Multiple sequence alignment - TraesCS7A01G308500

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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 TraesCS7A01G308500 chr7A 100.000 2339 0 0 1 2339 436737456 436739794 0.000000e+00 4320.0
1 TraesCS7A01G308500 chr7A 92.593 81 4 2 1527 1606 113812654 113812733 5.280000e-22 115.0
2 TraesCS7A01G308500 chr3D 93.491 845 49 3 4 847 263392169 263391330 0.000000e+00 1251.0
3 TraesCS7A01G308500 chr3D 93.278 848 52 2 2 848 263385331 263384488 0.000000e+00 1245.0
4 TraesCS7A01G308500 chr1D 93.388 847 50 3 1 846 462846842 462847683 0.000000e+00 1249.0
5 TraesCS7A01G308500 chr5D 93.075 852 51 8 1 849 85565045 85565891 0.000000e+00 1240.0
6 TraesCS7A01G308500 chr5D 93.822 518 31 1 847 1363 383586824 383587341 0.000000e+00 778.0
7 TraesCS7A01G308500 chr5D 84.957 698 86 9 1607 2287 417047113 417046418 0.000000e+00 689.0
8 TraesCS7A01G308500 chr5D 84.425 687 92 5 1615 2287 487530526 487531211 0.000000e+00 662.0
9 TraesCS7A01G308500 chr5D 80.658 760 111 25 1600 2339 497300807 497300064 7.300000e-155 556.0
10 TraesCS7A01G308500 chr5D 91.358 81 5 2 1527 1606 462949565 462949644 2.460000e-20 110.0
11 TraesCS7A01G308500 chr5D 95.000 60 3 0 2280 2339 497300013 497299954 6.880000e-16 95.3
12 TraesCS7A01G308500 chr5D 95.000 60 3 0 2280 2339 497300068 497300009 6.880000e-16 95.3
13 TraesCS7A01G308500 chr3A 93.278 848 46 6 1 847 659983202 659984039 0.000000e+00 1240.0
14 TraesCS7A01G308500 chr3A 93.254 845 49 5 4 846 544158670 544159508 0.000000e+00 1238.0
15 TraesCS7A01G308500 chr6A 93.160 848 51 4 1 847 184668786 184669627 0.000000e+00 1238.0
16 TraesCS7A01G308500 chr2D 93.136 845 52 3 4 847 431495566 431494727 0.000000e+00 1234.0
17 TraesCS7A01G308500 chr2D 94.788 518 26 1 847 1363 308681890 308681373 0.000000e+00 806.0
18 TraesCS7A01G308500 chr2D 94.402 518 28 1 847 1363 308678459 308677942 0.000000e+00 795.0
19 TraesCS7A01G308500 chr2D 92.683 82 2 4 1527 1606 340930293 340930214 5.280000e-22 115.0
20 TraesCS7A01G308500 chr2D 90.244 82 4 4 1527 1606 329566021 329566100 1.140000e-18 104.0
21 TraesCS7A01G308500 chr2A 93.051 849 52 4 4 850 445384270 445383427 0.000000e+00 1234.0
22 TraesCS7A01G308500 chr2A 93.834 519 31 1 847 1364 89174907 89175425 0.000000e+00 780.0
23 TraesCS7A01G308500 chr2A 93.654 520 32 1 847 1365 192002864 192003383 0.000000e+00 776.0
24 TraesCS7A01G308500 chr2A 91.250 80 5 2 1527 1605 82338592 82338670 8.840000e-20 108.0
25 TraesCS7A01G308500 chr4D 94.015 518 29 2 847 1363 469444986 469444470 0.000000e+00 784.0
26 TraesCS7A01G308500 chr4D 83.378 752 98 12 1615 2339 434931328 434930577 0.000000e+00 671.0
27 TraesCS7A01G308500 chr4D 84.615 676 81 15 1615 2270 439729030 439729702 0.000000e+00 651.0
28 TraesCS7A01G308500 chr4D 96.970 33 1 0 1365 1397 156570873 156570905 3.250000e-04 56.5
29 TraesCS7A01G308500 chr4D 96.970 33 1 0 1365 1397 259791153 259791185 3.250000e-04 56.5
30 TraesCS7A01G308500 chr2B 93.536 526 32 2 847 1370 793363810 793364335 0.000000e+00 782.0
31 TraesCS7A01G308500 chr3B 94.129 511 29 1 855 1364 161677992 161677482 0.000000e+00 776.0
32 TraesCS7A01G308500 chr3B 82.249 738 100 25 1625 2339 245350321 245349592 1.990000e-170 608.0
33 TraesCS7A01G308500 chr6D 93.642 519 32 1 847 1364 338920516 338921034 0.000000e+00 774.0
34 TraesCS7A01G308500 chr7D 84.253 743 84 17 1625 2339 571879560 571878823 0.000000e+00 693.0
35 TraesCS7A01G308500 chr7D 85.125 679 82 8 1625 2287 517354305 517353630 0.000000e+00 676.0
36 TraesCS7A01G308500 chr7D 83.644 697 95 10 1601 2279 153060854 153061549 2.530000e-179 638.0
37 TraesCS7A01G308500 chr7D 93.277 119 8 0 1405 1523 101436019 101436137 2.390000e-40 176.0
38 TraesCS7A01G308500 chr5A 83.134 753 97 18 1615 2339 657103597 657102847 0.000000e+00 660.0
39 TraesCS7A01G308500 chr5A 82.609 161 16 6 2191 2339 636994924 636994764 5.240000e-27 132.0
40 TraesCS7A01G308500 chr7B 82.174 690 105 11 1601 2272 115079957 115080646 5.600000e-161 577.0
41 TraesCS7A01G308500 chr7B 90.123 81 6 2 1527 1606 626033388 626033309 1.140000e-18 104.0
42 TraesCS7A01G308500 chr6B 93.827 81 5 0 1527 1607 270260276 270260356 3.160000e-24 122.0
43 TraesCS7A01G308500 chr1B 88.889 81 9 0 1527 1607 332331004 332331084 1.480000e-17 100.0
44 TraesCS7A01G308500 chr4B 88.889 81 7 2 1527 1606 665389106 665389185 5.320000e-17 99.0


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 TraesCS7A01G308500 chr7A 436737456 436739794 2338 False 4320.000000 4320 100.000000 1 2339 1 chr7A.!!$F2 2338
1 TraesCS7A01G308500 chr3D 263391330 263392169 839 True 1251.000000 1251 93.491000 4 847 1 chr3D.!!$R2 843
2 TraesCS7A01G308500 chr3D 263384488 263385331 843 True 1245.000000 1245 93.278000 2 848 1 chr3D.!!$R1 846
3 TraesCS7A01G308500 chr1D 462846842 462847683 841 False 1249.000000 1249 93.388000 1 846 1 chr1D.!!$F1 845
