Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 48 of 199
Found at i:14030358 original size:22 final size:22
Alignment explanation
Indices: 14030296--14030358 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
14030286 CCTGCTAGGT
* **
14030296 ACAAATCCCAAATATCACCGGC
1 ACAAAGCCCAAATATCACTAGC
**
14030318 ACAAAGCCTGAATATCACTAGC
1 ACAAAGCCCAAATATCACTAGC
14030340 ACAAAGCCCAAATATCACT
1 ACAAAGCCCAAATATCACT
14030359 GACGCAAAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.43, C:0.32, G:0.10, T:0.16
Consensus pattern (22 bp):
ACAAAGCCCAAATATCACTAGC
Found at i:14030366 original size:22 final size:22
Alignment explanation
Indices: 14030296--14030369 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
14030286 CCTGCTAGGT
* * *
14030296 ACAAATCCCAAATATCACCGGC
1 ACAAAGCCCAAATATCACTGAC
**
14030318 ACAAAGCCTGAATATCACT-AGC
1 ACAAAGCCCAAATATCACTGA-C
14030340 ACAAAGCCCAAATATCACTGAC
1 ACAAAGCCCAAATATCACTGAC
*
14030362 GCAAAGCC
1 ACAAAGCC
14030370 TGCTAGGCAC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 41 0.98
23 1 0.02
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (22 bp):
ACAAAGCCCAAATATCACTGAC
Found at i:14031275 original size:23 final size:22
Alignment explanation
Indices: 14031226--14031279 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
14031216 TCAAATCATG
*
14031226 AAATTTACCTTTTTAAAATTAC
1 AAATTTACCCTTTTAAAATTAC
*
14031248 GAATTTACCCTTTTAAAATCCTA-
1 AAATTTACCCTTTTAAAAT--TAC
14031271 AAATTTACC
1 AAATTTACC
14031280 ATGCAACCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.63
23 8 0.30
24 2 0.07
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATTTACCCTTTTAAAATTAC
Found at i:14031909 original size:12 final size:13
Alignment explanation
Indices: 14031892--14031920 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
14031882 AAGATTTCTT
14031892 TTGAAGCT-AGAA
1 TTGAAGCTGAGAA
14031904 TTGAAGCTGAGAA
1 TTGAAGCTGAGAA
14031917 TTGA
1 TTGA
14031921 GTATGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (13 bp):
TTGAAGCTGAGAA
Found at i:14036269 original size:16 final size:16
Alignment explanation
Indices: 14036248--14036279 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14036238 TGATAAAAAA
14036248 TATTATAATTAATAAT
1 TATTATAATTAATAAT
*
14036264 TATTATGATTAATAAT
1 TATTATAATTAATAAT
14036280 AATTTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TATTATAATTAATAAT
Found at i:14041558 original size:15 final size:15
Alignment explanation
Indices: 14041538--14041569 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14041528 AATTTCACTA
*
14041538 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
14041553 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
14041568 TT
1 TT
14041570 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:14050072 original size:20 final size:20
Alignment explanation
Indices: 14050049--14050086 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14050039 AAAAAAACTA
*
14050049 TATTTTAAAAATAAAATATT
1 TATTCTAAAAATAAAATATT
*
14050069 TATTCTAAAATTAAAATA
1 TATTCTAAAAATAAAATA
14050087 CTATTATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTCTAAAAATAAAATATT
Found at i:14050091 original size:19 final size:20
Alignment explanation
Indices: 14050049--14050091 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
14050039 AAAAAAACTA
* *
14050049 TATTTTAAAAATAAAATATT
1 TATTCTAAAAATAAAATATC
*
14050069 TATTCTAAAATTAAAATA-C
1 TATTCTAAAAATAAAATATC
14050088 TATT
1 TATT
14050092 ATTGTATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTCTAAAAATAAAATATC
Found at i:14057038 original size:21 final size:21
Alignment explanation
Indices: 14057012--14057079 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
14057002 ATGTGATATG
14057012 AATTAAATTTTATATTAGTGT
1 AATTAAATTTTATATTAGTGT
* *
14057033 AATTAATATTATTATGA-CA-TTT
1 AATTAA-ATT-TTAT-ATTAGTGT
*
14057055 AA-TAATTTTTATATTAGTGT
1 AATTAAATTTTATATTAGTGT
14057075 AATTA
1 AATTA
14057080 TTATTAAGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 6 0.17
21 11 0.31
22 7 0.19
23 5 0.14
24 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (21 bp):
AATTAAATTTTATATTAGTGT
Found at i:14057811 original size:40 final size:40
Alignment explanation
Indices: 14057760--14057841 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
14057750 CCGTTAATCG
* * * *
14057760 AATCGAAATATTTCGGTTAATTCG-GCTGATTAACCGAATT
1 AATCAAAATATTTCGATTAATTCGATCAG-TTAACCGAATT
14057800 AATCAAAATATTTCGATTAATTCGATCAGTTAACCGAATT
1 AATCAAAATATTTCGATTAATTCGATCAGTTAACCGAATT
14057840 AA
1 AA
14057842 CTGAGATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (40 bp):
AATCAAAATATTTCGATTAATTCGATCAGTTAACCGAATT
Found at i:14059322 original size:72 final size:73
Alignment explanation
Indices: 14059235--14059392 Score: 291
Period size: 72 Copynumber: 2.2 Consensus size: 73
14059225 CCCACCTCAT
14059235 GCAATGCAATATGACAAGCTCAAACAGATCAATACAATATCATTTAATTA-GCTTTAAATAGAAT
1 GCAAT-CAATATGACAAGCTCAAACAGATCAATACAATATCATTTAATTATGCTTTAAATAGAAT
*
14059299 AATACGGTA
65 AATACGATA
14059308 GCAATCAATATGACAAGCTCAAACAGATCAATACAATATCATTTAATTATGCTTTAAATAGAATA
1 GCAATCAATATGACAAGCTCAAACAGATCAATACAATATCATTTAATTATGCTTTAAATAGAATA
14059373 ATACGATA
66 ATACGATA
14059381 GCAATCAATATG
1 GCAATCAATATG
14059393 CTTATAATAG
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
72 44 0.53
73 39 0.47
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (73 bp):
GCAATCAATATGACAAGCTCAAACAGATCAATACAATATCATTTAATTATGCTTTAAATAGAATA
ATACGATA
Found at i:14059393 original size:34 final size:34
Alignment explanation
Indices: 14059285--14059429 Score: 98
Period size: 34 Copynumber: 4.1 Consensus size: 34
14059275 CATTTAATTA
**
14059285 GCTTTAAATAGAATAATACGGTAGCAATCAATAT
1 GCTTTAAATAGAATAATACAATAGCAATCAATAT
* * * * * *
14059319 GACAAGCTCAAACAG-ATCAATACAATATCATTTAATTAT
1 G-C---TTTAAATAGAAT-AATACAATAGCAATCAA-TAT
*
14059358 GCTTTAAATAGAATAATACGATAGCAATCAATAT
1 GCTTTAAATAGAATAATACAATAGCAATCAATAT
* *
14059392 GC-TTATAATAGTACAATACAATAGCAAAT-AATAT
1 GCTTTA-AATAGAATAATACAATAGC-AATCAATAT
14059426 GCTT
1 GCTT
14059430 ATGATAGGTC
Statistics
Matches: 83, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
33 3 0.04
34 29 0.35
35 24 0.29
36 2 0.02
37 2 0.02
38 19 0.23
39 4 0.05
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (34 bp):
GCTTTAAATAGAATAATACAATAGCAATCAATAT
Found at i:14060727 original size:12 final size:12
Alignment explanation
Indices: 14060710--14060734 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14060700 GGCCGAGTAG
14060710 CCAGGCCGTGTC
1 CCAGGCCGTGTC
14060722 CCAGGCCGTGTC
1 CCAGGCCGTGTC
14060734 C
1 C
14060735 TCACCCGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.32, T:0.16
Consensus pattern (12 bp):
CCAGGCCGTGTC
Found at i:14068200 original size:39 final size:40
Alignment explanation
Indices: 14068157--14068242 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 40
14068147 AAAAAATATA
*
14068157 TTTAATACAACAAAATATTTATTATATT-T-ATTTATGTTT
1 TTTAATACAACAAAATATTTATTATATTATGATAT-TGTTT
* *
14068196 TTTAATATAATAAAATATTTATTATATTATGATATTGTTT
1 TTTAATACAACAAAATATTTATTATATTATGATATTGTTT
14068236 TTTAATA
1 TTTAATA
14068243 TAAATACTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 26 0.62
40 13 0.31
41 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (40 bp):
TTTAATACAACAAAATATTTATTATATTATGATATTGTTT
Found at i:14069895 original size:23 final size:24
Alignment explanation
Indices: 14069850--14069904 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
14069840 AATTTATTCT
*
14069850 AAAACAAAATAGAATTAATTTTAA
1 AAAATAAAATAGAATTAATTTTAA
* *
14069874 AAAATAAAATATAATTGA-TTTAA
1 AAAATAAAATAGAATTAATTTTAA
*
14069897 AAATTAAA
1 AAAATAAA
14069905 TTAATTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATAAAATAGAATTAATTTTAA
Found at i:14069906 original size:17 final size:17
Alignment explanation
Indices: 14069879--14069922 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
14069869 TTTAAAAAAT
*
14069879 AAAATATAATTGATT-TA
1 AAAATA-AATTAATTCTA
14069896 AAAATTAAATTAATTCTA
1 AAAA-TAAATTAATTCTA
14069914 AAAATAAAT
1 AAAATAAAT
14069923 GAATAGGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AAAATAAATTAATTCTA
Found at i:14075178 original size:6 final size:6
Alignment explanation
Indices: 14075167--14075196 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
14075157 AAATGCCAAT
14075167 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC
1 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC
14075197 AGGGTGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.67, T:0.17
Consensus pattern (6 bp):
TGGGGC
Found at i:14075295 original size:14 final size:13
Alignment explanation
Indices: 14075278--14075353 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 13
14075268 ATTTAATTGA
14075278 TTTTAATTTTATATT
1 TTTTAATTTTA-A-T
14075293 TTTCTAATTTTGAAT
1 TTT-TAATTTT-AAT
*
14075308 TTTAAATTTTGAAT
1 TTTTAATTTT-AAT
* *
14075322 TTTGAATTTTAAAA
1 TTTTAATTTT-AAT
*
14075336 TTTTAATTTTATT
1 TTTTAATTTTAAT
14075349 TTTTA
1 TTTTA
14075354 TTAAATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
13 6 0.12
14 30 0.58
15 7 0.13
16 8 0.15
17 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:14075308 original size:7 final size:7
Alignment explanation
Indices: 14075298--14075345 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
14075288 ATATTTTTCT
14075298 AATTTTG
1 AATTTTG
*
14075305 AATTTTA
1 AATTTTG
14075312 AATTTTG
1 AATTTTG
14075319 AATTTTG
1 AATTTTG
*
14075326 AATTTTAA
1 AATTTT-G
14075334 AATTTT-
1 AATTTTG
14075340 AATTTT
1 AATTTT
14075346 ATTTTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.16
