Multiple sequence alignment - TraesCS5D01G295500

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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 TraesCS5D01G295500 chr5D 100.000 3039 0 0 1 3039 393571113 393568075 0.000000e+00 5613.0
1 TraesCS5D01G295500 chr5D 89.313 1048 78 13 1130 2162 393608568 393607540 0.000000e+00 1284.0
2 TraesCS5D01G295500 chr5D 98.142 646 11 1 2395 3039 35127112 35127757 0.000000e+00 1125.0
3 TraesCS5D01G295500 chr5D 98.140 645 11 1 2396 3039 16926267 16925623 0.000000e+00 1123.0
4 TraesCS5D01G295500 chr5D 97.281 662 17 1 2379 3039 530614384 530613723 0.000000e+00 1122.0
5 TraesCS5D01G295500 chr5D 87.403 643 52 9 1127 1765 393712196 393711579 0.000000e+00 712.0
6 TraesCS5D01G295500 chr5D 82.622 656 81 21 940 1574 393753156 393752513 1.590000e-152 549.0
7 TraesCS5D01G295500 chr5A 91.425 2309 110 33 1 2275 495341037 495338783 0.000000e+00 3086.0
8 TraesCS5D01G295500 chr5A 89.453 1043 75 18 1130 2152 495359580 495358553 0.000000e+00 1284.0
9 TraesCS5D01G295500 chr5A 80.779 385 57 14 940 1314 495841193 495840816 4.960000e-73 285.0
10 TraesCS5D01G295500 chr5B 88.763 1682 104 32 628 2253 473292502 473290850 0.000000e+00 1980.0
11 TraesCS5D01G295500 chr5B 87.775 1227 93 24 954 2153 473468206 473467010 0.000000e+00 1382.0
12 TraesCS5D01G295500 chr5B 86.166 1265 103 33 960 2187 473448839 473447610 0.000000e+00 1301.0
13 TraesCS5D01G295500 chr5B 83.053 655 82 22 945 1580 473626083 473625439 4.400000e-158 568.0
14 TraesCS5D01G295500 chr5B 83.418 392 39 15 939 1314 473455421 473455040 1.040000e-89 340.0
15 TraesCS5D01G295500 chr5B 83.234 167 23 5 40 201 125789690 125789856 6.790000e-32 148.0
16 TraesCS5D01G295500 chr5B 97.561 41 0 1 841 881 473468278 473468239 5.440000e-08 69.4
17 TraesCS5D01G295500 chr5B 92.857 42 2 1 540 580 704216144 704216103 3.270000e-05 60.2
18 TraesCS5D01G295500 chr5B 94.595 37 1 1 540 575 571191834 571191870 4.230000e-04 56.5
19 TraesCS5D01G295500 chr7D 98.905 639 6 1 2402 3039 224462474 224463112 0.000000e+00 1140.0
20 TraesCS5D01G295500 chr3D 98.748 639 7 1 2402 3039 491627753 491628391 0.000000e+00 1134.0
21 TraesCS5D01G295500 chr3D 98.746 638 7 1 2403 3039 42296840 42297477 0.000000e+00 1133.0
22 TraesCS5D01G295500 chr3D 98.148 648 10 2 2394 3039 367314518 367315165 0.000000e+00 1129.0
23 TraesCS5D01G295500 chr3D 97.561 656 11 4 2389 3039 488576206 488576861 0.000000e+00 1118.0
24 TraesCS5D01G295500 chr3D 82.979 94 16 0 2266 2359 259235717 259235624 5.400000e-13 86.1
25 TraesCS5D01G295500 chr1D 98.746 638 7 1 2403 3039 41437742 41438379 0.000000e+00 1133.0
26 TraesCS5D01G295500 chr6D 82.143 84 9 5 496 575 309074578 309074497 1.960000e-07 67.6
27 TraesCS5D01G295500 chr4B 94.737 38 0 1 320 355 66901630 66901593 1.180000e-04 58.4
28 TraesCS5D01G295500 chr4B 94.737 38 0 1 320 355 67037702 67037665 1.180000e-04 58.4


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 TraesCS5D01G295500 chr5D 393568075 393571113 3038 True 5613.0 5613 100.000 1 3039 1 chr5D.!!$R2 3038
1 TraesCS5D01G295500 chr5D 393607540 393608568 1028 True 1284.0 1284 89.313 1130 2162 1 chr5D.!!$R3 1032
2 TraesCS5D01G295500 chr5D 35127112 35127757 645 False 1125.0 1125 98.142 2395 3039 1 chr5D.!!$F1 644
3 TraesCS5D01G295500 chr5D 16925623 16926267 644 True 1123.0 1123 98.140 2396 3039 1 chr5D.!!$R1 643
4 TraesCS5D01G295500 chr5D 530613723 530614384 661 True 1122.0 1122 97.281 2379 3039 1 chr5D.!!$R6 660
5 TraesCS5D01G295500 chr5D 393711579 393712196 617 True 712.0 712 87.403 1127 1765 1 chr5D.!!$R4 638
6 TraesCS5D01G295500 chr5D 393752513 393753156 643 True 549.0 549 82.622 940 1574 1 chr5D.!!$R5 634
7 TraesCS5D01G295500 chr5A 495338783 495341037 2254 True 3086.0 3086 91.425 1 2275 1 chr5A.!!$R1 2274
8 TraesCS5D01G295500 chr5A 495358553 495359580 1027 True 1284.0 1284 89.453 1130 2152 1 chr5A.!!$R2 1022
9 TraesCS5D01G295500 chr5B 473290850 473292502 1652 True 1980.0 1980 88.763 628 2253 1 chr5B.!!$R1 1625
10 TraesCS5D01G295500 chr5B 473447610 473448839 1229 True 1301.0 1301 86.166 960 2187 1 chr5B.!!$R2 1227
11 TraesCS5D01G295500 chr5B 473467010 473468278 1268 True 725.7 1382 92.668 841 2153 2 chr5B.!!$R6 1312
12 TraesCS5D01G295500 chr5B 473625439 473626083 644 True 568.0 568 83.053 945 1580 1 chr5B.!!$R4 635
13 TraesCS5D01G295500 chr7D 224462474 224463112 638 False 1140.0 1140 98.905 2402 3039 1 chr7D.!!$F1 637