4 TraesCS7A01G308500 chr5D 85565045 85565891 846 False 1240.000000 1240 93.075000 1 849 1 chr5D.!!$F1 848
5 TraesCS7A01G308500 chr5D 383586824 383587341 517 False 778.000000 778 93.822000 847 1363 1 chr5D.!!$F2 516
6 TraesCS7A01G308500 chr5D 417046418 417047113 695 True 689.000000 689 84.957000 1607 2287 1 chr5D.!!$R1 680
7 TraesCS7A01G308500 chr5D 487530526 487531211 685 False 662.000000 662 84.425000 1615 2287 1 chr5D.!!$F4 672
8 TraesCS7A01G308500 chr5D 497299954 497300807 853 True 248.866667 556 90.219333 1600 2339 3 chr5D.!!$R2 739
9 TraesCS7A01G308500 chr3A 659983202 659984039 837 False 1240.000000 1240 93.278000 1 847 1 chr3A.!!$F2 846
10 TraesCS7A01G308500 chr3A 544158670 544159508 838 False 1238.000000 1238 93.254000 4 846 1 chr3A.!!$F1 842
11 TraesCS7A01G308500 chr6A 184668786 184669627 841 False 1238.000000 1238 93.160000 1 847 1 chr6A.!!$F1 846
12 TraesCS7A01G308500 chr2D 431494727 431495566 839 True 1234.000000 1234 93.136000 4 847 1 chr2D.!!$R2 843
13 TraesCS7A01G308500 chr2D 308677942 308681890 3948 True 800.500000 806 94.595000 847 1363 2 chr2D.!!$R3 516
14 TraesCS7A01G308500 chr2A 445383427 445384270 843 True 1234.000000 1234 93.051000 4 850 1 chr2A.!!$R1 846
15 TraesCS7A01G308500 chr2A 89174907 89175425 518 False 780.000000 780 93.834000 847 1364 1 chr2A.!!$F2 517
16 TraesCS7A01G308500 chr2A 192002864 192003383 519 False 776.000000 776 93.654000 847 1365 1 chr2A.!!$F3 518
17 TraesCS7A01G308500 chr4D 469444470 469444986 516 True 784.000000 784 94.015000 847 1363 1 chr4D.!!$R2 516
18 TraesCS7A01G308500 chr4D 434930577 434931328 751 True 671.000000 671 83.378000 1615 2339 1 chr4D.!!$R1 724
19 TraesCS7A01G308500 chr4D 439729030 439729702 672 False 651.000000 651 84.615000 1615 2270 1 chr4D.!!$F3 655
20 TraesCS7A01G308500 chr2B 793363810 793364335 525 False 782.000000 782 93.536000 847 1370 1 chr2B.!!$F1 523
21 TraesCS7A01G308500 chr3B 161677482 161677992 510 True 776.000000 776 94.129000 855 1364 1 chr3B.!!$R1 509
22 TraesCS7A01G308500 chr3B 245349592 245350321 729 True 608.000000 608 82.249000 1625 2339 1 chr3B.!!$R2 714
23 TraesCS7A01G308500 chr6D 338920516 338921034 518 False 774.000000 774 93.642000 847 1364 1 chr6D.!!$F1 517
24 TraesCS7A01G308500 chr7D 571878823 571879560 737 True 693.000000 693 84.253000 1625 2339 1 chr7D.!!$R2 714
25 TraesCS7A01G308500 chr7D 517353630 517354305 675 True 676.000000 676 85.125000 1625 2287 1 chr7D.!!$R1 662
26 TraesCS7A01G308500 chr7D 153060854 153061549 695 False 638.000000 638 83.644000 1601 2279 1 chr7D.!!$F2 678
27 TraesCS7A01G308500 chr5A 657102847 657103597 750 True 660.000000 660 83.134000 1615 2339 1 chr5A.!!$R2 724
28 TraesCS7A01G308500 chr7B 115079957 115080646 689 False 577.000000 577 82.174000 1601 2272 1 chr7B.!!$F1 671

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
430 434 0.035056 GTATGTGGCCAAGGAGCACT 60.035 55.0 7.24 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1502 0.033503 GGGTAACATCCTTGGGTGGG 60.034 60.0 4.82 0.0 39.74 4.61 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
213 214 0.693049 GAGAAAGGCCTCAAGGGTGA 59.307 55.000 5.23 0.00 37.43 4.02
294 296 3.177228 CTTCCTTCTCCTTCTCCCTTCA 58.823 50.000 0.00 0.00 0.00 3.02
364 367 4.399483 TCCTAGTAGGACTCCACACTTT 57.601 45.455 15.33 0.00 40.06 2.66
411 414 2.641815 CCTCCTCCCTCCATCCTTTATG 59.358 54.545 0.00 0.00 35.15 1.90
425 429 3.525609 TCCTTTATGTATGTGGCCAAGGA 59.474 43.478 7.24 10.38 36.75 3.36
430 434 0.035056 GTATGTGGCCAAGGAGCACT 60.035 55.000 7.24 0.00 0.00 4.40
509 514 4.597507 ACCATAATCCACCTCGGTCATATT 59.402 41.667 0.00 0.00 35.57 1.28
553 559 4.077300 TGTTCTGGTAGCATCATCATCC 57.923 45.455 0.00 0.00 0.00 3.51
597 603 1.269998 CGAAACTCTCCCTCGACACTT 59.730 52.381 0.00 0.00 34.52 3.16
712 718 5.417894 TGAAGACGTATGACTACATCAACCT 59.582 40.000 0.00 0.00 41.93 3.50
788 796 2.133553 CCTCTCGTTGCTATGCATCAG 58.866 52.381 0.19 0.33 38.76 2.90
943 952 3.118555 TCGGGGCGATCTTAAGAAATGAA 60.119 43.478 9.71 0.00 0.00 2.57
991 1001 3.146066 GGTAAGATTGACTGGTGTGCAA 58.854 45.455 0.00 0.00 0.00 4.08
1003 1013 2.692041 TGGTGTGCAAATGTGTTGATGA 59.308 40.909 0.00 0.00 0.00 2.92
1026 1036 4.982295 ACTGAAGCTTTGGCGTTAAAATTC 59.018 37.500 0.00 0.00 44.37 2.17
1055 1065 2.070654 CTTGCGCAAAGGACGGGTTT 62.071 55.000 25.01 0.00 31.68 3.27
1056 1066 2.050442 GCGCAAAGGACGGGTTTG 60.050 61.111 0.30 2.91 37.85 2.93
1122 1132 1.541379 TGAACGAAGGAGGACGATCA 58.459 50.000 0.00 0.00 38.52 2.92
1179 1189 2.747446 TCACTTAGCTTGCGATTTTCCC 59.253 45.455 0.00 0.00 0.00 3.97
1283 1293 1.079127 ATTGGCTCGAGGAACCACG 60.079 57.895 15.58 4.45 31.83 4.94
1312 1322 6.435591 TGCAATTGTACCAATCCTCATAAACA 59.564 34.615 7.40 0.00 0.00 2.83
1389 1399 1.888512 TGCATGAGAGCAAAAGTTCCC 59.111 47.619 0.00 0.00 42.46 3.97
