Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008397.1 Hibiscus syriacus cultivar Beakdansim tig00111166_pilon, whole genome shotgun sequence
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: 2560905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1615743 original size:3 final size:3
Alignment explanation
Indices: 1615735--1615769 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1615725 GGATACTATC
1615735 ATT ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1615770 ATAATGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1616466 original size:20 final size:20
Alignment explanation
Indices: 1616441--1616486 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1616431 CTATCATACT
1616441 GCCACCACTAATATTTGCTG
1 GCCACCACTAATATTTGCTG
1616461 GCCACCACTAATATTTGCTG
1 GCCACCACTAATATTTGCTG
1616481 GCCACC
1 GCCACC
1616487 CATGTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (20 bp):
GCCACCACTAATATTTGCTG
Found at i:1618521 original size:14 final size:13
Alignment explanation
Indices: 1618490--1618555 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
1618480 GTCATATAAT
*
1618490 AAAAATAAAATTT
1 AAAAATAAAATTA
*
1618503 GAAAATAAAATTAA
1 AAAAATAAAATT-A
**
1618517 AAAAATAAAATCC
1 AAAAATAAAATTA
* *
1618530 ATAAGTAAATATTA
1 AAAAATAAA-ATTA
*
1618544 GAAAATAAAATT
1 AAAAATAAAATT
1618556 CATAAAGTCA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
13 21 0.54
14 18 0.46
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (13 bp):
AAAAATAAAATTA
Found at i:1618538 original size:27 final size:27
Alignment explanation
Indices: 1618508--1618560 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1618498 AATTTGAAAA
1618508 TAAA-ATTAAAAAAATAAAATCCATAAG
1 TAAATATT-AAAAAATAAAATCCATAAG
* *
1618535 TAAATATTAGAAAATAAAATTCATAA
1 TAAATATTAAAAAATAAAATCCATAA
1618561 AGTCAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
TAAATATTAAAAAATAAAATCCATAAG
Found at i:1619099 original size:32 final size:32
Alignment explanation
Indices: 1619050--1619117 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
1619040 TTCATTAGTC
* *
1619050 AGTTAAAATGCTCTATCATACTGGGTCTGTAT
1 AGTTAAAATGCTCTATCACACTGGATCTGTAT
* *
1619082 AGTTAAATTGCTTTATCACACTGGATCTGTAT
1 AGTTAAAATGCTCTATCACACTGGATCTGTAT
1619114 AGTT
1 AGTT
1619118 TATCACACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (32 bp):
AGTTAAAATGCTCTATCACACTGGATCTGTAT
Found at i:1624828 original size:35 final size:35
Alignment explanation
Indices: 1624782--1624848 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1624772 ACTCCTCATG
1624782 TTGGAGTTGAGAATCGAAA-TTGAAAGCTTATACAC
1 TTGGAGTTGAGAAT-GAAACTTGAAAGCTTATACAC
* *
1624817 TTGGAGTTGAGAATTAAACTTGCAAGCTTATA
1 TTGGAGTTGAGAATGAAACTTGAAAGCTTATA
1624849 AATTAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 3 0.10
35 26 0.90
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (35 bp):
TTGGAGTTGAGAATGAAACTTGAAAGCTTATACAC
Found at i:1629715 original size:60 final size:59
Alignment explanation
Indices: 1629605--1629716 Score: 134
Period size: 60 Copynumber: 1.9 Consensus size: 59
1629595 TATAGGGTGT
** * ** *
1629605 TACTTTGTTGAGTCCCCAGCTATTGAAAGTTATAAAATGGTCCCTCGACTATAAAGTGA
1 TACTTTGTTGAGTCCCCAGCTATCAAAAGTTACAAAATAATCACTCGACTATAAAGTGA
** *
1629664 TACTTTGTTGAGTCCCTTGACTATCAAAAGTTACAAAATAATCACTTGACTAT
1 TACTTTGTTGAGTCCCCAG-CTATCAAAAGTTACAAAATAATCACTCGACTAT
1629717 TTATATATTC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 17 0.40
60 26 0.60
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (59 bp):
TACTTTGTTGAGTCCCCAGCTATCAAAAGTTACAAAATAATCACTCGACTATAAAGTGA
Found at i:1630148 original size:60 final size:60
Alignment explanation
Indices: 1630040--1630157 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 60
1630030 GTTGGGTGAC
*** * ***
1630040 CATTTCATAACTTTTAATAGTCTGGGGACTCAACAAAACAATGTCCTATAATCAAAGAAT
1 CATTTCATAACTTTTAATAGTAAAGAGACTCAACAAAACAACACCCTATAATCAAAGAAT
* * *
1630100 CATTTTATAACTTTTAATAGTAAAGAGACTCAACAAAGCAACACCCTATAATCGAAGA
1 CATTTCATAACTTTTAATAGTAAAGAGACTCAACAAAACAACACCCTATAATCAAAGA
1630158 CCATTTATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (60 bp):
CATTTCATAACTTTTAATAGTAAAGAGACTCAACAAAACAACACCCTATAATCAAAGAAT
Found at i:1636689 original size:26 final size:26
Alignment explanation
Indices: 1636660--1636709 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1636650 TGATGACAAG
1636660 TCAAATTTAACTTCAA-ATTCAACTTA
1 TCAAATTT-ACTTCAAGATTCAACTTA
* *
1636686 TCAACTTTATTTCAAGATTCAACT
1 TCAAATTTACTTCAAGATTCAACT
1636710 CAAGAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (26 bp):
TCAAATTTACTTCAAGATTCAACTTA
Found at i:1649556 original size:17 final size:18
Alignment explanation
Indices: 1649534--1649568 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1649524 TCACCCTAAT
1649534 AAAAAATAT-AATTATTA
1 AAAAAATATAAATTATTA
*
1649551 AAAAAATCTAAATTATTA
1 AAAAAATATAAATTATTA
1649569 CTTAATCTTT
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:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAAATATAAATTATTA
Found at i:1650102 original size:17 final size:17
Alignment explanation
Indices: 1650071--1650109 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1650061 AGTTTATTGG
1650071 TTTAAACTTAAAAAT-A
1 TTTAAACTTAAAAATAA
*
1650087 TTTAAATTTAAAAAATAA
1 TTTAAACTT-AAAAATAA
1650105 TTTAA
1 TTTAA
1650110 TCAATGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 6 0.30
18 6 0.30
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAACTTAAAAATAA
Found at i:1651693 original size:18 final size:18
Alignment explanation
Indices: 1651670--1651707 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1651660 TTTAATACTG
* *
1651670 TTGTTTTCATTGACTTTA
1 TTGTTTTAATTGAATTTA
1651688 TTGTTTTAATTGAATTTA
1 TTGTTTTAATTGAATTTA
1651706 TT
1 TT
1651708 TCGATTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (18 bp):
TTGTTTTAATTGAATTTA
Found at i:1657263 original size:23 final size:23
Alignment explanation
Indices: 1657216--1657263 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1657206 AATAACATAT
**
1657216 TAGGTAGCACTTATATAATGTAA
1 TAGGTAGCACTTATATAATAAAA
**
1657239 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
1657262 TA
1 TA
1657264 AGTATTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:1657792 original size:200 final size:198
Alignment explanation
Indices: 1657358--1657858 Score: 715
Period size: 200 Copynumber: 2.5 Consensus size: 198
1657348 ATTTTCTAAC
* * *
1657358 TAAACCGATATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGATTTCG
1 TAAACCGATATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCG
* *
1657423 ATGTTTTTGAGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACA
66 ATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACA
* *
1657486 TTCATTTGGAAAAAAATATCAACACAAACTTAAAAAGTGTCGATACATTATATAGACATATTTTC
130 TTCATTTGGAAAAAAATATCAACACAAACTTAAAAAGTATCGATACATTATATAGACATATTCTC
1657551 TCAT
195 TCAT
* * * * * * *
1657555 AAAACCGGTATATTTCTATC-AGGTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTC
1 TAAACCGATATATTTATACCGA-TTACATTGTAAATTTACCTATTACATTATAATTATCGATTTC
* *
1657619 GATGTTTTTGGGATCGATACTTTTAATAAATATATCGACACTTTATGCGTGCACCTCGTTTGACA
65 GATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACA
** * * * *
1657684 TTCATTCTGGACAAAATGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTGATC-TATT
130 TTCATT-TGGA-AAAAAATATCAACACAAACTTAAAAAGTATCGATACATTATATAGA-CATATT
1657748 CTCTCAT
192 CTCTCAT
1657755 TAAACCGATATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCG
1 TAAACCGATATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCG
*
1657820 AT-TTTTTGGGATCAATACTTTTAATAAATGTATCGACAC
66 ATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACAC
1657859 AAATTCCACA
Statistics
Matches: 266, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
196 3 0.01
197 72 0.27
198 43 0.16
199 39 0.15
200 107 0.40
201 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (198 bp):
TAAACCGATATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCG
ATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGACAT
TCATTTGGAAAAAAATATCAACACAAACTTAAAAAGTATCGATACATTATATAGACATATTCTCT
CAT
Found at i:1657966 original size:147 final size:148
Alignment explanation
Indices: 1657696--1658006 Score: 459
Period size: 147 Copynumber: 2.1 Consensus size: 148
1657686 CATTCTGGAC
* * * *
1657696 AAAATGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTGATCTATTCTCTCATTAAACC
1 AAAATGTATCGACACAAATTCAAAAAGTATCGATACATTATGTTGACCTATTATCTAATTAAACC
1657761 GATATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGAT-TTT
66 GATATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTT
1657825 TTGGGATCAATACTTTTA-
131 TTGGG-TCAATACTTTTAG
* * * *
1657843 ATAAATGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCTGTTATCTAATT-AAC
1 A-AAATGTATCGACACAAATTCAAAAAGTATCGATACATTATGTTGACCTATTATCTAATTAAAC
* * * *
1657907 C-AGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATGT
65 CGA-TATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGT
1657971 TTTTGGGTCAATACTTTTAG
129 TTTTGGGTCAATACTTTTAG
1657991 AAAATGTATCGACACA
1 AAAATGTATCGACACA
1658007 TATTTAGGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
146 1 0.01
147 87 0.59
148 60 0.41
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (148 bp):
AAAATGTATCGACACAAATTCAAAAAGTATCGATACATTATGTTGACCTATTATCTAATTAAACC
GATATATTTATACCGATTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTT
TTGGGTCAATACTTTTAG
Found at i:1658454 original size:15 final size:14
Alignment explanation
Indices: 1658430--1658471 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
1658420 GAAAGAAATG
1658430 AAAT-AAAATAAAA
1 AAATAAAAATAAAA
1658443 AAATACAAAATACAAA
1 AAATA-AAAATA-AAA
1658459 AAATAAAAATAAA
1 AAATAAAAATAAA
1658472 GTGAAGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 2 0.08
15 12 0.46
16 8 0.31
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATAAAAATAAAA
Found at i:1658492 original size:16 final size:17
Alignment explanation
Indices: 1658461--1658493 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1658451 AATACAAAAA
1658461 ATAAAAATAAAGTGAAG
1 ATAAAAATAAAGTGAAG
1658478 ATAAAAATAAA-TGAAG
1 ATAAAAATAAAGTGAAG
1658494 CAAATAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (17 bp):
ATAAAAATAAAGTGAAG
Found at i:1658577 original size:18 final size:18
Alignment explanation
Indices: 1658550--1658593 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1658540 CATAACTAAT
* *
1658550 AAATAAAAATAAAGAAGA
1 AAATACAAATAAAGAAAA
**
1658568 AAATACAAATAATTAAAA
1 AAATACAAATAAAGAAAA
1658586 AAATACAA
1 AAATACAA
1658594 GGGAGATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (18 bp):
AAATACAAATAAAGAAAA
Found at i:1658633 original size:8 final size:8
Alignment explanation
Indices: 1658611--1658711 Score: 58
Period size: 9 Copynumber: 11.6 Consensus size: 8
1658601 AAAAAGATAA
*
1658611 AAAAAAAG
1 AAAAAAAT
1658619 AATAAAAAT
1 AA-AAAAAT
1658628 AAAAAAAT
1 AAAAAAAT
* *
1658636 ACATAAATT
1 A-AAAAAAT
*
1658645 AATAAAAT
1 AAAAAAAT
* *
1658653 ACATAAAT
1 AAAAAAAT
1658661 AAGTAAAAAT
1 AA--AAAAAT
*
1658671 TAAAAAAT
1 AAAAAAAT
1658679 AATAAAAAT
1 AA-AAAAAT
1658688 AATAAAATAT
1 AA-AAAA-AT
*
1658698 AAATAAAT
1 AAAAAAAT
1658706 AGAAAA
1 A-AAAA
1658712 CAAAATATAA
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
8 31 0.42
9 32 0.44
10 10 0.14
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1658684 original size:17 final size:17
Alignment explanation
Indices: 1658613--1658831 Score: 82
Period size: 17 Copynumber: 12.8 Consensus size: 17
1658603 AAAGATAAAA
*
1658613 AAAAAGAATAAAAATAA-
1 AAAAATAAT-AAAATAAT
*
1658630 AAAAATACATAAATTAAT
1 AAAAATA-ATAAAATAAT
1658648 -AAAATACAT-AAATAAGT
1 AAAAATA-ATAAAATAA-T
1658665 AAAAATTAA-AAAATAAT
1 AAAAA-TAATAAAATAAT
1658682 AAAAATAATAAAAT-AT
1 AAAAATAATAAAATAAT
* *
1658698 AAATA-AATAGAA-AA-
1 AAAAATAATAAAATAAT
* **
1658712 CAAAAT-ATAAGGTAAT
1 AAAAATAATAAAATAAT
** * *
1658728 ATCGAA-AACAAAATAAG
1 A-AAAATAATAAAATAAT
*
1658745 AAATATAATTAAATATATAT
1 AAAAATAA-TAAA-ATA-AT
* *
1658765 AAAAACAATAATAGTAAT
