Multiple sequence alignment - TraesCS2B01G455600

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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 TraesCS2B01G455600 chr2B 100.000 2990 0 0 1 2990 650169737 650166748 0.000000e+00 5522.0
1 TraesCS2B01G455600 chr2B 86.170 188 14 5 1123 1310 650168378 650168203 3.040000e-45 193.0
2 TraesCS2B01G455600 chr2B 86.170 188 14 5 1360 1535 650168615 650168428 3.040000e-45 193.0
3 TraesCS2B01G455600 chr2B 85.484 186 24 1 2449 2634 549304553 549304371 1.090000e-44 191.0
4 TraesCS2B01G455600 chr2B 83.505 97 16 0 2538 2634 1778649 1778553 1.140000e-14 91.6
5 TraesCS2B01G455600 chr2D 92.600 1554 90 13 3 1535 544615053 544613504 0.000000e+00 2209.0
6 TraesCS2B01G455600 chr2D 89.507 934 56 18 1527 2457 544613554 544612660 0.000000e+00 1144.0
7 TraesCS2B01G455600 chr2D 83.103 290 32 6 1060 1345 544613745 544613469 6.400000e-62 248.0
8 TraesCS2B01G455600 chr2D 85.340 191 24 2 2444 2634 154109761 154109575 8.460000e-46 195.0
9 TraesCS2B01G455600 chr2D 89.796 147 14 1 2845 2990 544612463 544612317 1.420000e-43 187.0
10 TraesCS2B01G455600 chr2A 94.360 851 44 3 689 1535 686842974 686842124 0.000000e+00 1303.0
11 TraesCS2B01G455600 chr2A 92.173 741 48 5 1527 2266 686842174 686841443 0.000000e+00 1038.0
12 TraesCS2B01G455600 chr2A 84.648 469 47 13 321 770 686843399 686842937 7.610000e-121 444.0
13 TraesCS2B01G455600 chr2A 85.338 266 23 7 84 337 686843675 686843414 8.220000e-66 261.0
14 TraesCS2B01G455600 chr2A 82.712 295 34 8 1055 1345 686842370 686842089 2.300000e-61 246.0
15 TraesCS2B01G455600 chr2A 84.043 188 18 5 1360 1535 686842536 686842349 1.430000e-38 171.0
16 TraesCS2B01G455600 chr2A 93.204 103 7 0 2818 2920 686841336 686841234 5.160000e-33 152.0
17 TraesCS2B01G455600 chr5D 85.946 185 23 3 2452 2634 490607925 490607742 8.460000e-46 195.0
18 TraesCS2B01G455600 chr5D 86.286 175 20 4 2460 2633 216057415 216057244 1.420000e-43 187.0
19 TraesCS2B01G455600 chr7A 84.492 187 29 0 2448 2634 26885232 26885418 5.090000e-43 185.0
20 TraesCS2B01G455600 chr7A 83.422 187 30 1 2449 2634 13429025 13428839 3.960000e-39 172.0
21 TraesCS2B01G455600 chr3D 84.574 188 24 5 2449 2634 379458134 379458318 6.580000e-42 182.0
22 TraesCS2B01G455600 chr3D 76.757 185 43 0 2450 2634 313284265 313284449 1.470000e-18 104.0
23 TraesCS2B01G455600 chr4B 83.684 190 30 1 2450 2638 651976908 651977097 8.520000e-41 178.0
24 TraesCS2B01G455600 chr7B 83.422 187 29 2 2449 2634 151405849 151405664 3.960000e-39 172.0
25 TraesCS2B01G455600 chr7D 81.152 191 32 2 2444 2634 392764573 392764387 1.860000e-32 150.0
26 TraesCS2B01G455600 chr6A 75.709 247 44 8 2449 2681 60057161 60057405 3.150000e-20 110.0
27 TraesCS2B01G455600 chr3B 77.576 165 37 0 2470 2634 614203214 614203050 1.900000e-17 100.0
28 TraesCS2B01G455600 chr1D 92.157 51 4 0 211 261 392950920 392950970 4.130000e-09 73.1
29 TraesCS2B01G455600 chr1A 80.000 100 14 5 211 304 492270629 492270530 5.350000e-08 69.4
30 TraesCS2B01G455600 chr3A 93.023 43 3 0 2639 2681 24773814 24773772 2.490000e-06 63.9
31 TraesCS2B01G455600 chr5A 90.244 41 4 0 2641 2681 687055836 687055876 1.000000e-03 54.7
32 TraesCS2B01G455600 chr4A 90.244 41 4 0 2641 2681 704524785 704524745 1.000000e-03 54.7


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 TraesCS2B01G455600 chr2B 650166748 650169737 2989 True 1969.333333 5522 90.780000 1 2990 3 chr2B.!!$R3 2989
1 TraesCS2B01G455600 chr2D 544612317 544615053 2736 True 947.000000 2209 88.751500 3 2990 4 chr2D.!!$R2 2987
2 TraesCS2B01G455600 chr2A 686841234 686843675 2441 True 516.428571 1303 88.068286 84 2920 7 chr2A.!!$R1 2836

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
786 892 0.461961 AACCGATCTGAGCACTAGCC 59.538 55.0 0.0 0.0 43.56 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2676 2790 0.03213 CACTATGCCGCACCGATACT 59.968 55.0 0.0 0.0 0.0 2.12 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
28 29 5.927281 ACCTGGTCTTTGTATATGTACGT 57.073 39.130 0.00 0.00 33.36 3.57
29 30 6.290294 ACCTGGTCTTTGTATATGTACGTT 57.710 37.500 0.00 0.00 33.36 3.99
31 32 7.486647 ACCTGGTCTTTGTATATGTACGTTAG 58.513 38.462 0.00 0.00 33.36 2.34
32 33 7.123247 ACCTGGTCTTTGTATATGTACGTTAGT 59.877 37.037 0.00 0.00 33.36 2.24
41 42 8.044060 TGTATATGTACGTTAGTATGGCCTAC 57.956 38.462 3.32 4.18 35.01 3.18
115 116 5.491078 AGGAATGGGGAGATGTAAAGTTGTA 59.509 40.000 0.00 0.00 0.00 2.41
123 124 8.050930 GGGGAGATGTAAAGTTGTAAAGGATAA 58.949 37.037 0.00 0.00 0.00 1.75
185 186 5.964758 AGAGAGAGCACTTTAATGACTCAG 58.035 41.667 14.08 0.00 31.47 3.35
204 207 6.951971 ACTCAGAAGAAACAATGCTACCTAT 58.048 36.000 0.00 0.00 0.00 2.57
209 212 8.946085 CAGAAGAAACAATGCTACCTATACAAA 58.054 33.333 0.00 0.00 0.00 2.83
