Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 13 of 25
Found at i:1957517 original size:10 final size:10
Alignment explanation
Indices: 1957495--1957534 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1957485 ACATCAAATT
1957495 AATA-AATAA
1 AATATAATAA
1957504 AATA-AATAAA
1 AATATAAT-AA
1957514 AATATAATAA
1 AATATAATAA
1957524 AATATAATAA
1 AATATAATAA
1957534 A
1 A
1957535 TTATTGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 7 0.24
10 19 0.66
11 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AATATAATAA
Found at i:1957532 original size:25 final size:23
Alignment explanation
Indices: 1957490--1957535 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
1957480 TCCAAACATC
1957490 AAATTAATAAATAAAATAAATAA
1 AAATTAATAAATAAAATAAATAA
*
1957513 AAATATAATAAAATATAATAAAT
1 AAAT-TAAT-AAATAAAATAAAT
1957536 TATTGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 12 0.60
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATTAATAAATAAAATAAATAA
Found at i:1959020 original size:11 final size:11
Alignment explanation
Indices: 1959004--1959035 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1958994 TATATTTCAA
1959004 AAAAATAAAAT
1 AAAAATAAAAT
*
1959015 AAAAATATAAT
1 AAAAATAAAAT
1959026 AAAAATAAAA
1 AAAAATAAAA
1959036 ATATCATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1959032 original size:17 final size:17
Alignment explanation
Indices: 1959010--1959044 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1959000 TCAAAAAAAT
1959010 AAAATAAAAATATAATA
1 AAAATAAAAATATAATA
*
1959027 AAAATAAAAATATCATA
1 AAAATAAAAATATAATA
1959044 A
1 A
1959045 GTTATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATAAAAATATAATA
Found at i:1960440 original size:2 final size:2
Alignment explanation
Indices: 1960433--1960464 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1960423 GCTTATAGTG
1960433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1960465 ACATTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1960758 original size:13 final size:13
Alignment explanation
Indices: 1960740--1960764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1960730 ATTCACAATT
1960740 TTTTTTATTTTTA
1 TTTTTTATTTTTA
1960753 TTTTTTATTTTT
1 TTTTTTATTTTT
1960765 GTTGATCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:1961202 original size:14 final size:12
Alignment explanation
Indices: 1961177--1961235 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
1961167 TTTTTTTCAT
1961177 ATTTTTTAATTA
1 ATTTTTTAATTA
1961189 ATTTTTTATCATTAAA
1 ATTTTTTA--ATT--A
**
1961205 ATTTTTTAAACA
1 ATTTTTTAATTA
1961217 A--TTTTAATTA
1 ATTTTTTAATTA
1961227 ATTTTTTAA
1 ATTTTTTAA
1961236 ATAAAATAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
10 8 0.22
12 16 0.43
14 4 0.11
16 9 0.24
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTTTAATTA
Found at i:1964177 original size:17 final size:17
Alignment explanation
Indices: 1964144--1964196 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1964134 TTAAATATTC
*
1964144 ATTTACTTTTGTACTTTA
1 ATTTAATTTT-TACTTTA
1964162 ATTTAATTTTTACTTTA
1 ATTTAATTTTTACTTTA
* *
1964179 ATTTGATTTTTAATTTA
1 ATTTAATTTTTACTTTA
1964196 A
1 A
1964197 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (17 bp):
ATTTAATTTTTACTTTA
Found at i:1964787 original size:9 final size:9
Alignment explanation
Indices: 1964775--1964871 Score: 53
Period size: 8 Copynumber: 10.8 Consensus size: 9
1964765 TATTATAAAA
1964775 TTTATATAT
1 TTTATATAT
*
1964784 TTTATAAAT
1 TTTATATAT
1964793 TTTA-ATAT
1 TTTATATAT
*
1964801 TTTA-ATAA
1 TTTATATAT
1964809 TTTA-A-AT
1 TTTATATAT
*
1964816 TATT-TAAAT
1 T-TTATATAT
*
1964825 TTTA-AAAT
1 TTTATATAT
1964833 ATTTATATAT
1 -TTTATATAT
1964843 TTATATTATAT
1 TT-TA-TATAT
*
1964854 TTTAATTAAAT
1 TTT-A-TATAT
1964865 TTTATAT
1 TTTATAT
1964872 CATAATTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
7 2 0.03
8 24 0.33
9 23 0.32
10 7 0.10
11 16 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTATATAT
Found at i:1964788 original size:18 final size:17
Alignment explanation
Indices: 1964767--1964839 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 17
1964757 TTTTGACGTA
1964767 TTATAAAATTTATATATT
1 TTATAAAATTTA-ATATT
*
1964785 TTATAAATTTTAATATT
1 TTATAAAATTTAATATT
*
1964802 TTA-ATAATTTAA-ATT
1 TTATAAAATTTAATATT
* *
1964817 ATT-TAAATTTTAAAATAT
1 -TTATAAAATTTAATAT-T
1964835 TTATA
1 TTATA
1964840 TATTTATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.07
16 16 0.36
17 12 0.27
18 14 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATAAAATTTAATATT
Found at i:1964794 original size:17 final size:18
Alignment explanation
Indices: 1964767--1964804 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1964757 TTTTGACGTA
1964767 TTATAAAA-TTTATATATT
1 TTATAAAATTTTA-ATATT
1964785 TTAT-AAATTTTAATATT
1 TTATAAAATTTTAATATT
1964802 TTA
1 TTA
1964805 ATAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATAAAATTTTAATATT
Found at i:1964810 original size:17 final size:18
Alignment explanation
Indices: 1964767--1964871 Score: 71
Period size: 18 Copynumber: 5.8 Consensus size: 18
1964757 TTTTGACGTA
*
1964767 TTATAAAATTTATATATT
1 TTATAAATTTTATATATT
1964785 TTATAAATTTTA-ATATT
1 TTATAAATTTTATATATT
1964802 TTA-ATAA-TTTA-A-ATT
1 TTATA-AATTTTATATATT
*
1964817 ATT-TAAATTTTA-AAATAT
1 -TTATAAATTTTATATAT-T
*
1964835 TTATATATTTATATTATATT
1 TTATAAATTT-TA-TATATT
1964855 TTAATTAAATTTTATAT
1 TT-A-TAAATTTTATAT
1964872 CATAATTATA
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
15 5 0.07
16 14 0.20
17 14 0.20
18 18 0.25
19 2 0.03
20 6 0.08
21 6 0.08
22 6 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATAAATTTTATATATT
Found at i:1970210 original size:15 final size:15
Alignment explanation
Indices: 1970190--1970221 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1970180 TTTACAAAAA
1970190 TCGTATCTATTATTT
1 TCGTATCTATTATTT
1970205 TCGTATCTATTATTT
1 TCGTATCTATTATTT
1970220 TC
1 TC
1970222 AAAATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (15 bp):
TCGTATCTATTATTT
Found at i:1974877 original size:31 final size:32
Alignment explanation
Indices: 1974824--1974887 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
1974814 CAGCTAAATT
* * *
1974824 TTTTTCTTCTTCTATCTACTCTTT-TTTTTTC
1 TTTTTCTTCCTCTATATACTCTTTCTTTCTTC
1974855 TTTTTCTTCCTCTCATAT-CTCTTTCTTTCTTC
1 TTTTTCTTCCTCT-ATATACTCTTTCTTTCTTC
1974887 T
1 T
1974888 GTTTGAGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (32 bp):
TTTTTCTTCCTCTATATACTCTTTCTTTCTTC
Found at i:1976565 original size:31 final size:30
Alignment explanation
Indices: 1976530--1976589 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1976520 ACATAGAACA
*
1976530 TTACTACCTTAGCCATTAAAAGATAAAGAGT
1 TTACTACCTTA-ACATTAAAAGATAAAGAGT
* * *
1976561 TTACTATCTTAACTTTAAAAGATAGAGAG
1 TTACTACCTTAACATTAAAAGATAAAGAG
1976590 GGTAGAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (30 bp):
TTACTACCTTAACATTAAAAGATAAAGAGT
Found at i:1980813 original size:43 final size:43
Alignment explanation
Indices: 1980738--1980826 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
1980728 CTATATATTG
*
1980738 AACTAAACCCCTAATGAGCAATATGAAGTATGATTACTGGTCT
1 AACTAAACCCCTAATGAGCAATACGAAGTATGATTACTGGTCT
* *
1980781 AACTAAACCCCTAATGAGTAATACGAATTATGATTACTGGTCT
1 AACTAAACCCCTAATGAGCAATACGAAGTATGATTACTGGTCT
1980824 AAC
1 AAC
1980827 ATAATAATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (43 bp):
AACTAAACCCCTAATGAGCAATACGAAGTATGATTACTGGTCT
Found at i:1980893 original size:44 final size:38
Alignment explanation
Indices: 1980839--1980935 Score: 185
Period size: 38 Copynumber: 2.6 Consensus size: 38
1980829 AATAATGATT
1980839 ACTTTGAATTAGAATTAGTGTAACTATCTAGTTAGATC
1 ACTTTGAATTAGAATTAGTGTAACTATCTAGTTAGATC
1980877 ACTTTGAATTAGAATTAGTGTAACTATCTAGTTAGATC
1 ACTTTGAATTAGAATTAGTGTAACTATCTAGTTAGATC
*
1980915 ACTTTCAATTAGAATTAGTGT
1 ACTTTGAATTAGAATTAGTGT
1980936 TAAGTATATA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.40
Consensus pattern (38 bp):
ACTTTGAATTAGAATTAGTGTAACTATCTAGTTAGATC
Found at i:1981346 original size:52 final size:51
Alignment explanation
Indices: 1981068--1981684 Score: 379
Period size: 52 Copynumber: 11.8 Consensus size: 51
1981058 AATTAGTTAA
* * * * ** * *
1981068 ACTACTAATGACAAATTTGAAATAGAATTAGTGTAACTCTGTATTGAATTGA
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACT-AATATAGAATTGG
* * * * **
1981120 ACTTGTAATGGCCAATTTGAATTAAAATTAGTGTAACT-ATGCAGAATTGG
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACTAATATAGAATTGG
* * * * * *
1981170 ACTAGTAATGACCGATTTAAATTTAAAATTAGTCTAACT-ATATCGAATTAG
1 ACTAGTAATGACCAATTTCAA-TTAGAATTAGTGTAACTAATATAGAATTGG
* * *
1981221 ACCAGTAATGACCAATTAT-AATTAGAATTAGTATAAATATATTTATAGAATTGG
1 ACTAGTAATGACCAATT-TCAATTAGAATTAGTGTAACTA-A--TATAGAATTGG
** * * *
1981275 ACTAGTAATGACCGGTTTCAATTAGGATTAGTGCAACTAAGTATAGTATTGG
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACTAA-TATAGAATTGG
* * * *
1981327 ACTAGTAATGATCAATTTCAATTACAATTAGTGTAACCGT-ATATAAAAGTGG
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAA-C-TAATATAGAATTGG
* * * * *
1981379 ACTAGCAATGATCAATTTGAATTAGAATTAATGTAACTACATATTGAATTGG
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACTA-ATATAGAATTGG
* * * * * *
1981431 ACTACTAATGACCAATTTGAATCACAATTAGTGTAAGTATATTATTGAATTGG
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACTA-A-TATAGAATTGG
* * * * *
1981484 ACTTGTAA--ACCACTTTGAATTAGAATTAGTGTAAATGTATATAG-ATTGG
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACT-AATATAGAATTGG
* * * * *
1981533 ACTAGTAATAATCAATTTAAATT-GCAATTAGTGTAGCTGTATATAAAATTGGACTACTTGG
