Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009293.1 Hibiscus syriacus cultivar Beakdansim tig00113002_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: 65227
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:66 original size:12 final size:12
Alignment explanation
Indices: 51--185 Score: 93
Period size: 12 Copynumber: 11.2 Consensus size: 12
41 AATAAAAATA
*
51 ATAATATATAAC
1 ATAATATATAAT
*
63 ATAATA-ATTAT
1 ATAATATATAAT
*
74 ATACATA-ATATT
1 ATA-ATATATAAT
*
86 ATAATATATAGT
1 ATAATATATAAT
*
98 ATATATATAGACTAT
1 ATA-ATATATA--AT
113 ATAATATATAAT
1 ATAATATATAAT
125 ATAA-A-ATAAT
1 ATAATATATAAT
135 AT-ATATA-ATAT
1 ATAATATATA-AT
146 ATACACTATATAAT
1 ATA-A-TATATAAT
* *
160 ATACTATATAAA
1 ATAATATATAAT
*
172 ATAATAGATAAT
1 ATAATATATAAT
184 AT
1 AT
186 GGTATAATAA
Statistics
Matches: 98, Mismatches: 13, Indels: 24
0.73 0.10 0.18
Matches are distributed among these distances:
9 1 0.01
10 9 0.09
11 15 0.15
12 46 0.47
13 7 0.07
14 15 0.15
15 5 0.05
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:76 original size:2 final size:2
Alignment explanation
Indices: 71--169 Score: 63
Period size: 2 Copynumber: 52.0 Consensus size: 2
61 ACATAATAAT
* *
71 TA TA TA CA TA -A TA T- TA TA -A TA TA TA GTA TA TA TA TA GA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
*
112 TA TA -A TA TA TA -A TA TA -A AA TA -A TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
149 CA CTA TA TA -A TA TA CTA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA
170 AAATAATAGA
Statistics
Matches: 77, Mismatches: 7, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
1 9 0.12
2 62 0.81
3 6 0.08
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (2 bp):
TA
Found at i:100 original size:7 final size:7
Alignment explanation
Indices: 47--185 Score: 101
Period size: 7 Copynumber: 19.7 Consensus size: 7
37 AGTAAATAAA
47 AATA-AT
1 AATATAT
53 AATATAT
1 AATATAT
*
60 AACATAAT
1 AATAT-AT
68 AAT-TAT
1 AATATAT
*
74 -ATACAT
1 AATATAT
80 AATATTAT
1 AATA-TAT
88 AATATAT
1 AATATAT
*
95 AGTATAT
1 AATATAT
*
102 -ATATAG
1 AATATAT
*
108 ACTATAT
1 AATATAT
115 AATATAT
1 AATATAT
*
122 AATATAA
1 AATATAT
129 AATA-AT
1 AATATAT
135 -ATATAT
1 AATATAT
141 AATATAT
1 AATATAT
148 ACACTATAT
1 A-A-TATAT
157 AATATACT
1 AATATA-T
*
165 ATATAAAAT
1 A-AT-ATAT
*
174 AATAGAT
1 AATATAT
181 AATAT
1 AATAT
186 GGTATAATAA
Statistics
Matches: 105, Mismatches: 15, Indels: 25
0.72 0.10 0.17
Matches are distributed among these distances:
5 5 0.05
6 15 0.14
7 57 0.54
8 16 0.15
9 10 0.10
10 2 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:101 original size:9 final size:9
Alignment explanation
Indices: 48--185 Score: 72
Period size: 9 Copynumber: 14.8 Consensus size: 9
38 GTAAATAAAA
48 ATAATAATAT
1 ATAAT-ATAT
*
58 ATAACATA-
1 ATAATATAT
66 ATAAT-TAT
1 ATAATATAT
74 ATACATAATATT
1 ATA-AT-ATA-T
86 ATAATATAT
1 ATAATATAT
95 AGT-ATATAT
1 A-TAATATAT
*
104 ATAGA-CTAT
1 ATA-ATATAT
113 AT-A-ATAT
1 ATAATATAT
*
120 ATAATATAAA
1 ATAATAT-AT
130 ATAATATAT
1 ATAATATAT
139 ATAATATAT
1 ATAATATAT
*
148 ACACTATATAAT
1 ATA--ATAT-AT
*
160 ATACTATAT
1 ATAATATAT
* *
169 AAAATAATAG
1 ATAAT-ATAT
179 ATAATAT
1 ATAATAT
186 GGTATAATAA
Statistics
Matches: 100, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
7 8 0.08
8 9 0.09
9 40 0.40
10 27 0.27
11 8 0.08
12 8 0.08
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (9 bp):
ATAATATAT
Found at i:1239 original size:32 final size:32
Alignment explanation
Indices: 1198--1275 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
1188 TTTTTTTTCC
1198 TGTTTTAATTATGAATATATATTTATAAGACA
1 TGTTTTAATTATGAATATATATTTATAAGACA
1230 TGTTTTAATTATGAATATATATTTATAAGACA
