Multiple sequence alignment - TraesCS3D01G399800

Loading Multiple Alignment...

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 TraesCS3D01G399800 chr3D 100.000 3878 0 0 1 3878 514682219 514678342 0.000000e+00 7162.0
1 TraesCS3D01G399800 chr3B 90.056 2132 158 23 771 2872 676968365 676966258 0.000000e+00 2713.0
2 TraesCS3D01G399800 chr3B 93.167 761 43 7 1 756 676969365 676968609 0.000000e+00 1109.0
3 TraesCS3D01G399800 chr3B 91.633 490 31 4 3390 3878 676965632 676965152 0.000000e+00 669.0
4 TraesCS3D01G399800 chr3B 93.079 419 13 7 2877 3288 676966041 676965632 1.990000e-167 599.0
5 TraesCS3D01G399800 chr2A 79.860 1852 297 42 752 2565 764897793 764899606 0.000000e+00 1284.0
6 TraesCS3D01G399800 chr2A 94.017 117 6 1 3275 3391 187955930 187955815 3.980000e-40 176.0
7 TraesCS3D01G399800 chr2A 80.455 220 41 2 2654 2872 764899683 764899901 2.400000e-37 167.0
8 TraesCS3D01G399800 chr2A 92.593 54 4 0 3561 3614 652577003 652577056 1.160000e-10 78.7
9 TraesCS3D01G399800 chr2A 82.895 76 13 0 3565 3640 622287677 622287752 6.950000e-08 69.4
10 TraesCS3D01G399800 chr7B 80.489 1717 265 42 858 2563 746583435 746581778 0.000000e+00 1251.0
11 TraesCS3D01G399800 chr7B 80.489 1717 265 42 858 2563 746609819 746608162 0.000000e+00 1251.0
12 TraesCS3D01G399800 chr7B 85.596 604 85 2 1731 2333 748298842 748299444 1.970000e-177 632.0
13 TraesCS3D01G399800 chr7B 84.124 611 97 0 1723 2333 745472805 745473415 3.340000e-165 592.0
14 TraesCS3D01G399800 chr7B 80.081 738 115 14 842 1576 745446051 745446759 1.600000e-143 520.0
15 TraesCS3D01G399800 chr7B 81.636 648 94 12 932 1576 745471758 745472383 7.430000e-142 514.0
16 TraesCS3D01G399800 chr7B 81.240 645 97 13 932 1576 748297741 748298361 2.080000e-137 499.0
17 TraesCS3D01G399800 chr7B 94.958 119 6 0 3281 3399 559142191 559142309 1.840000e-43 187.0
18 TraesCS3D01G399800 chr7B 85.000 180 23 4 2656 2833 745473750 745473927 3.080000e-41 180.0
19 TraesCS3D01G399800 chr2D 82.491 851 114 14 752 1598 639127570 639128389 0.000000e+00 713.0
20 TraesCS3D01G399800 chr2D 80.267 375 71 2 1609 1983 639128427 639128798 2.950000e-71 279.0
21 TraesCS3D01G399800 chr1B 76.909 550 102 15 1024 1569 9647384 9647912 4.900000e-74 289.0
22 TraesCS3D01G399800 chr1B 92.063 126 8 2 3282 3406 624663028 624662904 3.980000e-40 176.0
23 TraesCS3D01G399800 chr1B 71.978 546 120 26 1781 2311 592366505 592365978 3.140000e-26 130.0
24 TraesCS3D01G399800 chr6B 92.308 130 8 2 3264 3392 705508993 705508865 2.380000e-42 183.0
25 TraesCS3D01G399800 chr6B 82.000 150 22 4 3717 3864 29779059 29778913 5.260000e-24 122.0
26 TraesCS3D01G399800 chr5D 94.017 117 7 0 3275 3391 424123539 424123655 1.110000e-40 178.0
27 TraesCS3D01G399800 chr5D 85.870 92 13 0 3561 3652 475520464 475520373 8.870000e-17 99.0
28 TraesCS3D01G399800 chr7D 90.441 136 10 2 3284 3419 474273737 474273605 3.980000e-40 176.0
29 TraesCS3D01G399800 chr7D 94.118 51 3 0 3558 3608 578488038 578488088 1.160000e-10 78.7
30 TraesCS3D01G399800 chr5A 94.017 117 6 1 3276 3392 9610334 9610219 3.980000e-40 176.0
31 TraesCS3D01G399800 chr5A 93.860 114 7 0 3282 3395 299771125 299771238 5.150000e-39 172.0
32 TraesCS3D01G399800 chr5A 93.860 114 7 0 3278 3391 385954756 385954869 5.150000e-39 172.0
33 TraesCS3D01G399800 chr5A 91.736 121 9 1 3282 3402 581101824 581101705 2.400000e-37 167.0
34 TraesCS3D01G399800 chr5A 88.172 93 11 0 3611 3703 340159060 340159152 1.140000e-20 111.0
35 TraesCS3D01G399800 chr5A 95.745 47 2 0 3560 3606 536432741 536432787 4.150000e-10 76.8
36 TraesCS3D01G399800 chr1D 93.277 119 7 1 3277 3395 222916446 222916563 1.430000e-39 174.0
37 TraesCS3D01G399800 chr1D 78.151 238 42 8 1781 2013 437292278 437292046 4.040000e-30 143.0
38 TraesCS3D01G399800 chr1D 94.444 54 3 0 3558 3611 308579483 308579536 2.480000e-12 84.2
39 TraesCS3D01G399800 chr7A 94.643 112 5 1 3285 3396 735739909 735739799 5.150000e-39 172.0
40 TraesCS3D01G399800 chr6A 90.840 131 7 5 3266 3392 545155557 545155686 1.850000e-38 171.0
41 TraesCS3D01G399800 chr5B 90.625 128 8 4 3271 3397 512985334 512985210 2.400000e-37 167.0
42 TraesCS3D01G399800 chr5B 96.226 53 2 0 3563 3615 617807501 617807553 1.920000e-13 87.9
43 TraesCS3D01G399800 chr1A 72.844 545 117 27 1781 2311 534275957 534276484 1.440000e-34 158.0
44 TraesCS3D01G399800 chr6D 89.831 59 6 0 3561 3619 114226965 114227023 4.150000e-10 76.8
45 TraesCS3D01G399800 chr2B 81.319 91 15 2 368 457 708020399 708020488 5.370000e-09 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 TraesCS3D01G399800 chr3D 514678342 514682219 3877 True 7162.000000 7162 100.000000 1 3878 1 chr3D.!!$R1 3877
1 TraesCS3D01G399800 chr3B 676965152 676969365 4213 True 1272.500000 2713 91.983750 1 3878 4 chr3B.!!$R1 3877
2 TraesCS3D01G399800 chr2A 764897793 764899901 2108 False 725.500000 1284 80.157500 752 2872 2 chr2A.!!$F3 2120
3 TraesCS3D01G399800 chr7B 746581778 746583435 1657 True 1251.000000 1251 80.489000 858 2563 1 chr7B.!!$R1 1705
4 TraesCS3D01G399800 chr7B 746608162 746609819 1657 True 1251.000000 1251 80.489000 858 2563 1 chr7B.!!$R2 1705
5 TraesCS3D01G399800 chr7B 748297741 748299444 1703 False 565.500000 632 83.418000 932 2333 2 chr7B.!!$F4 1401
6 TraesCS3D01G399800 chr7B 745446051 745446759 708 False 520.000000 520 80.081000 842 1576 1 chr7B.!!$F2 734
