Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004943.1 Hibiscus syriacus cultivar Beakdansim tig00011114_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: 51100
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4102 original size:21 final size:20
Alignment explanation
Indices: 4077--4130 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
4067 TTAGATGAAG
*
4077 TAGTATTGATACTGATTAAA
1 TAGTATTGATACCGATTAAA
* **
4097 TCAGTATCGATACCGATTAGG
1 T-AGTATTGATACCGATTAAA
4118 TAGTATTGATACC
1 TAGTATTGATACC
4131 ATGATAAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (20 bp):
TAGTATTGATACCGATTAAA
Found at i:4729 original size:59 final size:59
Alignment explanation
Indices: 4650--4809 Score: 241
Period size: 59 Copynumber: 2.7 Consensus size: 59
4640 ATGGCACTAA
** * **
4650 GTGTGC-AAAATGTTAAGAAATTCAAACTAAGTGTATGAATTTCTGTATTGGCCACTTT
1 GTGTGCTAAAATACTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGCCACTTT
* *
4708 GTGTGCTAAAATACTAAGAAATTCATACTAAGTGAATGAATTTCCATATTGGGCACTTT
1 GTGTGCTAAAATACTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGCCACTTT
*
4767 ATGTGCTAAAATACTAAGAAATTCATACTAAGTGTATGAATTT
1 GTGTGCTAAAATACTAAGAAATTCATACTAAGTGTATGAATTT
4810 TCGTATGGGC
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 6 0.07
59 86 0.93
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (59 bp):
GTGTGCTAAAATACTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGCCACTTT
Found at i:5294 original size:68 final size:68
Alignment explanation
Indices: 5103--5335 Score: 297
Period size: 68 Copynumber: 3.4 Consensus size: 68
5093 AATTTAACAT
* * * * * ** *
5103 AAATGTCTCATTTATGCCAGATAGATGAAATGCTAAGTGCCTTTGAGGCCTAACTATATATATGA
1 AAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGA
*
5168 CAG
66 TAG
5171 AAATGTGT-AATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTG
1 AAATGTGTCAA-TTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTG
5235 ATAG
65 ATAG
* * * *
5239 AAATGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAGACCTAACTGTGCAATTGG
1 AAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGA
5304 TAG
66 TAG
* ** *
5307 AAAGGTACCAATTATGCCAGCTAGATGAA
1 AAATGTGTCAATTATGCCAGTTAGATGAA
5336 CGATTAAATA
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
67 1 0.01
68 142 0.98
69 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (68 bp):
AAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGA
TAG
Found at i:5352 original size:68 final size:68
Alignment explanation
Indices: 5182--5353 Score: 173
Period size: 68 Copynumber: 2.5 Consensus size: 68
5172 AATGTGTAAT
* * * * * * * * **
5182 TTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGATAGAAATGTGT
1 TTATGCCAGCTAGATGAAAGACTAAATACATTTGAGACCTAACTGTGCAATTGATAGAAAGGTAC
5247 CAA
66 CAA
* * * * * * *
5250 TTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAGACCTAACTGTGCAATTGGTAGAAAGGTAC
1 TTATGCCAGCTAGATGAAAGACTAAATACATTTGAGACCTAACTGTGCAATTGATAGAAAGGTAC
5315 CAA
66 CAA
* *
5318 TTATGCCAGCTAGATGAACGATTAAATACATTTGAG
1 TTATGCCAGCTAGATGAAAGACTAAATACATTTGAG
5354 TAAGAGAATA
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 89 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
TTATGCCAGCTAGATGAAAGACTAAATACATTTGAGACCTAACTGTGCAATTGATAGAAAGGTAC
CAA
Found at i:5425 original size:81 final size:81
Alignment explanation
Indices: 5287--5681 Score: 562
Period size: 81 Copynumber: 4.9 Consensus size: 81
5277 GCCTTTGAGA
* * * **
5287 CCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGCTAGATGAACGATTAAATACATTTG
1 CCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
*
5352 AGTAAGAGAATAATAG
66 AGTAAAAGAATAATAG
* * *
5368 CCTAACTGTGCAATTAGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGCTAAATGCCGTTG
1 CCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
*
5433 AGTAAAACAATAATAG
66 AGTAAAAGAATAATAG
* * *
5449 CATAACTGTGCAATTGGTAGAAAGGTACCAATTATGCTAGTTAGATGAACGGTTAAATACCGTTG
1 CCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
5514 AGTAAAAGAATAATAG
66 AGTAAAAGAATAATAG
* * * *
5530 TCAAACTGTGCAATTGGTAGAAA-AGTACCAATTATG-CAGTTAGATAAACGGTTAAATACTGTT
1 CCTAACTGTGCAATTGGTAGAAAGA-TACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
* * *
5593 GACTAAAAGAATATTGG
65 GAGTAAAAGAATAATAG
*
5610 CCTAACTGTGCAATTGGTAGAAA-AGTATCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
1 CCTAACTGTGCAATTGGTAGAAAGA-TACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
5674 GAGTAAAA
65 GAGTAAAA
5682 CACATTAGAA
Statistics