244 247 3.120627 GCTCGAGCTCATATGAGGC 57.879 57.895 29.88 20.92 42.29 4.70
266 269 5.279456 GGCCAGGTGAACAGTAAAAATGAAT 60.279 40.000 0.00 0.00 0.00 2.57
364 408 4.640771 TTCTACAAATGTCCCAAGCTCT 57.359 40.909 0.00 0.00 0.00 4.09
410 460 0.745845 CACCCCGAGCTCATTCAAGG 60.746 60.000 15.40 5.28 0.00 3.61
428 478 5.399991 TCAAGGTTGGGACTAGAAGAGTAA 58.600 41.667 0.00 0.00 39.06 2.24
430 480 6.154706 TCAAGGTTGGGACTAGAAGAGTAATC 59.845 42.308 0.00 0.00 39.06 1.75
431 481 5.844601 AGGTTGGGACTAGAAGAGTAATCT 58.155 41.667 0.00 0.00 39.06 2.40
433 483 5.657302 GGTTGGGACTAGAAGAGTAATCTCA 59.343 44.000 0.00 0.00 42.66 3.27
437 487 5.894964 GGGACTAGAAGAGTAATCTCACCTT 59.105 44.000 0.00 0.00 42.66 3.50
461 511 9.409312 CTTCACAAACACTTATGCATGAAATAA 57.591 29.630 10.16 0.00 0.00 1.40
515 565 5.857822 CTTAGTTACAAAAGGCTAAGCGT 57.142 39.130 0.00 0.00 35.59 5.07
518 568 3.250040 AGTTACAAAAGGCTAAGCGTGTG 59.750 43.478 0.00 0.00 0.00 3.82
523 573 4.390909 ACAAAAGGCTAAGCGTGTGTATAC 59.609 41.667 0.00 0.00 0.00 1.47
525 575 4.402056 AAGGCTAAGCGTGTGTATACAT 57.598 40.909 9.18 0.00 39.39 2.29
526 576 4.402056 AGGCTAAGCGTGTGTATACATT 57.598 40.909 9.18 1.36 39.39 2.71
527 577 5.524971 AGGCTAAGCGTGTGTATACATTA 57.475 39.130 9.18 2.52 39.39 1.90
531 582 7.011109 AGGCTAAGCGTGTGTATACATTAAAAG 59.989 37.037 9.18 3.09 39.39 2.27
599 650 0.534873 TCAGCTAAGCATGTACCGCA 59.465 50.000 7.09 0.00 0.00 5.69
643 703 4.000325 ACACGTGCTGCACTTATCATTTA 59.000 39.130 28.04 0.00 31.34 1.40
786 892 0.461961 AACCGATCTGAGCACTAGCC 59.538 55.000 0.00 0.00 43.56 3.93
822 928 6.073602 CCAATTCAAGCAAGCTTTTAAACTCC 60.074 38.462 4.24 0.00 33.42 3.85
1047 1157 4.816984 AGATCCCCGTCGTCGCCT 62.817 66.667 0.00 0.00 35.54 5.52
1316 1426 0.592148 GTGGCGTCTCCGGAGTATAG 59.408 60.000 30.17 19.57 37.80 1.31
1341 1451 4.008933 GCTGACCACTGGAGGCGT 62.009 66.667 0.71 0.00 0.00 5.68
1414 1524 1.423056 GAGTACGTCCCGTCGACTG 59.577 63.158 14.70 7.04 41.54 3.51
1488 1598 4.838486 CGGCAGAGCTCGTCGTCC 62.838 72.222 19.55 11.72 0.00 4.79
1554 1664 2.450476 GGTTACTCCCCTTCTACGTCA 58.550 52.381 0.00 0.00 0.00 4.35
1555 1665 2.165234 GGTTACTCCCCTTCTACGTCAC 59.835 54.545 0.00 0.00 0.00 3.67
1556 1666 3.087781 GTTACTCCCCTTCTACGTCACT 58.912 50.000 0.00 0.00 0.00 3.41
1557 1667 1.546961 ACTCCCCTTCTACGTCACTG 58.453 55.000 0.00 0.00 0.00 3.66
1558 1668 1.203025 ACTCCCCTTCTACGTCACTGT 60.203 52.381 0.00 0.00 0.00 3.55
1559 1669 1.202582 CTCCCCTTCTACGTCACTGTG 59.797 57.143 0.17 0.17 0.00 3.66
1560 1670 0.389948 CCCCTTCTACGTCACTGTGC 60.390 60.000 2.12 0.00 0.00 4.57
1561 1671 0.389948 CCCTTCTACGTCACTGTGCC 60.390 60.000 2.12 0.00 0.00 5.01
1562 1672 0.732880 CCTTCTACGTCACTGTGCCG 60.733 60.000 9.90 9.90 0.00 5.69
1563 1673 0.240145 CTTCTACGTCACTGTGCCGA 59.760 55.000 18.63 1.03 0.00 5.54
1564 1674 0.240145 TTCTACGTCACTGTGCCGAG 59.760 55.000 18.63 10.62 0.00 4.63
1565 1675 0.887836 TCTACGTCACTGTGCCGAGT 60.888 55.000 18.63 9.79 0.00 4.18
1566 1676 0.729478 CTACGTCACTGTGCCGAGTG 60.729 60.000 18.63 5.97 44.14 3.51
1567 1677 2.137425 TACGTCACTGTGCCGAGTGG 62.137 60.000 18.63 0.00 43.16 4.00
1591 1701 0.032952 GCCGGAGTATATGCCGTTGA 59.967 55.000 5.05 0.00 45.85 3.18
1652 1762 3.299977 CACCCCGTCGACACCTCA 61.300 66.667 17.16 0.00 0.00 3.86
1668 1778 1.603236 CTCAGGAGCAGCGACCTTCT 61.603 60.000 10.78 0.00 33.91 2.85
1693 1803 4.748679 ACTACGCCGCGTCGACAC 62.749 66.667 23.94 4.66 41.54 3.67
1731 1841 1.828081 GTCACCGGATTACTCCCCC 59.172 63.158 9.46 0.00 38.45 5.40
1789 1899 3.374402 CGACTGCTCCGTGGAGGT 61.374 66.667 17.29 7.69 42.19 3.85
1948 2058 1.546476 GCTATCATCCGTACCAGAGGG 59.454 57.143 0.00 0.00 41.29 4.30
2047 2158 4.022242 CGGATGTTAGTCGGATTCATAGGT 60.022 45.833 0.00 0.00 0.00 3.08
2061 2172 5.435686 TTCATAGGTACCTTGCAGATTGT 57.564 39.130 22.11 0.00 0.00 2.71
2064 2175 6.346096 TCATAGGTACCTTGCAGATTGTAAC 58.654 40.000 22.11 0.00 0.00 2.50
2093 2207 7.520798 AGATATTGGATTCCTCATGCAAACTA 58.479 34.615 3.95 0.00 45.46 2.24
2249 2363 7.523293 TGACAGAATTTAATGTGGACACAAT 57.477 32.000 9.42 3.65 45.41 2.71
2327 2441 8.754991 TTTTTAAGATGGACCTAACAAACTGA 57.245 30.769 0.00 0.00 0.00 3.41
2328 2442 8.754991 TTTTAAGATGGACCTAACAAACTGAA 57.245 30.769 0.00 0.00 0.00 3.02
2329 2443 8.754991 TTTAAGATGGACCTAACAAACTGAAA 57.245 30.769 0.00 0.00 0.00 2.69
2330 2444 6.884280 AAGATGGACCTAACAAACTGAAAG 57.116 37.500 0.00 0.00 42.29 2.62
2331 2445 5.316987 AGATGGACCTAACAAACTGAAAGG 58.683 41.667 0.00 0.00 39.30 3.11
2332 2446 4.781775 TGGACCTAACAAACTGAAAGGA 57.218 40.909 0.00 0.00 39.30 3.36
2367 2481 0.317269 GGATGCGATGTTTGATGGCG 60.317 55.000 0.00 0.00 0.00 5.69
2370 2484 0.167908 TGCGATGTTTGATGGCGTTC 59.832 50.000 0.00 0.00 0.00 3.95
