Multiple sequence alignment - TraesCS5A01G321800

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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 TraesCS5A01G321800 chr5A 100.000 5946 0 0 1 5946 534462765 534468710 0.000000e+00 10981.0
1 TraesCS5A01G321800 chr5A 82.759 638 90 13 1417 2047 534570185 534570809 8.710000e-153 551.0
2 TraesCS5A01G321800 chr5A 80.833 600 90 12 3513 4102 534627509 534628093 1.180000e-121 448.0
3 TraesCS5A01G321800 chr5A 84.642 293 43 2 1757 2048 534371379 534371670 2.100000e-74 291.0
4 TraesCS5A01G321800 chr5A 78.005 441 69 21 4696 5123 534373559 534373984 9.890000e-63 252.0
5 TraesCS5A01G321800 chr5A 89.216 102 10 1 2071 2172 534464930 534465030 6.260000e-25 126.0
6 TraesCS5A01G321800 chr5A 91.304 46 3 1 582 626 534462884 534462839 1.790000e-05 62.1
7 TraesCS5A01G321800 chr5A 91.304 46 3 1 75 120 534463390 534463346 1.790000e-05 62.1
8 TraesCS5A01G321800 chrUn 93.403 1819 83 13 3401 5202 270058673 270056875 0.000000e+00 2660.0
9 TraesCS5A01G321800 chrUn 96.548 956 20 4 1 945 326861085 326860132 0.000000e+00 1570.0
10 TraesCS5A01G321800 chrUn 96.339 956 22 4 1 945 326864116 326863163 0.000000e+00 1559.0
11 TraesCS5A01G321800 chrUn 91.839 1115 58 20 944 2050 270061316 270060227 0.000000e+00 1524.0
12 TraesCS5A01G321800 chrUn 95.771 733 19 3 1 722 371912212 371912943 0.000000e+00 1171.0
13 TraesCS5A01G321800 chrUn 92.796 583 28 8 2828 3402 270059573 270058997 0.000000e+00 832.0
14 TraesCS5A01G321800 chrUn 86.349 630 79 4 1421 2048 325468880 325468256 0.000000e+00 680.0
15 TraesCS5A01G321800 chrUn 90.323 186 16 1 2318 2501 270060208 270060023 5.950000e-60 243.0
16 TraesCS5A01G321800 chrUn 89.894 188 12 4 2627 2810 270059810 270059626 9.960000e-58 235.0
17 TraesCS5A01G321800 chrUn 87.591 137 13 2 2485 2617 270060008 270059872 7.980000e-34 156.0
18 TraesCS5A01G321800 chrUn 95.122 41 2 0 582 622 326860966 326861006 1.380000e-06 65.8
19 TraesCS5A01G321800 chrUn 95.122 41 2 0 582 622 326863997 326864037 1.380000e-06 65.8
20 TraesCS5A01G321800 chrUn 93.182 44 3 0 582 625 371912331 371912288 1.380000e-06 65.8
21 TraesCS5A01G321800 chrUn 91.304 46 3 1 75 120 326860451 326860495 1.790000e-05 62.1
22 TraesCS5A01G321800 chrUn 91.304 46 3 1 75 120 326863482 326863526 1.790000e-05 62.1
23 TraesCS5A01G321800 chrUn 91.304 46 3 1 75 120 371912847 371912803 1.790000e-05 62.1
24 TraesCS5A01G321800 chr5D 93.403 1819 83 13 3401 5202 421161046 421159248 0.000000e+00 2660.0
25 TraesCS5A01G321800 chr5D 94.590 1294 54 10 2830 4115 421137120 421135835 0.000000e+00 1988.0
26 TraesCS5A01G321800 chr5D 90.656 1220 94 9 962 2175 421139019 421137814 0.000000e+00 1604.0
27 TraesCS5A01G321800 chr5D 94.471 1031 45 5 4179 5202 421134427 421133402 0.000000e+00 1578.0
28 TraesCS5A01G321800 chr5D 91.839 1115 58 20 944 2050 421163689 421162600 0.000000e+00 1524.0
29 TraesCS5A01G321800 chr5D 91.270 630 45 7 5201 5826 421159210 421158587 0.000000e+00 850.0
30 TraesCS5A01G321800 chr5D 91.111 630 45 7 5201 5826 421133364 421132742 0.000000e+00 843.0
31 TraesCS5A01G321800 chr5D 92.796 583 28 8 2828 3402 421161946 421161370 0.000000e+00 832.0
32 TraesCS5A01G321800 chr5D 86.981 530 51 9 2175 2698 421137908 421137391 1.110000e-161 580.0
33 TraesCS5A01G321800 chr5D 83.197 613 84 13 1443 2050 421089766 421089168 1.460000e-150 544.0
34 TraesCS5A01G321800 chr5D 85.941 441 62 0 1606 2046 420971186 420970746 6.980000e-129 472.0
35 TraesCS5A01G321800 chr5D 79.496 595 88 20 3516 4092 420969745 420969167 5.590000e-105 392.0
36 TraesCS5A01G321800 chr5D 78.311 438 69 20 4696 5121 421171939 421171516 5.910000e-65 259.0
37 TraesCS5A01G321800 chr5D 90.323 186 16 1 2318 2501 421162581 421162396 5.950000e-60 243.0
38 TraesCS5A01G321800 chr5D 89.894 188 12 4 2627 2810 421162183 421161999 9.960000e-58 235.0
39 TraesCS5A01G321800 chr5D 87.591 137 13 2 2485 2617 421162381 421162245 7.980000e-34 156.0
40 TraesCS5A01G321800 chr5D 100.000 71 0 0 4111 4181 421135860 421135790 1.340000e-26 132.0
41 TraesCS5A01G321800 chr5D 88.679 106 3 2 2714 2810 421137277 421137172 2.910000e-23 121.0
42 TraesCS5A01G321800 chr5B 92.085 1453 74 12 2830 4259 507189209 507190643 0.000000e+00 2008.0
43 TraesCS5A01G321800 chr5B 98.517 944 12 2 1 943 339473707 339474649 0.000000e+00 1664.0
44 TraesCS5A01G321800 chr5B 89.136 1215 93 18 959 2166 507187417 507188599 0.000000e+00 1476.0
45 TraesCS5A01G321800 chr5B 90.506 948 70 12 4263 5202 507191778 507192713 0.000000e+00 1234.0
46 TraesCS5A01G321800 chr5B 88.450 658 60 8 2165 2810 507188504 507189157 0.000000e+00 780.0
47 TraesCS5A01G321800 chr5B 86.414 633 79 4 1418 2048 507059161 507059788 0.000000e+00 686.0
48 TraesCS5A01G321800 chr5B 88.793 464 44 8 5201 5661 507192751 507193209 4.020000e-156 562.0
49 TraesCS5A01G321800 chr5B 82.043 607 90 14 1443 2044 507371260 507371852 3.200000e-137 499.0
50 TraesCS5A01G321800 chr5B 79.730 592 89 18 3515 4092 507586925 507587499 3.340000e-107 399.0
51 TraesCS5A01G321800 chr5B 78.636 440 66 22 4696 5121 507061730 507062155 3.530000e-67 267.0
52 TraesCS5A01G321800 chr5B 80.398 352 59 5 1443 1786 662856325 662855976 5.910000e-65 259.0
53 TraesCS5A01G321800 chr5B 93.182 44 3 0 582 625 339473825 339473782 1.380000e-06 65.8
54 TraesCS5A01G321800 chr5B 91.304 46 3 1 75 120 339474332 339474288 1.790000e-05 62.1
