Multiple sequence alignment - TraesCS7A01G245400

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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 TraesCS7A01G245400 chr7A 100.000 4339 0 0 1 4339 223521188 223525526 0.000000e+00 8013.0
1 TraesCS7A01G245400 chr7A 95.000 40 2 0 241 280 105519347 105519308 3.620000e-06 63.9
2 TraesCS7A01G245400 chr7B 94.472 3600 133 31 2 3556 189906271 189902693 0.000000e+00 5485.0
3 TraesCS7A01G245400 chr7B 88.020 601 18 19 3752 4339 189902700 189902141 0.000000e+00 662.0
4 TraesCS7A01G245400 chr7D 94.282 3585 133 29 1 3556 211631459 211635000 0.000000e+00 5419.0
5 TraesCS7A01G245400 chr7D 87.213 610 27 21 3752 4339 211634993 211635573 0.000000e+00 647.0
6 TraesCS7A01G245400 chr1A 93.298 373 14 3 1625 1995 508205541 508205178 1.370000e-149 540.0
7 TraesCS7A01G245400 chr1A 93.510 339 19 2 2543 2878 508202803 508202465 6.480000e-138 501.0
8 TraesCS7A01G245400 chr1A 94.161 137 7 1 2194 2330 508203963 508203828 1.580000e-49 207.0
9 TraesCS7A01G245400 chr6A 92.722 371 14 2 1625 1995 558036735 558037092 1.380000e-144 523.0
10 TraesCS7A01G245400 chr6A 93.510 339 19 2 2543 2878 558039477 558039815 6.480000e-138 501.0
11 TraesCS7A01G245400 chr6A 95.420 131 5 1 2194 2324 558038315 558038444 1.580000e-49 207.0
12 TraesCS7A01G245400 chr2A 94.395 339 16 2 2543 2878 651804636 651804298 6.430000e-143 518.0
13 TraesCS7A01G245400 chr2A 92.023 351 21 1 1645 1995 651807438 651807095 1.810000e-133 486.0
14 TraesCS7A01G245400 chr2A 94.161 137 7 1 2194 2330 651805877 651805742 1.580000e-49 207.0
15 TraesCS7A01G245400 chr4A 99.005 201 0 2 3557 3756 564147710 564147511 4.130000e-95 359.0
16 TraesCS7A01G245400 chr4A 93.333 195 1 1 3556 3750 597004982 597005164 1.190000e-70 278.0
17 TraesCS7A01G245400 chr4A 93.264 193 1 1 3557 3749 626387199 626387379 1.540000e-69 274.0
18 TraesCS7A01G245400 chr4A 89.583 48 5 0 233 280 229508072 229508119 1.300000e-05 62.1
19 TraesCS7A01G245400 chrUn 93.264 193 1 1 3557 3749 84241847 84242027 1.540000e-69 274.0
20 TraesCS7A01G245400 chr3B 92.821 195 2 1 3556 3750 539960667 539960849 5.530000e-69 272.0
21 TraesCS7A01G245400 chr3B 87.500 56 6 1 229 283 773735948 773735893 3.620000e-06 63.9
22 TraesCS7A01G245400 chr4B 93.194 191 1 1 3559 3749 606553844 606554022 1.990000e-68 270.0
23 TraesCS7A01G245400 chr4B 90.196 51 5 0 233 283 424913204 424913154 2.800000e-07 67.6
24 TraesCS7A01G245400 chr3A 92.784 194 2 1 3556 3749 64317891 64317710 1.990000e-68 270.0
25 TraesCS7A01G245400 chr2B 92.784 194 2 1 3557 3750 771775910 771775729 1.990000e-68 270.0
26 TraesCS7A01G245400 chr2B 84.772 197 28 2 3556 3750 46876688 46876884 3.420000e-46 196.0
27 TraesCS7A01G245400 chr1B 92.746 193 2 1 3557 3749 135250513 135250693 7.150000e-68 268.0
28 TraesCS7A01G245400 chr6B 91.584 202 3 3 3556 3757 433678758 433678945 2.570000e-67 267.0
29 TraesCS7A01G245400 chr6B 94.000 50 3 0 231 280 566529556 566529605 4.650000e-10 76.8
30 TraesCS7A01G245400 chr3D 89.796 49 5 0 232 280 12843637 12843589 3.620000e-06 63.9
31 TraesCS7A01G245400 chr5D 88.235 51 6 0 232 282 279273993 279273943 1.300000e-05 62.1


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 TraesCS7A01G245400 chr7A 223521188 223525526 4338 False 8013.000000 8013 100.000000 1 4339 1 chr7A.!!$F1 4338
1 TraesCS7A01G245400 chr7B 189902141 189906271 4130 True 3073.500000 5485 91.246000 2 4339 2 chr7B.!!$R1 4337
2 TraesCS7A01G245400 chr7D 211631459 211635573 4114 False 3033.000000 5419 90.747500 1 4339 2 chr7D.!!$F1 4338
3 TraesCS7A01G245400 chr1A 508202465 508205541 3076 True 416.000000 540 93.656333 1625 2878 3 chr1A.!!$R1 1253
4 TraesCS7A01G245400 chr6A 558036735 558039815 3080 False 410.333333 523 93.884000 1625 2878 3 chr6A.!!$F1 1253
5 TraesCS7A01G245400 chr2A 651804298 651807438 3140 True 403.666667 518 93.526333 1645 2878 3 chr2A.!!$R1 1233

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
636 640 0.249868 CGACCACTCCAGCAGAACAA 60.250 55.0 0.0 0.0 0.00 2.83 F
1098 1154 0.030908 CGAGGGGCAGATACGAGTTC 59.969 60.0 0.0 0.0 0.00 3.01 F
1478 1534 0.835971 TGCAGAAGCTCACCACCCTA 60.836 55.0 0.0 0.0 42.74 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 3971 0.608035 TCGGGCCACCTGATTCAAAC 60.608 55.000 4.39 0.0 33.41 2.93 R
2532 3974 2.668632 GTCGGGCCACCTGATTCA 59.331 61.111 4.39 0.0 41.38 2.57 R
3419 5405 1.065358 CGAAAACGCTAGCGAAAGGA 58.935 50.000 41.33 0.0 42.83 3.36 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
29 30 4.517285 TGTAGATTCAGGCTGGAATTCAC 58.483 43.478 15.73 13.42 37.61 3.18
39 40 5.010012 CAGGCTGGAATTCACTAAACTTTGT 59.990 40.000 6.61 0.00 0.00 2.83
83 84 7.573096 GCACTATGGACAATATTTATGTTCGGG 60.573 40.741 0.00 0.00 0.00 5.14
104 105 6.038825 TCGGGCTATGGTTTTGTTATGTATTG 59.961 38.462 0.00 0.00 0.00 1.90
226 227 4.510038 AATGTGTTCATTTGAGGCTGAC 57.490 40.909 0.00 0.00 40.88 3.51
228 229 1.197721 GTGTTCATTTGAGGCTGACCG 59.802 52.381 0.00 0.00 42.76 4.79
310 312 9.680315 GACCTAGATCACTTGTGTTGTATATAC 57.320 37.037 5.89 5.89 0.00 1.47
313 315 7.432148 AGATCACTTGTGTTGTATATACCCA 57.568 36.000 10.38 4.55 0.00 4.51
333 335 1.803334 TTGTAAGTCACCGCATGGAC 58.197 50.000 0.00 0.00 39.21 4.02
351 353 7.465379 CGCATGGACTAAAGATCGTTTGATTTA 60.465 37.037 9.48 0.00 34.09 1.40
353 355 8.664798 CATGGACTAAAGATCGTTTGATTTACA 58.335 33.333 9.48 0.00 34.09 2.41
358 360 8.380644 ACTAAAGATCGTTTGATTTACATGTCG 58.619 33.333 0.00 0.00 34.09 4.35
