Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 58 of 328
Found at i:16263539 original size:27 final size:27
Alignment explanation
Indices: 16263509--16263569 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
16263499 GAAATCAGTA
*
16263509 TAGTCTGAT-AGGACAATAAATATAAGG
1 TAGTCT-ATCAGGACAATAAACATAAGG
* * *
16263536 TAGTCTATCGGGACAGTAAACATAGGG
1 TAGTCTATCAGGACAATAAACATAAGG
16263563 TAGTCTA
1 TAGTCTA
16263570 CCGAGACAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (27 bp):
TAGTCTATCAGGACAATAAACATAAGG
Found at i:16263607 original size:27 final size:27
Alignment explanation
Indices: 16263519--16263609 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 27
16263509 TAGTCTGATA
* * *
16263519 GGACAATAAATATAAGGTAGTCTATCG
1 GGACAGTAAACATAGGGTAGTCTATCG
*
16263546 GGACAGTAAACATAGGGTAGTCTACCG
1 GGACAGTAAACATAGGGTAGTCTATCG
* * * *
16263573 AGACAGTAACCATGGGGTAGTCTGTCG
1 GGACAGTAAACATAGGGTAGTCTATCG
*
16263600 GGATAGTAAA
1 GGACAGTAAA
16263610 TACGAGGATT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.29, T:0.22
Consensus pattern (27 bp):
GGACAGTAAACATAGGGTAGTCTATCG
Found at i:16264846 original size:42 final size:43
Alignment explanation
Indices: 16264773--16264855 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
16264763 GAATTGAGTA
* **
16264773 CTTCGTTTACTCGATGTCATAGTTCAACTATGGTCTTACACAT
1 CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACACAT
*
16264816 CTTCATTTA-TCGATGTCATAGCCCAGCTATGGTCTTACAC
1 CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACAC
16264856 GAATCACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.78
43 8 0.22
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (43 bp):
CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACACAT
Found at i:16264897 original size:46 final size:47
Alignment explanation
Indices: 16264826--16264945 Score: 134
Period size: 47 Copynumber: 2.6 Consensus size: 47
16264816 CTTCATTTAT
* * * *
16264826 CGATGTCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAA
1 CGATGTCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAA
* * * * * *
16264872 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGTCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAA
*
16264919 CGATATCATATCCCAGATATGGTCTTA
1 CGATGTCATATCCCAGATATGGTCTTA
16264946 TACGGAAATC
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
46 25 0.42
47 35 0.58
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
CGATGTCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAA
Found at i:16265010 original size:31 final size:31
Alignment explanation
Indices: 16264975--16265146 Score: 206
Period size: 31 Copynumber: 5.5 Consensus size: 31
16264965 TTGTAGCCGA
*
16264975 AGCTACCACTATTCACTGATCAGGTAGCTAG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
* *
16265006 AGCTACCATTTTTCACTGATCAGGTAG-TCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCT-AG
* **
16265037 AGCTACCATTTTTCACTGATCAATTAGC-AG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
* *
16265067 AAGCTACCACTTTTCACTGATCAGGTAGCAAA
1 -AGCTACCACTTTTCACTGATCAGGTAGCTAG
*
16265099 AGCTACCACTTTTCACTGATCAGGTAGC-CG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
*
16265129 AAACTACCACTTTTCACT
1 -AGCTACCACTTTTCACT
16265147 TGTCATTTGT
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.02
31 120 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGCTAG
Found at i:16265052 original size:62 final size:62
Alignment explanation
Indices: 16264974--16265146 Score: 233
Period size: 62 Copynumber: 2.8 Consensus size: 62
16264964 CTTGTAGCCG
* * *
16264974 AAGCTACCACTATTCACTGATCAGGTAGCTAG-AGCTACCATTTTTCACTGATCAGGTAGTC-G
1 AAGCTACCACTTTTCACTGATCAGGTAGC-AGAAGCTACCACTTTTCACTGATCAGGTAG-CAA
* * **
16265036 GAGCTACCATTTTTCACTGATCAATTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
1 AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
* *
16265098 AAGCTACCACTTTTCACTGATCAGGTAGCCGAAACTACCACTTTTCACT
1 AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACT
16265147 TGTCATTTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
61 3 0.03
62 93 0.97
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (62 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
Found at i:16265136 original size:93 final size:93
Alignment explanation
Indices: 16264968--16265146 Score: 277
Period size: 93 Copynumber: 1.9 Consensus size: 93
16264958 TTGTCACTTG
* * * *
16264968 TAGCCGAAGCTACCACTATTCACTGATCAGGTAGCTAGAGCTACCATTTTTCACTGATCAGGTAG
1 TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
* * * *
16265033 TCGGAGCTACCATTTTTCACTGATCAAT
66 CCGAAACTACCACTTTTCACTGATCAAT
*
16265061 TAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
1 TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
16265126 CCGAAACTACCACTTTTCACT
66 CCGAAACTACCACTTTTCACT
16265147 TGTCATTTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (93 bp):
TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
CCGAAACTACCACTTTTCACTGATCAAT
Found at i:16265198 original size:51 final size:50
Alignment explanation
Indices: 16265122--16265217 Score: 129
Period size: 51 Copynumber: 1.9 Consensus size: 50
16265112 CACTGATCAG
* * *
16265122 GTAGCCGAAACTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAACTACCACTTATCACTT-TCACTTATCCTTGATCAGATAAGT
* **
16265173 GTAGCCGAAGCTATTACTTATCACTTTCACTTATCCTTGATCAGA
1 GTAGCCGAAACTACCACTTATCACTTTCACTTATCCTTGATCAGA
16265218 AAATGGATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 17 0.44
51 22 0.56
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (50 bp):
GTAGCCGAAACTACCACTTATCACTTTCACTTATCCTTGATCAGATAAGT
Found at i:16267716 original size:42 final size:43
Alignment explanation
Indices: 16267643--16267725 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
16267633 GAATTGAGTA
* **
16267643 CTTCGTTTACTCGATGTCATAGTTCAACTATGGTCTTACACAT
1 CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACACAT
*
16267686 CTTCATTTA-TCGATGTCATAGCCCAGCTATGGTCTTACAC
1 CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACAC
16267726 GAATCACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.78
43 8 0.22
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (43 bp):
CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACACAT
Found at i:16267767 original size:46 final size:46
Alignment explanation
Indices: 16267696--16267821 Score: 144
Period size: 47 Copynumber: 2.7 Consensus size: 46
16267686 CTTCATTTAT
* * * * *
16267696 CGATGTCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAA
1 CGATGTCATATCCCAGATATGGTCTTATACGAAGCACATATCACAA
* * * * *
16267742 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGTCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAA
*
16267789 CGATATCATATCCCAGATATGGTCTTATACGAA
1 CGATGTCATATCCCAGATATGGTCTTATACGAA
16267822 ATCATTTGTC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
46 27 0.42
47 38 0.58
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (46 bp):
CGATGTCATATCCCAGATATGGTCTTATACGAAGCACATATCACAA
Found at i:16267879 original size:31 final size:31
Alignment explanation
Indices: 16267844--16268015 Score: 206
Period size: 31 Copynumber: 5.5 Consensus size: 31
16267834 TTGTAGCCGA
*
16267844 AGCTACCACTATTCACTGATCAGGTAGCTAG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
* *
16267875 AGCTACCATTTTTCACTGATCAGGTAG-TCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCT-AG
* **
16267906 AGCTACCATTTTTCACTGATCAATTAGC-AG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
* *
16267936 AAGCTACCACTTTTCACTGATCAGGTAGCAAA
1 -AGCTACCACTTTTCACTGATCAGGTAGCTAG
*
16267968 AGCTACCACTTTTCACTGATCAGGTAGC-CG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
*
16267998 AAACTACCACTTTTCACT
1 -AGCTACCACTTTTCACT
16268016 TGTCATTTGT
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
30 2 0.02
31 120 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGCTAG
Found at i:16267921 original size:62 final size:62
Alignment explanation
Indices: 16267843--16268015 Score: 233
Period size: 62 Copynumber: 2.8 Consensus size: 62
16267833 CTTGTAGCCG
* * *
16267843 AAGCTACCACTATTCACTGATCAGGTAGCTAG-AGCTACCATTTTTCACTGATCAGGTAGTC-G
1 AAGCTACCACTTTTCACTGATCAGGTAGC-AGAAGCTACCACTTTTCACTGATCAGGTAG-CAA
* * **
16267905 GAGCTACCATTTTTCACTGATCAATTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
1 AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
* *
16267967 AAGCTACCACTTTTCACTGATCAGGTAGCCGAAACTACCACTTTTCACT
1 AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACT
16268016 TGTCATTTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
61 3 0.03
62 93 0.97
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (62 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
Found at i:16268005 original size:93 final size:93
Alignment explanation
Indices: 16267837--16268015 Score: 277
Period size: 93 Copynumber: 1.9 Consensus size: 93
16267827 TTGTCACTTG
* * * *
16267837 TAGCCGAAGCTACCACTATTCACTGATCAGGTAGCTAGAGCTACCATTTTTCACTGATCAGGTAG
1 TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