14 TraesCS5D01G295500 chr3D 491627753 491628391 638 False 1134.0 1134 98.748 2402 3039 1 chr3D.!!$F4 637
15 TraesCS5D01G295500 chr3D 42296840 42297477 637 False 1133.0 1133 98.746 2403 3039 1 chr3D.!!$F1 636
16 TraesCS5D01G295500 chr3D 367314518 367315165 647 False 1129.0 1129 98.148 2394 3039 1 chr3D.!!$F2 645
17 TraesCS5D01G295500 chr3D 488576206 488576861 655 False 1118.0 1118 97.561 2389 3039 1 chr3D.!!$F3 650
18 TraesCS5D01G295500 chr1D 41437742 41438379 637 False 1133.0 1133 98.746 2403 3039 1 chr1D.!!$F1 636

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
600 602 0.035317 AAGCCAGTGCAATGAGACGA 59.965 50.0 17.16 0.0 41.13 4.20 F
1389 1511 0.034756 CACATCTGGGTCCACGTCAA 59.965 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2055 0.634465 GTTCCTCCTCCTCCTCCTCT 59.366 60.0 0.0 0.0 0.0 3.69 R
2204 2390 0.744414 GGCTCGGTCAATGCTGCTTA 60.744 55.0 0.0 0.0 0.0 3.09 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
22 23 4.500116 GGTCGCGAGTCAGGGAGC 62.500 72.222 10.24 12.59 42.58 4.70
26 27 2.125753 GCGAGTCAGGGAGCTGTG 60.126 66.667 0.00 0.00 0.00 3.66
89 90 9.650371 CATTCTGGAATTTTACACATATACACG 57.350 33.333 0.00 0.00 0.00 4.49
114 115 5.985781 CACATCCTTGTGTACTTGTACAAC 58.014 41.667 14.23 9.77 46.68 3.32
121 122 5.864418 TGTGTACTTGTACAACTCTTCCT 57.136 39.130 14.23 0.00 0.00 3.36
124 125 6.041637 TGTGTACTTGTACAACTCTTCCTGAT 59.958 38.462 14.23 0.00 0.00 2.90
179 180 3.738745 AATCGGCTTCCATGGGGCC 62.739 63.158 28.29 28.29 42.18 5.80
195 196 2.342650 GCCGAGCTCCAAAATGCCA 61.343 57.895 8.47 0.00 0.00 4.92
222 223 4.526650 TCCTACAGCTTGACACTATGAACA 59.473 41.667 0.00 0.00 0.00 3.18
375 377 7.112528 TCACTATACAATTCGACACAAACAC 57.887 36.000 0.00 0.00 0.00 3.32
415 417 7.347222 ACACACCCAAGAAAGGATATATAGACA 59.653 37.037 0.00 0.00 0.00 3.41
417 419 7.162082 CACCCAAGAAAGGATATATAGACACC 58.838 42.308 0.00 0.00 0.00 4.16
436 438 1.403679 CCGAAAACAGCAACTTCACCA 59.596 47.619 0.00 0.00 0.00 4.17
437 439 2.159310 CCGAAAACAGCAACTTCACCAA 60.159 45.455 0.00 0.00 0.00 3.67
478 480 7.312657 ACATCAAGTGTACAATAAGCATCAG 57.687 36.000 0.00 0.00 39.91 2.90
481 483 9.049523 CATCAAGTGTACAATAAGCATCAGTAT 57.950 33.333 0.00 0.00 0.00 2.12
489 491 2.231215 AAGCATCAGTATGGAGTCGC 57.769 50.000 0.00 0.00 36.16 5.19
492 494 0.668535 CATCAGTATGGAGTCGCCGA 59.331 55.000 0.00 0.00 40.66 5.54
495 497 1.076923 AGTATGGAGTCGCCGAGGT 60.077 57.895 0.00 0.00 40.66 3.85
526 528 1.808945 GACAAGCCACCACAATGAGAG 59.191 52.381 0.00 0.00 0.00 3.20
532 534 1.004044 CCACCACAATGAGAGGAAGCT 59.996 52.381 0.00 0.00 0.00 3.74
541 543 1.270518 TGAGAGGAAGCTGTGCAAGAC 60.271 52.381 0.00 0.00 0.00 3.01
545 547 0.235926 GGAAGCTGTGCAAGACGAAC 59.764 55.000 0.00 0.00 0.00 3.95
549 551 1.487452 GCTGTGCAAGACGAACGTGA 61.487 55.000 4.19 0.00 0.00 4.35
554 556 1.618640 GCAAGACGAACGTGAGCTCC 61.619 60.000 12.15 1.40 0.00 4.70
555 557 0.318699 CAAGACGAACGTGAGCTCCA 60.319 55.000 12.15 0.00 0.00 3.86
556 558 0.387929 AAGACGAACGTGAGCTCCAA 59.612 50.000 12.15 0.00 0.00 3.53
557 559 0.039074 AGACGAACGTGAGCTCCAAG 60.039 55.000 12.15 4.92 0.00 3.61
558 560 1.006102 ACGAACGTGAGCTCCAAGG 60.006 57.895 12.15 1.45 0.00 3.61
559 561 2.383527 CGAACGTGAGCTCCAAGGC 61.384 63.158 12.15 0.00 0.00 4.35
560 562 2.357517 AACGTGAGCTCCAAGGCG 60.358 61.111 12.15 10.28 37.29 5.52
561 563 3.883744 AACGTGAGCTCCAAGGCGG 62.884 63.158 12.15 0.00 37.29 6.13
583 585 3.621794 CGCCTTCAGAAAGACAACAAAG 58.378 45.455 0.00 0.00 34.14 2.77
587 589 4.498682 CCTTCAGAAAGACAACAAAGCCAG 60.499 45.833 0.00 0.00 34.14 4.85
589 591 3.378112 TCAGAAAGACAACAAAGCCAGTG 59.622 43.478 0.00 0.00 0.00 3.66
592 594 1.473258 AGACAACAAAGCCAGTGCAA 58.527 45.000 0.00 0.00 41.13 4.08
593 595 2.034124 AGACAACAAAGCCAGTGCAAT 58.966 42.857 0.00 0.00 41.13 3.56
594 596 2.129607 GACAACAAAGCCAGTGCAATG 58.870 47.619 7.29 7.29 41.13 2.82
595 597 1.755959 ACAACAAAGCCAGTGCAATGA 59.244 42.857 17.16 0.00 41.13 2.57
596 598 2.223876 ACAACAAAGCCAGTGCAATGAG 60.224 45.455 17.16 7.00 41.13 2.90
597 599 1.985473 ACAAAGCCAGTGCAATGAGA 58.015 45.000 17.16 0.00 41.13 3.27
598 600 1.610522 ACAAAGCCAGTGCAATGAGAC 59.389 47.619 17.16 4.67 41.13 3.36
599 601 0.877071 AAAGCCAGTGCAATGAGACG 59.123 50.000 17.16 0.00 41.13 4.18
600 602 0.035317 AAGCCAGTGCAATGAGACGA 59.965 50.000 17.16 0.00 41.13 4.20
601 603 0.035317 AGCCAGTGCAATGAGACGAA 59.965 50.000 17.16 0.00 41.13 3.85
