Multiple sequence alignment - TraesCS7B01G079100

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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 TraesCS7B01G079100 chr7B 100.000 3814 0 0 650 4463 89203874 89207687 0.000000e+00 7044.0
1 TraesCS7B01G079100 chr7B 87.156 545 40 12 3686 4207 88974295 88973758 3.840000e-165 592.0
2 TraesCS7B01G079100 chr7B 100.000 206 0 0 1 206 89203225 89203430 9.060000e-102 381.0
3 TraesCS7B01G079100 chr7B 86.517 178 8 9 4287 4463 88973576 88973414 9.860000e-42 182.0
4 TraesCS7B01G079100 chr7D 93.707 2940 134 24 724 3631 127292581 127289661 0.000000e+00 4357.0
5 TraesCS7B01G079100 chr7D 89.302 430 21 10 3686 4096 127418863 127419286 2.380000e-142 516.0
6 TraesCS7B01G079100 chr7D 80.431 557 77 20 1108 1651 24521345 24520808 3.240000e-106 396.0
7 TraesCS7B01G079100 chr7D 74.913 578 110 22 1081 1651 24920235 24919686 9.650000e-57 231.0
8 TraesCS7B01G079100 chr7D 89.017 173 19 0 3684 3856 24424429 24424601 9.720000e-52 215.0
9 TraesCS7B01G079100 chr7D 96.330 109 2 1 4357 4463 127419541 127419649 1.280000e-40 178.0
10 TraesCS7B01G079100 chr7D 83.626 171 28 0 3686 3856 24500867 24501037 1.280000e-35 161.0
11 TraesCS7B01G079100 chr7D 95.000 60 3 0 4287 4346 127419489 127419548 1.320000e-15 95.3
12 TraesCS7B01G079100 chr7A 94.806 2753 110 15 905 3632 128051303 128048559 0.000000e+00 4261.0
13 TraesCS7B01G079100 chr7A 92.410 975 54 4 2280 3248 128024373 128023413 0.000000e+00 1373.0
14 TraesCS7B01G079100 chr7A 88.802 384 23 8 3686 4049 127910217 127909834 1.890000e-123 453.0
15 TraesCS7B01G079100 chr7A 80.108 558 77 22 1108 1651 25133716 25133179 7.000000e-103 385.0
16 TraesCS7B01G079100 chr7A 76.614 573 125 6 1082 1651 25360452 25359886 1.560000e-79 307.0
17 TraesCS7B01G079100 chr7A 89.017 173 19 0 3684 3856 24925865 24926037 9.720000e-52 215.0
18 TraesCS7B01G079100 chr7A 74.355 581 114 20 1081 1651 37847911 37848466 9.720000e-52 215.0
19 TraesCS7B01G079100 chr7A 96.748 123 4 0 2107 2229 128040264 128040142 5.850000e-49 206.0
20 TraesCS7B01G079100 chr7A 94.444 126 7 0 3342 3467 128022995 128022870 1.270000e-45 195.0
21 TraesCS7B01G079100 chr7A 83.041 171 29 0 3686 3856 24959419 24959589 5.980000e-34 156.0
22 TraesCS7B01G079100 chr7A 84.118 170 13 4 3473 3628 127924290 127924121 7.730000e-33 152.0
23 TraesCS7B01G079100 chr7A 71.970 528 137 10 2100 2620 25359479 25358956 1.290000e-30 145.0
24 TraesCS7B01G079100 chr7A 90.541 74 5 2 3630 3702 127910396 127910324 3.670000e-16 97.1
25 TraesCS7B01G079100 chr6B 100.000 206 0 0 1 206 140095620 140095825 9.060000e-102 381.0
26 TraesCS7B01G079100 chr6B 99.515 206 1 0 1 206 647392253 647392458 4.210000e-100 375.0
27 TraesCS7B01G079100 chr1B 100.000 206 0 0 1 206 39987415 39987620 9.060000e-102 381.0
28 TraesCS7B01G079100 chr4B 99.515 206 1 0 1 206 31986469 31986264 4.210000e-100 375.0
29 TraesCS7B01G079100 chr4B 99.515 206 1 0 1 206 668878543 668878748 4.210000e-100 375.0
30 TraesCS7B01G079100 chr4B 99.029 206 2 0 1 206 118510362 118510157 1.960000e-98 370.0
31 TraesCS7B01G079100 chr4A 99.515 206 1 0 1 206 670885168 670884963 4.210000e-100 375.0
32 TraesCS7B01G079100 chr4A 99.515 206 1 0 1 206 719935573 719935778 4.210000e-100 375.0
33 TraesCS7B01G079100 chr4A 75.043 577 105 25 1081 1651 708626391 708625848 9.650000e-57 231.0
34 TraesCS7B01G079100 chr4A 85.795 176 25 0 3684 3859 707251408 707251233 2.120000e-43 187.0
35 TraesCS7B01G079100 chr5B 99.510 204 1 0 2 205 660197815 660197612 5.450000e-99 372.0
36 TraesCS7B01G079100 chr6A 76.234 547 103 18 1108 1651 1831055 1831577 9.520000e-67 265.0
37 TraesCS7B01G079100 chr1A 80.412 97 8 7 4253 4338 582704198 582704294 3.730000e-06 63.9


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 TraesCS7B01G079100 chr7B 89203225 89207687 4462 False 3712.50 7044 100.0000 1 4463 2 chr7B.!!$F1 4462
1 TraesCS7B01G079100 chr7B 88973414 88974295 881 True 387.00 592 86.8365 3686 4463 2 chr7B.!!$R1 777
2 TraesCS7B01G079100 chr7D 127289661 127292581 2920 True 4357.00 4357 93.7070 724 3631 1 chr7D.!!$R3 2907
3 TraesCS7B01G079100 chr7D 24520808 24521345 537 True 396.00 396 80.4310 1108 1651 1 chr7D.!!$R1 543
4 TraesCS7B01G079100 chr7D 127418863 127419649 786 False 263.10 516 93.5440 3686 4463 3 chr7D.!!$F3 777
5 TraesCS7B01G079100 chr7D 24919686 24920235 549 True 231.00 231 74.9130 1081 1651 1 chr7D.!!$R2 570
6 TraesCS7B01G079100 chr7A 128048559 128051303 2744 True 4261.00 4261 94.8060 905 3632 1 chr7A.!!$R4 2727
7 TraesCS7B01G079100 chr7A 128022870 128024373 1503 True 784.00 1373 93.4270 2280 3467 2 chr7A.!!$R7 1187
8 TraesCS7B01G079100 chr7A 25133179 25133716 537 True 385.00 385 80.1080 1108 1651 1 chr7A.!!$R1 543
9 TraesCS7B01G079100 chr7A 127909834 127910396 562 True 275.05 453 89.6715 3630 4049 2 chr7A.!!$R6 419
10 TraesCS7B01G079100 chr7A 25358956 25360452 1496 True 226.00 307 74.2920 1082 2620 2 chr7A.!!$R5 1538
