Multiple sequence alignment - TraesCS1D01G211400

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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 TraesCS1D01G211400 chr1D 100.000 5534 0 0 1 5534 297370601 297376134 0.000000e+00 10220.0
1 TraesCS1D01G211400 chr1D 98.246 57 1 0 5236 5292 297375781 297375837 3.530000e-17 100.0
2 TraesCS1D01G211400 chr1D 98.246 57 1 0 5181 5237 297375836 297375892 3.530000e-17 100.0
3 TraesCS1D01G211400 chr1A 91.387 2380 141 36 1947 4281 369991594 369993954 0.000000e+00 3201.0
4 TraesCS1D01G211400 chr1A 91.104 978 56 6 4289 5237 369994142 369995117 0.000000e+00 1295.0
5 TraesCS1D01G211400 chr1A 84.292 974 73 34 991 1921 369990664 369991600 0.000000e+00 878.0
6 TraesCS1D01G211400 chr1A 91.582 297 21 3 5239 5534 369995064 369995357 1.860000e-109 407.0
7 TraesCS1D01G211400 chr1A 83.482 224 18 5 761 977 369990383 369990594 2.030000e-44 191.0
8 TraesCS1D01G211400 chr1B 92.671 2033 108 20 2276 4283 399793375 399795391 0.000000e+00 2891.0
9 TraesCS1D01G211400 chr1B 87.705 976 76 21 4289 5237 399795482 399796440 0.000000e+00 1098.0
10 TraesCS1D01G211400 chr1B 88.596 456 47 3 1469 1919 399792632 399793087 2.910000e-152 549.0
11 TraesCS1D01G211400 chr1B 89.905 317 27 3 1947 2260 399793083 399793397 2.400000e-108 403.0
12 TraesCS1D01G211400 chr1B 85.258 407 36 14 1040 1429 399792227 399792626 1.120000e-106 398.0
13 TraesCS1D01G211400 chr1B 88.704 301 29 4 5236 5534 399796384 399796681 4.070000e-96 363.0
14 TraesCS1D01G211400 chr2D 96.097 743 23 4 1 743 78332973 78332237 0.000000e+00 1206.0
15 TraesCS1D01G211400 chr7D 91.156 735 53 6 1 735 557845794 557845072 0.000000e+00 987.0
16 TraesCS1D01G211400 chr7D 89.564 757 58 11 1 749 306475960 306476703 0.000000e+00 941.0
17 TraesCS1D01G211400 chr7D 89.439 748 62 10 1 746 150598939 150599671 0.000000e+00 928.0
18 TraesCS1D01G211400 chr5B 90.280 751 57 9 1 749 192378312 192379048 0.000000e+00 968.0
19 TraesCS1D01G211400 chr5B 89.281 765 65 9 1 758 662050243 662049489 0.000000e+00 942.0
20 TraesCS1D01G211400 chr4B 89.934 755 61 6 1 750 131347201 131347945 0.000000e+00 959.0
21 TraesCS1D01G211400 chr4B 83.544 79 8 4 5400 5478 157667311 157667238 9.950000e-08 69.4
22 TraesCS1D01G211400 chr5D 89.467 750 62 10 1 747 420377815 420377080 0.000000e+00 931.0
23 TraesCS1D01G211400 chr4D 88.699 761 69 13 1 756 370671955 370672703 0.000000e+00 913.0
24 TraesCS1D01G211400 chr4D 93.333 75 4 1 4852 4925 447646697 447646623 5.860000e-20 110.0
25 TraesCS1D01G211400 chr4D 87.500 72 5 1 5414 5481 3593403 3593332 4.600000e-11 80.5
26 TraesCS1D01G211400 chrUn 91.045 67 6 0 5399 5465 81437424 81437358 2.120000e-14 91.6
27 TraesCS1D01G211400 chrUn 91.045 67 6 0 5399 5465 336023986 336023920 2.120000e-14 91.6
28 TraesCS1D01G211400 chrUn 88.235 68 4 2 5399 5466 41692919 41692856 1.650000e-10 78.7
29 TraesCS1D01G211400 chr3B 84.615 91 7 4 4989 5078 89374047 89373963 3.550000e-12 84.2
30 TraesCS1D01G211400 chr6B 84.810 79 8 1 5394 5472 455085184 455085258 5.940000e-10 76.8
31 TraesCS1D01G211400 chr5A 84.810 79 5 5 5395 5472 40616235 40616307 7.690000e-09 73.1
32 TraesCS1D01G211400 chr7B 83.333 78 6 6 5395 5472 368616870 368616940 1.290000e-06 65.8


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 TraesCS1D01G211400 chr1D 297370601 297376134 5533 False 3473.333333 10220 98.830667 1 5534 3 chr1D.!!$F1 5533
1 TraesCS1D01G211400 chr1A 369990383 369995357 4974 False 1194.400000 3201 88.369400 761 5534 5 chr1A.!!$F1 4773
2 TraesCS1D01G211400 chr1B 399792227 399796681 4454 False 950.333333 2891 88.806500 1040 5534 6 chr1B.!!$F1 4494
3 TraesCS1D01G211400 chr2D 78332237 78332973 736 True 1206.000000 1206 96.097000 1 743 1 chr2D.!!$R1 742
4 TraesCS1D01G211400 chr7D 557845072 557845794 722 True 987.000000 987 91.156000 1 735 1 chr7D.!!$R1 734
5 TraesCS1D01G211400 chr7D 306475960 306476703 743 False 941.000000 941 89.564000 1 749 1 chr7D.!!$F2 748
6 TraesCS1D01G211400 chr7D 150598939 150599671 732 False 928.000000 928 89.439000 1 746 1 chr7D.!!$F1 745
7 TraesCS1D01G211400 chr5B 192378312 192379048 736 False 968.000000 968 90.280000 1 749 1 chr5B.!!$F1 748
8 TraesCS1D01G211400 chr5B 662049489 662050243 754 True 942.000000 942 89.281000 1 758 1 chr5B.!!$R1 757
9 TraesCS1D01G211400 chr4B 131347201 131347945 744 False 959.000000 959 89.934000 1 750 1 chr4B.!!$F1 749
10 TraesCS1D01G211400 chr5D 420377080 420377815 735 True 931.000000 931 89.467000 1 747 1 chr5D.!!$R1 746
11 TraesCS1D01G211400 chr4D 370671955 370672703 748 False 913.000000 913 88.699000 1 756 1 chr4D.!!$F1 755

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
959 995 0.109132 CCAGCGATTTTCTGTTGCCC 60.109 55.000 0.00 0.00 0.00 5.36 F
1039 1129 0.319297 TCTGCGAGCATCATCGATGG 60.319 55.000 24.61 11.15 45.56 3.51 F
1275 1395 0.523072 TTCCAGTGAGTACGTACCGC 59.477 55.000 21.80 18.16 0.00 5.68 F
2845 2998 0.396435 ACCGAGAATGTGTCCAAGCA 59.604 50.000 0.00 0.00 0.00 3.91 F
2960 3113 1.153939 CTCCGAGGTGAGTGAAGCG 60.154 63.158 0.00 0.00 0.00 4.68 F
4455 4838 0.753262 GTCATGTCACCCCGAGCTAT 59.247 55.000 0.00 0.00 0.00 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2188 0.392336 GGCACCAACATTTTGCTGGA 59.608 50.000 4.05 0.0 35.69 3.86 R
