Multiple sequence alignment - TraesCS5A01G517800

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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 TraesCS5A01G517800 chr5A 100.000 2357 0 0 1 2357 680501091 680503447 0.000000e+00 4353
1 TraesCS5A01G517800 chr4B 82.967 1409 117 49 27 1367 642454545 642455898 0.000000e+00 1158
2 TraesCS5A01G517800 chr4B 93.666 742 42 4 1616 2357 642456710 642457446 0.000000e+00 1105
3 TraesCS5A01G517800 chr4D 94.290 683 38 1 1675 2357 499502677 499503358 0.000000e+00 1044
4 TraesCS5A01G517800 chr4D 82.278 1264 104 55 164 1367 499500650 499501853 0.000000e+00 983
5 TraesCS5A01G517800 chr1D 78.523 447 82 6 1916 2349 368319777 368319332 4.960000e-72 281
6 TraesCS5A01G517800 chr1B 78.261 437 78 11 1916 2336 492335584 492335149 4.990000e-67 265


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 TraesCS5A01G517800 chr5A 680501091 680503447 2356 False 4353.0 4353 100.0000 1 2357 1 chr5A.!!$F1 2356
1 TraesCS5A01G517800 chr4B 642454545 642457446 2901 False 1131.5 1158 88.3165 27 2357 2 chr4B.!!$F1 2330
2 TraesCS5A01G517800 chr4D 499500650 499503358 2708 False 1013.5 1044 88.2840 164 2357 2 chr4D.!!$F1 2193

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
533 543 0.033504 AGGAATGCGAAGTGTGTCGT 59.966 50.0 0.0 0.0 43.06 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1746 0.034089 ACCTGGCCCAATACAGAAGC 60.034 55.0 0.0 0.0 36.86 3.86 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
19 20 1.812235 CTGTAATCACTGGCACTGCA 58.188 50.000 2.82 0.00 0.00 4.41
20 21 1.736126 CTGTAATCACTGGCACTGCAG 59.264 52.381 13.48 13.48 0.00 4.41
21 22 0.449388 GTAATCACTGGCACTGCAGC 59.551 55.000 15.27 0.33 0.00 5.25
22 23 0.036590 TAATCACTGGCACTGCAGCA 59.963 50.000 15.27 2.62 35.83 4.41
23 24 0.611062 AATCACTGGCACTGCAGCAT 60.611 50.000 15.27 0.00 35.83 3.79
24 25 1.313091 ATCACTGGCACTGCAGCATG 61.313 55.000 15.27 6.81 40.87 4.06
60 61 5.180868 AGCACAGCTTAGTTTCTCTGAATTG 59.819 40.000 0.00 0.00 33.89 2.32
63 64 5.411053 ACAGCTTAGTTTCTCTGAATTGCTC 59.589 40.000 0.00 0.00 0.00 4.26
129 130 8.484214 TCTCTAAATAGAACTGTATGGCTCAT 57.516 34.615 0.00 0.00 0.00 2.90
130 131 9.588096 TCTCTAAATAGAACTGTATGGCTCATA 57.412 33.333 0.00 0.00 0.00 2.15
131 132 9.632807 CTCTAAATAGAACTGTATGGCTCATAC 57.367 37.037 14.78 14.78 44.74 2.39
132 133 8.297426 TCTAAATAGAACTGTATGGCTCATACG 58.703 37.037 15.92 13.56 46.69 3.06
145 146 2.729467 GCTCATACGTAGCTGATAGCCG 60.729 54.545 0.08 0.00 43.77 5.52
259 260 4.406173 CTCGCGAGCACGACAGGT 62.406 66.667 25.07 0.00 42.66 4.00
396 397 1.227263 CGGGCACATACCTTCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
425 432 0.181114 TGGTGCTGGTGCCTATGATC 59.819 55.000 0.00 0.00 38.71 2.92
430 438 2.440627 TGCTGGTGCCTATGATCATCTT 59.559 45.455 12.53 0.00 38.71 2.40
452 462 1.824852 TGCCTCTGAGCATCGTAGAAA 59.175 47.619 0.00 0.00 43.58 2.52
453 463 2.432146 TGCCTCTGAGCATCGTAGAAAT 59.568 45.455 0.00 0.00 43.58 2.17
454 464 2.799412 GCCTCTGAGCATCGTAGAAATG 59.201 50.000 0.00 0.00 43.58 2.32
455 465 3.739519 GCCTCTGAGCATCGTAGAAATGT 60.740 47.826 0.00 0.00 43.58 2.71
456 466 4.437239 CCTCTGAGCATCGTAGAAATGTT 58.563 43.478 0.00 0.00 43.58 2.71
508 518 7.651027 AAAATGCTACTGGCTCATCTTTTAT 57.349 32.000 0.00 0.00 42.39 1.40
533 543 0.033504 AGGAATGCGAAGTGTGTCGT 59.966 50.000 0.00 0.00 43.06 4.34
535 545 1.136690 GAATGCGAAGTGTGTCGTCA 58.863 50.000 0.00 0.00 43.06 4.35
540 550 2.353269 TGCGAAGTGTGTCGTCATTTTT 59.647 40.909 0.00 0.00 43.06 1.94
541 551 2.964768 GCGAAGTGTGTCGTCATTTTTC 59.035 45.455 0.00 0.00 43.06 2.29
544 554 4.446234 GAAGTGTGTCGTCATTTTTCTCG 58.554 43.478 0.00 0.00 0.00 4.04
547 557 2.798283 TGTGTCGTCATTTTTCTCGTCC 59.202 45.455 0.00 0.00 0.00 4.79
548 558 3.057734 GTGTCGTCATTTTTCTCGTCCT 58.942 45.455 0.00 0.00 0.00 3.85
549 559 3.121445 GTGTCGTCATTTTTCTCGTCCTC 59.879 47.826 0.00 0.00 0.00 3.71
550 560 3.005472 TGTCGTCATTTTTCTCGTCCTCT 59.995 43.478 0.00 0.00 0.00 3.69
551 561 3.608939 GTCGTCATTTTTCTCGTCCTCTC 59.391 47.826 0.00 0.00 0.00 3.20
552 562 2.924290 CGTCATTTTTCTCGTCCTCTCC 59.076 50.000 0.00 0.00 0.00 3.71
