Multiple sequence alignment - TraesCS5D01G213500

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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 TraesCS5D01G213500 chr5D 100.000 7123 0 0 1 7123 322792015 322784893 0.000000e+00 13154.0
1 TraesCS5D01G213500 chr5D 79.592 392 61 14 2461 2845 322788863 322788484 5.480000e-66 263.0
2 TraesCS5D01G213500 chr5D 79.592 392 61 14 3153 3532 322789555 322789171 5.480000e-66 263.0
3 TraesCS5D01G213500 chr5A 92.374 3501 141 42 13 3443 419369867 419366423 0.000000e+00 4870.0
4 TraesCS5D01G213500 chr5A 93.727 1865 81 14 4734 6597 419365092 419363263 0.000000e+00 2763.0
5 TraesCS5D01G213500 chr5A 93.912 1347 61 12 3357 4699 419366423 419365094 0.000000e+00 2013.0
6 TraesCS5D01G213500 chr5B 92.505 1868 64 26 101 1930 374453189 374451360 0.000000e+00 2604.0
7 TraesCS5D01G213500 chr5B 91.914 1818 91 21 4734 6533 374446319 374444540 0.000000e+00 2492.0
8 TraesCS5D01G213500 chr5B 94.766 1261 48 9 3357 4607 374449369 374448117 0.000000e+00 1947.0
9 TraesCS5D01G213500 chr5B 93.091 854 22 14 2287 3113 374451326 374450483 0.000000e+00 1216.0
10 TraesCS5D01G213500 chr5B 94.030 335 16 2 3112 3443 374449702 374449369 8.250000e-139 505.0
11 TraesCS5D01G213500 chr5B 82.674 531 62 17 6598 7123 708842175 708842680 1.820000e-120 444.0
12 TraesCS5D01G213500 chr5B 87.533 377 42 5 6598 6970 592795 592420 1.420000e-116 431.0
13 TraesCS5D01G213500 chr5B 88.991 109 10 1 4593 4699 374446429 374446321 4.480000e-27 134.0
14 TraesCS5D01G213500 chr5B 90.909 88 8 0 7036 7123 592384 592297 1.260000e-22 119.0
15 TraesCS5D01G213500 chr4D 92.179 537 27 6 6595 7120 381743756 381744288 0.000000e+00 745.0
16 TraesCS5D01G213500 chr4D 87.500 64 6 2 2165 2227 476314631 476314569 9.910000e-09 73.1
17 TraesCS5D01G213500 chr7D 88.065 553 35 10 6598 7123 582123272 582122724 1.690000e-175 627.0
18 TraesCS5D01G213500 chr3B 83.992 531 53 16 6598 7123 506729253 506728750 1.390000e-131 481.0
19 TraesCS5D01G213500 chr3B 83.681 527 59 18 6598 7121 515251667 515251165 8.360000e-129 472.0
20 TraesCS5D01G213500 chr3B 87.500 376 44 3 6598 6970 689992896 689993271 1.420000e-116 431.0
21 TraesCS5D01G213500 chr3B 82.090 536 56 21 6594 7123 98017973 98018474 8.540000e-114 422.0
22 TraesCS5D01G213500 chr3B 92.045 88 7 0 7036 7123 689993307 689993394 2.700000e-24 124.0
23 TraesCS5D01G213500 chr4A 89.182 379 35 4 6598 6970 658409559 658409181 1.080000e-127 468.0
24 TraesCS5D01G213500 chr2B 82.176 533 60 20 6598 7123 587231290 587230786 6.600000e-115 425.0
25 TraesCS5D01G213500 chr2B 81.439 528 61 20 6598 7123 67033060 67032568 1.440000e-106 398.0
26 TraesCS5D01G213500 chr2B 93.103 58 3 1 2152 2209 323085365 323085421 4.580000e-12 84.2
27 TraesCS5D01G213500 chr2A 93.103 58 3 1 2152 2209 285622293 285622349 4.580000e-12 84.2
28 TraesCS5D01G213500 chrUn 92.727 55 3 1 2162 2216 75920475 75920528 2.130000e-10 78.7
29 TraesCS5D01G213500 chr7B 94.231 52 2 1 2165 2216 724730023 724729973 2.130000e-10 78.7
30 TraesCS5D01G213500 chr6B 94.231 52 2 1 2165 2216 9990278 9990228 2.130000e-10 78.7
31 TraesCS5D01G213500 chr6A 94.231 52 2 1 2165 2216 432824797 432824747 2.130000e-10 78.7
32 TraesCS5D01G213500 chr1A 92.727 55 3 1 2162 2216 208881706 208881759 2.130000e-10 78.7


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 TraesCS5D01G213500 chr5D 322784893 322792015 7122 True 4560.000000 13154 86.394667 1 7123 3 chr5D.!!$R1 7122
1 TraesCS5D01G213500 chr5A 419363263 419369867 6604 True 3215.333333 4870 93.337667 13 6597 3 chr5A.!!$R1 6584
2 TraesCS5D01G213500 chr5B 374444540 374453189 8649 True 1483.000000 2604 92.549500 101 6533 6 chr5B.!!$R2 6432
3 TraesCS5D01G213500 chr5B 708842175 708842680 505 False 444.000000 444 82.674000 6598 7123 1 chr5B.!!$F1 525
4 TraesCS5D01G213500 chr4D 381743756 381744288 532 False 745.000000 745 92.179000 6595 7120 1 chr4D.!!$F1 525
5 TraesCS5D01G213500 chr7D 582122724 582123272 548 True 627.000000 627 88.065000 6598 7123 1 chr7D.!!$R1 525
6 TraesCS5D01G213500 chr3B 506728750 506729253 503 True 481.000000 481 83.992000 6598 7123 1 chr3B.!!$R1 525
7 TraesCS5D01G213500 chr3B 515251165 515251667 502 True 472.000000 472 83.681000 6598 7121 1 chr3B.!!$R2 523
8 TraesCS5D01G213500 chr3B 98017973 98018474 501 False 422.000000 422 82.090000 6594 7123 1 chr3B.!!$F1 529
9 TraesCS5D01G213500 chr2B 587230786 587231290 504 True 425.000000 425 82.176000 6598 7123 1 chr2B.!!$R2 525

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
383 387 0.034574 TATGAAACCGCTGCCCACAT 60.035 50.000 0.00 0.00 0.00 3.21 F
478 502 0.163788 CCGTCGAAACACACATGCTC 59.836 55.000 0.00 0.00 0.00 4.26 F
479 503 0.179275 CGTCGAAACACACATGCTCG 60.179 55.000 0.00 0.00 36.35 5.03 F
480 504 0.451135 GTCGAAACACACATGCTCGC 60.451 55.000 0.00 0.00 35.47 5.03 F
1993 2075 0.666913 AGATGGATGAAGCGCAATGC 59.333 50.000 11.47 6.22 46.98 3.56 F
2654 2761 1.453928 GGCCCACAAGCTACATCCC 60.454 63.158 0.00 0.00 0.00 3.85 F
3488 4480 0.390860 CACGGGCTTATCAGGAGAGG 59.609 60.000 0.00 0.00 0.00 3.69 F
