Multiple sequence alignment - TraesCS5B01G517500

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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 TraesCS5B01G517500 chr5B 100.000 6993 0 0 1 6993 680917435 680924427 0.000000e+00 12914.0
1 TraesCS5B01G517500 chr5B 79.350 615 71 28 6016 6627 501484604 501484043 1.420000e-101 381.0
2 TraesCS5B01G517500 chr5B 86.747 166 20 2 1272 1436 395925712 395925548 4.310000e-42 183.0
3 TraesCS5B01G517500 chr5D 92.102 7128 280 105 7 6993 539216818 539223803 0.000000e+00 9782.0
4 TraesCS5B01G517500 chr5D 81.157 536 43 28 6023 6552 2530201 2529718 1.840000e-100 377.0
5 TraesCS5B01G517500 chr5D 82.489 474 36 23 6016 6485 558059470 558059040 8.570000e-99 372.0
6 TraesCS5B01G517500 chr5D 92.063 126 10 0 1311 1436 337305489 337305364 2.000000e-40 178.0
7 TraesCS5B01G517500 chr5D 100.000 55 0 0 2386 2440 539219138 539219192 1.240000e-17 102.0
8 TraesCS5B01G517500 chr4A 91.296 6939 315 122 4 6816 629366621 629359846 0.000000e+00 9201.0
9 TraesCS5B01G517500 chr4A 94.898 98 5 0 6893 6990 629359605 629359508 3.380000e-33 154.0
10 TraesCS5B01G517500 chr4A 98.077 52 1 0 2389 2440 629364334 629364283 2.690000e-14 91.6
11 TraesCS5B01G517500 chr3B 79.741 617 59 37 6016 6627 573316232 573315677 3.060000e-103 387.0
12 TraesCS5B01G517500 chr3B 79.545 616 67 31 6016 6627 361841206 361841766 1.100000e-102 385.0
13 TraesCS5B01G517500 chr6B 77.060 619 76 31 6016 6627 33235405 33234846 5.300000e-76 296.0
14 TraesCS5B01G517500 chr6B 84.685 111 17 0 1854 1964 393598479 393598369 2.060000e-20 111.0
15 TraesCS5B01G517500 chr6A 77.986 427 89 4 5502 5924 47902516 47902941 5.380000e-66 263.0
16 TraesCS5B01G517500 chr5A 87.349 166 19 2 1272 1436 438475695 438475531 9.260000e-44 189.0
17 TraesCS5B01G517500 chr2D 82.143 112 18 2 1854 1964 618091928 618092038 2.080000e-15 95.3
18 TraesCS5B01G517500 chr2D 81.651 109 18 2 1857 1964 486315583 486315476 9.660000e-14 89.8


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 TraesCS5B01G517500 chr5B 680917435 680924427 6992 False 12914.000000 12914 100.000 1 6993 1 chr5B.!!$F1 6992
1 TraesCS5B01G517500 chr5B 501484043 501484604 561 True 381.000000 381 79.350 6016 6627 1 chr5B.!!$R2 611
2 TraesCS5B01G517500 chr5D 539216818 539223803 6985 False 9782.000000 9782 92.102 7 6993 1 chr5D.!!$F1 6986
3 TraesCS5B01G517500 chr4A 629359508 629366621 7113 True 3148.866667 9201 94.757 4 6990 3 chr4A.!!$R1 6986
4 TraesCS5B01G517500 chr3B 573315677 573316232 555 True 387.000000 387 79.741 6016 6627 1 chr3B.!!$R1 611
5 TraesCS5B01G517500 chr3B 361841206 361841766 560 False 385.000000 385 79.545 6016 6627 1 chr3B.!!$F1 611
6 TraesCS5B01G517500 chr6B 33234846 33235405 559 True 296.000000 296 77.060 6016 6627 1 chr6B.!!$R1 611

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
425 460 0.039256 GCACATGCGGCTCAAGAAAA 60.039 50.0 0.00 0.00 0.00 2.29 F
1536 1657 0.179067 TTGACGCGTTTTCTGGTCCT 60.179 50.0 15.53 0.00 0.00 3.85 F
2982 3120 0.108281 GGGAGACTTACCTTGACCGC 60.108 60.0 0.00 0.00 0.00 5.68 F
4328 4482 0.106015 AAGGCCCCATCTATGTTGGC 60.106 55.0 0.00 10.68 40.83 4.52 F
5263 5419 0.324943 TTCCACTTCTGGCCTACTGC 59.675 55.0 3.32 0.00 37.49 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2044 0.624795 GGTGGATCCTCTTTCCCCCT 60.625 60.0 14.23 0.0 28.94 4.79 R
3076 3214 0.955919 GGCCTTCCTTGTCGAACCTG 60.956 60.0 0.00 0.0 0.00 4.00 R
4860 5016 0.250640 AGCAACCAAGCTCCTGACTG 60.251 55.0 0.00 0.0 42.18 3.51 R
5797 5953 0.605319 GGACAATCACCCAGAACGCA 60.605 55.0 0.00 0.0 0.00 5.24 R
6672 6883 0.323178 AGAATCCTGGCCTTGCACTG 60.323 55.0 3.32 0.0 0.00 3.66 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
30 31 9.273016 TCTTTCCAGAAGAACAAACATTAGTAG 57.727 33.333 0.00 0.00 32.95 2.57
31 32 8.974060 TTTCCAGAAGAACAAACATTAGTAGT 57.026 30.769 0.00 0.00 32.95 2.73
