Multiple sequence alignment - TraesCS6A01G256400

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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 TraesCS6A01G256400 chr6A 100.000 3719 0 0 1 3719 475998944 476002662 0.000000e+00 6868.0
1 TraesCS6A01G256400 chr6D 92.871 3521 132 45 1 3451 336365237 336368708 0.000000e+00 5001.0
2 TraesCS6A01G256400 chr6B 93.154 3082 154 27 74 3112 484102089 484099022 0.000000e+00 4470.0
3 TraesCS6A01G256400 chr6B 87.395 357 31 8 3102 3455 484090840 484090495 7.480000e-107 398.0
4 TraesCS6A01G256400 chr2A 84.525 1454 223 2 1122 2574 653000214 653001666 0.000000e+00 1437.0
5 TraesCS6A01G256400 chr2D 84.240 1453 229 0 1122 2574 509229376 509230828 0.000000e+00 1415.0
6 TraesCS6A01G256400 chr2B 84.033 1453 232 0 1122 2574 598560814 598562266 0.000000e+00 1399.0
7 TraesCS6A01G256400 chr1A 74.728 1377 276 59 1242 2576 339915564 339914218 1.950000e-152 549.0
8 TraesCS6A01G256400 chr1D 74.419 1376 282 57 1242 2576 260588577 260589923 9.150000e-146 527.0
9 TraesCS6A01G256400 chr5D 73.761 545 115 24 1253 1783 412076948 412077478 4.900000e-44 189.0
10 TraesCS6A01G256400 chr5D 100.000 29 0 0 222 250 519629008 519629036 2.000000e-03 54.7
11 TraesCS6A01G256400 chr5A 73.713 544 117 23 1253 1783 523815649 523816179 4.900000e-44 189.0
12 TraesCS6A01G256400 chr5B 73.162 544 120 22 1253 1783 495019861 495020391 4.940000e-39 172.0
13 TraesCS6A01G256400 chr7D 76.733 202 47 0 1265 1466 255059139 255058938 3.040000e-21 113.0


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 TraesCS6A01G256400 chr6A 475998944 476002662 3718 False 6868 6868 100.000 1 3719 1 chr6A.!!$F1 3718
1 TraesCS6A01G256400 chr6D 336365237 336368708 3471 False 5001 5001 92.871 1 3451 1 chr6D.!!$F1 3450
2 TraesCS6A01G256400 chr6B 484099022 484102089 3067 True 4470 4470 93.154 74 3112 1 chr6B.!!$R2 3038
3 TraesCS6A01G256400 chr2A 653000214 653001666 1452 False 1437 1437 84.525 1122 2574 1 chr2A.!!$F1 1452
4 TraesCS6A01G256400 chr2D 509229376 509230828 1452 False 1415 1415 84.240 1122 2574 1 chr2D.!!$F1 1452
5 TraesCS6A01G256400 chr2B 598560814 598562266 1452 False 1399 1399 84.033 1122 2574 1 chr2B.!!$F1 1452
6 TraesCS6A01G256400 chr1A 339914218 339915564 1346 True 549 549 74.728 1242 2576 1 chr1A.!!$R1 1334
7 TraesCS6A01G256400 chr1D 260588577 260589923 1346 False 527 527 74.419 1242 2576 1 chr1D.!!$F1 1334

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
45 46 0.038159 CTAACGATCGATGCCTCCCC 60.038 60.000 24.34 0.0 0.00 4.81 F
765 826 0.462759 CTCACCTTCCTTCATCGGCC 60.463 60.000 0.00 0.0 0.00 6.13 F
960 1021 1.077068 CTCTCCCTCCTGAGCTCGT 60.077 63.158 9.64 0.0 32.22 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1113 2.358615 GATGCCATCGCCCGCATA 60.359 61.111 3.39 0.0 45.52 3.14 R
2598 2672 1.082756 GCTGCTCGGTTTTGTGTCG 60.083 57.895 0.00 0.0 0.00 4.35 R
2952 3033 0.179119 GCCATGCTCACTTTGATGCC 60.179 55.000 0.00 0.0 0.00 4.40 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
33 34 2.158579 ACCAACAAACCCCACTAACGAT 60.159 45.455 0.00 0.00 0.00 3.73
34 35 2.486592 CCAACAAACCCCACTAACGATC 59.513 50.000 0.00 0.00 0.00 3.69
35 36 2.088950 ACAAACCCCACTAACGATCG 57.911 50.000 14.88 14.88 0.00 3.69
36 37 1.619827 ACAAACCCCACTAACGATCGA 59.380 47.619 24.34 0.00 0.00 3.59
38 39 2.596904 AACCCCACTAACGATCGATG 57.403 50.000 24.34 13.47 0.00 3.84
41 42 0.389391 CCCACTAACGATCGATGCCT 59.611 55.000 24.34 0.00 0.00 4.75
42 43 1.603172 CCCACTAACGATCGATGCCTC 60.603 57.143 24.34 0.00 0.00 4.70
43 44 1.603172 CCACTAACGATCGATGCCTCC 60.603 57.143 24.34 0.00 0.00 4.30
44 45 0.674534 ACTAACGATCGATGCCTCCC 59.325 55.000 24.34 0.00 0.00 4.30
45 46 0.038159 CTAACGATCGATGCCTCCCC 60.038 60.000 24.34 0.00 0.00 4.81
61 66 1.554471 CCCCTAGCTACCCTCCCAT 59.446 63.158 0.00 0.00 0.00 4.00
65 70 2.695585 CCTAGCTACCCTCCCATTCTT 58.304 52.381 0.00 0.00 0.00 2.52
156 174 0.735978 TATCAGCGGTTCAGCACACG 60.736 55.000 0.00 0.00 40.15 4.49
157 175 2.715532 ATCAGCGGTTCAGCACACGT 62.716 55.000 0.00 0.00 40.15 4.49
199 217 6.238759 GGTCAGATGGTTATGTTCTTTATGGC 60.239 42.308 0.00 0.00 0.00 4.40
200 218 6.318648 GTCAGATGGTTATGTTCTTTATGGCA 59.681 38.462 0.00 0.00 0.00 4.92
222 267 3.627577 AGAACTTAGTGTTGGTGCTTGTG 59.372 43.478 0.00 0.00 39.30 3.33
248 293 2.697431 TTTCAGTTTTTCCGGCGATG 57.303 45.000 9.30 0.00 0.00 3.84
256 301 1.600023 TTTCCGGCGATGTTTGTTCT 58.400 45.000 9.30 0.00 0.00 3.01
264 309 3.059884 GCGATGTTTGTTCTGTGAGAGA 58.940 45.455 0.00 0.00 0.00 3.10
266 311 4.550422 CGATGTTTGTTCTGTGAGAGAGA 58.450 43.478 0.00 0.00 30.18 3.10
276 321 2.232452 CTGTGAGAGAGAATGTCCCGTT 59.768 50.000 0.00 0.00 0.00 4.44
283 328 5.014858 AGAGAGAATGTCCCGTTAACTACA 58.985 41.667 3.71 5.97 0.00 2.74
284 329 5.479375 AGAGAGAATGTCCCGTTAACTACAA 59.521 40.000 3.71 0.00 0.00 2.41
288 333 4.628963 ATGTCCCGTTAACTACAAAGGT 57.371 40.909 3.71 0.00 0.00 3.50
422 467 5.339085 GCTTGTATGTATTAGCGTCTACGTC 59.661 44.000 4.24 0.00 42.22 4.34
663 712 2.357517 CGCAGCCGAAGACAAGGT 60.358 61.111 0.00 0.00 36.29 3.50
765 826 0.462759 CTCACCTTCCTTCATCGGCC 60.463 60.000 0.00 0.00 0.00 6.13
