Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009123.1 Hibiscus syriacus cultivar Beakdansim tig00112613_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: 56522
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:7628 original size:15 final size:15
Alignment explanation
Indices: 7593--7621 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7583 GTGCTTCAAC
7593 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
7607 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
7622 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:7665 original size:24 final size:23
Alignment explanation
Indices: 7615--7670 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
7605 TTTTCTTTGC
*
7615 TTTTCTTCTTTTTGAGTGCTGGAT
1 TTTTCTTC-TTTTGAGTGCTGCAT
*
7639 TTTTCTTCTTTTGAGTGCTTCACT
1 TTTTCTTCTTTTGAGTGCTGCA-T
7663 TTTT-TTCT
1 TTTTCTTCT
7671 GATTTTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.07, C:0.16, G:0.14, T:0.62
Consensus pattern (23 bp):
TTTTCTTCTTTTGAGTGCTGCAT
Found at i:7770 original size:24 final size:25
Alignment explanation
Indices: 7741--7789 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
7731 CTGATTATCG
7741 CTTGATGTAAGG-CTTCTGATGCCA
1 CTTGATGTAAGGCCTTCTGATGCCA
7765 CTTGATGTAAGGCTCTTCTGATGCC
1 CTTGATGTAAGGC-CTTCTGATGCC
7790 TTAACAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.52
26 11 0.48
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (25 bp):
CTTGATGTAAGGCCTTCTGATGCCA
Found at i:12092 original size:33 final size:33
Alignment explanation
Indices: 12050--12118 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
12040 GTTGATGAAT
*
12050 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
12083 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
12116 GAA
1 GAA
12119 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:12123 original size:13 final size:12
Alignment explanation
Indices: 12104--12200 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
12094 TTATTGGCGT
12104 GATATGGTGATG
1 GATATGGTGATG
12116 GAATATGGTGAT-
1 G-ATATGGTGATG
*
12128 GATATAGGCG-T-
1 GATAT-GGTGATG
12139 GATAATGGTGATG
1 GAT-ATGGTGATG
12152 GACTATGGTGAT-
1 GA-TATGGTGATG
*
12164 GATATAGGCG-T-
1 GATAT-GGTGATG
*
12175 GATAATGGAGATG
1 GAT-ATGGTGATG
12188 GATTATGGTGATG
1 GA-TATGGTGATG
12201 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:12159 original size:36 final size:36
Alignment explanation
Indices: 12089--12201 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
12079 AATGGAAGGA
* *
12089 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
12124 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
12160 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
12196 TGATGA
1 TGATGA
12202 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:31991 original size:13 final size:13
Alignment explanation
Indices: 31973--32082 Score: 53
Period size: 13 Copynumber: 9.0 Consensus size: 13
31963 TAGGCGTGAA
31973 ATGGTGATGGAAT
1 ATGGTGATGGAAT
31986 ATGGTGAT-G-AT
1 ATGGTGATGGAAT
*
31997 ATAGGCG-T-G-AT
1 AT-GGTGATGGAAT
*
32008 AATGGTGATGGACT
1 -ATGGTGATGGAAT
32022 ATGGTGAT-G-AT
1 ATGGTGATGGAAT
*
32033 ATAGGCG-T-G-AT
1 AT-GGTGATGGAAT
*
32044 AATGGTGATGGAAG
1 -ATGGTGATGGAAT
32058 ATGGTGATGGAA-
1 ATGGTGATGGAAT
* *
32070 ATAGTAATGGAAT
1 ATGGTGATGGAAT
32083 GTTGATGGAG
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
11 21 0.27
12 24 0.31
13 30 0.39
14 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (13 bp):
ATGGTGATGGAAT
Found at i:32019 original size:36 final size:36
Alignment explanation
Indices: 31960--32066 Score: 189
Period size: 36 Copynumber: 3.0 Consensus size: 36
31950 GTTGGTTATA
31960 ATATAGGCGTGA-AATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
*
31995 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
*
32031 ATATAGGCGTGATAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
32067 GAAATAGTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 12 0.18
36 56 0.82
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.29
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGAATATGGTGATG
Found at i:33578 original size:21 final size:23
Alignment explanation
Indices: 33542--33584 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
33532 TGCTTATAAT
33542 AATATATAATGCATAAA-TAAGAA
1 AATATATAAT-CATAAAGTAAGAA
33565 AATATATAAT-ATAAAGTAAG
1 AATATATAATCATAAAGTAAG
33585 GTAGAACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 10 0.53
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.28
Consensus pattern (23 bp):
AATATATAATCATAAAGTAAGAA
Found at i:37198 original size:16 final size:16
Alignment explanation
Indices: 37167--37213 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
37157 TGGTAATGAA
37167 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
37184 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
37201 ATAAAAAAATGAA
1 ATAAAAAAATGAA
