Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008601.1 Hibiscus syriacus cultivar Beakdansim tig00111554_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: 61091
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:8507 original size:2 final size:2
Alignment explanation
Indices: 8500--8535 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8490 ATCCTTTCAA
8500 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
8536 CCTTTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12182 original size:37 final size:36
Alignment explanation
Indices: 12086--12257 Score: 109
Period size: 37 Copynumber: 4.7 Consensus size: 36
12076 GGAGGTTTTC
* * **
12086 AAATAGCAATTTATCTCACTTGAGATCA-TTTTTCTT
1 AAATAGAAATTTATCTCACTTGAGA-AAGTTTCACTT
* * *
12122 AAA-ACAAATTGTTTCTCGCTTGAGAAAGTTTCACTT
1 AAATAGAAATT-TATCTCACTTGAGAAAGTTTCACTT
* ** **
12158 AATATAGTAATTTATCTCACTTGAGATTGTTTTTTCTT
1 AA-ATAGAAATTTATCTCACTTGAGAAAG-TTTCACTT
* *
12196 AAA-ACAAACTGTT-TCTCGCTTGAGAAAGTTTCACTT
1 AAATAGAAA-T-TTATCTCACTTGAGAAAGTTTCACTT
* *
12232 GAAATAGCAATTTATCTCACTCGAGA
1 -AAATAGAAATTTATCTCACTTGAGA
12258 TTATTTTCTT
Statistics
Matches: 100, Mismatches: 26, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
35 6 0.06
36 34 0.34
37 42 0.42
38 18 0.18
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (36 bp):
AAATAGAAATTTATCTCACTTGAGAAAGTTTCACTT
Found at i:12213 original size:74 final size:72
Alignment explanation
Indices: 12086--12346 Score: 355
Period size: 72 Copynumber: 3.6 Consensus size: 72
12076 GGAGGTTTTC
**
12086 AAATAGCAATTTATCTCACTTGAGATCATTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATGTTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAAGT
12151 TTCACTT
66 TTCACTT
* *
12158 AATATAGTAATTTATCTCACTTGAGATTGTTTTTTCTTAAAACAAACTGTTTCTCGCTTGAGAAA
1 AA-ATAGCAATTTATCTCACTTGAGA-TGTTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAA
12223 GTTTCACTT
64 GTTTCACTT
* * * * *
12232 GAAATAGCAATTTATCTCACTCGAGAT-TATTTTCTTAAAACAAATTATTTCTCGCTGGAGAAAA
1 -AAATAGCAATTTATCTCACTTGAGATGTTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAAG
*
12296 TTTCACTCG
65 TTTCACT-T
* *
12305 AAATTGCAATTTATCTTACTTGAGAT-TGTTTTTCTTAAAACA
1 AAATAGCAATTTATCTCACTTGAGATGT-TTTTTCTTAAAACA
12347 TTTCCAAAAG
Statistics
Matches: 168, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
72 65 0.39
73 36 0.21
74 65 0.39
75 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (72 bp):
AAATAGCAATTTATCTCACTTGAGATGTTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAAGT
TTCACTT
Found at i:12412 original size:26 final size:26
Alignment explanation
Indices: 12382--12439 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
12372 ATAACTCATA
12382 TGAAGAGGAAGAAGGAGTTCATAGTC
1 TGAAGAGGAAGAAGGAGTTCATAGTC
12408 TGAAGAGGAAGAAGGAGTTCATAGTC
1 TGAAGAGGAAGAAGGAGTTCATAGTC
*
12434 TAAAGA
1 TGAAGA
12440 ACTCGTATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.19
Consensus pattern (26 bp):
TGAAGAGGAAGAAGGAGTTCATAGTC
Found at i:12462 original size:39 final size:39
Alignment explanation
Indices: 12405--12827 Score: 589
Period size: 39 Copynumber: 10.9 Consensus size: 39
12395 GGAGTTCATA
* *
12405 GTCTGAAGAGGAAGAAGGAGTTCATAGTCTAAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
*
12444 GTATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
* *
12483 GTCTGAAGAGAAAGAAGGAGTTCATAGTCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
