Multiple sequence alignment - TraesCS2B01G432800

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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 TraesCS2B01G432800 chr2B 100.000 2540 0 0 1 2540 622030779 622028240 0.000000e+00 4691
1 TraesCS2B01G432800 chr2B 89.372 2324 156 33 1 2296 435353333 435351073 0.000000e+00 2839
2 TraesCS2B01G432800 chr4A 91.321 2316 153 18 1 2296 574767503 574765216 0.000000e+00 3120
3 TraesCS2B01G432800 chr4A 91.185 1679 99 15 1 1656 602465167 602463515 0.000000e+00 2235
4 TraesCS2B01G432800 chr4A 89.345 1680 114 16 1 1656 218050778 218052416 0.000000e+00 2050
5 TraesCS2B01G432800 chr4A 90.354 622 44 9 1678 2296 602463520 602462912 0.000000e+00 802
6 TraesCS2B01G432800 chr4A 83.240 358 48 9 2186 2537 231003702 231004053 4.080000e-83 318
7 TraesCS2B01G432800 chr3A 91.034 2320 157 21 1 2300 224968248 224970536 0.000000e+00 3085
8 TraesCS2B01G432800 chr6A 90.842 2315 169 19 1 2296 394642529 394644819 0.000000e+00 3061
9 TraesCS2B01G432800 chr6A 80.261 765 88 24 1564 2296 561950152 561950885 3.750000e-143 518
10 TraesCS2B01G432800 chr6A 79.950 793 87 33 1564 2320 617383575 617382819 3.750000e-143 518
11 TraesCS2B01G432800 chr6A 79.974 764 90 24 1564 2296 462917679 462918410 2.920000e-139 505
12 TraesCS2B01G432800 chr5A 89.453 2323 152 40 1 2296 692979192 692981448 0.000000e+00 2846
13 TraesCS2B01G432800 chr5A 90.021 952 77 12 1353 2296 516607173 516608114 0.000000e+00 1216
14 TraesCS2B01G432800 chr5A 90.209 623 45 7 1678 2296 693959038 693959648 0.000000e+00 798
15 TraesCS2B01G432800 chr5A 80.273 806 99 32 1528 2296 599248402 599249184 1.030000e-153 553
16 TraesCS2B01G432800 chr5A 81.343 536 65 20 1772 2293 17572468 17571954 1.090000e-108 403
17 TraesCS2B01G432800 chr5A 93.798 129 8 0 1413 1541 246341097 246340969 7.170000e-46 195
18 TraesCS2B01G432800 chr1B 90.774 1680 104 14 1 1656 17134731 17136383 0.000000e+00 2196
19 TraesCS2B01G432800 chr1B 90.203 1674 106 22 2 1656 651732030 651730396 0.000000e+00 2130
20 TraesCS2B01G432800 chr1B 88.707 735 67 11 1566 2296 637283643 637282921 0.000000e+00 883
21 TraesCS2B01G432800 chr1B 89.809 628 46 10 1678 2301 41213583 41214196 0.000000e+00 789
22 TraesCS2B01G432800 chr1B 89.666 629 46 9 1678 2301 41175571 41176185 0.000000e+00 784
23 TraesCS2B01G432800 chr1B 88.083 386 32 6 1678 2059 17136378 17136753 1.790000e-121 446
24 TraesCS2B01G432800 chr1B 95.492 244 11 0 2297 2540 505816661 505816418 8.520000e-105 390
25 TraesCS2B01G432800 chr6B 90.720 1681 105 15 1 1656 617028554 617030208 0.000000e+00 2193
26 TraesCS2B01G432800 chr6B 90.519 886 71 7 1413 2296 423139266 423138392 0.000000e+00 1158
27 TraesCS2B01G432800 chr6B 90.214 889 71 7 1413 2296 101192031 101192908 0.000000e+00 1146
28 TraesCS2B01G432800 chr6B 90.369 623 43 10 1678 2296 399206901 399206292 0.000000e+00 802
29 TraesCS2B01G432800 chr6B 95.492 244 11 0 2297 2540 152238555 152238798 8.520000e-105 390
30 TraesCS2B01G432800 chr6B 76.481 591 78 30 1528 2088 345807271 345807830 5.390000e-67 265
31 TraesCS2B01G432800 chr5B 90.250 1682 112 16 1 1656 576501418 576503073 0.000000e+00 2150
32 TraesCS2B01G432800 chr5B 95.902 244 10 0 2297 2540 96530126 96529883 1.830000e-106 396
33 TraesCS2B01G432800 chr5B 95.902 244 10 0 2297 2540 134070729 134070486 1.830000e-106 396
34 TraesCS2B01G432800 chr5B 95.902 244 10 0 2297 2540 460454293 460454536 1.830000e-106 396
35 TraesCS2B01G432800 chr5B 95.492 244 11 0 2297 2540 285427666 285427423 8.520000e-105 390
36 TraesCS2B01G432800 chr5B 95.492 244 11 0 2297 2540 426127348 426127591 8.520000e-105 390
37 TraesCS2B01G432800 chr4B 88.435 735 68 10 1566 2296 11347194 11346473 0.000000e+00 870
38 TraesCS2B01G432800 chr4B 90.312 640 48 7 1413 2049 21166284 21166912 0.000000e+00 826
39 TraesCS2B01G432800 chr4B 95.902 244 10 0 2297 2540 23743245 23743002 1.830000e-106 396
40 TraesCS2B01G432800 chr1A 80.846 804 94 33 1528 2296 34918789 34918011 6.090000e-161 577
41 TraesCS2B01G432800 chr3B 95.902 244 10 0 2297 2540 449108278 449108035 1.830000e-106 396


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 TraesCS2B01G432800 chr2B 622028240 622030779 2539 True 4691.0 4691 100.0000 1 2540 1 chr2B.!!$R2 2539
1 TraesCS2B01G432800 chr2B 435351073 435353333 2260 True 2839.0 2839 89.3720 1 2296 1 chr2B.!!$R1 2295
2 TraesCS2B01G432800 chr4A 574765216 574767503 2287 True 3120.0 3120 91.3210 1 2296 1 chr4A.!!$R1 2295
3 TraesCS2B01G432800 chr4A 218050778 218052416 1638 False 2050.0 2050 89.3450 1 1656 1 chr4A.!!$F1 1655
4 TraesCS2B01G432800 chr4A 602462912 602465167 2255 True 1518.5 2235 90.7695 1 2296 2 chr4A.!!$R2 2295
5 TraesCS2B01G432800 chr3A 224968248 224970536 2288 False 3085.0 3085 91.0340 1 2300 1 chr3A.!!$F1 2299
6 TraesCS2B01G432800 chr6A 394642529 394644819 2290 False 3061.0 3061 90.8420 1 2296 1 chr6A.!!$F1 2295
7 TraesCS2B01G432800 chr6A 561950152 561950885 733 False 518.0 518 80.2610 1564 2296 1 chr6A.!!$F3 732
8 TraesCS2B01G432800 chr6A 617382819 617383575 756 True 518.0 518 79.9500 1564 2320 1 chr6A.!!$R1 756
9 TraesCS2B01G432800 chr6A 462917679 462918410 731 False 505.0 505 79.9740 1564 2296 1 chr6A.!!$F2 732
10 TraesCS2B01G432800 chr5A 692979192 692981448 2256 False 2846.0 2846 89.4530 1 2296 1 chr5A.!!$F3 2295
11 TraesCS2B01G432800 chr5A 516607173 516608114 941 False 1216.0 1216 90.0210 1353 2296 1 chr5A.!!$F1 943
