Multiple sequence alignment - TraesCS6A01G394900

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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 TraesCS6A01G394900 chr6A 100.000 5555 0 0 1 5555 608095090 608089536 0.000000e+00 10259
1 TraesCS6A01G394900 chr6A 89.143 175 17 2 2656 2828 608091777 608091603 3.370000e-52 217
2 TraesCS6A01G394900 chr6A 89.143 175 17 2 3314 3488 608092435 608092263 3.370000e-52 217
3 TraesCS6A01G394900 chr6B 90.619 4328 232 77 610 4840 703169832 703165582 0.000000e+00 5583
4 TraesCS6A01G394900 chr6B 87.204 719 52 21 4858 5555 703165597 703164898 0.000000e+00 782
5 TraesCS6A01G394900 chr6B 78.558 541 37 34 64 557 703170347 703169839 3.280000e-72 283
6 TraesCS6A01G394900 chr6B 88.571 175 18 2 3314 3488 703167767 703167595 1.570000e-50 211
7 TraesCS6A01G394900 chr6B 83.710 221 29 5 3763 3976 703167401 703167181 9.440000e-48 202
8 TraesCS6A01G394900 chr6B 87.429 175 20 2 2656 2828 703167125 703166951 3.390000e-47 200
9 TraesCS6A01G394900 chr6D 91.829 3647 210 30 1537 5135 461418512 461414906 0.000000e+00 5003
10 TraesCS6A01G394900 chr6D 94.231 468 15 9 974 1435 461419082 461418621 0.000000e+00 704
11 TraesCS6A01G394900 chr6D 88.742 302 21 8 5262 5555 461414704 461414408 1.900000e-94 357
12 TraesCS6A01G394900 chr6D 90.341 176 14 3 3314 3488 461417397 461417224 1.560000e-55 228
13 TraesCS6A01G394900 chr6D 85.714 217 22 4 2615 2828 461416742 461416532 2.610000e-53 220
14 TraesCS6A01G394900 chr6D 76.944 373 40 26 38 389 461419983 461419636 2.660000e-38 171
15 TraesCS6A01G394900 chr2A 87.615 218 19 4 1129 1340 745655782 745655997 4.300000e-61 246
16 TraesCS6A01G394900 chr2B 86.697 218 21 4 1129 1340 750002129 750002344 9.300000e-58 235
17 TraesCS6A01G394900 chr2D 78.286 350 76 0 4032 4381 615592761 615593110 5.600000e-55 226


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 TraesCS6A01G394900 chr6A 608089536 608095090 5554 True 3564.333333 10259 92.762000 1 5555 3 chr6A.!!$R1 5554
1 TraesCS6A01G394900 chr6B 703164898 703170347 5449 True 1210.166667 5583 86.015167 64 5555 6 chr6B.!!$R1 5491
2 TraesCS6A01G394900 chr6D 461414408 461419983 5575 True 1113.833333 5003 87.966833 38 5555 6 chr6D.!!$R1 5517

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
600 681 0.035630 ATGGCAGTGCAGACTCCTTC 60.036 55.000 18.61 0.0 0.00 3.46 F
602 683 0.036022 GGCAGTGCAGACTCCTTCTT 59.964 55.000 18.61 0.0 28.96 2.52 F
982 1097 0.323302 TGACTAACTGCCGCATTCCA 59.677 50.000 0.00 0.0 0.00 3.53 F
1635 1827 0.548510 AGTAGGCCCTGATTGCTTCC 59.451 55.000 0.00 0.0 0.00 3.46 F
1817 2017 1.503542 GAGCAAACCACGGAGCATG 59.496 57.895 0.00 0.0 0.00 4.06 F
1951 2151 1.755783 CAGGGGCAGAAGGAATGGC 60.756 63.158 0.00 0.0 42.19 4.40 F
3823 4061 2.105477 ACATGGATCCCACTATGTGAGC 59.895 50.000 13.23 0.0 39.71 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 2627 1.032114 GTGGTCCATGCCTAGCCAAC 61.032 60.000 0.00 0.00 0.00 3.77 R
2591 2791 2.991250 ACATCTTGGCACCATGAGTAC 58.009 47.619 10.99 0.00 34.39 2.73 R
2843 3044 1.224965 GAAGCTGCTATGGCTGTAGC 58.775 55.000 0.90 13.28 45.71 3.58 R
2844 3045 2.102084 TCTGAAGCTGCTATGGCTGTAG 59.898 50.000 0.90 0.00 40.19 2.74 R
3669 3907 0.895100 TTCTGGCGCAGGAAAGCATT 60.895 50.000 10.83 0.00 34.54 3.56 R
3840 4078 0.179084 GCTCCAGGTAGCAATGCGTA 60.179 55.000 0.00 0.00 42.30 4.42 R
5281 5668 0.609131 CCGGCACCAGGAACTCATTT 60.609 55.000 0.00 0.00 34.60 2.32 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
17 18 2.360980 CCTCCTCGTCCCTCACCT 59.639 66.667 0.00 0.00 0.00 4.00
18 19 1.755008 CCTCCTCGTCCCTCACCTC 60.755 68.421 0.00 0.00 0.00 3.85
19 20 1.000771 CTCCTCGTCCCTCACCTCA 60.001 63.158 0.00 0.00 0.00 3.86
20 21 1.304217 TCCTCGTCCCTCACCTCAC 60.304 63.158 0.00 0.00 0.00 3.51
21 22 1.304547 CCTCGTCCCTCACCTCACT 60.305 63.158 0.00 0.00 0.00 3.41
22 23 1.316706 CCTCGTCCCTCACCTCACTC 61.317 65.000 0.00 0.00 0.00 3.51
23 24 1.649390 CTCGTCCCTCACCTCACTCG 61.649 65.000 0.00 0.00 0.00 4.18
24 25 2.701780 CGTCCCTCACCTCACTCGG 61.702 68.421 0.00 0.00 0.00 4.63
25 26 1.606889 GTCCCTCACCTCACTCGGT 60.607 63.158 0.00 0.00 37.93 4.69
41 42 4.664677 GTGAGCGACACCAGCCGT 62.665 66.667 5.93 0.00 43.05 5.68
42 43 4.357947 TGAGCGACACCAGCCGTC 62.358 66.667 0.00 0.00 34.64 4.79
46 47 3.991051 CGACACCAGCCGTCCTGT 61.991 66.667 0.50 0.00 40.06 4.00
47 48 2.048127 GACACCAGCCGTCCTGTC 60.048 66.667 0.50 0.00 40.06 3.51
48 49 3.591254 GACACCAGCCGTCCTGTCC 62.591 68.421 0.50 0.00 40.06 4.02
49 50 3.625897 CACCAGCCGTCCTGTCCA 61.626 66.667 0.50 0.00 40.06 4.02
50 51 3.314331 ACCAGCCGTCCTGTCCAG 61.314 66.667 0.50 0.00 40.06 3.86
100 101 4.249513 GGCTGCTCCCTTCCATTC 57.750 61.111 0.00 0.00 0.00 2.67
101 102 1.454663 GGCTGCTCCCTTCCATTCC 60.455 63.158 0.00 0.00 0.00 3.01
102 103 1.454663 GCTGCTCCCTTCCATTCCC 60.455 63.158 0.00 0.00 0.00 3.97
262 286 1.427592 GAGGAATCGTGCTGCTGCTC 61.428 60.000 17.00 12.09 40.48 4.26
270 294 3.793144 GCTGCTGCTCGGGTTTCG 61.793 66.667 8.53 0.00 40.90 3.46