1 TGTTTTAATTATGAATATATATTTATAAGACA
1262 TGTTTTAATTATGA
1 TGTTTTAATTATGA
1276 TAATTTCACG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (32 bp):
TGTTTTAATTATGAATATATATTTATAAGACA
Found at i:1241 original size:18 final size:18
Alignment explanation
Indices: 1220--1273 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1210 GAATATATAT
1220 TTATAAGACATGTTTTAA
1 TTATAAGACATGTTTTAA
* * *
1238 TTAT--GA-AT-ATATAT
1 TTATAAGACATGTTTTAA
1252 TTATAAGACATGTTTTAA
1 TTATAAGACATGTTTTAA
1270 TTAT
1 TTAT
1274 GATAATTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
14 7 0.27
15 2 0.08
16 4 0.15
17 2 0.08
18 11 0.42
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (18 bp):
TTATAAGACATGTTTTAA
Found at i:5027 original size:12 final size:12
Alignment explanation
Indices: 5010--5035 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5000 TAGCTAAAGC
5010 ATACAAAAGTTG
1 ATACAAAAGTTG
5022 ATACAAAAGTTG
1 ATACAAAAGTTG
5034 AT
1 AT
5036 GTTCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (12 bp):
ATACAAAAGTTG
Found at i:11031 original size:19 final size:18
Alignment explanation
Indices: 10989--11031 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
10979 CGACCGTTAA
* *
10989 TATTTTTTATTGTATTTT
1 TATTTTTTATCGTATCTT
*
11007 TCTTTTTATATCGTATCTT
1 TATTTTT-TATCGTATCTT
11026 TATTTT
1 TATTTT
11032 ATTTTCTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72
Consensus pattern (18 bp):
TATTTTTTATCGTATCTT
Found at i:14707 original size:17 final size:18
Alignment explanation
Indices: 14685--14725 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
14675 TGTTATAATT
* *
14685 ATAAAAGTTCAAA-AAGC
1 ATAAAAGTTAAAATAAAC
14702 ATAAAAGTTAAAATAAAC
1 ATAAAAGTTAAAATAAAC
14720 ATAAAA
1 ATAAAA
14726 TTACTACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (18 bp):
ATAAAAGTTAAAATAAAC
Found at i:15376 original size:20 final size:21
Alignment explanation
Indices: 15351--15390 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
15341 ATTTTATTGA
15351 TTGTGTCCA-CTTGAAATTTT
1 TTGTGTCCATCTTGAAATTTT
15371 TTGTGTCCATCTTGAAATTT
1 TTGTGTCCATCTTGAAATTT
15391 GGGTTGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (21 bp):
TTGTGTCCATCTTGAAATTTT
Found at i:19376 original size:237 final size:237
Alignment explanation
Indices: 18948--19426 Score: 636
Period size: 237 Copynumber: 2.0 Consensus size: 237
18938 AATAGAGATC
* **
18948 ACCATCGCAAGAGGTCAGATAAAGAGGGCTGCTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
1 ACCATCGCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
* * ** * * *
19013 TTGAAGGAAGCAGAAAGCCGAGAGAGGAGTTTCCACGGGAAGAAATATAGATATGAGGATCAAGA
66 TTGAAGGAAGCAGAAAGCCGAGAGAAGAATCGCCACAGGAAGAAATACAAATATGAGGATCAAGA
* * ** **
19078 TGATGTTAAGAGGAACCATGACAAATCTAAGCGTGATAAATATTCTACTCAAGCTCCACGAAGTC
131 TGATATTAAAAGGAACCATGACAAATCTAAGCCAGATAAATATTCTACTCAAGCTCCACGAAGGA
* * * *
19143 TTGATGCTGATAAAAATCATGAAAAAGTTGGACCAGCTTCTG
196 TTGAAGCAGATAAAAATCAAGAAAAAGATGGACCAGCTTCTG
* *
19185 ACCATCTCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAATTGAGTCAGACTCAGAAGATGAA
1 ACCATCGCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
* * * * * **
19250 TTGAAGGAAGCAGAGAGTCGAGAGAAGAATCGCCGCAGGCAGAAATACAAATATGATGATCGTGA
66 TTGAAGGAAGCAGAAAGCCGAGAGAAGAATCGCCACAGGAAGAAATACAAATATGAGGATCAAGA
* * *
19315 TGATATTAAAAGGAACCATGATAAGTCTAAGCACAG-TAAATATTCTTCTCAAGCTCCACGAAGG
131 TGATATTAAAAGGAACCATGACAAATCTAAGC-CAGATAAATATTCTACTCAAGCTCCACGAAGG
* *
19379 ATTGAAGCAGATAAAAATCAAGAGAAAGATGGACCATCTTCTG
195 ATTGAAGCAGATAAAAATCAAGAAAAAGATGGACCAGCTTCTG
19422 ACCAT
1 ACCAT
19427 AGAGACATTG
Statistics
Matches: 207, Mismatches: 34, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