Matches: 279, Mismatches: 33, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
80 71 0.25
81 208 0.75
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (81 bp):
CCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTG
AGTAAAAGAATAATAG
Found at i:5561 original size:162 final size:161
Alignment explanation
Indices: 5289--5681 Score: 581
Period size: 161 Copynumber: 2.4 Consensus size: 161
5279 CTTTGAGACC
* * **
5289 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGCTAGATGAACGATTAAATACATTTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
* * *
5354 TAAGAGAATAATAGCCTAACTGTGCAATTAGTAGAAAGATACCAATTATGCCAGTTAGATGAACG
66 TAAAAGAATAATAGCCAAACTGTGCAATTAGTAGAAAGATACCAATTATG-CAGTTAGATAAACG
* *
5419 GCTAAATGCCGTTGAGTAAAACAATAATAGCA
130 GCTAAATACCGTTGACTAAAACAATAATAGCA
*
5451 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCTAGTTAGATGAACGGTTAAATACCGTTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
* *
5516 TAAAAGAATAATAGTCAAACTGTGCAATTGGTAGAAA-AGTACCAATTATGCAGTTAGATAAACG
66 TAAAAGAATAATAGCCAAACTGTGCAATTAGTAGAAAGA-TACCAATTATGCAGTTAGATAAACG
* * * * * *
5580 GTTAAATACTGTTGACTAAAAGAATATTGGCC
130 GCTAAATACCGTTGACTAAAACAATAATAGCA
* *
5612 TAACTGTGCAATTGGTAGAAAAGTATCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
5677 TAAAA
66 TAAAA
5682 CACATTAGAA
Statistics
Matches: 209, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
161 105 0.50
162 104 0.50
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (161 bp):
TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
TAAAAGAATAATAGCCAAACTGTGCAATTAGTAGAAAGATACCAATTATGCAGTTAGATAAACGG
CTAAATACCGTTGACTAAAACAATAATAGCA
Found at i:5773 original size:59 final size:59
Alignment explanation
Indices: 5697--5839 Score: 243
Period size: 59 Copynumber: 2.4 Consensus size: 59
5687 TAGAAAAGTG
* * *
5697 GTGTATGTATTTCCGTATTGGGCACTTTGTGTGCTAAAATACTAAGAAATTCATACTAA
1 GTGTATGAATTTTCGTATTGGGCACTTTGTATGCTAAAATACTAAGAAATTCATACTAA
*
5756 GTGTATGAATTTTCGTATTGGTCACTTTGTATGCTAAAATACTAAGAAATTCATACTAA
1 GTGTATGAATTTTCGTATTGGGCACTTTGTATGCTAAAATACTAAGAAATTCATACTAA
5815 GTGTATGAATTTTCGTA-TGGGCACT
1 GTGTATGAATTTTCGTATTGGGCACT
5840 ACGTGTACGA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 7 0.09
59 72 0.91
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (59 bp):
GTGTATGAATTTTCGTATTGGGCACTTTGTATGCTAAAATACTAAGAAATTCATACTAA
Found at i:6209 original size:68 final size:68
Alignment explanation
Indices: 6097--6315 Score: 321
Period size: 68 Copynumber: 3.2 Consensus size: 68
6087 AAAGATTAAT
* * * * * *
6097 AGGCCTAACTGTGCATTTAAAAGAAAGATATCATTTATGTCAGTTAGATGAAATGCTAAGTACCT
1 AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
6162 CTG
66 TTG
* * *
6165 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTACGTGCCT
1 AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6230 TTG
66 TTG
* * *
6233 AGGCCTAACTTTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6298 TTG
66 TTG
6301 AGGCCTAACTGTGCA
1 AGGCCTAACTGTGCA
6316 ATTGGTAGAA
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 135 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:6352 original size:68 final size:68
Alignment explanation
Indices: 6097--6341 Score: 303
Period size: 68 Copynumber: 3.6 Consensus size: 68
6087 AAAGATTAAT
* * * * * * * * *
6097 AGGCCTAACTGTGCATTTAAAAGAAAGATATCATTTATGTCAGTTAGATGAAATGCTAAGTACCT
1 AGGCCTAACTGTGCAATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
6162 CTG
66 TTG
* * *
6165 AGGCCTAACTGTGC-ATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTACGTGCC
1 AGGCCTAACTGTGCAAT-TGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
6229 TTTG
65 TTTG
* *
6233 AGGCCTAACTTTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
6298 TTG
66 TTG
* **
6301 AGGCCTAACTGTGCAATTGGTAGAAAAGGTACCAATTATGC
1 AGGCCTAACTGTGCAATTGATAG-AAAGGTGTCAATTATGC
6342 TGCTAGATGA
Statistics
Matches: 154, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 1 0.01
68 137 0.89
69 16 0.10
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCAATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:6370 original size:68 final size:68
Alignment explanation
Indices: 6097--6370 Score: 221
Period size: 68 Copynumber: 4.0 Consensus size: 68
6087 AAAGATTAAT
* * * * * * * * * *
6097 AGGCCTAACTGTGCATTTAAAAGAAAGATATCATTTATGTCAGTTAGATGAAATGCTAAGTACC-
1 AGGCCTAACTGTGCAATTGATAGAAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAATACCA
6161 TCTG
66 T-TG
* ** * * ** *
6165 AGGCCTAACTGTGC-ATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTACGTGCC
1 AGGCCTAACTGTGCAAT-TGATAGAAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAATACC
*
6229 TTTG
65 ATTG
* * ** * * * *
6233 AGGCCTAACTTTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCAATTGATAGAAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAATACCA
6298 TTG
66 TTG
* * * *
6301 AGGCCTAACTGTGCAATTGGTAGAAAAGGTACCAATTATG-CTGCTAGATGAACGGTTAAATACC
1 AGGCCTAACTGTGCAATTGATAG-AAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAATACC
6365 ATTG
65 ATTG
6369 AG
1 AG
6371 TAAAAGAATA
Statistics
Matches: 176, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
67 1 0.01
68 159 0.90
69 16 0.09
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCAATTGATAGAAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAATACCA
TTG
Found at i:6370 original size:136 final size:136
Alignment explanation
Indices: 6097--6370 Score: 309
Period size: 136 Copynumber: 2.0 Consensus size: 136
6087 AAAGATTAAT
* * *
6097 AGGCCTAACTGTGCATTTAAAAGAAAGATATCATTTATGTCAGTTAGATGAAATGCTAAGTACCT
1 AGGCCTAACTGTGCATTTAAAAGAAAGATATCAATTATGCCAGTTAGATGAAAGGCTAAGTACCT
** * * ** *
6162 CTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTACGTG
66 CTGAGGCCTAACTGTGCATATGACAGAAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAATA
*
6227 CCTTTG
131 CCATTG
* * * * * *
6233 AGGCCTAACTTTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTAAAAGAAAGATATCAATTATGCCAGTTAGATGAAAGGCTAAGTACCT
* ** * * *
6298 TTGAGGCCTAACTGTGCA-ATTGGTAGAAAAGGTACCAATTATG-CTGCTAGATGAACGGTTAAA
66 CTGAGGCCTAACTGTGCATA-TGACAG-AAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAA
6361 TACCATTG
129 TACCATTG
6369 AG
1 AG
6371 TAAAAGAATA
Statistics
Matches: 113, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
135 1 0.01
136 99 0.88
137 13 0.12
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (136 bp):
AGGCCTAACTGTGCATTTAAAAGAAAGATATCAATTATGCCAGTTAGATGAAAGGCTAAGTACCT
CTGAGGCCTAACTGTGCATATGACAGAAAGGTACCAATTATGCCAGCTAGATGAAAGGCTAAATA
CCATTG
Found at i:6445 original size:81 final size:81
Alignment explanation
Indices: 6303--6704 Score: 533
Period size: 81 Copynumber: 5.0 Consensus size: 81
6293 TGCCTTTGAG
* * * *
6303 GCCTAACTGTGCAATTGGTAGAAAAGGTACCAATTATG-CTGCTAGATGAACGGTTAAATACCAT
1 GCCTAACTGTGCAATTGGTAG-AAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
6367 TGAGTAAAAGAATAATA
65 TGAGTAAAAGAATAATA
* * * * *
6384 ACATAATTGTGCAATTAGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCATT
1 GCCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
**
6449 GAGTAAACCAATAATA
66 GAGTAAAAGAATAATA
* * *
6465 GCCTAACTGTGCAATTGGTAGAAAGATTCCAATTATGCCAGTTAGATGAAAGGTTAAATATCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
*
6530 GAGTAAAATAATAATA
66 GAGTAAAAGAATAATA
* * * * *
6546 GTCTAACTGTGCAATTGGTAGAAA-AGTACCAATTACGCCAGTTATATGAA-AGTTAAATATCGT
1 GCCTAACTGTGCAATTGGTAGAAAGA-TACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
* *
6609 TGAGTAAAATAATAATG
65 TGAGTAAAAGAATAATA
* * *
6626 GCCTAACTATGCAATTGGTAGAAAGGTACCAATTAT-ACAGTTAGATGAACGGTTAAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
6690 GAGTAAAAGAATAAT
66 GAGTAAAAGAATAAT
6705 GGTTAAACAC
Statistics
Matches: 283, Mismatches: 34, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
79 11 0.04
80 101 0.36
81 171 0.60
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (81 bp):
GCCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTT
GAGTAAAAGAATAATA
Found at i:6719 original size:29 final size:29
Alignment explanation
Indices: 6676--6735 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
6666 TTAGATGAAC
* *
6676 GGTTAAATACCGTTGAGTAAAAGAATAAT
1 GGTTAAACACCGTTGAATAAAAGAATAAT
* *
6705 GGTTAAACACTGTTGAATAAAAGAATGAT
1 GGTTAAACACCGTTGAATAAAAGAATAAT
6734 GG
1 GG
6736 ATTAGTTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (29 bp):
GGTTAAACACCGTTGAATAAAAGAATAAT
Found at i:7790 original size:2 final size:2
Alignment explanation
Indices: 7783--7814 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7773 TTAAATTCAT
7783 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
7815 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9173 original size:18 final size:18
Alignment explanation
Indices: 9150--9186 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9140 TGCATTAAAT
9150 GGTCTATAAGAAAATGAC
1 GGTCTATAAGAAAATGAC
*
9168 GGTCTATGAGAAAATGAC
1 GGTCTATAAGAAAATGAC
9186 G
1 G
9187 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (18 bp):
GGTCTATAAGAAAATGAC