553 563 3.367498 CGTCATTTTTCTCGTCCTCTCCT 60.367 47.826 0.00 0.00 0.00 3.69
554 564 3.929610 GTCATTTTTCTCGTCCTCTCCTG 59.070 47.826 0.00 0.00 0.00 3.86
555 565 3.578716 TCATTTTTCTCGTCCTCTCCTGT 59.421 43.478 0.00 0.00 0.00 4.00
556 566 3.662247 TTTTTCTCGTCCTCTCCTGTC 57.338 47.619 0.00 0.00 0.00 3.51
557 567 1.166129 TTTCTCGTCCTCTCCTGTCG 58.834 55.000 0.00 0.00 0.00 4.35
580 590 5.051441 CGATTTGCCAGATCGGATAATATCG 60.051 44.000 9.58 11.97 41.89 2.92
581 591 5.400066 TTTGCCAGATCGGATAATATCGA 57.600 39.130 7.64 0.00 39.79 3.59
582 592 4.371855 TGCCAGATCGGATAATATCGAC 57.628 45.455 7.64 0.00 38.25 4.20
583 593 3.181500 TGCCAGATCGGATAATATCGACG 60.181 47.826 7.64 0.00 38.25 5.12
584 594 3.364062 CCAGATCGGATAATATCGACGC 58.636 50.000 0.00 0.00 38.25 5.19
585 595 3.364062 CAGATCGGATAATATCGACGCC 58.636 50.000 0.00 0.00 38.25 5.68
586 596 2.358267 AGATCGGATAATATCGACGCCC 59.642 50.000 0.00 0.00 38.25 6.13
587 597 0.448990 TCGGATAATATCGACGCCCG 59.551 55.000 0.00 0.00 40.25 6.13
588 598 0.169672 CGGATAATATCGACGCCCGT 59.830 55.000 0.00 0.00 39.75 5.28
589 599 1.398041 CGGATAATATCGACGCCCGTA 59.602 52.381 0.00 0.00 39.75 4.02
590 600 2.159531 CGGATAATATCGACGCCCGTAA 60.160 50.000 0.00 0.00 39.75 3.18
591 601 3.670359 CGGATAATATCGACGCCCGTAAA 60.670 47.826 0.00 0.00 39.75 2.01
608 618 2.282701 AAATGCGCGCTCATCATTTT 57.717 40.000 33.29 15.90 37.17 1.82
610 620 1.019673 ATGCGCGCTCATCATTTTCT 58.980 45.000 33.29 0.00 0.00 2.52
612 622 1.186030 GCGCGCTCATCATTTTCTTG 58.814 50.000 26.67 0.00 0.00 3.02
613 623 1.202065 GCGCGCTCATCATTTTCTTGA 60.202 47.619 26.67 0.00 0.00 3.02
614 624 2.701807 CGCGCTCATCATTTTCTTGAG 58.298 47.619 5.56 0.00 39.87 3.02
620 630 6.327934 CGCTCATCATTTTCTTGAGGAATTT 58.672 36.000 0.00 0.00 36.14 1.82
634 644 4.222588 TGAGGAATTTAAACCTTGCCATGG 59.777 41.667 7.63 7.63 36.57 3.66
635 645 3.519107 AGGAATTTAAACCTTGCCATGGG 59.481 43.478 15.13 0.00 31.95 4.00
649 659 3.984193 ATGGGCGCTGTTGGAGAGC 62.984 63.158 7.64 0.00 46.21 4.09
655 665 1.336240 GCGCTGTTGGAGAGCAAATTT 60.336 47.619 0.00 0.00 46.20 1.82
657 667 2.680577 GCTGTTGGAGAGCAAATTTGG 58.319 47.619 19.47 2.11 36.40 3.28
694 710 6.691508 AGCCACAAGAAATCCAGTTTTAATC 58.308 36.000 0.00 0.00 0.00 1.75
700 716 8.695456 ACAAGAAATCCAGTTTTAATCAACACT 58.305 29.630 0.00 0.00 0.00 3.55
701 717 9.533253 CAAGAAATCCAGTTTTAATCAACACTT 57.467 29.630 0.00 0.00 0.00 3.16
708 724 9.126151 TCCAGTTTTAATCAACACTTAATGACA 57.874 29.630 0.00 0.00 0.00 3.58
709 725 9.743057 CCAGTTTTAATCAACACTTAATGACAA 57.257 29.630 0.00 0.00 0.00 3.18
822 847 3.439857 TGCAGGGAAGAAAATAGCACT 57.560 42.857 0.00 0.00 0.00 4.40
830 855 1.672881 AGAAAATAGCACTGCGCCATC 59.327 47.619 4.18 0.00 44.04 3.51
835 860 1.016627 TAGCACTGCGCCATCAATTC 58.983 50.000 4.18 0.00 44.04 2.17
836 861 1.584483 GCACTGCGCCATCAATTCG 60.584 57.895 4.18 0.00 32.94 3.34
938 991 2.029020 GGGAATCACTCCTTGCCAAAAC 60.029 50.000 0.00 0.00 44.68 2.43
976 1032 3.552068 CCAAAAACATTCCCGTTCTGTCC 60.552 47.826 0.00 0.00 0.00 4.02
1028 1101 5.968387 ATAAAACGGCTACGAGAAATCTG 57.032 39.130 0.00 0.00 44.60 2.90
1029 1102 1.641577 AACGGCTACGAGAAATCTGC 58.358 50.000 0.00 0.00 44.60 4.26
1046 1141 4.335584 CCTCTCTCGCCGCGATCC 62.336 72.222 17.22 0.00 34.61 3.36
1048 1143 3.126074 CTCTCTCGCCGCGATCCAA 62.126 63.158 17.22 1.69 34.61 3.53
1049 1144 2.202743 CTCTCGCCGCGATCCAAA 60.203 61.111 17.22 0.00 34.61 3.28
1050 1145 2.202743 TCTCGCCGCGATCCAAAG 60.203 61.111 17.22 3.35 34.61 2.77
1051 1146 2.509336 CTCGCCGCGATCCAAAGT 60.509 61.111 17.22 0.00 34.61 2.66
1097 1192 4.965858 GACCGATCGAGCGAGGCG 62.966 72.222 26.68 10.27 0.00 5.52
1099 1194 4.674904 CCGATCGAGCGAGGCGAG 62.675 72.222 26.68 1.94 41.49 5.03
1387 1531 2.554806 CATGCATGCATCTTCGTTGT 57.445 45.000 30.07 4.31 33.90 3.32
1389 1533 3.247442 CATGCATGCATCTTCGTTGTTT 58.753 40.909 30.07 2.89 33.90 2.83
1391 1535 3.307674 TGCATGCATCTTCGTTGTTTTC 58.692 40.909 18.46 0.00 0.00 2.29
1392 1536 3.243334 TGCATGCATCTTCGTTGTTTTCA 60.243 39.130 18.46 0.00 0.00 2.69
1396 1555 5.180367 TGCATCTTCGTTGTTTTCATTCA 57.820 34.783 0.00 0.00 0.00 2.57
