Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold118
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: 1286304
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 1 of 8
Found at i:3563 original size:13 final size:13
Alignment explanation
Indices: 3545--3570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3535 CAATTTTTTG
3545 TGTATCGATACAT
1 TGTATCGATACAT
3558 TGTATCGATACAT
1 TGTATCGATACAT
3571 ACTTGCTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4650 original size:29 final size:28
Alignment explanation
Indices: 4609--4663 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
4599 TCACCCATAT
* * *
4609 TATTTTTTTAATTTATTTTTTAAAAATA
1 TATTTTTTAAATTTAATCTTTAAAAATA
4637 TATTTTTTAAAATTTAATCTTTAAAAA
1 TATTTTTT-AAATTTAATCTTTAAAAA
4664 CTTAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTTTTAAATTTAATCTTTAAAAATA
Found at i:6356 original size:3 final size:3
Alignment explanation
Indices: 6350--6381 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6340 GAAGAAGAAG
*
6350 AAC AAC AAC AAC AAC AAC AAT AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
6382 AGGAGACGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:9808 original size:6 final size:6
Alignment explanation
Indices: 9799--9823 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9789 TGTCTATGCC
9799 GTGTCT GTGTCT GTGTCT GTGTCT G
1 GTGTCT GTGTCT GTGTCT GTGTCT G
9824 GTTATTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (6 bp):
GTGTCT
Found at i:10890 original size:31 final size:31
Alignment explanation
Indices: 10855--10916 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
10845 ACAAGGGTGT
*
10855 GAAAAGATCATCAATAAAGAAATA-TCCCACC
1 GAAAAAATCATCAATAAAGAAA-AGTCCCACC
10886 GAAAAAATCATCAATAAAGAAAAGTCCCACC
1 GAAAAAATCATCAATAAAGAAAAGTCCCACC
10917 TACTTTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.53, C:0.23, G:0.10, T:0.15
Consensus pattern (31 bp):
GAAAAAATCATCAATAAAGAAAAGTCCCACC
Found at i:11786 original size:16 final size:16
Alignment explanation
Indices: 11761--11794 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11751 AGTTTTTTTT
*
11761 TTTTTTAAACATTTAC
1 TTTTTAAAACATTTAC
11777 TTTTTAAAACATTTAC
1 TTTTTAAAACATTTAC
11793 TT
1 TT
11795 GCTTGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTAAAACATTTAC
Found at i:12742 original size:27 final size:26
Alignment explanation
Indices: 12685--12742 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
12675 TCTAATTAAT
**
12685 AATTTATTATATTTTTTAATATTTTA
1 AATTTATTATATTTTTTAATATTCAA
* *
12711 TATTTATTTTATTTATTTAATATTCAA
1 AATTTATTATATTT-TTTAATATTCAA
12738 AATTT
1 AATTT
12743 TTGAACAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
AATTTATTATATTTTTTAATATTCAA
Found at i:14558 original size:38 final size:38
Alignment explanation
Indices: 14506--14658 Score: 127
Period size: 38 Copynumber: 4.1 Consensus size: 38
14496 ACATAGGTCA
* * *
14506 AAACAAAAATTACTATTCTCAACTGGTGGCATTGTTAG
1 AAACAAAAACTACTATTCTTAACTGGTGGCATAGTTAG
* *
14544 AAACAAAAACTACTA-TCTTAACTGGTGGCATAATTCG
1 AAACAAAAACTACTATTCTTAACTGGTGGCATAGTTAG
* * * * *
14581 AAACAAAAA-TCATTATTCTAAATTGATAGCACT-GTTCA-
1 AAACAAAAACT-ACTATTCTTAACTGGTGGCA-TAGTT-AG
* * *
14619 AAACAAAAACCATTATTCTTAACTGGTTGCATAGTT-G
1 AAACAAAAACTACTATTCTTAACTGGTGGCATAGTTAG
14656 AAA
1 AAA
14659 ATACTTTCTG
Statistics
Matches: 91, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
36 1 0.01
37 34 0.37
38 55 0.60
39 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (38 bp):
AAACAAAAACTACTATTCTTAACTGGTGGCATAGTTAG
Found at i:14584 original size:37 final size:38
Alignment explanation
Indices: 14506--14589 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 38
14496 ACATAGGTCA
* **
14506 AAACAAAAATTACTATTCTCAACTGGTGGCATTGTTAG
1 AAACAAAAACTACTATTCTCAACTGGTGGCATAATTAG
* *
14544 AAACAAAAACTACTA-TCTTAACTGGTGGCATAATTCG
1 AAACAAAAACTACTATTCTCAACTGGTGGCATAATTAG
14581 AAACAAAAA
1 AAACAAAAA
14590 TCATTATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 27 0.66
38 14 0.34
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.26
Consensus pattern (38 bp):
AAACAAAAACTACTATTCTCAACTGGTGGCATAATTAG
Found at i:14585 original size:75 final size:76
Alignment explanation
Indices: 14506--14651 Score: 179
Period size: 75 Copynumber: 1.9 Consensus size: 76
14496 ACATAGGTCA
* * * * * *
14506 AAACAAAAATTACTATTCTCAACTGGTGGCATTGTT-AGAAACAAAAACTACTA-TCTTAACTGG
1 AAACAAAAATCACTATTCTAAACTGATAGCACTGTTCA-AAACAAAAACCACTATTCTTAACTGG
14569 TGGCATAATTCG
65 TGGCATAATTCG
* * *
14581 AAACAAAAATCATTATTCTAAATTGATAGCACTGTTCAAAACAAAAACCATTATTCTTAACTGGT
1 AAACAAAAATCACTATTCTAAACTGATAGCACTGTTCAAAACAAAAACCACTATTCTTAACTGGT
*
14646 TGCATA
66 GGCATA
14652 GTTGAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
75 42 0.71
76 17 0.29
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (76 bp):
AAACAAAAATCACTATTCTAAACTGATAGCACTGTTCAAAACAAAAACCACTATTCTTAACTGGT
GGCATAATTCG
Found at i:16238 original size:4 final size:4
Alignment explanation
Indices: 16229--16294 Score: 51
Period size: 4 Copynumber: 16.5 Consensus size: 4
16219 ATAATTGAGC
* * * * * *
16229 TATA TATA TATA CATA TGTA TATA TATA CATA TGTA TGTA TATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
16277 TACA TACA TATG TATA TA
1 TATA TATA TATA TATA TA
16295 ATACATATGT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:16252 original size:16 final size:16
Alignment explanation
Indices: 16231--16277 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
16221 AATTGAGCTA
16231 TATATATATACATATG
1 TATATATATACATATG
16247 TATATATATACATATG
1 TATATATATACATATG
*
16263 TATGTATATACATAT
1 TATATATATACATAT
16278 ACATACATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TATATATATACATATG
Found at i:16271 original size:26 final size:26
Alignment explanation
Indices: 16248--16302 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
16238 ATACATATGT
*
16248 ATATATATACATATGTATGTATATAC
1 ATATACATACATATGTATGTATATAC
*
16274 ATATACATACATATGTATATA-ATAC
1 ATATACATACATATGTATGTATATAC
16299 ATAT
1 ATAT
16303 GTATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (26 bp):
ATATACATACATATGTATGTATATAC
Found at i:16287 original size:16 final size:16
Alignment explanation
Indices: 16229--16302 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 16
16219 ATAATTGAGC
*
16229 TATATATATATACATA
1 TATATACATATACATA
* *
16245 TGTATATATATACATA
1 TATATACATATACATA
* **
16261 TGTATGTATATACATA
1 TATATACATATACATA
* **
16277 TACATACATATGTATA
1 TATATACATATACATA
16293 TA-ATACATAT
1 TATATACATAT
16303 GTATTATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
15 8 0.16
16 42 0.84
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (16 bp):
TATATACATATACATA
Found at i:16865 original size:33 final size:33
Alignment explanation
Indices: 16818--16897 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
16808 CAAAAATTTA
*
16818 AAATTTTCATAATTTGTATCGATACATCTGGGT
1 AAATTTTCACAATTTGTATCGATACATCTGGGT
*
16851 AAATTTTCACAATTTGTATTGATACATCTGGGT
1 AAATTTTCACAATTTGTATCGATACATCTGGGT
16884 AAATTTTCACAATT
1 AAATTTTCACAATT
16898 CTAGGTCCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (33 bp):
AAATTTTCACAATTTGTATCGATACATCTGGGT
Found at i:19371 original size:80 final size:77
Alignment explanation
Indices: 19287--19447 Score: 216
Period size: 79 Copynumber: 2.1 Consensus size: 77
19277 TTATTTATGT
* * * * **
19287 TTTTATTTTTAAAATACCTGATTTTTCATCCTCGGA-ATACTCCAACCCCGTTATTTTCGAGGGG
1 TTTTATTTTTAAAACA-CTGATTTTTCATCATCAGAGATACTCCAACCCCGTTA-TTTCAAAAGG
19351 ATACTCCAACCCCTGA
64 ATACTCC-ACCCCT-A
*
19367 TTTTATTTTTAAAACACTGATTTTTCATCATCAGAGATACTCCAACCTCGTTATTTCAAAAGGAT
1 TTTTATTTTTAAAACACTGATTTTTCATCATCAGAGATACTCCAACCCCGTTATTTCAAAAGGAT
19432 ACTCCACCCCTA
66 ACTCCACCCCTA
19444 TTTT
1 TTTT
19448 TATCTACAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
77 5 0.07
78 6 0.08
79 31 0.42
80 31 0.42
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (77 bp):
TTTTATTTTTAAAACACTGATTTTTCATCATCAGAGATACTCCAACCCCGTTATTTCAAAAGGAT
ACTCCACCCCTA
Found at i:31831 original size:19 final size:20
Alignment explanation
Indices: 31798--31844 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
31788 CTTCTTTTTT
31798 AAAAAAAAAACAAAAAAAGC
1 AAAAAAAAAACAAAAAAAGC
31818 AAAAACAAAAA-AAAAAAGAG-
1 AAAAA-AAAAACAAAAAA-AGC
31838 AAAAAAA
1 AAAAAAA
31845 TGAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.08
20 16 0.64
21 7 0.28
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAACAAAAAAAGC
Found at i:31852 original size:30 final size:29
Alignment explanation
Indices: 31798--31866 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
31788 CTTCTTTTTT
*
31798 AAAAAAAAA-ACAAAAAAAGCAAAAACAA
1 AAAAAAAAAGACAAAAAAAGAAAAAACAA
* * *
31826 AAAAAAAAAGAGAAAAAAATGAAAAAAGAG
1 AAAAAAAAAGACAAAAAAA-GAAAAAACAA
*
31856 AAAAGAAAAGA
1 AAAAAAAAAGA
31867 ACCTACTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 9 0.26
29 8 0.24
30 17 0.50
ACGTcount: A:0.83, C:0.04, G:0.12, T:0.01
Consensus pattern (29 bp):
AAAAAAAAAGACAAAAAAAGAAAAAACAA
Found at i:33009 original size:61 final size:60
Alignment explanation
Indices: 32830--33224 Score: 461
Period size: 61 Copynumber: 6.5 Consensus size: 60
32820 AACCTTTTAT
* * * *
32830 CCTTTCAGTCCTCGAAGAGCAGGACGCATTTCCCTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * * *
32890 ATTTCCAGTCCTCAAAGAGTAAGATGCCTTTT-TTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
32950 CCTTCCAGTCCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * **
33011 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGTTCACACAAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACG-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** *
33072 CCTTCCAGTCCTCAAAGAGCTGGACGCTTTCTCCTTGCAAAGCCCATACAAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACGCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
33133 CCTTCTAGTCC-CTAAAGAGTAAGACACTTTTCTTTTTCCTTTAAAGCCCACACAAGTTGGTGGC
1 CCTTCCAGTCCTC-AAAGAGCAGGACGCTTTTC-----CTTTTAAAGCCCACACAAGTTGGTGGC
33197 A
60 A
**
33198 CCTTTTAGTCCTCAAAGAGCAGGACGC
1 CCTTCCAGTCCTCAAAGAGCAGGACGC
33225 ACTTCATTTC
Statistics
Matches: 282, Mismatches: 43, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
60 78 0.28
61 158 0.56
65 45 0.16
66 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (60 bp):
CCTTCCAGTCCTCAAAGAGCAGGACGCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:33301 original size:41 final size:41
Alignment explanation
Indices: 33205--33429 Score: 170
Period size: 41 Copynumber: 5.4 Consensus size: 41
33195 GCACCTTTTA
* * *
33205 GTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCATTTCCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCC-T--TTTCCCTTT