326 378 1.880340 CGCCGCAACTCATCCTCTC 60.880 63.158 0.00 0.00 0.00 3.20
372 434 0.549950 CTCTGCCATCCTTCCATGGT 59.450 55.000 12.58 0.00 44.84 3.55
403 465 4.367023 CGGTTCGGTTCGGCAGGA 62.367 66.667 0.00 0.00 0.00 3.86
405 467 2.654877 GTTCGGTTCGGCAGGAGA 59.345 61.111 0.00 0.00 0.00 3.71
413 476 2.872858 GGTTCGGCAGGAGATTGATTAC 59.127 50.000 0.00 0.00 0.00 1.89
426 492 4.283212 AGATTGATTACCTAGCAGAGAGGC 59.717 45.833 0.00 0.00 37.63 4.70
450 523 1.165907 TCAATTGGATCATCGCGGCC 61.166 55.000 6.13 0.00 0.00 6.13
471 544 2.016393 CTCGCCGGCCTACAGATTCA 62.016 60.000 23.46 0.00 0.00 2.57
486 559 0.447801 ATTCAATTCTCACGCGTGCC 59.552 50.000 33.63 0.00 0.00 5.01
487 560 1.896339 TTCAATTCTCACGCGTGCCG 61.896 55.000 33.63 25.08 44.21 5.69
505 578 2.173382 CCTGCGCGTGTGTTTAGC 59.827 61.111 8.43 0.00 0.00 3.09
506 579 2.317609 CCTGCGCGTGTGTTTAGCT 61.318 57.895 8.43 0.00 0.00 3.32
509 582 0.509499 TGCGCGTGTGTTTAGCTTAC 59.491 50.000 8.43 0.00 0.00 2.34
536 613 4.561735 TTCGGTGTGAAATCAAGGTTTC 57.438 40.909 0.00 0.00 38.32 2.78
554 631 5.409211 GGTTTCACCTTCTAGTACTAGCAC 58.591 45.833 22.87 9.72 34.73 4.40
557 634 7.415429 GGTTTCACCTTCTAGTACTAGCACTAG 60.415 44.444 22.87 20.20 41.10 2.57
558 635 6.310764 TCACCTTCTAGTACTAGCACTAGT 57.689 41.667 23.63 14.40 45.50 2.57
560 637 7.855375 TCACCTTCTAGTACTAGCACTAGTAA 58.145 38.462 23.63 16.83 46.55 2.24
564 641 8.995220 CCTTCTAGTACTAGCACTAGTAAGATG 58.005 40.741 25.33 16.69 46.55 2.90
575 652 2.231215 AGTAAGATGGCGTGATGAGC 57.769 50.000 0.00 0.00 0.00 4.26
576 653 1.759445 AGTAAGATGGCGTGATGAGCT 59.241 47.619 0.00 0.00 34.52 4.09
579 656 1.953138 GATGGCGTGATGAGCTCGG 60.953 63.158 9.64 0.00 34.29 4.63
580 657 3.451556 ATGGCGTGATGAGCTCGGG 62.452 63.158 9.64 0.00 34.29 5.14
581 658 3.838271 GGCGTGATGAGCTCGGGA 61.838 66.667 9.64 0.00 34.29 5.14
585 662 1.596477 GTGATGAGCTCGGGATGGC 60.596 63.158 9.64 0.00 0.00 4.40
586 663 2.065789 TGATGAGCTCGGGATGGCA 61.066 57.895 9.64 0.00 0.00 4.92
587 664 1.301558 GATGAGCTCGGGATGGCAG 60.302 63.158 9.64 0.00 0.00 4.85
588 665 2.037620 GATGAGCTCGGGATGGCAGT 62.038 60.000 9.64 0.00 0.00 4.40
589 666 2.202987 GAGCTCGGGATGGCAGTG 60.203 66.667 0.00 0.00 0.00 3.66
594 675 2.821366 CGGGATGGCAGTGCAGAC 60.821 66.667 18.61 6.78 0.00 3.51
596 677 1.451028 GGGATGGCAGTGCAGACTC 60.451 63.158 18.61 7.14 0.00 3.36
600 681 0.035630 ATGGCAGTGCAGACTCCTTC 60.036 55.000 18.61 0.00 0.00 3.46
602 683 0.036022 GGCAGTGCAGACTCCTTCTT 59.964 55.000 18.61 0.00 28.96 2.52
628 709 5.787953 TGCCAAGAATTCAGATTTGTTCA 57.212 34.783 8.44 1.68 0.00 3.18
634 715 7.535258 CCAAGAATTCAGATTTGTTCAACTACG 59.465 37.037 8.44 0.00 0.00 3.51
639 720 7.633361 TTCAGATTTGTTCAACTACGACTAC 57.367 36.000 0.00 0.00 0.00 2.73
659 740 3.079578 ACTTGTCATTCATCTGTGCCAG 58.920 45.455 0.00 0.00 0.00 4.85
666 747 2.936919 TCATCTGTGCCAGTTCTTGT 57.063 45.000 2.68 0.00 32.61 3.16
669 750 4.256110 TCATCTGTGCCAGTTCTTGTATG 58.744 43.478 2.68 0.00 32.61 2.39
670 751 2.426522 TCTGTGCCAGTTCTTGTATGC 58.573 47.619 2.68 0.00 32.61 3.14
671 752 2.038952 TCTGTGCCAGTTCTTGTATGCT 59.961 45.455 2.68 0.00 32.61 3.79
672 753 2.417933 CTGTGCCAGTTCTTGTATGCTC 59.582 50.000 0.00 0.00 0.00 4.26
673 754 1.740025 GTGCCAGTTCTTGTATGCTCC 59.260 52.381 0.00 0.00 0.00 4.70
674 755 1.340017 TGCCAGTTCTTGTATGCTCCC 60.340 52.381 0.00 0.00 0.00 4.30
675 756 1.656652 CCAGTTCTTGTATGCTCCCG 58.343 55.000 0.00 0.00 0.00 5.14
676 757 1.009829 CAGTTCTTGTATGCTCCCGC 58.990 55.000 0.00 0.00 0.00 6.13
710 791 4.041049 CGTTTGCTGAATTTACACAAGCA 58.959 39.130 0.00 0.00 0.00 3.91
711 792 4.502282 CGTTTGCTGAATTTACACAAGCAA 59.498 37.500 4.39 4.39 38.73 3.91
712 793 5.331756 CGTTTGCTGAATTTACACAAGCAAG 60.332 40.000 8.24 0.00 40.96 4.01
713 794 3.641648 TGCTGAATTTACACAAGCAAGC 58.358 40.909 0.00 0.00 0.00 4.01
722 803 2.256591 ACAAGCAAGCCACGCTGAG 61.257 57.895 0.00 0.00 39.62 3.35
776 857 6.040166 TCCGTGTATCCTTACTGAATCCTTAC 59.960 42.308 0.00 0.00 0.00 2.34
787 868 5.738909 ACTGAATCCTTACACTGAATCTGG 58.261 41.667 0.00 0.00 0.00 3.86
837 923 7.014038 AGAGCATTTTTCAGTTCAGAATTCTGT 59.986 33.333 29.80 12.55 44.12 3.41
843 929 5.011090 TCAGTTCAGAATTCTGTATCCCG 57.989 43.478 29.80 16.84 44.12 5.14
853 939 0.811616 CTGTATCCCGTCTTGCCTGC 60.812 60.000 0.00 0.00 0.00 4.85
854 940 1.523938 GTATCCCGTCTTGCCTGCC 60.524 63.158 0.00 0.00 0.00 4.85
855 941 1.689233 TATCCCGTCTTGCCTGCCT 60.689 57.895 0.00 0.00 0.00 4.75
856 942 1.971505 TATCCCGTCTTGCCTGCCTG 61.972 60.000 0.00 0.00 0.00 4.85
860 946 2.031516 CGTCTTGCCTGCCTGACAG 61.032 63.158 0.00 0.00 46.77 3.51
873 959 2.035066 GCCTGACAGAACAACATGCTTT 59.965 45.455 3.32 0.00 0.00 3.51
876 962 2.290367 TGACAGAACAACATGCTTTCCG 59.710 45.455 0.00 0.00 0.00 4.30
881 967 4.618489 CAGAACAACATGCTTTCCGAAATC 59.382 41.667 0.00 0.00 0.00 2.17
882 968 4.520492 AGAACAACATGCTTTCCGAAATCT 59.480 37.500 0.00 0.00 0.00 2.40
886 972 5.473504 ACAACATGCTTTCCGAAATCTTACT 59.526 36.000 0.00 0.00 0.00 2.24
