Multiple sequence alignment - TraesCS7D01G294400

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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 TraesCS7D01G294400 chr7D 100.000 5043 0 0 1 5043 367391841 367386799 0.000000e+00 9313.0
1 TraesCS7D01G294400 chr7A 92.952 4157 130 49 761 4829 405952392 405948311 0.000000e+00 5903.0
2 TraesCS7D01G294400 chr7A 85.425 494 65 6 3 490 405953443 405952951 1.620000e-139 507.0
3 TraesCS7D01G294400 chr7A 93.421 228 11 4 488 712 405952607 405952381 8.090000e-88 335.0
4 TraesCS7D01G294400 chr7A 83.846 260 35 5 4785 5042 405069749 405069495 1.810000e-59 241.0
5 TraesCS7D01G294400 chr7A 87.826 115 6 5 1194 1301 405952731 405952618 1.470000e-25 128.0
6 TraesCS7D01G294400 chr7B 93.285 2904 85 32 757 3608 364697724 364700569 0.000000e+00 4181.0
7 TraesCS7D01G294400 chr7B 97.292 480 6 2 3618 4097 364700863 364701335 0.000000e+00 808.0
8 TraesCS7D01G294400 chr7B 96.034 353 10 1 4099 4451 364701524 364701872 5.660000e-159 571.0
9 TraesCS7D01G294400 chr7B 83.503 491 74 4 6 490 364674174 364674663 7.700000e-123 451.0
10 TraesCS7D01G294400 chr7B 95.652 230 6 3 4453 4681 364702032 364702258 2.870000e-97 366.0
11 TraesCS7D01G294400 chr7B 94.690 226 8 3 488 712 364697517 364697739 1.040000e-91 348.0
12 TraesCS7D01G294400 chr7B 85.906 298 27 6 4747 5043 364703585 364703868 2.280000e-78 303.0
13 TraesCS7D01G294400 chr7B 85.401 137 15 4 4877 5010 364906598 364906732 2.450000e-28 137.0
14 TraesCS7D01G294400 chr7B 90.099 101 4 3 1194 1289 364697388 364697487 5.300000e-25 126.0
15 TraesCS7D01G294400 chr1B 93.421 76 5 0 2 77 579967327 579967402 4.130000e-21 113.0
16 TraesCS7D01G294400 chr3A 90.541 74 7 0 3 76 277521536 277521609 1.160000e-16 99.0
17 TraesCS7D01G294400 chr2B 90.541 74 5 2 5 77 506051808 506051736 4.160000e-16 97.1
18 TraesCS7D01G294400 chr2D 97.778 45 1 0 33 77 7126671 7126627 1.510000e-10 78.7


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 TraesCS7D01G294400 chr7D 367386799 367391841 5042 True 9313.000000 9313 100.000000 1 5043 1 chr7D.!!$R1 5042
1 TraesCS7D01G294400 chr7A 405948311 405953443 5132 True 1718.250000 5903 89.906000 3 4829 4 chr7A.!!$R2 4826
2 TraesCS7D01G294400 chr7B 364697388 364703868 6480 False 957.571429 4181 93.279714 488 5043 7 chr7B.!!$F3 4555

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
239 244 0.178961 GAAGGGGTTTTGGGTGAGCT 60.179 55.0 0.00 0.0 0.0 4.09 F
711 1067 0.321671 CCCGCCTTTTGTCTCTCTCA 59.678 55.0 0.00 0.0 0.0 3.27 F
1092 1477 0.468585 ACGATCACCACCGGGCTATA 60.469 55.0 6.32 0.0 37.9 1.31 F
2394 2827 0.106318 AGCAGCCCCCATGATCTTTC 60.106 55.0 0.00 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1061 1446 0.460284 GTGATCGTGGCCTAGTGGTG 60.460 60.0 3.32 0.0 35.27 4.17 R
2380 2803 0.394216 TGTGCGAAAGATCATGGGGG 60.394 55.0 0.00 0.0 0.00 5.40 R
2688 3124 0.540597 GGAAGGCTGGAGCAGGTTTT 60.541 55.0 0.20 0.0 44.36 2.43 R
4046 4788 0.039437 CTACAGTTGACGCCGACAGT 60.039 55.0 0.00 0.0 32.17 3.55 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
31 32 4.746535 TTCATCTCCAATGCATGCAATT 57.253 36.364 26.68 16.11 0.00 2.32
39 40 6.016527 TCTCCAATGCATGCAATTAAGAGATC 60.017 38.462 26.68 0.00 0.00 2.75
40 41 5.010314 TCCAATGCATGCAATTAAGAGATCC 59.990 40.000 26.68 0.00 0.00 3.36
63 64 1.609208 CAAACCTGGTCACCCTCTTG 58.391 55.000 0.00 0.00 0.00 3.02
67 68 0.322008 CCTGGTCACCCTCTTGCTTC 60.322 60.000 0.00 0.00 0.00 3.86
82 83 1.421485 CTTCAGACATTGCGGCGAC 59.579 57.895 12.98 2.02 0.00 5.19
99 100 3.051479 CGCCCGGGTTTAGCGTTT 61.051 61.111 24.63 0.00 44.65 3.60
102 103 1.517210 GCCCGGGTTTAGCGTTTGAA 61.517 55.000 24.63 0.00 0.00 2.69
132 133 2.035442 GTCGAGTTCCAGCAAGGGC 61.035 63.158 0.00 0.00 38.24 5.19
137 138 1.607467 GTTCCAGCAAGGGCATGGT 60.607 57.895 0.00 0.00 44.61 3.55
144 145 3.965258 AAGGGCATGGTGGTGCGA 61.965 61.111 0.00 0.00 45.97 5.10
145 146 4.722700 AGGGCATGGTGGTGCGAC 62.723 66.667 0.00 0.00 45.97 5.19
184 189 4.154918 GTGATGCAAGAGAGAAACCGAATT 59.845 41.667 0.00 0.00 0.00 2.17
196 201 7.164803 AGAGAAACCGAATTCAGAGAAAGATT 58.835 34.615 6.22 0.00 0.00 2.40
199 204 5.165961 ACCGAATTCAGAGAAAGATTGGA 57.834 39.130 6.22 0.00 0.00 3.53
201 206 4.034975 CCGAATTCAGAGAAAGATTGGAGC 59.965 45.833 6.22 0.00 0.00 4.70