* *
33249 ATCCTCAAAGAGCATGACACACTTTATTTCCTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCCCTTT
* * ** * *
33290 GTCCTCGAAGAGTAGGATGCACTTTATTTCCGTTTCCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCCCTTT
* * * * * *
33331 TTCCTCAAAGAGTAAGACATA-TTTAATCTCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTT-ATTTCCTTTTCCCTTT
* ** * *
33372 GTCCTCAAGGAATAGGAC-CTA-TTTCA-TTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACAC-ACTTT-ATTTCCTTTTCCCTTT
33412 GTCCTCAAAGAGCAGGAC
1 GTCCTCAAAGAGCAGGAC
33430 GTATTTTTTT
Statistics
Matches: 145, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
40 30 0.21
41 87 0.60
43 1 0.01
44 27 0.19
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (41 bp):
GTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCCCTTT
Found at i:33429 original size:40 final size:39
Alignment explanation
Indices: 33322--33462 Score: 121
Period size: 34 Copynumber: 3.6 Consensus size: 39
33312 TTTATTTCCG
* * * * *
33322 TTTCCTTTTTTCCTCAAAGAGTAAGACATATTTAATCTCCTT
1 TTTCC-TTTGTCCTCAAAGAGCAGGACCTATTT-AT-TCTTT
* **
33364 TTTCCTTTGTCCTCAAGGAATAGGACCTATTTCATTCTTT
1 TTTCCTTTGTCCTCAAAGAGCAGGACCTATTT-ATTCTTT
*
33404 TTTCCTTTGTCCTCAAAGAGCAGGA-C---GTATT-TTT
1 TTTCCTTTGTCCTCAAAGAGCAGGACCTATTTATTCTTT
*
33438 TTTCCTTTGTGCTCAAAGAGCAGGA
1 TTTCCTTTGTCCTCAAAGAGCAGGA
33463 TGCCCCTTCT
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
34 27 0.31
35 3 0.03
36 1 0.01
39 1 0.01
40 26 0.30
41 24 0.28
42 5 0.06
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (39 bp):
TTTCCTTTGTCCTCAAAGAGCAGGACCTATTTATTCTTT
Found at i:34106 original size:20 final size:20
Alignment explanation
Indices: 34065--34107 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
34055 TACCTAGATA
*
34065 TATCGATACATTATTCATTG
1 TATCGATACATTATTCAATG
34085 TATCGATACATT-TCTCAATG
1 TATCGATACATTAT-TCAATG
34105 TAT
1 TAT
34108 TAATACATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (20 bp):
TATCGATACATTATTCAATG
Found at i:36526 original size:79 final size:79
Alignment explanation
Indices: 36440--36588 Score: 192
Period size: 79 Copynumber: 1.9 Consensus size: 79
36430 TCATTCATGT
* * * ** **
36440 TTTTATTTTTAAAATACCGATTTT-TCAACCTCGGGGATACTCCAACCTTGTTATTTTCGAGGGG
1 TTTTATTTCTAAAATACCGATTTTCT-AACATCAGGGATACTCCAACCCCGTTATTTTAAAGGGG
36504 ATACTCCAACCTTGA
65 ATACTCCAACCTTGA
* * *
36519 TTTTATTTCTAAAATATCGATTTTCTATCATCAGGGATACTCTAACCCCGTTATTTTAAAGGGGA
1 TTTTATTTCTAAAATACCGATTTTCTAACATCAGGGATACTCCAACCCCGTTATTTTAAAGGGGA
36584 TACTC
66 TACTC
36589 TACCCCCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 58 0.98
80 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (79 bp):
TTTTATTTCTAAAATACCGATTTTCTAACATCAGGGATACTCCAACCCCGTTATTTTAAAGGGGA
TACTCCAACCTTGA
Found at i:36602 original size:79 final size:80
Alignment explanation
Indices: 36439--36614 Score: 178
Period size: 79 Copynumber: 2.2 Consensus size: 80
36429 TTCATTCATG
* * * * ** **
36439 TTTTTATTTTTAAAATACCGATTTTTCAACCTCGGGGATACTCCAACCTTGTTATTTTCGAGGGG
1 TTTTTATTTCTAAAATATCGATTTTTCAACATCAGGGATACTCCAACCCCGTTATTTTAAAGGGG
***
36504 ATACTCCAACCTTGA
66 ATACTCCAACCCCCA
* *
36519 -TTTTATTTCTAAAATATCGA-TTTTCTATCATCAGGGATACTCTAACCCCGTTATTTTAAAGGG
1 TTTTTATTTCTAAAATATCGATTTTTC-AACATCAGGGATACTCCAACCCCGTTATTTTAAAGGG
*
36582 GATACT-CTACCCCCA
65 GATACTCCAACCCCCA
* *
36597 TTTTTATCTCCAAAATAT
1 TTTTTATTTCTAAAATAT
36615 TTAATTTTTC
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
78 10 0.13
79 68 0.87
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (80 bp):
TTTTTATTTCTAAAATATCGATTTTTCAACATCAGGGATACTCCAACCCCGTTATTTTAAAGGGG
ATACTCCAACCCCCA
Found at i:39045 original size:38 final size:38
Alignment explanation
Indices: 39001--39193 Score: 146
Period size: 38 Copynumber: 5.2 Consensus size: 38
38991 TTTAACCCTT
* *
39001 GTGGCATAGGTCAGAACAAAAATCATTATTCTTAACTA
1 GTGGCACAGGTCAAAACAAAAATCATTATTCTTAACTA
* * * *
39039 GTGGCA-TGGTTAGAAACAAAAACCATAATTCTTAACTA
1 GTGGCACAGGTCA-AAACAAAAATCATTATTCTTAACTA
* * * * *
39077 GTGACACAGTTCAAAACAAAAA-CTAATATTGTAAACTA
1 GTGGCACAGGTCAAAACAAAAATC-ATTATTCTTAACTA
* * * *
39115 GTGGCACAGTTCAAAACTAAATTCACTATT-TTAAACTA
1 GTGGCACAGGTCAAAACAAAAATCATTATTCTT-AACTA
* * * *
39153 GTGGCAC-CGTTAAAA-AAAACT-AGTATTCTTAACTA
1 GTGGCACAGGTCAAAACAAAAATCATTATTCTTAACTA
39188 GTGGCA
1 GTGGCA
39194 TGGTTGAAAC
Statistics
Matches: 125, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
35 16 0.13
36 6 0.05
37 11 0.09
38 88 0.70
39 4 0.03
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (38 bp):
GTGGCACAGGTCAAAACAAAAATCATTATTCTTAACTA
Found at i:39097 original size:76 final size:75
Alignment explanation
Indices: 39015--39203 Score: 176
Period size: 76 Copynumber: 2.5 Consensus size: 75
39005 CATAGGTCAG
*
39015 AACAAAAATCATTATTCTTAACTAGTGGCATGGTTAGAAACAAAAACCA-TAATTCTT-AACTAG
1 AACAAAAATCAATATTCTTAACTAGTGGCATGGTTAGAAACAAAAACCACT-ATT-TTAAACTAG
39078 TGACACAGTTCAA
64 TGACACAGTT-AA
* * ** * **
39091 AACAAAAA-CTAATATTGTAAACTAGTGGCACAGTTCA-AAACTAAATTCACTATTTTAAACTAG
1 AACAAAAATC-AATATTCTTAACTAGTGGCATGGTT-AGAAACAAAAACCACTATTTTAAACTAG
* *
39154 TGGCACCGTTAA
64 TGACACAGTTAA
* *
39166 AA-AAAACT-AGTATTCTTAACTAGTGGCATGGTT-GAAAC
1 AACAAAAATCAATATTCTTAACTAGTGGCATGGTTAGAAAC
39204 CAGTTTCTAA
Statistics
Matches: 91, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
72 4 0.04
73 20 0.22
74 4 0.04
75 7 0.08
76 54 0.59
77 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (75 bp):
AACAAAAATCAATATTCTTAACTAGTGGCATGGTTAGAAACAAAAACCACTATTTTAAACTAGTG
ACACAGTTAA
Found at i:40727 original size:13 final size:13
Alignment explanation
Indices: 40709--40733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40699 CAATTCATCA
40709 TGTATCGATACAT
1 TGTATCGATACAT
40722 TGTATCGATACA
1 TGTATCGATACA
40734 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40731 original size:33 final size:33
Alignment explanation
Indices: 40689--40753 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
40679 TTTAAATCAA
40689 TGTATCGATACAAT-T-CATCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
40722 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
40754 AACAGTAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:40827 original size:19 final size:19
Alignment explanation
Indices: 40783--40838 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
40773 TTGCCAGTTT
**
40783 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
40803 CATGTACCGATACAATGAA
1 CATGTATCGATACAATGAA
*
40822 CATGTATTGATACAATG
1 CATGTATCGATACAATG
40839 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:41481 original size:13 final size:13
Alignment explanation
Indices: 41465--41503 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
41455 TTTCTTTATG
*
41465 AATTTTTAATTGA
1 AATTCTTAATTGA
*
41478 AATTCTTGATT-A
1 AATTCTTAATTGA
41490 AATTCTTAATTGA
1 AATTCTTAATTGA
41503 A
1 A
41504 TTTATCACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (13 bp):
AATTCTTAATTGA
Found at i:42035 original size:17 final size:17
Alignment explanation
Indices: 42008--42040 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41998 AGACAAGCAA
42008 AAATAAAGAAATAAAATT
1 AAATAAAGAAA-AAAATT
42026 AAAT-AAGAAAAAAAT
1 AAATAAAGAAAAAAAT
42041 GGCCATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
AAATAAAGAAAAAAATT
Found at i:45652 original size:31 final size:31
Alignment explanation
Indices: 45617--45678 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
45607 AGTATTTCTT
45617 TAATCCTTAATTATATATAACACTTTCATTC
1 TAATCCTTAATTATATATAACACTTTCATTC
45648 TAATCCTTAATTATATATAACACTTTCATTC
1 TAATCCTTAATTATATATAACACTTTCATTC
45679 AAGATAGAAC
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:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (31 bp):
TAATCCTTAATTATATATAACACTTTCATTC
Found at i:47737 original size:20 final size:20
Alignment explanation
Indices: 47707--47753 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
47697 ATTTGTATTT
*
47707 ATACAATAAGTTAATGTATCA
1 ATAC-ATAAGTGAATGTATCA
*
47728 ATACATAAGTGAATGTATCG
1 ATACATAAGTGAATGTATCA
47748 ATACAT
1 ATACAT
47754 GCTTGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (20 bp):
ATACATAAGTGAATGTATCA
Found at i:47874 original size:32 final size:32
Alignment explanation
Indices: 47833--47909 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
47823 ACATTTTCAT
* *
47833 TGTATCGATACATTTTAGGTTTTTGACATAAA
1 TGTATCGATACATTCTAGGTTTTTGACACAAA
* *
47865 TGTATCGATACATTCTGGGTTTTTGACCCAAA
1 TGTATCGATACATTCTAGGTTTTTGACACAAA
47897 TGTATCGATACAT
1 TGTATCGATACAT
47910 GTAGCCAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATTCTAGGTTTTTGACACAAA
Found at i:48031 original size:21 final size:21
Alignment explanation
Indices: 48005--48044 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
47995 AAATGATCAA
48005 AATTCATGTCAATATCAAAAG
1 AATTCATGTCAATATCAAAAG
48026 AATTCATGTCAATATCAAA
1 AATTCATGTCAATATCAAA
48045 TGTCAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (21 bp):
AATTCATGTCAATATCAAAAG
Found at i:49601 original size:13 final size:13
Alignment explanation
Indices: 49583--49612 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
49573 ATAATTCTTC
*
49583 ATGTATCGATACA
1 ATGTATCAATACA
49596 ATGTATCAATACA
1 ATGTATCAATACA
49609 ATGT
1 ATGT
49613 CCCATGTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:55866 original size:20 final size:19
Alignment explanation
Indices: 55841--55895 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
55831 TTTTACCCAG
55841 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATT-AAAA
* **
55861 ATGTATCAATACATATATGA
1 ATGTATCGATACAT-TAAAA
55881 ATGTATCGATACATT
1 ATGTATCGATACATT
55896 CTATCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATTAAAA
Found at i:55951 original size:71 final size:71
Alignment explanation
Indices: 55830--56016 Score: 277
Period size: 71 Copynumber: 2.6 Consensus size: 71
55820 AAAGGTCACA
* *
55830 TTTTTACCCAGATGTATCGATACATTGAAAAATGTATCAATACATATATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATTGAATAATGTATCGATACATATATGAATGTATCGATACAT
55895 TCTATC
66 TCTATC
*** * * *
55901 TTTTTACCCAGATGTATCGATACATTCTTTAGTGTATCGATACATGTATGAATGTATTGATACAT
1 TTTTTACCCAGATGTATCGATACATTGAATAATGTATCGATACATATATGAATGTATCGATACAT
55966 TCTATC
66 TCTATC
*
55972 TTTTTACCCCA-ATATATCGATACATTGAATAATGTATCGATACAT
1 TTTTTA-CCCAGATGTATCGATACATTGAATAATGTATCGATACAT
56017 CTAGTTAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
71 98 0.96
72 4 0.04
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTGAATAATGTATCGATACATATATGAATGTATCGATACAT
TCTATC
Found at i:62664 original size:21 final size:21
