Multiple sequence alignment - TraesCS5D01G539600

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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 TraesCS5D01G539600 chr5D 100.000 3462 0 0 1 3462 551056601 551060062 0.000000e+00 6394.0
1 TraesCS5D01G539600 chr5D 86.002 1043 100 24 1627 2630 543503159 543502124 0.000000e+00 1075.0
2 TraesCS5D01G539600 chr5D 89.550 756 48 15 2699 3433 543502125 543501380 0.000000e+00 929.0
3 TraesCS5D01G539600 chr5D 87.003 654 60 13 997 1646 543503736 543503104 0.000000e+00 713.0
4 TraesCS5D01G539600 chr5D 74.330 1305 237 65 1026 2287 551447711 551448960 6.770000e-127 464.0
5 TraesCS5D01G539600 chr5D 79.668 482 87 10 1742 2215 552422095 552421617 1.540000e-88 337.0
6 TraesCS5D01G539600 chr5D 79.148 446 84 9 1781 2222 551739422 551739862 2.020000e-77 300.0
7 TraesCS5D01G539600 chr5D 76.651 424 81 11 1015 1423 551738698 551739118 5.820000e-53 219.0
8 TraesCS5D01G539600 chr5D 84.694 196 30 0 1015 1210 543536845 543536650 2.730000e-46 196.0
9 TraesCS5D01G539600 chr5D 84.343 198 31 0 1015 1212 551336813 551337010 9.800000e-46 195.0
10 TraesCS5D01G539600 chr5D 92.308 52 4 0 1378 1429 543536421 543536370 1.330000e-09 75.0
11 TraesCS5D01G539600 chr4A 88.170 2164 173 48 66 2200 616898446 616896337 0.000000e+00 2501.0
12 TraesCS5D01G539600 chr4A 87.962 731 71 12 2294 3017 616896231 616895511 0.000000e+00 846.0
13 TraesCS5D01G539600 chr4A 78.810 538 99 12 1712 2242 616229886 616229357 7.110000e-92 348.0
14 TraesCS5D01G539600 chr4A 81.319 182 27 1 1041 1215 616754838 616754657 1.300000e-29 141.0
15 TraesCS5D01G539600 chr4A 89.091 55 6 0 2241 2295 616896336 616896282 6.200000e-08 69.4
16 TraesCS5D01G539600 chr5B 86.250 960 104 7 2294 3230 685321800 685320846 0.000000e+00 1016.0
17 TraesCS5D01G539600 chr5B 89.264 652 64 5 1643 2292 685504350 685504997 0.000000e+00 811.0
18 TraesCS5D01G539600 chr5B 88.540 637 64 7 1641 2275 685322495 685321866 0.000000e+00 763.0
19 TraesCS5D01G539600 chr5B 87.812 640 76 2 1008 1646 685323092 685322454 0.000000e+00 749.0
20 TraesCS5D01G539600 chr5B 87.344 640 79 2 1008 1646 685503751 685504389 0.000000e+00 732.0
21 TraesCS5D01G539600 chr5B 74.846 1296 232 57 1038 2287 700237576 700236329 5.160000e-138 501.0
22 TraesCS5D01G539600 chr5B 86.683 398 42 2 2415 2802 685505138 685505534 6.860000e-117 431.0
23 TraesCS5D01G539600 chr5B 79.138 441 81 9 1782 2217 703716918 703717352 9.400000e-76 294.0
24 TraesCS5D01G539600 chr5B 91.542 201 15 1 3030 3230 685505560 685505758 3.400000e-70 276.0
25 TraesCS5D01G539600 chr5B 76.802 444 72 21 1012 1429 699597081 699597519 1.620000e-53 220.0
26 TraesCS5D01G539600 chr5B 85.572 201 29 0 1012 1212 700006965 700007165 9.730000e-51 211.0
27 TraesCS5D01G539600 chr5B 89.759 166 9 2 3276 3433 685320848 685320683 4.530000e-49 206.0
28 TraesCS5D01G539600 chr5B 87.730 163 12 2 3276 3430 685505756 685505918 2.120000e-42 183.0
29 TraesCS5D01G539600 chr5B 82.946 129 16 5 532 655 91466773 91466900 1.020000e-20 111.0
30 TraesCS5D01G539600 chr5B 90.909 66 4 1 2918 2981 693009576 693009511 1.710000e-13 87.9
31 TraesCS5D01G539600 chr5B 90.769 65 4 2 2630 2693 685501243 685501306 6.160000e-13 86.1
32 TraesCS5D01G539600 chr5B 92.308 52 4 0 1378 1429 700007355 700007406 1.330000e-09 75.0
33 TraesCS5D01G539600 chr1D 78.938 584 85 19 1034 1597 22968932 22968367 2.540000e-96 363.0
34 TraesCS5D01G539600 chr7D 78.389 509 78 19 1728 2222 22655231 22655721 5.620000e-78 302.0
35 TraesCS5D01G539600 chr1B 75.303 660 127 28 1782 2427 327488145 327488782 2.030000e-72 283.0
36 TraesCS5D01G539600 chr3D 88.462 78 8 1 532 609 161924379 161924455 3.680000e-15 93.5
37 TraesCS5D01G539600 chr3D 82.178 101 18 0 485 585 561705038 561704938 1.710000e-13 87.9
38 TraesCS5D01G539600 chr6D 80.000 115 17 6 527 638 294961442 294961553 2.860000e-11 80.5
39 TraesCS5D01G539600 chr1A 95.349 43 2 0 1244 1286 24153665 24153623 6.200000e-08 69.4


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 TraesCS5D01G539600 chr5D 551056601 551060062 3461 False 6394.000000 6394 100.000000 1 3462 1 chr5D.!!$F1 3461
1 TraesCS5D01G539600 chr5D 543501380 543503736 2356 True 905.666667 1075 87.518333 997 3433 3 chr5D.!!$R2 2436
2 TraesCS5D01G539600 chr5D 551447711 551448960 1249 False 464.000000 464 74.330000 1026 2287 1 chr5D.!!$F3 1261
3 TraesCS5D01G539600 chr5D 551738698 551739862 1164 False 259.500000 300 77.899500 1015 2222 2 chr5D.!!$F4 1207
4 TraesCS5D01G539600 chr4A 616895511 616898446 2935 True 1138.800000 2501 88.407667 66 3017 3 chr4A.!!$R3 2951
5 TraesCS5D01G539600 chr4A 616229357 616229886 529 True 348.000000 348 78.810000 1712 2242 1 chr4A.!!$R1 530
