Multiple sequence alignment - TraesCS3B01G452300

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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 TraesCS3B01G452300 chr3B 100.000 4758 0 0 1 4758 693471296 693466539 0.000000e+00 8787.0
1 TraesCS3B01G452300 chr3B 85.304 905 102 16 2897 3774 693645987 693645087 0.000000e+00 905.0
2 TraesCS3B01G452300 chr3B 85.123 894 88 27 1416 2288 693736964 693736095 0.000000e+00 872.0
3 TraesCS3B01G452300 chr3B 85.325 845 86 28 1398 2231 693647313 693646496 0.000000e+00 839.0
4 TraesCS3B01G452300 chr3B 86.823 554 52 8 1786 2339 693601671 693601139 2.450000e-167 599.0
5 TraesCS3B01G452300 chr3B 82.590 695 83 16 2901 3588 693728929 693728266 3.190000e-161 579.0
6 TraesCS3B01G452300 chr3B 79.062 640 95 24 3270 3887 693598656 693598034 2.060000e-108 403.0
7 TraesCS3B01G452300 chr3B 80.044 451 79 9 58 503 9429502 9429058 1.650000e-84 324.0
8 TraesCS3B01G452300 chr3B 82.407 324 42 5 2897 3211 693598975 693598658 7.850000e-68 268.0
9 TraesCS3B01G452300 chr3B 85.776 232 20 9 1210 1435 693602278 693602054 2.860000e-57 233.0
10 TraesCS3B01G452300 chr3B 80.180 333 44 11 1057 1375 693649641 693649317 3.700000e-56 230.0
11 TraesCS3B01G452300 chr3B 84.906 212 23 6 3655 3858 693726287 693726077 6.240000e-49 206.0
12 TraesCS3B01G452300 chr3B 89.189 148 16 0 3739 3886 693645042 693644895 8.130000e-43 185.0
13 TraesCS3B01G452300 chr3B 91.489 47 1 3 4019 4062 564019277 564019323 1.430000e-05 62.1
14 TraesCS3B01G452300 chr3D 92.121 4125 228 51 7 4099 525539663 525535604 0.000000e+00 5727.0
15 TraesCS3B01G452300 chr3D 86.090 913 96 15 2907 3792 525640429 525639521 0.000000e+00 953.0
16 TraesCS3B01G452300 chr3D 83.351 949 96 40 1424 2360 525641746 525640848 0.000000e+00 821.0
17 TraesCS3B01G452300 chr3D 85.870 552 57 5 1748 2292 525634702 525634165 6.910000e-158 568.0
18 TraesCS3B01G452300 chr3D 89.153 378 37 4 4309 4685 315487066 315486692 7.210000e-128 468.0
19 TraesCS3B01G452300 chr3D 89.008 373 36 4 4314 4686 292375958 292376325 1.560000e-124 457.0
20 TraesCS3B01G452300 chr3D 83.251 406 48 10 3270 3665 525632650 525632255 5.860000e-94 355.0
21 TraesCS3B01G452300 chr3D 77.534 592 117 11 103 687 316827261 316826679 4.560000e-90 342.0
22 TraesCS3B01G452300 chr3D 81.988 322 45 3 2897 3211 525632967 525632652 1.310000e-65 261.0
23 TraesCS3B01G452300 chr3D 87.417 151 11 4 3716 3858 525632138 525631988 2.950000e-37 167.0
24 TraesCS3B01G452300 chr3D 87.162 148 16 1 3758 3905 525639454 525639310 1.060000e-36 165.0
25 TraesCS3B01G452300 chr3A 93.958 3575 154 20 1124 4684 659624552 659621026 0.000000e+00 5349.0
26 TraesCS3B01G452300 chr3A 83.506 964 106 34 1416 2360 659858087 659857158 0.000000e+00 850.0
27 TraesCS3B01G452300 chr3A 81.039 1097 127 38 2901 3955 659822654 659821597 0.000000e+00 798.0
28 TraesCS3B01G452300 chr3A 84.564 596 66 11 1748 2339 659803243 659802670 6.910000e-158 568.0
29 TraesCS3B01G452300 chr3A 88.158 380 41 4 4309 4686 595657391 595657768 2.610000e-122 449.0
30 TraesCS3B01G452300 chr3A 94.444 234 12 1 895 1128 659630805 659630573 4.530000e-95 359.0
31 TraesCS3B01G452300 chr3A 85.303 347 39 5 3270 3606 659801158 659800814 9.800000e-92 348.0
32 TraesCS3B01G452300 chr3A 85.366 328 25 11 1210 1521 659803562 659803242 7.680000e-83 318.0
33 TraesCS3B01G452300 chr3A 79.733 449 73 9 268 709 1598287 1598724 4.620000e-80 309.0
34 TraesCS3B01G452300 chr3A 81.173 324 42 4 2901 3211 659801477 659801160 4.760000e-60 243.0
35 TraesCS3B01G452300 chr3A 90.722 97 8 1 4663 4758 260072700 260072796 1.390000e-25 128.0
36 TraesCS3B01G452300 chr3A 81.600 125 12 10 2610 2727 55482608 55482488 5.070000e-15 93.5
37 TraesCS3B01G452300 chr3A 94.340 53 2 1 4028 4079 36231291 36231343 3.950000e-11 80.5
38 TraesCS3B01G452300 chr3A 83.562 73 12 0 27 99 1647024 1646952 8.540000e-08 69.4
39 TraesCS3B01G452300 chr5D 90.296 371 33 3 4317 4686 417596827 417597195 2.570000e-132 483.0
40 TraesCS3B01G452300 chr5D 79.712 626 111 11 89 709 353517152 353517766 5.650000e-119 438.0
41 TraesCS3B01G452300 chr1D 89.182 379 37 4 4309 4686 63063443 63063068 2.000000e-128 470.0
42 TraesCS3B01G452300 chr7D 88.391 379 42 2 4309 4686 251308802 251308425 5.610000e-124 455.0
43 TraesCS3B01G452300 chr7D 78.998 619 102 20 92 704 47259869 47259273 9.590000e-107 398.0
44 TraesCS3B01G452300 chr7D 89.324 281 29 1 2626 2906 232354560 232354281 7.580000e-93 351.0
45 TraesCS3B01G452300 chr4D 88.220 382 40 5 4308 4686 357266139 357266518 7.260000e-123 451.0
