Multiple sequence alignment - TraesCS4A01G138600

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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 TraesCS4A01G138600 chr4A 100.000 2507 0 0 1 2507 205640573 205643079 0.000000e+00 4630.0
1 TraesCS4A01G138600 chr4A 92.685 998 54 3 1370 2348 205634088 205635085 0.000000e+00 1421.0
2 TraesCS4A01G138600 chr4A 90.494 547 35 10 1727 2260 409256844 409257386 0.000000e+00 706.0
3 TraesCS4A01G138600 chr4A 84.421 475 55 14 1 465 186728807 186729272 1.370000e-122 449.0
4 TraesCS4A01G138600 chr4A 91.739 230 17 2 570 797 404690445 404690216 4.020000e-83 318.0
5 TraesCS4A01G138600 chr4A 90.870 230 19 2 570 797 404671600 404671829 8.710000e-80 307.0
6 TraesCS4A01G138600 chr4A 88.372 215 13 6 1368 1571 286176119 286176332 5.350000e-62 248.0
7 TraesCS4A01G138600 chr4A 91.250 160 13 1 2349 2507 492740445 492740286 1.510000e-52 217.0
8 TraesCS4A01G138600 chr4A 91.603 131 9 2 1368 1496 261283305 261283175 1.980000e-41 180.0
9 TraesCS4A01G138600 chr4A 91.200 125 8 3 1374 1496 274463476 274463599 1.540000e-37 167.0
10 TraesCS4A01G138600 chr4A 89.189 111 11 1 822 932 270684860 270684969 1.210000e-28 137.0
11 TraesCS4A01G138600 chr4A 90.000 70 7 0 1640 1709 236054305 236054374 9.550000e-15 91.6
12 TraesCS4A01G138600 chr4A 94.340 53 2 1 1528 1580 538690895 538690946 2.070000e-11 80.5
13 TraesCS4A01G138600 chr2A 92.579 1361 77 2 14 1372 350309544 350310882 0.000000e+00 1932.0
14 TraesCS4A01G138600 chr2A 91.956 1007 57 6 1365 2348 350310945 350311950 0.000000e+00 1389.0
15 TraesCS4A01G138600 chr2A 90.875 526 36 8 1727 2245 343827585 343828105 0.000000e+00 695.0
16 TraesCS4A01G138600 chr2A 90.018 541 43 7 1727 2260 270446955 270447491 0.000000e+00 689.0
17 TraesCS4A01G138600 chr2A 87.823 542 50 12 1727 2261 181714269 181713737 2.740000e-174 621.0
18 TraesCS4A01G138600 chr2A 76.731 722 114 41 1666 2348 277913429 277914135 1.100000e-93 353.0
19 TraesCS4A01G138600 chr2A 76.593 722 115 41 1666 2348 277905243 277905949 5.130000e-92 348.0
20 TraesCS4A01G138600 chr2A 76.316 722 118 39 1666 2348 93770122 93770829 1.110000e-88 337.0
21 TraesCS4A01G138600 chr2A 76.039 722 121 38 1666 2348 93778308 93779016 6.690000e-86 327.0
22 TraesCS4A01G138600 chr2A 87.755 245 28 2 571 813 416734520 416734764 4.080000e-73 285.0
23 TraesCS4A01G138600 chr2A 76.789 573 88 35 3 555 767922089 767922636 1.900000e-71 279.0
24 TraesCS4A01G138600 chr2A 93.082 159 11 0 2349 2507 737084913 737085071 1.500000e-57 233.0
25 TraesCS4A01G138600 chr2A 91.304 161 12 1 2349 2507 204581911 204582071 4.200000e-53 219.0
26 TraesCS4A01G138600 chr2A 89.394 132 12 2 1208 1338 353297930 353297800 5.550000e-37 165.0
27 TraesCS4A01G138600 chr2A 91.525 118 9 1 1256 1372 52415457 52415340 7.180000e-36 161.0
28 TraesCS4A01G138600 chr2A 91.525 118 9 1 1256 1372 581536441 581536558 7.180000e-36 161.0
29 TraesCS4A01G138600 chr2A 89.831 118 11 1 1256 1372 169102242 169102359 1.550000e-32 150.0
30 TraesCS4A01G138600 chr2A 88.350 103 11 1 1666 1768 547105702 547105803 3.390000e-24 122.0
31 TraesCS4A01G138600 chr2A 89.474 95 10 0 1674 1768 546904569 546904663 1.220000e-23 121.0
32 TraesCS4A01G138600 chr5A 93.035 804 54 2 570 1372 145271015 145271817 0.000000e+00 1173.0
33 TraesCS4A01G138600 chr5A 92.584 445 32 1 826 1270 57247013 57246570 2.720000e-179 638.0
34 TraesCS4A01G138600 chr5A 92.290 441 33 1 830 1270 57282415 57281976 2.120000e-175 625.0
35 TraesCS4A01G138600 chr5A 91.031 446 38 2 825 1270 57314565 57314122 3.570000e-168 601.0
36 TraesCS4A01G138600 chr5A 89.247 465 36 11 1 456 66503847 66503388 1.010000e-158 569.0
37 TraesCS4A01G138600 chr5A 89.224 464 38 9 1 456 66511891 66511432 1.010000e-158 569.0
38 TraesCS4A01G138600 chr5A 85.529 463 55 8 9 466 579274365 579274820 8.120000e-130 473.0
39 TraesCS4A01G138600 chr5A 86.009 436 49 8 36 466 579258452 579258880 8.170000e-125 457.0
40 TraesCS4A01G138600 chr5A 80.174 459 64 15 1905 2348 403414203 403414649 4.020000e-83 318.0
41 TraesCS4A01G138600 chr5A 89.610 231 22 2 556 784 349308573 349308343 2.440000e-75 292.0
42 TraesCS4A01G138600 chr5A 75.355 633 101 38 1669 2260 128289344 128288726 1.150000e-63 254.0
43 TraesCS4A01G138600 chr5A 92.405 158 12 0 2350 2507 158055549 158055706 2.510000e-55 226.0
44 TraesCS4A01G138600 chr5A 94.776 134 6 1 1369 1501 638550103 638550236 9.090000e-50 207.0
45 TraesCS4A01G138600 chr5A 91.333 150 12 1 2199 2348 433500462 433500314 1.180000e-48 204.0
46 TraesCS4A01G138600 chr5A 90.132 152 14 1 2197 2348 453314266 453314416 1.970000e-46 196.0
47 TraesCS4A01G138600 chr3A 89.706 612 41 14 1640 2245 407834702 407835297 0.000000e+00 761.0
48 TraesCS4A01G138600 chr3A 87.816 632 48 9 1640 2245 407826913 407827541 0.000000e+00 713.0
49 TraesCS4A01G138600 chr3A 86.503 652 74 11 14 660 395223978 395224620 0.000000e+00 704.0
