Multiple sequence alignment - TraesCS7B01G080200

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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 TraesCS7B01G080200 chr7B 100.000 5390 0 0 1 5390 89949316 89954705 0.000000e+00 9954.0
1 TraesCS7B01G080200 chr7B 89.522 439 40 4 4953 5390 656194165 656193732 7.890000e-153 551.0
2 TraesCS7B01G080200 chr7A 92.780 2050 109 27 732 2760 128780865 128782896 0.000000e+00 2929.0
3 TraesCS7B01G080200 chr7A 91.803 793 36 4 3434 4224 128783591 128784356 0.000000e+00 1077.0
4 TraesCS7B01G080200 chr7A 94.420 681 31 5 2745 3422 128782931 128783607 0.000000e+00 1040.0
5 TraesCS7B01G080200 chr7A 85.610 549 59 5 28 558 128779136 128779682 4.720000e-155 558.0
6 TraesCS7B01G080200 chr7A 79.912 682 96 25 4719 5372 105644197 105644865 3.800000e-126 462.0
7 TraesCS7B01G080200 chr7A 85.642 397 31 14 4184 4578 128784358 128784730 1.410000e-105 394.0
8 TraesCS7B01G080200 chr7D 93.132 1587 85 12 834 2405 128784811 128786388 0.000000e+00 2305.0
9 TraesCS7B01G080200 chr7D 88.925 1237 85 23 2406 3601 128786416 128787641 0.000000e+00 1478.0
10 TraesCS7B01G080200 chr7D 90.943 806 38 16 3599 4372 128787734 128788536 0.000000e+00 1051.0
11 TraesCS7B01G080200 chr7D 79.424 695 100 26 4718 5388 183030871 183031546 8.230000e-123 451.0
12 TraesCS7B01G080200 chr7D 85.037 401 46 5 5000 5388 413445901 413446299 3.910000e-106 396.0
13 TraesCS7B01G080200 chr7D 93.023 215 14 1 4365 4578 128788794 128789008 4.050000e-81 313.0
14 TraesCS7B01G080200 chr7D 92.857 140 10 0 4580 4719 128789073 128789212 2.550000e-48 204.0
15 TraesCS7B01G080200 chr7D 82.857 105 17 1 1 104 436506117 436506013 5.750000e-15 93.5
16 TraesCS7B01G080200 chr7D 87.805 82 1 2 703 775 128784642 128784723 2.670000e-13 87.9
17 TraesCS7B01G080200 chr6B 86.605 433 53 2 4953 5385 597109505 597109078 1.760000e-129 473.0
18 TraesCS7B01G080200 chr6B 75.362 690 105 39 4719 5358 5555704 5556378 6.880000e-69 272.0
19 TraesCS7B01G080200 chr5D 79.659 703 99 27 4719 5388 27101521 27102212 2.940000e-127 466.0
20 TraesCS7B01G080200 chr5D 82.105 380 50 8 5000 5370 463083800 463083430 5.240000e-80 309.0
21 TraesCS7B01G080200 chr5D 83.858 254 36 3 2874 3123 259443622 259443874 2.510000e-58 237.0
22 TraesCS7B01G080200 chr5D 84.615 234 30 4 2855 3086 77916778 77917007 1.510000e-55 228.0
23 TraesCS7B01G080200 chr5D 83.410 217 27 8 2982 3197 522152780 522152988 5.510000e-45 193.0
24 TraesCS7B01G080200 chr5D 84.848 165 23 2 2856 3018 352828089 352828253 1.200000e-36 165.0
25 TraesCS7B01G080200 chr5D 89.189 74 7 1 2856 2928 403937774 403937701 2.070000e-14 91.6
26 TraesCS7B01G080200 chr5A 80.534 637 83 29 4718 5330 670229250 670229869 8.230000e-123 451.0
27 TraesCS7B01G080200 chr5A 77.711 664 92 32 4729 5355 342573874 342574518 6.640000e-94 355.0
28 TraesCS7B01G080200 chr5A 79.045 377 53 16 2856 3217 439874581 439874216 9.030000e-58 235.0
29 TraesCS7B01G080200 chr5A 81.633 294 43 11 2856 3142 510278638 510278349 3.250000e-57 233.0
30 TraesCS7B01G080200 chr5A 82.805 221 28 8 2979 3197 650288340 650288552 7.130000e-44 189.0
31 TraesCS7B01G080200 chr4D 83.081 396 49 7 5009 5388 493877517 493877124 1.440000e-90 344.0
32 TraesCS7B01G080200 chr4D 86.585 82 5 6 705 783 123147701 123147623 9.620000e-13 86.1
33 TraesCS7B01G080200 chr3B 76.257 716 100 37 4719 5386 25387740 25387047 3.130000e-82 316.0
34 TraesCS7B01G080200 chr3B 84.974 193 28 1 4953 5145 450824411 450824602 1.530000e-45 195.0
35 TraesCS7B01G080200 chr3B 71.598 676 136 29 14 640 662509600 662508932 3.390000e-27 134.0
36 TraesCS7B01G080200 chr2D 86.842 266 31 4 2856 3119 11394132 11393869 1.470000e-75 294.0
37 TraesCS7B01G080200 chr2A 82.941 340 36 14 2876 3197 11998620 11998285 2.460000e-73 287.0
38 TraesCS7B01G080200 chr5B 86.585 164 20 2 2856 3017 415799640 415799803 4.290000e-41 180.0
39 TraesCS7B01G080200 chr5B 79.583 240 30 10 2854 3087 403701748 403701522 2.600000e-33 154.0
40 TraesCS7B01G080200 chr4B 88.652 141 13 3 2939 3078 272067106 272067244 9.280000e-38 169.0
41 TraesCS7B01G080200 chr4B 89.552 67 4 3 706 772 187734967 187734904 1.240000e-11 82.4
42 TraesCS7B01G080200 chr1D 75.743 404 60 24 2856 3239 261744493 261744878 9.280000e-38 169.0
43 TraesCS7B01G080200 chr1D 100.000 29 0 0 703 731 457942189 457942217 3.000000e-03 54.7
44 TraesCS7B01G080200 chr2B 84.252 127 18 2 5 129 1211770 1211644 7.330000e-24 122.0
45 TraesCS7B01G080200 chr4A 88.889 72 5 3 703 774 446594547 446594615 9.620000e-13 86.1
46 TraesCS7B01G080200 chr1B 100.000 31 0 0 703 733 628002872 628002902 2.100000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G080200 chr7B 89949316 89954705 5389 False 9954.000000 9954 100.000000 1 5390 1 chr7B.!!$F1 5389
1 TraesCS7B01G080200 chr7A 128779136 128784730 5594 False 1199.600000 2929 90.051000 28 4578 5 chr7A.!!$F2 4550
