Multiple sequence alignment - TraesCS1A01G351400

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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 TraesCS1A01G351400 chr1A 100.000 5006 0 0 479 5484 535873791 535878796 0.000000e+00 9245
1 TraesCS1A01G351400 chr1A 100.000 309 0 0 1 309 535873313 535873621 6.160000e-159 571
2 TraesCS1A01G351400 chr1A 98.058 309 6 0 1 309 535864998 535865306 6.250000e-149 538
3 TraesCS1A01G351400 chr1A 97.087 309 9 0 1 309 255493857 255493549 6.300000e-144 521
4 TraesCS1A01G351400 chr7A 97.200 1786 42 5 1611 3392 142162008 142163789 0.000000e+00 3014
5 TraesCS1A01G351400 chr7A 97.021 1779 47 3 1617 3391 581919975 581918199 0.000000e+00 2987
6 TraesCS1A01G351400 chr7A 96.695 1785 50 5 1615 3393 142168885 142170666 0.000000e+00 2961
7 TraesCS1A01G351400 chr7A 98.960 1443 15 0 3391 4833 695715143 695716585 0.000000e+00 2582
8 TraesCS1A01G351400 chr7A 98.254 630 10 1 988 1616 695714519 695715148 0.000000e+00 1101
9 TraesCS1A01G351400 chr3A 97.077 1779 41 4 1617 3391 581826869 581828640 0.000000e+00 2987
10 TraesCS1A01G351400 chr3A 76.790 461 101 5 5005 5462 461793200 461793657 2.540000e-63 254
11 TraesCS1A01G351400 chr5A 96.865 1786 50 3 1615 3396 609669001 609667218 0.000000e+00 2983
12 TraesCS1A01G351400 chr5A 96.866 1787 47 5 1613 3392 609675881 609674097 0.000000e+00 2981
13 TraesCS1A01G351400 chr5A 96.633 1782 53 4 1615 3391 683839159 683840938 0.000000e+00 2952
14 TraesCS1A01G351400 chr5A 96.581 1784 52 4 1617 3392 683832294 683834076 0.000000e+00 2948
15 TraesCS1A01G351400 chr5A 99.099 1443 13 0 3391 4833 535690464 535691906 0.000000e+00 2593
16 TraesCS1A01G351400 chr5A 98.889 630 5 2 988 1616 535689841 535690469 0.000000e+00 1123
17 TraesCS1A01G351400 chr5A 97.461 512 12 1 479 990 145403863 145403353 0.000000e+00 872
18 TraesCS1A01G351400 chr5A 96.785 311 8 1 1 309 145404166 145403856 8.140000e-143 518
19 TraesCS1A01G351400 chr5A 95.806 310 12 1 1 309 407384016 407383707 2.950000e-137 499
20 TraesCS1A01G351400 chr5A 77.708 480 101 6 4832 5310 699868432 699868906 6.950000e-74 289
21 TraesCS1A01G351400 chr4A 96.747 1783 52 3 1615 3392 4682966 4681185 0.000000e+00 2966
22 TraesCS1A01G351400 chr4A 96.417 307 8 1 1 304 188014125 188014431 2.280000e-138 503
23 TraesCS1A01G351400 chr2A 99.099 1443 13 0 3391 4833 3421289 3419847 0.000000e+00 2593
24 TraesCS1A01G351400 chr2A 99.206 630 4 1 988 1616 3421913 3421284 0.000000e+00 1134
25 TraesCS1A01G351400 chr2A 99.804 509 1 0 479 987 368743927 368743419 0.000000e+00 935
26 TraesCS1A01G351400 chr2A 99.412 510 3 0 479 988 368735914 368735405 0.000000e+00 926
27 TraesCS1A01G351400 chr2A 98.814 506 5 1 482 987 479305758 479305254 0.000000e+00 900
28 TraesCS1A01G351400 chr2A 98.425 508 7 1 480 987 479314096 479313590 0.000000e+00 893
29 TraesCS1A01G351400 chrUn 98.474 1442 22 0 3391 4832 299171665 299173106 0.000000e+00 2542
30 TraesCS1A01G351400 chrUn 98.577 1405 20 0 3429 4833 320392814 320391410 0.000000e+00 2484
31 TraesCS1A01G351400 chrUn 98.095 630 11 1 988 1616 299171041 299171670 0.000000e+00 1096
32 TraesCS1A01G351400 chrUn 96.343 629 21 2 990 1616 320517779 320517151 0.000000e+00 1033
33 TraesCS1A01G351400 chrUn 96.343 629 21 2 990 1616 357771374 357772002 0.000000e+00 1033
34 TraesCS1A01G351400 chrUn 97.250 509 11 3 479 987 181277358 181277863 0.000000e+00 859
35 TraesCS1A01G351400 chrUn 95.793 309 13 0 1 309 181277057 181277365 2.950000e-137 499
36 TraesCS1A01G351400 chrUn 95.793 309 13 0 1 309 181285031 181285339 2.950000e-137 499
37 TraesCS1A01G351400 chr7D 98.474 1442 22 0 3391 4832 612449472 612448031 0.000000e+00 2542
38 TraesCS1A01G351400 chr7D 98.095 630 11 1 988 1616 612450096 612449467 0.000000e+00 1096
39 TraesCS1A01G351400 chr7D 75.703 498 120 1 4987 5484 292250292 292250788 1.180000e-61 248
40 TraesCS1A01G351400 chr2D 98.062 1445 26 1 3391 4833 627162310 627163754 0.000000e+00 2512
41 TraesCS1A01G351400 chr2D 98.089 628 9 3 988 1613 627161686 627162312 0.000000e+00 1090
42 TraesCS1A01G351400 chr3D 97.367 1443 36 2 3391 4832 51799345 51800786 0.000000e+00 2453
43 TraesCS1A01G351400 chr3D 76.000 500 115 5 4987 5484 441401707 441401211 2.540000e-63 254
44 TraesCS1A01G351400 chr6A 95.565 1443 60 4 3393 4834 134861786 134863225 0.000000e+00 2307
45 TraesCS1A01G351400 chr6A 98.254 630 10 1 988 1616 10198945 10199574 0.000000e+00 1101
46 TraesCS1A01G351400 chr6A 96.452 310 8 2 1 309 38089239 38089546 4.900000e-140 508
47 TraesCS1A01G351400 chr6A 95.498 311 11 3 1 309 425976843 425976534 1.370000e-135 494
48 TraesCS1A01G351400 chr6A 75.703 498 120 1 4987 5484 70548011 70547515 1.180000e-61 248
49 TraesCS1A01G351400 chr6A 75.429 525 114 14 4945 5462 457352247 457352763 1.970000e-59 241
50 TraesCS1A01G351400 chr4B 97.652 511 10 2 479 988 303079556 303079047 0.000000e+00 876
51 TraesCS1A01G351400 chr1B 97.446 509 13 0 479 987 213537016 213537524 0.000000e+00 869
52 TraesCS1A01G351400 chr3B 97.704 479 10 1 509 987 521359291 521358814 0.000000e+00 822
53 TraesCS1A01G351400 chr6D 77.708 480 100 7 4832 5310 159394702 159395175 2.500000e-73 287
54 TraesCS1A01G351400 chr6D 76.141 482 115 0 4987 5468 452434316 452433835 2.540000e-63 254
55 TraesCS1A01G351400 chr6B 77.389 429 95 2 5005 5432 115026327 115026754 2.540000e-63 254