50 TraesCS4A01G138600 chr3A 86.043 652 77 11 14 660 395215934 395216576 0.000000e+00 688.0
51 TraesCS4A01G138600 chr3A 93.211 383 25 1 888 1270 562690010 562689629 1.680000e-156 562.0
52 TraesCS4A01G138600 chr3A 90.862 383 35 0 888 1270 562698256 562697874 4.780000e-142 514.0
53 TraesCS4A01G138600 chr3A 81.942 515 82 9 1840 2348 150645091 150644582 2.300000e-115 425.0
54 TraesCS4A01G138600 chr3A 79.070 559 87 21 1806 2348 434707059 434706515 8.530000e-95 357.0
55 TraesCS4A01G138600 chr3A 77.565 575 89 29 1 557 371174386 371174938 6.730000e-81 311.0
56 TraesCS4A01G138600 chr3A 77.368 570 97 24 1 555 201152878 201153430 2.420000e-80 309.0
57 TraesCS4A01G138600 chr3A 77.470 577 81 36 1 555 734274307 734274856 1.460000e-77 300.0
58 TraesCS4A01G138600 chr3A 88.525 244 26 2 556 797 331447325 331447568 6.780000e-76 294.0
59 TraesCS4A01G138600 chr3A 89.177 231 23 2 570 798 331396075 331396305 1.130000e-73 287.0
60 TraesCS4A01G138600 chr3A 78.478 460 73 20 1913 2359 378670563 378670117 6.830000e-71 278.0
61 TraesCS4A01G138600 chr3A 90.000 140 10 4 2209 2348 222703647 222703512 7.130000e-41 178.0
62 TraesCS4A01G138600 chr3A 89.394 132 9 5 1210 1338 403938119 403938248 7.180000e-36 161.0
63 TraesCS4A01G138600 chr3A 92.105 114 8 1 1226 1338 403946368 403946481 2.580000e-35 159.0
64 TraesCS4A01G138600 chr3A 92.784 97 5 2 741 836 345556270 345556175 3.360000e-29 139.0
65 TraesCS4A01G138600 chr3A 91.667 60 2 2 1485 1544 201458070 201458126 2.070000e-11 80.5
66 TraesCS4A01G138600 chr3A 97.059 34 1 0 830 863 389746986 389747019 9.690000e-05 58.4
67 TraesCS4A01G138600 chr1A 87.092 643 58 16 1727 2348 507848703 507848065 0.000000e+00 704.0
68 TraesCS4A01G138600 chr1A 87.751 547 50 10 1727 2260 507856121 507855579 7.620000e-175 623.0
69 TraesCS4A01G138600 chr1A 90.634 331 25 3 1000 1330 126918088 126917764 3.830000e-118 435.0
70 TraesCS4A01G138600 chr1A 83.824 476 57 18 1 465 423609747 423609281 3.830000e-118 435.0
71 TraesCS4A01G138600 chr1A 91.038 212 13 5 1365 1571 293223194 293223404 5.280000e-72 281.0
72 TraesCS4A01G138600 chr1A 88.312 231 25 2 556 784 301935979 301936209 2.460000e-70 276.0
73 TraesCS4A01G138600 chr1A 90.909 209 13 5 1368 1571 543273669 543273462 2.460000e-70 276.0
74 TraesCS4A01G138600 chr1A 93.370 181 11 1 1368 1548 543281520 543281341 1.480000e-67 267.0
75 TraesCS4A01G138600 chr1A 75.991 429 77 17 138 555 348758399 348757986 5.470000e-47 198.0
76 TraesCS4A01G138600 chr1A 87.288 118 14 1 1256 1372 128729213 128729096 1.560000e-27 134.0
77 TraesCS4A01G138600 chr1A 96.053 76 3 0 1368 1443 52377962 52377887 9.420000e-25 124.0
78 TraesCS4A01G138600 chr1A 92.647 68 5 0 1642 1709 166990249 166990182 5.710000e-17 99.0
79 TraesCS4A01G138600 chr1A 96.154 52 2 0 1529 1580 185408616 185408667 4.440000e-13 86.1
80 TraesCS4A01G138600 chr1A 94.231 52 3 0 1529 1580 185416442 185416493 2.070000e-11 80.5
81 TraesCS4A01G138600 chr7A 90.030 331 27 3 1000 1330 186244526 186244850 8.290000e-115 424.0
82 TraesCS4A01G138600 chr7A 76.381 724 119 38 1666 2351 109573247 109573956 2.390000e-90 342.0
83 TraesCS4A01G138600 chr7A 92.453 159 12 0 2349 2507 325906125 325906283 6.980000e-56 228.0
84 TraesCS4A01G138600 chr7A 89.130 92 10 0 1677 1768 23919431 23919340 5.670000e-22 115.0
85 TraesCS4A01G138600 chr7A 88.043 92 11 0 1677 1768 24107671 24107580 2.640000e-20 110.0
86 TraesCS4A01G138600 chr7A 88.043 92 11 0 1677 1768 24115529 24115438 2.640000e-20 110.0
87 TraesCS4A01G138600 chr7A 89.552 67 6 1 1479 1544 233702628 233702694 1.600000e-12 84.2
88 TraesCS4A01G138600 chr7A 91.525 59 4 1 1528 1586 203641328 203641271 2.070000e-11 80.5
89 TraesCS4A01G138600 chr7A 95.833 48 1 1 1533 1580 586715624 586715578 2.670000e-10 76.8
90 TraesCS4A01G138600 chr6A 90.909 209 14 4 1368 1571 297360461 297360253 2.460000e-70 276.0
91 TraesCS4A01G138600 chr6A 91.772 158 12 1 2351 2507 259917738 259917581 4.200000e-53 219.0
92 TraesCS4A01G138600 chr6A 91.603 131 11 0 1208 1338 182799929 182799799 5.510000e-42 182.0
93 TraesCS4A01G138600 chr6A 87.342 158 18 2 849 1006 52110440 52110595 1.980000e-41 180.0
94 TraesCS4A01G138600 chr6A 85.443 158 21 2 849 1006 52074670 52074825 2.000000e-36 163.0
95 TraesCS4A01G138600 chr6A 92.537 67 5 0 1643 1709 262148556 262148490 2.050000e-16 97.1
96 TraesCS4A01G138600 chr6A 96.154 52 2 0 1529 1580 421133450 421133399 4.440000e-13 86.1
97 TraesCS4A01G138600 chr6A 94.231 52 3 0 1529 1580 421125267 421125216 2.070000e-11 80.5
98 TraesCS4A01G138600 chr3D 91.875 160 12 1 2349 2507 517952546 517952705 3.250000e-54 222.0
99 TraesCS4A01G138600 chr5D 91.195 159 14 0 2349 2507 258624346 258624188 1.510000e-52 217.0