12 TraesCS2B01G432800 chr5A 693959038 693959648 610 False 798.0 798 90.2090 1678 2296 1 chr5A.!!$F4 618
13 TraesCS2B01G432800 chr5A 599248402 599249184 782 False 553.0 553 80.2730 1528 2296 1 chr5A.!!$F2 768
14 TraesCS2B01G432800 chr5A 17571954 17572468 514 True 403.0 403 81.3430 1772 2293 1 chr5A.!!$R1 521
15 TraesCS2B01G432800 chr1B 651730396 651732030 1634 True 2130.0 2130 90.2030 2 1656 1 chr1B.!!$R3 1654
16 TraesCS2B01G432800 chr1B 17134731 17136753 2022 False 1321.0 2196 89.4285 1 2059 2 chr1B.!!$F3 2058
17 TraesCS2B01G432800 chr1B 637282921 637283643 722 True 883.0 883 88.7070 1566 2296 1 chr1B.!!$R2 730
18 TraesCS2B01G432800 chr1B 41213583 41214196 613 False 789.0 789 89.8090 1678 2301 1 chr1B.!!$F2 623
19 TraesCS2B01G432800 chr1B 41175571 41176185 614 False 784.0 784 89.6660 1678 2301 1 chr1B.!!$F1 623
20 TraesCS2B01G432800 chr6B 617028554 617030208 1654 False 2193.0 2193 90.7200 1 1656 1 chr6B.!!$F4 1655
21 TraesCS2B01G432800 chr6B 423138392 423139266 874 True 1158.0 1158 90.5190 1413 2296 1 chr6B.!!$R2 883
22 TraesCS2B01G432800 chr6B 101192031 101192908 877 False 1146.0 1146 90.2140 1413 2296 1 chr6B.!!$F1 883
23 TraesCS2B01G432800 chr6B 399206292 399206901 609 True 802.0 802 90.3690 1678 2296 1 chr6B.!!$R1 618
24 TraesCS2B01G432800 chr6B 345807271 345807830 559 False 265.0 265 76.4810 1528 2088 1 chr6B.!!$F3 560
25 TraesCS2B01G432800 chr5B 576501418 576503073 1655 False 2150.0 2150 90.2500 1 1656 1 chr5B.!!$F3 1655
26 TraesCS2B01G432800 chr4B 11346473 11347194 721 True 870.0 870 88.4350 1566 2296 1 chr4B.!!$R1 730
27 TraesCS2B01G432800 chr4B 21166284 21166912 628 False 826.0 826 90.3120 1413 2049 1 chr4B.!!$F1 636
28 TraesCS2B01G432800 chr1A 34918011 34918789 778 True 577.0 577 80.8460 1528 2296 1 chr1A.!!$R1 768

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
829 849 2.684881 AGGGTGATTAATTCTGCTTGCG 59.315 45.455 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2570 1.024271 GACTGCAGTTTTGACAGCCA 58.976 50.0 22.65 0.0 34.12 4.75 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
70 74 3.210227 TGTTCCATTGTGTCGTGAACAT 58.790 40.909 0.00 0.00 40.06 2.71
162 166 3.238597 AGAAGACTGGTTTCTCTGAGCT 58.761 45.455 0.00 0.00 29.05 4.09
236 240 5.652452 GGCTTGTTTACCTCATCCTTGTTAT 59.348 40.000 0.00 0.00 0.00 1.89
243 247 8.880750 GTTTACCTCATCCTTGTTATACTTGAC 58.119 37.037 0.00 0.00 0.00 3.18
285 296 7.337942 ACAGATTTGATAGAGATGGTTTGTTCC 59.662 37.037 0.00 0.00 0.00 3.62
344 355 6.438763 GTTTGTTTGTCCTAATCCTCTGTTG 58.561 40.000 0.00 0.00 0.00 3.33
400 411 5.826601 TGCGACAATATTCAGGCAATTTA 57.173 34.783 0.00 0.00 0.00 1.40
413 424 7.817418 TCAGGCAATTTAAGTTCTTGTTACT 57.183 32.000 0.00 0.00 0.00 2.24
414 425 8.911918 TCAGGCAATTTAAGTTCTTGTTACTA 57.088 30.769 0.00 0.00 0.00 1.82
464 475 6.360370 ACACTGGTAATTAAGAGAGAGCAA 57.640 37.500 0.00 0.00 0.00 3.91
517 528 2.869636 GCCTGAAGCATCTATCTTCCCG 60.870 54.545 0.00 0.00 42.97 5.14
601 612 6.566079 TGTGGAAGTGGATTTCTCTGATAT 57.434 37.500 0.00 0.00 0.00 1.63
630 648 5.391312 AAAGAAACAACATATGTGCTCCC 57.609 39.130 9.63 0.00 42.99 4.30
646 664 4.634443 GTGCTCCCGAAACATACTACATTT 59.366 41.667 0.00 0.00 0.00 2.32
651 669 7.361799 GCTCCCGAAACATACTACATTTTTCTT 60.362 37.037 0.00 0.00 0.00 2.52
653 671 7.662258 TCCCGAAACATACTACATTTTTCTTCA 59.338 33.333 0.00 0.00 0.00 3.02
774 792 3.382546 GGTGCCATGCTTCTTTCATGTAT 59.617 43.478 0.00 0.00 39.60 2.29
829 849 2.684881 AGGGTGATTAATTCTGCTTGCG 59.315 45.455 0.00 0.00 0.00 4.85
852 875 6.019881 GCGTGCTTCAAAGTTTTCAAATAACT 60.020 34.615 0.00 0.00 37.43 2.24
853 876 7.166804 GCGTGCTTCAAAGTTTTCAAATAACTA 59.833 33.333 0.00 0.00 34.88 2.24
854 877 8.469125 CGTGCTTCAAAGTTTTCAAATAACTAC 58.531 33.333 0.00 0.00 34.88 2.73
879 902 9.203163 ACTAGTTAATTAGTAGCATGGAGACTT 57.797 33.333 8.76 0.00 33.73 3.01
917 940 6.311200 GTCAACATTCTTGAACAGTTTGCTTT 59.689 34.615 0.00 0.00 0.00 3.51
947 970 5.825593 TCCTAGTCATTCAGAACCAACTT 57.174 39.130 0.00 0.00 0.00 2.66
948 971 5.551233 TCCTAGTCATTCAGAACCAACTTG 58.449 41.667 0.00 0.00 0.00 3.16
1048 1073 4.144297 AGAACCAAAGAATGTTGCTGCTA 58.856 39.130 0.00 0.00 0.00 3.49
1218 1243 0.744414 GGCAAGCCGCTGAGTTGATA 60.744 55.000 0.00 0.00 41.91 2.15
1236 1261 3.509967 TGATACGAGAGGAGCTTGTTGAA 59.490 43.478 0.00 0.00 41.55 2.69
1240 1265 2.694213 GAGAGGAGCTTGTTGAAGTCC 58.306 52.381 0.00 0.00 33.17 3.85
1273 1298 1.954146 GAGACCGAAGTTGCACGCA 60.954 57.895 0.00 0.00 0.00 5.24
1314 1339 0.183492 TGCAAAGAGTTGAGGCCACT 59.817 50.000 5.01 0.00 36.83 4.00
1327 1352 1.410850 GGCCACTGATGCTAGGGCTA 61.411 60.000 0.00 0.00 44.04 3.93
1328 1353 0.250081 GCCACTGATGCTAGGGCTAC 60.250 60.000 0.00 0.00 41.39 3.58
1359 1405 4.385358 TGCTAGATTTGCGTGTCTCATA 57.615 40.909 0.00 0.00 0.00 2.15
1363 1409 6.016276 TGCTAGATTTGCGTGTCTCATAGATA 60.016 38.462 0.00 0.00 0.00 1.98
1370 1416 3.362237 GCGTGTCTCATAGATATGTTCGC 59.638 47.826 0.03 0.00 35.26 4.70
1411 1457 2.233431 GGCATGGTTGATGTTGGCTTTA 59.767 45.455 0.00 0.00 34.14 1.85
1418 1465 5.009610 TGGTTGATGTTGGCTTTAGACTTTC 59.990 40.000 0.00 0.00 0.00 2.62
1441 1490 1.748493 TGTTGAGTTGTTTGGACCTGC 59.252 47.619 0.00 0.00 0.00 4.85
1464 1514 4.273480 CGGTTGATGAGTTTCTTTGACTGT 59.727 41.667 0.00 0.00 0.00 3.55
1632 1694 7.936847 TGTAATGATACTATTGGGCCTAAGTTG 59.063 37.037 7.87 2.45 32.98 3.16
