Multiple sequence alignment - TraesCS7B01G000900

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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 TraesCS7B01G000900 chr7B 100.000 4049 0 0 1 4049 256266 260314 0.000000e+00 7478.0
1 TraesCS7B01G000900 chr5D 89.277 1977 72 41 552 2481 562351850 562349967 0.000000e+00 2348.0
2 TraesCS7B01G000900 chr5D 86.808 1084 49 46 2415 3464 562350168 562349145 0.000000e+00 1123.0
3 TraesCS7B01G000900 chr5D 89.455 569 30 8 3498 4049 562348332 562347777 0.000000e+00 691.0
4 TraesCS7B01G000900 chr5B 88.614 1695 96 32 860 2481 712864328 712862658 0.000000e+00 1971.0
5 TraesCS7B01G000900 chr5B 93.365 1040 28 19 2433 3468 712862856 712861854 0.000000e+00 1500.0
6 TraesCS7B01G000900 chr5B 85.915 852 39 25 1 781 712865287 712864446 0.000000e+00 833.0
7 TraesCS7B01G000900 chr5B 89.162 489 22 5 3578 4049 712860965 712860491 7.540000e-162 580.0
8 TraesCS7B01G000900 chr5B 86.667 525 24 20 2959 3466 118165652 118165157 1.280000e-149 540.0
9 TraesCS7B01G000900 chr5B 97.590 83 2 0 3498 3580 712861111 712861029 4.220000e-30 143.0
10 TraesCS7B01G000900 chr6B 85.311 531 22 21 2960 3464 592468441 592467941 7.820000e-137 497.0
11 TraesCS7B01G000900 chr6B 85.333 75 11 0 166 240 702070833 702070759 1.210000e-10 78.7
12 TraesCS7B01G000900 chr3B 85.249 522 21 24 2960 3464 194479981 194480463 1.690000e-133 486.0


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 TraesCS7B01G000900 chr7B 256266 260314 4048 False 7478.000000 7478 100.000000 1 4049 1 chr7B.!!$F1 4048
1 TraesCS7B01G000900 chr5D 562347777 562351850 4073 True 1387.333333 2348 88.513333 552 4049 3 chr5D.!!$R1 3497
2 TraesCS7B01G000900 chr5B 712860491 712865287 4796 True 1005.400000 1971 90.929200 1 4049 5 chr5B.!!$R2 4048
3 TraesCS7B01G000900 chr6B 592467941 592468441 500 True 497.000000 497 85.311000 2960 3464 1 chr6B.!!$R1 504

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
64 65 1.743772 CGACTGTTGGTGGATCATCCC 60.744 57.143 0.0 0.0 35.03 3.85 F
856 964 2.277501 GCATCATGCGTGCGTTCC 60.278 61.111 0.0 0.0 31.71 3.62 F
1257 1383 0.033601 AAGTCCAACCAAGCACCACA 60.034 50.000 0.0 0.0 0.00 4.17 F
2350 2518 0.037160 TGAGCAGGAGCAGCAAATGA 59.963 50.000 0.0 0.0 45.49 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1362 0.257328 TGGTGCTTGGTTGGACTTGA 59.743 50.0 0.0 0.0 0.00 3.02 R
2331 2499 0.037160 TCATTTGCTGCTCCTGCTCA 59.963 50.0 0.0 0.0 40.48 4.26 R
2377 2545 0.107312 ATTCGCTGCTCCTGCTTCAT 60.107 50.0 0.0 0.0 40.48 2.57 R
3416 3673 0.038166 ATGGCGTCTGGGTGTTTGAT 59.962 50.0 0.0 0.0 0.00 2.57 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
24 25 5.104900 AGTTGAAATGTTCCCTCGCTACTAT 60.105 40.000 0.00 0.00 0.00 2.12
64 65 1.743772 CGACTGTTGGTGGATCATCCC 60.744 57.143 0.00 0.00 35.03 3.85
69 70 2.517919 GGTGGATCATCCCCAGCC 59.482 66.667 0.00 0.00 44.14 4.85
105 106 3.876914 TGCTCACGACTTGTCATCTTTTT 59.123 39.130 0.00 0.00 0.00 1.94
143 144 3.421844 GGGCTAACAGAAACCATGAACT 58.578 45.455 0.00 0.00 0.00 3.01
144 145 3.826729 GGGCTAACAGAAACCATGAACTT 59.173 43.478 0.00 0.00 0.00 2.66
154 175 8.137437 ACAGAAACCATGAACTTGTCAAATTAG 58.863 33.333 0.00 0.00 40.50 1.73
165 186 7.674471 ACTTGTCAAATTAGAGCCTCTTTAC 57.326 36.000 0.00 0.00 0.00 2.01
222 243 3.593442 AGGAAGATGTCTCCGAGAGAT 57.407 47.619 7.75 7.75 40.98 2.75
229 250 3.699779 TGTCTCCGAGAGATTTCATCG 57.300 47.619 0.00 0.00 40.98 3.84
234 255 6.183360 TGTCTCCGAGAGATTTCATCGTAATT 60.183 38.462 0.00 0.00 40.98 1.40
236 257 6.039382 TCTCCGAGAGATTTCATCGTAATTCA 59.961 38.462 0.00 0.00 33.35 2.57
251 272 7.389603 TCGTAATTCATAGTTATGCGAGTTG 57.610 36.000 0.00 0.00 33.76 3.16
319 340 7.440856 AGACGTCACCAAAATATGCAAAATTTT 59.559 29.630 19.50 14.23 37.08 1.82
320 341 7.351223 ACGTCACCAAAATATGCAAAATTTTG 58.649 30.769 27.57 27.57 46.60 2.44
342 363 7.606858 TTGAAGCAGATCTCAGATTACTTTG 57.393 36.000 0.00 0.00 0.00 2.77
346 367 4.384647 GCAGATCTCAGATTACTTTGGGGT 60.385 45.833 0.00 0.00 0.00 4.95
348 369 5.587844 CAGATCTCAGATTACTTTGGGGTTG 59.412 44.000 0.00 0.00 0.00 3.77
349 370 4.993705 TCTCAGATTACTTTGGGGTTGT 57.006 40.909 0.00 0.00 0.00 3.32
350 371 4.651778 TCTCAGATTACTTTGGGGTTGTG 58.348 43.478 0.00 0.00 0.00 3.33
351 372 4.349636 TCTCAGATTACTTTGGGGTTGTGA 59.650 41.667 0.00 0.00 0.00 3.58
352 373 4.651778 TCAGATTACTTTGGGGTTGTGAG 58.348 43.478 0.00 0.00 0.00 3.51
353 374 4.104102 TCAGATTACTTTGGGGTTGTGAGT 59.896 41.667 0.00 0.00 0.00 3.41
356 377 5.535030 AGATTACTTTGGGGTTGTGAGTTTC 59.465 40.000 0.00 0.00 0.00 2.78
369 390 5.808366 TGTGAGTTTCTCCAGTATTCACT 57.192 39.130 0.00 0.00 35.66 3.41
373 394 8.375506 TGTGAGTTTCTCCAGTATTCACTAAAT 58.624 33.333 0.00 0.00 35.66 1.40
419 459 7.231317 ACTTGTAATCTCTGGCTCAAAATTTCA 59.769 33.333 0.00 0.00 0.00 2.69
457 497 7.552050 TTGAGACCCACCAAAATATGAAATT 57.448 32.000 0.00 0.00 0.00 1.82
458 498 7.169158 TGAGACCCACCAAAATATGAAATTC 57.831 36.000 0.00 0.00 0.00 2.17
474 514 4.586841 TGAAATTCCAACCCTGGTTTGTAG 59.413 41.667 3.18 0.00 43.97 2.74
719 782 3.053831 ACAAACCACAATCTCTACCGG 57.946 47.619 0.00 0.00 0.00 5.28
752 823 8.396272 AGATCCTGGTAATTAATTACATGCAC 57.604 34.615 30.11 17.74 43.33 4.57
765 836 3.066291 ACATGCACTCGTTAATTCCCA 57.934 42.857 0.00 0.00 0.00 4.37