6 TraesCS5D01G539600 chr5B 685320683 685323092 2409 True 683.500000 1016 88.090250 1008 3433 4 chr5B.!!$R3 2425
7 TraesCS5D01G539600 chr5B 700236329 700237576 1247 True 501.000000 501 74.846000 1038 2287 1 chr5B.!!$R2 1249
8 TraesCS5D01G539600 chr5B 685501243 685505918 4675 False 419.850000 811 88.888667 1008 3430 6 chr5B.!!$F4 2422
9 TraesCS5D01G539600 chr1D 22968367 22968932 565 True 363.000000 363 78.938000 1034 1597 1 chr1D.!!$R1 563
10 TraesCS5D01G539600 chr1B 327488145 327488782 637 False 283.000000 283 75.303000 1782 2427 1 chr1B.!!$F1 645

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
661 677 0.039911 AGGTTCTGCTCCCTAGTCGT 59.96 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 4274 0.037697 TAGCCTGCTTACACACACCG 60.038 55.0 0.0 0.0 0.0 4.94 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
32 33 3.809905 GGTACCCATCAGGAAGATCAAC 58.190 50.000 0.00 0.00 39.89 3.18
33 34 2.698855 ACCCATCAGGAAGATCAACG 57.301 50.000 0.00 0.00 39.89 4.10
34 35 1.909302 ACCCATCAGGAAGATCAACGT 59.091 47.619 0.00 0.00 39.89 3.99
35 36 3.104512 ACCCATCAGGAAGATCAACGTA 58.895 45.455 0.00 0.00 39.89 3.57
36 37 3.517901 ACCCATCAGGAAGATCAACGTAA 59.482 43.478 0.00 0.00 39.89 3.18
37 38 3.871594 CCCATCAGGAAGATCAACGTAAC 59.128 47.826 0.00 0.00 38.24 2.50
38 39 4.503910 CCATCAGGAAGATCAACGTAACA 58.496 43.478 0.00 0.00 36.89 2.41
39 40 5.118990 CCATCAGGAAGATCAACGTAACAT 58.881 41.667 0.00 0.00 36.89 2.71
40 41 5.235186 CCATCAGGAAGATCAACGTAACATC 59.765 44.000 0.00 0.00 36.89 3.06
41 42 4.421058 TCAGGAAGATCAACGTAACATCG 58.579 43.478 0.00 0.00 0.00 3.84
42 43 4.157105 TCAGGAAGATCAACGTAACATCGA 59.843 41.667 0.00 0.00 34.70 3.59
43 44 4.862574 CAGGAAGATCAACGTAACATCGAA 59.137 41.667 0.00 0.00 34.70 3.71
44 45 5.004821 CAGGAAGATCAACGTAACATCGAAG 59.995 44.000 0.00 0.00 34.70 3.79
45 46 4.267928 GGAAGATCAACGTAACATCGAAGG 59.732 45.833 0.00 0.00 34.70 3.46
46 47 4.713824 AGATCAACGTAACATCGAAGGA 57.286 40.909 0.00 0.00 34.70 3.36
54 55 3.723172 CATCGAAGGATGGTGGCG 58.277 61.111 0.00 0.00 45.15 5.69
55 56 1.153369 CATCGAAGGATGGTGGCGT 60.153 57.895 0.00 0.00 45.15 5.68
57 58 0.828022 ATCGAAGGATGGTGGCGTAA 59.172 50.000 0.00 0.00 0.00 3.18
60 61 1.330521 CGAAGGATGGTGGCGTAATTG 59.669 52.381 0.00 0.00 0.00 2.32
61 62 2.639065 GAAGGATGGTGGCGTAATTGA 58.361 47.619 0.00 0.00 0.00 2.57
62 63 3.214328 GAAGGATGGTGGCGTAATTGAT 58.786 45.455 0.00 0.00 0.00 2.57
63 64 4.385825 GAAGGATGGTGGCGTAATTGATA 58.614 43.478 0.00 0.00 0.00 2.15
104 105 3.068873 GCATCGACCACTAGGAGATTTCT 59.931 47.826 0.00 0.00 38.69 2.52
113 114 5.235186 CCACTAGGAGATTTCTATTGTTGCG 59.765 44.000 0.00 0.00 36.89 4.85
120 121 7.556275 AGGAGATTTCTATTGTTGCGGAATTTA 59.444 33.333 0.00 0.00 0.00 1.40
130 131 6.142818 TGTTGCGGAATTTATTATTGGGAG 57.857 37.500 0.00 0.00 0.00 4.30
134 135 5.476599 TGCGGAATTTATTATTGGGAGGATG 59.523 40.000 0.00 0.00 0.00 3.51
166 167 3.617263 CACGGAGCTTACATACAAAGACC 59.383 47.826 0.00 0.00 0.00 3.85
169 170 3.118884 GGAGCTTACATACAAAGACCCGA 60.119 47.826 0.00 0.00 0.00 5.14
190 192 6.426025 CCCGATAGTTTTAGGGCTTATAACAC 59.574 42.308 11.36 0.96 37.07 3.32
227 240 9.543231 TCAGTAATATAATTAGGTAGGGTCTGG 57.457 37.037 0.00 0.00 0.00 3.86
228 241 8.759782 CAGTAATATAATTAGGTAGGGTCTGGG 58.240 40.741 0.00 0.00 0.00 4.45
229 242 8.470939 AGTAATATAATTAGGTAGGGTCTGGGT 58.529 37.037 0.00 0.00 0.00 4.51
230 243 9.774071 GTAATATAATTAGGTAGGGTCTGGGTA 57.226 37.037 0.00 0.00 0.00 3.69
235 248 3.899612 AGGTAGGGTCTGGGTATACTC 57.100 52.381 2.25 0.00 0.00 2.59
238 251 3.833070 GGTAGGGTCTGGGTATACTCATG 59.167 52.174 5.75 1.00 0.00 3.07
258 271 3.030291 TGGGCACAAAATCATACCCATC 58.970 45.455 0.00 0.00 42.38 3.51
265 278 6.183360 GCACAAAATCATACCCATCACATACA 60.183 38.462 0.00 0.00 0.00 2.29
268 281 6.942532 AAATCATACCCATCACATACACAC 57.057 37.500 0.00 0.00 0.00 3.82
276 289 4.381612 CCCATCACATACACACGACTAGTT 60.382 45.833 0.00 0.00 0.00 2.24
278 291 5.399013 CATCACATACACACGACTAGTTGA 58.601 41.667 17.37 3.13 0.00 3.18
282 295 6.373495 TCACATACACACGACTAGTTGAGTAT 59.627 38.462 17.37 16.21 39.06 2.12
290 303 3.128242 CGACTAGTTGAGTATGGTTCGGT 59.872 47.826 3.81 0.00 39.06 4.69
291 304 4.380233 CGACTAGTTGAGTATGGTTCGGTT 60.380 45.833 3.81 0.00 39.06 4.44
316 329 0.108709 CCATGGGCACGAAAATGTGG 60.109 55.000 2.85 0.00 40.26 4.17
318 331 0.887933 ATGGGCACGAAAATGTGGAC 59.112 50.000 0.00 0.00 40.26 4.02
320 333 1.512156 GGGCACGAAAATGTGGACGT 61.512 55.000 0.00 0.00 40.26 4.34
371 385 5.015515 TGCTCATGGGTAAAATTGTCATCA 58.984 37.500 0.00 0.00 0.00 3.07
376 390 7.715657 TCATGGGTAAAATTGTCATCATTAGC 58.284 34.615 0.00 0.00 0.00 3.09
378 392 5.362430 TGGGTAAAATTGTCATCATTAGCCC 59.638 40.000 13.39 0.00 41.26 5.19
381 395 6.041979 GGTAAAATTGTCATCATTAGCCCCAT 59.958 38.462 0.00 0.00 0.00 4.00
