Multiple sequence alignment - TraesCS7A01G522900

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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 TraesCS7A01G522900 chr7A 100.000 4545 0 0 1 4545 705683957 705688501 0.000000e+00 8394
1 TraesCS7A01G522900 chr7A 91.492 764 59 4 2761 3520 34788297 34789058 0.000000e+00 1046
2 TraesCS7A01G522900 chr7A 90.654 214 19 1 2249 2461 34787624 34787837 2.680000e-72 283
3 TraesCS7A01G522900 chr7B 88.895 3782 266 69 858 4545 705251174 705254895 0.000000e+00 4516
4 TraesCS7A01G522900 chr7D 94.517 1295 60 6 2249 3532 613869087 613870381 0.000000e+00 1988
5 TraesCS7A01G522900 chr7D 90.306 1403 84 23 858 2243 613867631 613868998 0.000000e+00 1790
6 TraesCS7A01G522900 chr7D 95.275 783 34 1 3763 4545 613870756 613871535 0.000000e+00 1238
7 TraesCS7A01G522900 chr7D 87.854 247 11 5 3527 3768 613870406 613870638 5.790000e-69 272
8 TraesCS7A01G522900 chr5A 87.241 627 56 9 1 626 68972990 68973593 0.000000e+00 693
9 TraesCS7A01G522900 chr5A 82.682 179 20 9 609 782 68973982 68974154 1.020000e-31 148
10 TraesCS7A01G522900 chr1B 87.574 169 18 3 692 858 645896976 645897143 4.640000e-45 193
11 TraesCS7A01G522900 chr2D 75.394 317 67 9 551 859 111210633 111210320 4.740000e-30 143
12 TraesCS7A01G522900 chr3B 75.000 320 63 16 551 859 816249459 816249772 1.030000e-26 132


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 TraesCS7A01G522900 chr7A 705683957 705688501 4544 False 8394.0 8394 100.0000 1 4545 1 chr7A.!!$F1 4544
1 TraesCS7A01G522900 chr7A 34787624 34789058 1434 False 664.5 1046 91.0730 2249 3520 2 chr7A.!!$F2 1271
2 TraesCS7A01G522900 chr7B 705251174 705254895 3721 False 4516.0 4516 88.8950 858 4545 1 chr7B.!!$F1 3687
3 TraesCS7A01G522900 chr7D 613867631 613871535 3904 False 1322.0 1988 91.9880 858 4545 4 chr7D.!!$F1 3687
4 TraesCS7A01G522900 chr5A 68972990 68974154 1164 False 420.5 693 84.9615 1 782 2 chr5A.!!$F1 781

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
84 85 0.031616 TTTTGGGTGGAAGCAAGGGT 60.032 50.0 0.00 0.00 34.77 4.34 F
795 1206 0.106708 TTTCTCGTCACCAGCTTGCT 59.893 50.0 0.00 0.00 0.00 3.91 F
926 1337 0.108898 CAGACACGAAGCCCAGAGAG 60.109 60.0 0.00 0.00 0.00 3.20 F
1520 1950 0.112218 TGCACTGGCCAATTAGGTGT 59.888 50.0 19.77 4.96 40.61 4.16 F
1606 2036 0.320508 GTTTTCTCCTCGGCTCCGTT 60.321 55.0 8.28 0.00 40.74 4.44 F
3091 3799 0.765510 AGGACTTGGCGAAACTCCTT 59.234 50.0 2.43 0.00 29.43 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2477 0.250467 ACAATGGCTGCTCTTCACGT 60.250 50.000 0.00 0.0 0.00 4.49 R
2757 3464 1.005215 AGTTGGAAGGGAGGAAGCATG 59.995 52.381 0.00 0.0 0.00 4.06 R
3091 3799 5.908831 ACCAACCATATCTTGATACCCTGTA 59.091 40.000 0.00 0.0 0.00 2.74 R
3490 4209 0.539051 GAGCCTTCCTCAGCTGCTTA 59.461 55.000 9.47 0.0 40.11 3.09 R
3502 4223 1.065126 ACATAGCAACCAGGAGCCTTC 60.065 52.381 0.00 0.0 0.00 3.46 R
4277 5198 0.038251 TGAGCTTCGACAAGTGCGAT 60.038 50.000 0.00 0.0 37.64 4.58 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 5.011533 TGCTTAGCTATGGAGGAAGATCTTC 59.988 44.000 24.68 24.68 38.80 2.87
34 35 5.369110 AGCTATGGAGGAAGATCTTCAACAT 59.631 40.000 31.29 28.85 41.20 2.71
48 49 6.688637 TCTTCAACATGCTCTAATCCATTG 57.311 37.500 0.00 0.00 0.00 2.82
59 60 4.464008 TCTAATCCATTGTTCTCATGCCC 58.536 43.478 0.00 0.00 0.00 5.36
62 63 2.170166 TCCATTGTTCTCATGCCCAAC 58.830 47.619 0.00 0.00 0.00 3.77
67 68 2.028130 TGTTCTCATGCCCAACGTTTT 58.972 42.857 0.00 0.00 0.00 2.43
84 85 0.031616 TTTTGGGTGGAAGCAAGGGT 60.032 50.000 0.00 0.00 34.77 4.34
97 98 4.584638 AGCAAGGGTGTGGTTTGATATA 57.415 40.909 0.00 0.00 0.00 0.86
98 99 4.270008 AGCAAGGGTGTGGTTTGATATAC 58.730 43.478 0.00 0.00 0.00 1.47
99 100 4.013728 GCAAGGGTGTGGTTTGATATACA 58.986 43.478 0.00 0.00 0.00 2.29
100 101 4.644685 GCAAGGGTGTGGTTTGATATACAT 59.355 41.667 0.00 0.00 0.00 2.29
101 102 5.221048 GCAAGGGTGTGGTTTGATATACATC 60.221 44.000 0.00 0.00 0.00 3.06
102 103 5.975988 AGGGTGTGGTTTGATATACATCT 57.024 39.130 0.00 0.00 31.93 2.90
103 104 5.930135 AGGGTGTGGTTTGATATACATCTC 58.070 41.667 0.00 0.00 31.93 2.75
104 105 5.063880 GGGTGTGGTTTGATATACATCTCC 58.936 45.833 0.00 0.00 31.93 3.71
105 106 5.397447 GGGTGTGGTTTGATATACATCTCCA 60.397 44.000 0.00 0.00 31.93 3.86
106 107 5.527582 GGTGTGGTTTGATATACATCTCCAC 59.472 44.000 12.93 12.93 42.03 4.02
107 108 6.112734 GTGTGGTTTGATATACATCTCCACA 58.887 40.000 16.29 16.29 44.88 4.17
108 109 6.258727 GTGTGGTTTGATATACATCTCCACAG 59.741 42.308 18.86 0.00 45.99 3.66
109 110 5.760253 GTGGTTTGATATACATCTCCACAGG 59.240 44.000 14.13 0.00 41.72 4.00
110 111 5.428457 TGGTTTGATATACATCTCCACAGGT 59.572 40.000 0.00 0.00 31.93 4.00
111 112 6.069673 TGGTTTGATATACATCTCCACAGGTT 60.070 38.462 0.00 0.00 31.93 3.50
112 113 7.126573 TGGTTTGATATACATCTCCACAGGTTA 59.873 37.037 0.00 0.00 31.93 2.85
113 114 7.441458 GGTTTGATATACATCTCCACAGGTTAC 59.559 40.741 0.00 0.00 31.93 2.50
114 115 7.669089 TTGATATACATCTCCACAGGTTACA 57.331 36.000 0.00 0.00 31.93 2.41
115 116 7.855784 TGATATACATCTCCACAGGTTACAT 57.144 36.000 0.00 0.00 31.93 2.29
116 117 7.896811 TGATATACATCTCCACAGGTTACATC 58.103 38.462 0.00 0.00 31.93 3.06
