Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 174 of 211
Found at i:54248803 original size:24 final size:24
Alignment explanation
Indices: 54248776--54248831 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
54248766 GCATGGCTTT
*
54248776 CAAACTCCGTCGCCGCTCATGATG
1 CAAACACCGTCGCCGCTCATGATG
* *
54248800 CAAACACTGTCGCCGTTCATGATG
1 CAAACACCGTCGCCGCTCATGATG
54248824 CAAACACC
1 CAAACACC
54248832 TCCACATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.20
Consensus pattern (24 bp):
CAAACACCGTCGCCGCTCATGATG
Found at i:54249152 original size:29 final size:29
Alignment explanation
Indices: 54249111--54249695 Score: 529
Period size: 29 Copynumber: 19.7 Consensus size: 29
54249101 TTTTGATATT
* * *
54249111 ATTTGATTAAAAACCCTAACCTTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* **
54249140 TTTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
54249169 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAACCTA
54249199 ATTTAATTAAAAACCCTAACCC--A--T-
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
54249223 -TTTAATTAAAAACCCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
54249251 TTTTAATTAAAAACCCAAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* **
54249280 TTTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
54249309 ATTTAATTAAAAA-CCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* **
54249337 TTTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
54249366 ATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCT-AACCCTAACCTA
*
54249396 ATTTAATTAAAAACCCTAACCCTAACC-C
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* **
54249424 ATTTCAATTAAAAACCCTAACCTTAATTTA
1 ATTT-AATTAAAAACCCTAACCCTAACCTA
***
54249454 ATTTAATTAAAAACCCTAATTTAATTAAAAACCCTA
1 ATTTAATTAAAAACCCTAA---CCCT---AA-CCTA
* * ** *****
54249490 ACCCTAACCCATTTTAATTAAAAACCCTAACCCTAATTTA
1 A--TTTA---ATTAAAAACCCTAACCCTAA-CC-----TA
**
54249530 ATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
54249559 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * **
54249588 TTTTAATTAAAAACCCTAACCTTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
**
54249617 ATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* **
54249646 ATTTAATTAAAAACCATAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
54249675 ATTTAATTAAAAACCCTAACC
1 ATTTAATTAAAAACCCTAACC
54249696 ATTAACAAAA
Statistics
Matches: 460, Mismatches: 68, Indels: 56
0.79 0.12 0.10
Matches are distributed among these distances:
23 21 0.05
25 2 0.00
27 1 0.00
28 28 0.06
29 310 0.67
30 58 0.13
32 2 0.00
35 20 0.04
36 3 0.01
38 5 0.01
40 3 0.01
41 7 0.02
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (29 bp):
ATTTAATTAAAAACCCTAACCCTAACCTA
Found at i:54249227 original size:58 final size:58
Alignment explanation
Indices: 54249111--54249695 Score: 704
Period size: 58 Copynumber: 10.4 Consensus size: 58
54249101 TTTTGATATT
* * * *
54249111 ATTTGATTAAAAACCCTAACCTTAACCCATTTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
54249169 ATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCC--A--T-
1 ATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
* * * ***
54249223 -TTTAATTAAAAACCCTAACCCTAACCCATTTTAATTAAAAACCCAAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
* ** ***
54249280 TTTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA-CCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
* ** **
54249337 TTTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAATTTA
* *
54249396 ATTTAATTAAAAACCCTAACCCTAACC-CATTTCAATTAAAAACCCTAACCTTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTT-AATTAAAAACCCTAACCCTAATTTA
***
54249454 ATTTAATT--AAA----AA--C---CCTAATTTAATTAAAAACCCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
* **
54249501 TTTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
* *
54249559 ATTTAATTAAAAACCCTAACCCTAACCTATTTTAATTAAAAACCCTAACCTTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
** *
54249617 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCATAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
54249675 ATTTAATTAAAAACCCTAACC
1 ATTTAATTAAAAACCCTAACC
54249696 ATTAACAAAA
Statistics
Matches: 463, Mismatches: 42, Indels: 44
0.84 0.08 0.08
Matches are distributed among these distances:
47 30 0.06
48 4 0.01
49 3 0.01
50 1 0.00
52 33 0.07
53 18 0.04
54 1 0.00
55 2 0.00
56 3 0.01
57 57 0.12
58 232 0.50
59 79 0.17
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (58 bp):
ATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTA
Found at i:54249321 original size:87 final size:87
Alignment explanation
Indices: 54249111--54249695 Score: 774
Period size: 87 Copynumber: 6.9 Consensus size: 87
54249101 TTTTGATATT
* * *** * *** *
54249111 ATTTGATTAAAAACCCTAACCTTAACCCATTTTAATTAAAAACCCTAACCCTAATTTAATTTAAT
1 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
**
54249176 TAAAAACCCTAAACCCTAACCTA
66 TAAAAACCCT-AACCCTAATTTA
54249199 ATTTAATTAAAAACCCTAACCC--A--T--TTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
1 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
* ***
54249258 TAAAAACCCAAACCCTAACCCA
66 TAAAAACCCTAACCCTAATTTA
*
54249280 TTTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAA-CCTAACCCTAACCCATTTTAAT
1 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
54249344 TAAAAACCCTAACCCTAATTTA
66 TAAAAACCCTAACCCTAATTTA
** *
54249366 ATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCCATTTCAA
1 ATTTAATTAAAAACCCT-AACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAA
*
54249431 TTAAAAACCCTAACCTTAATTTA
65 TTAAAAACCCTAACCCTAATTTA
54249454 ATTTAATT--AAA----AACCC-----TAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
1 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
54249508 TAAAAACCCTAACCCTAATTTA
66 TAAAAACCCTAACCCTAATTTA
*
54249530 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCTATTTTAAT
1 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
*
54249595 TAAAAACCCTAACCTTAATTTA
66 TAAAAACCCTAACCCTAATTTA
* *** *
54249617 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCATAACCCTAATTTAATTTAAT
1 ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
54249682 TAAAAACCCTAACC
66 TAAAAACCCTAACC
54249696 ATTAACAAAA
Statistics
Matches: 451, Mismatches: 27, Indels: 39
0.87 0.05 0.08
Matches are distributed among these distances:
76 66 0.15
78 3 0.01
81 37 0.08
82 45 0.10
83 1 0.00
85 1 0.00
86 60 0.13
87 168 0.37
88 70 0.16
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (87 bp):
ATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCCTAACCCATTTTAAT
TAAAAACCCTAACCCTAATTTA
Found at i:54249475 original size:18 final size:18
Alignment explanation
Indices: 54249452--54249490 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
54249442 AACCTTAATT
54249452 TAATTTAATTAAAAACCC
1 TAATTTAATTAAAAACCC
54249470 TAATTTAATTAAAAACCC
1 TAATTTAATTAAAAACCC
54249488 TAA
1 TAA
54249491 CCCTAACCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATTTAATTAAAAACCC
Found at i:54253501 original size:15 final size:15
Alignment explanation
Indices: 54253468--54253510 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54253458 AATAGATATT
* *
54253468 AATATAATATAAAGTA
1 AATAAAATA-AAAGGA
54253484 AATAAAATAAAAGGA
1 AATAAAATAAAAGGA
54253499 AATAAAA-AAAAG
1 AATAAAATAAAAG
54253511 CAAAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.20
15 12 0.48
16 8 0.32
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (15 bp):
AATAAAATAAAAGGA
Found at i:54254251 original size:18 final size:18
Alignment explanation
Indices: 54254224--54254268 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
54254214 GTGAGGTAAG
*
54254224 TATTAATATTAGTATTAA
1 TATTATTATTAGTATTAA
*
54254242 TATTATTATTAGTATTAT
1 TATTATTATTAGTATTAA
54254260 TATTATTAT
1 TATTATTAT
54254269 GAGTGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
TATTATTATTAGTATTAA
Found at i:54254265 original size:6 final size:6
Alignment explanation
Indices: 54254224--54254268 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
54254214 GTGAGGTAAG
* * * *
54254224 TATTAA TATTAG TATTAA TATTAT TATTAG TATTAT TATTAT TAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TAT
54254269 GAGTGGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (6 bp):
TATTAT
Found at i:54261040 original size:17 final size:16
Alignment explanation
Indices: 54260999--54261040 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
54260989 CTCTCCCACC
54260999 ACTAAAATAAAAATAA
1 ACTAAAATAAAAATAA
54261015 ACTAGAAATAAAATGATAA
1 ACTA-AAATAAAA--ATAA
54261034 AC-AAAAT
1 ACTAAAAT
54261041 CTTCTATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 1 0.04
19 6 0.26
ACGTcount: A:0.69, C:0.07, G:0.05, T:0.19
Consensus pattern (16 bp):
ACTAAAATAAAAATAA
Found at i:54266263 original size:49 final size:49
Alignment explanation
Indices: 54266186--54266282 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
54266176 TTATGCTATG
* *
54266186 CATTTCTAAACTTGGTCTTCCATTGTCTACACTCTTATCACTATTTATA
1 CATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTATTTATA
54266235 CATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTATTTAT
1 CATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTATTTAT
54266283 CCCTTCTAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTATTTATA
Found at i:54266616 original size:30 final size:30
Alignment explanation
Indices: 54266572--54266638 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
54266562 ATTTTAGGGG
*
54266572 TCACACACCCGTGTGACCAGGCCGTGTACC
1 TCACACGCCCGTGTGACCAGGCCGTGTACC
* * * * *
54266602 TCACACGCCTGTGTGGCTAGGTCGTGTGCC
1 TCACACGCCCGTGTGACCAGGCCGTGTACC
54266632 TCACACG
1 TCACACG
54266639 GCTGAGACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.36, G:0.27, T:0.21
Consensus pattern (30 bp):
TCACACGCCCGTGTGACCAGGCCGTGTACC
Found at i:54268371 original size:19 final size:18
Alignment explanation
Indices: 54268331--54268371 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
54268321 AATATTACAC
*
54268331 ATTTCAACTTCACATTAA
1 ATTTCAACTTCACACTAA
*
54268349 ATTTCAACTTTCACACTAT
1 ATTTCAAC-TTCACACTAA
54268368 ATTT
1 ATTT
54268372 TGCTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTCAACTTCACACTAA
Found at i:54274151 original size:99 final size:103
Alignment explanation
Indices: 54274019--54274204 Score: 245
Period size: 105 Copynumber: 1.8 Consensus size: 103
54274009 TTTTCTGTAC
* * ** * *
54274019 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCAT-A-TC-GGTGCCCATGCCAT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
*
54274081 GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
66 GTCCCAGACATGATCTTACGGGGGACCTCTCATCTCGG
*
54274119 TGCCAACGCCATGT-CCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATAA-CTC-A-GATGCCAATGC
54274183 CATGTCCCAGACATGATCTTAC
63 CATGTCCCAGACATGATCTTAC
54274205 ATGGGATCTC