2343 2481 1.025812 ATCGGGCTTCTGAGAGTACG 58.974 55.000 0.00 0.0 0.00 3.67 R
2951 3104 1.374252 TTCCGCCTTCGCTTCACTC 60.374 57.895 0.00 0.0 0.00 3.51 R
4011 4192 0.319040 GCTCTCACGCACAAGAGACA 60.319 55.000 9.70 0.0 41.28 3.41 R
4518 4901 0.396435 TGCATCAAGTTGACCGGACT 59.604 50.000 9.46 0.0 0.00 3.85 R
5369 5783 0.389757 GCCTATCCTCTTCCACCGAC 59.610 60.000 0.00 0.0 0.00 4.79 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
74 75 2.982130 GGACAGGCCGAGACACAT 59.018 61.111 0.00 0.00 0.00 3.21
83 84 3.279285 CGAGACACATCGGCATGAT 57.721 52.632 0.00 0.00 39.04 2.45
124 126 0.179089 ACTGCGCAATGCCACAAAAA 60.179 45.000 13.05 0.00 45.60 1.94
319 325 2.962569 CGAAGACGCTCTGGTCCA 59.037 61.111 0.00 0.00 37.66 4.02
441 459 3.695830 TGGGTGAGTAATGAAGTGGAC 57.304 47.619 0.00 0.00 0.00 4.02
450 470 7.602644 GTGAGTAATGAAGTGGACAGTAAATGA 59.397 37.037 0.00 0.00 0.00 2.57
464 489 4.627467 CAGTAAATGAAACCGTGAGAGGAG 59.373 45.833 0.00 0.00 34.73 3.69
710 739 0.531974 GAGGCGTGTGGTTGAGTTGA 60.532 55.000 0.00 0.00 0.00 3.18
750 779 6.067039 GTGGACGTTAGTGTTTTCGTAAATC 58.933 40.000 0.00 0.00 36.67 2.17
756 785 8.124199 ACGTTAGTGTTTTCGTAAATCAAATGT 58.876 29.630 0.00 0.00 34.78 2.71
757 786 8.406716 CGTTAGTGTTTTCGTAAATCAAATGTG 58.593 33.333 0.00 0.00 0.00 3.21
758 787 8.687301 GTTAGTGTTTTCGTAAATCAAATGTGG 58.313 33.333 0.00 0.00 0.00 4.17
759 788 5.689961 AGTGTTTTCGTAAATCAAATGTGGC 59.310 36.000 0.00 0.00 0.00 5.01
767 796 2.198827 ATCAAATGTGGCGAACCTGA 57.801 45.000 0.00 0.00 36.63 3.86
778 807 1.978542 CGAACCTGACCTGTTACGAG 58.021 55.000 0.00 0.00 0.00 4.18
789 818 5.532406 TGACCTGTTACGAGTTTGTAGTACT 59.468 40.000 0.00 0.00 0.00 2.73
793 822 9.401058 ACCTGTTACGAGTTTGTAGTACTATAT 57.599 33.333 5.75 0.00 0.00 0.86
841 870 2.812011 GGAGGATACACGTTGCAAGTTT 59.188 45.455 0.00 0.00 41.41 2.66
894 930 4.097863 GCTTTGCCCCGCGTGTAC 62.098 66.667 4.92 0.00 0.00 2.90
922 958 2.224499 GGCTCATCCAGATTTCTCCTCC 60.224 54.545 0.00 0.00 34.01 4.30
923 959 2.705127 GCTCATCCAGATTTCTCCTCCT 59.295 50.000 0.00 0.00 0.00 3.69
924 960 3.494749 GCTCATCCAGATTTCTCCTCCTG 60.495 52.174 0.00 0.00 0.00 3.86
925 961 3.710677 CTCATCCAGATTTCTCCTCCTGT 59.289 47.826 0.00 0.00 0.00 4.00
926 962 4.107072 TCATCCAGATTTCTCCTCCTGTT 58.893 43.478 0.00 0.00 0.00 3.16
927 963 5.280499 TCATCCAGATTTCTCCTCCTGTTA 58.720 41.667 0.00 0.00 0.00 2.41
928 964 5.129485 TCATCCAGATTTCTCCTCCTGTTAC 59.871 44.000 0.00 0.00 0.00 2.50
936 972 1.267261 CTCCTCCTGTTACGCGGATAG 59.733 57.143 12.47 6.29 0.00 2.08
940 976 1.605710 TCCTGTTACGCGGATAGCTAC 59.394 52.381 12.47 0.00 45.59 3.58
942 978 1.335810 CTGTTACGCGGATAGCTACCA 59.664 52.381 12.47 0.00 45.59 3.25
943 979 1.335810 TGTTACGCGGATAGCTACCAG 59.664 52.381 12.47 0.00 45.59 4.00
958 994 0.598065 ACCAGCGATTTTCTGTTGCC 59.402 50.000 0.00 0.00 0.00 4.52
959 995 0.109132 CCAGCGATTTTCTGTTGCCC 60.109 55.000 0.00 0.00 0.00 5.36
960 996 0.454957 CAGCGATTTTCTGTTGCCCG 60.455 55.000 0.00 0.00 0.00 6.13
961 997 0.605319 AGCGATTTTCTGTTGCCCGA 60.605 50.000 0.00 0.00 0.00 5.14
962 998 0.454452 GCGATTTTCTGTTGCCCGAC 60.454 55.000 0.00 0.00 0.00 4.79
963 999 1.156736 CGATTTTCTGTTGCCCGACT 58.843 50.000 0.00 0.00 0.00 4.18
964 1000 2.343101 CGATTTTCTGTTGCCCGACTA 58.657 47.619 0.00 0.00 0.00 2.59
986 1026 4.944372 GCACGCGCGGGCTAGTAT 62.944 66.667 46.53 15.41 42.14 2.12
987 1027 2.640989 CACGCGCGGGCTAGTATA 59.359 61.111 35.22 0.00 36.88 1.47
1035 1125 0.511653 CCATTCTGCGAGCATCATCG 59.488 55.000 0.00 0.00 45.48 3.84
1039 1129 0.319297 TCTGCGAGCATCATCGATGG 60.319 55.000 24.61 11.15 45.56 3.51
1040 1130 0.319297 CTGCGAGCATCATCGATGGA 60.319 55.000 24.61 12.15 45.56 3.41
1041 1131 0.598419 TGCGAGCATCATCGATGGAC 60.598 55.000 24.61 14.13 45.56 4.02
1109 1211 4.467107 GGAGGAGGAGGAGGCCGT 62.467 72.222 0.00 0.00 0.00 5.68
1110 1212 2.601868 GAGGAGGAGGAGGCCGTA 59.398 66.667 0.00 0.00 0.00 4.02
1114 1234 0.686769 GGAGGAGGAGGCCGTAAAGA 60.687 60.000 0.00 0.00 0.00 2.52
1118 1238 2.177233 AGGAGGAGGCCGTAAAGATCTA 59.823 50.000 0.00 0.00 0.00 1.98
1275 1395 0.523072 TTCCAGTGAGTACGTACCGC 59.477 55.000 21.80 18.16 0.00 5.68
1280 1400 4.894203 GAGTACGTACCGCCGCCG 62.894 72.222 21.80 0.00 0.00 6.46
1304 1425 1.650528 CTTCCTTCTCCTCCACCAGT 58.349 55.000 0.00 0.00 0.00 4.00
1318 1439 2.740055 CAGTGCCAGTGCGACCTC 60.740 66.667 0.00 0.00 41.78 3.85
1335 1456 5.568423 GCGACCTCTGAGATCAATCCATAAT 60.568 44.000 6.17 0.00 0.00 1.28
1336 1457 6.350528 GCGACCTCTGAGATCAATCCATAATA 60.351 42.308 6.17 0.00 0.00 0.98
1337 1458 7.632462 GCGACCTCTGAGATCAATCCATAATAT 60.632 40.741 6.17 0.00 0.00 1.28
1361 1482 3.323691 TGATCGAGTTGGAGGTTTCTTCA 59.676 43.478 0.00 0.00 0.00 3.02
1380 1501 7.406031 TCTTCAGTAGAAATCGACCAAGTAT 57.594 36.000 0.00 0.00 32.35 2.12
1388 1509 6.284459 AGAAATCGACCAAGTATCCAATCTC 58.716 40.000 0.00 0.00 0.00 2.75
1390 1511 5.815233 ATCGACCAAGTATCCAATCTCAT 57.185 39.130 0.00 0.00 0.00 2.90
1391 1512 6.918067 ATCGACCAAGTATCCAATCTCATA 57.082 37.500 0.00 0.00 0.00 2.15
1392 1513 6.085555 TCGACCAAGTATCCAATCTCATAC 57.914 41.667 0.00 0.00 0.00 2.39
1394 1515 5.692204 CGACCAAGTATCCAATCTCATACAC 59.308 44.000 0.00 0.00 0.00 2.90