2 TraesCS7B01G080200 chr7A 105644197 105644865 668 False 462.000000 462 79.912000 4719 5372 1 chr7A.!!$F1 653
3 TraesCS7B01G080200 chr7D 128784642 128789212 4570 False 906.483333 2305 91.114167 703 4719 6 chr7D.!!$F3 4016
4 TraesCS7B01G080200 chr7D 183030871 183031546 675 False 451.000000 451 79.424000 4718 5388 1 chr7D.!!$F1 670
5 TraesCS7B01G080200 chr6B 5555704 5556378 674 False 272.000000 272 75.362000 4719 5358 1 chr6B.!!$F1 639
6 TraesCS7B01G080200 chr5D 27101521 27102212 691 False 466.000000 466 79.659000 4719 5388 1 chr5D.!!$F1 669
7 TraesCS7B01G080200 chr5A 670229250 670229869 619 False 451.000000 451 80.534000 4718 5330 1 chr5A.!!$F3 612
8 TraesCS7B01G080200 chr5A 342573874 342574518 644 False 355.000000 355 77.711000 4729 5355 1 chr5A.!!$F1 626
9 TraesCS7B01G080200 chr3B 25387047 25387740 693 True 316.000000 316 76.257000 4719 5386 1 chr3B.!!$R1 667

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
367 383 0.107993 AGTGATCGGTAGACGGACGA 60.108 55.000 0.0 0.0 44.45 4.20 F
423 440 0.393077 ATGATTAACGGAGGGAGGCG 59.607 55.000 0.0 0.0 0.00 5.52 F
1395 2549 0.100146 GGTACCGAGGTTCACTAGCG 59.900 60.000 0.0 0.0 0.00 4.26 F
1418 2572 0.179029 CTCCGTTCCTTGTGGTGGTT 60.179 55.000 0.0 0.0 34.23 3.67 F
1791 2945 0.546747 CCCCCTTGTCTGGTCCTGTA 60.547 60.000 0.0 0.0 0.00 2.74 F
3141 4428 1.289530 AGGTGGGGGTCAGTTTGAAAA 59.710 47.619 0.0 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 2540 0.032952 AACGGAGCAACGCTAGTGAA 59.967 50.000 10.99 0.0 39.88 3.18 R
2221 3388 0.320421 TCGGGACCGCTGAAAAGAAG 60.320 55.000 5.75 0.0 39.59 2.85 R
2721 3935 2.900122 ATGCACAAAATCTCGTTCCG 57.100 45.000 0.00 0.0 0.00 4.30 R
3185 4472 3.717294 CTTCCACCCCTCCCACCG 61.717 72.222 0.00 0.0 0.00 4.94 R
3457 4747 6.013984 TCAAAATCCGAGGGAAGTAGTAGTTT 60.014 38.462 0.00 0.0 34.34 2.66 R
4646 6435 0.105593 GATCGATCCCAGAAGCTGCA 59.894 55.000 14.76 0.0 0.00 4.41 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
23 24 4.410400 GCTGGTGGGCCTACGCTT 62.410 66.667 13.72 0.00 35.27 4.68
24 25 2.436646 CTGGTGGGCCTACGCTTG 60.437 66.667 13.72 0.00 35.27 4.01
25 26 4.715523 TGGTGGGCCTACGCTTGC 62.716 66.667 13.72 0.00 35.27 4.01
56 57 0.768622 TCCCGTTCTTCCAACACCAT 59.231 50.000 0.00 0.00 0.00 3.55
57 58 0.881118 CCCGTTCTTCCAACACCATG 59.119 55.000 0.00 0.00 0.00 3.66
73 74 0.532573 CATGTCGGTGTAGTGAGCCT 59.467 55.000 0.00 0.00 0.00 4.58
105 106 3.272334 GCGATGCCGACATGGGAC 61.272 66.667 0.00 0.00 43.03 4.46
106 107 2.186644 CGATGCCGACATGGGACA 59.813 61.111 0.00 0.00 43.03 4.02
157 158 2.203832 TGGCCACTGGAGAGCTCA 60.204 61.111 17.77 0.00 0.00 4.26
163 164 1.381056 ACTGGAGAGCTCATCCGCT 60.381 57.895 17.77 6.14 44.33 5.52
169 170 1.139734 GAGCTCATCCGCTTGTCGA 59.860 57.895 9.40 0.00 41.08 4.20
172 173 1.215382 CTCATCCGCTTGTCGACCA 59.785 57.895 14.12 0.00 41.67 4.02
186 187 1.078426 GACCACAGTGGCGGCTATT 60.078 57.895 20.48 0.00 42.67 1.73
202 203 6.202226 GCGGCTATTTCCTTCTTTAATTCAG 58.798 40.000 0.00 0.00 0.00 3.02
211 212 4.568760 CCTTCTTTAATTCAGACGAGAGGC 59.431 45.833 0.00 0.00 42.06 4.70
221 222 4.069232 CGAGAGGCTGTCCCGCAA 62.069 66.667 6.02 0.00 39.21 4.85
249 250 2.132996 CAGAGCTCGAGGAGGCCAT 61.133 63.158 15.58 0.00 0.00 4.40
252 253 1.965754 GAGCTCGAGGAGGCCATGTT 61.966 60.000 15.58 0.00 0.00 2.71
263 264 0.324275 GGCCATGTTGGGTGTGGTAT 60.324 55.000 0.00 0.00 38.19 2.73
280 281 0.556258 TATCGAGAGGAGGCAGGGAA 59.444 55.000 0.00 0.00 0.00 3.97
317 333 1.469308 CGGGCGTTTAAATAACAGGCA 59.531 47.619 0.00 0.00 0.00 4.75
323 339 4.142469 GCGTTTAAATAACAGGCAGATGGT 60.142 41.667 0.00 0.00 0.00 3.55
338 354 1.982395 TGGTAGACCAGGTGGCGAG 60.982 63.158 0.00 0.00 42.01 5.03
357 373 3.067742 CGAGGTGGTTAATAGTGATCGGT 59.932 47.826 0.00 0.00 0.00 4.69
362 378 5.210715 GTGGTTAATAGTGATCGGTAGACG 58.789 45.833 0.00 0.00 46.11 4.18
365 381 5.447573 GTTAATAGTGATCGGTAGACGGAC 58.552 45.833 0.00 0.00 44.45 4.79
367 383 0.107993 AGTGATCGGTAGACGGACGA 60.108 55.000 0.00 0.00 44.45 4.20
369 385 1.332997 GTGATCGGTAGACGGACGAAT 59.667 52.381 0.00 0.00 44.45 3.34
371 387 1.600957 GATCGGTAGACGGACGAATGA 59.399 52.381 0.00 0.00 44.45 2.57
383 399 2.785258 GAATGAGCGGCGTTGGAC 59.215 61.111 9.37 0.00 0.00 4.02
414 431 2.217847 CGGCTACGAACATGATTAACGG 59.782 50.000 0.00 0.00 44.60 4.44
423 440 0.393077 ATGATTAACGGAGGGAGGCG 59.607 55.000 0.00 0.00 0.00 5.52
452 469 3.425094 CGGTTTATCATTTGAACGCGGAA 60.425 43.478 12.47 0.00 0.00 4.30
458 475 0.671251 ATTTGAACGCGGAAAAGGCA 59.329 45.000 12.47 0.00 0.00 4.75
459 476 0.671251 TTTGAACGCGGAAAAGGCAT 59.329 45.000 12.47 0.00 0.00 4.40
521 538 1.353103 CGCTTTAATGCTGGCTCCG 59.647 57.895 11.16 0.00 0.00 4.63
522 539 1.089481 CGCTTTAATGCTGGCTCCGA 61.089 55.000 11.16 0.00 0.00 4.55
532 549 1.000359 TGGCTCCGATGAGAGGTCA 60.000 57.895 0.00 0.00 41.42 4.02
