Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 130 of 276
Found at i:42033773 original size:83 final size:80
Alignment explanation
Indices: 42033590--42033813 Score: 328
Period size: 83 Copynumber: 2.8 Consensus size: 80
42033580 ACCCAAGTAT
* * *
42033590 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
42033653 TCACTAGCACAAATGC
65 TCACTAGCACAAATGC
*
42033669 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
42033733 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
42033752 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
42033814 CATCCGAATA
Statistics
Matches: 132, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
79 13 0.10
80 49 0.37
81 1 0.01
83 69 0.52
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:42037611 original size:55 final size:54
Alignment explanation
Indices: 42037552--42037656 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 54
42037542 AAAAAGGGCA
*
42037552 TGCGACACGTCCGTGCCTTAAG-ACCGTGGCCAAACCTGTTAAATT-AACACCGGTG
1 TGCGACACGACCGTGCC--AAGAACCGTGGCCAAACCTGTT-AATTGAACACCGGTG
* * *
42037607 TGCGACATGACTGTGCCAAGCAACCGTGGTCAAACCTGTTAATTGAACAC
1 TGCGACACGACCGTGCCAAG-AACCGTGGCCAAACCTGTTAATTGAACAC
42037657 GGGCATGGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
53 3 0.07
54 4 0.09
55 36 0.84
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (54 bp):
TGCGACACGACCGTGCCAAGAACCGTGGCCAAACCTGTTAATTGAACACCGGTG
Found at i:42039493 original size:68 final size:67
Alignment explanation
Indices: 42039421--42039570 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
42039411 CATCATGTGT
* * * *
42039421 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
42039483 ATGTAG
62 ATGTAG
** * *
42039489 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
42039554 AG
66 AG
42039556 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
42039571 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:42039526 original size:64 final size:64
Alignment explanation
Indices: 42039445--42039628 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
42039435 AGACATTATG
* *
42039445 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
42039509 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
42039574 AA
63 AA
* * * *
42039576 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
42039629 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:42045080 original size:50 final size:49
Alignment explanation
Indices: 42044966--42045152 Score: 200
Period size: 50 Copynumber: 3.8 Consensus size: 49
42044956 TGAGGTCGCA
* * *
42044966 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGT--GATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC--AGACTGTACG-TCACG
* ** *
42045017 TGTGTAGTGCTAAGTGCAGGCTACTACGTGTATTAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GT-ACGTCACG
* * *
42045067 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTCGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTACGTCACG
*
42045116 TGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
42045153 TAGCTTCGGC
Statistics
Matches: 117, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
47 1 0.01
48 4 0.03
49 40 0.34
50 41 0.35
51 31 0.26
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTACGTCACG
Found at i:42046807 original size:21 final size:21
Alignment explanation
Indices: 42046783--42046823 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
42046773 CCTTAATTTC
42046783 ATGTTTTATGCTTAGGCGAGT
1 ATGTTTTATGCTTAGGCGAGT
42046804 ATGTTTTATGCTTAGGCGAG
1 ATGTTTTATGCTTAGGCGAG
42046824 CATAGGAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (21 bp):
ATGTTTTATGCTTAGGCGAGT
Found at i:42050475 original size:29 final size:29
Alignment explanation
Indices: 42050412--42050479 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
42050402 TAATCAACCG
42050412 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
42050441 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
42050470 CGCACACTTA
1 CGCACACTTA
42050480 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:42050592 original size:174 final size:174
Alignment explanation
Indices: 42050301--42050628 Score: 593
Period size: 174 Copynumber: 1.9 Consensus size: 174
42050291 AACTCAAGGT
* * *
42050301 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
*
42050366 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
42050431 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
42050475 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
*
42050540 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
42050605 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
42050629 TGTACAATTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:42050620 original size:29 final size:30
Alignment explanation
Indices: 42050581--42050659 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
42050571 CTTAATAATC
42050581 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
42050611 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
42050640 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
42050660 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:42063636 original size:27 final size:27
Alignment explanation
Indices: 42063564--42063637 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
42063554 TTTGCCATAG
*
42063564 AGGCATTCCTTTCATATTACACCACAA
1 AGGCATTCCTTTCATATTGCACCACAA
*
42063591 AGGCATTCCTTTCATATTGCATCACAA
1 AGGCATTCCTTTCATATTGCACCACAA
42063618 AGGCATTCCTTTCATATTGC
1 AGGCATTCCTTTCATATTGC
42063638 GCAACAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (27 bp):
AGGCATTCCTTTCATATTGCACCACAA
Found at i:42073910 original size:13 final size:13
Alignment explanation
Indices: 42073892--42073930 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
42073882 ACGAAGCAGA
42073892 ACACGACCGTGTG
1 ACACGACCGTGTG
42073905 ACACGACCGTGTG
1 ACACGACCGTGTG
42073918 ACACGACCGTGTG
1 ACACGACCGTGTG
42073931 CACCAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACACGACCGTGTG
Found at i:42078962 original size:42 final size:42
Alignment explanation
Indices: 42078915--42079018 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
42078905 TATCGGGATG
* * *
42078915 TGAGATTCATGTAAGACCATGACTGGGACATTTGCATCGATA
1 TGAGATTCGTGTAAGACCATGACTAGGACATTGGCATCGATA
*
42078957 TGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
1 TGAGATTCGTGTAAGACCATGACTAGGACATTGGCATCGATA
42078999 TGAGATTCGTGTAAGACCAT
1 TGAGATTCGTGTAAGACCAT
42079019 AGCTAAGCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
TGAGATTCGTGTAAGACCATGACTAGGACATTGGCATCGATA
Found at i:42079032 original size:42 final size:42
Alignment explanation
Indices: 42078915--42079040 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
42078905 TATCGGGATG
* * ** *
42078915 TGAGATTCATGTAAGACCATGACTGGGACATTTGCATCGATA
1 TGAGATTCGTGTAAGACCATGTCTAAGACATTGGCATCGATA
*
42078957 TGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
1 TGAGATTCGTGTAAGACCATGTCTAAGACATTGGCATCGATA
42078999 TGAGATTCGTGTAAGACCATAG-CTAAG-CTATTGG-ATCGATA
1 TGAGATTCGTGTAAGACCAT-GTCTAAGAC-ATTGGCATCGATA
42079040 T
1 T
42079041 ACTATAACAT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
41 9 0.12
42 67 0.87
43 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
TGAGATTCGTGTAAGACCATGTCTAAGACATTGGCATCGATA
Found at i:42079953 original size:21 final size:21
Alignment explanation
Indices: 42079927--42079983 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
42079917 ATGGTATAAG
42079927 GTTGATGAATTGGTACATTTT
1 GTTGATGAATTGGTACATTTT
*
42079948 GTTGATGATGAATTGGTATATTTT
1 G-T--TGATGAATTGGTACATTTT
*
42079972 GTGGCATGAATT
1 GTTG-ATGAATT
42079984 ATATGATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 1 0.03
24 19 0.63
ACGTcount: A:0.25, C:0.04, G:0.26, T:0.46
Consensus pattern (21 bp):
GTTGATGAATTGGTACATTTT
Found at i:42086273 original size:29 final size:28
Alignment explanation
Indices: 42086237--42086314 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
42086227 TCATGAGATT
42086237 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
42086267 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
42086294 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
42086315 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:42086532 original size:174 final size:174
Alignment explanation
Indices: 42086267--42086594 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
42086257 AAATTGTACA
*
42086267 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
42086332 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
42086397 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
42086441 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
42086506 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
42086571 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
42086595 ACCTTGAGTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:42090995 original size:43 final size:43
Alignment explanation
Indices: 42090913--42090997 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
42090903 AGTAAGACCA
* * * *
42090913 TGGCATCGGTATGTGTTTACGAGTAAGACTCTGTCTGGGACAG
1 TGGCATCGATATGTGGTTACGAGTAAAACTCTGTATGGGACAG
42090956 TGGCATCGATATGTGGTTAC-ATGTAAAAC-CATGTATGGGACA
1 TGGCATCGATATGTGGTTACGA-GTAAAACTC-TGTATGGGACA
42090998 TTGATATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 2 0.06
43 34 0.94
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (43 bp):
TGGCATCGATATGTGGTTACGAGTAAAACTCTGTATGGGACAG
Found at i:42095514 original size:27 final size:27
Alignment explanation
Indices: 42095483--42095660 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
42095473 TAAATTGTAC
*
42095483 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
42095510 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42095536 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
42095564 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
42095592 AGCACTAAGTGTGCGACTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
42095619 AGCACTAAGTGTGC-AAGTTGATTATAT
1 AGCACTAAGTGTGCGAA-TTGACTATGT
*