4730 7437 0.104855 GTGTGGGATATCTGCTGCGA 59.895 55.000 2.05 0.00 0.00 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1414 0.546598 AATTCAGTCCCACCCGATCC 59.453 55.000 0.00 0.00 0.00 3.36 R
2379 2464 0.808755 GCACGTGAGGGGTTAAATGG 59.191 55.000 22.23 0.00 32.68 3.16 R
2654 2761 4.999950 GCTTCTGTATTGGATACCCAGATG 59.000 45.833 0.00 0.00 44.60 2.90 R
2720 2835 2.848691 CCAAGCAAATGGCCAAAGAAA 58.151 42.857 10.96 0.00 46.50 2.52 R
3207 4110 0.395586 TGTGCAACCTGAACTTGCCT 60.396 50.000 0.00 0.00 42.91 4.75 R
4711 7418 0.104855 TCGCAGCAGATATCCCACAC 59.895 55.000 0.00 0.00 0.00 3.82 R
5119 7828 0.246360 CTCACGGCTGTCATACACCA 59.754 55.000 0.00 0.00 0.00 4.17 R
6942 9681 0.041576 CGTCTAGCGTGCGTGCTATA 60.042 55.000 9.80 1.21 45.79 1.31 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
34 35 2.033424 GCGTTGGAGATGCCCTTAAATC 59.967 50.000 0.00 0.00 34.03 2.17
35 36 2.287915 CGTTGGAGATGCCCTTAAATCG 59.712 50.000 0.00 0.00 34.97 3.34
128 130 1.463444 GAAACGGTCGATTCTTGTGGG 59.537 52.381 6.20 0.00 0.00 4.61
137 139 4.873827 GTCGATTCTTGTGGGTTGCTTATA 59.126 41.667 0.00 0.00 0.00 0.98
138 140 5.527582 GTCGATTCTTGTGGGTTGCTTATAT 59.472 40.000 0.00 0.00 0.00 0.86
144 146 4.967084 TGTGGGTTGCTTATATCCGTAT 57.033 40.909 0.00 0.00 0.00 3.06
152 154 6.537660 GGTTGCTTATATCCGTATAATCCACC 59.462 42.308 0.00 0.00 32.36 4.61
157 159 2.369983 TCCGTATAATCCACCGAGGT 57.630 50.000 0.00 0.00 39.02 3.85
159 161 1.604693 CCGTATAATCCACCGAGGTGC 60.605 57.143 16.39 0.74 44.16 5.01
192 194 0.676782 AGTACCCAAAGCATCGTGGC 60.677 55.000 0.00 0.00 33.21 5.01
209 211 2.813100 GCAACGGTGGCAATCAAAG 58.187 52.632 0.90 0.00 0.00 2.77
215 217 3.596214 ACGGTGGCAATCAAAGTAGTAG 58.404 45.455 0.00 0.00 0.00 2.57
290 293 6.091986 AGCAAAAGAGATTCAGAAGATCGTTC 59.908 38.462 0.00 0.00 0.00 3.95
324 327 1.361993 CCTCTCGAGGCGAATCTGG 59.638 63.158 13.56 0.00 42.44 3.86
373 377 1.540363 CCGGGAGTCCATATGAAACCG 60.540 57.143 12.30 10.22 36.24 4.44
378 382 0.663153 GTCCATATGAAACCGCTGCC 59.337 55.000 3.65 0.00 0.00 4.85
381 385 0.381801 CATATGAAACCGCTGCCCAC 59.618 55.000 0.00 0.00 0.00 4.61
383 387 0.034574 TATGAAACCGCTGCCCACAT 60.035 50.000 0.00 0.00 0.00 3.21
384 388 1.597797 ATGAAACCGCTGCCCACATG 61.598 55.000 0.00 0.00 0.00 3.21
386 390 1.523154 GAAACCGCTGCCCACATGAA 61.523 55.000 0.00 0.00 0.00 2.57
387 391 0.899717 AAACCGCTGCCCACATGAAT 60.900 50.000 0.00 0.00 0.00 2.57
388 392 1.315257 AACCGCTGCCCACATGAATC 61.315 55.000 0.00 0.00 0.00 2.52
389 393 1.452651 CCGCTGCCCACATGAATCT 60.453 57.895 0.00 0.00 0.00 2.40
390 394 1.442526 CCGCTGCCCACATGAATCTC 61.443 60.000 0.00 0.00 0.00 2.75
393 397 2.029623 GCTGCCCACATGAATCTCAAT 58.970 47.619 0.00 0.00 0.00 2.57
421 425 6.716934 AATTACACTCCTCACGACATATCT 57.283 37.500 0.00 0.00 0.00 1.98
443 454 0.478507 ACCTCACCCTTTTCACCCAG 59.521 55.000 0.00 0.00 0.00 4.45
453 468 2.230189 TTTCACCCAGCACCAACCCA 62.230 55.000 0.00 0.00 0.00 4.51
471 495 1.096386 CAAACCCCCGTCGAAACACA 61.096 55.000 0.00 0.00 0.00 3.72
472 496 1.096967 AAACCCCCGTCGAAACACAC 61.097 55.000 0.00 0.00 0.00 3.82
473 497 2.109387 CCCCCGTCGAAACACACA 59.891 61.111 0.00 0.00 0.00 3.72
474 498 1.302192 CCCCCGTCGAAACACACAT 60.302 57.895 0.00 0.00 0.00 3.21
475 499 1.573829 CCCCCGTCGAAACACACATG 61.574 60.000 0.00 0.00 0.00 3.21
476 500 1.206578 CCCGTCGAAACACACATGC 59.793 57.895 0.00 0.00 0.00 4.06
477 501 1.227999 CCCGTCGAAACACACATGCT 61.228 55.000 0.00 0.00 0.00 3.79
478 502 0.163788 CCGTCGAAACACACATGCTC 59.836 55.000 0.00 0.00 0.00 4.26
479 503 0.179275 CGTCGAAACACACATGCTCG 60.179 55.000 0.00 0.00 36.35 5.03
480 504 0.451135 GTCGAAACACACATGCTCGC 60.451 55.000 0.00 0.00 35.47 5.03
543 573 4.081476 TCACTCTCACTCTCTCTCTCTCTG 60.081 50.000 0.00 0.00 0.00 3.35
544 574 3.201290 CTCTCACTCTCTCTCTCTCTGC 58.799 54.545 0.00 0.00 0.00 4.26
551 589 3.429080 CTCTCTCTCTGCGCTGGCC 62.429 68.421 14.70 0.00 38.85 5.36
692 730 1.228583 AGTCGAGCCACAGTGGAGA 60.229 57.895 24.96 15.38 40.96 3.71
762 812 2.853281 GCTGCCATTAAAACCGCGATAC 60.853 50.000 8.23 0.00 0.00 2.24
1180 1248 1.668294 CTCTCGGGACTGTGCTTGT 59.332 57.895 0.00 0.00 0.00 3.16
1345 1414 2.287103 TGTCTCGAGGTCGTAATCATCG 59.713 50.000 13.56 0.00 39.81 3.84
1550 1628 1.226888 CTTCCACTACGCCTACCGC 60.227 63.158 0.00 0.00 41.76 5.68
1665 1743 2.501128 ACGGGATGTCATCTGGCG 59.499 61.111 12.54 0.00 0.00 5.69
1798 1876 1.354040 CGATTCAGGTGTGTGCTCTC 58.646 55.000 0.00 0.00 0.00 3.20
1868 1948 3.960102 ACTCTGATTGTTGGCTGGAAAAA 59.040 39.130 0.00 0.00 0.00 1.94
1869 1949 4.590222 ACTCTGATTGTTGGCTGGAAAAAT 59.410 37.500 0.00 0.00 0.00 1.82
1870 1950 5.774690 ACTCTGATTGTTGGCTGGAAAAATA 59.225 36.000 0.00 0.00 0.00 1.40
1926 2006 6.409704 TGTGATCGAAATTTTGAGATCCTCT 58.590 36.000 19.97 3.52 38.85 3.69
1930 2010 4.093408 TCGAAATTTTGAGATCCTCTTGCG 59.907 41.667 3.86 0.00 0.00 4.85
1932 2012 5.063438 CGAAATTTTGAGATCCTCTTGCGTA 59.937 40.000 0.00 0.00 0.00 4.42
1993 2075 0.666913 AGATGGATGAAGCGCAATGC 59.333 50.000 11.47 6.22 46.98 3.56
