Multiple sequence alignment - TraesCS1A01G340200

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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 TraesCS1A01G340200 chr1A 100.000 5220 0 0 1 5220 530510955 530516174 0.000000e+00 9640.0
1 TraesCS1A01G340200 chr1B 88.088 2678 205 54 2610 5220 583396538 583399168 0.000000e+00 3073.0
2 TraesCS1A01G340200 chr1B 88.630 1935 143 36 7 1909 583393938 583395827 0.000000e+00 2283.0
3 TraesCS1A01G340200 chr1B 94.697 528 25 2 1905 2432 583395938 583396462 0.000000e+00 817.0
4 TraesCS1A01G340200 chr1B 89.944 179 15 2 2425 2602 314565532 314565708 1.460000e-55 228.0
5 TraesCS1A01G340200 chr1D 89.617 2456 188 39 4 2433 431954296 431956710 0.000000e+00 3061.0
6 TraesCS1A01G340200 chr1D 94.568 1344 53 11 3895 5220 431958127 431959468 0.000000e+00 2060.0
7 TraesCS1A01G340200 chr1D 93.596 1296 49 19 2610 3900 431956759 431958025 0.000000e+00 1903.0
8 TraesCS1A01G340200 chr1D 86.469 606 68 8 949 1545 369483188 369482588 0.000000e+00 652.0
9 TraesCS1A01G340200 chr1D 91.228 171 14 1 2424 2594 463381897 463382066 1.130000e-56 231.0
10 TraesCS1A01G340200 chr1D 77.311 119 23 3 525 643 415545114 415545000 3.370000e-07 67.6
11 TraesCS1A01G340200 chr6D 85.356 956 104 24 949 1888 59757743 59756808 0.000000e+00 957.0
12 TraesCS1A01G340200 chr6D 92.121 165 11 2 2432 2595 65394274 65394437 1.130000e-56 231.0
13 TraesCS1A01G340200 chr7D 83.891 956 95 30 949 1888 429959963 429959051 0.000000e+00 857.0
14 TraesCS1A01G340200 chr7D 87.097 62 8 0 5159 5220 205950276 205950215 2.610000e-08 71.3
15 TraesCS1A01G340200 chr5A 86.823 683 76 5 949 1620 545944153 545944832 0.000000e+00 750.0
16 TraesCS1A01G340200 chr5A 86.792 212 19 7 1681 1888 545944862 545945068 1.460000e-55 228.0
17 TraesCS1A01G340200 chr4B 88.315 445 38 12 1453 1888 603004960 603005399 5.990000e-144 521.0
18 TraesCS1A01G340200 chr4B 80.000 185 32 4 2432 2614 432813402 432813221 1.180000e-26 132.0
19 TraesCS1A01G340200 chr7B 87.865 445 39 13 1454 1888 559712236 559711797 4.660000e-140 508.0
20 TraesCS1A01G340200 chr7B 88.710 62 7 0 5159 5220 196278464 196278525 5.610000e-10 76.8
21 TraesCS1A01G340200 chr6B 87.661 389 39 7 1453 1833 693623120 693623507 1.330000e-120 444.0
22 TraesCS1A01G340200 chr6B 92.073 164 12 1 2431 2594 132353578 132353416 4.070000e-56 230.0
23 TraesCS1A01G340200 chr6B 88.950 181 18 2 2414 2594 720912234 720912056 6.800000e-54 222.0
24 TraesCS1A01G340200 chr4D 94.012 167 9 1 2428 2594 294699489 294699654 8.680000e-63 252.0
25 TraesCS1A01G340200 chr4D 91.566 166 13 1 2429 2594 34661691 34661527 1.460000e-55 228.0
26 TraesCS1A01G340200 chr2D 94.479 163 8 1 2432 2594 239722141 239722302 3.120000e-62 250.0
27 TraesCS1A01G340200 chr6A 90.643 171 15 1 2431 2601 363516233 363516402 5.260000e-55 226.0
28 TraesCS1A01G340200 chr6A 72.993 274 66 8 4947 5216 74239865 74240134 7.200000e-14 89.8
29 TraesCS1A01G340200 chr5D 82.474 194 23 9 2432 2619 331405048 331404860 5.410000e-35 159.0
30 TraesCS1A01G340200 chr3D 82.514 183 29 3 2432 2612 459335089 459335270 1.950000e-34 158.0
31 TraesCS1A01G340200 chr5B 94.340 53 2 1 949 1001 702409712 702409661 4.330000e-11 80.5


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 TraesCS1A01G340200 chr1A 530510955 530516174 5219 False 9640.000000 9640 100.000000 1 5220 1 chr1A.!!$F1 5219
1 TraesCS1A01G340200 chr1B 583393938 583399168 5230 False 2057.666667 3073 90.471667 7 5220 3 chr1B.!!$F2 5213
2 TraesCS1A01G340200 chr1D 431954296 431959468 5172 False 2341.333333 3061 92.593667 4 5220 3 chr1D.!!$F2 5216
3 TraesCS1A01G340200 chr1D 369482588 369483188 600 True 652.000000 652 86.469000 949 1545 1 chr1D.!!$R1 596
4 TraesCS1A01G340200 chr6D 59756808 59757743 935 True 957.000000 957 85.356000 949 1888 1 chr6D.!!$R1 939
5 TraesCS1A01G340200 chr7D 429959051 429959963 912 True 857.000000 857 83.891000 949 1888 1 chr7D.!!$R2 939
6 TraesCS1A01G340200 chr5A 545944153 545945068 915 False 489.000000 750 86.807500 949 1888 2 chr5A.!!$F1 939

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
49 50 0.396139 GCCATCCTGAATCCAGCCAA 60.396 55.0 0.0 0.0 39.07 4.52 F
193 195 0.550914 ACATCCACACCACCACACTT 59.449 50.0 0.0 0.0 0.00 3.16 F