7 TraesCS3D01G399800 chr7B 745471758 745473927 2169 False 428.666667 592 83.586667 932 2833 3 chr7B.!!$F3 1901
8 TraesCS3D01G399800 chr2D 639127570 639128798 1228 False 496.000000 713 81.379000 752 1983 2 chr2D.!!$F1 1231
9 TraesCS3D01G399800 chr1B 9647384 9647912 528 False 289.000000 289 76.909000 1024 1569 1 chr1B.!!$F1 545

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
415 416 0.032952 CGTCCCCTCGTTCTGTTTCA 59.967 55.0 0.0 0.0 0.00 2.69 F
1966 2534 0.319555 TTTCCTCGAACTCTGTGCGG 60.320 55.0 0.0 0.0 34.96 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2729 0.740868 ATGGCCATCACTCGTTGACG 60.741 55.0 14.09 0.0 36.92 4.35 R
2879 3492 0.026285 CCGTTTATTTCAGCCTCGCG 59.974 55.0 0.00 0.0 0.00 5.87 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
55 56 4.457949 ACGAAAGGGTCCAAATGACATAAC 59.542 41.667 0.00 0.00 46.38 1.89
58 59 6.350110 CGAAAGGGTCCAAATGACATAACAAT 60.350 38.462 0.00 0.00 46.38 2.71
73 74 7.016361 ACATAACAATCCGAATAAAGAGCAC 57.984 36.000 0.00 0.00 0.00 4.40
107 108 7.543947 CACATCAATCAAGTGCTATGAAGTA 57.456 36.000 0.00 0.00 0.00 2.24
139 140 4.345257 TGGTCAAGTAGATTATCCTGGAGC 59.655 45.833 1.52 0.00 0.00 4.70
168 169 4.421058 TGAACTTGTCGATTCTCCATACG 58.579 43.478 0.00 0.00 0.00 3.06
189 190 3.733344 GATGCGCCGCCAGGAAGTA 62.733 63.158 6.63 0.00 41.02 2.24
199 200 1.978542 CCAGGAAGTACTCGTGAACG 58.021 55.000 0.00 0.00 41.58 3.95
211 212 2.281517 TCGTGAACGACCACAACAATT 58.718 42.857 0.50 0.00 44.22 2.32
214 215 3.605231 CGTGAACGACCACAACAATTACC 60.605 47.826 0.00 0.00 43.02 2.85
227 228 6.144402 CACAACAATTACCATCTCAAAACTGC 59.856 38.462 0.00 0.00 0.00 4.40
259 260 1.445095 CTCCTGCTCCGATGAAGGG 59.555 63.158 2.46 0.00 0.00 3.95
261 262 0.909610 TCCTGCTCCGATGAAGGGTT 60.910 55.000 2.46 0.00 0.00 4.11
265 266 0.528684 GCTCCGATGAAGGGTTCTCG 60.529 60.000 0.00 0.00 33.31 4.04
269 270 1.471676 CCGATGAAGGGTTCTCGAAGG 60.472 57.143 8.92 0.00 34.50 3.46
296 297 8.013667 ACATCTCCCTTAACCTATTCATCTACT 58.986 37.037 0.00 0.00 0.00 2.57
370 371 7.378181 TGAAAAAGGCAAAAGATAATCACCTC 58.622 34.615 0.00 0.00 0.00 3.85
405 406 1.516386 CATCGTTGTCGTCCCCTCG 60.516 63.158 0.00 0.00 38.33 4.63
414 415 0.316204 TCGTCCCCTCGTTCTGTTTC 59.684 55.000 0.00 0.00 0.00 2.78
415 416 0.032952 CGTCCCCTCGTTCTGTTTCA 59.967 55.000 0.00 0.00 0.00 2.69
417 418 2.779506 GTCCCCTCGTTCTGTTTCAAT 58.220 47.619 0.00 0.00 0.00 2.57
423 424 5.278957 CCCCTCGTTCTGTTTCAATTGAAAT 60.279 40.000 30.63 0.00 44.69 2.17
432 433 5.221880 TGTTTCAATTGAAATGAAGCTCGG 58.778 37.500 30.63 0.00 44.69 4.63
433 434 5.221224 TGTTTCAATTGAAATGAAGCTCGGT 60.221 36.000 30.63 0.00 44.69 4.69
437 438 1.808411 TGAAATGAAGCTCGGTGGTC 58.192 50.000 0.00 0.00 0.00 4.02
483 484 3.138625 CGGTGCGGTGGGAGATAT 58.861 61.111 0.00 0.00 0.00 1.63
486 487 1.146041 GTGCGGTGGGAGATATGCA 59.854 57.895 0.00 0.00 0.00 3.96
505 506 2.189499 GGATTCCGGCAGTGGCATC 61.189 63.158 17.80 11.71 43.71 3.91
521 522 2.426406 ATCCATGAGCCGACGAGCA 61.426 57.895 10.28 0.00 34.23 4.26
546 547 4.665833 ATGCAATGATGATTGGTTCCTG 57.334 40.909 7.03 0.00 39.62 3.86
547 548 2.166870 TGCAATGATGATTGGTTCCTGC 59.833 45.455 7.03 0.00 39.62 4.85
549 550 2.424601 CAATGATGATTGGTTCCTGCGT 59.575 45.455 0.00 0.00 36.12 5.24
705 710 9.551734 CTGATCATAGTTCAGAATTCCAACATA 57.448 33.333 16.42 8.83 42.63 2.29
911 1144 9.533831 AAAGTACTTCCATATTTGAGTTTGGAT 57.466 29.630 8.95 0.00 38.04 3.41
1197 1439 1.747206 GCAGTGTATACCCTTGGCCTG 60.747 57.143 3.32 0.00 0.00 4.85
1211 1453 1.374758 GCCTGGTCTCACGACTTGG 60.375 63.158 0.00 0.00 40.10 3.61
1212 1454 1.293498 CCTGGTCTCACGACTTGGG 59.707 63.158 0.00 0.00 40.10 4.12
1213 1455 1.293498 CTGGTCTCACGACTTGGGG 59.707 63.158 0.00 0.00 40.10 4.96
1214 1456 1.152419 TGGTCTCACGACTTGGGGA 60.152 57.895 0.00 0.00 40.10 4.81
1215 1457 0.544357 TGGTCTCACGACTTGGGGAT 60.544 55.000 0.00 0.00 40.10 3.85
1216 1458 1.272816 TGGTCTCACGACTTGGGGATA 60.273 52.381 0.00 0.00 40.10 2.59
1217 1459 2.040178 GGTCTCACGACTTGGGGATAT 58.960 52.381 0.00 0.00 40.10 1.63
1218 1460 2.036089 GGTCTCACGACTTGGGGATATC 59.964 54.545 0.00 0.00 40.10 1.63
1219 1461 2.693591 GTCTCACGACTTGGGGATATCA 59.306 50.000 4.83 0.00 37.19 2.15
1220 1462 2.693591 TCTCACGACTTGGGGATATCAC 59.306 50.000 4.83 0.00 0.00 3.06
1221 1463 1.760613 TCACGACTTGGGGATATCACC 59.239 52.381 17.82 17.82 40.76 4.02
1313 1555 4.643784 ACCATTTCTTCTCATCCATCTTGC 59.356 41.667 0.00 0.00 0.00 4.01
1458 1700 1.797025 GCCCGATGCTTATAGTGTCC 58.203 55.000 0.00 0.00 36.87 4.02
1497 1739 7.459795 TGTTGTTGGAATTATCAAGTATGCA 57.540 32.000 0.00 0.00 0.00 3.96
1589 1831 0.608856 TTGCCAGACCATGATTGCGT 60.609 50.000 0.00 0.00 0.00 5.24
1611 1880 3.184628 AGAGGACATGAACAAGGATGGA 58.815 45.455 0.00 0.00 0.00 3.41
1618 1887 6.150641 GGACATGAACAAGGATGGATATGATG 59.849 42.308 0.00 0.00 0.00 3.07
1619 1888 6.844829 ACATGAACAAGGATGGATATGATGA 58.155 36.000 0.00 0.00 0.00 2.92
1638 1907 7.776933 TGATGACATTGTTTACATAGCTCTC 57.223 36.000 0.00 0.00 0.00 3.20
1641 1910 6.108687 TGACATTGTTTACATAGCTCTCTGG 58.891 40.000 0.00 0.00 0.00 3.86
1646 1915 5.479306 TGTTTACATAGCTCTCTGGTCAAC 58.521 41.667 0.00 0.00 0.00 3.18
1686 1955 9.685276 AATATCATTTCTGGACACAACATCTTA 57.315 29.630 0.00 0.00 0.00 2.10