37214 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:37841 original size:22 final size:23
Alignment explanation
Indices: 37813--37864 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
37803 ATTTAGAAGT
37813 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
* *
37835 TGGTGATGATATAGGTGTGATAA
1 TGGTGATAATATAGGCGTGATAA
37858 TGGTGAT
1 TGGTGAT
37865 GGACTATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:37897 original size:35 final size:36
Alignment explanation
Indices: 37833--37902 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 36
37823 ATAGGCGTGA
*
37833 TATGGTGATGATATAGGTGTGATAATGGTGATGGAC
1 TATGGCGATGATATAGGTGTGATAATGGTGATGGAC
37869 TATGGCGATGATATAGG-GTGATAATGGTGATGGA
1 TATGGCGATGATATAGGTGTGATAATGGTGATGGA
37903 AGATGGTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 17 0.52
36 16 0.48
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TATGGCGATGATATAGGTGTGATAATGGTGATGGAC
Found at i:37910 original size:13 final size:13
Alignment explanation
Indices: 37892--37916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37882 TAGGGTGATA
37892 ATGGTGATGGAAG
1 ATGGTGATGGAAG
37905 ATGGTGATGGAA
1 ATGGTGATGGAA
37917 ATAGTAATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:38365 original size:19 final size:20
Alignment explanation
Indices: 38318--38368 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
38308 GAAACCCCTT
**
38318 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
38338 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
38357 TGAAGATACATG
1 TGAAAATACATG
38369 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:41996 original size:22 final size:23
Alignment explanation
Indices: 41968--42019 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
41958 ATTTAGAAGT
41968 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
* *
41990 TGGTGATGATATAGGTGTGATAA
1 TGGTGATAATATAGGCGTGATAA
42013 TGGTGAT
1 TGGTGAT
42020 TGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:41999 original size:11 final size:11
Alignment explanation
Indices: 41985--42056 Score: 67
Period size: 11 Copynumber: 6.2 Consensus size: 11
41975 AATATAGGCG
41985 TGATATGGTGA
1 TGATATGGTGA
41996 TGATATAGGTG-
1 TGATAT-GGTGA
42007 TGATAATGGTGA
1 TGAT-ATGGTGA
42019 TTGACTATGGTGA
1 -TGA-TATGGTGA
*
42032 TGATATAGGCG-
1 TGATAT-GGTGA
42043 TGATAATGGTGA
1 TGAT-ATGGTGA
42055 TG
1 TG
42057 GAAGATGGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
11 24 0.47
12 16 0.31
13 10 0.20
14 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.35, T:0.35
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:42011 original size:36 final size:37
Alignment explanation
Indices: 41970--42049 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 37
41960 TTAGAAGTTG
*
41970 GTGATAATATAGGCG-TGA-TATGGTGATGATATAGGT
1 GTGATAATAT-GGCGATGACTATGGTGATGATATAGGC
*
42006 GTGAT-A-ATGGTGATTGACTATGGTGATGATATAGGC
1 GTGATAATATGGCGA-TGACTATGGTGATGATATAGGC
42042 GTGATAAT
1 GTGATAAT
42050 GGTGATGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
33 3 0.08
34 2 0.05
35 4 0.11
36 27 0.73
37 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.34
Consensus pattern (37 bp):
GTGATAATATGGCGATGACTATGGTGATGATATAGGC
Found at i:42050 original size:36 final size:36
Alignment explanation
Indices: 41987--42069 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
41977 TATAGGCGTG
* *
41987 ATATGGTGATGATATAGGTGTGATAATGGTGATTGA
1 ATATGGTGATGATATAGGCGTGATAATGGTGATGGA
*
42023 CTATGGTGATGATATAGGCGTGATAATGGTGATGGA
1 ATATGGTGATGATATAGGCGTGATAATGGTGATGGA
*
42059 AGATGGTGATG
1 ATATGGTGATG
42070 GAAATAGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.33
Consensus pattern (36 bp):
ATATGGTGATGATATAGGCGTGATAATGGTGATGGA
Found at i:42066 original size:13 final size:13
Alignment explanation
Indices: 42048--42072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42038 AGGCGTGATA
42048 ATGGTGATGGAAG
1 ATGGTGATGGAAG
42061 ATGGTGATGGAA
1 ATGGTGATGGAA
42073 ATAGTAATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:42522 original size:19 final size:20
Alignment explanation
Indices: 42475--42525 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
42465 GAAACCCCTT
**
42475 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
42495 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
42514 TGAAGATACATG
1 TGAAAATACATG
42526 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:46164 original size:22 final size:23
Alignment explanation
Indices: 46136--46187 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
46126 ATTTAGAAGT
46136 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
* *
46158 TGGTGATGATATAGGTGTGATAA
1 TGGTGATAATATAGGCGTGATAA
46181 TGGTGAT
1 TGGTGAT
46188 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:46167 original size:11 final size:11
Alignment explanation
Indices: 46153--46205 Score: 63
