Multiple sequence alignment - TraesCS4A01G257100

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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 TraesCS4A01G257100 chr4A 100.000 4458 0 0 1 4458 569883429 569878972 0.000000e+00 8233.0
1 TraesCS4A01G257100 chr4D 93.062 2825 110 30 3 2799 32496929 32499695 0.000000e+00 4052.0
2 TraesCS4A01G257100 chr4D 83.676 778 68 16 2822 3577 32499836 32500576 0.000000e+00 678.0
3 TraesCS4A01G257100 chr4D 82.667 600 44 29 3882 4455 32500908 32501473 1.120000e-130 477.0
4 TraesCS4A01G257100 chr4D 86.730 211 9 11 3666 3864 32500611 32500814 2.700000e-52 217.0
5 TraesCS4A01G257100 chr4B 90.245 1712 101 26 3 1690 47498014 47499683 0.000000e+00 2176.0
6 TraesCS4A01G257100 chr4B 88.624 1134 58 30 1694 2806 47499731 47500814 0.000000e+00 1314.0
7 TraesCS4A01G257100 chr4B 88.253 664 49 8 2822 3458 47500948 47501609 0.000000e+00 767.0
8 TraesCS4A01G257100 chr4B 83.010 412 26 23 4036 4431 47502106 47502489 2.570000e-87 333.0
9 TraesCS4A01G257100 chr4B 86.567 201 8 9 3677 3864 47501756 47501950 2.100000e-48 204.0
10 TraesCS4A01G257100 chr4B 100.000 46 0 0 3919 3964 47502065 47502110 7.950000e-13 86.1
11 TraesCS4A01G257100 chr7D 83.294 850 94 29 1934 2760 411026625 411025801 0.000000e+00 739.0
12 TraesCS4A01G257100 chr7D 84.718 602 79 10 951 1548 411027672 411027080 1.380000e-164 590.0
13 TraesCS4A01G257100 chr7D 77.147 652 87 32 2997 3615 411025513 411024891 5.560000e-84 322.0
14 TraesCS4A01G257100 chr7A 83.851 805 88 29 1934 2732 470888000 470888768 0.000000e+00 728.0
15 TraesCS4A01G257100 chr7A 84.786 631 82 10 924 1548 470886924 470887546 4.900000e-174 621.0
16 TraesCS4A01G257100 chr7A 76.409 674 100 36 2987 3628 470889163 470889809 4.330000e-80 309.0
17 TraesCS4A01G257100 chr7A 81.183 372 52 12 1181 1543 628917262 628917624 2.620000e-72 283.0
18 TraesCS4A01G257100 chr7A 84.211 228 29 4 1934 2156 628918080 628918305 9.710000e-52 215.0
19 TraesCS4A01G257100 chr2D 81.551 374 53 12 1181 1543 603592992 603592624 1.210000e-75 294.0
20 TraesCS4A01G257100 chr5D 81.016 374 55 12 1181 1543 297158346 297158714 2.620000e-72 283.0
21 TraesCS4A01G257100 chr5D 86.885 183 21 2 1934 2116 297159166 297159345 7.560000e-48 202.0
22 TraesCS4A01G257100 chr5A 79.787 376 56 14 1181 1543 534807964 534808332 5.720000e-64 255.0
23 TraesCS4A01G257100 chr5A 88.235 170 20 0 1934 2103 534808782 534808951 2.100000e-48 204.0
24 TraesCS4A01G257100 chr7B 81.169 308 43 10 1181 1477 713567974 713568277 2.680000e-57 233.0
25 TraesCS4A01G257100 chr7B 87.574 169 18 2 1948 2116 125856742 125856577 4.550000e-45 193.0
26 TraesCS4A01G257100 chr7B 87.647 170 16 4 1948 2116 713568776 713568941 4.550000e-45 193.0


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 TraesCS4A01G257100 chr4A 569878972 569883429 4457 True 8233.000000 8233 100.000000 1 4458 1 chr4A.!!$R1 4457
1 TraesCS4A01G257100 chr4D 32496929 32501473 4544 False 1356.000000 4052 86.533750 3 4455 4 chr4D.!!$F1 4452
2 TraesCS4A01G257100 chr4B 47498014 47502489 4475 False 813.350000 2176 89.449833 3 4431 6 chr4B.!!$F1 4428
3 TraesCS4A01G257100 chr7D 411024891 411027672 2781 True 550.333333 739 81.719667 951 3615 3 chr7D.!!$R1 2664
4 TraesCS4A01G257100 chr7A 470886924 470889809 2885 False 552.666667 728 81.682000 924 3628 3 chr7A.!!$F1 2704
5 TraesCS4A01G257100 chr7A 628917262 628918305 1043 False 249.000000 283 82.697000 1181 2156 2 chr7A.!!$F2 975
6 TraesCS4A01G257100 chr5D 297158346 297159345 999 False 242.500000 283 83.950500 1181 2116 2 chr5D.!!$F1 935
7 TraesCS4A01G257100 chr5A 534807964 534808951 987 False 229.500000 255 84.011000 1181 2103 2 chr5A.!!$F1 922
8 TraesCS4A01G257100 chr7B 713567974 713568941 967 False 213.000000 233 84.408000 1181 2116 2 chr7B.!!$F1 935

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
416 420 0.107654 GAGTAGGGGCATGTGGTGAC 60.108 60.000 0.00 0.0 33.92 3.67 F
418 422 0.107654 GTAGGGGCATGTGGTGACTC 60.108 60.000 0.00 0.0 36.12 3.36 F
422 426 0.326264 GGGCATGTGGTGACTCTTCT 59.674 55.000 0.00 0.0 35.58 2.85 F
425 429 1.002430 GCATGTGGTGACTCTTCTGGA 59.998 52.381 0.00 0.0 0.00 3.86 F
739 802 1.472728 CCTACCGGGAGAAAATCACCG 60.473 57.143 17.91 0.0 39.85 4.94 F
2806 3061 0.550914 TGCAAACTGTGGTTCCTCCT 59.449 50.000 0.00 0.0 34.14 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1343 0.596082 GTGTTACCCACGCAGCAAAT 59.404 50.000 0.0 0.0 35.77 2.32 R
1280 1345 3.739167 GTGTTACCCACGCAGCAA 58.261 55.556 0.0 0.0 35.77 3.91 R
1883 2077 6.773976 AGTTGAGGAACAATTTCTTCACAA 57.226 33.333 0.0 0.0 44.97 3.33 R
2594 2834 1.295423 GGTGGCTTCCTTCGCACTA 59.705 57.895 0.0 0.0 0.00 2.74 R
2817 3072 4.706842 ACACCACTTTCCTGTCAATAGT 57.293 40.909 0.0 0.0 0.00 2.12 R
3675 4269 0.033601 TATGCCACCATCCACCAACC 60.034 55.000 0.0 0.0 32.85 3.77 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
42 43 4.386954 CCTGCGCAATATGTCAGTATACAG 59.613 45.833 13.05 0.00 31.70 2.74
47 48 7.148323 TGCGCAATATGTCAGTATACAGTTTTT 60.148 33.333 8.16 0.00 31.70 1.94
48 49 7.164171 GCGCAATATGTCAGTATACAGTTTTTG 59.836 37.037 0.30 1.93 31.70 2.44
49 50 8.175069 CGCAATATGTCAGTATACAGTTTTTGT 58.825 33.333 5.50 0.00 43.96 2.83
93 95 1.180029 GCATCCCAAGTTCATGTGCT 58.820 50.000 0.00 0.00 0.00 4.40
96 98 2.189594 TCCCAAGTTCATGTGCTCTG 57.810 50.000 0.00 0.00 0.00 3.35