534 551 1.439644 GCTCCGATGAGAGGTCACC 59.560 63.158 0.00 0.00 41.42 4.02
545 562 3.775654 GGTCACCTCCGCTCTGGG 61.776 72.222 0.00 0.00 38.76 4.45
553 570 4.473520 CCGCTCTGGGCCGAATGT 62.474 66.667 0.00 0.00 37.74 2.71
571 588 3.741476 GGCGCTGGCACTTTGGAG 61.741 66.667 7.64 0.00 42.47 3.86
572 589 2.980233 GCGCTGGCACTTTGGAGT 60.980 61.111 0.00 0.00 39.62 3.85
581 598 3.290776 ACTTTGGAGTGACGCTGAC 57.709 52.632 0.00 0.00 33.99 3.51
582 599 0.753262 ACTTTGGAGTGACGCTGACT 59.247 50.000 0.00 0.00 33.99 3.41
583 600 1.143305 CTTTGGAGTGACGCTGACTG 58.857 55.000 0.00 0.00 0.00 3.51
584 601 0.880278 TTTGGAGTGACGCTGACTGC 60.880 55.000 0.00 0.00 38.57 4.40
585 602 1.748329 TTGGAGTGACGCTGACTGCT 61.748 55.000 0.00 0.00 40.11 4.24
586 603 1.005630 GGAGTGACGCTGACTGCTT 60.006 57.895 0.00 0.00 40.11 3.91
587 604 0.601311 GGAGTGACGCTGACTGCTTT 60.601 55.000 0.00 0.00 40.11 3.51
588 605 0.510359 GAGTGACGCTGACTGCTTTG 59.490 55.000 0.00 0.00 40.11 2.77
589 606 0.882042 AGTGACGCTGACTGCTTTGG 60.882 55.000 2.66 0.00 40.11 3.28
590 607 1.597854 TGACGCTGACTGCTTTGGG 60.598 57.895 2.66 0.00 40.11 4.12
631 648 1.281287 GAGAGGGTTTTGGGTAGGGTC 59.719 57.143 0.00 0.00 0.00 4.46
634 651 1.069775 GGGTTTTGGGTAGGGTCAGA 58.930 55.000 0.00 0.00 0.00 3.27
635 652 1.639108 GGGTTTTGGGTAGGGTCAGAT 59.361 52.381 0.00 0.00 0.00 2.90
636 653 2.042569 GGGTTTTGGGTAGGGTCAGATT 59.957 50.000 0.00 0.00 0.00 2.40
637 654 3.501568 GGGTTTTGGGTAGGGTCAGATTT 60.502 47.826 0.00 0.00 0.00 2.17
638 655 4.157246 GGTTTTGGGTAGGGTCAGATTTT 58.843 43.478 0.00 0.00 0.00 1.82
639 656 4.591498 GGTTTTGGGTAGGGTCAGATTTTT 59.409 41.667 0.00 0.00 0.00 1.94
663 680 4.382386 TTTTTGAGAAGAAGGGGTAGGG 57.618 45.455 0.00 0.00 0.00 3.53
664 681 2.735259 TTGAGAAGAAGGGGTAGGGT 57.265 50.000 0.00 0.00 0.00 4.34
665 682 2.249309 TGAGAAGAAGGGGTAGGGTC 57.751 55.000 0.00 0.00 0.00 4.46
666 683 1.435563 TGAGAAGAAGGGGTAGGGTCA 59.564 52.381 0.00 0.00 0.00 4.02
667 684 2.112190 GAGAAGAAGGGGTAGGGTCAG 58.888 57.143 0.00 0.00 0.00 3.51
668 685 1.722851 AGAAGAAGGGGTAGGGTCAGA 59.277 52.381 0.00 0.00 0.00 3.27
691 708 0.613572 TCGGAGGCATGTGTGGTAGA 60.614 55.000 0.00 0.00 0.00 2.59
692 709 0.460284 CGGAGGCATGTGTGGTAGAC 60.460 60.000 0.00 0.00 0.00 2.59
693 710 0.613260 GGAGGCATGTGTGGTAGACA 59.387 55.000 0.00 0.00 0.00 3.41
694 711 1.003118 GGAGGCATGTGTGGTAGACAA 59.997 52.381 0.00 0.00 35.91 3.18
695 712 2.356125 GGAGGCATGTGTGGTAGACAAT 60.356 50.000 0.00 0.00 35.91 2.71
696 713 2.939103 GAGGCATGTGTGGTAGACAATC 59.061 50.000 0.00 0.00 35.91 2.67
697 714 1.665679 GGCATGTGTGGTAGACAATCG 59.334 52.381 0.00 0.00 35.91 3.34
698 715 2.346803 GCATGTGTGGTAGACAATCGT 58.653 47.619 0.00 0.00 35.91 3.73
783 1911 4.263572 CCCACACCCCGACAGCAA 62.264 66.667 0.00 0.00 0.00 3.91
818 1972 2.661566 CCAAGCTCACGACACGCAG 61.662 63.158 0.00 0.00 0.00 5.18
819 1973 3.038417 AAGCTCACGACACGCAGC 61.038 61.111 0.00 0.00 36.66 5.25
822 1976 3.461982 CTCACGACACGCAGCGAC 61.462 66.667 24.65 11.31 0.00 5.19
1036 2190 1.068753 AGATCCCGCAGCATCTTCG 59.931 57.895 0.00 0.00 0.00 3.79
1071 2225 3.140814 GGTGCCGCTTGGGGATTC 61.141 66.667 7.95 0.00 38.95 2.52
1380 2534 1.993369 GCTGCCCAATTCGCTGGTAC 61.993 60.000 0.00 0.00 34.33 3.34
1386 2540 0.108329 CAATTCGCTGGTACCGAGGT 60.108 55.000 7.57 0.00 35.96 3.85
1392 2546 1.180029 GCTGGTACCGAGGTTCACTA 58.820 55.000 7.57 0.00 0.00 2.74
1393 2547 1.134560 GCTGGTACCGAGGTTCACTAG 59.865 57.143 7.57 2.22 0.00 2.57
1394 2548 1.134560 CTGGTACCGAGGTTCACTAGC 59.865 57.143 7.57 0.00 0.00 3.42
1395 2549 0.100146 GGTACCGAGGTTCACTAGCG 59.900 60.000 0.00 0.00 0.00 4.26
1418 2572 0.179029 CTCCGTTCCTTGTGGTGGTT 60.179 55.000 0.00 0.00 34.23 3.67
1436 2590 1.488705 TTGCAGGAAGATGACCGGGT 61.489 55.000 6.32 0.00 0.00 5.28
1520 2674 1.135632 CGAACTCCGAGAAGTCTGACC 60.136 57.143 3.76 0.00 41.76 4.02
1523 2677 1.305046 TCCGAGAAGTCTGACCCCC 60.305 63.158 3.76 0.00 0.00 5.40
1549 2703 1.964552 CCTACTACATCCTCGACGGT 58.035 55.000 0.00 0.00 0.00 4.83
1567 2721 3.088941 TTCCATCTACCAGGCGCCG 62.089 63.158 23.20 16.10 0.00 6.46
1655 2809 4.070716 AGAAATTCTGCAGTGAGGTTCTG 58.929 43.478 14.67 0.00 36.18 3.02
1736 2890 6.423862 CACAATTTTTCAGTGATTTTGCCAG 58.576 36.000 0.00 0.00 35.33 4.85
1739 2893 3.624326 TTTCAGTGATTTTGCCAGTCG 57.376 42.857 0.00 0.00 0.00 4.18
1768 2922 8.621532 AGTTGCAGAGTGTTAGATTGATTAAA 57.378 30.769 0.00 0.00 0.00 1.52
1769 2923 9.236006 AGTTGCAGAGTGTTAGATTGATTAAAT 57.764 29.630 0.00 0.00 0.00 1.40
1779 2933 8.757877 TGTTAGATTGATTAAATTTCCCCCTTG 58.242 33.333 0.00 0.00 0.00 3.61
1784 2938 5.022787 TGATTAAATTTCCCCCTTGTCTGG 58.977 41.667 0.00 0.00 0.00 3.86
1791 2945 0.546747 CCCCCTTGTCTGGTCCTGTA 60.547 60.000 0.00 0.00 0.00 2.74
1836 2990 7.766738 ATGCATCACATATCAAAAGCATTTTCA 59.233 29.630 0.00 0.00 41.46 2.69
