Multiple sequence alignment - TraesCS2B01G403000

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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 TraesCS2B01G403000 chr2B 100.000 5540 0 0 1 5540 571515212 571520751 0.000000e+00 10231
1 TraesCS2B01G403000 chr2A 94.086 2198 90 13 534 2707 631948804 631950985 0.000000e+00 3302
2 TraesCS2B01G403000 chr2A 88.011 1418 87 27 3438 4855 631952550 631953884 0.000000e+00 1600
3 TraesCS2B01G403000 chr2A 86.385 639 81 6 4903 5537 631953885 631954521 0.000000e+00 693
4 TraesCS2B01G403000 chr2A 82.175 662 45 32 2709 3344 631951204 631951818 8.290000e-138 501
5 TraesCS2B01G403000 chr2A 86.353 425 33 10 137 536 631948127 631948551 1.830000e-119 440
6 TraesCS2B01G403000 chr2A 94.581 203 11 0 3911 4113 714523110 714523312 1.160000e-81 315
7 TraesCS2B01G403000 chr2A 95.714 70 3 0 1 70 631878601 631878670 4.540000e-21 113
8 TraesCS2B01G403000 chr2D 88.810 1412 90 31 3438 4838 486504628 486505982 0.000000e+00 1670
9 TraesCS2B01G403000 chr2D 96.377 966 31 2 1704 2667 486500996 486501959 0.000000e+00 1587
10 TraesCS2B01G403000 chr2D 90.587 1158 71 9 569 1707 486499758 486500896 0.000000e+00 1500
11 TraesCS2B01G403000 chr2D 84.466 721 88 13 4821 5537 486574640 486575340 0.000000e+00 689
12 TraesCS2B01G403000 chr2D 92.357 471 27 6 2791 3260 486503237 486503699 0.000000e+00 662
13 TraesCS2B01G403000 chr2D 86.225 559 55 12 1 537 486496717 486497275 2.220000e-163 586
14 TraesCS2B01G403000 chr2D 77.725 211 36 10 4873 5077 32408492 32408697 9.750000e-23 119
15 TraesCS2B01G403000 chr7D 78.533 559 117 3 1763 2318 4794075 4794633 1.130000e-96 364
16 TraesCS2B01G403000 chr4A 78.393 560 116 5 1766 2321 738889298 738888740 5.280000e-95 359
17 TraesCS2B01G403000 chr4A 73.761 545 128 13 1786 2321 739273648 739274186 3.380000e-47 200
18 TraesCS2B01G403000 chr4A 71.380 877 218 24 1786 2647 739311339 739312197 1.220000e-46 198
19 TraesCS2B01G403000 chr7A 78.253 561 115 7 1763 2318 4626560 4627118 2.460000e-93 353
20 TraesCS2B01G403000 chr7A 93.596 203 13 0 3911 4113 646630453 646630251 2.510000e-78 303
21 TraesCS2B01G403000 chr7A 74.406 547 121 17 1786 2321 4069939 4069401 3.360000e-52 217
22 TraesCS2B01G403000 chr6B 93.564 202 13 0 3912 4113 7163717 7163918 9.020000e-78 302
23 TraesCS2B01G403000 chr6B 93.103 203 14 0 3911 4113 66691121 66691323 1.170000e-76 298
24 TraesCS2B01G403000 chr6B 71.365 901 224 26 1766 2643 18658347 18657458 2.620000e-48 204
25 TraesCS2B01G403000 chr3B 93.103 203 14 0 3911 4113 25306184 25305982 1.170000e-76 298
26 TraesCS2B01G403000 chr1B 93.103 203 14 0 3911 4113 635527098 635527300 1.170000e-76 298
27 TraesCS2B01G403000 chr5B 92.611 203 15 0 3911 4113 529033699 529033901 5.430000e-75 292
28 TraesCS2B01G403000 chr6D 71.556 900 224 24 1766 2643 10068558 10067669 1.210000e-51 215


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 TraesCS2B01G403000 chr2B 571515212 571520751 5539 False 10231.0 10231 100.0000 1 5540 1 chr2B.!!$F1 5539
1 TraesCS2B01G403000 chr2A 631948127 631954521 6394 False 1307.2 3302 87.4020 137 5537 5 chr2A.!!$F3 5400
2 TraesCS2B01G403000 chr2D 486496717 486505982 9265 False 1201.0 1670 90.8712 1 4838 5 chr2D.!!$F3 4837
3 TraesCS2B01G403000 chr2D 486574640 486575340 700 False 689.0 689 84.4660 4821 5537 1 chr2D.!!$F2 716
4 TraesCS2B01G403000 chr7D 4794075 4794633 558 False 364.0 364 78.5330 1763 2318 1 chr7D.!!$F1 555
5 TraesCS2B01G403000 chr4A 738888740 738889298 558 True 359.0 359 78.3930 1766 2321 1 chr4A.!!$R1 555
6 TraesCS2B01G403000 chr7A 4626560 4627118 558 False 353.0 353 78.2530 1763 2318 1 chr7A.!!$F1 555
7 TraesCS2B01G403000 chr7A 4069401 4069939 538 True 217.0 217 74.4060 1786 2321 1 chr7A.!!$R1 535
8 TraesCS2B01G403000 chr6B 18657458 18658347 889 True 204.0 204 71.3650 1766 2643 1 chr6B.!!$R1 877
9 TraesCS2B01G403000 chr6D 10067669 10068558 889 True 215.0 215 71.5560 1766 2643 1 chr6D.!!$R1 877

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
964 3705 0.528684 GCATGCGTCTCCTCTACCAC 60.529 60.0 0.00 0.00 0.00 4.16 F
1549 4302 0.102663 GGGTTCCGATCGACCTCTTC 59.897 60.0 21.34 5.38 36.18 2.87 F
2728 5884 0.620030 ATGCACATGTGACTAGGCCA 59.380 50.0 29.80 15.48 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2707 5599 0.379669 GCCTAGTCACATGTGCATGC 59.620 55.000 21.38 11.82 42.39 4.06 R
2941 7148 1.153647 CGCGCCAGTCTATTGGACA 60.154 57.895 0.00 0.00 46.72 4.02 R
4647 9946 0.035152 CCACCAATAGCCTCACTGCA 60.035 55.000 0.00 0.00 0.00 4.41 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
22 23 5.461032 CCTAAACCTGGAGCTAGATACAG 57.539 47.826 13.61 13.61 0.00 2.74
31 32 9.245481 ACCTGGAGCTAGATACAGTTTATATAC 57.755 37.037 18.75 0.00 0.00 1.47
36 37 9.771915 GAGCTAGATACAGTTTATATACGTTCC 57.228 37.037 0.00 0.00 0.00 3.62
45 46 7.147620 ACAGTTTATATACGTTCCCCATGAAGA 60.148 37.037 0.00 0.00 32.37 2.87
52 53 2.716217 GTTCCCCATGAAGAGGTTCTG 58.284 52.381 0.00 0.00 32.37 3.02
54 55 1.203428 TCCCCATGAAGAGGTTCTGGA 60.203 52.381 0.00 0.00 34.98 3.86
74 75 0.774276 TGGGTGAAGTTACATGGGCA 59.226 50.000 0.00 0.00 0.00 5.36
93 94 2.165167 CACAACCCAATCTCATGCTGT 58.835 47.619 0.00 0.00 0.00 4.40
105 106 1.908619 TCATGCTGTAGGAAAGGCTGA 59.091 47.619 0.00 0.00 0.00 4.26
113 114 4.164981 TGTAGGAAAGGCTGAAGGTCTAA 58.835 43.478 0.00 0.00 0.00 2.10
131 132 5.603767 GTCTAAGACAAGTTCGGTGTTCCG 61.604 50.000 0.00 0.00 44.03 4.30
