Multiple sequence alignment - TraesCS5D01G067900

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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 TraesCS5D01G067900 chr5D 100.000 6216 0 0 1 6216 63509061 63515276 0.000000e+00 11479.0
1 TraesCS5D01G067900 chr5D 88.721 727 46 17 2208 2927 560844772 560844075 0.000000e+00 856.0
2 TraesCS5D01G067900 chr5D 90.323 186 18 0 5005 5190 457522859 457523044 1.730000e-60 244.0
3 TraesCS5D01G067900 chr5D 92.308 65 4 1 6071 6135 63547878 63547941 2.390000e-14 91.6
4 TraesCS5D01G067900 chr5D 86.885 61 8 0 4664 4724 457522561 457522621 1.120000e-07 69.4
5 TraesCS5D01G067900 chr5A 89.388 5739 313 129 1 5602 52853700 52859279 0.000000e+00 6951.0
6 TraesCS5D01G067900 chr5A 84.950 598 78 5 2 592 367853640 367853048 4.150000e-166 595.0
7 TraesCS5D01G067900 chr5A 83.766 462 30 18 5689 6133 52859619 52860052 4.520000e-106 396.0
8 TraesCS5D01G067900 chr5A 89.175 194 13 6 5945 6135 53192236 53192424 1.040000e-57 235.0
9 TraesCS5D01G067900 chr5A 81.048 248 22 15 1049 1282 575323203 575323439 2.300000e-39 174.0
10 TraesCS5D01G067900 chr5B 92.314 3396 144 48 2111 5453 67038095 67034764 0.000000e+00 4717.0
11 TraesCS5D01G067900 chr5B 88.281 1408 76 35 716 2082 67039450 67038091 0.000000e+00 1604.0
12 TraesCS5D01G067900 chr5B 89.011 728 44 17 2208 2927 533945792 533945093 0.000000e+00 869.0
13 TraesCS5D01G067900 chr5B 89.451 692 42 14 5461 6135 67034353 67033676 0.000000e+00 845.0
14 TraesCS5D01G067900 chr5B 91.518 448 29 6 2000 2443 30021316 30021758 5.330000e-170 608.0
15 TraesCS5D01G067900 chr5B 90.625 224 13 4 2003 2222 395476484 395476265 2.190000e-74 291.0
16 TraesCS5D01G067900 chr5B 90.860 186 17 0 5005 5190 559462346 559462531 3.720000e-62 250.0
17 TraesCS5D01G067900 chr5B 81.377 247 23 12 1049 1282 559457063 559457299 4.950000e-41 180.0
18 TraesCS5D01G067900 chr5B 91.489 47 4 0 4678 4724 559462067 559462113 1.450000e-06 65.8
19 TraesCS5D01G067900 chr7D 89.684 727 39 17 2208 2927 143316768 143316071 0.000000e+00 894.0
20 TraesCS5D01G067900 chr7D 89.271 727 42 17 2208 2927 143349596 143348899 0.000000e+00 878.0
21 TraesCS5D01G067900 chr7D 93.525 278 12 3 2653 2927 184694288 184694014 5.800000e-110 409.0
22 TraesCS5D01G067900 chr7B 88.950 724 46 16 2208 2924 585075801 585076497 0.000000e+00 863.0
23 TraesCS5D01G067900 chr7B 85.235 596 78 5 1 593 450581502 450580914 6.890000e-169 604.0
24 TraesCS5D01G067900 chr7B 85.304 592 76 6 1 589 448731525 448732108 8.920000e-168 601.0
25 TraesCS5D01G067900 chr3B 87.500 568 64 5 1 562 9430161 9429595 0.000000e+00 649.0
26 TraesCS5D01G067900 chr3B 84.583 480 62 8 118 593 159307495 159307966 3.390000e-127 466.0
27 TraesCS5D01G067900 chr3B 93.204 206 12 2 2000 2205 760025028 760025231 1.010000e-77 302.0
28 TraesCS5D01G067900 chr3B 98.246 57 0 1 6138 6193 778298919 778298863 1.430000e-16 99.0
29 TraesCS5D01G067900 chr2B 86.600 597 69 6 1 593 14314951 14314362 0.000000e+00 649.0
30 TraesCS5D01G067900 chr2B 78.210 514 79 19 1 508 558046654 558047140 1.310000e-76 298.0
31 TraesCS5D01G067900 chr2B 86.154 65 9 0 623 687 557296752 557296816 3.110000e-08 71.3
32 TraesCS5D01G067900 chr2B 92.000 50 2 1 1 48 500887596 500887547 1.120000e-07 69.4
33 TraesCS5D01G067900 chr4A 91.236 445 32 6 2003 2443 675415132 675414691 3.210000e-167 599.0
34 TraesCS5D01G067900 chr4A 86.486 74 6 2 1771 1840 663200206 663200133 1.860000e-10 78.7
35 TraesCS5D01G067900 chr3D 83.417 597 66 16 1 593 105888247 105887680 1.990000e-144 523.0
36 TraesCS5D01G067900 chr3D 82.534 584 69 14 2 581 316952585 316952031 3.370000e-132 483.0
37 TraesCS5D01G067900 chr4D 93.525 278 12 3 2653 2927 506826950 506826676 5.800000e-110 409.0
38 TraesCS5D01G067900 chr4D 87.671 73 9 0 614 686 17428237 17428309 1.110000e-12 86.1
39 TraesCS5D01G067900 chr4D 84.848 66 10 0 621 686 483589912 483589977 4.020000e-07 67.6
40 TraesCS5D01G067900 chr4B 91.039 279 19 5 2169 2443 543723046 543723322 7.610000e-99 372.0
41 TraesCS5D01G067900 chr4B 89.427 227 18 3 2000 2222 546097540 546097764 1.320000e-71 281.0
42 TraesCS5D01G067900 chr4B 92.000 125 10 0 2000 2124 543722927 543723051 6.400000e-40 176.0
43 TraesCS5D01G067900 chr4B 91.964 112 9 0 2332 2443 459192384 459192495 2.320000e-34 158.0
44 TraesCS5D01G067900 chr4B 86.301 73 10 0 614 686 453263096 453263024 5.170000e-11 80.5
45 TraesCS5D01G067900 chr6B 92.233 206 13 2 2003 2208 105644230 105644028 7.880000e-74 289.0
46 TraesCS5D01G067900 chr6D 88.172 93 8 2 589 681 39574720 39574631 2.370000e-19 108.0
47 TraesCS5D01G067900 chr2D 90.164 61 6 0 623 683 8636514 8636574 5.170000e-11 80.5
48 TraesCS5D01G067900 chr2D 83.582 67 11 0 620 686 603132777 603132711 5.200000e-06 63.9
49 TraesCS5D01G067900 chr2A 87.097 62 8 0 622 683 654347079 654347140 3.110000e-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 TraesCS5D01G067900 chr5D 63509061 63515276 6215 False 11479.000000 11479 100.000000 1 6216 1 chr5D.!!$F1 6215