382 396 5.540400 AAATTGTCATCATTAGCCCCATG 57.460 39.130 0.00 0.00 0.00 3.66
383 397 1.985473 TGTCATCATTAGCCCCATGC 58.015 50.000 0.00 0.00 41.71 4.06
388 402 0.698886 TCATTAGCCCCATGCCCTCT 60.699 55.000 0.00 0.00 42.71 3.69
450 466 3.264897 CATGCGTCGCTGCCCTAC 61.265 66.667 19.50 0.00 0.00 3.18
451 467 4.873129 ATGCGTCGCTGCCCTACG 62.873 66.667 19.50 11.14 39.55 3.51
454 470 3.884350 CGTCGCTGCCCTACGCTA 61.884 66.667 4.31 0.00 38.78 4.26
455 471 2.278661 GTCGCTGCCCTACGCTAC 60.279 66.667 0.00 0.00 38.78 3.58
456 472 3.524606 TCGCTGCCCTACGCTACC 61.525 66.667 0.00 0.00 38.78 3.18
459 475 2.423898 GCTGCCCTACGCTACCTCA 61.424 63.158 0.00 0.00 38.78 3.86
469 485 4.135153 CTACCTCACTGCGCCGCT 62.135 66.667 11.67 0.00 0.00 5.52
508 524 1.066587 GCTCCCTTCGATCTGACCG 59.933 63.158 0.00 0.00 0.00 4.79
509 525 1.384989 GCTCCCTTCGATCTGACCGA 61.385 60.000 0.00 0.00 0.00 4.69
515 531 1.929806 TTCGATCTGACCGACCCACG 61.930 60.000 0.00 0.00 42.18 4.94
516 532 2.202756 GATCTGACCGACCCACGC 60.203 66.667 0.00 0.00 41.07 5.34
543 559 3.075005 CGGAGCGGGAGGAGGAAA 61.075 66.667 0.00 0.00 0.00 3.13
546 562 2.689034 AGCGGGAGGAGGAAAGGG 60.689 66.667 0.00 0.00 0.00 3.95
550 566 2.286502 GGAGGAGGAAAGGGCCCT 60.287 66.667 22.28 22.28 36.57 5.19
551 567 2.684499 GGAGGAGGAAAGGGCCCTG 61.684 68.421 29.50 0.00 33.36 4.45
616 632 3.162154 GGCTAGGGGAGGGGAACG 61.162 72.222 0.00 0.00 0.00 3.95
618 634 3.162154 CTAGGGGAGGGGAACGGC 61.162 72.222 0.00 0.00 0.00 5.68
656 672 0.755698 CGGCTAGGTTCTGCTCCCTA 60.756 60.000 0.00 0.00 32.08 3.53
661 677 0.039911 AGGTTCTGCTCCCTAGTCGT 59.960 55.000 0.00 0.00 0.00 4.34
662 678 0.173708 GGTTCTGCTCCCTAGTCGTG 59.826 60.000 0.00 0.00 0.00 4.35
663 679 0.173708 GTTCTGCTCCCTAGTCGTGG 59.826 60.000 0.00 0.00 0.00 4.94
664 680 0.251653 TTCTGCTCCCTAGTCGTGGT 60.252 55.000 0.00 0.00 0.00 4.16
667 683 0.622136 TGCTCCCTAGTCGTGGTCTA 59.378 55.000 0.00 0.00 0.00 2.59
670 686 2.683152 GCTCCCTAGTCGTGGTCTAGAA 60.683 54.545 0.00 0.00 37.62 2.10
671 687 3.618351 CTCCCTAGTCGTGGTCTAGAAA 58.382 50.000 0.00 0.00 37.62 2.52
672 688 4.208746 CTCCCTAGTCGTGGTCTAGAAAT 58.791 47.826 0.00 0.00 37.62 2.17
675 691 4.401519 CCCTAGTCGTGGTCTAGAAATTGA 59.598 45.833 0.00 0.00 37.62 2.57
676 692 5.341617 CCTAGTCGTGGTCTAGAAATTGAC 58.658 45.833 0.00 1.17 37.62 3.18
677 693 5.125739 CCTAGTCGTGGTCTAGAAATTGACT 59.874 44.000 17.73 17.73 37.62 3.41
679 695 5.471257 AGTCGTGGTCTAGAAATTGACTTC 58.529 41.667 11.23 0.00 31.85 3.01
680 696 5.244178 AGTCGTGGTCTAGAAATTGACTTCT 59.756 40.000 11.23 0.00 39.09 2.85
681 697 5.346281 GTCGTGGTCTAGAAATTGACTTCTG 59.654 44.000 0.00 0.00 36.34 3.02
682 698 5.243060 TCGTGGTCTAGAAATTGACTTCTGA 59.757 40.000 0.00 0.00 36.34 3.27
683 699 5.574830 CGTGGTCTAGAAATTGACTTCTGAG 59.425 44.000 0.00 0.00 36.34 3.35
685 701 6.367422 GTGGTCTAGAAATTGACTTCTGAGTG 59.633 42.308 0.00 0.00 36.34 3.51
686 702 6.267699 TGGTCTAGAAATTGACTTCTGAGTGA 59.732 38.462 0.00 0.00 36.34 3.41
688 704 7.277539 GGTCTAGAAATTGACTTCTGAGTGATG 59.722 40.741 0.00 0.00 36.34 3.07
689 705 5.876612 AGAAATTGACTTCTGAGTGATGC 57.123 39.130 0.00 0.00 35.88 3.91
690 706 5.558818 AGAAATTGACTTCTGAGTGATGCT 58.441 37.500 0.00 0.00 35.88 3.79
692 708 7.164122 AGAAATTGACTTCTGAGTGATGCTTA 58.836 34.615 0.00 0.00 35.88 3.09
695 711 7.750229 ATTGACTTCTGAGTGATGCTTAAAA 57.250 32.000 0.00 0.00 35.88 1.52
719 743 9.736023 AAAGTAGAGATTTGTTGTTGATTGTTC 57.264 29.630 0.00 0.00 0.00 3.18
730 754 3.498777 TGTTGATTGTTCGACGGCATAAA 59.501 39.130 0.00 0.00 38.88 1.40
733 757 6.128254 TGTTGATTGTTCGACGGCATAAAATA 60.128 34.615 0.00 0.00 38.88 1.40
737 761 7.808381 TGATTGTTCGACGGCATAAAATAAAAA 59.192 29.630 0.00 0.00 0.00 1.94
740 764 8.603983 TGTTCGACGGCATAAAATAAAAATAC 57.396 30.769 0.00 0.00 0.00 1.89
743 767 9.622004 TTCGACGGCATAAAATAAAAATACAAA 57.378 25.926 0.00 0.00 0.00 2.83
745 769 9.828220 CGACGGCATAAAATAAAAATACAAATG 57.172 29.630 0.00 0.00 0.00 2.32
758 782 4.829064 ATACAAATGTTGTTGTCGTGCT 57.171 36.364 0.00 0.00 42.22 4.40
759 783 2.796304 ACAAATGTTGTTGTCGTGCTG 58.204 42.857 0.00 0.00 42.22 4.41
760 784 1.518102 CAAATGTTGTTGTCGTGCTGC 59.482 47.619 0.00 0.00 0.00 5.25
839 866 4.883585 CCATTTCAAGTTGCTGATAGCCTA 59.116 41.667 0.00 0.00 41.51 3.93
840 867 5.220931 CCATTTCAAGTTGCTGATAGCCTAC 60.221 44.000 0.00 0.00 41.51 3.18
841 868 3.165058 TCAAGTTGCTGATAGCCTACG 57.835 47.619 0.00 0.00 41.51 3.51
842 869 2.496070 TCAAGTTGCTGATAGCCTACGT 59.504 45.455 0.00 0.00 41.51 3.57
843 870 2.860735 CAAGTTGCTGATAGCCTACGTC 59.139 50.000 0.00 0.00 41.51 4.34
844 871 1.065701 AGTTGCTGATAGCCTACGTCG 59.934 52.381 0.00 0.00 41.51 5.12
845 872 1.100510 TTGCTGATAGCCTACGTCGT 58.899 50.000 2.21 2.21 41.51 4.34