1267 1318 0.692756 TCGGGTGCCATCAGGGAATA 60.693 55.0 0.0 0.0 36.80 1.75 F
1491 1542 0.750850 ACGGGAGTGCATATAAGCGT 59.249 50.0 0.0 0.0 44.82 5.07 F
2444 2622 0.614134 ACCACCTACTCCCTCCGTTC 60.614 60.0 0.0 0.0 0.00 3.95 F
4174 4505 0.460284 CCGATTACGAAGCCTGCACT 60.460 55.0 0.0 0.0 42.66 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1433 0.106708 AAGAGCGTGCCAAGAACAGA 59.893 50.000 0.00 0.0 0.00 3.41 R
1435 1486 0.454196 AAAACGTGCACAGTGGGTTC 59.546 50.000 18.64 0.0 0.00 3.62 R
2423 2601 0.706433 ACGGAGGGAGTAGGTGGTAA 59.294 55.000 0.00 0.0 0.00 2.85 R
2578 2756 3.277416 AAACCTACTCCCTCTGTTCCT 57.723 47.619 0.00 0.0 0.00 3.36 R
4217 4552 0.033920 CCCCAAAAGGAAACTGCTGC 59.966 55.000 0.00 0.0 42.68 5.25 R
5183 5577 2.851195 AGCTTTGGTGTCATTCTCGTT 58.149 42.857 0.00 0.0 0.00 3.85 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
37 38 2.367512 GACCTCCCCTGCCATCCT 60.368 66.667 0.00 0.00 0.00 3.24
49 50 0.396139 GCCATCCTGAATCCAGCCAA 60.396 55.000 0.00 0.00 39.07 4.52
61 62 4.013702 AGCCAATGAAGCTGCTGG 57.986 55.556 1.35 1.03 39.69 4.85
62 63 1.381463 AGCCAATGAAGCTGCTGGA 59.619 52.632 1.35 0.00 39.69 3.86
63 64 0.680280 AGCCAATGAAGCTGCTGGAG 60.680 55.000 1.35 0.00 39.69 3.86
72 73 2.433994 GCTGCTGGAGGAGGAGGAG 61.434 68.421 0.00 0.00 40.48 3.69
74 75 2.366570 GCTGGAGGAGGAGGAGGT 59.633 66.667 0.00 0.00 0.00 3.85
80 81 0.923358 GAGGAGGAGGAGGTGAGAGA 59.077 60.000 0.00 0.00 0.00 3.10
97 98 6.071840 GGTGAGAGAAGCTAGTGAAAACTAGA 60.072 42.308 15.38 0.00 41.56 2.43
107 108 8.317679 AGCTAGTGAAAACTAGATGACTCAATT 58.682 33.333 15.38 0.00 41.56 2.32
148 150 8.402472 ACATGAAAGAAACATTAACGAGAAACA 58.598 29.630 0.00 0.00 0.00 2.83
150 152 7.981142 TGAAAGAAACATTAACGAGAAACACT 58.019 30.769 0.00 0.00 0.00 3.55
193 195 0.550914 ACATCCACACCACCACACTT 59.449 50.000 0.00 0.00 0.00 3.16
197 199 2.112198 CACACCACCACACTTGCGT 61.112 57.895 0.00 0.00 0.00 5.24
345 348 1.374560 TCACCGCGGAACATATTTGG 58.625 50.000 35.90 7.41 0.00 3.28
348 351 2.162608 CACCGCGGAACATATTTGGAAA 59.837 45.455 35.90 0.00 0.00 3.13
368 371 9.990360 TTGGAAAGGTTTGGATTTTATAGAAAC 57.010 29.630 0.00 0.00 0.00 2.78
396 399 7.579726 AGAAGAATGTTGAGATTCACGAAAAG 58.420 34.615 4.05 0.00 35.16 2.27
399 402 6.346919 AGAATGTTGAGATTCACGAAAAGTCG 60.347 38.462 4.05 0.00 40.10 4.18
441 444 1.069022 CAACCCGTGTCTCAAAGCATG 60.069 52.381 0.00 0.00 0.00 4.06
456 459 2.745100 ATGGCTGAGTGCTGCACG 60.745 61.111 25.39 13.68 39.64 5.34
513 516 1.575922 GCGTGTCTCAAAGCATGCA 59.424 52.632 21.98 0.00 44.44 3.96
515 518 1.891178 CGTGTCTCAAAGCATGCATG 58.109 50.000 22.70 22.70 0.00 4.06
532 535 3.504134 TGCATGCCGTGTACAGTAAATTT 59.496 39.130 16.68 0.00 0.00 1.82
533 536 4.695928 TGCATGCCGTGTACAGTAAATTTA 59.304 37.500 16.68 0.00 0.00 1.40
639 643 3.138884 TGCAAAACAGGATAGCAGTGA 57.861 42.857 0.00 0.00 0.00 3.41
649 653 2.072298 GATAGCAGTGATTCATCGGCC 58.928 52.381 0.00 0.00 0.00 6.13
653 657 1.202114 GCAGTGATTCATCGGCCAAAA 59.798 47.619 2.24 0.00 0.00 2.44
687 691 9.646522 ATTAAGTATACCATTTGAAGGAAGCAT 57.353 29.630 0.00 0.00 0.00 3.79
698 702 4.250464 TGAAGGAAGCATTTATCGTTCGT 58.750 39.130 0.00 0.00 41.15 3.85
699 703 4.693566 TGAAGGAAGCATTTATCGTTCGTT 59.306 37.500 0.00 0.00 41.15 3.85
700 704 4.859629 AGGAAGCATTTATCGTTCGTTC 57.140 40.909 0.00 0.00 0.00 3.95
702 706 4.567159 AGGAAGCATTTATCGTTCGTTCTC 59.433 41.667 0.00 0.00 0.00 2.87
717 730 2.032549 CGTTCTCTTTTGCACAGGTCAG 60.033 50.000 0.00 0.00 0.00 3.51
719 732 1.141657 TCTCTTTTGCACAGGTCAGCT 59.858 47.619 0.00 0.00 0.00 4.24
727 740 1.608590 GCACAGGTCAGCTTGCTTAAA 59.391 47.619 0.00 0.00 32.00 1.52
728 741 2.605580 GCACAGGTCAGCTTGCTTAAAC 60.606 50.000 0.00 0.00 32.00 2.01
738 751 3.075432 AGCTTGCTTAAACTTCCCCCTAA 59.925 43.478 0.00 0.00 0.00 2.69
745 758 8.493787 TGCTTAAACTTCCCCCTAAAAATTTA 57.506 30.769 0.00 0.00 0.00 1.40
851 872 5.051508 GCATATTGCGAGCCAAAAACAATAG 60.052 40.000 0.00 0.00 36.83 1.73
940 961 1.138464 GGGTAGACCGGGACAAATCTC 59.862 57.143 6.32 0.00 36.71 2.75
972 993 1.645402 CCAATCCCCCGGATCCAGTT 61.645 60.000 13.41 0.00 42.27 3.16
1037 1060 3.665675 AATCCGTCGAGCACCAGCC 62.666 63.158 0.00 0.00 43.56 4.85
1185 1234 1.274167 TCCCTTGTACACAGTAAGCCG 59.726 52.381 0.00 0.00 0.00 5.52