1633 1695 5.304686 TGATACTATTGGGCCTAAGTTGG 57.695 43.478 7.87 0.00 0.00 3.77
1688 1756 8.292444 TCATTTTATTCTCCTGTATTGGTTGG 57.708 34.615 0.00 0.00 0.00 3.77
1689 1757 7.341769 TCATTTTATTCTCCTGTATTGGTTGGG 59.658 37.037 0.00 0.00 0.00 4.12
1904 2016 2.707849 GCACATTGCCTCAGCCCAG 61.708 63.158 0.00 0.00 37.42 4.45
1955 2080 9.665719 CCAAAAGTAAATGTAAAAATGGGCTAT 57.334 29.630 0.00 0.00 0.00 2.97
1988 2113 5.389859 TCAGCCCATTAAAACAACTGATG 57.610 39.130 0.00 0.00 0.00 3.07
1989 2114 5.076182 TCAGCCCATTAAAACAACTGATGA 58.924 37.500 0.00 0.00 0.00 2.92
1991 2116 6.041409 TCAGCCCATTAAAACAACTGATGAAA 59.959 34.615 0.00 0.00 0.00 2.69
1996 2121 7.542130 CCCATTAAAACAACTGATGAAAGCTAC 59.458 37.037 0.00 0.00 0.00 3.58
1998 2123 9.683069 CATTAAAACAACTGATGAAAGCTACTT 57.317 29.630 0.00 0.00 0.00 2.24
2083 2208 2.722487 CTACGTGGCCTAGGCTCG 59.278 66.667 32.94 32.94 41.60 5.03
2104 2229 8.403236 GGCTCGTTAGTAATGACCATAATTTTT 58.597 33.333 14.13 0.00 0.00 1.94
2141 2266 4.080638 AGACCAAAATTTTGTTCAAGGGCA 60.081 37.500 24.80 0.00 32.72 5.36
2188 2314 2.994578 TCACGTTTGTTCGTTCTTGACA 59.005 40.909 0.00 0.00 42.27 3.58
2279 2410 6.204555 ACCAAAATGGGGAGTCATAATTGAT 58.795 36.000 0.87 0.00 43.37 2.57
2305 2436 9.890629 TCATATTTCTTGTAGTGCTATGAAGTT 57.109 29.630 0.00 0.00 0.00 2.66
2307 2438 6.706055 TTTCTTGTAGTGCTATGAAGTTCG 57.294 37.500 0.00 0.00 0.00 3.95
2308 2439 5.638596 TCTTGTAGTGCTATGAAGTTCGA 57.361 39.130 0.00 0.00 0.00 3.71
2309 2440 5.399858 TCTTGTAGTGCTATGAAGTTCGAC 58.600 41.667 0.00 0.00 0.00 4.20
2310 2441 5.183331 TCTTGTAGTGCTATGAAGTTCGACT 59.817 40.000 0.00 0.00 0.00 4.18
2311 2442 5.386958 TGTAGTGCTATGAAGTTCGACTT 57.613 39.130 0.00 0.00 41.95 3.01
2312 2443 5.161358 TGTAGTGCTATGAAGTTCGACTTG 58.839 41.667 5.20 0.00 38.80 3.16
2313 2444 4.258702 AGTGCTATGAAGTTCGACTTGT 57.741 40.909 5.20 0.00 38.80 3.16
2314 2445 4.632153 AGTGCTATGAAGTTCGACTTGTT 58.368 39.130 5.20 0.00 38.80 2.83
2315 2446 4.449068 AGTGCTATGAAGTTCGACTTGTTG 59.551 41.667 5.20 0.00 38.80 3.33
2316 2447 3.186409 TGCTATGAAGTTCGACTTGTTGC 59.814 43.478 5.20 6.93 38.80 4.17
2317 2448 3.186409 GCTATGAAGTTCGACTTGTTGCA 59.814 43.478 5.20 0.00 38.80 4.08
2318 2449 4.319477 GCTATGAAGTTCGACTTGTTGCAA 60.319 41.667 0.00 0.00 38.80 4.08
2319 2450 4.630894 ATGAAGTTCGACTTGTTGCAAA 57.369 36.364 0.00 0.00 38.80 3.68
2320 2451 4.014847 TGAAGTTCGACTTGTTGCAAAG 57.985 40.909 0.00 0.00 38.80 2.77
2321 2452 3.181501 TGAAGTTCGACTTGTTGCAAAGG 60.182 43.478 0.00 0.00 38.80 3.11
2322 2453 1.676006 AGTTCGACTTGTTGCAAAGGG 59.324 47.619 0.00 0.00 0.00 3.95
2323 2454 1.404035 GTTCGACTTGTTGCAAAGGGT 59.596 47.619 0.00 0.00 0.00 4.34
2324 2455 1.757682 TCGACTTGTTGCAAAGGGTT 58.242 45.000 0.00 0.00 0.00 4.11
2325 2456 2.096248 TCGACTTGTTGCAAAGGGTTT 58.904 42.857 0.00 0.00 0.00 3.27
2326 2457 2.494073 TCGACTTGTTGCAAAGGGTTTT 59.506 40.909 0.00 0.00 0.00 2.43
2327 2458 2.857748 CGACTTGTTGCAAAGGGTTTTC 59.142 45.455 0.00 0.00 0.00 2.29
2328 2459 2.857748 GACTTGTTGCAAAGGGTTTTCG 59.142 45.455 0.00 0.00 0.00 3.46
2329 2460 2.494073 ACTTGTTGCAAAGGGTTTTCGA 59.506 40.909 0.00 0.00 0.00 3.71
2330 2461 2.570442 TGTTGCAAAGGGTTTTCGAC 57.430 45.000 0.00 0.00 0.00 4.20
2331 2462 1.819288 TGTTGCAAAGGGTTTTCGACA 59.181 42.857 0.00 0.00 0.00 4.35
2332 2463 2.231478 TGTTGCAAAGGGTTTTCGACAA 59.769 40.909 0.00 0.00 0.00 3.18
2333 2464 2.857748 GTTGCAAAGGGTTTTCGACAAG 59.142 45.455 0.00 0.00 0.00 3.16
2334 2465 2.096248 TGCAAAGGGTTTTCGACAAGT 58.904 42.857 0.00 0.00 0.00 3.16
2335 2466 2.494073 TGCAAAGGGTTTTCGACAAGTT 59.506 40.909 0.00 0.00 0.00 2.66
2336 2467 3.113322 GCAAAGGGTTTTCGACAAGTTC 58.887 45.455 0.00 0.00 0.00 3.01
2337 2468 3.428316 GCAAAGGGTTTTCGACAAGTTCA 60.428 43.478 0.00 0.00 0.00 3.18
2338 2469 4.739195 CAAAGGGTTTTCGACAAGTTCAA 58.261 39.130 0.00 0.00 0.00 2.69
2339 2470 4.632538 AAGGGTTTTCGACAAGTTCAAG 57.367 40.909 0.00 0.00 0.00 3.02
2340 2471 2.949644 AGGGTTTTCGACAAGTTCAAGG 59.050 45.455 0.00 0.00 0.00 3.61
2341 2472 2.946990 GGGTTTTCGACAAGTTCAAGGA 59.053 45.455 0.00 0.00 0.00 3.36
2342 2473 3.003378 GGGTTTTCGACAAGTTCAAGGAG 59.997 47.826 0.00 0.00 0.00 3.69
2343 2474 3.626217 GGTTTTCGACAAGTTCAAGGAGT 59.374 43.478 0.00 0.00 0.00 3.85
2344 2475 4.095932 GGTTTTCGACAAGTTCAAGGAGTT 59.904 41.667 0.00 0.00 0.00 3.01
2345 2476 4.875544 TTTCGACAAGTTCAAGGAGTTG 57.124 40.909 0.00 0.00 36.31 3.16
2346 2477 3.812156 TCGACAAGTTCAAGGAGTTGA 57.188 42.857 3.00 0.00 41.13 3.18
2347 2478 3.454375 TCGACAAGTTCAAGGAGTTGAC 58.546 45.455 3.00 0.00 42.60 3.18
2348 2479 3.132289 TCGACAAGTTCAAGGAGTTGACT 59.868 43.478 3.00 0.00 42.60 3.41
2349 2480 4.340097 TCGACAAGTTCAAGGAGTTGACTA 59.660 41.667 3.00 0.00 42.60 2.59
2350 2481 4.444720 CGACAAGTTCAAGGAGTTGACTAC 59.555 45.833 3.00 0.00 42.60 2.73
2351 2482 4.369182 ACAAGTTCAAGGAGTTGACTACG 58.631 43.478 3.00 0.00 42.60 3.51
2352 2483 4.098960 ACAAGTTCAAGGAGTTGACTACGA 59.901 41.667 3.00 0.00 42.60 3.43
2353 2484 5.221461 ACAAGTTCAAGGAGTTGACTACGAT 60.221 40.000 3.00 0.00 42.60 3.73
2354 2485 4.810790 AGTTCAAGGAGTTGACTACGATG 58.189 43.478 0.00 0.00 42.60 3.84
2355 2486 4.523173 AGTTCAAGGAGTTGACTACGATGA 59.477 41.667 0.00 2.13 42.60 2.92
2356 2487 4.703645 TCAAGGAGTTGACTACGATGAG 57.296 45.455 0.00 0.00 37.79 2.90
2357 2488 4.332828 TCAAGGAGTTGACTACGATGAGA 58.667 43.478 0.00 0.00 37.79 3.27
2358 2489 4.156190 TCAAGGAGTTGACTACGATGAGAC 59.844 45.833 0.00 0.00 37.79 3.36