1 TraesCS5D01G067900 chr5D 560844075 560844772 697 True 856.000000 856 88.721000 2208 2927 1 chr5D.!!$R1 719
2 TraesCS5D01G067900 chr5A 52853700 52860052 6352 False 3673.500000 6951 86.577000 1 6133 2 chr5A.!!$F3 6132
3 TraesCS5D01G067900 chr5A 367853048 367853640 592 True 595.000000 595 84.950000 2 592 1 chr5A.!!$R1 590
4 TraesCS5D01G067900 chr5B 67033676 67039450 5774 True 2388.666667 4717 90.015333 716 6135 3 chr5B.!!$R3 5419
5 TraesCS5D01G067900 chr5B 533945093 533945792 699 True 869.000000 869 89.011000 2208 2927 1 chr5B.!!$R2 719
6 TraesCS5D01G067900 chr7D 143316071 143316768 697 True 894.000000 894 89.684000 2208 2927 1 chr7D.!!$R1 719
7 TraesCS5D01G067900 chr7D 143348899 143349596 697 True 878.000000 878 89.271000 2208 2927 1 chr7D.!!$R2 719
8 TraesCS5D01G067900 chr7B 585075801 585076497 696 False 863.000000 863 88.950000 2208 2924 1 chr7B.!!$F2 716
9 TraesCS5D01G067900 chr7B 450580914 450581502 588 True 604.000000 604 85.235000 1 593 1 chr7B.!!$R1 592
10 TraesCS5D01G067900 chr7B 448731525 448732108 583 False 601.000000 601 85.304000 1 589 1 chr7B.!!$F1 588
11 TraesCS5D01G067900 chr3B 9429595 9430161 566 True 649.000000 649 87.500000 1 562 1 chr3B.!!$R1 561
12 TraesCS5D01G067900 chr2B 14314362 14314951 589 True 649.000000 649 86.600000 1 593 1 chr2B.!!$R1 592
13 TraesCS5D01G067900 chr3D 105887680 105888247 567 True 523.000000 523 83.417000 1 593 1 chr3D.!!$R1 592
14 TraesCS5D01G067900 chr3D 316952031 316952585 554 True 483.000000 483 82.534000 2 581 1 chr3D.!!$R2 579

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
677 696 0.259065 TGAGAGGTCCGGCTGTAGAT 59.741 55.000 0.00 0.0 0.00 1.98 F
1489 1527 0.035152 TGCTGCCTGATCATCCGTTT 60.035 50.000 0.00 0.0 0.00 3.60 F
1836 1906 0.525668 GTCGACGACAGCAGGGTATG 60.526 60.000 22.66 0.0 32.09 2.39 F
1869 1939 0.625849 TCCTCCCCCTCTGCATTTTC 59.374 55.000 0.00 0.0 0.00 2.29 F
2367 2453 1.000233 TGCCTTTATGCCCACCCAG 60.000 57.895 0.00 0.0 0.00 4.45 F
3246 3412 1.089920 CTTGTCTTGCCCCATCTTCG 58.910 55.000 0.00 0.0 0.00 3.79 F
4207 4393 0.670162 CCCATCATTCCGCCACAATC 59.330 55.000 0.00 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2159 0.100146 GAACATAGCAGCAGCCAAGC 59.900 55.0 0.00 0.00 43.56 4.01 R
2928 3061 0.816825 ACACTCACACCAGCAAGCTG 60.817 55.0 14.91 14.91 43.26 4.24 R
3506 3675 0.179000 GTGCCTCCACACTCCATAGG 59.821 60.0 0.00 0.00 41.67 2.57 R
3507 3676 0.904649 TGTGCCTCCACACTCCATAG 59.095 55.0 0.00 0.00 46.51 2.23 R
4189 4375 0.670162 GGATTGTGGCGGAATGATGG 59.330 55.0 0.00 0.00 0.00 3.51 R
4779 4986 0.099436 GGCCGAATTCACACATCAGC 59.901 55.0 6.22 0.00 0.00 4.26 R
5654 6266 0.313672 GCGTCCAGGAGCTAGATCAG 59.686 60.0 10.68 1.45 0.00 2.90 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
100 101 8.746530 AGAATCAGACATAGAAATGCACATTTT 58.253 29.630 9.81 3.81 40.77 1.82
109 110 5.475719 AGAAATGCACATTTTGATCACCAG 58.524 37.500 9.81 0.00 40.77 4.00
121 122 4.849813 TGATCACCAGAAGATCACCAAT 57.150 40.909 2.00 0.00 44.98 3.16
127 128 3.524789 ACCAGAAGATCACCAATGGATCA 59.475 43.478 6.16 0.00 42.84 2.92
250 251 3.004354 TTCCTCGCCGGGCCTTTA 61.004 61.111 14.55 0.00 0.00 1.85
449 464 3.075005 AAGCCTTCTCCGCCGCTA 61.075 61.111 0.00 0.00 0.00 4.26
519 534 1.372499 CGTTCTTTCGTCGGAGGCA 60.372 57.895 0.00 0.00 0.00 4.75
530 549 2.202987 GGAGGCAGCGACCATCTG 60.203 66.667 0.69 0.00 34.79 2.90
543 562 4.002506 ATCTGCACCGCCGTGTGA 62.003 61.111 9.42 6.33 42.39 3.58
544 563 4.961511 TCTGCACCGCCGTGTGAC 62.962 66.667 9.42 2.76 42.39 3.67
545 564 4.969196 CTGCACCGCCGTGTGACT 62.969 66.667 9.42 0.00 42.39 3.41
567 586 3.077519 GCGGTAGACCCATGCGAGT 62.078 63.158 0.00 0.00 0.00 4.18
606 625 3.562232 TCCGGTTGGGTCGGCTTT 61.562 61.111 0.00 0.00 46.43 3.51
607 626 2.596338 CCGGTTGGGTCGGCTTTT 60.596 61.111 0.00 0.00 41.07 2.27
632 651 2.265904 CCAGTCAGTGACCGGACGA 61.266 63.158 19.25 0.00 40.26 4.20
640 659 3.512516 GACCGGACGACCTACCCG 61.513 72.222 9.46 0.00 42.64 5.28
648 667 1.444895 CGACCTACCCGGACGTTTG 60.445 63.158 0.73 0.00 44.21 2.93
677 696 0.259065 TGAGAGGTCCGGCTGTAGAT 59.741 55.000 0.00 0.00 0.00 1.98
688 707 3.743396 CCGGCTGTAGATGCTCTTAATTC 59.257 47.826 0.00 0.00 0.00 2.17
701 720 6.866480 TGCTCTTAATTCCAATAAAAGGCAG 58.134 36.000 0.00 0.00 0.00 4.85
774 804 2.751259 TCTGATCATCCAAAACTGCTGC 59.249 45.455 0.00 0.00 0.00 5.25
856 888 1.081376 CTCGACAGTCGACACACCC 60.081 63.158 21.92 1.01 44.82 4.61
857 889 1.792118 CTCGACAGTCGACACACCCA 61.792 60.000 21.92 0.00 44.82 4.51
1230 1265 1.593787 CAGCTCCTTCTCCTTCGCA 59.406 57.895 0.00 0.00 0.00 5.10
1233 1268 0.463620 GCTCCTTCTCCTTCGCATCT 59.536 55.000 0.00 0.00 0.00 2.90
1296 1331 0.655733 CGGTGCGTTTCTTGTCACTT 59.344 50.000 0.00 0.00 0.00 3.16
1424 1462 8.732413 TTTTTCAGATTGATTTCATCTGTTCG 57.268 30.769 9.23 0.00 41.70 3.95
1471 1509 8.408601 ACCAATTAGTAGCTGCTTTATTGAATG 58.591 33.333 26.36 17.88 0.00 2.67