1395 1516 5.930135 ACCAAGTATCCAATCTCATACACC 58.070 41.667 0.00 0.00 0.00 4.16
1396 1517 5.428457 ACCAAGTATCCAATCTCATACACCA 59.572 40.000 0.00 0.00 0.00 4.17
1398 1519 6.828273 CCAAGTATCCAATCTCATACACCAAA 59.172 38.462 0.00 0.00 0.00 3.28
1450 1572 2.291465 GCACAAGTCTGACTGAAATGCA 59.709 45.455 21.28 0.00 0.00 3.96
1453 1575 3.947196 ACAAGTCTGACTGAAATGCACAA 59.053 39.130 11.71 0.00 0.00 3.33
1482 1604 2.792674 CTCGCGTCTGTTTTGTTGACTA 59.207 45.455 5.77 0.00 0.00 2.59
1484 1606 2.283086 CGCGTCTGTTTTGTTGACTACA 59.717 45.455 0.00 0.00 34.12 2.74
1537 1667 7.601856 AGTTAGTCATAGCTAATCTCATCTGC 58.398 38.462 0.00 0.00 34.03 4.26
1538 1668 5.058149 AGTCATAGCTAATCTCATCTGCG 57.942 43.478 0.00 0.00 0.00 5.18
1548 1678 2.388735 TCTCATCTGCGGTCTAATGGT 58.611 47.619 0.00 0.00 0.00 3.55
1605 1740 2.919856 AGCAGACCTGGTGAGCGT 60.920 61.111 2.82 0.00 40.15 5.07
1625 1760 3.135994 GTTTACAGGCAGAACGAAAGGA 58.864 45.455 0.00 0.00 0.00 3.36
1626 1761 3.478857 TTACAGGCAGAACGAAAGGAA 57.521 42.857 0.00 0.00 0.00 3.36
1627 1762 2.341846 ACAGGCAGAACGAAAGGAAA 57.658 45.000 0.00 0.00 0.00 3.13
1631 1766 3.315191 CAGGCAGAACGAAAGGAAAAAGA 59.685 43.478 0.00 0.00 0.00 2.52
1639 1774 6.265422 AGAACGAAAGGAAAAAGATGGACAAT 59.735 34.615 0.00 0.00 0.00 2.71
1648 1783 3.356529 AAGATGGACAATCACCTGGAC 57.643 47.619 0.00 0.00 37.81 4.02
1656 1791 2.029290 ACAATCACCTGGACGAGTACAC 60.029 50.000 0.00 0.00 0.00 2.90
1672 1807 2.031516 CACTCGCCAGTGCTCCAAG 61.032 63.158 0.00 0.00 43.77 3.61
1706 1841 6.619874 GCAAACAGCCAAATCATCTTCATTTG 60.620 38.462 0.00 0.00 39.84 2.32
1729 1864 5.012893 GTCAACCTTCCAGATTCCAGAATT 58.987 41.667 0.00 0.00 0.00 2.17
1753 1888 1.214589 GCAGGAACGCGAGGAGTAA 59.785 57.895 15.93 0.00 0.00 2.24
1754 1889 0.802607 GCAGGAACGCGAGGAGTAAG 60.803 60.000 15.93 0.00 0.00 2.34
1755 1890 0.802607 CAGGAACGCGAGGAGTAAGC 60.803 60.000 15.93 0.00 0.00 3.09
1812 1947 2.564771 TCAAGTGTGAGAAGCTTGTGG 58.435 47.619 2.10 0.00 40.14 4.17
1820 1955 1.271102 GAGAAGCTTGTGGTCGAGAGT 59.729 52.381 2.10 0.00 0.00 3.24
1921 2056 8.797438 TGACAAGCACTTCTCTAGGTATATATG 58.203 37.037 0.00 0.00 0.00 1.78
1922 2057 8.713708 ACAAGCACTTCTCTAGGTATATATGT 57.286 34.615 0.00 0.00 0.00 2.29
1923 2058 8.580720 ACAAGCACTTCTCTAGGTATATATGTG 58.419 37.037 0.00 0.00 0.00 3.21
1924 2059 8.580720 CAAGCACTTCTCTAGGTATATATGTGT 58.419 37.037 0.00 0.00 0.00 3.72
1925 2060 9.809395 AAGCACTTCTCTAGGTATATATGTGTA 57.191 33.333 0.00 0.00 0.00 2.90
1926 2061 9.983024 AGCACTTCTCTAGGTATATATGTGTAT 57.017 33.333 0.00 0.00 0.00 2.29
1982 2117 1.001048 CGGCCATGGAGCACATATTTG 60.001 52.381 18.40 0.00 37.84 2.32
1993 2128 8.523915 TGGAGCACATATTTGTCAGATATTTT 57.476 30.769 0.00 0.00 32.34 1.82
1996 2131 9.793252 GAGCACATATTTGTCAGATATTTTGTT 57.207 29.630 0.00 0.00 32.34 2.83
2019 2154 8.128582 TGTTTGTCTGTTAATCACATCAGAAAC 58.871 33.333 0.00 0.00 38.40 2.78
2045 2183 9.335891 CTAATGCACGTTTCAAATACATAACAA 57.664 29.630 0.00 0.00 0.00 2.83
2050 2188 9.856803 GCACGTTTCAAATACATAACAAAAATT 57.143 25.926 0.00 0.00 0.00 1.82
2082 2220 2.829384 GGTGCCCAGGTCCAAGACA 61.829 63.158 0.00 0.00 33.68 3.41
2217 2355 6.395426 TCATGCACTTGATTTCTTCAGTTT 57.605 33.333 0.00 0.00 35.27 2.66
2224 2362 9.677567 GCACTTGATTTCTTCAGTTTTACATAA 57.322 29.630 0.00 0.00 35.27 1.90
2260 2398 8.655935 AATTCAGGATTTATGAGGTTTTGACT 57.344 30.769 0.00 0.00 0.00 3.41
2262 2400 7.452880 TCAGGATTTATGAGGTTTTGACTTG 57.547 36.000 0.00 0.00 0.00 3.16
2330 2468 6.316640 TCAAACCATCTTTCGTTCAAACTGTA 59.683 34.615 0.00 0.00 0.00 2.74
2343 2481 0.824759 AACTGTACGCAGGGAGGATC 59.175 55.000 0.00 0.00 46.62 3.36
2441 2579 0.868602 CCGCACGTCGAAACCGATAT 60.869 55.000 0.00 0.00 41.67 1.63
2579 2717 2.936912 GCACGTCTCTGTGGGCTCT 61.937 63.158 0.00 0.00 40.26 4.09
2708 2846 2.439338 AACACTGCACCGTGCCAA 60.439 55.556 20.67 2.10 44.23 4.52
2737 2875 5.415221 TCAGGTTGTTTGCTTTTTAACCAG 58.585 37.500 0.00 0.00 42.42 4.00
2738 2876 5.046950 TCAGGTTGTTTGCTTTTTAACCAGT 60.047 36.000 0.00 0.00 42.42 4.00
2739 2877 6.153000 TCAGGTTGTTTGCTTTTTAACCAGTA 59.847 34.615 0.00 0.00 42.42 2.74
2741 2879 6.153851 AGGTTGTTTGCTTTTTAACCAGTACT 59.846 34.615 0.00 0.00 42.42 2.73
2742 2880 6.474427 GGTTGTTTGCTTTTTAACCAGTACTC 59.526 38.462 0.00 0.00 40.31 2.59
2743 2881 6.139048 TGTTTGCTTTTTAACCAGTACTCC 57.861 37.500 0.00 0.00 0.00 3.85
2744 2882 5.889289 TGTTTGCTTTTTAACCAGTACTCCT 59.111 36.000 0.00 0.00 0.00 3.69
2747 2885 6.429521 TGCTTTTTAACCAGTACTCCTACT 57.570 37.500 0.00 0.00 33.01 2.57
2748 2886 7.543359 TGCTTTTTAACCAGTACTCCTACTA 57.457 36.000 0.00 0.00 31.46 1.82
2749 2887 7.381323 TGCTTTTTAACCAGTACTCCTACTAC 58.619 38.462 0.00 0.00 31.46 2.73
2757 2910 3.821600 CAGTACTCCTACTACGCATGGAT 59.178 47.826 0.00 0.00 31.46 3.41
2759 2912 5.472478 CAGTACTCCTACTACGCATGGATAA 59.528 44.000 0.00 0.00 31.46 1.75
2786 2939 4.571580 CAGGTGCATTTGTTTTTGACACAT 59.428 37.500 0.00 0.00 38.18 3.21
2809 2962 9.981114 ACATCGATGTAATGTAATGACTGATTA 57.019 29.630 29.05 0.00 39.68 1.75
2832 2985 0.472471 ACAGGCCAAGAAAACCGAGA 59.528 50.000 5.01 0.00 0.00 4.04
2838 2991 2.293399 GCCAAGAAAACCGAGAATGTGT 59.707 45.455 0.00 0.00 0.00 3.72