100 TraesCS4A01G138600 chr2D 91.250 160 13 1 2349 2507 156654429 156654270 1.510000e-52 217.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G138600 chr4A 205640573 205643079 2506 False 4630.0 4630 100.0000 1 2507 1 chr4A.!!$F3 2506
1 TraesCS4A01G138600 chr4A 205634088 205635085 997 False 1421.0 1421 92.6850 1370 2348 1 chr4A.!!$F2 978
2 TraesCS4A01G138600 chr4A 409256844 409257386 542 False 706.0 706 90.4940 1727 2260 1 chr4A.!!$F9 533
3 TraesCS4A01G138600 chr2A 350309544 350311950 2406 False 1660.5 1932 92.2675 14 2348 2 chr2A.!!$F15 2334
4 TraesCS4A01G138600 chr2A 343827585 343828105 520 False 695.0 695 90.8750 1727 2245 1 chr2A.!!$F8 518
5 TraesCS4A01G138600 chr2A 270446955 270447491 536 False 689.0 689 90.0180 1727 2260 1 chr2A.!!$F5 533
6 TraesCS4A01G138600 chr2A 181713737 181714269 532 True 621.0 621 87.8230 1727 2261 1 chr2A.!!$R2 534
7 TraesCS4A01G138600 chr2A 277913429 277914135 706 False 353.0 353 76.7310 1666 2348 1 chr2A.!!$F7 682
8 TraesCS4A01G138600 chr2A 277905243 277905949 706 False 348.0 348 76.5930 1666 2348 1 chr2A.!!$F6 682
9 TraesCS4A01G138600 chr2A 93770122 93770829 707 False 337.0 337 76.3160 1666 2348 1 chr2A.!!$F1 682
10 TraesCS4A01G138600 chr2A 93778308 93779016 708 False 327.0 327 76.0390 1666 2348 1 chr2A.!!$F2 682
11 TraesCS4A01G138600 chr2A 767922089 767922636 547 False 279.0 279 76.7890 3 555 1 chr2A.!!$F14 552
12 TraesCS4A01G138600 chr5A 145271015 145271817 802 False 1173.0 1173 93.0350 570 1372 1 chr5A.!!$F1 802
13 TraesCS4A01G138600 chr5A 128288726 128289344 618 True 254.0 254 75.3550 1669 2260 1 chr5A.!!$R6 591
14 TraesCS4A01G138600 chr3A 407834702 407835297 595 False 761.0 761 89.7060 1640 2245 1 chr3A.!!$F12 605
15 TraesCS4A01G138600 chr3A 407826913 407827541 628 False 713.0 713 87.8160 1640 2245 1 chr3A.!!$F11 605
16 TraesCS4A01G138600 chr3A 395223978 395224620 642 False 704.0 704 86.5030 14 660 1 chr3A.!!$F8 646
17 TraesCS4A01G138600 chr3A 395215934 395216576 642 False 688.0 688 86.0430 14 660 1 chr3A.!!$F7 646
18 TraesCS4A01G138600 chr3A 150644582 150645091 509 True 425.0 425 81.9420 1840 2348 1 chr3A.!!$R1 508
19 TraesCS4A01G138600 chr3A 434706515 434707059 544 True 357.0 357 79.0700 1806 2348 1 chr3A.!!$R5 542
20 TraesCS4A01G138600 chr3A 371174386 371174938 552 False 311.0 311 77.5650 1 557 1 chr3A.!!$F5 556
21 TraesCS4A01G138600 chr3A 201152878 201153430 552 False 309.0 309 77.3680 1 555 1 chr3A.!!$F1 554
22 TraesCS4A01G138600 chr3A 734274307 734274856 549 False 300.0 300 77.4700 1 555 1 chr3A.!!$F13 554
23 TraesCS4A01G138600 chr1A 507848065 507848703 638 True 704.0 704 87.0920 1727 2348 1 chr1A.!!$R7 621
24 TraesCS4A01G138600 chr1A 507855579 507856121 542 True 623.0 623 87.7510 1727 2260 1 chr1A.!!$R8 533
25 TraesCS4A01G138600 chr7A 109573247 109573956 709 False 342.0 342 76.3810 1666 2351 1 chr7A.!!$F1 685

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
262 269 0.257039 GCAAGATGGTGGGGTGATCT 59.743 55.0 0.0 0.0 0.0 2.75 F
711 738 0.322546 GGTTCAAGGGTCTCGGCAAT 60.323 55.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1533 0.338120 CCTCTCCTCTCTCCCACCTT 59.662 60.0 0.00 0.0 0.00 3.50 R
2382 2607 0.108138 CGGAGATCGTGCCTCCTTTT 60.108 55.0 14.86 0.0 46.15 2.27 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
62 64 7.013178 TGTTATTAACATGATGCGGATGACATT 59.987 33.333 5.14 0.00 36.25 2.71
92 97 7.929159 AGTTTTATGCAATTTGGAAAAGTTGG 58.071 30.769 0.00 0.00 0.00 3.77
131 136 1.401552 CATTGTCATCGTGGCGGAAAT 59.598 47.619 0.00 0.00 0.00 2.17
156 162 1.512156 GGGTGCCACGACAACGAATT 61.512 55.000 0.00 0.00 42.66 2.17
242 249 2.261671 GTGATGGGAGCGTGTCGT 59.738 61.111 0.00 0.00 0.00 4.34
262 269 0.257039 GCAAGATGGTGGGGTGATCT 59.743 55.000 0.00 0.00 0.00 2.75
291 306 1.291272 GTTCCCACGAGTTAGCGGT 59.709 57.895 0.00 0.00 35.12 5.68
294 309 1.033746 TCCCACGAGTTAGCGGTAGG 61.034 60.000 0.00 0.00 35.12 3.18
327 342 1.237285 GCAAGTGACAACTCGGGCAT 61.237 55.000 0.00 0.00 34.77 4.40
329 344 1.237285 AAGTGACAACTCGGGCATGC 61.237 55.000 9.90 9.90 34.77 4.06
368 391 5.393124 CAACTCATACATCACGCAACATTT 58.607 37.500 0.00 0.00 0.00 2.32
416 441 2.093500 ACCTCTGAAGCGTGCATTATCA 60.093 45.455 0.00 0.00 0.00 2.15
425 450 1.665679 CGTGCATTATCAGAGCGGTTT 59.334 47.619 0.00 0.00 0.00 3.27
557 582 0.452987 GTCGATGGTAGTGGTACGCA 59.547 55.000 0.00 0.00 44.14 5.24
568 593 2.093181 AGTGGTACGCATTTCATAGCCA 60.093 45.455 0.00 0.00 44.14 4.75
601 626 2.224209 ACGTTTCGAAGGTGGACTTGAT 60.224 45.455 0.00 0.00 40.21 2.57
709 736 1.701031 TTGGTTCAAGGGTCTCGGCA 61.701 55.000 0.00 0.00 0.00 5.69
711 738 0.322546 GGTTCAAGGGTCTCGGCAAT 60.323 55.000 0.00 0.00 0.00 3.56
725 752 2.098607 TCGGCAATGGTAGTCGTTCTAG 59.901 50.000 0.00 0.00 0.00 2.43
726 753 2.798499 CGGCAATGGTAGTCGTTCTAGG 60.798 54.545 0.00 0.00 0.00 3.02
727 754 2.202566 GCAATGGTAGTCGTTCTAGGC 58.797 52.381 0.00 0.00 0.00 3.93
728 755 2.418197 GCAATGGTAGTCGTTCTAGGCA 60.418 50.000 0.00 0.00 0.00 4.75