7 25 0.68
8 6 0.16
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (7 bp):
AATTTTG
Found at i:14075351 original size:6 final size:6
Alignment explanation
Indices: 14075277--14075350 Score: 51
Period size: 7 Copynumber: 10.8 Consensus size: 6
14075267 AATTTAATTG
14075277 ATTTTA ATTTTA TATTTTTCTA ATTTTGA ATTTTAA ATTTTGA ATTTTGA
1 ATTTTA ATTTTA -A--TTT-TA ATTTT-A ATTTT-A ATTTT-A ATTTT-A
14075327 ATTTTAAA ATTTTA ATTTT- ATTTT
1 ATTTT--A ATTTTA ATTTTA ATTTT
14075351 TTATTAAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
5 5 0.08
6 13 0.22
7 29 0.49
8 6 0.10
9 4 0.07
10 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:14075353 original size:21 final size:21
Alignment explanation
Indices: 14075297--14075345 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
14075287 TATATTTTTC
14075297 TAATTTTGAATTTT-AAATTT
1 TAATTTTGAATTTTAAAATTT
14075317 TGAATTTTGAATTTTAAAATTT
1 T-AATTTTGAATTTTAAAATTT
14075339 TAATTTT
1 TAATTTT
14075346 ATTTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.70
22 7 0.26
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (21 bp):
TAATTTTGAATTTTAAAATTT
Found at i:14078045 original size:15 final size:14
Alignment explanation
Indices: 14078009--14078064 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
14077999 ATATATAGGT
14078009 ATAATAATAATATATA
1 ATAATAATAATA-A-A
14078025 AT-ATAATAATAAA
1 ATAATAATAATAAA
*
14078038 AGTAATAATAACAAA
1 A-TAATAATAATAAA
14078053 ATTAATAA-AATA
1 A-TAATAATAATA
14078065 GACTAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 2 0.06
14 5 0.14
15 26 0.74
16 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:14078309 original size:19 final size:21
Alignment explanation
Indices: 14078271--14078309 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
14078261 CCTTTTTTAA
*
14078271 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
14078292 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
14078310 AAGAAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:14078498 original size:22 final size:23
Alignment explanation
Indices: 14078471--14078515 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
14078461 GGGTATATAC
14078471 AAATTAAATC-TCTAAGATTACA
1 AAATTAAATCTTCTAAGATTACA
*
14078493 AAATTATATCTTCTAAGATTACA
1 AAATTAAATCTTCTAAGATTACA
14078516 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (23 bp):
AAATTAAATCTTCTAAGATTACA
Found at i:14078523 original size:22 final size:23
Alignment explanation
Indices: 14078481--14078525 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
14078471 AAATTAAATC
*
14078481 TCTAAGATTACAAAATTATATCT
1 TCTAAGATTACAAAATCATATCT
*
14078504 TCTAAGATTAC-ATATCATATCT
1 TCTAAGATTACAAAATCATATCT
14078526 AAGATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATCT
Found at i:14078528 original size:19 final size:19
Alignment explanation
Indices: 14078504--14078578 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
14078494 AATTATATCT
14078504 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
*
14078523 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
* * *
14078544 TTTAAGATTGCATATTATA
1 TCTAAGATTACATATCATA
* *
14078563 TTTAAGATTGCATATC
1 TCTAAGATTACATATC
14078579 CTCGAAGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 31 0.65
21 17 0.35
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:14078541 original size:21 final size:21
Alignment explanation
Indices: 14078515--14078577 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
14078505 CTAAGATTAC
*
14078515 ATATCATATCTAAGATTGCAT
1 ATATCATATTTAAGATTGCAT
14078536 ATATCATATTTAAGATTGCAT
1 ATATCATATTTAAGATTGCAT
14078557 AT-T-ATATTTAAGATTGCAT
1 ATATCATATTTAAGATTGCAT
14078576 AT
1 AT
14078578 CCTCGAAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.44
20 1 0.02
21 22 0.54
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (21 bp):
ATATCATATTTAAGATTGCAT
Found at i:14079815 original size:20 final size:20
Alignment explanation
Indices: 14079781--14079826 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
14079771 TTTATATTCT
14079781 TTAAAAAATTATAAA-AAAA
1 TTAAAAAATTATAAAGAAAA
* *
14079800 TTAAAGAATATATAAAGAAAG
1 TTAAAAAAT-TATAAAGAAAA
14079821 TTAAAA
1 TTAAAA
14079827 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
20 6 0.27
21 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
TTAAAAAATTATAAAGAAAA
Found at i:14095123 original size:19 final size:17
Alignment explanation
Indices: 14095098--14095143 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
14095088 TATATATTTG
14095098 TTTTATAATTGTTTATAA
1 TTTTATAATTGTTT-TAA
14095116 TATTTAT-ATT-TTTTAA
1 T-TTTATAATTGTTTTAA
*
14095132 TGTTATAATTGT
1 TTTTATAATTGT
14095144 GATAAGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 4 0.17
18 4 0.17
19 5 0.21
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (17 bp):
TTTTATAATTGTTTTAA
Found at i:14100792 original size:40 final size:40
Alignment explanation
Indices: 14100756--14100874 Score: 134
Period size: 40 Copynumber: 3.0 Consensus size: 40
14100746 ACAAATGCCG
* * *
14100756 CTATAGATCGAGCATTAGAGACGCTTCTGGAAAAATGCCA
1 CTATAGATTGAGCATTAGAGACGCTTCTAGAAAAACGCCA
* *
14100796 CTAAAGATTGAGCATTA-ACGACGCTTTTAGAAAAACGCCA
1 CTATAGATTGAGCATTAGA-GACGCTTCTAGAAAAACGCCA
* * *
14100836 CTATAGGTTGATCATTAGCAG-TGCTTCTAGAAAAACGCC
1 CTATAGATTGAGCATTAG-AGACGCTTCTAGAAAAACGCC
14100875 GCAAAAAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
39 1 0.02
40 63 0.95
41 1 0.02
42 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (40 bp):
CTATAGATTGAGCATTAGAGACGCTTCTAGAAAAACGCCA
Found at i:14101600 original size:116 final size:116
Alignment explanation
Indices: 14101328--14101692 Score: 471
Period size: 116 Copynumber: 3.2 Consensus size: 116
14101318 AACGATGCCG
* * * * * * *
14101328 TTTTATTTGCATTTTTAGTGGCATTTTTACTAAAACGCTGCAAAAGGATATCTATTAGTGGCGGT
1 TTTTATCTGCGTTTTTAGTGGCATTTTTACTAAAATGCCGCAAAAGGATATGTGTTAGTGGCGTT
* ** * * *
14101393 TGTACGAAAAACGCAATAATTATGTTTAAAGTGTTTGCTAGACGTTGTCG-
66 TTTACGAAAAACGCAGCAATTATGTTTTAAGTGTTTGCTAAACATTGTCGT
** * *
14101443 TTTTATCTGCGTTTTTAGTGGTGTTTTTACTAAAATGCCGCAAGAGGATATGTGTTAGTGGCATT
1 TTTTATCTGCGTTTTTAGTGGCATTTTTACTAAAATGCCGCAAAAGGATATGTGTTAGTGGCGTT
* * * *
14101508 TTTACGGAAAATGCCGCAATTATGTTTTAAGTGTTTGCTAAACATTTTCGT
66 TTTACGAAAAACGCAGCAATTATGTTTTAAGTGTTTGCTAAACATTGTCGT
* * *
14101559 TTTTATCTGCGTTTCTAGTGGCATTTTGACTAAAATGCCGCAAAAGGATATGTGTTAGTGGTGTT
1 TTTTATCTGCGTTTTTAGTGGCATTTTTACTAAAATGCCGCAAAAGGATATGTGTTAGTGGCGTT
* * *
14101624 TTTACGAAAAACACTGCAATTATATTTTAAGTGTTTGCTAAACATTGTCGT
66 TTTACGAAAAACGCAGCAATTATGTTTTAAGTGTTTGCTAAACATTGTCGT
*
14101675 TTTTATCTGCGATTTTAG
1 TTTTATCTGCGTTTTTAG
14101693 CTGCGTTAGT
Statistics
Matches: 213, Mismatches: 36, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
115 94 0.44
116 119 0.56
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (116 bp):
TTTTATCTGCGTTTTTAGTGGCATTTTTACTAAAATGCCGCAAAAGGATATGTGTTAGTGGCGTT
TTTACGAAAAACGCAGCAATTATGTTTTAAGTGTTTGCTAAACATTGTCGT
Found at i:14101822 original size:23 final size:23
Alignment explanation
Indices: 14101796--14101917 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
14101786 CCCCACTCAG
*
14101796 ATTTCCCCAATTTCATTTCCCTA
1 ATTTCCCCAATTTCATTTCCCCA
*
14101819 ATTT-CCC-ATTTCCTATTCCCCCA
1 ATTTCCCCAATTT-C-ATTTCCCCA
* *
14101842 ATTTCTCCGATTTCATTTCCCCA
1 ATTTCCCCAATTTCATTTCCCCA
* *
14101865 ATTT-CCCAATTCCTTTTCCCCCA
1 ATTTCCCCAATTTCATTT-CCCCA
*
14101888 ATTTCCCCGATTTCATTTCCCCA
1 ATTTCCCCAATTTCATTTCCCCA
14101911 ATTTCCC
1 ATTTCCC
14101918 AACTGACCTG
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
21 4 0.05
22 13 0.16
23 48 0.59
24 13 0.16
25 4 0.05
ACGTcount: A:0.18, C:0.39, G:0.02, T:0.41
Consensus pattern (23 bp):
ATTTCCCCAATTTCATTTCCCCA
Found at i:14101855 original size:46 final size:46
Alignment explanation
Indices: 14101796--14101919 Score: 203
Period size: 46 Copynumber: 2.7 Consensus size: 46
14101786 CCCCACTCAG
* * *
14101796 ATTTCCCCAATTTCATTTCCCTAATTTCCCATTTCCTATTCCCCCA
1 ATTTCCCCGATTTCATTTCCCCAATTTCCCAATTCCTATTCCCCCA
* *
14101842 ATTTCTCCGATTTCATTTCCCCAATTTCCCAATTCCTTTTCCCCCA
1 ATTTCCCCGATTTCATTTCCCCAATTTCCCAATTCCTATTCCCCCA
14101888 ATTTCCCCGATTTCATTTCCCCAATTTCCCAA
1 ATTTCCCCGATTTCATTTCCCCAATTTCCCAA
14101920 CTGACCTGTC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.19, C:0.39, G:0.02, T:0.40
Consensus pattern (46 bp):
ATTTCCCCGATTTCATTTCCCCAATTTCCCAATTCCTATTCCCCCA
Found at i:14102077 original size:13 final size:12
Alignment explanation
Indices: 14102044--14102077 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14102034 GGTCAGATTC
*
14102044 TTTTGTTGGCAT
1 TTTTGTTGTCAT
14102056 TTTTGTTGTCAT
1 TTTTGTTGTCAT
14102068 TTTTGCTTGT
1 TTTTG-TTGT
14102078 TCCGTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.06, C:0.09, G:0.21, T:0.65
Consensus pattern (12 bp):
TTTTGTTGTCAT
Found at i:14103045 original size:46 final size:45
Alignment explanation
Indices: 14102976--14103063 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 45
14102966 TTACTTTTTT
* *
14102976 AAAAATCTTTAATTTCCATTATTTA-TTAGTCACTTAATTTCTAAA
1 AAAAATCTTTAATTTCCACTATTTACATA-TCACTTAATTTCTAAA
* *
14103021 AAAAATCTTTTAATTTTCACTATTTACATATTACTTAATTTCT
1 AAAAATC-TTTAATTTCCACTATTTACATATCACTTAATTTCT
14103064 TGGAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 7 0.19
46 28 0.76
47 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.49
Consensus pattern (45 bp):
AAAAATCTTTAATTTCCACTATTTACATATCACTTAATTTCTAAA
Found at i:14103328 original size:20 final size:21
Alignment explanation
Indices: 14103284--14103336 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