42095646 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42095661 GACTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 102 0.81
28 23 0.18
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:42095651 original size:82 final size:81
Alignment explanation
Indices: 42095480--42095660 Score: 222
Period size: 82 Copynumber: 2.2 Consensus size: 81
42095470 GATTAAATTG
* *
42095480 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42095545 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42095561 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGACTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
**
42095625 AAGTGTGC-AAGTTGATTA
64 AAGTGTGCGAA-TTGACCA
* *
42095643 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42095661 GACTCAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 20 0.24
82 64 0.76
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42104126 original size:18 final size:18
Alignment explanation
Indices: 42104103--42104142 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
42104093 ATCTTCCAAG
42104103 CTTAAATCAAGGTTCGTT
1 CTTAAATCAAGGTTCGTT
42104121 CTTAAATCAAGGTTCGTT
1 CTTAAATCAAGGTTCGTT
42104139 CTTA
1 CTTA
42104143 TTTGCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (18 bp):
CTTAAATCAAGGTTCGTT
Found at i:42104974 original size:43 final size:43
Alignment explanation
Indices: 42104905--42104996 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
42104895 AGTAAGACCA
* * * *
42104905 TGGCATCGATATGTGTTTACGAGTAAGACCCTGTCTGGGACAG
1 TGGCATCGATATGTGGTTACGAGTAAGACCATCTCTAGGACAG
* *
42104948 TGGCATCGATATGTGGTTGC-ATGTAAGACCATCTCTAGGACAT
1 TGGCATCGATATGTGGTTACGA-GTAAGACCATCTCTAGGACAG
42104991 TGGCAT
1 TGGCAT
42104997 TGTACGATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 41 0.98
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
TGGCATCGATATGTGGTTACGAGTAAGACCATCTCTAGGACAG
Found at i:42110522 original size:24 final size:26
Alignment explanation
Indices: 42110477--42110524 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
42110467 TTCTCTTAAA
*
42110477 TTTAATTTTATTCTAATAATTAATTT
1 TTTAATTTTATTCGAATAATTAATTT
*
42110503 TTTAA-TTTATT-GAATCATTAAT
1 TTTAATTTTATTCGAATAATTAAT
42110525 AATTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 6 0.30
26 5 0.25
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTAATTTTATTCGAATAATTAATTT
Found at i:42112855 original size:21 final size:23
Alignment explanation
Indices: 42112819--42112866 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
42112809 AATAATTAAC
*
42112819 TTTTATAAAATAATTTT-AGTTA
1 TTTTATAAAATAATTTTGAGTAA
*
42112841 TTTTAT-AATTAATTTTGAGTAA
1 TTTTATAAAATAATTTTGAGTAA
42112863 TTTT
1 TTTT
42112867 GGTTATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
TTTTATAAAATAATTTTGAGTAA
Found at i:42115898 original size:20 final size:21
Alignment explanation
Indices: 42115873--42115913 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42115863 CCCTTGAAAT
42115873 AGGGC-ATACGCCCGTGTGGA
1 AGGGCAATACGCCCGTGTGGA
*
42115893 AGGGCAATGCGCCCGTGTGGA
1 AGGGCAATACGCCCGTGTGGA
42115914 GCTTGTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.24, G:0.41, T:0.15
Consensus pattern (21 bp):
AGGGCAATACGCCCGTGTGGA
Found at i:42117288 original size:48 final size:48
Alignment explanation
Indices: 42117218--42117481 Score: 234
Period size: 48 Copynumber: 5.6 Consensus size: 48
42117208 TATCCGTACT
*
42117218 GATGCCATGTCCCAAACATGGTCTTACACTGACACCTCTATACGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCC
* *
42117266 GATGCCGTGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCC
* * *
42117314 GATGACATGTCCCAGACATGGTCTTACATTGACACATCTCATA---GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACCTCT-ATACGTGCC
* * *
42117360 GATG-CATGTTCCAGACAT-GTCTTACAGT-AGCTTACATCT-TGA-G-GCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-C--ACCTCTAT-ACGTGCC
* *
42117406 GATG-CATGTCCCAGACAT-GTATTACACT-AGCTCTCGTCTCA-A--TGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CAC-C-TCT-ATACGTGCC
*
42117452 GATGCCATGTCCTAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
42117482 AGCTCTCATA
Statistics
Matches: 186, Mismatches: 17, Indels: 26
0.81 0.07 0.11
Matches are distributed among these distances:
43 1 0.01
44 12 0.06
45 14 0.08
46 54 0.29
47 13 0.07
48 89 0.48
49 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACCTCTATACGTGCC
Found at i:42117410 original size:46 final size:46
Alignment explanation
Indices: 42117357--42117527 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 46
42117347 ACATCTCATA
* *
42117357 GCCGATGCATGTTCCAGACATGTCTTACAGTAGCT-TACATCTTGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCTTGAG
* * ** *
42117403 GCCGATGCATGTCCCAGACATGTATTACACTAGCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTTGAG
* ** *
42117449 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTTGAG
* *
42117497 GCCGATGCATGTCCCAAAAATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
42117528 GGCGCACAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 54 0.52
47 25 0.24
48 24 0.23
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTTGAG
Found at i:42117488 original size:48 final size:48
Alignment explanation
Indices: 42117066--42117490 Score: 231
Period size: 48 Copynumber: 8.9 Consensus size: 48
42117056 CATAGGGTAT
* * *
42117066 AATGCCGATGCCATGTCCTAGACATGGTCTTACAGT-G-GCTCATCCATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-C-TC
* * * * * **
42117114 AA-GTCGATGTCATGTCCCAGACATGGTTTTACACTAACTATCAAAATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC-ATCTC
* ** ** * * *
42117162 AAGGTTGACACCATATCCCAAACATGGTCTTACACTAGCTCTCACATATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATCTC
** * * * *
42117212 CGTACTGATGCCATGTCCCAAACATGGTCTTACACT-GACAC-C-TCT-
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATCTC
* *
42117257 ATACGTGCCGATGCCGTGTCCCAGACATGGTCTTACACT-GACAC-C-TCT-
1 A-A--TGCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATCTC
* * * * *
42117305 ATACGTGCTGATGACATGTCCCAGACATGGTCTTACA-TTG-ACACATCTC
1 A-A--TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC
* * *
42117354 -ATAGCCGATG-CATGTTCCAGACAT-GTCTTACAGTAGCT-TACATCTT
1 AAT-GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATCTC
* * * *
42117400 GAGGCCGATG-CATGTCCCAGACAT-GTATTACACTAGCTCTCGTCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC
*
42117446 AATGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCAT
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT
42117491 AATGTGGCCG
Statistics
Matches: 299, Mismatches: 56, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
44 8 0.03
45 16 0.05
46 59 0.20
47 47 0.16
48 100 0.33
49 33 0.11
50 35 0.12
51 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTC
Found at i:42117500 original size:94 final size:91
Alignment explanation
Indices: 42117183--42117527 Score: 258
Period size: 94 Copynumber: 3.7 Consensus size: 91
42117173 CATATCCCAA
* * * *
42117183 ACATGGTCTTACACTAGCTCTCACATATCCGT-ACTGATGCCATGTCCCAAACATGGTCTTACAC
1 ACATGGTCTTACACTAGCTCTCATA-AT--GTGGCCGATG-CATGTCCCAGACAT-GTCTTACAC
* * *
42117247 T-GACACCTCTATACGTGCCGATGCCGTGTCCCAG
61 TAGACACATC--T-CATGCCGATGCCATGT-CCAG
* * *
42117281 ACATGGTCTTACACT-GACACCTC-TATACGT-GCTGATGACATGTCCCAGACATGGTCTTACA-
1 ACATGGTCTTACACTAG-C-TCTCATA-ATGTGGCCGATG-CATGTCCCAGACAT-GTCTTACAC
*
42117342 TTGACACATCTCATAGCCGATG-CATGTTCCAG
61 TAGACACATCTCAT-GCCGATGCCATG-TCCAG
* ** * *
42117374 ACAT-GTCTTACAGTAGCT-TACATCTTGAGGCCGATGCATGTCCCAGACATGTATTACACTAGC
1 ACATGGTCTTACACTAGCTCT-CATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTAG-
* * *
42117437 TCTCGTCTCAATGCCGATGCCATGTCCTAG
64 ACACATCTC-ATGCCGATGCCATGTCC-AG
* *
42117467 ACATGGTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAAAAATGTCTTACACT
1 ACATGGTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACT
42117528 GGCGCACAAA
Statistics
Matches: 203, Mismatches: 28, Indels: 36
0.76 0.10 0.13
Matches are distributed among these distances:
90 8 0.04
91 18 0.09
92 33 0.16
93 26 0.13
94 56 0.28
95 2 0.01
96 37 0.18
97 1 0.00
98 19 0.09
99 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (91 bp):
ACATGGTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTAGAC
ACATCTCATGCCGATGCCATGTCCAG
Found at i:42124549 original size:49 final size:49
Alignment explanation
Indices: 42124492--42124723 Score: 275
Period size: 49 Copynumber: 4.7 Consensus size: 49
42124482 CTGGTATGCA
* *
42124492 TAGTAGCCTGAATTTAGTACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
** * *
42124541 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCCGGTACACG
* * ** * * * * *
42124591 TAGTAGACTACACTTAGTACTATTCACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCCGGTACACG
*
42124642 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
* *
42124691 TAGTAGCCTGCACTTAGTACTAGACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
42124724 TCACAATAGA
Statistics
Matches: 149, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 72 0.48
50 43 0.29
51 34 0.23
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
Found at i:42124651 original size:101 final size:100
Alignment explanation
Indices: 42124505--42124721 Score: 276
Period size: 101 Copynumber: 2.2 Consensus size: 100
42124495 TAGCCTGAAT
* * * *
42124505 TTAGTACTACACATGTGA-CCAA-TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACAT
1 TTAGTACTAGACACGTGATCGAAGTTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACAT
* *
42124568 GTGACCTAACCATCTGATACACGTAGTAGACTACAC
66 GCGACC-AACCATCCGATACACGTAGTAGACTACAC
** * *
42124604 TTAGTACTATTCACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACAT
1 TTAGTACTAGACACGTGATCGAAGTTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACAT
** * * *
42124669 GCGACCAATTATCCGGTACACGTAGTAGCCTGCAC
66 GCGACCAACCATCCGATACACGTAGTAGACTACAC
42124704 TTAGTACTAGACACGTGA
1 TTAGTACTAGACACGTGA
42124722 CCTCACAATA
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
99 15 0.15
100 42 0.42
101 43 0.43
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (100 bp):