602 604 0.445436 GCCAGTGCAATGAGACGAAG 59.555 55.000 17.16 0.00 37.47 3.79
603 605 0.445436 CCAGTGCAATGAGACGAAGC 59.555 55.000 17.16 0.00 0.00 3.86
604 606 1.436600 CAGTGCAATGAGACGAAGCT 58.563 50.000 8.85 0.00 0.00 3.74
605 607 2.610433 CAGTGCAATGAGACGAAGCTA 58.390 47.619 8.85 0.00 0.00 3.32
767 776 4.513442 TCATTTTCAGTTCCGATTCCGAT 58.487 39.130 0.00 0.00 38.22 4.18
769 778 3.603158 TTTCAGTTCCGATTCCGATCA 57.397 42.857 0.00 0.00 38.22 2.92
829 857 5.009631 GGGTGGCACATCTATATATGCAAA 58.990 41.667 20.82 0.00 44.52 3.68
901 942 1.227674 CGGGCACAGCTAGGGATTC 60.228 63.158 0.00 0.00 0.00 2.52
923 968 1.664333 GCTGCGCTATCTCTCAGCC 60.664 63.158 9.73 0.00 44.35 4.85
1176 1282 2.301346 GCTTGCTTAGCCCATGTATGT 58.699 47.619 0.29 0.00 44.48 2.29
1177 1283 3.476552 GCTTGCTTAGCCCATGTATGTA 58.523 45.455 0.29 0.00 44.48 2.29
1178 1284 3.882888 GCTTGCTTAGCCCATGTATGTAA 59.117 43.478 0.29 0.00 44.48 2.41
1179 1285 4.261197 GCTTGCTTAGCCCATGTATGTAAC 60.261 45.833 0.29 0.00 44.48 2.50
1180 1286 4.771114 TGCTTAGCCCATGTATGTAACT 57.229 40.909 0.29 0.00 0.00 2.24
1181 1287 5.880164 TGCTTAGCCCATGTATGTAACTA 57.120 39.130 0.29 0.00 0.00 2.24
1182 1288 6.433847 TGCTTAGCCCATGTATGTAACTAT 57.566 37.500 0.29 0.00 0.00 2.12
1185 1291 6.147821 GCTTAGCCCATGTATGTAACTATGTG 59.852 42.308 0.00 0.00 0.00 3.21
1389 1511 0.034756 CACATCTGGGTCCACGTCAA 59.965 55.000 0.00 0.00 0.00 3.18
1499 1627 1.460497 TACAGCCACCACCACTCCA 60.460 57.895 0.00 0.00 0.00 3.86
1540 1668 1.934463 CGCCATCATCGGTAAGCAC 59.066 57.895 0.00 0.00 0.00 4.40
1597 1736 7.888424 CATCCATCATATGCATAACCTTTTCA 58.112 34.615 11.13 0.00 0.00 2.69
1614 1753 1.812235 TCAGCTGGTACACTTGCATG 58.188 50.000 15.13 0.00 0.00 4.06
1659 1798 3.257624 CGGTGACCACTAGTCCTAACTTT 59.742 47.826 1.11 0.00 45.68 2.66
1663 1803 6.053650 GTGACCACTAGTCCTAACTTTTGTT 58.946 40.000 0.00 0.00 45.68 2.83
1664 1804 6.541278 GTGACCACTAGTCCTAACTTTTGTTT 59.459 38.462 0.00 0.00 45.68 2.83
1665 1805 6.764560 TGACCACTAGTCCTAACTTTTGTTTC 59.235 38.462 0.00 0.00 45.68 2.78
1729 1869 2.325583 AAAGTCACTTGAAGACCGCA 57.674 45.000 0.00 0.00 36.68 5.69
1744 1884 1.079681 CGCATGTGCATTTTGCCCT 60.080 52.632 5.77 0.00 44.23 5.19
1882 2022 2.124570 CCCACGGCCAATGGAGAG 60.125 66.667 22.21 4.29 39.87 3.20
1905 2048 0.913451 AAGGAGGATGTGGCAGCTCT 60.913 55.000 0.00 0.00 0.00 4.09
1909 2055 1.759445 GAGGATGTGGCAGCTCTAGAA 59.241 52.381 0.00 0.00 0.00 2.10
1941 2114 0.033642 GAGGAACATAGTAGCGCCCC 59.966 60.000 2.29 0.00 0.00 5.80
1984 2157 7.173390 CCCTTCCATTTTCTCGGTAATCTTATC 59.827 40.741 0.00 0.00 0.00 1.75
1988 2161 7.710907 TCCATTTTCTCGGTAATCTTATCACAG 59.289 37.037 0.00 0.00 0.00 3.66
2052 2235 4.093556 GCAAAGCTAGCGAGAAGTTAATGT 59.906 41.667 9.55 0.00 0.00 2.71
2119 2304 3.464907 CAAGGCCATGTATCAGACTCTG 58.535 50.000 5.01 0.00 0.00 3.35
2120 2305 1.415659 AGGCCATGTATCAGACTCTGC 59.584 52.381 5.01 0.00 0.00 4.26
2140 2325 7.549134 ACTCTGCGATTTTGAAGTTGATGTATA 59.451 33.333 0.00 0.00 0.00 1.47
2154 2339 7.907389 AGTTGATGTATAAGACTGAACTTCCA 58.093 34.615 0.00 0.00 0.00 3.53
2164 2349 3.195661 ACTGAACTTCCACGACAACTTC 58.804 45.455 0.00 0.00 0.00 3.01
2196 2381 6.870971 ACCGTGCAATTTACTCTCTTTTTA 57.129 33.333 0.00 0.00 0.00 1.52
2197 2382 7.448748 ACCGTGCAATTTACTCTCTTTTTAT 57.551 32.000 0.00 0.00 0.00 1.40
2264 2450 8.244113 GGAAACAAGGAAATAGATGTTTAGGTG 58.756 37.037 3.04 0.00 43.77 4.00
2275 2461 5.205056 AGATGTTTAGGTGTTCCCAACAAA 58.795 37.500 0.00 0.00 44.16 2.83
2276 2462 4.722361 TGTTTAGGTGTTCCCAACAAAC 57.278 40.909 0.00 0.00 44.16 2.93
2277 2463 4.345854 TGTTTAGGTGTTCCCAACAAACT 58.654 39.130 0.00 0.00 44.16 2.66
2278 2464 4.773149 TGTTTAGGTGTTCCCAACAAACTT 59.227 37.500 0.00 0.00 44.16 2.66
2279 2465 4.993029 TTAGGTGTTCCCAACAAACTTG 57.007 40.909 0.00 0.00 44.16 3.16
2280 2466 3.094484 AGGTGTTCCCAACAAACTTGA 57.906 42.857 0.00 0.00 44.16 3.02
2281 2467 2.758423 AGGTGTTCCCAACAAACTTGAC 59.242 45.455 0.00 0.00 44.16 3.18
2282 2468 2.494073 GGTGTTCCCAACAAACTTGACA 59.506 45.455 0.00 0.00 44.16 3.58
2283 2469 3.428862 GGTGTTCCCAACAAACTTGACAG 60.429 47.826 0.00 0.00 44.16 3.51
2284 2470 3.442273 GTGTTCCCAACAAACTTGACAGA 59.558 43.478 0.00 0.00 44.16 3.41
2285 2471 4.082463 GTGTTCCCAACAAACTTGACAGAA 60.082 41.667 0.00 0.00 44.16 3.02
2286 2472 4.709397 TGTTCCCAACAAACTTGACAGAAT 59.291 37.500 0.00 0.00 38.72 2.40
2287 2473 5.163561 TGTTCCCAACAAACTTGACAGAATC 60.164 40.000 0.00 0.00 38.72 2.52