Alignment explanation
Indices: 62604--62673 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 21
62594 GATCAGTTGA
*
62604 AAAGAAAAAGA-AAAGGAA-G
1 AAAGAAAAAGAGAAAGAAATG
*
62623 AGAGGAAAAA-AG-AAGACAATG
1 A-AAGAAAAAGAGAAAGA-AATG
62644 AAAGAAAAAGAGAAAGAAATG
1 AAAGAAAAAGAGAAAGAAATG
*
62665 -GAGAAAAAG
1 AAAGAAAAAG
62674 TTGGAAGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
19 5 0.12
20 24 0.59
21 8 0.20
22 4 0.10
ACGTcount: A:0.69, C:0.01, G:0.27, T:0.03
Consensus pattern (21 bp):
AAAGAAAAAGAGAAAGAAATG
Found at i:66487 original size:33 final size:33
Alignment explanation
Indices: 66450--66513 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
66440 AAATTCCAAG
66450 ATGTATCAATACAAAG-ATCAATGTATCGATACA
1 ATGTATCAATACAAAGAAT-AATGTATCGATACA
**
66483 ATGTATCAATACATTGAATAATGTATCGATA
1 ATGTATCAATACAAAGAATAATGTATCGATA
66514 TATTTCCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (33 bp):
ATGTATCAATACAAAGAATAATGTATCGATACA
Found at i:67330 original size:52 final size:49
Alignment explanation
Indices: 67311--67474 Score: 143
Period size: 49 Copynumber: 3.6 Consensus size: 49
67301 AAAGATGAGA
*
67311 AAGGTGCCGATGTGCTGATTGAAGGCCAACGACATCGGTCTTAAAGATG
1 AAGGTGCCGATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATG
* * * *
67360 AAGGTGCTGATGTGCTGATTCAAGGCCAAGGACATTGGGCTT---G-T-
1 AAGGTGCCGATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATG
* * * *
67404 ---GT--CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-C
1 AAGGTGCCGATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATG
* * *
67447 AAGGTGCCTATATGCTGATTGAAGGCCA
1 AAGGTGCCGATGTGCTGATTCAAGGCCA
67475 GCGATATTGG
Statistics
Matches: 92, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
39 30 0.33
41 2 0.02
42 1 0.01
45 1 0.01
46 3 0.03
48 18 0.20
49 37 0.40
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (49 bp):
AAGGTGCCGATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATG
Found at i:67484 original size:48 final size:48
Alignment explanation
Indices: 67406--67736 Score: 286
Period size: 48 Copynumber: 7.5 Consensus size: 48
67396 GGGCTTGTGT
*
67406 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
* * * *
67454 CTATATGCTGATTGAAGGCCAGCGATATTGGGCTT-------A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
* * *
67493 CAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAGGTTC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
* *
67541 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-------A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
* * * *
67580 CACTGTACTGATTCAAGGCCAGCGACATTGGTTTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
*
67628 CAATATGCTGATTCAAGGCCAGCGATATTAGG-CTT-------A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGACAAGGTGC
* * *
67667 CAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
*
67715 CAATATGTTGATTCAAGGCCAG
1 CAATATGCTGATTCAAGGCCAG
67737 TGATATTAAA
Statistics
Matches: 221, Mismatches: 33, Indels: 58
0.71 0.11 0.19
Matches are distributed among these distances:
38 2 0.01
39 96 0.43
41 3 0.01
46 3 0.01
48 115 0.52
49 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
Found at i:67513 original size:39 final size:39
Alignment explanation
Indices: 67459--67702 Score: 182
Period size: 39 Copynumber: 5.8 Consensus size: 39
67449 GGTGCCTATA
* *
67459 TGCTGATTGAAGGCCAGCGATATTGGGCTTATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* * * *
67498 TGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAGGTTCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTT-------A--TGCCAATG
* *
67546 TGCTGATTCAAGGCCAGCGATATTGGGCTTATGCCACTG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* ** *
67585 TACTGATTCAAGGCCAGCGACATTGGTTTTAAAGACAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTT-------A--TGCCAATG
* *
67633 TGCTGATTCAAGGCCAGCGATATTAGGCTTATGCCAATG
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
* *
67672 TGCTGATTCAAGGCCAACGACATTGGTCTTA
1 TGCTGATTCAAGGCCAGCGACATTGGGCTTA
67703 GAGACAAGGT
Statistics
Matches: 160, Mismatches: 27, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
39 92 0.57
41 2 0.01
46 2 0.01
48 64 0.40
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (39 bp):
TGCTGATTCAAGGCCAGCGACATTGGGCTTATGCCAATG
Found at i:67744 original size:87 final size:87
Alignment explanation
Indices: 67315--67743 Score: 626
Period size: 87 Copynumber: 4.9 Consensus size: 87
67305 ATGAGAAAGG
* * * * * ** *
67315 TGCCGATGTGCTGATTGAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCTGATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATT
* *
67380 CAAGGCCAAG-GACATTGGGCTTG
65 CAAGGCC-AGCGATATTGGGCTTA
* * *
67403 TGTCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCTATATGCTGATTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
67468 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* *
67490 TGCCAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGACAAGGTTCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
67555 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* * *
67577 TGCCACTGTACTGATTCAAGGCCAGCGACATTGGTTTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
*
67642 AAGGCCAGCGATATTAGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* * *
67664 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGAGACAAGGTGCCAATATGTTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
*
67729 AAGGCCAGTGATATT
66 AAGGCCAGCGATATT
67744 AAACGTAAAG
Statistics
Matches: 310, Mismatches: 30, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
86 2 0.01
87 270 0.87
88 38 0.12
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGGCTTA
Found at i:67856 original size:33 final size:33
Alignment explanation
Indices: 67750--68288 Score: 488
Period size: 34 Copynumber: 16.9 Consensus size: 33
67740 TATTAAACGT
** *
67750 AAAGGTGCCACTAAGTTGTGGTCTT-AAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
67782 AAAGGGATGCCACGGAAG-TGTGGGC-TAAAAGG-A
1 AAA-GG-TGCCACGG-AGTTGTGGACTTAAAAGGAA
*
67815 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
67848 CAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
67882 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
67915 CAAGGTGCCAC-AAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
**
67948 AAAGGTGCCATAGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
67981 AAAGAGTGCCATGAAGTTGTGGGCTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
68015 AAAGAATGCCATGGAGTTGTGGACTTAAAA-G--
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
*
68046 ---GGTGCCACGGAGTTATGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
68076 AAAGGTGCCACGGAGTTATGGACTTCAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
68106 ---GGTGCCACGGAGTTGTGGGCTTAAAAGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
**
68136 AAAGAGTGCTGCGGAGTTGTGGACTTAAAA-G--
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
** * *
68167 ---GGTGCCATAGAGTTGTGGACGTAAAAGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
68197 AAAGGTGCCACGGAGTTGTGGACTTCAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
68227 ---GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
68257 AGAGGGTGCCACGGAGTTGTGGACTTAAAAGG
1 A-AAGGTGCCACGGAGTTGTGGACTTAAAAGG
68289 GTGCTACTGA
Statistics
Matches: 416, Mismatches: 54, Indels: 72
0.77 0.10 0.13
Matches are distributed among these distances:
27 89 0.21
28 4 0.01
30 2 0.00
31 13 0.03
32 22 0.05
33 127 0.31
34 157 0.38
35 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:68052 original size:27 final size:27
Alignment explanation
Indices: 68021--68292 Score: 202
Period size: 27 Copynumber: 9.1 Consensus size: 27
68011 AGAAAAAGAA
*
68021 TGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
68048 TGCCACGGAGTTATGGACTTAAAAGGAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----GG
* *
68081 TGCCACGGAGTTATGGACTTCAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
68108 TGCCACGGAGTTGTGGGCTTAAAAGAAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAAG------G-G
**
68142 TGCTGCGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
** *
68169 TGCCATAGAGTTGTGGACGTAAAAGAAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAG------GG
*
68202 TGCCACGGAGTTGTGGACTTCAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
68229 TGCCACGGAGTTGTGGGCTTAAAAGGAAAGAGGG
1 TGCCACGGAGTTGTGGACTT------AAA-AGGG
68263 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
68290 TGC
1 TGC
68293 TACTGAGTCA
Statistics
Matches: 198, Mismatches: 21, Indels: 52
0.73 0.08 0.19
Matches are distributed among these distances:
27 95 0.48
28 5 0.03
32 1 0.01
33 51 0.26
34 46 0.23
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:68106 original size:60 final size:60
Alignment explanation
Indices: 67781--68292 Score: 537
Period size: 61 Copynumber: 8.2 Consensus size: 60
67771 TCTTAAAGGA
*
67781 AAAAGGGATGCCACGGAAG-TGTGGGC-TAAAAGG-AAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAGGG-TGCCACGG-AGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTT
*
67840 AAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC
1 AAAA-G-----GGTGCCACGGAGTTGTGGGC-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGAC
67905 TT
59 TT
* * **
67907 AAAAGGAACAAGGTGCCAC-AAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCATAGAGTTGTGGAC
1 AAAA-G-----GGTGCCACGGAGTTGTGGGC-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGAC
67971 TT
59 TT
* * * * *
67973 AAAAGGAAAAAGAGTGCCATGAAGTTGTGGGCTTAAAAAGAAAAAGAATGCCATGGAGTTGTGGA
1 AAAA-G-----G-GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGA
68038 CTT
58 CTT
* * *
68041 AAAAGGGTGCCACGGAGTTATGGACTTAAAAGGAAAAAGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTT
* * **
68101 CAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAAGAGTGCTGCGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGACTT
** * * *
68162 AAAAGGGTGCCATAGAGTTGTGGACGTAAAAGAAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTT
* *
68222 CAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAGAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAA-AAGGTGCCACGGAGTTGTGGACTT
68283 AAAAGGGTGC
1 AAAAGGGTGC
68293 TACTGAGTCA
Statistics
Matches: 399, Mismatches: 39, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
59 4 0.01
60 103 0.26
61 112 0.28
62 1 0.00
63 2 0.01
64 15 0.04
65 2 0.01
66 61 0.15
67 65 0.16
68 34 0.09
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (60 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTT
Found at i:68156 original size:121 final size:123
Alignment explanation
Indices: 67781--68292 Score: 558
Period size: 121 Copynumber: 4.1 Consensus size: 123
