Multiple sequence alignment - TraesCS6A01G207900

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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 TraesCS6A01G207900 chr6A 100.000 2339 0 0 1 2339 371337482 371339820 0.000000e+00 4320
1 TraesCS6A01G207900 chr1B 95.084 1363 64 2 1 1362 611789588 611790948 0.000000e+00 2143
2 TraesCS6A01G207900 chr6B 94.510 1366 63 6 1 1363 151678481 151679837 0.000000e+00 2097
3 TraesCS6A01G207900 chr6B 89.125 423 26 6 1362 1766 405056818 405056398 2.070000e-140 508
4 TraesCS6A01G207900 chr3B 94.555 1359 67 4 2 1359 418735711 418734359 0.000000e+00 2093
5 TraesCS6A01G207900 chr3B 91.507 471 35 2 1750 2216 726151669 726152138 0.000000e+00 643
6 TraesCS6A01G207900 chr4D 95.285 1315 52 6 1 1311 58941426 58940118 0.000000e+00 2076
7 TraesCS6A01G207900 chr4D 93.709 1367 76 7 1 1363 127148117 127149477 0.000000e+00 2039
8 TraesCS6A01G207900 chr4D 87.415 588 49 19 1767 2335 7406250 7405669 0.000000e+00 652
9 TraesCS6A01G207900 chr2B 94.135 1364 76 3 1 1362 30701341 30702702 0.000000e+00 2073
10 TraesCS6A01G207900 chr2B 90.136 588 38 14 1769 2338 720499798 720499213 0.000000e+00 747
11 TraesCS6A01G207900 chr2A 94.113 1359 75 3 3 1360 433378081 433376727 0.000000e+00 2061
12 TraesCS6A01G207900 chr2A 98.361 122 2 0 2218 2339 34125035 34125156 5.060000e-52 215
13 TraesCS6A01G207900 chr2D 93.855 1367 77 5 1 1363 273017911 273019274 0.000000e+00 2052
14 TraesCS6A01G207900 chr2D 89.587 557 34 17 1795 2335 89890021 89890569 0.000000e+00 686
15 TraesCS6A01G207900 chr2D 92.600 473 29 3 1755 2223 592352765 592352295 0.000000e+00 675
16 TraesCS6A01G207900 chr7D 93.773 1365 80 4 1 1363 232924947 232926308 0.000000e+00 2045
17 TraesCS6A01G207900 chr7D 95.238 462 15 3 1766 2223 419755524 419755066 0.000000e+00 725
18 TraesCS6A01G207900 chr7D 89.739 575 43 10 1767 2333 568173504 568172938 0.000000e+00 721
19 TraesCS6A01G207900 chr7D 92.243 477 30 4 1744 2216 169547938 169548411 0.000000e+00 669
20 TraesCS6A01G207900 chr7D 91.863 467 31 4 1755 2216 360237293 360237757 0.000000e+00 645
21 TraesCS6A01G207900 chr6D 95.228 461 16 2 1767 2223 391340925 391340467 0.000000e+00 725
22 TraesCS6A01G207900 chr6D 92.133 483 29 5 1748 2223 220337742 220337262 0.000000e+00 673
23 TraesCS6A01G207900 chr6D 88.923 325 16 8 1466 1773 263956095 263955774 1.310000e-102 383
24 TraesCS6A01G207900 chr5A 89.212 584 43 15 1766 2333 396212899 396212320 0.000000e+00 712
25 TraesCS6A01G207900 chr7B 89.043 575 53 6 1767 2333 661421607 661421035 0.000000e+00 704
26 TraesCS6A01G207900 chr3A 89.043 575 53 7 1767 2333 144631370 144630798 0.000000e+00 704
27 TraesCS6A01G207900 chr1D 92.308 481 31 3 1748 2223 97886782 97887261 0.000000e+00 678
28 TraesCS6A01G207900 chr3D 92.949 468 27 3 1755 2216 571694196 571694663 0.000000e+00 676
29 TraesCS6A01G207900 chr3D 86.745 596 55 17 1755 2333 446107109 446106521 1.960000e-180 641
30 TraesCS6A01G207900 chr5D 92.405 474 29 3 1754 2223 204250394 204249924 0.000000e+00 669


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 TraesCS6A01G207900 chr6A 371337482 371339820 2338 False 4320 4320 100.000 1 2339 1 chr6A.!!$F1 2338
1 TraesCS6A01G207900 chr1B 611789588 611790948 1360 False 2143 2143 95.084 1 1362 1 chr1B.!!$F1 1361
2 TraesCS6A01G207900 chr6B 151678481 151679837 1356 False 2097 2097 94.510 1 1363 1 chr6B.!!$F1 1362
3 TraesCS6A01G207900 chr3B 418734359 418735711 1352 True 2093 2093 94.555 2 1359 1 chr3B.!!$R1 1357
4 TraesCS6A01G207900 chr4D 58940118 58941426 1308 True 2076 2076 95.285 1 1311 1 chr4D.!!$R2 1310
5 TraesCS6A01G207900 chr4D 127148117 127149477 1360 False 2039 2039 93.709 1 1363 1 chr4D.!!$F1 1362
6 TraesCS6A01G207900 chr4D 7405669 7406250 581 True 652 652 87.415 1767 2335 1 chr4D.!!$R1 568
7 TraesCS6A01G207900 chr2B 30701341 30702702 1361 False 2073 2073 94.135 1 1362 1 chr2B.!!$F1 1361
8 TraesCS6A01G207900 chr2B 720499213 720499798 585 True 747 747 90.136 1769 2338 1 chr2B.!!$R1 569
9 TraesCS6A01G207900 chr2A 433376727 433378081 1354 True 2061 2061 94.113 3 1360 1 chr2A.!!$R1 1357
10 TraesCS6A01G207900 chr2D 273017911 273019274 1363 False 2052 2052 93.855 1 1363 1 chr2D.!!$F2 1362
11 TraesCS6A01G207900 chr2D 89890021 89890569 548 False 686 686 89.587 1795 2335 1 chr2D.!!$F1 540
12 TraesCS6A01G207900 chr7D 232924947 232926308 1361 False 2045 2045 93.773 1 1363 1 chr7D.!!$F2 1362
13 TraesCS6A01G207900 chr7D 568172938 568173504 566 True 721 721 89.739 1767 2333 1 chr7D.!!$R2 566
14 TraesCS6A01G207900 chr5A 396212320 396212899 579 True 712 712 89.212 1766 2333 1 chr5A.!!$R1 567
15 TraesCS6A01G207900 chr7B 661421035 661421607 572 True 704 704 89.043 1767 2333 1 chr7B.!!$R1 566
16 TraesCS6A01G207900 chr3A 144630798 144631370 572 True 704 704 89.043 1767 2333 1 chr3A.!!$R1 566
17 TraesCS6A01G207900 chr3D 446106521 446107109 588 True 641 641 86.745 1755 2333 1 chr3D.!!$R1 578

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