11 TraesCS7B01G079100 chr7A 37847911 37848466 555 False 215.00 215 74.3550 1081 1651 1 chr7A.!!$F3 570
12 TraesCS7B01G079100 chr4A 708625848 708626391 543 True 231.00 231 75.0430 1081 1651 1 chr4A.!!$R3 570
13 TraesCS7B01G079100 chr6A 1831055 1831577 522 False 265.00 265 76.2340 1108 1651 1 chr6A.!!$F1 543

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
44 45 0.038618 TTGCTCGAGCGTGTACACAT 60.039 50.0 30.75 13.23 45.83 3.21 F
702 703 0.108424 GAGCGACTGTTGGAGATGCT 60.108 55.0 0.00 0.00 38.05 3.79 F
703 704 0.108424 AGCGACTGTTGGAGATGCTC 60.108 55.0 0.00 0.00 32.53 4.26 F
704 705 0.108424 GCGACTGTTGGAGATGCTCT 60.108 55.0 0.00 0.00 0.00 4.09 F
2079 2177 0.244994 GAGAAGTCGAGAAGGCAGCA 59.755 55.0 0.00 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1962 2.182030 GTCGACGGAGCCAAGGAG 59.818 66.667 0.00 0.0 0.00 3.69 R
2066 2164 0.536724 TGCTAATGCTGCCTTCTCGA 59.463 50.000 0.00 0.0 40.48 4.04 R
2270 2368 0.603707 CAGGCTGTGGAAAGCGAAGA 60.604 55.000 6.28 0.0 44.52 2.87 R
2364 2462 1.248785 TGGAGAAGAAGACCGACGGG 61.249 60.000 20.00 0.0 40.11 5.28 R
4049 4656 0.041312 GCGCGCATAATTCAACGGAT 60.041 50.000 29.10 0.0 0.00 4.18 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
19 20 4.785453 GGCAGAGGGGCGAGGTTG 62.785 72.222 0.00 0.00 33.57 3.77
20 21 3.706373 GCAGAGGGGCGAGGTTGA 61.706 66.667 0.00 0.00 0.00 3.18
21 22 2.581354 CAGAGGGGCGAGGTTGAG 59.419 66.667 0.00 0.00 0.00 3.02
22 23 3.394836 AGAGGGGCGAGGTTGAGC 61.395 66.667 0.00 0.00 0.00 4.26
23 24 4.821589 GAGGGGCGAGGTTGAGCG 62.822 72.222 0.00 0.00 0.00 5.03
40 41 3.073446 GCTTGCTCGAGCGTGTAC 58.927 61.111 30.75 15.30 45.83 2.90
41 42 1.733041 GCTTGCTCGAGCGTGTACA 60.733 57.895 30.75 10.94 45.83 2.90
42 43 1.945776 GCTTGCTCGAGCGTGTACAC 61.946 60.000 30.75 16.32 45.83 2.90
43 44 0.663269 CTTGCTCGAGCGTGTACACA 60.663 55.000 30.75 9.36 45.83 3.72
44 45 0.038618 TTGCTCGAGCGTGTACACAT 60.039 50.000 30.75 13.23 45.83 3.21
45 46 0.456142 TGCTCGAGCGTGTACACATC 60.456 55.000 30.75 19.54 45.83 3.06
46 47 0.179161 GCTCGAGCGTGTACACATCT 60.179 55.000 23.61 19.75 0.00 2.90
47 48 1.732732 GCTCGAGCGTGTACACATCTT 60.733 52.381 23.61 7.45 0.00 2.40
48 49 1.914051 CTCGAGCGTGTACACATCTTG 59.086 52.381 24.98 21.61 0.00 3.02
49 50 0.992072 CGAGCGTGTACACATCTTGG 59.008 55.000 24.98 9.16 0.00 3.61
50 51 1.402325 CGAGCGTGTACACATCTTGGA 60.402 52.381 24.98 0.00 0.00 3.53
51 52 2.683968 GAGCGTGTACACATCTTGGAA 58.316 47.619 24.98 0.00 0.00 3.53
52 53 2.668457 GAGCGTGTACACATCTTGGAAG 59.332 50.000 24.98 7.05 0.00 3.46
53 54 2.037251 AGCGTGTACACATCTTGGAAGT 59.963 45.455 24.98 0.00 0.00 3.01
54 55 2.806244 GCGTGTACACATCTTGGAAGTT 59.194 45.455 24.98 0.00 0.00 2.66
55 56 3.120649 GCGTGTACACATCTTGGAAGTTC 60.121 47.826 24.98 0.00 0.00 3.01
56 57 4.055360 CGTGTACACATCTTGGAAGTTCA 58.945 43.478 24.98 0.00 0.00 3.18
57 58 4.690748 CGTGTACACATCTTGGAAGTTCAT 59.309 41.667 24.98 0.00 0.00 2.57
58 59 5.163953 CGTGTACACATCTTGGAAGTTCATC 60.164 44.000 24.98 0.00 0.00 2.92
59 60 5.934625 GTGTACACATCTTGGAAGTTCATCT 59.065 40.000 21.14 0.00 0.00 2.90
60 61 5.934043 TGTACACATCTTGGAAGTTCATCTG 59.066 40.000 5.01 0.00 0.00 2.90
61 62 4.330250 ACACATCTTGGAAGTTCATCTGG 58.670 43.478 5.01 0.00 0.00 3.86
62 63 3.128242 CACATCTTGGAAGTTCATCTGGC 59.872 47.826 5.01 0.00 0.00 4.85
63 64 2.496899 TCTTGGAAGTTCATCTGGCC 57.503 50.000 5.01 0.00 0.00 5.36
64 65 1.089920 CTTGGAAGTTCATCTGGCCG 58.910 55.000 5.01 0.00 0.00 6.13
65 66 0.960364 TTGGAAGTTCATCTGGCCGC 60.960 55.000 5.01 0.00 0.00 6.53
66 67 2.464459 GGAAGTTCATCTGGCCGCG 61.464 63.158 5.01 0.00 0.00 6.46
67 68 3.100862 GAAGTTCATCTGGCCGCGC 62.101 63.158 0.00 0.00 0.00 6.86
138 139 4.824166 CGTCCCGTACGTGCCGAG 62.824 72.222 15.21 0.00 46.72 4.63
139 140 4.487412 GTCCCGTACGTGCCGAGG 62.487 72.222 15.21 7.09 0.00 4.63
153 154 4.516195 GAGGGCGAGCCGGAGTTC 62.516 72.222 5.05 0.00 36.85 3.01
177 178 2.717485 GCGTATCTCCGCGGTGTA 59.283 61.111 27.15 14.32 44.69 2.90
178 179 1.370172 GCGTATCTCCGCGGTGTAG 60.370 63.158 27.15 15.99 44.69 2.74
179 180 1.370172 CGTATCTCCGCGGTGTAGC 60.370 63.158 27.15 14.89 0.00 3.58
180 181 1.783031 CGTATCTCCGCGGTGTAGCT 61.783 60.000 27.15 9.58 34.40 3.32
181 182 0.317938 GTATCTCCGCGGTGTAGCTG 60.318 60.000 27.15 7.84 34.40 4.24
182 183 2.071844 TATCTCCGCGGTGTAGCTGC 62.072 60.000 27.15 0.00 45.77 5.25
188 189 3.118454 CGGTGTAGCTGCCGTTGG 61.118 66.667 15.18 0.00 42.73 3.77
189 190 2.746277 GGTGTAGCTGCCGTTGGG 60.746 66.667 0.00 0.00 0.00 4.12
668 669 0.313987 AAAAGCTGCCTTTACCGTGC 59.686 50.000 0.00 0.00 40.30 5.34
669 670 1.852067 AAAGCTGCCTTTACCGTGCG 61.852 55.000 0.00 0.00 39.44 5.34
670 671 4.460873 GCTGCCTTTACCGTGCGC 62.461 66.667 0.00 0.00 0.00 6.09
671 672 4.147322 CTGCCTTTACCGTGCGCG 62.147 66.667 13.88 13.88 37.95 6.86
694 695 2.600388 TCGTTTGGAGCGACTGTTG 58.400 52.632 0.00 0.00 33.09 3.33
695 696 0.878523 TCGTTTGGAGCGACTGTTGG 60.879 55.000 0.00 0.00 33.09 3.77
696 697 0.878523 CGTTTGGAGCGACTGTTGGA 60.879 55.000 0.00 0.00 0.00 3.53
