Multiple sequence alignment - TraesCS2A01G132800

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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 TraesCS2A01G132800 chr2A 100.000 2297 0 0 1 2297 79746810 79749106 0.000000e+00 4242.0
1 TraesCS2A01G132800 chr2D 94.868 682 23 9 1625 2297 79418109 79418787 0.000000e+00 1055.0
2 TraesCS2A01G132800 chr2D 95.245 652 27 3 754 1402 644702282 644702932 0.000000e+00 1029.0
3 TraesCS2A01G132800 chr2D 94.939 652 29 3 754 1402 635068599 635067949 0.000000e+00 1018.0
4 TraesCS2A01G132800 chr2D 91.787 694 39 4 754 1444 39720624 39721302 0.000000e+00 950.0
5 TraesCS2A01G132800 chr2D 90.500 600 50 2 1 597 524085546 524084951 0.000000e+00 785.0
6 TraesCS2A01G132800 chr2D 94.891 137 7 0 618 754 524084879 524084743 4.970000e-52 215.0
7 TraesCS2A01G132800 chr7D 95.092 652 28 3 754 1402 626649283 626649933 0.000000e+00 1024.0
8 TraesCS2A01G132800 chr7D 90.818 599 53 1 1 599 530641266 530641862 0.000000e+00 800.0
9 TraesCS2A01G132800 chr7D 90.610 607 50 3 1 605 126665812 126665211 0.000000e+00 798.0
10 TraesCS2A01G132800 chr7D 90.452 597 53 3 1 596 532597953 532598546 0.000000e+00 784.0
11 TraesCS2A01G132800 chr7D 90.167 600 49 6 1 599 199908709 199909299 0.000000e+00 773.0
12 TraesCS2A01G132800 chr7D 86.400 375 23 13 408 755 220211795 220211422 3.580000e-103 385.0
13 TraesCS2A01G132800 chr7D 94.558 147 7 1 612 758 532598615 532598760 2.300000e-55 226.0
14 TraesCS2A01G132800 chr7D 97.368 38 1 0 1407 1444 626649924 626649961 5.300000e-07 65.8
15 TraesCS2A01G132800 chrUn 94.939 652 29 3 754 1402 45099810 45100460 0.000000e+00 1018.0
16 TraesCS2A01G132800 chrUn 94.939 652 29 3 754 1402 261514046 261513396 0.000000e+00 1018.0
17 TraesCS2A01G132800 chrUn 92.075 694 32 5 754 1444 186162802 186163475 0.000000e+00 955.0
18 TraesCS2A01G132800 chrUn 86.082 194 10 3 1253 1444 365031619 365031441 2.330000e-45 193.0
19 TraesCS2A01G132800 chrUn 95.455 44 2 0 1401 1444 261513411 261513368 1.140000e-08 71.3
20 TraesCS2A01G132800 chrUn 97.368 38 1 0 1407 1444 45100451 45100488 5.300000e-07 65.8
21 TraesCS2A01G132800 chr5B 94.939 652 29 3 754 1402 130613919 130614569 0.000000e+00 1018.0
22 TraesCS2A01G132800 chr5B 90.232 604 52 3 4 605 373759060 373758462 0.000000e+00 782.0
23 TraesCS2A01G132800 chr3D 94.939 652 29 3 754 1402 602890783 602890133 0.000000e+00 1018.0
24 TraesCS2A01G132800 chr3D 91.391 604 47 2 2 605 359690547 359689949 0.000000e+00 822.0
25 TraesCS2A01G132800 chr3D 92.517 147 8 3 612 757 480960108 480959964 8.320000e-50 207.0
26 TraesCS2A01G132800 chr3A 94.939 652 29 3 754 1402 725776859 725776209 0.000000e+00 1018.0
27 TraesCS2A01G132800 chr3A 93.750 144 8 1 612 755 77489250 77489108 4.970000e-52 215.0
28 TraesCS2A01G132800 chr7B 94.785 652 30 3 754 1402 743034682 743034032 0.000000e+00 1013.0
29 TraesCS2A01G132800 chr7B 95.455 44 2 0 1401 1444 743034047 743034004 1.140000e-08 71.3
30 TraesCS2A01G132800 chr1A 92.507 694 34 6 754 1444 334091876 334092554 0.000000e+00 977.0
31 TraesCS2A01G132800 chr2B 92.846 671 25 13 1648 2297 129664346 129663678 0.000000e+00 952.0
32 TraesCS2A01G132800 chr1D 90.115 607 53 3 1 605 32761355 32760754 0.000000e+00 782.0
33 TraesCS2A01G132800 chr5D 90.388 593 53 2 13 605 51510206 51509618 0.000000e+00 776.0
34 TraesCS2A01G132800 chr6D 94.521 146 7 1 612 757 211690147 211690291 8.260000e-55 224.0
35 TraesCS2A01G132800 chr6D 93.662 142 8 1 612 753 392572821 392572681 6.430000e-51 211.0
36 TraesCS2A01G132800 chr1B 93.103 145 9 1 612 756 460573634 460573491 6.430000e-51 211.0
37 TraesCS2A01G132800 chr4D 94.161 137 6 2 612 748 506343878 506344012 8.320000e-50 207.0
38 TraesCS2A01G132800 chr4A 95.455 44 2 0 1401 1444 48698483 48698526 1.140000e-08 71.3


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 TraesCS2A01G132800 chr2A 79746810 79749106 2296 False 4242.00 4242 100.0000 1 2297 1 chr2A.!!$F1 2296
1 TraesCS2A01G132800 chr2D 79418109 79418787 678 False 1055.00 1055 94.8680 1625 2297 1 chr2D.!!$F2 672
2 TraesCS2A01G132800 chr2D 644702282 644702932 650 False 1029.00 1029 95.2450 754 1402 1 chr2D.!!$F3 648
3 TraesCS2A01G132800 chr2D 635067949 635068599 650 True 1018.00 1018 94.9390 754 1402 1 chr2D.!!$R1 648
4 TraesCS2A01G132800 chr2D 39720624 39721302 678 False 950.00 950 91.7870 754 1444 1 chr2D.!!$F1 690
5 TraesCS2A01G132800 chr2D 524084743 524085546 803 True 500.00 785 92.6955 1 754 2 chr2D.!!$R2 753
6 TraesCS2A01G132800 chr7D 530641266 530641862 596 False 800.00 800 90.8180 1 599 1 chr7D.!!$F2 598
7 TraesCS2A01G132800 chr7D 126665211 126665812 601 True 798.00 798 90.6100 1 605 1 chr7D.!!$R1 604
8 TraesCS2A01G132800 chr7D 199908709 199909299 590 False 773.00 773 90.1670 1 599 1 chr7D.!!$F1 598
9 TraesCS2A01G132800 chr7D 626649283 626649961 678 False 544.90 1024 96.2300 754 1444 2 chr7D.!!$F4 690
10 TraesCS2A01G132800 chr7D 532597953 532598760 807 False 505.00 784 92.5050 1 758 2 chr7D.!!$F3 757
11 TraesCS2A01G132800 chrUn 186162802 186163475 673 False 955.00 955 92.0750 754 1444 1 chrUn.!!$F1 690
