Multiple sequence alignment - TraesCS2A01G253500

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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 TraesCS2A01G253500 chr2A 100.000 6769 0 0 1 6769 385444086 385450854 0.000000e+00 12501
1 TraesCS2A01G253500 chr2A 98.462 195 3 0 2323 2517 729554612 729554418 1.810000e-90 344
2 TraesCS2A01G253500 chr2D 95.914 4307 96 26 2518 6769 306342170 306346451 0.000000e+00 6905
3 TraesCS2A01G253500 chr2D 95.327 2311 52 12 44 2328 306339906 306342186 0.000000e+00 3618
4 TraesCS2A01G253500 chr2B 95.837 4300 112 40 2518 6769 374260348 374264628 0.000000e+00 6887
5 TraesCS2A01G253500 chr2B 95.647 2343 67 7 8 2328 374258035 374260364 0.000000e+00 3729
6 TraesCS2A01G253500 chr2B 98.462 195 3 0 2324 2518 580796952 580797146 1.810000e-90 344
7 TraesCS2A01G253500 chr5A 98.995 199 2 0 2324 2522 561167027 561167225 2.320000e-94 357
8 TraesCS2A01G253500 chr5A 96.618 207 3 4 2314 2517 355158483 355158688 2.340000e-89 340
9 TraesCS2A01G253500 chr7A 98.477 197 3 0 2322 2518 184334093 184333897 1.400000e-91 348
10 TraesCS2A01G253500 chr6B 97.525 202 1 4 2324 2521 338654709 338654910 6.500000e-90 342
11 TraesCS2A01G253500 chr6A 96.172 209 5 3 2335 2541 310143928 310143721 8.410000e-89 339
12 TraesCS2A01G253500 chr4B 94.954 218 6 5 2329 2545 530887090 530887303 3.020000e-88 337
13 TraesCS2A01G253500 chr1B 94.470 217 7 3 2325 2538 234818398 234818612 5.060000e-86 329


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 TraesCS2A01G253500 chr2A 385444086 385450854 6768 False 12501.0 12501 100.0000 1 6769 1 chr2A.!!$F1 6768
1 TraesCS2A01G253500 chr2D 306339906 306346451 6545 False 5261.5 6905 95.6205 44 6769 2 chr2D.!!$F1 6725
2 TraesCS2A01G253500 chr2B 374258035 374264628 6593 False 5308.0 6887 95.7420 8 6769 2 chr2B.!!$F2 6761

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
457 475 0.440371 CGCTTTGCTTCCGAGTTCTC 59.560 55.0 0.00 0.00 0.00 2.87 F
2400 2439 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.0 19.43 0.00 41.02 2.77 F
2485 2524 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.00 0.00 44.78 4.85 F
2498 2537 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.0 0.00 0.00 38.40 4.00 F
4752 4834 0.252479 AGCTGCACTTCCTGGATGAG 59.748 55.0 15.76 9.29 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 2448 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67 R
4017 4099 1.613630 ACGGAGGCCAGACAAGGAT 60.614 57.895 5.01 0.00 0.00 3.24 R
4752 4834 2.094659 CGGTGTGAGCGTGATGGTC 61.095 63.158 0.00 0.00 45.46 4.02 R
5055 5137 5.871524 TCAATGAACTGAGAGCATTACAGTC 59.128 40.000 0.00 0.00 42.81 3.51 R
6036 6121 0.801067 GACGTGCGGATCAGTACACC 60.801 60.000 13.76 1.76 0.00 4.16 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
135 148 4.606961 ACGCAAAAGACACAATAAAGTGG 58.393 39.130 0.00 0.00 43.72 4.00
372 390 1.905354 GTTGCCTTGCCTTGCCTCT 60.905 57.895 0.00 0.00 0.00 3.69
387 405 1.078567 CTCTCCTGCAACCCAGCTC 60.079 63.158 0.00 0.00 40.36 4.09
388 406 1.834856 CTCTCCTGCAACCCAGCTCA 61.835 60.000 0.00 0.00 40.36 4.26
389 407 1.376942 CTCCTGCAACCCAGCTCAG 60.377 63.158 0.00 0.00 40.36 3.35
390 408 3.060615 CCTGCAACCCAGCTCAGC 61.061 66.667 0.00 0.00 40.36 4.26
391 409 3.060615 CTGCAACCCAGCTCAGCC 61.061 66.667 0.00 0.00 34.21 4.85
392 410 4.666253 TGCAACCCAGCTCAGCCC 62.666 66.667 0.00 0.00 34.99 5.19
393 411 4.666253 GCAACCCAGCTCAGCCCA 62.666 66.667 0.00 0.00 0.00 5.36
394 412 2.115910 CAACCCAGCTCAGCCCAA 59.884 61.111 0.00 0.00 0.00 4.12
395 413 1.304713 CAACCCAGCTCAGCCCAAT 60.305 57.895 0.00 0.00 0.00 3.16
457 475 0.440371 CGCTTTGCTTCCGAGTTCTC 59.560 55.000 0.00 0.00 0.00 2.87
516 534 2.254350 GTTGTTTTCTCCGCCGCC 59.746 61.111 0.00 0.00 0.00 6.13
645 681 4.090588 TTTAGTGGGCGGGGCTCG 62.091 66.667 0.18 0.18 42.76 5.03
672 708 4.451629 TTTTAGTCCTCTTCTACCTGCG 57.548 45.455 0.00 0.00 0.00 5.18
704 740 6.755206 AGGTTAAAAGCTGTGGGTTTTTATC 58.245 36.000 10.37 3.69 46.69 1.75
729 765 5.253330 ACTGTCCTTGTGTTCTTTCTTTGA 58.747 37.500 0.00 0.00 0.00 2.69
750 786 6.092955 TGACAGTTAAGTGTTACACCTAGG 57.907 41.667 16.89 7.41 34.49 3.02
756 792 8.362639 CAGTTAAGTGTTACACCTAGGTTCTTA 58.637 37.037 13.15 10.99 34.49 2.10
808 844 6.124088 AGATTTGGCTCTTAAATTAGTGCG 57.876 37.500 0.00 0.00 35.93 5.34
810 846 2.985896 TGGCTCTTAAATTAGTGCGCT 58.014 42.857 9.73 4.58 35.93 5.92