167 168 2.959030 TGGACCATCTCTGGACTTATCG 59.041 50.000 0.00 0.00 46.37 2.92
212 213 2.359531 AGAGATAAAGCCTCGAGTTCCG 59.640 50.000 12.31 0.00 35.88 4.30
213 214 2.358267 GAGATAAAGCCTCGAGTTCCGA 59.642 50.000 12.31 0.00 46.35 4.55
233 234 3.295973 GAGCTGAACTCTAGGATGTCCT 58.704 50.000 6.81 6.81 42.62 3.85
263 265 5.865552 TGACACACGAGTATAAAGGTAAAGC 59.134 40.000 0.00 0.00 0.00 3.51
286 288 3.553508 CCAAAGCTTCAGGTTGTCCAATG 60.554 47.826 0.00 0.00 35.72 2.82
297 299 1.078848 GTCCAATGGCTCTGCGTCT 60.079 57.895 0.00 0.00 0.00 4.18
300 302 0.674581 CCAATGGCTCTGCGTCTTGA 60.675 55.000 0.00 0.00 0.00 3.02
351 353 3.935828 GTGCTTCTTCCTTCGCTTATCTT 59.064 43.478 0.00 0.00 0.00 2.40
370 373 5.710513 TCTTTTGGATGAAGGAACATGTG 57.289 39.130 0.00 0.00 0.00 3.21
371 374 5.139727 TCTTTTGGATGAAGGAACATGTGT 58.860 37.500 0.00 0.00 0.00 3.72
373 376 4.852134 TTGGATGAAGGAACATGTGTTG 57.148 40.909 0.00 0.00 38.56 3.33
374 377 3.831323 TGGATGAAGGAACATGTGTTGT 58.169 40.909 0.00 0.00 41.53 3.32
375 378 3.569277 TGGATGAAGGAACATGTGTTGTG 59.431 43.478 0.00 0.00 38.99 3.33
377 380 4.320494 GGATGAAGGAACATGTGTTGTGTC 60.320 45.833 0.00 0.00 38.99 3.67
385 412 3.930336 ACATGTGTTGTGTCGATCTCAT 58.070 40.909 0.00 0.00 37.11 2.90
506 533 3.594603 AGACACACGTAATGGAGAAGG 57.405 47.619 4.21 0.00 0.00 3.46
605 3338 6.994496 CACTATGTTGATTCTATGACCCACAT 59.006 38.462 0.00 0.00 42.39 3.21
609 3342 5.647658 TGTTGATTCTATGACCCACATGAAC 59.352 40.000 0.00 0.00 39.77 3.18
646 3379 1.228306 CCGTCCTCCTCCTATCGCT 60.228 63.158 0.00 0.00 0.00 4.93
785 3519 0.969149 CTTCCCAAACAAAGGGCTCC 59.031 55.000 0.00 0.00 46.36 4.70
834 3573 2.166459 TGTCTCTTCCATACAAGGCTCG 59.834 50.000 0.00 0.00 0.00 5.03
883 3622 1.032014 GCTCCTTCTGCTCTCTCGAT 58.968 55.000 0.00 0.00 0.00 3.59
891 3630 0.947960 TGCTCTCTCGATCGATCCAC 59.052 55.000 19.78 8.19 0.00 4.02
896 3635 3.655486 TCTCTCGATCGATCCACTAGTC 58.345 50.000 19.78 0.00 0.00 2.59
904 3643 5.617973 CGATCGATCCACTAGTCCATACTTG 60.618 48.000 19.51 0.00 37.15 3.16
945 3684 3.993234 GTGCTCGATCGCCGCATG 61.993 66.667 26.55 8.73 38.37 4.06
964 3705 0.528684 GCATGCGTCTCCTCTACCAC 60.529 60.000 0.00 0.00 0.00 4.16
973 3714 2.581246 TCTCCTCTACCACTAGCTCCAA 59.419 50.000 0.00 0.00 0.00 3.53
980 3721 0.678048 CCACTAGCTCCAACAAGCCC 60.678 60.000 0.00 0.00 43.56 5.19
983 3724 0.615331 CTAGCTCCAACAAGCCCAGA 59.385 55.000 0.00 0.00 43.56 3.86
1163 3916 4.484258 GCTCCTTCTCGCGCTCGT 62.484 66.667 5.56 0.00 36.96 4.18
1179 3932 2.532256 CGTCGGGCTCGTCGTCTAT 61.532 63.158 17.46 0.00 41.45 1.98
1181 3934 1.890979 TCGGGCTCGTCGTCTATCC 60.891 63.158 5.57 0.00 37.69 2.59
1222 3975 1.009900 GCCGACACGATAGGAGACG 60.010 63.158 0.00 0.00 43.77 4.18
1303 4056 3.382832 CGGAGAAGTCCACCGCCT 61.383 66.667 0.00 0.00 44.18 5.52
1472 4225 3.603532 ACTTGGATACGTACGTCTCTGA 58.396 45.455 26.53 15.04 42.51 3.27
1488 4241 6.655003 ACGTCTCTGAATACAAACATTTCCAT 59.345 34.615 0.00 0.00 0.00 3.41
1549 4302 0.102663 GGGTTCCGATCGACCTCTTC 59.897 60.000 21.34 5.38 36.18 2.87
1550 4303 1.104630 GGTTCCGATCGACCTCTTCT 58.895 55.000 18.66 0.00 33.08 2.85
1551 4304 1.065851 GGTTCCGATCGACCTCTTCTC 59.934 57.143 18.66 0.00 33.08 2.87
1552 4305 1.743958 GTTCCGATCGACCTCTTCTCA 59.256 52.381 18.66 0.00 0.00 3.27
1553 4306 2.350057 TCCGATCGACCTCTTCTCAT 57.650 50.000 18.66 0.00 0.00 2.90
1554 4307 2.222886 TCCGATCGACCTCTTCTCATC 58.777 52.381 18.66 0.00 0.00 2.92
1555 4308 1.069568 CCGATCGACCTCTTCTCATCG 60.070 57.143 18.66 0.00 35.72 3.84
1556 4309 1.867865 CGATCGACCTCTTCTCATCGA 59.132 52.381 10.26 0.00 46.59 3.59
1557 4310 2.349060 CGATCGACCTCTTCTCATCGAC 60.349 54.545 10.26 0.00 45.50 4.20
1558 4311 1.380524 TCGACCTCTTCTCATCGACC 58.619 55.000 0.00 0.00 38.59 4.79
1559 4312 1.065345 TCGACCTCTTCTCATCGACCT 60.065 52.381 0.00 0.00 38.59 3.85
1560 4313 1.332375 CGACCTCTTCTCATCGACCTC 59.668 57.143 0.00 0.00 36.70 3.85
1561 4314 2.650322 GACCTCTTCTCATCGACCTCT 58.350 52.381 0.00 0.00 0.00 3.69
1562 4315 2.616842 GACCTCTTCTCATCGACCTCTC 59.383 54.545 0.00 0.00 0.00 3.20
1591 4358 2.127003 GGTAAGTTGTTGCCGCGC 60.127 61.111 0.00 0.00 0.00 6.86
1592 4359 2.498887 GTAAGTTGTTGCCGCGCG 60.499 61.111 25.67 25.67 0.00 6.86
1593 4360 4.377661 TAAGTTGTTGCCGCGCGC 62.378 61.111 27.36 23.91 38.31 6.86
1663 4430 1.079503 GGTTCTAGCGTTTCTGGCTG 58.920 55.000 0.00 0.00 41.69 4.85
1671 4438 2.027625 GTTTCTGGCTGGACCGTCG 61.028 63.158 0.00 0.00 43.94 5.12
1672 4439 3.876589 TTTCTGGCTGGACCGTCGC 62.877 63.158 0.00 0.00 43.94 5.19
1729 4599 8.396272 ACTAGCTTTCATGTCTTAATTGTTGT 57.604 30.769 0.00 0.00 0.00 3.32
1732 4603 7.889469 AGCTTTCATGTCTTAATTGTTGTGAT 58.111 30.769 0.00 0.00 0.00 3.06
1733 4604 7.811236 AGCTTTCATGTCTTAATTGTTGTGATG 59.189 33.333 0.00 0.00 0.00 3.07
1734 4605 7.809331 GCTTTCATGTCTTAATTGTTGTGATGA 59.191 33.333 0.00 0.00 0.00 2.92
1735 4606 9.681692 CTTTCATGTCTTAATTGTTGTGATGAA 57.318 29.630 0.00 0.00 0.00 2.57
2241 5120 0.816373 GTACAGGACCGAGGACTTCC 59.184 60.000 0.00 0.00 0.00 3.46
2325 5204 0.901580 GGACTTCTACCCGGTGTCCA 60.902 60.000 16.48 0.00 44.59 4.02
2327 5206 1.214589 CTTCTACCCGGTGTCCACG 59.785 63.158 0.00 0.00 0.00 4.94
2647 5539 1.898154 CGTCCCTCCAGGTAACCAG 59.102 63.158 0.00 0.00 36.75 4.00
2657 5549 2.613977 CCAGGTAACCAGCTCACTCAAG 60.614 54.545 0.00 0.00 37.17 3.02
2660 5552 4.160439 CAGGTAACCAGCTCACTCAAGATA 59.840 45.833 0.00 0.00 37.17 1.98
2667 5559 3.698539 CAGCTCACTCAAGATAGGTCTCA 59.301 47.826 0.00 0.00 32.15 3.27
2669 5561 4.341806 AGCTCACTCAAGATAGGTCTCATG 59.658 45.833 0.00 0.00 32.15 3.07
