Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 137 of 325
Found at i:41667631 original size:24 final size:24
Alignment explanation
Indices: 41667604--41667652 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
41667594 TTCTAACACC
41667604 TTTAATGTAATCACCCTTCAATTG
1 TTTAATGTAATCACCCTTCAATTG
*
41667628 TTTAATGTGATCACCCTTCAATTG
1 TTTAATGTAATCACCCTTCAATTG
41667652 T
1 T
41667653 GTTGTACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (24 bp):
TTTAATGTAATCACCCTTCAATTG
Found at i:41669163 original size:12 final size:12
Alignment explanation
Indices: 41669146--41669180 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
41669136 ATATATATAT
41669146 ATACATGTCATG
1 ATACATGTCATG
41669158 ATACATGTCATG
1 ATACATGTCATG
*
41669170 ATACATATCAT
1 ATACATGTCAT
41669181 TCTCTTTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (12 bp):
ATACATGTCATG
Found at i:41677057 original size:28 final size:28
Alignment explanation
Indices: 41676999--41677064 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
41676989 CCAGGTTTTT
*
41676999 GGACACGGGCGTGTCTAGGCCGTGTGAG
1 GGACACGGGCGTGTCTAGGCCATGTGAG
* * * * *
41677027 GGAGACGGGTGTGTCTAGGCTATTTGGG
1 GGACACGGGCGTGTCTAGGCCATGTGAG
41677055 GGACACGGGC
1 GGACACGGGC
41677065 TAGGGACACA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.15, C:0.18, G:0.47, T:0.20
Consensus pattern (28 bp):
GGACACGGGCGTGTCTAGGCCATGTGAG
Found at i:41683686 original size:18 final size:18
Alignment explanation
Indices: 41683663--41683699 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
41683653 CCTAAAGGAC
*
41683663 TAGCTATCATCTTTTTCA
1 TAGCTATCATATTTTTCA
41683681 TAGCTATCATATTTTTCA
1 TAGCTATCATATTTTTCA
41683699 T
1 T
41683700 TCTTTCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (18 bp):
TAGCTATCATATTTTTCA
Found at i:41684561 original size:48 final size:48
Alignment explanation
Indices: 41684478--41684856 Score: 340
Period size: 48 Copynumber: 7.9 Consensus size: 48
41684468 ATACTAGGGT
* * *
41684478 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTG-
1 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGAC-TTTGA
* * *
41684526 TATGAGAGCTATTGTAAGACCATGTTTGGGACATGGCGTCGGCTTTGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACTTTGA
* * *
41684574 TATGTGAGCCAGTGTAAGACCATGTTT-GGAGCATGGCATCGGCATTT-A
1 TATGAGAGCTAGTGTAAGACCATGTTTGGGA-CATGGCATCGAC-TTTGA
* * * * *
41684622 TATGATAGATAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACTTTGA
* * * * *
41684670 TATGTA-ATCCAGTGTAAGACCATGTTTTGAACATGGGATCGACATTT-A
1 TATG-AGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGAC-TTTGA
* * * * *
41684718 TATGAAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACTTTGA
* * * **
41684766 CATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCGAT-A
1 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATC-G-A-CTTTGA
* * *
41684816 TATGAGAGCCAGTGCAAGACCATGTATT-GGACATGGTATCG
1 TATGAGAGCTAGTGTAAGACCATGT-TTGGGACATGGCATCG
41684857 GCATCTTACC
Statistics
Matches: 267, Mismatches: 51, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
47 10 0.04
48 212 0.79
49 10 0.04
50 32 0.12
51 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACTTTGA
Found at i:41684642 original size:96 final size:96
Alignment explanation
Indices: 41684478--41684858 Score: 501
Period size: 96 Copynumber: 3.9 Consensus size: 96
41684468 ATACTAGGGT
* * *
41684478 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTGTATGAGAGCTATTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAAAGCTAGTGTAA
* * * *
41684543 GACCATGTTTGGGACATGGCGTCGGCTTTGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
* * * *
41684574 TATGTGAGCCAGTGTAAGACCATGTTTGGAGCATGGCATCGGCATTTATATGATAGATAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAAAGCTAGTGTAA
*
41684639 GACCATGTCTGGGACATGGCATCGACCTCGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
* * * *
41684670 TATGTAATCCAGTGTAAGACCATGTTTTGAACATGGGATCGACATTTATATGAAAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAAAGCTAGTGTAA
41684735 GACCATGTCTGGGACATGGCATCGGCCTCGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
* * *** * * *
41684766 CATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCGATATATGAGAGCCAGTGC
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATC-G-ACATTTATATGAAAGCTAGTGT
* * *
41684831 AAGACCATGTATTGGACATGGTATCGGC
64 AAGACCATGTCTGGGACATGGCATCGGC
41684859 ATCTTACCTT
Statistics
Matches: 248, Mismatches: 35, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
96 206 0.83
97 1 0.00
98 41 0.17
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (96 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAAAGCTAGTGTAA
GACCATGTCTGGGACATGGCATCGGCCTCGA
Found at i:41684753 original size:144 final size:146
Alignment explanation
Indices: 41684479--41684856 Score: 414
Period size: 144 Copynumber: 2.6 Consensus size: 146
41684469 TACTAGGGTT
** * * * *
41684479 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTG-TATG-AGAGCTATTGTA
1 ATGTGAGATAGTGTAAGACCATGTTTGGAACATGGCATCGACACTCGATATGTAGAGCCAGTGTA
* * ** *
41684542 AGACCATGTTTGGGACATGGCG-TCGGCTTTGATATGTGAGCCAGTGTAAGACCATGTTTGGAGC
66 AGACCATGTTTTGGACATGG-GATCGACTTTGATATGAAAGCCAGTGTAAGACCATGTTGGGAGC
** *
41684606 ATGGCATCGGCATTTAT
130 ATGGCATCGGCATCGAC
* * *
41684623 ATGAT-AGATAGTGTAAGACCATGTCTGGGACATGGCATCGAC-CTCGATATGTA-ATCCAGTGT
1 ATG-TGAGATAGTGTAAGACCATGTTTGGAACATGGCATCGACACTCGATATGTAGAGCCAGTGT
* *
41684685 AAGACCATGTTTTGAACATGGGATCGACATTT-ATATGAAAGCTAGTGTAAGACCATGTCTGGGA
65 AAGACCATGTTTTGGACATGGGATCGAC-TTTGATATGAAAGCCAGTGTAAGACCATGT-TGGGA
*
41684749 -CATGGCATCGGCCTCGAC
128 GCATGGCATCGGCATCGAC
* * * *
41684767 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCAC-CGATATATGAGAGCCAGTGC
1 ATGTGAGATAGTGTAAGACCATGTTTGGAACATGGCATCGACACTCGATATGT-AGAGCCAGTGT
* *
41684831 AAGACCATGTATTGGACATGGTATCG
65 AAGACCATGTTTTGGACATGGGATCG
41684857 GCATCTTACC
Statistics
Matches: 194, Mismatches: 30, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
143 4 0.02
144 149 0.77
145 11 0.06
146 30 0.15
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (146 bp):
ATGTGAGATAGTGTAAGACCATGTTTGGAACATGGCATCGACACTCGATATGTAGAGCCAGTGTA
AGACCATGTTTTGGACATGGGATCGACTTTGATATGAAAGCCAGTGTAAGACCATGTTGGGAGCA
TGGCATCGGCATCGAC
Found at i:41691916 original size:50 final size:50
Alignment explanation
Indices: 41691793--41692237 Score: 365
Period size: 50 Copynumber: 8.8 Consensus size: 50
41691783 GTTCTGAGAA
* * * *
41691793 CACATGTGTAGTACTATGTGCAGGCTACTATGCGTTTGAGACAG-TT-TTTGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTA--CGTGT-A-CCAGATTGTTAGGT
* * * *
41691845 CACGTGTGTAGGATTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * * * * * *
41691895 CGCATGTGTTGTACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG-TTAGGT
* * * * * * *
41691946 CACGTATGTAGTACTATGTGCAAGCTATTACGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * *
41691996 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTCCGGATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
** * * * * * * *
41692046 TGCATGTGTAGTACTAAGTGCAGGGTACTATGCGTACC-CATTAACTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATT--GTTAGGT
* * * * *
41692097 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGATAAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * ** * *
41692147 CACGTGTATAGTACCAAGTATAGGCTACTACATGTACCAGATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* *
41692197 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
41692238 GAGCTTCGGT
Statistics
Matches: 302, Mismatches: 85, Indels: 14
0.75 0.21 0.03
Matches are distributed among these distances:
48 2 0.01
49 6 0.02
50 196 0.65
51 70 0.23
52 28 0.09
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
Found at i:41692002 original size:101 final size:102
Alignment explanation
Indices: 41691793--41692025 Score: 288
Period size: 101 Copynumber: 2.3 Consensus size: 102
41691783 GTTCTGAGAA
* *** * * *
41691793 CACATGTGTAGTACTATGTGCAGGCTACTATGCGTTTGAGACAGTTTTTGGTCACGTGTGTAGGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACAGTTTTCGATCACGTATGTAGGA
* * *
41691858 TTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGT
66 CTAAGTGCAAGCTACTACGTGTACCAAATGGTTAGGT
* * * * *
41691895 CGCATGTGTTGTACTAAGTGCAGGCTACTATGCGTACCCGATAG-TTTCGATCACGTATGTAGTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACAGTTTTCGATCACGTATGTAGGA
* * * *
41691959 CTATGTGCAAGCTATTACGTGTATCAGATGGTTAGGT
66 CTAAGTGCAAGCTACTACGTGTACCAAATGGTTAGGT
41691996 CACATGTGTAGTACTAAGTGCAGGCTACTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTA
41692026 CGTGTTCCGG
Statistics
Matches: 110, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
101 74 0.67
102 36 0.33
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (102 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGACAGTTTTCGATCACGTATGTAGGA
CTAAGTGCAAGCTACTACGTGTACCAAATGGTTAGGT
Found at i:41692118 original size:151 final size:151
Alignment explanation
Indices: 41691842--41692234 Score: 554
Period size: 151 Copynumber: 2.6 Consensus size: 151
41691832 GACAGTTTTT
* * * * *
41691842 GGTCACGTGTGTAGGATTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCGCATGTGTTGT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
** *
41691907 ACTAAGTGCAGGCTACTATGCGTACCCGATAGTTTCGATCACGTATGTAGTACTATGTGCAAGCT
66 ACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTATGTAGTACTAAGTGCAAGCT
* *
41691972 ATTACGTGTATCAGATGGTTA
131 ACTACGTGTATCAGATGGATA
* * * *
41691993 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTCCGGATTGATAGGTTGCATGTGTAGT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
* * *
41692058 ACTAAGTGCAGGGTACTATGCGTACCC-ATTAACTTCGATCACGTGTGTAGTACTAAGTGCAGGC
66 ACTAAGTGCAGGCTACTATGCGTACCCGA-TAACTTCGATCACGTATGTAGTACTAAGTGCAAGC
41692122 TACTACGTGTATCAGATGGATA
130 TACTACGTGTATCAGATGGATA
* * * ** * *
41692144 AGTCACGTGTATAGTACCAAGTATAGGCTACTACATGTACCAGATTGATAGGTCACATGTGTAGT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
41692209 ACTAAGTGCAGGCTACTATGCGTACC
66 ACTAAGTGCAGGCTACTATGCGTACC