1236 1285 2.371841 GCCCCTTGGATTTTGGTCTTTT 59.628 45.455 0.00 0.00 0.00 2.27
1240 1289 5.221904 CCCCTTGGATTTTGGTCTTTTTGAT 60.222 40.000 0.00 0.00 0.00 2.57
1267 1318 0.692756 TCGGGTGCCATCAGGGAATA 60.693 55.000 0.00 0.00 36.80 1.75
1405 1456 1.065551 GTTCTTGGCACGCTCTTTTGT 59.934 47.619 0.00 0.00 0.00 2.83
1431 1482 3.575630 TGTCGCAGTAGTTCAGATTCAC 58.424 45.455 0.00 0.00 0.00 3.18
1435 1486 2.668457 GCAGTAGTTCAGATTCACGGTG 59.332 50.000 0.56 0.56 0.00 4.94
1441 1492 1.052617 TCAGATTCACGGTGAACCCA 58.947 50.000 24.56 4.14 39.45 4.51
1450 1501 3.022287 GTGAACCCACTGTGCACG 58.978 61.111 13.13 9.67 43.59 5.34
1476 1527 2.099427 GGTTGTCTCTAGCTTCTACGGG 59.901 54.545 0.00 0.00 0.00 5.28
1482 1533 1.103803 CTAGCTTCTACGGGAGTGCA 58.896 55.000 0.00 0.00 46.80 4.57
1487 1538 3.895656 AGCTTCTACGGGAGTGCATATAA 59.104 43.478 9.73 0.00 46.80 0.98
1489 1540 3.936372 TCTACGGGAGTGCATATAAGC 57.064 47.619 0.00 0.00 46.80 3.09
1490 1541 2.228103 TCTACGGGAGTGCATATAAGCG 59.772 50.000 0.00 0.00 46.80 4.68
1491 1542 0.750850 ACGGGAGTGCATATAAGCGT 59.249 50.000 0.00 0.00 44.82 5.07
1494 1549 1.344763 GGGAGTGCATATAAGCGTCCT 59.655 52.381 16.45 4.35 39.19 3.85
1551 1606 3.701664 TGTCTCTGACTTGGCTCTGATA 58.298 45.455 0.00 0.00 33.15 2.15
1557 1612 7.229707 GTCTCTGACTTGGCTCTGATACTAATA 59.770 40.741 0.00 0.00 0.00 0.98
2041 2219 5.569355 TGAGCTTTCATATCCTTTTGACCA 58.431 37.500 0.00 0.00 0.00 4.02
2272 2450 3.864789 AGAGCTTCAGAAAAGGGTCAA 57.135 42.857 0.00 0.00 0.00 3.18
2399 2577 7.665559 TGTTAGAAAGTGTGCCTATCTCATTTT 59.334 33.333 0.00 0.00 33.00 1.82
2423 2601 2.652348 TGGGGAAATGGATGTACAACCT 59.348 45.455 21.41 3.01 0.00 3.50
2433 2611 4.223477 TGGATGTACAACCTTACCACCTAC 59.777 45.833 21.41 0.00 0.00 3.18
2434 2612 4.468868 GGATGTACAACCTTACCACCTACT 59.531 45.833 14.60 0.00 0.00 2.57
2435 2613 5.394993 GGATGTACAACCTTACCACCTACTC 60.395 48.000 14.60 0.00 0.00 2.59
2436 2614 3.834231 TGTACAACCTTACCACCTACTCC 59.166 47.826 0.00 0.00 0.00 3.85
2437 2615 2.263545 ACAACCTTACCACCTACTCCC 58.736 52.381 0.00 0.00 0.00 4.30
2439 2617 2.500504 CAACCTTACCACCTACTCCCTC 59.499 54.545 0.00 0.00 0.00 4.30
2440 2618 1.008084 ACCTTACCACCTACTCCCTCC 59.992 57.143 0.00 0.00 0.00 4.30
2442 2620 0.706433 TTACCACCTACTCCCTCCGT 59.294 55.000 0.00 0.00 0.00 4.69
2443 2621 0.706433 TACCACCTACTCCCTCCGTT 59.294 55.000 0.00 0.00 0.00 4.44
2444 2622 0.614134 ACCACCTACTCCCTCCGTTC 60.614 60.000 0.00 0.00 0.00 3.95
2445 2623 1.328430 CCACCTACTCCCTCCGTTCC 61.328 65.000 0.00 0.00 0.00 3.62
2447 2625 1.064166 CACCTACTCCCTCCGTTCCTA 60.064 57.143 0.00 0.00 0.00 2.94
2448 2626 1.642762 ACCTACTCCCTCCGTTCCTAA 59.357 52.381 0.00 0.00 0.00 2.69
2450 2628 3.306613 CCTACTCCCTCCGTTCCTAAAT 58.693 50.000 0.00 0.00 0.00 1.40
2451 2629 4.078980 ACCTACTCCCTCCGTTCCTAAATA 60.079 45.833 0.00 0.00 0.00 1.40
2452 2630 5.085219 CCTACTCCCTCCGTTCCTAAATAT 58.915 45.833 0.00 0.00 0.00 1.28
2453 2631 6.183361 ACCTACTCCCTCCGTTCCTAAATATA 60.183 42.308 0.00 0.00 0.00 0.86
2455 2633 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2456 2634 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2457 2635 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2458 2636 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2459 2637 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2460 2638 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2461 2639 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2462 2640 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2485 2663 8.645814 TTTTAGAGATTCCACTACAGACTACA 57.354 34.615 0.00 0.00 0.00 2.74
2486 2664 8.824756 TTTAGAGATTCCACTACAGACTACAT 57.175 34.615 0.00 0.00 0.00 2.29
2487 2665 9.916360 TTTAGAGATTCCACTACAGACTACATA 57.084 33.333 0.00 0.00 0.00 2.29
2488 2666 7.811117 AGAGATTCCACTACAGACTACATAC 57.189 40.000 0.00 0.00 0.00 2.39
2489 2667 6.483974 AGAGATTCCACTACAGACTACATACG 59.516 42.308 0.00 0.00 0.00 3.06
2490 2668 5.531659 AGATTCCACTACAGACTACATACGG 59.468 44.000 0.00 0.00 0.00 4.02
2491 2669 4.492494 TCCACTACAGACTACATACGGA 57.508 45.455 0.00 0.00 0.00 4.69
2492 2670 4.449131 TCCACTACAGACTACATACGGAG 58.551 47.826 0.00 0.00 0.00 4.63
2509 2687 5.160607 ACGGAGTAAAATGAGTGAATCCA 57.839 39.130 0.00 0.00 41.94 3.41
