Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008591.1 Hibiscus syriacus cultivar Beakdansim tig00111540_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1730314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1395369 original size:23 final size:23
Alignment explanation
Indices: 1395336--1395381 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1395326 AAGATGATTC
1395336 AAGTTCAAGCATATGTTATTAAT
1 AAGTTCAAGCATATGTTATTAAT
*
1395359 AAGTTCGAGCATATGTTATTAAT
1 AAGTTCAAGCATATGTTATTAAT
1395382 GATTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (23 bp):
AAGTTCAAGCATATGTTATTAAT
Found at i:1396142 original size:21 final size:21
Alignment explanation
Indices: 1396116--1396166 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1396106 AAGAACCTTG
1396116 TGCTCTACCAACTGAGCTGGA
1 TGCTCTACCAACTGAGCTGGA
1396137 TGCTCTACCAACTGAGCTGGA
1 TGCTCTACCAACTGAGCTGGA
1396158 TGCTCTACC
1 TGCTCTACC
1396167 TCAAGCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.25
Consensus pattern (21 bp):
TGCTCTACCAACTGAGCTGGA
Found at i:1399625 original size:14 final size:14
Alignment explanation
Indices: 1399608--1399767 Score: 78
Period size: 15 Copynumber: 11.3 Consensus size: 14
1399598 GAAAAATAAT
1399608 TTACGTAAAATGAA
1 TTACGTAAAATGAA
* **
1399622 TTACTGAAAAATGTT
1 TTAC-GTAAAATGAA
* *
1399637 TTATGTAAAAACGAA
1 TTACGT-AAAATGAA
* *
1399652 TTACAT-GAA--AA
1 TTACGTAAAATGAA
1399663 TTACGTAAAAATGAA
1 TTACGT-AAAATGAA
* **
1399678 TTACATGAAAACTGTT
1 TTACGT-AAAA-TGAA
*
1399694 TTACGTTAAATGAA
1 TTACGTAAAATGAA
**
1399708 TTAC-TAAAACTGTT
1 TTACGTAAAA-TGAA
1399722 TTACGTAAAATGAA
1 TTACGTAAAATGAA
**
1399736 TTAC-TAAAACTGTT
1 TTACGTAAAA-TGAA
*
1399750 TTACGTAAAATAAA
1 TTACGTAAAATGAA
1399764 TTAC
1 TTAC
1399768 ATTTCATGGA
Statistics
Matches: 104, Mismatches: 31, Indels: 22
0.66 0.20 0.14
Matches are distributed among these distances:
11 7 0.07
13 13 0.12
14 34 0.33
15 43 0.41
16 7 0.07
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (14 bp):
TTACGTAAAATGAA
Found at i:1399631 original size:28 final size:29
Alignment explanation
Indices: 1399607--1399767 Score: 192
Period size: 28 Copynumber: 5.7 Consensus size: 29
1399597 TGAAAAATAA
*
1399607 TTTACGTAAAATGAATTACTGAAAAATGT
1 TTTACGTAAAATGAATTACTGAAAACTGT
* *
1399636 TTTATGTAAAAACGAATTACATGAAAA----
1 TTTACGT-AAAATGAATTAC-TGAAAACTGT
1399663 -TTACGTAAAAATGAATTACATGAAAACTGT
1 TTTACGT-AAAATGAATTAC-TGAAAACTGT
*
1399693 TTTACGTTAAATGAATTACT-AAAACTGT
1 TTTACGTAAAATGAATTACTGAAAACTGT
1399721 TTTACGTAAAATGAATTACT-AAAACTGT
1 TTTACGTAAAATGAATTACTGAAAACTGT
*
1399749 TTTACGTAAAATAAATTAC
1 TTTACGTAAAATGAATTAC
1399768 ATTTCATGGA
Statistics
Matches: 118, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
26 24 0.20
28 53 0.45
29 7 0.06
30 22 0.19
31 12 0.10
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (29 bp):
TTTACGTAAAATGAATTACTGAAAACTGT
Found at i:1399632 original size:15 final size:15
Alignment explanation
Indices: 1399596--1399662 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
1399586 AATTGATTTT
1399596 CTGAAAAAT-AATTTA
1 CTGAAAAATGAA-TTA
*
1399611 C-GTAAAATGAATTA
1 CTGAAAAATGAATTA
**
1399625 CTGAAAAATGTTTTA
1 CTGAAAAATGAATTA
*
1399640 -TGTAAAAACGAATTA
1 CTG-AAAAATGAATTA
1399655 CATGAAAA
1 C-TGAAAA
1399663 TTACGTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
14 12 0.30
15 22 0.55
16 4 0.10
17 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (15 bp):
CTGAAAAATGAATTA
Found at i:1399679 original size:15 final size:15
Alignment explanation
Indices: 1399599--1399759 Score: 65
Period size: 14 Copynumber: 11.3 Consensus size: 15
1399589 TGATTTTCTG
1399599 AAAAAT-AATTTACGT
1 AAAAATGAA-TTACGT
1399614 -AAAATGAATTAC-T
1 AAAAATGAATTACGT
** *
1399627 GAAAAATGTTTTATGT
1 -AAAAATGAATTACGT
*
1399643 AAAAACGAATTAC--
1 AAAAATGAATTACGT
**
1399656 ATGAA--AATTACGT
1 AAAAATGAATTACGT
*
1399669 AAAAATGAATTACAT
1 AAAAATGAATTACGT
* **
1399684 GAAAACTGTTTTACGT
1 -AAAAATGAATTACGT
*
1399700 -TAAATGAATTAC-T
1 AAAAATGAATTACGT
* **
1399713 AAAACTGTTTTACGT
1 AAAAATGAATTACGT
1399728 -AAAATGAATTAC-T
1 AAAAATGAATTACGT
* **
1399741 AAAACTGTTTTACGT
1 AAAAATGAATTACGT
1399756 AAAA
1 AAAA
1399760 TAAATTACAT
Statistics
Matches: 103, Mismatches: 30, Indels: 26
0.65 0.19 0.16
Matches are distributed among these distances:
11 6 0.06
13 9 0.09
14 43 0.42
15 33 0.32
16 12 0.12
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (15 bp):
AAAAATGAATTACGT
Found at i:1399960 original size:25 final size:23
Alignment explanation
Indices: 1399909--1399960 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
1399899 TTGATTAAGT
* * *
1399909 TAATATTAAAAAAACAGTTTGAT
1 TAATATTAAAAAAAAAGTTAGAC
1399932 TAATGATTAAATAAAAAAGTTAGAC
1 TAAT-ATTAAA-AAAAAAGTTAGAC
1399957 TAAT
1 TAAT
1399961 TCGATTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 6 0.25
25 14 0.58
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (23 bp):
TAATATTAAAAAAAAAGTTAGAC
Found at i:1400117 original size:46 final size:44
Alignment explanation
Indices: 1400064--1400208 Score: 112
Period size: 48 Copynumber: 3.0 Consensus size: 44
1400054 ATTATTATAT
1400064 TAATATTAAATGTAAAAATTAATATTATTCATTATTAATAATTTAA
1 TAATATTAAAT-TAAAAATTAATATTATT-ATTATTAATAATTTAA
* * *
1400110 TAATATTATATTTAAAAAAATAAATACTATTAACTATATTAATAATTTATTA
1 TAATATTA-AATT--AAAAATTAATATTATT-A-T-TATTAATAATTTA--A
* * *
1400162 TACATTATTAAATTAAAAAATAATATAATATATTATT-ATAATATAA
1 TA-A-TATTAAATTAAAAATTAATATTAT-TATTATTAATAATTTAA
1400208 T
1 T
1400209 TGAGTATATA
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
46 11 0.14
47 2 0.03
48 22 0.28
49 5 0.06
50 14 0.18
51 12 0.15
52 4 0.05
53 4 0.05
54 5 0.06
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (44 bp):
TAATATTAAATTAAAAATTAATATTATTATTATTAATAATTTAA
Found at i:1400204 original size:51 final size:48
Alignment explanation
Indices: 1400064--1400204 Score: 123
Period size: 54 Copynumber: 2.9 Consensus size: 48
1400054 ATTATTATAT
* *
1400064 TAATATTAAATGTAAAAATTAATAT--TAT-TCATTATTAATAATTTAA
1 TAATATTAAAT-TAAAAAATAATATAATATATTATTATTAATAATTTAA
* *
1400110 TAATATTATATTTAAAAA-AATA-AATACTATTAACTATATTAATAATTTATTA
1 TAATATTAAATTAAAAAATAATATAATA-TATT-A-T-TATTAATAATTTA--A
1400162 TACATTATTAAATTAAAAAATAATATAATATATTATTA-TAATA
1 TA-A-TATTAAATTAAAAAATAATATAATATATTATTATTAATA
1400205 TAATTGAGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
44 4 0.05
45 7 0.09
46 11 0.14
47 1 0.01
48 1 0.01
49 1 0.01
50 13 0.17
51 5 0.07
52 5 0.07
53 2 0.03
54 14 0.18
55 8 0.11
56 4 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (48 bp):
TAATATTAAATTAAAAAATAATATAATATATTATTATTAATAATTTAA
Found at i:1400302 original size:19 final size:19
Alignment explanation
Indices: 1400280--1400331 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1400270 TAATATTTTC
1400280 ATTAAAATAATATTAAA-A
1 ATTAAAATAATATTAAATA
* *
1400298 TATTATATTAATATTAAATA
1 -ATTAAAATAATATTAAATA
*
1400318 AATAAAATAATATT
1 ATTAAAATAATATT
1400332 TTTTGAGTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAAATAATATTAAATA
Found at i:1400522 original size:29 final size:28
Alignment explanation
Indices: 1400469--1400532 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
1400459 ATTCATCACT
*
1400469 AAAAAATATTTTTCAGCTATTAAACACAA
1 AAAAAATATTTTTCAGCTATCAAAC-CAA
* * *
1400498 AAAAAATATTTTTCTGTTATCAAACTAA
1 AAAAAATATTTTTCAGCTATCAAACCAA
1400526 AAAAAAT
1 AAAAAAT
1400533 GAAAAAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAAAATATTTTTCAGCTATCAAACCAA
Found at i:1405942 original size:16 final size:16
Alignment explanation
Indices: 1405921--1405953 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1405911 CAAACCAAAT
1405921 TCATGTATGGATGGCA
1 TCATGTATGGATGGCA
1405937 TCATGTATGGATGGCA
1 TCATGTATGGATGGCA
1405953 T
1 T
1405954 ATCTTAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.33