67771 TCTTAAAGGA
*
67781 AAAAGGGATGCCACGGAAG-TGTGGGC-TAAAAGG-AAAAGGTGCCACAGAGTTGTGGACTTAAA
1 AAAAGGG-TGCCACGG-AGTTGTGGACTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGACTTAAA
67843 AGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGACTT
64 AGG----AGGTGCCACGGAGTTGTGGGC-TTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTT
* * * *
67907 AAAAGGAACAAGGTGCCAC-AAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCATAGAGTTGTGGAC
1 AAAA-G-----GGTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGGTGCCACAGAGTTGTGGAC
* * * *
67971 TTAAAAGGAAAAAGAGTGCCATGAAGTTGTGGGCTTAAAAAGAAAAAGAATGCCATGGAGTTGTG
59 TTAAAAGG----AG-GTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTTGTG
68036 GACTT
119 GACTT
* * * *
68041 AAAAGGGTGCCACGGAGTTATGGACTTAAAAGGAAAAAGGTGCCACGGAGTTATGGACTTCAAA-
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAG
**
68105 G-GGTGCCACGGAGTTGTGGGCTT-AAAAGAAAAAAGAGTGCTGCGGAGTTGTGGACTT
66 GAGGTGCCACGGAGTTGTGGGCTTAAAAAG-AAAAAGAGTGCCACGGAGTTGTGGACTT
** * * * *
68162 AAAAGGGTGCCATAGAGTTGTGGACGTAAAAGAAAAAAGGTGCCACGGAGTTGTGGACTTCAAA-
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAG
* * *
68226 G-GGTGCCACGGAGTTGTGGGCTTAAAAGGAAAGAGGGTGCCACGGAGTTGTGGACTT
66 GAGGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTT
68283 AAAAGGGTGC
1 AAAAGGGTGC
68293 TACTGAGTCA
Statistics
Matches: 338, Mismatches: 33, Indels: 35
0.83 0.08 0.09
Matches are distributed among these distances:
120 5 0.01
121 158 0.47
122 5 0.01
126 4 0.01
127 2 0.01
128 42 0.12
129 10 0.03
130 7 0.02
131 6 0.02
132 8 0.02
133 51 0.15
134 40 0.12
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (123 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAG
GAGGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:68341 original size:31 final size:31
Alignment explanation
Indices: 68305--68744 Score: 391
Period size: 31 Copynumber: 14.2 Consensus size: 31
68295 CTGAGTCACA
* *
68305 GACTTTTTGGAAAAGATGCTACTGAGTCGTG
1 GACTTTGTGGAAAAGATGCCACTGAGTCGTG
* * * * *
68336 AACTTTGAAGAGAAAAGATGCCATTGTGTTGTG
1 GACTTTG-TG-GAAAAGATGCCACTGAGTCGTG
*
68369 GACTTTGTAGAAAAGATGCCACT-ATGTCGTG
1 GACTTTGTGGAAAAGATGCCACTGA-GTCGTG
*
68400 GAC-TT-TGGAAAGAGATGCCACTAAGTCGTG
1 GACTTTGTGGAAA-AGATGCCACTGAGTCGTG
*
68430 GAC-TT-TGGAAAGAGATGCCACTGAGTCATG
1 GACTTTGTGGAAA-AGATGCCACTGAGTCGTG
* * * *
68460 GACTTGGAT-GAGAAGATGCCACTAAGTCATG
1 GACTTTG-TGGAAAAGATGCCACTGAGTCGTG
* **
68491 GACTTGGAAGAAAAGATGCCACTGAGTCGTG
1 GACTTTGTGGAAAAGATGCCACTGAGTCGTG
** *
68522 GACTTTGAAGAAAATATGCCACTGAGTCGTG
1 GACTTTGTGGAAAAGATGCCACTGAGTCGTG
** *
68553 GACTTTGAAGAAAAGATGCCACTG-TTCGTG
1 GACTTTGTGGAAAAGATGCCACTGAGTCGTG
* *
68583 GAC-TT-TGGAAAGAGATGCCATTCAGTCGTG
1 GACTTTGTGGAAA-AGATGCCACTGAGTCGTG
* *
68613 GAC-TT-TGGAAAGAGATGCCACTAAGTCATG
1 GACTTTGTGGAAA-AGATGCCACTGAGTCGTG
** *
68643 GACTTTGAAGAAAAGATGCCACTAAGTCGTG
1 GACTTTGTGGAAAAGATGCCACTGAGTCGTG
*
68674 GACTTTG-GGAAAAAAGACTGCCACTAAGTCGTG
1 GACTTTGTGG--AAAAGA-TGCCACTGAGTCGTG
* **
68707 GACTTGGAAGAAAAGATGCCACTGAGTCGTG
1 GACTTTGTGGAAAAGATGCCACTGAGTCGTG
68738 GACTTTG
1 GACTTTG
68745 AGAAGAGAGA
Statistics
Matches: 349, Mismatches: 43, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.01
29 16 0.05
30 93 0.27
31 169 0.48
32 20 0.06
33 46 0.13
34 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (31 bp):
GACTTTGTGGAAAAGATGCCACTGAGTCGTG
Found at i:68600 original size:183 final size:186
Alignment explanation
Indices: 68314--68745 Score: 656
Period size: 183 Copynumber: 2.3 Consensus size: 186
68304 AGACTTTTTG
* * * * * *
68314 GAAAAGATGCTACTGAGTCGTGAACTTTGAAGAGAAAAGATGCCATTGTGTTGTGGACTTTGTAG
1 GAAAAGATGCCACTGAGTCGTGGACTTTG-A-AGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
68379 AAAAGATGCCACTATGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGTGGACTTTGGAAAGAG
64 AAAAGATGCCACTATGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGTGGACTTTGGAAAGAG
* * *
68444 ATGCCACTGAGTCATGGACTTGGATGAGAAGATGCCACTAAGTCATGGAC-TT-GGAA
129 ATGCCACTAAGTCATGGACTTGGAAGAAAAGATGCCACTAAGTCATGGACTTTGGGAA
*
68500 GAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAATATGCCACTGAGTCGTGGACTTTGAAGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAA
* * *
68565 AAGATGCCACTGT-TCGTGGACTTTGGAAAGAGATGCCATTCAGTCGTGGACTTTGGAAAGAGAT
66 AAGATGCCACTATGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGTGGACTTTGGAAAGAGAT
* *
68629 GCCACTAAGTCATGGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTTTGGGAA
131 GCCACTAAGTCATGGACTTGGAAGAAAAGATGCCACTAAGTCATGGACTTTGGGAA
* *
68685 -AAAAGACTGCCACTAAGTCGTGGACTTGGAAGAAAAGATGCCACTGAGTCGTGGACTTTGA
1 GAAAAGA-TGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGA
68746 GAAGAGAGAT
Statistics
Matches: 225, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
183 92 0.41
184 50 0.22
185 56 0.25
186 27 0.12
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (186 bp):
GAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAGAA
AAGATGCCACTATGTCGTGGACTTTGGAAAGAGATGCCACTAAGTCGTGGACTTTGGAAAGAGAT
GCCACTAAGTCATGGACTTGGAAGAAAAGATGCCACTAAGTCATGGACTTTGGGAA
Found at i:70049 original size:18 final size:18
Alignment explanation
Indices: 70026--70063 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
70016 GCACTCTCTC
70026 TTTTTTTTTTG-TTTTTG
1 TTTTTTTTTTGTTTTTTG
70043 TTTTTTTTTTGTTTTTTG
1 TTTTTTTTTTGTTTTTTG
70061 TTT
1 TTT
70064 GTGTGTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (18 bp):
TTTTTTTTTTGTTTTTTG
Found at i:70058 original size:11 final size:11
Alignment explanation
Indices: 70026--70065 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
70016 GCACTCTCTC
70026 TTTTTT-TTTT
1 TTTTTTGTTTT
*
70036 GTTTTTGTTTT
1 TTTTTTGTTTT
70047 TTTTTTGTTTT
1 TTTTTTGTTTT
*
70058 TTGTTTGT
1 TTTTTTGT
70066 GTGTTTACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:75938 original size:19 final size:19
Alignment explanation
Indices: 75914--75974 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
75904 AGTGATACAT
75914 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
75933 TGTATCGAT-----ACTT-
1 TGTATCGATACAACACTTA
75946 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
75965 TGTATCGATA
1 TGTATCGATA
75975 TATTTACAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.25
14 4 0.11
18 4 0.11
19 19 0.53
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:75949 original size:32 final size:32
Alignment explanation
Indices: 75907--75974 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
75897 GCTTTGTAGT
75907 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
75939 GATACTTTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
75971 GATA
1 GATA
75975 TATTTACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:75951 original size:13 final size:14
Alignment explanation
Indices: 75928--75956 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
75918 TCGATACAAC
75928 ACTTATGTATCGAT
1 ACTTATGTATCGAT
75942 ACTT-TGTATCGAT
1 ACTTATGTATCGAT
75955 AC
1 AC
75957 AACACTTATG
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:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (14 bp):
ACTTATGTATCGAT
Found at i:80340 original size:33 final size:33
Alignment explanation
Indices: 80303--80367 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
80293 AATAGTACCC
*
80303 ATGTATCAATAC-ACAGAACTCACTATTGATACT
1 ATGTATCAATACTA-AGAACGCACTATTGATACT
*
80336 ATGTATCAATACTAAGAACGCAGTATTGATAC
1 ATGTATCAATACTAAGAACGCACTATTGATAC
80368 ATCTAGGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (33 bp):
ATGTATCAATACTAAGAACGCACTATTGATACT
Found at i:84908 original size:53 final size:53
Alignment explanation
Indices: 84788--84913 Score: 132
Period size: 52 Copynumber: 2.4 Consensus size: 53
84778 GTGATAAAGG
* ** * *
84788 TGCCAATATGCTGATTC-AGGACCAGTGATTTTAGGCTTATAGATGTAAAGAA
1 TGCCAATGTGCTGATTCAAGGACCAGTGACATTAGACTTATAGATGAAAAGAA
** * *
84840 TGTTAATGTGTTGATTCAAGG-TCAGTGACATTAGACTTGA-AGATGAAGAAGAA
1 TGCCAATGTGCTGATTCAAGGACCAGTGACATTAGACTT-ATAGATGAA-AAGAA
84893 TGCCAATGTGCTGATTCAAGG
1 TGCCAATGTGCTGATTCAAGG
84914 CCAACGACAT
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
52 32 0.54
53 27 0.46
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (53 bp):
TGCCAATGTGCTGATTCAAGGACCAGTGACATTAGACTTATAGATGAAAAGAA
Found at i:85054 original size:43 final size:43
Alignment explanation
Indices: 84990--85075 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
84980 CTTAAAGGTG
* *
84990 AAGGTGCTAATGTGCTAATTCAAGGCCAGCAACATTGGACTTA
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTA
* * *
85033 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTA
85076 GAAGAAGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (43 bp):
AAGGTGCCAATATGCTAATTCAAGGCCAGCAACATTGGACTTA
Found at i:85163 original size:28 final size:28
Alignment explanation
Indices: 85097--85531 Score: 462
Period size: 28 Copynumber: 15.5 Consensus size: 28
85087 CACCAACTTG
**
85097 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTG-AA-GGTTGCCACTGACT
* *
85126 TGTGTGCTTTTGAAGGTTGCCACTCG-TT
1 TGTGGGCTTTTGAAGGTTGCCACT-GACT
* *
85154 TATGGGC-TTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
85181 TGTGGTC-TTTGAAAAGG-TGCCGCTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
*
85209 TGTGGGCTTCTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
85237 TATGGGCTTTTGAACGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
85265 TGTGGGC-TTTGAAAAGG-TGCCACTAAAT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
* *
85293 TGTGGGCTTCTGAAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
85321 TGTGGGCTTTTGAAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
85349 TGTGGGC-TTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
*
85377 TGTGGGCTTCTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
85405 TGTGGGC-TTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
* *
85433 TGTAGGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
85461 TGTGGGCTTCTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
85489 TGTGGGC-TTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
*
85517 TGTGGGCTTTGGAAG
1 TGTGGGCTTTTGAAG
85532 CTGAGGAATG
Statistics
Matches: 345, Mismatches: 41, Indels: 42
0.81 0.10 0.10
Matches are distributed among these distances:
27 60 0.17
28 243 0.70
29 42 0.12
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:85267 original size:84 final size:83
Alignment explanation
Indices: 85097--85527 Score: 546
Period size: 84 Copynumber: 5.1 Consensus size: 83
85087 CACCAACTTG
* * * * * *
85097 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTGTGTGCTTTTGAAGGTTGCCACTCG-TTTATGGG
1 TGTGGGC-TTTGAAAAGG-TGCCACTAACTTGTGGGCTTCTGAAGGTTGCCACT-GACTTGTGGG