1693 1962 9.817809 TTTCTGGACACAACATCTTATCTATAC 57.182 33.333 0.00 0.00 0.00 1.47
1702 1971 8.470805 ACAACATCTTATCTATACCGGATGATC 58.529 37.037 9.46 0.00 35.80 2.92
1709 1978 0.408309 ATACCGGATGATCTCCCCGA 59.592 55.000 9.46 4.45 45.58 5.14
1711 1980 0.471971 ACCGGATGATCTCCCCGATT 60.472 55.000 9.46 6.12 45.58 3.34
1714 1995 0.322008 GGATGATCTCCCCGATTGGC 60.322 60.000 0.00 0.00 38.19 4.52
1717 1998 1.072159 GATCTCCCCGATTGGCCAG 59.928 63.158 5.11 0.00 30.84 4.85
1718 2235 2.403132 GATCTCCCCGATTGGCCAGG 62.403 65.000 5.11 3.55 30.84 4.45
1728 2245 1.492176 GATTGGCCAGGGAGAGATGAA 59.508 52.381 5.11 0.00 0.00 2.57
1736 2304 3.192212 CCAGGGAGAGATGAAAGCAAAAC 59.808 47.826 0.00 0.00 0.00 2.43
1738 2306 3.074412 GGGAGAGATGAAAGCAAAACGA 58.926 45.455 0.00 0.00 0.00 3.85
1740 2308 4.156739 GGGAGAGATGAAAGCAAAACGATT 59.843 41.667 0.00 0.00 0.00 3.34
1752 2320 6.515272 AGCAAAACGATTATCAAGATGGTT 57.485 33.333 0.00 0.00 0.00 3.67
1831 2399 8.035394 TCAGAACAAAGAGTGGTATCATACTTC 58.965 37.037 0.00 0.00 0.00 3.01
1868 2436 1.370414 CCGCTGTTGTTGCTTTCGG 60.370 57.895 0.00 0.00 0.00 4.30
1944 2512 2.325661 ATTCACTTTTTGGGGGAGGG 57.674 50.000 0.00 0.00 0.00 4.30
1966 2534 0.319555 TTTCCTCGAACTCTGTGCGG 60.320 55.000 0.00 0.00 34.96 5.69
2013 2581 1.380785 ATGGGCATGGCTGAAGGTG 60.381 57.895 19.78 0.00 0.00 4.00
2023 2591 1.576421 CTGAAGGTGCGAAAGTGGC 59.424 57.895 0.00 0.00 0.00 5.01
2136 2704 2.100605 ACTTTTCGAGCTGGATGACC 57.899 50.000 0.00 0.00 0.00 4.02
2161 2729 2.007608 GTACCCAAGCGAGAACATTCC 58.992 52.381 0.00 0.00 0.00 3.01
2197 2768 1.070038 CATGGTCAAATGGTTTGCGC 58.930 50.000 0.00 0.00 40.43 6.09
2253 2824 1.783284 TGAGCAAGCTGTTAGACACG 58.217 50.000 0.00 0.00 0.00 4.49
2305 2876 3.944015 GGAGTGTATTGCAGAGCAGATTT 59.056 43.478 0.00 0.00 40.61 2.17
2311 2882 2.105006 TGCAGAGCAGATTTGTCTCC 57.895 50.000 4.73 0.00 33.32 3.71
2316 2887 4.382470 GCAGAGCAGATTTGTCTCCTTAGA 60.382 45.833 4.73 0.00 31.78 2.10
2333 2916 4.502950 CCTTAGAGATCATGAAGGCTCCAC 60.503 50.000 15.75 2.01 32.54 4.02
2335 2918 2.699846 AGAGATCATGAAGGCTCCACTC 59.300 50.000 15.75 8.32 0.00 3.51
2355 2941 5.355071 CACTCAGTTTAGCAGCAAATGGATA 59.645 40.000 0.00 0.00 0.00 2.59
2360 2946 6.529125 CAGTTTAGCAGCAAATGGATAAACTG 59.471 38.462 20.76 20.76 46.29 3.16
2407 2993 4.888326 ATTGGTATTGTGGTGTTGCATT 57.112 36.364 0.00 0.00 0.00 3.56
2410 2996 5.791336 TGGTATTGTGGTGTTGCATTTAA 57.209 34.783 0.00 0.00 0.00 1.52
2412 2998 6.763355 TGGTATTGTGGTGTTGCATTTAATT 58.237 32.000 0.00 0.00 0.00 1.40
2425 3011 9.624697 TGTTGCATTTAATTACTGAGAAACATC 57.375 29.630 0.00 0.00 0.00 3.06
2434 3020 8.908786 AATTACTGAGAAACATCTGAGTGAAA 57.091 30.769 8.00 0.00 35.12 2.69
2496 3103 2.609737 GGAGGTATGCCGGAAACTATCG 60.610 54.545 5.05 0.00 40.50 2.92
2503 3110 2.295349 TGCCGGAAACTATCGAGATACC 59.705 50.000 5.05 0.00 0.00 2.73
2603 3216 0.676736 GAGCTTGAGGGGATAGTCCG 59.323 60.000 0.00 0.00 37.43 4.79
2607 3220 2.320781 CTTGAGGGGATAGTCCGTGAT 58.679 52.381 0.00 0.00 37.43 3.06
2609 3222 0.318762 GAGGGGATAGTCCGTGATGC 59.681 60.000 0.00 0.00 37.43 3.91
2640 3253 3.738982 TGTCGTGTCATCAAACAGGAAT 58.261 40.909 1.47 0.00 43.38 3.01
2641 3254 4.133820 TGTCGTGTCATCAAACAGGAATT 58.866 39.130 1.47 0.00 43.38 2.17
2646 3259 8.447833 GTCGTGTCATCAAACAGGAATTTATTA 58.552 33.333 1.47 0.00 43.38 0.98
2647 3260 9.004717 TCGTGTCATCAAACAGGAATTTATTAA 57.995 29.630 0.00 0.00 40.12 1.40
2648 3261 9.619316 CGTGTCATCAAACAGGAATTTATTAAA 57.381 29.630 0.00 0.00 37.24 1.52
2650 3263 9.638239 TGTCATCAAACAGGAATTTATTAAAGC 57.362 29.630 0.00 0.00 0.00 3.51
2651 3264 9.860898 GTCATCAAACAGGAATTTATTAAAGCT 57.139 29.630 0.00 0.00 0.00 3.74
2652 3265 9.859427 TCATCAAACAGGAATTTATTAAAGCTG 57.141 29.630 0.00 0.00 0.00 4.24
2767 3380 0.532573 GCTCATCACCTTCGTCTGGA 59.467 55.000 0.00 0.00 0.00 3.86
2777 3390 2.101415 CCTTCGTCTGGATGCTCATGTA 59.899 50.000 0.00 0.00 0.00 2.29
2816 3429 2.425143 TCACAATGGAGGAGGATTGC 57.575 50.000 0.00 0.00 33.59 3.56
2821 3434 0.467384 ATGGAGGAGGATTGCACTCG 59.533 55.000 0.00 0.00 35.82 4.18
2822 3435 1.144936 GGAGGAGGATTGCACTCGG 59.855 63.158 0.00 0.00 35.82 4.63
2833 3446 1.063649 GCACTCGGCAATGCTGATG 59.936 57.895 17.92 17.12 43.40 3.07
2834 3447 1.371337 GCACTCGGCAATGCTGATGA 61.371 55.000 17.92 3.72 43.40 2.92
2837 3450 0.511653 CTCGGCAATGCTGATGATCG 59.488 55.000 17.92 4.27 43.40 3.69
2840 3453 0.309922 GGCAATGCTGATGATCGTGG 59.690 55.000 4.82 0.00 0.00 4.94
2848 3461 2.587522 CTGATGATCGTGGTAGGAGGA 58.412 52.381 0.00 0.00 0.00 3.71
2872 3485 1.421480 GGAGGTATACGCCTTCCCTT 58.579 55.000 6.23 0.00 39.34 3.95
2873 3486 1.343789 GGAGGTATACGCCTTCCCTTC 59.656 57.143 6.23 0.00 39.34 3.46
2874 3487 1.000496 GAGGTATACGCCTTCCCTTCG 60.000 57.143 0.00 0.00 39.34 3.79
2875 3488 0.749049 GGTATACGCCTTCCCTTCGT 59.251 55.000 0.00 0.00 39.88 3.85
2876 3489 1.537562 GGTATACGCCTTCCCTTCGTG 60.538 57.143 0.00 0.00 37.61 4.35
2877 3490 1.406539 GTATACGCCTTCCCTTCGTGA 59.593 52.381 0.00 0.00 37.61 4.35
2879 3492 2.221906 TACGCCTTCCCTTCGTGAGC 62.222 60.000 0.00 0.00 37.61 4.26
2880 3493 2.815647 GCCTTCCCTTCGTGAGCG 60.816 66.667 0.00 0.00 39.92 5.03
2881 3494 2.815647 CCTTCCCTTCGTGAGCGC 60.816 66.667 0.00 0.00 38.14 5.92
2882 3495 3.181967 CTTCCCTTCGTGAGCGCG 61.182 66.667 0.00 0.00 38.14 6.86