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
99 27 0.38
100 13 0.18
102 2 0.03
105 30 0.42
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (103 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
GTCCCAGACATGATCTTACGGGGGACCTCTCATCTCGG
Found at i:54274156 original size:49 final size:50
Alignment explanation
Indices: 54274019--54274215 Score: 225
Period size: 50 Copynumber: 3.8 Consensus size: 50
54274009 TTTTCTGTAC
* * ** *
54274019 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
54274069 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
54274119 TGCCAACGCCATGT-CCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
* *
54274174 TGCCAATGCCATGTCCCAGACATGATCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54274216 TTACCCAAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
49 26 0.21
50 54 0.44
52 5 0.04
55 14 0.11
56 25 0.20
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:54276314 original size:19 final size:19
Alignment explanation
Indices: 54276290--54276331 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
54276280 ACCTTGGTTG
54276290 ATGATTTTGGTCATAATAA
1 ATGATTTTGGTCATAATAA
54276309 ATGATTTTGGTCATAATAA
1 ATGATTTTGGTCATAATAA
54276328 ATGA
1 ATGA
54276332 GGTATATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (19 bp):
ATGATTTTGGTCATAATAA
Found at i:54276646 original size:19 final size:20
Alignment explanation
Indices: 54276612--54276649 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
54276602 ATAGAGGTAA
54276612 TAAAGTGTGCATAATAATAT
1 TAAAGTGTGCATAATAATAT
54276632 TAAAGTGTG-ATAATAATA
1 TAAAGTGTGCATAATAATA
54276650 ATAATAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (20 bp):
TAAAGTGTGCATAATAATAT
Found at i:54286881 original size:15 final size:16
Alignment explanation
Indices: 54286861--54286890 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54286851 ATATATAATT
54286861 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
54286876 TAATAAATATTCTTA
1 TAATAAATATTCTTA
54286891 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:54286899 original size:38 final size:38
Alignment explanation
Indices: 54286851--54287146 Score: 117
Period size: 38 Copynumber: 7.5 Consensus size: 38
54286841 TTTAATAAAA
54286851 ATATATAATTTAATAAAATTCTTAATAATAAATATTCT
1 ATATATAATTTAATAAAATTCTTAATAATAAATATTCT
* * * *
54286889 -TATATGAATTTACTAAAA-TCATAAT-ATATA-ATCCT
1 ATATAT-AATTTAATAAAATTCTTAATAATAAATATTCT
* * * * *
54286924 ATAAAATATAATTTAA-AATAATTATTATTAAATATATTTTAAT
1 AT---ATATAATTTAATAA-AATTCTTAAT-AATAAATATT-CT
*
54286967 AAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 ----ATATATAATTTAATAAAATTCTTAATAATAAATATTCT
* * ** *
54287009 -TATATGAATTTACTAAAA-TCATAAT-ATATAATCCTGT
1 ATATAT-AATTTAATAAAATTCTTAATAATA-AATATTCT
* * * * * * *
54287046 AAAATATAATTTAA-ACTAATTATTATTAAATATATTTTAAT
1 -ATATATAATTTAATA-AAATTCTTAAT-AATAAATATT-CT
*
54287087 AAAATATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 ---ATATATAATTTAATAAAATTCTTAATAATAAATATTCT
*
54287128 -TATATGAATTTACTAAAAT
1 ATATAT-AATTTAATAAAAT
54287147 CATAATATTT
Statistics
Matches: 187, Mismatches: 42, Indels: 58
0.65 0.15 0.20
Matches are distributed among these distances:
35 4 0.02
36 7 0.04
37 35 0.19
38 50 0.27
39 16 0.09
40 3 0.02
41 10 0.05
42 9 0.05
43 29 0.16
44 20 0.11
45 2 0.01
47 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (38 bp):
ATATATAATTTAATAAAATTCTTAATAATAAATATTCT
Found at i:54286950 original size:120 final size:120
Alignment explanation
Indices: 54286815--54287154 Score: 628
Period size: 120 Copynumber: 2.8 Consensus size: 120
54286805 TTAATCATAT
* * *
54286815 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAAAATAATTATTATTAAATATATTTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
54286880 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATCCTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATCCTATAAAATATAA
54286935 TTTAAAATAATTATTATTAAATATATTTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATATTTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
54287000 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATCCTGTAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATCCTATAAAATATAA
*
54287055 TTTAAACTAATTATTATTAAATATATTTTAAT-AAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATATTTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
54287119 AAATATTCTTATATGAATTTACTAAAATCATAATAT
66 AAATATTCTTATATGAATTTACTAAAATCATAATAT
54287155 TTTATATGAA
Statistics
Matches: 215, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
119 68 0.32
120 147 0.68
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATATTTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATCCTATAAAATATAA
Found at i:54286974 original size:16 final size:17
Alignment explanation
Indices: 54286953--54286988 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
54286943 AATTATTATT
54286953 AAATATAT-TTTAATAA
1 AAATATATATTTAATAA
54286969 AAATATATAATTTAATAA
1 AAATATAT-ATTTAATAA
54286987 AA
1 AA
54286989 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATATATTTAATAA
Found at i:54287115 original size:17 final size:17
Alignment explanation
Indices: 54287075--54287108 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54287065 TTATTATTAA
*
54287075 ATATATTTTAATAAAAT
1 ATATAATTTAATAAAAT
54287092 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54287109 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54293378 original size:99 final size:99
Alignment explanation
Indices: 54293151--54293403 Score: 309
Period size: 98 Copynumber: 2.5 Consensus size: 99
54293141 AAAAAATATT
* *
54293151 TTTATAGTTATTTTGTAAGTAATTTATGATTAGTTTATAAATTGTTAGTG--TTTTGTGTTTTGT
1 TTTATAGTTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTTTGGGTTTTGT
****
54293214 GATTTATTAGTAATGTAAATTCTTTTTTAAAAAA
66 GATTTATTAGTAATGTAAATTCTTAAAAAAAAAA
* * *
54293248 TGTTATAGTTATTTCGTTAGTAATTTGTGATTAATTTATAAATTGTTAGTGTTTAGTTTAGGGTT
1 T-TTATAGTTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTT--TTT-GGGTT
*
54293313 TTGTGATTTTTTAGTAATGT-AA-T-TTAAAAAAAAAA
62 TTGTGATTTATTAGTAATGTAAATTCTTAAAAAAAAAA
* *
54293348 TTTATAATTTTTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTT
1 TTTATAGTTATTTTGTTAGTAATTTATGATTA-GTT-TATAAATTGTTAGTGTTTT
54293404 GTGATTTTTT
Statistics
Matches: 133, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
97 1 0.01
98 45 0.34
99 28 0.21
100 12 0.09
101 19 0.14
102 5 0.04
103 23 0.17
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (99 bp):
TTTATAGTTATTTTGTTAGTAATTTATGATTAGTTTATAAATTGTTAGTGTTTTTTGGGTTTTGT
GATTTATTAGTAATGTAAATTCTTAAAAAAAAAA
Found at i:54293436 original size:17 final size:18
Alignment explanation
Indices: 54293407--54293440 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
54293397 GTGTTTTGTG
54293407 ATTTTTTATTAATGTAAA
1 ATTTTTTATTAATGTAAA
54293425 ATTTTTTA-TAATGTAA
1 ATTTTTTATTAATGTAA
54293441 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTTTTATTAATGTAAA
Found at i:54293444 original size:15 final size:17
Alignment explanation
Indices: 54293407--54293444 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
54293397 GTGTTTTGTG
54293407 ATTTTTTATTAATGTAAA
1 ATTTTTTATTAATGT-AA
54293425 ATTTTTTA-TAATGT-A
1 ATTTTTTATTAATGTAA
54293440 ATTTT
1 ATTTT
54293445 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
17 6 0.30
18 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
ATTTTTTATTAATGTAA
Found at i:54293534 original size:27 final size:27
Alignment explanation
Indices: 54293477--54293534 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
54293467 TCATAGGAGT
* * * *
54293477 CACCAGTGGCGCCTATCAGATGGGAGT
1 CACCAGTGGCGCCTACCAAATGGCAGC
54293504 CACCAGTGGCGCCTACCAAATAGGCA-C
1 CACCAGTGGCGCCTACCAAAT-GGCAGC
54293531 CACC
1 CACC
54293535 TATCCCATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.14
Consensus pattern (27 bp):
CACCAGTGGCGCCTACCAAATGGCAGC
Found at i:54300160 original size:29 final size:30
Alignment explanation
Indices: 54300100--54300167 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
54300090 CGGTGTACTG
* *
54300100 AAAAATATTTTTGACGAAATAGGTTCT-GA
1 AAAAATATCTTTGACGAAATAGGTTCTAAA
* *
54300129 AAAAATATCTTTGACGAGAT-GAGTTTTAAA
1 AAAAATATCTTTGACGAAATAG-GTTCTAAA
54300159 AAAAATATC
1 AAAAATATC
54300168 CCATGAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 22 0.67
30 10 0.30
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (30 bp):
AAAAATATCTTTGACGAAATAGGTTCTAAA
Found at i:54306727 original size:43 final size:42
Alignment explanation
Indices: 54306582--54306787 Score: 299
Period size: 42 Copynumber: 4.9 Consensus size: 42
54306572 CTAAGAAAAT
* *
54306582 AAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTAAGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA
* *
54306624 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGTAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA
*
54306666 AAACGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTAGGAAGA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAA-A
* * *
54306709 AAACACCACTAACGATCATGTTCTTTAGCGGCGCTTAGGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA
54306751 AAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 AAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
54306788 TTTCACAAAC
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.01
42 107 0.73
43 38 0.26
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA
Found at i:54306804 original size:85 final size:84
Alignment explanation
Indices: 54306582--54306787 Score: 299
Period size: 85 Copynumber: 2.4 Consensus size: 84
54306572 CTAAGAAAAT
* *
54306582 AAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTTC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCACTAAAGATCATGTTC
* *
54306647 TTTAGCGGCGCTTTGTAAA
66 TTTAGCGGCGCTTAGGAAA
* * * *
54306666 AAACGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTAGGAAGAAAACACCACTAACGATCATGTT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAGAA-AAAACGCCACTAAAGATCATGTT
54306731 CTTTAGCGGCGCTTAGGAAA
65 CTTTAGCGGCGCTTAGGAAA
54306751 AAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 AAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
54306788 TTTCACAAAC
Statistics
Matches: 110, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
84 40 0.36
85 70 0.64
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (84 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCACTAAAGATCATGTTC
TTTAGCGGCGCTTAGGAAA
Found at i:54307060 original size:30 final size:30
Alignment explanation
Indices: 54307024--54307083 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
54307014 GCGTTAAAAG
54307024 TTAAAATGATAAAAATATTTATGCAATATA
1 TTAAAATGATAAAAATATTTATGCAATATA
54307054 TTAAAATGATAAAAATATTTATGCAATATA
1 TTAAAATGATAAAAATATTTATGCAATATA
