Multiple sequence alignment - TraesCS4D01G201300

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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 TraesCS4D01G201300 chr4D 100.000 4489 0 0 1 4489 348302981 348307469 0.000000e+00 8290.0
1 TraesCS4D01G201300 chr4D 94.000 50 3 0 1751 1800 348036262 348036311 4.820000e-10 76.8
2 TraesCS4D01G201300 chr4A 90.893 1109 55 22 1346 2415 117283051 117281950 0.000000e+00 1447.0
3 TraesCS4D01G201300 chr4A 88.879 1106 64 23 2494 3550 117281945 117280850 0.000000e+00 1306.0
4 TraesCS4D01G201300 chr4A 88.587 552 34 12 3 534 117284491 117283949 1.050000e-180 643.0
5 TraesCS4D01G201300 chr4A 83.652 679 44 18 582 1234 117283927 117283290 1.080000e-160 577.0
6 TraesCS4D01G201300 chr4A 92.000 50 4 0 1751 1800 117704831 117704782 2.240000e-08 71.3
7 TraesCS4D01G201300 chr2D 98.079 833 13 2 3660 4489 56189392 56188560 0.000000e+00 1447.0
8 TraesCS4D01G201300 chr2D 92.985 841 11 4 3662 4489 33946576 33945771 0.000000e+00 1182.0
9 TraesCS4D01G201300 chr2D 100.000 31 0 0 3150 3180 82325056 82325086 1.740000e-04 58.4
10 TraesCS4D01G201300 chr1D 98.195 831 10 3 3662 4489 474917412 474916584 0.000000e+00 1447.0
11 TraesCS4D01G201300 chr7D 97.467 829 20 1 3662 4489 276474041 276474869 0.000000e+00 1413.0
12 TraesCS4D01G201300 chr7D 95.054 829 19 4 3662 4489 293591210 293592017 0.000000e+00 1284.0
13 TraesCS4D01G201300 chr7D 93.133 830 27 12 3661 4489 52618179 52618979 0.000000e+00 1190.0
14 TraesCS4D01G201300 chr5D 97.112 831 21 2 3662 4489 213074544 213075374 0.000000e+00 1399.0
15 TraesCS4D01G201300 chr5D 96.908 841 11 3 3662 4489 563593625 563592787 0.000000e+00 1395.0
16 TraesCS4D01G201300 chr5D 77.885 104 18 4 2465 2564 367999983 368000085 4.850000e-05 60.2
17 TraesCS4D01G201300 chr4B 91.996 912 52 8 2209 3105 428465166 428466071 0.000000e+00 1260.0
18 TraesCS4D01G201300 chr4B 94.727 531 22 4 1683 2212 428463433 428463958 0.000000e+00 821.0
19 TraesCS4D01G201300 chr4B 88.321 548 34 13 3 534 428459817 428460350 8.190000e-177 630.0
20 TraesCS4D01G201300 chr4B 84.461 547 49 18 1125 1651 428461213 428461743 1.440000e-139 507.0
21 TraesCS4D01G201300 chr4B 82.895 456 41 22 715 1140 428460515 428460963 4.240000e-100 375.0
22 TraesCS4D01G201300 chr4B 90.308 227 17 5 3168 3390 428466076 428466301 4.390000e-75 292.0
23 TraesCS4D01G201300 chr4B 90.909 121 4 3 3546 3660 428466358 428466477 6.010000e-34 156.0
24 TraesCS4D01G201300 chr4B 93.069 101 3 1 620 720 428460385 428460481 1.300000e-30 145.0
25 TraesCS4D01G201300 chr4B 94.000 50 3 0 1751 1800 428191634 428191683 4.820000e-10 76.8
26 TraesCS4D01G201300 chr4B 100.000 37 0 0 556 592 428460339 428460375 8.060000e-08 69.4
27 TraesCS4D01G201300 chr6D 91.851 859 18 9 3659 4489 263962257 263961423 0.000000e+00 1151.0
28 TraesCS4D01G201300 chr6D 91.707 205 14 2 3658 3862 311262844 311263045 9.510000e-72 281.0
29 TraesCS4D01G201300 chr3B 88.284 845 55 16 3659 4489 262836817 262837631 0.000000e+00 972.0
30 TraesCS4D01G201300 chr2A 87.298 866 42 19 3661 4489 36028514 36029348 0.000000e+00 928.0
31 TraesCS4D01G201300 chr5B 89.873 79 4 4 3112 3188 433530572 433530648 1.030000e-16 99.0
32 TraesCS4D01G201300 chr6B 93.333 60 3 1 3118 3177 565749845 565749903 2.220000e-13 87.9
33 TraesCS4D01G201300 chr6A 89.706 68 7 0 3118 3185 161780130 161780197 2.220000e-13 87.9
34 TraesCS4D01G201300 chr1B 88.571 70 8 0 3111 3180 332093237 332093306 8.000000e-13 86.1
35 TraesCS4D01G201300 chr2B 100.000 31 0 0 3150 3180 134403489 134403519 1.740000e-04 58.4


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 TraesCS4D01G201300 chr4D 348302981 348307469 4488 False 8290.000000 8290 100.000000 1 4489 1 chr4D.!!$F2 4488
1 TraesCS4D01G201300 chr4A 117280850 117284491 3641 True 993.250000 1447 88.002750 3 3550 4 chr4A.!!$R2 3547
2 TraesCS4D01G201300 chr2D 56188560 56189392 832 True 1447.000000 1447 98.079000 3660 4489 1 chr2D.!!$R2 829
3 TraesCS4D01G201300 chr2D 33945771 33946576 805 True 1182.000000 1182 92.985000 3662 4489 1 chr2D.!!$R1 827
4 TraesCS4D01G201300 chr1D 474916584 474917412 828 True 1447.000000 1447 98.195000 3662 4489 1 chr1D.!!$R1 827
5 TraesCS4D01G201300 chr7D 276474041 276474869 828 False 1413.000000 1413 97.467000 3662 4489 1 chr7D.!!$F2 827
6 TraesCS4D01G201300 chr7D 293591210 293592017 807 False 1284.000000 1284 95.054000 3662 4489 1 chr7D.!!$F3 827
7 TraesCS4D01G201300 chr7D 52618179 52618979 800 False 1190.000000 1190 93.133000 3661 4489 1 chr7D.!!$F1 828
8 TraesCS4D01G201300 chr5D 213074544 213075374 830 False 1399.000000 1399 97.112000 3662 4489 1 chr5D.!!$F1 827
9 TraesCS4D01G201300 chr5D 563592787 563593625 838 True 1395.000000 1395 96.908000 3662 4489 1 chr5D.!!$R1 827
10 TraesCS4D01G201300 chr4B 428459817 428466477 6660 False 472.822222 1260 90.742889 3 3660 9 chr4B.!!$F2 3657
11 TraesCS4D01G201300 chr6D 263961423 263962257 834 True 1151.000000 1151 91.851000 3659 4489 1 chr6D.!!$R1 830
12 TraesCS4D01G201300 chr3B 262836817 262837631 814 False 972.000000 972 88.284000 3659 4489 1 chr3B.!!$F1 830
13 TraesCS4D01G201300 chr2A 36028514 36029348 834 False 928.000000 928 87.298000 3661 4489 1 chr2A.!!$F1 828

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
334 350 0.321122 CGGTGCTCCTTTCTTGCTCT 60.321 55.000 2.85 0.0 0.00 4.09 F
526 554 0.611714 TGCCTCGTAGTTTCTTCCCC 59.388 55.000 0.00 0.0 0.00 4.81 F