106 108 3.785486 TCATGTGCTCTGTATGTGCTAC 58.215 45.455 0.00 0.00 36.27 3.58
117 119 5.820947 TCTGTATGTGCTACGAGTGATTAGA 59.179 40.000 0.00 0.00 32.61 2.10
118 120 6.017852 TCTGTATGTGCTACGAGTGATTAGAG 60.018 42.308 0.00 0.00 32.61 2.43
119 121 3.422417 TGTGCTACGAGTGATTAGAGC 57.578 47.619 0.00 0.00 0.00 4.09
136 138 2.953821 CGCCCAAAATGTCGCTGT 59.046 55.556 0.00 0.00 0.00 4.40
160 162 7.710044 TGTTATGCTGCAACCCATAATTAAATG 59.290 33.333 6.36 0.00 36.60 2.32
179 181 6.492007 AAATGTCTGAATCACAGTGATGTC 57.508 37.500 17.11 15.32 45.86 3.06
220 223 5.242838 AGGGTAATTTCACGATGCTTGAAAA 59.757 36.000 2.72 0.00 44.14 2.29
239 242 5.984926 TGAAAATTGGCTTGTTCAATGTCTC 59.015 36.000 0.00 0.00 35.31 3.36
240 243 5.534207 AAATTGGCTTGTTCAATGTCTCA 57.466 34.783 0.00 0.00 35.31 3.27
243 246 2.622942 TGGCTTGTTCAATGTCTCAACC 59.377 45.455 0.00 0.00 0.00 3.77
259 262 0.250513 AACCGGGCTCATCTCAACTC 59.749 55.000 6.32 0.00 0.00 3.01
286 289 5.499268 CATTTTAAAATGTGTCACGCAGG 57.501 39.130 26.14 3.18 40.61 4.85
295 298 0.874390 TGTCACGCAGGCAGAAAATC 59.126 50.000 0.00 0.00 0.00 2.17
313 316 7.705325 CAGAAAATCCTGAGCAAATATTGGAAG 59.295 37.037 0.00 0.00 36.29 3.46
315 318 8.593945 AAAATCCTGAGCAAATATTGGAAGTA 57.406 30.769 0.00 0.00 0.00 2.24
317 320 7.573968 ATCCTGAGCAAATATTGGAAGTAAC 57.426 36.000 0.00 0.00 0.00 2.50
326 329 7.480810 CAAATATTGGAAGTAACCCTTGTAGC 58.519 38.462 0.00 0.00 32.03 3.58
327 330 4.650972 ATTGGAAGTAACCCTTGTAGCA 57.349 40.909 0.00 0.00 32.03 3.49
371 375 8.406297 GGATATATGAAAACTCTTGTGGAAACC 58.594 37.037 0.00 0.00 0.00 3.27
373 377 3.611970 TGAAAACTCTTGTGGAAACCGA 58.388 40.909 0.00 0.00 0.00 4.69
374 378 4.204012 TGAAAACTCTTGTGGAAACCGAT 58.796 39.130 0.00 0.00 0.00 4.18
375 379 4.274950 TGAAAACTCTTGTGGAAACCGATC 59.725 41.667 0.00 0.00 0.00 3.69
376 380 2.474410 ACTCTTGTGGAAACCGATCC 57.526 50.000 0.00 0.00 40.10 3.36
377 381 1.978580 ACTCTTGTGGAAACCGATCCT 59.021 47.619 3.98 0.00 40.35 3.24
378 382 2.372172 ACTCTTGTGGAAACCGATCCTT 59.628 45.455 3.98 0.00 40.35 3.36
379 383 3.181443 ACTCTTGTGGAAACCGATCCTTT 60.181 43.478 3.98 0.00 40.35 3.11
380 384 3.821033 CTCTTGTGGAAACCGATCCTTTT 59.179 43.478 3.98 0.00 40.35 2.27
381 385 4.975631 TCTTGTGGAAACCGATCCTTTTA 58.024 39.130 3.98 0.00 40.35 1.52
382 386 5.001232 TCTTGTGGAAACCGATCCTTTTAG 58.999 41.667 3.98 0.00 40.35 1.85
383 387 4.360951 TGTGGAAACCGATCCTTTTAGT 57.639 40.909 3.98 0.00 40.35 2.24
384 388 4.721132 TGTGGAAACCGATCCTTTTAGTT 58.279 39.130 3.98 0.00 40.35 2.24
385 389 5.134661 TGTGGAAACCGATCCTTTTAGTTT 58.865 37.500 3.98 0.00 40.35 2.66
386 390 5.009210 TGTGGAAACCGATCCTTTTAGTTTG 59.991 40.000 0.00 0.00 40.35 2.93
387 391 5.239963 GTGGAAACCGATCCTTTTAGTTTGA 59.760 40.000 0.00 0.00 40.35 2.69
388 392 6.007703 TGGAAACCGATCCTTTTAGTTTGAT 58.992 36.000 0.00 0.00 40.35 2.57
389 393 6.492087 TGGAAACCGATCCTTTTAGTTTGATT 59.508 34.615 0.00 0.00 40.35 2.57
390 394 7.014808 TGGAAACCGATCCTTTTAGTTTGATTT 59.985 33.333 0.00 0.00 40.35 2.17
391 395 7.870954 GGAAACCGATCCTTTTAGTTTGATTTT 59.129 33.333 0.00 0.00 36.50 1.82
392 396 9.902196 GAAACCGATCCTTTTAGTTTGATTTTA 57.098 29.630 0.00 0.00 31.14 1.52
394 398 9.855021 AACCGATCCTTTTAGTTTGATTTTATG 57.145 29.630 0.00 0.00 0.00 1.90
395 399 9.020731 ACCGATCCTTTTAGTTTGATTTTATGT 57.979 29.630 0.00 0.00 0.00 2.29
406 410 7.054751 AGTTTGATTTTATGTAGAGTAGGGGC 58.945 38.462 0.00 0.00 0.00 5.80
407 411 6.569127 TTGATTTTATGTAGAGTAGGGGCA 57.431 37.500 0.00 0.00 0.00 5.36
408 412 6.763715 TGATTTTATGTAGAGTAGGGGCAT 57.236 37.500 0.00 0.00 0.00 4.40
409 413 6.533730 TGATTTTATGTAGAGTAGGGGCATG 58.466 40.000 0.00 0.00 0.00 4.06
410 414 5.968676 TTTTATGTAGAGTAGGGGCATGT 57.031 39.130 0.00 0.00 0.00 3.21
411 415 4.955811 TTATGTAGAGTAGGGGCATGTG 57.044 45.455 0.00 0.00 0.00 3.21
412 416 1.496060 TGTAGAGTAGGGGCATGTGG 58.504 55.000 0.00 0.00 0.00 4.17
413 417 1.273609 TGTAGAGTAGGGGCATGTGGT 60.274 52.381 0.00 0.00 0.00 4.16
414 418 1.139058 GTAGAGTAGGGGCATGTGGTG 59.861 57.143 0.00 0.00 0.00 4.17
415 419 0.252696 AGAGTAGGGGCATGTGGTGA 60.253 55.000 0.00 0.00 0.00 4.02
416 420 0.107654 GAGTAGGGGCATGTGGTGAC 60.108 60.000 0.00 0.00 33.92 3.67
417 421 0.547712 AGTAGGGGCATGTGGTGACT 60.548 55.000 0.00 0.00 35.58 3.41
418 422 0.107654 GTAGGGGCATGTGGTGACTC 60.108 60.000 0.00 0.00 36.12 3.36
419 423 1.539869 AGGGGCATGTGGTGACTCT 60.540 57.895 0.00 0.00 43.98 3.24
420 424 1.380302 GGGGCATGTGGTGACTCTT 59.620 57.895 0.00 0.00 31.55 2.85
421 425 0.678048 GGGGCATGTGGTGACTCTTC 60.678 60.000 0.00 0.00 31.55 2.87
422 426 0.326264 GGGCATGTGGTGACTCTTCT 59.674 55.000 0.00 0.00 35.58 2.85
423 427 1.446907 GGCATGTGGTGACTCTTCTG 58.553 55.000 0.00 0.00 31.05 3.02
424 428 1.446907 GCATGTGGTGACTCTTCTGG 58.553 55.000 0.00 0.00 0.00 3.86
425 429 1.002430 GCATGTGGTGACTCTTCTGGA 59.998 52.381 0.00 0.00 0.00 3.86
426 430 2.550855 GCATGTGGTGACTCTTCTGGAA 60.551 50.000 0.00 0.00 0.00 3.53
427 431 3.743521 CATGTGGTGACTCTTCTGGAAA 58.256 45.455 0.00 0.00 0.00 3.13
428 432 3.924114 TGTGGTGACTCTTCTGGAAAA 57.076 42.857 0.00 0.00 0.00 2.29
429 433 4.437682 TGTGGTGACTCTTCTGGAAAAT 57.562 40.909 0.00 0.00 0.00 1.82
430 434 4.136796 TGTGGTGACTCTTCTGGAAAATG 58.863 43.478 0.00 0.00 0.00 2.32
431 435 3.057946 GTGGTGACTCTTCTGGAAAATGC 60.058 47.826 0.00 0.00 0.00 3.56
468 472 3.081061 TGCTCCACTACGATGCATTTTT 58.919 40.909 0.00 0.00 0.00 1.94
472 476 5.163754 GCTCCACTACGATGCATTTTTAAGT 60.164 40.000 0.00 0.00 0.00 2.24