846 873 1.957668 TGCTGATAGCCTACGTCGTA 58.042 50.000 4.78 4.78 41.51 3.43
847 874 2.501261 TGCTGATAGCCTACGTCGTAT 58.499 47.619 5.39 0.00 41.51 3.06
848 875 2.225727 TGCTGATAGCCTACGTCGTATG 59.774 50.000 5.39 4.38 41.51 2.39
849 876 2.225963 GCTGATAGCCTACGTCGTATGT 59.774 50.000 5.39 0.00 34.48 2.29
851 878 2.551032 TGATAGCCTACGTCGTATGTGG 59.449 50.000 5.39 5.22 0.00 4.17
860 887 3.071479 ACGTCGTATGTGGCTGAAAAAT 58.929 40.909 0.00 0.00 0.00 1.82
895 940 5.127845 TCTGAAAATTTTAACACAGCCCACA 59.872 36.000 2.75 0.00 0.00 4.17
897 942 4.744795 AAATTTTAACACAGCCCACACA 57.255 36.364 0.00 0.00 0.00 3.72
911 956 4.051167 CACAGAGCCCATGCCCCA 62.051 66.667 0.00 0.00 38.69 4.96
924 969 4.263572 CCCCACGCCTGTTGGACA 62.264 66.667 0.00 0.00 32.62 4.02
925 970 2.978010 CCCACGCCTGTTGGACAC 60.978 66.667 0.00 0.00 32.62 3.67
926 971 2.978010 CCACGCCTGTTGGACACC 60.978 66.667 0.00 0.00 34.57 4.16
927 972 2.978010 CACGCCTGTTGGACACCC 60.978 66.667 0.00 0.00 34.57 4.61
928 973 4.265056 ACGCCTGTTGGACACCCC 62.265 66.667 0.00 0.00 34.57 4.95
929 974 4.263572 CGCCTGTTGGACACCCCA 62.264 66.667 0.00 0.00 44.93 4.96
930 975 2.597510 GCCTGTTGGACACCCCAC 60.598 66.667 0.00 0.00 46.62 4.61
931 976 2.923035 CCTGTTGGACACCCCACA 59.077 61.111 0.00 0.00 46.62 4.17
932 977 1.228793 CCTGTTGGACACCCCACAA 59.771 57.895 0.00 0.00 46.62 3.33
933 978 0.823356 CCTGTTGGACACCCCACAAG 60.823 60.000 0.00 0.00 46.62 3.16
934 979 1.454847 TGTTGGACACCCCACAAGC 60.455 57.895 0.00 0.00 46.62 4.01
935 980 1.454847 GTTGGACACCCCACAAGCA 60.455 57.895 0.00 0.00 46.62 3.91
936 981 1.152777 TTGGACACCCCACAAGCAG 60.153 57.895 0.00 0.00 46.62 4.24
937 982 1.640593 TTGGACACCCCACAAGCAGA 61.641 55.000 0.00 0.00 46.62 4.26
939 984 1.968540 GACACCCCACAAGCAGAGC 60.969 63.158 0.00 0.00 0.00 4.09
940 985 2.674380 CACCCCACAAGCAGAGCC 60.674 66.667 0.00 0.00 0.00 4.70
941 986 3.971702 ACCCCACAAGCAGAGCCC 61.972 66.667 0.00 0.00 0.00 5.19
943 988 2.674380 CCCACAAGCAGAGCCCAC 60.674 66.667 0.00 0.00 0.00 4.61
944 989 2.113774 CCACAAGCAGAGCCCACA 59.886 61.111 0.00 0.00 0.00 4.17
1059 2568 3.064987 GCTGCCGGACGAGCTTCTA 62.065 63.158 5.05 0.00 32.12 2.10
1083 2592 1.458588 GATCTTCCTCCGCCTCCCT 60.459 63.158 0.00 0.00 0.00 4.20
1332 2856 1.602327 GGGACCGTCAGTACACTCCC 61.602 65.000 0.00 0.00 35.06 4.30
1423 2959 2.464459 CGCCGGATGAAGCTGGAAC 61.464 63.158 5.05 0.00 36.35 3.62
1506 3066 3.089874 CATGAGGGCCCCTTCCGA 61.090 66.667 21.43 0.00 31.76 4.55
1545 3108 2.818432 GGACATGAATGAGGATGATGGC 59.182 50.000 0.00 0.00 0.00 4.40
1557 3120 0.099259 ATGATGGCGATTGTGTTGCG 59.901 50.000 0.00 0.00 38.18 4.85
1598 3161 4.803426 GACGCCCGAGTGGAGCAG 62.803 72.222 0.00 0.00 37.45 4.24
1602 3165 2.759973 CCCGAGTGGAGCAGGCTA 60.760 66.667 0.00 0.00 37.49 3.93
2003 3572 7.307455 GCATAAAGTCATCGATCTAAAGGAACC 60.307 40.741 0.00 0.00 0.00 3.62
2231 3812 8.873144 TCCTTTTCTTTTCTGATGATTTGGAAT 58.127 29.630 0.00 0.00 0.00 3.01
2287 3874 9.050601 GGTGGAACAATTTAAAACATTGAATGA 57.949 29.630 12.80 0.00 44.16 2.57
2308 3947 4.216257 TGATTAGCCAAACTTTGAGTGCTC 59.784 41.667 2.87 0.00 30.26 4.26
2399 4039 7.429340 GCATATCAACTACTTTTTGGAATCACG 59.571 37.037 0.00 0.00 0.00 4.35
2402 4042 5.298276 TCAACTACTTTTTGGAATCACGCTT 59.702 36.000 0.00 0.00 0.00 4.68
2453 4093 2.060326 CTGCAAGGCATTGACAACAG 57.940 50.000 16.56 8.61 38.13 3.16
2457 4097 2.229543 GCAAGGCATTGACAACAGATGA 59.770 45.455 16.56 0.00 38.83 2.92
2496 4146 3.087031 CAGGAGGCAACATGAGAAATGT 58.913 45.455 0.00 0.00 41.41 2.71
2497 4147 3.508793 CAGGAGGCAACATGAGAAATGTT 59.491 43.478 0.00 0.00 42.38 2.71
2525 4175 2.740714 GCGACATGGGTCTTGCGAC 61.741 63.158 0.00 0.00 42.05 5.19
2542 4192 2.611971 GCGACCAGTGTCAGTATTTGGA 60.612 50.000 0.00 0.00 41.85 3.53
2546 4196 2.749621 CCAGTGTCAGTATTTGGAAGCC 59.250 50.000 0.00 0.00 0.00 4.35
2564 4214 1.268352 GCCGTTTTAATGCAGTGGTGA 59.732 47.619 0.00 0.00 0.00 4.02
2567 4217 4.380023 GCCGTTTTAATGCAGTGGTGATTA 60.380 41.667 0.00 0.00 0.00 1.75
2596 4246 6.998074 TCTCATAGTGTTGTTGGATTTTGTCT 59.002 34.615 0.00 0.00 0.00 3.41
2608 4258 1.229428 TTTTGTCTGCAAGCTCGAGG 58.771 50.000 15.58 0.00 35.82 4.63
2615 4265 1.227999 TGCAAGCTCGAGGTTTTCCG 61.228 55.000 26.38 16.25 46.35 4.30
2624 4274 1.397567 CGAGGTTTTCCGCACGTTAAC 60.398 52.381 0.00 0.00 46.35 2.01
2648 4298 3.372206 GTGTGTGTAAGCAGGCTAATGAG 59.628 47.826 0.00 0.00 0.00 2.90
2693 4343 5.710513 TTTCTTGCAGCATCAGTTATGTT 57.289 34.783 0.00 0.00 37.93 2.71
2757 4407 5.291971 AGCTTTGTCTTGCCATTGTAAAAG 58.708 37.500 0.00 0.00 0.00 2.27
2767 4417 4.695455 TGCCATTGTAAAAGCTCTACAGTC 59.305 41.667 8.24 0.00 31.17 3.51
2832 4486 4.094146 GCTTTAGAGCTGGTGATTTCTGTC 59.906 45.833 0.00 0.00 45.65 3.51
2855 4509 3.317430 GCCAAGAGATGATGATGGTTTCC 59.683 47.826 0.00 0.00 33.63 3.13