117 118 7.730332 TGATATACATCTCCACAGGTTACATCT 59.270 37.037 0.00 0.00 31.93 2.90
118 119 4.478206 ACATCTCCACAGGTTACATCTG 57.522 45.455 0.00 0.00 38.16 2.90
119 120 4.096681 ACATCTCCACAGGTTACATCTGA 58.903 43.478 0.00 0.00 36.22 3.27
159 160 8.203485 AGACATTCTCTGTGATCCTAGATTTTC 58.797 37.037 0.00 0.00 38.54 2.29
176 177 2.234300 TTCGGACAAAGACAGACCAC 57.766 50.000 0.00 0.00 0.00 4.16
186 187 5.934625 ACAAAGACAGACCACTCATCATTAC 59.065 40.000 0.00 0.00 0.00 1.89
213 214 8.877864 ATTATGTGGTCTATTTTTCACTCCAA 57.122 30.769 0.00 0.00 0.00 3.53
262 263 3.924918 ACCGATCCGATGACTTCTATG 57.075 47.619 0.00 0.00 0.00 2.23
266 267 0.744281 TCCGATGACTTCTATGCGCA 59.256 50.000 14.96 14.96 0.00 6.09
291 292 3.617535 AGGAGTCCCTTGCGATACT 57.382 52.632 5.25 0.00 40.78 2.12
303 304 2.030551 CGATACTGGAGCTACCGCA 58.969 57.895 0.00 0.00 42.61 5.69
315 316 1.134670 GCTACCGCAGAATCTTCCACT 60.135 52.381 0.00 0.00 35.78 4.00
319 320 2.567615 ACCGCAGAATCTTCCACTTAGT 59.432 45.455 0.00 0.00 0.00 2.24
325 326 5.423886 CAGAATCTTCCACTTAGTCCTTCC 58.576 45.833 0.00 0.00 0.00 3.46
327 328 5.188751 AGAATCTTCCACTTAGTCCTTCCTG 59.811 44.000 0.00 0.00 0.00 3.86
356 357 1.152756 GCACCCACCTGAACTTGGT 60.153 57.895 0.00 0.00 38.53 3.67
357 358 1.172812 GCACCCACCTGAACTTGGTC 61.173 60.000 0.00 0.00 35.28 4.02
403 404 2.612672 CGATCAACTCTGATGCTTGCAT 59.387 45.455 7.91 7.91 42.60 3.96
419 420 3.731728 ATGGCGGGTGCAGATGGT 61.732 61.111 0.00 0.00 45.35 3.55
420 421 3.286694 ATGGCGGGTGCAGATGGTT 62.287 57.895 0.00 0.00 45.35 3.67
430 431 2.046285 CAGATGGTTTGGCCCGGTC 61.046 63.158 0.00 0.00 36.04 4.79
436 437 1.313091 GGTTTGGCCCGGTCTGATTC 61.313 60.000 0.00 0.00 0.00 2.52
440 441 2.514824 GCCCGGTCTGATTCTGCC 60.515 66.667 0.00 0.00 0.00 4.85
450 451 2.912956 TCTGATTCTGCCTTACTGGGTT 59.087 45.455 0.00 0.00 36.00 4.11
455 456 1.351017 TCTGCCTTACTGGGTTCTTGG 59.649 52.381 0.00 0.00 36.00 3.61
461 462 4.721132 CCTTACTGGGTTCTTGGTGTAAA 58.279 43.478 0.00 0.00 0.00 2.01
462 463 4.517832 CCTTACTGGGTTCTTGGTGTAAAC 59.482 45.833 0.00 0.00 0.00 2.01
481 482 3.588277 CGTATTCGGGGATCACTGG 57.412 57.895 3.36 0.00 0.00 4.00
494 495 0.971959 TCACTGGCCCATTGATTGCC 60.972 55.000 0.00 0.00 45.56 4.52
542 544 2.127251 GCTTTTTGCAAAACTCCGAGG 58.873 47.619 23.79 4.15 42.31 4.63
543 545 2.481276 GCTTTTTGCAAAACTCCGAGGT 60.481 45.455 23.79 0.00 42.31 3.85
548 550 2.215196 TGCAAAACTCCGAGGTTACAC 58.785 47.619 0.00 0.00 0.00 2.90
549 551 2.215196 GCAAAACTCCGAGGTTACACA 58.785 47.619 0.00 0.00 0.00 3.72
573 575 1.556911 GTGATCATGGAGGTGGACTGT 59.443 52.381 0.00 0.00 0.00 3.55
574 576 1.833630 TGATCATGGAGGTGGACTGTC 59.166 52.381 0.00 0.00 0.00 3.51
576 578 2.919772 TCATGGAGGTGGACTGTCTA 57.080 50.000 7.85 0.00 0.00 2.59
585 587 3.515901 AGGTGGACTGTCTAAAGATGGTC 59.484 47.826 7.85 6.70 0.00 4.02
594 596 6.438741 ACTGTCTAAAGATGGTCAATCTCTGA 59.561 38.462 0.00 0.00 45.37 3.27
601 603 5.874093 AGATGGTCAATCTCTGAAACACTT 58.126 37.500 0.00 0.00 42.27 3.16
606 608 3.565482 TCAATCTCTGAAACACTTGCCAC 59.435 43.478 0.00 0.00 0.00 5.01
614 1020 3.243035 TGAAACACTTGCCACAATTCTCG 60.243 43.478 0.00 0.00 0.00 4.04
628 1034 1.896220 TTCTCGCTCAATTGTGGCTT 58.104 45.000 18.30 0.00 0.00 4.35
629 1035 1.896220 TCTCGCTCAATTGTGGCTTT 58.104 45.000 18.30 0.00 0.00 3.51
632 1038 4.009675 TCTCGCTCAATTGTGGCTTTTAT 58.990 39.130 18.30 0.00 0.00 1.40
647 1053 7.596995 TGTGGCTTTTATTTTAGTTGAAATCGG 59.403 33.333 0.00 0.00 31.96 4.18
651 1057 9.278734 GCTTTTATTTTAGTTGAAATCGGAGAG 57.721 33.333 0.00 0.00 43.63 3.20
662 1068 4.584743 TGAAATCGGAGAGCTAGCTAATGA 59.415 41.667 19.38 13.58 43.63 2.57
666 1072 5.537300 TCGGAGAGCTAGCTAATGATTTT 57.463 39.130 19.38 0.00 0.00 1.82
695 1106 4.579753 TGAGTCAACATGCAAATCAGTCAA 59.420 37.500 0.00 0.00 0.00 3.18
701 1112 8.236586 GTCAACATGCAAATCAGTCAACTAATA 58.763 33.333 0.00 0.00 0.00 0.98
702 1113 8.959548 TCAACATGCAAATCAGTCAACTAATAT 58.040 29.630 0.00 0.00 0.00 1.28
704 1115 7.934457 ACATGCAAATCAGTCAACTAATATCC 58.066 34.615 0.00 0.00 0.00 2.59
705 1116 7.776969 ACATGCAAATCAGTCAACTAATATCCT 59.223 33.333 0.00 0.00 0.00 3.24
706 1117 7.558161 TGCAAATCAGTCAACTAATATCCTG 57.442 36.000 0.00 0.00 0.00 3.86
713 1124 5.931146 CAGTCAACTAATATCCTGGCTCATC 59.069 44.000 0.00 0.00 0.00 2.92
719 1130 6.294473 ACTAATATCCTGGCTCATCTTTGTG 58.706 40.000 0.00 0.00 0.00 3.33
725 1136 2.977914 TGGCTCATCTTTGTGCTAGAC 58.022 47.619 0.00 0.00 41.12 2.59
726 1137 1.929836 GGCTCATCTTTGTGCTAGACG 59.070 52.381 0.00 0.00 41.12 4.18
727 1138 2.611518 GCTCATCTTTGTGCTAGACGT 58.388 47.619 0.00 0.00 38.89 4.34
768 1179 2.652590 GGAGAGCTGGCTCAATGAAAT 58.347 47.619 22.21 2.08 44.99 2.17
769 1180 2.617774 GGAGAGCTGGCTCAATGAAATC 59.382 50.000 22.21 10.33 44.99 2.17
770 1181 2.617774 GAGAGCTGGCTCAATGAAATCC 59.382 50.000 22.21 0.00 44.99 3.01
771 1182 2.241685 AGAGCTGGCTCAATGAAATCCT 59.758 45.455 22.21 0.00 44.99 3.24
772 1183 2.358267 GAGCTGGCTCAATGAAATCCTG 59.642 50.000 16.55 0.00 42.31 3.86
773 1184 2.025605 AGCTGGCTCAATGAAATCCTGA 60.026 45.455 0.00 0.00 0.00 3.86
774 1185 2.756760 GCTGGCTCAATGAAATCCTGAA 59.243 45.455 6.83 0.00 0.00 3.02