Found at i:9242 original size:32 final size:32
Alignment explanation
Indices: 9206--9291 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
9196 AAATGAAATA
9206 ATATATCACTGAAAAGTTTATGAAATAAAGTG
1 ATATATCACTGAAAAGTTTATGAAATAAAGTG
* * * *
9238 ATATATAATTGAAAAGTTTCTGAAATGAAGTG
1 ATATATCACTGAAAAGTTTATGAAATAAAGTG
9270 ATATATCACTGAAAAGTTTATG
1 ATATATCACTGAAAAGTTTATG
9292 TAATTGTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (32 bp):
ATATATCACTGAAAAGTTTATGAAATAAAGTG
Found at i:13662 original size:17 final size:17
Alignment explanation
Indices: 13628--13660 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13618 TTTTATTATA
13628 ATTATATAATTATATTT
1 ATTATATAATTATATTT
*
13645 ATTATTTAA-TATATTT
1 ATTATATAATTATATTT
13661 TACCTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATATAATTATATTT
Found at i:19229 original size:26 final size:27
Alignment explanation
Indices: 19187--19244 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
19177 ATGCATTTTC
* *
19187 TTTTTTACTTTAGTATATAT-TTTTAT
1 TTTTTTAATTTAGTATATATATATTAT
19213 TTTTTTAATATTA-TATATATATATTAT
1 TTTTTTAAT-TTAGTATATATATATTAT
19240 TTTTT
1 TTTTT
19245 ATTATCAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTTTTAATTTAGTATATATATATTAT
Found at i:19261 original size:2 final size:2
Alignment explanation
Indices: 19256--19310 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
19246 TTATCAGTTT
* * * *
19256 TA TA TA TA TA TA TA TA TA TA CTA TT TA TT TA TT TA TT TA T- TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
19298 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
19311 TATTTTTACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:19266 original size:38 final size:35
Alignment explanation
Indices: 19206--19317 Score: 133
Period size: 38 Copynumber: 3.1 Consensus size: 35
19196 TTAGTATATA
19206 TTTTTATTT-TTTTA-ATATTATATATATATATTAT
1 TTTTTATTTATTTTATATA-TATATATATATATTAT
19240 TTTTTATTATCAGTTTTATATATATATATATATATACTAT
1 TTTTTATT-T-A-TTTTATATATATATATATATAT--TAT
19280 TTATTTATTTA-TTTAT-TATATATATATATATTAT
1 TT-TTTATTTATTTTATATATATATATATATATTAT
19314 TTTT
1 TTTT
19318 ACTTTTTTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 17
0.80 0.00 0.20
Matches are distributed among these distances:
33 2 0.03
34 13 0.19
35 1 0.01
36 15 0.21
37 5 0.07
38 18 0.26
39 4 0.06
40 6 0.09
41 6 0.09
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (35 bp):
TTTTTATTTATTTTATATATATATATATATATTAT
Found at i:19327 original size:40 final size:37
Alignment explanation
Indices: 19206--19328 Score: 126
Period size: 40 Copynumber: 3.2 Consensus size: 37
19196 TTAGTATATA
*
19206 TTTTTATTT-TTTTAATAT-TATATATATA-TATTAT
1 TTTTTATTTATTTTTATATATATATATATATTATTAT
* *
19240 TTTTTATTATCAGTTTTATATATATATATATATATACTAT
1 TTTTTATT-T-ATTTTTATATATATATATATAT-TATTAT
*
19280 TTATTTATTTATTTATTATATATATATATATTATTTTTACT
1 TT-TTTATTTATTT-TTATATATATATATA-TATTATTA-T
19321 TTTTTATT
1 TTTTTATT
19329 ATTATTTTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
34 8 0.11
35 1 0.01
37 7 0.10
38 10 0.14
39 3 0.04
40 32 0.44
41 12 0.16
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (37 bp):
TTTTTATTTATTTTTATATATATATATATATTATTAT
Found at i:19343 original size:4 final size:4
Alignment explanation
Indices: 19277--19479 Score: 68
Period size: 4 Copynumber: 50.2 Consensus size: 4
19267 ATATATATAC
* *
19277 TATT TATT TATT TATT TATT ATATA TATA TATAT TA-T T-TT TACTT T-TT
1 TATT TATT TATT TATT TATT -TATT TATT TAT-T TATT TATT TA-TT TATT
* * * *
19325 TA-T TA-T TATTT TATT TATT TGTTT TATT TATA TATT T-TT TCTT CTTTT
1 TATT TATT TA-TT TATT TATT T-ATT TATT TATT TATT TATT TATT -TATT
* * * * * **
19373 TCTT TATT TTTT ATATT TATT TACT TA-C TATTT TATC T-TT GCTT TATT
1 TATT TATT TATT -TATT TATT TATT TATT TA-TT TATT TATT TATT TATT
* * *
19421 TATCT TATC T-TT TATT TAATT TGTT T-TT T-TT CATTT TCATT TAATT
1 TAT-T TATT TATT TATT T-ATT TATT TATT TATT TA-TT T-ATT T-ATT
19467 TATT TATT TATT T
1 TATT TATT TATT T
19480 CTTACCTTTT
Statistics
Matches: 153, Mismatches: 25, Indels: 42
0.70 0.11 0.19
Matches are distributed among these distances:
3 26 0.17
4 87 0.57
5 39 0.25
6 1 0.01
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:19393 original size:13 final size:12
Alignment explanation
Indices: 19277--19394 Score: 71
Period size: 13 Copynumber: 9.8 Consensus size: 12
19267 ATATATATAC
*
19277 TATTTATTTATT
1 TATTTATTTTTT
* *
19289 TATTTATTATATA
1 TATTTATT-TTTT
* * *
19302 TATATATATTAT
1 TATTTATTTTTT
*
19314 T-TTTACTTTTT
1 TATTTATTTTTT