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 TraesCS1A01G351400 chr1A 535873313 535878796 5483 False 4908.0 9245 100.0000 1 5484 2 chr1A.!!$F2 5483
1 TraesCS1A01G351400 chr7A 142162008 142163789 1781 False 3014.0 3014 97.2000 1611 3392 1 chr7A.!!$F1 1781
2 TraesCS1A01G351400 chr7A 581918199 581919975 1776 True 2987.0 2987 97.0210 1617 3391 1 chr7A.!!$R1 1774
3 TraesCS1A01G351400 chr7A 142168885 142170666 1781 False 2961.0 2961 96.6950 1615 3393 1 chr7A.!!$F2 1778
4 TraesCS1A01G351400 chr7A 695714519 695716585 2066 False 1841.5 2582 98.6070 988 4833 2 chr7A.!!$F3 3845
5 TraesCS1A01G351400 chr3A 581826869 581828640 1771 False 2987.0 2987 97.0770 1617 3391 1 chr3A.!!$F2 1774
6 TraesCS1A01G351400 chr5A 609667218 609669001 1783 True 2983.0 2983 96.8650 1615 3396 1 chr5A.!!$R2 1781
7 TraesCS1A01G351400 chr5A 609674097 609675881 1784 True 2981.0 2981 96.8660 1613 3392 1 chr5A.!!$R3 1779
8 TraesCS1A01G351400 chr5A 683839159 683840938 1779 False 2952.0 2952 96.6330 1615 3391 1 chr5A.!!$F2 1776
9 TraesCS1A01G351400 chr5A 683832294 683834076 1782 False 2948.0 2948 96.5810 1617 3392 1 chr5A.!!$F1 1775
10 TraesCS1A01G351400 chr5A 535689841 535691906 2065 False 1858.0 2593 98.9940 988 4833 2 chr5A.!!$F4 3845
11 TraesCS1A01G351400 chr5A 145403353 145404166 813 True 695.0 872 97.1230 1 990 2 chr5A.!!$R4 989
12 TraesCS1A01G351400 chr4A 4681185 4682966 1781 True 2966.0 2966 96.7470 1615 3392 1 chr4A.!!$R1 1777
13 TraesCS1A01G351400 chr2A 3419847 3421913 2066 True 1863.5 2593 99.1525 988 4833 2 chr2A.!!$R5 3845
14 TraesCS1A01G351400 chr2A 368743419 368743927 508 True 935.0 935 99.8040 479 987 1 chr2A.!!$R2 508
15 TraesCS1A01G351400 chr2A 368735405 368735914 509 True 926.0 926 99.4120 479 988 1 chr2A.!!$R1 509
16 TraesCS1A01G351400 chr2A 479305254 479305758 504 True 900.0 900 98.8140 482 987 1 chr2A.!!$R3 505
17 TraesCS1A01G351400 chr2A 479313590 479314096 506 True 893.0 893 98.4250 480 987 1 chr2A.!!$R4 507
18 TraesCS1A01G351400 chrUn 320391410 320392814 1404 True 2484.0 2484 98.5770 3429 4833 1 chrUn.!!$R1 1404
19 TraesCS1A01G351400 chrUn 299171041 299173106 2065 False 1819.0 2542 98.2845 988 4832 2 chrUn.!!$F4 3844
20 TraesCS1A01G351400 chrUn 320517151 320517779 628 True 1033.0 1033 96.3430 990 1616 1 chrUn.!!$R2 626
21 TraesCS1A01G351400 chrUn 357771374 357772002 628 False 1033.0 1033 96.3430 990 1616 1 chrUn.!!$F2 626
22 TraesCS1A01G351400 chrUn 181277057 181277863 806 False 679.0 859 96.5215 1 987 2 chrUn.!!$F3 986
23 TraesCS1A01G351400 chr7D 612448031 612450096 2065 True 1819.0 2542 98.2845 988 4832 2 chr7D.!!$R1 3844
24 TraesCS1A01G351400 chr2D 627161686 627163754 2068 False 1801.0 2512 98.0755 988 4833 2 chr2D.!!$F1 3845
25 TraesCS1A01G351400 chr3D 51799345 51800786 1441 False 2453.0 2453 97.3670 3391 4832 1 chr3D.!!$F1 1441
26 TraesCS1A01G351400 chr6A 134861786 134863225 1439 False 2307.0 2307 95.5650 3393 4834 1 chr6A.!!$F3 1441
27 TraesCS1A01G351400 chr6A 10198945 10199574 629 False 1101.0 1101 98.2540 988 1616 1 chr6A.!!$F1 628
28 TraesCS1A01G351400 chr6A 457352247 457352763 516 False 241.0 241 75.4290 4945 5462 1 chr6A.!!$F4 517
29 TraesCS1A01G351400 chr4B 303079047 303079556 509 True 876.0 876 97.6520 479 988 1 chr4B.!!$R1 509
30 TraesCS1A01G351400 chr1B 213537016 213537524 508 False 869.0 869 97.4460 479 987 1 chr1B.!!$F1 508

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
943 946 0.319083 TAAACGAGGTGACGTGGCAT 59.681 50.0 0.00 0.0 45.83 4.40 F
2486 2579 0.178947 GGATCTCATCCGGGACTCCT 60.179 60.0 0.00 0.0 40.13 3.69 F
2685 2778 0.892063 TCGGATGAACCACGATGTCA 59.108 50.0 0.00 0.0 38.90 3.58 F
2743 2836 1.433837 GCGGTATTGTACTTGCCCGG 61.434 60.0 13.67 0.0 36.05 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2743 2836 2.259505 GGATACCGACGATCGAATCC 57.740 55.000 24.34 19.05 43.74 3.01 R
3522 3619 4.216257 CCGACTTCCACATTTGACTCAAAT 59.784 41.667 10.71 10.71 43.71 2.32 R
4240 4338 5.423610 AGCCAACTCTATGATTCTGTACACT 59.576 40.000 0.00 0.00 0.00 3.55 R
4772 4873 7.745594 CACGCCGTAAGCTAAAATTTACTTTTA 59.254 33.333 0.00 0.00 40.39 1.52 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
42 43 2.046507 CCAGCAGGGCTCACTGAC 60.047 66.667 8.14 0.00 40.97 3.51
46 47 4.007644 CAGGGCTCACTGACGGCA 62.008 66.667 0.00 0.00 40.97 5.69
174 175 3.524606 GACGAATCCGGCGAGGGA 61.525 66.667 9.30 0.00 41.52 4.20
301 304 3.400590 GTGTCGCCGGTGTCGAAC 61.401 66.667 16.01 6.24 37.73 3.95
302 305 4.986587 TGTCGCCGGTGTCGAACG 62.987 66.667 16.01 1.42 37.73 3.95
908 911 5.942325 ATTTGAAAAGTTTCGAACCAACG 57.058 34.783 8.32 0.00 41.83 4.10
922 925 1.075542 CCAACGCGAGATTAGCAACA 58.924 50.000 15.93 0.00 34.19 3.33
923 926 1.061131 CCAACGCGAGATTAGCAACAG 59.939 52.381 15.93 0.00 34.19 3.16
943 946 0.319083 TAAACGAGGTGACGTGGCAT 59.681 50.000 0.00 0.00 45.83 4.40
956 959 1.473965 CGTGGCATCATTAGCAGAGGT 60.474 52.381 0.00 0.00 0.00 3.85
971 974 4.040461 AGCAGAGGTTCACTGTAGCTTAAA 59.960 41.667 0.00 0.00 37.64 1.52
1035 1038 8.287503 GCTGAAATTCAAAAAGATCTTGCAAAT 58.712 29.630 9.17 4.51 0.00 2.32
1302 1308 4.604156 TCTCTCTGTACCATGTCAGTGAT 58.396 43.478 0.00 0.00 34.97 3.06
1316 1322 5.755849 TGTCAGTGATACTACATCAGAGGA 58.244 41.667 0.00 0.00 0.00 3.71
1671 1678 3.802948 ACGTGTCACCAAGATCTATCC 57.197 47.619 0.00 0.00 0.00 2.59
2299 2319 1.774217 TCCCCTTCCACACTTGGCT 60.774 57.895 0.00 0.00 43.56 4.75
2306 2326 2.655090 TCCACACTTGGCTCATGAAA 57.345 45.000 0.00 0.00 43.56 2.69