801 893 6.152379 TCCTGTAATCGATCGATTCATTCAG 58.848 40.000 38.69 33.81 43.04 3.02
802 894 5.923114 CCTGTAATCGATCGATTCATTCAGT 59.077 40.000 38.69 20.36 43.04 3.41
804 912 5.625311 TGTAATCGATCGATTCATTCAGTCG 59.375 40.000 38.69 1.09 43.04 4.18
806 914 3.618698 TCGATCGATTCATTCAGTCGTC 58.381 45.455 15.15 0.00 36.77 4.20
817 925 7.504924 TTCATTCAGTCGTCCTTGTTAATTT 57.495 32.000 0.00 0.00 0.00 1.82
847 955 8.769891 TCATTTCATTTTGATTATGCATCATGC 58.230 29.630 0.19 1.35 41.82 4.06
856 964 2.277501 GCATCATGCGTGCGTTCC 60.278 61.111 0.00 0.00 31.71 3.62
857 965 2.404789 CATCATGCGTGCGTTCCC 59.595 61.111 0.00 0.00 0.00 3.97
858 966 2.824041 ATCATGCGTGCGTTCCCC 60.824 61.111 0.00 0.00 0.00 4.81
884 994 6.707608 CGTAGGATTGGAGATCATTTCATTCA 59.292 38.462 0.00 0.00 0.00 2.57
893 1003 7.447545 TGGAGATCATTTCATTCATTCCTGATC 59.552 37.037 0.00 0.00 38.39 2.92
1241 1367 3.953775 CCACCGCCCACCTCAAGT 61.954 66.667 0.00 0.00 0.00 3.16
1251 1377 0.954452 CACCTCAAGTCCAACCAAGC 59.046 55.000 0.00 0.00 0.00 4.01
1254 1380 0.954452 CTCAAGTCCAACCAAGCACC 59.046 55.000 0.00 0.00 0.00 5.01
1255 1381 0.257328 TCAAGTCCAACCAAGCACCA 59.743 50.000 0.00 0.00 0.00 4.17
1257 1383 0.033601 AAGTCCAACCAAGCACCACA 60.034 50.000 0.00 0.00 0.00 4.17
1258 1384 0.466189 AGTCCAACCAAGCACCACAG 60.466 55.000 0.00 0.00 0.00 3.66
1259 1385 1.152777 TCCAACCAAGCACCACAGG 60.153 57.895 0.00 0.00 0.00 4.00
1261 1387 2.906897 AACCAAGCACCACAGGCG 60.907 61.111 0.00 0.00 36.08 5.52
1265 1391 4.666253 AAGCACCACAGGCGCCAT 62.666 61.111 31.54 14.24 29.94 4.40
1271 1409 3.434319 CACAGGCGCCATCACCAC 61.434 66.667 31.54 0.00 0.00 4.16
1291 1429 2.687566 ATCACCACCGACCCTCCC 60.688 66.667 0.00 0.00 0.00 4.30
1355 1499 3.879885 CCCACCCACCGTGTCCAA 61.880 66.667 0.00 0.00 41.26 3.53
1433 1586 2.320367 CGACTCTGACCACGAAGAAAG 58.680 52.381 0.00 0.00 0.00 2.62
1617 1770 2.116983 CTCTCCACCACCACCACCAG 62.117 65.000 0.00 0.00 0.00 4.00
1620 1776 2.595463 CACCACCACCACCAGCAG 60.595 66.667 0.00 0.00 0.00 4.24
1638 1794 2.037136 GCAGCACGTCATGGAGCTT 61.037 57.895 0.00 0.00 34.61 3.74
1710 1869 3.443045 GACGGGCCCTACGACGAA 61.443 66.667 22.43 0.00 34.93 3.85
1800 1959 2.814336 TGATATGGACGACGATCTCCAG 59.186 50.000 10.90 0.00 39.99 3.86
1802 1961 1.037579 ATGGACGACGATCTCCAGCA 61.038 55.000 10.90 0.00 39.99 4.41
1833 1992 3.458163 GAGCCGTCGTCCATCCCA 61.458 66.667 0.00 0.00 0.00 4.37
1836 1995 3.849951 CCGTCGTCCATCCCAGGG 61.850 72.222 0.00 0.00 0.00 4.45
1837 1996 3.849951 CGTCGTCCATCCCAGGGG 61.850 72.222 5.33 0.92 0.00 4.79
1838 1997 4.176752 GTCGTCCATCCCAGGGGC 62.177 72.222 5.33 0.00 34.68 5.80
1857 2025 2.821366 CCGGCAGCGCAGAAGAAT 60.821 61.111 11.47 0.00 0.00 2.40
2045 2213 3.899981 CTGCGGGTGCCACTGCTTA 62.900 63.158 12.46 0.00 43.17 3.09
2046 2214 2.438434 GCGGGTGCCACTGCTTAT 60.438 61.111 5.54 0.00 39.64 1.73
2153 2321 1.684983 AGCAGAAGCAGCAACAATGTT 59.315 42.857 0.00 0.00 45.49 2.71
2244 2412 1.512310 CAGCGACTCTTCCGACGAC 60.512 63.158 0.00 0.00 0.00 4.34
2314 2482 3.738246 CACAGCAGCAGCAGCAGG 61.738 66.667 12.92 6.25 45.49 4.85
2315 2483 3.949980 ACAGCAGCAGCAGCAGGA 61.950 61.111 12.92 0.00 45.49 3.86
2316 2484 3.128188 CAGCAGCAGCAGCAGGAG 61.128 66.667 12.92 0.00 45.49 3.69
2317 2485 4.411981 AGCAGCAGCAGCAGGAGG 62.412 66.667 12.92 0.00 45.49 4.30
2318 2486 4.405671 GCAGCAGCAGCAGGAGGA 62.406 66.667 4.63 0.00 45.49 3.71
2319 2487 2.125065 CAGCAGCAGCAGGAGGAG 60.125 66.667 3.17 0.00 45.49 3.69
2320 2488 3.400928 AGCAGCAGCAGGAGGAGG 61.401 66.667 3.17 0.00 45.49 4.30
2321 2489 3.397439 GCAGCAGCAGGAGGAGGA 61.397 66.667 0.00 0.00 41.58 3.71
2322 2490 2.901813 CAGCAGCAGGAGGAGGAG 59.098 66.667 0.00 0.00 0.00 3.69
2323 2491 2.365370 AGCAGCAGGAGGAGGAGG 60.365 66.667 0.00 0.00 0.00 4.30
2324 2492 2.364842 GCAGCAGGAGGAGGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
2325 2493 2.433994 GCAGCAGGAGGAGGAGGAG 61.434 68.421 0.00 0.00 0.00 3.69
2326 2494 1.761667 CAGCAGGAGGAGGAGGAGG 60.762 68.421 0.00 0.00 0.00 4.30
2327 2495 2.252898 AGCAGGAGGAGGAGGAGGT 61.253 63.158 0.00 0.00 0.00 3.85
2328 2496 2.063378 GCAGGAGGAGGAGGAGGTG 61.063 68.421 0.00 0.00 0.00 4.00
2329 2497 1.382420 CAGGAGGAGGAGGAGGTGG 60.382 68.421 0.00 0.00 0.00 4.61
2330 2498 2.766229 GGAGGAGGAGGAGGTGGC 60.766 72.222 0.00 0.00 0.00 5.01
2331 2499 2.366570 GAGGAGGAGGAGGTGGCT 59.633 66.667 0.00 0.00 0.00 4.75
2332 2500 2.040278 AGGAGGAGGAGGTGGCTG 59.960 66.667 0.00 0.00 0.00 4.85
2333 2501 2.039624 GGAGGAGGAGGTGGCTGA 59.960 66.667 0.00 0.00 0.00 4.26
2334 2502 2.063378 GGAGGAGGAGGTGGCTGAG 61.063 68.421 0.00 0.00 0.00 3.35
2335 2503 2.686835 AGGAGGAGGTGGCTGAGC 60.687 66.667 0.00 0.00 0.00 4.26
2336 2504 3.005539 GGAGGAGGTGGCTGAGCA 61.006 66.667 6.82 0.00 0.00 4.26
2337 2505 2.583520 GAGGAGGTGGCTGAGCAG 59.416 66.667 6.82 0.00 0.00 4.24
2338 2506 3.007920 AGGAGGTGGCTGAGCAGG 61.008 66.667 6.82 0.00 0.00 4.85
2339 2507 3.005539 GGAGGTGGCTGAGCAGGA 61.006 66.667 6.82 0.00 0.00 3.86
2340 2508 2.583520 GAGGTGGCTGAGCAGGAG 59.416 66.667 6.82 0.00 0.00 3.69
2341 2509 3.678951 GAGGTGGCTGAGCAGGAGC 62.679 68.421 6.82 0.00 42.56 4.70
2342 2510 4.025858 GGTGGCTGAGCAGGAGCA 62.026 66.667 6.82 0.00 45.49 4.26
2343 2511 2.436292 GTGGCTGAGCAGGAGCAG 60.436 66.667 6.82 0.00 45.49 4.24
2347 2515 4.391869 CTGAGCAGGAGCAGCAAA 57.608 55.556 0.00 0.00 45.49 3.68