14103274 TTATTTATTT
14103284 TATATTTTTAAATATTAAAACC
1 TATATTTTT-AATATTAAAACC
**
14103306 TATATTTTTAATA-TATCACC
1 TATATTTTTAATATTAAAACC
14103326 TATATTTTTAA
1 TATATTTTTAA
14103337 ATTCATTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 16 0.55
21 4 0.14
22 9 0.31
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATTTTTAATATTAAAACC
Found at i:14103437 original size:37 final size:34
Alignment explanation
Indices: 14103352--14103443 Score: 121
Period size: 34 Copynumber: 2.6 Consensus size: 34
14103342 TTACTAATAA
* *
14103352 ATTTTTAAATTTTAAACATAATTATTTATTTTAT
1 ATTTTTAAATATTATACATAATTATTTATTTTAT
* *
14103386 GTTTTTAAATATTATATATAATTATTTATTTTTAAAT
1 ATTTTTAAATATTATACATAATTATTTA-TTTT--AT
14103423 ATTTTTAAATATTATACATAA
1 ATTTTTAAATATTATACATAA
14103444 AATTTTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
34 24 0.49
35 4 0.08
37 21 0.43
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (34 bp):
ATTTTTAAATATTATACATAATTATTTATTTTAT
Found at i:14103641 original size:9 final size:9
Alignment explanation
Indices: 14103550--14103808 Score: 127
Period size: 9 Copynumber: 27.7 Consensus size: 9
14103540 ACTAATTTCC
*
14103550 ACATAACAT
1 ACATAACTT
*
14103559 ACATAACTC
1 ACATAACTT
*
14103568 ACATAACAT
1 ACATAACTT
14103577 ACATAACTT
1 ACATAACTT
14103586 A-ATAACTT
1 ACATAACTT
* *
14103594 ATATATATCAT
1 ACATA-A-CTT
14103605 A-ACTCAACTT
1 ACA-T-AACTT
* *
14103615 AAATAACTC
1 ACATAACTT
14103624 ACATAACTT
1 ACATAACTT
14103633 ACATAACTT
1 ACATAACTT
* *
14103642 ATATATACCAT
1 ACATA-A-CTT
14103653 A-ACTCAACTT
1 ACA-T-AACTT
*
14103663 ACATAACTC
1 ACATAACTT
14103672 ACATAACTT
1 ACATAACTT
* *
14103681 ATATATATCAT
1 ACATA-A-CTT
14103692 A-ACTCAACTT
1 ACA-T-AACTT
14103702 ACATAA--T
1 ACATAACTT
*
14103709 ACATAAATAT
1 ACATAACT-T
* * *
14103719 ATATATCAT
1 ACATAACTT
14103728 ATCATAACTT
1 A-CATAACTT
*
14103738 ACATAACTC
1 ACATAACTT
14103747 ACATAACTT
1 ACATAACTT
14103756 ACATAACTT
1 ACATAACTT
14103765 A-ATAACTT
1 ACATAACTT
* * *
14103773 ATGTATATCAT
1 A--CATAACTT
14103784 ATCATAACTT
1 A-CATAACTT
14103794 ACATAACTT
1 ACATAACTT
*
14103803 GCATAA
1 ACATAA
14103809 TACATAAATA
Statistics
Matches: 193, Mismatches: 34, Indels: 46
0.71 0.12 0.17
Matches are distributed among these distances:
7 7 0.04
8 16 0.08
9 108 0.56
10 35 0.18
11 24 0.12
12 3 0.02
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (9 bp):
ACATAACTT
Found at i:14103654 original size:48 final size:47
Alignment explanation
Indices: 14103577--14103681 Score: 183
Period size: 48 Copynumber: 2.2 Consensus size: 47
14103567 CACATAACAT
*
14103577 ACATAACTTAATAACTTATATATATCATAACTCAACTTAAATAACTC
1 ACATAACTTAATAACTTATATATACCATAACTCAACTTAAATAACTC
*
14103624 ACATAACTTACATAACTTATATATACCATAACTCAACTTACATAACTC
1 ACATAACTTA-ATAACTTATATATACCATAACTCAACTTAAATAACTC
14103672 ACATAACTTA
1 ACATAACTTA
14103682 TATATATCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
47 10 0.18
48 45 0.82
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (47 bp):
ACATAACTTAATAACTTATATATACCATAACTCAACTTAAATAACTC
Found at i:14103667 original size:39 final size:39
Alignment explanation
Indices: 14103619--14103756 Score: 194
Period size: 39 Copynumber: 3.6 Consensus size: 39
14103609 CAACTTAAAT
* * *
14103619 AACTCACATAACTTACATAACTTATATATACCATAACTC
1 AACTTACATAACTCACATAACTTATATATATCATAACTC
14103658 AACTTACATAACTCACATAACTTATATATATCATAACTC
1 AACTTACATAACTCACATAACTTATATATATCATAACTC
* *
14103697 AACTTACATAA-T-ACATAA-ATATATATATCATATCAT-
1 AACTTACATAACTCACATAACTTATATATATCATAAC-TC
14103733 AACTTACATAACTCACATAACTTA
1 AACTTACATAACTCACATAACTTA
14103757 CATAACTTAA
Statistics
Matches: 89, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
36 25 0.28
37 8 0.09
38 7 0.08
39 49 0.55
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.33
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTATATATATCATAACTC
Found at i:14103669 original size:14 final size:14
Alignment explanation
Indices: 14103602--14103672 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 14
14103592 TTATATATAT
14103602 CATAACTCAACTTA
1 CATAACTCAACTTA
*
14103616 AATAACTCACATAACTTA
1 CATAACT--C--AACTTA
*
14103634 CATAACTTATA-TATA
1 CATAACTCA-ACT-TA
14103649 CCATAACTCAACTTA
1 -CATAACTCAACTTA
14103664 CATAACTCA
1 CATAACTCA
14103673 CATAACTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
14 17 0.38
15 6 0.13
16 10 0.22
18 12 0.27
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (14 bp):
CATAACTCAACTTA
Found at i:14106168 original size:13 final size:14
Alignment explanation
Indices: 14106152--14106180 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14106142 TTTTAAATAT
14106152 TTATAGT-GTTTAA
1 TTATAGTGGTTTAA
14106165 TTATAGTGGTTTAA
1 TTATAGTGGTTTAA
14106179 TT
1 TT
14106181 TTTGTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (14 bp):
TTATAGTGGTTTAA
Found at i:14107062 original size:43 final size:43
Alignment explanation
Indices: 14106956--14107157 Score: 142
Period size: 43 Copynumber: 4.7 Consensus size: 43
14106946 CGTTTTTAGT
* *
14106956 AAAGCGCCGCTAAAGAACATGACCTTTAGCAGCGTTTGTAATA
1 AAAGCGCCGCTAAAGATCATGACCTTTAGCAGCATTTGTAATA
* * * *
14106999 AAAGCGCCGCTAAAGGTCATGCCCTTTAGCGGCATTTGTGATA
1 AAAGCGCCGCTAAAGATCATGACCTTTAGCAGCATTTGTAATA
* * ** * * *
14107042 AAAGCACCGCTAAAGTTCATGTTCTTTA--ATG-ATGTTTTCTACA
1 AAAGCGCCGCTAAAGATCATGACCTTTAGCA-GCAT-TTGT-AATA
** * *
14107085 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGCTAA-A
1 AAAGCGCCGCTAAAGATCATGACCTTTAGCAGCATTTG-TAATA
* * * * *
14107128 ATAGTGCCTCTAAAGGTCATGACTTTTAGC
1 AAAGCGCCGCTAAAGATCATGACCTTTAGC
14107158 GGCTACCAAA
Statistics
Matches: 125, Mismatches: 27, Indels: 14
0.75 0.16 0.08
Matches are distributed among these distances:
41 2 0.02
42 4 0.03
43 113 0.90
44 4 0.03
45 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGATCATGACCTTTAGCAGCATTTGTAATA
Found at i:14108412 original size:21 final size:23
Alignment explanation
Indices: 14108387--14108431 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
14108377 ATAAATATAC
14108387 TATT-AATTTAA-TAATATTTAT
1 TATTAAATTTAACTAATATTTAT
14108408 TATTAAATTTAACCTAATATTTAT
1 TATTAAATTTAA-CTAATATTTAT
14108432 CTTGATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 7 0.33
24 10 0.48
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAAATTTAACTAATATTTAT
Found at i:14110749 original size:16 final size:16
Alignment explanation
Indices: 14110730--14110764 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14110720 TAGTAATTTT
14110730 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
14110746 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
14110762 AAT
1 AAT
14110765 TACAAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:14111441 original size:45 final size:45
Alignment explanation
Indices: 14111346--14111447 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
14111336 AAAGAAACGG
* * * *
14111346 ATAAGACCATAATTGAAAGACACTATGGCACTATACCAGAACTGA
1 ATAAGACCATAGTTGAAAGAAACTATGACACTATACCAGAAATGA
**
14111391 ATAAGACCATAGTTGAAAGAAACTATGACA-TCATACTGGAAATGA
1 ATAAGACCATAGTTGAAAGAAACTATGACACT-ATACCAGAAATGA
*
14111436 GTAAGACCATAG
1 ATAAGACCATAG
14111448 CTAAAAGACG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 1 0.02
45 48 0.98
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.21
Consensus pattern (45 bp):
ATAAGACCATAGTTGAAAGAAACTATGACACTATACCAGAAATGA
Found at i:14111468 original size:45 final size:44
Alignment explanation
Indices: 14111434--14111649 Score: 279
Period size: 45 Copynumber: 4.8 Consensus size: 44
14111424 TACTGGAAAT
* *
14111434 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCACGATTTTAAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCA-TATTTTAAC
* * *
14111479 GAGTAAGACCATAGCTTAAAGACGTTAAGGCATCACAATTTTAAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCA-TATTTTAAC
*
14111524 GAGTAAGACCATAGCTGAAAGACGTTATGGTATCATGATTTTAAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCAT-ATTTTAAC
* * * *
14111569 GAGTAAGACTATAGCTGAAAGACGTTATGGCATCACGATTCTAAT
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCA-TATTTTAAC
* * *
14111614 GAGTAAGACCATATCTGAAAGACATTATGACATCAT
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCAT
14111650 GAATCAGGGG
Statistics
Matches: 152, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
45 152 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (44 bp):
GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATATTTTAAC
Found at i:14111500 original size:90 final size:90
Alignment explanation
Indices: 14111392--14111590 Score: 238
Period size: 90 Copynumber: 2.2 Consensus size: 90
14111382 CAGAACTGAA
* * * *
14111392 TAAGACCATAG-TTGAAAGAAACTATGACATCATACTGGAAATGAGTAAGACCATAGCTAAAAGA
1 TAAGACCATAGCTT-AAAGAAACTAAGACATCACAATGGAAACGAGTAAGACCATAGCTAAAAGA
14111456 CGTTATGGCATCACGATTTTAACGAG
65 CGTTATGGCATCACGATTTTAACGAG
*** * *** *
14111482 TAAGACCATAGCTTAAAGACGTTAAGGCATCACAATTTTAACGAGTAAGACCATAGCTGAAAGAC
1 TAAGACCATAGCTTAAAGAAACTAAGACATCACAATGGAAACGAGTAAGACCATAGCTAAAAGAC
* *
14111547 GTTATGGTATCATGATTTTAACGAG
66 GTTATGGCATCACGATTTTAACGAG
* *
14111572 TAAGACTATAGCTGAAAGA
1 TAAGACCATAGCTTAAAGA
14111591 CGTTATGGCA
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
90 90 0.98
91 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (90 bp):
TAAGACCATAGCTTAAAGAAACTAAGACATCACAATGGAAACGAGTAAGACCATAGCTAAAAGAC
GTTATGGCATCACGATTTTAACGAG
Found at i:14111591 original size:90 final size:90
Alignment explanation
Indices: 14111434--14111651 Score: 328
Period size: 90 Copynumber: 2.4 Consensus size: 90
14111424 TACTGGAAAT
* * *
14111434 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCACGATTTTAACGAGTAAGACCATAGCTTAAA