887 973 5.803020 ACATGCTTTCCGAAATCTTACTC 57.197 39.130 0.00 0.00 0.00 2.59
888 974 5.245531 ACATGCTTTCCGAAATCTTACTCA 58.754 37.500 0.00 0.00 0.00 3.41
889 975 5.882557 ACATGCTTTCCGAAATCTTACTCAT 59.117 36.000 0.00 0.00 0.00 2.90
947 1049 3.004629 TCGTCATGTTTCAAGCAAAGCAT 59.995 39.130 0.00 0.00 0.00 3.79
951 1053 5.234757 GTCATGTTTCAAGCAAAGCATCAAA 59.765 36.000 0.00 0.00 0.00 2.69
952 1054 5.992829 TCATGTTTCAAGCAAAGCATCAAAT 59.007 32.000 0.00 0.00 0.00 2.32
953 1055 5.660629 TGTTTCAAGCAAAGCATCAAATG 57.339 34.783 0.00 0.00 0.00 2.32
968 1083 5.439721 CATCAAATGATGTTCCCCTGACTA 58.560 41.667 13.95 0.00 45.10 2.59
973 1088 2.027192 TGATGTTCCCCTGACTAACTGC 60.027 50.000 0.00 0.00 0.00 4.40
975 1090 0.391263 GTTCCCCTGACTAACTGCCG 60.391 60.000 0.00 0.00 0.00 5.69
976 1091 2.125106 CCCCTGACTAACTGCCGC 60.125 66.667 0.00 0.00 0.00 6.53
978 1093 1.221840 CCCTGACTAACTGCCGCAT 59.778 57.895 0.00 0.00 0.00 4.73
982 1097 0.323302 TGACTAACTGCCGCATTCCA 59.677 50.000 0.00 0.00 0.00 3.53
983 1098 1.065491 TGACTAACTGCCGCATTCCAT 60.065 47.619 0.00 0.00 0.00 3.41
984 1099 1.599542 GACTAACTGCCGCATTCCATC 59.400 52.381 0.00 0.00 0.00 3.51
985 1100 1.065491 ACTAACTGCCGCATTCCATCA 60.065 47.619 0.00 0.00 0.00 3.07
1052 1190 3.045142 GTCAAGGGACGACGACCA 58.955 61.111 17.82 0.00 33.68 4.02
1164 1305 2.069273 GACCTCAACTCCATCAACGTG 58.931 52.381 0.00 0.00 0.00 4.49
1384 1528 1.153745 GAGATCGCCGTCAAGCAGT 60.154 57.895 0.00 0.00 0.00 4.40
1421 1565 1.345741 CCAGGCAAGTTCTCTCTCACA 59.654 52.381 0.00 0.00 0.00 3.58
1432 1576 4.374689 TCTCTCTCACAGTCCTGTACTT 57.625 45.455 0.00 0.00 42.83 2.24
1436 1580 3.157881 TCTCACAGTCCTGTACTTCCTG 58.842 50.000 0.00 0.00 42.83 3.86
1437 1581 3.157881 CTCACAGTCCTGTACTTCCTGA 58.842 50.000 0.00 0.00 42.83 3.86
1438 1582 2.891580 TCACAGTCCTGTACTTCCTGAC 59.108 50.000 0.00 0.00 42.83 3.51
1456 1627 4.820284 TGACAGTCAGATAGCAGATACG 57.180 45.455 0.00 0.00 0.00 3.06
1495 1684 6.152661 CCACTTTTATGCATTACCAAGAGGAA 59.847 38.462 3.54 0.00 38.69 3.36
1511 1703 9.566432 ACCAAGAGGAATTATAACTCATTCATC 57.434 33.333 0.00 0.44 39.45 2.92
1512 1704 8.715998 CCAAGAGGAATTATAACTCATTCATCG 58.284 37.037 0.00 0.00 42.42 3.84
1533 1725 9.853555 TCATCGCAACAAATATAATTTGAACTT 57.146 25.926 16.94 1.34 33.83 2.66
1627 1819 2.196742 ATCCATTCAGTAGGCCCTGA 57.803 50.000 7.56 7.56 39.65 3.86
1635 1827 0.548510 AGTAGGCCCTGATTGCTTCC 59.451 55.000 0.00 0.00 0.00 3.46
1739 1932 4.079096 AGCCTAGGGTATAGTGAGTCAACT 60.079 45.833 12.99 0.00 0.00 3.16
1747 1940 5.069251 GGTATAGTGAGTCAACTAGTGCCAT 59.931 44.000 0.00 0.00 36.14 4.40
1817 2017 1.503542 GAGCAAACCACGGAGCATG 59.496 57.895 0.00 0.00 0.00 4.06
1864 2064 4.096681 TGCTTGATGAGTCCCTCTTAAGA 58.903 43.478 4.81 4.81 0.00 2.10
1901 2101 2.938956 AGCTTGAGCCACTAGTTTGT 57.061 45.000 0.00 0.00 43.38 2.83
1951 2151 1.755783 CAGGGGCAGAAGGAATGGC 60.756 63.158 0.00 0.00 42.19 4.40
2142 2342 4.158949 TCATGGCCAATGAGATTGAAAGTG 59.841 41.667 10.96 0.00 40.50 3.16
2148 2348 4.096081 CCAATGAGATTGAAAGTGGCTCTC 59.904 45.833 0.00 0.00 42.83 3.20
2201 2401 5.032846 TGAGGAGATGGACTTTCAGGTAAT 58.967 41.667 0.00 0.00 0.00 1.89
2213 2413 8.303876 GGACTTTCAGGTAATTCATTTGCTTTA 58.696 33.333 0.00 0.00 0.00 1.85
2510 2710 9.978044 ATCTACGGACCTAGAATTATTTTACAC 57.022 33.333 0.00 0.00 0.00 2.90
2591 2791 8.455903 AATGTATGATGTTCTAAAGATGTGGG 57.544 34.615 0.00 0.00 0.00 4.61
2716 2916 5.297278 TGGTATAATTGTTTCGGTGTATGCC 59.703 40.000 0.00 0.00 0.00 4.40
2848 3049 6.114767 TGAATAAGCATCAATGACAGCTACA 58.885 36.000 11.59 7.92 36.07 2.74
2907 3122 7.708051 TCATATCTACAAGTGACAAGAGTAGC 58.292 38.462 0.00 0.00 33.86 3.58
2999 3229 6.626302 TGTGCTATTATTTTGTTAGTTGGGC 58.374 36.000 0.00 0.00 0.00 5.36
3088 3318 3.275617 TTTTATGACAGATGGGTCCCG 57.724 47.619 2.65 0.00 36.97 5.14
3162 3392 3.494045 CTAAAGTGCTTGCTTTAGCCC 57.506 47.619 16.75 0.00 45.87 5.19
3205 3435 9.838339 AAGATTCTCCATGTACTAGTTTTATGG 57.162 33.333 19.13 19.13 39.66 2.74
3242 3473 5.066764 TGTTGCCACTTTGTTTAGTTCCTAC 59.933 40.000 0.00 0.00 0.00 3.18
3370 3608 6.326375 TCAAATGGTATAATTGTTTCGGTGC 58.674 36.000 0.00 0.00 0.00 5.01
3508 3746 7.689446 TGAAGCGTTAGTCAGAGCTATATAT 57.311 36.000 0.00 0.00 39.25 0.86
3666 3904 6.481434 ACTACCATAACAACTAGGGTGATC 57.519 41.667 2.93 0.00 44.46 2.92
3669 3907 5.030147 ACCATAACAACTAGGGTGATCTGA 58.970 41.667 2.93 0.00 43.14 3.27
3770 4008 9.571810 TGCTTTCATTAGTAATACATTTTGCAG 57.428 29.630 0.00 0.00 0.00 4.41
3823 4061 2.105477 ACATGGATCCCACTATGTGAGC 59.895 50.000 13.23 0.00 39.71 4.26
3835 4073 4.450419 CACTATGTGAGCCTAAGCAATAGC 59.550 45.833 0.00 0.00 43.56 2.97
3836 4074 5.741383 CACTATGTGAGCCTAAGCAATAGCT 60.741 44.000 0.00 0.00 44.71 3.32
3849 4087 3.482786 GCAATAGCTACATACGCATTGC 58.517 45.455 9.98 9.98 40.69 3.56
3850 4088 3.187227 GCAATAGCTACATACGCATTGCT 59.813 43.478 15.87 0.00 42.16 3.91
3851 4089 4.388773 GCAATAGCTACATACGCATTGCTA 59.611 41.667 15.87 0.00 42.16 3.49