2670 5562 4.619973 CTCACTCAAGATAGGTCTCATGC 58.380 47.826 0.00 0.00 32.15 4.06
2680 5572 5.601729 AGATAGGTCTCATGCTCTCATTTCA 59.398 40.000 0.00 0.00 0.00 2.69
2728 5884 0.620030 ATGCACATGTGACTAGGCCA 59.380 50.000 29.80 15.48 0.00 5.36
2740 5896 3.245514 TGACTAGGCCACCTTACTGTACT 60.246 47.826 5.01 0.00 34.61 2.73
2741 5897 3.097614 ACTAGGCCACCTTACTGTACTG 58.902 50.000 5.01 0.00 34.61 2.74
2744 5900 2.501723 AGGCCACCTTACTGTACTGATG 59.498 50.000 5.01 0.00 0.00 3.07
2746 5902 2.093447 GCCACCTTACTGTACTGATGCT 60.093 50.000 6.77 0.00 0.00 3.79
2748 5904 3.195610 CCACCTTACTGTACTGATGCTCA 59.804 47.826 6.77 0.00 0.00 4.26
2752 5908 6.204688 CACCTTACTGTACTGATGCTCAAAAA 59.795 38.462 6.77 0.00 0.00 1.94
2795 6978 4.666253 AGGTGCATGCCGGCTTGT 62.666 61.111 34.64 18.27 34.04 3.16
2797 6980 2.339556 GGTGCATGCCGGCTTGTAA 61.340 57.895 34.64 24.04 34.04 2.41
2802 6985 1.403679 GCATGCCGGCTTGTAAATACA 59.596 47.619 34.64 11.01 0.00 2.29
2803 6986 2.159310 GCATGCCGGCTTGTAAATACAA 60.159 45.455 34.64 10.48 43.32 2.41
2882 7079 1.373999 GCTGCACGTCTCTCTTGCT 60.374 57.895 0.00 0.00 41.11 3.91
2887 7084 1.066914 CACGTCTCTCTTGCTTGCTC 58.933 55.000 0.00 0.00 0.00 4.26
2890 7087 1.458827 CGTCTCTCTTGCTTGCTCAAC 59.541 52.381 0.00 0.00 0.00 3.18
3180 7387 7.229707 TCGAAATGAAATGTTCAAGGTTTCCTA 59.770 33.333 8.73 0.00 43.95 2.94
3181 7388 7.865385 CGAAATGAAATGTTCAAGGTTTCCTAA 59.135 33.333 8.73 0.00 43.95 2.69
3212 7419 1.852895 GGCGTGTTCATAGTGATCGAC 59.147 52.381 0.00 0.00 0.00 4.20
3219 7426 6.472486 CGTGTTCATAGTGATCGACATTAGTT 59.528 38.462 0.00 0.00 0.00 2.24
3222 7429 8.683615 TGTTCATAGTGATCGACATTAGTTAGT 58.316 33.333 0.00 0.00 0.00 2.24
3223 7430 9.171701 GTTCATAGTGATCGACATTAGTTAGTC 57.828 37.037 0.00 0.00 0.00 2.59
3224 7431 8.446599 TCATAGTGATCGACATTAGTTAGTCA 57.553 34.615 0.00 0.00 34.48 3.41
3225 7432 8.899771 TCATAGTGATCGACATTAGTTAGTCAA 58.100 33.333 0.00 0.00 34.48 3.18
3260 7467 2.811431 TGATGCACTAACCAAAAGGTCG 59.189 45.455 0.00 0.00 0.00 4.79
3262 7469 0.110373 GCACTAACCAAAAGGTCGCG 60.110 55.000 0.00 0.00 0.00 5.87
3265 7472 1.202557 ACTAACCAAAAGGTCGCGTGA 60.203 47.619 5.77 0.00 0.00 4.35
3266 7473 1.868498 CTAACCAAAAGGTCGCGTGAA 59.132 47.619 5.77 0.00 0.00 3.18
3267 7474 1.096416 AACCAAAAGGTCGCGTGAAA 58.904 45.000 5.77 0.00 0.00 2.69
3268 7475 1.096416 ACCAAAAGGTCGCGTGAAAA 58.904 45.000 5.77 0.00 0.00 2.29
3269 7476 1.679153 ACCAAAAGGTCGCGTGAAAAT 59.321 42.857 5.77 0.00 0.00 1.82
3270 7477 2.050691 CCAAAAGGTCGCGTGAAAATG 58.949 47.619 5.77 0.15 0.00 2.32
3271 7478 2.542824 CCAAAAGGTCGCGTGAAAATGT 60.543 45.455 5.77 0.00 0.00 2.71
3272 7479 3.112580 CAAAAGGTCGCGTGAAAATGTT 58.887 40.909 5.77 0.00 0.00 2.71
3273 7480 3.430333 AAAGGTCGCGTGAAAATGTTT 57.570 38.095 5.77 0.00 0.00 2.83
3274 7481 3.430333 AAGGTCGCGTGAAAATGTTTT 57.570 38.095 5.77 0.00 0.00 2.43
3275 7482 3.430333 AGGTCGCGTGAAAATGTTTTT 57.570 38.095 5.77 0.00 0.00 1.94
3276 7483 3.112580 AGGTCGCGTGAAAATGTTTTTG 58.887 40.909 5.77 0.00 0.00 2.44
3277 7484 3.109619 GGTCGCGTGAAAATGTTTTTGA 58.890 40.909 5.77 0.00 0.00 2.69
3278 7485 3.179599 GGTCGCGTGAAAATGTTTTTGAG 59.820 43.478 5.77 0.00 0.00 3.02
3279 7486 3.179599 GTCGCGTGAAAATGTTTTTGAGG 59.820 43.478 5.77 0.00 0.00 3.86
3309 7516 4.385146 GCTTTCTGCTGCTTCATTTCTTTC 59.615 41.667 0.00 0.00 38.95 2.62
3320 7527 6.017109 TGCTTCATTTCTTTCTACTTGTCCAC 60.017 38.462 0.00 0.00 0.00 4.02
3334 7541 0.759346 GTCCACTTCCAGGCGGATAT 59.241 55.000 0.00 0.00 42.41 1.63
3335 7542 1.048601 TCCACTTCCAGGCGGATATC 58.951 55.000 0.00 0.00 42.41 1.63
3347 7554 3.383825 AGGCGGATATCGTTTTCTAGTGT 59.616 43.478 0.00 0.00 41.72 3.55
3348 7555 4.581824 AGGCGGATATCGTTTTCTAGTGTA 59.418 41.667 0.00 0.00 41.72 2.90
3381 7588 9.574516 AACTTAACAATTCCACAGACTATTCTT 57.425 29.630 0.00 0.00 0.00 2.52
3407 7614 4.461992 TTTCTAACGGAAGCAAAAGACG 57.538 40.909 0.00 0.00 35.16 4.18
3408 7615 3.102052 TCTAACGGAAGCAAAAGACGT 57.898 42.857 0.00 0.00 39.74 4.34
3426 7633 7.724305 AAGACGTGCTTCTTTTTATTAGTCA 57.276 32.000 0.00 0.00 31.39 3.41
3427 7634 7.352719 AGACGTGCTTCTTTTTATTAGTCAG 57.647 36.000 0.00 0.00 0.00 3.51
3428 7635 7.152645 AGACGTGCTTCTTTTTATTAGTCAGA 58.847 34.615 0.00 0.00 0.00 3.27
3429 7636 7.656137 AGACGTGCTTCTTTTTATTAGTCAGAA 59.344 33.333 0.00 0.00 0.00 3.02
3430 7637 8.149973 ACGTGCTTCTTTTTATTAGTCAGAAA 57.850 30.769 0.00 0.00 0.00 2.52
3431 7638 8.068380 ACGTGCTTCTTTTTATTAGTCAGAAAC 58.932 33.333 0.00 0.00 0.00 2.78
3432 7639 8.283291 CGTGCTTCTTTTTATTAGTCAGAAACT 58.717 33.333 0.00 0.00 42.33 2.66
3433 7640 9.600646 GTGCTTCTTTTTATTAGTCAGAAACTC 57.399 33.333 0.00 0.00 39.55 3.01
3434 7641 9.337396 TGCTTCTTTTTATTAGTCAGAAACTCA 57.663 29.630 0.00 0.00 39.55 3.41
3435 7642 9.600646 GCTTCTTTTTATTAGTCAGAAACTCAC 57.399 33.333 0.00 0.00 39.55 3.51
3444 8702 5.028549 AGTCAGAAACTCACATCACAGTT 57.971 39.130 0.00 0.00 30.02 3.16
3461 8727 6.966021 TCACAGTTACATTAGTTTTGCCTTC 58.034 36.000 0.00 0.00 0.00 3.46
3478 8744 2.602878 CTTCCTTAAGTCGTAGCGCAA 58.397 47.619 11.47 0.00 0.00 4.85
3486 8761 1.611977 AGTCGTAGCGCAATATAGGCA 59.388 47.619 11.47 0.00 0.00 4.75
3487 8762 1.986378 GTCGTAGCGCAATATAGGCAG 59.014 52.381 11.47 0.00 0.00 4.85
3488 8763 1.883926 TCGTAGCGCAATATAGGCAGA 59.116 47.619 11.47 0.00 0.00 4.26
3489 8764 2.095212 TCGTAGCGCAATATAGGCAGAG 60.095 50.000 11.47 0.00 0.00 3.35
3490 8765 1.996191 GTAGCGCAATATAGGCAGAGC 59.004 52.381 11.47 0.00 0.00 4.09