853 914 1.438651 TTCTTCTGCCAACGATTCCG 58.561 50.000 0.00 0.00 42.50 4.30
960 1021 1.077068 CTCTCCCTCCTGAGCTCGT 60.077 63.158 9.64 0.00 32.22 4.18
965 1026 2.183811 CTCCTGAGCTCGTGCCAG 59.816 66.667 9.64 16.25 40.80 4.85
966 1027 4.074526 TCCTGAGCTCGTGCCAGC 62.075 66.667 9.64 4.41 40.80 4.85
1030 1092 3.299977 CCGACTCCACGGTCACCA 61.300 66.667 0.00 0.00 46.70 4.17
1041 1103 1.153706 GGTCACCATGTCGTACCGG 60.154 63.158 0.00 0.00 0.00 5.28
1088 1150 4.079961 GGCCCCTTTGCTCCCCAT 62.080 66.667 0.00 0.00 0.00 4.00
1089 1151 2.039462 GCCCCTTTGCTCCCCATT 59.961 61.111 0.00 0.00 0.00 3.16
1639 1701 4.787280 CCTCCCTGCCGGACCTCT 62.787 72.222 5.05 0.00 34.86 3.69
1953 2027 4.731612 CTGCCGAGCTGCGTCAGT 62.732 66.667 0.00 0.00 40.81 3.41
2053 2127 2.444388 TCCATGGGAATCTTGATCCAGG 59.556 50.000 13.02 0.00 38.80 4.45
2055 2129 1.600058 TGGGAATCTTGATCCAGGCT 58.400 50.000 0.00 0.00 38.80 4.58
2218 2292 2.877113 CATCGGCGTTCGCGTACA 60.877 61.111 16.24 0.00 43.62 2.90
2818 2893 6.634436 GCTGACAGAGTGACAATTTTTGTTAG 59.366 38.462 6.65 4.63 45.52 2.34
2952 3033 5.289675 CAGACTTCCTCACATTACTTTAGCG 59.710 44.000 0.00 0.00 0.00 4.26
2976 3057 0.896940 CAAAGTGAGCATGGCTGGGT 60.897 55.000 0.00 0.00 39.88 4.51
2977 3058 0.698238 AAAGTGAGCATGGCTGGGTA 59.302 50.000 0.00 0.00 39.88 3.69
2995 3076 5.268387 TGGGTATAGAATTTGTGGTTGCAT 58.732 37.500 0.00 0.00 0.00 3.96
3013 3094 0.544833 ATTTGCAGCCACCCCATGAA 60.545 50.000 0.00 0.00 0.00 2.57
3052 3133 1.205893 ACAACCAACAATGTGCCGTTT 59.794 42.857 0.00 0.00 0.00 3.60
3152 3233 2.936498 ACGCATTGGGAACTAGAATTCG 59.064 45.455 7.82 0.00 0.00 3.34
3181 3262 1.849823 GCAGGCTCCCATATCCCCT 60.850 63.158 0.00 0.00 0.00 4.79
3182 3263 1.846712 GCAGGCTCCCATATCCCCTC 61.847 65.000 0.00 0.00 0.00 4.30
3183 3264 0.178879 CAGGCTCCCATATCCCCTCT 60.179 60.000 0.00 0.00 0.00 3.69
3185 3266 1.802117 AGGCTCCCATATCCCCTCTTA 59.198 52.381 0.00 0.00 0.00 2.10
3208 3289 9.458374 CTTATATCGTTCAAAAGTGTGGTTTTT 57.542 29.630 0.00 0.00 0.00 1.94
3246 3327 1.884579 ACAGCACCATGAAGAAGCTTG 59.115 47.619 2.10 0.00 32.35 4.01
3247 3328 1.884579 CAGCACCATGAAGAAGCTTGT 59.115 47.619 2.10 0.00 32.35 3.16
3359 3445 2.328099 GCAACCGGCAGGAGTTCTG 61.328 63.158 10.86 0.00 46.03 3.02
3362 3448 2.046892 CCGGCAGGAGTTCTGGTG 60.047 66.667 0.00 0.00 43.54 4.17
3380 3469 9.573133 GTTCTGGTGTTTCATTAAGATAATTGG 57.427 33.333 0.00 0.00 0.00 3.16
3408 3497 8.793592 CAGTTTATAAGGAAACTAACCAAAGCT 58.206 33.333 1.47 0.00 45.70 3.74
3410 3499 8.573885 GTTTATAAGGAAACTAACCAAAGCTGT 58.426 33.333 0.00 0.00 42.68 4.40
3416 3505 5.975344 GGAAACTAACCAAAGCTGTTACAAC 59.025 40.000 0.00 0.00 0.00 3.32
3421 3510 4.705337 ACCAAAGCTGTTACAACGAAAA 57.295 36.364 0.00 0.00 0.00 2.29
3433 3522 0.517755 AACGAAAACACGCACACACA 59.482 45.000 0.00 0.00 36.70 3.72
3434 3523 0.179210 ACGAAAACACGCACACACAC 60.179 50.000 0.00 0.00 36.70 3.82
3435 3524 0.859788 CGAAAACACGCACACACACC 60.860 55.000 0.00 0.00 0.00 4.16
3436 3525 0.169230 GAAAACACGCACACACACCA 59.831 50.000 0.00 0.00 0.00 4.17
3437 3526 0.170116 AAAACACGCACACACACCAG 59.830 50.000 0.00 0.00 0.00 4.00
3443 3532 3.289834 CACACACACCAGCCCTGC 61.290 66.667 0.00 0.00 0.00 4.85
3444 3533 4.935495 ACACACACCAGCCCTGCG 62.935 66.667 0.00 0.00 0.00 5.18
3463 3552 3.164269 CTGCCTACCCGGAGCCAT 61.164 66.667 0.73 0.00 33.16 4.40
3464 3553 3.466791 CTGCCTACCCGGAGCCATG 62.467 68.421 0.73 0.00 33.16 3.66
3465 3554 3.161450 GCCTACCCGGAGCCATGA 61.161 66.667 0.73 0.00 33.16 3.07
3466 3555 2.822399 CCTACCCGGAGCCATGAC 59.178 66.667 0.73 0.00 33.16 3.06
3467 3556 2.417516 CTACCCGGAGCCATGACG 59.582 66.667 0.73 0.00 0.00 4.35
3468 3557 2.043752 TACCCGGAGCCATGACGA 60.044 61.111 0.73 0.00 0.00 4.20
3469 3558 2.351336 CTACCCGGAGCCATGACGAC 62.351 65.000 0.73 0.00 0.00 4.34
3470 3559 4.530857 CCCGGAGCCATGACGACC 62.531 72.222 0.73 0.00 0.00 4.79
3471 3560 4.530857 CCGGAGCCATGACGACCC 62.531 72.222 0.00 0.00 0.00 4.46
3472 3561 4.530857 CGGAGCCATGACGACCCC 62.531 72.222 0.00 0.00 0.00 4.95
3473 3562 4.530857 GGAGCCATGACGACCCCG 62.531 72.222 0.00 0.00 42.50 5.73
3477 3566 4.096003 CCATGACGACCCCGCCTT 62.096 66.667 0.00 0.00 39.95 4.35
3478 3567 2.727392 CCATGACGACCCCGCCTTA 61.727 63.158 0.00 0.00 39.95 2.69
3479 3568 1.520787 CATGACGACCCCGCCTTAC 60.521 63.158 0.00 0.00 39.95 2.34
3480 3569 1.985662 ATGACGACCCCGCCTTACA 60.986 57.895 0.00 0.00 39.95 2.41
3481 3570 1.546589 ATGACGACCCCGCCTTACAA 61.547 55.000 0.00 0.00 39.95 2.41
3482 3571 1.004679 GACGACCCCGCCTTACAAA 60.005 57.895 0.00 0.00 39.95 2.83
3483 3572 1.293963 GACGACCCCGCCTTACAAAC 61.294 60.000 0.00 0.00 39.95 2.93
3484 3573 2.036571 CGACCCCGCCTTACAAACC 61.037 63.158 0.00 0.00 0.00 3.27
3485 3574 1.377612 GACCCCGCCTTACAAACCT 59.622 57.895 0.00 0.00 0.00 3.50
3486 3575 0.614812 GACCCCGCCTTACAAACCTA 59.385 55.000 0.00 0.00 0.00 3.08
3487 3576 1.003464 GACCCCGCCTTACAAACCTAA 59.997 52.381 0.00 0.00 0.00 2.69
3488 3577 1.003928 ACCCCGCCTTACAAACCTAAG 59.996 52.381 0.00 0.00 0.00 2.18
3489 3578 1.092348 CCCGCCTTACAAACCTAAGC 58.908 55.000 0.00 0.00 0.00 3.09
3490 3579 1.612199 CCCGCCTTACAAACCTAAGCA 60.612 52.381 0.00 0.00 0.00 3.91