41692235 AGAGAGCTTC
Statistics
Matches: 212, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
150 1 0.00
151 211 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (151 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTATGTAGTACTAAGTGCAAGCT
ACTACGTGTATCAGATGGATA
Found at i:41692159 original size:101 final size:100
Alignment explanation
Indices: 41691995--41692226 Score: 252
Period size: 101 Copynumber: 2.3 Consensus size: 100
41691985 GATGGTTAGG
* * * ** *
41691995 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTCCGGATTGATAGGTTGCATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTCCAGATGGATAAGTCACATGTATAGTAC
* * * ** *
41692060 TAAGTGCAGGGTACTATGCGTACC-CATTAACTTCGA
66 CAAGTACAGGCTACTACACGTACCACATTAA--TAGA
* *
41692096 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAT-CAGATGGATAAGTCACGTGTATAGTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGT-TCCAGATGGATAAGTCACATGTATAGTA
* * * * *
41692160 CCAAGTATAGGCTACTACATGTACCAGATTGATAGG
65 CCAAGTACAGGCTACTACACGTACCACATTAATAGA
41692196 TCACATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTA
41692227 TGCGTACCAG
Statistics
Matches: 109, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
100 32 0.29
101 72 0.66
102 5 0.05
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTTCCAGATGGATAAGTCACATGTATAGTAC
CAAGTACAGGCTACTACACGTACCACATTAATAGA
Found at i:41707772 original size:30 final size:30
Alignment explanation
Indices: 41707717--41707876 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
41707707 ATAGTGAATC
41707717 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
41707746 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
41707776 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
41707805 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
41707833 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
41707863 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41707877 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:41707809 original size:59 final size:57
Alignment explanation
Indices: 41707717--41707876 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
41707707 ATAGTGAATC
*
41707717 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
41707776 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
41707833 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
41707877 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:41708378 original size:14 final size:14
Alignment explanation
Indices: 41708359--41708386 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41708349 TATACTTGAA
41708359 ATTTTACAAACATT
1 ATTTTACAAACATT
41708373 ATTTTACAAACATT
1 ATTTTACAAACATT
41708387 CTCCAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTTACAAACATT
Found at i:41715678 original size:29 final size:29
Alignment explanation
Indices: 41715646--41715746 Score: 116
Period size: 29 Copynumber: 3.5 Consensus size: 29
41715636 ATAGTGAATC
*
41715646 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAACT
*
41715675 CGCACACTTAGTGCTATATA--ATCAAACT
1 CGCACACTTAGTGCTATATATTTTC-AACT
* * * *
41715703 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATA-TATTTTCAACT
41715733 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41715747 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 20 0.33
29 21 0.34
30 17 0.28
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAACT
Found at i:41715739 original size:30 final size:29
Alignment explanation
Indices: 41715645--41715746 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
41715635 TATAGTGAAT
* * *
41715645 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
41715674 TCGCACACTTAGTGCTATATAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
41715702 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
41715732 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
41715747 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:41722925 original size:40 final size:40
Alignment explanation
Indices: 41722870--41723079 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41722860 AACATTGGAA
41722870 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41722910 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41722950 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41722990 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
41723029 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41723070 CTATATCCGG
1 ATATATCCGG
41723080 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41724825 original size:17 final size:18
Alignment explanation
Indices: 41724783--41724831 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
41724773 AGTTGAAAAG
41724783 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
41724802 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
41724819 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
41724832 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:41725720 original size:40 final size:40
Alignment explanation
Indices: 41725654--41725804 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
41725644 AAATTGAATG
* * *
41725654 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
41725693 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
41725733 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
41725773 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
41725805 ACGTGATCAT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 16 0.17
40 75 0.81
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41736380 original size:27 final size:27
Alignment explanation
Indices: 41736342--41736404 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
41736332 ATGGAATGGA
41736342 CTTTGTGGCAAACCATAAAAAGAAAGC
1 CTTTGTGGCAAACCATAAAAAGAAAGC
* * *
41736369 CTTTGTGGCAAATCATGAAATGAAAGC
1 CTTTGTGGCAAACCATAAAAAGAAAGC
*
41736396 ATTTGTGGC
1 CTTTGTGGC
41736405 GATCTCTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (27 bp):
CTTTGTGGCAAACCATAAAAAGAAAGC
Found at i:41738957 original size:40 final size:40
Alignment explanation
Indices: 41738858--41739038 Score: 197
Period size: 40 Copynumber: 4.5 Consensus size: 40
41738848 TTCGAATGAT
* * *
41738858 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
41738899 ATCCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAAA
1 ATCCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTA-CTAA
* *
41738940 AT-CGGGTTAAGTCCCGAAGGCATTTATGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * * *
41738979 ATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
41739020 A-CCGGGCTATGTCCCGAAG
1 ATCCGGGCTAAGTCCCGAAG
41739039 ACAATCTAGC
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
39 5 0.04
40 80 0.67
41 34 0.29
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:41739000 original size:80 final size:81
Alignment explanation
Indices: 41738861--41739038 Score: 225
Period size: 80 Copynumber: 2.2 Consensus size: 81
41738851 GAATGATATC
* * *
41738861 CGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATTG
41738926 TGCGAGTTACCAAAAT
66 TGCGAGTTACCAAAAT
* * *
41738942 CGGGTTAAGTCCCGAAGGCATTTATGC-GAGTTACTAAATCCGGG-CTAATTCCCGAAGGCAATT
1 CGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGGTC-AATTCCCGAAGGCAATT
* * * * *
41739005 GTGCGAATCACTATAAC
65 GTGCGAGTTACCAAAAT
*
41739022 CGGGCTATGTCCCGAAG
1 CGGGCTAAGTCCCGAAG
41739039 ACAATCTAGC
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 1 0.01
80 58 0.70
81 24 0.29
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (81 bp):
CGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATTG
TGCGAGTTACCAAAAT
Found at i:41739051 original size:80 final size:80
Alignment explanation
Indices: 41738860--41739078 Score: 201
Period size: 80 Copynumber: 2.7 Consensus size: 80
41738850 CGAATGATAT
* * * * * * *
41738860 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGACATCTATGC-GAGTTACTAAATCCGGGTCAATTCCCGAAGGCAATT
* *
41738925 GTGCGAGTTACCAAAA
65 GTGCGAATCACCAAAA
* * * *
41738941 TCGGGTTAAGTCCCGAAGGCATTTATGCGAGTTACTAAATCCGGG-CTAATTCCCGAAGGCAATT
1 CCGGGCTAAGTCCCGAAGACATCTATGCGAGTTACTAAATCCGGGTC-AATTCCCGAAGGCAATT
* *
41739005 GTGCGAATCACTATAA
65 GTGCGAATCACCAAAA
* ** * * *
41739021 CCGGGCTATGTCCCGAAGACAATCTA-GCGAGTCGCTATATCCGGTTAAATT-CCGAAGG
1 CCGGGCTAAGTCCCGAAGAC-ATCTATGCGAGTTACTAAATCCGGGTCAATTCCCGAAGG
41739079 TACGTGATTC
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
79 8 0.07
80 78 0.68
81 28 0.25
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGACATCTATGCGAGTTACTAAATCCGGGTCAATTCCCGAAGGCAATTG
TGCGAATCACCAAAA
Found at i:41742005 original size:68 final size:67
Alignment explanation
Indices: 41741933--41742082 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
41741923 CATCATGTGT
* * * *
41741933 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
41741995 ATGTAG
62 ATGTAG
** * *
41742001 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
41742066 AG
66 AG
41742068 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
41742083 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:41742038 original size:64 final size:64
Alignment explanation
Indices: 41741957--41742140 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
41741947 AGACATTATG
* *
41741957 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
41742021 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41742086 AA
63 AA
* * * *
41742088 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
41742141 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:41754307 original size:28 final size:29
Alignment explanation
Indices: 41754243--41754344 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 29
41754233 GTGACGAGAT
* * *
41754243 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
41754272 TGGCACTAAGTGTGCGA-TTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
41754300 TGGCACTATGTGTGCGGGCTT-GAATCACA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
41754329 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41754345 TGATTGAGTA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 25 0.42