872 908 3.507622 CCATTTCAGGTTCCAAGGAGTTC 59.492 47.826 0.00 0.00 0.00 3.01
880 919 4.342092 AGGTTCCAAGGAGTTCATTTGTTG 59.658 41.667 0.00 0.00 0.00 3.33
884 923 4.405358 TCCAAGGAGTTCATTTGTTGCTTT 59.595 37.500 0.00 0.00 0.00 3.51
886 925 5.234972 CCAAGGAGTTCATTTGTTGCTTTTC 59.765 40.000 0.00 0.00 0.00 2.29
887 926 4.948847 AGGAGTTCATTTGTTGCTTTTCC 58.051 39.130 0.00 0.00 0.00 3.13
893 932 2.202295 TTTGTTGCTTTTCCGTGAGC 57.798 45.000 0.00 0.00 39.33 4.26
989 1028 4.948004 CCTGTGTGATAGTAGGTACAGTCA 59.052 45.833 0.00 0.00 35.09 3.41
999 1038 1.001406 AGGTACAGTCACAAGCTCAGC 59.999 52.381 0.00 0.00 0.00 4.26
1004 1043 1.065926 CAGTCACAAGCTCAGCCCATA 60.066 52.381 0.00 0.00 0.00 2.74
1341 1380 2.028125 TTGACGGCCATCGGATCTCC 62.028 60.000 2.24 0.00 44.45 3.71
1440 1479 1.152881 CCTCCCTAGCAATGTGGCC 60.153 63.158 0.00 0.00 0.00 5.36
1563 1602 0.955919 CCGGGAACAACTTCTCAGGC 60.956 60.000 0.00 0.00 0.00 4.85
1884 1923 3.385577 AGAACTCAAGTTTCTCGCAGAC 58.614 45.455 0.00 0.00 38.56 3.51
2198 2237 8.434589 TCAGAATTTATGTTTTTGATCCCCTT 57.565 30.769 0.00 0.00 0.00 3.95
2219 2258 7.211573 CCCTTGCTATTTCATTTTATGCATGA 58.788 34.615 10.16 0.00 0.00 3.07
2319 2358 9.846248 CCTGGTTTCTTTCTTTATTTATGTCAG 57.154 33.333 0.00 0.00 0.00 3.51
2320 2359 9.346725 CTGGTTTCTTTCTTTATTTATGTCAGC 57.653 33.333 0.00 0.00 0.00 4.26
2321 2360 9.077885 TGGTTTCTTTCTTTATTTATGTCAGCT 57.922 29.630 0.00 0.00 0.00 4.24
2322 2361 9.346725 GGTTTCTTTCTTTATTTATGTCAGCTG 57.653 33.333 7.63 7.63 0.00 4.24
2357 2396 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2358 2397 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2359 2398 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2360 2399 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2361 2400 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2367 2406 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2368 2407 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2369 2408 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2370 2409 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2373 2412 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2385 2424 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2386 2425 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2387 2426 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2388 2427 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2389 2428 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2390 2429 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2391 2430 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2392 2431 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2393 2432 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2394 2433 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2395 2434 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2396 2435 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2397 2436 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2398 2437 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2399 2438 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2400 2439 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2401 2440 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2402 2441 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2403 2442 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2413 2452 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
2414 2453 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
2415 2454 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
2416 2455 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
2417 2456 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
2418 2457 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
2419 2458 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
2420 2459 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
2421 2460 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
2422 2461 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
2423 2462 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
2424 2463 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
2425 2464 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
2426 2465 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
2427 2466 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