TTAGTACTAGACACGTGATCGAAGTTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACAT
GCGACCAACCATCCGATACACGTAGTAGACTACAC
Found at i:42127166 original size:16 final size:16
Alignment explanation
Indices: 42127145--42127190 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
42127135 CACCCAGATT
* *
42127145 CACATAGTCACATATA
1 CACATAATCACATAAA
*
42127161 CACATAATCTCATAAA
1 CACATAATCACATAAA
*
42127177 CTCATAATCACATA
1 CACATAATCACATA
42127191 GTTCCCAGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (16 bp):
CACATAATCACATAAA
Found at i:42130720 original size:31 final size:31
Alignment explanation
Indices: 42130682--42130765 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
42130672 TTGTTACAGT
*
42130682 AAAGGCTTCGGCCCTGTGATATGAATAATGG
1 AAAGGCTTCGGCCCAGTGATATGAATAATGG
*
42130713 AAAGGCTTCGGCCCAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGG
42130744 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
42130766 TTGAGATTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGG
Found at i:42135685 original size:25 final size:26
Alignment explanation
Indices: 42135637--42135690 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
42135627 GAGGAAGTGC
* * *
42135637 AAAAGGGCTTTTTCCCCAGTTTATCA
1 AAAAGGGATTTTGCCCCAGATTATCA
*
42135663 AAAAGGGATTTTGCCCCA-ATTATTA
1 AAAAGGGATTTTGCCCCAGATTATCA
42135688 AAA
1 AAA
42135691 GAGGCTAGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (26 bp):
AAAAGGGATTTTGCCCCAGATTATCA
Found at i:42135941 original size:31 final size:31
Alignment explanation
Indices: 42135903--42135986 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
42135893 TTGTTACAGT
42135903 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
42135934 AAAGGCTTCGGCCCAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
42135965 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
42135987 CTGAGATTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:42155862 original size:22 final size:22
Alignment explanation
Indices: 42155837--42155904 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
42155827 CATGTTGGAA
*
42155837 TTTTGACGCATGCATGAGAAGT
1 TTTTGACCCATGCATGAGAAGT
42155859 TTTTGACCCATGCATGAGAAGT
1 TTTTGACCCATGCATGAGAAGT
42155881 TTTTGACCCATGCATGAGAAGT
1 TTTTGACCCATGCATGAGAAGT
42155903 TT
1 TT
42155905 GTGTGTTGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (22 bp):
TTTTGACCCATGCATGAGAAGT
Found at i:42161254 original size:62 final size:61
Alignment explanation
Indices: 42161156--42161278 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 61
42161146 TAGAGCTTTG
** * *
42161156 AGAAACTGAAAATGTTATTGATTGAGGCACCTGTGTTAATACAACTAAAATCAGGGAAAGA
1 AGAAACTGAAAATGTTATTGACCGAGGCACCAGTGTTAATACAACCAAAATCAGGGAAAGA
* * *
42161217 NAGAAATTGAAAATGTTATTGACCGAGGCACCAGTGTTAGTACAACCAGAATCAGGGAAAGA
1 -AGAAACTGAAAATGTTATTGACCGAGGCACCAGTGTTAATACAACCAAAATCAGGGAAAGA
42161279 GTTTGTGATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (61 bp):
AGAAACTGAAAATGTTATTGACCGAGGCACCAGTGTTAATACAACCAAAATCAGGGAAAGA
Found at i:42163891 original size:386 final size:386
Alignment explanation
Indices: 42163173--42163904 Score: 888
Period size: 386 Copynumber: 1.9 Consensus size: 386
42163163 AGGGTGGAAA
* * * *
42163173 GTTGTAACATCATGAAATAGGGCCTAGTTGGAACAGTGGTTTTGAGACCACAAATTTGAGATAAA
1 GTTGTAACATCATGAAATAGGGCCTAATCGGAACAGTGGTTTTCAGACCACAAATTCGAGATAAA
* * * *
42163238 AATAATTATTTTATGAGTATTATGAAGTCTGTGATGTGTATGCATGCTTATGTCAAAGTTTCATG
66 AATAATTATTTTATGAGTATTATGAAGTCTATGATATGTATGCATGATTATGTCAAAATTTCATG
* * * *
42163303 AAGAAATTCTATGCAAAAAATGTTTAATTGAACTTTAGGGACCGAATTGAATAAGATGCAAAACT
131 AAGAAATTCTATGCAAAAAATGCTTAATTGAACGTTAGGGACCAAATTGAATAAGATGCAAAAAT
** * *
42163368 TGTGTTCTAGAAGCTTTCAGCATGAAATTGCTTTAGATTATAAATTAGAAGGTCCTAATTAGCAA
196 TGCATTCTAGAAGCTTTCAGCATGAAATTGCTTTAGAATATAAATTAGAAGGTCCTAAATAGCAA
* * *
42163433 TTTGACCAATTTCTAAATATTTGGACAAAAATGGACATGCATAGGAAAAATTTGAAAGAAAGGCC
261 TTTGACCAATTTCTAAATATATGGACAAAAATGGACATGAATAGGAAAAATTTGAAAGAAAGGCA
*
42163498 TTAAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAATCAAGTGAAAAT
326 ATAAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAATCAAGTGAAAAT
* * * * *
42163559 GTTGTAATATCCTGAATTAGGGCCTAATCGGAATAGTGG-TTTCATGACCACAAATTCGAGATAG
1 GTTGTAACATCATGAAATAGGGCCTAATCGGAACAGTGGTTTTCA-GACCACAAATTCGAGATAA
* * * * * *
42163623 AAATAATTATTTTATGATTATTTTGAGGTCTATGATATG-ATTGCATGATTGTGTGAAAATTTCG
65 AAATAATTATTTTATGAGTATTATGAAGTCTATGATATGTA-TGCATGATTATGTCAAAATTTCA
* * ** *
42163687 TGAAGAAATTCTATGCATAAAGTGCTTAATTTGAA-GTTAGGGATTAAATTGAATAAGTTGCAAA
129 TGAAGAAATTCTATGCAAAAAATGCTTAA-TTGAACGTTAGGGACCAAATTGAATAAGATGCAAA
* * * *
42163751 AATTGCATTCTAGAAG-TTTCTAGTATGAAATTGCTTT-GAAATATTAATTAGGAGGTCTTAAAT
193 AATTGCATTCTAGAAGCTTTC-AGCATGAAATTGCTTTAG-AATATAAATTAGAAGGTCCTAAAT
* * * **
42163814 AGGAATTTGACCAATTTC-AAAGTCTATGGACAAATATTGGACATGAAT-GG-AATTTTTGGAAA
256 AGCAATTTGACCAATTTCTAAA-TATATGGACAAA-AATGGACATGAATAGGAAAAATTT-GAAA
** *
42163876 GTTTA-GTAATAAGGGCATTTTGGTCATTT
318 G-AAAGGCAATAAGGGCATTTTGGTCATTT
42163905 AGGGGTAAAA
Statistics
Matches: 289, Mismatches: 48, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
385 18 0.06
386 254 0.88
387 17 0.06
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (386 bp):
GTTGTAACATCATGAAATAGGGCCTAATCGGAACAGTGGTTTTCAGACCACAAATTCGAGATAAA
AATAATTATTTTATGAGTATTATGAAGTCTATGATATGTATGCATGATTATGTCAAAATTTCATG
AAGAAATTCTATGCAAAAAATGCTTAATTGAACGTTAGGGACCAAATTGAATAAGATGCAAAAAT
TGCATTCTAGAAGCTTTCAGCATGAAATTGCTTTAGAATATAAATTAGAAGGTCCTAAATAGCAA
TTTGACCAATTTCTAAATATATGGACAAAAATGGACATGAATAGGAAAAATTTGAAAGAAAGGCA
ATAAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAATCAAGTGAAAAT
Found at i:42165597 original size:27 final size:26
Alignment explanation
Indices: 42165553--42165604 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42165543 CTCACAGCAA
*
42165553 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
42165580 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
42165605 GCAACCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:42172965 original size:27 final size:26
Alignment explanation
Indices: 42172921--42172971 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
42172911 CTCGCTGCAA
*
42172921 TCTGGTGGCCTCGCCACATATATCTAT
1 TCTGGTGACCTCGCCACA-ATATCTAT
* *
42172948 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
42172972 GGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTAT
Found at i:42178847 original size:40 final size:38
Alignment explanation
Indices: 42178803--42178955 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 38
42178793 ACCAGCTTGT
42178803 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGA
1 AGCCTGCGGGTCTTTAAGCCCGGATA-AATTCCAGCA-GA
* * *
42178843 AGCCTGCGGGACTTTAAGCCCGGATAACATTCCAACATA
1 AGCCTGCGGGTCTTTAAGCCCGGATAA-ATTCCAGCAGA
42178882 TAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATGA
1 -AGCCTGCGGGTCTTTAAGCCCGGATA-AATTCCAGCA-GA
42178923 AGCCTGCGGGTCTTTAAGCCCGGATAACATTCC
1 AGCCTGCGGGTCTTTAAGCCCGGATAA-ATTCC
42178956 TCAAGTATCA
Statistics
Matches: 102, Mismatches: 6, Indels: 10
0.86 0.05 0.08
Matches are distributed among these distances:
39 3 0.03
40 97 0.95
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (38 bp):
AGCCTGCGGGTCTTTAAGCCCGGATAAATTCCAGCAGA
Found at i:42178896 original size:80 final size:80
Alignment explanation
Indices: 42178802--42178955 Score: 281
Period size: 80 Copynumber: 1.9 Consensus size: 80
42178792 TACCAGCTTG
42178802 TAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGACTTTAAGCCCGGA
1 TAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGACTTTAAGCCCGGA
42178867 TAACATTCCAACATA
66 TAACATTCCAACATA
* * *
42178882 TAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATGAAGCCTGCGGGTCTTTAAGCCCGGA
1 TAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGACTTTAAGCCCGGA
42178947 TAACATTCC
66 TAACATTCC
42178956 TCAAGTATCA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (80 bp):
TAGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGACTTTAAGCCCGGA
TAACATTCCAACATA
Found at i:42192545 original size:16 final size:19
Alignment explanation
Indices: 42192506--42192545 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
42192496 TTTACCGTCA
42192506 ATACA-CAGTGATGAATGT
1 ATACATCAGTGATGAATGT
42192524 ATACATCAG-GAT-AATG-
1 ATACATCAGTGATGAATGT
42192540 ATACAT
1 ATACAT
42192546 GTATAGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 4 0.19
18 8 0.38
19 3 0.14
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (19 bp):
ATACATCAGTGATGAATGT
Found at i:42193184 original size:3 final size:3
Alignment explanation
Indices: 42193176--42193208 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
42193166 AGCCCATATT
*
42193176 TTC TTC TTC TTC TTC TTC TTC TTC TTC TAC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
42193209 ATGAATTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:42197753 original size:28 final size:29
Alignment explanation
Indices: 42197722--42197785 Score: 67
Period size: 32 Copynumber: 2.1 Consensus size: 29
42197712 TCGTAAATAT
42197722 TAAA-TAATAATATTTACGAACTTGCTCG
1 TAAATTAATAATATTTACGAACTTGCTCG
** *
42197750 TAAAATTGTGTTAATATTTACTAACTTGCTCG
1 T-AAA-T-TAATAATATTTACGAACTTGCTCG
42197782 TAAA
1 TAAA
42197786 ATTGTGGTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 3 0.10
31 3 0.10
32 22 0.76
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
TAAATTAATAATATTTACGAACTTGCTCG
Found at i:42197770 original size:32 final size:32
Alignment explanation
Indices: 42197729--42197791 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
42197719 TATTAAATAA
42197729 TAATATTTACGAACTTGCTCGTAAAATTGTGT
1 TAATATTTACGAACTTGCTCGTAAAATTGTGT
*
42197761 TAATATTTACTAACTTGCTCGTAAAATTGTG
1 TAATATTTACGAACTTGCTCGTAAAATTGTG
42197792 GTCCCAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (32 bp):
TAATATTTACGAACTTGCTCGTAAAATTGTGT
Found at i:42198582 original size:66 final size:66
Alignment explanation
Indices: 42198469--42198592 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
42198459 ATTCGCTAGG
*