2374 2394 0.968405 GTGGTCCCAGTACGTTACCA 59.032 55.000 0.00 7.93 37.88 3.25
2395 2488 4.039366 CCAATAAACCCCGAAACTTTTCCA 59.961 41.667 0.00 0.00 33.68 3.53
2486 2579 0.178947 GGATCTCATCCGGGACTCCT 60.179 60.000 0.00 0.00 40.13 3.69
2549 2642 4.036027 CCTAGCGTCATCGAACCTTAAGTA 59.964 45.833 0.97 0.00 39.71 2.24
2685 2778 0.892063 TCGGATGAACCACGATGTCA 59.108 50.000 0.00 0.00 38.90 3.58
2743 2836 1.433837 GCGGTATTGTACTTGCCCGG 61.434 60.000 13.67 0.00 36.05 5.73
2839 2932 2.168521 TCATCCCGTGATCAACTCCTTC 59.831 50.000 0.00 0.00 0.00 3.46
2882 2975 2.363925 GTCCTACCGAGTGGGCCT 60.364 66.667 4.53 0.00 40.62 5.19
2899 2992 2.489437 GGCCTAGAGATACCTCTCCGTT 60.489 54.545 0.00 0.00 46.38 4.44
2900 2993 3.224269 GCCTAGAGATACCTCTCCGTTT 58.776 50.000 0.00 0.00 46.38 3.60
2955 3048 2.285083 CAACCCAACAGACACTTTCGA 58.715 47.619 0.00 0.00 0.00 3.71
2963 3056 4.189639 ACAGACACTTTCGAAGATACCC 57.810 45.455 0.00 0.00 35.04 3.69
2970 3063 2.857592 TTCGAAGATACCCGTAGTGC 57.142 50.000 0.00 0.00 35.04 4.40
3074 3167 7.282585 TCATGGTCTAAGGAAATGATACTTGG 58.717 38.462 0.00 0.00 0.00 3.61
3105 3198 7.549488 AGAAAAGCTTTAGCATACGAACTACAT 59.451 33.333 13.10 0.00 45.16 2.29
3118 3211 5.344066 ACGAACTACATGATCTTGTGCTAG 58.656 41.667 21.20 14.16 0.00 3.42
3234 3331 6.810911 ACTATTGATCAACGAGCTAGTCAAT 58.189 36.000 11.07 13.48 39.06 2.57
3515 3612 2.224670 TGGGGTTCACACCATACAACTC 60.225 50.000 0.00 0.00 46.28 3.01
3522 3619 3.070878 TCACACCATACAACTCTGCTTCA 59.929 43.478 0.00 0.00 0.00 3.02
3918 4016 9.167311 GACTTACACCAATCTTCATTTGTATCT 57.833 33.333 0.00 0.00 0.00 1.98
4845 4947 3.488423 CACTGGTTGGAGGAGCCT 58.512 61.111 0.00 0.00 37.63 4.58
4846 4948 1.763770 CACTGGTTGGAGGAGCCTT 59.236 57.895 0.00 0.00 37.63 4.35
4847 4949 0.322008 CACTGGTTGGAGGAGCCTTC 60.322 60.000 0.00 0.00 37.63 3.46
4848 4950 0.474660 ACTGGTTGGAGGAGCCTTCT 60.475 55.000 0.00 0.00 37.63 2.85
4849 4951 0.695347 CTGGTTGGAGGAGCCTTCTT 59.305 55.000 0.00 0.00 37.63 2.52
4850 4952 0.401738 TGGTTGGAGGAGCCTTCTTG 59.598 55.000 0.00 0.00 37.63 3.02
4851 4953 0.962855 GGTTGGAGGAGCCTTCTTGC 60.963 60.000 0.00 0.00 37.63 4.01
4852 4954 0.962855 GTTGGAGGAGCCTTCTTGCC 60.963 60.000 0.00 0.00 37.63 4.52
4853 4955 1.426251 TTGGAGGAGCCTTCTTGCCA 61.426 55.000 0.00 0.00 37.63 4.92
4854 4956 1.210204 TGGAGGAGCCTTCTTGCCAT 61.210 55.000 0.00 0.00 37.63 4.40
4855 4957 0.750911 GGAGGAGCCTTCTTGCCATG 60.751 60.000 0.00 0.00 0.00 3.66
4856 4958 0.034670 GAGGAGCCTTCTTGCCATGT 60.035 55.000 0.00 0.00 0.00 3.21
4857 4959 0.323178 AGGAGCCTTCTTGCCATGTG 60.323 55.000 0.00 0.00 0.00 3.21
4858 4960 0.610232 GGAGCCTTCTTGCCATGTGT 60.610 55.000 0.00 0.00 0.00 3.72
4859 4961 1.251251 GAGCCTTCTTGCCATGTGTT 58.749 50.000 0.00 0.00 0.00 3.32
4860 4962 2.436417 GAGCCTTCTTGCCATGTGTTA 58.564 47.619 0.00 0.00 0.00 2.41
4861 4963 3.019564 GAGCCTTCTTGCCATGTGTTAT 58.980 45.455 0.00 0.00 0.00 1.89
4862 4964 3.019564 AGCCTTCTTGCCATGTGTTATC 58.980 45.455 0.00 0.00 0.00 1.75
4863 4965 3.019564 GCCTTCTTGCCATGTGTTATCT 58.980 45.455 0.00 0.00 0.00 1.98
4864 4966 3.065925 GCCTTCTTGCCATGTGTTATCTC 59.934 47.826 0.00 0.00 0.00 2.75
4865 4967 3.310774 CCTTCTTGCCATGTGTTATCTCG 59.689 47.826 0.00 0.00 0.00 4.04
4866 4968 3.610040 TCTTGCCATGTGTTATCTCGT 57.390 42.857 0.00 0.00 0.00 4.18
4867 4969 3.937814 TCTTGCCATGTGTTATCTCGTT 58.062 40.909 0.00 0.00 0.00 3.85
4868 4970 5.079689 TCTTGCCATGTGTTATCTCGTTA 57.920 39.130 0.00 0.00 0.00 3.18
4869 4971 4.868171 TCTTGCCATGTGTTATCTCGTTAC 59.132 41.667 0.00 0.00 0.00 2.50
4870 4972 3.183754 TGCCATGTGTTATCTCGTTACG 58.816 45.455 0.00 0.00 0.00 3.18
4871 4973 2.034001 GCCATGTGTTATCTCGTTACGC 60.034 50.000 0.00 0.00 0.00 4.42
4872 4974 3.183754 CCATGTGTTATCTCGTTACGCA 58.816 45.455 0.00 0.00 36.80 5.24
4873 4975 3.000078 CCATGTGTTATCTCGTTACGCAC 60.000 47.826 0.00 1.88 35.39 5.34
4874 4976 3.285816 TGTGTTATCTCGTTACGCACA 57.714 42.857 8.93 8.93 33.71 4.57
4875 4977 3.840468 TGTGTTATCTCGTTACGCACAT 58.160 40.909 8.93 0.19 31.57 3.21
4876 4978 3.610677 TGTGTTATCTCGTTACGCACATG 59.389 43.478 8.93 0.00 31.57 3.21
4877 4979 2.601314 TGTTATCTCGTTACGCACATGC 59.399 45.455 0.00 0.00 37.78 4.06
4878 4980 1.847818 TATCTCGTTACGCACATGCC 58.152 50.000 0.00 0.00 37.91 4.40
4879 4981 0.108377 ATCTCGTTACGCACATGCCA 60.108 50.000 0.00 0.00 37.91 4.92
4880 4982 1.011968 TCTCGTTACGCACATGCCAC 61.012 55.000 0.00 0.00 37.91 5.01
4881 4983 2.095656 CGTTACGCACATGCCACG 59.904 61.111 0.00 1.19 37.91 4.94
4882 4984 2.663478 CGTTACGCACATGCCACGT 61.663 57.895 12.11 12.11 43.45 4.49
4883 4985 1.131826 GTTACGCACATGCCACGTC 59.868 57.895 10.98 0.00 40.99 4.34
4884 4986 2.030401 TTACGCACATGCCACGTCC 61.030 57.895 10.98 0.00 40.99 4.79
4889 4991 4.634703 ACATGCCACGTCCGCCAA 62.635 61.111 0.00 0.00 0.00 4.52
4890 4992 3.361158 CATGCCACGTCCGCCAAA 61.361 61.111 1.87 0.00 0.00 3.28
4891 4993 3.055719 ATGCCACGTCCGCCAAAG 61.056 61.111 1.87 0.00 0.00 2.77
4892 4994 3.842925 ATGCCACGTCCGCCAAAGT 62.843 57.895 1.87 0.00 0.00 2.66
4893 4995 4.025401 GCCACGTCCGCCAAAGTG 62.025 66.667 0.00 0.00 0.00 3.16
4894 4996 2.590575 CCACGTCCGCCAAAGTGT 60.591 61.111 0.00 0.00 33.14 3.55
4895 4997 2.604174 CCACGTCCGCCAAAGTGTC 61.604 63.158 0.00 0.00 33.14 3.67
4896 4998 1.885388 CACGTCCGCCAAAGTGTCA 60.885 57.895 0.00 0.00 0.00 3.58
4897 4999 1.070786 ACGTCCGCCAAAGTGTCAT 59.929 52.632 0.00 0.00 0.00 3.06
