Multiple sequence alignment - TraesCS7A01G066400

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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 TraesCS7A01G066400 chr7A 100.000 5275 0 0 1 5275 33360753 33366027 0.000000e+00 9742.0
1 TraesCS7A01G066400 chr7A 88.372 86 2 1 4801 4878 33365446 33365531 4.350000e-16 97.1
2 TraesCS7A01G066400 chr7A 88.372 86 2 1 4694 4779 33365553 33365630 4.350000e-16 97.1
3 TraesCS7A01G066400 chr4A 91.446 4489 216 80 515 4921 693274310 693278712 0.000000e+00 6008.0
4 TraesCS7A01G066400 chr4A 90.871 241 16 3 4918 5152 693278884 693279124 8.520000e-83 318.0
5 TraesCS7A01G066400 chr4A 88.043 92 2 2 4688 4779 693278587 693278669 3.360000e-17 100.0
6 TraesCS7A01G066400 chr4A 86.747 83 3 2 4801 4875 693278486 693278568 9.410000e-13 86.1
7 TraesCS7A01G066400 chr4A 100.000 30 0 0 2585 2614 670592883 670592854 7.380000e-04 56.5
8 TraesCS7A01G066400 chr7D 93.376 3895 178 44 1047 4922 33047262 33051095 0.000000e+00 5690.0
9 TraesCS7A01G066400 chr7D 94.132 409 23 1 1 409 33045528 33045935 5.800000e-174 621.0
10 TraesCS7A01G066400 chr7D 89.669 242 18 4 4918 5152 33051298 33051539 8.590000e-78 302.0
11 TraesCS7A01G066400 chr7D 83.861 316 26 10 496 796 33046564 33046869 1.450000e-70 278.0
12 TraesCS7A01G066400 chr7D 84.234 222 34 1 1 222 113124040 113124260 1.150000e-51 215.0
13 TraesCS7A01G066400 chr7D 95.690 116 5 0 5151 5266 126669804 126669689 2.510000e-43 187.0
14 TraesCS7A01G066400 chr7D 79.688 256 30 13 424 677 33046222 33046457 1.180000e-36 165.0
15 TraesCS7A01G066400 chr7D 88.372 86 2 1 4801 4878 33050862 33050947 4.350000e-16 97.1
16 TraesCS7A01G066400 chr7B 90.668 868 73 7 1673 2537 333749098 333748236 0.000000e+00 1147.0
17 TraesCS7A01G066400 chr7B 89.610 231 19 3 1 230 412038593 412038367 6.680000e-74 289.0
18 TraesCS7A01G066400 chr7B 83.105 219 36 1 4 222 140856030 140855813 1.160000e-46 198.0
19 TraesCS7A01G066400 chr7B 93.130 131 9 0 2202 2332 500213023 500213153 5.390000e-45 193.0
20 TraesCS7A01G066400 chr7B 81.008 258 34 10 1390 1636 333749355 333749102 1.940000e-44 191.0
21 TraesCS7A01G066400 chr2D 91.273 825 62 8 1775 2593 87170408 87171228 0.000000e+00 1116.0
22 TraesCS7A01G066400 chr2D 97.500 40 1 0 5064 5103 622228219 622228258 9.480000e-08 69.4
23 TraesCS7A01G066400 chr6D 89.735 565 52 6 1663 2224 460139898 460140459 0.000000e+00 717.0
24 TraesCS7A01G066400 chr6D 94.569 313 17 0 2222 2534 460154143 460154455 7.940000e-133 484.0
25 TraesCS7A01G066400 chr6D 93.333 45 2 1 5064 5107 249959300 249959344 1.230000e-06 65.8
26 TraesCS7A01G066400 chr5B 84.911 676 55 19 1663 2332 466530796 466531430 1.600000e-179 640.0
27 TraesCS7A01G066400 chr5B 84.302 344 30 11 1309 1638 466530472 466530805 1.100000e-81 315.0
28 TraesCS7A01G066400 chr5B 89.600 125 11 2 1124 1247 466530339 466530462 1.970000e-34 158.0
29 TraesCS7A01G066400 chr4B 86.022 372 33 10 1126 1496 560940762 560940409 1.070000e-101 381.0
30 TraesCS7A01G066400 chr3A 92.202 218 14 3 1 217 525299194 525299409 6.640000e-79 305.0
31 TraesCS7A01G066400 chr3A 97.436 39 1 0 5063 5101 9378552 9378514 3.410000e-07 67.6
32 TraesCS7A01G066400 chr3A 93.333 45 2 1 5064 5107 385525553 385525597 1.230000e-06 65.8
33 TraesCS7A01G066400 chr6A 84.234 222 34 1 1 222 21236121 21235901 1.150000e-51 215.0
34 TraesCS7A01G066400 chr6A 95.556 45 1 1 5064 5107 346592028 346591984 2.640000e-08 71.3
35 TraesCS7A01G066400 chr5A 82.819 227 38 1 6 232 426927393 426927618 8.960000e-48 202.0
36 TraesCS7A01G066400 chr5A 98.198 111 2 0 5147 5257 127831864 127831754 1.500000e-45 195.0
37 TraesCS7A01G066400 chr3B 82.883 222 36 2 4 225 572684786 572684567 1.160000e-46 198.0
38 TraesCS7A01G066400 chr2B 86.339 183 24 1 1 183 63817701 63817882 1.160000e-46 198.0
39 TraesCS7A01G066400 chr2B 99.074 108 1 0 5150 5257 178470149 178470042 1.500000e-45 195.0
40 TraesCS7A01G066400 chr2B 81.818 99 9 4 5064 5153 374800282 374800380 2.040000e-09 75.0
41 TraesCS7A01G066400 chr1A 98.198 111 2 0 5147 5257 134973599 134973489 1.500000e-45 195.0
42 TraesCS7A01G066400 chr1A 92.929 99 4 2 1926 2024 547727871 547727776 1.980000e-29 141.0
43 TraesCS7A01G066400 chr1A 90.411 73 7 0 1565 1637 547728147 547728075 4.350000e-16 97.1
44 TraesCS7A01G066400 chr3D 97.345 113 2 1 5146 5257 230765757 230765645 1.940000e-44 191.0
45 TraesCS7A01G066400 chr3D 93.333 45 2 1 5064 5107 292372798 292372754 1.230000e-06 65.8
46 TraesCS7A01G066400 chr5D 93.701 127 6 2 5145 5269 380324355 380324481 6.970000e-44 189.0
47 TraesCS7A01G066400 chr1D 96.491 114 4 0 5144 5257 349423038 349422925 6.970000e-44 189.0
48 TraesCS7A01G066400 chr6B 93.651 126 7 1 5137 5261 679091049 679090924 2.510000e-43 187.0
49 TraesCS7A01G066400 chr6B 97.778 45 0 1 5064 5107 337859095 337859139 5.660000e-10 76.8
50 TraesCS7A01G066400 chr1B 93.701 127 4 4 5134 5257 491085739 491085864 2.510000e-43 187.0
51 TraesCS7A01G066400 chr1B 100.000 28 0 0 2585 2612 643932531 643932558 1.000000e-02 52.8