2359 2490 3.958018 AGGAGTTGACTACGATGAGACT 58.042 45.455 0.00 0.00 0.00 3.24
2360 2491 4.337145 AGGAGTTGACTACGATGAGACTT 58.663 43.478 0.00 0.00 0.00 3.01
2361 2492 4.767928 AGGAGTTGACTACGATGAGACTTT 59.232 41.667 0.00 0.00 0.00 2.66
2362 2493 5.096849 GGAGTTGACTACGATGAGACTTTC 58.903 45.833 0.00 0.00 0.00 2.62
2363 2494 5.106078 GGAGTTGACTACGATGAGACTTTCT 60.106 44.000 0.00 0.00 0.00 2.52
2364 2495 5.945155 AGTTGACTACGATGAGACTTTCTC 58.055 41.667 0.00 0.00 43.65 2.87
2388 2519 4.471386 ACCCATAGTGATGCTTAAGTCTGT 59.529 41.667 4.02 0.00 0.00 3.41
2389 2520 5.053145 CCCATAGTGATGCTTAAGTCTGTC 58.947 45.833 4.02 0.00 0.00 3.51
2390 2521 5.053145 CCATAGTGATGCTTAAGTCTGTCC 58.947 45.833 4.02 0.00 0.00 4.02
2391 2522 3.238108 AGTGATGCTTAAGTCTGTCCG 57.762 47.619 4.02 0.00 0.00 4.79
2392 2523 2.826128 AGTGATGCTTAAGTCTGTCCGA 59.174 45.455 4.02 0.00 0.00 4.55
2393 2524 3.258372 AGTGATGCTTAAGTCTGTCCGAA 59.742 43.478 4.02 0.00 0.00 4.30
2394 2525 4.081420 AGTGATGCTTAAGTCTGTCCGAAT 60.081 41.667 4.02 0.00 0.00 3.34
2395 2526 4.268884 GTGATGCTTAAGTCTGTCCGAATC 59.731 45.833 4.02 0.00 0.00 2.52
2396 2527 3.953712 TGCTTAAGTCTGTCCGAATCA 57.046 42.857 4.02 0.00 0.00 2.57
2397 2528 4.471904 TGCTTAAGTCTGTCCGAATCAT 57.528 40.909 4.02 0.00 0.00 2.45
2398 2529 4.183865 TGCTTAAGTCTGTCCGAATCATG 58.816 43.478 4.02 0.00 0.00 3.07
2399 2530 4.184629 GCTTAAGTCTGTCCGAATCATGT 58.815 43.478 4.02 0.00 0.00 3.21
2400 2531 4.631813 GCTTAAGTCTGTCCGAATCATGTT 59.368 41.667 4.02 0.00 0.00 2.71
2401 2532 5.810587 GCTTAAGTCTGTCCGAATCATGTTA 59.189 40.000 4.02 0.00 0.00 2.41
2402 2533 6.019479 GCTTAAGTCTGTCCGAATCATGTTAG 60.019 42.308 4.02 0.00 0.00 2.34
2403 2534 3.786635 AGTCTGTCCGAATCATGTTAGC 58.213 45.455 0.00 0.00 0.00 3.09
2404 2535 3.195610 AGTCTGTCCGAATCATGTTAGCA 59.804 43.478 0.00 0.00 0.00 3.49
2405 2536 3.932710 GTCTGTCCGAATCATGTTAGCAA 59.067 43.478 0.00 0.00 0.00 3.91
2406 2537 4.572389 GTCTGTCCGAATCATGTTAGCAAT 59.428 41.667 0.00 0.00 0.00 3.56
2407 2538 5.065218 GTCTGTCCGAATCATGTTAGCAATT 59.935 40.000 0.00 0.00 0.00 2.32
2408 2539 5.065090 TCTGTCCGAATCATGTTAGCAATTG 59.935 40.000 0.00 0.00 0.00 2.32
2409 2540 4.037690 GTCCGAATCATGTTAGCAATTGC 58.962 43.478 23.05 23.05 42.49 3.56
2410 2541 3.066621 TCCGAATCATGTTAGCAATTGCC 59.933 43.478 26.45 12.24 43.38 4.52
2411 2542 3.038017 CGAATCATGTTAGCAATTGCCG 58.962 45.455 26.45 14.43 43.38 5.69
2412 2543 2.497107 ATCATGTTAGCAATTGCCGC 57.503 45.000 26.45 16.59 43.38 6.53
2413 2544 1.172175 TCATGTTAGCAATTGCCGCA 58.828 45.000 26.45 21.27 43.38 5.69
2414 2545 1.750206 TCATGTTAGCAATTGCCGCAT 59.250 42.857 26.45 22.40 43.38 4.73
2415 2546 2.166050 TCATGTTAGCAATTGCCGCATT 59.834 40.909 26.45 10.51 43.38 3.56
2416 2547 2.739885 TGTTAGCAATTGCCGCATTT 57.260 40.000 26.45 9.76 43.38 2.32
2417 2548 3.037431 TGTTAGCAATTGCCGCATTTT 57.963 38.095 26.45 9.01 43.38 1.82
2418 2549 4.179926 TGTTAGCAATTGCCGCATTTTA 57.820 36.364 26.45 7.96 43.38 1.52
2419 2550 4.753233 TGTTAGCAATTGCCGCATTTTAT 58.247 34.783 26.45 7.51 43.38 1.40
2420 2551 4.565962 TGTTAGCAATTGCCGCATTTTATG 59.434 37.500 26.45 0.00 43.38 1.90
2421 2552 3.523606 AGCAATTGCCGCATTTTATGA 57.476 38.095 26.45 0.00 43.38 2.15
2422 2553 4.062677 AGCAATTGCCGCATTTTATGAT 57.937 36.364 26.45 0.16 43.38 2.45
2423 2554 4.444536 AGCAATTGCCGCATTTTATGATT 58.555 34.783 26.45 0.00 43.38 2.57
2424 2555 5.599732 AGCAATTGCCGCATTTTATGATTA 58.400 33.333 26.45 0.00 43.38 1.75
2425 2556 6.225318 AGCAATTGCCGCATTTTATGATTAT 58.775 32.000 26.45 0.00 43.38 1.28
2426 2557 6.146510 AGCAATTGCCGCATTTTATGATTATG 59.853 34.615 26.45 0.00 43.38 1.90
2427 2558 6.145858 GCAATTGCCGCATTTTATGATTATGA 59.854 34.615 20.06 0.00 34.31 2.15
2428 2559 7.307278 GCAATTGCCGCATTTTATGATTATGAA 60.307 33.333 20.06 0.00 34.31 2.57
2429 2560 8.549548 CAATTGCCGCATTTTATGATTATGAAA 58.450 29.630 0.00 0.00 0.00 2.69
2430 2561 8.836268 ATTGCCGCATTTTATGATTATGAAAT 57.164 26.923 0.00 0.00 34.06 2.17
2431 2562 7.872163 TGCCGCATTTTATGATTATGAAATC 57.128 32.000 0.00 0.00 41.69 2.17
2432 2563 7.660112 TGCCGCATTTTATGATTATGAAATCT 58.340 30.769 0.00 0.00 41.83 2.40
2433 2564 7.595875 TGCCGCATTTTATGATTATGAAATCTG 59.404 33.333 0.00 0.00 41.83 2.90
2434 2565 7.062605 GCCGCATTTTATGATTATGAAATCTGG 59.937 37.037 8.93 8.93 41.83 3.86
2435 2566 7.062605 CCGCATTTTATGATTATGAAATCTGGC 59.937 37.037 0.00 0.00 41.83 4.85
2436 2567 7.595875 CGCATTTTATGATTATGAAATCTGGCA 59.404 33.333 0.00 0.00 41.83 4.92
2437 2568 9.263538 GCATTTTATGATTATGAAATCTGGCAA 57.736 29.630 0.00 0.00 41.83 4.52
2441 2572 9.767228 TTTATGATTATGAAATCTGGCAAATGG 57.233 29.630 0.00 0.00 41.83 3.16
2442 2573 5.603596 TGATTATGAAATCTGGCAAATGGC 58.396 37.500 0.00 0.00 41.83 4.40
2443 2574 5.364446 TGATTATGAAATCTGGCAAATGGCT 59.636 36.000 8.50 0.00 41.83 4.75
2444 2575 3.536956 ATGAAATCTGGCAAATGGCTG 57.463 42.857 8.50 7.93 44.01 4.85
2445 2576 2.250031 TGAAATCTGGCAAATGGCTGT 58.750 42.857 8.50 0.00 44.01 4.40
2446 2577 2.231964 TGAAATCTGGCAAATGGCTGTC 59.768 45.455 8.50 2.98 44.01 3.51
2447 2578 1.927487 AATCTGGCAAATGGCTGTCA 58.073 45.000 8.50 0.00 44.01 3.58
2448 2579 1.927487 ATCTGGCAAATGGCTGTCAA 58.073 45.000 8.50 0.00 44.01 3.18
2449 2580 1.702182 TCTGGCAAATGGCTGTCAAA 58.298 45.000 8.50 0.00 44.01 2.69
2450 2581 2.037901 TCTGGCAAATGGCTGTCAAAA 58.962 42.857 8.50 0.00 44.01 2.44
2451 2582 2.137523 CTGGCAAATGGCTGTCAAAAC 58.862 47.619 8.50 0.00 44.01 2.43