1 ACTAGTAATGACCAATTTCAATTAG-AATTAGTGTAAC--TA-AT---A-TAGA--A-TTGG
* * * * *
1981594 ACTAGTTATGAGCAATTTCAATTAGAATTTGTGTAATTATATATAGAATTTG
1 ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACTA-ATATAGAATTGG
* * * *
1981646 ACTAATCATGAGCC-ATTTTAATTAGAATTAGCGTAACTA
1 ACTAGTAATGA-CCAATTTCAATTAGAATTAGTGTAACTA
1981685 TAGATTCAAT
Statistics
Matches: 444, Mismatches: 92, Indels: 58
0.75 0.15 0.10
Matches are distributed among these distances:
49 12 0.03
50 44 0.10
51 87 0.20
52 189 0.43
53 26 0.06
54 40 0.09
55 3 0.01
56 2 0.00
57 2 0.00
59 5 0.01
60 1 0.00
61 32 0.07
62 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (51 bp):
ACTAGTAATGACCAATTTCAATTAGAATTAGTGTAACTAATATAGAATTGG
Found at i:1981740 original size:27 final size:24
Alignment explanation
Indices: 1981678--1981743 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1981668 TAGAATTAGC
* *
1981678 GTAACTATAGATTCAATTTCATTT
1 GTAACTATATATTCAATTGCATTT
1981702 GTAA-TA-AT-TTCAATTGCAATTGGT
1 GTAACTATATATTCAATTGC-ATT--T
1981726 GTAACTATATATTCAATT
1 GTAACTATATATTCAATT
1981744 AGACTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 8 0.24
22 4 0.12
23 2 0.06
24 9 0.26
25 2 0.06
26 2 0.06
27 7 0.21
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (24 bp):
GTAACTATATATTCAATTGCATTT
Found at i:1981787 original size:113 final size:113
Alignment explanation
Indices: 1981665--1981891 Score: 384
Period size: 113 Copynumber: 2.0 Consensus size: 113
1981655 GAGCCATTTT
* * *
1981665 AATTAGAATTAGCGTAACTATAGATTCAATT-TCATTTGTAATAATTTCAATTGCAATTGGTGTA
1 AATTAGAATTAGCGTAACTATAGATTCAATTCT-ACTTATAATAATTTCAATTGCAATTAGTGTA
1981729 ACTATATATTCAATTAGACTTGTAATTAGGAATTTCAATTAAAATTAGC
65 ACTATATATTCAATTAGACTTGTAATTAGGAATTTCAATTAAAATTAGC
*
1981778 AATTAGAATTAGCGTAACTATATATTCAATTCTACTTATAATAATTTCAATTGCAATTAGTGTAA
1 AATTAGAATTAGCGTAACTATAGATTCAATTCTACTTATAATAATTTCAATTGCAATTAGTGTAA
* *
1981843 TTATATATTCAATTAGACTTGTAATTGGGAATTTCAATTAAAATTAGC
66 CTATATATTCAATTAGACTTGTAATTAGGAATTTCAATTAAAATTAGC
1981891 A
1 A
1981892 TAACTATATA
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
113 106 0.99
114 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (113 bp):
AATTAGAATTAGCGTAACTATAGATTCAATTCTACTTATAATAATTTCAATTGCAATTAGTGTAA
CTATATATTCAATTAGACTTGTAATTAGGAATTTCAATTAAAATTAGC
Found at i:1981888 original size:52 final size:48
Alignment explanation
Indices: 1981777--1981908 Score: 147
Period size: 48 Copynumber: 2.7 Consensus size: 48
1981767 TTAAAATTAG
* **
1981777 CAATTAGAATTAGCGTAACTATATATTCAATTCTACTTATAATAATTT
1 CAATTAAAATTAGCGTAACTATATATTCAATTAGACTTATAATAATTT
** * * *
1981825 CAATTGCAATTAGTGTAATTATATATTCAATTAGACTTGTAATTGGGAATTT
1 CAATTAAAATTAGCGTAACTATATATTCAATTAGACTTATAA-T---AATTT
*
1981877 CAATTAAAATTAGCATAACTATATATTCAATT
1 CAATTAAAATTAGCGTAACTATATATTCAATT
1981909 GTATTGACTT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 35 0.51
49 1 0.01
52 32 0.47
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (48 bp):
CAATTAAAATTAGCGTAACTATATATTCAATTAGACTTATAATAATTT
Found at i:1988337 original size:10 final size:10
Alignment explanation
Indices: 1988322--1988351 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1988312 AAAAAATATT
1988322 TTATTTTTTA
1 TTATTTTTTA
1988332 TTA-TTTTTA
1 TTATTTTTTA
1988341 TTATTTTTTA
1 TTATTTTTTA
1988351 T
1 T
1988352 AAGGGTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTATTTTTTA
Found at i:1988722 original size:109 final size:109
Alignment explanation
Indices: 1988578--1988903 Score: 345
Period size: 109 Copynumber: 3.0 Consensus size: 109
1988568 AATTTACACG
* *
1988578 AAAAATGAATTA-CCTTATATAAAAGGCGTTCGTACG-CTACTTTATGACTCTAGACGATGATTT
1 AAAAATGAATTATCC-TATATAAAAGGCATTCGTACGTC-ACTTTACGACTCTAGACGATGATTT
* ** * *
1988641 ATTTTGAGGCCAATCTTTTGGTGCCCGAAT-TTACGTAATTAATGC
64 ATTTCGAAACCAATCTCTTGGTACCCGAATATTACGTAATTAATGC
* *
1988686 AAAAGATGAATTATCCTATATAAAGGGCATTCGTACGTCACTTTACGACTTTAGACGATGATTTA
1 AAAA-ATGAATTATCCTATATAAAAGGCATTCGTACGTCACTTTACGACTCTAGACGATGATTTA
* *
1988751 TTTCGAAACCAATCTCTTGGTACCTGAATATTACGTAATTAATGT
65 TTTCGAAACCAATCTCTTGGTACCCGAATATTACGTAATTAATGC
* * * *** * * *
1988796 AAAAATGAGTTATTCTATGTAAAAAATATTCGTACATCACTTTACGACTCTAAACGATAATTTAT
1 AAAAATGAATTATCCTATATAAAAGGCATTCGTACGTCACTTTACGACTCTAGACGATGATTTAT
*** ** * *
1988861 TTC-AGAGTTAATCTCTTAATGCCCGAATATTATGTAATTAATG
66 TTCGA-AACCAATCTCTTGGTACCCGAATATTACGTAATTAATG
1988904 TAAATTAAAT
Statistics
Matches: 183, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
108 5 0.03
109 157 0.86
110 21 0.11
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (109 bp):
AAAAATGAATTATCCTATATAAAAGGCATTCGTACGTCACTTTACGACTCTAGACGATGATTTAT
TTCGAAACCAATCTCTTGGTACCCGAATATTACGTAATTAATGC
Found at i:1992366 original size:22 final size:20
Alignment explanation
Indices: 1992341--1992380 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1992331 AGATAAAACT
1992341 AAAACTAAGATAAAAAAAAAGG
1 AAAACTAA-A-AAAAAAAAAGG
*
1992363 AAAAGTAAAAAAAAAAAA
1 AAAACTAAAAAAAAAAAA
1992381 TTTACTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (20 bp):
AAAACTAAAAAAAAAAAAGG
Found at i:1992959 original size:17 final size:16
Alignment explanation
Indices: 1992932--1992963 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1992922 TAAATATATT
1992932 ATTTAAAAATAAAATA
1 ATTTAAAAATAAAATA
1992948 ATTTATAAAATAAAAT
1 ATTTA-AAAATAAAAT
1992964 TCTATCTGAA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTTAAAAATAAAATA
Found at i:1993209 original size:35 final size:34
Alignment explanation
Indices: 1993127--1993210 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
1993117 TGAGGAATTG
* * *
1993127 AGTCCAAATTCTAAAGTTTTTGTATAAGGGGTCG
1 AGTCCAGATTCTAAAGTTTTTGTATAAGGAGTCA
* * *
1993161 AGTCCAGATTCTAAATTTTTTGTTTGAGAGAGTCA
1 AGTCCAGATTCTAAAGTTTTTGTATAAG-GAGTCA
*
1993196 AGTCTAGATTCTAAA
1 AGTCCAGATTCTAAA
1993211 CTAAAATGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 24 0.57
35 18 0.43
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (34 bp):
AGTCCAGATTCTAAAGTTTTTGTATAAGGAGTCA
Found at i:1997702 original size:21 final size:22
Alignment explanation
Indices: 1997668--1997727 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 22
1997658 CTGTTCATTT
*
1997668 TTTTTTCTACTCTTTCTCTTTC
1 TTTTTTCTACTCTTTCTCGTTC
*
1997690 TTTTTT-TAGTCTTTCTCGTTC
1 TTTTTTCTACTCTTTCTCGTTC
1997711 TTTTTTCTACTCTTTCT
1 TTTTTTCTACTCTTTCT
1997728 TTTGCTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.05, C:0.23, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTTTTCTACTCTTTCTCGTTC
Found at i:1997715 original size:22 final size:22
Alignment explanation
Indices: 1997667--1997727 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1997657 TCTGTTCATT
*
1997667 TTTTTTTCTACTCTTTCTCTTTC
1 TTTTTTT-TACTCTTTCTCGTTC
*
1997690 -TTTTTTTAGTCTTTCTCGTTC
1 TTTTTTTTACTCTTTCTCGTTC
*
1997711 TTTTTTCTACTCTTTCT
1 TTTTTTTTACTCTTTCT
1997728 TTTGCTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.05, C:0.23, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTTTTTTACTCTTTCTCGTTC
Found at i:1999300 original size:2 final size:2
Alignment explanation
Indices: 1999293--1999329 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1999283 TGTATGTATC
1999293 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1999330 CTATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1999336 original size:2 final size:2
Alignment explanation
Indices: 1999331--1999356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1999321 TGTGTGTGTC
1999331 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1999357 AAACCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2007020 original size:15 final size:14
Alignment explanation
Indices: 2006978--2007021 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2006968 TATTATATTT
*
2006978 TTTTTATAATTTAT
1 TTTTTATAATTTAA
*
2006992 TTTTTAAAATTTAA
1 TTTTTATAATTTAA
2007006 TTTTTATTAATTTAA
1 TTTTTA-TAATTTAA
2007021 T
1 T
2007022 ATATTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTATAATTTAA
Found at i:2007250 original size:20 final size:20
Alignment explanation
Indices: 2007199--2007250 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2007189 GTTAAAAACA
* *
2007199 AAACTTGATTTTTTTTAATT
1 AAACTTAATTTTTTTTAATC
* *
2007219 AAATTTAATTTTTTTTACTC
1 AAACTTAATTTTTTTTAATC
2007239 AAACTT-ATTTTT
1 AAACTTAATTTTT
2007251 GAAATTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (20 bp):
AAACTTAATTTTTTTTAATC
Found at i:2007278 original size:16 final size:17
Alignment explanation
Indices: 2007259--2007292 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2007249 TTGAAATTTA
*
2007259 ATATTTATAT-TTAAAT
1 ATATTTAAATATTAAAT
2007275 ATATTTAAATATTAAAT
1 ATATTTAAATATTAAAT
2007292 A
1 A
2007293 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTAAATATTAAAT
Found at i:2008807 original size:27 final size:28
Alignment explanation
Indices: 2008777--2008841 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
2008767 TGCTACTGCA
2008777 AATT-CAATAAACTTTTTTAAAAA-AATT
1 AATTACAA-AAACTTTTTTAAAAACAATT
***
2008804 AATTACAAAGGTTTTTTTAAAAACAATT
1 AATTACAAAAACTTTTTTAAAAACAATT
2008832 AATTACAAAA
1 AATTACAAAA
2008842 GTTTTTGGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (28 bp):
AATTACAAAAACTTTTTTAAAAACAATT
Found at i:2008821 original size:28 final size:28
Alignment explanation
Indices: 2008789--2008847 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
2008779 TTCAATAAAC
*
2008789 TTTTTTAAAAA-AATTAATTACAAAGGT
1 TTTTTTAAAAACAATTAATTACAAAAGT
2008816 TTTTTTAAAAACAATTAATTACAAAAGT
1 TTTTTTAAAAACAATTAATTACAAAAGT
2008844 TTTT
1 TTTT