2903 3727 3.001330 CGAGGCTGAAATAAACGGATGAC 59.999 47.826 0.00 0.00 0.00 3.06
2927 3751 3.110178 GCGCCGCTTCTTGTACGT 61.110 61.111 0.00 0.00 0.00 3.57
2928 3752 3.067846 GCGCCGCTTCTTGTACGTC 62.068 63.158 0.00 0.00 0.00 4.34
2929 3753 1.731613 CGCCGCTTCTTGTACGTCA 60.732 57.895 0.00 0.00 0.00 4.35
2930 3754 1.076533 CGCCGCTTCTTGTACGTCAT 61.077 55.000 0.00 0.00 0.00 3.06
2931 3755 0.645868 GCCGCTTCTTGTACGTCATC 59.354 55.000 0.00 0.00 0.00 2.92
2932 3756 0.914551 CCGCTTCTTGTACGTCATCG 59.085 55.000 0.00 0.00 43.34 3.84
2948 3772 2.679336 TCATCGTCATGGCATTTCTGTG 59.321 45.455 0.00 0.00 0.00 3.66
2960 3784 5.586243 TGGCATTTCTGTGTATCTTAAGCTC 59.414 40.000 0.00 0.00 0.00 4.09
3025 3849 4.618489 GTGTGTGTGATCAAATAAAGCAGC 59.382 41.667 0.00 0.00 0.00 5.25
3027 3851 4.855388 GTGTGTGATCAAATAAAGCAGCTG 59.145 41.667 10.11 10.11 0.00 4.24
3028 3852 4.082625 TGTGTGATCAAATAAAGCAGCTGG 60.083 41.667 17.12 0.00 0.00 4.85
3041 3865 1.672356 AGCTGGCTGCCGTTACTTG 60.672 57.895 14.98 0.00 44.23 3.16
3079 3907 5.003160 TGCTACTGATGTTTGTACTGCATT 58.997 37.500 0.00 0.00 0.00 3.56
3098 3926 5.005203 TGCATTTGCGTTCAAAAACTTGTAG 59.995 36.000 0.00 0.00 44.44 2.74
3135 3963 2.703416 ACTCCGGATTTTTAACCCGAC 58.297 47.619 3.57 0.00 45.58 4.79
3199 4028 1.376037 CTCCAGGCTCGGTTCAACC 60.376 63.158 0.00 0.00 34.05 3.77
3288 4119 5.886960 AAAGAGAACATTGGCATGTACTC 57.113 39.130 0.00 0.00 43.34 2.59
3289 4120 3.878778 AGAGAACATTGGCATGTACTCC 58.121 45.455 0.00 0.00 43.34 3.85
3290 4121 2.945668 GAGAACATTGGCATGTACTCCC 59.054 50.000 0.00 0.00 43.34 4.30
3291 4122 2.578021 AGAACATTGGCATGTACTCCCT 59.422 45.455 0.00 0.00 43.34 4.20
3292 4123 2.717639 ACATTGGCATGTACTCCCTC 57.282 50.000 0.00 0.00 42.24 4.30
3293 4124 1.212935 ACATTGGCATGTACTCCCTCC 59.787 52.381 0.00 0.00 42.24 4.30
3294 4125 0.469917 ATTGGCATGTACTCCCTCCG 59.530 55.000 0.00 0.00 0.00 4.63
3295 4126 0.907704 TTGGCATGTACTCCCTCCGT 60.908 55.000 0.00 0.00 0.00 4.69
3296 4127 0.907704 TGGCATGTACTCCCTCCGTT 60.908 55.000 0.00 0.00 0.00 4.44
3297 4128 0.179081 GGCATGTACTCCCTCCGTTC 60.179 60.000 0.00 0.00 0.00 3.95
3298 4129 0.824759 GCATGTACTCCCTCCGTTCT 59.175 55.000 0.00 0.00 0.00 3.01
3299 4130 2.029623 GCATGTACTCCCTCCGTTCTA 58.970 52.381 0.00 0.00 0.00 2.10
3300 4131 2.429610 GCATGTACTCCCTCCGTTCTAA 59.570 50.000 0.00 0.00 0.00 2.10
3301 4132 3.118884 GCATGTACTCCCTCCGTTCTAAA 60.119 47.826 0.00 0.00 0.00 1.85
3302 4133 4.443034 GCATGTACTCCCTCCGTTCTAAAT 60.443 45.833 0.00 0.00 0.00 1.40
3303 4134 5.671493 CATGTACTCCCTCCGTTCTAAATT 58.329 41.667 0.00 0.00 0.00 1.82
3304 4135 6.684613 GCATGTACTCCCTCCGTTCTAAATTA 60.685 42.308 0.00 0.00 0.00 1.40
3305 4136 7.442656 CATGTACTCCCTCCGTTCTAAATTAT 58.557 38.462 0.00 0.00 0.00 1.28
3306 4137 7.427989 TGTACTCCCTCCGTTCTAAATTATT 57.572 36.000 0.00 0.00 0.00 1.40
3307 4138 7.495055 TGTACTCCCTCCGTTCTAAATTATTC 58.505 38.462 0.00 0.00 0.00 1.75
3308 4139 5.598769 ACTCCCTCCGTTCTAAATTATTCG 58.401 41.667 0.00 0.00 0.00 3.34
3309 4140 5.128335 ACTCCCTCCGTTCTAAATTATTCGT 59.872 40.000 0.00 0.00 0.00 3.85
3310 4141 5.594926 TCCCTCCGTTCTAAATTATTCGTC 58.405 41.667 0.00 0.00 0.00 4.20
3311 4142 4.443394 CCCTCCGTTCTAAATTATTCGTCG 59.557 45.833 0.00 0.00 0.00 5.12
3312 4143 4.085210 CCTCCGTTCTAAATTATTCGTCGC 60.085 45.833 0.00 0.00 0.00 5.19
3313 4144 4.422840 TCCGTTCTAAATTATTCGTCGCA 58.577 39.130 0.00 0.00 0.00 5.10
3314 4145 4.501559 TCCGTTCTAAATTATTCGTCGCAG 59.498 41.667 0.00 0.00 0.00 5.18
3315 4146 4.501559 CCGTTCTAAATTATTCGTCGCAGA 59.498 41.667 0.00 0.00 0.00 4.26
3316 4147 5.005012 CCGTTCTAAATTATTCGTCGCAGAA 59.995 40.000 0.00 0.00 39.69 3.02
3317 4148 6.454583 CCGTTCTAAATTATTCGTCGCAGAAA 60.455 38.462 0.00 0.00 39.69 2.52
3318 4149 7.117454 CGTTCTAAATTATTCGTCGCAGAAAT 58.883 34.615 0.00 0.00 39.69 2.17
3319 4150 7.108851 CGTTCTAAATTATTCGTCGCAGAAATG 59.891 37.037 0.00 0.00 39.69 2.32
3320 4151 6.943981 TCTAAATTATTCGTCGCAGAAATGG 58.056 36.000 0.00 0.00 39.69 3.16
3321 4152 5.811399 AAATTATTCGTCGCAGAAATGGA 57.189 34.783 0.00 0.00 39.69 3.41
3322 4153 6.377327 AAATTATTCGTCGCAGAAATGGAT 57.623 33.333 0.00 0.00 39.69 3.41
3323 4154 4.794248 TTATTCGTCGCAGAAATGGATG 57.206 40.909 0.00 0.00 39.69 3.51
3324 4155 2.093306 TTCGTCGCAGAAATGGATGT 57.907 45.000 0.00 0.00 39.69 3.06
3325 4156 2.951457 TCGTCGCAGAAATGGATGTA 57.049 45.000 0.00 0.00 39.69 2.29
3326 4157 3.452755 TCGTCGCAGAAATGGATGTAT 57.547 42.857 0.00 0.00 39.69 2.29
3327 4158 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3328 4159 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
3329 4160 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
3330 4161 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3331 4162 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
3332 4163 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
3333 4164 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3334 4165 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3335 4166 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3336 4167 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3337 4168 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3365 4196 8.655935 ACATCTAGATACATCCATACATGTGA 57.344 34.615 9.11 0.00 37.57 3.58
3366 4197 8.526978 ACATCTAGATACATCCATACATGTGAC 58.473 37.037 9.11 0.00 37.57 3.67