1390 1400 2.165998 GCATGAGAGCAAAAGTTCCCT 58.834 47.619 0.00 0.00 0.00 4.20
1391 1401 2.560105 GCATGAGAGCAAAAGTTCCCTT 59.440 45.455 0.00 0.00 0.00 3.95
1392 1402 3.366781 GCATGAGAGCAAAAGTTCCCTTC 60.367 47.826 0.00 0.00 0.00 3.46
1393 1403 3.864789 TGAGAGCAAAAGTTCCCTTCT 57.135 42.857 0.00 0.00 0.00 2.85
1394 1404 4.170468 TGAGAGCAAAAGTTCCCTTCTT 57.830 40.909 0.00 0.00 0.00 2.52
1395 1405 3.885297 TGAGAGCAAAAGTTCCCTTCTTG 59.115 43.478 0.00 0.00 0.00 3.02
1396 1406 4.137543 GAGAGCAAAAGTTCCCTTCTTGA 58.862 43.478 0.00 0.00 0.00 3.02
1397 1407 4.734266 AGAGCAAAAGTTCCCTTCTTGAT 58.266 39.130 0.00 0.00 0.00 2.57
1398 1408 5.880901 AGAGCAAAAGTTCCCTTCTTGATA 58.119 37.500 0.00 0.00 0.00 2.15
1399 1409 5.942826 AGAGCAAAAGTTCCCTTCTTGATAG 59.057 40.000 0.00 0.00 0.00 2.08
1400 1410 5.012893 AGCAAAAGTTCCCTTCTTGATAGG 58.987 41.667 0.00 0.00 0.00 2.57
1401 1411 5.010282 GCAAAAGTTCCCTTCTTGATAGGA 58.990 41.667 0.00 0.00 34.56 2.94
1402 1412 5.124617 GCAAAAGTTCCCTTCTTGATAGGAG 59.875 44.000 0.00 0.00 34.56 3.69
1403 1413 4.495690 AAGTTCCCTTCTTGATAGGAGC 57.504 45.455 0.00 0.00 34.56 4.70
1404 1414 2.432510 AGTTCCCTTCTTGATAGGAGCG 59.567 50.000 0.00 0.00 35.04 5.03
1405 1415 1.414158 TCCCTTCTTGATAGGAGCGG 58.586 55.000 0.00 0.00 34.56 5.52
1406 1416 0.250081 CCCTTCTTGATAGGAGCGGC 60.250 60.000 0.00 0.00 34.56 6.53
1407 1417 0.250081 CCTTCTTGATAGGAGCGGCC 60.250 60.000 0.00 0.00 34.56 6.13
1408 1418 0.250081 CTTCTTGATAGGAGCGGCCC 60.250 60.000 0.00 0.00 37.37 5.80
1409 1419 2.028125 TTCTTGATAGGAGCGGCCCG 62.028 60.000 0.00 0.00 37.37 6.13
1410 1420 2.762459 TTGATAGGAGCGGCCCGT 60.762 61.111 4.45 0.00 37.37 5.28
1411 1421 2.701163 CTTGATAGGAGCGGCCCGTC 62.701 65.000 4.45 0.64 37.37 4.79
1412 1422 3.992317 GATAGGAGCGGCCCGTCC 61.992 72.222 14.50 14.50 37.37 4.79
1413 1423 4.853142 ATAGGAGCGGCCCGTCCA 62.853 66.667 21.42 11.30 37.37 4.02
1424 1434 3.000819 CCGTCCAGGGTAGCACCA 61.001 66.667 7.49 0.00 41.02 4.17
1425 1435 2.589157 CCGTCCAGGGTAGCACCAA 61.589 63.158 7.49 0.00 41.02 3.67
1426 1436 1.373435 CGTCCAGGGTAGCACCAAA 59.627 57.895 7.49 0.00 41.02 3.28
1427 1437 0.035439 CGTCCAGGGTAGCACCAAAT 60.035 55.000 7.49 0.00 41.02 2.32
1428 1438 1.208535 CGTCCAGGGTAGCACCAAATA 59.791 52.381 7.49 0.00 41.02 1.40
1429 1439 2.741878 CGTCCAGGGTAGCACCAAATAG 60.742 54.545 7.49 0.00 41.02 1.73
1430 1440 2.238898 GTCCAGGGTAGCACCAAATAGT 59.761 50.000 7.49 0.00 41.02 2.12
1431 1441 2.238646 TCCAGGGTAGCACCAAATAGTG 59.761 50.000 7.49 0.00 41.02 2.74
1432 1442 2.238646 CCAGGGTAGCACCAAATAGTGA 59.761 50.000 7.49 0.00 41.02 3.41
1433 1443 3.308117 CCAGGGTAGCACCAAATAGTGAA 60.308 47.826 7.49 0.00 41.02 3.18
1434 1444 3.941483 CAGGGTAGCACCAAATAGTGAAG 59.059 47.826 7.49 0.00 41.02 3.02
1435 1445 3.844211 AGGGTAGCACCAAATAGTGAAGA 59.156 43.478 7.49 0.00 41.02 2.87
1436 1446 4.475016 AGGGTAGCACCAAATAGTGAAGAT 59.525 41.667 7.49 0.00 41.02 2.40
1437 1447 5.044846 AGGGTAGCACCAAATAGTGAAGATT 60.045 40.000 7.49 0.00 41.02 2.40
1438 1448 5.066505 GGGTAGCACCAAATAGTGAAGATTG 59.933 44.000 7.49 0.00 41.02 2.67
1439 1449 5.880332 GGTAGCACCAAATAGTGAAGATTGA 59.120 40.000 0.00 0.00 40.34 2.57
1440 1450 6.037610 GGTAGCACCAAATAGTGAAGATTGAG 59.962 42.308 0.00 0.00 40.34 3.02
1441 1451 4.946157 AGCACCAAATAGTGAAGATTGAGG 59.054 41.667 0.00 0.00 40.34 3.86
1442 1452 4.096984 GCACCAAATAGTGAAGATTGAGGG 59.903 45.833 0.00 0.00 40.34 4.30
1443 1453 4.641989 CACCAAATAGTGAAGATTGAGGGG 59.358 45.833 0.00 0.00 40.34 4.79
1444 1454 3.633986 CCAAATAGTGAAGATTGAGGGGC 59.366 47.826 0.00 0.00 0.00 5.80
1445 1455 3.584733 AATAGTGAAGATTGAGGGGCC 57.415 47.619 0.00 0.00 0.00 5.80
1446 1456 2.270434 TAGTGAAGATTGAGGGGCCT 57.730 50.000 0.84 0.00 0.00 5.19
1447 1457 1.376649 AGTGAAGATTGAGGGGCCTT 58.623 50.000 0.84 0.00 0.00 4.35
1448 1458 1.713078 AGTGAAGATTGAGGGGCCTTT 59.287 47.619 0.84 0.00 0.00 3.11
1449 1459 2.919602 AGTGAAGATTGAGGGGCCTTTA 59.080 45.455 0.84 0.00 0.00 1.85
1450 1460 3.333680 AGTGAAGATTGAGGGGCCTTTAA 59.666 43.478 0.84 0.00 0.00 1.52
1451 1461 4.017130 AGTGAAGATTGAGGGGCCTTTAAT 60.017 41.667 5.29 5.29 0.00 1.40
1452 1462 5.193728 AGTGAAGATTGAGGGGCCTTTAATA 59.806 40.000 5.61 0.00 0.00 0.98
1453 1463 5.532779 GTGAAGATTGAGGGGCCTTTAATAG 59.467 44.000 5.61 0.00 0.00 1.73
1491 1501 9.566432 AAGTCAGCTTTAATCTATCCTATTTGG 57.434 33.333 0.00 0.00 37.10 3.28
1492 1502 7.663493 AGTCAGCTTTAATCTATCCTATTTGGC 59.337 37.037 0.00 0.00 35.26 4.52
1493 1503 6.942576 TCAGCTTTAATCTATCCTATTTGGCC 59.057 38.462 0.00 0.00 35.26 5.36
1494 1504 6.151817 CAGCTTTAATCTATCCTATTTGGCCC 59.848 42.308 0.00 0.00 35.26 5.80
1495 1505 6.010219 GCTTTAATCTATCCTATTTGGCCCA 58.990 40.000 0.00 0.00 35.26 5.36
1496 1506 6.071896 GCTTTAATCTATCCTATTTGGCCCAC 60.072 42.308 0.00 0.00 35.26 4.61
1497 1507 4.388577 AATCTATCCTATTTGGCCCACC 57.611 45.455 0.00 0.00 35.26 4.61
1498 1508 2.062636 TCTATCCTATTTGGCCCACCC 58.937 52.381 0.00 0.00 35.26 4.61