3491 8766 0.394192 AGCGCAATATAGGCAGAGCA 59.606 50.000 11.47 0.00 0.00 4.26
3492 8767 0.514691 GCGCAATATAGGCAGAGCAC 59.485 55.000 0.30 0.00 0.00 4.40
3493 8768 1.869774 CGCAATATAGGCAGAGCACA 58.130 50.000 0.00 0.00 0.00 4.57
3494 8769 1.528586 CGCAATATAGGCAGAGCACAC 59.471 52.381 0.00 0.00 0.00 3.82
3495 8770 2.564771 GCAATATAGGCAGAGCACACA 58.435 47.619 0.00 0.00 0.00 3.72
3496 8771 3.144506 GCAATATAGGCAGAGCACACAT 58.855 45.455 0.00 0.00 0.00 3.21
3497 8772 3.058432 GCAATATAGGCAGAGCACACATG 60.058 47.826 0.00 0.00 0.00 3.21
3687 8962 4.722700 CTCCGTTGTGCCCCTGGG 62.723 72.222 5.50 5.50 38.57 4.45
3719 8994 2.734670 CAACACAGGTGAGTTGCATTG 58.265 47.619 6.40 0.00 39.12 2.82
3720 8995 0.670162 ACACAGGTGAGTTGCATTGC 59.330 50.000 6.40 0.46 0.00 3.56
3721 8996 0.669619 CACAGGTGAGTTGCATTGCA 59.330 50.000 7.38 7.38 36.47 4.08
3722 8997 0.956633 ACAGGTGAGTTGCATTGCAG 59.043 50.000 11.76 0.12 40.61 4.41
3723 8998 0.242825 CAGGTGAGTTGCATTGCAGG 59.757 55.000 11.76 0.00 40.61 4.85
3724 8999 1.080298 GGTGAGTTGCATTGCAGGC 60.080 57.895 11.76 9.05 40.61 4.85
3725 9000 1.080298 GTGAGTTGCATTGCAGGCC 60.080 57.895 11.76 0.00 40.61 5.19
3741 9016 3.644606 CCCCCTCTGCACTGCACT 61.645 66.667 0.00 0.00 33.79 4.40
3745 9020 0.954449 CCCTCTGCACTGCACTTCTG 60.954 60.000 0.00 0.00 33.79 3.02
3746 9021 0.250209 CCTCTGCACTGCACTTCTGT 60.250 55.000 0.00 0.00 33.79 3.41
3747 9022 1.146637 CTCTGCACTGCACTTCTGTC 58.853 55.000 0.00 0.00 33.79 3.51
3748 9023 0.250038 TCTGCACTGCACTTCTGTCC 60.250 55.000 0.00 0.00 33.79 4.02
3749 9024 1.563435 CTGCACTGCACTTCTGTCCG 61.563 60.000 0.00 0.00 33.79 4.79
3750 9025 1.300931 GCACTGCACTTCTGTCCGA 60.301 57.895 0.00 0.00 0.00 4.55
3752 9027 1.354040 CACTGCACTTCTGTCCGATC 58.646 55.000 0.00 0.00 0.00 3.69
3755 9030 0.601057 TGCACTTCTGTCCGATCGAA 59.399 50.000 18.66 0.00 0.00 3.71
3756 9031 1.000394 TGCACTTCTGTCCGATCGAAA 60.000 47.619 18.66 0.63 0.00 3.46
3757 9032 1.656095 GCACTTCTGTCCGATCGAAAG 59.344 52.381 18.66 13.34 0.00 2.62
3758 9033 2.927014 GCACTTCTGTCCGATCGAAAGT 60.927 50.000 18.66 13.93 0.00 2.66
3759 9034 2.917971 CACTTCTGTCCGATCGAAAGTC 59.082 50.000 18.66 0.00 0.00 3.01
3760 9035 2.094649 ACTTCTGTCCGATCGAAAGTCC 60.095 50.000 18.66 0.00 0.00 3.85
3761 9036 0.450583 TCTGTCCGATCGAAAGTCCG 59.549 55.000 18.66 0.00 0.00 4.79
3762 9037 0.450583 CTGTCCGATCGAAAGTCCGA 59.549 55.000 18.66 0.00 43.16 4.55
3763 9038 0.883153 TGTCCGATCGAAAGTCCGAA 59.117 50.000 18.66 0.00 42.22 4.30
3764 9039 1.270274 TGTCCGATCGAAAGTCCGAAA 59.730 47.619 18.66 0.00 42.22 3.46
3765 9040 1.652619 GTCCGATCGAAAGTCCGAAAC 59.347 52.381 18.66 0.00 42.22 2.78
3766 9041 1.542915 TCCGATCGAAAGTCCGAAACT 59.457 47.619 18.66 0.00 42.22 2.66
3767 9042 1.654105 CCGATCGAAAGTCCGAAACTG 59.346 52.381 18.66 0.00 42.22 3.16
3768 9043 1.654105 CGATCGAAAGTCCGAAACTGG 59.346 52.381 10.26 0.00 42.22 4.00
3769 9044 2.000447 GATCGAAAGTCCGAAACTGGG 59.000 52.381 0.00 0.00 42.22 4.45
3797 9072 1.014352 GAGCACCAACGTTGACAGTT 58.986 50.000 29.35 15.46 0.00 3.16
3798 9073 1.003866 GAGCACCAACGTTGACAGTTC 60.004 52.381 29.35 19.38 0.00 3.01
3800 9075 0.303493 CACCAACGTTGACAGTTCGG 59.697 55.000 29.35 12.44 0.00 4.30
3801 9076 0.176219 ACCAACGTTGACAGTTCGGA 59.824 50.000 29.35 0.00 0.00 4.55
3803 9078 0.580104 CAACGTTGACAGTTCGGACC 59.420 55.000 23.90 0.00 0.00 4.46
3804 9079 0.462789 AACGTTGACAGTTCGGACCT 59.537 50.000 0.00 0.00 0.00 3.85
3805 9080 0.249322 ACGTTGACAGTTCGGACCTG 60.249 55.000 0.52 0.52 0.00 4.00
3806 9081 0.944311 CGTTGACAGTTCGGACCTGG 60.944 60.000 7.49 0.00 0.00 4.45
3807 9082 0.106149 GTTGACAGTTCGGACCTGGT 59.894 55.000 7.49 0.00 0.00 4.00
3808 9083 0.105964 TTGACAGTTCGGACCTGGTG 59.894 55.000 2.82 0.00 0.00 4.17
3809 9084 1.668151 GACAGTTCGGACCTGGTGC 60.668 63.158 2.82 6.05 0.00 5.01
3811 9086 4.003788 AGTTCGGACCTGGTGCGG 62.004 66.667 34.81 19.50 46.71 5.69
4020 9313 3.087031 CCGTCTACTTCTACCTGGTCAA 58.913 50.000 0.63 0.00 0.00 3.18
4136 9429 4.337274 TCGACCTTAATCTGCACGATCTTA 59.663 41.667 0.00 0.00 0.00 2.10
4157 9453 1.519455 CGTCAGGTCATCGAAGGCC 60.519 63.158 2.30 2.30 0.00 5.19
4178 9474 2.869354 CGATCTCGTTAAGGCCGTC 58.131 57.895 0.00 0.00 34.11 4.79
4205 9501 2.418910 CCTCGTCCCTGTGCTCGAT 61.419 63.158 0.00 0.00 0.00 3.59
4259 9555 9.595357 GTACGTTTCTTAAAGGAAATTCAGAAG 57.405 33.333 0.00 0.00 37.50 2.85
4260 9556 7.139392 ACGTTTCTTAAAGGAAATTCAGAAGC 58.861 34.615 0.00 0.00 37.50 3.86
4261 9557 6.303259 CGTTTCTTAAAGGAAATTCAGAAGCG 59.697 38.462 12.11 12.11 37.90 4.68
4262 9558 6.877611 TTCTTAAAGGAAATTCAGAAGCGT 57.122 33.333 0.00 0.00 0.00 5.07
4263 9559 6.481954 TCTTAAAGGAAATTCAGAAGCGTC 57.518 37.500 0.00 0.00 0.00 5.19
4264 9560 5.995282 TCTTAAAGGAAATTCAGAAGCGTCA 59.005 36.000 1.61 0.00 0.00 4.35
4265 9561 4.756084 AAAGGAAATTCAGAAGCGTCAG 57.244 40.909 1.61 0.00 0.00 3.51
4276 9572 3.483922 CAGAAGCGTCAGTCGACATATTC 59.516 47.826 19.50 12.07 42.74 1.75
4294 9590 8.004087 ACATATTCTGATTGATTGGTCTTTGG 57.996 34.615 0.00 0.00 0.00 3.28
4389 9686 2.818169 GGGCGGGAGGACATGCATA 61.818 63.158 0.00 0.00 0.00 3.14
4392 9689 1.498865 GCGGGAGGACATGCATAACG 61.499 60.000 0.00 0.00 0.00 3.18
4410 9707 3.055110 TCGCGCGTGTACCCTACA 61.055 61.111 30.98 2.41 36.08 2.74
4500 9797 1.959985 TCGATCAAGATCTGGGAGCTC 59.040 52.381 4.71 4.71 35.72 4.09
4544 9841 9.774071 TCCATATCCAGATTCATCATAAGTAGA 57.226 33.333 0.00 0.00 0.00 2.59
4576 9873 6.695292 CAATGTTTGCCTCAATAGTTTGAC 57.305 37.500 0.00 0.00 36.94 3.18