Consensus pattern (16 bp):
TCATGTATGGATGGCA
Found at i:1408844 original size:13 final size:13
Alignment explanation
Indices: 1408785--1408844 Score: 66
Period size: 13 Copynumber: 4.3 Consensus size: 13
1408775 TTTAAATGAT
1408785 AAACGAACATAAAC
1 AAACGAACA-AAAC
1408799 AAACGTAAACAAATAC
1 AAACG--AACAAA-AC
*
1408815 AAACGAACAAAAT
1 AAACGAACAAAAC
*
1408828 AAACGAACAACAC
1 AAACGAACAAAAC
1408841 AAAC
1 AAAC
1408845 ACAAAAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 16 0.40
14 11 0.28
15 2 0.05
16 11 0.28
ACGTcount: A:0.65, C:0.22, G:0.07, T:0.07
Consensus pattern (13 bp):
AAACGAACAAAAC
Found at i:1409123 original size:14 final size:14
Alignment explanation
Indices: 1409104--1409132 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1409094 GCTCTCTGTT
1409104 CGAACATAAATGAA
1 CGAACATAAATGAA
1409118 CGAACATAAATGAA
1 CGAACATAAATGAA
1409132 C
1 C
1409133 AAAAGTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:1409222 original size:43 final size:40
Alignment explanation
Indices: 1409170--1409265 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
1409160 TTCACGAACG
1409170 TAAATGAACGAACAAACCCTTTGTTCATGTTCGTTCATTTAA
1 TAAATGAACGAACAAA-CC-TTGTTCATGTTCGTTCATTTAA
* * *
1409212 TTAAACGAACGTA-AAATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACGAACAAACCTTGTTCATGTTCGTTCATTTAA
*
1409252 TAAATAAACGAACA
1 TAAATGAACGAACA
1409266 TAAACGAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
39 9 0.20
40 23 0.50
41 1 0.02
42 3 0.07
43 10 0.22
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (40 bp):
TAAATGAACGAACAAACCTTGTTCATGTTCGTTCATTTAA
Found at i:1418033 original size:30 final size:30
Alignment explanation
Indices: 1417958--1418036 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
1417948 TGTTAAATGT
*
1417958 ATTAATTTAGTCTCTCTATTAGAAGAATCA
1 ATTAAATTAGTCTCTCTATTAGAAGAATCA
* * * *
1417988 ATTTAAAATAATCTCTCTATTATAAGAATTA
1 A-TTAAATTAGTCTCTCTATTAGAAGAATCA
1418019 ATTAAATTAGTCTCTCTA
1 ATTAAATTAGTCTCTCTA
1418037 CAATTAAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 16 0.39
31 25 0.61
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (30 bp):
ATTAAATTAGTCTCTCTATTAGAAGAATCA
Found at i:1420028 original size:26 final size:26
Alignment explanation
Indices: 1419976--1420029 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1419966 TATACTTTTT
*
1419976 TATTTTTTATTAAAATAAACATTTAA
1 TATTTTTTATTAAAATAAACATATAA
* *
1420002 TATTTTATTTTTAAAATAATC-TATAA
1 TATTTT-TTATTAAAATAAACATATAA
1420028 TA
1 TA
1420030 ATTATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTTTTATTAAAATAAACATATAA
Found at i:1420187 original size:26 final size:26
Alignment explanation
Indices: 1420151--1420203 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1420141 ATATTTAGAA
1420151 ACATCGCTGTTCGATCTGGTCCGAAG
1 ACATCGCTGTTCGATCTGGTCCGAAG
1420177 ACATCGCTGTTCGATCTGGTCCGAAG
1 ACATCGCTGTTCGATCTGGTCCGAAG
1420203 A
1 A
1420204 AATCACTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (26 bp):
ACATCGCTGTTCGATCTGGTCCGAAG
Found at i:1432113 original size:52 final size:52
Alignment explanation
Indices: 1432035--1432136 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 52
1432025 CAAGTCATTC
* * *
1432035 TACTTTTGGATGGGATGATACGAGCATCTTAGTTCACTCGATCAATTAATTA
1 TACTTTAGGATGGGATAATACGAGCATCTTAGGTCACTCGATCAATTAATTA
* * *
1432087 TACTTTAGGATGGGATAATATGAGCATTTTCGGTCACTCGATCAATTAAT
1 TACTTTAGGATGGGATAATACGAGCATCTTAGGTCACTCGATCAATTAAT
1432137 GGATGACATC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (52 bp):
TACTTTAGGATGGGATAATACGAGCATCTTAGGTCACTCGATCAATTAATTA
Found at i:1439593 original size:18 final size:19
Alignment explanation
Indices: 1439558--1439594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1439548 CACGGAATGT
1439558 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1439578 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1439595 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1441786 original size:3 final size:3
Alignment explanation
Indices: 1441778--1441833 Score: 67
Period size: 3 Copynumber: 17.3 Consensus size: 3
1441768 AGTATTTTTA
*
1441778 TAT TAT TAT TATT TAT ATAT TAT TAT TAT TATT TAT ATAT TAT TAA TAT
1 TAT TAT TAT TA-T TAT -TAT TAT TAT TAT TA-T TAT -TAT TAT TAT TAT
1441827 TAT TAT T
1 TAT TAT T
1441834 TTTAGTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 35 0.74
4 12 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1441796 original size:17 final size:17
Alignment explanation
Indices: 1441756--1441837 Score: 77
Period size: 17 Copynumber: 5.1 Consensus size: 17
1441746 CAGTATAATA
* *
1441756 TATATTTTATATAGTATT
1 TATATATTAT-TATTATT
*
1441774 TTTATATTATTATTATT
1 TATATATTATTATTATT
1441791 TATATATTATTATTA-T
1 TATATATTATTATTATT
*
1441807 TATTTA-TA-TATTA-T
1 TATATATTATTATTATT
1441821 TA-ATATTATTATT-TT
1 TATATATTATTATTATT
1441836 TA
1 TA
1441838 GTTTTATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
13 2 0.04
14 10 0.18
15 9 0.16
16 6 0.11
17 20 0.36
18 8 0.15
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (17 bp):
TATATATTATTATTATT
Found at i:1441796 original size:37 final size:35
Alignment explanation
Indices: 1441754--1441835 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 35
1441744 TACAGTATAA
* *
1441754 TATATATTTTATATAGTATTTTTATATTATTATTATT
1 TATATATTTTAT-TAGTATTTATATATTATTAATA-T
*
1441791 TATATATTATTATTATTATTTATATATTATTAATAT
1 TATATATT-TTATTAGTATTTATATATTATTAATAT
1441827 TAT-TATTTT
1 TATATATTTT
1441836 TAGTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 2 0.05
35 4 0.10
36 4 0.10
37 27 0.66
38 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (35 bp):
TATATATTTTATTAGTATTTATATATTATTAATAT
Found at i:1441834 original size:23 final size:20
Alignment explanation
Indices: 1441754--1441830 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
1441744 TACAGTATAA
*
1441754 TATATATT-TTATATAGTATT
1 TATATATTATTAT-TATTATT
1441774 T-T-TA-TATTATTATTATT
1 TATATATTATTATTATTATT
1441791 TATATATTATTATTATTATT
1 TATATATTATTATTATTATT
*
1441811 TATATATTATTAATATTATT
1 TATATATTATTATTATTATT
1441831 ATTTTTAGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
17 8 0.16
18 7 0.14
19 3 0.06
20 33 0.65
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
TATATATTATTATTATTATT
Found at i:1443290 original size:19 final size:18
Alignment explanation
Indices: 1443266--1443308 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1443256 CAGAGGTAAG
*
1443266 TAATTTGGATTGAAAATTT
1 TAATTTGAATT-AAAATTT
* *
1443285 TAATTTTAATTAAATTTT
1 TAATTTGAATTAAAATTT
1443303 TAATTT
1 TAATTT
1443309 TTGTAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
TAATTTGAATTAAAATTT
Found at i:1444414 original size:20 final size:20
Alignment explanation
Indices: 1444389--1444481 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1444379 TTTTCCCAAT
1444389 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1444409 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1444429 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
** *
1444450 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1444471 TCGCAATGCGA
1 TCGCAATGCGA
1444482 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1444431 original size:41 final size:41
Alignment explanation
Indices: 1444386--1444481 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1444376 CGATTTTCCC
1444386 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1444427 AATTCGCAATGCGAATAAGTAAATCGCAATGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1444468 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1444482 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1444435 original size:21 final size:20
Alignment explanation
Indices: 1444389--1444481 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