729 756 3.741388 GCAATGGTAGTCGTTCTAGGCAT 60.741 47.826 0.00 0.00 0.00 4.40
730 757 4.051922 CAATGGTAGTCGTTCTAGGCATC 58.948 47.826 0.00 0.00 0.00 3.91
731 758 1.674441 TGGTAGTCGTTCTAGGCATCG 59.326 52.381 0.00 0.00 0.00 3.84
732 759 1.001597 GGTAGTCGTTCTAGGCATCGG 60.002 57.143 0.00 0.00 0.00 4.18
733 760 1.001597 GTAGTCGTTCTAGGCATCGGG 60.002 57.143 0.00 0.00 0.00 5.14
734 761 1.591863 GTCGTTCTAGGCATCGGGC 60.592 63.158 0.00 0.00 43.74 6.13
746 773 4.349682 TCGGGCATCGAGGTACTT 57.650 55.556 0.00 0.00 43.74 2.24
843 892 1.120530 GTCGGGGTACATGATGGTCT 58.879 55.000 0.00 0.00 0.00 3.85
860 909 0.616395 TCTGGGTCTTGGCGTATCCA 60.616 55.000 0.00 0.00 44.85 3.41
908 957 1.001048 TCGTGGTACTTGTCGTTCCAG 60.001 52.381 0.00 0.00 42.80 3.86
914 963 3.056035 GGTACTTGTCGTTCCAGGAAGAT 60.056 47.826 0.54 0.00 33.58 2.40
1032 1081 1.229177 TGGTGGCTGTGAGCTCCTA 60.229 57.895 12.15 0.00 41.99 2.94
1098 1147 1.144057 GGAGGTCGATGCGGTCAAT 59.856 57.895 0.00 0.00 0.00 2.57
1112 1161 1.538047 GTCAATGGGAAGAGCAGCAA 58.462 50.000 0.00 0.00 0.00 3.91
1115 1164 1.822990 CAATGGGAAGAGCAGCAACAT 59.177 47.619 0.00 0.00 0.00 2.71
1145 1194 2.359850 GGCATCGGACTTGGCACA 60.360 61.111 0.77 0.00 39.31 4.57
1158 1207 1.352622 TGGCACAGAACAAGGGAGGT 61.353 55.000 0.00 0.00 0.00 3.85
1206 1255 2.032681 GCGGGACTTGAGGCACTT 59.967 61.111 0.00 0.00 41.55 3.16
1280 1329 2.594303 CGAAGCAAGGTGGTGGCA 60.594 61.111 0.00 0.00 0.00 4.92
1287 1337 2.541907 AAGGTGGTGGCATGGCTCT 61.542 57.895 21.08 7.24 0.00 4.09
1365 1415 2.930562 GGCCAGGTGAGGTCCAGT 60.931 66.667 0.00 0.00 0.00 4.00
1580 1700 1.411651 GGGATCGAGGGAAAGAGGGG 61.412 65.000 0.00 0.00 0.00 4.79
1655 1775 1.430369 AAAGACTGGGCCTTGGAGCT 61.430 55.000 4.53 0.00 0.00 4.09
1656 1776 1.430369 AAGACTGGGCCTTGGAGCTT 61.430 55.000 4.53 0.00 0.00 3.74
1699 1819 2.521708 GCCTTGGCCAACTGGTGT 60.522 61.111 21.47 0.00 37.57 4.16
1705 1825 2.519302 GCCAACTGGTGTGGCTGT 60.519 61.111 8.18 0.00 44.72 4.40
1796 1964 6.017192 CCCATTTTAAGGCAAAACAGAAAAGG 60.017 38.462 0.00 0.00 38.90 3.11
1879 2059 5.049198 TCGCAATAATGATCTTGATCCAAGC 60.049 40.000 7.99 3.80 40.84 4.01
1899 2081 6.753279 CCAAGCAAAGTATAAATGGACATGTG 59.247 38.462 1.15 0.00 0.00 3.21
1900 2082 7.315142 CAAGCAAAGTATAAATGGACATGTGT 58.685 34.615 1.15 0.00 0.00 3.72
1901 2083 8.458052 CAAGCAAAGTATAAATGGACATGTGTA 58.542 33.333 1.15 0.00 0.00 2.90
1902 2084 8.574251 AGCAAAGTATAAATGGACATGTGTAA 57.426 30.769 1.15 0.00 0.00 2.41
2067 2251 2.031682 ACACGAAGCAGAAAAGACATGC 60.032 45.455 0.00 0.00 40.29 4.06
2078 2262 5.030295 AGAAAAGACATGCGATTATTTGCG 58.970 37.500 0.00 0.00 34.71 4.85
2091 2275 2.336554 ATTTGCGAGTGTGTTCATGC 57.663 45.000 0.00 0.00 0.00 4.06
2284 2509 9.172820 CAAAAATAAAAGGAGCAAGCAAAAATC 57.827 29.630 0.00 0.00 0.00 2.17
2299 2524 4.207019 GCAAAAATCAAACACACGGAGAAG 59.793 41.667 0.00 0.00 0.00 2.85
2309 2534 2.125512 CGGAGAAGCCCGGAACTG 60.126 66.667 0.73 0.00 45.43 3.16
2351 2576 1.421382 GTCTTGGCGCGTTACAGTTA 58.579 50.000 8.43 0.00 0.00 2.24
2352 2577 1.125566 GTCTTGGCGCGTTACAGTTAC 59.874 52.381 8.43 1.33 0.00 2.50
2353 2578 0.441145 CTTGGCGCGTTACAGTTACC 59.559 55.000 8.43 0.00 0.00 2.85
2354 2579 0.950071 TTGGCGCGTTACAGTTACCC 60.950 55.000 8.43 0.00 0.00 3.69
2355 2580 1.374505 GGCGCGTTACAGTTACCCA 60.375 57.895 8.43 0.00 0.00 4.51
2356 2581 1.629345 GGCGCGTTACAGTTACCCAC 61.629 60.000 8.43 0.00 0.00 4.61
2357 2582 1.947934 GCGCGTTACAGTTACCCACG 61.948 60.000 8.43 0.00 0.00 4.94
2358 2583 0.664166 CGCGTTACAGTTACCCACGT 60.664 55.000 0.00 0.00 33.36 4.49
2359 2584 1.063031 GCGTTACAGTTACCCACGTC 58.937 55.000 0.00 0.00 33.36 4.34
2360 2585 1.701704 CGTTACAGTTACCCACGTCC 58.298 55.000 0.00 0.00 0.00 4.79
2361 2586 1.701704 GTTACAGTTACCCACGTCCG 58.298 55.000 0.00 0.00 0.00 4.79
2362 2587 1.000274 GTTACAGTTACCCACGTCCGT 60.000 52.381 0.00 0.00 0.00 4.69
2363 2588 0.597568 TACAGTTACCCACGTCCGTG 59.402 55.000 12.66 12.66 45.02 4.94
2364 2589 1.364901 CAGTTACCCACGTCCGTGT 59.635 57.895 17.52 3.90 44.02 4.49
2365 2590 0.249573 CAGTTACCCACGTCCGTGTT 60.250 55.000 17.52 7.57 44.02 3.32
2366 2591 0.249573 AGTTACCCACGTCCGTGTTG 60.250 55.000 17.52 11.07 44.02 3.33
2367 2592 0.249405 GTTACCCACGTCCGTGTTGA 60.249 55.000 17.52 0.61 44.02 3.18
2368 2593 0.249405 TTACCCACGTCCGTGTTGAC 60.249 55.000 17.52 0.00 44.02 3.18
2369 2594 1.390383 TACCCACGTCCGTGTTGACA 61.390 55.000 17.52 1.74 44.02 3.58
2370 2595 1.954146 CCCACGTCCGTGTTGACAG 60.954 63.158 17.52 2.39 44.02 3.51
2371 2596 1.954146 CCACGTCCGTGTTGACAGG 60.954 63.158 17.52 0.00 44.02 4.00
2372 2597 1.066752 CACGTCCGTGTTGACAGGA 59.933 57.895 11.49 2.56 40.91 3.86
2373 2598 0.528901 CACGTCCGTGTTGACAGGAA 60.529 55.000 11.49 0.00 40.91 3.36
2374 2599 0.391597 ACGTCCGTGTTGACAGGAAT 59.608 50.000 5.47 0.00 35.60 3.01
2375 2600 1.068474 CGTCCGTGTTGACAGGAATC 58.932 55.000 5.47 0.00 35.60 2.52