385 387 4.468689 GGCGTGTAGGGGCTGGAC 62.469 72.222 0.00 0.00 0.00 4.02
417 419 1.086696 CAATACGGAGTGCCTTGGTG 58.913 55.000 0.00 0.00 45.73 4.17
476 479 1.134788 CCTTACGGGACTGTAAGCAGG 60.135 57.143 20.47 8.72 46.38 4.85
521 524 2.129555 ATCAGGACCCCACACACAGC 62.130 60.000 0.00 0.00 0.00 4.40
572 575 1.779569 TCAAACGAAGAGGCTCGAAC 58.220 50.000 9.22 3.85 41.44 3.95
636 640 0.249868 CGACCACTCCAGCAGAACAA 60.250 55.000 0.00 0.00 0.00 2.83
648 652 4.806247 CCAGCAGAACAAGCATACTAGTAC 59.194 45.833 4.31 0.00 0.00 2.73
726 747 2.081425 TTTCCCACATGCCAACACGC 62.081 55.000 0.00 0.00 0.00 5.34
761 784 2.668550 AAAAGTCGCCCCGAGCAC 60.669 61.111 0.00 0.00 44.04 4.40
872 904 2.284515 ATCCCCGAAATGCCCCTCAC 62.285 60.000 0.00 0.00 0.00 3.51
892 947 2.306512 ACGTAGGCCCCAAATAACAGAA 59.693 45.455 0.00 0.00 0.00 3.02
893 948 2.943033 CGTAGGCCCCAAATAACAGAAG 59.057 50.000 0.00 0.00 0.00 2.85
899 954 3.881713 GCCCCAAATAACAGAAGGGACAT 60.882 47.826 0.00 0.00 42.25 3.06
900 955 3.954258 CCCCAAATAACAGAAGGGACATC 59.046 47.826 0.00 0.00 42.25 3.06
913 968 0.471617 GGACATCATCCTCCAGGTGG 59.528 60.000 0.39 0.39 45.22 4.61
914 969 0.471617 GACATCATCCTCCAGGTGGG 59.528 60.000 7.76 1.45 36.34 4.61
915 970 0.253347 ACATCATCCTCCAGGTGGGT 60.253 55.000 7.76 0.00 38.11 4.51
966 1021 2.298661 CCCGGCCTAAACCCAGTCT 61.299 63.158 0.00 0.00 0.00 3.24
980 1036 2.931649 GTCTCCCCGGTTCCCCAA 60.932 66.667 0.00 0.00 0.00 4.12
983 1039 3.018805 TCCCCGGTTCCCCAATCC 61.019 66.667 0.00 0.00 0.00 3.01
1054 1110 1.345415 CAAGAAATGGCAGGGCTGTTT 59.655 47.619 0.00 0.00 0.00 2.83
1067 1123 2.742589 GGGCTGTTTGTTGTAGTCTAGC 59.257 50.000 0.00 0.00 0.00 3.42
1070 1126 2.055838 TGTTTGTTGTAGTCTAGCGCG 58.944 47.619 0.00 0.00 0.00 6.86
1096 1152 1.828660 CCGAGGGGCAGATACGAGT 60.829 63.158 0.00 0.00 0.00 4.18
1097 1153 1.392710 CCGAGGGGCAGATACGAGTT 61.393 60.000 0.00 0.00 0.00 3.01
1098 1154 0.030908 CGAGGGGCAGATACGAGTTC 59.969 60.000 0.00 0.00 0.00 3.01
1099 1155 1.404843 GAGGGGCAGATACGAGTTCT 58.595 55.000 0.00 0.00 0.00 3.01
1104 1160 3.449632 GGGCAGATACGAGTTCTTTCTC 58.550 50.000 0.00 0.00 0.00 2.87
1105 1161 3.449632 GGCAGATACGAGTTCTTTCTCC 58.550 50.000 0.00 0.00 0.00 3.71
1111 1167 1.071567 CGAGTTCTTTCTCCCGTCGC 61.072 60.000 0.00 0.00 0.00 5.19
1241 1297 4.101448 ACCGATGACCCTGGCAGC 62.101 66.667 9.56 0.00 0.00 5.25
1244 1300 4.101448 GATGACCCTGGCAGCGGT 62.101 66.667 22.53 22.53 34.13 5.68
1407 1463 4.544689 CCGAGCTCGAGACGCTGG 62.545 72.222 36.59 13.86 43.02 4.85
1478 1534 0.835971 TGCAGAAGCTCACCACCCTA 60.836 55.000 0.00 0.00 42.74 3.53
1514 1570 2.190578 CTGTCCGGCCAGATTCCC 59.809 66.667 6.67 0.00 34.23 3.97
1535 1591 4.570874 GGGATTGGGAGGCTCGCC 62.571 72.222 26.34 19.48 0.00 5.54
1544 1600 3.394836 AGGCTCGCCTCCTTGTCC 61.395 66.667 4.23 0.00 44.43 4.02
1799 1855 4.821589 CCGAGGCTCTGCGGGTTC 62.822 72.222 13.50 0.00 43.67 3.62
1823 1881 4.514577 AAGATCGAGTGCGCCGGG 62.515 66.667 4.18 0.00 37.46 5.73
2529 3971 4.639334 AGATAGTGGCACTGAATAGCATG 58.361 43.478 29.65 0.00 0.00 4.06
2532 3974 3.424703 AGTGGCACTGAATAGCATGTTT 58.575 40.909 21.37 0.00 0.00 2.83
3186 5171 2.165167 CCATCATCAATCATTCCGGGG 58.835 52.381 0.00 0.00 0.00 5.73
3263 5248 1.341531 TCCTTAGCTCCGCAGATTAGC 59.658 52.381 0.00 0.00 36.48 3.09
3264 5249 1.069204 CCTTAGCTCCGCAGATTAGCA 59.931 52.381 0.00 0.00 38.75 3.49
3265 5250 2.289320 CCTTAGCTCCGCAGATTAGCAT 60.289 50.000 0.00 0.00 38.75 3.79
3290 5275 7.531716 TCATTTGCCAACGTTATTAGGTTTAG 58.468 34.615 0.00 0.00 30.38 1.85
3291 5276 7.390996 TCATTTGCCAACGTTATTAGGTTTAGA 59.609 33.333 0.00 0.00 30.38 2.10
3324 5309 1.156736 AACCAGCCAAGAATCGTTCG 58.843 50.000 0.00 0.00 34.02 3.95
3345 5330 1.732259 CTGATGTGCGTTTGGTACTCC 59.268 52.381 0.00 0.00 31.78 3.85
3419 5405 3.972133 TGATCTGGACAATTTGCATCCT 58.028 40.909 4.96 0.00 33.34 3.24
3433 5419 0.103208 CATCCTCCTTTCGCTAGCGT 59.897 55.000 34.10 11.12 40.74 5.07
3482 5468 2.603173 GCACTTTCTCTTTTGCGGTGAG 60.603 50.000 0.00 0.00 0.00 3.51
3497 5484 2.872245 CGGTGAGAACTGAGAAAAAGCA 59.128 45.455 0.00 0.00 0.00 3.91
3566 5553 3.195002 GCGGTGCGAGCAATGCTA 61.195 61.111 8.12 0.00 39.88 3.49
3567 5554 3.009140 CGGTGCGAGCAATGCTAG 58.991 61.111 8.12 9.78 39.88 3.42
3568 5555 1.519234 CGGTGCGAGCAATGCTAGA 60.519 57.895 19.25 1.80 39.88 2.43
3569 5556 1.756375 CGGTGCGAGCAATGCTAGAC 61.756 60.000 19.25 12.93 39.88 2.59
3570 5557 1.633171 GTGCGAGCAATGCTAGACG 59.367 57.895 19.25 14.34 39.88 4.18
3571 5558 1.078759 GTGCGAGCAATGCTAGACGT 61.079 55.000 19.25 0.00 39.88 4.34
3572 5559 0.454196 TGCGAGCAATGCTAGACGTA 59.546 50.000 19.25 10.31 39.88 3.57
3573 5560 0.847035 GCGAGCAATGCTAGACGTAC 59.153 55.000 19.25 0.00 39.88 3.67
3574 5561 1.797713 GCGAGCAATGCTAGACGTACA 60.798 52.381 19.25 0.00 39.88 2.90
3575 5562 2.112522 CGAGCAATGCTAGACGTACAG 58.887 52.381 8.12 0.00 39.88 2.74
3576 5563 2.464865 GAGCAATGCTAGACGTACAGG 58.535 52.381 8.12 0.00 39.88 4.00
3577 5564 2.099263 GAGCAATGCTAGACGTACAGGA 59.901 50.000 8.12 0.00 39.88 3.86
3578 5565 2.496070 AGCAATGCTAGACGTACAGGAA 59.504 45.455 5.69 0.00 36.99 3.36
3579 5566 2.860735 GCAATGCTAGACGTACAGGAAG 59.139 50.000 0.00 0.00 0.00 3.46
3580 5567 3.676324 GCAATGCTAGACGTACAGGAAGT 60.676 47.826 0.00 0.00 0.00 3.01
3581 5568 4.495422 CAATGCTAGACGTACAGGAAGTT 58.505 43.478 0.00 0.00 0.00 2.66
3582 5569 5.647589 CAATGCTAGACGTACAGGAAGTTA 58.352 41.667 0.00 0.00 0.00 2.24