55 TraesCS5A01G321800 chr1B 78.628 889 167 17 1165 2044 632659923 632659049 8.650000e-158 568.0
56 TraesCS5A01G321800 chr1B 82.215 596 94 11 3513 4103 632657414 632656826 2.470000e-138 503.0
57 TraesCS5A01G321800 chr1B 85.586 111 16 0 2065 2175 279915646 279915536 3.770000e-22 117.0
58 TraesCS5A01G321800 chr6B 81.226 261 38 7 694 945 620653601 620653343 3.630000e-47 200.0
59 TraesCS5A01G321800 chr3A 85.561 187 27 0 758 944 688305032 688305218 4.700000e-46 196.0
60 TraesCS5A01G321800 chr3A 89.262 149 16 0 795 943 594325712 594325860 2.830000e-43 187.0
61 TraesCS5A01G321800 chr3A 87.069 116 9 4 2468 2577 745374308 745374423 6.260000e-25 126.0
62 TraesCS5A01G321800 chr3A 100.000 29 0 0 264 292 556349081 556349053 3.000000e-03 54.7
63 TraesCS5A01G321800 chr1A 88.961 154 17 0 790 943 538638324 538638171 2.190000e-44 191.0
64 TraesCS5A01G321800 chr1A 89.262 149 16 0 795 943 574825329 574825181 2.830000e-43 187.0
65 TraesCS5A01G321800 chr1A 86.486 111 15 0 2065 2175 531984913 531984803 8.090000e-24 122.0
66 TraesCS5A01G321800 chr2A 89.209 139 15 0 804 942 30174769 30174907 2.200000e-39 174.0
67 TraesCS5A01G321800 chr2A 87.500 128 9 2 2468 2588 604988079 604988206 2.230000e-29 141.0
68 TraesCS5A01G321800 chr3B 87.248 149 17 2 2175 2322 13053678 13053825 1.020000e-37 169.0
69 TraesCS5A01G321800 chr3B 85.906 149 19 2 2175 2322 104283669 104283816 2.220000e-34 158.0
70 TraesCS5A01G321800 chr6D 87.591 137 17 0 2186 2322 47793957 47794093 6.170000e-35 159.0
71 TraesCS5A01G321800 chr6D 87.591 137 17 0 2186 2322 466183323 466183459 6.170000e-35 159.0
72 TraesCS5A01G321800 chr4D 85.256 156 22 1 2165 2319 53756347 53756502 6.170000e-35 159.0
73 TraesCS5A01G321800 chr4D 88.034 117 8 2 2471 2581 299316631 299316515 3.740000e-27 134.0
74 TraesCS5A01G321800 chr3D 87.591 137 17 0 2186 2322 134598374 134598238 6.170000e-35 159.0
75 TraesCS5A01G321800 chr3D 87.591 137 17 0 2186 2322 593934765 593934901 6.170000e-35 159.0
76 TraesCS5A01G321800 chr7A 86.207 145 20 0 2175 2319 524701273 524701417 2.220000e-34 158.0
77 TraesCS5A01G321800 chr7A 86.614 127 8 4 2468 2585 27477729 27477855 1.340000e-26 132.0
78 TraesCS5A01G321800 chr6A 90.756 119 5 1 2471 2583 514475461 514475343 2.870000e-33 154.0
79 TraesCS5A01G321800 chr4B 89.744 117 6 2 2471 2581 371970550 371970434 1.730000e-30 145.0
80 TraesCS5A01G321800 chr2B 88.991 109 10 1 2067 2175 666651622 666651516 3.740000e-27 134.0
81 TraesCS5A01G321800 chr2D 88.288 111 12 1 2066 2175 621477716 621477826 1.340000e-26 132.0
82 TraesCS5A01G321800 chr2D 87.500 104 11 1 2071 2172 117830631 117830528 1.050000e-22 119.0
83 TraesCS5A01G321800 chr7D 86.555 119 13 3 2468 2585 136405416 136405532 1.740000e-25 128.0
84 TraesCS5A01G321800 chr4A 85.586 111 16 0 2065 2175 660523999 660523889 3.770000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G321800 chr5A 534462765 534468710 5945 False 5553.500000 10981 94.608000 1 5946 2 chr5A.!!$F4 5945
1 TraesCS5A01G321800 chr5A 534570185 534570809 624 False 551.000000 551 82.759000 1417 2047 1 chr5A.!!$F1 630
2 TraesCS5A01G321800 chr5A 534627509 534628093 584 False 448.000000 448 80.833000 3513 4102 1 chr5A.!!$F2 589
3 TraesCS5A01G321800 chr5A 534371379 534373984 2605 False 271.500000 291 81.323500 1757 5123 2 chr5A.!!$F3 3366
4 TraesCS5A01G321800 chrUn 326860132 326864116 3984 True 1564.500000 1570 96.443500 1 945 2 chrUn.!!$R3 944
5 TraesCS5A01G321800 chrUn 371912212 371912943 731 False 1171.000000 1171 95.771000 1 722 1 chrUn.!!$F1 721
6 TraesCS5A01G321800 chrUn 270056875 270061316 4441 True 941.666667 2660 90.974333 944 5202 6 chrUn.!!$R2 4258
7 TraesCS5A01G321800 chrUn 325468256 325468880 624 True 680.000000 680 86.349000 1421 2048 1 chrUn.!!$R1 627
8 TraesCS5A01G321800 chr5D 421132742 421139019 6277 True 978.000000 1988 92.355429 962 5826 7 chr5D.!!$R4 4864
9 TraesCS5A01G321800 chr5D 421158587 421163689 5102 True 928.571429 2660 91.016571 944 5826 7 chr5D.!!$R5 4882
10 TraesCS5A01G321800 chr5D 421089168 421089766 598 True 544.000000 544 83.197000 1443 2050 1 chr5D.!!$R1 607
11 TraesCS5A01G321800 chr5D 420969167 420971186 2019 True 432.000000 472 82.718500 1606 4092 2 chr5D.!!$R3 2486
12 TraesCS5A01G321800 chr5B 339473707 339474649 942 False 1664.000000 1664 98.517000 1 943 1 chr5B.!!$F1 942
13 TraesCS5A01G321800 chr5B 507187417 507193209 5792 False 1212.000000 2008 89.794000 959 5661 5 chr5B.!!$F5 4702
14 TraesCS5A01G321800 chr5B 507371260 507371852 592 False 499.000000 499 82.043000 1443 2044 1 chr5B.!!$F2 601
15 TraesCS5A01G321800 chr5B 507059161 507062155 2994 False 476.500000 686 82.525000 1418 5121 2 chr5B.!!$F4 3703
16 TraesCS5A01G321800 chr5B 507586925 507587499 574 False 399.000000 399 79.730000 3515 4092 1 chr5B.!!$F3 577
17 TraesCS5A01G321800 chr1B 632656826 632659923 3097 True 535.500000 568 80.421500 1165 4103 2 chr1B.!!$R2 2938

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
880 3923 3.610911 GAGGACCTGGATGACGATTTTT 58.389 45.455 0.00 0.00 0.00 1.94 F
1252 4295 0.544120 TTCCCCCGTAAACCTACCGT 60.544 55.000 0.00 0.00 0.00 4.83 F
2738 6192 0.399833 TGACATGTGTGGCCTTAGCA 59.600 50.000 1.15 0.00 42.56 3.49 F
2815 6279 0.657312 TGTCACACAGCTTGCGAAAG 59.343 50.000 0.00 0.00 0.00 2.62 F