237 206 1.00
238 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (237 bp):
ACCATCGCAAGACGTCAGATAAAGAGGGCAACTATCGCAGAACTGAGTCAGACTCAGAAGATGAA
TTGAAGGAAGCAGAAAGCCGAGAGAAGAATCGCCACAGGAAGAAATACAAATATGAGGATCAAGA
TGATATTAAAAGGAACCATGACAAATCTAAGCCAGATAAATATTCTACTCAAGCTCCACGAAGGA
TTGAAGCAGATAAAAATCAAGAAAAAGATGGACCAGCTTCTG
Found at i:20668 original size:21 final size:21
Alignment explanation
Indices: 20644--20696 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
20634 TCGGATTTCA
*
20644 ATCCGATCTGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
20665 ATCCGATCCGGATCGGTTTTT
1 ATCCGATCCGGATCGGTTTTT
20686 ATCCGATCCGG
1 ATCCGATCCGG
20697 TTTTTTCCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.36
Consensus pattern (21 bp):
ATCCGATCCGGATCGGTTTTT
Found at i:20810 original size:15 final size:15
Alignment explanation
Indices: 20792--20847 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
20782 TAACCGGTTT
20792 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
20807 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
20824 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
20839 CGATTTTAA
1 CGGTTTTAA
20848 TATTCCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:20820 original size:17 final size:17
Alignment explanation
Indices: 20795--20845 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
20785 CCGGTTTCGG
20795 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
20812 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
20827 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
20844 TT
1 TT
20846 AATATTCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:21243 original size:13 final size:13
Alignment explanation
Indices: 21222--21276 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
21212 AAGTTCGATA
*
21222 AATTCAAATACTT
1 AATTGAAATACTT
21235 AATTGAAATACTT
1 AATTGAAATACTT
* *
21248 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
21262 AATTGAAATACTT
1 AATTGAAATACTT
21275 AA
1 AA
21277 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:21307 original size:33 final size:33
Alignment explanation
Indices: 21262--21360 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
21252 AACTCAACAT
* * *
21262 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
21295 AATTCAAATACTTAAAAACTTCGAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
21328 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
21360 A
1 A
21361 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 11 0.18
33 50 0.82
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:21379 original size:21 final size:21
Alignment explanation
Indices: 21355--21394 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
21345 ACTTCAAGTT
21355 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
21376 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
21395 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:23708 original size:11 final size:12
Alignment explanation
Indices: 23687--23726 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
23677 TCCGGATAAA
23687 AACCGGTTTTTT
1 AACCGGTTTTTT
23699 AACCGGTTTTTTT
1 AACCGG-TTTTTT
23712 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
23726 A
1 A
23727 TTCGGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 6 0.24
15 6 0.24
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:23717 original size:15 final size:14
Alignment explanation
Indices: 23686--23725 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
23676 TTCCGGATAA
23686 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
23699 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