428 435 0.174845 GCGGACACTACATGGCACTA 59.825 55.0 0.0 0.0 38.59 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1388 1402 0.034337 GGGCACGAGGTTGAGTTACA 59.966 55.0 0.0 0.0 0.0 2.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.091549 ACATCAACATTTGGGAAGATGCT 58.908 39.130 0.00 0.00 37.07 3.79
393 397 4.120589 GGAAGTTATCTTGTCCGGCTAAG 58.879 47.826 0.00 3.63 33.64 2.18
428 435 0.174845 GCGGACACTACATGGCACTA 59.825 55.000 0.00 0.00 38.59 2.74
514 521 5.258841 TCTCAGGGTGTAGAAGATACGAAA 58.741 41.667 0.00 0.00 0.00 3.46
529 536 3.692791 ACGAAACACTTGCTTTTCCTC 57.307 42.857 0.00 0.00 0.00 3.71
615 624 1.137872 GATTGATCGTGCTGGAGAGGT 59.862 52.381 0.00 0.00 0.00 3.85
692 701 9.651718 GGTATGAAAATGTTCGAGAAATGATAC 57.348 33.333 0.00 0.00 36.46 2.24
723 733 4.229582 AGCTTGGTATCTATGGTGGGAAAA 59.770 41.667 0.00 0.00 0.00 2.29
729 739 3.343941 TCTATGGTGGGAAAAACGGAG 57.656 47.619 0.00 0.00 0.00 4.63
838 850 6.729690 TCTTCAAAGGTGTCCATGAAAAAT 57.270 33.333 0.00 0.00 33.50 1.82
931 944 1.047034 AGGGTACGATGGGGCAGTAC 61.047 60.000 0.00 0.00 39.78 2.73
973 986 3.582998 TTATTGCAGGAGGGAATGGAG 57.417 47.619 0.00 0.00 38.12 3.86
1027 1040 4.704057 CAGAGGCCTTAGCTCTCAAATTTT 59.296 41.667 6.77 0.00 38.22 1.82
1146 1159 3.799755 GCGGCGGCGACAATCTTT 61.800 61.111 36.87 0.00 0.00 2.52
1327 1341 8.330466 TCTCACAAACGATGTATTGGTTATTT 57.670 30.769 0.00 0.00 41.46 1.40
1398 1412 8.635877 ATCGATTCAGACTAATGTAACTCAAC 57.364 34.615 0.00 0.00 0.00 3.18
1399 1413 7.033791 TCGATTCAGACTAATGTAACTCAACC 58.966 38.462 0.00 0.00 0.00 3.77
1400 1414 7.036220 CGATTCAGACTAATGTAACTCAACCT 58.964 38.462 0.00 0.00 0.00 3.50
1401 1415 7.221067 CGATTCAGACTAATGTAACTCAACCTC 59.779 40.741 0.00 0.00 0.00 3.85
1402 1416 5.950883 TCAGACTAATGTAACTCAACCTCG 58.049 41.667 0.00 0.00 0.00 4.63
1403 1417 5.475909 TCAGACTAATGTAACTCAACCTCGT 59.524 40.000 0.00 0.00 0.00 4.18
1404 1418 5.573282 CAGACTAATGTAACTCAACCTCGTG 59.427 44.000 0.00 0.00 0.00 4.35
1405 1419 4.243270 ACTAATGTAACTCAACCTCGTGC 58.757 43.478 0.00 0.00 0.00 5.34
1406 1420 2.094762 ATGTAACTCAACCTCGTGCC 57.905 50.000 0.00 0.00 0.00 5.01
1407 1421 0.034337 TGTAACTCAACCTCGTGCCC 59.966 55.000 0.00 0.00 0.00 5.36
1408 1422 0.672711 GTAACTCAACCTCGTGCCCC 60.673 60.000 0.00 0.00 0.00 5.80
1409 1423 1.122632 TAACTCAACCTCGTGCCCCA 61.123 55.000 0.00 0.00 0.00 4.96
1410 1424 1.990160 AACTCAACCTCGTGCCCCAA 61.990 55.000 0.00 0.00 0.00 4.12
1411 1425 1.966451 CTCAACCTCGTGCCCCAAC 60.966 63.158 0.00 0.00 0.00 3.77
1412 1426 2.203280 CAACCTCGTGCCCCAACA 60.203 61.111 0.00 0.00 0.00 3.33
1413 1427 1.603455 CAACCTCGTGCCCCAACAT 60.603 57.895 0.00 0.00 0.00 2.71
1414 1428 0.322098 CAACCTCGTGCCCCAACATA 60.322 55.000 0.00 0.00 0.00 2.29
1415 1429 0.402504 AACCTCGTGCCCCAACATAA 59.597 50.000 0.00 0.00 0.00 1.90
1416 1430 0.035439 ACCTCGTGCCCCAACATAAG 60.035 55.000 0.00 0.00 0.00 1.73
1417 1431 0.748005 CCTCGTGCCCCAACATAAGG 60.748 60.000 0.00 0.00 0.00 2.69
1418 1432 0.251916 CTCGTGCCCCAACATAAGGA 59.748 55.000 0.00 0.00 0.00 3.36
1419 1433 0.251916 TCGTGCCCCAACATAAGGAG 59.748 55.000 0.00 0.00 0.00 3.69
1420 1434 0.251916 CGTGCCCCAACATAAGGAGA 59.748 55.000 0.00 0.00 0.00 3.71
1421 1435 1.743772 CGTGCCCCAACATAAGGAGAG 60.744 57.143 0.00 0.00 0.00 3.20
1422 1436 0.918983 TGCCCCAACATAAGGAGAGG 59.081 55.000 0.00 0.00 0.00 3.69
1423 1437 0.466372 GCCCCAACATAAGGAGAGGC 60.466 60.000 0.00 0.00 0.00 4.70
1424 1438 0.918983 CCCCAACATAAGGAGAGGCA 59.081 55.000 0.00 0.00 0.00 4.75
1425 1439 1.284785 CCCCAACATAAGGAGAGGCAA 59.715 52.381 0.00 0.00 0.00 4.52
1426 1440 2.369394 CCCAACATAAGGAGAGGCAAC 58.631 52.381 0.00 0.00 0.00 4.17
1446 1460 3.436028 CCCCCTCCCCGTCTCCTA 61.436 72.222 0.00 0.00 0.00 2.94
1447 1461 2.791406 CCCCCTCCCCGTCTCCTAT 61.791 68.421 0.00 0.00 0.00 2.57
1448 1462 1.236282 CCCCTCCCCGTCTCCTATT 59.764 63.158 0.00 0.00 0.00 1.73
1449 1463 1.122019 CCCCTCCCCGTCTCCTATTG 61.122 65.000 0.00 0.00 0.00 1.90
1450 1464 1.122019 CCCTCCCCGTCTCCTATTGG 61.122 65.000 0.00 0.00 0.00 3.16
1451 1465 0.398664 CCTCCCCGTCTCCTATTGGT 60.399 60.000 0.00 0.00 34.23 3.67
1452 1466 1.133262 CCTCCCCGTCTCCTATTGGTA 60.133 57.143 0.00 0.00 34.23 3.25
1453 1467 1.962100 CTCCCCGTCTCCTATTGGTAC 59.038 57.143 0.00 0.00 34.23 3.34
1454 1468 0.672342 CCCCGTCTCCTATTGGTACG 59.328 60.000 13.61 13.61 40.64 3.67
1455 1469 1.683943 CCCGTCTCCTATTGGTACGA 58.316 55.000 19.16 3.05 42.19 3.43
1456 1470 1.336125 CCCGTCTCCTATTGGTACGAC 59.664 57.143 19.16 11.71 42.19 4.34
1457 1471 2.019249 CCGTCTCCTATTGGTACGACA 58.981 52.381 19.16 0.00 42.19 4.35
1458 1472 2.621998 CCGTCTCCTATTGGTACGACAT 59.378 50.000 19.16 0.00 42.19 3.06
1459 1473 3.304525 CCGTCTCCTATTGGTACGACATC 60.305 52.174 19.16 0.00 42.19 3.06
1460 1474 3.314357 CGTCTCCTATTGGTACGACATCA 59.686 47.826 14.79 0.00 42.19 3.07
1461 1475 4.023107 CGTCTCCTATTGGTACGACATCAT 60.023 45.833 14.79 0.00 42.19 2.45
1462 1476 5.507482 CGTCTCCTATTGGTACGACATCATT 60.507 44.000 14.79 0.00 42.19 2.57
1463 1477 5.692204 GTCTCCTATTGGTACGACATCATTG 59.308 44.000 0.00 0.00 34.23 2.82
1464 1478 4.377021 TCCTATTGGTACGACATCATTGC 58.623 43.478 0.00 0.00 34.23 3.56