46 TraesCS3B01G452300 chr6D 88.127 379 43 2 4309 4686 148085104 148085481 2.610000e-122 449.0
47 TraesCS3B01G452300 chr6D 95.062 81 4 0 4678 4758 8159436 8159516 1.390000e-25 128.0
48 TraesCS3B01G452300 chr2B 79.777 628 104 13 89 711 14314247 14313638 7.310000e-118 435.0
49 TraesCS3B01G452300 chr2B 97.222 36 1 0 4026 4061 87422444 87422409 1.430000e-05 62.1
50 TraesCS3B01G452300 chr1A 78.768 617 99 20 98 706 550833907 550833315 7.470000e-103 385.0
51 TraesCS3B01G452300 chr1A 86.000 250 23 4 2630 2878 131291847 131291609 1.700000e-64 257.0
52 TraesCS3B01G452300 chr7B 77.704 601 111 18 92 684 448732214 448732799 3.520000e-91 346.0
53 TraesCS3B01G452300 chr7B 77.575 602 111 18 92 684 450580813 450580227 4.560000e-90 342.0
54 TraesCS3B01G452300 chr7B 94.737 38 1 1 4026 4062 536684256 536684219 1.850000e-04 58.4
55 TraesCS3B01G452300 chr2D 90.638 235 18 4 2628 2860 37610176 37610408 4.620000e-80 309.0
56 TraesCS3B01G452300 chr2D 88.119 101 8 4 4659 4756 15689780 15689879 3.010000e-22 117.0
57 TraesCS3B01G452300 chr5B 95.238 84 2 1 4677 4758 61763848 61763765 1.070000e-26 132.0
58 TraesCS3B01G452300 chr5A 96.250 80 1 2 4680 4758 191332677 191332599 3.860000e-26 130.0
59 TraesCS3B01G452300 chr5A 95.122 82 3 1 4677 4758 366019755 366019835 1.390000e-25 128.0
60 TraesCS3B01G452300 chr5A 91.209 91 6 2 4669 4758 642457091 642457002 6.470000e-24 122.0
61 TraesCS3B01G452300 chr4A 94.253 87 2 3 4674 4758 216045936 216046021 3.860000e-26 130.0
62 TraesCS3B01G452300 chr2A 96.250 80 2 1 4680 4758 171704955 171705034 3.860000e-26 130.0
63 TraesCS3B01G452300 chr7A 95.745 47 2 0 4023 4069 224975321 224975275 5.110000e-10 76.8
64 TraesCS3B01G452300 chr4B 85.507 69 10 0 533 601 581177857 581177925 6.600000e-09 73.1
65 TraesCS3B01G452300 chr1B 85.507 69 7 2 16 84 396119773 396119708 8.540000e-08 69.4
66 TraesCS3B01G452300 chrUn 95.238 42 2 0 4028 4069 84616569 84616528 3.070000e-07 67.6


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 TraesCS3B01G452300 chr3B 693466539 693471296 4757 True 8787.000000 8787 100.000000 1 4758 1 chr3B.!!$R2 4757
1 TraesCS3B01G452300 chr3B 693736095 693736964 869 True 872.000000 872 85.123000 1416 2288 1 chr3B.!!$R3 872
2 TraesCS3B01G452300 chr3B 693644895 693649641 4746 True 539.750000 905 84.999500 1057 3886 4 chr3B.!!$R5 2829
3 TraesCS3B01G452300 chr3B 693726077 693728929 2852 True 392.500000 579 83.748000 2901 3858 2 chr3B.!!$R6 957
4 TraesCS3B01G452300 chr3B 693598034 693602278 4244 True 375.750000 599 83.517000 1210 3887 4 chr3B.!!$R4 2677
5 TraesCS3B01G452300 chr3D 525535604 525539663 4059 True 5727.000000 5727 92.121000 7 4099 1 chr3D.!!$R3 4092
6 TraesCS3B01G452300 chr3D 525639310 525641746 2436 True 646.333333 953 85.534333 1424 3905 3 chr3D.!!$R5 2481
7 TraesCS3B01G452300 chr3D 316826679 316827261 582 True 342.000000 342 77.534000 103 687 1 chr3D.!!$R2 584
8 TraesCS3B01G452300 chr3D 525631988 525634702 2714 True 337.750000 568 84.631500 1748 3858 4 chr3D.!!$R4 2110
9 TraesCS3B01G452300 chr3A 659621026 659624552 3526 True 5349.000000 5349 93.958000 1124 4684 1 chr3A.!!$R3 3560
10 TraesCS3B01G452300 chr3A 659857158 659858087 929 True 850.000000 850 83.506000 1416 2360 1 chr3A.!!$R6 944
11 TraesCS3B01G452300 chr3A 659821597 659822654 1057 True 798.000000 798 81.039000 2901 3955 1 chr3A.!!$R5 1054
12 TraesCS3B01G452300 chr3A 659800814 659803562 2748 True 369.250000 568 84.101500 1210 3606 4 chr3A.!!$R7 2396
13 TraesCS3B01G452300 chr5D 353517152 353517766 614 False 438.000000 438 79.712000 89 709 1 chr5D.!!$F1 620
14 TraesCS3B01G452300 chr7D 47259273 47259869 596 True 398.000000 398 78.998000 92 704 1 chr7D.!!$R1 612
15 TraesCS3B01G452300 chr2B 14313638 14314247 609 True 435.000000 435 79.777000 89 711 1 chr2B.!!$R1 622
16 TraesCS3B01G452300 chr1A 550833315 550833907 592 True 385.000000 385 78.768000 98 706 1 chr1A.!!$R2 608
17 TraesCS3B01G452300 chr7B 448732214 448732799 585 False 346.000000 346 77.704000 92 684 1 chr7B.!!$F1 592
18 TraesCS3B01G452300 chr7B 450580227 450580813 586 True 342.000000 342 77.575000 92 684 1 chr7B.!!$R1 592

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
696 720 0.034089 ACTGGTATGAAAGGCCTGGC 60.034 55.0 5.69 11.05 0.00 4.85 F
698 722 0.034186 TGGTATGAAAGGCCTGGCTG 60.034 55.0 19.68 0.00 0.00 4.85 F
699 723 0.034089 GGTATGAAAGGCCTGGCTGT 60.034 55.0 19.68 3.18 0.00 4.40 F
778 802 0.164002 GTGGAAAAAGAGCGCTCGTC 59.836 55.0 30.39 23.73 34.09 4.20 F