775 1186 3.428589 GCTGGCTCAATGAAATCCTGAAC 60.429 47.826 6.83 0.00 0.00 3.18
776 1187 4.015084 CTGGCTCAATGAAATCCTGAACT 58.985 43.478 0.00 0.00 0.00 3.01
777 1188 4.410099 TGGCTCAATGAAATCCTGAACTT 58.590 39.130 0.00 0.00 0.00 2.66
778 1189 4.834496 TGGCTCAATGAAATCCTGAACTTT 59.166 37.500 0.00 0.00 0.00 2.66
779 1190 5.047802 TGGCTCAATGAAATCCTGAACTTTC 60.048 40.000 0.00 0.00 33.06 2.62
780 1191 5.184671 GGCTCAATGAAATCCTGAACTTTCT 59.815 40.000 0.00 0.00 33.50 2.52
781 1192 6.320944 GCTCAATGAAATCCTGAACTTTCTC 58.679 40.000 0.00 0.00 33.50 2.87
782 1193 6.486253 TCAATGAAATCCTGAACTTTCTCG 57.514 37.500 0.00 0.00 33.50 4.04
783 1194 5.997746 TCAATGAAATCCTGAACTTTCTCGT 59.002 36.000 0.00 0.00 33.50 4.18
784 1195 6.147821 TCAATGAAATCCTGAACTTTCTCGTC 59.852 38.462 0.00 0.00 33.50 4.20
785 1196 4.956085 TGAAATCCTGAACTTTCTCGTCA 58.044 39.130 0.00 0.00 33.50 4.35
786 1197 4.750098 TGAAATCCTGAACTTTCTCGTCAC 59.250 41.667 0.00 0.00 33.50 3.67
787 1198 2.814280 TCCTGAACTTTCTCGTCACC 57.186 50.000 0.00 0.00 0.00 4.02
788 1199 2.036387 TCCTGAACTTTCTCGTCACCA 58.964 47.619 0.00 0.00 0.00 4.17
789 1200 2.035961 TCCTGAACTTTCTCGTCACCAG 59.964 50.000 0.00 0.00 0.00 4.00
790 1201 1.795286 CTGAACTTTCTCGTCACCAGC 59.205 52.381 0.00 0.00 0.00 4.85
791 1202 1.412710 TGAACTTTCTCGTCACCAGCT 59.587 47.619 0.00 0.00 0.00 4.24
792 1203 2.158957 TGAACTTTCTCGTCACCAGCTT 60.159 45.455 0.00 0.00 0.00 3.74
793 1204 1.871080 ACTTTCTCGTCACCAGCTTG 58.129 50.000 0.00 0.00 0.00 4.01
794 1205 0.514691 CTTTCTCGTCACCAGCTTGC 59.485 55.000 0.00 0.00 0.00 4.01
795 1206 0.106708 TTTCTCGTCACCAGCTTGCT 59.893 50.000 0.00 0.00 0.00 3.91
796 1207 0.966179 TTCTCGTCACCAGCTTGCTA 59.034 50.000 0.00 0.00 0.00 3.49
797 1208 0.528017 TCTCGTCACCAGCTTGCTAG 59.472 55.000 0.00 0.00 0.00 3.42
808 1219 1.272781 GCTTGCTAGCTGACTGTACG 58.727 55.000 17.23 0.00 44.27 3.67
809 1220 1.135373 GCTTGCTAGCTGACTGTACGA 60.135 52.381 17.23 0.00 44.27 3.43
810 1221 2.791567 CTTGCTAGCTGACTGTACGAG 58.208 52.381 17.23 0.00 0.00 4.18
811 1222 1.095600 TGCTAGCTGACTGTACGAGG 58.904 55.000 17.23 0.00 0.00 4.63
812 1223 1.339727 TGCTAGCTGACTGTACGAGGA 60.340 52.381 17.23 0.00 0.00 3.71
813 1224 1.743958 GCTAGCTGACTGTACGAGGAA 59.256 52.381 7.70 0.00 0.00 3.36
814 1225 2.359531 GCTAGCTGACTGTACGAGGAAT 59.640 50.000 7.70 0.00 0.00 3.01
815 1226 2.949451 AGCTGACTGTACGAGGAATG 57.051 50.000 0.00 0.00 0.00 2.67
816 1227 1.134965 AGCTGACTGTACGAGGAATGC 60.135 52.381 0.00 0.00 0.00 3.56
817 1228 1.927895 CTGACTGTACGAGGAATGCC 58.072 55.000 0.00 0.00 0.00 4.40
833 1244 7.967890 AGGAATGCCTTTGTTTGAATAAAAG 57.032 32.000 0.00 0.00 43.90 2.27
834 1245 6.427853 AGGAATGCCTTTGTTTGAATAAAAGC 59.572 34.615 0.00 1.15 43.90 3.51
835 1246 6.427853 GGAATGCCTTTGTTTGAATAAAAGCT 59.572 34.615 7.66 0.00 30.67 3.74
836 1247 7.360353 GGAATGCCTTTGTTTGAATAAAAGCTC 60.360 37.037 7.66 0.43 30.67 4.09
837 1248 6.160576 TGCCTTTGTTTGAATAAAAGCTCT 57.839 33.333 7.66 0.00 30.67 4.09
838 1249 6.215845 TGCCTTTGTTTGAATAAAAGCTCTC 58.784 36.000 7.66 0.00 30.67 3.20
839 1250 6.040842 TGCCTTTGTTTGAATAAAAGCTCTCT 59.959 34.615 7.66 0.00 30.67 3.10
840 1251 7.230510 TGCCTTTGTTTGAATAAAAGCTCTCTA 59.769 33.333 7.66 0.00 30.67 2.43
841 1252 8.082242 GCCTTTGTTTGAATAAAAGCTCTCTAA 58.918 33.333 0.00 0.00 31.03 2.10
842 1253 9.965824 CCTTTGTTTGAATAAAAGCTCTCTAAA 57.034 29.630 0.00 0.00 31.03 1.85
846 1257 9.410556 TGTTTGAATAAAAGCTCTCTAAATTGC 57.589 29.630 0.00 0.00 0.00 3.56
847 1258 8.864024 GTTTGAATAAAAGCTCTCTAAATTGCC 58.136 33.333 0.00 0.00 0.00 4.52
848 1259 7.701539 TGAATAAAAGCTCTCTAAATTGCCA 57.298 32.000 0.00 0.00 0.00 4.92
849 1260 7.765307 TGAATAAAAGCTCTCTAAATTGCCAG 58.235 34.615 0.00 0.00 0.00 4.85
850 1261 7.611467 TGAATAAAAGCTCTCTAAATTGCCAGA 59.389 33.333 0.00 0.00 0.00 3.86
851 1262 7.944729 ATAAAAGCTCTCTAAATTGCCAGAA 57.055 32.000 0.00 0.00 0.00 3.02
852 1263 6.655078 AAAAGCTCTCTAAATTGCCAGAAA 57.345 33.333 0.00 0.00 0.00 2.52
853 1264 6.655078 AAAGCTCTCTAAATTGCCAGAAAA 57.345 33.333 0.00 0.00 0.00 2.29
854 1265 6.655078 AAGCTCTCTAAATTGCCAGAAAAA 57.345 33.333 0.00 0.00 0.00 1.94
899 1310 3.595819 GCAGTCAGCACCCCATTC 58.404 61.111 0.00 0.00 44.79 2.67
924 1335 1.079543 CCAGACACGAAGCCCAGAG 60.080 63.158 0.00 0.00 0.00 3.35
926 1337 0.108898 CAGACACGAAGCCCAGAGAG 60.109 60.000 0.00 0.00 0.00 3.20
970 1381 3.692593 ACGGCCCAGTTATACAATGAAAC 59.307 43.478 0.00 0.00 0.00 2.78
1015 1426 3.715097 GCACCTGCAGCCTCCTCT 61.715 66.667 8.66 0.00 41.59 3.69
1024 1435 1.686115 GCAGCCTCCTCTCTCTCTCTT 60.686 57.143 0.00 0.00 0.00 2.85
1031 1442 2.922955 TCCTCTCTCTCTCTTTCCAGGA 59.077 50.000 0.00 0.00 0.00 3.86
1032 1443 3.335183 TCCTCTCTCTCTCTTTCCAGGAA 59.665 47.826 0.00 0.00 0.00 3.36
1040 1451 3.224884 CTCTTTCCAGGAAGAGTCGTC 57.775 52.381 15.52 0.00 44.82 4.20
1041 1452 2.558795 CTCTTTCCAGGAAGAGTCGTCA 59.441 50.000 15.52 0.00 44.82 4.35
1042 1453 2.558795 TCTTTCCAGGAAGAGTCGTCAG 59.441 50.000 8.37 0.00 32.19 3.51
1043 1454 1.257743 TTCCAGGAAGAGTCGTCAGG 58.742 55.000 8.37 9.02 0.00 3.86
1044 1455 0.112606 TCCAGGAAGAGTCGTCAGGT 59.887 55.000 8.37 0.00 0.00 4.00
1045 1456 0.244994 CCAGGAAGAGTCGTCAGGTG 59.755 60.000 8.37 2.54 0.00 4.00