697 698 0.868406 GTTTGGAGCGACTGTTGGAG 59.132 55.000 0.00 0.00 0.00 3.86
698 699 0.756294 TTTGGAGCGACTGTTGGAGA 59.244 50.000 0.00 0.00 0.00 3.71
699 700 0.976641 TTGGAGCGACTGTTGGAGAT 59.023 50.000 0.00 0.00 0.00 2.75
700 701 0.247460 TGGAGCGACTGTTGGAGATG 59.753 55.000 0.00 0.00 0.00 2.90
701 702 1.086634 GGAGCGACTGTTGGAGATGC 61.087 60.000 0.00 0.00 0.00 3.91
702 703 0.108424 GAGCGACTGTTGGAGATGCT 60.108 55.000 0.00 0.00 38.05 3.79
703 704 0.108424 AGCGACTGTTGGAGATGCTC 60.108 55.000 0.00 0.00 32.53 4.26
704 705 0.108424 GCGACTGTTGGAGATGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
705 706 1.135139 GCGACTGTTGGAGATGCTCTA 59.865 52.381 0.00 0.00 0.00 2.43
706 707 2.417379 GCGACTGTTGGAGATGCTCTAA 60.417 50.000 0.00 0.00 0.00 2.10
707 708 3.443037 CGACTGTTGGAGATGCTCTAAG 58.557 50.000 0.00 0.00 31.92 2.18
708 709 3.119316 CGACTGTTGGAGATGCTCTAAGT 60.119 47.826 0.00 0.00 31.92 2.24
709 710 4.619394 CGACTGTTGGAGATGCTCTAAGTT 60.619 45.833 0.00 0.00 31.92 2.66
710 711 5.234466 ACTGTTGGAGATGCTCTAAGTTT 57.766 39.130 0.00 0.00 31.92 2.66
711 712 4.999950 ACTGTTGGAGATGCTCTAAGTTTG 59.000 41.667 0.00 0.00 31.92 2.93
712 713 5.221722 ACTGTTGGAGATGCTCTAAGTTTGA 60.222 40.000 0.00 0.00 31.92 2.69
713 714 5.620206 TGTTGGAGATGCTCTAAGTTTGAA 58.380 37.500 0.00 0.00 31.92 2.69
714 715 5.702670 TGTTGGAGATGCTCTAAGTTTGAAG 59.297 40.000 0.00 0.00 31.92 3.02
715 716 4.256920 TGGAGATGCTCTAAGTTTGAAGC 58.743 43.478 0.00 0.00 0.00 3.86
716 717 4.256920 GGAGATGCTCTAAGTTTGAAGCA 58.743 43.478 11.45 11.45 36.69 3.91
717 718 4.094146 GGAGATGCTCTAAGTTTGAAGCAC 59.906 45.833 11.34 7.68 35.03 4.40
718 719 4.006319 AGATGCTCTAAGTTTGAAGCACC 58.994 43.478 11.34 4.98 35.03 5.01
719 720 3.207265 TGCTCTAAGTTTGAAGCACCA 57.793 42.857 7.12 0.00 0.00 4.17
720 721 3.550820 TGCTCTAAGTTTGAAGCACCAA 58.449 40.909 7.12 0.00 0.00 3.67
721 722 3.315191 TGCTCTAAGTTTGAAGCACCAAC 59.685 43.478 7.12 0.00 0.00 3.77
722 723 3.565902 GCTCTAAGTTTGAAGCACCAACT 59.434 43.478 0.00 0.00 0.00 3.16
747 748 3.505680 CCAACAGTGGGATCGAAAAATCA 59.494 43.478 0.00 0.00 41.77 2.57
752 753 3.056107 AGTGGGATCGAAAAATCAGACGA 60.056 43.478 0.00 0.00 39.01 4.20
766 767 1.733399 GACGAGCGGGAACAGTGAC 60.733 63.158 0.00 0.00 0.00 3.67
769 770 2.847234 AGCGGGAACAGTGACCCA 60.847 61.111 22.52 0.00 45.83 4.51
772 773 0.893727 GCGGGAACAGTGACCCAAAT 60.894 55.000 22.52 0.00 45.83 2.32
780 781 6.209788 GGGAACAGTGACCCAAATTTATGTTA 59.790 38.462 19.67 0.00 44.96 2.41
795 796 8.986477 AATTTATGTTAGTTTCACATTGCCTC 57.014 30.769 0.00 0.00 36.28 4.70
796 797 7.759489 TTTATGTTAGTTTCACATTGCCTCT 57.241 32.000 0.00 0.00 36.28 3.69
797 798 8.856153 TTTATGTTAGTTTCACATTGCCTCTA 57.144 30.769 0.00 0.00 36.28 2.43
798 799 8.856153 TTATGTTAGTTTCACATTGCCTCTAA 57.144 30.769 0.00 0.00 36.28 2.10
799 800 6.554334 TGTTAGTTTCACATTGCCTCTAAC 57.446 37.500 0.00 0.00 37.40 2.34
800 801 6.058833 TGTTAGTTTCACATTGCCTCTAACA 58.941 36.000 9.70 9.70 41.40 2.41
801 802 6.017440 TGTTAGTTTCACATTGCCTCTAACAC 60.017 38.462 9.70 0.00 39.94 3.32
802 803 4.460263 AGTTTCACATTGCCTCTAACACA 58.540 39.130 0.00 0.00 0.00 3.72
804 805 4.350368 TTCACATTGCCTCTAACACAGA 57.650 40.909 0.00 0.00 0.00 3.41
816 817 4.673968 TCTAACACAGAGTACAGATGGGT 58.326 43.478 0.00 0.00 30.03 4.51
819 820 1.482593 CACAGAGTACAGATGGGTCCC 59.517 57.143 0.00 0.00 0.00 4.46
822 823 2.169352 CAGAGTACAGATGGGTCCCTTG 59.831 54.545 10.00 7.71 0.00 3.61
824 825 2.838202 GAGTACAGATGGGTCCCTTGAA 59.162 50.000 10.00 0.00 0.00 2.69
826 827 4.631234 AGTACAGATGGGTCCCTTGAATA 58.369 43.478 10.00 0.00 0.00 1.75
828 829 3.736094 ACAGATGGGTCCCTTGAATAGA 58.264 45.455 10.00 0.00 0.00 1.98
829 830 4.111577 ACAGATGGGTCCCTTGAATAGAA 58.888 43.478 10.00 0.00 0.00 2.10
830 831 4.080299 ACAGATGGGTCCCTTGAATAGAAC 60.080 45.833 10.00 0.00 0.00 3.01
831 832 3.459969 AGATGGGTCCCTTGAATAGAACC 59.540 47.826 10.00 0.00 37.92 3.62
832 833 2.638325 TGGGTCCCTTGAATAGAACCA 58.362 47.619 10.00 0.00 45.10 3.67
833 834 2.576191 TGGGTCCCTTGAATAGAACCAG 59.424 50.000 10.00 0.00 42.46 4.00
834 835 2.644676 GGTCCCTTGAATAGAACCAGC 58.355 52.381 0.00 0.00 0.00 4.85
835 836 2.239907 GGTCCCTTGAATAGAACCAGCT 59.760 50.000 0.00 0.00 0.00 4.24
836 837 3.274288 GTCCCTTGAATAGAACCAGCTG 58.726 50.000 6.78 6.78 0.00 4.24
837 838 2.912956 TCCCTTGAATAGAACCAGCTGT 59.087 45.455 13.81 0.00 0.00 4.40
838 839 3.012518 CCCTTGAATAGAACCAGCTGTG 58.987 50.000 13.81 6.81 0.00 3.66
841 842 4.323028 CCTTGAATAGAACCAGCTGTGAGA 60.323 45.833 13.81 0.00 0.00 3.27
848 849 4.723309 AGAACCAGCTGTGAGAAAAAGAT 58.277 39.130 13.81 0.00 0.00 2.40
863 864 3.494045 AAAGATAAGAAAAGCCAGCGC 57.506 42.857 0.00 0.00 0.00 5.92
870 871 2.041366 GAAAAGCCAGCGCGATCCTC 62.041 60.000 12.10 0.00 41.18 3.71
872 873 2.527951 AAAGCCAGCGCGATCCTCTT 62.528 55.000 12.10 3.00 41.18 2.85
894 895 1.824760 CATGCATGGACATGGCGGA 60.825 57.895 19.40 0.00 43.05 5.54
896 897 1.386525 ATGCATGGACATGGCGGAAC 61.387 55.000 13.63 0.00 39.16 3.62
934 938 3.302699 GTCTACGACTCGTGCATTTTACC 59.697 47.826 14.47 0.00 41.39 2.85
