Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 121 of 362
Found at i:40024897 original size:3 final size:3
Alignment explanation
Indices: 40024889--40024948 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
40024879 ACACAAAGCA
40024889 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
40024937 AAT AAC AAT AAT
1 AAT AAT AAT AAT
40024949 TTGTGATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40031046 original size:42 final size:42
Alignment explanation
Indices: 40030987--40031068 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
40030977 GGGTTATGTG
* *
40030987 TGATTTTGTGTAAGACCATATCTGGGATATGGCATCGATATT
1 TGATTTTGTGTAAGACCATATCTGAGACATGGCATCGATATT
* *
40031029 TGATTTTGTGTAAGACCATGTCTGAGACATGGCATTGATA
1 TGATTTTGTGTAAGACCATATCTGAGACATGGCATCGATA
40031069 CGAGATATCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (42 bp):
TGATTTTGTGTAAGACCATATCTGAGACATGGCATCGATATT
Found at i:40031082 original size:42 final size:42
Alignment explanation
Indices: 40030994--40031090 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
40030984 GTGTGATTTT
* * *** * *
40030994 GTGTAAGACCATATCTGGGATATGGCATCGATATTTGATTTT
1 GTGTAAGACCATATCTGAGACATGGCATCGATACGAGATATC
* *
40031036 GTGTAAGACCATGTCTGAGACATGGCATTGATACGAGATATC
1 GTGTAAGACCATATCTGAGACATGGCATCGATACGAGATATC
40031078 GTGTAAGACCATA
1 GTGTAAGACCATA
40031091 GTTGGGCTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (42 bp):
GTGTAAGACCATATCTGAGACATGGCATCGATACGAGATATC
Found at i:40040534 original size:18 final size:17
Alignment explanation
Indices: 40040513--40040548 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40040503 TAGAATTAGG
*
40040513 TTGAGAAAATTATTTAAT
1 TTGA-AAAATTAATTAAT
40040531 TTGAAAAATTAATTAAT
1 TTGAAAAATTAATTAAT
40040548 T
1 T
40040549 AAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (17 bp):
TTGAAAAATTAATTAAT
Found at i:40040540 original size:17 final size:17
Alignment explanation
Indices: 40040513--40040562 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 17
40040503 TAGAATTAGG
40040513 TTGAGAAAATTATTTAAT
1 TTGA-AAAATTATTTAAT
*
40040531 TTGAAAAATTAATTAA-
1 TTGAAAAATTATTTAAT
*
40040547 TT-AAAAATAATTTAAT
1 TTGAAAAATTATTTAAT
40040563 AAATAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 11 0.39
16 2 0.07
17 11 0.39
18 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TTGAAAAATTATTTAAT
Found at i:40043437 original size:17 final size:18
Alignment explanation
Indices: 40043415--40043450 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40043405 ATAATTAAGA
40043415 TAATTATAAT-ATTTGAT
1 TAATTATAATGATTTGAT
*
40043432 TAATTATTATGATTTGAT
1 TAATTATAATGATTTGAT
40043450 T
1 T
40043451 GTAATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (18 bp):
TAATTATAATGATTTGAT
Found at i:40049756 original size:34 final size:34
Alignment explanation
Indices: 40049713--40049780 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
40049703 AAAGAATGTA
40049713 ATCTTTCTTGTTCCAGTAGTGGATTAATAGGTGG
1 ATCTTTCTTGTTCCAGTAGTGGATTAATAGGTGG
*
40049747 ATCTTTCTTGTTCCAGTTGTGGATTAATAGGTGG
1 ATCTTTCTTGTTCCAGTAGTGGATTAATAGGTGG
40049781 TATTCATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.43
Consensus pattern (34 bp):
ATCTTTCTTGTTCCAGTAGTGGATTAATAGGTGG
Found at i:40058256 original size:40 final size:40
Alignment explanation
Indices: 40057946--40058250 Score: 420
Period size: 40 Copynumber: 7.7 Consensus size: 40
40057936 TTGAATGATG
* * * * *
40057946 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
40057986 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40058026 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
40058065 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40058105 TCCGGGTTAAGTCCCGAAGACATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
40058145 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40058185 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
40058226 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
40058251 AACGAGGAGC
Statistics
Matches: 242, Mismatches: 18, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
39 34 0.14
40 198 0.82
41 10 0.04
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40061614 original size:48 final size:48
Alignment explanation
Indices: 40061516--40061741 Score: 180
Period size: 48 Copynumber: 4.7 Consensus size: 48
40061506 TAATGTAAGC
* * *
40061516 CAGTATAAGA-CATGTCTGGGACAT-GCGTCCGCTACG---AGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGTATAGATGTGT
40061560 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGATGTGT
* * * * * * *
40061608 CAGTGTAAGACTATGTCTAGGATATGACATTGGCA--TAGAGATGTGAGAGC
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGATGT----GT
* * * * * *
40061658 CAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATTTCGAT-AGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATC-GGCACG-TATAGATGTGT
*
40061707 CACTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
40061742 TTACACCCTA
Statistics
Matches: 142, Mismatches: 27, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
44 9 0.06
45 17 0.12
46 14 0.10
48 40 0.28
49 30 0.21
50 26 0.18
51 2 0.01
54 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGATGTGT
Found at i:40067999 original size:48 final size:46
Alignment explanation
Indices: 40067899--40068163 Score: 215
Period size: 48 Copynumber: 5.7 Consensus size: 46
40067889 TTATTTGTGT
* *
40067899 GCCAGTGTAAGACATGTCT-GGACATGCATCAGCCAC-ATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGCACTATGATGAGA
* *
40067944 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACTAAGACGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACTATGATGAGA
* * *
40067992 GCTAGTGTAAGACATGTCTAGGACATGCATCGGC-CTTGTGATGTA-A
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCAC-TATGATG-AGA
* * * *
40068038 GCCAGTGTAAGACATGTCTGAGACATGCGTCAG--CTATGA-GATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACTATGATGA-GA
* *
40068082 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTAT-A-GATGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAC-TATGATGA-GA
* * *
40068130 GTCAGTGTAAGACCATGTTTGGGATATGGCATCG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
40068164 ACAAAGAGAT
Statistics
Matches: 185, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 15 0.08
45 27 0.15
46 53 0.29
47 24 0.13
48 61 0.33
49 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACTATGATGAGA
Found at i:40068045 original size:46 final size:45
Alignment explanation
Indices: 40067899--40068117 Score: 178
Period size: 46 Copynumber: 4.7 Consensus size: 45
40067889 TTATTTGTGT
* ** **
40067899 GCCAGTGTAAGACATGTCTGGACATGCATCAGCCACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGACATGCATCGGCCTTAAGATGAGA
*
40067944 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-TAAGACGAGA
1 GCCAGTGTAAGA-CATGTCT-GGACAT-GCATCGGC-CTTAAGATGAGA
* **
40067992 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTTGTGATGTA-A
1 GCCAGTGTAAGACATGTCT-GGACATGCATCGGCCTTAAGATG-AGA
* * * *
40068038 GCCAGTGTAAGACATGTCTGAGACATGCGTCAG-C-TATGA-GATGT
1 GCCAGTGTAAGACATGTCTG-GACATGCATCGGCCTTAAGATGA-GA
*
40068082 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GCCAGTGTAAGA-CATGTCT-GGACAT-GCATCGGC
40068118 ACGTATAGAT
Statistics
Matches: 143, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 15 0.10
45 27 0.19
46 54 0.38
47 20 0.14
48 24 0.17
49 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGACATGCATCGGCCTTAAGATGAGA
Found at i:40069328 original size:40 final size:41
Alignment explanation
Indices: 40069284--40069362 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 41
40069274 AGGTTTTTAG
40069284 ACACGGGCTA-AGACAC-AGGTGTGTCATGGCCGTGTGAGGA
1 ACACGGGCTATAGACACGAGGTGTGTCA-GGCCGTGTGAGGA
* *
40069324 ACACGGGCTATAGACACGGATGTGTGTCAGGCTGTGTGA
1 ACACGGGCTATAGACAC-GAGGTGTGTCAGGCCGTGTGA
40069363 AAACCCCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 10 0.29
41 6 0.18
42 9 0.26
43 9 0.26
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.20
Consensus pattern (41 bp):
ACACGGGCTATAGACACGAGGTGTGTCAGGCCGTGTGAGGA
Found at i:40079513 original size:46 final size:47
Alignment explanation
Indices: 40079409--40079625 Score: 180
Period size: 46 Copynumber: 4.6 Consensus size: 47
40079399 ACATTATGAG
* *
40079409 AGCCAGTGTAAGACCATGTTTAGGACATGGCATCGGCATT-GAGAAG-A
1 AGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGC-TTCGAGAAGTA
* * * *
40079456 GTGCTAGTGTAAGA-CATGTCTGGGACATGCTTCGGCTTCGAGACGTA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTTCGAGAAGTA
* * *
40079503 AGCCAGTGTAAG-GCATGTCTGGGACATGCATCGGCTACGAGAGGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTTCGAGAAGTA
* * *
40079548 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-AC-AGATATGCTA
1 AGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTTCGAGA-A-G-TA
**
40079596 GAGCTTGTGTAAGACCATGTCTGGGACATG
1 -AGCCAGTGTAAGACCATGTCTGGGACATG
40079626 GCATTGGCAC
Statistics
Matches: 140, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
44 13 0.09
45 18 0.13
46 59 0.42
47 14 0.10
48 11 0.08
49 1 0.01
50 24 0.17
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTTCGAGAAGTA
Found at i:40081822 original size:22 final size:21
Alignment explanation
Indices: 40081773--40081826 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
40081763 CGGCCTGTAG
**
40081773 CACGGGCGTGTCCCGGGGTCA
1 CACGGGCGTGTCCCGGGACCA
* *
40081794 CAAGGGCGTGTCCCTTGGACCA
1 CACGGGCGTGTCCC-GGGACCA
40081816 CACGGGCGTGT
1 CACGGGCGTGT
40081827 GAGCCTGCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.13, C:0.31, G:0.39, T:0.17
Consensus pattern (21 bp):
CACGGGCGTGTCCCGGGACCA
Found at i:40082205 original size:18 final size:18