1602 3762 0.891904 TGCCCCTTAAACAAGCCGAC 60.892 55.0 0.00 0.00 0.00 4.79 F
2444 6161 0.776810 TGGGATTCAAAGGACAGCCA 59.223 50.0 0.00 0.00 36.29 4.75 F
2875 7444 0.829182 CCAAGGGCAGGCTTTGTTCT 60.829 55.0 16.46 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 3677 0.460987 CAGTGCCTCGAGATGAACCC 60.461 60.000 15.71 0.0 0.00 4.11 R
1523 3678 1.086634 GCAGTGCCTCGAGATGAACC 61.087 60.000 15.71 0.0 0.00 3.62 R
2114 4426 1.130777 AGCCACCTTTGCCATTTTGT 58.869 45.000 0.00 0.0 0.00 2.83 R
2142 4454 2.760374 GATTCCATCCGTCCATCAGAC 58.240 52.381 0.00 0.0 42.54 3.51 R
2878 7447 0.459489 AGACTTCGAGATGCTCAGGC 59.541 55.000 0.00 0.0 39.26 4.85 R
3250 7856 1.000506 TCTTCCTCCTCGTCGTTTTGG 59.999 52.381 0.00 0.0 0.00 3.28 R
4500 11250 0.748729 ACGTTTGAGCGACCCCAAAA 60.749 50.000 0.00 0.0 34.52 2.44 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
71 72 2.262915 GTCCCTCTCCTGTGCACG 59.737 66.667 13.13 7.03 0.00 5.34
113 114 2.033448 GGCACCAACACCCATCGA 59.967 61.111 0.00 0.00 0.00 3.59
156 157 0.613260 CGGGGAAAGGAGATGACACA 59.387 55.000 0.00 0.00 0.00 3.72
193 195 2.645567 CTGTCCTGTCGTCGCTGT 59.354 61.111 0.00 0.00 0.00 4.40
207 215 3.023949 GCTGTGCGAGGGACAGGAT 62.024 63.158 17.09 0.00 41.08 3.24
219 227 0.980231 GACAGGATGGTCCAGCTCCT 60.980 60.000 8.08 8.08 43.62 3.69
224 232 2.527951 GATGGTCCAGCTCCTGCGTT 62.528 60.000 0.00 0.00 45.42 4.84
336 344 1.476891 GCCATCACCTCTTCGTAGTCA 59.523 52.381 0.00 0.00 0.00 3.41
389 397 6.710278 TGGACATTGTAGTTGATGAGATCAA 58.290 36.000 0.00 0.00 46.30 2.57
406 414 3.101643 TCAAAATCGGAGAGGGAGAGA 57.898 47.619 0.00 0.00 43.63 3.10
408 416 3.838317 TCAAAATCGGAGAGGGAGAGAAA 59.162 43.478 0.00 0.00 43.63 2.52
419 427 0.458716 GGAGAGAAAAGGACGGAGCG 60.459 60.000 0.00 0.00 0.00 5.03
420 428 0.526662 GAGAGAAAAGGACGGAGCGA 59.473 55.000 0.00 0.00 0.00 4.93
421 429 0.528470 AGAGAAAAGGACGGAGCGAG 59.472 55.000 0.00 0.00 0.00 5.03
422 430 0.526662 GAGAAAAGGACGGAGCGAGA 59.473 55.000 0.00 0.00 0.00 4.04
423 431 0.528470 AGAAAAGGACGGAGCGAGAG 59.472 55.000 0.00 0.00 0.00 3.20
424 432 0.526662 GAAAAGGACGGAGCGAGAGA 59.473 55.000 0.00 0.00 0.00 3.10
518 527 4.631740 TGGGCCGGACCTGACAGA 62.632 66.667 30.93 1.49 39.10 3.41
573 597 6.451340 TCCATCCTATATTTGGGCTGGATATT 59.549 38.462 6.98 0.00 34.34 1.28
582 606 1.679898 GCTGGATATTAGGGGCGCT 59.320 57.895 7.64 9.68 0.00 5.92
605 629 1.072505 AGCCCGGTCGTTTGTTCAT 59.927 52.632 0.00 0.00 0.00 2.57
611 635 2.380660 CGGTCGTTTGTTCATGGTTTG 58.619 47.619 0.00 0.00 0.00 2.93
612 636 2.032302 CGGTCGTTTGTTCATGGTTTGA 59.968 45.455 0.00 0.00 0.00 2.69
613 637 3.487711 CGGTCGTTTGTTCATGGTTTGAA 60.488 43.478 0.00 0.00 42.09 2.69
614 638 4.425520 GGTCGTTTGTTCATGGTTTGAAA 58.574 39.130 0.00 0.00 45.71 2.69
616 640 5.336744 GTCGTTTGTTCATGGTTTGAAAGA 58.663 37.500 0.00 0.00 45.71 2.52
617 641 5.977129 GTCGTTTGTTCATGGTTTGAAAGAT 59.023 36.000 0.00 0.00 45.71 2.40
618 642 6.142320 GTCGTTTGTTCATGGTTTGAAAGATC 59.858 38.462 0.00 0.00 45.71 2.75
619 643 6.039270 TCGTTTGTTCATGGTTTGAAAGATCT 59.961 34.615 0.00 0.00 45.71 2.75
621 645 5.710513 TGTTCATGGTTTGAAAGATCTGG 57.289 39.130 0.00 0.00 45.71 3.86
624 648 5.710513 TCATGGTTTGAAAGATCTGGTTG 57.289 39.130 0.00 0.00 0.00 3.77
625 649 4.523943 TCATGGTTTGAAAGATCTGGTTGG 59.476 41.667 0.00 0.00 0.00 3.77
629 653 5.188751 TGGTTTGAAAGATCTGGTTGGTTTT 59.811 36.000 0.00 0.00 0.00 2.43
630 654 6.112734 GGTTTGAAAGATCTGGTTGGTTTTT 58.887 36.000 0.00 0.00 0.00 1.94
631 655 6.257849 GGTTTGAAAGATCTGGTTGGTTTTTC 59.742 38.462 0.00 0.00 0.00 2.29
632 656 6.790232 TTGAAAGATCTGGTTGGTTTTTCT 57.210 33.333 0.00 0.00 0.00 2.52
633 657 6.790232 TGAAAGATCTGGTTGGTTTTTCTT 57.210 33.333 0.00 0.00 0.00 2.52
634 658 7.181569 TGAAAGATCTGGTTGGTTTTTCTTT 57.818 32.000 0.00 0.00 35.34 2.52
635 659 7.619965 TGAAAGATCTGGTTGGTTTTTCTTTT 58.380 30.769 0.00 0.00 33.44 2.27
636 660 8.100164 TGAAAGATCTGGTTGGTTTTTCTTTTT 58.900 29.630 0.00 0.00 33.44 1.94
663 687 3.319198 AATGACCGGACGGCCTGT 61.319 61.111 9.46 3.00 39.32 4.00
664 688 3.310860 AATGACCGGACGGCCTGTC 62.311 63.158 23.91 23.91 45.54 3.51
672 696 4.250305 ACGGCCTGTCCAAGCGTT 62.250 61.111 0.00 0.00 34.01 4.84
679 703 1.541233 CCTGTCCAAGCGTTTGAGACT 60.541 52.381 23.35 0.00 36.39 3.24
684 708 2.301870 TCCAAGCGTTTGAGACTGGTAT 59.698 45.455 14.10 0.00 36.36 2.73
687 711 3.678056 AGCGTTTGAGACTGGTATGAA 57.322 42.857 0.00 0.00 0.00 2.57
690 714 3.125316 GCGTTTGAGACTGGTATGAAAGG 59.875 47.826 0.00 0.00 0.00 3.11