2452 2583 1.761784 TGGCAAATGGCTGTCAAAACT 59.238 42.857 8.50 0.00 44.01 2.66
2453 2584 2.137523 GGCAAATGGCTGTCAAAACTG 58.862 47.619 0.00 0.00 44.01 3.16
2454 2585 1.528161 GCAAATGGCTGTCAAAACTGC 59.472 47.619 0.00 0.00 46.38 4.40
2461 2592 3.427161 GCTGTCAAAACTGCAGTCTTT 57.573 42.857 21.95 18.42 46.36 2.52
2462 2593 4.552166 GCTGTCAAAACTGCAGTCTTTA 57.448 40.909 21.95 0.11 46.36 1.85
2463 2594 4.920376 GCTGTCAAAACTGCAGTCTTTAA 58.080 39.130 21.95 6.54 46.36 1.52
2464 2595 5.523369 GCTGTCAAAACTGCAGTCTTTAAT 58.477 37.500 21.95 0.00 46.36 1.40
2465 2596 5.400485 GCTGTCAAAACTGCAGTCTTTAATG 59.600 40.000 21.95 12.57 46.36 1.90
2466 2597 5.830912 TGTCAAAACTGCAGTCTTTAATGG 58.169 37.500 21.95 10.48 0.00 3.16
2467 2598 5.592282 TGTCAAAACTGCAGTCTTTAATGGA 59.408 36.000 21.95 12.33 0.00 3.41
2468 2599 6.265196 TGTCAAAACTGCAGTCTTTAATGGAT 59.735 34.615 21.95 0.00 0.00 3.41
2469 2600 7.147976 GTCAAAACTGCAGTCTTTAATGGATT 58.852 34.615 21.95 3.32 0.00 3.01
2470 2601 7.653311 GTCAAAACTGCAGTCTTTAATGGATTT 59.347 33.333 21.95 9.82 0.00 2.17
2471 2602 7.867403 TCAAAACTGCAGTCTTTAATGGATTTC 59.133 33.333 21.95 0.00 0.00 2.17
2472 2603 7.530426 AAACTGCAGTCTTTAATGGATTTCT 57.470 32.000 21.95 0.00 0.00 2.52
2473 2604 7.530426 AACTGCAGTCTTTAATGGATTTCTT 57.470 32.000 21.95 0.00 0.00 2.52
2474 2605 8.635765 AACTGCAGTCTTTAATGGATTTCTTA 57.364 30.769 21.95 0.00 0.00 2.10
2475 2606 8.635765 ACTGCAGTCTTTAATGGATTTCTTAA 57.364 30.769 15.25 0.00 0.00 1.85
2476 2607 9.077885 ACTGCAGTCTTTAATGGATTTCTTAAA 57.922 29.630 15.25 0.00 0.00 1.52
2477 2608 9.565213 CTGCAGTCTTTAATGGATTTCTTAAAG 57.435 33.333 5.25 7.97 42.37 1.85
2478 2609 9.295825 TGCAGTCTTTAATGGATTTCTTAAAGA 57.704 29.630 11.47 11.47 45.09 2.52
2509 2640 9.461312 TTGTATATGATGCAACTAGAAGGTTTT 57.539 29.630 0.00 0.00 29.78 2.43
2510 2641 8.892723 TGTATATGATGCAACTAGAAGGTTTTG 58.107 33.333 0.00 0.00 0.00 2.44
2511 2642 7.944729 ATATGATGCAACTAGAAGGTTTTGT 57.055 32.000 0.00 0.00 0.00 2.83
2512 2643 5.689383 TGATGCAACTAGAAGGTTTTGTC 57.311 39.130 0.00 0.00 0.00 3.18
2513 2644 4.213270 TGATGCAACTAGAAGGTTTTGTCG 59.787 41.667 0.00 0.00 0.00 4.35
2514 2645 3.799366 TGCAACTAGAAGGTTTTGTCGA 58.201 40.909 0.00 0.00 0.00 4.20
2515 2646 4.385825 TGCAACTAGAAGGTTTTGTCGAT 58.614 39.130 0.00 0.00 0.00 3.59
2516 2647 4.451096 TGCAACTAGAAGGTTTTGTCGATC 59.549 41.667 0.00 0.00 0.00 3.69
2517 2648 4.142881 GCAACTAGAAGGTTTTGTCGATCC 60.143 45.833 0.00 0.00 0.00 3.36
2518 2649 5.238583 CAACTAGAAGGTTTTGTCGATCCT 58.761 41.667 0.00 0.00 0.00 3.24
2519 2650 6.395629 CAACTAGAAGGTTTTGTCGATCCTA 58.604 40.000 0.00 0.00 0.00 2.94
2520 2651 6.600882 ACTAGAAGGTTTTGTCGATCCTAA 57.399 37.500 0.00 0.00 0.00 2.69
2521 2652 7.001099 ACTAGAAGGTTTTGTCGATCCTAAA 57.999 36.000 0.00 0.00 0.00 1.85
2522 2653 7.097834 ACTAGAAGGTTTTGTCGATCCTAAAG 58.902 38.462 0.00 0.00 0.00 1.85
2523 2654 5.246307 AGAAGGTTTTGTCGATCCTAAAGG 58.754 41.667 0.00 0.00 0.00 3.11
2524 2655 4.635699 AGGTTTTGTCGATCCTAAAGGT 57.364 40.909 0.00 0.00 36.34 3.50
2525 2656 4.324267 AGGTTTTGTCGATCCTAAAGGTG 58.676 43.478 0.00 0.00 36.34 4.00
2526 2657 3.119955 GGTTTTGTCGATCCTAAAGGTGC 60.120 47.826 0.00 0.00 36.34 5.01
2527 2658 3.695830 TTTGTCGATCCTAAAGGTGCT 57.304 42.857 0.00 0.00 36.34 4.40
2528 2659 4.811969 TTTGTCGATCCTAAAGGTGCTA 57.188 40.909 0.00 0.00 36.34 3.49
2529 2660 4.811969 TTGTCGATCCTAAAGGTGCTAA 57.188 40.909 0.00 0.00 36.34 3.09
2530 2661 4.119442 TGTCGATCCTAAAGGTGCTAAC 57.881 45.455 0.00 0.00 36.34 2.34
2531 2662 3.512329 TGTCGATCCTAAAGGTGCTAACA 59.488 43.478 0.00 0.00 36.34 2.41
2532 2663 4.020928 TGTCGATCCTAAAGGTGCTAACAA 60.021 41.667 0.00 0.00 36.34 2.83
2533 2664 4.933400 GTCGATCCTAAAGGTGCTAACAAA 59.067 41.667 0.00 0.00 36.34 2.83
2534 2665 5.063564 GTCGATCCTAAAGGTGCTAACAAAG 59.936 44.000 0.00 0.00 36.34 2.77
2535 2666 4.935808 CGATCCTAAAGGTGCTAACAAAGT 59.064 41.667 0.00 0.00 36.34 2.66
2536 2667 5.163854 CGATCCTAAAGGTGCTAACAAAGTG 60.164 44.000 0.00 0.00 36.34 3.16
2537 2668 5.043737 TCCTAAAGGTGCTAACAAAGTGT 57.956 39.130 0.00 0.00 36.34 3.55
2538 2669 4.819630 TCCTAAAGGTGCTAACAAAGTGTG 59.180 41.667 0.00 0.00 36.34 3.82
2539 2670 3.436700 AAAGGTGCTAACAAAGTGTGC 57.563 42.857 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.970662 TGAAAGAATCACTGCATTAGCC 57.029 40.909 0.00 0.00 34.39 3.93
23 24 7.704789 AAGAAACAATTGAAAGAATCACTGC 57.295 32.000 13.59 0.00 37.92 4.40
70 74 4.315803 CCTTACGAGCCTCTTTCTGAAAA 58.684 43.478 4.18 0.00 0.00 2.29
162 166 8.964772 AGAAACTTACTATCGCCTTCTTAACTA 58.035 33.333 0.00 0.00 0.00 2.24
236 240 8.161699 TGTCGAGCATATAATGTAGTCAAGTA 57.838 34.615 0.00 0.00 0.00 2.24
243 247 8.748380 TCAAATCTGTCGAGCATATAATGTAG 57.252 34.615 0.00 0.00 0.00 2.74
317 328 5.048713 CAGAGGATTAGGACAAACAAACCAC 60.049 44.000 0.00 0.00 0.00 4.16
319 330 5.070685 ACAGAGGATTAGGACAAACAAACC 58.929 41.667 0.00 0.00 0.00 3.27
344 355 5.912396 CCAAAATGAATATGCAATGCAATGC 59.088 36.000 19.99 19.99 43.62 3.56
400 411 5.013183 ACCTGCTGGATAGTAACAAGAACTT 59.987 40.000 17.64 0.00 37.04 2.66
436 447 7.550906 GCTCTCTCTTAATTACCAGTGTTCAAT 59.449 37.037 0.00 0.00 0.00 2.57
517 528 1.157585 GTTTCTCCACTCCGAAAGCC 58.842 55.000 0.00 0.00 30.51 4.35
553 564 8.954350 CAAGTCCTAAACATTTCATTCAGATCT 58.046 33.333 0.00 0.00 0.00 2.75
601 612 9.062524 AGCACATATGTTGTTTCTTTAGTACAA 57.937 29.630 5.37 0.00 36.00 2.41