Alignment explanation
Indices: 40082175--40082234 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
40082165 GAACAGTTCT
* *
40082175 CATAAAATTAGTAGTGCA
1 CATAAAATAAGTAATGCA
* *
40082193 CATATAATAAGTAATTCA
1 CATAAAATAAGTAATGCA
*
40082211 CATAAAATAAGAAGAT-CA
1 CATAAAATAAGTA-ATGCA
40082229 CATAAA
1 CATAAA
40082235 TTATAAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 33 0.94
19 2 0.06
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (18 bp):
CATAAAATAAGTAATGCA
Found at i:40082280 original size:17 final size:17
Alignment explanation
Indices: 40082258--40082366 Score: 103
Period size: 17 Copynumber: 6.4 Consensus size: 17
40082248 TCAAACATTT
40082258 GTTCATATAAAATAACA
1 GTTCATATAAAATAACA
*
40082275 GTTCATACT-AAATGACA
1 GTTCATA-TAAAATAACA
* * *
40082292 GCTCATACAAAATAATA
1 GTTCATATAAAATAACA
* *
40082309 GTTCATATGAAATATCA
1 GTTCATATAAAATAACA
**
40082326 GTTCATATTGAATAACA
1 GTTCATATAAAATAACA
* **
40082343 ATTCATGCAAAATAACA
1 GTTCATATAAAATAACA
40082360 GTTCATA
1 GTTCATA
40082367 CTCCATCATA
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
17 69 0.99
18 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (17 bp):
GTTCATATAAAATAACA
Found at i:40082328 original size:51 final size:51
Alignment explanation
Indices: 40082258--40082366 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
40082248 TCAAACATTT
* * *
40082258 GTTCATATAAAATAACAGTTCATACTAAATGACAGCTCATACAAAATAATA
1 GTTCATATAAAATAACAGTTCATACTAAATAACAACTCATACAAAATAACA
* * * * * *
40082309 GTTCATATGAAATATCAGTTCATATTGAATAACAATTCATGCAAAATAACA
1 GTTCATATAAAATAACAGTTCATACTAAATAACAACTCATACAAAATAACA
40082360 GTTCATA
1 GTTCATA
40082367 CTCCATCATA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (51 bp):
GTTCATATAAAATAACAGTTCATACTAAATAACAACTCATACAAAATAACA
Found at i:40083358 original size:27 final size:28
Alignment explanation
Indices: 40083307--40083475 Score: 170
Period size: 29 Copynumber: 6.0 Consensus size: 28
40083297 CGAAAACATT
*
40083307 ACAAAACCCATCCATATATATTATATAAA
1 ACAAAACCCAT-CATATATATTATATATA
* *
40083336 ACAAGACCCAT-ATATATA-T-TATATG
1 ACAAAACCCATCATATATATTATATATA
*
40083361 ACAAAACTCA-C-TCATATATTATATATA
1 ACAAAACCCATCAT-ATATATTATATATA
* *
40083388 ACAAAATCCATGCATATATATGATATATA
1 ACAAAACCCAT-CATATATATTATATATA
40083417 ACAAAACCCATACATATATATTATATATA
1 ACAAAACCCAT-CATATATATTATATATA
*
40083446 AC-AAACCCATGCATGTATATATATTATATA
1 ACAAAACCCAT-CATATATAT-TA-TATATA
40083476 TATAATAAAG
Statistics
Matches: 117, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
24 1 0.01
25 17 0.15
26 2 0.02
27 20 0.17
28 16 0.14
29 54 0.46
30 7 0.06
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (28 bp):
ACAAAACCCATCATATATATTATATATA
Found at i:40083465 original size:81 final size:79
Alignment explanation
Indices: 40083307--40083468 Score: 175
Period size: 81 Copynumber: 2.0 Consensus size: 79
40083297 CGAAAACATT
* *
40083307 ACAAAACCCATCCATATATATTATATAAAACAAGACCCATATATATATTATATGACAAAACTCAC
1 ACAAAACCCATCCATATATATGATATAAAACAAAACCCATATATATATTATATGACAAAA--CAC
* *
40083372 TCATATATTATATATA
64 CCATACATTATATATA
* * * *
40083388 ACAAAATCCATGCATATATATGATATATAACAAAACCCATACATATATATTATAT-ATAACAA-A
1 ACAAAACCCATCCATATATATGATATAAAACAAAACCCAT--ATATATATTATATGACAA-AACA
*
40083451 CCCATGCATGTATATATA
63 CCCATACAT-TATATATA
40083469 TTATATATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
80 7 0.10
81 43 0.63
82 3 0.04
83 15 0.22
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.30
Consensus pattern (79 bp):
ACAAAACCCATCCATATATATGATATAAAACAAAACCCATATATATATTATATGACAAAACACCC
ATACATTATATATA
Found at i:40084500 original size:78 final size:78
Alignment explanation
Indices: 40084371--40084531 Score: 313
Period size: 78 Copynumber: 2.1 Consensus size: 78
40084361 AACACCATTA
*
40084371 AACCATTCCAATATTATAGATCAAAGCCTATTACTCTCTATACCAAGAACTTAACTAATTTTGTC
1 AACCATTCCAATATTATAGATCAAAGCCTATTAATCTCTATACCAAGAACTTAACTAATTTTGTC
40084436 AAAATAGTTGTTT
66 AAAATAGTTGTTT
40084449 AACCATTCCAATATTATAGATCAAAGCCTATTAATCTCTATACCAAGAACTTAACTAATTTTGTC
1 AACCATTCCAATATTATAGATCAAAGCCTATTAATCTCTATACCAAGAACTTAACTAATTTTGTC
40084514 AAAATAGTTGTTT
66 AAAATAGTTGTTT
40084527 AACCA
1 AACCA
40084532 CTCAAATCTC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (78 bp):
AACCATTCCAATATTATAGATCAAAGCCTATTAATCTCTATACCAAGAACTTAACTAATTTTGTC
AAAATAGTTGTTT
Found at i:40086612 original size:11 final size:11
Alignment explanation
Indices: 40086596--40086621 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40086586 AGTTTATATG
40086596 TAATAATAATT
1 TAATAATAATT
40086607 TAATAATAATT
1 TAATAATAATT
40086618 TAAT
1 TAAT
40086622 TATTCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATAATAATT
Found at i:40088031 original size:12 final size:12
Alignment explanation
Indices: 40087994--40088031 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40087984 TTTTAATTTT
40087994 AAAAT-TTTTAA
1 AAAATATTTTAA
*
40088005 AAAATATTATAA
1 AAAATATTTTAA
40088017 AAAATATTTTTAA
1 AAAATA-TTTTAA
40088030 AA
1 AA
40088032 TTAAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 5 0.22
12 11 0.48
13 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:40095396 original size:23 final size:23
Alignment explanation
Indices: 40095370--40095415 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40095360 AAGCTCAAAA
40095370 AATGAACCTAATAAAGACTTTGT
1 AATGAACCTAATAAAGACTTTGT
40095393 AATGAACCTAATAAAGACTTTGT
1 AATGAACCTAATAAAGACTTTGT
40095416 CATAAAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (23 bp):
AATGAACCTAATAAAGACTTTGT
Found at i:40099847 original size:40 final size:40
Alignment explanation
Indices: 40099789--40099864 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
40099779 TCTCAACTTC
* * *
40099789 ATACTTGATTATTAATCTTAATGCATTATGTTGGAACATT
1 ATACTTGATAATCAATCTTAATGCATTATGGTGGAACATT
* *
40099829 ATACTTGATAATCCATCTTAGTGCATTATGGTGGAA
1 ATACTTGATAATCAATCTTAATGCATTATGGTGGAA
40099865 TACAAAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (40 bp):
ATACTTGATAATCAATCTTAATGCATTATGGTGGAACATT
Found at i:40104296 original size:93 final size:93
Alignment explanation
Indices: 40104184--40104355 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
40104174 CGCCCATAAG
*
40104184 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
40104248 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
40104277 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40104342 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
40104356 TCAACATCCT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40104350 original size:46 final size:46
Alignment explanation
Indices: 40104177--40104352 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
40104167 TGTAACCCGC
* *
40104177 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
40104223 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
40104273 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40104316 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40104353 TGCTCAACAT
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40111283 original size:93 final size:93
Alignment explanation
Indices: 40111171--40111342 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
40111161 CGCCCATAAG
*
40111171 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
40111235 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
40111264 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40111329 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
40111343 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40111337 original size:46 final size:46
Alignment explanation
Indices: 40111164--40111339 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
40111154 TGTAACCCGC
* *
40111164 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
40111210 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
40111260 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40111303 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40111340 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40132642 original size:39 final size:38
Alignment explanation
Indices: 40132606--40132788 Score: 208
Period size: 39 Copynumber: 4.7 Consensus size: 38
40132596 TCTACTCGTT
*
40132606 CAAATGCCTTCGGACATAGCCCGG-TTACAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATT--AGTAACTCGCA
*
40132645 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGA-TTAGTAACTCGCA
* *
40132684 CCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGG-ATTAGTAACTCGCA
* * * *
40132723 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
40132764 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
40132789 CATCATTCGA
Statistics
Matches: 125, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
39 81 0.65
40 31 0.25
41 13 0.10
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:40134994 original size:7 final size:7
Alignment explanation
Indices: 40134982--40135008 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40134972 CAAGGAGATG
40134982 AAAGGTC
1 AAAGGTC
40134989 AAAGGTC
1 AAAGGTC
40134996 AAAGGTC
1 AAAGGTC
40135003 AAAGGT
1 AAAGGT
40135009 TGAGGAAGAC
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:0.44, C:0.11, G:0.30, T:0.15
Consensus pattern (7 bp):
AAAGGTC
Found at i:40138046 original size:24 final size:26
Alignment explanation
Indices: 40138001--40138048 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
40137991 AATGCACAAA
* *
40138001 TTTGAAAAGAATTTCTTGAAAACACC
1 TTTGAAAAGAATTCCTTCAAAACACC
40138027 TTTG-AAA-AATTCCTTCAAAACA
1 TTTGAAAAGAATTCCTTCAAAACA
40138049 ATATTCTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 3 0.15
26 4 0.20
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (26 bp):