2391 2505 2.024176 TTGCCTGCTTATCGGTTCTC 57.976 50.000 0.00 0.00 0.00 2.87
2408 2522 5.500931 CGGTTCTCGATCTTAGCAAAATGTC 60.501 44.000 0.00 0.00 42.43 3.06
2450 2564 2.381961 AGTGGGGGAGCCAGAAAAATTA 59.618 45.455 0.00 0.00 0.00 1.40
2453 2567 4.341235 GTGGGGGAGCCAGAAAAATTATAC 59.659 45.833 0.00 0.00 0.00 1.47
2454 2568 4.231890 TGGGGGAGCCAGAAAAATTATACT 59.768 41.667 0.00 0.00 0.00 2.12
2455 2569 4.827835 GGGGGAGCCAGAAAAATTATACTC 59.172 45.833 0.00 0.00 0.00 2.59
2456 2570 4.515567 GGGGAGCCAGAAAAATTATACTCG 59.484 45.833 0.00 0.00 0.00 4.18
2458 2572 4.816925 GGAGCCAGAAAAATTATACTCGCT 59.183 41.667 0.00 0.00 30.49 4.93
2459 2573 5.297029 GGAGCCAGAAAAATTATACTCGCTT 59.703 40.000 0.00 0.00 28.29 4.68
2460 2574 6.364945 AGCCAGAAAAATTATACTCGCTTC 57.635 37.500 0.00 0.00 0.00 3.86
2461 2575 5.880332 AGCCAGAAAAATTATACTCGCTTCA 59.120 36.000 0.00 0.00 0.00 3.02
2462 2576 6.543831 AGCCAGAAAAATTATACTCGCTTCAT 59.456 34.615 0.00 0.00 0.00 2.57
2463 2577 7.067494 AGCCAGAAAAATTATACTCGCTTCATT 59.933 33.333 0.00 0.00 0.00 2.57
2465 2579 9.226345 CCAGAAAAATTATACTCGCTTCATTTC 57.774 33.333 0.00 0.00 0.00 2.17
2466 2580 9.773328 CAGAAAAATTATACTCGCTTCATTTCA 57.227 29.630 0.00 0.00 0.00 2.69
2471 2585 9.888878 AAATTATACTCGCTTCATTTCATGATG 57.111 29.630 0.00 0.00 39.39 3.07
2472 2586 8.613060 ATTATACTCGCTTCATTTCATGATGT 57.387 30.769 0.00 0.00 39.39 3.06
2473 2587 9.710900 ATTATACTCGCTTCATTTCATGATGTA 57.289 29.630 0.00 0.00 39.39 2.29
2474 2588 5.980698 ACTCGCTTCATTTCATGATGTAG 57.019 39.130 0.00 0.00 39.39 2.74
2475 2589 5.423015 ACTCGCTTCATTTCATGATGTAGT 58.577 37.500 0.00 3.97 39.39 2.73
2476 2590 5.292834 ACTCGCTTCATTTCATGATGTAGTG 59.707 40.000 9.15 9.15 39.39 2.74
2477 2591 4.034394 TCGCTTCATTTCATGATGTAGTGC 59.966 41.667 10.14 5.35 39.39 4.40
2478 2592 4.201841 CGCTTCATTTCATGATGTAGTGCA 60.202 41.667 0.00 0.00 39.39 4.57
2479 2593 5.505159 CGCTTCATTTCATGATGTAGTGCAT 60.505 40.000 0.00 0.00 39.39 3.96
2492 2606 3.964718 TGCATCAGCGCTTTTCGA 58.035 50.000 7.50 1.25 46.23 3.71
2493 2607 1.789751 TGCATCAGCGCTTTTCGAG 59.210 52.632 7.50 0.00 46.23 4.04
2494 2608 0.670239 TGCATCAGCGCTTTTCGAGA 60.670 50.000 7.50 0.00 46.23 4.04
2495 2609 0.654683 GCATCAGCGCTTTTCGAGAT 59.345 50.000 7.50 2.95 41.67 2.75
2496 2610 1.063174 GCATCAGCGCTTTTCGAGATT 59.937 47.619 7.50 0.00 41.67 2.40
2497 2611 2.476854 GCATCAGCGCTTTTCGAGATTT 60.477 45.455 7.50 0.00 41.67 2.17
2498 2612 3.242413 GCATCAGCGCTTTTCGAGATTTA 60.242 43.478 7.50 0.00 41.67 1.40
2499 2613 4.727734 GCATCAGCGCTTTTCGAGATTTAA 60.728 41.667 7.50 0.00 41.67 1.52
2500 2614 5.323900 CATCAGCGCTTTTCGAGATTTAAA 58.676 37.500 7.50 0.00 41.67 1.52
2501 2615 5.545658 TCAGCGCTTTTCGAGATTTAAAT 57.454 34.783 7.50 0.00 41.67 1.40
2502 2616 5.938322 TCAGCGCTTTTCGAGATTTAAATT 58.062 33.333 7.50 0.00 41.67 1.82
2503 2617 6.378582 TCAGCGCTTTTCGAGATTTAAATTT 58.621 32.000 7.50 0.00 41.67 1.82
2504 2618 6.305399 TCAGCGCTTTTCGAGATTTAAATTTG 59.695 34.615 7.50 0.00 41.67 2.32
2505 2619 6.305399 CAGCGCTTTTCGAGATTTAAATTTGA 59.695 34.615 7.50 0.00 41.67 2.69
2506 2620 6.305638 AGCGCTTTTCGAGATTTAAATTTGAC 59.694 34.615 2.64 0.00 41.67 3.18
2507 2621 6.452480 GCGCTTTTCGAGATTTAAATTTGACC 60.452 38.462 0.00 0.00 41.67 4.02
2508 2622 6.580791 CGCTTTTCGAGATTTAAATTTGACCA 59.419 34.615 1.43 0.00 41.67 4.02
2509 2623 7.273381 CGCTTTTCGAGATTTAAATTTGACCAT 59.727 33.333 1.43 0.00 41.67 3.55
2510 2624 9.567848 GCTTTTCGAGATTTAAATTTGACCATA 57.432 29.630 1.43 0.00 0.00 2.74
2524 2638 9.810545 AAATTTGACCATATATTTAACCAACGG 57.189 29.630 0.00 0.00 0.00 4.44
2525 2639 6.945938 TTGACCATATATTTAACCAACGGG 57.054 37.500 0.00 0.00 41.29 5.28
2526 2640 6.249911 TGACCATATATTTAACCAACGGGA 57.750 37.500 0.00 0.00 38.05 5.14
2527 2641 6.056884 TGACCATATATTTAACCAACGGGAC 58.943 40.000 0.00 0.00 38.05 4.46
2528 2642 5.379187 ACCATATATTTAACCAACGGGACC 58.621 41.667 0.00 0.00 38.05 4.46
2529 2643 4.453136 CCATATATTTAACCAACGGGACCG 59.547 45.833 9.56 9.56 46.03 4.79
2530 2644 3.910568 ATATTTAACCAACGGGACCGA 57.089 42.857 18.80 0.00 42.83 4.69
2531 2645 1.812235 ATTTAACCAACGGGACCGAC 58.188 50.000 18.80 0.00 42.83 4.79
2532 2646 0.758123 TTTAACCAACGGGACCGACT 59.242 50.000 18.80 0.78 42.83 4.18
2533 2647 0.033781 TTAACCAACGGGACCGACTG 59.966 55.000 18.80 13.26 42.83 3.51
2534 2648 2.438951 TAACCAACGGGACCGACTGC 62.439 60.000 18.80 0.00 42.83 4.40
2560 2674 6.687081 CGGGAGCAAAAATTATACCACTAA 57.313 37.500 0.00 0.00 0.00 2.24
2561 2675 7.090953 CGGGAGCAAAAATTATACCACTAAA 57.909 36.000 0.00 0.00 0.00 1.85
2562 2676 7.712797 CGGGAGCAAAAATTATACCACTAAAT 58.287 34.615 0.00 0.00 0.00 1.40
2563 2677 8.194769 CGGGAGCAAAAATTATACCACTAAATT 58.805 33.333 0.00 0.00 0.00 1.82