1 AAAAATAATAA-AATAAT
*** *
1658783 AGTTATAATAAAA-AAA
1 AAAAATAATAAAATAAT
1658799 AAGAAATAAATAAAATAAT
1 AA-AAAT-AATAAAATAAT
1658818 AAAAAATAATAAAA
1 -AAAAATAATAAAA
1658832 ATATGAAATG
Statistics
Matches: 145, Mismatches: 35, Indels: 43
0.65 0.16 0.19
Matches are distributed among these distances:
14 6 0.04
15 9 0.06
16 18 0.12
17 47 0.32
18 39 0.27
19 16 0.11
20 10 0.07
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (17 bp):
AAAAATAATAAAATAAT
Found at i:1658691 original size:43 final size:41
Alignment explanation
Indices: 1658621--1658703 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 41
1658611 AAAAAAAGAA
*
1658621 TAAAAATAAAAAAATACATAAATTAATAAAATACATAAATAAG
1 TAAAAATAAAAAAATACATAAAATAATAAAAT--ATAAATAAG
*
1658664 TAAAAATTAAAAAATA-ATAAAAATAATAAAATATAAATAA
1 TAAAAATAAAAAAATACAT-AAAATAATAAAATATAAATAA
1658704 ATAGAAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 8 0.22
42 2 0.05
43 27 0.73
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.24
Consensus pattern (41 bp):
TAAAAATAAAAAAATACATAAAATAATAAAATATAAATAAG
Found at i:1658719 original size:22 final size:24
Alignment explanation
Indices: 1658691--1658742 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1658681 TAAAAATAAT
1658691 AAAATATAA-ATAA-ATAGAAAAC
1 AAAATATAAGATAATATAGAAAAC
* *
1658713 AAAATATAAGGTAATATCGAAAAC
1 AAAATATAAGATAATATAGAAAAC
1658737 AAAATA
1 AAAATA
1658743 AGAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
23 3 0.12
24 14 0.54
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (24 bp):
AAAATATAAGATAATATAGAAAAC
Found at i:1658810 original size:18 final size:17
Alignment explanation
Indices: 1658787--1658832 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1658777 AGTAATAGTT
1658787 ATAATAAAAAA-AAAGAA
1 ATAATAAAAAATAAA-AA
1658804 ATAAATAAAATAATAAAAA
1 AT-AATAAAA-AATAAAAA
1658823 ATAATAAAAA
1 ATAATAAAAA
1658833 TATGAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 14 0.54
19 6 0.23
20 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
ATAATAAAAAATAAAAA
Found at i:1660691 original size:37 final size:34
Alignment explanation
Indices: 1660647--1660769 Score: 194
Period size: 33 Copynumber: 3.6 Consensus size: 34
1660637 AACTCGAAGG
*
1660647 TTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGG-TTT
*
1660682 TTGTGTGTGTTTCAAGAGAAACAATCTCAAAGG-TT
1 TT-T-TGTGTTTCAAGAGAAACAATTTCAAAGGTTT
1660717 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
1660751 TTTTGTGTTTCAAGAGAAA
1 TTTTGTGTTTCAAGAGAAA
1660770 TTGTCTCCAG
Statistics
Matches: 82, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
33 27 0.33
34 22 0.27
35 6 0.07
36 1 0.01
37 26 0.32
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.41
Consensus pattern (34 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
Found at i:1660796 original size:70 final size:70
Alignment explanation
Indices: 1660652--1660862 Score: 199
Period size: 70 Copynumber: 3.1 Consensus size: 70
1660642 GAAGGTTTTG
* ** *
1660652 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGTGTTTCAAGAGAAACAATCT-CA--AAG
1 TGTTTCAAGAGAAACAATTTCAAAGG-TTTTT-T-TGTGTTTCAAGAGAAACTGTCTCCAGGGAG
***
1660714 G-TTTTTT
63 GCAAATTT
*
1660721 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAATTGTCTCCAGGGAGGC
1 -TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGGC
1660786 AAATTT
65 AAATTT
* *
1660792 TGTTTCAAGAGAAAC-ATATTCAAAGG----TTGGTGTTTCAAGAGAAACTGTCTCAAGGG-GGA
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGG-
*
1660851 CAAAATT
64 CAAATTT
1660858 TGTTT
1 TGTTT
1660863 AATGTAAAAC
Statistics
Matches: 123, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
65 2 0.02
66 38 0.31
67 19 0.15
68 3 0.02
69 7 0.06
70 51 0.41
71 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (70 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGGCA
AATTT
Found at i:1660860 original size:66 final size:65
Alignment explanation
Indices: 1660722--1660921 Score: 192
Period size: 66 Copynumber: 3.0 Consensus size: 65
1660712 AGGTTTTTTG
* *
1660722 TGTTTCAAGAGAAACA-ATTTCAAAGGTTTTTTTGTGTTTCAAGAGAAATTGTCTCCAGGGAGG-
1 TGTTTCAAGAGAAACATA-TTCAAAGG-----TTGTGTTTCAAGAGAAACTGTCTCAAGGG-GGA
*
1660785 CAAATTT
59 CAAAATT
1660792 TGTTTCAAGAGAAACATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGGGGGACAAAAT
1 TGTTTCAAGAGAAACATATTCAAAGGTT-GTGTTTCAAGAGAAACTGTCTCAAGGGGGACAAAAT
1660857 T
65 T
* * * * * *
1660858 TGTTT-AATGTA-AAACATATTCAAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAA
1 TGTTTCAA-G-AGAAACATATTC-AAAGGTTGTGTTTCAAGAGAAACTGTCTCAAGGGGGACAAA
1660921 A
63 A
1660922 CTTTATTCTA
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
65 6 0.05
66 77 0.67
67 7 0.06
70 24 0.21
71 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (65 bp):
TGTTTCAAGAGAAACATATTCAAAGGTTGTGTTTCAAGAGAAACTGTCTCAAGGGGGACAAAATT
Found at i:1661077 original size:36 final size:36
Alignment explanation
Indices: 1661020--1661105 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
1661010 TCAATGTTTA
* * * *
1661020 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1661056 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
** *
1661092 CATTTCAGGGGAAA
1 TGTTTCAAGGGAAA
1661106 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:1661131 original size:101 final size:101
Alignment explanation
Indices: 1660992--1661292 Score: 505
Period size: 101 Copynumber: 3.0 Consensus size: 101
1660982 AAAGATTTTG
*
1660992 TTTCAAGAGAAACTGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
*
1661057 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGATAAAATTCA
* * ** *
1661094 TTTCAGGGGAAATGTTTTCAATGTTTATATTTCAAGAGAAACGGTCACAAGGGAGACAAAATTTG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTG
1661159 TTTCAAGGGAAAC-AGTCTCAAGAGAGATAAAATTCA
66 TTTCAAGGGAAACTA-TCTCAAGAGAGATAAAATTCA
*
1661195 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAATTTTG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTG
1661260 TTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
66 TTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1661293 CTTGTTTTAA
Statistics
Matches: 184, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
100 1 0.01
101 172 0.93
102 11 0.06
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTG
TTTCAAGGGAAACTATCTCAAGAGAGATAAAATTCA
Found at i:1661171 original size:36 final size:36
Alignment explanation
Indices: 1661122--1661206 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
1661112 CAATGTTTAT
* * * *
1661122 ATTTCAAGAGAAACGGTCACAAGGGAGACAAAATTT
1 ATTTCAAGGGAAACAGTCACAAGAGAGACAAAATTC
* * *
1661158 GTTTCAAGGGAAACAGTCTCAAGAGAGATAAAATTC
1 ATTTCAAGGGAAACAGTCACAAGAGAGACAAAATTC
1661194 ATTTCAAGGGAAA
1 ATTTCAAGGGAAA
1661207 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (36 bp):
ATTTCAAGGGAAACAGTCACAAGAGAGACAAAATTC
Found at i:1661327 original size:37 final size:36
Alignment explanation
Indices: 1661289--1661419 Score: 102
Period size: 36 Copynumber: 3.6 Consensus size: 36
1661279 AAGAGAGATA
*
1661289 AAATCTTGTTTTAAGAAAAACAATCTTGAGGGAAAT
1 AAATCTTCTTTTAAGAAAAACAATCTTGAGGGAAAT
** * ** ** * * *
1661325 AAATCTTCTTTCGAGTAAAACGGTCTCAAGTGAGAC
1 AAATCTTCTTTTAAGAAAAACAATCTTGAGGGAAAT
* *
1661361 AAAGTC-TGTTTTAAGAAAAAAAAATCTTGAGGGAAAT
1 AAA-TCTTCTTTTAAG-AAAAACAATCTTGAGGGAAAT
* *
1661398 AAATCTTCTTTTGAGTAAAACA
1 AAATCTTCTTTTAAGAAAAACA
1661420 GTCTCAAGTG
Statistics
Matches: 65, Mismatches: 27, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
36 41 0.63
37 24 0.37
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (36 bp):
AAATCTTCTTTTAAGAAAAACAATCTTGAGGGAAAT
Found at i:1661381 original size:73 final size:73
Alignment explanation
Indices: 1661275--1661450 Score: 273
Period size: 73 Copynumber: 2.4 Consensus size: 73
1661265 AGGGAAACTA
* * * *
1661275 TCTCAAGAGAGATAAAATCTTGTTTTAAG-AAAAACAATCTTGAGGGAAATAAATCTTCTTTCGA
1 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAAAAAATCTTGAGGGAAATAAATCTTCTTTCGA
*
1661339 GTAAAACGG
65 GTAAAACAG
*
1661348 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAAAAAATCTTGAGGGAAATAAATCTTCTTTTGAG
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAAAAAATCTTGAGGGAAATAAATCTTCTTTCGAG
1661413 TAAAACAG
66 TAAAACAG
*
1661421 TCTCAAGTGAGACAAGGTCTGTTTTAAGAA
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAA
1661451 TGATAATCTC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
72 9 0.09
73 86 0.91
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (73 bp):
TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAAAAAATCTTGAGGGAAATAAATCTTCTTTCGAG
TAAAACAG
Found at i:1662655 original size:184 final size:185
Alignment explanation
Indices: 1662346--1662714 Score: 731
Period size: 184 Copynumber: 2.0 Consensus size: 185
1662336 TTGGTTAGGG
1662346 CTCGCCCCTCTTTCTTGGTTTGATATTTTAATCGGATGCGACCAAAATGACACAACTAGCATAAT
1 CTCGCCCCTCTTTCTTGGTTTGATATTTTAATCGGATGCGACCAAAATGACACAACTAGCATAAT
1662411 CAATGGCTAGACCTTTTAGAAAACTTCTATTTCAGTTCTCTAAAATCTTTCATTTGTTCAAGTTT
66 CAATGGCTAGACCTTTTAGAAAACTTCTATTTCAGTTCTCTAAAATCTTTCATTTGTTCAAGTTT
1662476 TGTAAGCTCCTCTAACAAAGGTGGTGCAGAAATATCGGTCT-AAAATGAAATTCT
131 TGTAAGCTCCTCTAACAAAGGTGGTGCAGAAATATCGGTCTAAAAATGAAATTCT
1662530 CTCGCCCCTCTTTCTTGGTTTGATATTTTAATCGGATGCGACCAAAATGACACAACTAGCATAAT
1 CTCGCCCCTCTTTCTTGGTTTGATATTTTAATCGGATGCGACCAAAATGACACAACTAGCATAAT
1662595 CAATGGCTAGACCTTTTAGAAAACTTCTATTTCAGTTCTCTAAAATCTTTCATTTGTTCAAGTTT
66 CAATGGCTAGACCTTTTAGAAAACTTCTATTTCAGTTCTCTAAAATCTTTCATTTGTTCAAGTTT
1662660 TGTAAGCTCCTCTAACAAAGGTGGTGCAGAAATATCGGTCTAAAAATGAAATTCT
131 TGTAAGCTCCTCTAACAAAGGTGGTGCAGAAATATCGGTCTAAAAATGAAATTCT
1662715 TGAGTGCTCG
Statistics
Matches: 184, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
184 171 0.93
185 13 0.07
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (185 bp):
CTCGCCCCTCTTTCTTGGTTTGATATTTTAATCGGATGCGACCAAAATGACACAACTAGCATAAT
CAATGGCTAGACCTTTTAGAAAACTTCTATTTCAGTTCTCTAAAATCTTTCATTTGTTCAAGTTT
TGTAAGCTCCTCTAACAAAGGTGGTGCAGAAATATCGGTCTAAAAATGAAATTCT
Found at i:1668551 original size:16 final size:16
Alignment explanation
Indices: 1668526--1668568 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1668516 ATTAATGTGG
* *
1668526 TTTTTAAAATCTCACT
1 TTTTTTAAATCGCACT
*
1668542 TTTTTTAAATCGCATT
1 TTTTTTAAATCGCACT
1668558 TGTTTTTAAAT
1 T-TTTTTAAAT
1668569 TAAAAGGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTTTTAAATCGCACT
Found at i:1668563 original size:17 final size:17
Alignment explanation
Indices: 1668525--1668568 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1668515 AATTAATGTG
*
1668525 GTTTTTAAAATCTCACTT
1 GTTTTT-AAATCGCACTT
*
1668543 -TTTTTAAATCGCATTT
1 GTTTTTAAATCGCACTT
1668559 GTTTTTAAAT
1 GTTTTTAAAT
1668569 TAAAAGGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (17 bp):
GTTTTTAAATCGCACTT
Found at i:1669468 original size:50 final size:45
Alignment explanation
Indices: 1669353--1669441 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 45
1669343 TCGAATAAAT
* *
1669353 GCATGCGAACTAGATATCATGCGGTTAGGTTTATTTTTTGAACAA
1 GCATGCGAAGTAGATATCATGCGGTTAGGTTTATTTTGTGAACAA
*
1669398 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTCGTGAA
1 GCATGCGAAGTAGATATCATGCGGTTAGG-TTTATTTT-GTGAA
1669442 TAACAAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 28 0.70
46 8 0.20
47 4 0.10
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (45 bp):
GCATGCGAAGTAGATATCATGCGGTTAGGTTTATTTTGTGAACAA
Found at i:1679144 original size:30 final size:30
Alignment explanation
Indices: 1679126--1679225 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
1679116 AAATAATAAT
*
1679126 AAAAATGAGAAAAAGAAAAAGAAGAAAAGA
1 AAAAATGAGAAAAAGAAAAAAAAGAAAAGA
* *
1679156 AAAAATGAGAAAAA-ATAAAAATGAAAA-A
1 AAAAATGAGAAAAAGAAAAAAAAGAAAAGA
* *
1679184 AAATAA--AG-AAAAGTAAAAAGAGAAAAATGA
1 AAA-AATGAGAAAAAGAAAAAAAAG-AAAA-GA
*
1679214 AAAAAAGAGAAA
1 AAAAATGAGAAA
1679226 TAAAAGGAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
26 4 0.07
27 7 0.13
28 8 0.15
29 14 0.25
30 18 0.33
31 2 0.04
32 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (30 bp):
AAAAATGAGAAAAAGAAAAAAAAGAAAAGA