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTTTAACGAGTAAGACCATAGCTGAAA
*
14111499 GACGTTAAGGCATCACAATTTTAAC
66 GACGTTAAGGCATCACAATTCTAAC
* *
14111524 GAGTAAGACCATAGCTGAAAGACGTTATGGTATCATGATTTTAACGAGTAAGACTATAGCTGAAA
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTTTAACGAGTAAGACCATAGCTGAAA
* * *
14111589 GACGTTATGGCATCACGATTCTAAT
66 GACGTTAAGGCATCACAATTCTAAC
* * *
14111614 GAGTAAGACCATATCTGAAAGACATTATGACATCATGA
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGA
14111652 ATCAGGGGAA
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 115 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (90 bp):
GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGATTTTAACGAGTAAGACCATAGCTGAAA
GACGTTAAGGCATCACAATTCTAAC
Found at i:14111688 original size:135 final size:134
Alignment explanation
Indices: 14111389--14111648 Score: 306
Period size: 135 Copynumber: 1.9 Consensus size: 134
14111379 TACCAGAACT
* * ** *** *
14111389 GAATAAGACCATAGTTGAAAGAAACTATGACATCAT-ACTGGAAATGAGTAAGACCATAGCTAAA
1 GAATAAGACCATAGCTGAAAGACACTATGGTATCATGA-TTTTAACGAGTAAGACCATAGCTAAA
* * * *
14111453 AGACGTTATGGCATCACGATTTTAACGAGTAAGACCATAGCTTAAAGACGTTAAGGCATCACAAT
65 AGACGTTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAAAGACATTAAGACATCACAA-
*
14111518 TTTAAC
129 TTCAAC
* ** * *
14111524 GAGTAAGACCATAGCTGAAAGACGTTATGGTATCATGATTTTAACGAGTAAGACTATAGCTGAAA
1 GAATAAGACCATAGCTGAAAGACACTATGGTATCATGATTTTAACGAGTAAGACCATAGCTAAAA
* * *
14111589 GACGTTATGGCATCACGATTCTAATGAGTAAGACCATATCTGAAAGACATTATGACATCA
66 GACGTTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAAAGACATTAAGACATCA
14111649 TGAATCAGGG
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
135 103 0.99
136 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.25
Consensus pattern (134 bp):
GAATAAGACCATAGCTGAAAGACACTATGGTATCATGATTTTAACGAGTAAGACCATAGCTAAAA
GACGTTATGGCATCACGATTCTAACGAGTAAGACCATAGCTGAAAGACATTAAGACATCACAATT
CAAC
Found at i:14112678 original size:50 final size:50
Alignment explanation
Indices: 14112619--14112719 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
14112609 TGAATTAAGT
14112619 ATGTTTTGGGTCATTTTTGGGTACACACAGCCTGGGACCTAGGCTGTCAC
1 ATGTTTTGGGTCATTTTTGGGTACACACAGCCTGGGACCTAGGCTGTCAC
14112669 ATGTTTTGGGTCATTTTTGGGTACACACAGCCTGGGACCTAGGCTGTCAC
1 ATGTTTTGGGTCATTTTTGGGTACACACAGCCTGGGACCTAGGCTGTCAC
14112719 A
1 A
14112720 CGCCGTGTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.32
Consensus pattern (50 bp):
ATGTTTTGGGTCATTTTTGGGTACACACAGCCTGGGACCTAGGCTGTCAC
Found at i:14113444 original size:21 final size:21
Alignment explanation
Indices: 14113418--14113459 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
14113408 TTTTATGATG
14113418 ATTAGAAACATTTGTACATGA
1 ATTAGAAACATTTGTACATGA
*
14113439 ATTAGAAGCATTTGTACATGA
1 ATTAGAAACATTTGTACATGA
14113460 TTTGAGGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
ATTAGAAACATTTGTACATGA
Found at i:14131940 original size:26 final size:26
Alignment explanation
Indices: 14131904--14131969 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
14131894 ACATATTTTC
*
14131904 TCAAAATTTTACTAAGGGCAGAATCG
1 TCAAAATTTTACTAAGGGCAAAATCG
* * *
14131930 TCAAAATTTTACCAAGGGTAAAATTG
1 TCAAAATTTTACTAAGGGCAAAATCG
*
14131956 TTAAAATTTTACTA
1 TCAAAATTTTACTA
14131970 GGAGTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACTAAGGGCAAAATCG
Found at i:14131976 original size:26 final size:25
Alignment explanation
Indices: 14131904--14131979 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
14131894 ACATATTTTC
* *
14131904 TCAAAATTTTACTAAGGGCAGAATCG
1 TCAAAATTTTACT-AGGGTAAAATCG
* *
14131930 TCAAAATTTTACCAAGGGTAAAATTG
1 TCAAAATTTTA-CTAGGGTAAAATCG
*
14131956 TTAAAATTTTACTAGGAGTAAAAT
1 TCAAAATTTTACTAGG-GTAAAAT
14131980 AGATATGGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
25 4 0.10
26 37 0.88
27 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (25 bp):
TCAAAATTTTACTAGGGTAAAATCG
Found at i:14141906 original size:25 final size:26
Alignment explanation
Indices: 14141867--14141934 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
14141857 TTCTTGAAAT
14141867 TTTACTAGGGG-AAAATAGTCAAA-A
1 TTTACTAGGGGTAAAATAGTCAAAGA
* *
14141891 TTTACTAGGGGTAAAATTGTCAAAGT
1 TTTACTAGGGGTAAAATAGTCAAAGA
*
14141917 TTTGCT-GGGGTAAAATAG
1 TTTACTAGGGGTAAAATAG
14141935 AAATGAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 11 0.29
25 22 0.58
26 5 0.13
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (26 bp):
TTTACTAGGGGTAAAATAGTCAAAGA
Found at i:14142884 original size:9 final size:9
Alignment explanation
Indices: 14142870--14142901 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
14142860 GATCAAGTAA
14142870 AATTAAATT
1 AATTAAATT
14142879 AATTAAATT
1 AATTAAATT
14142888 AATTTAAATT
1 AA-TTAAATT
14142898 AATT
1 AATT
14142902 TGATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTAAATT
Found at i:14142896 original size:10 final size:10
Alignment explanation
Indices: 14142872--14142902 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
14142862 TCAAGTAAAA
14142872 TTAAATTAA-
1 TTAAATTAAT
14142881 TTAAATTAAT
1 TTAAATTAAT
14142891 TTAAATTAAT
1 TTAAATTAAT
14142901 TT
1 TT
14142903 GATATTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:14143445 original size:69 final size:68
Alignment explanation
Indices: 14143328--14143461 Score: 196
Period size: 69 Copynumber: 2.0 Consensus size: 68
14143318 ATTATTTTAA
* * * * * *
14143328 TAAATTTAATTTAATATTTATTTTGATAGTATTTTATTAATTTAATATTAAAGTGGTTATCTTAA
1 TAAATTTAATCTAATATTTATCTTAATAGTATTATATTAAATTAATATTAAAGTGATTATCTTAA
14143393 AAT
66 AAT
*
14143396 TAAATTTAATCTAATATTTATCTTAATAAGTATTATATTAAATTAATATTAAAGTGATTATTTTA
1 TAAATTTAATCTAATATTTATCTTAAT-AGTATTATATTAAATTAATATTAAAGTGATTATCTTA
14143461 A
65 A
14143462 TTATATTTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
68 24 0.41
69 34 0.59
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (68 bp):
TAAATTTAATCTAATATTTATCTTAATAGTATTATATTAAATTAATATTAAAGTGATTATCTTAA
AAT
Found at i:14147181 original size:17 final size:17
Alignment explanation
Indices: 14147159--14147195 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
14147149 GTGTATAAAA
14147159 ATGTATTTTGATGCAAG
1 ATGTATTTTGATGCAAG
14147176 ATGTATTTTGATGCAAG
1 ATGTATTTTGATGCAAG
14147193 ATG
1 ATG
14147196 GAAAATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (17 bp):
ATGTATTTTGATGCAAG
Found at i:14151523 original size:14 final size:13
Alignment explanation
Indices: 14151499--14151550 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
14151489 TTTTATGAAT
14151499 TAAAAAATAATTA
1 TAAAAAATAATTA
14151512 TAAAAGAATAATTA
1 TAAAA-AATAATTA
* *
14151526 TATTAAAATAAATCA
1 TA-AAAAAT-AATTA
14151541 TATAAAAATA
1 TA-AAAAATA
14151551 TTTAATATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 5 0.15
14 14 0.42
15 14 0.42
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
TAAAAAATAATTA
Found at i:14155316 original size:13 final size:13
Alignment explanation
Indices: 14155298--14155325 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
14155288 CTTTTCTATT
14155298 ATTCAATGGGTTA
1 ATTCAATGGGTTA
14155311 ATTCAATGGGTTA
1 ATTCAATGGGTTA
14155324 AT
1 AT
14155326 GTCTCAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (13 bp):
ATTCAATGGGTTA
Found at i:14155896 original size:90 final size:91
Alignment explanation
Indices: 14155717--14155886 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 91
14155707 GCGGCACCGG
*
14155717 TGAATTTTAAAAAAAAACAATGTCAGATAAAAAGCTGAGACAAGAAAAAATATTTTTTAATGGGT
1 TGAATTTTAAAAAAAAACAATGTCAGATAAAAAGCTGAGACAAGAAAAAATATTTTTTAATAGGT
*
14155782 GTCATCAGTGTGTCAAGCAACACCAA
66 GTCATCAGTGTATCAAGCAACACCAA
* *** * * *
14155808 TGAATTTTTAAAAAAAATGGTGTCA-A-AAAAAGTTGCGACAGGAAAAAAATATTTTTTAATAGG
1 TGAATTTTAAAAAAAAACAATGTCAGATAAAAAGCTGAGACAAG-AAAAAATATTTTTTAATAGG
* *
14155871 TGTCGTCGGTGTATCA
65 TGTCATCAGTGTATCA
14155887 TGTGACACCA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
89 13 0.19
90 33 0.49
91 21 0.31
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (91 bp):
TGAATTTTAAAAAAAAACAATGTCAGATAAAAAGCTGAGACAAGAAAAAATATTTTTTAATAGGT
GTCATCAGTGTATCAAGCAACACCAA
Found at i:14167150 original size:15 final size:15
Alignment explanation
Indices: 14167130--14167182 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
14167120 CACCTTAAAC
14167130 ACAAATATAGTCTTT
1 ACAAATATAGTCTTT
* * * **
14167145 ACAAATAAAAATATAA
1 ACAAAT-ATAGTCTTT
14167161 ACAAATATAGTCTTT
1 ACAAATATAGTCTTT
14167176 ACAAATA
1 ACAAATA
14167183 AAAATATAAT
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (15 bp):
ACAAATATAGTCTTT
Found at i:14167166 original size:31 final size:31
Alignment explanation
Indices: 14167130--14167191 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
14167120 CACCTTAAAC
14167130 ACAAATATAGTCTTTACAAATAAAAATATAA
1 ACAAATATAGTCTTTACAAATAAAAATATAA
14167161 ACAAATATAGTCTTTACAAATAAAAATATAA
1 ACAAATATAGTCTTTACAAATAAAAATATAA
14167192 TCTTAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (31 bp):
ACAAATATAGTCTTTACAAATAAAAATATAA
Found at i:14167213 original size:13 final size:14
Alignment explanation
Indices: 14167190--14167218 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
14167180 ATAAAAATAT
14167190 AATCTTAAATATTA
1 AATCTTAAATATTA
14167204 AATC-TAAATATTA
1 AATCTTAAATATTA
14167217 AA
1 AA
14167219 AATAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATCTTAAATATTA
Found at i:14167246 original size:18 final size:18
Alignment explanation
Indices: 14167194--14167250 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
14167184 AAATATAATC