12 TraesCS2A01G132800 chrUn 261513368 261514046 678 True 544.65 1018 95.1970 754 1444 2 chrUn.!!$R2 690
13 TraesCS2A01G132800 chrUn 45099810 45100488 678 False 541.90 1018 96.1535 754 1444 2 chrUn.!!$F2 690
14 TraesCS2A01G132800 chr5B 130613919 130614569 650 False 1018.00 1018 94.9390 754 1402 1 chr5B.!!$F1 648
15 TraesCS2A01G132800 chr5B 373758462 373759060 598 True 782.00 782 90.2320 4 605 1 chr5B.!!$R1 601
16 TraesCS2A01G132800 chr3D 602890133 602890783 650 True 1018.00 1018 94.9390 754 1402 1 chr3D.!!$R3 648
17 TraesCS2A01G132800 chr3D 359689949 359690547 598 True 822.00 822 91.3910 2 605 1 chr3D.!!$R1 603
18 TraesCS2A01G132800 chr3A 725776209 725776859 650 True 1018.00 1018 94.9390 754 1402 1 chr3A.!!$R2 648
19 TraesCS2A01G132800 chr7B 743034004 743034682 678 True 542.15 1013 95.1200 754 1444 2 chr7B.!!$R1 690
20 TraesCS2A01G132800 chr1A 334091876 334092554 678 False 977.00 977 92.5070 754 1444 1 chr1A.!!$F1 690
21 TraesCS2A01G132800 chr2B 129663678 129664346 668 True 952.00 952 92.8460 1648 2297 1 chr2B.!!$R1 649
22 TraesCS2A01G132800 chr1D 32760754 32761355 601 True 782.00 782 90.1150 1 605 1 chr1D.!!$R1 604
23 TraesCS2A01G132800 chr5D 51509618 51510206 588 True 776.00 776 90.3880 13 605 1 chr5D.!!$R1 592

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
842 903 0.105964 TTGCACGTGTGGTTCTAGCT 59.894 50.0 18.38 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2397 0.478072 ATGTTCTGGTGGAAGGTGCA 59.522 50.0 0.0 0.0 34.23 4.57 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
179 180 3.295973 CAACAGGAGAAAACCCTTGGAA 58.704 45.455 0.00 0.00 0.00 3.53
388 393 1.073199 CAGGTTCCTGCCCGAGTTT 59.927 57.895 5.89 0.00 0.00 2.66
402 407 2.679996 GTTTTGGAGCCCGGCCAT 60.680 61.111 5.55 0.00 34.90 4.40
520 525 4.154347 CGGTGAGGCAGAGAGGGC 62.154 72.222 0.00 0.00 0.00 5.19
576 586 4.282496 GAGAGTGGAGGGAGTTATGAGAA 58.718 47.826 0.00 0.00 0.00 2.87
696 757 1.833934 AGCCCAGGCAACCAAACAG 60.834 57.895 12.03 0.00 44.88 3.16
697 758 2.871253 GCCCAGGCAACCAAACAGG 61.871 63.158 3.12 0.00 41.75 4.00
698 759 2.736531 CCAGGCAACCAAACAGGC 59.263 61.111 0.00 0.00 43.14 4.85
699 760 2.736531 CAGGCAACCAAACAGGCC 59.263 61.111 0.00 0.00 46.77 5.19
701 762 2.421314 GGCAACCAAACAGGCCAC 59.579 61.111 5.01 0.00 45.70 5.01
702 763 2.027460 GCAACCAAACAGGCCACG 59.973 61.111 5.01 0.00 43.14 4.94
703 764 2.027460 CAACCAAACAGGCCACGC 59.973 61.111 5.01 0.00 43.14 5.34
704 765 2.441164 AACCAAACAGGCCACGCA 60.441 55.556 5.01 0.00 43.14 5.24
705 766 2.781158 AACCAAACAGGCCACGCAC 61.781 57.895 5.01 0.00 43.14 5.34
706 767 3.215568 CCAAACAGGCCACGCACA 61.216 61.111 5.01 0.00 0.00 4.57
707 768 2.563798 CCAAACAGGCCACGCACAT 61.564 57.895 5.01 0.00 0.00 3.21
708 769 1.081242 CAAACAGGCCACGCACATC 60.081 57.895 5.01 0.00 0.00 3.06
709 770 2.268076 AAACAGGCCACGCACATCC 61.268 57.895 5.01 0.00 0.00 3.51
710 771 4.722700 ACAGGCCACGCACATCCC 62.723 66.667 5.01 0.00 0.00 3.85
735 796 3.766691 CCTGGTTGGGCTGCATGC 61.767 66.667 11.82 11.82 41.94 4.06
736 797 4.124351 CTGGTTGGGCTGCATGCG 62.124 66.667 14.09 9.16 44.05 4.73
757 818 1.081708 CAACCAAACGCGCCCTTAC 60.082 57.895 5.73 0.00 0.00 2.34
760 821 2.686816 CCAAACGCGCCCTTACTGG 61.687 63.158 5.73 0.00 0.00 4.00
775 836 1.183676 ACTGGTCGGTCCGCTAGTTT 61.184 55.000 15.44 0.00 39.52 2.66
839 900 2.319136 AACTTGCACGTGTGGTTCTA 57.681 45.000 18.38 0.00 0.00 2.10
842 903 0.105964 TTGCACGTGTGGTTCTAGCT 59.894 50.000 18.38 0.00 0.00 3.32
876 937 5.850614 TCGGTATCTAATAACCTTGCTTCC 58.149 41.667 0.00 0.00 33.34 3.46
919 980 7.725844 CCTCTCCTAACTATTGCCCATTTATTT 59.274 37.037 0.00 0.00 0.00 1.40
992 1054 9.305555 TCTTCTATTATTAAGTACGGCTGGTAT 57.694 33.333 0.00 0.00 32.74 2.73
1011 1073 5.062934 TGGTATCATTTCGATGTGTTTCGAC 59.937 40.000 0.00 0.00 46.94 4.20
1080 1142 4.160642 TCCACTTCCTACTCGCAGTATA 57.839 45.455 0.00 0.00 29.08 1.47
1162 1224 9.469807 AAAGTTTATGTTTTTATGTGATCGCAA 57.530 25.926 13.91 0.03 0.00 4.85
1166 1228 8.978564 TTATGTTTTTATGTGATCGCAACATT 57.021 26.923 22.03 7.01 35.53 2.71
1198 1260 1.202348 CTGAATTTTCCACGGAAGCCC 59.798 52.381 0.00 0.00 35.38 5.19
1382 1488 2.017782 GCTGTGTCTCGATCTCCTACA 58.982 52.381 0.00 0.00 0.00 2.74
1383 1489 2.223386 GCTGTGTCTCGATCTCCTACAC 60.223 54.545 9.32 9.32 40.61 2.90
1384 1490 3.010420 CTGTGTCTCGATCTCCTACACA 58.990 50.000 15.08 15.08 45.88 3.72
1385 1491 3.621558 TGTGTCTCGATCTCCTACACAT 58.378 45.455 13.05 0.00 43.90 3.21
1386 1492 3.378427 TGTGTCTCGATCTCCTACACATG 59.622 47.826 13.05 0.00 43.90 3.21
1387 1493 3.628032 GTGTCTCGATCTCCTACACATGA 59.372 47.826 0.00 0.00 40.08 3.07
1388 1494 4.096532 GTGTCTCGATCTCCTACACATGAA 59.903 45.833 0.00 0.00 40.08 2.57
1389 1495 4.705023 TGTCTCGATCTCCTACACATGAAA 59.295 41.667 0.00 0.00 0.00 2.69
1390 1496 5.163612 TGTCTCGATCTCCTACACATGAAAG 60.164 44.000 0.00 0.00 0.00 2.62
1391 1497 5.066634 GTCTCGATCTCCTACACATGAAAGA 59.933 44.000 0.00 0.00 0.00 2.52
1392 1498 5.830457 TCTCGATCTCCTACACATGAAAGAT 59.170 40.000 0.00 0.00 0.00 2.40
1393 1499 6.998673 TCTCGATCTCCTACACATGAAAGATA 59.001 38.462 0.00 0.00 0.00 1.98