2288 2474 4.531854 TCCCAACAAACTTGACAGAATCA 58.468 39.130 0.00 0.00 34.65 2.57
2289 2475 4.338118 TCCCAACAAACTTGACAGAATCAC 59.662 41.667 0.00 0.00 36.92 3.06
2290 2476 4.097741 CCCAACAAACTTGACAGAATCACA 59.902 41.667 0.00 0.00 36.92 3.58
2291 2477 5.394005 CCCAACAAACTTGACAGAATCACAA 60.394 40.000 0.00 0.00 36.92 3.33
2292 2478 5.516339 CCAACAAACTTGACAGAATCACAAC 59.484 40.000 0.00 0.00 36.92 3.32
2293 2479 6.324819 CAACAAACTTGACAGAATCACAACT 58.675 36.000 0.00 0.00 36.92 3.16
2294 2480 6.124088 ACAAACTTGACAGAATCACAACTC 57.876 37.500 0.00 0.00 36.92 3.01
2295 2481 5.882557 ACAAACTTGACAGAATCACAACTCT 59.117 36.000 0.00 0.00 36.92 3.24
2296 2482 5.998454 AACTTGACAGAATCACAACTCTG 57.002 39.130 0.00 0.00 43.90 3.35
2305 2491 7.606858 CAGAATCACAACTCTGTTGTATGAT 57.393 36.000 14.52 11.58 35.38 2.45
2306 2492 8.037382 CAGAATCACAACTCTGTTGTATGATT 57.963 34.615 19.65 19.65 35.38 2.57
2307 2493 8.173775 CAGAATCACAACTCTGTTGTATGATTC 58.826 37.037 27.23 27.23 39.52 2.52
2308 2494 8.099537 AGAATCACAACTCTGTTGTATGATTCT 58.900 33.333 29.14 29.14 41.79 2.40
2309 2495 7.606858 ATCACAACTCTGTTGTATGATTCTG 57.393 36.000 14.52 2.41 31.64 3.02
2310 2496 5.409520 TCACAACTCTGTTGTATGATTCTGC 59.590 40.000 14.52 0.00 31.64 4.26
2311 2497 5.179929 CACAACTCTGTTGTATGATTCTGCA 59.820 40.000 14.52 0.00 31.64 4.41
2312 2498 5.764686 ACAACTCTGTTGTATGATTCTGCAA 59.235 36.000 13.51 0.00 28.57 4.08
2313 2499 5.869753 ACTCTGTTGTATGATTCTGCAAC 57.130 39.130 0.00 0.00 40.89 4.17
2314 2500 5.555017 ACTCTGTTGTATGATTCTGCAACT 58.445 37.500 14.56 0.00 41.04 3.16
2315 2501 6.000219 ACTCTGTTGTATGATTCTGCAACTT 59.000 36.000 14.56 0.00 41.04 2.66
2316 2502 6.488006 ACTCTGTTGTATGATTCTGCAACTTT 59.512 34.615 14.56 0.00 41.04 2.66
2317 2503 7.661437 ACTCTGTTGTATGATTCTGCAACTTTA 59.339 33.333 14.56 5.13 41.04 1.85
2318 2504 8.565896 TCTGTTGTATGATTCTGCAACTTTAT 57.434 30.769 14.56 0.00 41.04 1.40
2319 2505 8.453320 TCTGTTGTATGATTCTGCAACTTTATG 58.547 33.333 14.56 0.00 41.04 1.90
2320 2506 8.334263 TGTTGTATGATTCTGCAACTTTATGA 57.666 30.769 14.56 0.00 41.04 2.15
2321 2507 8.959548 TGTTGTATGATTCTGCAACTTTATGAT 58.040 29.630 14.56 0.00 41.04 2.45
2322 2508 9.443283 GTTGTATGATTCTGCAACTTTATGATC 57.557 33.333 0.00 0.00 38.41 2.92
2323 2509 8.158169 TGTATGATTCTGCAACTTTATGATCC 57.842 34.615 0.00 0.00 0.00 3.36
2324 2510 7.774625 TGTATGATTCTGCAACTTTATGATCCA 59.225 33.333 0.00 0.00 0.00 3.41
2325 2511 7.649533 ATGATTCTGCAACTTTATGATCCAA 57.350 32.000 0.00 0.00 0.00 3.53
2326 2512 7.465353 TGATTCTGCAACTTTATGATCCAAA 57.535 32.000 0.00 0.00 0.00 3.28
2327 2513 7.315142 TGATTCTGCAACTTTATGATCCAAAC 58.685 34.615 0.00 0.00 0.00 2.93
2328 2514 6.899393 TTCTGCAACTTTATGATCCAAACT 57.101 33.333 0.00 0.00 0.00 2.66
2329 2515 7.994425 TTCTGCAACTTTATGATCCAAACTA 57.006 32.000 0.00 0.00 0.00 2.24
2330 2516 7.994425 TCTGCAACTTTATGATCCAAACTAA 57.006 32.000 0.00 0.00 0.00 2.24
2331 2517 7.816640 TCTGCAACTTTATGATCCAAACTAAC 58.183 34.615 0.00 0.00 0.00 2.34
2332 2518 6.919721 TGCAACTTTATGATCCAAACTAACC 58.080 36.000 0.00 0.00 0.00 2.85
2333 2519 6.719370 TGCAACTTTATGATCCAAACTAACCT 59.281 34.615 0.00 0.00 0.00 3.50
2334 2520 7.094377 TGCAACTTTATGATCCAAACTAACCTC 60.094 37.037 0.00 0.00 0.00 3.85
2335 2521 7.121315 GCAACTTTATGATCCAAACTAACCTCT 59.879 37.037 0.00 0.00 0.00 3.69
2336 2522 8.669243 CAACTTTATGATCCAAACTAACCTCTC 58.331 37.037 0.00 0.00 0.00 3.20
2337 2523 8.152023 ACTTTATGATCCAAACTAACCTCTCT 57.848 34.615 0.00 0.00 0.00 3.10
2338 2524 8.043710 ACTTTATGATCCAAACTAACCTCTCTG 58.956 37.037 0.00 0.00 0.00 3.35
2339 2525 7.733773 TTATGATCCAAACTAACCTCTCTGA 57.266 36.000 0.00 0.00 0.00 3.27
2340 2526 6.821616 ATGATCCAAACTAACCTCTCTGAT 57.178 37.500 0.00 0.00 0.00 2.90
2341 2527 6.627087 TGATCCAAACTAACCTCTCTGATT 57.373 37.500 0.00 0.00 0.00 2.57
2342 2528 6.644347 TGATCCAAACTAACCTCTCTGATTC 58.356 40.000 0.00 0.00 0.00 2.52
2343 2529 6.441924 TGATCCAAACTAACCTCTCTGATTCT 59.558 38.462 0.00 0.00 0.00 2.40
2344 2530 7.619698 TGATCCAAACTAACCTCTCTGATTCTA 59.380 37.037 0.00 0.00 0.00 2.10
2345 2531 7.979786 TCCAAACTAACCTCTCTGATTCTAT 57.020 36.000 0.00 0.00 0.00 1.98
2346 2532 7.786030 TCCAAACTAACCTCTCTGATTCTATG 58.214 38.462 0.00 0.00 0.00 2.23
2347 2533 6.481644 CCAAACTAACCTCTCTGATTCTATGC 59.518 42.308 0.00 0.00 0.00 3.14
2348 2534 7.271511 CAAACTAACCTCTCTGATTCTATGCT 58.728 38.462 0.00 0.00 0.00 3.79
2349 2535 7.430760 AACTAACCTCTCTGATTCTATGCTT 57.569 36.000 0.00 0.00 0.00 3.91