29 35 0.58
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:41759902 original size:42 final size:42
Alignment explanation
Indices: 41759843--41759927 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
41759833 GGTACTTACC
41759843 TTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTAT
1 TTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTAT
41759885 TTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTAT
1 TTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTAT
41759927 T
1 T
41759928 AAGATGGCGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (42 bp):
TTTGATTGAATTCGCTTACAACAATAGTTTTCAATCAAGTAT
Found at i:41762252 original size:29 final size:28
Alignment explanation
Indices: 41762220--41762322 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41762210 GTGACGAGAT
* *
41762220 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
41762249 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
41762278 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
41762307 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41762323 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:41764184 original size:12 final size:12
Alignment explanation
Indices: 41764167--41764200 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
41764157 CCAAGGTTTT
41764167 GCACACGGGCTA
1 GCACACGGGCTA
41764179 GCACACGGGCTA
1 GCACACGGGCTA
*
41764191 GGACACGGGC
1 GCACACGGGC
41764201 GTGTCATGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.38, T:0.06
Consensus pattern (12 bp):
GCACACGGGCTA
Found at i:41766360 original size:51 final size:50
Alignment explanation
Indices: 41766187--41766410 Score: 229
Period size: 49 Copynumber: 4.5 Consensus size: 50
41766177 AAGCTATCAA
* * *
41766187 GTACGCATAGTAGCCTGCACTGAGTACTACACA--TGCAACCAATTATCCG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTG-ATCCAATTATCCG
* * * * * * *
41766236 GTACATATAGTAGCCTACACTAAGTACTGCACACGTGATCTAACTATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCCAATTATCCG
* * * *
41766286 ATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCCAA-TTATCCG
** * *
41766337 GTATGCATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAATTATCCG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCCAATTATCCG
* *
41766386 ATACACGTAGTAGCCTGCACTTAGT
1 GTACACATAGTAGCCTGCACTTAGT
41766411 CCTAACTTTT
Statistics
Matches: 142, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 55 0.39
50 48 0.34
51 39 0.27
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (50 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACACGTGATCCAATTATCCG
Found at i:41769093 original size:29 final size:29
Alignment explanation
Indices: 41769060--41769117 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41769050 CCCTTTACTA
41769060 AGAAAACCAATTCATGAGGGAATTTCAAT
1 AGAAAACCAATTCATGAGGGAATTTCAAT
41769089 AGAAAACCAATTCATGAGGGAATTTCAAT
1 AGAAAACCAATTCATGAGGGAATTTCAAT
41769118 CAATACATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (29 bp):
AGAAAACCAATTCATGAGGGAATTTCAAT
Found at i:41771443 original size:49 final size:49
Alignment explanation
Indices: 41771375--41771619 Score: 267
Period size: 49 Copynumber: 4.9 Consensus size: 49
41771365 TAGCCAAAGC
* *
41771375 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACAT-TCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGT-GACCAAT
* * *
41771424 TATCTAGTACACGTTGTAGCCTGCACTTAGTACTACACATGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC-AAT
* * * * * * *
41771474 CATTTGATACATGTAGTAGCCTGCACTTATTACTACACACGTGATCAAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-T
* ** * *
41771525 TATCGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGTAACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * *
41771574 TATCCGGTACACGTAGTAGCCTGCGCTTAGTACTACACACGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
41771620 TCAAAATAGA
Statistics
Matches: 158, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
49 80 0.51
50 44 0.28
51 34 0.22
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
Found at i:41775050 original size:46 final size:46
Alignment explanation
Indices: 41774983--41775154 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
41774973 AACCCGCCCC
*
41774983 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
41775029 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * * * *
41775077 TCA-CGAACTCGGACTCAACTGAACGAGTTCGGACATTCGCTTCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
41775122 -AAGGTGAACTCGGACTCAACTGAACGAGTTCGG
1 TAA-GTGAACTCGGACTCAACTCAACGAGTTCGG
41775155 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 3 0.03
46 60 0.57
47 27 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:41775095 original size:93 final size:93
Alignment explanation
Indices: 41774988--41775158 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
41774978 GCCCCTAAGT
* *
41774988 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAA-GTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA-AAGGTGAACTCGGACTCAACTCA
41775052 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
41775081 GAACTCGGACTCAACTGAACGAGTTCGGACATTCGCTTCCAAAGGTGAACTCGGACTCAACTGAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAAAGGTGAACTCGGACTCAACTCAA
41775146 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41775159 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAAAGGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41782033 original size:46 final size:46
Alignment explanation
Indices: 41781966--41782136 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
41781956 AACCCGCCCC
* *
41781966 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCATCCA
*
41782012 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGCATCCA
* * * *
41782060 TCA-CGAACTCGGACTCAACTGAACGAGTTC-GACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCATCCA
* *
41782104 TAGGTGAACTCGGACTCAACTCAATGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
41782137 ATGCTCAACC
Statistics
Matches: 102, Mismatches: 13, Indels: 20
0.76 0.10 0.15
Matches are distributed among these distances:
41 2 0.02
42 4 0.04
43 2 0.02
44 1 0.01
45 24 0.24
46 33 0.32
47 25 0.25
48 3 0.03
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCATCCA
Found at i:41782133 original size:92 final size:93
Alignment explanation
Indices: 41781971--41782140 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 93
41781961 GCCCCTAAGT
* *
41781971 GAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41782036 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
41782064 GAACTCGGACTCAACTGAACGAGTTC-GACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
41782128 TGAGTTCGGATGC
66 CGAGTTCGGATGC
41782141 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 48 0.68
93 23 0.32
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41792107 original size:20 final size:20
Alignment explanation
Indices: 41792084--41792121 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41792074 CACATCCAAA
*
41792084 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
41792104 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
41792122 GTGAATAAAC
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:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:41792674 original size:25 final size:25
Alignment explanation
Indices: 41792646--41792724 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
41792636 ATCCTAGCCT
41792646 GAGAGGTTAAGCAATTGAGAGATAA
1 GAGAGGTTAAGCAATTGAGAGATAA
* **
41792671 GAGA-GTT--CCAATTTTGTTAGATAA
1 GAGAGGTTAAGCAA--TTGAGAGATAA
* *
41792695 GAGAGGTTAAGCAACTGAGAAATAA
1 GAGAGGTTAAGCAATTGAGAGATAA
41792720 GAGAG
1 GAGAG
41792725 TTCCTAAATC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 3 0.07
24 16 0.39
25 19 0.46
27 3 0.07
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (25 bp):
GAGAGGTTAAGCAATTGAGAGATAA
Found at i:41799589 original size:51 final size:49
Alignment explanation
Indices: 41799534--41799672 Score: 139
Period size: 51 Copynumber: 2.9 Consensus size: 49
41799524 CTACTTCATA
* *
41799534 ACATGTAACACATCCATAATGAACTTGGACCTCTCAACGAGCTCGAATG
1 ACATGTAACGCATCCATAATGAACTCGGACCTCTCAACGAGCTCGAATG
* * * * *
41799583 TTACATG-AATCGCATCCATCATGAACTCGGACCACTTAACAAGCTCAAATG
1 --ACATGTAA-CGCATCCATAATGAACTCGGACCTCTCAACGAGCTCGAATG
41799634 -C---T-A-GCATCCATAATGAACTCGGACCTCTCAACGAGCTCG
1 ACATGTAACGCATCCATAATGAACTCGGACCTCTCAACGAGCTCG
41799673 GATGCCACAT
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
43 31 0.42
45 1 0.01
48 1 0.01
50 2 0.03
51 39 0.53
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (49 bp):
ACATGTAACGCATCCATAATGAACTCGGACCTCTCAACGAGCTCGAATG
Found at i:41805071 original size:24 final size:24
Alignment explanation
Indices: 41804827--41805069 Score: 441
Period size: 24 Copynumber: 10.1 Consensus size: 24
41804817 GCAAAGACCA
41804827 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41804851 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41804875 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41804899 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41804923 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
41804947 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41804971 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41804995 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41805019 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
* *
41805043 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
41805067 TAT
1 TAT
41805070 AGTCACATTC
Statistics
Matches: 213, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 213 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:41813238 original size:40 final size:40
Alignment explanation
Indices: 41813193--41813359 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
41813183 CGGAATATAA
*
41813193 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41813233 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41813273 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41813313 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41813352 CCGGATAT