2564 2678 9.884636 GGGAGCAAAAATTATACCACTAAATTT 57.115 29.630 0.00 0.00 35.01 1.82
2579 2693 9.153721 ACCACTAAATTTGTATCGAAAATACGA 57.846 29.630 0.00 0.00 46.04 3.43
2580 2694 9.976255 CCACTAAATTTGTATCGAAAATACGAA 57.024 29.630 0.00 0.00 45.16 3.85
2587 2701 9.702726 ATTTGTATCGAAAATACGAAATCAGTG 57.297 29.630 0.00 0.00 45.16 3.66
2588 2702 6.701937 TGTATCGAAAATACGAAATCAGTGC 58.298 36.000 0.00 0.00 45.16 4.40
2589 2703 6.533723 TGTATCGAAAATACGAAATCAGTGCT 59.466 34.615 0.00 0.00 45.16 4.40
2590 2704 7.703197 TGTATCGAAAATACGAAATCAGTGCTA 59.297 33.333 0.00 0.00 45.16 3.49
2591 2705 7.715265 ATCGAAAATACGAAATCAGTGCTAT 57.285 32.000 0.00 0.00 45.16 2.97
2592 2706 8.812147 ATCGAAAATACGAAATCAGTGCTATA 57.188 30.769 0.00 0.00 45.16 1.31
2593 2707 8.637281 TCGAAAATACGAAATCAGTGCTATAA 57.363 30.769 0.00 0.00 39.34 0.98
2594 2708 9.256477 TCGAAAATACGAAATCAGTGCTATAAT 57.744 29.630 0.00 0.00 39.34 1.28
2595 2709 9.864034 CGAAAATACGAAATCAGTGCTATAATT 57.136 29.630 0.00 0.00 35.09 1.40
2600 2714 7.849804 ACGAAATCAGTGCTATAATTTCTGT 57.150 32.000 10.69 8.27 36.45 3.41
2601 2715 8.268850 ACGAAATCAGTGCTATAATTTCTGTT 57.731 30.769 10.69 0.00 36.45 3.16
2602 2716 8.177663 ACGAAATCAGTGCTATAATTTCTGTTG 58.822 33.333 10.69 1.49 36.45 3.33
2603 2717 7.164826 CGAAATCAGTGCTATAATTTCTGTTGC 59.835 37.037 10.69 0.00 36.45 4.17
2604 2718 5.818136 TCAGTGCTATAATTTCTGTTGCC 57.182 39.130 0.00 0.00 0.00 4.52
2605 2719 4.332543 TCAGTGCTATAATTTCTGTTGCCG 59.667 41.667 0.00 0.00 0.00 5.69
2606 2720 4.094887 CAGTGCTATAATTTCTGTTGCCGT 59.905 41.667 0.00 0.00 0.00 5.68
2607 2721 4.332819 AGTGCTATAATTTCTGTTGCCGTC 59.667 41.667 0.00 0.00 0.00 4.79
2608 2722 3.308595 TGCTATAATTTCTGTTGCCGTCG 59.691 43.478 0.00 0.00 0.00 5.12
2609 2723 2.825086 ATAATTTCTGTTGCCGTCGC 57.175 45.000 0.00 0.00 0.00 5.19
2610 2724 1.514003 TAATTTCTGTTGCCGTCGCA 58.486 45.000 0.00 0.00 45.49 5.10
2621 2735 4.086178 CGTCGCAGTCGGTCTCGT 62.086 66.667 0.00 0.00 35.06 4.18
2622 2736 2.254651 GTCGCAGTCGGTCTCGTT 59.745 61.111 0.00 0.00 37.69 3.85
2623 2737 2.081212 GTCGCAGTCGGTCTCGTTG 61.081 63.158 0.00 0.00 37.69 4.10
2624 2738 2.805353 CGCAGTCGGTCTCGTTGG 60.805 66.667 0.00 0.00 37.69 3.77
2625 2739 2.338984 GCAGTCGGTCTCGTTGGT 59.661 61.111 0.00 0.00 37.69 3.67
2626 2740 1.300697 GCAGTCGGTCTCGTTGGTT 60.301 57.895 0.00 0.00 37.69 3.67
2627 2741 0.038892 GCAGTCGGTCTCGTTGGTTA 60.039 55.000 0.00 0.00 37.69 2.85
2628 2742 1.603678 GCAGTCGGTCTCGTTGGTTAA 60.604 52.381 0.00 0.00 37.69 2.01
2629 2743 2.746269 CAGTCGGTCTCGTTGGTTAAA 58.254 47.619 0.00 0.00 37.69 1.52
2630 2744 3.323243 CAGTCGGTCTCGTTGGTTAAAT 58.677 45.455 0.00 0.00 37.69 1.40
2631 2745 3.744426 CAGTCGGTCTCGTTGGTTAAATT 59.256 43.478 0.00 0.00 37.69 1.82
2632 2746 4.212636 CAGTCGGTCTCGTTGGTTAAATTT 59.787 41.667 0.00 0.00 37.69 1.82
2633 2747 5.406175 CAGTCGGTCTCGTTGGTTAAATTTA 59.594 40.000 0.00 0.00 37.69 1.40
2634 2748 5.636543 AGTCGGTCTCGTTGGTTAAATTTAG 59.363 40.000 0.00 0.00 37.69 1.85
2635 2749 5.634859 GTCGGTCTCGTTGGTTAAATTTAGA 59.365 40.000 0.00 0.00 37.69 2.10
2636 2750 6.312180 GTCGGTCTCGTTGGTTAAATTTAGAT 59.688 38.462 0.00 0.00 37.69 1.98
2637 2751 6.532657 TCGGTCTCGTTGGTTAAATTTAGATC 59.467 38.462 0.00 0.00 37.69 2.75
2638 2752 6.534079 CGGTCTCGTTGGTTAAATTTAGATCT 59.466 38.462 0.00 0.00 0.00 2.75
2639 2753 7.254017 CGGTCTCGTTGGTTAAATTTAGATCTC 60.254 40.741 0.00 0.00 0.00 2.75
2640 2754 7.548075 GGTCTCGTTGGTTAAATTTAGATCTCA 59.452 37.037 0.00 0.00 0.00 3.27
2641 2755 8.932791 GTCTCGTTGGTTAAATTTAGATCTCAA 58.067 33.333 0.00 0.00 0.00 3.02
2642 2756 9.496873 TCTCGTTGGTTAAATTTAGATCTCAAA 57.503 29.630 0.00 0.00 0.00 2.69
2674 2788 5.375417 TGCACTACATTGTGAAATGAAGG 57.625 39.130 5.49 0.00 40.12 3.46
2675 2789 4.218200 TGCACTACATTGTGAAATGAAGGG 59.782 41.667 5.49 0.00 40.12 3.95
2676 2790 4.458989 GCACTACATTGTGAAATGAAGGGA 59.541 41.667 5.49 0.00 40.12 4.20
2677 2791 5.392380 GCACTACATTGTGAAATGAAGGGAG 60.392 44.000 5.49 0.00 40.12 4.30
2678 2792 5.707298 CACTACATTGTGAAATGAAGGGAGT 59.293 40.000 5.49 0.00 40.12 3.85
2679 2793 6.878923 CACTACATTGTGAAATGAAGGGAGTA 59.121 38.462 5.49 0.00 40.12 2.59
2680 2794 7.554118 CACTACATTGTGAAATGAAGGGAGTAT 59.446 37.037 5.49 0.00 40.12 2.12
2681 2795 7.770897 ACTACATTGTGAAATGAAGGGAGTATC 59.229 37.037 5.49 0.00 34.39 2.24
2682 2796 5.586243 ACATTGTGAAATGAAGGGAGTATCG 59.414 40.000 5.49 0.00 32.82 2.92
2683 2797 4.137116 TGTGAAATGAAGGGAGTATCGG 57.863 45.455 0.00 0.00 34.37 4.18
2684 2798 3.517901 TGTGAAATGAAGGGAGTATCGGT 59.482 43.478 0.00 0.00 34.37 4.69
2685 2799 3.871594 GTGAAATGAAGGGAGTATCGGTG 59.128 47.826 0.00 0.00 34.37 4.94
2686 2800 2.622064 AATGAAGGGAGTATCGGTGC 57.378 50.000 0.00 0.00 34.37 5.01
2687 2801 0.389391 ATGAAGGGAGTATCGGTGCG 59.611 55.000 0.00 0.00 34.37 5.34