52 TraesCS7A01G066400 chr2A 82.653 98 9 4 5064 5153 386294347 386294444 4.380000e-11 80.5


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 TraesCS7A01G066400 chr7A 33360753 33366027 5274 False 3312.066667 9742 92.24800 1 5275 3 chr7A.!!$F1 5274
1 TraesCS7A01G066400 chr4A 693274310 693279124 4814 False 1628.025000 6008 89.27675 515 5152 4 chr4A.!!$F1 4637
2 TraesCS7A01G066400 chr7D 33045528 33051539 6011 False 1192.183333 5690 88.18300 1 5152 6 chr7D.!!$F2 5151
3 TraesCS7A01G066400 chr7B 333748236 333749355 1119 True 669.000000 1147 85.83800 1390 2537 2 chr7B.!!$R3 1147
4 TraesCS7A01G066400 chr2D 87170408 87171228 820 False 1116.000000 1116 91.27300 1775 2593 1 chr2D.!!$F1 818
5 TraesCS7A01G066400 chr6D 460139898 460140459 561 False 717.000000 717 89.73500 1663 2224 1 chr6D.!!$F2 561
6 TraesCS7A01G066400 chr5B 466530339 466531430 1091 False 371.000000 640 86.27100 1124 2332 3 chr5B.!!$F1 1208

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
876 1461 0.033109 CTCCCAAACCCCAGAATCCC 60.033 60.000 0.0 0.0 0.00 3.85 F
877 1462 1.001631 CCCAAACCCCAGAATCCCC 59.998 63.158 0.0 0.0 0.00 4.81 F
2298 3062 0.250727 TGTGTGGTTAAGCCTGGAGC 60.251 55.000 0.0 0.0 44.25 4.70 F
3351 4124 0.881118 CTATCTCCTCGCTCTCAGGC 59.119 60.000 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 3062 1.647213 CACGTCAACAATCGTACCTCG 59.353 52.381 0.0 0.0 38.52 4.63 R
2730 3499 3.092301 AGAAAGCATCCACTAAAAGGCC 58.908 45.455 0.0 0.0 0.00 5.19 R
4100 4874 0.178992 CCAACAGCCTGTCCCAAAGA 60.179 55.000 0.0 0.0 0.00 2.52 R
4341 5115 0.040958 GTGTGCTCCTGCGTTTTCTG 60.041 55.000 0.0 0.0 43.34 3.02 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
52 53 6.420903 GCACAAAGTAATTTTCTTCAACTCCC 59.579 38.462 0.00 0.00 0.00 4.30
100 101 2.241281 TTCCAACTCCACCGATCCTA 57.759 50.000 0.00 0.00 0.00 2.94
117 118 1.068333 CCTACAATTTTGCACTGCGCT 60.068 47.619 9.73 0.00 43.06 5.92
162 163 1.147376 CCAGGTGTTGACCCGTTCA 59.853 57.895 0.00 0.00 44.40 3.18
164 165 0.884704 CAGGTGTTGACCCGTTCAGG 60.885 60.000 0.00 0.00 44.40 3.86
259 260 2.844839 ACGCCTAGCCCTCATCCC 60.845 66.667 0.00 0.00 0.00 3.85
299 300 3.004126 TGGGAGGGCATATGAAGGTAT 57.996 47.619 6.97 0.00 0.00 2.73
309 310 0.530650 ATGAAGGTATGTCGCCTGCG 60.531 55.000 4.92 4.92 34.29 5.18
312 313 2.573609 AAGGTATGTCGCCTGCGGAC 62.574 60.000 12.06 9.07 40.25 4.79
330 331 2.555199 GACCCCACATGATTCTCTTCG 58.445 52.381 0.00 0.00 0.00 3.79
332 333 2.093447 ACCCCACATGATTCTCTTCGTC 60.093 50.000 0.00 0.00 0.00 4.20
343 344 3.917329 TCTCTTCGTCGACATTTGTCT 57.083 42.857 17.16 0.00 42.66 3.41
344 345 4.238761 TCTCTTCGTCGACATTTGTCTT 57.761 40.909 17.16 0.00 42.66 3.01
363 364 7.101652 TGTCTTTCTGTAGATCTATGTGGAC 57.898 40.000 5.57 10.13 0.00 4.02
365 366 5.299531 TCTTTCTGTAGATCTATGTGGACCG 59.700 44.000 5.57 0.00 0.00 4.79
371 372 2.959707 AGATCTATGTGGACCGGTCTTC 59.040 50.000 32.52 24.22 0.00 2.87
376 377 1.364901 GTGGACCGGTCTTCGTTCA 59.635 57.895 32.52 18.64 37.11 3.18
377 378 0.037605 GTGGACCGGTCTTCGTTCAT 60.038 55.000 32.52 0.00 37.11 2.57
392 393 3.105203 CGTTCATTGTGTTTGTGTGTCC 58.895 45.455 0.00 0.00 0.00 4.02
417 418 8.567285 CATAGGTTGGATACTTTTGAGAAACT 57.433 34.615 0.00 0.00 37.61 2.66
419 420 5.701290 AGGTTGGATACTTTTGAGAAACTCG 59.299 40.000 0.00 0.00 32.40 4.18
420 421 5.699458 GGTTGGATACTTTTGAGAAACTCGA 59.301 40.000 0.00 0.00 32.40 4.04
421 422 6.204108 GGTTGGATACTTTTGAGAAACTCGAA 59.796 38.462 0.00 0.00 32.64 3.71
422 423 7.291567 GTTGGATACTTTTGAGAAACTCGAAG 58.708 38.462 0.00 0.00 35.58 3.79
423 424 6.755206 TGGATACTTTTGAGAAACTCGAAGA 58.245 36.000 15.90 3.63 35.58 2.87
424 425 7.214381 TGGATACTTTTGAGAAACTCGAAGAA 58.786 34.615 15.90 3.54 35.58 2.52
425 426 7.713507 TGGATACTTTTGAGAAACTCGAAGAAA 59.286 33.333 15.90 8.20 35.58 2.52
432 705 6.530913 TGAGAAACTCGAAGAAACATTGAG 57.469 37.500 0.00 0.00 34.09 3.02
439 712 6.226787 ACTCGAAGAAACATTGAGAGTTCAT 58.773 36.000 0.00 0.00 34.27 2.57
440 713 6.708054 ACTCGAAGAAACATTGAGAGTTCATT 59.292 34.615 0.00 0.00 34.27 2.57
441 714 7.095439 ACTCGAAGAAACATTGAGAGTTCATTC 60.095 37.037 0.00 0.00 34.27 2.67
444 717 7.533222 CGAAGAAACATTGAGAGTTCATTCAAG 59.467 37.037 0.00 0.00 36.81 3.02
448 721 9.520204 GAAACATTGAGAGTTCATTCAAGAAAA 57.480 29.630 0.00 0.00 36.81 2.29
449 722 9.525409 AAACATTGAGAGTTCATTCAAGAAAAG 57.475 29.630 0.00 0.00 36.81 2.27
451 724 8.348507 ACATTGAGAGTTCATTCAAGAAAAGAC 58.651 33.333 0.00 0.00 36.81 3.01
452 725 6.530913 TGAGAGTTCATTCAAGAAAAGACG 57.469 37.500 0.00 0.00 0.00 4.18
456 729 1.804151 TCATTCAAGAAAAGACGGCCG 59.196 47.619 26.86 26.86 0.00 6.13
459 732 1.082104 CAAGAAAAGACGGCCGTGC 60.082 57.895 39.65 26.09 0.00 5.34
473 746 2.359478 GTGCCGACGGGAATGGTT 60.359 61.111 17.22 0.00 34.06 3.67
477 750 1.029947 GCCGACGGGAATGGTTGATT 61.030 55.000 17.22 0.00 34.06 2.57
479 752 0.650512 CGACGGGAATGGTTGATTCG 59.349 55.000 0.00 0.00 41.45 3.34
509 783 2.104792 AGGCTTTGCTCTTGTCACTGTA 59.895 45.455 0.00 0.00 0.00 2.74