2350 2536 7.430760 ACTAACCTCTCTGATTCTATGCTTT 57.569 36.000 0.00 0.00 0.00 3.51
2351 2537 7.856415 ACTAACCTCTCTGATTCTATGCTTTT 58.144 34.615 0.00 0.00 0.00 2.27
2352 2538 8.982723 ACTAACCTCTCTGATTCTATGCTTTTA 58.017 33.333 0.00 0.00 0.00 1.52
2353 2539 9.474920 CTAACCTCTCTGATTCTATGCTTTTAG 57.525 37.037 0.00 0.00 0.00 1.85
2354 2540 7.430760 ACCTCTCTGATTCTATGCTTTTAGT 57.569 36.000 0.00 0.00 0.00 2.24
2355 2541 7.496747 ACCTCTCTGATTCTATGCTTTTAGTC 58.503 38.462 0.00 0.00 0.00 2.59
2356 2542 6.928492 CCTCTCTGATTCTATGCTTTTAGTCC 59.072 42.308 0.00 0.00 0.00 3.85
2357 2543 7.418368 CCTCTCTGATTCTATGCTTTTAGTCCA 60.418 40.741 0.00 0.00 0.00 4.02
2358 2544 7.268586 TCTCTGATTCTATGCTTTTAGTCCAC 58.731 38.462 0.00 0.00 0.00 4.02
2359 2545 6.946340 TCTGATTCTATGCTTTTAGTCCACA 58.054 36.000 0.00 0.00 0.00 4.17
2360 2546 6.818644 TCTGATTCTATGCTTTTAGTCCACAC 59.181 38.462 0.00 0.00 0.00 3.82
2361 2547 5.880332 TGATTCTATGCTTTTAGTCCACACC 59.120 40.000 0.00 0.00 0.00 4.16
2362 2548 4.216411 TCTATGCTTTTAGTCCACACCC 57.784 45.455 0.00 0.00 0.00 4.61
2363 2549 2.969821 ATGCTTTTAGTCCACACCCA 57.030 45.000 0.00 0.00 0.00 4.51
2364 2550 1.975660 TGCTTTTAGTCCACACCCAC 58.024 50.000 0.00 0.00 0.00 4.61
2365 2551 0.872388 GCTTTTAGTCCACACCCACG 59.128 55.000 0.00 0.00 0.00 4.94
2366 2552 1.519408 CTTTTAGTCCACACCCACGG 58.481 55.000 0.00 0.00 0.00 4.94
2367 2553 1.071071 CTTTTAGTCCACACCCACGGA 59.929 52.381 0.00 0.00 0.00 4.69
2368 2554 1.354101 TTTAGTCCACACCCACGGAT 58.646 50.000 0.00 0.00 32.83 4.18
2369 2555 2.234896 TTAGTCCACACCCACGGATA 57.765 50.000 0.00 0.00 32.83 2.59
2370 2556 2.234896 TAGTCCACACCCACGGATAA 57.765 50.000 0.00 0.00 32.83 1.75
2371 2557 1.580059 AGTCCACACCCACGGATAAT 58.420 50.000 0.00 0.00 32.83 1.28
2372 2558 2.754465 AGTCCACACCCACGGATAATA 58.246 47.619 0.00 0.00 32.83 0.98
2373 2559 3.314693 AGTCCACACCCACGGATAATAT 58.685 45.455 0.00 0.00 32.83 1.28
2374 2560 3.714798 AGTCCACACCCACGGATAATATT 59.285 43.478 0.00 0.00 32.83 1.28
2375 2561 4.165372 AGTCCACACCCACGGATAATATTT 59.835 41.667 0.00 0.00 32.83 1.40
2376 2562 5.367352 AGTCCACACCCACGGATAATATTTA 59.633 40.000 0.00 0.00 32.83 1.40
2377 2563 6.043938 AGTCCACACCCACGGATAATATTTAT 59.956 38.462 0.00 0.00 32.83 1.40
2385 2571 8.626526 ACCCACGGATAATATTTATGAAACAAC 58.373 33.333 0.00 0.00 0.00 3.32
2386 2572 8.625651 CCCACGGATAATATTTATGAAACAACA 58.374 33.333 0.00 0.00 0.00 3.33
2406 2592 3.265479 ACATTTCTCCCTCCTTCCTGAAG 59.735 47.826 0.00 0.00 38.14 3.02
2675 2862 1.002134 ATGAAGCACCCGAACCTGG 60.002 57.895 0.00 0.00 0.00 4.45
2798 2985 3.179830 GTCACAGTAGACAATAGTGGCG 58.820 50.000 0.00 0.00 38.10 5.69
2811 2998 1.450312 GTGGCGTGCTCAATAGGCT 60.450 57.895 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.131638 TTTGTGAGACACAGCTCCCT 58.868 50.000 4.82 0.00 45.39 4.20
22 23 2.355756 CTGTGGGTTTTGTGAGACACAG 59.644 50.000 8.03 8.03 45.39 3.66
26 27 2.480419 CGATCTGTGGGTTTTGTGAGAC 59.520 50.000 0.00 0.00 0.00 3.36
160 161 1.758122 GCCCCATGGAAGCCGATTT 60.758 57.895 15.22 0.00 0.00 2.17
161 162 2.123726 GCCCCATGGAAGCCGATT 60.124 61.111 15.22 0.00 0.00 3.34
162 163 4.209866 GGCCCCATGGAAGCCGAT 62.210 66.667 24.68 0.00 36.84 4.18
165 166 4.883354 CTCGGCCCCATGGAAGCC 62.883 72.222 27.45 27.45 43.53 4.35
167 168 3.764160 GAGCTCGGCCCCATGGAAG 62.764 68.421 15.22 5.21 0.00 3.46
171 172 3.643595 TTTGGAGCTCGGCCCCATG 62.644 63.158 7.83 0.00 0.00 3.66
172 173 2.228841 ATTTTGGAGCTCGGCCCCAT 62.229 55.000 7.83 0.00 0.00 4.00
173 174 2.917897 ATTTTGGAGCTCGGCCCCA 61.918 57.895 7.83 0.00 0.00 4.96
179 180 1.747355 AGAATGGCATTTTGGAGCTCG 59.253 47.619 14.93 0.00 0.00 5.03
195 196 5.658634 TCATAGTGTCAAGCTGTAGGAGAAT 59.341 40.000 0.00 0.00 0.00 2.40
354 356 6.007079 CGTGTGTTTGTGTCGAATTGTATAG 58.993 40.000 0.00 0.00 0.00 1.31
375 377 2.402572 TGTGTGTTGTGGTGGCGTG 61.403 57.895 0.00 0.00 0.00 5.34
415 417 1.404035 GGTGAAGTTGCTGTTTTCGGT 59.596 47.619 0.00 0.00 0.00 4.69
417 419 2.842208 TGGTGAAGTTGCTGTTTTCG 57.158 45.000 0.00 0.00 0.00 3.46
436 438 6.403866 TGATGTTTGCTTGGAGTTGTATTT 57.596 33.333 0.00 0.00 0.00 1.40
437 439 6.040842 ACTTGATGTTTGCTTGGAGTTGTATT 59.959 34.615 0.00 0.00 0.00 1.89
478 480 1.359475 GACCTCGGCGACTCCATAC 59.641 63.158 4.99 0.00 34.01 2.39
481 483 4.361971 AGGACCTCGGCGACTCCA 62.362 66.667 23.92 0.00 34.01 3.86
489 491 2.826337 TCCATGATGAGGACCTCGG 58.174 57.895 16.81 11.08 32.35 4.63
