Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005070.1 Hibiscus syriacus cultivar Beakdansim tig00011381_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67839
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2700 original size:12 final size:12
Alignment explanation
Indices: 2680--2750 Score: 79
Period size: 12 Copynumber: 5.9 Consensus size: 12
2670 ACAAAGATAT
* *
2680 CAGAGATCATAA
1 CAGAAATCAGAA
*
2692 CAGAAATCAGAG
1 CAGAAATCAGAA
*
2704 CAGAAATCAAAA
1 CAGAAATCAGAA
*
2716 CAGAATTCAGAA
1 CAGAAATCAGAA
* *
2728 CATAAATCATAA
1 CAGAAATCAGAA
2740 CAGAAATCAGA
1 CAGAAATCAGA
2751 TAAAATATTC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:2712 original size:24 final size:24
Alignment explanation
Indices: 2680--2750 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
2670 ACAAAGATAT
* *
2680 CAGAGATCATAACAGAAATCAGAG
1 CAGAAATCATAACAGAAATCAGAA
* *
2704 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCATAACAGAAATCAGAA
*
2728 CATAAATCATAACAGAAATCAGA
1 CAGAAATCATAACAGAAATCAGA
2751 TAAAATATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (24 bp):
CAGAAATCATAACAGAAATCAGAA
Found at i:4159 original size:17 final size:17
Alignment explanation
Indices: 4138--4183 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
4128 AGTCAATGCC
*
4138 AGTCAACGGTCAGTTCA
1 AGTCAACGGTCAGTGCA
*
4155 GGTCAACGGTCAGTGCA
1 AGTCAACGGTCAGTGCA
4172 AGTCAACGGTCA
1 AGTCAACGGTCA
4184 ATGGCTCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (17 bp):
AGTCAACGGTCAGTGCA
Found at i:15720 original size:12 final size:12
Alignment explanation
Indices: 15703--15809 Score: 90
Period size: 12 Copynumber: 8.9 Consensus size: 12
15693 ACATAGATAT
15703 CAGAAATCAGAA
1 CAGAAATCAGAA
*
15715 CAGAAATCAGAG
1 CAGAAATCAGAA
* *
15727 CATAAATCAGAG
1 CAGAAATCAGAA
* *
15739 CATAAATCATAA
1 CAGAAATCAGAA
*
15751 CAGAATTCA-AA
1 CAGAAATCAGAA
*
15762 GCAGAAAGCAGAA
1 -CAGAAATCAGAA
* * * *
15775 AAGAACTTAGAG
1 CAGAAATCAGAA
15787 CAGAAATCAGAA
1 CAGAAATCAGAA
*
15799 TAGAAATCAGA
1 CAGAAATCAGA
15810 TAAAATATTC
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
11 2 0.03
12 71 0.95
13 2 0.03
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:17196 original size:13 final size:13
Alignment explanation
Indices: 17178--17204 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17168 TTAACTTTTT
17178 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
17191 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
17204 G
1 G
17205 CCGATCAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:18414 original size:54 final size:54
Alignment explanation
Indices: 18224--18418 Score: 309
Period size: 55 Copynumber: 3.6 Consensus size: 54
18214 TGCAGAAAGT
* *
18224 TAAGAAATTCATACTATGTGTATGAATTTTCGTATGGGCACTTTGTGTGCAAACC
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAA-C
*
18279 TAAGAAATTCATACTAAGTGTATGAATTTCCATATGGGCACTTTGTGTGCAATAC
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAA-AC
* * *
18334 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATATGTGCTAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAC
*
18388 TAAGAAATCCATACTAAGTGTATGAATTTCC