695 719 1.561542 AGACTGGTATGAAAGGCCTGG 59.438 52.381 5.69 0.00 0.00 4.45
696 720 0.034089 ACTGGTATGAAAGGCCTGGC 60.034 55.000 5.69 11.05 0.00 4.85
697 721 0.257039 CTGGTATGAAAGGCCTGGCT 59.743 55.000 19.68 0.00 0.00 4.75
698 722 0.034186 TGGTATGAAAGGCCTGGCTG 60.034 55.000 19.68 0.00 0.00 4.85
699 723 0.034089 GGTATGAAAGGCCTGGCTGT 60.034 55.000 19.68 3.18 0.00 4.40
700 724 1.211949 GGTATGAAAGGCCTGGCTGTA 59.788 52.381 19.68 1.45 0.00 2.74
701 725 2.565841 GTATGAAAGGCCTGGCTGTAG 58.434 52.381 19.68 0.00 0.00 2.74
702 726 1.289160 ATGAAAGGCCTGGCTGTAGA 58.711 50.000 19.68 0.51 0.00 2.59
703 727 1.289160 TGAAAGGCCTGGCTGTAGAT 58.711 50.000 19.68 0.00 0.00 1.98
714 738 3.470709 TGGCTGTAGATGCTCTAATTGC 58.529 45.455 0.00 0.00 29.58 3.56
726 750 8.975295 AGATGCTCTAATTGCCTATTTTCTTTT 58.025 29.630 0.00 0.00 0.00 2.27
728 752 8.353423 TGCTCTAATTGCCTATTTTCTTTTCT 57.647 30.769 0.00 0.00 0.00 2.52
731 755 9.780413 CTCTAATTGCCTATTTTCTTTTCTGAC 57.220 33.333 0.00 0.00 0.00 3.51
748 772 6.968131 TTCTGACTTAATATCACTGTGCAC 57.032 37.500 10.75 10.75 0.00 4.57
751 775 7.161404 TCTGACTTAATATCACTGTGCACTTT 58.839 34.615 19.41 1.13 0.00 2.66
752 776 7.118245 TCTGACTTAATATCACTGTGCACTTTG 59.882 37.037 19.41 14.57 0.00 2.77
753 777 6.934083 TGACTTAATATCACTGTGCACTTTGA 59.066 34.615 19.41 19.28 0.00 2.69
754 778 7.607607 TGACTTAATATCACTGTGCACTTTGAT 59.392 33.333 26.60 26.60 33.31 2.57
755 779 7.755591 ACTTAATATCACTGTGCACTTTGATG 58.244 34.615 29.28 20.01 31.20 3.07
756 780 7.607607 ACTTAATATCACTGTGCACTTTGATGA 59.392 33.333 29.28 20.46 31.20 2.92
757 781 6.432607 AATATCACTGTGCACTTTGATGAG 57.567 37.500 29.28 16.72 31.20 2.90
758 782 2.497138 TCACTGTGCACTTTGATGAGG 58.503 47.619 19.41 0.00 0.00 3.86
759 783 1.538512 CACTGTGCACTTTGATGAGGG 59.461 52.381 19.41 1.76 0.00 4.30
760 784 1.143684 ACTGTGCACTTTGATGAGGGT 59.856 47.619 19.41 0.00 0.00 4.34
761 785 1.538512 CTGTGCACTTTGATGAGGGTG 59.461 52.381 19.41 0.00 0.00 4.61
762 786 0.883833 GTGCACTTTGATGAGGGTGG 59.116 55.000 10.32 0.00 0.00 4.61
763 787 0.770499 TGCACTTTGATGAGGGTGGA 59.230 50.000 0.00 0.00 0.00 4.02
764 788 1.144708 TGCACTTTGATGAGGGTGGAA 59.855 47.619 0.00 0.00 0.00 3.53
765 789 2.238521 GCACTTTGATGAGGGTGGAAA 58.761 47.619 0.00 0.00 0.00 3.13
766 790 2.627699 GCACTTTGATGAGGGTGGAAAA 59.372 45.455 0.00 0.00 0.00 2.29
767 791 3.069443 GCACTTTGATGAGGGTGGAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
768 792 4.797275 GCACTTTGATGAGGGTGGAAAAAG 60.797 45.833 0.00 0.00 0.00 2.27
769 793 4.584325 CACTTTGATGAGGGTGGAAAAAGA 59.416 41.667 0.00 0.00 0.00 2.52
770 794 4.829492 ACTTTGATGAGGGTGGAAAAAGAG 59.171 41.667 0.00 0.00 0.00 2.85
771 795 2.795329 TGATGAGGGTGGAAAAAGAGC 58.205 47.619 0.00 0.00 0.00 4.09
772 796 1.740025 GATGAGGGTGGAAAAAGAGCG 59.260 52.381 0.00 0.00 0.00 5.03
773 797 0.889186 TGAGGGTGGAAAAAGAGCGC 60.889 55.000 0.00 0.00 0.00 5.92
774 798 0.606673 GAGGGTGGAAAAAGAGCGCT 60.607 55.000 11.27 11.27 0.00 5.92
775 799 0.606673 AGGGTGGAAAAAGAGCGCTC 60.607 55.000 30.01 30.01 0.00 5.03
776 800 1.497722 GGTGGAAAAAGAGCGCTCG 59.502 57.895 30.39 0.00 34.09 5.03
777 801 1.228657 GGTGGAAAAAGAGCGCTCGT 61.229 55.000 30.39 25.69 34.09 4.18
778 802 0.164002 GTGGAAAAAGAGCGCTCGTC 59.836 55.000 30.39 23.73 34.09 4.20
802 826 4.400845 CAGCAGATCGACACATTTTCTTG 58.599 43.478 0.00 0.00 0.00 3.02
803 827 4.067896 AGCAGATCGACACATTTTCTTGT 58.932 39.130 0.00 0.00 0.00 3.16
804 828 4.153117 AGCAGATCGACACATTTTCTTGTC 59.847 41.667 0.00 0.00 39.05 3.18
872 900 1.062148 GCTTATCGTTCCAAACCGCTC 59.938 52.381 0.00 0.00 0.00 5.03
937 965 2.141312 CAAGGGTTTGGGGTTTGGG 58.859 57.895 0.00 0.00 0.00 4.12
986 1014 4.827835 CCCGATCTGATTGACCTAGAGTTA 59.172 45.833 6.46 0.00 0.00 2.24
1058 1086 2.124570 CCGCATTAGTGGCAGCCT 60.125 61.111 14.15 0.00 38.83 4.58
1060 1088 2.528743 CGCATTAGTGGCAGCCTCG 61.529 63.158 14.15 0.00 0.00 4.63
1493 3648 7.458397 TGATTTACTAACTTGGTCTGATTGGT 58.542 34.615 0.00 0.00 0.00 3.67
1516 3671 7.967854 TGGTTTATCATCGATTGCAAAGTTTAG 59.032 33.333 1.71 0.00 0.00 1.85
1522 3677 9.941664 ATCATCGATTGCAAAGTTTAGATAAAG 57.058 29.630 1.71 0.00 0.00 1.85
1523 3678 8.397906 TCATCGATTGCAAAGTTTAGATAAAGG 58.602 33.333 1.71 0.00 0.00 3.11
1532 3687 8.184848 GCAAAGTTTAGATAAAGGGTTCATCTC 58.815 37.037 0.00 0.00 31.60 2.75
1571 3731 3.385193 CCAAATTGGGTGGTTGTTCTC 57.615 47.619 3.60 0.00 32.67 2.87
1589 3749 1.074566 CTCCAGAACTTTCTTGCCCCT 59.925 52.381 0.00 0.00 34.74 4.79
1602 3762 0.891904 TGCCCCTTAAACAAGCCGAC 60.892 55.000 0.00 0.00 0.00 4.79