2688 2802 1.067582 GAAGGGAGTATCGGTGCGG 59.932 63.158 0.00 0.00 34.37 5.69
2689 2803 2.973180 GAAGGGAGTATCGGTGCGGC 62.973 65.000 0.00 0.00 34.37 6.53
2711 2825 6.404293 CGGCATAGTGTTATTAAGCAAGGTTT 60.404 38.462 0.00 0.00 0.00 3.27
2712 2826 6.751888 GGCATAGTGTTATTAAGCAAGGTTTG 59.248 38.462 0.00 0.00 0.00 2.93
2723 2837 1.839424 CAAGGTTTGGGAGGGCTAAG 58.161 55.000 0.00 0.00 0.00 2.18
2724 2838 1.075536 CAAGGTTTGGGAGGGCTAAGT 59.924 52.381 0.00 0.00 0.00 2.24
2726 2840 0.392595 GGTTTGGGAGGGCTAAGTCG 60.393 60.000 0.00 0.00 0.00 4.18
2728 2842 1.061546 TTTGGGAGGGCTAAGTCGTT 58.938 50.000 0.00 0.00 0.00 3.85
2787 2905 3.244976 GAATGAAACTGAATGTTGGCCG 58.755 45.455 0.00 0.00 39.13 6.13
2791 2909 2.755469 CTGAATGTTGGCCGGGGG 60.755 66.667 2.18 0.00 0.00 5.40
2826 2944 0.543277 CTGCCTCTGCCAATGTAGGA 59.457 55.000 0.00 0.00 36.33 2.94
2828 2946 1.565759 TGCCTCTGCCAATGTAGGAAT 59.434 47.619 0.00 0.00 36.33 3.01
2906 3053 2.435372 TTGAGTTGTTTGGCTCCACT 57.565 45.000 0.00 0.00 0.00 4.00
2912 3059 2.890945 GTTGTTTGGCTCCACTTGGTAT 59.109 45.455 0.00 0.00 36.34 2.73
2940 3087 5.471556 TTGATGTCGGTCAACCTAACTAA 57.528 39.130 0.00 0.00 33.41 2.24
2942 3089 5.475719 TGATGTCGGTCAACCTAACTAAAG 58.524 41.667 0.00 0.00 0.00 1.85
2943 3090 5.244402 TGATGTCGGTCAACCTAACTAAAGA 59.756 40.000 0.00 0.00 0.00 2.52
2944 3091 5.733620 TGTCGGTCAACCTAACTAAAGAT 57.266 39.130 0.00 0.00 0.00 2.40
2945 3092 6.105397 TGTCGGTCAACCTAACTAAAGATT 57.895 37.500 0.00 0.00 0.00 2.40
2946 3093 6.161381 TGTCGGTCAACCTAACTAAAGATTC 58.839 40.000 0.00 0.00 0.00 2.52
2947 3094 6.161381 GTCGGTCAACCTAACTAAAGATTCA 58.839 40.000 0.00 0.00 0.00 2.57
2948 3095 6.817140 GTCGGTCAACCTAACTAAAGATTCAT 59.183 38.462 0.00 0.00 0.00 2.57
2983 3131 8.234546 CGTTGGCAGAATACTTGTAGTTTATTT 58.765 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.173339 ACATATACAAAGACCAGGTTGTCTG 58.827 40.000 0.00 0.08 44.68 3.51
11 12 8.909671 GCCATACTAACGTACATATACAAAGAC 58.090 37.037 0.00 0.00 0.00 3.01
21 22 3.304928 GCGTAGGCCATACTAACGTACAT 60.305 47.826 5.01 0.00 31.68 2.29
28 29 2.885266 CTCTGAGCGTAGGCCATACTAA 59.115 50.000 5.01 0.00 41.24 2.24
29 30 2.505405 CTCTGAGCGTAGGCCATACTA 58.495 52.381 5.01 0.00 41.24 1.82
31 32 0.315568 CCTCTGAGCGTAGGCCATAC 59.684 60.000 5.01 3.78 41.24 2.39
32 33 0.185175 TCCTCTGAGCGTAGGCCATA 59.815 55.000 5.01 0.00 41.24 2.74
41 42 1.333636 ACTCCCCATTCCTCTGAGCG 61.334 60.000 0.00 0.00 0.00 5.03
115 116 9.927668 CAATTTTTCACCTATGTGTTATCCTTT 57.072 29.630 0.00 0.00 43.26 3.11
123 124 7.106439 TCACAACAATTTTTCACCTATGTGT 57.894 32.000 0.00 0.00 43.26 3.72
185 186 9.162764 TCTTTGTATAGGTAGCATTGTTTCTTC 57.837 33.333 0.00 0.00 0.00 2.87
204 207 7.116376 CGAGCTAAGAAACTTCATGTCTTTGTA 59.884 37.037 1.34 0.00 33.70 2.41
209 212 5.392767 TCGAGCTAAGAAACTTCATGTCT 57.607 39.130 0.00 0.00 0.00 3.41
244 247 8.792633 TCTTATTCATTTTTACTGTTCACCTGG 58.207 33.333 0.00 0.00 0.00 4.45
385 429 0.620556 ATGAGCTCGGGGTGAACAAT 59.379 50.000 9.64 0.00 0.00 2.71
386 430 0.400213 AATGAGCTCGGGGTGAACAA 59.600 50.000 9.64 0.00 0.00 2.83
410 460 6.406065 GGTGAGATTACTCTTCTAGTCCCAAC 60.406 46.154 0.00 0.00 42.99 3.77
428 478 5.182001 GCATAAGTGTTTGTGAAGGTGAGAT 59.818 40.000 0.00 0.00 0.00 2.75
430 480 4.275689 TGCATAAGTGTTTGTGAAGGTGAG 59.724 41.667 0.00 0.00 0.00 3.51
431 481 4.203226 TGCATAAGTGTTTGTGAAGGTGA 58.797 39.130 0.00 0.00 0.00 4.02
433 483 4.826733 TCATGCATAAGTGTTTGTGAAGGT 59.173 37.500 0.00 0.00 0.00 3.50
437 487 9.926158 AATTATTTCATGCATAAGTGTTTGTGA 57.074 25.926 0.00 0.00 0.00 3.58
526 576 9.671279 GCTTAGTACCAACTTATAACCCTTTTA 57.329 33.333 0.00 0.00 37.15 1.52
527 577 7.613022 GGCTTAGTACCAACTTATAACCCTTTT 59.387 37.037 0.00 0.00 37.15 2.27
531 582 5.131642 AGGGCTTAGTACCAACTTATAACCC 59.868 44.000 0.00 0.00 37.15 4.11
578 629 1.858091 CGGTACATGCTTAGCTGAGG 58.142 55.000 7.72 0.00 0.00 3.86
583 634 4.545823 TTTTATGCGGTACATGCTTAGC 57.454 40.909 10.23 0.00 40.06 3.09
613 665 4.969196 CAGCACGTGTGGCCGTCT 62.969 66.667 18.38 0.07 39.45 4.18
619 671 0.443869 GATAAGTGCAGCACGTGTGG 59.556 55.000 22.63 10.72 39.64 4.17
651 712 6.533730 CCTGTATAAATCATGAGGGCACTTA 58.466 40.000 0.09 0.00 0.00 2.24
786 892 0.597568 TTGAATTGGCTTCGGCTGTG 59.402 50.000 0.00 0.00 41.44 3.66
913 1019 2.279918 GTTCCGTGTGAGCGTGGT 60.280 61.111 0.00 0.00 0.00 4.16
1341 1451 1.447140 GTAATCTGGTGACGCCGCA 60.447 57.895 0.00 0.00 41.21 5.69
1356 1466 4.465512 GAGGTCGACGGCGCGTAA 62.466 66.667 5.31 0.00 41.37 3.18
1438 1548 4.579384 CCGGGTGTGCTGGTTGGT 62.579 66.667 0.00 0.00 0.00 3.67
1442 1552 3.767630 GACAACCGGGTGTGCTGGT 62.768 63.158 34.08 2.89 37.68 4.00
1488 1598 1.969208 GTAGAAGGGGAGTAATCCGGG 59.031 57.143 0.00 0.00 0.00 5.73