207 212 4.019051 TCAGAGAAAGATTGGAGCATGGAA 60.019 41.667 0.00 0.00 0.00 3.53
212 217 2.492025 AGATTGGAGCATGGAAGGGTA 58.508 47.619 0.00 0.00 0.00 3.69
216 221 1.149401 GAGCATGGAAGGGTAGGGC 59.851 63.158 0.00 0.00 0.00 5.19
218 223 2.689691 GCATGGAAGGGTAGGGCCA 61.690 63.158 6.18 0.00 39.65 5.36
232 237 1.913262 GGCCAGGAAGGGGTTTTGG 60.913 63.158 0.00 0.00 38.09 3.28
239 244 0.178961 GAAGGGGTTTTGGGTGAGCT 60.179 55.000 0.00 0.00 0.00 4.09
279 284 1.069935 GGCTGCTATTCGGACTCCC 59.930 63.158 0.00 0.00 0.00 4.30
289 294 2.034221 GGACTCCCGCAAAGCCTT 59.966 61.111 0.00 0.00 0.00 4.35
290 295 1.603739 GGACTCCCGCAAAGCCTTT 60.604 57.895 0.00 0.00 0.00 3.11
305 310 7.471721 GCAAAGCCTTTAAAGTTTGTTTTGAT 58.528 30.769 23.46 3.65 33.33 2.57
311 316 7.045031 GCCTTTAAAGTTTGTTTTGATTTTGCG 60.045 33.333 14.03 0.00 0.00 4.85
313 318 9.535270 CTTTAAAGTTTGTTTTGATTTTGCGAA 57.465 25.926 7.07 0.00 0.00 4.70
331 336 4.544001 AAAAAGTGCGTCCGGACA 57.456 50.000 32.80 13.27 38.98 4.02
332 337 3.015516 AAAAAGTGCGTCCGGACAT 57.984 47.368 32.80 13.61 38.98 3.06
335 340 1.935933 AAAGTGCGTCCGGACATATC 58.064 50.000 32.80 19.10 38.98 1.63
340 345 2.900167 CGTCCGGACATATCGGCGA 61.900 63.158 32.80 13.87 46.43 5.54
356 361 2.737376 GAACCGACACAGACCCGC 60.737 66.667 0.00 0.00 0.00 6.13
357 362 3.509137 GAACCGACACAGACCCGCA 62.509 63.158 0.00 0.00 0.00 5.69
374 379 1.745087 CGCATTGGATGGCTAAACACT 59.255 47.619 0.00 0.00 0.00 3.55
379 384 2.432444 TGGATGGCTAAACACTTTCGG 58.568 47.619 0.00 0.00 0.00 4.30
381 386 2.418976 GGATGGCTAAACACTTTCGGAC 59.581 50.000 0.00 0.00 0.00 4.79
384 389 2.224670 TGGCTAAACACTTTCGGACCAT 60.225 45.455 0.00 0.00 0.00 3.55
420 425 2.024176 CGGACATTTCAAGGATCCGT 57.976 50.000 5.98 0.00 45.73 4.69
425 430 4.485163 GACATTTCAAGGATCCGTTTTGG 58.515 43.478 5.98 0.00 40.09 3.28
435 440 1.533625 TCCGTTTTGGAGATGCCTTG 58.466 50.000 0.00 0.00 43.74 3.61
437 442 1.200020 CCGTTTTGGAGATGCCTTGAC 59.800 52.381 0.00 0.00 42.00 3.18
438 443 1.879380 CGTTTTGGAGATGCCTTGACA 59.121 47.619 0.00 0.00 37.63 3.58
440 445 3.610114 CGTTTTGGAGATGCCTTGACAAG 60.610 47.826 8.31 8.31 37.63 3.16
441 446 2.957402 TTGGAGATGCCTTGACAAGT 57.043 45.000 14.03 0.00 37.63 3.16
443 448 2.783135 TGGAGATGCCTTGACAAGTTC 58.217 47.619 14.03 7.91 37.63 3.01
450 456 1.600413 GCCTTGACAAGTTCGCCAAAG 60.600 52.381 14.03 0.00 0.00 2.77
471 477 2.818130 AACTACCTAAACCGTGCGAA 57.182 45.000 0.00 0.00 0.00 4.70
482 488 0.515564 CCGTGCGAAAAACCAGGTAG 59.484 55.000 0.00 0.00 0.00 3.18
483 489 1.504359 CGTGCGAAAAACCAGGTAGA 58.496 50.000 0.00 0.00 0.00 2.59
484 490 1.459592 CGTGCGAAAAACCAGGTAGAG 59.540 52.381 0.00 0.00 0.00 2.43
485 491 2.490991 GTGCGAAAAACCAGGTAGAGT 58.509 47.619 0.00 0.00 0.00 3.24
582 937 9.926158 CTACTCATATATCTCTTGTCAATTGCT 57.074 33.333 0.00 0.00 0.00 3.91
603 958 1.665679 CAAACCGTGAGAATCCGATGG 59.334 52.381 0.00 0.00 31.82 3.51
621 976 4.491676 GATGGCATGCATCATCATTAACC 58.508 43.478 23.90 3.95 39.47 2.85
699 1055 4.729918 CTTCAGCTGCCCCGCCTT 62.730 66.667 9.47 0.00 0.00 4.35
700 1056 4.284550 TTCAGCTGCCCCGCCTTT 62.285 61.111 9.47 0.00 0.00 3.11
701 1057 3.808218 TTCAGCTGCCCCGCCTTTT 62.808 57.895 9.47 0.00 0.00 2.27
702 1058 4.060038 CAGCTGCCCCGCCTTTTG 62.060 66.667 0.00 0.00 0.00 2.44
703 1059 4.603535 AGCTGCCCCGCCTTTTGT 62.604 61.111 0.00 0.00 0.00 2.83
704 1060 4.056125 GCTGCCCCGCCTTTTGTC 62.056 66.667 0.00 0.00 0.00 3.18
705 1061 2.282462 CTGCCCCGCCTTTTGTCT 60.282 61.111 0.00 0.00 0.00 3.41
706 1062 2.282180 TGCCCCGCCTTTTGTCTC 60.282 61.111 0.00 0.00 0.00 3.36
707 1063 2.034221 GCCCCGCCTTTTGTCTCT 59.966 61.111 0.00 0.00 0.00 3.10
708 1064 2.041115 GCCCCGCCTTTTGTCTCTC 61.041 63.158 0.00 0.00 0.00 3.20
709 1065 1.679898 CCCCGCCTTTTGTCTCTCT 59.320 57.895 0.00 0.00 0.00 3.10
710 1066 0.391793 CCCCGCCTTTTGTCTCTCTC 60.392 60.000 0.00 0.00 0.00 3.20
711 1067 0.321671 CCCGCCTTTTGTCTCTCTCA 59.678 55.000 0.00 0.00 0.00 3.27
712 1068 1.433534 CCGCCTTTTGTCTCTCTCAC 58.566 55.000 0.00 0.00 0.00 3.51
713 1069 1.001406 CCGCCTTTTGTCTCTCTCACT 59.999 52.381 0.00 0.00 0.00 3.41
714 1070 2.333014 CGCCTTTTGTCTCTCTCACTC 58.667 52.381 0.00 0.00 0.00 3.51
715 1071 2.288457 CGCCTTTTGTCTCTCTCACTCA 60.288 50.000 0.00 0.00 0.00 3.41
716 1072 3.063485 GCCTTTTGTCTCTCTCACTCAC 58.937 50.000 0.00 0.00 0.00 3.51
717 1073 3.244044 GCCTTTTGTCTCTCTCACTCACT 60.244 47.826 0.00 0.00 0.00 3.41