2856 4510 4.789807 CCAAGAGATGATGATGGTTTCCT 58.210 43.478 0.00 0.00 0.00 3.36
2860 4514 7.222161 CAAGAGATGATGATGGTTTCCTCATA 58.778 38.462 0.00 0.00 39.11 2.15
2861 4515 7.384524 AGAGATGATGATGGTTTCCTCATAA 57.615 36.000 0.00 0.00 39.11 1.90
2891 4545 9.520204 CTCACTGGTATGCCTTAATTAATTTTG 57.480 33.333 5.91 0.00 35.27 2.44
2959 4614 8.239038 AGAGTAAAGAGTATAGCATGCAGTTA 57.761 34.615 21.98 3.75 0.00 2.24
3032 4696 7.168219 TGAAATATTGAGCTGTAAGTTGAGGT 58.832 34.615 0.00 0.00 35.30 3.85
3072 4736 5.104444 AGGATCTGAGTTGCATGAAGATCTT 60.104 40.000 7.95 7.95 41.85 2.40
3073 4737 6.099413 AGGATCTGAGTTGCATGAAGATCTTA 59.901 38.462 8.25 0.00 41.85 2.10
3074 4738 6.935771 GGATCTGAGTTGCATGAAGATCTTAT 59.064 38.462 8.25 0.01 41.85 1.73
3095 4759 8.467598 TCTTATAGAGGTTTTACTGCTACAGTG 58.532 37.037 10.42 0.00 45.01 3.66
3096 4760 3.665190 AGAGGTTTTACTGCTACAGTGC 58.335 45.455 10.42 0.00 45.01 4.40
3144 4808 8.031848 AGGTTGCTATTTGTTGCATATTTTTG 57.968 30.769 0.00 0.00 39.07 2.44
3146 4810 7.094848 GGTTGCTATTTGTTGCATATTTTTGGT 60.095 33.333 0.00 0.00 39.07 3.67
3151 4815 4.597404 TGTTGCATATTTTTGGTCTGCA 57.403 36.364 0.00 0.00 40.79 4.41
3157 4821 4.676196 GCATATTTTTGGTCTGCAGTGGAG 60.676 45.833 14.67 5.07 33.13 3.86
3177 4841 7.288852 AGTGGAGATAATAGTAGACTGCAATGT 59.711 37.037 0.00 0.00 31.61 2.71
3180 4844 7.039363 GGAGATAATAGTAGACTGCAATGTCCT 60.039 40.741 2.65 0.00 37.66 3.85
3238 4902 3.261897 ACTGCTAGGCTACAGTGTTCATT 59.738 43.478 21.15 3.53 45.19 2.57
3240 4904 3.007940 TGCTAGGCTACAGTGTTCATTGT 59.992 43.478 0.00 6.25 0.00 2.71
3241 4905 4.221924 TGCTAGGCTACAGTGTTCATTGTA 59.778 41.667 0.00 7.67 0.00 2.41
3243 4907 5.063564 GCTAGGCTACAGTGTTCATTGTAAC 59.936 44.000 0.00 5.38 30.06 2.50
3272 4936 9.762381 TTTTGGTTTATTATATTCCAGACTGGT 57.238 29.630 21.06 5.61 39.03 4.00
3274 4938 8.974060 TGGTTTATTATATTCCAGACTGGTTC 57.026 34.615 21.06 0.00 39.03 3.62
3275 4939 8.553153 TGGTTTATTATATTCCAGACTGGTTCA 58.447 33.333 21.06 7.27 39.03 3.18
3276 4940 8.837389 GGTTTATTATATTCCAGACTGGTTCAC 58.163 37.037 21.06 5.12 39.03 3.18
3277 4941 9.391006 GTTTATTATATTCCAGACTGGTTCACA 57.609 33.333 21.06 0.00 39.03 3.58
3387 5057 2.159282 GCTCTGTTCCAAATGCCTGATG 60.159 50.000 0.00 0.00 0.00 3.07
3388 5058 2.426024 CTCTGTTCCAAATGCCTGATGG 59.574 50.000 0.00 0.00 35.49 3.51
3426 5098 6.988622 TCATTTCATGGGCAAAATGAATTC 57.011 33.333 14.57 0.00 44.60 2.17
3430 5102 3.845398 TCATGGGCAAAATGAATTCCCTT 59.155 39.130 2.27 0.00 37.83 3.95
3433 5105 3.261390 TGGGCAAAATGAATTCCCTTCTG 59.739 43.478 2.27 0.00 37.83 3.02
3434 5106 3.515104 GGGCAAAATGAATTCCCTTCTGA 59.485 43.478 2.27 0.00 34.75 3.27
3435 5107 4.382362 GGGCAAAATGAATTCCCTTCTGAG 60.382 45.833 2.27 0.00 34.75 3.35
3436 5108 4.221482 GGCAAAATGAATTCCCTTCTGAGT 59.779 41.667 2.27 0.00 34.75 3.41
3437 5109 5.279657 GGCAAAATGAATTCCCTTCTGAGTT 60.280 40.000 2.27 0.00 34.75 3.01
3438 5110 5.636543 GCAAAATGAATTCCCTTCTGAGTTG 59.363 40.000 2.27 0.19 34.75 3.16
3439 5111 5.990120 AAATGAATTCCCTTCTGAGTTGG 57.010 39.130 2.27 0.00 34.75 3.77
3440 5112 2.795329 TGAATTCCCTTCTGAGTTGGC 58.205 47.619 2.27 0.00 34.75 4.52
3441 5113 2.376518 TGAATTCCCTTCTGAGTTGGCT 59.623 45.455 2.27 0.00 34.75 4.75
3442 5114 2.503895 ATTCCCTTCTGAGTTGGCTG 57.496 50.000 0.00 0.00 0.00 4.85
3443 5115 1.140312 TTCCCTTCTGAGTTGGCTGT 58.860 50.000 0.00 0.00 0.00 4.40
3444 5116 2.024176 TCCCTTCTGAGTTGGCTGTA 57.976 50.000 0.00 0.00 0.00 2.74
3445 5117 2.551270 TCCCTTCTGAGTTGGCTGTAT 58.449 47.619 0.00 0.00 0.00 2.29
3446 5118 2.912956 TCCCTTCTGAGTTGGCTGTATT 59.087 45.455 0.00 0.00 0.00 1.89
3447 5119 3.330701 TCCCTTCTGAGTTGGCTGTATTT 59.669 43.478 0.00 0.00 0.00 1.40
3448 5120 4.082125 CCCTTCTGAGTTGGCTGTATTTT 58.918 43.478 0.00 0.00 0.00 1.82
3449 5121 4.524328 CCCTTCTGAGTTGGCTGTATTTTT 59.476 41.667 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.118738 ACGTTGATCTTCCTGATGGGTAC 60.119 47.826 0.00 0.00 35.14 3.34
13 14 3.104512 ACGTTGATCTTCCTGATGGGTA 58.895 45.455 0.00 0.00 35.14 3.69
15 16 2.698855 ACGTTGATCTTCCTGATGGG 57.301 50.000 0.00 0.00 35.14 4.00
16 17 4.503910 TGTTACGTTGATCTTCCTGATGG 58.496 43.478 0.00 0.00 35.14 3.51
17 18 5.051441 CGATGTTACGTTGATCTTCCTGATG 60.051 44.000 0.00 0.00 35.14 3.07
18 19 5.043903 CGATGTTACGTTGATCTTCCTGAT 58.956 41.667 0.00 0.00 38.27 2.90
19 20 4.157105 TCGATGTTACGTTGATCTTCCTGA 59.843 41.667 0.00 0.00 34.70 3.86
20 21 4.421058 TCGATGTTACGTTGATCTTCCTG 58.579 43.478 0.00 0.00 34.70 3.86
21 22 4.713824 TCGATGTTACGTTGATCTTCCT 57.286 40.909 0.00 0.00 34.70 3.36
22 23 4.267928 CCTTCGATGTTACGTTGATCTTCC 59.732 45.833 0.00 0.00 34.70 3.46
23 24 5.100259 TCCTTCGATGTTACGTTGATCTTC 58.900 41.667 0.00 0.00 34.70 2.87