4898 5000 0.534203 ACGTCCGCCAAAGTGTCATT 60.534 50.000 0.00 0.00 0.00 2.57
4899 5001 1.270412 ACGTCCGCCAAAGTGTCATTA 60.270 47.619 0.00 0.00 0.00 1.90
4900 5002 1.393539 CGTCCGCCAAAGTGTCATTAG 59.606 52.381 0.00 0.00 0.00 1.73
4901 5003 1.130561 GTCCGCCAAAGTGTCATTAGC 59.869 52.381 0.00 0.00 0.00 3.09
4902 5004 1.164411 CCGCCAAAGTGTCATTAGCA 58.836 50.000 0.00 0.00 0.00 3.49
4903 5005 1.131126 CCGCCAAAGTGTCATTAGCAG 59.869 52.381 0.00 0.00 0.00 4.24
4904 5006 2.076100 CGCCAAAGTGTCATTAGCAGA 58.924 47.619 0.00 0.00 0.00 4.26
4905 5007 2.483877 CGCCAAAGTGTCATTAGCAGAA 59.516 45.455 0.00 0.00 0.00 3.02
4906 5008 3.667960 CGCCAAAGTGTCATTAGCAGAAC 60.668 47.826 0.00 0.00 0.00 3.01
4907 5009 3.366374 GCCAAAGTGTCATTAGCAGAACC 60.366 47.826 0.00 0.00 0.00 3.62
4908 5010 3.820467 CCAAAGTGTCATTAGCAGAACCA 59.180 43.478 0.00 0.00 0.00 3.67
4909 5011 4.460382 CCAAAGTGTCATTAGCAGAACCAT 59.540 41.667 0.00 0.00 0.00 3.55
4910 5012 5.392380 CCAAAGTGTCATTAGCAGAACCATC 60.392 44.000 0.00 0.00 0.00 3.51
4911 5013 3.878778 AGTGTCATTAGCAGAACCATCC 58.121 45.455 0.00 0.00 0.00 3.51
4912 5014 3.521126 AGTGTCATTAGCAGAACCATCCT 59.479 43.478 0.00 0.00 0.00 3.24
4913 5015 3.873952 GTGTCATTAGCAGAACCATCCTC 59.126 47.826 0.00 0.00 0.00 3.71
4914 5016 3.519107 TGTCATTAGCAGAACCATCCTCA 59.481 43.478 0.00 0.00 0.00 3.86
4915 5017 3.873952 GTCATTAGCAGAACCATCCTCAC 59.126 47.826 0.00 0.00 0.00 3.51
4916 5018 3.118261 TCATTAGCAGAACCATCCTCACC 60.118 47.826 0.00 0.00 0.00 4.02
4917 5019 0.824109 TAGCAGAACCATCCTCACCG 59.176 55.000 0.00 0.00 0.00 4.94
4918 5020 1.194781 AGCAGAACCATCCTCACCGT 61.195 55.000 0.00 0.00 0.00 4.83
4919 5021 0.321653 GCAGAACCATCCTCACCGTT 60.322 55.000 0.00 0.00 0.00 4.44
4920 5022 1.882352 GCAGAACCATCCTCACCGTTT 60.882 52.381 0.00 0.00 0.00 3.60
4921 5023 2.076863 CAGAACCATCCTCACCGTTTC 58.923 52.381 0.00 0.00 0.00 2.78
4922 5024 1.978580 AGAACCATCCTCACCGTTTCT 59.021 47.619 0.00 0.00 0.00 2.52
4923 5025 2.076863 GAACCATCCTCACCGTTTCTG 58.923 52.381 0.00 0.00 0.00 3.02
4924 5026 1.348064 ACCATCCTCACCGTTTCTGA 58.652 50.000 0.00 0.00 0.00 3.27
4925 5027 1.276421 ACCATCCTCACCGTTTCTGAG 59.724 52.381 0.00 0.00 35.78 3.35
4926 5028 1.550524 CCATCCTCACCGTTTCTGAGA 59.449 52.381 0.00 0.00 37.90 3.27
4927 5029 2.417924 CCATCCTCACCGTTTCTGAGAG 60.418 54.545 0.00 0.00 37.90 3.20
4928 5030 1.257743 TCCTCACCGTTTCTGAGAGG 58.742 55.000 0.00 0.00 45.64 3.69
4929 5031 0.247736 CCTCACCGTTTCTGAGAGGG 59.752 60.000 5.48 5.48 41.65 4.30
4930 5032 0.247736 CTCACCGTTTCTGAGAGGGG 59.752 60.000 11.07 2.10 37.90 4.79
4931 5033 1.376037 CACCGTTTCTGAGAGGGGC 60.376 63.158 11.07 0.00 0.00 5.80
4932 5034 1.536662 ACCGTTTCTGAGAGGGGCT 60.537 57.895 11.07 0.00 0.00 5.19
4933 5035 1.219393 CCGTTTCTGAGAGGGGCTC 59.781 63.158 0.00 0.00 44.21 4.70
4952 5054 1.760480 AAGCACCCCCAACAACCAC 60.760 57.895 0.00 0.00 0.00 4.16
4955 5057 1.530655 CACCCCCAACAACCACTCC 60.531 63.158 0.00 0.00 0.00 3.85
4969 5071 2.425592 CTCCGGTCCAGTGTTGCA 59.574 61.111 0.00 0.00 0.00 4.08
4970 5072 1.669115 CTCCGGTCCAGTGTTGCAG 60.669 63.158 0.00 0.00 0.00 4.41
4973 5075 0.249120 CCGGTCCAGTGTTGCAGATA 59.751 55.000 0.00 0.00 0.00 1.98
4978 5080 3.624861 GGTCCAGTGTTGCAGATAGATTG 59.375 47.826 0.00 0.00 0.00 2.67
4979 5081 3.624861 GTCCAGTGTTGCAGATAGATTGG 59.375 47.826 0.00 0.00 0.00 3.16
4981 5083 3.624861 CCAGTGTTGCAGATAGATTGGAC 59.375 47.826 0.00 0.00 0.00 4.02
4982 5084 4.511527 CAGTGTTGCAGATAGATTGGACT 58.488 43.478 0.00 0.00 0.00 3.85
4983 5085 4.940046 CAGTGTTGCAGATAGATTGGACTT 59.060 41.667 0.00 0.00 0.00 3.01
4984 5086 5.064452 CAGTGTTGCAGATAGATTGGACTTC 59.936 44.000 0.00 0.00 0.00 3.01
4990 5092 3.006323 CAGATAGATTGGACTTCCGGGAG 59.994 52.174 8.71 8.71 39.43 4.30
4991 5093 1.120530 TAGATTGGACTTCCGGGAGC 58.879 55.000 10.62 2.19 39.43 4.70
4992 5094 1.521681 GATTGGACTTCCGGGAGCG 60.522 63.158 10.62 0.00 39.43 5.03
4993 5095 2.925162 GATTGGACTTCCGGGAGCGG 62.925 65.000 10.62 0.00 39.43 5.52
5021 5123 3.379880 GCCATGGCTTGCCAAAGA 58.620 55.556 29.98 0.00 35.19 2.52
5022 5124 1.217244 GCCATGGCTTGCCAAAGAG 59.783 57.895 29.98 8.52 35.19 2.85
5028 5130 2.956987 CTTGCCAAAGAGCCACCG 59.043 61.111 0.00 0.00 35.19 4.94
5031 5133 4.043200 GCCAAAGAGCCACCGCAC 62.043 66.667 0.00 0.00 37.52 5.34
5032 5134 3.726517 CCAAAGAGCCACCGCACG 61.727 66.667 0.00 0.00 37.52 5.34
5033 5135 4.389576 CAAAGAGCCACCGCACGC 62.390 66.667 0.00 0.00 37.52 5.34
5059 5161 4.007457 GCAGAAGGCATGGAAGCA 57.993 55.556 0.00 0.00 43.97 3.91
5081 5183 1.300971 CCTCGCATTCCACACCACAG 61.301 60.000 0.00 0.00 0.00 3.66
5083 5185 0.320683 TCGCATTCCACACCACAGAG 60.321 55.000 0.00 0.00 0.00 3.35
5091 5193 2.034687 CACCACAGAGGGGGCAAG 59.965 66.667 0.00 0.00 43.89 4.01
5098 5200 1.462238 AGAGGGGGCAAGTGTCAGT 60.462 57.895 0.00 0.00 0.00 3.41
5099 5201 1.302832 GAGGGGGCAAGTGTCAGTG 60.303 63.158 0.00 0.00 0.00 3.66
5101 5203 1.136329 AGGGGGCAAGTGTCAGTGAT 61.136 55.000 0.00 0.00 0.00 3.06
5105 5207 1.677217 GGGCAAGTGTCAGTGATCTCC 60.677 57.143 0.00 0.00 0.00 3.71
5108 5210 2.344950 CAAGTGTCAGTGATCTCCAGC 58.655 52.381 0.00 0.00 0.00 4.85
5109 5211 0.901124 AGTGTCAGTGATCTCCAGCC 59.099 55.000 0.00 0.00 0.00 4.85
5110 5212 0.107945 GTGTCAGTGATCTCCAGCCC 60.108 60.000 0.00 0.00 0.00 5.19
5111 5213 1.267574 TGTCAGTGATCTCCAGCCCC 61.268 60.000 0.00 0.00 0.00 5.80
5114 5216 2.764128 GTGATCTCCAGCCCCCGA 60.764 66.667 0.00 0.00 0.00 5.14