3367 4198 8.526147 CATCTAGATACATCCATACATGTGACA 58.474 37.037 9.11 0.00 37.57 3.58
3368 4199 8.477419 TCTAGATACATCCATACATGTGACAA 57.523 34.615 9.11 0.00 37.57 3.18
3369 4200 8.579863 TCTAGATACATCCATACATGTGACAAG 58.420 37.037 9.11 0.00 37.57 3.16
3370 4201 7.129457 AGATACATCCATACATGTGACAAGT 57.871 36.000 9.11 0.00 37.57 3.16
3371 4202 8.250143 AGATACATCCATACATGTGACAAGTA 57.750 34.615 9.11 2.98 37.57 2.24
3372 4203 8.704668 AGATACATCCATACATGTGACAAGTAA 58.295 33.333 9.11 0.00 37.57 2.24
3373 4204 9.494271 GATACATCCATACATGTGACAAGTAAT 57.506 33.333 9.11 0.00 37.57 1.89
3374 4205 9.851686 ATACATCCATACATGTGACAAGTAATT 57.148 29.630 9.11 0.00 37.57 1.40
3375 4206 8.213518 ACATCCATACATGTGACAAGTAATTC 57.786 34.615 9.11 0.00 35.57 2.17
3376 4207 6.902224 TCCATACATGTGACAAGTAATTCG 57.098 37.500 9.11 0.00 0.00 3.34
3377 4208 5.815222 TCCATACATGTGACAAGTAATTCGG 59.185 40.000 9.11 4.27 0.00 4.30
3378 4209 5.815222 CCATACATGTGACAAGTAATTCGGA 59.185 40.000 9.11 0.00 0.00 4.55
3379 4210 6.315144 CCATACATGTGACAAGTAATTCGGAA 59.685 38.462 9.11 0.00 0.00 4.30
3380 4211 5.607119 ACATGTGACAAGTAATTCGGAAC 57.393 39.130 0.00 0.00 0.00 3.62
3445 4276 8.641155 CAACTAATTATGTGTGTTTCATGCAAG 58.359 33.333 0.00 0.00 0.00 4.01
3448 4279 5.764487 TTATGTGTGTTTCATGCAAGTGA 57.236 34.783 0.00 0.00 0.00 3.41
3474 4305 0.512952 ACAAATGCGCGTGTTCTCTC 59.487 50.000 8.43 0.00 0.00 3.20
3497 4328 4.503817 CCTTCTCTTGTCAAGTCATGGACA 60.504 45.833 12.30 0.00 41.93 4.02
3498 4329 3.995199 TCTCTTGTCAAGTCATGGACAC 58.005 45.455 12.30 0.00 43.22 3.67
3513 4344 4.679412 CACCATTTGTGCTTGGCC 57.321 55.556 0.00 0.00 38.34 5.36
3533 4364 0.601558 ACAAGAGCAAATGCAGCCAG 59.398 50.000 8.28 0.00 45.16 4.85
3534 4365 0.108804 CAAGAGCAAATGCAGCCAGG 60.109 55.000 8.28 0.00 45.16 4.45
3535 4366 1.255667 AAGAGCAAATGCAGCCAGGG 61.256 55.000 8.28 0.00 45.16 4.45
3536 4367 1.679977 GAGCAAATGCAGCCAGGGA 60.680 57.895 8.28 0.00 45.16 4.20
3537 4368 1.664321 GAGCAAATGCAGCCAGGGAG 61.664 60.000 8.28 0.00 45.16 4.30
3538 4369 1.679977 GCAAATGCAGCCAGGGAGA 60.680 57.895 0.00 0.00 41.59 3.71
3539 4370 1.041447 GCAAATGCAGCCAGGGAGAT 61.041 55.000 0.00 0.00 41.59 2.75
3575 4406 0.109342 CGGCTTAGGGCATCTCCAAT 59.891 55.000 0.00 0.00 44.01 3.16
3642 4473 2.281070 AGCCGGCCATCTAATGCG 60.281 61.111 26.15 0.00 0.00 4.73
3686 4517 7.042254 ACACTATTTGAACTAACTGGACGAAAC 60.042 37.037 0.00 0.00 0.00 2.78
3694 4525 5.607477 ACTAACTGGACGAAACTCATCAAA 58.393 37.500 0.00 0.00 0.00 2.69
3695 4526 4.813296 AACTGGACGAAACTCATCAAAC 57.187 40.909 0.00 0.00 0.00 2.93
3706 4537 0.035036 TCATCAAACACGGCGGGTTA 59.965 50.000 29.50 14.58 0.00 2.85
3802 4633 7.453752 ACATATTCCTAGGAATTAAGGTCGCTA 59.546 37.037 35.95 18.10 41.55 4.26
3826 4657 4.021916 TGACCTGGTTTAGTAGTAGGAGC 58.978 47.826 0.00 0.00 32.86 4.70
3829 4660 4.264262 ACCTGGTTTAGTAGTAGGAGCTCA 60.264 45.833 17.19 0.00 32.86 4.26
3831 4662 5.010213 CCTGGTTTAGTAGTAGGAGCTCATC 59.990 48.000 17.19 5.01 0.00 2.92
3858 4689 7.275779 TGTTCGATCTCTCACTTGTATTTTAGC 59.724 37.037 0.00 0.00 0.00 3.09
3865 4696 7.936847 TCTCTCACTTGTATTTTAGCTTTTGGA 59.063 33.333 0.00 0.00 0.00 3.53
3867 4698 8.908903 TCTCACTTGTATTTTAGCTTTTGGAAA 58.091 29.630 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.032924 GGACCCTTTCGTGTGTTTGAAG 59.967 50.000 0.00 0.00 0.00 3.02
55 56 5.920840 TCTATCGTGCTCTTTATTCGGATTG 59.079 40.000 0.00 0.00 0.00 2.67
58 59 5.509716 TTCTATCGTGCTCTTTATTCGGA 57.490 39.130 0.00 0.00 0.00 4.55
73 74 6.190264 CACTTGATTGATGTGCTTTCTATCG 58.810 40.000 0.00 0.00 30.89 2.92
118 119 5.799827 AGCTCCAGGATAATCTACTTGAC 57.200 43.478 0.00 0.00 0.00 3.18
123 124 7.120051 TCATACCTAGCTCCAGGATAATCTAC 58.880 42.308 9.63 0.00 39.18 2.59
139 140 6.183360 TGGAGAATCGACAAGTTCATACCTAG 60.183 42.308 0.00 0.00 34.37 3.02
181 182 2.983402 TCGTTCACGAGTACTTCCTG 57.017 50.000 0.00 0.00 44.22 3.86
199 200 5.957842 TTGAGATGGTAATTGTTGTGGTC 57.042 39.130 0.00 0.00 0.00 4.02
211 212 4.350368 TGACTGCAGTTTTGAGATGGTA 57.650 40.909 22.65 0.00 0.00 3.25
214 215 5.411977 AGAAGATGACTGCAGTTTTGAGATG 59.588 40.000 22.65 0.00 0.00 2.90
227 228 2.500910 AGCAGGAGGAAGAAGATGACTG 59.499 50.000 0.00 0.00 0.00 3.51
259 260 2.104170 AGGGAGATGTCCTTCGAGAAC 58.896 52.381 9.08 0.00 43.36 3.01
261 262 2.534042 AAGGGAGATGTCCTTCGAGA 57.466 50.000 9.08 0.00 40.31 4.04
265 266 6.099845 TGAATAGGTTAAGGGAGATGTCCTTC 59.900 42.308 9.08 2.18 43.02 3.46
269 270 7.309770 AGATGAATAGGTTAAGGGAGATGTC 57.690 40.000 0.00 0.00 0.00 3.06
387 388 1.516386 CGAGGGGACGACAACGATG 60.516 63.158 0.00 0.00 42.66 3.84
405 406 7.357859 CGAGCTTCATTTCAATTGAAACAGAAC 60.358 37.037 30.64 25.42 45.55 3.01
414 415 3.057315 ACCACCGAGCTTCATTTCAATTG 60.057 43.478 0.00 0.00 0.00 2.32
415 416 3.157087 ACCACCGAGCTTCATTTCAATT 58.843 40.909 0.00 0.00 0.00 2.32
417 418 2.151202 GACCACCGAGCTTCATTTCAA 58.849 47.619 0.00 0.00 0.00 2.69
423 424 3.282745 GAGCGACCACCGAGCTTCA 62.283 63.158 0.00 0.00 41.84 3.02
432 433 0.454600 TGGACGAATAGAGCGACCAC 59.545 55.000 0.00 0.00 45.60 4.16
437 438 0.924090 GCTTGTGGACGAATAGAGCG 59.076 55.000 0.00 0.00 0.00 5.03
466 467 1.300931 CATATCTCCCACCGCACCG 60.301 63.158 0.00 0.00 0.00 4.94
472 473 2.290577 GGAATCCTGCATATCTCCCACC 60.291 54.545 0.00 0.00 0.00 4.61
483 484 2.046023 CACTGCCGGAATCCTGCA 60.046 61.111 17.24 17.24 41.22 4.41