1472 1510 7.380602 CCAATTAGTAGCTGCTTTATTGAATGC 59.619 37.037 26.36 0.00 36.50 3.56
1473 1511 7.814264 ATTAGTAGCTGCTTTATTGAATGCT 57.186 32.000 10.41 0.00 36.81 3.79
1474 1512 5.496133 AGTAGCTGCTTTATTGAATGCTG 57.504 39.130 7.79 0.00 36.81 4.41
1476 1514 2.199236 GCTGCTTTATTGAATGCTGCC 58.801 47.619 13.10 0.00 46.27 4.85
1477 1515 2.159142 GCTGCTTTATTGAATGCTGCCT 60.159 45.455 13.10 0.00 46.27 4.75
1478 1516 3.444916 CTGCTTTATTGAATGCTGCCTG 58.555 45.455 0.00 0.00 36.81 4.85
1479 1517 3.090790 TGCTTTATTGAATGCTGCCTGA 58.909 40.909 0.00 0.00 36.81 3.86
1480 1518 3.702548 TGCTTTATTGAATGCTGCCTGAT 59.297 39.130 0.00 0.00 36.81 2.90
1481 1519 4.202080 TGCTTTATTGAATGCTGCCTGATC 60.202 41.667 0.00 0.00 36.81 2.92
1482 1520 4.202080 GCTTTATTGAATGCTGCCTGATCA 60.202 41.667 0.00 0.00 33.88 2.92
1483 1521 5.509163 GCTTTATTGAATGCTGCCTGATCAT 60.509 40.000 0.00 0.00 33.88 2.45
1484 1522 5.700722 TTATTGAATGCTGCCTGATCATC 57.299 39.130 0.00 0.00 0.00 2.92
1485 1523 1.977056 TGAATGCTGCCTGATCATCC 58.023 50.000 0.00 0.00 0.00 3.51
1486 1524 0.873054 GAATGCTGCCTGATCATCCG 59.127 55.000 0.00 0.00 0.00 4.18
1487 1525 0.182061 AATGCTGCCTGATCATCCGT 59.818 50.000 0.00 0.00 0.00 4.69
1488 1526 0.182061 ATGCTGCCTGATCATCCGTT 59.818 50.000 0.00 0.00 0.00 4.44
1489 1527 0.035152 TGCTGCCTGATCATCCGTTT 60.035 50.000 0.00 0.00 0.00 3.60
1490 1528 0.659957 GCTGCCTGATCATCCGTTTC 59.340 55.000 0.00 0.00 0.00 2.78
1491 1529 0.933097 CTGCCTGATCATCCGTTTCG 59.067 55.000 0.00 0.00 0.00 3.46
1492 1530 0.534873 TGCCTGATCATCCGTTTCGA 59.465 50.000 0.00 0.00 0.00 3.71
1493 1531 1.066502 TGCCTGATCATCCGTTTCGAA 60.067 47.619 0.00 0.00 0.00 3.71
1494 1532 2.006888 GCCTGATCATCCGTTTCGAAA 58.993 47.619 6.47 6.47 0.00 3.46
1495 1533 2.418628 GCCTGATCATCCGTTTCGAAAA 59.581 45.455 13.10 0.00 0.00 2.29
1496 1534 3.119990 GCCTGATCATCCGTTTCGAAAAA 60.120 43.478 13.10 1.64 0.00 1.94
1615 1655 4.094294 GGCAGGAAAACAACAACCTTTTTC 59.906 41.667 0.00 0.00 38.14 2.29
1617 1657 5.411361 GCAGGAAAACAACAACCTTTTTCTT 59.589 36.000 6.12 0.00 38.65 2.52
1618 1658 6.072728 GCAGGAAAACAACAACCTTTTTCTTT 60.073 34.615 6.12 0.00 38.65 2.52
1619 1659 7.518161 CAGGAAAACAACAACCTTTTTCTTTC 58.482 34.615 6.12 0.00 38.65 2.62
1622 1662 8.511321 GGAAAACAACAACCTTTTTCTTTCATT 58.489 29.630 6.12 0.00 38.65 2.57
1623 1663 9.541724 GAAAACAACAACCTTTTTCTTTCATTC 57.458 29.630 0.00 0.00 36.64 2.67
1624 1664 6.885735 ACAACAACCTTTTTCTTTCATTCG 57.114 33.333 0.00 0.00 0.00 3.34
1653 1721 3.815401 TCGATCTCGATCAGATACTGCAA 59.185 43.478 7.59 0.00 42.48 4.08
1765 1835 4.463879 CTCTCCCACAGCAGCGGG 62.464 72.222 0.00 0.00 44.60 6.13
1836 1906 0.525668 GTCGACGACAGCAGGGTATG 60.526 60.000 22.66 0.00 32.09 2.39
1869 1939 0.625849 TCCTCCCCCTCTGCATTTTC 59.374 55.000 0.00 0.00 0.00 2.29
1907 1980 4.021719 AGTGATGAACTGCCAATTTCCTTG 60.022 41.667 0.00 0.00 37.88 3.61
1909 1982 4.022068 TGATGAACTGCCAATTTCCTTGTC 60.022 41.667 0.00 0.00 32.61 3.18
1912 1985 3.733443 ACTGCCAATTTCCTTGTCAAC 57.267 42.857 0.00 0.00 32.61 3.18
2001 2083 6.838382 AGGTGATTTTACTTGTACTCCTGTT 58.162 36.000 0.00 0.00 0.00 3.16
2015 2097 1.939934 TCCTGTTTTGACTGCAACTCG 59.060 47.619 0.00 0.00 32.79 4.18
2025 2107 3.098636 GACTGCAACTCGTTGAAACAAC 58.901 45.455 13.57 0.00 42.93 3.32
2028 2110 3.902150 TGCAACTCGTTGAAACAACAAA 58.098 36.364 13.57 2.18 42.93 2.83
2076 2159 5.291178 TGTGAATTTTGAATGAGCTGGTTG 58.709 37.500 0.00 0.00 0.00 3.77
2216 2301 9.350357 GCAACTAAGTTTATAAGTTTTTAGGGC 57.650 33.333 9.89 9.19 31.21 5.19
2244 2330 9.387123 GCTGTAAATTTCTTCTGTTTTCTAGTG 57.613 33.333 0.00 0.00 0.00 2.74
2358 2444 9.897744 ATGAATTTAATACGATGTGCCTTTATG 57.102 29.630 0.00 0.00 0.00 1.90
2359 2445 7.860373 TGAATTTAATACGATGTGCCTTTATGC 59.140 33.333 0.00 0.00 0.00 3.14
2367 2453 1.000233 TGCCTTTATGCCCACCCAG 60.000 57.895 0.00 0.00 0.00 4.45
2389 2475 4.279420 AGTGAAGCAGCGTCATATCATAGA 59.721 41.667 14.48 0.00 0.00 1.98
2453 2539 2.440627 AGCAACTGGATCATGCCATCTA 59.559 45.455 0.00 0.00 40.93 1.98
2492 2579 8.267894 AGGCATTTAACAGACATTAGTGAGTAT 58.732 33.333 0.00 0.00 0.00 2.12
2641 2737 1.821136 CTTCCATGCCCTTGTCTTTCC 59.179 52.381 0.00 0.00 0.00 3.13
2707 2803 4.319333 GCAAGTGTGAGTGAACTGAATGAG 60.319 45.833 0.00 0.00 0.00 2.90
2785 2881 5.163673 GGTCCAGCAGATGAGATTTTCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
2803 2929 2.795231 TCCTGAGGAAAAGCAGATGG 57.205 50.000 0.00 0.00 34.06 3.51
2816 2942 1.332997 GCAGATGGGAATTGAGAAGCG 59.667 52.381 0.00 0.00 0.00 4.68
2842 2972 4.142337 TGCCACACAATGATTCAGCAATAG 60.142 41.667 0.00 0.00 0.00 1.73
2843 2973 4.142315 GCCACACAATGATTCAGCAATAGT 60.142 41.667 0.00 0.00 0.00 2.12
2844 2974 5.066375 GCCACACAATGATTCAGCAATAGTA 59.934 40.000 0.00 0.00 0.00 1.82
2846 2976 7.682741 GCCACACAATGATTCAGCAATAGTATT 60.683 37.037 0.00 0.00 0.00 1.89
2928 3061 9.755804 ATTTCAAACTGAAGAAAGGAAGAAATC 57.244 29.630 0.00 0.00 37.70 2.17