TTTGAAAAGAATTCCTTCAAAACACC
Found at i:40144494 original size:26 final size:25
Alignment explanation
Indices: 40144444--40144492 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
40144434 ATAAACTATT
*
40144444 AATAATTCAATAAATTGAAAATTTA
1 AATAATTAAATAAATTGAAAATTTA
40144469 AATAATTAAATAAAATT-AAAATTT
1 AATAATTAAAT-AAATTGAAAATTT
40144493 TAGGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AATAATTAAATAAATTGAAAATTTA
Found at i:40145165 original size:22 final size:19
Alignment explanation
Indices: 40145126--40145167 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
40145116 TGTAAAATTG
40145126 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
40145145 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
40145167 A
1 A
40145168 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:40147510 original size:20 final size:20
Alignment explanation
Indices: 40147487--40147526 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40147477 GGTGGGAGTT
* *
40147487 TCATGTCTCGTTATCTGATG
1 TCATGTCTCATTATCCGATG
40147507 TCATGTCTCATTATCCGATG
1 TCATGTCTCATTATCCGATG
40147527 CCCTAGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (20 bp):
TCATGTCTCATTATCCGATG
Found at i:40148937 original size:26 final size:25
Alignment explanation
Indices: 40148895--40148988 Score: 72
Period size: 23 Copynumber: 3.9 Consensus size: 25
40148885 CCGCTATTCC
* * *
40148895 GAGCT-ATGATCAGTAAGCTCCTCTT
1 GAGCTGATGAACAATAAGCT-CTATT
40148920 GAGCTGATGAACAATAAGCTCTATT
1 GAGCTGATGAACAATAAGCTCTATT
***
40148945 GAGCTGA--AATGGTAAGCTCTGA-T
1 GAGCTGATGAACAATAAGCTCT-ATT
*
40148968 GAGCTGA-AAACAATAAGCTCT
1 GAGCTGATGAACAATAAGCTCT
40148989 TACGAGCTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 18 0.32
24 11 0.19
25 16 0.28
26 12 0.21
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (25 bp):
GAGCTGATGAACAATAAGCTCTATT
Found at i:40152156 original size:50 final size:50
Alignment explanation
Indices: 40152031--40152220 Score: 231
Period size: 50 Copynumber: 3.8 Consensus size: 50
40152021 AGCCGAAGCT
* * * *
40152031 ATCTGATACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* * * * *
40152080 ATCCGGTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTCACC
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* *
40152130 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCGACTTAA-C
1 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
* *
40152179 AGTATGGTACACCGTAGTAGCCTGCACTTAGTACTACACACG
1 A-TCTGATACA-CGTAGTAGCCTGCACTTAGTACTACACACG
40152221 TGTATTCACA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 40 0.34
50 50 0.42
51 29 0.24
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (50 bp):
ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCTAACC
Found at i:40155155 original size:26 final size:27
Alignment explanation
Indices: 40155101--40155155 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
40155091 TTGTCGTAAA
*
40155101 TTCAAATCTTTTTGATTCATCAAATAT
1 TTCAAATCTTTTTGATTCATCAAAGAT
40155128 TTCAAA-CTTTTGTGA-TCAGT-AAAGAT
1 TTCAAATCTTTT-TGATTCA-TCAAAGAT
40155154 TT
1 TT
40155156 GACATTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (27 bp):
TTCAAATCTTTTTGATTCATCAAAGAT
Found at i:40159580 original size:50 final size:50
Alignment explanation
Indices: 40159462--40159687 Score: 251
Period size: 50 Copynumber: 4.5 Consensus size: 50
40159452 CATATACGCA
* * * *
40159462 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
* *
40159511 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
* * * * *
40159561 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTCAT-TGAGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CCATCTGA-TACACG
* * * * * *
40159612 TAGTAGCCTACACTTAGTACTACACATGCGACTTAA-TAGTATGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCA-TCTGATACACG
40159662 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
40159688 CGTGTATTCA
Statistics
Matches: 149, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
49 32 0.21
50 77 0.52
51 40 0.27
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
Found at i:40159660 original size:101 final size:99
Alignment explanation
Indices: 40159462--40159687 Score: 269
Period size: 101 Copynumber: 2.3 Consensus size: 99
40159452 CATATACGCA
* *
40159462 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACATAGTAGCCTACACTTA
* * *
40159527 GTACTACACACGTGACCTCACCATCTGATACACG
66 GTACTACACACGCGACCTCAACATATGATACACG
* * * *
40159561 TAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTC-AT-TGAGTACGCATAGTAGCCTACA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA--CAATCCG-GTACACATAGTAGCCTACA
* * * *
40159624 CTTAGTACTACACATGCGA-CTTAATAGTATGGTACACG
62 CTTAGTACTACACACGCGACCTCAACA-TATGATACACG
40159662 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
40159688 CGTGTATTCA
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
99 30 0.28
100 8 0.07
101 70 0.64
102 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCCGGTACACATAGTAGCCTACACTTA
GTACTACACACGCGACCTCAACATATGATACACG
Found at i:40161174 original size:32 final size:32
Alignment explanation
Indices: 40161137--40161199 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
40161127 GCATATATTC
40161137 ATAAATCAAAGAATAACAATCACATACATATA
1 ATAAATCAAAGAATAACAATCACATACATATA
* *
40161169 ATAAATCAAAGGATAACAATCACTTACATAT
1 ATAAATCAAAGAATAACAATCACATACATAT
40161200 TTATATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.24
Consensus pattern (32 bp):
ATAAATCAAAGAATAACAATCACATACATATA
Found at i:40165354 original size:11 final size:11
Alignment explanation
Indices: 40165318--40165373 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40165308 CATGGTATGT
40165318 ATGATATGCAC
1 ATGATATGCAC
* *
40165329 ATGACATG--T
1 ATGATATGCAC
40165338 ATGATATGCAC
1 ATGATATGCAC
*
40165349 ATGATATG--T
1 ATGATATGCAC
40165358 ATGATATGCAC
1 ATGATATGCAC
40165369 ATGAT
1 ATGAT
40165374 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40165373 original size:20 final size:20
Alignment explanation
Indices: 40165307--40165373 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
40165297 ATTTTGATAA
*
40165307 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40165327 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
40165347 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
40165367 ACATGAT
1 ACATGAT
40165374 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40165451 original size:26 final size:24
Alignment explanation
Indices: 40165422--40165544 Score: 151
Period size: 25 Copynumber: 5.0 Consensus size: 24
40165412 GGAGGAAGTG
40165422 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
40165446 GATAAAAGGGCTTATGCCCCAGTTAT
1 --TAAAAGGGCTTATGCCCCAGTTAT
*
40165472 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
* *
40165497 TAAAAGGGATT-TTCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
40165520 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
40165545 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
23 18 0.21
24 13 0.15
25 31 0.36
26 24 0.28
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:40165776 original size:31 final size:31
Alignment explanation
Indices: 40165738--40165801 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40165728 CGTTTACAAT
*
40165738 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAACATGA
**
40165769 AAAGGCTTCGGCCCAGTGTTATGAAACATGA
1 AAAGGCTTCGGCCCAGTAATATGAAACATGA
40165800 AA
1 AA
40165802 TATGAAAAGG
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:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAACATGA
Found at i:40171411 original size:47 final size:47
Alignment explanation
Indices: 40171353--40171707 Score: 570
Period size: 47 Copynumber: 7.6 Consensus size: 47
40171343 GATAATTGTG
40171353 ATGTG-AA-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40171398 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40171445 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40171492 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40171541 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40171588 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
40171635 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40171682 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
40171708 TCCCGAAGGG
Statistics
Matches: 288, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
45 5 0.02
46 2 0.01
47 235 0.82
49 46 0.16
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40171573 original size:143 final size:141
Alignment explanation
Indices: 40171353--40171707 Score: 588
Period size: 143 Copynumber: 2.5 Consensus size: 141
40171343 GATAATTGTG
40171353 ATGTG-AA-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40171416 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
66 GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
40171481 CAATGTGATGA
131 CAATGTGATGA
40171492 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
40171557 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATG
64 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
*
40171622 GCCGATGTGATGA
129 GCCAATGTGATGA
* * * * * * * *
40171635 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40171700 GTGATAAG
66 GTGATAAG
40171708 TCCCGAAGGG
Statistics
Matches: 202, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
139 5 0.02
140 2 0.01
141 56 0.28
143 139 0.69
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (141 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
CAATGTGATGA
Found at i:40173897 original size:38 final size:38
Alignment explanation
Indices: 40173833--40173907 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