1394 1500 7.502561 TCTCGATCTCCTACACATGAAAGATAA 59.497 37.037 0.00 0.00 0.00 1.75
1395 1501 7.652727 TCGATCTCCTACACATGAAAGATAAG 58.347 38.462 0.00 0.00 0.00 1.73
1396 1502 7.502561 TCGATCTCCTACACATGAAAGATAAGA 59.497 37.037 0.00 0.00 0.00 2.10
1397 1503 8.303156 CGATCTCCTACACATGAAAGATAAGAT 58.697 37.037 0.00 0.00 0.00 2.40
1399 1505 8.539117 TCTCCTACACATGAAAGATAAGATCA 57.461 34.615 0.00 0.00 0.00 2.92
1405 1511 7.743104 ACACATGAAAGATAAGATCACGAAAC 58.257 34.615 0.00 0.00 0.00 2.78
1435 1541 1.400530 GGAGACGGGGTCCTATGGTG 61.401 65.000 0.00 0.00 32.18 4.17
1444 1550 2.474112 GGTCCTATGGTGTGGGTCTTA 58.526 52.381 0.00 0.00 0.00 2.10
1445 1551 2.841881 GGTCCTATGGTGTGGGTCTTAA 59.158 50.000 0.00 0.00 0.00 1.85
1446 1552 3.458487 GGTCCTATGGTGTGGGTCTTAAT 59.542 47.826 0.00 0.00 0.00 1.40
1447 1553 4.079958 GGTCCTATGGTGTGGGTCTTAATT 60.080 45.833 0.00 0.00 0.00 1.40
1448 1554 5.123936 GTCCTATGGTGTGGGTCTTAATTC 58.876 45.833 0.00 0.00 0.00 2.17
1449 1555 4.165372 TCCTATGGTGTGGGTCTTAATTCC 59.835 45.833 0.00 0.00 0.00 3.01
1450 1556 4.080015 CCTATGGTGTGGGTCTTAATTCCA 60.080 45.833 0.00 0.00 0.00 3.53
1455 1561 1.997606 GTGGGTCTTAATTCCACGACG 59.002 52.381 0.00 0.00 41.03 5.12
1456 1562 1.066716 TGGGTCTTAATTCCACGACGG 60.067 52.381 0.00 0.00 0.00 4.79
1457 1563 1.205417 GGGTCTTAATTCCACGACGGA 59.795 52.381 0.00 0.00 44.40 4.69
1464 1570 2.599281 TCCACGACGGAAGCCTCA 60.599 61.111 0.00 0.00 42.52 3.86
1465 1571 2.125912 CCACGACGGAAGCCTCAG 60.126 66.667 0.00 0.00 36.56 3.35
1466 1572 2.636412 CCACGACGGAAGCCTCAGA 61.636 63.158 0.00 0.00 36.56 3.27
1467 1573 1.289066 CACGACGGAAGCCTCAGAA 59.711 57.895 0.00 0.00 0.00 3.02
1468 1574 0.319555 CACGACGGAAGCCTCAGAAA 60.320 55.000 0.00 0.00 0.00 2.52
1469 1575 0.319641 ACGACGGAAGCCTCAGAAAC 60.320 55.000 0.00 0.00 0.00 2.78
1470 1576 0.038159 CGACGGAAGCCTCAGAAACT 60.038 55.000 0.00 0.00 0.00 2.66
1471 1577 1.433534 GACGGAAGCCTCAGAAACTG 58.566 55.000 0.00 0.00 0.00 3.16
1472 1578 0.603975 ACGGAAGCCTCAGAAACTGC 60.604 55.000 0.00 0.00 0.00 4.40
1473 1579 0.603707 CGGAAGCCTCAGAAACTGCA 60.604 55.000 0.00 0.00 0.00 4.41
1474 1580 1.831580 GGAAGCCTCAGAAACTGCAT 58.168 50.000 0.00 0.00 0.00 3.96
1475 1581 1.471684 GGAAGCCTCAGAAACTGCATG 59.528 52.381 0.00 0.00 0.00 4.06
1476 1582 1.471684 GAAGCCTCAGAAACTGCATGG 59.528 52.381 0.00 0.00 0.00 3.66
1477 1583 0.964358 AGCCTCAGAAACTGCATGGC 60.964 55.000 15.96 15.96 39.92 4.40
1478 1584 1.246056 GCCTCAGAAACTGCATGGCA 61.246 55.000 17.55 0.00 39.65 4.92
1479 1585 1.471119 CCTCAGAAACTGCATGGCAT 58.529 50.000 0.00 0.00 38.13 4.40
1480 1586 1.822990 CCTCAGAAACTGCATGGCATT 59.177 47.619 0.00 0.00 38.13 3.56
1481 1587 2.159282 CCTCAGAAACTGCATGGCATTC 60.159 50.000 0.00 0.00 38.13 2.67
1482 1588 1.820519 TCAGAAACTGCATGGCATTCC 59.179 47.619 0.00 0.00 38.13 3.01
1492 1598 3.642938 TGGCATTCCAGCGTAAGTT 57.357 47.368 0.00 0.00 37.47 2.66
1493 1599 1.904287 TGGCATTCCAGCGTAAGTTT 58.096 45.000 0.00 0.00 37.47 2.66
1494 1600 2.235016 TGGCATTCCAGCGTAAGTTTT 58.765 42.857 0.00 0.00 37.47 2.43
1495 1601 2.227865 TGGCATTCCAGCGTAAGTTTTC 59.772 45.455 0.00 0.00 37.47 2.29
1496 1602 2.488153 GGCATTCCAGCGTAAGTTTTCT 59.512 45.455 0.00 0.00 41.68 2.52
1497 1603 3.492313 GCATTCCAGCGTAAGTTTTCTG 58.508 45.455 0.00 0.00 41.68 3.02
1498 1604 3.058224 GCATTCCAGCGTAAGTTTTCTGT 60.058 43.478 0.00 0.00 41.68 3.41
1499 1605 4.153475 GCATTCCAGCGTAAGTTTTCTGTA 59.847 41.667 0.00 0.00 41.68 2.74
1500 1606 5.671329 GCATTCCAGCGTAAGTTTTCTGTAG 60.671 44.000 0.00 0.00 41.68 2.74
1501 1607 4.595762 TCCAGCGTAAGTTTTCTGTAGT 57.404 40.909 0.00 0.00 41.68 2.73
1502 1608 5.710513 TCCAGCGTAAGTTTTCTGTAGTA 57.289 39.130 0.00 0.00 41.68 1.82
1503 1609 6.276832 TCCAGCGTAAGTTTTCTGTAGTAT 57.723 37.500 0.00 0.00 41.68 2.12
1504 1610 6.097356 TCCAGCGTAAGTTTTCTGTAGTATG 58.903 40.000 0.00 0.00 41.68 2.39
1505 1611 5.867716 CCAGCGTAAGTTTTCTGTAGTATGT 59.132 40.000 0.00 0.00 41.68 2.29
1506 1612 6.034683 CCAGCGTAAGTTTTCTGTAGTATGTC 59.965 42.308 0.00 0.00 41.68 3.06
1507 1613 6.807230 CAGCGTAAGTTTTCTGTAGTATGTCT 59.193 38.462 0.00 0.00 41.68 3.41
1508 1614 7.966753 CAGCGTAAGTTTTCTGTAGTATGTCTA 59.033 37.037 0.00 0.00 41.68 2.59
1509 1615 8.182881 AGCGTAAGTTTTCTGTAGTATGTCTAG 58.817 37.037 0.00 0.00 41.68 2.43
1510 1616 7.044183 GCGTAAGTTTTCTGTAGTATGTCTAGC 60.044 40.741 0.00 0.00 41.68 3.42
1511 1617 7.431668 CGTAAGTTTTCTGTAGTATGTCTAGCC 59.568 40.741 0.00 0.00 0.00 3.93
1512 1618 6.223351 AGTTTTCTGTAGTATGTCTAGCCC 57.777 41.667 0.00 0.00 0.00 5.19
1513 1619 5.958987 AGTTTTCTGTAGTATGTCTAGCCCT 59.041 40.000 0.00 0.00 0.00 5.19
1514 1620 5.854010 TTTCTGTAGTATGTCTAGCCCTG 57.146 43.478 0.00 0.00 0.00 4.45
1515 1621 3.223435 TCTGTAGTATGTCTAGCCCTGC 58.777 50.000 0.00 0.00 0.00 4.85
1516 1622 2.959030 CTGTAGTATGTCTAGCCCTGCA 59.041 50.000 0.00 0.00 0.00 4.41
1517 1623 3.371034 TGTAGTATGTCTAGCCCTGCAA 58.629 45.455 0.00 0.00 0.00 4.08
1518 1624 3.384789 TGTAGTATGTCTAGCCCTGCAAG 59.615 47.826 0.00 0.00 0.00 4.01
1519 1625 2.472029 AGTATGTCTAGCCCTGCAAGT 58.528 47.619 0.00 0.00 0.00 3.16