473 477 6.036735 GCTCCACTACGATGCATTTTTAAGTA 59.963 38.462 0.00 0.00 0.00 2.24
493 497 7.818493 AAGTATATAGTATGAACATGCGCAG 57.182 36.000 18.32 10.85 0.00 5.18
512 516 4.438744 CGCAGAACTCTTTTGGAAACTGTT 60.439 41.667 0.00 0.00 0.00 3.16
543 606 3.976793 ATTTTGCTCCACTATGATGCG 57.023 42.857 0.00 0.00 0.00 4.73
547 610 2.279741 TGCTCCACTATGATGCGTTTC 58.720 47.619 0.00 0.00 0.00 2.78
558 621 7.326063 CACTATGATGCGTTTCGAAGTATCATA 59.674 37.037 23.86 23.86 36.81 2.15
568 631 9.193133 CGTTTCGAAGTATCATAGGTTTCATAT 57.807 33.333 0.00 0.00 0.00 1.78
586 649 4.101430 TCATATGCATGCTTGACCAGAGTA 59.899 41.667 20.33 0.00 31.73 2.59
601 664 4.600111 ACCAGAGTACAAAAATGGGACCTA 59.400 41.667 0.00 0.00 35.26 3.08
614 677 8.575649 AAAATGGGACCTACTGTTAAACATAG 57.424 34.615 0.00 0.00 0.00 2.23
691 754 7.012989 ACTGTTTTACCTTGTAGAATCCAACAC 59.987 37.037 0.00 0.00 0.00 3.32
739 802 1.472728 CCTACCGGGAGAAAATCACCG 60.473 57.143 17.91 0.00 39.85 4.94
901 964 2.228545 TTGCAGGCATTTATGGACCA 57.771 45.000 0.00 0.00 0.00 4.02
1155 1218 2.201732 GCATCCTGCAGCATGATTTTG 58.798 47.619 22.05 4.26 44.26 2.44
1274 1339 7.707624 ATGCAATCTTGTTTTCCTTCTCATA 57.292 32.000 0.00 0.00 0.00 2.15
1278 1343 9.113838 GCAATCTTGTTTTCCTTCTCATAGATA 57.886 33.333 0.00 0.00 0.00 1.98
1518 1591 3.668447 TGATCTGAGGACTGTTTTCTGC 58.332 45.455 0.00 0.00 0.00 4.26
1572 1657 3.000727 CGGTATCGGGGCATCTTTTATC 58.999 50.000 0.00 0.00 0.00 1.75
1573 1658 3.556213 CGGTATCGGGGCATCTTTTATCA 60.556 47.826 0.00 0.00 0.00 2.15
1883 2077 5.748402 TGAGTTGAGCATTTCCATATGAGT 58.252 37.500 3.65 0.00 0.00 3.41
2594 2834 5.242393 GCTTACATTGAGGCATGTAATGGAT 59.758 40.000 8.73 0.00 46.86 3.41
2615 2855 2.347490 GCGAAGGAAGCCACCAGA 59.653 61.111 0.00 0.00 0.00 3.86
2753 3006 4.201822 GCTTCAAACTTCACTCGTTCACTT 60.202 41.667 0.00 0.00 0.00 3.16
2754 3007 4.857871 TCAAACTTCACTCGTTCACTTG 57.142 40.909 0.00 0.00 0.00 3.16
2755 3008 4.250464 TCAAACTTCACTCGTTCACTTGT 58.750 39.130 0.00 0.00 0.00 3.16
2756 3009 4.693566 TCAAACTTCACTCGTTCACTTGTT 59.306 37.500 0.00 0.00 0.00 2.83
2757 3010 5.180492 TCAAACTTCACTCGTTCACTTGTTT 59.820 36.000 0.00 0.00 0.00 2.83
2758 3011 5.622770 AACTTCACTCGTTCACTTGTTTT 57.377 34.783 0.00 0.00 0.00 2.43
2759 3012 6.730960 AACTTCACTCGTTCACTTGTTTTA 57.269 33.333 0.00 0.00 0.00 1.52
2800 3055 8.303876 CCTAATAACTAAATGCAAACTGTGGTT 58.696 33.333 0.00 0.00 37.24 3.67
2806 3061 0.550914 TGCAAACTGTGGTTCCTCCT 59.449 50.000 0.00 0.00 34.14 3.69
2809 3064 1.142870 CAAACTGTGGTTCCTCCTCCA 59.857 52.381 0.00 0.00 34.14 3.86
2810 3065 1.518367 AACTGTGGTTCCTCCTCCAA 58.482 50.000 0.00 0.00 35.38 3.53
2811 3066 0.765510 ACTGTGGTTCCTCCTCCAAC 59.234 55.000 0.00 0.00 35.38 3.77
2812 3067 0.764890 CTGTGGTTCCTCCTCCAACA 59.235 55.000 0.00 0.00 35.38 3.33
2816 3071 2.304761 GTGGTTCCTCCTCCAACATACA 59.695 50.000 0.00 0.00 35.38 2.29
2817 3072 2.983192 TGGTTCCTCCTCCAACATACAA 59.017 45.455 0.00 0.00 37.07 2.41
2818 3073 3.244770 TGGTTCCTCCTCCAACATACAAC 60.245 47.826 0.00 0.00 37.07 3.32
2819 3074 3.009143 GGTTCCTCCTCCAACATACAACT 59.991 47.826 0.00 0.00 0.00 3.16
2829 3207 6.367374 TCCAACATACAACTATTGACAGGA 57.633 37.500 0.00 0.00 0.00 3.86
2844 3222 3.055385 TGACAGGAAAGTGGTGTATAGGC 60.055 47.826 0.00 0.00 0.00 3.93
2846 3224 3.587506 ACAGGAAAGTGGTGTATAGGCTT 59.412 43.478 0.00 0.00 0.00 4.35
2851 3229 6.828785 AGGAAAGTGGTGTATAGGCTTAAATG 59.171 38.462 0.00 0.00 0.00 2.32
2863 3241 5.824904 AGGCTTAAATGTGTTATCTGCTG 57.175 39.130 0.00 0.00 0.00 4.41
2995 3549 5.677091 GCAAATGCTACTTGTGTCTTATGGG 60.677 44.000 0.00 0.00 38.21 4.00
3154 3708 6.060136 CCAAATGAATCTGATAAGCCTCTCA 58.940 40.000 0.00 0.00 0.00 3.27
3158 3712 8.763984 AATGAATCTGATAAGCCTCTCAAAAT 57.236 30.769 0.00 0.00 0.00 1.82
3166 3720 0.097150 GCCTCTCAAAATTCGTCGCC 59.903 55.000 0.00 0.00 0.00 5.54
3215 3780 0.966875 CATTGCCCTGCAGCCTTGTA 60.967 55.000 8.66 0.00 40.61 2.41
3239 3804 2.348472 TCCCTCAACAAGATCCCACTT 58.652 47.619 0.00 0.00 0.00 3.16
3287 3852 1.522355 CCGCACGAGCATGGAGAAT 60.522 57.895 5.50 0.00 42.27 2.40
3305 3870 5.221009 GGAGAATTCCATCAGCATTCTGTTC 60.221 44.000 0.65 0.00 43.45 3.18
3337 3914 5.779922 TCGTCTATGACCATATTGCCTTAC 58.220 41.667 0.00 0.00 0.00 2.34
3354 3932 3.005897 CCTTACGGCTGCTGACATATACT 59.994 47.826 16.72 0.00 0.00 2.12
3368 3946 7.463469 TGACATATACTGCATTTCACTAACG 57.537 36.000 0.00 0.00 0.00 3.18
3381 3959 7.270579 GCATTTCACTAACGAAAGAAACCATAC 59.729 37.037 0.00 0.00 38.24 2.39
3387 3965 3.417101 ACGAAAGAAACCATACATGCCA 58.583 40.909 0.00 0.00 0.00 4.92
3394 3973 0.185901 ACCATACATGCCATCACCCC 59.814 55.000 0.00 0.00 0.00 4.95
3430 4009 1.459450 GAGTATTTTTCGCCAGGGCA 58.541 50.000 11.42 0.00 42.06 5.36
3454 4033 3.011760 GCGCGAAAACTCCCAGTCG 62.012 63.158 12.10 0.00 36.59 4.18
3458 4037 1.068055 GCGAAAACTCCCAGTCGTAGA 60.068 52.381 0.00 0.00 35.93 2.59
3465 4044 2.100197 CTCCCAGTCGTAGATGTTCCA 58.900 52.381 0.00 0.00 40.67 3.53
3467 4046 3.889538 CTCCCAGTCGTAGATGTTCCATA 59.110 47.826 0.00 0.00 40.67 2.74
3469 4048 4.523173 TCCCAGTCGTAGATGTTCCATATC 59.477 45.833 0.00 0.00 40.67 1.63
3470 4049 4.322049 CCCAGTCGTAGATGTTCCATATCC 60.322 50.000 0.00 0.00 40.67 2.59
3472 4051 4.280929 CAGTCGTAGATGTTCCATATCCCA 59.719 45.833 0.00 0.00 40.67 4.37
3473 4052 5.047021 CAGTCGTAGATGTTCCATATCCCAT 60.047 44.000 0.00 0.00 40.67 4.00