2008 2090 2.401720 GCAATGCGTTGAAAAACTCTCG 59.598 45.455 22.81 0.00 37.53 4.04
2026 2108 3.739300 TCTCGACGAATTGAAGTTCCAAC 59.261 43.478 0.00 0.00 0.00 3.77
2277 2361 3.211045 TGTGCTACACTTTTTCCTCACC 58.789 45.455 0.00 0.00 35.11 4.02
2283 2367 3.074412 ACACTTTTTCCTCACCGCTATG 58.926 45.455 0.00 0.00 0.00 2.23
2338 2423 2.749280 TACACACTGGATGAGCTGTG 57.251 50.000 0.00 0.00 38.57 3.66
2379 2464 4.517075 GCATTGACTTTAGAATAGGCCCTC 59.483 45.833 0.00 0.00 0.00 4.30
2654 2761 1.453928 GGCCCACAAGCTACATCCC 60.454 63.158 0.00 0.00 0.00 3.85
2760 2875 2.019984 GCTGGTGGCCTTCTTATTGAG 58.980 52.381 3.32 0.00 34.27 3.02
2894 3012 3.107402 TGCCACCCTATTTTGCCATTA 57.893 42.857 0.00 0.00 0.00 1.90
2957 3076 6.877611 TTTTCCAACTGGATGTTCTCTAAC 57.122 37.500 0.00 0.00 44.98 2.34
3063 3182 5.352569 CCAGGTTGAATTCTAGATGTGTCAC 59.647 44.000 7.05 0.00 0.00 3.67
3077 3196 7.812690 AGATGTGTCACAATGCATGTTATAT 57.187 32.000 10.28 0.00 41.46 0.86
3215 4118 5.179452 ACCAATACTATGACAGGCAAGTT 57.821 39.130 0.00 0.00 0.00 2.66
3243 4146 6.526674 GGTTGCACATTTGTACTTTATGCTAC 59.473 38.462 12.17 12.17 36.86 3.58
3286 4192 2.500910 CTGGCAATGACTCTTCCTCTCT 59.499 50.000 0.00 0.00 0.00 3.10
3287 4193 2.499289 TGGCAATGACTCTTCCTCTCTC 59.501 50.000 0.00 0.00 0.00 3.20
3309 4215 5.322754 TCGGAAGAGGTAGTATTATCAGGG 58.677 45.833 0.00 0.00 34.84 4.45
3323 4229 8.652290 AGTATTATCAGGGGATAGACTTGAAAC 58.348 37.037 0.00 0.00 37.31 2.78
3390 4296 5.649395 TCAATGGAAAGATGAGTGTTGGATC 59.351 40.000 0.00 0.00 0.00 3.36
3456 4448 5.463724 GCTTGTGGTCTTACTGATATGTAGC 59.536 44.000 0.00 0.00 0.00 3.58
3464 4456 5.536538 TCTTACTGATATGTAGCTGGGTCTG 59.463 44.000 0.00 0.00 0.00 3.51
3472 4464 1.877576 TAGCTGGGTCTGTCTGCACG 61.878 60.000 0.00 0.00 0.00 5.34
3488 4480 0.390860 CACGGGCTTATCAGGAGAGG 59.609 60.000 0.00 0.00 0.00 3.69
3493 4485 1.475930 GGCTTATCAGGAGAGGCAACC 60.476 57.143 0.56 0.00 36.15 3.77
3600 4592 4.649088 ACCACTTTTGCAAACTTAGTCC 57.351 40.909 12.39 0.00 0.00 3.85
3616 4608 9.969001 AAACTTAGTCCTGGCACTATAAATTTA 57.031 29.630 0.00 0.00 0.00 1.40
3753 4745 2.436109 GGAGCTCCTTGTGGCCAA 59.564 61.111 26.25 0.00 0.00 4.52
3851 4843 2.145397 TGGGTGCAGGTGTTGTTTTA 57.855 45.000 0.00 0.00 0.00 1.52
3887 4880 4.525100 GGTCTAGATCTAAGGCAAGTAGGG 59.475 50.000 3.57 0.00 0.00 3.53
3957 4950 1.076332 GTTGTCACGGGATGCACTAC 58.924 55.000 0.00 0.00 0.00 2.73
3989 4982 3.416119 TTGACGTATGGATCAGTCGAC 57.584 47.619 7.70 7.70 36.49 4.20
4012 5005 0.538584 TGTGCTTCAGATCTGCCGAT 59.461 50.000 18.36 0.00 0.00 4.18
4109 5102 0.393537 GTGGGCCATCTCCTTCTGTG 60.394 60.000 10.70 0.00 0.00 3.66
4116 5109 2.420642 CATCTCCTTCTGTGTGTGTGG 58.579 52.381 0.00 0.00 0.00 4.17
4117 5110 0.758734 TCTCCTTCTGTGTGTGTGGG 59.241 55.000 0.00 0.00 0.00 4.61
4138 5131 0.401738 CCTGCCCTTTGACCTCTTCA 59.598 55.000 0.00 0.00 0.00 3.02
4150 5143 5.164620 TGACCTCTTCAACAATCAGCATA 57.835 39.130 0.00 0.00 0.00 3.14
4248 5241 3.864789 TCATCCATCTAAGGCTTTCCC 57.135 47.619 4.45 0.00 0.00 3.97
4274 5267 3.140814 GCGTGCCATCTTTCCCCC 61.141 66.667 0.00 0.00 0.00 5.40
4318 5311 1.676006 CCCGGAAAATTTGGATCTCCG 59.324 52.381 17.52 17.52 46.78 4.63
4418 5419 4.935352 AAACTTGTTGGTATGCATGTGT 57.065 36.364 10.16 0.00 0.00 3.72
4488 5489 5.329399 TGTACTGCCACCCTTTCAAAATAT 58.671 37.500 0.00 0.00 0.00 1.28
4489 5490 5.777732 TGTACTGCCACCCTTTCAAAATATT 59.222 36.000 0.00 0.00 0.00 1.28
4490 5491 6.948886 TGTACTGCCACCCTTTCAAAATATTA 59.051 34.615 0.00 0.00 0.00 0.98
4491 5492 6.926630 ACTGCCACCCTTTCAAAATATTAA 57.073 33.333 0.00 0.00 0.00 1.40
4492 5493 7.309770 ACTGCCACCCTTTCAAAATATTAAA 57.690 32.000 0.00 0.00 0.00 1.52
4527 5530 2.463752 ACTGCCAGGCATCATGATTTT 58.536 42.857 16.64 0.00 38.13 1.82
4627 7334 7.147724 CCTTGTCTGGTCTGGAATGTTATAGTA 60.148 40.741 0.00 0.00 0.00 1.82
4629 7336 6.183360 TGTCTGGTCTGGAATGTTATAGTAGC 60.183 42.308 0.00 0.00 0.00 3.58
4630 7337 5.897250 TCTGGTCTGGAATGTTATAGTAGCA 59.103 40.000 0.00 0.00 0.00 3.49
4632 7339 6.953101 TGGTCTGGAATGTTATAGTAGCAAA 58.047 36.000 0.00 0.00 0.00 3.68
4638 7345 8.116651 TGGAATGTTATAGTAGCAAAGCAAAA 57.883 30.769 0.00 0.00 0.00 2.44
4647 7354 6.648879 AGTAGCAAAGCAAAAACTCCATTA 57.351 33.333 0.00 0.00 0.00 1.90
4692 7399 0.467106 TGGCCTGCAAGCAAACACTA 60.467 50.000 9.97 0.00 0.00 2.74
4694 7401 1.273327 GGCCTGCAAGCAAACACTATT 59.727 47.619 9.97 0.00 0.00 1.73
4695 7402 2.599659 GCCTGCAAGCAAACACTATTC 58.400 47.619 1.41 0.00 0.00 1.75
4697 7404 3.829948 CCTGCAAGCAAACACTATTCTG 58.170 45.455 0.00 0.00 0.00 3.02
4699 7406 4.470462 CTGCAAGCAAACACTATTCTGTC 58.530 43.478 0.00 0.00 0.00 3.51
4701 7408 5.304778 TGCAAGCAAACACTATTCTGTCTA 58.695 37.500 0.00 0.00 0.00 2.59
4702 7409 5.409520 TGCAAGCAAACACTATTCTGTCTAG 59.590 40.000 0.00 0.00 0.00 2.43
4703 7410 5.409826 GCAAGCAAACACTATTCTGTCTAGT 59.590 40.000 0.00 0.00 0.00 2.57
4710 7417 4.677584 CACTATTCTGTCTAGTGTCTGCC 58.322 47.826 9.64 0.00 40.66 4.85
4711 7418 2.949451 ATTCTGTCTAGTGTCTGCCG 57.051 50.000 0.00 0.00 0.00 5.69
4712 7419 1.617322 TTCTGTCTAGTGTCTGCCGT 58.383 50.000 0.00 0.00 0.00 5.68