54307084 CACTATGACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (30 bp):
TTAAAATGATAAAAATATTTATGCAATATA
Found at i:54307269 original size:12 final size:12
Alignment explanation
Indices: 54307237--54307272 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
54307227 TTTTGAACCT
*
54307237 CTGCTTCTATCG
1 CTGCTTCTCTCG
54307249 CTGCTTCTCTCG
1 CTGCTTCTCTCG
54307261 CTGCTTCTCTCG
1 CTGCTTCTCTCG
54307273 TTGCGGCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.39, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:54307287 original size:21 final size:21
Alignment explanation
Indices: 54307261--54307329 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
54307251 GCTTCTCTCG
* *
54307261 CTGCTTCTCTCGTTGCGGCTT
1 CTGCTTCTCTCGTTGCAGCCT
* *
54307282 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGTTGCAGCCT
*
54307303 CTGCTTCCCTCGTTGTC-GCCT
1 CTGCTTCTCTCGTTG-CAGCCT
54307324 CTGCTT
1 CTGCTT
54307330 TAAGTTGTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.01, C:0.38, G:0.20, T:0.41
Consensus pattern (21 bp):
CTGCTTCTCTCGTTGCAGCCT
Found at i:54309955 original size:9 final size:9
Alignment explanation
Indices: 54309938--54310449 Score: 235
Period size: 9 Copynumber: 59.2 Consensus size: 9
54309928 TAAGTATAAT
*
54309938 TAAGCTATG
1 TAAGTTATG
54309947 TAAGTTATG
1 TAAGTTATG
54309956 T-A-TTATG
1 TAAGTTATG
54309963 TAAGTTAT-
1 TAAGTTATG
*
54309971 TTA-TTATG
1 TAAGTTATG
* *
54309979 AAAATTATG
1 TAAGTTATG
*
54309988 TAAGTTGTG
1 TAAGTTATG
54309997 T-A-TTATG
1 TAAGTTATG
*
54310004 -AA--AAT-
1 TAAGTTATG
* *
54310009 TATGCTATG
1 TAAGTTATG
54310018 TAAGTTATG
1 TAAGTTATG
* *
54310027 TAAGTCATA
1 TAAGTTATG
54310036 TAAGTTATG
1 TAAGTTATG
54310045 T-A-TTATG
1 TAAGTTATG
54310052 TAAGTTATG
1 TAAGTTATG
54310061 TAAGTTAT-
1 TAAGTTATG
*
54310069 TTA-TTATG
1 TAAGTTATG
* * *
54310077 AAAATTAAG
1 TAAGTTATG
54310086 TAAGTTATG
1 TAAGTTATG
*
54310095 TAATTTATG
1 TAAGTTATG
*
54310104 -AA-TAAT-
1 TAAGTTATG
*** *
54310110 TAAAAAAATA
1 T-AAGTTATG
54310120 TAAGTTATG
1 TAAGTTATG
54310129 TAAG-T-TG
1 TAAGTTATG
54310136 TAAGTTATG
1 TAAGTTATG
54310145 TAAGTTATG
1 TAAGTTATG
*
54310154 TATA-ATAT-
1 TA-AGTTATG
54310162 TAA-TTAAT-
1 TAAGTT-ATG
54310170 TAAGTTATG
1 TAAGTTATG
54310179 TAAGTTATG
1 TAAGTTATG
*
54310188 TATAATATTAATG
1 --TAA-GTT-ATG
54310201 TAAGTTATG
1 TAAGTTATG
*
54310210 TAATTTATG
1 TAAGTTATG
*
54310219 TATAATATTAATG
1 --TAA-GTT-ATG
54310232 TAAGTTATG
1 TAAGTTATG
*
54310241 TAATTTATG
1 TAAGTTATG
*
54310250 -AA-TAAT-
1 TAAGTTATG
***
54310256 TAAAAAATG
1 TAAGTTATG
54310265 TAAGTTATG
1 TAAGTTATG
54310274 TAAG-T-TG
1 TAAGTTATG
54310281 TAAGTTATG
1 TAAGTTATG
54310290 TAAGTTATG
1 TAAGTTATG
*
54310299 TATA-ATAT-
1 TA-AGTTATG
54310307 TAA-TTAAT-
1 TAAGTT-ATG
54310315 TAAGTTATG
1 TAAGTTATG
*
54310324 TAATTTATG
1 TAAGTTATG
*
54310333 TATAATATTAATG
1 --TAA-GTT-ATG
54310346 TAAGTTATG
1 TAAGTTATG
54310355 TAAG-T-TG
1 TAAGTTATG
54310362 TAAGTTATG
1 TAAGTTATG
54310371 TAAGTTATG
1 TAAGTTATG
*
54310380 TATA-ATAT-
1 TA-AGTTATG
54310388 TAA-TTAAT-
1 TAAGTT-ATG
54310396 TAAGTTATG
1 TAAGTTATG
54310405 TAAGTTATG
1 TAAGTTATG
*
54310414 TATA-ATAT-
1 TA-AGTTATG
54310422 TAA-TTAAT-
1 TAAGTT-ATG
54310430 TAAGTTATG
1 TAAGTTATG
54310439 TAAGTTATG
1 TAAGTTATG
54310448 TA
1 TA
54310450 TAATACTAAT
Statistics
Matches: 396, Mismatches: 53, Indels: 108
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.01
7 59 0.15
8 64 0.16
9 226 0.57
10 11 0.03
11 18 0.05
12 6 0.02
13 9 0.02
ACGTcount: A:0.39, C:0.01, G:0.15, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:54309964 original size:16 final size:16
Alignment explanation
Indices: 54309943--54310062 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
54309933 ATAATTAAGC
54309943 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
54309959 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
54309975 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
54309984 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
54310000 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
54310014 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
54310032 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
54310048 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
54310063 AGTTATTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 11 0.14
15 2 0.03
16 45 0.56
17 1 0.01
18 12 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:54309985 original size:25 final size:25
Alignment explanation
Indices: 54309957--54310111 Score: 129
Period size: 25 Copynumber: 6.2 Consensus size: 25
54309947 TAAGTTATGT
54309957 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
54309982 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
54310007 ATTATGCTATG-TA---AGTTATGTAA
1 ATTATG-TAAGTTATTTA-TTATGAAA
* * * * *
54310030 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
*
54310055 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
54310080 ATTAAGTAAGTTATGTAATTTATGAATA
1 ATTATGTAAGTTAT-TTA-TTATGAA-A
54310108 ATTA
1 ATTA
54310112 AAAAAATATA
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
22 4 0.04
23 12 0.11
25 71 0.68
26 6 0.06
27 7 0.07
28 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:54310089 original size:34 final size:34
Alignment explanation
Indices: 54309983--54310102 Score: 100
Period size: 34 Copynumber: 3.4 Consensus size: 34
54309973 ATTATGAAAA
* *
54309983 TTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAG
1 TTATGTAAGTTATTTATTATGAAAATTA----A-GTAAG
* * * *
54310022 TTATGTAAGTCATATAAGTTATG--TATTATGTAAG
1 TTATGTAAGTTAT-TTA-TTATGAAAATTAAGTAAG
54310056 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
1 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
*
54310090 TTATGTAATTTAT
1 TTATGTAAGTTAT
54310103 GAATAATTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
32 5 0.08
33 2 0.03
34 38 0.58
39 15 0.23
40 1 0.02
41 5 0.08
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.46
Consensus pattern (34 bp):
TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
Found at i:54310139 original size:50 final size:50
Alignment explanation
Indices: 54310085--54310184 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
54310075 TGAAAATTAA
*
54310085 GTAAGTTATGTAATTTATGAATAAT-TAAAAAAATATAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTTATGAATAATATAAAAAAAT-TAAGTTATGTAAGTT
* * **
54310135 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTTATGAATAATATAAAAAAATTAAGTTATGTAAGTT
54310185 ATGTATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 38 0.86
51 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (50 bp):
GTAAGTTATGTAAGTTATGAATAATATAAAAAAATTAAGTTATGTAAGTT
Found at i:54310141 original size:16 final size:16
Alignment explanation
Indices: 54310120--54310150 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54310110 TAAAAAAATA
54310120 TAAGTTATGTAAGTTG
1 TAAGTTATGTAAGTTG
54310136 TAAGTTATGTAAGTT
1 TAAGTTATGTAAGTT
54310151 ATGTATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (16 bp):
TAAGTTATGTAAGTTG
Found at i:54310174 original size:34 final size:34
Alignment explanation
Indices: 54310136--54310465 Score: 187
Period size: 34 Copynumber: 10.0 Consensus size: 34
54310126 ATGTAAGTTG
54310136 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
*
54310170 TAAGTTATGTAAGTTATGTATAATATTAA-T--G
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* *
54310201 TAAGTTATGTAATTTATGTATAATATTAA-T--G
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* * **
54310232 TAAGTTATGTAATTTATGAAT-A-ATTAAAAAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* *
54310264 GTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGT-ATAATAT
1 -TAAGTTATGTAAG-T-TATG-TA--TAA--TAT-TAATTA-AT
54310307 TAA-TTAAT-TAAGTTATG--TAAT-TT-ATGT-A-
1 TAAGTT-ATGTAAGTTATGTATAATATTAAT-TAAT
* *
54310335 TAATATTAATGTAAGTTATGTA-AGT-TGTAAGTT-AT
1 TAA-GTT-ATGTAAGTTATGTATAATAT-TAA-TTAAT
54310370 GTAAGTTATGT-A-T-------AATATTAATTAAT
1 -TAAGTTATGTAAGTTATGTATAATATTAATTAAT
54310396 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
*
54310430 TAAGTTATGTAAGTTATGTATAATACTAATGTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAAT-TAAT
54310465 T
1 T
54310466 TTTGCCAAAC
Statistics
Matches: 242, Mismatches: 15, Indels: 77
0.72 0.04 0.23
Matches are distributed among these distances:
25 12 0.05
26 8 0.03
27 2 0.01
28 3 0.01
29 6 0.02
30 9 0.04
31 60 0.25
32 5 0.02
33 15 0.06
34 82 0.34
35 11 0.05
36 4 0.02
38 1 0.00
39 4 0.02
40 1 0.00
41 6 0.02
42 10 0.04
43 3 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (34 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAAT
Found at i:54310174 original size:84 final size:84
Alignment explanation
Indices: 54310033--54310193 Score: 227
Period size: 84 Copynumber: 1.9 Consensus size: 84
54310023 TATGTAAGTC
* * *
54310033 ATATAAGTTATGTATTATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAA
1 ATATAAGTTATGTAGTATGTAAGTTATGTAAGTTATGTATAATGAAAATTAAGTAAGTTATGTAA
*
54310098 TTTATGAATAATTAAAAAA
66 GTTATGAATAATTAAAAAA
* *
54310117 ATATAAGTTATGTAAGT-TGTAAGTTATGTAAGTTATGTATAAT-ATTAATTAATTAAGTTATGT
1 ATATAAGTTATGT-AGTATGTAAGTTATGTAAGTTATGTATAATGA-AAATTAAGTAAGTTATGT
*
54310180 AAGTTATGTATAAT
64 AAGTTATGAATAAT
54310194 ATTAATGTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
83 1 0.01
84 65 0.96
85 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (84 bp):
ATATAAGTTATGTAGTATGTAAGTTATGTAAGTTATGTATAATGAAAATTAAGTAAGTTATGTAA
GTTATGAATAATTAAAAAA
Found at i:54310205 original size:65 final size:64
Alignment explanation
Indices: 54310134--54310360 Score: 225
Period size: 65 Copynumber: 3.8 Consensus size: 64
54310124 TTATGTAAGT
* * **
54310134 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAA-T-ATT
1 TGTAAGTTATGTAAGTTATGTATAATATTAA-T--GTAAGTTATGTAAGTTATGAATAATTAAAA
54310197 AA
63 AA
* *
54310199 TGTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAA
1 TGTAAGTTATGTAAGTTATGTATAATATTAATGTAAGTTATGTAAGTTATGAATAATTAAAAAA
* **
54310263 TGTAAGTTATGTAAG-T-TG--TAA-GTT-ATGTAAGTTA--T--G-TAT-AAT-ATTAATTAA
1 TGTAAGTTATGTAAGTTATGTATAATATTAATGTAAGTTATGTAAGTTATGAATAATTAAAAAA
*
54310314 T-TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTT
1 TGTAAGTTATGTAAGTTATGTATAATATTAATGTAAGTTATGTAAGTT
54310361 GTAAGTTATG
Statistics
Matches: 136, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
50 12 0.09
51 9 0.07
52 5 0.04
53 3 0.02
54 3 0.02
55 2 0.01
56 11 0.08
58 11 0.08
59 2 0.01
60 4 0.03
61 1 0.01
62 23 0.17
63 2 0.01
64 18 0.13
65 30 0.22
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (64 bp):
TGTAAGTTATGTAAGTTATGTATAATATTAATGTAAGTTATGTAAGTTATGAATAATTAAAAAA
Found at i:54310278 original size:145 final size:145
Alignment explanation
Indices: 54310045--54310357 Score: 524
Period size: 145 Copynumber: 2.1 Consensus size: 145