527 555 0.611714 GCCTCGTAGTTTCTTCCCCA 59.388 55.000 0.00 0.0 0.00 4.96 F
1025 1136 0.670546 GCGTCTCCAGCAAGCAAGTA 60.671 55.000 0.00 0.0 34.19 2.24 F
1026 1137 1.071605 CGTCTCCAGCAAGCAAGTAC 58.928 55.000 0.00 0.0 0.00 2.73 F
2844 6262 1.134729 GGAAATGAATGGCATTGCGGT 60.135 47.619 19.07 0.0 46.25 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1868 0.107897 TGTCACACGTGAGCAAAGGT 60.108 50.000 25.01 0.00 40.75 3.50 R
2083 4277 0.454600 CCAGCAATGCATCACAGGTC 59.545 55.000 8.35 0.00 0.00 3.85 R
2106 4300 1.051008 TTGTCCAGAGCAGCTTCTGA 58.949 50.000 15.63 4.50 45.95 3.27 R
2844 6262 1.003959 TGCTTGGTCTGCGCATACA 60.004 52.632 24.86 15.18 0.00 2.29 R
2975 6393 1.103803 TGTATGTCTGGACGGAGCTC 58.896 55.000 4.71 4.71 0.00 4.09 R
4381 7958 0.257039 GCCACCATGTCCATCCTCTT 59.743 55.000 0.00 0.00 0.00 2.85 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
20 21 0.997196 GTATCTCGGTGTCGGTTTGC 59.003 55.000 0.00 0.00 36.95 3.68
39 40 2.420722 TGCGTTATTTTCCAATCCCGAC 59.579 45.455 0.00 0.00 0.00 4.79
91 93 5.014858 AGATTGCTTGAAGATGTGACCAAT 58.985 37.500 0.00 0.00 0.00 3.16
115 121 1.269012 ACCAAACATGCCAGGGAATG 58.731 50.000 4.66 4.66 37.19 2.67
127 133 1.952296 CAGGGAATGGCTGCAGAATAC 59.048 52.381 20.43 4.47 0.00 1.89
128 134 0.947244 GGGAATGGCTGCAGAATACG 59.053 55.000 20.43 0.00 0.00 3.06
129 135 1.668419 GGAATGGCTGCAGAATACGT 58.332 50.000 20.43 2.32 0.00 3.57
131 137 1.331756 GAATGGCTGCAGAATACGTGG 59.668 52.381 20.43 0.00 0.00 4.94
132 138 0.541392 ATGGCTGCAGAATACGTGGA 59.459 50.000 20.43 0.00 0.00 4.02
133 139 0.323302 TGGCTGCAGAATACGTGGAA 59.677 50.000 20.43 0.00 0.00 3.53
134 140 1.271108 TGGCTGCAGAATACGTGGAAA 60.271 47.619 20.43 0.00 0.00 3.13
136 142 2.414161 GGCTGCAGAATACGTGGAAAAC 60.414 50.000 20.43 0.00 0.00 2.43
137 143 2.484264 GCTGCAGAATACGTGGAAAACT 59.516 45.455 20.43 0.00 0.00 2.66
203 210 5.557891 GCATATAGGCCATGCTTTTAGAG 57.442 43.478 17.12 0.00 44.35 2.43
299 314 1.127582 GTGCTGAATGCTCGTGAACTC 59.872 52.381 0.00 0.00 43.37 3.01
300 315 1.001293 TGCTGAATGCTCGTGAACTCT 59.999 47.619 0.00 0.00 43.37 3.24
301 316 1.658095 GCTGAATGCTCGTGAACTCTC 59.342 52.381 0.00 0.00 38.95 3.20
330 346 0.875059 GAACCGGTGCTCCTTTCTTG 59.125 55.000 8.52 0.00 0.00 3.02
334 350 0.321122 CGGTGCTCCTTTCTTGCTCT 60.321 55.000 2.85 0.00 0.00 4.09
347 363 8.462016 TCCTTTCTTGCTCTTATCAATTTTAGC 58.538 33.333 0.00 0.00 0.00 3.09
463 491 8.749841 ATGCGTACTTAATCAGTTCATATCTC 57.250 34.615 0.00 0.00 36.88 2.75
492 520 2.084546 GATGCCACAAACCTGTCCTAC 58.915 52.381 0.00 0.00 31.64 3.18
498 526 1.000955 ACAAACCTGTCCTACTCGCTG 59.999 52.381 0.00 0.00 0.00 5.18
522 550 0.963962 TCGGTGCCTCGTAGTTTCTT 59.036 50.000 0.00 0.00 0.00 2.52
523 551 1.068055 TCGGTGCCTCGTAGTTTCTTC 60.068 52.381 0.00 0.00 0.00 2.87
524 552 1.723220 GGTGCCTCGTAGTTTCTTCC 58.277 55.000 0.00 0.00 0.00 3.46
525 553 1.675116 GGTGCCTCGTAGTTTCTTCCC 60.675 57.143 0.00 0.00 0.00 3.97
526 554 0.611714 TGCCTCGTAGTTTCTTCCCC 59.388 55.000 0.00 0.00 0.00 4.81
527 555 0.611714 GCCTCGTAGTTTCTTCCCCA 59.388 55.000 0.00 0.00 0.00 4.96
528 556 1.209747 GCCTCGTAGTTTCTTCCCCAT 59.790 52.381 0.00 0.00 0.00 4.00
529 557 2.433239 GCCTCGTAGTTTCTTCCCCATA 59.567 50.000 0.00 0.00 0.00 2.74
530 558 3.740452 GCCTCGTAGTTTCTTCCCCATAC 60.740 52.174 0.00 0.00 0.00 2.39
531 559 3.490419 CCTCGTAGTTTCTTCCCCATACG 60.490 52.174 0.00 0.00 37.83 3.06
532 560 3.355378 TCGTAGTTTCTTCCCCATACGA 58.645 45.455 1.50 1.50 41.68 3.43
533 561 3.379372 TCGTAGTTTCTTCCCCATACGAG 59.621 47.826 1.50 0.00 39.79 4.18
534 562 3.129988 CGTAGTTTCTTCCCCATACGAGT 59.870 47.826 0.00 0.00 38.54 4.18
535 563 4.381292 CGTAGTTTCTTCCCCATACGAGTT 60.381 45.833 0.00 0.00 38.54 3.01
536 564 4.635699 AGTTTCTTCCCCATACGAGTTT 57.364 40.909 0.00 0.00 0.00 2.66
537 565 4.981812 AGTTTCTTCCCCATACGAGTTTT 58.018 39.130 0.00 0.00 0.00 2.43
538 566 5.382616 AGTTTCTTCCCCATACGAGTTTTT 58.617 37.500 0.00 0.00 0.00 1.94
618 653 1.339610 CAACGAGCTCCAGGGAGATAG 59.660 57.143 19.34 15.13 41.31 2.08
655 690 2.936498 CAAAGTCACTGTCCAAACGAGT 59.064 45.455 0.00 0.00 0.00 4.18
656 691 2.981859 AGTCACTGTCCAAACGAGTT 57.018 45.000 0.00 0.00 0.00 3.01
657 692 4.395959 AAGTCACTGTCCAAACGAGTTA 57.604 40.909 0.00 0.00 0.00 2.24
658 693 4.395959 AGTCACTGTCCAAACGAGTTAA 57.604 40.909 0.00 0.00 0.00 2.01
705 740 2.683968 TCAACCATCGACTACAACAGC 58.316 47.619 0.00 0.00 0.00 4.40
749 823 1.403647 GCGTATGTGCGGCCTATATCA 60.404 52.381 0.00 0.00 0.00 2.15
805 894 0.995728 CGCTCGCTTCTTCTTCTTCC 59.004 55.000 0.00 0.00 0.00 3.46
806 895 1.670087 CGCTCGCTTCTTCTTCTTCCA 60.670 52.381 0.00 0.00 0.00 3.53
807 896 2.626840 GCTCGCTTCTTCTTCTTCCAT 58.373 47.619 0.00 0.00 0.00 3.41
860 961 3.546218 GCTCGCTCAAAGTTTTCTTCGTT 60.546 43.478 0.00 0.00 39.48 3.85
861 962 4.588278 CTCGCTCAAAGTTTTCTTCGTTT 58.412 39.130 0.00 0.00 39.48 3.60
862 963 4.584394 TCGCTCAAAGTTTTCTTCGTTTC 58.416 39.130 0.00 0.00 39.48 2.78
863 964 4.331717 TCGCTCAAAGTTTTCTTCGTTTCT 59.668 37.500 0.00 0.00 39.48 2.52
864 965 5.028375 CGCTCAAAGTTTTCTTCGTTTCTT 58.972 37.500 0.00 0.00 39.48 2.52
865 966 5.169738 CGCTCAAAGTTTTCTTCGTTTCTTC 59.830 40.000 0.00 0.00 39.48 2.87
866 967 6.258899 GCTCAAAGTTTTCTTCGTTTCTTCT 58.741 36.000 0.00 0.00 39.48 2.85
867 968 6.747739 GCTCAAAGTTTTCTTCGTTTCTTCTT 59.252 34.615 0.00 0.00 39.48 2.52
868 969 7.044641 GCTCAAAGTTTTCTTCGTTTCTTCTTC 60.045 37.037 0.00 0.00 39.48 2.87