4713 7420 0.881796 TCTGTCTAGTGTCTGCCGTG 59.118 55.000 0.00 0.00 0.00 4.94
4714 7421 0.598562 CTGTCTAGTGTCTGCCGTGT 59.401 55.000 0.00 0.00 0.00 4.49
4715 7422 0.313987 TGTCTAGTGTCTGCCGTGTG 59.686 55.000 0.00 0.00 0.00 3.82
4716 7423 0.388649 GTCTAGTGTCTGCCGTGTGG 60.389 60.000 0.00 0.00 38.77 4.17
4717 7424 1.079819 CTAGTGTCTGCCGTGTGGG 60.080 63.158 0.00 0.00 39.58 4.61
4718 7425 1.532078 TAGTGTCTGCCGTGTGGGA 60.532 57.895 0.00 0.00 38.47 4.37
4719 7426 0.902984 TAGTGTCTGCCGTGTGGGAT 60.903 55.000 0.00 0.00 38.47 3.85
4720 7427 0.902984 AGTGTCTGCCGTGTGGGATA 60.903 55.000 0.00 0.00 38.47 2.59
4721 7428 0.178068 GTGTCTGCCGTGTGGGATAT 59.822 55.000 0.00 0.00 38.47 1.63
4722 7429 0.464036 TGTCTGCCGTGTGGGATATC 59.536 55.000 0.00 0.00 38.47 1.63
4723 7430 0.753262 GTCTGCCGTGTGGGATATCT 59.247 55.000 2.05 0.00 38.47 1.98
4724 7431 0.752658 TCTGCCGTGTGGGATATCTG 59.247 55.000 2.05 0.00 38.47 2.90
4725 7432 0.882042 CTGCCGTGTGGGATATCTGC 60.882 60.000 2.05 0.00 38.47 4.26
4726 7433 1.337384 TGCCGTGTGGGATATCTGCT 61.337 55.000 2.05 0.00 38.47 4.24
4727 7434 0.882042 GCCGTGTGGGATATCTGCTG 60.882 60.000 2.05 0.00 38.47 4.41
4728 7435 0.882042 CCGTGTGGGATATCTGCTGC 60.882 60.000 2.05 0.00 38.47 5.25
4729 7436 1.217585 CGTGTGGGATATCTGCTGCG 61.218 60.000 2.05 0.00 0.00 5.18
4730 7437 0.104855 GTGTGGGATATCTGCTGCGA 59.895 55.000 2.05 0.00 0.00 5.10
4731 7438 1.051008 TGTGGGATATCTGCTGCGAT 58.949 50.000 2.05 10.75 0.00 4.58
4732 7439 2.029020 GTGTGGGATATCTGCTGCGATA 60.029 50.000 13.61 13.61 0.00 2.92
4761 7468 7.399765 CCTTGATCATGGAGGATATCTCTTAGT 59.600 40.741 20.45 0.00 42.10 2.24
4764 7471 7.732140 TGATCATGGAGGATATCTCTTAGTTGT 59.268 37.037 2.05 0.00 42.10 3.32
4781 7488 4.067896 AGTTGTCCATGTGCTGACTTAAG 58.932 43.478 0.00 0.00 32.67 1.85
4798 7505 6.543465 TGACTTAAGTCCCATGCATTCATTAG 59.457 38.462 28.43 0.00 44.15 1.73
4834 7541 8.936864 GCTTTGTGTACATTGATTAAGTAGAGT 58.063 33.333 0.00 0.00 0.00 3.24
4853 7560 9.947433 AGTAGAGTTACTATACAGCTATACCAG 57.053 37.037 17.74 0.00 38.35 4.00
4855 7562 8.624367 AGAGTTACTATACAGCTATACCAGTG 57.376 38.462 0.00 0.00 0.00 3.66
4856 7563 8.219178 AGAGTTACTATACAGCTATACCAGTGT 58.781 37.037 0.00 0.00 0.00 3.55
4857 7564 8.167605 AGTTACTATACAGCTATACCAGTGTG 57.832 38.462 0.00 0.00 0.00 3.82
4859 7566 3.753294 ATACAGCTATACCAGTGTGGC 57.247 47.619 0.00 0.00 42.67 5.01
4860 7567 1.573108 ACAGCTATACCAGTGTGGCT 58.427 50.000 0.00 0.00 42.67 4.75
4862 7569 3.104512 ACAGCTATACCAGTGTGGCTTA 58.895 45.455 2.67 0.00 42.67 3.09
4863 7570 3.118738 ACAGCTATACCAGTGTGGCTTAC 60.119 47.826 2.67 0.00 42.67 2.34
4870 7578 2.002586 CCAGTGTGGCTTACTGATTCG 58.997 52.381 18.80 3.39 46.52 3.34
4905 7613 9.946165 TCTGTAATTATGTACATTAGAGTGACG 57.054 33.333 14.77 0.00 33.59 4.35
4930 7638 5.974156 TTGGATCTTCCTTCCATGTGATA 57.026 39.130 0.00 0.00 42.69 2.15
4935 7643 7.238305 TGGATCTTCCTTCCATGTGATATGTAT 59.762 37.037 0.00 0.00 38.35 2.29
4943 7651 8.456471 CCTTCCATGTGATATGTATAATGCAAG 58.544 37.037 0.00 0.00 0.00 4.01
4945 7653 6.885918 TCCATGTGATATGTATAATGCAAGGG 59.114 38.462 0.00 0.00 0.00 3.95
4963 7671 0.313987 GGTTTGCACAGGCTACAACC 59.686 55.000 0.00 0.00 41.91 3.77
4965 7673 0.184933 TTTGCACAGGCTACAACCCT 59.815 50.000 0.00 0.00 41.91 4.34
4974 7682 4.522789 ACAGGCTACAACCCTAAAAATGTG 59.477 41.667 0.00 0.00 0.00 3.21
5056 7765 4.241590 TGCATGCTTGTTAACCTTTCTG 57.758 40.909 20.33 0.00 0.00 3.02
5057 7766 3.005684 TGCATGCTTGTTAACCTTTCTGG 59.994 43.478 20.33 0.00 42.93 3.86
5058 7767 3.578688 CATGCTTGTTAACCTTTCTGGC 58.421 45.455 2.48 0.00 40.22 4.85
5059 7768 2.944129 TGCTTGTTAACCTTTCTGGCT 58.056 42.857 2.48 0.00 40.22 4.75
5060 7769 3.295973 TGCTTGTTAACCTTTCTGGCTT 58.704 40.909 2.48 0.00 40.22 4.35
5061 7770 3.704061 TGCTTGTTAACCTTTCTGGCTTT 59.296 39.130 2.48 0.00 40.22 3.51
5062 7771 4.202111 TGCTTGTTAACCTTTCTGGCTTTC 60.202 41.667 2.48 0.00 40.22 2.62
5063 7772 4.038042 GCTTGTTAACCTTTCTGGCTTTCT 59.962 41.667 2.48 0.00 40.22 2.52
5066 7775 4.821805 TGTTAACCTTTCTGGCTTTCTCTG 59.178 41.667 2.48 0.00 40.22 3.35
5109 7818 6.233434 TGTATCTCATGCTGTGACTTTTTCT 58.767 36.000 0.00 0.00 32.22 2.52
5119 7828 5.534207 TGTGACTTTTTCTTGCATGGAAT 57.466 34.783 0.00 0.00 0.00 3.01
5222 7931 5.529800 ACTTTACAACGTGCAGAGGTTTAAT 59.470 36.000 0.00 0.00 0.00 1.40
5305 8014 8.397906 TGAATTTATCCTTAGCTGTTTCAATCG 58.602 33.333 0.00 0.00 0.00 3.34
5505 8214 4.081642 TGAGCACCATTCTAACCACTACTC 60.082 45.833 0.00 0.00 0.00 2.59
5509 8218 6.384305 AGCACCATTCTAACCACTACTCTAAT 59.616 38.462 0.00 0.00 0.00 1.73
5512 8221 5.992217 CCATTCTAACCACTACTCTAATGGC 59.008 44.000 0.00 0.00 36.69 4.40
5520 8229 2.292918 ACTACTCTAATGGCCTCCACCA 60.293 50.000 3.32 0.00 45.82 4.17
5527 8236 2.044946 GGCCTCCACCATCACCAC 60.045 66.667 0.00 0.00 0.00 4.16
5530 8239 2.290287 CCTCCACCATCACCACGGA 61.290 63.158 0.00 0.00 0.00 4.69
5559 8268 1.770658 CTATGATTCAGTGGGGCTGGA 59.229 52.381 0.00 0.00 45.08 3.86
5569 8278 2.668632 GGGCTGGAATCGACACCA 59.331 61.111 11.15 11.15 34.81 4.17