3852 4090 5.668866 GCAATAGCTACATACGCATTGCTAC 60.669 44.000 15.87 0.00 42.16 3.58
3853 4091 2.755650 AGCTACATACGCATTGCTACC 58.244 47.619 7.12 0.00 0.00 3.18
3857 4095 1.484653 ACATACGCATTGCTACCTGGA 59.515 47.619 7.12 0.00 0.00 3.86
3895 4133 5.126222 GCTTGCTTTAGCTCCCTTTAGAAAT 59.874 40.000 3.10 0.00 42.66 2.17
3899 4137 7.172342 TGCTTTAGCTCCCTTTAGAAATTGTA 58.828 34.615 3.10 0.00 42.66 2.41
3900 4138 7.336931 TGCTTTAGCTCCCTTTAGAAATTGTAG 59.663 37.037 3.10 0.00 42.66 2.74
3930 4168 5.932303 TCTCCATGTACTAGTTTTGTGAAGC 59.068 40.000 0.00 0.00 0.00 3.86
3936 4174 7.385778 TGTACTAGTTTTGTGAAGCTTGTTT 57.614 32.000 2.10 0.00 34.87 2.83
3941 4179 8.736244 ACTAGTTTTGTGAAGCTTGTTTTCTTA 58.264 29.630 2.10 0.00 30.57 2.10
3963 4203 7.500892 TCTTATTGCCAGTTTGTTTAGTTCAGA 59.499 33.333 0.00 0.00 0.00 3.27
3971 4211 7.273381 CCAGTTTGTTTAGTTCAGAACAACTTG 59.727 37.037 15.85 7.20 43.24 3.16
3982 4222 7.552687 AGTTCAGAACAACTTGAACTTGATACA 59.447 33.333 15.85 0.00 40.45 2.29
4146 4408 2.967615 GAGCTTATCACCGGCCGC 60.968 66.667 22.85 2.59 0.00 6.53
4219 4481 3.909430 GTGAAACCGTACATCTCTGACA 58.091 45.455 0.00 0.00 0.00 3.58
4330 4592 0.760945 CCTCCTCCGGCTATCCAAGT 60.761 60.000 0.00 0.00 0.00 3.16
4365 4627 2.609459 GAGCGAGGTGTATGAAATGGTG 59.391 50.000 0.00 0.00 0.00 4.17
4383 4645 0.881796 TGCAGAAGATCGTCGACAGT 59.118 50.000 17.16 2.46 0.00 3.55
4416 4678 3.790437 CCGGAGCCTCCACTGCAT 61.790 66.667 12.13 0.00 35.91 3.96
4482 4744 1.283321 GGGTCATTGAAGAGGAGGCTT 59.717 52.381 0.00 0.00 0.00 4.35
4488 4750 2.030027 TGAAGAGGAGGCTTCAGGAA 57.970 50.000 0.00 0.00 46.73 3.36
4500 4762 2.814336 GCTTCAGGAATTCAAGTTCGGT 59.186 45.455 7.93 0.00 0.00 4.69
4524 4786 4.082523 CAGATCGTGTGGCGGGGT 62.083 66.667 0.00 0.00 41.72 4.95
4721 4985 0.391395 CTCTGGTCTGAGCTGCAAGG 60.391 60.000 8.47 0.00 0.00 3.61
4746 5011 4.202172 TGTGAATCAGTAGGTCGTTTGTGA 60.202 41.667 0.00 0.00 0.00 3.58
4785 5051 3.438434 GCCTTCCATCTTGTGAACTCTTC 59.562 47.826 0.00 0.00 0.00 2.87
4788 5054 5.767168 CCTTCCATCTTGTGAACTCTTCTTT 59.233 40.000 0.00 0.00 0.00 2.52
4822 5095 5.821204 ACTAATCTTGTTTGTGCACAACTC 58.179 37.500 31.17 24.79 35.28 3.01
4836 5113 5.060940 GTGCACAACTCAAAAACTGTCTTTC 59.939 40.000 13.17 0.00 0.00 2.62
4842 5119 8.360390 ACAACTCAAAAACTGTCTTTCTTTTCT 58.640 29.630 0.00 0.00 0.00 2.52
4843 5120 9.196552 CAACTCAAAAACTGTCTTTCTTTTCTT 57.803 29.630 0.00 0.00 0.00 2.52
4845 5122 9.764363 ACTCAAAAACTGTCTTTCTTTTCTTTT 57.236 25.926 0.00 0.00 0.00 2.27
4847 5124 9.981114 TCAAAAACTGTCTTTCTTTTCTTTTCT 57.019 25.926 0.00 0.00 0.00 2.52
4906 5183 3.003689 GGTTGTATGCAGGGAATGATTCG 59.996 47.826 0.00 0.00 0.00 3.34
4916 5193 2.951642 GGGAATGATTCGGATTCAAGCA 59.048 45.455 6.67 0.00 32.34 3.91
4936 5213 3.437049 GCAAAGATGTGACCTGAACCTAC 59.563 47.826 0.00 0.00 0.00 3.18
4956 5233 2.311542 ACTGGATTTCTGCCCACCAATA 59.688 45.455 0.00 0.00 0.00 1.90
4979 5256 0.315568 GGATGCGCCTTATCTCGAGT 59.684 55.000 13.13 2.46 0.00 4.18
4981 5258 1.789464 GATGCGCCTTATCTCGAGTTG 59.211 52.381 13.13 1.35 0.00 3.16
4983 5260 0.876342 GCGCCTTATCTCGAGTTGGG 60.876 60.000 13.13 11.73 0.00 4.12
4984 5261 0.876342 CGCCTTATCTCGAGTTGGGC 60.876 60.000 21.90 21.90 35.33 5.36
4988 5265 1.137872 CTTATCTCGAGTTGGGCTGCT 59.862 52.381 13.13 0.00 0.00 4.24
5094 5371 2.902486 TGCTCACATCAGAAAGAGACCT 59.098 45.455 0.00 0.00 0.00 3.85
5150 5537 3.259374 CACATACATAGGGGAGGCTACAG 59.741 52.174 0.00 0.00 0.00 2.74
5167 5554 1.270358 ACAGGTCAGCTCGACTTTTCC 60.270 52.381 13.59 0.82 44.70 3.13
5208 5595 8.044060 TGATTGATCATTTGTTACCAGAGAAC 57.956 34.615 0.00 0.00 0.00 3.01
5219 5606 7.660030 TGTTACCAGAGAACAGATGATGATA 57.340 36.000 0.00 0.00 33.03 2.15
5234 5621 4.522114 TGATGATAAAAATCTCCACCGCA 58.478 39.130 0.00 0.00 0.00 5.69
5243 5630 3.576078 ATCTCCACCGCAAATAATCCA 57.424 42.857 0.00 0.00 0.00 3.41
5250 5637 3.088532 ACCGCAAATAATCCAGCAAAGA 58.911 40.909 0.00 0.00 0.00 2.52
5261 5648 1.667236 CAGCAAAGATCATGCCGGTA 58.333 50.000 17.02 0.00 44.91 4.02
5262 5649 1.331756 CAGCAAAGATCATGCCGGTAC 59.668 52.381 17.02 0.00 44.91 3.34
5267 5654 0.828022 AGATCATGCCGGTACCGAAA 59.172 50.000 35.41 22.29 42.83 3.46
5284 5671 4.096732 CGAAATTTCGCCAGAGGAAAAT 57.903 40.909 26.01 0.00 44.26 1.82
5285 5672 3.853671 CGAAATTTCGCCAGAGGAAAATG 59.146 43.478 26.01 0.00 44.26 2.32
5286 5673 4.379394 CGAAATTTCGCCAGAGGAAAATGA 60.379 41.667 26.01 0.00 44.26 2.57
5287 5674 4.708726 AATTTCGCCAGAGGAAAATGAG 57.291 40.909 0.00 0.00 37.00 2.90
5288 5675 2.859165 TTCGCCAGAGGAAAATGAGT 57.141 45.000 0.00 0.00 0.00 3.41
5290 5677 2.699954 TCGCCAGAGGAAAATGAGTTC 58.300 47.619 0.00 0.00 0.00 3.01
5298 5686 1.546029 GGAAAATGAGTTCCTGGTGCC 59.454 52.381 0.00 0.00 43.32 5.01
5319 5707 1.280421 GGTCTCATTCTGCTGTTCCCT 59.720 52.381 0.00 0.00 0.00 4.20
5331 5719 2.810400 GCTGTTCCCTTGTTGCTGTAGA 60.810 50.000 0.00 0.00 0.00 2.59
5332 5720 3.679389 CTGTTCCCTTGTTGCTGTAGAT 58.321 45.455 0.00 0.00 0.00 1.98
5337 5725 4.575885 TCCCTTGTTGCTGTAGATTGTAC 58.424 43.478 0.00 0.00 0.00 2.90
