 2.43
2410 3554 2.846754 GGGAGGGGAGCCAGCTAG 60.847 72.222 0.00 0.00 0.00 3.42
2411 3555 4.499116 GGGGAGGGGAGCCAGCTA 62.499 72.222 0.00 0.00 0.00 3.32
2496 3642 2.446802 GGCGAGGGGAGGGAGAAT 60.447 66.667 0.00 0.00 0.00 2.40
2537 3683 3.773370 CCGATCTAGCCGGGCTTA 58.227 61.111 29.02 16.44 43.05 3.09
3046 4567 2.301738 GGGCCCAGAGCACCTAAGT 61.302 63.158 19.95 0.00 46.50 2.24
3272 4795 2.257371 CGACGCCGAAGAAGTCCA 59.743 61.111 0.00 0.00 38.22 4.02
3312 4835 1.905894 AGAAGAGGGGTTGAAGCTCTC 59.094 52.381 16.06 16.06 0.00 3.20
3321 4844 0.827368 GAGCATCGAGAAGAGGGGTT 59.173 55.000 0.00 0.00 0.00 4.11
3339 4862 2.508439 GACGAAGATTGCGCCCGA 60.508 61.111 4.18 0.00 0.00 5.14
3521 5045 1.812922 CTAGCTTGGTCCTGCTGCG 60.813 63.158 16.68 7.02 40.08 5.18
3592 5116 1.504900 CCAACGGACGAGACGATCA 59.495 57.895 0.00 0.00 34.93 2.92
3722 5246 3.055719 CACACGGCCATGACCACC 61.056 66.667 5.45 0.00 0.00 4.61
3723 5247 3.055719 CCACACGGCCATGACCAC 61.056 66.667 5.45 0.00 0.00 4.16
3724 5248 4.343323 CCCACACGGCCATGACCA 62.343 66.667 5.45 0.00 0.00 4.02
4337 7856 0.537143 CCCCAGCACTACACAAGCAA 60.537 55.000 0.00 0.00 0.00 3.91
4342 7861 2.579657 CGACCCCCAGCACTACACA 61.580 63.158 0.00 0.00 0.00 3.72
4344 7863 2.203728 ACGACCCCCAGCACTACA 60.204 61.111 0.00 0.00 0.00 2.74
4420 7939 0.246635 ACATCCAGGTACAGACGCAC 59.753 55.000 0.00 0.00 0.00 5.34
4456 7975 2.793585 GCTTTCGCCCCGCTTTATAAAC 60.794 50.000 0.00 0.00 0.00 2.01
4458 7977 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98
4495 8014 6.716173 TCTGATCATTTTCACTTGACATCCAA 59.284 34.615 0.00 0.00 0.00 3.53
4496 8015 6.149973 GTCTGATCATTTTCACTTGACATCCA 59.850 38.462 0.00 0.00 0.00 3.41
4497 8016 6.149973 TGTCTGATCATTTTCACTTGACATCC 59.850 38.462 0.00 0.00 28.88 3.51
4641 8177 2.882137 GGTTCCGTTCCAACAAATGAGA 59.118 45.455 0.00 0.00 0.00 3.27
4649 8185 2.076863 CTGATGAGGTTCCGTTCCAAC 58.923 52.381 0.00 0.00 0.00 3.77
4686 8223 9.971922 CATCTTTCCTTCAGTTAATTTTCTGTT 57.028 29.630 8.64 0.00 33.89 3.16
4742 8279 4.275936 GCCTAAAGAATTGACGCATGGTAT 59.724 41.667 0.00 0.00 0.00 2.73
4743 8280 3.625764 GCCTAAAGAATTGACGCATGGTA 59.374 43.478 0.00 0.00 0.00 3.25
4744 8281 2.423538 GCCTAAAGAATTGACGCATGGT 59.576 45.455 0.00 0.00 0.00 3.55
4745 8282 2.423185 TGCCTAAAGAATTGACGCATGG 59.577 45.455 0.00 0.00 0.00 3.66
4746 8283 3.763097 TGCCTAAAGAATTGACGCATG 57.237 42.857 0.00 0.00 0.00 4.06
4747 8284 3.119495 GGTTGCCTAAAGAATTGACGCAT 60.119 43.478 0.00 0.00 0.00 4.73
4764 8301 9.432077 CAAAAATGTTGTTTATTACTTGGTTGC 57.568 29.630 0.00 0.00 0.00 4.17
4851 8388 6.927294 ATTGCTTGGTGTAGAGCTTAATAC 57.073 37.500 0.00 0.00 39.60 1.89
4898 8439 6.835174 AGACTGCCACATCAGTATCATTTAT 58.165 36.000 0.00 0.00 46.40 1.40
4906 8447 3.447586 GGTCTAAGACTGCCACATCAGTA 59.552 47.826 0.00 0.00 46.40 2.74
4959 8500 4.572985 TTGGTTCTGTGAGCTTCATTTG 57.427 40.909 0.00 0.00 0.00 2.32
4996 8540 3.944087 AGGCAAGCTACTTAACTTGGAG 58.056 45.455 5.04 0.00 42.82 3.86
5133 8706 8.763984 TTCCAAAACTTAACCAATACAACCTA 57.236 30.769 0.00 0.00 0.00 3.08