718 1074 4.555262 CCTTTTGTCTCTCTCACTCACTC 58.445 47.826 0.00 0.00 0.00 3.51
719 1075 4.280677 CCTTTTGTCTCTCTCACTCACTCT 59.719 45.833 0.00 0.00 0.00 3.24
720 1076 5.446143 TTTTGTCTCTCTCACTCACTCTC 57.554 43.478 0.00 0.00 0.00 3.20
721 1077 4.365514 TTGTCTCTCTCACTCACTCTCT 57.634 45.455 0.00 0.00 0.00 3.10
722 1078 3.937814 TGTCTCTCTCACTCACTCTCTC 58.062 50.000 0.00 0.00 0.00 3.20
723 1079 3.582647 TGTCTCTCTCACTCACTCTCTCT 59.417 47.826 0.00 0.00 0.00 3.10
724 1080 4.184629 GTCTCTCTCACTCACTCTCTCTC 58.815 52.174 0.00 0.00 0.00 3.20
725 1081 4.081420 GTCTCTCTCACTCACTCTCTCTCT 60.081 50.000 0.00 0.00 0.00 3.10
726 1082 4.160439 TCTCTCTCACTCACTCTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
727 1083 4.096681 TCTCTCACTCACTCTCTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
728 1084 4.160439 TCTCTCACTCACTCTCTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
729 1085 3.837731 TCTCACTCACTCTCTCTCTCTCA 59.162 47.826 0.00 0.00 0.00 3.27
730 1086 3.935203 CTCACTCACTCTCTCTCTCTCAC 59.065 52.174 0.00 0.00 0.00 3.51
731 1087 3.582647 TCACTCACTCTCTCTCTCTCACT 59.417 47.826 0.00 0.00 0.00 3.41
732 1088 3.935203 CACTCACTCTCTCTCTCTCACTC 59.065 52.174 0.00 0.00 0.00 3.51
733 1089 3.582647 ACTCACTCTCTCTCTCTCACTCA 59.417 47.826 0.00 0.00 0.00 3.41
734 1090 3.935203 CTCACTCTCTCTCTCTCACTCAC 59.065 52.174 0.00 0.00 0.00 3.51
735 1091 3.582647 TCACTCTCTCTCTCTCACTCACT 59.417 47.826 0.00 0.00 0.00 3.41
736 1092 3.935203 CACTCTCTCTCTCTCACTCACTC 59.065 52.174 0.00 0.00 0.00 3.51
737 1093 3.840666 ACTCTCTCTCTCTCACTCACTCT 59.159 47.826 0.00 0.00 0.00 3.24
738 1094 4.081420 ACTCTCTCTCTCTCACTCACTCTC 60.081 50.000 0.00 0.00 0.00 3.20
739 1095 4.096681 TCTCTCTCTCTCACTCACTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
740 1096 4.160439 TCTCTCTCTCTCACTCACTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
741 1097 4.096681 TCTCTCTCTCACTCACTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
742 1098 4.160439 TCTCTCTCTCACTCACTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
743 1099 4.096681 TCTCTCTCACTCACTCTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
744 1100 4.160439 TCTCTCTCACTCACTCTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
745 1101 4.096681 TCTCTCACTCACTCTCTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
746 1102 4.160439 TCTCTCACTCACTCTCTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
747 1103 4.096681 TCTCACTCACTCTCTCTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
748 1104 4.160439 TCTCACTCACTCTCTCTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
749 1105 4.096681 TCACTCACTCTCTCTCTCTCTCT 58.903 47.826 0.00 0.00 0.00 3.10
750 1106 4.160439 TCACTCACTCTCTCTCTCTCTCTC 59.840 50.000 0.00 0.00 0.00 3.20
751 1107 4.081476 CACTCACTCTCTCTCTCTCTCTCA 60.081 50.000 0.00 0.00 0.00 3.27
752 1108 4.081420 ACTCACTCTCTCTCTCTCTCTCAC 60.081 50.000 0.00 0.00 0.00 3.51
753 1109 4.096681 TCACTCTCTCTCTCTCTCTCACT 58.903 47.826 0.00 0.00 0.00 3.41
754 1110 4.160439 TCACTCTCTCTCTCTCTCTCACTC 59.840 50.000 0.00 0.00 0.00 3.51
755 1111 4.081476 CACTCTCTCTCTCTCTCTCACTCA 60.081 50.000 0.00 0.00 0.00 3.41
756 1112 4.081420 ACTCTCTCTCTCTCTCTCACTCAC 60.081 50.000 0.00 0.00 0.00 3.51
757 1113 4.096681 TCTCTCTCTCTCTCTCACTCACT 58.903 47.826 0.00 0.00 0.00 3.41
758 1114 4.160439 TCTCTCTCTCTCTCTCACTCACTC 59.840 50.000 0.00 0.00 0.00 3.51
759 1115 3.837731 TCTCTCTCTCTCTCACTCACTCA 59.162 47.826 0.00 0.00 0.00 3.41
900 1285 5.163395 CCATCCTTCTACCAGGAAACTAGAC 60.163 48.000 0.00 0.00 46.50 2.59
903 1288 4.160626 CCTTCTACCAGGAAACTAGACAGG 59.839 50.000 0.00 0.00 40.21 4.00
954 1339 2.030363 ACACACACAACACACAACCAAG 60.030 45.455 0.00 0.00 0.00 3.61
970 1355 3.893961 AAGCTGCTTGGGGGAAGGC 62.894 63.158 15.16 0.00 31.56 4.35
992 1377 3.634448 CGAGAGAGAGAGAGAGAGAGAGT 59.366 52.174 0.00 0.00 0.00 3.24
1060 1445 4.803426 GTCTCCCCGCGAGTGCAG 62.803 72.222 8.23 0.00 42.97 4.41
1068 1453 2.048222 GCGAGTGCAGCACCACTA 60.048 61.111 22.41 0.00 45.55 2.74
1089 1474 4.082523 CACGATCACCACCGGGCT 62.083 66.667 6.32 0.00 37.90 5.19
1092 1477 0.468585 ACGATCACCACCGGGCTATA 60.469 55.000 6.32 0.00 37.90 1.31
1284 1669 3.860605 ATGCTGCGGCCCATACGA 61.861 61.111 16.57 0.00 37.74 3.43