869 970 6.959311 TCAAAGTTTTCTTCGTTTCTTCTTCG 59.041 34.615 0.00 0.00 39.48 3.79
870 971 6.418585 AAGTTTTCTTCGTTTCTTCTTCGT 57.581 33.333 0.00 0.00 34.76 3.85
903 1004 1.218316 CCCACCTTCAGCCGTACTC 59.782 63.158 0.00 0.00 0.00 2.59
917 1018 2.289010 CCGTACTCCCGTTTACCAGTTT 60.289 50.000 0.00 0.00 0.00 2.66
919 1020 3.732212 GTACTCCCGTTTACCAGTTTGT 58.268 45.455 0.00 0.00 0.00 2.83
927 1028 3.242188 CGTTTACCAGTTTGTATAGCGGC 60.242 47.826 0.00 0.00 0.00 6.53
952 1053 7.855904 GCAGTGCTTTATATACGCTTACAAAAT 59.144 33.333 8.18 0.00 0.00 1.82
962 1072 5.114785 ACGCTTACAAAATGTACATTGCA 57.885 34.783 21.46 0.00 31.69 4.08
963 1073 4.915085 ACGCTTACAAAATGTACATTGCAC 59.085 37.500 21.46 6.84 31.69 4.57
964 1074 4.914504 CGCTTACAAAATGTACATTGCACA 59.085 37.500 21.46 5.61 31.69 4.57
974 1084 1.667830 CATTGCACACGTCCCGAGT 60.668 57.895 0.00 0.00 0.00 4.18
1024 1135 1.963338 GCGTCTCCAGCAAGCAAGT 60.963 57.895 0.00 0.00 34.19 3.16
1025 1136 0.670546 GCGTCTCCAGCAAGCAAGTA 60.671 55.000 0.00 0.00 34.19 2.24
1026 1137 1.071605 CGTCTCCAGCAAGCAAGTAC 58.928 55.000 0.00 0.00 0.00 2.73
1044 1159 4.153411 AGTACTACTGCACAGTTCCTTCT 58.847 43.478 8.86 0.00 42.54 2.85
1045 1160 4.589374 AGTACTACTGCACAGTTCCTTCTT 59.411 41.667 8.86 0.00 42.54 2.52
1089 1204 1.623359 GCGCGATCACTAGATGGATC 58.377 55.000 12.10 5.33 37.22 3.36
1112 1231 2.997303 TCTACTCTATGATCGCTCGCTC 59.003 50.000 0.00 0.00 0.00 5.03
1128 1247 3.116300 TCGCTCATCGCTCTATGAAAAC 58.884 45.455 0.00 0.00 35.51 2.43
1143 1527 4.893424 TGAAAACTCTGTAGGTTTGCAC 57.107 40.909 0.00 0.00 42.80 4.57
1144 1528 4.265893 TGAAAACTCTGTAGGTTTGCACA 58.734 39.130 0.00 0.00 42.80 4.57
1145 1529 4.335315 TGAAAACTCTGTAGGTTTGCACAG 59.665 41.667 0.00 0.00 42.80 3.66
1146 1530 2.550830 ACTCTGTAGGTTTGCACAGG 57.449 50.000 2.20 0.00 42.01 4.00
1147 1531 2.047061 ACTCTGTAGGTTTGCACAGGA 58.953 47.619 2.20 0.00 42.01 3.86
1148 1532 2.438021 ACTCTGTAGGTTTGCACAGGAA 59.562 45.455 2.20 0.00 42.01 3.36
1149 1533 3.070018 CTCTGTAGGTTTGCACAGGAAG 58.930 50.000 2.20 0.00 42.01 3.46
1150 1534 2.703536 TCTGTAGGTTTGCACAGGAAGA 59.296 45.455 2.20 0.00 42.01 2.87
1179 1563 2.589157 CCGCCTACCTTGACACCCA 61.589 63.158 0.00 0.00 0.00 4.51
1235 1725 7.064253 GCAACCAGGTTGTGTTATTACTACTAG 59.936 40.741 29.46 2.47 44.40 2.57
1253 1743 8.411991 ACTACTAGTACTTTGCTTTCTTCTCT 57.588 34.615 0.00 0.00 0.00 3.10
1261 1751 7.163001 ACTTTGCTTTCTTCTCTGAAACTTT 57.837 32.000 0.00 0.00 33.11 2.66
1266 1756 8.506168 TGCTTTCTTCTCTGAAACTTTCTTTA 57.494 30.769 3.22 0.00 33.11 1.85
1279 1769 9.677567 TGAAACTTTCTTTACTCAAATATGTGC 57.322 29.630 3.22 0.00 0.00 4.57
1280 1770 9.677567 GAAACTTTCTTTACTCAAATATGTGCA 57.322 29.630 0.00 0.00 0.00 4.57
1282 1772 9.683069 AACTTTCTTTACTCAAATATGTGCAAG 57.317 29.630 0.00 0.00 0.00 4.01
1284 1774 5.868257 TCTTTACTCAAATATGTGCAAGCG 58.132 37.500 0.00 0.00 0.00 4.68
1285 1775 2.549633 ACTCAAATATGTGCAAGCGC 57.450 45.000 0.00 0.00 39.24 5.92
1315 1843 7.639072 CGAGATCTTCATGTTCATGTTCATTTC 59.361 37.037 11.73 6.79 0.00 2.17
1316 1844 8.577048 AGATCTTCATGTTCATGTTCATTTCT 57.423 30.769 11.73 6.39 0.00 2.52
1318 1846 7.748691 TCTTCATGTTCATGTTCATTTCTGA 57.251 32.000 11.73 0.00 0.00 3.27
1319 1847 8.344446 TCTTCATGTTCATGTTCATTTCTGAT 57.656 30.769 11.73 0.00 0.00 2.90
1320 1848 9.452287 TCTTCATGTTCATGTTCATTTCTGATA 57.548 29.630 11.73 0.00 0.00 2.15
1321 1849 9.499585 CTTCATGTTCATGTTCATTTCTGATAC 57.500 33.333 11.73 0.00 0.00 2.24
1322 1850 8.564509 TCATGTTCATGTTCATTTCTGATACA 57.435 30.769 11.73 0.00 31.58 2.29
1323 1851 9.181061 TCATGTTCATGTTCATTTCTGATACAT 57.819 29.630 11.73 0.00 35.43 2.29
1324 1852 9.447040 CATGTTCATGTTCATTTCTGATACATC 57.553 33.333 4.80 0.00 34.12 3.06
1325 1853 7.687445 TGTTCATGTTCATTTCTGATACATCG 58.313 34.615 0.00 0.00 34.12 3.84
1326 1854 7.548780 TGTTCATGTTCATTTCTGATACATCGA 59.451 33.333 0.00 0.00 34.12 3.59
1327 1855 8.554528 GTTCATGTTCATTTCTGATACATCGAT 58.445 33.333 0.00 0.00 34.12 3.59
1328 1856 8.302965 TCATGTTCATTTCTGATACATCGATC 57.697 34.615 0.00 0.00 34.12 3.69
1329 1857 8.146412 TCATGTTCATTTCTGATACATCGATCT 58.854 33.333 0.00 0.00 34.12 2.75
1330 1858 7.936950 TGTTCATTTCTGATACATCGATCTC 57.063 36.000 0.00 0.00 0.00 2.75
1331 1859 7.720442 TGTTCATTTCTGATACATCGATCTCT 58.280 34.615 0.00 0.00 0.00 3.10
1332 1860 7.650903 TGTTCATTTCTGATACATCGATCTCTG 59.349 37.037 0.00 0.00 0.00 3.35
1333 1861 6.155136 TCATTTCTGATACATCGATCTCTGC 58.845 40.000 0.00 0.00 0.00 4.26
1334 1862 3.820777 TCTGATACATCGATCTCTGCG 57.179 47.619 0.00 0.00 0.00 5.18
1335 1863 3.142174 TCTGATACATCGATCTCTGCGT 58.858 45.455 0.00 0.00 0.00 5.24
1336 1864 4.315803 TCTGATACATCGATCTCTGCGTA 58.684 43.478 0.00 0.00 0.00 4.42
1337 1865 4.938226 TCTGATACATCGATCTCTGCGTAT 59.062 41.667 0.00 0.00 0.00 3.06
1338 1866 5.412904 TCTGATACATCGATCTCTGCGTATT 59.587 40.000 0.00 0.00 0.00 1.89
1339 1867 6.013842 TGATACATCGATCTCTGCGTATTT 57.986 37.500 0.00 0.00 0.00 1.40
1340 1868 7.119262 TCTGATACATCGATCTCTGCGTATTTA 59.881 37.037 0.00 0.00 0.00 1.40
1341 1869 7.021790 TGATACATCGATCTCTGCGTATTTAC 58.978 38.462 0.00 0.00 0.00 2.01
1344 1872 4.913335 TCGATCTCTGCGTATTTACCTT 57.087 40.909 0.00 0.00 0.00 3.50
1351 1879 3.682858 TCTGCGTATTTACCTTTGCTCAC 59.317 43.478 0.00 0.00 0.00 3.51
1358 1886 1.860676 TACCTTTGCTCACGTGTGAC 58.139 50.000 21.06 12.33 35.46 3.67
1362 1890 1.665679 CTTTGCTCACGTGTGACAAGT 59.334 47.619 21.06 0.00 34.59 3.16