59 60 5.719563 AGTAAATCCCTTTTTGTACCATGGG 59.280 40.000 18.09 0.00 36.14 4.00
86 87 2.037136 CCCAAGCAGCGACCTTCTG 61.037 63.158 0.00 0.00 34.79 3.02
88 89 2.359230 AAGCAGCGACCTTCTGGC 60.359 61.111 0.00 0.00 36.63 4.85
102 103 0.772124 TCTGGCCTCCTTTCCCAAGT 60.772 55.000 3.32 0.00 0.00 3.16
103 104 0.113190 CTGGCCTCCTTTCCCAAGTT 59.887 55.000 3.32 0.00 0.00 2.66
104 105 0.560688 TGGCCTCCTTTCCCAAGTTT 59.439 50.000 3.32 0.00 0.00 2.66
112 114 2.419851 CCTTTCCCAAGTTTGCAAAGCA 60.420 45.455 13.26 0.00 36.47 3.91
123 125 0.254178 TGCAAAGCAGAGGATCCTCC 59.746 55.000 33.81 21.49 43.70 4.30
166 169 6.705825 GGCTACCAAATTTTCATTTTCACACT 59.294 34.615 0.00 0.00 29.41 3.55
171 174 8.206189 ACCAAATTTTCATTTTCACACTCTGAT 58.794 29.630 0.00 0.00 29.41 2.90
173 176 9.472361 CAAATTTTCATTTTCACACTCTGATCT 57.528 29.630 0.00 0.00 29.41 2.75
182 185 7.430992 TTTCACACTCTGATCTTTGATCTTG 57.569 36.000 8.71 3.06 0.00 3.02
211 219 1.740025 GAAATAGATAGCGCCCATGCC 59.260 52.381 2.29 0.00 34.65 4.40
224 232 0.447801 CCATGCCGTTTTTCCTCTCG 59.552 55.000 0.00 0.00 0.00 4.04
226 234 1.394917 CATGCCGTTTTTCCTCTCGAG 59.605 52.381 5.93 5.93 0.00 4.04
227 235 0.677288 TGCCGTTTTTCCTCTCGAGA 59.323 50.000 15.70 15.70 0.00 4.04
280 290 1.901464 GACACCCCAACCAACGCAT 60.901 57.895 0.00 0.00 0.00 4.73
291 301 4.162690 AACGCATCCCCGCTCTCC 62.163 66.667 0.00 0.00 0.00 3.71
297 307 3.460478 ATCCCCGCTCTCCCTCTCC 62.460 68.421 0.00 0.00 0.00 3.71
403 438 0.829990 CTCCTCCCCTTTCTCTCTGC 59.170 60.000 0.00 0.00 0.00 4.26
423 458 3.266964 GCACATGCGGCTCAAGAA 58.733 55.556 0.00 0.00 0.00 2.52
424 459 1.580942 GCACATGCGGCTCAAGAAA 59.419 52.632 0.00 0.00 0.00 2.52
425 460 0.039256 GCACATGCGGCTCAAGAAAA 60.039 50.000 0.00 0.00 0.00 2.29
492 527 2.549349 CCGTGGTTACAAGCAAGGTACT 60.549 50.000 15.25 0.00 46.35 2.73
493 528 2.735134 CGTGGTTACAAGCAAGGTACTC 59.265 50.000 0.00 0.00 38.49 2.59
494 529 3.072211 GTGGTTACAAGCAAGGTACTCC 58.928 50.000 0.00 0.00 38.49 3.85
496 531 4.020839 GTGGTTACAAGCAAGGTACTCCTA 60.021 45.833 0.00 0.00 44.35 2.94
497 532 4.020839 TGGTTACAAGCAAGGTACTCCTAC 60.021 45.833 0.00 0.00 44.35 3.18
515 550 3.910767 CCTACCGATTATTAACTCGTCGC 59.089 47.826 0.00 0.00 33.11 5.19
516 551 3.425577 ACCGATTATTAACTCGTCGCA 57.574 42.857 0.00 0.00 33.11 5.10
517 552 3.772932 ACCGATTATTAACTCGTCGCAA 58.227 40.909 0.00 0.00 33.11 4.85
592 630 0.543174 AGAGAGAGAAACGCAGGGGT 60.543 55.000 0.00 0.00 0.00 4.95
593 631 0.390472 GAGAGAGAAACGCAGGGGTG 60.390 60.000 0.00 0.00 0.00 4.61
594 632 1.122019 AGAGAGAAACGCAGGGGTGT 61.122 55.000 0.00 0.00 40.06 4.16
595 633 0.951040 GAGAGAAACGCAGGGGTGTG 60.951 60.000 0.00 0.00 37.91 3.82
596 634 1.966451 GAGAAACGCAGGGGTGTGG 60.966 63.158 0.00 0.00 37.91 4.17
633 671 0.252742 GAGAAAGTGAGGGGAGGGGA 60.253 60.000 0.00 0.00 0.00 4.81
635 673 1.229984 AAAGTGAGGGGAGGGGAGG 60.230 63.158 0.00 0.00 0.00 4.30
718 756 0.229753 GAGCTGTCGAAACACACACG 59.770 55.000 0.00 0.00 0.00 4.49
803 851 4.485834 CCGATTCGTCCCGTCGCA 62.486 66.667 5.20 0.00 34.25 5.10
888 943 1.402787 CCCTTCCCCAATTCATTCCG 58.597 55.000 0.00 0.00 0.00 4.30
910 965 2.694616 TTCCCCATTCCCCTCCCG 60.695 66.667 0.00 0.00 0.00 5.14
913 968 3.738481 CCCATTCCCCTCCCGCAA 61.738 66.667 0.00 0.00 0.00 4.85
914 969 2.603008 CCATTCCCCTCCCGCAAT 59.397 61.111 0.00 0.00 0.00 3.56
915 970 1.529244 CCATTCCCCTCCCGCAATC 60.529 63.158 0.00 0.00 0.00 2.67
916 971 1.529244 CATTCCCCTCCCGCAATCC 60.529 63.158 0.00 0.00 0.00 3.01
924 979 4.954970 CCCGCAATCCATCCCCCG 62.955 72.222 0.00 0.00 0.00 5.73
1100 1188 1.016653 GTGAGTCCTTCGCTTCTGGC 61.017 60.000 0.00 0.00 33.43 4.85
1103 1191 1.807573 GTCCTTCGCTTCTGGCTCG 60.808 63.158 0.00 0.00 39.13 5.03
1105 1193 3.191539 CTTCGCTTCTGGCTCGGC 61.192 66.667 0.00 0.00 39.13 5.54
1192 1292 2.437180 GCGGGGTTTCGGTTAGGG 60.437 66.667 0.00 0.00 0.00 3.53