1520 1626 2.432510 AGTATGTCTAGCCCTGCAAGTC 59.567 50.000 0.00 0.00 0.00 3.01
1521 1627 1.279496 ATGTCTAGCCCTGCAAGTCA 58.721 50.000 0.00 0.00 0.00 3.41
1522 1628 1.055849 TGTCTAGCCCTGCAAGTCAA 58.944 50.000 0.00 0.00 0.00 3.18
1523 1629 1.002430 TGTCTAGCCCTGCAAGTCAAG 59.998 52.381 0.00 0.00 0.00 3.02
1524 1630 1.276421 GTCTAGCCCTGCAAGTCAAGA 59.724 52.381 0.00 0.00 0.00 3.02
1525 1631 1.276421 TCTAGCCCTGCAAGTCAAGAC 59.724 52.381 0.00 0.00 0.00 3.01
1526 1632 1.002430 CTAGCCCTGCAAGTCAAGACA 59.998 52.381 2.72 0.00 0.00 3.41
1527 1633 0.403271 AGCCCTGCAAGTCAAGACAT 59.597 50.000 2.72 0.00 0.00 3.06
1528 1634 1.630369 AGCCCTGCAAGTCAAGACATA 59.370 47.619 2.72 0.00 0.00 2.29
1529 1635 2.040278 AGCCCTGCAAGTCAAGACATAA 59.960 45.455 2.72 0.00 0.00 1.90
1530 1636 2.421424 GCCCTGCAAGTCAAGACATAAG 59.579 50.000 2.72 0.00 0.00 1.73
1531 1637 3.679389 CCCTGCAAGTCAAGACATAAGT 58.321 45.455 2.72 0.00 0.00 2.24
1532 1638 4.074970 CCCTGCAAGTCAAGACATAAGTT 58.925 43.478 2.72 0.00 0.00 2.66
1533 1639 4.083110 CCCTGCAAGTCAAGACATAAGTTG 60.083 45.833 2.72 0.00 0.00 3.16
1534 1640 4.756642 CCTGCAAGTCAAGACATAAGTTGA 59.243 41.667 2.72 0.00 0.00 3.18
1542 1648 6.590234 TCAAGACATAAGTTGACAGCTAGA 57.410 37.500 0.00 0.00 0.00 2.43
1543 1649 6.993079 TCAAGACATAAGTTGACAGCTAGAA 58.007 36.000 0.00 0.00 0.00 2.10
1544 1650 6.868864 TCAAGACATAAGTTGACAGCTAGAAC 59.131 38.462 0.00 0.00 0.00 3.01
1545 1651 5.725362 AGACATAAGTTGACAGCTAGAACC 58.275 41.667 0.00 0.00 0.00 3.62
1546 1652 5.246203 AGACATAAGTTGACAGCTAGAACCA 59.754 40.000 0.00 0.00 0.00 3.67
1547 1653 6.054860 ACATAAGTTGACAGCTAGAACCAT 57.945 37.500 0.00 0.00 0.00 3.55
1548 1654 7.124298 AGACATAAGTTGACAGCTAGAACCATA 59.876 37.037 0.00 0.00 0.00 2.74
1549 1655 7.620880 ACATAAGTTGACAGCTAGAACCATAA 58.379 34.615 0.00 0.00 0.00 1.90
1550 1656 7.549488 ACATAAGTTGACAGCTAGAACCATAAC 59.451 37.037 0.00 0.00 0.00 1.89
1551 1657 5.483685 AGTTGACAGCTAGAACCATAACA 57.516 39.130 0.00 0.00 0.00 2.41
1552 1658 6.054860 AGTTGACAGCTAGAACCATAACAT 57.945 37.500 0.00 0.00 0.00 2.71
1553 1659 6.476378 AGTTGACAGCTAGAACCATAACATT 58.524 36.000 0.00 0.00 0.00 2.71
1554 1660 6.372659 AGTTGACAGCTAGAACCATAACATTG 59.627 38.462 0.00 0.00 0.00 2.82
1555 1661 4.635765 TGACAGCTAGAACCATAACATTGC 59.364 41.667 0.00 0.00 0.00 3.56
1556 1662 3.947834 ACAGCTAGAACCATAACATTGCC 59.052 43.478 0.00 0.00 0.00 4.52
1557 1663 3.947196 CAGCTAGAACCATAACATTGCCA 59.053 43.478 0.00 0.00 0.00 4.92
1558 1664 3.947834 AGCTAGAACCATAACATTGCCAC 59.052 43.478 0.00 0.00 0.00 5.01
1559 1665 3.694072 GCTAGAACCATAACATTGCCACA 59.306 43.478 0.00 0.00 0.00 4.17
1560 1666 4.339247 GCTAGAACCATAACATTGCCACAT 59.661 41.667 0.00 0.00 0.00 3.21
1561 1667 5.163519 GCTAGAACCATAACATTGCCACATT 60.164 40.000 0.00 0.00 0.00 2.71
1562 1668 5.743636 AGAACCATAACATTGCCACATTT 57.256 34.783 0.00 0.00 0.00 2.32
1563 1669 5.723295 AGAACCATAACATTGCCACATTTC 58.277 37.500 0.00 0.00 0.00 2.17
1564 1670 5.481473 AGAACCATAACATTGCCACATTTCT 59.519 36.000 0.00 0.00 0.00 2.52
1565 1671 5.743636 ACCATAACATTGCCACATTTCTT 57.256 34.783 0.00 0.00 0.00 2.52
1566 1672 5.481105 ACCATAACATTGCCACATTTCTTG 58.519 37.500 0.00 0.00 0.00 3.02
1567 1673 5.011943 ACCATAACATTGCCACATTTCTTGT 59.988 36.000 0.00 0.00 39.91 3.16
1568 1674 5.933463 CCATAACATTGCCACATTTCTTGTT 59.067 36.000 0.00 0.00 36.00 2.83
1569 1675 6.427547 CCATAACATTGCCACATTTCTTGTTT 59.572 34.615 0.00 0.00 36.00 2.83
1570 1676 5.989551 AACATTGCCACATTTCTTGTTTC 57.010 34.783 0.00 0.00 36.00 2.78
1571 1677 4.379652 ACATTGCCACATTTCTTGTTTCC 58.620 39.130 0.00 0.00 36.00 3.13
1572 1678 4.141756 ACATTGCCACATTTCTTGTTTCCA 60.142 37.500 0.00 0.00 36.00 3.53
1573 1679 4.478206 TTGCCACATTTCTTGTTTCCAA 57.522 36.364 0.00 0.00 36.00 3.53
1574 1680 4.686191 TGCCACATTTCTTGTTTCCAAT 57.314 36.364 0.00 0.00 36.00 3.16
1575 1681 5.033589 TGCCACATTTCTTGTTTCCAATT 57.966 34.783 0.00 0.00 36.00 2.32
1576 1682 4.815308 TGCCACATTTCTTGTTTCCAATTG 59.185 37.500 0.00 0.00 36.00 2.32
1577 1683 4.319694 GCCACATTTCTTGTTTCCAATTGC 60.320 41.667 0.00 0.00 36.00 3.56
1578 1684 4.084433 CCACATTTCTTGTTTCCAATTGCG 60.084 41.667 0.00 0.00 36.00 4.85
1579 1685 4.507388 CACATTTCTTGTTTCCAATTGCGT 59.493 37.500 0.00 0.00 36.00 5.24
1580 1686 4.507388 ACATTTCTTGTTTCCAATTGCGTG 59.493 37.500 0.00 0.00 33.74 5.34
1581 1687 2.791383 TCTTGTTTCCAATTGCGTGG 57.209 45.000 0.00 0.00 40.33 4.94
1582 1688 2.028130 TCTTGTTTCCAATTGCGTGGT 58.972 42.857 0.00 0.00 39.88 4.16
1583 1689 3.215151 TCTTGTTTCCAATTGCGTGGTA 58.785 40.909 0.00 0.00 39.88 3.25
1584 1690 3.252215 TCTTGTTTCCAATTGCGTGGTAG 59.748 43.478 0.00 0.00 39.88 3.18
1585 1691 2.852449 TGTTTCCAATTGCGTGGTAGA 58.148 42.857 0.00 0.00 39.88 2.59
1586 1692 3.417101 TGTTTCCAATTGCGTGGTAGAT 58.583 40.909 0.00 0.00 39.88 1.98
1587 1693 3.823873 TGTTTCCAATTGCGTGGTAGATT 59.176 39.130 0.00 0.00 39.88 2.40
1588 1694 5.004448 TGTTTCCAATTGCGTGGTAGATTA 58.996 37.500 0.00 0.00 39.88 1.75
1589 1695 5.473846 TGTTTCCAATTGCGTGGTAGATTAA 59.526 36.000 0.00 0.00 39.88 1.40
1590 1696 6.151985 TGTTTCCAATTGCGTGGTAGATTAAT 59.848 34.615 0.00 0.00 39.88 1.40