40173823 AATCCGAGTT
*
40173833 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
40173871 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
40173908 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:40174020 original size:40 final size:40
Alignment explanation
Indices: 40173961--40174275 Score: 482
Period size: 40 Copynumber: 8.1 Consensus size: 40
40173951 AGGTCTCGAC
40173961 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40174000 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40174040 GATGTATCC-GGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
40174079 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40174119 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
40174159 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* *
40174199 GAT-TATCC-GGCT-A--CCCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * *
40174234 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40174274 GA
1 GA
40174276 CGTGTATTCG
Statistics
Matches: 256, Mismatches: 13, Indels: 13
0.91 0.05 0.05
Matches are distributed among these distances:
35 22 0.09
36 5 0.02
37 5 0.02
38 4 0.02
39 48 0.19
40 172 0.67
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:40174102 original size:79 final size:80
Alignment explanation
Indices: 40173961--40174275 Score: 482
Period size: 79 Copynumber: 4.0 Consensus size: 80
40173951 AGGTCTCGAC
40173961 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
40174025 AGCATTCATGCTAGT
66 AGCATTCATGCTAGT
*
40174040 GATGTATCC-GGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
40174104 AGCATTCGTGCTAGT
66 AGCATTCATGCTAGT
*
40174119 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
*
40174184 AGCATTCGTGCTAGT
66 AGCATTCATGCTAGT
* * * * *
40174199 GAT-TATCC-GGCT-A--CCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* *
40174259 AGCAATCATGCTGGT
66 AGCATTCATGCTAGT
40174274 GA
1 GA
40174276 CGTGTATTCG
Statistics
Matches: 223, Mismatches: 11, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
75 55 0.25
77 1 0.00
78 4 0.02
79 86 0.39
80 77 0.35
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
AGCATTCATGCTAGT
Found at i:40174206 original size:119 final size:119
Alignment explanation
Indices: 40173961--40174275 Score: 489
Period size: 119 Copynumber: 2.7 Consensus size: 119
40173951 AGGTCTCGAC
*
40173961 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
40174025 AGCATTCATGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCATGCTAGT
66 AGCATTCATGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
40174079 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* *
40174144 AGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
66 AGCATTCATGCTAGTGATGTATCC-GGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * *
40174199 GAT-TATCC-GGCT-A--CCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAG
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
* *
40174259 AGCAATCATGCTGGTGA
66 AGCATTCATGCTAGTGA
40174276 CGTGTATTCG
Statistics
Matches: 184, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
115 57 0.31
117 1 0.01
118 8 0.04
119 87 0.47
120 31 0.17
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (119 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAG
AGCATTCATGCTAGTGATGTATCCGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:40177816 original size:47 final size:47
Alignment explanation
Indices: 40177758--40178249 Score: 834
Period size: 47 Copynumber: 10.6 Consensus size: 47
40177748 GATAATTGTG
40177758 ATGTG-AA-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40177803 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40177850 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40177897 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC-ATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40177943 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40177990 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC---GTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
40178034 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40178083 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40178130 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
40178177 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
40178224 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
40178250 TCCCGAAGGG
Statistics
Matches: 425, Mismatches: 14, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
44 18 0.04
45 5 0.01
46 74 0.17
47 310 0.73
49 18 0.04
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:40177972 original size:140 final size:141
Alignment explanation
Indices: 40177758--40178249 Score: 834
Period size: 140 Copynumber: 3.5 Consensus size: 141
40177748 GATAATTGTG
40177758 ATGTG-AA-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40177821 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
66 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
40177886 CGATGTGATGA
131 CGATGTGATGA
40177897 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC-ATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40177961 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
66 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
40178026 C---GTGATGA
131 CGATGTGATGA
40178034 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* *
40178099 ATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATG
64 ATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
40178164 GCCGATGTGATGA
129 GCCGATGTGATGA
* * * * * * * *
40178177 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40178242 GTGATAAG
66 GTGATAAG
40178250 TCCCGAAGGG
Statistics
Matches: 335, Mismatches: 10, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
137 18 0.05
139 31 0.09
140 186 0.56
141 82 0.24
143 18 0.05
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (141 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
CGATGTGATGA
Found at i:40184408 original size:11 final size:11
Alignment explanation
Indices: 40184372--40184427 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
40184362 CATGGTATGT
40184372 ATGATATGCAC
1 ATGATATGCAC
* *
40184383 ATGACATG--T
1 ATGATATGCAC
40184392 ATGATATGCAC
1 ATGATATGCAC
*
40184403 ATGATATG--T
1 ATGATATGCAC
40184412 ATGATATGCAC
1 ATGATATGCAC
40184423 ATGAT
1 ATGAT
40184428 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40184427 original size:20 final size:20
Alignment explanation
Indices: 40184361--40184427 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
40184351 GTTTTGATAA
*
40184361 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40184381 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
40184401 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
40184421 ACATGAT
1 ACATGAT
40184428 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40184657 original size:24 final size:25
Alignment explanation
Indices: 40184478--40184646 Score: 263
Period size: 25 Copynumber: 6.9 Consensus size: 25
40184468 AGGAAGTGTA
**
40184478 AAAGGGCTTATGCCTTAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
40184503 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
40184528 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
* *
40184553 AAAGGGCTTATTCCCCAATTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
40184578 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
*
40184602 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
40184626 AAAGGGCTT-TGCCCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTAT
40184647 TAAAAGAGGC
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
23 12 0.09
24 33 0.24
25 92 0.67
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:40184903 original size:31 final size:31
Alignment explanation
Indices: 40184865--40184928 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
40184855 CGTTTACAGT
* *
40184865 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAACATGA
**
40184896 AAAGGCTTCAGCCCAGTGTTATGAAACATGA
1 AAAGGCTTCAGCCCAGTAATATGAAACATGA
40184927 AA
1 AA
40184929 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAACATGA
Found at i:40187613 original size:41 final size:41
Alignment explanation
Indices: 40187566--40187647 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
40187556 CAATAATGTC
*
40187566 AACATGATAAATCTTTAACAGTTTCAAAATTTAAGGTACGG
1 AACATGATAAATCTTTAACAGTTTCAAAATTTAAGATACGG
40187607 AACATGATAAATCTTTAACAGTTTCAAAATTTAAGATACGG
1 AACATGATAAATCTTTAACAGTTTCAAAATTTAAGATACGG
40187648 GCTAGCTAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (41 bp):
AACATGATAAATCTTTAACAGTTTCAAAATTTAAGATACGG
Found at i:40191110 original size:82 final size:81
Alignment explanation
Indices: 40190966--40191130 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 81
40190956 GTAATAGTTA
*
40190966 TTTGTACCTTTCCCATGCCTCATACAAGGACTCATCATCCATTTGTTGGAAAGCAGTAATCTCAT
1 TTTGTACCTTTCCCATGCCTCATACAAGGACTCATCATCCATTTGTTGGAAAGCAATAATCTCAT
40191031 TCCTCAACTTAGCATTC
66 TCCTCAA-TTAGCATTC
* * *
40191048 TTTGTACCTTTCCCATGCCTCATATAAGGACTCATCATCTATTTGTTGGAAAGCAATGATCTCAT
1 TTTGTACCTTTCCCATGCCTCATACAAGGACTCATCATCCATTTGTTGGAAAGCAATAATCTCAT
40191113 TCCTCAATTAGCATTC
66 TCCTCAATTAGCATTC
40191129 TT
1 TT
40191131 GCTAGGAGGT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 11 0.14
82 68 0.86
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (81 bp):
TTTGTACCTTTCCCATGCCTCATACAAGGACTCATCATCCATTTGTTGGAAAGCAATAATCTCAT
TCCTCAATTAGCATTC
Found at i:40192292 original size:29 final size:25
Alignment explanation
Indices: 40192232--40192282 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40192222 AATTTTAATA
40192232 AGCAAATGTGTTAATGCACATACAT
1 AGCAAATGTGTTAATGCACATACAT