5338 5726 4.286032 TCCCTTGTTGCTGTAGATTGTACT 59.714 41.667 0.00 0.00 0.00 2.73
5339 5727 4.393062 CCCTTGTTGCTGTAGATTGTACTG 59.607 45.833 0.00 0.00 0.00 2.74
5340 5728 4.142816 CCTTGTTGCTGTAGATTGTACTGC 60.143 45.833 13.69 13.69 41.02 4.40
5341 5729 4.001618 TGTTGCTGTAGATTGTACTGCA 57.998 40.909 17.72 17.72 45.89 4.41
5354 5744 0.472044 TACTGCACTGTTGGCTGGAA 59.528 50.000 0.00 0.00 34.89 3.53
5355 5745 1.103398 ACTGCACTGTTGGCTGGAAC 61.103 55.000 0.00 0.00 34.89 3.62
5408 5808 5.416639 TGAACACTTTCCATTCCATCATCAG 59.583 40.000 0.00 0.00 0.00 2.90
5418 5818 5.374071 CATTCCATCATCAGAACATCTCCA 58.626 41.667 0.00 0.00 0.00 3.86
5427 5827 0.767998 GAACATCTCCATCCTCCCCC 59.232 60.000 0.00 0.00 0.00 5.40
5429 5829 0.046242 ACATCTCCATCCTCCCCCAA 59.954 55.000 0.00 0.00 0.00 4.12
5441 5845 0.613572 TCCCCCAATTTTTCTCCGGC 60.614 55.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.755008 GAGGTGAGGGACGAGGAGG 60.755 68.421 0.00 0.00 0.00 4.30
2 3 1.304217 GTGAGGTGAGGGACGAGGA 60.304 63.158 0.00 0.00 0.00 3.71
3 4 1.304547 AGTGAGGTGAGGGACGAGG 60.305 63.158 0.00 0.00 0.00 4.63
4 5 1.649390 CGAGTGAGGTGAGGGACGAG 61.649 65.000 0.00 0.00 0.00 4.18
5 6 1.674651 CGAGTGAGGTGAGGGACGA 60.675 63.158 0.00 0.00 0.00 4.20
6 7 2.701780 CCGAGTGAGGTGAGGGACG 61.702 68.421 0.00 0.00 0.00 4.79
7 8 1.606889 ACCGAGTGAGGTGAGGGAC 60.607 63.158 0.00 0.00 44.07 4.46
8 9 2.851801 ACCGAGTGAGGTGAGGGA 59.148 61.111 0.00 0.00 44.07 4.20
24 25 4.664677 ACGGCTGGTGTCGCTCAC 62.665 66.667 0.00 2.71 46.43 3.51
25 26 4.357947 GACGGCTGGTGTCGCTCA 62.358 66.667 0.00 0.00 46.43 4.26
30 31 2.048127 GACAGGACGGCTGGTGTC 60.048 66.667 8.63 8.63 35.60 3.67
31 32 3.626924 GGACAGGACGGCTGGTGT 61.627 66.667 0.00 0.00 0.00 4.16
32 33 3.596066 CTGGACAGGACGGCTGGTG 62.596 68.421 0.00 0.00 0.00 4.17
33 34 3.314331 CTGGACAGGACGGCTGGT 61.314 66.667 0.00 0.00 0.00 4.00
43 44 2.750657 GGATGGAGGCCCTGGACAG 61.751 68.421 0.00 0.00 0.00 3.51
44 45 2.692368 GGATGGAGGCCCTGGACA 60.692 66.667 0.00 0.00 0.00 4.02
45 46 3.493303 GGGATGGAGGCCCTGGAC 61.493 72.222 0.00 0.00 42.56 4.02
50 51 4.843331 TGGGAGGGATGGAGGCCC 62.843 72.222 0.00 0.00 46.40 5.80
51 52 2.696125 TTGGGAGGGATGGAGGCC 60.696 66.667 0.00 0.00 0.00 5.19
52 53 2.597903 GTTGGGAGGGATGGAGGC 59.402 66.667 0.00 0.00 0.00 4.70
92 93 2.624293 GGGAAAGGGAAGGGAATGGAAG 60.624 54.545 0.00 0.00 0.00 3.46
93 94 1.361197 GGGAAAGGGAAGGGAATGGAA 59.639 52.381 0.00 0.00 0.00 3.53
94 95 1.007607 GGGAAAGGGAAGGGAATGGA 58.992 55.000 0.00 0.00 0.00 3.41
95 96 1.010795 AGGGAAAGGGAAGGGAATGG 58.989 55.000 0.00 0.00 0.00 3.16
96 97 1.063642 GGAGGGAAAGGGAAGGGAATG 60.064 57.143 0.00 0.00 0.00 2.67
97 98 1.309876 GGAGGGAAAGGGAAGGGAAT 58.690 55.000 0.00 0.00 0.00 3.01
98 99 1.205460 CGGAGGGAAAGGGAAGGGAA 61.205 60.000 0.00 0.00 0.00 3.97
99 100 1.615424 CGGAGGGAAAGGGAAGGGA 60.615 63.158 0.00 0.00 0.00 4.20
100 101 2.998949 CGGAGGGAAAGGGAAGGG 59.001 66.667 0.00 0.00 0.00 3.95
101 102 2.272471 GCGGAGGGAAAGGGAAGG 59.728 66.667 0.00 0.00 0.00 3.46
102 103 2.272471 GGCGGAGGGAAAGGGAAG 59.728 66.667 0.00 0.00 0.00 3.46
166 176 1.956170 GTGATGATAGGCGCACGGG 60.956 63.158 10.83 0.00 0.00 5.28
167 177 1.956170 GGTGATGATAGGCGCACGG 60.956 63.158 10.83 0.00 32.24 4.94
208 222 4.803908 CCGGGCAGGAAGGGAAGC 62.804 72.222 0.00 0.00 45.00 3.86
326 378 1.076192 AGGCGGGGGTAGTGAGTAG 60.076 63.158 0.00 0.00 0.00 2.57
360 422 2.632028 CGATCTCAGACCATGGAAGGAT 59.368 50.000 21.47 13.47 0.00 3.24
389 451 0.391130 CAATCTCCTGCCGAACCGAA 60.391 55.000 0.00 0.00 0.00 4.30
403 465 4.283212 GCCTCTCTGCTAGGTAATCAATCT 59.717 45.833 0.00 0.00 36.43 2.40
405 467 4.230455 AGCCTCTCTGCTAGGTAATCAAT 58.770 43.478 0.00 0.00 40.56 2.57
413 476 0.968405 GATGGAGCCTCTCTGCTAGG 59.032 60.000 0.00 0.00 42.95 3.02
463 536 2.413112 CACGCGTGAGAATTGAATCTGT 59.587 45.455 34.93 0.00 0.00 3.41
487 560 2.173382 CTAAACACACGCGCAGGC 59.827 61.111 5.73 0.00 0.00 4.85
489 562 0.787787 TAAGCTAAACACACGCGCAG 59.212 50.000 5.73 0.55 0.00 5.18
493 566 4.461992 TTGAAGTAAGCTAAACACACGC 57.538 40.909 0.00 0.00 0.00 5.34
494 567 5.783654 CGAATTGAAGTAAGCTAAACACACG 59.216 40.000 0.00 0.00 0.00 4.49
496 569 5.761234 ACCGAATTGAAGTAAGCTAAACACA 59.239 36.000 0.00 0.00 0.00 3.72
497 570 6.077838 CACCGAATTGAAGTAAGCTAAACAC 58.922 40.000 0.00 0.00 0.00 3.32
500 573 5.992829 TCACACCGAATTGAAGTAAGCTAAA 59.007 36.000 0.00 0.00 0.00 1.85
501 574 5.543714 TCACACCGAATTGAAGTAAGCTAA 58.456 37.500 0.00 0.00 0.00 3.09
502 575 5.142061 TCACACCGAATTGAAGTAAGCTA 57.858 39.130 0.00 0.00 0.00 3.32
503 576 4.002906 TCACACCGAATTGAAGTAAGCT 57.997 40.909 0.00 0.00 0.00 3.74
505 578 6.898041 TGATTTCACACCGAATTGAAGTAAG 58.102 36.000 0.00 0.00 33.36 2.34
506 579 6.869315 TGATTTCACACCGAATTGAAGTAA 57.131 33.333 0.00 0.00 33.36 2.24
509 582 5.156355 CCTTGATTTCACACCGAATTGAAG 58.844 41.667 0.00 0.00 33.36 3.02
548 625 3.315470 TCACGCCATCTTACTAGTGCTAG 59.685 47.826 5.39 4.80 39.04 3.42
554 631 3.005261 AGCTCATCACGCCATCTTACTAG 59.995 47.826 0.00 0.00 0.00 2.57