2376 2601 1.439679 GTCCGTGTTGACAGGAATCC 58.560 55.000 5.47 0.00 35.60 3.01
2377 2602 0.323629 TCCGTGTTGACAGGAATCCC 59.676 55.000 0.00 0.00 33.92 3.85
2378 2603 0.324943 CCGTGTTGACAGGAATCCCT 59.675 55.000 0.00 0.00 45.74 4.20
2379 2604 1.271379 CCGTGTTGACAGGAATCCCTT 60.271 52.381 0.00 0.00 42.02 3.95
2380 2605 2.027561 CCGTGTTGACAGGAATCCCTTA 60.028 50.000 0.00 0.00 42.02 2.69
2381 2606 3.558321 CCGTGTTGACAGGAATCCCTTAA 60.558 47.826 0.00 0.00 42.02 1.85
2382 2607 4.069304 CGTGTTGACAGGAATCCCTTAAA 58.931 43.478 0.00 0.00 42.02 1.52
2383 2608 4.517453 CGTGTTGACAGGAATCCCTTAAAA 59.483 41.667 0.00 0.00 42.02 1.52
2384 2609 5.009210 CGTGTTGACAGGAATCCCTTAAAAA 59.991 40.000 0.00 0.00 42.02 1.94
2403 2628 3.532155 GGAGGCACGATCTCCGCT 61.532 66.667 7.46 0.00 41.01 5.52
2404 2629 2.496817 GAGGCACGATCTCCGCTT 59.503 61.111 0.00 0.00 43.32 4.68
2405 2630 1.880340 GAGGCACGATCTCCGCTTG 60.880 63.158 0.00 0.00 43.32 4.01
2406 2631 2.892425 GGCACGATCTCCGCTTGG 60.892 66.667 0.00 0.00 43.32 3.61
2407 2632 2.184322 GCACGATCTCCGCTTGGA 59.816 61.111 0.00 0.00 43.32 3.53
2408 2633 1.227380 GCACGATCTCCGCTTGGAT 60.227 57.895 0.00 0.00 42.17 3.41
2409 2634 0.032130 GCACGATCTCCGCTTGGATA 59.968 55.000 0.00 0.00 42.17 2.59
2410 2635 1.538204 GCACGATCTCCGCTTGGATAA 60.538 52.381 0.00 0.00 42.17 1.75
2411 2636 2.398498 CACGATCTCCGCTTGGATAAG 58.602 52.381 0.00 0.00 42.17 1.73
2412 2637 2.034685 CACGATCTCCGCTTGGATAAGA 59.965 50.000 0.00 0.00 42.17 2.10
2413 2638 2.034812 ACGATCTCCGCTTGGATAAGAC 59.965 50.000 0.00 0.00 42.17 3.01
2414 2639 2.034685 CGATCTCCGCTTGGATAAGACA 59.965 50.000 0.00 0.00 42.17 3.41
2415 2640 2.961526 TCTCCGCTTGGATAAGACAC 57.038 50.000 0.00 0.00 42.17 3.67
2416 2641 1.134367 TCTCCGCTTGGATAAGACACG 59.866 52.381 0.00 0.00 42.17 4.49
2417 2642 0.459585 TCCGCTTGGATAAGACACGC 60.460 55.000 0.00 0.00 36.65 5.34
2418 2643 1.429148 CCGCTTGGATAAGACACGCC 61.429 60.000 0.00 0.00 35.92 5.68
2419 2644 0.739462 CGCTTGGATAAGACACGCCA 60.739 55.000 0.00 0.00 35.92 5.69
2420 2645 1.448985 GCTTGGATAAGACACGCCAA 58.551 50.000 0.00 0.00 38.02 4.52
2421 2646 2.017049 GCTTGGATAAGACACGCCAAT 58.983 47.619 0.00 0.00 39.46 3.16
2422 2647 3.202906 GCTTGGATAAGACACGCCAATA 58.797 45.455 0.00 0.00 39.46 1.90
2423 2648 3.625764 GCTTGGATAAGACACGCCAATAA 59.374 43.478 0.00 0.00 39.46 1.40
2424 2649 4.095782 GCTTGGATAAGACACGCCAATAAA 59.904 41.667 0.00 0.00 39.46 1.40
2425 2650 5.730568 GCTTGGATAAGACACGCCAATAAAG 60.731 44.000 0.00 0.00 39.46 1.85
2426 2651 3.625764 TGGATAAGACACGCCAATAAAGC 59.374 43.478 0.00 0.00 0.00 3.51
2427 2652 3.003378 GGATAAGACACGCCAATAAAGCC 59.997 47.826 0.00 0.00 0.00 4.35
2428 2653 1.904287 AAGACACGCCAATAAAGCCA 58.096 45.000 0.00 0.00 0.00 4.75
2429 2654 1.165270 AGACACGCCAATAAAGCCAC 58.835 50.000 0.00 0.00 0.00 5.01
2430 2655 0.179200 GACACGCCAATAAAGCCACG 60.179 55.000 0.00 0.00 0.00 4.94
2431 2656 0.887387 ACACGCCAATAAAGCCACGT 60.887 50.000 0.00 0.00 0.00 4.49
2432 2657 0.179200 CACGCCAATAAAGCCACGTC 60.179 55.000 0.00 0.00 0.00 4.34
2433 2658 0.321298 ACGCCAATAAAGCCACGTCT 60.321 50.000 0.00 0.00 0.00 4.18
2434 2659 0.802494 CGCCAATAAAGCCACGTCTT 59.198 50.000 0.00 0.00 0.00 3.01
2435 2660 1.199097 CGCCAATAAAGCCACGTCTTT 59.801 47.619 7.33 7.33 39.40 2.52
2436 2661 2.595386 GCCAATAAAGCCACGTCTTTG 58.405 47.619 11.40 0.00 36.95 2.77
2437 2662 2.671070 GCCAATAAAGCCACGTCTTTGG 60.671 50.000 11.40 7.04 36.95 3.28
2438 2663 2.817258 CCAATAAAGCCACGTCTTTGGA 59.183 45.455 11.40 0.00 39.24 3.53
2439 2664 3.365969 CCAATAAAGCCACGTCTTTGGAC 60.366 47.826 11.40 0.00 39.24 4.02
2440 2665 2.623878 TAAAGCCACGTCTTTGGACA 57.376 45.000 11.40 0.00 42.21 4.02
2441 2666 1.981256 AAAGCCACGTCTTTGGACAT 58.019 45.000 1.74 0.00 42.21 3.06
2442 2667 1.238439 AAGCCACGTCTTTGGACATG 58.762 50.000 0.00 0.00 42.21 3.21
2445 2670 2.555123 CACGTCTTTGGACATGGGG 58.445 57.895 0.00 0.00 42.21 4.96
2446 2671 1.303317 ACGTCTTTGGACATGGGGC 60.303 57.895 0.00 0.00 42.21 5.80
2447 2672 2.398554 CGTCTTTGGACATGGGGCG 61.399 63.158 0.00 0.00 42.21 6.13
2448 2673 1.002624 GTCTTTGGACATGGGGCGA 60.003 57.895 0.00 0.00 41.75 5.54
2449 2674 1.002624 TCTTTGGACATGGGGCGAC 60.003 57.895 0.00 0.00 0.00 5.19
2450 2675 2.359354 TTTGGACATGGGGCGACG 60.359 61.111 0.00 0.00 0.00 5.12
2451 2676 2.796483 CTTTGGACATGGGGCGACGA 62.796 60.000 0.00 0.00 0.00 4.20
2452 2677 2.796483 TTTGGACATGGGGCGACGAG 62.796 60.000 0.00 0.00 0.00 4.18
2462 2687 3.870606 GCGACGAGCCAGCTAAAA 58.129 55.556 0.00 0.00 40.81 1.52
2463 2688 1.420312 GCGACGAGCCAGCTAAAAC 59.580 57.895 0.00 0.00 40.81 2.43
2464 2689 1.702299 CGACGAGCCAGCTAAAACG 59.298 57.895 0.00 0.00 0.00 3.60
2465 2690 1.683790 CGACGAGCCAGCTAAAACGG 61.684 60.000 0.00 0.00 0.00 4.44
2466 2691 0.669625 GACGAGCCAGCTAAAACGGT 60.670 55.000 0.00 0.00 0.00 4.83