1391 1919 1.330521 CAGGTTGTACATGGCGTATGC 59.669 52.381 0.00 0.00 40.59 3.14
1492 2024 2.584835 TTTCCCTCCACATGAGTTGG 57.415 50.000 0.00 0.00 39.65 3.77
1568 2100 2.332654 GGTACCAGGGTTTGCAGCG 61.333 63.158 7.15 0.00 0.00 5.18
1666 3830 7.344871 AGGTGTGGCTAGACTAAAATACATAGT 59.655 37.037 0.00 0.00 36.34 2.12
1695 3888 9.202273 CTCCTATTTAGATGAGTGTTAAGATGC 57.798 37.037 0.00 0.00 0.00 3.91
1823 4016 5.242393 CCAAATTGAGTCCTGATGTGAGTTT 59.758 40.000 0.00 0.00 0.00 2.66
2045 4239 4.202315 TGGCAAGAGCTAAGAACACTTGTA 60.202 41.667 9.88 0.00 41.70 2.41
2046 4240 4.755123 GGCAAGAGCTAAGAACACTTGTAA 59.245 41.667 9.88 0.00 41.70 2.41
2047 4241 5.412904 GGCAAGAGCTAAGAACACTTGTAAT 59.587 40.000 9.88 0.00 41.70 1.89
2093 4287 3.865446 TGCTGATTACTGACCTGTGATG 58.135 45.455 0.00 0.00 0.00 3.07
2106 4300 1.749063 CTGTGATGCATTGCTGGTCAT 59.251 47.619 10.49 0.00 0.00 3.06
2107 4301 1.746787 TGTGATGCATTGCTGGTCATC 59.253 47.619 10.49 4.71 36.70 2.92
2159 4353 6.725369 TCTCCCTTTCAAAATTTGATGATGGA 59.275 34.615 9.41 11.53 39.84 3.41
2171 4365 7.787623 ATTTGATGATGGACCTTTCTTTCTT 57.212 32.000 0.00 0.00 0.00 2.52
2250 5653 4.552276 GGCAATTTAAAGAACTAACGTCGC 59.448 41.667 0.00 0.00 0.00 5.19
2315 5718 7.174413 TGTTGATGGATTCCAAGTATTCTTCA 58.826 34.615 9.98 3.41 36.95 3.02
2336 5739 7.544566 TCTTCACCAACATAAAGAACTACGATC 59.455 37.037 0.00 0.00 0.00 3.69
2390 5793 3.678056 TCAAGGTAGCAAGAACACGAT 57.322 42.857 0.00 0.00 0.00 3.73
2447 5850 5.068198 GCTCCATGAAGCCTGATATTTCAAA 59.932 40.000 0.00 0.00 36.22 2.69
2458 5861 9.783081 AGCCTGATATTTCAAAATTCAACTTTT 57.217 25.926 0.00 0.00 0.00 2.27
2642 6053 7.649306 GTGTAGCTCAAATCTTGAACACATTTT 59.351 33.333 13.88 0.00 43.38 1.82
2844 6262 1.134729 GGAAATGAATGGCATTGCGGT 60.135 47.619 19.07 0.00 46.25 5.68
2975 6393 1.606350 GATCTCGCGCCCGAAATACG 61.606 60.000 0.00 0.00 43.87 3.06
3092 6510 9.484806 AAATGGAGATCATTGGACTCTTATTTT 57.515 29.630 0.00 0.00 44.68 1.82
3158 6580 7.320499 CAGTTTAAATTAGACTGCCAAAACG 57.680 36.000 10.16 0.00 34.97 3.60
3174 6596 6.913673 TGCCAAAACGTCTTACATTTAAGAAC 59.086 34.615 2.91 0.00 44.35 3.01
3179 6601 7.653767 AACGTCTTACATTTAAGAACAGAGG 57.346 36.000 2.91 0.00 44.35 3.69
3181 6603 7.889469 ACGTCTTACATTTAAGAACAGAGGTA 58.111 34.615 2.91 0.00 44.35 3.08
3229 6654 9.445786 CACATAAAACGTTTATCAAAGTCTTGT 57.554 29.630 15.03 2.26 33.94 3.16
3291 6716 1.737793 GGTTTAACCTGCTCATCCACG 59.262 52.381 6.92 0.00 34.73 4.94
3302 6730 2.094417 GCTCATCCACGAGTGTTTTAGC 59.906 50.000 2.36 2.99 35.33 3.09
3369 6799 1.893315 AGGATTTTCCCCCGATCTCA 58.107 50.000 0.00 0.00 37.19 3.27
3397 6827 6.733509 AGGAAGTCATTGTAGTAGTACTCCT 58.266 40.000 5.96 7.71 0.00 3.69
3414 6844 2.500098 CTCCTTCCGTCCAAGTAATCCA 59.500 50.000 0.00 0.00 0.00 3.41
3418 6848 1.829222 TCCGTCCAAGTAATCCAGGAC 59.171 52.381 0.00 0.00 45.46 3.85
3436 6866 7.243824 TCCAGGACGGAGGTAATATTACTTAT 58.756 38.462 21.86 10.76 39.64 1.73
3437 6867 8.393259 TCCAGGACGGAGGTAATATTACTTATA 58.607 37.037 21.86 0.00 39.64 0.98
3497 6958 4.196971 ACGTGCAGATATAAGGGTTTTCC 58.803 43.478 0.00 0.00 39.75 3.13
3519 6980 0.534877 TGGATTTGGATCGGCCGATG 60.535 55.000 43.46 7.75 40.66 3.84
3520 6981 0.250295 GGATTTGGATCGGCCGATGA 60.250 55.000 43.46 26.78 40.66 2.92
3521 6982 0.868406 GATTTGGATCGGCCGATGAC 59.132 55.000 43.46 32.93 40.66 3.06
3522 6983 0.535102 ATTTGGATCGGCCGATGACC 60.535 55.000 43.46 35.79 40.66 4.02
3529 6990 4.033894 GGCCGATGACCGATGAAG 57.966 61.111 0.00 0.00 41.76 3.02
3530 6991 2.247437 GGCCGATGACCGATGAAGC 61.247 63.158 0.00 0.00 41.76 3.86
3531 6992 1.521457 GCCGATGACCGATGAAGCA 60.521 57.895 0.00 0.00 41.76 3.91
3532 6993 0.882042 GCCGATGACCGATGAAGCAT 60.882 55.000 0.00 0.00 41.76 3.79
3533 6994 1.586422 CCGATGACCGATGAAGCATT 58.414 50.000 0.00 0.00 41.76 3.56
3534 6995 1.262417 CCGATGACCGATGAAGCATTG 59.738 52.381 0.00 0.00 41.76 2.82
3535 6996 1.333524 CGATGACCGATGAAGCATTGC 60.334 52.381 0.00 0.00 41.76 3.56
3536 6997 1.002033 GATGACCGATGAAGCATTGCC 60.002 52.381 4.70 0.00 0.00 4.52
3537 6998 0.322366 TGACCGATGAAGCATTGCCA 60.322 50.000 4.70 0.00 0.00 4.92
3538 6999 0.810648 GACCGATGAAGCATTGCCAA 59.189 50.000 4.70 0.00 0.00 4.52
3539 7000 1.406539 GACCGATGAAGCATTGCCAAT 59.593 47.619 4.70 0.00 0.00 3.16
3540 7001 1.135527 ACCGATGAAGCATTGCCAATG 59.864 47.619 13.11 13.11 41.85 2.82
3541 7002 1.135527 CCGATGAAGCATTGCCAATGT 59.864 47.619 18.10 0.00 41.01 2.71
3542 7003 2.358582 CCGATGAAGCATTGCCAATGTA 59.641 45.455 18.10 4.20 41.01 2.29
3543 7004 3.005050 CCGATGAAGCATTGCCAATGTAT 59.995 43.478 18.10 7.89 41.01 2.29
3544 7005 3.978855 CGATGAAGCATTGCCAATGTATG 59.021 43.478 18.10 0.00 41.01 2.39
3545 7006 3.167921 TGAAGCATTGCCAATGTATGC 57.832 42.857 18.10 5.98 43.78 3.14
3546 7007 2.121786 GAAGCATTGCCAATGTATGCG 58.878 47.619 18.10 0.00 46.97 4.73
3547 7008 1.105457 AGCATTGCCAATGTATGCGT 58.895 45.000 18.10 0.00 46.97 5.24
3548 7009 1.202203 GCATTGCCAATGTATGCGTG 58.798 50.000 18.10 0.00 41.01 5.34
3549 7010 1.202203 CATTGCCAATGTATGCGTGC 58.798 50.000 9.30 0.00 34.18 5.34
3550 7011 0.816373 ATTGCCAATGTATGCGTGCA 59.184 45.000 0.00 0.00 0.00 4.57
3551 7012 0.170784 TTGCCAATGTATGCGTGCAG 59.829 50.000 2.42 0.00 0.00 4.41
3552 7013 0.676151 TGCCAATGTATGCGTGCAGA 60.676 50.000 2.42 0.00 0.00 4.26
3553 7014 0.664761 GCCAATGTATGCGTGCAGAT 59.335 50.000 2.42 0.00 0.00 2.90
3554 7015 1.872952 GCCAATGTATGCGTGCAGATA 59.127 47.619 2.42 0.00 0.00 1.98