* * * *
12522 GTTTGAAGAGGAAGAAAGAGTTCATAGTTTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
* **
12561 GTTTGAAGAGGAAGAAGGAGTTCATGGTCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
* *
12600 ATATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
**
12639 GTCTGAAGAGGAAGAAAAAGGTT-ATAATCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGA-GTTCATAATCTGAAGAACTC
* * *
12678 GTCTGAAAATGAAGAAGGAGTTCATAGTCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
*
12717 GTCTGAAGAGGAAGAATGAGTTCATAATCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
* *
12756 GTCTGAAGA-GAAAAAAGAGTTCATAATCTGAAGAACTC
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
* * * *
12794 ATCTAAAGAGGAAAAATGAGTTCATAATCTGAAG
1 GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAG
12828 GGGAAGAAGG
Statistics
Matches: 346, Mismatches: 35, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
38 37 0.11
39 306 0.88
40 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.22
Consensus pattern (39 bp):
GTCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
Found at i:12572 original size:117 final size:117
Alignment explanation
Indices: 12405--13052 Score: 795
Period size: 117 Copynumber: 5.7 Consensus size: 117
12395 GGAGTTCATA
* * * *
12405 GTCTGAAGAGGAAGAAGGAGTTCATAGTCTAAAGAACTCGTATGAAGAGGAAGAAGGAGTTCATA
1 GTCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATA
*
12470 ATCTGAAGAACTCGTCTGAAGAGAAAGAAGGAGTTCATAGTCTGAAGAACTC
66 ATCTGAAGAACTCGTCTGAAGAGAAAGAAGGAGTTCATAATCTGAAGAACTC
* * * * *
12522 GTTTGAAGAGGAAGAAAGAGTTCATAGTTTGAAGAACTCGTTTGAAGAGGAAGAAGGAGTTCATG
1 GTCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATA
* * * *
12587 GTCTGAAGAACTCATATGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTC
66 ATCTGAAGAACTCGTCTGAAGAGAAAGAAGGAGTTCATAATCTGAAGAACTC
* * *
12639 GTCTGAAGAGGAAGAAAAAGGTT-ATAATCTGAAGAACTCGTCTGAAAATGAAGAAGGAGTTCAT
1 GTCTGAAGAGGAAGAAAGA-GTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCAT
* * *
12703 AGTCTGAAGAACTCGTCTGAAGAGGAAGAATGAGTTCATAATCTGAAGAACTC
65 AATCTGAAGAACTCGTCTGAAGAGAAAGAAGGAGTTCATAATCTGAAGAACTC
* * * * *
12756 GTCTGAAGA-GAAAAAAGAGTTCATAATCTGAAGAACTCATCTAAAGAGGAAAAATGAGTTCATA
1 GTCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATA
12820 ATCT---GAA---G---G--G-G-AAGAAGGAGTTCATAATCTGAAGAACTC
66 ATCTGAAGAACTCGTCTGAAGAGAAAGAAGGAGTTCATAATCTGAAGAACTC
* * * * * * *
12859 GTTTGAATAGGAAGAAGGAGATCATAATCTGAAGAACTCGTCTGAATAGGAAAAATGAGTTCATA
1 GTCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATA
* *
12924 ATCTGAAGAACTCGTCTGAAGAGAAAAAAGGAGTTCATAATCTGAATAACTC
66 ATCTGAAGAACTCGTCTGAAGAGAAAGAAGGAGTTCATAATCTGAAGAACTC
* * * * * * **
12976 ATATGAAGAGGAAGAAGGAGTTCATAATTTGAAGAACTCATCTGAAGAGAAAGAATAAGTTCATA
1 GTCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATA
*
13041 GTCTGAAGAACT
66 ATCTGAAGAACT
13053 TATTCAACCT
Statistics
Matches: 462, Mismatches: 53, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
103 34 0.07
104 54 0.12
105 1 0.00
107 4 0.01
110 2 0.00
113 4 0.01
115 4 0.01
116 47 0.10
117 309 0.67
118 3 0.01
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.22
Consensus pattern (117 bp):
GTCTGAAGAGGAAGAAAGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGTTCATA
ATCTGAAGAACTCGTCTGAAGAGAAAGAAGGAGTTCATAATCTGAAGAACTC
Found at i:12832 original size:26 final size:26
Alignment explanation