1591 1697 6.767524 TTCCAATTGCGTGGTAGATTAATT 57.232 33.333 0.00 0.00 39.88 1.40
1592 1698 7.867305 TTCCAATTGCGTGGTAGATTAATTA 57.133 32.000 0.00 0.00 39.88 1.40
1593 1699 7.254227 TCCAATTGCGTGGTAGATTAATTAC 57.746 36.000 0.00 0.00 39.88 1.89
1594 1700 7.051623 TCCAATTGCGTGGTAGATTAATTACT 58.948 34.615 0.00 0.00 39.88 2.24
1595 1701 7.225931 TCCAATTGCGTGGTAGATTAATTACTC 59.774 37.037 0.00 0.00 39.88 2.59
1596 1702 6.764877 ATTGCGTGGTAGATTAATTACTCG 57.235 37.500 0.00 5.80 0.00 4.18
1597 1703 5.503662 TGCGTGGTAGATTAATTACTCGA 57.496 39.130 17.52 0.00 0.00 4.04
1598 1704 5.516996 TGCGTGGTAGATTAATTACTCGAG 58.483 41.667 11.84 11.84 0.00 4.04
1599 1705 4.916249 GCGTGGTAGATTAATTACTCGAGG 59.084 45.833 18.41 0.00 0.00 4.63
1600 1706 5.278169 GCGTGGTAGATTAATTACTCGAGGA 60.278 44.000 18.41 4.89 0.00 3.71
1601 1707 6.569994 GCGTGGTAGATTAATTACTCGAGGAT 60.570 42.308 18.41 7.57 0.00 3.24
1602 1708 7.022384 CGTGGTAGATTAATTACTCGAGGATC 58.978 42.308 18.41 1.79 0.00 3.36
1603 1709 7.308408 CGTGGTAGATTAATTACTCGAGGATCA 60.308 40.741 18.41 0.00 33.17 2.92
1604 1710 8.524487 GTGGTAGATTAATTACTCGAGGATCAT 58.476 37.037 18.41 0.00 33.17 2.45
1605 1711 8.523658 TGGTAGATTAATTACTCGAGGATCATG 58.476 37.037 18.41 0.00 33.17 3.07
1606 1712 7.489757 GGTAGATTAATTACTCGAGGATCATGC 59.510 40.741 18.41 0.00 33.17 4.06
1607 1713 6.402222 AGATTAATTACTCGAGGATCATGCC 58.598 40.000 18.41 0.29 33.17 4.40
1608 1714 2.732412 ATTACTCGAGGATCATGCCG 57.268 50.000 18.41 0.00 33.17 5.69
1609 1715 0.032130 TTACTCGAGGATCATGCCGC 59.968 55.000 18.41 0.00 33.17 6.53
1610 1716 1.106944 TACTCGAGGATCATGCCGCA 61.107 55.000 18.41 0.00 33.17 5.69
1611 1717 1.664017 CTCGAGGATCATGCCGCAG 60.664 63.158 3.91 0.00 33.17 5.18
1612 1718 2.107750 CGAGGATCATGCCGCAGT 59.892 61.111 0.00 0.00 33.17 4.40
1613 1719 1.106944 TCGAGGATCATGCCGCAGTA 61.107 55.000 0.00 0.00 33.17 2.74
1614 1720 0.941463 CGAGGATCATGCCGCAGTAC 60.941 60.000 0.00 0.00 33.17 2.73
1615 1721 0.390860 GAGGATCATGCCGCAGTACT 59.609 55.000 0.00 0.00 33.17 2.73
1616 1722 0.390860 AGGATCATGCCGCAGTACTC 59.609 55.000 0.00 0.00 0.00 2.59
1617 1723 0.390860 GGATCATGCCGCAGTACTCT 59.609 55.000 0.00 0.00 0.00 3.24
1618 1724 1.495878 GATCATGCCGCAGTACTCTG 58.504 55.000 0.00 0.00 43.87 3.35
1619 1725 0.105593 ATCATGCCGCAGTACTCTGG 59.894 55.000 0.00 5.67 41.57 3.86
1620 1726 0.970427 TCATGCCGCAGTACTCTGGA 60.970 55.000 13.03 0.00 41.57 3.86
1621 1727 0.105593 CATGCCGCAGTACTCTGGAT 59.894 55.000 13.03 0.00 41.57 3.41
1622 1728 0.833287 ATGCCGCAGTACTCTGGATT 59.167 50.000 13.03 0.00 41.57 3.01
1623 1729 0.613260 TGCCGCAGTACTCTGGATTT 59.387 50.000 13.03 0.00 41.57 2.17
1662 1770 4.935205 TGACTATCACAAATTCTGGAACCG 59.065 41.667 0.00 0.00 0.00 4.44
1663 1771 5.160607 ACTATCACAAATTCTGGAACCGA 57.839 39.130 0.00 0.00 0.00 4.69
1664 1772 4.935808 ACTATCACAAATTCTGGAACCGAC 59.064 41.667 0.00 0.00 0.00 4.79
1687 1795 6.303839 ACCAGAAGCCAATAACTGAAAACTA 58.696 36.000 0.00 0.00 32.90 2.24
1688 1796 6.431234 ACCAGAAGCCAATAACTGAAAACTAG 59.569 38.462 0.00 0.00 32.90 2.57
1912 2027 2.983512 AGGACTCGCATCCTCTTGT 58.016 52.632 1.67 0.00 46.92 3.16
1933 2048 9.362151 TCTTGTAAAGGAACATGGAAAAACTAT 57.638 29.630 0.00 0.00 46.24 2.12
2036 2151 2.159043 AGGATAACATCTCTGTGCACGG 60.159 50.000 20.12 20.12 35.22 4.94
2064 2179 4.876107 CCTCCGAATTGCTAACACTAACAT 59.124 41.667 0.00 0.00 0.00 2.71
2109 2224 1.079543 CAGAACTAGCTGCGGCACT 60.080 57.895 21.93 1.65 41.70 4.40
2289 2418 2.107378 TGCACCTTCCACCAGAACATTA 59.893 45.455 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.428622 CCGTCGGGGTTTTCACCT 59.571 61.111 2.34 0.00 43.65 4.00
96 97 2.815211 CCGATGCCACAGGTCGTG 60.815 66.667 0.00 0.00 45.92 4.35
159 160 3.566351 CTTCCAAGGGTTTTCTCCTGTT 58.434 45.455 0.00 0.00 34.34 3.16
213 215 2.032528 CGCTGCTTCTTGGGACCA 59.967 61.111 0.00 0.00 0.00 4.02
375 380 1.374947 CTCCAAAACTCGGGCAGGA 59.625 57.895 0.00 0.00 0.00 3.86
616 661 2.742372 CTGGTCCGGCGGAAACTG 60.742 66.667 32.91 24.41 31.38 3.16
637 698 2.027192 CACAGACCTTAAAGCAGGCCTA 60.027 50.000 3.98 0.00 37.47 3.93
644 705 1.923227 GCCCGCACAGACCTTAAAGC 61.923 60.000 0.00 0.00 0.00 3.51
655 716 3.893763 CGTTTTGTGGCCCGCACA 61.894 61.111 0.00 0.00 0.00 4.57
718 779 3.766691 GCATGCAGCCCAACCAGG 61.767 66.667 14.21 0.00 37.23 4.45
719 780 4.124351 CGCATGCAGCCCAACCAG 62.124 66.667 19.57 0.00 41.38 4.00
728 789 3.223710 TTTGGTTGCCCGCATGCAG 62.224 57.895 19.57 6.15 43.21 4.41
729 790 3.229501 TTTGGTTGCCCGCATGCA 61.230 55.556 19.57 0.00 40.07 3.96
730 791 2.738139 GTTTGGTTGCCCGCATGC 60.738 61.111 7.91 7.91 0.00 4.06
731 792 2.430582 CGTTTGGTTGCCCGCATG 60.431 61.111 0.00 0.00 0.00 4.06
732 793 4.356442 GCGTTTGGTTGCCCGCAT 62.356 61.111 0.00 0.00 45.12 4.73
738 799 2.910345 TAAGGGCGCGTTTGGTTGC 61.910 57.895 8.43 0.00 0.00 4.17
739 800 1.081708 GTAAGGGCGCGTTTGGTTG 60.082 57.895 8.43 0.00 0.00 3.77
740 801 1.228033 AGTAAGGGCGCGTTTGGTT 60.228 52.632 8.43 0.00 0.00 3.67
741 802 1.964373 CAGTAAGGGCGCGTTTGGT 60.964 57.895 8.43 0.00 0.00 3.67
742 803 2.686816 CCAGTAAGGGCGCGTTTGG 61.687 63.158 8.43 0.00 0.00 3.28