2348 2516 2.869636 CTGAGCAGGAGCAGCAAAT 58.130 52.632 0.00 0.00 45.49 2.32
2349 2517 0.452184 CTGAGCAGGAGCAGCAAATG 59.548 55.000 0.00 0.00 45.49 2.32
2350 2518 0.037160 TGAGCAGGAGCAGCAAATGA 59.963 50.000 0.00 0.00 45.49 2.57
2351 2519 0.450983 GAGCAGGAGCAGCAAATGAC 59.549 55.000 0.00 0.00 45.49 3.06
2352 2520 1.136147 GCAGGAGCAGCAAATGACG 59.864 57.895 0.00 0.00 41.58 4.35
2353 2521 1.300971 GCAGGAGCAGCAAATGACGA 61.301 55.000 0.00 0.00 41.58 4.20
2354 2522 1.376543 CAGGAGCAGCAAATGACGAT 58.623 50.000 0.00 0.00 0.00 3.73
2355 2523 1.063616 CAGGAGCAGCAAATGACGATG 59.936 52.381 0.00 0.00 0.00 3.84
2356 2524 0.379669 GGAGCAGCAAATGACGATGG 59.620 55.000 0.00 0.00 0.00 3.51
2357 2525 1.372582 GAGCAGCAAATGACGATGGA 58.627 50.000 0.00 0.00 0.00 3.41
2358 2526 1.329906 GAGCAGCAAATGACGATGGAG 59.670 52.381 0.00 0.00 0.00 3.86
2359 2527 0.248377 GCAGCAAATGACGATGGAGC 60.248 55.000 0.00 0.00 0.00 4.70
2360 2528 1.089112 CAGCAAATGACGATGGAGCA 58.911 50.000 0.00 0.00 0.00 4.26
2361 2529 1.063616 CAGCAAATGACGATGGAGCAG 59.936 52.381 0.00 0.00 0.00 4.24
2362 2530 0.379669 GCAAATGACGATGGAGCAGG 59.620 55.000 0.00 0.00 0.00 4.85
2363 2531 2.013563 GCAAATGACGATGGAGCAGGA 61.014 52.381 0.00 0.00 0.00 3.86
2364 2532 1.938577 CAAATGACGATGGAGCAGGAG 59.061 52.381 0.00 0.00 0.00 3.69
2365 2533 0.179062 AATGACGATGGAGCAGGAGC 60.179 55.000 0.00 0.00 42.56 4.70
2366 2534 1.332889 ATGACGATGGAGCAGGAGCA 61.333 55.000 0.00 0.00 45.49 4.26
2367 2535 1.227205 GACGATGGAGCAGGAGCAG 60.227 63.158 0.00 0.00 45.49 4.24
2368 2536 2.108566 CGATGGAGCAGGAGCAGG 59.891 66.667 0.00 0.00 45.49 4.85
2369 2537 2.429767 CGATGGAGCAGGAGCAGGA 61.430 63.158 0.00 0.00 45.49 3.86
2370 2538 1.446791 GATGGAGCAGGAGCAGGAG 59.553 63.158 0.00 0.00 45.49 3.69
2371 2539 2.663423 GATGGAGCAGGAGCAGGAGC 62.663 65.000 0.00 0.00 45.49 4.70
2372 2540 3.397439 GGAGCAGGAGCAGGAGCA 61.397 66.667 0.00 0.00 45.49 4.26
2373 2541 2.187424 GAGCAGGAGCAGGAGCAG 59.813 66.667 0.00 0.00 45.49 4.24
2374 2542 4.098722 AGCAGGAGCAGGAGCAGC 62.099 66.667 0.00 0.00 45.49 5.25
2376 2544 3.767806 CAGGAGCAGGAGCAGCGA 61.768 66.667 0.00 0.00 45.49 4.93
2377 2545 2.999648 AGGAGCAGGAGCAGCGAA 61.000 61.111 0.00 0.00 45.49 4.70
2378 2546 2.188994 GGAGCAGGAGCAGCGAAT 59.811 61.111 0.00 0.00 45.49 3.34
2379 2547 2.178890 GGAGCAGGAGCAGCGAATG 61.179 63.158 0.00 0.00 45.49 2.67
2380 2548 1.153489 GAGCAGGAGCAGCGAATGA 60.153 57.895 0.00 0.00 45.49 2.57
2381 2549 0.742281 GAGCAGGAGCAGCGAATGAA 60.742 55.000 0.00 0.00 45.49 2.57
2382 2550 0.743701 AGCAGGAGCAGCGAATGAAG 60.744 55.000 0.00 0.00 45.49 3.02
2383 2551 1.720301 CAGGAGCAGCGAATGAAGC 59.280 57.895 0.00 0.00 0.00 3.86
2384 2552 1.022982 CAGGAGCAGCGAATGAAGCA 61.023 55.000 0.00 0.00 37.01 3.91
2385 2553 0.743701 AGGAGCAGCGAATGAAGCAG 60.744 55.000 0.00 0.00 37.01 4.24
2386 2554 1.712977 GGAGCAGCGAATGAAGCAGG 61.713 60.000 0.00 0.00 37.01 4.85
2387 2555 0.742281 GAGCAGCGAATGAAGCAGGA 60.742 55.000 0.00 0.00 37.01 3.86
2388 2556 0.743701 AGCAGCGAATGAAGCAGGAG 60.744 55.000 0.00 0.00 37.01 3.69
2389 2557 1.720301 CAGCGAATGAAGCAGGAGC 59.280 57.895 0.00 0.00 42.56 4.70
2390 2558 1.022982 CAGCGAATGAAGCAGGAGCA 61.023 55.000 0.00 0.00 45.49 4.26
2391 2559 0.743701 AGCGAATGAAGCAGGAGCAG 60.744 55.000 0.00 0.00 45.49 4.24
2392 2560 1.720301 CGAATGAAGCAGGAGCAGC 59.280 57.895 0.00 0.00 45.49 5.25
2393 2561 1.720301 GAATGAAGCAGGAGCAGCG 59.280 57.895 0.00 0.00 45.49 5.18
2394 2562 0.742281 GAATGAAGCAGGAGCAGCGA 60.742 55.000 0.00 0.00 45.49 4.93
2395 2563 0.321919 AATGAAGCAGGAGCAGCGAA 60.322 50.000 0.00 0.00 45.49 4.70
2396 2564 0.107312 ATGAAGCAGGAGCAGCGAAT 60.107 50.000 0.00 0.00 45.49 3.34
2397 2565 1.022982 TGAAGCAGGAGCAGCGAATG 61.023 55.000 0.00 0.00 45.49 2.67
2398 2566 0.742281 GAAGCAGGAGCAGCGAATGA 60.742 55.000 0.00 0.00 45.49 2.57
2399 2567 0.321919 AAGCAGGAGCAGCGAATGAA 60.322 50.000 0.00 0.00 45.49 2.57
2400 2568 0.743701 AGCAGGAGCAGCGAATGAAG 60.744 55.000 0.00 0.00 45.49 3.02
2401 2569 1.720301 CAGGAGCAGCGAATGAAGC 59.280 57.895 0.00 0.00 0.00 3.86
2402 2570 1.022982 CAGGAGCAGCGAATGAAGCA 61.023 55.000 0.00 0.00 37.01 3.91
2403 2571 0.743701 AGGAGCAGCGAATGAAGCAG 60.744 55.000 0.00 0.00 37.01 4.24
2404 2572 1.062206 GAGCAGCGAATGAAGCAGC 59.938 57.895 0.00 0.00 45.59 5.25
2405 2573 2.872557 GCAGCGAATGAAGCAGCA 59.127 55.556 0.00 0.00 44.79 4.41
2406 2574 1.226323 GCAGCGAATGAAGCAGCAG 60.226 57.895 0.00 0.00 44.79 4.24
2407 2575 1.919956 GCAGCGAATGAAGCAGCAGT 61.920 55.000 0.00 0.00 44.79 4.40
2408 2576 0.520404 CAGCGAATGAAGCAGCAGTT 59.480 50.000 0.00 0.00 37.01 3.16
2409 2577 0.520404 AGCGAATGAAGCAGCAGTTG 59.480 50.000 0.00 0.00 37.01 3.16
2410 2578 0.455633 GCGAATGAAGCAGCAGTTGG 60.456 55.000 0.00 0.00 34.19 3.77
2411 2579 0.455633 CGAATGAAGCAGCAGTTGGC 60.456 55.000 0.00 0.00 45.30 4.52
2420 2588 2.033141 GCAGTTGGCTGAGCAGGA 59.967 61.111 6.82 0.00 45.28 3.86
2421 2589 2.039405 GCAGTTGGCTGAGCAGGAG 61.039 63.158 6.82 0.00 45.28 3.69
2422 2590 2.039405 CAGTTGGCTGAGCAGGAGC 61.039 63.158 6.82 0.00 45.28 4.70
2423 2591 2.033141 GTTGGCTGAGCAGGAGCA 59.967 61.111 6.82 0.00 45.49 4.26
2424 2592 2.039405 GTTGGCTGAGCAGGAGCAG 61.039 63.158 6.82 0.00 45.49 4.24