2949 3088 1.097547 GCTTGCTGGTGTGAGTGTGT 61.098 55.000 0.00 0.00 0.00 3.72
2956 3095 2.628178 CTGGTGTGAGTGTGTCCTTCTA 59.372 50.000 0.00 0.00 0.00 2.10
3036 3193 2.174349 GTCTTCGGCGCTTGCTTG 59.826 61.111 7.64 0.00 39.13 4.01
3037 3194 3.726517 TCTTCGGCGCTTGCTTGC 61.727 61.111 7.64 0.00 39.13 4.01
3038 3195 3.730761 CTTCGGCGCTTGCTTGCT 61.731 61.111 7.64 0.00 39.13 3.91
3039 3196 3.259425 CTTCGGCGCTTGCTTGCTT 62.259 57.895 7.64 0.00 39.13 3.91
3064 3221 4.370917 TGTGCAAAAGAAGCTTTGATTCC 58.629 39.130 0.00 0.00 38.35 3.01
3160 3317 2.487986 CCCCACTGAGCTTTGAACTTCT 60.488 50.000 0.00 0.00 0.00 2.85
3184 3341 6.326161 TCTCTCTCTCTCTCTCTCTGGATAT 58.674 44.000 0.00 0.00 0.00 1.63
3220 3385 4.154296 GCTTGCAGGCCTATGGAG 57.846 61.111 10.18 2.26 0.00 3.86
3246 3412 1.089920 CTTGTCTTGCCCCATCTTCG 58.910 55.000 0.00 0.00 0.00 3.79
3263 3429 3.250040 TCTTCGCTTTGACCTTTAGCAAC 59.750 43.478 0.00 0.00 34.62 4.17
3309 3475 1.747709 CTCTCATGTCCCCAGCTTTG 58.252 55.000 0.00 0.00 0.00 2.77
3329 3495 7.042187 AGCTTTGTCTTCTAATCTAATGATGCG 60.042 37.037 0.00 0.00 32.44 4.73
3425 3594 3.072184 AGTGCCTCCATGATTATGTCCTC 59.928 47.826 0.00 0.00 32.21 3.71
3466 3635 4.529219 TATGGCACGCCTCGGCAG 62.529 66.667 9.92 3.70 42.76 4.85
3496 3665 6.556639 TCATCAACTAGATCTATGCCCTAGT 58.443 40.000 2.11 0.00 43.34 2.57
3501 3670 5.909760 ACTAGATCTATGCCCTAGTTGGAT 58.090 41.667 2.11 0.00 39.84 3.41
3502 3671 6.326970 ACTAGATCTATGCCCTAGTTGGATT 58.673 40.000 2.11 0.00 39.84 3.01
3503 3672 7.479579 ACTAGATCTATGCCCTAGTTGGATTA 58.520 38.462 2.11 0.00 39.84 1.75
3504 3673 7.956315 ACTAGATCTATGCCCTAGTTGGATTAA 59.044 37.037 2.11 0.00 39.84 1.40
3505 3674 7.010339 AGATCTATGCCCTAGTTGGATTAAC 57.990 40.000 0.00 0.00 39.65 2.01
3506 3675 5.562298 TCTATGCCCTAGTTGGATTAACC 57.438 43.478 0.00 0.00 40.24 2.85
3507 3676 3.595190 ATGCCCTAGTTGGATTAACCC 57.405 47.619 0.00 0.00 40.24 4.11
3508 3677 2.568979 TGCCCTAGTTGGATTAACCCT 58.431 47.619 0.00 0.00 40.24 4.34
3509 3678 3.738434 TGCCCTAGTTGGATTAACCCTA 58.262 45.455 0.00 0.00 40.24 3.53
3510 3679 4.312487 TGCCCTAGTTGGATTAACCCTAT 58.688 43.478 0.00 0.00 40.24 2.57
3511 3680 4.104102 TGCCCTAGTTGGATTAACCCTATG 59.896 45.833 0.00 0.00 40.24 2.23
3512 3681 4.506802 GCCCTAGTTGGATTAACCCTATGG 60.507 50.000 0.00 0.00 40.24 2.74
3513 3682 4.911522 CCCTAGTTGGATTAACCCTATGGA 59.088 45.833 0.00 0.00 40.24 3.41
3514 3683 5.013183 CCCTAGTTGGATTAACCCTATGGAG 59.987 48.000 0.00 0.00 40.24 3.86
3515 3684 5.607171 CCTAGTTGGATTAACCCTATGGAGT 59.393 44.000 0.00 0.00 40.24 3.85
3516 3685 5.373812 AGTTGGATTAACCCTATGGAGTG 57.626 43.478 0.00 0.00 40.24 3.51
3547 3716 3.829886 ATGATTTGTGTACACTTGGCG 57.170 42.857 25.60 0.00 0.00 5.69
3588 3760 3.764885 GCGTGTGCTTTCAATTAGGAT 57.235 42.857 0.00 0.00 38.39 3.24
3604 3784 1.202806 AGGATCCACCACACACTGTTG 60.203 52.381 15.82 0.00 42.04 3.33
3643 3823 3.860641 CTTTGGGCACTGACAAAAAGTT 58.139 40.909 0.00 0.00 36.29 2.66
3656 3836 7.042791 ACTGACAAAAAGTTTTCACAACACAAG 60.043 33.333 0.32 0.00 0.00 3.16
4197 4383 2.094675 CCACTGGTGAACCCATCATTC 58.905 52.381 1.93 0.00 44.15 2.67
4199 4385 1.340017 ACTGGTGAACCCATCATTCCG 60.340 52.381 0.00 0.00 44.15 4.30
4200 4386 0.679640 TGGTGAACCCATCATTCCGC 60.680 55.000 0.00 0.00 40.97 5.54
4202 4388 0.679640 GTGAACCCATCATTCCGCCA 60.680 55.000 0.00 0.00 40.97 5.69
4203 4389 0.679640 TGAACCCATCATTCCGCCAC 60.680 55.000 0.00 0.00 31.50 5.01
4207 4393 0.670162 CCCATCATTCCGCCACAATC 59.330 55.000 0.00 0.00 0.00 2.67
4210 4396 1.605710 CATCATTCCGCCACAATCCTC 59.394 52.381 0.00 0.00 0.00 3.71
4274 4460 1.626654 CGTTTCTTGATCGGCAGCGT 61.627 55.000 0.00 0.00 0.00 5.07
4804 5011 4.644234 TGATGTGTGAATTCGGCCATTAAT 59.356 37.500 2.24 0.00 0.00 1.40
4933 5140 2.540101 GGCGTGCTATAGCTTTGTAGTG 59.460 50.000 24.61 7.34 42.66 2.74
5191 5398 4.514577 CGCCTCCTCGCCATCGTT 62.515 66.667 0.00 0.00 36.96 3.85
5229 5437 2.126463 ATGATCGCCGCCGTATCG 60.126 61.111 0.00 0.00 35.54 2.92
5232 5440 4.702081 ATCGCCGCCGTATCGAGC 62.702 66.667 0.00 0.00 35.61 5.03
5266 5474 2.421424 GTGGTGATCTGATTGACCTTGC 59.579 50.000 16.39 7.23 0.00 4.01
5312 5520 5.508200 TGCTATTGTTTTCTTTGTTCCGT 57.492 34.783 0.00 0.00 0.00 4.69
5340 5549 7.222161 TCCTGTAAGTTTTAGTTTCTTCTCCC 58.778 38.462 0.00 0.00 0.00 4.30
5439 5648 0.981183 TGAACCGTGGTAGCCTCATT 59.019 50.000 0.00 0.00 0.00 2.57
5453 5662 7.715249 TGGTAGCCTCATTTATGTTTGATCTAC 59.285 37.037 0.00 0.00 32.67 2.59
5454 5663 7.934120 GGTAGCCTCATTTATGTTTGATCTACT 59.066 37.037 0.00 0.00 33.28 2.57
5487 6099 3.008375 TGGGAACAGGAAGAACATCTCAG 59.992 47.826 0.00 0.00 35.01 3.35
5526 6138 6.361748 GTCACTGTACTACAAAGGTTTACTCG 59.638 42.308 0.00 0.00 0.00 4.18
5532 6144 4.831710 ACTACAAAGGTTTACTCGGTCTCT 59.168 41.667 0.00 0.00 0.00 3.10
5653 6265 1.008938 ACAAGATCTCTGCCCCTACCT 59.991 52.381 0.00 0.00 0.00 3.08
5654 6266 1.691434 CAAGATCTCTGCCCCTACCTC 59.309 57.143 0.00 0.00 0.00 3.85
5767 6666 0.462789 GAATTGCTGGGGCCATTCTG 59.537 55.000 4.39 0.00 43.18 3.02