3491 3580 2.156098 CCGCCTTACAAACCTAAGCAA 58.844 47.619 0.00 0.00 0.00 3.91
3492 3581 2.095415 CCGCCTTACAAACCTAAGCAAC 60.095 50.000 0.00 0.00 0.00 4.17
3493 3582 2.412325 CGCCTTACAAACCTAAGCAACG 60.412 50.000 0.00 0.00 0.00 4.10
3494 3583 2.667448 GCCTTACAAACCTAAGCAACGC 60.667 50.000 0.00 0.00 0.00 4.84
3495 3584 2.550606 CCTTACAAACCTAAGCAACGCA 59.449 45.455 0.00 0.00 0.00 5.24
3496 3585 3.551551 CTTACAAACCTAAGCAACGCAC 58.448 45.455 0.00 0.00 0.00 5.34
3497 3586 1.384525 ACAAACCTAAGCAACGCACA 58.615 45.000 0.00 0.00 0.00 4.57
3498 3587 1.953686 ACAAACCTAAGCAACGCACAT 59.046 42.857 0.00 0.00 0.00 3.21
3499 3588 2.360801 ACAAACCTAAGCAACGCACATT 59.639 40.909 0.00 0.00 0.00 2.71
3500 3589 2.979813 CAAACCTAAGCAACGCACATTC 59.020 45.455 0.00 0.00 0.00 2.67
3501 3590 2.185004 ACCTAAGCAACGCACATTCT 57.815 45.000 0.00 0.00 0.00 2.40
3502 3591 2.504367 ACCTAAGCAACGCACATTCTT 58.496 42.857 0.00 0.00 0.00 2.52
3503 3592 2.484264 ACCTAAGCAACGCACATTCTTC 59.516 45.455 0.00 0.00 0.00 2.87
3504 3593 2.474526 CCTAAGCAACGCACATTCTTCG 60.475 50.000 0.00 0.00 0.00 3.79
3505 3594 0.385974 AAGCAACGCACATTCTTCGC 60.386 50.000 0.00 0.00 0.00 4.70
3506 3595 1.797537 GCAACGCACATTCTTCGCC 60.798 57.895 0.00 0.00 0.00 5.54
3507 3596 1.154225 CAACGCACATTCTTCGCCC 60.154 57.895 0.00 0.00 0.00 6.13
3508 3597 2.332654 AACGCACATTCTTCGCCCC 61.333 57.895 0.00 0.00 0.00 5.80
3509 3598 3.864686 CGCACATTCTTCGCCCCG 61.865 66.667 0.00 0.00 0.00 5.73
3510 3599 2.435938 GCACATTCTTCGCCCCGA 60.436 61.111 0.00 0.00 0.00 5.14
3511 3600 2.464459 GCACATTCTTCGCCCCGAG 61.464 63.158 0.00 0.00 37.14 4.63
3512 3601 1.815421 CACATTCTTCGCCCCGAGG 60.815 63.158 0.00 0.00 37.14 4.63
3513 3602 2.291043 ACATTCTTCGCCCCGAGGT 61.291 57.895 0.00 0.00 37.14 3.85
3514 3603 1.521681 CATTCTTCGCCCCGAGGTC 60.522 63.158 0.00 0.00 37.14 3.85
3515 3604 3.077519 ATTCTTCGCCCCGAGGTCG 62.078 63.158 0.00 0.00 37.14 4.79
3517 3606 4.796231 CTTCGCCCCGAGGTCGTG 62.796 72.222 0.00 0.00 37.14 4.35
3535 3624 4.717629 CTCCGCACAAGCCGACGA 62.718 66.667 0.00 0.00 37.52 4.20
3538 3627 2.126618 CGCACAAGCCGACGACTA 60.127 61.111 0.00 0.00 37.52 2.59
3539 3628 2.152699 CGCACAAGCCGACGACTAG 61.153 63.158 0.00 0.00 37.52 2.57
3540 3629 2.445438 GCACAAGCCGACGACTAGC 61.445 63.158 0.00 0.00 33.58 3.42
3542 3631 3.248171 CAAGCCGACGACTAGCGC 61.248 66.667 0.00 0.00 46.04 5.92
3543 3632 3.441290 AAGCCGACGACTAGCGCT 61.441 61.111 17.26 17.26 46.04 5.92
3544 3633 2.110967 AAGCCGACGACTAGCGCTA 61.111 57.895 17.75 17.75 46.04 4.26
3545 3634 1.651240 AAGCCGACGACTAGCGCTAA 61.651 55.000 19.37 2.45 46.04 3.09
3546 3635 1.008767 GCCGACGACTAGCGCTAAT 60.009 57.895 19.37 8.76 46.04 1.73
3547 3636 1.269444 GCCGACGACTAGCGCTAATG 61.269 60.000 19.37 13.01 46.04 1.90
3548 3637 0.029035 CCGACGACTAGCGCTAATGT 59.971 55.000 19.37 16.13 46.04 2.71
3549 3638 1.113253 CGACGACTAGCGCTAATGTG 58.887 55.000 19.37 9.23 46.04 3.21
3550 3639 1.267882 CGACGACTAGCGCTAATGTGA 60.268 52.381 19.37 0.00 46.04 3.58
3551 3640 2.110226 GACGACTAGCGCTAATGTGAC 58.890 52.381 19.37 6.22 46.04 3.67
3552 3641 1.202268 ACGACTAGCGCTAATGTGACC 60.202 52.381 19.37 1.68 46.04 4.02
3553 3642 1.478137 GACTAGCGCTAATGTGACCG 58.522 55.000 19.37 6.55 0.00 4.79
3554 3643 1.065102 GACTAGCGCTAATGTGACCGA 59.935 52.381 19.37 0.00 0.00 4.69
3555 3644 1.681793 ACTAGCGCTAATGTGACCGAT 59.318 47.619 19.37 0.00 0.00 4.18
3556 3645 2.287668 ACTAGCGCTAATGTGACCGATC 60.288 50.000 19.37 0.00 0.00 3.69
3557 3646 0.459899 AGCGCTAATGTGACCGATCA 59.540 50.000 8.99 0.00 0.00 2.92
3558 3647 0.855349 GCGCTAATGTGACCGATCAG 59.145 55.000 0.00 0.00 34.75 2.90
3560 3649 1.221414 GCTAATGTGACCGATCAGGC 58.779 55.000 3.85 0.00 46.52 4.85
3561 3650 1.202580 GCTAATGTGACCGATCAGGCT 60.203 52.381 3.85 0.00 46.52 4.58
3562 3651 2.748605 CTAATGTGACCGATCAGGCTC 58.251 52.381 3.85 0.00 46.52 4.70
3563 3652 1.198713 AATGTGACCGATCAGGCTCT 58.801 50.000 3.85 0.00 46.52 4.09
3564 3653 0.749649 ATGTGACCGATCAGGCTCTC 59.250 55.000 3.85 0.00 46.52 3.20
3565 3654 0.323816 TGTGACCGATCAGGCTCTCT 60.324 55.000 3.85 0.00 46.52 3.10
3566 3655 1.064685 TGTGACCGATCAGGCTCTCTA 60.065 52.381 3.85 0.00 46.52 2.43
3567 3656 1.606668 GTGACCGATCAGGCTCTCTAG 59.393 57.143 3.85 0.00 46.52 2.43
3568 3657 1.490910 TGACCGATCAGGCTCTCTAGA 59.509 52.381 3.85 0.00 46.52 2.43
3569 3658 2.151202 GACCGATCAGGCTCTCTAGAG 58.849 57.143 13.98 13.98 46.52 2.43
3589 3678 1.805869 CACTGAGGTGCTCTCCAAAG 58.194 55.000 5.44 0.46 41.76 2.77
3590 3679 0.036022 ACTGAGGTGCTCTCCAAAGC 59.964 55.000 5.44 0.00 41.76 3.51
3591 3680 0.676151 CTGAGGTGCTCTCCAAAGCC 60.676 60.000 5.44 0.00 41.77 4.35
3592 3681 1.743252 GAGGTGCTCTCCAAAGCCG 60.743 63.158 0.00 0.00 41.77 5.52
3593 3682 2.032681 GGTGCTCTCCAAAGCCGT 59.967 61.111 0.00 0.00 41.77 5.68
3594 3683 1.600916 GGTGCTCTCCAAAGCCGTT 60.601 57.895 0.00 0.00 41.77 4.44
3595 3684 1.576421 GTGCTCTCCAAAGCCGTTG 59.424 57.895 0.00 0.00 41.77 4.10
3605 3694 2.863401 AAAGCCGTTGGTTTGACTTC 57.137 45.000 0.00 0.00 40.50 3.01
3606 3695 1.029681 AAGCCGTTGGTTTGACTTCC 58.970 50.000 0.00 0.00 0.00 3.46
3607 3696 0.822121 AGCCGTTGGTTTGACTTCCC 60.822 55.000 0.00 0.00 0.00 3.97