23712 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
23726 ATTCGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:25013 original size:31 final size:33
Alignment explanation
Indices: 24946--25031 Score: 133
Period size: 32 Copynumber: 2.7 Consensus size: 33
24936 GTTCAGGTAT
24946 TAAAATGAAACAAAAAGTTAAC-ATCGTGATAC
1 TAAAATGAAACAAAAAGTTAACGATCGTGATAC
24978 TAAAATGAAACAAAAAGTTAACGA-CGTG-TAC
1 TAAAATGAAACAAAAAGTTAACGATCGTGATAC
* *
25009 TAAAATGAGACAAAAAGTAAACG
1 TAAAATGAAACAAAAAGTTAACG
25032 TTAGGTACCG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
31 24 0.47
32 26 0.51
33 1 0.02
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.19
Consensus pattern (33 bp):
TAAAATGAAACAAAAAGTTAACGATCGTGATAC
Found at i:27776 original size:45 final size:45
Alignment explanation
Indices: 27712--27805 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
27702 AATCCGTCCA
27712 TCGTGACTTAGTCCTCGGTTAAGTAGCGAATCTAAGATATTAAAC
1 TCGTGACTTAGTCCTCGGTTAAGTAGCGAATCTAAGATATTAAAC
27757 TCGTGACTTAGTCCTCGGTTAAGTAGCGAATCTAAGATATTAAAC
1 TCGTGACTTAGTCCTCGGTTAAGTAGCGAATCTAAGATATTAAAC
27802 TCGT
1 TCGT
27806 AATTAACTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (45 bp):
TCGTGACTTAGTCCTCGGTTAAGTAGCGAATCTAAGATATTAAAC
Found at i:31539 original size:38 final size:36
Alignment explanation
Indices: 31504--31573 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
31494 TACAAATTGT
*
31504 AAAATATTTATATATTTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAATTAAATTC
* *
31541 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
31574 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 13 0.43
37 17 0.57
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:36000 original size:17 final size:18
Alignment explanation
Indices: 35959--36004 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
35949 ATATATAGTG
35959 CAGAAAAACAGTTTTGGT
1 CAGAAAAACAGTTTTGGT
35977 CAGAAAAACAGTTTTGGT
1 CAGAAAAACAGTTTTGGT
* *
35995 TAAAAAAACA
1 CAGAAAAACA
36005 TTGAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (18 bp):
CAGAAAAACAGTTTTGGT
Found at i:36115 original size:16 final size:16
Alignment explanation
Indices: 36094--36131 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
36084 TTTACTTTCT
36094 TTGATTTTATCTTCCC
1 TTGATTTTATCTTCCC
36110 TTGATTTTATCTTCCC
1 TTGATTTTATCTTCCC
36126 TTGATT
1 TTGATT
36132 AATCCTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.13, C:0.21, G:0.08, T:0.58
Consensus pattern (16 bp):
TTGATTTTATCTTCCC
Found at i:39545 original size:20 final size:19
Alignment explanation
Indices: 39517--39572 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
39507 CAAAAACACA
* *
39517 TCTTGGTATCGATACTAGCC
1 TCTTAGTATCGATACCA-CC
39537 TCTTAGTATCGATACCACC
1 TCTTAGTATCGATACCACC
*
39556 CCTTTAGTATCGATACC
1 TC-TTAGTATCGATACC
39573 CTCTTAAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (19 bp):
TCTTAGTATCGATACCACC
Found at i:48915 original size:90 final size:90
Alignment explanation
Indices: 48794--48971 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
48784 TAATCTCGAA
* * * * *
48794 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
48859 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
48884 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
48949 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
48972 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:49442 original size:2 final size:2
Alignment explanation
Indices: 49435--49505 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
49425 TTGTTTTGTT
49435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