5810 6709 2.565834 GAGCCCTGTTGGTTCTGTAGTA 59.434 50.000 0.00 0.00 40.97 1.82
5824 6723 6.403878 GTTCTGTAGTATAGGAGGTTTGCAA 58.596 40.000 0.00 0.00 0.00 4.08
5848 6748 7.840342 ACAACAACTCTGCATCTATCTAAAG 57.160 36.000 0.00 0.00 0.00 1.85
5855 6755 7.829725 ACTCTGCATCTATCTAAAGCTATGAG 58.170 38.462 0.00 0.00 0.00 2.90
5931 6851 2.440980 GGGATTGCAGGACCAGGC 60.441 66.667 0.00 0.00 0.00 4.85
6002 6935 5.065914 TGAATCATAAGCATTAGCAGTCCC 58.934 41.667 0.00 0.00 45.49 4.46
6044 6977 0.250858 TGCTGTCCTGGTTGGTGATG 60.251 55.000 0.00 0.00 37.07 3.07
6046 6979 0.401738 CTGTCCTGGTTGGTGATGGT 59.598 55.000 0.00 0.00 37.07 3.55
6080 7014 3.369756 ACGCTGATACATTTGTGGTTACG 59.630 43.478 0.00 0.00 0.00 3.18
6087 7021 2.105134 ACATTTGTGGTTACGGAGACCA 59.895 45.455 3.09 3.09 44.59 4.02
6116 7050 5.237344 GCTGGAATGACAATGTACTATGGAC 59.763 44.000 0.00 0.00 0.00 4.02
6117 7051 6.306643 TGGAATGACAATGTACTATGGACA 57.693 37.500 0.00 0.00 0.00 4.02
6145 7079 8.966155 AGGGACTTTTAAAAGGGAAAATATGA 57.034 30.769 27.23 0.00 40.31 2.15
6146 7080 9.387397 AGGGACTTTTAAAAGGGAAAATATGAA 57.613 29.630 27.23 0.00 40.31 2.57
6147 7081 9.653287 GGGACTTTTAAAAGGGAAAATATGAAG 57.347 33.333 27.23 3.05 40.31 3.02
6148 7082 9.653287 GGACTTTTAAAAGGGAAAATATGAAGG 57.347 33.333 27.23 2.70 40.31 3.46
6154 7088 7.482169 AAAAGGGAAAATATGAAGGAGAACC 57.518 36.000 0.00 0.00 0.00 3.62
6164 7098 2.685202 AGGAGAACCTGGTACCAGC 58.315 57.895 32.98 20.83 45.92 4.85
6165 7099 1.218316 GGAGAACCTGGTACCAGCG 59.782 63.158 32.98 26.78 42.35 5.18
6166 7100 1.448013 GAGAACCTGGTACCAGCGC 60.448 63.158 32.98 23.11 42.35 5.92
6167 7101 2.167398 GAGAACCTGGTACCAGCGCA 62.167 60.000 32.98 2.24 42.35 6.09
6168 7102 2.032071 AACCTGGTACCAGCGCAC 59.968 61.111 32.98 0.00 42.35 5.34
6169 7103 3.546714 AACCTGGTACCAGCGCACC 62.547 63.158 32.98 9.24 42.35 5.01
6170 7104 4.778143 CCTGGTACCAGCGCACCC 62.778 72.222 32.98 1.64 42.35 4.61
6171 7105 3.706373 CTGGTACCAGCGCACCCT 61.706 66.667 28.48 0.00 37.24 4.34
6172 7106 2.284039 TGGTACCAGCGCACCCTA 60.284 61.111 11.60 0.00 33.61 3.53
6173 7107 1.686325 CTGGTACCAGCGCACCCTAT 61.686 60.000 28.48 0.00 37.24 2.57
6174 7108 0.397394 TGGTACCAGCGCACCCTATA 60.397 55.000 11.60 0.00 33.61 1.31
6175 7109 0.974383 GGTACCAGCGCACCCTATAT 59.026 55.000 11.47 0.00 0.00 0.86
6176 7110 1.337823 GGTACCAGCGCACCCTATATG 60.338 57.143 11.47 0.00 0.00 1.78
6177 7111 0.320374 TACCAGCGCACCCTATATGC 59.680 55.000 11.47 0.00 39.81 3.14
6178 7112 1.071299 CCAGCGCACCCTATATGCA 59.929 57.895 11.47 0.00 43.57 3.96
6179 7113 0.534877 CCAGCGCACCCTATATGCAA 60.535 55.000 11.47 0.00 43.57 4.08
6180 7114 1.308047 CAGCGCACCCTATATGCAAA 58.692 50.000 11.47 0.00 43.57 3.68
6181 7115 1.675483 CAGCGCACCCTATATGCAAAA 59.325 47.619 11.47 0.00 43.57 2.44
6182 7116 2.098934 CAGCGCACCCTATATGCAAAAA 59.901 45.455 11.47 0.00 43.57 1.94
6203 7137 5.405935 AAAAATTAGTAAAGGGCAGCCTG 57.594 39.130 12.43 0.00 0.00 4.85
6204 7138 2.736670 ATTAGTAAAGGGCAGCCTGG 57.263 50.000 12.43 0.00 0.00 4.45
6205 7139 1.368374 TTAGTAAAGGGCAGCCTGGT 58.632 50.000 12.43 0.00 0.00 4.00
6206 7140 0.618458 TAGTAAAGGGCAGCCTGGTG 59.382 55.000 12.43 0.00 0.00 4.17
6207 7141 2.035626 TAAAGGGCAGCCTGGTGC 59.964 61.111 12.43 12.66 43.19 5.01
6208 7142 2.839609 TAAAGGGCAGCCTGGTGCA 61.840 57.895 21.31 0.00 45.93 4.57
6209 7143 2.153898 TAAAGGGCAGCCTGGTGCAT 62.154 55.000 21.31 7.89 45.93 3.96
6210 7144 4.753662 AGGGCAGCCTGGTGCATG 62.754 66.667 21.31 0.00 45.93 4.06
6212 7146 2.045045 GGCAGCCTGGTGCATGTA 60.045 61.111 21.31 0.00 45.93 2.29
6213 7147 2.117156 GGCAGCCTGGTGCATGTAG 61.117 63.158 21.31 0.00 45.93 2.74
6214 7148 2.768492 GCAGCCTGGTGCATGTAGC 61.768 63.158 15.83 6.00 43.41 3.58
6215 7149 1.077930 CAGCCTGGTGCATGTAGCT 60.078 57.895 14.15 2.03 45.94 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 4.520179 CATTGGTGATCTTCTGGTGATCA 58.480 43.478 0.00 0.00 45.33 2.92
109 110 3.889815 TGGTGATCCATTGGTGATCTTC 58.110 45.455 1.86 0.00 39.48 2.87
121 122 1.004161 TGGCGATCTTTTGGTGATCCA 59.996 47.619 0.00 0.00 42.66 3.41
127 128 2.955660 TGAACTTTGGCGATCTTTTGGT 59.044 40.909 0.00 0.00 0.00 3.67
196 197 5.445845 GCCGTCTTCGTCTTTAATTTCAAA 58.554 37.500 0.00 0.00 35.01 2.69
543 562 3.674050 ATGGGTCTACCGCCGGAGT 62.674 63.158 11.71 3.70 44.64 3.85
544 563 2.838225 ATGGGTCTACCGCCGGAG 60.838 66.667 11.71 0.00 44.64 4.63
545 564 3.151710 CATGGGTCTACCGCCGGA 61.152 66.667 11.71 0.00 44.64 5.14
567 586 0.733150 CTGACGAGGACGCATGACTA 59.267 55.000 0.00 0.00 43.96 2.59
616 635 2.266627 GGTCGTCCGGTCACTGACT 61.267 63.158 9.08 0.00 32.47 3.41
622 641 2.361610 GGGTAGGTCGTCCGGTCA 60.362 66.667 0.00 0.00 39.05 4.02
632 651 0.540365 TCTCAAACGTCCGGGTAGGT 60.540 55.000 0.00 0.00 41.99 3.08
648 667 1.320507 GGACCTCTCATACCCGTCTC 58.679 60.000 0.00 0.00 0.00 3.36
677 696 6.437162 ACTGCCTTTTATTGGAATTAAGAGCA 59.563 34.615 0.00 0.00 0.00 4.26
774 804 8.192774 TCTCATTATTTGCAAGCCTATCTTTTG 58.807 33.333 0.00 0.00 31.27 2.44