2008848 GGCTATAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (28 bp):
TTTTTTAAAAACAATTAATTACAAAAGT
Found at i:2009252 original size:3 final size:3
Alignment explanation
Indices: 2009244--2009295 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
2009234 CACGAGGTCC
*
2009244 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2009292 ATA A
1 ATA A
2009296 GATTATTCAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2009461 original size:77 final size:77
Alignment explanation
Indices: 2009313--2009461 Score: 210
Period size: 77 Copynumber: 1.9 Consensus size: 77
2009303 CACACAGGAA
* * *
2009313 ATAAAAAATTTTAATGCAAACTATTTTATTTATTTTATAATTAGTTTTTTTATCATTTTTTAAAT
1 ATAAAAAATTTTAATACAAACTATTTTATTTATTTTATAATTAGTTTTTTTATCAATTTTGAAAT
*
2009378 CGAGTTAATATC
66 CAAGTTAATATC
* * * *
2009390 ATAAAAAATTTTATTACAGACTATTTTATTTATTTTATAATT-GATTTTTTTATTAATTTTGCAA
1 ATAAAAAATTTTAATACAAACTATTTTATTTATTTTATAATTAG-TTTTTTTATCAATTTTGAAA
2009454 TCAAGTTA
65 TCAAGTTA
2009462 TTATTATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 1 0.02
77 62 0.98
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.52
Consensus pattern (77 bp):
ATAAAAAATTTTAATACAAACTATTTTATTTATTTTATAATTAGTTTTTTTATCAATTTTGAAAT
CAAGTTAATATC
Found at i:2010664 original size:18 final size:19
Alignment explanation
Indices: 2010643--2010682 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2010633 AAATATTCAA
* *
2010643 TTTTTTAAGAATATTA-TT
1 TTTTTTAAAAAAATTACTT
2010661 TTTTTTAAAAAAATTACTT
1 TTTTTTAAAAAAATTACTT
2010680 TTT
1 TTT
2010683 ACAATCATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTTTAAAAAAATTACTT
Found at i:2011014 original size:22 final size:21
Alignment explanation
Indices: 2010983--2011025 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
2010973 TACTTTAGTT
2010983 TTATTTAAAATAAATAAATTA
1 TTATTTAAAATAAATAAATTA
*
2011004 TTATTTAAAAATAAATTAATTA
1 TTATTT-AAAATAAATAAATTA
2011026 AATGAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTATTTAAAATAAATAAATTA
Found at i:2011992 original size:2 final size:2
Alignment explanation
Indices: 2011987--2012015 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2011977 TAACCTTTTC
2011987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2012016 GGTAAACTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2013060 original size:19 final size:19
Alignment explanation
Indices: 2013019--2013061 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2013009 CGAAATTTAT
*
2013019 AAAATAATATATGTTTAAT
1 AAAATAATATATGTTTAAA
*
2013038 AAAAT-ATATATTTTTTAAA
1 AAAATAATATA-TGTTTAAA
2013057 AAAAT
1 AAAAT
2013062 GCACATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAATAATATATGTTTAAA
Found at i:2013346 original size:2 final size:2
Alignment explanation
Indices: 2013339--2013374 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2013329 TCTAAGGTAA
2013339 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2013375 GTGTTTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2018971 original size:22 final size:22
Alignment explanation
Indices: 2018925--2018972 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2018915 AACATAAATC
* * * *
2018925 AGGAAACTAATTCCATTGAATT
1 AGGAAACTAATCCCACTAAACT
2018947 AGGAAACTAATCCCACTAAACT
1 AGGAAACTAATCCCACTAAACT
2018969 AGGA
1 AGGA
2018973 GATTGACTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (22 bp):
AGGAAACTAATCCCACTAAACT
Found at i:2018986 original size:19 final size:19
Alignment explanation
Indices: 2018962--2019000 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2018952 ACTAATCCCA
2018962 CTAAACTAGGAGATTGACT
1 CTAAACTAGGAGATTGACT
2018981 CTAAACTAGGAGATTGACT
1 CTAAACTAGGAGATTGACT
2019000 C
1 C
2019001 CAACAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (19 bp):
CTAAACTAGGAGATTGACT
Found at i:2020993 original size:18 final size:18
Alignment explanation
Indices: 2020970--2021006 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2020960 TTCTAGAGAT
2020970 TCAGGTTCT-GACACATGG
1 TCAGGTT-TGGACACATGG
2020988 TCAGGTTTGGACACATGG
1 TCAGGTTTGGACACATGG
2021006 T
1 T
2021007 TTGGTGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (18 bp):
TCAGGTTTGGACACATGG
Found at i:2024465 original size:15 final size:15
Alignment explanation
Indices: 2024445--2024476 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2024435 TTCTTCTGTT
*
2024445 TTGCCTTTGGTTTTA
1 TTGCCTTTGATTTTA
2024460 TTGCCTTTGATTTTA
1 TTGCCTTTGATTTTA
2024475 TT
1 TT
2024477 ATCACAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.16, T:0.62
Consensus pattern (15 bp):
TTGCCTTTGATTTTA
Found at i:2027904 original size:2 final size:2
Alignment explanation
Indices: 2027899--2027935 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2027889 AATTTTTTTG
*
2027899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2027936 CAATTTTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2040027 original size:13 final size:13
Alignment explanation
Indices: 2040009--2040034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2039999 TGGGAAAGGA
2040009 TTGGTTCAAAAAT
1 TTGGTTCAAAAAT
2040022 TTGGTTCAAAAAT
1 TTGGTTCAAAAAT
2040035 ACTTTCTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGGTTCAAAAAT
Found at i:2046502 original size:21 final size:20
Alignment explanation
Indices: 2046477--2046529 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
2046467 TACAAGCCAA
**
2046477 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA-TACTTGG
2046498 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
2046517 TGTATCGATACAA
1 TGTATCGATACAA
2046530 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:2046535 original size:19 final size:18
Alignment explanation
Indices: 2046477--2046535 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 18
2046467 TACAAGCCAA
2046477 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA---TTTGG
*
2046498 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
2046517 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
2046536 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
21 12 0.35
22 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:2047215 original size:20 final size:20
Alignment explanation
Indices: 2047192--2047230 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2047182 ATTAAGTCGA
2047192 ATCAAACTTAATCAATTTAG
1 ATCAAACTTAATCAATTTAG
2047212 ATCAAACTTAATCAATTTA
1 ATCAAACTTAATCAATTTA
2047231 ACTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (20 bp):
ATCAAACTTAATCAATTTAG
Found at i:2047457 original size:19 final size:19
Alignment explanation
Indices: 2047406--2047459 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
2047396 AATTATAAAA
2047406 AATACCATATAAGATTTTT
1 AATACCATATAAGATTTTT
*
2047425 AAT----TAT-A-CTTTTT
1 AATACCATATAAGATTTTT
2047438 AATACCATATAAGATTTTT
1 AATACCATATAAGATTTTT
2047457 AAT
1 AAT
2047460 TAGAATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
13 8 0.30
14 1 0.04
15 3 0.11
17 3 0.11
18 1 0.04
19 11 0.41
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (19 bp):
AATACCATATAAGATTTTT
Found at i:2048596 original size:9 final size:9
Alignment explanation
Indices: 2048582--2048607 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2048572 TGCTTCTAGT
2048582 TCTTTTATG
1 TCTTTTATG
2048591 TCTTTTATG
1 TCTTTTATG
2048600 TCTTTTAT
1 TCTTTTAT
2048608 TTTGCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.69
Consensus pattern (9 bp):
TCTTTTATG
Found at i:2051665 original size:13 final size:13
Alignment explanation
Indices: 2051647--2051672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2051637 ACATTTGGTC
2051647 ATGTATCGATACA
1 ATGTATCGATACA
2051660 ATGTATCGATACA
1 ATGTATCGATACA
2051673 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2051667 original size:33 final size:32
Alignment explanation
Indices: 2051625--2051692 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
2051615 TGTTACAAGC
2051625 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
2051658 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
2051690 CAA
1 CAA
2051693 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:2054272 original size:13 final size:13
Alignment explanation
Indices: 2054254--2054292 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2054244 ATAATTGCCA
2054254 TGTATCGATACAG
1 TGTATCGATACAG
*
2054267 TGTATCGATACAA
1 TGTATCGATACAG
2054280 TGTATCGATACAG
1 TGTATCGATACAG
2054293 AGAACTGCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2058766 original size:3 final size:3
Alignment explanation
Indices: 2058758--2058788 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2058748 TATGAGTCAC
*
2058758 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
2058789 GTCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:2063128 original size:19 final size:19
Alignment explanation
Indices: 2063104--2063170 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
2063094 ATTCAACGAT
2063104 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
2063123 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
2063137 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
2063155 TTGTATCGATACATAA
1 TTGTATCGATACATAA
2063171 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:2063141 original size:32 final size:32
Alignment explanation
Indices: 2063105--2063167 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
2063095 TTCAACGATT
2063105 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2063137 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
2063168 TAATTAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2063142 original size:13 final size:13