1652 2043 5.457140 TCTTGTTGTGGCGATGTAAAATTC 58.543 37.500 0.00 0.00 0.00 2.17
1769 2160 2.094762 ACCTTACCACTCACGCATTC 57.905 50.000 0.00 0.00 0.00 2.67
1836 2235 7.885399 ACTAAGTTTGATTGAACTGCTAATCCT 59.115 33.333 0.00 0.00 39.68 3.24
1953 2352 3.626670 CCGTAGCAGTGCTAGTTACTACT 59.373 47.826 25.09 0.00 42.11 2.57
1954 2353 4.813161 CCGTAGCAGTGCTAGTTACTACTA 59.187 45.833 25.09 0.00 42.11 1.82
1955 2354 5.277250 CCGTAGCAGTGCTAGTTACTACTAC 60.277 48.000 25.09 19.42 42.11 2.73
2040 2463 1.767759 AAGGCAGAGAGAGAGAGAGC 58.232 55.000 0.00 0.00 0.00 4.09
2042 2465 1.447317 GGCAGAGAGAGAGAGAGCGG 61.447 65.000 0.00 0.00 0.00 5.52
2394 2827 0.106318 AGCAGCCCCCATGATCTTTC 60.106 55.000 0.00 0.00 0.00 2.62
2400 2833 1.683943 CCCCATGATCTTTCGCACAT 58.316 50.000 0.00 0.00 0.00 3.21
2688 3124 8.328758 CCCTTTGGAATATATAGATGCCAACTA 58.671 37.037 17.90 5.48 35.35 2.24
2776 3212 2.257676 GCTTCGAGAACGGGTCGT 59.742 61.111 3.70 0.00 43.97 4.34
2865 3301 1.616159 CCACACGGAATGGAAGGTTT 58.384 50.000 0.00 0.00 39.87 3.27
2961 3397 4.164030 AGGTAGGCATCACACAATCACATA 59.836 41.667 0.00 0.00 0.00 2.29
3072 3508 6.613153 AACTATCAGCAGGAGAACTAGTTT 57.387 37.500 10.02 0.00 28.07 2.66
3109 3545 6.318900 GCCTGCTCCATATGTAAAAACTACTT 59.681 38.462 1.24 0.00 0.00 2.24
3110 3546 7.148069 GCCTGCTCCATATGTAAAAACTACTTT 60.148 37.037 1.24 0.00 0.00 2.66
3138 3580 8.618677 AGTAAAGACAACTGGCTTAAGTAAAAC 58.381 33.333 4.02 0.00 43.96 2.43
3157 3599 1.203928 CTCGTGGATTAAGCGAGCTG 58.796 55.000 0.00 0.00 44.03 4.24
3207 3649 5.610398 TGTCATGTGCTCTCTTTGACTTAA 58.390 37.500 0.00 0.00 0.00 1.85
3301 3743 2.359531 CGGCTGTTTTTGTAAACCCTGA 59.640 45.455 0.00 0.00 42.39 3.86
3302 3744 3.713288 GGCTGTTTTTGTAAACCCTGAC 58.287 45.455 0.00 0.00 42.39 3.51
3331 3773 9.911788 AGAATCAGTTCCAAGTAAATGTGATAT 57.088 29.630 0.00 0.00 34.81 1.63
3341 3788 7.254455 CCAAGTAAATGTGATATCAGGACGAAC 60.254 40.741 5.42 1.18 0.00 3.95
3364 3819 2.353803 GGGAGTATACATTGCGCCCTAG 60.354 54.545 4.18 0.00 38.87 3.02
3403 3858 1.955778 TGGTCTGTCCGTTTTACTCGA 59.044 47.619 0.00 0.00 39.52 4.04
3405 3860 2.030451 GGTCTGTCCGTTTTACTCGACT 60.030 50.000 0.00 0.00 0.00 4.18
3406 3861 3.189287 GGTCTGTCCGTTTTACTCGACTA 59.811 47.826 0.00 0.00 0.00 2.59
3435 3890 0.749454 CTTAAGCCGGCCTGAATGCT 60.749 55.000 26.15 0.00 35.08 3.79
3686 4425 6.154363 TCCCCACATTTTCTTGTCATATTTCC 59.846 38.462 0.00 0.00 0.00 3.13
3700 4439 5.648092 GTCATATTTCCGGGAAATGGATAGG 59.352 44.000 34.51 21.33 41.55 2.57
4046 4788 1.667830 CAACGCCGGAGCTGAAGAA 60.668 57.895 5.05 0.00 36.60 2.52
4069 4811 0.961857 TCGGCGTCAACTGTAGCCTA 60.962 55.000 6.85 3.60 46.85 3.93
4237 5166 3.733077 CGATCTCCAATGAAAAGCAAGCC 60.733 47.826 0.00 0.00 0.00 4.35
4341 5270 4.587976 ACTAGTAGCCAGACAGTTAGGA 57.412 45.455 0.00 0.00 0.00 2.94
4343 5272 4.951094 ACTAGTAGCCAGACAGTTAGGAAG 59.049 45.833 0.00 0.00 0.00 3.46
4383 5312 4.201841 TGTGAATCATGCATGCTTTCTACG 60.202 41.667 27.71 0.25 0.00 3.51
4670 5761 2.871182 TAGTAAGCAGGTGCATCTCG 57.129 50.000 0.00 0.00 45.16 4.04
4819 7191 2.904866 GCGTGACCAAGGCCAACA 60.905 61.111 5.01 0.00 33.42 3.33
4820 7192 3.030652 CGTGACCAAGGCCAACAC 58.969 61.111 5.01 6.62 0.00 3.32
4821 7193 1.821759 CGTGACCAAGGCCAACACA 60.822 57.895 5.01 0.00 0.00 3.72
4823 7195 0.385390 GTGACCAAGGCCAACACAAG 59.615 55.000 5.01 0.00 0.00 3.16
4825 7197 0.755327 GACCAAGGCCAACACAAGGT 60.755 55.000 5.01 0.99 0.00 3.50
4826 7198 1.042559 ACCAAGGCCAACACAAGGTG 61.043 55.000 5.01 0.00 39.75 4.00
4827 7199 0.754957 CCAAGGCCAACACAAGGTGA 60.755 55.000 5.01 0.00 36.96 4.02
4828 7200 0.385390 CAAGGCCAACACAAGGTGAC 59.615 55.000 5.01 0.00 36.96 3.67
4830 7202 2.551912 GGCCAACACAAGGTGACCG 61.552 63.158 0.00 0.00 36.96 4.79
4831 7203 2.551912 GCCAACACAAGGTGACCGG 61.552 63.158 0.00 0.00 36.96 5.28
4832 7204 1.896660 CCAACACAAGGTGACCGGG 60.897 63.158 6.32 0.00 36.96 5.73
4833 7205 2.203294 AACACAAGGTGACCGGGC 60.203 61.111 6.32 1.57 36.96 6.13
4834 7206 3.785122 AACACAAGGTGACCGGGCC 62.785 63.158 3.83 3.98 36.96 5.80
4867 7239 0.736053 TGAAACCCAACAAGACGCAC 59.264 50.000 0.00 0.00 0.00 5.34
4869 7241 1.133407 GAAACCCAACAAGACGCACAA 59.867 47.619 0.00 0.00 0.00 3.33
4871 7243 0.678366 ACCCAACAAGACGCACAACA 60.678 50.000 0.00 0.00 0.00 3.33
4877 7249 4.407818 CAACAAGACGCACAACAACTTAA 58.592 39.130 0.00 0.00 0.00 1.85