942 951 4.081420 ACTCGTGCATTTTACCAGAGAGAT 60.081 41.667 0.00 0.00 0.00 2.75
955 964 2.295909 CAGAGAGATCCTTTCCGCTAGG 59.704 54.545 0.00 0.00 39.46 3.02
972 985 2.789409 AGGTAGCCGAGCAAAAATCT 57.211 45.000 0.00 0.00 0.00 2.40
1098 1116 1.006758 TGGAACCTGACGTCCTCCTAT 59.993 52.381 14.12 0.00 0.00 2.57
1669 1741 2.993008 ATGCGCCTCATGACCAGT 59.007 55.556 4.18 0.00 33.26 4.00
1864 1962 3.316573 CTTGCAGAGACCGACCCCC 62.317 68.421 0.00 0.00 0.00 5.40
2061 2159 2.045045 CGGAGCAATGGCCAAGGA 60.045 61.111 10.96 0.00 42.56 3.36
2066 2164 0.407139 AGCAATGGCCAAGGAGAAGT 59.593 50.000 10.96 0.00 42.56 3.01
2078 2176 0.459411 GGAGAAGTCGAGAAGGCAGC 60.459 60.000 0.00 0.00 0.00 5.25
2079 2177 0.244994 GAGAAGTCGAGAAGGCAGCA 59.755 55.000 0.00 0.00 0.00 4.41
2080 2178 0.901124 AGAAGTCGAGAAGGCAGCAT 59.099 50.000 0.00 0.00 0.00 3.79
2097 2195 1.584175 CATTAGCAGCAGCAGAGGAG 58.416 55.000 3.17 0.00 45.49 3.69
2193 2291 2.510238 CCCTTCTTCCTGCTCGCG 60.510 66.667 0.00 0.00 0.00 5.87
2229 2327 3.138798 GCCATGGTGCTGCTCCTG 61.139 66.667 20.19 14.98 0.00 3.86
2616 2717 4.749310 AGGCAGTTCTCCGCGCTG 62.749 66.667 5.56 2.99 0.00 5.18
2715 2816 0.749454 AGGTGAAGCATTCCATCGCC 60.749 55.000 0.00 0.00 46.93 5.54
2722 2823 0.249489 GCATTCCATCGCCGAGTACT 60.249 55.000 0.00 0.00 0.00 2.73
3315 3435 1.375396 GCTCATGGTGTACGTGGCA 60.375 57.895 0.00 0.00 36.71 4.92
3475 3919 5.373812 ACATGTTTAGGAGGAGGGTTATG 57.626 43.478 0.00 0.00 0.00 1.90
3478 3922 4.172807 TGTTTAGGAGGAGGGTTATGTGT 58.827 43.478 0.00 0.00 0.00 3.72
3484 3928 4.292306 AGGAGGAGGGTTATGTGTGAATTT 59.708 41.667 0.00 0.00 0.00 1.82
3485 3929 5.491078 AGGAGGAGGGTTATGTGTGAATTTA 59.509 40.000 0.00 0.00 0.00 1.40
3488 3932 7.996644 GGAGGAGGGTTATGTGTGAATTTATTA 59.003 37.037 0.00 0.00 0.00 0.98
3527 3975 6.092944 TGTTACCTTTAAGTGTTGTGTCAGTG 59.907 38.462 0.00 0.00 0.00 3.66
3536 3984 2.741517 TGTTGTGTCAGTGAGTTGTGTG 59.258 45.455 0.00 0.00 0.00 3.82
3566 4015 3.695556 TGATTTCCCTACGTACGTGATGA 59.304 43.478 30.25 19.11 0.00 2.92
3580 4029 3.911719 GATGAAATCACCAGCCCCT 57.088 52.632 0.00 0.00 44.70 4.79
3581 4030 2.149973 GATGAAATCACCAGCCCCTT 57.850 50.000 0.00 0.00 44.70 3.95
3610 4070 3.976793 TTGCTCTGTTTCTTGCTTCTG 57.023 42.857 0.00 0.00 0.00 3.02
3632 4092 4.225942 TGAATTCTGACTAGGACAATGCCT 59.774 41.667 7.05 2.15 42.15 4.75
3633 4093 3.616956 TTCTGACTAGGACAATGCCTG 57.383 47.619 6.50 0.97 39.08 4.85
3634 4094 2.540383 TCTGACTAGGACAATGCCTGT 58.460 47.619 6.50 3.55 42.61 4.00
3635 4095 3.708451 TCTGACTAGGACAATGCCTGTA 58.292 45.455 6.50 0.00 38.84 2.74
3647 4107 3.481903 CCTGTACGCTGCAGCACG 61.482 66.667 36.03 23.84 42.21 5.34
3813 4397 4.722700 GGCCAGCACGGTCACCAT 62.723 66.667 0.00 0.00 40.18 3.55
3849 4433 2.184322 CGCCACGTACAGCCATCT 59.816 61.111 0.00 0.00 0.00 2.90
3856 4440 1.623811 ACGTACAGCCATCTGAACCTT 59.376 47.619 0.00 0.00 42.95 3.50
3892 4476 3.006133 TGGTCGGTGGCTGCCATA 61.006 61.111 26.22 10.91 35.28 2.74
3915 4499 2.418471 GCATCAGTCTGGAACTCTGGAG 60.418 54.545 0.00 0.00 35.45 3.86
3927 4534 3.459710 ACTCTGGAGTACTGGCTAAGT 57.540 47.619 0.00 0.00 40.43 2.24
3945 4552 6.404513 GGCTAAGTTACAGTCGTTAGAGATGT 60.405 42.308 0.00 0.00 33.57 3.06
4051 4658 4.755546 CTCTCGGCGAGCGATATC 57.244 61.111 31.01 0.00 31.99 1.63
4052 4659 1.135731 CTCTCGGCGAGCGATATCC 59.864 63.158 31.01 0.00 31.99 2.59
4053 4660 2.202362 CTCGGCGAGCGATATCCG 60.202 66.667 25.31 6.73 42.96 4.18
4054 4661 2.967473 CTCGGCGAGCGATATCCGT 61.967 63.158 25.31 0.00 42.28 4.69
4055 4662 2.050351 CGGCGAGCGATATCCGTT 60.050 61.111 0.00 0.00 41.15 4.44
4056 4663 2.365068 CGGCGAGCGATATCCGTTG 61.365 63.158 0.00 0.00 41.15 4.10
4081 4688 1.208259 TGCGCGCACATGTATAAGAG 58.792 50.000 33.09 0.00 0.00 2.85
4086 4693 2.802247 GCGCACATGTATAAGAGCATCA 59.198 45.455 0.30 0.00 37.82 3.07
4133 4740 6.814043 AGAAGTAACGACAGAGTAAACCTTT 58.186 36.000 0.00 0.00 0.00 3.11
4134 4741 7.945134 AGAAGTAACGACAGAGTAAACCTTTA 58.055 34.615 0.00 0.00 0.00 1.85
4138 4745 5.779529 ACGACAGAGTAAACCTTTAGTGA 57.220 39.130 0.00 0.00 0.00 3.41
4153 4760 9.722184 AACCTTTAGTGAAGTAGTTTTATCTCC 57.278 33.333 0.00 0.00 33.29 3.71
4154 4761 9.102453 ACCTTTAGTGAAGTAGTTTTATCTCCT 57.898 33.333 0.00 0.00 33.29 3.69
4182 4789 5.754543 TTTGGTCGTTTTTAACCGATCTT 57.245 34.783 0.00 0.00 35.31 2.40
4184 4791 4.634199 TGGTCGTTTTTAACCGATCTTCT 58.366 39.130 0.00 0.00 35.31 2.85
4198 4805 7.113658 ACCGATCTTCTAAATTTAGCAGAGA 57.886 36.000 25.02 21.86 36.69 3.10
4211 4818 6.780706 TTTAGCAGAGAAAAACTTAGGTCG 57.219 37.500 0.00 0.00 0.00 4.79
4213 4820 3.071167 AGCAGAGAAAAACTTAGGTCGGT 59.929 43.478 0.00 0.00 0.00 4.69
4235 4966 1.071471 CACTCAAAGGTGCCGGACT 59.929 57.895 5.05 0.00 0.00 3.85
4238 4969 1.228124 TCAAAGGTGCCGGACTTGG 60.228 57.895 5.05 3.58 0.00 3.61
4239 4970 1.228124 CAAAGGTGCCGGACTTGGA 60.228 57.895 5.05 0.00 0.00 3.53
4240 4971 1.228154 AAAGGTGCCGGACTTGGAC 60.228 57.895 5.05 0.00 0.00 4.02