2428 2596 3.767806 CTGAGCAGGAGCAGCGGA 61.768 66.667 0.00 0.00 45.49 5.54
2429 2597 3.079478 TGAGCAGGAGCAGCGGAT 61.079 61.111 0.00 0.00 45.49 4.18
2430 2598 2.588314 GAGCAGGAGCAGCGGATG 60.588 66.667 0.00 0.00 45.49 3.51
2431 2599 3.079478 AGCAGGAGCAGCGGATGA 61.079 61.111 0.00 0.00 45.49 2.92
3051 3243 0.944386 GCTTCTTCCGCAAGTGACAA 59.056 50.000 0.00 0.00 0.00 3.18
3052 3244 1.334149 GCTTCTTCCGCAAGTGACAAC 60.334 52.381 0.00 0.00 0.00 3.32
3053 3245 1.939934 CTTCTTCCGCAAGTGACAACA 59.060 47.619 0.00 0.00 0.00 3.33
3054 3246 1.295792 TCTTCCGCAAGTGACAACAC 58.704 50.000 0.00 0.00 46.24 3.32
3064 3256 2.022808 GTGACAACACATGCGTCTTG 57.977 50.000 0.00 0.00 45.32 3.02
3065 3257 1.330521 GTGACAACACATGCGTCTTGT 59.669 47.619 0.00 0.00 45.32 3.16
3080 3301 4.384547 GCGTCTTGTCTTCTTCTCTTCTTC 59.615 45.833 0.00 0.00 0.00 2.87
3088 3309 7.001674 TGTCTTCTTCTCTTCTTCTCTGTAGT 58.998 38.462 0.00 0.00 0.00 2.73
3103 3324 5.185828 TCTCTGTAGTAGACAACACATGCAT 59.814 40.000 0.00 0.00 37.70 3.96
3115 3337 2.707791 ACACATGCATGCCTCCTATACT 59.292 45.455 26.53 0.00 0.00 2.12
3116 3338 3.244353 ACACATGCATGCCTCCTATACTC 60.244 47.826 26.53 0.00 0.00 2.59
3117 3339 2.028658 ACATGCATGCCTCCTATACTCG 60.029 50.000 26.53 0.00 0.00 4.18
3118 3340 1.995376 TGCATGCCTCCTATACTCGA 58.005 50.000 16.68 0.00 0.00 4.04
3167 3389 3.506067 ACCCAAGGAAGAAAGCAAATACG 59.494 43.478 0.00 0.00 0.00 3.06
3168 3390 3.506067 CCCAAGGAAGAAAGCAAATACGT 59.494 43.478 0.00 0.00 0.00 3.57
3169 3391 4.698304 CCCAAGGAAGAAAGCAAATACGTA 59.302 41.667 0.00 0.00 0.00 3.57
3183 3405 7.971455 AGCAAATACGTACCTTTTACTGATTC 58.029 34.615 0.00 0.00 0.00 2.52
3184 3406 7.822822 AGCAAATACGTACCTTTTACTGATTCT 59.177 33.333 0.00 0.00 0.00 2.40
3185 3407 8.448615 GCAAATACGTACCTTTTACTGATTCTT 58.551 33.333 0.00 0.00 0.00 2.52
3186 3408 9.755064 CAAATACGTACCTTTTACTGATTCTTG 57.245 33.333 0.00 0.00 0.00 3.02
3187 3409 5.857822 ACGTACCTTTTACTGATTCTTGC 57.142 39.130 0.00 0.00 0.00 4.01
3189 3411 4.935808 CGTACCTTTTACTGATTCTTGCCT 59.064 41.667 0.00 0.00 0.00 4.75
3190 3412 5.163854 CGTACCTTTTACTGATTCTTGCCTG 60.164 44.000 0.00 0.00 0.00 4.85
3191 3413 3.507622 ACCTTTTACTGATTCTTGCCTGC 59.492 43.478 0.00 0.00 0.00 4.85
3261 3514 9.306280 CATATCGTAACGAATCTTTATGCTTTG 57.694 33.333 0.00 0.00 39.99 2.77
3341 3598 1.227823 TGACCACCAAGCAACCGAG 60.228 57.895 0.00 0.00 0.00 4.63
3353 3610 1.674322 AACCGAGAAATGCCCACCG 60.674 57.895 0.00 0.00 0.00 4.94
3359 3616 1.448893 GAAATGCCCACCGACGCTA 60.449 57.895 0.00 0.00 0.00 4.26
3364 3621 0.466007 TGCCCACCGACGCTACTATA 60.466 55.000 0.00 0.00 0.00 1.31
3365 3622 0.886563 GCCCACCGACGCTACTATAT 59.113 55.000 0.00 0.00 0.00 0.86
3366 3623 1.135460 GCCCACCGACGCTACTATATC 60.135 57.143 0.00 0.00 0.00 1.63
3367 3624 1.471684 CCCACCGACGCTACTATATCC 59.528 57.143 0.00 0.00 0.00 2.59
3370 3627 3.427638 CCACCGACGCTACTATATCCATG 60.428 52.174 0.00 0.00 0.00 3.66
3378 3635 4.437524 CGCTACTATATCCATGACACCTCG 60.438 50.000 0.00 0.00 0.00 4.63
3394 3651 0.815615 CTCGTTCCCCTATGCCTTGC 60.816 60.000 0.00 0.00 0.00 4.01
3404 3661 1.959282 CTATGCCTTGCCCATCTTTCC 59.041 52.381 0.00 0.00 0.00 3.13
3405 3662 0.688749 ATGCCTTGCCCATCTTTCCC 60.689 55.000 0.00 0.00 0.00 3.97
3406 3663 1.000866 GCCTTGCCCATCTTTCCCT 59.999 57.895 0.00 0.00 0.00 4.20
3407 3664 0.615827 GCCTTGCCCATCTTTCCCTT 60.616 55.000 0.00 0.00 0.00 3.95
3408 3665 1.478631 CCTTGCCCATCTTTCCCTTC 58.521 55.000 0.00 0.00 0.00 3.46
3409 3666 1.006400 CCTTGCCCATCTTTCCCTTCT 59.994 52.381 0.00 0.00 0.00 2.85
3410 3667 2.097825 CTTGCCCATCTTTCCCTTCTG 58.902 52.381 0.00 0.00 0.00 3.02
3411 3668 0.323725 TGCCCATCTTTCCCTTCTGC 60.324 55.000 0.00 0.00 0.00 4.26
3412 3669 0.323725 GCCCATCTTTCCCTTCTGCA 60.324 55.000 0.00 0.00 0.00 4.41
3413 3670 1.687368 GCCCATCTTTCCCTTCTGCAT 60.687 52.381 0.00 0.00 0.00 3.96
3414 3671 2.743553 CCCATCTTTCCCTTCTGCATT 58.256 47.619 0.00 0.00 0.00 3.56
3415 3672 2.692041 CCCATCTTTCCCTTCTGCATTC 59.308 50.000 0.00 0.00 0.00 2.67
3416 3673 3.359033 CCATCTTTCCCTTCTGCATTCA 58.641 45.455 0.00 0.00 0.00 2.57
3428 3685 2.821378 TCTGCATTCATCAAACACCCAG 59.179 45.455 0.00 0.00 0.00 4.45
3464 3729 1.974236 CCCTCACACTTGTCTCCTTCT 59.026 52.381 0.00 0.00 0.00 2.85
3468 3733 4.321601 CCTCACACTTGTCTCCTTCTACTG 60.322 50.000 0.00 0.00 0.00 2.74
3469 3734 4.470602 TCACACTTGTCTCCTTCTACTGA 58.529 43.478 0.00 0.00 0.00 3.41
3470 3735 5.080337 TCACACTTGTCTCCTTCTACTGAT 58.920 41.667 0.00 0.00 0.00 2.90
3471 3736 5.540337 TCACACTTGTCTCCTTCTACTGATT 59.460 40.000 0.00 0.00 0.00 2.57
3474 3739 6.268847 ACACTTGTCTCCTTCTACTGATTCTT 59.731 38.462 0.00 0.00 0.00 2.52
3475 3740 6.589523 CACTTGTCTCCTTCTACTGATTCTTG 59.410 42.308 0.00 0.00 0.00 3.02
3477 3742 4.081420 TGTCTCCTTCTACTGATTCTTGCC 60.081 45.833 0.00 0.00 0.00 4.52
3478 3743 4.161377 GTCTCCTTCTACTGATTCTTGCCT 59.839 45.833 0.00 0.00 0.00 4.75
3479 3744 4.161189 TCTCCTTCTACTGATTCTTGCCTG 59.839 45.833 0.00 0.00 0.00 4.85
3495 4551 4.040645 TGCAGAGGGAGTAGCAGG 57.959 61.111 0.00 0.00 32.48 4.85
3603 4741 9.581099 GTAATAACTAAATGTTTTCACCCATGG 57.419 33.333 4.14 4.14 39.89 3.66
3621 4759 1.370900 GCACGCTGCAGGAAAGTTG 60.371 57.895 17.12 1.11 44.26 3.16
3678 4820 2.627699 CGGGCATTGGTAGGCATAATTT 59.372 45.455 0.00 0.00 31.29 1.82
3679 4821 3.823873 CGGGCATTGGTAGGCATAATTTA 59.176 43.478 0.00 0.00 31.29 1.40