2816 6280 0.657840 GTCACACAGCTTGCGAAAGT 59.342 50.000 4.74 0.00 0.00 2.66 F
3075 6980 1.370064 GTTAGGTGGCACCGACACT 59.630 57.895 29.76 15.44 44.90 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 5865 2.438800 AGGCTAGTCGTAGTGGTGAT 57.561 50.000 0.00 0.0 0.00 3.06 R
3075 6980 2.147958 GACCGCAACCATGTTCTGTAA 58.852 47.619 0.00 0.0 0.00 2.41 R
3657 8208 3.016031 TGCGAACATATGCAAGTGGATT 58.984 40.909 1.58 0.0 38.34 3.01 R
4510 11664 3.614092 CATATGTGGTGTCTTGGCTTCT 58.386 45.455 0.00 0.0 0.00 2.85 R
4583 11737 5.335740 CCAAGTTATCTCCATAGTCGCGTAT 60.336 44.000 5.77 0.0 0.00 3.06 R
5067 12236 3.957497 ACATTTGACTTGCAACCTTGGTA 59.043 39.130 0.00 0.0 35.91 3.25 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
880 3923 3.610911 GAGGACCTGGATGACGATTTTT 58.389 45.455 0.00 0.00 0.00 1.94
952 3995 5.220710 GTGCACTTCACTCCATCCTATAT 57.779 43.478 10.32 0.00 42.38 0.86
1064 4107 2.032620 CAGTGTTAGCCCCTCGATAGT 58.967 52.381 0.00 0.00 37.40 2.12
1155 4198 2.354773 GATTCCTCGGCGGCTACG 60.355 66.667 7.21 0.00 44.63 3.51
1156 4199 3.843117 GATTCCTCGGCGGCTACGG 62.843 68.421 7.21 4.50 41.36 4.02
1252 4295 0.544120 TTCCCCCGTAAACCTACCGT 60.544 55.000 0.00 0.00 0.00 4.83
1325 4368 5.934043 GCAGCATCCAAGTATGTATACATGA 59.066 40.000 25.48 15.13 34.79 3.07
1352 4398 9.819267 ATACTCTTACCAGTAAAAGCATACTTC 57.181 33.333 0.00 0.00 33.90 3.01
1353 4399 7.676947 ACTCTTACCAGTAAAAGCATACTTCA 58.323 34.615 0.00 0.00 33.90 3.02
1375 4421 4.327357 CACGATTTTGTCACTAGCTAGGTG 59.673 45.833 24.35 18.36 36.17 4.00
1410 4465 1.069022 AGTGCATGCGTGTGTCAAATC 60.069 47.619 14.09 0.00 0.00 2.17
1411 4466 1.069022 GTGCATGCGTGTGTCAAATCT 60.069 47.619 14.09 0.00 0.00 2.40
1412 4467 1.197492 TGCATGCGTGTGTCAAATCTC 59.803 47.619 14.09 0.00 0.00 2.75
1413 4468 1.197492 GCATGCGTGTGTCAAATCTCA 59.803 47.619 0.00 0.00 0.00 3.27
1414 4469 2.350676 GCATGCGTGTGTCAAATCTCAA 60.351 45.455 0.00 0.00 0.00 3.02
1415 4470 3.852939 GCATGCGTGTGTCAAATCTCAAA 60.853 43.478 0.00 0.00 0.00 2.69
1419 4474 4.202000 TGCGTGTGTCAAATCTCAAATGTT 60.202 37.500 0.00 0.00 0.00 2.71
1434 4489 4.288366 TCAAATGTTAGGTGACAGATGGGA 59.712 41.667 0.00 0.00 32.19 4.37
1512 4579 2.431771 CGACGATTGACACCGCCA 60.432 61.111 0.00 0.00 0.00 5.69
1710 4777 2.681778 CACTCCTCCTGGCGTCCT 60.682 66.667 0.00 0.00 0.00 3.85
2069 5325 1.032794 CGTCCTAGCTATGCACTCCA 58.967 55.000 0.00 0.00 0.00 3.86
2077 5333 2.017049 GCTATGCACTCCATCCGTTTT 58.983 47.619 0.00 0.00 35.34 2.43
2155 5414 8.684973 AGACGTATTTTAGAGTGTATGTTCAC 57.315 34.615 0.00 0.00 38.46 3.18
2157 5416 9.136952 GACGTATTTTAGAGTGTATGTTCACTT 57.863 33.333 0.00 0.00 46.81 3.16
2165 5424 7.986085 AGAGTGTATGTTCACTTATTTTGCT 57.014 32.000 0.98 0.00 46.81 3.91
2166 5425 8.034058 AGAGTGTATGTTCACTTATTTTGCTC 57.966 34.615 0.98 0.00 46.81 4.26
2167 5426 7.119846 AGAGTGTATGTTCACTTATTTTGCTCC 59.880 37.037 0.98 0.00 46.81 4.70
2168 5427 6.021596 GTGTATGTTCACTTATTTTGCTCCG 58.978 40.000 0.00 0.00 35.68 4.63
2169 5428 5.703592 TGTATGTTCACTTATTTTGCTCCGT 59.296 36.000 0.00 0.00 0.00 4.69
2170 5429 6.874664 TGTATGTTCACTTATTTTGCTCCGTA 59.125 34.615 0.00 0.00 0.00 4.02
2171 5430 7.551262 TGTATGTTCACTTATTTTGCTCCGTAT 59.449 33.333 0.00 0.00 0.00 3.06
2172 5431 6.176975 TGTTCACTTATTTTGCTCCGTATG 57.823 37.500 0.00 0.00 0.00 2.39
2173 5432 5.703592 TGTTCACTTATTTTGCTCCGTATGT 59.296 36.000 0.00 0.00 0.00 2.29
2174 5433 6.874664 TGTTCACTTATTTTGCTCCGTATGTA 59.125 34.615 0.00 0.00 0.00 2.29
2175 5434 7.388224 TGTTCACTTATTTTGCTCCGTATGTAA 59.612 33.333 0.00 0.00 0.00 2.41
2176 5435 8.395633 GTTCACTTATTTTGCTCCGTATGTAAT 58.604 33.333 0.00 0.00 0.00 1.89
2177 5436 7.915508 TCACTTATTTTGCTCCGTATGTAATG 58.084 34.615 0.00 0.00 0.00 1.90
2178 5437 7.551262 TCACTTATTTTGCTCCGTATGTAATGT 59.449 33.333 0.00 0.00 0.00 2.71
2179 5438 8.822855 CACTTATTTTGCTCCGTATGTAATGTA 58.177 33.333 0.00 0.00 0.00 2.29
2180 5439 9.386010 ACTTATTTTGCTCCGTATGTAATGTAA 57.614 29.630 0.00 0.00 0.00 2.41
2181 5440 9.864034 CTTATTTTGCTCCGTATGTAATGTAAG 57.136 33.333 0.00 0.00 0.00 2.34
2182 5441 9.602568 TTATTTTGCTCCGTATGTAATGTAAGA 57.397 29.630 0.00 0.00 0.00 2.10
2183 5442 6.897259 TTTGCTCCGTATGTAATGTAAGAC 57.103 37.500 0.00 0.00 0.00 3.01
2184 5443 4.940463 TGCTCCGTATGTAATGTAAGACC 58.060 43.478 0.00 0.00 0.00 3.85
2185 5444 4.647853 TGCTCCGTATGTAATGTAAGACCT 59.352 41.667 0.00 0.00 0.00 3.85
2186 5445 5.128171 TGCTCCGTATGTAATGTAAGACCTT 59.872 40.000 0.00 0.00 0.00 3.50
2187 5446 6.047231 GCTCCGTATGTAATGTAAGACCTTT 58.953 40.000 0.00 0.00 0.00 3.11
2188 5447 6.537660 GCTCCGTATGTAATGTAAGACCTTTT 59.462 38.462 0.00 0.00 0.00 2.27
2189 5448 7.707893 GCTCCGTATGTAATGTAAGACCTTTTA 59.292 37.037 0.00 0.00 0.00 1.52
2190 5449 9.245962 CTCCGTATGTAATGTAAGACCTTTTAG 57.754 37.037 0.00 0.00 0.00 1.85
2191 5450 8.970020 TCCGTATGTAATGTAAGACCTTTTAGA 58.030 33.333 0.00 0.00 0.00 2.10
2192 5451 9.245962 CCGTATGTAATGTAAGACCTTTTAGAG 57.754 37.037 0.00 0.00 0.00 2.43
2215 5474 8.843262 AGAGATTTCAATATGAATTGCATTCGA 58.157 29.630 0.00 0.00 41.96 3.71
2261 5520 8.560374 AGAGTGTAGTTTCACTTATTTTGCTTC 58.440 33.333 0.98 0.00 46.81 3.86
2325 5586 3.541713 CGGAGGGAGTAGCTGCCC 61.542 72.222 11.94 11.94 43.25 5.36
2418 5684 5.622770 TTTTCTCCGAGCCAGATAAAAAC 57.377 39.130 0.00 0.00 0.00 2.43
2543 5845 8.874744 TGAAGGTAGTAACATAGACTAGTGTT 57.125 34.615 0.00 0.34 41.16 3.32