* * * *
16267902 TCGGAGCTACCATTTTTCACTGATCAAT
66 CCGAAACTACCACTTTTCACTGATCAAT
*
16267930 TAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
1 TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
16267995 CCGAAACTACCACTTTTCACT
66 CCGAAACTACCACTTTTCACT
16268016 TGTCATTTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (93 bp):
TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
CCGAAACTACCACTTTTCACTGATCAAT
Found at i:16268089 original size:50 final size:51
Alignment explanation
Indices: 16267991--16268119 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
16267981 CACTGATCAG
* * * * *
16267991 GTAGCCGAAACTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
*
16268042 GTAGCCGAAGCTATTACTTATCACTT-TCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
16268092 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
16268120 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 47 0.67
51 23 0.33
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
Found at i:16272412 original size:17 final size:17
Alignment explanation
Indices: 16272392--16272425 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16272382 TGTTATTAAA
*
16272392 GGTTAAAATGGTAAAAT
1 GGTTAAAATGATAAAAT
16272409 GGTTAAAATGATAAAAT
1 GGTTAAAATGATAAAAT
16272426 AATTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (17 bp):
GGTTAAAATGATAAAAT
Found at i:16272431 original size:17 final size:17
Alignment explanation
Indices: 16272394--16272434 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
16272384 TTATTAAAGG
* **
16272394 TTAAAATGGTAAAATGG
1 TTAAAATGATAAAATAA
16272411 TTAAAATGATAAAATAA
1 TTAAAATGATAAAATAA
16272428 TTAAAAT
1 TTAAAAT
16272435 AAAGCCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (17 bp):
TTAAAATGATAAAATAA
Found at i:16272772 original size:15 final size:17
Alignment explanation
Indices: 16272749--16272780 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16272739 TGAAAATGCA
16272749 AAATGATT-AAATTATG
1 AAATGATTAAAATTATG
16272765 AAAT-ATTAAAATTATG
1 AAATGATTAAAATTATG
16272781 TGGTTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
AAATGATTAAAATTATG
Found at i:16274696 original size:27 final size:26
Alignment explanation
Indices: 16274666--16274717 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
16274656 GGAAAAATCG
16274666 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGTGG--ATATGTGCAAAGTTATT
* *
16274693 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAAGTTAT
16274718 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAAGTTATT
Found at i:16275882 original size:43 final size:43
Alignment explanation
Indices: 16275834--16275983 Score: 153
Period size: 43 Copynumber: 3.5 Consensus size: 43
16275824 GTTACCAAGA
16275834 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* *
16275877 TGTGATTACGTGTAAGACCATGTATGGGACATTGGCA-T-TAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * * * * * *
16275918 TAATCGATTTCGTGTGAGACCCTGTCTAGGACAGTGGCATCG-AT
1 T-GT-GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
*
16275962 ATGTGATAACATGTAAGACCAT
1 -TGTGATTACATGTAAGACCAT
16275984 ATCTAGGATA
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
41 4 0.05
42 2 0.02
43 76 0.88
44 3 0.03
45 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:16276548 original size:29 final size:29
Alignment explanation
Indices: 16276516--16276571 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
16276506 GATAGAATGA
16276516 TGAAACCATATGAATTATATCATGTTTGG
1 TGAAACCATATGAATTATATCATGTTTGG
*
16276545 TGAAATCATATGAATTATATCATGTTT
1 TGAAACCATATGAATTATATCATGTTT
16276572 TGAGTAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (29 bp):
TGAAACCATATGAATTATATCATGTTTGG
Found at i:16281781 original size:19 final size:20
Alignment explanation
Indices: 16281747--16281786 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
16281737 AAATTGAATC
16281747 AAATTAAACTTTCATGCATA
1 AAATTAAACTTTCATGCATA
* *
16281767 AAATTATAC-TTCATGTATA
1 AAATTAAACTTTCATGCATA
16281786 A
1 A
16281787 CATTGTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATTAAACTTTCATGCATA
Found at i:16282979 original size:4 final size:4
Alignment explanation
Indices: 16282970--16282996 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16282960 TCTGATCTCG
16282970 GTTA GTTA GTTA GTTA GTTA GTTA GTT
1 GTTA GTTA GTTA GTTA GTTA GTTA GTT
16282997 GACATATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
GTTA
Found at i:16288800 original size:14 final size:14
Alignment explanation
Indices: 16288781--16288834 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
16288771 GGTCATCAAA
16288781 TTATTTAAAAATTT
1 TTATTTAAAAATTT
* *
16288795 TTATTTAAATTATTAAA
1 TTATTTAAA-AATT--T
16288812 TTATTTAAAAATTT
1 TTATTTAAAAATTT
*
16288826 TCATTTAAA
1 TTATTTAAA
16288835 TTATTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.53
15 3 0.09
16 3 0.09
17 9 0.28
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATTTAAAAATTT
Found at i:16288813 original size:31 final size:31
Alignment explanation
Indices: 16288778--16288870 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
16288768 AATGGTCATC
16288778 AAATTATTTAAAAATTTTTATTTAAATTATT
1 AAATTATTTAAAAATTTTTATTTAAATTATT
*
16288809 AAATTATTTAAAAATTTTCATTTAAATTATT
1 AAATTATTTAAAAATTTTTATTTAAATTATT
** *
16288840 AAATTATTTAAAAAAATTTATTTAATTTATT
1 AAATTATTTAAAAATTTTTATTTAAATTATT
16288871 GGGCTATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
AAATTATTTAAAAATTTTTATTTAAATTATT
Found at i:16288817 original size:17 final size:17
Alignment explanation
Indices: 16288795--16288851 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
16288785 TTAAAAATTT
16288795 TTATTTAAATTATTAAA
1 TTATTTAAATTATTAAA
*
16288812 TTATTTAAA-AATT---
1 TTATTTAAATTATTAAA
16288825 TTCATTTAAATTATTAAA
1 TT-ATTTAAATTATTAAA
16288843 TTATTTAAA
1 TTATTTAAA
16288852 AAAATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 2 0.06
14 7 0.21
15 3 0.09
16 3 0.09
17 16 0.48
18 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTTAAATTATTAAA
Found at i:16291588 original size:20 final size:20
Alignment explanation
Indices: 16291561--16291599 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16291551 TGTTTATTTT
*
16291561 ATTTCAT-AATTTTTTAAAA
1 ATTTCATAAATATTTTAAAA
16291580 ATTTACATAAATATTTTAAA
1 ATTT-CATAAATATTTTAAA
16291600 TTATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTCATAAATATTTTAAAA
Found at i:16291690 original size:18 final size:19
Alignment explanation
Indices: 16291651--16291688 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16291641 TATTTTTTAT
16291651 ATTTTAAAATTTATGAGAA
1 ATTTTAAAATTTATGAGAA
* *
16291670 ATTTTAAATTTTATTAGAA
1 ATTTTAAAATTTATGAGAA
16291689 TTAGGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (19 bp):
ATTTTAAAATTTATGAGAA
Found at i:16294134 original size:46 final size:47
Alignment explanation
Indices: 16293949--16294261 Score: 226
Period size: 46 Copynumber: 6.7 Consensus size: 47
16293939 GGGTATAATA
* * *
16293949 CTGATGCCATGTCTCAGACATAGTCTTACACTGGCT-CATCCATC-AAG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTACAT-C-TCGTAG
* *
16293996 -TCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTACATATCCGT-G
1 CT-GATGCCATGTCCCAGACATGGTCTTACACT-G-GC-TACATCT-CGTAG
*
16294046 -TCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACATCTCGTAG
1 CT-GATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCGTAG
*
16294092 CTGATG-CATGTCCTAGACAT-GTCTTACACTGGCTTACATCTCG-AGG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGC-TACATCTCGTA-G
** * ** *
16294138 CCAATG-CATGTCCCAGACAT-GTCTTACACTAGCTATTGTCTC-AATG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTA-CATCTCGTA-G
* * *
16294184 CCGATGCCATGTCCCAGACATGGTCTTACACTGGATCT-CATAAT-GTGG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGG--CTACAT-CTCGTAG
*
16294232 TTGATG-CATGTCCCAGACAT-GTCTTACACT
1 CTGATGCCATGTCCCAGACATGGTCTTACACT
16294262 AGCACACAAA
Statistics
Matches: 221, Mismatches: 25, Indels: 41
0.77 0.09 0.14
Matches are distributed among these distances:
44 12 0.05
45 19 0.09
46 70 0.32
47 57 0.26
48 19 0.09
49 4 0.02
50 37 0.17
51 3 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTACATCTCGTAG
Found at i:16294210 original size:94 final size:91
Alignment explanation
Indices: 16293951--16294267 Score: 288
Period size: 94 Copynumber: 3.4 Consensus size: 91
16293941 GTATAATACT
* * * *
16293951 GATGCCATGTCTCAGACATAGTCTTACACTGGCTCATC-CATCAAGTCGATGCCATGTCCCAGAC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCACATCTCAT--AGCCGATGCCATGTCCCAGAC
* *
16294015 ATGGTCTTACACTAGCTCTTACATATCCGTGTC
62 ATGGTCTTACACT-G-GCTTACATAT-CGGGTC
* * *
16294048 GATGCCATGTCCCAGACATGGTCTTACACT-GACACATCTCGTAGCTGATG-CATGTCCTAGACA
1 GATG-CATGTCCCAGACAT-GTCTTACACTAG-CACATCTCATAGCCGATGCCATGTCCCAGACA
* *
16294111 T-GTCTTACACTGGCTTACATCTCGAGGCC
63 TGGTCTTACACTGGCTTACATATCG-GGTC
* **
16294140 AATGCATGTCCCAGACATGTCTTACACTAGCTATTGTCTCA-ATGCCGATGCCATGTCCCAGACA
1 GATGCATGTCCCAGACATGTCTTACACTAGC-A-CATCTCATA-GCCGATGCCATGTCCCAGACA