495 497 1.288188 TGGCTTGTCCATGATGAGGA 58.712 50.000 0.00 0.00 40.72 3.71
526 528 0.235926 GTTCGTCTTGCACAGCTTCC 59.764 55.000 0.00 0.00 0.00 3.46
532 534 1.487452 GCTCACGTTCGTCTTGCACA 61.487 55.000 0.00 0.00 0.00 4.57
541 543 2.383527 GCCTTGGAGCTCACGTTCG 61.384 63.158 17.19 0.00 0.00 3.95
558 560 2.742372 TCTTTCTGAAGGCGCCGC 60.742 61.111 23.20 18.21 33.56 6.53
559 561 1.227999 TTGTCTTTCTGAAGGCGCCG 61.228 55.000 23.20 6.78 40.42 6.46
560 562 0.238553 GTTGTCTTTCTGAAGGCGCC 59.761 55.000 21.89 21.89 40.42 6.53
561 563 0.944386 TGTTGTCTTTCTGAAGGCGC 59.056 50.000 0.00 0.00 40.42 6.53
562 564 3.621794 CTTTGTTGTCTTTCTGAAGGCG 58.378 45.455 0.00 0.00 40.42 5.52
563 565 3.375642 GCTTTGTTGTCTTTCTGAAGGC 58.624 45.455 0.00 0.00 38.00 4.35
564 566 3.381272 TGGCTTTGTTGTCTTTCTGAAGG 59.619 43.478 0.00 0.00 33.56 3.46
565 567 4.096984 ACTGGCTTTGTTGTCTTTCTGAAG 59.903 41.667 0.00 0.00 0.00 3.02
566 568 4.016444 ACTGGCTTTGTTGTCTTTCTGAA 58.984 39.130 0.00 0.00 0.00 3.02
567 569 3.378112 CACTGGCTTTGTTGTCTTTCTGA 59.622 43.478 0.00 0.00 0.00 3.27
568 570 3.699067 CACTGGCTTTGTTGTCTTTCTG 58.301 45.455 0.00 0.00 0.00 3.02
571 573 1.824230 TGCACTGGCTTTGTTGTCTTT 59.176 42.857 0.00 0.00 41.91 2.52
583 585 0.445436 CTTCGTCTCATTGCACTGGC 59.555 55.000 4.01 0.00 41.68 4.85
587 589 2.932614 ACATAGCTTCGTCTCATTGCAC 59.067 45.455 0.00 0.00 0.00 4.57
589 591 2.932614 ACACATAGCTTCGTCTCATTGC 59.067 45.455 0.00 0.00 0.00 3.56
592 594 8.336801 TGTATATACACATAGCTTCGTCTCAT 57.663 34.615 11.62 0.00 0.00 2.90
593 595 7.660208 TCTGTATATACACATAGCTTCGTCTCA 59.340 37.037 11.62 0.00 31.93 3.27
594 596 7.958567 GTCTGTATATACACATAGCTTCGTCTC 59.041 40.741 11.62 0.00 31.93 3.36
595 597 7.360185 CGTCTGTATATACACATAGCTTCGTCT 60.360 40.741 11.62 0.00 31.93 4.18
596 598 6.737301 CGTCTGTATATACACATAGCTTCGTC 59.263 42.308 11.62 0.00 31.93 4.20
597 599 6.204301 ACGTCTGTATATACACATAGCTTCGT 59.796 38.462 11.62 10.15 31.93 3.85
598 600 6.520104 CACGTCTGTATATACACATAGCTTCG 59.480 42.308 11.62 9.66 31.93 3.79
599 601 6.305877 GCACGTCTGTATATACACATAGCTTC 59.694 42.308 11.62 0.00 31.93 3.86
600 602 6.150318 GCACGTCTGTATATACACATAGCTT 58.850 40.000 11.62 0.00 31.93 3.74
601 603 5.617087 CGCACGTCTGTATATACACATAGCT 60.617 44.000 11.62 0.00 31.93 3.32
602 604 4.553815 CGCACGTCTGTATATACACATAGC 59.446 45.833 11.62 10.82 31.93 2.97
603 605 4.553815 GCGCACGTCTGTATATACACATAG 59.446 45.833 11.62 2.74 31.93 2.23
604 606 4.469552 GCGCACGTCTGTATATACACATA 58.530 43.478 11.62 0.00 31.93 2.29
605 607 3.305964 GCGCACGTCTGTATATACACAT 58.694 45.455 11.62 0.00 31.93 3.21
677 679 6.739112 ACTCTGAAGCTGGTCAAATTTTTAC 58.261 36.000 0.00 0.00 0.00 2.01
681 683 4.500375 GCAACTCTGAAGCTGGTCAAATTT 60.500 41.667 0.00 0.00 0.00 1.82
767 776 1.004560 CTCAACAGCCGAGCCTTGA 60.005 57.895 0.00 0.00 0.00 3.02
936 981 4.306471 ATCGAGCGAGCGAGCGAG 62.306 66.667 13.62 0.41 44.26 5.03
937 982 4.300743 GATCGAGCGAGCGAGCGA 62.301 66.667 11.47 11.47 44.26 4.93
1171 1277 7.823149 AAAAGACGGACACATAGTTACATAC 57.177 36.000 0.00 0.00 0.00 2.39
1172 1278 7.274033 CGAAAAAGACGGACACATAGTTACATA 59.726 37.037 0.00 0.00 0.00 2.29
1173 1279 6.090358 CGAAAAAGACGGACACATAGTTACAT 59.910 38.462 0.00 0.00 0.00 2.29
1174 1280 5.403166 CGAAAAAGACGGACACATAGTTACA 59.597 40.000 0.00 0.00 0.00 2.41
1175 1281 5.403466 ACGAAAAAGACGGACACATAGTTAC 59.597 40.000 0.00 0.00 34.93 2.50
1176 1282 5.403166 CACGAAAAAGACGGACACATAGTTA 59.597 40.000 0.00 0.00 34.93 2.24
1177 1283 4.210537 CACGAAAAAGACGGACACATAGTT 59.789 41.667 0.00 0.00 34.93 2.24
1178 1284 3.739300 CACGAAAAAGACGGACACATAGT 59.261 43.478 0.00 0.00 34.93 2.12
1179 1285 3.739300 ACACGAAAAAGACGGACACATAG 59.261 43.478 0.00 0.00 34.93 2.23
1180 1286 3.719924 ACACGAAAAAGACGGACACATA 58.280 40.909 0.00 0.00 34.93 2.29
1181 1287 2.542595 GACACGAAAAAGACGGACACAT 59.457 45.455 0.00 0.00 34.93 3.21
1182 1288 1.928503 GACACGAAAAAGACGGACACA 59.071 47.619 0.00 0.00 34.93 3.72
1185 1291 1.188791 GTCGACACGAAAAAGACGGAC 59.811 52.381 11.55 0.00 37.72 4.79
1389 1511 2.771763 CTTCCTGCGAGCCACGAAGT 62.772 60.000 7.87 0.00 45.48 3.01
1540 1668 1.597027 GTTCAGGTGTGGTGGTCGG 60.597 63.158 0.00 0.00 0.00 4.79
1597 1736 1.527034 CACATGCAAGTGTACCAGCT 58.473 50.000 13.82 0.00 34.83 4.24
1744 1884 3.254166 GGTGCAAAATCTGAAAGCTCTCA 59.746 43.478 0.00 0.00 0.00 3.27
1882 2022 2.440980 GCCACATCCTCCTTGCCC 60.441 66.667 0.00 0.00 0.00 5.36