1688 3850 3.334691 TCTGATTGTTGTTTCCGGCTAG 58.665 45.455 0.00 0.00 0.00 3.42
1893 4202 1.304713 CCCTTGCACAATGGAGGCT 60.305 57.895 0.00 0.00 0.00 4.58
1922 4234 1.884579 CCCATTGCCTGTATCTGATGC 59.115 52.381 0.00 0.00 0.00 3.91
2142 4454 2.417719 GCAAAGGTGGCTATAGATCGG 58.582 52.381 3.21 0.00 0.00 4.18
2347 4663 1.802069 TGCAGTATTTAGCACGCACA 58.198 45.000 0.00 0.00 35.51 4.57
2350 4666 3.555547 TGCAGTATTTAGCACGCACATAG 59.444 43.478 0.00 0.00 35.51 2.23
2363 4744 7.241376 AGCACGCACATAGTAGTTTAATTTTC 58.759 34.615 0.00 0.00 0.00 2.29
2444 6161 0.776810 TGGGATTCAAAGGACAGCCA 59.223 50.000 0.00 0.00 36.29 4.75
2699 7268 9.574516 GTTGTTATATTAATCAAGGATCAGGGT 57.425 33.333 0.00 0.00 0.00 4.34
2756 7325 5.127693 ACAAGCTACTTAGTGTCTCACTG 57.872 43.478 11.92 0.16 45.01 3.66
2842 7411 2.283173 CAGGCCCCCAACAAGGTC 60.283 66.667 0.00 0.00 34.66 3.85
2852 7421 2.432444 CCAACAAGGTCGGCTATGAAA 58.568 47.619 0.00 0.00 0.00 2.69
2871 7440 2.999063 CCCCAAGGGCAGGCTTTG 60.999 66.667 11.58 11.58 35.35 2.77
2872 7441 2.203684 CCCAAGGGCAGGCTTTGT 60.204 61.111 16.46 0.00 0.00 2.83
2873 7442 1.838396 CCCAAGGGCAGGCTTTGTT 60.838 57.895 16.46 0.00 0.00 2.83
2875 7444 0.829182 CCAAGGGCAGGCTTTGTTCT 60.829 55.000 16.46 0.00 0.00 3.01
2876 7445 1.547675 CCAAGGGCAGGCTTTGTTCTA 60.548 52.381 16.46 0.00 0.00 2.10
2877 7446 2.450476 CAAGGGCAGGCTTTGTTCTAT 58.550 47.619 10.44 0.00 0.00 1.98
2878 7447 2.134789 AGGGCAGGCTTTGTTCTATG 57.865 50.000 0.00 0.00 0.00 2.23
2909 7482 5.388408 TCTCGAAGTCTTCCTTTAAGGAC 57.612 43.478 13.98 3.12 45.78 3.85
2962 7545 7.436430 TGTAGTCTTACTGTACTTGTCTGAG 57.564 40.000 0.00 0.00 0.00 3.35
3202 7808 1.986378 CGTCTAAGAGTCTGTTTGCCG 59.014 52.381 0.00 0.00 0.00 5.69
3562 8192 3.737559 TGCCCAGAACTTGATACCATT 57.262 42.857 0.00 0.00 0.00 3.16
3694 10306 0.468400 ATGACTACTCGCTCCCCTCC 60.468 60.000 0.00 0.00 0.00 4.30
4017 10762 5.932303 TGAGCTTATTACTTGTGGTCTGAAC 59.068 40.000 0.00 0.00 0.00 3.18
4046 10791 2.606751 ATACTCCCTCCGTCCCATAG 57.393 55.000 0.00 0.00 0.00 2.23
4055 10800 4.404640 CCTCCGTCCCATAGTATAAGACA 58.595 47.826 10.67 0.00 0.00 3.41
4121 10866 4.993705 AAGAACAACTTATGGGAGTGGA 57.006 40.909 0.00 0.00 37.03 4.02
4122 10867 4.559862 AGAACAACTTATGGGAGTGGAG 57.440 45.455 0.00 0.00 0.00 3.86
4123 10868 4.168101 AGAACAACTTATGGGAGTGGAGA 58.832 43.478 0.00 0.00 0.00 3.71
4124 10869 4.597507 AGAACAACTTATGGGAGTGGAGAA 59.402 41.667 0.00 0.00 0.00 2.87
4125 10870 4.287766 ACAACTTATGGGAGTGGAGAAC 57.712 45.455 0.00 0.00 0.00 3.01
4126 10871 3.650942 ACAACTTATGGGAGTGGAGAACA 59.349 43.478 0.00 0.00 0.00 3.18
4127 10872 4.104102 ACAACTTATGGGAGTGGAGAACAA 59.896 41.667 0.00 0.00 0.00 2.83
4128 10873 4.287766 ACTTATGGGAGTGGAGAACAAC 57.712 45.455 0.00 0.00 0.00 3.32
4129 10874 3.910627 ACTTATGGGAGTGGAGAACAACT 59.089 43.478 0.00 0.00 0.00 3.16
4130 10875 4.351111 ACTTATGGGAGTGGAGAACAACTT 59.649 41.667 0.00 0.00 0.00 2.66
4131 10876 5.546499 ACTTATGGGAGTGGAGAACAACTTA 59.454 40.000 0.00 0.00 0.00 2.24
4132 10877 6.215636 ACTTATGGGAGTGGAGAACAACTTAT 59.784 38.462 0.00 0.00 0.00 1.73
4133 10878 4.286297 TGGGAGTGGAGAACAACTTATG 57.714 45.455 0.00 0.00 0.00 1.90
4134 10879 3.009033 TGGGAGTGGAGAACAACTTATGG 59.991 47.826 0.00 0.00 0.00 2.74
4222 10969 1.391577 ATGGCGCAACTTATCATGCA 58.608 45.000 10.83 0.00 42.68 3.96
4306 11053 4.417426 AGCCATAAAGTACGTAGCCAAT 57.583 40.909 0.00 0.00 0.00 3.16
4349 11096 8.827177 AACAACTTTGAGAATATGACGTTAGA 57.173 30.769 0.00 0.00 0.00 2.10
4356 11103 7.080353 TGAGAATATGACGTTAGAAGAACGA 57.920 36.000 15.99 0.00 45.64 3.85
4358 11105 7.856398 TGAGAATATGACGTTAGAAGAACGATC 59.144 37.037 15.99 10.08 45.64 3.69
4361 11108 9.608617 GAATATGACGTTAGAAGAACGATCATA 57.391 33.333 22.26 22.26 45.64 2.15
4391 11138 5.697633 TCGACCCAAGACTTGTTTGTTATAC 59.302 40.000 14.03 0.00 0.00 1.47
4429 11179 7.375834 TCGTCAGAAGTCAGTTGTTATAACAT 58.624 34.615 18.69 2.48 38.95 2.71
4457 11207 6.423001 AGTGTTAACGTGTGAATTAGTTCCTC 59.577 38.462 0.26 0.00 33.26 3.71
4461 11211 3.323979 ACGTGTGAATTAGTTCCTCAGGT 59.676 43.478 0.00 10.40 34.61 4.00
4500 11250 7.028926 AGTCACTTCTTATCGTACGATGAAT 57.971 36.000 34.91 21.82 36.17 2.57
4503 11253 8.592998 GTCACTTCTTATCGTACGATGAATTTT 58.407 33.333 34.91 14.89 36.17 1.82
4509 11259 3.264104 TCGTACGATGAATTTTGGGGTC 58.736 45.455 15.28 0.00 0.00 4.46
4526 11276 1.419374 GTCGCTCAAACGTCATCTGT 58.581 50.000 0.00 0.00 0.00 3.41
4527 11277 2.592194 GTCGCTCAAACGTCATCTGTA 58.408 47.619 0.00 0.00 0.00 2.74