856 888 5.912396 GGTTTTATACATGTGTGTGTGTGTG 59.088 40.000 9.11 0.00 39.39 3.82
857 889 5.277586 CGGTTTTATACATGTGTGTGTGTGT 60.278 40.000 9.11 0.00 39.39 3.72
1310 1345 3.808834 AGACCGATTTCTTTTTCCCCT 57.191 42.857 0.00 0.00 0.00 4.79
1311 1346 4.866508 AAAGACCGATTTCTTTTTCCCC 57.133 40.909 1.99 0.00 42.09 4.81
1424 1462 4.929211 GGTCAAATAAAAACAGGATGCCAC 59.071 41.667 0.00 0.00 42.53 5.01
1471 1509 0.659957 GAAACGGATGATCAGGCAGC 59.340 55.000 0.09 0.00 0.00 5.25
1472 1510 0.933097 CGAAACGGATGATCAGGCAG 59.067 55.000 0.09 0.00 0.00 4.85
1473 1511 0.534873 TCGAAACGGATGATCAGGCA 59.465 50.000 0.09 0.00 0.00 4.75
1474 1512 1.651987 TTCGAAACGGATGATCAGGC 58.348 50.000 0.09 0.00 0.00 4.85
1475 1513 4.678509 TTTTTCGAAACGGATGATCAGG 57.321 40.909 10.79 0.00 0.00 3.86
1494 1532 2.169769 CCATGGATCAGGCAGCATTTTT 59.830 45.455 5.56 0.00 0.00 1.94
1495 1533 1.760613 CCATGGATCAGGCAGCATTTT 59.239 47.619 5.56 0.00 0.00 1.82
1496 1534 1.410004 CCATGGATCAGGCAGCATTT 58.590 50.000 5.56 0.00 0.00 2.32
1615 1655 6.138449 GAGATCGATGATCACGAATGAAAG 57.862 41.667 19.30 0.00 41.12 2.62
1653 1721 4.324267 ACTCAAAACGCTGCCTAGTTAAT 58.676 39.130 0.00 0.00 0.00 1.40
1836 1906 1.346068 GGGAGGATGAGATGGTACTGC 59.654 57.143 0.00 0.00 0.00 4.40
1837 1907 1.974236 GGGGAGGATGAGATGGTACTG 59.026 57.143 0.00 0.00 0.00 2.74
1841 1911 0.104725 GAGGGGGAGGATGAGATGGT 60.105 60.000 0.00 0.00 0.00 3.55
1869 1939 8.449397 CAGTTCATCACTTCATCTAAAAGAAGG 58.551 37.037 7.05 0.00 44.20 3.46
1907 1980 6.405842 CCTGGCCTTTAATTTATCCAGTTGAC 60.406 42.308 3.32 0.00 39.42 3.18
1909 1982 5.682212 GCCTGGCCTTTAATTTATCCAGTTG 60.682 44.000 7.66 0.00 39.42 3.16
1912 1985 4.218312 AGCCTGGCCTTTAATTTATCCAG 58.782 43.478 16.57 0.00 40.43 3.86
2001 2083 3.189495 TGTTTCAACGAGTTGCAGTCAAA 59.811 39.130 10.83 3.90 40.24 2.69
2015 2097 6.366061 GGATTATCTGCCTTTGTTGTTTCAAC 59.634 38.462 5.78 5.78 0.00 3.18
2028 2110 7.008941 AGCATGATTAAAAGGATTATCTGCCT 58.991 34.615 0.00 0.00 35.61 4.75
2051 2134 3.924686 CCAGCTCATTCAAAATTCACAGC 59.075 43.478 0.00 0.00 0.00 4.40
2076 2159 0.100146 GAACATAGCAGCAGCCAAGC 59.900 55.000 0.00 0.00 43.56 4.01
2195 2278 8.736244 CAGCTGCCCTAAAAACTTATAAACTTA 58.264 33.333 0.00 0.00 0.00 2.24
2197 2280 6.719829 ACAGCTGCCCTAAAAACTTATAAACT 59.280 34.615 15.27 0.00 0.00 2.66
2198 2281 6.920817 ACAGCTGCCCTAAAAACTTATAAAC 58.079 36.000 15.27 0.00 0.00 2.01
2201 2284 8.817092 ATTTACAGCTGCCCTAAAAACTTATA 57.183 30.769 15.27 0.00 0.00 0.98
2202 2285 7.718334 ATTTACAGCTGCCCTAAAAACTTAT 57.282 32.000 15.27 0.00 0.00 1.73
2203 2286 7.533289 AATTTACAGCTGCCCTAAAAACTTA 57.467 32.000 15.27 0.00 0.00 2.24
2205 2288 6.267699 AGAAATTTACAGCTGCCCTAAAAACT 59.732 34.615 15.27 9.26 0.00 2.66
2206 2289 6.455647 AGAAATTTACAGCTGCCCTAAAAAC 58.544 36.000 15.27 7.41 0.00 2.43
2211 2294 4.943705 CAGAAGAAATTTACAGCTGCCCTA 59.056 41.667 15.27 0.00 0.00 3.53
2216 2301 9.604626 CTAGAAAACAGAAGAAATTTACAGCTG 57.395 33.333 13.48 13.48 0.00 4.24
2244 2330 1.692519 ACCAGTCTGACAGGTTGTACC 59.307 52.381 18.02 0.00 33.97 3.34
2282 2368 1.301165 GCCAAGCCTGCAACCAAAG 60.301 57.895 0.00 0.00 0.00 2.77
2331 2417 9.897744 ATAAAGGCACATCGTATTAAATTCATG 57.102 29.630 0.00 0.00 0.00 3.07
2358 2444 2.674380 CTGCTTCACTGGGTGGGC 60.674 66.667 0.00 4.29 33.87 5.36
2359 2445 2.674380 GCTGCTTCACTGGGTGGG 60.674 66.667 0.00 0.00 33.87 4.61
2367 2453 4.550422 TCTATGATATGACGCTGCTTCAC 58.450 43.478 11.22 0.00 0.00 3.18
2453 2539 8.989131 TCTGTTAAATGCCTACCTAATTAGAGT 58.011 33.333 14.28 11.91 0.00 3.24
2492 2579 6.139679 AGTCCCTGATTCTTTCATTTACCA 57.860 37.500 0.00 0.00 32.72 3.25
2496 2586 6.983906 ACAAAGTCCCTGATTCTTTCATTT 57.016 33.333 0.00 0.00 32.72 2.32
2530 2620 1.683385 GCCCAATCACCAGGCTTTATC 59.317 52.381 0.00 0.00 43.62 1.75
2620 2712 2.519013 GAAAGACAAGGGCATGGAAGT 58.481 47.619 0.00 0.00 0.00 3.01
2739 2835 2.997980 TGACCAAAGCTTGACTTGACA 58.002 42.857 0.00 0.00 39.09 3.58
2785 2881 1.283029 TCCCATCTGCTTTTCCTCAGG 59.717 52.381 0.00 0.00 0.00 3.86
2803 2929 2.032178 GTGGCATACGCTTCTCAATTCC 59.968 50.000 0.00 0.00 38.60 3.01
2816 2942 3.129113 TGCTGAATCATTGTGTGGCATAC 59.871 43.478 7.51 7.51 0.00 2.39
2842 2972 6.092122 GCCAACCAGATTTGCCTTAAAAATAC 59.908 38.462 0.00 0.00 0.00 1.89
2843 2973 6.169800 GCCAACCAGATTTGCCTTAAAAATA 58.830 36.000 0.00 0.00 0.00 1.40
2844 2974 5.003160 GCCAACCAGATTTGCCTTAAAAAT 58.997 37.500 0.00 0.00 0.00 1.82
2846 2976 3.389329 TGCCAACCAGATTTGCCTTAAAA 59.611 39.130 0.00 0.00 0.00 1.52
2928 3061 0.816825 ACACTCACACCAGCAAGCTG 60.817 55.000 14.91 14.91 43.26 4.24
3006 3159 2.749621 GCCGAAGACCATCAAATCAAGT 59.250 45.455 0.00 0.00 0.00 3.16
3039 3196 2.166050 TCAAAGCTTCTTTTGCACAGCA 59.834 40.909 0.00 0.00 37.83 4.41
3160 3317 3.994317 TCCAGAGAGAGAGAGAGAGAGA 58.006 50.000 0.00 0.00 0.00 3.10
3184 3341 1.308047 CCACAGTGTGTGCTGCTTTA 58.692 50.000 21.48 0.00 46.51 1.85