1444379 TTTTCCCAAT
*
1444389 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1444409 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1444429 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
**
1444450 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1444471 TCGCAATGCGA
1 TCGCAATGCGA
1444482 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 30 0.50
21 30 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1444495 original size:20 final size:20
Alignment explanation
Indices: 1444470--1444564 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1444460 AATTGGGAAA
*
1444470 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1444490 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1444511 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1444531 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1444551 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1444565 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1444512 original size:41 final size:41
Alignment explanation
Indices: 1444467--1444544 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1444457 GCGAATTGGG
* * *
1444467 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
1444508 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
1444545 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:1444780 original size:22 final size:22
Alignment explanation
Indices: 1444752--1444795 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1444742 CACTCTCTCA
1444752 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1444774 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1444796 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1445084 original size:20 final size:20
Alignment explanation
Indices: 1445059--1445096 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1445049 CGATTCTCTC
1445059 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1445079 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1445097 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1446436 original size:18 final size:18
Alignment explanation
Indices: 1446415--1446459 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1446405 TCCAATTCGG
*
1446415 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1446433 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1446451 GAGCCATCA
1 GAGCCATCA
1446460 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1446986 original size:19 final size:20
Alignment explanation
Indices: 1446932--1446987 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1446922 TAGTTTACTT
* *
1446932 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
1446952 TTGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1446972 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
1446988 AAATCGCAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1446993 original size:19 final size:19
Alignment explanation
Indices: 1446971--1447034 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
1446961 GGAAATGGCT
1446971 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1446990 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1447004 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1447023 ATCGCAATGCGA
1 ATCGCAATGCGA
1447035 TTTTTGTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 22 0.61
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1447075 original size:19 final size:19
Alignment explanation
Indices: 1447060--1447163 Score: 111
Period size: 19 Copynumber: 5.4 Consensus size: 19
1447050 GCGATTTTGT
1447060 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1447078 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1447097 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
1447117 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1447136 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1447156 TGTTGCGA
1 CGTTGCGA
1447164 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 8 0.11
19 36 0.49
20 29 0.40
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1447121 original size:39 final size:38
Alignment explanation
Indices: 1447071--1447144 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
1447061 GTTGCGATTT
**
1447071 CATTTCGCGTTGCGATTTTCATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
*
1447109 CATTTCCGCGTTGCGATAGTCATTTCGCGTTGCGAT
1 CATTT-CGCGTTGCGATAGTCATTTCGCATTGCGAT
1447145 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (38 bp):
CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
Found at i:1449028 original size:14 final size:14
Alignment explanation
Indices: 1449009--1449044 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1448999 ATTGTTTAAT
1449009 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1449023 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1449037 TGATTTGT
1 TGATTTGT
1449045 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1449262 original size:19 final size:19
Alignment explanation
Indices: 1449240--1449337 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1449230 GGAAATTACT
1449240 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1449259 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1449273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1449292 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1449306 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1449325 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1449338 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1449282 original size:33 final size:33
Alignment explanation
Indices: 1449240--1449333 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1449230 GGAAATTACT
1449240 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1449273 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1449306 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1449334 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1449355 original size:19 final size:20
Alignment explanation
Indices: 1449333--1449375 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1449323 AAATCGCAAC
1449333 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1449352 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1449372 GCGA
1 GCGA
1449376 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1449360 original size:14 final size:14
Alignment explanation
Indices: 1449361--1449394 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1449351 TGCGATTTTC
1449361 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1449375 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1449389 ATTTTC
1 ATTTTC
1449395 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1449536 original size:14 final size:14
Alignment explanation
Indices: 1449517--1449553 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1449507 CATCAATTAA
1449517 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1449531 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1449545 ACAAATCAA
1 ACAAATCAA
1449554 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1450995 original size:42 final size:42
Alignment explanation
Indices: 1450949--1451032 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1450939 CGATGACAGT
* * *
1450949 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1450991 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1451033 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1453148 original size:19 final size:19
Alignment explanation
Indices: 1453031--1453215 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1453021 TCTTTTGGTT
*