1465 1479 4.100963 TCCTATTGGTACGACATCATTGCT 59.899 41.667 0.00 0.00 34.23 3.91
1466 1480 5.303333 TCCTATTGGTACGACATCATTGCTA 59.697 40.000 0.00 0.00 34.23 3.49
1467 1481 6.014584 TCCTATTGGTACGACATCATTGCTAT 60.015 38.462 0.00 0.00 34.23 2.97
1468 1482 6.650807 CCTATTGGTACGACATCATTGCTATT 59.349 38.462 0.00 0.00 0.00 1.73
1469 1483 5.984233 TTGGTACGACATCATTGCTATTC 57.016 39.130 0.00 0.00 0.00 1.75
1470 1484 4.377021 TGGTACGACATCATTGCTATTCC 58.623 43.478 0.00 0.00 0.00 3.01
1471 1485 4.141824 TGGTACGACATCATTGCTATTCCA 60.142 41.667 0.00 0.00 0.00 3.53
1472 1486 4.814234 GGTACGACATCATTGCTATTCCAA 59.186 41.667 0.00 0.00 0.00 3.53
1473 1487 5.470098 GGTACGACATCATTGCTATTCCAAT 59.530 40.000 0.00 0.00 35.90 3.16
1474 1488 6.017109 GGTACGACATCATTGCTATTCCAATT 60.017 38.462 0.00 0.00 33.35 2.32
1475 1489 6.455360 ACGACATCATTGCTATTCCAATTT 57.545 33.333 0.00 0.00 33.35 1.82
1476 1490 6.267817 ACGACATCATTGCTATTCCAATTTG 58.732 36.000 0.00 0.00 33.35 2.32
1477 1491 6.127647 ACGACATCATTGCTATTCCAATTTGT 60.128 34.615 0.00 0.00 34.35 2.83
1478 1492 6.415867 CGACATCATTGCTATTCCAATTTGTC 59.584 38.462 12.86 12.86 39.48 3.18
1479 1493 6.576185 ACATCATTGCTATTCCAATTTGTCC 58.424 36.000 0.00 0.00 33.35 4.02
1480 1494 5.596836 TCATTGCTATTCCAATTTGTCCC 57.403 39.130 0.00 0.00 33.35 4.46
1481 1495 5.022122 TCATTGCTATTCCAATTTGTCCCA 58.978 37.500 0.00 0.00 33.35 4.37
1482 1496 5.662208 TCATTGCTATTCCAATTTGTCCCAT 59.338 36.000 0.00 0.00 33.35 4.00
1483 1497 6.156602 TCATTGCTATTCCAATTTGTCCCATT 59.843 34.615 0.00 0.00 33.35 3.16
1484 1498 5.341872 TGCTATTCCAATTTGTCCCATTG 57.658 39.130 0.00 0.00 0.00 2.82
1485 1499 5.022122 TGCTATTCCAATTTGTCCCATTGA 58.978 37.500 0.00 0.00 34.05 2.57
1486 1500 5.483231 TGCTATTCCAATTTGTCCCATTGAA 59.517 36.000 0.00 0.00 34.05 2.69
1487 1501 6.013898 TGCTATTCCAATTTGTCCCATTGAAA 60.014 34.615 0.00 0.00 34.05 2.69
1488 1502 7.049754 GCTATTCCAATTTGTCCCATTGAAAT 58.950 34.615 0.00 0.00 34.05 2.17
1489 1503 7.553760 GCTATTCCAATTTGTCCCATTGAAATT 59.446 33.333 0.00 0.00 34.05 1.82
1490 1504 9.452287 CTATTCCAATTTGTCCCATTGAAATTT 57.548 29.630 0.00 0.00 34.05 1.82
1491 1505 8.709272 ATTCCAATTTGTCCCATTGAAATTTT 57.291 26.923 0.00 0.00 34.05 1.82
1492 1506 7.507733 TCCAATTTGTCCCATTGAAATTTTG 57.492 32.000 0.00 0.00 34.05 2.44
1493 1507 7.059156 TCCAATTTGTCCCATTGAAATTTTGT 58.941 30.769 0.00 0.00 34.05 2.83
1494 1508 8.213679 TCCAATTTGTCCCATTGAAATTTTGTA 58.786 29.630 0.00 0.00 34.05 2.41
1495 1509 8.505625 CCAATTTGTCCCATTGAAATTTTGTAG 58.494 33.333 0.00 0.00 34.05 2.74
1496 1510 8.505625 CAATTTGTCCCATTGAAATTTTGTAGG 58.494 33.333 0.00 0.00 34.05 3.18
1497 1511 6.739331 TTGTCCCATTGAAATTTTGTAGGT 57.261 33.333 0.00 0.00 0.00 3.08
1498 1512 7.841282 TTGTCCCATTGAAATTTTGTAGGTA 57.159 32.000 0.00 0.00 0.00 3.08
1499 1513 7.461182 TGTCCCATTGAAATTTTGTAGGTAG 57.539 36.000 0.00 0.00 0.00 3.18
1500 1514 7.007723 TGTCCCATTGAAATTTTGTAGGTAGT 58.992 34.615 0.00 0.00 0.00 2.73
1501 1515 7.507616 TGTCCCATTGAAATTTTGTAGGTAGTT 59.492 33.333 0.00 0.00 0.00 2.24
1502 1516 9.016438 GTCCCATTGAAATTTTGTAGGTAGTTA 57.984 33.333 0.00 0.00 0.00 2.24
1503 1517 9.762381 TCCCATTGAAATTTTGTAGGTAGTTAT 57.238 29.630 0.00 0.00 0.00 1.89
1530 1544 5.774498 GGATACATCCAAGGAATTGGTTC 57.226 43.478 6.89 0.00 46.38 3.62
1531 1545 4.275936 GGATACATCCAAGGAATTGGTTCG 59.724 45.833 6.89 0.52 46.38 3.95
1532 1546 3.433306 ACATCCAAGGAATTGGTTCGA 57.567 42.857 6.89 0.00 42.62 3.71
1533 1547 3.968265 ACATCCAAGGAATTGGTTCGAT 58.032 40.909 6.89 0.00 42.62 3.59
1534 1548 3.696051 ACATCCAAGGAATTGGTTCGATG 59.304 43.478 6.89 6.03 42.62 3.84
1535 1549 2.722094 TCCAAGGAATTGGTTCGATGG 58.278 47.619 6.89 0.28 42.62 3.51
1536 1550 1.750778 CCAAGGAATTGGTTCGATGGG 59.249 52.381 0.00 0.00 37.22 4.00
1537 1551 1.134946 CAAGGAATTGGTTCGATGGGC 59.865 52.381 0.00 0.00 35.10 5.36
1538 1552 0.625849 AGGAATTGGTTCGATGGGCT 59.374 50.000 0.00 0.00 35.10 5.19
1539 1553 1.005924 AGGAATTGGTTCGATGGGCTT 59.994 47.619 0.00 0.00 35.10 4.35
1540 1554 1.405463 GGAATTGGTTCGATGGGCTTC 59.595 52.381 0.00 0.00 35.10 3.86
1541 1555 1.405463 GAATTGGTTCGATGGGCTTCC 59.595 52.381 0.00 0.00 0.00 3.46
1542 1556 0.748005 ATTGGTTCGATGGGCTTCCG 60.748 55.000 0.00 0.00 0.00 4.30
1543 1557 3.202706 GGTTCGATGGGCTTCCGC 61.203 66.667 0.00 0.00 0.00 5.54
1544 1558 2.435938 GTTCGATGGGCTTCCGCA 60.436 61.111 0.00 0.00 38.10 5.69
1545 1559 1.819632 GTTCGATGGGCTTCCGCAT 60.820 57.895 0.00 0.00 46.03 4.73
1546 1560 0.531974 GTTCGATGGGCTTCCGCATA 60.532 55.000 0.00 0.00 43.74 3.14
1547 1561 0.179234 TTCGATGGGCTTCCGCATAA 59.821 50.000 0.00 0.00 43.74 1.90
1548 1562 0.531974 TCGATGGGCTTCCGCATAAC 60.532 55.000 0.00 0.00 43.74 1.89
1549 1563 1.507141 CGATGGGCTTCCGCATAACC 61.507 60.000 0.00 0.00 43.74 2.85
1550 1564 0.465460 GATGGGCTTCCGCATAACCA 60.465 55.000 0.00 0.00 43.74 3.67
1551 1565 0.466189 ATGGGCTTCCGCATAACCAG 60.466 55.000 0.00 0.00 42.15 4.00
1552 1566 1.077716 GGGCTTCCGCATAACCAGT 60.078 57.895 0.00 0.00 38.10 4.00
1553 1567 0.679960 GGGCTTCCGCATAACCAGTT 60.680 55.000 0.00 0.00 38.10 3.16