* *
16294204 TGGTCTTACACTGGATCT-CATAAT-GTGGTT
63 TGGTCTTACACTGGCT-TACAT-ATCG-GGTC
16294234 GATGCATGTCCCAGACATGTCTTACACTAGCACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCACA
16294268 CAAATAACCC
Statistics
Matches: 184, Mismatches: 25, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
90 11 0.06
91 19 0.10
92 23 0.12
93 15 0.08
94 59 0.32
95 15 0.08
96 7 0.04
97 33 0.18
98 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (91 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACATCTCATAGCCGATGCCATGTCCCAGACATGG
TCTTACACTGGCTTACATATCGGGTC
Found at i:16294993 original size:13 final size:13
Alignment explanation
Indices: 16294971--16295007 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
16294961 CAAAAACACA
16294971 AAAAGT-ATCAAG
1 AAAAGTCATCAAG
16294983 AAAAGTCATCAAG
1 AAAAGTCATCAAG
16294996 AAAAGTCATCAA
1 AAAAGTCATCAA
16295008 AATCACTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (13 bp):
AAAAGTCATCAAG
Found at i:16299799 original size:15 final size:13
Alignment explanation
Indices: 16299766--16299790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16299756 GTTTGTCATT
16299766 AAAATATTTTTTA
1 AAAATATTTTTTA
16299779 AAAATATTTTTT
1 AAAATATTTTTT
16299791 TAGAAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAAATATTTTTTA
Found at i:16299803 original size:16 final size:14
Alignment explanation
Indices: 16299766--16299799 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
16299756 GTTTGTCATT
16299766 AAAATA-TTTTTTA
1 AAAATATTTTTTTA
16299779 AAAATATTTTTTTA
1 AAAATATTTTTTTA
16299793 GAAAATA
1 -AAAATA
16299800 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 7 0.37
15 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AAAATATTTTTTTA
Found at i:16299817 original size:19 final size:20
Alignment explanation
Indices: 16299783--16299832 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
16299773 TTTTTAAAAA
*
16299783 TATTTTTTTAGAAAATAATT
1 TATTTTTCTAGAAAATAATT
*
16299803 TATTTTTCTAG-AAATGATT
1 TATTTTTCTAGAAAATAATT
16299822 TATTTTTCTAG
1 TATTTTTCTAG
16299833 TGTTTGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (20 bp):
TATTTTTCTAGAAAATAATT
Found at i:16300352 original size:32 final size:29
Alignment explanation
Indices: 16300294--16300354 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 29
16300284 TGACTCAAGT
*
16300294 TTTTGATAATTAAAAAAATTAGAAAATAA
1 TTTTGATAATTAAAAAAATTAAAAAATAA
16300323 TTTTGATAATTTAATACAAAATTAAAAAATAA
1 TTTTGATAA-TTAA-A-AAAATTAAAAAATAA
16300355 AATAAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 9 0.32
30 4 0.14
31 1 0.04
32 14 0.50
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
TTTTGATAATTAAAAAAATTAAAAAATAA
Found at i:16301019 original size:7 final size:7
Alignment explanation
Indices: 16301007--16301033 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
16300997 AATCATTTAC
16301007 TTTTGAA
1 TTTTGAA
16301014 TTTTGAA
1 TTTTGAA
16301021 TTTTGAA
1 TTTTGAA
16301028 TTTTGA
1 TTTTGA
16301034 TTATTAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (7 bp):
TTTTGAA
Found at i:16302143 original size:14 final size:15
Alignment explanation
Indices: 16302121--16302152 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
16302111 GAATTATGTT
16302121 AGTTGTATTATCATA
1 AGTTGTATTATCATA
16302136 AGTT-TATTATCATA
1 AGTTGTATTATCATA
16302150 AGT
1 AGT
16302153 ATAAATCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (15 bp):
AGTTGTATTATCATA
Found at i:16303668 original size:13 final size:13
Alignment explanation
Indices: 16303637--16303661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16303627 ATTTTACTCT
16303637 TTTTTTATTTTTA
1 TTTTTTATTTTTA
16303650 TTTTTTATTTTT
1 TTTTTTATTTTT
16303662 TTCTTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:16304190 original size:11 final size:11
Alignment explanation
Indices: 16304174--16304203 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16304164 GTATATATTG
16304174 TATATATTATA
1 TATATATTATA
*
16304185 TTTATATTATA
1 TATATATTATA
16304196 TATATATT
1 TATATATT
16304204 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:16304258 original size:21 final size:23
Alignment explanation
Indices: 16304232--16304274 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16304222 ATACTTCTTG
*
16304232 TATATT-TC-CATGTATATACTT
1 TATATTGTCTCATGTACATACTT
16304253 TATATTGTCTCATGTACATACT
1 TATATTGTCTCATGTACATACT
16304275 CTGAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 2 0.11
23 11 0.58
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (23 bp):
TATATTGTCTCATGTACATACTT
Found at i:16318085 original size:2 final size:2
Alignment explanation
Indices: 16318078--16318114 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16318068 AAAATATAAA
16318078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16318115 AACACTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16327416 original size:62 final size:60
Alignment explanation
Indices: 16327291--16327417 Score: 141
Period size: 62 Copynumber: 2.1 Consensus size: 60
16327281 ATCCTAAATA
* * ** * *
16327291 TAAAAAATTCAATAAATTTAGCCTCAATGTTTGCAAAATTTGTCATTTTAGTTCTAATGC
1 TAAAAAATTCAATAAATTAAACCTCAACATTTACAAAATTTGTCAATTTAGTTCTAATGC
*
16327351 TAAAAAATTCAATAAATTCAAACTCTCAACATTTACAAAATCTT-TCAATTTAG-TCTCAATTC
1 TAAAAAATTCAATAAATT-AAAC-CTCAACATTTACAAAAT-TTGTCAATTTAGTTCT-AATGC
16327413 TAAAA
1 TAAAA
16327418 TTTTTTAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
60 18 0.32
61 5 0.09
62 31 0.55
63 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.37
Consensus pattern (60 bp):
TAAAAAATTCAATAAATTAAACCTCAACATTTACAAAATTTGTCAATTTAGTTCTAATGC
Found at i:16333458 original size:21 final size:21
Alignment explanation
Indices: 16333429--16333470 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16333419 TTGGGTTGAT
* *
16333429 GTCTTGAGACAAGACGAATAA
1 GTCTCGAGACAAGAAGAATAA
*
16333450 GTCTCGAGATAAGAAGAATAA
1 GTCTCGAGACAAGAAGAATAA
16333471 AAGTTGTCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (21 bp):
GTCTCGAGACAAGAAGAATAA
Found at i:16334679 original size:41 final size:41
Alignment explanation
Indices: 16334619--16334703 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
16334609 CCTCGCAAAG
*
16334619 TTGCGAGGAGTATTCGCATGTCT-CCTTTGCGAGGCATTCCA
1 TTGCGAGGAGTATTCGCATGTCTACC-TCGCGAGGCATTCCA
* *
16334660 TTGCGAGGAGTACTT-GCATGTTTACCTCGCGAGGCATTCTA
1 TTGCGAGGAGTA-TTCGCATGTCTACCTCGCGAGGCATTCCA
16334701 TTG
1 TTG
16334704 TGTTCACCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (41 bp):
TTGCGAGGAGTATTCGCATGTCTACCTCGCGAGGCATTCCA
Found at i:16334941 original size:2 final size:2
Alignment explanation
Indices: 16334934--16334967 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16334924 TTTCACTTTA
16334934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16334968 TAGTAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16335148 original size:24 final size:24
Alignment explanation
Indices: 16335120--16335180 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
16335110 TAAATATATT
*
16335120 ATATGTTATTATTATATCATTTTA
1 ATATGTTATTATTATATAATTTTA
16335144 ATATGAATT-TT-TTATATAATTTTA
1 ATATG--TTATTATTATATAATTTTA
*
16335168 ATATATTATTATT
1 ATATGTTATTATT
16335181 TAAAATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 2 0.06
23 2 0.06
24 23 0.74
25 2 0.06
26 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (24 bp):
ATATGTTATTATTATATAATTTTA
Found at i:16337373 original size:14 final size:13
Alignment explanation
Indices: 16337333--16337412 Score: 63
Period size: 13 Copynumber: 6.7 Consensus size: 13
16337323 TTATTGTATT
16337333 TATTTGATTTAAT-
1 TATTT-ATTTAATA
16337346 TATTT-TTTAA-A
1 TATTTATTTAATA
16337357 TATTATATTTAATA
1 TATT-TATTTAATA
16337371 TA-TTATTT--T-
1 TATTTATTTAATA
16337380 TA-TTATTTAA-A
1 TATTTATTTAATA
16337391 TATTATATTTAATA
1 TATT-TATTTAATA
16337405 TA-TTATTT
1 TATTTATTT
16337413 TTATTATACT
Statistics
Matches: 57, Mismatches: 0, Indels: 21
0.73 0.00 0.27
Matches are distributed among these distances:
9 8 0.14
10 1 0.02
11 11 0.19
12 12 0.21
13 19 0.33
14 6 0.11
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (13 bp):
TATTTATTTAATA
Found at i:16337389 original size:34 final size:34
Alignment explanation
Indices: 16337345--16337419 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
16337335 TTTGATTTAA
*
16337345 TTATTTTTTAAATATTATATTTAATATATTATTT
1 TTATTATTTAAATATTATATTTAATATATTATTT
16337379 TTATTATTTAAATATTATATTTAATATATTATTT
1 TTATTATTTAAATATTATATTTAATATATTATTT
16337413 TTATTAT
1 TTATTAT
16337420 ACTCAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (34 bp):
TTATTATTTAAATATTATATTTAATATATTATTT
Found at i:16337393 original size:20 final size:21
Alignment explanation
Indices: 16337362--16337401 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
16337352 TTAAATATTA
*
16337362 TATTTAATATATTATTTTTAT
1 TATTTAATATATTATATTTAT
16337383 TATTTAA-ATATTATATTTA
1 TATTTAATATATTATATTTA
16337402 ATATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTAATATATTATATTTAT
Found at i:16337415 original size:14 final size:14
Alignment explanation
Indices: 16337344--16337420 Score: 57
Period size: 14 Copynumber: 5.1 Consensus size: 14
16337334 ATTTGATTTA
16337344 ATTATTTTTTAA-AT
1 ATTA-TTTTTAATAT
*
16337358 ATTATATTTAATAT
1 ATTATTTTTAATAT
16337372 ATTATTTTTATTATTTAAAT
1 ATTATTTTTA--A--T--AT
*
16337392 ATTATATTTAATAT
1 ATTATTTTTAATAT
*
16337406 ATTATTTTTATTAT
1 ATTATTTTTAATAT
16337420 A
1 A
16337421 CTCAATAGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.12
14 30 0.59
16 2 0.04
18 2 0.04
20 11 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTTTAATAT
Found at i:16343670 original size:131 final size:131
Alignment explanation
Indices: 16343436--16343827 Score: 633
Period size: 131 Copynumber: 3.0 Consensus size: 131
16343426 TAATTATTCA
* * ** *
16343436 TTTAAAAATTCTT-AAAAGCGAAGGAAATGTTCGATGTTTGGCAATTCGGGAAATCGTGCCCTAT
1 TTTAAAAACTCTTCAAAA-CGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTAT
* * *
16343500 CGTGCTGGGTTGCGATTTCCCGTTCGTTCAAAACAATCGAATATTCCTTTGGAACTTCACTCATG
65 CGTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCACTCATG
16343565 TC
130 TC
* *
16343567 TTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTTGGGGAATCGTGCCCTGTC
1 TTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
16343632 GTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCACTCATGT
66 GTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCACTCATGT
16343697 C
131 C
16343698 TTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
1 TTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
* * * * *
16343763 GTGCTGGGTTGCGATCTCCTGTTTGTTCAACATAACCGAATATTCCTTTAGAATTTCACTCATGT
66 GTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCACTCATGT
16343828 TCTCTAAATT
Statistics
Matches: 243, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 239 0.98
132 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (131 bp):
TTTAAAAACTCTTCAAAACGAAGGTAATACTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
GTGCTGGGTTGCGATTTCCTGTTTGTTCAAAACAATCGAATATTCCTTTGGAATTTCACTCATGT
C
Found at i:16345320 original size:37 final size:37
Alignment explanation
Indices: 16345270--16345344 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
16345260 TTCCCAATTA
16345270 TAAAGACAGTTTAGTCTTTCTTCTAAATCCACATGAT
1 TAAAGACAGTTTAGTCTTTCTTCTAAATCCACATGAT
16345307 TAAAGACAGTTTAGTCTTTCTTCTAAATCCACATGAT
1 TAAAGACAGTTTAGTCTTTCTTCTAAATCCACATGAT
16345344 T
1 T
16345345 CTTCTTTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (37 bp):
TAAAGACAGTTTAGTCTTTCTTCTAAATCCACATGAT
Found at i:16351086 original size:3 final size:3
Alignment explanation
Indices: 16351078--16351180 Score: 52
Period size: 3 Copynumber: 33.3 Consensus size: 3
16351068 ATATATATAA
* * ** * *
16351078 ATT ATT ATT ATT ATT -TGT TTT ATT TTT AAC CTT ATT TTT A-T ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
16351122 ATAT ATT A-T ATA ATT ATTT ATT ATAT ATT ATT -TAT ATT ATT ATT ATTT
1 AT-T ATT ATT ATT ATT A-TT ATT AT-T ATT ATT AT-T ATT ATT ATT A-TT
16351170 ATT ATAT ATT A
1 ATT AT-T ATT A
16351181 ATTTTCACGA
Statistics
Matches: 76, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
2 6 0.08
3 53 0.70
4 17 0.22
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:16351128 original size:7 final size:7
Alignment explanation
Indices: 16351116--16351180 Score: 78
Period size: 7 Copynumber: 9.0 Consensus size: 7
16351106 ACCTTATTTT
16351116 TATATTA
1 TATATTA
16351123 TATATTA
1 TATATTA
16351130 TATAATTA
1 TAT-ATTA
*
16351138 TTTATTA
1 TATATTA
16351145 TATATTA
1 TATATTA
16351152 TTTATATTA
1 --TATATTA
16351161 T-TATTA
1 TATATTA
*
16351167 TTTATTA
1 TATATTA
16351174 TATATTA
1 TATATTA
16351181 ATTTTCACGA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
6 6 0.12
7 32 0.63
8 6 0.12
9 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTA
Found at i:16351137 original size:15 final size:14
Alignment explanation
Indices: 16351116--16351180 Score: 78
Period size: 15 Copynumber: 4.5 Consensus size: 14
16351106 ACCTTATTTT
16351116 TATATTATATATTA
1 TATATTATATATTA
*
16351130 TATAATTATTTATTA
1 TAT-ATTATATATTA
16351145 TATATTATTTATATTA
1 TATATTA--TATATTA
*
16351161 T-TATTATTTATTA
1 TATATTATATATTA
16351174 TATATTA
1 TATATTA
16351181 ATTTTCACGA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
13 7 0.16
14 12 0.27
15 18 0.41
16 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATTATATATTA
Found at i:16351144 original size:22 final size:22
Alignment explanation
Indices: 16351053--16351359 Score: 116
Period size: 22 Copynumber: 14.1 Consensus size: 22
16351043 TATTTATTTC
16351053 TATTATTATATATATATATATAT
1 TATTATTATATAT-TATATATAT
* * * *
16351076 AAATTATTAT-TATTATTTGTTT
1 -TATTATTATATATTATATATAT
* **
16351098 TATTTTTA-ACCTTAT-T-T-T
1 TATTATTATATATTATATATAT
16351116 TA-TATTATATATTATATA-AT
1 TATTATTATATATTATATATAT
*
16351136 TATTTATTATATATTATTTATAT
1 TA-TTATTATATATTATATATAT
*
16351159 TATTATTATTTATTATATATTAAT
1 TATTATTATATATTATATA-T-AT
** * * *
16351183 T-TTCACGAAATATTAT-TTTTT
1 TATT-ATTATATATTATATATAT
*
16351204 TA-CATTAT-TATTAT-TATAT
1 TATTATTATATATTATATATAT
*
16351223 T-TT-TGTATA-A-TATATTTAT
1 TATTAT-TATATATTATATATAT
16351242 TAATTATATATATATTATAT-TAT
1 T-ATTAT-TATATATTATATATAT
* *
16351265 TTTTACATATATACTTTCATATTATAT
1 TATTA-TTATATA--TT-ATAT-ATAT
*
16351292 TATAATTAT-T-TTATATTATAT
1 TATTATTATATATTATA-TATAT
*
16351313 TATT-TTATACTATTATATATTT
1 TATTATTATA-TATTATATATAT
*
16351335 TTTTATCTATATATTAT-TATCAT
1 TATTAT-TATATATTATATAT-AT
16351358 TA
1 TA
16351360 AAGGTTTTAA
Statistics
Matches: 210, Mismatches: 39, Indels: 69
0.66 0.12 0.22
Matches are distributed among these distances:
17 4 0.02
18 12 0.06
19 21 0.10
20 10 0.05
21 24 0.11
22 65 0.31
23 30 0.14
24 30 0.14
25 5 0.02
26 3 0.01
27 6 0.03
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (22 bp):
TATTATTATATATTATATATAT
Found at i:16351149 original size:29 final size:28
Alignment explanation
Indices: 16351116--16351359 Score: 107
Period size: 29 Copynumber: 8.5 Consensus size: 28
16351106 ACCTTATTTT
16351116 TATATTA-TATATTATATAATTATTTATTA
1 TATATTATTATATTAT-T-ATTATTTATTA
16351145 TATATTATTTATATTATTATTATTTATTA
1 TATATTA-TTATATTATTATTATTTATTA
* ** * *
16351174 TATATTAATTTTCACGAAATATTATTT-TTT
1 TATATT-ATTAT-A-TTATTATTATTTATTA
* * *
16351204 TACATTATTATTATTA-TATTTTTGTATAA
1 TATATTATTA-TATTATTATTATT-TATTA
*
16351233 TATATTTATTA-ATTA-TA-TATATATTA
1 TATA-TTATTATATTATTATTATTTATTA
* * *
16351259 TATTATTTTTACA-TATATACTT-TCATATTA
1 TA-TATTATTATATTAT-TA-TTAT-TTATTA
* * *
16351289 TATTATAATTATTTTA-TATTATATTATTT
1 TA-TATTATTATATTATTATTAT-TTATTA
*
16351318 TATACTATTATA-TATT-TT-TTTATCTA
1 TATATTATTATATTATTATTATTTAT-TA
16351344 TATATTATTATCATTA
1 TATATTATTAT-ATTA
16351360 AAGGTTTTAA
Statistics
Matches: 164, Mismatches: 29, Indels: 45
0.69 0.12 0.19
Matches are distributed among these distances:
25 4 0.02
26 25 0.15
27 16 0.10
28 22 0.13
29 45 0.27
30 33 0.20
31 19 0.12
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.60
Consensus pattern (28 bp):
TATATTATTATATTATTATTATTTATTA
Found at i:16351250 original size:15 final size:16
Alignment explanation
Indices: 16351232--16351351 Score: 67
Period size: 15 Copynumber: 7.8 Consensus size: 16
16351222 TTTTTGTATA
*
16351232 ATATATTTATTA-ATT
1 ATATATATATTATATT
16351247 ATATATATATTATATT
1 ATATATATATTATATT
* *
16351263 AT-T-TTTA-CATA-T
1 ATATATATATTATATT
*
16351275 ATACTTTCATATTATATT
1 ATA-TAT-ATATTATATT
*
16351293 ATA-ATTATTTTATATT
1 ATATA-TATATTATATT
* *
16351309 ATAT-TATTTTATACT
1 ATATATATATTATATT
* *
16351324 AT-TATATATTTTTTT
1 ATATATATATTATATT
*
16351339 ATCTATATATTAT
1 ATATATATATTAT
16351352 TATCATTAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 21
0.70 0.11 0.18
Matches are distributed among these distances:
12 3 0.04
13 3 0.04
14 5 0.06
15 34 0.42
16 28 0.35
17 4 0.05
18 4 0.05
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATATATTATATT
Found at i:16351346 original size:34 final size:34
Alignment explanation
Indices: 16351289--16351354 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
16351279 TTTCATATTA
16351289 TATTATAATTATTTTATATTATATTATT-TTATAC
1 TATTATAATTATTTTATATTATA-TATTATTATAC
16351323 TATTATATATT-TTTT-TATCTATATATTATTAT
1 TATTATA-ATTATTTTATAT-TATATATTATTAT
16351355 CATTAAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 7 0.24
34 19 0.66
35 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (34 bp):
TATTATAATTATTTTATATTATATATTATTATAC
Found at i:16351655 original size:18 final size:17
Alignment explanation
Indices: 16351597--16351655 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
16351587 TTCTAAACCA
*
16351597 ATATATATTTTTATTTT
1 ATATAAATTTTTATTTT
*
16351614 ATATATAATTATTATTCTT
1 ATATA-AATTTTTATT-TT
* *
16351633 TTATAAATTTTTGTTATT
1 ATATAAATTTTTATT-TT
16351651 ATATA
1 ATATA
16351656 TTATATATTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
17 5 0.15
18 22 0.67
19 6 0.18
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
ATATAAATTTTTATTTT