743 804 1.908066 GACCAGTAAGGGCGCGTTTG 61.908 60.000 8.43 0.00 43.89 2.93
744 805 1.670083 GACCAGTAAGGGCGCGTTT 60.670 57.895 8.43 0.00 43.89 3.60
745 806 2.047560 GACCAGTAAGGGCGCGTT 60.048 61.111 8.43 0.00 43.89 4.84
750 811 2.582978 GGACCGACCAGTAAGGGC 59.417 66.667 0.00 0.00 44.64 5.19
751 812 2.890371 CGGACCGACCAGTAAGGG 59.110 66.667 8.64 0.00 43.89 3.95
752 813 1.033746 TAGCGGACCGACCAGTAAGG 61.034 60.000 20.50 0.00 45.67 2.69
757 818 0.813184 TAAACTAGCGGACCGACCAG 59.187 55.000 20.50 12.88 38.90 4.00
760 821 1.136285 GCGTAAACTAGCGGACCGAC 61.136 60.000 20.50 9.27 0.00 4.79
775 836 5.290158 GTGATAACTTCTTCGGATTTGCGTA 59.710 40.000 0.00 0.00 0.00 4.42
966 1028 7.592885 ACCAGCCGTACTTAATAATAGAAGA 57.407 36.000 0.00 0.00 0.00 2.87
1080 1142 2.398588 TGAGCCGGGATCATTAAGAGT 58.601 47.619 11.64 0.00 0.00 3.24
1166 1228 7.918562 CCGTGGAAAATTCAGACTTTCTTTTTA 59.081 33.333 4.78 0.00 33.06 1.52
1198 1260 6.634436 GCACCTAAGATCAAATATTTTGAGCG 59.366 38.462 11.28 2.30 39.56 5.03
1228 1290 6.320164 CACCCGAACAATAATATTCCAAAGGA 59.680 38.462 0.00 0.00 0.00 3.36
1382 1488 7.905604 TGTTTCGTGATCTTATCTTTCATGT 57.094 32.000 0.00 0.00 0.00 3.21
1385 1491 9.869757 TCTTATGTTTCGTGATCTTATCTTTCA 57.130 29.630 0.00 0.00 0.00 2.69
1389 1495 9.613957 CGTATCTTATGTTTCGTGATCTTATCT 57.386 33.333 0.00 0.00 0.00 1.98
1390 1496 8.851416 CCGTATCTTATGTTTCGTGATCTTATC 58.149 37.037 0.00 0.00 0.00 1.75
1391 1497 7.813148 CCCGTATCTTATGTTTCGTGATCTTAT 59.187 37.037 0.00 0.00 0.00 1.73
1392 1498 7.013559 TCCCGTATCTTATGTTTCGTGATCTTA 59.986 37.037 0.00 0.00 0.00 2.10
1393 1499 5.983720 CCCGTATCTTATGTTTCGTGATCTT 59.016 40.000 0.00 0.00 0.00 2.40
1394 1500 5.301045 TCCCGTATCTTATGTTTCGTGATCT 59.699 40.000 0.00 0.00 0.00 2.75
1395 1501 5.526115 TCCCGTATCTTATGTTTCGTGATC 58.474 41.667 0.00 0.00 0.00 2.92
1396 1502 5.301045 TCTCCCGTATCTTATGTTTCGTGAT 59.699 40.000 0.00 0.00 0.00 3.06
1397 1503 4.641541 TCTCCCGTATCTTATGTTTCGTGA 59.358 41.667 0.00 0.00 0.00 4.35
1399 1505 4.497006 CGTCTCCCGTATCTTATGTTTCGT 60.497 45.833 0.00 0.00 0.00 3.85
1405 1511 1.544691 CCCCGTCTCCCGTATCTTATG 59.455 57.143 0.00 0.00 33.66 1.90
1435 1541 1.997606 CGTCGTGGAATTAAGACCCAC 59.002 52.381 11.54 11.54 45.07 4.61
1448 1554 2.125912 CTGAGGCTTCCGTCGTGG 60.126 66.667 0.00 0.00 40.09 4.94
1449 1555 0.319555 TTTCTGAGGCTTCCGTCGTG 60.320 55.000 0.00 0.00 0.00 4.35
1450 1556 0.319641 GTTTCTGAGGCTTCCGTCGT 60.320 55.000 0.00 0.00 0.00 4.34
1451 1557 0.038159 AGTTTCTGAGGCTTCCGTCG 60.038 55.000 0.00 0.00 0.00 5.12
1452 1558 1.433534 CAGTTTCTGAGGCTTCCGTC 58.566 55.000 0.00 0.00 32.44 4.79
1453 1559 0.603975 GCAGTTTCTGAGGCTTCCGT 60.604 55.000 0.66 0.00 32.44 4.69
1454 1560 0.603707 TGCAGTTTCTGAGGCTTCCG 60.604 55.000 0.66 0.00 32.44 4.30
1455 1561 1.471684 CATGCAGTTTCTGAGGCTTCC 59.528 52.381 0.00 0.00 32.44 3.46
1456 1562 1.471684 CCATGCAGTTTCTGAGGCTTC 59.528 52.381 0.00 0.00 32.44 3.86
1457 1563 1.542492 CCATGCAGTTTCTGAGGCTT 58.458 50.000 0.00 0.00 32.44 4.35
1458 1564 0.964358 GCCATGCAGTTTCTGAGGCT 60.964 55.000 15.53 0.00 40.04 4.58
1459 1565 1.246056 TGCCATGCAGTTTCTGAGGC 61.246 55.000 15.77 15.77 41.92 4.70
1460 1566 1.471119 ATGCCATGCAGTTTCTGAGG 58.529 50.000 0.00 0.95 43.65 3.86
1461 1567 2.159282 GGAATGCCATGCAGTTTCTGAG 60.159 50.000 0.00 0.00 43.65 3.35
1462 1568 1.820519 GGAATGCCATGCAGTTTCTGA 59.179 47.619 0.00 0.00 43.65 3.27
1463 1569 1.546923 TGGAATGCCATGCAGTTTCTG 59.453 47.619 0.00 0.00 43.65 3.02
1464 1570 1.822990 CTGGAATGCCATGCAGTTTCT 59.177 47.619 0.00 0.00 44.91 2.52
1465 1571 1.738030 GCTGGAATGCCATGCAGTTTC 60.738 52.381 8.78 0.00 44.91 2.78
1466 1572 0.248289 GCTGGAATGCCATGCAGTTT 59.752 50.000 8.78 0.00 44.91 2.66
1467 1573 1.895238 GCTGGAATGCCATGCAGTT 59.105 52.632 8.78 0.00 44.91 3.16
1468 1574 2.412323 CGCTGGAATGCCATGCAGT 61.412 57.895 12.87 0.00 44.91 4.40
1469 1575 1.096967 TACGCTGGAATGCCATGCAG 61.097 55.000 12.87 3.41 44.91 4.41
1470 1576 0.679321 TTACGCTGGAATGCCATGCA 60.679 50.000 12.87 0.00 44.91 3.96
1471 1577 0.029834 CTTACGCTGGAATGCCATGC 59.970 55.000 0.00 0.00 44.91 4.06
1472 1578 1.382522 ACTTACGCTGGAATGCCATG 58.617 50.000 0.00 0.00 44.91 3.66
1473 1579 2.128771 AACTTACGCTGGAATGCCAT 57.871 45.000 0.00 0.00 44.91 4.40
1474 1580 1.904287 AAACTTACGCTGGAATGCCA 58.096 45.000 0.00 0.00 43.47 4.92
1475 1581 2.488153 AGAAAACTTACGCTGGAATGCC 59.512 45.455 0.00 0.00 0.00 4.40
1476 1582 3.058224 ACAGAAAACTTACGCTGGAATGC 60.058 43.478 0.00 0.00 32.82 3.56
1477 1583 4.749245 ACAGAAAACTTACGCTGGAATG 57.251 40.909 0.00 0.00 32.82 2.67
1478 1584 5.548406 ACTACAGAAAACTTACGCTGGAAT 58.452 37.500 0.00 0.00 32.82 3.01
1479 1585 4.952460 ACTACAGAAAACTTACGCTGGAA 58.048 39.130 0.00 0.00 32.82 3.53
1480 1586 4.595762 ACTACAGAAAACTTACGCTGGA 57.404 40.909 0.00 0.00 32.82 3.86
1481 1587 5.867716 ACATACTACAGAAAACTTACGCTGG 59.132 40.000 0.00 0.00 32.82 4.85
1482 1588 6.807230 AGACATACTACAGAAAACTTACGCTG 59.193 38.462 0.00 0.00 34.65 5.18
1483 1589 6.921914 AGACATACTACAGAAAACTTACGCT 58.078 36.000 0.00 0.00 0.00 5.07