2467 2692 0.250166 ACGAGCCAGCTAAAACGGTT 60.250 50.000 0.00 0.00 0.00 4.44
2468 2693 0.442699 CGAGCCAGCTAAAACGGTTC 59.557 55.000 0.00 0.00 0.00 3.62
2469 2694 0.442699 GAGCCAGCTAAAACGGTTCG 59.557 55.000 0.00 0.00 0.00 3.95
2470 2695 1.154282 GCCAGCTAAAACGGTTCGC 60.154 57.895 0.00 0.00 0.00 4.70
2471 2696 1.847890 GCCAGCTAAAACGGTTCGCA 61.848 55.000 9.67 0.00 0.00 5.10
2472 2697 0.589223 CCAGCTAAAACGGTTCGCAA 59.411 50.000 9.67 0.00 0.00 4.85
2473 2698 1.399727 CCAGCTAAAACGGTTCGCAAG 60.400 52.381 9.67 2.60 0.00 4.01
2474 2699 1.263217 CAGCTAAAACGGTTCGCAAGT 59.737 47.619 9.67 0.00 39.48 3.16
2475 2700 2.477375 CAGCTAAAACGGTTCGCAAGTA 59.523 45.455 9.67 0.00 39.48 2.24
2476 2701 2.735134 AGCTAAAACGGTTCGCAAGTAG 59.265 45.455 9.67 0.00 39.48 2.57
2477 2702 2.477754 GCTAAAACGGTTCGCAAGTAGT 59.522 45.455 2.89 0.00 39.48 2.73
2478 2703 3.663493 GCTAAAACGGTTCGCAAGTAGTG 60.663 47.826 2.89 0.00 39.48 2.74
2479 2704 1.223187 AAACGGTTCGCAAGTAGTGG 58.777 50.000 0.00 0.00 39.48 4.00
2480 2705 1.226030 AACGGTTCGCAAGTAGTGGC 61.226 55.000 0.00 0.00 39.48 5.01
2481 2706 1.374252 CGGTTCGCAAGTAGTGGCT 60.374 57.895 0.00 0.00 39.48 4.75
2482 2707 1.626654 CGGTTCGCAAGTAGTGGCTG 61.627 60.000 0.00 0.00 39.48 4.85
2483 2708 1.298859 GGTTCGCAAGTAGTGGCTGG 61.299 60.000 0.00 0.00 39.48 4.85
2484 2709 1.003839 TTCGCAAGTAGTGGCTGGG 60.004 57.895 0.00 0.00 39.48 4.45
2485 2710 3.127533 CGCAAGTAGTGGCTGGGC 61.128 66.667 0.00 0.00 0.00 5.36
2486 2711 2.034066 GCAAGTAGTGGCTGGGCA 59.966 61.111 0.00 0.00 0.00 5.36
2487 2712 2.042831 GCAAGTAGTGGCTGGGCAG 61.043 63.158 0.00 0.00 0.00 4.85
2488 2713 1.377725 CAAGTAGTGGCTGGGCAGG 60.378 63.158 0.00 0.00 0.00 4.85
2497 2722 2.753043 CTGGGCAGGCATGGTGTC 60.753 66.667 0.00 0.00 0.00 3.67
2498 2723 3.572447 CTGGGCAGGCATGGTGTCA 62.572 63.158 0.00 0.00 0.00 3.58
2499 2724 2.043652 GGGCAGGCATGGTGTCAT 60.044 61.111 0.00 0.00 0.00 3.06
2500 2725 1.227102 GGGCAGGCATGGTGTCATA 59.773 57.895 0.00 0.00 31.33 2.15
2501 2726 0.178981 GGGCAGGCATGGTGTCATAT 60.179 55.000 0.00 0.00 31.33 1.78
2502 2727 1.242076 GGCAGGCATGGTGTCATATC 58.758 55.000 0.00 0.00 31.33 1.63
2503 2728 1.477377 GGCAGGCATGGTGTCATATCA 60.477 52.381 0.00 0.00 31.33 2.15
2504 2729 1.605710 GCAGGCATGGTGTCATATCAC 59.394 52.381 0.00 0.00 37.57 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 8.668510 TTTTCCAAATTGCATAAAACTTGCTA 57.331 26.923 0.00 0.00 40.77 3.49
92 97 4.768130 ATGCTTCATATCATGCTCTTGC 57.232 40.909 0.00 0.00 40.20 4.01
131 136 1.697082 TTGTCGTGGCACCCCTTACA 61.697 55.000 12.86 6.22 0.00 2.41
156 162 1.960417 TGTCGTGGCATCACTTTCAA 58.040 45.000 0.00 0.00 41.53 2.69
173 179 2.153366 ACCGAAAACCGATACGTTGT 57.847 45.000 0.00 0.00 41.76 3.32
242 249 0.034186 GATCACCCCACCATCTTGCA 60.034 55.000 0.00 0.00 0.00 4.08
291 306 1.279749 TGCTCGGTCCTCCTCTCCTA 61.280 60.000 0.00 0.00 0.00 2.94
294 309 0.968393 ACTTGCTCGGTCCTCCTCTC 60.968 60.000 0.00 0.00 0.00 3.20
327 342 0.539207 TGCACCCTATGTTTGCAGCA 60.539 50.000 0.00 0.00 41.29 4.41
329 344 1.888512 AGTTGCACCCTATGTTTGCAG 59.111 47.619 0.00 0.00 46.46 4.41
390 415 3.165058 TGCACGCTTCAGAGGTATAAG 57.835 47.619 0.00 0.00 0.00 1.73
416 441 1.006102 CACCGACTCAAACCGCTCT 60.006 57.895 0.00 0.00 0.00 4.09
425 450 2.581216 ACTTCCTCTACACCGACTCA 57.419 50.000 0.00 0.00 0.00 3.41
543 568 3.620427 ATGAAATGCGTACCACTACCA 57.380 42.857 0.00 0.00 0.00 3.25
557 582 4.663120 TGTACCCCTACATGGCTATGAAAT 59.337 41.667 17.90 0.00 37.73 2.17
568 593 2.170166 TCGAAACGTGTACCCCTACAT 58.830 47.619 0.00 0.00 35.28 2.29
594 619 4.130286 AGGGAGTCGAATTCATCAAGTC 57.870 45.455 6.22 0.59 0.00 3.01
709 736 3.243434 CGATGCCTAGAACGACTACCATT 60.243 47.826 0.00 0.00 0.00 3.16
711 738 1.674441 CGATGCCTAGAACGACTACCA 59.326 52.381 0.00 0.00 0.00 3.25
729 756 1.672854 CCAAGTACCTCGATGCCCGA 61.673 60.000 0.00 0.00 46.35 5.14
730 757 1.227263 CCAAGTACCTCGATGCCCG 60.227 63.158 0.00 0.00 40.25 6.13
731 758 1.523938 GCCAAGTACCTCGATGCCC 60.524 63.158 0.00 0.00 0.00 5.36
732 759 0.179045 ATGCCAAGTACCTCGATGCC 60.179 55.000 0.00 0.00 0.00 4.40
733 760 1.599542 GAATGCCAAGTACCTCGATGC 59.400 52.381 0.00 0.00 0.00 3.91
734 761 3.185246 AGAATGCCAAGTACCTCGATG 57.815 47.619 0.00 0.00 0.00 3.84
735 762 3.535561 CAAGAATGCCAAGTACCTCGAT 58.464 45.455 0.00 0.00 0.00 3.59
736 763 2.354704 CCAAGAATGCCAAGTACCTCGA 60.355 50.000 0.00 0.00 0.00 4.04
737 764 2.009774 CCAAGAATGCCAAGTACCTCG 58.990 52.381 0.00 0.00 0.00 4.63
738 765 2.026262 TCCCAAGAATGCCAAGTACCTC 60.026 50.000 0.00 0.00 0.00 3.85
739 766 1.992557 TCCCAAGAATGCCAAGTACCT 59.007 47.619 0.00 0.00 0.00 3.08
740 767 2.507407 TCCCAAGAATGCCAAGTACC 57.493 50.000 0.00 0.00 0.00 3.34
741 768 3.381590 GGAATCCCAAGAATGCCAAGTAC 59.618 47.826 0.00 0.00 0.00 2.73
742 769 3.631250 GGAATCCCAAGAATGCCAAGTA 58.369 45.455 0.00 0.00 0.00 2.24
743 770 2.460669 GGAATCCCAAGAATGCCAAGT 58.539 47.619 0.00 0.00 0.00 3.16