4878 7250 4.011058 ACAAGACGCACAACAACTTAAC 57.989 40.909 0.00 0.00 0.00 2.01
4900 7272 2.611225 CTTCCTCCCGATGAAGAAGG 57.389 55.000 4.28 0.00 40.30 3.46
4905 7277 1.139654 CTCCCGATGAAGAAGGCATCA 59.860 52.381 0.00 0.00 41.66 3.07
4917 7289 1.742761 AGGCATCAAGTGGATCAACG 58.257 50.000 0.00 0.00 32.57 4.10
4924 7296 3.186047 GTGGATCAACGGACGGCG 61.186 66.667 4.80 4.80 0.00 6.46
4955 7327 2.777913 ACCCTATTCCCCTTTCTCCTC 58.222 52.381 0.00 0.00 0.00 3.71
4957 7329 2.976185 CCCTATTCCCCTTTCTCCTCTC 59.024 54.545 0.00 0.00 0.00 3.20
4977 7349 6.037786 TCTCTGTTCGTCCAATTCTTGTAT 57.962 37.500 0.00 0.00 0.00 2.29
4978 7350 6.100004 TCTCTGTTCGTCCAATTCTTGTATC 58.900 40.000 0.00 0.00 0.00 2.24
4986 7358 5.235186 CGTCCAATTCTTGTATCCATGAGTC 59.765 44.000 0.00 0.00 0.00 3.36
4999 7371 4.390264 TCCATGAGTCGTAATCGAGATCT 58.610 43.478 0.00 0.00 46.96 2.75
5000 7372 5.548406 TCCATGAGTCGTAATCGAGATCTA 58.452 41.667 0.00 0.00 46.96 1.98
5001 7373 5.995897 TCCATGAGTCGTAATCGAGATCTAA 59.004 40.000 0.00 0.00 46.96 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.674623 GCATTGGAGATGAAAGAACTGCTG 60.675 45.833 0.00 0.00 0.00 4.41
1 2 3.442977 GCATTGGAGATGAAAGAACTGCT 59.557 43.478 0.00 0.00 0.00 4.24
2 3 3.192001 TGCATTGGAGATGAAAGAACTGC 59.808 43.478 0.00 0.00 0.00 4.40
4 5 4.142227 GCATGCATTGGAGATGAAAGAACT 60.142 41.667 14.21 0.00 0.00 3.01
5 6 4.110482 GCATGCATTGGAGATGAAAGAAC 58.890 43.478 14.21 0.00 0.00 3.01
6 7 3.764972 TGCATGCATTGGAGATGAAAGAA 59.235 39.130 18.46 0.00 0.00 2.52
7 8 3.358118 TGCATGCATTGGAGATGAAAGA 58.642 40.909 18.46 0.00 0.00 2.52
11 12 5.595133 TCTTAATTGCATGCATTGGAGATGA 59.405 36.000 23.37 9.71 0.00 2.92
31 32 2.168521 CCAGGTTTGCTCGGATCTCTTA 59.831 50.000 0.00 0.00 0.00 2.10
39 40 1.966451 GGTGACCAGGTTTGCTCGG 60.966 63.158 0.00 0.00 0.00 4.63
40 41 3.655481 GGTGACCAGGTTTGCTCG 58.345 61.111 0.00 0.00 0.00 5.03
63 64 2.099062 CGCCGCAATGTCTGAAGC 59.901 61.111 0.00 0.00 0.00 3.86
99 100 2.028294 ACTCGACTACTCCGTCTCTTCA 60.028 50.000 0.00 0.00 0.00 3.02
102 103 2.620242 GAACTCGACTACTCCGTCTCT 58.380 52.381 0.00 0.00 0.00 3.10
113 114 1.674057 CCCTTGCTGGAACTCGACT 59.326 57.895 0.00 0.00 38.35 4.18
132 133 2.541547 ATCCTGGTCGCACCACCATG 62.542 60.000 4.16 0.63 44.79 3.66
145 146 1.377202 CACCGTTCCACCATCCTGG 60.377 63.158 0.00 0.00 45.02 4.45
150 151 0.251121 TTGCATCACCGTTCCACCAT 60.251 50.000 0.00 0.00 0.00 3.55
160 161 1.734465 CGGTTTCTCTCTTGCATCACC 59.266 52.381 0.00 0.00 0.00 4.02
184 189 3.520721 TCCATGCTCCAATCTTTCTCTGA 59.479 43.478 0.00 0.00 0.00 3.27
196 201 0.988145 CCCTACCCTTCCATGCTCCA 60.988 60.000 0.00 0.00 0.00 3.86
199 204 2.386935 GGCCCTACCCTTCCATGCT 61.387 63.158 0.00 0.00 0.00 3.79
201 206 1.533711 CTGGCCCTACCCTTCCATG 59.466 63.158 0.00 0.00 37.83 3.66
207 212 2.042930 CCTTCCTGGCCCTACCCT 59.957 66.667 0.00 0.00 37.83 4.34
212 217 2.097727 AAAACCCCTTCCTGGCCCT 61.098 57.895 0.00 0.00 0.00 5.19
216 221 0.831711 CACCCAAAACCCCTTCCTGG 60.832 60.000 0.00 0.00 0.00 4.45
218 223 0.482887 CTCACCCAAAACCCCTTCCT 59.517 55.000 0.00 0.00 0.00 3.36
232 237 2.187946 CGACATCCCCAGCTCACC 59.812 66.667 0.00 0.00 0.00 4.02
239 244 0.398522 ATAGGACTGCGACATCCCCA 60.399 55.000 0.00 0.00 35.38 4.96
279 284 5.463499 AAACAAACTTTAAAGGCTTTGCG 57.537 34.783 22.32 12.11 0.00 4.85
280 285 6.836953 TCAAAACAAACTTTAAAGGCTTTGC 58.163 32.000 22.32 0.00 0.00 3.68
285 290 7.045031 CGCAAAATCAAAACAAACTTTAAAGGC 60.045 33.333 19.14 6.11 0.00 4.35
288 293 9.878599 TTTCGCAAAATCAAAACAAACTTTAAA 57.121 22.222 0.00 0.00 0.00 1.52
289 294 9.878599 TTTTCGCAAAATCAAAACAAACTTTAA 57.121 22.222 0.00 0.00 0.00 1.52
290 295 9.878599 TTTTTCGCAAAATCAAAACAAACTTTA 57.121 22.222 0.00 0.00 0.00 1.85
319 324 3.917870 CGATATGTCCGGACGCAC 58.082 61.111 28.70 18.01 0.00 5.34
326 331 3.932289 GGTTCGCCGATATGTCCG 58.068 61.111 0.00 0.00 0.00 4.79
337 342 2.737376 GGGTCTGTGTCGGTTCGC 60.737 66.667 0.00 0.00 0.00 4.70
340 345 2.391724 AATGCGGGTCTGTGTCGGTT 62.392 55.000 0.00 0.00 0.00 4.44
344 349 0.392998 ATCCAATGCGGGTCTGTGTC 60.393 55.000 0.00 0.00 34.36 3.67
346 351 1.378882 CCATCCAATGCGGGTCTGTG 61.379 60.000 0.00 0.00 34.36 3.66
356 361 4.414852 CGAAAGTGTTTAGCCATCCAATG 58.585 43.478 0.00 0.00 0.00 2.82
357 362 3.443681 CCGAAAGTGTTTAGCCATCCAAT 59.556 43.478 0.00 0.00 0.00 3.16