3475 4064 5.869888 GTCGTAGATGTTCCATATCCCATTC 59.130 44.000 0.00 0.00 40.67 2.67
3480 4069 4.993705 TGTTCCATATCCCATTCCTACC 57.006 45.455 0.00 0.00 0.00 3.18
3505 4094 0.529773 GCAGGATTGCGGTCGTCATA 60.530 55.000 0.00 0.00 41.13 2.15
3507 4096 2.276201 CAGGATTGCGGTCGTCATAAA 58.724 47.619 0.00 0.00 0.00 1.40
3508 4097 2.675844 CAGGATTGCGGTCGTCATAAAA 59.324 45.455 0.00 0.00 0.00 1.52
3531 4120 2.549332 GCAGTCTGCTCCCTCAAAC 58.451 57.895 17.89 0.00 40.96 2.93
3572 4164 0.668535 GTGTGAGGTTGTTTCCCAGC 59.331 55.000 0.00 0.00 0.00 4.85
3579 4171 0.032540 GTTGTTTCCCAGCTGGCAAG 59.967 55.000 28.39 14.31 0.00 4.01
3580 4172 0.106268 TTGTTTCCCAGCTGGCAAGA 60.106 50.000 28.39 16.60 0.00 3.02
3581 4173 0.823356 TGTTTCCCAGCTGGCAAGAC 60.823 55.000 28.39 20.87 0.00 3.01
3583 4175 0.106268 TTTCCCAGCTGGCAAGACAA 60.106 50.000 28.39 12.60 0.00 3.18
3592 4185 1.528586 CTGGCAAGACAAGAGACAACG 59.471 52.381 0.00 0.00 0.00 4.10
3628 4222 3.061965 CCTGGTGCTTCGTTTTGTTTTTG 59.938 43.478 0.00 0.00 0.00 2.44
3629 4223 2.413453 TGGTGCTTCGTTTTGTTTTTGC 59.587 40.909 0.00 0.00 0.00 3.68
3647 4241 2.035155 TCTCGAAGCCGTCCTGGA 59.965 61.111 0.00 0.00 42.00 3.86
3648 4242 1.379977 TCTCGAAGCCGTCCTGGAT 60.380 57.895 0.00 0.00 42.00 3.41
3651 4245 0.970937 TCGAAGCCGTCCTGGATCTT 60.971 55.000 0.00 4.14 42.00 2.40
3652 4246 0.528684 CGAAGCCGTCCTGGATCTTC 60.529 60.000 18.38 18.38 42.00 2.87
3653 4247 0.827368 GAAGCCGTCCTGGATCTTCT 59.173 55.000 19.86 6.87 42.00 2.85
3654 4248 0.827368 AAGCCGTCCTGGATCTTCTC 59.173 55.000 0.00 0.00 42.00 2.87
3655 4249 0.032615 AGCCGTCCTGGATCTTCTCT 60.033 55.000 0.00 0.00 42.00 3.10
3656 4250 0.827368 GCCGTCCTGGATCTTCTCTT 59.173 55.000 0.00 0.00 42.00 2.85
3657 4251 1.472376 GCCGTCCTGGATCTTCTCTTG 60.472 57.143 0.00 0.00 42.00 3.02
3658 4252 1.827969 CCGTCCTGGATCTTCTCTTGT 59.172 52.381 0.00 0.00 42.00 3.16
3659 4253 2.159170 CCGTCCTGGATCTTCTCTTGTC 60.159 54.545 0.00 0.00 42.00 3.18
3660 4254 2.478709 CGTCCTGGATCTTCTCTTGTCG 60.479 54.545 0.00 0.00 0.00 4.35
3661 4255 2.494073 GTCCTGGATCTTCTCTTGTCGT 59.506 50.000 0.00 0.00 0.00 4.34
3662 4256 2.755655 TCCTGGATCTTCTCTTGTCGTC 59.244 50.000 0.00 0.00 0.00 4.20
3663 4257 2.478709 CCTGGATCTTCTCTTGTCGTCG 60.479 54.545 0.00 0.00 0.00 5.12
3664 4258 1.135373 TGGATCTTCTCTTGTCGTCGC 60.135 52.381 0.00 0.00 0.00 5.19
3665 4259 1.133407 GGATCTTCTCTTGTCGTCGCT 59.867 52.381 0.00 0.00 0.00 4.93
3666 4260 2.446282 GATCTTCTCTTGTCGTCGCTC 58.554 52.381 0.00 0.00 0.00 5.03
3667 4261 1.524848 TCTTCTCTTGTCGTCGCTCT 58.475 50.000 0.00 0.00 0.00 4.09
3668 4262 1.880675 TCTTCTCTTGTCGTCGCTCTT 59.119 47.619 0.00 0.00 0.00 2.85
3669 4263 1.982223 CTTCTCTTGTCGTCGCTCTTG 59.018 52.381 0.00 0.00 0.00 3.02
3670 4264 0.952280 TCTCTTGTCGTCGCTCTTGT 59.048 50.000 0.00 0.00 0.00 3.16
3671 4265 1.056103 CTCTTGTCGTCGCTCTTGTG 58.944 55.000 0.00 0.00 0.00 3.33
3672 4266 0.318699 TCTTGTCGTCGCTCTTGTGG 60.319 55.000 0.00 0.00 0.00 4.17
3673 4267 0.597637 CTTGTCGTCGCTCTTGTGGT 60.598 55.000 0.00 0.00 0.00 4.16
3674 4268 0.179094 TTGTCGTCGCTCTTGTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
3675 4269 0.874175 TGTCGTCGCTCTTGTGGTTG 60.874 55.000 0.00 0.00 0.00 3.77
3678 4272 1.157870 CGTCGCTCTTGTGGTTGGTT 61.158 55.000 0.00 0.00 0.00 3.67
3684 4278 0.626382 TCTTGTGGTTGGTTGGTGGA 59.374 50.000 0.00 0.00 0.00 4.02
3713 4307 6.890268 TGGCATATATACGTCCTCTGTAAGAT 59.110 38.462 0.00 0.00 45.62 2.40
3726 4320 8.085296 GTCCTCTGTAAGATACATGGTTAGATG 58.915 40.741 0.00 0.00 45.62 2.90
3747 4341 0.322816 TGCTGAAATCCCAGGCAGTC 60.323 55.000 0.00 0.00 34.82 3.51
3774 4371 8.778059 GGGGATATAGATGATTGGGTAAATACA 58.222 37.037 0.00 0.00 0.00 2.29
3775 4372 9.614792 GGGATATAGATGATTGGGTAAATACAC 57.385 37.037 0.00 0.00 0.00 2.90
3826 4428 3.060602 GTTCTCCTCTGAAACCAACTCG 58.939 50.000 0.00 0.00 0.00 4.18
3856 4463 5.094812 CAGATCGCTGCTGTATATTCTCTC 58.905 45.833 0.00 0.00 34.95 3.20
3857 4464 4.764308 AGATCGCTGCTGTATATTCTCTCA 59.236 41.667 0.00 0.00 0.00 3.27
3861 4468 5.094812 CGCTGCTGTATATTCTCTCATCTC 58.905 45.833 0.00 0.00 0.00 2.75
3862 4469 5.106197 CGCTGCTGTATATTCTCTCATCTCT 60.106 44.000 0.00 0.00 0.00 3.10
3864 4471 7.153985 GCTGCTGTATATTCTCTCATCTCTTT 58.846 38.462 0.00 0.00 0.00 2.52
3901 4589 6.500684 TCTGGTTTATCTCTTGTGCATTTC 57.499 37.500 0.00 0.00 0.00 2.17
3909 4597 1.275856 TCTTGTGCATTTCCCATTGCC 59.724 47.619 0.00 0.00 38.08 4.52
3914 4602 1.433064 CATTTCCCATTGCCGGTCG 59.567 57.895 1.90 0.00 0.00 4.79
3964 4652 2.359850 TTGTGCCCTAGCTTGCCG 60.360 61.111 0.00 0.00 40.80 5.69
3984 4672 4.381411 CCGTCTCTTTTGGTTTCTCTCTT 58.619 43.478 0.00 0.00 0.00 2.85
3985 4673 4.449405 CCGTCTCTTTTGGTTTCTCTCTTC 59.551 45.833 0.00 0.00 0.00 2.87
3994 4682 9.455847 CTTTTGGTTTCTCTCTTCTGTATTTTG 57.544 33.333 0.00 0.00 0.00 2.44
3995 4683 7.510549 TTGGTTTCTCTCTTCTGTATTTTGG 57.489 36.000 0.00 0.00 0.00 3.28
3996 4684 6.601332 TGGTTTCTCTCTTCTGTATTTTGGT 58.399 36.000 0.00 0.00 0.00 3.67
3997 4685 7.060421 TGGTTTCTCTCTTCTGTATTTTGGTT 58.940 34.615 0.00 0.00 0.00 3.67
3999 4687 7.445707 GGTTTCTCTCTTCTGTATTTTGGTTCT 59.554 37.037 0.00 0.00 0.00 3.01
4019 4712 3.756434 TCTTGCTTATAGTTTGTGTGGCC 59.244 43.478 0.00 0.00 0.00 5.36
4029 4722 1.178276 TTGTGTGGCCGACTTGTTTT 58.822 45.000 0.00 0.00 0.00 2.43
4051 4749 1.656441 GTTTGACTGCTGCTGTGGG 59.344 57.895 17.10 0.00 0.00 4.61
4109 4818 4.242475 CTGTGTCCTTACGCTTTGTCATA 58.758 43.478 0.00 0.00 37.03 2.15