Indices: 12794--12854 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
12784 TGAAGAACTC
* *
12794 ATCTAAAGAGGAAAAATGAGTTCATA
1 ATCTGAAGAGGAAAAAGGAGTTCATA
* *
12820 ATCTGAAGGGGAAGAAGGAGTTCATA
1 ATCTGAAGAGGAAAAAGGAGTTCATA
12846 ATCTGAAGA
1 ATCTGAAGA
12855 ACTCGTTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.21
Consensus pattern (26 bp):
ATCTGAAGAGGAAAAAGGAGTTCATA
Found at i:12834 original size:142 final size:143
Alignment explanation
Indices: 12688--12969 Score: 458
Period size: 142 Copynumber: 2.0 Consensus size: 143
12678 GTCTGAAAAT
* * *
12688 GAAGAAGGAGTTCATAGTCTGAAGAACTCGTCTGAAGAGGAAGAATGAGTTCATAATCTGAAGAA
1 GAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGATCATAATCTGAAGAA
* *
12753 CTCGTCTGAAGA-GAAAAAAGAGTTCATAATCTGAAGAACTCATCTAAAGAGGAAAAATGAGTTC
66 CTCGTCTGAAGAGGAAAAAAGAGTTCATAATCTGAAGAACTCATCTAAAGAGAAAAAAGGAGTTC
12817 ATAATCTGAAGGG
131 ATAATCTGAAGGG
* *
12830 GAAGAAGGAGTTCATAATCTGAAGAACTCGTTTGAATAGGAAGAAGGAGATCATAATCTGAAGAA
1 GAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGATCATAATCTGAAGAA
* * * *
12895 CTCGTCTGAATAGGAAAAATGAGTTCATAATCTGAAGAACTCGTCTGAAGAGAAAAAAGGAGTTC
66 CTCGTCTGAAGAGGAAAAAAGAGTTCATAATCTGAAGAACTCATCTAAAGAGAAAAAAGGAGTTC
12960 ATAATCTGAA
131 ATAATCTGAA
12970 TAACTCATAT
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
142 71 0.55
143 57 0.45
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (143 bp):
GAAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGGAGATCATAATCTGAAGAA
CTCGTCTGAAGAGGAAAAAAGAGTTCATAATCTGAAGAACTCATCTAAAGAGAAAAAAGGAGTTC
ATAATCTGAAGGG
Found at i:12855 original size:20 final size:20
Alignment explanation
Indices: 12830--12894 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
12820 ATCTGAAGGG
12830 GAAGAAGGAGTTCATAATCT
1 GAAGAAGGAGTTCATAATCT
*** **
12850 GAAGAACTCGTT--TGAATAG
1 GAAGAAGGAGTTCAT-AATCT
*
12869 GAAGAAGGAGATCATAATCT
1 GAAGAAGGAGTTCATAATCT
12889 GAAGAA
1 GAAGAA
12895 CTCGTCTGAA
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 1 0.03
19 11 0.35
20 18 0.58
21 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.22
Consensus pattern (20 bp):
GAAGAAGGAGTTCATAATCT
Found at i:12884 original size:39 final size:39
Alignment explanation
Indices: 12821--13052 Score: 302
Period size: 39 Copynumber: 5.9 Consensus size: 39
12811 GAGTTCATAA
*
12821 TCTGAAGGGGAAGAAGGAGTTCATAATCTGAAGAACTCG
1 TCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCG
* * *
12860 TTTGAATAGGAAGAAGGAGATCATAATCTGAAGAACTCG
1 TCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCG
* * *
12899 TCTGAATAGGAAAAATGAGTTCATAATCTGAAGAACTCG
1 TCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCG
* * * *
12938 TCTGAAGAGAAAAAAGGAGTTCATAATCTGAATAACTCA
1 TCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCG
* * *
12977 TATGAAGAGGAAGAAGGAGTTCATAATTTGAAGAACTCA
1 TCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCG
* ** *
13016 TCTGAAGAGAAAGAATAAGTTCATAGTCTGAAGAACT
1 TCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACT
13053 TATTCAACCT
Statistics
Matches: 169, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 169 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (39 bp):
TCTGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCG
Found at i:12944 original size:181 final size:182
Alignment explanation
Indices: 12640--13010 Score: 575
Period size: 181 Copynumber: 2.0 Consensus size: 182
12630 GAAGAACTCG
* * *