4555 11305 5.346551 CGGTGATCATAACGACAACTTACAA 59.653 40.000 0.00 0.00 0.00 2.41
4579 11329 6.340522 AGTTCATCAAAAAGTTTGACAAGGG 58.659 36.000 5.59 0.00 0.00 3.95
4595 11345 6.314917 TGACAAGGGACTATATAGCTCATGA 58.685 40.000 9.78 0.00 38.49 3.07
4661 11411 1.671054 CGGTGTGACGGCTTCCATT 60.671 57.895 0.00 0.00 0.00 3.16
4670 11420 1.361668 CGGCTTCCATTGTCGTCTGG 61.362 60.000 0.00 0.00 0.00 3.86
4684 11434 1.459348 TCTGGCCAGACACAGGTGA 60.459 57.895 32.00 6.38 35.47 4.02
4685 11435 1.302033 CTGGCCAGACACAGGTGAC 60.302 63.158 29.88 0.00 0.00 3.67
4686 11436 2.032681 GGCCAGACACAGGTGACC 59.967 66.667 6.40 0.00 0.00 4.02
4687 11437 2.818169 GGCCAGACACAGGTGACCA 61.818 63.158 3.63 0.00 0.00 4.02
4688 11438 1.598130 GCCAGACACAGGTGACCAC 60.598 63.158 3.63 0.00 0.00 4.16
4689 11439 2.044806 GCCAGACACAGGTGACCACT 62.045 60.000 3.63 0.00 0.00 4.00
4690 11440 0.250038 CCAGACACAGGTGACCACTG 60.250 60.000 3.63 0.06 41.64 3.66
4692 11442 1.134401 CAGACACAGGTGACCACTGTT 60.134 52.381 3.63 0.00 46.38 3.16
4693 11443 1.134401 AGACACAGGTGACCACTGTTG 60.134 52.381 3.63 0.00 46.38 3.33
4694 11444 0.107214 ACACAGGTGACCACTGTTGG 60.107 55.000 3.63 0.00 46.38 3.77
4695 11445 0.180171 CACAGGTGACCACTGTTGGA 59.820 55.000 3.63 0.00 46.38 3.53
4696 11446 0.916086 ACAGGTGACCACTGTTGGAA 59.084 50.000 3.63 0.00 46.38 3.53
4697 11447 1.283613 ACAGGTGACCACTGTTGGAAA 59.716 47.619 3.63 0.00 46.38 3.13
4698 11448 2.091885 ACAGGTGACCACTGTTGGAAAT 60.092 45.455 3.63 0.00 46.38 2.17
4699 11449 3.137544 ACAGGTGACCACTGTTGGAAATA 59.862 43.478 3.63 0.00 46.38 1.40
4700 11450 4.202567 ACAGGTGACCACTGTTGGAAATAT 60.203 41.667 3.63 0.00 46.38 1.28
4701 11451 6.267099 ACAGGTGACCACTGTTGGAAATATG 61.267 44.000 3.63 0.00 46.38 1.78
4708 11458 4.780815 CACTGTTGGAAATATGCCCTAGA 58.219 43.478 0.00 0.00 0.00 2.43
4709 11459 4.818546 CACTGTTGGAAATATGCCCTAGAG 59.181 45.833 0.00 0.00 0.00 2.43
4710 11460 4.141390 ACTGTTGGAAATATGCCCTAGAGG 60.141 45.833 0.00 0.00 39.47 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.353437 ACGAAGGCGGACACGGAC 62.353 66.667 5.57 0.00 43.17 4.79
1 2 4.047059 GACGAAGGCGGACACGGA 62.047 66.667 5.57 0.00 43.17 4.69
39 40 4.400109 GACGCGACGGAGCAGTCA 62.400 66.667 15.93 0.00 40.98 3.41
50 51 3.062466 CACAGGAGAGGGACGCGA 61.062 66.667 15.93 0.00 0.00 5.87
53 54 2.262915 GTGCACAGGAGAGGGACG 59.737 66.667 13.17 0.00 0.00 4.79
113 114 4.101448 GCTCCTCCACACGGGCAT 62.101 66.667 0.00 0.00 36.21 4.40
193 195 2.284625 ACCATCCTGTCCCTCGCA 60.285 61.111 0.00 0.00 0.00 5.10
207 215 3.240134 GAACGCAGGAGCTGGACCA 62.240 63.158 0.00 0.00 39.10 4.02
336 344 3.453679 GACTCCGGCTCCGAGCTT 61.454 66.667 19.68 0.07 41.99 3.74
389 397 3.198853 CCTTTTCTCTCCCTCTCCGATTT 59.801 47.826 0.00 0.00 0.00 2.17
406 414 0.528470 CTCTCTCGCTCCGTCCTTTT 59.472 55.000 0.00 0.00 0.00 2.27
408 416 0.746563 CTCTCTCTCGCTCCGTCCTT 60.747 60.000 0.00 0.00 0.00 3.36
419 427 3.550437 AGCTCACTCTCTCTCTCTCTC 57.450 52.381 0.00 0.00 0.00 3.20
420 428 3.389329 CCTAGCTCACTCTCTCTCTCTCT 59.611 52.174 0.00 0.00 0.00 3.10
421 429 3.495100 CCCTAGCTCACTCTCTCTCTCTC 60.495 56.522 0.00 0.00 0.00 3.20
422 430 2.439507 CCCTAGCTCACTCTCTCTCTCT 59.560 54.545 0.00 0.00 0.00 3.10
423 431 2.172717 ACCCTAGCTCACTCTCTCTCTC 59.827 54.545 0.00 0.00 0.00 3.20
424 432 2.205342 ACCCTAGCTCACTCTCTCTCT 58.795 52.381 0.00 0.00 0.00 3.10
478 487 2.113139 GCCCCCACATATGTCCCG 59.887 66.667 5.07 0.00 0.00 5.14
514 523 2.267006 CAGGGCGCATCTGTCTGT 59.733 61.111 10.83 0.00 0.00 3.41
582 606 3.552384 AAACGACCGGGCTGACCA 61.552 61.111 5.33 0.00 40.22 4.02
589 613 0.887387 ACCATGAACAAACGACCGGG 60.887 55.000 6.32 0.00 0.00 5.73
605 629 3.909732 ACCAACCAGATCTTTCAAACCA 58.090 40.909 0.00 0.00 0.00 3.67
611 635 8.492673 AAAAAGAAAAACCAACCAGATCTTTC 57.507 30.769 0.00 0.00 35.31 2.62
633 657 1.604755 CGGTCATTGTCCGGTCAAAAA 59.395 47.619 17.94 6.61 43.68 1.94
634 658 1.231221 CGGTCATTGTCCGGTCAAAA 58.769 50.000 17.94 6.96 43.68 2.44
635 659 2.921374 CGGTCATTGTCCGGTCAAA 58.079 52.632 17.94 3.52 43.68 2.69
636 660 4.685447 CGGTCATTGTCCGGTCAA 57.315 55.556 16.44 16.44 43.68 3.18
641 665 2.508439 CCGTCCGGTCATTGTCCG 60.508 66.667 14.32 14.32 46.49 4.79
642 666 2.818274 GCCGTCCGGTCATTGTCC 60.818 66.667 7.66 0.00 37.65 4.02
663 687 0.468226 ACCAGTCTCAAACGCTTGGA 59.532 50.000 0.00 0.00 33.01 3.53
664 688 2.163818 TACCAGTCTCAAACGCTTGG 57.836 50.000 0.00 0.00 33.01 3.61
672 696 2.912956 AGGCCTTTCATACCAGTCTCAA 59.087 45.455 0.00 0.00 0.00 3.02
679 703 0.034186 CAGCCAGGCCTTTCATACCA 60.034 55.000 8.22 0.00 0.00 3.25