2845 2998 0.396435 ACCGAGAATGTGTCCAAGCA 59.604 50.000 0.00 0.00 0.00 3.91
2936 3089 3.487202 CGTGACAACGCCATCCGG 61.487 66.667 0.00 0.00 43.98 5.14
2952 3105 4.019983 GGAAGCTCTCCGAGGTGA 57.980 61.111 0.00 0.00 39.62 4.02
2960 3113 1.153939 CTCCGAGGTGAGTGAAGCG 60.154 63.158 0.00 0.00 0.00 4.68
2966 3119 2.383527 GGTGAGTGAAGCGAAGGCG 61.384 63.158 0.00 0.00 46.35 5.52
3125 3278 3.041940 CAGGCGACGCGGAACTTT 61.042 61.111 14.61 0.00 0.00 2.66
3242 3396 5.940470 ACAGTTCCAGCAAGAGGTAAATTAG 59.060 40.000 0.00 0.00 0.00 1.73
3286 3440 1.755959 TGCCTGTGCATTTGTTTCAGT 59.244 42.857 0.00 0.00 44.23 3.41
3296 3450 4.678742 GCATTTGTTTCAGTTCTTGAGAGC 59.321 41.667 0.00 0.00 37.07 4.09
3318 3499 3.555586 CCAAGGGTCAAAAATGCTGAAGG 60.556 47.826 0.00 0.00 0.00 3.46
3319 3500 1.620323 AGGGTCAAAAATGCTGAAGGC 59.380 47.619 0.00 0.00 42.22 4.35
3320 3501 1.620323 GGGTCAAAAATGCTGAAGGCT 59.380 47.619 0.00 0.00 42.39 4.58
3321 3502 2.611224 GGGTCAAAAATGCTGAAGGCTG 60.611 50.000 0.00 0.00 42.39 4.85
3323 3504 3.243839 GGTCAAAAATGCTGAAGGCTGAA 60.244 43.478 0.00 0.00 42.39 3.02
3324 3505 3.737774 GTCAAAAATGCTGAAGGCTGAAC 59.262 43.478 0.00 0.00 42.39 3.18
3325 3506 3.384146 TCAAAAATGCTGAAGGCTGAACA 59.616 39.130 0.00 0.00 42.39 3.18
3351 3532 4.151883 AGATGTTTAATGGTGCAGGTTGT 58.848 39.130 0.00 0.00 0.00 3.32
3424 3605 3.200593 GAGGCATCAGCGCTGGTG 61.201 66.667 39.86 39.86 44.25 4.17
3427 3608 2.177531 GCATCAGCGCTGGTGTTG 59.822 61.111 41.80 29.68 43.37 3.33
3629 3810 1.228245 GCCAACCTGGTCAGCAAGA 60.228 57.895 14.26 0.00 40.46 3.02
3755 3936 1.582968 GTGTACTCCTTCGGCGTCA 59.417 57.895 6.85 0.00 0.00 4.35
3847 4028 2.279120 GAGATGGAGGCGCTCGTG 60.279 66.667 7.64 0.00 0.00 4.35
4011 4192 1.004560 CCATGTCTGTCGCACCAGT 60.005 57.895 0.00 0.00 34.02 4.00
4071 4270 5.369404 TCATCTGCCCAATTTCTCAGGTATA 59.631 40.000 0.00 0.00 0.00 1.47
4072 4271 5.708736 TCTGCCCAATTTCTCAGGTATAA 57.291 39.130 0.00 0.00 0.00 0.98
4073 4272 6.266131 TCTGCCCAATTTCTCAGGTATAAT 57.734 37.500 0.00 0.00 0.00 1.28
4074 4273 7.387265 TCTGCCCAATTTCTCAGGTATAATA 57.613 36.000 0.00 0.00 0.00 0.98
4090 4289 7.068103 CAGGTATAATAATTGTTGAGTTGCCCA 59.932 37.037 0.00 0.00 0.00 5.36
4150 4350 4.893608 ACTTTTGTGGTTTCAAGTTTGCT 58.106 34.783 0.00 0.00 0.00 3.91
4192 4392 4.805219 CCACCACAAAATACAGGTTTAGC 58.195 43.478 0.00 0.00 30.44 3.09
4260 4460 9.890085 CGAATACAATTTGAATAATTTGTGCTG 57.110 29.630 2.79 0.00 39.42 4.41
4263 4463 7.675962 ACAATTTGAATAATTTGTGCTGCAT 57.324 28.000 5.27 0.00 38.34 3.96
4329 4712 3.350219 TTGCAGGAGGTTATGAGGAAC 57.650 47.619 0.00 0.00 0.00 3.62
4341 4724 2.526873 AGGAACCCTCACACGGCT 60.527 61.111 0.00 0.00 0.00 5.52
4455 4838 0.753262 GTCATGTCACCCCGAGCTAT 59.247 55.000 0.00 0.00 0.00 2.97
4512 4895 3.663995 CATCAACAAAAGATGCCACCA 57.336 42.857 0.00 0.00 36.77 4.17
4518 4901 1.811965 CAAAAGATGCCACCACGATCA 59.188 47.619 0.00 0.00 0.00 2.92
4608 4991 8.655901 TCAGCTCCACATTTGGTGTATATATTA 58.344 33.333 0.00 0.00 46.44 0.98
4634 5017 6.854091 ACTACCTTGTTGTTTTTGGGTTTA 57.146 33.333 0.00 0.00 0.00 2.01
4648 5031 8.831550 GTTTTTGGGTTTATGAGTTGCAAAATA 58.168 29.630 0.00 0.00 0.00 1.40
4666 5049 6.019075 GCAAAATACGATCTACTGTGCATGTA 60.019 38.462 0.00 0.00 0.00 2.29
4676 5059 5.994668 TCTACTGTGCATGTATTCAAACACA 59.005 36.000 9.41 9.41 39.43 3.72
4805 5189 6.480651 GCTAAAGCCTCCTAATTCTGAACTAC 59.519 42.308 0.00 0.00 34.31 2.73
4807 5191 5.606348 AGCCTCCTAATTCTGAACTACAG 57.394 43.478 0.00 0.00 46.97 2.74
4812 5196 7.394816 CCTCCTAATTCTGAACTACAGGAAAA 58.605 38.462 10.48 0.00 45.76 2.29
4815 5199 9.096823 TCCTAATTCTGAACTACAGGAAAAGTA 57.903 33.333 8.03 0.00 45.76 2.24
4822 5206 7.672660 TCTGAACTACAGGAAAAGTATGGAGTA 59.327 37.037 0.00 0.00 45.76 2.59
4827 5211 9.263446 ACTACAGGAAAAGTATGGAGTATTACA 57.737 33.333 0.00 0.00 36.34 2.41
4959 5346 4.449743 ACATAAGTGTTCGTACGTTGCAAT 59.550 37.500 16.05 9.10 34.01 3.56
4962 5349 1.527736 GTGTTCGTACGTTGCAATGGA 59.472 47.619 22.20 11.93 0.00 3.41
4983 5370 7.444629 TGGAGACATACATATTACTCCGTAC 57.555 40.000 0.00 0.00 44.46 3.67
5058 5446 6.736853 CGACGTGATTGATTCCTTTTCTTAAC 59.263 38.462 0.00 0.00 0.00 2.01
5067 5455 7.309920 TGATTCCTTTTCTTAACGTTAATGGC 58.690 34.615 20.39 7.07 0.00 4.40
5145 5557 6.213195 TGACCATGATATGTGTGCCTGATATA 59.787 38.462 0.00 0.00 0.00 0.86
5195 5607 2.620251 TAGAGATTGGCCGTGATTGG 57.380 50.000 0.00 0.00 0.00 3.16
5215 5627 4.855340 TGGTTCCTTCCCATAAAGACATC 58.145 43.478 0.00 0.00 0.00 3.06
5220 5632 6.485830 TCCTTCCCATAAAGACATCACTAG 57.514 41.667 0.00 0.00 0.00 2.57
5240 5652 8.642432 TCACTAGATATACCAAAGATTGAGTGG 58.358 37.037 0.00 0.00 38.46 4.00
5241 5653 7.386299 CACTAGATATACCAAAGATTGAGTGGC 59.614 40.741 0.00 0.00 35.72 5.01
5242 5654 5.625150 AGATATACCAAAGATTGAGTGGCC 58.375 41.667 0.00 0.00 35.72 5.36
5243 5655 2.107950 TACCAAAGATTGAGTGGCCG 57.892 50.000 0.00 0.00 35.72 6.13
5244 5656 0.110486 ACCAAAGATTGAGTGGCCGT 59.890 50.000 0.00 0.00 35.72 5.68
5245 5657 0.523072 CCAAAGATTGAGTGGCCGTG 59.477 55.000 0.00 0.00 0.00 4.94
5246 5658 1.522668 CAAAGATTGAGTGGCCGTGA 58.477 50.000 0.00 0.00 0.00 4.35
5247 5659 2.086869 CAAAGATTGAGTGGCCGTGAT 58.913 47.619 0.00 0.00 0.00 3.06
5248 5660 2.489329 CAAAGATTGAGTGGCCGTGATT 59.511 45.455 0.00 0.00 0.00 2.57