1534 1644 2.165234 GTGACGTAGAAGGGGAGTAACC 59.835 54.545 0.00 0.00 38.08 2.85
1535 1645 3.087781 AGTGACGTAGAAGGGGAGTAAC 58.912 50.000 0.00 0.00 0.00 2.50
1536 1646 3.087031 CAGTGACGTAGAAGGGGAGTAA 58.913 50.000 0.00 0.00 0.00 2.24
1537 1647 2.040813 ACAGTGACGTAGAAGGGGAGTA 59.959 50.000 0.00 0.00 0.00 2.59
1538 1648 1.203025 ACAGTGACGTAGAAGGGGAGT 60.203 52.381 0.00 0.00 0.00 3.85
1539 1649 1.202582 CACAGTGACGTAGAAGGGGAG 59.797 57.143 0.00 0.00 0.00 4.30
1540 1650 1.254026 CACAGTGACGTAGAAGGGGA 58.746 55.000 0.00 0.00 0.00 4.81
1541 1651 0.389948 GCACAGTGACGTAGAAGGGG 60.390 60.000 4.15 0.00 0.00 4.79
1542 1652 0.389948 GGCACAGTGACGTAGAAGGG 60.390 60.000 4.15 0.00 0.00 3.95
1543 1653 0.732880 CGGCACAGTGACGTAGAAGG 60.733 60.000 21.48 0.00 45.41 3.46
1544 1654 2.725644 CGGCACAGTGACGTAGAAG 58.274 57.895 21.48 0.00 45.41 2.85
1545 1655 4.957266 CGGCACAGTGACGTAGAA 57.043 55.556 21.48 0.00 45.41 2.10
1569 1679 4.573162 GGCATATACTCCGGCGAC 57.427 61.111 9.30 0.00 0.00 5.19
1591 1701 4.008933 GCGCCTCCAGTGGTCAGT 62.009 66.667 9.54 0.00 0.00 3.41
1652 1762 1.594310 GAAGAAGGTCGCTGCTCCT 59.406 57.895 7.30 7.30 35.34 3.69
2047 2158 4.530553 TCTCCTGTTACAATCTGCAAGGTA 59.469 41.667 0.00 0.00 0.00 3.08
2061 2172 7.683578 CATGAGGAATCCAATATCTCCTGTTA 58.316 38.462 0.61 0.00 38.45 2.41
2064 2175 4.942483 GCATGAGGAATCCAATATCTCCTG 59.058 45.833 0.61 0.00 38.45 3.86
2126 2240 2.287009 CGGCAAACAGGAAAGAAGTGAC 60.287 50.000 0.00 0.00 0.00 3.67
2313 2427 4.072839 CCCTCCTTTCAGTTTGTTAGGTC 58.927 47.826 0.00 0.00 0.00 3.85
2315 2429 4.202472 ACTCCCTCCTTTCAGTTTGTTAGG 60.202 45.833 0.00 0.00 0.00 2.69
2316 2430 4.974399 ACTCCCTCCTTTCAGTTTGTTAG 58.026 43.478 0.00 0.00 0.00 2.34
2319 2433 4.019231 GGATACTCCCTCCTTTCAGTTTGT 60.019 45.833 0.00 0.00 0.00 2.83
2320 2434 4.019321 TGGATACTCCCTCCTTTCAGTTTG 60.019 45.833 0.00 0.00 35.03 2.93
2322 2436 3.803340 TGGATACTCCCTCCTTTCAGTT 58.197 45.455 0.00 0.00 35.03 3.16
2324 2438 5.379706 AATTGGATACTCCCTCCTTTCAG 57.620 43.478 0.00 0.00 35.03 3.02
2325 2439 5.509498 CAAATTGGATACTCCCTCCTTTCA 58.491 41.667 0.00 0.00 35.03 2.69
2326 2440 4.889995 CCAAATTGGATACTCCCTCCTTTC 59.110 45.833 6.04 0.00 40.96 2.62
2327 2441 4.544152 TCCAAATTGGATACTCCCTCCTTT 59.456 41.667 11.23 0.00 42.67 3.11
2328 2442 4.119155 TCCAAATTGGATACTCCCTCCTT 58.881 43.478 11.23 0.00 42.67 3.36
2329 2443 3.747852 TCCAAATTGGATACTCCCTCCT 58.252 45.455 11.23 0.00 42.67 3.69
2367 2481 2.084546 ACCGATAAGCAGGCAAAGAAC 58.915 47.619 0.00 0.00 0.00 3.01
2370 2484 2.352960 GAGAACCGATAAGCAGGCAAAG 59.647 50.000 0.00 0.00 0.00 2.77
2391 2505 2.286418 GGGCGACATTTTGCTAAGATCG 60.286 50.000 0.00 6.28 31.91 3.69
2421 2535 2.980177 GCTCCCCCACTAACCACCC 61.980 68.421 0.00 0.00 0.00 4.61
2469 2583 1.742761 AAAGCGCTGATGCACTACAT 58.257 45.000 12.58 0.00 43.54 2.29
2470 2584 1.464608 GAAAAGCGCTGATGCACTACA 59.535 47.619 12.58 0.00 39.64 2.74
2471 2585 1.527793 CGAAAAGCGCTGATGCACTAC 60.528 52.381 12.58 0.00 39.64 2.73
2472 2586 0.721154 CGAAAAGCGCTGATGCACTA 59.279 50.000 12.58 0.00 39.64 2.74
2473 2587 0.950555 TCGAAAAGCGCTGATGCACT 60.951 50.000 12.58 0.00 40.61 4.40
2474 2588 0.519999 CTCGAAAAGCGCTGATGCAC 60.520 55.000 12.58 0.00 40.61 4.57
2475 2589 0.670239 TCTCGAAAAGCGCTGATGCA 60.670 50.000 12.58 0.00 40.61 3.96
2476 2590 0.654683 ATCTCGAAAAGCGCTGATGC 59.345 50.000 12.58 0.00 40.61 3.91
2477 2591 3.395858 AAATCTCGAAAAGCGCTGATG 57.604 42.857 12.58 1.02 40.61 3.07
2478 2592 5.545658 TTTAAATCTCGAAAAGCGCTGAT 57.454 34.783 12.58 5.05 40.61 2.90
2479 2593 5.545658 ATTTAAATCTCGAAAAGCGCTGA 57.454 34.783 12.58 2.15 40.61 4.26
2480 2594 6.305399 TCAAATTTAAATCTCGAAAAGCGCTG 59.695 34.615 12.58 0.00 40.61 5.18
2481 2595 6.305638 GTCAAATTTAAATCTCGAAAAGCGCT 59.694 34.615 2.64 2.64 40.61 5.92
2482 2596 6.450276 GTCAAATTTAAATCTCGAAAAGCGC 58.550 36.000 0.00 0.00 40.61 5.92
2483 2597 6.580791 TGGTCAAATTTAAATCTCGAAAAGCG 59.419 34.615 0.10 0.00 42.69 4.68
2484 2598 7.867445 TGGTCAAATTTAAATCTCGAAAAGC 57.133 32.000 0.10 0.00 0.00 3.51
2498 2612 9.810545 CCGTTGGTTAAATATATGGTCAAATTT 57.189 29.630 0.00 0.00 0.00 1.82
2499 2613 8.417884 CCCGTTGGTTAAATATATGGTCAAATT 58.582 33.333 0.00 0.00 0.00 1.82
2500 2614 7.780745 TCCCGTTGGTTAAATATATGGTCAAAT 59.219 33.333 0.00 0.00 0.00 2.32
2501 2615 7.067251 GTCCCGTTGGTTAAATATATGGTCAAA 59.933 37.037 0.00 0.00 0.00 2.69
2502 2616 6.543100 GTCCCGTTGGTTAAATATATGGTCAA 59.457 38.462 0.00 0.00 0.00 3.18
2503 2617 6.056884 GTCCCGTTGGTTAAATATATGGTCA 58.943 40.000 0.00 0.00 0.00 4.02
2504 2618 5.471116 GGTCCCGTTGGTTAAATATATGGTC 59.529 44.000 0.00 0.00 0.00 4.02
2505 2619 5.379187 GGTCCCGTTGGTTAAATATATGGT 58.621 41.667 0.00 0.00 0.00 3.55
2506 2620 4.453136 CGGTCCCGTTGGTTAAATATATGG 59.547 45.833 0.00 0.00 34.35 2.74