1554 1568 0.451783 GGCTTCCGCATAACCAGTTG 59.548 55.000 0.00 0.00 38.10 3.16
1555 1569 0.451783 GCTTCCGCATAACCAGTTGG 59.548 55.000 0.00 0.00 37.38 3.77
1556 1570 1.948611 GCTTCCGCATAACCAGTTGGA 60.949 52.381 4.92 0.00 36.01 3.53
1557 1571 2.432444 CTTCCGCATAACCAGTTGGAA 58.568 47.619 4.92 0.00 38.94 3.53
1558 1572 2.107950 TCCGCATAACCAGTTGGAAG 57.892 50.000 4.92 0.00 38.94 3.46
1559 1573 1.349688 TCCGCATAACCAGTTGGAAGT 59.650 47.619 4.92 0.00 38.94 3.01
1560 1574 2.568062 TCCGCATAACCAGTTGGAAGTA 59.432 45.455 4.92 0.00 38.94 2.24
1561 1575 3.199071 TCCGCATAACCAGTTGGAAGTAT 59.801 43.478 4.92 0.00 38.94 2.12
1562 1576 4.406326 TCCGCATAACCAGTTGGAAGTATA 59.594 41.667 4.92 0.00 38.94 1.47
1563 1577 4.750098 CCGCATAACCAGTTGGAAGTATAG 59.250 45.833 4.92 0.00 38.94 1.31
1564 1578 5.452776 CCGCATAACCAGTTGGAAGTATAGA 60.453 44.000 4.92 0.00 38.94 1.98
1565 1579 6.223852 CGCATAACCAGTTGGAAGTATAGAT 58.776 40.000 4.92 0.00 38.94 1.98
1566 1580 6.706270 CGCATAACCAGTTGGAAGTATAGATT 59.294 38.462 4.92 0.00 38.94 2.40
1567 1581 7.226720 CGCATAACCAGTTGGAAGTATAGATTT 59.773 37.037 4.92 0.00 38.94 2.17
1568 1582 9.555727 GCATAACCAGTTGGAAGTATAGATTTA 57.444 33.333 4.92 0.00 38.94 1.40
1571 1585 8.451908 AACCAGTTGGAAGTATAGATTTATGC 57.548 34.615 4.92 0.00 38.94 3.14
1572 1586 7.573710 ACCAGTTGGAAGTATAGATTTATGCA 58.426 34.615 4.92 0.00 38.94 3.96
1573 1587 8.220559 ACCAGTTGGAAGTATAGATTTATGCAT 58.779 33.333 3.79 3.79 38.94 3.96
1574 1588 9.725019 CCAGTTGGAAGTATAGATTTATGCATA 57.275 33.333 1.16 1.16 37.39 3.14
1594 1608 8.821686 TGCATAAATTATCTCCTTTCTCCAAA 57.178 30.769 0.00 0.00 0.00 3.28
1595 1609 9.425248 TGCATAAATTATCTCCTTTCTCCAAAT 57.575 29.630 0.00 0.00 0.00 2.32
1596 1610 9.688592 GCATAAATTATCTCCTTTCTCCAAATG 57.311 33.333 0.00 0.00 0.00 2.32
1598 1612 6.721704 AATTATCTCCTTTCTCCAAATGGC 57.278 37.500 0.00 0.00 34.44 4.40
1599 1613 5.456921 TTATCTCCTTTCTCCAAATGGCT 57.543 39.130 0.00 0.00 34.44 4.75
1600 1614 3.356529 TCTCCTTTCTCCAAATGGCTC 57.643 47.619 0.00 0.00 34.44 4.70
1601 1615 2.644299 TCTCCTTTCTCCAAATGGCTCA 59.356 45.455 0.00 0.00 34.44 4.26
1602 1616 3.074390 TCTCCTTTCTCCAAATGGCTCAA 59.926 43.478 0.00 0.00 34.44 3.02
1603 1617 3.157087 TCCTTTCTCCAAATGGCTCAAC 58.843 45.455 0.00 0.00 34.44 3.18
1604 1618 3.160269 CCTTTCTCCAAATGGCTCAACT 58.840 45.455 0.00 0.00 34.44 3.16
1605 1619 3.192212 CCTTTCTCCAAATGGCTCAACTC 59.808 47.826 0.00 0.00 34.44 3.01
1606 1620 2.099141 TCTCCAAATGGCTCAACTCG 57.901 50.000 0.00 0.00 34.44 4.18
1607 1621 1.623311 TCTCCAAATGGCTCAACTCGA 59.377 47.619 0.00 0.00 34.44 4.04
1608 1622 1.734465 CTCCAAATGGCTCAACTCGAC 59.266 52.381 0.00 0.00 34.44 4.20
1609 1623 1.071542 TCCAAATGGCTCAACTCGACA 59.928 47.619 0.00 0.00 34.44 4.35
1610 1624 1.879380 CCAAATGGCTCAACTCGACAA 59.121 47.619 0.00 0.00 0.00 3.18
1611 1625 2.095567 CCAAATGGCTCAACTCGACAAG 60.096 50.000 0.00 0.00 0.00 3.16
1612 1626 2.807967 CAAATGGCTCAACTCGACAAGA 59.192 45.455 0.00 0.00 0.00 3.02
1623 1637 2.839486 TCGACAAGAGATGGCAACTT 57.161 45.000 0.00 0.00 36.57 2.66
1624 1638 3.126001 TCGACAAGAGATGGCAACTTT 57.874 42.857 0.00 0.00 36.57 2.66
1625 1639 3.067106 TCGACAAGAGATGGCAACTTTC 58.933 45.455 0.00 0.00 36.57 2.62
1626 1640 2.159787 CGACAAGAGATGGCAACTTTCG 60.160 50.000 0.00 9.52 36.57 3.46
1627 1641 1.537202 ACAAGAGATGGCAACTTTCGC 59.463 47.619 0.00 0.00 37.61 4.70
1628 1642 1.808945 CAAGAGATGGCAACTTTCGCT 59.191 47.619 0.00 0.00 32.74 4.93
1629 1643 1.731720 AGAGATGGCAACTTTCGCTC 58.268 50.000 0.00 0.00 37.61 5.03
1630 1644 1.002430 AGAGATGGCAACTTTCGCTCA 59.998 47.619 0.00 0.00 37.61 4.26
1631 1645 1.806542 GAGATGGCAACTTTCGCTCAA 59.193 47.619 0.00 0.00 37.61 3.02
1632 1646 1.537202 AGATGGCAACTTTCGCTCAAC 59.463 47.619 0.00 0.00 37.61 3.18
1633 1647 1.266718 GATGGCAACTTTCGCTCAACA 59.733 47.619 0.00 0.00 37.61 3.33
1634 1648 0.662619 TGGCAACTTTCGCTCAACAG 59.337 50.000 0.00 0.00 37.61 3.16
1635 1649 0.661483 GGCAACTTTCGCTCAACAGC 60.661 55.000 0.00 0.00 42.96 4.40
1636 1650 0.661483 GCAACTTTCGCTCAACAGCC 60.661 55.000 0.00 0.00 43.56 4.85
1637 1651 0.040067 CAACTTTCGCTCAACAGCCC 60.040 55.000 0.00 0.00 43.56 5.19
1638 1652 1.507141 AACTTTCGCTCAACAGCCCG 61.507 55.000 0.00 0.00 43.56 6.13
1639 1653 2.668212 TTTCGCTCAACAGCCCGG 60.668 61.111 0.00 0.00 43.56 5.73
1640 1654 3.171828 TTTCGCTCAACAGCCCGGA 62.172 57.895 0.73 0.00 43.56 5.14
1641 1655 2.463589 TTTCGCTCAACAGCCCGGAT 62.464 55.000 0.73 0.00 43.56 4.18
1642 1656 1.609635 TTCGCTCAACAGCCCGGATA 61.610 55.000 0.73 0.00 43.56 2.59
1643 1657 1.153449 CGCTCAACAGCCCGGATAA 60.153 57.895 0.73 0.00 43.56 1.75
1644 1658 0.532862 CGCTCAACAGCCCGGATAAT 60.533 55.000 0.73 0.00 43.56 1.28
1645 1659 0.947244 GCTCAACAGCCCGGATAATG 59.053 55.000 0.73 0.00 40.14 1.90
1646 1660 0.947244 CTCAACAGCCCGGATAATGC 59.053 55.000 0.73 0.00 0.00 3.56
1647 1661 0.546122 TCAACAGCCCGGATAATGCT 59.454 50.000 0.73 0.00 35.25 3.79
1648 1662 1.064758 TCAACAGCCCGGATAATGCTT 60.065 47.619 0.73 0.00 31.77 3.91
1649 1663 2.171659 TCAACAGCCCGGATAATGCTTA 59.828 45.455 0.73 0.00 31.77 3.09