42198469 TCCAAACTAACGATTGCAATTAGCCAAGCCCACTGGCAACCCCAATTCGCTAGGCCTACTAGTGA
1 TCCAAACTAACGATTGCAATTAGCCAAGCCCACTGGCAACCCCAATTCGCCAGGCCTACTAGTGA
42198534 A
66 A
* * * * *
42198535 TCCAAACTGATGATTGCAATTCA-CCAAGCCTACTGGCGACCCTAATTCGCCAGGCCTA
1 TCCAAACTAACGATTGCAATT-AGCCAAGCCCACTGGCAACCCCAATTCGCCAGGCCTA
42198593 TTGGTAAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
66 50 0.98
67 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (66 bp):
TCCAAACTAACGATTGCAATTAGCCAAGCCCACTGGCAACCCCAATTCGCCAGGCCTACTAGTGA
A
Found at i:42200076 original size:24 final size:25
Alignment explanation
Indices: 42200035--42200081 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
42200025 AAATTTCGGA
*
42200035 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
42200059 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
42200082 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:42204165 original size:25 final size:27
Alignment explanation
Indices: 42204101--42204171 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 27
42204091 AATGCTCATA
*
42204101 CGAGCACATA-AACGGGAAGCTCTCTCT
1 CGAGC-CATATAACGGGAAGCTCTATCT
*
42204128 CGAGCCATATAACGGGAAGCTC-ATGT
1 CGAGCCATATAACGGGAAGCTCTATCT
*
42204154 -GAGCCATGTAACGGGAAG
1 CGAGCCATATAACGGGAAG
42204172 TTGATTCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
25 17 0.43
26 6 0.15
27 17 0.43
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (27 bp):
CGAGCCATATAACGGGAAGCTCTATCT
Found at i:42204320 original size:25 final size:25
Alignment explanation
Indices: 42204253--42204338 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
42204243 AGCTCCGGAT
*
42204253 AGCCATATATTAGGAAGCTCATGAAAG
1 AGCCATATATTAGGAAGCTC--CAAAG
* **
42204280 AGCC-TTTAATCGGGAAGCTCCAAAG
1 AGCCATAT-ATTAGGAAGCTCCAAAG
*
42204305 AGCCATATATTAGGAAGAT-CAAGAG
1 AGCCATATATTAGGAAGCTCCAA-AG
42204330 AGCCA-ATAT
1 AGCCATATAT
42204339 CAAGATGATC
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
24 7 0.15
25 23 0.48
26 4 0.08
27 14 0.29
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (25 bp):
AGCCATATATTAGGAAGCTCCAAAG
Found at i:42207943 original size:27 final size:27
Alignment explanation
Indices: 42207912--42208089 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42207902 TAAATTGTAC
42207912 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42207939 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42207965 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42207993 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42208021 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42208048 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42208075 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42208090 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42208026 original size:82 final size:81
Alignment explanation
Indices: 42207913--42208068 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42207903 AAATTGTACA
* *
42207913 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42207977 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42207994 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42208059 TGCGAGTTGA
65 TGCGAATTGA
42208069 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42208080 original size:82 final size:81
Alignment explanation
Indices: 42207909--42208089 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42207899 GATTAAATTG
* *
42207909 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42207974 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42207990 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42208054 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42208072 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42208090 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42218715 original size:28 final size:29
Alignment explanation
Indices: 42218684--42218747 Score: 67
Period size: 32 Copynumber: 2.1 Consensus size: 29
42218674 TCGTAAATAT
42218684 TAAA-TAATAATATTTACGAACTTGCTCG
1 TAAATTAATAATATTTACGAACTTGCTCG
** *
42218712 TAAAATTGTGTTAATATTTACTAACTTGCTCG
1 T-AAA-T-TAATAATATTTACGAACTTGCTCG
42218744 TAAA
1 TAAA
42218748 ATTGTGGTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.03
29 3 0.10
31 3 0.10
32 22 0.76
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
TAAATTAATAATATTTACGAACTTGCTCG
Found at i:42218732 original size:32 final size:32
Alignment explanation
Indices: 42218691--42218753 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
42218681 TATTAAATAA
42218691 TAATATTTACGAACTTGCTCGTAAAATTGTGT
1 TAATATTTACGAACTTGCTCGTAAAATTGTGT
*
42218723 TAATATTTACTAACTTGCTCGTAAAATTGTG
1 TAATATTTACGAACTTGCTCGTAAAATTGTG
42218754 GTCCCAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (32 bp):
TAATATTTACGAACTTGCTCGTAAAATTGTGT
Found at i:42219544 original size:66 final size:66
Alignment explanation
Indices: 42219431--42219554 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
42219421 ATTCGCTAGG
*
42219431 TCCAAACTAACGATTGCAATTAGCCAAGCCCACTGGCAACCCCAATTCGCTAGGCCTACTAGTGA
1 TCCAAACTAACGATTGCAATTAGCCAAGCCCACTGGCAACCCCAATTCGCCAGGCCTACTAGTGA
42219496 A
66 A
* * * * *
42219497 TCCAAACTGATGATTGCAATTCA-CCAAGCCTACTGGCGACCCTAATTCGCCAGGCCTA
1 TCCAAACTAACGATTGCAATT-AGCCAAGCCCACTGGCAACCCCAATTCGCCAGGCCTA
42219555 TTGGTAAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
66 50 0.98
67 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (66 bp):
TCCAAACTAACGATTGCAATTAGCCAAGCCCACTGGCAACCCCAATTCGCCAGGCCTACTAGTGA
A
Found at i:42221038 original size:24 final size:25
Alignment explanation
Indices: 42220997--42221043 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
42220987 AAATTTCGGA
*
42220997 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
42221021 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
42221044 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:42225127 original size:25 final size:27
Alignment explanation
Indices: 42225063--42225133 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 27
42225053 AATGCTCATA
*
42225063 CGAGCACATA-AACGGGAAGCTCTCTCT
1 CGAGC-CATATAACGGGAAGCTCTATCT
*
42225090 CGAGCCATATAACGGGAAGCTC-ATGT
1 CGAGCCATATAACGGGAAGCTCTATCT
*
42225116 -GAGCCATGTAACGGGAAG
1 CGAGCCATATAACGGGAAG
42225134 TTGATTCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
25 17 0.43
26 6 0.15
27 17 0.43
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (27 bp):
CGAGCCATATAACGGGAAGCTCTATCT
Found at i:42225282 original size:25 final size:25
Alignment explanation
Indices: 42225215--42225300 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
42225205 AGCTCCGGAT
*
42225215 AGCCATATATTAGGAAGCTCATGAAAG
1 AGCCATATATTAGGAAGCTC--CAAAG
* **
42225242 AGCC-TTTAATCGGGAAGCTCCAAAG
1 AGCCATAT-ATTAGGAAGCTCCAAAG
*
42225267 AGCCATATATTAGGAAGAT-CAAGAG
1 AGCCATATATTAGGAAGCTCCAA-AG
42225292 AGCCA-ATAT
1 AGCCATATAT
42225301 CAAGATGATC
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
24 7 0.15
25 23 0.48
26 4 0.08
27 14 0.29
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (25 bp):
AGCCATATATTAGGAAGCTCCAAAG
Found at i:42232931 original size:27 final size:27
Alignment explanation
Indices: 42232901--42232979 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 27
42232891 ATTCAAGAAT
42232901 GCTCACACGAGCACATA-AACGGGAAGC
1 GCTCACACGAGC-CATATAACGGGAAGC
* * *
42232928 GCTCTCTCGAGCCATATAATGGGAA--
1 GCTCACACGAGCCATATAACGGGAAGC
*** *
42232953 GCTCATGTGAGCCATGTAACGGGAAGC
1 GCTCACACGAGCCATATAACGGGAAGC
42232980 TTATACGAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
25 19 0.47
26 4 0.10
27 17 0.43
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.16
Consensus pattern (27 bp):
GCTCACACGAGCCATATAACGGGAAGC
Found at i:42234631 original size:24 final size:26
Alignment explanation
Indices: 42234604--42234662 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
42234594 AAGCTCATAT
*
42234604 GAGCCAATA-AT-AGGAAGCTCCAGA
1 GAGCCAATATATCAGGAAGCTCAAGA
*
42234628 GAGCC-ATATATCATGAAGCTCAAGA
1 GAGCCAATATATCAGGAAGCTCAAGA
42234653 GAGCCAATAT
1 GAGCCAATAT
42234663 TGAGATGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.10
24 7 0.23
25 16 0.53
26 4 0.13
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (26 bp):
GAGCCAATATATCAGGAAGCTCAAGA
Found at i:42237045 original size:27 final size:27
Alignment explanation
Indices: 42237014--42237191 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42237004 TAAATTGTAC
42237014 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42237041 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42237067 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42237095 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42237123 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42237150 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42237177 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42237192 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42237128 original size:82 final size:81
Alignment explanation
Indices: 42237015--42237170 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42237005 AAATTGTACA
* *
42237015 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42237079 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42237096 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42237161 TGCGAGTTGA
65 TGCGAATTGA
42237171 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42237182 original size:82 final size:81
Alignment explanation
Indices: 42237011--42237191 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42237001 GATTAAATTG
* *
42237011 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42237076 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42237092 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42237156 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42237174 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42237192 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42238243 original size:18 final size:18
Alignment explanation