511 785 2.096019 GCTTTGCTCTTGTCACTGTAGC 60.096 50.000 0.00 0.00 0.00 3.58
513 787 2.154854 TGCTCTTGTCACTGTAGCAC 57.845 50.000 0.00 0.00 38.22 4.40
531 805 3.601685 CCGGTTGTGGTTGGTGGC 61.602 66.667 0.00 0.00 0.00 5.01
560 834 1.529744 AGGACCAAGTGAAAAGGGGA 58.470 50.000 0.00 0.00 0.00 4.81
561 835 1.425448 AGGACCAAGTGAAAAGGGGAG 59.575 52.381 0.00 0.00 0.00 4.30
562 836 1.145119 GGACCAAGTGAAAAGGGGAGT 59.855 52.381 0.00 0.00 0.00 3.85
580 854 4.935808 GGGAGTAGATTGTTTGTCACGAAT 59.064 41.667 0.00 0.00 0.00 3.34
598 872 6.040391 TCACGAATTGGAAAAGGAAGATTGTT 59.960 34.615 0.00 0.00 0.00 2.83
607 881 7.394359 TGGAAAAGGAAGATTGTTTCTATCCTG 59.606 37.037 7.64 0.00 39.69 3.86
608 882 6.765915 AAAGGAAGATTGTTTCTATCCTGC 57.234 37.500 0.00 0.00 39.69 4.85
617 891 4.569943 TGTTTCTATCCTGCTTCTCACAC 58.430 43.478 0.00 0.00 0.00 3.82
621 895 0.534412 ATCCTGCTTCTCACACGGAG 59.466 55.000 0.00 0.00 45.49 4.63
700 1255 4.200283 CTGAGCCTCCGCCGAGAC 62.200 72.222 3.41 0.00 38.52 3.36
714 1269 2.997897 AGACCCACGAGCTGTCCC 60.998 66.667 0.00 0.00 0.00 4.46
721 1276 4.154347 CGAGCTGTCCCTGGCCTC 62.154 72.222 3.32 0.00 0.00 4.70
767 1335 4.415332 GCCGCCGTCTCGTCTGAA 62.415 66.667 0.00 0.00 0.00 3.02
768 1336 2.504244 CCGCCGTCTCGTCTGAAC 60.504 66.667 0.00 0.00 0.00 3.18
769 1337 2.561885 CGCCGTCTCGTCTGAACT 59.438 61.111 0.00 0.00 0.00 3.01
770 1338 1.512310 CGCCGTCTCGTCTGAACTC 60.512 63.158 0.00 0.00 0.00 3.01
876 1461 0.033109 CTCCCAAACCCCAGAATCCC 60.033 60.000 0.00 0.00 0.00 3.85
877 1462 1.001631 CCCAAACCCCAGAATCCCC 59.998 63.158 0.00 0.00 0.00 4.81
878 1463 1.001631 CCAAACCCCAGAATCCCCC 59.998 63.158 0.00 0.00 0.00 5.40
879 1464 1.379843 CAAACCCCAGAATCCCCCG 60.380 63.158 0.00 0.00 0.00 5.73
1537 2258 1.409381 CCCATTCCTCTTCCCTTCTGC 60.409 57.143 0.00 0.00 0.00 4.26
1545 2284 1.625818 TCTTCCCTTCTGCTCTGTTCC 59.374 52.381 0.00 0.00 0.00 3.62
1557 2296 3.190874 GCTCTGTTCCCGAAATCAGTAG 58.809 50.000 0.00 0.00 0.00 2.57
1561 2300 2.280628 GTTCCCGAAATCAGTAGCCAG 58.719 52.381 0.00 0.00 0.00 4.85
1575 2314 2.810439 AGCCAGAGATAGATTGACGC 57.190 50.000 0.00 0.00 0.00 5.19
1697 2444 2.512515 GACCTCACCATCAGCGGC 60.513 66.667 0.00 0.00 0.00 6.53
1804 2557 5.065613 TCCTTCCATCCCATCCATAAAAG 57.934 43.478 0.00 0.00 0.00 2.27
1805 2558 3.575687 CCTTCCATCCCATCCATAAAAGC 59.424 47.826 0.00 0.00 0.00 3.51
1806 2559 3.243359 TCCATCCCATCCATAAAAGCC 57.757 47.619 0.00 0.00 0.00 4.35
1824 2578 7.833285 AAAAGCCTTCCAATTCTGTTAACTA 57.167 32.000 7.22 0.00 0.00 2.24
1829 2583 5.220854 CCTTCCAATTCTGTTAACTATGGCG 60.221 44.000 7.22 3.58 0.00 5.69
1848 2602 4.697828 TGGCGATGTCAAAATTAAGTGCTA 59.302 37.500 0.00 0.00 0.00 3.49
1859 2613 7.825270 TCAAAATTAAGTGCTACCGGAATCTTA 59.175 33.333 9.46 6.84 0.00 2.10
1920 2674 7.581213 AACAATTCACTAGTGTTTGATTCCA 57.419 32.000 30.40 8.96 41.94 3.53
2004 2761 1.608590 ACTTGTTTGGTCCATTGAGCG 59.391 47.619 0.00 0.00 41.98 5.03
2087 2846 2.469826 TGATAATTAGCCTGCGTCACG 58.530 47.619 0.00 0.00 0.00 4.35
2298 3062 0.250727 TGTGTGGTTAAGCCTGGAGC 60.251 55.000 0.00 0.00 44.25 4.70
2353 3117 5.930837 TTGCTTCCTTTCCTCTTTTGAAA 57.069 34.783 0.00 0.00 0.00 2.69
2504 3273 6.227522 TGACTTCCGAGACATTGTCATTTTA 58.772 36.000 18.57 1.01 34.60 1.52
2524 3293 5.801350 TTAATCAGCTCATTCCTGAAACG 57.199 39.130 0.00 0.00 42.12 3.60
2527 3296 1.391485 CAGCTCATTCCTGAAACGACG 59.609 52.381 0.00 0.00 32.03 5.12
2537 3306 6.788684 TTCCTGAAACGACGATTGATTTTA 57.211 33.333 0.00 0.00 0.00 1.52
2632 3401 5.538433 ACTTCTAGATAGATCAGACCTTGGC 59.462 44.000 0.00 0.00 31.40 4.52
2664 3433 5.439721 TGGATGATATGCTGCTAAAACAGT 58.560 37.500 0.00 0.00 39.96 3.55
2666 3435 5.278169 GGATGATATGCTGCTAAAACAGTGG 60.278 44.000 0.00 0.00 39.96 4.00
2667 3436 3.947196 TGATATGCTGCTAAAACAGTGGG 59.053 43.478 0.00 0.00 39.96 4.61
2697 3466 4.202090 CCATTTTAGAATTGGAGCTGCCTC 60.202 45.833 1.53 0.00 37.63 4.70
2720 3489 8.882736 CCTCTTTGTTTTGCTTATTTTTCTGTT 58.117 29.630 0.00 0.00 0.00 3.16
2765 3534 6.599244 TGGATGCTTTCTATCGAAATCAGTTT 59.401 34.615 0.00 0.00 38.29 2.66
2959 3728 2.602878 GTCATGCAGAAATTGTGCTGG 58.397 47.619 16.01 8.21 41.78 4.85
2964 3733 1.547372 GCAGAAATTGTGCTGGGATGT 59.453 47.619 7.92 0.00 37.96 3.06
2980 3749 2.480419 GGATGTCACTCTGTTTTCCACG 59.520 50.000 0.00 0.00 0.00 4.94
3003 3772 5.794945 CGTTAATATGTTGTTGCTTGTCCTG 59.205 40.000 0.00 0.00 0.00 3.86
3011 3780 5.825679 TGTTGTTGCTTGTCCTGTACTATTT 59.174 36.000 0.00 0.00 0.00 1.40
3013 3782 5.373222 TGTTGCTTGTCCTGTACTATTTGT 58.627 37.500 0.00 0.00 0.00 2.83
3058 3827 7.124573 ACAAAAAGCTCCCAAGTCTTTATTT 57.875 32.000 0.00 0.00 32.31 1.40
3099 3868 6.374333 GGCACCAGATAATCAAACTAGTTTCA 59.626 38.462 18.00 6.07 0.00 2.69
3116 3887 9.127277 ACTAGTTTCAATGGCTACTTTTTGTTA 57.873 29.630 0.00 0.00 0.00 2.41
3351 4124 0.881118 CTATCTCCTCGCTCTCAGGC 59.119 60.000 0.00 0.00 0.00 4.85
3411 4185 8.697507 AGTCCTGAATTTGTGACTTTATTTCT 57.302 30.769 0.00 0.00 34.53 2.52
3416 4190 7.939782 TGAATTTGTGACTTTATTTCTGCAGA 58.060 30.769 13.74 13.74 0.00 4.26