4110 4819 3.991773 TGTGTCCTTACGCTTTGTCATAC 59.008 43.478 0.00 0.00 37.03 2.39
4111 4820 3.991773 GTGTCCTTACGCTTTGTCATACA 59.008 43.478 0.00 0.00 33.16 2.29
4112 4821 4.091509 GTGTCCTTACGCTTTGTCATACAG 59.908 45.833 0.00 0.00 33.16 2.74
4113 4822 4.243270 GTCCTTACGCTTTGTCATACAGT 58.757 43.478 0.00 0.00 0.00 3.55
4118 4830 8.252417 TCCTTACGCTTTGTCATACAGTAATAA 58.748 33.333 0.00 0.00 0.00 1.40
4119 4831 8.875803 CCTTACGCTTTGTCATACAGTAATAAA 58.124 33.333 0.00 0.00 0.00 1.40
4124 4836 9.210426 CGCTTTGTCATACAGTAATAAATGTTC 57.790 33.333 0.00 0.00 0.00 3.18
4137 4849 5.690464 ATAAATGTTCTGACTGCTCTCCT 57.310 39.130 0.00 0.00 0.00 3.69
4143 4855 1.342496 TCTGACTGCTCTCCTTGTGTG 59.658 52.381 0.00 0.00 0.00 3.82
4175 4887 9.475620 AGAAAGAAAAGGAAAGGAAGAGTAAAA 57.524 29.630 0.00 0.00 0.00 1.52
4210 4922 0.955428 GACAGACGCTTGAATGCCCA 60.955 55.000 0.00 0.00 0.00 5.36
4241 4953 3.223423 ACATGACTTGTCACTCGCTAG 57.777 47.619 5.53 0.00 30.89 3.42
4243 4955 2.991434 TGACTTGTCACTCGCTAGAC 57.009 50.000 0.00 0.00 35.37 2.59
4245 4957 1.813786 GACTTGTCACTCGCTAGACCT 59.186 52.381 0.00 0.00 33.89 3.85
4246 4958 1.813786 ACTTGTCACTCGCTAGACCTC 59.186 52.381 0.00 0.00 33.89 3.85
4247 4959 0.803117 TTGTCACTCGCTAGACCTCG 59.197 55.000 0.00 0.00 33.89 4.63
4248 4960 1.062845 GTCACTCGCTAGACCTCGC 59.937 63.158 0.00 0.00 0.00 5.03
4249 4961 2.113433 TCACTCGCTAGACCTCGCC 61.113 63.158 0.00 0.00 0.00 5.54
4250 4962 3.203412 ACTCGCTAGACCTCGCCG 61.203 66.667 0.00 0.00 0.00 6.46
4251 4963 2.895865 CTCGCTAGACCTCGCCGA 60.896 66.667 0.00 0.00 0.00 5.54
4252 4964 2.887889 CTCGCTAGACCTCGCCGAG 61.888 68.421 7.25 7.25 0.00 4.63
4253 4965 2.895865 CGCTAGACCTCGCCGAGA 60.896 66.667 17.19 0.00 0.00 4.04
4254 4966 2.887889 CGCTAGACCTCGCCGAGAG 61.888 68.421 17.19 8.36 46.44 3.20
4270 4985 1.774856 GAGAGGAGAGGAGGACTAGCT 59.225 57.143 0.00 0.00 0.00 3.32
4272 4987 0.472471 AGGAGAGGAGGACTAGCTCG 59.528 60.000 0.00 0.00 0.00 5.03
4274 4989 1.503818 GAGAGGAGGACTAGCTCGCG 61.504 65.000 0.00 0.00 0.00 5.87
4275 4990 3.189010 GAGGAGGACTAGCTCGCGC 62.189 68.421 0.00 0.00 0.00 6.86
4276 4991 3.518998 GGAGGACTAGCTCGCGCA 61.519 66.667 8.75 0.00 39.10 6.09
4277 4992 2.278271 GAGGACTAGCTCGCGCAC 60.278 66.667 8.75 0.00 39.10 5.34
4278 4993 3.052620 GAGGACTAGCTCGCGCACA 62.053 63.158 8.75 0.00 39.10 4.57
4279 4994 2.580867 GGACTAGCTCGCGCACAG 60.581 66.667 8.75 3.11 39.10 3.66
4280 4995 2.179517 GACTAGCTCGCGCACAGT 59.820 61.111 8.75 1.88 39.10 3.55
4282 4997 2.179267 CTAGCTCGCGCACAGTCA 59.821 61.111 8.75 0.00 39.10 3.41
4283 4998 1.226802 CTAGCTCGCGCACAGTCAT 60.227 57.895 8.75 0.00 39.10 3.06
4304 5019 3.213206 ACATTCACTCACTGGAGCAAA 57.787 42.857 0.00 0.00 45.42 3.68
4305 5020 3.144506 ACATTCACTCACTGGAGCAAAG 58.855 45.455 0.00 0.00 45.42 2.77
4306 5021 3.144506 CATTCACTCACTGGAGCAAAGT 58.855 45.455 0.00 0.00 45.42 2.66
4307 5022 4.202357 ACATTCACTCACTGGAGCAAAGTA 60.202 41.667 0.00 0.00 45.42 2.24
4308 5023 3.667497 TCACTCACTGGAGCAAAGTAG 57.333 47.619 0.00 0.00 45.42 2.57
4369 5084 2.378547 TCAGGTTGGTAGGCAGGATTTT 59.621 45.455 0.00 0.00 0.00 1.82
4412 5127 1.538047 GGCTCTTGGTTGAATGCAGA 58.462 50.000 0.00 0.00 0.00 4.26
4413 5128 1.200948 GGCTCTTGGTTGAATGCAGAC 59.799 52.381 0.00 0.00 0.00 3.51
4418 5133 0.821301 TGGTTGAATGCAGACGCCAA 60.821 50.000 0.00 0.00 37.32 4.52
4419 5134 0.109597 GGTTGAATGCAGACGCCAAG 60.110 55.000 0.00 0.00 37.32 3.61
4420 5135 0.593128 GTTGAATGCAGACGCCAAGT 59.407 50.000 0.00 0.00 37.32 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.087646 GGGACAGAGCAAAATGAGTCC 58.912 52.381 0.00 0.00 43.60 3.85
1 2 2.746362 CAGGGACAGAGCAAAATGAGTC 59.254 50.000 0.00 0.00 0.00 3.36
6 7 1.589716 GCGCAGGGACAGAGCAAAAT 61.590 55.000 0.30 0.00 40.75 1.82
42 43 4.022762 ACAGGGCCAAAACAAAACAAAAAC 60.023 37.500 6.18 0.00 0.00 2.43
47 48 2.569404 AGAACAGGGCCAAAACAAAACA 59.431 40.909 6.18 0.00 0.00 2.83
48 49 3.260475 AGAACAGGGCCAAAACAAAAC 57.740 42.857 6.18 0.00 0.00 2.43
49 50 3.386402 CCTAGAACAGGGCCAAAACAAAA 59.614 43.478 6.18 0.00 41.26 2.44
93 95 4.983671 AATCACTCGTAGCACATACAGA 57.016 40.909 0.00 0.00 33.65 3.41
96 98 4.912766 GCTCTAATCACTCGTAGCACATAC 59.087 45.833 0.00 0.00 0.00 2.39
106 108 0.179111 TTGGGCGCTCTAATCACTCG 60.179 55.000 9.62 0.00 0.00 4.18
117 119 2.672996 AGCGACATTTTGGGCGCT 60.673 55.556 10.51 10.51 45.69 5.92
118 120 2.504681 CAGCGACATTTTGGGCGC 60.505 61.111 5.07 5.07 42.63 6.53
119 121 0.519519 TAACAGCGACATTTTGGGCG 59.480 50.000 0.00 0.00 0.00 6.13
136 138 7.790027 ACATTTAATTATGGGTTGCAGCATAA 58.210 30.769 2.05 0.00 0.00 1.90
160 162 4.814147 TCAGACATCACTGTGATTCAGAC 58.186 43.478 20.13 10.07 46.27 3.51
220 223 4.262164 GGTTGAGACATTGAACAAGCCAAT 60.262 41.667 0.00 0.00 35.59 3.16
239 242 0.036010 AGTTGAGATGAGCCCGGTTG 60.036 55.000 0.00 0.00 0.00 3.77
240 243 0.250513 GAGTTGAGATGAGCCCGGTT 59.749 55.000 0.00 0.00 0.00 4.44
243 246 1.144936 GGGAGTTGAGATGAGCCCG 59.855 63.158 0.00 0.00 0.00 6.13
275 278 0.593128 ATTTTCTGCCTGCGTGACAC 59.407 50.000 0.00 0.00 0.00 3.67
284 287 2.592102 TTGCTCAGGATTTTCTGCCT 57.408 45.000 0.00 0.00 34.91 4.75
285 288 3.881937 ATTTGCTCAGGATTTTCTGCC 57.118 42.857 0.00 0.00 34.91 4.85
286 289 5.751990 CCAATATTTGCTCAGGATTTTCTGC 59.248 40.000 0.00 0.00 34.91 4.26
295 298 5.067805 GGGTTACTTCCAATATTTGCTCAGG 59.932 44.000 0.00 0.00 0.00 3.86