1404 1563 7.643764 TCTTCGTTGTTTTCATTCATTCTTGTC 59.356 33.333 0.00 0.00 0.00 3.18
1408 1567 5.451908 TGTTTTCATTCATTCTTGTCTCGC 58.548 37.500 0.00 0.00 0.00 5.03
1409 1568 3.997319 TTCATTCATTCTTGTCTCGCG 57.003 42.857 0.00 0.00 0.00 5.87
1410 1569 3.230743 TCATTCATTCTTGTCTCGCGA 57.769 42.857 9.26 9.26 0.00 5.87
1418 1577 1.543941 CTTGTCTCGCGATCGCATCC 61.544 60.000 36.45 21.74 42.06 3.51
1422 1581 1.665916 CTCGCGATCGCATCCCATT 60.666 57.895 36.45 0.00 42.06 3.16
1423 1582 1.621301 CTCGCGATCGCATCCCATTC 61.621 60.000 36.45 7.19 42.06 2.67
1427 1586 2.143122 GCGATCGCATCCCATTCTTTA 58.857 47.619 33.89 0.00 41.49 1.85
1430 1589 4.670221 GCGATCGCATCCCATTCTTTATTC 60.670 45.833 33.89 0.00 41.49 1.75
1441 1601 7.343357 TCCCATTCTTTATTCGTAGGATTGTT 58.657 34.615 0.00 0.00 0.00 2.83
1442 1602 7.282224 TCCCATTCTTTATTCGTAGGATTGTTG 59.718 37.037 0.00 0.00 0.00 3.33
1443 1603 7.067008 CCCATTCTTTATTCGTAGGATTGTTGT 59.933 37.037 0.00 0.00 0.00 3.32
1444 1604 8.458843 CCATTCTTTATTCGTAGGATTGTTGTT 58.541 33.333 0.00 0.00 0.00 2.83
1445 1605 9.840427 CATTCTTTATTCGTAGGATTGTTGTTT 57.160 29.630 0.00 0.00 0.00 2.83
1453 1620 5.086058 CGTAGGATTGTTGTTTGTATGTGC 58.914 41.667 0.00 0.00 0.00 4.57
1454 1621 4.519540 AGGATTGTTGTTTGTATGTGCC 57.480 40.909 0.00 0.00 0.00 5.01
1459 1626 7.613801 AGGATTGTTGTTTGTATGTGCCTAATA 59.386 33.333 0.00 0.00 0.00 0.98
1463 1630 5.224562 TGTTTGTATGTGCCTAATAACGC 57.775 39.130 0.00 0.00 0.00 4.84
1467 1634 0.462937 ATGTGCCTAATAACGCGCCA 60.463 50.000 5.73 0.00 34.58 5.69
1471 1638 0.941542 GCCTAATAACGCGCCATTGA 59.058 50.000 5.73 0.00 0.00 2.57
1473 1640 2.739913 GCCTAATAACGCGCCATTGATA 59.260 45.455 5.73 0.00 0.00 2.15
1474 1641 3.424433 GCCTAATAACGCGCCATTGATAC 60.424 47.826 5.73 0.00 0.00 2.24
1478 1645 1.151777 AACGCGCCATTGATACGAGG 61.152 55.000 5.73 0.00 0.00 4.63
1479 1646 1.299850 CGCGCCATTGATACGAGGA 60.300 57.895 0.00 0.00 0.00 3.71
1480 1647 1.278172 CGCGCCATTGATACGAGGAG 61.278 60.000 0.00 0.00 0.00 3.69
1481 1648 0.032130 GCGCCATTGATACGAGGAGA 59.968 55.000 0.00 0.00 0.00 3.71
1482 1649 1.337260 GCGCCATTGATACGAGGAGAT 60.337 52.381 0.00 0.00 0.00 2.75
1483 1650 2.600731 CGCCATTGATACGAGGAGATC 58.399 52.381 0.00 0.00 0.00 2.75
1484 1651 2.230025 CGCCATTGATACGAGGAGATCT 59.770 50.000 0.00 0.00 0.00 2.75
1485 1652 3.671971 CGCCATTGATACGAGGAGATCTC 60.672 52.174 14.75 14.75 39.10 2.75
1486 1653 3.509575 GCCATTGATACGAGGAGATCTCT 59.490 47.826 21.81 8.41 40.30 3.10
1487 1654 4.380444 GCCATTGATACGAGGAGATCTCTC 60.380 50.000 21.81 15.30 40.30 3.20
1497 1664 1.805428 GAGATCTCTCCAGAGCGGCC 61.805 65.000 15.80 0.00 40.26 6.13
1504 1671 4.292178 CCAGAGCGGCCGAGGATC 62.292 72.222 33.48 19.98 0.00 3.36
1516 1683 2.984871 GAGGATCGAAGGAAGCAGC 58.015 57.895 0.00 0.00 0.00 5.25
1517 1684 0.463620 GAGGATCGAAGGAAGCAGCT 59.536 55.000 0.00 0.00 0.00 4.24
1518 1685 0.177604 AGGATCGAAGGAAGCAGCTG 59.822 55.000 10.11 10.11 0.00 4.24
1519 1686 0.107945 GGATCGAAGGAAGCAGCTGT 60.108 55.000 16.64 0.00 0.00 4.40
1520 1687 1.005340 GATCGAAGGAAGCAGCTGTG 58.995 55.000 16.64 0.00 0.00 3.66
1521 1688 0.392193 ATCGAAGGAAGCAGCTGTGG 60.392 55.000 16.64 0.00 0.00 4.17
1522 1689 2.037136 CGAAGGAAGCAGCTGTGGG 61.037 63.158 16.64 0.00 0.00 4.61
1523 1690 2.282745 AAGGAAGCAGCTGTGGGC 60.283 61.111 16.64 0.00 42.19 5.36
1543 1710 6.015940 GTGGGCTGGATTCCAATAAGAAATAG 60.016 42.308 6.88 0.00 34.47 1.73
1544 1711 6.071320 GGGCTGGATTCCAATAAGAAATAGT 58.929 40.000 6.88 0.00 30.80 2.12
1546 1713 7.175119 GGGCTGGATTCCAATAAGAAATAGTAC 59.825 40.741 6.88 0.00 30.80 2.73
1547 1714 7.939588 GGCTGGATTCCAATAAGAAATAGTACT 59.060 37.037 6.88 0.00 30.80 2.73
1548 1715 9.998106 GCTGGATTCCAATAAGAAATAGTACTA 57.002 33.333 6.88 4.77 30.80 1.82
1551 1718 9.438228 GGATTCCAATAAGAAATAGTACTAGGC 57.562 37.037 8.85 0.46 0.00 3.93
1552 1719 9.998106 GATTCCAATAAGAAATAGTACTAGGCA 57.002 33.333 8.85 0.00 0.00 4.75
1553 1720 9.780186 ATTCCAATAAGAAATAGTACTAGGCAC 57.220 33.333 8.85 0.65 0.00 5.01
1554 1721 7.431249 TCCAATAAGAAATAGTACTAGGCACG 58.569 38.462 8.85 0.00 0.00 5.34