1448 1548 2.158608 CCTCAAGGGTTTGTTCCACTCT 60.159 50.000 0.00 0.00 35.73 3.24
1449 1549 3.142174 CTCAAGGGTTTGTTCCACTCTC 58.858 50.000 0.00 0.00 35.73 3.20
1450 1550 1.873591 CAAGGGTTTGTTCCACTCTCG 59.126 52.381 0.00 0.00 0.00 4.04
1451 1551 0.250338 AGGGTTTGTTCCACTCTCGC 60.250 55.000 0.00 0.00 0.00 5.03
1452 1552 0.250338 GGGTTTGTTCCACTCTCGCT 60.250 55.000 0.00 0.00 0.00 4.93
1453 1553 1.594331 GGTTTGTTCCACTCTCGCTT 58.406 50.000 0.00 0.00 0.00 4.68
1533 1654 1.265905 GGATTTGACGCGTTTTCTGGT 59.734 47.619 15.53 0.00 0.00 4.00
1534 1655 2.571206 GATTTGACGCGTTTTCTGGTC 58.429 47.619 15.53 0.00 0.00 4.02
1536 1657 0.179067 TTGACGCGTTTTCTGGTCCT 60.179 50.000 15.53 0.00 0.00 3.85
1543 1664 2.922335 GCGTTTTCTGGTCCTGATTTGC 60.922 50.000 0.00 0.00 0.00 3.68
1545 1666 3.610114 CGTTTTCTGGTCCTGATTTGCTG 60.610 47.826 0.00 0.00 0.00 4.41
1546 1667 1.538047 TTCTGGTCCTGATTTGCTGC 58.462 50.000 0.00 0.00 0.00 5.25
1547 1668 0.322816 TCTGGTCCTGATTTGCTGCC 60.323 55.000 0.00 0.00 0.00 4.85
1768 1893 3.068590 CACCAATGGCCAGATGGTAATTC 59.931 47.826 33.89 0.00 45.45 2.17
1779 1904 6.129179 CCAGATGGTAATTCATTAACCACCT 58.871 40.000 0.00 0.00 31.29 4.00
1817 1942 5.604231 TCCTCTGCCATAATATCAGACTGTT 59.396 40.000 1.59 0.00 33.72 3.16
1820 1945 6.057533 TCTGCCATAATATCAGACTGTTTGG 58.942 40.000 1.59 0.38 32.48 3.28
1872 2005 0.322726 TGTAGGTCGACGACATCCCA 60.323 55.000 27.77 18.18 33.68 4.37
1911 2044 3.755628 CCTTCCTTCGTCGGCGGA 61.756 66.667 10.62 0.00 38.89 5.54
1971 2104 1.508088 CCTTCCTGGTGCGCATTTC 59.492 57.895 15.91 7.44 0.00 2.17
2022 2155 3.153919 GCTGTAACAATGGTTCAGGGAA 58.846 45.455 7.03 0.00 38.45 3.97
2038 2171 3.642141 AGGGAAACTGATGGTTGTTTGT 58.358 40.909 0.00 0.00 38.29 2.83
2039 2172 3.384467 AGGGAAACTGATGGTTGTTTGTG 59.616 43.478 0.00 0.00 38.29 3.33
2040 2173 3.132111 GGGAAACTGATGGTTGTTTGTGT 59.868 43.478 0.00 0.00 38.29 3.72
2239 2372 2.615489 ACGACACTAGAAACTCGCTC 57.385 50.000 0.00 0.00 0.00 5.03
2240 2373 1.878088 ACGACACTAGAAACTCGCTCA 59.122 47.619 0.00 0.00 0.00 4.26
2256 2389 5.011090 TCGCTCAGCATCTATTAGTTTGT 57.989 39.130 0.00 0.00 0.00 2.83
2289 2422 6.528072 CGCCTTTCTGATTAATTCTTGGTTTC 59.472 38.462 0.00 0.00 0.00 2.78
2293 2426 8.795786 TTTCTGATTAATTCTTGGTTTCAACG 57.204 30.769 0.00 0.00 0.00 4.10
2297 2430 2.793278 ATTCTTGGTTTCAACGGCAC 57.207 45.000 0.00 0.00 0.00 5.01
2304 2437 4.010667 TGGTTTCAACGGCACTAGTATT 57.989 40.909 0.00 0.00 0.00 1.89
2332 2465 7.118971 GTCAAACAGACTAGAGATTTCATGCTT 59.881 37.037 0.00 0.00 44.09 3.91
2334 2467 5.347342 ACAGACTAGAGATTTCATGCTTCG 58.653 41.667 0.00 0.00 0.00 3.79
2389 2522 7.555965 ACCTAAAATGCCAAAAGAATATCCAC 58.444 34.615 0.00 0.00 0.00 4.02
2405 2538 0.452184 CCACTAGAGTGTCGCGATGT 59.548 55.000 14.06 0.00 44.21 3.06
2437 2570 6.019108 AGAGGACCTAAAATGCCAAAAGAAT 58.981 36.000 0.00 0.00 0.00 2.40
2440 2573 9.131791 GAGGACCTAAAATGCCAAAAGAATATA 57.868 33.333 0.00 0.00 0.00 0.86
2467 2600 7.053498 ACATTTTGCTAAAACAGGGAAACAAT 58.947 30.769 0.00 0.00 32.37 2.71
2468 2601 7.555914 ACATTTTGCTAAAACAGGGAAACAATT 59.444 29.630 0.00 0.00 32.37 2.32
2469 2602 7.929941 TTTTGCTAAAACAGGGAAACAATTT 57.070 28.000 0.00 0.00 0.00 1.82
2486 2619 3.982576 ATTTGGCGAATTCGTATTCCC 57.017 42.857 27.24 19.54 42.22 3.97
2489 2622 3.102052 TGGCGAATTCGTATTCCCTAC 57.898 47.619 27.24 8.53 42.22 3.18
2490 2623 2.431419 TGGCGAATTCGTATTCCCTACA 59.569 45.455 27.24 10.76 42.22 2.74
2491 2624 3.070446 TGGCGAATTCGTATTCCCTACAT 59.930 43.478 27.24 0.00 42.22 2.29
2492 2625 4.062991 GGCGAATTCGTATTCCCTACATT 58.937 43.478 27.24 0.00 42.22 2.71
2493 2626 4.514066 GGCGAATTCGTATTCCCTACATTT 59.486 41.667 27.24 0.00 42.22 2.32
2529 2662 2.086869 GCTGCATTTGTCTAAGCTGGA 58.913 47.619 0.00 0.00 0.00 3.86
2535 2668 4.397417 GCATTTGTCTAAGCTGGATGAAGT 59.603 41.667 0.00 0.00 0.00 3.01