3583 5570 4.691860 TGCTAGACGTACAGGAAGTTAC 57.308 45.455 0.00 0.00 0.00 2.50
3584 5571 4.074259 TGCTAGACGTACAGGAAGTTACA 58.926 43.478 0.00 0.00 0.00 2.41
3585 5572 4.155462 TGCTAGACGTACAGGAAGTTACAG 59.845 45.833 0.00 0.00 0.00 2.74
3586 5573 4.438472 GCTAGACGTACAGGAAGTTACAGG 60.438 50.000 0.00 0.00 0.00 4.00
3587 5574 2.824341 AGACGTACAGGAAGTTACAGGG 59.176 50.000 0.00 0.00 0.00 4.45
3588 5575 1.897802 ACGTACAGGAAGTTACAGGGG 59.102 52.381 0.00 0.00 0.00 4.79
3589 5576 1.206371 CGTACAGGAAGTTACAGGGGG 59.794 57.143 0.00 0.00 0.00 5.40
3590 5577 2.263545 GTACAGGAAGTTACAGGGGGT 58.736 52.381 0.00 0.00 0.00 4.95
3591 5578 1.829138 ACAGGAAGTTACAGGGGGTT 58.171 50.000 0.00 0.00 0.00 4.11
3592 5579 2.141067 ACAGGAAGTTACAGGGGGTTT 58.859 47.619 0.00 0.00 0.00 3.27
3593 5580 3.329277 ACAGGAAGTTACAGGGGGTTTA 58.671 45.455 0.00 0.00 0.00 2.01
3594 5581 3.073503 ACAGGAAGTTACAGGGGGTTTAC 59.926 47.826 0.00 0.00 0.00 2.01
3595 5582 2.303890 AGGAAGTTACAGGGGGTTTACG 59.696 50.000 0.00 0.00 0.00 3.18
3596 5583 2.616256 GGAAGTTACAGGGGGTTTACGG 60.616 54.545 0.00 0.00 0.00 4.02
3597 5584 0.986527 AGTTACAGGGGGTTTACGGG 59.013 55.000 0.00 0.00 0.00 5.28
3598 5585 0.035152 GTTACAGGGGGTTTACGGGG 60.035 60.000 0.00 0.00 0.00 5.73
3599 5586 1.851065 TTACAGGGGGTTTACGGGGC 61.851 60.000 0.00 0.00 0.00 5.80
3600 5587 2.769145 TACAGGGGGTTTACGGGGCT 62.769 60.000 0.00 0.00 0.00 5.19
3601 5588 3.335729 AGGGGGTTTACGGGGCTG 61.336 66.667 0.00 0.00 0.00 4.85
3602 5589 3.654143 GGGGGTTTACGGGGCTGT 61.654 66.667 0.00 0.00 0.00 4.40
3603 5590 2.437449 GGGGTTTACGGGGCTGTT 59.563 61.111 0.00 0.00 0.00 3.16
3604 5591 1.974875 GGGGTTTACGGGGCTGTTG 60.975 63.158 0.00 0.00 0.00 3.33
3605 5592 1.974875 GGGTTTACGGGGCTGTTGG 60.975 63.158 0.00 0.00 0.00 3.77
3606 5593 1.974875 GGTTTACGGGGCTGTTGGG 60.975 63.158 0.00 0.00 0.00 4.12
3607 5594 1.974875 GTTTACGGGGCTGTTGGGG 60.975 63.158 0.00 0.00 0.00 4.96
3608 5595 2.462626 TTTACGGGGCTGTTGGGGT 61.463 57.895 0.00 0.00 0.00 4.95
3609 5596 2.700407 TTTACGGGGCTGTTGGGGTG 62.700 60.000 0.00 0.00 0.00 4.61
3612 5599 3.897122 GGGGCTGTTGGGGTGTGA 61.897 66.667 0.00 0.00 0.00 3.58
3613 5600 2.440599 GGGCTGTTGGGGTGTGAT 59.559 61.111 0.00 0.00 0.00 3.06
3614 5601 1.228862 GGGCTGTTGGGGTGTGATT 60.229 57.895 0.00 0.00 0.00 2.57
3615 5602 1.535204 GGGCTGTTGGGGTGTGATTG 61.535 60.000 0.00 0.00 0.00 2.67
3616 5603 1.535204 GGCTGTTGGGGTGTGATTGG 61.535 60.000 0.00 0.00 0.00 3.16
3617 5604 1.966762 CTGTTGGGGTGTGATTGGC 59.033 57.895 0.00 0.00 0.00 4.52
3618 5605 0.827089 CTGTTGGGGTGTGATTGGCA 60.827 55.000 0.00 0.00 0.00 4.92
3619 5606 0.827089 TGTTGGGGTGTGATTGGCAG 60.827 55.000 0.00 0.00 0.00 4.85
3620 5607 0.539438 GTTGGGGTGTGATTGGCAGA 60.539 55.000 0.00 0.00 0.00 4.26
3621 5608 0.251297 TTGGGGTGTGATTGGCAGAG 60.251 55.000 0.00 0.00 0.00 3.35
3622 5609 1.133181 TGGGGTGTGATTGGCAGAGA 61.133 55.000 0.00 0.00 0.00 3.10
3623 5610 0.257039 GGGGTGTGATTGGCAGAGAT 59.743 55.000 0.00 0.00 0.00 2.75
3624 5611 1.673168 GGGTGTGATTGGCAGAGATC 58.327 55.000 0.00 0.00 0.00 2.75
3625 5612 1.211457 GGGTGTGATTGGCAGAGATCT 59.789 52.381 0.00 0.00 0.00 2.75
3626 5613 2.435805 GGGTGTGATTGGCAGAGATCTA 59.564 50.000 0.00 0.00 0.00 1.98
3627 5614 3.118261 GGGTGTGATTGGCAGAGATCTAA 60.118 47.826 0.00 0.00 0.00 2.10
3628 5615 4.445448 GGGTGTGATTGGCAGAGATCTAAT 60.445 45.833 0.00 0.00 0.00 1.73
3629 5616 5.128919 GGTGTGATTGGCAGAGATCTAATT 58.871 41.667 0.00 0.00 0.00 1.40
3630 5617 6.291377 GGTGTGATTGGCAGAGATCTAATTA 58.709 40.000 0.00 0.00 0.00 1.40
3631 5618 6.426328 GGTGTGATTGGCAGAGATCTAATTAG 59.574 42.308 6.11 6.11 0.00 1.73
3632 5619 7.212976 GTGTGATTGGCAGAGATCTAATTAGA 58.787 38.462 17.32 17.32 36.65 2.10
3633 5620 7.712639 GTGTGATTGGCAGAGATCTAATTAGAA 59.287 37.037 18.79 3.46 35.69 2.10
3634 5621 7.930325 TGTGATTGGCAGAGATCTAATTAGAAG 59.070 37.037 18.79 8.18 35.69 2.85
3635 5622 7.387397 GTGATTGGCAGAGATCTAATTAGAAGG 59.613 40.741 18.79 8.18 35.69 3.46
3636 5623 5.815233 TGGCAGAGATCTAATTAGAAGGG 57.185 43.478 18.79 8.49 35.69 3.95
3637 5624 4.040952 TGGCAGAGATCTAATTAGAAGGGC 59.959 45.833 18.79 16.16 35.69 5.19
3638 5625 4.040952 GGCAGAGATCTAATTAGAAGGGCA 59.959 45.833 18.79 0.00 35.69 5.36
3639 5626 5.237048 GCAGAGATCTAATTAGAAGGGCAG 58.763 45.833 18.79 8.97 35.69 4.85
3640 5627 5.792741 CAGAGATCTAATTAGAAGGGCAGG 58.207 45.833 18.79 3.07 35.69 4.85
3641 5628 4.285775 AGAGATCTAATTAGAAGGGCAGGC 59.714 45.833 18.79 3.95 35.69 4.85
3642 5629 3.329225 AGATCTAATTAGAAGGGCAGGCC 59.671 47.826 18.79 4.33 35.69 5.19
3643 5630 2.376855 ATCTAATTAGAAGGGCAGGCCC 59.623 50.000 21.90 21.90 44.39 5.80
3644 5631 4.217601 ATCTAATTAGAAGGGCAGGCCCA 61.218 47.826 29.88 10.42 45.47 5.36
3645 5632 6.283304 ATCTAATTAGAAGGGCAGGCCCAC 62.283 50.000 29.88 21.95 45.47 4.61
3652 5639 4.284550 GGCAGGCCCACCAGTGAA 62.285 66.667 0.00 0.00 39.06 3.18
3653 5640 2.203480 GCAGGCCCACCAGTGAAA 60.203 61.111 0.00 0.00 39.06 2.69
3654 5641 1.832167 GCAGGCCCACCAGTGAAAA 60.832 57.895 0.00 0.00 39.06 2.29
3655 5642 1.187567 GCAGGCCCACCAGTGAAAAT 61.188 55.000 0.00 0.00 39.06 1.82
3656 5643 0.890683 CAGGCCCACCAGTGAAAATC 59.109 55.000 0.00 0.00 39.06 2.17
3657 5644 0.482446 AGGCCCACCAGTGAAAATCA 59.518 50.000 0.00 0.00 39.06 2.57
3658 5645 0.890683 GGCCCACCAGTGAAAATCAG 59.109 55.000 0.00 0.00 35.26 2.90
3659 5646 0.890683 GCCCACCAGTGAAAATCAGG 59.109 55.000 0.00 0.00 0.00 3.86
3660 5647 1.549203 CCCACCAGTGAAAATCAGGG 58.451 55.000 0.00 0.00 0.00 4.45