1499 1509 1.780309 CTATCCTATTTGGCCCACCCA 59.220 52.381 0.00 0.00 43.51 4.51
1506 1516 2.863484 TGGCCCACCCAAGGATGT 60.863 61.111 0.00 0.00 41.82 3.06
1507 1517 2.445155 GGCCCACCCAAGGATGTT 59.555 61.111 0.00 0.00 0.00 2.71
1508 1518 1.143329 TGGCCCACCCAAGGATGTTA 61.143 55.000 0.00 0.00 41.82 2.41
1509 1519 0.683179 GGCCCACCCAAGGATGTTAC 60.683 60.000 0.00 0.00 0.00 2.50
1510 1520 0.683179 GCCCACCCAAGGATGTTACC 60.683 60.000 0.00 0.00 0.00 2.85
1511 1521 0.033503 CCCACCCAAGGATGTTACCC 60.034 60.000 0.00 0.00 0.00 3.69
1512 1522 0.999712 CCACCCAAGGATGTTACCCT 59.000 55.000 0.00 0.00 35.03 4.34
1513 1523 2.201830 CCACCCAAGGATGTTACCCTA 58.798 52.381 0.00 0.00 32.77 3.53
1514 1524 2.172717 CCACCCAAGGATGTTACCCTAG 59.827 54.545 0.00 0.00 32.77 3.02
1515 1525 1.844497 ACCCAAGGATGTTACCCTAGC 59.156 52.381 0.00 0.00 32.77 3.42
1516 1526 2.127708 CCCAAGGATGTTACCCTAGCT 58.872 52.381 0.00 0.00 32.77 3.32
1517 1527 2.104963 CCCAAGGATGTTACCCTAGCTC 59.895 54.545 0.00 0.00 32.77 4.09
1518 1528 2.104963 CCAAGGATGTTACCCTAGCTCC 59.895 54.545 0.00 0.00 32.77 4.70
1519 1529 1.705873 AGGATGTTACCCTAGCTCCG 58.294 55.000 0.00 0.00 30.92 4.63
1520 1530 0.033642 GGATGTTACCCTAGCTCCGC 59.966 60.000 0.00 0.00 0.00 5.54
1521 1531 0.033642 GATGTTACCCTAGCTCCGCC 59.966 60.000 0.00 0.00 0.00 6.13
1522 1532 0.689745 ATGTTACCCTAGCTCCGCCA 60.690 55.000 0.00 0.00 0.00 5.69
1523 1533 1.143401 GTTACCCTAGCTCCGCCAC 59.857 63.158 0.00 0.00 0.00 5.01
1524 1534 1.001248 TTACCCTAGCTCCGCCACT 59.999 57.895 0.00 0.00 0.00 4.00
1525 1535 1.327690 TTACCCTAGCTCCGCCACTG 61.328 60.000 0.00 0.00 0.00 3.66
1526 1536 4.537433 CCCTAGCTCCGCCACTGC 62.537 72.222 0.00 0.00 0.00 4.40
1527 1537 3.465403 CCTAGCTCCGCCACTGCT 61.465 66.667 0.00 0.00 40.43 4.24
1528 1538 2.581354 CTAGCTCCGCCACTGCTT 59.419 61.111 0.00 0.00 38.15 3.91
1529 1539 1.520342 CTAGCTCCGCCACTGCTTC 60.520 63.158 0.00 0.00 38.15 3.86
1530 1540 1.954362 CTAGCTCCGCCACTGCTTCT 61.954 60.000 0.00 0.00 38.15 2.85
1531 1541 1.949847 TAGCTCCGCCACTGCTTCTC 61.950 60.000 0.00 0.00 38.15 2.87
1532 1542 2.659016 CTCCGCCACTGCTTCTCA 59.341 61.111 0.00 0.00 34.43 3.27
1533 1543 1.004560 CTCCGCCACTGCTTCTCAA 60.005 57.895 0.00 0.00 34.43 3.02
1534 1544 1.294659 CTCCGCCACTGCTTCTCAAC 61.295 60.000 0.00 0.00 34.43 3.18
1535 1545 2.328099 CCGCCACTGCTTCTCAACC 61.328 63.158 0.00 0.00 34.43 3.77
1536 1546 2.328099 CGCCACTGCTTCTCAACCC 61.328 63.158 0.00 0.00 34.43 4.11
1537 1547 1.228245 GCCACTGCTTCTCAACCCA 60.228 57.895 0.00 0.00 33.53 4.51
1538 1548 1.518903 GCCACTGCTTCTCAACCCAC 61.519 60.000 0.00 0.00 33.53 4.61
1539 1549 0.109342 CCACTGCTTCTCAACCCACT 59.891 55.000 0.00 0.00 0.00 4.00
1540 1550 1.477558 CCACTGCTTCTCAACCCACTT 60.478 52.381 0.00 0.00 0.00 3.16
1541 1551 2.301346 CACTGCTTCTCAACCCACTTT 58.699 47.619 0.00 0.00 0.00 2.66
1542 1552 2.689983 CACTGCTTCTCAACCCACTTTT 59.310 45.455 0.00 0.00 0.00 2.27
1543 1553 2.689983 ACTGCTTCTCAACCCACTTTTG 59.310 45.455 0.00 0.00 0.00 2.44
1544 1554 2.031120 TGCTTCTCAACCCACTTTTGG 58.969 47.619 0.00 0.00 43.50 3.28
1557 1567 5.376854 CCACTTTTGGGTGTTTGATAGAG 57.623 43.478 0.00 0.00 39.57 2.43
1558 1568 4.827284 CCACTTTTGGGTGTTTGATAGAGT 59.173 41.667 0.00 0.00 39.57 3.24
1559 1569 5.278463 CCACTTTTGGGTGTTTGATAGAGTG 60.278 44.000 0.00 0.00 39.57 3.51
1560 1570 5.299279 CACTTTTGGGTGTTTGATAGAGTGT 59.701 40.000 0.00 0.00 33.04 3.55
1561 1571 6.485313 CACTTTTGGGTGTTTGATAGAGTGTA 59.515 38.462 0.00 0.00 33.04 2.90
1562 1572 7.174946 CACTTTTGGGTGTTTGATAGAGTGTAT 59.825 37.037 0.00 0.00 33.04 2.29
1563 1573 7.174946 ACTTTTGGGTGTTTGATAGAGTGTATG 59.825 37.037 0.00 0.00 0.00 2.39
1564 1574 6.367374 TTGGGTGTTTGATAGAGTGTATGA 57.633 37.500 0.00 0.00 0.00 2.15
1565 1575 5.977635 TGGGTGTTTGATAGAGTGTATGAG 58.022 41.667 0.00 0.00 0.00 2.90
1566 1576 5.104941 TGGGTGTTTGATAGAGTGTATGAGG 60.105 44.000 0.00 0.00 0.00 3.86
1567 1577 5.128827 GGGTGTTTGATAGAGTGTATGAGGA 59.871 44.000 0.00 0.00 0.00 3.71
1568 1578 6.276847 GGTGTTTGATAGAGTGTATGAGGAG 58.723 44.000 0.00 0.00 0.00 3.69
1569 1579 6.127310 GGTGTTTGATAGAGTGTATGAGGAGT 60.127 42.308 0.00 0.00 0.00 3.85
1570 1580 6.754209 GTGTTTGATAGAGTGTATGAGGAGTG 59.246 42.308 0.00 0.00 0.00 3.51
1571 1581 5.521906 TTGATAGAGTGTATGAGGAGTGC 57.478 43.478 0.00 0.00 0.00 4.40
1572 1582 4.536765 TGATAGAGTGTATGAGGAGTGCA 58.463 43.478 0.00 0.00 0.00 4.57
1573 1583 5.143369 TGATAGAGTGTATGAGGAGTGCAT 58.857 41.667 0.00 0.00 0.00 3.96
1574 1584 3.815856 AGAGTGTATGAGGAGTGCATG 57.184 47.619 0.00 0.00 0.00 4.06
1575 1585 3.369175 AGAGTGTATGAGGAGTGCATGA 58.631 45.455 0.00 0.00 0.00 3.07
1576 1586 3.384146 AGAGTGTATGAGGAGTGCATGAG 59.616 47.826 0.00 0.00 0.00 2.90
1577 1587 3.102972 AGTGTATGAGGAGTGCATGAGT 58.897 45.455 0.00 0.00 0.00 3.41
1578 1588 3.131933 AGTGTATGAGGAGTGCATGAGTC 59.868 47.826 0.00 0.00 0.00 3.36