Found at i:1679185 original size:15 final size:15
Alignment explanation
Indices: 1679123--1679219 Score: 72
Period size: 16 Copynumber: 6.1 Consensus size: 15
1679113 AAAAAATAAT
*
1679123 AATAAAAATGAGAAA
1 AATAAAAATGAAAAA
*
1679138 AAGAAAAA-GAAGAAA
1 AATAAAAATGAA-AAA
1679153 AGA-AAAAATGAGAAAA
1 A-ATAAAAATGA-AAAA
1679169 AATAAAAATGAAAAAA
1 AATAAAAATG-AAAAA
*
1679185 AATAAAGAAAAGTAAAAA
1 AAT-AA-AAATG-AAAAA
* *
1679203 GAGAAAAATGAAAAA
1 AATAAAAATGAAAAA
1679218 AA
1 AA
1679220 GAGAAATAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.03
15 23 0.35
16 25 0.38
17 6 0.09
18 10 0.15
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
AATAAAAATGAAAAA
Found at i:1679226 original size:15 final size:13
Alignment explanation
Indices: 1679086--1679210 Score: 76
Period size: 14 Copynumber: 8.9 Consensus size: 13
1679076 AAGAAGAAAT
1679086 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
*
1679099 AAATGA-AAAATGAA
1 AAAAGAGAAAA--AA
* *
1679113 AAAAAATAATAATAA
1 AAAAGAGAA-AA-AA
*
1679128 AAATGAGAAAAAGA
1 AAAAGAGAAAAA-A
1679142 AAAAGAAGAAAAGAA
1 AAAAG-AGAAAA-AA
1679157 AAAATGAGAAAAAA
1 AAAA-GAGAAAAAA
1679171 TAAAA-ATGAAAAAA
1 -AAAAGA-GAAAAAA
*
1679185 AATAA-AGAAAAGTA
1 AA-AAGAGAAAA-AA
1679199 AAAAGAGAAAAA
1 AAAAGAGAAAAA
1679211 TGAAAAAAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
12 4 0.04
13 16 0.18
14 34 0.38
15 31 0.35
16 4 0.04
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (13 bp):
AAAAGAGAAAAAA
Found at i:1680681 original size:55 final size:52
Alignment explanation
Indices: 1680391--1680749 Score: 368
Period size: 51 Copynumber: 6.8 Consensus size: 52
1680381 AACAAGTTCG
* * **
1680391 TTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTA
* * **
1680442 TTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTA
*
1680493 TTGAAGATT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTA
1 TTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTA
* *
1680544 TTGAAGA-TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTTTT
1 TTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACG---TTTA
* * * * *
1680598 TTTAAGATTGTTCAAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTA
1 TTGAAGA---TTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTA
* * * *
1680653 CTGAAGATTATTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTA
1 TTGAAG---ATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTA
* *
1680708 CTGAAGATTGTTCGAGTCTTATACTC-CATGAAAGAATAGGGA
1 TTGAAGA---TTCGAGTCTTATACTCTC-TGAAGGAATAGGGA
1680750 ACAAACCCGC
Statistics
Matches: 275, Mismatches: 18, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.00
51 142 0.52
52 1 0.00
54 10 0.04
55 85 0.31
58 36 0.13
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (52 bp):
TTGAAGATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTA
Found at i:1680771 original size:110 final size:110
Alignment explanation
Indices: 1680551--1680755 Score: 259
Period size: 110 Copynumber: 1.8 Consensus size: 110
1680541 TTATTGAAGA
* * * ** *
1680551 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTTTTTTTAAGATTGTTCAAGTC
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACG--TTTTACTGAAGATTGTTCAAGTC
* * * * *
1680616 TTATACTCCCTGAACGAATAGGGAGCAGACACGTTTACTGAAGATTAT
64 TTATACTCCATGAAAGAATAGGGAACAAACACGATTA-TGAAGATTAT
* *
1680664 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACG-TTTACTGAAGATTGTTCGAGTCTT
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTTACTGAAGATTGTTCAAGTCTT
1680728 ATACTCCATGAAAGAATAGGGAACAAAC
66 ATACTCCATGAAAGAATAGGGAACAAAC
1680756 CCGCCATTTG
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
110 44 0.55
113 36 0.45
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (110 bp):
TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTTACTGAAGATTGTTCAAGTCTT
ATACTCCATGAAAGAATAGGGAACAAACACGATTATGAAGATTAT
Found at i:1683505 original size:16 final size:16
Alignment explanation
Indices: 1683480--1683522 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1683470 ATTGATGTGG
* *
1683480 TTTTTAAAATCTCACT
1 TTTTTTAAATCGCACT
*
1683496 TTTTTTAAATCGCATT
1 TTTTTTAAATCGCACT
1683512 TGTTTTTAAAT
1 T-TTTTTAAAT
1683523 TAAAAGGAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTTTTAAATCGCACT
Found at i:1683517 original size:17 final size:17
Alignment explanation
Indices: 1683479--1683522 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1683469 AATTGATGTG
*
1683479 GTTTTTAAAATCTCACTT
1 GTTTTT-AAATCGCACTT
*
1683497 -TTTTTAAATCGCATTT
1 GTTTTTAAATCGCACTT
1683513 GTTTTTAAAT
1 GTTTTTAAAT
1683523 TAAAAGGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (17 bp):
GTTTTTAAATCGCACTT
Found at i:1684332 original size:7 final size:7
Alignment explanation
Indices: 1684314--1684435 Score: 77
Period size: 7 Copynumber: 16.1 Consensus size: 7
1684304 TATAAGGGAG
1684314 ATAAAAA
1 ATAAAAA
1684321 GATAAAAA
1 -ATAAAAA
*
1684329 ATAAAGA
1 ATAAAAA
1684336 AT-AAAA
1 ATAAAAA
1684342 ATAAAAA
1 ATAAAAA
1684349 A-AAGAAA
1 ATAA-AAA
* *
1684356 TTAAATA
1 ATAAAAA
1684363 ATAAAATA
1 ATAAAA-A
1684371 CATAAATAA
1 -ATAAA-AA
*
1684380 GTAAAAA
1 ATAAAAA
*
1684387 TAGAAAATA
1 -ATAAAA-A
1684396 ATAAAAA
1 ATAAAAA
1684403 ATAATATAA
1 ATAA-A-AA
1684412 TATAAATAA
1 -ATAAA-AA
1684421 ATAAAAA
1 ATAAAAA
*
1684428 ACAAAAA
1 ATAAAAA
1684435 A
1 A
1684436 ATAAGGTAAT
Statistics
Matches: 92, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
6 7 0.08
7 38 0.41
8 29 0.32
9 13 0.14
10 5 0.05
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (7 bp):
ATAAAAA
Found at i:1684352 original size:18 final size:22
Alignment explanation
Indices: 1684322--1684368 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
1684312 AGATAAAAAG
1684322 ATAAAAAATAAAG-AA-TAAA-A
1 ATAAA-AATAAAGAAATTAAATA
1684342 ATAAAAA-AAAGAAATTAAATA
1 ATAAAAATAAAGAAATTAAATA
1684363 ATAAAA
1 ATAAAA
1684369 TACATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 9 0.38
21 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (22 bp):
ATAAAAATAAAGAAATTAAATA
Found at i:1684403 original size:17 final size:17
Alignment explanation
Indices: 1684322--1684405 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
1684312 AGATAAAAAG
*
1684322 ATAAAAAATAAAGAATAAAA
1 ATAAAAAAT--AGAA-AATA
* *
1684342 ATAAAAAAAAGAAATTAA
1 ATAAAAAATAGAAAAT-A
*
1684360 ATAATAAAATACATAAATA
1 ATAA-AAAATAGA-AAATA
1684379 AGT-AAAAATAGAAAATA
1 A-TAAAAAATAGAAAATA
1684396 ATAAAAAATA
1 ATAAAAAATA
1684406 ATATAATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
16 1 0.02
17 14 0.27
18 16 0.31
19 9 0.17
20 12 0.23
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (17 bp):
ATAAAAAATAGAAAATA
Found at i:1684438 original size:25 final size:25
Alignment explanation
Indices: 1684382--1684438 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1684372 ATAAATAAGT
*
1684382 AAAAATAGAAAATAATAAAAAATAA
1 AAAAATAGAAAATAATAAAAAACAA
* * *
1684407 TATAATA-TAAATAAATAAAAAACAA
1 AAAAATAGAAAAT-AATAAAAAACAA
1684432 AAAAATA
1 AAAAATA
1684439 AGGTAATATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (25 bp):
AAAAATAGAAAATAATAAAAAACAA
Found at i:1688178 original size:19 final size:19
Alignment explanation
Indices: 1688154--1688197 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1688144 ATTCACATAC
1688154 AAAATTATAAATCGTATAA
1 AAAATTATAAATCGTATAA
* * *
1688173 AAAATTATGAATTGTATAC
1 AAAATTATAAATCGTATAA
1688192 AAAATT
1 AAAATT
1688198 TCCCCTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAATTATAAATCGTATAA
Found at i:1690182 original size:198 final size:200
Alignment explanation
Indices: 1689818--1691010 Score: 1403
Period size: 200 Copynumber: 6.0 Consensus size: 200
1689808 GCGTAATTTA
* *
1689818 AAAAAGTAT-AGACACAACTTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAATC
1 AAAAAGTATCA-ACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACC
*
1689882 GGTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTT
65 GGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * *
1689947 TTGGGATCAATACAATTT-TAAATGTATCGAAACTTTATGCGTGCACCTC-GTTGGGCATTCATT
130 TTGGGATCAATACATTTTATAAATGTATCGACACTTTATTCGTGCACCTCTGTTGGGCATTCATT
*
1690010 CTGGTC
195 CTGGAC
* * *
1690016 AACAAGTATCAACACAATTTTAAAAAGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
1 AAAAAGTATCAACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * * * * *
1690081 GTATATTTATATC-GTTACATTGTAAACTTAACTATTACATTATAATTATCGGTTTCAATGTTTT
66 GTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * * * *
1690145 TGGGATCGATACGTTTTATAAATGTATCAACACTTTATGT-GTGCA-CTCTTTTAGGCATTCATT
131 TGGGATCAATACATTTTATAAATGTATCGACACTTTAT-TCGTGCACCTCTGTTGGGCATTCATT
1690208 CTGGAC
195 CTGGAC
* ** * * * * * * * **
1690214 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGATGTAAACATATTCTCTCATAAAAAT
1 AAAAAGTATCAACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAAT-TAACC
* * * *
1690279 GGTATATTTCTATCGGCTACATTGTAAAGTTACCTATTACATTATAATTATCGATTTCGATGTTT
65 GGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * * *
1690344 TTGGGATCGATACATTTTATAAATGTATCTACACTTTATACGTGCA-CTCTTTTAGGCATTCATT
130 TTGGGATCAATACATTTTATAAATGTATCGACACTTTATTCGTGCACCTCTGTTGGGCATTCATT
1690408 CTGGAC
195 CTGGAC
* * * * * * *
1690414 AAAAAGTATCGACACAAATTCCACAAA-TGTCGATACATGATGTAGACCTATTCTCTCATAAAAC
1 AAAAAGTATCAACACAAATT-TAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAAT-TAAC
* * * * *
1690478 CGATATATTTCTACCGGTTACATTGGAAATTTACCTATTACATTATATTTATTGGTTTTGATGTT
64 CGGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * * * *
1690543 TTTAGGG-TCAATACGTTTTATAAATGTATTGATACTTTATTCATGCATCTC-GTTGGGCATTTA
129 TTT-GGGATCAATACATTTTATAAATGTATCGACACTTTATTCGTGCACCTCTGTTGGGCATTCA
*
1690606 TTCTGGTC
193 TTCTGGAC
* *
1690614 AAAACGTAT-AGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAA-TAATC
1 AAAAAGTATCA-ACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACC
* * * *
1690677 GGTATATTTCTACCGATTACATTGGAAAATTGACCTATTACATTATAATTATC-TTATTTGATG-
65 GGTATATTTCTACCGGTTACATTGGAAAGTT-ACCTATTACATTATAATTATCGGT-TTCGATGT
* * * * * *
1690740 TTTTGGGATCAATACTTTTTATAAATGTATTGACATTTTATTCATGCACCTCAGTTGGTCATTCA
128 TTTTGGGATCAATACATTTTATAAATGTATCGACACTTTATTCGTGCACCTCTGTTGGGCATTCA
1690805 TTCTGGAC
193 TTCTGGAC
* * *
1690813 AAAAAATATCAACAC-AATATAAAAAGTGTCGATATATTATGTAGACCTATTTTCTAATTAACCG
1 AAAAAGTATCAACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* * * *
1690877 GTATATATCTACCGGTTACATTGGAAATTTACCTATTACATTATAATTATC-ATATTCGATATTT
66 GTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGGT-TTCGATGTTT
** * * *
1690941 TTGCAATCGATAC-TTTTAATAAATGTATCGACATTTTATTCGTGCACCTCGGTTGGGCATTCAT
130 TTGGGATCAATACATTTT-ATAAATGTATCGACACTTTATTCGTGCACCTCTGTTGGGCATTCAT
1691005 TCTGGA
194 TCTGGA
1691011 GATTACTGAA
Statistics
Matches: 866, Mismatches: 109, Indels: 39
0.85 0.11 0.04
Matches are distributed among these distances:
197 68 0.08
198 305 0.35
199 166 0.19
200 318 0.37
201 9 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (200 bp):
AAAAAGTATCAACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
GTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCAATACATTTTATAAATGTATCGACACTTTATTCGTGCACCTCTGTTGGGCATTCATTC
TGGAC
Found at i:1692286 original size:18 final size:18
Alignment explanation
Indices: 1692263--1692299 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1692253 CAAAATTTAT
1692263 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1692281 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1692299 A
1 A
1692300 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1694482 original size:110 final size:104
Alignment explanation
Indices: 1694299--1695157 Score: 781
Period size: 98 Copynumber: 8.3 Consensus size: 104
1694289 AATATTGTTC
* * * *
1694299 CGAGTCCAATAACCTCCGCTGTGAAGTTGAAATTGGTTATGGAACCGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-TCTGGAACC-GGAAATTGTTTGTTGACA
* * *
1694364 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGAATATTGT-T
64 ATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTG----TTGTCT
* * * *
1694408 CCGAGTCCAATAACCTCCGCTGTGAAGTTGAAATTGGTTATGGAACCGGGAAATTATTTGTTGAC