1905 2048 2.140224 CCTCCTCCTCCTCCTCTTCTA 58.860 57.143 0.00 0.00 0.00 2.10
1909 2055 0.634465 GTTCCTCCTCCTCCTCCTCT 59.366 60.000 0.00 0.00 0.00 3.69
1963 2136 7.041780 CCTGTGATAAGATTACCGAGAAAATGG 60.042 40.741 0.00 0.00 0.00 3.16
1984 2157 3.989787 GCCGGCAAAACCCCTGTG 61.990 66.667 24.80 0.00 33.26 3.66
1988 2161 3.238497 AAAGGCCGGCAAAACCCC 61.238 61.111 30.85 8.87 33.26 4.95
2052 2235 8.642935 TCATTGGGTTTAACATGAACTCATTA 57.357 30.769 0.00 0.00 37.34 1.90
2119 2304 8.391106 AGTCTTATACATCAACTTCAAAATCGC 58.609 33.333 0.00 0.00 0.00 4.58
2120 2305 9.694520 CAGTCTTATACATCAACTTCAAAATCG 57.305 33.333 0.00 0.00 0.00 3.34
2140 2325 3.118738 AGTTGTCGTGGAAGTTCAGTCTT 60.119 43.478 5.01 0.00 0.00 3.01
2164 2349 6.694411 AGAGTAAATTGCACGGTTAGTATACG 59.306 38.462 0.00 0.00 0.00 3.06
2196 2381 7.573843 GCTCGGTCAATGCTGCTTATAAATTAT 60.574 37.037 0.00 0.00 0.00 1.28
2197 2382 6.293407 GCTCGGTCAATGCTGCTTATAAATTA 60.293 38.462 0.00 0.00 0.00 1.40
2204 2390 0.744414 GGCTCGGTCAATGCTGCTTA 60.744 55.000 0.00 0.00 0.00 3.09
2216 2402 4.881850 CCTATTTCAAAATGTAGGCTCGGT 59.118 41.667 0.00 0.00 0.00 4.69
2218 2404 6.677781 TTCCTATTTCAAAATGTAGGCTCG 57.322 37.500 0.00 0.00 28.53 5.03
2264 2450 4.712122 TTCTGTCAAGTTTGTTGGGAAC 57.288 40.909 0.00 0.00 0.00 3.62
2275 2461 5.028549 ACAGAGTTGTGATTCTGTCAAGT 57.971 39.130 1.53 0.00 46.25 3.16
2281 2467 7.606858 ATCATACAACAGAGTTGTGATTCTG 57.393 36.000 21.89 5.12 43.21 3.02
2282 2468 8.099537 AGAATCATACAACAGAGTTGTGATTCT 58.900 33.333 29.45 29.45 45.44 2.40
2283 2469 8.173775 CAGAATCATACAACAGAGTTGTGATTC 58.826 37.037 27.50 27.50 43.52 2.52
2284 2470 7.361542 GCAGAATCATACAACAGAGTTGTGATT 60.362 37.037 21.89 20.66 37.85 2.57
2285 2471 6.093219 GCAGAATCATACAACAGAGTTGTGAT 59.907 38.462 21.89 14.99 37.67 3.06
2286 2472 5.409520 GCAGAATCATACAACAGAGTTGTGA 59.590 40.000 21.89 13.62 37.67 3.58
2287 2473 5.179929 TGCAGAATCATACAACAGAGTTGTG 59.820 40.000 21.89 9.31 37.67 3.33
2288 2474 5.308014 TGCAGAATCATACAACAGAGTTGT 58.692 37.500 18.17 18.17 39.87 3.32
2289 2475 5.868043 TGCAGAATCATACAACAGAGTTG 57.132 39.130 8.24 8.24 0.00 3.16
2290 2476 6.000219 AGTTGCAGAATCATACAACAGAGTT 59.000 36.000 12.98 0.00 43.74 3.01
2291 2477 5.555017 AGTTGCAGAATCATACAACAGAGT 58.445 37.500 12.98 0.00 43.74 3.24
2292 2478 6.492007 AAGTTGCAGAATCATACAACAGAG 57.508 37.500 12.98 0.00 43.74 3.35
2293 2479 6.882610 AAAGTTGCAGAATCATACAACAGA 57.117 33.333 12.98 0.00 43.74 3.41
2294 2480 8.453320 TCATAAAGTTGCAGAATCATACAACAG 58.547 33.333 12.98 2.00 43.74 3.16
2295 2481 8.334263 TCATAAAGTTGCAGAATCATACAACA 57.666 30.769 12.98 0.00 43.74 3.33
2296 2482 9.443283 GATCATAAAGTTGCAGAATCATACAAC 57.557 33.333 5.33 5.33 42.08 3.32
2297 2483 8.623903 GGATCATAAAGTTGCAGAATCATACAA 58.376 33.333 0.00 0.00 0.00 2.41
2298 2484 7.774625 TGGATCATAAAGTTGCAGAATCATACA 59.225 33.333 0.00 0.00 0.00 2.29
2299 2485 8.158169 TGGATCATAAAGTTGCAGAATCATAC 57.842 34.615 0.00 0.00 0.00 2.39
2300 2486 8.750515 TTGGATCATAAAGTTGCAGAATCATA 57.249 30.769 0.00 0.00 0.00 2.15
2301 2487 7.649533 TTGGATCATAAAGTTGCAGAATCAT 57.350 32.000 0.00 0.00 0.00 2.45
2302 2488 7.177216 AGTTTGGATCATAAAGTTGCAGAATCA 59.823 33.333 0.00 0.00 0.00 2.57
2303 2489 7.542025 AGTTTGGATCATAAAGTTGCAGAATC 58.458 34.615 0.00 0.00 0.00 2.52
2304 2490 7.472334 AGTTTGGATCATAAAGTTGCAGAAT 57.528 32.000 0.00 0.00 0.00 2.40
2305 2491 6.899393 AGTTTGGATCATAAAGTTGCAGAA 57.101 33.333 0.00 0.00 0.00 3.02
2306 2492 7.094377 GGTTAGTTTGGATCATAAAGTTGCAGA 60.094 37.037 7.16 0.00 0.00 4.26
2307 2493 7.029563 GGTTAGTTTGGATCATAAAGTTGCAG 58.970 38.462 7.16 0.00 0.00 4.41
2308 2494 6.719370 AGGTTAGTTTGGATCATAAAGTTGCA 59.281 34.615 7.16 0.00 0.00 4.08
2309 2495 7.121315 AGAGGTTAGTTTGGATCATAAAGTTGC 59.879 37.037 7.16 2.81 0.00 4.17
2310 2496 8.567285 AGAGGTTAGTTTGGATCATAAAGTTG 57.433 34.615 7.16 0.00 0.00 3.16
2311 2497 8.606830 AGAGAGGTTAGTTTGGATCATAAAGTT 58.393 33.333 7.16 0.00 0.00 2.66
2312 2498 8.043710 CAGAGAGGTTAGTTTGGATCATAAAGT 58.956 37.037 0.00 1.38 0.00 2.66
2313 2499 8.260818 TCAGAGAGGTTAGTTTGGATCATAAAG 58.739 37.037 0.00 0.00 0.00 1.85
2314 2500 8.146053 TCAGAGAGGTTAGTTTGGATCATAAA 57.854 34.615 0.00 0.00 0.00 1.40
2315 2501 7.733773 TCAGAGAGGTTAGTTTGGATCATAA 57.266 36.000 0.00 0.00 0.00 1.90
2316 2502 7.921041 ATCAGAGAGGTTAGTTTGGATCATA 57.079 36.000 0.00 0.00 0.00 2.15
2317 2503 6.821616 ATCAGAGAGGTTAGTTTGGATCAT 57.178 37.500 0.00 0.00 0.00 2.45