3680 4822 4.462483 CGGGCATTGGTAGGCATAATTTAT 59.538 41.667 0.00 0.00 31.29 1.40
3681 4823 5.047377 CGGGCATTGGTAGGCATAATTTATT 60.047 40.000 0.00 0.00 31.29 1.40
3772 4931 2.684001 TCATTCCGTTGCCTATTCGT 57.316 45.000 0.00 0.00 0.00 3.85
3784 4943 4.529446 TGCCTATTCGTTTCGACAAAAAC 58.471 39.130 0.00 0.00 34.89 2.43
3813 4972 4.582869 TCAGCTGAAAGTATGTGCTTCAT 58.417 39.130 15.67 0.00 40.25 2.57
3814 4973 5.733676 TCAGCTGAAAGTATGTGCTTCATA 58.266 37.500 15.67 0.00 37.91 2.15
3815 4974 6.351711 TCAGCTGAAAGTATGTGCTTCATAT 58.648 36.000 15.67 0.00 40.54 1.78
3816 4975 7.500141 TCAGCTGAAAGTATGTGCTTCATATA 58.500 34.615 15.67 0.00 40.54 0.86
3875 5034 4.142381 CCACTTAAAACCCAGCTAAGCATC 60.142 45.833 0.00 0.00 0.00 3.91
3878 5037 2.717639 AAACCCAGCTAAGCATCGAT 57.282 45.000 0.00 0.00 0.00 3.59
3905 5064 2.672961 TGCAGGAATTCTACAGGACG 57.327 50.000 5.23 0.00 0.00 4.79
3908 5067 2.544685 CAGGAATTCTACAGGACGCAG 58.455 52.381 5.23 0.00 0.00 5.18
3909 5068 1.134670 AGGAATTCTACAGGACGCAGC 60.135 52.381 5.23 0.00 0.00 5.25
3937 5096 4.112634 TGGGTCCTTTGTCAAGCTTTAT 57.887 40.909 0.00 0.00 0.00 1.40
4033 5192 6.866010 TTGTATAGCATATGCAAGGAGTTG 57.134 37.500 28.62 0.00 45.16 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.138304 CGAACCACAAGATCTTTCACCA 58.862 45.455 4.86 0.00 0.00 4.17
105 106 1.774856 GCCCCTTAAGCCCTTCATCTA 59.225 52.381 0.00 0.00 0.00 1.98
113 114 0.916809 TCTGTTAGCCCCTTAAGCCC 59.083 55.000 0.00 0.00 0.00 5.19
114 115 2.753452 GTTTCTGTTAGCCCCTTAAGCC 59.247 50.000 0.00 0.00 0.00 4.35
115 116 2.753452 GGTTTCTGTTAGCCCCTTAAGC 59.247 50.000 0.00 0.00 0.00 3.09
121 122 2.492088 GTTCATGGTTTCTGTTAGCCCC 59.508 50.000 0.00 0.00 0.00 5.80
143 144 7.174946 CCAAGTAAAGAGGCTCTAATTTGACAA 59.825 37.037 24.43 1.93 0.00 3.18
144 145 6.655003 CCAAGTAAAGAGGCTCTAATTTGACA 59.345 38.462 24.43 2.22 0.00 3.58
165 186 4.707030 TGCAAGATGAAATACTGCCAAG 57.293 40.909 0.00 0.00 0.00 3.61
192 213 5.141182 GGAGACATCTTCCTAGTGGTATCA 58.859 45.833 0.00 0.00 34.23 2.15
222 243 8.582433 TCGCATAACTATGAATTACGATGAAA 57.418 30.769 0.77 0.00 35.75 2.69
229 250 7.478520 ACCAACTCGCATAACTATGAATTAC 57.521 36.000 0.77 0.00 35.75 1.89
234 255 5.242434 ACAAACCAACTCGCATAACTATGA 58.758 37.500 0.77 0.00 35.75 2.15
236 257 5.293569 GCTACAAACCAACTCGCATAACTAT 59.706 40.000 0.00 0.00 0.00 2.12
244 265 1.135689 CCATGCTACAAACCAACTCGC 60.136 52.381 0.00 0.00 0.00 5.03
251 272 6.859420 AAATTGAAAACCATGCTACAAACC 57.141 33.333 0.00 0.00 0.00 3.27
281 302 4.915704 TGGTGACGTCTGAAATTGTTTTC 58.084 39.130 17.92 0.00 41.39 2.29
282 303 4.974368 TGGTGACGTCTGAAATTGTTTT 57.026 36.364 17.92 0.00 0.00 2.43
319 340 6.111382 CCAAAGTAATCTGAGATCTGCTTCA 58.889 40.000 0.00 0.00 0.00 3.02
320 341 5.526846 CCCAAAGTAATCTGAGATCTGCTTC 59.473 44.000 0.00 0.00 0.00 3.86
329 350 4.651778 TCACAACCCCAAAGTAATCTGAG 58.348 43.478 0.00 0.00 0.00 3.35
342 363 1.143073 ACTGGAGAAACTCACAACCCC 59.857 52.381 0.00 0.00 31.08 4.95
346 367 6.174720 AGTGAATACTGGAGAAACTCACAA 57.825 37.500 0.00 0.00 35.34 3.33
348 369 8.779354 ATTTAGTGAATACTGGAGAAACTCAC 57.221 34.615 0.00 0.00 37.78 3.51
404 444 3.306294 GGAACCCTGAAATTTTGAGCCAG 60.306 47.826 0.00 0.00 0.00 4.85
405 445 2.632512 GGAACCCTGAAATTTTGAGCCA 59.367 45.455 0.00 0.00 0.00 4.75
474 514 1.754226 TGGGTTCAAGCTCCAACAAAC 59.246 47.619 9.35 1.52 0.00 2.93
569 616 3.571828 TCTCTCTCAAACTGAGGACACAG 59.428 47.826 3.92 0.00 44.39 3.66
592 639 5.828859 GCTACTACTATTCTTGTCTCCTCCA 59.171 44.000 0.00 0.00 0.00 3.86
677 740 0.689623 AGGAAGGAAGGCAGTCAGTG 59.310 55.000 0.00 0.00 0.00 3.66
752 823 3.181474 GGAGAGGAGTGGGAATTAACGAG 60.181 52.174 0.00 0.00 0.00 4.18
765 836 3.434453 CGATTACAGGAGAGGAGAGGAGT 60.434 52.174 0.00 0.00 0.00 3.85
801 893 8.742554 AAATGAATGAAATTAACAAGGACGAC 57.257 30.769 0.00 0.00 36.07 4.34
802 894 8.572185 TGAAATGAATGAAATTAACAAGGACGA 58.428 29.630 0.00 0.00 36.07 4.20
847 955 4.807039 CCTACGGGGGAACGCACG 62.807 72.222 11.63 11.63 45.96 5.34
853 961 0.340558 TCTCCAATCCTACGGGGGAA 59.659 55.000 2.86 0.00 39.02 3.97
855 963 0.977395 GATCTCCAATCCTACGGGGG 59.023 60.000 0.00 0.00 35.33 5.40
856 964 1.717032 TGATCTCCAATCCTACGGGG 58.283 55.000 0.00 0.00 0.00 5.73
857 965 4.202357 TGAAATGATCTCCAATCCTACGGG 60.202 45.833 0.00 0.00 0.00 5.28
858 966 4.960938 TGAAATGATCTCCAATCCTACGG 58.039 43.478 0.00 0.00 0.00 4.02
884 994 5.823570 CAGCAGAAGAAGAATGATCAGGAAT 59.176 40.000 0.09 0.00 0.00 3.01
893 1003 7.375106 AGACAATAACAGCAGAAGAAGAATG 57.625 36.000 0.00 0.00 0.00 2.67
1134 1260 4.477975 GCGGTGAGGACGAGGACG 62.478 72.222 0.00 0.00 45.75 4.79
1165 1291 2.888863 GCTGTGGAGGAGGACGAG 59.111 66.667 0.00 0.00 0.00 4.18
1194 1320 0.606096 TGTAGACATGTGGGTCGTGG 59.394 55.000 1.15 0.00 42.62 4.94
1197 1323 2.448926 TGTTGTAGACATGTGGGTCG 57.551 50.000 1.15 0.00 42.62 4.79
1203 1329 4.256920 GGCTGATCTTGTTGTAGACATGT 58.743 43.478 0.00 0.00 38.26 3.21
1236 1362 0.257328 TGGTGCTTGGTTGGACTTGA 59.743 50.000 0.00 0.00 0.00 3.02
1240 1366 1.455383 CCTGTGGTGCTTGGTTGGAC 61.455 60.000 0.00 0.00 0.00 4.02
1241 1367 1.152777 CCTGTGGTGCTTGGTTGGA 60.153 57.895 0.00 0.00 0.00 3.53
1251 1377 3.434319 GTGATGGCGCCTGTGGTG 61.434 66.667 29.70 0.00 36.10 4.17
1254 1380 3.434319 GTGGTGATGGCGCCTGTG 61.434 66.667 29.70 0.00 45.15 3.66