1 -CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-TCTGGAACC-GGAAATTGTTTGTTGAC
* * * *
1694473 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
63 AATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * *
1694515 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCT-GAA-C-GAAA-T-CTTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG-GTCTGGAACCGGAAATTGTTTGTTGACAA
* *
1694575 TCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
65 TCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * ** * *
1694615 CGAGTCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-TCTGGAA-CCGGAAATTGTTTGTTGACA
* * *
1694680 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
1694721 CGAGTGGCACGATATCCTCCG-TCGTGGAGTTGAAATCGTGG-ATGAAACTGAAAAGTTGTTCGT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAAT--TGGTCTGGAACCGGAAA-TTGTTTGT
*
1694784 TGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
1694830 CGAATCCAATATCCTTCGCTGTGAAGTTGAAGTTGG-CT----CC-GAAATTGCTTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTCTGGAACCGGAAATTGTTTGTTGACAAT
* *
1694889 CAGCCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
1694928 TGGGTCCAATATCCTTCGCTGTGAAGTTGAGATTGG-CT-----CTGAAATTGTTTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTCTGGAACCGGAAATTGTTTGTTGACAAT
* * *
1694987 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCAT
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTC-T
* * * * * *
1695027 -GGGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATT-ATTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-TCTGGAAC-CGGAAATTGTTTGTTGACA
* ** *
1695090 ACCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTATTGTCT
64 ATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
1695131 CGAGTCCAATATCCTTCGCTGTGAAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGT
1695158 CAAAATTGAC
Statistics
Matches: 648, Mismatches: 73, Indels: 61
0.83 0.09 0.08
Matches are distributed among these distances:
97 1 0.00
98 168 0.26
99 4 0.01
100 82 0.13
101 3 0.00
102 4 0.01
104 9 0.01
105 68 0.10
106 116 0.18
107 3 0.00
108 8 0.01
109 79 0.12
110 100 0.15
111 3 0.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTCTGGAACCGGAAATTGTTTGTTGACAAT
CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1694840 original size:215 final size:202
Alignment explanation
Indices: 1694347--1695157 Score: 709
Period size: 206 Copynumber: 3.9 Consensus size: 202
1694337 ATGGAACCGG
* * * * *
1694347 GAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGAATATTGT-TCCG
1 GAAATTGTTCGTTGACAATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTG----TTGTCT-CG
* * * * ** * **
1694411 AGTCCAATAACCTCCGCTGTGAAGTTGAAATTGGTTATGGAACCGGGAAATTATTTGTTGACAGT
61 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA--ATGAAA-TGTTTGTTGACAAC
* * * * * *
1694476 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT--CTAATATCCTTCGCTGTGA
122 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCCAATATCCTCCGCTGTGA
1694539 AGTTGAAATT-GACTCT
187 AGTTGAAATTGGA-TCT
* * * *
1694555 GAACGAAATCTT-GTTGACAATCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
1 G-A--AATTGTTCGTTGACAATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAG
* *
1694619 TCCAATATCCTTCACTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCA
63 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA--TG--AAATGTTTGTTGACAACCA
* * *
1694684 GCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCG-TCGTGG
124 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC-CAATATCCTCCGCT-GTGA
1694748 AGTTGAAATCGTGGATGAAACT
187 AGTTGAAAT--TGGAT----CT
* *
1694770 GAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAAT
1 G-AAA-TTGTTCGTTGACAATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT
* * * * **
1694835 CCAATATCCTTCGCTGTGAAGTTGAAGTTGGCTCCGAAAT----TGCTTGTCGACAGTCAGCCGT
64 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATGAAATGTTTGTTGACAACCAGCCGT
* * * * * * *
1694896 CCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTG-G-GTCCAATATCCTTCGCTGTGAAGTTGAG
129 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCCAATATCCTCCGCTGTGAAGTTGAA
*
1694959 ATTGGCTCT
194 ATTGGATCT
* * * * * * *
1694968 GAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCAT-GGGTC
1 GAAATTGTTCGTTGACAATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTC-TCGAGTC
* *
1695032 CAATATCCTTCGCCGTGAAGTTGAAATTGGCCCTGAAACTGGGAAAT-TATTGTTGACAACCAGC
65 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-T--GAAATGT-TTGTTGACAACCAGC
* * *
1695096 CGTCCCTTCATTGTGAAGTTGAACTTGTATTGTCTCGAGT--CCAATATCCTTCGCTGTGAAGT
126 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCCAATATCCTCCGCTGTGAAGT
1695158 CAAAATTGAC
Statistics
Matches: 495, Mismatches: 75, Indels: 71
0.77 0.12 0.11
Matches are distributed among these distances:
196 83 0.17
197 5 0.01
198 3 0.01
202 4 0.01
203 66 0.13
204 22 0.04
205 7 0.01
206 89 0.18
207 50 0.10
208 3 0.01
209 22 0.04
210 37 0.07
211 7 0.01
212 2 0.00
213 3 0.01
214 3 0.01
215 89 0.18
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (202 bp):
GAAATTGTTCGTTGACAATCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATGAAATGTTTGTTGACAACCAGCCGTCC
CTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCCAATATCCTCCGCTGTGAAGTTGAAAT
TGGATCT
Found at i:1694906 original size:55 final size:53
Alignment explanation
Indices: 1694842--1695013 Score: 152
Period size: 55 Copynumber: 3.4 Consensus size: 53
1694832 AATCCAATAT
1694842 CCTTCGCTGTGAAGTTGA-AGTTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGTC
1 CCTTCGCTGTGAAGTTGAGA-TTGGCT-CGAAATTG-TTGTCGACAGTCAGCCGTC
* ** * *
1694897 CCTTCGCTGTGAAGTTGAGCTTGTGCT-G-TCTTG-GGTC--CAAT-A----T-
1 CCTTCGCTGTGAAGTTGAGATTG-GCTCGAAATTGTTGTCGACAGTCAGCCGTC
*
1694940 CCTTCGCTGTGAAGTTGAGATTGGCTCTGAAATTGTTTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGATTGGCTC-GAAATTG-TTGTCGACAGTCAGCCGTC
1694995 CCTTCGCTGTGAAGTTGAG
1 CCTTCGCTGTGAAGTTGAG
1695014 CTTGTGCTGT
Statistics
Matches: 91, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
42 3 0.03
43 22 0.24
44 2 0.02
45 3 0.03
47 3 0.03
48 1 0.01
49 6 0.07
50 1 0.01
51 3 0.03
53 3 0.03
54 1 0.01
55 40 0.44
56 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (53 bp):
CCTTCGCTGTGAAGTTGAGATTGGCTCGAAATTGTTGTCGACAGTCAGCCGTC
Found at i:1695607 original size:68 final size:67
Alignment explanation
Indices: 1695452--1695674 Score: 227
Period size: 68 Copynumber: 3.3 Consensus size: 67
1695442 CAGATGATGC
* ** * * * * * *
1695452 TTCAAGAGAAATTGTCTCAAAAGAGACAGAACTCGTTTCAAGGGAAA-CAATCTCAAAGATATTT
1 TTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTT
1695516 GTTGT
64 G-TGT
* ** **
1695521 TTCATGAGAAAGGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATTTTG
1 TTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGATTTTG
1695586 TGT
65 TGT
* * *
1695589 TTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-T
1 TTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGT
1695652 GT
66 GT
*
1695654 TTCAAGGGAAACTGTCTCAAG
1 TTCAAGAGAAACTGTCTCAAG
1695675 ATAGATGAAA
Statistics
Matches: 129, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
65 22 0.17
66 3 0.02
67 23 0.18
68 31 0.24
69 29 0.22
70 18 0.14
71 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGT
GT
Found at i:1695690 original size:65 final size:67
Alignment explanation
Indices: 1695452--1695910 Score: 238
Period size: 65 Copynumber: 6.7 Consensus size: 67
1695442 CAGATGATGC
* * * * * * *
1695452 TTCAAGAGAAATTGTCTCAAAAGAGACAGAACTCGTTTCAAGGGAAA-CAATCTCAAAGATATTT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTT
1695516 GTTGT
64 G-TGT
* ** * * **
1695521 TTCATGAGAAAGGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATTTTG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGATTTTG
1695586 TGT
65 TGT
* * *
1695589 TTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-T
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGT
1695652 GT
66 GT
* * * * * **
1695654 TTCAAGGGAAACTGTCTCAAGATAGATGAAAA-TTGTTTCAAGAGAAAT-TGTCTCAAGAGAGAC
1 TTCAAGAGAAACTGTCTCAAGAGAGA-CAAAATTTGTTTTAAGGGAAATAAAT-TC-A-A-AG--
** *
1695717 AAAACTT-AGT
59 --ATTTTGTGT
* * * ** * * * * * *
1695727 TCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATA-TTT-T
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGT
1695790 GT
66 GT
* * * *
1695792 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGGGAAACTGTCTCAAGA-T-AGAC
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-----T-AA-ATTCA-AA
**
1695855 GAAATT-TGT
58 GATTTTGTGT
* *
1695864 TTAAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
1695911 CTGTCTCAAG
Statistics
Matches: 299, Mismatches: 68, Indels: 43
0.73 0.17 0.10
Matches are distributed among these distances:
64 1 0.00
65 81 0.27
66 9 0.03
67 24 0.08
68 33 0.11
69 29 0.10
70 20 0.07
71 8 0.03
72 53 0.18
73 39 0.13
74 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.28
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGT
GT
Found at i:1695703 original size:15 final size:15
Alignment explanation
Indices: 1695683--1695713 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1695673 AGATAGATGA
*
1695683 AAATTGTTTCAAGAG
1 AAATTGTCTCAAGAG
1695698 AAATTGTCTCAAGAG
1 AAATTGTCTCAAGAG
1695713 A
1 A
1695714 GACAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (15 bp):
AAATTGTCTCAAGAG
Found at i:1695706 original size:36 final size:35
Alignment explanation
Indices: 1695650--1695930 Score: 236
Period size: 36 Copynumber: 8.0 Consensus size: 35
1695640 TTCAAAGATT
* * *
1695650 TTGTTTCAAGGGAAACTGTCTCAAGATAGATGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGA-CAAAA
*
1695686 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1695721 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
1695759 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
1695788 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1695823 TTTATTTAAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
1695860 TTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1695895 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1695931 CTCTTCTAGT
Statistics
Matches: 199, Mismatches: 30, Indels: 32
0.76 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 10 0.05
36 130 0.65
37 32 0.16
38 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1695753 original size:138 final size:137
Alignment explanation
Indices: 1695592--1695911 Score: 410
Period size: 138 Copynumber: 2.3 Consensus size: 137
1695582 TTTGTGTTTC
* * * *
1695592 AAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTC
* * * * *
1695657 AAGGGAAACTGTCTCAAGATAGATGAAAA-TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
66 AAGGGAAACTGTCTCAAGAGAGA-CAAAATTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
1695721 CTTAGTTCCA
130 -TTAGTT-CA
** * * * *
1695731 AA-AGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTC
* * *
1695795 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGGGAAACTGTCTCAAGATAGACGAAAT
66 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAAT
* *
1695860 TTGTTTA
131 TAGTTCA
*
1695867 AAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1695912 TGTCTCAAGA
Statistics
Matches: 154, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
136 3 0.02
137 46 0.30
138 103 0.67
139 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (137 bp):
AAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTC
AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAAT
TAGTTCA
Found at i:1695952 original size:35 final size:36
Alignment explanation
Indices: 1695792--1695964 Score: 154
Period size: 36 Copynumber: 4.8 Consensus size: 36
1695782 AATATTTTGT
* * **
1695792 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
1695828 TTAAAGGGAAACTGTCTCAAGATAGACGAAATTTG-
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * *
1695863 TTTAAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
1695900 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
1695934 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
1695965 TCTTGTTTTA
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
34 5 0.04
35 27 0.23