3661 5648 1.549203 CCACCAGTGAAAATCAGGGG 58.451 55.000 0.00 0.85 0.00 4.79
3662 5649 1.549203 CACCAGTGAAAATCAGGGGG 58.451 55.000 0.00 0.00 0.00 5.40
3663 5650 1.075374 CACCAGTGAAAATCAGGGGGA 59.925 52.381 0.00 0.00 29.43 4.81
3664 5651 1.786441 ACCAGTGAAAATCAGGGGGAA 59.214 47.619 0.00 0.00 0.00 3.97
3665 5652 2.178984 ACCAGTGAAAATCAGGGGGAAA 59.821 45.455 0.00 0.00 0.00 3.13
3666 5653 3.238597 CCAGTGAAAATCAGGGGGAAAA 58.761 45.455 0.00 0.00 0.00 2.29
3667 5654 3.840078 CCAGTGAAAATCAGGGGGAAAAT 59.160 43.478 0.00 0.00 0.00 1.82
3668 5655 4.081476 CCAGTGAAAATCAGGGGGAAAATC 60.081 45.833 0.00 0.00 0.00 2.17
3669 5656 4.527816 CAGTGAAAATCAGGGGGAAAATCA 59.472 41.667 0.00 0.00 0.00 2.57
3670 5657 4.774200 AGTGAAAATCAGGGGGAAAATCAG 59.226 41.667 0.00 0.00 0.00 2.90
3671 5658 4.081476 GTGAAAATCAGGGGGAAAATCAGG 60.081 45.833 0.00 0.00 0.00 3.86
3672 5659 2.854736 AATCAGGGGGAAAATCAGGG 57.145 50.000 0.00 0.00 0.00 4.45
3673 5660 0.936691 ATCAGGGGGAAAATCAGGGG 59.063 55.000 0.00 0.00 0.00 4.79
3674 5661 1.221213 TCAGGGGGAAAATCAGGGGG 61.221 60.000 0.00 0.00 0.00 5.40
3688 5675 2.203209 GGGGGCGCCAGTTAGATG 60.203 66.667 30.85 0.00 0.00 2.90
3689 5676 2.742116 GGGGGCGCCAGTTAGATGA 61.742 63.158 30.85 0.00 0.00 2.92
3690 5677 1.223487 GGGGCGCCAGTTAGATGAA 59.777 57.895 30.85 0.00 0.00 2.57
3691 5678 0.815615 GGGGCGCCAGTTAGATGAAG 60.816 60.000 30.85 0.00 0.00 3.02
3692 5679 1.440145 GGGCGCCAGTTAGATGAAGC 61.440 60.000 30.85 0.98 0.00 3.86
3693 5680 1.440145 GGCGCCAGTTAGATGAAGCC 61.440 60.000 24.80 0.00 36.13 4.35
3694 5681 0.744414 GCGCCAGTTAGATGAAGCCA 60.744 55.000 0.00 0.00 0.00 4.75
3695 5682 1.009829 CGCCAGTTAGATGAAGCCAC 58.990 55.000 0.00 0.00 0.00 5.01
3696 5683 1.009829 GCCAGTTAGATGAAGCCACG 58.990 55.000 0.00 0.00 0.00 4.94
3697 5684 1.676014 GCCAGTTAGATGAAGCCACGT 60.676 52.381 0.00 0.00 0.00 4.49
3698 5685 2.699954 CCAGTTAGATGAAGCCACGTT 58.300 47.619 0.00 0.00 0.00 3.99
3699 5686 2.673368 CCAGTTAGATGAAGCCACGTTC 59.327 50.000 0.00 0.00 0.00 3.95
3700 5687 3.589988 CAGTTAGATGAAGCCACGTTCT 58.410 45.455 0.00 0.00 0.00 3.01
3701 5688 3.369147 CAGTTAGATGAAGCCACGTTCTG 59.631 47.826 0.00 0.00 0.00 3.02
3702 5689 3.006967 AGTTAGATGAAGCCACGTTCTGT 59.993 43.478 0.00 0.00 0.00 3.41
3703 5690 2.550830 AGATGAAGCCACGTTCTGTT 57.449 45.000 0.00 0.00 0.00 3.16
3704 5691 2.417719 AGATGAAGCCACGTTCTGTTC 58.582 47.619 0.00 0.00 0.00 3.18
3705 5692 1.464997 GATGAAGCCACGTTCTGTTCC 59.535 52.381 0.00 0.00 0.00 3.62
3706 5693 0.468226 TGAAGCCACGTTCTGTTCCT 59.532 50.000 0.00 0.00 0.00 3.36
3707 5694 0.868406 GAAGCCACGTTCTGTTCCTG 59.132 55.000 0.00 0.00 0.00 3.86
3708 5695 0.180406 AAGCCACGTTCTGTTCCTGT 59.820 50.000 0.00 0.00 0.00 4.00
3709 5696 1.045407 AGCCACGTTCTGTTCCTGTA 58.955 50.000 0.00 0.00 0.00 2.74
3710 5697 1.414919 AGCCACGTTCTGTTCCTGTAA 59.585 47.619 0.00 0.00 0.00 2.41
3711 5698 2.158871 AGCCACGTTCTGTTCCTGTAAA 60.159 45.455 0.00 0.00 0.00 2.01
3712 5699 2.223377 GCCACGTTCTGTTCCTGTAAAG 59.777 50.000 0.00 0.00 0.00 1.85
3713 5700 3.463944 CCACGTTCTGTTCCTGTAAAGT 58.536 45.455 0.00 0.00 0.00 2.66
3714 5701 3.875134 CCACGTTCTGTTCCTGTAAAGTT 59.125 43.478 0.00 0.00 0.00 2.66
3715 5702 4.334481 CCACGTTCTGTTCCTGTAAAGTTT 59.666 41.667 0.00 0.00 0.00 2.66
3716 5703 5.163693 CCACGTTCTGTTCCTGTAAAGTTTT 60.164 40.000 0.00 0.00 0.00 2.43
3717 5704 5.737290 CACGTTCTGTTCCTGTAAAGTTTTG 59.263 40.000 0.00 0.00 0.00 2.44
3718 5705 5.413523 ACGTTCTGTTCCTGTAAAGTTTTGT 59.586 36.000 0.00 0.00 0.00 2.83
3719 5706 6.594937 ACGTTCTGTTCCTGTAAAGTTTTGTA 59.405 34.615 0.00 0.00 0.00 2.41
3720 5707 7.281549 ACGTTCTGTTCCTGTAAAGTTTTGTAT 59.718 33.333 0.00 0.00 0.00 2.29
3721 5708 7.797123 CGTTCTGTTCCTGTAAAGTTTTGTATC 59.203 37.037 0.00 0.00 0.00 2.24
3722 5709 8.617809 GTTCTGTTCCTGTAAAGTTTTGTATCA 58.382 33.333 0.00 0.00 0.00 2.15
3723 5710 8.740123 TCTGTTCCTGTAAAGTTTTGTATCAA 57.260 30.769 0.00 0.00 0.00 2.57
3724 5711 9.349713 TCTGTTCCTGTAAAGTTTTGTATCAAT 57.650 29.630 0.00 0.00 0.00 2.57
3725 5712 9.612620 CTGTTCCTGTAAAGTTTTGTATCAATC 57.387 33.333 0.00 0.00 0.00 2.67
3726 5713 9.126151 TGTTCCTGTAAAGTTTTGTATCAATCA 57.874 29.630 0.00 0.00 0.00 2.57
3727 5714 9.394477 GTTCCTGTAAAGTTTTGTATCAATCAC 57.606 33.333 0.00 0.00 0.00 3.06
3728 5715 8.106247 TCCTGTAAAGTTTTGTATCAATCACC 57.894 34.615 0.00 0.00 0.00 4.02
3729 5716 7.175990 TCCTGTAAAGTTTTGTATCAATCACCC 59.824 37.037 0.00 0.00 0.00 4.61
3730 5717 7.176690 CCTGTAAAGTTTTGTATCAATCACCCT 59.823 37.037 0.00 0.00 0.00 4.34
3731 5718 7.881142 TGTAAAGTTTTGTATCAATCACCCTG 58.119 34.615 0.00 0.00 0.00 4.45
3732 5719 6.976934 AAAGTTTTGTATCAATCACCCTGT 57.023 33.333 0.00 0.00 0.00 4.00
3733 5720 9.005777 GTAAAGTTTTGTATCAATCACCCTGTA 57.994 33.333 0.00 0.00 0.00 2.74
3734 5721 8.650143 AAAGTTTTGTATCAATCACCCTGTAT 57.350 30.769 0.00 0.00 0.00 2.29
3735 5722 7.630242 AGTTTTGTATCAATCACCCTGTATG 57.370 36.000 0.00 0.00 0.00 2.39
3736 5723 7.175104 AGTTTTGTATCAATCACCCTGTATGT 58.825 34.615 0.00 0.00 0.00 2.29
3737 5724 7.336931 AGTTTTGTATCAATCACCCTGTATGTC 59.663 37.037 0.00 0.00 0.00 3.06
3738 5725 6.560003 TTGTATCAATCACCCTGTATGTCT 57.440 37.500 0.00 0.00 0.00 3.41
3739 5726 7.669089 TTGTATCAATCACCCTGTATGTCTA 57.331 36.000 0.00 0.00 0.00 2.59
3740 5727 7.290110 TGTATCAATCACCCTGTATGTCTAG 57.710 40.000 0.00 0.00 0.00 2.43
3741 5728 6.839134 TGTATCAATCACCCTGTATGTCTAGT 59.161 38.462 0.00 0.00 0.00 2.57