374 379 4.655921 GGATGGCATGGTCCGAAA 57.344 55.556 3.81 0.00 0.00 3.46
379 384 2.180204 CCGTTCGGATGGCATGGTC 61.180 63.158 3.81 0.00 0.00 4.02
381 386 1.748879 AACCGTTCGGATGGCATGG 60.749 57.895 18.28 0.38 35.16 3.66
384 389 3.053291 GCAACCGTTCGGATGGCA 61.053 61.111 18.28 0.00 35.16 4.92
393 398 1.001815 CTTGAAATGTCCGCAACCGTT 60.002 47.619 0.00 0.00 0.00 4.44
406 411 4.662278 TCTCCAAAACGGATCCTTGAAAT 58.338 39.130 10.75 0.00 45.19 2.17
407 412 4.093472 TCTCCAAAACGGATCCTTGAAA 57.907 40.909 10.75 0.00 45.19 2.69
420 425 3.565307 ACTTGTCAAGGCATCTCCAAAA 58.435 40.909 16.85 0.00 37.29 2.44
425 430 1.129437 GCGAACTTGTCAAGGCATCTC 59.871 52.381 16.85 4.02 0.00 2.75
431 436 1.946768 TCTTTGGCGAACTTGTCAAGG 59.053 47.619 16.85 0.55 34.49 3.61
435 440 3.692791 AGTTTCTTTGGCGAACTTGTC 57.307 42.857 0.00 0.00 0.00 3.18
437 442 3.564225 AGGTAGTTTCTTTGGCGAACTTG 59.436 43.478 0.00 0.00 0.00 3.16
438 443 3.816994 AGGTAGTTTCTTTGGCGAACTT 58.183 40.909 0.00 0.00 0.00 2.66
440 445 5.446709 GTTTAGGTAGTTTCTTTGGCGAAC 58.553 41.667 0.00 0.00 0.00 3.95
441 446 4.516321 GGTTTAGGTAGTTTCTTTGGCGAA 59.484 41.667 0.00 0.00 0.00 4.70
443 448 3.120442 CGGTTTAGGTAGTTTCTTTGGCG 60.120 47.826 0.00 0.00 0.00 5.69
450 456 2.676076 TCGCACGGTTTAGGTAGTTTC 58.324 47.619 0.00 0.00 0.00 2.78
471 477 2.809299 GCCGTGAACTCTACCTGGTTTT 60.809 50.000 3.84 0.00 0.00 2.43
555 908 9.703892 GCAATTGACAAGAGATATATGAGTAGT 57.296 33.333 10.34 0.00 0.00 2.73
582 937 2.616960 CATCGGATTCTCACGGTTTGA 58.383 47.619 0.00 0.00 0.00 2.69
603 958 4.021807 TGATGGGTTAATGATGATGCATGC 60.022 41.667 11.82 11.82 0.00 4.06
621 976 1.184970 GGGTGGGGTTTGTGTGATGG 61.185 60.000 0.00 0.00 0.00 3.51
699 1055 4.724399 AGAGAGTGAGTGAGAGAGACAAA 58.276 43.478 0.00 0.00 0.00 2.83
700 1056 4.041567 AGAGAGAGTGAGTGAGAGAGACAA 59.958 45.833 0.00 0.00 0.00 3.18
701 1057 3.582647 AGAGAGAGTGAGTGAGAGAGACA 59.417 47.826 0.00 0.00 0.00 3.41
702 1058 4.081420 AGAGAGAGAGTGAGTGAGAGAGAC 60.081 50.000 0.00 0.00 0.00 3.36
703 1059 4.096681 AGAGAGAGAGTGAGTGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
704 1060 4.161189 AGAGAGAGAGAGTGAGTGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
705 1061 4.096681 AGAGAGAGAGAGTGAGTGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
706 1062 4.081476 TGAGAGAGAGAGAGTGAGTGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
707 1063 3.837731 TGAGAGAGAGAGAGTGAGTGAGA 59.162 47.826 0.00 0.00 0.00 3.27
708 1064 3.935203 GTGAGAGAGAGAGAGTGAGTGAG 59.065 52.174 0.00 0.00 0.00 3.51
709 1065 3.582647 AGTGAGAGAGAGAGAGTGAGTGA 59.417 47.826 0.00 0.00 0.00 3.41
710 1066 3.935203 GAGTGAGAGAGAGAGAGTGAGTG 59.065 52.174 0.00 0.00 0.00 3.51
711 1067 3.582647 TGAGTGAGAGAGAGAGAGTGAGT 59.417 47.826 0.00 0.00 0.00 3.41
712 1068 3.935203 GTGAGTGAGAGAGAGAGAGTGAG 59.065 52.174 0.00 0.00 0.00 3.51
713 1069 3.582647 AGTGAGTGAGAGAGAGAGAGTGA 59.417 47.826 0.00 0.00 0.00 3.41
714 1070 3.935203 GAGTGAGTGAGAGAGAGAGAGTG 59.065 52.174 0.00 0.00 0.00 3.51
715 1071 3.840666 AGAGTGAGTGAGAGAGAGAGAGT 59.159 47.826 0.00 0.00 0.00 3.24
716 1072 4.161189 AGAGAGTGAGTGAGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
717 1073 4.096681 AGAGAGTGAGTGAGAGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
718 1074 4.161189 AGAGAGAGTGAGTGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
719 1075 4.096681 AGAGAGAGTGAGTGAGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
720 1076 4.161189 AGAGAGAGAGTGAGTGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
721 1077 4.096681 AGAGAGAGAGTGAGTGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
722 1078 4.161189 AGAGAGAGAGAGTGAGTGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
723 1079 4.096681 AGAGAGAGAGAGTGAGTGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
724 1080 4.161189 AGAGAGAGAGAGAGTGAGTGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
725 1081 4.096681 AGAGAGAGAGAGAGTGAGTGAGA 58.903 47.826 0.00 0.00 0.00 3.27
726 1082 4.161189 AGAGAGAGAGAGAGAGTGAGTGAG 59.839 50.000 0.00 0.00 0.00 3.51
727 1083 4.096681 AGAGAGAGAGAGAGAGTGAGTGA 58.903 47.826 0.00 0.00 0.00 3.41
728 1084 4.081476 TGAGAGAGAGAGAGAGAGTGAGTG 60.081 50.000 0.00 0.00 0.00 3.51
729 1085 4.081420 GTGAGAGAGAGAGAGAGAGTGAGT 60.081 50.000 0.00 0.00 0.00 3.41