380 384 8.208903 GCCCCTACTCTACATAAAATCAAACTA 58.791 37.037 0.00 0.00 0.00 2.24
381 385 7.054751 GCCCCTACTCTACATAAAATCAAACT 58.945 38.462 0.00 0.00 0.00 2.66
382 386 6.826741 TGCCCCTACTCTACATAAAATCAAAC 59.173 38.462 0.00 0.00 0.00 2.93
383 387 6.964464 TGCCCCTACTCTACATAAAATCAAA 58.036 36.000 0.00 0.00 0.00 2.69
384 388 6.569127 TGCCCCTACTCTACATAAAATCAA 57.431 37.500 0.00 0.00 0.00 2.57
385 389 6.101150 ACATGCCCCTACTCTACATAAAATCA 59.899 38.462 0.00 0.00 0.00 2.57
386 390 6.428159 CACATGCCCCTACTCTACATAAAATC 59.572 42.308 0.00 0.00 0.00 2.17
387 391 6.299141 CACATGCCCCTACTCTACATAAAAT 58.701 40.000 0.00 0.00 0.00 1.82
388 392 5.397447 CCACATGCCCCTACTCTACATAAAA 60.397 44.000 0.00 0.00 0.00 1.52
389 393 4.102524 CCACATGCCCCTACTCTACATAAA 59.897 45.833 0.00 0.00 0.00 1.40
390 394 3.646162 CCACATGCCCCTACTCTACATAA 59.354 47.826 0.00 0.00 0.00 1.90
391 395 3.239449 CCACATGCCCCTACTCTACATA 58.761 50.000 0.00 0.00 0.00 2.29
392 396 2.050144 CCACATGCCCCTACTCTACAT 58.950 52.381 0.00 0.00 0.00 2.29
393 397 1.273609 ACCACATGCCCCTACTCTACA 60.274 52.381 0.00 0.00 0.00 2.74
394 398 1.139058 CACCACATGCCCCTACTCTAC 59.861 57.143 0.00 0.00 0.00 2.59
395 399 1.007842 TCACCACATGCCCCTACTCTA 59.992 52.381 0.00 0.00 0.00 2.43
396 400 0.252696 TCACCACATGCCCCTACTCT 60.253 55.000 0.00 0.00 0.00 3.24
397 401 0.107654 GTCACCACATGCCCCTACTC 60.108 60.000 0.00 0.00 0.00 2.59
398 402 0.547712 AGTCACCACATGCCCCTACT 60.548 55.000 0.00 0.00 0.00 2.57
399 403 0.107654 GAGTCACCACATGCCCCTAC 60.108 60.000 0.00 0.00 0.00 3.18
400 404 0.252696 AGAGTCACCACATGCCCCTA 60.253 55.000 0.00 0.00 0.00 3.53
401 405 1.136329 AAGAGTCACCACATGCCCCT 61.136 55.000 0.00 0.00 0.00 4.79
402 406 0.678048 GAAGAGTCACCACATGCCCC 60.678 60.000 0.00 0.00 0.00 5.80
403 407 0.326264 AGAAGAGTCACCACATGCCC 59.674 55.000 0.00 0.00 0.00 5.36
404 408 1.446907 CAGAAGAGTCACCACATGCC 58.553 55.000 0.00 0.00 0.00 4.40
405 409 1.002430 TCCAGAAGAGTCACCACATGC 59.998 52.381 0.00 0.00 0.00 4.06
406 410 3.407424 TTCCAGAAGAGTCACCACATG 57.593 47.619 0.00 0.00 0.00 3.21
407 411 4.437682 TTTTCCAGAAGAGTCACCACAT 57.562 40.909 0.00 0.00 0.00 3.21
408 412 3.924114 TTTTCCAGAAGAGTCACCACA 57.076 42.857 0.00 0.00 0.00 4.17
409 413 3.057946 GCATTTTCCAGAAGAGTCACCAC 60.058 47.826 0.00 0.00 0.00 4.16
410 414 3.149196 GCATTTTCCAGAAGAGTCACCA 58.851 45.455 0.00 0.00 0.00 4.17
411 415 3.149196 TGCATTTTCCAGAAGAGTCACC 58.851 45.455 0.00 0.00 0.00 4.02
412 416 4.836125 TTGCATTTTCCAGAAGAGTCAC 57.164 40.909 0.00 0.00 0.00 3.67
413 417 5.775686 CATTTGCATTTTCCAGAAGAGTCA 58.224 37.500 0.00 0.00 0.00 3.41
414 418 4.624452 GCATTTGCATTTTCCAGAAGAGTC 59.376 41.667 0.00 0.00 41.59 3.36
415 419 4.282703 AGCATTTGCATTTTCCAGAAGAGT 59.717 37.500 5.20 0.00 45.16 3.24
416 420 4.817517 AGCATTTGCATTTTCCAGAAGAG 58.182 39.130 5.20 0.00 45.16 2.85
417 421 4.877378 AGCATTTGCATTTTCCAGAAGA 57.123 36.364 5.20 0.00 45.16 2.87
418 422 8.706492 TTATAAGCATTTGCATTTTCCAGAAG 57.294 30.769 5.20 0.00 45.16 2.85
419 423 9.669887 AATTATAAGCATTTGCATTTTCCAGAA 57.330 25.926 5.20 0.00 45.16 3.02
420 424 9.669887 AAATTATAAGCATTTGCATTTTCCAGA 57.330 25.926 5.20 0.00 45.16 3.86
431 435 9.023967 GTAGTGGAGCAAAATTATAAGCATTTG 57.976 33.333 13.03 13.03 36.19 2.32
468 472 8.736244 TCTGCGCATGTTCATACTATATACTTA 58.264 33.333 12.24 0.00 0.00 2.24
472 476 7.602753 AGTTCTGCGCATGTTCATACTATATA 58.397 34.615 12.24 0.00 0.00 0.86
473 477 6.459066 AGTTCTGCGCATGTTCATACTATAT 58.541 36.000 12.24 0.00 0.00 0.86
483 487 2.287788 CCAAAAGAGTTCTGCGCATGTT 60.288 45.455 12.24 0.00 0.00 2.71
488 492 2.033424 AGTTTCCAAAAGAGTTCTGCGC 59.967 45.455 0.00 0.00 0.00 6.09
489 493 3.065371 ACAGTTTCCAAAAGAGTTCTGCG 59.935 43.478 0.00 0.00 0.00 5.18
491 495 7.168135 GCATTAACAGTTTCCAAAAGAGTTCTG 59.832 37.037 0.00 0.00 0.00 3.02
493 497 7.203218 AGCATTAACAGTTTCCAAAAGAGTTC 58.797 34.615 0.00 0.00 0.00 3.01
547 610 7.889589 TGCATATGAAACCTATGATACTTCG 57.110 36.000 6.97 0.00 0.00 3.79
558 621 3.382546 GGTCAAGCATGCATATGAAACCT 59.617 43.478 21.98 0.00 36.36 3.50
568 631 1.347378 TGTACTCTGGTCAAGCATGCA 59.653 47.619 21.98 0.00 0.00 3.96
586 649 6.608002 TGTTTAACAGTAGGTCCCATTTTTGT 59.392 34.615 0.00 0.00 0.00 2.83
641 704 7.037438 GTGCTCACAATCAACAATAATCCAAT 58.963 34.615 0.00 0.00 0.00 3.16
660 723 5.284861 TCTACAAGGTAAAACAGTGCTCA 57.715 39.130 0.00 0.00 0.00 4.26
661 724 6.128254 GGATTCTACAAGGTAAAACAGTGCTC 60.128 42.308 0.00 0.00 0.00 4.26
691 754 3.819337 CAGGATCCACATGATTGCCTAAG 59.181 47.826 15.82 0.00 32.41 2.18
739 802 6.238429 CGAGTGGACTAGTTGTAGTAATCTCC 60.238 46.154 0.00 0.00 39.78 3.71
901 964 2.086869 CATTTGAGGAGGCGACAATGT 58.913 47.619 0.00 0.00 0.00 2.71
1274 1339 2.943033 GTTACCCACGCAGCAAATATCT 59.057 45.455 0.00 0.00 0.00 1.98
1278 1343 0.596082 GTGTTACCCACGCAGCAAAT 59.404 50.000 0.00 0.00 35.77 2.32
1280 1345 3.739167 GTGTTACCCACGCAGCAA 58.261 55.556 0.00 0.00 35.77 3.91
1883 2077 6.773976 AGTTGAGGAACAATTTCTTCACAA 57.226 33.333 0.00 0.00 44.97 3.33
2594 2834 1.295423 GGTGGCTTCCTTCGCACTA 59.705 57.895 0.00 0.00 0.00 2.74
2615 2855 5.163581 CGAAAGCTCATTCAAATTCCCAGAT 60.164 40.000 0.00 0.00 0.00 2.90
2753 3006 8.856153 TTAGGTTCATGCTAGAACATAAAACA 57.144 30.769 19.20 4.84 45.83 2.83
2800 3055 5.724370 TCAATAGTTGTATGTTGGAGGAGGA 59.276 40.000 0.00 0.00 0.00 3.71
2806 3061 6.367374 TCCTGTCAATAGTTGTATGTTGGA 57.633 37.500 0.00 0.00 0.00 3.53