2547 2680 1.130561 GGATGAAGTTGTAACTGCGCC 59.869 52.381 4.18 0.00 37.39 6.53
2569 2702 5.765182 GCCAGTGCCATTTAGTAATGACTAT 59.235 40.000 0.00 0.00 43.12 2.12
2690 2828 8.812147 TGTAAAATGTGTTACTAGACTCTGTG 57.188 34.615 0.00 0.00 35.41 3.66
2952 3090 3.855668 TGATCAATTCCCCAAGTGGTTT 58.144 40.909 0.00 0.00 0.00 3.27
2982 3120 0.108281 GGGAGACTTACCTTGACCGC 60.108 60.000 0.00 0.00 0.00 5.68
3072 3210 4.573201 TGGAACTAACTGCTTGTGTTGTAC 59.427 41.667 0.00 0.00 0.00 2.90
3076 3214 4.809426 ACTAACTGCTTGTGTTGTACTGTC 59.191 41.667 0.00 0.00 0.00 3.51
3456 3594 2.161855 CAGCCACTTTGCTATGTTCCA 58.838 47.619 0.00 0.00 40.32 3.53
3732 3883 2.017049 CTTTGCCCTAATGAAGTCCGG 58.983 52.381 0.00 0.00 0.00 5.14
3744 3895 2.701951 TGAAGTCCGGTTTTGTCTACCT 59.298 45.455 0.00 0.00 33.35 3.08
3906 4057 2.036992 TGTTTTGGATGCATTTTCGGCT 59.963 40.909 0.00 0.00 0.00 5.52
4003 4154 1.721926 GTCTCTGCTGTGCTAACGAAC 59.278 52.381 0.00 0.00 0.00 3.95
4078 4229 4.685924 CAGTCAAGGAAGCAATGTGTTTT 58.314 39.130 0.00 0.00 0.00 2.43
4114 4265 6.628919 TTGGTAGGAAAGAAAGTTTGCTAC 57.371 37.500 16.48 16.48 46.10 3.58
4214 4365 9.739276 ATGTAAGACTTGGATTTCATGTTTCTA 57.261 29.630 0.00 0.00 34.42 2.10
4273 4427 6.590234 ATGAAGTTTCCCTAACATTTGTCC 57.410 37.500 0.00 0.00 39.30 4.02
4328 4482 0.106015 AAGGCCCCATCTATGTTGGC 60.106 55.000 0.00 10.68 40.83 4.52
4331 4485 1.447317 GCCCCATCTATGTTGGCACG 61.447 60.000 13.13 0.00 41.07 5.34
4361 4515 0.830648 TTAGAAGGCAGGCGCTGTAT 59.169 50.000 7.64 0.00 38.60 2.29
4523 4677 6.319911 AGAGGTTGTTTTTCAAGAAGGAAGAG 59.680 38.462 0.00 0.00 36.66 2.85
4565 4719 4.083802 GCACTTAGTGAAATTGACGAAGCT 60.084 41.667 17.40 0.00 35.23 3.74
4568 4722 1.537202 AGTGAAATTGACGAAGCTGCC 59.463 47.619 0.00 0.00 0.00 4.85
4590 4744 3.153919 GCAGGTACCACTCAATTTCCAA 58.846 45.455 15.94 0.00 0.00 3.53
4593 4747 4.023193 CAGGTACCACTCAATTTCCAACAC 60.023 45.833 15.94 0.00 0.00 3.32
4600 4756 5.507315 CCACTCAATTTCCAACACTGGTTAC 60.507 44.000 0.00 0.00 43.97 2.50
4860 5016 2.638363 ACAGACTGGGGAAAAGAGGTAC 59.362 50.000 7.51 0.00 0.00 3.34
4883 5039 1.900498 AGGAGCTTGGTTGCTGTGC 60.900 57.895 0.00 0.00 44.17 4.57
4884 5040 2.253452 GAGCTTGGTTGCTGTGCG 59.747 61.111 0.00 0.00 44.17 5.34
4885 5041 3.886329 GAGCTTGGTTGCTGTGCGC 62.886 63.158 0.00 0.00 44.17 6.09
4897 5053 2.044832 CTGTGCGCTGCTGATTAGGC 62.045 60.000 9.73 0.00 0.00 3.93
4918 5074 4.418392 GCAGTTCAAATATCTGTTGCCTG 58.582 43.478 0.00 0.00 32.41 4.85
4927 5083 8.710239 TCAAATATCTGTTGCCTGGTAGTAATA 58.290 33.333 0.00 0.00 0.00 0.98
4936 5092 9.860650 TGTTGCCTGGTAGTAATAAATCATAAT 57.139 29.630 0.00 0.00 0.00 1.28
5056 5212 6.759827 GGTCGATTTACTGCATACCTAAAAGA 59.240 38.462 0.00 0.00 0.00 2.52
5074 5230 2.519013 AGACCTGCATTCAAAGGTTCC 58.481 47.619 0.00 0.00 46.97 3.62
5128 5284 1.125093 TTCTTCGGTGGGCTCTTGGA 61.125 55.000 0.00 0.00 0.00 3.53
5182 5338 2.306847 CTTTGGTATGGGTATGGTGGC 58.693 52.381 0.00 0.00 0.00 5.01
5263 5419 0.324943 TTCCACTTCTGGCCTACTGC 59.675 55.000 3.32 0.00 37.49 4.40
5352 5508 7.462571 TTGTAGTTCTATCTGCTGTGAAGTA 57.537 36.000 0.00 0.00 0.00 2.24
5383 5539 4.199310 GGTACGATTTAAACCTTACCCCC 58.801 47.826 4.21 0.00 0.00 5.40
5464 5620 6.985117 TCTTTTCATCTGCATTTTTGCTACT 58.015 32.000 0.00 0.00 35.49 2.57
5545 5701 2.304761 GTTCTGGGTCATTGGAGGTGTA 59.695 50.000 0.00 0.00 0.00 2.90
5557 5713 1.071385 GGAGGTGTATCTGCCCATCTG 59.929 57.143 0.00 0.00 0.00 2.90
5797 5953 2.900546 TCTCTTCGGGAAGCTCTTCTTT 59.099 45.455 9.23 0.00 39.45 2.52
5800 5956 0.670546 TCGGGAAGCTCTTCTTTGCG 60.671 55.000 9.23 0.00 39.45 4.85
5941 6097 0.106918 TGCGTGTGAACCCTTTCCTT 60.107 50.000 0.00 0.00 0.00 3.36
6009 6169 3.970640 ACCTAGGAGATGAAAGGATGGAC 59.029 47.826 17.98 0.00 33.16 4.02
6010 6170 3.006323 CCTAGGAGATGAAAGGATGGACG 59.994 52.174 1.05 0.00 0.00 4.79