54310035 ATAAGTTATG
54310045 TATT-ATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTATGAATAA
1 TATTAATGTAAGTTATGT-A---ATTTATTATGAAAATTAAGTAAGTTATGTAATTTATGAATAA
54310109 TTAAAAAAATATAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
62 TTAAAAAAATATAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
54310174 TTATGTAAGTTATGTATAA
127 TTATGTAAGTTATGTATAA
*
54310193 TATTAATGTAAGTTATGTAATTTATGTAT-AATATTAATGTAAGTTATGTAATTTATGAATAATT
1 TATTAATGTAAGTTATGTAATTTAT-TATGAAAATTAA-GTAAGTTATGTAATTTATGAATAATT
*
54310257 -AAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTT
64 AAAAAAATATAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTT
*
54310321 ATGTAATTTATGTATAA
129 ATGTAAGTTATGTATAA
54310338 TATTAATGTAAGTTATGTAA
1 TATTAATGTAAGTTATGTAA
54310358 GTTGTAAGTT
Statistics
Matches: 159, Mismatches: 3, Indels: 9
0.93 0.02 0.05
Matches are distributed among these distances:
145 112 0.70
146 29 0.18
148 5 0.03
149 13 0.08
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (145 bp):
TATTAATGTAAGTTATGTAATTTATTATGAAAATTAAGTAAGTTATGTAATTTATGAATAATTAA
AAAAATATAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTAT
GTAAGTTATGTATAA
Found at i:54310284 original size:16 final size:16
Alignment explanation
Indices: 54310263--54310376 Score: 71
Period size: 16 Copynumber: 7.1 Consensus size: 16
54310253 AATTAAAAAA
54310263 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
54310279 TGTAAGTTATGTAAGTT
1 TGTAAGTTATGTAAG-T
*
54310296 ATGTATA-ATAT-TAA-T
1 -TGTA-AGTTATGTAAGT
*
54310311 TAATTAAGTTATGTAA-T
1 T--GTAAGTTATGTAAGT
* *
54310328 T-TATGTATAATATTAA--
1 TGTAAGT-T-AT-GTAAGT
54310344 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
54310360 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
54310376 T
1 T
54310377 ATGTATAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 26
0.70 0.06 0.23
Matches are distributed among these distances:
14 8 0.10
15 5 0.06
16 41 0.53
17 16 0.21
18 7 0.09
19 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:54310292 original size:49 final size:50
Alignment explanation
Indices: 54310230--54310326 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 50
54310220 ATAATATTAA
*
54310230 TGTAAGTTATGTAATTTATGAAT-A-ATTAAAAAATGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGTTATGAATAATATTAAAAAAT-TAAGTTATGTAAGT
* **
54310279 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAA
1 TGTAAGTTATGTAAGTTATGAATAATATTAAAAAATTAAGTTATGTAA
54310327 TTTATGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 21 0.50
50 13 0.31
51 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.43
Consensus pattern (50 bp):
TGTAAGTTATGTAAGTTATGAATAATATTAAAAAATTAAGTTATGTAAGT
Found at i:54310368 original size:47 final size:43
Alignment explanation
Indices: 54310227--54310660 Score: 187
Period size: 43 Copynumber: 10.0 Consensus size: 43
54310217 TGTATAATAT
* * **
54310227 TAATGTAAGTTATGTAATTTATGAAT-A-ATTAAAAAATGTAAG
1 TAATGTAAGTTATGTAAGTTATGTATAATATTAATTAAT-TAAG
* * * *
54310269 TTATGTAAG-T-TGTAAGTTATGTA-AGTTATGT-ATAATATTAAT
1 TAATGTAAGTTATGTAAGTTATGTATA-ATAT-TAATTA-ATTAAG
* *
54310311 TAAT-TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATG
1 TAATGTAAGTTATGTAAGTTATGTATAATATTAAT-TAA-TTAAG
54310355 TAAGTTGTAAGTTATGTAAGTTATGTAT-A-A-T-ATTAA-T---
1 TAA--TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
54310392 TAAT-TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
1 TAATGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
* * * * *
54310434 TTATGTAAGTTATGTATAATACTAATGTA-ATTTTTGCCAA--ACATT--T
1 TAATGTAAGTTATGTA-AGT--T-ATGTATAATATT---AATTA-ATTAAG
* * ** *
54310480 TAATGTAAGTTATGTAATTTATGAATAATTAAAAAATGTAAGTTATG
1 TAATGTAAGTTATGTAAGTTATGTATAA-T-ATTAAT-TAA-TTAAG
54310527 TAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
1 TAA--TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
* * * * * *
54310572 TTATGTAATTTATGTATAATATTAATGTA-AGTTATGT-ATAATATTAAT
1 TAATGTAAGTTATG--TAA-GTT-ATGTATA-ATAT-TAATTA-ATTAAG
* *
54310620 TAAT-TAAGTTATGTAATTTATGTATAATATTTATTAATTAA
1 TAATGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAA
54310661 TTAAGTTATG
Statistics
Matches: 299, Mismatches: 42, Indels: 102
0.67 0.09 0.23
Matches are distributed among these distances:
34 21 0.07
35 2 0.01
36 1 0.00
37 4 0.01
38 5 0.02
39 1 0.00
40 12 0.04
41 5 0.02
42 39 0.13
43 57 0.19
44 16 0.05
45 18 0.06
46 28 0.09
47 52 0.17
48 13 0.04
49 25 0.08
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.46
Consensus pattern (43 bp):
TAATGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
Found at i:54310529 original size:9 final size:9
Alignment explanation
Indices: 54310515--54310643 Score: 71
Period size: 9 Copynumber: 14.6 Consensus size: 9
54310505 TAATTAAAAA
54310515 ATGTAAGTT
1 ATGTAAGTT
54310524 ATGTAAG-T
1 ATGTAAGTT
54310532 -TGTAAGTT
1 ATGTAAGTT
54310540 ATGTAAGTT
1 ATGTAAGTT
*
54310549 ATGTATA-AT
1 ATGTA-AGTT
54310558 AT-TAA-TT
1 ATGTAAGTT
54310565 AAT-TAAGTT
1 -ATGTAAGTT
*
54310574 ATGTAATTT
1 ATGTAAGTT
*
54310583 ATGTATAATATT
1 ATG--TAA-GTT
54310595 AATGTAAGTT
1 -ATGTAAGTT
*
54310605 ATGTATA-AT
1 ATGTA-AGTT
54310614 AT-TAA-TT
1 ATGTAAGTT
54310621 AAT-TAAGTT
1 -ATGTAAGTT
*
54310630 ATGTAATTT
1 ATGTAAGTT
54310639 ATGTA
1 ATGTA
54310644 TAATATTTAT
Statistics
Matches: 98, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
7 10 0.10
8 20 0.20
9 53 0.54
10 4 0.04
11 6 0.06
12 2 0.02
13 3 0.03
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:54310537 original size:16 final size:16
Alignment explanation
Indices: 54310516--54310548 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54310506 AATTAAAAAA
54310516 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
54310532 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
54310548 T
1 T
54310549 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:54310541 original size:49 final size:50
Alignment explanation
Indices: 54310483--54310635 Score: 148
Period size: 56 Copynumber: 3.0 Consensus size: 50
54310473 AACATTTTAA
*
54310483 TGTAAGTTATGTAATTTATGAAT-A-ATTAAAAAATGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGTTATGAATAATATTAAAAAAT-TAAGTTATGTAAGT
* ** *
54310532 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTT
1 TGTAAGTTATGTAAGTTATGAATAATATTAAAAAATTAAGTTATGTAA-GT
* * **
54310583 ATGTATAATATTAATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAA
1 -TG--TAA-GTT-ATGTAAGTTATGAATAATATTAAAAAATTAAGTTATGTAA
54310636 TTTATGTATA
Statistics
Matches: 90, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
49 21 0.23
50 13 0.14
51 9 0.10
52 2 0.02
54 3 0.03
55 2 0.02
56 40 0.44
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (50 bp):
TGTAAGTTATGTAAGTTATGAATAATATTAAAAAATTAAGTTATGTAAGT
Found at i:54310553 original size:138 final size:138
Alignment explanation
Indices: 54310396--54310647 Score: 400
Period size: 138 Copynumber: 1.8 Consensus size: 138
54310386 ATTAATTAAT
54310396 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
1 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
* *
54310461 TAATTTTTGCCA-AACATT-TTAATGTAAGTTATGTAATTTATGAATAATTAAAAAATGTAAGTT
66 TAAGTTATG-CATAACATTATTAAT-TAAGTTATGTAATTTATGAATAATTAAAAAATGTAAGTT
54310524 ATGTAAGTTG
129 ATGTAAGTTG
* *
54310534 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATG
1 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
* * *
54310599 TAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAAT
66 TAAGTTATGCATAACATT-ATTAATTAAGTTATGTAATTTATGAATAAT
54310648 ATTTATTAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
137 1 0.01
138 75 0.72
139 23 0.22
140 5 0.05
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.46
Consensus pattern (138 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
TAAGTTATGCATAACATTATTAATTAAGTTATGTAATTTATGAATAATTAAAAAATGTAAGTTAT
GTAAGTTG
Found at i:54310566 original size:253 final size:256
Alignment explanation
Indices: 54310136--54310609 Score: 830
Period size: 253 Copynumber: 1.8 Consensus size: 256
54310126 ATGTAAGTTG
*
54310136 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATATTAATG
1 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
* *
54310201 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAATGT
66 TAAGTTATGCAA--TA-GCAT-ATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAATGT
54310266 AAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTA
127 AAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTA
54310331 TGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAAT
192 TGTATAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAAT
54310396 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
1 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
* *
54310461 TAATTTTTGCCAA-A-CAT-T-TTAATGTAAGTTATGTAATTTATGAATAATTAAAAAATGTAAG
66 TAAGTTATG-CAATAGCATATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAATGTAAG
54310522 TTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGT
130 TTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGT
54310587 ATAATATTAATGTAAGTTATGTA
195 ATAATATTAATGTAAGTTATGTA
54310610 TAATATTAAT
Statistics
Matches: 208, Mismatches: 5, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
253 131 0.63
254 1 0.00
256 2 0.01
258 1 0.00
260 71 0.34
261 2 0.01
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (256 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATACTAATG
TAAGTTATGCAATAGCATATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAATGTAAGT
TATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTA
TAATATTAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAAT
Found at i:54310571 original size:25 final size:25
Alignment explanation
Indices: 54310543--54310634 Score: 112
Period size: 25 Copynumber: 3.4 Consensus size: 25
54310533 GTAAGTTATG
54310543 TAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTATAATATTAATTAAT
* *
54310568 TAAGTTATGTAATTTATGTATAATATTAAT
1 TAAGTTATGT-A--TA-ATATTA-ATTAAT
54310598 GTAAGTTATGTATAATATTAATTAAT
1 -TAAGTTATGTATAATATTAATTAAT
54310624 TAAGTTATGTA
1 TAAGTTATGTA
54310635 ATTTATGTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
25 21 0.37
26 7 0.12
27 4 0.07
28 4 0.07
29 4 0.07
30 7 0.12
31 10 0.18
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (25 bp):
TAAGTTATGTATAATATTAATTAAT
Found at i:54310606 original size:22 final size:22
Alignment explanation
Indices: 54310574--54310619 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
54310564 TAATTAAGTT
*
54310574 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
54310596 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
54310618 AT
1 AT
54310620 TAATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:54310609 original size:56 final size:56
Alignment explanation
Indices: 54310540--54310650 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