557 634 2.131183 GAGCTCATCACGCCATCTTAC 58.869 52.381 9.40 0.00 0.00 2.34
558 635 1.269257 CGAGCTCATCACGCCATCTTA 60.269 52.381 15.40 0.00 0.00 2.10
560 637 1.067084 CGAGCTCATCACGCCATCT 59.933 57.895 15.40 0.00 0.00 2.90
564 641 3.157217 ATCCCGAGCTCATCACGCC 62.157 63.158 15.40 0.00 0.00 5.68
575 652 2.513204 CTGCACTGCCATCCCGAG 60.513 66.667 0.00 0.00 0.00 4.63
576 653 3.002583 TCTGCACTGCCATCCCGA 61.003 61.111 0.00 0.00 0.00 5.14
579 656 1.451028 GGAGTCTGCACTGCCATCC 60.451 63.158 0.00 0.00 34.93 3.51
580 657 0.035630 AAGGAGTCTGCACTGCCATC 60.036 55.000 0.00 0.00 41.91 3.51
581 658 0.035630 GAAGGAGTCTGCACTGCCAT 60.036 55.000 0.00 0.00 41.91 4.40
585 662 1.345741 TGGAAGAAGGAGTCTGCACTG 59.654 52.381 0.00 0.00 36.40 3.66
586 663 1.722034 TGGAAGAAGGAGTCTGCACT 58.278 50.000 0.00 0.00 36.40 4.40
587 664 2.354259 CATGGAAGAAGGAGTCTGCAC 58.646 52.381 0.00 0.00 36.40 4.57
588 665 1.339438 GCATGGAAGAAGGAGTCTGCA 60.339 52.381 0.00 0.00 36.40 4.41
589 666 1.377536 GCATGGAAGAAGGAGTCTGC 58.622 55.000 0.00 0.00 36.40 4.26
594 675 2.795231 TCTTGGCATGGAAGAAGGAG 57.205 50.000 0.00 0.00 0.00 3.69
596 677 3.765511 TGAATTCTTGGCATGGAAGAAGG 59.234 43.478 7.05 0.00 41.53 3.46
600 681 5.593679 AATCTGAATTCTTGGCATGGAAG 57.406 39.130 7.05 0.00 0.00 3.46
602 683 4.773674 ACAAATCTGAATTCTTGGCATGGA 59.226 37.500 7.05 0.00 0.00 3.41
674 755 0.715638 CAAACGAAACCGTACGTGCG 60.716 55.000 19.61 19.61 42.43 5.34
675 756 0.988336 GCAAACGAAACCGTACGTGC 60.988 55.000 15.21 10.81 42.43 5.34
676 757 0.578211 AGCAAACGAAACCGTACGTG 59.422 50.000 15.21 8.32 42.43 4.49
677 758 0.578211 CAGCAAACGAAACCGTACGT 59.422 50.000 15.21 0.00 44.57 3.57
678 759 0.854062 TCAGCAAACGAAACCGTACG 59.146 50.000 8.69 8.69 39.67 3.67
679 760 3.531262 ATTCAGCAAACGAAACCGTAC 57.469 42.857 0.00 0.00 39.67 3.67
680 761 4.555348 AAATTCAGCAAACGAAACCGTA 57.445 36.364 0.00 0.00 39.67 4.02
681 762 3.430333 AAATTCAGCAAACGAAACCGT 57.570 38.095 0.00 0.00 42.82 4.83
682 763 4.145756 GTGTAAATTCAGCAAACGAAACCG 59.854 41.667 0.00 0.00 0.00 4.44
710 791 1.808945 CAAGAATTCTCAGCGTGGCTT 59.191 47.619 8.78 0.00 36.40 4.35
711 792 1.446907 CAAGAATTCTCAGCGTGGCT 58.553 50.000 8.78 0.00 40.77 4.75
712 793 0.179179 GCAAGAATTCTCAGCGTGGC 60.179 55.000 8.78 1.11 0.00 5.01
713 794 1.446907 AGCAAGAATTCTCAGCGTGG 58.553 50.000 20.58 4.07 33.76 4.94
722 803 9.657121 GAATTAGCAATACAGTAGCAAGAATTC 57.343 33.333 0.00 0.00 32.42 2.17
776 857 4.320057 GCAGTGTTTCTTCCAGATTCAGTG 60.320 45.833 0.00 0.00 34.66 3.66
787 868 4.900635 TTTCTTCAGGCAGTGTTTCTTC 57.099 40.909 0.00 0.00 0.00 2.87
837 923 1.689233 AGGCAGGCAAGACGGGATA 60.689 57.895 0.00 0.00 0.00 2.59
843 929 0.250467 TTCTGTCAGGCAGGCAAGAC 60.250 55.000 1.12 11.33 45.08 3.01
853 939 3.304928 GGAAAGCATGTTGTTCTGTCAGG 60.305 47.826 0.00 0.00 0.00 3.86
854 940 3.607775 CGGAAAGCATGTTGTTCTGTCAG 60.608 47.826 0.00 0.00 0.00 3.51
855 941 2.290367 CGGAAAGCATGTTGTTCTGTCA 59.710 45.455 0.00 0.00 0.00 3.58
856 942 2.548057 TCGGAAAGCATGTTGTTCTGTC 59.452 45.455 11.37 0.00 0.00 3.51
860 946 4.798574 AGATTTCGGAAAGCATGTTGTTC 58.201 39.130 19.57 4.50 0.00 3.18
861 947 4.853924 AGATTTCGGAAAGCATGTTGTT 57.146 36.364 19.57 0.00 0.00 2.83
867 953 6.115446 TGATGAGTAAGATTTCGGAAAGCAT 58.885 36.000 19.57 11.12 0.00 3.79
873 959 6.485830 AAGGATGATGAGTAAGATTTCGGA 57.514 37.500 0.00 0.00 0.00 4.55
876 962 7.056635 TGGGAAAGGATGATGAGTAAGATTTC 58.943 38.462 0.00 0.00 0.00 2.17
881 967 5.358160 GGTTTGGGAAAGGATGATGAGTAAG 59.642 44.000 0.00 0.00 0.00 2.34
882 968 5.015178 AGGTTTGGGAAAGGATGATGAGTAA 59.985 40.000 0.00 0.00 0.00 2.24
886 972 3.333381 TCAGGTTTGGGAAAGGATGATGA 59.667 43.478 0.00 0.00 0.00 2.92
887 973 3.700538 TCAGGTTTGGGAAAGGATGATG 58.299 45.455 0.00 0.00 0.00 3.07
888 974 4.402616 TTCAGGTTTGGGAAAGGATGAT 57.597 40.909 0.00 0.00 0.00 2.45
889 975 3.893753 TTCAGGTTTGGGAAAGGATGA 57.106 42.857 0.00 0.00 0.00 2.92
947 1049 5.014123 AGTTAGTCAGGGGAACATCATTTGA 59.986 40.000 0.00 0.00 0.00 2.69
951 1053 3.370953 GCAGTTAGTCAGGGGAACATCAT 60.371 47.826 0.00 0.00 0.00 2.45
952 1054 2.027192 GCAGTTAGTCAGGGGAACATCA 60.027 50.000 0.00 0.00 0.00 3.07
953 1055 2.633488 GCAGTTAGTCAGGGGAACATC 58.367 52.381 0.00 0.00 0.00 3.06
968 1083 0.608856 TGTGATGGAATGCGGCAGTT 60.609 50.000 9.25 3.08 0.00 3.16
973 1088 1.725665 CTGCTGTGATGGAATGCGG 59.274 57.895 0.00 0.00 0.00 5.69
975 1090 0.100682 CTGCTGCTGTGATGGAATGC 59.899 55.000 0.00 0.00 0.00 3.56
976 1091 0.100682 GCTGCTGCTGTGATGGAATG 59.899 55.000 8.53 0.00 36.03 2.67
978 1093 2.036571 CGCTGCTGCTGTGATGGAA 61.037 57.895 13.93 0.00 36.97 3.53
1031 1169 1.006571 TCGTCGTCCCTTGACTTGC 60.007 57.895 0.00 0.00 39.47 4.01
1164 1305 4.492160 TCGGCGCTCATGTCGGAC 62.492 66.667 7.64 0.00 0.00 4.79
1384 1528 2.114411 GACCCCCTTGCGGTTCAA 59.886 61.111 0.00 0.00 32.27 2.69
1398 1542 0.980423 AGAGAGAACTTGCCTGGACC 59.020 55.000 0.00 0.00 0.00 4.46
1421 1565 3.158676 GACTGTCAGGAAGTACAGGACT 58.841 50.000 4.53 0.00 45.94 3.85