1579 1589 2.432146 TGTATGAGGAGTGCATGAGTCC 59.568 50.000 0.00 3.91 43.97 3.85
1580 1590 1.576577 ATGAGGAGTGCATGAGTCCA 58.423 50.000 16.56 3.15 45.89 4.02
1581 1591 0.610174 TGAGGAGTGCATGAGTCCAC 59.390 55.000 16.56 12.50 45.89 4.02
1582 1592 0.610174 GAGGAGTGCATGAGTCCACA 59.390 55.000 16.56 0.00 45.89 4.17
1583 1593 0.322975 AGGAGTGCATGAGTCCACAC 59.677 55.000 16.56 6.36 45.89 3.82
1584 1594 0.322975 GGAGTGCATGAGTCCACACT 59.677 55.000 8.95 8.95 45.66 3.55
1585 1595 1.436600 GAGTGCATGAGTCCACACTG 58.563 55.000 12.85 0.00 43.16 3.66
1586 1596 1.001293 GAGTGCATGAGTCCACACTGA 59.999 52.381 12.85 0.00 43.16 3.41
1587 1597 1.151668 GTGCATGAGTCCACACTGAC 58.848 55.000 0.00 0.00 30.63 3.51
1589 1599 1.417517 TGCATGAGTCCACACTGACTT 59.582 47.619 0.00 0.00 45.41 3.01
1590 1600 2.632512 TGCATGAGTCCACACTGACTTA 59.367 45.455 0.00 0.00 45.41 2.24
1591 1601 3.070878 TGCATGAGTCCACACTGACTTAA 59.929 43.478 0.00 0.00 45.41 1.85
1592 1602 3.433615 GCATGAGTCCACACTGACTTAAC 59.566 47.826 0.00 0.00 45.41 2.01
1593 1603 4.631131 CATGAGTCCACACTGACTTAACA 58.369 43.478 0.00 0.00 45.41 2.41
1594 1604 4.054780 TGAGTCCACACTGACTTAACAC 57.945 45.455 0.00 0.00 45.41 3.32
1595 1605 3.449377 TGAGTCCACACTGACTTAACACA 59.551 43.478 0.00 0.00 45.41 3.72
1596 1606 4.081365 TGAGTCCACACTGACTTAACACAA 60.081 41.667 0.00 0.00 45.41 3.33
1597 1607 4.839121 AGTCCACACTGACTTAACACAAA 58.161 39.130 0.00 0.00 42.92 2.83
1598 1608 5.437060 AGTCCACACTGACTTAACACAAAT 58.563 37.500 0.00 0.00 42.92 2.32
1599 1609 6.588204 AGTCCACACTGACTTAACACAAATA 58.412 36.000 0.00 0.00 42.92 1.40
1613 1623 4.261801 ACACAAATACACTAGGGATGTGC 58.738 43.478 18.14 0.00 40.10 4.57
1620 1630 2.910319 ACACTAGGGATGTGCTTGGTAA 59.090 45.455 0.00 0.00 38.86 2.85
1641 1655 2.257409 CTGCATTAGGTCCGGCCAGT 62.257 60.000 15.92 0.67 40.61 4.00
1702 1721 1.008361 CATTGAAAAGTTGGCCCGCG 61.008 55.000 0.00 0.00 0.00 6.46
1735 1754 1.524165 CCTCTCAGCCTGCATCTGC 60.524 63.158 10.32 3.49 42.50 4.26
1751 1770 0.449388 CTGCAGGAACGCTCAAATCC 59.551 55.000 5.57 0.00 0.00 3.01
1763 1782 3.335579 GCTCAAATCCACCGTTTCTACT 58.664 45.455 0.00 0.00 0.00 2.57
1829 1849 1.003928 TCTTGCACCAGAGCATGTGAT 59.996 47.619 0.00 0.00 45.19 3.06
1830 1850 1.400846 CTTGCACCAGAGCATGTGATC 59.599 52.381 0.00 0.00 45.19 2.92
1834 1856 0.545171 ACCAGAGCATGTGATCCCTG 59.455 55.000 0.00 0.00 0.00 4.45
1868 1986 4.140924 ACTTTGTTTCTTCTTCCCCTCCAT 60.141 41.667 0.00 0.00 0.00 3.41
1880 2001 2.131023 CCCCTCCATTAAGCTCCTCTT 58.869 52.381 0.00 0.00 38.79 2.85
1883 2004 5.094387 CCCCTCCATTAAGCTCCTCTTATA 58.906 45.833 0.00 0.00 37.14 0.98
1886 2007 7.108847 CCCTCCATTAAGCTCCTCTTATATTG 58.891 42.308 0.00 0.00 37.14 1.90
2002 2267 9.868277 TTTTTGTGATCAGTTCATAGTTTTGTT 57.132 25.926 0.00 0.00 36.54 2.83
2082 5029 2.126463 CGTCATGCACGGTCGACT 60.126 61.111 16.46 0.00 45.46 4.18
2134 5108 7.320443 TCATCTTATAGTTTCACATTGCACC 57.680 36.000 0.00 0.00 0.00 5.01
2139 5113 9.290988 TCTTATAGTTTCACATTGCACCTTTTA 57.709 29.630 0.00 0.00 0.00 1.52
2155 5129 4.090930 ACCTTTTATGTTTCGACGATCGTG 59.909 41.667 28.12 17.50 41.35 4.35
2172 5146 3.777478 TCGTGGACGATTCAATCTAACC 58.223 45.455 0.00 0.00 44.22 2.85
2177 5171 5.875359 GTGGACGATTCAATCTAACCTCTTT 59.125 40.000 0.00 0.00 0.00 2.52
2194 5192 7.274603 ACCTCTTTCTCGTGAAGTATATACC 57.725 40.000 9.32 0.00 33.28 2.73
2240 5239 4.042187 ACACTCATTAAGCTTGGTCTCCTT 59.958 41.667 9.86 0.00 0.00 3.36
2243 5242 4.253685 TCATTAAGCTTGGTCTCCTTTCG 58.746 43.478 9.86 0.00 0.00 3.46
2307 5317 1.006825 CGCGTGCTGTTACACTAGCA 61.007 55.000 0.00 0.00 46.79 3.49
2315 5325 0.037605 GTTACACTAGCACCACCGCT 60.038 55.000 0.00 0.00 46.26 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 4.760204 CCCAATATGAATTCCCGTAACTCC 59.240 45.833 2.27 0.00 0.00 3.85
244 245 1.636769 GCCCCCTTTCCCTAGTCCAG 61.637 65.000 0.00 0.00 0.00 3.86
294 296 6.217693 ACCTCCTACATGGAATAGGAAAAAGT 59.782 38.462 11.44 5.05 46.05 2.66
411 414 0.035056 AGTGCTCCTTGGCCACATAC 60.035 55.000 3.88 0.00 0.00 2.39
425 429 2.634940 ACTTGTGTGTCTATGGAGTGCT 59.365 45.455 0.00 0.00 0.00 4.40
430 434 5.482163 TGATCAACTTGTGTGTCTATGGA 57.518 39.130 0.00 0.00 0.00 3.41
509 514 3.383229 TGCCTAAGCACCGCTACA 58.617 55.556 0.00 0.00 46.52 2.74
529 535 4.758773 TGATGATGCTACCAGAACATGA 57.241 40.909 0.00 0.00 0.00 3.07
553 559 2.506217 CGACGGTGTGATGACGGG 60.506 66.667 0.00 0.00 0.00 5.28
597 603 3.073678 CCACGAACTCATGATCCAACAA 58.926 45.455 0.00 0.00 0.00 2.83
712 718 1.724623 GCAGAAGCGTTATGACAACGA 59.275 47.619 13.23 0.00 45.64 3.85
788 796 3.302935 CGCACACACAAGATCTATCATGC 60.303 47.826 0.00 1.19 0.00 4.06
795 803 1.893137 TCCTACGCACACACAAGATCT 59.107 47.619 0.00 0.00 0.00 2.75
796 804 2.363788 TCCTACGCACACACAAGATC 57.636 50.000 0.00 0.00 0.00 2.75
797 805 2.831685 TTCCTACGCACACACAAGAT 57.168 45.000 0.00 0.00 0.00 2.40
798 806 2.831685 ATTCCTACGCACACACAAGA 57.168 45.000 0.00 0.00 0.00 3.02