6011 6171 2.752030 AGGAGATGAAAGGATGGACGA 58.248 47.619 0.00 0.00 0.00 4.20
6019 6179 5.565592 TGAAAGGATGGACGATCAAAATG 57.434 39.130 0.00 0.00 31.91 2.32
6064 6224 4.162320 TGAAGGTGTTTTTGTGCCCATAAA 59.838 37.500 0.00 0.00 0.00 1.40
6219 6388 0.110486 GGCAACCCTTCTTCACCTCA 59.890 55.000 0.00 0.00 0.00 3.86
6220 6389 1.239347 GCAACCCTTCTTCACCTCAC 58.761 55.000 0.00 0.00 0.00 3.51
6221 6390 1.897560 CAACCCTTCTTCACCTCACC 58.102 55.000 0.00 0.00 0.00 4.02
6222 6391 1.421646 CAACCCTTCTTCACCTCACCT 59.578 52.381 0.00 0.00 0.00 4.00
6223 6392 1.353091 ACCCTTCTTCACCTCACCTC 58.647 55.000 0.00 0.00 0.00 3.85
6251 6420 2.680913 CGGCCACGAAGAAGCAAGG 61.681 63.158 2.24 0.00 44.60 3.61
6258 6427 3.589988 CACGAAGAAGCAAGGATACAGT 58.410 45.455 0.00 0.00 41.41 3.55
6263 6432 2.093235 AGAAGCAAGGATACAGTCAGCC 60.093 50.000 0.00 0.00 41.41 4.85
6265 6434 1.630369 AGCAAGGATACAGTCAGCCAA 59.370 47.619 0.00 0.00 41.41 4.52
6266 6435 2.012673 GCAAGGATACAGTCAGCCAAG 58.987 52.381 0.00 0.00 41.41 3.61
6267 6436 2.616510 GCAAGGATACAGTCAGCCAAGT 60.617 50.000 0.00 0.00 41.41 3.16
6335 6532 5.509498 TGACCTTGATTTAAATGGAGAGGG 58.491 41.667 5.17 2.25 0.00 4.30
6391 6589 0.679505 TCGTCTGTATGCTATGCCCC 59.320 55.000 0.00 0.00 0.00 5.80
6397 6595 2.040813 CTGTATGCTATGCCCCAAGGAT 59.959 50.000 0.00 0.00 33.47 3.24
6522 6723 9.981114 CTTGTTTTGGTAAATTCTAAACTGGAT 57.019 29.630 0.00 0.00 31.71 3.41
6566 6768 4.202080 CCCATTCATCTGCACATTGTTAGG 60.202 45.833 0.00 0.00 0.00 2.69
6597 6799 6.760291 TCTTCTTGTTCCTCTTTCTAGTTCC 58.240 40.000 0.00 0.00 0.00 3.62
6649 6860 8.210946 CCAGATTTCCATTAGTGTAGGTATCAA 58.789 37.037 0.00 0.00 0.00 2.57
6663 6874 9.129209 GTGTAGGTATCAAGAAAAATTGAAAGC 57.871 33.333 0.00 0.00 42.21 3.51
6664 6875 8.303876 TGTAGGTATCAAGAAAAATTGAAAGCC 58.696 33.333 0.00 0.00 42.21 4.35
6665 6876 7.544804 AGGTATCAAGAAAAATTGAAAGCCT 57.455 32.000 0.00 0.00 42.21 4.58
6666 6877 7.381323 AGGTATCAAGAAAAATTGAAAGCCTG 58.619 34.615 8.18 0.00 42.21 4.85
6667 6878 7.233348 AGGTATCAAGAAAAATTGAAAGCCTGA 59.767 33.333 8.18 0.00 42.21 3.86
6668 6879 7.329471 GGTATCAAGAAAAATTGAAAGCCTGAC 59.671 37.037 0.00 0.00 42.21 3.51
6669 6880 6.469782 TCAAGAAAAATTGAAAGCCTGACT 57.530 33.333 0.00 0.00 36.28 3.41
6670 6881 6.275335 TCAAGAAAAATTGAAAGCCTGACTG 58.725 36.000 0.00 0.00 36.28 3.51
6671 6882 4.625028 AGAAAAATTGAAAGCCTGACTGC 58.375 39.130 0.00 0.00 0.00 4.40
6672 6883 3.391506 AAAATTGAAAGCCTGACTGCC 57.608 42.857 0.00 0.00 0.00 4.85
6673 6884 1.999648 AATTGAAAGCCTGACTGCCA 58.000 45.000 0.00 0.00 0.00 4.92
6674 6885 1.542492 ATTGAAAGCCTGACTGCCAG 58.458 50.000 0.00 0.00 42.55 4.85
6698 6909 3.282885 CAAGGCCAGGATTCTTAACTCC 58.717 50.000 5.01 0.00 0.00 3.85
6719 6930 0.834687 AAGGGAGGAACGGTGCTGTA 60.835 55.000 0.00 0.00 0.00 2.74
6758 6969 1.413767 CGATTCTGCGACCGACCAAG 61.414 60.000 0.00 0.00 0.00 3.61
6762 6973 4.373116 TGCGACCGACCAAGAGCC 62.373 66.667 0.00 0.00 0.00 4.70
6774 6985 3.285484 ACCAAGAGCCAGCTATGAATTG 58.715 45.455 6.51 0.00 0.00 2.32
6777 6988 1.134280 AGAGCCAGCTATGAATTGCGT 60.134 47.619 0.00 0.00 33.76 5.24
6788 6999 1.269174 TGAATTGCGTCCACATGGTTG 59.731 47.619 0.00 0.00 36.34 3.77
6825 7036 0.675522 CCGTGGTCCATGGTTACACC 60.676 60.000 20.77 17.79 35.92 4.16
6826 7037 0.323629 CGTGGTCCATGGTTACACCT 59.676 55.000 18.49 0.00 39.58 4.00
6827 7038 1.271163 CGTGGTCCATGGTTACACCTT 60.271 52.381 18.49 0.00 39.58 3.50
6828 7039 2.027929 CGTGGTCCATGGTTACACCTTA 60.028 50.000 18.49 0.06 39.58 2.69
6829 7040 3.340928 GTGGTCCATGGTTACACCTTAC 58.659 50.000 18.49 8.07 39.58 2.34
6830 7041 2.980379 TGGTCCATGGTTACACCTTACA 59.020 45.455 18.49 0.00 39.58 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.707938 AATGTTTGTTCTTCTGGAAAGAAAAG 57.292 30.769 2.02 0.00 37.93 2.27
1 2 9.801873 CTAATGTTTGTTCTTCTGGAAAGAAAA 57.198 29.630 2.02 0.00 37.93 2.29