Found at i:16365305 original size:3 final size:3
Alignment explanation
Indices: 16365297--16365425 Score: 70
Period size: 3 Copynumber: 41.7 Consensus size: 3
16365287 TATTTATTTC
* *
16365297 TAT TAT TAT ATAT ATAT AAAT TAT TAT TAT TAT TAT TAT T-T GTTT TAT
1 TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * ** * *
16365345 TTT TAA CCT TAT TTT TA- TAT TAT ATAT TA- TAT AAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
16365388 TAT ATAT TAT T-T ATAT TAT TAT TATT TAT TAT ATAT TA
1 TAT -TAT TAT TAT -TAT TAT TAT TA-T TAT TAT -TAT TA
16365426 CTTTTCACGA
Statistics
Matches: 99, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
2 8 0.08
3 67 0.68
4 24 0.24
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:16365372 original size:7 final size:7
Alignment explanation
Indices: 16365360--16365425 Score: 71
Period size: 7 Copynumber: 9.0 Consensus size: 7
16365350 ACCTTATTTT
16365360 TATATTA
1 TATATTA
16365367 TATATTA
1 TATATTA
16365374 TATAATTA
1 TAT-ATTA
*
16365382 TTTTATTA
1 -TATATTA
16365390 TATATTA
1 TATATTA
16365397 TTTATATTA
1 --TATATTA
16365406 T-TATTA
1 TATATTA
*
16365412 TTTATTA
1 TATATTA
16365419 TATATTA
1 TATATTA
16365426 CTTTTCACGA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
6 6 0.12
7 28 0.55
8 8 0.16
9 9 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTA
Found at i:16365390 original size:16 final size:15
Alignment explanation
Indices: 16365360--16365599 Score: 105
Period size: 15 Copynumber: 15.6 Consensus size: 15
16365350 ACCTTATTTT
*
16365360 TATATTA-TATATTA
1 TATATTATTTTATTA
16365374 TATAATTATTTTATTA
1 TAT-ATTATTTTATTA
16365390 TATATTATTTATATTA
1 TATATTATTT-TATTA
16365406 T-TATTA-TTTATTA
1 TATATTATTTTATTA
**
16365419 TATATTACTTTTCACGA
1 TATATTA-TTTT-ATTA
* *
16365436 AATATTA--TTATTT
1 TATATTATTTTATTA
*
16365449 TACATTATTATTATTA
1 TATATTATT-TTATTA
*
16365465 CAT-TT-TTTGTA-TA
1 TATATTATTT-TATTA
*
16365478 TATATT-TATTAATTA
1 TATATTAT-TTTATTA
16365493 TATA-TA---TATTA
1 TATATTATTTTATTA
*
16365504 TATATTATTTTTACATA
1 TATATTA-TTTTA-TTA
16365521 TATACTTTCATATTATATTA
1 TATA--TT-AT-TT-TATTA
16365541 TA-ATTATTTTA-TA
1 TATATTATTTTATTA
16365554 TTATATTATTTTATACTA
1 -TATATTATTTTAT--TA
16365572 TTATATATATTTTTATCTA
1 -TATAT-TA-TTTTAT-TA
16365591 TATATTATT
1 TATATTATT
16365600 ATCATTAAAG
Statistics
Matches: 176, Mismatches: 17, Indels: 64
0.68 0.07 0.25
Matches are distributed among these distances:
11 8 0.05
12 2 0.01
13 19 0.11
14 25 0.14
15 37 0.21
16 30 0.17
17 18 0.10
18 13 0.07
19 9 0.05
20 13 0.07
21 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (15 bp):
TATATTATTTTATTA
Found at i:16365540 original size:5 final size:5
Alignment explanation
Indices: 16365530--16365582 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
16365520 ATATACTTTC
* * *
16365530 ATATT ATATT ATAATT ATTTT ATATT ATATT ATTTT ATACT ATTATAT
1 ATATT ATATT AT-ATT ATATT ATATT ATATT ATATT ATATT A-TAT-T
16365578 ATATT
1 ATATT
16365583 TTTATCTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 27 0.69
6 10 0.26
7 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:16365541 original size:85 final size:87
Alignment explanation
Indices: 16365359--16365579 Score: 202
Period size: 85 Copynumber: 2.6 Consensus size: 87
16365349 AACCTTATTT
* * *
16365359 TTATATTATATATTATATAATTATTTTATTATATATTATTTATATTATTATTATTTATTATATAT
1 TTATATTAT-TATTAT-TAATTATTTTAGTATATATTATTTATATAATTATTATATATTATATAT
* *
16365424 TACTTTTCACGAAATATTATTATT
64 TACTTTTCACGAAATATTATCATA
*
16365448 TTACATTATTATTATTACATT-TTTT-GTATATA-TATTTAT-TAATTATATATATATTATATAT
1 TTATATTATTATTATTA-ATTATTTTAGTATATATTATTTATATAATTAT-TATATATTATATAT
* *
16365509 TA-TTTTTAC-ATATA-TA-C-T-
64 TACTTTTCACGAAATATTATCATA
*
16365527 TTCATATTA-TATTA-TAATTATTTTA-TATTATATTATTT-TAT-ACTATTATATAT
1 TT-ATATTATTATTATTAATTATTTTAGTA-TATATTATTTATATAATTATTATATAT
16365580 ATTTTTATCT
Statistics
Matches: 115, Mismatches: 9, Indels: 27
0.76 0.06 0.18
Matches are distributed among these distances:
77 3 0.03
78 15 0.13
79 16 0.14
80 12 0.10
82 2 0.02
83 4 0.03
84 12 0.10
85 22 0.19
86 6 0.05
87 6 0.05
88 9 0.08
89 8 0.07
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (87 bp):
TTATATTATTATTATTAATTATTTTAGTATATATTATTTATATAATTATTATATATTATATATTA
CTTTTCACGAAATATTATCATA
Found at i:16371208 original size:24 final size:24
Alignment explanation
Indices: 16371172--16371221 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
16371162 AAGCTTAAGG
*
16371172 TCCCTAAGTATCAAAAATACATTT
1 TCCCTAAGCATCAAAAATACATTT
*
16371196 TCCCTGAGCATCAAAAATACATTT
1 TCCCTAAGCATCAAAAATACATTT
16371220 TC
1 TC
16371222 AGAAAACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (24 bp):
TCCCTAAGCATCAAAAATACATTT
Found at i:16378349 original size:18 final size:18
Alignment explanation
Indices: 16378278--16378349 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
16378268 AAGTTTTTGA
* * *
16378278 AGAAAGGAAGAGAAGAAG
1 AGAAGGGAAGGGAAAAAG
*
16378296 AAGAAGGAGAA-GGAAAAGG
1 -AGAAGG-GAAGGGAAAAAG
* *
16378315 AG-AGGG-CGGGAAGAAG
1 AGAAGGGAAGGGAAAAAG
16378331 AGAAGGGAAGGGAAAAAG
1 AGAAGGGAAGGGAAAAAG
16378349 A
1 A
16378350 AAGAAAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
16 9 0.22
17 7 0.17
18 11 0.28
19 10 0.25
20 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.44, T:0.00
Consensus pattern (18 bp):
AGAAGGGAAGGGAAAAAG
Found at i:16380332 original size:20 final size:20
Alignment explanation
Indices: 16380309--16380362 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
16380299 GATTTAGGAT
*
16380309 TTATTTTTATTTATCTTCAA
1 TTATTTTTATTTATATTCAA
* * *
16380329 TTATCTTTAATTATATTTAA
1 TTATTTTTATTTATATTCAA
*
16380349 TTATTTGTATTTAT
1 TTATTTTTATTTAT
16380363 TTCTAGGAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTTTTATTTATATTCAA
Found at i:16384107 original size:18 final size:18
Alignment explanation
Indices: 16384084--16384118 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16384074 TATTTCTCTA
* *
16384084 TATTTTTATTTTTTATTT
1 TATTTTAATTATTTATTT
16384102 TATTTTAATTATTTATT
1 TATTTTAATTATTTATT
16384119 ATTTTATCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTAATTATTTATTT
Found at i:16384113 original size:21 final size:21
Alignment explanation
Indices: 16384089--16384140 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
16384079 CTCTATATTT
* *
16384089 TTATTTTTTATTTTATTTTAA
1 TTATTTATTATTTTATCTTAA
16384110 TTATTTATTATTTTATCTTAA
1 TTATTTATTATTTTATCTTAA
*
16384131 TGATTTATTA
1 TTATTTATTA
16384141 CGTAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTATTTATTATTTTATCTTAA
Found at i:16384441 original size:4 final size:4
Alignment explanation
Indices: 16384434--16384461 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
16384424 TTCTTTCGCC
16384434 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
16384462 CCACATCGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:16386652 original size:10 final size:10
Alignment explanation
Indices: 16386637--16386688 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
16386627 TAAATTTAGG
16386637 ATTTATTTTT
1 ATTTATTTTT
* *
16386647 ATTTATCTTC
1 ATTTATTTTT
* *
16386657 AATTATCTTT
1 ATTTATTTTT
*
16386667 ATTTATTTAT
1 ATTTATTTTT
16386677 ATTTATCTTTT
1 ATTTAT-TTTT
16386688 A
1 A
16386689 GAATTTAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
10 29 0.88
11 4 0.12
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:16386686 original size:20 final size:21
Alignment explanation
Indices: 16386637--16386686 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
16386627 TAAATTTAGG
*
16386637 ATTTATTTTTATTTATCTTCA
1 ATTTATCTTTATTTATCTTCA
16386658 A-TTATCTTTATTTAT-TT-A
1 ATTTATCTTTATTTATCTTCA
16386676 TATTTATCTTT
1 -ATTTATCTTT
16386687 TAGAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 3 0.12
20 21 0.81
21 1 0.04
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTATCTTTATTTATCTTCA
Found at i:16387427 original size:17 final size:18
Alignment explanation
Indices: 16387399--16387432 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
16387389 TATTCTCCAT
16387399 TTTAATTTTCGCAATTTA
1 TTTAATTTTCGCAATTTA
16387417 TTTAA-TTTCGCAATTT
1 TTTAATTTTCGCAATTT
16387433 CAATTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTTCGCAATTTA
Found at i:16389743 original size:20 final size:20
Alignment explanation
Indices: 16389720--16389778 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
16389710 TAAACATGGT
16389720 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
* *
16389740 ATGTATGATATGAACATGAT
1 ATGTATGATATGCACATGAC
16389760 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
16389779 GGTATTCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:16389856 original size:24 final size:24
Alignment explanation
Indices: 16389829--16390020 Score: 244
Period size: 24 Copynumber: 8.0 Consensus size: 24
16389819 GAGGAAGTGC
16389829 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
16389853 AAAAGGGCTTCTGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