36 79 0.68
37 5 0.04
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:1695971 original size:71 final size:72
Alignment explanation
Indices: 1695799--1695972 Score: 219
Period size: 72 Copynumber: 2.4 Consensus size: 72
1695789 TGTTTCAAGG
* * * *
1695799 GAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATCTGT
*
1695864 TTAAAGA
66 CTAAAGA
*
1695871 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTCT-
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAA-TCTG
**
1695935 TCTAGTGA
65 TCTAAAGA
* *
1695943 -AAACGGTCTCAAGCGAGAC-AAATCTTGTTT
1 GAAACTGTCTCAAGAGAGACAAAAT-TTGTTT
1695973 TAAGAAAAAT
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
70 4 0.04
71 23 0.26
72 61 0.68
73 2 0.02
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (72 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATCTGT
CTAAAGA
Found at i:1696858 original size:22 final size:22
Alignment explanation
Indices: 1696833--1696883 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1696823 TTGTGTTTGG
1696833 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1696855 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1696877 TCAAAGG
1 TCAAAGG
1696884 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1697542 original size:22 final size:22
Alignment explanation
Indices: 1697490--1697546 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
1697480 TTTTTGTCCC
*
1697490 CTTTTTTATTTTTG-TTCTTGT
1 CTTTTTTCTTTTTGCTTCTTGT
* *
1697511 -TTTTTCCTTTTTGCTTCTTTT
1 CTTTTTTCTTTTTGCTTCTTGT
1697532 CTTTTTTCTTTTTGC
1 CTTTTTTCTTTTTGC
1697547 CCTTTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 11 0.37
21 6 0.20
22 13 0.43
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.75
Consensus pattern (22 bp):
CTTTTTTCTTTTTGCTTCTTGT
Found at i:1697553 original size:22 final size:23
Alignment explanation
Indices: 1697510--1697552 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1697500 TTTGTTCTTG
*
1697510 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
1697533 TTTTTT-CTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
1697553 TATTCTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:1700967 original size:4 final size:4
Alignment explanation
Indices: 1700958--1700985 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1700948 AATGTTAGTA
1700958 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1700986 GACGAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:1702196 original size:26 final size:27
Alignment explanation
Indices: 1702134--1702206 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
1702124 AGTAAATAAA
* *
1702134 AAAAATAATAGTTATATATATAATAACT
1 AAAAATAATA-TTAAATATATAAGAACT
* *
1702162 TAAAA-AATATTAAATATATTAGAA-T
1 AAAAATAATATTAAATATATAAGAACT
*
1702187 AAAAATAATAAT-AATATATA
1 AAAAATAATATTAAATATATA
1702207 CTTAATAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 12 0.32
26 17 0.46
27 4 0.11
28 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (27 bp):
AAAAATAATATTAAATATATAAGAACT
Found at i:1702636 original size:35 final size:36
Alignment explanation
Indices: 1702587--1702676 Score: 112
Period size: 35 Copynumber: 2.5 Consensus size: 36
1702577 GTGCTTGTGG
1702587 ATCCTATCTTTAGGAGTTTAAAACATAGCA-AATTCT
1 ATCCTAT-TTTAGGAGTTTAAAACATAGCAGAATTCT
* * *
1702623 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTAAAACATAGCAGAATTCT
*
1702658 ATCCTATTTTTGAGAGTTT
1 ATCCTATTTTAG-GAGTTT
1702677 GAATCCTAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 10 0.21
35 25 0.53
36 10 0.21
37 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTAAAACATAGCAGAATTCT
Found at i:1704059 original size:6 final size:6
Alignment explanation
Indices: 1704052--1704085 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1704042 GTTTGGATCA
* *
1704052 TCATCA TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1704086 TGACCGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:1705159 original size:15 final size:15
Alignment explanation
Indices: 1705139--1705167 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1705129 GGAGGTTGTC
1705139 GTTGAGAAGAGCTTG
1 GTTGAGAAGAGCTTG
1705154 GTTGAGAAGAGCTT
1 GTTGAGAAGAGCTT
1705168 TGAGAAAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.38, T:0.28
Consensus pattern (15 bp):
GTTGAGAAGAGCTTG
Found at i:1705265 original size:23 final size:23
Alignment explanation
Indices: 1705235--1705281 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1705225 GTTACATTGG
1705235 AACACAAACACATTAACGAAAAA
1 AACACAAACACATTAACGAAAAA
*
1705258 AACACAAACACATTAAGGAAAAA
1 AACACAAACACATTAACGAAAAA
1705281 A
1 A
1705282 GAGTCCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.66, C:0.19, G:0.06, T:0.09
Consensus pattern (23 bp):
AACACAAACACATTAACGAAAAA
Found at i:1706246 original size:201 final size:201
Alignment explanation
Indices: 1705491--1707052 Score: 2147
Period size: 200 Copynumber: 7.8 Consensus size: 201
1705481 GAGAAATTTA
* * * *
1705491 AAAAAGTATCGACACAAATTTAAAATGTGTTGATACATTATGTAGACCTATTCTCTCTTAATACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* ** * * * * *
1705556 GGTATATTTATACCGGTTACATTGGAAAATTACAAATTATATTTTAATTATCGATTTCAAT-TTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
1705620 TTGGGATCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGCACCTAGTTTGGGTATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
1705685 CTGGAC
196 CTGGAC
* * *
1705691 AAAAAATATCGACACAAATTTAAAAAATGTTGATACATTATGTAGACCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * * * *
1705756 GGTATATTTATATCGGTTACATTG-GAAATT--TTCTT--ATTATAATTATGAGTTTCGATATTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
*
1705816 TTGGGATCGATACTTTTTATAAATGTATCGATACTTTATGCGTGCACCTAGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
*
1705881 CTGGTC
196 CTGGAC
* * * * * * * *
1705887 AAAATGTATCGACACAAATTTAAAAAGTGTCGATATAATATGTAGACCTATTTTCTAAT-TATCT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * *
1705951 TGTATATTTCTACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATATTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* *
1706016 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
1706081 CTGGAC
196 CTGGAC
* ** *
1706087 AAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTAGATATATTCTCTCATAAAATC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * *
1706152 GGTATATTTATACCGGTTACATTGGAAATTTACCTATTATATTATAATTATGGGTTTCGATATTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
*
1706217 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
*
1706282 CTGGTC
196 CTGGAC
* * * *
1706288 AAAACGTATCGACACAAATTTAAAAAATGTCGAAACATTATGTAGACATATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * * *
1706353 AGTATGTTTATACAGGTTACATT-AGAAATTTACCTATTACATTATAATTATGTGTTTCGATGTT
66 GGTATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
*
1706417 TTTGGGATCGATACTTTTTATAAATGTATCGACATTTTATGCGTGCACCTAGTTTGGGCATTCAT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCAT
**
1706482 TCTGGTT
195 TCTGGAC
* * * * * * * * *
1706489 AAAAAGTATCGACAAAAATTAAAAAAGTGTCGATACAGTATATAGACCTATTTTCTAAT-TATCT
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * *
1706553 GGTATATTTCTACCAGTTACATTGAAAAATTACCTATTACATTATAATTATTGGTTTTGATGTTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * * *
1706618 TTGAGATTGATACTTTTTATAAATGTATCGACATTTTATGCGTGCACTTAGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
*
1706683 CTAGAC
196 CTGGAC
* * * * *
1706689 ATAAACTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAAC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
*
1706754 GGTATATTTATACC-GTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
1706818 TTGGGATCGATACATTTTATAAATGTTTCGACACTTTATGCATGCACCTAGTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
*
1706883 TTGGAC
196 CTGGAC
* * * ** *
1706889 AAAACGTATTGACACAAATTTCAAAAGTGTC-ATTACATTATGTTTACATATTCTCTCATAAAAC
1 AAAAAGTATCGACACAAATTTAAAAAGTGTCGA-TACATTATGTAGACCTATTCTCTCATAAAAC
*
1706953 CGATATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
65 CGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
1707018 TTTGGGATCGAGACTTTTTATAAATGTATCAACAC
130 TTTGGGATCGATACTTTTTATAAATGTATCGACAC
1707053 ATCTGTTTAC
Statistics
Matches: 1205, Mismatches: 145, Indels: 23
0.88 0.11 0.02
Matches are distributed among these distances:
195 39 0.03
196 127 0.11
197 2 0.00
198 3 0.00
199 6 0.00
200 572 0.47
201 456 0.38
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (201 bp):
AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
CTGGAC
Found at i:1706513 original size:401 final size:402
Alignment explanation
Indices: 1705491--1707052 Score: 2149
Period size: 401 Copynumber: 3.9 Consensus size: 402
1705481 GAGAAATTTA
* * * * *
1705491 AAAAAGTATCGACACAAATTTAAAATGTGTTGATACATTATGTAGACCTATTCTCTCTTAATACC
1 AAAACGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* ** * * * * *
1705556 GGTATATTTATACCGGTTACATTGGAAAATTACAAATTATATTTTAATTATCGATTTCAAT-TTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTT
* * *
1705620 TTGGGATCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGCACCTAGTTTGGGTATTCATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
* * ** *
1705685 CTGGACAAAAAATATCGACACAAATTTAAAAAATGTTGATACATTATGTAGACCTATTCTCTCAT
196 CTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTAGACATATTCTCTCAT
* * * * *
1705750 AAAACCGGTATATTTATATCGGTTACATTG-GAAATT--TTCTT--ATTATAATTATGAGTTTCG
261 AAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCG
*
1705810 ATATTTTTGGGATCGATACTTTTTATAAATGTATCGATACTTTATGCGTGCACCTAGTTTGGGCA
326 ATATTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCA
1705875 TTCATTCTGGTC
391 TTCATTCTGGTC
* * * * * * * *
1705887 AAAATGTATCGACACAAATTTAAAAAGTGTCGATATAATATGTAGACCTATTTTCTAAT-TATCT
1 AAAACGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * *
1705951 TGTATATTTCTACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATATTT
66 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTT
*
1706016 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGGCATTCATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
*
1706081 CTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTAGATATATTCTCTCAT
196 CTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTAGACATATTCTCTCAT
* * * *
1706146 AAAATCGGTATATTTATACCGGTTACATTGGAAATTTACCTATTATATTATAATTATGGGTTTCG
261 AAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCG
*
1706211 ATATTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTAGTTTGGGCA
326 ATATTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCA
1706276 TTCATTCTGGTC
391 TTCATTCTGGTC
* * *
1706288 AAAACGTATCGACACAAATTTAAAAAATGTCGAAACATTATGTAGACATATTCTCTCATAAAACC
1 AAAACGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
* * * *
1706353 AGTATGTTTATACAGGTTACATT-AGAAATTTACCTATTACATTATAATTAT-GTGTTTCGATGT
66 GGTATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATAG-GTTTCGATGT
* *
1706416 TTTTGGGATCGATACTTTTTATAAATGTATCGACATTTTATGCGTGCACCTAGTTTGGGCATTCA
129 TTTTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCA
** * * * * * * * *
1706481 TTCTGGTTAAAAAGTATCGACAAAAATTAAAAAAGTGTCGATACAGTATATAGACCTATTTTCTA
194 TTCTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTAGACATATTCTCTC
* * * * * *
1706546 AT-TATCTGGTATATTTCTACCAGTTACATTGAAAAATTACCTATTACATTATAATTATTGGTTT
259 ATAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTT
* * * * * *
1706610 TGATGTTTTTGAGATTGATACTTTTTATAAATGTATCGACATTTTATGCGTGCACTTAGTTTGGG
324 CGATATTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGG
* *
1706675 CATTCATTCTAGAC
389 CATTCATTCTGGTC
* * *
1706689 ATAAAC-TATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAAA
1 A-AAACGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAAC
* *
1706753 CGGTATATTTATACC-GTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTTGATGTT
65 CGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGTT
* *
1706817 TTTGGGATCGATACATTTTATAAATGTTTCGACACTTTATGCATGCACCTAGTTTGGGCATTCAT
130 TTTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCAT
* * * * * **