1453031 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1453050 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1453070 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1453088 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1453104 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1453122 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1453137 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1453157 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1453176 GAAATGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
*
1453195 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1453214 GA
1 GA
1453216 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 60 0.44
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1453169 original size:39 final size:38
Alignment explanation
Indices: 1453031--1453215 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
1453021 TCTTTTGGTT
* *
1453031 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
1453070 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
1453104 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
1453137 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
* *
1453176 GAAATGAAAATCGCAACGTGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1453214 GA
1 GA
1453216 TTTTGGTTTC
Statistics
Matches: 125, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
33 42 0.34
34 16 0.13
35 2 0.02
38 23 0.18
39 28 0.22
40 14 0.11
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1453244 original size:19 final size:19
Alignment explanation
Indices: 1453211--1453255 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1453201 AAAATCGCAA
*
1453211 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1453230 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1453249 TGCGATT
1 TGCGATT
1453256 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1453835 original size:20 final size:20
Alignment explanation
Indices: 1453807--1453858 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1453797 CGCTAAGTAA
* *
1453807 ATCGCGTTGCGAAAGTCAGT
1 ATCGTGTTGCGAAAGTAAGT
1453827 ATCGTGTTGCGAAAGTAAGT
1 ATCGTGTTGCGAAAGTAAGT
1453847 ATC-TCGTTGCGA
1 ATCGT-GTTGCGA
1453859 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGTGTTGCGAAAGTAAGT
Found at i:1453919 original size:41 final size:41
Alignment explanation
Indices: 1453889--1453984 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
1453879 ATAGTCAGTA
* * * *
1453889 TCGCATTGGGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
1453930 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
1453971 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1453985 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1453922 original size:21 final size:21
Alignment explanation
Indices: 1453889--1453981 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 21
1453879 ATAGTCAGTA
*
1453889 TCGCATTGGGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1453910 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
1453930 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1453951 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1453971 TCGCATTGCGA
1 TCGCATTGCGA
1453982 ATTGGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.56
21 25 0.44
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1453933 original size:20 final size:20
Alignment explanation
Indices: 1453908--1453981 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1453898 GATTTTCCCA
*
1453908 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
1453928 ATTCGCATTGCGAATTTCCCA
1 ATTCGCATTGCG-ATTTACTT
*
1453949 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
1453969 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1453982 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:1456810 original size:2 final size:2
Alignment explanation
Indices: 1456803--1456843 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1456793 TCATAAAATC
1456803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1456844 AAGTAGAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1457626 original size:24 final size:22
Alignment explanation
Indices: 1457599--1457643 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1457589 TATCAAAATC
1457599 ATGATCTA-GTAGTATATTGTAAAA
1 ATGAT-TATGTAGT-TATT-TAAAA
1457623 ATGATTATGTAGTTATTTAAA
1 ATGATTATGTAGTTATTTAAA
1457644 TCACATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (22 bp):
ATGATTATGTAGTTATTTAAAA
Found at i:1457745 original size:32 final size:32
Alignment explanation
Indices: 1457690--1457761 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1457680 TCTCATGATT
* * *
1457690 TACCCAAGAGAGTGTCTTAGGGCCTGAGAGCC
1 TACCCAATAAAGTGTCTTAGGGCCTCAGAGCC
* *
1457722 TACCCAATAAAGTTTCTTGGGGCCTCAGAGCC
1 TACCCAATAAAGTGTCTTAGGGCCTCAGAGCC
1457754 TACCCAAT
1 TACCCAAT
1457762 GGTTACCTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (32 bp):
TACCCAATAAAGTGTCTTAGGGCCTCAGAGCC
Found at i:1465191 original size:22 final size:22
Alignment explanation
Indices: 1465162--1465206 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1465152 AAAAAATGTT
*
1465162 GAAAAAAATAGCAGTTCGAAAAA
1 GAAAAAAA-AACAGTTCGAAAAA
*
1465185 GAAAAAAAAACTGTTCGAAAAA
1 GAAAAAAAAACAGTTCGAAAAA
1465207 AAGACATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (22 bp):
GAAAAAAAAACAGTTCGAAAAA
Found at i:1469486 original size:3 final size:3
Alignment explanation
Indices: 1469478--1469502 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1469468 TTTGTTAGTA
1469478 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1469503 GAATTAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1477275 original size:16 final size:16
Alignment explanation
Indices: 1477251--1477284 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1477241 TATCGCCGAC
*
1477251 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1477267 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1477283 CG
1 CG
1477285 TGAATAGTAA
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:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1480059 original size:23 final size:23
Alignment explanation
Indices: 1480012--1480069 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1480002 GTTTATATAG
1480012 TATTATTATATTATATAATAATAA
1 TATTATTAT-TTATATAATAATAA
* *
1480036 TATTATTATTTATATATTACTAA
1 TATTATTATTTATATAATAATAA
1480059 TATTATTATTT
1 TATTATTATTT
1480070 TTAGTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTATTATTTATATAATAATAA
Found at i:1482670 original size:119 final size:119
Alignment explanation
Indices: 1482459--1482695 Score: 456
Period size: 119 Copynumber: 2.0 Consensus size: 119
1482449 TTATTACTAC
1482459 ATATATATATTAATTGTGGTATTCTTGAAATATTATATAAATCTATATCAGATATTATATTTTAA
1 ATATATATATTAATTGTGGTATTCTTGAAATATTATATAAATCTATATCAGATATTATATTTTAA
1482524 GTGTAAATTACAAATTTCATCATTAAATTTTATTCTCTTATTTTATTCACTGAT
66 GTGTAAATTACAAATTTCATCATTAAATTTTATTCTCTTATTTTATTCACTGAT
*
1482578 ATATATATCTTAATTGTGGTATTCTTGAAATATTATATAAATCTATATCAGATATTATATTTTAA
1 ATATATATATTAATTGTGGTATTCTTGAAATATTATATAAATCTATATCAGATATTATATTTTAA
*
1482643 GTGTAAATTACAAATTTTATCATTAAATTTTATTCTCTTATTTTATTCACTGA
66 GTGTAAATTACAAATTTCATCATTAAATTTTATTCTCTTATTTTATTCACTGA
1482696 ACCTTAAAAG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (119 bp):
ATATATATATTAATTGTGGTATTCTTGAAATATTATATAAATCTATATCAGATATTATATTTTAA
GTGTAAATTACAAATTTCATCATTAAATTTTATTCTCTTATTTTATTCACTGAT
Found at i:1486446 original size:32 final size:32
Alignment explanation
Indices: 1486397--1486462 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1486387 TGATTTACTG
* *
1486397 AAAAAAGTGTCTTGGGGCCT-GAGAGCCTATCC
1 AAAAAAGTGTCTCGGGGCCTCG-GAGCCTACCC
*
1486429 AAAAAAGTTTCTCGGGGCCTCGGAGCCTACCC
1 AAAAAAGTGTCTCGGGGCCTCGGAGCCTACCC
1486461 AA
1 AA
1486463 GGGTCACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (32 bp):
AAAAAAGTGTCTCGGGGCCTCGGAGCCTACCC
Found at i:1489659 original size:28 final size:29
Alignment explanation