2573 5875 8.738106 ACACTAGTCTAAGTTAATCACCACTAC 58.262 37.037 0.00 0.00 0.00 2.73
2593 5895 3.922910 ACGACTAGCCTAAAAGTGTTCC 58.077 45.455 0.00 0.00 0.00 3.62
2638 5995 9.747898 TGATATGAGGTTACCAGTTAAAACATT 57.252 29.630 3.51 0.00 0.00 2.71
2642 5999 6.016610 TGAGGTTACCAGTTAAAACATTCTGC 60.017 38.462 3.51 0.00 0.00 4.26
2654 6011 8.717821 GTTAAAACATTCTGCAGACATACACTA 58.282 33.333 18.03 0.00 0.00 2.74
2658 6015 9.448438 AAACATTCTGCAGACATACACTATAAA 57.552 29.630 18.03 0.00 0.00 1.40
2738 6192 0.399833 TGACATGTGTGGCCTTAGCA 59.600 50.000 1.15 0.00 42.56 3.49
2811 6275 2.001872 TGATATGTCACACAGCTTGCG 58.998 47.619 0.00 0.00 0.00 4.85
2812 6276 2.270923 GATATGTCACACAGCTTGCGA 58.729 47.619 0.00 0.00 0.00 5.10
2813 6277 2.162319 TATGTCACACAGCTTGCGAA 57.838 45.000 0.00 0.00 0.00 4.70
2814 6278 1.308047 ATGTCACACAGCTTGCGAAA 58.692 45.000 0.00 0.00 0.00 3.46
2815 6279 0.657312 TGTCACACAGCTTGCGAAAG 59.343 50.000 0.00 0.00 0.00 2.62
2816 6280 0.657840 GTCACACAGCTTGCGAAAGT 59.342 50.000 4.74 0.00 0.00 2.66
2819 6283 2.939756 TCACACAGCTTGCGAAAGTTTA 59.060 40.909 4.74 0.00 0.00 2.01
2821 6285 4.752604 TCACACAGCTTGCGAAAGTTTATA 59.247 37.500 4.74 0.00 0.00 0.98
2822 6286 5.082059 CACACAGCTTGCGAAAGTTTATAG 58.918 41.667 4.74 0.00 0.00 1.31
2823 6287 4.994852 ACACAGCTTGCGAAAGTTTATAGA 59.005 37.500 4.74 0.00 0.00 1.98
2824 6288 5.120830 ACACAGCTTGCGAAAGTTTATAGAG 59.879 40.000 4.74 0.00 0.00 2.43
2826 6290 4.034510 CAGCTTGCGAAAGTTTATAGAGGG 59.965 45.833 4.74 0.00 0.00 4.30
2828 6292 4.271291 GCTTGCGAAAGTTTATAGAGGGAG 59.729 45.833 4.74 0.00 0.00 4.30
2835 6334 8.976471 GCGAAAGTTTATAGAGGGAGTATTAAC 58.024 37.037 0.00 0.00 0.00 2.01
3075 6980 1.370064 GTTAGGTGGCACCGACACT 59.630 57.895 29.76 15.44 44.90 3.55
3657 8208 5.334028 CCATTTCATTTAGCGATGCACGATA 60.334 40.000 11.94 7.55 45.77 2.92
3790 8342 7.147549 TGGTCTGAAGGTATATTTTCTACCCAG 60.148 40.741 14.43 0.00 39.63 4.45
3810 8374 7.758495 ACCCAGCTTATATGTTTTTCGTAAAG 58.242 34.615 0.00 0.00 0.00 1.85
4243 10190 6.590234 AAACCACCCATTTGATCTACTTTC 57.410 37.500 0.00 0.00 0.00 2.62
4346 11494 6.904626 AGTTATAGATGCACCAAGGAGAAAT 58.095 36.000 0.00 0.00 0.00 2.17
4417 11567 7.549147 AACTAGGTGAGGTGTACTATGAAAA 57.451 36.000 0.00 0.00 0.00 2.29
4419 11569 7.556844 ACTAGGTGAGGTGTACTATGAAAATG 58.443 38.462 0.00 0.00 0.00 2.32
4501 11655 2.026729 CCCCTCCTCCTCTTCTTTTGAC 60.027 54.545 0.00 0.00 0.00 3.18
4510 11664 6.463049 CCTCCTCTTCTTTTGACAGTGAACTA 60.463 42.308 0.00 0.00 0.00 2.24
4514 11668 7.170658 CCTCTTCTTTTGACAGTGAACTAGAAG 59.829 40.741 13.45 13.45 38.96 2.85
4636 11790 4.199310 GTGGGCATACATGAATACACACT 58.801 43.478 0.00 0.00 0.00 3.55
4787 11947 5.070313 AGGTTTCTTTTGCAGGCTTTGATTA 59.930 36.000 0.00 0.00 0.00 1.75
4946 12106 8.783833 TTCAGAATCCATCAAGAAAGAGTAAG 57.216 34.615 0.00 0.00 0.00 2.34
5087 12256 4.021192 CCATACCAAGGTTGCAAGTCAAAT 60.021 41.667 0.00 0.00 36.26 2.32
5088 12257 3.457610 ACCAAGGTTGCAAGTCAAATG 57.542 42.857 0.00 0.00 36.26 2.32
5089 12258 2.765699 ACCAAGGTTGCAAGTCAAATGT 59.234 40.909 0.00 0.00 36.26 2.71
5090 12259 3.957497 ACCAAGGTTGCAAGTCAAATGTA 59.043 39.130 0.00 0.00 36.26 2.29
5091 12260 4.588528 ACCAAGGTTGCAAGTCAAATGTAT 59.411 37.500 0.00 0.00 36.26 2.29
5093 12262 6.266558 ACCAAGGTTGCAAGTCAAATGTATTA 59.733 34.615 0.00 0.00 36.26 0.98
5094 12263 6.808212 CCAAGGTTGCAAGTCAAATGTATTAG 59.192 38.462 0.00 0.00 36.26 1.73
5263 12476 0.839946 GGTACTCTGTGCCCATGGAT 59.160 55.000 15.22 0.00 32.14 3.41
5330 12543 6.215845 TCCACAGTGTAATGATATCACATCG 58.784 40.000 7.78 0.52 34.94 3.84
5468 12681 3.202906 TCCAAGCTATCGCCATGTAAAC 58.797 45.455 0.00 0.00 36.60 2.01
5473 12686 2.034001 GCTATCGCCATGTAAACGACAC 60.034 50.000 0.00 0.00 42.17 3.67
5487 12700 7.677309 TGTAAACGACACCGAATACATTTATG 58.323 34.615 0.00 0.00 36.39 1.90
5521 12737 2.005451 CTCCATCAAAGGCTCTCAACG 58.995 52.381 0.00 0.00 0.00 4.10
5542 12758 6.530913 ACGATGATTTGAGATTATTGGTCG 57.469 37.500 0.00 0.00 0.00 4.79
5585 12801 3.109151 ACCCGATTGATACAACACCCTA 58.891 45.455 0.00 0.00 0.00 3.53
5592 12808 7.386851 CGATTGATACAACACCCTATAGGATT 58.613 38.462 21.07 8.55 39.89 3.01
5610 12826 0.100682 TTTCTCCCTCTCGCGATTCG 59.899 55.000 10.36 0.62 40.15 3.34
5622 12838 1.083489 GCGATTCGTTCAATCCACCA 58.917 50.000 8.03 0.00 38.17 4.17
5671 12887 7.427214 ACAAGCTAGAAACTATATCCTTCGTC 58.573 38.462 0.00 0.00 0.00 4.20
5676 12892 4.338682 AGAAACTATATCCTTCGTCGCACT 59.661 41.667 0.00 0.00 0.00 4.40
5706 12922 1.072331 CCGAATGCCTAAGTAGCCCAT 59.928 52.381 0.00 0.00 0.00 4.00
5712 12928 2.438021 TGCCTAAGTAGCCCATCGAAAT 59.562 45.455 0.00 0.00 0.00 2.17
5730 12946 1.639635 ATGATTCTCCCGCCTTGCCT 61.640 55.000 0.00 0.00 0.00 4.75
5736 12952 3.058160 CCCGCCTTGCCTGTTCTG 61.058 66.667 0.00 0.00 0.00 3.02
5737 12953 3.058160 CCGCCTTGCCTGTTCTGG 61.058 66.667 0.00 0.00 0.00 3.86
5757 12973 4.929479 TGGGCATGTTAACTAGTCCATTT 58.071 39.130 16.73 0.00 0.00 2.32
5766 12984 1.338769 ACTAGTCCATTTCGTGCACCC 60.339 52.381 12.15 0.00 0.00 4.61
5792 13010 1.064803 CCGTATTTGCCGCATTAAGCA 59.935 47.619 0.00 0.00 46.13 3.91
5803 13021 3.065233 CCGCATTAAGCAGCAAACTATCA 59.935 43.478 0.00 0.00 46.13 2.15
5823 13041 1.381191 TGCTCCGGATAGGCACTGA 60.381 57.895 12.49 0.00 41.52 3.41
5826 13044 1.749334 CTCCGGATAGGCACTGACCC 61.749 65.000 3.57 0.00 41.52 4.46
5827 13045 2.417516 CGGATAGGCACTGACCCG 59.582 66.667 0.00 0.00 41.52 5.28