2428 2467 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2429 2468 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2430 2469 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2431 2470 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2432 2471 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2433 2472 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2434 2473 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2435 2474 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2436 2475 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2437 2476 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2438 2477 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2439 2478 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2451 2490 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2452 2491 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2453 2492 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2454 2493 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2455 2494 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2456 2495 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2457 2496 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2458 2497 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2459 2498 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2460 2499 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2461 2500 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2462 2501 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2463 2502 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
2464 2503 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
2465 2504 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
2466 2505 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
2467 2506 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
2468 2507 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
2469 2508 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
2470 2509 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
2471 2510 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
2472 2511 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
2484 2523 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2485 2524 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2486 2525 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2487 2526 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2488 2527 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2489 2528 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2490 2529 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2491 2530 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2492 2531 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2493 2532 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2494 2533 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2495 2534 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2496 2535 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2497 2536 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2498 2537 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2499 2538 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2503 2542 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2504 2543 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2505 2544 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2506 2545 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2507 2546 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2508 2547 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2509 2548 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2510 2549 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2524 2563 2.270434 AGGCTCCCCTTCTTATGTCA 57.730 50.000 0.00 0.00 38.74 3.58
2727 2767 7.044052 GCATTGCCTACAAACTAAATCGATTTC 60.044 37.037 25.89 8.97 39.77 2.17
2916 2958 1.202110 GCATTTCACGCATCTCACCAG 60.202 52.381 0.00 0.00 0.00 4.00
2973 3016 3.340928 TGACATGATGAGAAGCAGGTTG 58.659 45.455 0.00 0.00 0.00 3.77
3030 3079 1.835494 TGACCCAACAAACCAAACGA 58.165 45.000 0.00 0.00 0.00 3.85
3059 3108 9.920133 TTGTTTAAATAAACTGCAATATGCTGA 57.080 25.926 14.84 0.00 43.79 4.26
3060 3109 9.571810 TGTTTAAATAAACTGCAATATGCTGAG 57.428 29.630 14.84 2.65 43.79 3.35
3061 3110 9.787532 GTTTAAATAAACTGCAATATGCTGAGA 57.212 29.630 14.84 1.82 43.79 3.27