Indices: 1489602--1489659 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1489592 TGTGACAAAG
* *
1489602 TATAATAATTATTTTATAATTTTGATAAA
1 TATAATAAATATTTTATAATTTTGAAAAA
*
1489631 TATAA-AAATATTTTATAATTTTTAAAAA
1 TATAATAAATATTTTATAATTTTGAAAAA
1489659 T
1 T
1489660 TTCATGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TATAATAAATATTTTATAATTTTGAAAAA
Found at i:1490791 original size:3 final size:3
Alignment explanation
Indices: 1490783--1490807 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1490773 TTTGTTAGTA
1490783 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1490808 GAATTAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1503384 original size:13 final size:13
Alignment explanation
Indices: 1503366--1503403 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1503356 GATTTCTCAG
1503366 AAATGAAGATAGA
1 AAATGAAGATAGA
1503379 AAATGAAGATA-A
1 AAATGAAGATAGA
*
1503391 CAA-GAAGATAGA
1 AAATGAAGATAGA
1503403 A
1 A
1503404 GAAAATCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 7 0.32
12 4 0.18
13 11 0.50
ACGTcount: A:0.63, C:0.03, G:0.21, T:0.13
Consensus pattern (13 bp):
AAATGAAGATAGA
Found at i:1503964 original size:42 final size:41
Alignment explanation
Indices: 1503917--1504013 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
1503907 ACAATTTAAG
* * *
1503917 TCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGAGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * * *
1503959 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGAGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
* *
1504000 TCATTCGTGCCATC
1 TCCTTCGAGCCATC
1504014 CATAAGACCT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (41 bp):
TCCTTCGAGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:1504240 original size:13 final size:13
Alignment explanation
Indices: 1504222--1504246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1504212 TGAAGCAAAT
1504222 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1504235 CCATCAGTAAGT
1 CCATCAGTAAGT
1504247 CTTTCGAGCA
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:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1504293 original size:42 final size:42
Alignment explanation
Indices: 1504234--1504335 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
1504224 ATCAGTAAGT
1504234 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
* * *
1504276 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
*
1504318 GCCATCAGTAAGTTTTTC
1 GCCATCAGTAAGTCTTTC
1504336 AGGTAAAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
Found at i:1504347 original size:42 final size:42
Alignment explanation
Indices: 1504234--1504372 Score: 149
Period size: 42 Copynumber: 3.3 Consensus size: 42
1504224 ATCAGTAAGT
** * * *
1504234 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTCCAG
1 GCCATCAGTAAGTCTTTCGAGCAAAATGATTAAATCCTTCGG
**
1504276 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCAAAATGATTAAATCCTTCGG
* *
1504318 GCCATCAGTAAGTTTTTC-AGGTAAAATGA-TAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGA-GCAAAATGATTAAATCCTTCGG
*
1504359 GTCATCCA-TAAGTC
1 GCCAT-CAGTAAGTC
1504373 CTTTGGGTAG
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 22 0.26
42 64 0.74
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCAAAATGATTAAATCCTTCGG
Found at i:1504908 original size:53 final size:53
Alignment explanation
Indices: 1504796--1504916 Score: 156
Period size: 53 Copynumber: 2.3 Consensus size: 53
1504786 ATAATCACAC
* *
1504796 CAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCTATAGG
1 CAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAAGGAGCGAACCGATAGG
* * * *
1504849 CAGAAGATTGTTCGAGTTTTACTCCTTGAAGCAAGAAGGAGCGAACCCGCT-GG
1 CAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAAGGAGCGAA-CCGATAGG
1504902 TC-GAAGATTGTTCAA
1 -CAGAAGATTGTTCAA
1504917 AAAAGAGGGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 55 0.93
54 4 0.07
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAAGGAGCGAACCGATAGG
Found at i:1508114 original size:24 final size:23
Alignment explanation
Indices: 1508085--1508139 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1508075 AATTGAATTT
*
1508085 AAAATT-CAATTAATGAGAATTTCC
1 AAAATTACAATTAATGA-AACTT-C
*
1508109 AAAATTACCATTAATGAAACTTC
1 AAAATTACAATTAATGAAACTTC
1508132 AAAATTAC
1 AAAATTAC
1508140 CAAATGTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.32
24 10 0.36
25 9 0.32
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (23 bp):
AAAATTACAATTAATGAAACTTC
Found at i:1508138 original size:23 final size:25
Alignment explanation
Indices: 1508085--1508141 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
1508075 AATTGAATTT
* *
1508085 AAAATT-CAATTAATGAGAATTTCC
1 AAAATTACCATTAATGAGAACTTCC
1508109 AAAATTACCATTAATGA-AACTT-C
1 AAAATTACCATTAATGAGAACTTCC
1508132 AAAATTACCA
1 AAAATTACCA
1508142 AATGTCATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 11 0.37
24 10 0.33
25 9 0.30
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (25 bp):
AAAATTACCATTAATGAGAACTTCC
Found at i:1508591 original size:16 final size:16
Alignment explanation
Indices: 1508572--1508607 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1508562 TGACATCAGG
*
1508572 TTCAGTTCGGGTTAAT
1 TTCAGTTCGGATTAAT
*
1508588 TTCAGTTCGGATTGAT
1 TTCAGTTCGGATTAAT
1508604 TTCA
1 TTCA
1508608 TTTCAGGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (16 bp):
TTCAGTTCGGATTAAT
Found at i:1508933 original size:2 final size:2
Alignment explanation
Indices: 1508773--1508925 Score: 65
Period size: 2 Copynumber: 78.5 Consensus size: 2
1508763 GAAAAAAATA
* **
1508773 AT AT AT GT AT AT AT AT -T A- AT AT -T AT AT AT ACT -T AT GC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
1508812 AT AT AT AT AT AT AT AT AT AA AT AT A- AA AT AC AT A- AT A- AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * *
1508852 AT GT AT AT AT AT A- AGT AT AT GT A- AGT AT AT AT AT GT GAT GT
1 AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT -AT AT
* * *
1508893 AT GT AC AC A- AGT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
1508926 AGTATATAAT
Statistics
Matches: 113, Mismatches: 22, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
1 10 0.09
2 97 0.86
3 6 0.05
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1509301 original size:27 final size:26
Alignment explanation
Indices: 1509230--1509330 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 26
1509220 TTCTCTATTC
1509230 TCTCTAAATTTCTC-AATTTCCCTCTAT
1 TCTC-AAATTT-TCAAATTTCCCTCTAT
* ** *
1509257 TCCCAAATATCCCCAATTTCCCTCTAT
1 TCTCAAAT-TTTCAAATTTCCCTCTAT
*
1509284 TCTCAAAATTTTCAAATTTCACTCTAAAT
1 TCTC-AAATTTTCAAATTTCCCTCT--AT
1509313 TCTC-AATTTTCCAAATTT
1 TCTCAAATTTT-CAAATTT
1509331 TTTCAATTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.08
27 38 0.63
28 11 0.18
29 6 0.10
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (26 bp):
TCTCAAATTTTCAAATTTCCCTCTAT
Found at i:1509346 original size:37 final size:38
Alignment explanation
Indices: 1509292--1509392 Score: 143
Period size: 37 Copynumber: 2.7 Consensus size: 38
1509282 ATTCTCAAAA
* *
1509292 TTTTCAAATTTCACTCTAAATTCTCAATTTTCC-AAATT
1 TTTTC-AATTTCCCTCTAAATTCTCAATTTCCCAAAATT
*
1509330 TTTTCAATTTCCCTCTAAATTCCCAATTTCCCAAAATT
1 TTTTCAATTTCCCTCTAAATTCTCAATTTCCCAAAATT
*
1509368 TCTT-AATTTCCCTCTAAATTCTCAA
1 TTTTCAATTTCCCTCTAAATTCTCAA
1509393 ATAAAATCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
37 44 0.77
38 13 0.23
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.45
Consensus pattern (38 bp):
TTTTCAATTTCCCTCTAAATTCTCAATTTCCCAAAATT
Found at i:1509358 original size:19 final size:19
Alignment explanation
Indices: 1509334--1509388 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1509324 CAAATTTTTT
1509334 CAATTTCCCTCTAAATTCC
1 CAATTTCCCTCTAAATTCC