3608 3697 1.802337 GCCGTTGGTTTGACTTCCCC 61.802 60.000 0.00 0.00 0.00 4.81
3609 3698 1.512156 CCGTTGGTTTGACTTCCCCG 61.512 60.000 0.00 0.00 0.00 5.73
3610 3699 1.512156 CGTTGGTTTGACTTCCCCGG 61.512 60.000 0.00 0.00 0.00 5.73
3611 3700 1.529713 TTGGTTTGACTTCCCCGGC 60.530 57.895 0.00 0.00 0.00 6.13
3612 3701 2.114411 GGTTTGACTTCCCCGGCA 59.886 61.111 0.00 0.00 0.00 5.69
3613 3702 1.971695 GGTTTGACTTCCCCGGCAG 60.972 63.158 0.00 0.00 0.00 4.85
3614 3703 2.282180 TTTGACTTCCCCGGCAGC 60.282 61.111 0.00 0.00 0.00 5.25
3615 3704 3.860930 TTTGACTTCCCCGGCAGCC 62.861 63.158 0.00 0.00 0.00 4.85
3634 3723 4.218578 CGAGGCAGCGCTCCAGAT 62.219 66.667 22.44 7.11 0.00 2.90
3635 3724 2.188994 GAGGCAGCGCTCCAGATT 59.811 61.111 22.44 6.82 0.00 2.40
3636 3725 1.451028 GAGGCAGCGCTCCAGATTT 60.451 57.895 22.44 6.51 0.00 2.17
3637 3726 1.001641 AGGCAGCGCTCCAGATTTT 60.002 52.632 22.44 3.74 0.00 1.82
3638 3727 0.610232 AGGCAGCGCTCCAGATTTTT 60.610 50.000 22.44 3.15 0.00 1.94
3639 3728 1.094785 GGCAGCGCTCCAGATTTTTA 58.905 50.000 7.13 0.00 0.00 1.52
3640 3729 1.064654 GGCAGCGCTCCAGATTTTTAG 59.935 52.381 7.13 0.00 0.00 1.85
3641 3730 2.009774 GCAGCGCTCCAGATTTTTAGA 58.990 47.619 7.13 0.00 0.00 2.10
3642 3731 2.615912 GCAGCGCTCCAGATTTTTAGAT 59.384 45.455 7.13 0.00 0.00 1.98
3643 3732 3.065925 GCAGCGCTCCAGATTTTTAGATT 59.934 43.478 7.13 0.00 0.00 2.40
3644 3733 4.439289 GCAGCGCTCCAGATTTTTAGATTT 60.439 41.667 7.13 0.00 0.00 2.17
3645 3734 5.644644 CAGCGCTCCAGATTTTTAGATTTT 58.355 37.500 7.13 0.00 0.00 1.82
3646 3735 5.514204 CAGCGCTCCAGATTTTTAGATTTTG 59.486 40.000 7.13 0.00 0.00 2.44
3647 3736 5.415701 AGCGCTCCAGATTTTTAGATTTTGA 59.584 36.000 2.64 0.00 0.00 2.69
3648 3737 5.513141 GCGCTCCAGATTTTTAGATTTTGAC 59.487 40.000 0.00 0.00 0.00 3.18
3649 3738 6.030228 CGCTCCAGATTTTTAGATTTTGACC 58.970 40.000 0.00 0.00 0.00 4.02
3650 3739 6.030228 GCTCCAGATTTTTAGATTTTGACCG 58.970 40.000 0.00 0.00 0.00 4.79
3651 3740 5.949735 TCCAGATTTTTAGATTTTGACCGC 58.050 37.500 0.00 0.00 0.00 5.68
3652 3741 5.710099 TCCAGATTTTTAGATTTTGACCGCT 59.290 36.000 0.00 0.00 0.00 5.52
3653 3742 5.801947 CCAGATTTTTAGATTTTGACCGCTG 59.198 40.000 0.00 0.00 0.00 5.18
3654 3743 5.287035 CAGATTTTTAGATTTTGACCGCTGC 59.713 40.000 0.00 0.00 0.00 5.25
3655 3744 4.846779 TTTTTAGATTTTGACCGCTGCT 57.153 36.364 0.00 0.00 0.00 4.24
3656 3745 4.419522 TTTTAGATTTTGACCGCTGCTC 57.580 40.909 0.00 0.00 0.00 4.26
3657 3746 3.334583 TTAGATTTTGACCGCTGCTCT 57.665 42.857 0.00 0.00 0.00 4.09
3658 3747 4.465632 TTAGATTTTGACCGCTGCTCTA 57.534 40.909 0.00 0.00 0.00 2.43
3659 3748 2.898705 AGATTTTGACCGCTGCTCTAG 58.101 47.619 0.00 0.00 0.00 2.43
3660 3749 2.234908 AGATTTTGACCGCTGCTCTAGT 59.765 45.455 0.00 0.00 0.00 2.57
3661 3750 2.543777 TTTTGACCGCTGCTCTAGTT 57.456 45.000 0.00 0.00 0.00 2.24
3662 3751 3.671008 TTTTGACCGCTGCTCTAGTTA 57.329 42.857 0.00 0.00 0.00 2.24
3663 3752 2.941453 TTGACCGCTGCTCTAGTTAG 57.059 50.000 0.00 0.00 0.00 2.34
3664 3753 2.124277 TGACCGCTGCTCTAGTTAGA 57.876 50.000 0.00 0.00 0.00 2.10
3665 3754 2.656002 TGACCGCTGCTCTAGTTAGAT 58.344 47.619 0.00 0.00 0.00 1.98
3666 3755 3.816994 TGACCGCTGCTCTAGTTAGATA 58.183 45.455 0.00 0.00 0.00 1.98
3667 3756 3.815962 TGACCGCTGCTCTAGTTAGATAG 59.184 47.826 0.00 0.00 0.00 2.08
3668 3757 2.554893 ACCGCTGCTCTAGTTAGATAGC 59.445 50.000 12.13 12.13 38.23 2.97
3669 3758 2.094957 CCGCTGCTCTAGTTAGATAGCC 60.095 54.545 14.62 4.15 38.30 3.93
3670 3759 2.554462 CGCTGCTCTAGTTAGATAGCCA 59.446 50.000 14.62 1.90 38.30 4.75
3671 3760 3.610585 CGCTGCTCTAGTTAGATAGCCAC 60.611 52.174 14.62 2.25 38.30 5.01
3672 3761 3.305744 GCTGCTCTAGTTAGATAGCCACC 60.306 52.174 11.51 0.00 36.89 4.61
3673 3762 2.885266 TGCTCTAGTTAGATAGCCACCG 59.115 50.000 0.00 0.00 0.00 4.94
3674 3763 3.147629 GCTCTAGTTAGATAGCCACCGA 58.852 50.000 0.00 0.00 0.00 4.69
3675 3764 3.189702 GCTCTAGTTAGATAGCCACCGAG 59.810 52.174 0.00 0.00 0.00 4.63
3676 3765 3.147629 TCTAGTTAGATAGCCACCGAGC 58.852 50.000 0.00 0.00 0.00 5.03
3678 3767 1.957877 AGTTAGATAGCCACCGAGCTC 59.042 52.381 2.73 2.73 43.67 4.09
3679 3768 1.681793 GTTAGATAGCCACCGAGCTCA 59.318 52.381 15.40 0.00 43.67 4.26
3680 3769 2.067365 TAGATAGCCACCGAGCTCAA 57.933 50.000 15.40 0.00 43.67 3.02
3681 3770 0.749649 AGATAGCCACCGAGCTCAAG 59.250 55.000 15.40 6.88 43.67 3.02
3682 3771 0.747255 GATAGCCACCGAGCTCAAGA 59.253 55.000 15.40 0.00 43.67 3.02
3683 3772 1.342819 GATAGCCACCGAGCTCAAGAT 59.657 52.381 15.40 0.00 43.67 2.40
3684 3773 0.461548 TAGCCACCGAGCTCAAGATG 59.538 55.000 15.40 5.58 43.67 2.90
3685 3774 2.467826 GCCACCGAGCTCAAGATGC 61.468 63.158 15.40 5.53 0.00 3.91
3686 3775 2.169789 CCACCGAGCTCAAGATGCG 61.170 63.158 15.40 0.00 35.28 4.73
3687 3776 2.169789 CACCGAGCTCAAGATGCGG 61.170 63.158 15.40 10.43 46.83 5.69
3688 3777 2.351244 ACCGAGCTCAAGATGCGGA 61.351 57.895 15.40 0.00 44.43 5.54
3689 3778 1.880340 CCGAGCTCAAGATGCGGAC 60.880 63.158 15.40 0.00 44.43 4.79
3690 3779 1.153765 CGAGCTCAAGATGCGGACA 60.154 57.895 15.40 0.00 35.28 4.02
3691 3780 1.416813 CGAGCTCAAGATGCGGACAC 61.417 60.000 15.40 0.00 35.28 3.67
3692 3781 0.108424 GAGCTCAAGATGCGGACACT 60.108 55.000 9.40 0.00 35.28 3.55