486 487 2.615227 GATGCCACTGCCGGAATCCT 62.615 60.000 5.05 0.00 35.26 3.24
505 506 2.125552 TTGCTCGTCGGCTCATGG 60.126 61.111 7.14 0.00 0.00 3.66
521 522 4.439057 GAACCAATCATCATTGCATGCTT 58.561 39.130 20.33 3.31 38.53 3.91
546 547 9.874215 AAGAGTTCTAGTTTGTAATTAAAACGC 57.126 29.630 13.06 1.49 41.41 4.84
583 584 8.511465 ACTCAAAATCAGAATTCATTTCGTTG 57.489 30.769 8.44 5.06 39.46 4.10
584 585 9.533253 AAACTCAAAATCAGAATTCATTTCGTT 57.467 25.926 8.44 7.60 39.46 3.85
808 1041 2.928334 ACTGGAAGATAGCAATGCTGG 58.072 47.619 19.25 0.62 37.03 4.85
911 1144 7.391554 GCAAGATGGGAAAGTAGCATATAATCA 59.608 37.037 0.00 0.00 0.00 2.57
1211 1453 3.323775 TCCCCTTTAGTGGTGATATCCC 58.676 50.000 0.00 1.87 0.00 3.85
1212 1454 6.443849 TGATATCCCCTTTAGTGGTGATATCC 59.556 42.308 17.15 6.26 39.17 2.59
1213 1455 7.331791 GTGATATCCCCTTTAGTGGTGATATC 58.668 42.308 14.67 14.67 39.66 1.63
1214 1456 6.215636 GGTGATATCCCCTTTAGTGGTGATAT 59.784 42.308 0.00 0.00 32.81 1.63
1215 1457 5.546499 GGTGATATCCCCTTTAGTGGTGATA 59.454 44.000 0.00 0.00 0.00 2.15
1216 1458 4.351111 GGTGATATCCCCTTTAGTGGTGAT 59.649 45.833 0.00 0.00 0.00 3.06
1217 1459 3.714798 GGTGATATCCCCTTTAGTGGTGA 59.285 47.826 0.00 0.00 0.00 4.02
1218 1460 3.458118 TGGTGATATCCCCTTTAGTGGTG 59.542 47.826 5.78 0.00 0.00 4.17
1219 1461 3.458487 GTGGTGATATCCCCTTTAGTGGT 59.542 47.826 5.78 0.00 0.00 4.16
1220 1462 3.716872 AGTGGTGATATCCCCTTTAGTGG 59.283 47.826 5.78 0.00 0.00 4.00
1221 1463 4.408921 TCAGTGGTGATATCCCCTTTAGTG 59.591 45.833 5.78 0.00 0.00 2.74
1222 1464 4.631234 TCAGTGGTGATATCCCCTTTAGT 58.369 43.478 5.78 0.00 0.00 2.24
1223 1465 5.630415 TTCAGTGGTGATATCCCCTTTAG 57.370 43.478 5.78 0.00 30.85 1.85
1224 1466 6.364701 CATTTCAGTGGTGATATCCCCTTTA 58.635 40.000 5.78 0.00 30.85 1.85
1225 1467 4.946160 TTTCAGTGGTGATATCCCCTTT 57.054 40.909 5.78 0.00 30.85 3.11
1226 1468 4.796606 CATTTCAGTGGTGATATCCCCTT 58.203 43.478 5.78 0.00 30.85 3.95
1227 1469 3.435601 GCATTTCAGTGGTGATATCCCCT 60.436 47.826 5.78 1.80 30.85 4.79
1228 1470 2.887152 GCATTTCAGTGGTGATATCCCC 59.113 50.000 0.00 0.00 30.85 4.81
1313 1555 1.120530 AGTAATAGTGTCCTGCCCGG 58.879 55.000 0.00 0.00 0.00 5.73
1458 1700 3.210358 ACAACAAACACAAAGACACCG 57.790 42.857 0.00 0.00 0.00 4.94
1497 1739 5.365314 ACTCTTGAGAGACCAAGTTCTTTCT 59.635 40.000 14.61 0.00 44.74 2.52
1589 1831 4.361783 TCCATCCTTGTTCATGTCCTCTA 58.638 43.478 0.00 0.00 0.00 2.43
1618 1887 6.109359 ACCAGAGAGCTATGTAAACAATGTC 58.891 40.000 0.00 0.00 0.00 3.06
1619 1888 6.054860 ACCAGAGAGCTATGTAAACAATGT 57.945 37.500 0.00 0.00 0.00 2.71
1638 1907 4.012895 GCACGTGGCGTTGACCAG 62.013 66.667 18.88 0.00 41.46 4.00
1646 1915 0.796312 GATATTATGGGCACGTGGCG 59.204 55.000 32.35 0.90 46.16 5.69
1709 1978 1.600058 TTCATCTCTCCCTGGCCAAT 58.400 50.000 7.01 0.00 0.00 3.16
1711 1980 0.914644 CTTTCATCTCTCCCTGGCCA 59.085 55.000 4.71 4.71 0.00 5.36
1714 1995 2.795231 TTGCTTTCATCTCTCCCTGG 57.205 50.000 0.00 0.00 0.00 4.45
1717 1998 3.074412 TCGTTTTGCTTTCATCTCTCCC 58.926 45.455 0.00 0.00 0.00 4.30
1718 2235 4.954092 ATCGTTTTGCTTTCATCTCTCC 57.046 40.909 0.00 0.00 0.00 3.71
1720 2237 7.615582 TGATAATCGTTTTGCTTTCATCTCT 57.384 32.000 0.00 0.00 0.00 3.10
1728 2245 6.515272 ACCATCTTGATAATCGTTTTGCTT 57.485 33.333 0.00 0.00 0.00 3.91
1752 2320 9.489084 GCATACATCACACTAAGAATAATACCA 57.511 33.333 0.00 0.00 0.00 3.25
1868 2436 4.829064 TTGTCACTTGCAAGGAACATAC 57.171 40.909 29.18 16.78 0.00 2.39
1944 2512 2.348591 CGCACAGAGTTCGAGGAAAAAC 60.349 50.000 0.00 0.00 0.00 2.43
1953 2521 1.493772 TAAACACCGCACAGAGTTCG 58.506 50.000 0.00 0.00 0.00 3.95
1966 2534 5.418840 AGGGTGACATCATGGAAATAAACAC 59.581 40.000 0.00 0.00 0.00 3.32
2013 2581 1.900237 CAAGCTTATGCCACTTTCGC 58.100 50.000 0.00 0.00 40.80 4.70
2023 2591 2.756760 AGGACAACATGGCAAGCTTATG 59.243 45.455 0.00 1.95 0.00 1.90
2115 2683 3.596214 GGTCATCCAGCTCGAAAAGTTA 58.404 45.455 0.00 0.00 0.00 2.24
2136 2704 2.501223 TTCTCGCTTGGGTACTGCCG 62.501 60.000 0.00 0.00 38.44 5.69
2161 2729 0.740868 ATGGCCATCACTCGTTGACG 60.741 55.000 14.09 0.00 36.92 4.35
2197 2768 4.300189 TCTTTTCAACATGGACCAAACG 57.700 40.909 0.00 0.00 0.00 3.60
2253 2824 1.754803 TCATCCACATCCACGTACTCC 59.245 52.381 0.00 0.00 0.00 3.85
2311 2882 4.344679 AGTGGAGCCTTCATGATCTCTAAG 59.655 45.833 15.34 2.47 0.00 2.18
2316 2887 2.435069 CTGAGTGGAGCCTTCATGATCT 59.565 50.000 0.00 0.00 0.00 2.75
2320 2891 2.486472 AACTGAGTGGAGCCTTCATG 57.514 50.000 0.00 0.00 0.00 3.07
2333 2916 4.978083 ATCCATTTGCTGCTAAACTGAG 57.022 40.909 0.00 0.00 0.00 3.35
2335 2918 6.529125 CAGTTTATCCATTTGCTGCTAAACTG 59.471 38.462 22.51 22.51 43.58 3.16
2407 2993 9.996554 TTCACTCAGATGTTTCTCAGTAATTAA 57.003 29.630 0.00 0.00 29.75 1.40
2412 2998 8.585018 TGTATTTCACTCAGATGTTTCTCAGTA 58.415 33.333 0.00 0.00 29.75 2.74
2425 3011 5.885230 TTTGCCTCATGTATTTCACTCAG 57.115 39.130 0.00 0.00 0.00 3.35
2496 3103 4.816925 GCCAAAAGGTACATCAGGTATCTC 59.183 45.833 0.00 0.00 42.70 2.75
2603 3216 1.125021 CGACAACGTCAAGAGCATCAC 59.875 52.381 0.00 0.00 32.22 3.06
2626 3239 9.859427 CAGCTTTAATAAATTCCTGTTTGATGA 57.141 29.630 0.00 0.00 0.00 2.92
2640 3253 6.958767 AGCTAACTCCTCCAGCTTTAATAAA 58.041 36.000 0.00 0.00 42.95 1.40
2641 3254 6.561519 AGCTAACTCCTCCAGCTTTAATAA 57.438 37.500 0.00 0.00 42.95 1.40