* *
1509353 CAATTT-CC-CAAAATTTCT
1 CAATTTCCCTCTAAA-TTCC
*
1509371 TAATTTCCCTCTAAATTC
1 CAATTTCCCTCTAAATTC
1509389 TCAAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 11 0.38
20 4 0.14
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (19 bp):
CAATTTCCCTCTAAATTCC
Found at i:1509672 original size:13 final size:13
Alignment explanation
Indices: 1509649--1509692 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1509639 TGAAATTAAT
*
1509649 TTAATGATTATAA
1 TTAAGGATTATAA
1509662 TTAA-GATTTATAA
1 TTAAGGA-TTATAA
1509675 TATAAGGATTATAA
1 T-TAAGGATTATAA
1509689 TTAA
1 TTAA
1509693 TATACAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (13 bp):
TTAAGGATTATAA
Found at i:1509843 original size:16 final size:16
Alignment explanation
Indices: 1509822--1509873 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1509812 TATAACTTAT
1509822 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATATC
*
1509838 AAGTCAGATAAATATC
1 AAGTCAGGTAAATATC
* *
1509854 ATA-TCAGGTCAATAAC
1 A-AGTCAGGTAAATATC
1509870 AAGT
1 AAGT
1509874 TGAATTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (16 bp):
AAGTCAGGTAAATATC
Found at i:1511307 original size:12 final size:12
Alignment explanation
Indices: 1511282--1511349 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
1511272 ACGAAGATAT
* *
1511282 CAGAAATCAAAA
1 CAGAATTCAGAA
1511294 CAGAATTCAGAA
1 CAGAATTCAGAA
1511306 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1511318 CAGAA-TC-CAT
1 CAGAATTCAGAA
*
1511328 CAGAAATCAGAA
1 CAGAATTCAGAA
1511340 CAGAATTCAG
1 CAGAATTCAG
1511350 GTCATTTATC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
10 6 0.13
11 6 0.13
12 32 0.71
13 1 0.02
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.15
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1511347 original size:46 final size:46
Alignment explanation
Indices: 1511280--1511369 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
1511270 AAACGAAGAT
1511280 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
* ** **
1511326 ATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAAT
1511370 TCAAGTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (46 bp):
ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC
Found at i:1511384 original size:24 final size:24
Alignment explanation
Indices: 1511281--1511386 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
1511271 AACGAAGATA
*
1511281 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
1511304 AACAGATATCAGAACAGAA-TCCA-
1 -TCAGAAATCAGAACAGAATTCAAG
*
1511327 TCAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
***
1511351 TCATTTATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
1511375 TCGGAAATCAGA
1 TCAGAAATCAGA
1511387 TAAAATATTT
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
22 16 0.25
23 4 0.06
24 44 0.69
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:1513013 original size:63 final size:63
Alignment explanation
Indices: 1512914--1513036 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
1512904 TGCTTTCTTG
1512914 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1512977 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1513037 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:1513980 original size:13 final size:13
Alignment explanation
Indices: 1513962--1513993 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1513952 CGCCGGTCAA
1513962 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1513975 CGGGTCAACGGGT
1 CGGGTCAACGGGT
1513988 CGGGTC
1 CGGGTC
1513994 GGGTCAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:1513997 original size:31 final size:31
Alignment explanation
Indices: 1513962--1514028 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1513952 CGCCGGTCAA
* * *
1513962 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGAGTCGGATAAACGGGTCGGGT
*
1513993 CGGGTCAACTAGTCGGATAAACGGGTCGGGT
1 CGGGTCAACGAGTCGGATAAACGGGTCGGGT
1514024 CGGGT
1 CGGGT
1514029 TGGGTTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGAGTCGGATAAACGGGTCGGGT
Found at i:1514007 original size:18 final size:18
Alignment explanation
Indices: 1513970--1514008 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1513960 AACGGGTCAA
*
1513970 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGAGT
*
1513988 CGGGTCGGGTCAACTAGT
1 CGGGTCGGGTCAACGAGT
1514006 CGG
1 CGG
1514009 ATAAACGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGAGT
Found at i:1517810 original size:62 final size:63
Alignment explanation
Indices: 1517732--1517853 Score: 228
Period size: 63 Copynumber: 2.0 Consensus size: 63
1517722 TGCTTTCTTG
1517732 AACACTCTCTGATCTTG-AACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
*
1517794 AACACTCTCTGATCTTGAAACGGTTCTCTTAACATACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1517854 CCTAGGATTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 17 0.29
63 41 0.71
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.35
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:1518487 original size:190 final size:191
Alignment explanation
Indices: 1518163--1518550 Score: 751
Period size: 190 Copynumber: 2.0 Consensus size: 191
1518153 TTATATTAAT
*
1518163 CATTCGATCCGTAATCAGTTACAGAATTTCTGCAACATTCATATCGAGTGTATAATTTATTTTAA
1 CATTCGATCCGTAATCAGTTACAGAATTTCTACAACATTCATATCGAGTGTATAATTTATTTTAA
1518228 CTCCACCAAAGTGACCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGT
66 CTCCACCAAAGTGACCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGT
*
1518293 ATAAAGAGGTAGTAAAGTATTACCTCGATTTCCGTGCAATACTGATCGACCATAAAAATTC
131 ATAAAGAGGTAGCAAAGTATTACCTCGATTTCCGTGCAATACTGATCGACCATAAAAATTC
1518354 CATTCGATCCGTAATCAGTTACAGAATTTCTACAACATTCATATCGAGTGTATAATTTA-TTTAA
1 CATTCGATCCGTAATCAGTTACAGAATTTCTACAACATTCATATCGAGTGTATAATTTATTTTAA
1518418 CTCCACCAAAGTGACCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGT
66 CTCCACCAAAGTGACCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGT
1518483 ATAAAGAGGTAGCAAAGTATTACCTCGATTTCCGTGCAATACTGATCGACCATAAAAATTC
131 ATAAAGAGGTAGCAAAGTATTACCTCGATTTCCGTGCAATACTGATCGACCATAAAAATTC
1518544 CATTCGA
1 CATTCGA
1518551 ACGCCTTTGA
Statistics
Matches: 195, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
190 137 0.70
191 58 0.30
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (191 bp):
CATTCGATCCGTAATCAGTTACAGAATTTCTACAACATTCATATCGAGTGTATAATTTATTTTAA
CTCCACCAAAGTGACCAACATTATCTTATTCATGCATTTACCAATATCAACATGTTCCATAAAGT
ATAAAGAGGTAGCAAAGTATTACCTCGATTTCCGTGCAATACTGATCGACCATAAAAATTC
Found at i:1521855 original size:23 final size:23
Alignment explanation
Indices: 1521825--1521870 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1521815 TGAGGAGGCC
1521825 AATGGACAATCAAGTTAACACAG
1 AATGGACAATCAAGTTAACACAG
1521848 AATGGACAATCAAGTTAACACAG
1 AATGGACAATCAAGTTAACACAG
1521871 TTTACAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (23 bp):
AATGGACAATCAAGTTAACACAG
Found at i:1521930 original size:32 final size:33
Alignment explanation
Indices: 1521889--1521953 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
1521879 ACAAGGCAGG
1521889 GATTTCATCGATGAGAACACCGGTA-CGTGATC
1 GATTTCATCGATGAGAACACCGGTACCGTGATC
1521921 GATTTCATCGATGAGAACACCGGTACCGTGATC
1 GATTTCATCGATGAGAACACCGGTACCGTGATC
1521954 CAAAACTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (33 bp):
GATTTCATCGATGAGAACACCGGTACCGTGATC
Found at i:1522605 original size:162 final size:163
Alignment explanation
Indices: 1522338--1522663 Score: 636
Period size: 162 Copynumber: 2.0 Consensus size: 163
1522328 TCATGTCGTC
1522338 CAGTAAGTAATCCTAATGCAAAGTGGACTATGCTGTGGGTCTTTTATTTGTATTAGCATTATTTC
1 CAGTAAGTAATCCTAATGCAAAGTGGACTATGCTGTGGGTCTTTTATTTGTATTAGCATTATTTC
1522403 AGTTTAATTTTGTATTATCTTTATTTTACCATTTGATGTGCCAATC-TATATATCAACTTAAGGT
66 AGTTTAATTTTGTATTATCTTTATTTTACCATTTGATGTGCCAATCATATATATCAACTTAAGGT