1555 1722 7.069085 TCCAATAAGAAATAGTACTAGGCACGT 59.931 37.037 8.85 1.79 0.00 4.49
1556 1723 7.381678 CCAATAAGAAATAGTACTAGGCACGTC 59.618 40.741 8.85 0.02 0.00 4.34
1557 1724 5.909621 AAGAAATAGTACTAGGCACGTCA 57.090 39.130 8.85 0.00 0.00 4.35
1558 1725 5.909621 AGAAATAGTACTAGGCACGTCAA 57.090 39.130 8.85 0.00 0.00 3.18
1559 1726 6.276832 AGAAATAGTACTAGGCACGTCAAA 57.723 37.500 8.85 0.00 0.00 2.69
1560 1727 6.331061 AGAAATAGTACTAGGCACGTCAAAG 58.669 40.000 8.85 0.00 0.00 2.77
1561 1728 5.909621 AATAGTACTAGGCACGTCAAAGA 57.090 39.130 8.85 0.00 0.00 2.52
1562 1729 5.909621 ATAGTACTAGGCACGTCAAAGAA 57.090 39.130 8.85 0.00 0.00 2.52
1563 1730 4.595762 AGTACTAGGCACGTCAAAGAAA 57.404 40.909 0.00 0.00 0.00 2.52
1564 1731 4.952460 AGTACTAGGCACGTCAAAGAAAA 58.048 39.130 0.00 0.00 0.00 2.29
1565 1732 4.989168 AGTACTAGGCACGTCAAAGAAAAG 59.011 41.667 0.00 0.00 0.00 2.27
1566 1733 4.067972 ACTAGGCACGTCAAAGAAAAGA 57.932 40.909 0.00 0.00 0.00 2.52
1567 1734 4.448210 ACTAGGCACGTCAAAGAAAAGAA 58.552 39.130 0.00 0.00 0.00 2.52
1568 1735 4.879545 ACTAGGCACGTCAAAGAAAAGAAA 59.120 37.500 0.00 0.00 0.00 2.52
1569 1736 4.918810 AGGCACGTCAAAGAAAAGAAAT 57.081 36.364 0.00 0.00 0.00 2.17
1570 1737 6.708949 ACTAGGCACGTCAAAGAAAAGAAATA 59.291 34.615 0.00 0.00 0.00 1.40
1571 1738 6.002062 AGGCACGTCAAAGAAAAGAAATAG 57.998 37.500 0.00 0.00 0.00 1.73
1572 1739 5.531287 AGGCACGTCAAAGAAAAGAAATAGT 59.469 36.000 0.00 0.00 0.00 2.12
1573 1740 6.708949 AGGCACGTCAAAGAAAAGAAATAGTA 59.291 34.615 0.00 0.00 0.00 1.82
1574 1741 7.015877 GGCACGTCAAAGAAAAGAAATAGTAG 58.984 38.462 0.00 0.00 0.00 2.57
1575 1742 6.520104 GCACGTCAAAGAAAAGAAATAGTAGC 59.480 38.462 0.00 0.00 0.00 3.58
1576 1743 7.572759 CACGTCAAAGAAAAGAAATAGTAGCA 58.427 34.615 0.00 0.00 0.00 3.49
1577 1744 7.742089 CACGTCAAAGAAAAGAAATAGTAGCAG 59.258 37.037 0.00 0.00 0.00 4.24
1578 1745 7.095187 ACGTCAAAGAAAAGAAATAGTAGCAGG 60.095 37.037 0.00 0.00 0.00 4.85
1579 1746 7.530863 GTCAAAGAAAAGAAATAGTAGCAGGG 58.469 38.462 0.00 0.00 0.00 4.45
1580 1747 6.151144 TCAAAGAAAAGAAATAGTAGCAGGGC 59.849 38.462 0.00 0.00 0.00 5.19
1581 1748 5.443230 AGAAAAGAAATAGTAGCAGGGCT 57.557 39.130 0.00 0.00 43.41 5.19
1582 1749 5.821097 AGAAAAGAAATAGTAGCAGGGCTT 58.179 37.500 0.00 0.00 40.44 4.35
1590 1757 3.550437 AGTAGCAGGGCTTCTGTATTG 57.450 47.619 0.00 0.00 45.08 1.90
1597 1764 0.753111 GGCTTCTGTATTGGGCCAGG 60.753 60.000 6.23 0.00 42.08 4.45
1603 1770 2.092429 TCTGTATTGGGCCAGGTGATTC 60.092 50.000 6.23 0.00 0.00 2.52
1604 1771 1.922447 TGTATTGGGCCAGGTGATTCT 59.078 47.619 6.23 0.00 0.00 2.40
1607 1775 3.756082 ATTGGGCCAGGTGATTCTTTA 57.244 42.857 6.23 0.00 0.00 1.85
1608 1776 2.806945 TGGGCCAGGTGATTCTTTAG 57.193 50.000 0.00 0.00 0.00 1.85
1609 1777 1.284785 TGGGCCAGGTGATTCTTTAGG 59.715 52.381 0.00 0.00 0.00 2.69
1610 1778 1.285078 GGGCCAGGTGATTCTTTAGGT 59.715 52.381 4.39 0.00 0.00 3.08
1613 1781 3.561313 GGCCAGGTGATTCTTTAGGTGAA 60.561 47.826 0.00 0.00 0.00 3.18
1675 2429 4.631813 GGTCGTAGTCTTCCTAGTCGTTTA 59.368 45.833 0.00 0.00 0.00 2.01
1676 2430 5.446607 GGTCGTAGTCTTCCTAGTCGTTTAC 60.447 48.000 0.00 0.00 0.00 2.01
1690 2444 4.043761 TCGTTTACTTGACGAAATTCGC 57.956 40.909 15.90 8.90 45.45 4.70
1691 2445 3.490155 TCGTTTACTTGACGAAATTCGCA 59.510 39.130 15.90 11.41 45.45 5.10
1756 2510 3.182372 GCACGAGTCTTCCAAAATTTTGC 59.818 43.478 22.90 10.62 36.86 3.68
1758 2512 4.442073 CACGAGTCTTCCAAAATTTTGCTG 59.558 41.667 22.90 14.87 36.86 4.41
1817 2571 1.211212 CACCTGATCCTTGATCCTGCA 59.789 52.381 1.88 0.00 38.20 4.41
1884 2638 0.895530 TCTTACCTGCAGGGAACTCG 59.104 55.000 35.42 21.82 40.21 4.18
1932 2686 1.882623 GAGTGTTCCTCCAGCCTTTTG 59.117 52.381 0.00 0.00 33.79 2.44
1935 2689 2.034685 GTGTTCCTCCAGCCTTTTGTTC 59.965 50.000 0.00 0.00 0.00 3.18
1944 2698 1.404035 AGCCTTTTGTTCAACACGTCC 59.596 47.619 0.00 0.00 0.00 4.79
2087 2841 0.464036 TTTCCCGATGGTGATCTCCG 59.536 55.000 9.20 0.00 0.00 4.63
2239 2993 4.825422 CACACCAGCTATATGATACCAGG 58.175 47.826 0.00 0.00 0.00 4.45
2248 3002 5.104527 GCTATATGATACCAGGCCCATGTAA 60.105 44.000 0.00 0.00 0.00 2.41