Indices: 42238216--42238251 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42238206 AGCATCAGTA
42238216 TTGAAGCCCCGTGTAGGG
1 TTGAAGCCCCGTGTAGGG
*
42238234 TTGAATCCCCGTGTAGGG
1 TTGAAGCCCCGTGTAGGG
42238252 AGATATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (18 bp):
TTGAAGCCCCGTGTAGGG
Found at i:42245254 original size:27 final size:27
Alignment explanation
Indices: 42245223--42245400 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42245213 TAAATTGTAC
42245223 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42245250 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42245276 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42245304 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42245332 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42245359 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42245386 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42245401 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42245337 original size:82 final size:81
Alignment explanation
Indices: 42245224--42245379 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42245214 AAATTGTACA
* *
42245224 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42245288 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42245305 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42245370 TGCGAGTTGA
65 TGCGAATTGA
42245380 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42245391 original size:82 final size:81
Alignment explanation
Indices: 42245220--42245400 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42245210 GATTAAATTG
* *
42245220 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42245285 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42245301 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42245365 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42245383 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42245401 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42246525 original size:137 final size:137
Alignment explanation
Indices: 42246279--42246551 Score: 519
Period size: 137 Copynumber: 2.0 Consensus size: 137
42246269 TCAGATTTTT
*
42246279 GTGGGACAGGGCCAGAACGGTTTCTGGATTCCCTGCTCTGACTTTGGAAATTCATTATAAATTAA
1 GTGGGACAGGGCCAGAACGGTTTCTGGATTCCCTGCTCCGACTTTGGAAATTCATTATAAATTAA
*
42246344 CCAGAGATAATTAGGGTCTTACCATATATGTATAGATTCCTCTCTGAGTCTAGTTTTCATAGAAA
66 CCAGAGATAATTAGGGTCTTACCATATATGTATAGATTCCTCTCTAAGTCTAGTTTTCATAGAAA
42246409 CAAACGG
131 CAAACGG
42246416 GTGGGACAGGGCCAGAACGGTTTCTGGATTCCCTGCTCCGACTTTGGAAATTCATTATAAATTAA
1 GTGGGACAGGGCCAGAACGGTTTCTGGATTCCCTGCTCCGACTTTGGAAATTCATTATAAATTAA
*
42246481 CCAGAGATAATTAGGGTCTTACCATATATGTATAGATTTCTCTCTAAGTCTAGTTTTCATAGAAA
66 CCAGAGATAATTAGGGTCTTACCATATATGTATAGATTCCTCTCTAAGTCTAGTTTTCATAGAAA
42246546 CAAACG
131 CAAACG
42246552 ACATCAGTAT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (137 bp):
GTGGGACAGGGCCAGAACGGTTTCTGGATTCCCTGCTCCGACTTTGGAAATTCATTATAAATTAA
CCAGAGATAATTAGGGTCTTACCATATATGTATAGATTCCTCTCTAAGTCTAGTTTTCATAGAAA
CAAACGG
Found at i:42253582 original size:27 final size:27
Alignment explanation
Indices: 42253551--42253728 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42253541 TAAATTGTAC
42253551 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42253578 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42253604 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42253632 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42253660 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42253687 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42253714 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42253729 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42253665 original size:82 final size:81
Alignment explanation
Indices: 42253552--42253707 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42253542 AAATTGTACA
* *
42253552 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42253616 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42253633 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42253698 TGCGAGTTGA
65 TGCGAATTGA
42253708 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42253719 original size:82 final size:81
Alignment explanation
Indices: 42253548--42253728 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42253538 GATTAAATTG
* *
42253548 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42253613 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42253629 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42253693 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42253711 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42253729 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42258583 original size:4 final size:4
Alignment explanation
Indices: 42258569--42258599 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
42258559 CTAAATTGGA
42258569 AATT GAATT AATT AATT AATT AATT AATT AA
1 AATT -AATT AATT AATT AATT AATT AATT AA
42258600 AAGATCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:42262190 original size:45 final size:45
Alignment explanation
Indices: 42262126--42262495 Score: 566
Period size: 45 Copynumber: 8.2 Consensus size: 45
42262116 CGAACTTCGG
* *
42262126 GCCTAGTAGGCTATAATGCCGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
*
42262171 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTTGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
* *
42262216 GCCTAGCTGGCTATGATGCTGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
*
42262261 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTTGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
* *
42262306 GCCTAGCTGGCTATGATGCTGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
42262351 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
* *
42262396 GCCTAGCAGGCTATAATGCCGGTGAGATACTATTCGGG-CTTTCGA
1 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTT-GA
* * * * *
42262441 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TAATCAGGCC-TCGA
1 GCCTAGCAGGCTATGATGCCGGTGAGAT-ATTATTCGGGCCTTTGA
42262485 GCCTAGCAGGC
1 GCCTAGCAGGC
42262496 GAAATGCCGA
Statistics
Matches: 302, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
44 17 0.06
45 283 0.94
46 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
Found at i:42284667 original size:13 final size:13
Alignment explanation
Indices: 42284649--42284676 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42284639 GAAGCACGGT
42284649 TCACACGGGCGTG
1 TCACACGGGCGTG
42284662 TCACACGGGCGTG
1 TCACACGGGCGTG
42284675 TC
1 TC
42284677 CCTGCCGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (13 bp):
TCACACGGGCGTG
Found at i:42288281 original size:3 final size:3
Alignment explanation
Indices: 42288275--42288310 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
42288265 TTTTTCTCTT
42288275 TTA TTA TTA -TA TTA TTA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42288311 TACTAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:42288289 original size:11 final size:11
Alignment explanation
Indices: 42288275--42288306 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
42288265 TTTTTCTCTT
42288275 TTATTATTATA
1 TTATTATTATA
42288286 TTATTATTATA
1 TTATTATTATA
42288297 TTATTATTAT
1 TTATTATTAT
42288307 TATTTACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTATTATA
Found at i:42288294 original size:14 final size:15
Alignment explanation
Indices: 42288275--42288310 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
42288265 TTTTTCTCTT
42288275 TTATTATTA-TATTA
1 TTATTATTATTATTA
42288289 TTATTA-TATTATTA
1 TTATTATTATTATTA
42288303 TTATTATT
1 TTATTATT
42288311 TACTAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 17 0.85
15 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTATTATTATTA
Found at i:42288943 original size:7 final size:7
Alignment explanation
Indices: 42288931--42289042 Score: 52
Period size: 7 Copynumber: 15.7 Consensus size: 7
42288921 AGTAATTAAT
42288931 CTAAACC
1 CTAAACC
42288938 CTAAACC
1 CTAAACC
*
42288945 TCTTAACCC
1 -C-TAAACC
*
42288954 CT-ATCC
1 CTAAACC
*
42288960 CATAAACA
1 C-TAAACC
*
42288968 CTAAACA
1 CTAAACC
42288975 CTAAACC
1 CTAAACC
*
42288982 CTTAACC
1 CTAAACC
*
42288989 CTTAACAC
1 CTAAAC-C
42288997 C-AAACC
1 CTAAACC
*
42289003 CTTACACC
1 C-TAAACC
*
42289011 TTAAACTC
1 CTAAAC-C
*
42289019 C--AGCC
1 CTAAACC
*
42289024 CTAACCC
1 CTAAACC
42289031 CTAAACC
1 CTAAACC
42289038 CTAAA
1 CTAAA
42289043 TCATAATTCC
Statistics
Matches: 81, Mismatches: 14, Indels: 20
0.70 0.12 0.17
Matches are distributed among these distances:
5 2 0.02
6 8 0.10
7 54 0.67
8 12 0.15
9 5 0.06
ACGTcount: A:0.38, C:0.41, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:42289001 original size:21 final size:21
Alignment explanation
Indices: 42288971--42289014 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42288961 ATAAACACTA
*
42288971 AACACTAAACCCTTA-ACCCTT
1 AACACCAAACCCTTACA-CCTT
42288992 AACACCAAACCCTTACACCTT
1 AACACCAAACCCTTACACCTT
42289013 AA
1 AA
42289015 ACTCCAGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (21 bp):
AACACCAAACCCTTACACCTT
Found at i:42289393 original size:41 final size:41
Alignment explanation
Indices: 42289348--42289527 Score: 218
Period size: 41 Copynumber: 4.4 Consensus size: 41
42289338 GTTATATGAC
*
42289348 TTTTAGCGGCGTTTTTCCAAAAACACCGCTAATGTTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAACACCGCTAATGCTCTGGT
* *
42289389 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAACACCGCTAATGCTCTGGT
* * * **
42289430 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTATT
1 TTTTAGCGGCGTTTTTCCAAAAACACCGCTAATGCTCTGGT
* * * * * *
42289471 TTTTAGTGGCATTTTTTACTAAAGCACCGCTATTGCTCT-GT
1 TTTTAGCGGC-GTTTTTCCAAAAACACCGCTAATGCTCTGGT
42289512 TTTTAGCGGCGTTTTT
1 TTTTAGCGGCGTTTTT
42289528 GGTAAAACGT
Statistics
Matches: 122, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
40 5 0.04
41 95 0.78
42 22 0.18
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAACACCGCTAATGCTCTGGT
Found at i:42289557 original size:41 final size:41