3220 3385 3.376918 GGCAAGACAAGGGCTGCC 61.377 66.667 11.05 11.05 35.20 4.85
3246 3412 2.608016 GCAGGTTGCTAAAGGTCAAAGC 60.608 50.000 0.00 0.00 40.96 3.51
3263 3429 3.137176 TGATTAGGGATGAGAAAGGCAGG 59.863 47.826 0.00 0.00 0.00 4.85
3309 3475 7.938563 AGAACGCATCATTAGATTAGAAGAC 57.061 36.000 0.00 0.00 30.20 3.01
3425 3594 3.512035 TGCACACACCACTTGCAG 58.488 55.556 0.00 0.00 41.29 4.41
3466 3635 6.128063 GGCATAGATCTAGTTGATGAATTGCC 60.128 42.308 16.68 16.68 36.88 4.52
3467 3636 6.128063 GGGCATAGATCTAGTTGATGAATTGC 60.128 42.308 8.70 8.56 35.14 3.56
3468 3637 7.166851 AGGGCATAGATCTAGTTGATGAATTG 58.833 38.462 8.70 0.00 35.14 2.32
3469 3638 7.327064 AGGGCATAGATCTAGTTGATGAATT 57.673 36.000 8.70 0.00 35.14 2.17
3496 3665 4.080015 CCACACTCCATAGGGTTAATCCAA 60.080 45.833 7.70 0.00 37.20 3.53
3498 3667 3.714798 TCCACACTCCATAGGGTTAATCC 59.285 47.826 0.00 0.00 37.20 3.01
3499 3668 4.202367 CCTCCACACTCCATAGGGTTAATC 60.202 50.000 0.00 0.00 37.20 1.75
3501 3670 3.112263 CCTCCACACTCCATAGGGTTAA 58.888 50.000 0.00 0.00 37.20 2.01
3502 3671 2.759355 CCTCCACACTCCATAGGGTTA 58.241 52.381 0.00 0.00 37.20 2.85
3503 3672 1.584724 CCTCCACACTCCATAGGGTT 58.415 55.000 0.00 0.00 37.20 4.11
3504 3673 0.983378 GCCTCCACACTCCATAGGGT 60.983 60.000 0.00 0.00 41.23 4.34
3505 3674 0.982852 TGCCTCCACACTCCATAGGG 60.983 60.000 0.00 0.00 0.00 3.53
3506 3675 0.179000 GTGCCTCCACACTCCATAGG 59.821 60.000 0.00 0.00 41.67 2.57
3507 3676 0.904649 TGTGCCTCCACACTCCATAG 59.095 55.000 0.00 0.00 46.51 2.23
3508 3677 3.081048 TGTGCCTCCACACTCCATA 57.919 52.632 0.00 0.00 46.51 2.74
3509 3678 3.905454 TGTGCCTCCACACTCCAT 58.095 55.556 0.00 0.00 46.51 3.41
3579 3751 3.691118 CAGTGTGTGGTGGATCCTAATTG 59.309 47.826 14.23 0.00 37.07 2.32
3604 3784 4.749598 CCAAAGCAGGTTGTTTAATTGGAC 59.250 41.667 0.00 0.00 38.64 4.02
3621 3801 2.204237 CTTTTTGTCAGTGCCCAAAGC 58.796 47.619 7.54 0.00 44.14 3.51
3643 3823 5.689514 CAGTGTTCAAACTTGTGTTGTGAAA 59.310 36.000 0.00 0.00 36.26 2.69
3656 3836 6.145534 TGACTCGTATCAATCAGTGTTCAAAC 59.854 38.462 0.00 0.00 0.00 2.93
3755 3940 7.141363 GCCAGAAAATACTATTAGCACCATTG 58.859 38.462 0.00 0.00 0.00 2.82
4189 4375 0.670162 GGATTGTGGCGGAATGATGG 59.330 55.000 0.00 0.00 0.00 3.51
4197 4383 1.143838 TGATCGAGGATTGTGGCGG 59.856 57.895 0.00 0.00 0.00 6.13
4199 4385 1.737838 TTGTGATCGAGGATTGTGGC 58.262 50.000 0.00 0.00 0.00 5.01
4200 4386 2.615447 CCATTGTGATCGAGGATTGTGG 59.385 50.000 0.00 0.00 0.00 4.17
4202 4388 2.292267 GCCATTGTGATCGAGGATTGT 58.708 47.619 0.00 0.00 0.00 2.71
4203 4389 1.605710 GGCCATTGTGATCGAGGATTG 59.394 52.381 0.00 0.00 0.00 2.67
4207 4393 1.233019 GATGGCCATTGTGATCGAGG 58.767 55.000 21.84 0.00 0.00 4.63
4210 4396 1.944035 CCGATGGCCATTGTGATCG 59.056 57.895 27.92 21.83 37.93 3.69
4493 4682 2.095161 AGTTGTTCTCGTCCTGATCGAC 60.095 50.000 0.00 0.00 33.71 4.20
4725 4924 5.537188 AGATCAAGAACAGTGTGAGAAGTC 58.463 41.667 0.00 0.00 0.00 3.01
4726 4925 5.543507 AGATCAAGAACAGTGTGAGAAGT 57.456 39.130 0.00 0.00 0.00 3.01
4732 4931 6.148315 TGCAATAGAAGATCAAGAACAGTGTG 59.852 38.462 0.00 0.00 0.00 3.82
4733 4932 6.233434 TGCAATAGAAGATCAAGAACAGTGT 58.767 36.000 0.00 0.00 0.00 3.55
4763 4970 7.062839 CACACATCAGCTAAGAGTTAAGAGAAC 59.937 40.741 0.00 0.00 0.00 3.01
4766 4973 6.625362 TCACACATCAGCTAAGAGTTAAGAG 58.375 40.000 0.00 0.00 0.00 2.85
4767 4974 6.590234 TCACACATCAGCTAAGAGTTAAGA 57.410 37.500 0.00 0.00 0.00 2.10
4768 4975 7.840342 ATTCACACATCAGCTAAGAGTTAAG 57.160 36.000 0.00 0.00 0.00 1.85
4769 4976 7.063426 CGAATTCACACATCAGCTAAGAGTTAA 59.937 37.037 6.22 0.00 0.00 2.01
4770 4977 6.531594 CGAATTCACACATCAGCTAAGAGTTA 59.468 38.462 6.22 0.00 0.00 2.24
4771 4978 5.349817 CGAATTCACACATCAGCTAAGAGTT 59.650 40.000 6.22 0.00 0.00 3.01
4772 4979 4.867047 CGAATTCACACATCAGCTAAGAGT 59.133 41.667 6.22 0.00 0.00 3.24
4775 4982 3.242543 GCCGAATTCACACATCAGCTAAG 60.243 47.826 6.22 0.00 0.00 2.18
4779 4986 0.099436 GGCCGAATTCACACATCAGC 59.901 55.000 6.22 0.00 0.00 4.26
4933 5140 1.652563 GAGACAAAACCACACGGCC 59.347 57.895 0.00 0.00 34.57 6.13
4974 5181 1.734477 CAACTCCGGCGTCAGTGAG 60.734 63.158 6.01 7.38 0.00 3.51
4975 5182 2.338620 CAACTCCGGCGTCAGTGA 59.661 61.111 6.01 0.00 0.00 3.41
5235 5443 2.282180 ATCACCACGGGTTGCACC 60.282 61.111 0.00 0.00 37.60 5.01
5237 5445 1.302431 CAGATCACCACGGGTTGCA 60.302 57.895 0.00 0.00 31.02 4.08
5245 5453 2.421424 GCAAGGTCAATCAGATCACCAC 59.579 50.000 12.26 0.97 0.00 4.16
5266 5474 8.012241 GCAAGAACTACAAGAACACATTTCTAG 58.988 37.037 0.00 0.00 0.00 2.43
5312 5520 9.543783 GAGAAGAAACTAAAACTTACAGGAGAA 57.456 33.333 0.00 0.00 0.00 2.87
5340 5549 3.601435 TCACTCAAGTCTAGACGAGAGG 58.399 50.000 32.34 25.25 39.60 3.69
5453 5662 5.237236 TCCTGTTCCCAAGGTTACTTAAG 57.763 43.478 0.00 0.00 34.49 1.85
5454 5663 5.370289 TCTTCCTGTTCCCAAGGTTACTTAA 59.630 40.000 0.00 0.00 34.49 1.85
5487 6099 0.604780 AGTGACACACTGAGCCATGC 60.605 55.000 8.59 0.00 43.63 4.06
5526 6138 3.330267 CAGCCTACAAAGACAAGAGACC 58.670 50.000 0.00 0.00 0.00 3.85