5828 13046 2.125326 CGGATAGGCACTGACCCGA 61.125 63.158 0.00 0.00 44.34 5.14
5829 13047 1.742768 GGATAGGCACTGACCCGAG 59.257 63.158 0.00 0.00 41.52 4.63
5830 13048 1.068250 GATAGGCACTGACCCGAGC 59.932 63.158 0.00 0.00 41.52 5.03
5831 13049 2.685387 GATAGGCACTGACCCGAGCG 62.685 65.000 0.00 0.00 41.52 5.03
5832 13050 3.931190 TAGGCACTGACCCGAGCGA 62.931 63.158 0.00 0.00 41.52 4.93
5834 13052 4.357947 GCACTGACCCGAGCGACA 62.358 66.667 0.00 0.00 0.00 4.35
5835 13053 2.338620 CACTGACCCGAGCGACAA 59.661 61.111 0.00 0.00 0.00 3.18
5836 13054 1.734477 CACTGACCCGAGCGACAAG 60.734 63.158 0.00 0.00 0.00 3.16
5837 13055 1.901948 ACTGACCCGAGCGACAAGA 60.902 57.895 0.00 0.00 0.00 3.02
5838 13056 1.153939 CTGACCCGAGCGACAAGAG 60.154 63.158 0.00 0.00 0.00 2.85
5839 13057 1.587043 CTGACCCGAGCGACAAGAGA 61.587 60.000 0.00 0.00 0.00 3.10
5840 13058 0.965866 TGACCCGAGCGACAAGAGAT 60.966 55.000 0.00 0.00 0.00 2.75
5841 13059 0.526524 GACCCGAGCGACAAGAGATG 60.527 60.000 0.00 0.00 0.00 2.90
5842 13060 1.227089 CCCGAGCGACAAGAGATGG 60.227 63.158 0.00 0.00 0.00 3.51
5843 13061 1.227089 CCGAGCGACAAGAGATGGG 60.227 63.158 0.00 0.00 0.00 4.00
5844 13062 1.880340 CGAGCGACAAGAGATGGGC 60.880 63.158 0.00 0.00 34.05 5.36
5845 13063 1.522580 GAGCGACAAGAGATGGGCC 60.523 63.158 0.00 0.00 34.28 5.80
5846 13064 2.892425 GCGACAAGAGATGGGCCG 60.892 66.667 0.00 0.00 0.00 6.13
5847 13065 2.892640 CGACAAGAGATGGGCCGA 59.107 61.111 0.00 0.00 0.00 5.54
5848 13066 1.519455 CGACAAGAGATGGGCCGAC 60.519 63.158 0.00 0.00 0.00 4.79
5849 13067 1.596934 GACAAGAGATGGGCCGACA 59.403 57.895 0.00 0.00 0.00 4.35
5850 13068 0.741221 GACAAGAGATGGGCCGACAC 60.741 60.000 0.00 0.00 0.00 3.67
5851 13069 1.296392 CAAGAGATGGGCCGACACA 59.704 57.895 0.00 0.00 0.00 3.72
5852 13070 1.021390 CAAGAGATGGGCCGACACAC 61.021 60.000 0.00 0.00 0.00 3.82
5853 13071 1.194781 AAGAGATGGGCCGACACACT 61.195 55.000 0.00 0.00 0.00 3.55
5854 13072 1.194781 AGAGATGGGCCGACACACTT 61.195 55.000 0.00 0.00 0.00 3.16
5855 13073 0.321653 GAGATGGGCCGACACACTTT 60.322 55.000 0.00 0.00 0.00 2.66
5856 13074 0.606401 AGATGGGCCGACACACTTTG 60.606 55.000 0.00 0.00 0.00 2.77
5857 13075 0.605319 GATGGGCCGACACACTTTGA 60.605 55.000 0.00 0.00 0.00 2.69
5858 13076 0.606401 ATGGGCCGACACACTTTGAG 60.606 55.000 0.00 0.00 0.00 3.02
5859 13077 1.070786 GGGCCGACACACTTTGAGA 59.929 57.895 0.00 0.00 0.00 3.27
5860 13078 0.951040 GGGCCGACACACTTTGAGAG 60.951 60.000 0.00 0.00 0.00 3.20
5861 13079 0.951040 GGCCGACACACTTTGAGAGG 60.951 60.000 0.00 0.00 0.00 3.69
5862 13080 0.249911 GCCGACACACTTTGAGAGGT 60.250 55.000 0.00 0.00 0.00 3.85
5863 13081 1.810412 GCCGACACACTTTGAGAGGTT 60.810 52.381 0.00 0.00 0.00 3.50
5864 13082 2.547218 GCCGACACACTTTGAGAGGTTA 60.547 50.000 0.00 0.00 0.00 2.85
5865 13083 3.057734 CCGACACACTTTGAGAGGTTAC 58.942 50.000 0.00 0.00 0.00 2.50
5866 13084 3.491964 CCGACACACTTTGAGAGGTTACA 60.492 47.826 0.00 0.00 0.00 2.41
5867 13085 4.307432 CGACACACTTTGAGAGGTTACAT 58.693 43.478 0.00 0.00 0.00 2.29
5868 13086 5.466819 CGACACACTTTGAGAGGTTACATA 58.533 41.667 0.00 0.00 0.00 2.29
5869 13087 5.573282 CGACACACTTTGAGAGGTTACATAG 59.427 44.000 0.00 0.00 0.00 2.23
5870 13088 6.420913 ACACACTTTGAGAGGTTACATAGT 57.579 37.500 0.00 0.00 0.00 2.12
5871 13089 6.223852 ACACACTTTGAGAGGTTACATAGTG 58.776 40.000 0.00 0.00 44.87 2.74
5872 13090 5.120830 CACACTTTGAGAGGTTACATAGTGC 59.879 44.000 14.09 0.00 43.98 4.40
5873 13091 5.012148 ACACTTTGAGAGGTTACATAGTGCT 59.988 40.000 14.09 3.82 43.98 4.40
5874 13092 6.210784 ACACTTTGAGAGGTTACATAGTGCTA 59.789 38.462 14.09 0.00 43.98 3.49
5875 13093 6.754209 CACTTTGAGAGGTTACATAGTGCTAG 59.246 42.308 0.00 0.00 38.44 3.42
5876 13094 4.920640 TGAGAGGTTACATAGTGCTAGC 57.079 45.455 8.10 8.10 0.00 3.42
5877 13095 3.637229 TGAGAGGTTACATAGTGCTAGCC 59.363 47.826 13.29 3.49 0.00 3.93
5878 13096 3.637229 GAGAGGTTACATAGTGCTAGCCA 59.363 47.826 13.29 0.00 0.00 4.75
5879 13097 4.030913 AGAGGTTACATAGTGCTAGCCAA 58.969 43.478 13.29 0.00 0.00 4.52
5880 13098 4.120589 GAGGTTACATAGTGCTAGCCAAC 58.879 47.826 13.29 4.48 0.00 3.77
5881 13099 3.118371 AGGTTACATAGTGCTAGCCAACC 60.118 47.826 13.29 12.93 35.49 3.77
5882 13100 3.370103 GGTTACATAGTGCTAGCCAACCA 60.370 47.826 13.29 0.00 35.38 3.67
5883 13101 2.698855 ACATAGTGCTAGCCAACCAG 57.301 50.000 13.29 0.34 0.00 4.00
5884 13102 1.909302 ACATAGTGCTAGCCAACCAGT 59.091 47.619 13.29 1.01 0.00 4.00
5885 13103 2.305927 ACATAGTGCTAGCCAACCAGTT 59.694 45.455 13.29 0.00 0.00 3.16
5886 13104 3.244911 ACATAGTGCTAGCCAACCAGTTT 60.245 43.478 13.29 0.00 0.00 2.66
5887 13105 2.364972 AGTGCTAGCCAACCAGTTTT 57.635 45.000 13.29 0.00 0.00 2.43
5888 13106 2.666317 AGTGCTAGCCAACCAGTTTTT 58.334 42.857 13.29 0.00 0.00 1.94
5889 13107 2.362077 AGTGCTAGCCAACCAGTTTTTG 59.638 45.455 13.29 0.00 0.00 2.44
5890 13108 2.360801 GTGCTAGCCAACCAGTTTTTGA 59.639 45.455 13.29 0.00 0.00 2.69
5891 13109 3.027412 TGCTAGCCAACCAGTTTTTGAA 58.973 40.909 13.29 0.00 0.00 2.69
5892 13110 3.068024 TGCTAGCCAACCAGTTTTTGAAG 59.932 43.478 13.29 0.00 0.00 3.02
5893 13111 2.602257 AGCCAACCAGTTTTTGAAGC 57.398 45.000 0.00 0.00 0.00 3.86
5894 13112 1.138859 AGCCAACCAGTTTTTGAAGCC 59.861 47.619 0.00 0.00 0.00 4.35
5895 13113 1.138859 GCCAACCAGTTTTTGAAGCCT 59.861 47.619 0.00 0.00 0.00 4.58
5896 13114 2.419990 GCCAACCAGTTTTTGAAGCCTT 60.420 45.455 0.00 0.00 0.00 4.35