2253 3007 5.276440 TGATACCAGGCCCATGTAATTTTT 58.724 37.500 0.00 0.00 0.00 1.94
2265 3019 5.861787 CCATGTAATTTTTCGGTTCCACTTC 59.138 40.000 0.00 0.00 0.00 3.01
2282 3036 2.866762 ACTTCGTGTTCTTTGAGAGTGC 59.133 45.455 0.00 0.00 0.00 4.40
2290 3044 0.947244 CTTTGAGAGTGCCGCACTTT 59.053 50.000 26.38 21.26 45.44 2.66
2292 3046 0.179059 TTGAGAGTGCCGCACTTTGA 60.179 50.000 26.38 13.24 45.44 2.69
2336 3090 1.461127 GTGGATTCAGCAACGTCTCAC 59.539 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.812235 CTGCAGTGCCAGTGATTACA 58.188 50.000 13.72 0.00 0.00 2.41
3 4 0.036590 TGCTGCAGTGCCAGTGATTA 59.963 50.000 16.64 0.00 35.28 1.75
5 6 1.001269 ATGCTGCAGTGCCAGTGAT 60.001 52.632 16.64 4.45 35.28 3.06
6 7 1.969589 CATGCTGCAGTGCCAGTGA 60.970 57.895 16.64 2.36 35.28 3.41
7 8 2.566529 CATGCTGCAGTGCCAGTG 59.433 61.111 16.64 2.59 35.28 3.66
8 9 3.371063 GCATGCTGCAGTGCCAGT 61.371 61.111 16.64 0.00 44.26 4.00
17 18 0.742505 TTCTTATGCTGGCATGCTGC 59.257 50.000 18.92 21.23 44.08 5.25
18 19 1.269102 GCTTCTTATGCTGGCATGCTG 60.269 52.381 18.92 12.01 37.82 4.41
19 20 1.030457 GCTTCTTATGCTGGCATGCT 58.970 50.000 18.92 0.00 37.82 3.79
20 21 0.742505 TGCTTCTTATGCTGGCATGC 59.257 50.000 17.09 9.90 37.82 4.06
21 22 1.746787 TGTGCTTCTTATGCTGGCATG 59.253 47.619 17.09 2.84 37.82 4.06
22 23 2.022195 CTGTGCTTCTTATGCTGGCAT 58.978 47.619 12.76 12.76 40.19 4.40
23 24 1.456296 CTGTGCTTCTTATGCTGGCA 58.544 50.000 0.00 0.00 0.00 4.92
24 25 0.100146 GCTGTGCTTCTTATGCTGGC 59.900 55.000 0.00 0.00 0.00 4.85
25 26 1.747709 AGCTGTGCTTCTTATGCTGG 58.252 50.000 0.00 0.00 33.89 4.85
26 27 3.937706 ACTAAGCTGTGCTTCTTATGCTG 59.062 43.478 8.14 0.00 46.77 4.41
27 28 4.213564 ACTAAGCTGTGCTTCTTATGCT 57.786 40.909 8.14 0.00 46.77 3.79
28 29 4.954092 AACTAAGCTGTGCTTCTTATGC 57.046 40.909 8.14 0.00 46.77 3.14
29 30 6.593382 AGAGAAACTAAGCTGTGCTTCTTATG 59.407 38.462 8.14 0.00 46.77 1.90
30 31 6.593382 CAGAGAAACTAAGCTGTGCTTCTTAT 59.407 38.462 8.14 0.00 46.77 1.73
31 32 5.928839 CAGAGAAACTAAGCTGTGCTTCTTA 59.071 40.000 8.14 0.00 46.77 2.10
32 33 4.754114 CAGAGAAACTAAGCTGTGCTTCTT 59.246 41.667 8.14 1.70 46.77 2.52
71 72 9.855361 CATATGTTAATTCAGAGAAACTAAGCG 57.145 33.333 0.00 0.00 0.00 4.68
122 123 2.229062 GCTATCAGCTACGTATGAGCCA 59.771 50.000 5.20 0.00 41.06 4.75
129 130 4.572909 TCTATTCGGCTATCAGCTACGTA 58.427 43.478 0.00 0.00 41.99 3.57
130 131 3.409570 TCTATTCGGCTATCAGCTACGT 58.590 45.455 0.00 0.00 41.99 3.57
131 132 4.624336 ATCTATTCGGCTATCAGCTACG 57.376 45.455 0.00 0.00 41.99 3.51
132 133 4.564769 GCAATCTATTCGGCTATCAGCTAC 59.435 45.833 0.00 0.00 41.99 3.58
145 146 8.261492 TCTCTCAGTTTTCTTGCAATCTATTC 57.739 34.615 0.00 0.00 0.00 1.75
194 195 7.340232 CCTGTGATTAGGAGGAAAATGATTTCA 59.660 37.037 3.97 0.00 42.14 2.69
202 203 2.569853 TCGCCTGTGATTAGGAGGAAAA 59.430 45.455 0.00 0.00 40.42 2.29
211 212 3.904800 TTCCATCTTCGCCTGTGATTA 57.095 42.857 0.00 0.00 0.00 1.75
216 217 2.859165 TTCTTTCCATCTTCGCCTGT 57.141 45.000 0.00 0.00 0.00 4.00
396 397 0.035630 ACCAGCACCAGCAAGAGATC 60.036 55.000 0.00 0.00 45.49 2.75
452 462 6.072673 GGTCGTTTTCAGGAGAAACATAACAT 60.073 38.462 0.00 0.00 43.09 2.71
453 463 5.237779 GGTCGTTTTCAGGAGAAACATAACA 59.762 40.000 0.00 0.00 43.09 2.41
454 464 5.237779 TGGTCGTTTTCAGGAGAAACATAAC 59.762 40.000 0.00 0.00 43.09 1.89
455 465 5.369833 TGGTCGTTTTCAGGAGAAACATAA 58.630 37.500 0.00 0.00 43.09 1.90
456 466 4.963373 TGGTCGTTTTCAGGAGAAACATA 58.037 39.130 0.00 0.00 43.09 2.29
522 532 4.025979 ACGAGAAAAATGACGACACACTTC 60.026 41.667 0.00 0.00 0.00 3.01
533 543 3.578716 ACAGGAGAGGACGAGAAAAATGA 59.421 43.478 0.00 0.00 0.00 2.57
535 545 3.367498 CGACAGGAGAGGACGAGAAAAAT 60.367 47.826 0.00 0.00 0.00 1.82
540 550 0.542333 ATCGACAGGAGAGGACGAGA 59.458 55.000 0.00 0.00 36.49 4.04
541 551 1.384525 AATCGACAGGAGAGGACGAG 58.615 55.000 0.00 0.00 36.49 4.18
544 554 1.646189 GCAAATCGACAGGAGAGGAC 58.354 55.000 0.00 0.00 0.00 3.85
547 557 3.840831 TGGCAAATCGACAGGAGAG 57.159 52.632 0.00 0.00 0.00 3.20
553 563 0.534873 TCCGATCTGGCAAATCGACA 59.465 50.000 23.82 7.67 46.89 4.35