5120 5222 1.377333 CTCCAGCCCCCGAGAAAAC 60.377 63.158 0.00 0.00 0.00 2.43
5126 5228 2.423538 CAGCCCCCGAGAAAACTTATTG 59.576 50.000 0.00 0.00 0.00 1.90
5128 5230 2.619590 GCCCCCGAGAAAACTTATTGGA 60.620 50.000 0.00 0.00 0.00 3.53
5132 5234 4.270008 CCCGAGAAAACTTATTGGACCAT 58.730 43.478 0.00 0.00 0.00 3.55
5138 5240 6.245408 AGAAAACTTATTGGACCATGTAGCA 58.755 36.000 0.00 0.00 0.00 3.49
5141 5243 4.526970 ACTTATTGGACCATGTAGCAAGG 58.473 43.478 0.00 0.00 0.00 3.61
5144 5246 1.367346 TGGACCATGTAGCAAGGGAA 58.633 50.000 0.00 0.00 0.00 3.97
5147 5249 3.245586 TGGACCATGTAGCAAGGGAATTT 60.246 43.478 0.00 0.00 0.00 1.82
5149 5251 4.016444 GACCATGTAGCAAGGGAATTTGA 58.984 43.478 0.00 0.00 0.00 2.69
5152 5254 4.380867 CCATGTAGCAAGGGAATTTGACAC 60.381 45.833 0.00 0.00 0.00 3.67
5155 5257 4.278170 TGTAGCAAGGGAATTTGACACAAG 59.722 41.667 0.00 0.00 0.00 3.16
5156 5258 3.565307 AGCAAGGGAATTTGACACAAGA 58.435 40.909 0.00 0.00 0.00 3.02
5157 5259 3.319122 AGCAAGGGAATTTGACACAAGAC 59.681 43.478 0.00 0.00 0.00 3.01
5162 5264 2.228822 GGAATTTGACACAAGACGCCAT 59.771 45.455 0.00 0.00 0.00 4.40
5168 5270 0.311790 ACACAAGACGCCATGCAAAG 59.688 50.000 0.00 0.00 0.00 2.77
5171 5273 0.877071 CAAGACGCCATGCAAAGACT 59.123 50.000 0.00 0.00 0.00 3.24
5226 5328 3.982372 TTCCAGATGGCGCGACGAC 62.982 63.158 12.10 4.87 34.27 4.34
5243 5345 4.431131 CCATCCGGTGCCCTGCTT 62.431 66.667 0.00 0.00 0.00 3.91
5244 5346 3.136123 CATCCGGTGCCCTGCTTG 61.136 66.667 0.00 0.00 0.00 4.01
5245 5347 3.329889 ATCCGGTGCCCTGCTTGA 61.330 61.111 0.00 0.00 0.00 3.02
5246 5348 2.905996 ATCCGGTGCCCTGCTTGAA 61.906 57.895 0.00 0.00 0.00 2.69
5285 5387 3.274586 CGCTCGTCCATGGCCATG 61.275 66.667 34.82 34.82 38.51 3.66
5288 5390 4.854924 TCGTCCATGGCCATGCGG 62.855 66.667 36.08 25.46 37.49 5.69
5291 5393 1.228245 GTCCATGGCCATGCGGTAT 60.228 57.895 36.08 3.09 37.49 2.73
5303 5405 2.725641 CGGTATGCGGATCGGACA 59.274 61.111 4.16 2.42 0.00 4.02
5310 5412 1.215647 GCGGATCGGACAGTGAAGT 59.784 57.895 4.16 0.00 0.00 3.01
5312 5414 1.350193 CGGATCGGACAGTGAAGTTG 58.650 55.000 0.00 0.00 0.00 3.16
5315 5417 0.321653 ATCGGACAGTGAAGTTGCCC 60.322 55.000 0.00 0.00 0.00 5.36
5316 5418 2.317609 CGGACAGTGAAGTTGCCCG 61.318 63.158 0.00 0.00 0.00 6.13
5317 5419 1.070786 GGACAGTGAAGTTGCCCGA 59.929 57.895 0.00 0.00 0.00 5.14
5348 5450 1.379044 CCAGGCAAGGGTGTCATCC 60.379 63.158 0.00 0.00 0.00 3.51
5350 5452 2.438434 GGCAAGGGTGTCATCCGG 60.438 66.667 0.00 0.00 0.00 5.14
5351 5453 2.668632 GCAAGGGTGTCATCCGGA 59.331 61.111 6.61 6.61 0.00 5.14
5352 5454 1.002624 GCAAGGGTGTCATCCGGAA 60.003 57.895 9.01 0.00 0.00 4.30
5353 5455 1.305930 GCAAGGGTGTCATCCGGAAC 61.306 60.000 9.01 3.13 0.00 3.62
5354 5456 0.036164 CAAGGGTGTCATCCGGAACA 59.964 55.000 9.01 6.55 0.00 3.18
5357 5459 1.005394 GGTGTCATCCGGAACACGT 60.005 57.895 25.69 0.96 42.24 4.49
5360 5462 1.005394 GTCATCCGGAACACGTGGT 60.005 57.895 21.57 14.94 42.24 4.16
5365 5467 2.357034 CGGAACACGTGGTGAGGG 60.357 66.667 21.57 0.00 36.96 4.30
5368 5470 4.619227 AACACGTGGTGAGGGGCG 62.619 66.667 21.57 0.00 36.96 6.13
5378 5480 3.797353 GAGGGGCGGATGCTGGAA 61.797 66.667 0.00 0.00 42.25 3.53
5381 5483 1.150536 GGGGCGGATGCTGGAAATA 59.849 57.895 0.00 0.00 42.25 1.40
5382 5484 0.467290 GGGGCGGATGCTGGAAATAA 60.467 55.000 0.00 0.00 42.25 1.40
5383 5485 1.620822 GGGCGGATGCTGGAAATAAT 58.379 50.000 0.00 0.00 42.25 1.28
5384 5486 1.541588 GGGCGGATGCTGGAAATAATC 59.458 52.381 0.00 0.00 42.25 1.75
5387 5489 2.485814 GCGGATGCTGGAAATAATCTCC 59.514 50.000 0.00 0.00 38.39 3.71
5394 5496 3.681594 GCTGGAAATAATCTCCACGTCCA 60.682 47.826 0.00 0.00 38.07 4.02
5395 5497 4.708177 CTGGAAATAATCTCCACGTCCAT 58.292 43.478 0.00 0.00 38.07 3.41
5396 5498 5.741964 GCTGGAAATAATCTCCACGTCCATA 60.742 44.000 0.00 0.00 38.07 2.74
5412 5514 1.486211 CATAGGGAGGAAGTGTCGGT 58.514 55.000 0.00 0.00 0.00 4.69
5414 5516 0.113776 TAGGGAGGAAGTGTCGGTGT 59.886 55.000 0.00 0.00 0.00 4.16
5417 5519 0.531200 GGAGGAAGTGTCGGTGTAGG 59.469 60.000 0.00 0.00 0.00 3.18
5420 5522 0.531200 GGAAGTGTCGGTGTAGGAGG 59.469 60.000 0.00 0.00 0.00 4.30
5432 5534 0.388294 GTAGGAGGTCCATACGCCAC 59.612 60.000 0.00 0.00 38.89 5.01
5433 5535 0.260816 TAGGAGGTCCATACGCCACT 59.739 55.000 0.00 0.00 38.89 4.00
5434 5536 1.043673 AGGAGGTCCATACGCCACTC 61.044 60.000 0.00 0.00 38.89 3.51
5438 5540 2.766651 TCCATACGCCACTCCCCC 60.767 66.667 0.00 0.00 0.00 5.40
5474 5576 3.799755 GCCACGCGCCTTAACCTG 61.800 66.667 5.73 0.00 0.00 4.00
5475 5577 3.799755 CCACGCGCCTTAACCTGC 61.800 66.667 5.73 0.00 0.00 4.85
5476 5578 3.047280 CACGCGCCTTAACCTGCA 61.047 61.111 5.73 0.00 0.00 4.41
5477 5579 2.281208 ACGCGCCTTAACCTGCAA 60.281 55.556 5.73 0.00 0.00 4.08
5478 5580 2.325082 ACGCGCCTTAACCTGCAAG 61.325 57.895 5.73 0.00 0.00 4.01
5479 5581 2.325082 CGCGCCTTAACCTGCAAGT 61.325 57.895 0.00 0.00 0.00 3.16
5480 5582 1.502190 GCGCCTTAACCTGCAAGTC 59.498 57.895 0.00 0.00 0.00 3.01
5481 5583 0.955919 GCGCCTTAACCTGCAAGTCT 60.956 55.000 0.00 0.00 0.00 3.24
5482 5584 1.079503 CGCCTTAACCTGCAAGTCTC 58.920 55.000 0.00 0.00 0.00 3.36
5483 5585 1.454201 GCCTTAACCTGCAAGTCTCC 58.546 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 3.989698 CTGCCCTCTACACGTGCCG 62.990 68.421 17.22 6.92 0.00 5.69
46 47 0.681564 CCTCTCTGCCCTCTACACGT 60.682 60.000 0.00 0.00 0.00 4.49
908 911 3.611113 TCGTTTACTGTTGCTAATCTCGC 59.389 43.478 0.00 0.00 0.00 5.03
922 925 0.319297 GCCACGTCACCTCGTTTACT 60.319 55.000 0.00 0.00 42.27 2.24