3693 3782 0.390866 AGCTCAAGATGCGGACACTG 60.391 55.000 0.00 0.00 35.28 3.66
3694 3783 1.975363 GCTCAAGATGCGGACACTGC 61.975 60.000 0.00 0.00 0.00 4.40
3695 3784 0.390866 CTCAAGATGCGGACACTGCT 60.391 55.000 0.00 0.00 0.00 4.24
3696 3785 0.671472 TCAAGATGCGGACACTGCTG 60.671 55.000 0.00 0.00 0.00 4.41
3697 3786 1.376424 AAGATGCGGACACTGCTGG 60.376 57.895 0.00 0.00 0.00 4.85
3698 3787 2.046892 GATGCGGACACTGCTGGT 60.047 61.111 0.00 0.00 0.00 4.00
3707 3796 3.970332 ACTGCTGGTGACCACAGA 58.030 55.556 28.49 6.73 38.20 3.41
3708 3797 1.750930 ACTGCTGGTGACCACAGAG 59.249 57.895 28.49 16.05 38.20 3.35
3709 3798 1.050988 ACTGCTGGTGACCACAGAGT 61.051 55.000 28.49 16.57 38.20 3.24
3710 3799 0.320247 CTGCTGGTGACCACAGAGTC 60.320 60.000 21.75 3.27 38.20 3.36
3711 3800 1.373497 GCTGGTGACCACAGAGTCG 60.373 63.158 0.00 0.00 39.77 4.18
3712 3801 2.041976 CTGGTGACCACAGAGTCGT 58.958 57.895 0.00 0.00 39.77 4.34
3713 3802 0.039074 CTGGTGACCACAGAGTCGTC 60.039 60.000 0.00 0.00 39.77 4.20
3714 3803 0.753848 TGGTGACCACAGAGTCGTCA 60.754 55.000 0.00 0.00 39.77 4.35
3715 3804 0.387929 GGTGACCACAGAGTCGTCAA 59.612 55.000 0.00 0.00 35.68 3.18
3716 3805 1.488527 GTGACCACAGAGTCGTCAAC 58.511 55.000 0.00 0.00 35.68 3.18
3717 3806 1.107945 TGACCACAGAGTCGTCAACA 58.892 50.000 0.00 0.00 39.77 3.33
3718 3807 1.478916 TGACCACAGAGTCGTCAACAA 59.521 47.619 0.00 0.00 39.77 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.067974 GTTAGTGGGGTTTGTTGGTGC 59.932 52.381 0.00 0.00 0.00 5.01
33 34 1.726192 TAGCTAGGGGGAGGCATCGA 61.726 60.000 0.00 0.00 0.00 3.59
34 35 1.228894 TAGCTAGGGGGAGGCATCG 60.229 63.158 0.00 0.00 0.00 3.84
35 36 1.195442 GGTAGCTAGGGGGAGGCATC 61.195 65.000 0.00 0.00 0.00 3.91
36 37 1.152008 GGTAGCTAGGGGGAGGCAT 60.152 63.158 0.00 0.00 0.00 4.40
38 39 2.527123 GGGTAGCTAGGGGGAGGC 60.527 72.222 0.00 0.00 0.00 4.70
41 42 2.409937 GGGAGGGTAGCTAGGGGGA 61.410 68.421 0.00 0.00 0.00 4.81
42 43 2.049792 ATGGGAGGGTAGCTAGGGGG 62.050 65.000 0.00 0.00 0.00 5.40
43 44 0.104409 AATGGGAGGGTAGCTAGGGG 60.104 60.000 0.00 0.00 0.00 4.79
44 45 1.132689 AGAATGGGAGGGTAGCTAGGG 60.133 57.143 0.00 0.00 0.00 3.53
45 46 2.407340 AGAATGGGAGGGTAGCTAGG 57.593 55.000 0.00 0.00 0.00 3.02
156 174 1.269998 ACCTAGACTCACTTCGCACAC 59.730 52.381 0.00 0.00 0.00 3.82
157 175 1.540267 GACCTAGACTCACTTCGCACA 59.460 52.381 0.00 0.00 0.00 4.57
199 217 3.627577 ACAAGCACCAACACTAAGTTCTG 59.372 43.478 0.00 0.00 38.74 3.02
200 218 3.627577 CACAAGCACCAACACTAAGTTCT 59.372 43.478 0.00 0.00 38.74 3.01
207 252 6.648879 AATAAATACACAAGCACCAACACT 57.351 33.333 0.00 0.00 0.00 3.55
222 267 6.316319 TCGCCGGAAAAACTGAAATAAATAC 58.684 36.000 5.05 0.00 0.00 1.89
248 293 5.178438 GGACATTCTCTCTCACAGAACAAAC 59.822 44.000 0.00 0.00 32.65 2.93
256 301 1.924731 ACGGGACATTCTCTCTCACA 58.075 50.000 0.00 0.00 0.00 3.58
264 309 5.221783 ACCTTTGTAGTTAACGGGACATTCT 60.222 40.000 10.53 0.00 0.00 2.40
266 311 4.758165 CACCTTTGTAGTTAACGGGACATT 59.242 41.667 10.53 0.00 0.00 2.71
276 321 6.041637 AGTCATCACAGACACCTTTGTAGTTA 59.958 38.462 0.00 0.00 40.98 2.24
283 328 4.422073 TGAAGTCATCACAGACACCTTT 57.578 40.909 0.00 0.00 40.98 3.11
284 329 4.630644 ATGAAGTCATCACAGACACCTT 57.369 40.909 0.00 0.00 41.93 3.50
313 358 6.397272 AGAGAGTGAGAAGACACATCATTTC 58.603 40.000 0.00 0.00 42.45 2.17
401 446 5.525012 ACAGACGTAGACGCTAATACATACA 59.475 40.000 1.14 0.00 44.43 2.29
410 455 5.111989 AGTACAATACAGACGTAGACGCTA 58.888 41.667 1.14 0.00 44.43 4.26
506 554 1.135689 GCACGATGCAATTTCGGTTCT 60.136 47.619 12.42 0.00 44.26 3.01
663 712 0.108963 ACGTCCGGTTTTTGGATGGA 59.891 50.000 0.00 0.00 45.10 3.41
870 931 2.356313 ACGAGACAAGCCGCTGTG 60.356 61.111 0.00 0.00 0.00 3.66
1041 1103 2.546494 GCCCGCATACTCACCATGC 61.546 63.158 0.00 0.00 44.31 4.06
1051 1113 2.358615 GATGCCATCGCCCGCATA 60.359 61.111 3.39 0.00 45.52 3.14
1088 1150 4.980805 GCACGACCACCTCCGCAA 62.981 66.667 0.00 0.00 0.00 4.85
1125 1187 2.545596 CGGCTTGCAAGTGAGCACA 61.546 57.895 26.55 0.00 45.61 4.57
1953 2027 2.574018 CCACCACTCGAGGCAGACA 61.574 63.158 18.41 0.00 0.00 3.41
2053 2127 4.822036 AGATGTAGATGAGTGACGTAGC 57.178 45.455 0.00 0.00 0.00 3.58
2055 2129 4.579340 GGGAAGATGTAGATGAGTGACGTA 59.421 45.833 0.00 0.00 0.00 3.57
2202 2276 2.103538 ATGTACGCGAACGCCGAT 59.896 55.556 15.93 2.48 45.53 4.18
2424 2498 2.687805 CCAGAACGCGAGGACGAGA 61.688 63.158 15.93 0.00 41.48 4.04
2598 2672 1.082756 GCTGCTCGGTTTTGTGTCG 60.083 57.895 0.00 0.00 0.00 4.35
2818 2893 8.451908 AAAACTCTATACAGATTACCAATGGC 57.548 34.615 0.00 0.00 0.00 4.40
2866 2947 8.121167 GAATCCTTTCGACTTCTGTAATACTG 57.879 38.462 0.00 0.00 0.00 2.74
2952 3033 0.179119 GCCATGCTCACTTTGATGCC 60.179 55.000 0.00 0.00 0.00 4.40
2995 3076 0.544833 ATTCATGGGGTGGCTGCAAA 60.545 50.000 0.50 0.00 0.00 3.68
3037 3118 6.814076 TTAAAGTTAAACGGCACATTGTTG 57.186 33.333 0.00 0.00 0.00 3.33
3169 3250 5.483174 ACGATATAAGAGGGGATATGGGA 57.517 43.478 0.00 0.00 0.00 4.37
3181 3262 7.972832 AACCACACTTTTGAACGATATAAGA 57.027 32.000 0.00 0.00 0.00 2.10
3182 3263 9.458374 AAAAACCACACTTTTGAACGATATAAG 57.542 29.630 0.00 0.00 0.00 1.73