4668 9967 1.745141 GCAGTGAGGCTATTGGTGGAG 60.745 57.143 0.00 0.00 0.00 3.86
4670 9969 2.026822 CAGTGAGGCTATTGGTGGAGTT 60.027 50.000 0.00 0.00 0.00 3.01
4674 9973 3.266772 TGAGGCTATTGGTGGAGTTCAAT 59.733 43.478 0.00 0.00 37.38 2.57
4681 9980 7.363793 GGCTATTGGTGGAGTTCAATTGTATTT 60.364 37.037 5.13 0.00 35.50 1.40
4805 10104 6.662865 TTGGGAATGTAAAAATGAGAGCAA 57.337 33.333 0.00 0.00 0.00 3.91
4861 10160 3.359515 AAGCGGTGGTGCGCGTATA 62.360 57.895 8.43 0.00 40.67 1.47
4862 10161 2.638330 AAGCGGTGGTGCGCGTATAT 62.638 55.000 8.43 0.00 40.67 0.86
4888 10187 2.745968 TGAAGGGTCAAACCAAGCTTT 58.254 42.857 0.00 0.00 41.02 3.51
4890 10189 3.634910 TGAAGGGTCAAACCAAGCTTTAC 59.365 43.478 0.00 0.00 41.02 2.01
4901 10200 8.691797 TCAAACCAAGCTTTACTACTCAAATTT 58.308 29.630 0.00 0.00 0.00 1.82
4942 10243 0.987294 AGGGTCATGGGTTCAGACAG 59.013 55.000 0.00 0.00 34.04 3.51
4984 10286 3.703556 TCCAAAAATGTGAGAACTTGGCA 59.296 39.130 0.00 0.00 34.57 4.92
4992 10294 4.469657 TGTGAGAACTTGGCAAACCTATT 58.530 39.130 0.00 0.00 36.63 1.73
5052 10354 3.118905 ACAAGTGTGAGAAGAAGCTCC 57.881 47.619 0.00 0.00 33.95 4.70
5088 10390 2.383442 ATGATAGCACCGTACCCTCT 57.617 50.000 0.00 0.00 0.00 3.69
5169 10471 0.537143 TGGAGCGCCAAATGTTCTGT 60.537 50.000 6.75 0.00 42.49 3.41
5218 10520 1.599542 GCTTCCAACATCGCTACATCC 59.400 52.381 0.00 0.00 0.00 3.51
5226 10528 2.626266 ACATCGCTACATCCGTAATCCA 59.374 45.455 0.00 0.00 0.00 3.41
5234 10536 4.073293 ACATCCGTAATCCACAAGATCC 57.927 45.455 0.00 0.00 32.47 3.36
5269 10571 4.666512 TGCCTTGAAAATTTCCTAGCTCT 58.333 39.130 3.00 0.00 0.00 4.09
5271 10573 5.539955 TGCCTTGAAAATTTCCTAGCTCTTT 59.460 36.000 3.00 0.00 0.00 2.52
5279 10581 1.447838 CCTAGCTCTTTTCGGCGCA 60.448 57.895 10.83 0.00 0.00 6.09
5293 10595 4.891727 CGCACTCCCGCCGCTAAT 62.892 66.667 0.00 0.00 0.00 1.73
5336 10638 4.280929 AGATCCCGACATCGACATGAATTA 59.719 41.667 0.00 0.00 43.02 1.40
5377 10679 2.883574 CGCATAGTTGGTTTCGGTAGA 58.116 47.619 0.00 0.00 0.00 2.59
5383 10685 2.701951 AGTTGGTTTCGGTAGAGTCCAA 59.298 45.455 0.00 0.00 38.02 3.53
5386 10688 1.622312 GGTTTCGGTAGAGTCCAAGGT 59.378 52.381 0.00 0.00 0.00 3.50
5394 10696 0.419459 AGAGTCCAAGGTGGGGATCT 59.581 55.000 0.00 0.00 38.32 2.75
5409 10711 0.395686 GATCTGATGCTGCTAGGCCA 59.604 55.000 5.01 0.00 0.00 5.36
5415 10717 1.776975 ATGCTGCTAGGCCAGGATCC 61.777 60.000 5.01 2.48 39.30 3.36
5417 10719 3.527775 CTGCTAGGCCAGGATCCGC 62.528 68.421 5.01 4.41 0.00 5.54
5431 10733 2.698274 GGATCCGCCCCAAACAATATTT 59.302 45.455 0.00 0.00 0.00 1.40
5432 10734 3.133901 GGATCCGCCCCAAACAATATTTT 59.866 43.478 0.00 0.00 0.00 1.82
5450 10752 1.017177 TTGTGTCTTATGCGCCGGTC 61.017 55.000 4.18 0.00 0.00 4.79
5473 10775 2.576002 GCGTTTGCACAAACTGGCG 61.576 57.895 20.53 10.88 46.21 5.69
5477 10779 3.748071 TTGCACAAACTGGCGCACG 62.748 57.895 10.83 0.70 31.18 5.34
5491 10794 3.068881 CACGCCCCTCTCCTTTGA 58.931 61.111 0.00 0.00 0.00 2.69
5497 10800 1.519719 CCCTCTCCTTTGAGCTCGG 59.480 63.158 9.64 4.39 38.58 4.63
5501 10804 4.082523 TCCTTTGAGCTCGGCCCG 62.083 66.667 9.64 0.00 0.00 6.13
5514 10817 1.603326 TCGGCCCGTTTAACACTTTTC 59.397 47.619 1.63 0.00 0.00 2.29
5516 10819 2.350102 CGGCCCGTTTAACACTTTTCTC 60.350 50.000 0.00 0.00 0.00 2.87
5518 10821 3.058432 GGCCCGTTTAACACTTTTCTCTC 60.058 47.826 0.00 0.00 0.00 3.20
5519 10822 3.363673 GCCCGTTTAACACTTTTCTCTCG 60.364 47.826 0.00 0.00 0.00 4.04
5520 10823 3.805971 CCCGTTTAACACTTTTCTCTCGT 59.194 43.478 0.00 0.00 0.00 4.18
5523 10826 5.005971 CCGTTTAACACTTTTCTCTCGTTCA 59.994 40.000 0.00 0.00 0.00 3.18
5539 10844 1.765750 GTTCAAAACGTTTCTCGCACG 59.234 47.619 15.01 0.00 44.19 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.972832 GGGGAACGTATATAAACTGTATCTAGC 59.027 40.741 0.00 0.00 0.00 3.42
14 15 8.938801 TGGGGAACGTATATAAACTGTATCTA 57.061 34.615 0.00 0.00 0.00 1.98
22 23 6.649557 CCTCTTCATGGGGAACGTATATAAAC 59.350 42.308 0.00 0.00 0.00 2.01
31 32 1.279271 AGAACCTCTTCATGGGGAACG 59.721 52.381 0.00 0.00 0.00 3.95
36 37 2.422519 CCATCCAGAACCTCTTCATGGG 60.423 54.545 0.00 0.00 32.84 4.00
45 46 1.747444 ACTTCACCCATCCAGAACCT 58.253 50.000 0.00 0.00 0.00 3.50
52 53 2.654863 CCCATGTAACTTCACCCATCC 58.345 52.381 0.00 0.00 0.00 3.51
54 55 1.357420 TGCCCATGTAACTTCACCCAT 59.643 47.619 0.00 0.00 0.00 4.00
74 75 2.592102 ACAGCATGAGATTGGGTTGT 57.408 45.000 0.00 0.00 39.69 3.32
93 94 4.466726 GTCTTAGACCTTCAGCCTTTCCTA 59.533 45.833 0.00 0.00 0.00 2.94
105 106 3.387050 ACACCGAACTTGTCTTAGACCTT 59.613 43.478 10.10 0.00 0.00 3.50
131 132 2.158667 TGGTCCAAAACTCCAGTCCTTC 60.159 50.000 0.00 0.00 0.00 3.46
137 138 3.341823 CAGAGATGGTCCAAAACTCCAG 58.658 50.000 15.70 8.83 34.62 3.86
146 147 2.959030 CGATAAGTCCAGAGATGGTCCA 59.041 50.000 0.00 0.00 0.00 4.02
167 168 1.444553 CACTTCTCGACACCTCGGC 60.445 63.158 0.00 0.00 40.58 5.54
190 191 3.564644 CGGAACTCGAGGCTTTATCTCTA 59.435 47.826 18.41 0.00 42.43 2.43
212 213 3.068024 CAGGACATCCTAGAGTTCAGCTC 59.932 52.174 0.00 0.00 46.65 4.09
213 214 3.030291 CAGGACATCCTAGAGTTCAGCT 58.970 50.000 0.00 0.00 46.65 4.24
215 216 2.697751 CCCAGGACATCCTAGAGTTCAG 59.302 54.545 0.00 0.00 46.65 3.02
233 234 0.901827 ATACTCGTGTGTCATGCCCA 59.098 50.000 0.00 0.00 0.00 5.36
263 265 0.961753 GGACAACCTGAAGCTTTGGG 59.038 55.000 19.29 16.97 0.00 4.12
275 277 1.885871 GCAGAGCCATTGGACAACC 59.114 57.895 6.95 0.00 0.00 3.77
286 288 0.603975 AAGGTTCAAGACGCAGAGCC 60.604 55.000 0.00 0.00 35.60 4.70