923 926 0.598158 TGCCACGTCACCTCGTTTAC 60.598 55.000 0.00 0.00 42.27 2.01
943 946 4.382040 GCTACAGTGAACCTCTGCTAATGA 60.382 45.833 0.00 0.00 36.50 2.57
956 959 4.383335 CCCGGGTATTTAAGCTACAGTGAA 60.383 45.833 14.18 0.00 0.00 3.18
971 974 0.468585 TCTATGTGACGCCCGGGTAT 60.469 55.000 24.63 10.89 0.00 2.73
1035 1038 0.179059 TGACCTCTTCTGCGCAACAA 60.179 50.000 13.05 6.40 0.00 2.83
1302 1308 7.284944 GCTACCTTTAGTTCCTCTGATGTAGTA 59.715 40.741 0.00 0.00 0.00 1.82
1316 1322 5.925509 TGTCAACAAGAGCTACCTTTAGTT 58.074 37.500 0.00 0.00 0.00 2.24
1671 1678 1.466167 CTCGTTGCTGGTTTCTCCATG 59.534 52.381 0.00 0.00 46.12 3.66
2374 2394 4.897076 ACTGGAAAAGTTTCGGGGTTTATT 59.103 37.500 0.00 0.00 34.57 1.40
2395 2488 2.422945 GGGAAGTCCTGTTTTGGTCACT 60.423 50.000 0.00 0.00 35.95 3.41
2486 2579 6.228995 TGTATGTGGTTACCGAATGTTGTTA 58.771 36.000 0.00 0.00 0.00 2.41
2743 2836 2.259505 GGATACCGACGATCGAATCC 57.740 55.000 24.34 19.05 43.74 3.01
2839 2932 6.747659 CATCATAATGTGCACAATGTGATG 57.252 37.500 37.96 37.96 43.65 3.07
2899 2992 4.069304 CTGGGATTTTTCACTCCGTGTAA 58.931 43.478 0.00 0.00 34.79 2.41
2900 2993 3.071892 ACTGGGATTTTTCACTCCGTGTA 59.928 43.478 0.00 0.00 34.79 2.90
2912 3005 3.262420 CACGAATCGAGACTGGGATTTT 58.738 45.455 10.55 0.00 33.25 1.82
2955 3048 1.861982 AGGTGCACTACGGGTATCTT 58.138 50.000 17.98 0.00 0.00 2.40
2963 3056 4.110482 GGTGACTATAAAGGTGCACTACG 58.890 47.826 17.98 1.40 0.00 3.51
2970 3063 5.107133 CGTAACTGGGTGACTATAAAGGTG 58.893 45.833 0.00 0.00 0.00 4.00
3074 3167 6.715464 TCGTATGCTAAAGCTTTTCTAATGC 58.285 36.000 18.47 12.25 42.66 3.56
3105 3198 3.374764 TCCTAAGCCTAGCACAAGATCA 58.625 45.455 0.00 0.00 0.00 2.92
3118 3211 2.644676 GACAAGACCCAATCCTAAGCC 58.355 52.381 0.00 0.00 0.00 4.35
3209 3302 5.822278 TGACTAGCTCGTTGATCAATAGTC 58.178 41.667 25.71 25.71 38.61 2.59
3234 3331 4.223953 CCATGTCCCTAGTAAGCCTCTAA 58.776 47.826 0.00 0.00 0.00 2.10
3522 3619 4.216257 CCGACTTCCACATTTGACTCAAAT 59.784 41.667 10.71 10.71 43.71 2.32
3913 4011 9.405587 GCAACATAGAAGATCTCAACTAGATAC 57.594 37.037 0.00 0.00 45.35 2.24
3918 4016 6.544928 TGGCAACATAGAAGATCTCAACTA 57.455 37.500 0.00 1.29 46.17 2.24
4240 4338 5.423610 AGCCAACTCTATGATTCTGTACACT 59.576 40.000 0.00 0.00 0.00 3.55
4772 4873 7.745594 CACGCCGTAAGCTAAAATTTACTTTTA 59.254 33.333 0.00 0.00 40.39 1.52
4834 4936 1.380302 GGCAAGAAGGCTCCTCCAA 59.620 57.895 0.00 0.00 40.24 3.53
4835 4937 1.210204 ATGGCAAGAAGGCTCCTCCA 61.210 55.000 0.00 0.00 44.55 3.86
4836 4938 0.750911 CATGGCAAGAAGGCTCCTCC 60.751 60.000 0.00 0.00 44.55 4.30
4837 4939 0.034670 ACATGGCAAGAAGGCTCCTC 60.035 55.000 0.00 0.00 44.55 3.71
4838 4940 0.323178 CACATGGCAAGAAGGCTCCT 60.323 55.000 0.00 0.00 44.55 3.69
4839 4941 0.610232 ACACATGGCAAGAAGGCTCC 60.610 55.000 0.00 0.00 44.55 4.70
4840 4942 1.251251 AACACATGGCAAGAAGGCTC 58.749 50.000 0.00 0.00 44.55 4.70
4841 4943 2.584835 TAACACATGGCAAGAAGGCT 57.415 45.000 0.00 0.00 44.55 4.58
4842 4944 3.019564 AGATAACACATGGCAAGAAGGC 58.980 45.455 0.00 0.00 44.50 4.35
4843 4945 3.310774 CGAGATAACACATGGCAAGAAGG 59.689 47.826 0.00 0.00 0.00 3.46
4844 4946 3.935203 ACGAGATAACACATGGCAAGAAG 59.065 43.478 0.00 0.00 0.00 2.85
4845 4947 3.937814 ACGAGATAACACATGGCAAGAA 58.062 40.909 0.00 0.00 0.00 2.52
4846 4948 3.610040 ACGAGATAACACATGGCAAGA 57.390 42.857 0.00 0.00 0.00 3.02
4847 4949 4.259810 CGTAACGAGATAACACATGGCAAG 60.260 45.833 0.00 0.00 0.00 4.01
4848 4950 3.615056 CGTAACGAGATAACACATGGCAA 59.385 43.478 0.00 0.00 0.00 4.52
4849 4951 3.183754 CGTAACGAGATAACACATGGCA 58.816 45.455 0.00 0.00 0.00 4.92
4850 4952 2.034001 GCGTAACGAGATAACACATGGC 60.034 50.000 0.00 0.00 0.00 4.40
4851 4953 3.000078 GTGCGTAACGAGATAACACATGG 60.000 47.826 0.00 0.00 0.00 3.66
4852 4954 3.610677 TGTGCGTAACGAGATAACACATG 59.389 43.478 0.00 0.00 32.06 3.21
4853 4955 3.840468 TGTGCGTAACGAGATAACACAT 58.160 40.909 0.00 0.00 32.06 3.21
4854 4956 3.285816 TGTGCGTAACGAGATAACACA 57.714 42.857 0.00 0.00 34.43 3.72
4855 4957 3.541516 GCATGTGCGTAACGAGATAACAC 60.542 47.826 0.00 0.00 0.00 3.32
4856 4958 2.601314 GCATGTGCGTAACGAGATAACA 59.399 45.455 0.00 0.00 0.00 2.41
4857 4959 2.034001 GGCATGTGCGTAACGAGATAAC 60.034 50.000 0.00 0.00 43.26 1.89
4858 4960 2.198406 GGCATGTGCGTAACGAGATAA 58.802 47.619 0.00 0.00 43.26 1.75
4859 4961 1.135333 TGGCATGTGCGTAACGAGATA 59.865 47.619 0.00 0.00 43.26 1.98
4860 4962 0.108377 TGGCATGTGCGTAACGAGAT 60.108 50.000 0.00 0.00 43.26 2.75
4861 4963 1.011968 GTGGCATGTGCGTAACGAGA 61.012 55.000 0.00 0.00 43.26 4.04
4862 4964 1.419922 GTGGCATGTGCGTAACGAG 59.580 57.895 0.00 0.00 43.26 4.18
4863 4965 2.376538 CGTGGCATGTGCGTAACGA 61.377 57.895 16.40 0.00 41.96 3.85
4864 4966 2.095656 CGTGGCATGTGCGTAACG 59.904 61.111 10.53 10.53 43.26 3.18
4865 4967 1.131826 GACGTGGCATGTGCGTAAC 59.868 57.895 18.67 0.00 43.26 2.50
4866 4968 2.030401 GGACGTGGCATGTGCGTAA 61.030 57.895 18.67 0.00 43.26 3.18
4867 4969 2.433491 GGACGTGGCATGTGCGTA 60.433 61.111 18.67 0.00 43.26 4.42
4872 4974 4.634703 TTGGCGGACGTGGCATGT 62.635 61.111 13.11 13.11 44.53 3.21
4873 4975 3.326889 CTTTGGCGGACGTGGCATG 62.327 63.158 4.87 4.87 44.53 4.06
4874 4976 3.055719 CTTTGGCGGACGTGGCAT 61.056 61.111 10.04 0.00 44.53 4.40
4875 4977 4.555709 ACTTTGGCGGACGTGGCA 62.556 61.111 10.04 4.36 43.36 4.92
4876 4978 4.025401 CACTTTGGCGGACGTGGC 62.025 66.667 0.00 0.00 0.00 5.01
4877 4979 2.590575 ACACTTTGGCGGACGTGG 60.591 61.111 0.00 0.00 0.00 4.94