2318 2504 6.441924 AGAATCAGAGAGGTTAGTTTGGATCA 59.558 38.462 0.00 0.00 0.00 2.92
2319 2505 6.883744 AGAATCAGAGAGGTTAGTTTGGATC 58.116 40.000 0.00 0.00 0.00 3.36
2320 2506 6.882768 AGAATCAGAGAGGTTAGTTTGGAT 57.117 37.500 0.00 0.00 0.00 3.41
2321 2507 7.633772 GCATAGAATCAGAGAGGTTAGTTTGGA 60.634 40.741 0.00 0.00 0.00 3.53
2322 2508 6.481644 GCATAGAATCAGAGAGGTTAGTTTGG 59.518 42.308 0.00 0.00 0.00 3.28
2323 2509 7.271511 AGCATAGAATCAGAGAGGTTAGTTTG 58.728 38.462 0.00 0.00 0.00 2.93
2324 2510 7.430760 AGCATAGAATCAGAGAGGTTAGTTT 57.569 36.000 0.00 0.00 0.00 2.66
2325 2511 7.430760 AAGCATAGAATCAGAGAGGTTAGTT 57.569 36.000 0.00 0.00 0.00 2.24
2326 2512 7.430760 AAAGCATAGAATCAGAGAGGTTAGT 57.569 36.000 0.00 0.00 0.00 2.24
2327 2513 9.474920 CTAAAAGCATAGAATCAGAGAGGTTAG 57.525 37.037 0.00 0.00 0.00 2.34
2328 2514 8.982723 ACTAAAAGCATAGAATCAGAGAGGTTA 58.017 33.333 0.00 0.00 0.00 2.85
2329 2515 7.856415 ACTAAAAGCATAGAATCAGAGAGGTT 58.144 34.615 0.00 0.00 0.00 3.50
2330 2516 7.418483 GGACTAAAAGCATAGAATCAGAGAGGT 60.418 40.741 0.00 0.00 0.00 3.85
2331 2517 6.928492 GGACTAAAAGCATAGAATCAGAGAGG 59.072 42.308 0.00 0.00 0.00 3.69
2332 2518 7.437862 GTGGACTAAAAGCATAGAATCAGAGAG 59.562 40.741 0.00 0.00 0.00 3.20
2333 2519 7.093333 TGTGGACTAAAAGCATAGAATCAGAGA 60.093 37.037 0.00 0.00 0.00 3.10
2334 2520 7.010923 GTGTGGACTAAAAGCATAGAATCAGAG 59.989 40.741 0.00 0.00 0.00 3.35
2335 2521 6.818644 GTGTGGACTAAAAGCATAGAATCAGA 59.181 38.462 0.00 0.00 0.00 3.27
2336 2522 6.037610 GGTGTGGACTAAAAGCATAGAATCAG 59.962 42.308 0.00 0.00 0.00 2.90
2337 2523 5.880332 GGTGTGGACTAAAAGCATAGAATCA 59.120 40.000 0.00 0.00 0.00 2.57
2338 2524 5.297029 GGGTGTGGACTAAAAGCATAGAATC 59.703 44.000 0.00 0.00 0.00 2.52
2339 2525 5.193679 GGGTGTGGACTAAAAGCATAGAAT 58.806 41.667 0.00 0.00 0.00 2.40
2340 2526 4.042311 TGGGTGTGGACTAAAAGCATAGAA 59.958 41.667 0.00 0.00 0.00 2.10
2341 2527 3.585289 TGGGTGTGGACTAAAAGCATAGA 59.415 43.478 0.00 0.00 0.00 1.98
2342 2528 3.689649 GTGGGTGTGGACTAAAAGCATAG 59.310 47.826 0.00 0.00 0.00 2.23
2343 2529 3.681593 GTGGGTGTGGACTAAAAGCATA 58.318 45.455 0.00 0.00 0.00 3.14
2344 2530 2.514803 GTGGGTGTGGACTAAAAGCAT 58.485 47.619 0.00 0.00 0.00 3.79
2345 2531 1.812324 CGTGGGTGTGGACTAAAAGCA 60.812 52.381 0.00 0.00 0.00 3.91
2346 2532 0.872388 CGTGGGTGTGGACTAAAAGC 59.128 55.000 0.00 0.00 0.00 3.51
2347 2533 1.071071 TCCGTGGGTGTGGACTAAAAG 59.929 52.381 0.00 0.00 0.00 2.27
2348 2534 1.129917 TCCGTGGGTGTGGACTAAAA 58.870 50.000 0.00 0.00 0.00 1.52
2349 2535 1.354101 ATCCGTGGGTGTGGACTAAA 58.646 50.000 0.00 0.00 37.02 1.85
2350 2536 2.234896 TATCCGTGGGTGTGGACTAA 57.765 50.000 0.00 0.00 37.02 2.24
2351 2537 2.234896 TTATCCGTGGGTGTGGACTA 57.765 50.000 0.00 0.00 37.02 2.59
2352 2538 1.580059 ATTATCCGTGGGTGTGGACT 58.420 50.000 0.00 0.00 37.02 3.85
2353 2539 3.764237 ATATTATCCGTGGGTGTGGAC 57.236 47.619 0.00 0.00 37.02 4.02
2354 2540 4.781775 AAATATTATCCGTGGGTGTGGA 57.218 40.909 0.00 0.00 38.95 4.02
2355 2541 6.234920 TCATAAATATTATCCGTGGGTGTGG 58.765 40.000 0.00 0.00 0.00 4.17
2356 2542 7.737972 TTCATAAATATTATCCGTGGGTGTG 57.262 36.000 0.00 0.00 0.00 3.82
2357 2543 7.776030 TGTTTCATAAATATTATCCGTGGGTGT 59.224 33.333 0.00 0.00 0.00 4.16
2358 2544 8.160521 TGTTTCATAAATATTATCCGTGGGTG 57.839 34.615 0.00 0.00 0.00 4.61
2359 2545 8.626526 GTTGTTTCATAAATATTATCCGTGGGT 58.373 33.333 0.00 0.00 0.00 4.51
2360 2546 8.625651 TGTTGTTTCATAAATATTATCCGTGGG 58.374 33.333 0.00 0.00 0.00 4.61
2371 2557 8.966868 GGAGGGAGAAATGTTGTTTCATAAATA 58.033 33.333 3.68 0.00 0.00 1.40
2372 2558 7.675619 AGGAGGGAGAAATGTTGTTTCATAAAT 59.324 33.333 3.68 0.00 0.00 1.40
2373 2559 7.010160 AGGAGGGAGAAATGTTGTTTCATAAA 58.990 34.615 3.68 0.00 0.00 1.40
2374 2560 6.552008 AGGAGGGAGAAATGTTGTTTCATAA 58.448 36.000 3.68 0.00 0.00 1.90
2375 2561 6.139679 AGGAGGGAGAAATGTTGTTTCATA 57.860 37.500 3.68 0.00 0.00 2.15
2376 2562 5.003096 AGGAGGGAGAAATGTTGTTTCAT 57.997 39.130 3.68 0.00 0.00 2.57
2377 2563 4.453480 AGGAGGGAGAAATGTTGTTTCA 57.547 40.909 3.68 0.00 0.00 2.69
2385 2571 3.883669 CTTCAGGAAGGAGGGAGAAATG 58.116 50.000 1.01 0.00 34.87 2.32
2675 2862 2.297033 TCATGAAAAGGTTGCTCTTGGC 59.703 45.455 0.00 0.00 42.22 4.52
2798 2985 2.352960 GCTACACAAGCCTATTGAGCAC 59.647 50.000 0.00 0.00 46.25 4.40
2811 2998 3.190744 CAGTTACTCTCCGAGCTACACAA 59.809 47.826 0.00 0.00 32.04 3.33


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

AutoCloner maintained by Alex Coulton.