3555 7016 2.485426 GCCAATGTATGCGTGCAGATAT 59.515 45.455 2.42 0.00 0.00 1.63
3556 7017 3.684305 GCCAATGTATGCGTGCAGATATA 59.316 43.478 2.42 0.00 0.00 0.86
3557 7018 4.154015 GCCAATGTATGCGTGCAGATATAA 59.846 41.667 2.42 0.00 0.00 0.98
3558 7019 5.672073 GCCAATGTATGCGTGCAGATATAAG 60.672 44.000 2.42 0.00 0.00 1.73
3559 7020 5.163824 CCAATGTATGCGTGCAGATATAAGG 60.164 44.000 2.42 2.48 0.00 2.69
3560 7021 3.925379 TGTATGCGTGCAGATATAAGGG 58.075 45.455 0.00 0.00 0.00 3.95
3561 7022 3.323691 TGTATGCGTGCAGATATAAGGGT 59.676 43.478 0.00 0.00 0.00 4.34
3562 7023 3.492102 ATGCGTGCAGATATAAGGGTT 57.508 42.857 0.00 0.00 0.00 4.11
3563 7024 3.275617 TGCGTGCAGATATAAGGGTTT 57.724 42.857 0.00 0.00 0.00 3.27
3564 7025 3.616219 TGCGTGCAGATATAAGGGTTTT 58.384 40.909 0.00 0.00 0.00 2.43
3565 7026 4.013728 TGCGTGCAGATATAAGGGTTTTT 58.986 39.130 0.00 0.00 0.00 1.94
3566 7027 4.095782 TGCGTGCAGATATAAGGGTTTTTC 59.904 41.667 0.00 0.00 0.00 2.29
3567 7028 4.497507 GCGTGCAGATATAAGGGTTTTTCC 60.498 45.833 0.00 0.00 0.00 3.13
3568 7029 4.881850 CGTGCAGATATAAGGGTTTTTCCT 59.118 41.667 0.00 0.00 39.17 3.36
3570 7031 6.564328 GTGCAGATATAAGGGTTTTTCCTTG 58.436 40.000 6.41 0.00 45.87 3.61
3571 7032 5.656416 TGCAGATATAAGGGTTTTTCCTTGG 59.344 40.000 6.41 0.00 45.87 3.61
3572 7033 5.891551 GCAGATATAAGGGTTTTTCCTTGGA 59.108 40.000 6.41 0.00 45.87 3.53
3573 7034 6.551227 GCAGATATAAGGGTTTTTCCTTGGAT 59.449 38.462 6.41 0.31 45.87 3.41
3574 7035 7.069950 GCAGATATAAGGGTTTTTCCTTGGATT 59.930 37.037 6.41 0.00 45.87 3.01
3575 7036 8.981659 CAGATATAAGGGTTTTTCCTTGGATTT 58.018 33.333 6.41 0.00 45.87 2.17
3576 7037 8.981659 AGATATAAGGGTTTTTCCTTGGATTTG 58.018 33.333 6.41 0.00 45.87 2.32
3577 7038 8.909423 ATATAAGGGTTTTTCCTTGGATTTGA 57.091 30.769 6.41 0.00 45.87 2.69
3578 7039 5.966853 AAGGGTTTTTCCTTGGATTTGAA 57.033 34.783 0.00 0.00 44.78 2.69
3579 7040 6.514012 AAGGGTTTTTCCTTGGATTTGAAT 57.486 33.333 0.00 0.00 44.78 2.57
3580 7041 6.114187 AGGGTTTTTCCTTGGATTTGAATC 57.886 37.500 0.00 0.00 32.13 2.52
3581 7042 4.929211 GGGTTTTTCCTTGGATTTGAATCG 59.071 41.667 0.00 0.00 34.89 3.34
3582 7043 4.929211 GGTTTTTCCTTGGATTTGAATCGG 59.071 41.667 0.00 0.00 36.27 4.18
4040 7561 2.038007 AGGAGCTGCGGGAAGAGA 59.962 61.111 0.00 0.00 0.00 3.10
4095 7670 4.554036 GTGGGGAGCTGCCGGATC 62.554 72.222 19.04 4.63 37.63 3.36
4096 7671 4.804420 TGGGGAGCTGCCGGATCT 62.804 66.667 19.04 0.00 37.63 2.75
4097 7672 4.247380 GGGGAGCTGCCGGATCTG 62.247 72.222 19.04 0.00 37.63 2.90
4098 7673 3.474570 GGGAGCTGCCGGATCTGT 61.475 66.667 9.14 0.00 37.63 3.41
4099 7674 2.202987 GGAGCTGCCGGATCTGTG 60.203 66.667 5.05 0.00 0.00 3.66
4100 7675 2.894387 GAGCTGCCGGATCTGTGC 60.894 66.667 5.05 4.52 0.00 4.57
4101 7676 4.827087 AGCTGCCGGATCTGTGCG 62.827 66.667 5.05 2.54 39.07 5.34
4107 7682 3.190849 CGGATCTGTGCGGCTGTG 61.191 66.667 0.00 0.00 35.34 3.66
4108 7683 2.821366 GGATCTGTGCGGCTGTGG 60.821 66.667 0.00 0.00 0.00 4.17
4109 7684 2.821366 GATCTGTGCGGCTGTGGG 60.821 66.667 0.00 0.00 0.00 4.61
4110 7685 4.415150 ATCTGTGCGGCTGTGGGG 62.415 66.667 0.00 0.00 0.00 4.96
4381 7958 4.994471 CTGCTGCGTCAGGTGGCA 62.994 66.667 8.57 0.00 37.63 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.670674 GCAAACCGACACCGAGATACA 60.671 52.381 0.00 0.00 38.22 2.29
1 2 0.997196 GCAAACCGACACCGAGATAC 59.003 55.000 0.00 0.00 38.22 2.24
18 19 2.420722 GTCGGGATTGGAAAATAACGCA 59.579 45.455 0.00 0.00 0.00 5.24
20 21 4.688511 TTGTCGGGATTGGAAAATAACG 57.311 40.909 0.00 0.00 0.00 3.18
39 40 8.502161 AAGTTAAAATAGCGTGTAAGCTTTTG 57.498 30.769 3.20 0.00 46.80 2.44
91 93 2.042297 TCCCTGGCATGTTTGGTTATCA 59.958 45.455 0.00 0.00 0.00 2.15
115 121 1.448985 TTTCCACGTATTCTGCAGCC 58.551 50.000 9.47 0.00 0.00 4.85
127 133 1.228033 ACCCCCGAAGTTTTCCACG 60.228 57.895 0.00 0.00 0.00 4.94
128 134 0.466739 ACACCCCCGAAGTTTTCCAC 60.467 55.000 0.00 0.00 0.00 4.02
129 135 0.259356 AACACCCCCGAAGTTTTCCA 59.741 50.000 0.00 0.00 0.00 3.53
131 137 0.031585 GCAACACCCCCGAAGTTTTC 59.968 55.000 0.00 0.00 0.00 2.29
132 138 0.684805 TGCAACACCCCCGAAGTTTT 60.685 50.000 0.00 0.00 0.00 2.43
133 139 0.684805 TTGCAACACCCCCGAAGTTT 60.685 50.000 0.00 0.00 0.00 2.66
134 140 0.469144 ATTGCAACACCCCCGAAGTT 60.469 50.000 0.00 0.00 0.00 2.66
136 142 1.762708 ATATTGCAACACCCCCGAAG 58.237 50.000 0.00 0.00 0.00 3.79
137 143 3.586470 ATATATTGCAACACCCCCGAA 57.414 42.857 0.00 0.00 0.00 4.30
203 210 7.348201 CAGTTTGTCTGTCTGTCTGTTTATTC 58.652 38.462 0.00 0.00 39.17 1.75
299 314 4.003648 AGCACCGGTTCATTAAGAAAGAG 58.996 43.478 2.97 0.00 38.13 2.85
300 315 4.000988 GAGCACCGGTTCATTAAGAAAGA 58.999 43.478 2.97 0.00 38.13 2.52
301 316 3.127030 GGAGCACCGGTTCATTAAGAAAG 59.873 47.826 2.97 0.00 38.13 2.62
330 346 6.094048 TGTGGACAGCTAAAATTGATAAGAGC 59.906 38.462 0.00 0.00 0.00 4.09
334 350 5.703592 ACGTGTGGACAGCTAAAATTGATAA 59.296 36.000 0.00 0.00 0.00 1.75
347 363 0.601046 ATCAGCACACGTGTGGACAG 60.601 55.000 40.73 25.59 45.72 3.51
492 520 1.878522 GGCACCGACATACAGCGAG 60.879 63.158 0.00 0.00 0.00 5.03
498 526 0.737219 ACTACGAGGCACCGACATAC 59.263 55.000 6.32 0.00 0.00 2.39
545 573 2.226912 CTCGTACGGGGAATTGCAAAAA 59.773 45.455 16.52 0.00 0.00 1.94
546 574 1.807742 CTCGTACGGGGAATTGCAAAA 59.192 47.619 16.52 0.00 0.00 2.44
547 575 1.444836 CTCGTACGGGGAATTGCAAA 58.555 50.000 16.52 0.00 0.00 3.68
548 576 0.391927 CCTCGTACGGGGAATTGCAA 60.392 55.000 30.89 0.00 38.23 4.08
549 577 1.219664 CCTCGTACGGGGAATTGCA 59.780 57.895 30.89 0.00 38.23 4.08