5897 13115 3.457234 CCAACCAGTTTTTGAAGCCTTC 58.543 45.455 0.00 0.00 0.00 3.46
5898 13116 3.132824 CCAACCAGTTTTTGAAGCCTTCT 59.867 43.478 5.96 0.00 0.00 2.85
5899 13117 4.340950 CCAACCAGTTTTTGAAGCCTTCTA 59.659 41.667 5.96 0.00 0.00 2.10
5900 13118 5.507985 CCAACCAGTTTTTGAAGCCTTCTAG 60.508 44.000 5.96 0.00 0.00 2.43
5901 13119 4.793201 ACCAGTTTTTGAAGCCTTCTAGT 58.207 39.130 5.96 0.00 0.00 2.57
5902 13120 5.937111 ACCAGTTTTTGAAGCCTTCTAGTA 58.063 37.500 5.96 0.00 0.00 1.82
5903 13121 5.998363 ACCAGTTTTTGAAGCCTTCTAGTAG 59.002 40.000 5.96 0.00 0.00 2.57
5904 13122 5.412904 CCAGTTTTTGAAGCCTTCTAGTAGG 59.587 44.000 10.96 10.96 38.40 3.18
5905 13123 5.998363 CAGTTTTTGAAGCCTTCTAGTAGGT 59.002 40.000 16.04 0.00 37.63 3.08
5906 13124 6.147985 CAGTTTTTGAAGCCTTCTAGTAGGTC 59.852 42.308 16.04 7.93 37.63 3.85
5907 13125 4.820894 TTTGAAGCCTTCTAGTAGGTCC 57.179 45.455 16.04 6.98 37.63 4.46
5908 13126 2.748388 TGAAGCCTTCTAGTAGGTCCC 58.252 52.381 16.04 6.68 37.63 4.46
5909 13127 2.040939 GAAGCCTTCTAGTAGGTCCCC 58.959 57.143 16.04 0.59 37.63 4.81
5910 13128 1.320962 AGCCTTCTAGTAGGTCCCCT 58.679 55.000 16.04 2.83 37.63 4.79
5911 13129 1.062810 AGCCTTCTAGTAGGTCCCCTG 60.063 57.143 16.04 0.00 37.63 4.45
5912 13130 1.063114 GCCTTCTAGTAGGTCCCCTGA 60.063 57.143 16.04 0.00 37.63 3.86
5913 13131 2.626149 GCCTTCTAGTAGGTCCCCTGAA 60.626 54.545 16.04 0.00 37.63 3.02
5914 13132 3.930035 CCTTCTAGTAGGTCCCCTGAAT 58.070 50.000 7.24 0.00 34.61 2.57
5915 13133 3.898741 CCTTCTAGTAGGTCCCCTGAATC 59.101 52.174 7.24 0.00 34.61 2.52
5916 13134 4.388118 CCTTCTAGTAGGTCCCCTGAATCT 60.388 50.000 7.24 0.00 34.61 2.40
5917 13135 4.186077 TCTAGTAGGTCCCCTGAATCTG 57.814 50.000 0.00 0.00 34.61 2.90
5918 13136 2.950990 AGTAGGTCCCCTGAATCTGT 57.049 50.000 0.00 0.00 34.61 3.41
5919 13137 3.207044 AGTAGGTCCCCTGAATCTGTT 57.793 47.619 0.00 0.00 34.61 3.16
5920 13138 3.532102 AGTAGGTCCCCTGAATCTGTTT 58.468 45.455 0.00 0.00 34.61 2.83
5921 13139 3.916989 AGTAGGTCCCCTGAATCTGTTTT 59.083 43.478 0.00 0.00 34.61 2.43
5922 13140 3.903530 AGGTCCCCTGAATCTGTTTTT 57.096 42.857 0.00 0.00 29.57 1.94
5945 13163 9.639601 TTTTTGTTTGTTTTCTTTGTTGGTTTT 57.360 22.222 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 9.994432 TTTCAAATATTGTTTGCGAACATTTTT 57.006 22.222 20.12 15.63 44.71 1.94
781 3824 1.447140 GCTGGCGTCGTCAACCATA 60.447 57.895 0.00 0.00 31.79 2.74
880 3923 3.623060 GTCACGTAGGTCCACGAACTATA 59.377 47.826 17.22 0.00 44.69 1.31
952 3995 8.748179 ATCTGTAGGTAGTAGGTGTAGGTATA 57.252 38.462 0.00 0.00 0.00 1.47
1155 4198 2.123033 GGCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1156 4199 1.457455 CAGGCTCCTCCTCCTCCTC 60.457 68.421 0.00 0.00 45.52 3.71
1157 4200 2.236959 GACAGGCTCCTCCTCCTCCT 62.237 65.000 0.00 0.00 45.52 3.69
1158 4201 1.760480 GACAGGCTCCTCCTCCTCC 60.760 68.421 0.00 0.00 45.52 4.30
1179 4222 2.820178 TCCATGAGTCTTGCAGTAGGA 58.180 47.619 0.00 0.00 0.00 2.94
1352 4398 4.327357 CACCTAGCTAGTGACAAAATCGTG 59.673 45.833 19.31 11.53 37.42 4.35
1353 4399 4.021368 ACACCTAGCTAGTGACAAAATCGT 60.021 41.667 19.31 3.32 38.63 3.73
1375 4421 3.443054 TGCACTCACGCGTTTAATTAC 57.557 42.857 10.22 0.00 33.35 1.89
1410 4465 4.637534 CCCATCTGTCACCTAACATTTGAG 59.362 45.833 0.00 0.00 0.00 3.02
1411 4466 4.288366 TCCCATCTGTCACCTAACATTTGA 59.712 41.667 0.00 0.00 0.00 2.69
1412 4467 4.588899 TCCCATCTGTCACCTAACATTTG 58.411 43.478 0.00 0.00 0.00 2.32
1413 4468 4.927267 TCCCATCTGTCACCTAACATTT 57.073 40.909 0.00 0.00 0.00 2.32
1414 4469 4.589908 GTTCCCATCTGTCACCTAACATT 58.410 43.478 0.00 0.00 0.00 2.71
1415 4470 3.369471 CGTTCCCATCTGTCACCTAACAT 60.369 47.826 0.00 0.00 0.00 2.71
1419 4474 1.191535 CCGTTCCCATCTGTCACCTA 58.808 55.000 0.00 0.00 0.00 3.08
1500 4567 2.668212 CACGGTGGCGGTGTCAAT 60.668 61.111 0.00 0.00 31.52 2.57
2062 5137 8.617809 TCTTATATTTAAAAACGGATGGAGTGC 58.382 33.333 0.00 0.00 0.00 4.40
2063 5319 9.931210 GTCTTATATTTAAAAACGGATGGAGTG 57.069 33.333 0.00 0.00 0.00 3.51
2129 5388 9.778993 GTGAACATACACTCTAAAATACGTCTA 57.221 33.333 0.00 0.00 37.73 2.59
2130 5389 8.521176 AGTGAACATACACTCTAAAATACGTCT 58.479 33.333 0.00 0.00 46.36 4.18
2131 5390 8.684973 AGTGAACATACACTCTAAAATACGTC 57.315 34.615 0.00 0.00 46.36 4.34
2144 5403 6.021596 CGGAGCAAAATAAGTGAACATACAC 58.978 40.000 0.00 0.00 40.60 2.90
2145 5404 5.703592 ACGGAGCAAAATAAGTGAACATACA 59.296 36.000 0.00 0.00 0.00 2.29
2146 5405 6.178239 ACGGAGCAAAATAAGTGAACATAC 57.822 37.500 0.00 0.00 0.00 2.39
2147 5406 7.551262 ACATACGGAGCAAAATAAGTGAACATA 59.449 33.333 0.00 0.00 0.00 2.29
2148 5407 6.374333 ACATACGGAGCAAAATAAGTGAACAT 59.626 34.615 0.00 0.00 0.00 2.71
2149 5408 5.703592 ACATACGGAGCAAAATAAGTGAACA 59.296 36.000 0.00 0.00 0.00 3.18
2150 5409 6.178239 ACATACGGAGCAAAATAAGTGAAC 57.822 37.500 0.00 0.00 0.00 3.18
2151 5410 7.908827 TTACATACGGAGCAAAATAAGTGAA 57.091 32.000 0.00 0.00 0.00 3.18
2152 5411 7.551262 ACATTACATACGGAGCAAAATAAGTGA 59.449 33.333 0.00 0.00 0.00 3.41
2153 5412 7.693952 ACATTACATACGGAGCAAAATAAGTG 58.306 34.615 0.00 0.00 0.00 3.16
2154 5413 7.859325 ACATTACATACGGAGCAAAATAAGT 57.141 32.000 0.00 0.00 0.00 2.24
2155 5414 9.864034 CTTACATTACATACGGAGCAAAATAAG 57.136 33.333 0.00 0.00 0.00 1.73
2156 5415 9.602568 TCTTACATTACATACGGAGCAAAATAA 57.397 29.630 0.00 0.00 0.00 1.40