1 TAAGAAATTCATACTAAGTGTATGAATTTCC
18419 ATAGGGGAAA
Statistics
Matches: 131, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
54 32 0.24
55 98 0.75
56 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (54 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAC
Found at i:18715 original size:68 final size:68
Alignment explanation
Indices: 18636--19179 Score: 721
Period size: 68 Copynumber: 8.0 Consensus size: 68
18626 AAGATTAATA
* * *
18636 GCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAATGGCAAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18701 GAG
66 GAG
* * * *
18704 GCCTAACTGTGCATTTGACATATATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18769 GAG
66 GAG
* * *
18772 GCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTATGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
18837 GAA
66 GAG
** * * * *
18840 GCCTATTTGTGCATTTGAGATAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGACTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18905 GAG
66 GAG
* * * *
18908 GCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCGAGTTAGATGAAAAGCTAAATGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18973 GAG
66 GAG
* * * * * *
18976 GCCCAATTGTGCATTAGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTTCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19041 GAG
66 GAG
* * *
19044 GCCTAACTGTTCATTTGACAGAAAGGTTTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
19109 AAG
66 GAG
* * * * * * * *
19112 GCCTAGCAGTGCATTTGGA-AGAAAGGTGTAAATCATGCCAATTAGATGAAAAGTTAAATGCCTT
1 GCCTAACTGTGCATTT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
19176 TGAG
65 TGAG
19180 TAAAACACTA
Statistics
Matches: 413, Mismatches: 62, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
68 411 1.00
69 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:18998 original size:204 final size:204
Alignment explanation
Indices: 18635--19179 Score: 795
Period size: 204 Copynumber: 2.7 Consensus size: 204
18625 AAAGATTAAT
* *
18635 AGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAATGGCAAAGTGCCTT
1 AGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
* * * * *
18700 TGAGGCCTAACTGTGCATTTGACATATATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGT
66 TGAGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAAGCTAAATGC
* * *
18765 CTTTGAGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTATG
131 CTTTGAGGCCCAACTGTGCATTAGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAG
18830 TGCCTTTGA
196 TGCCTTTGA
** * * *
18839 AGCCTATTTGTGCATTTGAGATAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGACTT
1 AGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
*
18904 TGAGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCGAGTTAGATGAAAAGCTAAATGC
66 TGAGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAAGCTAAATGC
*
18969 CTTTGAGGCCCAATTGTGCATTAGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAG
131 CTTTGAGGCCCAACTGTGCATTAGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAG
*
19034 TTCCTTTGA
196 TGCCTTTGA
* * * * *
19043 GGCCTAACTGTTCATTTGACAGAAAGGTTTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTT
1 AGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
* * * * * * * *
19108 TAAGGCCTAGCAGTGCATTTGGA-AGAAAGGTGTAAATCATGCCAATTAGATGAAAAGTTAAATG
66 TGAGGCCTAACTGTGCATTT-GACATAAAGGTGTCAATTATGCCAGTTAGATGAAAAGCTAAATG
19172 CCTTTGAG
130 CCTTTGAG
19180 TAAAACACTA
Statistics
Matches: 303, Mismatches: 37, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
204 301 0.99
205 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (204 bp):
AGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGAGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAAGCTAAATGC
CTTTGAGGCCCAACTGTGCATTAGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAG
TGCCTTTGA
Found at i:19275 original size:46 final size:45
Alignment explanation
Indices: 19204--19344 Score: 183
Period size: 46 Copynumber: 3.1 Consensus size: 45
19194 TATAACAATG
* * *
19204 CATAATATCGTATAAAAGAGCATGAAAGGATGCCATAAAGGAAATA
1 CATAATAGCGTAT-AAAGGGCATGAAAGGATGCCATAAATGAAATA
* * * *
19250 TATAATAGCGTAGAAAGGGGCATGAAAGAATGCCATAAATGAAATG
1 CATAATAGCGTATAAA-GGGCATGAAAGGATGCCATAAATGAAATA
* *
19296 CATAATAGCGTATAAAAGGCATGAAAGGATGCCATAAATGAAATG
1 CATAATAGCGTATAAAGGGCATGAAAGGATGCCATAAATGAAATA
19341 CATA
1 CATA
19345 GGGGTGCATT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
45 34 0.41
46 49 0.59
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.20
Consensus pattern (45 bp):
CATAATAGCGTATAAAGGGCATGAAAGGATGCCATAAATGAAATA
Found at i:19332 original size:45 final size:45
Alignment explanation
Indices: 19200--19389 Score: 209
Period size: 45 Copynumber: 4.2 Consensus size: 45
19190 GATGTATAAC
* *
19200 AATGCATAATATCGTATAAAAGAGCATGAAAGGATGCCATAAAGGA
1 AATGCATAATAGCGTATAAAAG-GCATGAAAGGATGCCATAAATGA
** * * *
19246 AATATATAATAGCGTAGAAAGGGGCATGAAAGAATGCCATAAATGA
1 AATGCATAATAGCGTATAAA-AGGCATGAAAGGATGCCATAAATGA
19292 AATGCATAATAGCGTATAAAAGGCATGAAAGGATGCCATAAATGA
1 AATGCATAATAGCGTATAAAAGGCATGAAAGGATGCCATAAATGA
*** * * * ** *
19337 AATGCATAGGGGTGCATTATCGGCATGAAAGGATGCCATAATTGA
1 AATGCATAATAGCGTATAAAAGGCATGAAAGGATGCCATAAATGA
*
19382 GATGCATA
1 AATGCATA
19390 TGGTTCATTA
Statistics
Matches: 121, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
45 66 0.55
46 54 0.45
47 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (45 bp):
AATGCATAATAGCGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:23106 original size:293 final size:294
Alignment explanation
Indices: 22529--23748 Score: 1075
Period size: 293 Copynumber: 4.1 Consensus size: 294
22519 TGGTTCAAGT
* **
22529 GGAAAAATAATCACTTTGAACCAATTGGTTTTGTCTAACGTTATACTTTAGGTTGAAACCTTGAA
1 GGAAAAGTAATCACTTTGAACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTTGAA
* * * * * *
22594 TGTTCAGGCATAGCAAACCAAATGGAAACCCATAACGATTTATGATTTTTTGTCACAATATGTTG
66 TGTACAGGCATAGTAAACCAAATTGAAACCCATAACGACTTATGA-TGTTT-TCACAACATGTTG
* ** * * *
22659 GTAACAAACC-TTATAATTGTAACATGAGTTGGAATGCACCGAGTTTGAAGATTTATCCTGACGA
129 GTAACAAACCTTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACGA
* * *
22723 GTTCTAAAACTTAGTTAATGAGTTTTGATACTCTAAACCTAAATTGTTACCAGGAACAACCTAAA
194 GTTCTAAAACTTAGTCAATGAGTTTCGATACTCGAAACCTAAATTGTTACCAGGAACAACCTAAA