5382 8961 4.099881 ACTTGTGTGCTTCCATTGAACAAT 59.900 37.500 0.00 0.00 0.00 2.71
5397 8976 1.069703 CGACAGGCATCAACTTGTGTG 60.070 52.381 0.00 0.00 0.00 3.82
5404 8983 1.442769 ACATGACGACAGGCATCAAC 58.557 50.000 0.00 0.00 44.33 3.18
5555 9138 9.185680 AGTTGTAACTAGACAAACCTTTTCAAT 57.814 29.630 0.00 0.00 40.88 2.57
5669 9252 0.749454 GGCCAGCATCCTTGACGATT 60.749 55.000 0.00 0.00 0.00 3.34
5818 9402 2.159296 GGTATGATGGGCAACGGTTTTC 60.159 50.000 0.00 0.00 37.60 2.29
5824 9408 2.158957 ACTAGTGGTATGATGGGCAACG 60.159 50.000 0.00 0.00 37.60 4.10
5840 9424 0.729116 GCATGTGCGCAATCACTAGT 59.271 50.000 14.00 0.00 37.81 2.57
6003 9634 9.533253 AGAAGAACACATGGAAATTTTAACTTG 57.467 29.630 0.00 0.00 0.00 3.16
6008 9639 7.286546 TCCACAGAAGAACACATGGAAATTTTA 59.713 33.333 0.00 0.00 33.34 1.52
6010 9641 5.598005 TCCACAGAAGAACACATGGAAATTT 59.402 36.000 0.00 0.00 33.34 1.82
6049 9681 8.793592 AGCATTATAACTATGTGACGACTCATA 58.206 33.333 8.83 8.83 33.28 2.15
6057 9689 9.331282 AGAAAAGGAGCATTATAACTATGTGAC 57.669 33.333 0.00 0.00 0.00 3.67
6100 9740 2.202295 TTGCTTTTTCAGTTGCCGTC 57.798 45.000 0.00 0.00 0.00 4.79
6102 9742 5.404968 TGAAATATTGCTTTTTCAGTTGCCG 59.595 36.000 0.00 0.00 37.03 5.69
6104 9744 8.946935 GTTTTGAAATATTGCTTTTTCAGTTGC 58.053 29.630 0.00 0.00 41.42 4.17
6197 9842 2.106511 AGGCCAGTAACAGCAGAGAAAA 59.893 45.455 5.01 0.00 0.00 2.29
6223 9869 4.720046 AGAAAAAGGTTCCTCAGAGGTTC 58.280 43.478 16.65 10.49 36.53 3.62
6249 9896 2.375174 ACTTCCAACATCCCTGCTAACA 59.625 45.455 0.00 0.00 0.00 2.41
6363 10015 3.756069 ACGAGAGTCGGAATTTCTTACG 58.244 45.455 0.86 0.00 45.59 3.18
6383 10037 3.959478 TGTCAAGACAGACACGGAC 57.041 52.632 0.00 0.00 43.18 4.79
6452 10106 1.537202 GACCAGCACTCCAACACAATC 59.463 52.381 0.00 0.00 0.00 2.67
6565 10238 4.162131 GGCATTTGGAATCCCACATAAGTT 59.838 41.667 0.00 0.00 43.41 2.66
6567 10240 3.705579 TGGCATTTGGAATCCCACATAAG 59.294 43.478 0.00 0.00 43.41 1.73
6659 10364 1.615384 GGCCTGATTGACCTTGCTTCT 60.615 52.381 0.00 0.00 0.00 2.85
6660 10365 0.813821 GGCCTGATTGACCTTGCTTC 59.186 55.000 0.00 0.00 0.00 3.86
6661 10366 0.613012 GGGCCTGATTGACCTTGCTT 60.613 55.000 0.84 0.00 0.00 3.91
6664 10369 0.890683 GTTGGGCCTGATTGACCTTG 59.109 55.000 4.53 0.00 0.00 3.61
6665 10370 0.251787 GGTTGGGCCTGATTGACCTT 60.252 55.000 4.53 0.00 0.00 3.50
6667 10372 4.018409 GGTTGGGCCTGATTGACC 57.982 61.111 4.53 0.00 0.00 4.02
6748 10522 1.439679 CAGCGTCAGTTTACCCCTTC 58.560 55.000 0.00 0.00 0.00 3.46
6855 10629 0.250513 CCTACAGAGAAGGCCACCAC 59.749 60.000 5.01 0.00 0.00 4.16
6889 10663 6.041637 ACACTGGAGTCAAACACTACAATCTA 59.958 38.462 0.00 0.00 46.19 1.98
6949 10723 4.223032 GTCTTGACTGGTTCAGGAGGAATA 59.777 45.833 0.00 0.00 40.82 1.75
7039 10813 0.880278 CGTGGCTGGTTGGATATCGG 60.880 60.000 0.00 0.00 0.00 4.18
7048 10822 0.678950 CCAAAATTCCGTGGCTGGTT 59.321 50.000 0.00 0.00 0.00 3.67
7086 10860 2.844122 GCCGATTTTCGTAAGGCAAT 57.156 45.000 0.00 0.00 46.48 3.56
7096 10870 2.723124 ACATGTTGGTGCCGATTTTC 57.277 45.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.