2507 2621 5.178067 GTCGGTCCCGTTGGTTAAATATATG 59.822 44.000 5.52 0.00 40.74 1.78
2508 2622 5.070847 AGTCGGTCCCGTTGGTTAAATATAT 59.929 40.000 5.52 0.00 40.74 0.86
2509 2623 4.405358 AGTCGGTCCCGTTGGTTAAATATA 59.595 41.667 5.52 0.00 40.74 0.86
2510 2624 3.198417 AGTCGGTCCCGTTGGTTAAATAT 59.802 43.478 5.52 0.00 40.74 1.28
2511 2625 2.566724 AGTCGGTCCCGTTGGTTAAATA 59.433 45.455 5.52 0.00 40.74 1.40
2512 2626 1.348696 AGTCGGTCCCGTTGGTTAAAT 59.651 47.619 5.52 0.00 40.74 1.40
2513 2627 0.758123 AGTCGGTCCCGTTGGTTAAA 59.242 50.000 5.52 0.00 40.74 1.52
2514 2628 0.033781 CAGTCGGTCCCGTTGGTTAA 59.966 55.000 5.52 0.00 40.74 2.01
2515 2629 1.667151 CAGTCGGTCCCGTTGGTTA 59.333 57.895 5.52 0.00 40.74 2.85
2516 2630 2.424302 CAGTCGGTCCCGTTGGTT 59.576 61.111 5.52 0.00 40.74 3.67
2517 2631 4.309950 GCAGTCGGTCCCGTTGGT 62.310 66.667 5.52 0.00 40.74 3.67
2530 2644 4.947147 TTTTGCTCCCGCCGCAGT 62.947 61.111 0.00 0.00 38.80 4.40
2531 2645 2.490993 AATTTTTGCTCCCGCCGCAG 62.491 55.000 0.00 0.00 38.80 5.18
2532 2646 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
2533 2647 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
2534 2648 2.287368 GGTATAATTTTTGCTCCCGCCG 60.287 50.000 0.00 0.00 34.43 6.46
2535 2649 2.691011 TGGTATAATTTTTGCTCCCGCC 59.309 45.455 0.00 0.00 34.43 6.13
2536 2650 3.380320 AGTGGTATAATTTTTGCTCCCGC 59.620 43.478 0.00 0.00 0.00 6.13
2537 2651 6.687081 TTAGTGGTATAATTTTTGCTCCCG 57.313 37.500 0.00 0.00 0.00 5.14
2538 2652 9.884636 AAATTTAGTGGTATAATTTTTGCTCCC 57.115 29.630 0.00 0.00 29.68 4.30
2553 2667 9.153721 TCGTATTTTCGATACAAATTTAGTGGT 57.846 29.630 0.00 0.00 34.85 4.16
2554 2668 9.976255 TTCGTATTTTCGATACAAATTTAGTGG 57.024 29.630 0.00 0.00 39.57 4.00
2561 2675 9.702726 CACTGATTTCGTATTTTCGATACAAAT 57.297 29.630 0.00 0.00 39.57 2.32
2562 2676 7.690637 GCACTGATTTCGTATTTTCGATACAAA 59.309 33.333 0.00 0.00 39.57 2.83
2563 2677 7.064134 AGCACTGATTTCGTATTTTCGATACAA 59.936 33.333 0.00 0.00 39.57 2.41
2564 2678 6.533723 AGCACTGATTTCGTATTTTCGATACA 59.466 34.615 0.00 0.00 39.57 2.29
2565 2679 6.934210 AGCACTGATTTCGTATTTTCGATAC 58.066 36.000 0.00 0.00 39.57 2.24
2566 2680 8.812147 ATAGCACTGATTTCGTATTTTCGATA 57.188 30.769 0.00 0.00 39.57 2.92
2567 2681 7.715265 ATAGCACTGATTTCGTATTTTCGAT 57.285 32.000 0.00 0.00 39.57 3.59
2568 2682 8.637281 TTATAGCACTGATTTCGTATTTTCGA 57.363 30.769 0.00 0.00 38.08 3.71
2569 2683 9.864034 AATTATAGCACTGATTTCGTATTTTCG 57.136 29.630 0.00 0.00 0.00 3.46
2574 2688 9.547753 ACAGAAATTATAGCACTGATTTCGTAT 57.452 29.630 0.00 0.37 41.20 3.06
2575 2689 8.942338 ACAGAAATTATAGCACTGATTTCGTA 57.058 30.769 0.00 0.00 41.20 3.43
2576 2690 7.849804 ACAGAAATTATAGCACTGATTTCGT 57.150 32.000 0.00 7.90 41.20 3.85
2577 2691 7.164826 GCAACAGAAATTATAGCACTGATTTCG 59.835 37.037 0.00 7.49 41.20 3.46
2578 2692 7.433425 GGCAACAGAAATTATAGCACTGATTTC 59.567 37.037 0.00 7.34 38.27 2.17
2579 2693 7.260603 GGCAACAGAAATTATAGCACTGATTT 58.739 34.615 0.00 0.00 33.53 2.17
2580 2694 6.458751 CGGCAACAGAAATTATAGCACTGATT 60.459 38.462 0.00 0.00 33.53 2.57
2581 2695 5.008019 CGGCAACAGAAATTATAGCACTGAT 59.992 40.000 0.00 0.00 33.53 2.90
2582 2696 4.332543 CGGCAACAGAAATTATAGCACTGA 59.667 41.667 0.00 0.00 33.53 3.41
2583 2697 4.094887 ACGGCAACAGAAATTATAGCACTG 59.905 41.667 0.00 0.00 35.14 3.66
2584 2698 4.261801 ACGGCAACAGAAATTATAGCACT 58.738 39.130 0.00 0.00 0.00 4.40
2585 2699 4.588278 GACGGCAACAGAAATTATAGCAC 58.412 43.478 0.00 0.00 0.00 4.40
2586 2700 3.308595 CGACGGCAACAGAAATTATAGCA 59.691 43.478 0.00 0.00 0.00 3.49
2587 2701 3.844943 GCGACGGCAACAGAAATTATAGC 60.845 47.826 0.00 0.00 39.62 2.97
2588 2702 3.861834 GCGACGGCAACAGAAATTATAG 58.138 45.455 0.00 0.00 39.62 1.31
2589 2703 3.936902 GCGACGGCAACAGAAATTATA 57.063 42.857 0.00 0.00 39.62 0.98
2590 2704 2.825086 GCGACGGCAACAGAAATTAT 57.175 45.000 0.00 0.00 39.62 1.28
2604 2718 3.590443 AACGAGACCGACTGCGACG 62.590 63.158 0.00 0.00 40.82 5.12
2605 2719 2.081212 CAACGAGACCGACTGCGAC 61.081 63.158 0.00 0.00 40.82 5.19
2606 2720 2.254350 CAACGAGACCGACTGCGA 59.746 61.111 0.00 0.00 40.82 5.10
2607 2721 2.805353 CCAACGAGACCGACTGCG 60.805 66.667 0.00 0.00 39.50 5.18
2608 2722 0.038892 TAACCAACGAGACCGACTGC 60.039 55.000 0.00 0.00 39.50 4.40
2609 2723 2.427232 TTAACCAACGAGACCGACTG 57.573 50.000 0.00 0.00 39.50 3.51
2610 2724 3.672767 ATTTAACCAACGAGACCGACT 57.327 42.857 0.00 0.00 39.50 4.18
2611 2725 4.737353 AAATTTAACCAACGAGACCGAC 57.263 40.909 0.00 0.00 39.50 4.79
2612 2726 5.782047 TCTAAATTTAACCAACGAGACCGA 58.218 37.500 0.00 0.00 39.50 4.69
2613 2727 6.534079 AGATCTAAATTTAACCAACGAGACCG 59.466 38.462 0.00 0.00 42.50 4.79
2614 2728 7.548075 TGAGATCTAAATTTAACCAACGAGACC 59.452 37.037 0.00 0.00 0.00 3.85