4878 4980 1.227999 ATGACACTTTGGCGGACGTG 61.228 55.000 0.00 0.00 0.00 4.49
4879 4981 0.534203 AATGACACTTTGGCGGACGT 60.534 50.000 0.00 0.00 0.00 4.34
4880 4982 1.393539 CTAATGACACTTTGGCGGACG 59.606 52.381 0.00 0.00 0.00 4.79
4881 4983 1.130561 GCTAATGACACTTTGGCGGAC 59.869 52.381 0.00 0.00 0.00 4.79
4882 4984 1.271108 TGCTAATGACACTTTGGCGGA 60.271 47.619 0.00 0.00 33.71 5.54
4883 4985 1.131126 CTGCTAATGACACTTTGGCGG 59.869 52.381 0.00 0.00 33.71 6.13
4884 4986 2.076100 TCTGCTAATGACACTTTGGCG 58.924 47.619 0.00 0.00 33.71 5.69
4885 4987 3.366374 GGTTCTGCTAATGACACTTTGGC 60.366 47.826 0.00 0.00 0.00 4.52
4886 4988 3.820467 TGGTTCTGCTAATGACACTTTGG 59.180 43.478 0.00 0.00 0.00 3.28
4887 4989 5.392380 GGATGGTTCTGCTAATGACACTTTG 60.392 44.000 0.00 0.00 0.00 2.77
4888 4990 4.702131 GGATGGTTCTGCTAATGACACTTT 59.298 41.667 0.00 0.00 0.00 2.66
4889 4991 4.018960 AGGATGGTTCTGCTAATGACACTT 60.019 41.667 0.00 0.00 0.00 3.16
4890 4992 3.521126 AGGATGGTTCTGCTAATGACACT 59.479 43.478 0.00 0.00 0.00 3.55
4891 4993 3.873952 GAGGATGGTTCTGCTAATGACAC 59.126 47.826 0.00 0.00 0.00 3.67
4892 4994 3.519107 TGAGGATGGTTCTGCTAATGACA 59.481 43.478 0.00 0.00 0.00 3.58
4893 4995 3.873952 GTGAGGATGGTTCTGCTAATGAC 59.126 47.826 0.00 0.00 0.00 3.06
4894 4996 3.118261 GGTGAGGATGGTTCTGCTAATGA 60.118 47.826 0.00 0.00 0.00 2.57
4895 4997 3.209410 GGTGAGGATGGTTCTGCTAATG 58.791 50.000 0.00 0.00 0.00 1.90
4896 4998 2.158900 CGGTGAGGATGGTTCTGCTAAT 60.159 50.000 0.00 0.00 0.00 1.73
4897 4999 1.207089 CGGTGAGGATGGTTCTGCTAA 59.793 52.381 0.00 0.00 0.00 3.09
4898 5000 0.824109 CGGTGAGGATGGTTCTGCTA 59.176 55.000 0.00 0.00 0.00 3.49
4899 5001 1.194781 ACGGTGAGGATGGTTCTGCT 61.195 55.000 0.00 0.00 0.00 4.24
4900 5002 0.321653 AACGGTGAGGATGGTTCTGC 60.322 55.000 0.00 0.00 0.00 4.26
4901 5003 2.076863 GAAACGGTGAGGATGGTTCTG 58.923 52.381 0.00 0.00 0.00 3.02
4902 5004 1.978580 AGAAACGGTGAGGATGGTTCT 59.021 47.619 0.00 0.00 0.00 3.01
4903 5005 2.076863 CAGAAACGGTGAGGATGGTTC 58.923 52.381 0.00 0.00 0.00 3.62
4904 5006 1.697432 TCAGAAACGGTGAGGATGGTT 59.303 47.619 0.00 0.00 0.00 3.67
4905 5007 1.276421 CTCAGAAACGGTGAGGATGGT 59.724 52.381 0.00 0.00 38.24 3.55
4906 5008 1.550524 TCTCAGAAACGGTGAGGATGG 59.449 52.381 0.47 0.00 41.62 3.51
4907 5009 2.417924 CCTCTCAGAAACGGTGAGGATG 60.418 54.545 12.15 0.00 44.79 3.51
4908 5010 1.827969 CCTCTCAGAAACGGTGAGGAT 59.172 52.381 12.15 0.00 44.79 3.24
4909 5011 1.257743 CCTCTCAGAAACGGTGAGGA 58.742 55.000 12.15 0.00 44.79 3.71
4910 5012 0.247736 CCCTCTCAGAAACGGTGAGG 59.752 60.000 11.08 11.08 41.62 3.86
4911 5013 0.247736 CCCCTCTCAGAAACGGTGAG 59.752 60.000 0.00 0.00 42.51 3.51
4912 5014 1.827399 GCCCCTCTCAGAAACGGTGA 61.827 60.000 0.00 0.00 0.00 4.02
4913 5015 1.376037 GCCCCTCTCAGAAACGGTG 60.376 63.158 0.00 0.00 0.00 4.94
4914 5016 1.536662 AGCCCCTCTCAGAAACGGT 60.537 57.895 0.00 0.00 0.00 4.83
4915 5017 1.219393 GAGCCCCTCTCAGAAACGG 59.781 63.158 0.00 0.00 41.51 4.44
4916 5018 1.975327 TGAGCCCCTCTCAGAAACG 59.025 57.895 0.00 0.00 46.34 3.60
4923 5025 2.270527 GGTGCTTGAGCCCCTCTC 59.729 66.667 0.00 0.00 42.23 3.20
4924 5026 3.334054 GGGTGCTTGAGCCCCTCT 61.334 66.667 17.30 0.00 43.68 3.69
4929 5031 2.991540 GTTGGGGGTGCTTGAGCC 60.992 66.667 0.00 0.00 42.09 4.70
4930 5032 1.832167 TTGTTGGGGGTGCTTGAGC 60.832 57.895 0.00 0.00 42.50 4.26
4931 5033 1.463553 GGTTGTTGGGGGTGCTTGAG 61.464 60.000 0.00 0.00 0.00 3.02
4932 5034 1.456705 GGTTGTTGGGGGTGCTTGA 60.457 57.895 0.00 0.00 0.00 3.02
4933 5035 1.760086 TGGTTGTTGGGGGTGCTTG 60.760 57.895 0.00 0.00 0.00 4.01
4934 5036 1.760480 GTGGTTGTTGGGGGTGCTT 60.760 57.895 0.00 0.00 0.00 3.91
4935 5037 2.123468 GTGGTTGTTGGGGGTGCT 60.123 61.111 0.00 0.00 0.00 4.40
4936 5038 2.123468 AGTGGTTGTTGGGGGTGC 60.123 61.111 0.00 0.00 0.00 5.01
4937 5039 1.530655 GGAGTGGTTGTTGGGGGTG 60.531 63.158 0.00 0.00 0.00 4.61
4938 5040 2.931921 GGAGTGGTTGTTGGGGGT 59.068 61.111 0.00 0.00 0.00 4.95
4939 5041 2.282180 CGGAGTGGTTGTTGGGGG 60.282 66.667 0.00 0.00 0.00 5.40
4940 5042 2.282180 CCGGAGTGGTTGTTGGGG 60.282 66.667 0.00 0.00 0.00 4.96
4952 5054 1.669115 CTGCAACACTGGACCGGAG 60.669 63.158 9.46 0.79 0.00 4.63
4955 5057 1.204704 TCTATCTGCAACACTGGACCG 59.795 52.381 0.00 0.00 0.00 4.79
4958 5060 3.519107 TCCAATCTATCTGCAACACTGGA 59.481 43.478 0.00 0.00 0.00 3.86
4961 5063 4.833478 AGTCCAATCTATCTGCAACACT 57.167 40.909 0.00 0.00 0.00 3.55
4969 5071 3.235200 CTCCCGGAAGTCCAATCTATCT 58.765 50.000 0.73 0.00 35.14 1.98
4970 5072 2.289133 GCTCCCGGAAGTCCAATCTATC 60.289 54.545 0.73 0.00 35.14 2.08
4973 5075 1.908483 GCTCCCGGAAGTCCAATCT 59.092 57.895 0.73 0.00 35.14 2.40
4993 5095 3.749981 CCATGGCTACGGAATGGC 58.250 61.111 0.00 0.00 34.82 4.40
5006 5108 4.904466 GCTCTTTGGCAAGCCATG 57.096 55.556 15.49 11.01 46.64 3.66
5028 5130 3.857854 CTGCAGATGTCCGCGTGC 61.858 66.667 8.42 7.88 36.42 5.34
5031 5133 2.169789 CCTTCTGCAGATGTCCGCG 61.170 63.158 19.04 0.00 0.00 6.46
5032 5134 2.467826 GCCTTCTGCAGATGTCCGC 61.468 63.158 19.04 14.44 40.77 5.54
5033 5135 3.805267 GCCTTCTGCAGATGTCCG 58.195 61.111 19.04 8.47 40.77 4.79
5059 5161 0.327924 TGGTGTGGAATGCGAGGATT 59.672 50.000 0.00 0.00 0.00 3.01
5066 5168 0.962356 CCCTCTGTGGTGTGGAATGC 60.962 60.000 0.00 0.00 0.00 3.56
5068 5170 1.500783 CCCCCTCTGTGGTGTGGAAT 61.501 60.000 0.00 0.00 0.00 3.01
5081 5183 1.302832 CACTGACACTTGCCCCCTC 60.303 63.158 0.00 0.00 0.00 4.30