1706882 TTTGGACAAAACGTATTGACACAAATTTCAAAAGTGTCATTACATTATGTTTACATATTCTCTCA
195 TCTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTAGACATATTCTCTCA
*
1706947 TAAAACCGATATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTC
260 TAAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTC
* * *
1707012 GATGTTTTTGGGATCGAGACTTTTTATAAATGTATCAACAC
325 GATATTTTTGGGATCGATACTTTTTATAAATGTATCGACAC
1707053 ATCTGTTTAC
Statistics
Matches: 1017, Mismatches: 136, Indels: 21
0.87 0.12 0.02
Matches are distributed among these distances:
395 52 0.05
396 202 0.20
397 4 0.00
399 3 0.00
400 153 0.15
401 426 0.42
402 177 0.17
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (402 bp):
AAAACGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACC
GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTT
TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCATTCATT
CTGGACAAAAAGTATCGACACAAATTTAAAAAGTGTCAATACATTATGTAGACATATTCTCTCAT
AAAACCGGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCG
ATATTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTGGGCA
TTCATTCTGGTC
Found at i:1707525 original size:19 final size:19
Alignment explanation
Indices: 1707501--1707549 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1707491 TTACATTCAC
1707501 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
1707520 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
1707539 ATACAAAATTA
1 ATACAAAATTA
1707550 ACTCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:1710592 original size:365 final size:361
Alignment explanation
Indices: 1709879--1710716 Score: 1148
Period size: 365 Copynumber: 2.3 Consensus size: 361
1709869 TACGCGTACT
* * *
1709879 TATTAAAGTA-CTGGCACTTTCAATATATCCAGTAGCGCTTTATC-GTTTTGTCATTTAAAGACC
1 TATTAAAGTATC-GACACTTTCAATATATCCAGTAGCGCTTTACCGGTTTTGTC-TTT-TAGACC
* *
1709942 GGTTTTGTCATATTTTTTCCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACAC
63 GGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
*
1710007 TTTATAGGCGCTATTACTGCATCTCTTTTAAATTCCCAAAGTGTCGATACTTATATTAAAGTATC
128 TTTATAGGCGCTATTACTGCATCTCTTTTAAATTCCCAAAGTGTCGATACTTATATTAAACTATC
* * ** *
1710072 GACACTTTTAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGGGACTGGTTTTGTCATAT
193 GACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTC-AAACCGGTTTTGTCATAT
**
1710137 TTTTACCTGTTATATCGTTATGGATCGATACTTTTTTATAAAATATCGACACTTTATACGCGCTA
257 TTTTACCTGTTATATCGTTATGGATCGATACAGTTTTATAAAATATCGACACTTTATACGCGCTA
*
1710202 TTGCTGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
322 TTACTGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
* *
1710242 TATTAAAGTATCGACACTTTCAATATATCCATTAGCGCTTTACCGGTTTTGTCTTTTCGGGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCGGTTTTGTCTTTT--AGACCG
* *
1710307 GTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACACT
64 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* * * * *
1710372 TTATAGGCGTTATTATTTCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTAT-TTCAATCTAAT
129 TTATAGGCGCTATTACTGCATCTCTTTTAAATTCCCAAAGTGTCGATACTTATATT-AAACT-AT
*
1710436 CGATACTTTCAACATATCCGGTAGCGCTTTACC-GATTTTGTCATAATT-AAACCGGTTTTGTCA
192 CGACACTTTCAACATATCCGGTAGCGCTTTACCAG-TTTTGTCAT--TTCAAACCGGTTTTGTCA
* * * *
1710499 TATTTTTACCTGTTATATTGTTATGGATTGATACAGTTTTATAAAGTATCGACACTTTATAGGCG
254 TATTTTTACCTGTTATATCGTTATGGATCGATACAGTTTTATAAAATATCGACACTTTATACGCG
*
1710564 CTATTATTGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
319 CTATTACTGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
** * * * * *
1710607 T-TTCAATCTAATCGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATTAAAC
1 TATT-AAAGT-ATCGACACTTTCAATATATCCAGTAGCGCTTTACCGGTTTTGTC-T-TTTAGAC
** *
1710671 CGGTTTTGTCATATTTTTACCTGTTATATTAATATGGATTGATACA
62 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1710717 GATTGATACG
Statistics
Matches: 419, Mismatches: 43, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
363 44 0.11
364 130 0.31
365 157 0.37
366 83 0.20
367 3 0.01
368 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (361 bp):
TATTAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCGGTTTTGTCTTTTAGACCGGT
TTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
ATAGGCGCTATTACTGCATCTCTTTTAAATTCCCAAAGTGTCGATACTTATATTAAACTATCGAC
ACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCAAACCGGTTTTGTCATATTTTT
ACCTGTTATATCGTTATGGATCGATACAGTTTTATAAAATATCGACACTTTATACGCGCTATTAC
TGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
Found at i:1710717 original size:183 final size:181
Alignment explanation
Indices: 1709893--1710716 Score: 1127
Period size: 182 Copynumber: 4.5 Consensus size: 181
1709883 AAAGTACTGG
* * *
1709893 CACTTTCAATATATCCAGTAGCGCTTTATC-GTTTTGTCATTTAAAGACCGGTTTTGTCATATTT
1 CACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCAA-ACCGGTTTTGTCATATTT
* *
1709957 TTTCCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATT
65 TTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATT
* *
1710022 ACTGCATCTCTTTTAAATTCCCAAAGTGTCGATACTTATATTAAAGTATCGA
130 ACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTATATTAAACTATCGA
* * ** *
1710074 CACTTTTAATATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGGGACTGGTTTTGTCATATTT
1 CACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC-AAACCGGTTTTGTCATATTT
* * * *
1710139 TTACCTGTTATATCGTTATGGATCGATACTTTTTTATAAAATATCGACACTTTATACGCGCTATT
65 TTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATT
* * *
1710204 GCTGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTATATTAAAGTATCGA
130 ACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTATATTAAACTATCGA
** * **
1710256 CACTTTCAATATATCCATTAGCGCTTTACCGGTTTTGTCTTTTCGGGACCGGTTTTGTCATATTT
1 CACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTC-AAACCGGTTTTGTCATATTT
* * *
1710321 TTACATGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACACTTTATAGGCGTTATT
65 TTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATT
* * *
1710386 ATTTCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTAT-TTCAATCTAATCGA
130 ACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTATATT-AAACT-ATCGA
* * *
1710439 TACTTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATT-AAACCGGTTTTGTCATATT
1 CACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCAT--TTCAAACCGGTTTTGTCATATT
* *
1710503 TTTACCTGTTATATTGTTATGGATTGATACAGTTTTATAAAGTATCGACACTTTATAGGCGCTAT
64 TTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTAT
* * *
1710568 TATTGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTAT-TTCAATCTAATCGA
129 TACTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTATATT-AAACT-ATCGA
* *
1710622 TACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATT-AAACCGGTTTTGTCATATT
1 CACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCAT--TTCAAACCGGTTTTGTCATATT
** *
1710686 TTTACCTGTTATATTAATATGGATTGATACA
64 TTTACCTGTTATATTGTTATGGATCGATACA
1710717 GATTGATACG
Statistics
Matches: 586, Mismatches: 51, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
181 29 0.05
182 294 0.50
183 261 0.45
185 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
CACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCAAACCGGTTTTGTCATATTTT
TACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTA
CTGCTTCTCTTTTAAATTCCCAAAGTGTCGATACTTATATTAAACTATCGA
Found at i:1710722 original size:10 final size:10
Alignment explanation
Indices: 1710707--1710736 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1710697 TATTAATATG
1710707 GATTGATACA
1 GATTGATACA
*
1710717 GATTGATACG
1 GATTGATACA
1710727 GATTGATACA
1 GATTGATACA
1710737 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (10 bp):
GATTGATACA
Found at i:1719849 original size:11 final size:12
Alignment explanation
Indices: 1719833--1719864 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1719823 CAGTATATTA
1719833 TATTATT-TTTT
1 TATTATTATTTT
1719844 TATTATTATTTT
1 TATTATTATTTT
1719856 T-TTATTATT
1 TATTATTATT
1719865 ATTAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:1719852 original size:14 final size:14
Alignment explanation
Indices: 1719833--1719881 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
1719823 CAGTATATTA
1719833 TATTATTTTTTTAT
1 TATTATTTTTTTAT
1719847 TATTATTTTTTTAT
1 TATTATTTTTTTAT
**
1719861 TATTATTAATTTAT
1 TATTATTTTTTTAT
1719875 ATATTAT
1 -TATTAT
1719882 AATTGTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 26 0.81
15 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTTTTTAT
Found at i:1721264 original size:29 final size:28
Alignment explanation
Indices: 1721232--1721292 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1721222 TTTAATTTAT
1721232 TTCAATTTAGTCCTTTAAATTTTTAGTTA
1 TTCAATTTAGTCCTTTAAA-TTTTAGTTA
* ** * *
1721261 TTCATTTTTTTCTTTTTAATTTTAGTTA
1 TTCAATTTAGTCCTTTAAATTTTAGTTA
1721289 TTCA
1 TTCA
1721293 TTATTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (28 bp):
TTCAATTTAGTCCTTTAAATTTTAGTTA
Found at i:1721283 original size:28 final size:28
Alignment explanation
Indices: 1721252--1721312 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
1721242 TCCTTTAAAT
1721252 TTTTAGTTATTCATT-TTTTTCTTTTTAA
1 TTTTAGTTATTCATTATTTTTC-TTTTAA
1721280 TTTTAGTTATTCATTATTTTTCTTTTAA
1 TTTTAGTTATTCATTATTTTTCTTTTAA
1721308 TTTTA
1 TTTTA
1721313 ATGTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (28 bp):
TTTTAGTTATTCATTATTTTTCTTTTAA
Found at i:1721327 original size:29 final size:29
Alignment explanation
Indices: 1721252--1721319 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
1721242 TCCTTTAAAT
*
1721252 TTTTAGTTATTCATT-TTTTTCTTTTTAA
1 TTTTAATTATTCATTATTTTTCTTTTTAA
*
1721280 TTTTAGTTATTCATTATTTTTC-TTTTAA
1 TTTTAATTATTCATTATTTTTCTTTTTAA
1721308 TTTTAATGTATT
1 TTTTAAT-TATT
1721320 TTTTATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (29 bp):
TTTTAATTATTCATTATTTTTCTTTTTAA
Found at i:1730685 original size:24 final size:27
Alignment explanation
Indices: 1730647--1730702 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 27
1730637 ATCATAGAGA
* *
1730647 ATATATTATTGTATT-ATTTTCAATTT
1 ATATATTATTGTATTAAATTTAAATTT
1730673 ATATATT-TT-TATTAAATTTAAATTT
1 ATATATTATTGTATTAAATTTAAATTT
1730698 ATATA
1 ATATA
1730703 AATTTTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 4 0.15
25 16 0.59
26 7 0.26
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATATATTATTGTATTAAATTTAAATTT
Found at i:1734388 original size:106 final size:106
Alignment explanation
Indices: 1734203--1735217 Score: 1475
Period size: 106 Copynumber: 10.0 Consensus size: 106
1734193 GTATTGTTCC
* ** * * *
1734203 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACA
* * *
1734267 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGCTG-CATG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
*
1734309 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1734374 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1734415 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1734480 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1734521 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1734574 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1734615 GAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1734680 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1734721 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1734774 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1734815 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1734880 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1734921 GAGTCCAATATCCTTCGTTGTGAAGTTG-AA---G-T-TG-----G-GAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1734974 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1735015 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1735080 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1735120 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-G----G-----GA-AA-TTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
1735173 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1735214 GAGT
1 GAGT
1735218 GGCACGATAT
Statistics
Matches: 846, Mismatches: 24, Indels: 90
0.88 0.03 0.09