*
19325 TA-TTATTATTT
1 TATTTATTTTTT
19336 TATTTATTTGTTT
1 TATTTATTT-TTT
* *
19349 TATTTATATATT
1 TATTTATTTTTT
*
19361 T-TTTCTTCTTTT
1 TATTTATT-TTTT
*
19373 TCTTTATTTTTT
1 TATTTATTTTTT
19385 ATATTTATTT
1 -TATTTATTT
19395 ACTTACTATT
Statistics
Matches: 79, Mismatches: 20, Indels: 13
0.71 0.18 0.12
Matches are distributed among these distances:
11 20 0.25
12 26 0.33
13 33 0.42
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (12 bp):
TATTTATTTTTT
Found at i:22538 original size:11 final size:11
Alignment explanation
Indices: 22519--22574 Score: 67
Period size: 11 Copynumber: 4.7 Consensus size: 11
22509 AGATTCAATC
*
22519 AGAACAAAAAG
1 AGAAAAAAAAG
22530 AGAAAAAAAAG
1 AGAAAAAAAAG
22541 AGAAAAAGCAAAG
1 AGAAAAA--AAAG
22554 AGAAAATAAAAAG
1 AG-AAA-AAAAAG
22567 AGAAAAAA
1 AGAAAAAA
22575 CAAAGGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
11 20 0.50
12 3 0.08
13 12 0.30
14 3 0.08
15 2 0.05
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:22555 original size:13 final size:12
Alignment explanation
Indices: 22526--22584 Score: 68
Period size: 13 Copynumber: 4.8 Consensus size: 12
22516 ATCAGAACAA
22526 AAAGAGAAAAA-
1 AAAGAGAAAAAC
22537 AAAGAGAAAAAGC
1 AAAGAGAAAAA-C
*
22550 AAAGAGAAAATAA
1 AAAGAGAAAA-AC
22563 AAAGAGAAAAAAC
1 AAAGAG-AAAAAC
22576 AAAG-GAAAA
1 AAAGAGAAAA
22585 TTGAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 15 0.36
12 1 0.02
13 21 0.50
14 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (12 bp):
AAAGAGAAAAAC
Found at i:22564 original size:26 final size:26
Alignment explanation
Indices: 22526--22585 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
22516 ATCAGAACAA
*
22526 AAAGAG-AAA-AAAAAGAGAAAAAGC
1 AAAGAGAAAATAAAAAGAGAAAAAAC
22550 AAAGAGAAAATAAAAAGAGAAAAAAC
1 AAAGAGAAAATAAAAAGAGAAAAAAC
22576 AAAG-GAAAAT
1 AAAGAGAAAAT
22586 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 6 0.18
25 9 0.27
26 18 0.55
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (26 bp):
AAAGAGAAAATAAAAAGAGAAAAAAC
Found at i:22768 original size:69 final size:69
Alignment explanation
Indices: 22657--22794 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
22647 GATTCAAACT
*
22657 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
22722 TCAA
66 TCAA
* * *
22726 ATGAGATTGATCAAGTATAATTATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
22791 TCAA
66 TCAA
22795 GAGAGAGACA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCA
TCAA
Found at i:23755 original size:32 final size:32
Alignment explanation
Indices: 23718--23837 Score: 129
Period size: 32 Copynumber: 3.8 Consensus size: 32
23708 GGAACAATGA
23718 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGAAGATTCAACATCAAATGTTG
** *
23750 GGGCAT-TGTTTTAGATTTAACATCAAATGTTG
1 GGGCATCT-TTGAAGATTCAACATCAAATGTTG
* * * *
23782 GGGTATTTTTTG-AGATTCAACATCGAATATTG
1 GGGCA-TCTTTGAAGATTCAACATCAAATGTTG
23814 GGGCATCTTTGGAA-ATTCAACATC
1 GGGCATCTTT-GAAGATTCAACATC
23838 CTGATGTAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
31 5 0.07
32 63 0.86
33 4 0.05
34 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (32 bp):
GGGCATCTTTGAAGATTCAACATCAAATGTTG
Found at i:24707 original size:106 final size:105
Alignment explanation
Indices: 24414--24688 Score: 399
Period size: 106 Copynumber: 2.6 Consensus size: 105
24404 ATATTGTGCC
* * ** * *
24414 ACTCGAGACAACACAAGTTCAACTCCACAACGAAGGGATGATTGGTTATCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
24479 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAG
*
24520 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTACC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-CC
* * * *
24585 AATTTCGGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAG
* *
24626 ACTCGAGACAACACAAGCTCAACTTCACAACGAA-GGAGCGGCTGGCTGTCAACAAACAATTTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGGCTGGTTGTCAACAAACAATTTC
24689 TTAGCTCCAG
Statistics
Matches: 153, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
105 4 0.03
106 149 0.97
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (105 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAG
Found at i:24745 original size:59 final size:59
Alignment explanation
Indices: 24661--24779 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
24651 CACAACGAAG
24661 GAGCGGCTGGCTGTCAACAAACAATTTCTTAGCTCCAGAGCCAATTTTAAGTTCACGGC
1 GAGCGGCTGGCTGTCAACAAACAATTTCTTAGCTCCAGAGCCAATTTTAAGTTCACGGC
24720 GAGCGGCTGGCTGTCAACAAACAATTTCTTAGCTCCAGAGCCAATTTTAAGTTCACGGC