2809 3064 7.174946 CCACTTTCCTGTCAATAGTTGTATGTT 59.825 37.037 0.00 0.00 0.00 2.71
2810 3065 6.655003 CCACTTTCCTGTCAATAGTTGTATGT 59.345 38.462 0.00 0.00 0.00 2.29
2811 3066 6.655003 ACCACTTTCCTGTCAATAGTTGTATG 59.345 38.462 0.00 0.00 0.00 2.39
2812 3067 6.655003 CACCACTTTCCTGTCAATAGTTGTAT 59.345 38.462 0.00 0.00 0.00 2.29
2816 3071 5.048846 ACACCACTTTCCTGTCAATAGTT 57.951 39.130 0.00 0.00 0.00 2.24
2817 3072 4.706842 ACACCACTTTCCTGTCAATAGT 57.293 40.909 0.00 0.00 0.00 2.12
2818 3073 6.986817 CCTATACACCACTTTCCTGTCAATAG 59.013 42.308 0.00 0.00 0.00 1.73
2819 3074 6.631766 GCCTATACACCACTTTCCTGTCAATA 60.632 42.308 0.00 0.00 0.00 1.90
2829 3207 6.946009 ACACATTTAAGCCTATACACCACTTT 59.054 34.615 0.00 0.00 0.00 2.66
2844 3222 9.906660 TTTTTACCAGCAGATAACACATTTAAG 57.093 29.630 0.00 0.00 0.00 1.85
2877 3256 7.213678 AGTTGTATCTTGATAGGAGCTTAAGC 58.786 38.462 20.09 20.09 42.49 3.09
2995 3549 2.163211 GAGAGGCCTGCAAATTCACTTC 59.837 50.000 12.00 0.00 0.00 3.01
3145 3699 1.464997 GCGACGAATTTTGAGAGGCTT 59.535 47.619 0.00 0.00 0.00 4.35
3154 3708 1.804748 GAGTGAAGGGCGACGAATTTT 59.195 47.619 0.00 0.00 0.00 1.82
3158 3712 0.319555 CAAGAGTGAAGGGCGACGAA 60.320 55.000 0.00 0.00 0.00 3.85
3166 3720 3.737850 AGAAGCTCAACAAGAGTGAAGG 58.262 45.455 0.00 0.00 46.47 3.46
3218 3783 2.348472 AGTGGGATCTTGTTGAGGGAA 58.652 47.619 0.00 0.00 0.00 3.97
3287 3852 2.290260 ACCGAACAGAATGCTGATGGAA 60.290 45.455 8.02 0.00 45.17 3.53
3299 3864 3.928727 AGACGAAACATACCGAACAGA 57.071 42.857 0.00 0.00 0.00 3.41
3305 3870 4.036567 TGGTCATAGACGAAACATACCG 57.963 45.455 0.00 0.00 32.65 4.02
3337 3914 1.143305 GCAGTATATGTCAGCAGCCG 58.857 55.000 0.00 0.00 0.00 5.52
3344 3921 7.262048 TCGTTAGTGAAATGCAGTATATGTCA 58.738 34.615 0.00 0.00 32.63 3.58
3354 3932 5.066634 TGGTTTCTTTCGTTAGTGAAATGCA 59.933 36.000 0.00 0.00 37.24 3.96
3368 3946 5.343249 GTGATGGCATGTATGGTTTCTTTC 58.657 41.667 3.81 0.00 0.00 2.62
3381 3959 3.214123 CTGCGGGGTGATGGCATG 61.214 66.667 3.81 0.00 35.91 4.06
3394 3973 0.320247 CTCCTGCTAATAGCCCTGCG 60.320 60.000 10.06 0.00 41.51 5.18
3430 4009 1.067821 TGGGAGTTTTCGCGCAATTTT 59.932 42.857 8.75 0.00 39.23 1.82
3480 4069 2.515523 CCGCAATCCTGCCCTCTG 60.516 66.667 0.00 0.00 46.56 3.35
3485 4074 3.195698 GACGACCGCAATCCTGCC 61.196 66.667 0.00 0.00 46.56 4.85
3517 4106 0.687354 GTCTGGTTTGAGGGAGCAGA 59.313 55.000 2.24 2.24 46.09 4.26
3531 4120 3.553508 CCTGCACAAATTTTCCAGTCTGG 60.554 47.826 13.21 13.21 39.43 3.86
3572 4164 1.528586 CGTTGTCTCTTGTCTTGCCAG 59.471 52.381 0.00 0.00 0.00 4.85
3579 4171 4.982916 ACTAACATGACGTTGTCTCTTGTC 59.017 41.667 0.00 0.00 38.63 3.18
3580 4172 4.945246 ACTAACATGACGTTGTCTCTTGT 58.055 39.130 0.00 0.00 38.63 3.16
3581 4173 5.907197 AACTAACATGACGTTGTCTCTTG 57.093 39.130 0.00 0.00 38.63 3.02
3583 4175 5.162075 GCTAACTAACATGACGTTGTCTCT 58.838 41.667 0.00 0.00 38.63 3.10
3592 4185 2.678336 GCACCAGGCTAACTAACATGAC 59.322 50.000 0.00 0.00 40.25 3.06
3629 4223 1.388065 ATCCAGGACGGCTTCGAGAG 61.388 60.000 0.00 0.00 37.63 3.20
3647 4241 2.088423 AGAGCGACGACAAGAGAAGAT 58.912 47.619 0.00 0.00 0.00 2.40
3648 4242 1.524848 AGAGCGACGACAAGAGAAGA 58.475 50.000 0.00 0.00 0.00 2.87
3651 4245 0.952280 ACAAGAGCGACGACAAGAGA 59.048 50.000 0.00 0.00 0.00 3.10
3652 4246 1.056103 CACAAGAGCGACGACAAGAG 58.944 55.000 0.00 0.00 0.00 2.85
3653 4247 0.318699 CCACAAGAGCGACGACAAGA 60.319 55.000 0.00 0.00 0.00 3.02
3654 4248 0.597637 ACCACAAGAGCGACGACAAG 60.598 55.000 0.00 0.00 0.00 3.16
3655 4249 0.179094 AACCACAAGAGCGACGACAA 60.179 50.000 0.00 0.00 0.00 3.18
3656 4250 0.874175 CAACCACAAGAGCGACGACA 60.874 55.000 0.00 0.00 0.00 4.35
3657 4251 1.557443 CCAACCACAAGAGCGACGAC 61.557 60.000 0.00 0.00 0.00 4.34
3658 4252 1.300620 CCAACCACAAGAGCGACGA 60.301 57.895 0.00 0.00 0.00 4.20
3659 4253 1.157870 AACCAACCACAAGAGCGACG 61.158 55.000 0.00 0.00 0.00 5.12
3660 4254 0.307760 CAACCAACCACAAGAGCGAC 59.692 55.000 0.00 0.00 0.00 5.19
3661 4255 0.817634 CCAACCAACCACAAGAGCGA 60.818 55.000 0.00 0.00 0.00 4.93
3662 4256 1.101049 ACCAACCAACCACAAGAGCG 61.101 55.000 0.00 0.00 0.00 5.03
3663 4257 0.385390 CACCAACCAACCACAAGAGC 59.615 55.000 0.00 0.00 0.00 4.09
3664 4258 1.032014 CCACCAACCAACCACAAGAG 58.968 55.000 0.00 0.00 0.00 2.85
3665 4259 0.626382 TCCACCAACCAACCACAAGA 59.374 50.000 0.00 0.00 0.00 3.02
3666 4260 1.340889 CATCCACCAACCAACCACAAG 59.659 52.381 0.00 0.00 0.00 3.16
3667 4261 1.407936 CATCCACCAACCAACCACAA 58.592 50.000 0.00 0.00 0.00 3.33
3668 4262 0.468958 CCATCCACCAACCAACCACA 60.469 55.000 0.00 0.00 0.00 4.17
3669 4263 0.469144 ACCATCCACCAACCAACCAC 60.469 55.000 0.00 0.00 0.00 4.16
3670 4264 0.468958 CACCATCCACCAACCAACCA 60.469 55.000 0.00 0.00 0.00 3.67
3671 4265 1.184970 CCACCATCCACCAACCAACC 61.185 60.000 0.00 0.00 0.00 3.77
3672 4266 1.815817 GCCACCATCCACCAACCAAC 61.816 60.000 0.00 0.00 0.00 3.77
3673 4267 1.532794 GCCACCATCCACCAACCAA 60.533 57.895 0.00 0.00 0.00 3.67
3674 4268 2.091640 ATGCCACCATCCACCAACCA 62.092 55.000 0.00 0.00 0.00 3.67
3675 4269 0.033601 TATGCCACCATCCACCAACC 60.034 55.000 0.00 0.00 32.85 3.77
3678 4272 3.055458 CGTATATATGCCACCATCCACCA 60.055 47.826 0.00 0.00 32.85 4.17
3684 4278 4.160439 CAGAGGACGTATATATGCCACCAT 59.840 45.833 14.17 0.00 35.44 3.55
3713 4307 4.486125 TTCAGCAGCATCTAACCATGTA 57.514 40.909 0.00 0.00 0.00 2.29
3726 4320 1.664321 CTGCCTGGGATTTCAGCAGC 61.664 60.000 0.00 0.00 34.67 5.25