* *
85160 CTTTGAAGGTTGCCACTAACT
63 CTTTGAAAGTTGCCACTGACT
* * * *
85181 TGTGGTCTTTGAAAAGGTGCCGCTGACTTGTGGGCTTCTGAAGGTTGCCACTGACTTATGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGC-T
*
85246 TTGAACGTTGCCACTGACT
65 TTGAAAGTTGCCACTGACT
* *
85265 TGTGGGCTTTGAAAAGGTGCCACTAAATTGTGGGCTTCTGAAGGTTGCCATTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGC-T
* *
85330 TTGAAGGTTGCCATTGACT
65 TTGAAAGTTGCCACTGACT
* *
85349 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGCTT
* *
85414 TGAAAAGGTGCCACTAACT
66 TG-AAAGTTGCCACTGACT
*
85433 TGTAGGCTTTTG--AAGGTTGCCACTAACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGC
1 TGTGGGC-TTTGAAAAGG-TGCCACTAACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGC
*
85496 TTTGAAAAGGTGCCACTGACT
64 TTTG-AAAGTTGCCACTGACT
85517 TGTGGGCTTTG
1 TGTGGGCTTTG
85528 GAAGCTGAGG
Statistics
Matches: 310, Mismatches: 31, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
82 3 0.01
83 55 0.18
84 248 0.80
85 4 0.01
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (83 bp):
TGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTCTGAAGGTTGCCACTGACTTGTGGGCTT
TGAAAGTTGCCACTGACT
Found at i:85943 original size:37 final size:37
Alignment explanation
Indices: 85893--85977 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
85883 AAAAACGAAG
85893 CACAAATGCATCATGCAAAAGGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAAGGAAATGTTATGAATGT
*
85930 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAAGGAAATGTTATGAATGT
85967 CACAAATGCAT
1 CACAAATGCAT
85978 GATTGTGGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (37 bp):
CACAAATGCATCATGCAAAAGGAAATGTTATGAATGT
Found at i:92581 original size:13 final size:13
Alignment explanation
Indices: 92563--92587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
92553 CATAAAGTGT
92563 TGTATCGATACAA
1 TGTATCGATACAA
92576 TGTATCGATACA
1 TGTATCGATACA
92588 TATTTATTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:92724 original size:32 final size:32
Alignment explanation
Indices: 92683--92759 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
92673 CACTGATCTT
*
92683 TGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGA
92715 TGTATCGATACATGCAAGCAAATTTGCCCAGA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGA
92747 TGTATCGATACAT
1 TGTATCGATACAT
92760 TACTAAATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (32 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGA
Found at i:94924 original size:24 final size:26
Alignment explanation
Indices: 94897--94947 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
94887 ATTAAAAAAT
94897 TATTCAT-C-GGGGACACTCCAACCC
1 TATTCATCCAGGGGACACTCCAACCC
*
94921 TATTCCTCCGAGGGGACACTCCAACCC
1 TATTCATCC-AGGGGACACTCCAACCC
94948 CGTTTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 1 0.04
27 16 0.70
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.20
Consensus pattern (26 bp):
TATTCATCCAGGGGACACTCCAACCC
Found at i:106663 original size:1 final size:1
Alignment explanation
Indices: 106659--106727 Score: 75
Period size: 1 Copynumber: 69.0 Consensus size: 1
106649 CGTCCTCCAC
* * * * * * *
106659 AAAAAAAAAAAAGAAAAAAAAACAAAACAAAACAAAAAAAAAAACAAAAAACAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
106724 AAAA
1 AAAA
106728 GGGTCCGGAT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.90, C:0.09, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:106696 original size:32 final size:31
Alignment explanation
Indices: 106659--106727 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 31
106649 CGTCCTCCAC
*
106659 AAAAAAAAAAAAGAAAAAA-AAACAAAACAAA
1 AAAAAAAAAAAACAAAAAACAAA-AAAACAAA
106690 ACAAAAAAAAAAACAAAAAACAAAAAAACAAA
1 A-AAAAAAAAAAACAAAAAACAAAAAAACAAA
106722 AAAAAA
1 AAAAAA
106728 GGGTCCGGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 6 0.17
32 26 0.74
33 3 0.09
ACGTcount: A:0.90, C:0.09, G:0.01, T:0.00
Consensus pattern (31 bp):
AAAAAAAAAAAACAAAAAACAAAAAAACAAA
Found at i:108206 original size:43 final size:43
Alignment explanation
Indices: 108143--108232 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
108133 TCATCTTCAT
* *
108143 CTTTAAGTCCAATGTAGCTGGCCTTGAATCGGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
108186 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
108229 CTTT
1 CTTT
108233 TCCACCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:108250 original size:52 final size:52
Alignment explanation
Indices: 108183--108391 Score: 238
Period size: 52 Copynumber: 4.0 Consensus size: 52
108173 GGCACATTGG
* *
108183 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTC
1 CACCTTTAAGTCCAATATAGCTGGCCGTGAATCAGCATATTGGCACCTTTTC
* * *
108235 CACCTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACATTTTC
1 CACCTTTAAGTCCAATATAGCTGGCCGTGAATCAGCATATTGGCACCTTTTC
* * * * * *
108287 CATCTTTAACTTCAATGTAGCTGGCCGTGAATCAGCACATTGACATCCTTTTTC
1 CACCTTTAAGTCCAATATAGCTGGCCGTGAATCAGCATATTGGCA-CC-TTTTC
* * * * * *
108341 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 -CACCTTTAAGTCCAATATAGCTGGCCGTGAATCAGCATATTGGCACCTTT
108392 ATCACTTTTC
Statistics
Matches: 132, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
52 86 0.65
53 4 0.03
54 6 0.05
55 36 0.27
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (52 bp):
CACCTTTAAGTCCAATATAGCTGGCCGTGAATCAGCATATTGGCACCTTTTC
Found at i:108449 original size:67 final size:67
Alignment explanation
Indices: 108341--108534 Score: 298
Period size: 67 Copynumber: 2.9 Consensus size: 67
108331 ATCCTTTTTC
*
108341 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCAT
1 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCAT
108406 CT
66 CT
*
108408 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTTTCAT
1 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCAT
108473 CT
66 CT
* * * * * * *
108475 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTT
108535 AAAACCTAAT
Statistics
Matches: 117, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 113 0.97
68 4 0.03
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (67 bp):
TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCAT
CT
Found at i:108584 original size:53 final size:52
Alignment explanation
Indices: 108475--108669 Score: 128
Period size: 52 Copynumber: 3.7 Consensus size: 52
108465 TTTTTCATCT
** * * * **
108475 TCATCTTTAAGTCC-AATATTGCTGGCCTTGAATCAGCATATTGGCA-CCTTC
1 TCATCTTTAAAACCTAATATCGCTGGCCGTGAATCAGCACATT-GCATTTTTC
* * * *
108526 ATCATCTTTAAAACCTAATGTTGTTGGCCTTGAATCAGCACATTAGCATTTTTC
1 -TCATCTTTAAAACCTAATATCGCTGGCCGTGAATCAGCACATT-GCATTTTTC
* ** * *
108580 TCATC-TTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATCCTTTTTC
1 TCATCTTTAAAACCTAATATCGCTGGCCGTGAATCAGCACATTG-CA---TTTTTC
* * *
108635 TCATCTTT-GAACCCAATATCGTTGGCCGTGAATCA
1 TCATCTTTAAAACCTAATATCGCTGGCCGTGAATCA
108670 ACGTATTGGT
Statistics
Matches: 114, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
51 1 0.01
52 44 0.39
53 33 0.29
54 3 0.03
55 31 0.27
56 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (52 bp):
TCATCTTTAAAACCTAATATCGCTGGCCGTGAATCAGCACATTGCATTTTTC
Found at i:109388 original size:13 final size:12
Alignment explanation
Indices: 109344--109424 Score: 61
Period size: 13 Copynumber: 7.1 Consensus size: 12
109334 CTGCCAAAAA
109344 ATGTATCGATAC
1 ATGTATCGATAC
109356 AT-TACTC-A-A-
1 ATGTA-TCGATAC
*
109365 ATGTATTGATAC
1 ATGTATCGATAC
109377 ATTGTATCGATAC
1 A-TGTATCGATAC
109390 AT-TACTC-A-A-
1 ATGTA-TCGATAC
109399 ATGTATCGATAC
1 ATGTATCGATAC
109411 ATTGTATCGATAC
1 A-TGTATCGATAC
109424 A
1 A
109425 CTGATCTTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 23
0.69 0.03 0.29
Matches are distributed among these distances:
9 7 0.13
10 8 0.15
11 8 0.15
12 9 0.16
13 23 0.42
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:109388 original size:34 final size:34
Alignment explanation
Indices: 109345--109424 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
109335 TGCCAAAAAA
*
109345 TGTATCGATACATTACTCAAATGTATTGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
109379 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
109413 TGTATCGATACA
1 TGTATCGATACA
109425 CTGATCTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGATACAT
Found at i:109489 original size:52 final size:52
Alignment explanation
Indices: 109433--109561 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
109423 CACTGATCTT
109433 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
109485 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
109537 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
109562 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:115026 original size:49 final size:49
Alignment explanation
Indices: 114963--115355 Score: 357
Period size: 49 Copynumber: 8.0 Consensus size: 49
114953 GGTGGCATCT
* *
114963 TCTTCTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTA
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
* * * * *
115013 TCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA-C----
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
*
115057 -CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
* * *
115105 CCCTCTTGAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACGCTTCTCA
1 -TCT-TTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCAC-CTT-T-A
* * * * *
115159 TCTTTTAAGACCAATGTCACTGGCCTTGAATCAACATATTGGCATCTTCA
1 TC-TTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
*** * * * *
115209 TCTTTAAGTCTGGTATTGCTGGCCTTGAATCAGCATATTGGCACCGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
* * * * * *
115258 TCTTTAAGACCAATGTCGTTGGCCATGAATCAACACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
** * ** * *
115307 TCACTAAGTCCGATATCATTGGCCTTGAATCAACATTTTGGCATCTTTA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
115356 ACATTCCTAA
Statistics
Matches: 279, Mismatches: 52, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
43 38 0.14
44 1 0.00
48 1 0.00
49 147 0.53
50 9 0.03
51 38 0.14
52 6 0.02
53 37 0.13
54 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTA
Found at i:115079 original size:43 final size:43
Alignment explanation
Indices: 115014--115104 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 43
115004 GCACCTTTAT
* *
115014 CTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
115057 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
115100 CTTTA
1 CTTTA
115105 CCCTCTTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:115382 original size:52 final size:49
Alignment explanation
Indices: 114967--115401 Score: 229
Period size: 49 Copynumber: 8.8 Consensus size: 49