2510 2688 4.935808 ACGGAGTAAAATGAGTGAATCCAC 59.064 41.667 0.00 0.00 41.94 4.02
2511 2689 4.935205 CGGAGTAAAATGAGTGAATCCACA 59.065 41.667 0.00 0.00 45.54 4.17
2512 2690 5.163854 CGGAGTAAAATGAGTGAATCCACAC 60.164 44.000 0.00 0.00 45.54 3.82
2523 2701 6.808008 AGTGAATCCACACTCTAAAACATG 57.192 37.500 0.00 0.00 46.36 3.21
2524 2702 6.299141 AGTGAATCCACACTCTAAAACATGT 58.701 36.000 0.00 0.00 46.36 3.21
2525 2703 6.428159 AGTGAATCCACACTCTAAAACATGTC 59.572 38.462 0.00 0.00 46.36 3.06
2526 2704 6.428159 GTGAATCCACACTCTAAAACATGTCT 59.572 38.462 0.00 0.00 42.72 3.41
2527 2705 7.602644 GTGAATCCACACTCTAAAACATGTCTA 59.397 37.037 0.00 0.00 42.72 2.59
2528 2706 8.321353 TGAATCCACACTCTAAAACATGTCTAT 58.679 33.333 0.00 0.00 0.00 1.98
2529 2707 9.817809 GAATCCACACTCTAAAACATGTCTATA 57.182 33.333 0.00 0.00 0.00 1.31
2555 2733 6.835174 ACATCCGTATGTAGTCCTTAGTAGA 58.165 40.000 0.00 0.00 44.66 2.59
2556 2734 7.285566 ACATCCGTATGTAGTCCTTAGTAGAA 58.714 38.462 0.00 0.00 44.66 2.10
2557 2735 7.943447 ACATCCGTATGTAGTCCTTAGTAGAAT 59.057 37.037 0.00 0.00 44.66 2.40
2558 2736 7.741027 TCCGTATGTAGTCCTTAGTAGAATG 57.259 40.000 0.00 0.00 0.00 2.67
2559 2737 7.285566 TCCGTATGTAGTCCTTAGTAGAATGT 58.714 38.462 0.00 0.00 0.00 2.71
2560 2738 7.443575 TCCGTATGTAGTCCTTAGTAGAATGTC 59.556 40.741 0.00 0.00 0.00 3.06
2561 2739 7.444792 CCGTATGTAGTCCTTAGTAGAATGTCT 59.555 40.741 0.00 0.00 0.00 3.41
2562 2740 9.486497 CGTATGTAGTCCTTAGTAGAATGTCTA 57.514 37.037 0.00 0.00 0.00 2.59
2566 2744 9.970553 TGTAGTCCTTAGTAGAATGTCTAGAAA 57.029 33.333 0.00 0.00 28.01 2.52
2589 2767 9.549078 GAAAGACTTATATTTAGGAACAGAGGG 57.451 37.037 0.00 0.00 0.00 4.30
2590 2768 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
2591 2769 8.485578 AGACTTATATTTAGGAACAGAGGGAG 57.514 38.462 0.00 0.00 0.00 4.30
2599 2777 3.599348 AGGAACAGAGGGAGTAGGTTTT 58.401 45.455 0.00 0.00 0.00 2.43
2679 2892 9.998106 TGGTAGGCAATACTATTAAAAGATCTC 57.002 33.333 0.00 0.00 34.56 2.75
2701 2914 6.269077 TCTCAGGTAAATTGTGTTCAGGAGTA 59.731 38.462 0.00 0.00 0.00 2.59
2733 2946 5.653507 TGCAGGTCATATTTTGAATCTTGC 58.346 37.500 0.00 0.00 35.70 4.01
2886 3099 1.826720 GCAAAATTGGCTGATCCTGGA 59.173 47.619 0.00 0.00 35.26 3.86
3110 3323 6.270695 ACCCAGTGGATTTGATCTTCATTTTT 59.729 34.615 11.95 0.00 34.81 1.94
3534 3747 8.624776 CCACATATTTCTCTGAAACCTTAATCC 58.375 37.037 0.00 0.00 0.00 3.01
3558 3771 9.591792 TCCTCTATGCATATATTCGAGAAATTG 57.408 33.333 17.23 4.87 0.00 2.32
3633 3846 3.119245 AGCTCCAAATAATGCAGCTGTTG 60.119 43.478 16.64 10.35 39.02 3.33
3637 3854 4.523943 TCCAAATAATGCAGCTGTTGTCTT 59.476 37.500 16.64 4.78 0.00 3.01
3647 3864 4.855388 GCAGCTGTTGTCTTATTGATGTTG 59.145 41.667 16.64 0.00 0.00 3.33
3651 3868 5.630680 GCTGTTGTCTTATTGATGTTGGTTG 59.369 40.000 0.00 0.00 0.00 3.77
3663 3880 8.816640 ATTGATGTTGGTTGAATTAAGTTCAC 57.183 30.769 0.00 0.00 46.14 3.18
3664 3881 7.340122 TGATGTTGGTTGAATTAAGTTCACA 57.660 32.000 0.00 0.00 46.14 3.58
3665 3882 7.776107 TGATGTTGGTTGAATTAAGTTCACAA 58.224 30.769 0.00 0.00 46.14 3.33
3666 3883 8.420222 TGATGTTGGTTGAATTAAGTTCACAAT 58.580 29.630 0.00 0.00 46.14 2.71
3667 3884 9.906660 GATGTTGGTTGAATTAAGTTCACAATA 57.093 29.630 0.00 0.00 46.14 1.90
3690 3907 6.851222 ATCAGACAATTTACATAGGAAGCG 57.149 37.500 0.00 0.00 0.00 4.68
3717 3934 3.008330 ACTGCATCTTCATGAGTTGCTC 58.992 45.455 20.38 3.22 46.56 4.26
3719 3936 2.026542 TGCATCTTCATGAGTTGCTCCT 60.027 45.455 20.38 0.00 46.56 3.69
3749 3966 6.613699 TGGCAGGATGTGATAAAATTAGGAT 58.386 36.000 0.00 0.00 39.31 3.24
3753 3970 7.231317 GCAGGATGTGATAAAATTAGGATTGGA 59.769 37.037 0.00 0.00 39.31 3.53
3805 4022 5.506815 CGAGTTTCAGTATAGCATACCCGAA 60.507 44.000 0.00 0.00 0.00 4.30
3829 4049 4.158394 TGAGATAAAACATGCCTGAAAGCC 59.842 41.667 0.00 0.00 0.00 4.35
3859 4079 2.212652 TCGTTGCATCATGCTATCCAC 58.787 47.619 11.84 0.00 45.31 4.02
3863 4083 4.295870 GTTGCATCATGCTATCCACATTG 58.704 43.478 11.84 0.00 45.31 2.82
3933 4264 5.690865 TCTGACAGTACCCATTTTCACTTT 58.309 37.500 1.59 0.00 0.00 2.66
4111 4442 2.637382 CCATTTGGGTAGGGCTTGTTTT 59.363 45.455 0.00 0.00 0.00 2.43
4174 4505 0.460284 CCGATTACGAAGCCTGCACT 60.460 55.000 0.00 0.00 42.66 4.40
4176 4507 0.924090 GATTACGAAGCCTGCACTCG 59.076 55.000 10.80 10.80 0.00 4.18