3064 3113 4.367386 AAACTGCAATATGCTGAGAAGC 57.633 40.909 14.84 0.00 45.31 3.86
3079 3156 5.582269 GCTGAGAAGCAGTTCATGTGTATTA 59.418 40.000 0.00 0.00 46.62 0.98
3166 3245 5.758784 GGTAGATCATTTACCACTGTAAGGC 59.241 44.000 0.00 0.00 40.26 4.35
3308 3390 1.066645 TGATGCTTCACAGATGCGTCT 60.067 47.619 20.55 1.48 44.05 4.18
3588 3670 1.952296 GATCTACCATTGCTTGCTGGG 59.048 52.381 5.98 2.10 36.82 4.45
3843 3925 2.941720 CCTCAGCTCCAATCAGTTTAGC 59.058 50.000 0.00 0.00 0.00 3.09
4017 4099 3.234353 CAGCCTCCCTGATGATGTAGTA 58.766 50.000 0.00 0.00 44.64 1.82
4752 4834 0.252479 AGCTGCACTTCCTGGATGAG 59.748 55.000 15.76 9.29 0.00 2.90
5055 5137 3.998341 TGGCTAGCTTTTTGTACGGTAAG 59.002 43.478 15.72 0.00 0.00 2.34
5059 5141 5.163982 GCTAGCTTTTTGTACGGTAAGACTG 60.164 44.000 7.70 0.00 0.00 3.51
5169 5254 5.049405 GTCATTAACTCAACCTTCCTGTGTG 60.049 44.000 0.00 0.00 0.00 3.82
5339 5424 2.046892 CTGGACGGCCTTGACCTG 60.047 66.667 9.82 0.00 34.31 4.00
5510 5595 1.066257 CTTTGGTGTTGCGCTGCTT 59.934 52.632 9.73 0.00 0.00 3.91
5561 5646 0.544357 TCATCACGGGGTCTGAAGGT 60.544 55.000 0.00 0.00 0.00 3.50
5744 5829 0.393537 GGCCTGGGATCAAGTCTGTG 60.394 60.000 0.00 0.00 0.00 3.66
5865 5950 1.165270 GTAGGTGTGTGGCATCAACC 58.835 55.000 7.20 7.20 0.00 3.77
5907 5992 1.547372 GCAATGTCTCATTGGTTGCCT 59.453 47.619 19.44 0.00 39.27 4.75
5978 6063 5.880332 TGCAAGTAGATTAGCCAACTTTAGG 59.120 40.000 0.00 0.00 29.93 2.69
6036 6121 6.576662 TCTTCTGTAGTTTACTCCTGTCAG 57.423 41.667 0.00 0.00 0.00 3.51
6124 6210 5.241285 TGATTTGACAGCAGTGCTTATCAAA 59.759 36.000 34.74 34.74 36.40 2.69
6230 6317 4.095483 GGATGAATCTGTAGCCAACTTGTG 59.905 45.833 0.00 0.00 0.00 3.33
6231 6318 4.085357 TGAATCTGTAGCCAACTTGTGT 57.915 40.909 0.00 0.00 0.00 3.72
6403 6496 4.217118 AGGTGCTCAGATTCATCACAAAAC 59.783 41.667 0.00 0.00 0.00 2.43
6422 6515 6.938030 ACAAAACCAAACCTCATTCGTAGATA 59.062 34.615 0.00 0.00 35.04 1.98
6474 6608 1.378250 CTCAGCCAAGCCTTCAGGG 60.378 63.158 0.00 0.00 35.18 4.45
6485 6619 2.497107 CCTTCAGGGCGCATAAAATG 57.503 50.000 10.83 0.00 0.00 2.32
6487 6621 2.033801 CCTTCAGGGCGCATAAAATGAG 59.966 50.000 10.83 0.00 0.00 2.90
6488 6622 2.418368 TCAGGGCGCATAAAATGAGT 57.582 45.000 10.83 0.00 32.30 3.41
6489 6623 2.722094 TCAGGGCGCATAAAATGAGTT 58.278 42.857 10.83 0.00 32.30 3.01
6490 6624 2.423185 TCAGGGCGCATAAAATGAGTTG 59.577 45.455 10.83 0.00 32.30 3.16
6491 6625 2.164219 CAGGGCGCATAAAATGAGTTGT 59.836 45.455 10.83 0.00 32.30 3.32
6492 6626 3.376859 CAGGGCGCATAAAATGAGTTGTA 59.623 43.478 10.83 0.00 32.30 2.41
6493 6627 4.036734 CAGGGCGCATAAAATGAGTTGTAT 59.963 41.667 10.83 0.00 32.30 2.29
6494 6628 4.644685 AGGGCGCATAAAATGAGTTGTATT 59.355 37.500 10.83 0.00 32.30 1.89
6495 6629 4.976116 GGGCGCATAAAATGAGTTGTATTC 59.024 41.667 10.83 0.00 32.30 1.75
6496 6630 5.221048 GGGCGCATAAAATGAGTTGTATTCT 60.221 40.000 10.83 0.00 32.30 2.40
6497 6631 6.017440 GGGCGCATAAAATGAGTTGTATTCTA 60.017 38.462 10.83 0.00 32.30 2.10
6498 6632 7.072030 GGCGCATAAAATGAGTTGTATTCTAG 58.928 38.462 10.83 0.00 32.30 2.43
6499 6633 7.254795 GGCGCATAAAATGAGTTGTATTCTAGT 60.255 37.037 10.83 0.00 32.30 2.57
6500 6634 7.584123 GCGCATAAAATGAGTTGTATTCTAGTG 59.416 37.037 0.30 0.00 32.30 2.74
6501 6635 8.604035 CGCATAAAATGAGTTGTATTCTAGTGT 58.396 33.333 0.00 0.00 0.00 3.55
6510 6644 9.692749 TGAGTTGTATTCTAGTGTTACTTTGAG 57.307 33.333 0.00 0.00 0.00 3.02
6511 6645 9.909644 GAGTTGTATTCTAGTGTTACTTTGAGA 57.090 33.333 0.00 0.00 0.00 3.27
6512 6646 9.694137 AGTTGTATTCTAGTGTTACTTTGAGAC 57.306 33.333 0.00 0.00 0.00 3.36
6513 6647 8.636843 GTTGTATTCTAGTGTTACTTTGAGACG 58.363 37.037 0.00 0.00 0.00 4.18
6552 6686 6.814954 TCCTATCACTTGGCTTTCTCTTAT 57.185 37.500 0.00 0.00 0.00 1.73
6553 6687 7.914427 TCCTATCACTTGGCTTTCTCTTATA 57.086 36.000 0.00 0.00 0.00 0.98
6587 6722 3.380320 AGGTTCTAACAAGCACCACAAAC 59.620 43.478 0.00 0.00 0.00 2.93
6594 6729 1.391157 AAGCACCACAAACGGCACAT 61.391 50.000 0.00 0.00 0.00 3.21
6596 6731 0.386731 GCACCACAAACGGCACATAC 60.387 55.000 0.00 0.00 0.00 2.39
6631 6766 5.235516 AGGAAACAGTCAATAACTACCACG 58.764 41.667 0.00 0.00 36.07 4.94
6687 6822 3.871006 GCCACTCCAAAACAAAAAGAAGG 59.129 43.478 0.00 0.00 0.00 3.46
6690 6825 5.337169 CCACTCCAAAACAAAAAGAAGGACA 60.337 40.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.985847 GCAGTTGTCCACAGGGCC 60.986 66.667 0.00 0.00 0.00 5.80