12640 TCTGAAGAGGAAGAAAAAGGTTATAATCTGAAGAACTCGTCTGAAAATGAAGAAGGAGTTCATAG
1 TCTGAAGAGGAAGAAAAAGGTTATAATCTGAAGAACTCGTCTGAAAAGGAAGAAGGAGATCATAA
*
12705 TCTGAAGAACTCGTCTGAAGAGGAAGAATGAGTTCATAATCTGAAGAACTCGTCTGAAGAGAAAA
66 TCTGAAGAACTCGTCTGAAGAGGAAAAATGAGTTCATAATCTGAAGAACTCGTCTGAAGAGAAAA
* *
12770 AA-GAGTTCATAATCTGAAGAACTCATCTAAAGAGGAAAAATGAGTTCATAA
131 AAGGAGTTCATAATCTGAAGAACTCATATAAAGAGGAAAAAGGAGTTCATAA
* ** * *
12821 TCTGAAGGGGAAGAAGGA-GTTCATAATCTGAAGAACTCGTTTGAATAGGAAGAAGGAGATCATA
1 TCTGAAGAGGAAGAAAAAGGTT-ATAATCTGAAGAACTCGTCTGAAAAGGAAGAAGGAGATCATA
*
12885 ATCTGAAGAACTCGTCTGAATAGGAAAAATGAGTTCATAATCTGAAGAACTCGTCTGAAGAGAAA
65 ATCTGAAGAACTCGTCTGAAGAGGAAAAATGAGTTCATAATCTGAAGAACTCGTCTGAAGAGAAA
* * *
12950 AAAGGAGTTCATAATCTGAATAACTCATATGAAGAGGAAGAAGGAGTTCATAA
130 AAAGGAGTTCATAATCTGAAGAACTCATATAAAGAGGAAAAAGGAGTTCATAA
*
13003 TTTGAAGA
1 TCTGAAGA
13011 ACTCATCTGA
Statistics
Matches: 171, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
180 3 0.02
181 118 0.69
182 50 0.29
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (182 bp):
TCTGAAGAGGAAGAAAAAGGTTATAATCTGAAGAACTCGTCTGAAAAGGAAGAAGGAGATCATAA
TCTGAAGAACTCGTCTGAAGAGGAAAAATGAGTTCATAATCTGAAGAACTCGTCTGAAGAGAAAA
AAGGAGTTCATAATCTGAAGAACTCATATAAAGAGGAAAAAGGAGTTCATAA
Found at i:13252 original size:3 final size:3
Alignment explanation
Indices: 13244--13279 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
13234 TTTTTATTTG
* *
13244 TTA TTA TTA TTA TTA ATA TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13280 CAGGCCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:14973 original size:20 final size:20
Alignment explanation
Indices: 14948--14985 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
14938 CACTAATCCT
14948 TTTTTATTATTAAAAAGACC
1 TTTTTATTATTAAAAAGACC
14968 TTTTTATTATTAAAAAGA
1 TTTTTATTATTAAAAAGA
14986 ACGAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTTATTATTAAAAAGACC
Found at i:15062 original size:28 final size:27
Alignment explanation
Indices: 15015--15067 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
15005 CAAACCAATT
*
15015 ACTCTTTTAAAATAATATTTTCTTAAAA
1 ACTCTTTTAAAAGAATATTTT-TTAAAA
15043 ACTCTTTTAAAAG-ATAATTTTTTAA
1 ACTCTTTTAAAAGAAT-ATTTTTTAA
15068 GTATTCGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (27 bp):
ACTCTTTTAAAAGAATATTTTTTAAAA
Found at i:21421 original size:2 final size:2
Alignment explanation
Indices: 21414--21444 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21404 GTAGATAGAA
21414 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
21445 TGACGCTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23305 original size:10 final size:10
Alignment explanation
Indices: 23290--23314 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
23280 CCTCGTTATT
23290 CTAAGCTTTG
1 CTAAGCTTTG
23300 CTAAGCTTTG
1 CTAAGCTTTG
23310 CTAAG
1 CTAAG
23315 TTTTACCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (10 bp):
CTAAGCTTTG
Found at i:27555 original size:136 final size:136
Alignment explanation
Indices: 27310--27658 Score: 524
Period size: 136 Copynumber: 2.6 Consensus size: 136
27300 TTGTTAGATT
* * * *
27310 GAACAAGTTCTTCGCATTATGAACTTCTTCTCTC-TTTT-GGATGAGTTTTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
* * ** * *
27373 CTTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTG
66 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTC-ATGAATCGAGTG