1255 1381 3.952508 TGTGGTGATGGCGCCTGT 61.953 61.111 29.70 16.88 45.15 4.00
1257 1383 3.272364 ATGTGTGGTGATGGCGCCT 62.272 57.895 29.70 13.55 45.15 5.52
1258 1384 2.751436 ATGTGTGGTGATGGCGCC 60.751 61.111 22.73 22.73 45.13 6.53
1259 1385 2.039974 TGATGTGTGGTGATGGCGC 61.040 57.895 0.00 0.00 0.00 6.53
1261 1387 0.608856 TGGTGATGTGTGGTGATGGC 60.609 55.000 0.00 0.00 0.00 4.40
1262 1388 1.167851 GTGGTGATGTGTGGTGATGG 58.832 55.000 0.00 0.00 0.00 3.51
1264 1390 0.321564 CGGTGGTGATGTGTGGTGAT 60.322 55.000 0.00 0.00 0.00 3.06
1265 1391 1.070615 CGGTGGTGATGTGTGGTGA 59.929 57.895 0.00 0.00 0.00 4.02
1271 1409 1.079127 GAGGGTCGGTGGTGATGTG 60.079 63.158 0.00 0.00 0.00 3.21
1291 1429 0.526524 GAGGAGTCGCTGGATTCGTG 60.527 60.000 0.00 0.00 30.14 4.35
1397 1550 2.271800 AGTCGGTTGATTCTGATTCGC 58.728 47.619 0.00 0.00 0.00 4.70
1433 1586 3.982241 GCTGGTGGTTGTGCTGCC 61.982 66.667 0.00 0.00 0.00 4.85
1617 1770 2.743538 TCCATGACGTGCTGCTGC 60.744 61.111 8.89 8.89 40.20 5.25
1620 1776 2.037136 AAGCTCCATGACGTGCTGC 61.037 57.895 0.00 0.00 35.79 5.25
1710 1869 0.826672 AGTCGGGGAAGTTGTCGTCT 60.827 55.000 0.00 0.00 0.00 4.18
1800 1959 4.947147 TCCGGTGGTGCTTGGTGC 62.947 66.667 0.00 0.00 43.25 5.01
1802 1961 4.643387 GCTCCGGTGGTGCTTGGT 62.643 66.667 0.00 0.00 38.91 3.67
1816 1975 3.432051 CTGGGATGGACGACGGCTC 62.432 68.421 0.00 0.00 0.00 4.70
1840 1999 2.821366 ATTCTTCTGCGCTGCCGG 60.821 61.111 9.73 0.00 34.32 6.13
1841 2000 2.402388 CATTCTTCTGCGCTGCCG 59.598 61.111 9.73 2.50 37.57 5.69
1845 2004 2.001361 GCATGGCATTCTTCTGCGCT 62.001 55.000 9.73 0.00 43.23 5.92
1857 2025 2.741985 CGTCGGAACAGCATGGCA 60.742 61.111 0.00 0.00 43.62 4.92
1996 2164 2.049185 TGGACGAGGAGCTGCTCTC 61.049 63.158 29.52 23.78 41.15 3.20
2041 2209 2.019984 GGCATAGGCATAGGCATAAGC 58.980 52.381 17.33 12.21 46.62 3.09
2042 2210 3.641434 AGGCATAGGCATAGGCATAAG 57.359 47.619 17.33 0.00 40.04 1.73
2043 2211 5.039920 CATAGGCATAGGCATAGGCATAA 57.960 43.478 17.33 1.61 38.30 1.90
2044 2212 4.694760 CATAGGCATAGGCATAGGCATA 57.305 45.455 17.33 14.57 39.97 3.14
2045 2213 3.572632 CATAGGCATAGGCATAGGCAT 57.427 47.619 17.33 12.60 39.97 4.40
2127 2295 2.224378 TGTTGCTGCTTCTGCTTCTACT 60.224 45.455 0.00 0.00 40.48 2.57
2128 2296 2.146342 TGTTGCTGCTTCTGCTTCTAC 58.854 47.619 0.00 0.00 40.48 2.59
2129 2297 2.549064 TGTTGCTGCTTCTGCTTCTA 57.451 45.000 0.00 0.00 40.48 2.10
2244 2412 1.004560 ACCAGGCAGTGTCATGTCG 60.005 57.895 0.00 0.00 0.00 4.35
2314 2482 2.063378 CAGCCACCTCCTCCTCCTC 61.063 68.421 0.00 0.00 0.00 3.71
2315 2483 2.040278 CAGCCACCTCCTCCTCCT 59.960 66.667 0.00 0.00 0.00 3.69
2316 2484 2.039624 TCAGCCACCTCCTCCTCC 59.960 66.667 0.00 0.00 0.00 4.30
2317 2485 2.730524 GCTCAGCCACCTCCTCCTC 61.731 68.421 0.00 0.00 0.00 3.71
2318 2486 2.686835 GCTCAGCCACCTCCTCCT 60.687 66.667 0.00 0.00 0.00 3.69
2319 2487 3.005539 TGCTCAGCCACCTCCTCC 61.006 66.667 0.00 0.00 0.00 4.30
2320 2488 2.583520 CTGCTCAGCCACCTCCTC 59.416 66.667 0.00 0.00 0.00 3.71
2321 2489 3.007920 CCTGCTCAGCCACCTCCT 61.008 66.667 0.00 0.00 0.00 3.69
2322 2490 3.005539 TCCTGCTCAGCCACCTCC 61.006 66.667 0.00 0.00 0.00 4.30
2323 2491 2.583520 CTCCTGCTCAGCCACCTC 59.416 66.667 0.00 0.00 0.00 3.85
2324 2492 3.715097 GCTCCTGCTCAGCCACCT 61.715 66.667 0.00 0.00 36.03 4.00
2325 2493 3.972971 CTGCTCCTGCTCAGCCACC 62.973 68.421 0.00 0.00 40.48 4.61
2326 2494 2.436292 CTGCTCCTGCTCAGCCAC 60.436 66.667 0.00 0.00 40.48 5.01
2330 2498 0.452184 CATTTGCTGCTCCTGCTCAG 59.548 55.000 0.00 0.00 40.48 3.35
2331 2499 0.037160 TCATTTGCTGCTCCTGCTCA 59.963 50.000 0.00 0.00 40.48 4.26
2332 2500 0.450983 GTCATTTGCTGCTCCTGCTC 59.549 55.000 0.00 0.00 40.48 4.26
2333 2501 1.303799 CGTCATTTGCTGCTCCTGCT 61.304 55.000 0.00 0.00 40.48 4.24
2334 2502 1.136147 CGTCATTTGCTGCTCCTGC 59.864 57.895 0.00 0.00 40.20 4.85
2335 2503 1.063616 CATCGTCATTTGCTGCTCCTG 59.936 52.381 0.00 0.00 0.00 3.86
2336 2504 1.376543 CATCGTCATTTGCTGCTCCT 58.623 50.000 0.00 0.00 0.00 3.69
2337 2505 0.379669 CCATCGTCATTTGCTGCTCC 59.620 55.000 0.00 0.00 0.00 4.70
2338 2506 1.329906 CTCCATCGTCATTTGCTGCTC 59.670 52.381 0.00 0.00 0.00 4.26
2339 2507 1.376543 CTCCATCGTCATTTGCTGCT 58.623 50.000 0.00 0.00 0.00 4.24
2340 2508 0.248377 GCTCCATCGTCATTTGCTGC 60.248 55.000 0.00 0.00 0.00 5.25
2341 2509 1.063616 CTGCTCCATCGTCATTTGCTG 59.936 52.381 0.00 0.00 0.00 4.41
2342 2510 1.376543 CTGCTCCATCGTCATTTGCT 58.623 50.000 0.00 0.00 0.00 3.91
2343 2511 0.379669 CCTGCTCCATCGTCATTTGC 59.620 55.000 0.00 0.00 0.00 3.68
2344 2512 1.938577 CTCCTGCTCCATCGTCATTTG 59.061 52.381 0.00 0.00 0.00 2.32
2345 2513 1.745141 GCTCCTGCTCCATCGTCATTT 60.745 52.381 0.00 0.00 36.03 2.32
2346 2514 0.179062 GCTCCTGCTCCATCGTCATT 60.179 55.000 0.00 0.00 36.03 2.57
2347 2515 1.332889 TGCTCCTGCTCCATCGTCAT 61.333 55.000 0.00 0.00 40.48 3.06
2348 2516 1.953231 CTGCTCCTGCTCCATCGTCA 61.953 60.000 0.00 0.00 40.48 4.35
2349 2517 1.227205 CTGCTCCTGCTCCATCGTC 60.227 63.158 0.00 0.00 40.48 4.20
2350 2518 2.729479 CCTGCTCCTGCTCCATCGT 61.729 63.158 0.00 0.00 40.48 3.73
2351 2519 2.108566 CCTGCTCCTGCTCCATCG 59.891 66.667 0.00 0.00 40.48 3.84
2352 2520 1.446791 CTCCTGCTCCTGCTCCATC 59.553 63.158 0.00 0.00 40.48 3.51
2353 2521 2.744243 GCTCCTGCTCCTGCTCCAT 61.744 63.158 0.00 0.00 40.48 3.41