554 564 1.871080 ATCCGATCTGGCAAATCGAC 58.129 50.000 23.82 0.00 46.89 4.20
555 565 3.744238 TTATCCGATCTGGCAAATCGA 57.256 42.857 23.82 10.72 46.89 3.59
556 566 5.051441 CGATATTATCCGATCTGGCAAATCG 60.051 44.000 16.02 16.02 44.29 3.34
557 567 6.019479 GTCGATATTATCCGATCTGGCAAATC 60.019 42.308 0.00 0.00 37.14 2.17
585 595 1.083401 GATGAGCGCGCATTTACGG 60.083 57.895 35.10 0.00 0.00 4.02
586 596 0.233074 ATGATGAGCGCGCATTTACG 59.767 50.000 35.10 0.00 0.00 3.18
587 597 2.389713 AATGATGAGCGCGCATTTAC 57.610 45.000 35.10 19.59 0.00 2.01
588 598 3.065233 AGAAAATGATGAGCGCGCATTTA 59.935 39.130 35.10 19.23 40.28 1.40
589 599 2.159338 AGAAAATGATGAGCGCGCATTT 60.159 40.909 35.10 25.04 42.25 2.32
590 600 1.402968 AGAAAATGATGAGCGCGCATT 59.597 42.857 35.10 20.54 33.96 3.56
591 601 1.019673 AGAAAATGATGAGCGCGCAT 58.980 45.000 35.10 27.04 0.00 4.73
596 606 4.952262 TTCCTCAAGAAAATGATGAGCG 57.048 40.909 0.00 0.00 39.36 5.03
597 607 9.643693 TTTAAATTCCTCAAGAAAATGATGAGC 57.356 29.630 0.00 0.00 39.36 4.26
608 618 5.144100 TGGCAAGGTTTAAATTCCTCAAGA 58.856 37.500 0.00 0.00 33.09 3.02
610 620 5.279910 CCATGGCAAGGTTTAAATTCCTCAA 60.280 40.000 0.00 0.00 33.09 3.02
612 622 4.383010 CCCATGGCAAGGTTTAAATTCCTC 60.383 45.833 6.09 0.00 33.09 3.71
613 623 3.519107 CCCATGGCAAGGTTTAAATTCCT 59.481 43.478 6.09 0.00 35.34 3.36
614 624 3.872696 CCCATGGCAAGGTTTAAATTCC 58.127 45.455 6.09 0.00 0.00 3.01
634 644 1.589716 ATTTGCTCTCCAACAGCGCC 61.590 55.000 2.29 0.00 40.01 6.53
635 645 0.242017 AATTTGCTCTCCAACAGCGC 59.758 50.000 0.00 0.00 40.01 5.92
639 649 2.037901 TGCCAAATTTGCTCTCCAACA 58.962 42.857 12.92 0.00 31.97 3.33
640 650 2.818130 TGCCAAATTTGCTCTCCAAC 57.182 45.000 12.92 0.00 31.97 3.77
655 665 8.932434 TTCTTGTGGCTATAAATATAATGCCA 57.068 30.769 8.54 8.54 46.59 4.92
675 691 9.533253 AAGTGTTGATTAAAACTGGATTTCTTG 57.467 29.630 0.00 0.00 0.00 3.02
780 796 6.252967 CATTCATGCACTGGTAGTACAAAA 57.747 37.500 2.06 0.00 0.00 2.44
781 797 5.878332 CATTCATGCACTGGTAGTACAAA 57.122 39.130 2.06 0.00 0.00 2.83
799 822 4.400567 AGTGCTATTTTCTTCCCTGCATTC 59.599 41.667 0.00 0.00 0.00 2.67
804 827 2.096496 CGCAGTGCTATTTTCTTCCCTG 59.904 50.000 14.33 0.00 0.00 4.45
811 836 1.401552 TGATGGCGCAGTGCTATTTTC 59.598 47.619 14.33 4.46 45.89 2.29
855 880 9.214957 CGCTCACTAATTCCACCATTATTATTA 57.785 33.333 0.00 0.00 0.00 0.98
856 881 7.174946 CCGCTCACTAATTCCACCATTATTATT 59.825 37.037 0.00 0.00 0.00 1.40
976 1032 4.135153 CCGCCCGTGGAGACAGAG 62.135 72.222 0.00 0.00 44.46 3.35
995 1051 5.333568 CGTAGCCGTTTTATTTATACAGGGC 60.334 44.000 0.00 0.00 38.29 5.19
996 1052 5.984926 TCGTAGCCGTTTTATTTATACAGGG 59.015 40.000 0.00 0.00 35.01 4.45
1028 1101 4.992294 GATCGCGGCGAGAGAGGC 62.992 72.222 29.64 11.06 39.91 4.70
1029 1102 4.335584 GGATCGCGGCGAGAGAGG 62.336 72.222 29.64 0.00 39.91 3.69
1046 1141 1.268625 GCGTTAGGGTTTGGGACTTTG 59.731 52.381 0.00 0.00 0.00 2.77
1048 1143 0.604511 CGCGTTAGGGTTTGGGACTT 60.605 55.000 0.00 0.00 0.00 3.01
1049 1144 1.004200 CGCGTTAGGGTTTGGGACT 60.004 57.895 0.00 0.00 0.00 3.85
1050 1145 0.603439 TTCGCGTTAGGGTTTGGGAC 60.603 55.000 5.77 0.00 0.00 4.46
1051 1146 0.603439 GTTCGCGTTAGGGTTTGGGA 60.603 55.000 5.77 0.00 0.00 4.37
1096 1191 4.227134 CATCCCGACCCTGCCTCG 62.227 72.222 0.00 0.00 0.00 4.63
1097 1192 2.143419 ATCATCCCGACCCTGCCTC 61.143 63.158 0.00 0.00 0.00 4.70
1098 1193 2.040464 ATCATCCCGACCCTGCCT 60.040 61.111 0.00 0.00 0.00 4.75
1099 1194 2.111878 CATCATCCCGACCCTGCC 59.888 66.667 0.00 0.00 0.00 4.85
1382 1526 6.085458 CGAGACAAGAATGAATGAAAACAACG 59.915 38.462 0.00 0.00 0.00 4.10
1383 1527 6.129352 GCGAGACAAGAATGAATGAAAACAAC 60.129 38.462 0.00 0.00 0.00 3.32
1384 1528 5.914635 GCGAGACAAGAATGAATGAAAACAA 59.085 36.000 0.00 0.00 0.00 2.83
1385 1529 5.451908 GCGAGACAAGAATGAATGAAAACA 58.548 37.500 0.00 0.00 0.00 2.83
1386 1530 4.551126 CGCGAGACAAGAATGAATGAAAAC 59.449 41.667 0.00 0.00 0.00 2.43
1387 1531 4.450757 TCGCGAGACAAGAATGAATGAAAA 59.549 37.500 3.71 0.00 33.31 2.29
1389 1533 3.584834 TCGCGAGACAAGAATGAATGAA 58.415 40.909 3.71 0.00 33.31 2.57
1391 1535 3.361435 CGATCGCGAGACAAGAATGAATG 60.361 47.826 16.66 0.00 46.97 2.67