40192257 AGCAAATGTGTTAATGCACATACAT
1 AGCAAATGTGTTAATGCACATACAT
40192282 A
1 A
40192283 CTTATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (25 bp):
AGCAAATGTGTTAATGCACATACAT
Found at i:40192985 original size:39 final size:39
Alignment explanation
Indices: 40192929--40193005 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
40192919 TTTAGTTTGT
*
40192929 GTCTTTAATTATGTCATAGTTTGAACATCATTAATATGA
1 GTCTTTAATTATATCATAGTTTGAACATCATTAATATGA
40192968 GTCTTTAATTATATCATAGTTTGAACATCATTAATATG
1 GTCTTTAATTATATCATAGTTTGAACATCATTAATATG
40193006 TGTTCTACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (39 bp):
GTCTTTAATTATATCATAGTTTGAACATCATTAATATGA
Found at i:40195249 original size:22 final size:22
Alignment explanation
Indices: 40195223--40195266 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40195213 GAAAATAATC
40195223 AAAATTAATCAAAATTAATTAT
1 AAAATTAATCAAAATTAATTAT
* *
40195245 AAAATTAATTAAATTTAATTAT
1 AAAATTAATCAAAATTAATTAT
40195267 GTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAATCAAAATTAATTAT
Found at i:40195257 original size:10 final size:10
Alignment explanation
Indices: 40195214--40195265 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
40195204 CAAACTGTCG
*
40195214 AAAA-TAATC
1 AAAATTAATT
*
40195223 AAAATTAATC
1 AAAATTAATT
40195233 AAAATTAATTAT
1 AAAATTAA-T-T
40195245 AAAATTAATT
1 AAAATTAATT
*
40195255 AAATTTAATT
1 AAAATTAATT
40195265 A
1 A
40195266 TGTTAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 4 0.11
10 24 0.63
11 2 0.05
12 8 0.21
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTAATT
Found at i:40196364 original size:14 final size:13
Alignment explanation
Indices: 40196337--40196375 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
40196327 TGAAATTTCA
40196337 TATATTTTTATATT
1 TATATTTTT-TATT
*
40196351 TTTATTGTTTTATT
1 TATATT-TTTTATT
40196365 TATATTTTTTA
1 TATATTTTTTA
40196376 GAGTTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.23
14 14 0.64
15 3 0.14
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TATATTTTTTATT
Found at i:40198090 original size:27 final size:27
Alignment explanation
Indices: 40198053--40198105 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
40198043 CACTATGGGA
40198053 AAAAAAAAAAGAATGAAATGTTTGTAG
1 AAAAAAAAAAGAATGAAATGTTTGTAG
40198080 AAAAAAAAAAGAATGAAATGTTTGTA
1 AAAAAAAAAAGAATGAAATGTTTGTA
40198106 ATATGTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (27 bp):
AAAAAAAAAAGAATGAAATGTTTGTAG
Found at i:40199086 original size:26 final size:26
Alignment explanation
Indices: 40199056--40199166 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
40199046 AGCATGGCTG
* *
40199056 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
40199082 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
40199110 CCAGAA-TGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
40199136 CCAGATCAGATAATTGTGGC-GTAGCCA
1 CCAGAACAGATAA-TGTGGCAG-AGCCA
40199163 CCAG
1 CCAG
40199167 GATGCTTCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
26 28 0.38
27 30 0.41
28 15 0.21
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40199155 original size:27 final size:27
Alignment explanation
Indices: 40199056--40199166 Score: 106
Period size: 26 Copynumber: 4.1 Consensus size: 27
40199046 AGCATGGCTG
* * *
40199056 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGATCAGATAATTGTGGCAGAGCCA
* *
40199082 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAT-CAGATAATTGTGGCAGAGCCA
40199110 CCAGA--ATGAT-ATATGTGGCAGAGCCA
1 CCAGATCA-GATAAT-TGTGGCAGAGCCA
40199136 CCAGATCAGATAATTGTGGC-GTAGCCA
1 CCAGATCAGATAATTGTGGCAG-AGCCA
40199163 CCAG
1 CCAG
40199167 GATGCTTCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
25 3 0.04
26 26 0.37
27 24 0.34
28 18 0.25
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (27 bp):
CCAGATCAGATAATTGTGGCAGAGCCA
Found at i:40205484 original size:93 final size:93
Alignment explanation
Indices: 40205325--40205495 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
40205315 CGCCCATAAG
* * * *
40205325 CGAACTCGGACTCAAGTCAATGAGCTTGGGCGTTCGCATCCATAAGTGAACTCGGAATCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGAATCAACTCA
40205390 ACGAGCTCGGATGTCTAGTTACATTTCA
66 ACGAGCTCGGATGTCTAGTTACATTTCA
*
40205418 CGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGGAATCAACTC
*
40205482 AACGAGTTCGGATG
65 AACGAGCTCGGATG
40205496 CTCAACCATC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGAATCAACTCA
ACGAGCTCGGATGTCTAGTTACATTTCA
Found at i:40205488 original size:46 final size:46
Alignment explanation
Indices: 40205318--40205493 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
40205308 TGTAACCCGC
* * *
40205318 CCATAAGCGAACTCGGACTCAAGTCAATGAGCTT-GGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TTCGGACGTTCGCAT
* * * * * *
40205364 CCATAAGTGAACTCGGAATCAACTCAACGAGCTCGGATGTCTAG-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGT-TCGCAT
* * *
40205410 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
40205457 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40205494 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
45 3 0.03
46 65 0.63
47 33 0.32
48 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:40207002 original size:19 final size:18
Alignment explanation
Indices: 40206970--40207020 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
40206960 AACATAATTC
* *
40206970 ATTC-ATTTCTCATACAT
1 ATTCAATTTCACATAAAT
40206987 GATTCAATTTCACATAAAT
1 -ATTCAATTTCACATAAAT
*
40207006 A-TCAATTTAACATAA
1 ATTCAATTTCACATAA
40207021 TCATATTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 13 0.45
18 5 0.17
19 11 0.38
ACGTcount: A:0.41, C:0.18, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTCAATTTCACATAAAT
Found at i:40208544 original size:43 final size:43
Alignment explanation
Indices: 40208497--40208611 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
40208487 GATGTCACTA
* * *
40208497 TCCCAGGCAGGGTTTTACACGA-AATCA-AATAACGATGCCAATG
1 TCCCAGACAGGGTCTTACA-GATAATCACAAT-ACAATGCCAATG
*
40208540 TCCCAGACATGGTCTTACAGATAATCACAATACAATGCCAATG
1 TCCCAGACAGGGTCTTACAGATAATCACAATACAATGCCAATG
* *
40208583 TCCCAGACATGATCTTACATG-TAATCACA
1 TCCCAGACAGGGTCTTACA-GATAATCACA
40208612 TCTCAGCAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
42 2 0.03
43 58 0.91
44 4 0.06
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (43 bp):
TCCCAGACAGGGTCTTACAGATAATCACAATACAATGCCAATG
Found at i:40217586 original size:27 final size:27
Alignment explanation
Indices: 40217556--40217711 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
40217546 TGCTATTCAC
* *
40217556 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * * *
40217583 TCAAATCGCACCCTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
40217610 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
40217638 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
40217665 TCCTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
40217692 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
40217712 TGTACAATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 81 0.78
28 22 0.21
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:40217627 original size:55 final size:55
Alignment explanation
Indices: 40217561--40217712 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
40217551 TTCACTCAAC
* * *
40217561 TCGCACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTACAT
* ** * * *
40217616 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
* *
40217670 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
40217713 GTACAATTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 40 0.50
55 40 0.50
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
Found at i:40225686 original size:27 final size:27
Alignment explanation
Indices: 40225656--40225810 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
40225646 TGCTATTCAC
* *
40225656 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * *
40225683 TCAAATCGCAC-CTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
40225709 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
40225737 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
40225764 TCCTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
40225791 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
40225811 TGTACAATTT
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
26 15 0.14
27 74 0.71
28 15 0.14
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:40225719 original size:54 final size:55
Alignment explanation
Indices: 40225661--40225811 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
40225651 TTCACTCAAC
* *
40225661 TCGCACACTTAGTGCCACGTAATCAAATCGCAC-CTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTACAT
* ** * * *
40225715 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
* *
40225769 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
40225812 GTACAATTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
54 68 0.85
55 12 0.15
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTACAT
Found at i:40227799 original size:17 final size:16
Alignment explanation
Indices: 40227748--40227806 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
40227738 TAATCACTTC
40227748 AATATTAAATT-AATT
1 AATATTAAATTAAATT
40227763 AATATATATAA--AAATT
1 AATAT-TA-AATTAAATT
*
40227779 AATATTAGATTAAATTT
1 AATATTAAATTAAA-TT
40227796 AATATTAAATT
1 AATATTAAATT
40227807 GTATTAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 1 0.03
15 7 0.19
16 14 0.39
17 14 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
AATATTAAATTAAATT
Found at i:40227852 original size:27 final size:27
Alignment explanation