5249 5661 1.742761 AGATTGAGTGGCCGTGATTG 58.257 50.000 0.00 0.00 0.00 2.67
5250 5662 0.734889 GATTGAGTGGCCGTGATTGG 59.265 55.000 0.00 0.00 0.00 3.16
5251 5663 0.038166 ATTGAGTGGCCGTGATTGGT 59.962 50.000 0.00 0.00 0.00 3.67
5252 5664 0.179004 TTGAGTGGCCGTGATTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
5253 5665 0.605319 TGAGTGGCCGTGATTGGTTC 60.605 55.000 0.00 0.00 0.00 3.62
5254 5666 1.303317 AGTGGCCGTGATTGGTTCC 60.303 57.895 0.00 0.00 0.00 3.62
5255 5667 1.303317 GTGGCCGTGATTGGTTCCT 60.303 57.895 0.00 0.00 0.00 3.36
5256 5668 0.893727 GTGGCCGTGATTGGTTCCTT 60.894 55.000 0.00 0.00 0.00 3.36
5257 5669 0.608035 TGGCCGTGATTGGTTCCTTC 60.608 55.000 0.00 0.00 0.00 3.46
5258 5670 1.313091 GGCCGTGATTGGTTCCTTCC 61.313 60.000 0.00 0.00 0.00 3.46
5259 5671 1.313091 GCCGTGATTGGTTCCTTCCC 61.313 60.000 0.00 0.00 0.00 3.97
5260 5672 0.037590 CCGTGATTGGTTCCTTCCCA 59.962 55.000 0.00 0.00 0.00 4.37
5261 5673 1.340991 CCGTGATTGGTTCCTTCCCAT 60.341 52.381 0.00 0.00 0.00 4.00
5262 5674 2.092646 CCGTGATTGGTTCCTTCCCATA 60.093 50.000 0.00 0.00 0.00 2.74
5263 5675 3.616219 CGTGATTGGTTCCTTCCCATAA 58.384 45.455 0.00 0.00 0.00 1.90
5264 5676 4.013728 CGTGATTGGTTCCTTCCCATAAA 58.986 43.478 0.00 0.00 0.00 1.40
5265 5677 4.096382 CGTGATTGGTTCCTTCCCATAAAG 59.904 45.833 0.00 0.00 0.00 1.85
5266 5678 5.261216 GTGATTGGTTCCTTCCCATAAAGA 58.739 41.667 0.00 0.00 0.00 2.52
5267 5679 5.125578 GTGATTGGTTCCTTCCCATAAAGAC 59.874 44.000 0.00 0.00 0.00 3.01
5268 5680 4.733077 TTGGTTCCTTCCCATAAAGACA 57.267 40.909 0.00 0.00 0.00 3.41
5269 5681 4.946160 TGGTTCCTTCCCATAAAGACAT 57.054 40.909 0.00 0.00 0.00 3.06
5270 5682 4.855340 TGGTTCCTTCCCATAAAGACATC 58.145 43.478 0.00 0.00 0.00 3.06
5271 5683 4.290985 TGGTTCCTTCCCATAAAGACATCA 59.709 41.667 0.00 0.00 0.00 3.07
5272 5684 4.640647 GGTTCCTTCCCATAAAGACATCAC 59.359 45.833 0.00 0.00 0.00 3.06
5273 5685 5.501156 GTTCCTTCCCATAAAGACATCACT 58.499 41.667 0.00 0.00 0.00 3.41
5274 5686 6.352737 GGTTCCTTCCCATAAAGACATCACTA 60.353 42.308 0.00 0.00 0.00 2.74
5275 5687 6.485830 TCCTTCCCATAAAGACATCACTAG 57.514 41.667 0.00 0.00 0.00 2.57
5276 5688 6.202331 TCCTTCCCATAAAGACATCACTAGA 58.798 40.000 0.00 0.00 0.00 2.43
5277 5689 6.846505 TCCTTCCCATAAAGACATCACTAGAT 59.153 38.462 0.00 0.00 33.87 1.98
5278 5690 8.010697 TCCTTCCCATAAAGACATCACTAGATA 58.989 37.037 0.00 0.00 31.88 1.98
5279 5691 8.820831 CCTTCCCATAAAGACATCACTAGATAT 58.179 37.037 0.00 0.00 31.88 1.63
5282 5694 9.256228 TCCCATAAAGACATCACTAGATATACC 57.744 37.037 0.00 0.00 31.88 2.73
5283 5695 9.035890 CCCATAAAGACATCACTAGATATACCA 57.964 37.037 0.00 0.00 31.88 3.25
5353 5766 7.790823 TGGGGTAAAAGCGATTTAATAGTAC 57.209 36.000 0.00 0.00 35.33 2.73
5432 5846 1.075536 GGTGGTGGGGAGAAAACTGAT 59.924 52.381 0.00 0.00 0.00 2.90
5441 5855 6.659242 GTGGGGAGAAAACTGATTGAAAGATA 59.341 38.462 0.00 0.00 0.00 1.98
5509 5923 6.563037 ACTAAACCCTCCTAATTTCTCTCC 57.437 41.667 0.00 0.00 0.00 3.71
5510 5924 6.030082 ACTAAACCCTCCTAATTTCTCTCCA 58.970 40.000 0.00 0.00 0.00 3.86
5516 5930 3.457749 CTCCTAATTTCTCTCCAGGCCTT 59.542 47.826 0.00 0.00 0.00 4.35
5527 5941 0.698818 CCAGGCCTTCAAGTTACCCT 59.301 55.000 0.00 0.00 0.00 4.34
5529 5943 2.307686 CCAGGCCTTCAAGTTACCCTTA 59.692 50.000 0.00 0.00 0.00 2.69
5532 5946 5.016831 CAGGCCTTCAAGTTACCCTTAAAT 58.983 41.667 0.00 0.00 0.00 1.40
5533 5947 6.184789 CAGGCCTTCAAGTTACCCTTAAATA 58.815 40.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 126 1.152756 AGTCCCGTGCTTGCCTTTT 60.153 52.632 0.00 0.00 0.00 2.27
127 129 4.021925 GGAGTCCCGTGCTTGCCT 62.022 66.667 0.00 0.00 0.00 4.75
177 179 0.673985 ATTCATCGAGATTCCGGCGA 59.326 50.000 9.30 0.00 38.51 5.54
227 231 2.505819 TCCTTGCCTCCATTACTTCTCC 59.494 50.000 0.00 0.00 0.00 3.71
228 232 3.914426 TCCTTGCCTCCATTACTTCTC 57.086 47.619 0.00 0.00 0.00 2.87
229 233 4.018050 ACATTCCTTGCCTCCATTACTTCT 60.018 41.667 0.00 0.00 0.00 2.85
441 459 4.566004 TCCTCTCACGGTTTCATTTACTG 58.434 43.478 0.00 0.00 0.00 2.74
450 470 1.918800 CCCCCTCCTCTCACGGTTT 60.919 63.158 0.00 0.00 0.00 3.27
710 739 1.593209 CACACGTGTGGGCGTTAGT 60.593 57.895 35.65 1.12 43.83 2.24
730 759 8.124199 ACATTTGATTTACGAAAACACTAACGT 58.876 29.630 0.00 0.00 41.66 3.99
750 779 0.240945 GGTCAGGTTCGCCACATTTG 59.759 55.000 0.00 0.00 40.60 2.32
756 785 0.034337 GTAACAGGTCAGGTTCGCCA 59.966 55.000 0.00 0.00 40.60 5.69
757 786 1.012486 CGTAACAGGTCAGGTTCGCC 61.012 60.000 0.00 0.00 37.60 5.54
758 787 0.038892 TCGTAACAGGTCAGGTTCGC 60.039 55.000 0.00 0.00 0.00 4.70
759 788 1.268899 ACTCGTAACAGGTCAGGTTCG 59.731 52.381 0.00 0.00 0.00 3.95
767 796 7.693969 ATAGTACTACAAACTCGTAACAGGT 57.306 36.000 4.31 0.00 0.00 4.00
797 826 2.097466 CCTTCGCAGTGTCACAAGTTTT 59.903 45.455 5.62 0.00 0.00 2.43
798 827 1.670811 CCTTCGCAGTGTCACAAGTTT 59.329 47.619 5.62 0.00 0.00 2.66
799 828 1.299541 CCTTCGCAGTGTCACAAGTT 58.700 50.000 5.62 0.00 0.00 2.66
800 829 1.160329 GCCTTCGCAGTGTCACAAGT 61.160 55.000 5.62 0.00 34.03 3.16
825 854 2.577700 TCCCAAACTTGCAACGTGTAT 58.422 42.857 0.00 0.00 0.00 2.29
841 870 4.974438 AGCGGGTCCCAGTTCCCA 62.974 66.667 9.12 0.00 43.57 4.37
878 907 2.666862 TGTACACGCGGGGCAAAG 60.667 61.111 15.46 0.00 0.00 2.77