1 CCGGATAT
41813360 CATTCAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
39 14 0.13
40 90 0.87
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41813343 original size:80 final size:79
Alignment explanation
Indices: 41813209--41813359 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
41813199 TTAATCACGT
*
41813209 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
41813274 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
41813289 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
41813352 CCGGATAT
64 CCGGATAT
41813360 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:41816284 original size:40 final size:40
Alignment explanation
Indices: 41816120--41816286 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 40
41816110 AAATTGAATG
* * **
41816120 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGATT
* * **
41816159 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
*
41816199 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGCT-ATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAG-TGATT
* *
41816239 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGATT
41816279 ATATCCGG
1 ATATCCGG
41816287 TTATATTCCG
Statistics
Matches: 104, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
39 18 0.17
40 83 0.80
41 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
Found at i:41823671 original size:46 final size:46
Alignment explanation
Indices: 41823621--41823793 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
41823611 TGGTTGAGCA
41823621 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41823667 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41823712 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
41823760 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41823794 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41823777 original size:93 final size:93
Alignment explanation
Indices: 41823618--41823788 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41823608 GGATGGTTGA
* *
41823618 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41823683 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41823711 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41823776 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41823789 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41824051 original size:19 final size:20
Alignment explanation
Indices: 41824014--41824051 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41824004 ATAAGGTGGT
41824014 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
41824034 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
41824052 TGGTGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:41836685 original size:39 final size:39
Alignment explanation
Indices: 41836583--41836758 Score: 266
Period size: 40 Copynumber: 4.5 Consensus size: 39
41836573 GGATGATAAC
41836583 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41836622 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 -CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41836662 CGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAAT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
41836702 CGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA-T
*
41836742 C-GGCTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
41836759 TACTTGGTTT
Statistics
Matches: 127, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
39 53 0.42
40 74 0.58
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (39 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41836714 original size:79 final size:80
Alignment explanation
Indices: 41836583--41836758 Score: 270
Period size: 79 Copynumber: 2.2 Consensus size: 80
41836573 GGATGATAAC
* *
41836583 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGA
41836648 GCGAGTTA-CTATA-T
66 GCGAG-TAGCTATATT
*
41836662 CGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAAT-CGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-ATCCGGGCTAAGTCCCGAAGGCATTTG
41836726 AGCGAGTAGCTATATT
65 AGCGAGTAGCTATATT
*
41836742 C-GGCTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
41836759 TACTTGGTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
78 2 0.02
79 83 0.93
80 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGA
GCGAGTAGCTATATT
Found at i:41843337 original size:22 final size:22
Alignment explanation
Indices: 41843311--41843356 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
41843301 GAGAAACTCT
41843311 TTACGCTTCTGGTCTACAAATC
1 TTACGCTTCTGGTCTACAAATC
41843333 TTACGCTTCTGGTCTACAAATC
1 TTACGCTTCTGGTCTACAAATC
41843355 TT
1 TT
41843357 TCACTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (22 bp):
TTACGCTTCTGGTCTACAAATC
Found at i:41847314 original size:17 final size:17
Alignment explanation
Indices: 41847282--41847315 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41847272 TAAAATATTA
**
41847282 TTAAAAAAATTTAAAAT
1 TTAAAAAAATAAAAAAT
41847299 TTAAAAAAATAAAAAAT
1 TTAAAAAAATAAAAAAT
41847316 GGTTTAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAAATAAAAAAT
Found at i:41853282 original size:19 final size:20
Alignment explanation
Indices: 41853258--41853307 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
41853248 TACAAGATAC
41853258 AAAATAAAAATATATTTT-A
1 AAAATAAAAATATATTTTCA
* *
41853277 AAAATAATACAATTTATTTTCT
1 AAAATAA-A-AATATATTTTCA
41853299 AAAATAAAA
1 AAAATAAAA
41853308 TTAATTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.27
20 2 0.08
21 10 0.38
22 7 0.27
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATAAAAATATATTTTCA
Found at i:41853346 original size:35 final size:35
Alignment explanation
Indices: 41853307--41853379 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
41853297 CTAAAATAAA
41853307 ATTAATTTTTGT-ATTATTTAATTAAGTT-GATACTT
1 ATTAATTTTT-TCATTATTTAATTAAGTTCG-TACTT
*
41853342 ATTAATTTTTTCATTATTTAATTAGGTTCGTACTT
1 ATTAATTTTTTCATTATTTAATTAAGTTCGTACTT
41853377 ATT
1 ATT
41853380 TGTTCAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 1 0.03
35 33 0.94
36 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (35 bp):
ATTAATTTTTTCATTATTTAATTAAGTTCGTACTT
Found at i:41857554 original size:26 final size:26
Alignment explanation
Indices: 41857525--41857578 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
41857515 TAAGTCAAAA
* * *
41857525 TTTTTTTCTCCTTGTAATTTG-ACTT
1 TTTTTTTGTCTTTGTAAATTGAACTT
41857550 TTTTTTTGTCTTTGTAAATTGAACTT
1 TTTTTTTGTCTTTGTAAATTGAACTT
41857576 TTT
1 TTT
41857579 GTCCCCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.15, C:0.11, G:0.09, T:0.65
Consensus pattern (26 bp):
TTTTTTTGTCTTTGTAAATTGAACTT
Found at i:41859915 original size:47 final size:47
Alignment explanation
Indices: 41859643--41859915 Score: 393
Period size: 47 Copynumber: 5.8 Consensus size: 47
41859633 CCCTTCGGGA
* * * * ** *
41859643 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCCCTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41859690 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
41859737 CTTATCACATATATATACCTTCACATTCAGCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41859784 CTTATCACATATATACACTTTCACATTCATCACATCTGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41859831 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41859880 CTTATCACATATATACACTTTCACATTCATCACATC
1 CTTATCACATATATACACTTTCACATTCATCACATC
41859916 AAATCCTAAA
Statistics
Matches: 205, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
47 159 0.78
49 46 0.22
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41868276 original size:49 final size:49
Alignment explanation
Indices: 41868204--41868390 Score: 275
Period size: 49 Copynumber: 3.8 Consensus size: 49
41868194 TGAGGTCACG
41868204 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * ** * *
41868253 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
* *
41868303 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
41868352 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
41868391 GCTTCGGCTA
Statistics
Matches: 120, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
49 78 0.65
50 42 0.35
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:41868367 original size:99 final size:99
Alignment explanation
Indices: 41868196--41868389 Score: 352
Period size: 99 Copynumber: 2.0 Consensus size: 99
41868186 AGCTATTGTG
41868196 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
* *
41868261 ACTAAGTGCAGGCTACTATGTGTATCAGATGGTT
66 ACTAAGTGCAGGCTACTATGCGTACCAGATGGTT
* *
41868295 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGTATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
41868360 ACTAAGTGCAGGCTACTATGCGTACCAGAT
66 ACTAAGTGCAGGCTACTATGCGTACCAGAT
41868390 AGCTTCGGCT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (99 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTATGCGTACCAGATGGTT
Found at i:41869829 original size:30 final size:30
Alignment explanation
Indices: 41869794--41869866 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
41869784 GTACAGGGCT
* *
41869794 CACACGCCCGTGTGGTCAGGCCGTGTACTA
1 CACACGCCCGTATGGTCAGGCCATGTACTA
*
41869824 CACACGCCCGTATGGTCAGGTCATGTACTA
1 CACACGCCCGTATGGTCAGGCCATGTACTA
41869854 CACACGCCCGTAT
1 CACACGCCCGTAT
41869867 TCGTAACCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.21, C:0.34, G:0.25, T:0.21
Consensus pattern (30 bp):
CACACGCCCGTATGGTCAGGCCATGTACTA
Found at i:41872483 original size:50 final size:49
Alignment explanation
Indices: 41872316--41872530 Score: 277
Period size: 49 Copynumber: 4.3 Consensus size: 49
41872306 CTGGTACGCA
* *
41872316 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
*
41872365 TAGTAGCCTGCACTTAGTACTACACACATGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* ** * *
41872414 TAGTAGCCTGCACTTAGTACTGCACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * ** * *
41872464 TAGTAGCCTGCACTTAGTACTACACACGTGGTCGAAGTTATTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGT-GACCAA-TTATCCGGTACACG