2157 5416 9.037737 GTCTTACATTACATACGGAGCAAAATA 57.962 33.333 0.00 0.00 0.00 1.40
2158 5417 7.012044 GGTCTTACATTACATACGGAGCAAAAT 59.988 37.037 0.00 0.00 0.00 1.82
2159 5418 6.314400 GGTCTTACATTACATACGGAGCAAAA 59.686 38.462 0.00 0.00 0.00 2.44
2160 5419 5.813672 GGTCTTACATTACATACGGAGCAAA 59.186 40.000 0.00 0.00 0.00 3.68
2161 5420 5.128171 AGGTCTTACATTACATACGGAGCAA 59.872 40.000 0.00 0.00 0.00 3.91
2162 5421 4.647853 AGGTCTTACATTACATACGGAGCA 59.352 41.667 0.00 0.00 0.00 4.26
2163 5422 5.197682 AGGTCTTACATTACATACGGAGC 57.802 43.478 0.00 0.00 0.00 4.70
2164 5423 9.245962 CTAAAAGGTCTTACATTACATACGGAG 57.754 37.037 0.00 0.00 0.00 4.63
2165 5424 8.970020 TCTAAAAGGTCTTACATTACATACGGA 58.030 33.333 0.00 0.00 0.00 4.69
2166 5425 9.245962 CTCTAAAAGGTCTTACATTACATACGG 57.754 37.037 0.00 0.00 0.00 4.02
2325 5586 2.791560 GTGATCATCAGTCCATCGAACG 59.208 50.000 0.00 0.00 0.00 3.95
2439 5705 7.663081 CCTTCATACATGCCAAGAGTATATTGT 59.337 37.037 0.00 0.00 0.00 2.71
2497 5764 9.806203 CCTTCATAATGCAAAATGTCATAGAAA 57.194 29.630 10.44 0.00 0.00 2.52
2543 5845 9.470399 TGGTGATTAACTTAGACTAGTGTCATA 57.530 33.333 0.00 0.00 45.20 2.15
2563 5865 2.438800 AGGCTAGTCGTAGTGGTGAT 57.561 50.000 0.00 0.00 0.00 3.06
2573 5875 2.921754 CGGAACACTTTTAGGCTAGTCG 59.078 50.000 0.00 0.00 0.00 4.18
2593 5895 8.673711 TCATATCAAGGTTTGGATAAGAAAACG 58.326 33.333 0.00 0.00 37.19 3.60
2708 6096 5.126061 GGCCACACATGTCAAGAGATAAAAT 59.874 40.000 0.00 0.00 0.00 1.82
2738 6192 7.442364 AGACGCACACAGAAGCATAATTATAAT 59.558 33.333 0.00 0.00 0.00 1.28
2774 6237 8.646900 TGACATATCACCTAATATTACAGCACA 58.353 33.333 0.00 0.00 0.00 4.57
2821 6285 9.059023 AGGACAAAATTAGTTAATACTCCCTCT 57.941 33.333 0.00 0.00 35.78 3.69
2822 6286 9.682465 AAGGACAAAATTAGTTAATACTCCCTC 57.318 33.333 0.00 0.00 35.78 4.30
2884 6777 4.001652 AGCACATCATTGACAGTCTTCAG 58.998 43.478 1.31 0.00 0.00 3.02
2886 6779 3.126514 CCAGCACATCATTGACAGTCTTC 59.873 47.826 1.31 0.00 0.00 2.87
2887 6780 3.079578 CCAGCACATCATTGACAGTCTT 58.920 45.455 1.31 0.00 0.00 3.01
3075 6980 2.147958 GACCGCAACCATGTTCTGTAA 58.852 47.619 0.00 0.00 0.00 2.41
3288 7288 3.765026 ACTTGCGTGTTGAAAATCGTTT 58.235 36.364 0.00 0.00 0.00 3.60
3312 7315 6.610830 ACATTCATATGAAAAGTAATGGGCCA 59.389 34.615 21.50 9.61 37.61 5.36
3657 8208 3.016031 TGCGAACATATGCAAGTGGATT 58.984 40.909 1.58 0.00 38.34 3.01
3790 8342 6.480285 TCGGCTTTACGAAAAACATATAAGC 58.520 36.000 0.00 0.00 40.34 3.09
3810 8374 7.272731 GGAGTTTCTTAATTTGTGTAATTCGGC 59.727 37.037 0.00 0.00 37.60 5.54
3863 8429 9.787435 ACAGTCACAAACTTGGATAATAACTAA 57.213 29.630 0.00 0.00 35.45 2.24
3884 8462 5.106908 GCTAGGATTGTCAAGTCAAACAGTC 60.107 44.000 0.00 0.00 32.96 3.51
4112 8690 9.883142 TGAGTTGAGTTTGATAAAATTTTGGTT 57.117 25.926 13.76 0.00 0.00 3.67
4323 11469 7.573968 AATTTCTCCTTGGTGCATCTATAAC 57.426 36.000 0.00 0.00 0.00 1.89
4346 11494 8.445275 TGGTCCGTCTAGTTATATACGTTTAA 57.555 34.615 0.00 0.00 31.53 1.52
4501 11655 3.743396 GTGTCTTGGCTTCTAGTTCACTG 59.257 47.826 0.00 0.00 0.00 3.66
4510 11664 3.614092 CATATGTGGTGTCTTGGCTTCT 58.386 45.455 0.00 0.00 0.00 2.85
4583 11737 5.335740 CCAAGTTATCTCCATAGTCGCGTAT 60.336 44.000 5.77 0.00 0.00 3.06
4679 11834 6.391227 TCTCTTTTCTTTCCATGGTGAAAC 57.609 37.500 20.95 0.00 31.28 2.78
4716 11876 7.206687 GGTGGCCGAATGATTGAATTTTATAA 58.793 34.615 0.00 0.00 0.00 0.98
4787 11947 8.705594 AGTGTTATTATAACTCTGGTAGTGCAT 58.294 33.333 15.96 0.00 38.88 3.96
4946 12106 4.399303 AGGCACTAAGTAATTCACCATTGC 59.601 41.667 0.00 0.00 36.02 3.56
5067 12236 3.957497 ACATTTGACTTGCAACCTTGGTA 59.043 39.130 0.00 0.00 35.91 3.25
5087 12256 8.268605 TGTCCAACAATAATAGTGCCTAATACA 58.731 33.333 0.00 0.00 0.00 2.29
5088 12257 8.671384 TGTCCAACAATAATAGTGCCTAATAC 57.329 34.615 0.00 0.00 0.00 1.89
5089 12258 9.860650 ATTGTCCAACAATAATAGTGCCTAATA 57.139 29.630 3.57 0.00 46.11 0.98
5090 12259 8.632679 CATTGTCCAACAATAATAGTGCCTAAT 58.367 33.333 5.08 0.00 46.22 1.73
5091 12260 7.831690 TCATTGTCCAACAATAATAGTGCCTAA 59.168 33.333 5.08 0.00 46.22 2.69
5093 12262 6.186957 TCATTGTCCAACAATAATAGTGCCT 58.813 36.000 5.08 0.00 46.22 4.75
5094 12263 6.449635 TCATTGTCCAACAATAATAGTGCC 57.550 37.500 5.08 0.00 46.22 5.01
5263 12476 7.014326 TGCCACATTATTGGTAAACAAAGTGTA 59.986 33.333 0.00 0.00 43.46 2.90
5396 12609 4.301628 GCCAATGGACAAGAGACAAAAAG 58.698 43.478 2.05 0.00 0.00 2.27
5521 12737 7.439356 TCAGACGACCAATAATCTCAAATCATC 59.561 37.037 0.00 0.00 0.00 2.92
5542 12758 2.096218 GCGTTGGTGAGTTTGATCAGAC 60.096 50.000 8.31 8.31 0.00 3.51
5610 12826 6.071391 ACCAACTTGATTATGGTGGATTGAAC 60.071 38.462 13.67 0.00 45.47 3.18
5668 12884 3.250323 CTGCCGATCAGTGCGACG 61.250 66.667 0.00 0.00 38.02 5.12
5691 12907 8.600449 AATCATTTCGATGGGCTACTTAGGCA 62.600 42.308 11.57 0.00 41.15 4.75
5706 12922 0.830648 AGGCGGGAGAATCATTTCGA 59.169 50.000 0.00 0.00 36.93 3.71
5712 12928 2.272146 GGCAAGGCGGGAGAATCA 59.728 61.111 0.00 0.00 36.25 2.57
5730 12946 4.564821 GGACTAGTTAACATGCCCAGAACA 60.565 45.833 8.61 0.00 0.00 3.18
5736 12952 4.035208 CGAAATGGACTAGTTAACATGCCC 59.965 45.833 8.61 2.50 0.00 5.36
5737 12953 4.634443 ACGAAATGGACTAGTTAACATGCC 59.366 41.667 8.61 4.30 0.00 4.40
5739 12955 5.121611 TGCACGAAATGGACTAGTTAACATG 59.878 40.000 8.61 2.40 0.00 3.21
5740 12956 5.121768 GTGCACGAAATGGACTAGTTAACAT 59.878 40.000 8.61 0.00 45.77 2.71
5772 12990 1.064803 TGCTTAATGCGGCAAATACGG 59.935 47.619 6.82 1.10 46.63 4.02