*
14167194 TTAAATATTAAATCTAAATA
1 TTAAATATT-AAT-AAAATA
* *
14167214 TTAAA-AATAATTAAAATT
1 TTAAATATTAA-TAAAATA
14167232 TTAAATATTAATAAAATA
1 TTAAATATTAATAAAATA
14167250 T
1 T
14167251 AAAAATTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 18 0.60
19 7 0.23
20 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAATATTAATAAAATA
Found at i:14181259 original size:26 final size:26
Alignment explanation
Indices: 14181230--14181311 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
14181220 ATACCGCAGT
14181230 TCTTTGTGAGCTTCCT-ATTATATGGC
1 TCTTTGTGAGCTTCCTAATTA-ATGGC
* * * *
14181256 TCTTCGTGAACTTCCTGATTAAAGGC
1 TCTTTGTGAGCTTCCTAATTAATGGC
*
14181282 TCTTTCTGAGCTTCCTAATTAATGGC
1 TCTTTGTGAGCTTCCTAATTAATGGC
14181308 TCTT
1 TCTT
14181312 CGGAGTTTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 43 0.91
27 4 0.09
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (26 bp):
TCTTTGTGAGCTTCCTAATTAATGGC
Found at i:14181440 original size:24 final size:23
Alignment explanation
Indices: 14181236--14181440 Score: 74
Period size: 24 Copynumber: 8.3 Consensus size: 23
14181226 CAGTTCTTTG
14181236 TGAGCTTCCT-ATTATATGGCTCTT
1 TGAGCTTCCTGA-T-TATGGCTCTT
* *
14181260 CGTGAACTTCCTGATTAAAGGCTCTTT
1 --TGAGCTTCCTGATT-ATGGCTC-TT
*
14181287 CTGAGCTTCCTAATTAATGGCTCTT
1 -TGAGCTTCCTGATT-ATGGCTCTT
* * * * *
14181312 CGGAGTTTCCTGATAATGACTCGCT
1 -TGAGCTTCCTGATTATGGCTC-TT
* * * * *
14181337 TGAACTTCCTAATATATAGCTATCC
1 TGAGCTTCCTGAT-TATGGCTCT-T
* * *
14181362 AGACCTTCCCG-TTAATGGCTCTT
1 TGAGCTTCCTGATT-ATGGCTCTT
* *
14181385 TGGAGCTACCTG-TTATTGGCTCACT
1 T-GAGCTTCCTGATTA-TGGCTC-TT
14181410 TGAGCTTCCTGATTATGGCTCTT
1 TGAGCTTCCTGATTATGGCTCTT
14181433 ATGAGCTT
1 -TGAGCTT
14181441 TCCGTTATAT
Statistics
Matches: 131, Mismatches: 36, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
23 3 0.02
24 59 0.45
25 31 0.24
26 35 0.27
27 3 0.02
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (23 bp):
TGAGCTTCCTGATTATGGCTCTT
Found at i:14183801 original size:27 final size:27
Alignment explanation
Indices: 14183763--14183831 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
14183753 TGTAATCCTT
* * **
14183763 GTGTTTATTGTCCCAACGATCTACTTC
1 GTGTTTAATGTCCCAACGAACTACCCC
14183790 GTGTTTAATGTCCCAACGAACTACCCC
1 GTGTTTAATGTCCCAACGAACTACCCC
*
14183817 GTGTTTACTGTCCCA
1 GTGTTTAATGTCCCA
14183832 GTAGACTACC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (27 bp):
GTGTTTAATGTCCCAACGAACTACCCC
Found at i:14185679 original size:20 final size:21
Alignment explanation
Indices: 14185650--14185688 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14185640 AAAGTGGGCA
14185650 AACAACCATTTTT-AACCTTG
1 AACAACCATTTTTCAACCTTG
*
14185670 AACAATCATTTTTCAACCT
1 AACAACCATTTTTCAACCT
14185689 ATTTAACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (21 bp):
AACAACCATTTTTCAACCTTG
Found at i:14187432 original size:27 final size:27
Alignment explanation
Indices: 14187402--14187453 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
14187392 ATATTTAATT
14187402 ATTA-TAACATAATTAAATTGTACTTAA
1 ATTATTAACAT-ATTAAATTGTACTTAA
* *
14187429 ATTATTAACATATTGAATTTTACTT
1 ATTATTAACATATTAAATTGTACTT
14187454 CATTTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (27 bp):
ATTATTAACATATTAAATTGTACTTAA
Found at i:14190251 original size:3 final size:3
Alignment explanation
Indices: 14190224--14190265 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
14190214 TTTTATTAAT
* *
14190224 TTA TTAA TTA TT- TTA TTA CTA TTA TTA TTA TTG TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14190266 GTATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:14190778 original size:16 final size:17
Alignment explanation
Indices: 14190744--14190788 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
14190734 TAGTTTTCTT
*
14190744 TATATGTATACTTTCATA
1 TATATGTATA-TATCATA
14190762 TATATGTATATAT-ATA
1 TATATGTATATATCATA
14190778 TATATGTATAT
1 TATATGTATAT
14190789 TATTGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 14 0.54
17 2 0.08
18 10 0.38
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (17 bp):
TATATGTATATATCATA
Found at i:14191575 original size:11 final size:11
Alignment explanation
Indices: 14191559--14191583 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14191549 TAAACAATCG
14191559 ATTCGGTACCA
1 ATTCGGTACCA
14191570 ATTCGGTACCA
1 ATTCGGTACCA
14191581 ATT
1 ATT
14191584 TTCTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (11 bp):
ATTCGGTACCA
Found at i:14212585 original size:42 final size:43
Alignment explanation
Indices: 14212520--14212610 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 43
14212510 ACGGCTTGAC
*
14212520 ACACGGGTATGTGACACGACCGTGTGACCCTACTTAG-AGAGTT
1 ACACGGGTATGGGACACGACCGTGTGACCCTACTTAGAAG-GTT
* * * *
14212563 ACACGGGT-TGGGACACGGCCGTGTGTCCCTAGTTCGAAGGTT
1 ACACGGGTATGGGACACGACCGTGTGACCCTACTTAGAAGGTT
14212605 ACACGG
1 ACACGG
14212611 CCTGAGACAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 32 0.76
43 10 0.24
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.22
Consensus pattern (43 bp):
ACACGGGTATGGGACACGACCGTGTGACCCTACTTAGAAGGTT
Found at i:14212620 original size:42 final size:42
Alignment explanation
Indices: 14212532--14212631 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
14212522 ACGGGTATGT
* * ** *
14212532 GACACGACCGTGTGACCCTACTTAGAGAGTTACACGGGTTGG
1 GACACGGCCGTGTGTCCCTACTTAGAGAGTTACACGGCCTGA
* *
14212574 GACACGGCCGTGTGTCCCTAGTTCGA-AGGTTACACGGCCTGA
1 GACACGGCCGTGTGTCCCTACTTAGAGA-GTTACACGGCCTGA
14212616 GACACAGG-CGTGTGTC
1 GACAC-GGCCGTGTGTC
14212632 TCAGCCGTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.94
43 2 0.04
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (42 bp):
GACACGGCCGTGTGTCCCTACTTAGAGAGTTACACGGCCTGA
Found at i:14215538 original size:17 final size:18
Alignment explanation
Indices: 14215508--14215546 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
14215498 ATTAACACTT
* *
14215508 AAAATAATATTATATAGA
1 AAAATAATAGTATATACA
14215526 AAAATAAT-GTATATACA
1 AAAATAATAGTATATACA
14215543 AAAA
1 AAAA
14215547 ATGTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAATAATAGTATATACA
Found at i:14217141 original size:50 final size:50
Alignment explanation
Indices: 14217077--14217684 Score: 320
Period size: 50 Copynumber: 12.1 Consensus size: 50
14217067 TCGTAACTTC
* * * * *
14217077 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTT
1 AATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
* * * * * *
14217127 AATCTGTTCCACTGCACTGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTT
1 AATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
* * * * * *
14217177 AATCTTTTTAACTGCAATGTCAGGGAGGCCAGACTCACTGTTATGGCTTT
1 AATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
* * ** * * * * * *
14217227 CATCTGTTCCACTGCACCGCCTGGGAGGTAAGATTCGCTGTTGTAGCTTT
1 AATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
* * * * *
14217277 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTT
1 AATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
* * * * *
14217327 AATCTGTTCCACTGC-ATCG-CTTGGGAAGTAAGATTCGCTGTTGTAGCTTT
1 AATCTGTTCAACTGCAAT-GTC-AGGGAAGCAAGATTCACTGTTGTGGCTTT
* * * *
14217377 AATCTTTTTAACTGCAATGTCAGGGAGGCCAA-ATTCACCGTTGTGGCTTT
1 AATCTGTTCAACTGCAATGTCAGGGAAG-CAAGATTCACTGTTGTGGCTTT
* * * * * * ** * ** *
14217427 AATCTGCTCTACTGCACTGGCTGAGAGAGTGAGATTC-GTCACTGTGACTTT
1 AATCTGTTCAACTGCAATGTCAGGGA-AGCAAGATTCACT-GTTGTGGCTTT
* *** * *
14217478 AATCCT-TTTAACTGCAATGTCAAAAAAGCAAGATTTACCGTTGTGGCTTT
1 AAT-CTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
* * * * * * ** *
14217528 AATCTGCTCTACTGCACTGGCTGAGAGAGTGAGATT---TGTCACTGTGACTTT
1 AATCTGTTCAACTGCAATGTCAGGGA-AGCAAGATTCACTGT---TGTGGCTTT
* * *
14217579 AATCCT-TTTAACTGGAATGTC-GGGAAAGCAAGATTCACAGTTGTGGCTTT
1 AAT-CTGTTCAACTGCAATGTCAGGG-AAGCAAGATTCACTGTTGTGGCTTT
* * * * * * *
14217629 AATCTATTTC-ACTGCATTGCCATGGAGGTAAGATTCACTGTTGTAGCTTT
1 AATCT-GTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
14217679 AATCTG
1 AATCTG
14217685 CAATGTCGAG
Statistics
Matches: 401, Mismatches: 134, Indels: 47
0.69 0.23 0.08
Matches are distributed among these distances:
48 2 0.00
49 7 0.02
50 321 0.80
51 65 0.16
52 4 0.01
53 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
AATCTGTTCAACTGCAATGTCAGGGAAGCAAGATTCACTGTTGTGGCTTT
Found at i:14217258 original size:100 final size:100
Alignment explanation
Indices: 14217077--14217734 Score: 690
Period size: 100 Copynumber: 6.7 Consensus size: 100
14217067 TCGTAACTTC
* *
14217077 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGC
1 AATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGC
* *
14217142 ACTGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTT
66 ACTGCCTGGGAGGTAAGATTCGCTGTTGTAGCTTT
* * * * * *
14217177 AATCTTTTTAACTGCAATGTCAGGGAGGCCAGACTCACTGTTATGGCTTTCATCTGTTCCACTGC
1 AATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGC
*
14217242 ACCGCCTGGGAGGTAAGATTCGCTGTTGTAGCTTT
66 ACTGCCTGGGAGGTAAGATTCGCTGTTGTAGCTTT
* *
14217277 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGC
1 AATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGC
* *
14217342 A-TCGCTTGGGAAGTAAGATTCGCTGTTGTAGCTTT
66 ACT-GCCTGGGAGGTAAGATTCGCTGTTGTAGCTTT
* * *
14217377 AATCTTTTTAACTGCAATGTCAGGGAGGCCAA-ATTCACCGTTGTGGCTTTAATCTGCTCTACTG
1 AATCTTTTTAACTGCAATGTCAGGGAAG-CAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTG
* * *
14217441 CACTGGCTGAGAGAGTGAGATTCGTCACTG-TG-A-CTTT
65 CACTGCCTGGGAG-GTAAGATTCG---CTGTTGTAGCTTT
* *** * * *
14217478 AATCCTTTTAACTGCAATGTCAAAAAAGCAAGATTTACCGTTGTGGCTTTAATCTGCTCTACTGC
1 AATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGC
* * * *
14217543 ACTGGCTGAGAGAGTGAGATTTGTCACTG-TG-A-CTTT
66 ACTGCCTGGGAG-GTAAGA--T-TCGCTGTTGTAGCTTT
* * * * *
14217579 AATCCTTTTAACTGGAATGTC-GGGAAAGCAAGATTCACAGTTGTGGCTTTAATCTATTTCACTG
1 AATCTTTTTAACTGCAATGTCAGGG-AAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTG
* *
14217643 CATTGCCAT-GGAGGTAAGATTCACTGTTGTAGCTTT
65 CACTGCC-TGGGAGGTAAGATTCGCTGTTGTAGCTTT
* *
14217679 AA------T--CTGCAATGTC-GAGGAAGCAAGATTTACCGTTGTAGCTTTAATCTGTTCC-CTG
1 AATCTTTTTAACTGCAATGTCAG-GGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTG
14217734 C
65 C
14217735 TCTTGAAGAT
Statistics
Matches: 482, Mismatches: 59, Indels: 43
0.83 0.10 0.07
Matches are distributed among these distances:
91 4 0.01
92 40 0.08
93 2 0.00
94 1 0.00
97 6 0.01
98 3 0.01
99 1 0.00
100 253 0.52
101 162 0.34
102 2 0.00
103 3 0.01
104 5 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (100 bp):
AATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGC
ACTGCCTGGGAGGTAAGATTCGCTGTTGTAGCTTT
Found at i:14218989 original size:7 final size:7
Alignment explanation
Indices: 14218972--14219040 Score: 58
Period size: 7 Copynumber: 10.1 Consensus size: 7
14218962 TTAGCCTCTC
14218972 CATTTTT
1 CATTTTT
14218979 -ATTTTT
1 CATTTTT
14218985 CA-TTTT
1 CATTTTT
14218991 CATTTTT
1 CATTTTT
*
14218998 C-CTTTT
1 CATTTTT
14219004 CATTTTT
1 CATTTTT
*
14219011 --GTTTT
1 CATTTTT
14219016 CACTTTTTT
1 CA--TTTTT
14219025 CATTTTT
1 CATTTTT
14219032 CATATTTT
1 CAT-TTTT
14219040 C
1 C
14219041 TGACTCAGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
5 4 0.08
6 17 0.34
7 18 0.36
8 5 0.10
9 6 0.12
ACGTcount: A:0.13, C:0.16, G:0.01, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:14218990 original size:13 final size:13
Alignment explanation
Indices: 14218972--14219040 Score: 68
Period size: 13 Copynumber: 5.1 Consensus size: 13
14218962 TTAGCCTCTC
*
14218972 CATTTTTATTTTT
1 CATTTTCATTTTT
14218985 CATTTTCATTTTT
1 CATTTTCATTTTT
*
14218998 CCTTTTCATTTTT
1 CATTTTCATTTTT
*
14219011 -GTTTTCACTTTTTT
1 CATTTTCA--TTTTT
14219025 CATTTTTCATATTTT
1 CA-TTTTCAT-TTTT
14219040 C
1 C
14219041 TGACTCAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
12 6 0.13
13 24 0.51
14 6 0.13
15 5 0.11
16 6 0.13
ACGTcount: A:0.13, C:0.16, G:0.01, T:0.70
Consensus pattern (13 bp):
CATTTTCATTTTT
Found at i:14218996 original size:19 final size:19
Alignment explanation
Indices: 14218972--14219009 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14218962 TTAGCCTCTC
*
14218972 CATTTTTATTTTTCATTTT
1 CATTTTTACTTTTCATTTT
*
14218991 CATTTTTCCTTTTCATTTT
1 CATTTTTACTTTTCATTTT
14219010 TGTTTTCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (19 bp):
CATTTTTACTTTTCATTTT
Found at i:14219021 original size:19 final size:18
Alignment explanation
Indices: 14218981--14219022 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
14218971 CCATTTTTAT
14218981 TTTTCATTTTCATTTTTCC
1 TTTTCATTTT-ATTTTTCC
14219000 TTTTCATTTT-TGTTTTCAC
1 TTTTCATTTTAT-TTTTC-C
14219019 TTTT
1 TTTT
14219023 TTCATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.05
18 5 0.24
19 15 0.71
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTCATTTTATTTTTCC
Found at i:14224608 original size:14 final size:15
Alignment explanation
Indices: 14224577--14224613 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
14224567 GAGAACTTGA
14224577 TATAAATAATAGTATG
1 TATAAA-AATAGTATG
14224593 TATAAAAATA-TATG
1 TATAAAAATAGTATG
14224607 TATAAAA
1 TATAAAA
14224614 GTTGAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 4 0.19
16 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (15 bp):
TATAAAAATAGTATG
Found at i:14224836 original size:17 final size:18
Alignment explanation
Indices: 14224797--14224830 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14224787 TATTAACACT
*
14224797 TAAAATAATATTATATAG
1 TAAAATAATAGTATATAG
14224815 TAAAATAAT-GTATATA
1 TAAAATAATAGTATATA
14224831 CGAAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAAATAATAGTATATAG
Found at i:14242882 original size:8 final size:9
Alignment explanation
Indices: 14242858--14242883 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
14242848 GAAAACTATA
14242858 GTGTTTTTG
1 GTGTTTTTG
14242867 GTGTTTTTG
1 GTGTTTTTG
14242876 GTGTTTTT
1 GTGTTTTT
14242884 TCTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (9 bp):
GTGTTTTTG
Found at i:14246029 original size:52 final size:52
Alignment explanation
Indices: 14245958--14246109 Score: 268
Period size: 52 Copynumber: 2.9 Consensus size: 52
14245948 ATCAAGTGAC
* **
14245958 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
14246010 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
*
14246062 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
14246110 AGTGATAAGT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 96 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:14246127 original size:37 final size:37
Alignment explanation
Indices: 14246083--14246229 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
14246073 TGATAGCTTC
*
14246083 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
14246120 GGCTACACTTATCTGATCAAGAAATAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
14246157 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
14246194 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
14246229 G
1 G
14246230 ATCATACGTA
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 88 0.85
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:14248904 original size:18 final size:20
Alignment explanation
Indices: 14248881--14248924 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14248871 AATTAGATTT
*
14248881 TAAAAAT-TCA-ATTAAAAA
1 TAAAAATATCATAATAAAAA
*
14248899 TAAAAATATTATAATAAAAA
1 TAAAAATATCATAATAAAAA
14248919 TAAAAA
1 TAAAAA
14248925 AATGGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAAATATCATAATAAAAA
Found at i:14255133 original size:25 final size:25
Alignment explanation
Indices: 14255105--14255196 Score: 114
Period size: 25 Copynumber: 3.7 Consensus size: 25
14255095 TCTGACCCAC
14255105 AGCTCGTGTGAGCATACCGATTTAT
1 AGCTCGTGTGAGCATACCGATTTAT
* * *
14255130 AGCTCGTGAT-AGCATACCAATCTAC
1 AGCTCGTG-TGAGCATACCGATTTAT
* *
14255155 AGCTCGAGTGAGCATACCGATTCAT
1 AGCTCGTGTGAGCATACCGATTTAT
*
14255180 AGCTCGTATGAGCATAC
1 AGCTCGTGTGAGCATAC
14255197 ATGTACATGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.02
25 53 0.96
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (25 bp):
AGCTCGTGTGAGCATACCGATTTAT
Found at i:14257872 original size:20 final size:18
Alignment explanation
Indices: 14257822--14257873 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
14257812 TTACAAGATA
14257822 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
14257839 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
14257859 AATATTAAATTAATA
1 AATATTAAATTAATA
14257874 AAATACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:14258363 original size:19 final size:19
Alignment explanation
Indices: 14258325--14258364 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
14258315 AAAATATCAT
* *
14258325 ATTAATTTTAATTAATTTG
1 ATTAATTTAAATTAACTTG
*
14258344 ATTAATTTAAATTTACTTG
1 ATTAATTTAAATTAACTTG
14258363 AT
1 AT
14258365 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTAACTTG
Found at i:14259776 original size:16 final size:17
Alignment explanation
Indices: 14259739--14259784 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
14259729 ATTAAATTTG
*
14259739 ATTTAATATTTATCTTA
1 ATTTAATATTTATATTA
14259756 A--TAATATTT-TATTA
1 ATTTAATATTTATATTA
*
14259770 ATTTAATATTAATAT
1 ATTTAATATTTATAT
14259785 GAGTAGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
16 7 0.29
17 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTAATATTTATATTA
Found at i:14261788 original size:28 final size:28
Alignment explanation
Indices: 14261757--14261824 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
14261747 AGTGAGGGCC
*
14261757 TAGCCCGATACAATAATAGTGTGAACCT
1 TAGCCCAATACAATAATAGTGTGAACCT
**
14261785 TAGCCCAATACAATAATAGTGTGGGCCT
1 TAGCCCAATACAATAATAGTGTGAACCT
14261813 TAGCCCAATACA
1 TAGCCCAATACA
14261825 GTAACAGTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (28 bp):
TAGCCCAATACAATAATAGTGTGAACCT
Found at i:14261964 original size:26 final size:26
Alignment explanation
Indices: 14261935--14261989 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
14261925 AACACACCAA
* *
14261935 TATCGCAGTAAAGCTGCCAGTAATAG
1 TATCGCAGTAAAGCTGCCAATAACAG
*
14261961 TATCGCAGTGAAGCTGCCAATAACAG
1 TATCGCAGTAAAGCTGCCAATAACAG
14261987 TAT
1 TAT
14261990 ATGTGGCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (26 bp):
TATCGCAGTAAAGCTGCCAATAACAG
Found at i:14262191 original size:53 final size:53
Alignment explanation
Indices: 14262133--14262268 Score: 184
Period size: 54 Copynumber: 2.5 Consensus size: 53
14262123 TAACAGTTAT
*
14262133 TTTACCTTATGGGGGTATTTCGGTCATTTTACCCTA-TGGGGTATTTCGGTCA
1 TTTACCTTATGGGGGTATTTCGGTCATTTTACCCTATTAGGGTATTTCGGTCA
* * * *
14262185 TCTTACCCTATGGGGATATTTCAGTCATTTTACCCTATTAGGGTATTTTGGTCA
1 T-TTACCTTATGGGGGTATTTCGGTCATTTTACCCTATTAGGGTATTTCGGTCA
* *
14262239 TTCTACCTTATGGCGGTATTTCGATCATTT
1 TT-TACCTTATGGGGGTATTTCGGTCATTT
14262269 ATTGATCGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
52 1 0.01
53 33 0.46
54 37 0.52
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (53 bp):
TTTACCTTATGGGGGTATTTCGGTCATTTTACCCTATTAGGGTATTTCGGTCA
Found at i:14262231 original size:27 final size:26
Alignment explanation
Indices: 14262126--14262268 Score: 144
Period size: 27 Copynumber: 5.3 Consensus size: 26
14262116 TGAGGTATAA