938 947 5.183140 CCACGATGAACCTACCTTTTTCATT 59.817 40.000 0.00 0.00 39.53 2.57
943 952 2.290705 CCCCACGATGAACCTACCTTTT 60.291 50.000 0.00 0.00 0.00 2.27
966 976 4.142600 GCACACCAGTCAATCTTACCATTC 60.143 45.833 0.00 0.00 0.00 2.67
991 1001 5.508489 CCAAAGCTTCAGTCATCAACACATT 60.508 40.000 0.00 0.00 0.00 2.71
1003 1013 4.584327 ATTTTAACGCCAAAGCTTCAGT 57.416 36.364 0.00 0.00 36.60 3.41
1026 1036 1.643868 TTTGCGCAAGTGATAGGCCG 61.644 55.000 23.68 0.00 41.68 6.13
1154 1164 5.863935 GGAAAATCGCAAGCTAAGTGAAAAT 59.136 36.000 6.45 0.00 37.18 1.82
1365 1375 3.083122 ACTTTTGCTCTCATGCATCCT 57.917 42.857 0.00 0.00 42.96 3.24
1366 1376 3.428589 GGAACTTTTGCTCTCATGCATCC 60.429 47.826 0.00 0.00 42.96 3.51
1368 1378 2.494870 GGGAACTTTTGCTCTCATGCAT 59.505 45.455 0.00 0.00 42.96 3.96
1370 1380 2.165998 AGGGAACTTTTGCTCTCATGC 58.834 47.619 0.00 0.00 37.44 4.06
1384 1394 2.483889 CCGCTCCTATCAAGAAGGGAAC 60.484 54.545 0.00 0.00 34.66 3.62
1385 1395 1.762957 CCGCTCCTATCAAGAAGGGAA 59.237 52.381 0.00 0.00 34.66 3.97
1386 1396 1.414158 CCGCTCCTATCAAGAAGGGA 58.586 55.000 0.00 0.00 34.66 4.20
1387 1397 0.250081 GCCGCTCCTATCAAGAAGGG 60.250 60.000 0.00 0.00 34.66 3.95
1388 1398 0.250081 GGCCGCTCCTATCAAGAAGG 60.250 60.000 0.00 0.00 35.26 3.46
1389 1399 0.250081 GGGCCGCTCCTATCAAGAAG 60.250 60.000 0.00 0.00 34.39 2.85
1390 1400 1.830145 GGGCCGCTCCTATCAAGAA 59.170 57.895 0.00 0.00 34.39 2.52
1391 1401 2.498941 CGGGCCGCTCCTATCAAGA 61.499 63.158 15.42 0.00 34.39 3.02
1392 1402 2.029666 CGGGCCGCTCCTATCAAG 59.970 66.667 15.42 0.00 34.39 3.02
1393 1403 2.762459 ACGGGCCGCTCCTATCAA 60.762 61.111 28.71 0.00 34.39 2.57
1394 1404 3.224324 GACGGGCCGCTCCTATCA 61.224 66.667 28.71 0.00 34.39 2.15
1395 1405 3.992317 GGACGGGCCGCTCCTATC 61.992 72.222 28.71 14.95 34.39 2.08
1396 1406 4.853142 TGGACGGGCCGCTCCTAT 62.853 66.667 32.51 15.10 40.66 2.57
1407 1417 2.119484 TTTGGTGCTACCCTGGACGG 62.119 60.000 0.00 0.00 37.50 4.79
1408 1418 0.035439 ATTTGGTGCTACCCTGGACG 60.035 55.000 0.00 0.00 37.50 4.79
1409 1419 2.238898 ACTATTTGGTGCTACCCTGGAC 59.761 50.000 0.00 0.00 37.50 4.02
1410 1420 2.238646 CACTATTTGGTGCTACCCTGGA 59.761 50.000 0.00 0.00 37.50 3.86
1411 1421 2.238646 TCACTATTTGGTGCTACCCTGG 59.761 50.000 3.33 0.00 37.50 4.45
1412 1422 3.627395 TCACTATTTGGTGCTACCCTG 57.373 47.619 3.33 0.00 37.50 4.45
1413 1423 3.844211 TCTTCACTATTTGGTGCTACCCT 59.156 43.478 3.33 0.00 37.50 4.34
1414 1424 4.216411 TCTTCACTATTTGGTGCTACCC 57.784 45.455 3.33 0.00 37.50 3.69
1415 1425 5.880332 TCAATCTTCACTATTTGGTGCTACC 59.120 40.000 0.00 0.00 39.22 3.18
1416 1426 6.037610 CCTCAATCTTCACTATTTGGTGCTAC 59.962 42.308 0.00 0.00 37.16 3.58
1417 1427 6.115446 CCTCAATCTTCACTATTTGGTGCTA 58.885 40.000 0.00 0.00 37.16 3.49
1418 1428 4.946157 CCTCAATCTTCACTATTTGGTGCT 59.054 41.667 0.00 0.00 37.16 4.40
1419 1429 4.096984 CCCTCAATCTTCACTATTTGGTGC 59.903 45.833 0.00 0.00 37.16 5.01
1420 1430 4.641989 CCCCTCAATCTTCACTATTTGGTG 59.358 45.833 0.00 0.00 38.44 4.17
1421 1431 4.860022 CCCCTCAATCTTCACTATTTGGT 58.140 43.478 0.00 0.00 0.00 3.67
1422 1432 3.633986 GCCCCTCAATCTTCACTATTTGG 59.366 47.826 0.00 0.00 0.00 3.28
1423 1433 3.633986 GGCCCCTCAATCTTCACTATTTG 59.366 47.826 0.00 0.00 0.00 2.32
1424 1434 3.529319 AGGCCCCTCAATCTTCACTATTT 59.471 43.478 0.00 0.00 0.00 1.40
1425 1435 3.126453 AGGCCCCTCAATCTTCACTATT 58.874 45.455 0.00 0.00 0.00 1.73
1426 1436 2.781667 AGGCCCCTCAATCTTCACTAT 58.218 47.619 0.00 0.00 0.00 2.12
1427 1437 2.270434 AGGCCCCTCAATCTTCACTA 57.730 50.000 0.00 0.00 0.00 2.74
1428 1438 1.376649 AAGGCCCCTCAATCTTCACT 58.623 50.000 0.00 0.00 0.00 3.41
1429 1439 2.222227 AAAGGCCCCTCAATCTTCAC 57.778 50.000 0.00 0.00 0.00 3.18
1430 1440 4.608170 ATTAAAGGCCCCTCAATCTTCA 57.392 40.909 0.00 0.00 0.00 3.02
1431 1441 5.073428 CCTATTAAAGGCCCCTCAATCTTC 58.927 45.833 0.00 0.00 38.97 2.87
1432 1442 4.731929 TCCTATTAAAGGCCCCTCAATCTT 59.268 41.667 0.00 0.00 46.10 2.40
1433 1443 4.315993 TCCTATTAAAGGCCCCTCAATCT 58.684 43.478 0.00 0.00 46.10 2.40
1434 1444 4.724279 TCCTATTAAAGGCCCCTCAATC 57.276 45.455 0.00 0.00 46.10 2.67
1435 1445 5.043356 ACTTTCCTATTAAAGGCCCCTCAAT 60.043 40.000 0.00 0.00 46.10 2.57
1436 1446 4.293901 ACTTTCCTATTAAAGGCCCCTCAA 59.706 41.667 0.00 0.00 46.10 3.02
1437 1447 3.856206 ACTTTCCTATTAAAGGCCCCTCA 59.144 43.478 0.00 0.00 46.10 3.86
1438 1448 4.521536 ACTTTCCTATTAAAGGCCCCTC 57.478 45.455 0.00 0.00 46.10 4.30
1439 1449 6.607809 ATTACTTTCCTATTAAAGGCCCCT 57.392 37.500 0.00 0.00 46.10 4.79
1440 1450 8.771521 TTAATTACTTTCCTATTAAAGGCCCC 57.228 34.615 0.00 0.00 46.10 5.80
1465 1475 9.566432 CCAAATAGGATAGATTAAAGCTGACTT 57.434 33.333 0.00 0.00 41.22 3.01
1466 1476 7.663493 GCCAAATAGGATAGATTAAAGCTGACT 59.337 37.037 0.00 0.00 41.22 3.41
1467 1477 7.094592 GGCCAAATAGGATAGATTAAAGCTGAC 60.095 40.741 0.00 0.00 41.22 3.51