1650 1664 3.149196 CAACAGCCCGGATAATGCTTAT 58.851 45.455 0.73 0.00 31.77 1.73
1651 1665 3.059352 ACAGCCCGGATAATGCTTATC 57.941 47.619 0.73 7.14 41.00 1.75
1652 1666 2.639839 ACAGCCCGGATAATGCTTATCT 59.360 45.455 0.73 0.00 41.37 1.98
1653 1667 3.838317 ACAGCCCGGATAATGCTTATCTA 59.162 43.478 0.73 0.00 41.37 1.98
1654 1668 4.286032 ACAGCCCGGATAATGCTTATCTAA 59.714 41.667 0.73 0.00 41.37 2.10
1655 1669 5.221843 ACAGCCCGGATAATGCTTATCTAAA 60.222 40.000 0.73 0.00 41.37 1.85
1656 1670 5.352569 CAGCCCGGATAATGCTTATCTAAAG 59.647 44.000 0.73 0.00 41.37 1.85
1657 1671 5.013183 AGCCCGGATAATGCTTATCTAAAGT 59.987 40.000 0.73 0.00 41.37 2.66
1658 1672 5.705905 GCCCGGATAATGCTTATCTAAAGTT 59.294 40.000 0.73 0.00 41.37 2.66
1659 1673 6.348540 GCCCGGATAATGCTTATCTAAAGTTG 60.349 42.308 0.73 0.00 41.37 3.16
1660 1674 6.934645 CCCGGATAATGCTTATCTAAAGTTGA 59.065 38.462 0.73 0.00 41.37 3.18
1661 1675 7.118390 CCCGGATAATGCTTATCTAAAGTTGAG 59.882 40.741 0.73 0.00 41.37 3.02
1662 1676 7.872993 CCGGATAATGCTTATCTAAAGTTGAGA 59.127 37.037 0.00 0.00 41.37 3.27
1663 1677 8.920665 CGGATAATGCTTATCTAAAGTTGAGAG 58.079 37.037 12.59 0.00 41.37 3.20
1664 1678 9.213799 GGATAATGCTTATCTAAAGTTGAGAGG 57.786 37.037 12.59 0.00 41.37 3.69
1665 1679 9.988815 GATAATGCTTATCTAAAGTTGAGAGGA 57.011 33.333 0.00 0.00 39.12 3.71
1666 1680 9.995003 ATAATGCTTATCTAAAGTTGAGAGGAG 57.005 33.333 0.00 0.00 0.00 3.69
1667 1681 7.667575 ATGCTTATCTAAAGTTGAGAGGAGA 57.332 36.000 6.77 0.00 0.00 3.71
1668 1682 7.667575 TGCTTATCTAAAGTTGAGAGGAGAT 57.332 36.000 6.77 0.00 0.00 2.75
1669 1683 8.083828 TGCTTATCTAAAGTTGAGAGGAGATT 57.916 34.615 6.77 0.00 0.00 2.40
1670 1684 8.543774 TGCTTATCTAAAGTTGAGAGGAGATTT 58.456 33.333 6.77 0.00 0.00 2.17
1678 1692 8.850007 AAAGTTGAGAGGAGATTTACTAAACC 57.150 34.615 0.00 0.00 0.00 3.27
1679 1693 7.800300 AGTTGAGAGGAGATTTACTAAACCT 57.200 36.000 0.00 0.00 0.00 3.50
1680 1694 8.896722 AGTTGAGAGGAGATTTACTAAACCTA 57.103 34.615 0.00 0.00 0.00 3.08
1681 1695 9.495382 AGTTGAGAGGAGATTTACTAAACCTAT 57.505 33.333 0.00 0.00 0.00 2.57
1682 1696 9.752961 GTTGAGAGGAGATTTACTAAACCTATC 57.247 37.037 0.00 0.00 36.63 2.08
1683 1697 9.488762 TTGAGAGGAGATTTACTAAACCTATCA 57.511 33.333 0.00 0.00 41.69 2.15
1684 1698 9.488762 TGAGAGGAGATTTACTAAACCTATCAA 57.511 33.333 0.00 0.00 40.90 2.57
1701 1715 8.438676 ACCTATCAATCTTTTCCTAAATCACG 57.561 34.615 0.00 0.00 0.00 4.35
1702 1716 8.047310 ACCTATCAATCTTTTCCTAAATCACGT 58.953 33.333 0.00 0.00 0.00 4.49
1703 1717 9.542462 CCTATCAATCTTTTCCTAAATCACGTA 57.458 33.333 0.00 0.00 0.00 3.57
1711 1725 9.932207 TCTTTTCCTAAATCACGTAATACTTCA 57.068 29.630 0.00 0.00 0.00 3.02
1748 1762 9.740239 ATGGATTGAACGATGAATTTAAATCTG 57.260 29.630 0.10 0.00 0.00 2.90
1749 1763 8.739039 TGGATTGAACGATGAATTTAAATCTGT 58.261 29.630 0.10 0.00 0.00 3.41
1750 1764 9.573133 GGATTGAACGATGAATTTAAATCTGTT 57.427 29.630 0.10 2.76 0.00 3.16
1775 1789 7.426929 ACTAATATTAGCGCATGAAGGAAAG 57.573 36.000 20.24 0.00 34.09 2.62
1971 1988 7.163441 TGGTTAAGTTTCCTAACCATAGACAC 58.837 38.462 9.79 0.00 45.67 3.67
1992 2009 3.558006 ACGTGTTGTCATTTGATGAACGA 59.442 39.130 15.58 0.47 40.37 3.85
2143 2161 1.620819 CTCCCGGATACCAGAGGAATG 59.379 57.143 0.73 0.00 0.00 2.67
2170 2189 3.001838 GTGTGCTATCAAACGTCACAACA 59.998 43.478 5.66 0.00 39.07 3.33
2267 2308 1.660607 CTACGCACACGCAAGATCATT 59.339 47.619 0.00 0.00 45.53 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.622811 GTGGCACAATTTGGGATCCAA 59.377 47.619 15.23 0.00 44.16 3.53
97 101 6.314784 GGTCAATCAAATCTACGACTTTTGG 58.685 40.000 0.00 0.00 32.52 3.28
298 302 9.569122 GGAATATTTTAGTTTGCTCCCATACTA 57.431 33.333 0.00 0.00 35.36 1.82
428 435 0.700564 AGTGTTGCCTGACATGGGAT 59.299 50.000 0.00 0.00 0.00 3.85
514 521 4.689612 TCTACAGAGGAAAAGCAAGTGT 57.310 40.909 0.00 0.00 0.00 3.55
529 536 3.320673 ACCTCCTTCGCTTTTCTACAG 57.679 47.619 0.00 0.00 0.00 2.74
656 665 6.460814 CGAACATTTTCATACCCCATAATGCA 60.461 38.462 0.00 0.00 0.00 3.96
692 701 5.719085 ACCATAGATACCAAGCTGAGATAGG 59.281 44.000 0.00 0.00 0.00 2.57
723 733 2.301870 TCCTTGTGCACTAATCTCCGTT 59.698 45.455 19.41 0.00 0.00 4.44
729 739 7.377766 TGAGTTAATTCCTTGTGCACTAATC 57.622 36.000 19.41 6.77 0.00 1.75
838 850 2.029892 AAGGACATTGCCAACCCCCA 62.030 55.000 0.00 0.00 0.00 4.96
931 944 2.820787 ACCTACCTTTGTCGTCTCTCAG 59.179 50.000 0.00 0.00 0.00 3.35
973 986 1.227639 TCCGCGCAGTAGTCTATCTC 58.772 55.000 8.75 0.00 0.00 2.75
1027 1040 2.165437 CCCTTTGCGCTAAATTTAGGCA 59.835 45.455 25.09 25.09 36.14 4.75
1099 1112 2.038813 TCCTCCGTCCTGCATGGA 59.961 61.111 0.00 1.25 43.86 3.41
1146 1159 5.163374 ACAAGCATAGTGATAGCAGTCATCA 60.163 40.000 0.00 0.00 0.00 3.07
1257 1271 3.253432 GCTCCTCAAACCAATTCGAAGTT 59.747 43.478 3.35 0.00 0.00 2.66
1264 1278 5.888161 CACTAATAGGCTCCTCAAACCAATT 59.112 40.000 0.00 0.00 0.00 2.32
1372 1386 9.088512 GTTGAGTTACATTAGTCTGAATCGATT 57.911 33.333 11.20 11.20 0.00 3.34
1373 1387 7.707035 GGTTGAGTTACATTAGTCTGAATCGAT 59.293 37.037 0.00 0.00 0.00 3.59
1374 1388 7.033791 GGTTGAGTTACATTAGTCTGAATCGA 58.966 38.462 0.00 0.00 0.00 3.59