1915 3071 7.931046 TCTACTTCTTACCTCTTCTTCTACCT 58.069 38.462 0.00 0.00 0.00 3.08
2031 3194 7.037438 CCAGCTGATTTTATGCATTGTAGTTT 58.963 34.615 17.39 0.00 0.00 2.66
2052 3218 5.756195 TTGTGACTGGAAGAATGAAACTG 57.244 39.130 0.00 0.00 37.43 3.16
2053 3219 4.136796 TGTGACTGGAAGAATGAAACTGG 58.863 43.478 0.00 0.00 37.43 4.00
2094 3260 4.022849 GGTCAGGATAATGCAGTAATTGGC 60.023 45.833 0.00 0.00 0.00 4.52
2099 3265 4.275936 GGATAATGCAGTAATTGGCTCGTT 59.724 41.667 0.00 0.00 0.00 3.85
2187 3354 1.734465 GTTTCAGAATCAGCAGGTCCG 59.266 52.381 0.00 0.00 0.00 4.79
2268 3435 9.635404 TTTAATTCCTTACTCCTTTGTGAAAGA 57.365 29.630 0.00 0.00 41.02 2.52
2269 3436 9.635404 TTAATTCCTTACTCCTTTGTGAAAGAA 57.365 29.630 0.00 0.00 41.02 2.52
2347 3514 9.750125 CTAATTTTGAATAGCCATTTTACCCTC 57.250 33.333 0.00 0.00 0.00 4.30
2353 3520 6.158695 TGAATAGCCATTTTACCCTCTCTCTT 59.841 38.462 0.00 0.00 0.00 2.85
2564 3761 7.465900 TTCTGGGGAATCTGGTTTCTATAAT 57.534 36.000 0.00 0.00 0.00 1.28
2585 3782 2.639286 GTTCGCCAACTGCACTGG 59.361 61.111 5.81 5.81 41.33 4.00
2764 3987 6.056428 AGGTTTTGCAACTTTTAGTCGTAG 57.944 37.500 0.00 0.00 32.90 3.51
2929 4204 7.278461 TCAACGTAGGAAATTTTTGATTGGA 57.722 32.000 0.00 0.00 0.00 3.53
2950 4226 5.936372 TGGATTGAGATTAGATATGCTGTGC 59.064 40.000 0.00 0.00 0.00 4.57
3017 4304 4.280425 TGGGATTGTGTACGTACAACTACA 59.720 41.667 28.89 19.43 42.74 2.74
3042 4329 4.506758 AGTTGATTTTGTTGCTTGCTTGT 58.493 34.783 0.00 0.00 0.00 3.16
3078 4365 9.462174 CTTGCTATTGGCGATTTATTTGATTTA 57.538 29.630 0.00 0.00 45.43 1.40
3097 4384 6.920210 TGATTTATGTTGATTGTTTTGCACGA 59.080 30.769 0.00 0.00 0.00 4.35
3141 4428 1.289530 AGGTGGGGGTCAGTTTGAAAA 59.710 47.619 0.00 0.00 0.00 2.29
3142 4429 1.686587 GGTGGGGGTCAGTTTGAAAAG 59.313 52.381 0.00 0.00 0.00 2.27
3380 4669 4.918810 AAAGTTTGAGTCCATGTGAACC 57.081 40.909 0.00 0.00 0.00 3.62
3475 4765 6.461110 TGATTAAACTACTACTTCCCTCGG 57.539 41.667 0.00 0.00 0.00 4.63
3559 4849 0.316841 GAAATTGGTTCCTTGCCGCA 59.683 50.000 0.00 0.00 0.00 5.69
3651 5036 7.306574 GCAAAACAAAAGTAGCATAACTGGAAC 60.307 37.037 0.00 0.00 0.00 3.62
3658 5043 6.803154 AGTAGCATAACTGGAACTTTTGTC 57.197 37.500 0.00 0.00 0.00 3.18
3869 5256 4.837860 ACAAAGCAAATTGGGGAGACATAA 59.162 37.500 0.00 0.00 34.56 1.90
3906 5293 7.095102 GCACATGATATGTACTGATGCACATTA 60.095 37.037 0.00 0.00 42.70 1.90
3943 5356 5.420725 AGTTGTGTCTGATGCACCTTATA 57.579 39.130 0.00 0.00 36.11 0.98
3956 5369 3.676324 GCACCTTATACGAGTTCTGCTGT 60.676 47.826 0.00 0.00 0.00 4.40
3961 5374 5.515626 CCTTATACGAGTTCTGCTGTTGTAC 59.484 44.000 0.00 0.00 0.00 2.90
4012 5425 4.389687 GCCTTGTCAACCATTTGCTAATTG 59.610 41.667 0.00 0.00 32.17 2.32
4034 5447 3.683822 GCTCCAGACTTCTGACATCTTTG 59.316 47.826 7.87 0.00 46.59 2.77
4208 5664 4.460382 AGATTTCAATGAGATTGTGCCGTT 59.540 37.500 0.00 0.00 41.02 4.44
4225 5681 5.798434 GTGCCGTTGATCAAGTAAAATTACC 59.202 40.000 8.80 0.00 34.19 2.85
4238 5694 5.941647 AGTAAAATTACCGCCACACTAATGT 59.058 36.000 0.00 0.00 35.21 2.71
4239 5695 5.715434 AAAATTACCGCCACACTAATGTT 57.285 34.783 0.00 0.00 36.72 2.71
4286 5743 7.885399 AGTAGAAATTTGTAATTCCTGAGCTGT 59.115 33.333 0.00 0.00 0.00 4.40
4338 5796 4.037446 ACTTCGACTGATCCTTGATAGCTC 59.963 45.833 0.00 0.00 0.00 4.09
4395 6119 9.613428 TGATAAACTTATTCCATTAGGACACAG 57.387 33.333 0.00 0.00 45.73 3.66
4402 6126 8.621532 TTATTCCATTAGGACACAGCAATATC 57.378 34.615 0.00 0.00 45.73 1.63
4403 6127 5.628797 TCCATTAGGACACAGCAATATCA 57.371 39.130 0.00 0.00 39.61 2.15
4468 6193 0.623723 ATCGGCCACTTTACCCACAT 59.376 50.000 2.24 0.00 0.00 3.21
4514 6239 0.676466 TTGTTACATGCTCTGGGCCG 60.676 55.000 0.00 0.00 40.92 6.13
4545 6271 9.923143 TGGACACTTTATATACTGGATAAATCG 57.077 33.333 0.00 0.00 30.41 3.34
4553 6279 2.478292 ACTGGATAAATCGTGTCCCCT 58.522 47.619 0.00 0.00 0.00 4.79
4578 6304 4.750941 AGGAATTTGATGTCCCTGGAAAA 58.249 39.130 0.00 0.00 34.13 2.29
4627 6416 2.570415 TCACGGAGGGCAATTGTTTA 57.430 45.000 7.40 0.00 0.00 2.01
4670 6459 0.034616 CTTCTGGGATCGATCCTGCC 59.965 60.000 36.72 23.99 46.35 4.85
4671 6460 0.690744 TTCTGGGATCGATCCTGCCA 60.691 55.000 36.72 26.71 46.35 4.92
4674 6463 1.227674 GGGATCGATCCTGCCACAC 60.228 63.158 36.72 19.14 46.35 3.82
4686 6475 1.673920 CTGCCACACCAAAAACTACGT 59.326 47.619 0.00 0.00 0.00 3.57
4687 6476 1.671845 TGCCACACCAAAAACTACGTC 59.328 47.619 0.00 0.00 0.00 4.34
4759 6548 0.985760 TTTTAGGCACTAGGGGCGAA 59.014 50.000 13.61 11.78 44.25 4.70
4767 6556 0.630134 ACTAGGGGCGAACTAGGTCT 59.370 55.000 6.16 0.00 41.70 3.85
4769 6558 0.465097 TAGGGGCGAACTAGGTCTCG 60.465 60.000 6.16 6.51 38.11 4.04
4779 6568 3.278072 TAGGTCTCGGTCACGCCCT 62.278 63.158 0.00 0.00 40.69 5.19
4780 6569 1.913951 TAGGTCTCGGTCACGCCCTA 61.914 60.000 0.00 0.00 40.69 3.53
4828 6622 2.396590 AACGTGACATTTCCCGCTAT 57.603 45.000 0.00 0.00 0.00 2.97
4872 6684 4.250305 AGCGCCACAAAGTCCGGT 62.250 61.111 2.29 0.00 0.00 5.28