5605 8314 1.152830 TGGGGCCAAGACAGAAACC 59.847 57.895 4.39 0.00 0.00 3.27
5659 8368 1.351350 TCTCCAGAAGAGGTCGACAGA 59.649 52.381 18.91 5.11 43.44 3.41
5823 8532 3.942115 GTCTTCTGTCCTGCCCTTATTTC 59.058 47.826 0.00 0.00 0.00 2.17
5829 8538 4.023291 TGTCCTGCCCTTATTTCATTTCC 58.977 43.478 0.00 0.00 0.00 3.13
5834 8543 5.656416 CCTGCCCTTATTTCATTTCCTTGTA 59.344 40.000 0.00 0.00 0.00 2.41
6133 8855 3.694072 CAGTACCTCTGAGACAGGAGAAG 59.306 52.174 6.17 0.00 46.27 2.85
6134 8856 3.589735 AGTACCTCTGAGACAGGAGAAGA 59.410 47.826 6.17 0.00 34.75 2.87
6135 8857 3.534357 ACCTCTGAGACAGGAGAAGAA 57.466 47.619 6.17 0.00 34.75 2.52
6160 8882 3.440173 AGCACAGATGAAAACAATACCGG 59.560 43.478 0.00 0.00 0.00 5.28
6259 8983 2.607892 GCGTGTGTGAGGTGAAGGC 61.608 63.158 0.00 0.00 0.00 4.35
6260 8984 1.961277 CGTGTGTGAGGTGAAGGCC 60.961 63.158 0.00 0.00 0.00 5.19
6261 8985 1.451936 GTGTGTGAGGTGAAGGCCT 59.548 57.895 0.00 0.00 42.53 5.19
6301 9029 5.253330 ACTATAGTGATCTGCTAGGCTCTC 58.747 45.833 4.10 0.00 0.00 3.20
6302 9030 1.703411 AGTGATCTGCTAGGCTCTCC 58.297 55.000 0.00 0.00 0.00 3.71
6303 9031 0.678950 GTGATCTGCTAGGCTCTCCC 59.321 60.000 0.00 0.00 0.00 4.30
6304 9032 0.262876 TGATCTGCTAGGCTCTCCCA 59.737 55.000 0.00 0.00 35.39 4.37
6336 9064 0.107312 ATCCACATGCTCTCCTGCAC 60.107 55.000 0.00 0.00 46.33 4.57
6556 9285 2.564471 CCTCAAGCAGGCCAAGAAG 58.436 57.895 5.01 0.00 34.56 2.85
6566 9295 1.947456 AGGCCAAGAAGTGTTCGTTTC 59.053 47.619 5.01 0.00 34.02 2.78
6567 9296 1.333791 GGCCAAGAAGTGTTCGTTTCG 60.334 52.381 0.00 0.00 34.02 3.46
6573 9302 4.516092 AGAAGTGTTCGTTTCGAGTTTG 57.484 40.909 0.00 0.00 37.14 2.93
6581 9310 3.992643 TCGTTTCGAGTTTGGTCCATTA 58.007 40.909 0.00 0.00 0.00 1.90
6588 9317 5.014858 TCGAGTTTGGTCCATTAGTCTACT 58.985 41.667 0.00 0.00 0.00 2.57
6590 9319 6.660521 TCGAGTTTGGTCCATTAGTCTACTAA 59.339 38.462 5.11 5.11 42.04 2.24
6591 9320 7.341256 TCGAGTTTGGTCCATTAGTCTACTAAT 59.659 37.037 9.14 9.14 46.81 1.73
6593 9322 7.793036 AGTTTGGTCCATTAGTCTACTAATCC 58.207 38.462 11.55 10.78 44.77 3.01
6595 9324 7.743116 TTGGTCCATTAGTCTACTAATCCAA 57.257 36.000 20.14 20.14 44.77 3.53
6596 9325 7.120923 TGGTCCATTAGTCTACTAATCCAAC 57.879 40.000 11.55 9.89 44.77 3.77
6637 9366 3.805971 GTGCCTAAACTTGTCTGTTACGT 59.194 43.478 0.00 0.00 0.00 3.57
6639 9368 4.271533 TGCCTAAACTTGTCTGTTACGTTG 59.728 41.667 0.00 0.00 0.00 4.10
6680 9410 7.938563 TTGTAAAATACACAAAAGTGATGCC 57.061 32.000 2.22 0.00 38.63 4.40
6974 9713 3.298317 CGCTAGACGCCAAGACTAATAC 58.702 50.000 0.00 0.00 34.21 1.89
6975 9714 3.298317 GCTAGACGCCAAGACTAATACG 58.702 50.000 0.00 0.00 0.00 3.06
6976 9715 3.243002 GCTAGACGCCAAGACTAATACGT 60.243 47.826 0.00 0.00 36.30 3.57
6977 9716 4.024556 GCTAGACGCCAAGACTAATACGTA 60.025 45.833 0.00 0.00 33.31 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.097286 GGGCATCTCCAACGCTATTAAAAA 59.903 41.667 0.00 0.00 36.21 1.94
5 6 3.630312 GGGCATCTCCAACGCTATTAAAA 59.370 43.478 0.00 0.00 36.21 1.52
6 7 3.118038 AGGGCATCTCCAACGCTATTAAA 60.118 43.478 0.00 0.00 36.21 1.52
7 8 2.438021 AGGGCATCTCCAACGCTATTAA 59.562 45.455 0.00 0.00 36.21 1.40
8 9 2.047061 AGGGCATCTCCAACGCTATTA 58.953 47.619 0.00 0.00 36.21 0.98
9 10 0.839946 AGGGCATCTCCAACGCTATT 59.160 50.000 0.00 0.00 36.21 1.73
10 11 0.839946 AAGGGCATCTCCAACGCTAT 59.160 50.000 0.00 0.00 36.21 2.97
11 12 1.491668 TAAGGGCATCTCCAACGCTA 58.508 50.000 0.00 0.00 36.21 4.26
49 50 8.377453 TGTCAAGAAAAGACACCTTCCCTAGG 62.377 46.154 0.06 0.06 40.80 3.02
50 51 4.998033 GTCAAGAAAAGACACCTTCCCTAG 59.002 45.833 0.00 0.00 36.06 3.02
52 53 3.202151 TGTCAAGAAAAGACACCTTCCCT 59.798 43.478 0.00 0.00 40.80 4.20
53 54 3.551846 TGTCAAGAAAAGACACCTTCCC 58.448 45.455 0.00 0.00 40.80 3.97
128 130 6.255020 CGGTGGATTATACGGATATAAGCAAC 59.745 42.308 0.00 3.81 40.61 4.17
137 139 2.561419 CACCTCGGTGGATTATACGGAT 59.439 50.000 8.22 0.00 42.00 4.18
138 140 1.958579 CACCTCGGTGGATTATACGGA 59.041 52.381 8.22 0.00 42.00 4.69
144 146 1.063492 TCTAGGCACCTCGGTGGATTA 60.063 52.381 17.16 0.00 45.49 1.75
159 161 0.179108 GGTACTTGTGCCGCTCTAGG 60.179 60.000 8.41 0.00 0.00 3.02
192 194 2.552315 ACTACTTTGATTGCCACCGTTG 59.448 45.455 0.00 0.00 0.00 4.10
209 211 4.816925 GCCTGGTTTTGGATCATCTACTAC 59.183 45.833 0.00 0.00 0.00 2.73
215 217 0.101219 GCGCCTGGTTTTGGATCATC 59.899 55.000 0.00 0.00 0.00 2.92
336 339 6.182627 ACTCCCGGGGTTAATTTTAACTTAG 58.817 40.000 23.50 6.91 42.00 2.18
373 377 1.466856 TTGAGATTCATGTGGGCAGC 58.533 50.000 0.00 0.00 0.00 5.25
378 382 9.642327 TGTAATTTTTCATTGAGATTCATGTGG 57.358 29.630 0.00 0.00 0.00 4.17
383 387 9.300681 AGGAGTGTAATTTTTCATTGAGATTCA 57.699 29.630 0.00 0.00 0.00 2.57
384 388 9.780413 GAGGAGTGTAATTTTTCATTGAGATTC 57.220 33.333 0.00 0.00 0.00 2.52
386 390 8.734386 GTGAGGAGTGTAATTTTTCATTGAGAT 58.266 33.333 0.00 0.00 0.00 2.75
387 391 7.095229 CGTGAGGAGTGTAATTTTTCATTGAGA 60.095 37.037 0.00 0.00 0.00 3.27
388 392 7.017645 CGTGAGGAGTGTAATTTTTCATTGAG 58.982 38.462 0.00 0.00 0.00 3.02
389 393 6.708502 TCGTGAGGAGTGTAATTTTTCATTGA 59.291 34.615 0.00 0.00 0.00 2.57