Matches are distributed among these distances:
93 53 0.06
94 264 0.31
95 10 0.01
96 4 0.00
98 1 0.00
99 3 0.00
100 5 0.01
101 3 0.00
104 5 0.01
105 42 0.05
106 454 0.54
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1734550 original size:43 final size:43
Alignment explanation
Indices: 1734489--1734644 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
1734479 ACCAGCGGTC
1734489 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
1734532 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
1734582 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
1734626 CCCTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
1734645 ATTGGCTCTG
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
43 39 0.47
44 1 0.01
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 1 0.01
51 22 0.27
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:1734614 original size:94 final size:94
Alignment explanation
Indices: 1734453--1735217 Score: 1127
Period size: 94 Copynumber: 7.8 Consensus size: 94
1734443 AAATTGGTTC
* *
1734453 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1734518 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
1734547 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1734612 CTGGAGTCCAATATCCCTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
1734641 TGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAATTGG----GAAATT-----G-T--TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1734706 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1734747 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1734812 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1734841 TGAAATTGACTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTTGTCGTGAAGTTG
1 TGAAATTG-----G-----GA-AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1734906 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1734947 TGAAGTTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1735012 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGT
1735041 TGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1 TGAAA-----T-TG-----G-GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1735106 AACTTGCGTTGTCT-GAGTCCAATATCCTTCGTTGTGAAGT
54 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1735146 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1735211 CTTGAGT
66 CTGGAGT
1735218 GGCACGATAT
Statistics
Matches: 623, Mismatches: 11, Indels: 74
0.88 0.02 0.10
Matches are distributed among these distances:
93 57 0.09
94 273 0.44
95 2 0.00
96 3 0.00
97 1 0.00
98 6 0.01
99 4 0.01
100 3 0.00
101 1 0.00
102 6 0.01
103 1 0.00
104 3 0.00
105 34 0.05
106 229 0.37
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGT
Found at i:1734690 original size:200 final size:200
Alignment explanation
Indices: 1734347--1735217 Score: 1618
Period size: 200 Copynumber: 4.4 Consensus size: 200
1734337 AAATTGGCTC
* * *
1734347 TGAAATTGAGAAGTTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1734412 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
1734477 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1734542 GAAGT
196 GAAGT
1734547 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
1734612 CTGGAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
1734677 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1734742 GAAGT
196 GAAGT
*
1734747 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1734812 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
*
1734877 CAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1734942 GAAGT
196 GAAGT
*
1734947 TGAAGTTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1735012 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
1735077 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAGTCCAATATCCTTCGTTGT
131 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1735141 GAAGT
196 GAAGT
*
1735146 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1735211 CTTGAGT
66 CTGGAGT
1735218 GGCACGATAT
Statistics
Matches: 652, Mismatches: 19, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
199 95 0.15
200 557 0.85
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (200 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
GAAGT
Found at i:1734750 original size:43 final size:43
Alignment explanation
Indices: 1734689--1734844 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
1734679 ACCAGCGGTC
1734689 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * ** ***
1734732 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
*
1734782 CCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
1734826 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
1734845 ATTGACTCTG
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 39 0.48
44 1 0.01
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 1 0.01
51 21 0.26
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:1734958 original size:400 final size:400
Alignment explanation
Indices: 1734203--1735217 Score: 1705
Period size: 400 Copynumber: 2.5 Consensus size: 400
1734193 GTATTGTTCC
** * *
1734203 GAGTCCAATAT-CCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTG-GAAAATTGTTTATTGAC
1 GAGTCCAATATCCCT-CGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAATTGTTTATTGAC
* * *
1734266 AACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGCTG-CATGGAGTCCAATATCCTTCGTTGT
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGTTGT
*
1734330 GAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGA
128 GAAGTTGAAATT-G----G-----GA-AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
**
1734395 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATT
181 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATT
1734460 GAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
246 GAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
1734525 CCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
311 CCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
1734590 CGTGAAGTTGAACTTGCGTTGTCTG
376 CGTGAAGTTGAACTTGCGTTGTCTG
* *
1734615 GAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAA
1 GAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1734680 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
1734745 GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTT
131 GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
1734810 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTATT
196 GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTATT
*
1734875 GACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
261 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
*
1734940 GTGAAGTTGAAGTTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
326 GTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
1735005 GCGTTGTCTG
391 GCGTTGTCTG
*
1735015 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1735080 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
1735144 GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTT
131 GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
*
1735209 GTCTTGAGT
196 GTCTGGAGT
1735218 GGCACGATAT
Statistics
Matches: 579, Mismatches: 21, Indels: 19
0.94 0.03 0.03
Matches are distributed among these distances:
399 95 0.16
400 351 0.61
401 2 0.00
402 2 0.00
407 1 0.00
411 1 0.00
412 122 0.21
413 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (400 bp):
GAGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
GTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTATT
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
GTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTG
Found at i:1744925 original size:21 final size:20
Alignment explanation
Indices: 1744859--1744927 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 20
1744849 AATAATTATT
*
1744859 AAAAATCATATTTACTTTCAA
1 AAAAATCATATTTA-TTTTAA
* *
1744880 AAAAATAAAATTATAATTATT--
1 AAAAATCATATT-T-ATT-TTAA
1744901 AAAAATCATATTTATTTTGAA
1 AAAAATCATATTTATTTT-AA
1744922 AAAAAT
1 AAAAAT
1744928 AAAATTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 1 0.03
21 26 0.70
22 3 0.08
23 2 0.05
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAAATCATATTTATTTTAA
Found at i:1744934 original size:21 final size:20
Alignment explanation
Indices: 1744868--1744935 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
1744858 TAAAAATCAT
*
1744868 ATTTACTTTCAAAAAAATAAA
1 ATTTA-TTTTAAAAAAATAAA
* *
1744889 ATTATAATTATT--AAAAATCAT
1 ATT-T-ATT-TTAAAAAAATAAA
1744910 ATTTATTTTGAAAAAAATAAA
1 ATTTATTTT-AAAAAAATAAA
1744931 ATTTA
1 ATTTA
1744936 ATTAAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
18 2 0.06
19 3 0.08
20 1 0.03
21 25 0.69
22 3 0.08
23 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (20 bp):
ATTTATTTTAAAAAAATAAA
Found at i:1744960 original size:42 final size:42
Alignment explanation
Indices: 1744850--1744939 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
1744840 GAAAAATTCA
* *
1744850 ATAATTATTAAAAATCATATTTACTTTCAAAAAAATAAAATT
1 ATAATTATTAAAAATCATATTTATTTTGAAAAAAATAAAATT
1744892 ATAATTATTAAAAATCATATTTATTTTGAAAAAAATAAAATT
1 ATAATTATTAAAAATCATATTTATTTTGAAAAAAATAAAATT
1744934 -TAATTA
1 ATAATTA
1744940 AATTATAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 6 0.13
42 40 0.87
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (42 bp):
ATAATTATTAAAAATCATATTTATTTTGAAAAAAATAAAATT
Found at i:1745914 original size:3 final size:3
Alignment explanation
Indices: 1745906--1745933 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1745896 CCGTATTTTG
1745906 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1745934 ATTCTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1755421 original size:64 final size:64
Alignment explanation
Indices: 1755342--1755474 Score: 230
Period size: 64 Copynumber: 2.1 Consensus size: 64
1755332 AACACACAGC
* *
1755342 AATGAAGCTGTGTCCTGGCTTAAAGACATGATAAAGAAAACAAGGGTCTAAATCCTGAAATCCA
1 AATGAAGCTGTGTCCTGCCTGAAAGACATGATAAAGAAAACAAGGGTCTAAATCCTGAAATCCA
* *
1755406 AATGAAGCTGTGTCCTTCCTGAAAGACATGATAAATAAAACAAGGGTCTAAATCCTGAAATCCA
1 AATGAAGCTGTGTCCTGCCTGAAAGACATGATAAAGAAAACAAGGGTCTAAATCCTGAAATCCA
1755470 AATGA
1 AATGA
1755475 CAACTTTGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (64 bp):
AATGAAGCTGTGTCCTGCCTGAAAGACATGATAAAGAAAACAAGGGTCTAAATCCTGAAATCCA
Found at i:1758172 original size:17 final size:17
Alignment explanation
Indices: 1758138--1758189 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1758128 ATCGGATAAA
* *
1758138 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
1758155 TTTATTAATTTACTGAG
1 TTTATTAATTTACAGAG
*
1758172 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
1758187 TTT
1 TTT
1758190 CTACTGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:1762225 original size:29 final size:30
Alignment explanation
Indices: 1762188--1762251 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1762178 AAATGGCATT
* * *
1762188 AATGACTCAATTACAAATTTTTAA-AATAC
1 AATGGCTCAATTACAAATTATTAATAATAA
*
1762217 AATGGCTCAATTATAAATTATTAATAATAA
1 AATGGCTCAATTACAAATTATTAATAATAA
1762247 AATGG
1 AATGG
1762252 TTTATGATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (30 bp):
AATGGCTCAATTACAAATTATTAATAATAA
Found at i:1764544 original size:30 final size:28
Alignment explanation
Indices: 1764502--1764582 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 28
1764492 AATACACATA
*
1764502 AAAGGACTAAATTGAAATAAATTTAAAATG
1 AAAGGACTAAATTAAAATAAA-TT-AAATG
*
1764532 AAAGGA-TGAAATTAAAATTAATTAAATG
1 AAAGGACT-AAATTAAAATAAATTAAATG
* * *
1764560 -AAGGACCAAAATACAATAAATTA
1 AAAGGACTAAATTAAAATAAATTA
1764583 TAAACTAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 18 0.42
28 5 0.12
29 3 0.07
30 17 0.40
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.25
Consensus pattern (28 bp):
AAAGGACTAAATTAAAATAAATTAAATG
Found at i:1765387 original size:11 final size:12
Alignment explanation
Indices: 1765371--1765420 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
1765361 ATTAATTGAA
1765371 TAAACCT-AAAC
1 TAAACCTAAAAC
1765382 TAAACCTAAAA-
1 TAAACCTAAAAC