* *
22788 TTGTATACGTTTAAGTCACATTTTAGTTTGAAAACT-
259 TTGTAAACGTTTAAGTCACATTTTAGGTTGAAAA-TA
* *
22824 GGAAAA-TCA-CACTTTGAACCAATTTGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTTGAA
1 GGAAAAGTAATCACTTTGAACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTTGAA
** * *
22887 TGTACTTGCATAGTAAACCAAATTGAAGCCCATAACGACTTATGATGCTTTCACAACATGTTGGT
66 TGTACAGGCATAGTAAACCAAATTGAAACCCATAACGACTTATGATGTTTTCACAACATGTTGGT
* * *
22952 AACAAACCTTTATAATTTTAACATGAGTTGGAATGCGCTAAGTTCAAAAATTTAACCCGACGAGT
131 AACAAACCTTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACGAGT
*
23017 TCTAAAACTTAGTCAATGAGTTTCGATACT-GAGAACCTAAATTGTTACGAGGAACAACCTAAAT
196 TCTAAAACTTAGTCAATGAGTTTCGATACTCGA-AACCTAAATTGTTACCAGGAACAACCTAAAT
* * * *
23081 TATTAAACGTTTAGGTTATATTTTAGGTTGAAAATA
260 T-GTAAACGTTTAAGTCACATTTTAGGTTGAAAATA
* **
23117 GGAAAAGTAATCAC-TTGAAACCTATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTCAA
1 GGAAAAGTAATCACTTTG-AACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTTGA
* * * * *
23181 ATGTACAGGAATAGTAAACAAAATTGAAACTCATAGCGACCTATGATGTTTTCACAACATGTCAT
65 ATGTACAGGCATAGTAAACCAAATTGAAACCCATAACGACTTATGATGTTTTCACAACATG---T
** * * * * ** * * ** *
23246 TATTAACAAACTTTTGTAATTGTAACATGAGTTGGAATGTATCGAA-TTTGAAGATTTATCTTGT
127 TGGTAACAAACCTTTATAATTGTAACATGAGTTGGAATGCA-CCAAGTTCAAAAATTTAACCCGA
* * * * * * **
23310 CGCA-TTTTGAAACTTAGTCATTGAGTTTCAATACT-GAGAACCTTAAGTGTTACCACTAACAAC
191 CG-AGTTCTAAAACTTAGTCAATGAGTTTCGATACTCGA-AACCTAAATTGTTACCAGGAACAAC
* * * *
23373 CTAAAATGCGACGATGTTATAGGTTTACGTCACATTTTAGGTT-AAAAGCA
254 CT-AAAT-------TG-TAAACGTTTAAGTCACATTTTAGGTTGAAAA-TA
* * ** * * *** * * *
23423 GAAAAAGTAATTACTTCAAAGCAATAGGTTTTGCCCAACATTATACTTCATGTTGAAACCTTGAA
1 GGAAAAGTAATCACTTTGAACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTTGAA
* * * * * * * *
23488 AG-ATCAGACATAGTAAATCAAATTGAAACCCATAAAGAAC-TATGACGTTTGTAACAATATCTT
66 TGTA-CAGGCATAGTAAACCAAATTGAAACCCATAACG-ACTTATGATGTTT-TCACAACATGTT
* * ** * *
23551 GGTAACAGACCTTTATAATTGTAACATGAGTTGGAATGCACCGAGTTTGAAGATTTATCCCGACG
128 GGTAACAAACCTTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACG
* * * * ** * **
23616 AGTT-TCGAAATTTAATCAATGAGTTTTGATACTAAAAACCTCAAA-TGTTTCCAATAACAACCT
193 AGTTCT-AAAACTTAGTCAATGAGTTTCGATACTCGAAACCT-AAATTGTTACCAGGAACAACCT
* * * ** *
23679 AAGTTGTTATAGGTTTTGGTCACATCTTAGGTTGAAAACT-
256 AAATTG-TAAACGTTTAAGTCACATTTTAGGTTGAAAA-TA
* * *
23719 GGAAAAATTATCACTTTGAACTAATTGGTT
1 GGAAAAGTAATCACTTTGAACCAATTGGTT
23749 ATTTTTAACG
Statistics
Matches: 753, Mismatches: 140, Indels: 63
0.79 0.15 0.07
Matches are distributed among these distances:
291 23 0.03
292 110 0.15
293 121 0.16
294 7 0.01
295 103 0.14
296 47 0.06
297 4 0.01
298 100 0.13
299 8 0.01
303 7 0.01
304 98 0.13
305 8 0.01
306 107 0.14
307 10 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (294 bp):
GGAAAAGTAATCACTTTGAACCAATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTTGAA
TGTACAGGCATAGTAAACCAAATTGAAACCCATAACGACTTATGATGTTTTCACAACATGTTGGT
AACAAACCTTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACGAGT
TCTAAAACTTAGTCAATGAGTTTCGATACTCGAAACCTAAATTGTTACCAGGAACAACCTAAATT