41872515 TAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTA
41872531 TTCATCATAT
Statistics
Matches: 144, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
49 77 0.53
50 42 0.29
51 25 0.17
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:41874979 original size:30 final size:30
Alignment explanation
Indices: 41874944--41875003 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
41874934 CAAGAAAACT
41874944 GAATAAAAAAATCCAAAATAGAA-AAACCCA
1 GAATAAAAAAATCCAAAATA-AAGAAACCCA
* *
41874974 GAATAAAGAAATCCAGAATAAAGAAACCCA
1 GAATAAAAAAATCCAAAATAAAGAAACCCA
41875004 AGATATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.63, C:0.17, G:0.10, T:0.10
Consensus pattern (30 bp):
GAATAAAAAAATCCAAAATAAAGAAACCCA
Found at i:41874996 original size:15 final size:15
Alignment explanation
Indices: 41874944--41874999 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
41874934 CAAGAAAACT
*
41874944 GAATAAAAAAATCCA
1 GAATAAAGAAATCCA
* *
41874959 AAATAGAA-AAACCCA
1 GAATA-AAGAAATCCA
41874974 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
41874989 GAATAAAGAAA
1 GAATAAAGAAA
41875000 CCCAAGATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
14 2 0.06
15 31 0.89
16 2 0.06
ACGTcount: A:0.66, C:0.12, G:0.11, T:0.11
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:41878110 original size:50 final size:49
Alignment explanation
Indices: 41877933--41878122 Score: 265
Period size: 48 Copynumber: 3.9 Consensus size: 49
41877923 GTAGCCAAGC
* * * *
41877933 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
41877982 TATCTGGTACATGTAGTAG-CTACACTTAGTACTACACACGTGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * *
41878030 TATCCGGTACACGTACTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* *
41878080 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTG
41878123 GTTGAAGTTA
Statistics
Matches: 124, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
48 42 0.34
49 41 0.33
50 41 0.33
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:41885543 original size:38 final size:38
Alignment explanation
Indices: 41885501--41885649 Score: 174
Period size: 38 Copynumber: 3.9 Consensus size: 38
41885491 GTAGGCTATA
*
41885501 TGCTGGAATTATATCCGGGTTAAATCCGGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
41885539 TGCTGGTAA-TATATCCAGGTTAAATCCTGCAGGCTTCA
1 TGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
41885577 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
41885615 TGCTGGTATTATATCTGAGCTTAAAGTCCCGCAGG
1 TGCTGGAATTATATCCG-GGTTAAA-TCCCGCAGG
41885650 TTTTGTGTTG
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.01
38 78 0.81
39 8 0.08
40 9 0.09
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:41893607 original size:38 final size:38
Alignment explanation
Indices: 41893546--41893734 Score: 193
Period size: 38 Copynumber: 4.9 Consensus size: 38
41893536 ATTTGATGTG
* *
41893546 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGAATTA
41893586 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA-TA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG-AATTA
* ** *
41893624 TATCCGTGTTAAATCCCATAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
* * *
41893662 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
* * * *
41893700 TATCTGAGCTTAAAGTCCCGCAGGTTTTGTGCTGG
1 TATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGG
41893735 TGACTAGATT
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
37 2 0.02
38 88 0.69
39 13 0.10
40 25 0.20
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGAATTA
Found at i:41894601 original size:2 final size:2
Alignment explanation
Indices: 41894594--41894638 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
41894584 ATAATAAAAG
41894594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41894636 AT A
1 AT A
41894639 AAATTGGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41901541 original size:51 final size:50
Alignment explanation
Indices: 41901464--41901562 Score: 144
Period size: 51 Copynumber: 2.0 Consensus size: 50
41901454 TAGATGCGAG
* * *
41901464 CATCTGAGCTCGTTGAGAGGTCTGAGTTCATAATGGATGTGATTCATGTAA
1 CATCTAAGCTCGTTGAAAGGTCTGAGTTCATAATGGATGT-ATACATGTAA
* *
41901515 CATCTAAGCTCGTTGAAAGGTTTGAGTTCATTATGGATGTATACATGT
1 CATCTAAGCTCGTTGAAAGGTCTGAGTTCATAATGGATGTATACATGT
41901563 TATGAGGTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 7 0.16
51 36 0.84
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.35
Consensus pattern (50 bp):
CATCTAAGCTCGTTGAAAGGTCTGAGTTCATAATGGATGTATACATGTAA
Found at i:41903431 original size:22 final size:22
Alignment explanation
Indices: 41903391--41903433 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41903381 GTGTTGGAGA
* *
41903391 CACATGGGCGTGTCCCTGTGTC
1 CACACGGGCGTGTCACTGTGTC
*
41903413 CACACGGGCGTGTGACTGTGT
1 CACACGGGCGTGTCACTGTGT
41903434 TTTAGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.28, G:0.35, T:0.26
Consensus pattern (22 bp):
CACACGGGCGTGTCACTGTGTC
Found at i:41911434 original size:42 final size:42
Alignment explanation
Indices: 41911388--41911485 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
41911378 TCCTTGACGT
* * *
41911388 GGTCTTACATGTAATCAAATATC-ATGCCACTGTCCCAGACAG
1 GGTCTTACACGTAATCAAATA-CGATGCCAATGTCCAAGACAG
* *
41911430 GGTCTTACACGAAATCAAATACGATGCCAATGTCCAAGACAT
1 GGTCTTACACGTAATCAAATACGATGCCAATGTCCAAGACAG
41911472 GGTCTTACACGTAA
1 GGTCTTACACGTAA
41911486 ATCATACGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 48 0.98
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (42 bp):
GGTCTTACACGTAATCAAATACGATGCCAATGTCCAAGACAG
Found at i:41911519 original size:44 final size:42
Alignment explanation
Indices: 41911387--41911527 Score: 133
Period size: 42 Copynumber: 3.3 Consensus size: 42
41911377 ATCCTTGACG
* * ** *
41911387 TGGTCTTACATGTAATCAAATATC-ATGCCACTGTCCCAGACA
1 TGGTCTTACACGAAATCAAATA-CGATGCCAAAGTCCAAGACA
* *
41911429 GGGTCTTACACGAAATCAAATACGATGCCAATGTCCAAGACA
1 TGGTCTTACACGAAATCAAATACGATGCCAAAGTCCAAGACA
* * * *
41911471 TGGTCTTACACGTAAATCATACGT-CGATGCCAAAGTCCTATACG
1 TGGTCTTACACG-AAATCA-A-ATACGATGCCAAAGTCCAAGACA
41911515 TGGTCTTACACGA
1 TGGTCTTACACGA
41911528 TAACACATAT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 46 0.55
43 7 0.08
44 29 0.35
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAAATACGATGCCAAAGTCCAAGACA
Found at i:41915580 original size:40 final size:40
Alignment explanation
Indices: 41915531--41915720 Score: 174
Period size: 40 Copynumber: 4.8 Consensus size: 40
41915521 ATCACGATTT
*
41915531 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* * *
41915571 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAATTACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* * *
41915611 GCATAAATGTCC-TCGGGACTTAGCCCGGAT-GTA-GCCACTA
1 GCACAAATG-CCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
* * * ** *
41915651 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* *
41915691 GCATTAAAT--CTTCGGGACTTAGCCCGGATA
1 GCA-CAAATGCCTTCGGGTCTTAGCCCGGATA
41915721 TCATTCAATT
Statistics
Matches: 120, Mismatches: 23, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
39 22 0.18
40 92 0.77
41 6 0.05
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:41915619 original size:80 final size:81
Alignment explanation
Indices: 41915535--41915720 Score: 233
Period size: 80 Copynumber: 2.3 Consensus size: 81
41915525 CGATTTGCAC
* * *
41915535 AAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTCGCACGAA-TGCCTTCGGGTCTTAGCCCG
1 AAATGCCTTCGGGACTTAGCCCGGATAGAA-GCACTAGCAC-AATTGCCTTCGGGTCTTAACCCG
*
41915598 GATATAATTACTAGCA-T
64 GATATAATTACCAGCATT
*
41915615 AAATGTCC-TCGGGACTTAGCCCGGAT-GTAGCCACTAGCACAATTGCCTTCGGGTCTTAACCCG
1 AAATG-CCTTCGGGACTTAGCCCGGATAGAAG-CACTAGCACAATTGCCTTCGGGTCTTAACCCG
*
41915678 GATATAATTTCCAGCATT
64 GATATAATTACCAGCATT
41915696 AAAT--CTTCGGGACTTAGCCCGGATA
1 AAATGCCTTCGGGACTTAGCCCGGATA
41915721 TCATTCAATT
Statistics
Matches: 93, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
78 2 0.02
79 22 0.24
80 62 0.67
81 7 0.08
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
AAATGCCTTCGGGACTTAGCCCGGATAGAAGCACTAGCACAATTGCCTTCGGGTCTTAACCCGGA
TATAATTACCAGCATT
Found at i:41923696 original size:40 final size:40
Alignment explanation
Indices: 41923647--41923797 Score: 173
Period size: 40 Copynumber: 3.8 Consensus size: 40
41923637 ATCACGATTT
*
41923647 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* * *
41923687 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAATTACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* * *
41923727 GCATAAATGTCC-TCGGGACTTAGCCCGGAT-GTA-GCCACTA
1 GCACAAATG-CCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
* *
41923767 GCACAATTGCCTTCGGGTCTTAACCCGGATA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATA
41923798 TAATTTCCAG
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
39 3 0.03
40 87 0.95
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:41923735 original size:80 final size:81
Alignment explanation
Indices: 41923651--41923837 Score: 226
Period size: 80 Copynumber: 2.3 Consensus size: 81
41923641 CGATTTGCAC
* * *
41923651 AAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTCGCACGAA-TGCCTTCGGGTCTTAGCCCG
1 AAATGCCTTCGGGACTTAGCCCGGATAGAA-GCACTAGCAC-AATTGCCTTCGGGTCTTAACCCG
*
41923714 GATATAATTACTAGCA-T
64 GATATAATTACCAGCATT
*
41923731 AAATGTCC-TCGGGACTTAGCCCGGAT-GTAGCCACTAGCACAATTGCCTTCGGGTCTTAACCCG
1 AAATG-CCTTCGGGACTTAGCCCGGATAGAAG-CACTAGCACAATTGCCTTCGGGTCTTAACCCG
*
41923794 GATATAATTTCCAGCATT
64 GATATAATTACCAGCATT
41923812 AACAT--CTTCGGGACTTAGCCCGGATA
1 AA-ATGCCTTCGGGACTTAGCCCGGATA
41923838 TCATTCAATT
Statistics
Matches: 93, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
78 1 0.01
79 5 0.05
80 80 0.86
81 5 0.05
82 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (81 bp):
AAATGCCTTCGGGACTTAGCCCGGATAGAAGCACTAGCACAATTGCCTTCGGGTCTTAACCCGGA
TATAATTACCAGCATT
Found at i:41937135 original size:37 final size:37
Alignment explanation