Alignment explanation
Indices: 42289348--42289557 Score: 187
Period size: 41 Copynumber: 5.1 Consensus size: 41
42289338 GTTATATGAC
* * *
42289348 TTTTAGCGGCGTTTTTCCAAAAACACCGCTAATGTTCTG-G
1 TTTTAGCGGCGTTTTTACAAAAACGCCGCTAATGCTCTGTG
42289388 TTTTTAGCGGCG-TTTTACCAAAAACGCCGCTAATGCTCTG-G
1 -TTTTAGCGGCGTTTTTA-CAAAAACGCCGCTAATGCTCTGTG
* * *
42289429 TTTTTAGCGGCG-TTTTACCAAAAGCGCCGCTAATGCTCTATT
1 -TTTTAGCGGCGTTTTTA-CAAAAACGCCGCTAATGCTCTGTG
* * * * * *
42289471 TTTTAGTGGCATTTTTTACTAAAGCACCGCTATTGCTCTGT-
1 TTTTAGCGGC-GTTTTTACAAAAACGCCGCTAATGCTCTGTG
*** * *
42289512 TTTTAGCGGCGTTTTTGGTAAAACGTCGCTATTGCTCTGTG
1 TTTTAGCGGCGTTTTTACAAAAACGCCGCTAATGCTCTGTG
42289553 TTTTA
1 TTTTA
42289558 CAATTTTTGC
Statistics
Matches: 145, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
40 28 0.19
41 93 0.64
42 19 0.13
43 5 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTACAAAAACGCCGCTAATGCTCTGTG
Found at i:42292324 original size:30 final size:30
Alignment explanation
Indices: 42292290--42292350 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
42292280 TCCTTAACTC
42292290 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
42292320 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
42292350 A
1 A
42292351 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:42294960 original size:27 final size:27
Alignment explanation
Indices: 42294929--42295022 Score: 102
Period size: 27 Copynumber: 3.5 Consensus size: 27
42294919 TTAGTTTACC
* *
42294929 AAATTACTGAAATACCTTCGACTTGTA
1 AAATTACCGAAATACCTTCGATTTGTA
* * *
42294956 AAATTACCAAAATACC-CCGATTTATA
1 AAATTACCGAAATACCTTCGATTTGTA
*
42294982 AAATTACCCAAATATCCTT-GATTTGTA
1 AAATTACCGAAATA-CCTTCGATTTGTA
*
42295009 AAATTACTGAAATA
1 AAATTACCGAAATA
42295023 AGATAGAATT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 20 0.36
27 35 0.64
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (27 bp):
AAATTACCGAAATACCTTCGATTTGTA
Found at i:42295057 original size:27 final size:27
Alignment explanation
Indices: 42295027--42295180 Score: 200
Period size: 27 Copynumber: 5.7 Consensus size: 27
42295017 GAAATAAGAT
42295027 AGAATTACCATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* * *
42295054 AGAATTACCGTTTTATCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
*
42295081 AGAATTACCGTTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
** * *
42295108 AGAATTGTCGTTTTACCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
* * *
42295135 AGAATTACTATTTTACCATTGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
42295162 AGAATTACTATTTTACCCT
1 AGAATTACCATTTTACCCT
42295181 ATTACCGTTT
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 111 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (27 bp):
AGAATTACCATTTTACCCTCGATTTAC
Found at i:42295088 original size:54 final size:54
Alignment explanation
Indices: 42295025--42295265 Score: 252
Period size: 54 Copynumber: 4.7 Consensus size: 54
42295015 CTGAAATAAG
* * *
42295025 ATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTATCCTCGATTT
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTT
** *
42295079 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTGTCGTTTTACCCTCGATTT
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTT
** * * *
42295133 ATAGAATTACTATTTTACCATTGATTTACAGAATTACTATTTTA-CC-C-----
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTT
*
42295180 -T---ATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTT
** * * *
42295230 ATAGAATTATTGTTTTATCCTTGATTTACAAAATTA
1 ATAGAATTACCGTTTTACCCTCGATTTACAGAATTA
42295266 TTGAAATACC
Statistics
Matches: 152, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
43 33 0.22
44 2 0.01
45 1 0.01
46 1 0.01
51 1 0.01
52 1 0.01
53 2 0.01
54 111 0.73
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (54 bp):
ATAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTT
Found at i:42295219 original size:97 final size:97
Alignment explanation
Indices: 42295084--42295265 Score: 285
Period size: 97 Copynumber: 1.9 Consensus size: 97
42295074 GATTTATAGA
** *
42295084 ATTACCGTTTTACCCTCGATTTACAGAATTGTCGTTTTACCCTCGATTTATAGAATTACTATTTT
1 ATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACTATTTT
*
42295149 A-CCATTGATTTACAGAATTACTATTTTACCCT
66 ATCC-TTGATTTACAAAATTACTATTTTACCCT
* * *
42295181 ATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATTGTTTT
1 ATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACTATTTT
42295246 ATCCTTGATTTACAAAATTA
66 ATCCTTGATTTACAAAATTA
42295266 TTGAAATACC
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
97 75 0.97
98 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (97 bp):
ATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACTATTTT
ATCCTTGATTTACAAAATTACTATTTTACCCT
Found at i:42295231 original size:27 final size:27
Alignment explanation
Indices: 42295181--42295238 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
42295171 ATTTTACCCT
*
42295181 ATTACCGTTTTACCCTCGATTTATAGA
1 ATTACCATTTTACCCTCGATTTATAGA
42295208 ATTACCATTTTACCCTCGATTTATAGA
1 ATTACCATTTTACCCTCGATTTATAGA
42295235 ATTA
1 ATTA
42295239 TTGTTTTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (27 bp):
ATTACCATTTTACCCTCGATTTATAGA
Found at i:42295245 original size:27 final size:27
Alignment explanation
Indices: 42295187--42295268 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
42295177 CCCTATTACC
**
42295187 GTTTTACCCTCGATTTATAGAATTACC
1 GTTTTACCCTCGATTTATAGAATTATT
*
42295214 ATTTTACCCTCGATTTATAGAATTATT
1 GTTTTACCCTCGATTTATAGAATTATT
* * * *
42295241 GTTTTATCCTTGATTTACAAAATTATT
1 GTTTTACCCTCGATTTATAGAATTATT
42295268 G
1 G
42295269 AAATACCCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (27 bp):
GTTTTACCCTCGATTTATAGAATTATT
Found at i:42295285 original size:124 final size:124
Alignment explanation
Indices: 42295057--42295293 Score: 316
Period size: 124 Copynumber: 1.9 Consensus size: 124
42295047 GATTTACAGA
* * *
42295057 ATTACCGTTTTATCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTGTCGTTTT
1 ATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTT
* * ** *
42295122 ACCCTCGATTTATAGAATTACTATTTTACCATTGATTTACAGAATTACTATTTTACCCT
66 ACCCTCGATTTACAAAATTACTATAATACCATTGATTTACAAAATTACTATTTTACCCT
* *
42295181 ATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATTGTTTT
1 ATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTT
* * * *
42295246 ATCCTTGATTTACAAAATTATTGA-AATACCCTT-AGTTTACAAAATTAC
66 ACCCTCGATTTACAAAATTACT-ATAATACCATTGA-TTTACAAAATTAC
42295294 CAAAATACCC
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
123 1 0.01
124 95 0.98
125 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (124 bp):
ATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGTTTT
ACCCTCGATTTACAAAATTACTATAATACCATTGATTTACAAAATTACTATTTTACCCT
Found at i:42295299 original size:27 final size:27
Alignment explanation
Indices: 42295269--42295412 Score: 121
Period size: 27 Copynumber: 5.4 Consensus size: 27
42295259 AAAATTATTG
*
42295269 AAATACCCTTAGTTTACAAAATTACCA
1 AAATACCCTTAGTTTATAAAATTACCA
* * *
42295296 AAATACCC-TCGATCAGTAAAATTACCA
1 AAATACCCTTAGTTTA-TAAAATTACCA
* * * *
42295323 AAATACCCCTGGTTTGTAAAATTACTA
1 AAATACCCTTAGTTTATAAAATTACCA
* * * *
42295350 AAATACCCCTGGTTTGTAAAATTACTA
1 AAATACCCTTAGTTTATAAAATTACCA
* * * *
42295377 AAATACCCTGA-CTTGTAAAATTACCG
1 AAATACCCTTAGTTTATAAAATTACCA
42295403 AAATACCCTT
1 AAATACCCTT
42295413 GTAGGGTAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
26 25 0.25
27 71 0.72
28 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATACCCTTAGTTTATAAAATTACCA
Found at i:42295320 original size:151 final size:151
Alignment explanation
Indices: 42295030--42295308 Score: 326
Period size: 151 Copynumber: 1.8 Consensus size: 151
42295020 ATAAGATAGA
* *
42295030 ATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTATCCTCGATTTATAGAATTACCGTTTT
1 ATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTT
* * *** * * * * *** * *
42295095 ACCCTCGATTTACAGAATTGTCGTTTTACCCTCGATTTATAGAATTACTATTTTACCATTGATTT
66 ACCCTCGATTTACAAAATTATCGAAATACCCTAGATTTACAAAATTACCAAAATACCATCGATGT
42295160 ACAGAATTACTATTTTACCCT
131 ACAGAATTACTATTTTACCCT
* * **
42295181 ATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATTGTTTT
1 ATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTT
* * * *
42295246 ATCCTTGATTTACAAAATTATTGAAATACCCTTAG-TTTACAAAATTACCAAAATACCCTCGAT
66 ACCCTCGATTTACAAAATTATCGAAATACCC-TAGATTTACAAAATTACCAAAATACCATCGAT
42295309 CAGTAAAATT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
151 102 0.98
152 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (151 bp):
ATTACCATTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTT
ACCCTCGATTTACAAAATTATCGAAATACCCTAGATTTACAAAATTACCAAAATACCATCGATGT
ACAGAATTACTATTTTACCCT
Found at i:42295392 original size:26 final size:26
Alignment explanation
Indices: 42295286--42295411 Score: 153
Period size: 27 Copynumber: 4.7 Consensus size: 26
42295276 CTTAGTTTAC
**
42295286 AAAATTACCAAAATACCCTCGATCAGT
1 AAAATTACCAAAATACCCT-GATTTGT
*
42295313 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATA-CCCTGATTTGT
* *
42295340 AAAATTACTAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATA-CCCTGATTTGT
* *
42295367 AAAATTACTAAAATACCCTGACTTGT
1 AAAATTACCAAAATACCCTGATTTGT
*
42295393 AAAATTACCGAAATACCCT
1 AAAATTACCAAAATACCCT
42295412 TGTAGGGTAG
Statistics
Matches: 90, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
26 26 0.29
27 60 0.67
28 4 0.04
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTGATTTGT
Found at i:42295434 original size:27 final size:27
Alignment explanation
Indices: 42295395--42295652 Score: 385
Period size: 27 Copynumber: 9.6 Consensus size: 27
42295385 TGACTTGTAA
*
42295395 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42295422 AATTACC-AGAATACCCCTGTAAGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
42295449 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42295476 AATTATC-ACAATACCCCTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
* *