624 642 4.481368 AATGTAGTATGTTTCGGGAGCA 57.519 40.909 0.00 0.00 0.00 4.26
630 648 9.530129 GAGTGAAGAAAAATGTAGTATGTTTCG 57.470 33.333 0.00 0.00 34.21 3.46
646 664 3.874383 TGGGAACATGGAGTGAAGAAA 57.126 42.857 0.00 0.00 33.40 2.52
715 733 5.181245 CAGGTAAGGATACACAACAAACCAG 59.819 44.000 0.00 0.00 41.41 4.00
731 749 6.349860 GCACCAGGTTTATTAAACAGGTAAGG 60.350 42.308 23.76 17.08 44.36 2.69
811 831 2.848302 GCACGCAAGCAGAATTAATCAC 59.152 45.455 0.00 0.00 45.62 3.06
829 849 9.516314 AGTAGTTATTTGAAAACTTTGAAGCAC 57.484 29.630 0.00 0.00 38.18 4.40
852 875 9.863650 AGTCTCCATGCTACTAATTAACTAGTA 57.136 33.333 3.93 3.93 34.03 1.82
853 876 8.770010 AGTCTCCATGCTACTAATTAACTAGT 57.230 34.615 1.75 1.75 36.16 2.57
854 877 9.469807 CAAGTCTCCATGCTACTAATTAACTAG 57.530 37.037 0.00 0.00 0.00 2.57
907 930 8.188139 TGACTAGGAAACTTTAAAAGCAAACTG 58.812 33.333 0.00 0.00 43.67 3.16
917 940 8.215050 TGGTTCTGAATGACTAGGAAACTTTAA 58.785 33.333 0.00 0.00 43.67 1.52
947 970 4.763279 AGAAAGATGCACACATGTCATTCA 59.237 37.500 0.00 0.00 36.35 2.57
948 971 5.306532 AGAAAGATGCACACATGTCATTC 57.693 39.130 0.00 0.00 36.35 2.67
1025 1050 3.385755 AGCAGCAACATTCTTTGGTTCTT 59.614 39.130 0.00 0.00 35.00 2.52
1048 1073 6.712095 TCTTTAGTGAGAATGTCAGCAACAAT 59.288 34.615 0.00 0.00 42.37 2.71
1161 1186 6.531948 GCTTGTACTCTAGTTCTTGTACATGG 59.468 42.308 8.74 0.00 42.83 3.66
1218 1243 1.689273 ACTTCAACAAGCTCCTCTCGT 59.311 47.619 0.00 0.00 32.09 4.18
1236 1261 4.466015 GTCTCCTCTGATTTCTTCTGGACT 59.534 45.833 0.00 0.00 0.00 3.85
1240 1265 3.445450 TCGGTCTCCTCTGATTTCTTCTG 59.555 47.826 0.00 0.00 0.00 3.02
1273 1298 3.510360 AGTAACAACTGATACTCTGCGGT 59.490 43.478 0.00 0.00 29.16 5.68
1314 1339 2.914908 TGCTGTAGCCCTAGCATCA 58.085 52.632 0.80 0.00 44.36 3.07
1359 1405 8.732746 AAACTATTTTACCTGCGAACATATCT 57.267 30.769 0.00 0.00 0.00 1.98
1363 1409 7.916914 ACTAAACTATTTTACCTGCGAACAT 57.083 32.000 0.00 0.00 0.00 2.71
1370 1416 8.567948 CCATGCCATACTAAACTATTTTACCTG 58.432 37.037 0.00 0.00 0.00 4.00
1411 1457 5.220854 CCAAACAACTCAACATCGAAAGTCT 60.221 40.000 0.00 0.00 0.00 3.24
1418 1465 2.878406 AGGTCCAAACAACTCAACATCG 59.122 45.455 0.00 0.00 0.00 3.84
1441 1490 4.273480 ACAGTCAAAGAAACTCATCAACCG 59.727 41.667 0.00 0.00 0.00 4.44
1489 1539 3.828451 CTCATCAAACCACAACCAATCCT 59.172 43.478 0.00 0.00 0.00 3.24
1688 1756 2.166821 TCATTGCACAATTTGGCACC 57.833 45.000 10.75 0.00 40.23 5.01
1689 1757 4.752661 AAATCATTGCACAATTTGGCAC 57.247 36.364 10.75 0.00 40.23 5.01
1752 1857 7.450074 CCAGCCCACTCATACAATTTAGTATA 58.550 38.462 0.00 0.00 33.12 1.47
1848 1960 2.781403 ATCATTAATTGGGCCAGCCT 57.219 45.000 6.23 0.00 36.10 4.58
1904 2016 3.126343 CACGGCCTGTTAATGTTAGTTCC 59.874 47.826 0.00 0.00 0.00 3.62
1991 2116 9.218525 ACATGGATGCCTAATATATAAGTAGCT 57.781 33.333 0.00 0.00 0.00 3.32
1999 2124 9.931698 AAATGATGACATGGATGCCTAATATAT 57.068 29.630 0.00 0.00 36.79 0.86
2002 2127 8.361889 CAAAAATGATGACATGGATGCCTAATA 58.638 33.333 0.00 0.00 36.79 0.98
2005 2130 5.452216 GCAAAAATGATGACATGGATGCCTA 60.452 40.000 0.00 0.00 36.79 3.93
2006 2131 4.682320 GCAAAAATGATGACATGGATGCCT 60.682 41.667 0.00 0.00 36.79 4.75
2132 2257 1.304381 GGTCATGGCTGCCCTTGAA 60.304 57.895 17.53 0.00 44.19 2.69
2141 2266 6.071165 CCTTTTCTAGAATTTTGGTCATGGCT 60.071 38.462 5.89 0.00 0.00 4.75
2188 2314 1.906574 TCGGAAGGTCAATAGTTGGCT 59.093 47.619 0.00 0.00 35.12 4.75
2238 2369 4.671880 TTGGTCGTTAATTCGTCATTGG 57.328 40.909 0.00 0.00 0.00 3.16
2279 2410 9.890629 AACTTCATAGCACTACAAGAAATATGA 57.109 29.630 5.58 0.00 0.00 2.15
2296 2427 4.990543 TGCAACAAGTCGAACTTCATAG 57.009 40.909 0.00 0.00 36.03 2.23
2297 2428 5.277779 CCTTTGCAACAAGTCGAACTTCATA 60.278 40.000 0.00 0.00 36.03 2.15
2298 2429 4.498009 CCTTTGCAACAAGTCGAACTTCAT 60.498 41.667 0.00 0.00 36.03 2.57
2299 2430 3.181501 CCTTTGCAACAAGTCGAACTTCA 60.182 43.478 0.00 0.00 36.03 3.02
2300 2431 3.363178 CCTTTGCAACAAGTCGAACTTC 58.637 45.455 0.00 0.00 36.03 3.01
2301 2432 2.099098 CCCTTTGCAACAAGTCGAACTT 59.901 45.455 0.00 0.00 39.39 2.66
2302 2433 1.676006 CCCTTTGCAACAAGTCGAACT 59.324 47.619 0.00 0.00 0.00 3.01
2303 2434 1.404035 ACCCTTTGCAACAAGTCGAAC 59.596 47.619 0.00 0.00 0.00 3.95
2304 2435 1.757682 ACCCTTTGCAACAAGTCGAA 58.242 45.000 0.00 0.00 0.00 3.71
2305 2436 1.757682 AACCCTTTGCAACAAGTCGA 58.242 45.000 0.00 0.00 0.00 4.20
2306 2437 2.577449 AAACCCTTTGCAACAAGTCG 57.423 45.000 0.00 0.00 0.00 4.18
2307 2438 2.857748 CGAAAACCCTTTGCAACAAGTC 59.142 45.455 0.00 0.00 0.00 3.01
2308 2439 2.494073 TCGAAAACCCTTTGCAACAAGT 59.506 40.909 0.00 0.00 0.00 3.16
2309 2440 2.857748 GTCGAAAACCCTTTGCAACAAG 59.142 45.455 0.00 0.00 0.00 3.16
2310 2441 2.231478 TGTCGAAAACCCTTTGCAACAA 59.769 40.909 0.00 0.00 0.00 2.83
2311 2442 1.819288 TGTCGAAAACCCTTTGCAACA 59.181 42.857 0.00 0.00 0.00 3.33
2312 2443 2.570442 TGTCGAAAACCCTTTGCAAC 57.430 45.000 0.00 0.00 0.00 4.17
2313 2444 2.494073 ACTTGTCGAAAACCCTTTGCAA 59.506 40.909 0.00 0.00 0.00 4.08
2314 2445 2.096248 ACTTGTCGAAAACCCTTTGCA 58.904 42.857 0.00 0.00 0.00 4.08
2315 2446 2.863401 ACTTGTCGAAAACCCTTTGC 57.137 45.000 0.00 0.00 0.00 3.68
2316 2447 4.364415 TGAACTTGTCGAAAACCCTTTG 57.636 40.909 0.00 0.00 0.00 2.77
2317 2448 4.142249 CCTTGAACTTGTCGAAAACCCTTT 60.142 41.667 0.00 0.00 0.00 3.11
2318 2449 3.380320 CCTTGAACTTGTCGAAAACCCTT 59.620 43.478 0.00 0.00 0.00 3.95
2319 2450 2.949644 CCTTGAACTTGTCGAAAACCCT 59.050 45.455 0.00 0.00 0.00 4.34