550 578 0.392060 AACCTCGTACGGGGAATTGC 60.392 55.000 39.87 0.00 38.23 3.56
551 579 1.648504 GAACCTCGTACGGGGAATTG 58.351 55.000 39.87 14.11 38.23 2.32
552 580 0.538584 GGAACCTCGTACGGGGAATT 59.461 55.000 39.87 24.77 38.23 2.17
553 581 0.325016 AGGAACCTCGTACGGGGAAT 60.325 55.000 39.87 26.89 38.23 3.01
554 582 0.331278 TAGGAACCTCGTACGGGGAA 59.669 55.000 39.87 16.32 38.23 3.97
595 630 0.108424 CTCCCTGGAGCTCGTTGAAG 60.108 60.000 7.83 0.00 35.31 3.02
618 653 1.464997 CTTTGGTCGGTAGCTCTTTGC 59.535 52.381 0.00 0.00 43.29 3.68
655 690 4.933400 GCCGAGGACACTGACTTTAATTAA 59.067 41.667 0.00 0.00 0.00 1.40
656 691 4.020928 TGCCGAGGACACTGACTTTAATTA 60.021 41.667 0.00 0.00 0.00 1.40
657 692 3.244422 TGCCGAGGACACTGACTTTAATT 60.244 43.478 0.00 0.00 0.00 1.40
658 693 2.301870 TGCCGAGGACACTGACTTTAAT 59.698 45.455 0.00 0.00 0.00 1.40
782 856 1.133407 AGAAGAAGAAGCGAGCGGTAG 59.867 52.381 0.00 0.00 0.00 3.18
805 894 2.659897 GACGGCCGAGCTAGCATG 60.660 66.667 35.90 8.43 0.00 4.06
806 895 3.147595 TGACGGCCGAGCTAGCAT 61.148 61.111 35.90 6.14 0.00 3.79
807 896 4.129737 GTGACGGCCGAGCTAGCA 62.130 66.667 35.90 16.05 0.00 3.49
860 961 5.622460 GCTGATGGAGAAGTACGAAGAAGAA 60.622 44.000 0.00 0.00 0.00 2.52
861 962 4.142359 GCTGATGGAGAAGTACGAAGAAGA 60.142 45.833 0.00 0.00 0.00 2.87
862 963 4.109050 GCTGATGGAGAAGTACGAAGAAG 58.891 47.826 0.00 0.00 0.00 2.85
863 964 3.119101 GGCTGATGGAGAAGTACGAAGAA 60.119 47.826 0.00 0.00 0.00 2.52
864 965 2.427453 GGCTGATGGAGAAGTACGAAGA 59.573 50.000 0.00 0.00 0.00 2.87
865 966 2.482142 GGGCTGATGGAGAAGTACGAAG 60.482 54.545 0.00 0.00 0.00 3.79
866 967 1.480954 GGGCTGATGGAGAAGTACGAA 59.519 52.381 0.00 0.00 0.00 3.85
867 968 1.112113 GGGCTGATGGAGAAGTACGA 58.888 55.000 0.00 0.00 0.00 3.43
868 969 0.105039 GGGGCTGATGGAGAAGTACG 59.895 60.000 0.00 0.00 0.00 3.67
869 970 1.134371 GTGGGGCTGATGGAGAAGTAC 60.134 57.143 0.00 0.00 0.00 2.73
870 971 1.204146 GTGGGGCTGATGGAGAAGTA 58.796 55.000 0.00 0.00 0.00 2.24
898 999 3.732212 ACAAACTGGTAAACGGGAGTAC 58.268 45.455 0.00 0.00 46.69 2.73
903 1004 3.307782 CGCTATACAAACTGGTAAACGGG 59.692 47.826 0.00 0.00 0.00 5.28
917 1018 2.971660 TAAAGCACTGCCGCTATACA 57.028 45.000 0.00 0.00 42.89 2.29
919 1020 5.337554 CGTATATAAAGCACTGCCGCTATA 58.662 41.667 0.00 0.00 42.89 1.31
927 1028 9.158364 CATTTTGTAAGCGTATATAAAGCACTG 57.842 33.333 12.29 0.00 0.00 3.66
952 1053 2.921374 GGGACGTGTGCAATGTACA 58.079 52.632 0.00 0.00 28.94 2.90
974 1084 1.483827 CCAGCAGCTAGTGATCAGGAA 59.516 52.381 0.00 0.00 0.00 3.36
1024 1135 5.297547 CAAAGAAGGAACTGTGCAGTAGTA 58.702 41.667 5.18 0.00 41.58 1.82
1025 1136 4.130118 CAAAGAAGGAACTGTGCAGTAGT 58.870 43.478 5.18 0.00 41.58 2.73
1026 1137 3.058639 GCAAAGAAGGAACTGTGCAGTAG 60.059 47.826 5.18 0.00 46.71 2.57
1044 1159 5.469479 GGCAGCAGAGTAATTTTAAGCAAA 58.531 37.500 0.00 0.00 0.00 3.68
1045 1160 4.379394 CGGCAGCAGAGTAATTTTAAGCAA 60.379 41.667 0.00 0.00 0.00 3.91
1073 1188 6.878923 AGAGTAGAAGATCCATCTAGTGATCG 59.121 42.308 14.93 0.00 35.76 3.69
1089 1204 3.435327 AGCGAGCGATCATAGAGTAGAAG 59.565 47.826 0.00 0.00 0.00 2.85
1112 1231 5.689514 CCTACAGAGTTTTCATAGAGCGATG 59.310 44.000 0.00 0.00 0.00 3.84
1128 1247 2.839486 TCCTGTGCAAACCTACAGAG 57.161 50.000 5.99 0.00 45.46 3.35
1149 1533 1.455959 TAGGCGGGAGAGCTTCCTC 60.456 63.158 12.71 4.70 45.98 3.71
1150 1534 1.758906 GTAGGCGGGAGAGCTTCCT 60.759 63.158 12.71 4.92 45.98 3.36
1179 1563 2.856000 AGGTGGCTGCTGGGAAGT 60.856 61.111 0.00 0.00 0.00 3.01
1235 1725 7.252965 AGTTTCAGAGAAGAAAGCAAAGTAC 57.747 36.000 0.00 0.00 38.11 2.73
1253 1743 9.677567 GCACATATTTGAGTAAAGAAAGTTTCA 57.322 29.630 17.65 0.00 0.00 2.69
1261 1751 5.673568 GCGCTTGCACATATTTGAGTAAAGA 60.674 40.000 0.00 0.00 38.92 2.52
1266 1756 1.811965 TGCGCTTGCACATATTTGAGT 59.188 42.857 9.73 0.00 45.56 3.41
1278 1768 4.565704 GATCTCGCGTGCGCTTGC 62.566 66.667 9.73 11.94 39.59 4.01
1279 1769 2.340246 GAAGATCTCGCGTGCGCTTG 62.340 60.000 9.73 1.22 39.59 4.01
1280 1770 2.125912 AAGATCTCGCGTGCGCTT 60.126 55.556 9.73 7.72 39.59 4.68
1282 1772 2.233654 ATGAAGATCTCGCGTGCGC 61.234 57.895 9.79 0.00 39.59 6.09
1284 1774 1.002366 AACATGAAGATCTCGCGTGC 58.998 50.000 5.77 0.00 0.00 5.34
1285 1775 2.262211 TGAACATGAAGATCTCGCGTG 58.738 47.619 5.77 3.13 0.00 5.34
1287 1777 2.862536 ACATGAACATGAAGATCTCGCG 59.137 45.455 19.56 0.00 41.20 5.87
1292 1820 8.456471 TCAGAAATGAACATGAACATGAAGATC 58.544 33.333 19.56 12.27 41.20 2.75
1297 1825 8.564509 TGTATCAGAAATGAACATGAACATGA 57.435 30.769 19.56 0.54 41.20 3.07
1315 1843 3.550950 ACGCAGAGATCGATGTATCAG 57.449 47.619 0.54 0.00 0.00 2.90
1316 1844 5.629079 AATACGCAGAGATCGATGTATCA 57.371 39.130 0.54 0.00 0.00 2.15
1318 1846 6.151312 AGGTAAATACGCAGAGATCGATGTAT 59.849 38.462 0.54 0.00 0.00 2.29
1319 1847 5.472478 AGGTAAATACGCAGAGATCGATGTA 59.528 40.000 0.54 0.00 0.00 2.29
1320 1848 4.278669 AGGTAAATACGCAGAGATCGATGT 59.721 41.667 0.54 0.00 0.00 3.06
1321 1849 4.799678 AGGTAAATACGCAGAGATCGATG 58.200 43.478 0.54 0.00 0.00 3.84
1322 1850 5.455056 AAGGTAAATACGCAGAGATCGAT 57.545 39.130 0.00 0.00 0.00 3.59
1323 1851 4.913335 AAGGTAAATACGCAGAGATCGA 57.087 40.909 0.00 0.00 0.00 3.59
1324 1852 4.318121 GCAAAGGTAAATACGCAGAGATCG 60.318 45.833 0.00 0.00 0.00 3.69
1325 1853 4.811557 AGCAAAGGTAAATACGCAGAGATC 59.188 41.667 0.00 0.00 0.00 2.75
1326 1854 4.770795 AGCAAAGGTAAATACGCAGAGAT 58.229 39.130 0.00 0.00 0.00 2.75