390 394 6.797033 GTCGTGAGGAGTGTAATTTTTCATTG 59.203 38.462 0.00 0.00 0.00 2.82
393 397 5.361427 TGTCGTGAGGAGTGTAATTTTTCA 58.639 37.500 0.00 0.00 0.00 2.69
421 425 1.133606 GGGTGAAAAGGGTGAGGTTCA 60.134 52.381 0.00 0.00 0.00 3.18
443 454 3.238497 GGGGGTTTGGGTTGGTGC 61.238 66.667 0.00 0.00 0.00 5.01
453 468 1.096967 GTGTGTTTCGACGGGGGTTT 61.097 55.000 0.00 0.00 0.00 3.27
471 495 0.660488 TTGTTTGTTCGCGAGCATGT 59.340 45.000 26.28 0.00 0.00 3.21
472 496 1.752753 TTTGTTTGTTCGCGAGCATG 58.247 45.000 26.28 0.00 0.00 4.06
473 497 2.483583 TTTTGTTTGTTCGCGAGCAT 57.516 40.000 26.28 0.00 0.00 3.79
474 498 2.264109 TTTTTGTTTGTTCGCGAGCA 57.736 40.000 22.26 22.26 0.00 4.26
496 520 2.294791 AGTAGCAGCGGCAATAGTAGAG 59.705 50.000 12.44 0.00 44.61 2.43
543 573 4.884257 CATTGCCATGGCCAGCGC 62.884 66.667 33.44 15.94 41.09 5.92
544 574 4.215742 CCATTGCCATGGCCAGCG 62.216 66.667 33.44 18.45 43.95 5.18
551 589 1.867233 GTAGTACTCGCCATTGCCATG 59.133 52.381 0.00 0.00 0.00 3.66
692 730 3.252458 GGATTTAATTTATGGAGCGGCGT 59.748 43.478 9.37 0.00 0.00 5.68
762 812 5.527582 GGCATTAATGGCCGGATTAGTATAG 59.472 44.000 27.12 0.00 46.49 1.31
928 978 0.036306 ACAGACCCGGAAAGCGAAAT 59.964 50.000 0.73 0.00 0.00 2.17
1157 1225 2.203788 ACAGTCCCGAGAGCCCAA 60.204 61.111 0.00 0.00 0.00 4.12
1180 1248 3.196469 CAGAACTCCAGTGGCAAGAGATA 59.804 47.826 15.11 0.00 0.00 1.98
1345 1414 0.546598 AATTCAGTCCCACCCGATCC 59.453 55.000 0.00 0.00 0.00 3.36
1472 1541 3.243053 TGGTGGTACGGGTGGTGG 61.243 66.667 0.00 0.00 0.00 4.61
1829 1907 5.620206 TCAGAGTAATGCACTGGAGAAAAA 58.380 37.500 0.00 0.00 37.72 1.94
1830 1908 5.227569 TCAGAGTAATGCACTGGAGAAAA 57.772 39.130 0.00 0.00 37.72 2.29
1831 1909 4.890158 TCAGAGTAATGCACTGGAGAAA 57.110 40.909 0.00 0.00 37.72 2.52
1870 1950 8.637986 TGAAAATGTAAACTAAGCCAACAAGAT 58.362 29.630 0.00 0.00 0.00 2.40
1926 2006 8.963130 CAAAAACATTTTTCTACTCATACGCAA 58.037 29.630 0.00 0.00 38.23 4.85
1993 2075 3.829066 TTCGTCGAGAGTTTTTCAACG 57.171 42.857 0.00 0.00 38.03 4.10
1998 2080 5.986004 ACTTCAATTCGTCGAGAGTTTTT 57.014 34.783 0.00 0.00 0.00 1.94
2008 2090 7.760340 AGATACTAGTTGGAACTTCAATTCGTC 59.240 37.037 0.00 0.00 40.37 4.20
2115 2199 4.663334 AGGTTAACCAAGAAAGCCTTAGG 58.337 43.478 26.26 0.00 38.89 2.69
2338 2423 1.794222 CGCCAGATTGTTCCCGTTC 59.206 57.895 0.00 0.00 0.00 3.95
2379 2464 0.808755 GCACGTGAGGGGTTAAATGG 59.191 55.000 22.23 0.00 32.68 3.16
2654 2761 4.999950 GCTTCTGTATTGGATACCCAGATG 59.000 45.833 0.00 0.00 44.60 2.90
2720 2835 2.848691 CCAAGCAAATGGCCAAAGAAA 58.151 42.857 10.96 0.00 46.50 2.52
2760 2875 2.699321 GGAGGGACCCAACTAGTACATC 59.301 54.545 14.60 0.00 0.00 3.06
2857 2975 5.465724 GGGTGGCAAATAAATCGTAGAGTAG 59.534 44.000 0.00 0.00 43.63 2.57
2873 2991 3.464878 TGGCAAAATAGGGTGGCAA 57.535 47.368 0.00 0.00 46.13 4.52
2957 3076 1.086696 AATGTGCCCGATTGTTCTCG 58.913 50.000 0.00 0.00 38.37 4.04
3207 4110 0.395586 TGTGCAACCTGAACTTGCCT 60.396 50.000 0.00 0.00 42.91 4.75
3215 4118 6.676950 CATAAAGTACAAATGTGCAACCTGA 58.323 36.000 4.49 0.00 34.36 3.86
3243 4146 2.098607 CACAGCAAATGTATGGCTCTGG 59.901 50.000 0.00 0.00 41.41 3.86
3249 4152 1.470285 GCCAGCACAGCAAATGTATGG 60.470 52.381 6.94 6.94 44.95 2.74
3286 4192 5.322754 CCCTGATAATACTACCTCTTCCGA 58.677 45.833 0.00 0.00 0.00 4.55
3287 4193 4.463186 CCCCTGATAATACTACCTCTTCCG 59.537 50.000 0.00 0.00 0.00 4.30
3304 4210 2.093658 GCGTTTCAAGTCTATCCCCTGA 60.094 50.000 0.00 0.00 0.00 3.86
3309 4215 2.007608 GTGGGCGTTTCAAGTCTATCC 58.992 52.381 0.00 0.00 0.00 2.59
3323 4229 1.153549 GAGAGGTAGCTTGTGGGCG 60.154 63.158 0.00 0.00 37.29 6.13
3412 4318 2.848691 CCAAGCAAATGGCCAAAGAAA 58.151 42.857 10.96 0.00 46.50 2.52
3456 4448 2.047844 CCGTGCAGACAGACCCAG 60.048 66.667 0.00 0.00 0.00 4.45
3464 4456 0.811616 CCTGATAAGCCCGTGCAGAC 60.812 60.000 0.00 0.00 41.13 3.51
3472 4464 0.839946 TTGCCTCTCCTGATAAGCCC 59.160 55.000 0.00 0.00 0.00 5.19
3493 4485 4.096984 GCTTCCAATTAGAGGACCATGTTG 59.903 45.833 0.00 0.00 34.19 3.33
3501 4493 5.481473 AGCAAAAATGCTTCCAATTAGAGGA 59.519 36.000 0.00 0.00 43.52 3.71
3600 4592 9.149225 TGCACATTTTTAAATTTATAGTGCCAG 57.851 29.630 23.17 9.89 40.06 4.85
3712 4704 6.418523 CCCCACAAGAACGTTATTTTAACAAC 59.581 38.462 5.22 0.00 0.00 3.32
3725 4717 1.376037 GGAGCTCCCCACAAGAACG 60.376 63.158 23.19 0.00 0.00 3.95
3808 4800 2.457366 AAGGTCCAGCTAGTGTTTCG 57.543 50.000 0.00 0.00 0.00 3.46
3851 4843 8.840200 TTAGATCTAGACCCAGTGAACTAAAT 57.160 34.615 2.02 0.00 0.00 1.40
3989 4982 2.543012 CGGCAGATCTGAAGCACATTAG 59.457 50.000 27.04 0.00 0.00 1.73
4012 5005 2.889170 TGGTTAAGCCAATAGGTGCA 57.111 45.000 1.51 0.00 45.94 4.57
4117 5110 0.402121 AAGAGGTCAAAGGGCAGGAC 59.598 55.000 0.00 0.00 0.00 3.85
4150 5143 7.392766 TCCATCCCTCTGATAATTGTACATT 57.607 36.000 0.00 0.00 30.56 2.71
4165 5158 5.995446 AGAACTGAAACTATTCCATCCCTC 58.005 41.667 0.00 0.00 34.49 4.30
4219 5212 6.060788 AGCCTTAGATGGATGAAATCTCAAC 58.939 40.000 0.00 0.00 44.71 3.18
4274 5267 9.594478 GGGTATTATGAAACACCATTTAAAAGG 57.406 33.333 7.92 7.92 32.42 3.11
4289 5282 7.782644 AGATCCAAATTTTCCGGGTATTATGAA 59.217 33.333 0.00 0.00 0.00 2.57