1484 1590 7.044183 GCTAGACATACTACAGAAAACTTACGC 60.044 40.741 0.00 0.00 0.00 4.42
1485 1591 7.431668 GGCTAGACATACTACAGAAAACTTACG 59.568 40.741 0.00 0.00 0.00 3.18
1486 1592 7.705752 GGGCTAGACATACTACAGAAAACTTAC 59.294 40.741 0.00 0.00 0.00 2.34
1487 1593 7.618512 AGGGCTAGACATACTACAGAAAACTTA 59.381 37.037 0.00 0.00 0.00 2.24
1488 1594 6.440965 AGGGCTAGACATACTACAGAAAACTT 59.559 38.462 0.00 0.00 0.00 2.66
1489 1595 5.958987 AGGGCTAGACATACTACAGAAAACT 59.041 40.000 0.00 0.00 0.00 2.66
1490 1596 6.043411 CAGGGCTAGACATACTACAGAAAAC 58.957 44.000 0.00 0.00 0.00 2.43
1491 1597 5.395324 GCAGGGCTAGACATACTACAGAAAA 60.395 44.000 0.00 0.00 0.00 2.29
1492 1598 4.099573 GCAGGGCTAGACATACTACAGAAA 59.900 45.833 0.00 0.00 0.00 2.52
1493 1599 3.637229 GCAGGGCTAGACATACTACAGAA 59.363 47.826 0.00 0.00 0.00 3.02
1494 1600 3.223435 GCAGGGCTAGACATACTACAGA 58.777 50.000 0.00 0.00 0.00 3.41
1495 1601 2.959030 TGCAGGGCTAGACATACTACAG 59.041 50.000 0.00 0.00 0.00 2.74
1496 1602 3.026707 TGCAGGGCTAGACATACTACA 57.973 47.619 0.00 0.00 0.00 2.74
1497 1603 3.385111 ACTTGCAGGGCTAGACATACTAC 59.615 47.826 0.00 0.00 35.20 2.73
1498 1604 3.637229 GACTTGCAGGGCTAGACATACTA 59.363 47.826 0.00 0.00 35.20 1.82
1499 1605 2.432510 GACTTGCAGGGCTAGACATACT 59.567 50.000 0.00 0.00 35.20 2.12
1500 1606 2.168521 TGACTTGCAGGGCTAGACATAC 59.831 50.000 2.27 0.00 32.95 2.39
1501 1607 2.466846 TGACTTGCAGGGCTAGACATA 58.533 47.619 2.27 0.00 32.95 2.29
1502 1608 1.279496 TGACTTGCAGGGCTAGACAT 58.721 50.000 2.27 0.00 32.95 3.06
1503 1609 1.002430 CTTGACTTGCAGGGCTAGACA 59.998 52.381 7.36 4.00 35.18 3.41
1504 1610 1.276421 TCTTGACTTGCAGGGCTAGAC 59.724 52.381 11.70 0.00 35.20 2.59
1505 1611 1.276421 GTCTTGACTTGCAGGGCTAGA 59.724 52.381 11.70 11.70 35.20 2.43
1506 1612 1.002430 TGTCTTGACTTGCAGGGCTAG 59.998 52.381 6.80 6.80 37.42 3.42
1507 1613 1.055849 TGTCTTGACTTGCAGGGCTA 58.944 50.000 2.27 0.00 0.00 3.93
1508 1614 0.403271 ATGTCTTGACTTGCAGGGCT 59.597 50.000 2.27 0.00 0.00 5.19
1509 1615 2.113860 TATGTCTTGACTTGCAGGGC 57.886 50.000 0.00 0.00 0.00 5.19
1510 1616 3.679389 ACTTATGTCTTGACTTGCAGGG 58.321 45.455 0.00 0.00 0.00 4.45
1511 1617 4.756642 TCAACTTATGTCTTGACTTGCAGG 59.243 41.667 0.00 0.00 0.00 4.85
1512 1618 5.237127 TGTCAACTTATGTCTTGACTTGCAG 59.763 40.000 12.31 0.77 42.93 4.41
1513 1619 5.122519 TGTCAACTTATGTCTTGACTTGCA 58.877 37.500 12.31 0.00 42.93 4.08
1514 1620 5.673337 TGTCAACTTATGTCTTGACTTGC 57.327 39.130 12.31 0.00 42.93 4.01
1515 1621 5.468072 AGCTGTCAACTTATGTCTTGACTTG 59.532 40.000 12.31 8.06 42.93 3.16
1516 1622 5.615289 AGCTGTCAACTTATGTCTTGACTT 58.385 37.500 12.31 0.00 42.93 3.01
1517 1623 5.220710 AGCTGTCAACTTATGTCTTGACT 57.779 39.130 12.31 0.00 42.93 3.41
1518 1624 6.390721 TCTAGCTGTCAACTTATGTCTTGAC 58.609 40.000 0.00 6.63 42.84 3.18
1519 1625 6.590234 TCTAGCTGTCAACTTATGTCTTGA 57.410 37.500 0.00 0.00 0.00 3.02
1520 1626 6.091441 GGTTCTAGCTGTCAACTTATGTCTTG 59.909 42.308 0.00 0.00 0.00 3.02
1521 1627 6.166982 GGTTCTAGCTGTCAACTTATGTCTT 58.833 40.000 0.00 0.00 0.00 3.01
1522 1628 5.246203 TGGTTCTAGCTGTCAACTTATGTCT 59.754 40.000 0.00 0.00 0.00 3.41
1523 1629 5.479306 TGGTTCTAGCTGTCAACTTATGTC 58.521 41.667 0.00 0.00 0.00 3.06
1524 1630 5.483685 TGGTTCTAGCTGTCAACTTATGT 57.516 39.130 0.00 0.00 0.00 2.29
1525 1631 7.549134 TGTTATGGTTCTAGCTGTCAACTTATG 59.451 37.037 0.00 0.00 0.00 1.90
1526 1632 7.620880 TGTTATGGTTCTAGCTGTCAACTTAT 58.379 34.615 0.00 0.00 0.00 1.73
1527 1633 6.999950 TGTTATGGTTCTAGCTGTCAACTTA 58.000 36.000 0.00 0.00 0.00 2.24
1528 1634 5.865085 TGTTATGGTTCTAGCTGTCAACTT 58.135 37.500 0.00 0.00 0.00 2.66
1529 1635 5.483685 TGTTATGGTTCTAGCTGTCAACT 57.516 39.130 0.00 0.00 0.00 3.16
1530 1636 6.546395 CAATGTTATGGTTCTAGCTGTCAAC 58.454 40.000 0.00 0.00 0.00 3.18
1531 1637 5.123820 GCAATGTTATGGTTCTAGCTGTCAA 59.876 40.000 0.00 0.00 0.00 3.18
1532 1638 4.635765 GCAATGTTATGGTTCTAGCTGTCA 59.364 41.667 0.00 0.00 0.00 3.58
1533 1639 4.035675 GGCAATGTTATGGTTCTAGCTGTC 59.964 45.833 0.00 0.00 0.00 3.51
1534 1640 3.947834 GGCAATGTTATGGTTCTAGCTGT 59.052 43.478 0.00 0.00 0.00 4.40
1535 1641 3.947196 TGGCAATGTTATGGTTCTAGCTG 59.053 43.478 0.00 0.00 0.00 4.24
1536 1642 3.947834 GTGGCAATGTTATGGTTCTAGCT 59.052 43.478 0.00 0.00 0.00 3.32
1537 1643 3.694072 TGTGGCAATGTTATGGTTCTAGC 59.306 43.478 0.00 0.00 0.00 3.42
1538 1644 6.455360 AATGTGGCAATGTTATGGTTCTAG 57.545 37.500 0.00 0.00 0.00 2.43
1539 1645 6.663093 AGAAATGTGGCAATGTTATGGTTCTA 59.337 34.615 0.00 0.00 0.00 2.10
1540 1646 5.481473 AGAAATGTGGCAATGTTATGGTTCT 59.519 36.000 0.00 0.00 0.00 3.01
1541 1647 5.723295 AGAAATGTGGCAATGTTATGGTTC 58.277 37.500 0.00 0.00 0.00 3.62
1542 1648 5.743636 AGAAATGTGGCAATGTTATGGTT 57.256 34.783 0.00 0.00 0.00 3.67
1543 1649 5.011943 ACAAGAAATGTGGCAATGTTATGGT 59.988 36.000 0.00 0.00 41.93 3.55
1544 1650 5.481105 ACAAGAAATGTGGCAATGTTATGG 58.519 37.500 0.00 0.00 41.93 2.74
1545 1651 7.360269 GGAAACAAGAAATGTGGCAATGTTATG 60.360 37.037 0.00 0.00 42.99 1.90
1546 1652 6.650390 GGAAACAAGAAATGTGGCAATGTTAT 59.350 34.615 0.00 0.00 42.99 1.89
1547 1653 5.988561 GGAAACAAGAAATGTGGCAATGTTA 59.011 36.000 0.00 0.00 42.99 2.41