4241 4972 1.990160 AAAGGTGCCGGACTTGGACA 61.990 55.000 5.05 0.00 0.00 4.02
4242 4973 2.668550 GGTGCCGGACTTGGACAC 60.669 66.667 5.05 0.66 36.17 3.67
4243 4974 2.110213 GTGCCGGACTTGGACACA 59.890 61.111 5.05 0.00 36.60 3.72
4244 4975 1.961277 GTGCCGGACTTGGACACAG 60.961 63.158 5.05 0.00 36.60 3.66
4245 4976 2.426023 GCCGGACTTGGACACAGT 59.574 61.111 5.05 0.00 0.00 3.55
4246 4977 1.668151 GCCGGACTTGGACACAGTC 60.668 63.158 5.05 0.00 0.00 3.51
4247 4978 1.745890 CCGGACTTGGACACAGTCA 59.254 57.895 0.00 0.00 33.68 3.41
4248 4979 0.321671 CCGGACTTGGACACAGTCAT 59.678 55.000 0.00 0.00 33.68 3.06
4249 4980 1.673033 CCGGACTTGGACACAGTCATC 60.673 57.143 0.00 0.00 33.68 2.92
4250 4981 1.714794 GGACTTGGACACAGTCATCG 58.285 55.000 12.96 0.00 33.68 3.84
4251 4982 1.272490 GGACTTGGACACAGTCATCGA 59.728 52.381 12.96 0.00 33.68 3.59
4252 4983 2.600731 GACTTGGACACAGTCATCGAG 58.399 52.381 0.00 0.00 33.68 4.04
4253 4984 1.273606 ACTTGGACACAGTCATCGAGG 59.726 52.381 0.00 0.00 33.68 4.63
4254 4985 1.546029 CTTGGACACAGTCATCGAGGA 59.454 52.381 0.00 0.00 33.68 3.71
4255 4986 0.888619 TGGACACAGTCATCGAGGAC 59.111 55.000 21.99 21.99 38.08 3.85
4256 4987 0.179161 GGACACAGTCATCGAGGACG 60.179 60.000 23.00 19.31 42.62 4.79
4257 4988 0.522180 GACACAGTCATCGAGGACGT 59.478 55.000 23.00 19.90 42.62 4.34
4258 4989 0.241213 ACACAGTCATCGAGGACGTG 59.759 55.000 32.65 32.65 42.62 4.49
4259 4990 0.521735 CACAGTCATCGAGGACGTGA 59.478 55.000 31.83 13.70 42.62 4.35
4260 4991 1.068541 CACAGTCATCGAGGACGTGAA 60.069 52.381 31.83 0.25 42.62 3.18
4261 4992 1.068472 ACAGTCATCGAGGACGTGAAC 60.068 52.381 25.50 6.48 42.62 3.18
4262 4993 1.200252 CAGTCATCGAGGACGTGAACT 59.800 52.381 23.00 3.08 42.62 3.01
4263 4994 1.200252 AGTCATCGAGGACGTGAACTG 59.800 52.381 23.00 0.00 42.62 3.16
4264 4995 0.109272 TCATCGAGGACGTGAACTGC 60.109 55.000 0.00 0.00 40.69 4.40
4265 4996 0.109086 CATCGAGGACGTGAACTGCT 60.109 55.000 0.00 0.00 40.69 4.24
4266 4997 1.132453 CATCGAGGACGTGAACTGCTA 59.868 52.381 0.00 0.00 40.69 3.49
4267 4998 0.520404 TCGAGGACGTGAACTGCTAC 59.480 55.000 0.00 0.00 40.69 3.58
4268 4999 0.522180 CGAGGACGTGAACTGCTACT 59.478 55.000 0.00 0.00 34.56 2.57
4269 5000 1.736126 CGAGGACGTGAACTGCTACTA 59.264 52.381 0.00 0.00 34.56 1.82
4282 5013 3.746409 CTACTACGACCGGCGGTGC 62.746 68.421 39.41 25.24 46.49 5.01
4316 5057 0.372679 CGCAAGTATGTGCTCAGCTG 59.627 55.000 7.63 7.63 42.62 4.24
4320 5061 3.528532 CAAGTATGTGCTCAGCTGATGA 58.471 45.455 18.63 3.54 36.21 2.92
4331 5072 4.130857 CTCAGCTGATGAAAGATGCTCAT 58.869 43.478 18.63 0.00 37.52 2.90
4350 5091 8.773033 TGCTCATCATCCTAGCATATAGATAA 57.227 34.615 0.00 0.00 41.15 1.75
4351 5092 9.205513 TGCTCATCATCCTAGCATATAGATAAA 57.794 33.333 0.00 0.00 41.15 1.40
4352 5093 9.474920 GCTCATCATCCTAGCATATAGATAAAC 57.525 37.037 0.00 0.00 36.26 2.01
4355 5096 9.761504 CATCATCCTAGCATATAGATAAACTGG 57.238 37.037 0.00 0.00 0.00 4.00
4356 5097 9.720874 ATCATCCTAGCATATAGATAAACTGGA 57.279 33.333 0.00 0.00 0.00 3.86
4357 5098 9.194972 TCATCCTAGCATATAGATAAACTGGAG 57.805 37.037 0.00 0.00 0.00 3.86
4358 5099 7.411486 TCCTAGCATATAGATAAACTGGAGC 57.589 40.000 0.00 0.00 0.00 4.70
4359 5100 6.954102 TCCTAGCATATAGATAAACTGGAGCA 59.046 38.462 0.00 0.00 0.00 4.26
4360 5101 7.621285 TCCTAGCATATAGATAAACTGGAGCAT 59.379 37.037 0.00 0.00 0.00 3.79
4361 5102 8.918116 CCTAGCATATAGATAAACTGGAGCATA 58.082 37.037 0.00 0.00 0.00 3.14
4373 5114 9.851686 ATAAACTGGAGCATATATTTGTCAAGA 57.148 29.630 6.95 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.785453 CAACCTCGCCCCTCTGCC 62.785 72.222 0.00 0.00 0.00 4.85
4 5 2.581354 CTCAACCTCGCCCCTCTG 59.419 66.667 0.00 0.00 0.00 3.35
5 6 3.394836 GCTCAACCTCGCCCCTCT 61.395 66.667 0.00 0.00 0.00 3.69
6 7 4.821589 CGCTCAACCTCGCCCCTC 62.822 72.222 0.00 0.00 0.00 4.30
23 24 1.733041 TGTACACGCTCGAGCAAGC 60.733 57.895 34.69 19.78 42.21 4.01
24 25 0.663269 TGTGTACACGCTCGAGCAAG 60.663 55.000 34.69 27.25 42.21 4.01
25 26 0.038618 ATGTGTACACGCTCGAGCAA 60.039 50.000 34.69 15.56 42.21 3.91
26 27 0.456142 GATGTGTACACGCTCGAGCA 60.456 55.000 34.69 14.70 42.21 4.26
27 28 0.179161 AGATGTGTACACGCTCGAGC 60.179 55.000 27.64 27.64 37.78 5.03
28 29 1.914051 CAAGATGTGTACACGCTCGAG 59.086 52.381 20.61 8.45 0.00 4.04
29 30 1.402325 CCAAGATGTGTACACGCTCGA 60.402 52.381 20.61 3.42 0.00 4.04
30 31 0.992072 CCAAGATGTGTACACGCTCG 59.008 55.000 20.61 10.08 0.00 5.03
31 32 2.363788 TCCAAGATGTGTACACGCTC 57.636 50.000 20.61 18.36 0.00 5.03
32 33 2.037251 ACTTCCAAGATGTGTACACGCT 59.963 45.455 20.61 16.81 0.00 5.07
33 34 2.413837 ACTTCCAAGATGTGTACACGC 58.586 47.619 20.61 14.88 0.00 5.34
34 35 4.055360 TGAACTTCCAAGATGTGTACACG 58.945 43.478 20.61 6.21 0.00 4.49
35 36 5.934625 AGATGAACTTCCAAGATGTGTACAC 59.065 40.000 19.36 19.36 0.00 2.90
36 37 5.934043 CAGATGAACTTCCAAGATGTGTACA 59.066 40.000 0.00 0.00 0.00 2.90
37 38 5.352569 CCAGATGAACTTCCAAGATGTGTAC 59.647 44.000 0.00 0.00 0.00 2.90
38 39 5.491070 CCAGATGAACTTCCAAGATGTGTA 58.509 41.667 0.00 0.00 0.00 2.90