1522467 GAATTTTTAAAATTTTAAGAAATAAAAATAAAA
131 GAATTTTTAAAATTTTAAGAAATAAAAATAAAA
1522500 CAGTAAGTAATCCTAATGCAAAGTGGACTATGCTGTGGGTCTTTTATTTGTATTAGCATTATTTC
1 CAGTAAGTAATCCTAATGCAAAGTGGACTATGCTGTGGGTCTTTTATTTGTATTAGCATTATTTC
1522565 AGTTTAATTTTGTATTATCTTTATTTTACCATTTGATGTGCCAATCTATATATATCAACTTAAGG
66 AGTTTAATTTTGTATTATCTTTATTTTACCATTTGATGTGCCAATC-ATATATATCAACTTAAGG
1522630 TGAATTTTTAAAATTTTAAGAAATAAAAATAAAA
130 TGAATTTTTAAAATTTTAAGAAATAAAAATAAAA
1522664 AAATATTAAA
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
162 111 0.69
164 51 0.31
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (163 bp):
CAGTAAGTAATCCTAATGCAAAGTGGACTATGCTGTGGGTCTTTTATTTGTATTAGCATTATTTC
AGTTTAATTTTGTATTATCTTTATTTTACCATTTGATGTGCCAATCATATATATCAACTTAAGGT
GAATTTTTAAAATTTTAAGAAATAAAAATAAAA
Found at i:1523103 original size:38 final size:38
Alignment explanation
Indices: 1523052--1523127 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
1523042 TCTCAAAAAA
* *
1523052 TCGGGTCAAATGGAAGATAT-ATATTTTTCAGGTCGGGT
1 TCGGATCAAATGGAAGATATAAAATTTTT-AGGTCGGGT
* *
1523090 TCGGATCACATGGAAGATTTAAAATTTTTAGGTCGGGT
1 TCGGATCAAATGGAAGATATAAAATTTTTAGGTCGGGT
1523128 GAACCTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 26 0.79
39 7 0.21
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.34
Consensus pattern (38 bp):
TCGGATCAAATGGAAGATATAAAATTTTTAGGTCGGGT
Found at i:1524467 original size:20 final size:20
Alignment explanation
Indices: 1524442--1524534 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1524432 TTTCCCCAAT
1524442 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1524462 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1524482 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1524503 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1524524 TCGCAATGCGA
1 TCGCAATGCGA
1524535 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1524484 original size:41 final size:41
Alignment explanation
Indices: 1524439--1524534 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1524429 CGATTTCCCC
1524439 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1524480 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1524521 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1524535 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1524488 original size:21 final size:20
Alignment explanation
Indices: 1524442--1524534 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1524432 TTTCCCCAAT
*
1524442 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1524462 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1524482 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1524503 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1524524 TCGCAATGCGA
1 TCGCAATGCGA
1524535 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1524547 original size:41 final size:41
Alignment explanation
Indices: 1524461--1524595 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1524451 GAATAAGTAA
* * *
1524461 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1524502 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1524543 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1524584 TTCGCAACGCGA
1 ATCGCAACGCGA
1524596 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1524548 original size:20 final size:20
Alignment explanation
Indices: 1524523--1524617 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1524513 AATTGGGAAA
*
1524523 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1524543 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1524564 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1524584 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1524604 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1524618 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1524833 original size:22 final size:22
Alignment explanation
Indices: 1524805--1524848 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1524795 CACTCTCTCA
1524805 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1524827 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1524849 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1525135 original size:20 final size:20
Alignment explanation
Indices: 1525110--1525147 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1525100 TGCGATTCTC
1525110 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1525130 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1525148 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1526471 original size:18 final size:18
Alignment explanation
Indices: 1526450--1526494 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1526440 TCCACTTCGG
*
1526450 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
1526468 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
1526486 GAGCCATCA
1 GAGCCATCA
1526495 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1527021 original size:19 final size:20
Alignment explanation
Indices: 1526967--1527033 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1526957 TAGTTTACTT
* *
1526967 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1526987 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1527007 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1527026 TCGCAACG
1 TCGCAACG
1527034 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1527041 original size:14 final size:14
Alignment explanation
Indices: 1527022--1527078 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
1527012 ATGCGAAATG
1527022 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1527036 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1527052 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1527068 AAAATCACAAC
1 AAAATCGCAAC
1527079 ACGAAATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.51, C:0.26, G:0.14, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1527064 original size:32 final size:33
Alignment explanation
Indices: 1527006--1527096 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
1526996 GGAAATGGCT
*
1527006 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1527039 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* *
1527071 ATCACAACACGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1527097 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1527119 original size:19 final size:18
Alignment explanation
Indices: 1527097--1527186 Score: 70
Period size: 14 Copynumber: 5.3 Consensus size: 18
1527087 AAAATCGCAA
1527097 TGCGATTTGTGTTTCGCGT
1 TGCGATTT-TGTTTCGCGT
1527116 TGCGATTTTG--TC-C-T
1 TGCGATTTTGTTTCGCGT
**
1527130 TGCGATTTCATTTCGCGT
1 TGCGATTTTGTTTCGCGT
1527148 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
* *
1527162 TGCGATTTTCATTTCGCAT
1 TGCGATTTT-GTTTCGCGT
1527181 TGCGAT
1 TGCGAT
1527187 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
14 21 0.38
15 1 0.02
16 5 0.09
17 2 0.04
18 11 0.20
19 16 0.29
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1527147 original size:32 final size:33
Alignment explanation
Indices: 1527108--1527186 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1527098 GCGATTTGTG
1527108 TTTCGCGTTGCGATTTTGTCCTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCCTTGCGATTTTCA
*
1527140 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCCTTGCGATTTTCA
*
1527173 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1527187 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCCTTGCGATTTTCA
Found at i:1527205 original size:20 final size:19
Alignment explanation
Indices: 1527171--1527225 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1527161 TTGCGATTTT
*