5803 13021 1.381872 AGTGCCTATCCGGAGCAGT 60.382 57.895 16.47 16.52 37.15 4.40
5823 13041 1.513158 CATCTCTTGTCGCTCGGGT 59.487 57.895 0.00 0.00 0.00 5.28
5826 13044 1.880340 GCCCATCTCTTGTCGCTCG 60.880 63.158 0.00 0.00 0.00 5.03
5827 13045 1.522580 GGCCCATCTCTTGTCGCTC 60.523 63.158 0.00 0.00 0.00 5.03
5828 13046 2.586792 GGCCCATCTCTTGTCGCT 59.413 61.111 0.00 0.00 0.00 4.93
5829 13047 2.892425 CGGCCCATCTCTTGTCGC 60.892 66.667 0.00 0.00 0.00 5.19
5830 13048 1.519455 GTCGGCCCATCTCTTGTCG 60.519 63.158 0.00 0.00 0.00 4.35
5831 13049 0.741221 GTGTCGGCCCATCTCTTGTC 60.741 60.000 0.00 0.00 0.00 3.18
5832 13050 1.296715 GTGTCGGCCCATCTCTTGT 59.703 57.895 0.00 0.00 0.00 3.16
5833 13051 1.021390 GTGTGTCGGCCCATCTCTTG 61.021 60.000 0.00 0.00 0.00 3.02
5834 13052 1.194781 AGTGTGTCGGCCCATCTCTT 61.195 55.000 0.00 0.00 0.00 2.85
5835 13053 1.194781 AAGTGTGTCGGCCCATCTCT 61.195 55.000 0.00 0.00 0.00 3.10
5836 13054 0.321653 AAAGTGTGTCGGCCCATCTC 60.322 55.000 0.00 0.00 0.00 2.75
5837 13055 0.606401 CAAAGTGTGTCGGCCCATCT 60.606 55.000 0.00 0.00 0.00 2.90
5838 13056 0.605319 TCAAAGTGTGTCGGCCCATC 60.605 55.000 0.00 0.00 0.00 3.51
5839 13057 0.606401 CTCAAAGTGTGTCGGCCCAT 60.606 55.000 0.00 0.00 0.00 4.00
5840 13058 1.227823 CTCAAAGTGTGTCGGCCCA 60.228 57.895 0.00 0.00 0.00 5.36
5841 13059 0.951040 CTCTCAAAGTGTGTCGGCCC 60.951 60.000 0.00 0.00 0.00 5.80
5842 13060 0.951040 CCTCTCAAAGTGTGTCGGCC 60.951 60.000 0.00 0.00 0.00 6.13
5843 13061 0.249911 ACCTCTCAAAGTGTGTCGGC 60.250 55.000 0.00 0.00 0.00 5.54
5844 13062 2.240493 AACCTCTCAAAGTGTGTCGG 57.760 50.000 0.00 0.00 0.00 4.79
5845 13063 3.713288 TGTAACCTCTCAAAGTGTGTCG 58.287 45.455 0.00 0.00 0.00 4.35
5846 13064 6.366332 CACTATGTAACCTCTCAAAGTGTGTC 59.634 42.308 0.00 0.00 0.00 3.67
5847 13065 6.223852 CACTATGTAACCTCTCAAAGTGTGT 58.776 40.000 0.00 0.00 0.00 3.72
5848 13066 5.120830 GCACTATGTAACCTCTCAAAGTGTG 59.879 44.000 0.00 0.00 36.38 3.82
5849 13067 5.012148 AGCACTATGTAACCTCTCAAAGTGT 59.988 40.000 0.00 0.00 36.38 3.55
5850 13068 5.482908 AGCACTATGTAACCTCTCAAAGTG 58.517 41.667 0.00 0.00 36.92 3.16
5851 13069 5.746990 AGCACTATGTAACCTCTCAAAGT 57.253 39.130 0.00 0.00 0.00 2.66
5852 13070 5.751028 GCTAGCACTATGTAACCTCTCAAAG 59.249 44.000 10.63 0.00 0.00 2.77
5853 13071 5.395324 GGCTAGCACTATGTAACCTCTCAAA 60.395 44.000 18.24 0.00 0.00 2.69
5854 13072 4.099573 GGCTAGCACTATGTAACCTCTCAA 59.900 45.833 18.24 0.00 0.00 3.02
5855 13073 3.637229 GGCTAGCACTATGTAACCTCTCA 59.363 47.826 18.24 0.00 0.00 3.27
5856 13074 3.637229 TGGCTAGCACTATGTAACCTCTC 59.363 47.826 18.24 0.00 0.00 3.20
5857 13075 3.643237 TGGCTAGCACTATGTAACCTCT 58.357 45.455 18.24 0.00 0.00 3.69
5858 13076 4.120589 GTTGGCTAGCACTATGTAACCTC 58.879 47.826 18.24 0.00 0.00 3.85
5859 13077 3.118371 GGTTGGCTAGCACTATGTAACCT 60.118 47.826 18.24 0.00 34.86 3.50
5860 13078 3.203716 GGTTGGCTAGCACTATGTAACC 58.796 50.000 18.24 13.66 0.00 2.85
5861 13079 3.869065 TGGTTGGCTAGCACTATGTAAC 58.131 45.455 18.24 8.98 0.00 2.50
5862 13080 3.517901 ACTGGTTGGCTAGCACTATGTAA 59.482 43.478 18.24 0.00 0.00 2.41
5863 13081 3.104512 ACTGGTTGGCTAGCACTATGTA 58.895 45.455 18.24 0.00 0.00 2.29
5864 13082 1.909302 ACTGGTTGGCTAGCACTATGT 59.091 47.619 18.24 4.93 0.00 2.29
5865 13083 2.698855 ACTGGTTGGCTAGCACTATG 57.301 50.000 18.24 4.29 0.00 2.23
5866 13084 3.721087 AAACTGGTTGGCTAGCACTAT 57.279 42.857 18.24 0.00 0.00 2.12
5867 13085 3.502123 AAAACTGGTTGGCTAGCACTA 57.498 42.857 18.24 3.97 0.00 2.74
5868 13086 2.362077 CAAAAACTGGTTGGCTAGCACT 59.638 45.455 18.24 0.00 0.00 4.40
5869 13087 2.360801 TCAAAAACTGGTTGGCTAGCAC 59.639 45.455 18.24 6.87 0.00 4.40
5870 13088 2.660572 TCAAAAACTGGTTGGCTAGCA 58.339 42.857 18.24 0.25 0.00 3.49
5871 13089 3.642705 CTTCAAAAACTGGTTGGCTAGC 58.357 45.455 6.04 6.04 0.00 3.42
5872 13090 3.552890 GGCTTCAAAAACTGGTTGGCTAG 60.553 47.826 0.00 0.00 0.00 3.42
5873 13091 2.364002 GGCTTCAAAAACTGGTTGGCTA 59.636 45.455 0.00 0.00 0.00 3.93
5874 13092 1.138859 GGCTTCAAAAACTGGTTGGCT 59.861 47.619 0.00 0.00 0.00 4.75
5875 13093 1.138859 AGGCTTCAAAAACTGGTTGGC 59.861 47.619 0.00 0.00 0.00 4.52
5876 13094 3.132824 AGAAGGCTTCAAAAACTGGTTGG 59.867 43.478 27.70 0.00 0.00 3.77
5877 13095 4.391405 AGAAGGCTTCAAAAACTGGTTG 57.609 40.909 27.70 0.00 0.00 3.77
5878 13096 5.201243 ACTAGAAGGCTTCAAAAACTGGTT 58.799 37.500 27.70 6.77 0.00 3.67
5879 13097 4.793201 ACTAGAAGGCTTCAAAAACTGGT 58.207 39.130 27.70 11.87 0.00 4.00
5880 13098 5.412904 CCTACTAGAAGGCTTCAAAAACTGG 59.587 44.000 27.70 16.01 0.00 4.00
5881 13099 5.998363 ACCTACTAGAAGGCTTCAAAAACTG 59.002 40.000 27.70 13.05 40.62 3.16
5882 13100 6.189036 ACCTACTAGAAGGCTTCAAAAACT 57.811 37.500 27.70 9.62 40.62 2.66
5883 13101 5.411977 GGACCTACTAGAAGGCTTCAAAAAC 59.588 44.000 27.70 11.29 40.62 2.43
5884 13102 5.514310 GGGACCTACTAGAAGGCTTCAAAAA 60.514 44.000 27.70 10.48 40.62 1.94
5885 13103 4.019591 GGGACCTACTAGAAGGCTTCAAAA 60.020 45.833 27.70 12.49 40.62 2.44
5886 13104 3.518303 GGGACCTACTAGAAGGCTTCAAA 59.482 47.826 27.70 14.87 40.62 2.69
5887 13105 3.105283 GGGACCTACTAGAAGGCTTCAA 58.895 50.000 27.70 10.14 40.62 2.69
5888 13106 2.748388 GGGACCTACTAGAAGGCTTCA 58.252 52.381 27.70 13.41 40.62 3.02
5919 13137 9.639601 AAAACCAACAAAGAAAACAAACAAAAA 57.360 22.222 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.