4343 5336 2.969821 ACCAACTTCACCTGGCAATA 57.030 45.000 0.00 0.00 36.03 1.90
4418 5419 4.541973 TCTATGCAGAGCTCTGTTTCAA 57.458 40.909 37.25 21.48 45.45 2.69
4468 5469 6.926630 TTAATATTTTGAAAGGGTGGCAGT 57.073 33.333 0.00 0.00 0.00 4.40
4491 5492 5.473504 CCTGGCAGTACATGTAGTTCTTTTT 59.526 40.000 14.43 0.00 0.00 1.94
4492 5493 5.003804 CCTGGCAGTACATGTAGTTCTTTT 58.996 41.667 14.43 0.00 0.00 2.27
4553 5556 5.302823 AGCCCAAAATTGATGCTATTCCTAC 59.697 40.000 7.93 0.00 35.37 3.18
4584 5587 3.885297 ACAAGGGAAGTGTTTCATGTCAG 59.115 43.478 0.00 0.00 34.90 3.51
4587 5590 3.885297 CAGACAAGGGAAGTGTTTCATGT 59.115 43.478 0.00 0.00 34.90 3.21
4588 5591 3.254166 CCAGACAAGGGAAGTGTTTCATG 59.746 47.826 0.00 0.00 34.90 3.07
4595 7302 1.271054 CCAGACCAGACAAGGGAAGTG 60.271 57.143 0.00 0.00 0.00 3.16
4600 7307 1.352352 ACATTCCAGACCAGACAAGGG 59.648 52.381 0.00 0.00 0.00 3.95
4627 7334 6.762333 AGAATAATGGAGTTTTTGCTTTGCT 58.238 32.000 0.00 0.00 0.00 3.91
4629 7336 8.822652 AGAAGAATAATGGAGTTTTTGCTTTG 57.177 30.769 0.00 0.00 0.00 2.77
4630 7337 9.836864 AAAGAAGAATAATGGAGTTTTTGCTTT 57.163 25.926 0.00 0.00 0.00 3.51
4632 7339 9.836864 AAAAAGAAGAATAATGGAGTTTTTGCT 57.163 25.926 0.00 0.00 0.00 3.91
4660 7367 2.276409 GGCCACCTGCATGGATCA 59.724 61.111 10.63 0.00 43.02 2.92
4692 7399 2.094494 CACGGCAGACACTAGACAGAAT 60.094 50.000 0.00 0.00 0.00 2.40
4694 7401 0.881796 CACGGCAGACACTAGACAGA 59.118 55.000 0.00 0.00 0.00 3.41
4695 7402 0.598562 ACACGGCAGACACTAGACAG 59.401 55.000 0.00 0.00 0.00 3.51
4697 7404 0.388649 CCACACGGCAGACACTAGAC 60.389 60.000 0.00 0.00 0.00 2.59
4699 7406 1.079819 CCCACACGGCAGACACTAG 60.080 63.158 0.00 0.00 0.00 2.57
4701 7408 0.902984 TATCCCACACGGCAGACACT 60.903 55.000 0.00 0.00 0.00 3.55
4702 7409 0.178068 ATATCCCACACGGCAGACAC 59.822 55.000 0.00 0.00 0.00 3.67
4703 7410 0.464036 GATATCCCACACGGCAGACA 59.536 55.000 0.00 0.00 0.00 3.41
4704 7411 0.753262 AGATATCCCACACGGCAGAC 59.247 55.000 0.00 0.00 0.00 3.51
4705 7412 0.752658 CAGATATCCCACACGGCAGA 59.247 55.000 0.00 0.00 0.00 4.26
4706 7413 0.882042 GCAGATATCCCACACGGCAG 60.882 60.000 0.00 0.00 0.00 4.85
4707 7414 1.146041 GCAGATATCCCACACGGCA 59.854 57.895 0.00 0.00 0.00 5.69
4708 7415 0.882042 CAGCAGATATCCCACACGGC 60.882 60.000 0.00 0.00 0.00 5.68
4709 7416 0.882042 GCAGCAGATATCCCACACGG 60.882 60.000 0.00 0.00 0.00 4.94
4710 7417 1.217585 CGCAGCAGATATCCCACACG 61.218 60.000 0.00 0.00 0.00 4.49
4711 7418 0.104855 TCGCAGCAGATATCCCACAC 59.895 55.000 0.00 0.00 0.00 3.82
4712 7419 1.051008 ATCGCAGCAGATATCCCACA 58.949 50.000 0.00 0.00 0.00 4.17
4713 7420 3.319137 TTATCGCAGCAGATATCCCAC 57.681 47.619 0.00 0.00 33.60 4.61
4714 7421 3.118629 GGATTATCGCAGCAGATATCCCA 60.119 47.826 0.00 0.00 33.60 4.37
4715 7422 3.133721 AGGATTATCGCAGCAGATATCCC 59.866 47.826 18.55 15.66 34.72 3.85
4716 7423 4.399004 AGGATTATCGCAGCAGATATCC 57.601 45.455 16.75 16.75 34.57 2.59
4717 7424 5.414360 TCAAGGATTATCGCAGCAGATATC 58.586 41.667 7.49 0.00 33.60 1.63
4718 7425 5.411831 TCAAGGATTATCGCAGCAGATAT 57.588 39.130 7.49 0.00 33.60 1.63
4719 7426 4.871933 TCAAGGATTATCGCAGCAGATA 57.128 40.909 0.00 0.00 32.39 1.98
4720 7427 3.758755 TCAAGGATTATCGCAGCAGAT 57.241 42.857 0.00 0.00 34.79 2.90
4721 7428 3.070015 TGATCAAGGATTATCGCAGCAGA 59.930 43.478 0.00 0.00 0.00 4.26
4722 7429 3.396560 TGATCAAGGATTATCGCAGCAG 58.603 45.455 0.00 0.00 0.00 4.24
4723 7430 3.473923 TGATCAAGGATTATCGCAGCA 57.526 42.857 0.00 0.00 0.00 4.41
4724 7431 3.126514 CCATGATCAAGGATTATCGCAGC 59.873 47.826 11.68 0.00 0.00 5.25
4725 7432 4.572909 TCCATGATCAAGGATTATCGCAG 58.427 43.478 15.63 0.00 0.00 5.18
4726 7433 4.564199 CCTCCATGATCAAGGATTATCGCA 60.564 45.833 19.51 0.00 32.53 5.10
4727 7434 3.937706 CCTCCATGATCAAGGATTATCGC 59.062 47.826 19.51 0.00 32.53 4.58
4728 7435 5.411831 TCCTCCATGATCAAGGATTATCG 57.588 43.478 19.51 7.99 34.26 2.92
4729 7436 8.936787 AGATATCCTCCATGATCAAGGATTATC 58.063 37.037 25.48 23.57 45.57 1.75
4730 7437 8.873156 AGATATCCTCCATGATCAAGGATTAT 57.127 34.615 25.48 19.87 45.57 1.28
4731 7438 8.127692 AGAGATATCCTCCATGATCAAGGATTA 58.872 37.037 25.48 15.42 45.57 1.75
4732 7439 6.967056 AGAGATATCCTCCATGATCAAGGATT 59.033 38.462 25.48 16.20 45.57 3.01
4761 7468 4.065088 GACTTAAGTCAGCACATGGACAA 58.935 43.478 27.12 0.00 44.18 3.18
4764 7471 2.027192 GGGACTTAAGTCAGCACATGGA 60.027 50.000 31.30 0.00 46.47 3.41
4781 7488 3.484407 AGAGCTAATGAATGCATGGGAC 58.516 45.455 0.00 0.00 34.26 4.46
4834 7541 6.015688 GCCACACTGGTATAGCTGTATAGTAA 60.016 42.308 13.26 0.00 40.46 2.24
4850 7557 2.002586 CGAATCAGTAAGCCACACTGG 58.997 52.381 9.36 0.00 42.98 4.00
4852 7559 1.276421 AGCGAATCAGTAAGCCACACT 59.724 47.619 0.00 0.00 0.00 3.55
4853 7560 1.726853 AGCGAATCAGTAAGCCACAC 58.273 50.000 0.00 0.00 0.00 3.82
4855 7562 3.166489 AGTAGCGAATCAGTAAGCCAC 57.834 47.619 0.00 0.00 0.00 5.01
4856 7563 3.887621 AAGTAGCGAATCAGTAAGCCA 57.112 42.857 0.00 0.00 0.00 4.75
4857 7564 6.144724 CAGAATAAGTAGCGAATCAGTAAGCC 59.855 42.308 0.00 0.00 0.00 4.35