3423 4197 4.273318 ACTTTATTTCTGCAGATGGGACC 58.727 43.478 19.04 0.00 0.00 4.46
3599 4373 3.244770 CCAACCCTACAGGAAGCTTTGTA 60.245 47.826 0.00 5.59 39.89 2.41
3626 4400 2.663879 GCAAACACTGCGTGATCTTCTG 60.664 50.000 14.18 1.38 42.37 3.02
3716 4490 1.956477 GGTGAATTTGTCAGTGTGGCT 59.044 47.619 0.00 0.00 36.74 4.75
3770 4544 4.910304 AGAGGCAGGGTTCACATAATCTAT 59.090 41.667 0.00 0.00 0.00 1.98
3773 4547 4.202461 GGCAGGGTTCACATAATCTATGGA 60.202 45.833 0.00 0.00 40.47 3.41
3809 4583 1.416401 TCTCTTGCAGGGTTTCGAGTT 59.584 47.619 0.00 0.00 0.00 3.01
4238 5012 0.468029 CTGTGGTGGTGGAAAGGCTT 60.468 55.000 0.00 0.00 0.00 4.35
4245 5019 1.286248 GGTGGAAAGGCTTAGGAGGA 58.714 55.000 0.00 0.00 0.00 3.71
4269 5043 3.006110 CACAGATGGCCACAAATCAAACT 59.994 43.478 8.16 0.00 0.00 2.66
4340 5114 1.509644 CTGCTTCGCCAGTTGCTTCA 61.510 55.000 0.00 0.00 38.05 3.02
4341 5115 1.081840 GCTTCGCCAGTTGCTTCAC 60.082 57.895 0.00 0.00 38.05 3.18
4364 5138 2.324014 AAACGCAGGAGCACACAGGA 62.324 55.000 0.00 0.00 42.27 3.86
4392 5167 2.642311 TGCCTTAACCAGATCTGTTCCA 59.358 45.455 21.11 5.81 0.00 3.53
4427 5202 2.680805 CGTCTTGGCATCTACCATTGGT 60.681 50.000 13.94 13.94 40.13 3.67
4469 5244 3.476552 TGGTGGAAACAGTCATGTCTTC 58.523 45.455 0.00 0.00 44.46 2.87
4486 5261 1.873591 CTTCGGTGGTGGAACAAAGAG 59.126 52.381 0.00 0.00 44.16 2.85
4501 5276 2.322355 AAGAGCAGGGATCATGTTCG 57.678 50.000 7.90 0.00 33.60 3.95
4502 5277 0.179062 AGAGCAGGGATCATGTTCGC 60.179 55.000 11.79 11.79 33.60 4.70
4510 5285 0.504384 GATCATGTTCGCATCCGTCG 59.496 55.000 0.00 0.00 35.23 5.12
4591 5366 1.139654 CGATTCTCATCTGCTTCCCCA 59.860 52.381 0.00 0.00 0.00 4.96
4660 5435 3.678056 AGTCTTGTGTTCATTCGCCTA 57.322 42.857 0.00 0.00 0.00 3.93
4672 5447 4.380531 TCATTCGCCTATTCAATCCTGTC 58.619 43.478 0.00 0.00 0.00 3.51
4678 5453 4.723309 GCCTATTCAATCCTGTCATCCTT 58.277 43.478 0.00 0.00 0.00 3.36
4799 5574 6.270000 TGTGAATTCAGGTTCTTTCTCCTCTA 59.730 38.462 8.80 0.00 30.91 2.43
4885 5660 1.155424 TCCAGTTTGTGACGGCGTTC 61.155 55.000 16.19 11.61 0.00 3.95
4982 6063 9.667107 TTGTTTCTTATAGACTAATGTTCCCAG 57.333 33.333 0.00 0.00 0.00 4.45
5035 6116 2.094675 TCGTGTAGGCTGTAGTAACCC 58.905 52.381 0.00 0.00 0.00 4.11
5037 6118 2.159282 CGTGTAGGCTGTAGTAACCCAG 60.159 54.545 0.00 0.00 0.00 4.45
5152 6239 9.959721 TCTATGGAAAAATGGGCTAATATCTAC 57.040 33.333 0.00 0.00 0.00 2.59
5153 6240 9.965902 CTATGGAAAAATGGGCTAATATCTACT 57.034 33.333 0.00 0.00 0.00 2.57
5154 6241 8.870075 ATGGAAAAATGGGCTAATATCTACTC 57.130 34.615 0.00 0.00 0.00 2.59
5155 6242 7.231467 TGGAAAAATGGGCTAATATCTACTCC 58.769 38.462 0.00 0.00 0.00 3.85
5156 6243 6.659668 GGAAAAATGGGCTAATATCTACTCCC 59.340 42.308 0.00 0.00 0.00 4.30
5157 6244 7.408013 AAAAATGGGCTAATATCTACTCCCT 57.592 36.000 0.00 0.00 34.89 4.20
5158 6245 6.628644 AAATGGGCTAATATCTACTCCCTC 57.371 41.667 0.00 0.00 34.89 4.30
5159 6246 4.062490 TGGGCTAATATCTACTCCCTCC 57.938 50.000 0.00 0.00 34.89 4.30
5160 6247 3.025262 GGGCTAATATCTACTCCCTCCG 58.975 54.545 0.00 0.00 0.00 4.63
5161 6248 3.563915 GGGCTAATATCTACTCCCTCCGT 60.564 52.174 0.00 0.00 0.00 4.69
5162 6249 4.087907 GGCTAATATCTACTCCCTCCGTT 58.912 47.826 0.00 0.00 0.00 4.44
5163 6250 4.158209 GGCTAATATCTACTCCCTCCGTTC 59.842 50.000 0.00 0.00 0.00 3.95
5164 6251 4.765856 GCTAATATCTACTCCCTCCGTTCA 59.234 45.833 0.00 0.00 0.00 3.18
5165 6252 5.106078 GCTAATATCTACTCCCTCCGTTCAG 60.106 48.000 0.00 0.00 0.00 3.02
5166 6253 4.726035 ATATCTACTCCCTCCGTTCAGA 57.274 45.455 0.00 0.00 0.00 3.27
5167 6254 2.893215 TCTACTCCCTCCGTTCAGAA 57.107 50.000 0.00 0.00 0.00 3.02
5168 6255 3.383698 TCTACTCCCTCCGTTCAGAAT 57.616 47.619 0.00 0.00 0.00 2.40
5169 6256 3.709587 TCTACTCCCTCCGTTCAGAATT 58.290 45.455 0.00 0.00 0.00 2.17
5170 6257 4.863548 TCTACTCCCTCCGTTCAGAATTA 58.136 43.478 0.00 0.00 0.00 1.40
5171 6258 3.889520 ACTCCCTCCGTTCAGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
5172 6259 3.442076 ACTCCCTCCGTTCAGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
5173 6260 3.838903 ACTCCCTCCGTTCAGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
5174 6261 4.184629 CTCCCTCCGTTCAGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
5175 6262 3.581332 TCCCTCCGTTCAGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
5176 6263 3.933332 CCCTCCGTTCAGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
5177 6264 4.322801 CCCTCCGTTCAGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
5178 6265 4.865365 CCTCCGTTCAGAATTACTTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
5179 6266 4.482386 TCCGTTCAGAATTACTTGTCTCG 58.518 43.478 0.00 0.00 0.00 4.04
5180 6267 3.612860 CCGTTCAGAATTACTTGTCTCGG 59.387 47.826 0.00 0.00 0.00 4.63
5181 6268 4.482386 CGTTCAGAATTACTTGTCTCGGA 58.518 43.478 0.00 0.00 0.00 4.55
5182 6269 4.921515 CGTTCAGAATTACTTGTCTCGGAA 59.078 41.667 0.00 0.00 0.00 4.30
5183 6270 5.404366 CGTTCAGAATTACTTGTCTCGGAAA 59.596 40.000 0.00 0.00 0.00 3.13
5184 6271 6.090898 CGTTCAGAATTACTTGTCTCGGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