3742 5729 8.002459 TGTATCAATCACCCTGTATGTCTAGTA 58.998 37.037 0.00 0.00 0.00 1.82
3743 5730 9.026121 GTATCAATCACCCTGTATGTCTAGTAT 57.974 37.037 0.00 0.00 0.00 2.12
3744 5731 7.914427 TCAATCACCCTGTATGTCTAGTATT 57.086 36.000 0.00 0.00 0.00 1.89
3745 5732 9.601810 ATCAATCACCCTGTATGTCTAGTATTA 57.398 33.333 0.00 0.00 0.00 0.98
3746 5733 9.601810 TCAATCACCCTGTATGTCTAGTATTAT 57.398 33.333 0.00 0.00 0.00 1.28
3749 5736 8.190326 TCACCCTGTATGTCTAGTATTATTGG 57.810 38.462 0.00 0.00 0.00 3.16
3750 5737 8.008332 TCACCCTGTATGTCTAGTATTATTGGA 58.992 37.037 0.00 0.00 0.00 3.53
3751 5738 8.816894 CACCCTGTATGTCTAGTATTATTGGAT 58.183 37.037 0.00 0.00 0.00 3.41
3752 5739 8.816894 ACCCTGTATGTCTAGTATTATTGGATG 58.183 37.037 0.00 0.00 0.00 3.51
3753 5740 7.766278 CCCTGTATGTCTAGTATTATTGGATGC 59.234 40.741 0.00 0.00 0.00 3.91
3754 5741 7.489435 CCTGTATGTCTAGTATTATTGGATGCG 59.511 40.741 0.00 0.00 0.00 4.73
3755 5742 7.320399 TGTATGTCTAGTATTATTGGATGCGG 58.680 38.462 0.00 0.00 0.00 5.69
3756 5743 5.801531 TGTCTAGTATTATTGGATGCGGT 57.198 39.130 0.00 0.00 0.00 5.68
3757 5744 5.538118 TGTCTAGTATTATTGGATGCGGTG 58.462 41.667 0.00 0.00 0.00 4.94
3758 5745 4.389077 GTCTAGTATTATTGGATGCGGTGC 59.611 45.833 0.00 0.00 0.00 5.01
3799 5786 1.464997 GACCCTGAAAGATGCGACAAC 59.535 52.381 0.00 0.00 34.07 3.32
3833 5820 2.447887 GCGTCCATCAGTGTCAGCG 61.448 63.158 0.00 0.00 0.00 5.18
3853 5840 2.979813 CGCATTGTCTTTTTACCTGTGC 59.020 45.455 0.00 0.00 0.00 4.57
3862 5849 3.545124 TTACCTGTGCCCTGCCGTG 62.545 63.158 0.00 0.00 0.00 4.94
3968 5970 0.830444 TTCAGTGGCCCGTGTCTAGT 60.830 55.000 0.00 0.00 0.00 2.57
3969 5971 1.215647 CAGTGGCCCGTGTCTAGTC 59.784 63.158 0.00 0.00 0.00 2.59
3970 5972 1.076906 AGTGGCCCGTGTCTAGTCT 59.923 57.895 0.00 0.00 0.00 3.24
3971 5973 0.330604 AGTGGCCCGTGTCTAGTCTA 59.669 55.000 0.00 0.00 0.00 2.59
3972 5974 0.739561 GTGGCCCGTGTCTAGTCTAG 59.260 60.000 0.00 0.00 0.00 2.43
3999 6001 2.806244 CCTGGTACGGTTTCTTGTTGAG 59.194 50.000 0.00 0.00 0.00 3.02
4001 6003 2.171027 TGGTACGGTTTCTTGTTGAGGT 59.829 45.455 0.00 0.00 0.00 3.85
4018 6020 2.307686 GAGGTGAAATGGGTTCCCTACA 59.692 50.000 9.43 1.97 37.16 2.74
4061 6063 3.840666 TCTTGCTGAAGAATGGAGGTAGT 59.159 43.478 0.00 0.00 35.14 2.73
4203 6216 4.219507 CCCTCGCACTGTAATCATCTCTAT 59.780 45.833 0.00 0.00 0.00 1.98
4261 6274 5.105063 GGAAAGCTGACAAAATATGAAGGC 58.895 41.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.441718 TTAGTGAATTCCAGCCTGAATCT 57.558 39.130 2.27 0.00 33.91 2.40
15 16 5.010012 ACAAAGTTTAGTGAATTCCAGCCTG 59.990 40.000 2.27 0.00 0.00 4.85
196 197 7.981225 GCCTCAAATGAACACATTTATAACCAT 59.019 33.333 7.67 0.00 40.72 3.55
199 200 8.243426 TCAGCCTCAAATGAACACATTTATAAC 58.757 33.333 7.67 0.91 40.72 1.89
222 223 7.122204 TGGATCATAGTATAACATACCGGTCAG 59.878 40.741 12.40 7.67 0.00 3.51
223 224 6.949463 TGGATCATAGTATAACATACCGGTCA 59.051 38.462 12.40 0.00 0.00 4.02
224 225 7.400599 TGGATCATAGTATAACATACCGGTC 57.599 40.000 12.40 0.00 0.00 4.79
225 226 7.786046 TTGGATCATAGTATAACATACCGGT 57.214 36.000 13.98 13.98 0.00 5.28
226 227 9.667107 AATTTGGATCATAGTATAACATACCGG 57.333 33.333 0.00 0.00 0.00 5.28
310 312 1.401552 CATGCGGTGACTTACAATGGG 59.598 52.381 0.00 0.00 0.00 4.00
313 315 2.027192 AGTCCATGCGGTGACTTACAAT 60.027 45.455 0.00 0.00 0.00 2.71
333 335 8.380644 ACGACATGTAAATCAAACGATCTTTAG 58.619 33.333 0.00 0.00 0.00 1.85
417 419 6.528072 GGATGTTTCCGATTTTCAAATCTGTC 59.472 38.462 9.95 0.00 41.99 3.51
476 479 4.782019 TTTGATTACTGGTTGATGGTGC 57.218 40.909 0.00 0.00 0.00 5.01
521 524 4.802051 CGGCACATGGGACTGGGG 62.802 72.222 0.00 0.00 0.00 4.96
636 640 9.324008 TCATACTCCTACTAGTACTAGTATGCT 57.676 37.037 32.85 22.31 44.76 3.79
704 725 0.887247 TGTTGGCATGTGGGAAATCG 59.113 50.000 0.00 0.00 0.00 3.34
726 747 7.692705 GCGACTTTTGCTAAAGGAGTAATTAAG 59.307 37.037 21.83 0.00 44.10 1.85
761 784 2.123342 GTGGATTCGATCGAAGCTCTG 58.877 52.381 36.12 0.00 40.05 3.35
802 826 4.505970 CTGGAGGGGGAGGGGGAG 62.506 77.778 0.00 0.00 0.00 4.30
836 868 1.212616 GATGGAGATTCGAACCGCAG 58.787 55.000 0.00 0.00 0.00 5.18
872 904 2.702592 TCTGTTATTTGGGGCCTACG 57.297 50.000 0.84 0.00 0.00 3.51
899 954 2.587060 AATACCCACCTGGAGGATGA 57.413 50.000 12.14 0.00 38.94 2.92
900 955 2.158608 GGAAATACCCACCTGGAGGATG 60.159 54.545 12.14 0.00 38.94 3.51
909 964 2.353579 CGAAATGACGGAAATACCCACC 59.646 50.000 0.00 0.00 34.64 4.61
913 968 3.126343 ACTTGCGAAATGACGGAAATACC 59.874 43.478 0.00 0.00 42.19 2.73
914 969 4.336532 ACTTGCGAAATGACGGAAATAC 57.663 40.909 0.00 0.00 42.19 1.89
915 970 6.483385 TTTACTTGCGAAATGACGGAAATA 57.517 33.333 0.00 0.00 42.19 1.40
980 1036 1.002274 AAGAGGACAGCCGAGGGAT 59.998 57.895 0.00 0.00 39.96 3.85
983 1039 1.671901 GGAGAAGAGGACAGCCGAGG 61.672 65.000 0.00 0.00 39.96 4.63
1054 1110 0.179171 GCTCGCGCTAGACTACAACA 60.179 55.000 13.89 0.00 0.00 3.33
1070 1126 3.764160 CTGCCCCTCGGAATGGCTC 62.764 68.421 15.86 0.01 45.56 4.70
1096 1152 1.438651 CATTGCGACGGGAGAAAGAA 58.561 50.000 0.00 0.00 0.00 2.52
1097 1153 0.391130 CCATTGCGACGGGAGAAAGA 60.391 55.000 0.00 0.00 0.00 2.52
1098 1154 1.982073 GCCATTGCGACGGGAGAAAG 61.982 60.000 0.00 0.00 0.00 2.62
1099 1155 2.038269 GCCATTGCGACGGGAGAAA 61.038 57.895 0.00 0.00 0.00 2.52
1241 1297 2.701780 CCTCCAGGTGTCGAGACCG 61.702 68.421 24.53 18.62 41.35 4.79
1244 1300 1.304217 GTCCCTCCAGGTGTCGAGA 60.304 63.158 0.00 0.00 36.75 4.04
1478 1534 1.598130 GAAGTTGTGCGCCAGGTCT 60.598 57.895 4.18 0.27 0.00 3.85