16389877 AAAGGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
16389901 AAAAGGGCTT-TTCTCCCAATTATC
1 AAAAGGGCTTATGC-CCCAGTTATT
*
16389925 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
16389949 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
16389973 AAAAGGGCTTTTGCCCTAGTTTTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
16389997 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
16390021 ATGATAAAGC
Statistics
Matches: 143, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.01
24 130 0.91
25 11 0.08
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:16400327 original size:22 final size:21
Alignment explanation
Indices: 16400293--16400341 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
16400283 AGTAGCACCC
* *
16400293 TCCCCCTCATTTTCCTTCTTCCT
1 TCCCCTTCATTTT-CATCTT-CT
16400316 TCCCCTTC-TTTTCATCTTCT
1 TCCCCTTCATTTTCATCTTCT
16400336 TCCCCT
1 TCCCCT
16400342 ACCCCAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 5 0.21
22 4 0.17
23 7 0.29
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (21 bp):
TCCCCTTCATTTTCATCTTCT
Found at i:16400351 original size:6 final size:6
Alignment explanation
Indices: 16400337--16400370 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
16400327 TCATCTTCTT
*
16400337 CCCCTA CCCCAA CCCCAA CCCCAA CCCCAA CCCC
1 CCCCAA CCCCAA CCCCAA CCCCAA CCCCAA CCCC
16400371 TACTCCCTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.26, C:0.71, G:0.00, T:0.03
Consensus pattern (6 bp):
CCCCAA
Found at i:16401774 original size:27 final size:27
Alignment explanation
Indices: 16401743--16401811 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
16401733 TTTAGTTTCC
* *
16401743 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTACTAAAATACCCCCGACTTATA
* * *
16401770 AAATTACCAAAGTACCCCCGATTTATA
1 AAATTACTAAAATACCCCCGACTTATA
16401797 AAATTACTAAAATAC
1 AAATTACTAAAATAC
16401812 TCCTGTAAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.28
Consensus pattern (27 bp):
AAATTACTAAAATACCCCCGACTTATA
Found at i:16401851 original size:27 final size:27
Alignment explanation
Indices: 16401821--16402008 Score: 209
Period size: 27 Copynumber: 7.0 Consensus size: 27
16401811 CTCCTGTAAG
*
16401821 ATAGAATTATCGTTTTACCCTCGATTT
1 ATAGAATTACCGTTTTACCCTCGATTT
*
16401848 ATAGAATTACCATTTTACCCTCGATTT
1 ATAGAATTACCGTTTTACCCTCGATTT
* *
16401875 ATAGAATTATCGTTTTACTCTCGATTT
1 ATAGAATTACCGTTTTACCCTCGATTT
* *
16401902 ATAGAATTACCATTTTACCCTCAATTT
1 ATAGAATTACCGTTTTACCCTCGATTT
* *
16401929 ACAAAATTACCGTTTTACCCTC-AGTTT
1 ATAGAATTACCGTTTTACCCTCGA-TTT
* * *
16401956 ACAAAATTACTGTTTTACCCTC-AGTTT
1 ATAGAATTACCGTTTTACCCTCGA-TTT
* * * *
16401983 ACAAAATTATCATTTTACCCTCGATT
1 ATAGAATTACCGTTTTACCCTCGATT
16402009 GTGAAATTAC
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 141 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.41
Consensus pattern (27 bp):
ATAGAATTACCGTTTTACCCTCGATTT
Found at i:16401879 original size:54 final size:53
Alignment explanation
Indices: 16401825--16402008 Score: 244
Period size: 54 Copynumber: 3.4 Consensus size: 53
16401815 TGTAAGATAG
* *
16401825 AATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAG
1 AATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTC-ATTTACAA
*
16401879 AATTATCGTTTTACTCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAA
1 AATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTC-ATTTACAA
* * * **
16401933 AATTACCGTTTTACCCTC-AGTTTACAAAATTACTGTTTTACCCTCAGTTTACAA
1 AATTATCGTTTTACCCTCGA-TTTATAGAATTACCATTTTACCCTCA-TTTACAA
*
16401987 AATTATCATTTTACCCTCGATT
1 AATTATCGTTTTACCCTCGATT
16402009 GTGAAATTAC
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.02
54 112 0.97
55 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (53 bp):
AATTATCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCATTTACAA
Found at i:16402030 original size:27 final size:26
Alignment explanation
Indices: 16402000--16402189 Score: 136
Period size: 27 Copynumber: 7.0 Consensus size: 26
16401990 TATCATTTTA
*
16402000 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTAAAATTACTGAAATAC
* * * **
16402027 CCCT-ATAGGATAGAGTTACCAAAATAC
1 CCCTGAT-TG-TAAAATTACTGAAATAC
* *
16402054 CCCTAGTTTGTAAAATTACCGAAATAC
1 CCCT-GATTGTAAAATTACTGAAATAC
*
16402081 CCCTAGTTTGTAAAATTACTGAAATAC
1 CCCT-GATTGTAAAATTACTGAAATAC
* *
16402108 CACTGGTTTGTAAAATTACAT-AAATAC
1 CCCT-GATTGTAAAATTAC-TGAAATAC
*
16402135 CCCTGATT-TACAAAATTACAGAAATAC
1 CCCTGATTGT--AAAATTACTGAAATAC
*
16402162 CCCTGATT-TACAAAATTACAGAAATAC
1 CCCTGATTGT--AAAATTACTGAAATAC
16402189 C
1 C
16402190 ATTGACTTTC
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
25 3 0.02
26 4 0.03
27 128 0.93
28 2 0.01
29 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.28
Consensus pattern (26 bp):
CCCTGATTGTAAAATTACTGAAATAC
Found at i:16402150 original size:54 final size:54
Alignment explanation
Indices: 16402048--16402189 Score: 178
Period size: 54 Copynumber: 2.6 Consensus size: 54
16402038 AGAGTTACCA
* * ** *
16402048 AAATACCCCTAGTTTGTAAAATTACCGAAATACCCCTAGTTTGTAAAATTACTG
1 AAATACCCCTGGTTTGTAAAATTACAGAAATACCCCTAGTTTACAAAATTACAG
* *
16402102 AAATACCACTGGTTTGTAAAATTACATAAATACCCCT-GATTTACAAAATTACAG
1 AAATACCCCTGGTTTGTAAAATTACAGAAATACCCCTAG-TTTACAAAATTACAG
* **
16402156 AAATACCCCTGATTTACAAAATTACAGAAATACC
1 AAATACCCCTGGTTTGTAAAATTACAGAAATACC
16402190 ATTGACTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
53 1 0.01
54 74 0.99
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (54 bp):
AAATACCCCTGGTTTGTAAAATTACAGAAATACCCCTAGTTTACAAAATTACAG
Found at i:16402228 original size:56 final size:54
Alignment explanation
Indices: 16402065--16402245 Score: 168
Period size: 54 Copynumber: 3.3 Consensus size: 54
16402055 CCTAGTTTGT
* * ** * **
16402065 AAAATTACCGAAATACCCCT-AGTTTGTAAAATTACTGAAATACCACTGGTTTGT
1 AAAATTACAGAAATACCACTGA-TTTACAAAATTACAGAAATACCACTGGTTTAC
* * * *
16402119 AAAATTACATAAATACCCCTGATTTACAAAATTACAGAAATACCCCTGATTTAC
1 AAAATTACAGAAATACCACTGATTTACAAAATTACAGAAATACCACTGGTTTAC
* ** *
16402173 AAAATTACAGAAATACCATTGACTTT-CTAAAAATTGTAGAAATACCATTGGTTTAC
1 AAAATTACAGAAATACCACTGA-TTTAC--AAAATTACAGAAATACCACTGGTTTAC
*
16402229 AAAATTACTGAAATACC
1 AAAATTACAGAAATACC
16402246 CTTGGTTTGT
Statistics
Matches: 105, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
54 63 0.60
55 4 0.04
56 38 0.36
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (54 bp):
AAAATTACAGAAATACCACTGATTTACAAAATTACAGAAATACCACTGGTTTAC
Found at i:16402339 original size:28 final size:27
Alignment explanation
Indices: 16402307--16402368 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
16402297 ACCCCTAATA
16402307 GGTAAAAAGACCGTAAAACCCCATGTAG
1 GGTAAAAAGACCGTAAAA-CCCATGTAG
** * * *
16402335 GGTAAAGTGACCGTAATACCCTTGTAT
1 GGTAAAAAGACCGTAAAACCCATGTAG
16402362 GGTAAAA
1 GGTAAAA
16402369 TGACGAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (27 bp):
GGTAAAAAGACCGTAAAACCCATGTAG
Found at i:16402372 original size:27 final size:28
Alignment explanation
Indices: 16402307--16402372 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
16402297 ACCCCTAATA
*
16402307 GGTAAAAAGACCGTAAAACCCCATGTAG
1 GGTAAAATGACCGTAAAACCCCATGTAG
* * * *
16402335 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAAAACCCCATGTAG
16402362 GGTAAAATGAC
1 GGTAAAATGAC
16402373 GAATATGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (28 bp):
GGTAAAATGACCGTAAAACCCCATGTAG
Found at i:16403240 original size:24 final size:25
Alignment explanation
Indices: 16403169--16403238 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
16403159 AGGAAGGGCT
* * *
16403169 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
16403194 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
16403219 AAAAAGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
16403239 ATTAAAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:16403447 original size:42 final size:42
Alignment explanation
Indices: 16403385--16403475 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
16403375 TAGTCTCCCC
* *
16403385 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCAAAAATTCATTGACATTACATGTGATATTG
16403427 AAATGGGCTTGCAAAAATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCAAAAATTCATTGACATTACATGTGATATTG
16403469 AAATGGG
1 AAATGGG
16403476 ACTAAGGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCAAAAATTCATTGACATTACATGTGATATTG
Found at i:16404291 original size:31 final size:31
Alignment explanation
Indices: 16404250--16404313 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
16404240 CCTTTTCATA
*
16404250 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
16404281 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
16404312 TT
1 TT
16404314 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:16404558 original size:24 final size:24
Alignment explanation
Indices: 16404506--16404694 Score: 260
Period size: 24 Copynumber: 8.0 Consensus size: 24
16404496 GCTTTATCAT
*
16404506 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