1327 1855 4.181578 GAGCAAAGGTAAATACGCAGAGA 58.818 43.478 0.00 0.00 0.00 3.10
1328 1856 3.932710 TGAGCAAAGGTAAATACGCAGAG 59.067 43.478 0.00 0.00 0.00 3.35
1329 1857 3.682858 GTGAGCAAAGGTAAATACGCAGA 59.317 43.478 0.00 0.00 0.00 4.26
1330 1858 3.483574 CGTGAGCAAAGGTAAATACGCAG 60.484 47.826 0.00 0.00 0.00 5.18
1331 1859 2.413796 CGTGAGCAAAGGTAAATACGCA 59.586 45.455 0.00 0.00 0.00 5.24
1332 1860 2.414138 ACGTGAGCAAAGGTAAATACGC 59.586 45.455 0.00 0.00 34.01 4.42
1333 1861 3.430895 ACACGTGAGCAAAGGTAAATACG 59.569 43.478 25.01 0.00 36.48 3.06
1334 1862 4.449743 TCACACGTGAGCAAAGGTAAATAC 59.550 41.667 25.01 0.00 34.14 1.89
1335 1863 4.449743 GTCACACGTGAGCAAAGGTAAATA 59.550 41.667 25.01 0.00 40.75 1.40
1336 1864 3.250040 GTCACACGTGAGCAAAGGTAAAT 59.750 43.478 25.01 0.00 40.75 1.40
1337 1865 2.610374 GTCACACGTGAGCAAAGGTAAA 59.390 45.455 25.01 0.00 40.75 2.01
1338 1866 2.206750 GTCACACGTGAGCAAAGGTAA 58.793 47.619 25.01 0.00 40.75 2.85
1339 1867 1.137282 TGTCACACGTGAGCAAAGGTA 59.863 47.619 25.01 0.00 40.75 3.08
1340 1868 0.107897 TGTCACACGTGAGCAAAGGT 60.108 50.000 25.01 0.00 40.75 3.50
1341 1869 1.003545 CTTGTCACACGTGAGCAAAGG 60.004 52.381 25.01 8.40 40.75 3.11
1344 1872 1.396648 CAACTTGTCACACGTGAGCAA 59.603 47.619 25.01 19.70 40.75 3.91
1351 1879 3.135225 TGTAATCCCAACTTGTCACACG 58.865 45.455 0.00 0.00 0.00 4.49
1358 1886 5.067273 TGTACAACCTGTAATCCCAACTTG 58.933 41.667 0.00 0.00 34.21 3.16
1362 1890 4.594970 CCATGTACAACCTGTAATCCCAA 58.405 43.478 0.00 0.00 34.21 4.12
1492 2024 5.123936 AGTGAACCTAACCAAAGAAGACAC 58.876 41.667 0.00 0.00 0.00 3.67
1618 2150 3.694072 TGATTCTTGGGGTAAATCTTGCG 59.306 43.478 0.00 0.00 31.99 4.85
1666 3830 9.475620 TCTTAACACTCATCTAAATAGGAGACA 57.524 33.333 0.00 0.00 0.00 3.41
1823 4016 7.759433 GCTATTGCAGCCTTTAAAGACAAAATA 59.241 33.333 16.98 11.60 45.23 1.40
1903 4096 4.672587 TTTCAGGATCCTAAGGTCATCG 57.327 45.455 15.67 0.00 0.00 3.84
2083 4277 0.454600 CCAGCAATGCATCACAGGTC 59.545 55.000 8.35 0.00 0.00 3.85
2093 4287 1.202268 GCTTCTGATGACCAGCAATGC 60.202 52.381 0.00 0.00 42.62 3.56
2106 4300 1.051008 TTGTCCAGAGCAGCTTCTGA 58.949 50.000 15.63 4.50 45.95 3.27
2107 4301 1.888215 TTTGTCCAGAGCAGCTTCTG 58.112 50.000 8.25 8.25 43.35 3.02
2159 4353 2.755952 ACTGGCCAAGAAAGAAAGGT 57.244 45.000 7.01 0.00 0.00 3.50
2250 5653 1.956477 CCACCTGTTTCCAGTTCCAAG 59.044 52.381 0.00 0.00 36.95 3.61
2315 5718 5.046159 TGGGATCGTAGTTCTTTATGTTGGT 60.046 40.000 0.00 0.00 0.00 3.67
2390 5793 5.401531 AAACGCTACACTCCTGAAAGATA 57.598 39.130 0.00 0.00 34.07 1.98
2473 5876 9.887406 CCTATGTAAACGTGTACTTTTTCATTT 57.113 29.630 16.66 0.00 31.37 2.32
2475 5878 7.879160 TCCCTATGTAAACGTGTACTTTTTCAT 59.121 33.333 16.66 5.31 32.75 2.57
2476 5879 7.215789 TCCCTATGTAAACGTGTACTTTTTCA 58.784 34.615 16.66 0.00 0.00 2.69
2477 5880 7.656707 TCCCTATGTAAACGTGTACTTTTTC 57.343 36.000 16.66 0.00 0.00 2.29
2844 6262 1.003959 TGCTTGGTCTGCGCATACA 60.004 52.632 24.86 15.18 0.00 2.29
2975 6393 1.103803 TGTATGTCTGGACGGAGCTC 58.896 55.000 4.71 4.71 0.00 4.09
3124 6546 9.260002 CAGTCTAATTTAAACTGCCAAAACATT 57.740 29.630 0.00 0.00 34.55 2.71
3146 6568 4.483476 AATGTAAGACGTTTTGGCAGTC 57.517 40.909 0.83 0.00 35.30 3.51
3229 6654 9.953565 AGCATAGTGTACTTTAATTGGTTAAGA 57.046 29.630 0.00 0.00 31.81 2.10
3291 6716 7.445945 AGTCCTATGATATGGCTAAAACACTC 58.554 38.462 0.00 0.00 0.00 3.51
3341 6770 3.502211 CGGGGGAAAATCCTTTATGATCG 59.498 47.826 0.00 0.00 36.57 3.69
3345 6774 4.729868 AGATCGGGGGAAAATCCTTTATG 58.270 43.478 0.00 0.00 36.57 1.90
3350 6780 1.893315 TGAGATCGGGGGAAAATCCT 58.107 50.000 0.00 0.00 36.57 3.24
3357 6787 2.787339 TCCTTAATGAGATCGGGGGA 57.213 50.000 0.00 0.00 0.00 4.81
3358 6788 2.706190 ACTTCCTTAATGAGATCGGGGG 59.294 50.000 0.00 0.00 0.00 5.40
3397 6827 2.235402 GTCCTGGATTACTTGGACGGAA 59.765 50.000 0.00 0.00 39.39 4.30
3414 6844 9.240734 CTGTATAAGTAATATTACCTCCGTCCT 57.759 37.037 19.74 0.00 34.19 3.85
3418 6848 9.240734 AGTCCTGTATAAGTAATATTACCTCCG 57.759 37.037 19.74 4.93 34.19 4.63
3454 6884 3.715628 AAAAACAGCAGATGTCACCAC 57.284 42.857 0.00 0.00 43.00 4.16
3497 6958 1.447317 CGGCCGATCCAAATCCAAGG 61.447 60.000 24.07 0.00 34.01 3.61
3519 6980 0.810648 TTGGCAATGCTTCATCGGTC 59.189 50.000 4.82 0.00 0.00 4.79
3520 6981 1.135527 CATTGGCAATGCTTCATCGGT 59.864 47.619 25.69 0.00 31.20 4.69
3521 6982 1.135527 ACATTGGCAATGCTTCATCGG 59.864 47.619 33.90 12.55 42.69 4.18
3522 6983 2.572191 ACATTGGCAATGCTTCATCG 57.428 45.000 33.90 13.22 42.69 3.84
3523 6984 3.739300 GCATACATTGGCAATGCTTCATC 59.261 43.478 33.90 17.57 42.69 2.92
3524 6985 3.724374 GCATACATTGGCAATGCTTCAT 58.276 40.909 33.90 20.90 42.69 2.57
3525 6986 2.479901 CGCATACATTGGCAATGCTTCA 60.480 45.455 33.90 19.77 43.01 3.02
3526 6987 2.121786 CGCATACATTGGCAATGCTTC 58.878 47.619 33.90 20.99 43.01 3.86
3527 6988 1.477700 ACGCATACATTGGCAATGCTT 59.522 42.857 33.90 21.41 43.01 3.91
3528 6989 1.105457 ACGCATACATTGGCAATGCT 58.895 45.000 33.90 24.01 43.01 3.79
3529 6990 1.202203 CACGCATACATTGGCAATGC 58.798 50.000 33.90 23.29 42.69 3.56
3530 6991 1.202203 GCACGCATACATTGGCAATG 58.798 50.000 32.73 32.73 44.48 2.82
3531 6992 0.816373 TGCACGCATACATTGGCAAT 59.184 45.000 6.96 6.96 0.00 3.56
3532 6993 0.170784 CTGCACGCATACATTGGCAA 59.829 50.000 0.68 0.68 0.00 4.52
3533 6994 0.676151 TCTGCACGCATACATTGGCA 60.676 50.000 0.00 0.00 0.00 4.92
3534 6995 0.664761 ATCTGCACGCATACATTGGC 59.335 50.000 0.00 0.00 0.00 4.52