5083 5185 0.678048 GATCACTGACACTTGCCCCC 60.678 60.000 0.00 0.00 0.00 5.40
5087 5189 2.344950 CTGGAGATCACTGACACTTGC 58.655 52.381 0.00 0.00 0.00 4.01
5090 5192 0.901124 GGCTGGAGATCACTGACACT 59.099 55.000 0.00 0.00 0.00 3.55
5091 5193 0.107945 GGGCTGGAGATCACTGACAC 60.108 60.000 0.00 0.00 0.00 3.67
5098 5200 2.444706 CTCGGGGGCTGGAGATCA 60.445 66.667 0.00 0.00 31.90 2.92
5099 5201 1.338136 TTTCTCGGGGGCTGGAGATC 61.338 60.000 4.13 0.00 38.95 2.75
5101 5203 1.537889 TTTTCTCGGGGGCTGGAGA 60.538 57.895 0.00 0.00 37.52 3.71
5105 5207 2.420058 ATAAGTTTTCTCGGGGGCTG 57.580 50.000 0.00 0.00 0.00 4.85
5108 5210 3.014623 GTCCAATAAGTTTTCTCGGGGG 58.985 50.000 0.00 0.00 0.00 5.40
5109 5211 3.014623 GGTCCAATAAGTTTTCTCGGGG 58.985 50.000 0.00 0.00 0.00 5.73
5110 5212 3.681593 TGGTCCAATAAGTTTTCTCGGG 58.318 45.455 0.00 0.00 0.00 5.14
5111 5213 4.700213 ACATGGTCCAATAAGTTTTCTCGG 59.300 41.667 0.00 0.00 0.00 4.63
5114 5216 6.245408 TGCTACATGGTCCAATAAGTTTTCT 58.755 36.000 0.00 0.00 0.00 2.52
5120 5222 3.885297 CCCTTGCTACATGGTCCAATAAG 59.115 47.826 0.00 0.00 0.00 1.73
5126 5228 2.736670 ATTCCCTTGCTACATGGTCC 57.263 50.000 0.00 0.00 0.00 4.46
5128 5230 3.763897 GTCAAATTCCCTTGCTACATGGT 59.236 43.478 0.00 0.00 0.00 3.55
5132 5234 3.826524 TGTGTCAAATTCCCTTGCTACA 58.173 40.909 0.00 0.00 0.00 2.74
5138 5240 2.293399 GCGTCTTGTGTCAAATTCCCTT 59.707 45.455 0.00 0.00 0.00 3.95
5141 5243 1.606668 TGGCGTCTTGTGTCAAATTCC 59.393 47.619 0.00 0.00 0.00 3.01
5144 5246 1.068333 GCATGGCGTCTTGTGTCAAAT 60.068 47.619 4.72 0.00 0.00 2.32
5147 5249 0.817229 TTGCATGGCGTCTTGTGTCA 60.817 50.000 4.72 0.00 0.00 3.58
5149 5251 0.311790 CTTTGCATGGCGTCTTGTGT 59.688 50.000 4.72 0.00 0.00 3.72
5152 5254 0.877071 AGTCTTTGCATGGCGTCTTG 59.123 50.000 0.00 0.00 0.00 3.02
5155 5257 1.291877 ACGAGTCTTTGCATGGCGTC 61.292 55.000 0.00 0.00 0.00 5.19
5156 5258 0.037697 TACGAGTCTTTGCATGGCGT 60.038 50.000 0.00 0.00 0.00 5.68
5157 5259 0.370273 GTACGAGTCTTTGCATGGCG 59.630 55.000 0.00 0.00 0.00 5.69
5162 5264 2.489971 CCAAAGGTACGAGTCTTTGCA 58.510 47.619 13.71 0.00 44.87 4.08
5168 5270 0.535797 CTCCCCCAAAGGTACGAGTC 59.464 60.000 0.00 0.00 0.00 3.36
5171 5273 1.536907 TGCTCCCCCAAAGGTACGA 60.537 57.895 0.00 0.00 0.00 3.43
5243 5345 2.046023 CCATCGGCAGGTGCTTCA 60.046 61.111 1.26 0.00 41.70 3.02
5244 5346 2.109126 GTCCATCGGCAGGTGCTTC 61.109 63.158 1.26 0.00 41.70 3.86
5245 5347 2.045926 GTCCATCGGCAGGTGCTT 60.046 61.111 1.26 0.00 41.70 3.91
5246 5348 4.457496 CGTCCATCGGCAGGTGCT 62.457 66.667 1.26 0.00 41.70 4.40
5249 5351 4.148825 GAGCGTCCATCGGCAGGT 62.149 66.667 0.00 0.00 40.26 4.00
5284 5386 3.220658 TCCGATCCGCATACCGCA 61.221 61.111 0.00 0.00 42.60 5.69
5285 5387 2.733593 GTCCGATCCGCATACCGC 60.734 66.667 0.00 0.00 35.03 5.68
5288 5390 0.384309 TCACTGTCCGATCCGCATAC 59.616 55.000 0.00 0.00 0.00 2.39
5291 5393 1.215382 CTTCACTGTCCGATCCGCA 59.785 57.895 0.00 0.00 0.00 5.69
5294 5396 1.079503 GCAACTTCACTGTCCGATCC 58.920 55.000 0.00 0.00 0.00 3.36
5297 5399 1.070786 GGGCAACTTCACTGTCCGA 59.929 57.895 0.00 0.00 0.00 4.55
5300 5402 0.249911 AGTCGGGCAACTTCACTGTC 60.250 55.000 0.00 0.00 0.00 3.51
5316 5418 2.815647 CTGGGCGCCGAAGAAGTC 60.816 66.667 22.54 3.93 0.00 3.01
5317 5419 4.394712 CCTGGGCGCCGAAGAAGT 62.395 66.667 24.99 0.00 0.00 3.01
5338 5440 1.740296 CGTGTTCCGGATGACACCC 60.740 63.158 26.28 9.54 42.35 4.61
5340 5442 1.289109 CCACGTGTTCCGGATGACAC 61.289 60.000 23.82 23.82 42.01 3.67
5345 5447 1.292223 CTCACCACGTGTTCCGGAT 59.708 57.895 15.65 0.00 42.24 4.18
5348 5450 2.357034 CCCTCACCACGTGTTCCG 60.357 66.667 15.65 0.92 44.03 4.30
5350 5452 2.668550 GCCCCTCACCACGTGTTC 60.669 66.667 15.65 0.00 34.79 3.18
5351 5453 4.619227 CGCCCCTCACCACGTGTT 62.619 66.667 15.65 0.00 34.79 3.32
5365 5467 2.485814 GAGATTATTTCCAGCATCCGCC 59.514 50.000 0.00 0.00 39.83 6.13
5368 5470 3.499918 CGTGGAGATTATTTCCAGCATCC 59.500 47.826 4.60 0.00 45.00 3.51
5369 5471 4.130118 ACGTGGAGATTATTTCCAGCATC 58.870 43.478 4.60 0.00 45.00 3.91
5373 5475 4.137116 TGGACGTGGAGATTATTTCCAG 57.863 45.455 4.60 2.87 45.00 3.86
5378 5480 4.489737 TCCCTATGGACGTGGAGATTATT 58.510 43.478 0.00 0.00 35.03 1.40
5381 5483 2.320781 CTCCCTATGGACGTGGAGATT 58.679 52.381 11.00 0.00 45.93 2.40
5382 5484 1.481428 CCTCCCTATGGACGTGGAGAT 60.481 57.143 16.67 0.00 45.93 2.75
5383 5485 0.106167 CCTCCCTATGGACGTGGAGA 60.106 60.000 16.67 0.74 45.93 3.71
5384 5486 0.106167 TCCTCCCTATGGACGTGGAG 60.106 60.000 9.78 9.78 43.29 3.86
5387 5489 1.137086 CACTTCCTCCCTATGGACGTG 59.863 57.143 0.00 5.29 43.80 4.49
5394 5496 1.273098 ACACCGACACTTCCTCCCTAT 60.273 52.381 0.00 0.00 0.00 2.57
5395 5497 0.113776 ACACCGACACTTCCTCCCTA 59.886 55.000 0.00 0.00 0.00 3.53
5396 5498 0.113776 TACACCGACACTTCCTCCCT 59.886 55.000 0.00 0.00 0.00 4.20
5412 5514 0.032912 TGGCGTATGGACCTCCTACA 60.033 55.000 0.00 0.00 36.82 2.74
5414 5516 0.260816 AGTGGCGTATGGACCTCCTA 59.739 55.000 0.00 0.00 36.82 2.94
5417 5519 1.442148 GGAGTGGCGTATGGACCTC 59.558 63.158 0.00 0.00 0.00 3.85
5420 5522 2.504519 GGGGAGTGGCGTATGGAC 59.495 66.667 0.00 0.00 0.00 4.02
5462 5564 0.955919 AGACTTGCAGGTTAAGGCGC 60.956 55.000 1.80 0.00 38.23 6.53
5463 5565 1.079503 GAGACTTGCAGGTTAAGGCG 58.920 55.000 1.80 0.00 38.23 5.52
5464 5566 1.454201 GGAGACTTGCAGGTTAAGGC 58.546 55.000 1.80 0.00 33.25 4.35


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

AutoCloner maintained by Alex Coulton.