3208 3289 3.627577 GCTGTTCTGTTTCTTCCAGTCAA 59.372 43.478 0.00 0.00 0.00 3.18
3209 3290 3.206150 GCTGTTCTGTTTCTTCCAGTCA 58.794 45.455 0.00 0.00 0.00 3.41
3210 3291 3.002759 GTGCTGTTCTGTTTCTTCCAGTC 59.997 47.826 0.00 0.00 0.00 3.51
3211 3292 2.945668 GTGCTGTTCTGTTTCTTCCAGT 59.054 45.455 0.00 0.00 0.00 4.00
3212 3293 2.291741 GGTGCTGTTCTGTTTCTTCCAG 59.708 50.000 0.00 0.00 0.00 3.86
3213 3294 2.297701 GGTGCTGTTCTGTTTCTTCCA 58.702 47.619 0.00 0.00 0.00 3.53
3214 3295 2.297701 TGGTGCTGTTCTGTTTCTTCC 58.702 47.619 0.00 0.00 0.00 3.46
3215 3296 3.565482 TCATGGTGCTGTTCTGTTTCTTC 59.435 43.478 0.00 0.00 0.00 2.87
3225 3306 2.283145 AGCTTCTTCATGGTGCTGTT 57.717 45.000 0.00 0.00 32.32 3.16
3268 3353 6.377146 AGCTTGAAAGTTTCTTTCCAACTACA 59.623 34.615 16.33 0.00 33.12 2.74
3270 3355 7.404671 AAGCTTGAAAGTTTCTTTCCAACTA 57.595 32.000 16.33 0.00 33.12 2.24
3280 3365 3.867493 AGCAGCAAAAGCTTGAAAGTTTC 59.133 39.130 8.75 8.75 39.87 2.78
3355 3441 8.250332 GCCAATTATCTTAATGAAACACCAGAA 58.750 33.333 0.00 0.00 0.00 3.02
3359 3445 6.872920 TGGCCAATTATCTTAATGAAACACC 58.127 36.000 0.61 0.00 0.00 4.16
3380 3469 7.457024 TTGGTTAGTTTCCTTATAAACTGGC 57.543 36.000 11.25 4.98 46.49 4.85
3398 3487 5.814764 TTTCGTTGTAACAGCTTTGGTTA 57.185 34.783 0.00 0.00 0.00 2.85
3408 3497 2.159037 TGTGCGTGTTTTCGTTGTAACA 59.841 40.909 0.00 0.00 32.21 2.41
3410 3499 2.159037 TGTGTGCGTGTTTTCGTTGTAA 59.841 40.909 0.00 0.00 0.00 2.41
3416 3505 0.859788 GGTGTGTGTGCGTGTTTTCG 60.860 55.000 0.00 0.00 0.00 3.46
3421 3510 3.202001 GCTGGTGTGTGTGCGTGT 61.202 61.111 0.00 0.00 0.00 4.49
3448 3537 3.161450 TCATGGCTCCGGGTAGGC 61.161 66.667 9.56 9.56 42.19 3.93
3449 3538 2.822399 GTCATGGCTCCGGGTAGG 59.178 66.667 0.00 0.00 42.97 3.18
3450 3539 2.125326 TCGTCATGGCTCCGGGTAG 61.125 63.158 0.00 0.00 0.00 3.18
3451 3540 2.043752 TCGTCATGGCTCCGGGTA 60.044 61.111 0.00 0.00 0.00 3.69
3452 3541 3.771160 GTCGTCATGGCTCCGGGT 61.771 66.667 0.00 0.00 0.00 5.28
3453 3542 4.530857 GGTCGTCATGGCTCCGGG 62.531 72.222 0.00 0.00 0.00 5.73
3454 3543 4.530857 GGGTCGTCATGGCTCCGG 62.531 72.222 0.00 0.00 0.00 5.14
3455 3544 4.530857 GGGGTCGTCATGGCTCCG 62.531 72.222 0.00 0.00 0.00 4.63
3456 3545 4.530857 CGGGGTCGTCATGGCTCC 62.531 72.222 0.00 0.00 0.00 4.70
3460 3549 2.727392 TAAGGCGGGGTCGTCATGG 61.727 63.158 0.00 0.00 44.51 3.66
3461 3550 1.520787 GTAAGGCGGGGTCGTCATG 60.521 63.158 0.00 0.00 44.51 3.07
3462 3551 1.546589 TTGTAAGGCGGGGTCGTCAT 61.547 55.000 0.00 0.00 44.51 3.06
3463 3552 1.756408 TTTGTAAGGCGGGGTCGTCA 61.756 55.000 0.00 0.00 44.51 4.35
3464 3553 1.004679 TTTGTAAGGCGGGGTCGTC 60.005 57.895 0.00 0.00 42.03 4.20
3465 3554 1.301953 GTTTGTAAGGCGGGGTCGT 60.302 57.895 0.00 0.00 38.89 4.34
3466 3555 2.036571 GGTTTGTAAGGCGGGGTCG 61.037 63.158 0.00 0.00 39.81 4.79
3467 3556 0.614812 TAGGTTTGTAAGGCGGGGTC 59.385 55.000 0.00 0.00 0.00 4.46
3468 3557 1.003928 CTTAGGTTTGTAAGGCGGGGT 59.996 52.381 0.00 0.00 0.00 4.95
3469 3558 1.746470 CTTAGGTTTGTAAGGCGGGG 58.254 55.000 0.00 0.00 0.00 5.73
3470 3559 1.092348 GCTTAGGTTTGTAAGGCGGG 58.908 55.000 0.00 0.00 31.60 6.13
3471 3560 1.816074 TGCTTAGGTTTGTAAGGCGG 58.184 50.000 0.00 0.00 31.60 6.13
3472 3561 2.412325 CGTTGCTTAGGTTTGTAAGGCG 60.412 50.000 0.00 0.00 31.60 5.52
3473 3562 2.667448 GCGTTGCTTAGGTTTGTAAGGC 60.667 50.000 0.00 0.00 34.07 4.35
3474 3563 2.550606 TGCGTTGCTTAGGTTTGTAAGG 59.449 45.455 0.00 0.00 31.60 2.69
3475 3564 3.002862 TGTGCGTTGCTTAGGTTTGTAAG 59.997 43.478 0.00 0.00 33.74 2.34
3476 3565 2.943690 TGTGCGTTGCTTAGGTTTGTAA 59.056 40.909 0.00 0.00 0.00 2.41
3477 3566 2.562635 TGTGCGTTGCTTAGGTTTGTA 58.437 42.857 0.00 0.00 0.00 2.41
3478 3567 1.384525 TGTGCGTTGCTTAGGTTTGT 58.615 45.000 0.00 0.00 0.00 2.83
3479 3568 2.704725 ATGTGCGTTGCTTAGGTTTG 57.295 45.000 0.00 0.00 0.00 2.93
3480 3569 2.884639 AGAATGTGCGTTGCTTAGGTTT 59.115 40.909 0.00 0.00 0.00 3.27
3481 3570 2.504367 AGAATGTGCGTTGCTTAGGTT 58.496 42.857 0.00 0.00 0.00 3.50
3482 3571 2.185004 AGAATGTGCGTTGCTTAGGT 57.815 45.000 0.00 0.00 0.00 3.08
3483 3572 2.474526 CGAAGAATGTGCGTTGCTTAGG 60.475 50.000 0.00 0.00 0.00 2.69
3484 3573 2.762472 CGAAGAATGTGCGTTGCTTAG 58.238 47.619 0.00 0.00 0.00 2.18
3485 3574 1.136085 GCGAAGAATGTGCGTTGCTTA 60.136 47.619 0.00 0.00 0.00 3.09
3486 3575 0.385974 GCGAAGAATGTGCGTTGCTT 60.386 50.000 0.00 0.00 0.00 3.91
3487 3576 1.207593 GCGAAGAATGTGCGTTGCT 59.792 52.632 0.00 0.00 0.00 3.91
3488 3577 1.797537 GGCGAAGAATGTGCGTTGC 60.798 57.895 0.00 0.00 0.00 4.17
3489 3578 1.154225 GGGCGAAGAATGTGCGTTG 60.154 57.895 0.00 0.00 0.00 4.10
3490 3579 2.332654 GGGGCGAAGAATGTGCGTT 61.333 57.895 0.00 0.00 0.00 4.84
3491 3580 2.746277 GGGGCGAAGAATGTGCGT 60.746 61.111 0.00 0.00 0.00 5.24
3492 3581 3.864686 CGGGGCGAAGAATGTGCG 61.865 66.667 0.00 0.00 0.00 5.34
3493 3582 2.435938 TCGGGGCGAAGAATGTGC 60.436 61.111 0.00 0.00 31.06 4.57
3494 3583 1.815421 CCTCGGGGCGAAGAATGTG 60.815 63.158 0.00 0.00 34.74 3.21
3495 3584 2.240162 GACCTCGGGGCGAAGAATGT 62.240 60.000 0.00 0.00 34.74 2.71
3496 3585 1.521681 GACCTCGGGGCGAAGAATG 60.522 63.158 0.00 0.00 34.74 2.67
3497 3586 2.901042 GACCTCGGGGCGAAGAAT 59.099 61.111 0.00 0.00 34.74 2.40