1046 1457 0.244994 CAGGAAGAGTCGTCAGGTGG 59.755 60.000 8.37 0.00 0.00 4.61
1047 1458 0.900647 AGGAAGAGTCGTCAGGTGGG 60.901 60.000 8.37 0.00 0.00 4.61
1048 1459 0.898789 GGAAGAGTCGTCAGGTGGGA 60.899 60.000 8.37 0.00 0.00 4.37
1055 1477 4.008933 GTCAGGTGGGAGCAGCGT 62.009 66.667 0.00 0.00 0.00 5.07
1250 1672 3.589988 CTCGACAGTAAGCATGTTCCTT 58.410 45.455 0.00 0.00 0.00 3.36
1260 1682 2.158900 AGCATGTTCCTTCTCATACCCG 60.159 50.000 0.00 0.00 0.00 5.28
1262 1684 0.539986 TGTTCCTTCTCATACCCGCC 59.460 55.000 0.00 0.00 0.00 6.13
1278 1700 0.729116 CGCCGTTCAGATCAAGCAAT 59.271 50.000 0.00 0.00 0.00 3.56
1311 1733 3.822996 TCGAGCTTAGTCTCAAAGAACG 58.177 45.455 0.00 0.00 33.41 3.95
1361 1783 2.147436 TCAAATCTTGCGTTTTGGGC 57.853 45.000 0.00 0.00 34.38 5.36
1362 1784 1.410517 TCAAATCTTGCGTTTTGGGCA 59.589 42.857 0.00 0.00 38.93 5.36
1371 1793 1.769733 CGTTTTGGGCATGAACTGTG 58.230 50.000 0.00 0.00 0.00 3.66
1380 1802 4.469586 TGGGCATGAACTGTGAAGTAGATA 59.530 41.667 0.00 0.00 0.00 1.98
1384 1806 6.109359 GCATGAACTGTGAAGTAGATACCTT 58.891 40.000 0.00 0.00 0.00 3.50
1385 1807 7.265673 GCATGAACTGTGAAGTAGATACCTTA 58.734 38.462 0.00 0.00 0.00 2.69
1386 1808 7.928706 GCATGAACTGTGAAGTAGATACCTTAT 59.071 37.037 0.00 0.00 0.00 1.73
1389 1811 8.910944 TGAACTGTGAAGTAGATACCTTATACC 58.089 37.037 0.00 0.00 0.00 2.73
1390 1812 8.834004 AACTGTGAAGTAGATACCTTATACCA 57.166 34.615 0.00 0.00 0.00 3.25
1391 1813 8.466617 ACTGTGAAGTAGATACCTTATACCAG 57.533 38.462 0.00 0.00 0.00 4.00
1392 1814 8.060075 ACTGTGAAGTAGATACCTTATACCAGT 58.940 37.037 0.00 0.00 0.00 4.00
1393 1815 9.570468 CTGTGAAGTAGATACCTTATACCAGTA 57.430 37.037 0.00 0.00 0.00 2.74
1394 1816 9.347240 TGTGAAGTAGATACCTTATACCAGTAC 57.653 37.037 0.00 0.00 0.00 2.73
1422 1844 6.321848 TGCCTGCAATATGTATGATGAAAG 57.678 37.500 0.00 0.00 0.00 2.62
1423 1845 5.159209 GCCTGCAATATGTATGATGAAAGC 58.841 41.667 0.00 0.00 0.00 3.51
1425 1847 6.149973 GCCTGCAATATGTATGATGAAAGCTA 59.850 38.462 0.00 0.00 0.00 3.32
1426 1848 7.524912 CCTGCAATATGTATGATGAAAGCTAC 58.475 38.462 0.00 0.00 0.00 3.58
1476 1906 6.788218 AGATTTTGAACTGGGAGAGAGAATT 58.212 36.000 0.00 0.00 0.00 2.17
1485 1915 4.096681 TGGGAGAGAGAATTGTCTGCTAA 58.903 43.478 10.29 0.00 35.69 3.09
1511 1941 2.045045 GGCTATGTGCACTGGCCA 60.045 61.111 29.22 4.71 45.15 5.36
1520 1950 0.112218 TGCACTGGCCAATTAGGTGT 59.888 50.000 19.77 4.96 40.61 4.16
1576 2006 2.840974 CGTTTCTGTCGCAGGGATT 58.159 52.632 6.95 0.00 31.51 3.01
1603 2033 1.448013 CGGTTTTCTCCTCGGCTCC 60.448 63.158 0.00 0.00 0.00 4.70
1606 2036 0.320508 GTTTTCTCCTCGGCTCCGTT 60.321 55.000 8.28 0.00 40.74 4.44
1667 2097 3.329889 TGCTCCGGGCCTTCATGT 61.330 61.111 0.84 0.00 40.92 3.21
1708 2138 4.093291 CCCCTGCTCTTCGCTGCT 62.093 66.667 0.00 0.00 40.11 4.24
1711 2141 2.511145 CTGCTCTTCGCTGCTCCC 60.511 66.667 0.00 0.00 40.11 4.30
1720 2150 1.078214 CGCTGCTCCCATGAAGGAA 60.078 57.895 0.00 0.00 41.22 3.36
1918 2358 1.678101 GTAATTGTGCAGGATGAGGGC 59.322 52.381 0.00 0.00 39.69 5.19
1951 2391 5.358160 AGCTTGGCAGTACAGGAAATATTTC 59.642 40.000 18.22 18.22 36.46 2.17
2034 2477 7.013846 CCCTTTGTTTACTTGATGGTTAGTTGA 59.986 37.037 0.00 0.00 0.00 3.18
2038 2481 6.018588 TGTTTACTTGATGGTTAGTTGACGTG 60.019 38.462 0.00 0.00 0.00 4.49
2042 2485 4.594123 TGATGGTTAGTTGACGTGAAGA 57.406 40.909 0.00 0.00 0.00 2.87
2043 2486 4.556233 TGATGGTTAGTTGACGTGAAGAG 58.444 43.478 0.00 0.00 0.00 2.85
2044 2487 2.750948 TGGTTAGTTGACGTGAAGAGC 58.249 47.619 0.00 0.00 0.00 4.09
2060 2503 1.350351 AGAGCAGCCATTGTCTCTGTT 59.650 47.619 0.00 0.00 38.22 3.16
2067 2513 5.278463 GCAGCCATTGTCTCTGTTAAAAAGA 60.278 40.000 0.00 0.00 0.00 2.52
2071 2517 8.424133 AGCCATTGTCTCTGTTAAAAAGAAAAT 58.576 29.630 0.00 0.00 28.98 1.82
2079 2525 9.762933 TCTCTGTTAAAAAGAAAATTTGGATGG 57.237 29.630 0.00 0.00 0.00 3.51
2100 2548 9.556030 GGATGGTTTCTAGAAAAATTTAAGACG 57.444 33.333 19.30 0.00 31.33 4.18
2164 2612 2.864343 ACGGAACAACAGCTATATTCGC 59.136 45.455 0.00 0.00 0.00 4.70
2207 2655 6.384305 ACTTGTATAAGCATCAGTTCTAGGGT 59.616 38.462 0.00 0.00 37.43 4.34
2243 2691 4.698583 AGCTATCGTTACTGTCTTTCGT 57.301 40.909 0.00 0.00 0.00 3.85
2281 2813 6.711277 AGAGTTAACTCATCTGGCAATGTTA 58.289 36.000 31.80 0.00 45.21 2.41
2288 2820 4.650734 TCATCTGGCAATGTTACAGACAA 58.349 39.130 6.59 0.00 43.29 3.18
2427 2959 3.499918 AGGATCGTTGTTCTGCTTTCTTG 59.500 43.478 0.00 0.00 0.00 3.02
2455 2987 4.990526 ACATCAAAGGTGAGGTTGATTCT 58.009 39.130 0.00 0.00 46.28 2.40
2502 3082 5.514169 TCACAGACTGATCTACCTCAAGAT 58.486 41.667 10.08 0.00 38.95 2.40
2535 3122 8.880878 ATTGTTTAATTACCACAAAACTGGAC 57.119 30.769 11.62 0.00 34.19 4.02
2544 3131 5.686753 ACCACAAAACTGGACTTGTATACA 58.313 37.500 0.08 0.08 34.04 2.29
2658 3270 2.910205 CAGTCACTCTGTGCACCAG 58.090 57.895 15.69 12.74 42.97 4.00
2713 3420 3.479489 TGAAATGATGTGTGCTGACTGT 58.521 40.909 0.00 0.00 0.00 3.55
2776 3483 1.272147 ACATGCTTCCTCCCTTCCAAC 60.272 52.381 0.00 0.00 0.00 3.77
2829 3537 0.987294 CAGGACTGGGACATGGTCTT 59.013 55.000 0.00 0.00 38.20 3.01
3091 3799 0.765510 AGGACTTGGCGAAACTCCTT 59.234 50.000 2.43 0.00 29.43 3.36
3103 3811 4.622220 GCGAAACTCCTTACAGGGTATCAA 60.622 45.833 0.00 0.00 35.59 2.57