4889 6701 1.315690 GGTGATCATCATGCCACAGG 58.684 55.000 0.00 0.00 0.00 4.00
4891 6703 2.372264 GTGATCATCATGCCACAGGTT 58.628 47.619 0.00 0.00 0.00 3.50
4906 6719 4.766891 CCACAGGTTGGTGATCAAATAACT 59.233 41.667 0.00 0.00 41.10 2.24
4911 6733 8.576442 ACAGGTTGGTGATCAAATAACTTAAAG 58.424 33.333 0.00 0.00 37.08 1.85
4912 6734 8.576442 CAGGTTGGTGATCAAATAACTTAAAGT 58.424 33.333 0.00 0.00 37.08 2.66
4914 6736 9.406828 GGTTGGTGATCAAATAACTTAAAGTTC 57.593 33.333 0.00 0.00 37.08 3.01
4915 6737 9.113876 GTTGGTGATCAAATAACTTAAAGTTCG 57.886 33.333 0.00 0.00 37.08 3.95
4918 6740 6.464834 GTGATCAAATAACTTAAAGTTCGGCG 59.535 38.462 0.00 0.00 39.51 6.46
4952 6792 1.071894 CGCGTAGACGATGCATCAAAG 60.072 52.381 25.70 12.48 40.42 2.77
4956 6796 0.254178 AGACGATGCATCAAAGGGCT 59.746 50.000 25.70 14.11 0.00 5.19
4958 6798 1.033746 ACGATGCATCAAAGGGCTGG 61.034 55.000 25.70 8.95 0.00 4.85
4959 6799 1.033746 CGATGCATCAAAGGGCTGGT 61.034 55.000 25.70 0.00 0.00 4.00
4982 6838 2.586635 TCGGCGCGACTTTTGTGT 60.587 55.556 12.10 0.00 0.00 3.72
4984 6840 2.003443 CGGCGCGACTTTTGTGTTG 61.003 57.895 12.10 0.00 0.00 3.33
4986 6842 1.657181 GCGCGACTTTTGTGTTGGG 60.657 57.895 12.10 0.00 37.35 4.12
4987 6843 1.657181 CGCGACTTTTGTGTTGGGC 60.657 57.895 0.00 0.00 0.00 5.36
4988 6844 1.657181 GCGACTTTTGTGTTGGGCG 60.657 57.895 0.00 0.00 0.00 6.13
4989 6845 1.725066 CGACTTTTGTGTTGGGCGT 59.275 52.632 0.00 0.00 0.00 5.68
4992 6848 1.336755 GACTTTTGTGTTGGGCGTCAT 59.663 47.619 0.00 0.00 0.00 3.06
4993 6849 1.066908 ACTTTTGTGTTGGGCGTCATG 59.933 47.619 0.00 0.00 0.00 3.07
4994 6850 0.387202 TTTTGTGTTGGGCGTCATGG 59.613 50.000 0.00 0.00 0.00 3.66
4995 6851 0.466372 TTTGTGTTGGGCGTCATGGA 60.466 50.000 0.00 0.00 0.00 3.41
4996 6852 0.888736 TTGTGTTGGGCGTCATGGAG 60.889 55.000 0.00 0.00 0.00 3.86
4997 6853 2.040544 GTGTTGGGCGTCATGGAGG 61.041 63.158 0.00 0.00 0.00 4.30
4998 6854 3.134127 GTTGGGCGTCATGGAGGC 61.134 66.667 2.51 2.51 41.88 4.70
5050 6948 4.719369 GTCGTGGAGGCGTCGCTT 62.719 66.667 18.11 9.97 0.00 4.68
5123 7030 1.075970 AGGATGAGGCCACGCTCTA 60.076 57.895 5.01 0.00 0.00 2.43
5127 7034 1.050988 ATGAGGCCACGCTCTACCAT 61.051 55.000 5.01 0.00 0.00 3.55
5148 7055 0.179001 AACCACGCCTTAACCTGCTT 60.179 50.000 0.00 0.00 0.00 3.91
5281 7233 1.518352 CATCAACGCCGACCATCGA 60.518 57.895 0.00 0.00 43.74 3.59
5298 7250 3.140325 TCGAGCCATGGTTTTCTCTTT 57.860 42.857 14.67 0.00 0.00 2.52
5308 7260 2.224892 GGTTTTCTCTTTCCTCTGGGCT 60.225 50.000 0.00 0.00 0.00 5.19
5350 7302 0.678950 TGCAGTGTTCGATGGACTCA 59.321 50.000 0.00 0.00 0.00 3.41
5362 7314 3.558411 GACTCATGCAGACGCGCC 61.558 66.667 5.73 0.00 42.97 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.410400 AAGCGTAGGCCCACCAGC 62.410 66.667 0.00 0.00 41.24 4.85
7 8 2.436646 CAAGCGTAGGCCCACCAG 60.437 66.667 0.00 0.00 41.24 4.00
8 9 4.715523 GCAAGCGTAGGCCCACCA 62.716 66.667 0.00 0.00 41.24 4.17
13 14 3.497031 GTTCGGCAAGCGTAGGCC 61.497 66.667 3.28 0.00 46.80 5.19
14 15 3.849953 CGTTCGGCAAGCGTAGGC 61.850 66.667 0.00 0.00 40.37 3.93
15 16 2.431942 ACGTTCGGCAAGCGTAGG 60.432 61.111 0.00 0.00 37.07 3.18
16 17 2.726691 CCACGTTCGGCAAGCGTAG 61.727 63.158 0.23 0.00 37.07 3.51
17 18 2.735478 CCACGTTCGGCAAGCGTA 60.735 61.111 0.23 0.00 37.07 4.42
36 37 0.107831 TGGTGTTGGAAGAACGGGAG 59.892 55.000 0.00 0.00 0.00 4.30
41 42 2.969443 CGACATGGTGTTGGAAGAAC 57.031 50.000 0.00 0.00 0.00 3.01
56 57 1.964448 CAGGCTCACTACACCGACA 59.036 57.895 0.00 0.00 0.00 4.35
57 58 1.446272 GCAGGCTCACTACACCGAC 60.446 63.158 0.00 0.00 0.00 4.79
94 95 1.447838 CCTCGTTGTCCCATGTCGG 60.448 63.158 0.00 0.00 0.00 4.79
96 97 0.736325 CGTCCTCGTTGTCCCATGTC 60.736 60.000 0.00 0.00 0.00 3.06
146 147 3.536164 AGCGGATGAGCTCTCCAG 58.464 61.111 23.52 18.41 45.67 3.86
157 158 1.079819 CTGTGGTCGACAAGCGGAT 60.080 57.895 18.91 0.00 41.33 4.18
163 164 2.279851 CGCCACTGTGGTCGACAA 60.280 61.111 27.80 2.10 40.46 3.18
169 170 0.676782 GAAATAGCCGCCACTGTGGT 60.677 55.000 26.48 10.53 44.42 4.16
172 173 0.328258 AAGGAAATAGCCGCCACTGT 59.672 50.000 0.00 0.00 0.00 3.55
186 187 6.398918 CCTCTCGTCTGAATTAAAGAAGGAA 58.601 40.000 4.47 0.00 0.00 3.36
202 203 4.500116 GCGGGACAGCCTCTCGTC 62.500 72.222 3.40 0.00 45.59 4.20
211 212 4.020617 TCCCTGCTTGCGGGACAG 62.021 66.667 21.01 5.56 45.67 3.51
221 222 0.685785 TCGAGCTCTGAATCCCTGCT 60.686 55.000 12.85 0.00 36.63 4.24
227 228 0.031994 GCCTCCTCGAGCTCTGAATC 59.968 60.000 12.85 0.00 0.00 2.52
228 229 1.398958 GGCCTCCTCGAGCTCTGAAT 61.399 60.000 12.85 0.00 0.00 2.57
232 233 2.132996 CATGGCCTCCTCGAGCTCT 61.133 63.158 12.85 0.00 0.00 4.09
249 250 1.548719 CTCTCGATACCACACCCAACA 59.451 52.381 0.00 0.00 0.00 3.33
252 253 0.333652 TCCTCTCGATACCACACCCA 59.666 55.000 0.00 0.00 0.00 4.51
263 264 1.682684 GTTCCCTGCCTCCTCTCGA 60.683 63.158 0.00 0.00 0.00 4.04