16404531 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
16404555 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
16404578 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
16404602 ATAACTGGGGCATAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
16404625 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
16404649 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
16404672 ATAACTGGGGCACAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
16404695 TCACTTCCTC
Statistics
Matches: 150, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
23 65 0.43
24 73 0.49
25 12 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:16404582 original size:47 final size:47
Alignment explanation
Indices: 16404505--16404695 Score: 285
Period size: 47 Copynumber: 4.0 Consensus size: 47
16404495 TGCTTTATCA
* *
16404505 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-C-TTTAATAACTGGGGCATAAGCCCTTTT
*
16404554 TATAACTGGGGCATAAGCCCTTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTT
* *
16404601 GATAACTGGGGCATAAGCCCTTTGATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTT
* *
16404648 GATAACTGGGGCATAAGCCCTTTAATAACTGGGGCACAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTT
16404695 T
1 T
16404696 CACTTCCTCC
Statistics
Matches: 132, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
47 114 0.86
48 5 0.04
49 13 0.10
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (47 bp):
TATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:16404585 original size:23 final size:23
Alignment explanation
Indices: 16404527--16404693 Score: 244
Period size: 23 Copynumber: 7.1 Consensus size: 23
16404517 CCTAGCCTCT
*
16404527 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
16404550 TTTTTATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
16404574 TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
16404597 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
16404621 TTTGATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
16404644 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
16404668 TTTAATAACTGGGGCACAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
16404691 TTT
1 TTT
16404694 TTCACTTCCT
Statistics
Matches: 133, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
23 68 0.51
24 65 0.49
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:16404766 original size:9 final size:9
Alignment explanation
Indices: 16404752--16404828 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
16404742 CATCCGTGTG
16404752 CATATCATA
1 CATATCATA
*
16404761 CATATCATGTG
1 CATATCA--TA
16404772 CATATCATA
1 CATATCATA
* *
16404781 CATGTCATGTG
1 CATATCA--TA
16404792 CATATCATA
1 CATATCATA
*
16404801 CATATCATGTG
1 CATATCA--TA
16404812 CATATCATA
1 CATATCATA
16404821 CATATCAT
1 CATATCAT
16404829 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:16404771 original size:20 final size:20
Alignment explanation
Indices: 16404748--16404830 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
16404738 TGAACATCCG
16404748 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
16404768 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
16404788 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
16404808 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
16404828 TGT
1 TGT
16404831 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:16404777 original size:11 final size:11
Alignment explanation
Indices: 16404748--16404819 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
16404738 TGAACATCCG
16404748 TGTGCATATCA
1 TGTGCATATCA
*
16404759 --TACATATCA
1 TGTGCATATCA
16404768 TGTGCATATCA
1 TGTGCATATCA
* *
16404779 --TACATGTCA
1 TGTGCATATCA
16404788 TGTGCATATCA
1 TGTGCATATCA
*
16404799 --TACATATCA
1 TGTGCATATCA
16404808 TGTGCATATCA
1 TGTGCATATCA
16404819 T
1 T
16404820 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:16404913 original size:25 final size:25
Alignment explanation
Indices: 16404867--16404916 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16404857 ATATATAAAC
* * * *
16404867 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
16404892 CCTAGGGGCAAAACGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
16404917 TATTATAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:16408225 original size:31 final size:31
Alignment explanation
Indices: 16408184--16408247 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
16408174 CCTTTTCATA
*
16408184 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
16408215 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
16408246 TT
1 TT
16408248 ACGTAAACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:16408514 original size:47 final size:48
Alignment explanation
Indices: 16408437--16408627 Score: 282
Period size: 47 Copynumber: 4.0 Consensus size: 48
16408427 TGCTTTATCA
* *
16408437 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
16408486 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* *
16408533 GATAACT-GGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
16408580 GATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
16408627 T
1 T
16408628 CACTTCCTCC
Statistics
Matches: 131, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
46 12 0.09
47 89 0.68
48 17 0.13
49 13 0.10
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:16408517 original size:23 final size:24
Alignment explanation
Indices: 16408438--16408626 Score: 269
Period size: 24 Copynumber: 8.0 Consensus size: 24
16408428 GCTTTATCAT
*
16408438 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
16408463 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
16408487 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
16408510 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
16408534 ATAACT-GGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
16408557 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
16408581 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
16408604 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
16408627 TCACTTCCTC
Statistics
Matches: 151, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
23 65 0.43
24 74 0.49
25 12 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:16408699 original size:9 final size:9
Alignment explanation
Indices: 16408685--16408761 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
16408675 ATCTCGTGTG
16408685 CATATCATA
1 CATATCATA
*
16408694 CATATCATGTG
1 CATATCA--TA
16408705 CATATCATA
1 CATATCATA
* *
16408714 CATGTCATGTG
1 CATATCA--TA
16408725 CATATCATA
1 CATATCATA
*
16408734 CATATCATGTG
1 CATATCA--TA
16408745 CATATCATA
1 CATATCATA
16408754 CATATCAT
1 CATATCAT
16408762 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:16408704 original size:20 final size:20
Alignment explanation
Indices: 16408681--16408763 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
16408671 GAACATCTCG
16408681 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
16408701 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
16408721 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
16408741 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
16408761 TGT
1 TGT
16408764 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:16408710 original size:11 final size:11
Alignment explanation
Indices: 16408681--16408752 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
16408671 GAACATCTCG
16408681 TGTGCATATCA
1 TGTGCATATCA
*
16408692 --TACATATCA
1 TGTGCATATCA
16408701 TGTGCATATCA
1 TGTGCATATCA
* *
16408712 --TACATGTCA
1 TGTGCATATCA
16408721 TGTGCATATCA
1 TGTGCATATCA
*
16408732 --TACATATCA
1 TGTGCATATCA
16408741 TGTGCATATCA
1 TGTGCATATCA
16408752 T
1 T
16408753 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:16408846 original size:25 final size:25
Alignment explanation
Indices: 16408800--16408847 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
16408790 ATATATAAAC
* * * *
16408800 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
16408825 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
16408848 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:16412159 original size:31 final size:31
Alignment explanation
Indices: 16412118--16412181 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
16412108 CCTTTTCATA
*
16412118 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
16412149 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
16412180 TT
1 TT
16412182 ACGGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:16412450 original size:47 final size:48
Alignment explanation
Indices: 16412373--16412563 Score: 257
Period size: 47 Copynumber: 4.0 Consensus size: 48
16412363 TGCTTTATCA
* *
16412373 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
*
16412422 TATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
16412469 GATAACTGGGGCATAAGCCCTTTTGAA-AACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTT-AATAACTGGGGCATAAGCCCTTTT
* * *
16412517 GATAACT-GGGCATAAGCCC-TTTAATAATTGGGGCATAAGCCTTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