39 40 4.330250 CCAGATGAACTTCCAAGATGTGT 58.670 43.478 0.00 0.00 0.00 3.72
40 41 3.128242 GCCAGATGAACTTCCAAGATGTG 59.872 47.826 0.00 0.00 0.00 3.21
41 42 3.350833 GCCAGATGAACTTCCAAGATGT 58.649 45.455 0.00 0.00 0.00 3.06
42 43 2.686915 GGCCAGATGAACTTCCAAGATG 59.313 50.000 0.00 0.00 0.00 2.90
43 44 2.681976 CGGCCAGATGAACTTCCAAGAT 60.682 50.000 2.24 0.00 0.00 2.40
44 45 1.339055 CGGCCAGATGAACTTCCAAGA 60.339 52.381 2.24 0.00 0.00 3.02
45 46 1.089920 CGGCCAGATGAACTTCCAAG 58.910 55.000 2.24 0.00 0.00 3.61
46 47 0.960364 GCGGCCAGATGAACTTCCAA 60.960 55.000 2.24 0.00 0.00 3.53
47 48 1.377202 GCGGCCAGATGAACTTCCA 60.377 57.895 2.24 0.00 0.00 3.53
48 49 2.464459 CGCGGCCAGATGAACTTCC 61.464 63.158 2.24 0.00 0.00 3.46
49 50 3.093278 CGCGGCCAGATGAACTTC 58.907 61.111 2.24 0.00 0.00 3.01
50 51 3.127533 GCGCGGCCAGATGAACTT 61.128 61.111 8.83 0.00 0.00 2.66
136 137 4.516195 GAACTCCGGCTCGCCCTC 62.516 72.222 0.00 0.00 0.00 4.30
161 162 1.370172 GCTACACCGCGGAGATACG 60.370 63.158 35.90 15.33 0.00 3.06
162 163 0.317938 CAGCTACACCGCGGAGATAC 60.318 60.000 35.90 17.91 34.40 2.24
163 164 2.030551 CAGCTACACCGCGGAGATA 58.969 57.895 35.90 18.95 34.40 1.98
164 165 2.808315 CAGCTACACCGCGGAGAT 59.192 61.111 35.90 15.83 34.40 2.75
165 166 4.129737 GCAGCTACACCGCGGAGA 62.130 66.667 35.90 15.31 34.40 3.71
172 173 2.746277 CCCAACGGCAGCTACACC 60.746 66.667 0.00 0.00 0.00 4.16
649 650 0.313987 GCACGGTAAAGGCAGCTTTT 59.686 50.000 7.74 7.74 0.00 2.27
650 651 1.852067 CGCACGGTAAAGGCAGCTTT 61.852 55.000 0.00 0.00 0.00 3.51
651 652 2.325082 CGCACGGTAAAGGCAGCTT 61.325 57.895 0.00 0.00 0.00 3.74
652 653 2.742372 CGCACGGTAAAGGCAGCT 60.742 61.111 0.00 0.00 0.00 4.24
653 654 4.460873 GCGCACGGTAAAGGCAGC 62.461 66.667 0.30 0.00 0.00 5.25
654 655 4.147322 CGCGCACGGTAAAGGCAG 62.147 66.667 8.75 0.00 34.97 4.85
676 677 0.878523 CCAACAGTCGCTCCAAACGA 60.879 55.000 0.00 0.00 37.17 3.85
677 678 0.878523 TCCAACAGTCGCTCCAAACG 60.879 55.000 0.00 0.00 0.00 3.60
678 679 0.868406 CTCCAACAGTCGCTCCAAAC 59.132 55.000 0.00 0.00 0.00 2.93
679 680 0.756294 TCTCCAACAGTCGCTCCAAA 59.244 50.000 0.00 0.00 0.00 3.28
680 681 0.976641 ATCTCCAACAGTCGCTCCAA 59.023 50.000 0.00 0.00 0.00 3.53
681 682 0.247460 CATCTCCAACAGTCGCTCCA 59.753 55.000 0.00 0.00 0.00 3.86
682 683 1.086634 GCATCTCCAACAGTCGCTCC 61.087 60.000 0.00 0.00 0.00 4.70
683 684 0.108424 AGCATCTCCAACAGTCGCTC 60.108 55.000 0.00 0.00 0.00 5.03
684 685 0.108424 GAGCATCTCCAACAGTCGCT 60.108 55.000 0.00 0.00 34.58 4.93
685 686 2.378028 GAGCATCTCCAACAGTCGC 58.622 57.895 0.00 0.00 0.00 5.19
697 698 3.753272 TGGTGCTTCAAACTTAGAGCATC 59.247 43.478 0.00 0.34 34.72 3.91
698 699 3.754965 TGGTGCTTCAAACTTAGAGCAT 58.245 40.909 0.00 0.00 34.72 3.79
699 700 3.207265 TGGTGCTTCAAACTTAGAGCA 57.793 42.857 0.00 0.00 0.00 4.26
700 701 3.565902 AGTTGGTGCTTCAAACTTAGAGC 59.434 43.478 0.00 0.00 0.00 4.09
701 702 4.816385 TCAGTTGGTGCTTCAAACTTAGAG 59.184 41.667 0.67 0.00 0.00 2.43
702 703 4.574828 GTCAGTTGGTGCTTCAAACTTAGA 59.425 41.667 0.67 0.00 0.00 2.10
703 704 4.261197 GGTCAGTTGGTGCTTCAAACTTAG 60.261 45.833 0.67 0.00 0.00 2.18
704 705 3.630312 GGTCAGTTGGTGCTTCAAACTTA 59.370 43.478 0.67 0.00 0.00 2.24
705 706 2.427095 GGTCAGTTGGTGCTTCAAACTT 59.573 45.455 0.67 0.00 0.00 2.66
706 707 2.024414 GGTCAGTTGGTGCTTCAAACT 58.976 47.619 0.00 0.00 0.00 2.66
707 708 1.748493 TGGTCAGTTGGTGCTTCAAAC 59.252 47.619 0.00 0.00 0.00 2.93
708 709 2.136298 TGGTCAGTTGGTGCTTCAAA 57.864 45.000 0.00 0.00 0.00 2.69
709 710 1.748493 GTTGGTCAGTTGGTGCTTCAA 59.252 47.619 0.00 0.00 0.00 2.69
710 711 1.340502 TGTTGGTCAGTTGGTGCTTCA 60.341 47.619 0.00 0.00 0.00 3.02
711 712 1.334869 CTGTTGGTCAGTTGGTGCTTC 59.665 52.381 0.00 0.00 39.17 3.86
712 713 1.392589 CTGTTGGTCAGTTGGTGCTT 58.607 50.000 0.00 0.00 39.17 3.91
713 714 3.100545 CTGTTGGTCAGTTGGTGCT 57.899 52.632 0.00 0.00 39.17 4.40
722 723 1.052617 TTCGATCCCACTGTTGGTCA 58.947 50.000 0.00 0.00 42.10 4.02
747 748 1.901948 TCACTGTTCCCGCTCGTCT 60.902 57.895 0.00 0.00 0.00 4.18
752 753 1.990160 TTTGGGTCACTGTTCCCGCT 61.990 55.000 11.57 0.00 46.13 5.52
766 767 8.442384 GCAATGTGAAACTAACATAAATTTGGG 58.558 33.333 0.00 0.00 37.27 4.12
769 770 9.423061 GAGGCAATGTGAAACTAACATAAATTT 57.577 29.630 0.00 0.00 37.27 1.82
772 773 7.759489 AGAGGCAATGTGAAACTAACATAAA 57.241 32.000 0.00 0.00 37.27 1.40
780 781 4.460263 TGTGTTAGAGGCAATGTGAAACT 58.540 39.130 0.00 0.00 38.04 2.66
795 796 4.142138 GGACCCATCTGTACTCTGTGTTAG 60.142 50.000 0.00 0.00 0.00 2.34
796 797 3.767673 GGACCCATCTGTACTCTGTGTTA 59.232 47.826 0.00 0.00 0.00 2.41
797 798 2.567615 GGACCCATCTGTACTCTGTGTT 59.432 50.000 0.00 0.00 0.00 3.32
798 799 2.180276 GGACCCATCTGTACTCTGTGT 58.820 52.381 0.00 0.00 0.00 3.72
799 800 1.482593 GGGACCCATCTGTACTCTGTG 59.517 57.143 5.33 0.00 0.00 3.66
800 801 1.362932 AGGGACCCATCTGTACTCTGT 59.637 52.381 14.60 0.00 0.00 3.41
801 802 2.166907 AGGGACCCATCTGTACTCTG 57.833 55.000 14.60 0.00 0.00 3.35
802 803 2.044492 TCAAGGGACCCATCTGTACTCT 59.956 50.000 14.60 0.00 0.00 3.24