1 2 2.985847 GGCAGTTGTCCACAGGGC 60.986 66.667 0.00 0.00 0.00 5.19
2 3 1.488705 TAGGGCAGTTGTCCACAGGG 61.489 60.000 5.44 0.00 43.78 4.45
3 4 0.620556 ATAGGGCAGTTGTCCACAGG 59.379 55.000 5.44 0.00 43.78 4.00
4 5 2.496899 AATAGGGCAGTTGTCCACAG 57.503 50.000 5.44 0.00 43.78 3.66
5 6 4.102524 CCTATAATAGGGCAGTTGTCCACA 59.897 45.833 5.44 0.00 43.78 4.17
6 7 4.642429 CCTATAATAGGGCAGTTGTCCAC 58.358 47.826 5.44 0.00 43.78 4.02
135 148 3.382015 TTTTTGTTTTTCTGCTTGCGC 57.618 38.095 0.00 0.00 0.00 6.09
372 390 2.752358 CTGAGCTGGGTTGCAGGA 59.248 61.111 0.00 0.00 34.99 3.86
387 405 0.685131 TGATTGGGCTGATTGGGCTG 60.685 55.000 0.00 0.00 0.00 4.85
388 406 0.263765 ATGATTGGGCTGATTGGGCT 59.736 50.000 0.00 0.00 0.00 5.19
389 407 0.677842 GATGATTGGGCTGATTGGGC 59.322 55.000 0.00 0.00 0.00 5.36
390 408 1.335145 GGATGATTGGGCTGATTGGG 58.665 55.000 0.00 0.00 0.00 4.12
391 409 1.335145 GGGATGATTGGGCTGATTGG 58.665 55.000 0.00 0.00 0.00 3.16
392 410 1.335145 GGGGATGATTGGGCTGATTG 58.665 55.000 0.00 0.00 0.00 2.67
393 411 0.178981 CGGGGATGATTGGGCTGATT 60.179 55.000 0.00 0.00 0.00 2.57
394 412 1.457604 CGGGGATGATTGGGCTGAT 59.542 57.895 0.00 0.00 0.00 2.90
395 413 2.756042 CCGGGGATGATTGGGCTGA 61.756 63.158 0.00 0.00 0.00 4.26
457 475 1.060308 CCTTACCGCGCAAATGACG 59.940 57.895 8.75 0.00 0.00 4.35
495 513 1.285950 GGCGGAGAAAACAACTGGC 59.714 57.895 0.00 0.00 0.00 4.85
516 534 1.097547 AATCCTCGAAATGCAGGGCG 61.098 55.000 0.00 0.00 0.00 6.13
645 681 4.936411 GGTAGAAGAGGACTAAAAAGTGCC 59.064 45.833 0.00 0.00 0.00 5.01
672 708 5.336451 CCCACAGCTTTTAACCTCCAATAAC 60.336 44.000 0.00 0.00 0.00 1.89
704 740 5.567138 AAGAAAGAACACAAGGACAGTTG 57.433 39.130 0.00 0.00 0.00 3.16
729 765 6.325804 AGAACCTAGGTGTAACACTTAACTGT 59.674 38.462 17.14 0.00 39.98 3.55
756 792 7.816411 AGCATCCAGGTAATAATAGGAAAACT 58.184 34.615 0.00 0.00 31.17 2.66
773 809 2.758979 AGCCAAATCTTTGAGCATCCAG 59.241 45.455 14.34 0.00 40.55 3.86
810 846 0.179020 CCACAGGTCCTGCTTTCACA 60.179 55.000 19.40 0.00 34.37 3.58
872 908 2.472488 GCTCACGGAAAAGCAACAAATG 59.528 45.455 0.00 0.00 38.42 2.32
880 919 2.556287 CCACGCTCACGGAAAAGC 59.444 61.111 0.00 0.00 46.04 3.51
884 923 4.680237 CAGCCCACGCTCACGGAA 62.680 66.667 0.00 0.00 43.95 4.30
908 947 0.098376 CTTTCAGCTTGATCTGCGCC 59.902 55.000 4.18 0.00 34.19 6.53
910 949 0.731417 CCCTTTCAGCTTGATCTGCG 59.269 55.000 0.00 0.00 34.19 5.18
989 1028 2.292267 CGAAATATGGGCTGAGCTTGT 58.708 47.619 3.72 0.00 0.00 3.16
999 1038 2.282180 CCCGGGGCGAAATATGGG 60.282 66.667 14.71 0.00 0.00 4.00
1004 1043 2.423064 GCATTTCCCGGGGCGAAAT 61.423 57.895 23.50 16.66 39.87 2.17
1164 1203 3.532155 AGGAGCGCGAGGATGTCC 61.532 66.667 12.10 0.70 0.00 4.02
1284 1323 4.024143 GCGCCATTGCACACGACA 62.024 61.111 0.00 0.00 37.32 4.35
1464 1503 0.320421 ACCGGTTGTTGGAGATGTCG 60.320 55.000 0.00 0.00 0.00 4.35
1563 1602 1.108776 CAATGGAGTCAGGCAATGGG 58.891 55.000 0.00 0.00 0.00 4.00
1647 1686 0.608640 TCCGAAGACCTTTCAGAGCC 59.391 55.000 0.00 0.00 0.00 4.70
1884 1923 9.591792 TTCAGATATACAACTGTCTCTGAAATG 57.408 33.333 19.60 1.51 40.78 2.32
1932 1971 3.404869 ACTCCATCTATCAGTGACCCA 57.595 47.619 0.00 0.00 0.00 4.51
2198 2237 8.582433 CATGTCATGCATAAAATGAAATAGCA 57.418 30.769 0.00 0.00 35.87 3.49
2329 2368 4.518249 CACCAGGTTGCCCTTTTTAAAAA 58.482 39.130 12.62 12.62 39.89 1.94
2330 2369 3.682999 GCACCAGGTTGCCCTTTTTAAAA 60.683 43.478 0.00 0.00 39.89 1.52
2331 2370 2.158885 GCACCAGGTTGCCCTTTTTAAA 60.159 45.455 0.00 0.00 39.89 1.52
2332 2371 1.414550 GCACCAGGTTGCCCTTTTTAA 59.585 47.619 0.00 0.00 39.89 1.52
2333 2372 1.044611 GCACCAGGTTGCCCTTTTTA 58.955 50.000 0.00 0.00 39.89 1.52
2334 2373 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
2335 2374 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2336 2375 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2337 2376 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2338 2377 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2339 2378 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2340 2379 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2341 2380 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2342 2381 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2343 2382 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2368 2407 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2369 2408 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2370 