2615 2729 8.475331 TGAGATCTAAATTTAACCAACGAGAC 57.525 34.615 0.00 0.00 0.00 3.36
2616 2730 9.496873 TTTGAGATCTAAATTTAACCAACGAGA 57.503 29.630 0.00 0.00 0.00 4.04
2647 2761 9.577110 CTTCATTTCACAATGTAGTGCATTTAT 57.423 29.630 3.42 0.00 44.82 1.40
2648 2762 8.028354 CCTTCATTTCACAATGTAGTGCATTTA 58.972 33.333 3.42 0.00 44.82 1.40
2649 2763 6.869913 CCTTCATTTCACAATGTAGTGCATTT 59.130 34.615 3.42 0.00 44.82 2.32
2651 2765 5.105635 CCCTTCATTTCACAATGTAGTGCAT 60.106 40.000 0.00 0.00 40.78 3.96
2652 2766 4.218200 CCCTTCATTTCACAATGTAGTGCA 59.782 41.667 0.00 0.00 40.78 4.57
2653 2767 4.458989 TCCCTTCATTTCACAATGTAGTGC 59.541 41.667 0.00 0.00 40.78 4.40
2654 2768 5.707298 ACTCCCTTCATTTCACAATGTAGTG 59.293 40.000 0.00 0.00 40.78 2.74
2655 2769 5.880901 ACTCCCTTCATTTCACAATGTAGT 58.119 37.500 0.00 0.00 40.78 2.73
2656 2770 7.042456 CGATACTCCCTTCATTTCACAATGTAG 60.042 40.741 0.00 0.00 40.78 2.74
2657 2771 6.761242 CGATACTCCCTTCATTTCACAATGTA 59.239 38.462 0.00 0.00 40.78 2.29
2658 2772 5.586243 CGATACTCCCTTCATTTCACAATGT 59.414 40.000 0.00 0.00 40.78 2.71
2659 2773 5.008019 CCGATACTCCCTTCATTTCACAATG 59.992 44.000 0.00 0.00 41.25 2.82
2660 2774 5.126067 CCGATACTCCCTTCATTTCACAAT 58.874 41.667 0.00 0.00 0.00 2.71
2661 2775 4.019681 ACCGATACTCCCTTCATTTCACAA 60.020 41.667 0.00 0.00 0.00 3.33
2662 2776 3.517901 ACCGATACTCCCTTCATTTCACA 59.482 43.478 0.00 0.00 0.00 3.58
2663 2777 3.871594 CACCGATACTCCCTTCATTTCAC 59.128 47.826 0.00 0.00 0.00 3.18
2664 2778 3.681594 GCACCGATACTCCCTTCATTTCA 60.682 47.826 0.00 0.00 0.00 2.69
2665 2779 2.872858 GCACCGATACTCCCTTCATTTC 59.127 50.000 0.00 0.00 0.00 2.17
2666 2780 2.741878 CGCACCGATACTCCCTTCATTT 60.742 50.000 0.00 0.00 0.00 2.32
2667 2781 1.202533 CGCACCGATACTCCCTTCATT 60.203 52.381 0.00 0.00 0.00 2.57
2668 2782 0.389391 CGCACCGATACTCCCTTCAT 59.611 55.000 0.00 0.00 0.00 2.57
2669 2783 1.672854 CCGCACCGATACTCCCTTCA 61.673 60.000 0.00 0.00 0.00 3.02
2670 2784 1.067582 CCGCACCGATACTCCCTTC 59.932 63.158 0.00 0.00 0.00 3.46
2671 2785 3.090219 GCCGCACCGATACTCCCTT 62.090 63.158 0.00 0.00 0.00 3.95
2672 2786 3.537874 GCCGCACCGATACTCCCT 61.538 66.667 0.00 0.00 0.00 4.20
2673 2787 1.812686 TATGCCGCACCGATACTCCC 61.813 60.000 0.00 0.00 0.00 4.30
2674 2788 0.388649 CTATGCCGCACCGATACTCC 60.389 60.000 0.00 0.00 0.00 3.85
2675 2789 0.314302 ACTATGCCGCACCGATACTC 59.686 55.000 0.00 0.00 0.00 2.59
2676 2790 0.032130 CACTATGCCGCACCGATACT 59.968 55.000 0.00 0.00 0.00 2.12
2677 2791 0.249322 ACACTATGCCGCACCGATAC 60.249 55.000 0.00 0.00 0.00 2.24
2678 2792 0.462375 AACACTATGCCGCACCGATA 59.538 50.000 0.00 0.00 0.00 2.92
2679 2793 0.462375 TAACACTATGCCGCACCGAT 59.538 50.000 0.00 0.00 0.00 4.18
2680 2794 0.462375 ATAACACTATGCCGCACCGA 59.538 50.000 0.00 0.00 0.00 4.69
2681 2795 1.295792 AATAACACTATGCCGCACCG 58.704 50.000 0.00 0.00 0.00 4.94
2682 2796 3.303791 GCTTAATAACACTATGCCGCACC 60.304 47.826 0.00 0.00 0.00 5.01
2683 2797 3.311322 TGCTTAATAACACTATGCCGCAC 59.689 43.478 0.00 0.00 0.00 5.34
2684 2798 3.536570 TGCTTAATAACACTATGCCGCA 58.463 40.909 0.00 0.00 0.00 5.69
2685 2799 4.527564 CTTGCTTAATAACACTATGCCGC 58.472 43.478 0.00 0.00 0.00 6.53
2686 2800 4.574828 ACCTTGCTTAATAACACTATGCCG 59.425 41.667 0.00 0.00 0.00 5.69
2687 2801 6.451064 AACCTTGCTTAATAACACTATGCC 57.549 37.500 0.00 0.00 0.00 4.40
2688 2802 6.751888 CCAAACCTTGCTTAATAACACTATGC 59.248 38.462 0.00 0.00 0.00 3.14
2689 2803 7.122055 TCCCAAACCTTGCTTAATAACACTATG 59.878 37.037 0.00 0.00 0.00 2.23
2711 2825 1.941377 TTAACGACTTAGCCCTCCCA 58.059 50.000 0.00 0.00 0.00 4.37
2712 2826 3.555527 ATTTAACGACTTAGCCCTCCC 57.444 47.619 0.00 0.00 0.00 4.30
2741 2855 6.641314 CGTTAGATTGACGATTATTACCTGCT 59.359 38.462 0.00 0.00 42.82 4.24
2769 2887 0.958091 CCGGCCAACATTCAGTTTCA 59.042 50.000 2.24 0.00 38.74 2.69
2843 2961 9.755804 GGTAAGTACTTTGAACTTGTAGTAGTT 57.244 33.333 14.49 0.00 40.92 2.24
2859 3006 8.747471 ACTAAGCTTTCTATTCGGTAAGTACTT 58.253 33.333 13.68 13.68 0.00 2.24
2906 3053 2.682352 CCGACATCAACATGCATACCAA 59.318 45.455 0.00 0.00 32.57 3.67
2912 3059 1.889545 TTGACCGACATCAACATGCA 58.110 45.000 0.00 0.00 33.62 3.96
2940 3087 6.061441 TGCCAACGGAATACATATGAATCTT 58.939 36.000 10.38 0.00 0.00 2.40
2942 3089 5.700832 TCTGCCAACGGAATACATATGAATC 59.299 40.000 10.38 4.32 0.00 2.52
2943 3090 5.620206 TCTGCCAACGGAATACATATGAAT 58.380 37.500 10.38 0.00 0.00 2.57
2944 3091 5.029807 TCTGCCAACGGAATACATATGAA 57.970 39.130 10.38 0.00 0.00 2.57
2945 3092 4.681074 TCTGCCAACGGAATACATATGA 57.319 40.909 10.38 0.00 0.00 2.15
2954 3102 3.134574 ACAAGTATTCTGCCAACGGAA 57.865 42.857 0.00 0.00 45.15 4.30


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

AutoCloner maintained by Alex Coulton.