5185 6272 6.968131 TCAGAATTACTTGTCTCGGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
5186 6273 5.874810 TCAGAATTACTTGTCTCGGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
5187 6274 5.874810 CAGAATTACTTGTCTCGGAAATGGA 59.125 40.000 0.00 0.00 0.00 3.41
5188 6275 6.540189 CAGAATTACTTGTCTCGGAAATGGAT 59.460 38.462 0.00 0.00 0.00 3.41
5189 6276 6.540189 AGAATTACTTGTCTCGGAAATGGATG 59.460 38.462 0.00 0.00 0.00 3.51
5190 6277 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
5191 6278 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
5192 6279 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
5193 6280 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
5194 6281 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
5195 6282 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
5196 6283 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
5197 6284 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
5198 6285 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
5199 6286 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
5200 6287 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
5201 6288 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
5202 6289 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
5203 6290 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
5204 6291 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
5229 6316 8.783833 ATATGTGTAGATACATCCATTTCTGC 57.216 34.615 0.00 0.00 41.31 4.26
5230 6317 5.049828 TGTGTAGATACATCCATTTCTGCG 58.950 41.667 0.00 0.00 38.63 5.18
5231 6318 5.163457 TGTGTAGATACATCCATTTCTGCGA 60.163 40.000 0.00 0.00 38.63 5.10
5232 6319 5.175856 GTGTAGATACATCCATTTCTGCGAC 59.824 44.000 0.00 0.00 38.63 5.19
5233 6320 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
5234 6321 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
5235 6322 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
5236 6323 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
5237 6324 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
5238 6325 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
5239 6326 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
5240 6327 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
5241 6328 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
5242 6329 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
5243 6330 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
5244 6331 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
5245 6332 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
5246 6333 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
5247 6334 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
5248 6335 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
5249 6336 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
5250 6337 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
5251 6338 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
5252 6339 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
5253 6340 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
5254 6341 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
5255 6342 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
5256 6343 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
5257 6344 1.856629 ATTCCGAACGGAGGGAGTAA 58.143 50.000 15.34 0.34 46.06 2.24
5258 6345 1.631405 TTCCGAACGGAGGGAGTAAA 58.369 50.000 15.34 0.00 46.06 2.01
5259 6346 1.631405 TCCGAACGGAGGGAGTAAAA 58.369 50.000 12.04 0.00 39.76 1.52
5260 6347 2.181975 TCCGAACGGAGGGAGTAAAAT 58.818 47.619 12.04 0.00 39.76 1.82
5261 6348 3.364549 TCCGAACGGAGGGAGTAAAATA 58.635 45.455 12.04 0.00 39.76 1.40
5262 6349 3.962718 TCCGAACGGAGGGAGTAAAATAT 59.037 43.478 12.04 0.00 39.76 1.28
5263 6350 5.139727 TCCGAACGGAGGGAGTAAAATATA 58.860 41.667 12.04 0.00 39.76 0.86
5264 6351 5.598005 TCCGAACGGAGGGAGTAAAATATAA 59.402 40.000 12.04 0.00 39.76 0.98
5265 6352 6.098124 TCCGAACGGAGGGAGTAAAATATAAA 59.902 38.462 12.04 0.00 39.76 1.40
5266 6353 6.423001 CCGAACGGAGGGAGTAAAATATAAAG 59.577 42.308 7.53 0.00 37.50 1.85
5267 6354 6.982724 CGAACGGAGGGAGTAAAATATAAAGT 59.017 38.462 0.00 0.00 0.00 2.66
5268 6355 7.493645 CGAACGGAGGGAGTAAAATATAAAGTT 59.506 37.037 0.00 0.00 0.00 2.66
5269 6356 9.170734 GAACGGAGGGAGTAAAATATAAAGTTT 57.829 33.333 0.00 0.00 0.00 2.66
5270 6357 8.502105 ACGGAGGGAGTAAAATATAAAGTTTG 57.498 34.615 0.00 0.00 0.00 2.93
5271 6358 8.105197 ACGGAGGGAGTAAAATATAAAGTTTGT 58.895 33.333 0.00 0.00 0.00 2.83
5272 6359 9.603921 CGGAGGGAGTAAAATATAAAGTTTGTA 57.396 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.611518 CTCCACAGAAACTAGGAAGCG 58.388 52.381 0.00 0.00 0.00 4.68
133 134 3.877508 GTCAACACCTGGCTATTCCATAC 59.122 47.826 0.00 0.00 45.50 2.39
149 150 1.525077 GCACCTGAACGGGTCAACA 60.525 57.895 1.95 0.00 37.52 3.33
162 163 3.699894 CAGGACTGGAGCGCACCT 61.700 66.667 24.52 12.09 0.00 4.00