24 25 5.068234 TCCTTCGATGTTACGTTGATCTT 57.932 39.130 0.00 0.00 34.70 2.40
25 26 4.713824 TCCTTCGATGTTACGTTGATCT 57.286 40.909 0.00 0.00 34.70 2.75
26 27 4.209288 CCATCCTTCGATGTTACGTTGATC 59.791 45.833 0.00 0.00 43.87 2.92
27 28 4.119862 CCATCCTTCGATGTTACGTTGAT 58.880 43.478 0.00 0.00 43.87 2.57
29 30 3.062099 CACCATCCTTCGATGTTACGTTG 59.938 47.826 0.00 0.00 43.87 4.10
31 32 2.418197 CCACCATCCTTCGATGTTACGT 60.418 50.000 0.00 0.00 43.87 3.57
32 33 2.201732 CCACCATCCTTCGATGTTACG 58.798 52.381 0.00 0.00 43.87 3.18
33 34 1.940613 GCCACCATCCTTCGATGTTAC 59.059 52.381 0.00 0.00 43.87 2.50
34 35 1.472552 CGCCACCATCCTTCGATGTTA 60.473 52.381 0.00 0.00 43.87 2.41
35 36 0.744414 CGCCACCATCCTTCGATGTT 60.744 55.000 0.00 0.00 43.87 2.71
36 37 1.153369 CGCCACCATCCTTCGATGT 60.153 57.895 0.00 0.00 43.87 3.06
37 38 0.104120 TACGCCACCATCCTTCGATG 59.896 55.000 0.00 0.00 44.80 3.84
38 39 0.828022 TTACGCCACCATCCTTCGAT 59.172 50.000 0.00 0.00 0.00 3.59
39 40 0.828022 ATTACGCCACCATCCTTCGA 59.172 50.000 0.00 0.00 0.00 3.71
40 41 1.330521 CAATTACGCCACCATCCTTCG 59.669 52.381 0.00 0.00 0.00 3.79
41 42 2.639065 TCAATTACGCCACCATCCTTC 58.361 47.619 0.00 0.00 0.00 3.46
42 43 2.799126 TCAATTACGCCACCATCCTT 57.201 45.000 0.00 0.00 0.00 3.36
43 44 3.391296 ACTATCAATTACGCCACCATCCT 59.609 43.478 0.00 0.00 0.00 3.24
44 45 3.740115 ACTATCAATTACGCCACCATCC 58.260 45.455 0.00 0.00 0.00 3.51
45 46 5.295787 TGAAACTATCAATTACGCCACCATC 59.704 40.000 0.00 0.00 34.30 3.51
46 47 5.189928 TGAAACTATCAATTACGCCACCAT 58.810 37.500 0.00 0.00 34.30 3.55
49 50 5.965334 CACATGAAACTATCAATTACGCCAC 59.035 40.000 0.00 0.00 42.54 5.01
50 51 5.645929 ACACATGAAACTATCAATTACGCCA 59.354 36.000 0.00 0.00 42.54 5.69
52 53 7.021196 ACAACACATGAAACTATCAATTACGC 58.979 34.615 0.00 0.00 42.54 4.42
53 54 9.689075 CTACAACACATGAAACTATCAATTACG 57.311 33.333 0.00 0.00 42.54 3.18
57 58 7.066284 GCCTCTACAACACATGAAACTATCAAT 59.934 37.037 0.00 0.00 42.54 2.57
60 61 5.874810 TGCCTCTACAACACATGAAACTATC 59.125 40.000 0.00 0.00 0.00 2.08
61 62 5.804639 TGCCTCTACAACACATGAAACTAT 58.195 37.500 0.00 0.00 0.00 2.12
62 63 5.222079 TGCCTCTACAACACATGAAACTA 57.778 39.130 0.00 0.00 0.00 2.24
63 64 4.085357 TGCCTCTACAACACATGAAACT 57.915 40.909 0.00 0.00 0.00 2.66
104 105 8.239038 TCCCAATAATAAATTCCGCAACAATA 57.761 30.769 0.00 0.00 0.00 1.90
113 114 5.721480 CCCCATCCTCCCAATAATAAATTCC 59.279 44.000 0.00 0.00 0.00 3.01
120 121 1.788915 CACCCCCATCCTCCCAATAAT 59.211 52.381 0.00 0.00 0.00 1.28
124 125 2.616893 CCACCCCCATCCTCCCAA 60.617 66.667 0.00 0.00 0.00 4.12
166 167 6.987992 TGTGTTATAAGCCCTAAAACTATCGG 59.012 38.462 0.00 0.00 0.00 4.18
169 170 9.695155 AACATGTGTTATAAGCCCTAAAACTAT 57.305 29.630 0.00 0.00 36.32 2.12
215 228 3.136896 TGAGTATACCCAGACCCTACCT 58.863 50.000 0.00 0.00 0.00 3.08
217 230 3.833070 CCATGAGTATACCCAGACCCTAC 59.167 52.174 0.00 0.00 0.00 3.18
218 231 3.181410 CCCATGAGTATACCCAGACCCTA 60.181 52.174 0.00 0.00 0.00 3.53
219 232 2.427889 CCCATGAGTATACCCAGACCCT 60.428 54.545 0.00 0.00 0.00 4.34
221 234 1.348036 GCCCATGAGTATACCCAGACC 59.652 57.143 0.00 0.00 0.00 3.85
224 237 1.768275 TGTGCCCATGAGTATACCCAG 59.232 52.381 0.00 0.00 0.00 4.45
225 238 1.886422 TGTGCCCATGAGTATACCCA 58.114 50.000 0.00 0.00 0.00 4.51
227 240 4.887071 TGATTTTGTGCCCATGAGTATACC 59.113 41.667 0.00 0.00 0.00 2.73
228 241 6.639632 ATGATTTTGTGCCCATGAGTATAC 57.360 37.500 0.00 0.00 0.00 1.47
229 242 6.714810 GGTATGATTTTGTGCCCATGAGTATA 59.285 38.462 0.00 0.00 0.00 1.47
230 243 5.536161 GGTATGATTTTGTGCCCATGAGTAT 59.464 40.000 0.00 0.00 0.00 2.12
231 244 4.887071 GGTATGATTTTGTGCCCATGAGTA 59.113 41.667 0.00 0.00 0.00 2.59
232 245 3.701040 GGTATGATTTTGTGCCCATGAGT 59.299 43.478 0.00 0.00 0.00 3.41
235 248 2.765135 TGGGTATGATTTTGTGCCCATG 59.235 45.455 0.00 0.00 44.05 3.66
238 251 3.030291 TGATGGGTATGATTTTGTGCCC 58.970 45.455 0.00 0.00 40.33 5.36
258 271 4.795268 ACTCAACTAGTCGTGTGTATGTG 58.205 43.478 0.00 0.00 30.33 3.21
265 278 4.379186 CGAACCATACTCAACTAGTCGTGT 60.379 45.833 0.00 0.00 39.80 4.49
268 281 3.128242 ACCGAACCATACTCAACTAGTCG 59.872 47.826 0.00 0.00 39.80 4.18
276 289 2.093869 GGCAGTAACCGAACCATACTCA 60.094 50.000 0.00 0.00 0.00 3.41
278 291 1.208776 GGGCAGTAACCGAACCATACT 59.791 52.381 0.00 0.00 0.00 2.12
282 295 0.322098 CATGGGCAGTAACCGAACCA 60.322 55.000 0.00 0.00 0.00 3.67
316 329 2.865343 CCACATGGGTAGAGTACGTC 57.135 55.000 0.00 0.00 0.00 4.34
365 379 1.251251 GGCATGGGGCTAATGATGAC 58.749 55.000 0.00 0.00 44.01 3.06
371 385 1.849116 CAGAGGGCATGGGGCTAAT 59.151 57.895 0.00 0.00 44.01 1.73
447 463 4.692129 CGCAGTGAGGTAGCGTAG 57.308 61.111 0.00 0.00 45.82 3.51
452 468 4.135153 AGCGGCGCAGTGAGGTAG 62.135 66.667 35.02 0.00 0.00 3.18