Alignment explanation
Indices: 2063124--2063148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2063114 ACATAAGTGT
2063124 TGTATCGATACAA
1 TGTATCGATACAA
2063137 TGTATCGATACA
1 TGTATCGATACA
2063149 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2068101 original size:227 final size:227
Alignment explanation
Indices: 2067706--2068159 Score: 881
Period size: 227 Copynumber: 2.0 Consensus size: 227
2067696 ACCAAGTCCT
2067706 TAGTAGCCTAGAGCAGTAATAGAAAGATTACATCCAATTAACAAATTAGATACCAGCTAGTAAAG
1 TAGTAGCCTAGAGCAGTAATAGAAAGATTACATCCAATTAACAAATTAGATACCAGCTAGTAAAG
*
2067771 CAAAATTAGATACCGATTTCCCTCTTGACCTGTTCCTAATGTTAGGCAACCTACGCCTATTACAA
66 CAAAATTAGATACCGATTTCCCTCTTGACCTGTTCCTAATGTTAGGCAACCTACACCTATTACAA
2067836 AGAAGTTTGCAATCCTCAACTCTATAATAAACTCTATCTTAAGAGAAAACAAAAAGAATCATCTA
131 AGAAGTTTGCAATCCTCAACTCTATAATAAACTCTATCTTAAGAGAAAACAAAAAGAATCATCTA
*
2067901 GTTTTCAAGCTGTATCACCAAAGAAAACCAGG
196 GTTTTCAAGCTATATCACCAAAGAAAACCAGG
2067933 TAGTAGCCTAGAGCAGTAATAGAAAGATTACATCCAATTAACAAATTAGATACCAGCTAGTAAAG
1 TAGTAGCCTAGAGCAGTAATAGAAAGATTACATCCAATTAACAAATTAGATACCAGCTAGTAAAG
2067998 CAAAATTAGATACCGATTTCCCTCTTGACCTGTTCCTAATGTTAGGCAACCTACACCTATTACAA
66 CAAAATTAGATACCGATTTCCCTCTTGACCTGTTCCTAATGTTAGGCAACCTACACCTATTACAA
*
2068063 AGAAGTTTGCAATCCTCAACTCTATAATAAACTCTATCTTAGGAGAAAACAAAAAGAATCATCTA
131 AGAAGTTTGCAATCCTCAACTCTATAATAAACTCTATCTTAAGAGAAAACAAAAAGAATCATCTA
2068128 GTTTTCAAGCTATATCACCAAAGAAAACCAGG
196 GTTTTCAAGCTATATCACCAAAGAAAACCAGG
2068160 GTTACAGCAA
Statistics
Matches: 224, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
227 224 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (227 bp):
TAGTAGCCTAGAGCAGTAATAGAAAGATTACATCCAATTAACAAATTAGATACCAGCTAGTAAAG
CAAAATTAGATACCGATTTCCCTCTTGACCTGTTCCTAATGTTAGGCAACCTACACCTATTACAA
AGAAGTTTGCAATCCTCAACTCTATAATAAACTCTATCTTAAGAGAAAACAAAAAGAATCATCTA
GTTTTCAAGCTATATCACCAAAGAAAACCAGG
Found at i:2069174 original size:34 final size:35
Alignment explanation
Indices: 2069136--2069202 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2069126 CCTTACAACA
2069136 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2069170 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2069203 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2069666 original size:21 final size:20
Alignment explanation
Indices: 2069641--2069693 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
2069631 TACAAGCCAA
**
2069641 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA-TACTTGG
2069662 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
2069681 TGTATCGATACAA
1 TGTATCGATACAA
2069694 GTTTGGCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:2069699 original size:19 final size:18
Alignment explanation
Indices: 2069641--2069699 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 18
2069631 TACAAGCCAA
2069641 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA---TTTGG
*
2069662 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
2069681 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
2069700 CTATTGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
21 12 0.35
22 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:2071471 original size:13 final size:13
Alignment explanation
Indices: 2071453--2071477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2071443 ACTCAAGCAA
2071453 TGTATCGATACAT
1 TGTATCGATACAT
2071466 TGTATCGATACA
1 TGTATCGATACA
2071478 ATCTGGAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2072581 original size:13 final size:13
Alignment explanation
Indices: 2072563--2072588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2072553 AATTTTTTGG
2072563 TGTATCGATACAT
1 TGTATCGATACAT
2072576 TGTATCGATACAT
1 TGTATCGATACAT
2072589 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2076736 original size:26 final size:26
Alignment explanation
Indices: 2076686--2076736 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2076676 GATAGTATTA
* * *
2076686 ATAAAGTTTAACTTTATTTGGGATTG
1 ATAAAGTTCAACTTTATATGAGATTG
2076712 ATAAAGTTCAACTTTATATGAGATT
1 ATAAAGTTCAACTTTATATGAGATT
2076737 CTAAATAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (26 bp):
ATAAAGTTCAACTTTATATGAGATTG
Found at i:2081444 original size:15 final size:16
Alignment explanation
Indices: 2081419--2081449 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2081409 TTTATGAATA
2081419 TTTTAATATATAAAAT
1 TTTTAATATATAAAAT
2081435 TTTTAA-ATATAAAAT
1 TTTTAATATATAAAAT
2081450 AAATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAATATATAAAAT
Found at i:2082014 original size:16 final size:16
Alignment explanation
Indices: 2081992--2082037 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
2081982 TTCGGGCAGG
2081992 TTCGGGTTCAGGCTCA
1 TTCGGGTTCAGGCTCA
* * *
2082008 TTTGGGTTCATGCTCG
1 TTCGGGTTCAGGCTCA
2082024 TTCGGGTTCAGGCT
1 TTCGGGTTCAGGCT
2082038 TTTTTCAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.09, C:0.22, G:0.33, T:0.37
Consensus pattern (16 bp):
TTCGGGTTCAGGCTCA
Found at i:2082083 original size:16 final size:16
Alignment explanation
Indices: 2082062--2082095 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2082052 TTCGGACTCT
2082062 TTCAGGTTCAGGCTTA
1 TTCAGGTTCAGGCTTA
*
2082078 TTCAGGTTCGGGCTTA
1 TTCAGGTTCAGGCTTA
2082094 TT
1 TT
2082096 TAGGCTCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.41
Consensus pattern (16 bp):
TTCAGGTTCAGGCTTA
Found at i:2082104 original size:16 final size:16
Alignment explanation
Indices: 2082062--2082105 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2082052 TTCGGACTCT
* *
2082062 TTCAGGTTCAGGCTTA
1 TTCAGGCTCGGGCTTA
*
2082078 TTCAGGTTCGGGCTTA
1 TTCAGGCTCGGGCTTA
*
2082094 TTTAGGCTCGGG
1 TTCAGGCTCGGG
2082106 TTTAGGTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.36
Consensus pattern (16 bp):
TTCAGGCTCGGGCTTA
Found at i:2082302 original size:18 final size:18
Alignment explanation
Indices: 2082279--2082321 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2082269 TCTATATTTA
2082279 TATATAAAATTAATTTTT
1 TATATAAAATTAATTTTT
2082297 TATATAAAATTAATTTTT
1 TATATAAAATTAATTTTT
*
2082315 TAAATAA
1 TATATAA
2082322 TTTATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATAAAATTAATTTTT
Found at i:2083477 original size:16 final size:16
Alignment explanation
Indices: 2083458--2083488 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2083448 GGGTTCGAGC
*
2083458 TTTCTCTAGTTCGGAT
1 TTTCTCAAGTTCGGAT
2083474 TTTCTCAAGTTCGGA
1 TTTCTCAAGTTCGGA
2083489 CAATTTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (16 bp):
TTTCTCAAGTTCGGAT
Found at i:2084344 original size:53 final size:53
Alignment explanation
Indices: 2084272--2084378 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
2084262 AAACCGATAT
2084272 ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
1 ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
* *
2084325 ACCAAATCACACAGTTACATATACATATATCAATATGAAAATAAAAATAATAC
1 ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
2084378 A
1 A
2084379 TTGACTAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.22
Consensus pattern (53 bp):
ACCAAATCACACAGATACATATACATACATCAATATGAAAATAAAAATAATAC
Found at i:2089077 original size:26 final size:26
Alignment explanation
Indices: 2089047--2089100 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2089037 AAACCCTAAC
*
2089047 CCTAATTGACGCCAACCAAACCAAAT
1 CCTAATTGACCCCAACCAAACCAAAT
* *
2089073 CCTAATTGACCCCAATCAAACTAAAT
1 CCTAATTGACCCCAACCAAACCAAAT
2089099 CC
1 CC
2089101 AATCTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.35, G:0.06, T:0.19
Consensus pattern (26 bp):
CCTAATTGACCCCAACCAAACCAAAT
Found at i:2089817 original size:16 final size:16
Alignment explanation
Indices: 2089779--2089898 Score: 65
Period size: 16 Copynumber: 7.6 Consensus size: 16
2089769 TAAAAATTTT
*
2089779 AATTAATTT-ATTTAA
1 AATTAATTTAATTAAA
*
2089794 ATTTAATTTAATTAAA
1 AATTAATTTAATTAAA
*
2089810 AATTAA-TTAA--AATT
1 AATTAATTTAATTAA-A
*
2089824 AATTAATTTAAATATAA
1 AATTAATTTAATTA-AA
*
2089841 AATT-ATTTAAATTTAA
1 AATTAATTT-AATTAAA
*
2089857 AA-TAATTTAAATATAA
1 AATTAATTTAATTA-AA
* **
2089873 AATAAATCGAATATAAA
1 AATTAATTTAAT-TAAA
2089890 AA-TAATTTA
1 AATTAATTTA
2089899 TACTTAAAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
13 2 0.03
14 6 0.08
15 20 0.26
16 30 0.38
17 17 0.22
18 3 0.04
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
AATTAATTTAATTAAA
Found at i:2089817 original size:31 final size:30
Alignment explanation
Indices: 2089779--2089867 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 30
2089769 TAAAAATTTT
2089779 AATTAATTTATTTAAATTTAATTTAA-TTAAA
1 AATTAA-TTATTTAAATTTAA-TTAATTTAAA
2089810 AATTAATTA---AAA-TTAATTAATTTAAA
1 AATTAATTATTTAAATTTAATTAATTTAAA
* * *
2089836 TATAAAATTATTTAAATTTAAAATAATTTAAA
1 AAT-TAATTATTTAAATTT-AATTAATTTAAA
2089868 TATAAAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
25 4 0.08
26 11 0.23
27 8 0.17
30 6 0.12
31 8 0.17
32 11 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATTAATTATTTAAATTTAATTAATTTAAA
Found at i:2089890 original size:32 final size:33
Alignment explanation
Indices: 2089827--2089898 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
2089817 TAAAATTAAT
* * * *
2089827 TAATTTAAATATAAAATTATTTAAAT-TTAAAA
1 TAATTTAAATATAAAATAAATCAAATATAAAAA
*
2089859 TAATTTAAATATAAAATAAATCGAATATAAAAA
1 TAATTTAAATATAAAATAAATCAAATATAAAAA
2089892 TAATTTA
1 TAATTTA
2089899 TACTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (33 bp):
TAATTTAAATATAAAATAAATCAAATATAAAAA