730 1086 4.161189 AGTGAGAGAGAGAGAGAGAGTGAG 59.839 50.000 0.00 0.00 0.00 3.51
731 1087 4.096681 AGTGAGAGAGAGAGAGAGAGTGA 58.903 47.826 0.00 0.00 0.00 3.41
732 1088 4.081476 TGAGTGAGAGAGAGAGAGAGAGTG 60.081 50.000 0.00 0.00 0.00 3.51
733 1089 4.081420 GTGAGTGAGAGAGAGAGAGAGAGT 60.081 50.000 0.00 0.00 0.00 3.24
734 1090 4.161189 AGTGAGTGAGAGAGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
735 1091 4.096681 AGTGAGTGAGAGAGAGAGAGAGA 58.903 47.826 0.00 0.00 0.00 3.10
736 1092 4.081476 TGAGTGAGTGAGAGAGAGAGAGAG 60.081 50.000 0.00 0.00 0.00 3.20
737 1093 3.837731 TGAGTGAGTGAGAGAGAGAGAGA 59.162 47.826 0.00 0.00 0.00 3.10
738 1094 3.935203 GTGAGTGAGTGAGAGAGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
739 1095 3.582647 AGTGAGTGAGTGAGAGAGAGAGA 59.417 47.826 0.00 0.00 0.00 3.10
740 1096 3.935203 GAGTGAGTGAGTGAGAGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
741 1097 3.582647 AGAGTGAGTGAGTGAGAGAGAGA 59.417 47.826 0.00 0.00 0.00 3.10
742 1098 3.935203 GAGAGTGAGTGAGTGAGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
743 1099 3.582647 AGAGAGTGAGTGAGTGAGAGAGA 59.417 47.826 0.00 0.00 0.00 3.10
744 1100 3.935203 GAGAGAGTGAGTGAGTGAGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
745 1101 3.582647 AGAGAGAGTGAGTGAGTGAGAGA 59.417 47.826 0.00 0.00 0.00 3.10
746 1102 3.935203 GAGAGAGAGTGAGTGAGTGAGAG 59.065 52.174 0.00 0.00 0.00 3.20
747 1103 3.582647 AGAGAGAGAGTGAGTGAGTGAGA 59.417 47.826 0.00 0.00 0.00 3.27
748 1104 3.935203 GAGAGAGAGAGTGAGTGAGTGAG 59.065 52.174 0.00 0.00 0.00 3.51
749 1105 3.326297 TGAGAGAGAGAGTGAGTGAGTGA 59.674 47.826 0.00 0.00 0.00 3.41
750 1106 3.673902 TGAGAGAGAGAGTGAGTGAGTG 58.326 50.000 0.00 0.00 0.00 3.51
751 1107 4.365514 TTGAGAGAGAGAGTGAGTGAGT 57.634 45.455 0.00 0.00 0.00 3.41
752 1108 4.518590 TGTTTGAGAGAGAGAGTGAGTGAG 59.481 45.833 0.00 0.00 0.00 3.51
753 1109 4.464947 TGTTTGAGAGAGAGAGTGAGTGA 58.535 43.478 0.00 0.00 0.00 3.41
754 1110 4.518590 TCTGTTTGAGAGAGAGAGTGAGTG 59.481 45.833 0.00 0.00 0.00 3.51
755 1111 4.518970 GTCTGTTTGAGAGAGAGAGTGAGT 59.481 45.833 0.00 0.00 0.00 3.41
756 1112 4.518590 TGTCTGTTTGAGAGAGAGAGTGAG 59.481 45.833 0.00 0.00 0.00 3.51
757 1113 4.464947 TGTCTGTTTGAGAGAGAGAGTGA 58.535 43.478 0.00 0.00 0.00 3.41
758 1114 4.844998 TGTCTGTTTGAGAGAGAGAGTG 57.155 45.455 0.00 0.00 0.00 3.51
759 1115 5.738783 GCTTTGTCTGTTTGAGAGAGAGAGT 60.739 44.000 0.00 0.00 29.79 3.24
922 1307 4.268884 GTGTTGTGTGTGTCTTCTCTTCTC 59.731 45.833 0.00 0.00 0.00 2.87
970 1355 3.634448 ACTCTCTCTCTCTCTCTCTCTCG 59.366 52.174 0.00 0.00 0.00 4.04
992 1377 4.765449 AGAGCTCCATTGCGCGCA 62.765 61.111 33.09 33.09 37.81 6.09
1060 1445 1.521681 GATCGTGGCCTAGTGGTGC 60.522 63.158 3.32 0.00 35.27 5.01
1061 1446 0.460284 GTGATCGTGGCCTAGTGGTG 60.460 60.000 3.32 0.00 35.27 4.17
1062 1447 1.614241 GGTGATCGTGGCCTAGTGGT 61.614 60.000 3.32 0.00 35.27 4.16
1063 1448 1.144057 GGTGATCGTGGCCTAGTGG 59.856 63.158 3.32 0.00 0.00 4.00
1064 1449 0.460284 GTGGTGATCGTGGCCTAGTG 60.460 60.000 3.32 0.00 0.00 2.74
1065 1450 1.614241 GGTGGTGATCGTGGCCTAGT 61.614 60.000 3.32 0.00 0.00 2.57
1066 1451 1.144057 GGTGGTGATCGTGGCCTAG 59.856 63.158 3.32 0.00 0.00 3.02
1067 1452 2.717044 CGGTGGTGATCGTGGCCTA 61.717 63.158 3.32 0.00 0.00 3.93
1068 1453 4.082523 CGGTGGTGATCGTGGCCT 62.083 66.667 3.32 0.00 0.00 5.19
1089 1474 1.325355 CGAAGAACCTCCCGCCTATA 58.675 55.000 0.00 0.00 0.00 1.31
1092 1477 3.391382 CCGAAGAACCTCCCGCCT 61.391 66.667 0.00 0.00 0.00 5.52
1154 1539 1.092921 AAACGGAAGCTGCAACGACA 61.093 50.000 15.43 0.00 0.00 4.35
1350 1741 3.039588 CAGTAACACGGCGCGGTT 61.040 61.111 18.85 19.11 0.00 4.44
1769 2160 7.836842 AGTTAAAGGGGCATTAATAAGTGTTG 58.163 34.615 0.00 0.00 0.00 3.33
1836 2235 6.716284 TCTCTCATCTTAGTCTCACTCAAGA 58.284 40.000 0.00 0.00 0.00 3.02
2040 2463 1.376609 GCTTAACCACATCTGCCCCG 61.377 60.000 0.00 0.00 0.00 5.73
2042 2465 1.098050 CTGCTTAACCACATCTGCCC 58.902 55.000 0.00 0.00 0.00 5.36
2379 2802 1.453745 TGCGAAAGATCATGGGGGC 60.454 57.895 0.00 0.00 0.00 5.80
2380 2803 0.394216 TGTGCGAAAGATCATGGGGG 60.394 55.000 0.00 0.00 0.00 5.40
2381 2804 1.605710 GATGTGCGAAAGATCATGGGG 59.394 52.381 0.00 0.00 0.00 4.96
2383 2806 2.286831 GCAGATGTGCGAAAGATCATGG 60.287 50.000 0.00 0.00 40.71 3.66
2384 2807 2.983166 GCAGATGTGCGAAAGATCATG 58.017 47.619 0.00 0.00 40.71 3.07