2 3 8.966868 ACTAATGTTTGTTCTTCTGGAAAGAAA 58.033 29.630 2.02 0.00 37.93 2.52
30 31 4.600692 ACAAAAAGGGATTTACTGCCAC 57.399 40.909 0.00 0.00 37.96 5.01
31 32 4.525100 GGTACAAAAAGGGATTTACTGCCA 59.475 41.667 0.00 0.00 37.96 4.92
59 60 0.099436 CGCTGCTTGGGCTGAAATAC 59.901 55.000 0.00 0.00 39.31 1.89
86 87 0.969149 CAAACTTGGGAAAGGAGGCC 59.031 55.000 0.00 0.00 0.00 5.19
88 89 1.703411 TGCAAACTTGGGAAAGGAGG 58.297 50.000 0.00 0.00 0.00 4.30
102 103 2.440409 GAGGATCCTCTGCTTTGCAAA 58.560 47.619 31.11 12.14 38.41 3.68
103 104 2.119801 GAGGATCCTCTGCTTTGCAA 57.880 50.000 31.11 0.00 38.41 4.08
104 105 3.869623 GAGGATCCTCTGCTTTGCA 57.130 52.632 31.11 0.00 39.80 4.08
123 125 1.582937 CTGTACGCGTCTGCCTACG 60.583 63.158 18.63 0.00 45.58 3.51
166 169 8.588472 TCTCTGTTTACAAGATCAAAGATCAGA 58.412 33.333 9.43 0.48 0.00 3.27
182 185 5.405873 GGGCGCTATCTATTTCTCTGTTTAC 59.594 44.000 7.64 0.00 0.00 2.01
211 219 3.661936 CGCTTTTCTCGAGAGGAAAAACG 60.662 47.826 15.94 15.62 40.11 3.60
224 232 4.547406 ACAAGGTTGTTACGCTTTTCTC 57.453 40.909 0.00 0.00 38.47 2.87
280 290 4.144727 GGAGAGGGAGAGCGGGGA 62.145 72.222 0.00 0.00 0.00 4.81
297 307 2.022934 GTTGACCCTAGACTCCTACCG 58.977 57.143 0.00 0.00 0.00 4.02
298 308 3.025262 CTGTTGACCCTAGACTCCTACC 58.975 54.545 0.00 0.00 0.00 3.18
354 370 2.809601 GACGGTGTGGCGCTACTG 60.810 66.667 24.82 18.79 0.00 2.74
492 527 4.319766 GCGACGAGTTAATAATCGGTAGGA 60.320 45.833 0.00 0.00 43.12 2.94
493 528 3.910767 GCGACGAGTTAATAATCGGTAGG 59.089 47.826 0.00 1.42 43.12 3.18
494 529 4.530388 TGCGACGAGTTAATAATCGGTAG 58.470 43.478 0.00 4.73 43.12 3.18
495 530 4.550577 TGCGACGAGTTAATAATCGGTA 57.449 40.909 0.00 0.00 43.12 4.02
496 531 3.425577 TGCGACGAGTTAATAATCGGT 57.574 42.857 0.00 0.12 43.12 4.69
497 532 3.548668 TGTTGCGACGAGTTAATAATCGG 59.451 43.478 0.00 0.00 43.12 4.18
545 580 1.618888 CGGTTCCCTACTCCCTCTGAA 60.619 57.143 0.00 0.00 0.00 3.02
546 581 0.033405 CGGTTCCCTACTCCCTCTGA 60.033 60.000 0.00 0.00 0.00 3.27
547 582 0.033405 TCGGTTCCCTACTCCCTCTG 60.033 60.000 0.00 0.00 0.00 3.35
548 583 0.033306 GTCGGTTCCCTACTCCCTCT 60.033 60.000 0.00 0.00 0.00 3.69
552 587 0.816373 GACTGTCGGTTCCCTACTCC 59.184 60.000 0.00 0.00 0.00 3.85
592 630 2.039724 TACACCCACCCACCCACA 60.040 61.111 0.00 0.00 0.00 4.17
593 631 1.838073 CTCTACACCCACCCACCCAC 61.838 65.000 0.00 0.00 0.00 4.61
594 632 1.537889 CTCTACACCCACCCACCCA 60.538 63.158 0.00 0.00 0.00 4.51
595 633 1.229400 TCTCTACACCCACCCACCC 60.229 63.158 0.00 0.00 0.00 4.61
596 634 0.252103 TCTCTCTACACCCACCCACC 60.252 60.000 0.00 0.00 0.00 4.61
663 701 2.740447 CCCAGTTTTTGTACTACTCGCC 59.260 50.000 0.00 0.00 0.00 5.54
814 868 1.021202 CGATGTGGTGTGGTGTGTTT 58.979 50.000 0.00 0.00 0.00 2.83
888 943 0.393944 GAGGGGAATGGGGAACGAAC 60.394 60.000 0.00 0.00 0.00 3.95
1143 1243 3.108521 CGACACGGAGAAGAACAGG 57.891 57.895 0.00 0.00 0.00 4.00
1174 1274 2.816520 CCTAACCGAAACCCCGCG 60.817 66.667 0.00 0.00 0.00 6.46
1175 1275 2.437180 CCCTAACCGAAACCCCGC 60.437 66.667 0.00 0.00 0.00 6.13
1185 1285 0.035739 TGAGAAACGGCACCCTAACC 59.964 55.000 0.00 0.00 0.00 2.85
1186 1286 1.886886 TTGAGAAACGGCACCCTAAC 58.113 50.000 0.00 0.00 0.00 2.34
1189 1289 0.693049 AGATTGAGAAACGGCACCCT 59.307 50.000 0.00 0.00 0.00 4.34
1192 1292 3.330267 AGAAGAGATTGAGAAACGGCAC 58.670 45.455 0.00 0.00 0.00 5.01
1448 1548 2.261671 GGCCGAGAGTGAAAGCGA 59.738 61.111 0.00 0.00 0.00 4.93
1449 1549 2.815647 GGGCCGAGAGTGAAAGCG 60.816 66.667 0.00 0.00 0.00 4.68
1450 1550 2.035442 GTGGGCCGAGAGTGAAAGC 61.035 63.158 0.00 0.00 0.00 3.51
1451 1551 1.376037 GGTGGGCCGAGAGTGAAAG 60.376 63.158 0.00 0.00 0.00 2.62
1452 1552 2.747686 GGTGGGCCGAGAGTGAAA 59.252 61.111 0.00 0.00 0.00 2.69
1453 1553 3.319198 GGGTGGGCCGAGAGTGAA 61.319 66.667 0.00 0.00 34.97 3.18
1533 1654 4.007457 GCAGGCAGCAAATCAGGA 57.993 55.556 0.00 0.00 44.79 3.86