Indices: 40227822--40227876 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
40227812 AAAATAATAG
40227822 AATGTTTATCTACAAGATAAACATTAA
1 AATGTTTATCTACAAGATAAACATTAA
40227849 AATGTTTATCTACAAGATAAACATTAA
1 AATGTTTATCTACAAGATAAACATTAA
40227876 A
1 A
40227877 TTAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (27 bp):
AATGTTTATCTACAAGATAAACATTAA
Found at i:40229549 original size:16 final size:16
Alignment explanation
Indices: 40229528--40229558 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40229518 CTATGCATGC
*
40229528 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
40229544 AAAATACAAAAGACA
1 AAAATACAAAAGACA
40229559 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:40231307 original size:49 final size:48
Alignment explanation
Indices: 40231234--40231439 Score: 195
Period size: 49 Copynumber: 4.2 Consensus size: 48
40231224 ATGTGTGTGT
40231234 CAGTGTAAGACCTGTCTAGGACATGGCATTGACACAGATAACTGAGAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATTGACACAGATAA-TGAGAGC
* ** * * * *
40231283 CAGTGTAAGACCTATCTAAAACATGGTATCGGCCTCAAGAT-ATGCA-AGC
1 CAGTGTAAGACCTGTCTAGGACATGGCAT-TGACAC-AGATAATG-AGAGC
* * * *
40231332 TAGTGCAAGACCTGTCTGGGACATGGCATTGACACAGATAAGTGAGAAC
1 CAGTGTAAGACCTGTCTAGGACATGGCATTGACACAGATAA-TGAGAGC
* * *
40231381 CAGTGTAAGACCTGTCTAGGACATGGCATCGACTA-AGAT-GTAAGAGC
1 CAGTGTAAGACCTGTCTAGGACATGGCATTGAC-ACAGATAATGAGAGC
*
40231428 TAGTGTAAGACC
1 CAGTGTAAGACC
40231440 ATGTTTGGAA
Statistics
Matches: 124, Mismatches: 26, Indels: 16
0.75 0.16 0.10
Matches are distributed among these distances:
47 20 0.16
48 5 0.04
49 89 0.72
50 6 0.05
51 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (48 bp):
CAGTGTAAGACCTGTCTAGGACATGGCATTGACACAGATAATGAGAGC
Found at i:40245161 original size:19 final size:20
Alignment explanation
Indices: 40245124--40245161 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40245114 ATAAGGTGGT
40245124 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
40245144 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
40245162 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:40256077 original size:104 final size:102
Alignment explanation
Indices: 40255916--40256137 Score: 365
Period size: 104 Copynumber: 2.2 Consensus size: 102
40255906 TTGTATATAA
** * *
40255916 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
40255981 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
*
40256019 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
40256083 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
40256122 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
40256138 GATATCCATT
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
103 48 0.43
104 63 0.56
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:40256189 original size:70 final size:72
Alignment explanation
Indices: 40256057--40256207 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
40256047 TCATTGGTGG
* *
40256057 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
40256121 GAGGGGT
66 GAGGGGT
***
40256128 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
40256192 GAGGGGT
66 GAGGGGT
40256199 TGCTAAGTG
1 TGCTAAGTG
40256208 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 24 0.32
71 50 0.68
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:40263647 original size:104 final size:104
Alignment explanation
Indices: 40263467--40263690 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
40263457 TGTATATAAA
** * *
40263467 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
40263532 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
40263571 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
40263635 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
40263675 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
40263691 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:40263742 original size:71 final size:72
Alignment explanation
Indices: 40263609--40263760 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
40263599 TCATTGGTGG
* *
40263609 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
40263674 GAGGGGT
66 GAGGGGT
***
40263681 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
40263745 GAGGGGT
66 GAGGGGT
40263752 TGCTAAGTG
1 TGCTAAGTG
40263761 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:40267122 original size:42 final size:42
Alignment explanation
Indices: 40267063--40267184 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
40267053 TAGGGTTAGT
* *
40267063 TGAGATTACGTGTAAGACCATATTTGGGATATGGCATCGAAA
1 TGAGATTACATGTAAGACCATATATGGGATATGGCATCGAAA
* * * *
40267105 TGAGATTTCATGTAAGACCATAGATGGGCTACTGGCATCGATA
1 TGAGATTACATGTAAGACCATATATGGGATA-TGGCATCGAAA
** * *
40267148 TGAGATCCCATGTAAGACCATATCTGGGATGTGGCAT
1 TGAGATTACATGTAAGACCATATATGGGATATGGCAT
40267185 TAGTATGGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 32 0.48
43 35 0.52
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (42 bp):
TGAGATTACATGTAAGACCATATATGGGATATGGCATCGAAA
Found at i:40267315 original size:20 final size:20
Alignment explanation
Indices: 40267269--40267315 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40267259 CGTCAATGTT
40267269 TAAGTTGTGAAAGACTATAG
1 TAAGTTGTGAAAGACTATAG
* *
40267289 TATGTTGTGAAAGATTAT-G
1 TAAGTTGTGAAAGACTATAG
40267308 ATAAGTTG
1 -TAAGTTG
40267316 CAAGTTGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATAG
Found at i:40272085 original size:13 final size:13
Alignment explanation
Indices: 40272067--40272095 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40272057 GGTTGTTTAT
40272067 TAAACTAATTAAC
1 TAAACTAATTAAC
40272080 TAAACTAATTAAC
1 TAAACTAATTAAC
40272093 TAA
1 TAA
40272096 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:40277989 original size:47 final size:47
Alignment explanation
Indices: 40277935--40278219 Score: 453
Period size: 47 Copynumber: 6.1 Consensus size: 47
40277925 GATTTTATGA
** * * *
40277935 GATGAATGTGAATGTGTATATATGAGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
40277982 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
40278029 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
40278076 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
40278123 GATGAATGTGAACATGCATATATGTGATAAGGTTGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* * ** *
40278170 GATGAATGTGTACATGCATATGTGTGATAAGGTAGAATGGCTAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
40278217 GAT
1 GAT
40278220 AAACGTGGAA
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 225 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:40278031 original size:22 final size:22
Alignment explanation
Indices: 40278004--40278125 Score: 72
Period size: 22 Copynumber: 5.3 Consensus size: 22
40277994 CATGCATATG
40278004 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
40278026 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
40278051 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
40278073 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
40278098 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
40278120 TGTGAT
1 TGTGAT
40278126 GAATGTGAAC
Statistics
Matches: 74, Mismatches: 12, Indels: 28
0.65 0.11 0.25
Matches are distributed among these distances:
22 22 0.30
23 18 0.24
24 18 0.24
25 16 0.22
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:40278219 original size:22 final size:22
Alignment explanation
Indices: 40278144--40278221 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 22
40278134 ACATGCATAT
* *
40278144 ATGTGATAAGGTTGAATGGCCA
1 ATGTGATAAGGTAGAATGGCTA
*
40278166 ATGTGATGAATGTGTA-CAT-GCATA
1 ATGTGAT-AA-G-GTAGAATGGC-TA
*
40278190 TGTGTGATAAGGTAGAATGGCTA
1 -ATGTGATAAGGTAGAATGGCTA
40278213 ATGTGATAA
1 ATGTGATAA
40278222 ACGTGGAAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
22 18 0.42
23 9 0.21
24 8 0.19
25 8 0.19
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.31
Consensus pattern (22 bp):
ATGTGATAAGGTAGAATGGCTA
Found at i:40278241 original size:141 final size:141
Alignment explanation
Indices: 40277942--40278265 Score: 454
Period size: 141 Copynumber: 2.3 Consensus size: 141
40277932 TGAGATGAAT
* * * *
40277942 GTGAATGTGTATATATGAGATAAGGCCTAATGGCCAATGTGATGAATGTGAACATGCATATGTGT
1 GTGAACGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGT
*
40278007 GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
66 GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
* *
40278072 ATGTGATGAAT
131 ATGTGATAAAC
* *
40278083 GTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGT
1 GTGAACGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGT
** * * * *
40278148 GATAAGGTTGAATGGCCAATGTGATGAATGTGTACATGCATATGTGTGATAAGGTAGAATGGCTA
66 GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
40278213 ATGTGATAAAC
131 ATGTGATAAAC
** *
40278224 GTGGAA-GTGTATATATGTGGCGAA-GCCGAATGGCTAATGTGA
1 GT-GAACGTGTATATATGT-GATAAGGCCGAATGGCCAATGTGA
40278266 GATATGTATG
Statistics
Matches: 161, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
141 155 0.96
142 6 0.04
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.27
Consensus pattern (141 bp):
GTGAACGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGT
GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
ATGTGATAAAC
Found at i:40280695 original size:40 final size:40
Alignment explanation
Indices: 40280635--40280897 Score: 427
Period size: 40 Copynumber: 6.6 Consensus size: 40
40280625 ATTTGAATAC
* *
40280635 ATCCAGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
40280675 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
*
40280715 ATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