Found at i:2089924 original size:49 final size:48
Alignment explanation
Indices: 2089834--2089926 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 48
2089824 AATTAATTTA
* * **
2089834 AATATAAAATTATTTAAATTTAAAATAATTTAAATATAAAATAAATCG
1 AATATAAAATAATTTAAACTTAAAATAATACAAATATAAAATAAATCG
*
2089882 AATATAAAAATAATTTATACTTAAAATAATACAAAT-TCAAAATAA
1 AATAT-AAAATAATTTAAACTTAAAATAATACAAATAT-AAAATAA
2089927 CTCAAATCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
48 6 0.16
49 32 0.84
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (48 bp):
AATATAAAATAATTTAAACTTAAAATAATACAAATATAAAATAAATCG
Found at i:2090073 original size:27 final size:28
Alignment explanation
Indices: 2090043--2090107 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
2090033 TTAATTAATT
*
2090043 TAAATTTAAAAT-AATAC-AAATTTAAAA
1 TAAATTTAAAATCAA-ACTAAATATAAAA
*
2090070 TAAA-TAAAAATCAAACTAAATATAAAA
1 TAAATTTAAAATCAAACTAAATATAAAA
2090097 -ATAATTTAAAA
1 TA-AATTTAAAA
2090108 ATTTAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 9 0.29
27 17 0.55
28 5 0.16
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (28 bp):
TAAATTTAAAATCAAACTAAATATAAAA
Found at i:2090080 original size:17 final size:16
Alignment explanation
Indices: 2090044--2090080 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
2090034 TAATTAATTT
*
2090044 AAATTTAAAATAATAC
1 AAATTTAAAATAATAA
2090060 AAATTTAAAATAAATAA
1 AAATTTAAAAT-AATAA
2090077 AAAT
1 AAAT
2090081 CAAACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTTAAAATAATAA
Found at i:2090138 original size:18 final size:20
Alignment explanation
Indices: 2090117--2090164 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2090107 AATTTAAATT
2090117 AACTTAA-TCA-TAACTCAA
1 AACTTAATTCATTAACTCAA
2090135 AAC-TAATTCATTAACTCAA
1 AACTTAATTCATTAACTCAA
2090154 AAC-TAATTCAT
1 AACTTAATTCAT
2090165 CATTCATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.11
18 6 0.21
19 19 0.68
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (20 bp):
AACTTAATTCATTAACTCAA
Found at i:2090151 original size:19 final size:19
Alignment explanation
Indices: 2090127--2090164 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2090117 AACTTAATCA
2090127 TAACTCAAAACTAATTCAT
1 TAACTCAAAACTAATTCAT
2090146 TAACTCAAAACTAATTCAT
1 TAACTCAAAACTAATTCAT
2090165 CATTCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (19 bp):
TAACTCAAAACTAATTCAT
Found at i:2093968 original size:20 final size:20
Alignment explanation
Indices: 2093943--2093980 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2093933 CAGAACCTAG
*
2093943 AATGTATGGATACAATTTTA
1 AATGTATCGATACAATTTTA
2093963 AATGTATCGATACAATTT
1 AATGTATCGATACAATTT
2093981 CCTTTCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACAATTTTA
Found at i:2094047 original size:20 final size:20
Alignment explanation
Indices: 2094004--2094077 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
2093994 CACATGGTTC
***
2094004 TGTATCGATACATTTCAAGCA
1 TGTATCGATACA-TTCACTTA
2094025 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
2094045 TGTAT-GAATACATTGC-CTTA
1 TGTATCG-ATACATT-CACTTA
*
2094065 TTGTATTGATACA
1 -TGTATCGATACA
2094078 AATTGTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.02
20 21 0.46
21 23 0.50
22 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:2094076 original size:21 final size:20
Alignment explanation
Indices: 2094024--2094077 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
2094014 CATTTCAAGC
*
2094024 ATGTATCGATACATTCACTT
1 ATGTATTGATACATTCACTT
2094044 ATGTA-TGAATACATTGC-CTT
1 ATGTATTG-ATACATT-CACTT
2094064 ATTGTATTGATACA
1 A-TGTATTGATACA
2094078 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.03
20 16 0.55
21 10 0.34
22 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATTGATACATTCACTT
Found at i:2094740 original size:17 final size:18
Alignment explanation
Indices: 2094707--2094741 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2094697 TTTATTTTAA
2094707 ATGAAATTAGGTTTATTT
1 ATGAAATTAGGTTTATTT
*
2094725 ATGAAATT-GTTTTATTT
1 ATGAAATTAGGTTTATTT
2094742 TTAGGCCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
ATGAAATTAGGTTTATTT
Found at i:2099409 original size:74 final size:74
Alignment explanation
Indices: 2099235--2099913 Score: 719
Period size: 74 Copynumber: 9.4 Consensus size: 74
2099225 AAAAACGTTC
* * * * *
2099235 TACTCTTTAAGGACTGAAAAAGATAAAGGATACCACCAGCTAATGTGGGCTTTAAAGAAAAA-AA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
* *
2099299 AAGGTATCC
66 AAGGCATCT
* * * * * * *
2099308 CACTCTTTAAGGATTGAAAAAGGTAAAGAGTGCCACCAGCTTATATGGGCTCTGAAGAAAAAGAA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
2099373 AAGGCATCT
66 AAGGCATCT
* * * * * * *
2099382 TATTCTTTGAGGACTGAAAAAGATAAAGTGTGCCACTAACCTGTATGGGCTTTGAAGAAAAAGAA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
2099447 AAGG-AGTCT
66 AAGGCA-TCT
* * * *
2099456 TGCTCCTTGAGGATTGAAAAAGGTAAAGGGT-------GC--ATGTGGGCTTTGAAGAAAAAGAA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
* *
2099512 AATGCGTCT
66 AAGGCATCT
* * *
2099521 TGCTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACTAGCTTGTGTGGGCTTTGAAGAAAAAGAA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
*
2099586 AAGGCATCC
66 AAGGCATCT
* * * * * *
2099595 TGCTCTTTAAAGACTGAAAACAG-TAAAGGGTGCCACTAACTTATGTGGGCCTTGAAG-AAAA-A
1 TACTCTTTGAGGACTGAAAA-AGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGA
2099657 AAA-GCATCT
65 AAAGGCATCT
* * * * * *
2099666 TAGTTTTTGAAGACTAAAAAAGATAAAGGGTGCCACCAGCTTATGTGGACTTTAAAGAAAAAAAA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTT---GAAGAAAAA
2099731 GAAAAGGCATCT
63 GAAAAGGCATCT
*
2099743 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAACTTATGTGGGCTTTGAAG--AAA-AA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
2099805 AAGGCATCT
66 AAGGCATCT
* * * * *
2099814 TACTCTTTGAGGACTGAAAAAGGTAAAAGGTGTCACCAGCTTGTATGGGCTTTGAAGAAAAAGAA
1 TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
* *
2099879 AATGCATCC
66 AAGGCATCT
*
2099888 TACTCTTTAAGGACTGAAAAAGATAA
1 TACTCTTTGAGGACTGAAAAAGATAA
2099914 GTTTAGATAC
Statistics
Matches: 509, Mismatches: 74, Indels: 45
0.81 0.12 0.07
Matches are distributed among these distances:
65 55 0.11
67 1 0.00
70 2 0.00
71 108 0.21
72 9 0.02
73 60 0.12
74 211 0.41
75 6 0.01
76 4 0.01
77 53 0.10
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (74 bp):
TACTCTTTGAGGACTGAAAAAGATAAAGGGTGCCACCAGCTTATGTGGGCTTTGAAGAAAAAGAA
AAGGCATCT
Found at i:2099501 original size:65 final size:65
Alignment explanation
Indices: 2099427--2099553 Score: 209
Period size: 65 Copynumber: 2.0 Consensus size: 65
2099417 CTAACCTGTA
* *
2099427 TGGGCTTTGAAGAAAAAGAAAAGGAGTCTTGCTCCTTGAGGATTGAAAAAGGTAAAGGGTGCATG
1 TGGGCTTTGAAGAAAAAGAAAAGGAGTCTTGCTCCTTGAGGACTGAAAAAGATAAAGGGTGCATG
* * *
2099492 TGGGCTTTGAAGAAAAAGAAAATGCGTCTTGCTCTTTGAGGACTGAAAAAGATAAAGGGTGC
1 TGGGCTTTGAAGAAAAAGAAAAGGAGTCTTGCTCCTTGAGGACTGAAAAAGATAAAGGGTGC
2099554 CACTAGCTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.35, C:0.10, G:0.31, T:0.24
Consensus pattern (65 bp):
TGGGCTTTGAAGAAAAAGAAAAGGAGTCTTGCTCCTTGAGGACTGAAAAAGATAAAGGGTGCATG
Found at i:2101487 original size:80 final size:79
Alignment explanation
Indices: 2101374--2101576 Score: 228
Period size: 80 Copynumber: 2.6 Consensus size: 79
2101364 AATAACAGGG
* * * * * * *
2101374 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
2101438 AAAAAAAAAATCGGGA
65 -AAAAAAAAACCGGGA
* * *
2101454 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * *
2101519 GAATAAAGCCGGGG
66 AAAAAAAACCGGGA
* *
2101533 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
2101577 GAAATAACGA
Statistics
Matches: 104, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
79 51 0.49
80 53 0.51
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCGGGA
Found at i:2101568 original size:28 final size:28
Alignment explanation
Indices: 2101528--2101599 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2101518 GGAATAAAGC
** *
2101528 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2101556 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
2101584 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2101600 TCGACTATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:2101697 original size:53 final size:53
Alignment explanation
Indices: 2101587--2101711 Score: 164
Period size: 53 Copynumber: 2.4 Consensus size: 53
2101577 GAAATAACGA
* * * *
2101587 GGTTGGAGTATCCTCGACT-ATGAAAAATTGGTATTCTTGGAAATAAAATCGG
1 GGTTGGAGTATCCTCGATTAAGGAAAAATTGGTATTCTTGAAAATAAAACCGG
* * *
2101639 AGTTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTT-TTGAAAATAAAACCGG
1 GGTTGGAGTATCCTCGATT-AAGGAAAAATTGGTATTCTTGAAAATAAAACCGG
2101692 GGTTGGAGTATCCTCGATTA
1 GGTTGGAGTATCCTCGATTA
2101712 TGAAAAGTCA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
52 17 0.27
53 31 0.50
54 14 0.23
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (53 bp):
GGTTGGAGTATCCTCGATTAAGGAAAAATTGGTATTCTTGAAAATAAAACCGG
Found at i:2101774 original size:28 final size:27
Alignment explanation
Indices: 2101742--2101806 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 27
2101732 AATAAAGTCA
**
2101742 GGGTTGGAGTATCCCCTCGGAAGTAACG
1 GGGTTGGAGTATCCCCGAGGAA-TAACG
*
2101770 GGGTTGGAGTATCCCCGATGAATAACG
1 GGGTTGGAGTATCCCCGAGGAATAACG
2101797 GGGTTGGAGT
1 GGGTTGGAGT
2101807 GTCCTCGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAATAACG
Found at i:2101803 original size:27 final size:28
Alignment explanation
Indices: 2101742--2101815 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 28
2101732 AATAAAGTCA
***
2101742 GGGTTGGAGTATCCCCTCGGAAGTAACG