280 281 4.778143 GCATCCAACCTCCGCCGT 62.778 66.667 0.00 0.00 0.00 5.68
317 333 1.330655 CGCCACCTGGTCTACCATCT 61.331 60.000 1.51 0.00 46.46 2.90
323 339 1.982395 CACCTCGCCACCTGGTCTA 60.982 63.158 0.00 0.00 37.57 2.59
329 345 1.485066 CTATTAACCACCTCGCCACCT 59.515 52.381 0.00 0.00 0.00 4.00
338 354 5.527033 GTCTACCGATCACTATTAACCACC 58.473 45.833 0.00 0.00 0.00 4.61
357 373 1.725665 CCGCTCATTCGTCCGTCTA 59.274 57.895 0.00 0.00 0.00 2.59
362 378 2.813908 AACGCCGCTCATTCGTCC 60.814 61.111 0.00 0.00 35.18 4.79
365 381 2.813474 TCCAACGCCGCTCATTCG 60.813 61.111 0.00 0.00 0.00 3.34
367 383 0.460284 CTAGTCCAACGCCGCTCATT 60.460 55.000 0.00 0.00 0.00 2.57
369 385 2.571757 CTAGTCCAACGCCGCTCA 59.428 61.111 0.00 0.00 0.00 4.26
371 387 2.108278 AAACCTAGTCCAACGCCGCT 62.108 55.000 0.00 0.00 0.00 5.52
383 399 2.163010 TGTTCGTAGCCGAGAAACCTAG 59.837 50.000 0.00 0.00 45.24 3.02
414 431 4.493747 CGTTCGTCCGCCTCCCTC 62.494 72.222 0.00 0.00 0.00 4.30
423 440 4.932268 TCAAATGATAAACCGTTCGTCC 57.068 40.909 0.00 0.00 0.00 4.79
452 469 0.251922 ATCCTGGTGCACATGCCTTT 60.252 50.000 20.43 0.00 41.18 3.11
458 475 2.438975 CCGCATCCTGGTGCACAT 60.439 61.111 20.43 0.00 45.30 3.21
459 476 3.952508 ACCGCATCCTGGTGCACA 61.953 61.111 20.43 3.92 45.30 4.57
499 516 1.517039 GCCAGCATTAAAGCGGTGC 60.517 57.895 12.68 7.59 40.15 5.01
501 518 1.032114 GGAGCCAGCATTAAAGCGGT 61.032 55.000 12.68 0.06 40.15 5.68
553 570 4.577677 TCCAAAGTGCCAGCGCCA 62.578 61.111 2.29 0.00 0.00 5.69
563 580 0.753262 AGTCAGCGTCACTCCAAAGT 59.247 50.000 0.00 0.00 35.60 2.66
567 584 2.340078 GCAGTCAGCGTCACTCCA 59.660 61.111 0.00 0.00 0.00 3.86
576 593 3.741476 CCGCCCAAAGCAGTCAGC 61.741 66.667 0.00 0.00 44.04 4.26
577 594 3.058160 CCCGCCCAAAGCAGTCAG 61.058 66.667 0.00 0.00 44.04 3.51
578 595 2.632602 TTTCCCGCCCAAAGCAGTCA 62.633 55.000 0.00 0.00 44.04 3.41
579 596 1.866853 CTTTCCCGCCCAAAGCAGTC 61.867 60.000 0.00 0.00 44.04 3.51
580 597 1.903404 CTTTCCCGCCCAAAGCAGT 60.903 57.895 0.00 0.00 44.04 4.40
581 598 2.639327 CCTTTCCCGCCCAAAGCAG 61.639 63.158 0.00 0.00 44.04 4.24
582 599 2.600173 CCTTTCCCGCCCAAAGCA 60.600 61.111 0.00 0.00 44.04 3.91
583 600 3.381983 CCCTTTCCCGCCCAAAGC 61.382 66.667 0.00 0.00 38.52 3.51
584 601 3.381983 GCCCTTTCCCGCCCAAAG 61.382 66.667 0.00 0.00 0.00 2.77
602 619 2.692273 AAAACCCTCTCACCACCCGC 62.692 60.000 0.00 0.00 0.00 6.13
605 622 0.539669 CCCAAAACCCTCTCACCACC 60.540 60.000 0.00 0.00 0.00 4.61
610 627 1.368374 CCCTACCCAAAACCCTCTCA 58.632 55.000 0.00 0.00 0.00 3.27
613 630 1.004394 CTGACCCTACCCAAAACCCTC 59.996 57.143 0.00 0.00 0.00 4.30
642 659 3.725267 ACCCTACCCCTTCTTCTCAAAAA 59.275 43.478 0.00 0.00 0.00 1.94
643 660 3.329814 GACCCTACCCCTTCTTCTCAAAA 59.670 47.826 0.00 0.00 0.00 2.44
644 661 2.910977 GACCCTACCCCTTCTTCTCAAA 59.089 50.000 0.00 0.00 0.00 2.69
645 662 2.158066 TGACCCTACCCCTTCTTCTCAA 60.158 50.000 0.00 0.00 0.00 3.02
646 663 1.435563 TGACCCTACCCCTTCTTCTCA 59.564 52.381 0.00 0.00 0.00 3.27
647 664 2.112190 CTGACCCTACCCCTTCTTCTC 58.888 57.143 0.00 0.00 0.00 2.87
648 665 1.722851 TCTGACCCTACCCCTTCTTCT 59.277 52.381 0.00 0.00 0.00 2.85
649 666 2.249309 TCTGACCCTACCCCTTCTTC 57.751 55.000 0.00 0.00 0.00 2.87
650 667 2.846827 CAATCTGACCCTACCCCTTCTT 59.153 50.000 0.00 0.00 0.00 2.52
651 668 2.225908 ACAATCTGACCCTACCCCTTCT 60.226 50.000 0.00 0.00 0.00 2.85
652 669 2.170817 GACAATCTGACCCTACCCCTTC 59.829 54.545 0.00 0.00 0.00 3.46
653 670 2.197465 GACAATCTGACCCTACCCCTT 58.803 52.381 0.00 0.00 0.00 3.95
654 671 1.880941 GACAATCTGACCCTACCCCT 58.119 55.000 0.00 0.00 0.00 4.79
655 672 0.464452 CGACAATCTGACCCTACCCC 59.536 60.000 0.00 0.00 0.00 4.95
656 673 0.464452 CCGACAATCTGACCCTACCC 59.536 60.000 0.00 0.00 0.00 3.69
657 674 1.409427 CTCCGACAATCTGACCCTACC 59.591 57.143 0.00 0.00 0.00 3.18
658 675 1.409427 CCTCCGACAATCTGACCCTAC 59.591 57.143 0.00 0.00 0.00 3.18
659 676 1.776662 CCTCCGACAATCTGACCCTA 58.223 55.000 0.00 0.00 0.00 3.53
660 677 1.617947 GCCTCCGACAATCTGACCCT 61.618 60.000 0.00 0.00 0.00 4.34
661 678 1.153349 GCCTCCGACAATCTGACCC 60.153 63.158 0.00 0.00 0.00 4.46
662 679 0.179000 ATGCCTCCGACAATCTGACC 59.821 55.000 0.00 0.00 0.00 4.02
663 680 1.293924 CATGCCTCCGACAATCTGAC 58.706 55.000 0.00 0.00 0.00 3.51
664 681 0.904649 ACATGCCTCCGACAATCTGA 59.095 50.000 0.00 0.00 0.00 3.27
665 682 1.012086 CACATGCCTCCGACAATCTG 58.988 55.000 0.00 0.00 0.00 2.90
666 683 0.615331 ACACATGCCTCCGACAATCT 59.385 50.000 0.00 0.00 0.00 2.40
667 684 0.729116 CACACATGCCTCCGACAATC 59.271 55.000 0.00 0.00 0.00 2.67
668 685 0.677731 CCACACATGCCTCCGACAAT 60.678 55.000 0.00 0.00 0.00 2.71
691 708 1.349688 TGGCCCTCACTTTACGATTGT 59.650 47.619 0.00 0.00 0.00 2.71
692 709 2.107950 TGGCCCTCACTTTACGATTG 57.892 50.000 0.00 0.00 0.00 2.67
693 710 2.433436 GTTGGCCCTCACTTTACGATT 58.567 47.619 0.00 0.00 0.00 3.34