40280755 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* * *
40280795 ATCCGGGCTAAGACCCAAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* * *
40280835 ATCTGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* *
40280875 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
40280898 ATTGAGCTTG
Statistics
Matches: 207, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 207 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
Found at i:40283186 original size:43 final size:42
Alignment explanation
Indices: 40283096--40283217 Score: 163
Period size: 43 Copynumber: 2.9 Consensus size: 42
40283086 TAAGGGTAGT
*
40283096 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
1 TGAGATTACGTGTAAGACCATATATGGGATATGGCATCGATA
* * *
40283138 TGAGATTTCGTGTAAGACCATAGATGGGCTATTGGCATCGATA
1 TGAGATTACGTGTAAGACCATATATGGGATA-TGGCATCGATA
** * *
40283181 TGAGATCCCATGTAAGACCATATATGGGGTATGGCAT
1 TGAGATTACGTGTAAGACCATATATGGGATATGGCAT
40283218 TAGTATGGTA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
42 33 0.47
43 37 0.53
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATATGGGATATGGCATCGATA
Found at i:40284319 original size:18 final size:19
Alignment explanation
Indices: 40284296--40284331 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40284286 ACACCTTGAT
*
40284296 CTGAAGCCCA-AAGTCTAG
1 CTGAAGCACATAAGTCTAG
40284314 CTGAAGCACATAAGTCTA
1 CTGAAGCACATAAGTCTA
40284332 AACGAAAGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (19 bp):
CTGAAGCACATAAGTCTAG
Found at i:40284451 original size:39 final size:39
Alignment explanation
Indices: 40284314--40284435 Score: 174
Period size: 39 Copynumber: 3.2 Consensus size: 39
40284304 CAAAGTCTAG
* *
40284314 CTGAAGCACATAAGT-CTAAACGAAAGCCTGAAGGCTAA
1 CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
* * **
40284352 CTAAAGCACACAAGTGCTAAAAGGAAGCCCAAAGGCTAA
1 CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
*
40284391 CTGAAGCACACAAGTGTTAAACGGAAGCCTGAAGGCTAA
1 CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
40284430 CTGAAG
1 CTGAAG
40284436 GTCATCAGAG
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 13 0.18
39 59 0.82
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (39 bp):
CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
Found at i:40289128 original size:21 final size:21
Alignment explanation
Indices: 40289103--40289167 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 21
40289093 AAGGCTAACT
40289103 GAAGCACACAAGTGCTAAATG
1 GAAGCACACAAGTGCTAAATG
*
40289124 GAAGC-C-CGAAG-GCTAACT-
1 GAAGCACAC-AAGTGCTAAATG
*
40289142 GAAGCACACAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAATG
40289163 GAAGC
1 GAAGC
40289168 CTGAAGGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 10 0.28
21 10 0.28
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAATG
Found at i:40289200 original size:39 final size:39
Alignment explanation
Indices: 40289048--40289184 Score: 204
Period size: 39 Copynumber: 3.5 Consensus size: 39
40289038 TCATGATCTA
* * * * *
40289048 AAGCCCGAAGTCTAGCTGAAGCACATAAGT-CTAAACGA
1 AAGCCTGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
*
40289086 AAGCCTGAAGGCTAACTGAAGCACACAAGTGCTAAATGG
1 AAGCCTGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
*
40289125 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
1 AAGCCTGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
40289164 AAGCCTGAAGGCTAACTGAAG
1 AAGCCTGAAGGCTAACTGAAG
40289185 GTCATCAGAG
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
38 26 0.29
39 63 0.71
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (39 bp):
AAGCCTGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
Found at i:40297916 original size:31 final size:31
Alignment explanation
Indices: 40297871--40297954 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
40297861 TTAGTCTTGA
* *
40297871 CATAT-ACTGGGCCGAATCCTTTCCATAAAT
1 CATATCACAGGGCCGAAGCCTTTCCATAAAT
* *
40297901 CATATCACAGTGCCGAAGCCTTTTCATAAAT
1 CATATCACAGGGCCGAAGCCTTTCCATAAAT
*
40297932 CATATCACTGGGCCGAAGCCTTT
1 CATATCACAGGGCCGAAGCCTTT
40297955 ACTGTAAACG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 5 0.11
31 42 0.89
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (31 bp):
CATATCACAGGGCCGAAGCCTTTCCATAAAT
Found at i:40298025 original size:42 final size:42
Alignment explanation
Indices: 40297978--40298111 Score: 241
Period size: 42 Copynumber: 3.2 Consensus size: 42
40297968 TGGCCCTTAG
* *
40297978 GCCCATTTCAATATCACATGTAATGTTAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
40298020 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
40298062 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
40298104 TCCCATTT
1 GCCCATTT
40298112 GGGGAGACTA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:40298287 original size:25 final size:25
Alignment explanation
Indices: 40298259--40298328 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
40298249 CTCTTTTAAT
40298259 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
40298284 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
40298309 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
40298329 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 38 0.90
26 4 0.10
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:40299168 original size:27 final size:27
Alignment explanation
Indices: 40299138--40299202 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
40299128 GGGCATATTC
40299138 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
40299165 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
* *
40299192 ATCTTTTTACC
1 GTCATTTTACC
40299203 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:40299286 original size:27 final size:27
Alignment explanation
Indices: 40299233--40299466 Score: 164
Period size: 27 Copynumber: 8.6 Consensus size: 27
40299223 TTTCATCCTA
* * * *
40299233 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* **
40299260 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * ** * *
40299287 TAATGGTATTTCTATAATTTTTAGAAAGT
1 CAAGGGTATTTCGGTAA-TTTTACAAA-C
** ** *
40299316 CAAGGGTATTTCTATAATTTTGTAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * *
40299343 CATGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
** *
40299370 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
40299397 C-AGTGGTATTTCGGTAATTTTACAAAC
1 CAAG-GGTATTTCGGTAATTTTACAAAC
* * *
40299424 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * *
40299451 TAGGGGTATTTTGGTA
1 CAAGGGTATTTCGGTA
40299467 CTTCTATCCT
Statistics
Matches: 168, Mismatches: 35, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
26 2 0.01
27 136 0.81
28 15 0.09
29 15 0.09
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTCGGTAATTTTACAAAC
Found at i:40299405 original size:54 final size:54
Alignment explanation
Indices: 40299346--40299502 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 54
40299336 TGTAAATCAT
*
40299346 GGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCGGTAATTTCACAAACCAG
* * * * *
40299400 TGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTCACAAACCAG
* * ** *
40299454 GGGTATTTTGGTACTTCTATCCTAC-AGGGGTATTTCAGTAATTTCACAA
1 GGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTCGGTAATTTCACAA
40299503 TCGAGGGTAA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
54 81 0.94
55 5 0.06
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGGTAATTTCACAAACCAG
Found at i:40299486 original size:81 final size:81
Alignment explanation
Indices: 40299346--40299502 Score: 194
Period size: 81 Copynumber: 1.9 Consensus size: 81
40299336 TGTAAATCAT
* * *
40299346 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTCGG
1 GGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTCAG
*
40299411 TAATTTTACAAACTAG
66 TAATTTCACAAACTAG
* * **
40299427 GGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGGT-ACTTCTATCCTA-CAGGGGTATTT
1 GGGTATTTTGGTAATTTTACAAA-TAGAGGGTATTTCGGTAATTTC-A-CAAACCAGGGGTATTT
40299489 CAGTAATTTCACAA
63 CAGTAATTTCACAA
40299503 TCGAGGGTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
80 4 0.06
81 57 0.88
82 4 0.06
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTTCACAAACCAGGGGTATTTCAG
TAATTTCACAAACTAG
Found at i:40299509 original size:27 final size:27
Alignment explanation
Indices: 40299346--40299509 Score: 136
Period size: 27 Copynumber: 6.1 Consensus size: 27
40299336 TGTAAATCAT
* * *
40299346 GGGTATTTTGGTAATTTTACAAATTGA-
1 GGGTATTTCGGTAATTTCACAAA-CGAG
*
40299373 GGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTCGGTAATTTCACAAACGAG
* * *
40299400 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTCACAAACGAG
* * *
40299427 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTCACAAACGAG
* * **
40299454 GGGTATTTTGGT-ACTTCTATCCTAC-AG
1 GGGTATTTCGGTAATTTC-A-CAAACGAG
* *
40299481 GGGTATTTCAGTAATTTCACAATCGAG
1 GGGTATTTCGGTAATTTCACAAACGAG
40299508 GG
1 GG
40299510 TAAAACGATA
Statistics
Matches: 113, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
26 6 0.05
27 100 0.88
28 7 0.06
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTCACAAACGAG
Found at i:40299566 original size:54 final size:54
Alignment explanation
Indices: 40299501--40299676 Score: 264
Period size: 54 Copynumber: 3.3 Consensus size: 54
40299491 GTAATTTCAC
* *
40299501 AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGTAAACTGGTAATTTTGTA
1 AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGTAAACTGGTAATTCTATA
*
40299555 AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGTAAACTGGTAATTCTATA
* ** * *
40299609 AATTGAGCATAAAACGGTAATTTTGTAAATCGAGGGTGAAAC-GGTAATTCTATA
1 AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGT-AAACTGGTAATTCTATA