Period size: 11 Copynumber: 4.5 Consensus size: 11
46143 AATATAGGCG
46153 TGATATGGTGA
1 TGATATGGTGA
46164 TGATATAGGTG-
1 TGATAT-GGTGA
46175 TGATAATGGTGA
1 TGAT-ATGGTGA
46187 TGGACTATGGTGA
1 T-GA-TATGGTGA
46200 TGATAT
1 TGATAT
46206 AGGCGTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
11 17 0.46
12 9 0.24
13 10 0.27
14 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.34, T:0.36
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:46196 original size:36 final size:36
Alignment explanation
Indices: 46156--46226 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
46146 ATAGGCGTGA
*
46156 TATGGTGATGATATAGGTGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
46192 TATGGTGATGATATAGGCGTTATAATGGTGATGGA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGA
46227 AGATAGTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.03, G:0.35, T:0.34
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:46236 original size:36 final size:36
Alignment explanation
Indices: 46160--46237 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
46150 GCGTGATATG
* ** *
46160 GTGATGATATAGGTGTGATAATGGTGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGAAGATA
*
46196 GTGATGATATAGGCGTTATAATGGTGATGGAAGATA
1 GTGATGATATAGGCGTGATAATGGTGATGGAAGATA
46232 GTGATG
1 GTGATG
46238 GAAATAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGAAGATA
Found at i:46237 original size:13 final size:12
Alignment explanation
Indices: 46219--46252 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
46209 CGTTATAATG
46219 GTGATGGAAGATA
1 GTGATGGAA-ATA
46232 GTGATGGAAATA
1 GTGATGGAAATA
*
46244 GTAATGGAA
1 GTGATGGAA
46253 TGTTGATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (12 bp):
GTGATGGAAATA
Found at i:46687 original size:19 final size:20
Alignment explanation
Indices: 46640--46690 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
46630 GAAACCCCTT
**
46640 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
46660 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
46679 TGAATATACATG
1 TGAAAATACATG
46691 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:49908 original size:11 final size:11
Alignment explanation
Indices: 49892--49919 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
49882 TGTAGGAGTC
49892 TTTTCTTTTCT
1 TTTTCTTTTCT
49903 TTTTCTTTTCT
1 TTTTCTTTTCT
49914 TTTTCT
1 TTTTCT
49920 CATTGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:50337 original size:13 final size:13
Alignment explanation
Indices: 50319--50430 Score: 57
Period size: 13 Copynumber: 9.2 Consensus size: 13
50309 TATAGGCGTG
50319 ATATGGTGATGGA
1 ATATGGTGATGGA
50332 ATATGGTGAT-G-
1 ATATGGTGATGGA
*
50343 ATATAGGCG-T-G-
1 ATAT-GGTGATGGA
50354 ATAATGGTGATGGA
1 AT-ATGGTGATGGA
*
50368 CTATGGTGAT-G-
1 ATATGGTGATGGA
*
50379 ATATAGGCG-T-G-
1 ATAT-GGTGATGGA
50390 ATAATGGTGATGGA
1 AT-ATGGTGATGGA
*
50404 AGATGGTGATGGA
1 ATATGGTGATGGA
* *
50417 A-ATAGTAATGGA
1 ATATGGTGATGGA
50429 AT
1 AT
50431 GTTGATGGAG
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
11 21 0.27
12 24 0.30
13 32 0.41
14 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:50373 original size:36 final size:36
Alignment explanation
Indices: 50300--50414 Score: 196
Period size: 36 Copynumber: 3.2 Consensus size: 36
50290 ATTTAGAAGT
*
50300 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
50335 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
50371 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
50407 TGGTGATG
1 TGGTGATG
50415 GAAATAGTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 20 0.27
36 55 0.73
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:50437 original size:72 final size:71
Alignment explanation
Indices: 50300--50439 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 71
50290 ATTTAGAAGT
* * ** *
50300 TGGTGATAATATAGGCGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATAATATAGGCGTGATATGGTGATGGAAGATGGTGATGAAATAGGAATGAGAATGGTGAT
50365 GGACTA
66 GGACTA
* * *
50371 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGATGGTGATGGAAATAGTAATG-GAATGTTG
1 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAAGATGGTGAT-GAAATAGGAATGAGAATGGTG
50435 ATGGA
64 ATGGA
50440 GTTGGCGTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
71 20 0.34
72 31 0.53
73 8 0.14
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.30
Consensus pattern (71 bp):
TGGTGATAATATAGGCGTGATATGGTGATGGAAGATGGTGATGAAATAGGAATGAGAATGGTGAT
GGACTA
Found at i:54827 original size:24 final size:23
Alignment explanation
Indices: 54787--54832 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
54777 AAGAAATCAG
54787 AAAATCAAAAGAAATTAAAGCAA
1 AAAATCAAAAGAAATTAAAGCAA
* *
54810 AAAATTAAGAAGAAATTACAGCA
1 AAAATCAA-AAGAAATTAAAGCA
54833 TTAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.65, C:0.09, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAATCAAAAGAAATTAAAGCAA
Done.