114957 GCATCTTCTT
* * * * * * * *
114967 CTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATCT
1 CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCA
* *
115016 TTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCACC-T--T--
1 CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCA
* * * * * * * *
115060 -TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCCT
1 CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCA-TCA
* * * * * *
115109 CTTGAGTCCAATATTGCTGGCCTTGAATCAACATATTGGCACGCTTC-TCA
1 C-TAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCAC-CTTCATCA
** * * *
115159 TCTTTTAAGACCAATGTCACTGGCCTTGAATCAACATATTGGCATCTTCATCT
1 -C---TAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCA
* * *** * * * * * * *
115212 TTAAGTCTGGTATTGCTGGCCTTGAATCAGCATATTGGCACCGTCATCT
1 CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCA
* *
115261 TTAAGACCAATGTCGTTGGCCATGAATCAACACATTGGCACCTTCATCA
1 CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCA
* * * * ** *
115310 CTAAGTCCGATATCATTGGCCTTGAATCAACATTTTGGCATCTTTAACATTC-
1 CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCA-CCTT--CA-TCA
* ** *
115362 CTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCA
1 CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCA
115402 TTTTTCTTCA
Statistics
Matches: 304, Mismatches: 65, Indels: 31
0.76 0.16 0.08
Matches are distributed among these distances:
43 37 0.12
44 1 0.00
46 1 0.00
48 1 0.00
49 143 0.47
50 4 0.01
51 38 0.12
52 40 0.13
53 39 0.13
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
CTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCATCA
Found at i:129585 original size:4 final size:4
Alignment explanation
Indices: 129576--129640 Score: 73
Period size: 4 Copynumber: 16.5 Consensus size: 4
129566 ACAAAAAAGA
* *
129576 AAAC AAAC AAA- AAAT AAAA AAAC AAAAC AAAAC AAA- AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC -AAAC -AAAC AAAC AAAC AAAC AAAC
129624 AAAC AAAC AAA- AAAC AA
1 AAAC AAAC AAAC AAAC AA
129641 CAACAAAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
3 9 0.16
4 37 0.67
5 9 0.16
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.02
Consensus pattern (4 bp):
AAAC
Found at i:129596 original size:25 final size:22
Alignment explanation
Indices: 129568--129637 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
129558 CGTCCTCTAC
*
129568 AAAAAAGAAAACAAACAAAAAA
1 AAAAAAAAAAACAAACAAAAAA
129590 TAAAAAAACAAAACAAAACAAAAAA
1 -AAAAAAA-AAAAC-AAACAAAAAA
* *
129615 CAAACAAACAAACAAACAAAAAA
1 -AAAAAAAAAAACAAACAAAAAA
129638 CAACAACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.39
24 9 0.22
25 16 0.39
ACGTcount: A:0.83, C:0.14, G:0.01, T:0.01
Consensus pattern (22 bp):
AAAAAAAAAAACAAACAAAAAA
Found at i:129597 original size:8 final size:8
Alignment explanation
Indices: 129568--129637 Score: 63
Period size: 8 Copynumber: 8.6 Consensus size: 8
129558 CGTCCTCTAC
*
129568 AAAAAAGA
1 AAAAAACA
129576 AAACAAAC-
1 AAA-AAACA
*
129584 AAAAAATA
1 AAAAAACA
129592 AAAAAACA
1 AAAAAACA
129600 AAACAAA-A
1 AAA-AAACA
129608 CAAAAAACA
1 -AAAAAACA
*
129617 AACAAACA
1 AAAAAACA
*
129625 AACAAACA
1 AAAAAACA
129633 AAAAA
1 AAAAA
129638 CAACAACAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
7 3 0.06
8 39 0.75
9 10 0.19
ACGTcount: A:0.83, C:0.14, G:0.01, T:0.01
Consensus pattern (8 bp):
AAAAAACA
Found at i:129602 original size:24 final size:24
Alignment explanation
Indices: 129568--129640 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 24
129558 CGTCCTCTAC
* *
129568 AAAAAAGAAAACAAACAAAAAATA
1 AAAAAACAAAACAAACAAAAAACA
129592 AAAAAACAAAACAAAACAAAAAACA
1 AAAAAACAAAAC-AAACAAAAAACA
*
129617 AACAAAC-AAACAAACAAAAAACA
1 AAAAAACAAAACAAACAAAAAACA
129640 A
1 A
129641 CAACAAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 13 0.29
24 15 0.33
25 17 0.38
ACGTcount: A:0.82, C:0.15, G:0.01, T:0.01
Consensus pattern (24 bp):
AAAAAACAAAACAAACAAAAAACA
Found at i:129610 original size:29 final size:29
Alignment explanation
Indices: 129570--129635 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
129560 TCCTCTACAA
* *
129570 AAAAGAAAACAAACAAA-AAATAAAAAAAC
1 AAAACAAAACAAA-AAACAAACAAAAAAAC
*
129599 AAAACAAAACAAAAAACAAACAAACAAAC
1 AAAACAAAACAAAAAACAAACAAAAAAAC
129628 -AAACAAAA
1 AAAACAAAA
129636 AACAACAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.02
Consensus pattern (29 bp):
AAAACAAAACAAAAAACAAACAAAAAAAC
Found at i:129614 original size:12 final size:12
Alignment explanation
Indices: 129566--129649 Score: 86
Period size: 12 Copynumber: 7.0 Consensus size: 12
129556 GGCGTCCTCT
129566 ACAAAA-AAGAAA
1 ACAAAACAA-AAA
129578 AC-AAACAAAAA
1 ACAAAACAAAAA
* *
129589 ATAAAAAAACAAA
1 ACAAAACAA-AAA
129602 ACAAAACAAAAA
1 ACAAAACAAAAA
129614 AC-AAACAAACAA
1 ACAAAACAAA-AA
129626 AC-AAACAAAAA
1 ACAAAACAAAAA
129637 ACAACAACAAAAA
1 ACAA-AACAAAAA
129650 GGGTCGGGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
11 18 0.29
12 26 0.42
13 18 0.29
ACGTcount: A:0.81, C:0.17, G:0.01, T:0.01
Consensus pattern (12 bp):
ACAAAACAAAAA
Found at i:129615 original size:36 final size:35
Alignment explanation
Indices: 129566--129649 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 35
129556 GGCGTCCTCT
129566 ACAAAA-AAGAAAACAAACAAA-AAATAAAAAAACAAA
1 ACAAAACAA-AAAACAAACAAACAAA-AAAAAAA-AAA
* *
129602 ACAAAACAAAAAACAAACAAACAAACAAACAAAAA
1 ACAAAACAAAAAACAAACAAACAAAAAAAAAAAAA
129637 ACAACAACAAAAA
1 ACAA-AACAAAAA
129650 GGGTCGGGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 7 0.16
36 31 0.72
37 5 0.12
ACGTcount: A:0.81, C:0.17, G:0.01, T:0.01
Consensus pattern (35 bp):
ACAAAACAAAAAACAAACAAACAAAAAAAAAAAAA
Found at i:129636 original size:29 final size:27
Alignment explanation
Indices: 129580--129649 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
129570 AAAAGAAAAC
*
129580 AAACAAA-AAATAAAAAAACAAAACAAA
1 AAACAAACAAACAAAAAAAC-AAACAAA
* *
129607 ACAAAAAACAAACAAACAAACAAACAAA
1 A-AACAAACAAACAAAAAAACAAACAAA
129635 AAAC-AAC-AACAAAAA
1 AAACAAACAAACAAAAA
129650 GGGTCGGGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.19
26 3 0.08
27 3 0.08
28 13 0.36
29 10 0.28
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.01
Consensus pattern (27 bp):
AAACAAACAAACAAAAAAACAAACAAA
Found at i:131214 original size:13 final size:13
Alignment explanation
Indices: 131196--131221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
131186 TACAGCAAGT
131196 ATGTATCGATACA
1 ATGTATCGATACA
131209 ATGTATCGATACA
1 ATGTATCGATACA
131222 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:133471 original size:21 final size:21
Alignment explanation
Indices: 133438--133482 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
133428 TTGCAAGATG
*
133438 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
133460 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
133480 AAA
1 AAA
133483 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:135306 original size:15 final size:15
Alignment explanation
Indices: 135286--135316 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
135276 TAAAAATGTC
*
135286 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
135301 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
135316 C
1 C
135317 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:137405 original size:13 final size:13
Alignment explanation
Indices: 137387--137412 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
137377 ACATTTTTCT
137387 TTGTATCGATACA
1 TTGTATCGATACA
137400 TTGTATCGATACA
1 TTGTATCGATACA
137413 AGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:137576 original size:20 final size:19
Alignment explanation
Indices: 137535--137577 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
137525 ATCTTTTGCA
137535 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
137555 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
137575 AAA
1 AAA
137578 ACTAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:139444 original size:20 final size:20
Alignment explanation
Indices: 139419--139458 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
139409 GGAAGTCAGA
139419 TTACAGGTTTAAGAAAGGAG
1 TTACAGGTTTAAGAAAGGAG
139439 TTACAGGTTTAAGAAAGGAG
1 TTACAGGTTTAAGAAAGGAG
139459 AATGATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (20 bp):
TTACAGGTTTAAGAAAGGAG
Found at i:140004 original size:13 final size:13
Alignment explanation
Indices: 139986--140011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
139976 TACAGCAAGT
139986 ATGTATCGATACA
1 ATGTATCGATACA
139999 ATGTATCGATACA
1 ATGTATCGATACA
140012 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:141078 original size:29 final size:29
Alignment explanation
Indices: 141035--141261 Score: 230
Period size: 29 Copynumber: 8.0 Consensus size: 29
141025 CATTCCTCAC
*
141035 CTTTT-CAAAGCCCACAAGTCAGTCGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
141063 CATTTCCAAAGCCCACAAGTCAGTGGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* * *
141092 C-CTTCAAAAGCCCATAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
141120 CTTTTCTAAAGCCCATAAGTCAGTGGCAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
141149 CTTTTCCAAAGCCCACAAGTTAGTGGCAA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* * * ** *
141178 C-CTTCAAAAGCCCACAAGTTAGTAACACC
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA-T
* *
141207 CCTTT-C-AAGCCCACAAGTCAGTGGTAT
1 CTTTTCCAAAGCCCACAAGTCAGTGGCAT
* *
141234 CTTTTCAAAAGCCCACAAGTTAGTGGCA
1 CTTTTCCAAAGCCCACAAGTCAGTGGCA
141262 ACCTTCAAAA
Statistics
Matches: 164, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
27 4 0.02
28 66 0.40
29 92 0.56
30 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (29 bp):
CTTTTCCAAAGCCCACAAGTCAGTGGCAT
Found at i:141110 original size:28 final size:28
Alignment explanation
Indices: 141041--141306 Score: 223
Period size: 29 Copynumber: 9.3 Consensus size: 28
141031 TCACCTTTTC
* * * *
141041 AAAGCCCACAAGTCAGTCGCATCATTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
141070 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
141098 AAAGCCCATAAGTCAGTGGCATCTTTTCT
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
* * * *
141127 AAAGCCCATAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
141156 AAAGCCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* ** *
141184 AAAGCCCACAAGTTAGTAACACCCCTTTC-
1 AAAGCCCACAAGTCAGTGGCA-ACC-TTCA
* * *
141213 -AAGCCCACAAGTCAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
141241 AAAGCCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* **
141269 AAAGCACACAAGTTGGT-GCAACCCTTTCA
1 AAAGCCCACAAGTCAGTGGCAA-CC-TTCA