40299663 AATCGAGGGTAAAA
1 AATCGAGGGTAAAA
40299677 TGGTAATTCT
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
54 106 0.97
55 3 0.03
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (54 bp):
AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGTAAACTGGTAATTCTATA
Found at i:40299612 original size:81 final size:81
Alignment explanation
Indices: 40299501--40299692 Score: 260
Period size: 81 Copynumber: 2.4 Consensus size: 81
40299491 GTAATTTCAC
* * * * **
40299501 AATCGAGGGTAAAACGATAATTTTGTAAATTGAGGGT-AAACTGGTAATTTTGTAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGCATAAAAC-GGTAATTTTGTAAATCGAGGGT
* *
40299565 AAAACGATAATTTTGTA
65 AAAACGATAATTCTATA
* *
40299582 AATTGAGGGTAAAATGGTAATTCTATAAATTGAGCATAAAACGGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGCATAAAACGGTAATTTTGTAAATCGAGGGTA
*
40299647 AAACGGTAATTCTATA
66 AAACGATAATTCTATA
*
40299663 AATCGAGGGTAAAATGGTAATTCTACAAAT
1 AATCGAGGGTAAAATGGTAATTCTATAAAT
40299693 CGAAGGCATT
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
81 93 0.96
82 4 0.04
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATTGAGCATAAAACGGTAATTTTGTAAATCGAGGGTA
AAACGATAATTCTATA
Found at i:40299695 original size:27 final size:27
Alignment explanation
Indices: 40299501--40299684 Score: 226
Period size: 27 Copynumber: 6.8 Consensus size: 27
40299491 GTAATTTCAC
*
40299501 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
40299528 AATTGAGGGT-AAACTGGTAATTTTGTA
1 AATCGAGGGTAAAAC-GGTAATTTTGTA
*
40299555 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * * *
40299582 AATTGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* **
40299609 AATTGAGCATAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
40299636 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
40299663 AATCGAGGGTAAAATGGTAATT
1 AATCGAGGGTAAAACGGTAATT
40299685 CTACAAATCG
Statistics
Matches: 133, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
26 4 0.03
27 125 0.94
28 4 0.03
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:40302957 original size:2 final size:2
Alignment explanation
Indices: 40302940--40302978 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
40302930 ACACAATTGT
* *
40302940 TC TC TT TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40302979 TTTTCTGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:40303330 original size:20 final size:20
Alignment explanation
Indices: 40303305--40303351 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
40303295 TTTAAGCCTC
40303305 ACACGCCCGTGTGCTTTGAG
1 ACACGCCCGTGTGCTTTGAG
*
40303325 ACACGCCCGTGTGCTTTGGG
1 ACACGCCCGTGTGCTTTGAG
40303345 ACACGCC
1 ACACGCC
40303352 TGTTTCCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.34, G:0.30, T:0.21
Consensus pattern (20 bp):
ACACGCCCGTGTGCTTTGAG
Found at i:40308881 original size:121 final size:121
Alignment explanation
Indices: 40308661--40308888 Score: 312
Period size: 121 Copynumber: 1.9 Consensus size: 121
40308651 TCACGAAAGT
* * * *
40308661 TTCACACAATCATGCAATCATATCATAGACCTCAAAATAATTATAAAATAATTATTTCTATCTCA
1 TTCACACAAGCATGCAATCATAACATAAACCTCAAAATAATCATAAAATAATTATTTCTATCTCA
* * * * *
40308726 AATTTGTGGTCTCGACACCACTATTTTGATTAGGCCGTAATTCAGGATATCACACA
66 AATTTGTGGTCTCAAAACCACTATTCTGACTAGGCCCTAATTCAGGATATCACACA
* * *
40308782 TTCACACAAGCATGCATTCATAACATAAACCTCATAATAATCATAAAATAGTTATTTCTATCTCA
1 TTCACACAAGCATGCAATCATAACATAAACCTCAAAATAATCATAAAATAATTATTTCTATCTCA
** * *
40308847 GTTTTGTGGTCTCAAAACCATTGTTCTGACTAGGCCCTAATT
66 AATTTGTGGTCTCAAAACCACTATTCTGACTAGGCCCTAATT
40308889 TGGGATGTTA
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
121 91 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (121 bp):
TTCACACAAGCATGCAATCATAACATAAACCTCAAAATAATCATAAAATAATTATTTCTATCTCA
AATTTGTGGTCTCAAAACCACTATTCTGACTAGGCCCTAATTCAGGATATCACACA
Found at i:40310528 original size:18 final size:19
Alignment explanation
Indices: 40310469--40310518 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
40310459 AATATGATTA
*
40310469 ACATTTTGAAAAATGGCTC
1 ACATTTTGAAAAATGACTC
40310488 ACATTTTGAAAAATGACTC
1 ACATTTTGAAAAATGACTC
40310507 ACATTTTGAAAA
1 ACATTTTGAAAA
40310519 TGAATGACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (19 bp):
ACATTTTGAAAAATGACTC
Found at i:40311109 original size:65 final size:65
Alignment explanation
Indices: 40311005--40311134 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
40310995 TACGCAAAGT
40311005 ACAAAAACATATCTTCGCTTACACAGAGACTCAAACTCAAGACAACAGCGT-AAACAAAAACTTA
1 ACAAAAACATATCTTCGCTTACACAGAGACTCAAACTCAAGACAACAGC-TCAAACAAAAACTTA
40311069 A
65 A
*
40311070 ACAAAAACATATCTTCGCTTACACAGAGACTCAAACTCAAGACAACAGCTCAATCAAAAACTTAA
1 ACAAAAACATATCTTCGCTTACACAGAGACTCAAACTCAAGACAACAGCTCAAACAAAAACTTAA
40311135 CCATTGAACC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 1 0.02
65 62 0.98
ACGTcount: A:0.48, C:0.25, G:0.08, T:0.18
Consensus pattern (65 bp):
ACAAAAACATATCTTCGCTTACACAGAGACTCAAACTCAAGACAACAGCTCAAACAAAAACTTAA
Found at i:40312721 original size:23 final size:23
Alignment explanation
Indices: 40312695--40312739 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
40312685 ATAAATGAAT
40312695 CTTGGATATATTCTACTTGGATC
1 CTTGGATATATTCTACTTGGATC
*
40312718 CTTGGATCTATTCTACTTGGAT
1 CTTGGATATATTCTACTTGGAT
40312740 TTTGTCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (23 bp):
CTTGGATATATTCTACTTGGATC
Found at i:40314898 original size:17 final size:17
Alignment explanation
Indices: 40314876--40314915 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40314866 TAAAATTGGG
40314876 TTGAGAAGATT-ATTTAA
1 TTGAGAA-ATTAATTTAA
*
40314893 TTGAGAAATTAATTTAT
1 TTGAGAAATTAATTTAA
40314910 TTGAGA
1 TTGAGA
40314916 TGTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (17 bp):
TTGAGAAATTAATTTAA
Found at i:40316344 original size:29 final size:30
Alignment explanation
Indices: 40316302--40316358 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
40316292 ATGCACCACC
*
40316302 ATTTTACAGATTTTATAGTTTTGCCACTGG
1 ATTTTACAAATTTTATAGTTTTGCCACTGG
40316332 ATTTT-CAAATTTTATAGTTTTGCCACT
1 ATTTTACAAATTTTATAGTTTTGCCACT
40316359 ATTTTCCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (30 bp):
ATTTTACAAATTTTATAGTTTTGCCACTGG
Found at i:40316402 original size:58 final size:57
Alignment explanation
Indices: 40316297--40316445 Score: 138
Period size: 58 Copynumber: 2.6 Consensus size: 57
40316287 TGACCATGCA
* * *
40316297 CCACCATTTTACAGATTTTATAGTTTTGCCACTGGATTTTCAAATTTTAT-AGTTTTG
1 CCACTATTTTACAGATTTTACAGTTTTGCCACTGGATTTTCAAATTTT-TCAGTTCTG
* * * ** *
40316354 CCACTATTTTCCAGATTTTACATTTTCTGTCACTGTTTTTTCATATTTTTCAGTTCTG
1 CCACTATTTTACAGATTTTACAGTTT-TGCCACTGGATTTTCAAATTTTTCAGTTCTG
* ** * *
40316412 CCACTGTTTTTTTAGATTTTACTGTTTTACCACT
1 CCACT-ATTTTACAGATTTTACAGTTTTGCCACT
40316446 TTTTTTAAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
57 23 0.32
58 34 0.47
59 16 0.22
ACGTcount: A:0.20, C:0.19, G:0.10, T:0.51
Consensus pattern (57 bp):
CCACTATTTTACAGATTTTACAGTTTTGCCACTGGATTTTCAAATTTTTCAGTTCTG
Found at i:40316444 original size:29 final size:29
Alignment explanation
Indices: 40316303--40316451 Score: 86
Period size: 29 Copynumber: 5.2 Consensus size: 29
40316293 TGCACCACCA
* * * * *
40316303 TTTTACAGATTTTATAGTTTTGCCACTGG
1 TTTTTCAGATTTTACAGTTCTACCACTGT
* * * * * *
40316332 ATTTTCAAATTTTATAGTTTTGCCACT-A
1 TTTTTCAGATTTTACAGTTCTACCACTGT
* * **
40316360 TTTTCCAGATTTTACATTTTCTGTCACTGT
1 TTTTTCAGATTTTACA-GTTCTACCACTGT
* * *
40316390 TTTTTCATATTTTTCAGTTCTGCCACTGT
1 TTTTTCAGATTTTACAGTTCTACCACTGT
* * *
40316419 TTTTTTAGATTTTACTGTTTTACCACT-T
1 TTTTTCAGATTTTACAGTTCTACCACTGT
40316447 TTTTT
1 TTTTT
40316452 AAAAAATTTA
Statistics
Matches: 95, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
28 18 0.19
29 64 0.67
30 13 0.14
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (29 bp):
TTTTTCAGATTTTACAGTTCTACCACTGT
Found at i:40330229 original size:23 final size:24
Alignment explanation
Indices: 40330187--40330234 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
40330177 AATTTCTTGA
*
40330187 GAGACATTGGCATGGAAATATCAT
1 GAGACATTAGCATGGAAATATCAT
*
40330211 GAGA-ATTAGCATGGTAATATCAT
1 GAGACATTAGCATGGAAATATCAT
40330234 G
1 G
40330235 GGTATGAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (24 bp):
GAGACATTAGCATGGAAATATCAT
Found at i:40335917 original size:28 final size:28
Alignment explanation
Indices: 40335885--40335983 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 28
40335875 ATAATAAGCC
*
40335885 CGCACACTTAGTGCT-TAGTAGTCGAACT
1 CGCACACTTAGTGCTATA-TAATCGAACT
40335913 CGCACACTTAGTGCTATATAATC-AACCT
1 CGCACACTTAGTGCTATATAATCGAA-CT
* * *
40335941 CGCACACTTAGTGCTATACAATTTGAACC
1 CGCACACTTAGTGCTATATAA-TCGAACT
40335970 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40335984 CAATCTCATG
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
27 2 0.03
28 41 0.65
29 18 0.29
30 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCGAACT
Found at i:40341328 original size:39 final size:40
Alignment explanation
Indices: 40341211--40341434 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
40341201 GCTCCTCGTT
* *
40341211 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
40341251 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
40341291 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
40341330 CAATTGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
40341369 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
* *
40341410 CAAA-GCTTTCAGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40341435 CATCATTCAA
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 70 0.42
40 77 0.47
41 16 0.10
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Done.