2354 2522 3.397439 GCTCCTGCTCCTGCTCCA 61.397 66.667 0.00 0.00 40.48 3.86
2355 2523 3.388703 CTGCTCCTGCTCCTGCTCC 62.389 68.421 0.00 0.00 40.48 4.70
2356 2524 2.187424 CTGCTCCTGCTCCTGCTC 59.813 66.667 0.00 0.00 40.48 4.26
2357 2525 4.098722 GCTGCTCCTGCTCCTGCT 62.099 66.667 0.00 0.00 40.48 4.24
2359 2527 2.590391 ATTCGCTGCTCCTGCTCCTG 62.590 60.000 0.00 0.00 40.48 3.86
2360 2528 2.365586 ATTCGCTGCTCCTGCTCCT 61.366 57.895 0.00 0.00 40.48 3.69
2361 2529 2.178890 CATTCGCTGCTCCTGCTCC 61.179 63.158 0.00 0.00 40.48 4.70
2362 2530 0.742281 TTCATTCGCTGCTCCTGCTC 60.742 55.000 0.00 0.00 40.48 4.26
2363 2531 0.743701 CTTCATTCGCTGCTCCTGCT 60.744 55.000 0.00 0.00 40.48 4.24
2364 2532 1.720301 CTTCATTCGCTGCTCCTGC 59.280 57.895 0.00 0.00 40.20 4.85
2365 2533 1.022982 TGCTTCATTCGCTGCTCCTG 61.023 55.000 0.00 0.00 0.00 3.86
2366 2534 0.743701 CTGCTTCATTCGCTGCTCCT 60.744 55.000 0.00 0.00 0.00 3.69
2367 2535 1.712977 CCTGCTTCATTCGCTGCTCC 61.713 60.000 0.00 0.00 0.00 4.70
2368 2536 0.742281 TCCTGCTTCATTCGCTGCTC 60.742 55.000 0.00 0.00 0.00 4.26
2369 2537 0.743701 CTCCTGCTTCATTCGCTGCT 60.744 55.000 0.00 0.00 0.00 4.24
2370 2538 1.720301 CTCCTGCTTCATTCGCTGC 59.280 57.895 0.00 0.00 0.00 5.25
2371 2539 1.022982 TGCTCCTGCTTCATTCGCTG 61.023 55.000 0.00 0.00 40.48 5.18
2372 2540 0.743701 CTGCTCCTGCTTCATTCGCT 60.744 55.000 0.00 0.00 40.48 4.93
2373 2541 1.720301 CTGCTCCTGCTTCATTCGC 59.280 57.895 0.00 0.00 40.48 4.70
2374 2542 1.720301 GCTGCTCCTGCTTCATTCG 59.280 57.895 0.00 0.00 40.48 3.34
2375 2543 0.742281 TCGCTGCTCCTGCTTCATTC 60.742 55.000 0.00 0.00 40.48 2.67
2376 2544 0.321919 TTCGCTGCTCCTGCTTCATT 60.322 50.000 0.00 0.00 40.48 2.57
2377 2545 0.107312 ATTCGCTGCTCCTGCTTCAT 60.107 50.000 0.00 0.00 40.48 2.57
2378 2546 1.022982 CATTCGCTGCTCCTGCTTCA 61.023 55.000 0.00 0.00 40.48 3.02
2379 2547 0.742281 TCATTCGCTGCTCCTGCTTC 60.742 55.000 0.00 0.00 40.48 3.86
2380 2548 0.321919 TTCATTCGCTGCTCCTGCTT 60.322 50.000 0.00 0.00 40.48 3.91
2381 2549 0.743701 CTTCATTCGCTGCTCCTGCT 60.744 55.000 0.00 0.00 40.48 4.24
2382 2550 1.720301 CTTCATTCGCTGCTCCTGC 59.280 57.895 0.00 0.00 40.20 4.85
2383 2551 1.022982 TGCTTCATTCGCTGCTCCTG 61.023 55.000 0.00 0.00 0.00 3.86
2384 2552 0.743701 CTGCTTCATTCGCTGCTCCT 60.744 55.000 0.00 0.00 0.00 3.69
2385 2553 1.720301 CTGCTTCATTCGCTGCTCC 59.280 57.895 0.00 0.00 0.00 4.70
2386 2554 1.062206 GCTGCTTCATTCGCTGCTC 59.938 57.895 0.00 0.00 45.27 4.26
2387 2555 3.185155 GCTGCTTCATTCGCTGCT 58.815 55.556 0.00 0.00 45.27 4.24
2389 2557 0.520404 AACTGCTGCTTCATTCGCTG 59.480 50.000 0.00 0.00 0.00 5.18
2390 2558 0.520404 CAACTGCTGCTTCATTCGCT 59.480 50.000 0.00 0.00 0.00 4.93
2391 2559 0.455633 CCAACTGCTGCTTCATTCGC 60.456 55.000 0.00 0.00 0.00 4.70
2392 2560 0.455633 GCCAACTGCTGCTTCATTCG 60.456 55.000 0.00 0.00 36.87 3.34
2393 2561 3.413522 GCCAACTGCTGCTTCATTC 57.586 52.632 0.00 0.00 36.87 2.67
2403 2571 2.033141 TCCTGCTCAGCCAACTGC 59.967 61.111 0.00 0.00 44.10 4.40
2404 2572 2.039405 GCTCCTGCTCAGCCAACTG 61.039 63.158 0.00 0.00 45.95 3.16
2405 2573 2.350514 GCTCCTGCTCAGCCAACT 59.649 61.111 0.00 0.00 36.03 3.16
2406 2574 2.033141 TGCTCCTGCTCAGCCAAC 59.967 61.111 0.00 0.00 40.48 3.77
2407 2575 2.350134 CTGCTCCTGCTCAGCCAA 59.650 61.111 0.00 0.00 40.48 4.52
2411 2579 3.091499 ATCCGCTGCTCCTGCTCAG 62.091 63.158 0.00 0.00 40.48 3.35
2412 2580 3.079478 ATCCGCTGCTCCTGCTCA 61.079 61.111 0.00 0.00 40.48 4.26
2413 2581 2.584261 TTCATCCGCTGCTCCTGCTC 62.584 60.000 0.00 0.00 40.48 4.26
2414 2582 2.590391 CTTCATCCGCTGCTCCTGCT 62.590 60.000 0.00 0.00 40.48 4.24
2415 2583 2.124983 TTCATCCGCTGCTCCTGC 60.125 61.111 0.00 0.00 40.20 4.85
2416 2584 2.178890 GCTTCATCCGCTGCTCCTG 61.179 63.158 0.00 0.00 0.00 3.86
2417 2585 2.188994 GCTTCATCCGCTGCTCCT 59.811 61.111 0.00 0.00 0.00 3.69
2418 2586 2.124983 TGCTTCATCCGCTGCTCC 60.125 61.111 0.00 0.00 0.00 4.70
2419 2587 2.178890 CCTGCTTCATCCGCTGCTC 61.179 63.158 0.00 0.00 0.00 4.26
2420 2588 2.124819 CCTGCTTCATCCGCTGCT 60.125 61.111 0.00 0.00 0.00 4.24
2421 2589 3.885521 GCCTGCTTCATCCGCTGC 61.886 66.667 0.00 0.00 0.00 5.25
2422 2590 3.570638 CGCCTGCTTCATCCGCTG 61.571 66.667 0.00 0.00 0.00 5.18
2423 2591 4.845580 CCGCCTGCTTCATCCGCT 62.846 66.667 0.00 0.00 0.00 5.52
3051 3243 2.533266 AGAAGACAAGACGCATGTGT 57.467 45.000 12.68 12.68 0.00 3.72
3052 3244 3.062763 AGAAGAAGACAAGACGCATGTG 58.937 45.455 4.30 4.30 0.00 3.21
3053 3245 3.006323 AGAGAAGAAGACAAGACGCATGT 59.994 43.478 0.00 0.00 0.00 3.21
3054 3246 3.583806 AGAGAAGAAGACAAGACGCATG 58.416 45.455 0.00 0.00 0.00 4.06
3056 3248 3.319405 AGAAGAGAAGAAGACAAGACGCA 59.681 43.478 0.00 0.00 0.00 5.24
3057 3249 3.908213 AGAAGAGAAGAAGACAAGACGC 58.092 45.455 0.00 0.00 0.00 5.19
3059 3251 6.863126 CAGAGAAGAAGAGAAGAAGACAAGAC 59.137 42.308 0.00 0.00 0.00 3.01
3060 3252 6.549364 ACAGAGAAGAAGAGAAGAAGACAAGA 59.451 38.462 0.00 0.00 0.00 3.02
3062 3254 6.723298 ACAGAGAAGAAGAGAAGAAGACAA 57.277 37.500 0.00 0.00 0.00 3.18
3063 3255 7.001674 ACTACAGAGAAGAAGAGAAGAAGACA 58.998 38.462 0.00 0.00 0.00 3.41
3064 3256 7.448748 ACTACAGAGAAGAAGAGAAGAAGAC 57.551 40.000 0.00 0.00 0.00 3.01
3065 3257 8.598916 TCTACTACAGAGAAGAAGAGAAGAAGA 58.401 37.037 0.00 0.00 0.00 2.87