1527171 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1527190 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1527210 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1527226 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1529255 original size:18 final size:18
Alignment explanation
Indices: 1529232--1529266 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1529222 AACGAGAAAA
1529232 TCGCAATGCGAAATGAAC
1 TCGCAATGCGAAATGAAC
1529250 TCGCAATGCGAAATGAA
1 TCGCAATGCGAAATGAA
1529267 AATCGCAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (18 bp):
TCGCAATGCGAAATGAAC
Found at i:1529369 original size:20 final size:20
Alignment explanation
Indices: 1529312--1529369 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
1529302 TCGCATTGCG
* *
1529312 ATTTTCTCGTTGCGATAACC
1 ATTTTCACGTTGCGATAGCC
*
1529332 ATTTTCGCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
1529352 ATTTTCACGTTGCGATAG
1 ATTTTCACGTTGCGATAG
1529370 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:1530479 original size:24 final size:24
Alignment explanation
Indices: 1530423--1530481 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
1530413 AGTCAGTATT
* *
1530423 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
1530447 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
1530471 CGAATTTTGAT
1 CGAAATTTGAT
1530482 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:1532976 original size:19 final size:19
Alignment explanation
Indices: 1532954--1533051 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1532944 GGAAATTACT
1532954 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1532973 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1532987 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1533006 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
1533020 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1533039 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1533052 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1532996 original size:33 final size:33
Alignment explanation
Indices: 1532954--1533047 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1532944 GGAAATTACT
1532954 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1532987 ATCGCAATGCGAAATGAAAATCGCAATGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1533020 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1533048 CGAATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1533069 original size:19 final size:20
Alignment explanation
Indices: 1533047--1533089 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1533037 AAATCGCAAC
1533047 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1533066 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1533086 GCGA
1 GCGA
1533090 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1533074 original size:14 final size:14
Alignment explanation
Indices: 1533075--1533108 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1533065 TGCGATTTTC
1533075 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1533089 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1533103 ATTTTC
1 ATTTTC
1533109 ATTTCGCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1533248 original size:14 final size:14
Alignment explanation
Indices: 1533229--1533265 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1533219 CATCAATTAA
1533229 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1533243 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1533257 ACAAATCAA
1 ACAAATCAA
1533266 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1534705 original size:42 final size:42
Alignment explanation
Indices: 1534656--1534739 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1534646 CGATGACAGT
* * *
1534656 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1534698 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1534740 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1536746 original size:20 final size:19
Alignment explanation
Indices: 1536715--1536876 Score: 99
Period size: 20 Copynumber: 8.8 Consensus size: 19
1536705 GTCTTTGGTT
1536715 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1536734 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1536755 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1536774 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
1536788 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
*** * *
1536804 CCCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1536822 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
1536842 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1536861 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1536877 TGCGATTTGG
Statistics
Matches: 111, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
14 10 0.09
15 7 0.06
16 5 0.05
17 2 0.02
18 3 0.03
19 35 0.32
20 47 0.42
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1536783 original size:34 final size:33
Alignment explanation
Indices: 1536740--1536839 Score: 137
Period size: 34 Copynumber: 3.0 Consensus size: 33
1536730 ACGAGATAAT
*
1536740 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1536774 GAGAATCGCAACGCGAAATGACTATCGCGACCCA
1 GAGAATCGCAACGCGAAATGACTATCGC-AACCA
* **
1536808 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1536840 GCGAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
33 17 0.29
34 42 0.71
ACGTcount: A:0.39, C:0.27, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1536898 original size:18 final size:18
Alignment explanation
Indices: 1536877--1536919 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1536867 AAAATCGCAA
*
1536877 TGCGATTTGGTTTCGCGT
1 TGCGATTTGATTTCGCGT
*
1536895 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTGATTTCGCGT
1536914 TGCGAT
1 TGCGAT
1536920 AGTCATTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTGATTTCGCGT
Found at i:1536944 original size:19 final size:19
Alignment explanation
Indices: 1536887--1536945 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1536877 TGCGATTTGG
* *
1536887 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTCTCA
**
1536906 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTCTCA
1536925 TTTCCGCG-TGCGATTCTCA
1 TTT-CGCGTTGCGATTCTCA
1536944 TT
1 TT
1536946 CTCGAACTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 30 0.88
20 4 0.12
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TTTCGCGTTGCGATTCTCA
Found at i:1537538 original size:20 final size:20
Alignment explanation
Indices: 1537453--1537546 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1537443 CGCTATGTAA
*
1537453 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
1537473 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1537493 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1537514 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1537534 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1537547 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1537565 original size:41 final size:41
Alignment explanation
Indices: 1537535--1537630 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
1537525 ATAGTCAGTA
* * *
1537535 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
1537576 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
1537617 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1537631 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1537579 original size:20 final size:20
Alignment explanation
Indices: 1537535--1537627 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1537525 ATAGTCAGTA
* **
1537535 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1537556 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1537576 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
1537597 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1537617 TCGCATTGCGA
1 TCGCATTGCGA
1537628 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Done.