4179 4510 1.100510 TACGAAGCCTGCACTCGTAT 58.899 50.000 17.22 3.45 38.10 3.06
4217 4552 5.521735 TGTCCAAAATGAAAATTGGTGAACG 59.478 36.000 4.62 0.00 45.12 3.95
4267 4602 2.477825 CCACATTCTGCCGTCTCATAG 58.522 52.381 0.00 0.00 0.00 2.23
4311 4652 2.093235 CCCTGATCTCTTCACCTTGTCC 60.093 54.545 0.00 0.00 0.00 4.02
4358 4699 6.584954 GCTGCTCATATAACGAATGTTGTAG 58.415 40.000 0.00 0.00 39.12 2.74
4422 4763 2.578021 ACCTATGCATGGACTTTGGAGT 59.422 45.455 12.26 0.00 39.32 3.85
4571 4935 4.677779 GCCTTTGTTGCATTATCGGTCAAT 60.678 41.667 0.00 0.00 0.00 2.57
4754 5148 8.340618 AGTAATCCTTATATTTTGCGATGCAT 57.659 30.769 0.00 0.00 38.76 3.96
4861 5255 3.247648 GGCGGGCTTTTTCTTTCTTTTTC 59.752 43.478 0.00 0.00 0.00 2.29
4868 5262 5.290885 GCTTTTTCTTTCTTTTTCCAGCGAA 59.709 36.000 0.00 0.00 0.00 4.70
4900 5294 9.045223 CATCATAGTAATGTCATTCTCCGAAAA 57.955 33.333 0.07 0.00 34.50 2.29
4943 5337 8.017418 TGTTTTGGACAAATTTCTTGGATACT 57.983 30.769 0.00 0.00 34.69 2.12
5129 5523 5.930837 ACTTGACAAAATGGGAAACAAGA 57.069 34.783 0.00 0.00 37.34 3.02
5183 5577 4.578928 GGTTTCTTCCTTGTTAGCAGTTCA 59.421 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.600107 GGGTGGTCGACCTATGCAA 59.400 57.895 33.39 11.17 45.33 4.08
1 2 2.363975 GGGGTGGTCGACCTATGCA 61.364 63.158 33.39 11.97 45.33 3.96
2 3 2.504519 GGGGTGGTCGACCTATGC 59.495 66.667 33.39 20.12 45.33 3.14
3 4 1.755395 TCGGGGTGGTCGACCTATG 60.755 63.158 33.39 18.76 45.33 2.23
4 5 2.685366 TCGGGGTGGTCGACCTAT 59.315 61.111 33.39 0.00 45.33 2.57
30 31 0.396139 TTGGCTGGATTCAGGATGGC 60.396 55.000 2.40 0.00 41.19 4.40
37 38 2.519771 AGCTTCATTGGCTGGATTCA 57.480 45.000 0.00 0.00 38.73 2.57
49 50 0.619832 TCCTCCTCCAGCAGCTTCAT 60.620 55.000 0.00 0.00 0.00 2.57
59 60 0.851332 TCTCACCTCCTCCTCCTCCA 60.851 60.000 0.00 0.00 0.00 3.86
60 61 0.106217 CTCTCACCTCCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
61 62 0.923358 TCTCTCACCTCCTCCTCCTC 59.077 60.000 0.00 0.00 0.00 3.71
62 63 1.287739 CTTCTCTCACCTCCTCCTCCT 59.712 57.143 0.00 0.00 0.00 3.69
63 64 1.775385 CTTCTCTCACCTCCTCCTCC 58.225 60.000 0.00 0.00 0.00 4.30
72 73 4.888917 AGTTTTCACTAGCTTCTCTCACC 58.111 43.478 0.00 0.00 0.00 4.02
117 118 9.450807 CTCGTTAATGTTTCTTTCATGTTCTTT 57.549 29.630 0.00 0.00 0.00 2.52
153 155 8.178964 GGATGTTTGTTTGCGTCTATGTTATAA 58.821 33.333 0.00 0.00 0.00 0.98
156 158 5.470437 TGGATGTTTGTTTGCGTCTATGTTA 59.530 36.000 0.00 0.00 0.00 2.41
169 171 1.754226 GTGGTGGTGTGGATGTTTGTT 59.246 47.619 0.00 0.00 0.00 2.83
197 199 1.610363 TTATGTTTGCGAAGTGGGCA 58.390 45.000 0.00 0.00 38.93 5.36
330 333 2.422127 ACCTTTCCAAATATGTTCCGCG 59.578 45.455 0.00 0.00 0.00 6.46
368 371 6.891624 TCGTGAATCTCAACATTCTTCTTTG 58.108 36.000 0.00 0.00 34.35 2.77
376 379 5.679906 CGACTTTTCGTGAATCTCAACATT 58.320 37.500 0.00 0.00 40.61 2.71
396 399 2.080286 TTGTCCAAGAAGCTAGCGAC 57.920 50.000 9.55 9.97 0.00 5.19
399 402 4.695455 TGTATGTTTGTCCAAGAAGCTAGC 59.305 41.667 6.62 6.62 0.00 3.42
495 498 0.169672 ATGCATGCTTTGAGACACGC 59.830 50.000 20.33 0.00 0.00 5.34
513 516 7.649973 TGTTTTAAATTTACTGTACACGGCAT 58.350 30.769 0.00 0.00 0.00 4.40
515 518 7.911362 TTGTTTTAAATTTACTGTACACGGC 57.089 32.000 0.00 0.00 0.00 5.68
600 604 6.893958 TTGCATGAAAATTTACAAACACGT 57.106 29.167 0.00 0.00 0.00 4.49
601 605 7.689812 TGTTTTGCATGAAAATTTACAAACACG 59.310 29.630 0.00 0.00 35.96 4.49
602 606 8.886816 TGTTTTGCATGAAAATTTACAAACAC 57.113 26.923 0.00 0.00 35.96 3.32
603 607 8.180267 CCTGTTTTGCATGAAAATTTACAAACA 58.820 29.630 0.00 0.00 35.96 2.83
604 608 8.394121 TCCTGTTTTGCATGAAAATTTACAAAC 58.606 29.630 0.00 0.00 35.96 2.93
607 611 9.421806 CTATCCTGTTTTGCATGAAAATTTACA 57.578 29.630 0.00 0.90 35.96 2.41
608 612 8.382875 GCTATCCTGTTTTGCATGAAAATTTAC 58.617 33.333 0.00 0.00 35.96 2.01
609 613 8.093307 TGCTATCCTGTTTTGCATGAAAATTTA 58.907 29.630 0.00 0.00 35.96 1.40
610 614 6.935771 TGCTATCCTGTTTTGCATGAAAATTT 59.064 30.769 0.00 0.00 35.96 1.82
684 688 5.002561 GCAAAAGAGAACGAACGATAAATGC 59.997 40.000 0.14 0.00 0.00 3.56
687 691 5.006844 TGTGCAAAAGAGAACGAACGATAAA 59.993 36.000 0.14 0.00 0.00 1.40
698 702 1.949525 GCTGACCTGTGCAAAAGAGAA 59.050 47.619 0.00 0.00 0.00 2.87
699 703 1.141657 AGCTGACCTGTGCAAAAGAGA 59.858 47.619 0.00 0.00 0.00 3.10