1 GGGTTGGAGTATCCCCGATGAAGTAACG
2101770 GGGTTGGAGTATCCCCGATGAA-TAACG
1 GGGTTGGAGTATCCCCGATGAAGTAACG
* *
2101797 GGGTTGGAGTGTCCTCGAT
1 GGGTTGGAGTATCCCCGAT
2101816 TGTGAAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAGTAACG
Found at i:2101870 original size:54 final size:51
Alignment explanation
Indices: 2101799--2101929 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 51
2101789 GAATAACGGG
* * * *
2101799 GTTGGAGTGTCCTCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TTTTGAAAATAAAATCGGA
*
2101853 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGA
*
2101904 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
2101930 TTGAGAAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
51 36 0.54
52 4 0.06
53 10 0.15
54 17 0.25
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:2104301 original size:13 final size:13
Alignment explanation
Indices: 2104283--2104308 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2104273 ACAAAGATCC
2104283 ATGTATCGATACA
1 ATGTATCGATACA
2104296 ATGTATCGATACA
1 ATGTATCGATACA
2104309 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2104304 original size:33 final size:33
Alignment explanation
Indices: 2104262--2104328 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2104252 AAAATTTCCA
***
2104262 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2104295 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2104328 A
1 A
2104329 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2104372 original size:19 final size:19
Alignment explanation
Indices: 2104348--2104402 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
2104338 CAGTAGCTAA
*
2104348 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
2104367 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
2104386 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2104403 TTGTTGAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:2104485 original size:21 final size:21
Alignment explanation
Indices: 2104461--2104514 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
2104451 TTGTAGGATG
2104461 TATCGATACATTCCACAAATA
1 TATCGATACATTCCACAAATA
*
2104482 TATCGATACATTCCACAAATG
1 TATCGATACATTCCACAAATA
2104503 TATCGATACATT
1 TATCGATACATT
2104515 TGGATAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (21 bp):
TATCGATACATTCCACAAATA
Found at i:2104945 original size:13 final size:13
Alignment explanation
Indices: 2104929--2104958 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2104919 ATACATTGTT
2104929 CATTGTATCGATA
1 CATTGTATCGATA
2104942 CATTGTATCGATA
1 CATTGTATCGATA
2104955 CATT
1 CATT
2104959 CTAGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2105014 original size:20 final size:20
Alignment explanation
Indices: 2104991--2105028 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2104981 ATACATTTTG
*
2104991 CATTGTATCGATACATTGCC
1 CATTATATCGATACATTGCC
2105011 CATTATATCGATACATTG
1 CATTATATCGATACATTG
2105029 TATTGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
CATTATATCGATACATTGCC
Found at i:2105037 original size:33 final size:33
Alignment explanation
Indices: 2104991--2105060 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2104981 ATACATTTTG
2104991 CATTGTATCGATACATTGCCCATTATATCGATA
1 CATTGTATCGATACATTGCCCATTATATCGATA
* * * *
2105024 CATTGTATTGATACATTGCTCATTGTATCGATT
1 CATTGTATCGATACATTGCCCATTATATCGATA
2105057 CATT
1 CATT
2105061 TTACAATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACATTGCCCATTATATCGATA
Found at i:2107536 original size:51 final size:51
Alignment explanation
Indices: 2107379--2107545 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 51
2107369 ATTTTTCATC
* ** **
2107379 TCGGGGATACTCCAA-TCCCGGTTCCATTTCCAAAACA-TCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACT-AATTTTTCACAA
* * ** **
2107430 TCGGGGATACTCCAACTGCGATTTT-TTT-AAAAACACCGATTTACCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAA
2107479 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAA
* *
2107530 TTGGGGATATTCCAAC
1 TCGGGGATACTCCAAC
2107546 CTCGTTATTT
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
49 37 0.40
50 6 0.06
51 49 0.53
52 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAA
Found at i:2107729 original size:52 final size:52
Alignment explanation
Indices: 2107667--2107784 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 52
2107657 TTATTTCCGA
* *
2107667 GGGGATACTCCAACCT-CAATTTTATTTTCTAAAATACGAATTTT-TCATAATC
1 GGGGATACTCCAACCTCCAATTTTATTTTC-AAAACACCAATTTTCT-ATAATC
* *
2107719 GGGGATACTCCAA-CTCCGATTTTATTTTCAAAACACCAATTTTCTATAATT
1 GGGGATACTCCAACCTCCAATTTTATTTTCAAAACACCAATTTTCTATAATC
*
2107770 AGGGATACTCCAACC
1 GGGGATACTCCAACC
2107785 CTGTTATTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
51 31 0.53
52 27 0.47
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (52 bp):
GGGGATACTCCAACCTCCAATTTTATTTTCAAAACACCAATTTTCTATAATC
Found at i:2107898 original size:238 final size:236
Alignment explanation
Indices: 2107474--2108049 Score: 823
Period size: 238 Copynumber: 2.4 Consensus size: 236
2107464 ACCGATTTAC
* * * *
2107474 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTT-TCACAATTGGGGAT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCT-ATAATTAGGGAT
* *
2107538 ATTCCAA-CCTCGTTATTTCTGAGGAGATACTCCAACCTTGGCTTTATATCTAAAATATTGATTT
65 ACTCCAACCCT-GTTATTTCTGAGG-GATACTCCAACCTCGGCTTTATATCTAAAATATTGATTT
* ** * * * *
2107602 TTCATAATCGGAGGTACTCCAACCTTGTTATGTCATCGGGGATACTCCAATTCCGTTATTTCCGA
128 TTCATAATCGGAGGCACTCCAACCCCGTTATGTCATCAGCGATACTCCAATCCCGTTATTTCCAA
* * *
2107667 GGGGATACTCCAACCTCAATTTTATTTTCTAAAATACGAATTTTT
193 AGGGATACTCCAACCTCAATTTTA-TTTCTAAAATACCAATATTT
*
2107712 CATAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATA
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATA
* *
2107777 CTCCAACCCTGTTATTTCTGAGAGGATACTCCAGCCTCGGTTTTATATCTAAAATATTGATTTTT
66 CTCCAACCCTGTTATTTCTGAG-GGATACTCCAACCTCGGCTTTATATCTAAAATATTGATTTTT
* * *
2107842 CATAATCGGGGGCACTCCAACCCCGTTATGTCATCAGCGATGCTCCAATCCCGTTATTTCTAAAG
130 CATAATCGGAGGCACTCCAACCCCGTTATGTCATCAGCGATACTCCAATCCCGTTATTTCCAAAG
* *
2107907 GGATACTCCAATCTCGATTTTATTTCTAAAATACCAATATTT
195 GGATACTCCAACCTCAATTTTATTTCTAAAATACCAATATTT
* * * *
2107949 CACAATCGGGAATACTCCAATTCTGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATA
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATA
*
2108014 CTCCAACCCTGTTATTTCCGAGGGGATACTCCAACC
66 CTCCAACCCTGTTATTTCTGA-GGGATACTCCAACC
2108050 CTGATTTTAG
Statistics
Matches: 303, Mismatches: 31, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
237 110 0.36
238 188 0.62
239 5 0.02
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (236 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATA
CTCCAACCCTGTTATTTCTGAGGGATACTCCAACCTCGGCTTTATATCTAAAATATTGATTTTTC
ATAATCGGAGGCACTCCAACCCCGTTATGTCATCAGCGATACTCCAATCCCGTTATTTCCAAAGG
GATACTCCAACCTCAATTTTATTTCTAAAATACCAATATTT
Found at i:2107966 original size:51 final size:51
Alignment explanation
Indices: 2107905--2108019 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
2107895 TTATTTCTAA
*
2107905 AGGGATACTCCAA-TCTCGATTTTA-TTTCTAAAATACCAATATTTC-ACAATC
1 AGGGATACTCCAATTCT-GATTTTATTTTC-AAAACACCAAT-TTTCTACAATC
*
2107956 -GGGAATACTCCAATTCTGATTTTATTTTCAAAACACCAATTTTCTATAATC
1 AGGG-ATACTCCAATTCTGATTTTATTTTCAAAACACCAATTTTCTACAATC
2108007 AGGGATACTCCAA
1 AGGGATACTCCAA
2108020 CCCTGTTATT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
50 7 0.12
51 40 0.70
52 10 0.18
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (51 bp):
AGGGATACTCCAATTCTGATTTTATTTTCAAAACACCAATTTTCTACAATC
Found at i:2108043 original size:79 final size:79
Alignment explanation
Indices: 2107960--2108187 Score: 339
Period size: 79 Copynumber: 2.9 Consensus size: 79
2107950 ACAATCGGGA
** * *
2107960 ATACTCCAATTCTGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACCCTG
1 ATACTCCAACCCTGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAACCCTG
2108025 TTATTTCCGAGGGG
66 TTATTTCCGAGGGG
* * *
2108039 ATACTCCAACCCTGATTTTAGTTTCAAAATACCGATTTTCTATAATTAGGGATACTCCAACCCTG
1 ATACTCCAACCCTGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAACCCTG
*
2108104 TTATTTCTGAGGGG
66 TTATTTCCGAGGGG
* * * * *
2108118 ATACTCCAACCCTGATTTTACTTCCAAAACACCGATTTTCCATAATCGGGGATACTCCAGCCCCG
1 ATACTCCAACCCTGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAACCCTG
2108183 TTATT
66 TTATT
2108188 ATCTCCAAAA
Statistics
Matches: 134, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 134 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (79 bp):
ATACTCCAACCCTGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAACCCTG
TTATTTCCGAGGGG
Found at i:2108098 original size:237 final size:235
Alignment explanation
Indices: 2107433--2108107 Score: 817
Period size: 238 Copynumber: 2.9 Consensus size: 235
2107423 TTCTTAATCG
* * * *
2107433 GGGATACTCCAACTGCGATTTT-TTT-AAAAACACCGATTTACCACAATCGGGGATACTCCAACT
1 GGGATACTCCAACT-CGATTTTATTTCTAAAATACCAATTT-TCACAATCGGGGATACTCCAACT
* * * * *
2107496 CCGATTTTATTTCCAAAACACTAATTTT-TCACAATTGGGGATATTCCAA-CCTCGTTATTTCTG
64 CCGATTTTATTTTCAAAACACCAATTTTCT-ATAATTAGGGATACTCCAACCCT-GTTATTTCTG
* * * *
2107559 AGGAGATACTCCAACCTTGGCTTTATATCTAAAATATTGATTTTTCATAA-TCGGAGGTACTCCA
127 AGGGGATACTCCAACCCTGGTTTTATATCTAAAATATTGATTTTTCATAATTAGG-GGTACTCCA
* * * * * *
2107623 ACCTTGTTATGTCATCGGGGATACTCCAATTCCGTTATTTCCGAG
191 ACCCTGTTATGTCATCAGCGATACTCCAATCCCGTTATTTCCAAA
* * *
2107668 GGGATACTCCAACCTCAATTTTATTTTCTAAAATACGAATTTTTCATAATCGGGGATACTCCAAC
1 GGGATACTCCAA-CTCGATTTTA-TTTCTAAAATACCAA-TTTTCACAATCGGGGATACTCCAAC