GTAAACGTTTAAGTCACATTTTAGGTTGAAAATA
Found at i:23711 original size:602 final size:587
Alignment explanation
Indices: 22528--23748 Score: 1267
Period size: 602 Copynumber: 2.1 Consensus size: 587
22518 TTGGTTCAAG
* **
22528 TGGAAAAATAATCACTTTGAACCAATTGGTTTTGTCTAACGTTATACTTTAGGTTGAAACCTTGA
1 TGGAAAAATAATCAC-TTGAACCAATTGGTTTTGACTAACGTTATACTTTAGGTTGAAACCTCAA
* * * ** * *
22593 ATGTTCAGGCATAGCAAACCAAATGGAAACCCATAACGATTTATGATTTTTTGTCACAATATGTT
65 ATGTACAGGAATAGCAAACAAAATGGAAACCCATAACGACCTATGATTGTTTGTCACAACATGTT
* *
22658 GGTAACAAACCTTATAATTGTAACATGAGTTGGAATGCACCGAGTTTGAAGATTTATCCTGACGA
130 AGTAACAAACCTTATAATTGTAACATGAGTTGGAATGCACCGAATTTGAAGATTTATCCTGACGA
* ** * * *
22723 GTTCTAAAACTTAGTTAATGAGTTTTGATACTCTAAACCTAAATTGTTACCAGGAACAACCTAAA
195 GTTCTAAAACTTAGTCAATGAGTTTCAATACTCGAAACCTAAAGTGTTACCACGAACAACCTAAA
* * * * ** **
22788 TTGTATACGTTTAAGTCACATTTTAGTTTGAAAACTGGAAAATCACACTTTGAACCAATTTGTTT
260 TTGTATACGTTTAAGTCACATTTTAGGTTGAAAACAGAAAAATAACACTTCAAACCAATAGGTTT
** * * * * *
22853 TGAGTAACGTTATACTTTAGGTTGAAACCTTGAATGTACTTGCATAGTAAACCAAATTGAAGCCC
325 TGACCAACATTATACTTCAGGTTGAAACCTTGAAAGTACTAGCATAGTAAACCAAATTGAAACCC
* * * * *
22918 ATAACGACTTATGATGCTTTCACAACATGTTGGTAACAAACCTTTATAATTTTAACATGAGTTGG
390 ATAAAGACTTATGACGCTTTAACAACATCTTGGTAACAAACCTTTATAATTGTAACATGAGTTGG
* * * *
22983 AATGCGCTAAGTTCAAAAATTTAACCCGACGAGTTCTAAAACTTAGTCAATGAGTTTCGATACTG
455 AATGCACCAAGTTCAAAAATTTAACCCGACGAGTTCTAAAACTTAATCAATGAGTTTCGATACTA
* * * * * *
23048 AGAACCTAAATTGTTACGAGGAACAACCTAAATTATTAAACGTTTAGGTTATATTTTAGGTTGAA
520 AAAACCTAAATTGTTACCAAGAACAACCTAAATTATTAAACGTTTAGGTCACATCTTAGGTTGAA
23113 AA-
585 AAC
* * *
23115 TAGGAAAAGTAATCACTTGAAACCTATTGGTTTTGAGTAACGTTATACTTTAGGTTGAAACCTCA
1 T-GGAAAAATAATCACTTG-AACCAATTGGTTTTGACTAACGTTATACTTTAGGTTGAAACCTCA
* * * *
23180 AATGTACAGGAATAGTAAACAAAATTGAAACTCATAGCGACCTATGA-TGTTT-TCACAACATGT
64 AATGTACAGGAATAGCAAACAAAATGGAAACCCATAACGACCTATGATTGTTTGTCACAACATG-
* * * * * *
23243 CATTATTAACAAACTTTTGTAATTGTAACATGAGTTGGAATGTATCGAATTTGAAGATTTATCTT
128 --TTAGTAACAAAC-CTTATAATTGTAACATGAGTTGGAATGCACCGAATTTGAAGATTTATCCT
* * * * * *
23308 GTCGCA-TTTTGAAACTTAGTCATTGAGTTTCAATACT-GAGAACCTTAAGTGTTACCACTAACA
190 GACG-AGTTCTAAAACTTAGTCAATGAGTTTCAATACTCGA-AACCTAAAGTGTTACCACGAACA
* * *
23371 ACCTAAAATGCGACGATGTTATAGGTTTACGTCACATTTTAGGTT-AAAAGCAGAAAAAGTAATT
253 ACCT-AAAT-------TG-TATACGTTTAAGTCACATTTTAGGTTGAAAA-CAGAAAAA-TAA-C
* * *
23435 ACTTCAAAGCAATAGGTTTTGCCCAACATTATACTTCATGTTGAAACCTTGAAAG-A-TCAGACA
306 ACTTCAAACCAATAGGTTTTGACCAACATTATACTTCAGGTTGAAACCTTGAAAGTACT-AG-CA
* * * *
23498 TAGTAAATCAAATTGAAACCCATAAAGAAC-TATGACGTTTGTAACAATATCTTGGTAACAGACC
369 TAGTAAACCAAATTGAAACCCATAAAG-ACTTATGACGCTT-TAACAACATCTTGGTAACAAACC
* ** * * *
23562 TTTATAATTGTAACATGAGTTGGAATGCACCGAGTTTGAAGATTTATCCCGACGAGTT-TCGAAA
432 TTTATAATTGTAACATGAGTTGGAATGCACCAAGTTCAAAAATTTAACCCGACGAGTTCT-AAAA
* * * * * * *
23626 TTTAATCAATGAGTTTTGATACTAAAAACCTCAAA-TGTTTCCAATAACAACCTAAGTTGTTATA
496 CTTAATCAATGAGTTTCGATACTAAAAACCT-AAATTGTTACCAAGAACAACCTAAATTATTAAA
* *
23690 GGTTTTGGTCACATCTTAGGTTGAAAAC
560 CGTTTAGGTCACATCTTAGGTTGAAAAC
* *
23718 TGGAAAAATTATCACTTTGAACTAATTGGTT