700 704 1.602311 AGCTGACCTGTGCAAAAGAG 58.398 50.000 0.00 0.00 0.00 2.85
702 706 1.866880 GCAAGCTGACCTGTGCAAAAG 60.867 52.381 0.95 0.00 36.97 2.27
717 730 1.924731 AGGGGGAAGTTTAAGCAAGC 58.075 50.000 0.00 0.00 0.00 4.01
719 732 7.381789 AATTTTTAGGGGGAAGTTTAAGCAA 57.618 32.000 0.00 0.00 0.00 3.91
727 740 9.624037 AATACCTTTAAATTTTTAGGGGGAAGT 57.376 29.630 17.64 3.90 0.00 3.01
745 758 8.420222 TGTTCATTGTCACATTCAAATACCTTT 58.580 29.630 0.00 0.00 0.00 3.11
796 812 8.911662 GCGTGTCAAAAATGTATTTACAAAGAT 58.088 29.630 0.00 0.00 39.99 2.40
797 813 7.915923 TGCGTGTCAAAAATGTATTTACAAAGA 59.084 29.630 0.00 0.00 39.99 2.52
798 814 8.055609 TGCGTGTCAAAAATGTATTTACAAAG 57.944 30.769 0.00 0.00 39.99 2.77
799 815 7.168302 CCTGCGTGTCAAAAATGTATTTACAAA 59.832 33.333 0.00 0.00 39.99 2.83
800 816 6.638873 CCTGCGTGTCAAAAATGTATTTACAA 59.361 34.615 0.00 0.00 39.99 2.41
801 817 6.017026 TCCTGCGTGTCAAAAATGTATTTACA 60.017 34.615 0.00 0.00 40.98 2.41
802 818 6.375377 TCCTGCGTGTCAAAAATGTATTTAC 58.625 36.000 0.00 0.00 0.00 2.01
803 819 6.561737 TCCTGCGTGTCAAAAATGTATTTA 57.438 33.333 0.00 0.00 0.00 1.40
804 820 5.446143 TCCTGCGTGTCAAAAATGTATTT 57.554 34.783 0.00 0.00 0.00 1.40
805 821 4.615912 GCTCCTGCGTGTCAAAAATGTATT 60.616 41.667 0.00 0.00 0.00 1.89
806 822 3.119849 GCTCCTGCGTGTCAAAAATGTAT 60.120 43.478 0.00 0.00 0.00 2.29
807 823 2.225491 GCTCCTGCGTGTCAAAAATGTA 59.775 45.455 0.00 0.00 0.00 2.29
851 872 1.667830 TAACGTGCAGCACTCTGGC 60.668 57.895 23.15 0.00 40.65 4.85
940 961 0.243636 GGATTGGAAAGGCACGGTTG 59.756 55.000 0.00 0.00 0.00 3.77
972 993 1.301716 GACTTGTGCTGGGAGCGAA 60.302 57.895 0.00 0.00 46.26 4.70
1185 1234 4.475135 GGGAAGCAGAGGGTCGGC 62.475 72.222 0.00 0.00 37.86 5.54
1236 1285 3.157881 TGGCACCCGAAAACATAATCAA 58.842 40.909 0.00 0.00 0.00 2.57
1240 1289 2.752354 CTGATGGCACCCGAAAACATAA 59.248 45.455 0.00 0.00 0.00 1.90
1382 1433 0.106708 AAGAGCGTGCCAAGAACAGA 59.893 50.000 0.00 0.00 0.00 3.41
1405 1456 5.774498 ATCTGAACTACTGCGACATGATA 57.226 39.130 0.00 0.00 0.00 2.15
1431 1482 2.203139 TGCACAGTGGGTTCACCG 60.203 61.111 1.84 0.00 44.64 4.94
1435 1486 0.454196 AAAACGTGCACAGTGGGTTC 59.546 50.000 18.64 0.00 0.00 3.62
1441 1492 0.885196 ACAACCAAAACGTGCACAGT 59.115 45.000 18.64 12.84 0.00 3.55
1449 1500 4.058817 AGAAGCTAGAGACAACCAAAACG 58.941 43.478 0.00 0.00 0.00 3.60
1450 1501 5.118817 CGTAGAAGCTAGAGACAACCAAAAC 59.881 44.000 0.00 0.00 0.00 2.43
1476 1527 2.797156 CACAGGACGCTTATATGCACTC 59.203 50.000 10.84 4.56 0.00 3.51
1482 1533 5.360144 AGAGTACAACACAGGACGCTTATAT 59.640 40.000 0.00 0.00 0.00 0.86
1487 1538 1.329256 AGAGTACAACACAGGACGCT 58.671 50.000 0.00 0.00 0.00 5.07
1489 1540 3.909776 TGTAGAGTACAACACAGGACG 57.090 47.619 0.00 0.00 35.38 4.79
1522 1577 5.437060 AGCCAAGTCAGAGACAACTAAAAA 58.563 37.500 0.00 0.00 34.60 1.94
1542 1597 9.664332 ATGAACATGAATATTAGTATCAGAGCC 57.336 33.333 0.00 0.00 0.00 4.70
1551 1606 9.524106 CAATGCACAATGAACATGAATATTAGT 57.476 29.630 0.00 0.00 0.00 2.24
1557 1612 4.570930 TGCAATGCACAATGAACATGAAT 58.429 34.783 2.72 0.00 31.71 2.57
2062 2240 3.697542 CCTGATCTTGTCATGCCATTTCA 59.302 43.478 0.00 0.00 35.97 2.69
2318 2496 8.723365 ACCTGATGATAAGGTCCATATTAAACA 58.277 33.333 0.00 0.00 45.13 2.83
2370 2548 7.168219 TGAGATAGGCACACTTTCTAACAATT 58.832 34.615 0.00 0.00 37.58 2.32
2371 2549 6.711277 TGAGATAGGCACACTTTCTAACAAT 58.289 36.000 0.00 0.00 37.58 2.71
2375 2553 7.665559 ACAAAATGAGATAGGCACACTTTCTAA 59.334 33.333 0.00 0.00 37.58 2.10
2399 2577 3.816398 TGTACATCCATTTCCCCAACA 57.184 42.857 0.00 0.00 0.00 3.33
2423 2601 0.706433 ACGGAGGGAGTAGGTGGTAA 59.294 55.000 0.00 0.00 0.00 2.85
2433 2611 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2434 2612 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2435 2613 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2436 2614 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2459 2637 9.085645 TGTAGTCTGTAGTGGAATCTCTAAAAA 57.914 33.333 0.00 0.00 0.00 1.94
2460 2638 8.645814 TGTAGTCTGTAGTGGAATCTCTAAAA 57.354 34.615 0.00 0.00 0.00 1.52
2461 2639 8.824756 ATGTAGTCTGTAGTGGAATCTCTAAA 57.175 34.615 0.00 0.00 0.00 1.85
2462 2640 9.339850 GTATGTAGTCTGTAGTGGAATCTCTAA 57.660 37.037 0.00 0.00 0.00 2.10