2320 2451 2.946990 TCCTTGAACTTGTCGAAAACCC 59.053 45.455 0.00 0.00 0.00 4.11
2321 2452 3.626217 ACTCCTTGAACTTGTCGAAAACC 59.374 43.478 0.00 0.00 0.00 3.27
2322 2453 4.877323 ACTCCTTGAACTTGTCGAAAAC 57.123 40.909 0.00 0.00 0.00 2.43
2323 2454 4.938832 TCAACTCCTTGAACTTGTCGAAAA 59.061 37.500 0.00 0.00 33.20 2.29
2324 2455 4.331717 GTCAACTCCTTGAACTTGTCGAAA 59.668 41.667 0.00 0.00 38.17 3.46
2325 2456 3.869246 GTCAACTCCTTGAACTTGTCGAA 59.131 43.478 0.00 0.00 38.17 3.71
2326 2457 3.132289 AGTCAACTCCTTGAACTTGTCGA 59.868 43.478 0.00 0.00 38.17 4.20
2327 2458 3.458189 AGTCAACTCCTTGAACTTGTCG 58.542 45.455 0.00 0.00 38.17 4.35
2328 2459 4.444720 CGTAGTCAACTCCTTGAACTTGTC 59.555 45.833 0.00 0.00 38.17 3.18
2329 2460 4.098960 TCGTAGTCAACTCCTTGAACTTGT 59.901 41.667 0.00 0.00 38.17 3.16
2330 2461 4.617959 TCGTAGTCAACTCCTTGAACTTG 58.382 43.478 0.00 0.00 38.17 3.16
2331 2462 4.931661 TCGTAGTCAACTCCTTGAACTT 57.068 40.909 0.00 0.00 38.17 2.66
2332 2463 4.523173 TCATCGTAGTCAACTCCTTGAACT 59.477 41.667 0.00 0.00 38.17 3.01
2333 2464 4.806330 TCATCGTAGTCAACTCCTTGAAC 58.194 43.478 0.00 0.00 38.17 3.18
2334 2465 4.765339 TCTCATCGTAGTCAACTCCTTGAA 59.235 41.667 0.00 0.00 38.17 2.69
2335 2466 4.156190 GTCTCATCGTAGTCAACTCCTTGA 59.844 45.833 0.00 0.00 33.76 3.02
2336 2467 4.156922 AGTCTCATCGTAGTCAACTCCTTG 59.843 45.833 0.00 0.00 0.00 3.61
2337 2468 4.337145 AGTCTCATCGTAGTCAACTCCTT 58.663 43.478 0.00 0.00 0.00 3.36
2338 2469 3.958018 AGTCTCATCGTAGTCAACTCCT 58.042 45.455 0.00 0.00 0.00 3.69
2339 2470 4.705337 AAGTCTCATCGTAGTCAACTCC 57.295 45.455 0.00 0.00 0.00 3.85
2340 2471 5.945155 AGAAAGTCTCATCGTAGTCAACTC 58.055 41.667 0.00 0.00 0.00 3.01
2341 2472 5.945155 GAGAAAGTCTCATCGTAGTCAACT 58.055 41.667 0.32 0.00 42.90 3.16
2364 2495 4.813161 CAGACTTAAGCATCACTATGGGTG 59.187 45.833 1.29 0.00 46.60 4.61
2365 2496 4.471386 ACAGACTTAAGCATCACTATGGGT 59.529 41.667 1.29 0.00 33.38 4.51
2366 2497 5.028549 ACAGACTTAAGCATCACTATGGG 57.971 43.478 1.29 0.00 33.38 4.00
2367 2498 5.053145 GGACAGACTTAAGCATCACTATGG 58.947 45.833 1.29 0.00 33.38 2.74
2368 2499 4.742167 CGGACAGACTTAAGCATCACTATG 59.258 45.833 1.29 0.00 36.09 2.23
2378 2509 6.019479 GCTAACATGATTCGGACAGACTTAAG 60.019 42.308 0.00 0.00 0.00 1.85
2380 2511 5.105513 TGCTAACATGATTCGGACAGACTTA 60.106 40.000 0.00 0.00 0.00 2.24
2382 2513 3.195610 TGCTAACATGATTCGGACAGACT 59.804 43.478 0.00 0.00 0.00 3.24
2383 2514 3.521560 TGCTAACATGATTCGGACAGAC 58.478 45.455 0.00 0.00 0.00 3.51
2384 2515 3.885724 TGCTAACATGATTCGGACAGA 57.114 42.857 0.00 0.00 0.00 3.41
2385 2516 5.268544 CAATTGCTAACATGATTCGGACAG 58.731 41.667 0.00 0.00 0.00 3.51
2388 2519 3.066621 GGCAATTGCTAACATGATTCGGA 59.933 43.478 28.42 0.00 41.70 4.55
2389 2520 3.374745 GGCAATTGCTAACATGATTCGG 58.625 45.455 28.42 0.00 41.70 4.30
2390 2521 3.038017 CGGCAATTGCTAACATGATTCG 58.962 45.455 28.42 15.73 41.70 3.34
2391 2522 2.791004 GCGGCAATTGCTAACATGATTC 59.209 45.455 28.42 8.02 41.70 2.52
2392 2523 2.166050 TGCGGCAATTGCTAACATGATT 59.834 40.909 28.42 0.00 41.70 2.57
2393 2524 1.750206 TGCGGCAATTGCTAACATGAT 59.250 42.857 28.42 0.00 41.70 2.45
2394 2525 1.172175 TGCGGCAATTGCTAACATGA 58.828 45.000 28.42 4.79 41.70 3.07
2395 2526 2.212869 ATGCGGCAATTGCTAACATG 57.787 45.000 28.42 13.10 41.70 3.21
2396 2527 2.965572 AATGCGGCAATTGCTAACAT 57.034 40.000 28.42 23.67 41.70 2.71
2397 2528 2.739885 AAATGCGGCAATTGCTAACA 57.260 40.000 28.42 22.65 41.70 2.41
2398 2529 4.803088 TCATAAAATGCGGCAATTGCTAAC 59.197 37.500 28.42 18.22 41.70 2.34
2399 2530 5.003692 TCATAAAATGCGGCAATTGCTAA 57.996 34.783 28.42 15.26 41.70 3.09
2400 2531 4.645762 TCATAAAATGCGGCAATTGCTA 57.354 36.364 28.42 16.12 41.70 3.49
2401 2532 3.523606 TCATAAAATGCGGCAATTGCT 57.476 38.095 28.42 10.61 41.70 3.91
2402 2533 4.799419 AATCATAAAATGCGGCAATTGC 57.201 36.364 22.47 22.47 41.14 3.56
2403 2534 7.640616 TCATAATCATAAAATGCGGCAATTG 57.359 32.000 6.82 0.00 0.00 2.32
2404 2535 8.659925 TTTCATAATCATAAAATGCGGCAATT 57.340 26.923 6.82 0.87 0.00 2.32
2405 2536 8.836268 ATTTCATAATCATAAAATGCGGCAAT 57.164 26.923 6.82 0.00 0.00 3.56
2406 2537 8.143193 AGATTTCATAATCATAAAATGCGGCAA 58.857 29.630 6.82 0.00 42.18 4.52
2407 2538 7.595875 CAGATTTCATAATCATAAAATGCGGCA 59.404 33.333 4.58 4.58 42.18 5.69
2408 2539 7.062605 CCAGATTTCATAATCATAAAATGCGGC 59.937 37.037 0.00 0.00 42.18 6.53
2409 2540 7.062605 GCCAGATTTCATAATCATAAAATGCGG 59.937 37.037 0.00 0.00 42.18 5.69
2410 2541 7.595875 TGCCAGATTTCATAATCATAAAATGCG 59.404 33.333 0.00 0.00 42.18 4.73
2411 2542 8.821147 TGCCAGATTTCATAATCATAAAATGC 57.179 30.769 0.00 0.00 42.18 3.56
2415 2546 9.767228 CCATTTGCCAGATTTCATAATCATAAA 57.233 29.630 0.00 0.00 42.18 1.40
2416 2547 7.874016 GCCATTTGCCAGATTTCATAATCATAA 59.126 33.333 0.00 0.00 42.18 1.90
2417 2548 7.233962 AGCCATTTGCCAGATTTCATAATCATA 59.766 33.333 0.00 0.00 40.94 2.15
2418 2549 6.042781 AGCCATTTGCCAGATTTCATAATCAT 59.957 34.615 0.00 0.00 40.94 2.45
2419 2550 5.364446 AGCCATTTGCCAGATTTCATAATCA 59.636 36.000 0.00 0.00 40.94 2.57
2420 2551 5.694910 CAGCCATTTGCCAGATTTCATAATC 59.305 40.000 0.00 0.00 42.71 1.75
2421 2552 5.129815 ACAGCCATTTGCCAGATTTCATAAT 59.870 36.000 0.00 0.00 42.71 1.28
2422 2553 4.467082 ACAGCCATTTGCCAGATTTCATAA 59.533 37.500 0.00 0.00 42.71 1.90
2423 2554 4.025360 ACAGCCATTTGCCAGATTTCATA 58.975 39.130 0.00 0.00 42.71 2.15
2424 2555 2.835764 ACAGCCATTTGCCAGATTTCAT 59.164 40.909 0.00 0.00 42.71 2.57