217 218 1.966451 CCTTGTGACACTTCGGGCC 60.966 63.158 7.20 0.00 0.00 5.80
222 223 3.330267 GTGGAGATCCTTGTGACACTTC 58.670 50.000 7.20 0.00 36.82 3.01
280 281 2.644798 ACATACCTTCATATGCCCTCCC 59.355 50.000 0.00 0.00 36.21 4.30
309 310 2.743183 CGAAGAGAATCATGTGGGGTCC 60.743 54.545 0.00 0.00 37.82 4.46
312 313 2.555199 GACGAAGAGAATCATGTGGGG 58.445 52.381 0.00 0.00 37.82 4.96
343 344 4.341235 CCGGTCCACATAGATCTACAGAAA 59.659 45.833 4.10 0.00 0.00 2.52
344 345 3.889538 CCGGTCCACATAGATCTACAGAA 59.110 47.826 4.10 0.00 0.00 3.02
363 364 1.508632 ACACAATGAACGAAGACCGG 58.491 50.000 0.00 0.00 43.93 5.28
365 366 4.035017 CACAAACACAATGAACGAAGACC 58.965 43.478 0.00 0.00 0.00 3.85
371 372 3.105203 GGACACACAAACACAATGAACG 58.895 45.455 0.00 0.00 0.00 3.95
376 377 4.469657 ACCTATGGACACACAAACACAAT 58.530 39.130 0.00 0.00 0.00 2.71
377 378 3.892284 ACCTATGGACACACAAACACAA 58.108 40.909 0.00 0.00 0.00 3.33
392 393 8.567285 AGTTTCTCAAAAGTATCCAACCTATG 57.433 34.615 0.00 0.00 0.00 2.23
409 410 6.280643 TCTCAATGTTTCTTCGAGTTTCTCA 58.719 36.000 0.00 0.00 0.00 3.27
411 412 6.284459 ACTCTCAATGTTTCTTCGAGTTTCT 58.716 36.000 0.00 0.00 0.00 2.52
412 413 6.532365 ACTCTCAATGTTTCTTCGAGTTTC 57.468 37.500 0.00 0.00 0.00 2.78
413 414 6.538742 TGAACTCTCAATGTTTCTTCGAGTTT 59.461 34.615 0.00 0.00 39.51 2.66
414 415 6.049149 TGAACTCTCAATGTTTCTTCGAGTT 58.951 36.000 0.00 0.00 41.37 3.01
417 418 6.705825 TGAATGAACTCTCAATGTTTCTTCGA 59.294 34.615 0.00 0.00 34.49 3.71
419 420 8.562892 TCTTGAATGAACTCTCAATGTTTCTTC 58.437 33.333 0.00 0.00 34.49 2.87
420 421 8.455903 TCTTGAATGAACTCTCAATGTTTCTT 57.544 30.769 0.00 0.00 34.49 2.52
421 422 8.455903 TTCTTGAATGAACTCTCAATGTTTCT 57.544 30.769 0.00 0.00 34.49 2.52
422 423 9.520204 TTTTCTTGAATGAACTCTCAATGTTTC 57.480 29.630 0.00 0.00 34.49 2.78
423 424 9.525409 CTTTTCTTGAATGAACTCTCAATGTTT 57.475 29.630 0.00 0.00 34.49 2.83
424 425 8.906867 TCTTTTCTTGAATGAACTCTCAATGTT 58.093 29.630 0.00 0.00 34.49 2.71
425 426 8.348507 GTCTTTTCTTGAATGAACTCTCAATGT 58.651 33.333 0.00 0.00 34.49 2.71
432 705 4.467735 GCCGTCTTTTCTTGAATGAACTC 58.532 43.478 0.00 0.00 0.00 3.01
439 712 0.941542 CACGGCCGTCTTTTCTTGAA 59.058 50.000 31.80 0.00 0.00 2.69
440 713 1.503818 GCACGGCCGTCTTTTCTTGA 61.504 55.000 31.80 0.00 0.00 3.02
441 714 1.082104 GCACGGCCGTCTTTTCTTG 60.082 57.895 31.80 16.24 0.00 3.02
456 729 2.359478 AACCATTCCCGTCGGCAC 60.359 61.111 5.50 0.00 0.00 5.01
459 732 1.014352 GAATCAACCATTCCCGTCGG 58.986 55.000 3.60 3.60 35.66 4.79
467 740 3.328382 TCGAGGTTCGAATCAACCATT 57.672 42.857 11.72 0.00 46.90 3.16
479 752 0.799393 GAGCAAAGCCTTCGAGGTTC 59.201 55.000 0.00 0.00 37.80 3.62
491 764 3.059325 GTGCTACAGTGACAAGAGCAAAG 60.059 47.826 6.85 0.00 44.25 2.77
509 783 2.518349 CAACCACAACCGGGTGCT 60.518 61.111 22.38 3.68 36.82 4.40
511 785 2.124067 ACCAACCACAACCGGGTG 60.124 61.111 20.60 20.60 43.96 4.61
513 787 2.909965 CCACCAACCACAACCGGG 60.910 66.667 6.32 0.00 0.00 5.73
531 805 0.535102 ACTTGGTCCTTGGCGTTCAG 60.535 55.000 0.00 0.00 0.00 3.02
560 834 5.995282 TCCAATTCGTGACAAACAATCTACT 59.005 36.000 0.00 0.00 0.00 2.57
561 835 6.236017 TCCAATTCGTGACAAACAATCTAC 57.764 37.500 0.00 0.00 0.00 2.59
562 836 6.869315 TTCCAATTCGTGACAAACAATCTA 57.131 33.333 0.00 0.00 0.00 1.98
580 854 7.950124 AGGATAGAAACAATCTTCCTTTTCCAA 59.050 33.333 0.00 0.00 40.11 3.53
598 872 2.166459 CCGTGTGAGAAGCAGGATAGAA 59.834 50.000 0.00 0.00 0.00 2.10
604 878 4.586618 CTCCGTGTGAGAAGCAGG 57.413 61.111 0.00 0.00 44.42 4.85
700 1255 4.087892 CCAGGGACAGCTCGTGGG 62.088 72.222 5.02 0.00 36.75 4.61
764 1332 0.756294 TCTTGCCGGTTCAGAGTTCA 59.244 50.000 1.90 0.00 0.00 3.18
765 1333 1.149148 GTCTTGCCGGTTCAGAGTTC 58.851 55.000 1.90 0.00 0.00 3.01
766 1334 0.600255 CGTCTTGCCGGTTCAGAGTT 60.600 55.000 1.90 0.00 0.00 3.01
767 1335 1.006102 CGTCTTGCCGGTTCAGAGT 60.006 57.895 1.90 0.00 0.00 3.24
768 1336 2.383527 GCGTCTTGCCGGTTCAGAG 61.384 63.158 1.90 0.00 37.76 3.35
769 1337 2.357034 GCGTCTTGCCGGTTCAGA 60.357 61.111 1.90 0.00 37.76 3.27
851 1427 4.062032 GGGGTTTGGGAGAGGGGC 62.062 72.222 0.00 0.00 0.00 5.80
1530 2251 0.321671 TTCGGGAACAGAGCAGAAGG 59.678 55.000 0.00 0.00 0.00 3.46
1537 2258 3.190874 GCTACTGATTTCGGGAACAGAG 58.809 50.000 0.00 0.00 34.88 3.35
1545 2284 3.742433 ATCTCTGGCTACTGATTTCGG 57.258 47.619 0.00 0.00 0.00 4.30
1557 2296 2.223923 ACTGCGTCAATCTATCTCTGGC 60.224 50.000 0.00 0.00 0.00 4.85
1561 2300 2.033550 ACCGACTGCGTCAATCTATCTC 59.966 50.000 8.91 0.00 35.23 2.75
1585 2332 0.376152 GGACAGCTGCACAATCATCG 59.624 55.000 15.27 0.00 0.00 3.84
1697 2444 4.814294 GGCTGGTACGTGGCGAGG 62.814 72.222 0.00 0.00 0.00 4.63
1804 2557 5.450550 GCCATAGTTAACAGAATTGGAAGGC 60.451 44.000 8.61 3.83 0.00 4.35
1805 2558 5.220854 CGCCATAGTTAACAGAATTGGAAGG 60.221 44.000 8.61 0.00 0.00 3.46
1806 2559 5.584649 TCGCCATAGTTAACAGAATTGGAAG 59.415 40.000 8.61 5.48 0.00 3.46
1824 2578 4.158394 AGCACTTAATTTTGACATCGCCAT 59.842 37.500 0.00 0.00 0.00 4.40
1829 2583 5.353123 TCCGGTAGCACTTAATTTTGACATC 59.647 40.000 0.00 0.00 0.00 3.06