3181 3894 2.936498 CACCCAAGTAAACATAGGCTCG 59.064 50.000 0.00 0.00 0.00 5.03
3185 3898 4.369182 CCAAGTAAACATAGGCTCGTAGG 58.631 47.826 0.00 0.00 0.00 3.18
3215 3931 2.223340 ACAAAACTTGCGCTCTTCTGTG 60.223 45.455 9.73 1.27 0.00 3.66
3502 4223 2.079925 GGAAACAGTAAGCAGCTGAGG 58.920 52.381 20.43 1.46 37.40 3.86
3544 4295 6.603095 TGTGTATTTGTTTTGGTTTTGCAAC 58.397 32.000 0.00 0.00 0.00 4.17
3580 4331 4.508047 GCCTATCCATTCCCATCTCATGTT 60.508 45.833 0.00 0.00 0.00 2.71
3583 4334 4.589647 TCCATTCCCATCTCATGTTTCA 57.410 40.909 0.00 0.00 0.00 2.69
3670 4441 4.698780 CCATGATATGCTGGTGATAACAGG 59.301 45.833 0.00 0.00 36.48 4.00
3679 4450 3.517901 CTGGTGATAACAGGTTACCAGGA 59.482 47.826 18.52 0.00 35.17 3.86
3682 4453 4.881850 GGTGATAACAGGTTACCAGGATTG 59.118 45.833 3.51 0.00 0.00 2.67
3739 4516 6.265196 TCTTGTGAAGATTGGTAAGTTTGCAT 59.735 34.615 0.00 0.00 31.20 3.96
3740 4517 6.403866 TGTGAAGATTGGTAAGTTTGCATT 57.596 33.333 0.00 0.00 0.00 3.56
3741 4518 7.517614 TGTGAAGATTGGTAAGTTTGCATTA 57.482 32.000 0.00 0.00 0.00 1.90
3742 4519 7.367285 TGTGAAGATTGGTAAGTTTGCATTAC 58.633 34.615 0.85 0.85 33.29 1.89
3756 4541 7.644490 AGTTTGCATTACGAAACATGAAGTAA 58.356 30.769 0.00 4.76 35.00 2.24
3775 4683 9.135189 TGAAGTAACTGTAAACTACCAACTAGA 57.865 33.333 0.00 0.00 0.00 2.43
3847 4755 4.679373 GGAATGATCCTAGAGCAGTTGA 57.321 45.455 0.00 0.00 42.93 3.18
3867 4783 3.244764 CTCAGGCATGCTGAGTTGT 57.755 52.632 26.16 2.57 42.30 3.32
3877 4793 2.182827 TGCTGAGTTGTAGAGGCAGAT 58.817 47.619 0.00 0.00 0.00 2.90
3878 4794 3.365472 TGCTGAGTTGTAGAGGCAGATA 58.635 45.455 0.00 0.00 0.00 1.98
3879 4795 3.131223 TGCTGAGTTGTAGAGGCAGATAC 59.869 47.826 0.00 0.00 0.00 2.24
3936 4852 2.806244 GCCCTAAATATACACAGCACGG 59.194 50.000 0.00 0.00 0.00 4.94
3951 4867 0.248458 CACGGCTTGTTCAAAGCGTT 60.248 50.000 4.15 0.00 43.89 4.84
3975 4891 5.105595 TGCATGATCGAGATATACTTCAGGG 60.106 44.000 0.00 0.00 0.00 4.45
3977 4893 6.095580 GCATGATCGAGATATACTTCAGGGTA 59.904 42.308 0.00 0.00 0.00 3.69
4113 5034 3.668447 TGCTGAACTTTCTGAGGATCAC 58.332 45.455 0.00 0.00 42.56 3.06
4115 5036 3.257393 CTGAACTTTCTGAGGATCACCG 58.743 50.000 0.00 0.00 42.56 4.94
4169 5090 1.201647 CTTGGCCTTGTGATGCTCTTG 59.798 52.381 3.32 0.00 0.00 3.02
4180 5101 2.012673 GATGCTCTTGCCGACAAAGAT 58.987 47.619 0.00 0.00 38.71 2.40
4233 5154 0.615331 GATGAACAGAGGCCTCACCA 59.385 55.000 33.90 23.42 43.14 4.17
4277 5198 3.559171 GCTCATACTTCTTCACAACCCCA 60.559 47.826 0.00 0.00 0.00 4.96
4460 5381 0.041090 ATTCAAACCGGGGGCTTGAT 59.959 50.000 6.32 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.094464 TGAGAACAATGGATTAGAGCATGTTG 59.906 38.462 0.00 0.00 0.00 3.33
34 35 4.577693 GCATGAGAACAATGGATTAGAGCA 59.422 41.667 0.00 0.00 0.00 4.26
48 49 2.793278 AAAACGTTGGGCATGAGAAC 57.207 45.000 0.00 0.00 0.00 3.01
59 60 1.134965 TGCTTCCACCCAAAAACGTTG 60.135 47.619 0.00 0.00 0.00 4.10
62 63 1.537990 CCTTGCTTCCACCCAAAAACG 60.538 52.381 0.00 0.00 0.00 3.60
67 68 1.152567 CACCCTTGCTTCCACCCAA 60.153 57.895 0.00 0.00 0.00 4.12
73 74 0.389025 CAAACCACACCCTTGCTTCC 59.611 55.000 0.00 0.00 0.00 3.46
97 98 4.096681 TCAGATGTAACCTGTGGAGATGT 58.903 43.478 0.00 0.00 33.57 3.06
98 99 4.743057 TCAGATGTAACCTGTGGAGATG 57.257 45.455 0.00 0.00 33.57 2.90
99 100 4.780021 AGTTCAGATGTAACCTGTGGAGAT 59.220 41.667 0.00 0.00 33.57 2.75
100 101 4.160329 AGTTCAGATGTAACCTGTGGAGA 58.840 43.478 0.00 0.00 33.57 3.71
101 102 4.221703 AGAGTTCAGATGTAACCTGTGGAG 59.778 45.833 0.00 0.00 33.57 3.86
102 103 4.160329 AGAGTTCAGATGTAACCTGTGGA 58.840 43.478 0.00 0.00 33.57 4.02
103 104 4.543590 AGAGTTCAGATGTAACCTGTGG 57.456 45.455 0.00 0.00 33.57 4.17
104 105 4.692625 CCAAGAGTTCAGATGTAACCTGTG 59.307 45.833 0.00 0.00 33.57 3.66
105 106 4.348168 ACCAAGAGTTCAGATGTAACCTGT 59.652 41.667 0.00 0.00 33.57 4.00
106 107 4.899502 ACCAAGAGTTCAGATGTAACCTG 58.100 43.478 0.00 0.00 0.00 4.00
107 108 4.841246 AGACCAAGAGTTCAGATGTAACCT 59.159 41.667 0.00 0.00 0.00 3.50
108 109 5.153950 AGACCAAGAGTTCAGATGTAACC 57.846 43.478 0.00 0.00 0.00 2.85
109 110 7.121463 TCTCTAGACCAAGAGTTCAGATGTAAC 59.879 40.741 0.00 0.00 43.02 2.50
110 111 7.121463 GTCTCTAGACCAAGAGTTCAGATGTAA 59.879 40.741 0.00 0.00 43.02 2.41
111 112 6.600032 GTCTCTAGACCAAGAGTTCAGATGTA 59.400 42.308 0.00 0.00 43.02 2.29
112 113 5.417580 GTCTCTAGACCAAGAGTTCAGATGT 59.582 44.000 0.00 0.00 43.02 3.06
113 114 5.417266 TGTCTCTAGACCAAGAGTTCAGATG 59.583 44.000 7.63 0.00 44.15 2.90
114 115 5.575157 TGTCTCTAGACCAAGAGTTCAGAT 58.425 41.667 7.63 0.00 44.15 2.90
115 116 4.986783 TGTCTCTAGACCAAGAGTTCAGA 58.013 43.478 7.63 0.00 44.15 3.27
116 117 5.913137 ATGTCTCTAGACCAAGAGTTCAG 57.087 43.478 7.63 0.00 44.15 3.02
117 118 6.013379 AGAATGTCTCTAGACCAAGAGTTCA 58.987 40.000 7.63 0.24 44.15 3.18
118 119 6.524101 AGAATGTCTCTAGACCAAGAGTTC 57.476 41.667 7.63 3.55 44.15 3.01
119 120 6.524101 GAGAATGTCTCTAGACCAAGAGTT 57.476 41.667 7.63 0.00 44.15 3.01
151 152 5.221561 TGGTCTGTCTTTGTCCGAAAATCTA 60.222 40.000 0.00 0.00 0.00 1.98
159 160 1.068588 TGAGTGGTCTGTCTTTGTCCG 59.931 52.381 0.00 0.00 0.00 4.79
186 187 9.613428 TGGAGTGAAAAATAGACCACATAATAG 57.387 33.333 0.00 0.00 32.35 1.73