684 708 1.065199 CATCTACAGCCAGGCCTTTCA 60.065 52.381 8.22 0.00 0.00 2.69
687 711 1.225704 GCATCTACAGCCAGGCCTT 59.774 57.895 8.22 0.00 0.00 4.35
690 714 4.453093 GAGCATCTACAGCCAGGC 57.547 61.111 1.84 1.84 0.00 4.85
701 725 9.242477 GAAAAGAAAATAGGCAATTAGAGCATC 57.758 33.333 0.00 0.00 0.00 3.91
702 726 8.975295 AGAAAAGAAAATAGGCAATTAGAGCAT 58.025 29.630 0.00 0.00 0.00 3.79
703 727 8.246180 CAGAAAAGAAAATAGGCAATTAGAGCA 58.754 33.333 0.00 0.00 0.00 4.26
726 750 6.286240 AGTGCACAGTGATATTAAGTCAGA 57.714 37.500 21.04 0.00 0.00 3.27
728 752 6.934083 TCAAAGTGCACAGTGATATTAAGTCA 59.066 34.615 21.04 0.00 0.00 3.41
731 755 7.977904 TCATCAAAGTGCACAGTGATATTAAG 58.022 34.615 25.89 17.15 0.00 1.85
748 772 4.321527 GCTCTTTTTCCACCCTCATCAAAG 60.322 45.833 0.00 0.00 0.00 2.77
751 775 2.795329 GCTCTTTTTCCACCCTCATCA 58.205 47.619 0.00 0.00 0.00 3.07
752 776 1.740025 CGCTCTTTTTCCACCCTCATC 59.260 52.381 0.00 0.00 0.00 2.92
753 777 1.826385 CGCTCTTTTTCCACCCTCAT 58.174 50.000 0.00 0.00 0.00 2.90
754 778 0.889186 GCGCTCTTTTTCCACCCTCA 60.889 55.000 0.00 0.00 0.00 3.86
755 779 0.606673 AGCGCTCTTTTTCCACCCTC 60.607 55.000 2.64 0.00 0.00 4.30
756 780 0.606673 GAGCGCTCTTTTTCCACCCT 60.607 55.000 29.88 0.00 0.00 4.34
757 781 1.876664 GAGCGCTCTTTTTCCACCC 59.123 57.895 29.88 0.00 0.00 4.61
758 782 1.228657 ACGAGCGCTCTTTTTCCACC 61.229 55.000 32.88 5.58 0.00 4.61
759 783 0.164002 GACGAGCGCTCTTTTTCCAC 59.836 55.000 32.88 8.95 0.00 4.02
760 784 1.282248 CGACGAGCGCTCTTTTTCCA 61.282 55.000 32.88 0.00 0.00 3.53
761 785 1.416434 CGACGAGCGCTCTTTTTCC 59.584 57.895 32.88 12.49 0.00 3.13
773 797 1.936880 GTCGATCTGCTGCGACGAG 60.937 63.158 0.00 0.00 45.81 4.18
774 798 2.100410 GTCGATCTGCTGCGACGA 59.900 61.111 0.00 0.78 45.81 4.20
777 801 0.108662 AATGTGTCGATCTGCTGCGA 60.109 50.000 0.00 0.00 0.00 5.10
778 802 0.723414 AAATGTGTCGATCTGCTGCG 59.277 50.000 0.00 0.00 0.00 5.18
802 826 3.453679 AAGAGAGCGGAGGCGGAC 61.454 66.667 0.00 0.00 46.35 4.79
803 827 3.452786 CAAGAGAGCGGAGGCGGA 61.453 66.667 0.00 0.00 46.35 5.54
804 828 4.521062 CCAAGAGAGCGGAGGCGG 62.521 72.222 0.00 0.00 46.35 6.13
856 884 1.468520 CAATGAGCGGTTTGGAACGAT 59.531 47.619 0.00 0.00 0.00 3.73
872 900 2.203126 GGGAGCCGAGAGCCAATG 60.203 66.667 0.00 0.00 45.47 2.82
959 987 1.281867 AGGTCAATCAGATCGGGCAAA 59.718 47.619 0.00 0.00 30.60 3.68
1107 1135 0.877213 TCATGATGCGCCTGATGTCG 60.877 55.000 11.40 0.00 0.00 4.35
1220 1254 0.234884 CGTTCAAGCCAAACGGAGAC 59.765 55.000 7.70 0.00 44.27 3.36
1516 3671 3.181465 TGCCTCGAGATGAACCCTTTATC 60.181 47.826 15.71 0.00 0.00 1.75
1521 3676 0.616111 AGTGCCTCGAGATGAACCCT 60.616 55.000 15.71 0.00 0.00 4.34
1522 3677 0.460987 CAGTGCCTCGAGATGAACCC 60.461 60.000 15.71 0.00 0.00 4.11
1523 3678 1.086634 GCAGTGCCTCGAGATGAACC 61.087 60.000 15.71 0.00 0.00 3.62
1532 3687 2.256461 GCCAAAAGCAGTGCCTCG 59.744 61.111 12.58 0.00 42.97 4.63
1571 3731 2.001076 AAGGGGCAAGAAAGTTCTGG 57.999 50.000 0.00 0.00 37.65 3.86
1589 3749 2.303175 AGCAAAGGTCGGCTTGTTTAA 58.697 42.857 0.00 0.00 36.92 1.52
1632 3793 9.169592 TGAATACGAAATACCCTTCTTTAAAGG 57.830 33.333 15.13 2.60 37.17 3.11
1637 3799 6.415573 AGCTGAATACGAAATACCCTTCTTT 58.584 36.000 0.00 0.00 0.00 2.52
1640 3802 7.964604 ATTAGCTGAATACGAAATACCCTTC 57.035 36.000 0.00 0.00 0.00 3.46
1688 3850 1.747355 CCAATGGCTGATCAAGTGGTC 59.253 52.381 4.53 0.00 0.00 4.02
1830 4135 5.071384 TCATCACAGAGATAACATGGATGCT 59.929 40.000 0.00 0.00 34.43 3.79
2114 4426 1.130777 AGCCACCTTTGCCATTTTGT 58.869 45.000 0.00 0.00 0.00 2.83
2142 4454 2.760374 GATTCCATCCGTCCATCAGAC 58.240 52.381 0.00 0.00 42.54 3.51
2343 4659 9.763465 TTTAGCGAAAATTAAACTACTATGTGC 57.237 29.630 0.00 0.00 0.00 4.57
2350 4666 9.601971 TGACATGTTTAGCGAAAATTAAACTAC 57.398 29.630 0.00 0.00 39.39 2.73
2429 6146 3.323751 GCATTTGGCTGTCCTTTGAAT 57.676 42.857 0.00 0.00 40.25 2.57
2444 6161 8.917088 ACAAATATAGCCATACAGAAAGCATTT 58.083 29.630 0.00 0.00 43.98 2.32
2756 7325 8.499403 AGCATTACTTTTTCATCTCCTCTTAC 57.501 34.615 0.00 0.00 0.00 2.34
2796 7365 7.391148 AGTCACTAGTTGCTTTTCTCAAAAA 57.609 32.000 0.00 0.00 33.42 1.94
2842 7411 0.751643 CCTTGGGGGTTTCATAGCCG 60.752 60.000 0.00 0.00 45.75 5.52
2865 7434 3.201225 TGCTCAGGCATAGAACAAAGCC 61.201 50.000 0.00 0.00 44.28 4.35
2866 7435 2.086869 TGCTCAGGCATAGAACAAAGC 58.913 47.619 0.00 0.00 44.28 3.51
2878 7447 0.459489 AGACTTCGAGATGCTCAGGC 59.541 55.000 0.00 0.00 39.26 4.85
2962 7545 4.056050 AGACACACATGAACCGAGTAAAC 58.944 43.478 0.00 0.00 0.00 2.01