3498 3587 3.755628 CGACCTCGGGGCGAAGAA 61.756 66.667 12.28 0.00 34.74 2.52
3500 3589 4.796231 CACGACCTCGGGGCGAAG 62.796 72.222 22.70 11.77 44.95 3.79
3518 3607 4.717629 TCGTCGGCTTGTGCGGAG 62.718 66.667 0.00 0.00 46.61 4.63
3520 3609 3.620300 TAGTCGTCGGCTTGTGCGG 62.620 63.158 3.90 0.00 40.82 5.69
3521 3610 2.126618 TAGTCGTCGGCTTGTGCG 60.127 61.111 3.90 0.00 40.82 5.34
3522 3611 2.445438 GCTAGTCGTCGGCTTGTGC 61.445 63.158 3.90 3.99 38.76 4.57
3523 3612 2.152699 CGCTAGTCGTCGGCTTGTG 61.153 63.158 3.90 5.99 0.00 3.33
3524 3613 2.178521 CGCTAGTCGTCGGCTTGT 59.821 61.111 3.90 0.00 0.00 3.16
3525 3614 2.319011 TAGCGCTAGTCGTCGGCTTG 62.319 60.000 14.45 3.86 41.07 4.01
3526 3615 1.651240 TTAGCGCTAGTCGTCGGCTT 61.651 55.000 17.98 0.00 41.07 4.35
3527 3616 1.445716 ATTAGCGCTAGTCGTCGGCT 61.446 55.000 17.98 4.10 41.07 5.52
3528 3617 1.008767 ATTAGCGCTAGTCGTCGGC 60.009 57.895 17.98 0.00 41.07 5.54
3529 3618 0.029035 ACATTAGCGCTAGTCGTCGG 59.971 55.000 17.98 5.00 41.07 4.79
3530 3619 1.113253 CACATTAGCGCTAGTCGTCG 58.887 55.000 17.98 5.38 41.07 5.12
3531 3620 2.110226 GTCACATTAGCGCTAGTCGTC 58.890 52.381 17.98 4.74 41.07 4.20
3532 3621 1.202268 GGTCACATTAGCGCTAGTCGT 60.202 52.381 17.98 12.83 41.07 4.34
3533 3622 1.478137 GGTCACATTAGCGCTAGTCG 58.522 55.000 17.98 12.19 42.12 4.18
3534 3623 1.065102 TCGGTCACATTAGCGCTAGTC 59.935 52.381 17.98 2.54 40.07 2.59
3535 3624 1.100510 TCGGTCACATTAGCGCTAGT 58.899 50.000 17.98 12.45 40.07 2.57
3536 3625 2.287608 TGATCGGTCACATTAGCGCTAG 60.288 50.000 17.98 9.71 40.07 3.42
3537 3626 1.679153 TGATCGGTCACATTAGCGCTA 59.321 47.619 14.45 14.45 40.07 4.26
3538 3627 0.459899 TGATCGGTCACATTAGCGCT 59.540 50.000 17.26 17.26 40.07 5.92
3539 3628 0.855349 CTGATCGGTCACATTAGCGC 59.145 55.000 0.00 0.00 40.07 5.92
3540 3629 1.491670 CCTGATCGGTCACATTAGCG 58.508 55.000 0.00 0.00 41.54 4.26
3541 3630 1.202580 AGCCTGATCGGTCACATTAGC 60.203 52.381 0.00 0.00 34.25 3.09
3542 3631 2.363680 AGAGCCTGATCGGTCACATTAG 59.636 50.000 0.00 0.00 34.25 1.73
3543 3632 2.362397 GAGAGCCTGATCGGTCACATTA 59.638 50.000 0.00 0.00 34.25 1.90
3544 3633 1.137872 GAGAGCCTGATCGGTCACATT 59.862 52.381 0.00 0.00 34.25 2.71
3545 3634 0.749649 GAGAGCCTGATCGGTCACAT 59.250 55.000 0.00 0.00 34.25 3.21
3546 3635 0.323816 AGAGAGCCTGATCGGTCACA 60.324 55.000 0.00 0.00 34.25 3.58
3547 3636 1.606668 CTAGAGAGCCTGATCGGTCAC 59.393 57.143 0.00 0.00 34.25 3.67
3548 3637 1.490910 TCTAGAGAGCCTGATCGGTCA 59.509 52.381 0.00 0.00 34.25 4.02
3549 3638 2.151202 CTCTAGAGAGCCTGATCGGTC 58.849 57.143 15.05 0.00 35.13 4.79
3550 3639 2.270352 CTCTAGAGAGCCTGATCGGT 57.730 55.000 15.05 0.00 35.13 4.69
3571 3660 0.036022 GCTTTGGAGAGCACCTCAGT 59.964 55.000 8.16 0.00 43.76 3.41
3572 3661 0.676151 GGCTTTGGAGAGCACCTCAG 60.676 60.000 8.16 0.00 44.49 3.35
3573 3662 1.376466 GGCTTTGGAGAGCACCTCA 59.624 57.895 8.16 0.00 44.49 3.86
3574 3663 1.743252 CGGCTTTGGAGAGCACCTC 60.743 63.158 0.00 0.00 44.49 3.85
3575 3664 2.056906 AACGGCTTTGGAGAGCACCT 62.057 55.000 0.00 0.00 44.49 4.00
3576 3665 1.600916 AACGGCTTTGGAGAGCACC 60.601 57.895 0.00 0.00 44.49 5.01
3577 3666 1.576421 CAACGGCTTTGGAGAGCAC 59.424 57.895 0.00 0.00 44.49 4.40
3578 3667 4.063529 CAACGGCTTTGGAGAGCA 57.936 55.556 0.00 0.00 44.49 4.26
3585 3674 2.459934 GAAGTCAAACCAACGGCTTTG 58.540 47.619 0.00 0.00 34.63 2.77
3586 3675 1.407618 GGAAGTCAAACCAACGGCTTT 59.592 47.619 0.00 0.00 0.00 3.51
3587 3676 1.029681 GGAAGTCAAACCAACGGCTT 58.970 50.000 0.00 0.00 0.00 4.35
3588 3677 0.822121 GGGAAGTCAAACCAACGGCT 60.822 55.000 0.00 0.00 0.00 5.52
3589 3678 1.658114 GGGAAGTCAAACCAACGGC 59.342 57.895 0.00 0.00 0.00 5.68
3590 3679 1.512156 CGGGGAAGTCAAACCAACGG 61.512 60.000 0.00 0.00 0.00 4.44
3591 3680 1.512156 CCGGGGAAGTCAAACCAACG 61.512 60.000 0.00 0.00 0.00 4.10
3592 3681 1.802337 GCCGGGGAAGTCAAACCAAC 61.802 60.000 2.18 0.00 0.00 3.77
3593 3682 1.529713 GCCGGGGAAGTCAAACCAA 60.530 57.895 2.18 0.00 0.00 3.67
3594 3683 2.114411 GCCGGGGAAGTCAAACCA 59.886 61.111 2.18 0.00 0.00 3.67
3595 3684 1.971695 CTGCCGGGGAAGTCAAACC 60.972 63.158 2.18 0.00 0.00 3.27
3596 3685 2.626780 GCTGCCGGGGAAGTCAAAC 61.627 63.158 2.18 0.00 0.00 2.93
3597 3686 2.282180 GCTGCCGGGGAAGTCAAA 60.282 61.111 2.18 0.00 0.00 2.69
3598 3687 4.344865 GGCTGCCGGGGAAGTCAA 62.345 66.667 1.35 0.00 0.00 3.18
3617 3706 3.729965 AATCTGGAGCGCTGCCTCG 62.730 63.158 26.87 14.45 32.57 4.63
3618 3707 1.028868 AAAATCTGGAGCGCTGCCTC 61.029 55.000 26.87 6.10 0.00 4.70
3619 3708 0.610232 AAAAATCTGGAGCGCTGCCT 60.610 50.000 26.87 8.22 0.00 4.75
3620 3709 1.064654 CTAAAAATCTGGAGCGCTGCC 59.935 52.381 26.87 20.82 0.00 4.85
3621 3710 2.009774 TCTAAAAATCTGGAGCGCTGC 58.990 47.619 23.36 23.36 0.00 5.25
3622 3711 4.889832 AATCTAAAAATCTGGAGCGCTG 57.110 40.909 18.48 0.00 0.00 5.18
3623 3712 5.415701 TCAAAATCTAAAAATCTGGAGCGCT 59.584 36.000 11.27 11.27 0.00 5.92
3624 3713 5.513141 GTCAAAATCTAAAAATCTGGAGCGC 59.487 40.000 0.00 0.00 0.00 5.92
3625 3714 6.030228 GGTCAAAATCTAAAAATCTGGAGCG 58.970 40.000 0.00 0.00 0.00 5.03
3626 3715 6.030228 CGGTCAAAATCTAAAAATCTGGAGC 58.970 40.000 0.00 0.00 0.00 4.70