27437 ATAGGTC
130 ATAGGTC
27444 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
* * * *
27509 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
66 CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
27574 TAGGTC
131 TAGGTC
* *
27580 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
27645 CTCCATTGAAAATG
66 CTCCATTGAAAATG
27659 CTGATCCACC
Statistics
Matches: 195, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 31 0.16
135 4 0.02
136 159 0.82
137 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGTCATGAATCGAGTGA
TAGGTC
Found at i:28644 original size:1 final size:1
Alignment explanation
Indices: 28630--28686 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
28620 TCCTTCTTCA
* * * * * **
28630 TTTTTCTTTCTTTTTTTTTCTTTTTTTTTTCTTCTTTTTTTTTCATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28687 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:28650 original size:24 final size:23
Alignment explanation
Indices: 28623--28686 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
28613 TGAACCCTCC
28623 TTCTTCATTTTTCTTTCTTTTTTT
1 TTCTTCATTTTT-TTTCTTTTTTT
28647 TTCTT--TTTTTTTTCTTCTTTTT
1 TTCTTCATTTTTTTTCTT-TTTTT
28669 TT-TTCATTTTTTTT-TTTT
1 TTCTTCATTTTTTTTCTTTT
28687 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 10 0.27
22 14 0.38
23 8 0.22
24 5 0.14
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (23 bp):
TTCTTCATTTTTTTTCTTTTTTT
Found at i:28687 original size:14 final size:13
Alignment explanation
Indices: 28630--28689 Score: 79
Period size: 14 Copynumber: 4.6 Consensus size: 13
28620 TCCTTCTTCA
28630 TTTTTCTTTCTTTT
1 TTTTTCTTT-TTTT
28644 TTTTTC--TTTTT
1 TTTTTCTTTTTTT
*
28655 TTTTTCTTCTTTT
1 TTTTTCTTTTTTT
28668 TTTTTCATTTTTTT
1 TTTTTC-TTTTTTT
28682 TTTTTCTT
1 TTTTTCTT
28690 CAAGCATAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 10 0.24
12 1 0.02
13 12 0.29
14 18 0.44
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:28688 original size:24 final size:23
Alignment explanation
Indices: 28630--28689 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 23
28620 TCCTTCTTCA
*
28630 TTTTTCTTTCTTTTTTTTTCTTT
1 TTTTTTTTTCTTTTTTTTTCTTT
28653 TTTTTTTCTTCTTTTTTTTTCATTT
1 TTTTTTT-TTCTTTTTTTTTC-TTT
28678 TTTTTTTTTCTT
1 TTTTTTTTTCTT
28690 CAAGCATAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 6 0.18
24 18 0.53
25 10 0.29
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.87
Consensus pattern (23 bp):
TTTTTTTTTCTTTTTTTTTCTTT
Found at i:56861 original size:38 final size:38
Alignment explanation
Indices: 56782--56856 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 38
56772 CAATACTAGC
56782 ATAAGAATATTGATACCTATTTTTAAAAAATAATTTCA
1 ATAAGAATATTGATACCTATTTTTAAAAAATAATTTCA
**
56820 ATAAGAATA-TGATACCTATTTTT-TTAAATAATTTCA
1 ATAAGAATATTGATACCTATTTTTAAAAAATAATTTCA
56856 A
1 A
56857 AATAAATGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 12 0.34
37 14 0.40
38 9 0.26
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (38 bp):
ATAAGAATATTGATACCTATTTTTAAAAAATAATTTCA
Found at i:60474 original size:5 final size:5
Alignment explanation
Indices: 60466--60519 Score: 99
Period size: 5 Copynumber: 10.8 Consensus size: 5
60456 GTCAGGCTTA
*
60466 ATATA ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
60516 ATAT
1 ATAT
60520 AAATAATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.41
Consensus pattern (5 bp):
ATATG
Done.