297 299 2.238521 GACTCCAATGCCAAGGTTCAA 58.761 47.619 0.00 0.00 0.00 2.69
300 302 0.779997 AGGACTCCAATGCCAAGGTT 59.220 50.000 0.00 0.00 0.00 3.50
351 353 4.648762 ACAACACATGTTCCTTCATCCAAA 59.351 37.500 0.00 0.00 40.06 3.28
370 373 5.062308 GTCAAAGGTATGAGATCGACACAAC 59.938 44.000 0.00 1.36 0.00 3.32
371 374 5.168569 GTCAAAGGTATGAGATCGACACAA 58.831 41.667 0.00 0.00 0.00 3.33
373 376 4.744570 TGTCAAAGGTATGAGATCGACAC 58.255 43.478 0.00 0.00 0.00 3.67
374 377 5.451937 GGATGTCAAAGGTATGAGATCGACA 60.452 44.000 7.93 0.00 45.95 4.35
375 378 4.985409 GGATGTCAAAGGTATGAGATCGAC 59.015 45.833 7.93 0.00 45.95 4.20
377 380 5.207110 AGGATGTCAAAGGTATGAGATCG 57.793 43.478 7.93 0.00 45.95 3.69
385 412 3.491766 AGAGGGAGGATGTCAAAGGTA 57.508 47.619 0.00 0.00 0.00 3.08
605 3338 3.307906 CGACCAGGACCCGGTTCA 61.308 66.667 0.00 0.00 36.69 3.18
673 3406 0.979187 GGTGAACGGGGTCTATGGGA 60.979 60.000 0.00 0.00 0.00 4.37
785 3519 1.325640 CAGTGTGGCGATGATCTTTCG 59.674 52.381 12.46 12.46 39.55 3.46
834 3573 3.187700 CGGGCGATATTTATAGACAGCC 58.812 50.000 0.00 0.00 42.32 4.85
883 3622 4.533815 ACAAGTATGGACTAGTGGATCGA 58.466 43.478 0.00 0.00 33.58 3.59
891 3630 3.021695 TCACGGGACAAGTATGGACTAG 58.978 50.000 0.00 0.00 33.58 2.57
896 3635 2.482721 GTGTTTCACGGGACAAGTATGG 59.517 50.000 0.00 0.00 0.00 2.74
904 3643 0.736053 TGCTTTGTGTTTCACGGGAC 59.264 50.000 0.00 0.00 37.14 4.46
945 3684 0.528684 GTGGTAGAGGAGACGCATGC 60.529 60.000 7.91 7.91 0.00 4.06
964 3705 0.615331 TCTGGGCTTGTTGGAGCTAG 59.385 55.000 0.00 0.00 42.32 3.42
973 3714 0.390860 CGCTAGCTATCTGGGCTTGT 59.609 55.000 13.93 0.00 40.74 3.16
980 3721 2.371158 GCTGCGCGCTAGCTATCTG 61.371 63.158 33.28 15.67 42.32 2.90
1163 3916 1.890979 GGATAGACGACGAGCCCGA 60.891 63.158 0.00 0.00 39.50 5.14
1179 3932 4.738998 CCGCCATGCCCTTGTGGA 62.739 66.667 0.00 0.00 37.72 4.02
1202 3955 1.826921 TCTCCTATCGTGTCGGCCC 60.827 63.158 0.00 0.00 0.00 5.80
1208 3961 1.666054 GACCTCGTCTCCTATCGTGT 58.334 55.000 0.00 0.00 0.00 4.49
1210 3963 1.159098 GCGACCTCGTCTCCTATCGT 61.159 60.000 0.00 0.00 42.22 3.73
1213 3966 1.153208 ACGCGACCTCGTCTCCTAT 60.153 57.895 15.93 0.00 38.44 2.57
1214 3967 2.267006 ACGCGACCTCGTCTCCTA 59.733 61.111 15.93 0.00 38.44 2.94
1278 4031 2.637383 GGACTTCTCCGACACGCCT 61.637 63.158 0.00 0.00 0.00 5.52
1472 4225 9.777297 AGTTAGCAAAATGGAAATGTTTGTATT 57.223 25.926 0.00 0.00 35.22 1.89
1488 4241 2.685897 ACGCAAGACCAAGTTAGCAAAA 59.314 40.909 0.00 0.00 43.62 2.44
1549 4302 1.885887 GGATCTGGAGAGGTCGATGAG 59.114 57.143 0.00 0.00 28.76 2.90
1550 4303 1.479573 GGGATCTGGAGAGGTCGATGA 60.480 57.143 0.00 0.00 28.76 2.92
1551 4304 0.965439 GGGATCTGGAGAGGTCGATG 59.035 60.000 0.00 0.00 28.76 3.84
1552 4305 0.558220 TGGGATCTGGAGAGGTCGAT 59.442 55.000 0.00 0.00 28.76 3.59
1553 4306 0.335019 TTGGGATCTGGAGAGGTCGA 59.665 55.000 0.00 0.00 28.76 4.20
1554 4307 0.461961 GTTGGGATCTGGAGAGGTCG 59.538 60.000 0.00 0.00 28.76 4.79
1555 4308 0.461961 CGTTGGGATCTGGAGAGGTC 59.538 60.000 0.00 0.00 0.00 3.85
1556 4309 0.978146 CCGTTGGGATCTGGAGAGGT 60.978 60.000 0.00 0.00 34.06 3.85
1557 4310 0.978146 ACCGTTGGGATCTGGAGAGG 60.978 60.000 0.00 0.00 36.97 3.69
1558 4311 1.776662 TACCGTTGGGATCTGGAGAG 58.223 55.000 0.00 0.00 36.97 3.20
1559 4312 2.108168 CTTACCGTTGGGATCTGGAGA 58.892 52.381 0.00 0.00 36.97 3.71
1560 4313 1.831736 ACTTACCGTTGGGATCTGGAG 59.168 52.381 0.00 0.00 36.97 3.86
1561 4314 1.946984 ACTTACCGTTGGGATCTGGA 58.053 50.000 0.00 0.00 36.97 3.86
1562 4315 2.781681 AACTTACCGTTGGGATCTGG 57.218 50.000 0.00 0.00 33.72 3.86
1591 4358 4.908687 TGGATTGATCGGCCGGCG 62.909 66.667 27.83 16.23 0.00 6.46
1592 4359 2.974698 CTGGATTGATCGGCCGGC 60.975 66.667 27.83 21.18 0.00 6.13
1593 4360 1.595382 GTCTGGATTGATCGGCCGG 60.595 63.158 27.83 6.80 0.00 6.13
1649 4416 1.295423 GGTCCAGCCAGAAACGCTA 59.705 57.895 0.00 0.00 33.91 4.26
1663 4430 2.709475 GCATTGATGCGACGGTCC 59.291 61.111 1.91 0.00 44.67 4.46
1672 4439 0.528901 CATTGGGCCGTGCATTGATG 60.529 55.000 0.00 0.00 0.00 3.07
1684 4451 3.736483 ATCGCACGATCATTGGGC 58.264 55.556 0.00 0.00 0.00 5.36
2241 5120 2.097038 GCAGCAGGTCGTAGTGCAG 61.097 63.158 8.04 2.11 42.47 4.41
2613 5501 3.801997 CGCCCAGCCCTTGAGGAT 61.802 66.667 0.00 0.00 38.24 3.24
2647 5539 4.619973 CATGAGACCTATCTTGAGTGAGC 58.380 47.826 0.00 0.00 34.34 4.26
2657 5549 5.851720 TGAAATGAGAGCATGAGACCTATC 58.148 41.667 0.00 0.00 34.26 2.08
2660 5552 4.774660 ATGAAATGAGAGCATGAGACCT 57.225 40.909 0.00 0.00 34.26 3.85
2667 5559 2.957006 GCCAGGAATGAAATGAGAGCAT 59.043 45.455 0.00 0.00 35.92 3.79
2669 5561 2.372264 TGCCAGGAATGAAATGAGAGC 58.628 47.619 0.00 0.00 0.00 4.09
2670 5562 4.261072 CGATTGCCAGGAATGAAATGAGAG 60.261 45.833 0.00 0.00 0.00 3.20
2680 5572 1.153168 CGGGTCGATTGCCAGGAAT 60.153 57.895 0.00 0.00 0.00 3.01
2707 5599 0.379669 GCCTAGTCACATGTGCATGC 59.620 55.000 21.38 11.82 42.39 4.06
2752 5908 2.223947 GCCGGTGGAAGTCAATGTTTTT 60.224 45.455 1.90 0.00 0.00 1.94
2756 6935 1.303317 GGCCGGTGGAAGTCAATGT 60.303 57.895 1.90 0.00 0.00 2.71
2890 7087 9.842444 CGACAGTTGGTTTGTTTTAATTTTATG 57.158 29.630 0.00 0.00 0.00 1.90
2941 7148 1.153647 CGCGCCAGTCTATTGGACA 60.154 57.895 0.00 0.00 46.72 4.02
2994 7201 5.357878 GTCATCACCAGGAAATGATTGCTAA 59.642 40.000 10.49 0.00 34.65 3.09
3152 7359 7.384932 GGAAACCTTGAACATTTCATTTCGAAT 59.615 33.333 0.00 0.00 37.19 3.34
3160 7367 7.889873 TCTTTAGGAAACCTTGAACATTTCA 57.110 32.000 0.00 0.00 38.04 2.69
3180 7387 3.476552 TGAACACGCCTTCTTCATCTTT 58.523 40.909 0.00 0.00 0.00 2.52