1566 1687 4.172232 TCCTCCTCATCCCCGGGG 62.172 72.222 35.80 35.80 0.00 5.73
1768 1893 4.218200 TGTGAGATTTGCAGGTGGTTAATG 59.782 41.667 0.00 0.00 0.00 1.90
1779 1904 2.873245 GCAGAGGAGTGTGAGATTTGCA 60.873 50.000 0.00 0.00 0.00 4.08
1911 2044 0.624795 GGTGGATCCTCTTTCCCCCT 60.625 60.000 14.23 0.00 28.94 4.79
1971 2104 7.766283 TGCTAGTAGGAGATGATGATATTTCG 58.234 38.462 0.00 0.00 0.00 3.46
2022 2155 3.056250 TGCAACACAAACAACCATCAGTT 60.056 39.130 0.00 0.00 40.16 3.16
2040 2173 0.961019 GGATCTTGGTTGCACTGCAA 59.039 50.000 12.59 12.59 46.80 4.08
2239 2372 7.848051 CGCTAAAGAACAAACTAATAGATGCTG 59.152 37.037 0.00 0.00 0.00 4.41
2240 2373 7.466050 GCGCTAAAGAACAAACTAATAGATGCT 60.466 37.037 0.00 0.00 0.00 3.79
2256 2389 7.336931 AGAATTAATCAGAAAGGCGCTAAAGAA 59.663 33.333 7.64 0.00 0.00 2.52
2289 2422 2.967362 TGACCAATACTAGTGCCGTTG 58.033 47.619 5.39 5.53 0.00 4.10
2293 2426 4.392138 GTCTGTTTGACCAATACTAGTGCC 59.608 45.833 5.39 0.00 39.69 5.01
2297 2430 8.282455 TCTCTAGTCTGTTTGACCAATACTAG 57.718 38.462 0.00 0.00 46.46 2.57
2304 2437 6.419484 TGAAATCTCTAGTCTGTTTGACCA 57.581 37.500 0.00 0.00 46.46 4.02
2334 2467 1.475441 GCACATCGCGACACTCTAGC 61.475 60.000 12.93 5.29 0.00 3.42
2354 2487 1.591619 GCATTTTAGGTCGTCTACGGC 59.408 52.381 2.24 0.00 44.28 5.68
2362 2495 6.918022 GGATATTCTTTTGGCATTTTAGGTCG 59.082 38.462 0.00 0.00 0.00 4.79
2389 2522 2.571528 GCACATCGCGACACTCTAG 58.428 57.895 12.93 0.00 0.00 2.43
2440 2573 7.731054 TGTTTCCCTGTTTTAGCAAAATGTAT 58.269 30.769 0.00 0.00 32.22 2.29
2458 2591 2.666022 CGAATTCGCCAAATTGTTTCCC 59.334 45.455 15.93 0.00 37.70 3.97
2493 2626 9.177608 ACAAATGCAGCAGTTTTAAGATAGATA 57.822 29.630 5.07 0.00 0.00 1.98
2529 2662 1.806542 CTGGCGCAGTTACAACTTCAT 59.193 47.619 10.83 0.00 37.08 2.57
2535 2668 2.258013 GGCACTGGCGCAGTTACAA 61.258 57.895 10.83 0.00 42.59 2.41
2601 2735 5.240891 TCTTCCTTGCAGTCAAAGATACAG 58.759 41.667 0.00 0.00 0.00 2.74
2690 2828 9.952188 AAATCAAGAAAAAGTTAGTACTCAAGC 57.048 29.630 0.00 0.00 31.99 4.01
2952 3090 4.482772 AGGTAAGTCTCCCTCTCAATAGGA 59.517 45.833 0.00 0.00 39.15 2.94
2982 3120 4.320494 GCAGTAACCAACCTCAATGTCAAG 60.320 45.833 0.00 0.00 0.00 3.02
3076 3214 0.955919 GGCCTTCCTTGTCGAACCTG 60.956 60.000 0.00 0.00 0.00 4.00
3886 4037 2.687370 AGCCGAAAATGCATCCAAAAC 58.313 42.857 0.00 0.00 0.00 2.43
3906 4057 9.311676 TGCTACTACTAGCTATAGAGAAGACTA 57.688 37.037 3.21 0.00 45.20 2.59
4003 4154 3.434641 CCAAGTTCAGCATATATGGAGCG 59.565 47.826 14.51 0.00 0.00 5.03
4114 4265 1.238439 ATCTTTGTGGGAACTGCACG 58.762 50.000 0.00 0.00 0.00 5.34
4273 4427 6.764308 AACCTTTCATGTTGATCTGTATGG 57.236 37.500 0.00 0.00 0.00 2.74
4331 4485 3.274288 CTGCCTTCTAAAGACACATCCC 58.726 50.000 0.00 0.00 0.00 3.85
4361 4515 3.772387 TGTTTTGGGAGCATCATAACCA 58.228 40.909 0.00 0.00 36.25 3.67
4523 4677 1.004927 GCGTACGCAGGTGATTGATTC 60.005 52.381 33.90 0.00 41.49 2.52
4547 4701 2.742053 GGCAGCTTCGTCAATTTCACTA 59.258 45.455 0.00 0.00 0.00 2.74
4565 4719 1.836999 ATTGAGTGGTACCTGCGGCA 61.837 55.000 14.36 1.29 0.00 5.69
4568 4722 1.737793 GGAAATTGAGTGGTACCTGCG 59.262 52.381 14.36 0.00 0.00 5.18
4590 4744 9.256228 TGAAGATATTTCTAGAGTAACCAGTGT 57.744 33.333 0.00 0.00 0.00 3.55
4860 5016 0.250640 AGCAACCAAGCTCCTGACTG 60.251 55.000 0.00 0.00 42.18 3.51
4897 5053 4.460382 ACCAGGCAACAGATATTTGAACTG 59.540 41.667 0.00 0.00 41.41 3.16
4901 5057 5.435686 ACTACCAGGCAACAGATATTTGA 57.564 39.130 0.00 0.00 41.41 2.69
5056 5212 1.247567 CGGAACCTTTGAATGCAGGT 58.752 50.000 0.00 0.00 46.04 4.00
5074 5230 1.633171 CGAAAGATTGAGAGGCGCG 59.367 57.895 0.00 0.00 0.00 6.86
5128 5284 6.991531 GGTTGCTGAAGAAGATCTCAATAGAT 59.008 38.462 0.00 0.00 45.46 1.98
5161 5317 2.306847 CCACCATACCCATACCAAAGC 58.693 52.381 0.00 0.00 0.00 3.51
5182 5338 7.713764 AAATCTTTCCAAAAATTTCAGTCCG 57.286 32.000 0.00 0.00 0.00 4.79