694 711 1.339727 GGTTGGCCCTCACTTTACGAT 60.340 52.381 0.00 0.00 0.00 3.73
695 712 0.035739 GGTTGGCCCTCACTTTACGA 59.964 55.000 0.00 0.00 0.00 3.43
696 713 0.036306 AGGTTGGCCCTCACTTTACG 59.964 55.000 0.00 0.00 40.71 3.18
697 714 1.534729 CAGGTTGGCCCTCACTTTAC 58.465 55.000 0.00 0.00 43.86 2.01
698 715 0.404040 CCAGGTTGGCCCTCACTTTA 59.596 55.000 0.00 0.00 43.86 1.85
745 1826 3.561528 GGCTGGGCCTAGGTATAATTTCC 60.562 52.174 18.96 2.99 46.69 3.13
775 1856 4.099170 GCTGCTGCCTTGCTGTCG 62.099 66.667 3.85 0.00 34.93 4.35
956 2110 3.235481 TCGTGGGTCGGCTTTGGA 61.235 61.111 0.00 0.00 40.32 3.53
959 2113 4.675029 CCGTCGTGGGTCGGCTTT 62.675 66.667 0.00 0.00 42.47 3.51
1060 2214 1.607801 GGGCAACAGAATCCCCAAGC 61.608 60.000 0.00 0.00 37.46 4.01
1071 2225 3.499737 GACATCGCCGGGCAACAG 61.500 66.667 20.71 7.97 39.74 3.16
1342 2496 2.043450 AGAGAGGAGGAGTGGCGG 60.043 66.667 0.00 0.00 0.00 6.13
1344 2498 2.781158 GCGAGAGAGGAGGAGTGGC 61.781 68.421 0.00 0.00 0.00 5.01
1347 2501 1.752694 GCAGCGAGAGAGGAGGAGT 60.753 63.158 0.00 0.00 0.00 3.85
1380 2534 1.352156 GCAACGCTAGTGAACCTCGG 61.352 60.000 10.99 0.00 0.00 4.63
1386 2540 0.032952 AACGGAGCAACGCTAGTGAA 59.967 50.000 10.99 0.00 39.88 3.18
1392 2546 1.961277 CAAGGAACGGAGCAACGCT 60.961 57.895 0.00 0.00 43.88 5.07
1393 2547 2.251642 ACAAGGAACGGAGCAACGC 61.252 57.895 0.00 0.00 37.37 4.84
1394 2548 1.569493 CACAAGGAACGGAGCAACG 59.431 57.895 0.00 0.00 40.31 4.10
1395 2549 0.818040 ACCACAAGGAACGGAGCAAC 60.818 55.000 0.00 0.00 38.69 4.17
1418 2572 1.488705 AACCCGGTCATCTTCCTGCA 61.489 55.000 0.00 0.00 0.00 4.41
1436 2590 1.080772 CGCTCAGCACGTACTCCAA 60.081 57.895 0.00 0.00 0.00 3.53
1520 2674 1.115930 ATGTAGTAGGCGAGCAGGGG 61.116 60.000 0.00 0.00 0.00 4.79
1523 2677 1.268352 GAGGATGTAGTAGGCGAGCAG 59.732 57.143 0.00 0.00 0.00 4.24
1549 2703 2.908015 GGCGCCTGGTAGATGGAA 59.092 61.111 22.15 0.00 0.00 3.53
1655 2809 3.961182 TCGTTGTCAGTGAGTGAACTAC 58.039 45.455 0.00 0.00 36.74 2.73
1710 2864 5.220815 GGCAAAATCACTGAAAAATTGTGCA 60.221 36.000 10.62 0.00 42.74 4.57
1736 2890 0.598680 ACACTCTGCAACTCAGCGAC 60.599 55.000 0.00 0.00 42.56 5.19
1739 2893 3.032017 TCTAACACTCTGCAACTCAGC 57.968 47.619 0.00 0.00 42.56 4.26
1768 2922 0.704664 GGACCAGACAAGGGGGAAAT 59.295 55.000 0.00 0.00 0.00 2.17
1769 2923 0.402861 AGGACCAGACAAGGGGGAAA 60.403 55.000 0.00 0.00 0.00 3.13
1772 2926 0.546747 TACAGGACCAGACAAGGGGG 60.547 60.000 0.00 0.00 0.00 5.40
1779 2933 4.894784 TCTGAAATGTTACAGGACCAGAC 58.105 43.478 0.00 0.00 35.20 3.51
1784 2938 5.420409 CCCTACTCTGAAATGTTACAGGAC 58.580 45.833 0.00 0.00 35.20 3.85
1791 2945 4.080356 TGCATAGCCCTACTCTGAAATGTT 60.080 41.667 0.00 0.00 0.00 2.71
1836 2990 1.617850 TCCAATTTTGAGCATGCCGTT 59.382 42.857 15.66 0.00 0.00 4.44
2031 3194 4.136796 CCAGTTTCATTCTTCCAGTCACA 58.863 43.478 0.00 0.00 0.00 3.58
2052 3218 1.067635 CCAAATGTACCACTGCTTGCC 60.068 52.381 0.00 0.00 0.00 4.52
2053 3219 1.613437 ACCAAATGTACCACTGCTTGC 59.387 47.619 0.00 0.00 0.00 4.01
2187 3354 7.822822 TGACTTTAGAGTTACCATCTTTTAGGC 59.177 37.037 0.00 0.00 35.88 3.93
2221 3388 0.320421 TCGGGACCGCTGAAAAGAAG 60.320 55.000 5.75 0.00 39.59 2.85
2293 3460 5.139727 ACCATGGAAATCTGTCAAGAAACA 58.860 37.500 21.47 0.00 35.59 2.83
2328 3495 5.667626 AGAGAGAGGGTAAAATGGCTATTCA 59.332 40.000 0.00 0.00 0.00 2.57
2329 3496 6.181206 AGAGAGAGGGTAAAATGGCTATTC 57.819 41.667 0.00 0.00 0.00 1.75
2338 3505 6.431234 GCAATCTTTGAAGAGAGAGGGTAAAA 59.569 38.462 0.00 0.00 38.66 1.52
2347 3514 6.873076 ACAGAGTAAGCAATCTTTGAAGAGAG 59.127 38.462 0.00 0.00 38.66 3.20
2353 3520 7.283127 AGTCAAAACAGAGTAAGCAATCTTTGA 59.717 33.333 0.00 0.00 33.85 2.69
2721 3935 2.900122 ATGCACAAAATCTCGTTCCG 57.100 45.000 0.00 0.00 0.00 4.30
2764 3987 8.020861 TGCAGAACTCATAATTTTGCAAAATC 57.979 30.769 31.78 19.96 37.62 2.17
2867 4141 4.025401 CCTGTTGCAACGACGGGC 62.025 66.667 23.79 3.04 36.79 6.13
2929 4204 4.934001 CCGCACAGCATATCTAATCTCAAT 59.066 41.667 0.00 0.00 0.00 2.57
3017 4304 4.952460 AGCAAGCAACAAAATCAACTCAT 58.048 34.783 0.00 0.00 0.00 2.90
3034 4321 6.251655 AGCAAGAAATCTCTTACAAGCAAG 57.748 37.500 0.00 0.00 40.05 4.01
3042 4329 5.670485 TCGCCAATAGCAAGAAATCTCTTA 58.330 37.500 0.00 0.00 40.05 2.10
3078 4365 4.566545 TCTCGTGCAAAACAATCAACAT 57.433 36.364 0.00 0.00 0.00 2.71
3097 4384 6.136155 TCCTTGTTTCTGGGAAAAGAAATCT 58.864 36.000 2.97 0.00 45.37 2.40
3185 4472 3.717294 CTTCCACCCCTCCCACCG 61.717 72.222 0.00 0.00 0.00 4.94
3256 4545 9.575783 AGAAATAGAGATAAGAAAACTGACGAC 57.424 33.333 0.00 0.00 0.00 4.34
3380 4669 7.499438 TTTATTTGTTTCAAACAGTGTGTCG 57.501 32.000 2.58 0.00 43.27 4.35
3426 4716 6.752351 ACAATCTGTACTGCTAAATACACTCG 59.248 38.462 0.00 0.00 0.00 4.18
3457 4747 6.013984 TCAAAATCCGAGGGAAGTAGTAGTTT 60.014 38.462 0.00 0.00 34.34 2.66
3469 4759 7.986085 ATTACAGATTATCAAAATCCGAGGG 57.014 36.000 0.00 0.00 0.00 4.30