54310530 GTTGTAAGTT
54310540 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
54310596 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATT
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATT
54310651 TATTAATTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (56 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
Found at i:54310637 original size:172 final size:168
Alignment explanation
Indices: 54310199--54310609 Score: 497
Period size: 172 Copynumber: 2.5 Consensus size: 168
54310189 ATAATATTAA
* * * * *
54310199 TGTAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGAATAAT-TAAA
1 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATATTAA
** * * * * *
54310260 AAATGTAAGTTATGTAAG-T-TGTA-AGT--T-ATGTAAGTTATG-TATAATATTAATTAATTAA
66 TTA-GTAAGTTATGTAAGATATGTATAATACTAATGTAATTTTTGCCA-AACATT--TTAATTAA
* **
54310318 GTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGT
127 GTTATGTAATTTATGAATAATAAAAATGTAAGTTATGTAAGT
54310360 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATATTAA
1 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATATTAA
* *
54310425 TTAATTAAGTTATGTAAGTTATGTATAATACTAATGTAATTTTTGCCAAACATTTTAATGTAAGT
66 TT-AGTAAGTTATGTAAGATATGTATAATACTAATGTAATTTTTGCCAAACATTTTAAT-TAAGT
54310490 TATGTAATTTATGAATAATTAAAAAATGTAAGTTATGTAAGT
129 TATGTAATTTATGAATAA-T-AAAAATGTAAGTTATGTAAGT
*
54310532 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATATTAA
54310597 -T-GTAAGTTATGTA
66 TTAGTAAGTTATGTA
54310610 TAATATTAAT
Statistics
Matches: 217, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
161 30 0.14
162 1 0.00
164 22 0.10
165 16 0.07
166 2 0.01
167 4 0.02
168 2 0.01
169 16 0.07
170 23 0.11
171 17 0.08
172 84 0.39
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (168 bp):
TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAAGTTATGTATAATATTAA
TTAGTAAGTTATGTAAGATATGTATAATACTAATGTAATTTTTGCCAAACATTTTAATTAAGTTA
TGTAATTTATGAATAATAAAAATGTAAGTTATGTAAGT
Found at i:54310641 original size:34 final size:37
Alignment explanation
Indices: 54310596--54310674 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 37
54310586 TATAATATTA
*
54310596 ATGTAAGTTATGTAT-A-A-TATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATATTATTAATTAATTAAGTT
54310630 ATGTAATTTATGTATAATATTTATTAATTAATTAAGTT
1 ATGTAATTTATGTATAATA-TTATTAATTAATTAAGTT
54310668 ATGTAAT
1 ATGTAAT
54310675 CGAGGATGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 14 0.35
35 1 0.03
36 1 0.03
38 24 0.60
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (37 bp):
ATGTAATTTATGTATAATATTATTAATTAATTAAGTT
Found at i:54311243 original size:18 final size:18
Alignment explanation
Indices: 54311220--54311308 Score: 92
Period size: 18 Copynumber: 4.8 Consensus size: 18
54311210 ATATATAAAT
54311220 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
54311238 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
* *
54311260 TTTTAGTCA-GTAATATA
1 TTTAAGTAATGTAATATA
*
54311277 TTTAAGTACTGTAATATA
1 TTTAAGTAATGTAATATA
*
54311295 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
54311309 GTAAGTAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
17 12 0.20
18 29 0.49
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.14
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:54311284 original size:39 final size:43
Alignment explanation
Indices: 54311193--54311295 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 43
54311183 AGCTAATTTT
54311193 TATTTAAGTAATGTAATATATATAAATTTTAAGTAATGTAATA
1 TATTTAAGTAATGTAATATATATAAATTTTAAGTAATGTAATA
* *
54311236 TATTTAAGTAATGTAA-GT-TATAAATTTT-AGTCA-GTAATA
1 TATTTAAGTAATGTAATATATATAAATTTTAAGTAATGTAATA
*
54311275 TATTTAAGTACTGTAATATAT
1 TATTTAAGTAATGTAATATAT
54311296 TTTAGTAAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
39 21 0.39
40 5 0.09
41 11 0.20
42 1 0.02
43 16 0.30
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (43 bp):
TATTTAAGTAATGTAATATATATAAATTTTAAGTAATGTAATA
Found at i:54314455 original size:114 final size:114
Alignment explanation
Indices: 54314307--54314975 Score: 1020
Period size: 114 Copynumber: 5.9 Consensus size: 114
54314297 TAAATTATTT
* * *
54314307 TAAATCCTTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTTTCTAAAAACGCCACTAAATCCCCGACAGCTCAGAAAAC
54314372 GGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
54314421 TAAATCCCTAAGCATTAGTGGCGCTTTTCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTTTCTAAAAACGCCACTAAATCCCCGACAGCTCAGAAAAC
* *
54314486 GGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTTCCAAAAAAGCCGC
66 GGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * * *
54314535 TAAAGCCCTAAGCATTAGCGGCGC-TTACATAGAAACGCCACTAAATCCCTGACAGCTCAGAAAA
1 TAAATCCCTGAGCATTAGCGGCGCTTTTC-TAAAAACGCCACTAAATCCCCGACAGCTCAGAAAA
54314599 CGGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
65 CGGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
** *
54314649 TAAATCCCTGAGCATTAGCGGCGCTTACCTAGAAACGCCACTAAATCCCCGACAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTTTCTAAAAACGCCACTAAATCCCCGACAGCTCAGAAAAC
* * * *
54314714 GGTGTCGTTGGCCATAGGTATTTTTGTGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* *
54314763 TAAATCCCTGAGCATTAGCGGCGCTTTTCTAAAAACGCCGCTAAATCCTCGACAGCTCAGAAAAC
1 TAAATCCCTGAGCATTAGCGGCGCTTTTCTAAAAACGCCACTAAATCCCCGACAGCTCAGAAAAC
* * *
54314828 GGCATCGTTGGTCTTAGGTATTTTTGTGGCGCTTTCCCAAAAATGCCGC
66 GGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * * *
54314877 TAAATCACTGAGCATTAGCGGCGC-TTTCTTAGAAACGCCACTAAATCCCCAAAAGCTCCGAAAA
1 TAAATCCCTGAGCATTAGCGGCGCTTTTC-TAAAAACGCCACTAAATCCCCGACAGCTCAGAAAA
*
54314941 CGGCGTCGTTGGGCTTAGGTA-TTTTGCGGCGCTTT
65 CGGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTT
54314976 TCTGGAAACG
Statistics
Matches: 509, Mismatches: 43, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
113 20 0.04
114 487 0.96
115 2 0.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (114 bp):
TAAATCCCTGAGCATTAGCGGCGCTTTTCTAAAAACGCCACTAAATCCCCGACAGCTCAGAAAAC
GGCGTCGTTGGTCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:54315520 original size:31 final size:31
Alignment explanation
Indices: 54315461--54315524 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
54315451 TAAGAAAGAG
**
54315461 TTTGAGAGATTTTTGAGAGTGGATTGAGAAA
1 TTTGAGAGATTTTTGAGAGTAAATTGAGAAA
54315492 TTTGAGAGATTTTTGAGAG-AAATGTGAGAAA
1 TTTGAGAGATTTTTGAGAGTAAAT-TGAGAAA
54315523 TT
1 TT
54315525 AGTAGGTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (31 bp):
TTTGAGAGATTTTTGAGAGTAAATTGAGAAA
Found at i:54317117 original size:15 final size:15
Alignment explanation
Indices: 54317099--54317131 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
54317089 ACCACCGGCA
54317099 CCTCCACCTATGACG
1 CCTCCACCTATGACG
*
54317114 CCTCCATCTATGACG
1 CCTCCACCTATGACG
54317129 CCT
1 CCT
54317132 AATTCAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.45, G:0.12, T:0.24
Consensus pattern (15 bp):
CCTCCACCTATGACG
Found at i:54332907 original size:41 final size:41
Alignment explanation
Indices: 54332848--54333064 Score: 371
Period size: 41 Copynumber: 5.3 Consensus size: 41
54332838 GTTTAGAATT
54332848 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
*
54332889 GATGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
*
54332930 AGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* *
54332971 GGTGATCTGAATCAGGCTATAAGCCTAGTAGGCTAAATGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
* * *
54333012 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
54333053 GGTGATCTGAAT
1 GGTGATCTGAAT
54333065 ATGTTAAATT
Statistics
Matches: 164, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 164 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
Found at i:54338534 original size:16 final size:17
Alignment explanation
Indices: 54338513--54338544 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54338503 AATTTTTAAA
54338513 AAATA-TTTTAAATTTG
1 AAATATTTTTAAATTTG
54338529 AAATATTTTTAAATTT
1 AAATATTTTTAAATTT
54338545 ATAGTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AAATATTTTTAAATTTG
Found at i:54339340 original size:94 final size:94
Alignment explanation
Indices: 54339174--54339353 Score: 326
Period size: 94 Copynumber: 1.9 Consensus size: 94
54339164 AGTAGTTGGT
*
54339174 AAGAAGGATTGATGTGCATCCTGCAGGCAATTAATTGGACCATGAAAATACATGGAAAGGAGGGT
1 AAGAAGGATTAATGTGCATCCTGCAGGCAATTAATTGGACCATGAAAATACATGGAAAGGAGGGT
54339239 AGCTAAAAAGGT-GGGGAGGGGGAAGGGGA
66 AGCT-AAAAGGTGGGGGAGGGGGAAGGGGA
*
54339268 AAGAGGGATTAATGTGCATCCTGCAGGCAATTAATTGGACCATGAAAATACATGGAAAGGAGGGT
1 AAGAAGGATTAATGTGCATCCTGCAGGCAATTAATTGGACCATGAAAATACATGGAAAGGAGGGT
54339333 AGCTAAAAGGTGGGGGAGGGG
66 AGCTAAAAGGTGGGGGAGGGG
54339354 AGTTACATGT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
93 7 0.08
94 76 0.92
ACGTcount: A:0.36, C:0.10, G:0.37, T:0.18
Consensus pattern (94 bp):
AAGAAGGATTAATGTGCATCCTGCAGGCAATTAATTGGACCATGAAAATACATGGAAAGGAGGGT
AGCTAAAAGGTGGGGGAGGGGGAAGGGGA
Found at i:54339897 original size:27 final size:27
Alignment explanation
Indices: 54339866--54339921 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
54339856 TATAAGCGGT
* * *
54339866 GCAAAGAACACCGCTACATATAACGCC
1 GCAAAAAACACCACTACAGATAACGCC
* *
54339893 GCAAAAAACGCCATTACAGATAACGCC
1 GCAAAAAACACCACTACAGATAACGCC
54339920 GC
1 GC
54339922 TAAATTTTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.32, G:0.16, T:0.11
Consensus pattern (27 bp):
GCAAAAAACACCACTACAGATAACGCC
Found at i:54340102 original size:43 final size:41
Alignment explanation
Indices: 54340032--54340191 Score: 112
Period size: 43 Copynumber: 3.7 Consensus size: 41
54340022 CACTTTGACT
* * *
54340032 AAAAACGCCGCTACAGAAT-ATGATCTTTAGTGGCACTTTTCTC
1 AAAAACGCCACTA-A-AATCATGTTCTTTAGCGGC-CTTTTCTC
* *
54340075 ACAAACGCCACTAAAATTCATGTTCTTTAGCGGCGTTTT-T-
1 AAAAACGCCACTAAAA-TCATGTTCTTTAGCGGCCTTTTCTC
* * *
54340115 AGTAAATGCACCACTAAAAATCATGTTCTATAGCGGCGCTTTTC-C
1 A--AAA-ACGCCACT-AAAATCATGTTCTTTAGCGGC-CTTTTCTC
*
54340160 TAAAAACGCCACTAAAGATCATGTTTTTTAGC
1 -AAAAACGCCACTAAA-ATCATGTTCTTTAGC
54340192 AGCGTTCTTG
Statistics
Matches: 92, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 11 0.12
43 65 0.71
44 11 0.12
46 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (41 bp):
AAAAACGCCACTAAAATCATGTTCTTTAGCGGCCTTTTCTC
Found at i:54348156 original size:12 final size:13
Alignment explanation
Indices: 54348133--54348157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54348123 GGGGAATTAA
54348133 TTTGGGGAAAAAT
1 TTTGGGGAAAAAT
54348146 TTTGGGGAAAAA
1 TTTGGGGAAAAA
54348158 GAAAGGGGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (13 bp):
TTTGGGGAAAAAT
Found at i:54348251 original size:63 final size:62
Alignment explanation
Indices: 54348146--54348281 Score: 150
Period size: 63 Copynumber: 2.2 Consensus size: 62