42295503 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42295530 AATTACCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42295557 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
42295584 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
42295611 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
42295638 AATTATCGAGATACC
1 AATTACCGAAATACC
42295653 TTCTGAGGTA
Statistics
Matches: 212, Mismatches: 15, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
26 2 0.01
27 209 0.99
28 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:42303484 original size:23 final size:23
Alignment explanation
Indices: 42303458--42303504 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
42303448 TATTCTATTG
*
42303458 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
42303481 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
42303504 T
1 T
42303505 AATGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:42304885 original size:13 final size:13
Alignment explanation
Indices: 42304862--42304899 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
42304852 TTTAATTTTA
42304862 TTTTA-TTTTATT
1 TTTTATTTTTATT
42304874 TTTTATTTTTATT
1 TTTTATTTTTATT
* *
42304887 TTATGTTTTTATT
1 TTTTATTTTTATT
42304900 AATTTCACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:42304885 original size:18 final size:19
Alignment explanation
Indices: 42304857--42304899 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
42304847 TGATGTTTAA
42304857 TTTTA-TTTTATTTTAT-T
1 TTTTATTTTTATTTTATGT
42304874 TTTTATTTTTATTTTATGT
1 TTTTATTTTTATTTTATGT
42304893 TTTTATT
1 TTTTATT
42304900 AATTTCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.21
18 11 0.46
19 8 0.33
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTATTTTATGT
Found at i:42304904 original size:23 final size:23
Alignment explanation
Indices: 42304853--42304904 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
42304843 ATAATGATGT
*
42304853 TTAA-TTTTATTTTATTTTATTT
1 TTAATTTTTATTTTATTTTATTA
*
42304875 TTTATTTTTATTTTATGTTT-TTA
1 TTAATTTTTATTTTAT-TTTATTA
42304898 TTAATTT
1 TTAATTT
42304905 CACCTTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 3 0.12
23 19 0.76
24 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (23 bp):
TTAATTTTTATTTTATTTTATTA
Found at i:42306876 original size:13 final size:13
Alignment explanation
Indices: 42306858--42306898 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
42306848 AAAGCACGAC
42306858 TCACACGGGCGTG
1 TCACACGGGCGTG
*
42306871 TCACACAGGCGTG
1 TCACACGGGCGTG
*
42306884 TCACACGAGCGTG
1 TCACACGGGCGTG
42306897 TC
1 TC
42306899 CCTGCCAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.17
Consensus pattern (13 bp):
TCACACGGGCGTG
Found at i:42314475 original size:10 final size:11
Alignment explanation
Indices: 42314456--42314480 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42314446 TAAAACAACC
42314456 AAAAGAAAAAA
1 AAAAGAAAAAA
42314467 AAAAGAAAAAA
1 AAAAGAAAAAA
42314478 AAA
1 AAA
42314481 TCAGATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:42315501 original size:14 final size:13
Alignment explanation
Indices: 42315476--42315509 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
42315466 TTTTTTTTAC
42315476 TTTAA-TTTTTTG
1 TTTAATTTTTTTG
42315488 TTTAATTTTCTTTG
1 TTTAATTTT-TTTG
42315502 TTTAATTT
1 TTTAATTT
42315510 AATCATGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 3 0.15
14 12 0.60
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTAATTTTTTTG
Found at i:42321009 original size:23 final size:22
Alignment explanation
Indices: 42320965--42321045 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
42320955 GTTAACAATA
*
42320965 ATAATAAT-ATATGTTAGTAAGG
1 ATAATAATAATATG-TAGAAAGG
42320987 ATAATAATAATATGTAGAAAAGG
1 ATAATAATAATATGTAG-AAAGG
** *
42321010 GGAATAATAATA-GTAG-TAGG
1 ATAATAATAATATGTAGAAAGG
*
42321030 AGTAATAATACTATGT
1 A-TAATAATAATATGT
42321046 TAATAAGAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.06
21 9 0.19
22 17 0.35
23 19 0.40
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.31
Consensus pattern (22 bp):
ATAATAATAATATGTAGAAAGG
Found at i:42321126 original size:3 final size:3
Alignment explanation
Indices: 42321046--42321446 Score: 150
Period size: 3 Copynumber: 136.3 Consensus size: 3
42321036 AATACTATGT
* * * * * *
42321046 TAA TAA GAA TAA TAG TAA TAG TAA TAC TAA AAA GGTAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA TAA
* * * * * *
42321093 AAA TAA AAA TAA AAA TAA AAA TAA TAG TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * ***
42321141 TAA TAG TAA TAA -AA CAGA GAA AAA CAA CAA -CA TAA CGG TAA -AA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
42321184 GTAA TAA TAA TAA TAA TTA TAA T-A TAA -AA TTAA TGA T-A TAA TAA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* ** * *
42321228 T-G TAA TAA TAA TAA GCA -AA TAA GT-A TAA AAA GAA -AA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * * ** * * ** *
42321269 TCA TAG TAA TAA TAG TTG TAG TAA TAA TAA TAG TAA GGA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
42321317 TAA T-A TAA AAA TGA TAG TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
42321363 TAA TAA TAA TGAA -AG TAG TGGA -AA TAA TGA TAG TAA T-A TAA TAG
1 TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
42321407 TAG GAA TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
42321447 GGCAAAACAG
Statistics
Matches: 289, Mismatches: 85, Indels: 48
0.68 0.20 0.11
Matches are distributed among these distances:
2 26 0.09
3 252 0.87
4 9 0.03
5 2 0.01
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:42328142 original size:20 final size:19
Alignment explanation
Indices: 42328117--42328158 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
42328107 CTTTTTTATC
42328117 CTTCTCTTATCTCTTCCCCT
1 CTTCTCTTATCT-TTCCCCT
* *
42328137 CTTCTCTTTTCTTTCTCCT
1 CTTCTCTTATCTTTCCCCT
42328156 CTT
1 CTT
42328159 AATTCTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (19 bp):
CTTCTCTTATCTTTCCCCT
Found at i:42329089 original size:27 final size:27
Alignment explanation
Indices: 42329058--42329115 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
42329048 ATTAAACTAT
* *
42329058 CCCTAAGTATG-AAAATTACCGTTTTAC
1 CCCTAAG-ATGCAAAATAACCGTTATAC
*
42329085 CCCT-AGGTGCAAAATAACCGTTATAC
1 CCCTAAGATGCAAAATAACCGTTATAC
42329111 CCCTA
1 CCCTA
42329116 GGGTTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 2 0.08
26 20 0.77
27 4 0.15
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (27 bp):
CCCTAAGATGCAAAATAACCGTTATAC
Found at i:42333485 original size:35 final size:35
Alignment explanation
Indices: 42333446--42333562 Score: 128
Period size: 35 Copynumber: 3.3 Consensus size: 35
42333436 TACTCTTTGT
* *
42333446 TTGGCTTGTTTCGATTGGACTAGCTCTTATAAGCA
1 TTGGCGTGTTTCGATTGGACTAGCTCTTATGAGCA
* * * *
42333481 TTGGCGTGTTTCGGTTGAACTGGTTCTTATGAGCA
1 TTGGCGTGTTTCGATTGGACTAGCTCTTATGAGCA
* *
42333516 TTGGCGTG-TTCTAGTTGGACTAGCTCTTGTGAGCA
1 TTGGCGTGTTTCGA-TTGGACTAGCTCTTATGAGCA
*
42333551 TTTGCTGTGTTT
1 TTGGC-GTGTTT
42333563 TGGAGGGATT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
34 3 0.05
35 58 0.88
36 3 0.05
37 2 0.03
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.42
Consensus pattern (35 bp):
TTGGCGTGTTTCGATTGGACTAGCTCTTATGAGCA
Found at i:42341817 original size:25 final size:25
Alignment explanation
Indices: 42341787--42341836 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
42341777 ATGATGGTAC
*
42341787 ATGATATAT-TGATATATTGAAATGG
1 ATGATATATGT-ATATAATGAAATGG
42341812 ATGATATATGTATATAATGAAATGG
1 ATGATATATGTATATAATGAAATGG
42341837 TAAGATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (25 bp):
ATGATATATGTATATAATGAAATGG
Found at i:42343223 original size:22 final size:23
Alignment explanation
Indices: 42343198--42343248 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
42343188 GGTGCCTTTT
*
42343198 AAGGGCTTAT-GTACATG-TGCAA
1 AAGGGATTATAGTACATGTTG-AA
42343220 AAGGGATTATAGGTACATGTTGAA
1 AAGGGATTATA-GTACATGTTGAA
42343244 AAGGG
1 AAGGG
42343249 TGAGAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 9 0.36
24 14 0.56
25 2 0.08
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.25
Consensus pattern (23 bp):
AAGGGATTATAGTACATGTTGAA
Found at i:42345698 original size:19 final size:21
Alignment explanation
Indices: 42345655--42345704 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 21
42345645 TGTCCCTTTT
42345655 TGCATT-CATTTCATTCATCA
1 TGCATTACATTTCATTCATCA
*
42345675 -ACATTACATTTCA-TCAT-A
1 TGCATTACATTTCATTCATCA
*
42345693 TGCATTAAATTT
1 TGCATTACATTT
42345705 TAGAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.04
19 17 0.68
20 7 0.28
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (21 bp):
TGCATTACATTTCATTCATCA
Found at i:42349904 original size:74 final size:74
Alignment explanation
Indices: 42349818--42349972 Score: 292
Period size: 74 Copynumber: 2.1 Consensus size: 74
42349808 TATCTATGAC
42349818 AAATCAATAAACAATTACCACATTTAACATAATAATCCATTTTCAATCTCAATTTCCAAATACAT
1 AAATCAATAAACAATTACCACATTTAACATAATAATCCATTTTCAATCTCAATTTCCAAATACAT
*
42349883 CCGTCCATA
66 CCATCCATA
42349892 AAATCAATAAACAATTACCACATTTAACATAATAATCCATTTTCAATCTCAATTTCCAAATACAT
1 AAATCAATAAACAATTACCACATTTAACATAATAATCCATTTTCAATCTCAATTTCCAAATACAT
42349957 CCATCCATA
66 CCATCCATA
*
42349966 ATATCAA
1 AAATCAA
42349973 GCATATCTCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.31
Consensus pattern (74 bp):
AAATCAATAAACAATTACCACATTTAACATAATAATCCATTTTCAATCTCAATTTCCAAATACAT
CCATCCATA
Found at i:42351151 original size:43 final size:42
Alignment explanation
Indices: 42350996--42351170 Score: 131
Period size: 43 Copynumber: 4.1 Consensus size: 42
42350986 TCACACATAT
* * *
42350996 CATA-CAATGCCAACGTCCCAGACGTGGTTTTACATGTAATCA
1 CATATCAATGCCAATGTCCCAGACGTGGTCTTACACG-AATCA
* * * * * *
42351038 TATCTCGATGCCACTGTCTCAGATAG-GGTCTTACACGAATCA
1 CATATCAATGCCAATGTCCCAGA-CGTGGTCTTACACGAATCA
* ** * * *
42351080 AATA-CGGTGCCGATGTCCCGGACATGGTCTTACACGTAATCA
1 CATATCAATGCCAATGTCCCAGACGTGGTCTTACACG-AATCA
** *
42351122 CATATCAATGCCAATGTCCCAGGTGTGGTCTTACATGAATACA