804 805 2.642171 TCAAGGGACCCATCTGTACT 57.358 50.000 14.60 0.00 0.00 2.73
806 807 4.890988 TCTATTCAAGGGACCCATCTGTA 58.109 43.478 14.60 1.14 0.00 2.74
816 817 2.912956 ACAGCTGGTTCTATTCAAGGGA 59.087 45.455 19.93 0.00 0.00 4.20
819 820 4.825422 TCTCACAGCTGGTTCTATTCAAG 58.175 43.478 19.93 0.36 0.00 3.02
822 823 6.428159 TCTTTTTCTCACAGCTGGTTCTATTC 59.572 38.462 19.93 0.00 0.00 1.75
824 825 5.869579 TCTTTTTCTCACAGCTGGTTCTAT 58.130 37.500 19.93 0.00 0.00 1.98
826 827 4.156455 TCTTTTTCTCACAGCTGGTTCT 57.844 40.909 19.93 0.00 0.00 3.01
828 829 6.299141 TCTTATCTTTTTCTCACAGCTGGTT 58.701 36.000 19.93 0.00 0.00 3.67
829 830 5.869579 TCTTATCTTTTTCTCACAGCTGGT 58.130 37.500 19.93 0.24 0.00 4.00
830 831 6.808008 TTCTTATCTTTTTCTCACAGCTGG 57.192 37.500 19.93 7.28 0.00 4.85
831 832 7.325579 GCTTTTCTTATCTTTTTCTCACAGCTG 59.674 37.037 13.48 13.48 0.00 4.24
832 833 7.366513 GCTTTTCTTATCTTTTTCTCACAGCT 58.633 34.615 0.00 0.00 0.00 4.24
833 834 6.584184 GGCTTTTCTTATCTTTTTCTCACAGC 59.416 38.462 0.00 0.00 0.00 4.40
834 835 7.651808 TGGCTTTTCTTATCTTTTTCTCACAG 58.348 34.615 0.00 0.00 0.00 3.66
835 836 7.581213 TGGCTTTTCTTATCTTTTTCTCACA 57.419 32.000 0.00 0.00 0.00 3.58
836 837 6.584184 GCTGGCTTTTCTTATCTTTTTCTCAC 59.416 38.462 0.00 0.00 0.00 3.51
837 838 6.568462 CGCTGGCTTTTCTTATCTTTTTCTCA 60.568 38.462 0.00 0.00 0.00 3.27
838 839 5.797434 CGCTGGCTTTTCTTATCTTTTTCTC 59.203 40.000 0.00 0.00 0.00 2.87
841 842 4.237724 GCGCTGGCTTTTCTTATCTTTTT 58.762 39.130 0.00 0.00 35.83 1.94
848 849 1.006832 GATCGCGCTGGCTTTTCTTA 58.993 50.000 5.56 0.00 36.88 2.10
863 864 3.741860 GCATGGGCAAGAGGATCG 58.258 61.111 0.00 0.00 39.54 3.69
894 895 1.203287 GACTTTCTACTACGGCCGGTT 59.797 52.381 31.76 15.49 0.00 4.44
896 897 1.101331 AGACTTTCTACTACGGCCGG 58.899 55.000 31.76 15.62 0.00 6.13
923 927 4.775236 AGGATCTCTCTGGTAAAATGCAC 58.225 43.478 0.00 0.00 0.00 4.57
934 938 2.295909 CCTAGCGGAAAGGATCTCTCTG 59.704 54.545 0.00 0.00 36.08 3.35
955 964 3.241995 CGTGTAGATTTTTGCTCGGCTAC 60.242 47.826 0.00 0.00 0.00 3.58
966 979 2.450609 ACGGAGTGCGTGTAGATTTT 57.549 45.000 9.56 0.00 42.51 1.82
1098 1116 3.573772 CTCGTTGCTCTGGTCCGCA 62.574 63.158 0.00 0.00 0.00 5.69
1857 1955 3.787001 GAGCCAAGGAGGGGGTCG 61.787 72.222 0.00 0.00 42.40 4.79
1864 1962 2.182030 GTCGACGGAGCCAAGGAG 59.818 66.667 0.00 0.00 0.00 3.69
2061 2159 0.901124 ATGCTGCCTTCTCGACTTCT 59.099 50.000 0.00 0.00 0.00 2.85
2066 2164 0.536724 TGCTAATGCTGCCTTCTCGA 59.463 50.000 0.00 0.00 40.48 4.04
2078 2176 1.134461 ACTCCTCTGCTGCTGCTAATG 60.134 52.381 17.00 4.89 40.48 1.90
2079 2177 1.202330 ACTCCTCTGCTGCTGCTAAT 58.798 50.000 17.00 0.00 40.48 1.73
2080 2178 0.979665 AACTCCTCTGCTGCTGCTAA 59.020 50.000 17.00 3.91 40.48 3.09
2097 2195 2.814336 GTCCTTCATCACCTGGAACAAC 59.186 50.000 0.00 0.00 38.70 3.32
2167 2265 2.351276 GAAGAAGGGGCTCGCCAA 59.649 61.111 10.51 0.00 37.98 4.52
2193 2291 1.817209 CGGGAGGAGCAGGTAGTTC 59.183 63.158 0.00 0.00 0.00 3.01
2229 2327 1.868251 GACGACGATGACGAGGCAC 60.868 63.158 0.00 0.00 42.66 5.01
2270 2368 0.603707 CAGGCTGTGGAAAGCGAAGA 60.604 55.000 6.28 0.00 44.52 2.87
2277 2375 1.376466 GCTCCTCAGGCTGTGGAAA 59.624 57.895 31.43 15.98 39.27 3.13
2364 2462 1.248785 TGGAGAAGAAGACCGACGGG 61.249 60.000 20.00 0.00 40.11 5.28
2616 2717 3.827898 CCGAGACGGCAGGACCTC 61.828 72.222 0.00 0.00 41.17 3.85
2715 2816 2.626892 GACGTCGCTGATAAGTACTCG 58.373 52.381 0.00 0.00 0.00 4.18
3174 3294 1.519455 CGACATCTCCGCCAACTCC 60.519 63.158 0.00 0.00 0.00 3.85
3178 3298 4.812476 CGCCGACATCTCCGCCAA 62.812 66.667 0.00 0.00 0.00 4.52
3444 3888 4.473196 TCCTCCTAAACATGTTCCATGCTA 59.527 41.667 12.39 0.00 0.00 3.49
3504 3948 6.408035 TCACTGACACAACACTTAAAGGTAA 58.592 36.000 0.00 0.00 0.00 2.85
3508 3952 6.128282 ACAACTCACTGACACAACACTTAAAG 60.128 38.462 0.00 0.00 0.00 1.85
3515 3959 2.741517 CACACAACTCACTGACACAACA 59.258 45.455 0.00 0.00 0.00 3.33
3521 3969 3.982475 TCTGATCACACAACTCACTGAC 58.018 45.455 0.00 0.00 0.00 3.51
3527 3975 6.404074 GGGAAATCATTCTGATCACACAACTC 60.404 42.308 0.00 0.00 35.76 3.01
3536 3984 5.629849 CGTACGTAGGGAAATCATTCTGATC 59.370 44.000 7.22 0.00 35.76 2.92
3550 3999 4.036567 TGATTTCATCACGTACGTAGGG 57.963 45.455 22.34 12.88 33.59 3.53
3566 4015 0.190815 ACCAAAGGGGCTGGTGATTT 59.809 50.000 0.00 0.00 45.67 2.17
3577 4026 4.871933 ACAGAGCAAATTAACCAAAGGG 57.128 40.909 0.00 0.00 41.29 3.95
3578 4027 6.515832 AGAAACAGAGCAAATTAACCAAAGG 58.484 36.000 0.00 0.00 0.00 3.11
3579 4028 7.517259 GCAAGAAACAGAGCAAATTAACCAAAG 60.517 37.037 0.00 0.00 0.00 2.77
3580 4029 6.257630 GCAAGAAACAGAGCAAATTAACCAAA 59.742 34.615 0.00 0.00 0.00 3.28
3581 4030 5.752955 GCAAGAAACAGAGCAAATTAACCAA 59.247 36.000 0.00 0.00 0.00 3.67
3610 4070 4.574013 CAGGCATTGTCCTAGTCAGAATTC 59.426 45.833 0.00 0.00 33.95 2.17
3647 4107 3.866582 CTGCCGGAGTCCATCCCC 61.867 72.222 5.05 0.00 46.50 4.81
3867 4451 2.046892 CCACCGACCAGAGCAAGG 60.047 66.667 0.00 0.00 0.00 3.61