3535 6996 5.163824 CCTTATATCTGCACGCATACATTGG 60.164 44.000 0.00 0.00 0.00 3.16
3536 6997 5.163824 CCCTTATATCTGCACGCATACATTG 60.164 44.000 0.00 0.00 0.00 2.82
3537 6998 4.937620 CCCTTATATCTGCACGCATACATT 59.062 41.667 0.00 0.00 0.00 2.71
3538 6999 4.020218 ACCCTTATATCTGCACGCATACAT 60.020 41.667 0.00 0.00 0.00 2.29
3539 7000 3.323691 ACCCTTATATCTGCACGCATACA 59.676 43.478 0.00 0.00 0.00 2.29
3540 7001 3.926616 ACCCTTATATCTGCACGCATAC 58.073 45.455 0.00 0.00 0.00 2.39
3541 7002 4.617253 AACCCTTATATCTGCACGCATA 57.383 40.909 0.00 0.00 0.00 3.14
3542 7003 3.492102 AACCCTTATATCTGCACGCAT 57.508 42.857 0.00 0.00 0.00 4.73
3543 7004 3.275617 AAACCCTTATATCTGCACGCA 57.724 42.857 0.00 0.00 0.00 5.24
3544 7005 4.497507 GGAAAAACCCTTATATCTGCACGC 60.498 45.833 0.00 0.00 0.00 5.34
3545 7006 4.881850 AGGAAAAACCCTTATATCTGCACG 59.118 41.667 0.00 0.00 40.05 5.34
3546 7007 6.405842 CCAAGGAAAAACCCTTATATCTGCAC 60.406 42.308 0.00 0.00 44.30 4.57
3547 7008 5.656416 CCAAGGAAAAACCCTTATATCTGCA 59.344 40.000 0.00 0.00 44.30 4.41
3548 7009 5.891551 TCCAAGGAAAAACCCTTATATCTGC 59.108 40.000 0.00 0.00 44.30 4.26
3549 7010 8.539117 AATCCAAGGAAAAACCCTTATATCTG 57.461 34.615 0.00 0.00 44.30 2.90
3550 7011 8.981659 CAAATCCAAGGAAAAACCCTTATATCT 58.018 33.333 0.00 0.00 44.30 1.98
3551 7012 8.977412 TCAAATCCAAGGAAAAACCCTTATATC 58.023 33.333 0.00 0.00 44.30 1.63
3552 7013 8.909423 TCAAATCCAAGGAAAAACCCTTATAT 57.091 30.769 0.00 0.00 44.30 0.86
3553 7014 8.728596 TTCAAATCCAAGGAAAAACCCTTATA 57.271 30.769 0.00 0.00 44.30 0.98
3554 7015 7.625498 TTCAAATCCAAGGAAAAACCCTTAT 57.375 32.000 0.00 0.00 44.30 1.73
3555 7016 7.524698 CGATTCAAATCCAAGGAAAAACCCTTA 60.525 37.037 0.00 0.00 44.30 2.69
3556 7017 5.966853 TTCAAATCCAAGGAAAAACCCTT 57.033 34.783 0.00 0.00 46.91 3.95
3557 7018 5.279456 CGATTCAAATCCAAGGAAAAACCCT 60.279 40.000 0.00 0.00 33.89 4.34
3558 7019 4.929211 CGATTCAAATCCAAGGAAAAACCC 59.071 41.667 0.00 0.00 33.89 4.11
3559 7020 4.929211 CCGATTCAAATCCAAGGAAAAACC 59.071 41.667 0.00 0.00 33.72 3.27
3560 7021 4.388773 GCCGATTCAAATCCAAGGAAAAAC 59.611 41.667 0.00 0.00 31.68 2.43
3561 7022 4.562552 GGCCGATTCAAATCCAAGGAAAAA 60.563 41.667 0.00 0.00 31.68 1.94
3562 7023 3.056179 GGCCGATTCAAATCCAAGGAAAA 60.056 43.478 0.00 0.00 31.68 2.29
3563 7024 2.495669 GGCCGATTCAAATCCAAGGAAA 59.504 45.455 0.00 0.00 31.68 3.13
3564 7025 2.099405 GGCCGATTCAAATCCAAGGAA 58.901 47.619 0.00 0.00 31.68 3.36
3565 7026 1.762708 GGCCGATTCAAATCCAAGGA 58.237 50.000 0.00 0.00 31.68 3.36
3566 7027 0.381801 CGGCCGATTCAAATCCAAGG 59.618 55.000 24.07 0.00 31.68 3.61
3567 7028 1.378531 TCGGCCGATTCAAATCCAAG 58.621 50.000 27.28 0.00 31.68 3.61
3568 7029 1.675483 CATCGGCCGATTCAAATCCAA 59.325 47.619 37.36 7.68 31.62 3.53
3569 7030 1.134250 TCATCGGCCGATTCAAATCCA 60.134 47.619 37.36 8.29 31.62 3.41
3570 7031 1.264288 GTCATCGGCCGATTCAAATCC 59.736 52.381 37.36 15.72 31.62 3.01
3571 7032 2.032549 CAGTCATCGGCCGATTCAAATC 60.033 50.000 37.36 21.46 31.62 2.17
3572 7033 1.942657 CAGTCATCGGCCGATTCAAAT 59.057 47.619 37.36 21.54 31.62 2.32
3573 7034 1.066502 TCAGTCATCGGCCGATTCAAA 60.067 47.619 37.36 19.97 31.62 2.69
3574 7035 0.534873 TCAGTCATCGGCCGATTCAA 59.465 50.000 37.36 22.51 31.62 2.69
3575 7036 0.752658 ATCAGTCATCGGCCGATTCA 59.247 50.000 37.36 23.90 31.62 2.57
3576 7037 1.143305 CATCAGTCATCGGCCGATTC 58.857 55.000 37.36 29.64 31.62 2.52
3577 7038 0.752658 TCATCAGTCATCGGCCGATT 59.247 50.000 37.36 21.46 31.62 3.34
3578 7039 0.752658 TTCATCAGTCATCGGCCGAT 59.247 50.000 34.60 34.60 34.81 4.18
3579 7040 0.103026 CTTCATCAGTCATCGGCCGA 59.897 55.000 33.12 33.12 0.00 5.54
3580 7041 1.493950 GCTTCATCAGTCATCGGCCG 61.494 60.000 22.12 22.12 0.00 6.13
3581 7042 0.462581 TGCTTCATCAGTCATCGGCC 60.463 55.000 0.00 0.00 0.00 6.13
3582 7043 1.590932 ATGCTTCATCAGTCATCGGC 58.409 50.000 0.00 0.00 0.00 5.54
3644 7105 6.470278 AGGGAGTAGTTTTATTTACTGCGTT 58.530 36.000 0.00 0.00 38.61 4.84
3645 7106 6.046290 AGGGAGTAGTTTTATTTACTGCGT 57.954 37.500 0.00 0.00 38.61 5.24
4040 7561 1.071471 CTCCTCACCGCCACAGTTT 59.929 57.895 0.00 0.00 0.00 2.66
4089 7664 4.457496 ACAGCCGCACAGATCCGG 62.457 66.667 0.00 0.00 46.94 5.14
4090 7665 3.190849 CACAGCCGCACAGATCCG 61.191 66.667 0.00 0.00 0.00 4.18
4091 7666 2.821366 CCACAGCCGCACAGATCC 60.821 66.667 0.00 0.00 0.00 3.36
4092 7667 2.821366 CCCACAGCCGCACAGATC 60.821 66.667 0.00 0.00 0.00 2.75
4093 7668 4.415150 CCCCACAGCCGCACAGAT 62.415 66.667 0.00 0.00 0.00 2.90
4097 7672 4.643387 AACTCCCCACAGCCGCAC 62.643 66.667 0.00 0.00 0.00 5.34
4098 7673 4.641645 CAACTCCCCACAGCCGCA 62.642 66.667 0.00 0.00 0.00 5.69
4100 7675 4.335647 AGCAACTCCCCACAGCCG 62.336 66.667 0.00 0.00 0.00 5.52
4101 7676 2.674380 CAGCAACTCCCCACAGCC 60.674 66.667 0.00 0.00 0.00 4.85
4102 7677 3.368571 GCAGCAACTCCCCACAGC 61.369 66.667 0.00 0.00 0.00 4.40
4103 7678 1.303888 ATGCAGCAACTCCCCACAG 60.304 57.895 0.00 0.00 0.00 3.66
4104 7679 1.303561 GATGCAGCAACTCCCCACA 60.304 57.895 0.00 0.00 0.00 4.17
4105 7680 1.001641 AGATGCAGCAACTCCCCAC 60.002 57.895 4.07 0.00 0.00 4.61
4106 7681 1.001764 CAGATGCAGCAACTCCCCA 60.002 57.895 4.07 0.00 0.00 4.96
4107 7682 1.001641 ACAGATGCAGCAACTCCCC 60.002 57.895 4.07 0.00 0.00 4.81
4108 7683 2.177950 CACAGATGCAGCAACTCCC 58.822 57.895 4.07 0.00 0.00 4.30
4381 7958 0.257039 GCCACCATGTCCATCCTCTT 59.743 55.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.