141298 AAAGCCCAC
1 AAAGCCCAC
141307 CCAAGTTGGT
Statistics
Matches: 199, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
27 8 0.04
28 83 0.42
29 105 0.53
30 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:141131 original size:57 final size:57
Alignment explanation
Indices: 141041--141281 Score: 263
Period size: 57 Copynumber: 4.2 Consensus size: 57
141031 TCACCTTTTC
* * *
141041 AAAGCCCACAAGTCAGTCGCATCATTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * * * *
141098 AAAGCCCATAAGTCAGTGGCATCTTTTCTAAAGCCCATAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-CTTCA
* * * * ** *
141156 AAAGCCCACAAGTTAGTGGCAAC-CTTCAAAAGCCCACAAGTTAGTAACACCCCTTTC-
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCA-ACC-TTCA
* *
141213 -AAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
*
141269 AAAGCACACAAGT
1 AAAGCCCACAAGT
141282 TGGTGCAACC
Statistics
Matches: 151, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
55 3 0.02
56 21 0.14
57 100 0.66
58 27 0.18
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:141186 original size:86 final size:86
Alignment explanation
Indices: 141034--141281 Score: 356
Period size: 85 Copynumber: 2.9 Consensus size: 86
141024 ACATTCCTCA
* * *
141034 CCTTTTCAAAGCCCACAAGTCAGTCGCATCATTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTTAGTGGCAACCTTCAA
* **
141099 AAGCCCATAAGTCAGTGGCA-
66 AAGCCCACAAGTCAGTAACAC
* *
141119 TCTTTTCTAAAGCCCATAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTTAGTGGCAACCTTCA
1 CCTTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTTAGTGGCAACCTTCA
*
141184 AAAGCCCACAAGTTAGTAACAC
65 AAAGCCCACAAGTCAGTAACAC
* * *
141206 CCCTTTC-AAGCCCACAAGTCAGTGGTATCTTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCAA
1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTTAGTGGCAACCTTCAA
*
141270 AAGCACACAAGT
66 AAGCCCACAAGT
141282 TGGTGCAACC
Statistics
Matches: 146, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
85 71 0.49
86 70 0.48
87 5 0.03
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (86 bp):
CCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTTAGTGGCAACCTTCAA
AAGCCCACAAGTCAGTAACAC
Found at i:141297 original size:57 final size:58
Alignment explanation
Indices: 141041--141320 Score: 252
Period size: 57 Copynumber: 4.9 Consensus size: 58
141031 TCACCTTTTC
* * * *
141041 AAAGCCCACAAGTCAGTCGC-ATCATTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAATCCTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCA
* * * * * * * *
141098 AAAGCCCATAAGTCAGTGGC-ATCTTTTCTAAAGCCCATAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAATCCTTTCAAAAGCCCACAAGTTAGTGGCAAC-CTTCA
* ** *
141156 AAAGCCCACAAGTTAGTGGCAA-CC-TTCAAAAGCCCACAAGTTAGTAACACCCCTTTC-
1 AAAGCCCACAAGTCAGTGGCAATCCTTTCAAAAGCCCACAAGTTAGTGGCA-ACC-TTCA
* *
141213 -AAGCCCACAAGTCAGTGG-TATCTTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAATCCTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCA
* ** * *
141269 AAAGCACACAAGTTGGT-GCAACCCTTTCAAAAGCCCACCCAAGTTGGTGGCA
1 AAAGCCCACAAGTCAGTGGCAATCCTTTCAAAAGCCCA--CAAGTTAGTGGCA
141321 TCTTCTTCTA
Statistics
Matches: 181, Mismatches: 31, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
55 4 0.02
56 21 0.12
57 117 0.65
58 26 0.14
59 13 0.07
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (58 bp):
AAAGCCCACAAGTCAGTGGCAATCCTTTCAAAAGCCCACAAGTTAGTGGCAACCTTCA
Found at i:141299 original size:29 final size:28
Alignment explanation
Indices: 141236--141317 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 28
141226 AGTGGTATCT
* *
141236 TTTCAAAAGCCCACAAGTTAGTGGCAACC
1 TTTCAAAAGCACACAAGTTGGT-GCAACC
141265 -TTCAAAAGCACACAAGTTGGTGCAACCC
1 TTTCAAAAGCACACAAGTTGGTGCAA-CC
*
141293 TTTCAAAAGCCCACCCAAGTTGGTG
1 TTTCAAAAG--CACACAAGTTGGTG
141318 GCATCTTCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 4 0.09
28 21 0.46
29 8 0.17
31 13 0.28
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (28 bp):
TTTCAAAAGCACACAAGTTGGTGCAACC
Found at i:141400 original size:49 final size:49
Alignment explanation
Indices: 141324--141761 Score: 366
Period size: 49 Copynumber: 8.9 Consensus size: 49
141314 GGTGGCATCT
*
141324 TCTTCTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTAGCACCTTTA
1 TCTT-TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * *
141374 TCTTTAAGACCAATGTCGTTGCCCTTGAATCAGCACATTGGCA-C----
1 TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
* * *
141418 -CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTA
1 TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * * * *
141466 CCCTCTTGAGTCCAATATTGCTAGCCTTGAATCAGCATATTAGCACCCTTCTCA
1 -TCT-TTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCA-CCTT-T-A
* * * * * *
141520 TCTTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCATCTTTA
1 TC-TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
*** * * *
141570 TCTTTAAGTCTGGTATCGTTGGCCTTGAATCAGCATTTTGGCACCATCA
1 TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * * *
141619 TCTTTAAGACCATTGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * *
141668 TCTTTAAGTCCGATATCGTTGGCCTTAAATTAGCATATTGGCATCTTTA
1 TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * * ** *
141717 ACATTCCTAAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGC
1 TC-TT--TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGC
141762 GTTCTTCTTC
Statistics
Matches: 307, Mismatches: 66, Indels: 28
0.77 0.16 0.07
Matches are distributed among these distances:
43 36 0.12
44 1 0.00
48 1 0.00
49 151 0.49
50 11 0.04
51 36 0.12
52 35 0.11
53 34 0.11
54 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTA
Found at i:141423 original size:43 final size:43
Alignment explanation
Indices: 141375--141465 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
141365 GCACCTTTAT
* *
141375 CTTTAAGACCAATGTCGTTGCCCTTGAATCAGCACATTGGCAC
1 CTTTAAGACCAATATCGCTGCCCTTGAATCAGCACATTGGCAC
* * * * *
141418 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCAT
1 CTTTAAGACCAATATCGCTGCCCTTGAATCAGCACATTGGCAC
141461 CTTTA
1 CTTTA
141466 CCCTCTTGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (43 bp):
CTTTAAGACCAATATCGCTGCCCTTGAATCAGCACATTGGCAC
Found at i:141674 original size:147 final size:148
Alignment explanation
Indices: 141329--141761 Score: 439
Period size: 147 Copynumber: 2.9 Consensus size: 148
141319 CATCTTCTTC
* * *
141329 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTAAGACCAATGTCGTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCATCTTTAAGACCAATGTCGTT
*
141394 GCCCTTGAATCAGCACATTGGCA-C----CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATA
66 GGCCTTGAATCAGCACATTGGCATCTTTACTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATA
* * *
141454 TTGGCATCTTTACCCTCT
131 TTGGCACCATCACCCTCT
* * * *
141472 TGAGTCCAATATTGCTAGCCTTGAATCAGCATATTAGCACCCTTCTCATCTTTTAAGACCAATGT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTAGCA-CC-T-TCATC-TTTAAGACCAATGT
* * ** *
141537 CGCTGGCCTTGAATCAACACATTGGCATCTTTATCTTTAAGTCTGGTATCGTTGGCCTTGAATCA
62 CGTTGGCCTTGAATCAGCACATTGGCATCTTTA-CTTTAAGTCTAATATCGCTGGCCTTGAATCA
* *
141602 GCATTTTGGCACCATCA-TCT-T
126 GCATATTGGCACCATCACCCTCT
* * * * * *
141623 TAAGACCATTGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCGATATCGTT
1 TAAGACCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCATCTTTAAGACCAATGTCGTT
* * * * * * **
141688 GGCCTTAAATTAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCTGGCCTTGTCTCAG
66 GGCCTTGAATCAGCACATTGGCATCTTT-AC-TT--TAAGTCTAATATCGCTGGCCTTGAATCAG
*
141753 CACATTGGC
127 CATATTGGC
141762 GTTCTTCTTC
Statistics
Matches: 235, Mismatches: 41, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
143 35 0.15
144 2 0.01
145 1 0.00
146 4 0.02
147 77 0.33
148 9 0.04
149 1 0.00
150 30 0.13
151 33 0.14
152 2 0.01
153 41 0.17
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (148 bp):
TAAGACCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTCATCTTTAAGACCAATGTCGTT
GGCCTTGAATCAGCACATTGGCATCTTTACTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATA
TTGGCACCATCACCCTCT
Found at i:142684 original size:33 final size:33
Alignment explanation
Indices: 142627--142692 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
142617 GCCAAAGAAA
*
142627 TGTATCAATACATTATTCAATGTATCGTTACAT
1 TGTATCAATACATTATTCAATGTATCGATACAT
**
142660 TGTATCAATACATTGA-TCCTTGTATCGATACAT
1 TGTATCAATACATT-ATTCAATGTATCGATACAT
142693 CTAGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (33 bp):
TGTATCAATACATTATTCAATGTATCGATACAT
Found at i:153387 original size:32 final size:30
Alignment explanation
Indices: 153351--153409 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
153341 GAAATCAAAT
153351 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
153383 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
153410 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:153688 original size:13 final size:13
Alignment explanation
Indices: 153670--153695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
153660 AATTTTTTTG
153670 TGTATCGATACAT
1 TGTATCGATACAT
153683 TGTATCGATACAT
1 TGTATCGATACAT
153696 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:162103 original size:51 final size:50
Alignment explanation
Indices: 162043--162228 Score: 187
Period size: 51 Copynumber: 3.9 Consensus size: 50
162033 TTTTAACTAG
* *
162043 ATGTATCGATACATTAAAAAATATATCGATACATATAGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATATATCAATACAT-TAGGTAAAAAGACAGA
* * *
162094 ATGTATCGATAAATTGAAGAATATATCGATACATTCA--T------AC---
1 ATGTATCGATACATTGAAAAATATATCAATACATT-AGGTAAAAAGACAGA
*
162134 ATGTATCGATACATTGAAAAATGTATCAATACATCTAGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATATATCAATACAT-TAGGTAAAAAGACAGA
* * *
162185 ATGTATTGATACATTGAAAAATGTATCAATACATCAGGTAAAAA
1 ATGTATCGATACATTGAAAAATATATCAATACATTAGGTAAAAA
162229 TGTGACTTTT
Statistics
Matches: 113, Mismatches: 9, Indels: 27
0.76 0.06 0.18
Matches are distributed among these distances:
40 31 0.27
41 1 0.01
42 1 0.01
43 2 0.02
48 2 0.02
49 1 0.01
50 10 0.09
51 65 0.58
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATATATCAATACATTAGGTAAAAAGACAGA
Found at i:162140 original size:20 final size:20
Alignment explanation
Indices: 162093--162167 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
162083 AAAAAGACAG
* * *
162093 AATGTATCGATAAATTGAAG
1 AATGTATCGATACATTCAAA
* *
162113 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
162133 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
*
162153 AATGTATCAATACAT
1 AATGTATCGATACAT
162168 CTAGGTAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:162201 original size:91 final size:91