3573 4863 7.145932 ACATAAACAGAAGGAACATGTAAGC 57.854 36.000 0.00 0.00 0.00 3.09
3651 5036 6.664515 TCCGCTGTAAATAACAAGACAAAAG 58.335 36.000 0.00 0.00 37.74 2.27
3658 5043 6.236017 TCTGTTTCCGCTGTAAATAACAAG 57.764 37.500 0.00 0.00 37.74 3.16
3808 5193 8.612619 CATCATGTACCAAGTAACAGGAAATAC 58.387 37.037 0.00 0.00 0.00 1.89
3813 5198 4.534500 ACCATCATGTACCAAGTAACAGGA 59.466 41.667 0.00 0.00 0.00 3.86
3906 5293 2.958355 CACAACTTTCTTGGGGACACAT 59.042 45.455 0.00 0.00 42.67 3.21
3943 5356 1.687123 AGGTACAACAGCAGAACTCGT 59.313 47.619 0.00 0.00 0.00 4.18
3956 5369 3.712733 ACACACTTGGGAGTAAGGTACAA 59.287 43.478 0.00 0.00 33.90 2.41
3961 5374 3.485463 TGAACACACTTGGGAGTAAGG 57.515 47.619 0.00 0.00 33.90 2.69
4012 5425 3.608316 AAGATGTCAGAAGTCTGGAGC 57.392 47.619 8.42 0.00 43.91 4.70
4208 5664 5.004448 TGTGGCGGTAATTTTACTTGATCA 58.996 37.500 0.00 0.00 34.16 2.92
4225 5681 4.678509 ACAACATAACATTAGTGTGGCG 57.321 40.909 0.00 0.00 38.92 5.69
4266 5723 6.071728 CCTTCACAGCTCAGGAATTACAAATT 60.072 38.462 0.00 0.00 0.00 1.82
4286 5743 1.134220 AGAAAACGGTCTGCACCTTCA 60.134 47.619 0.00 0.00 41.17 3.02
4300 5757 6.200286 TCAGTCGAAGTGTACATTCAGAAAAC 59.800 38.462 0.00 0.00 0.00 2.43
4338 5796 1.981256 ACCACAAACTGGCCTTACAG 58.019 50.000 3.32 0.00 45.32 2.74
4395 6119 0.383231 GCTGTGGCCAGTGATATTGC 59.617 55.000 5.11 0.00 41.02 3.56
4402 6126 3.036577 CAAGTGCTGTGGCCAGTG 58.963 61.111 5.11 2.39 41.02 3.66
4403 6127 2.908940 GCAAGTGCTGTGGCCAGT 60.909 61.111 5.11 0.00 41.02 4.00
4468 6193 3.553508 GCTCATTTTCAAGCAGCTTTGGA 60.554 43.478 4.38 0.00 38.42 3.53
4543 6269 1.358152 AATTCCTTCAGGGGACACGA 58.642 50.000 0.00 0.00 34.78 4.35
4545 6271 3.154827 TCAAATTCCTTCAGGGGACAC 57.845 47.619 0.00 0.00 34.78 3.67
4553 6279 3.333381 TCCAGGGACATCAAATTCCTTCA 59.667 43.478 0.00 0.00 31.90 3.02
4578 6304 3.053842 AGACCATCATGGCATTGAGAAGT 60.054 43.478 2.52 0.00 42.67 3.01
4627 6416 0.679002 AGACGCCTTGCATGCTGATT 60.679 50.000 20.33 0.00 0.00 2.57
4645 6434 0.106335 ATCGATCCCAGAAGCTGCAG 59.894 55.000 10.11 10.11 0.00 4.41
4646 6435 0.105593 GATCGATCCCAGAAGCTGCA 59.894 55.000 14.76 0.00 0.00 4.41
4686 6475 2.038269 GTTTTCCCAGCGATGGCGA 61.038 57.895 15.97 10.63 46.35 5.54
4687 6476 2.485122 GTTTTCCCAGCGATGGCG 59.515 61.111 15.97 8.10 46.35 5.69
4713 6502 2.478746 CGATGGCCCGAAAACACG 59.521 61.111 0.00 0.00 0.00 4.49
4748 6537 0.630134 AGACCTAGTTCGCCCCTAGT 59.370 55.000 0.00 0.00 31.82 2.57
4759 6548 2.045131 GGCGTGACCGAGACCTAGT 61.045 63.158 0.00 0.00 35.63 2.57
4812 6605 4.695217 TTTTGATAGCGGGAAATGTCAC 57.305 40.909 0.00 0.00 0.00 3.67
4863 6666 2.292267 GCATGATGATCACCGGACTTT 58.708 47.619 9.46 0.00 0.00 2.66
4872 6684 2.371306 CAACCTGTGGCATGATGATCA 58.629 47.619 0.00 0.00 0.00 2.92
4889 6701 9.113876 CGAACTTTAAGTTATTTGATCACCAAC 57.886 33.333 10.57 0.00 38.80 3.77
4891 6703 7.574217 GCCGAACTTTAAGTTATTTGATCACCA 60.574 37.037 10.57 0.00 38.80 4.17
4894 6706 6.148150 ACGCCGAACTTTAAGTTATTTGATCA 59.852 34.615 10.57 0.00 38.80 2.92
4939 6779 1.033746 CCAGCCCTTTGATGCATCGT 61.034 55.000 21.34 0.00 0.00 3.73
4941 6781 0.743097 GACCAGCCCTTTGATGCATC 59.257 55.000 20.14 20.14 0.00 3.91
4969 6825 1.657181 GCCCAACACAAAAGTCGCG 60.657 57.895 0.00 0.00 0.00 5.87
4970 6826 1.657181 CGCCCAACACAAAAGTCGC 60.657 57.895 0.00 0.00 0.00 5.19
4975 6831 0.387202 CCATGACGCCCAACACAAAA 59.613 50.000 0.00 0.00 0.00 2.44
4977 6833 0.888736 CTCCATGACGCCCAACACAA 60.889 55.000 0.00 0.00 0.00 3.33
4978 6834 1.302431 CTCCATGACGCCCAACACA 60.302 57.895 0.00 0.00 0.00 3.72
4981 6837 3.134127 GCCTCCATGACGCCCAAC 61.134 66.667 0.00 0.00 0.00 3.77
4982 6838 4.776322 CGCCTCCATGACGCCCAA 62.776 66.667 0.00 0.00 0.00 4.12
4987 6843 4.457496 ACCAGCGCCTCCATGACG 62.457 66.667 2.29 0.00 0.00 4.35
4988 6844 2.512515 GACCAGCGCCTCCATGAC 60.513 66.667 2.29 0.00 0.00 3.06
4989 6845 4.147449 CGACCAGCGCCTCCATGA 62.147 66.667 2.29 0.00 0.00 3.07
5061 6959 4.308458 CAACTCCCACGCCGACCA 62.308 66.667 0.00 0.00 0.00 4.02
5095 7002 1.202746 GGCCTCATCCTGAACCAGATC 60.203 57.143 0.00 0.00 32.44 2.75
5123 7030 1.530323 GTTAAGGCGTGGTTCATGGT 58.470 50.000 0.00 0.00 0.00 3.55
5127 7034 0.887387 GCAGGTTAAGGCGTGGTTCA 60.887 55.000 0.00 0.00 0.00 3.18
5180 7090 1.809271 CGACCTGGCATTCCTGATGAG 60.809 57.143 0.00 0.00 38.03 2.90
5181 7091 0.178767 CGACCTGGCATTCCTGATGA 59.821 55.000 0.00 0.00 38.03 2.92
5182 7092 0.816825 CCGACCTGGCATTCCTGATG 60.817 60.000 0.00 0.00 38.85 3.07
5262 7214 2.525248 CGATGGTCGGCGTTGATGG 61.525 63.158 6.85 0.00 36.00 3.51
5281 7233 3.075134 AGAGGAAAGAGAAAACCATGGCT 59.925 43.478 13.04 0.00 0.00 4.75
5285 7237 3.815757 GCCCAGAGGAAAGAGAAAACCAT 60.816 47.826 0.00 0.00 33.47 3.55
5350 7302 4.129737 ACTACGGCGCGTCTGCAT 62.130 61.111 9.90 0.00 41.54 3.96


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

AutoCloner maintained by Alex Coulton.