1468 1478 6.942576 GGCCAAATAGGATAGATTAAAGCTGA 59.057 38.462 0.00 0.00 41.22 4.26
1469 1479 6.151817 GGGCCAAATAGGATAGATTAAAGCTG 59.848 42.308 4.39 0.00 41.22 4.24
1470 1480 6.183361 TGGGCCAAATAGGATAGATTAAAGCT 60.183 38.462 2.13 0.00 41.22 3.74
1471 1481 6.010219 TGGGCCAAATAGGATAGATTAAAGC 58.990 40.000 2.13 0.00 41.22 3.51
1472 1482 6.434340 GGTGGGCCAAATAGGATAGATTAAAG 59.566 42.308 8.40 0.00 41.22 1.85
1473 1483 6.311735 GGTGGGCCAAATAGGATAGATTAAA 58.688 40.000 8.40 0.00 41.22 1.52
1474 1484 5.222254 GGGTGGGCCAAATAGGATAGATTAA 60.222 44.000 8.40 0.00 41.22 1.40
1475 1485 4.291249 GGGTGGGCCAAATAGGATAGATTA 59.709 45.833 8.40 0.00 41.22 1.75
1476 1486 3.076032 GGGTGGGCCAAATAGGATAGATT 59.924 47.826 8.40 0.00 41.22 2.40
1477 1487 2.649816 GGGTGGGCCAAATAGGATAGAT 59.350 50.000 8.40 0.00 41.22 1.98
1478 1488 2.062636 GGGTGGGCCAAATAGGATAGA 58.937 52.381 8.40 0.00 41.22 1.98
1479 1489 1.780309 TGGGTGGGCCAAATAGGATAG 59.220 52.381 8.40 0.00 41.22 2.08
1480 1490 1.914272 TGGGTGGGCCAAATAGGATA 58.086 50.000 8.40 0.00 41.22 2.59
1481 1491 1.014804 TTGGGTGGGCCAAATAGGAT 58.985 50.000 8.40 0.00 41.22 3.24
1482 1492 0.334676 CTTGGGTGGGCCAAATAGGA 59.665 55.000 8.40 0.00 41.22 2.94
1483 1493 0.687427 CCTTGGGTGGGCCAAATAGG 60.687 60.000 8.40 9.37 41.84 2.57
1484 1494 0.334676 TCCTTGGGTGGGCCAAATAG 59.665 55.000 8.40 3.34 36.17 1.73
1485 1495 1.014804 ATCCTTGGGTGGGCCAAATA 58.985 50.000 8.40 0.00 36.17 1.40
1486 1496 0.618393 CATCCTTGGGTGGGCCAAAT 60.618 55.000 8.40 0.00 36.17 2.32
1487 1497 1.229145 CATCCTTGGGTGGGCCAAA 60.229 57.895 8.40 0.00 36.17 3.28
1488 1498 2.029892 AACATCCTTGGGTGGGCCAA 62.030 55.000 8.40 0.00 36.17 4.52
1489 1499 1.143329 TAACATCCTTGGGTGGGCCA 61.143 55.000 0.00 0.00 36.17 5.36
1490 1500 0.683179 GTAACATCCTTGGGTGGGCC 60.683 60.000 4.82 0.00 0.00 5.80
1491 1501 0.683179 GGTAACATCCTTGGGTGGGC 60.683 60.000 4.82 0.00 0.00 5.36
1492 1502 0.033503 GGGTAACATCCTTGGGTGGG 60.034 60.000 4.82 0.00 39.74 4.61
1493 1503 0.999712 AGGGTAACATCCTTGGGTGG 59.000 55.000 4.82 0.00 39.74 4.61
1494 1504 2.421529 GCTAGGGTAACATCCTTGGGTG 60.422 54.545 0.00 0.00 35.92 4.61
1495 1505 1.844497 GCTAGGGTAACATCCTTGGGT 59.156 52.381 0.00 0.00 35.92 4.51
1496 1506 2.104963 GAGCTAGGGTAACATCCTTGGG 59.895 54.545 0.00 0.00 35.92 4.12
1497 1507 2.104963 GGAGCTAGGGTAACATCCTTGG 59.895 54.545 0.00 0.00 35.92 3.61
1498 1508 2.224066 CGGAGCTAGGGTAACATCCTTG 60.224 54.545 0.00 0.00 35.92 3.61
1499 1509 2.040178 CGGAGCTAGGGTAACATCCTT 58.960 52.381 0.00 0.00 35.92 3.36
1500 1510 1.705873 CGGAGCTAGGGTAACATCCT 58.294 55.000 0.00 0.00 38.36 3.24
1519 1529 1.228245 TGGGTTGAGAAGCAGTGGC 60.228 57.895 0.00 0.00 41.61 5.01
1520 1530 0.109342 AGTGGGTTGAGAAGCAGTGG 59.891 55.000 0.00 0.00 0.00 4.00
1521 1531 1.972872 AAGTGGGTTGAGAAGCAGTG 58.027 50.000 0.00 0.00 0.00 3.66
1522 1532 2.689983 CAAAAGTGGGTTGAGAAGCAGT 59.310 45.455 0.00 0.00 0.00 4.40
1523 1533 2.035066 CCAAAAGTGGGTTGAGAAGCAG 59.965 50.000 0.00 0.00 41.77 4.24
1524 1534 2.031120 CCAAAAGTGGGTTGAGAAGCA 58.969 47.619 0.00 0.00 41.77 3.91
1525 1535 2.800881 CCAAAAGTGGGTTGAGAAGC 57.199 50.000 0.00 0.00 41.77 3.86
1535 1545 4.827284 ACTCTATCAAACACCCAAAAGTGG 59.173 41.667 0.00 0.00 45.53 4.00
1536 1546 5.299279 ACACTCTATCAAACACCCAAAAGTG 59.701 40.000 0.00 0.00 43.65 3.16
1537 1547 5.445964 ACACTCTATCAAACACCCAAAAGT 58.554 37.500 0.00 0.00 0.00 2.66
1538 1548 7.390440 TCATACACTCTATCAAACACCCAAAAG 59.610 37.037 0.00 0.00 0.00 2.27
1539 1549 7.227873 TCATACACTCTATCAAACACCCAAAA 58.772 34.615 0.00 0.00 0.00 2.44
1540 1550 6.774673 TCATACACTCTATCAAACACCCAAA 58.225 36.000 0.00 0.00 0.00 3.28
1541 1551 6.367374 TCATACACTCTATCAAACACCCAA 57.633 37.500 0.00 0.00 0.00 4.12
1542 1552 5.104941 CCTCATACACTCTATCAAACACCCA 60.105 44.000 0.00 0.00 0.00 4.51
1543 1553 5.128827 TCCTCATACACTCTATCAAACACCC 59.871 44.000 0.00 0.00 0.00 4.61
1544 1554 6.127310 ACTCCTCATACACTCTATCAAACACC 60.127 42.308 0.00 0.00 0.00 4.16
1545 1555 6.754209 CACTCCTCATACACTCTATCAAACAC 59.246 42.308 0.00 0.00 0.00 3.32
1546 1556 6.628175 GCACTCCTCATACACTCTATCAAACA 60.628 42.308 0.00 0.00 0.00 2.83
1547 1557 5.751028 GCACTCCTCATACACTCTATCAAAC 59.249 44.000 0.00 0.00 0.00 2.93
1548 1558 5.422012 TGCACTCCTCATACACTCTATCAAA 59.578 40.000 0.00 0.00 0.00 2.69
1549 1559 4.956075 TGCACTCCTCATACACTCTATCAA 59.044 41.667 0.00 0.00 0.00 2.57
1550 1560 4.536765 TGCACTCCTCATACACTCTATCA 58.463 43.478 0.00 0.00 0.00 2.15
1551 1561 5.242615 TCATGCACTCCTCATACACTCTATC 59.757 44.000 0.00 0.00 0.00 2.08
1552 1562 5.143369 TCATGCACTCCTCATACACTCTAT 58.857 41.667 0.00 0.00 0.00 1.98
1553 1563 4.536765 TCATGCACTCCTCATACACTCTA 58.463 43.478 0.00 0.00 0.00 2.43
1554 1564 3.369175 TCATGCACTCCTCATACACTCT 58.631 45.455 0.00 0.00 0.00 3.24
1555 1565 3.131933 ACTCATGCACTCCTCATACACTC 59.868 47.826 0.00 0.00 0.00 3.51