744 771 1.406539 CGGAATCCCAAGAATGCCAAG 59.593 52.381 0.00 0.00 0.00 3.61
745 772 1.005332 TCGGAATCCCAAGAATGCCAA 59.995 47.619 0.00 0.00 0.00 4.52
746 773 0.623194 TCGGAATCCCAAGAATGCCA 59.377 50.000 0.00 0.00 0.00 4.92
786 835 1.445410 GTCTACGTGGTGATGCGCA 60.445 57.895 14.96 14.96 0.00 6.09
843 892 4.138665 TGGATACGCCAAGACCCA 57.861 55.556 0.00 0.00 45.87 4.51
860 909 0.102300 GTTTCGCCAAGCACACCTTT 59.898 50.000 0.00 0.00 0.00 3.11
898 947 2.632996 AGAACATCTTCCTGGAACGACA 59.367 45.455 4.68 0.00 0.00 4.35
908 957 4.865365 CCAAGACTTACGAGAACATCTTCC 59.135 45.833 0.00 0.00 0.00 3.46
914 963 4.931661 AACTCCAAGACTTACGAGAACA 57.068 40.909 15.14 0.00 0.00 3.18
992 1041 4.830765 GCGCCGCCATGTACCTCA 62.831 66.667 0.00 0.00 0.00 3.86
1032 1081 2.685380 CCTCTCCTTCCCCTGCGT 60.685 66.667 0.00 0.00 0.00 5.24
1098 1147 0.401356 TCATGTTGCTGCTCTTCCCA 59.599 50.000 0.00 0.00 0.00 4.37
1112 1161 1.815421 GCCATCCGCTTCGTCATGT 60.815 57.895 0.00 0.00 0.00 3.21
1115 1164 1.521457 GATGCCATCCGCTTCGTCA 60.521 57.895 0.00 0.00 38.78 4.35
1145 1194 0.474660 AGCTCCACCTCCCTTGTTCT 60.475 55.000 0.00 0.00 0.00 3.01
1206 1255 2.134287 GCCTAGTCCCATCGCCTCA 61.134 63.158 0.00 0.00 0.00 3.86
1272 1321 2.753043 CCAGAGCCATGCCACCAC 60.753 66.667 0.00 0.00 0.00 4.16
1280 1329 4.479993 GACGCCAGCCAGAGCCAT 62.480 66.667 0.00 0.00 41.25 4.40
1332 1382 2.529744 GCCTTCCTCCACCACCACT 61.530 63.158 0.00 0.00 0.00 4.00
1402 1522 2.538141 CCCACCTTGAGCCAGGGAA 61.538 63.158 9.77 0.00 42.25 3.97
1413 1533 0.338120 CCTCTCCTCTCTCCCACCTT 59.662 60.000 0.00 0.00 0.00 3.50
1501 1621 0.609957 TCCGCTCGTTCCTCCTACAA 60.610 55.000 0.00 0.00 0.00 2.41
1580 1700 1.342819 CAATCCCTCCTGTCGATCTCC 59.657 57.143 0.00 0.00 0.00 3.71
1655 1775 2.598787 CGCCCTTCCCACTGGGTAA 61.599 63.158 14.25 6.43 44.74 2.85
1656 1776 3.006728 CGCCCTTCCCACTGGGTA 61.007 66.667 14.25 3.43 44.74 3.69
1744 1882 4.083565 GAGAGATATTTAGGCGGAGAGGT 58.916 47.826 0.00 0.00 0.00 3.85
1781 1937 2.698274 TCCTTCCCTTTTCTGTTTTGCC 59.302 45.455 0.00 0.00 0.00 4.52
1782 1938 4.607293 ATCCTTCCCTTTTCTGTTTTGC 57.393 40.909 0.00 0.00 0.00 3.68
1796 1964 5.305902 CCCTACCTCTCTTTCTTATCCTTCC 59.694 48.000 0.00 0.00 0.00 3.46
1901 2083 9.323985 TCAAATGAGTTCGAATCCAAAATTTTT 57.676 25.926 0.00 0.00 0.00 1.94
1902 2084 8.885494 TCAAATGAGTTCGAATCCAAAATTTT 57.115 26.923 0.00 0.00 0.00 1.82
2048 2230 1.195448 CGCATGTCTTTTCTGCTTCGT 59.805 47.619 0.00 0.00 33.75 3.85
2067 2251 4.320667 TGAACACACTCGCAAATAATCG 57.679 40.909 0.00 0.00 0.00 3.34
2078 2262 3.486375 CGGAATCATGCATGAACACACTC 60.486 47.826 31.79 19.30 40.69 3.51
2284 2509 1.841663 CGGGCTTCTCCGTGTGTTTG 61.842 60.000 0.00 0.00 44.60 2.93
2299 2524 0.744771 GACTTCCATCAGTTCCGGGC 60.745 60.000 0.00 0.00 0.00 6.13
2308 2533 2.171003 TGCTCGAGAAGACTTCCATCA 58.829 47.619 18.75 0.00 0.00 3.07
2309 2534 2.949451 TGCTCGAGAAGACTTCCATC 57.051 50.000 18.75 3.21 0.00 3.51
2339 2564 0.664166 ACGTGGGTAACTGTAACGCG 60.664 55.000 3.53 3.53 32.81 6.01
2355 2580 0.391597 ATTCCTGTCAACACGGACGT 59.608 50.000 0.00 0.00 40.72 4.34
2356 2581 1.068474 GATTCCTGTCAACACGGACG 58.932 55.000 0.00 0.00 40.72 4.79
2357 2582 1.439679 GGATTCCTGTCAACACGGAC 58.560 55.000 0.00 0.00 38.29 4.79
2358 2583 0.323629 GGGATTCCTGTCAACACGGA 59.676 55.000 2.01 0.00 0.00 4.69
2359 2584 0.324943 AGGGATTCCTGTCAACACGG 59.675 55.000 2.01 0.00 42.98 4.94
2360 2585 2.185004 AAGGGATTCCTGTCAACACG 57.815 50.000 0.00 0.00 44.07 4.49
2361 2586 6.399639 TTTTTAAGGGATTCCTGTCAACAC 57.600 37.500 0.00 0.00 44.07 3.32
2381 2606 1.676014 CGGAGATCGTGCCTCCTTTTT 60.676 52.381 14.86 0.00 46.15 1.94
2382 2607 0.108138 CGGAGATCGTGCCTCCTTTT 60.108 55.000 14.86 0.00 46.15 2.27
2383 2608 1.517832 CGGAGATCGTGCCTCCTTT 59.482 57.895 14.86 0.00 46.15 3.11
2384 2609 3.082579 GCGGAGATCGTGCCTCCTT 62.083 63.158 14.86 0.00 46.15 3.36
2385 2610 3.532155 GCGGAGATCGTGCCTCCT 61.532 66.667 14.86 0.00 46.15 3.69
2386 2611 3.082579 AAGCGGAGATCGTGCCTCC 62.083 63.158 9.41 9.41 45.16 4.30
2387 2612 1.880340 CAAGCGGAGATCGTGCCTC 60.880 63.158 3.69 0.00 41.72 4.70
2388 2613 2.185350 CAAGCGGAGATCGTGCCT 59.815 61.111 3.69 0.00 41.72 4.75
2389 2614 2.892425 CCAAGCGGAGATCGTGCC 60.892 66.667 3.69 0.00 41.72 5.01
2390 2615 2.184322 TCCAAGCGGAGATCGTGC 59.816 61.111 0.00 0.00 41.72 5.34
2399 2624 1.429148 GGCGTGTCTTATCCAAGCGG 61.429 60.000 0.00 0.00 38.05 5.52
2400 2625 0.739462 TGGCGTGTCTTATCCAAGCG 60.739 55.000 0.00 0.00 38.05 4.68
2401 2626 1.448985 TTGGCGTGTCTTATCCAAGC 58.551 50.000 0.00 0.00 34.01 4.01
2402 2627 5.730568 GCTTTATTGGCGTGTCTTATCCAAG 60.731 44.000 0.00 0.00 41.32 3.61
2403 2628 4.095782 GCTTTATTGGCGTGTCTTATCCAA 59.904 41.667 0.00 0.00 42.10 3.53
2404 2629 3.625764 GCTTTATTGGCGTGTCTTATCCA 59.374 43.478 0.00 0.00 0.00 3.41
2405 2630 3.003378 GGCTTTATTGGCGTGTCTTATCC 59.997 47.826 0.00 0.00 0.00 2.59