1535 1591 1.961180 AATCGAGGCGGGACAAGGAG 61.961 60.000 0.00 0.00 0.00 3.69
1544 1600 1.521681 GGAGGACAAATCGAGGCGG 60.522 63.158 0.00 0.00 0.00 6.13
1799 1855 1.880340 GCACTCGATCTTGAGCGGG 60.880 63.158 6.61 6.61 39.68 6.13
1823 1881 1.207791 TTCTTGGCTCATCCCTCTCC 58.792 55.000 0.00 0.00 0.00 3.71
1964 2022 2.667418 CACTGCAGCACTAGCCCT 59.333 61.111 15.27 0.00 43.56 5.19
2006 2291 2.360852 TCCTCGTCCCTGGTCGTC 60.361 66.667 2.94 0.00 0.00 4.20
2529 3971 0.608035 TCGGGCCACCTGATTCAAAC 60.608 55.000 4.39 0.00 33.41 2.93
2532 3974 2.668632 GTCGGGCCACCTGATTCA 59.331 61.111 4.39 0.00 41.38 2.57
3186 5171 2.106683 CGGGTCATGGCTTCCGTTC 61.107 63.158 6.82 0.00 37.92 3.95
3263 5248 5.890334 ACCTAATAACGTTGGCAAATGATG 58.110 37.500 11.99 0.00 0.00 3.07
3264 5249 6.524101 AACCTAATAACGTTGGCAAATGAT 57.476 33.333 11.99 0.00 0.00 2.45
3265 5250 5.968528 AACCTAATAACGTTGGCAAATGA 57.031 34.783 11.99 0.00 0.00 2.57
3290 5275 2.678324 CTGGTTTCTTCACCGTCTCTC 58.322 52.381 0.00 0.00 40.09 3.20
3291 5276 1.270358 GCTGGTTTCTTCACCGTCTCT 60.270 52.381 0.00 0.00 40.09 3.10
3324 5309 1.128692 GAGTACCAAACGCACATCAGC 59.871 52.381 0.00 0.00 0.00 4.26
3363 5348 1.655885 TACATACACGGCCGCGAAGA 61.656 55.000 28.58 6.68 0.00 2.87
3419 5405 1.065358 CGAAAACGCTAGCGAAAGGA 58.935 50.000 41.33 0.00 42.83 3.36
3433 5419 2.339403 TGCTGCTGCATTCCGAAAA 58.661 47.368 14.93 0.00 45.31 2.29
3468 5454 2.478134 CTCAGTTCTCACCGCAAAAGAG 59.522 50.000 0.00 0.00 0.00 2.85
3469 5455 2.102420 TCTCAGTTCTCACCGCAAAAGA 59.898 45.455 0.00 0.00 0.00 2.52
3470 5456 2.483876 TCTCAGTTCTCACCGCAAAAG 58.516 47.619 0.00 0.00 0.00 2.27
3471 5457 2.613026 TCTCAGTTCTCACCGCAAAA 57.387 45.000 0.00 0.00 0.00 2.44
3472 5458 2.613026 TTCTCAGTTCTCACCGCAAA 57.387 45.000 0.00 0.00 0.00 3.68
3497 5484 0.971386 CAAGAAAGCCACCAGCCAAT 59.029 50.000 0.00 0.00 45.47 3.16
3556 5543 2.099263 TCCTGTACGTCTAGCATTGCTC 59.901 50.000 15.81 0.00 40.44 4.26
3557 5544 2.100197 TCCTGTACGTCTAGCATTGCT 58.900 47.619 16.63 16.63 43.41 3.91
3558 5545 2.579207 TCCTGTACGTCTAGCATTGC 57.421 50.000 0.00 0.00 0.00 3.56
3559 5546 4.111375 ACTTCCTGTACGTCTAGCATTG 57.889 45.455 0.00 0.00 0.00 2.82
3560 5547 4.803098 AACTTCCTGTACGTCTAGCATT 57.197 40.909 0.00 0.00 0.00 3.56
3561 5548 4.703575 TGTAACTTCCTGTACGTCTAGCAT 59.296 41.667 0.00 0.00 0.00 3.79
3562 5549 4.074259 TGTAACTTCCTGTACGTCTAGCA 58.926 43.478 0.00 0.00 0.00 3.49
3563 5550 4.438472 CCTGTAACTTCCTGTACGTCTAGC 60.438 50.000 0.00 0.00 0.00 3.42
3564 5551 4.096081 CCCTGTAACTTCCTGTACGTCTAG 59.904 50.000 0.00 0.00 0.00 2.43
3565 5552 4.012374 CCCTGTAACTTCCTGTACGTCTA 58.988 47.826 0.00 0.00 0.00 2.59
3566 5553 2.824341 CCCTGTAACTTCCTGTACGTCT 59.176 50.000 0.00 0.00 0.00 4.18
3567 5554 2.094338 CCCCTGTAACTTCCTGTACGTC 60.094 54.545 0.00 0.00 0.00 4.34
3568 5555 1.897802 CCCCTGTAACTTCCTGTACGT 59.102 52.381 0.00 0.00 0.00 3.57
3569 5556 1.206371 CCCCCTGTAACTTCCTGTACG 59.794 57.143 0.00 0.00 0.00 3.67
3570 5557 2.263545 ACCCCCTGTAACTTCCTGTAC 58.736 52.381 0.00 0.00 0.00 2.90
3571 5558 2.727429 ACCCCCTGTAACTTCCTGTA 57.273 50.000 0.00 0.00 0.00 2.74
3572 5559 1.829138 AACCCCCTGTAACTTCCTGT 58.171 50.000 0.00 0.00 0.00 4.00
3573 5560 2.971901 AAACCCCCTGTAACTTCCTG 57.028 50.000 0.00 0.00 0.00 3.86
3574 5561 2.303890 CGTAAACCCCCTGTAACTTCCT 59.696 50.000 0.00 0.00 0.00 3.36
3575 5562 2.616256 CCGTAAACCCCCTGTAACTTCC 60.616 54.545 0.00 0.00 0.00 3.46
3576 5563 2.616256 CCCGTAAACCCCCTGTAACTTC 60.616 54.545 0.00 0.00 0.00 3.01
3577 5564 1.352017 CCCGTAAACCCCCTGTAACTT 59.648 52.381 0.00 0.00 0.00 2.66
3578 5565 0.986527 CCCGTAAACCCCCTGTAACT 59.013 55.000 0.00 0.00 0.00 2.24
3579 5566 0.035152 CCCCGTAAACCCCCTGTAAC 60.035 60.000 0.00 0.00 0.00 2.50
3580 5567 1.851065 GCCCCGTAAACCCCCTGTAA 61.851 60.000 0.00 0.00 0.00 2.41
3581 5568 2.300197 GCCCCGTAAACCCCCTGTA 61.300 63.158 0.00 0.00 0.00 2.74
3582 5569 3.654143 GCCCCGTAAACCCCCTGT 61.654 66.667 0.00 0.00 0.00 4.00
3583 5570 3.335729 AGCCCCGTAAACCCCCTG 61.336 66.667 0.00 0.00 0.00 4.45
3584 5571 3.335729 CAGCCCCGTAAACCCCCT 61.336 66.667 0.00 0.00 0.00 4.79
3585 5572 3.214190 AACAGCCCCGTAAACCCCC 62.214 63.158 0.00 0.00 0.00 5.40
3586 5573 1.974875 CAACAGCCCCGTAAACCCC 60.975 63.158 0.00 0.00 0.00 4.95
3587 5574 1.974875 CCAACAGCCCCGTAAACCC 60.975 63.158 0.00 0.00 0.00 4.11
3588 5575 1.974875 CCCAACAGCCCCGTAAACC 60.975 63.158 0.00 0.00 0.00 3.27
3589 5576 1.974875 CCCCAACAGCCCCGTAAAC 60.975 63.158 0.00 0.00 0.00 2.01
3590 5577 2.437002 CCCCAACAGCCCCGTAAA 59.563 61.111 0.00 0.00 0.00 2.01
3591 5578 2.855014 ACCCCAACAGCCCCGTAA 60.855 61.111 0.00 0.00 0.00 3.18
3592 5579 3.642503 CACCCCAACAGCCCCGTA 61.643 66.667 0.00 0.00 0.00 4.02
3595 5582 2.730129 AATCACACCCCAACAGCCCC 62.730 60.000 0.00 0.00 0.00 5.80
3596 5583 1.228862 AATCACACCCCAACAGCCC 60.229 57.895 0.00 0.00 0.00 5.19
3597 5584 1.535204 CCAATCACACCCCAACAGCC 61.535 60.000 0.00 0.00 0.00 4.85
3598 5585 1.966762 CCAATCACACCCCAACAGC 59.033 57.895 0.00 0.00 0.00 4.40
3599 5586 0.827089 TGCCAATCACACCCCAACAG 60.827 55.000 0.00 0.00 0.00 3.16
3600 5587 0.827089 CTGCCAATCACACCCCAACA 60.827 55.000 0.00 0.00 0.00 3.33
3601 5588 0.539438 TCTGCCAATCACACCCCAAC 60.539 55.000 0.00 0.00 0.00 3.77
3602 5589 0.251297 CTCTGCCAATCACACCCCAA 60.251 55.000 0.00 0.00 0.00 4.12
3603 5590 1.133181 TCTCTGCCAATCACACCCCA 61.133 55.000 0.00 0.00 0.00 4.96
3604 5591 0.257039 ATCTCTGCCAATCACACCCC 59.743 55.000 0.00 0.00 0.00 4.95