1375 1389 7.036220 AGGTTGAGTTACATTAGTCTGAATCG 58.964 38.462 0.00 0.00 0.00 3.34
1376 1390 7.221067 CGAGGTTGAGTTACATTAGTCTGAATC 59.779 40.741 0.00 0.00 0.00 2.52
1377 1391 7.036220 CGAGGTTGAGTTACATTAGTCTGAAT 58.964 38.462 0.00 0.00 0.00 2.57
1378 1392 6.015688 ACGAGGTTGAGTTACATTAGTCTGAA 60.016 38.462 0.00 0.00 0.00 3.02
1379 1393 5.475909 ACGAGGTTGAGTTACATTAGTCTGA 59.524 40.000 0.00 0.00 0.00 3.27
1380 1394 5.573282 CACGAGGTTGAGTTACATTAGTCTG 59.427 44.000 0.00 0.00 0.00 3.51
1381 1395 5.710984 CACGAGGTTGAGTTACATTAGTCT 58.289 41.667 0.00 0.00 0.00 3.24
1382 1396 4.326548 GCACGAGGTTGAGTTACATTAGTC 59.673 45.833 0.00 0.00 0.00 2.59
1383 1397 4.243270 GCACGAGGTTGAGTTACATTAGT 58.757 43.478 0.00 0.00 0.00 2.24
1384 1398 3.617263 GGCACGAGGTTGAGTTACATTAG 59.383 47.826 0.00 0.00 0.00 1.73
1385 1399 3.592059 GGCACGAGGTTGAGTTACATTA 58.408 45.455 0.00 0.00 0.00 1.90
1386 1400 2.423577 GGCACGAGGTTGAGTTACATT 58.576 47.619 0.00 0.00 0.00 2.71
1387 1401 1.338769 GGGCACGAGGTTGAGTTACAT 60.339 52.381 0.00 0.00 0.00 2.29
1388 1402 0.034337 GGGCACGAGGTTGAGTTACA 59.966 55.000 0.00 0.00 0.00 2.41
1389 1403 0.672711 GGGGCACGAGGTTGAGTTAC 60.673 60.000 0.00 0.00 0.00 2.50
1390 1404 1.122632 TGGGGCACGAGGTTGAGTTA 61.123 55.000 0.00 0.00 0.00 2.24
1391 1405 1.990160 TTGGGGCACGAGGTTGAGTT 61.990 55.000 0.00 0.00 0.00 3.01
1392 1406 2.448582 TTGGGGCACGAGGTTGAGT 61.449 57.895 0.00 0.00 0.00 3.41
1393 1407 1.966451 GTTGGGGCACGAGGTTGAG 60.966 63.158 0.00 0.00 0.00 3.02
1394 1408 2.063015 ATGTTGGGGCACGAGGTTGA 62.063 55.000 0.00 0.00 0.00 3.18
1395 1409 0.322098 TATGTTGGGGCACGAGGTTG 60.322 55.000 0.00 0.00 0.00 3.77
1396 1410 0.402504 TTATGTTGGGGCACGAGGTT 59.597 50.000 0.00 0.00 0.00 3.50
1397 1411 0.035439 CTTATGTTGGGGCACGAGGT 60.035 55.000 0.00 0.00 0.00 3.85
1398 1412 0.748005 CCTTATGTTGGGGCACGAGG 60.748 60.000 0.00 0.00 0.00 4.63
1399 1413 0.251916 TCCTTATGTTGGGGCACGAG 59.748 55.000 0.00 0.00 0.00 4.18
1400 1414 0.251916 CTCCTTATGTTGGGGCACGA 59.748 55.000 0.00 0.00 0.00 4.35
1401 1415 0.251916 TCTCCTTATGTTGGGGCACG 59.748 55.000 0.00 0.00 0.00 5.34
1402 1416 1.408822 CCTCTCCTTATGTTGGGGCAC 60.409 57.143 0.00 0.00 0.00 5.01
1403 1417 0.918983 CCTCTCCTTATGTTGGGGCA 59.081 55.000 0.00 0.00 0.00 5.36
1404 1418 0.466372 GCCTCTCCTTATGTTGGGGC 60.466 60.000 0.00 0.00 0.00 5.80
1405 1419 0.918983 TGCCTCTCCTTATGTTGGGG 59.081 55.000 0.00 0.00 0.00 4.96
1406 1420 2.025887 AGTTGCCTCTCCTTATGTTGGG 60.026 50.000 0.00 0.00 0.00 4.12
1407 1421 3.274288 GAGTTGCCTCTCCTTATGTTGG 58.726 50.000 0.00 0.00 34.69 3.77
1429 1443 2.327958 AATAGGAGACGGGGAGGGGG 62.328 65.000 0.00 0.00 0.00 5.40
1430 1444 1.122019 CAATAGGAGACGGGGAGGGG 61.122 65.000 0.00 0.00 0.00 4.79
1431 1445 1.122019 CCAATAGGAGACGGGGAGGG 61.122 65.000 0.00 0.00 36.89 4.30
1432 1446 0.398664 ACCAATAGGAGACGGGGAGG 60.399 60.000 0.00 0.00 38.69 4.30
1433 1447 1.962100 GTACCAATAGGAGACGGGGAG 59.038 57.143 0.00 0.00 38.69 4.30
1434 1448 1.751733 CGTACCAATAGGAGACGGGGA 60.752 57.143 0.00 0.00 41.13 4.81
1435 1449 0.672342 CGTACCAATAGGAGACGGGG 59.328 60.000 0.00 0.00 41.13 5.73
1436 1450 1.336125 GTCGTACCAATAGGAGACGGG 59.664 57.143 11.59 0.00 43.31 5.28
1437 1451 2.019249 TGTCGTACCAATAGGAGACGG 58.981 52.381 11.59 0.00 43.31 4.79
1438 1452 3.314357 TGATGTCGTACCAATAGGAGACG 59.686 47.826 0.00 0.00 43.96 4.18
1439 1453 4.913335 TGATGTCGTACCAATAGGAGAC 57.087 45.455 0.00 0.00 38.69 3.36
1440 1454 5.739070 GCAATGATGTCGTACCAATAGGAGA 60.739 44.000 0.00 0.00 38.69 3.71
1441 1455 4.449068 GCAATGATGTCGTACCAATAGGAG 59.551 45.833 0.00 0.00 38.69 3.69
1442 1456 4.100963 AGCAATGATGTCGTACCAATAGGA 59.899 41.667 0.00 0.00 38.69 2.94
1443 1457 4.380531 AGCAATGATGTCGTACCAATAGG 58.619 43.478 0.00 0.00 42.21 2.57
1444 1458 7.148573 GGAATAGCAATGATGTCGTACCAATAG 60.149 40.741 0.00 0.00 0.00 1.73
1445 1459 6.649141 GGAATAGCAATGATGTCGTACCAATA 59.351 38.462 0.00 0.00 0.00 1.90
1446 1460 5.470098 GGAATAGCAATGATGTCGTACCAAT 59.530 40.000 0.00 0.00 0.00 3.16
1447 1461 4.814234 GGAATAGCAATGATGTCGTACCAA 59.186 41.667 0.00 0.00 0.00 3.67
1448 1462 4.141824 TGGAATAGCAATGATGTCGTACCA 60.142 41.667 0.00 0.00 0.00 3.25
1449 1463 4.377021 TGGAATAGCAATGATGTCGTACC 58.623 43.478 0.00 0.00 0.00 3.34
1450 1464 5.984233 TTGGAATAGCAATGATGTCGTAC 57.016 39.130 0.00 0.00 0.00 3.67
1451 1465 7.066887 ACAAATTGGAATAGCAATGATGTCGTA 59.933 33.333 0.00 0.00 0.00 3.43
1452 1466 6.127647 ACAAATTGGAATAGCAATGATGTCGT 60.128 34.615 0.00 0.00 0.00 4.34
1453 1467 6.267817 ACAAATTGGAATAGCAATGATGTCG 58.732 36.000 0.00 0.00 0.00 4.35
1454 1468 6.698766 GGACAAATTGGAATAGCAATGATGTC 59.301 38.462 5.49 5.49 37.52 3.06
1455 1469 6.407299 GGGACAAATTGGAATAGCAATGATGT 60.407 38.462 0.00 0.00 0.00 3.06
1456 1470 5.987347 GGGACAAATTGGAATAGCAATGATG 59.013 40.000 0.00 0.00 0.00 3.07
1457 1471 5.662208 TGGGACAAATTGGAATAGCAATGAT 59.338 36.000 0.00 0.00 31.92 2.45
1458 1472 5.022122 TGGGACAAATTGGAATAGCAATGA 58.978 37.500 0.00 0.00 31.92 2.57
1459 1473 5.341872 TGGGACAAATTGGAATAGCAATG 57.658 39.130 0.00 0.00 31.92 2.82
1476 1490 7.462571 ACTACCTACAAAATTTCAATGGGAC 57.537 36.000 0.00 0.00 0.00 4.46