903 939 3.710677 ACAGGAGGAGAAATCTGGATGAG 59.289 47.826 0.00 0.00 0.00 2.90
905 941 4.500499 AACAGGAGGAGAAATCTGGATG 57.500 45.455 0.00 0.00 0.00 3.51
909 945 3.190874 GCGTAACAGGAGGAGAAATCTG 58.809 50.000 0.00 0.00 0.00 2.90
922 958 1.335810 TGGTAGCTATCCGCGTAACAG 59.664 52.381 4.92 0.00 45.59 3.16
923 959 1.335810 CTGGTAGCTATCCGCGTAACA 59.664 52.381 4.92 0.00 45.59 2.41
924 960 1.929482 GCTGGTAGCTATCCGCGTAAC 60.929 57.143 4.92 0.00 45.59 2.50
925 961 0.313043 GCTGGTAGCTATCCGCGTAA 59.687 55.000 4.92 0.00 45.59 3.18
926 962 1.848932 CGCTGGTAGCTATCCGCGTA 61.849 60.000 28.24 0.00 45.59 4.42
927 963 2.728817 GCTGGTAGCTATCCGCGT 59.271 61.111 4.92 0.00 45.59 6.01
928 964 2.201436 ATCGCTGGTAGCTATCCGCG 62.201 60.000 29.99 29.99 45.59 6.46
936 972 2.729156 GCAACAGAAAATCGCTGGTAGC 60.729 50.000 0.00 0.00 37.69 3.58
940 976 0.109132 GGGCAACAGAAAATCGCTGG 60.109 55.000 0.00 0.00 37.69 4.85
942 978 0.605319 TCGGGCAACAGAAAATCGCT 60.605 50.000 0.00 0.00 38.06 4.93
943 979 0.454452 GTCGGGCAACAGAAAATCGC 60.454 55.000 0.00 0.00 44.36 4.58
952 988 2.735478 CGCGTTAGTCGGGCAACA 60.735 61.111 0.00 0.00 44.64 3.33
1022 1112 0.598419 GTCCATCGATGATGCTCGCA 60.598 55.000 26.86 0.00 38.59 5.10
1025 1115 1.135046 CGTGTCCATCGATGATGCTC 58.865 55.000 26.86 14.26 38.59 4.26
1109 1211 1.470285 GCACCGCCACGTAGATCTTTA 60.470 52.381 0.00 0.00 0.00 1.85
1110 1212 0.739813 GCACCGCCACGTAGATCTTT 60.740 55.000 0.00 0.00 0.00 2.52
1280 1400 1.258445 TGGAGGAGAAGGAAGCGACC 61.258 60.000 0.00 0.00 0.00 4.79
1281 1402 0.108567 GTGGAGGAGAAGGAAGCGAC 60.109 60.000 0.00 0.00 0.00 5.19
1304 1425 2.917227 TCAGAGGTCGCACTGGCA 60.917 61.111 0.00 0.00 41.24 4.92
1318 1439 9.465985 CGATCAGATATTATGGATTGATCTCAG 57.534 37.037 9.69 0.00 39.00 3.35
1335 1456 4.956700 AGAAACCTCCAACTCGATCAGATA 59.043 41.667 0.00 0.00 0.00 1.98
1336 1457 3.772025 AGAAACCTCCAACTCGATCAGAT 59.228 43.478 0.00 0.00 0.00 2.90
1337 1458 3.165875 AGAAACCTCCAACTCGATCAGA 58.834 45.455 0.00 0.00 0.00 3.27
1361 1482 6.540438 TTGGATACTTGGTCGATTTCTACT 57.460 37.500 0.00 0.00 37.61 2.57
1450 1572 1.129251 CAGACGCGAGATTGCAATTGT 59.871 47.619 15.93 4.02 34.15 2.71
1453 1575 1.442769 AACAGACGCGAGATTGCAAT 58.557 45.000 15.93 12.83 34.15 3.56
1465 1587 8.891928 CAAAATATGTAGTCAACAAAACAGACG 58.108 33.333 0.00 0.00 42.70 4.18
1482 1604 8.028354 TGCGATTTGATCAGAAACAAAATATGT 58.972 29.630 9.26 0.00 46.82 2.29
1484 1606 8.246180 ACTGCGATTTGATCAGAAACAAAATAT 58.754 29.630 9.26 0.00 39.01 1.28
1537 1667 2.095263 CACTGCCAAAACCATTAGACCG 60.095 50.000 0.00 0.00 0.00 4.79
1538 1668 2.231235 CCACTGCCAAAACCATTAGACC 59.769 50.000 0.00 0.00 0.00 3.85
1548 1678 0.752054 CTTGCTTCCCACTGCCAAAA 59.248 50.000 0.00 0.00 0.00 2.44
1574 1709 0.321387 TCTGCTCTCAGCTTGCTTGG 60.321 55.000 0.00 0.00 42.97 3.61
1605 1740 3.478857 TCCTTTCGTTCTGCCTGTAAA 57.521 42.857 0.00 0.00 0.00 2.01
1625 1760 4.524328 GTCCAGGTGATTGTCCATCTTTTT 59.476 41.667 0.00 0.00 32.34 1.94
1626 1761 4.082125 GTCCAGGTGATTGTCCATCTTTT 58.918 43.478 0.00 0.00 32.34 2.27
1627 1762 3.690460 GTCCAGGTGATTGTCCATCTTT 58.310 45.455 0.00 0.00 32.34 2.52
1631 1766 1.208052 CTCGTCCAGGTGATTGTCCAT 59.792 52.381 0.00 0.00 0.00 3.41
1639 1774 1.531423 GAGTGTACTCGTCCAGGTGA 58.469 55.000 0.00 0.00 32.78 4.02
1672 1807 0.961019 TGGCTGTTTGCACCTTCATC 59.039 50.000 0.00 0.00 45.15 2.92
1706 1841 3.703001 TCTGGAATCTGGAAGGTTGAC 57.297 47.619 0.00 0.00 37.45 3.18
1729 1864 0.179111 CCTCGCGTTCCTGCAGATTA 60.179 55.000 17.39 0.00 34.15 1.75
1753 1888 2.608623 AGGGCAATTTAGTTTGGTGCT 58.391 42.857 0.00 0.00 35.53 4.40
1754 1889 3.244044 TGAAGGGCAATTTAGTTTGGTGC 60.244 43.478 0.00 0.00 34.42 5.01
1755 1890 4.599047 TGAAGGGCAATTTAGTTTGGTG 57.401 40.909 0.00 0.00 0.00 4.17
1812 1947 0.512085 ACGACGTCTTCACTCTCGAC 59.488 55.000 14.70 0.00 0.00 4.20
1820 1955 0.824595 TCCCCTTCACGACGTCTTCA 60.825 55.000 14.70 0.00 0.00 3.02
1945 2080 9.212593 TCCATGGCCGCACATATATATATATAT 57.787 33.333 16.45 16.45 36.61 0.86
1946 2081 8.602472 TCCATGGCCGCACATATATATATATA 57.398 34.615 13.72 13.60 0.00 0.86
1947 2082 7.494922 TCCATGGCCGCACATATATATATAT 57.505 36.000 6.96 9.12 0.00 0.86
1948 2083 6.574269 GCTCCATGGCCGCACATATATATATA 60.574 42.308 17.69 4.92 0.00 0.86
1949 2084 5.798132 CTCCATGGCCGCACATATATATAT 58.202 41.667 6.96 0.00 0.00 0.86
1950 2085 4.503123 GCTCCATGGCCGCACATATATATA 60.503 45.833 17.69 0.00 0.00 0.86
1951 2086 3.745480 GCTCCATGGCCGCACATATATAT 60.745 47.826 17.69 0.00 0.00 0.86
1966 2101 7.683437 ATATCTGACAAATATGTGCTCCATG 57.317 36.000 0.00 0.00 40.74 3.66
1993 2128 7.800155 TTCTGATGTGATTAACAGACAAACA 57.200 32.000 0.00 0.00 43.64 2.83
1996 2131 9.554395 TTAGTTTCTGATGTGATTAACAGACAA 57.446 29.630 0.00 0.00 43.64 3.18
1997 2132 9.725019 ATTAGTTTCTGATGTGATTAACAGACA 57.275 29.630 0.00 0.00 43.64 3.41
2008 2143 4.668576 ACGTGCATTAGTTTCTGATGTG 57.331 40.909 0.00 0.00 31.37 3.21
2009 2144 5.689383 AAACGTGCATTAGTTTCTGATGT 57.311 34.783 10.71 0.00 35.92 3.06
2019 2154 8.888332 TGTTATGTATTTGAAACGTGCATTAG 57.112 30.769 0.00 0.00 0.00 1.73
2045 2183 4.036616 GCACCAACATTTTGCTGGAATTTT 59.963 37.500 4.05 0.00 35.69 1.82
2050 2188 0.392336 GGCACCAACATTTTGCTGGA 59.608 50.000 4.05 0.00 35.69 3.86