3605 5592 1.211457 AGATCTCTGCCAATCACACCC 59.789 52.381 0.00 0.00 0.00 4.61
3606 5593 2.706339 AGATCTCTGCCAATCACACC 57.294 50.000 0.00 0.00 0.00 4.16
3607 5594 7.212976 TCTAATTAGATCTCTGCCAATCACAC 58.787 38.462 11.24 0.00 0.00 3.82
3608 5595 7.365497 TCTAATTAGATCTCTGCCAATCACA 57.635 36.000 11.24 0.00 0.00 3.58
3609 5596 7.387397 CCTTCTAATTAGATCTCTGCCAATCAC 59.613 40.741 15.82 0.00 31.40 3.06
3610 5597 7.448420 CCTTCTAATTAGATCTCTGCCAATCA 58.552 38.462 15.82 0.00 31.40 2.57
3611 5598 6.878389 CCCTTCTAATTAGATCTCTGCCAATC 59.122 42.308 15.82 0.00 31.40 2.67
3612 5599 6.746614 GCCCTTCTAATTAGATCTCTGCCAAT 60.747 42.308 15.82 0.00 31.40 3.16
3613 5600 5.455326 GCCCTTCTAATTAGATCTCTGCCAA 60.455 44.000 15.82 0.00 31.40 4.52
3614 5601 4.040952 GCCCTTCTAATTAGATCTCTGCCA 59.959 45.833 15.82 0.00 31.40 4.92
3615 5602 4.040952 TGCCCTTCTAATTAGATCTCTGCC 59.959 45.833 15.82 2.90 31.40 4.85
3616 5603 5.220710 TGCCCTTCTAATTAGATCTCTGC 57.779 43.478 15.82 13.72 31.40 4.26
3617 5604 5.792741 CCTGCCCTTCTAATTAGATCTCTG 58.207 45.833 15.82 9.26 31.40 3.35
3618 5605 4.285775 GCCTGCCCTTCTAATTAGATCTCT 59.714 45.833 15.82 0.00 31.40 3.10
3619 5606 4.564613 GGCCTGCCCTTCTAATTAGATCTC 60.565 50.000 15.82 6.77 31.40 2.75
3620 5607 3.329225 GGCCTGCCCTTCTAATTAGATCT 59.671 47.826 15.82 0.00 31.40 2.75
3621 5608 3.680490 GGCCTGCCCTTCTAATTAGATC 58.320 50.000 15.82 6.77 31.40 2.75
3622 5609 3.797559 GGCCTGCCCTTCTAATTAGAT 57.202 47.619 15.82 0.00 31.40 1.98
3635 5622 3.808218 TTTCACTGGTGGGCCTGCC 62.808 63.158 4.53 8.00 37.23 4.85
3636 5623 1.187567 ATTTTCACTGGTGGGCCTGC 61.188 55.000 4.53 0.00 37.23 4.85
3637 5624 0.890683 GATTTTCACTGGTGGGCCTG 59.109 55.000 4.53 0.00 39.33 4.85
3638 5625 0.482446 TGATTTTCACTGGTGGGCCT 59.518 50.000 4.53 0.00 35.27 5.19
3639 5626 0.890683 CTGATTTTCACTGGTGGGCC 59.109 55.000 0.00 0.00 0.00 5.80
3640 5627 0.890683 CCTGATTTTCACTGGTGGGC 59.109 55.000 0.70 0.00 0.00 5.36
3641 5628 1.549203 CCCTGATTTTCACTGGTGGG 58.451 55.000 0.70 0.00 0.00 4.61
3642 5629 1.549203 CCCCTGATTTTCACTGGTGG 58.451 55.000 0.70 0.00 0.00 4.61
3643 5630 1.075374 TCCCCCTGATTTTCACTGGTG 59.925 52.381 0.00 0.00 0.00 4.17
3644 5631 1.455822 TCCCCCTGATTTTCACTGGT 58.544 50.000 0.00 0.00 0.00 4.00
3645 5632 2.603075 TTCCCCCTGATTTTCACTGG 57.397 50.000 0.00 0.00 0.00 4.00
3646 5633 4.527816 TGATTTTCCCCCTGATTTTCACTG 59.472 41.667 0.00 0.00 0.00 3.66
3647 5634 4.750941 TGATTTTCCCCCTGATTTTCACT 58.249 39.130 0.00 0.00 0.00 3.41
3648 5635 4.081476 CCTGATTTTCCCCCTGATTTTCAC 60.081 45.833 0.00 0.00 0.00 3.18
3649 5636 4.095946 CCTGATTTTCCCCCTGATTTTCA 58.904 43.478 0.00 0.00 0.00 2.69
3650 5637 3.452264 CCCTGATTTTCCCCCTGATTTTC 59.548 47.826 0.00 0.00 0.00 2.29
3651 5638 3.453868 CCCTGATTTTCCCCCTGATTTT 58.546 45.455 0.00 0.00 0.00 1.82
3652 5639 2.293118 CCCCTGATTTTCCCCCTGATTT 60.293 50.000 0.00 0.00 0.00 2.17
3653 5640 1.291939 CCCCTGATTTTCCCCCTGATT 59.708 52.381 0.00 0.00 0.00 2.57
3654 5641 0.936691 CCCCTGATTTTCCCCCTGAT 59.063 55.000 0.00 0.00 0.00 2.90
3655 5642 1.221213 CCCCCTGATTTTCCCCCTGA 61.221 60.000 0.00 0.00 0.00 3.86
3656 5643 1.311059 CCCCCTGATTTTCCCCCTG 59.689 63.158 0.00 0.00 0.00 4.45
3657 5644 3.871333 CCCCCTGATTTTCCCCCT 58.129 61.111 0.00 0.00 0.00 4.79
3671 5658 2.203209 CATCTAACTGGCGCCCCC 60.203 66.667 26.77 0.00 0.00 5.40
3672 5659 0.815615 CTTCATCTAACTGGCGCCCC 60.816 60.000 26.77 0.00 0.00 5.80
3673 5660 1.440145 GCTTCATCTAACTGGCGCCC 61.440 60.000 26.77 6.44 0.00 6.13
3674 5661 1.440145 GGCTTCATCTAACTGGCGCC 61.440 60.000 22.73 22.73 0.00 6.53
3675 5662 0.744414 TGGCTTCATCTAACTGGCGC 60.744 55.000 0.00 0.00 0.00 6.53
3676 5663 1.009829 GTGGCTTCATCTAACTGGCG 58.990 55.000 0.00 0.00 0.00 5.69
3677 5664 1.009829 CGTGGCTTCATCTAACTGGC 58.990 55.000 0.00 0.00 0.00 4.85
3678 5665 2.386661 ACGTGGCTTCATCTAACTGG 57.613 50.000 0.00 0.00 0.00 4.00
3679 5666 3.369147 CAGAACGTGGCTTCATCTAACTG 59.631 47.826 0.00 0.00 0.00 3.16
3680 5667 3.006967 ACAGAACGTGGCTTCATCTAACT 59.993 43.478 0.00 0.00 0.00 2.24
3681 5668 3.326747 ACAGAACGTGGCTTCATCTAAC 58.673 45.455 0.00 0.00 0.00 2.34
3682 5669 3.678056 ACAGAACGTGGCTTCATCTAA 57.322 42.857 0.00 0.00 0.00 2.10
3683 5670 3.585862 GAACAGAACGTGGCTTCATCTA 58.414 45.455 0.00 0.00 0.00 1.98
3684 5671 2.417719 GAACAGAACGTGGCTTCATCT 58.582 47.619 0.00 0.00 0.00 2.90
3685 5672 1.464997 GGAACAGAACGTGGCTTCATC 59.535 52.381 0.00 0.00 0.00 2.92
3686 5673 1.072331 AGGAACAGAACGTGGCTTCAT 59.928 47.619 0.00 0.00 0.00 2.57
3687 5674 0.468226 AGGAACAGAACGTGGCTTCA 59.532 50.000 0.00 0.00 0.00 3.02
3688 5675 0.868406 CAGGAACAGAACGTGGCTTC 59.132 55.000 0.00 0.00 0.00 3.86
3689 5676 0.180406 ACAGGAACAGAACGTGGCTT 59.820 50.000 0.00 0.00 0.00 4.35
3690 5677 1.045407 TACAGGAACAGAACGTGGCT 58.955 50.000 0.00 0.00 0.00 4.75
3691 5678 1.873698 TTACAGGAACAGAACGTGGC 58.126 50.000 0.00 0.00 0.00 5.01
3692 5679 3.463944 ACTTTACAGGAACAGAACGTGG 58.536 45.455 0.00 0.00 0.00 4.94
3693 5680 5.479716 AAACTTTACAGGAACAGAACGTG 57.520 39.130 0.00 0.00 0.00 4.49
3694 5681 5.413523 ACAAAACTTTACAGGAACAGAACGT 59.586 36.000 0.00 0.00 0.00 3.99
3695 5682 5.875930 ACAAAACTTTACAGGAACAGAACG 58.124 37.500 0.00 0.00 0.00 3.95
3696 5683 8.617809 TGATACAAAACTTTACAGGAACAGAAC 58.382 33.333 0.00 0.00 0.00 3.01
3697 5684 8.740123 TGATACAAAACTTTACAGGAACAGAA 57.260 30.769 0.00 0.00 0.00 3.02
3698 5685 8.740123 TTGATACAAAACTTTACAGGAACAGA 57.260 30.769 0.00 0.00 0.00 3.41