3747 4341 5.950544 TTACCCAATCATCTATATCCCCG 57.049 43.478 0.00 0.00 0.00 5.73
3774 4371 8.562949 ACCCAAGAATTACTACCTGTATATGT 57.437 34.615 0.00 0.00 0.00 2.29
3775 4372 9.273016 CAACCCAAGAATTACTACCTGTATATG 57.727 37.037 0.00 0.00 0.00 1.78
3776 4373 8.437575 CCAACCCAAGAATTACTACCTGTATAT 58.562 37.037 0.00 0.00 0.00 0.86
3777 4374 7.624478 TCCAACCCAAGAATTACTACCTGTATA 59.376 37.037 0.00 0.00 0.00 1.47
3872 4555 5.470098 GCACAAGAGATAAACCAGAAAGACA 59.530 40.000 0.00 0.00 0.00 3.41
3886 4574 3.118884 GCAATGGGAAATGCACAAGAGAT 60.119 43.478 0.00 0.00 42.12 2.75
3892 4580 1.590665 CGGCAATGGGAAATGCACA 59.409 52.632 0.00 0.00 44.32 4.57
3893 4581 1.153588 CCGGCAATGGGAAATGCAC 60.154 57.895 0.00 0.00 44.32 4.57
3909 4597 3.554692 GGTGAATGCGCTCGACCG 61.555 66.667 9.73 0.00 0.00 4.79
3914 4602 0.390340 TGAGTGAGGTGAATGCGCTC 60.390 55.000 9.73 0.00 39.09 5.03
3964 4652 6.052360 ACAGAAGAGAGAAACCAAAAGAGAC 58.948 40.000 0.00 0.00 0.00 3.36
3984 4672 9.515226 AACTATAAGCAAGAACCAAAATACAGA 57.485 29.630 0.00 0.00 0.00 3.41
3994 4682 5.699839 CCACACAAACTATAAGCAAGAACC 58.300 41.667 0.00 0.00 0.00 3.62
3995 4683 5.154222 GCCACACAAACTATAAGCAAGAAC 58.846 41.667 0.00 0.00 0.00 3.01
3996 4684 4.217550 GGCCACACAAACTATAAGCAAGAA 59.782 41.667 0.00 0.00 0.00 2.52
3997 4685 3.756434 GGCCACACAAACTATAAGCAAGA 59.244 43.478 0.00 0.00 0.00 3.02
3999 4687 2.486203 CGGCCACACAAACTATAAGCAA 59.514 45.455 2.24 0.00 0.00 3.91
4019 4712 4.342772 CAGTCAAACCTCAAAACAAGTCG 58.657 43.478 0.00 0.00 0.00 4.18
4029 4722 0.181114 ACAGCAGCAGTCAAACCTCA 59.819 50.000 0.00 0.00 0.00 3.86
4109 4818 7.390027 AGAGCAGTCAGAACATTTATTACTGT 58.610 34.615 0.00 0.00 36.20 3.55
4110 4819 7.010923 GGAGAGCAGTCAGAACATTTATTACTG 59.989 40.741 0.00 0.00 36.74 2.74
4111 4820 7.044798 GGAGAGCAGTCAGAACATTTATTACT 58.955 38.462 0.00 0.00 0.00 2.24
4112 4821 7.044798 AGGAGAGCAGTCAGAACATTTATTAC 58.955 38.462 0.00 0.00 0.00 1.89
4113 4822 7.187824 AGGAGAGCAGTCAGAACATTTATTA 57.812 36.000 0.00 0.00 0.00 0.98
4118 4830 3.072184 ACAAGGAGAGCAGTCAGAACATT 59.928 43.478 0.00 0.00 0.00 2.71
4119 4831 2.636893 ACAAGGAGAGCAGTCAGAACAT 59.363 45.455 0.00 0.00 0.00 2.71
4121 4833 2.224161 ACACAAGGAGAGCAGTCAGAAC 60.224 50.000 0.00 0.00 0.00 3.01
4124 4836 1.342496 TCACACAAGGAGAGCAGTCAG 59.658 52.381 0.00 0.00 0.00 3.51
4127 4839 3.281727 TTTTCACACAAGGAGAGCAGT 57.718 42.857 0.00 0.00 0.00 4.40
4175 4887 0.846427 TGTCTCCTCTGCCCCCATTT 60.846 55.000 0.00 0.00 0.00 2.32
4176 4888 1.229951 TGTCTCCTCTGCCCCCATT 60.230 57.895 0.00 0.00 0.00 3.16
4178 4890 2.284921 CTGTCTCCTCTGCCCCCA 60.285 66.667 0.00 0.00 0.00 4.96
4179 4891 2.039624 TCTGTCTCCTCTGCCCCC 59.960 66.667 0.00 0.00 0.00 5.40
4180 4892 2.716017 CGTCTGTCTCCTCTGCCCC 61.716 68.421 0.00 0.00 0.00 5.80
4181 4893 2.888863 CGTCTGTCTCCTCTGCCC 59.111 66.667 0.00 0.00 0.00 5.36
4185 4897 1.621992 TTCAAGCGTCTGTCTCCTCT 58.378 50.000 0.00 0.00 0.00 3.69
4210 4922 2.300152 ACAAGTCATGTCTCGTGTCCAT 59.700 45.455 0.00 0.00 37.96 3.41
4237 4949 3.027292 CTCTCGGCGAGGTCTAGC 58.973 66.667 33.93 0.00 36.06 3.42
4245 4957 2.190843 CTCCTCTCCTCTCGGCGA 59.809 66.667 10.14 10.14 0.00 5.54
4246 4958 2.904866 CCTCCTCTCCTCTCGGCG 60.905 72.222 0.00 0.00 0.00 6.46
4247 4959 1.826487 GTCCTCCTCTCCTCTCGGC 60.826 68.421 0.00 0.00 0.00 5.54
4248 4960 1.071699 CTAGTCCTCCTCTCCTCTCGG 59.928 61.905 0.00 0.00 0.00 4.63
4249 4961 1.542547 GCTAGTCCTCCTCTCCTCTCG 60.543 61.905 0.00 0.00 0.00 4.04
4250 4962 1.774856 AGCTAGTCCTCCTCTCCTCTC 59.225 57.143 0.00 0.00 0.00 3.20
4251 4963 1.774856 GAGCTAGTCCTCCTCTCCTCT 59.225 57.143 0.00 0.00 0.00 3.69
4252 4964 1.542547 CGAGCTAGTCCTCCTCTCCTC 60.543 61.905 0.00 0.00 0.00 3.71
4253 4965 0.472471 CGAGCTAGTCCTCCTCTCCT 59.528 60.000 0.00 0.00 0.00 3.69
4254 4966 1.170290 GCGAGCTAGTCCTCCTCTCC 61.170 65.000 0.00 0.00 0.00 3.71
4270 4985 1.277326 GAATGTATGACTGTGCGCGA 58.723 50.000 12.10 0.00 0.00 5.87
4272 4987 2.002586 AGTGAATGTATGACTGTGCGC 58.997 47.619 0.00 0.00 0.00 6.09
4274 4989 4.092529 CAGTGAGTGAATGTATGACTGTGC 59.907 45.833 0.00 0.00 0.00 4.57
4275 4990 4.628766 CCAGTGAGTGAATGTATGACTGTG 59.371 45.833 0.00 0.00 0.00 3.66
4276 4991 4.528206 TCCAGTGAGTGAATGTATGACTGT 59.472 41.667 0.00 0.00 0.00 3.55
4277 4992 5.077134 TCCAGTGAGTGAATGTATGACTG 57.923 43.478 0.00 0.00 0.00 3.51
4278 4993 4.382470 GCTCCAGTGAGTGAATGTATGACT 60.382 45.833 0.00 0.00 40.95 3.41
4279 4994 3.868077 GCTCCAGTGAGTGAATGTATGAC 59.132 47.826 0.00 0.00 40.95 3.06
4280 4995 3.515104 TGCTCCAGTGAGTGAATGTATGA 59.485 43.478 0.00 0.00 40.95 2.15
4282 4997 4.558226 TTGCTCCAGTGAGTGAATGTAT 57.442 40.909 0.00 0.00 40.95 2.29
4283 4998 4.202357 ACTTTGCTCCAGTGAGTGAATGTA 60.202 41.667 0.00 0.00 40.95 2.29
4304 5019 6.299805 TGAGCCAACATTCAATACTCTACT 57.700 37.500 0.00 0.00 0.00 2.57
4305 5020 5.007136 GCTGAGCCAACATTCAATACTCTAC 59.993 44.000 0.00 0.00 0.00 2.59
4306 5021 5.118990 GCTGAGCCAACATTCAATACTCTA 58.881 41.667 0.00 0.00 0.00 2.43
4307 5022 3.944015 GCTGAGCCAACATTCAATACTCT 59.056 43.478 0.00 0.00 0.00 3.24
4308 5023 3.691118 TGCTGAGCCAACATTCAATACTC 59.309 43.478 0.23 0.00 0.00 2.59
4369 5084 1.066929 ACTGTCACGTGCAGATATGCA 60.067 47.619 32.33 11.76 43.22 3.96
4420 5135 8.413309 TTGAGCAAAGGTTACTAGAGTAGTAA 57.587 34.615 0.00 2.98 46.03 2.24


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

AutoCloner maintained by Alex Coulton.