486 502 1.103987 TCAGATCGAAGGGAGCTCGG 61.104 60.000 7.83 0.00 40.01 4.63
499 515 2.202756 GCGTGGGTCGGTCAGATC 60.203 66.667 0.00 0.00 40.26 2.75
598 614 3.162154 GTTCCCCTCCCCTAGCCG 61.162 72.222 0.00 0.00 0.00 5.52
600 616 3.162154 CCGTTCCCCTCCCCTAGC 61.162 72.222 0.00 0.00 0.00 3.42
601 617 3.162154 GCCGTTCCCCTCCCCTAG 61.162 72.222 0.00 0.00 0.00 3.02
637 653 0.755698 TAGGGAGCAGAACCTAGCCG 60.756 60.000 0.00 0.00 38.30 5.52
648 664 0.622136 TAGACCACGACTAGGGAGCA 59.378 55.000 0.00 0.00 0.00 4.26
656 672 5.244178 AGAAGTCAATTTCTAGACCACGACT 59.756 40.000 7.81 7.81 35.70 4.18
658 674 5.243060 TCAGAAGTCAATTTCTAGACCACGA 59.757 40.000 0.00 0.00 35.70 4.35
661 677 6.267699 TCACTCAGAAGTCAATTTCTAGACCA 59.732 38.462 0.00 0.00 35.70 4.02
662 678 6.692486 TCACTCAGAAGTCAATTTCTAGACC 58.308 40.000 0.00 0.00 35.70 3.85
663 679 7.201513 GCATCACTCAGAAGTCAATTTCTAGAC 60.202 40.741 0.00 0.00 35.70 2.59
664 680 6.815641 GCATCACTCAGAAGTCAATTTCTAGA 59.184 38.462 0.00 0.00 35.70 2.43
667 683 5.558818 AGCATCACTCAGAAGTCAATTTCT 58.441 37.500 0.00 0.00 37.90 2.52
670 686 7.750229 TTTAAGCATCACTCAGAAGTCAATT 57.250 32.000 0.00 0.00 31.71 2.32
671 687 7.446625 ACTTTTAAGCATCACTCAGAAGTCAAT 59.553 33.333 0.00 0.00 31.71 2.57
672 688 6.767902 ACTTTTAAGCATCACTCAGAAGTCAA 59.232 34.615 0.00 0.00 31.71 3.18
675 691 7.671302 TCTACTTTTAAGCATCACTCAGAAGT 58.329 34.615 0.00 0.00 35.60 3.01
676 692 8.031864 TCTCTACTTTTAAGCATCACTCAGAAG 58.968 37.037 0.00 0.00 0.00 2.85
677 693 7.896811 TCTCTACTTTTAAGCATCACTCAGAA 58.103 34.615 0.00 0.00 0.00 3.02
679 695 8.715191 AATCTCTACTTTTAAGCATCACTCAG 57.285 34.615 0.00 0.00 0.00 3.35
680 696 8.939929 CAAATCTCTACTTTTAAGCATCACTCA 58.060 33.333 0.00 0.00 0.00 3.41
681 697 8.940952 ACAAATCTCTACTTTTAAGCATCACTC 58.059 33.333 0.00 0.00 0.00 3.51
682 698 8.854614 ACAAATCTCTACTTTTAAGCATCACT 57.145 30.769 0.00 0.00 0.00 3.41
683 699 9.334693 CAACAAATCTCTACTTTTAAGCATCAC 57.665 33.333 0.00 0.00 0.00 3.06
685 701 9.899226 AACAACAAATCTCTACTTTTAAGCATC 57.101 29.630 0.00 0.00 0.00 3.91
686 702 9.683069 CAACAACAAATCTCTACTTTTAAGCAT 57.317 29.630 0.00 0.00 0.00 3.79
688 704 9.899226 ATCAACAACAAATCTCTACTTTTAAGC 57.101 29.630 0.00 0.00 0.00 3.09
695 711 7.441157 TCGAACAATCAACAACAAATCTCTACT 59.559 33.333 0.00 0.00 0.00 2.57
719 743 9.828220 CATTTGTATTTTTATTTTATGCCGTCG 57.172 29.630 0.00 0.00 0.00 5.12
733 757 6.533367 AGCACGACAACAACATTTGTATTTTT 59.467 30.769 0.00 0.00 44.59 1.94
737 761 4.536065 CAGCACGACAACAACATTTGTAT 58.464 39.130 0.00 0.00 44.59 2.29
740 764 1.518102 GCAGCACGACAACAACATTTG 59.482 47.619 0.00 0.00 0.00 2.32
743 767 1.100463 TGGCAGCACGACAACAACAT 61.100 50.000 0.00 0.00 0.00 2.71
745 769 1.298339 GTGGCAGCACGACAACAAC 60.298 57.895 0.00 0.00 30.71 3.32
789 813 1.527034 TGCCAAAGCATGAGAGTGTC 58.473 50.000 0.00 0.00 46.52 3.67
839 866 2.157834 TTTTCAGCCACATACGACGT 57.842 45.000 5.52 5.52 0.00 4.34
840 867 3.120338 ACATTTTTCAGCCACATACGACG 60.120 43.478 0.00 0.00 0.00 5.12
841 868 4.403453 GACATTTTTCAGCCACATACGAC 58.597 43.478 0.00 0.00 0.00 4.34
842 869 3.124466 CGACATTTTTCAGCCACATACGA 59.876 43.478 0.00 0.00 0.00 3.43
843 870 3.120338 ACGACATTTTTCAGCCACATACG 60.120 43.478 0.00 0.00 0.00 3.06
844 871 4.083537 TGACGACATTTTTCAGCCACATAC 60.084 41.667 0.00 0.00 0.00 2.39
845 872 4.068599 TGACGACATTTTTCAGCCACATA 58.931 39.130 0.00 0.00 0.00 2.29
846 873 2.884012 TGACGACATTTTTCAGCCACAT 59.116 40.909 0.00 0.00 0.00 3.21
847 874 2.293170 TGACGACATTTTTCAGCCACA 58.707 42.857 0.00 0.00 0.00 4.17
848 875 3.347958 TTGACGACATTTTTCAGCCAC 57.652 42.857 0.00 0.00 0.00 5.01
849 876 4.377839 TTTTGACGACATTTTTCAGCCA 57.622 36.364 0.00 0.00 0.00 4.75
851 878 5.914635 TCAGATTTTGACGACATTTTTCAGC 59.085 36.000 0.00 0.00 0.00 4.26
860 887 9.574458 TGTTAAAATTTTCAGATTTTGACGACA 57.426 25.926 6.72 0.00 43.12 4.35
895 940 4.052518 GTGGGGCATGGGCTCTGT 62.053 66.667 0.00 0.00 41.58 3.41
911 956 4.265056 GGGGTGTCCAACAGGCGT 62.265 66.667 0.00 0.00 35.00 5.68
915 960 1.455383 GCTTGTGGGGTGTCCAACAG 61.455 60.000 0.00 0.00 46.92 3.16
921 966 1.968540 GCTCTGCTTGTGGGGTGTC 60.969 63.158 0.00 0.00 0.00 3.67
922 967 2.113986 GCTCTGCTTGTGGGGTGT 59.886 61.111 0.00 0.00 0.00 4.16
923 968 2.674380 GGCTCTGCTTGTGGGGTG 60.674 66.667 0.00 0.00 0.00 4.61
924 969 3.971702 GGGCTCTGCTTGTGGGGT 61.972 66.667 0.00 0.00 0.00 4.95
925 970 3.970410 TGGGCTCTGCTTGTGGGG 61.970 66.667 0.00 0.00 0.00 4.96
926 971 2.674380 GTGGGCTCTGCTTGTGGG 60.674 66.667 0.00 0.00 0.00 4.61
927 972 2.113774 TGTGGGCTCTGCTTGTGG 59.886 61.111 0.00 0.00 0.00 4.17
928 973 2.263741 GGTGTGGGCTCTGCTTGTG 61.264 63.158 0.00 0.00 0.00 3.33
929 974 2.113986 GGTGTGGGCTCTGCTTGT 59.886 61.111 0.00 0.00 0.00 3.16
930 975 1.970114 CTGGTGTGGGCTCTGCTTG 60.970 63.158 0.00 0.00 0.00 4.01