2409 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2371 2410 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2372 2411 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2373 2412 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2374 2413 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2375 2414 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2376 2415 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2377 2416 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2378 2417 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2379 2418 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2380 2419 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2381 2420 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2382 2421 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2383 2422 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2384 2423 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2385 2424 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2386 2425 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2387 2426 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2392 2431 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
2393 2432 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
2394 2433 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
2395 2434 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
2396 2435 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
2397 2436 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
2398 2437 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
2399 2438 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
2400 2439 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
2401 2440 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
2402 2441 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
2403 2442 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
2404 2443 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
2405 2444 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
2406 2445 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
2407 2446 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
2408 2447 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
2409 2448 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2410 2449 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2411 2450 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2412 2451 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2413 2452 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2414 2453 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2415 2454 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2416 2455 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2417 2456 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2418 2457 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2419 2458 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2420 2459 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2421 2460 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2422 2461 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2423 2462 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2424 2463 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2425 2464 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2426 2465 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2427 2466 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2428 2467 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2429 2468 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2443 2482 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
2444 2483 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
2445 2484 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
2446 2485 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
2447 2486 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
2448 2487 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
2449 2488 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
2450 2489 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
2451 2490 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
2452 2491 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
2467 2506 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2468 2507 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2469 2508 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2470 2509 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2471 2510 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2472 2511 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2473 2512 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2474 2513 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2475 2514 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2476 2515 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2477 2516 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2478 2517 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2479 2518 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2480 2519 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2481 2520 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2486 2525 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2487 2526 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2488 2527 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2489 2528 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2490 2529 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2491 2530 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2492 2531 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2500 2539 1.910580 TAAGAAGGGGAGCCTTGGCG 61.911 60.000 5.95 0.00 0.00 5.69
2501 2540 0.553333 ATAAGAAGGGGAGCCTTGGC 59.447 55.000 2.97 2.97 0.00 4.52
2502 2541 1.566231 ACATAAGAAGGGGAGCCTTGG 59.434 52.381 0.00 0.00 0.00 3.61
2503 2542 2.239654 TGACATAAGAAGGGGAGCCTTG 59.760 50.000 0.00 0.00 0.00 3.61
2504 2543 2.507471 CTGACATAAGAAGGGGAGCCTT 59.493 50.000 0.00 0.00 0.00 4.35
2505 2544 2.122768 CTGACATAAGAAGGGGAGCCT 58.877 52.381 0.00 0.00 0.00 4.58
2506 2545 1.475930 GCTGACATAAGAAGGGGAGCC 60.476 57.143 0.00 0.00 0.00 4.70
2507 2546 1.488393 AGCTGACATAAGAAGGGGAGC 59.512 52.381 0.00 0.00 0.00 4.70
2508 2547 2.768527 TCAGCTGACATAAGAAGGGGAG 59.231 50.000 13.74 0.00 0.00 4.30
2509 2548 2.832838 TCAGCTGACATAAGAAGGGGA 58.167 47.619 13.74 0.00 0.00 4.81
2510 2549 3.853355 ATCAGCTGACATAAGAAGGGG 57.147 47.619 20.97 0.00 0.00 4.79
2511 2550 5.416952 ACAAAATCAGCTGACATAAGAAGGG 59.583 40.000 20.97 3.23 0.00 3.95
2512 2551 6.506500 ACAAAATCAGCTGACATAAGAAGG 57.493 37.500 20.97 4.57 0.00 3.46
2513 2552 9.499585 CATAACAAAATCAGCTGACATAAGAAG 57.500 33.333 20.97 6.44 0.00 2.85
2514 2553 9.230122 TCATAACAAAATCAGCTGACATAAGAA 57.770 29.630 20.97 3.44 0.00 2.52
2515 2554 8.668353 GTCATAACAAAATCAGCTGACATAAGA 58.332 33.333 20.97 5.78 33.49 2.10
2516 2555 8.453320 TGTCATAACAAAATCAGCTGACATAAG 58.547 33.333 20.97 10.79 37.27 1.73
2517 2556 8.334263 TGTCATAACAAAATCAGCTGACATAA 57.666 30.769 20.97 0.00 37.27 1.90
2518 2557 7.920160 TGTCATAACAAAATCAGCTGACATA 57.080 32.000 20.97 6.50 37.27 2.29
2519 2558 6.822667 TGTCATAACAAAATCAGCTGACAT 57.177 33.333 20.97 8.45 37.27 3.06
2520 2559 6.631971 TTGTCATAACAAAATCAGCTGACA 57.368 33.333 20.97 5.70 42.34 3.58
2635 2674 7.514784 TGTGATTCTGAACAGACAATTTGAT 57.485 32.000 2.79 0.00 37.14 2.57
2721 2760 4.003648 AGTAGTTGCAAAGGAGGAAATCG 58.996 43.478 0.00 0.00 0.00 3.34
2727 2767 4.082571 CCAATCAAGTAGTTGCAAAGGAGG 60.083 45.833 0.00 0.00 33.23 4.30
2904 2946 2.898729 AATAGGTCTGGTGAGATGCG 57.101 50.000 0.00 0.00 0.00 4.73
2910 2952 4.962362 TCAGCAATCTAATAGGTCTGGTGA 59.038 41.667 10.98 10.98 38.55 4.02
3057 3106 5.874810 GGTAATACACATGAACTGCTTCTCA 59.125 40.000 0.00 0.00 0.00 3.27
3058 3107 5.874810 TGGTAATACACATGAACTGCTTCTC 59.125 40.000 0.00 0.00 0.00 2.87
3059 3108 5.804639 TGGTAATACACATGAACTGCTTCT 58.195 37.500 0.00 0.00 0.00 2.85
3060 3109 6.683974 ATGGTAATACACATGAACTGCTTC 57.316 37.500 0.00 0.00 0.00 3.86
3061 3110 7.829211 ACTAATGGTAATACACATGAACTGCTT 59.171 33.333 0.00 0.00 0.00 3.91
3062 3111 7.338710 ACTAATGGTAATACACATGAACTGCT 58.661 34.615 0.00 0.00 0.00 4.24
3079 3156 4.475016 ACCCAGCAGAAGATTACTAATGGT 59.525 41.667 0.00 0.00 0.00 3.55
3166 3245 1.482182 TGCATACTGTAGGCCACTCTG 59.518 52.381 20.20 1.22 33.95 3.35
3588 3670 3.244033 AGATCTAACACAGTGCAGCTC 57.756 47.619 0.00 0.00 0.00 4.09
3843 3925 4.767928 AGTAGATTAGCAGGAATAGGACCG 59.232 45.833 0.00 0.00 0.00 4.79
4017 4099 1.613630 ACGGAGGCCAGACAAGGAT 60.614 57.895 5.01 0.00 0.00 3.24
4752 4834 2.094659 CGGTGTGAGCGTGATGGTC 61.095 63.158 0.00 0.00 45.46 4.02