3699 5686 9.612620 GATTGATACAAAACTTTACAGGAACAG 57.387 33.333 0.00 0.00 0.00 3.16
3700 5687 9.126151 TGATTGATACAAAACTTTACAGGAACA 57.874 29.630 0.00 0.00 0.00 3.18
3701 5688 9.394477 GTGATTGATACAAAACTTTACAGGAAC 57.606 33.333 0.00 0.00 0.00 3.62
3702 5689 8.573035 GGTGATTGATACAAAACTTTACAGGAA 58.427 33.333 0.00 0.00 0.00 3.36
3703 5690 7.175990 GGGTGATTGATACAAAACTTTACAGGA 59.824 37.037 0.00 0.00 0.00 3.86
3704 5691 7.176690 AGGGTGATTGATACAAAACTTTACAGG 59.823 37.037 0.00 0.00 0.00 4.00
3705 5692 8.023128 CAGGGTGATTGATACAAAACTTTACAG 58.977 37.037 0.00 0.00 0.00 2.74
3706 5693 7.504238 ACAGGGTGATTGATACAAAACTTTACA 59.496 33.333 0.00 0.00 0.00 2.41
3707 5694 7.882179 ACAGGGTGATTGATACAAAACTTTAC 58.118 34.615 0.00 0.00 0.00 2.01
3708 5695 9.747898 ATACAGGGTGATTGATACAAAACTTTA 57.252 29.630 0.00 0.00 0.00 1.85
3709 5696 6.976934 ACAGGGTGATTGATACAAAACTTT 57.023 33.333 0.00 0.00 0.00 2.66
3710 5697 7.669722 ACATACAGGGTGATTGATACAAAACTT 59.330 33.333 0.00 0.00 0.00 2.66
3711 5698 7.175104 ACATACAGGGTGATTGATACAAAACT 58.825 34.615 0.00 0.00 0.00 2.66
3712 5699 7.336931 AGACATACAGGGTGATTGATACAAAAC 59.663 37.037 0.00 0.00 0.00 2.43
3713 5700 7.402054 AGACATACAGGGTGATTGATACAAAA 58.598 34.615 0.00 0.00 0.00 2.44
3714 5701 6.957631 AGACATACAGGGTGATTGATACAAA 58.042 36.000 0.00 0.00 0.00 2.83
3715 5702 6.560003 AGACATACAGGGTGATTGATACAA 57.440 37.500 0.00 0.00 0.00 2.41
3716 5703 6.839134 ACTAGACATACAGGGTGATTGATACA 59.161 38.462 0.00 0.00 0.00 2.29
3717 5704 7.291411 ACTAGACATACAGGGTGATTGATAC 57.709 40.000 0.00 0.00 0.00 2.24
3718 5705 9.601810 AATACTAGACATACAGGGTGATTGATA 57.398 33.333 0.00 0.00 0.00 2.15
3719 5706 8.497910 AATACTAGACATACAGGGTGATTGAT 57.502 34.615 0.00 0.00 0.00 2.57
3720 5707 7.914427 AATACTAGACATACAGGGTGATTGA 57.086 36.000 0.00 0.00 0.00 2.57
3723 5710 8.816894 CCAATAATACTAGACATACAGGGTGAT 58.183 37.037 0.00 0.00 0.00 3.06
3724 5711 8.008332 TCCAATAATACTAGACATACAGGGTGA 58.992 37.037 0.00 0.00 0.00 4.02
3725 5712 8.190326 TCCAATAATACTAGACATACAGGGTG 57.810 38.462 0.00 0.00 0.00 4.61
3726 5713 8.816894 CATCCAATAATACTAGACATACAGGGT 58.183 37.037 0.00 0.00 0.00 4.34
3727 5714 7.766278 GCATCCAATAATACTAGACATACAGGG 59.234 40.741 0.00 0.00 0.00 4.45
3728 5715 7.489435 CGCATCCAATAATACTAGACATACAGG 59.511 40.741 0.00 0.00 0.00 4.00
3729 5716 7.489435 CCGCATCCAATAATACTAGACATACAG 59.511 40.741 0.00 0.00 0.00 2.74
3730 5717 7.039293 ACCGCATCCAATAATACTAGACATACA 60.039 37.037 0.00 0.00 0.00 2.29
3731 5718 7.275779 CACCGCATCCAATAATACTAGACATAC 59.724 40.741 0.00 0.00 0.00 2.39
3732 5719 7.320399 CACCGCATCCAATAATACTAGACATA 58.680 38.462 0.00 0.00 0.00 2.29
3733 5720 6.166279 CACCGCATCCAATAATACTAGACAT 58.834 40.000 0.00 0.00 0.00 3.06
3734 5721 5.538118 CACCGCATCCAATAATACTAGACA 58.462 41.667 0.00 0.00 0.00 3.41
3735 5722 4.389077 GCACCGCATCCAATAATACTAGAC 59.611 45.833 0.00 0.00 0.00 2.59
3736 5723 4.283467 AGCACCGCATCCAATAATACTAGA 59.717 41.667 0.00 0.00 0.00 2.43
3737 5724 4.389992 CAGCACCGCATCCAATAATACTAG 59.610 45.833 0.00 0.00 0.00 2.57
3738 5725 4.202315 ACAGCACCGCATCCAATAATACTA 60.202 41.667 0.00 0.00 0.00 1.82
3739 5726 3.141398 CAGCACCGCATCCAATAATACT 58.859 45.455 0.00 0.00 0.00 2.12
3740 5727 2.878406 ACAGCACCGCATCCAATAATAC 59.122 45.455 0.00 0.00 0.00 1.89
3741 5728 3.207265 ACAGCACCGCATCCAATAATA 57.793 42.857 0.00 0.00 0.00 0.98
3742 5729 2.057137 ACAGCACCGCATCCAATAAT 57.943 45.000 0.00 0.00 0.00 1.28
3743 5730 2.285083 GTACAGCACCGCATCCAATAA 58.715 47.619 0.00 0.00 0.00 1.40
3744 5731 1.208293 TGTACAGCACCGCATCCAATA 59.792 47.619 0.00 0.00 0.00 1.90
3745 5732 0.035534 TGTACAGCACCGCATCCAAT 60.036 50.000 0.00 0.00 0.00 3.16
3746 5733 0.953471 GTGTACAGCACCGCATCCAA 60.953 55.000 0.00 0.00 42.10 3.53
3747 5734 1.375396 GTGTACAGCACCGCATCCA 60.375 57.895 0.00 0.00 42.10 3.41
3748 5735 3.486263 GTGTACAGCACCGCATCC 58.514 61.111 0.00 0.00 42.10 3.51
3755 5742 1.524008 GGCCCAAAGGTGTACAGCAC 61.524 60.000 25.75 5.96 46.97 4.40
3756 5743 1.228429 GGCCCAAAGGTGTACAGCA 60.228 57.895 25.75 0.00 34.57 4.41
3757 5744 1.228429 TGGCCCAAAGGTGTACAGC 60.228 57.895 17.29 17.29 34.57 4.40
3758 5745 0.110486 ACTGGCCCAAAGGTGTACAG 59.890 55.000 0.00 0.00 34.57 2.74
3799 5786 4.767255 GCAGCCCCTCCTGTGTCG 62.767 72.222 0.00 0.00 35.28 4.35
3833 5820 3.317150 GGCACAGGTAAAAAGACAATGC 58.683 45.455 0.00 0.00 0.00 3.56
3870 5857 2.986979 TGCATGCACAGCCACAGG 60.987 61.111 18.46 0.00 0.00 4.00
3871 5858 2.257371 GTGCATGCACAGCCACAG 59.743 61.111 39.12 0.00 45.53 3.66
3925 5920 2.052237 CGCGTGTTGCCACTGAAC 60.052 61.111 0.00 0.00 42.08 3.18
3926 5921 3.276091 CCGCGTGTTGCCACTGAA 61.276 61.111 4.92 0.00 42.08 3.02
3929 5924 3.876589 CTACCCGCGTGTTGCCACT 62.877 63.158 4.92 0.00 42.08 4.00
3930 5925 3.419759 CTACCCGCGTGTTGCCAC 61.420 66.667 4.92 0.00 42.08 5.01
3931 5926 4.690719 CCTACCCGCGTGTTGCCA 62.691 66.667 4.92 0.00 42.08 4.92
3972 5974 1.293963 GAAACCGTACCAGGCGAACC 61.294 60.000 0.00 0.00 33.69 3.62
4018 6020 6.059787 AGAATCTCAGGCTGTCATTAAAGT 57.940 37.500 15.27 0.00 0.00 2.66
4057 6059 2.416547 ACTGCGAATGTGCAATGACTAC 59.583 45.455 0.00 0.00 45.74 2.73
4081 6083 1.294041 TGGCACCCATGACCAATCTA 58.706 50.000 0.00 0.00 29.67 1.98
4203 6216 5.564651 GCATCCGAAAATCAAGAACTCCAAA 60.565 40.000 0.00 0.00 0.00 3.28
4281 6295 0.535780 TGCTGCCACAGTGAAAGGAG 60.536 55.000 0.62 0.00 33.43 3.69


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

AutoCloner maintained by Alex Coulton.