Alignment explanation
Indices: 162043--162218 Score: 271
Period size: 91 Copynumber: 1.9 Consensus size: 91
162033 TTTTAACTAG
*
162043 ATGTATCGATACATTAAAAAATATATCGATACATATAGGTAAAAAGACAGAATGTATCGATAAAT
1 ATGTATCGATACATTAAAAAATATATCAATACATATAGGTAAAAAGACAGAATGTATCGATAAAT
* *
162108 TGAAGAATATATCGATACATTCATAC
66 TGAAAAATATATCAATACATTCATAC
* * * * *
162134 ATGTATCGATACATTGAAAAATGTATCAATACATCTAGGTAAAAAGACAGAATGTATTGATACAT
1 ATGTATCGATACATTAAAAAATATATCAATACATATAGGTAAAAAGACAGAATGTATCGATAAAT
*
162199 TGAAAAATGTATCAATACAT
66 TGAAAAATATATCAATACAT
162219 CAGGTAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.29
Consensus pattern (91 bp):
ATGTATCGATACATTAAAAAATATATCAATACATATAGGTAAAAAGACAGAATGTATCGATAAAT
TGAAAAATATATCAATACATTCATAC
Found at i:163171 original size:13 final size:13
Alignment explanation
Indices: 163153--163186 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
163143 GTATTGCTTA
163153 GTATCGATGCAAT
1 GTATCGATGCAAT
163166 GTATCGATGCAAT
1 GTATCGATGCAAT
163179 GTATCGAT
1 GTATCGAT
163187 ACATGTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (13 bp):
GTATCGATGCAAT
Found at i:163319 original size:24 final size:23
Alignment explanation
Indices: 163264--163330 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
163254 CTTTTAATTG
*
163264 ATGCATCA-TGTTCATTATTACT
1 ATGCATCACTGTTCATTATCACT
* *
163286 GTTCATCACTGTTCATATATCACT
1 ATGCATCACTGTTCAT-TATCACT
*
163310 ATGCATCACTATTCATGTATC
1 ATGCATCACTGTTCAT-TATC
163331 GAGACAGTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 6 0.17
23 7 0.19
24 23 0.64
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (23 bp):
ATGCATCACTGTTCATTATCACT
Found at i:166135 original size:9 final size:9
Alignment explanation
Indices: 166121--166154 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
166111 TCCAAGTCAC
166121 CATCATTAT
1 CATCATTAT
166130 CATCATTAT
1 CATCATTAT
166139 CATC-TTCAT
1 CATCATT-AT
166148 CATCATT
1 CATCATT
166155 GATGGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:168614 original size:23 final size:24
Alignment explanation
Indices: 168587--168633 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
168577 TTGCTGAAAA
168587 TTTGTT-TTCAATTG-ATTTATGTT
1 TTTGTTCTT-AATTGAATTTATGTT
*
168610 TTTGTTCTTAATTGAATTTGTGTT
1 TTTGTTCTTAATTGAATTTATGTT
168634 CAATTCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.64
Consensus pattern (24 bp):
TTTGTTCTTAATTGAATTTATGTT
Found at i:169057 original size:30 final size:28
Alignment explanation
Indices: 169016--169083 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
169006 GATCTTGTGC
* *
169016 TATTATTGATGTTTATTGCATGATTATTAT
1 TATT-TTGATGTTTA-TGCATGATGATTAA
*
169046 TGATTTTGATGTTTATGGATGATGATTAA
1 T-ATTTTGATGTTTATGCATGATGATTAA
169075 TATTTTGAT
1 TATTTTGAT
169084 TGAATATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.24
29 12 0.35
30 11 0.32
31 3 0.09
ACGTcount: A:0.26, C:0.01, G:0.18, T:0.54
Consensus pattern (28 bp):
TATTTTGATGTTTATGCATGATGATTAA
Found at i:170963 original size:33 final size:32
Alignment explanation
Indices: 170921--170983 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
170911 TATACACCCA
*
170921 AATGTATCGATATATATTACTTAGTATCGATAC
1 AATGTATCGATACATATTACTTA-TATCGATAC
* *
170954 AATGTATCGATACATGTTCCTTATATCGAT
1 AATGTATCGATACATATTACTTATATCGAT
170984 GCATCATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (32 bp):
AATGTATCGATACATATTACTTATATCGATAC
Found at i:171117 original size:24 final size:22
Alignment explanation
Indices: 171049--171132 Score: 91
Period size: 24 Copynumber: 3.7 Consensus size: 22
171039 TTGATACATT
*
171049 ACTGTTCAT-TAT-TGTTCATC
1 ACTGTTCATGTATCAGTTCATC
*
171069 ACTGTTTTATGTATCACAGTTCATC
1 ACTG-TTCATGTAT--CAGTTCATC
171094 ACTGTTCATGTATCAGTATGCATC
1 ACTGTTCATGTATCAGT-T-CATC
171118 ACTGTTCATGTATCA
1 ACTGTTCATGTATCA
171133 ATCAGTGTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
20 4 0.07
21 4 0.07
22 7 0.13
23 1 0.02
24 27 0.50
25 11 0.20
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (22 bp):
ACTGTTCATGTATCAGTTCATC
Found at i:171253 original size:20 final size:19
Alignment explanation
Indices: 171207--171253 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
171197 AATTTCAAGT
*
171207 GCATGTATCGATACATTAT
1 GCATGTATCGATACATTAA
*
171226 GAATTGTATCGATACATTAAA
1 GCA-TGTATCGATACATT-AA
171247 GCATGTA
1 GCATGTA
171254 AGTGCGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (19 bp):
GCATGTATCGATACATTAA
Found at i:172252 original size:32 final size:32
Alignment explanation
Indices: 172161--172255 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 32
172151 TGGTGATTTG
* *
172161 AAAAAAGTTGCCACCAACTTGCGTGGGCCTTA
1 AAAAAAGTTGCCACCAACTTGTGTGGGCTTTA
* * * *
172193 AAAAAAGATGCCACTAACTTGTATGGGCTTTC
1 AAAAAAGTTGCCACCAACTTGTGTGGGCTTTA
* * *
172225 AAAAGAGTTGCCACCGACTTATGTGGGCTTT
1 AAAAAAGTTGCCACCAACTTGTGTGGGCTTT
172256 GAAAGGGTAT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (32 bp):
AAAAAAGTTGCCACCAACTTGTGTGGGCTTTA
Found at i:172305 original size:28 final size:28
Alignment explanation
Indices: 172195--172774 Score: 537
Period size: 28 Copynumber: 20.2 Consensus size: 28
172185 GGGCCTTAAA
* * *
172195 AAAAGATGCCACTAACTTGTATGGGCTTTC
1 AAAAGGTGCCACTGACTTG--TGGGCTTTG
*
172225 AAAAGAGTTGCCACCGACTTATGTGGGCTTTG
1 AAAAG-G-TGCCACTGAC-T-TGTGGGCTTTG
* * *
172257 AAAGGGTATGCCATTGACTTGTGGGTTTTG
1 AAAAGG--TGCCACTGACTTGTGGGCTTTG
* *
172287 AAATGGTGCCACTGACTTGTTGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
172315 AAAAGATGCCATTGACTTGTGGGCTTT-
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
172342 AAAATGATGCCACTAACTTGTGGGCTTTA
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
* * *
172371 AAAAGATGCCACTAACTTATGGGCTTT-
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
172398 AAAAGGATGCCACTAACTTATGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
172427 AAAAGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
172455 -AAA-GTACGCCACTGACTTATGGGC-TTC
1 AAAAGGT--GCCACTGACTTGTGGGCTTTG
172482 AAAATGGTGCCACTGACTTGTGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
* * * *
172511 AAAGGGTATGGCACTGACTTATGGGCTTCG
1 AAAAGG--TGCCACTGACTTGTGGGCTTTG
*
172541 AAAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
* *
172570 AAATGATGCCACTGACTTGTGGGCTTT-
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
172597 AAAAGGATGCCACTGTCTTGTGAGG-TTTG
1 AAAAGG-TGCCACTGACTTGTG-GGCTTTG
*
172626 AAAGGGTGCCACTGACTTGTGGGCTTT-
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
172653 AAAAGGGTATTCCATTGACTTGTGGGCTTTG
1 AAAA-GG--TGCCACTGACTTGTGGGCTTTG
* *
172684 AAAAGGGTGCCACTGACTTATGGGCGTTG
1 AAAA-GGTGCCACTGACTTGTGGGCTTTG
* * *
172713 AAAAGATGCCATTGACTTGTAGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* * *
172741 AAAAGATGCCATTTACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
172769 AAAAGG
1 AAAAGG
172775 GTCGTATTGA
Statistics
Matches: 463, Mismatches: 61, Indels: 54
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.00
27 23 0.05
28 270 0.58
29 64 0.14
30 63 0.14
31 11 0.02
32 28 0.06
33 1 0.00
34 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (28 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:172592 original size:143 final size:140
Alignment explanation
Indices: 172201--172772 Score: 612
Period size: 143 Copynumber: 4.0 Consensus size: 140
172191 TAAAAAAAGA
* * *
172201 TGCCACTAACTTGTATGGGCTTTCAAAAGAGT-TGCCACCGACTTATGTGGGCTTTG-AAAGGGT
1 TGCCACTGACTTG--TGGGCTTT--AAAGGGTATGCCACTGACTTA--TGGGC-TTGAAAAGGG-
* * * * * * * *
172264 ATGCCATTGACTTGTGGGTTTTGAAATGGTGCCACTGACTTGTTGGCTTTGAAAAGATGCCATTG
58 -TGCCACTAACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAAGATGCCACTG
*
172329 ACTTGTGGGCTTTAAAATGA
121 ACTTGTGGGCTTTAAAATGG
* ** * * *
172349 TGCCACTAACTTGTGGGCTTTAAAAAG-ATGCCACTAACTTATGGGCTTTAAAAGGATGCCACTA
1 TGCCACTGACTTGTGGGCTTTAAAGGGTATGCCACTGACTTATGGGCTTGAAAAGGGTGCCACTA
* *
172413 ACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGTACGCCACTGACTTATGGG
66 ACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAG-ATGCCACTGACTTGTGGG
*
172478 CTTCAAAATGG
130 CTTTAAAATGG
*
172489 TGCCACTGACTTGTGGGCTTTGAAAGGGTATGGCACTGACTTATGGGCTTCGAAAAGGGTGCCAC
1 TGCCACTGACTTGTGGGCTTT-AAAGGGTATGCCACTGACTTATGGGCTT-GAAAAGGGTGCCAC
* * * *
172554 TAACTTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCACTGTCTTGTG
64 TAACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAA-GATGCCACTGACTTGTG
* *
172619 AGG-TTTGAAAGGG
128 -GGCTTTAAAATGG
* * *
172632 TGCCACTGACTTGTGGGCTTTAAAAGGGTATTCCATTGACTTGTGGGCTTTGAAAAGGGTGCCAC
1 TGCCACTGACTTGTGGGCTTT-AAAGGGTATGCCACTGACTTATGGGC-TTGAAAAGGGTGCCAC
* * * * * *
172697 TGACTTATGGGCGTTGAAAAGATGCCATTGACTTGTAGGCTTTGAAAAGATGCCATTTACTTGTG
64 TAACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTG-AAAGATGCCACTGACTTGTG
172762 GGCTTTGAAAA
128 GGCTTT-AAAA
172773 GGGTCGTATT
Statistics
Matches: 363, Mismatches: 49, Indels: 28
0.82 0.11 0.06
Matches are distributed among these distances:
139 4 0.01
140 87 0.24
141 6 0.02
142 31 0.09
143 187 0.52
144 27 0.07
146 8 0.02
148 13 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (140 bp):
TGCCACTGACTTGTGGGCTTTAAAGGGTATGCCACTGACTTATGGGCTTGAAAAGGGTGCCACTA
ACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTTGTGGGC
TTTAAAATGG
Found at i:172824 original size:13 final size:13
Alignment explanation
Indices: 172808--172868 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 13
172798 ACAAAGTTTC
172808 TGACAAACATTCT
1 TGACAAACATTCT
**
172821 TGACAAATGTTCT
1 TGACAAACATTCT
* *
172834 TGACGATACTTTCT
1 TGAC-AAACATTCT
*
172848 TGACAACCATTTCT
1 TGACAAACA-TTCT
172862 TGACAAA
1 TGACAAA
172869 TGGTGAATTG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
13 17 0.46
14 20 0.54
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (13 bp):
TGACAAACATTCT
Found at i:174078 original size:10 final size:9
Alignment explanation
Indices: 174059--174092 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
174049 TGTTTGTTTA
174059 TTTTTTGGT
1 TTTTTTGGT
174068 TTTTTTGGGT
1 TTTTTT-GGT
*
174078 TTTTTTTGT
1 TTTTTTGGT
174087 TTTTTT
1 TTTTTT
174093 TTTGTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (9 bp):
TTTTTTGGT
Found at i:184437 original size:27 final size:28
Alignment explanation
Indices: 184407--184465 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
184397 AAAAGAGGAA
184407 GATCGATAGATGAATCG-CCATCTAACC
1 GATCGATAGATGAATCGCCCATCTAACC
* *
184434 GATCGGTAGATGAATTGCCCATCTAACC
1 GATCGATAGATGAATCGCCCATCTAACC
184462 GATC
1 GATC
184466 CTCGATGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (28 bp):
GATCGATAGATGAATCGCCCATCTAACC
Done.