2107733 TCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATACTCCAACCCTGTTATTTCTGA
63 TCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATACTCCAACCCTGTTATTTCTGA
* * ** *
2107798 GAGGATACTCC-AGCCTCGGTTTTATATCTAAAATATTGATTTTTCATAATCGGGGGCACTCCAA
128 GGGGATACTCCAACCCT-GGTTTTATATCTAAAATATTGATTTTTCATAATTAGGGGTACTCCAA
* * *
2107862 CCCCGTTATGTCATCAGCGATGCTCCAATCCCGTTATTTCTAAA
192 CCCTGTTATGTCATCAGCGATACTCCAATCCCGTTATTTCCAAA
* *
2107906 GGGATACTCCAATCTCGATTTTATTTCTAAAATACCAATATTTCACAATCGGGAATACTCCAATT
1 GGGATACTCCAA-CTCGATTTTATTTCTAAAATACCAAT-TTTCACAATCGGGGATACTCCAACT
* * *
2107971 CTGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTCCGAG
64 CCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATACTCCAACCCTGTTATTTCTGAG
* * ** *
2108036 GGGATACTCCAACCCTGATTTTAGTTTC-AAAATACCGA-TTTTCTATAATTAGGGATACTCCAA
129 GGGATACTCCAACCCTGGTTTTA-TATCTAAAATATTGATTTTTC-ATAATTAGGGGTACTCCAA
2108099 CCCTGTTAT
192 CCCTGTTAT
2108108 TTCTGAGGGG
Statistics
Matches: 378, Mismatches: 49, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
235 18 0.05
236 8 0.02
237 150 0.40
238 193 0.51
239 9 0.02
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (235 bp):
GGGATACTCCAACTCGATTTTATTTCTAAAATACCAATTTTCACAATCGGGGATACTCCAACTCC
GATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATACTCCAACCCTGTTATTTCTGAGGG
GATACTCCAACCCTGGTTTTATATCTAAAATATTGATTTTTCATAATTAGGGGTACTCCAACCCT
GTTATGTCATCAGCGATACTCCAATCCCGTTATTTCCAAA
Found at i:2116085 original size:42 final size:42
Alignment explanation
Indices: 2115857--2117545 Score: 370
Period size: 42 Copynumber: 40.5 Consensus size: 42
2115847 GACTAAGCCA
* * * * *
2115857 ACAAGTAAACAAAGGATAAAGAAGTTGACCGGGATTGAA-CA
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * *
2115898 ACAAGTCAACAAAGGATAAA-AAGATTTACTCGAGACTAAATCG
1 ACAAGTCAACAAAGGATAAAGAA-ATTAAC-CGAGATTGAACCG
* * * *
2115941 ACAAG-CAAAAAAAGGATAAAGAAGTTAACCGGGATTGAACTG
1 ACAAGTC-AACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * * *
2115983 ACATGTCAATAAAGGATGAAA-AGATTTAACCGAGACT-AAGCCA
1 ACAAGTCAACAAAGGAT-AAAGA-AATTAACCGAGATTGAA-CCG
* * *
2116026 ACAGGTAAACAAAGGATAAAGAAATTGACCGAGATTGAACCG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * ** * * *
2116068 ACAAGTCAATAAGGGATAAA-AGGGTT-ACTCGGGACT-AAGCTG
1 ACAAGTCAACAAAGGATAAAGA-AATTAAC-CGAGATTGAA-CCG
* * * * * * *
2116110 ATAGGTAAACAAAGGATAAA-AAAGTTGATCGGGATTAAACCG
1 ACAAGTCAACAAAGGATAAAGAAA-TTAACCGAGATTGAACCG
* * * * * * *
2116152 ATATGTCAACAAAGGATAAAAAAATTGATCGGGATTGAACTG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * * * **
2116194 ACAAGTCAACAAAAGATAAAAGGATTTACCCGAGACT-AAGTTG
1 ACAAGTCAACAAAGGAT-AAAGAAATTAACCGAGATTGAA-CCG
* * * * * *
2116237 ACAGGTAAACAAAAGATAAA-ATAGTTGACCGAGATTGAACTG
1 ACAAGTCAACAAAGGATAAAGA-AATTAACCGAGATTGAACCG
* *
2116279 ACAAGTTAACAAAGGATAAA-AGGATTAACCCGAGATT-AAGCCG
1 ACAAGTCAACAAAGGATAAAGA-AATTAA-CCGAGATTGAA-CCG
* * * ** * * * * **
2116322 ACAGGTAAATAAAATATAAAGAAGTTGACCAAGGTTGAACTA
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
*
2116364 AGAAGTCAACAAAGGAT-----AA--AA--G-GA-T-AAGCCG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAA-CCG
* * * * * **
2116395 ACAGGTAAACAAAGGATAAAGAAGTTGACC-AGGGTTGAATTG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGA-GATTGAACCG
* *
2116437 AAAAGTCAACAAAGGAT-----AA--AA--G-GA-T-AAGCCA
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAA-CCG
* * * * * * *
2116468 ATAAGTAAACAAAGGACAAAGAAATTGACCGGGATAGAACTG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * *
2116510 ACAAGTCAACAAAGGATAAA-AGGATTTACCGAGACT-AAGCTG
1 ACAAGTCAACAAAGGATAAAGA-AATTAACCGAGATTGAA-CCG
* ** * *
2116552 ACATGGAAAC-AA--ATAAA-AAAGTTGAA-TGAGATTGAACTG
1 ACAAGTCAACAAAGGATAAAGAAA-TT-AACCGAGATTGAACCG
* * * * *
2116591 ACAAGTCAACAAAAGATAAA-AAGATTTACTCGGGACTGAGCCG
1 ACAAGTCAACAAAGGATAAAGAA-ATTAAC-CGAGATTGAACCG
* * * * *
2116634 ATAGGTAAACAAAGGATAAA-AAAGTTAAACGGGATTGAACCG
1 ACAAGTCAACAAAGGATAAAGAAA-TTAACCGAGATTGAACCG
* * * * * * *
2116676 ACAAGTTAACAAAGGATAAAAGGATTTACCCGAGACTGAGCTG
1 ACAAGTCAACAAAGGAT-AAAGAAATTAACCGAGATTGAACCG
* * **
2116719 A-TAGATAAACAAAGGATAAAGAAATTAACTAAGATTGAACCG
1 ACAAG-TCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * * * * *
2116761 ATAAGTCAACAAAGGATAAA-AGGATTTACCTGGGACTGAGCCA
1 ACAAGTCAACAAAGGATAAAGA-AATTAACC-GAGATTGAACCG
* * * * * * *
2116804 ATAGGTAAACAAAGGATAAAGAAATTGACTGGGATTGAACTG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * *
2116846 ACAAGTCAACAAAGGATAAA-AAGATTTACCCAAGACT-AAGCCA
1 ACAAGTCAACAAAGGATAAAGAA-A-TTAACCGAGATTGAA-CCG
* * * * ** *
2116889 ATAGGTAAACAAAGGATAAAGAAGTTGGCCAAGATTGAACCG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * *
2116931 GCAAGTCAACAAAGGATAAA-AACATTTACTCAAGATT-AAGCTG
1 ACAAGTCAACAAAGGATAAAGAA-ATTAAC-CGAGATTGAA-CCG
* * * * * * *
2116974 ATAGGTAAACAAAGGATAAA-AATGTTTACC-AGAGTTCAACTG
1 ACAAGTCAACAAAGGATAAAGAA-ATTAACCGAGA-TTGAACCG
* * * * * **
2117016 AGAAGTCAACAATGGATAAA-AAGATTTACTCAAGACTGAGTCG
1 ACAAGTCAACAAAGGATAAAGAA-ATTAAC-CGAGATTGAACCG
* * * * * **
2117059 ACAAGTAAACAAAGGATAAA-AAATTGATCGGGATAGAACTA
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * * *
2117100 ATAAGTCAACAAAAGGATAAA-AAGATTTATCC-AGGACTGAGCTG
1 ACAAGTCAAC-AAAGGATAAAGAA-A-TTAACCGA-GATTGAACCG
** * * * *
2117144 ACCGGTAAATAAAGGATAAAGAAGTTGAA-CGA-AGTTAAACCG
1 ACAAGTCAACAAAGGATAAAGAAATT-AACCGAGA-TTGAACCG
* * **
2117186 ACAAGTCAACAAAGGATAAA-AGGATTTACTCGAGACTT-AGTCG
1 ACAAGTCAACAAAGGATAAAGA-AATTAAC-CGAGA-TTGAACCG
* * * *
2117229 AC-AGTTAAACAAAGGATAAAGAAGTTGAA-CGGGATTGAACTG
1 ACAAG-TCAACAAAGGATAAAGAAATT-AACCGAGATTGAACCG
* * * * * *
2117271 ACAAGTTAACAAAGGATAAAAGGATTTACCCGAGATTGAGCTG
1 ACAAGTCAACAAAGGAT-AAAGAAATTAACCGAGATTGAACCG
* * * * * *
2117314 ACAGGTAAATAAAGGATAAAGAAATTGA-CAAGGATTGAACCA
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGA-GATTGAACCG
* * * * *
2117356 ACAAGTCAACAAAGGATAAA-AAGATTTACATGGGACT-AAGCCA
1 ACAAGTCAACAAAGGATAAAGAA-ATTAAC-CGAGATTGAA-CCG
* * * * * * *
2117399 ACAAGTAAATAAAAGATAAAGAAATTGATCGGGATTGAACCA
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
* * * *
2117441 ACATGTCAACAAAGGATAAA-ATAATTTACCTGGGATT-AAGCCA
1 ACAAGTCAACAAAGGATAAAGA-AATTAACC-GAGATTGAA-CCG
* * * * *
2117484 ATAGGTAAACAAAGGATAAAGAAGTTGACC-AGGATTGAACCG
1 ACAAGTCAACAAAGGATAAAGAAATTAACCGA-GATTGAACCG
* *
2117526 ATAAGTCAACAGAGGATAAA
1 ACAAGTCAACAAAGGATAAA
2117546 AAGATTTACT
Statistics
Matches: 1187, Mismatches: 344, Indels: 233
0.67 0.20 0.13
Matches are distributed among these distances:
30 4 0.00
31 31 0.03
32 2 0.00
35 2 0.00
36 3 0.00
37 2 0.00
38 3 0.00
39 23 0.02
40 8 0.01
41 68 0.06
42 576 0.49
43 431 0.36
44 34 0.03
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.18
Consensus pattern (42 bp):
ACAAGTCAACAAAGGATAAAGAAATTAACCGAGATTGAACCG
Found at i:2116126 original size:169 final size:169
Alignment explanation
Indices: 2115847--2116173 Score: 424
Period size: 169 Copynumber: 1.9 Consensus size: 169
2115837 GGTTACTTAG
* *
2115847 GACTAAGCCAACAAGTAAACAAAGGATAAAGAAGTTGACCGGGATTGAACAACAAGTCAACAAAG
1 GACTAAGCCAACAAGTAAACAAAGGATAAAGAAATTGACCGAGATTGAACAACAAGTCAACAAAG
* *
2115912 GATAAAAAGATTTACTCGAGACTAAATCGACAAGCAAAAAAAGGATAAAGAAGTTAACCGGGATT
66 GATAAAAAGAGTTACTCGAGACTAAATCGACAAGCAAAAAAAGGATAAAAAAGTTAACCGGGATT
* * * *
2115977 GAACTGACATGTCAATAAAGGATGAAAAGATTTAACCGA
131 AAACCGACATGTCAACAAAGGATAAAAAGATTTAACCGA
* * * *
2116016 GACTAAGCCAACAGGTAAACAAAGGATAAAGAAATTGACCGAGATTGAACCGACAAGTCAATAAG
1 GACTAAGCCAACAAGTAAACAAAGGATAAAGAAATTGACCGAGATTGAA-CAACAAGTCAACAAA
* * * * * * * * *
2116081 GGAT-AAAAGGGTTACTCGGGACT-AAGCTGATAGGTAAACAAAGGATAAAAAAGTTGATCGGGA
65 GGATAAAAAGAGTTACTCGAGACTAAATC-GACAAGCAAAAAAAGGATAAAAAAGTTAACCGGGA
*
2116144 TTAAACCGATATGTCAACAAAGGATAAAAA
129 TTAAACCGACATGTCAACAAAGGATAAAAA
2116174 AATTGATCGG
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
168 3 0.02
169 115 0.86
170 16 0.12
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (169 bp):
GACTAAGCCAACAAGTAAACAAAGGATAAAGAAATTGACCGAGATTGAACAACAAGTCAACAAAG
GATAAAAAGAGTTACTCGAGACTAAATCGACAAGCAAAAAAAGGATAAAAAAGTTAACCGGGATT
AAACCGACATGTCAACAAAGGATAAAAAGATTTAACCGA
Found at i:2116248 original size:43 final size:43
Alignment explanation
Indices: 2116191--2116341 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 43
2116181 CGGGATTGAA
* * *
2116191 CTGACAAGTCAACAAAAGATAAAAGGATTTACCCGAGACTAAG
1 CTGACAAGTAAACAAAAGATAAAAGGATTAACCCGAGATTAAG
* * * *
2116234 TTGACAGGTAAACAAAAGATAAAA-TAGTTGA-CCGAGATTGAA-
1 CTGACAAGTAAACAAAAGATAAAAGGA-TTAACCCGAGATT-AAG
* *
2116276 CTGACAAGTTAACAAAGGATAAAAGGATTAACCCGAGATTAAG
1 CTGACAAGTAAACAAAAGATAAAAGGATTAACCCGAGATTAAG
* * * *
2116319 CCGACAGGTAAATAAAATATAAA
1 CTGACAAGTAAACAAAAGATAAA
2116342 GAAGTTGACC
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
42 33 0.39
43 52 0.61
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (43 bp):
CTGACAAGTAAACAAAAGATAAAAGGATTAACCCGAGATTAAG
Found at i:2116273 original size:85 final size:85
Alignment explanation
Indices: 2116159--2117588 Score: 1190
Period size: 85 Copynumber: 17.2 Consensus size: 85
2116149 CCGATATGTC
* * * * *
2116159 AACAAAGGATAAAAAAATTGATCGGGATTGAACTGACAAGTCAACAAAAGATAAAAGGATTTACC
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
**
2116224 CGAGACTAAGTTGACAGGTA
66 CGAGACTAAGCCGACAGGTA
* * *
2116244 AACAAAAGATAAA-ATAGTTGACCGAGATTGAACTGACAAGTTAACAAAGGATAAAAGGATTAAC
1 AACAAAGGATAAAGA-AGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTAC
*
2116308 CCGAGATTAAGCCGACAGGTA
65 CCGAGACTAAGCCGACAGGTA
* ** * * * *
2116329 AATAAAATATAAAGAAGTTGACCAAGGTTGAACTAAGAAGTCAACAAAGGAT--AA--A---A--
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