1556 1566 3.102972 ACTCATGCACTCCTCATACACT 58.897 45.455 0.00 0.00 0.00 3.55
1557 1567 3.452474 GACTCATGCACTCCTCATACAC 58.548 50.000 0.00 0.00 0.00 2.90
1558 1568 2.432146 GGACTCATGCACTCCTCATACA 59.568 50.000 0.00 0.00 0.00 2.29
1559 1569 2.432146 TGGACTCATGCACTCCTCATAC 59.568 50.000 0.00 0.00 0.00 2.39
1560 1570 2.432146 GTGGACTCATGCACTCCTCATA 59.568 50.000 0.00 0.00 43.49 2.15
1561 1571 1.209019 GTGGACTCATGCACTCCTCAT 59.791 52.381 0.00 0.00 43.49 2.90
1562 1572 0.610174 GTGGACTCATGCACTCCTCA 59.390 55.000 0.00 0.00 43.49 3.86
1563 1573 0.610174 TGTGGACTCATGCACTCCTC 59.390 55.000 0.00 0.00 46.76 3.71
1564 1574 0.322975 GTGTGGACTCATGCACTCCT 59.677 55.000 0.00 0.00 46.76 3.69
1565 1575 0.322975 AGTGTGGACTCATGCACTCC 59.677 55.000 0.00 0.00 46.76 3.85
1566 1576 1.001293 TCAGTGTGGACTCATGCACTC 59.999 52.381 0.00 0.00 46.76 3.51
1567 1577 1.051008 TCAGTGTGGACTCATGCACT 58.949 50.000 0.00 0.08 46.76 4.40
1568 1578 1.151668 GTCAGTGTGGACTCATGCAC 58.848 55.000 0.00 0.00 46.81 4.57
1569 1579 1.051008 AGTCAGTGTGGACTCATGCA 58.949 50.000 0.00 0.00 44.63 3.96
1570 1580 3.923354 AGTCAGTGTGGACTCATGC 57.077 52.632 0.00 0.00 44.63 4.06
1576 1586 5.751243 ATTTGTGTTAAGTCAGTGTGGAC 57.249 39.130 0.00 0.00 38.08 4.02
1577 1587 6.259167 GTGTATTTGTGTTAAGTCAGTGTGGA 59.741 38.462 0.00 0.00 0.00 4.02
1578 1588 6.260050 AGTGTATTTGTGTTAAGTCAGTGTGG 59.740 38.462 0.00 0.00 0.00 4.17
1579 1589 7.246674 AGTGTATTTGTGTTAAGTCAGTGTG 57.753 36.000 0.00 0.00 0.00 3.82
1580 1590 7.656137 CCTAGTGTATTTGTGTTAAGTCAGTGT 59.344 37.037 0.00 0.00 0.00 3.55
1581 1591 7.117812 CCCTAGTGTATTTGTGTTAAGTCAGTG 59.882 40.741 0.00 0.00 0.00 3.66
1582 1592 7.015877 TCCCTAGTGTATTTGTGTTAAGTCAGT 59.984 37.037 0.00 0.00 0.00 3.41
1583 1593 7.383687 TCCCTAGTGTATTTGTGTTAAGTCAG 58.616 38.462 0.00 0.00 0.00 3.51
1584 1594 7.305813 TCCCTAGTGTATTTGTGTTAAGTCA 57.694 36.000 0.00 0.00 0.00 3.41
1585 1595 7.822822 ACATCCCTAGTGTATTTGTGTTAAGTC 59.177 37.037 0.00 0.00 0.00 3.01
1586 1596 7.606456 CACATCCCTAGTGTATTTGTGTTAAGT 59.394 37.037 0.00 0.00 32.44 2.24
1587 1597 7.414098 GCACATCCCTAGTGTATTTGTGTTAAG 60.414 40.741 0.00 0.00 39.17 1.85
1588 1598 6.373216 GCACATCCCTAGTGTATTTGTGTTAA 59.627 38.462 0.00 0.00 39.17 2.01
1589 1599 5.878116 GCACATCCCTAGTGTATTTGTGTTA 59.122 40.000 0.00 0.00 39.17 2.41
1590 1600 4.700213 GCACATCCCTAGTGTATTTGTGTT 59.300 41.667 0.00 0.00 39.17 3.32
1591 1601 4.019321 AGCACATCCCTAGTGTATTTGTGT 60.019 41.667 0.00 0.00 39.17 3.72
1592 1602 4.517285 AGCACATCCCTAGTGTATTTGTG 58.483 43.478 0.00 0.00 39.17 3.33
1593 1603 4.844349 AGCACATCCCTAGTGTATTTGT 57.156 40.909 0.00 0.00 39.17 2.83
1594 1604 4.336433 CCAAGCACATCCCTAGTGTATTTG 59.664 45.833 0.00 0.00 39.17 2.32
1595 1605 4.018415 ACCAAGCACATCCCTAGTGTATTT 60.018 41.667 0.00 0.00 39.17 1.40
1596 1606 3.523564 ACCAAGCACATCCCTAGTGTATT 59.476 43.478 0.00 0.00 39.17 1.89
1597 1607 3.115390 ACCAAGCACATCCCTAGTGTAT 58.885 45.455 0.00 0.00 39.17 2.29
1598 1608 2.546899 ACCAAGCACATCCCTAGTGTA 58.453 47.619 0.00 0.00 39.17 2.90
1599 1609 1.362224 ACCAAGCACATCCCTAGTGT 58.638 50.000 0.00 0.00 39.17 3.55
1702 1721 0.603975 AGAGGTGCTTTGAGTTCCGC 60.604 55.000 0.00 0.00 0.00 5.54
1735 1754 0.804989 GGTGGATTTGAGCGTTCCTG 59.195 55.000 0.00 0.00 0.00 3.86
1751 1770 2.618053 CTTGGCCTAGTAGAAACGGTG 58.382 52.381 3.32 0.00 0.00 4.94
1883 2004 9.753674 TGAATTAGAAGGGACATAAGAAACAAT 57.246 29.630 0.00 0.00 0.00 2.71
1886 2007 8.451748 GTGTGAATTAGAAGGGACATAAGAAAC 58.548 37.037 0.00 0.00 0.00 2.78
1894 2143 4.503910 CGATGTGTGAATTAGAAGGGACA 58.496 43.478 0.00 0.00 0.00 4.02
1907 2156 2.009051 GATTGATGCACCGATGTGTGA 58.991 47.619 0.00 0.00 44.65 3.58
1927 2176 8.939201 TCTTTTTCATGTAGAGCTTATCTCAG 57.061 34.615 0.00 0.00 44.35 3.35
2002 2267 9.400638 GAACATGAAATTAAACATTTACGGTCA 57.599 29.630 0.00 0.00 0.00 4.02
2031 2296 9.169592 CAAAATTCATCCAAAATAGCTCCAAAT 57.830 29.630 0.00 0.00 0.00 2.32
2134 5108 4.325204 TCCACGATCGTCGAAACATAAAAG 59.675 41.667 19.84 1.89 43.74 2.27
2139 5113 1.625616 GTCCACGATCGTCGAAACAT 58.374 50.000 19.84 0.00 43.74 2.71
2155 5129 6.342111 AGAAAGAGGTTAGATTGAATCGTCC 58.658 40.000 0.00 4.23 0.00 4.79
2172 5146 7.273320 TGGGTATATACTTCACGAGAAAGAG 57.727 40.000 12.54 0.00 32.35 2.85
2177 5171 7.174426 CACACTATGGGTATATACTTCACGAGA 59.826 40.741 12.54 0.00 0.00 4.04
2194 5192 7.815641 TGTCATTAACACAAATCACACTATGG 58.184 34.615 0.00 0.00 31.20 2.74
2223 5222 4.020128 AGACGAAAGGAGACCAAGCTTAAT 60.020 41.667 0.00 0.00 0.00 1.40
2240 5239 1.402325 CGGTGTAGCATGACAGACGAA 60.402 52.381 0.00 0.00 34.53 3.85
2243 5242 1.084370 GCCGGTGTAGCATGACAGAC 61.084 60.000 1.90 0.00 0.00 3.51
2272 5271 3.441290 CGGGAGAGGAGCGACGTT 61.441 66.667 0.00 0.00 0.00 3.99
2315 5325 0.391597 GGTTGAGAGGAACGACACCA 59.608 55.000 0.00 0.00 0.00 4.17
2318 5328 0.966920 GGAGGTTGAGAGGAACGACA 59.033 55.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.