3080 3301 4.809673 TGCATGTGTTGTCTACTACAGAG 58.190 43.478 0.00 0.00 39.87 3.35
3088 3309 2.358957 GAGGCATGCATGTGTTGTCTA 58.641 47.619 26.79 0.00 0.00 2.59
3103 3324 3.328050 TGAGAGATCGAGTATAGGAGGCA 59.672 47.826 0.00 0.00 0.00 4.75
3115 3337 2.808906 TTGAGGTCCTGAGAGATCGA 57.191 50.000 0.00 0.00 0.00 3.59
3116 3338 2.692557 ACATTGAGGTCCTGAGAGATCG 59.307 50.000 0.00 0.00 0.00 3.69
3117 3339 5.860941 TTACATTGAGGTCCTGAGAGATC 57.139 43.478 0.00 0.00 0.00 2.75
3118 3340 6.627087 TTTTACATTGAGGTCCTGAGAGAT 57.373 37.500 0.00 0.00 0.00 2.75
3167 3389 5.392057 GCAGGCAAGAATCAGTAAAAGGTAC 60.392 44.000 0.00 0.00 0.00 3.34
3168 3390 4.700213 GCAGGCAAGAATCAGTAAAAGGTA 59.300 41.667 0.00 0.00 0.00 3.08
3169 3391 3.507622 GCAGGCAAGAATCAGTAAAAGGT 59.492 43.478 0.00 0.00 0.00 3.50
3187 3409 2.988010 TAATGTACAGAGCCTGCAGG 57.012 50.000 29.34 29.34 34.37 4.85
3189 3411 5.928976 ACATAATAATGTACAGAGCCTGCA 58.071 37.500 0.33 0.00 44.66 4.41
3190 3412 6.591834 CCTACATAATAATGTACAGAGCCTGC 59.408 42.308 0.33 0.00 44.66 4.85
3191 3413 7.896811 TCCTACATAATAATGTACAGAGCCTG 58.103 38.462 0.33 1.16 44.66 4.85
3233 3483 8.988064 AGCATAAAGATTCGTTACGATATGAT 57.012 30.769 21.75 15.93 35.23 2.45
3234 3484 8.812147 AAGCATAAAGATTCGTTACGATATGA 57.188 30.769 21.75 4.71 35.23 2.15
3235 3485 9.306280 CAAAGCATAAAGATTCGTTACGATATG 57.694 33.333 8.67 13.59 35.23 1.78
3261 3514 4.722855 GCGTGGTGGTGCATTGCC 62.723 66.667 6.12 0.00 0.00 4.52
3341 3598 1.448893 TAGCGTCGGTGGGCATTTC 60.449 57.895 7.30 0.00 0.00 2.17
3353 3610 4.459685 AGGTGTCATGGATATAGTAGCGTC 59.540 45.833 0.00 0.00 0.00 5.19
3359 3616 4.281182 GGAACGAGGTGTCATGGATATAGT 59.719 45.833 0.00 0.00 0.00 2.12
3364 3621 0.541863 GGGAACGAGGTGTCATGGAT 59.458 55.000 0.00 0.00 0.00 3.41
3365 3622 1.550130 GGGGAACGAGGTGTCATGGA 61.550 60.000 0.00 0.00 0.00 3.41
3366 3623 1.078426 GGGGAACGAGGTGTCATGG 60.078 63.158 0.00 0.00 0.00 3.66
3367 3624 1.191535 TAGGGGAACGAGGTGTCATG 58.808 55.000 0.00 0.00 0.00 3.07
3370 3627 0.179081 GCATAGGGGAACGAGGTGTC 60.179 60.000 0.00 0.00 0.00 3.67
3378 3635 1.455773 GGGCAAGGCATAGGGGAAC 60.456 63.158 0.00 0.00 0.00 3.62
3394 3651 2.449137 ATGCAGAAGGGAAAGATGGG 57.551 50.000 0.00 0.00 0.00 4.00
3404 3661 3.367703 GGGTGTTTGATGAATGCAGAAGG 60.368 47.826 0.00 0.00 0.00 3.46
3405 3662 3.256383 TGGGTGTTTGATGAATGCAGAAG 59.744 43.478 0.00 0.00 0.00 2.85
3406 3663 3.229293 TGGGTGTTTGATGAATGCAGAA 58.771 40.909 0.00 0.00 0.00 3.02
3407 3664 2.821378 CTGGGTGTTTGATGAATGCAGA 59.179 45.455 0.00 0.00 0.00 4.26
3408 3665 2.821378 TCTGGGTGTTTGATGAATGCAG 59.179 45.455 0.00 0.00 0.00 4.41
3409 3666 2.557924 GTCTGGGTGTTTGATGAATGCA 59.442 45.455 0.00 0.00 0.00 3.96
3410 3667 2.414559 CGTCTGGGTGTTTGATGAATGC 60.415 50.000 0.00 0.00 0.00 3.56
3411 3668 2.414559 GCGTCTGGGTGTTTGATGAATG 60.415 50.000 0.00 0.00 0.00 2.67
3412 3669 1.812571 GCGTCTGGGTGTTTGATGAAT 59.187 47.619 0.00 0.00 0.00 2.57
3413 3670 1.234821 GCGTCTGGGTGTTTGATGAA 58.765 50.000 0.00 0.00 0.00 2.57
3414 3671 0.605319 GGCGTCTGGGTGTTTGATGA 60.605 55.000 0.00 0.00 0.00 2.92
3415 3672 0.888736 TGGCGTCTGGGTGTTTGATG 60.889 55.000 0.00 0.00 0.00 3.07
3416 3673 0.038166 ATGGCGTCTGGGTGTTTGAT 59.962 50.000 0.00 0.00 0.00 2.57
3428 3685 0.749454 AGGGCAGAATTCATGGCGTC 60.749 55.000 18.35 10.66 43.74 5.19
3464 3729 2.093288 CCTCTGCAGGCAAGAATCAGTA 60.093 50.000 15.13 0.00 30.98 2.74
3468 3733 0.254178 TCCCTCTGCAGGCAAGAATC 59.746 55.000 15.13 0.00 38.72 2.52
3469 3734 0.255318 CTCCCTCTGCAGGCAAGAAT 59.745 55.000 15.13 0.00 38.72 2.40
3470 3735 1.130054 ACTCCCTCTGCAGGCAAGAA 61.130 55.000 15.13 0.00 38.72 2.52
3471 3736 0.252239 TACTCCCTCTGCAGGCAAGA 60.252 55.000 15.13 5.24 38.72 3.02
3474 3739 2.362369 GCTACTCCCTCTGCAGGCA 61.362 63.158 15.13 0.00 38.72 4.75
3475 3740 2.308968 CTGCTACTCCCTCTGCAGGC 62.309 65.000 15.13 7.14 46.24 4.85
3478 3743 1.687146 CCCTGCTACTCCCTCTGCA 60.687 63.158 0.00 0.00 0.00 4.41
3479 3744 0.762461 ATCCCTGCTACTCCCTCTGC 60.762 60.000 0.00 0.00 0.00 4.26
3584 4722 4.244862 GTGCCATGGGTGAAAACATTTAG 58.755 43.478 15.13 0.00 0.00 1.85
3599 4737 2.537792 CTTTCCTGCAGCGTGCCATG 62.538 60.000 8.66 0.00 44.23 3.66
3600 4738 2.282391 TTTCCTGCAGCGTGCCAT 60.282 55.556 8.66 0.00 44.23 4.40
3601 4739 2.979676 CTTTCCTGCAGCGTGCCA 60.980 61.111 8.66 0.00 44.23 4.92
3602 4740 2.555547 AACTTTCCTGCAGCGTGCC 61.556 57.895 8.66 0.00 44.23 5.01
3603 4741 1.370900 CAACTTTCCTGCAGCGTGC 60.371 57.895 8.66 3.44 45.29 5.34
3621 4759 4.800993 CACAGGTGAGTCGTTGAAGATATC 59.199 45.833 0.00 0.00 0.00 1.63
3772 4931 4.499019 GCTGATTCTGGGTTTTTGTCGAAA 60.499 41.667 0.00 0.00 0.00 3.46
3784 4943 4.334759 CACATACTTTCAGCTGATTCTGGG 59.665 45.833 19.04 8.53 34.91 4.45
3891 5050 1.929836 CTGCTGCGTCCTGTAGAATTC 59.070 52.381 0.00 0.00 30.84 2.17
3908 5067 2.118294 AAAGGACCCAAGCCCTGC 59.882 61.111 0.00 0.00 32.12 4.85
3909 5068 0.895559 GACAAAGGACCCAAGCCCTG 60.896 60.000 0.00 0.00 32.12 4.45
3937 5096 3.137687 TGCTCCACGCAGAGTTCA 58.862 55.556 4.42 0.00 45.47 3.18
3954 5113 5.351465 ACAAATCTGAAAAGACGTGCGATAT 59.649 36.000 0.00 0.00 0.00 1.63
3957 5116 2.869801 ACAAATCTGAAAAGACGTGCGA 59.130 40.909 0.00 0.00 0.00 5.10
3961 5120 2.032030 CGCCACAAATCTGAAAAGACGT 60.032 45.455 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.