3202 7808 6.292596 GCTCTATTGAATCTGAATCGAACCAC 60.293 42.308 0.00 0.00 0.00 4.16
3250 7856 1.000506 TCTTCCTCCTCGTCGTTTTGG 59.999 52.381 0.00 0.00 0.00 3.28
3391 8009 1.215423 AGGATGGCATACACCCCTTTC 59.785 52.381 13.22 0.00 33.22 2.62
3562 8192 1.257743 CTTCACCTTCGTCCTCCTCA 58.742 55.000 0.00 0.00 0.00 3.86
4017 10762 5.353400 GGACGGAGGGAGTATTTGTTAAAAG 59.647 44.000 0.00 0.00 0.00 2.27
4046 10791 9.405587 TGTTTAGCTTGCAAAAATGTCTTATAC 57.594 29.630 0.00 0.00 0.00 1.47
4055 10800 8.661352 ACATAAGTTGTTTAGCTTGCAAAAAT 57.339 26.923 0.00 0.00 33.74 1.82
4115 10860 4.020128 ACTCCCATAAGTTGTTCTCCACTC 60.020 45.833 0.00 0.00 0.00 3.51
4116 10861 3.910627 ACTCCCATAAGTTGTTCTCCACT 59.089 43.478 0.00 0.00 0.00 4.00
4117 10862 4.003648 CACTCCCATAAGTTGTTCTCCAC 58.996 47.826 0.00 0.00 0.00 4.02
4118 10863 3.009033 CCACTCCCATAAGTTGTTCTCCA 59.991 47.826 0.00 0.00 0.00 3.86
4119 10864 3.263425 TCCACTCCCATAAGTTGTTCTCC 59.737 47.826 0.00 0.00 0.00 3.71
4120 10865 4.553330 TCCACTCCCATAAGTTGTTCTC 57.447 45.455 0.00 0.00 0.00 2.87
4121 10866 4.104102 TGTTCCACTCCCATAAGTTGTTCT 59.896 41.667 0.00 0.00 0.00 3.01
4122 10867 4.394729 TGTTCCACTCCCATAAGTTGTTC 58.605 43.478 0.00 0.00 0.00 3.18
4123 10868 4.447138 TGTTCCACTCCCATAAGTTGTT 57.553 40.909 0.00 0.00 0.00 2.83
4124 10869 4.335416 CATGTTCCACTCCCATAAGTTGT 58.665 43.478 0.00 0.00 0.00 3.32
4125 10870 3.129287 GCATGTTCCACTCCCATAAGTTG 59.871 47.826 0.00 0.00 0.00 3.16
4126 10871 3.010584 AGCATGTTCCACTCCCATAAGTT 59.989 43.478 0.00 0.00 0.00 2.66
4127 10872 2.578021 AGCATGTTCCACTCCCATAAGT 59.422 45.455 0.00 0.00 0.00 2.24
4128 10873 3.287867 AGCATGTTCCACTCCCATAAG 57.712 47.619 0.00 0.00 0.00 1.73
4129 10874 4.853468 TTAGCATGTTCCACTCCCATAA 57.147 40.909 0.00 0.00 0.00 1.90
4130 10875 4.853468 TTTAGCATGTTCCACTCCCATA 57.147 40.909 0.00 0.00 0.00 2.74
4131 10876 3.737559 TTTAGCATGTTCCACTCCCAT 57.262 42.857 0.00 0.00 0.00 4.00
4132 10877 3.181434 ACTTTTAGCATGTTCCACTCCCA 60.181 43.478 0.00 0.00 0.00 4.37
4133 10878 3.421844 ACTTTTAGCATGTTCCACTCCC 58.578 45.455 0.00 0.00 0.00 4.30
4134 10879 6.569179 TTTACTTTTAGCATGTTCCACTCC 57.431 37.500 0.00 0.00 0.00 3.85
4175 10920 8.188799 TGTACTCTGTAGGATAAAAGATTGTCG 58.811 37.037 0.00 0.00 0.00 4.35
4222 10969 6.373495 GGTACCTAACAAAGTTCCATCGAAAT 59.627 38.462 4.06 0.00 0.00 2.17
4341 11088 7.909777 TCAATATGATCGTTCTTCTAACGTC 57.090 36.000 9.76 7.68 43.47 4.34
4349 11096 5.696724 GGGTCGATTCAATATGATCGTTCTT 59.303 40.000 13.00 0.00 37.73 2.52
4356 11103 6.179906 AGTCTTGGGTCGATTCAATATGAT 57.820 37.500 0.00 0.00 0.00 2.45
4358 11105 5.586243 ACAAGTCTTGGGTCGATTCAATATG 59.414 40.000 16.85 0.00 34.12 1.78
4361 11108 4.021102 ACAAGTCTTGGGTCGATTCAAT 57.979 40.909 16.85 0.00 34.12 2.57
4391 11138 6.808704 TGACTTCTGACGATTGTATCTCAAAG 59.191 38.462 0.00 0.00 39.62 2.77
4406 11153 7.602644 TCCATGTTATAACAACTGACTTCTGAC 59.397 37.037 21.57 0.00 43.03 3.51
4429 11179 5.603596 ACTAATTCACACGTTAACACTCCA 58.396 37.500 6.39 0.00 0.00 3.86
4440 11190 3.926616 ACCTGAGGAACTAATTCACACG 58.073 45.455 4.99 0.00 41.55 4.49
4457 11207 6.489700 AGTGACTATGATACTCTCATGACCTG 59.510 42.308 0.00 0.00 44.48 4.00
4461 11211 8.759481 AAGAAGTGACTATGATACTCTCATGA 57.241 34.615 0.00 0.00 44.48 3.07
4500 11250 0.748729 ACGTTTGAGCGACCCCAAAA 60.749 50.000 0.00 0.00 34.52 2.44
4503 11253 2.029964 GACGTTTGAGCGACCCCA 59.970 61.111 0.00 0.00 35.59 4.96
4509 11259 2.729360 TGTTACAGATGACGTTTGAGCG 59.271 45.455 0.00 0.00 37.94 5.03
4526 11276 4.437772 TGTCGTTATGATCACCGTGTTA 57.562 40.909 0.00 0.00 0.00 2.41
4527 11277 3.306917 TGTCGTTATGATCACCGTGTT 57.693 42.857 0.00 0.00 0.00 3.32
4555 11305 6.154363 TCCCTTGTCAAACTTTTTGATGAACT 59.846 34.615 4.72 0.00 0.00 3.01
4579 11329 7.416964 AATCCCACTCATGAGCTATATAGTC 57.583 40.000 22.83 8.13 0.00 2.59
4582 11332 6.214208 AGCAAATCCCACTCATGAGCTATATA 59.786 38.462 22.83 4.21 0.00 0.86
4595 11345 1.079127 CGTCGGAGCAAATCCCACT 60.079 57.895 0.00 0.00 46.50 4.00
4617 11367 4.534103 AGGGCCATAAGAATATCTCTCCAC 59.466 45.833 6.18 0.00 31.02 4.02
4670 11420 1.598130 GTGGTCACCTGTGTCTGGC 60.598 63.158 0.00 0.00 0.00 4.85
4684 11434 2.042979 AGGGCATATTTCCAACAGTGGT 59.957 45.455 0.00 0.00 46.11 4.16
4686 11436 4.780815 TCTAGGGCATATTTCCAACAGTG 58.219 43.478 0.00 0.00 0.00 3.66
4687 11437 4.141390 CCTCTAGGGCATATTTCCAACAGT 60.141 45.833 0.00 0.00 0.00 3.55
4688 11438 4.392940 CCTCTAGGGCATATTTCCAACAG 58.607 47.826 0.00 0.00 0.00 3.16
4689 11439 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.