1432 1576 3.372440 TCTGCTATCTGACTGTCAGGA 57.628 47.619 31.26 20.73 44.39 3.86
1436 1580 3.003793 TGCGTATCTGCTATCTGACTGTC 59.996 47.826 0.00 0.00 35.36 3.51
1437 1581 2.952310 TGCGTATCTGCTATCTGACTGT 59.048 45.455 0.00 0.00 35.36 3.55
1438 1582 3.004210 AGTGCGTATCTGCTATCTGACTG 59.996 47.826 0.00 0.00 35.36 3.51
1451 1622 9.635520 AAAAGTGGTATATATACAGTGCGTATC 57.364 33.333 21.56 4.62 41.25 2.24
1456 1627 9.214957 TGCATAAAAGTGGTATATATACAGTGC 57.785 33.333 21.56 17.16 34.98 4.40
1529 1721 8.778358 CAAGTCTAAAGATGCAGAACTTAAGTT 58.222 33.333 20.67 20.67 41.64 2.66
1530 1722 8.150945 TCAAGTCTAAAGATGCAGAACTTAAGT 58.849 33.333 1.12 1.12 0.00 2.24
1533 1725 7.896811 TCTCAAGTCTAAAGATGCAGAACTTA 58.103 34.615 0.00 0.00 0.00 2.24
1534 1726 6.763355 TCTCAAGTCTAAAGATGCAGAACTT 58.237 36.000 0.00 0.00 0.00 2.66
1535 1727 6.352016 TCTCAAGTCTAAAGATGCAGAACT 57.648 37.500 0.00 0.00 0.00 3.01
1550 1742 7.279758 CCTGGATTAGTTTCAAGATCTCAAGTC 59.720 40.741 0.00 0.00 0.00 3.01
1635 1827 3.896648 ATAAACTATGCCGCATTTCCG 57.103 42.857 11.97 1.01 0.00 4.30
1739 1932 4.019771 TGTTGTTCCTGTATGATGGCACTA 60.020 41.667 0.00 0.00 0.00 2.74
1747 1940 5.011635 TCAGTTAGCTGTTGTTCCTGTATGA 59.988 40.000 6.47 0.00 43.05 2.15
1817 2017 5.880341 GTGGAACTGAAATGCTGGTATAAC 58.120 41.667 0.00 0.00 0.00 1.89
1951 2151 4.466828 CCAAGCACGTTCATTTCTGTTAG 58.533 43.478 0.00 0.00 0.00 2.34
2166 2366 4.282957 TCCATCTCCTCATGCAGATACTTC 59.717 45.833 0.00 0.00 0.00 3.01
2213 2413 7.665559 TCAGTTAGTTTTTGTATTGATCAGCCT 59.334 33.333 0.00 0.00 0.00 4.58
2424 2624 1.928046 TCCATGCCTAGCCAACCCA 60.928 57.895 0.00 0.00 0.00 4.51
2427 2627 1.032114 GTGGTCCATGCCTAGCCAAC 61.032 60.000 0.00 0.00 0.00 3.77
2536 2736 9.314321 CAAGACCGATAATTGTAAAGACTATGT 57.686 33.333 0.00 0.00 0.00 2.29
2541 2741 6.417191 TGCAAGACCGATAATTGTAAAGAC 57.583 37.500 0.00 0.00 0.00 3.01
2548 2748 7.914871 TCATACATTTTGCAAGACCGATAATTG 59.085 33.333 0.00 0.00 0.00 2.32
2555 2755 4.985413 ACATCATACATTTTGCAAGACCG 58.015 39.130 0.00 0.00 0.00 4.79
2591 2791 2.991250 ACATCTTGGCACCATGAGTAC 58.009 47.619 10.99 0.00 34.39 2.73
2833 3034 3.572632 ATGGCTGTAGCTGTCATTGAT 57.427 42.857 0.00 0.00 41.70 2.57
2843 3044 1.224965 GAAGCTGCTATGGCTGTAGC 58.775 55.000 0.90 13.28 45.71 3.58
2844 3045 2.102084 TCTGAAGCTGCTATGGCTGTAG 59.898 50.000 0.90 0.00 40.19 2.74
2848 3049 2.573369 CATTCTGAAGCTGCTATGGCT 58.427 47.619 0.90 0.00 42.31 4.75
2977 3197 6.842437 TGCCCAACTAACAAAATAATAGCA 57.158 33.333 0.00 0.00 0.00 3.49
2999 3229 5.046591 TGAAACCAGGGTTCTGTACTCTATG 60.047 44.000 18.56 0.00 34.47 2.23
3033 3263 6.166279 TGGTTGTCTTTTGTGCAAAATACAA 58.834 32.000 24.36 24.36 46.00 2.41
3088 3318 2.434884 TGCTTAGCCTCGCACAGC 60.435 61.111 0.29 1.26 36.71 4.40
3162 3392 7.766738 GGAGAATCTTCTACAACTTCTAAAGGG 59.233 40.741 0.00 0.00 38.07 3.95
3214 3444 8.772844 AGGAACTAAACAAAGTGGCAACAAGAT 61.773 37.037 0.00 0.00 46.31 2.40
3278 3509 8.033038 GGAACCATGTTTTAGGAAAAGTTATCC 58.967 37.037 0.00 0.00 37.22 2.59
3370 3608 5.980715 TGCACATTTAAGCATCAATAGCATG 59.019 36.000 0.00 0.00 35.51 4.06
3447 3685 3.045634 TCCTTTCCAGGACTTCAGTTGA 58.954 45.455 0.00 0.00 45.20 3.18
3508 3746 4.060900 CTGTGAAGCTGCTAGAAGAAACA 58.939 43.478 0.90 0.00 0.00 2.83
3666 3904 1.138247 GGCGCAGGAAAGCATTCAG 59.862 57.895 10.83 0.00 37.29 3.02
3669 3907 0.895100 TTCTGGCGCAGGAAAGCATT 60.895 50.000 10.83 0.00 34.54 3.56
3835 4073 3.059884 CCAGGTAGCAATGCGTATGTAG 58.940 50.000 0.00 0.00 0.00 2.74
3836 4074 2.696187 TCCAGGTAGCAATGCGTATGTA 59.304 45.455 0.00 0.00 0.00 2.29
3840 4078 0.179084 GCTCCAGGTAGCAATGCGTA 60.179 55.000 0.00 0.00 42.30 4.42
3841 4079 1.450312 GCTCCAGGTAGCAATGCGT 60.450 57.895 0.00 0.00 42.30 5.24
3842 4080 2.182842 GGCTCCAGGTAGCAATGCG 61.183 63.158 0.00 0.00 44.64 4.73
3843 4081 1.825622 GGGCTCCAGGTAGCAATGC 60.826 63.158 0.00 0.00 44.64 3.56
3844 4082 1.152881 GGGGCTCCAGGTAGCAATG 60.153 63.158 0.00 0.00 44.64 2.82
3845 4083 2.386935 GGGGGCTCCAGGTAGCAAT 61.387 63.158 4.16 0.00 44.64 3.56
3846 4084 3.015145 GGGGGCTCCAGGTAGCAA 61.015 66.667 4.16 0.00 44.64 3.91
3866 4104 1.889170 GGGAGCTAAAGCAAGCACTTT 59.111 47.619 4.54 5.01 45.30 2.66
3912 4150 6.995511 AACAAGCTTCACAAAACTAGTACA 57.004 33.333 0.00 0.00 0.00 2.90
3914 4152 8.276252 AGAAAACAAGCTTCACAAAACTAGTA 57.724 30.769 0.00 0.00 0.00 1.82
3930 4168 7.538303 AACAAACTGGCAATAAGAAAACAAG 57.462 32.000 0.00 0.00 0.00 3.16
3936 4174 8.001881 TGAACTAAACAAACTGGCAATAAGAA 57.998 30.769 0.00 0.00 0.00 2.52
3941 4179 6.127479 TGTTCTGAACTAAACAAACTGGCAAT 60.127 34.615 20.18 0.00 32.69 3.56
3963 4203 8.902806 TCAAAGATGTATCAAGTTCAAGTTGTT 58.097 29.630 4.85 0.00 30.75 2.83
3971 4211 6.535150 TGGACGATCAAAGATGTATCAAGTTC 59.465 38.462 0.00 0.00 0.00 3.01
3982 4222 8.258007 TGTTAGTTTAGATGGACGATCAAAGAT 58.742 33.333 0.00 0.00 32.86 2.40
4215 4477 4.713946 GGGAACCGCTTGATGTCA 57.286 55.556 0.00 0.00 40.86 3.58
4302 4564 4.821589 CGGAGGAGGCAGCGGTTC 62.822 72.222 0.00 0.00 0.00 3.62