232 233 1.480789 TCGGATCGGTTCCATCTTCA 58.519 50.000 5.97 0.00 45.78 3.02
238 239 1.136305 GAAGTCATCGGATCGGTTCCA 59.864 52.381 5.97 0.00 45.78 3.53
241 242 3.553096 GCATAGAAGTCATCGGATCGGTT 60.553 47.826 0.00 0.00 0.00 4.44
250 251 2.478134 GGTCATGCGCATAGAAGTCATC 59.522 50.000 24.84 9.39 0.00 2.92
262 263 2.109126 GGACTCCTTGGTCATGCGC 61.109 63.158 0.00 0.00 37.91 6.09
282 283 0.384309 CGGTAGCTCCAGTATCGCAA 59.616 55.000 0.00 0.00 35.57 4.85
288 289 1.681793 GATTCTGCGGTAGCTCCAGTA 59.318 52.381 0.00 1.76 45.42 2.74
291 292 1.137086 GAAGATTCTGCGGTAGCTCCA 59.863 52.381 0.00 0.00 45.42 3.86
303 304 5.188751 CAGGAAGGACTAAGTGGAAGATTCT 59.811 44.000 0.00 0.00 0.00 2.40
319 320 1.216064 CCATCCATGTCCAGGAAGGA 58.784 55.000 8.60 8.60 44.78 3.36
325 326 1.454479 GGGTGCCATCCATGTCCAG 60.454 63.158 0.00 0.00 0.00 3.86
327 328 1.754234 GTGGGTGCCATCCATGTCC 60.754 63.158 0.00 0.00 35.28 4.02
356 357 7.627513 GCACCATCCGTTGTAATTTTTATCTGA 60.628 37.037 0.00 0.00 0.00 3.27
357 358 6.472163 GCACCATCCGTTGTAATTTTTATCTG 59.528 38.462 0.00 0.00 0.00 2.90
403 404 3.505790 AAACCATCTGCACCCGCCA 62.506 57.895 0.00 0.00 37.32 5.69
415 416 1.863155 ATCAGACCGGGCCAAACCAT 61.863 55.000 1.76 0.00 42.05 3.55
419 420 0.322456 CAGAATCAGACCGGGCCAAA 60.322 55.000 1.76 0.00 0.00 3.28
420 421 1.299648 CAGAATCAGACCGGGCCAA 59.700 57.895 1.76 0.00 0.00 4.52
430 431 3.054802 AGAACCCAGTAAGGCAGAATCAG 60.055 47.826 0.00 0.00 35.39 2.90
436 437 1.073923 ACCAAGAACCCAGTAAGGCAG 59.926 52.381 0.00 0.00 35.39 4.85
440 441 4.517832 GGTTTACACCAAGAACCCAGTAAG 59.482 45.833 0.00 0.00 43.61 2.34
481 482 1.227060 GCTTCGGCAATCAATGGGC 60.227 57.895 0.00 0.00 41.33 5.36
509 510 2.756829 CAAAAAGCACACCATCATGCA 58.243 42.857 0.00 0.00 44.59 3.96
573 575 7.604164 GTGTTTCAGAGATTGACCATCTTTAGA 59.396 37.037 0.00 0.00 42.92 2.10
574 576 7.605691 AGTGTTTCAGAGATTGACCATCTTTAG 59.394 37.037 0.00 0.00 42.92 1.85
576 578 6.302269 AGTGTTTCAGAGATTGACCATCTTT 58.698 36.000 0.00 0.00 42.92 2.52
585 587 3.316029 TGTGGCAAGTGTTTCAGAGATTG 59.684 43.478 0.00 0.00 0.00 2.67
594 596 2.543653 GCGAGAATTGTGGCAAGTGTTT 60.544 45.455 4.66 0.00 0.00 2.83
601 603 1.825090 ATTGAGCGAGAATTGTGGCA 58.175 45.000 12.05 0.00 0.00 4.92
606 608 2.163010 AGCCACAATTGAGCGAGAATTG 59.837 45.455 13.59 13.39 43.53 2.32
614 1020 7.889589 ACTAAAATAAAAGCCACAATTGAGC 57.110 32.000 13.59 14.27 0.00 4.26
628 1034 8.561738 AGCTCTCCGATTTCAACTAAAATAAA 57.438 30.769 0.00 0.00 0.00 1.40
629 1035 9.314321 CTAGCTCTCCGATTTCAACTAAAATAA 57.686 33.333 0.00 0.00 0.00 1.40
632 1038 5.581085 GCTAGCTCTCCGATTTCAACTAAAA 59.419 40.000 7.70 0.00 0.00 1.52
666 1072 8.143193 ACTGATTTGCATGTTGACTCATAAAAA 58.857 29.630 0.00 0.00 0.00 1.94
675 1086 4.863491 AGTTGACTGATTTGCATGTTGAC 58.137 39.130 0.00 0.00 0.00 3.18
684 1095 6.769822 AGCCAGGATATTAGTTGACTGATTTG 59.230 38.462 0.00 0.00 0.00 2.32
690 1101 5.843421 AGATGAGCCAGGATATTAGTTGACT 59.157 40.000 0.00 0.00 0.00 3.41
695 1106 6.294473 CACAAAGATGAGCCAGGATATTAGT 58.706 40.000 0.00 0.00 0.00 2.24
701 1112 1.284198 AGCACAAAGATGAGCCAGGAT 59.716 47.619 0.00 0.00 43.26 3.24
702 1113 0.694771 AGCACAAAGATGAGCCAGGA 59.305 50.000 0.00 0.00 43.26 3.86
704 1115 2.935201 GTCTAGCACAAAGATGAGCCAG 59.065 50.000 0.00 0.00 43.26 4.85
705 1116 2.675032 CGTCTAGCACAAAGATGAGCCA 60.675 50.000 0.00 0.00 43.26 4.75
706 1117 1.929836 CGTCTAGCACAAAGATGAGCC 59.070 52.381 0.00 0.00 43.26 4.70
713 1124 0.792640 CAGGCACGTCTAGCACAAAG 59.207 55.000 0.00 0.00 0.00 2.77
746 1157 2.178890 CATTGAGCCAGCTCTCCGC 61.179 63.158 19.71 0.00 43.12 5.54
761 1172 5.997746 TGACGAGAAAGTTCAGGATTTCATT 59.002 36.000 0.00 0.00 37.78 2.57
768 1179 2.035961 CTGGTGACGAGAAAGTTCAGGA 59.964 50.000 0.00 0.00 0.00 3.86
769 1180 2.408050 CTGGTGACGAGAAAGTTCAGG 58.592 52.381 0.00 0.00 0.00 3.86
770 1181 1.795286 GCTGGTGACGAGAAAGTTCAG 59.205 52.381 0.00 0.00 0.00 3.02
771 1182 1.412710 AGCTGGTGACGAGAAAGTTCA 59.587 47.619 0.00 0.00 0.00 3.18
772 1183 2.156343 AGCTGGTGACGAGAAAGTTC 57.844 50.000 0.00 0.00 0.00 3.01
773 1184 2.213499 CAAGCTGGTGACGAGAAAGTT 58.787 47.619 0.00 0.00 0.00 2.66
774 1185 1.871080 CAAGCTGGTGACGAGAAAGT 58.129 50.000 0.00 0.00 0.00 2.66
775 1186 0.514691 GCAAGCTGGTGACGAGAAAG 59.485 55.000 0.00 0.00 0.00 2.62
776 1187 0.106708 AGCAAGCTGGTGACGAGAAA 59.893 50.000 0.00 0.00 0.00 2.52
777 1188 0.966179 TAGCAAGCTGGTGACGAGAA 59.034 50.000 4.53 0.00 0.00 2.87
778 1189 0.528017 CTAGCAAGCTGGTGACGAGA 59.472 55.000 4.53 0.00 0.00 4.04
779 1190 1.080995 GCTAGCAAGCTGGTGACGAG 61.081 60.000 10.63 0.00 45.85 4.18
780 1191 1.079819 GCTAGCAAGCTGGTGACGA 60.080 57.895 10.63 0.00 45.85 4.20
781 1192 3.479370 GCTAGCAAGCTGGTGACG 58.521 61.111 10.63 0.00 45.85 4.35
790 1201 2.478709 CCTCGTACAGTCAGCTAGCAAG 60.479 54.545 18.83 9.26 0.00 4.01
791 1202 1.472878 CCTCGTACAGTCAGCTAGCAA 59.527 52.381 18.83 0.90 0.00 3.91
792 1203 1.095600 CCTCGTACAGTCAGCTAGCA 58.904 55.000 18.83 0.00 0.00 3.49
793 1204 1.380524 TCCTCGTACAGTCAGCTAGC 58.619 55.000 6.62 6.62 0.00 3.42
794 1205 3.793801 GCATTCCTCGTACAGTCAGCTAG 60.794 52.174 0.00 0.00 0.00 3.42