1 GAGCGGCTGGCTGTCAACAAACAATTTCTTAGCTCCAGAGCCAATTTTAAGTTCACGGC
24779 G
1 G
24780 GAGGATATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (59 bp):
GAGCGGCTGGCTGTCAACAAACAATTTCTTAGCTCCAGAGCCAATTTTAAGTTCACGGC
Found at i:25168 original size:87 final size:89
Alignment explanation
Indices: 25024--25221 Score: 319
Period size: 87 Copynumber: 2.2 Consensus size: 89
25014 TTTTGGAACT
*
25024 AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATGAATTTAATCTCG
1 AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATAAATTTAATCTCG
25089 ATTGAGATAGTTTCCCTTGAAACA
66 ATTGAGATAGTTTCCCTTGAAACA
* * *
25113 AAATTTTGTCTCCCTTGA-A-ACATAAACATTGAAAATATTTCTCTTGAAATAAATTTTATCTCG
1 AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATAAATTTAATCTCG
* * *
25176 CTTGGGGTAGTTTCCCTTGAAACA
66 ATTGAGATAGTTTCCCTTGAAACA
25200 AAATTTTGTCTCCCTTGAGACA
1 AAATTTTGTCTCCCTTGAGACA
25222 GTTTCTCTTG
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
87 79 0.79
88 2 0.02
89 19 0.19
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (89 bp):
AAATTTTGTCTCCCTTGAGACACATAAACATTGAAAACATTTCCCTTGAAATAAATTTAATCTCG
ATTGAGATAGTTTCCCTTGAAACA
Found at i:25206 original size:37 final size:37
Alignment explanation
Indices: 25150--25338 Score: 114
Period size: 37 Copynumber: 5.4 Consensus size: 37
25140 ATTGAAAATA
* * * **
25150 TTTCTCTTGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCTCTTGAAACAAAATTTTATCTCCCTTGAGACAG
* *
25186 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAAATTTTATCTCCCTTGAGACAG
* * *
25223 TTTCTCTTGAAACATAA----A----CATTGAAAACA-
1 TTTCTCTTGAAACAAAATTTTATCTCCCTTG-AGACAG
** * ** *
25252 TTTC-CTTTGAAA-TTAATTTTGTCTATCTTGAGATAG
1 TTTCTC-TTGAAACAAAATTTTATCTCCCTTGAGACAG
* *
25288 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAAATTTTATCTCCCTTGAGACAG
25325 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
25339 TAAACCTTGA
Statistics
Matches: 115, Mismatches: 24, Indels: 27
0.69 0.14 0.16
Matches are distributed among these distances:
28 4 0.03
29 14 0.12
30 4 0.03
35 3 0.03
36 24 0.21
37 66 0.57
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAATTTTATCTCCCTTGAGACAG
Found at i:25247 original size:102 final size:101
Alignment explanation
Indices: 25126--25365 Score: 372
Period size: 102 Copynumber: 2.3 Consensus size: 101
25116 TTTTGTCTCC
* * * *
25126 CTTGAAACATAAACATTGAAAATATTTCTCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTC-CTTGAAATAAATTTTATCTAGCTTGAGATAGTTTCC
25191 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
65 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* * *
25228 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTATCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCC-TTGAAATAAATTTTATCTAGCTTGAGATAGTTTCC
25293 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
65 CTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
25330 CTTGAAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 CTTGAAACATAAACATTGAAAACATTT-CCTTGAAA
25366 CACAAAATAT
Statistics
Matches: 127, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
101 1 0.01
102 124 0.98
103 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (101 bp):
CTTGAAACATAAACATTGAAAACATTTCCTTGAAATAAATTTTATCTAGCTTGAGATAGTTTCCC
TTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:25458 original size:37 final size:37
Alignment explanation
Indices: 25407--25504 Score: 153
Period size: 36 Copynumber: 2.7 Consensus size: 37
25397 CGAGTTTTGT
* *
25407 GACAGTTTCTCTTGAAACAAAATCTAGTCTCTCTTGA
1 GACAGTTTCCCTTGAAACAAAATCTAGTCTCTCTTAA
* *
25444 GACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTAA
1 GACAGTTTCCCTTGAAACAAAATCTAGTCTCTCTTAA
25480 GACAGTTTCCCTTGAAACAAAATCT
1 GACAGTTTCCCTTGAAACAAAATCT
25505 TTGAATATCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 33 0.60
37 22 0.40
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (37 bp):
GACAGTTTCCCTTGAAACAAAATCTAGTCTCTCTTAA
Found at i:25576 original size:102 final size:103
Alignment explanation
Indices: 25412--25602 Score: 262
Period size: 102 Copynumber: 1.9 Consensus size: 103
25402 TTTGTGACAG
*
25412 TTTCTCTTGAAACAAAATCTAGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
1 TTTCTCTTGAAACAAAATCTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
25477 TAAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCT
66 TAAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCT
* * * * *
25515 TTTC-CTTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCT
1 TTTCTCTTGAAACAAAATCTAGTCTCCCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCT
* **
25577 CTTGAGACAGTTTCTTTTGAAACAAA
64 CTTAAGACAGTTTCCCTTGAAACAAA
25603 TTTTGTCCCT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
100 4 0.05
101 26 0.34
102 43 0.56
103 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (103 bp):
TTTCTCTTGAAACAAAATCTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
TAAGACAGTTTCCCTTGAAACAAAATCTTTGAATATCT
Found at i:25581 original size:37 final size:36
Alignment explanation
Indices: 25520--25638 Score: 168
Period size: 36 Copynumber: 3.3 Consensus size: 36
25510 TATCTTTTCC
* *
25520 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
*
25556 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
25593 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
25629 TTGAAACAAA
1 TTGAAACAAA
25639 AAAAAACCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.01
36 41 0.55
37 31 0.42
38 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:25649 original size:36 final size:36
Alignment explanation
Indices: 25575--25649 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
25565 AGTTTTGTCT
* ******
25575 CTCTTGAGACAGTTTCTTTTGAAACAAATTTTGTCC
1 CTCTTGAGACAGTTTCTCTTGAAACAAAAAAAAACC
25611 CTCTTGAGACAGTTTCTCTTGAAACAAAAAAAAACC
1 CTCTTGAGACAGTTTCTCTTGAAACAAAAAAAAACC
25647 CTC
1 CTC
25650 GAATTTGTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (36 bp):
CTCTTGAGACAGTTTCTCTTGAAACAAAAAAAAACC
Found at i:26886 original size:39 final size:40
Alignment explanation
Indices: 26843--26981 Score: 146
Period size: 39 Copynumber: 3.5 Consensus size: 40
26833 TTTACTTTAG
26843 TATATATTTTTATTTTTT-TAGATTATATATATATATATA
1 TATATATTTTTATTTTTTATAGATTATATATATATATATA
* *
26882 TATATATTATTT-TTTTATTATCAG-TTTTAT-TA-ATTTATA
1 TATATATT-TTTATTTT-TTAT-AGATTATATATATATATATA
* **
26921 TATATATTTACTATTTTTTATTTATTATATATATATATATA
1 TATATATTT-TTATTTTTTATAGATTATATATATATATATA
26962 TAT-TATTTTTACTTTTTTAT
1 TATATATTTTTA-TTTTTTAT
26982 TATTATTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
38 1 0.01
39 38 0.46
40 26 0.32
41 15 0.18
42 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (40 bp):
TATATATTTTTATTTTTTATAGATTATATATATATATATA
Found at i:26942 original size:7 final size:7
Alignment explanation
Indices: 26907--27015 Score: 50
Period size: 7 Copynumber: 15.4 Consensus size: 7
26897 TATTATCAGT
26907 TTTATTAA
1 TTTATT-A
26915 TTTA-TA
1 TTTATTA
*
26921 TATA-TA
1 TTTATTA
*
26927 TTTACTA
1 TTTATTA
*
26934 TTTTTTA
1 TTTATTA
26941 TTTATTA
1 TTTATTA
*
26948 TATA-TA
1 TTTATTA
*
26954 TATATATA
1 TTTAT-TA
26962 TATTATT-
1 T-TTATTA
*
26969 TTTACTTT
1 TTTA-TTA
26977 TTTATTA
1 TTTATTA
*
26984 TTATTTTA
1 TT-TATTA
26992 TTTATT-
1 TTTATTA
26998 TGTT-TTA
1 T-TTATTA
27005 TTTATATA
1 TTTAT-TA
27013 TTT
1 TTT
27016 TTTTCTTCTT
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
6 23 0.29
7 31 0.39
8 23 0.29
9 3 0.04
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (7 bp):
TTTATTA
Found at i:26959 original size:33 final size:34
Alignment explanation
Indices: 26907--26971 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
26897 TATTATCAGT
* *
26907 TTTATTAATTTATATATATATTTACTATTTTTTA
1 TTTATTAATATATATATATATATACTATTTTTTA
*
26941 TTTATT-ATATATATATATATATATTATTTTT
1 TTTATTAATATATATATATATATACTATTTTT
26972 ACTTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 22 0.79
34 6 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (34 bp):
TTTATTAATATATATATATATATACTATTTTTTA
Found at i:26988 original size:76 final size:77
Alignment explanation
Indices: 26830--26971 Score: 211
Period size: 76 Copynumber: 1.9 Consensus size: 77
26820 ATGCATTTTC
* *
26830 TTTT-TTACTTTAGTATATATTTTTATTTTTTTAGATTATATATATATATATATATATATTATTT
1 TTTTATTAATTTAGTATATATATTTATTTTTTTAGATTATATATATATATATATATATATTATTT
26894 TTTTATTATCAG
66 TTTTATTATCAG
*
26906 TTTTATTAATTTA-TATATATATTTACTATTTTTTA-TTTAT-TATATATATATATATATATTAT
1 TTTTATTAATTTAGTATATATATTTA-T-TTTTTTAGATTATATATATATATATATATATATTAT
26968 TTTT
64 TTTT
26972 ACTTTTTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
76 41 0.68
77 12 0.20
78 7 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (77 bp):
TTTTATTAATTTAGTATATATATTTATTTTTTTAGATTATATATATATATATATATATATTATTT
TTTTATTATCAG
Found at i:27003 original size:13 final size:12
Alignment explanation
Indices: 26969--27056 Score: 67
Period size: 13 Copynumber: 7.3 Consensus size: 12
26959 ATATATTATT
*
26969 TTTACTTTTTTA
1 TTTATTTTTTTA
*
26981 -TTATTATTTTA
1 TTTATTTTTTTA
26992 TTTATTTGTTTTA
1 TTTATTT-TTTTA