5352 5508 4.694037 GGTTTAAATCGTACCAGACTTGCT 59.306 41.667 0.00 0.00 32.12 3.91
5383 5539 3.243535 GCAAGACAGAACCAAAAGGGAAG 60.244 47.826 0.00 0.00 41.15 3.46
5440 5596 6.864685 CAGTAGCAAAAATGCAGATGAAAAGA 59.135 34.615 3.41 0.00 37.25 2.52
5464 5620 4.689705 GCCCATCTCATTTCCAGAATACCA 60.690 45.833 0.00 0.00 0.00 3.25
5545 5701 1.033746 CGGCAAACAGATGGGCAGAT 61.034 55.000 0.00 0.00 0.00 2.90
5605 5761 1.295792 TTGTTGTGACGGTGAAGCTC 58.704 50.000 0.00 0.00 0.00 4.09
5797 5953 0.605319 GGACAATCACCCAGAACGCA 60.605 55.000 0.00 0.00 0.00 5.24
5800 5956 3.356529 AGATGGACAATCACCCAGAAC 57.643 47.619 0.00 0.00 37.81 3.01
6009 6169 5.295045 TCCACATGATGACTCATTTTGATCG 59.705 40.000 0.00 0.00 40.20 3.69
6010 6170 6.318144 ACTCCACATGATGACTCATTTTGATC 59.682 38.462 0.00 0.00 40.20 2.92
6011 6171 6.185511 ACTCCACATGATGACTCATTTTGAT 58.814 36.000 0.00 0.00 40.20 2.57
6019 6179 7.615582 TCAAAATTACTCCACATGATGACTC 57.384 36.000 0.00 0.00 0.00 3.36
6071 6231 1.143889 GGGGATGGAGGAATGGAAGAC 59.856 57.143 0.00 0.00 0.00 3.01
6219 6388 2.031163 GCCGAACTGCACAGAGGT 59.969 61.111 4.31 0.00 0.00 3.85
6220 6389 2.743928 GGCCGAACTGCACAGAGG 60.744 66.667 4.31 6.01 0.00 3.69
6221 6390 2.031012 TGGCCGAACTGCACAGAG 59.969 61.111 4.31 0.00 0.00 3.35
6222 6391 2.280797 GTGGCCGAACTGCACAGA 60.281 61.111 4.31 0.00 0.00 3.41
6223 6392 3.716006 CGTGGCCGAACTGCACAG 61.716 66.667 0.00 0.00 35.63 3.66
6247 6416 3.265791 GACTTGGCTGACTGTATCCTTG 58.734 50.000 0.00 0.00 0.00 3.61
6251 6420 3.257393 CACTGACTTGGCTGACTGTATC 58.743 50.000 0.00 0.00 0.00 2.24
6258 6427 2.418368 AACAACACTGACTTGGCTGA 57.582 45.000 0.00 0.00 0.00 4.26
6263 6432 5.036737 GGACAATGAAACAACACTGACTTG 58.963 41.667 0.00 0.00 0.00 3.16
6265 6434 4.269183 TGGACAATGAAACAACACTGACT 58.731 39.130 0.00 0.00 0.00 3.41
6266 6435 4.601019 CTGGACAATGAAACAACACTGAC 58.399 43.478 0.00 0.00 0.00 3.51
6267 6436 3.066621 GCTGGACAATGAAACAACACTGA 59.933 43.478 0.00 0.00 0.00 3.41
6335 6532 7.709269 TCGGCTCACTTACATACATTTTATC 57.291 36.000 0.00 0.00 0.00 1.75
6436 6637 4.256920 GCATTCTTGCCTTACAGAGAGAA 58.743 43.478 0.00 0.00 43.38 2.87
6509 6710 5.893255 TGCAGGCATTTATCCAGTTTAGAAT 59.107 36.000 0.00 0.00 0.00 2.40
6566 6768 6.484977 AGAAAGAGGAACAAGAAGATGACAAC 59.515 38.462 0.00 0.00 0.00 3.32
6597 6799 5.599732 AGCAGATGAAGCATAGAACTAGTG 58.400 41.667 0.00 0.00 0.00 2.74
6649 6860 4.502087 GGCAGTCAGGCTTTCAATTTTTCT 60.502 41.667 0.00 0.00 40.24 2.52
6656 6867 3.025924 CTGGCAGTCAGGCTTTCAA 57.974 52.632 6.28 0.00 44.55 2.69
6657 6868 4.806936 CTGGCAGTCAGGCTTTCA 57.193 55.556 6.28 0.00 44.55 2.69
6671 6882 1.304713 AATCCTGGCCTTGCACTGG 60.305 57.895 3.32 0.76 0.00 4.00
6672 6883 0.323178 AGAATCCTGGCCTTGCACTG 60.323 55.000 3.32 0.00 0.00 3.66
6673 6884 0.407139 AAGAATCCTGGCCTTGCACT 59.593 50.000 3.32 0.00 0.00 4.40
6674 6885 2.128771 TAAGAATCCTGGCCTTGCAC 57.871 50.000 3.32 0.00 0.00 4.57
6678 6889 2.092914 CGGAGTTAAGAATCCTGGCCTT 60.093 50.000 3.32 0.00 33.12 4.35
6698 6909 2.434359 GCACCGTTCCTCCCTTCG 60.434 66.667 0.00 0.00 0.00 3.79
6706 6917 0.517316 CAAAGCTACAGCACCGTTCC 59.483 55.000 3.70 0.00 45.16 3.62
6707 6918 0.517316 CCAAAGCTACAGCACCGTTC 59.483 55.000 3.70 0.00 45.16 3.95
6709 6920 1.966451 GCCAAAGCTACAGCACCGT 60.966 57.895 3.70 0.00 45.16 4.83
6710 6921 2.870372 GCCAAAGCTACAGCACCG 59.130 61.111 3.70 0.00 45.16 4.94
6758 6969 1.262683 GACGCAATTCATAGCTGGCTC 59.737 52.381 0.00 0.00 0.00 4.70
6762 6973 2.009051 TGTGGACGCAATTCATAGCTG 58.991 47.619 0.00 0.00 0.00 4.24
6774 6985 4.101790 CGCCAACCATGTGGACGC 62.102 66.667 5.96 3.22 41.65 5.19
6777 6988 2.672651 CAGCGCCAACCATGTGGA 60.673 61.111 2.29 0.00 41.65 4.02
6788 6999 4.543084 GCGAGCAAATCCAGCGCC 62.543 66.667 2.29 0.00 41.65 6.53
6896 7239 6.371548 GCAGTCATATCTTTTGTCAAGTACCA 59.628 38.462 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.