54348136 GGGGAAAAAT
* * * * * **
54348146 TTTGGGGAAAAAGAAAGGGGTCTGTGAAAGAAACTTAGGGATTTC-AGGGAGAGGGGGAACTGA
1 TTTGGGAAAAAAGAAAGAGGTCTGTGAAAAAAAATTAAGGATTTCGA-AAAGA-GGGGAACTGA
*
54348209 TTTGGGAAAAAAGAAAGAGGTTTAG-GAAAAAAAATTAAGGATTTCGAAAAGAGGGGAACTGA
1 TTTGGGAAAAAAGAAAGAGGTCT-GTGAAAAAAAATTAAGGATTTCGAAAAGAGGGGAACTGA
54348271 TTTGTGGAAAA
1 TTTG-GGAAAA
54348282 GAATTTGAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
62 14 0.23
63 46 0.74
64 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.34, T:0.21
Consensus pattern (62 bp):
TTTGGGAAAAAAGAAAGAGGTCTGTGAAAAAAAATTAAGGATTTCGAAAAGAGGGGAACTGA
Found at i:54348428 original size:39 final size:40
Alignment explanation
Indices: 54348347--54348430 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
54348337 TTTGTTGCGA
* * *
54348347 TTTTCTCATAAATGCTGCTAATGTCTTACCTTTTGTAGCAT
1 TTTTCTCATAAA-GCCGCTAATATCTTACCTTTTGGAGCAT
*
54348388 TTTTCTCATAAA-CCGTTAATATCTTACCTTTTGCGA-CAT
1 TTTTCTCATAAAGCCGCTAATATCTTACCTTTTG-GAGCAT
54348427 TTTT
1 TTTT
54348431 TAGTTAACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 25 0.66
40 1 0.03
41 12 0.32
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.48
Consensus pattern (40 bp):
TTTTCTCATAAAGCCGCTAATATCTTACCTTTTGGAGCAT
Found at i:54350078 original size:41 final size:41
Alignment explanation
Indices: 54350033--54350206 Score: 258
Period size: 41 Copynumber: 4.2 Consensus size: 41
54350023 ACTGGCACTT
*
54350033 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
*
54350074 AGCCTACTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
* * *
54350115 AGCCTGCTAGACTTAAAGTTTGAAATGTTGCACCGGCGACA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
** * * *
54350156 AGCCTGCTAGACTTAAAGTCTGAAACATATCACTGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
54350197 AGCCTGCTAG
1 AGCCTGCTAG
54350207 GCACCGAGCC
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 119 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
Found at i:54352848 original size:18 final size:17
Alignment explanation
Indices: 54352794--54352848 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
54352784 TTTTCTAATC
54352794 TTTTTATCTTTTCA-TTG
1 TTTTT-TCTTTTCATTTG
* * *
54352811 -TTTTTCATTTCCTTTC
1 TTTTTTCTTTTCATTTG
54352827 TTTTTGTCTTTTCATTTG
1 TTTTT-TCTTTTCATTTG
54352845 TTTT
1 TTTT
54352849 CATTTTTCCT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 4 0.14
18 13 0.45
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTTTCTTTTCATTTG
Found at i:54352849 original size:23 final size:23
Alignment explanation
Indices: 54352808--54352855 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54352798 TATCTTTTCA
54352808 TTGTTTTTCATTTCCTTTC-TTT
1 TTGTTTTTCATTTCCTTTCATTT
**
54352830 TTGTCTTTTCATTTGTTTTCATTT
1 TTGT-TTTTCATTTCCTTTCATTT
54352854 TT
1 TT
54352856 CCTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (23 bp):
TTGTTTTTCATTTCCTTTCATTT
Found at i:54352860 original size:23 final size:23
Alignment explanation
Indices: 54352812--54352861 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
54352802 TTTTCATTGT
*
54352812 TTTTCATTTCCTTTCTTTTTGTC
1 TTTTCATTTCCTTTCTTTTTGCC
**
54352835 TTTTCATTTGTTTTCATTTTT-CC
1 TTTTCATTTCCTTTC-TTTTTGCC
54352858 TTTT
1 TTTT
54352862 AAAATAGACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTCATTTCCTTTCTTTTTGCC
Found at i:54358563 original size:21 final size:20
Alignment explanation
Indices: 54358529--54358601 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
54358519 TTTAAAATAA
54358529 AAAATTTGTAAAATTTATATAG
1 AAAATTT-TAAAATTTAT-TAG
**
54358551 AAAATTTTAAAATTTATTTT
1 AAAATTTTAAAATTTATTAG
* *
54358571 AAAAATATAAAATTTATT-G
1 AAAATTTTAAAATTTATTAG
*
54358590 AAAATATTAAAA
1 AAAATTTTAAAA
54358602 ATTTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 9 0.21
20 17 0.40
21 10 0.23
22 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAATTTTAAAATTTATTAG
Found at i:54358893 original size:18 final size:19
Alignment explanation
Indices: 54358872--54358908 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54358862 AAATCATAAT
54358872 AATTTTAAAAT-ATTTTAA
1 AATTTTAAAATAATTTTAA
*
54358890 AATTTTATAATAATTTTAA
1 AATTTTAAAATAATTTTAA
54358909 TTTTTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTAAAATAATTTTAA
Found at i:54359178 original size:19 final size:19
Alignment explanation
Indices: 54359139--54359181 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
54359129 GTATAATAAA
* *
54359139 TTTTACAATTTTTAAGGAT
1 TTTTACAACTTTTAAAGAT
*
54359158 TTTTACAACTTTTAAATAT
1 TTTTACAACTTTTAAAGAT
54359177 TTTTA
1 TTTTA
54359182 AATAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTACAACTTTTAAAGAT
Found at i:54361586 original size:5 final size:5
Alignment explanation
Indices: 54361551--54361601 Score: 63
Period size: 5 Copynumber: 10.6 Consensus size: 5
54361541 AACATAAGGA
*
54361551 AGAAG AGAGGG AGAAG A-AAG A-AAG A-AAG AGAAG AGAAG AGAAG AGAAG
1 AGAAG AGA-AG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG
54361599 AGA
1 AGA
54361602 GAAAGGGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 12 0.29
5 26 0.62
6 4 0.10
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:54361599 original size:28 final size:28
Alignment explanation
Indices: 54361551--54361606 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
54361541 AACATAAGGA
*
54361551 AGAAGAGAGGGAGAAGAAAGAAAGAAAG
1 AGAAGAGAGAGAGAAGAAAGAAAGAAAG
*
54361579 AGAAGAGA-AGAGAAGAGAAGAGAGAAAG
1 AGAAGAGAGAGAGAAGA-AAGAAAGAAAG
54361607 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (28 bp):
AGAAGAGAGAGAGAAGAAAGAAAGAAAG
Found at i:54364638 original size:32 final size:32
Alignment explanation
Indices: 54364592--54364697 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
54364582 CAAGTCAAAT
* * *
54364592 GTGTGCCACTTGTGGAATGGGCATGATCAGTG
1 GTGTGCCGCCTGTGGAATGGGCATGACCAGTG
***
54364624 GTGTGCCGCCTGTGGAATGGGCATGACCAACC
1 GTGTGCCGCCTGTGGAATGGGCATGACCAGTG
* * * *
54364656 G-ATGCCGCTTGTGAAATGGGCATGGCCAGTG
1 GTGTGCCGCCTGTGGAATGGGCATGACCAGTG
54364687 GTGTGCCGCCT
1 GTGTGCCGCCT
54364698 TTCTCTAAGG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 24 0.41
32 34 0.59
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.24
Consensus pattern (32 bp):
GTGTGCCGCCTGTGGAATGGGCATGACCAGTG
Found at i:54369343 original size:13 final size:13
Alignment explanation
Indices: 54369327--54369354 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
54369317 ATTGTCGTAC
54369327 TATAAAATCGTGT
1 TATAAAATCGTGT
54369340 TATAAAATCGTGT
1 TATAAAATCGTGT
54369353 TA
1 TA
54369355 GTAGTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
TATAAAATCGTGT
Found at i:54372048 original size:27 final size:27
Alignment explanation
Indices: 54372014--54372074 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
54372004 AAAAATAATT
54372014 AAAATATTATAACTTTTTTTATTTACC
1 AAAATATTATAACTTTTTTTATTTACC
* *
54372041 AAAATATTATAATTTTTTTTATTTATC
1 AAAATATTATAACTTTTTTTATTTACC
54372068 AAAATAT
1 AAAATAT
54372075 ACCAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAATATTATAACTTTTTTTATTTACC
Found at i:54372478 original size:19 final size:19
Alignment explanation
Indices: 54372454--54372519 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
54372444 ATTAAAATAG
54372454 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
54372473 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
54372491 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
54372510 TTTAATTTAA
1 TTTAATTTAA
54372520 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:54372801 original size:18 final size:19
Alignment explanation
Indices: 54372752--54372810 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
54372742 ATTTTATATT
54372752 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* * *
54372771 TTAAGTGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
54372789 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
54372808 TTA
1 TTA
54372811 CTTAATTAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.37
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:54373508 original size:27 final size:27
Alignment explanation
Indices: 54373478--54373539 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
54373468 TTTTTTTGGT
*
54373478 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
54373505 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
54373532 ATATTTTG
1 ATATTTTG
54373540 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:54373813 original size:114 final size:115
Alignment explanation
Indices: 54373613--54373844 Score: 394
Period size: 114 Copynumber: 2.0 Consensus size: 115
54373603 ATTGAGATCC
* * * *
54373613 TTTTAAGCATTTAATAGTAATTACCCCGATTCTAATGAGTGCGAAAAACTTGATAGAGCGATATA
1 TTTTAAGCATTCAATAATAATTACCCCGATTCTAATGAGTGCGAAAAACTTAATAGAGCCATATA
*
54373678 TAATTAAACTTAGCACACATAGATGTTGAACTAGCCCT-AAAAACGTATT
66 TAACTAAACTTAGCACACATAGATGTTGAACTAGCCCTAAAAAACGTATT
*
54373727 TTTTAAGCATTCAATAATAATTACCCCGATTCTAATGAGTGCGAAAAACTTAATAGTGCCATATA
1 TTTTAAGCATTCAATAATAATTACCCCGATTCTAATGAGTGCGAAAAACTTAATAGAGCCATATA
*
54373792 TAACTAAACTTAGCACACATAGATGTTGAACTAGCCCTAAAAAACTTATT
66 TAACTAAACTTAGCACACATAGATGTTGAACTAGCCCTAAAAAACGTATT
54373842 TTT
1 TTT
54373845 AGACATAGCC
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 97 0.88
115 13 0.12
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (115 bp):
TTTTAAGCATTCAATAATAATTACCCCGATTCTAATGAGTGCGAAAAACTTAATAGAGCCATATA
TAACTAAACTTAGCACACATAGATGTTGAACTAGCCCTAAAAAACGTATT
Found at i:54374124 original size:29 final size:29
Alignment explanation
Indices: 54374070--54374125 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
54374060 ACTCCCAATA
* * *
54374070 ATTTTTATTTAATTTTTTATATTTTAATG
1 ATTTTTATTTAATTTTTAAAAATTTAATG
54374099 ATTTTT-TTTGAATTTTTAAAAATTTAA
1 ATTTTTATTT-AATTTTTAAAAATTTAA
54374126 AAAATTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (29 bp):
ATTTTTATTTAATTTTTAAAAATTTAATG
Found at i:54375871 original size:10 final size:9
Alignment explanation
Indices: 54375844--54375870 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
54375834 ATTTTTGTAT
54375844 TTTTTAAAA
1 TTTTTAAAA
54375853 TTTTTAAAA
1 TTTTTAAAA
54375862 TTTTTAAAA
1 TTTTTAAAA
54375871 AATTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:54382197 original size:23 final size:23
Alignment explanation
Indices: 54382171--54382220 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
54382161 ACTCGACTCA
* *
54382171 AACTCGAATTACT-TATTCAAGTT
1 AACTCGAATAACTCAATTCAA-TT
54382194 AACTCGAATAACTCAATTCAATT
1 AACTCGAATAACTCAATTCAATT
54382217 AACT
1 AACT
54382221 TAAAATTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (23 bp):
AACTCGAATAACTCAATTCAATT
Found at i:54387678 original size:16 final size:17
Alignment explanation