2082 2220 1.971481 TGTGCATGACTTCAAGTGCT 58.029 45.000 0.00 0.00 38.37 4.40
2217 2355 8.318412 TCCTGAATTACTTGAGCTGTTATGTAA 58.682 33.333 0.00 0.00 0.00 2.41
2224 2362 8.049117 TCATAAATCCTGAATTACTTGAGCTGT 58.951 33.333 0.00 0.00 0.00 4.40
2241 2379 7.214467 TCACAAGTCAAAACCTCATAAATCC 57.786 36.000 0.00 0.00 0.00 3.01
2330 2468 1.076923 AGTACGATCCTCCCTGCGT 60.077 57.895 0.00 0.00 40.42 5.24
2343 2481 1.025812 ATCGGGCTTCTGAGAGTACG 58.974 55.000 0.00 0.00 0.00 3.67
2441 2579 2.905075 ACTGCATTATTACTGCTCGCA 58.095 42.857 7.43 0.00 40.34 5.10
2632 2770 4.437524 CGAACGAGCTAGAAGAATCACTCA 60.438 45.833 0.00 0.00 0.00 3.41
2636 2774 4.156190 AGTTCGAACGAGCTAGAAGAATCA 59.844 41.667 21.87 0.00 33.97 2.57
2708 2846 5.796424 AAAAGCAAACAACCTGATCATCT 57.204 34.783 0.00 0.00 0.00 2.90
2737 2875 5.954296 TTATCCATGCGTAGTAGGAGTAC 57.046 43.478 0.00 0.00 32.91 2.73
2738 2876 7.231925 TGAATTTATCCATGCGTAGTAGGAGTA 59.768 37.037 0.00 0.00 32.91 2.59
2739 2877 6.041637 TGAATTTATCCATGCGTAGTAGGAGT 59.958 38.462 0.00 0.00 32.91 3.85
2741 2879 6.413783 TGAATTTATCCATGCGTAGTAGGA 57.586 37.500 0.00 0.00 34.12 2.94
2742 2880 5.639506 CCTGAATTTATCCATGCGTAGTAGG 59.360 44.000 0.00 0.00 0.00 3.18
2743 2881 6.146184 CACCTGAATTTATCCATGCGTAGTAG 59.854 42.308 0.00 0.00 0.00 2.57
2744 2882 5.989168 CACCTGAATTTATCCATGCGTAGTA 59.011 40.000 0.00 0.00 0.00 1.82
2747 2885 3.563808 GCACCTGAATTTATCCATGCGTA 59.436 43.478 0.00 0.00 0.00 4.42
2748 2886 2.358898 GCACCTGAATTTATCCATGCGT 59.641 45.455 0.00 0.00 0.00 5.24
2749 2887 2.358582 TGCACCTGAATTTATCCATGCG 59.641 45.455 0.00 0.00 33.90 4.73
2757 2910 7.550551 TGTCAAAAACAAATGCACCTGAATTTA 59.449 29.630 3.94 0.00 31.67 1.40
2759 2912 5.879223 TGTCAAAAACAAATGCACCTGAATT 59.121 32.000 3.94 0.00 34.03 2.17
2809 2962 3.492337 TCGGTTTTCTTGGCCTGTAATT 58.508 40.909 3.32 0.00 0.00 1.40
2832 2985 2.553904 CCTCCTTCTGCTTGGACACATT 60.554 50.000 0.00 0.00 0.00 2.71
2838 2991 1.661463 ATGTCCTCCTTCTGCTTGGA 58.339 50.000 0.00 0.00 0.00 3.53
2845 2998 2.122768 CCTTGGCTATGTCCTCCTTCT 58.877 52.381 0.00 0.00 0.00 2.85
2925 3078 2.125106 GAGCTTCCGGATGGCGTT 60.125 61.111 18.22 5.58 34.14 4.84
2948 3101 2.383527 CGCCTTCGCTTCACTCACC 61.384 63.158 0.00 0.00 0.00 4.02
2950 3103 2.048222 CCGCCTTCGCTTCACTCA 60.048 61.111 0.00 0.00 0.00 3.41
2951 3104 1.374252 TTCCGCCTTCGCTTCACTC 60.374 57.895 0.00 0.00 0.00 3.51
2952 3105 1.668151 GTTCCGCCTTCGCTTCACT 60.668 57.895 0.00 0.00 0.00 3.41
2960 3113 1.743252 CTGCTCCAGTTCCGCCTTC 60.743 63.158 0.00 0.00 0.00 3.46
2966 3119 1.446966 GACTCGCTGCTCCAGTTCC 60.447 63.158 0.00 0.00 33.43 3.62
3125 3278 3.291101 GACCTTGGTGGCGTCGCTA 62.291 63.158 18.11 8.52 40.22 4.26
3242 3396 2.105766 ACTACACGAGGGGGTACAATC 58.894 52.381 0.00 0.00 0.00 2.67
3296 3450 3.555586 CCTTCAGCATTTTTGACCCTTGG 60.556 47.826 0.00 0.00 0.00 3.61
3318 3499 5.355350 ACCATTAAACATCTAGCTGTTCAGC 59.645 40.000 12.12 15.88 38.38 4.26
3319 3500 6.676456 GCACCATTAAACATCTAGCTGTTCAG 60.676 42.308 12.12 3.67 38.38 3.02
3320 3501 5.123820 GCACCATTAAACATCTAGCTGTTCA 59.876 40.000 12.12 3.53 38.38 3.18
3321 3502 5.123820 TGCACCATTAAACATCTAGCTGTTC 59.876 40.000 12.12 0.00 38.38 3.18
3323 3504 4.588899 TGCACCATTAAACATCTAGCTGT 58.411 39.130 0.00 0.00 0.00 4.40
3324 3505 4.036027 CCTGCACCATTAAACATCTAGCTG 59.964 45.833 0.00 0.00 0.00 4.24
3325 3506 4.202441 CCTGCACCATTAAACATCTAGCT 58.798 43.478 0.00 0.00 0.00 3.32
3327 3508 5.415701 ACAACCTGCACCATTAAACATCTAG 59.584 40.000 0.00 0.00 0.00 2.43
3328 3509 5.321102 ACAACCTGCACCATTAAACATCTA 58.679 37.500 0.00 0.00 0.00 1.98
3329 3510 4.151883 ACAACCTGCACCATTAAACATCT 58.848 39.130 0.00 0.00 0.00 2.90
3330 3511 4.519540 ACAACCTGCACCATTAAACATC 57.480 40.909 0.00 0.00 0.00 3.06
3331 3512 4.100808 ACAACAACCTGCACCATTAAACAT 59.899 37.500 0.00 0.00 0.00 2.71
3332 3513 3.449018 ACAACAACCTGCACCATTAAACA 59.551 39.130 0.00 0.00 0.00 2.83
3333 3514 4.053469 ACAACAACCTGCACCATTAAAC 57.947 40.909 0.00 0.00 0.00 2.01
3334 3515 4.081420 ACAACAACAACCTGCACCATTAAA 60.081 37.500 0.00 0.00 0.00 1.52
3338 3519 1.484038 ACAACAACAACCTGCACCAT 58.516 45.000 0.00 0.00 0.00 3.55
3351 3532 2.158827 TGCCTCACTCTGCTTACAACAA 60.159 45.455 0.00 0.00 0.00 2.83
3412 3593 1.376424 CTCCAACACCAGCGCTGAT 60.376 57.895 38.06 21.54 0.00 2.90
3415 3596 1.598130 GAACTCCAACACCAGCGCT 60.598 57.895 2.64 2.64 0.00 5.92
3418 3599 1.610886 GGTAGGAACTCCAACACCAGC 60.611 57.143 0.00 0.00 41.75 4.85
3421 3602 0.971386 TCGGTAGGAACTCCAACACC 59.029 55.000 0.00 1.85 41.75 4.16
3594 3775 1.215647 GCGTCGAGGAGGATGTTGT 59.784 57.895 9.75 0.00 0.00 3.32
3649 3830 3.458163 GTCATGGTCGGGAGGCGA 61.458 66.667 0.00 0.00 33.19 5.54
3700 3881 1.381872 CTCCCCGGTGATCAGGAGT 60.382 63.158 16.91 0.00 40.91 3.85
4011 4192 0.319040 GCTCTCACGCACAAGAGACA 60.319 55.000 9.70 0.00 41.28 3.41
4071 4270 9.566432 TTAAAATTGGGCAACTCAACAATTATT 57.434 25.926 0.00 0.00 41.24 1.40
4072 4271 9.566432 TTTAAAATTGGGCAACTCAACAATTAT 57.434 25.926 0.00 0.00 41.24 1.28
4073 4272 8.964476 TTTAAAATTGGGCAACTCAACAATTA 57.036 26.923 0.00 0.00 41.24 1.40
4074 4273 7.772757 TCTTTAAAATTGGGCAACTCAACAATT 59.227 29.630 0.00 0.00 43.20 2.32