1848 2602 3.585732 TCAGGAAAAGGTAAGATTCCGGT 59.414 43.478 0.00 0.00 45.78 5.28
1859 2613 3.009033 TGTCGATGGAATCAGGAAAAGGT 59.991 43.478 0.00 0.00 45.97 3.50
1933 2689 9.774742 GAAACCTTGATGATAATCAAACACTAC 57.225 33.333 6.93 0.00 39.73 2.73
1934 2690 9.739276 AGAAACCTTGATGATAATCAAACACTA 57.261 29.630 6.93 0.00 39.73 2.74
2035 2792 9.619316 TTCAATGGACACAAATAAGTTAATTCG 57.381 29.630 0.00 0.00 0.00 3.34
2197 2958 3.673902 TCGATTGAGCTGATCCAAAACA 58.326 40.909 0.00 0.00 0.00 2.83
2298 3062 1.647213 CACGTCAACAATCGTACCTCG 59.353 52.381 0.00 0.00 38.52 4.63
2353 3117 8.579006 CAGATAACATGTATATGGCCACAAAAT 58.421 33.333 8.16 1.79 38.66 1.82
2504 3273 3.686726 GTCGTTTCAGGAATGAGCTGATT 59.313 43.478 0.00 0.00 34.03 2.57
2537 3306 8.038944 CACAGGATCATGGAAATGAAAATCTTT 58.961 33.333 12.66 0.00 33.83 2.52
2632 3401 5.816258 AGCAGCATATCATCCAGATTAATCG 59.184 40.000 9.78 5.27 38.19 3.34
2666 3435 3.132824 CCAATTCTAAAATGGGAGTGGCC 59.867 47.826 0.00 0.00 38.12 5.36
2667 3436 4.023291 TCCAATTCTAAAATGGGAGTGGC 58.977 43.478 0.00 0.00 39.65 5.01
2675 3444 4.643784 AGAGGCAGCTCCAATTCTAAAATG 59.356 41.667 5.21 0.00 37.29 2.32
2720 3489 6.732896 TCCACTAAAAGGCCATAACAAAAA 57.267 33.333 5.01 0.00 0.00 1.94
2730 3499 3.092301 AGAAAGCATCCACTAAAAGGCC 58.908 45.455 0.00 0.00 0.00 5.19
2765 3534 5.684704 CAGAATGGCTTGGTTAGATTCCTA 58.315 41.667 0.00 0.00 0.00 2.94
2865 3634 5.295787 TGACAGCACCTTTTAAAGTACACTG 59.704 40.000 3.91 7.97 0.00 3.66
2868 3637 5.278266 GCATGACAGCACCTTTTAAAGTACA 60.278 40.000 0.00 0.00 0.00 2.90
2936 3705 3.073678 AGCACAATTTCTGCATGACGTA 58.926 40.909 0.00 0.00 37.08 3.57
2959 3728 2.480419 CGTGGAAAACAGAGTGACATCC 59.520 50.000 0.00 0.00 0.00 3.51
2964 3733 6.932400 ACATATTAACGTGGAAAACAGAGTGA 59.068 34.615 0.00 0.00 0.00 3.41
2980 3749 6.677913 ACAGGACAAGCAACAACATATTAAC 58.322 36.000 0.00 0.00 0.00 2.01
3028 3797 6.362248 AGACTTGGGAGCTTTTTGTACTAAA 58.638 36.000 0.00 0.00 0.00 1.85
3058 3827 5.045942 TCTGGTGCCAGATTCAAACTATACA 60.046 40.000 16.28 0.00 46.80 2.29
3099 3868 7.775053 TGAGGAATAACAAAAAGTAGCCATT 57.225 32.000 0.00 0.00 0.00 3.16
3116 3887 5.219468 TGGAAAATTACCCCATGAGGAAT 57.781 39.130 0.00 0.00 38.24 3.01
3351 4124 7.087639 ACACCAAACCATGATTATAAAACACG 58.912 34.615 0.00 0.00 0.00 4.49
3411 4185 3.399181 GTCCCGGTCCCATCTGCA 61.399 66.667 0.00 0.00 0.00 4.41
3416 4190 2.424234 CCATTTTATGTCCCGGTCCCAT 60.424 50.000 0.00 1.59 0.00 4.00
3423 4197 2.014128 AGTTCGCCATTTTATGTCCCG 58.986 47.619 0.00 0.00 0.00 5.14
3626 4400 4.632153 TGTTCTTCTCTGTAGCAAAGTCC 58.368 43.478 0.00 0.00 0.00 3.85
3671 4445 1.864082 CCAAATGTTGAACCGGCAAAC 59.136 47.619 0.00 4.25 0.00 2.93
3716 4490 2.235891 TCTAGCTCGTTCACAACCTCA 58.764 47.619 0.00 0.00 0.00 3.86
3770 4544 5.584913 AGAGATAGGTCTTTTGAGAGTCCA 58.415 41.667 0.00 0.00 33.97 4.02
3773 4547 5.247110 TGCAAGAGATAGGTCTTTTGAGAGT 59.753 40.000 11.48 0.00 44.93 3.24
4100 4874 0.178992 CCAACAGCCTGTCCCAAAGA 60.179 55.000 0.00 0.00 0.00 2.52
4238 5012 1.062198 TGGCCATCTGTGATCCTCCTA 60.062 52.381 0.00 0.00 0.00 2.94
4245 5019 3.090210 TGATTTGTGGCCATCTGTGAT 57.910 42.857 9.72 0.00 0.00 3.06
4269 5043 1.618837 AGTTCTCTAGGCGTTTCAGCA 59.381 47.619 0.00 0.00 39.27 4.41
4333 5107 1.065401 CCTGCGTTTTCTGTGAAGCAA 59.935 47.619 0.00 0.00 34.04 3.91
4340 5114 0.463654 TGTGCTCCTGCGTTTTCTGT 60.464 50.000 0.00 0.00 43.34 3.41
4341 5115 0.040958 GTGTGCTCCTGCGTTTTCTG 60.041 55.000 0.00 0.00 43.34 3.02
4381 5156 5.954153 ATCACTCTGATTGGAACAGATCT 57.046 39.130 0.00 0.00 42.32 2.75
4384 5159 4.621510 CGGAATCACTCTGATTGGAACAGA 60.622 45.833 2.17 0.00 46.20 3.41
4427 5202 4.099266 CCAATTGTCAGTTTCAAACCTCCA 59.901 41.667 4.43 0.00 0.00 3.86
4469 5244 0.817634 TGCTCTTTGTTCCACCACCG 60.818 55.000 0.00 0.00 0.00 4.94
4486 5261 0.590195 GATGCGAACATGATCCCTGC 59.410 55.000 0.00 0.00 36.35 4.85
4501 5276 2.202756 GGAGGACACGACGGATGC 60.203 66.667 0.00 0.00 0.00 3.91
4502 5277 2.052690 AGGGAGGACACGACGGATG 61.053 63.158 0.00 0.00 0.00 3.51
4510 5285 0.765510 AACAGGAACAGGGAGGACAC 59.234 55.000 0.00 0.00 0.00 3.67
4591 5366 1.563924 TTACCGCCTGTGACACCTAT 58.436 50.000 2.45 0.00 0.00 2.57
4686 5461 5.942826 ACCAAAGAACAAAATTGCCAAAAGA 59.057 32.000 0.00 0.00 0.00 2.52
4687 5462 6.193514 ACCAAAGAACAAAATTGCCAAAAG 57.806 33.333 0.00 0.00 0.00 2.27
4809 5584 9.268268 TCAACACTAACTTATGTTACCAAAGAG 57.732 33.333 0.00 0.00 36.92 2.85
4885 5660 2.502510 GCAATGCCGTGCGTCAAG 60.503 61.111 0.00 0.00 34.21 3.02
4895 5675 0.240678 TGATGACACAACGCAATGCC 59.759 50.000 0.00 0.00 0.00 4.40
4982 6063 2.105006 TCATCACTGAGCTTTCCTGC 57.895 50.000 0.00 0.00 0.00 4.85
5010 6091 6.332630 GGTTACTACAGCCTACACGAATTTA 58.667 40.000 0.00 0.00 0.00 1.40
5111 6192 8.754991 TTTTCCATAGACTTGGTCAAACTTTA 57.245 30.769 0.52 0.00 38.01 1.85
5152 6239 4.184629 CAAGTAATTCTGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
5153 6240 3.581332 ACAAGTAATTCTGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