1 TGGAAAAATAATCAC-TTGAACCAATTGGTT
23749 ATTTTTAACG
Statistics
Matches: 510, Mismatches: 96, Indels: 41
0.79 0.15 0.06
Matches are distributed among these distances:
586 9 0.02
587 8 0.02
588 91 0.18
589 11 0.02
590 95 0.19
591 5 0.01
598 6 0.01
599 30 0.06
600 4 0.01
601 78 0.15
602 166 0.33
603 7 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (587 bp):
TGGAAAAATAATCACTTGAACCAATTGGTTTTGACTAACGTTATACTTTAGGTTGAAACCTCAAA
TGTACAGGAATAGCAAACAAAATGGAAACCCATAACGACCTATGATTGTTTGTCACAACATGTTA
GTAACAAACCTTATAATTGTAACATGAGTTGGAATGCACCGAATTTGAAGATTTATCCTGACGAG
TTCTAAAACTTAGTCAATGAGTTTCAATACTCGAAACCTAAAGTGTTACCACGAACAACCTAAAT
TGTATACGTTTAAGTCACATTTTAGGTTGAAAACAGAAAAATAACACTTCAAACCAATAGGTTTT
GACCAACATTATACTTCAGGTTGAAACCTTGAAAGTACTAGCATAGTAAACCAAATTGAAACCCA
TAAAGACTTATGACGCTTTAACAACATCTTGGTAACAAACCTTTATAATTGTAACATGAGTTGGA
ATGCACCAAGTTCAAAAATTTAACCCGACGAGTTCTAAAACTTAATCAATGAGTTTCGATACTAA
AAACCTAAATTGTTACCAAGAACAACCTAAATTATTAAACGTTTAGGTCACATCTTAGGTTGAAA
AC
Found at i:24030 original size:39 final size:39
Alignment explanation
Indices: 23984--24141 Score: 151
Period size: 39 Copynumber: 4.0 Consensus size: 39
23974 AGATTGGTGT
* * **
23984 AACCGAAAATGTT-TCAAACCATATAATGTTTTAGGTTGC
1 AACCGAAAATATTACCAAA-CATATAACATTTTAGGTTGC
* *
24023 AACCGAAAATATTACCAAACATATAATATTGTAGGTTGATGC
1 AACCGAAAATATTACCAAACATATAACATTTTAGG-T--TGC
* * *
24065 AACCGAAAATGTTTA--AATCATGTAACATTTTAGGTTGC
1 AACCGAAAAT-ATTACCAAACATATAACATTTTAGGTTGC
*
24103 ATACCGGAAATATTACCAAACATATAACATTTTAGGTTG
1 A-ACCGAAAATATTACCAAACATATAACATTTTAGGTTG
24142 ATTATATTTC
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
38 7 0.07
39 34 0.35
40 26 0.27
41 15 0.15
42 13 0.13
43 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (39 bp):
AACCGAAAATATTACCAAACATATAACATTTTAGGTTGC
Found at i:24114 original size:81 final size:81
Alignment explanation
Indices: 23946--24143 Score: 254
Period size: 81 Copynumber: 2.4 Consensus size: 81
23936 AAAAGTTACT
* * * * * * *
23946 GAAAATGTAACCAAACATAAAATATTCTAGATTGGTGTAACCGAAAATGTTTCAAACCATATAAT
1 GAAAATATTACCAAACATATAATATTCTAGGTTGATGCAACCGAAAATGTTTCAAACCATATAAC
*
24011 GTTTTAGGTTGCAACC
66 ATTTTAGGTTGCAACC
* * *
24027 GAAAATATTACCAAACATATAATATTGTAGGTTGATGCAACCGAAAATGTTT-AAATCATGTAAC
1 GAAAATATTACCAAACATATAATATTCTAGGTTGATGCAACCGAAAATGTTTCAAACCATATAAC
24091 ATTTTAGGTTGCATACC
66 ATTTTAGGTTGCA-ACC
* * *
24108 GGAAATATTACCAAACATATAACATTTTAGGTTGAT
1 GAAAATATTACCAAACATATAATATTCTAGGTTGAT
24144 TATATTTCTT
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 21 0.21
81 81 0.79
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (81 bp):
GAAAATATTACCAAACATATAATATTCTAGGTTGATGCAACCGAAAATGTTTCAAACCATATAAC
ATTTTAGGTTGCAACC
Found at i:28668 original size:2 final size:2
Alignment explanation
Indices: 28661--28698 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28651 GATGTGTTAG
28661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28699 GAGTTTGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29158 original size:2 final size:2
Alignment explanation
Indices: 29151--29177 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29141 CCTAGTCCAT