* *
14262126 CAGTTATTTTACCTTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
*
14262153 CGGTCATTTTACCCTATGGGGTATTT
1 CAGTCATTTTACCCTATGGGGTATTT
* *
14262179 CGGTCATCTTACCCTATGGGGATATTT
1 CAGTCATTTTACCCTATGGGG-TATTT
*
14262206 CAGTCATTTTACCCTATTAGGGTATTT
1 CAGTCATTTTACCCTA-TGGGGTATTT
** * *
14262233 TGGTCATTCTACCTTATGGCGGTATTT
1 CAGTCATTTTACCCTATGG-GGTATTT
14262260 C-GATCATTT
1 CAG-TCATTT
14262269 ATTGATCGCT
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
26 32 0.33
27 62 0.63
28 4 0.04
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (26 bp):
CAGTCATTTTACCCTATGGGGTATTT
Found at i:14264925 original size:69 final size:69
Alignment explanation
Indices: 14264769--14264926 Score: 262
Period size: 69 Copynumber: 2.3 Consensus size: 69
14264759 TCCATACCTG
* *
14264769 AGCTATGGTCTTATACCCTACAATCCTCGTGTTTACTATCCTGGAAGACTCTTTTGGTTGCCATA
1 AGCTATGGTCTTATACCTTACAATCCTAGTGTTTACTATCCTGGAAGACTCTTTTGGTTGCCATA
14264834 ACCA
66 ACCA
* *
14264838 AGCTATGGTCTTAAACCTTACAATCCTAGTGTTTACTGTCCTGGAAGACTCTTTTGGTTGCCATA
1 AGCTATGGTCTTATACCTTACAATCCTAGTGTTTACTATCCTGGAAGACTCTTTTGGTTGCCATA
*
14264903 ATCA
66 ACCA
*
14264907 GGCTATGGTCTTATACCTTA
1 AGCTATGGTCTTATACCTTA
14264927 TACCTCTTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 82 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (69 bp):
AGCTATGGTCTTATACCTTACAATCCTAGTGTTTACTATCCTGGAAGACTCTTTTGGTTGCCATA
ACCA
Found at i:14266958 original size:44 final size:45
Alignment explanation
Indices: 14266904--14267021 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 45
14266894 TACTAGCAGT
* *
14266904 TTAA-TTGCAAAAACTGGTGGTTTATCCA-AACTTACTGGCAAC-TT
1 TTAACTTGC-AAAACTGGTGGTTTATCCACAAC-TACTGACAACGTA
* * * * *
14266948 TTATC-TGC-AAACTTGTTGTGTATGCACAACTACTGACAACGTA
1 TTAACTTGCAAAACTGGTGGTTTATCCACAACTACTGACAACGTA
14266991 TTAACTTGCAAAACTGGTGGTTTATCCACAA
1 TTAACTTGCAAAACTGGTGGTTTATCCACAA
14267022 ACTTATTGCT
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
42 23 0.40
43 8 0.14
44 9 0.16
45 17 0.30
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (45 bp):
TTAACTTGCAAAACTGGTGGTTTATCCACAACTACTGACAACGTA
Found at i:14267065 original size:89 final size:90
Alignment explanation
Indices: 14266913--14267293 Score: 290
Period size: 90 Copynumber: 4.3 Consensus size: 90
14266903 TTTAATTGCA
* * * ** *
14266913 AAAACTGGTGGTTTAT-C--CAAACTTACTGGC-AACTTTTATCTGCAAACTTGTTGTGTATGCA
1 AAAACTGGTGGTTCATCCATCAAACTTACT-GCTAGCTTTTATCTACAAACCCGTTGTGTATTCA
* * *
14266974 CAACTACTGACAACGTATTAACTTGC
65 CAACTAATGACAATGTATTAACCTGC
* * *
14267000 AAAACTGGTGGTTTATCCA-CAAACTTATTGCTAGTTTTTATCTACAAACCCGTTGTGTATTCAC
1 AAAACTGGTGGTTCATCCATCAAACTTACTGCTAGCTTTTATCTACAAACCCGTTGTGTATTCAC
* * * *
14267064 AACTATTAATAGTGTATTAACCTGC
66 AACTAATGACAATGTATTAACCTGC
* * * * *** * * * * *
14267089 AACATTAGTGGTTCATCCATGATTTTTACTGGTAGTTTTTATCTACAAACTCATTTTGTATTCAC
1 AAAACTGGTGGTTCATCCATCAAACTTACTGCTAGCTTTTATCTACAAACCCGTTGTGTATTCAC
* *
14267154 AACTAATGGCAATGTATTAACCTAC
66 AACTAATGACAATGTATTAACCTGC
* * * *** * *
14267179 AATACCGGTGGTTCATCCATGATTTTTACTGGTAGCTTTTATCTACAAACCCGTTGTGTACTCAC
1 AAAACTGGTGGTTCATCCATCAAACTTACTGCTAGCTTTTATCTACAAACCCGTTGTGTATTCAC
* ** *
14267244 AACTAGTGGTAGTGTATTAACCTG-
66 AACTAATGACAATGTATTAACCTGC
* * *
14267268 AAATATTGTTAGTTCATCCA-CAAACT
1 AAA-ACTGGTGGTTCATCCATCAAACT
14267294 AAAGTTTCCG
Statistics
Matches: 235, Mismatches: 54, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
87 16 0.07
88 3 0.01
89 73 0.31
90 143 0.61
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (90 bp):
AAAACTGGTGGTTCATCCATCAAACTTACTGCTAGCTTTTATCTACAAACCCGTTGTGTATTCAC
AACTAATGACAATGTATTAACCTGC
Found at i:14267157 original size:90 final size:90
Alignment explanation
Indices: 14267031--14267267 Score: 330
Period size: 90 Copynumber: 2.6 Consensus size: 90
14267021 AACTTATTGC
* ** **
14267031 TAGTTTTTATCTACAAACCCGTTGTGTATTCACAACTATTAATAGTGTATTAACCTGCAACATTA
1 TAGTTTTTATCTACAAACCCGTTGTGTATTCACAACTAATGGTAGTGTATTAACCTGCAACACCA
14267096 GTGGTTCATCCATGATTTTTACTGG
66 GTGGTTCATCCATGATTTTTACTGG
* * * * * * * *
14267121 TAGTTTTTATCTACAAACTCATTTTGTATTCACAACTAATGGCAATGTATTAACCTACAATACCG
1 TAGTTTTTATCTACAAACCCGTTGTGTATTCACAACTAATGGTAGTGTATTAACCTGCAACACCA
14267186 GTGGTTCATCCATGATTTTTACTGG
66 GTGGTTCATCCATGATTTTTACTGG
* * *
14267211 TAGCTTTTATCTACAAACCCGTTGTGTACTCACAACTAGTGGTAGTGTATTAACCTG
1 TAGTTTTTATCTACAAACCCGTTGTGTATTCACAACTAATGGTAGTGTATTAACCTG
14267268 AAATATTGTT
Statistics
Matches: 125, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 125 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (90 bp):
TAGTTTTTATCTACAAACCCGTTGTGTATTCACAACTAATGGTAGTGTATTAACCTGCAACACCA
GTGGTTCATCCATGATTTTTACTGG
Found at i:14273237 original size:39 final size:39
Alignment explanation
Indices: 14273140--14273526 Score: 381
Period size: 39 Copynumber: 9.9 Consensus size: 39
14273130 TAGAAATACG
* * *
14273140 GTGATTATACAGGCTATGCGCCTAGCAGGCTTTGTGCC-
1 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* * *
14273178 GATG-TTATTCGGGTTAAGTGCCTAGTAGGCTTTGTGCCA
1 G-TGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* * * *
14273217 GTGAATATTCAGGTTAAGTGCCTAGCCGTG-TTTGTGTCA
1 GTGATTATTCAGGCTAAGTGCCTAGCAG-GCTTTGTGCCA
* *
14273256 GTGACTATTCAGGCTAAGTGCCTAGCAGGCATTGTGCC-
1 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* * *
14273294 GTTGATTATTCAGGCTATGTGCCTAGCAGGCTTTGTGTCG
1 G-TGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* * * **
14273334 GTGATTATTCGGGCTAAGTGCCCAACAGGCTTTGTG-TT
1 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* *
14273372 GCTGATTATTCAGGCTCAGTGCCTAGCAGGCTTTGTGTCA
1 G-TGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* * * *
14273412 ATGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGTCG
1 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
** * * *
14273451 GTGATTATTTGGGCTATGTGCCTAGCAGGCTTTAT-ACA
1 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
** *
14273489 GGTGATTATTCAGGCTTTGTGCCTAGTAGGCTTTGTGC
1 -GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGC
14273527 TGGTGTATTG
Statistics
Matches: 290, Mismatches: 48, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
38 35 0.12
39 253 0.87
40 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (39 bp):
GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
Found at i:14273354 original size:117 final size:116
Alignment explanation
Indices: 14273140--14273526 Score: 454
Period size: 117 Copynumber: 3.3 Consensus size: 116
14273130 TAGAAATACG
* * * * *
14273140 GTGATTATACAGGCTATGCGCCTAGCAGGCTTTGTGCCGATG-TTATTCGGGTTAAGTGCCTAGT
1 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCGATGATTATTCGGGCTAAGTGCCTAGC
* * * * * *
14273204 AGGCTTTGTGCCAGTGAATATTCAGGTTAAGTGCCTAGCCGTG-TTTGTGTCA
66 AGGCTTTGTGTCGGTGATTATTCGGGCTAAGTGCCTAGCAG-GCTTTGTGT-A
* * * * *
14273256 GTGACTATTCAGGCTAAGTGCCTAGCAGGCATTGTGCCGTTGATTATTCAGGCTATGTGCCTAGC
1 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCGATGATTATTCGGGCTAAGTGCCTAGC
* * *
14273321 AGGCTTTGTGTCGGTGATTATTCGGGCTAAGTGCCCAACAGGCTTTGTGTT
66 AGGCTTTGTGTCGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGTA
* * *
14273372 GCTGATTATTCAGGCTCAGTGCCTAGCAGGCTTTGTGTCAATGATTATTCGGGCTAAGTGCCTAG
1 G-TGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCGATGATTATTCGGGCTAAGTGCCTAG
* * * **
14273437 CAGGCTTTGTGTCGGTGATTATTTGGGCTATGTGCCTAGCAGGCTTTATACA
65 CAGGCTTTGTGTCGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGTA
** *
14273489 GGTGATTATTCAGGCTTTGTGCCTAGTAGGCTTTGTGC
1 -GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGC
14273527 TGGTGTATTG
Statistics
Matches: 228, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
116 38 0.17
117 189 0.83
118 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (116 bp):
GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCGATGATTATTCGGGCTAAGTGCCTAGC
AGGCTTTGTGTCGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGTA
Found at i:14280153 original size:17 final size:17
Alignment explanation
Indices: 14280133--14280182 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
14280123 GTTTAGTATT
14280133 TTTGGATAAATTATTGA
1 TTTGGATAAATTATTGA
*
14280150 TTTGAGA-AAATTAGTTAA
1 TTTG-GATAAATTA-TTGA
14280168 TTT-GATAAATT-TTGA
1 TTTGGATAAATTATTGA
14280183 GTTAAGGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 15 0.54
18 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (17 bp):
TTTGGATAAATTATTGA
Found at i:14280542 original size:39 final size:39
Alignment explanation
Indices: 14280496--14280962 Score: 618
Period size: 39 Copynumber: 12.0 Consensus size: 39
14280486 AATAGAAATA
*
14280496 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGT
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * *
14280535 CGATGATTATTCGGGATATGTGCCTAGTAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * *
14280574 TGGTGATTATTTGGGCTAAGTGCCTAGTAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
*
14280613 TGGTGATTATTCGGGCTATA-TGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTA-AGTGCCTAGCAGGCTTTGTGC
* *
14280652 TGGTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* *
14280691 CGCTGATTATTCGGGCTTAGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
14280730 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* * * *
14280769 CGGAT-ATTATTTGAGCTATGTACCTAGCAGGCTTTGTGC
1 CGG-TGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* *
14280808 CGGTGATTATTCGGGCTATGTGCCTAGTAGGCTTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* *
14280847 CGGTGATTATTCGGGCTATGTGCCTAGTAGGCTTTGT-C
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
* ** * **