5055 5137 5.871524 TCAATGAACTGAGAGCATTACAGTC 59.128 40.000 0.00 0.00 42.81 3.51
5059 5141 7.148188 TGGAAATCAATGAACTGAGAGCATTAC 60.148 37.037 4.75 0.00 31.54 1.89
5153 5238 4.008074 ACATACACACAGGAAGGTTGAG 57.992 45.455 0.00 0.00 0.00 3.02
5163 5248 4.809673 TCTGCTCAGTAACATACACACAG 58.190 43.478 0.00 0.00 0.00 3.66
5169 5254 3.053455 GCCGATCTGCTCAGTAACATAC 58.947 50.000 1.31 0.00 0.00 2.39
5191 5276 4.095400 GAGGGCCTCTCCTCCCCA 62.095 72.222 26.44 0.00 45.75 4.96
5510 5595 3.385384 CGGCCAGTCAGGAGCTCA 61.385 66.667 17.19 0.00 41.22 4.26
5744 5829 6.584563 GCTAGATTGATGAAAGATCCTCGTAC 59.415 42.308 0.00 0.00 0.00 3.67
5865 5950 1.817357 TCTGAACTTGCAGGCATCAG 58.183 50.000 19.97 19.97 39.04 2.90
5907 5992 1.373246 GTACAACACGGCGGCACTA 60.373 57.895 13.24 0.00 0.00 2.74
6036 6121 0.801067 GACGTGCGGATCAGTACACC 60.801 60.000 13.76 1.76 0.00 4.16
6230 6317 3.255888 GGTTTCCCTCCAATTCAGTGAAC 59.744 47.826 7.96 0.00 0.00 3.18
6231 6318 3.496331 GGTTTCCCTCCAATTCAGTGAA 58.504 45.455 8.27 8.27 0.00 3.18
6403 6496 5.914033 TCCTTATCTACGAATGAGGTTTGG 58.086 41.667 0.00 0.00 34.74 3.28
6474 6608 7.584123 CACTAGAATACAACTCATTTTATGCGC 59.416 37.037 0.00 0.00 0.00 6.09
6475 6609 8.604035 ACACTAGAATACAACTCATTTTATGCG 58.396 33.333 0.00 0.00 0.00 4.73
6484 6618 9.692749 CTCAAAGTAACACTAGAATACAACTCA 57.307 33.333 0.00 0.00 0.00 3.41
6485 6619 9.909644 TCTCAAAGTAACACTAGAATACAACTC 57.090 33.333 0.00 0.00 0.00 3.01
6487 6621 8.636843 CGTCTCAAAGTAACACTAGAATACAAC 58.363 37.037 0.00 0.00 0.00 3.32
6488 6622 8.570488 TCGTCTCAAAGTAACACTAGAATACAA 58.430 33.333 0.00 0.00 0.00 2.41
6489 6623 8.019669 GTCGTCTCAAAGTAACACTAGAATACA 58.980 37.037 0.00 0.00 0.00 2.29
6490 6624 8.235905 AGTCGTCTCAAAGTAACACTAGAATAC 58.764 37.037 0.00 0.00 0.00 1.89
6491 6625 8.235226 CAGTCGTCTCAAAGTAACACTAGAATA 58.765 37.037 0.00 0.00 0.00 1.75
6492 6626 7.085116 CAGTCGTCTCAAAGTAACACTAGAAT 58.915 38.462 0.00 0.00 0.00 2.40
6493 6627 6.436261 CAGTCGTCTCAAAGTAACACTAGAA 58.564 40.000 0.00 0.00 0.00 2.10
6494 6628 5.562307 GCAGTCGTCTCAAAGTAACACTAGA 60.562 44.000 0.00 0.00 0.00 2.43
6495 6629 4.617645 GCAGTCGTCTCAAAGTAACACTAG 59.382 45.833 0.00 0.00 0.00 2.57
6496 6630 4.037089 TGCAGTCGTCTCAAAGTAACACTA 59.963 41.667 0.00 0.00 0.00 2.74
6497 6631 3.181479 TGCAGTCGTCTCAAAGTAACACT 60.181 43.478 0.00 0.00 0.00 3.55
6498 6632 3.120792 TGCAGTCGTCTCAAAGTAACAC 58.879 45.455 0.00 0.00 0.00 3.32
6499 6633 3.446310 TGCAGTCGTCTCAAAGTAACA 57.554 42.857 0.00 0.00 0.00 2.41
6500 6634 4.992381 ATTGCAGTCGTCTCAAAGTAAC 57.008 40.909 0.00 0.00 0.00 2.50
6501 6635 6.310467 GTCATATTGCAGTCGTCTCAAAGTAA 59.690 38.462 0.00 0.00 0.00 2.24
6502 6636 5.805486 GTCATATTGCAGTCGTCTCAAAGTA 59.195 40.000 0.00 0.00 0.00 2.24
6503 6637 4.627467 GTCATATTGCAGTCGTCTCAAAGT 59.373 41.667 0.00 0.00 0.00 2.66
6504 6638 4.627035 TGTCATATTGCAGTCGTCTCAAAG 59.373 41.667 0.00 0.00 0.00 2.77
6505 6639 4.565022 TGTCATATTGCAGTCGTCTCAAA 58.435 39.130 0.00 0.00 0.00 2.69
6506 6640 4.186856 TGTCATATTGCAGTCGTCTCAA 57.813 40.909 0.00 0.00 0.00 3.02
6507 6641 3.866883 TGTCATATTGCAGTCGTCTCA 57.133 42.857 0.00 0.00 0.00 3.27
6508 6642 4.210120 GGATTGTCATATTGCAGTCGTCTC 59.790 45.833 0.00 0.00 0.00 3.36
6509 6643 4.122776 GGATTGTCATATTGCAGTCGTCT 58.877 43.478 0.00 0.00 0.00 4.18
6510 6644 4.122776 AGGATTGTCATATTGCAGTCGTC 58.877 43.478 0.00 0.00 0.00 4.20
6511 6645 4.142609 AGGATTGTCATATTGCAGTCGT 57.857 40.909 0.00 0.00 0.00 4.34
6512 6646 5.928264 TGATAGGATTGTCATATTGCAGTCG 59.072 40.000 0.00 0.00 0.00 4.18
6513 6647 6.933521 AGTGATAGGATTGTCATATTGCAGTC 59.066 38.462 0.00 0.00 0.00 3.51
6552 6686 4.283467 TGTTAGAACCTGCAAGAGAAGCTA 59.717 41.667 0.00 0.00 34.07 3.32
6553 6687 3.071602 TGTTAGAACCTGCAAGAGAAGCT 59.928 43.478 0.00 0.00 34.07 3.74
6587 6722 3.513680 TGGTTAGTAGTGTATGTGCCG 57.486 47.619 0.00 0.00 0.00 5.69
6594 6729 6.324512 TGACTGTTTCCTTGGTTAGTAGTGTA 59.675 38.462 0.00 0.00 0.00 2.90
6596 6731 5.607477 TGACTGTTTCCTTGGTTAGTAGTG 58.393 41.667 0.00 0.00 0.00 2.74
6631 6766 2.985896 TGAGCTGGTATTTGGTGTAGC 58.014 47.619 0.00 0.00 0.00 3.58
6687 6822 4.162320 TCTGGATTAGAGGAACATGGTGTC 59.838 45.833 0.00 0.00 0.00 3.67
6690 6825 5.222870 AGATCTGGATTAGAGGAACATGGT 58.777 41.667 0.00 0.00 39.20 3.55


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

AutoCloner maintained by Alex Coulton.