931 976 2.433446 CTGGTGTGGGCTCTGCTT 59.567 61.111 0.00 0.00 0.00 3.91
932 977 4.341783 GCTGGTGTGGGCTCTGCT 62.342 66.667 0.00 0.00 0.00 4.24
933 978 4.341783 AGCTGGTGTGGGCTCTGC 62.342 66.667 0.00 0.00 32.98 4.26
937 982 1.529244 GTTTGAGCTGGTGTGGGCT 60.529 57.895 0.00 0.00 41.88 5.19
939 984 1.402787 AAAGTTTGAGCTGGTGTGGG 58.597 50.000 0.00 0.00 0.00 4.61
940 985 2.223805 GGAAAAGTTTGAGCTGGTGTGG 60.224 50.000 0.00 0.00 0.00 4.17
941 986 2.223805 GGGAAAAGTTTGAGCTGGTGTG 60.224 50.000 0.00 0.00 0.00 3.82
943 988 1.341209 GGGGAAAAGTTTGAGCTGGTG 59.659 52.381 0.00 0.00 0.00 4.17
944 989 1.063266 TGGGGAAAAGTTTGAGCTGGT 60.063 47.619 0.00 0.00 0.00 4.00
1111 2620 3.710722 CTTGCAGGCGAGGGAGGT 61.711 66.667 0.32 0.00 0.00 3.85
1485 3045 1.225704 GAAGGGGCCCTCATGACAG 59.774 63.158 28.97 0.00 30.89 3.51
1506 3066 1.079819 CAGGCCGATGACGACAACT 60.080 57.895 0.00 0.00 42.66 3.16
1598 3161 2.758736 ATGAGAATCCGAGCATAGCC 57.241 50.000 0.00 0.00 0.00 3.93
1602 3165 4.277672 CCATCAAAATGAGAATCCGAGCAT 59.722 41.667 0.00 0.00 34.61 3.79
1608 3171 4.280819 TCCACCCATCAAAATGAGAATCC 58.719 43.478 0.00 0.00 34.61 3.01
2003 3572 3.386932 TGGGATTTTGAATGGGGAGAG 57.613 47.619 0.00 0.00 0.00 3.20
2278 3864 7.816031 ACTCAAAGTTTGGCTAATCATTCAATG 59.184 33.333 15.47 0.00 0.00 2.82
2279 3865 7.816031 CACTCAAAGTTTGGCTAATCATTCAAT 59.184 33.333 15.47 0.00 0.00 2.57
2287 3874 4.217118 CAGAGCACTCAAAGTTTGGCTAAT 59.783 41.667 15.47 6.31 0.00 1.73
2318 3958 9.903682 GCATGAGCATAATTAGATGTAACATTT 57.096 29.630 0.00 0.00 41.58 2.32
2340 3980 2.916702 TGCACTCATAGGTAGGCATG 57.083 50.000 0.00 0.00 0.00 4.06
2381 4021 8.556213 TTATAAGCGTGATTCCAAAAAGTAGT 57.444 30.769 0.00 0.00 0.00 2.73
2399 4039 7.223387 CCTTTCTGCAAACATGGATTTATAAGC 59.777 37.037 0.00 0.00 0.00 3.09
2402 4042 6.667414 ACCCTTTCTGCAAACATGGATTTATA 59.333 34.615 0.00 0.00 0.00 0.98
2453 4093 6.349944 CCTGCCCTTAAGCATATTCAATCATC 60.350 42.308 0.00 0.00 43.09 2.92
2457 4097 5.065613 TCCTGCCCTTAAGCATATTCAAT 57.934 39.130 0.00 0.00 43.09 2.57
2496 4146 3.426615 ACCCATGTCGCCTTCAAATAAA 58.573 40.909 0.00 0.00 0.00 1.40
2497 4147 3.013921 GACCCATGTCGCCTTCAAATAA 58.986 45.455 0.00 0.00 0.00 1.40
2525 4175 2.749621 GGCTTCCAAATACTGACACTGG 59.250 50.000 0.00 0.00 0.00 4.00
2542 4192 1.960689 ACCACTGCATTAAAACGGCTT 59.039 42.857 0.00 0.00 0.00 4.35
2546 4196 7.810766 AAATAATCACCACTGCATTAAAACG 57.189 32.000 0.00 0.00 0.00 3.60
2567 4217 9.480053 CAAAATCCAACAACACTATGAGAAAAT 57.520 29.630 0.00 0.00 0.00 1.82
2596 4246 1.227999 CGGAAAACCTCGAGCTTGCA 61.228 55.000 6.99 0.00 0.00 4.08
2615 4265 1.207390 TACACACACCGTTAACGTGC 58.793 50.000 25.15 0.00 37.74 5.34
2624 4274 0.037697 TAGCCTGCTTACACACACCG 60.038 55.000 0.00 0.00 0.00 4.94
2648 4298 7.787725 AATTGGAGGTTCATTACGAGATAAC 57.212 36.000 0.00 0.00 0.00 1.89
2757 4407 4.488126 CTATGAGAGCAGACTGTAGAGC 57.512 50.000 3.99 0.00 0.00 4.09
2820 4474 1.734465 CTCTTGGCGACAGAAATCACC 59.266 52.381 0.00 0.00 44.54 4.02
2832 4486 2.251409 ACCATCATCATCTCTTGGCG 57.749 50.000 0.00 0.00 0.00 5.69
2855 4509 3.750130 GCATACCAGTGAGCCATTATGAG 59.250 47.826 0.00 0.00 0.00 2.90
2856 4510 3.496692 GGCATACCAGTGAGCCATTATGA 60.497 47.826 9.60 0.00 46.26 2.15
2860 4514 3.502164 GGCATACCAGTGAGCCATT 57.498 52.632 9.60 0.00 46.26 3.16
2891 4545 4.702131 ACCTCCAGCACTAATCAAATTCAC 59.298 41.667 0.00 0.00 0.00 3.18
2909 4563 2.191128 AACATCAGCACTTGACCTCC 57.809 50.000 0.00 0.00 38.99 4.30
3032 4696 4.100035 CAGATCCTGCCATACTGTCAGTTA 59.900 45.833 11.54 0.00 0.00 2.24
3072 4736 6.406624 GGCACTGTAGCAGTAAAACCTCTATA 60.407 42.308 1.16 0.00 43.43 1.31
3073 4737 5.420409 GCACTGTAGCAGTAAAACCTCTAT 58.580 41.667 1.16 0.00 43.43 1.98
3074 4738 4.322499 GGCACTGTAGCAGTAAAACCTCTA 60.322 45.833 1.16 0.00 43.43 2.43
3095 4759 3.073274 ACCTAACAGATTTGTGGAGGC 57.927 47.619 14.41 0.00 41.64 4.70
3096 4760 6.992715 CCTAATACCTAACAGATTTGTGGAGG 59.007 42.308 13.37 13.37 42.74 4.30
3144 4808 4.946478 ACTATTATCTCCACTGCAGACC 57.054 45.455 23.35 0.00 0.00 3.85
3146 4810 6.488344 CAGTCTACTATTATCTCCACTGCAGA 59.512 42.308 23.35 0.00 0.00 4.26
3151 4815 7.288852 ACATTGCAGTCTACTATTATCTCCACT 59.711 37.037 0.00 0.00 0.00 4.00
3157 4821 7.928706 ACAAGGACATTGCAGTCTACTATTATC 59.071 37.037 0.00 0.00 43.15 1.75
3177 4841 7.904558 ATACATCTTCATCTCACTACAAGGA 57.095 36.000 0.00 0.00 0.00 3.36
3216 4880 2.248248 TGAACACTGTAGCCTAGCAGT 58.752 47.619 2.40 2.40 45.69 4.40
3266 4930 7.454260 AATAAGGAAAATCTGTGAACCAGTC 57.546 36.000 0.00 0.00 42.19 3.51
3423 5095 1.707427 ACAGCCAACTCAGAAGGGAAT 59.293 47.619 0.00 0.00 0.00 3.01
3426 5098 3.356529 AATACAGCCAACTCAGAAGGG 57.643 47.619 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.