2649 3262 1.477295 ACGTAAGCTAACTCCTCCAGC 59.523 52.381 0.00 0.00 45.62 4.85
2650 3263 2.492484 ACACGTAAGCTAACTCCTCCAG 59.508 50.000 0.00 0.00 45.62 3.86
2651 3264 2.230508 CACACGTAAGCTAACTCCTCCA 59.769 50.000 0.00 0.00 45.62 3.86
2652 3265 2.416972 CCACACGTAAGCTAACTCCTCC 60.417 54.545 0.00 0.00 45.62 4.30
2734 3347 3.791586 GAGCTCCCCTCCTGTGCC 61.792 72.222 0.87 0.00 34.35 5.01
2777 3390 0.765903 ATCTCCGAGGCCATGGATGT 60.766 55.000 18.40 0.00 32.83 3.06
2816 3429 1.263484 GATCATCAGCATTGCCGAGTG 59.737 52.381 4.70 0.00 0.00 3.51
2821 3434 0.309922 CCACGATCATCAGCATTGCC 59.690 55.000 4.70 0.00 0.00 4.52
2822 3435 1.019673 ACCACGATCATCAGCATTGC 58.980 50.000 0.00 0.00 0.00 3.56
2833 3446 1.889829 CTCCATCCTCCTACCACGATC 59.110 57.143 0.00 0.00 0.00 3.69
2834 3447 1.481428 CCTCCATCCTCCTACCACGAT 60.481 57.143 0.00 0.00 0.00 3.73
2837 3450 1.710816 CTCCTCCATCCTCCTACCAC 58.289 60.000 0.00 0.00 0.00 4.16
2840 3453 3.837399 ATACCTCCTCCATCCTCCTAC 57.163 52.381 0.00 0.00 0.00 3.18
2848 3461 2.249139 GAAGGCGTATACCTCCTCCAT 58.751 52.381 10.71 0.00 39.93 3.41
2879 3492 0.026285 CCGTTTATTTCAGCCTCGCG 59.974 55.000 0.00 0.00 0.00 5.87
2880 3493 1.365699 TCCGTTTATTTCAGCCTCGC 58.634 50.000 0.00 0.00 0.00 5.03
2881 3494 3.001330 GTCATCCGTTTATTTCAGCCTCG 59.999 47.826 0.00 0.00 0.00 4.63
2882 3495 3.312697 GGTCATCCGTTTATTTCAGCCTC 59.687 47.826 0.00 0.00 0.00 4.70
2885 3498 3.013921 TGGGTCATCCGTTTATTTCAGC 58.986 45.455 0.00 0.00 38.76 4.26
2886 3499 5.008019 CAGATGGGTCATCCGTTTATTTCAG 59.992 44.000 4.48 0.00 41.36 3.02
2903 3727 4.845580 AGAAGCGGCGCAGATGGG 62.846 66.667 35.02 0.00 0.00 4.00
2927 3751 2.679336 CACAGAAATGCCATGACGATGA 59.321 45.455 0.00 0.00 0.00 2.92
2928 3752 2.421073 ACACAGAAATGCCATGACGATG 59.579 45.455 0.00 0.00 0.00 3.84
2929 3753 2.715046 ACACAGAAATGCCATGACGAT 58.285 42.857 0.00 0.00 0.00 3.73
2930 3754 2.183478 ACACAGAAATGCCATGACGA 57.817 45.000 0.00 0.00 0.00 4.20
2931 3755 3.873361 AGATACACAGAAATGCCATGACG 59.127 43.478 0.00 0.00 0.00 4.35
2932 3756 5.824904 AAGATACACAGAAATGCCATGAC 57.175 39.130 0.00 0.00 0.00 3.06
2948 3772 2.789893 CCAAGACGCGAGCTTAAGATAC 59.210 50.000 15.93 0.00 0.00 2.24
2960 3784 1.498865 AAGAAGCACACCAAGACGCG 61.499 55.000 3.53 3.53 0.00 6.01
3025 3849 1.076332 GTACAAGTAACGGCAGCCAG 58.924 55.000 13.30 7.00 0.00 4.85
3027 3851 2.094338 ACTAGTACAAGTAACGGCAGCC 60.094 50.000 0.00 0.00 0.00 4.85
3028 3852 3.119566 AGACTAGTACAAGTAACGGCAGC 60.120 47.826 0.00 0.00 0.00 5.25
3041 3865 4.936411 TCAGTAGCACAGTCAGACTAGTAC 59.064 45.833 1.67 3.15 0.00 2.73
3079 3907 7.164498 CGATTTACTACAAGTTTTTGAACGCAA 59.836 33.333 0.00 0.00 37.73 4.85
3098 3926 4.085210 CCGGAGTATTCGCTTTCGATTTAC 60.085 45.833 0.00 0.00 45.04 2.01
3116 3944 2.702261 TGTCGGGTTAAAAATCCGGAG 58.298 47.619 11.34 0.00 43.54 4.63
3199 4028 5.808042 AATATGCAAGTCTTACACAGCTG 57.192 39.130 13.48 13.48 31.43 4.24
3271 4102 2.945668 GAGGGAGTACATGCCAATGTTC 59.054 50.000 0.00 0.00 44.94 3.18
3288 4119 4.443394 CGACGAATAATTTAGAACGGAGGG 59.557 45.833 0.00 0.00 0.00 4.30
3289 4120 4.085210 GCGACGAATAATTTAGAACGGAGG 60.085 45.833 0.00 0.00 0.00 4.30
3290 4121 4.501559 TGCGACGAATAATTTAGAACGGAG 59.498 41.667 0.00 0.00 0.00 4.63
3291 4122 4.422840 TGCGACGAATAATTTAGAACGGA 58.577 39.130 0.00 0.00 0.00 4.69
3292 4123 4.501559 TCTGCGACGAATAATTTAGAACGG 59.498 41.667 0.00 0.00 0.00 4.44
3293 4124 5.615495 TCTGCGACGAATAATTTAGAACG 57.385 39.130 0.00 0.00 0.00 3.95
3294 4125 7.373441 CCATTTCTGCGACGAATAATTTAGAAC 59.627 37.037 0.00 0.00 0.00 3.01
3295 4126 7.279090 TCCATTTCTGCGACGAATAATTTAGAA 59.721 33.333 0.00 0.00 0.00 2.10
3296 4127 6.759356 TCCATTTCTGCGACGAATAATTTAGA 59.241 34.615 0.00 0.00 0.00 2.10
3297 4128 6.943981 TCCATTTCTGCGACGAATAATTTAG 58.056 36.000 0.00 0.00 0.00 1.85
3298 4129 6.912203 TCCATTTCTGCGACGAATAATTTA 57.088 33.333 0.00 0.00 0.00 1.40
3299 4130 5.811399 TCCATTTCTGCGACGAATAATTT 57.189 34.783 0.00 0.00 0.00 1.82
3300 4131 5.296780 ACATCCATTTCTGCGACGAATAATT 59.703 36.000 0.00 0.00 0.00 1.40
3301 4132 4.816385 ACATCCATTTCTGCGACGAATAAT 59.184 37.500 0.00 0.00 0.00 1.28
3302 4133 4.188462 ACATCCATTTCTGCGACGAATAA 58.812 39.130 0.00 0.00 0.00 1.40
3303 4134 3.792401 ACATCCATTTCTGCGACGAATA 58.208 40.909 0.00 0.00 0.00 1.75
3304 4135 2.632377 ACATCCATTTCTGCGACGAAT 58.368 42.857 0.00 0.00 0.00 3.34
3305 4136 2.093306 ACATCCATTTCTGCGACGAA 57.907 45.000 0.00 0.00 0.00 3.85
3306 4137 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
3307 4138 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
3308 4139 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3309 4140 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3310 4141 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3311 4142 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3339 4170 9.753674 TCACATGTATGGATGTATCTAGATGTA 57.246 33.333 15.79 4.44 34.69 2.29
3340 4171 8.526978 GTCACATGTATGGATGTATCTAGATGT 58.473 37.037 15.79 1.25 34.69 3.06
3341 4172 8.526147 TGTCACATGTATGGATGTATCTAGATG 58.474 37.037 15.79 0.00 34.69 2.90
3342 4173 8.655935 TGTCACATGTATGGATGTATCTAGAT 57.344 34.615 10.73 10.73 34.69 1.98
3343 4174 8.477419 TTGTCACATGTATGGATGTATCTAGA 57.523 34.615 0.00 0.00 34.69 2.43
3344 4175 8.363390 ACTTGTCACATGTATGGATGTATCTAG 58.637 37.037 0.00 0.00 34.69 2.43