Indices: 41937085--41937218 Score: 259
Period size: 37 Copynumber: 3.6 Consensus size: 37
41937075 TTATTACAAA
41937085 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
41937122 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
41937159 GTCTTACCCGGACATAATCTCCACACGTAGTCATCAG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
41937196 GTCTTACCCGGACATAATCTCCA
1 GTCTTACCCGGACATAATCTCCA
41937219 AGTTTCATGT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:41937329 original size:48 final size:48
Alignment explanation
Indices: 41937253--41937731 Score: 742
Period size: 48 Copynumber: 10.0 Consensus size: 48
41937243 GTTACAACAC
* * *
41937253 TCACATTAGCCATTCGGCTTTACCACATATTCTTATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * *
41937301 TCACATTCGCCATTCGGCTTTACGACATATGCATATCTCATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
41937349 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * * *
41937397 TCACATTCGCCATTCGGCTTTACCACATCTACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
41937445 TCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* **
41937493 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACGTATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* **
41937541 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACGTATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
41937589 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
41937637 TCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * *
41937685 TCACATTAGCCATTCGGCTTTACCACATACACATATCACACATATAT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
41937732 ATATTTATCT
Statistics
Matches: 400, Mismatches: 31, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 400 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (48 bp):
TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
Found at i:41944265 original size:12 final size:12
Alignment explanation
Indices: 41944248--41944275 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41944238 TGTAATCAAA
41944248 TATCGATGACAG
1 TATCGATGACAG
41944260 TATCGATGACAG
1 TATCGATGACAG
41944272 TATC
1 TATC
41944276 CCAGACAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (12 bp):
TATCGATGACAG
Found at i:41944357 original size:44 final size:42
Alignment explanation
Indices: 41944284--41944381 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 42
41944274 TCCCAGACAG
* ** *
41944284 GGTCTTACACGAAATCAAATACGATGCCAACGTCTTAGACGT
1 GGTCTTACATGAAATCAAATACGATGCCAACGTCCCAAACGT
*
41944326 GGTCTTACATGTAAATCATAAGT-CGATGCCAACGTCCCAAATGT
1 GGTCTTACATG-AAATCA-AA-TACGATGCCAACGTCCCAAACGT
41944370 GGTCTTACATGA
1 GGTCTTACATGA
41944382 TAACACATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
42 10 0.21
43 7 0.15
44 30 0.62
45 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (42 bp):
GGTCTTACATGAAATCAAATACGATGCCAACGTCCCAAACGT
Found at i:41949845 original size:48 final size:48
Alignment explanation
Indices: 41949769--41950139 Score: 401
Period size: 48 Copynumber: 7.8 Consensus size: 48
41949759 ACTGTGCTAA
* *
41949769 ATGTGACTGTGTAAGACCATGTCGGGGACATGGCATCAGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
*
41949817 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGGATC-GACGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAG-CGATGATAT
* * * * * *
41949865 GTATGCCTGTTTAAGA-CATGCCTAGGACATGGCATCAGGGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
** *
41949912 ATGTG-CTAGTGTAAGACCATGTCTGGGACATGGCATTGGTGATGATAT
1 ATGTGCCT-GTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
* *
41949960 ATGTGCCTGTGGAAGACCATGTCTGGGACATGGCATCAACGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
* * * * * *
41950008 GTGTTCCTGTGTAAGACCATGTCTGGGACATGTCATCGGTGATAATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
* * * * **
41950056 GTGTGCCAGTGTATGACCATGTTTGGGACATGGCATTGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
* ** *
41950104 GTG-GATTTATGTAAGACCATGT-TAGGGACATGGCAT
1 ATGTG-CCTGTGTAAGACCATGTCT-GGGACATGGCAT
41950140 TGGTGCTTTA
Statistics
Matches: 272, Mismatches: 44, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
46 2 0.01
47 38 0.14
48 230 0.85
49 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (48 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCAGCGATGATAT
Found at i:41952115 original size:31 final size:31
Alignment explanation
Indices: 41952072--41952135 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41952062 CCTGTTCATA
41952072 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
41952103 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
41952134 TT
1 TT
41952136 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:41952375 original size:24 final size:24
Alignment explanation
Indices: 41952328--41952495 Score: 270
Period size: 24 Copynumber: 7.0 Consensus size: 24
41952318 ACTTTATCAT
*
41952328 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
41952353 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
41952378 ATAACTGGGGCATAAG-CCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41952401 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41952425 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41952449 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41952473 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
41952496 GCACTTCCTC
Statistics
Matches: 137, Mismatches: 1, Indels: 11
0.92 0.01 0.07
Matches are distributed among these distances:
23 22 0.16
24 85 0.62
25 27 0.20
26 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:41952566 original size:9 final size:9
Alignment explanation
Indices: 41952552--41952608 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
41952542 ATCTCGTGTG
41952552 CATATCATA
1 CATATCATA
*
41952561 CATATCATGTG
1 CATATCA--TA
41952572 CATATCATA
1 CATATCATA
* *
41952581 CATGTCATGTG
1 CATATCA--TA
41952592 CATATCATA
1 CATATCATA
41952601 CATATCAT
1 CATATCAT
41952609 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:41952571 original size:20 final size:20
Alignment explanation
Indices: 41952548--41952610 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
41952538 GAACATCTCG
41952548 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
41952568 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
41952588 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
41952608 TGT
1 TGT
41952611 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:41952692 original size:24 final size:25
Alignment explanation
Indices: 41952647--41952693 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
41952637 ATATATAAAC
* *
41952647 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCATAAAGGTCATTTTTA
41952672 CCTAGGGGCA-AAAGGTCATTTT
1 CCTAGGGGCATAAAGGTCATTTT
41952694 CATATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (25 bp):
CCTAGGGGCATAAAGGTCATTTTTA
Found at i:41959317 original size:14 final size:14
Alignment explanation
Indices: 41959265--41959317 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
41959255 AAAAATAGAA
41959265 ATTTAAAACT-TTG
1 ATTTAAAACTCTTG
*
41959278 ATTTGAAAACTCCCTTT
1 ATTT-AAAACT--CTTG
*
41959295 ATTTTAAACTCTTG
1 ATTTAAAACTCTTG
41959309 ATTTAAAAC
1 ATTTAAAAC
41959318 AGAAAAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
13 4 0.12
14 17 0.53
16 5 0.16
17 6 0.19
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (14 bp):
ATTTAAAACTCTTG
Found at i:41960218 original size:31 final size:31
Alignment explanation
Indices: 41960175--41960238 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41960165 CCTTTTCATA
41960175 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
41960206 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
41960237 TT
1 TT
41960239 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:41960507 original size:23 final size:24
Alignment explanation
Indices: 41960431--41960550 Score: 165
Period size: 24 Copynumber: 5.0 Consensus size: 24
41960421 GCTTTATCAT
*
41960431 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
41960456 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
*
41960481 ATAACTGAGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41960504 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41960528 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
41960551 GCACTCCTCC
Statistics
Matches: 87, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
23 23 0.26
24 34 0.39
25 24 0.28
26 6 0.07
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:41960540 original size:47 final size:47
Alignment explanation
Indices: 41960452--41960549 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 47
41960442 CCTAGCCTCT
41960452 TTTAATAACTGGGGCAAAGCCCTTTTTTAATAACTGAGGCATAAGCCC
1 TTTAATAACTGGGGCAAAGCCC-TTTTTAATAACTGAGGCATAAGCCC
*
41960500 TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCA-AAGCCCTTTTTAATAACTGAGGCATAAGCCC
41960547 TTT
1 TTT
41960550 TGCACTCCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
47 26 0.54
48 16 0.33
49 6 0.12
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (47 bp):
TTTAATAACTGGGGCAAAGCCCTTTTTAATAACTGAGGCATAAGCCC
Found at i:41960625 original size:20 final size:20
Alignment explanation
Indices: 41960602--41960664 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
41960592 GAACATCTCG
41960602 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
41960622 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
*
41960642 TGTGTATATCATACATATCA
1 TGTGCATATCATACATATCA
41960662 TGT
1 TGT
41960665 TTCAAAATCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:41963121 original size:24 final size:24
Alignment explanation
Indices: 41962898--41963119 Score: 363
Period size: 24 Copynumber: 9.1 Consensus size: 24
41962888 GCAAAGACCA
41962898 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41962922 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41962946 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
41962970 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41962994 TATGGCACTATGTGTGCGATTTACTAC