*
1765393 GAAA-CTAAAAC
1 TAAACCTAAAAC
*
1765404 TAAAACTAAAAC
1 TAAACCTAAAAC
1765416 TAAAC
1 TAAAC
1765421 TAAGTATCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 6 0.18
11 13 0.39
12 14 0.42
ACGTcount: A:0.62, C:0.20, G:0.02, T:0.16
Consensus pattern (12 bp):
TAAACCTAAAAC
Found at i:1765397 original size:22 final size:22
Alignment explanation
Indices: 1765378--1765423 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1765368 GAATAAACCT
*
1765378 AAACTAAACCTAAAAGAAACTA
1 AAACTAAAACTAAAAGAAACTA
*
1765400 AAACTAAAACTAAAACTAAACTA
1 AAACTAAAACTAAAA-GAAACTA
1765423 A
1 A
1765424 GTATCTCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.65, C:0.17, G:0.02, T:0.15
Consensus pattern (22 bp):
AAACTAAAACTAAAAGAAACTA
Found at i:1765399 original size:16 final size:16
Alignment explanation
Indices: 1765378--1765408 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1765368 GAATAAACCT
*
1765378 AAACTAAACCTAAAAG
1 AAACTAAAACTAAAAG
1765394 AAACTAAAACTAAAA
1 AAACTAAAACTAAAA
1765409 CTAAAACTAA
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:0.68, C:0.16, G:0.03, T:0.13
Consensus pattern (16 bp):
AAACTAAAACTAAAAG
Found at i:1765403 original size:6 final size:6
Alignment explanation
Indices: 1765394--1765423 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1765384 AACCTAAAAG
1765394 AAACTA AAACTA AAACTA AAACT- AAACTA A
1 AAACTA AAACTA AAACTA AAACTA AAACTA A
1765424 GTATCTCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
AAACTA
Found at i:1765883 original size:17 final size:17
Alignment explanation
Indices: 1765863--1765898 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1765853 GTTAAATGGT
*
1765863 AGTTTTTCAGTTAAGCC
1 AGTTTTTCAGTTAAACC
1765880 AGTTTTTCAGTTAAACC
1 AGTTTTTCAGTTAAACC
1765897 AG
1 AG
1765899 CTTTCTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (17 bp):
AGTTTTTCAGTTAAACC
Found at i:1768591 original size:17 final size:17
Alignment explanation
Indices: 1768571--1768605 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1768561 GTTAAAGGGT
*
1768571 AGTTTTTCAGTTAAGCC
1 AGTTTTTCAATTAAGCC
1768588 AGTTTTTCAATTAAGCC
1 AGTTTTTCAATTAAGCC
1768605 A
1 A
1768606 CCTTTCTATT
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:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (17 bp):
AGTTTTTCAATTAAGCC
Found at i:1776405 original size:20 final size:20
Alignment explanation
Indices: 1776380--1776446 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
1776370 TTTTCCCAAT
1776380 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1776400 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
1776421 TCGCAATGCGAATAAGTAGA
1 TCGCAATGCGAATAAGTAAA
1776441 TCGCAA
1 TCGCAA
1776447 CGTGAATTGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1776423 original size:21 final size:21
Alignment explanation
Indices: 1776397--1776472 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
1776387 GCGAATAAGT
1776397 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1776418 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
* *
1776438 AGATCGCAACGTGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1776459 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1776473 TACTTACTAT
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.34
21 27 0.66
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1776486 original size:20 final size:20
Alignment explanation
Indices: 1776461--1776554 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1776451 AATTGGGAAA
*
1776461 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
1776481 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
1776502 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1776522 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
1776542 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1776555 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1776487 original size:41 final size:41
Alignment explanation
Indices: 1776380--1776472 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
1776370 TTTTCCCAAT
*
1776380 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAGATCGCAACGCGAATTGGGAAAA
*
1776421 TCGCAATGCGAATAAGTAGATCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAGATCGCAACGCGAATTGGGAAAA
1776462 TCGCAATGCGA
1 TCGCAATGCGA
1776473 TACTTACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAGATCGCAACGCGAATTGGGAAAA
Found at i:1776503 original size:41 final size:41
Alignment explanation
Indices: 1776458--1776535 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
1776448 GTGAATTGGG
* * *
1776458 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAA
*
1776499 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
1776536 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAA
Found at i:1777129 original size:20 final size:19
Alignment explanation
Indices: 1777075--1777142 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1777065 TTCGAGAATG
1777075 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1777095 ACTATCGCAACGCGAAAGTA
1 AAAATCGCAACGCGAAA-TA
**
1777115 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1777134 AAAATCGCA
1 AAAATCGCA
1777143 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.32
20 28 0.68
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1777184 original size:20 final size:19
Alignment explanation
Indices: 1777138--1777303 Score: 118
Period size: 20 Copynumber: 9.1 Consensus size: 19
1777128 GAAACCAAAA
*
1777138 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1777157 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
1777176 TCGCGGTTGCAATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
1777196 TTGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1777212 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1777229 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1777243 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1777262 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1777282 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1777302 TC
1 TC
1777304 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.34
20 47 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1777219 original size:39 final size:39
Alignment explanation
Indices: 1777143--1777219 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
1777133 CAAAATCGCA
* * **
1777143 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCAATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
*
1777182 TTGCAATTTTCATTTTGCGTTGCGATTGTCT-GGTCGCG
1 TTGCAATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
1777220 ATAGTCATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (39 bp):
TTGCAATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:1777273 original size:34 final size:33
Alignment explanation
Indices: 1777191--1777278 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
1777181 GTTGCAATTT
* * *
1777191 TCATTTTGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1777224 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1777257 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1777279 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1779366 original size:42 final size:42
Alignment explanation
Indices: 1779306--1779428 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
1779296 GCCCGACTCG
* * *
1779306 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1779348 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* ** * *
1779390 AC-AGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTA-TCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1779429 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
41 1 0.02
42 61 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1780805 original size:14 final size:14
Alignment explanation
Indices: 1780786--1780821 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1780776 ATTGTTTAAT
1780786 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1780800 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1780814 TGATTTGT
1 TGATTTGT
1780822 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1781046 original size:33 final size:32
Alignment explanation
Indices: 1781004--1781130 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
1780994 ATTAAATTCG
*
1781004 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CAT
* *
1781037 CGTTGCGATTTTCATTTCGCATTGTGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCAT
*
1781070 CGTTGCGATTTTCATTTCGCATTGCGATTCTTT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-AT
1781103 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1781131 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCAT
Found at i:1781093 original size:66 final size:66
Alignment explanation
Indices: 1780997--1781126 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
1780987 ACGCGAAATT
*
1780997 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1781062 G
66 G
**
1781063 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
1781127 CGATAGTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
G
Found at i:1783439 original size:12 final size:12
Alignment explanation
Indices: 1783422--1783446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1783412 TCTTCGGGGA
1783422 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1783434 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1783446 C
1 C
1783447 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1783655 original size:24 final size:24
Alignment explanation
Indices: 1783621--1783674 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1783611 CTGAAACATC
* *
1783621 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
1783645 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
1783669 ATCAAA
1 ATCAAA
1783675 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1784677 original size:19 final size:19
Alignment explanation
Indices: 1784655--1784708 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1784645 ATCGCAACGA
1784655 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1784674 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
* *
1784693 GCAAATCGCATTGCGA
1 GAAAATCGCAATGCGA
1784709 TTTTCTCGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.17
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1784739 original size:19 final size:19
Alignment explanation
Indices: 1784698--1784765 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1784688 GAAATGCAAA
1784698 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1784714 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1784731 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1784750 TCGCATTGTGATTTTC
1 TCGCATTGCGATTTTC
1784766 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1786823 original size:20 final size:19
Alignment explanation
Indices: 1786788--1786854 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1786778 GAAACTTAAA
1786788 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1786807 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1786827 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1786846 ATCGCAACG
1 ATCGCAACG
1786855 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1786862 original size:14 final size:14
Alignment explanation
Indices: 1786843--1786900 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1786833 ATGCGAAATG
1786843 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1786857 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1786873 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1786889 AAAATCGCAACG
1 AAAATCGCAACG
1786901 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1786885 original size:32 final size:33
Alignment explanation
Indices: 1786827--1786905 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1786817 GGAAATGGCT
*
1786827 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1786860 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1786892 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1786906 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Done.