1477 1491 9.762381 ATAACTACCTACAAAATTTCAATGGGA 57.238 29.630 0.00 0.00 0.00 4.37
1491 1505 8.867097 GGATGTATCCTTCAATAACTACCTACA 58.133 37.037 3.63 0.00 43.73 2.74
1517 1531 1.134946 GCCCATCGAACCAATTCCTTG 59.865 52.381 0.00 0.00 0.00 3.61
1518 1532 1.005924 AGCCCATCGAACCAATTCCTT 59.994 47.619 0.00 0.00 0.00 3.36
1519 1533 0.625849 AGCCCATCGAACCAATTCCT 59.374 50.000 0.00 0.00 0.00 3.36
1520 1534 1.405463 GAAGCCCATCGAACCAATTCC 59.595 52.381 0.00 0.00 0.00 3.01
1521 1535 1.405463 GGAAGCCCATCGAACCAATTC 59.595 52.381 0.00 0.00 0.00 2.17
1522 1536 1.474330 GGAAGCCCATCGAACCAATT 58.526 50.000 0.00 0.00 0.00 2.32
1523 1537 0.748005 CGGAAGCCCATCGAACCAAT 60.748 55.000 0.00 0.00 0.00 3.16
1524 1538 1.376683 CGGAAGCCCATCGAACCAA 60.377 57.895 0.00 0.00 0.00 3.67
1525 1539 2.267642 CGGAAGCCCATCGAACCA 59.732 61.111 0.00 0.00 0.00 3.67
1537 1551 2.107950 TCCAACTGGTTATGCGGAAG 57.892 50.000 0.00 0.00 36.34 3.46
1538 1552 2.224670 ACTTCCAACTGGTTATGCGGAA 60.225 45.455 0.00 0.00 36.34 4.30
1539 1553 1.349688 ACTTCCAACTGGTTATGCGGA 59.650 47.619 0.00 0.00 36.34 5.54
1540 1554 1.821216 ACTTCCAACTGGTTATGCGG 58.179 50.000 0.00 0.00 36.34 5.69
1541 1555 5.597806 TCTATACTTCCAACTGGTTATGCG 58.402 41.667 0.00 0.00 36.34 4.73
1542 1556 8.451908 AAATCTATACTTCCAACTGGTTATGC 57.548 34.615 0.00 0.00 36.34 3.14
1545 1559 9.555727 GCATAAATCTATACTTCCAACTGGTTA 57.444 33.333 0.00 0.00 36.34 2.85
1546 1560 8.052748 TGCATAAATCTATACTTCCAACTGGTT 58.947 33.333 0.00 0.00 36.34 3.67
1547 1561 7.573710 TGCATAAATCTATACTTCCAACTGGT 58.426 34.615 0.00 0.00 36.34 4.00
1548 1562 8.627208 ATGCATAAATCTATACTTCCAACTGG 57.373 34.615 0.00 0.00 0.00 4.00
1568 1582 9.425248 TTTGGAGAAAGGAGATAATTTATGCAT 57.575 29.630 3.79 3.79 29.97 3.96
1569 1583 8.821686 TTTGGAGAAAGGAGATAATTTATGCA 57.178 30.769 0.00 0.00 0.00 3.96
1570 1584 9.688592 CATTTGGAGAAAGGAGATAATTTATGC 57.311 33.333 0.00 0.00 0.00 3.14
1572 1586 8.864087 GCCATTTGGAGAAAGGAGATAATTTAT 58.136 33.333 0.00 0.00 37.39 1.40
1573 1587 8.061304 AGCCATTTGGAGAAAGGAGATAATTTA 58.939 33.333 0.00 0.00 37.39 1.40
1574 1588 6.899631 AGCCATTTGGAGAAAGGAGATAATTT 59.100 34.615 0.00 0.00 37.39 1.82
1575 1589 6.438620 AGCCATTTGGAGAAAGGAGATAATT 58.561 36.000 0.00 0.00 37.39 1.40
1576 1590 6.023334 AGCCATTTGGAGAAAGGAGATAAT 57.977 37.500 0.00 0.00 37.39 1.28
1577 1591 5.044919 TGAGCCATTTGGAGAAAGGAGATAA 60.045 40.000 0.00 0.00 37.39 1.75
1578 1592 4.474651 TGAGCCATTTGGAGAAAGGAGATA 59.525 41.667 0.00 0.00 37.39 1.98
1579 1593 3.267812 TGAGCCATTTGGAGAAAGGAGAT 59.732 43.478 0.00 0.00 37.39 2.75
1580 1594 2.644299 TGAGCCATTTGGAGAAAGGAGA 59.356 45.455 0.00 0.00 37.39 3.71
1581 1595 3.077484 TGAGCCATTTGGAGAAAGGAG 57.923 47.619 0.00 0.00 37.39 3.69
1582 1596 3.157087 GTTGAGCCATTTGGAGAAAGGA 58.843 45.455 0.00 0.00 37.39 3.36
1583 1597 3.160269 AGTTGAGCCATTTGGAGAAAGG 58.840 45.455 0.00 0.00 37.39 3.11
1584 1598 3.120060 CGAGTTGAGCCATTTGGAGAAAG 60.120 47.826 0.00 0.00 37.39 2.62
1585 1599 2.813754 CGAGTTGAGCCATTTGGAGAAA 59.186 45.455 0.00 0.00 37.39 2.52
1586 1600 2.038426 TCGAGTTGAGCCATTTGGAGAA 59.962 45.455 0.00 0.00 37.39 2.87
1587 1601 1.623311 TCGAGTTGAGCCATTTGGAGA 59.377 47.619 0.00 0.00 37.39 3.71
1588 1602 1.734465 GTCGAGTTGAGCCATTTGGAG 59.266 52.381 0.00 0.00 37.39 3.86
1589 1603 1.071542 TGTCGAGTTGAGCCATTTGGA 59.928 47.619 0.00 0.00 37.39 3.53
1590 1604 1.522668 TGTCGAGTTGAGCCATTTGG 58.477 50.000 0.00 0.00 38.53 3.28
1591 1605 2.807967 TCTTGTCGAGTTGAGCCATTTG 59.192 45.455 0.00 0.00 0.00 2.32
1592 1606 3.070018 CTCTTGTCGAGTTGAGCCATTT 58.930 45.455 0.00 0.00 34.95 2.32
1593 1607 2.300152 TCTCTTGTCGAGTTGAGCCATT 59.700 45.455 0.00 0.00 40.75 3.16
1594 1608 1.895798 TCTCTTGTCGAGTTGAGCCAT 59.104 47.619 0.00 0.00 40.75 4.40
1595 1609 1.328279 TCTCTTGTCGAGTTGAGCCA 58.672 50.000 0.00 0.00 40.75 4.75
1596 1610 2.266554 CATCTCTTGTCGAGTTGAGCC 58.733 52.381 0.00 0.00 40.39 4.70
1597 1611 2.266554 CCATCTCTTGTCGAGTTGAGC 58.733 52.381 0.00 0.00 40.39 4.26
1598 1612 2.266554 GCCATCTCTTGTCGAGTTGAG 58.733 52.381 0.00 0.00 40.39 3.02
1599 1613 1.618343 TGCCATCTCTTGTCGAGTTGA 59.382 47.619 0.00 0.00 40.39 3.18
1600 1614 2.084610 TGCCATCTCTTGTCGAGTTG 57.915 50.000 0.00 0.00 40.75 3.16
1601 1615 2.037772 AGTTGCCATCTCTTGTCGAGTT 59.962 45.455 0.00 0.00 40.75 3.01
1602 1616 1.620819 AGTTGCCATCTCTTGTCGAGT 59.379 47.619 0.00 0.00 40.75 4.18
1603 1617 2.376808 AGTTGCCATCTCTTGTCGAG 57.623 50.000 0.00 0.00 41.30 4.04
1604 1618 2.839486 AAGTTGCCATCTCTTGTCGA 57.161 45.000 0.00 0.00 0.00 4.20
1605 1619 2.159787 CGAAAGTTGCCATCTCTTGTCG 60.160 50.000 0.00 0.00 0.00 4.35
1606 1620 2.413371 GCGAAAGTTGCCATCTCTTGTC 60.413 50.000 0.00 0.00 0.00 3.18
1607 1621 1.537202 GCGAAAGTTGCCATCTCTTGT 59.463 47.619 0.00 0.00 0.00 3.16
1608 1622 1.808945 AGCGAAAGTTGCCATCTCTTG 59.191 47.619 0.00 0.00 0.00 3.02
1609 1623 2.079925 GAGCGAAAGTTGCCATCTCTT 58.920 47.619 0.00 0.00 0.00 2.85
1610 1624 1.002430 TGAGCGAAAGTTGCCATCTCT 59.998 47.619 0.00 0.00 0.00 3.10
1611 1625 1.442769 TGAGCGAAAGTTGCCATCTC 58.557 50.000 0.00 0.00 0.00 2.75