4859 7566 9.731819 TTACAGAATAAGTAGCGAATCAGTAAG 57.268 33.333 0.00 0.00 0.00 2.34
4898 7606 2.028020 AGGAAGATCCAAACCGTCACTC 60.028 50.000 0.00 0.00 39.61 3.51
4943 7651 0.313987 GTTGTAGCCTGTGCAAACCC 59.686 55.000 0.00 0.00 41.13 4.11
4945 7653 0.313987 GGGTTGTAGCCTGTGCAAAC 59.686 55.000 0.00 0.00 37.72 2.93
4954 7662 4.082408 GGTCACATTTTTAGGGTTGTAGCC 60.082 45.833 0.00 0.00 35.59 3.93
5056 7765 3.471680 ACAACTTCTCACAGAGAAAGCC 58.528 45.455 10.33 0.00 46.18 4.35
5057 7766 5.269313 CAAACAACTTCTCACAGAGAAAGC 58.731 41.667 10.33 0.00 46.18 3.51
5058 7767 5.163723 TGCAAACAACTTCTCACAGAGAAAG 60.164 40.000 10.33 7.49 46.18 2.62
5059 7768 4.699735 TGCAAACAACTTCTCACAGAGAAA 59.300 37.500 10.33 0.00 46.18 2.52
5060 7769 4.260985 TGCAAACAACTTCTCACAGAGAA 58.739 39.130 8.94 8.94 45.01 2.87
5061 7770 3.872696 TGCAAACAACTTCTCACAGAGA 58.127 40.909 0.00 0.00 36.86 3.10
5062 7771 4.514441 AGATGCAAACAACTTCTCACAGAG 59.486 41.667 0.00 0.00 0.00 3.35
5063 7772 4.274214 CAGATGCAAACAACTTCTCACAGA 59.726 41.667 0.00 0.00 0.00 3.41
5066 7775 4.558538 ACAGATGCAAACAACTTCTCAC 57.441 40.909 0.00 0.00 0.00 3.51
5109 7818 3.694926 TGTCATACACCATTCCATGCAA 58.305 40.909 0.00 0.00 0.00 4.08
5119 7828 0.246360 CTCACGGCTGTCATACACCA 59.754 55.000 0.00 0.00 0.00 4.17
5222 7931 3.251484 AGGGAGAGGAACACTTTGATGA 58.749 45.455 0.00 0.00 0.00 2.92
5305 8014 6.036191 GCACTACTACAAGACAGGATTTTAGC 59.964 42.308 0.00 0.00 0.00 3.09
5509 8218 2.531428 TGGTGATGGTGGAGGCCA 60.531 61.111 5.01 0.00 43.48 5.36
5512 8221 2.268920 CCGTGGTGATGGTGGAGG 59.731 66.667 0.00 0.00 0.00 4.30
5520 8229 1.371183 CACTGGTGTCCGTGGTGAT 59.629 57.895 0.00 0.00 0.00 3.06
5527 8236 2.205074 GAATCATAGCACTGGTGTCCG 58.795 52.381 2.64 0.00 0.00 4.79
5530 8239 3.603532 CACTGAATCATAGCACTGGTGT 58.396 45.455 2.64 0.00 0.00 4.16
5569 8278 4.589908 CCCCACTTATACTTGACAGCTTT 58.410 43.478 0.00 0.00 0.00 3.51
5659 8368 2.043852 ACCGAGAGCTCACCGGAT 60.044 61.111 37.40 24.89 45.58 4.18
5823 8532 7.485913 CGGACAAATCTCATTTACAAGGAAATG 59.514 37.037 10.79 10.79 44.68 2.32
5829 8538 6.456181 GCTCTCGGACAAATCTCATTTACAAG 60.456 42.308 0.00 0.00 0.00 3.16
5834 8543 3.274288 GGCTCTCGGACAAATCTCATTT 58.726 45.455 0.00 0.00 0.00 2.32
5844 8553 1.372499 CGAAAACGGCTCTCGGACA 60.372 57.895 0.00 0.00 44.45 4.02
5845 8554 1.071567 CTCGAAAACGGCTCTCGGAC 61.072 60.000 0.00 0.00 44.45 4.79
5846 8555 1.211969 CTCGAAAACGGCTCTCGGA 59.788 57.895 0.00 0.00 44.45 4.55
5872 8581 9.692749 CTTTTTCTTCCAATTTTAGGGACTTAC 57.307 33.333 0.00 0.00 41.75 2.34
6071 8793 3.039011 GTTCTCTTCCCACCATAGCCTA 58.961 50.000 0.00 0.00 0.00 3.93
6133 8855 6.803807 GGTATTGTTTTCATCTGTGCTTCTTC 59.196 38.462 0.00 0.00 0.00 2.87
6134 8856 6.568462 CGGTATTGTTTTCATCTGTGCTTCTT 60.568 38.462 0.00 0.00 0.00 2.52
6135 8857 5.106555 CGGTATTGTTTTCATCTGTGCTTCT 60.107 40.000 0.00 0.00 0.00 2.85
6160 8882 1.375523 ATGTCAACGGCGAAGTCCC 60.376 57.895 16.62 0.00 0.00 4.46
6259 8983 3.983741 AGTTCAGTTTCTCAAGACGAGG 58.016 45.455 0.00 0.00 42.55 4.63
6260 8984 7.483375 CACTATAGTTCAGTTTCTCAAGACGAG 59.517 40.741 1.56 0.00 43.80 4.18
6261 8985 7.174426 TCACTATAGTTCAGTTTCTCAAGACGA 59.826 37.037 1.56 0.00 0.00 4.20
6284 9008 0.678950 GGGAGAGCCTAGCAGATCAC 59.321 60.000 0.00 0.00 0.00 3.06
6301 9029 1.145531 TGGATGGCCACATAATCTGGG 59.854 52.381 8.16 0.00 39.92 4.45
6302 9030 2.662535 TGGATGGCCACATAATCTGG 57.337 50.000 8.16 0.00 39.92 3.86
6326 9054 0.593128 CCAAAAACCGTGCAGGAGAG 59.407 55.000 8.24 0.00 45.00 3.20
6336 9064 2.661195 CGCAATCTAAAGCCAAAAACCG 59.339 45.455 0.00 0.00 0.00 4.44
6551 9280 4.201783 CCAAACTCGAAACGAACACTTCTT 60.202 41.667 0.00 0.00 34.74 2.52
6553 9282 3.063045 ACCAAACTCGAAACGAACACTTC 59.937 43.478 0.00 0.00 34.74 3.01
6556 9285 2.286008 GGACCAAACTCGAAACGAACAC 60.286 50.000 0.00 0.00 34.74 3.32
6566 9295 5.326200 AGTAGACTAATGGACCAAACTCG 57.674 43.478 0.00 0.00 0.00 4.18
6567 9296 7.927092 GGATTAGTAGACTAATGGACCAAACTC 59.073 40.741 17.56 2.73 46.07 3.01
6573 9302 6.040166 TCGTTGGATTAGTAGACTAATGGACC 59.960 42.308 17.56 13.27 46.07 4.46
6588 9317 9.825109 TCATGATGTATTTAACTCGTTGGATTA 57.175 29.630 0.00 0.00 0.00 1.75
6590 9319 7.987458 ACTCATGATGTATTTAACTCGTTGGAT 59.013 33.333 0.00 0.00 0.00 3.41
6591 9320 7.277760 CACTCATGATGTATTTAACTCGTTGGA 59.722 37.037 0.00 0.00 0.00 3.53
6593 9322 6.901887 GCACTCATGATGTATTTAACTCGTTG 59.098 38.462 0.00 0.00 0.00 4.10
6595 9324 5.523916 GGCACTCATGATGTATTTAACTCGT 59.476 40.000 0.00 0.00 0.00 4.18
6596 9325 5.755375 AGGCACTCATGATGTATTTAACTCG 59.245 40.000 0.00 0.00 0.00 4.18
6673 9402 1.737236 TGCGACAAGTTATGGCATCAC 59.263 47.619 1.65 2.79 36.57 3.06
6680 9410 0.179225 GCACCGTGCGACAAGTTATG 60.179 55.000 7.96 0.00 31.71 1.90
6942 9681 0.041576 CGTCTAGCGTGCGTGCTATA 60.042 55.000 9.80 1.21 45.79 1.31
6974 9713 9.898806 GCGATAGTAGACTGTATAAGTAATACG 57.101 37.037 0.00 0.00 40.31 3.06
6977 9716 9.947433 AGAGCGATAGTAGACTGTATAAGTAAT 57.053 33.333 0.00 0.00 37.66 1.89


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

AutoCloner maintained by Alex Coulton.