3627 3716 6.030228 GCGGTCAAAATCTAAAAATCTGGAG 58.970 40.000 0.00 0.00 0.00 3.86
3628 3717 5.710099 AGCGGTCAAAATCTAAAAATCTGGA 59.290 36.000 0.00 0.00 0.00 3.86
3629 3718 5.801947 CAGCGGTCAAAATCTAAAAATCTGG 59.198 40.000 0.00 0.00 0.00 3.86
3630 3719 5.287035 GCAGCGGTCAAAATCTAAAAATCTG 59.713 40.000 0.00 0.00 0.00 2.90
3631 3720 5.183904 AGCAGCGGTCAAAATCTAAAAATCT 59.816 36.000 0.00 0.00 0.00 2.40
3632 3721 5.402398 AGCAGCGGTCAAAATCTAAAAATC 58.598 37.500 0.00 0.00 0.00 2.17
3633 3722 5.183904 AGAGCAGCGGTCAAAATCTAAAAAT 59.816 36.000 9.70 0.00 31.89 1.82
3634 3723 4.518970 AGAGCAGCGGTCAAAATCTAAAAA 59.481 37.500 9.70 0.00 31.89 1.94
3635 3724 4.072131 AGAGCAGCGGTCAAAATCTAAAA 58.928 39.130 9.70 0.00 31.89 1.52
3636 3725 3.674997 AGAGCAGCGGTCAAAATCTAAA 58.325 40.909 9.70 0.00 31.89 1.85
3637 3726 3.334583 AGAGCAGCGGTCAAAATCTAA 57.665 42.857 9.70 0.00 31.89 2.10
3638 3727 3.447586 ACTAGAGCAGCGGTCAAAATCTA 59.552 43.478 0.00 0.00 31.89 1.98
3639 3728 2.234908 ACTAGAGCAGCGGTCAAAATCT 59.765 45.455 0.00 0.00 31.89 2.40
3640 3729 2.622436 ACTAGAGCAGCGGTCAAAATC 58.378 47.619 0.00 0.00 31.89 2.17
3641 3730 2.770164 ACTAGAGCAGCGGTCAAAAT 57.230 45.000 0.00 0.00 31.89 1.82
3642 3731 2.543777 AACTAGAGCAGCGGTCAAAA 57.456 45.000 0.00 0.00 31.89 2.44
3643 3732 2.823747 TCTAACTAGAGCAGCGGTCAAA 59.176 45.455 0.00 0.00 31.89 2.69
3644 3733 2.443416 TCTAACTAGAGCAGCGGTCAA 58.557 47.619 0.00 0.00 31.89 3.18
3645 3734 2.124277 TCTAACTAGAGCAGCGGTCA 57.876 50.000 0.00 0.00 31.89 4.02
3646 3735 3.365565 GCTATCTAACTAGAGCAGCGGTC 60.366 52.174 0.00 0.43 35.78 4.79
3647 3736 2.554893 GCTATCTAACTAGAGCAGCGGT 59.445 50.000 0.00 0.00 35.78 5.68
3648 3737 2.094957 GGCTATCTAACTAGAGCAGCGG 60.095 54.545 0.00 0.00 41.55 5.52
3649 3738 2.554462 TGGCTATCTAACTAGAGCAGCG 59.446 50.000 0.00 0.00 41.55 5.18
3650 3739 3.305744 GGTGGCTATCTAACTAGAGCAGC 60.306 52.174 0.00 11.87 40.68 5.25
3651 3740 3.057876 CGGTGGCTATCTAACTAGAGCAG 60.058 52.174 0.00 0.00 35.50 4.24
3652 3741 2.885266 CGGTGGCTATCTAACTAGAGCA 59.115 50.000 0.00 0.00 35.50 4.26
3653 3742 3.147629 TCGGTGGCTATCTAACTAGAGC 58.852 50.000 0.00 0.00 35.50 4.09
3654 3743 3.189702 GCTCGGTGGCTATCTAACTAGAG 59.810 52.174 0.00 0.00 35.50 2.43
3655 3744 3.147629 GCTCGGTGGCTATCTAACTAGA 58.852 50.000 0.00 0.00 36.65 2.43
3656 3745 3.150767 AGCTCGGTGGCTATCTAACTAG 58.849 50.000 0.00 0.00 41.16 2.57
3657 3746 3.147629 GAGCTCGGTGGCTATCTAACTA 58.852 50.000 0.00 0.00 43.20 2.24
3658 3747 1.957877 GAGCTCGGTGGCTATCTAACT 59.042 52.381 0.00 0.00 43.20 2.24
3659 3748 1.681793 TGAGCTCGGTGGCTATCTAAC 59.318 52.381 9.64 0.00 43.20 2.34
3660 3749 2.067365 TGAGCTCGGTGGCTATCTAA 57.933 50.000 9.64 0.00 43.20 2.10
3661 3750 1.957177 CTTGAGCTCGGTGGCTATCTA 59.043 52.381 9.64 0.00 43.20 1.98
3662 3751 0.749649 CTTGAGCTCGGTGGCTATCT 59.250 55.000 9.64 0.00 43.20 1.98
3663 3752 0.747255 TCTTGAGCTCGGTGGCTATC 59.253 55.000 9.64 0.00 43.20 2.08
3664 3753 1.069823 CATCTTGAGCTCGGTGGCTAT 59.930 52.381 9.64 0.00 43.20 2.97
3665 3754 0.461548 CATCTTGAGCTCGGTGGCTA 59.538 55.000 9.64 0.00 43.20 3.93
3666 3755 1.220206 CATCTTGAGCTCGGTGGCT 59.780 57.895 9.64 0.00 46.11 4.75
3667 3756 2.467826 GCATCTTGAGCTCGGTGGC 61.468 63.158 9.64 5.37 0.00 5.01
3668 3757 2.169789 CGCATCTTGAGCTCGGTGG 61.170 63.158 9.64 0.00 0.00 4.61
3669 3758 2.169789 CCGCATCTTGAGCTCGGTG 61.170 63.158 9.64 3.23 35.75 4.94
3670 3759 2.185350 CCGCATCTTGAGCTCGGT 59.815 61.111 9.64 0.00 35.75 4.69
3671 3760 1.880340 GTCCGCATCTTGAGCTCGG 60.880 63.158 9.64 5.25 41.30 4.63
3672 3761 1.153765 TGTCCGCATCTTGAGCTCG 60.154 57.895 9.64 0.00 0.00 5.03
3673 3762 0.108424 AGTGTCCGCATCTTGAGCTC 60.108 55.000 6.82 6.82 0.00 4.09
3674 3763 0.390866 CAGTGTCCGCATCTTGAGCT 60.391 55.000 0.00 0.00 0.00 4.09
3675 3764 1.975363 GCAGTGTCCGCATCTTGAGC 61.975 60.000 0.00 0.00 0.00 4.26
3676 3765 0.390866 AGCAGTGTCCGCATCTTGAG 60.391 55.000 0.00 0.00 0.00 3.02
3677 3766 0.671472 CAGCAGTGTCCGCATCTTGA 60.671 55.000 0.00 0.00 0.00 3.02
3678 3767 1.642037 CCAGCAGTGTCCGCATCTTG 61.642 60.000 0.00 0.00 0.00 3.02
3679 3768 1.376424 CCAGCAGTGTCCGCATCTT 60.376 57.895 0.00 0.00 0.00 2.40
3680 3769 2.267006 CCAGCAGTGTCCGCATCT 59.733 61.111 0.00 0.00 0.00 2.90
3681 3770 2.046892 ACCAGCAGTGTCCGCATC 60.047 61.111 0.00 0.00 0.00 3.91
3682 3771 2.359107 CACCAGCAGTGTCCGCAT 60.359 61.111 0.00 0.00 41.93 4.73
3690 3779 1.050988 ACTCTGTGGTCACCAGCAGT 61.051 55.000 19.76 10.30 35.62 4.40
3691 3780 0.320247 GACTCTGTGGTCACCAGCAG 60.320 60.000 16.32 16.32 35.52 4.24
3692 3781 1.748403 GACTCTGTGGTCACCAGCA 59.252 57.895 0.00 0.00 36.35 4.41
3693 3782 1.373497 CGACTCTGTGGTCACCAGC 60.373 63.158 0.00 0.00 36.12 4.85
3694 3783 0.039074 GACGACTCTGTGGTCACCAG 60.039 60.000 0.00 0.00 40.20 4.00
3695 3784 0.753848 TGACGACTCTGTGGTCACCA 60.754 55.000 10.60 0.00 43.97 4.17
3696 3785 2.038690 TGACGACTCTGTGGTCACC 58.961 57.895 10.60 0.00 43.97 4.02
3698 3787 1.107945 TGTTGACGACTCTGTGGTCA 58.892 50.000 10.60 10.60 46.28 4.02
3699 3788 2.218953 TTGTTGACGACTCTGTGGTC 57.781 50.000 6.02 6.02 40.72 4.02


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

AutoCloner maintained by Alex Coulton.