2116385 -G-GA-TAAGCCGACAGGTA
66 CGAGACTAAGCCGACAGGTA
* * *
2116402 AACAAAGGATAAAGAAGTTGACC-AGGGTTGAATTGAAAAGTCAACAAAGGATAAAAGGA--TA-
1 AACAAAGGATAAAGAAGTTGACCGA-GATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTAC
* *
2116463 ---AG-CCAA---TA-A-GTA
65 CCGAGACTAAGCCGACAGGTA
* * * *
2116475 AACAAAGGACAAAGAAATTGACCGGGATAGAACTGACAAGTCAACAAAGGATAAAAGGATTTA-C
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
*
2116539 CGAGACTAAGCTGACATGG-A
66 CGAGACTAAGCCGACA-GGTA
* ** * * *
2116559 AAC-AA--ATAAAAAAGTTGAATGAGATTGAACTGACAAGTCAACAAAAGATAAAAAGATTTACT
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
* * *
2116621 CGGGACTGAGCCGATAGGTA
66 CGAGACTAAGCCGACAGGTA
* * * * * *
2116641 AACAAAGGATAAAAAAGTTAAACGGGATTGAACCGACAAGTTAACAAAGGATAAAAGGATTTACC
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
* * * *
2116706 CGAGACTGAGCTGATAGATA
66 CGAGACTAAGCCGACAGGTA
* * ** * *
2116726 AACAAAGGATAAAGAAATTAACTAAGATTGAACCGATAAGTCAACAAAGGATAAAAGGATTTACC
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
* * * * *
2116791 TGGGACTGAGCCAATAGGTA
66 CGAGACTAAGCCGACAGGTA
* * * *
2116811 AACAAAGGATAAAGAAATTGACTGGGATTGAACTGACAAGTCAACAAAGGATAAAAAGATTTACC
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
* * *
2116876 CAAGACTAAGCCAATAGGTA
66 CGAGACTAAGCCGACAGGTA
* * * * ** *
2116896 AACAAAGGATAAAGAAGTTGGCCAAGATTGAACCGGCAAGTCAACAAAGGATAAAAACATTTACT
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
* * * *
2116961 CAAGATTAAGCTGATAGGTA
66 CGAGACTAAGCCGACAGGTA
* * * * *
2116981 AACAAAGGATAAA-AATGTTTACC-AGAGTTCAACTGAGAAGTCAACAATGGATAAAAAGATTTA
1 AACAAAGGATAAAGAA-GTTGACCGAGA-TTGAACTGACAAGTCAACAAAGGATAAAAGGATTTA
* * * * *
2117044 CTCAAGACTGAGTCGACAAGTA
64 CCCGAGACTAAGCCGACAGGTA
* * * * * * * *
2117066 AACAAAGGATAAA-AAATTGATCGGGATAGAACTAATAAGTCAACAAAAGGATAAAAAGATTTAT
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAAC-AAAGGATAAAAGGATTTAC
* * *
2117130 CC-AGGACTGAGCTGACCGGTA
65 CCGA-GACTAAGCCGACAGGTA
* * * *
2117151 AATAAAGGATAAAGAAGTTGAACGA-AGTTAAACCGACAAGTCAACAAAGGATAAAAGGATTTAC
1 AACAAAGGATAAAGAAGTTGACCGAGA-TTGAACTGACAAGTCAACAAAGGATAAAAGGATTTAC
* * * *
2117215 TCGAGACTTAGTCGACAGTTA
65 CCGAGACTAAGCCGACAGGTA
* * *
2117236 AACAAAGGATAAAGAAGTTGAACGGGATTGAACTGACAAGTTAACAAAGGATAAAAGGATTTACC
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
* * *
2117301 CGAGATTGAGCTGACAGGTA
66 CGAGACTAAGCCGACAGGTA
* * * ** *
2117321 AATAAAGGATAAAGAAATTGA-CAAGGATTGAACCAACAAGTCAACAAAGGATAAAAAGATTTAC
1 AACAAAGGATAAAGAAGTTGACCGA-GATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTAC
** * * *
2117385 ATGGGACTAAGCCAACAAGTA
65 CCGAGACTAAGCCGACAGGTA
* * * * * ** * **
2117406 AATAAAAGATAAAGAAATTGATCGGGATTGAACCAACATGTCAACAAAGGATAAAATAATTTACC
1 AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
* * * * *
2117471 TGGGATTAAGCCAATAGGTA
66 CGAGACTAAGCCGACAGGTA
* * * *
2117491 AACAAAGGATAAAGAAGTTGACC-AGGATTGAACCGATAAGTCAACAGAGGATAAAAAGATTTAC
1 AACAAAGGATAAAGAAGTTGACCGA-GATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTAC
* * * *
2117555 TCTAGACTAAGTCGATAGGTA
65 CCGAGACTAAGCCGACAGGTA
*
2117576 AATAAAGGATAAA
1 AACAAAGGATAAA
2117589 AATGTTAACT
Statistics
Matches: 1109, Mismatches: 196, Indels: 80
0.80 0.14 0.06
Matches are distributed among these distances:
72 1 0.00
73 112 0.10
74 3 0.00
75 6 0.01
77 1 0.00
78 7 0.01
79 3 0.00
81 49 0.04
82 17 0.02
83 7 0.01
84 30 0.03
85 848 0.76
86 25 0.02
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (85 bp):
AACAAAGGATAAAGAAGTTGACCGAGATTGAACTGACAAGTCAACAAAGGATAAAAGGATTTACC
CGAGACTAAGCCGACAGGTA
Found at i:2116392 original size:73 final size:72
Alignment explanation
Indices: 2116315--2116534 Score: 289
Period size: 73 Copynumber: 3.0 Consensus size: 72
2116305 AACCCGAGAT
* ** *
2116315 TAAGCCGACAGGTAAATAAAATATAAAGAAGTTGACCAAGGTTGAACTAAGAAGTCAACAAAGGA
1 TAAGCCGACAGGTAAACAAAGGATAAAGAAGTTGACCAGGGTTGAACTAA-AAGTCAACAAAGGA
2116380 TAAAAGGA
65 TAAAAGGA
*
2116388 TAAGCCGACAGGTAAACAAAGGATAAAGAAGTTGACCAGGGTTGAATTGAAAAGTCAACAAAGGA
1 TAAGCCGACAGGTAAACAAAGGATAAAGAAGTTGACCAGGGTTGAACT-AAAAGTCAACAAAGGA
2116453 TAAAAGGA
65 TAAAAGGA
* * * * * * *
2116461 TAAGCCAATAAGTAAACAAAGGACAAAGAAATTGACC-GGGATAGAACTGACAAGTCAACAAAGG
1 TAAGCCGACAGGTAAACAAAGGATAAAGAAGTTGACCAGGG-TTGAACT-AAAAGTCAACAAAGG
2116525 ATAAAAGGA
64 ATAAAAGGA
2116534 T
1 T
2116535 TTACCGAGAC
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
72 3 0.02
73 127 0.96
74 2 0.02
ACGTcount: A:0.50, C:0.12, G:0.23, T:0.15
Consensus pattern (72 bp):
TAAGCCGACAGGTAAACAAAGGATAAAGAAGTTGACCAGGGTTGAACTAAAAGTCAACAAAGGAT
AAAAGGA
Found at i:2117694 original size:41 final size:40
Alignment explanation
Indices: 2117643--2117777 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 40
2117633 TGGCCAAGGT
* *
2117643 AAAATCGATAAAGCCAATGTGTTAGAAGGGTTAACTAGGGA
1 AAAATCGATAAAGCCAATG-ATTAGAAGGGTTGACTAGGGA
* * * * *
2117684 AAAATTGATAAAGTCAACTAATTAGAA-GGTTGGCTAGGGCC
1 AAAATCGATAAAGCCAA-TGATTAGAAGGGTTGACTAGGG-A
2117725 AAAAT-GATAAAGCCAATAGATTAGAAGGGTTGACTAGGGA
1 AAAATCGATAAAGCCAAT-GATTAGAAGGGTTGACTAGGGA
2117765 AAAATCGATAAAG
1 AAAATCGATAAAG
2117778 TTAATGAGAA
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.01
40 32 0.41
41 44 0.56
42 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.21
Consensus pattern (40 bp):
AAAATCGATAAAGCCAATGATTAGAAGGGTTGACTAGGGA
Found at i:2117707 original size:81 final size:81
Alignment explanation
Indices: 2117592--2117778 Score: 211
Period size: 81 Copynumber: 2.3 Consensus size: 81
2117582 GGATAAAAAT
* * * *
2117592 GTTAACT-GGGAATAAACTGA-CAAGTTAACCAATTAAAAGGGTGGCCAAGG-TAAAATCGATAA
1 GTTAACTAGGGAA-AAATTGATAAAGTCAACCAATTAAAAGGGTGGCCAAGGCCAAAAT-GATAA
*
2117654 AGCCAAT-GTGTTAGAAGG
64 AGCCAATAG-ATTAGAAGG
* * * * *
2117672 GTTAACTAGGGAAAAATTGATAAAGTCAACTAATTAGAAGGTTGGCTAGGGCCAAAATGATAAAG
1 GTTAACTAGGGAAAAATTGATAAAGTCAACCAATTAAAAGGGTGGCCAAGGCCAAAATGATAAAG
2117737 CCAATAGATTAGAAGG
66 CCAATAGATTAGAAGG
* *
2117753 GTTGACTAGGGAAAAATCGATAAAGT
1 GTTAACTAGGGAAAAATTGATAAAGT
2117779 TAATGAGAAT
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
80 13 0.14
81 72 0.79
82 6 0.07
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (81 bp):
GTTAACTAGGGAAAAATTGATAAAGTCAACCAATTAAAAGGGTGGCCAAGGCCAAAATGATAAAG
CCAATAGATTAGAAGG
Found at i:2117733 original size:40 final size:40
Alignment explanation
Indices: 2117664--2117778 Score: 144
Period size: 40 Copynumber: 2.8 Consensus size: 40
2117654 AGCCAATGTG
*
2117664 TTAGAAGGGTTAACTAGGGAAAAATTGATAAAGTCAACTA-A
1 TTAGAAGGGTTGACTAGGGAAAAA-TGATAAAGTCAA-TAGA
* * *
2117705 TTAGAA-GGTTGGCTAGGGCCAAAATGATAAAGCCAATAGA
1 TTAGAAGGGTTGACTAGGG-AAAAATGATAAAGTCAATAGA
2117745 TTAGAAGGGTTGACTAGGGAAAAATCGATAAAGT
1 TTAGAAGGGTTGACTAGGGAAAAAT-GATAAAGT
2117779 TAATGAGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
39 2 0.03
40 33 0.52
41 28 0.44
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (40 bp):
TTAGAAGGGTTGACTAGGGAAAAATGATAAAGTCAATAGA
Found at i:2117836 original size:46 final size:46
Alignment explanation
Indices: 2117783--2118030 Score: 209
Period size: 46 Copynumber: 5.4 Consensus size: 46
2117773 TAAAGTTAAT
* *
2117783 GAGAATGAAAAAGGTTTGACCAGGGTGGTAA-TCGATATAGTCAAAC
1 GAGAATGAAAAAGGTTTGACTAGGGTGGTAACT-GATACAGTCAAAC
* * * * * * *
2117829 GAGAATGAAAAGGGTTTGACTAGAGTGATGACTGACACAATCAAAT
1 GAGAATGAAAAAGGTTTGACTAGGGTGGTAACTGATACAGTCAAAC
* * * *
2117875 GA-AGAT-AAAAAGGGTTTCACCAGGGTGTTAACTAATACAGTCAAAC
1 GAGA-ATGAAAAA-GGTTTGACTAGGGTGGTAACTGATACAGTCAAAC
* * * * *
2117921 -ACAAAAGAAAAGGGTTTGATTAGGGTGGTAACCGATACAGTCAAAC
1 GA-GAATGAAAAAGGTTTGACTAGGGTGGTAACTGATACAGTCAAAC
* * * * *
2117967 AAGAACGAAAATGGTTTAACTAGGGTGGTAACTGATACAGTCAAAT
1 GAGAATGAAAAAGGTTTGACTAGGGTGGTAACTGATACAGTCAAAC
2118013 GA-AGATGAAAAAGGTTTG
1 GAGA-ATGAAAAAGGTTTG
2118031 TTTGGTAAAG
Statistics
Matches: 156, Mismatches: 38, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
45 7 0.04
46 142 0.91
47 7 0.04
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (46 bp):
GAGAATGAAAAAGGTTTGACTAGGGTGGTAACTGATACAGTCAAAC
Found at i:2119006 original size:20 final size:21
Alignment explanation
Indices: 2118981--2119026 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
2118971 TTAAATGCAT
2118981 GTATCGAT-ATATTATGAAAA
1 GTATCGATAATATTATGAAAA
2119001 GTATCGATACATATTATGAAAA
1 GTATCGATA-ATATTATGAAAA
2119023 GTAT
1 GTAT
2119027 AGGGTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.33
22 16 0.67
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
GTATCGATAATATTATGAAAA
Found at i:2120551 original size:12 final size:12
Alignment explanation
Indices: 2120536--2120568 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2120526 ACCATCAAAA
2120536 ATGATGAAGATG
1 ATGATGAAGATG
2120548 ATGATGATA-ATG
1 ATGATGA-AGATG
2120560 ATGATGAAG
1 ATGATGAAG
2120569 TTGACTCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
ATGATGAAGATG
Found at i:2126125 original size:64 final size:64
Alignment explanation
Indices: 2126023--2126164 Score: 230
Period size: 64 Copynumber: 2.2 Consensus size: 64
2126013 CCGAAAAAGG
* *
2126023 TATGATTGGGAATGTGTAGGCGGTTCCCCCTTTGTGGTCATATGACATCCCTAAAAGAAAGGGA
1 TATGATTGGGAATGTGCAGGCGGTTCCCCCTTTATGGTCATATGACATCCCTAAAAGAAAGGGA
* * * *
2126087 TATGATTAGGAATGTGCGGGCTGTTCCCCCTTTATGGTCATATGACGTCCCTAAAAGAAAGGGA
1 TATGATTGGGAATGTGCAGGCGGTTCCCCCTTTATGGTCATATGACATCCCTAAAAGAAAGGGA
2126151 TATGATTGGGAATG
1 TATGATTGGGAATG
2126165 AGTGGTCAGG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 71 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (64 bp):
TATGATTGGGAATGTGCAGGCGGTTCCCCCTTTATGGTCATATGACATCCCTAAAAGAAAGGGA
Done.