1 TATGGCACTATGTGTGCGA-TT--TAC
*
41963021 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41963045 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41963069 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
41963093 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
41963117 TAT
1 TAT
41963120 AGTCATTCGG
Statistics
Matches: 189, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
24 164 0.87
25 2 0.01
26 2 0.01
27 21 0.11
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:41965169 original size:39 final size:39
Alignment explanation
Indices: 41965043--41965171 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 39
41965033 ATGCTGGAAA
* * *
41965043 TTATATCCGGGTTAAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCT-AAGACCCGAAGGCATTTGTGCGAGT-G
* * * **
41965084 CTACATCCGGGCTAAGA-CCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TG
*
41965123 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTG
41965162 TTATATCCGG
1 TTATATCCGG
41965172 TTATATTCCG
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
39 40 0.57
40 20 0.29
41 10 0.14
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG
Found at i:41973006 original size:40 final size:39
Alignment explanation
Indices: 41972940--41973085 Score: 138
Period size: 40 Copynumber: 3.8 Consensus size: 39
41972930 AAATTGAATG
*
41972940 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-TGCTGGAAATT
* * ****
41972979 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-TGCTGGAAATT
* * *
41973019 ACATCCGGGCTAAGACCCGAAGGC-ATTCG-TGCGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTTGCTG-GAAATT
*
41973057 CTATCCGGGCTAAGACCCGAAGGC-ATTTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTTG
41973086 TGCACGTGGT
Statistics
Matches: 86, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
37 1 0.01
38 29 0.34
39 16 0.19
40 40 0.47
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTTGCTGGAAATT
Found at i:41973103 original size:78 final size:78
Alignment explanation
Indices: 41972940--41973104 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 78
41972930 AAATTGAATG
*
41972940 ATATCCGGGCTAAGCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGCCCGAAGACAATTATGC-GGAAATTATATCCGGGCTAAGACCCGAAGGCAA
41973005 TTGTGCTAGTGGCT
65 TTGTGCTAGTGGCT
* * * * *
41973019 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GACATTCTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAG-CCCGAAGACAATT-ATGCGGAAATTATATCCGGGCTAAGACCCGAAGGCA
* *
41973082 TTTGTGC-ACGTGGTT
64 ATTGTGCTA-GTGGCT
41973097 ATATCCGG
1 ATATCCGG
41973105 TTATATTCCG
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
77 1 0.01
78 46 0.62
79 16 0.22
80 11 0.15
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (78 bp):
ATATCCGGGCTAAGCCCGAAGACAATTATGCGGAAATTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCTAGTGGCT
Found at i:41984548 original size:42 final size:43
Alignment explanation
Indices: 41984486--41984589 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
41984476 AAGTCTGAAG
* * * *
41984486 TCGTTGAGTGGTCCGGGTTCATGATATATGTG-GCATCCGAGC
1 TCGTTGAGTGGTCCGAGTTCATGATAGATGCGAGCATCCAAGC
* *
41984528 TCGTTGAGTGGTCCGAGTTCATTATGGATGCGAGCATCCAAGC
1 TCGTTGAGTGGTCCGAGTTCATGATAGATGCGAGCATCCAAGC
* *
41984571 TCGTTAAGTGGTCTGAGTT
1 TCGTTGAGTGGTCCGAGTT
41984590 TATAATGGAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 27 0.51
43 26 0.49
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (43 bp):
TCGTTGAGTGGTCCGAGTTCATGATAGATGCGAGCATCCAAGC
Found at i:41984581 original size:43 final size:42
Alignment explanation
Indices: 41984486--41984600 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 42
41984476 AAGTCTGAAG
* * ** * *
41984486 TCGTTGAGTGGTCCGGGTTCATGATATATGTGGCATCCGAGC
1 TCGTTGAGTGGTCCGAGTTCATAATGGATGCGGCATCCAAGC
*
41984528 TCGTTGAGTGGTCCGAGTTCATTATGGATGCGAGCATCCAAGC
1 TCGTTGAGTGGTCCGAGTTCATAATGGATGCG-GCATCCAAGC
* * *
41984571 TCGTTAAGTGGTCTGAGTTTATAATGGATG
1 TCGTTGAGTGGTCCGAGTTCATAATGGATG
41984601 TGATACATGT
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 27 0.44
43 35 0.56
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (42 bp):
TCGTTGAGTGGTCCGAGTTCATAATGGATGCGGCATCCAAGC
Found at i:41986055 original size:2 final size:2
Alignment explanation
Indices: 41986043--41986072 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
41986033 TATGGTGAAA
41986043 AT AT CAT 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 A
41986073 AACTGATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41989218 original size:35 final size:35
Alignment explanation
Indices: 41989172--41989243 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
41989162 TCGAGAAAAT
41989172 AGAATGCTCAGAATTGAGCACACGGGCAGAGACAC
1 AGAATGCTCAGAATTGAGCACACGGGCAGAGACAC
41989207 AGAATGCTCAGAATTGAGCACACGGGCAGAGACAC
1 AGAATGCTCAGAATTGAGCACACGGGCAGAGACAC
41989242 AG
1 AG
41989244 GCGTGTGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.29, T:0.11
Consensus pattern (35 bp):
AGAATGCTCAGAATTGAGCACACGGGCAGAGACAC
Found at i:41993550 original size:2 final size:2
Alignment explanation
Indices: 41993543--41993567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41993533 AAGACTAGTC
41993543 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 A
41993568 CATGTCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41995055 original size:30 final size:30
Alignment explanation
Indices: 41995021--41995081 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41995011 TCCTTAACTC
41995021 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
41995051 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
41995081 A
1 A
41995082 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:42010771 original size:16 final size:16
Alignment explanation
Indices: 42010752--42010782 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42010742 CTTCTTCACT
42010752 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
42010768 TACTTACTTACTTAA
1 TACTCACTTACTTAA
42010783 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:42010788 original size:20 final size:20
Alignment explanation
Indices: 42010749--42010788 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42010739 AAACTTCTTC
* *
42010749 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
42010769 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
42010789 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:42011104 original size:53 final size:54
Alignment explanation
Indices: 42010975--42011229 Score: 238
Period size: 55 Copynumber: 4.8 Consensus size: 54
42010965 ACACGGGTAC
* ** * *
42010975 CTTACCATTGCCATAACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
42011024 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
42011077 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* ** * * *
42011132 CTTATCAATGCCATGTATTGATATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
42011185 CCTTACCAATTTCCATGCCTTGGCATGGCCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
42011230 AAACCCTAAT
Statistics
Matches: 167, Mismatches: 28, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 2 0.01
53 49 0.29
54 10 0.06
55 66 0.40
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:42011166 original size:108 final size:110
Alignment explanation
Indices: 42011022--42011222 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
42011012 ATCCTTTTGA
* * *
42011022 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTATTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
*
42011085 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGCCTTACATGGGACCTTTGCCTTATAGT
* * * *
42011130 AACTTATCAATGCCATGTATTGATATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTATTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
42011195 TTCCATGCCTTGGCATGGCCTTACATGG
66 TGCCATGCCTTGGCATGGCCTTACATGG
42011223 TATCCTTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.58
109 7 0.09
110 26 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTATTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGCCTTACATGGGACCTTTGCCTTATAGT
Found at i:42020976 original size:27 final size:28
Alignment explanation
Indices: 42020946--42021015 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
42020936 ATAATAAGTC
*
42020946 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
42020973 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
42021001 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42021016 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42028906 original size:27 final size:28
Alignment explanation
Indices: 42028876--42028945 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
42028866 ATAATAAGTC
*
42028876 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
42028903 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
42028931 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42028946 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42032827 original size:32 final size:31
Alignment explanation
Indices: 42032785--42032858 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 31
42032775 GCCCTAGGCC
* * *
42032785 ACATGTGCGTGGGTGACCGCACGGCCCATAAT
1 ACATGGGCGTGGGAGACCACACGGCCCA-AAT
* * **
42032817 ACATGGGCGTGTGAGTCCACACGGCCCACCT
1 ACATGGGCGTGGGAGACCACACGGCCCAAAT
42032848 ACATGGGCGTG
1 ACATGGGCGTG
42032859 TGCCCCTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 12 0.34
32 23 0.66
ACGTcount: A:0.20, C:0.30, G:0.32, T:0.18
Consensus pattern (31 bp):
ACATGGGCGTGGGAGACCACACGGCCCAAAT
Found at i:42038312 original size:45 final size:46
Alignment explanation
Indices: 42038248--42038422 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
42038238 TGTAACCCGC
*
42038248 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
42038293 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
42038343 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
42038386 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42038423 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 36 0.32