*
27005 TTTATATATTTT-
1 TTTAT-TTTTTTA
* *
27017 TTTCTTCTTTTTC
1 TTTATT-TTTTTA
27030 TTTATTTTTTTA
1 TTTATTTTTTTA
27042 --TATTTATTTTA
1 TTTATTT-TTTTA
27053 TTTA
1 TTTA
27057 CTACTTTATC
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 5 0.08
11 15 0.25
12 18 0.30
13 21 0.35
14 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:27011 original size:47 final size:48
Alignment explanation
Indices: 26937--27056 Score: 117
Period size: 47 Copynumber: 2.6 Consensus size: 48
26927 TTTACTATTT
* * *
26937 TTTA-TTTATTATATATA-TATATATATAT-TATTTTTACTT-TTTTAT-
1 TTTATTTTATTATATTTATTTTATTTATATAT-TTTTTACTTCTTTT-TC
* *
26982 TATTATTTTATT-TATTTGTTTTATTTATATATTTTTTTCTTCTTTTTC
1 T-TTATTTTATTATATTTATTTTATTTATATATTTTTTACTTCTTTTTC
*
27030 TTTATTTTTTTATATTTATTTTATTTA
1 TTTATTTTATTATATTTATTTTATTTA
27057 CTACTTTATC
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
45 1 0.02
46 7 0.11
47 33 0.54
48 20 0.33
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72
Consensus pattern (48 bp):
TTTATTTTATTATATTTATTTTATTTATATATTTTTTACTTCTTTTTC
Found at i:27014 original size:17 final size:16
Alignment explanation
Indices: 26934--27019 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 16
26924 ATATTTACTA
26934 TTTTTTATTTAT-TAT
1 TTTTTTATTTATATAT
* * * *
26949 ATATATATATATATAT
1 TTTTTTATTTATATAT
*
26965 TATTTTTACTTT-TTTAT
1 T-TTTTTA-TTTATATAT
* * *
26982 TATTAT-TTTATTTAT
1 TTTTTTATTTATATAT
26997 TTGTTTTATTTATATAT
1 TT-TTTTATTTATATAT
27014 TTTTTT
1 TTTTTT
27020 CTTCTTTTTC
Statistics
Matches: 51, Mismatches: 14, Indels: 11
0.67 0.18 0.14
Matches are distributed among these distances:
14 3 0.06
15 14 0.27
16 13 0.25
17 19 0.37
18 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (16 bp):
TTTTTTATTTATATAT
Found at i:27027 original size:24 final size:23
Alignment explanation
Indices: 26958--27041 Score: 75
Period size: 23 Copynumber: 3.6 Consensus size: 23
26948 TATATATATA
26958 TATATATTATTTTTACTTTTTTAT
1 TATATATT-TTTTTACTTTTTTAT
*
26982 TAT-TATTTTATTTATTTGTTTTATT
1 TATATATTTT-TTTACTT-TTTTA-T
*
27007 TATATATTTTTTT-CTTCTTT-T
1 TATATATTTTTTTACTTTTTTAT
* *
27028 TCTTTATTTTTTTA
1 TATATATTTTTTTA
27042 TATTTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 12 0.24
22 2 0.04
23 13 0.26
24 10 0.20
25 7 0.14
26 6 0.12
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (23 bp):
TATATATTTTTTTACTTTTTTAT
Found at i:27069 original size:37 final size:38
Alignment explanation
Indices: 26992--27069 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 38
26982 TATTATTTTA
* * *
26992 TTTATTTGTTTTATTTATATATTTTTTTCTTCTTTTTC
1 TTTATTTGTTTTATTTATATATTTTTTACTACTTTATC
27030 TTTATTT-TTTTATATT-TAT-TTTATTTACTACTTTATC
1 TTTATTTGTTTTAT-TTATATATTT-TTTACTACTTTATC
27067 TTT
1 TTT
27070 GCTTTCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 3 0.09
37 23 0.66
38 9 0.26
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (38 bp):
TTTATTTGTTTTATTTATATATTTTTTACTACTTTATC
Found at i:49305 original size:33 final size:32
Alignment explanation
Indices: 49266--49336 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
49256 GACGCCGAAA
*
49266 TTAACCCAAAGCAAAAGCAACCTGAACCAAATT
1 TTAACCCAAACCAAAAGCAACCTGAACCAAA-T
* * *
49299 TTAACCCGATCCAAAAGCAACCTGAACCGAAT
1 TTAACCCAAACCAAAAGCAACCTGAACCAAAT
49331 TTAACC
1 TTAACC
49337 TGACCCGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.44, C:0.30, G:0.10, T:0.17
Consensus pattern (32 bp):
TTAACCCAAACCAAAAGCAACCTGAACCAAAT
Found at i:50336 original size:41 final size:41
Alignment explanation
Indices: 50290--50388 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
50280 CAAGAAAAAA
* * * *
50290 AAACGCGGCTATATACTAGTATTTTAGTGGCATTTTTGAAC
1 AAACGCCGCTAAAGACTAGTATTTTAGTGGCATTTTTAAAC
* * *
50331 AAACGCCGCTAAAGACTCGTGTTTTAGTGGCGTTTTTAAAC
1 AAACGCCGCTAAAGACTAGTATTTTAGTGGCATTTTTAAAC
*
50372 AAATGCCGCTAAAGACT
1 AAACGCCGCTAAAGACT
50389 TGTACATTAG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTAGTATTTTAGTGGCATTTTTAAAC
Found at i:50409 original size:41 final size:41
Alignment explanation
Indices: 50313--50401 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
50303 TACTAGTATT
* * ***
50313 TTAGTGGCATTTTTGAACAAACGCCGCTAAAGACTCGTGTT
1 TTAGTGGCATTTTTAAACAAATGCCGCTAAAGACTCGTACA
* *
50354 TTAGTGGCGTTTTTAAACAAATGCCGCTAAAGACTTGTACA
1 TTAGTGGCATTTTTAAACAAATGCCGCTAAAGACTCGTACA
50395 TTAGTGG
1 TTAGTGG
50402 TTTTTTTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (41 bp):
TTAGTGGCATTTTTAAACAAATGCCGCTAAAGACTCGTACA
Done.