3892 4476 2.093075 CCAGAGTTCCAGACTGATGCAT 60.093 50.000 0.00 0.00 39.19 3.96
3899 4483 3.426615 CAGTACTCCAGAGTTCCAGACT 58.573 50.000 5.49 0.08 42.54 3.24
3915 4499 4.431661 ACGACTGTAACTTAGCCAGTAC 57.568 45.455 0.00 0.00 39.43 2.73
3927 4534 5.409520 ACGTGTACATCTCTAACGACTGTAA 59.590 40.000 0.00 0.00 37.66 2.41
3945 4552 4.211164 GCTAATTGATGCATGCTACGTGTA 59.789 41.667 20.33 4.08 0.00 2.90
4049 4656 0.041312 GCGCGCATAATTCAACGGAT 60.041 50.000 29.10 0.00 0.00 4.18
4051 4658 1.061729 TGCGCGCATAATTCAACGG 59.938 52.632 33.09 0.00 0.00 4.44
4052 4659 0.520205 TGTGCGCGCATAATTCAACG 60.520 50.000 38.62 0.00 0.00 4.10
4053 4660 1.513994 CATGTGCGCGCATAATTCAAC 59.486 47.619 38.62 21.70 0.00 3.18
4054 4661 1.132073 ACATGTGCGCGCATAATTCAA 59.868 42.857 38.62 16.62 0.00 2.69
4055 4662 0.731994 ACATGTGCGCGCATAATTCA 59.268 45.000 38.62 29.05 0.00 2.57
4056 4663 2.661504 TACATGTGCGCGCATAATTC 57.338 45.000 38.62 24.07 0.00 2.17
4111 4718 7.650903 CACTAAAGGTTTACTCTGTCGTTACTT 59.349 37.037 0.00 0.00 0.00 2.24
4118 4725 8.358895 ACTACTTCACTAAAGGTTTACTCTGTC 58.641 37.037 0.00 0.00 39.47 3.51
4119 4726 8.247666 ACTACTTCACTAAAGGTTTACTCTGT 57.752 34.615 0.00 0.00 39.47 3.41
4129 4736 9.945904 AAGGAGATAAAACTACTTCACTAAAGG 57.054 33.333 0.00 0.00 36.44 3.11
4149 4756 9.518906 GTTAAAAACGACCAAAATTTAAGGAGA 57.481 29.630 14.59 0.00 0.00 3.71
4153 4760 8.337741 TCGGTTAAAAACGACCAAAATTTAAG 57.662 30.769 0.00 0.00 33.69 1.85
4154 4761 8.868635 ATCGGTTAAAAACGACCAAAATTTAA 57.131 26.923 4.77 0.00 42.39 1.52
4171 4778 9.314321 CTCTGCTAAATTTAGAAGATCGGTTAA 57.686 33.333 28.69 10.42 42.96 2.01
4174 4781 7.113658 TCTCTGCTAAATTTAGAAGATCGGT 57.886 36.000 28.69 0.00 42.96 4.69
4193 4800 5.120363 GCTTACCGACCTAAGTTTTTCTCTG 59.880 44.000 0.00 0.00 0.00 3.35
4198 4805 4.711399 AGTGCTTACCGACCTAAGTTTTT 58.289 39.130 0.00 0.00 0.00 1.94
4207 4814 1.270678 ACCTTTGAGTGCTTACCGACC 60.271 52.381 0.00 0.00 0.00 4.79
4208 4815 1.798813 CACCTTTGAGTGCTTACCGAC 59.201 52.381 0.00 0.00 0.00 4.79
4235 4966 1.272490 GTCCTCGATGACTGTGTCCAA 59.728 52.381 12.95 0.00 32.39 3.53
4238 4969 0.522180 ACGTCCTCGATGACTGTGTC 59.478 55.000 17.14 0.00 40.62 3.67
4239 4970 0.241213 CACGTCCTCGATGACTGTGT 59.759 55.000 23.63 12.72 40.62 3.72
4240 4971 0.521735 TCACGTCCTCGATGACTGTG 59.478 55.000 24.81 24.81 39.19 3.66
4241 4972 1.068472 GTTCACGTCCTCGATGACTGT 60.068 52.381 17.14 13.59 40.62 3.55
4242 4973 1.200252 AGTTCACGTCCTCGATGACTG 59.800 52.381 17.14 13.86 40.62 3.51
4243 4974 1.200252 CAGTTCACGTCCTCGATGACT 59.800 52.381 17.14 3.72 40.62 3.41
4244 4975 1.618861 CAGTTCACGTCCTCGATGAC 58.381 55.000 10.48 10.48 40.62 3.06
4245 4976 0.109272 GCAGTTCACGTCCTCGATGA 60.109 55.000 0.00 0.00 40.62 2.92
4246 4977 0.109086 AGCAGTTCACGTCCTCGATG 60.109 55.000 0.00 0.00 40.62 3.84
4247 4978 1.132643 GTAGCAGTTCACGTCCTCGAT 59.867 52.381 0.00 0.00 40.62 3.59
4248 4979 0.520404 GTAGCAGTTCACGTCCTCGA 59.480 55.000 0.00 0.00 40.62 4.04
4249 4980 0.522180 AGTAGCAGTTCACGTCCTCG 59.478 55.000 0.00 0.00 43.34 4.63
4250 4981 2.475852 CGTAGTAGCAGTTCACGTCCTC 60.476 54.545 0.00 0.00 0.00 3.71
4251 4982 1.467734 CGTAGTAGCAGTTCACGTCCT 59.532 52.381 0.00 0.00 0.00 3.85
4252 4983 1.466167 TCGTAGTAGCAGTTCACGTCC 59.534 52.381 0.00 0.00 34.39 4.79
4253 4984 2.503871 GTCGTAGTAGCAGTTCACGTC 58.496 52.381 0.00 0.00 34.39 4.34
4254 4985 1.198637 GGTCGTAGTAGCAGTTCACGT 59.801 52.381 0.00 0.00 34.39 4.49
4255 4986 1.789410 CGGTCGTAGTAGCAGTTCACG 60.789 57.143 0.00 0.00 0.00 4.35
4256 4987 1.467035 CCGGTCGTAGTAGCAGTTCAC 60.467 57.143 0.00 0.00 0.00 3.18
4257 4988 0.806868 CCGGTCGTAGTAGCAGTTCA 59.193 55.000 0.00 0.00 0.00 3.18
4258 4989 0.525029 GCCGGTCGTAGTAGCAGTTC 60.525 60.000 1.90 0.00 0.00 3.01
4259 4990 1.509923 GCCGGTCGTAGTAGCAGTT 59.490 57.895 1.90 0.00 0.00 3.16
4260 4991 2.758089 CGCCGGTCGTAGTAGCAGT 61.758 63.158 1.90 0.00 0.00 4.40
4261 4992 2.024305 CGCCGGTCGTAGTAGCAG 59.976 66.667 1.90 0.00 0.00 4.24
4262 4993 3.511595 CCGCCGGTCGTAGTAGCA 61.512 66.667 15.38 0.00 36.19 3.49
4263 4994 3.512516 ACCGCCGGTCGTAGTAGC 61.513 66.667 1.02 0.00 36.19 3.58
4264 4995 2.406401 CACCGCCGGTCGTAGTAG 59.594 66.667 5.41 0.00 31.02 2.57
4265 4996 3.814268 GCACCGCCGGTCGTAGTA 61.814 66.667 5.41 0.00 31.02 1.82
4331 5072 9.194972 CTCCAGTTTATCTATATGCTAGGATGA 57.805 37.037 7.05 0.00 0.00 2.92
4348 5089 9.679661 TTCTTGACAAATATATGCTCCAGTTTA 57.320 29.630 0.00 0.00 0.00 2.01
4349 5090 8.579850 TTCTTGACAAATATATGCTCCAGTTT 57.420 30.769 0.00 0.00 0.00 2.66
4350 5091 8.579850 TTTCTTGACAAATATATGCTCCAGTT 57.420 30.769 0.00 0.00 0.00 3.16
4351 5092 8.579850 TTTTCTTGACAAATATATGCTCCAGT 57.420 30.769 0.00 0.00 0.00 4.00
4360 5101 9.944663 GGCGTCATATTTTTCTTGACAAATATA 57.055 29.630 11.87 3.05 39.75 0.86
4361 5102 8.465999 TGGCGTCATATTTTTCTTGACAAATAT 58.534 29.630 8.23 8.23 39.75 1.28
4362 5103 7.821652 TGGCGTCATATTTTTCTTGACAAATA 58.178 30.769 0.00 4.95 39.75 1.40


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

AutoCloner maintained by Alex Coulton.