2425 2556 2.231964 GACAGCCATTTGCCAGATTTCA 59.768 45.455 0.00 0.00 42.71 2.69
2426 2557 2.231964 TGACAGCCATTTGCCAGATTTC 59.768 45.455 0.00 0.00 42.71 2.17
2427 2558 2.250031 TGACAGCCATTTGCCAGATTT 58.750 42.857 0.00 0.00 42.71 2.17
2428 2559 1.927487 TGACAGCCATTTGCCAGATT 58.073 45.000 0.00 0.00 42.71 2.40
2429 2560 1.927487 TTGACAGCCATTTGCCAGAT 58.073 45.000 0.00 0.00 42.71 2.90
2430 2561 1.702182 TTTGACAGCCATTTGCCAGA 58.298 45.000 0.00 0.00 42.71 3.86
2431 2562 2.137523 GTTTTGACAGCCATTTGCCAG 58.862 47.619 0.00 0.00 42.71 4.85
2432 2563 1.761784 AGTTTTGACAGCCATTTGCCA 59.238 42.857 0.00 0.00 42.71 4.92
2433 2564 2.137523 CAGTTTTGACAGCCATTTGCC 58.862 47.619 0.00 0.00 42.71 4.52
2434 2565 1.528161 GCAGTTTTGACAGCCATTTGC 59.472 47.619 0.00 0.00 41.71 3.68
2435 2566 2.798283 CTGCAGTTTTGACAGCCATTTG 59.202 45.455 5.25 0.00 0.00 2.32
2436 2567 2.431782 ACTGCAGTTTTGACAGCCATTT 59.568 40.909 15.25 0.00 34.12 2.32
2437 2568 2.034124 ACTGCAGTTTTGACAGCCATT 58.966 42.857 15.25 0.00 34.12 3.16
2438 2569 1.610522 GACTGCAGTTTTGACAGCCAT 59.389 47.619 22.65 0.00 34.12 4.40
2439 2570 1.024271 GACTGCAGTTTTGACAGCCA 58.976 50.000 22.65 0.00 34.12 4.75
2440 2571 1.312815 AGACTGCAGTTTTGACAGCC 58.687 50.000 22.65 4.43 34.12 4.85
2441 2572 3.427161 AAAGACTGCAGTTTTGACAGC 57.573 42.857 22.65 5.23 34.12 4.40
2442 2573 5.916883 CCATTAAAGACTGCAGTTTTGACAG 59.083 40.000 22.65 12.32 35.74 3.51
2443 2574 5.592282 TCCATTAAAGACTGCAGTTTTGACA 59.408 36.000 22.65 9.47 0.00 3.58
2444 2575 6.072112 TCCATTAAAGACTGCAGTTTTGAC 57.928 37.500 22.65 7.67 0.00 3.18
2445 2576 6.899393 ATCCATTAAAGACTGCAGTTTTGA 57.101 33.333 22.65 18.19 0.00 2.69
2446 2577 7.869429 AGAAATCCATTAAAGACTGCAGTTTTG 59.131 33.333 22.65 10.19 0.00 2.44
2447 2578 7.955918 AGAAATCCATTAAAGACTGCAGTTTT 58.044 30.769 22.65 19.29 0.00 2.43
2448 2579 7.530426 AGAAATCCATTAAAGACTGCAGTTT 57.470 32.000 22.65 13.35 0.00 2.66
2449 2580 7.530426 AAGAAATCCATTAAAGACTGCAGTT 57.470 32.000 22.65 7.90 0.00 3.16
2450 2581 8.635765 TTAAGAAATCCATTAAAGACTGCAGT 57.364 30.769 21.88 21.88 0.00 4.40
2451 2582 9.565213 CTTTAAGAAATCCATTAAAGACTGCAG 57.435 33.333 13.48 13.48 45.49 4.41
2452 2583 9.295825 TCTTTAAGAAATCCATTAAAGACTGCA 57.704 29.630 13.38 0.00 45.87 4.41
2482 2613 8.438676 AACCTTCTAGTTGCATCATATACAAC 57.561 34.615 0.00 0.00 43.12 3.32
2483 2614 9.461312 AAAACCTTCTAGTTGCATCATATACAA 57.539 29.630 0.00 0.00 0.00 2.41
2484 2615 8.892723 CAAAACCTTCTAGTTGCATCATATACA 58.107 33.333 0.00 0.00 0.00 2.29
2485 2616 8.893727 ACAAAACCTTCTAGTTGCATCATATAC 58.106 33.333 0.00 0.00 0.00 1.47
2486 2617 9.109393 GACAAAACCTTCTAGTTGCATCATATA 57.891 33.333 0.00 0.00 0.00 0.86
2487 2618 7.201644 CGACAAAACCTTCTAGTTGCATCATAT 60.202 37.037 0.00 0.00 0.00 1.78
2488 2619 6.092122 CGACAAAACCTTCTAGTTGCATCATA 59.908 38.462 0.00 0.00 0.00 2.15
2489 2620 5.106555 CGACAAAACCTTCTAGTTGCATCAT 60.107 40.000 0.00 0.00 0.00 2.45
2490 2621 4.213270 CGACAAAACCTTCTAGTTGCATCA 59.787 41.667 0.00 0.00 0.00 3.07
2491 2622 4.451096 TCGACAAAACCTTCTAGTTGCATC 59.549 41.667 0.00 0.00 0.00 3.91
2492 2623 4.385825 TCGACAAAACCTTCTAGTTGCAT 58.614 39.130 0.00 0.00 0.00 3.96
2493 2624 3.799366 TCGACAAAACCTTCTAGTTGCA 58.201 40.909 0.00 0.00 0.00 4.08
2494 2625 4.142881 GGATCGACAAAACCTTCTAGTTGC 60.143 45.833 0.00 0.00 0.00 4.17
2495 2626 5.238583 AGGATCGACAAAACCTTCTAGTTG 58.761 41.667 0.00 0.00 0.00 3.16
2496 2627 5.485209 AGGATCGACAAAACCTTCTAGTT 57.515 39.130 0.00 0.00 0.00 2.24
2497 2628 6.600882 TTAGGATCGACAAAACCTTCTAGT 57.399 37.500 0.00 0.00 34.42 2.57
2498 2629 6.535508 CCTTTAGGATCGACAAAACCTTCTAG 59.464 42.308 0.00 0.00 37.39 2.43
2499 2630 6.013984 ACCTTTAGGATCGACAAAACCTTCTA 60.014 38.462 2.06 0.00 38.94 2.10
2500 2631 5.221864 ACCTTTAGGATCGACAAAACCTTCT 60.222 40.000 2.06 0.00 38.94 2.85
2501 2632 5.001874 ACCTTTAGGATCGACAAAACCTTC 58.998 41.667 2.06 0.00 38.94 3.46
2502 2633 4.760204 CACCTTTAGGATCGACAAAACCTT 59.240 41.667 2.06 0.00 38.94 3.50
2503 2634 4.324267 CACCTTTAGGATCGACAAAACCT 58.676 43.478 2.06 0.00 38.94 3.50
2504 2635 3.119955 GCACCTTTAGGATCGACAAAACC 60.120 47.826 2.06 0.00 38.94 3.27
2505 2636 3.751698 AGCACCTTTAGGATCGACAAAAC 59.248 43.478 2.06 0.00 38.94 2.43
2506 2637 4.015872 AGCACCTTTAGGATCGACAAAA 57.984 40.909 2.06 0.00 38.94 2.44
2507 2638 3.695830 AGCACCTTTAGGATCGACAAA 57.304 42.857 2.06 0.00 38.94 2.83
2508 2639 4.020928 TGTTAGCACCTTTAGGATCGACAA 60.021 41.667 2.06 0.00 38.94 3.18
2509 2640 3.512329 TGTTAGCACCTTTAGGATCGACA 59.488 43.478 2.06 2.62 38.94 4.35
2510 2641 4.119442 TGTTAGCACCTTTAGGATCGAC 57.881 45.455 2.06 0.40 38.94 4.20
2511 2642 4.811969 TTGTTAGCACCTTTAGGATCGA 57.188 40.909 2.06 0.00 38.94 3.59
2512 2643 4.935808 ACTTTGTTAGCACCTTTAGGATCG 59.064 41.667 2.06 0.00 38.94 3.69
2513 2644 5.705905 ACACTTTGTTAGCACCTTTAGGATC 59.294 40.000 2.06 0.00 38.94 3.36
2514 2645 5.473504 CACACTTTGTTAGCACCTTTAGGAT 59.526 40.000 2.06 0.00 38.94 3.24
2515 2646 4.819630 CACACTTTGTTAGCACCTTTAGGA 59.180 41.667 2.06 0.00 38.94 2.94
2516 2647 4.556699 GCACACTTTGTTAGCACCTTTAGG 60.557 45.833 0.00 0.00 42.17 2.69
2517 2648 4.537015 GCACACTTTGTTAGCACCTTTAG 58.463 43.478 0.00 0.00 0.00 1.85
2518 2649 4.561735 GCACACTTTGTTAGCACCTTTA 57.438 40.909 0.00 0.00 0.00 1.85
2519 2650 3.436700 GCACACTTTGTTAGCACCTTT 57.563 42.857 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.