Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 20
Found at i:3571417 original size:35 final size:39
Alignment explanation
Indices: 3571366--3571447 Score: 113
Period size: 37 Copynumber: 2.2 Consensus size: 39
3571356 TATAATTTTA
3571366 AATACAAAAAACTTACAATAA-G-TATTAAATGGTAAAT
1 AATACAAAAAACTTACAATAACGCTATTAAATGGTAAAT
3571403 AATA-AAAAAA-TTACAATAACTGCTATTAAATGGT-AAT
1 AATACAAAAAACTTACAATAAC-GCTATTAAATGGTAAAT
3571440 AA-ACAAAA
1 AATACAAAA
3571448 TTAACAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
35 9 0.22
36 7 0.17
37 14 0.34
38 11 0.27
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.26
Consensus pattern (39 bp):
AATACAAAAAACTTACAATAACGCTATTAAATGGTAAAT
Found at i:3575323 original size:17 final size:18
Alignment explanation
Indices: 3575291--3575324 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3575281 TAGTTAAATA
3575291 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
3575309 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
3575325 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:3576521 original size:31 final size:31
Alignment explanation
Indices: 3576464--3576522 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3576454 ATCAATGAAA
3576464 TATTTAAATGGTTTCAATATTACTACCTAAC
1 TATTTAAATGGTTTCAATATTACTACCTAAC
3576495 TATTTAAATGGTTTCAATA-TAGCTACCT
1 TATTTAAATGGTTTCAATATTA-CTACCT
3576523 TCTATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (31 bp):
TATTTAAATGGTTTCAATATTACTACCTAAC
Found at i:3580742 original size:18 final size:17
Alignment explanation
Indices: 3580703--3580741 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3580693 TTATCATACC
*
3580703 TTTTTAAATAAGATTTA
1 TTTTTAAATAAGATATA
3580720 TTTTTAAATTAA-ATATA
1 TTTTTAAA-TAAGATATA
3580737 TTTTT
1 TTTTT
3580742 TTGTAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTTAAATAAGATATA
Found at i:3590736 original size:13 final size:13
Alignment explanation
Indices: 3590718--3590752 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3590708 TAATATATCC
3590718 TTTAAAATTATAT
1 TTTAAAATTATAT
3590731 TTTAAAA-TATAT
1 TTTAAAATTATAT
*
3590743 TTAAAAATTA
1 TTTAAAATTA
3590753 AAAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTAAAATTATAT
Found at i:3591152 original size:20 final size:21
Alignment explanation
Indices: 3591127--3591165 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3591117 CCGAAAATGT
*
3591127 TAAAAA-ATTAATATTTTAGA
1 TAAAAATAATAATATTTTAGA
3591147 TAAAAATAATAATATTTTA
1 TAAAAATAATAATATTTTA
3591166 AGTATCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAGA
Found at i:3591817 original size:26 final size:26
Alignment explanation
Indices: 3591788--3591905 Score: 82
Period size: 26 Copynumber: 4.5 Consensus size: 26
3591778 TCAAATTCAT
3591788 AATATTTTATATATATTAACTTAAAA
1 AATATTTTATATATATTAACTTAAAA
3591814 AATA-TTT-T-TATATTAACTTATTAAA
1 AATATTTTATATATATTAACTTA--AAA
* * **
3591839 TATATTTTATTATTAAATTAA-TTTTAA
1 AATATTTTA-TA-TATATTAACTTAAAA
* * *
3591866 AATATTTTATATTATTTTCATTTAAATA
1 AATATTTTATA-TATATTAACTTAAA-A
*
3591894 GATATTTTATAT
1 AATATTTTATAT
3591906 TAAAATTTAT
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
23 12 0.17