1392 1536 2.791560 CGATCGCGAGACAAGAATGAAT 59.208 45.455 16.66 0.00 46.97 2.57
1396 1555 0.179137 TGCGATCGCGAGACAAGAAT 60.179 50.000 32.64 0.00 46.97 2.40
1404 1563 1.621301 GAATGGGATGCGATCGCGAG 61.621 60.000 32.64 2.31 44.36 5.03
1408 1567 4.434725 CGAATAAAGAATGGGATGCGATCG 60.435 45.833 11.69 11.69 0.00 3.69
1409 1568 4.452455 ACGAATAAAGAATGGGATGCGATC 59.548 41.667 0.00 0.00 0.00 3.69
1410 1569 4.389374 ACGAATAAAGAATGGGATGCGAT 58.611 39.130 0.00 0.00 0.00 4.58
1418 1577 7.985476 ACAACAATCCTACGAATAAAGAATGG 58.015 34.615 0.00 0.00 0.00 3.16
1422 1581 8.385898 ACAAACAACAATCCTACGAATAAAGA 57.614 30.769 0.00 0.00 0.00 2.52
1427 1586 7.526608 CACATACAAACAACAATCCTACGAAT 58.473 34.615 0.00 0.00 0.00 3.34
1430 1589 5.086058 GCACATACAAACAACAATCCTACG 58.914 41.667 0.00 0.00 0.00 3.51
1441 1601 4.201734 CGCGTTATTAGGCACATACAAACA 60.202 41.667 0.00 0.00 34.90 2.83
1442 1602 4.268522 CGCGTTATTAGGCACATACAAAC 58.731 43.478 0.00 0.00 34.90 2.93
1443 1603 3.242478 GCGCGTTATTAGGCACATACAAA 60.242 43.478 8.43 0.00 34.90 2.83
1444 1604 2.285756 GCGCGTTATTAGGCACATACAA 59.714 45.455 8.43 0.00 34.90 2.41
1445 1605 1.862201 GCGCGTTATTAGGCACATACA 59.138 47.619 8.43 0.00 34.90 2.29
1453 1620 3.181534 CGTATCAATGGCGCGTTATTAGG 60.182 47.826 8.43 0.00 0.00 2.69
1454 1621 3.671459 TCGTATCAATGGCGCGTTATTAG 59.329 43.478 8.43 4.64 0.00 1.73
1459 1626 1.151777 CCTCGTATCAATGGCGCGTT 61.152 55.000 8.43 0.00 0.00 4.84
1463 1630 2.230025 AGATCTCCTCGTATCAATGGCG 59.770 50.000 0.00 0.00 0.00 5.69
1478 1645 1.659794 GCCGCTCTGGAGAGATCTC 59.340 63.158 15.29 15.29 44.74 2.75
1479 1646 1.832167 GGCCGCTCTGGAGAGATCT 60.832 63.158 7.89 0.00 44.74 2.75
1480 1647 2.733945 GGCCGCTCTGGAGAGATC 59.266 66.667 7.89 0.00 44.74 2.75
1481 1648 3.222855 CGGCCGCTCTGGAGAGAT 61.223 66.667 14.67 0.00 44.74 2.75
1482 1649 4.426313 TCGGCCGCTCTGGAGAGA 62.426 66.667 23.51 0.00 44.74 3.10
1483 1650 3.898509 CTCGGCCGCTCTGGAGAG 61.899 72.222 23.51 5.96 44.75 3.20
1486 1653 4.841617 ATCCTCGGCCGCTCTGGA 62.842 66.667 23.51 23.56 42.00 3.86
1487 1654 4.292178 GATCCTCGGCCGCTCTGG 62.292 72.222 23.51 19.09 42.50 3.86
1488 1655 4.637489 CGATCCTCGGCCGCTCTG 62.637 72.222 23.51 10.27 36.00 3.35
1489 1656 4.877619 TCGATCCTCGGCCGCTCT 62.878 66.667 23.51 4.40 40.88 4.09
1490 1657 3.832720 CTTCGATCCTCGGCCGCTC 62.833 68.421 23.51 13.18 40.88 5.03
1492 1659 4.951963 CCTTCGATCCTCGGCCGC 62.952 72.222 23.51 4.66 40.88 6.53
1497 1664 0.873743 GCTGCTTCCTTCGATCCTCG 60.874 60.000 0.00 0.00 42.10 4.63
1504 1671 2.037136 CCCACAGCTGCTTCCTTCG 61.037 63.158 15.27 0.00 0.00 3.79
1505 1672 2.338785 GCCCACAGCTGCTTCCTTC 61.339 63.158 15.27 0.00 38.99 3.46
1515 1682 0.685458 ATTGGAATCCAGCCCACAGC 60.685 55.000 0.86 0.00 44.25 4.40
1516 1683 2.734755 TATTGGAATCCAGCCCACAG 57.265 50.000 0.86 0.00 33.81 3.66
1517 1684 2.580322 TCTTATTGGAATCCAGCCCACA 59.420 45.455 0.86 0.00 33.81 4.17
1518 1685 3.297134 TCTTATTGGAATCCAGCCCAC 57.703 47.619 0.86 0.00 33.81 4.61
1519 1686 4.329638 TTTCTTATTGGAATCCAGCCCA 57.670 40.909 0.86 0.00 33.81 5.36
1520 1687 6.071320 ACTATTTCTTATTGGAATCCAGCCC 58.929 40.000 0.86 0.00 33.81 5.19
1521 1688 7.939588 AGTACTATTTCTTATTGGAATCCAGCC 59.060 37.037 0.86 0.00 33.81 4.85
1522 1689 8.910351 AGTACTATTTCTTATTGGAATCCAGC 57.090 34.615 0.86 0.00 33.81 4.85
1531 1698 7.919091 TGACGTGCCTAGTACTATTTCTTATTG 59.081 37.037 2.33 0.00 0.00 1.90
1543 1710 4.986659 TCTTTTCTTTGACGTGCCTAGTAC 59.013 41.667 0.00 0.00 0.00 2.73
1544 1711 5.204409 TCTTTTCTTTGACGTGCCTAGTA 57.796 39.130 0.00 0.00 0.00 1.82
1546 1713 5.418310 TTTCTTTTCTTTGACGTGCCTAG 57.582 39.130 0.00 0.00 0.00 3.02
1547 1714 6.708949 ACTATTTCTTTTCTTTGACGTGCCTA 59.291 34.615 0.00 0.00 0.00 3.93
1548 1715 4.918810 ATTTCTTTTCTTTGACGTGCCT 57.081 36.364 0.00 0.00 0.00 4.75
1549 1716 5.758924 ACTATTTCTTTTCTTTGACGTGCC 58.241 37.500 0.00 0.00 0.00 5.01
1550 1717 6.520104 GCTACTATTTCTTTTCTTTGACGTGC 59.480 38.462 0.00 0.00 0.00 5.34
1551 1718 7.572759 TGCTACTATTTCTTTTCTTTGACGTG 58.427 34.615 0.00 0.00 0.00 4.49
1552 1719 7.095187 CCTGCTACTATTTCTTTTCTTTGACGT 60.095 37.037 0.00 0.00 0.00 4.34