29151 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29178 TAGTTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30254 original size:56 final size:54
Alignment explanation
Indices: 30179--30345 Score: 183
Period size: 56 Copynumber: 3.0 Consensus size: 54
30169 TACCATATTT
* * *
30179 TAGATTGAAGCACAGAGGTGCTCAATCGTCCCTAAAAGTACAAAGGTGCCAGATCC
1 TAGATTGAAGCACAAAGGTGCTCAATCGTCCC-AAAA-CACAAAGGTGCCAGATCA
* **
30235 TAGATTGAAGCACAAAGGTGCTCAATCATCCCAAAACACTGAGGTGCCAGATCA
1 TAGATTGAAGCACAAAGGTGCTCAATCGTCCCAAAACACAAAGGTGCCAGATCA
* * * * *
30289 TAGATTGATGCAAAAATGTGCTCAATAGTCCCAAAGCACACAGAGGTGCTCAG-TCA
1 TAGATTGAAGCACAAAGGTGCTCAATCGTCCCAAA--ACACAAAGGTGC-CAGATCA
30345 T
1 T
30346 TTTTAACTGC
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
54 44 0.46
55 4 0.04
56 45 0.47
57 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (54 bp):
TAGATTGAAGCACAAAGGTGCTCAATCGTCCCAAAACACAAAGGTGCCAGATCA
Found at i:36521 original size:86 final size:84
Alignment explanation
Indices: 36376--36545 Score: 322
Period size: 86 Copynumber: 2.0 Consensus size: 84
36366 TTCCTCCCAT
36376 CACTACCACTGATTTAGCCACACCAACCAAGTACAATGGTAAGAGCAAGGAAAGCCCCAGCCTCA
1 CACTACCACTGATTTAGCCACACCAACCAAGTACAATGGTAAGAGCAAGGAAAGCCCCAGCCTC-
36441 ACACAAGTTTTGAACGTTTCC
65 ACACAAG-TTTGAACGTTTCC
36462 CACTACCACTGATTTAGCCACACCAACCAAGTACAATGGTAAGAGCAAGGAAAGCCCCAGCCTCA
1 CACTACCACTGATTTAGCCACACCAACCAAGTACAATGGTAAGAGCAAGGAAAGCCCCAGCCTCA
36527 CACAAGTTTGAACGTTTCC
66 CACAAGTTTGAACGTTTCC
36546 AAACGTCGAA
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 13 0.15
85 7 0.08
86 64 0.76
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.18
Consensus pattern (84 bp):
CACTACCACTGATTTAGCCACACCAACCAAGTACAATGGTAAGAGCAAGGAAAGCCCCAGCCTCA
CACAAGTTTGAACGTTTCC
Found at i:52031 original size:32 final size:32
Alignment explanation
Indices: 51995--52063 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
51985 CCTTGTGCTA
* *
51995 GTATAATTAGAATCAGGAAAAGACTATGTAGT
1 GTATAATCAGAATCAGAAAAAGACTATGTAGT
* * *
52027 GTATAATCATAATCATAAAAAGACTGTGTAGT
1 GTATAATCAGAATCAGAAAAAGACTATGTAGT
*
52059 CTATA
1 GTATA
52064 GAGATGCATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (32 bp):
GTATAATCAGAATCAGAAAAAGACTATGTAGT
Found at i:65732 original size:12 final size:12
Alignment explanation
Indices: 65713--65746 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
65703 GAATGTTTTA
65713 TCTGATTTCTAAT
1 TCTGATTTCT-AT
65726 T-TGATTTCTAT
1 TCTGATTTCTAT
65737 TCTGATTTCT
1 TCTGATTTCT
65747 GATATGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 16 0.80
13 1 0.05
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (12 bp):
TCTGATTTCTAT
Found at i:65745 original size:24 final size:24
Alignment explanation
Indices: 65713--65767 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
65703 GAATGTTTTA
* *
65713 TCTGATTTCTAATTTGATTTCTAT
1 TCTGATTTCTAATATGAATTCTAT
* *
65737 TCTGATTTCTGATATGAATTCTGT
1 TCTGATTTCTAATATGAATTCTAT
65761 TCTGATT
1 TCTGATT
65768 CCTGTATCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.55
Consensus pattern (24 bp):
TCTGATTTCTAATATGAATTCTAT
Done.