24 1 0.01
25 9 0.12
26 15 0.21
27 14 0.19
28 12 0.17
29 2 0.03
30 7 0.10
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (26 bp):
AATATTTTATATATATTAACTTAAAA
Found at i:3591851 original size:27 final size:26
Alignment explanation
Indices: 3591788--3591875 Score: 87
Period size: 23 Copynumber: 3.4 Consensus size: 26
3591778 TCAAATTCAT
*
3591788 AATATTTTATATATATTAACTTA-AAA
1 AATATTTTAT-TATATTAACTTATTAA
3591814 AATA-TTT-TTATATTAACTTATTAA
1 AATATTTTATTATATTAACTTATTAA
3591838 ATATATTTTATTATTAAATTAA-TT-TTAA
1 A-ATATTTTATTA-T--ATTAACTTATTAA
3591866 AATATTTTAT
1 AATATTTTAT
3591876 ATTATTTTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
23 12 0.22
24 4 0.07
25 6 0.11
26 7 0.13
27 12 0.22
28 6 0.11
29 2 0.04
30 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
AATATTTTATTATATTAACTTATTAA
Found at i:3592069 original size:31 final size:31
Alignment explanation
Indices: 3592034--3592102 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
3592024 GTGATAACCT
3592034 TATCTTAATTAAATAAAAACAAAAGTGAACA
1 TATCTTAATTAAATAAAAACAAAAGTGAACA
* **
3592065 TATCTTAATTAAATAAAAACGAAAGTGATTA
1 TATCTTAATTAAATAAAAACAAAAGTGAACA
3592096 TATCTTA
1 TATCTTA
3592103 TGTTTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (31 bp):
TATCTTAATTAAATAAAAACAAAAGTGAACA
Found at i:3592511 original size:7 final size:7
Alignment explanation
Indices: 3592499--3592525 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3592489 AATAATTATT
3592499 ATTATAA
1 ATTATAA
3592506 ATTATAA
1 ATTATAA
3592513 ATTATAA
1 ATTATAA
3592520 ATTATA
1 ATTATA
3592526 TGCATCATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTATAA
Found at i:3595440 original size:17 final size:18
Alignment explanation
Indices: 3595418--3595453 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3595408 AAGGTTATAA
*
3595418 TAAAAAAACTA-ATAATT
1 TAAAAAAACGATATAATT
3595435 TAAAAAAACGATATAATT
1 TAAAAAAACGATATAATT
3595453 T
1 T
3595454 TCAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAAAAACGATATAATT
Found at i:3598651 original size:6 final size:6
Alignment explanation
Indices: 3598640--3598670 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3598630 TTAGAAATAT
3598640 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
3598671 GAATTTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:3604551 original size:15 final size:15
Alignment explanation
Indices: 3604531--3604573 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
3604521 CCGACAAAAT
3604531 TTCACTATTCATGAA
1 TTCACTATTCATGAA
**
3604546 TTCACTATTCACAAA
1 TTCACTATTCATGAA
3604561 TTCACTATTCATG
1 TTCACTATTCATG
3604574 TGAATAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.40
Consensus pattern (15 bp):
TTCACTATTCATGAA
Found at i:3605172 original size:15 final size:15
Alignment explanation
Indices: 3605147--3605185 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3605137 ATAATTAAAA
3605147 TATTATTTATTTAATC
1 TATT-TTTATTTAATC
*
3605163 TATTTTTATTTATTC
1 TATTTTTATTTAATC
*
3605178 AATTTTTA
1 TATTTTTA
3605186 AAAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTATTTAATC
Found at i:3610194 original size:21 final size:21
Alignment explanation