5154 6241 3.933332 GACAAGTAATTCTGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
5155 6242 4.822026 AGACAAGTAATTCTGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
5156 6243 4.559251 CGAGACAAGTAATTCTGAACGGAG 59.441 45.833 0.00 0.00 0.00 4.63
5157 6244 4.482386 CGAGACAAGTAATTCTGAACGGA 58.518 43.478 0.00 0.00 0.00 4.69
5158 6245 3.612860 CCGAGACAAGTAATTCTGAACGG 59.387 47.826 0.00 0.00 0.00 4.44
5159 6246 4.482386 TCCGAGACAAGTAATTCTGAACG 58.518 43.478 0.00 0.00 0.00 3.95
5160 6247 6.780706 TTTCCGAGACAAGTAATTCTGAAC 57.219 37.500 0.00 0.00 0.00 3.18
5161 6248 6.371548 CCATTTCCGAGACAAGTAATTCTGAA 59.628 38.462 0.00 0.00 0.00 3.02
5162 6249 5.874810 CCATTTCCGAGACAAGTAATTCTGA 59.125 40.000 0.00 0.00 0.00 3.27
5163 6250 5.874810 TCCATTTCCGAGACAAGTAATTCTG 59.125 40.000 0.00 0.00 0.00 3.02
5164 6251 6.049955 TCCATTTCCGAGACAAGTAATTCT 57.950 37.500 0.00 0.00 0.00 2.40
5165 6252 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
5166 6253 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
5167 6254 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
5168 6255 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
5169 6256 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
5170 6257 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
5171 6258 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
5172 6259 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
5173 6260 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
5174 6261 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
5175 6262 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
5176 6263 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
5177 6264 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
5178 6265 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
5203 6290 9.224267 GCAGAAATGGATGTATCTACACATATT 57.776 33.333 0.00 0.00 39.25 1.28
5204 6291 7.547019 CGCAGAAATGGATGTATCTACACATAT 59.453 37.037 0.00 0.00 39.25 1.78
5205 6292 6.868339 CGCAGAAATGGATGTATCTACACATA 59.132 38.462 0.00 0.00 39.25 2.29
5206 6293 5.698089 CGCAGAAATGGATGTATCTACACAT 59.302 40.000 0.00 0.00 41.83 3.21
5207 6294 5.049828 CGCAGAAATGGATGTATCTACACA 58.950 41.667 0.00 0.00 39.30 3.72
5208 6295 5.175856 GTCGCAGAAATGGATGTATCTACAC 59.824 44.000 0.00 0.00 39.69 2.90
5209 6296 5.163457 TGTCGCAGAAATGGATGTATCTACA 60.163 40.000 0.00 0.00 39.69 2.74
5210 6297 5.289595 TGTCGCAGAAATGGATGTATCTAC 58.710 41.667 0.00 0.00 39.69 2.59
5211 6298 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
5212 6299 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
5213 6300 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
5214 6301 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
5215 6302 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
5216 6303 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
5217 6304 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
5218 6305 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
5219 6306 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
5220 6307 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
5221 6308 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
5222 6309 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
5223 6310 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
5224 6311 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
5225 6312 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
5226 6313 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
5227 6314 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
5228 6315 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
5229 6316 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
5230 6317 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
5231 6318 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
5232 6319 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
5233 6320 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
5234 6321 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
5235 6322 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
5236 6323 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
5237 6324 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
5238 6325 1.856629 TTACTCCCTCCGTTCGGAAT 58.143 50.000 14.79 2.09 33.41 3.01
5239 6326 1.631405 TTTACTCCCTCCGTTCGGAA 58.369 50.000 14.79 0.04 33.41 4.30
5240 6327 1.631405 TTTTACTCCCTCCGTTCGGA 58.369 50.000 13.34 13.34 0.00 4.55
5241 6328 2.685850 ATTTTACTCCCTCCGTTCGG 57.314 50.000 4.74 4.74 0.00 4.30
5242 6329 6.982724 ACTTTATATTTTACTCCCTCCGTTCG 59.017 38.462 0.00 0.00 0.00 3.95
5243 6330 8.728337 AACTTTATATTTTACTCCCTCCGTTC 57.272 34.615 0.00 0.00 0.00 3.95
5244 6331 8.953313 CAAACTTTATATTTTACTCCCTCCGTT 58.047 33.333 0.00 0.00 0.00 4.44
5245 6332 8.105197 ACAAACTTTATATTTTACTCCCTCCGT 58.895 33.333 0.00 0.00 0.00 4.69
5246 6333 8.502105 ACAAACTTTATATTTTACTCCCTCCG 57.498 34.615 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.