3181 7388 3.126001 TGAACACGCCTTCTTCATCTT 57.874 42.857 0.00 0.00 0.00 2.40
3212 7419 7.653767 AGGAGTTTTCGTTGACTAACTAATG 57.346 36.000 0.00 0.00 34.60 1.90
3219 7426 5.524971 TCAGAAGGAGTTTTCGTTGACTA 57.475 39.130 0.00 0.00 31.94 2.59
3222 7429 3.498397 GCATCAGAAGGAGTTTTCGTTGA 59.502 43.478 0.00 0.00 31.94 3.18
3223 7430 3.250762 TGCATCAGAAGGAGTTTTCGTTG 59.749 43.478 0.00 0.00 31.94 4.10
3224 7431 3.251004 GTGCATCAGAAGGAGTTTTCGTT 59.749 43.478 0.00 0.00 34.32 3.85
3225 7432 2.808543 GTGCATCAGAAGGAGTTTTCGT 59.191 45.455 0.00 0.00 32.33 3.85
3260 7467 5.710613 TTTCCTCAAAAACATTTTCACGC 57.289 34.783 0.00 0.00 0.00 5.34
3286 7493 3.572604 AGAAATGAAGCAGCAGAAAGC 57.427 42.857 0.00 0.00 46.19 3.51
3309 7516 1.673033 CGCCTGGAAGTGGACAAGTAG 60.673 57.143 0.00 0.00 0.00 2.57
3348 7555 8.793592 GTCTGTGGAATTGTTAAGTTATTCCTT 58.206 33.333 17.49 0.00 44.88 3.36
3389 7596 2.661979 GCACGTCTTTTGCTTCCGTTAG 60.662 50.000 0.00 0.00 37.00 2.34
3390 7597 1.262151 GCACGTCTTTTGCTTCCGTTA 59.738 47.619 0.00 0.00 37.00 3.18
3393 7600 4.515107 GCACGTCTTTTGCTTCCG 57.485 55.556 0.00 0.00 37.00 4.30
3407 7614 9.600646 GAGTTTCTGACTAATAAAAAGAAGCAC 57.399 33.333 0.00 0.00 39.19 4.40
3408 7615 9.337396 TGAGTTTCTGACTAATAAAAAGAAGCA 57.663 29.630 0.00 0.00 39.19 3.91
3418 7625 7.896811 ACTGTGATGTGAGTTTCTGACTAATA 58.103 34.615 0.00 0.00 39.19 0.98
3421 7628 5.791336 ACTGTGATGTGAGTTTCTGACTA 57.209 39.130 0.00 0.00 39.19 2.59
3422 7629 4.679373 ACTGTGATGTGAGTTTCTGACT 57.321 40.909 0.00 0.00 42.70 3.41
3423 7630 5.753438 TGTAACTGTGATGTGAGTTTCTGAC 59.247 40.000 0.00 0.00 34.28 3.51
3425 7632 6.791887 ATGTAACTGTGATGTGAGTTTCTG 57.208 37.500 0.00 0.00 34.28 3.02
3426 7633 8.150945 ACTAATGTAACTGTGATGTGAGTTTCT 58.849 33.333 0.00 0.00 34.28 2.52
3427 7634 8.311650 ACTAATGTAACTGTGATGTGAGTTTC 57.688 34.615 0.00 0.00 34.28 2.78
3428 7635 8.677148 AACTAATGTAACTGTGATGTGAGTTT 57.323 30.769 0.00 0.00 34.28 2.66
3429 7636 8.677148 AAACTAATGTAACTGTGATGTGAGTT 57.323 30.769 0.00 0.00 36.40 3.01
3430 7637 8.559536 CAAAACTAATGTAACTGTGATGTGAGT 58.440 33.333 0.00 0.00 0.00 3.41
3431 7638 7.535258 GCAAAACTAATGTAACTGTGATGTGAG 59.465 37.037 0.00 0.00 0.00 3.51
3432 7639 7.359595 GCAAAACTAATGTAACTGTGATGTGA 58.640 34.615 0.00 0.00 0.00 3.58
3433 7640 6.582295 GGCAAAACTAATGTAACTGTGATGTG 59.418 38.462 0.00 0.00 0.00 3.21
3434 7641 6.490040 AGGCAAAACTAATGTAACTGTGATGT 59.510 34.615 0.00 0.00 0.00 3.06
3435 7642 6.913170 AGGCAAAACTAATGTAACTGTGATG 58.087 36.000 0.00 0.00 0.00 3.07
3436 7643 7.309194 GGAAGGCAAAACTAATGTAACTGTGAT 60.309 37.037 0.00 0.00 0.00 3.06
3444 8702 7.118680 CGACTTAAGGAAGGCAAAACTAATGTA 59.881 37.037 7.53 0.00 41.29 2.29
3461 8727 4.857588 CCTATATTGCGCTACGACTTAAGG 59.142 45.833 9.73 0.11 0.00 2.69
3490 8765 4.406069 GTGCTTTATGTACTGCATGTGTG 58.594 43.478 0.00 0.00 38.47 3.82
3491 8766 3.125146 CGTGCTTTATGTACTGCATGTGT 59.875 43.478 0.00 0.00 38.47 3.72
3492 8767 3.485711 CCGTGCTTTATGTACTGCATGTG 60.486 47.826 0.00 0.00 39.85 3.21
3493 8768 2.677836 CCGTGCTTTATGTACTGCATGT 59.322 45.455 0.00 0.00 39.85 3.21
3494 8769 2.677836 ACCGTGCTTTATGTACTGCATG 59.322 45.455 0.00 0.00 40.79 4.06
3495 8770 2.985896 ACCGTGCTTTATGTACTGCAT 58.014 42.857 0.00 0.00 41.42 3.96
3496 8771 2.465860 ACCGTGCTTTATGTACTGCA 57.534 45.000 0.00 0.00 0.00 4.41
3497 8772 5.479716 AATTACCGTGCTTTATGTACTGC 57.520 39.130 0.00 0.00 0.00 4.40
3498 8773 7.404203 GGTTAATTACCGTGCTTTATGTACTG 58.596 38.462 0.00 0.00 37.12 2.74
3525 8800 3.146066 GACTGCATGTTGGTAAGGAACA 58.854 45.455 0.00 0.00 37.70 3.18
3526 8801 2.159627 CGACTGCATGTTGGTAAGGAAC 59.840 50.000 0.00 0.00 0.00 3.62
3687 8962 4.077188 GTGTTGCTCTGCCGACGC 62.077 66.667 0.00 0.00 0.00 5.19
3720 8995 4.421515 CAGTGCAGAGGGGGCCTG 62.422 72.222 0.84 0.00 31.76 4.85
3724 8999 3.201707 AAGTGCAGTGCAGAGGGGG 62.202 63.158 20.42 0.00 40.08 5.40
3725 9000 1.673665 GAAGTGCAGTGCAGAGGGG 60.674 63.158 20.42 0.00 40.08 4.79
3733 9008 1.354040 GATCGGACAGAAGTGCAGTG 58.646 55.000 0.00 0.00 35.57 3.66
3740 9015 2.531206 GGACTTTCGATCGGACAGAAG 58.469 52.381 16.41 13.31 0.00 2.85
3741 9016 1.135489 CGGACTTTCGATCGGACAGAA 60.135 52.381 16.41 0.00 0.00 3.02
3745 9020 1.652619 GTTTCGGACTTTCGATCGGAC 59.347 52.381 16.41 0.00 39.03 4.79
3746 9021 1.542915 AGTTTCGGACTTTCGATCGGA 59.457 47.619 16.41 2.60 39.03 4.55
3747 9022 1.654105 CAGTTTCGGACTTTCGATCGG 59.346 52.381 16.41 1.30 39.03 4.18
3748 9023 1.654105 CCAGTTTCGGACTTTCGATCG 59.346 52.381 9.36 9.36 39.03 3.69
3749 9024 2.000447 CCCAGTTTCGGACTTTCGATC 59.000 52.381 0.00 0.00 39.03 3.69
3750 9025 1.944430 GCCCAGTTTCGGACTTTCGAT 60.944 52.381 0.00 0.00 39.03 3.59
3752 9027 1.866925 GCCCAGTTTCGGACTTTCG 59.133 57.895 0.00 0.00 36.10 3.46
3755 9030 1.147600 AACGCCCAGTTTCGGACTT 59.852 52.632 0.00 0.00 40.88 3.01
3756 9031 2.826702 AACGCCCAGTTTCGGACT 59.173 55.556 0.00 0.00 40.88 3.85
3763 9038 0.465460 TGCTCTGAAAACGCCCAGTT 60.465 50.000 0.00 0.00 46.76 3.16
3764 9039 1.148273 TGCTCTGAAAACGCCCAGT 59.852 52.632 0.00 0.00 0.00 4.00
3765 9040 1.576421 GTGCTCTGAAAACGCCCAG 59.424 57.895 0.00 0.00 0.00 4.45
3766 9041 1.896660 GGTGCTCTGAAAACGCCCA 60.897 57.895 0.00 0.00 0.00 5.36
3767 9042 1.452145 TTGGTGCTCTGAAAACGCCC 61.452 55.000 0.00 0.00 32.87 6.13
3768 9043 0.317854 GTTGGTGCTCTGAAAACGCC 60.318 55.000 0.00 0.00 34.48 5.68
3769 9044 0.657368 CGTTGGTGCTCTGAAAACGC 60.657 55.000 0.00 0.00 37.42 4.84