Indices: 3610164--3610209 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3610154 TTTTCATCGA
* *
3610164 GTATCGTTACCCAACGGTAAG
1 GTATCATTACCAAACGGTAAG
* *
3610185 GTATCATTACCAAAGGGTGAG
1 GTATCATTACCAAACGGTAAG
3610206 GTAT
1 GTAT
3610210 TGGTACCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (21 bp):
GTATCATTACCAAACGGTAAG
Found at i:3611318 original size:22 final size:22
Alignment explanation
Indices: 3611276--3611338 Score: 99
Period size: 22 Copynumber: 2.8 Consensus size: 22
3611266 GTGAAATTTG
*
3611276 TCCCGAAGGACCTCATGTATATA
1 TCCCGAATGACCT-ATGTATATA
*
3611299 TCCCGAATGACCTATGTATATG
1 TCCCGAATGACCTATGTATATA
3611321 TCCCGAATGACCTATGTA
1 TCCCGAATGACCTATGTA
3611339 ACCCTTGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 26 0.68
23 12 0.32
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (22 bp):
TCCCGAATGACCTATGTATATA
Found at i:3613056 original size:24 final size:21
Alignment explanation
Indices: 3613029--3613085 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
3613019 GTGCTAAGGA
3613029 ACTTTAGTATATTAGTGTTAATGC
1 ACTTTAGTATA--A-TGTTAATGC
* *
3613053 ACTTTCGTATCAATGTTGATGC
1 ACTTTAGTAT-AATGTTAATGC
3613075 ACTTTAGTATA
1 ACTTTAGTATA
3613086 CCAGTGCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.03
22 17 0.59
23 1 0.03
24 9 0.31
25 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (21 bp):
ACTTTAGTATAATGTTAATGC
Found at i:3615224 original size:22 final size:22
Alignment explanation
Indices: 3615174--3615230 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
3615164 AGAAAAGGGC
3615174 TGGTATCGATAC-TTTAGTTTG
1 TGGTATCGATACTTTTAGTTTG
* *
3615195 -AGTATCGATACTTTTGGTTTG
1 TGGTATCGATACTTTTAGTTTG
*
3615216 TGGTATCGATGCTTT
1 TGGTATCGATACTTT
3615231 CCTGAGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 10 0.33
21 8 0.27
22 12 0.40
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.47
Consensus pattern (22 bp):
TGGTATCGATACTTTTAGTTTG
Found at i:3617807 original size:137 final size:138
Alignment explanation
Indices: 3617579--3617945 Score: 360
Period size: 138 Copynumber: 2.7 Consensus size: 138
3617569 TAGTCCTTGA
* * * *
3617579 TTTTACCCGAGGTTCCAT-TTTTGGTTATTCGATTCAATAATT-AGCTAAAATTCGATTA-ATTT
1 TTTTGCCCGAGGTT--ATATTTTGGTTATTTGATTTAATAATTGA-CTAAAATT-GATTAGGTTT
** * * *
3617641 GTAATATTAGAGCCTCCATTTTA-CATTAA-TTTCACT-TTAGTCCTTTAATTTGTA-AGAGTTT
62 -TAATATTAGAGCCTCCATTTTAGGTTTAATTTTCA-TGTTAGTACTGTAA-TTG-AGAGAATTT
** *
3617702 TTGATTTGGTCATCGC
123 TCAATTTGGTCATCAC
* *
3617718 TTTTGCCCGAGGTTATATTTTGGTTATTTGATTTAATAATTGACTAATATTGATTAGGTTTTAAC
1 TTTTGCCCGAGGTTATATTTTGGTTATTTGATTTAATAATTGACTAAAATTGATTAGGTTTTAAT
3617783 ATTAGAGCCTCCA-TTTAGGTTTAATTTTCATGTTAGTACTGTAATTGAGGAGAATTTTCAATTT
66 ATTAGAGCCTCCATTTTAGGTTTAATTTTCATGTTAGTACTGTAATTGA-GAGAATTTTCAATTT
* *
3617847 TGTCCTCAC
130 GGTCATCAC
* * *
3617856 TTTTGCCCGAGGTT-TAGTTTTGATTATTTGATTTAAAAATTTG-CTAAAATTGATTAGG-ATTA
1 TTTTGCCCGAGGTTATA-TTTTGGTTATTTGATTTAATAA-TTGACTAAAATTGATTAGGTTTTA
* *
3617918 ATATTAGAACCTTCATTTTTAGGTTTAA
64 ATATTAGAGCCTCCA-TTTTAGGTTTAA
3617946 CCCTTAAGTT
Statistics
Matches: 193, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
136 5 0.03