2394 2827 5.516996 AATCATAAGATTTGCAGATGTGCG 58.483 37.500 10.60 0.00 43.76 5.34
2688 3124 0.540597 GGAAGGCTGGAGCAGGTTTT 60.541 55.000 0.20 0.00 44.36 2.43
2776 3212 2.801421 GTCGCAGATCTCGCCAGA 59.199 61.111 10.34 0.00 40.67 3.86
2865 3301 0.878086 TGTCATCGTCGTTTGCAGCA 60.878 50.000 0.00 0.00 0.00 4.41
3109 3545 9.835389 TTACTTAAGCCAGTTGTCTTTACTAAA 57.165 29.630 1.29 0.00 0.00 1.85
3110 3546 9.835389 TTTACTTAAGCCAGTTGTCTTTACTAA 57.165 29.630 1.29 0.00 0.00 2.24
3123 3565 4.312443 TCCACGAGTTTTACTTAAGCCAG 58.688 43.478 1.29 0.00 0.00 4.85
3157 3599 2.827921 AGGTGACATCAATTGAAAGGCC 59.172 45.455 13.09 11.05 0.00 5.19
3207 3649 4.722279 ACCTAAAGTATAGCAAAGCCCTCT 59.278 41.667 0.00 0.00 0.00 3.69
3250 3692 5.417580 AGCATGCGGGTAAAAGATAAAAAGA 59.582 36.000 13.01 0.00 0.00 2.52
3251 3693 5.650543 AGCATGCGGGTAAAAGATAAAAAG 58.349 37.500 13.01 0.00 0.00 2.27
3252 3694 5.184096 TGAGCATGCGGGTAAAAGATAAAAA 59.816 36.000 13.01 0.00 0.00 1.94
3253 3695 4.702612 TGAGCATGCGGGTAAAAGATAAAA 59.297 37.500 13.01 0.00 0.00 1.52
3254 3696 4.265893 TGAGCATGCGGGTAAAAGATAAA 58.734 39.130 13.01 0.00 0.00 1.40
3255 3697 3.879998 TGAGCATGCGGGTAAAAGATAA 58.120 40.909 13.01 0.00 0.00 1.75
3256 3698 3.552132 TGAGCATGCGGGTAAAAGATA 57.448 42.857 13.01 0.00 0.00 1.98
3257 3699 2.418368 TGAGCATGCGGGTAAAAGAT 57.582 45.000 13.01 0.00 0.00 2.40
3331 3773 2.526888 ATACTCCCAGTTCGTCCTGA 57.473 50.000 5.80 0.00 34.23 3.86
3341 3788 1.512926 GGCGCAATGTATACTCCCAG 58.487 55.000 10.83 0.00 0.00 4.45
3364 3819 1.923864 CAAACGGCTGTTCCAAAACAC 59.076 47.619 12.25 0.00 40.45 3.32
3423 3878 1.009829 GAGTTACAGCATTCAGGCCG 58.990 55.000 0.00 0.00 0.00 6.13
3686 4425 5.291905 AGTACTTTCCTATCCATTTCCCG 57.708 43.478 0.00 0.00 0.00 5.14
4046 4788 0.039437 CTACAGTTGACGCCGACAGT 60.039 55.000 0.00 0.00 32.17 3.55
4341 5270 5.134661 TCACACCCTTTAATTCGTTTCCTT 58.865 37.500 0.00 0.00 0.00 3.36
4343 5272 5.441709 TTCACACCCTTTAATTCGTTTCC 57.558 39.130 0.00 0.00 0.00 3.13
4605 5696 3.814842 TGAAACTAACTGCATGGACACAG 59.185 43.478 0.00 0.00 39.86 3.66
4654 5745 1.269257 CGATCGAGATGCACCTGCTTA 60.269 52.381 10.26 0.00 42.66 3.09
4695 5786 6.721704 AAACTGCAAGATCTCCTTTCTTTT 57.278 33.333 0.00 0.00 37.43 2.27
4696 5787 6.721704 AAAACTGCAAGATCTCCTTTCTTT 57.278 33.333 0.00 0.00 37.43 2.52
4697 5788 6.721704 AAAAACTGCAAGATCTCCTTTCTT 57.278 33.333 0.00 0.00 37.43 2.52
4722 5813 0.232303 GAGAGCGTGTTGTTCAACGG 59.768 55.000 10.43 6.67 0.00 4.44
4723 5814 0.232303 GGAGAGCGTGTTGTTCAACG 59.768 55.000 10.43 2.59 0.00 4.10
4726 5817 0.318699 CGAGGAGAGCGTGTTGTTCA 60.319 55.000 0.00 0.00 0.00 3.18
4727 5818 1.618640 GCGAGGAGAGCGTGTTGTTC 61.619 60.000 0.00 0.00 0.00 3.18
4729 5820 2.049063 GCGAGGAGAGCGTGTTGT 60.049 61.111 0.00 0.00 0.00 3.32
4801 7173 4.025401 GTTGGCCTTGGTCACGCG 62.025 66.667 3.53 3.53 0.00 6.01
4808 7180 0.754957 TCACCTTGTGTTGGCCTTGG 60.755 55.000 3.32 0.00 34.79 3.61
4838 7210 3.145473 TGGGTTTCACTGGGCCCAG 62.145 63.158 44.27 44.27 45.40 4.45
4847 7219 0.736053 TGCGTCTTGTTGGGTTTCAC 59.264 50.000 0.00 0.00 0.00 3.18
4867 7239 3.154710 GGAGGAAGGGGTTAAGTTGTTG 58.845 50.000 0.00 0.00 0.00 3.33
4869 7241 1.709115 GGGAGGAAGGGGTTAAGTTGT 59.291 52.381 0.00 0.00 0.00 3.32
4871 7243 0.989602 CGGGAGGAAGGGGTTAAGTT 59.010 55.000 0.00 0.00 0.00 2.66
4877 7249 0.983378 CTTCATCGGGAGGAAGGGGT 60.983 60.000 13.68 0.00 43.28 4.95
4878 7250 0.691078 TCTTCATCGGGAGGAAGGGG 60.691 60.000 19.34 0.06 45.97 4.79
4900 7272 1.398390 GTCCGTTGATCCACTTGATGC 59.602 52.381 0.00 0.00 32.41 3.91
4905 7277 1.375523 GCCGTCCGTTGATCCACTT 60.376 57.895 0.00 0.00 0.00 3.16
4929 7301 5.248705 GGAGAAAGGGGAATAGGGTATGTAG 59.751 48.000 0.00 0.00 0.00 2.74
4931 7303 3.981375 GGAGAAAGGGGAATAGGGTATGT 59.019 47.826 0.00 0.00 0.00 2.29
4933 7305 4.175065 AGAGGAGAAAGGGGAATAGGGTAT 59.825 45.833 0.00 0.00 0.00 2.73
4934 7306 3.540687 AGAGGAGAAAGGGGAATAGGGTA 59.459 47.826 0.00 0.00 0.00 3.69
4977 7349 4.390264 AGATCTCGATTACGACTCATGGA 58.610 43.478 0.00 0.00 43.81 3.41
4978 7350 4.757799 AGATCTCGATTACGACTCATGG 57.242 45.455 0.00 0.00 43.81 3.66
4986 7358 9.149556 GATCACGATATTTAGATCTCGATTACG 57.850 37.037 0.00 3.18 35.95 3.18
5015 7387 8.113462 AGTAGGGTTGGATCTAATCTCTATCTC 58.887 40.741 1.78 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.