1612 1626 1.537202 GTTGAGCGAAAGTTGCCATCT 59.463 47.619 0.00 0.00 0.00 2.90
1613 1627 1.266718 TGTTGAGCGAAAGTTGCCATC 59.733 47.619 0.00 0.00 0.00 3.51
1614 1628 1.267806 CTGTTGAGCGAAAGTTGCCAT 59.732 47.619 0.00 0.00 0.00 4.40
1615 1629 0.662619 CTGTTGAGCGAAAGTTGCCA 59.337 50.000 0.00 0.00 0.00 4.92
1616 1630 0.661483 GCTGTTGAGCGAAAGTTGCC 60.661 55.000 0.00 0.00 34.87 4.52
1617 1631 2.788535 GCTGTTGAGCGAAAGTTGC 58.211 52.632 0.00 0.00 34.87 4.17
1626 1640 0.947244 CATTATCCGGGCTGTTGAGC 59.053 55.000 0.00 0.00 45.40 4.26
1627 1641 0.947244 GCATTATCCGGGCTGTTGAG 59.053 55.000 0.00 0.00 0.00 3.02
1628 1642 0.546122 AGCATTATCCGGGCTGTTGA 59.454 50.000 0.00 0.00 36.34 3.18
1629 1643 1.392589 AAGCATTATCCGGGCTGTTG 58.607 50.000 0.00 0.00 38.04 3.33
1630 1644 3.508845 ATAAGCATTATCCGGGCTGTT 57.491 42.857 0.00 0.00 36.28 3.16
1640 1654 9.995003 CTCCTCTCAACTTTAGATAAGCATTAT 57.005 33.333 0.00 0.00 45.61 1.28
1641 1655 9.201989 TCTCCTCTCAACTTTAGATAAGCATTA 57.798 33.333 0.00 0.00 33.48 1.90
1642 1656 8.083828 TCTCCTCTCAACTTTAGATAAGCATT 57.916 34.615 0.00 0.00 0.00 3.56
1643 1657 7.667575 TCTCCTCTCAACTTTAGATAAGCAT 57.332 36.000 0.00 0.00 0.00 3.79
1644 1658 7.667575 ATCTCCTCTCAACTTTAGATAAGCA 57.332 36.000 0.00 0.00 0.00 3.91
1645 1659 8.956533 AAATCTCCTCTCAACTTTAGATAAGC 57.043 34.615 0.00 0.00 0.00 3.09
1652 1666 9.939802 GGTTTAGTAAATCTCCTCTCAACTTTA 57.060 33.333 0.00 0.00 0.00 1.85
1653 1667 8.661345 AGGTTTAGTAAATCTCCTCTCAACTTT 58.339 33.333 2.36 0.00 0.00 2.66
1654 1668 8.208575 AGGTTTAGTAAATCTCCTCTCAACTT 57.791 34.615 2.36 0.00 0.00 2.66
1655 1669 7.800300 AGGTTTAGTAAATCTCCTCTCAACT 57.200 36.000 2.36 0.00 0.00 3.16
1656 1670 9.752961 GATAGGTTTAGTAAATCTCCTCTCAAC 57.247 37.037 11.73 0.00 33.06 3.18
1657 1671 9.488762 TGATAGGTTTAGTAAATCTCCTCTCAA 57.511 33.333 11.73 0.00 33.06 3.02
1658 1672 9.488762 TTGATAGGTTTAGTAAATCTCCTCTCA 57.511 33.333 11.73 11.69 33.06 3.27
1675 1689 8.893727 CGTGATTTAGGAAAAGATTGATAGGTT 58.106 33.333 0.00 0.00 0.00 3.50
1676 1690 8.047310 ACGTGATTTAGGAAAAGATTGATAGGT 58.953 33.333 0.00 0.00 0.00 3.08
1677 1691 8.438676 ACGTGATTTAGGAAAAGATTGATAGG 57.561 34.615 0.00 0.00 0.00 2.57
1685 1699 9.932207 TGAAGTATTACGTGATTTAGGAAAAGA 57.068 29.630 0.00 0.00 0.00 2.52
1722 1736 9.740239 CAGATTTAAATTCATCGTTCAATCCAT 57.260 29.630 1.43 0.00 0.00 3.41
1723 1737 8.739039 ACAGATTTAAATTCATCGTTCAATCCA 58.261 29.630 1.43 0.00 0.00 3.41
1724 1738 9.573133 AACAGATTTAAATTCATCGTTCAATCC 57.427 29.630 1.43 0.00 0.00 3.01
1742 1756 9.489084 TCATGCGCTAATATTAGTAACAGATTT 57.511 29.630 20.89 3.14 33.32 2.17
1743 1757 9.489084 TTCATGCGCTAATATTAGTAACAGATT 57.511 29.630 20.89 3.42 33.32 2.40
1744 1758 9.144747 CTTCATGCGCTAATATTAGTAACAGAT 57.855 33.333 20.89 5.45 33.32 2.90
1745 1759 7.598869 CCTTCATGCGCTAATATTAGTAACAGA 59.401 37.037 20.89 12.46 33.32 3.41
1746 1760 7.598869 TCCTTCATGCGCTAATATTAGTAACAG 59.401 37.037 20.89 10.73 33.32 3.16
1747 1761 7.438564 TCCTTCATGCGCTAATATTAGTAACA 58.561 34.615 20.89 16.62 33.32 2.41
1748 1762 7.884816 TCCTTCATGCGCTAATATTAGTAAC 57.115 36.000 20.89 12.45 33.32 2.50
1749 1763 8.896320 TTTCCTTCATGCGCTAATATTAGTAA 57.104 30.769 20.89 9.52 33.32 2.24
1750 1764 8.364894 TCTTTCCTTCATGCGCTAATATTAGTA 58.635 33.333 20.89 10.38 33.32 1.82
1751 1765 7.217200 TCTTTCCTTCATGCGCTAATATTAGT 58.783 34.615 20.89 1.52 33.32 2.24
1752 1766 7.658179 TCTTTCCTTCATGCGCTAATATTAG 57.342 36.000 16.79 16.79 0.00 1.73
1753 1767 7.361201 GCATCTTTCCTTCATGCGCTAATATTA 60.361 37.037 9.73 0.00 34.01 0.98
1754 1768 6.569226 GCATCTTTCCTTCATGCGCTAATATT 60.569 38.462 9.73 0.00 34.01 1.28
1755 1769 5.106396 GCATCTTTCCTTCATGCGCTAATAT 60.106 40.000 9.73 0.00 34.01 1.28
1756 1770 4.214119 GCATCTTTCCTTCATGCGCTAATA 59.786 41.667 9.73 0.00 34.01 0.98
1757 1771 3.004106 GCATCTTTCCTTCATGCGCTAAT 59.996 43.478 9.73 0.00 34.01 1.73
1758 1772 2.355756 GCATCTTTCCTTCATGCGCTAA 59.644 45.455 9.73 0.00 34.01 3.09
1759 1773 1.942657 GCATCTTTCCTTCATGCGCTA 59.057 47.619 9.73 0.00 34.01 4.26
1760 1774 0.737219 GCATCTTTCCTTCATGCGCT 59.263 50.000 9.73 0.00 34.01 5.92
1761 1775 0.248784 GGCATCTTTCCTTCATGCGC 60.249 55.000 0.00 0.00 43.32 6.09
1762 1776 0.383231 GGGCATCTTTCCTTCATGCG 59.617 55.000 0.00 0.00 43.32 4.73
1763 1777 1.772836 AGGGCATCTTTCCTTCATGC 58.227 50.000 0.00 0.00 41.93 4.06
1764 1778 4.387598 CTCTAGGGCATCTTTCCTTCATG 58.612 47.826 0.00 0.00 34.75 3.07
1844 1859 9.740710 AAGTTTCCTGTTAATACAATTCTAGCT 57.259 29.630 0.00 0.00 32.92 3.32
1862 1877 5.241403 TCCACACATGTATCAAGTTTCCT 57.759 39.130 0.00 0.00 0.00 3.36
1971 1988 4.084589 TCTCGTTCATCAAATGACAACACG 60.085 41.667 5.83 5.83 39.71 4.49
2105 2123 5.047306 CCGGGAGTTGCATAATCTCATAGTA 60.047 44.000 0.00 0.00 0.00 1.82
2143 2161 1.535462 ACGTTTGATAGCACACAAGGC 59.465 47.619 0.00 0.00 0.00 4.35
2267 2308 2.543641 CTCTCGTTGCTATGCATCACA 58.456 47.619 0.19 0.00 38.76 3.58
2310 2354 2.818432 ACACTTCCGTTGTCGATCTACT 59.182 45.455 0.00 0.00 39.71 2.57


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

AutoCloner maintained by Alex Coulton.