2463 2641 7.656542 CGTATGTAGTCTGTAGTGGAATCTCTA 59.343 40.741 0.00 0.00 0.00 2.43
2464 2642 6.483974 CGTATGTAGTCTGTAGTGGAATCTCT 59.516 42.308 0.00 0.00 0.00 3.10
2465 2643 6.293516 CCGTATGTAGTCTGTAGTGGAATCTC 60.294 46.154 0.00 0.00 0.00 2.75
2466 2644 5.531659 CCGTATGTAGTCTGTAGTGGAATCT 59.468 44.000 0.00 0.00 0.00 2.40
2467 2645 5.530171 TCCGTATGTAGTCTGTAGTGGAATC 59.470 44.000 0.00 0.00 0.00 2.52
2468 2646 5.443283 TCCGTATGTAGTCTGTAGTGGAAT 58.557 41.667 0.00 0.00 0.00 3.01
2469 2647 4.847198 TCCGTATGTAGTCTGTAGTGGAA 58.153 43.478 0.00 0.00 0.00 3.53
2470 2648 4.080695 ACTCCGTATGTAGTCTGTAGTGGA 60.081 45.833 0.00 0.00 0.00 4.02
2471 2649 4.197750 ACTCCGTATGTAGTCTGTAGTGG 58.802 47.826 0.00 0.00 0.00 4.00
2472 2650 6.915544 TTACTCCGTATGTAGTCTGTAGTG 57.084 41.667 0.00 0.00 0.00 2.74
2473 2651 7.928307 TTTTACTCCGTATGTAGTCTGTAGT 57.072 36.000 0.00 0.00 0.00 2.73
2474 2652 8.618677 TCATTTTACTCCGTATGTAGTCTGTAG 58.381 37.037 0.00 0.00 0.00 2.74
2475 2653 8.510243 TCATTTTACTCCGTATGTAGTCTGTA 57.490 34.615 0.00 0.00 0.00 2.74
2476 2654 7.122353 ACTCATTTTACTCCGTATGTAGTCTGT 59.878 37.037 0.00 0.00 0.00 3.41
2477 2655 7.432545 CACTCATTTTACTCCGTATGTAGTCTG 59.567 40.741 0.00 0.00 0.00 3.51
2478 2656 7.338703 TCACTCATTTTACTCCGTATGTAGTCT 59.661 37.037 0.00 0.00 0.00 3.24
2479 2657 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2480 2658 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2481 2659 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2482 2660 7.924412 GGATTCACTCATTTTACTCCGTATGTA 59.076 37.037 0.00 0.00 0.00 2.29
2483 2661 6.761714 GGATTCACTCATTTTACTCCGTATGT 59.238 38.462 0.00 0.00 0.00 2.29
2484 2662 6.761242 TGGATTCACTCATTTTACTCCGTATG 59.239 38.462 0.00 0.00 0.00 2.39
2485 2663 6.761714 GTGGATTCACTCATTTTACTCCGTAT 59.238 38.462 0.00 0.00 40.58 3.06
2486 2664 6.103997 GTGGATTCACTCATTTTACTCCGTA 58.896 40.000 0.00 0.00 40.58 4.02
2487 2665 4.935808 GTGGATTCACTCATTTTACTCCGT 59.064 41.667 0.00 0.00 40.58 4.69
2488 2666 4.935205 TGTGGATTCACTCATTTTACTCCG 59.065 41.667 5.55 0.00 43.94 4.63
2489 2667 5.940470 AGTGTGGATTCACTCATTTTACTCC 59.060 40.000 5.55 0.00 44.07 3.85
2501 2679 6.428159 AGACATGTTTTAGAGTGTGGATTCAC 59.572 38.462 0.00 0.00 43.87 3.18
2502 2680 6.533730 AGACATGTTTTAGAGTGTGGATTCA 58.466 36.000 0.00 0.00 0.00 2.57
2503 2681 8.723942 ATAGACATGTTTTAGAGTGTGGATTC 57.276 34.615 0.00 0.00 0.00 2.52
2519 2697 9.682465 ACTACATACGGATGTATATAGACATGT 57.318 33.333 20.64 12.10 45.42 3.21
2521 2699 9.339850 GGACTACATACGGATGTATATAGACAT 57.660 37.037 20.64 12.70 45.42 3.06
2522 2700 8.546322 AGGACTACATACGGATGTATATAGACA 58.454 37.037 20.64 2.07 45.42 3.41
2523 2701 8.961294 AGGACTACATACGGATGTATATAGAC 57.039 38.462 20.64 10.95 45.42 2.59
2528 2706 9.881649 CTACTAAGGACTACATACGGATGTATA 57.118 37.037 20.64 9.08 45.42 1.47
2529 2707 8.600668 TCTACTAAGGACTACATACGGATGTAT 58.399 37.037 20.64 11.04 45.42 2.29
2530 2708 7.966812 TCTACTAAGGACTACATACGGATGTA 58.033 38.462 19.32 19.32 44.77 2.29
2532 2710 7.741027 TTCTACTAAGGACTACATACGGATG 57.259 40.000 5.94 5.94 39.16 3.51
2533 2711 7.943447 ACATTCTACTAAGGACTACATACGGAT 59.057 37.037 0.00 0.00 0.00 4.18
2534 2712 7.285566 ACATTCTACTAAGGACTACATACGGA 58.714 38.462 0.00 0.00 0.00 4.69
2535 2713 7.444792 AGACATTCTACTAAGGACTACATACGG 59.555 40.741 0.00 0.00 0.00 4.02
2536 2714 8.380743 AGACATTCTACTAAGGACTACATACG 57.619 38.462 0.00 0.00 0.00 3.06
2540 2718 9.970553 TTTCTAGACATTCTACTAAGGACTACA 57.029 33.333 0.00 0.00 0.00 2.74
2563 2741 9.549078 CCCTCTGTTCCTAAATATAAGTCTTTC 57.451 37.037 0.00 0.00 0.00 2.62
2564 2742 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
2565 2743 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
2566 2744 8.068733 ACTCCCTCTGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
2567 2745 8.252624 ACTCCCTCTGTTCCTAAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
2568 2746 9.369672 CTACTCCCTCTGTTCCTAAATATAAGT 57.630 37.037 0.00 0.00 0.00 2.24
2569 2747 8.808092 CCTACTCCCTCTGTTCCTAAATATAAG 58.192 40.741 0.00 0.00 0.00 1.73
2570 2748 8.294690 ACCTACTCCCTCTGTTCCTAAATATAA 58.705 37.037 0.00 0.00 0.00 0.98
2571 2749 7.834046 ACCTACTCCCTCTGTTCCTAAATATA 58.166 38.462 0.00 0.00 0.00 0.86
2572 2750 6.694611 ACCTACTCCCTCTGTTCCTAAATAT 58.305 40.000 0.00 0.00 0.00 1.28