2406 2631 3.625764 TGGCTTTATTGGCGTGTCTTATC 59.374 43.478 0.00 0.00 35.06 1.75
2407 2632 3.377172 GTGGCTTTATTGGCGTGTCTTAT 59.623 43.478 0.00 0.00 35.06 1.73
2408 2633 2.745281 GTGGCTTTATTGGCGTGTCTTA 59.255 45.455 0.00 0.00 35.06 2.10
2409 2634 1.539827 GTGGCTTTATTGGCGTGTCTT 59.460 47.619 0.00 0.00 35.06 3.01
2410 2635 1.165270 GTGGCTTTATTGGCGTGTCT 58.835 50.000 0.00 0.00 35.06 3.41
2411 2636 0.179200 CGTGGCTTTATTGGCGTGTC 60.179 55.000 0.00 0.00 35.06 3.67
2412 2637 0.887387 ACGTGGCTTTATTGGCGTGT 60.887 50.000 0.00 0.00 35.06 4.49
2413 2638 0.179200 GACGTGGCTTTATTGGCGTG 60.179 55.000 0.00 0.00 35.06 5.34
2414 2639 0.321298 AGACGTGGCTTTATTGGCGT 60.321 50.000 0.00 0.00 35.06 5.68
2415 2640 0.802494 AAGACGTGGCTTTATTGGCG 59.198 50.000 0.00 0.00 35.06 5.69
2416 2641 2.595386 CAAAGACGTGGCTTTATTGGC 58.405 47.619 0.00 0.00 36.39 4.52
2417 2642 2.817258 TCCAAAGACGTGGCTTTATTGG 59.183 45.455 0.00 0.00 38.68 3.16
2418 2643 3.252215 TGTCCAAAGACGTGGCTTTATTG 59.748 43.478 0.00 0.00 46.74 1.90
2419 2644 3.482436 TGTCCAAAGACGTGGCTTTATT 58.518 40.909 0.00 0.00 46.74 1.40
2420 2645 3.134574 TGTCCAAAGACGTGGCTTTAT 57.865 42.857 0.00 0.00 46.74 1.40
2421 2646 2.623878 TGTCCAAAGACGTGGCTTTA 57.376 45.000 0.00 0.00 46.74 1.85
2422 2647 1.981256 ATGTCCAAAGACGTGGCTTT 58.019 45.000 0.00 0.00 46.74 3.51
2423 2648 3.725754 ATGTCCAAAGACGTGGCTT 57.274 47.368 0.00 0.00 46.74 4.35
2428 2653 1.303317 GCCCCATGTCCAAAGACGT 60.303 57.895 0.00 0.00 46.74 4.34
2429 2654 2.398554 CGCCCCATGTCCAAAGACG 61.399 63.158 0.00 0.00 46.74 4.18
2430 2655 1.002624 TCGCCCCATGTCCAAAGAC 60.003 57.895 0.00 0.00 43.83 3.01
2431 2656 1.002624 GTCGCCCCATGTCCAAAGA 60.003 57.895 0.00 0.00 0.00 2.52
2432 2657 2.398554 CGTCGCCCCATGTCCAAAG 61.399 63.158 0.00 0.00 0.00 2.77
2433 2658 2.359354 CGTCGCCCCATGTCCAAA 60.359 61.111 0.00 0.00 0.00 3.28
2434 2659 3.309436 CTCGTCGCCCCATGTCCAA 62.309 63.158 0.00 0.00 0.00 3.53
2435 2660 3.770040 CTCGTCGCCCCATGTCCA 61.770 66.667 0.00 0.00 0.00 4.02
2445 2670 1.420312 GTTTTAGCTGGCTCGTCGC 59.580 57.895 0.00 0.00 38.13 5.19
2446 2671 1.683790 CCGTTTTAGCTGGCTCGTCG 61.684 60.000 0.00 1.12 0.00 5.12
2447 2672 0.669625 ACCGTTTTAGCTGGCTCGTC 60.670 55.000 0.00 0.00 0.00 4.20
2448 2673 0.250166 AACCGTTTTAGCTGGCTCGT 60.250 50.000 0.00 0.00 0.00 4.18
2449 2674 0.442699 GAACCGTTTTAGCTGGCTCG 59.557 55.000 0.00 0.00 0.00 5.03
2450 2675 0.442699 CGAACCGTTTTAGCTGGCTC 59.557 55.000 0.00 0.00 0.00 4.70
2451 2676 1.574702 GCGAACCGTTTTAGCTGGCT 61.575 55.000 0.00 0.00 0.00 4.75
2452 2677 1.154282 GCGAACCGTTTTAGCTGGC 60.154 57.895 0.00 0.00 0.00 4.85
2453 2678 0.589223 TTGCGAACCGTTTTAGCTGG 59.411 50.000 0.00 0.00 0.00 4.85
2454 2679 1.263217 ACTTGCGAACCGTTTTAGCTG 59.737 47.619 0.00 5.01 0.00 4.24
2455 2680 1.589803 ACTTGCGAACCGTTTTAGCT 58.410 45.000 0.00 0.00 0.00 3.32
2456 2681 2.477754 ACTACTTGCGAACCGTTTTAGC 59.522 45.455 0.00 0.00 0.00 3.09
2457 2682 3.120786 CCACTACTTGCGAACCGTTTTAG 60.121 47.826 0.00 0.00 0.00 1.85
2458 2683 2.801679 CCACTACTTGCGAACCGTTTTA 59.198 45.455 0.00 0.00 0.00 1.52
2459 2684 1.600485 CCACTACTTGCGAACCGTTTT 59.400 47.619 0.00 0.00 0.00 2.43
2460 2685 1.223187 CCACTACTTGCGAACCGTTT 58.777 50.000 0.00 0.00 0.00 3.60
2461 2686 1.226030 GCCACTACTTGCGAACCGTT 61.226 55.000 0.00 0.00 0.00 4.44
2462 2687 1.666872 GCCACTACTTGCGAACCGT 60.667 57.895 0.00 0.00 0.00 4.83
2463 2688 1.374252 AGCCACTACTTGCGAACCG 60.374 57.895 0.00 0.00 0.00 4.44
2464 2689 1.298859 CCAGCCACTACTTGCGAACC 61.299 60.000 0.00 0.00 0.00 3.62
2465 2690 1.298859 CCCAGCCACTACTTGCGAAC 61.299 60.000 0.00 0.00 0.00 3.95
2466 2691 1.003839 CCCAGCCACTACTTGCGAA 60.004 57.895 0.00 0.00 0.00 4.70
2467 2692 2.662596 CCCAGCCACTACTTGCGA 59.337 61.111 0.00 0.00 0.00 5.10
2468 2693 3.127533 GCCCAGCCACTACTTGCG 61.128 66.667 0.00 0.00 0.00 4.85
2469 2694 2.034066 TGCCCAGCCACTACTTGC 59.966 61.111 0.00 0.00 0.00 4.01
2470 2695 1.377725 CCTGCCCAGCCACTACTTG 60.378 63.158 0.00 0.00 0.00 3.16
2471 2696 3.081554 CCTGCCCAGCCACTACTT 58.918 61.111 0.00 0.00 0.00 2.24
2472 2697 3.721706 GCCTGCCCAGCCACTACT 61.722 66.667 0.00 0.00 0.00 2.57
2473 2698 3.350031 ATGCCTGCCCAGCCACTAC 62.350 63.158 0.00 0.00 0.00 2.73
2474 2699 3.016971 ATGCCTGCCCAGCCACTA 61.017 61.111 0.00 0.00 0.00 2.74
2475 2700 4.753662 CATGCCTGCCCAGCCACT 62.754 66.667 0.00 0.00 0.00 4.00
2480 2705 2.753043 GACACCATGCCTGCCCAG 60.753 66.667 0.00 0.00 0.00 4.45
2481 2706 1.569943 TATGACACCATGCCTGCCCA 61.570 55.000 0.00 0.00 34.31 5.36
2482 2707 0.178981 ATATGACACCATGCCTGCCC 60.179 55.000 0.00 0.00 34.31 5.36
2483 2708 1.242076 GATATGACACCATGCCTGCC 58.758 55.000 0.00 0.00 34.31 4.85
2484 2709 1.605710 GTGATATGACACCATGCCTGC 59.394 52.381 0.00 0.00 35.07 4.85


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

AutoCloner maintained by Alex Coulton.