1548 1654 4.815846 GGAAACAAGAAATGTGGCAATGTT 59.184 37.500 0.00 0.00 42.99 2.71
1549 1655 4.141756 TGGAAACAAGAAATGTGGCAATGT 60.142 37.500 0.00 0.00 42.99 2.71
1550 1656 4.378774 TGGAAACAAGAAATGTGGCAATG 58.621 39.130 0.00 0.00 42.99 2.82
1551 1657 4.686191 TGGAAACAAGAAATGTGGCAAT 57.314 36.364 0.00 0.00 42.99 3.56
1565 1671 2.852449 TCTACCACGCAATTGGAAACA 58.148 42.857 7.72 0.00 39.24 2.83
1566 1672 4.434713 AATCTACCACGCAATTGGAAAC 57.565 40.909 7.72 0.00 39.24 2.78
1567 1673 6.767524 ATTAATCTACCACGCAATTGGAAA 57.232 33.333 7.72 0.00 39.24 3.13
1568 1674 6.767524 AATTAATCTACCACGCAATTGGAA 57.232 33.333 7.72 0.00 39.24 3.53
1569 1675 7.051623 AGTAATTAATCTACCACGCAATTGGA 58.948 34.615 7.72 0.00 39.24 3.53
1570 1676 7.259290 AGTAATTAATCTACCACGCAATTGG 57.741 36.000 7.72 0.00 43.04 3.16
1571 1677 7.042992 TCGAGTAATTAATCTACCACGCAATTG 60.043 37.037 10.87 0.00 0.00 2.32
1572 1678 6.982141 TCGAGTAATTAATCTACCACGCAATT 59.018 34.615 10.87 0.00 0.00 2.32
1573 1679 6.509656 TCGAGTAATTAATCTACCACGCAAT 58.490 36.000 10.87 0.00 0.00 3.56
1574 1680 5.893687 TCGAGTAATTAATCTACCACGCAA 58.106 37.500 10.87 0.00 0.00 4.85
1575 1681 5.503662 TCGAGTAATTAATCTACCACGCA 57.496 39.130 10.87 0.00 0.00 5.24
1576 1682 4.916249 CCTCGAGTAATTAATCTACCACGC 59.084 45.833 12.31 0.00 0.00 5.34
1577 1683 6.309712 TCCTCGAGTAATTAATCTACCACG 57.690 41.667 12.31 0.00 0.00 4.94
1578 1684 7.883217 TGATCCTCGAGTAATTAATCTACCAC 58.117 38.462 12.31 0.35 0.00 4.16
1579 1685 8.523658 CATGATCCTCGAGTAATTAATCTACCA 58.476 37.037 12.31 1.90 0.00 3.25
1580 1686 7.489757 GCATGATCCTCGAGTAATTAATCTACC 59.510 40.741 12.31 0.00 0.00 3.18
1581 1687 7.489757 GGCATGATCCTCGAGTAATTAATCTAC 59.510 40.741 12.31 0.00 0.00 2.59
1582 1688 7.548097 GGCATGATCCTCGAGTAATTAATCTA 58.452 38.462 12.31 0.00 0.00 1.98
1583 1689 6.402222 GGCATGATCCTCGAGTAATTAATCT 58.598 40.000 12.31 0.00 0.00 2.40
1584 1690 5.289675 CGGCATGATCCTCGAGTAATTAATC 59.710 44.000 12.31 2.80 0.00 1.75
1585 1691 5.171476 CGGCATGATCCTCGAGTAATTAAT 58.829 41.667 12.31 0.93 0.00 1.40
1586 1692 4.556233 CGGCATGATCCTCGAGTAATTAA 58.444 43.478 12.31 0.00 0.00 1.40
1587 1693 3.614150 GCGGCATGATCCTCGAGTAATTA 60.614 47.826 12.31 1.92 0.00 1.40
1588 1694 2.868044 GCGGCATGATCCTCGAGTAATT 60.868 50.000 12.31 0.00 0.00 1.40
1589 1695 1.337260 GCGGCATGATCCTCGAGTAAT 60.337 52.381 12.31 4.38 0.00 1.89
1590 1696 0.032130 GCGGCATGATCCTCGAGTAA 59.968 55.000 12.31 0.00 0.00 2.24
1591 1697 1.106944 TGCGGCATGATCCTCGAGTA 61.107 55.000 12.31 0.00 0.00 2.59
1592 1698 2.360949 CTGCGGCATGATCCTCGAGT 62.361 60.000 12.31 0.00 0.00 4.18
1593 1699 1.664017 CTGCGGCATGATCCTCGAG 60.664 63.158 5.13 5.13 0.00 4.04
1594 1700 1.106944 TACTGCGGCATGATCCTCGA 61.107 55.000 1.75 0.00 0.00 4.04
1595 1701 0.941463 GTACTGCGGCATGATCCTCG 60.941 60.000 1.75 0.00 0.00 4.63
1596 1702 0.390860 AGTACTGCGGCATGATCCTC 59.609 55.000 1.75 0.00 0.00 3.71
1597 1703 0.390860 GAGTACTGCGGCATGATCCT 59.609 55.000 1.75 0.00 0.00 3.24
1598 1704 0.390860 AGAGTACTGCGGCATGATCC 59.609 55.000 1.75 0.00 0.00 3.36
1599 1705 1.495878 CAGAGTACTGCGGCATGATC 58.504 55.000 1.75 0.00 37.33 2.92
1600 1706 0.105593 CCAGAGTACTGCGGCATGAT 59.894 55.000 1.75 0.00 42.25 2.45
1601 1707 0.970427 TCCAGAGTACTGCGGCATGA 60.970 55.000 1.75 0.00 42.25 3.07
1602 1708 0.105593 ATCCAGAGTACTGCGGCATG 59.894 55.000 1.75 0.00 42.25 4.06
1603 1709 0.833287 AATCCAGAGTACTGCGGCAT 59.167 50.000 1.75 0.00 42.25 4.40
1604 1710 0.613260 AAATCCAGAGTACTGCGGCA 59.387 50.000 0.00 1.29 42.25 5.69
1605 1711 1.739067 AAAATCCAGAGTACTGCGGC 58.261 50.000 0.00 0.00 42.25 6.53
1606 1712 3.600388 AGAAAAATCCAGAGTACTGCGG 58.400 45.455 0.00 0.00 42.25 5.69
1607 1713 4.932200 AGAAGAAAAATCCAGAGTACTGCG 59.068 41.667 0.00 0.00 42.25 5.18
1608 1714 6.809630 AAGAAGAAAAATCCAGAGTACTGC 57.190 37.500 0.00 0.00 42.25 4.40
1644 1750 3.081804 GGTCGGTTCCAGAATTTGTGAT 58.918 45.455 0.00 0.00 0.00 3.06
1646 1752 2.226330 TGGTCGGTTCCAGAATTTGTG 58.774 47.619 0.00 0.00 33.19 3.33
1662 1770 5.241728 AGTTTTCAGTTATTGGCTTCTGGTC 59.758 40.000 0.00 0.00 0.00 4.02
1663 1771 5.140454 AGTTTTCAGTTATTGGCTTCTGGT 58.860 37.500 0.00 0.00 0.00 4.00
1664 1772 5.712152 AGTTTTCAGTTATTGGCTTCTGG 57.288 39.130 0.00 0.00 0.00 3.86
1742 1854 5.989168 TGGTATTACAGTGTCTTGTCTGTTG 59.011 40.000 0.00 0.00 43.39 3.33
1745 1857 6.398095 TGATGGTATTACAGTGTCTTGTCTG 58.602 40.000 0.00 0.00 37.65 3.51
1912 2027 9.362151 ACTCAATAGTTTTTCCATGTTCCTTTA 57.638 29.630 0.00 0.00 29.00 1.85
1933 2048 4.804665 TGACATTACGTTTTGACGACTCAA 59.195 37.500 5.91 0.00 34.39 3.02
2036 2151 1.132453 GTTAGCAATTCGGAGGGTTGC 59.868 52.381 13.51 13.51 44.28 4.17
2046 2161 9.243637 TGTCAAAAATGTTAGTGTTAGCAATTC 57.756 29.630 0.00 0.00 0.00 2.17
2109 2224 1.553248 AGTGTAAATCTGCGTGGCCTA 59.447 47.619 3.32 0.00 0.00 3.93
2245 2364 7.611467 TGCAGATTCTTGTGATGTTACCTTAAT 59.389 33.333 0.00 0.00 0.00 1.40
2268 2397 0.478072 ATGTTCTGGTGGAAGGTGCA 59.522 50.000 0.00 0.00 34.23 4.57


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

AutoCloner maintained by Alex Coulton.