3345 4176 8.250143 ACTTGTCACATGTATGGATGTATCTA 57.750 34.615 0.00 0.00 34.69 1.98
3346 4177 7.129457 ACTTGTCACATGTATGGATGTATCT 57.871 36.000 0.00 0.00 34.69 1.98
3347 4178 8.887036 TTACTTGTCACATGTATGGATGTATC 57.113 34.615 0.00 0.00 34.69 2.24
3348 4179 9.851686 AATTACTTGTCACATGTATGGATGTAT 57.148 29.630 0.00 0.00 34.69 2.29
3349 4180 9.325198 GAATTACTTGTCACATGTATGGATGTA 57.675 33.333 0.00 0.00 34.69 2.29
3350 4181 7.011389 CGAATTACTTGTCACATGTATGGATGT 59.989 37.037 0.00 0.00 37.01 3.06
3351 4182 7.347448 CGAATTACTTGTCACATGTATGGATG 58.653 38.462 0.00 0.00 0.00 3.51
3352 4183 6.483307 CCGAATTACTTGTCACATGTATGGAT 59.517 38.462 0.00 0.00 0.00 3.41
3353 4184 5.815222 CCGAATTACTTGTCACATGTATGGA 59.185 40.000 0.00 0.00 0.00 3.41
3354 4185 5.815222 TCCGAATTACTTGTCACATGTATGG 59.185 40.000 0.00 5.37 0.00 2.74
3355 4186 6.902224 TCCGAATTACTTGTCACATGTATG 57.098 37.500 0.00 0.00 0.00 2.39
3356 4187 6.035650 CGTTCCGAATTACTTGTCACATGTAT 59.964 38.462 0.00 0.00 0.00 2.29
3357 4188 5.346551 CGTTCCGAATTACTTGTCACATGTA 59.653 40.000 0.00 0.00 0.00 2.29
3358 4189 4.151689 CGTTCCGAATTACTTGTCACATGT 59.848 41.667 1.42 1.42 0.00 3.21
3359 4190 4.435518 CCGTTCCGAATTACTTGTCACATG 60.436 45.833 0.00 0.00 0.00 3.21
3360 4191 3.682858 CCGTTCCGAATTACTTGTCACAT 59.317 43.478 0.00 0.00 0.00 3.21
3361 4192 3.061322 CCGTTCCGAATTACTTGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
3362 4193 3.319755 TCCGTTCCGAATTACTTGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
3363 4194 3.581755 CTCCGTTCCGAATTACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3364 4195 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3365 4196 2.564062 TCCTCCGTTCCGAATTACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
3366 4197 3.241067 TCCTCCGTTCCGAATTACTTG 57.759 47.619 0.00 0.00 0.00 3.16
3367 4198 3.260128 ACTTCCTCCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
3368 4199 2.830321 ACTTCCTCCGTTCCGAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
3369 4200 3.242549 ACTTCCTCCGTTCCGAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
3370 4201 4.403432 ACATACTTCCTCCGTTCCGAATTA 59.597 41.667 0.00 0.00 0.00 1.40
3371 4202 3.197116 ACATACTTCCTCCGTTCCGAATT 59.803 43.478 0.00 0.00 0.00 2.17
3372 4203 2.764572 ACATACTTCCTCCGTTCCGAAT 59.235 45.455 0.00 0.00 0.00 3.34
3373 4204 2.173519 ACATACTTCCTCCGTTCCGAA 58.826 47.619 0.00 0.00 0.00 4.30
3374 4205 1.843368 ACATACTTCCTCCGTTCCGA 58.157 50.000 0.00 0.00 0.00 4.55
3375 4206 2.165845 AGAACATACTTCCTCCGTTCCG 59.834 50.000 0.00 0.00 37.31 4.30
3376 4207 3.056035 ACAGAACATACTTCCTCCGTTCC 60.056 47.826 0.00 0.00 37.31 3.62
3377 4208 4.189639 ACAGAACATACTTCCTCCGTTC 57.810 45.455 0.00 0.00 36.95 3.95
3378 4209 4.039973 TGAACAGAACATACTTCCTCCGTT 59.960 41.667 0.00 0.00 0.00 4.44
3379 4210 3.576982 TGAACAGAACATACTTCCTCCGT 59.423 43.478 0.00 0.00 0.00 4.69
3380 4211 3.927142 GTGAACAGAACATACTTCCTCCG 59.073 47.826 0.00 0.00 0.00 4.63
3381 4212 3.927142 CGTGAACAGAACATACTTCCTCC 59.073 47.826 0.00 0.00 0.00 4.30
3382 4213 4.557205 ACGTGAACAGAACATACTTCCTC 58.443 43.478 0.00 0.00 0.00 3.71
3383 4214 4.602340 ACGTGAACAGAACATACTTCCT 57.398 40.909 0.00 0.00 0.00 3.36
3384 4215 5.467705 AGTACGTGAACAGAACATACTTCC 58.532 41.667 0.00 0.00 0.00 3.46
3385 4216 6.147581 TGAGTACGTGAACAGAACATACTTC 58.852 40.000 0.00 0.00 0.00 3.01
3386 4217 6.080648 TGAGTACGTGAACAGAACATACTT 57.919 37.500 0.00 0.00 0.00 2.24
3387 4218 5.700722 TGAGTACGTGAACAGAACATACT 57.299 39.130 0.00 0.00 0.00 2.12
3388 4219 6.090783 TGATGAGTACGTGAACAGAACATAC 58.909 40.000 0.00 0.00 0.00 2.39
3389 4220 6.262193 TGATGAGTACGTGAACAGAACATA 57.738 37.500 0.00 0.00 0.00 2.29
3395 4226 6.073819 TGACAAAATGATGAGTACGTGAACAG 60.074 38.462 0.00 0.00 0.00 3.16
3432 4263 2.780065 TGCTCACTTGCATGAAACAC 57.220 45.000 6.60 0.00 38.12 3.32
3445 4276 1.606606 GCGCATTTGTAGTTGCTCAC 58.393 50.000 0.30 0.00 36.71 3.51
3448 4279 0.110238 CACGCGCATTTGTAGTTGCT 60.110 50.000 5.73 0.00 36.71 3.91
3451 4282 1.871039 AGAACACGCGCATTTGTAGTT 59.129 42.857 5.73 4.64 0.00 2.24
3474 4305 3.999663 GTCCATGACTTGACAAGAGAAGG 59.000 47.826 21.95 16.12 0.00 3.46
3497 4328 1.047596 TGTGGCCAAGCACAAATGGT 61.048 50.000 7.24 0.00 39.00 3.55
3498 4329 0.106335 TTGTGGCCAAGCACAAATGG 59.894 50.000 7.24 0.00 38.22 3.16
3509 4340 1.114119 TGCATTTGCTCTTGTGGCCA 61.114 50.000 0.00 0.00 42.66 5.36
3513 4344 0.315886 TGGCTGCATTTGCTCTTGTG 59.684 50.000 0.50 0.00 42.66 3.33
3642 4473 5.235305 AGTGTTTGAAATGTATGCGGATC 57.765 39.130 0.00 0.00 0.00 3.36
3677 4508 2.542178 CGTGTTTGATGAGTTTCGTCCA 59.458 45.455 0.00 0.00 31.51 4.02
3686 4517 1.234615 AACCCGCCGTGTTTGATGAG 61.235 55.000 0.00 0.00 0.00 2.90
3694 4525 2.078392 CTTTAATGTAACCCGCCGTGT 58.922 47.619 0.00 0.00 0.00 4.49
3695 4526 1.202098 GCTTTAATGTAACCCGCCGTG 60.202 52.381 0.00 0.00 0.00 4.94
3763 4594 7.622081 TCCTAGGAATATGTGTCTTAAACCTCA 59.378 37.037 9.71 0.00 0.00 3.86
3802 4633 5.262804 CTCCTACTACTAAACCAGGTCACT 58.737 45.833 0.00 0.00 0.00 3.41
3826 4657 4.898829 AGTGAGAGATCGAACAGATGAG 57.101 45.455 0.00 0.00 40.26 2.90
3829 4660 6.707440 ATACAAGTGAGAGATCGAACAGAT 57.293 37.500 0.00 0.00 43.51 2.90
3831 4662 7.588143 AAAATACAAGTGAGAGATCGAACAG 57.412 36.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.