49477 TA TA TA TA TA TA TG TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49506 GTATGATTGG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49607 original size:25 final size:26
Alignment explanation
Indices: 49560--49626 Score: 109
Period size: 25 Copynumber: 2.6 Consensus size: 26
49550 TCGAGACCAC
49560 AAGCTTAGAAAAGCTAGATATAGTGA
1 AAGCTTAGAAAAGCTAGATATAGTGA
*
49586 AAGCTTAG-AAATCTAGATATAGTGA
1 AAGCTTAGAAAAGCTAGATATAGTGA
*
49611 AAGCTTAGTAAAGCTA
1 AAGCTTAGAAAAGCTA
49627 TATTGGTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 24 0.63
26 14 0.37
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (26 bp):
AAGCTTAGAAAAGCTAGATATAGTGA
Found at i:50318 original size:29 final size:29
Alignment explanation
Indices: 50276--50334 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
50266 ATTTTCACCT
50276 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
50305 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
50334 A
1 A
50335 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:54996 original size:29 final size:29
Alignment explanation
Indices: 54954--55012 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54944 ATTTTCACCT
54954 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
54983 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
55012 A
1 A
55013 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:58783 original size:7 final size:7
Alignment explanation
Indices: 58771--58804 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
58761 ATAATACACT
58771 TTTTTTA
1 TTTTTTA
58778 TTTTTTA
1 TTTTTTA
58785 -TTTTTA
1 TTTTTTA
58791 -TTTTTA
1 TTTTTTA
58797 TTTTTTA
1 TTTTTTA
58804 T
1 T
58805 AATTACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:58788 original size:6 final size:6
Alignment explanation
Indices: 58772--58801 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
58762 TAATACACTT
58772 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTT
58802 TATAATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:59180 original size:16 final size:16
Alignment explanation
Indices: 59159--59189 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59149 ACTTTCTTTA
59159 ATTTTATCTTCCCTTG
1 ATTTTATCTTCCCTTG
59175 ATTTTATCTTCCCTT
1 ATTTTATCTTCCCTT
59190 TATTAATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTATCTTCCCTTG
Found at i:60080 original size:24 final size:24
Alignment explanation
Indices: 59990--60075 Score: 106
Period size: 24 Copynumber: 3.6 Consensus size: 24
59980 AACAATTAAG
59990 GGAATTATCTTTTGCAATTTATTA
1 GGAATTATCTTTTGCAATTTATTA
*
60014 GGAATTATCTTTTGCAATTTCTTTA
1 GGAATTATCTTTTGCAATTT-ATTA
*
60039 -CAATTTATC-TTTGC-ATTTATTA
1 GGAA-TTATCTTTTGCAATTTATTA
60061 GGAATTATCTCTTTG
1 GGAATTATCT-TTTG
60076 GATTTTTAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
22 8 0.15
23 6 0.11
24 31 0.58
25 8 0.15
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
GGAATTATCTTTTGCAATTTATTA
Found at i:62670 original size:20 final size:20
Alignment explanation
Indices: 62642--62693 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
62632 TGCATTCTCG
*
62642 GTATTGATAC-CAACCCTGTA
1 GTATCGATACTCAACCCTG-A
* *
62662 GTATCGATACTCAAGCGTGA
1 GTATCGATACTCAACCCTGA
62682 GTATCGATACTC
1 GTATCGATACTC
62694 CCTTGAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (20 bp):
GTATCGATACTCAACCCTGA
Found at i:62887 original size:7 final size:7
Alignment explanation
Indices: 62875--62903 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
62865 ATGAATTTTC
62875 TTTATAT
1 TTTATAT
62882 TTTATAT
1 TTTATAT
62889 TTTATAT
1 TTTATAT
62896 TTTATAT
1 TTTATAT
62903 T
1 T
62904 GATGATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATAT
Done.