14280885 AGGTGATTATTCGGGCTTTGTTCCTAAAAGG-TTTGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
** *
14280923 CGGTGATTATTCGGGCTTTGTGCCTAGCAGGCTATGTGC
1 CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
14280962 C
1 C
14280963 AGTGTATTGG
Statistics
Matches: 385, Mismatches: 37, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
37 5 0.01
38 57 0.15
39 321 0.83
40 2 0.01
ACGTcount: A:0.16, C:0.18, G:0.31, T:0.35
Consensus pattern (39 bp):
CGGTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGC
Found at i:14280824 original size:23 final size:23
Alignment explanation
Indices: 14280798--14280870 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 23
14280788 GTACCTAGCA
*
14280798 GGCTTTGTGCCGGTGATTATTCG
1 GGCTATGTGCCGGTGATTATTCG
*
14280821 GGCTATGTGCC--T-AGTA----
1 GGCTATGTGCCGGTGATTATTCG
*
14280837 GGCTTTGTGCCGGTGATTATTCG
1 GGCTATGTGCCGGTGATTATTCG
14280860 GGCTATGTGCC
1 GGCTATGTGCC
14280871 TAGTAGGCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
16 10 0.26
18 1 0.03
19 3 0.08
20 3 0.08
21 1 0.03
23 20 0.53
ACGTcount: A:0.11, C:0.19, G:0.34, T:0.36
Consensus pattern (23 bp):
GGCTATGTGCCGGTGATTATTCG
Found at i:14284598 original size:16 final size:17
Alignment explanation
Indices: 14284577--14284614 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
14284567 TTCAATATGG
*
14284577 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
14284593 ATTTTACTACTGTATTTT
1 ATTTTACTA-TGTATTTT
14284611 ATTT
1 ATTT
14284615 GAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:14286760 original size:22 final size:22
Alignment explanation
Indices: 14286718--14286778 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
14286708 GGATATTATA
** *
14286718 TGATATGATATGTTATAAGATGC
1 TGATATGATATGACATGAGAT-C
14286741 -GATATGATATGACATGAGATC
1 TGATATGATATGACATGAGATC
* *
14286762 TGATTTGATTTGACATG
1 TGATATGATATGACATG
14286779 TTATTAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (22 bp):
TGATATGATATGACATGAGATC
Found at i:14288011 original size:19 final size:19
Alignment explanation
Indices: 14287987--14288024 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
14287977 CCTTCAGTTG
14287987 GAATCTTCGTAAAATAATT
1 GAATCTTCGTAAAATAATT
14288006 GAATCTTCGTAAAATAATT
1 GAATCTTCGTAAAATAATT
14288025 TTGCATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
GAATCTTCGTAAAATAATT
Found at i:14292102 original size:13 final size:13
Alignment explanation
Indices: 14292084--14292108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14292074 TGTCGTTCCA
14292084 GTGACTTAATTTG
1 GTGACTTAATTTG
14292097 GTGACTTAATTT
1 GTGACTTAATTT
14292109 CATGGTTGTG
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
GTGACTTAATTTG
Found at i:14292481 original size:63 final size:60
Alignment explanation
Indices: 14292411--14292553 Score: 177
Period size: 61 Copynumber: 2.4 Consensus size: 60
14292401 TTTTTCTAAT
* * * *
14292411 ATTATATATTTTTATTTTTATTAATTCATATTTTAATAATAATTATATTAAGAATGTTATTAA
1 ATTATATATTTTTATTTTTATTAATT-ATA-TTTAATAATAAATAGATTAA-AATATAATTAA
14292474 ATTATATATTTTTA-TTTTATTAAATTATATTTAATAATAAATAGATTAAAATATAATTAA
1 ATTATATATTTTTATTTTTATT-AATTATATTTAATAATAAATAGATTAAAATATAATTAA
*
14292534 A--ATAT-TTATTATTTTTATTA
1 ATTATATATTTTTATTTTTATTA
14292554 CATTTAATAA
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
57 6 0.08
58 11 0.15
60 10 0.14
61 18 0.25
62 10 0.14
63 18 0.25
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (60 bp):
ATTATATATTTTTATTTTTATTAATTATATTTAATAATAAATAGATTAAAATATAATTAA
Found at i:14293414 original size:41 final size:41
Alignment explanation
Indices: 14293356--14293593 Score: 266
Period size: 41 Copynumber: 5.8 Consensus size: 41
14293346 AGAGTTTTGG
*
14293356 GGGCATTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
* * *
14293397 GGGGCTTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
* * *
14293438 AGGG-ATTTAGCGGCGTTTTTGAAAAAG-AGCCCCTAATGTTC
1 -GGGCCTTTAGCGGCGTTTTTGAAAAAGCA-CCGCTAATGCTC
* **
14293479 GGGCCTTTAGCGGCGTTTTTGGAAAAGTGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
** * *
14293520 GTACCTTTTGTGGCGTTTTT-AGAAAAGCACCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGA-AAAAGCACCGCTAATGCTC
** * *
14293561 GTACCTTTAGCTGCGTTTTTGAAAAAGCGCCGC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGC
14293594 AAATAATAAA
Statistics
Matches: 166, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
40 3 0.02
41 159 0.96
42 4 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTC
Found at i:14293580 original size:123 final size:122
Alignment explanation
Indices: 14293356--14293587 Score: 297
Period size: 123 Copynumber: 1.9 Consensus size: 122
14293346 AGAGTTTTGG
**
14293356 GGGCATTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGGGCTTTAGCGACGTTTTTGAAA
1 GGGCATTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGACCTTTAGCGACGTTTTTGAAA
*
14293421 AAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTTGAAAAAGAGCCCCTAATGTTC
66 AAGCACCGCTAATGCTCA-GGATTTAGCGGCGTTTTTGAAAAAGAGCCCCTAATGTTC
* * ** * * * *
14293479 GGGCCTTTAGCGGCGTTTTTGGAAAAGTGCCGCTAATGCTCGTACCTTTTGTGGCGTTTTT-AGA
1 GGGCATTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGACCTTTAGCGACGTTTTTGA-A
* *
14293543 AAAGCACCGCTAATGCTC-GTACCTTTAGCTGCGTTTTTGAAAAAG
65 AAAGCACCGCTAATGCTCAGGA--TTTAGCGGCGTTTTTGAAAAAG
14293588 CGCCGCAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
121 2 0.02
122 1 0.01
123 90 0.97
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (122 bp):
GGGCATTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCGGACCTTTAGCGACGTTTTTGAAA
AAGCACCGCTAATGCTCAGGATTTAGCGGCGTTTTTGAAAAAGAGCCCCTAATGTTC
Found at i:14294710 original size:27 final size:28
Alignment explanation
Indices: 14294681--14294746 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
14294671 CAGTTTTGAG
*
14294681 TTTAGGGTTTAGGGTTTAGGGTTT-AGG
1 TTTAGGGTTTAGGGATTAGGGTTTAAGG
* * * *
14294708 TTTAGGGCTTGGGGATTGGGGTTTAAGA
1 TTTAGGGTTTAGGGATTAGGGTTTAAGG
*
14294736 TTTAGAGTTTA
1 TTTAGGGTTTA
14294747 CATTTTAGTG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.18, C:0.02, G:0.38, T:0.42
Consensus pattern (28 bp):
TTTAGGGTTTAGGGATTAGGGTTTAAGG
Found at i:14294711 original size:6 final size:7
Alignment explanation
Indices: 14294680--14294746 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
14294670 ACAGTTTTGA
14294680 GTTTAGG
1 GTTTAGG
14294687 GTTTAGG
1 GTTTAGG
14294694 GTTTAGG
1 GTTTAGG
14294701 GTTTA-G
1 GTTTAGG
14294707 GTTTAGG
1 GTTTAGG
* *
14294714 GCTTGGG
1 GTTTAGG
* *
14294721 GATTGGG
1 GTTTAGG
*
14294728 GTTTAAG
1 GTTTAGG
* *
14294735 ATTTAGA
1 GTTTAGG
14294742 GTTTA
1 GTTTA
14294747 CATTTTAGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
6 6 0.12
7 43 0.88
ACGTcount: A:0.18, C:0.01, G:0.39, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:14295193 original size:24 final size:25
Alignment explanation
Indices: 14295157--14295204 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
14295147 TTAAAATGAA
14295157 TTTTAAAAGATTT-TAAACTTTTAT
1 TTTTAAAAGATTTATAAACTTTTAT
* * *
14295181 TTTTATAATATTTATATACTTTTA
1 TTTTAAAAGATTTATAAACTTTTA
14295205 AAGAAAAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTAAAAGATTTATAAACTTTTAT
Found at i:14295446 original size:41 final size:41
Alignment explanation
Indices: 14295399--14295485 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
14295389 AAGTTCTATG
*
14295399 ATTTTGGGCCGACTTTGTTATACGGGCAAATCCATATAAAA
1 ATTTTGGGCCGACTTTGTTATACGAGCAAATCCATATAAAA
**
14295440 ATTTTGGGCCGACTTTGTTATACGAGCTTATCCATATAAAA
1 ATTTTGGGCCGACTTTGTTATACGAGCAAATCCATATAAAA
14295481 ATTTT
1 ATTTT
14295486 ATCCATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (41 bp):
ATTTTGGGCCGACTTTGTTATACGAGCAAATCCATATAAAA
Found at i:14299328 original size:43 final size:43
Alignment explanation
Indices: 14299239--14299480 Score: 360
Period size: 43 Copynumber: 5.6 Consensus size: 43
14299229 ATAATTTTTT
* * ** * *
14299239 TAAAGGTTAT-GTTTTTAGCGGCGTTTGTGACAAAAAACGCCAC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTG-GGAAAAGCGCCGC
*
14299282 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
14299325 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGAGAAAAGTGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* *
14299368 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGAGCAGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
14299411 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
14299454 TAAAGGTCATGGTCTTTAGCGGCGTTT
1 TAAAGGTCATGGTCTTTAGCGGCGTTT
14299481 ATTTCTAAAA
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
43 164 0.91
44 17 0.09
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (43 bp):
TAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:14302761 original size:23 final size:24
Alignment explanation
Indices: 14302714--14302770 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 24
14302704 TGGGCTAGGA
*
14302714 TAATTTTATTAATCAATTCAACAT
1 TAATTTTATTAAGCAATTCAACAT
14302738 TAATTTTATTAAGCAA-TCAACAT
1 TAATTTTATTAAGCAATTCAACAT
14302761 TAATTTTATT
1 TAATTTTATT
14302771 TCGATCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTTTATTAAGCAATTCAACAT
Found at i:14303775 original size:27 final size:27
Alignment explanation
Indices: 14303745--14303807 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
14303735 GAAAAAGAAT
14303745 AGAAGAGAAAGAAGATTCAGCCAGCAG
1 AGAAGAGAAAGAAGATTCAGCCAGCAG
** *
14303772 AGAAGAGAAAGAAGATTTGGCCAGTAG
1 AGAAGAGAAAGAAGATTCAGCCAGCAG
14303799 AGAAGAGAA
1 AGAAGAGAA
14303808 GAGAGAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.32, T:0.10
Consensus pattern (27 bp):
AGAAGAGAAAGAAGATTCAGCCAGCAG
Done.