46 29 0.26
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:42038413 original size:93 final size:92
Alignment explanation
Indices: 42038255--42038425 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 92
42038245 CGCCCATAAG
*
42038255 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42038320 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
42038347 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42038412 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
42038426 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 28 0.37
93 48 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42045933 original size:93 final size:93
Alignment explanation
Indices: 42045821--42045992 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
42045811 CGCCCATAAG
*
42045821 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
42045885 AACGAGCTCGGATGCCTAGTTACATCTCA
65 AACGAGCTCGGATGCCTAGTTACATCTCA
*
42045914 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
42045979 ACGAGTTCGGATGC
66 ACGAGCTCGGATGC
42045993 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:42045984 original size:46 final size:46
Alignment explanation
Indices: 42045814--42045989 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
42045804 TGTAACCCGC
*
42045814 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCAT
* *
42045860 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
42045910 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
42045953 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
42045990 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 62 0.56
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:42053565 original size:13 final size:14
Alignment explanation
Indices: 42053528--42053564 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
42053518 AGGATCGAAT
42053528 AAAAGAAAAATTAG
1 AAAAGAAAAATTAG
42053542 AAAAGAAAAATTAG
1 AAAAGAAAAATTAG
42053556 AAAAGAAAA
1 AAAAGAAAA
42053565 TAAAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (14 bp):
AAAAGAAAAATTAG
Found at i:42056064 original size:6 final size:6
Alignment explanation
Indices: 42056062--42056098 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
42056052 TAATAAAAAT
*
42056062 AAAATA AAA-CA AAAACA AAAACA AAAAC- AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAA
42056099 TTTAAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 9 0.32
6 19 0.68
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAACA
Found at i:42056076 original size:11 final size:11
Alignment explanation
Indices: 42056053--42056113 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
42056043 AGTTGAGATT
42056053 AATAAAA-ATAA
1 AATAAAACA-AA
42056064 AATAAAACAAA
1 AATAAAACAAA
*
42056075 AACAAAAACAAA
1 AA-TAAAACAAA
*
42056087 AACAAAACAAA
1 AATAAAACAAA
*
42056098 ATTTAAAACAAGA
1 A-ATAAAACAA-A
42056111 AAT
1 AAT
42056114 TGAAGTTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 20 0.49
12 19 0.46
13 2 0.05
ACGTcount: A:0.77, C:0.10, G:0.02, T:0.11
Consensus pattern (11 bp):
AATAAAACAAA
Found at i:42056082 original size:17 final size:17
Alignment explanation
Indices: 42056062--42056108 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
42056052 TAATAAAAAT
42056062 AAAATAAAACAAAAACA
1 AAAATAAAACAAAAACA
*
42056079 AAAACAAAA-ACAAAACA
1 AAAATAAAACA-AAAACA
*
42056096 AAATTTAAAACAA
1 AAA-ATAAAACAA
42056109 GAAATTGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.04
17 17 0.71
18 5 0.21
19 1 0.04
ACGTcount: A:0.79, C:0.13, G:0.00, T:0.09
Consensus pattern (17 bp):
AAAATAAAACAAAAACA
Found at i:42056084 original size:12 final size:11
Alignment explanation
Indices: 42056062--42056098 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
42056052 TAATAAAAAT
*
42056062 AAAATAAAACA
1 AAAACAAAACA
42056073 AAAACAAAAACA
1 AAAAC-AAAACA
42056085 AAAACAAAACA
1 AAAACAAAACA
42056096 AAA
1 AAA
42056099 TTTAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAACAAAACA
Found at i:42058971 original size:12 final size:12
Alignment explanation
Indices: 42058954--42058979 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42058944 GTGTCGCAGG
42058954 CCATGTGCCAGA
1 CCATGTGCCAGA
42058966 CCATGTGCCAGA
1 CCATGTGCCAGA
42058978 CC
1 CC
42058980 GTGTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (12 bp):
CCATGTGCCAGA
Found at i:42062736 original size:40 final size:40
Alignment explanation
Indices: 42062708--42062902 Score: 243
Period size: 40 Copynumber: 4.9 Consensus size: 40
42062698 TCATAGTGAT
42062708 TAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
1 TAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
* *
42062748 TAATTTCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTAC
1 TAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
* * *
42062788 AAATTCCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTAC
1 TAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
* * *
42062828 T-ATATCCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGAC
1 TAAT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
* * * * *
42062868 -CATACCGGGCTAAGACCCGACGGC-CTTGTGCGAGT
1 TAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
42062903 GGTTATATCC
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
38 9 0.07
39 20 0.15
40 106 0.79
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC
Found at i:42062917 original size:38 final size:40
Alignment explanation
Indices: 42062712--42062927 Score: 183
Period size: 40 Copynumber: 5.5 Consensus size: 40
42062702 AGTGATTAAT
* * *
42062712 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
1 TCCGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA
* * * * * *
42062751 TTTCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTAC-AAA
1 -TCCGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA
* * ** *
42062791 TTCCGGGATAAGTCCCGAAGGCAATTGTGCGAGTTACTATA
1 -TCCGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA
* * *
42062832 TCCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACCATA
1 TCCGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA
* **
42062872 -CCGGGCTAAGACCCGACGGCC-TTGTGCGAGTGGTTATA
1 TCCGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA
42062910 TCC-GGCTAA-ATCCCGAAG
1 TCCGGGCTAAGA-CCCGAAG
42062928 ATAATTGGGT
Statistics
Matches: 152, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.01
38 25 0.16
39 22 0.14
40 102 0.67
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA
Found at i:42065210 original size:22 final size:23
Alignment explanation
Indices: 42065185--42065227 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
42065175 AAAGCCGAGG
42065185 AGCTCAGTAT-GGAG-AAAAGAAA
1 AGCTCA-TATGGGAGCAAAAGAAA
*
42065207 AGCTGATATGGGAGCAAAAGA
1 AGCTCATATGGGAGCAAAAGA
42065228 GTTTCGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 9 0.50
23 6 0.33
ACGTcount: A:0.47, C:0.09, G:0.30, T:0.14
Consensus pattern (23 bp):
AGCTCATATGGGAGCAAAAGAAA
Found at i:42070939 original size:40 final size:40
Alignment explanation
Indices: 42070881--42071105 Score: 240
Period size: 40 Copynumber: 5.7 Consensus size: 40
42070871 CTAACGGGGT
** * * * *
42070881 TAAGTCCCGAAGAAATTTGTGCTAGTGATTAATTTCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
42070921 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTTCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
* * *
42070961 TAAGTCCCGAAGGTATTTGTGCGAGTTACAAATTCCGGGA
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
* *
42071001 TAAGTCCCAAAGGCAATTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* * * *
42071041 TAAGTCCCGAAGGCCTTTGTGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* * *
42071081 TAAGACCCGACGGC-CTTGTGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCGAGT
42071106 GGTTATATCC
Statistics
Matches: 160, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 11 0.07
40 149 0.93
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:42071114 original size:39 final size:40
Alignment explanation
Indices: 42070916--42071130 Score: 179
Period size: 40 Copynumber: 5.4 Consensus size: 40
42070906 TGATTAATTT
* * * *
42070916 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTT
1 CGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA-TC
* ** * *
42070956 CGGGCTAAGTCCCGAAGGTATTTGTGCGAGTTAC-AAATTC
1 CGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATA-TC
* * * ** *
42070996 CGGGATAAGTCCCAAAGGCAATTGTGCGAGTTACTATATC
1 CGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATATC
* * *
42071036 CGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACCATATC
1 CGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATATC
* **
42071076 CGGGCTAAGACCCGACGGCC-TTGTGCGAGTGGTTATATC
1 CGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATATC
42071115 C-GGCTAA-ATCCCGAAG
1 CGGGCTAAGA-CCCGAAG
42071131 ATAATTGGGT
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 12 0.08
39 17 0.11
40 119 0.79
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGACCCGAAGGCCTTTGTGCGAGTGACTATATC
Found at i:42080177 original size:50 final size:49
Alignment explanation
Indices: 42080109--42080298 Score: 202
Period size: 50 Copynumber: 3.8 Consensus size: 49
42080099 GCATCTTAAG
**
42080109 TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGA
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATTATC-GA
* * * *
42080159 TACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGG
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-TTATC-GA
** * * * *
42080210 TATGCATAATAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCA
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATTATCGA
* * *
42080258 GTACACGTAGTAGCTTGCACTTAGTACTACACACATGACCT
1 -TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCT
42080299 CACAATAGAT
Statistics
Matches: 113, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
49 36 0.32
50 41 0.36
51 36 0.32
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (49 bp):
TACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAATTATCGA
Done.