795 1206 2.099263 GCATTCCTCGTACAGTCAGCTA 59.901 50.000 0.00 0.00 0.00 3.32
796 1207 1.134965 GCATTCCTCGTACAGTCAGCT 60.135 52.381 0.00 0.00 0.00 4.24
797 1208 1.281899 GCATTCCTCGTACAGTCAGC 58.718 55.000 0.00 0.00 0.00 4.26
798 1209 1.478510 AGGCATTCCTCGTACAGTCAG 59.521 52.381 0.00 0.00 38.72 3.51
799 1210 1.557099 AGGCATTCCTCGTACAGTCA 58.443 50.000 0.00 0.00 38.72 3.41
800 1211 2.673368 CAAAGGCATTCCTCGTACAGTC 59.327 50.000 0.00 0.00 43.40 3.51
801 1212 2.038557 ACAAAGGCATTCCTCGTACAGT 59.961 45.455 0.00 0.00 43.40 3.55
802 1213 2.699954 ACAAAGGCATTCCTCGTACAG 58.300 47.619 0.00 0.00 43.40 2.74
803 1214 2.851263 ACAAAGGCATTCCTCGTACA 57.149 45.000 0.00 0.00 43.40 2.90
804 1215 3.500680 TCAAACAAAGGCATTCCTCGTAC 59.499 43.478 0.00 0.00 43.40 3.67
805 1216 3.745799 TCAAACAAAGGCATTCCTCGTA 58.254 40.909 0.00 0.00 43.40 3.43
806 1217 2.582052 TCAAACAAAGGCATTCCTCGT 58.418 42.857 0.00 0.00 43.40 4.18
807 1218 3.641437 TTCAAACAAAGGCATTCCTCG 57.359 42.857 0.00 0.00 43.40 4.63
808 1219 7.360353 GCTTTTATTCAAACAAAGGCATTCCTC 60.360 37.037 0.00 0.00 43.40 3.71
810 1221 6.427853 AGCTTTTATTCAAACAAAGGCATTCC 59.572 34.615 3.88 0.00 38.71 3.01
811 1222 7.386025 AGAGCTTTTATTCAAACAAAGGCATTC 59.614 33.333 3.88 0.00 38.71 2.67
812 1223 7.219322 AGAGCTTTTATTCAAACAAAGGCATT 58.781 30.769 3.88 0.00 38.71 3.56
813 1224 6.762333 AGAGCTTTTATTCAAACAAAGGCAT 58.238 32.000 3.88 0.00 38.71 4.40
814 1225 6.040842 AGAGAGCTTTTATTCAAACAAAGGCA 59.959 34.615 3.88 0.00 38.71 4.75
815 1226 6.450545 AGAGAGCTTTTATTCAAACAAAGGC 58.549 36.000 0.00 0.00 37.09 4.35
816 1227 9.965824 TTTAGAGAGCTTTTATTCAAACAAAGG 57.034 29.630 0.00 0.00 0.00 3.11
820 1231 9.410556 GCAATTTAGAGAGCTTTTATTCAAACA 57.589 29.630 0.00 0.00 0.00 2.83
821 1232 8.864024 GGCAATTTAGAGAGCTTTTATTCAAAC 58.136 33.333 0.00 0.00 0.00 2.93
822 1233 8.584157 TGGCAATTTAGAGAGCTTTTATTCAAA 58.416 29.630 0.00 0.00 0.00 2.69
823 1234 8.121305 TGGCAATTTAGAGAGCTTTTATTCAA 57.879 30.769 0.00 0.00 0.00 2.69
824 1235 7.611467 TCTGGCAATTTAGAGAGCTTTTATTCA 59.389 33.333 0.00 0.00 0.00 2.57
825 1236 7.989826 TCTGGCAATTTAGAGAGCTTTTATTC 58.010 34.615 0.00 0.00 0.00 1.75
826 1237 7.944729 TCTGGCAATTTAGAGAGCTTTTATT 57.055 32.000 0.00 0.00 0.00 1.40
827 1238 7.944729 TTCTGGCAATTTAGAGAGCTTTTAT 57.055 32.000 0.00 0.00 0.00 1.40
828 1239 7.759489 TTTCTGGCAATTTAGAGAGCTTTTA 57.241 32.000 0.00 0.00 0.00 1.52
829 1240 6.655078 TTTCTGGCAATTTAGAGAGCTTTT 57.345 33.333 0.00 0.00 0.00 2.27
830 1241 6.655078 TTTTCTGGCAATTTAGAGAGCTTT 57.345 33.333 0.00 0.00 0.00 3.51
831 1242 6.655078 TTTTTCTGGCAATTTAGAGAGCTT 57.345 33.333 0.00 0.00 0.00 3.74
853 1264 5.477607 AATAAAGTTTAGGGGCGCTTTTT 57.522 34.783 10.13 8.51 33.78 1.94
854 1265 6.605995 AGATAATAAAGTTTAGGGGCGCTTTT 59.394 34.615 10.13 6.79 33.78 2.27
855 1266 6.127101 AGATAATAAAGTTTAGGGGCGCTTT 58.873 36.000 10.13 0.00 35.62 3.51
856 1267 5.691896 AGATAATAAAGTTTAGGGGCGCTT 58.308 37.500 10.13 0.00 0.00 4.68
899 1310 2.342279 TTCGTGTCTGGGCCGAAG 59.658 61.111 0.00 0.00 35.85 3.79
956 1367 4.342772 CTGCTGCGGTTTCATTGTATAAC 58.657 43.478 0.00 0.00 0.00 1.89
957 1368 3.181501 GCTGCTGCGGTTTCATTGTATAA 60.182 43.478 10.62 0.00 0.00 0.98
1003 1414 0.395586 GAGAGAGAGAGGAGGCTGCA 60.396 60.000 9.23 0.00 0.00 4.41
1009 1420 3.053693 TCCTGGAAAGAGAGAGAGAGGAG 60.054 52.174 0.00 0.00 0.00 3.69
1010 1421 2.922955 TCCTGGAAAGAGAGAGAGAGGA 59.077 50.000 0.00 0.00 0.00 3.71
1013 1424 4.666412 TCTTCCTGGAAAGAGAGAGAGA 57.334 45.455 10.86 0.00 31.71 3.10
1024 1435 1.257743 CCTGACGACTCTTCCTGGAA 58.742 55.000 9.14 9.14 0.00 3.53
1031 1442 1.536943 GCTCCCACCTGACGACTCTT 61.537 60.000 0.00 0.00 0.00 2.85
1032 1443 1.979693 GCTCCCACCTGACGACTCT 60.980 63.158 0.00 0.00 0.00 3.24
1038 1449 3.941657 GACGCTGCTCCCACCTGAC 62.942 68.421 0.00 0.00 0.00 3.51
1039 1450 3.695606 GACGCTGCTCCCACCTGA 61.696 66.667 0.00 0.00 0.00 3.86
1250 1672 0.681887 TCTGAACGGCGGGTATGAGA 60.682 55.000 13.24 0.29 0.00 3.27
1260 1682 2.927553 AATTGCTTGATCTGAACGGC 57.072 45.000 0.00 0.00 0.00 5.68
1311 1733 2.266055 CCTCAGTCGGTTCCTGGC 59.734 66.667 0.00 0.00 0.00 4.85
1380 1802 5.885912 CAGGCAATTTGTACTGGTATAAGGT 59.114 40.000 12.53 0.00 0.00 3.50
1384 1806 4.849518 TGCAGGCAATTTGTACTGGTATA 58.150 39.130 18.39 0.00 0.00 1.47
1385 1807 3.696045 TGCAGGCAATTTGTACTGGTAT 58.304 40.909 18.39 0.00 0.00 2.73
1386 1808 3.147553 TGCAGGCAATTTGTACTGGTA 57.852 42.857 18.39 3.91 0.00 3.25
1387 1809 1.993956 TGCAGGCAATTTGTACTGGT 58.006 45.000 18.39 0.00 0.00 4.00
1388 1810 3.598019 ATTGCAGGCAATTTGTACTGG 57.402 42.857 13.44 6.75 43.32 4.00
1394 1816 7.149307 TCATCATACATATTGCAGGCAATTTG 58.851 34.615 25.55 25.55 43.32 2.32
1422 1844 4.017808 TCCTGACCTCAAGAACTAGTAGC 58.982 47.826 0.00 0.00 0.00 3.58
1423 1845 5.502079 TCTCCTGACCTCAAGAACTAGTAG 58.498 45.833 0.00 0.00 0.00 2.57
1425 1847 4.390129 TCTCCTGACCTCAAGAACTAGT 57.610 45.455 0.00 0.00 0.00 2.57
1426 1848 4.159506 CCTTCTCCTGACCTCAAGAACTAG 59.840 50.000 0.00 0.00 0.00 2.57
1476 1906 2.573462 AGCCATTCTTCCTTAGCAGACA 59.427 45.455 0.00 0.00 0.00 3.41
1485 1915 2.240667 AGTGCACATAGCCATTCTTCCT 59.759 45.455 21.04 0.00 44.83 3.36