4132 4332 5.049818 CACAAAAGCAAACTTGAAACCACAA 60.050 36.000 0.00 0.00 35.85 3.33
4150 4350 1.407258 GCCACTACACCAAGCACAAAA 59.593 47.619 0.00 0.00 0.00 2.44
4192 4392 7.959689 TTGGTCATATTCAAACAAACATTGG 57.040 32.000 0.00 0.00 34.12 3.16
4240 4440 9.644993 CATATGCAGCACAAATTATTCAAATTG 57.355 29.630 0.00 0.00 31.92 2.32
4329 4712 4.007644 TCTGCAGCCGTGTGAGGG 62.008 66.667 9.47 0.00 0.00 4.30
4341 4724 1.888018 GTAGGTGTAGCCGTCTGCA 59.112 57.895 0.00 0.00 44.83 4.41
4467 4850 5.315348 TGCTGCATATAATTCTGTATGGCA 58.685 37.500 0.00 0.00 29.64 4.92
4512 4895 0.966920 AAGTTGACCGGACTGATCGT 59.033 50.000 9.46 0.00 0.00 3.73
4518 4901 0.396435 TGCATCAAGTTGACCGGACT 59.604 50.000 9.46 0.00 0.00 3.85
4608 4991 5.512298 ACCCAAAAACAACAAGGTAGTACT 58.488 37.500 0.00 0.00 0.00 2.73
4612 4995 7.493367 TCATAAACCCAAAAACAACAAGGTAG 58.507 34.615 0.00 0.00 0.00 3.18
4616 4999 7.676104 GCAACTCATAAACCCAAAAACAACAAG 60.676 37.037 0.00 0.00 0.00 3.16
4634 5017 6.818644 ACAGTAGATCGTATTTTGCAACTCAT 59.181 34.615 0.00 0.00 0.00 2.90
4648 5031 5.262588 TGAATACATGCACAGTAGATCGT 57.737 39.130 6.93 0.00 0.00 3.73
4805 5189 6.483640 GCCTGTAATACTCCATACTTTTCCTG 59.516 42.308 0.00 0.00 0.00 3.86
4807 5191 6.592870 AGCCTGTAATACTCCATACTTTTCC 58.407 40.000 0.00 0.00 0.00 3.13
4812 5196 5.394738 TGCTAGCCTGTAATACTCCATACT 58.605 41.667 13.29 0.00 0.00 2.12
4815 5199 4.408921 TGTTGCTAGCCTGTAATACTCCAT 59.591 41.667 13.29 0.00 0.00 3.41
4822 5206 3.981071 TCTGTGTTGCTAGCCTGTAAT 57.019 42.857 13.29 0.00 0.00 1.89
4827 5211 2.816087 CACAAATCTGTGTTGCTAGCCT 59.184 45.455 13.29 0.00 46.68 4.58
4853 5237 2.677875 CTTGAACCTGGGCTGGCC 60.678 66.667 14.23 14.23 0.00 5.36
4945 5332 2.063266 GTCTCCATTGCAACGTACGAA 58.937 47.619 24.41 5.86 0.00 3.85
5012 5399 8.404000 ACGTCGAATCTCTACAAATACTGTATT 58.596 33.333 7.22 7.22 39.82 1.89
5058 5446 7.591057 CACACATAAATATTCAGGCCATTAACG 59.409 37.037 5.01 0.00 0.00 3.18
5195 5607 5.501156 AGTGATGTCTTTATGGGAAGGAAC 58.499 41.667 0.00 0.00 0.00 3.62
5215 5627 7.386299 GCCACTCAATCTTTGGTATATCTAGTG 59.614 40.741 0.00 0.00 32.50 2.74
5220 5632 4.452455 CGGCCACTCAATCTTTGGTATATC 59.548 45.833 2.24 0.00 32.50 1.63
5233 5645 0.179004 AACCAATCACGGCCACTCAA 60.179 50.000 2.24 0.00 0.00 3.02
5234 5646 0.605319 GAACCAATCACGGCCACTCA 60.605 55.000 2.24 0.00 0.00 3.41
5235 5647 1.305930 GGAACCAATCACGGCCACTC 61.306 60.000 2.24 0.00 0.00 3.51
5236 5648 1.303317 GGAACCAATCACGGCCACT 60.303 57.895 2.24 0.00 0.00 4.00
5237 5649 0.893727 AAGGAACCAATCACGGCCAC 60.894 55.000 2.24 0.00 0.00 5.01
5238 5650 0.608035 GAAGGAACCAATCACGGCCA 60.608 55.000 2.24 0.00 0.00 5.36
5239 5651 1.313091 GGAAGGAACCAATCACGGCC 61.313 60.000 0.00 0.00 0.00 6.13
5240 5652 1.313091 GGGAAGGAACCAATCACGGC 61.313 60.000 0.00 0.00 0.00 5.68
5241 5653 0.037590 TGGGAAGGAACCAATCACGG 59.962 55.000 0.00 0.00 34.44 4.94
5242 5654 2.128771 ATGGGAAGGAACCAATCACG 57.871 50.000 0.00 0.00 42.17 4.35
5243 5655 5.125578 GTCTTTATGGGAAGGAACCAATCAC 59.874 44.000 0.00 0.00 42.17 3.06
5244 5656 5.222233 TGTCTTTATGGGAAGGAACCAATCA 60.222 40.000 0.00 0.00 42.17 2.57
5245 5657 5.261216 TGTCTTTATGGGAAGGAACCAATC 58.739 41.667 0.00 0.00 42.17 2.67
5246 5658 5.269554 TGTCTTTATGGGAAGGAACCAAT 57.730 39.130 0.00 0.00 42.17 3.16
5247 5659 4.733077 TGTCTTTATGGGAAGGAACCAA 57.267 40.909 0.00 0.00 42.17 3.67
5248 5660 4.290985 TGATGTCTTTATGGGAAGGAACCA 59.709 41.667 0.00 0.00 43.22 3.67
5249 5661 4.640647 GTGATGTCTTTATGGGAAGGAACC 59.359 45.833 0.00 0.00 0.00 3.62
5250 5662 5.501156 AGTGATGTCTTTATGGGAAGGAAC 58.499 41.667 0.00 0.00 0.00 3.62
5251 5663 5.779241 AGTGATGTCTTTATGGGAAGGAA 57.221 39.130 0.00 0.00 0.00 3.36
5252 5664 6.202331 TCTAGTGATGTCTTTATGGGAAGGA 58.798 40.000 0.00 0.00 0.00 3.36
5253 5665 6.485830 TCTAGTGATGTCTTTATGGGAAGG 57.514 41.667 0.00 0.00 0.00 3.46
5256 5668 9.256228 GGTATATCTAGTGATGTCTTTATGGGA 57.744 37.037 0.00 0.00 34.32 4.37
5257 5669 9.035890 TGGTATATCTAGTGATGTCTTTATGGG 57.964 37.037 0.00 0.00 34.32 4.00
5277 5689 9.004717 TGTCGAAACAAATCAATCTTTGGTATA 57.995 29.630 0.00 0.00 39.83 1.47
5278 5690 7.881142 TGTCGAAACAAATCAATCTTTGGTAT 58.119 30.769 0.00 0.00 39.83 2.73
5279 5691 7.227711 TCTGTCGAAACAAATCAATCTTTGGTA 59.772 33.333 0.00 0.00 39.83 3.25
5280 5692 6.039270 TCTGTCGAAACAAATCAATCTTTGGT 59.961 34.615 0.00 0.00 39.83 3.67
5281 5693 6.437928 TCTGTCGAAACAAATCAATCTTTGG 58.562 36.000 0.00 0.00 39.83 3.28
5282 5694 9.611284 TTATCTGTCGAAACAAATCAATCTTTG 57.389 29.630 0.00 0.00 41.02 2.77
5285 5697 9.612620 GTTTTATCTGTCGAAACAAATCAATCT 57.387 29.630 0.00 0.00 34.24 2.40
5286 5698 8.850452 GGTTTTATCTGTCGAAACAAATCAATC 58.150 33.333 0.00 0.00 35.53 2.67
5287 5699 8.356657 TGGTTTTATCTGTCGAAACAAATCAAT 58.643 29.630 0.00 0.00 35.53 2.57
5328 5740 7.994334 TGTACTATTAAATCGCTTTTACCCCAT 59.006 33.333 0.00 0.00 29.47 4.00
5353 5766 3.190535 CACCGACTTTTACCCCTTCAATG 59.809 47.826 0.00 0.00 0.00 2.82
5369 5783 0.389757 GCCTATCCTCTTCCACCGAC 59.610 60.000 0.00 0.00 0.00 4.79
5509 5923 2.586648 AAGGGTAACTTGAAGGCCTG 57.413 50.000 5.69 0.00 38.21 4.85
5510 5924 4.734843 TTTAAGGGTAACTTGAAGGCCT 57.265 40.909 0.00 0.00 40.37 5.19


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

AutoCloner maintained by Alex Coulton.