4317 4579 2.658593 CGCGACTTGGATAGCCGG 60.659 66.667 0.00 0.00 36.79 6.13
4324 4586 4.735132 CTTCGGGCGCGACTTGGA 62.735 66.667 26.59 9.93 0.00 3.53
4326 4588 2.509336 ATCTTCGGGCGCGACTTG 60.509 61.111 26.59 17.88 0.00 3.16
4330 4592 4.873129 GCTCATCTTCGGGCGCGA 62.873 66.667 23.01 23.01 0.00 5.87
4365 4627 1.263776 CACTGTCGACGATCTTCTGC 58.736 55.000 11.62 0.00 0.00 4.26
4410 4672 0.464373 CCGAGCCATGGTAATGCAGT 60.464 55.000 14.67 0.00 31.93 4.40
4416 4678 1.600107 GGACACCGAGCCATGGTAA 59.400 57.895 14.67 0.00 37.72 2.85
4443 4705 0.951040 CTTTCTTGGTCCGCTTCGCT 60.951 55.000 0.00 0.00 0.00 4.93
4482 4744 2.552315 GCAACCGAACTTGAATTCCTGA 59.448 45.455 2.27 0.00 0.00 3.86
4500 4762 2.741985 CACACGATCTGGCGGCAA 60.742 61.111 14.48 4.62 35.12 4.52
4524 4786 6.012508 AGGTCTTAATGATCTCAGGTTTCCAA 60.013 38.462 0.00 0.00 27.85 3.53
4542 4804 3.282021 GCATCCATTTCAGCAGGTCTTA 58.718 45.455 0.00 0.00 0.00 2.10
4675 4939 1.670811 ACAAACACAAGACGGCTCAAG 59.329 47.619 0.00 0.00 0.00 3.02
4721 4985 4.510340 ACAAACGACCTACTGATTCACAAC 59.490 41.667 0.00 0.00 0.00 3.32
4746 5011 2.962859 AGGCTGAAACTGGACCAAAAT 58.037 42.857 0.00 0.00 0.00 1.82
4785 5051 9.646427 AAACAAGATTAGTACTCTGCTAGAAAG 57.354 33.333 0.00 0.00 0.00 2.62
4788 5054 8.029522 CACAAACAAGATTAGTACTCTGCTAGA 58.970 37.037 0.00 0.00 0.00 2.43
4861 5138 5.221501 CCCTTTCCACATGAAAAATGACAGT 60.222 40.000 0.00 0.00 42.25 3.55
4906 5183 3.760684 AGGTCACATCTTTGCTTGAATCC 59.239 43.478 0.00 0.00 0.00 3.01
4916 5193 4.263068 CCAGTAGGTTCAGGTCACATCTTT 60.263 45.833 0.00 0.00 0.00 2.52
4936 5213 1.856629 ATTGGTGGGCAGAAATCCAG 58.143 50.000 0.00 0.00 33.13 3.86
4956 5233 0.972883 GAGATAAGGCGCATCCTCCT 59.027 55.000 10.83 0.00 46.94 3.69
4974 5251 0.674581 CATTCAGCAGCCCAACTCGA 60.675 55.000 0.00 0.00 0.00 4.04
4979 5256 1.282738 TCAGATCATTCAGCAGCCCAA 59.717 47.619 0.00 0.00 0.00 4.12
4981 5258 2.048444 TTCAGATCATTCAGCAGCCC 57.952 50.000 0.00 0.00 0.00 5.19
4983 5260 5.932883 TCAGATATTCAGATCATTCAGCAGC 59.067 40.000 0.00 0.00 0.00 5.25
4984 5261 7.413548 GCATCAGATATTCAGATCATTCAGCAG 60.414 40.741 0.00 0.00 0.00 4.24
4988 5265 6.879458 CCAGCATCAGATATTCAGATCATTCA 59.121 38.462 0.00 0.00 0.00 2.57
5094 5371 6.601332 AGAAATTCTCCCAGTTGTACAAAGA 58.399 36.000 10.51 6.35 0.00 2.52
5167 5554 4.936891 TCAATCATGTAGACAGTCCGATG 58.063 43.478 0.00 0.00 0.00 3.84
5208 5595 6.567321 GCGGTGGAGATTTTTATCATCATCTG 60.567 42.308 0.00 0.00 0.00 2.90
5219 5606 5.186797 TGGATTATTTGCGGTGGAGATTTTT 59.813 36.000 0.00 0.00 0.00 1.94
5234 5621 5.508489 CGGCATGATCTTTGCTGGATTATTT 60.508 40.000 17.41 0.00 41.73 1.40
5243 5630 1.668419 GTACCGGCATGATCTTTGCT 58.332 50.000 17.09 4.62 40.03 3.91
5250 5637 2.341846 AATTTCGGTACCGGCATGAT 57.658 45.000 32.80 16.56 40.25 2.45
5267 5654 3.690460 ACTCATTTTCCTCTGGCGAAAT 58.310 40.909 0.00 0.00 0.00 2.17
5279 5666 1.200020 CGGCACCAGGAACTCATTTTC 59.800 52.381 0.00 0.00 34.60 2.29
5281 5668 0.609131 CCGGCACCAGGAACTCATTT 60.609 55.000 0.00 0.00 34.60 2.32
5284 5671 2.847234 ACCGGCACCAGGAACTCA 60.847 61.111 0.00 0.00 34.60 3.41
5285 5672 2.047179 GACCGGCACCAGGAACTC 60.047 66.667 0.00 0.00 34.60 3.01
5286 5673 2.526873 AGACCGGCACCAGGAACT 60.527 61.111 0.00 2.09 43.88 3.01
5287 5674 2.047179 GAGACCGGCACCAGGAAC 60.047 66.667 0.00 0.00 0.00 3.62
5288 5675 1.488705 AATGAGACCGGCACCAGGAA 61.489 55.000 0.00 0.00 0.00 3.36
5290 5677 1.450312 GAATGAGACCGGCACCAGG 60.450 63.158 0.00 0.00 0.00 4.45
5292 5679 1.296392 CAGAATGAGACCGGCACCA 59.704 57.895 0.00 0.00 39.69 4.17
5298 5686 1.363744 GGAACAGCAGAATGAGACCG 58.636 55.000 0.00 0.00 39.69 4.79
5319 5707 4.213270 GTGCAGTACAATCTACAGCAACAA 59.787 41.667 0.00 0.00 40.64 2.83
5331 5719 1.881973 CAGCCAACAGTGCAGTACAAT 59.118 47.619 0.00 0.00 0.00 2.71
5332 5720 1.308047 CAGCCAACAGTGCAGTACAA 58.692 50.000 0.00 0.00 0.00 2.41
5337 5725 1.656441 GTTCCAGCCAACAGTGCAG 59.344 57.895 0.00 0.00 0.00 4.41
5338 5726 1.827789 GGTTCCAGCCAACAGTGCA 60.828 57.895 0.00 0.00 0.00 4.57
5339 5727 1.391157 TTGGTTCCAGCCAACAGTGC 61.391 55.000 0.00 0.00 42.98 4.40
5340 5728 1.067516 CTTTGGTTCCAGCCAACAGTG 59.932 52.381 0.00 0.00 46.98 3.66
5341 5729 1.064017 TCTTTGGTTCCAGCCAACAGT 60.064 47.619 0.00 0.00 46.98 3.55
5354 5744 7.147915 TGCAGAAAGTAACAGAATTTCTTTGGT 60.148 33.333 0.00 0.00 40.40 3.67
5355 5745 7.168135 GTGCAGAAAGTAACAGAATTTCTTTGG 59.832 37.037 0.00 0.00 40.40 3.28
5358 5748 7.067494 ACTGTGCAGAAAGTAACAGAATTTCTT 59.933 33.333 6.17 0.00 42.09 2.52
5408 5808 0.767998 GGGGGAGGATGGAGATGTTC 59.232 60.000 0.00 0.00 0.00 3.18
5418 5818 2.358195 CGGAGAAAAATTGGGGGAGGAT 60.358 50.000 0.00 0.00 0.00 3.24
5427 5827 2.518949 CATGTCGCCGGAGAAAAATTG 58.481 47.619 10.32 0.00 0.00 2.32
5429 5829 1.094785 CCATGTCGCCGGAGAAAAAT 58.905 50.000 10.32 1.15 0.00 1.82
5441 5845 0.946528 CACCCATATGCACCATGTCG 59.053 55.000 8.81 2.49 0.00 4.35


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

AutoCloner maintained by Alex Coulton.