1 CATATCAATGCCAATGTCCCAGACGTGGTCTTACACGAAT-CA
42351165 CATATC
1 CATATC
42351171 GAAAATCCTA
Statistics
Matches: 100, Mismatches: 27, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
41 24 0.24
42 20 0.20
43 55 0.55
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (42 bp):
CATATCAATGCCAATGTCCCAGACGTGGTCTTACACGAATCA
Found at i:42354115 original size:79 final size:82
Alignment explanation
Indices: 42354004--42354188 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
42353994 GCTACTCGTT
* *
42354004 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
42354067 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
42354084 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
42354147 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
42354164 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42354189 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:42354188 original size:40 final size:40
Alignment explanation
Indices: 42353985--42354188 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
42353975 CGGAATTTAA
** *
42353985 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42354025 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42354065 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42354104 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42354144 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42354184 CCGGA
1 CCGGA
42354189 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42362090 original size:79 final size:79
Alignment explanation
Indices: 42361979--42362202 Score: 301
Period size: 79 Copynumber: 2.8 Consensus size: 79
42361969 GCTACTCGTT
* * *
42361979 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
42362044 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
42362059 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
42362122 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
42362137 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
42362201 GA
64 GA
42362203 CATCATTCAA
Statistics
Matches: 129, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
78 36 0.28
79 59 0.46
80 34 0.26
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:42362093 original size:39 final size:40
Alignment explanation
Indices: 42361979--42362202 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
42361969 GCTACTCGTT
* *
42361979 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
42362019 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
42362059 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
42362098 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
42362137 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
42362178 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42362203 CATCATTCAA
Statistics
Matches: 166, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 77 0.46
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:42372055 original size:47 final size:48
Alignment explanation
Indices: 42371904--42372162 Score: 164
Period size: 47 Copynumber: 5.5 Consensus size: 48
42371894 TGATTTGTGC
* * * *
42371904 GCCAGTGTAAGACATGTCTGGGACATGCTTCAG-C-C-ACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATGA-GATA
* * * *
42371950 GCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATGGAGATGAG-T-
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGACATGAGATA
** *
42371998 GCCAAAGTAAGACATGTTTGGGACATGCATCGGCCTCGACA-GAGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATGAGATA
* * * * * * **
42372045 GCCAGTGTAAGACGTGTCTGGGACACGCATTGG-AT-AAGATTTG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATGAGATA
* * * * *
42372089 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CACG-CATATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACAT-GA-GATA
42372137 GCCAGTGTAAGATCATGTCTGGGACA
1 GCCAGTGTAAGA-CATGTCTGGGACA
42372163 ACGCATCTGT
Statistics
Matches: 161, Mismatches: 38, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
44 30 0.19
45 7 0.04
46 27 0.17
47 54 0.34
48 25 0.16
49 13 0.08
50 1 0.01
51 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (48 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACATGAGATA
Found at i:42374676 original size:26 final size:26
Alignment explanation
Indices: 42374647--42374754 Score: 146
Period size: 26 Copynumber: 4.2 Consensus size: 26
42374637 TGGTACAAAT
42374647 TGATAATGGGTTAGGTAAAAGTTCCA
1 TGATAATGGGTTAGGTAAAAGTTCCA
* *
42374673 TGATAATGGATTAGGTAGATA-TTCCA
1 TGATAATGGGTTAGGTA-AAAGTTCCA
* *
42374699 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAAAGTTCCA
* *
42374725 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAAAGTTCCA
42374751 TGAT
1 TGAT
42374755 GGGCATTTCA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
25 1 0.01
26 69 0.96
27 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAAAGTTCCA
Found at i:42374709 original size:52 final size:52
Alignment explanation
Indices: 42374647--42374754 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
42374637 TGGTACAAAT
*
42374647 TGATAATGGGTTAGGTAAAAGTTCCATGATAATGGATTAGGTAGATATTCCA
1 TGATAATGGGTTAGGTAAAAGTTCCATGATAATGGATTAGGTAAATATTCCA
* * * *
42374699 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAAAGTTCCATGATAATGGATTAGGTAAATATTCCA
42374751 TGAT
1 TGAT
42374755 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAAAGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:42377154 original size:44 final size:44
Alignment explanation
Indices: 42377076--42377550 Score: 373
Period size: 44 Copynumber: 10.8 Consensus size: 44
42377066 TACCATAGTG
* * * *
42377076 AATCTTATCTCCTTGAAA-TTGCAGTGGAGTAGATTAAAGCTATA
1 AATCTTATCTCCCT-AAAGTTGCAGTGGAGCAGATTAAAGCCACA
* *
42377120 AATCTAATCTCCCTAAAGTTACAGTAGG-GCAGATTAAAGCCACA
1 AATCTTATCTCCCTAAAGTTGCAGT-GGAGCAGATTAAAGCCACA
** * * *
42377164 AGGCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAA-CCACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AAAGCCACA
* * ** * * * * *
42377208 AGTCTTATTTCTTTGAAGTTGCAGTGGAACGGATTGAAGCTACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * *
42377252 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * * *
42377296 CATCTTCTCTCCCTGAAGTTACAGTGGAGCAGATTAATGCCACG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * *
42377340 AATCTAATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
* *
42377384 AATCTTATCTCCTTGAAA-TTGCAGTGGAGCAGATTAAAACCACA
1 AATCTTATCTCCCT-AAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * * ** *
42377428 AATCTAATCTCGCTAAGGTTGAAGTGGAGCAGATTGAAGTTACG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * * * * * ** *
42377472 AACCTTATCTCCCTGAAGTTACAATGTAGTAGATTGAAGGAACT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
* * * *
42377516 AATTTTATATCCCTAAAGTTACAATGGAGCAGATT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT
42377551 GAAATAACAA
Statistics
Matches: 341, Mismatches: 83, Indels: 14
0.78 0.19 0.03
Matches are distributed among these distances:
43 9 0.03
44 324 0.95
45 8 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
Found at i:42377315 original size:132 final size:132
Alignment explanation
Indices: 42377075--42377550 Score: 448
Period size: 132 Copynumber: 3.6 Consensus size: 132
42377065 CTACCATAGT
* * * * *
42377075 GAATCTTATCTCCTTGAAATTGCAGTGGAGTAGATTAAAGCTATAAATCTAATCTCCCTAAAGTT
1 GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTAAAGTT
* * * *
42377140 ACAGTAGG-GCAGATTAAAGCCACAAGGCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAA-A
66 GCAGT-GGAGCAGATTAAAGCCACAA-TCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAATA
42377203 CCAC
129 CCAC
* * * *
42377207 -AAGTCTTATTTCTTTGAAGTTGCAGTGGAACGGATTGAAGCTACAAATCTTATCTCCCTAAAGT
1 GAA-TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTAAAGT
* * * *
42377271 TGCAGTGGAGTAGATTGAAGCTACACATCTTCTCTCCCTGAAGTT-ACAGTGGAGCAGATT-AAT
65 TGCAGTGGAGCAGATTAAAGCCACA-ATCTTATCTCCCTGAAGTTGA-AGTGGAGCAGATTGAAT
*
42377334 GCCAC
128 ACCAC
* * * * *
42377339 GAATCTAATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCTTGAAA-T
1 GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCT-AAAGT
* * *
42377403 TGCAGTGGAGCAGATTAAAACCACAAATCTAATCTCGCT-AAGGTTGAAGTGGAGCAGATTGAAG
65 TGCAGTGGAGCAGATTAAAGCCAC-AATCTTATCTCCCTGAA-GTTGAAGTGGAGCAGATTGAA-
*
42377467 T--TAC
127 TACCAC
* * * * * * ** * * *
42377471 GAACCTTATCTCCCTGAAGTTACAATGTAGTAGATTGAAGGAACTAATTTTATATCCCTAAAGTT
1 GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTAAAGTT
* *
42377536 ACAATGGAGCAGATT
66 GCAGTGGAGCAGATT
42377551 GAAATAACAA
Statistics
Matches: 280, Mismatches: 51, Indels: 26
0.78 0.14 0.07
Matches are distributed among these distances:
131 11 0.04
132 258 0.92
133 10 0.04
134 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (132 bp):
GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTAAAGTT
GCAGTGGAGCAGATTAAAGCCACAATCTTATCTCCCTGAAGTTGAAGTGGAGCAGATTGAATACC
AC
Found at i:42377579 original size:44 final size:44
Alignment explanation
Indices: 42377305--42377579 Score: 111
Period size: 44 Copynumber: 6.2 Consensus size: 44
42377295 ACATCTTCTC
* * * * *
42377305 TCCCTGAAGTTACAGTGGAGCAGATT-AATGCCACGAAT-CTAATC
1 TCCCTGAAGTTACAATGGAGCAGATTGAAAG-AACAAATCCT-ATA
* ** * * * *
42377349 TCCCTAAAGTTGTAGTGGAGCAGATTG-AAGCTACAAATCTTATC
1 TCCCTGAAGTTACAATGGAGCAGATTGAAAG-AACAAATCCTATA
* * * * * **
42377393 TCCTTGAAATTGCAGTGGAGCAGATTAAAACCACAAAT-CTA-A
1 TCCCTGAAGTTACAATGGAGCAGATTGAAAGAACAAATCCTATA
* * * *
42377435 TCTCGCT-AAGGTTGA-AGTGGAGCAGATTG-AAGTTACGAA-CCTTATC
1 TC-C-CTGAA-GTT-ACAATGGAGCAGATTGAAAG-AACAAATCC-TATA
* * * * **
42377481 TCCCTGAAGTTACAATGTAGTAGATTGAAGGAACTAATTTTATA
1 TCCCTGAAGTTACAATGGAGCAGATTGAAAGAACAAATCCTATA
* *
42377525 TCCCTAAAGTTACAATGGAGCAGATTGAAATAACAAATCCTATA
1 TCCCTGAAGTTACAATGGAGCAGATTGAAAGAACAAATCCTATA
42377569 -CCTCTGAAGTT
1 TCC-CTGAAGTT
42377580 GCAGTGGGTT
Statistics
Matches: 173, Mismatches: 42, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
42 2 0.01
43 10 0.06
44 149 0.86
45 10 0.06
46 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (44 bp):
TCCCTGAAGTTACAATGGAGCAGATTGAAAGAACAAATCCTATA
Done.