Indices: 54387657--54387689 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54387647 TATAGAAAAA
54387657 AAAAATG-GACCATTGG
1 AAAAATGTGACCATTGG
*
54387673 AAAAATGTGATCATTGG
1 AAAAATGTGACCATTGG
54387690 TCTAATTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAAATGTGACCATTGG
Found at i:54387743 original size:53 final size:53
Alignment explanation
Indices: 54387675--54387832 Score: 271
Period size: 53 Copynumber: 3.0 Consensus size: 53
54387665 ACCATTGGAA
* * * *
54387675 AAATGTGATCATTGGTCTAATTAGTCGTTGGTCTCAATGGTTAGAAAATCAAG
1 AAATGTGACCGTTGGTCTAAATAGCCGTTGGTCTCAATGGTTAGAAAATCAAG
*
54387728 AAATGTGACCGTTGGTCTAAATAGCCGTTGGTCTCAACGGTTAGAAAATCAAG
1 AAATGTGACCGTTGGTCTAAATAGCCGTTGGTCTCAATGGTTAGAAAATCAAG
54387781 AAATGTGACCGTTGGTCTAAATAGCCGTTGGTCTCAATGGTTAGAAAATCAA
1 AAATGTGACCGTTGGTCTAAATAGCCGTTGGTCTCAATGGTTAGAAAATCAA
54387833 CGACGGTGAT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 99 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (53 bp):
AAATGTGACCGTTGGTCTAAATAGCCGTTGGTCTCAATGGTTAGAAAATCAAG
Found at i:54390448 original size:29 final size:30
Alignment explanation
Indices: 54390403--54390463 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
54390393 CAAAAAACTC
54390403 TCAAATTTCTTCCTAAATTTCTCAAAGCTT
1 TCAAATTTCTTCCTAAATTTCTCAAAGCTT
54390433 TCAAA-TTC-TCCTTAAATTTCTCAAAGCTT
1 TCAAATTTCTTCC-TAAATTTCTCAAAGCTT
54390462 TC
1 TC
54390464 TTTAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 3 0.10
29 22 0.73
30 5 0.17
ACGTcount: A:0.30, C:0.25, G:0.03, T:0.43
Consensus pattern (30 bp):
TCAAATTTCTTCCTAAATTTCTCAAAGCTT
Found at i:54390669 original size:10 final size:11
Alignment explanation
Indices: 54390654--54390682 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
54390644 AATTTTTTTC
54390654 TTTTATTTAA-
1 TTTTATTTAAT
54390664 TTTTATTTAAT
1 TTTTATTTAAT
54390675 TTTTATTT
1 TTTTATTT
54390683 TATATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTATTTAAT
Found at i:54391625 original size:7 final size:7
Alignment explanation
Indices: 54391615--54391639 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54391605 AGTCATTTCA
54391615 TATTTAG
1 TATTTAG
54391622 TATTTAG
1 TATTTAG
54391629 TATTTAG
1 TATTTAG
54391636 TATT
1 TATT
54391640 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:54392752 original size:57 final size:59
Alignment explanation
Indices: 54392644--54392757 Score: 144
Period size: 57 Copynumber: 2.0 Consensus size: 59
54392634 TGTGTAAACT
* * ***
54392644 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTTAATATTTTAATAGTAAATTA
1 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGTAATAG-AAATTA
*
54392704 TTTTTATA-T-TTT-ATTTAATAAAATAGAAGTTCTTTTGAATAAGGTAATAGAAAT
1 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGTAATAGAAAT
54392758 AATGCAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
56 4 0.08
57 32 0.67
58 3 0.06
59 1 0.02
60 8 0.17
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (59 bp):
TTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGTAATAGAAATTA
Found at i:54395441 original size:17 final size:17
Alignment explanation
Indices: 54395419--54395452 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54395409 GATAAGTCTG
54395419 CACCATCGCCTCCAAGC
1 CACCATCGCCTCCAAGC
54395436 CACCATCGCCTCCAAGC
1 CACCATCGCCTCCAAGC
54395453 TACAACCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.53, G:0.12, T:0.12
Consensus pattern (17 bp):
CACCATCGCCTCCAAGC
Found at i:54396033 original size:126 final size:125
Alignment explanation
Indices: 54395803--54396294 Score: 740
Period size: 126 Copynumber: 3.9 Consensus size: 125
54395793 AAGGCCAAAC
* * *
54395803 AGGAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTGTTTCATCAATTTTGCTGACAGTACA
1 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCA
*
54395868 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTTATTTTT
66 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTTATTTTT
* * *
54395928 CAAGAACTACTGTAGAAAAATAGCGTCCACGTGAGAGCTTTTTTCATCATTTTTGCTGACAGTGC
1 -AGGAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGC
54395993 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAACTATT-TTTTT
65 ATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAA-T-TTATTTTT
* * * *
54396055 AGGAACTACTGTAGAAAAATAGCGCCCACGTGGGAGC-TTTTTCATCGATTTTGCTGACAGTGCA
1 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCA
* * *
54396119 TCCTGCTTGAAGCGTTTTTG--ACTATTTGTTCATAACTGTCTTCTCAAAATTATTTTTTT
66 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATT-TATTTTT
* *
54396178 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTATCAATTTTGCTGACAGTGCA
1 AGGAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCA
* * * *
54396243 TCCTGCTTGAAGCTTTTTTTACACTGTTTGTTCAGAACTGTCTTCTCAAAAT
66 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAAT
54396295 AAATTGAATA
Statistics
Matches: 337, Mismatches: 22, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
121 1 0.00
122 2 0.01
123 67 0.20
124 43 0.13
125 45 0.13
126 171 0.51
127 6 0.02
128 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (125 bp):
AGGAACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCA
TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATTTATTTTT
Found at i:54396244 original size:249 final size:251
Alignment explanation
Indices: 54395803--54396293 Score: 781
Period size: 249 Copynumber: 2.0 Consensus size: 251
54395793 AAGGCCAAAC
*
54395803 AGGAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTGTTTCATCAATTTTGCTGACAGTACA
1 AGGAACTACTGTAGAAAAAGAGCACCCACGTGAGAGCTTGTTTCATCAATTTTGCTGACAGTACA
54395868 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAAAACCGTCTTCTCAAAATTTATTTTTCAAGA
66 TCCTGCTTGAAGCGTTTTTGA-ACTATTTGTTCAAAACCGTCTTCTCAAAATTTATTTTTCAAGA
* *
54395933 ACTACTGTAGAAAAATAGCGTCCACGTGAGAGCTTTTTTCATCATTTTTGCTGACAGTGCATCCT
130 ACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCT
54395998 GCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAACTATTTTTTT
195 GCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAACTATTTTTTT
* * * * *
54396055 AGGAACTACTGTAGAAAAATAGCGCCCACGTGGGAGCTT-TTTCATCGATTTTGCTGACAGTGCA
1 AGGAACTACTGTAGAAAAAGAGCACCCACGTGAGAGCTTGTTTCATCAATTTTGCTGACAGTACA
* * * *
54396119 TCCTGCTTGAAGCGTTTTTG-ACTATTTGTTCATAACTGTCTTCTCAAAA-TTATTTTTTTAGGA
66 TCCTGCTTGAAGCGTTTTTGAACTATTTGTTCAAAACCGTCTTCTCAAAATTTA-TTTTTCAAGA
* *
54396182 ACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTATCAATTTTGCTGACAGTGCATCCT
130 ACTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCT
* * * *
54396247 GCTTGAAGCTTTTTTTACACTGTTTGTTCAGAACTGTCTTCTCAAAA
195 GCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAA
54396294 TAAATTGAAT
Statistics
Matches: 220, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
248 3 0.01
249 139 0.63
251 43 0.20
252 35 0.16
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (251 bp):
AGGAACTACTGTAGAAAAAGAGCACCCACGTGAGAGCTTGTTTCATCAATTTTGCTGACAGTACA
TCCTGCTTGAAGCGTTTTTGAACTATTTGTTCAAAACCGTCTTCTCAAAATTTATTTTTCAAGAA
CTACTGTAGAAAAAGAGCGTCCACGTGAGAGCTTTTTTCATCAATTTTGCTGACAGTGCATCCTG
CTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAACTATTTTTTT
Found at i:54396432 original size:33 final size:34
Alignment explanation
Indices: 54396393--54396477 Score: 127
Period size: 33 Copynumber: 2.5 Consensus size: 34
54396383 TTTAAAAAAA
*
54396393 CTAAACCCTAATTTAATTAATTTCTTAAAAACCC
1 CTAAACCCTAATTTAATTAATTTATTAAAAACCC
*
54396427 C-AAACCCTAATTTAATTAATTTATTTAAAACCC
1 CTAAACCCTAATTTAATTAATTTATTAAAAACCC
* *
54396460 CTAAAACGTAATTTAATT
1 CTAAACCCTAATTTAATT
54396478 TAAAAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 31 0.67
34 15 0.33
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.36
Consensus pattern (34 bp):
CTAAACCCTAATTTAATTAATTTATTAAAAACCC
Found at i:54404458 original size:19 final size:21
Alignment explanation
Indices: 54404423--54404472 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
54404413 TATATATATT
*
54404423 TTTAAAACAATATTGAT-A-AA
1 TTTAAAA-AATAGTGATAATAA
54404443 TTTAAAAAATAGTGATAATAA
1 TTTAAAAAATAGTGATAATAA
54404464 TTTAAAAAA
1 TTTAAAAAA
54404473 ATGTATTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.30
20 8 0.30
21 11 0.41
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (21 bp):
TTTAAAAAATAGTGATAATAA
Found at i:54404473 original size:22 final size:20
Alignment explanation
Indices: 54404423--54404474 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
54404413 TATATATATT
* *
54404423 TTTAAAACAATATTGATAAA
1 TTTAAAAAAATAGTGATAAA
54404443 TTT-AAAAAATAGTGATAATAA
1 TTTAAAAAAATAGTGAT-A-AA
54404464 TTTAAAAAAAT
1 TTTAAAAAAAT
54404475 GTATTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 5 0.19
22 7 0.26
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (20 bp):
TTTAAAAAAATAGTGATAAA
Found at i:54404766 original size:24 final size:25
Alignment explanation
Indices: 54404729--54404780 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
54404719 TTAAATAAAT
* *
54404729 ATATATAGTAAATTCAAAA-TGTCA
1 ATATATAATAAATTCAAAAGTATCA
* *
54404753 ATATATAATGAATTTAAAAGTATCA
1 ATATATAATAAATTCAAAAGTATCA
54404778 ATA
1 ATA
54404781 ACAAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (25 bp):
ATATATAATAAATTCAAAAGTATCA
Found at i:54405296 original size:11 final size:12
Alignment explanation
Indices: 54405280--54405311 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
54405270 GTCCCGTGTT
54405280 TAAAACC-AAAA
1 TAAAACCTAAAA
54405291 TAAAACCTAAAA
1 TAAAACCTAAAA
54405303 -AAAACCTAA
1 TAAAACCTAA
54405312 CACTTCCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.69, C:0.19, G:0.00, T:0.12
Consensus pattern (12 bp):
TAAAACCTAAAA
Found at i:54408258 original size:5 final size:5
Alignment explanation
Indices: 54408248--54408359 Score: 210
Period size: 5 Copynumber: 22.8 Consensus size: 5
54408238 TTTGTTTTAC
54408248 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
54408297 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
54408347 TATAA TAT-A TATA
1 TATAA TATAA TATA
54408360 CTTAAATGTT
Statistics
Matches: 105, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.08
5 97 0.92
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:54415641 original size:224 final size:224
Alignment explanation
Indices: 54415251--54415702 Score: 760
Period size: 224 Copynumber: 2.0 Consensus size: 224
54415241 CACACACCCG
* * *
54415251 TGTGGCTGGCCGTGTGAGCACACCTGTGTCTTAGGTCATGTGGTATTTGAAGTAGGGTACATGGT
1 TGTGGCTGGCCGTGTGAGCACACCCGTGTCTTAGGCCATGTGGTATTTGAAGTAGGGTACACGGT
* * * * *
54415316 GGCGTCCCCAGCCCGTGTAACTCTCTGACTTGTAATACATTTAAGTGCAGGGGTTACACGGCCAA
66 CGCGTCCCCAGCCCATGTAACTCTCTAACTTGCAATACATTTAAGTGCAGGGGTCACACGGCCAA
*
54415381 GCCACACGCCCGTGTGCTAGGCCGCGTGTAAAAACCTGGGCATTCTGTTTGAAATTTTAAGGTAT
131 GCCACAAGCCCGTGTGCTAGGCCGCGTGTAAAAACCTGGGCATTCTGTTTGAAATTTTAAGGTAT
54415446 AGGGGACACACGGCCAAACCACACGCACA