5532 6144 0.476338 TGCCCAGCCTACAAAGACAA 59.524 50.000 0.00 0.00 0.00 3.18
5626 6238 3.274288 GGGCAGAGATCTTGTTAAGGTG 58.726 50.000 0.00 0.00 0.00 4.00
5633 6245 1.008938 AGGTAGGGGCAGAGATCTTGT 59.991 52.381 0.00 0.00 0.00 3.16
5653 6265 1.974265 CGTCCAGGAGCTAGATCAGA 58.026 55.000 10.68 0.37 0.00 3.27
5654 6266 0.313672 GCGTCCAGGAGCTAGATCAG 59.686 60.000 10.68 1.45 0.00 2.90
5824 6723 6.314896 GCTTTAGATAGATGCAGAGTTGTTGT 59.685 38.462 0.00 0.00 0.00 3.32
5848 6748 2.424557 CTCCATGCCATCACTCATAGC 58.575 52.381 0.00 0.00 0.00 2.97
5855 6755 0.818445 CTCCAGCTCCATGCCATCAC 60.818 60.000 0.00 0.00 44.23 3.06
5931 6851 3.472283 ACAGCCTCATTCAGAGCTATG 57.528 47.619 0.69 0.69 43.31 2.23
6002 6935 2.409870 GCATCAAAGCCCAGGTCCG 61.410 63.158 0.00 0.00 0.00 4.79
6054 6987 4.575885 ACCACAAATGTATCAGCGTAACT 58.424 39.130 0.00 0.00 0.00 2.24
6056 6989 5.062433 CGTAACCACAAATGTATCAGCGTAA 59.938 40.000 0.00 0.00 0.00 3.18
6058 6991 3.369756 CGTAACCACAAATGTATCAGCGT 59.630 43.478 0.00 0.00 0.00 5.07
6059 6992 3.242284 CCGTAACCACAAATGTATCAGCG 60.242 47.826 0.00 0.00 0.00 5.18
6061 6994 5.291128 GTCTCCGTAACCACAAATGTATCAG 59.709 44.000 0.00 0.00 0.00 2.90
6080 7014 3.817647 GTCATTCCAGCAATATGGTCTCC 59.182 47.826 0.00 0.00 41.43 3.71
6087 7021 9.006839 CATAGTACATTGTCATTCCAGCAATAT 57.993 33.333 0.00 0.00 32.33 1.28
6090 7024 5.589855 CCATAGTACATTGTCATTCCAGCAA 59.410 40.000 0.00 0.00 0.00 3.91
6116 7050 8.746052 ATTTTCCCTTTTAAAAGTCCCTTTTG 57.254 30.769 23.04 8.04 42.61 2.44
6134 7068 4.889995 CCAGGTTCTCCTTCATATTTTCCC 59.110 45.833 0.00 0.00 43.07 3.97
6135 7069 5.510430 ACCAGGTTCTCCTTCATATTTTCC 58.490 41.667 0.00 0.00 43.07 3.13
6137 7071 6.011981 TGGTACCAGGTTCTCCTTCATATTTT 60.012 38.462 11.60 0.00 43.07 1.82
6138 7072 5.491078 TGGTACCAGGTTCTCCTTCATATTT 59.509 40.000 11.60 0.00 43.07 1.40
6139 7073 5.036916 TGGTACCAGGTTCTCCTTCATATT 58.963 41.667 11.60 0.00 43.07 1.28
6140 7074 4.631234 TGGTACCAGGTTCTCCTTCATAT 58.369 43.478 11.60 0.00 43.07 1.78
6141 7075 4.030913 CTGGTACCAGGTTCTCCTTCATA 58.969 47.826 31.15 0.00 43.07 2.15
6142 7076 2.840651 CTGGTACCAGGTTCTCCTTCAT 59.159 50.000 31.15 0.00 43.07 2.57
6143 7077 2.257207 CTGGTACCAGGTTCTCCTTCA 58.743 52.381 31.15 0.00 43.07 3.02
6144 7078 1.066071 GCTGGTACCAGGTTCTCCTTC 60.066 57.143 36.91 17.33 43.07 3.46
6145 7079 0.984995 GCTGGTACCAGGTTCTCCTT 59.015 55.000 36.91 0.00 43.07 3.36
6146 7080 1.258445 CGCTGGTACCAGGTTCTCCT 61.258 60.000 36.91 0.00 46.37 3.69
6147 7081 1.218316 CGCTGGTACCAGGTTCTCC 59.782 63.158 36.91 21.13 43.77 3.71
6148 7082 1.448013 GCGCTGGTACCAGGTTCTC 60.448 63.158 36.91 21.78 43.77 2.87
6149 7083 2.214216 TGCGCTGGTACCAGGTTCT 61.214 57.895 36.91 0.00 43.77 3.01
6150 7084 2.033194 GTGCGCTGGTACCAGGTTC 61.033 63.158 36.91 22.45 43.77 3.62
6151 7085 2.032071 GTGCGCTGGTACCAGGTT 59.968 61.111 36.91 0.00 43.77 3.50
6157 7091 1.939838 GCATATAGGGTGCGCTGGTAC 60.940 57.143 9.73 0.00 32.29 3.34
6158 7092 0.320374 GCATATAGGGTGCGCTGGTA 59.680 55.000 9.73 0.00 32.29 3.25
6159 7093 1.071471 GCATATAGGGTGCGCTGGT 59.929 57.895 9.73 0.00 32.29 4.00
6160 7094 0.534877 TTGCATATAGGGTGCGCTGG 60.535 55.000 9.73 0.00 45.37 4.85
6161 7095 1.308047 TTTGCATATAGGGTGCGCTG 58.692 50.000 9.73 0.00 45.37 5.18
6162 7096 2.051334 TTTTGCATATAGGGTGCGCT 57.949 45.000 9.73 0.00 45.37 5.92
6163 7097 2.861462 TTTTTGCATATAGGGTGCGC 57.139 45.000 0.00 0.00 45.37 6.09
6181 7115 4.222810 CCAGGCTGCCCTTTACTAATTTTT 59.777 41.667 16.57 0.00 40.33 1.94
6182 7116 3.769300 CCAGGCTGCCCTTTACTAATTTT 59.231 43.478 16.57 0.00 40.33 1.82
6183 7117 3.245622 ACCAGGCTGCCCTTTACTAATTT 60.246 43.478 16.57 0.00 40.33 1.82
6184 7118 2.311841 ACCAGGCTGCCCTTTACTAATT 59.688 45.455 16.57 0.00 40.33 1.40
6185 7119 1.923148 ACCAGGCTGCCCTTTACTAAT 59.077 47.619 16.57 0.00 40.33 1.73
6186 7120 1.004277 CACCAGGCTGCCCTTTACTAA 59.996 52.381 16.57 0.00 40.33 2.24
6187 7121 0.618458 CACCAGGCTGCCCTTTACTA 59.382 55.000 16.57 0.00 40.33 1.82
6188 7122 1.380302 CACCAGGCTGCCCTTTACT 59.620 57.895 16.57 0.00 40.33 2.24
6189 7123 2.343426 GCACCAGGCTGCCCTTTAC 61.343 63.158 16.57 0.00 40.33 2.01
6190 7124 2.035626 GCACCAGGCTGCCCTTTA 59.964 61.111 16.57 0.00 40.33 1.85
6191 7125 3.534704 ATGCACCAGGCTGCCCTTT 62.535 57.895 16.57 0.00 45.15 3.11
6192 7126 3.988678 ATGCACCAGGCTGCCCTT 61.989 61.111 16.57 0.00 45.15 3.95
6193 7127 4.753662 CATGCACCAGGCTGCCCT 62.754 66.667 16.57 0.00 45.15 5.19
6194 7128 3.643595 TACATGCACCAGGCTGCCC 62.644 63.158 16.57 0.00 45.15 5.36
6195 7129 2.045045 TACATGCACCAGGCTGCC 60.045 61.111 11.65 11.65 45.15 4.85
6196 7130 2.768492 GCTACATGCACCAGGCTGC 61.768 63.158 9.56 0.00 45.15 5.25
6197 7131 1.077930 AGCTACATGCACCAGGCTG 60.078 57.895 7.75 7.75 45.94 4.85
6198 7132 3.408229 AGCTACATGCACCAGGCT 58.592 55.556 0.00 0.00 45.94 4.58


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

AutoCloner maintained by Alex Coulton.