2573 2751 6.101274 ACCTACTCCCTCTGTTCCTAAATA 57.899 41.667 0.00 0.00 0.00 1.40
2574 2752 4.961585 ACCTACTCCCTCTGTTCCTAAAT 58.038 43.478 0.00 0.00 0.00 1.40
2575 2753 4.415224 ACCTACTCCCTCTGTTCCTAAA 57.585 45.455 0.00 0.00 0.00 1.85
2576 2754 4.415224 AACCTACTCCCTCTGTTCCTAA 57.585 45.455 0.00 0.00 0.00 2.69
2577 2755 4.415224 AAACCTACTCCCTCTGTTCCTA 57.585 45.455 0.00 0.00 0.00 2.94
2578 2756 3.277416 AAACCTACTCCCTCTGTTCCT 57.723 47.619 0.00 0.00 0.00 3.36
2579 2757 5.243981 GTTAAAACCTACTCCCTCTGTTCC 58.756 45.833 0.00 0.00 0.00 3.62
2580 2758 5.243981 GGTTAAAACCTACTCCCTCTGTTC 58.756 45.833 4.58 0.00 45.75 3.18
2581 2759 5.238624 GGTTAAAACCTACTCCCTCTGTT 57.761 43.478 4.58 0.00 45.75 3.16
2582 2760 4.904895 GGTTAAAACCTACTCCCTCTGT 57.095 45.455 4.58 0.00 45.75 3.41
2671 2884 7.175641 CCTGAACACAATTTACCTGAGATCTTT 59.824 37.037 0.00 0.00 0.00 2.52
2679 2892 7.504924 TTTACTCCTGAACACAATTTACCTG 57.495 36.000 0.00 0.00 0.00 4.00
2733 2946 5.802956 TGTTTCAGGCACTTAAAAACTTTCG 59.197 36.000 0.00 0.00 33.04 3.46
3558 3771 8.854614 AAACCATCCAACTCTAGCAATATATC 57.145 34.615 0.00 0.00 0.00 1.63
3565 3778 8.271458 TCATAAATAAACCATCCAACTCTAGCA 58.729 33.333 0.00 0.00 0.00 3.49
3613 3826 4.157289 AGACAACAGCTGCATTATTTGGAG 59.843 41.667 15.27 0.00 45.96 3.86
3618 3831 7.395190 TCAATAAGACAACAGCTGCATTATT 57.605 32.000 15.27 13.51 0.00 1.40
3621 3834 5.184479 ACATCAATAAGACAACAGCTGCATT 59.816 36.000 15.27 0.00 0.00 3.56
3622 3835 4.703575 ACATCAATAAGACAACAGCTGCAT 59.296 37.500 15.27 0.00 0.00 3.96
3664 3881 8.993121 CGCTTCCTATGTAAATTGTCTGATATT 58.007 33.333 0.00 0.00 0.00 1.28
3665 3882 7.604164 CCGCTTCCTATGTAAATTGTCTGATAT 59.396 37.037 0.00 0.00 0.00 1.63
3666 3883 6.929049 CCGCTTCCTATGTAAATTGTCTGATA 59.071 38.462 0.00 0.00 0.00 2.15
3667 3884 5.760253 CCGCTTCCTATGTAAATTGTCTGAT 59.240 40.000 0.00 0.00 0.00 2.90
3674 3891 4.772886 AGTCCCGCTTCCTATGTAAATT 57.227 40.909 0.00 0.00 0.00 1.82
3681 3898 1.041437 GCAGTAGTCCCGCTTCCTAT 58.959 55.000 0.00 0.00 0.00 2.57
3688 3905 0.175760 TGAAGATGCAGTAGTCCCGC 59.824 55.000 0.00 0.00 0.00 6.13
3690 3907 3.133721 ACTCATGAAGATGCAGTAGTCCC 59.866 47.826 0.00 0.00 0.00 4.46
3717 3934 3.497103 TCACATCCTGCCAATGATAGG 57.503 47.619 0.00 0.00 0.00 2.57
3719 3936 8.481492 AATTTTATCACATCCTGCCAATGATA 57.519 30.769 0.00 0.00 32.42 2.15
3805 4022 5.163478 GGCTTTCAGGCATGTTTTATCTCAT 60.163 40.000 0.00 0.00 40.97 2.90
3829 4049 4.377124 GCATGATGCAACGATCTATGAGTG 60.377 45.833 13.36 0.00 44.26 3.51
3859 4079 7.367159 ACATGACAATTTAATGTTGCCAATG 57.633 32.000 0.00 5.80 32.57 2.82
3863 4083 8.700722 TGAATACATGACAATTTAATGTTGCC 57.299 30.769 0.00 0.00 36.08 4.52
3899 4230 8.964533 ATGGGTACTGTCAGATCTATTTCTAT 57.035 34.615 6.91 0.00 0.00 1.98
3901 4232 7.682787 AATGGGTACTGTCAGATCTATTTCT 57.317 36.000 6.91 0.00 0.00 2.52
3933 4264 4.503910 CTCGTCATCCACCTGTGATAAAA 58.496 43.478 0.00 0.00 0.00 1.52
4079 4410 1.303309 CCCAAATGGAGTCATCGAGC 58.697 55.000 0.00 0.00 37.39 5.03
4111 4442 4.610605 TCCTTAATGGACACGAAGTTGA 57.389 40.909 0.00 0.00 38.50 3.18
4174 4505 4.424626 GACACTTGAAGCTGATGATACGA 58.575 43.478 0.00 0.00 0.00 3.43
4176 4507 4.507710 TGGACACTTGAAGCTGATGATAC 58.492 43.478 0.00 0.00 0.00 2.24
4179 4510 3.490439 TTGGACACTTGAAGCTGATGA 57.510 42.857 0.00 0.00 0.00 2.92
4217 4552 0.033920 CCCCAAAAGGAAACTGCTGC 59.966 55.000 0.00 0.00 42.68 5.25
4249 4584 3.895232 AACTATGAGACGGCAGAATGT 57.105 42.857 0.00 0.00 39.31 2.71
4358 4699 4.491676 ACAATCACATGAAAAGATGCAGC 58.508 39.130 0.00 0.00 0.00 5.25
4434 4775 6.547880 ACACCAACACACACAAAATATAGGAA 59.452 34.615 0.00 0.00 0.00 3.36
4524 4884 7.816995 GGCATTACAAACATCATCCTTGTAAAA 59.183 33.333 9.83 0.00 44.39 1.52
4754 5148 0.882927 GACGCCAGCTTTGTACCACA 60.883 55.000 0.00 0.00 0.00 4.17
4861 5255 6.603237 TTACTATGATGAATTGTTCGCTGG 57.397 37.500 0.00 0.00 0.00 4.85
4895 5289 4.844267 ACGTGGAAGTTGAGAAATTTTCG 58.156 39.130 3.57 0.00 34.02 3.46
4943 5337 5.221382 GGAACATACACTCGAAGGCCTTATA 60.221 44.000 20.54 8.63 0.00 0.98
5153 5547 6.097554 TGCTAACAAGGAAGAAACCATTTTCA 59.902 34.615 0.31 0.00 43.29 2.69
5183 5577 2.851195 AGCTTTGGTGTCATTCTCGTT 58.149 42.857 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.