196 AGGGGACACACGGCCAAACCACACGCACA
54415475 TGTGGCTGGCCGTGTGAGCACACCCGTGTCTTAGGCCATGTGGTATTTGAAGTAGGGTACACGGT
1 TGTGGCTGGCCGTGTGAGCACACCCGTGTCTTAGGCCATGTGGTATTTGAAGTAGGGTACACGGT
*
54415540 CGTGTCCCCAGCCCATGTAACTCTCTAACTTGCAATACATTTAAGTGCAGGGGTCACACGGCCAA
66 CGCGTCCCCAGCCCATGTAACTCTCTAACTTGCAATACATTTAAGTGCAGGGGTCACACGGCCAA
* * * * *
54415605 GCCACAATCCCGTGTGCTAGGCTGTGTGTAAAAACCTGGGTATTCTGTTTGAAATTTTAAGGTCT
131 GCCACAAGCCCGTGTGCTAGGCCGCGTGTAAAAACCTGGGCATTCTGTTTGAAATTTTAAGGTAT
*
54415670 AGGGGACACACGGCCAAACCACACGCCCA
196 AGGGGACACACGGCCAAACCACACGCACA
54415699 TGTG
1 TGTG
54415703 TCAAGCCGTG
Statistics
Matches: 212, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
224 212 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (224 bp):
TGTGGCTGGCCGTGTGAGCACACCCGTGTCTTAGGCCATGTGGTATTTGAAGTAGGGTACACGGT
CGCGTCCCCAGCCCATGTAACTCTCTAACTTGCAATACATTTAAGTGCAGGGGTCACACGGCCAA
GCCACAAGCCCGTGTGCTAGGCCGCGTGTAAAAACCTGGGCATTCTGTTTGAAATTTTAAGGTAT
AGGGGACACACGGCCAAACCACACGCACA
Found at i:54422654 original size:3 final size:3
Alignment explanation
Indices: 54422646--54422676 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
54422636 TATATATTTG
54422646 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54422677 GGGATTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:54426472 original size:39 final size:39
Alignment explanation
Indices: 54426423--54426498 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
54426413 ACAGGTGTCA
*
54426423 TGTGACCAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
*
54426462 TGTGAACAGGCTGGGTCAAGTTTGTCTGGTTCAAATT
1 TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATT
54426499 TATCCAGCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.36
Consensus pattern (39 bp):
TGTGAACAGGCTGGGTCAAATTTGTCTGGTTCAAATTCT
Found at i:54429820 original size:21 final size:21
Alignment explanation
Indices: 54429794--54429838 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
54429784 TTCCACACCT
*
54429794 ATGTTAGTTGAATTGGAGTAA
1 ATGTTAGTTGAATTCGAGTAA
*
54429815 ATGTTAGTTGGATTCGAGTAA
1 ATGTTAGTTGAATTCGAGTAA
54429836 ATG
1 ATG
54429839 AGAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (21 bp):
ATGTTAGTTGAATTCGAGTAA
Found at i:54432401 original size:3 final size:3
Alignment explanation
Indices: 54432393--54432438 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
54432383 ATAAATTAAA
* *
54432393 TAT TAT TA- TAT TA- TAT TAT TAT AAT GTAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
54432437 TA
1 TA
54432439 ACTAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:54432410 original size:13 final size:13
Alignment explanation
Indices: 54432392--54432438 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
54432382 TATAAATTAA
54432392 ATATTATTATATT
1 ATATTATTATATT
*
54432405 ATATTATTATAAT
1 ATATTATTATATT
* *
54432418 GTATTATTAT-TA
1 ATATTATTATATT
54432430 ATATTATTA
1 ATATTATTA
54432439 ACTAATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
ATATTATTATATT
Found at i:54432927 original size:17 final size:18
Alignment explanation
Indices: 54432905--54432938 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54432895 TAAATGAGTT
54432905 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
54432922 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
54432939 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:54435176 original size:16 final size:17
Alignment explanation
Indices: 54435149--54435187 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
54435139 TTTAATTTTC
54435149 AAAATTTCAAAAAAATA
1 AAAATTTCAAAAAAATA
54435166 AAAATTT-AAAAAAATA
1 AAAATTTCAAAAAAATA
54435182 AAAATT
1 AAAATT
54435188 GCATTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTTCAAAAAAATA
Found at i:54435223 original size:30 final size:30
Alignment explanation
Indices: 54435183--54435283 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
54435173 AAAAAAATAA
* *
54435183 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
54435213 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
54435243 AAATTTCACTTAGACCCCT-AACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
54435272 AAATTTCATTTT
1 AAATTTCATTTT
54435284 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.38
30 38 0.62
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.45
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:54435297 original size:29 final size:28
Alignment explanation
Indices: 54435183--54435298 Score: 92
Period size: 29 Copynumber: 4.0 Consensus size: 28
54435173 AAAAAAATAA
* * *
54435183 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTT-AACCCTAAAC-TTTCTT
*
54435213 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTAACCC-TAAACTTTC-TT
*
54435243 AAATTTCA-CTTAGACCCCT-AACTTTCATT
1 AAATTTCATTTTA-A-CCCTAAACTTTC-TT
* *
54435272 AAATTTCATTTTAATCCTAAATTTTCT
1 AAATTTCATTTTAACCCTAAACTTTCT
54435299 AAAAATTACA
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.06
29 33 0.47
30 30 0.43
31 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.45
Consensus pattern (28 bp):
AAATTTCATTTTAACCCTAAACTTTCTT
Found at i:54435890 original size:8 final size:8
Alignment explanation
Indices: 54435872--54435926 Score: 67
Period size: 8 Copynumber: 6.8 Consensus size: 8
54435862 CCAGCAGAAA
54435872 AAAAAAGAG
1 AAAAAA-AG
54435881 AAAAAAAG
1 AAAAAAAG
*
54435889 AAAAAGAG
1 AAAAAAAG
*
54435897 AGAAAAAG
1 AAAAAAAG
54435905 -AAAAAAG
1 AAAAAAAG
54435912 AAAAACAAG
1 AAAAA-AAG
54435921 AAAAAA
1 AAAAAA
54435927 GGGGTTCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
7 6 0.15
8 20 0.50
9 14 0.35
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:54435894 original size:16 final size:16
Alignment explanation
Indices: 54435869--54435925 Score: 82
Period size: 16 Copynumber: 3.6 Consensus size: 16
54435859 AGCCCAGCAG
54435869 AAAA-AAAAAGAGAAA
1 AAAAGAAAAAGAGAAA
*
54435884 AAAAGAAAAAGAGAGA
1 AAAAGAAAAAGAGAAA
54435900 AAAAGAAAAA-AGAAA
1 AAAAGAAAAAGAGAAA
54435915 AACAAGAAAAA
1 AA-AAGAAAAA
54435926 AGGGGTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 10 0.26
16 28 0.74
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAGAAA
Found at i:54435922 original size:22 final size:23
Alignment explanation
Indices: 54435882--54435925 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
54435872 AAAAAAGAGA
*
54435882 AAAAAAGAAAAAGAGAGAAAAAG
1 AAAAAAGAAAAACAGAGAAAAAG
54435905 AAAAAAGAAAAACA-AGAAAAA
1 AAAAAAGAAAAACAGAGAAAAA
54435926 AGGGGTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAACAGAGAAAAAG
Found at i:54435927 original size:33 final size:30
Alignment explanation
Indices: 54435867--54435925 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
54435857 CCAGCCCAGC
*
54435867 AGAAAAAAAAAGAGAAAAAAAGAAAAAGAG
1 AGAAAAAAAAAAAGAAAAAAAGAAAAAGAG
54435897 AGAAAAAGAAAAAAGAAAAACAAGAAAAA
1 AGAAAAA-AAAAAAGAAAAA-AAGAAAAA
54435926 AGGGGTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.27
31 11 0.42
32 8 0.31
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (30 bp):
AGAAAAAAAAAAAGAAAAAAAGAAAAAGAG
Found at i:54436110 original size:26 final size:27
Alignment explanation
Indices: 54436067--54436118 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
54436057 ATATTTTGGC
54436067 ATTTATATTTTTAATTTATTTAATTTA
1 ATTTATATTTTTAATTTATTTAATTTA
* *
54436094 ATTTA-ATTTTTATTTTATTTTATTT
1 ATTTATATTTTTAATTTATTTAATTT
54436119 TAAATACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
ATTTATATTTTTAATTTATTTAATTTA
Found at i:54436316 original size:21 final size:20
Alignment explanation
Indices: 54436284--54436325 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
54436274 TCGCGTTTCG
54436284 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
54436304 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
54436325 A
1 A
54436326 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:54436326 original size:19 final size:19
Alignment explanation
Indices: 54436284--54436325 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
54436274 TCGCGTTTCG
54436284 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
54436304 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
54436324 AA
1 AA
54436326 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:54436453 original size:18 final size:18
Alignment explanation
Indices: 54436430--54436841 Score: 201
Period size: 17 Copynumber: 23.3 Consensus size: 18
54436420 GAAAAATCAG
54436430 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
54436448 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
54436466 AAAAA-TTCCAT-TTTTC
1 AAAAATTTTCGTGTTTTC
* *
54436482 AAAATTTTTCGTGTTTTTTT
1 AAAAATTTTCGTG--TTTTC
* * * *
54436502 AAAAAATTCCAT-ATTTC
1 AAAAATTTTCGTGTTTTC
* *
54436519 TAAAATTTTCGTG-TTTA
1 AAAAATTTTCGTGTTTTC
* *
54436536 AAAAAATTTCGTATTTTC
1 AAAAATTTTCGTGTTTTC
* ** *
54436554 AAAATTTTTTATTTTTTTC
1 AAAA-ATTTTCGTGTTTTC
* *
54436573 AACAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
54436590 ACAAATTCTCGTATTTT-
1 AAAAATTTTCGTGTTTTC
* ** *
54436607 AAAATTTTTTATGTTTTA
1 AAAAATTTTCGTGTTTTC
54436625 AAAAATAAATTTC-TCGTGTTTC
1 AAAAAT---TTTCGT-GT-TTTC
* *
54436647 -AAAATTGTCATG-TTT-
1 AAAAATTTTCGTGTTTTC
*
54436662 AAAAATTTTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
54436679 TAAAATGTTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
**
54436696 -AAAATCCTCGTGTTTTTC
1 AAAAATTTTCGTG-TTTTC
* *
54436714 AAAAATTCTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
54436731 AAAAATCTTCTTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
54436749 -AAAATTCTAGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
54436765 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
54436783 AAAAATTTCCCCTGTTTTC
1 AAAAATTT-TCGTGTTTTC
* *
54436802 AAAAATTCTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
* *
54436819 AAAAATTTTCTTTTTTTC
1 AAAAATTTTCGTGTTTTC
54436837 AAAAA
1 AAAAA
54436842 AAAAAACTTC
Statistics
Matches: 295, Mismatches: 73, Indels: 52
0.70 0.17 0.12
Matches are distributed among these distances:
16 39 0.13
17 115 0.39
18 77 0.26
19 38 0.13
20 13 0.04
21 10 0.03
22 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:54436528 original size:37 final size:36
Alignment explanation
Indices: 54436444--54436534 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 36
54436434 ATTTTCGTGT
* *
54436444 TTTCAAAAATTTTCGTG---TTTTCAAAAATTCCATT
1 TTTC-AAAATTTTCGTGTTTTTTTAAAAAATTCCATA
54436478 TTTCAAAATTTTTCGTGTTTTTTTAAAAAATTCCATA
1 TTTCAAAA-TTTTCGTGTTTTTTTAAAAAATTCCATA
54436515 TTTCTAAAATTTTCGTGTTT
1 TTTC-AAAATTTTCGTGTTT
54436535 AAAAAAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.08
34 12 0.24
37 30 0.60
38 4 0.08
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.52
Consensus pattern (36 bp):
TTTCAAAATTTTCGTGTTTTTTTAAAAAATTCCATA
Done.