1553 1720 7.237173 CCTGCTACTATTTCTTTTCTTTGACG 58.763 38.462 0.00 0.00 0.00 4.35
1554 1721 7.530863 CCCTGCTACTATTTCTTTTCTTTGAC 58.469 38.462 0.00 0.00 0.00 3.18
1555 1722 6.151144 GCCCTGCTACTATTTCTTTTCTTTGA 59.849 38.462 0.00 0.00 0.00 2.69
1556 1723 6.151817 AGCCCTGCTACTATTTCTTTTCTTTG 59.848 38.462 0.00 0.00 36.99 2.77
1557 1724 6.249192 AGCCCTGCTACTATTTCTTTTCTTT 58.751 36.000 0.00 0.00 36.99 2.52
1558 1725 5.821097 AGCCCTGCTACTATTTCTTTTCTT 58.179 37.500 0.00 0.00 36.99 2.52
1559 1726 5.443230 AGCCCTGCTACTATTTCTTTTCT 57.557 39.130 0.00 0.00 36.99 2.52
1560 1727 5.883115 AGAAGCCCTGCTACTATTTCTTTTC 59.117 40.000 0.00 0.00 38.25 2.29
1561 1728 5.649831 CAGAAGCCCTGCTACTATTTCTTTT 59.350 40.000 0.00 0.00 38.25 2.27
1562 1729 5.189180 CAGAAGCCCTGCTACTATTTCTTT 58.811 41.667 0.00 0.00 38.25 2.52
1563 1730 4.226168 ACAGAAGCCCTGCTACTATTTCTT 59.774 41.667 3.85 0.00 46.81 2.52
1564 1731 3.777522 ACAGAAGCCCTGCTACTATTTCT 59.222 43.478 3.85 0.00 46.81 2.52
1565 1732 4.143986 ACAGAAGCCCTGCTACTATTTC 57.856 45.455 3.85 0.00 46.81 2.17
1566 1733 5.896073 ATACAGAAGCCCTGCTACTATTT 57.104 39.130 3.85 0.00 46.81 1.40
1567 1734 5.455326 CCAATACAGAAGCCCTGCTACTATT 60.455 44.000 3.85 0.00 46.81 1.73
1568 1735 4.040952 CCAATACAGAAGCCCTGCTACTAT 59.959 45.833 3.85 0.00 46.81 2.12
1569 1736 3.388024 CCAATACAGAAGCCCTGCTACTA 59.612 47.826 3.85 0.00 46.81 1.82
1570 1737 2.171448 CCAATACAGAAGCCCTGCTACT 59.829 50.000 3.85 0.00 46.81 2.57
1571 1738 2.565841 CCAATACAGAAGCCCTGCTAC 58.434 52.381 3.85 0.00 46.81 3.58
1572 1739 1.490490 CCCAATACAGAAGCCCTGCTA 59.510 52.381 3.85 0.00 46.81 3.49
1573 1740 0.257039 CCCAATACAGAAGCCCTGCT 59.743 55.000 3.85 0.00 46.81 4.24
1574 1741 1.387295 GCCCAATACAGAAGCCCTGC 61.387 60.000 3.85 0.00 46.81 4.85
1576 1743 1.214305 TGGCCCAATACAGAAGCCCT 61.214 55.000 0.00 0.00 43.18 5.19
1577 1744 0.753111 CTGGCCCAATACAGAAGCCC 60.753 60.000 0.00 0.00 43.18 5.19
1578 1745 0.753111 CCTGGCCCAATACAGAAGCC 60.753 60.000 0.00 0.00 44.13 4.35
1579 1746 0.034089 ACCTGGCCCAATACAGAAGC 60.034 55.000 0.00 0.00 36.86 3.86
1580 1747 1.281867 TCACCTGGCCCAATACAGAAG 59.718 52.381 0.00 0.00 36.86 2.85
1581 1748 1.367346 TCACCTGGCCCAATACAGAA 58.633 50.000 0.00 0.00 36.86 3.02
1582 1749 1.595311 ATCACCTGGCCCAATACAGA 58.405 50.000 0.00 0.00 36.86 3.41
1590 1757 1.285078 ACCTAAAGAATCACCTGGCCC 59.715 52.381 0.00 0.00 0.00 5.80
1630 2384 0.533032 TTGGTATGATGCGTGGTCGA 59.467 50.000 0.00 0.00 39.71 4.20
1632 2386 1.062002 CGTTTGGTATGATGCGTGGTC 59.938 52.381 0.00 0.00 0.00 4.02
1633 2387 1.083489 CGTTTGGTATGATGCGTGGT 58.917 50.000 0.00 0.00 0.00 4.16
1635 2389 3.895806 CCGTTTGGTATGATGCGTG 57.104 52.632 0.00 0.00 0.00 5.34
1675 2429 1.531149 CACCTGCGAATTTCGTCAAGT 59.469 47.619 19.10 13.82 42.81 3.16
1676 2430 1.798223 TCACCTGCGAATTTCGTCAAG 59.202 47.619 19.10 13.78 42.81 3.02
1690 2444 3.011818 TCAGCAAATGTAGCATCACCTG 58.988 45.455 0.00 0.00 0.00 4.00
1691 2445 3.012518 GTCAGCAAATGTAGCATCACCT 58.987 45.455 0.00 0.00 0.00 4.00
1740 2494 2.476241 CGGCAGCAAAATTTTGGAAGAC 59.524 45.455 27.60 13.53 38.57 3.01
1756 2510 3.242091 CGTCATGAATTGTTCTACGGCAG 60.242 47.826 0.00 0.00 31.89 4.85
1758 2512 2.927477 TCGTCATGAATTGTTCTACGGC 59.073 45.455 0.00 0.00 34.31 5.68
1817 2571 1.150536 ACCATTGCCACCGTCAAGT 59.849 52.632 0.00 0.00 0.00 3.16
1929 2683 1.661617 CTGACGGACGTGTTGAACAAA 59.338 47.619 0.00 0.00 0.00 2.83
1932 2686 1.563173 GCTGACGGACGTGTTGAAC 59.437 57.895 0.53 0.00 0.00 3.18
1944 2698 3.669036 CTCGAGGACACCGCTGACG 62.669 68.421 3.91 0.00 39.67 4.35
2087 2841 1.719780 CAAGGCTAACGTTGTCGAGAC 59.280 52.381 11.99 1.66 40.62 3.36
2155 2909 3.254411 TGGTGAGCGATGATCTACTGATC 59.746 47.826 0.00 0.00 46.89 2.92
2239 2993 3.056465 TGGAACCGAAAAATTACATGGGC 60.056 43.478 0.00 0.00 0.00 5.36
2265 3019 0.508641 CGGCACTCTCAAAGAACACG 59.491 55.000 0.00 0.00 0.00 4.49
2290 3044 2.661537 CCGTTCAGTGTGCGCTCA 60.662 61.111 9.73 8.97 0.00 4.26
2299 3053 1.538135 ACCCCTTAGCCCGTTCAGT 60.538 57.895 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.