3809 9084 4.312231 CAACTGCACGCACACCCG 62.312 66.667 0.00 0.00 0.00 5.28
3810 9085 3.964875 CCAACTGCACGCACACCC 61.965 66.667 0.00 0.00 0.00 4.61
3811 9086 2.899838 TCCAACTGCACGCACACC 60.900 61.111 0.00 0.00 0.00 4.16
3812 9087 1.785041 ATGTCCAACTGCACGCACAC 61.785 55.000 0.00 0.00 0.00 3.82
3813 9088 1.506309 GATGTCCAACTGCACGCACA 61.506 55.000 0.00 0.00 0.00 4.57
3814 9089 1.207593 GATGTCCAACTGCACGCAC 59.792 57.895 0.00 0.00 0.00 5.34
3815 9090 2.316867 CGATGTCCAACTGCACGCA 61.317 57.895 0.00 0.00 0.00 5.24
3816 9091 1.959899 CTCGATGTCCAACTGCACGC 61.960 60.000 0.00 0.00 0.00 5.34
3817 9092 1.354337 CCTCGATGTCCAACTGCACG 61.354 60.000 0.00 0.00 0.00 5.34
3895 9188 2.738521 CTGCAGTTGTACGGCGCT 60.739 61.111 6.90 0.00 42.26 5.92
4033 9326 0.250640 AGAAGTGGGTGCTGAGCTTG 60.251 55.000 5.83 0.00 0.00 4.01
4136 9429 1.471676 GCCTTCGATGACCTGACGATT 60.472 52.381 0.00 0.00 36.02 3.34
4178 9474 4.208686 GGGACGAGGCTGCCGTAG 62.209 72.222 13.96 11.05 40.67 3.51
4188 9484 1.226802 CATCGAGCACAGGGACGAG 60.227 63.158 0.00 0.00 38.12 4.18
4189 9485 2.710902 CCATCGAGCACAGGGACGA 61.711 63.158 0.00 0.00 39.01 4.20
4205 9501 4.039603 TCTCACTGACAGATCTTCTCCA 57.960 45.455 10.08 0.00 0.00 3.86
4261 9557 7.307042 CCAATCAATCAGAATATGTCGACTGAC 60.307 40.741 17.92 4.13 45.71 3.51
4262 9558 6.703165 CCAATCAATCAGAATATGTCGACTGA 59.297 38.462 17.92 11.13 42.26 3.41
4263 9559 6.481313 ACCAATCAATCAGAATATGTCGACTG 59.519 38.462 17.92 5.47 0.00 3.51
4264 9560 6.586344 ACCAATCAATCAGAATATGTCGACT 58.414 36.000 17.92 4.95 0.00 4.18
4265 9561 6.703607 AGACCAATCAATCAGAATATGTCGAC 59.296 38.462 9.11 9.11 0.00 4.20
4276 9572 3.760151 TGAGCCAAAGACCAATCAATCAG 59.240 43.478 0.00 0.00 0.00 2.90
4318 9615 5.174037 ACCTATCACAAAAATCCTCGGAA 57.826 39.130 0.00 0.00 0.00 4.30
4323 9620 8.599624 AATGATCAACCTATCACAAAAATCCT 57.400 30.769 0.00 0.00 38.65 3.24
4333 9630 5.299949 CACGATGGAATGATCAACCTATCA 58.700 41.667 18.63 5.72 40.07 2.15
4392 9689 2.577911 GTAGGGTACACGCGCGAC 60.578 66.667 39.36 24.32 0.00 5.19
4410 9707 2.622436 GCAGAGTCGTAGATTGCCTTT 58.378 47.619 0.00 0.00 40.67 3.11
4500 9797 2.213499 GGACGGATGTAGGCTGAATTG 58.787 52.381 0.00 0.00 0.00 2.32
4576 9873 5.011125 AGCTGCTACCCTACATTGTATACAG 59.989 44.000 0.00 0.00 0.00 2.74
4646 9945 1.409241 CCACCAATAGCCTCACTGCAT 60.409 52.381 0.00 0.00 0.00 3.96
4647 9946 0.035152 CCACCAATAGCCTCACTGCA 60.035 55.000 0.00 0.00 0.00 4.41
4674 9973 9.482627 CCACTTATTTTGTGGCTAAAAATACAA 57.517 29.630 13.75 0.12 46.73 2.41
4704 10003 3.919216 AGTCACACTATTCAGACACAGC 58.081 45.455 0.00 0.00 33.56 4.40
4767 10066 6.881570 ACATTCCCAAAATCCTTCATCATTC 58.118 36.000 0.00 0.00 0.00 2.67
4805 10104 7.449395 TCTTGAAACATGTTCTTCCATTCATCT 59.551 33.333 12.39 0.00 0.00 2.90
4869 10168 3.889538 AGTAAAGCTTGGTTTGACCCTTC 59.110 43.478 0.00 0.00 37.50 3.46
4871 10170 3.595190 AGTAAAGCTTGGTTTGACCCT 57.405 42.857 0.00 0.00 37.50 4.34
4876 10175 8.871686 AAATTTGAGTAGTAAAGCTTGGTTTG 57.128 30.769 0.00 0.00 0.00 2.93
4881 10180 9.121517 CATGTGAAATTTGAGTAGTAAAGCTTG 57.878 33.333 0.00 0.00 0.00 4.01
4883 10182 8.621532 TCATGTGAAATTTGAGTAGTAAAGCT 57.378 30.769 0.00 0.00 0.00 3.74
4984 10286 3.119990 CGAACACCGATGCAAATAGGTTT 60.120 43.478 0.00 0.00 41.76 3.27
4992 10294 0.037697 AGCTACGAACACCGATGCAA 60.038 50.000 0.00 0.00 41.76 4.08
5088 10390 2.548057 GACATTCACAAAGGCAGTCGAA 59.452 45.455 0.00 0.00 0.00 3.71
5163 10465 3.067833 GAGGGTTTAGCACTGACAGAAC 58.932 50.000 10.08 2.42 0.00 3.01
5169 10471 1.276421 GCAGAGAGGGTTTAGCACTGA 59.724 52.381 0.00 0.00 0.00 3.41
5207 10509 2.626266 TGTGGATTACGGATGTAGCGAT 59.374 45.455 0.00 0.00 0.00 4.58
5218 10520 3.206150 CTTGGGGATCTTGTGGATTACG 58.794 50.000 0.00 0.00 34.33 3.18
5226 10528 0.622665 CTCAGCCTTGGGGATCTTGT 59.377 55.000 0.00 0.00 33.58 3.16
5252 10554 5.335661 GCCGAAAAGAGCTAGGAAATTTTCA 60.336 40.000 11.09 0.00 38.95 2.69
5279 10581 2.444140 AGGATTAGCGGCGGGAGT 60.444 61.111 9.78 0.00 0.00 3.85
5364 10666 2.038033 CCTTGGACTCTACCGAAACCAA 59.962 50.000 0.00 0.00 35.05 3.67
5377 10679 0.119155 TCAGATCCCCACCTTGGACT 59.881 55.000 0.00 0.00 40.96 3.85
5383 10685 1.992519 GCAGCATCAGATCCCCACCT 61.993 60.000 0.00 0.00 0.00 4.00
5386 10688 1.054231 CTAGCAGCATCAGATCCCCA 58.946 55.000 0.00 0.00 0.00 4.96
5394 10696 1.058428 ATCCTGGCCTAGCAGCATCA 61.058 55.000 3.32 0.00 0.00 3.07
5409 10711 0.923358 TATTGTTTGGGGCGGATCCT 59.077 50.000 10.75 0.00 34.39 3.24
5431 10733 1.004320 ACCGGCGCATAAGACACAA 60.004 52.632 10.83 0.00 0.00 3.33
5432 10734 1.447140 GACCGGCGCATAAGACACA 60.447 57.895 10.83 0.00 0.00 3.72
5434 10736 1.447140 GTGACCGGCGCATAAGACA 60.447 57.895 10.83 0.00 0.00 3.41
5450 10752 2.287059 GTTTGTGCAAACGCCTGTG 58.713 52.632 11.35 0.00 40.85 3.66
5473 10775 2.747855 CAAAGGAGAGGGGCGTGC 60.748 66.667 0.00 0.00 0.00 5.34
5477 10779 1.223211 GAGCTCAAAGGAGAGGGGC 59.777 63.158 9.40 0.00 44.26 5.80
5487 10790 0.250381 TTAAACGGGCCGAGCTCAAA 60.250 50.000 35.78 14.22 0.00 2.69
5491 10794 1.670083 GTGTTAAACGGGCCGAGCT 60.670 57.895 35.78 18.18 0.00 4.09
5497 10800 3.363673 CGAGAGAAAAGTGTTAAACGGGC 60.364 47.826 0.00 0.00 0.00 6.13
5501 10804 8.572976 GTTTTGAACGAGAGAAAAGTGTTAAAC 58.427 33.333 0.00 0.00 0.00 2.01
5519 10822 1.765750 CGTGCGAGAAACGTTTTGAAC 59.234 47.619 15.89 11.67 44.60 3.18
5520 10823 2.079941 CGTGCGAGAAACGTTTTGAA 57.920 45.000 15.89 0.07 44.60 2.69


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

AutoCloner maintained by Alex Coulton.