1511 1941 2.890945 GCACCAACCAAGACACCTAATT 59.109 45.455 0.00 0.00 0.00 1.40
1520 1950 1.271543 CCTGATGAGCACCAACCAAGA 60.272 52.381 0.00 0.00 0.00 3.02
1576 2006 3.894547 GAGAAAACCGCCGCCCAGA 62.895 63.158 0.00 0.00 0.00 3.86
1603 2033 1.066215 TCCTCCATGACCATCACAACG 60.066 52.381 0.00 0.00 0.00 4.10
1606 2036 1.833630 GAGTCCTCCATGACCATCACA 59.166 52.381 0.00 0.00 35.83 3.58
1705 2135 1.691219 GGGTTCCTTCATGGGAGCA 59.309 57.895 7.07 0.00 43.62 4.26
1708 2138 2.978946 GCGGGGTTCCTTCATGGGA 61.979 63.158 0.00 0.00 36.20 4.37
1711 2141 1.815421 CGAGCGGGGTTCCTTCATG 60.815 63.158 0.00 0.00 0.00 3.07
1918 2358 2.706339 ACTGCCAAGCTATCCTCAAG 57.294 50.000 0.00 0.00 0.00 3.02
1951 2391 1.327690 TGGAATTCCTCTCGTCCCCG 61.328 60.000 24.73 0.00 36.82 5.73
2034 2477 0.250467 ACAATGGCTGCTCTTCACGT 60.250 50.000 0.00 0.00 0.00 4.49
2038 2481 2.008329 CAGAGACAATGGCTGCTCTTC 58.992 52.381 0.00 0.00 36.80 2.87
2042 2485 3.423539 TTAACAGAGACAATGGCTGCT 57.576 42.857 0.00 0.00 33.03 4.24
2043 2486 4.503741 TTTTAACAGAGACAATGGCTGC 57.496 40.909 0.00 0.00 33.03 5.25
2044 2487 6.317789 TCTTTTTAACAGAGACAATGGCTG 57.682 37.500 0.00 0.00 35.81 4.85
2074 2520 9.556030 CGTCTTAAATTTTTCTAGAAACCATCC 57.444 33.333 17.51 0.13 0.00 3.51
2099 2546 6.146184 ACACTGACAATGTGATACTTCTTTCG 59.854 38.462 0.00 0.00 38.65 3.46
2100 2548 7.426929 ACACTGACAATGTGATACTTCTTTC 57.573 36.000 0.00 0.00 38.65 2.62
2261 2792 6.371548 GTCTGTAACATTGCCAGATGAGTTAA 59.628 38.462 5.05 0.00 37.54 2.01
2263 2794 4.697352 GTCTGTAACATTGCCAGATGAGTT 59.303 41.667 5.05 0.00 37.54 3.01
2270 2801 4.539870 CTTGTTGTCTGTAACATTGCCAG 58.460 43.478 0.00 0.00 40.00 4.85
2281 2813 4.022849 GCTAAATTCCTGCTTGTTGTCTGT 60.023 41.667 0.00 0.00 0.00 3.41
2288 2820 3.700538 TCATGGCTAAATTCCTGCTTGT 58.299 40.909 0.00 0.00 0.00 3.16
2427 2959 3.222603 ACCTCACCTTTGATGTTTGGAC 58.777 45.455 0.00 0.00 26.81 4.02
2455 2987 9.625747 TGATAACAAGCTCAACAATATATCCAA 57.374 29.630 0.00 0.00 0.00 3.53
2535 3122 8.057812 GCAAAATGCATCAGATTGTATACAAG 57.942 34.615 22.03 10.16 44.26 3.16
2658 3270 3.381590 GCCTTCCCAAAATATCCACACTC 59.618 47.826 0.00 0.00 0.00 3.51
2713 3420 1.067425 GTGCTGCATCAAGCCATCAAA 60.067 47.619 5.27 0.00 44.83 2.69
2751 3458 3.274288 GAAGGGAGGAAGCATGTAACTG 58.726 50.000 0.00 0.00 0.00 3.16
2757 3464 1.005215 AGTTGGAAGGGAGGAAGCATG 59.995 52.381 0.00 0.00 0.00 4.06
3091 3799 5.908831 ACCAACCATATCTTGATACCCTGTA 59.091 40.000 0.00 0.00 0.00 2.74
3103 3811 7.888021 TGAACATGTAGAAAACCAACCATATCT 59.112 33.333 0.00 0.00 0.00 1.98
3181 3894 4.738252 GCAAGTTTTGTTTACAGCACCTAC 59.262 41.667 0.00 0.00 0.00 3.18
3185 3898 2.034926 GCGCAAGTTTTGTTTACAGCAC 60.035 45.455 0.30 0.00 41.68 4.40
3215 3931 3.304026 TCGATGTAAATGGCGTCGTTAAC 59.696 43.478 0.00 0.00 43.45 2.01
3346 4062 3.636231 CCACCAGACGAAGGCCCA 61.636 66.667 0.00 0.00 0.00 5.36
3352 4068 1.191489 TGCCTGATCCACCAGACGAA 61.191 55.000 0.00 0.00 36.29 3.85
3490 4209 0.539051 GAGCCTTCCTCAGCTGCTTA 59.461 55.000 9.47 0.00 40.11 3.09
3502 4223 1.065126 ACATAGCAACCAGGAGCCTTC 60.065 52.381 0.00 0.00 0.00 3.46
3580 4331 8.908903 AGTTGTATACACCAAAAACTGAATGAA 58.091 29.630 4.68 0.00 0.00 2.57
3583 4334 9.744468 GAAAGTTGTATACACCAAAAACTGAAT 57.256 29.630 4.68 0.00 0.00 2.57
3670 4441 5.767816 AAGAAACACACAATCCTGGTAAC 57.232 39.130 0.00 0.00 0.00 2.50
3679 4450 4.826733 TCTGTGCCATAAGAAACACACAAT 59.173 37.500 0.00 0.00 38.07 2.71
3682 4453 5.874810 TCTATCTGTGCCATAAGAAACACAC 59.125 40.000 0.00 0.00 38.07 3.82
3739 4516 9.316730 AGTTTACAGTTACTTCATGTTTCGTAA 57.683 29.630 0.00 0.00 0.00 3.18
3740 4517 8.876275 AGTTTACAGTTACTTCATGTTTCGTA 57.124 30.769 0.00 0.00 0.00 3.43
3741 4518 7.781548 AGTTTACAGTTACTTCATGTTTCGT 57.218 32.000 0.00 0.00 0.00 3.85
3742 4519 8.219105 GGTAGTTTACAGTTACTTCATGTTTCG 58.781 37.037 0.00 0.00 0.00 3.46
3756 4541 6.164176 GCATGTCTAGTTGGTAGTTTACAGT 58.836 40.000 0.00 0.00 0.00 3.55
3775 4683 3.262660 TGAGGTTCTCTCTTCATGCATGT 59.737 43.478 25.43 2.03 42.86 3.21
3867 4783 8.548880 ACCTTGTAAATTAGTATCTGCCTCTA 57.451 34.615 0.00 0.00 0.00 2.43
3877 4793 7.288158 ACCTTGCCAAAACCTTGTAAATTAGTA 59.712 33.333 0.00 0.00 0.00 1.82
3878 4794 6.099125 ACCTTGCCAAAACCTTGTAAATTAGT 59.901 34.615 0.00 0.00 0.00 2.24
3879 4795 6.521162 ACCTTGCCAAAACCTTGTAAATTAG 58.479 36.000 0.00 0.00 0.00 1.73
3936 4852 1.190763 CATGCAACGCTTTGAACAAGC 59.809 47.619 7.19 0.00 39.77 4.01
3951 4867 5.105595 CCCTGAAGTATATCTCGATCATGCA 60.106 44.000 0.00 0.00 0.00 3.96
3975 4891 2.799978 GCAAAAGCAATGTTGGGTGTAC 59.200 45.455 0.00 0.00 0.00 2.90
3977 4893 1.209019 TGCAAAAGCAATGTTGGGTGT 59.791 42.857 0.00 0.00 0.00 4.16
4088 5009 1.805345 CCTCAGAAAGTTCAGCAGCAG 59.195 52.381 0.00 0.00 0.00 4.24
4115 5036 3.532155 AGCGTCTCCGATCAGGGC 61.532 66.667 0.00 0.00 41.52 5.19
4169 5090 2.892784 AGCTAGGTATCTTTGTCGGC 57.107 50.000 0.00 0.00 0.00 5.54
4233 5154 0.905357 CTCGAGGACTTCCATTGGGT 59.095 55.000 3.91 0.00 38.89 4.51
4277 5198 0.038251 TGAGCTTCGACAAGTGCGAT 60.038 50.000 0.00 0.00 37.64 4.58
4460 5381 2.698274 TGTGAGGCTGAGAACTAACACA 59.302 45.455 0.00 0.00 35.24 3.72


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

AutoCloner maintained by Alex Coulton.