16412563 T
1 T
16412564 CACTTCCTCC
Statistics
Matches: 130, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
45 2 0.02
46 22 0.17
47 56 0.43
48 35 0.27
49 15 0.12
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:16412453 original size:23 final size:24
Alignment explanation
Indices: 16412374--16412562 Score: 244
Period size: 24 Copynumber: 8.0 Consensus size: 24
16412364 GCTTTATCAT
*
16412374 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
16412399 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
16412423 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
16412446 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
16412470 ATAACTGGGGCATAAGCCCTTTTGA
1 ATAACTGGGGCATAAGCCCTTTT-A
*
16412495 A-AACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
16412518 ATAACT-GGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
16412540 ATAATTGGGGCATAAGCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTT
16412563 TCACTTCCTC
Statistics
Matches: 145, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.06
23 45 0.31
24 79 0.54
25 13 0.09
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:16412474 original size:71 final size:72
Alignment explanation
Indices: 16412374--16412563 Score: 253
Period size: 71 Copynumber: 2.7 Consensus size: 72
16412364 GCTTTATCAT
* * *
16412374 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTTAAAACTGGGGCATAA
16412438 GCCC-TTTA
64 GCCCTTTTA
* * *
16412446 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGAAAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTAAAACTGGGGCATAAGC
*
16412511 CCTTTTG
66 CCTTTTA
* *
16412518 ATAACT-GGGCATAAGCCC-TTTAATAATTGGGGCATAAGCCTTTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTT
16412564 CACTTCCTCC
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
70 24 0.23
71 60 0.57
72 21 0.20
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTAAAACTGGGGCATAAGC
CCTTTTA
Found at i:16412635 original size:9 final size:9
Alignment explanation
Indices: 16412621--16412697 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
16412611 ATCTCGTGTG
16412621 CATATCATA
1 CATATCATA
*
16412630 CATATCATGTG
1 CATATCA--TA
16412641 CATATCATA
1 CATATCATA
* *
16412650 CATGTCATGTG
1 CATATCA--TA
16412661 CATATCATA
1 CATATCATA
*
16412670 CATATCATGTG
1 CATATCA--TA
16412681 CATATCATA
1 CATATCATA
16412690 CATATCAT
1 CATATCAT
16412698 GTTTATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 31 0.57
11 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:16412640 original size:20 final size:20
Alignment explanation
Indices: 16412617--16412699 Score: 157
Period size: 20 Copynumber: 4.2 Consensus size: 20
16412607 GAACATCTCG
16412617 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
16412637 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
16412657 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
16412677 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
16412697 TGT
1 TGT
16412700 TTATCAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:16412646 original size:11 final size:11
Alignment explanation
Indices: 16412617--16412688 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
16412607 GAACATCTCG
16412617 TGTGCATATCA
1 TGTGCATATCA
*
16412628 --TACATATCA
1 TGTGCATATCA
16412637 TGTGCATATCA
1 TGTGCATATCA
* *
16412648 --TACATGTCA
1 TGTGCATATCA
16412657 TGTGCATATCA
1 TGTGCATATCA
*
16412668 --TACATATCA
1 TGTGCATATCA
16412677 TGTGCATATCA
1 TGTGCATATCA
16412688 T
1 T
16412689 ACATATCATG
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 23 0.49
11 24 0.51
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:16412782 original size:25 final size:25
Alignment explanation
Indices: 16412736--16412783 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
16412726 ATATATAAAC
* * * *
16412736 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
16412761 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
16412784 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:16414315 original size:31 final size:31
Alignment explanation
Indices: 16414277--16414358 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
16414267 GTTACACTTT
*
16414277 GGCCCAGTGATATGGTTTATGAAAAGGCTTC
1 GGCCCAGTGATATGATTTATGAAAAGGCTTC
16414308 GGCCCAGTGATATGATTTATGAAAAGGCTTC
1 GGCCCAGTGATATGATTTATGAAAAGGCTTC
** *
16414339 AACCCACTGATATGATTTAT
1 GGCCCAGTGATATGATTTAT
16414359 TGGGATTACA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (31 bp):
GGCCCAGTGATATGATTTATGAAAAGGCTTC
Found at i:16418473 original size:30 final size:30
Alignment explanation
Indices: 16418438--16418494 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
16418428 TAGGCACTTC
* *
16418438 CACACGGGTAAACCACACGCTCGTGTGAGG
1 CACACGGGCAAACCACACGCTCATGTGAGG
*
16418468 CACACGGGCAATCCACACGCTCATGTG
1 CACACGGGCAAACCACACGCTCATGTG
16418495 TCATGGCCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.14
Consensus pattern (30 bp):
CACACGGGCAAACCACACGCTCATGTGAGG
Found at i:16419997 original size:14 final size:14
Alignment explanation
Indices: 16419978--16420006 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16419968 TGGAACAAAC
16419978 TTTGTAATATAAAT
1 TTTGTAATATAAAT
16419992 TTTGTAATATAAAT
1 TTTGTAATATAAAT
16420006 T
1 T
16420007 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:16420044 original size:62 final size:62
Alignment explanation
Indices: 16419962--16420116 Score: 256
Period size: 62 Copynumber: 2.5 Consensus size: 62
16419952 TTATAACACG
* *
16419962 AAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAATACATTACAATATT
1 AAAAATTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAATACATTACAACATT
* * *
16420024 AAAAATTGGAACAAATTTTGTAATATAAATTTTGTTATATAAATTAAATACATTATAACATT
1 AAAAATTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAATACATTACAACATT
*
16420086 AAAAATTGGAACAAACTTTGTACTATAAATT
1 AAAAATTGGAACAAACTTTGTAATATAAATT
16420117 AGGTACATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 86 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (62 bp):
AAAAATTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAATACATTACAACATT
Found at i:16420055 original size:14 final size:14
Alignment explanation
Indices: 16420036--16420068 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16420026 AAATTGGAAC
16420036 AAATTTTGTAATAT
1 AAATTTTGTAATAT
*
16420050 AAATTTTGTTATAT
1 AAATTTTGTAATAT
16420064 AAATT
1 AAATT
16420069 AAATACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
AAATTTTGTAATAT
Found at i:16423709 original size:16 final size:16
Alignment explanation
Indices: 16423690--16423732 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
16423680 CTTTAGCCAT
16423690 ATTTACTTTTAGTGCA
1 ATTTACTTTTAGTGCA
* **
16423706 ATTTATTTTTAGTTTA
1 ATTTACTTTTAGTGCA
16423722 ATTTCACTTTT
1 ATTT-ACTTTT
16423733 CTAACTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (16 bp):
ATTTACTTTTAGTGCA
Found at i:16425153 original size:20 final size:20
Alignment explanation
Indices: 16425104--16425159 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
16425094 GATAGGGGCA
* *
16425104 CATGCCTGTGTGGCCTGGTG
1 CATGCCCGTGTGGCCTGGAG
* * *
16425124 AACGCTCGTGTGGCCTGGAG
1 CATGCCCGTGTGGCCTGGAG
16425144 CATGCCCGTGTGGCCT
1 CATGCCCGTGTGGCCT
16425160 ACCCGTGGGC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.25
Consensus pattern (20 bp):
CATGCCCGTGTGGCCTGGAG
Found at i:16436211 original size:27 final size:27
Alignment explanation
Indices: 16436171--16436245 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
16436161 GCAATTGGTA
16436171 CCGCCTATCAGATAGGCACCACCAGTG
1 CCGCCTATCAGATAGGCACCACCAGTG
* * *** *
16436198 CTGCCTACCAGATAGGGGTCACTAGTG
1 CCGCCTATCAGATAGGCACCACCAGTG
*
16436225 CCACCTATCAGATAGGCACCA
1 CCGCCTATCAGATAGGCACCA
16436246 TACCCCCATA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (27 bp):
CCGCCTATCAGATAGGCACCACCAGTG
Found at i:16436799 original size:20 final size:20
Alignment explanation
Indices: 16436774--16436871 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 20
16436764 TTTATATATT
*
16436774 TTTTAGAATTTTTTTAAAAA
1 TTTTAGAATTTTTTAAAAAA
16436794 TTTTAGAATTTTTTAAAAAATATAAA
1 TTTTAGAATTTTTT----AA-A-AAA
* * *
16436820 TTTTGGAATTTTAT-AAATA
1 TTTTAGAATTTTTTAAAAAA
16436839 TTTT-GAATTTTTTAAAAATA
1 TTTTAGAATTTTTTAAAAA-A
16436859 TTTT-GAATTTTTT
1 TTTTAGAATTTTTT
16436872 TGTAATTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
18 8 0.12
19 9 0.14
20 29 0.45
21 1 0.02
24 1 0.02
25 1 0.02
26 15 0.23
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (20 bp):
TTTTAGAATTTTTTAAAAAA
Found at i:16436821 original size:18 final size:19
Alignment explanation
Indices: 16436777--16436823 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
16436767 ATATATTTTT
* *
16436777 TAGAATTTTTTTAAAAATTT
1 TAGAA-TTTTTTAAAAAATA
16436797 TAGAATTTTTTAAAAAATA
1 TAGAATTTTTTAAAAAATA
16436816 TA-AATTTT
1 TAGAATTTT
16436824 GGAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
TAGAATTTTTTAAAAAATA
Done.