137 48 0.25
138 112 0.58
139 28 0.15
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (138 bp):
TTTTGCCCGAGGTTATATTTTGGTTATTTGATTTAATAATTGACTAAAATTGATTAGGTTTTAAT
ATTAGAGCCTCCATTTTAGGTTTAATTTTCATGTTAGTACTGTAATTGAGAGAATTTTCAATTTG
GTCATCAC
Found at i:3618932 original size:31 final size:31
Alignment explanation
Indices: 3618884--3618961 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
3618874 CTTTTAAAAC
**
3618884 TTGCAATACAATCCCCCAACATTTAGT-TCGT
1 TTGCAATATGATCCCCCAACATTTAGTCT-GT
*
3618915 TTGTAATATGATCCCCCAACATTTAGTCTGT
1 TTGCAATATGATCCCCCAACATTTAGTCTGT
*
3618946 TTGCAATATGGTCCCC
1 TTGCAATATGATCCCC
3618962 GACCGTTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.35
Consensus pattern (31 bp):
TTGCAATATGATCCCCCAACATTTAGTCTGT
Found at i:3620930 original size:31 final size:32
Alignment explanation
Indices: 3620895--3620957 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
3620885 ACGGTCGGAG
3620895 ACCATATTGCAAACAGACTAAATGTT-GGGGA
1 ACCATATTGCAAACAGACTAAATGTTAGGGGA
3620926 ACCATATTGCAAACAGACTAAATGTTAGGGGA
1 ACCATATTGCAAACAGACTAAATGTTAGGGGA
3620958 CTGTATTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (32 bp):
ACCATATTGCAAACAGACTAAATGTTAGGGGA
Found at i:3621769 original size:57 final size:57
Alignment explanation
Indices: 3621681--3621847 Score: 246
Period size: 57 Copynumber: 2.9 Consensus size: 57
3621671 TCGAATGCCC
*
3621681 AACTCCAACCCTCTCAGAGGAGTTCAGTGGGTTCGAATGCCCCAAATCAAGGTCGTG
1 AACTCCAACCCTCTCAGAGGAGTTCAGTGGGTTCGAATGCCCCAAATCGAGGTCGTG
* * * * *
3621738 AACTCCAATCCTCTCAGAAGAATTCAGTGGGTTCGAATGCCCCAAATCGAGATTGTG
1 AACTCCAACCCTCTCAGAGGAGTTCAGTGGGTTCGAATGCCCCAAATCGAGGTCGTG
* *
3621795 AGCTCCAACCCTCTCAGAGGAGTTCAGCT-GGTTCGAATACCCCAAATCGAGGT
1 AACTCCAACCCTCTCAGAGGAGTTCAG-TGGGTTCGAATGCCCCAAATCGAGGT
3621848 AGGAAACTGC
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
57 96 0.99
58 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (57 bp):
AACTCCAACCCTCTCAGAGGAGTTCAGTGGGTTCGAATGCCCCAAATCGAGGTCGTG
Found at i:3624554 original size:16 final size:17
Alignment explanation
Indices: 3624527--3624559 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3624517 TCATATTCTC
3624527 TTCTTCATTCTCTTTAT
1 TTCTTCATTCTCTTTAT
3624544 TTCTT-ATTCTCTTTAT
1 TTCTTCATTCTCTTTAT
3624560 CTCCACCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTTCATTCTCTTTAT
Found at i:3625441 original size:21 final size:21
Alignment explanation
Indices: 3625391--3625441 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3625381 GGTAGGCTGA
* *
3625391 TATCCATACCAGATAAATTGG
1 TATCCATATCAGATAAACTGG
* *
3625412 TATCCATATCGGATGAACTGG
1 TATCCATATCAGATAAACTGG
3625433 TATCCATAT
1 TATCCATAT
3625442 TGAAGGCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (21 bp):
TATCCATATCAGATAAACTGG
Found at i:3628600 original size:15 final size:15
Alignment explanation
Indices: 3628574--3628611 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3628564 AGGTGTCACA
3628574 TTGACT-TTCAAACT
1 TTGACTCTTCAAACT
3628588 TTGACTCTTCAAACT
1 TTGACTCTTCAAACT
3628603 TTGACTCTT
1 TTGACTCTT
3628612 GACAAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.45
Consensus pattern (15 bp):
TTGACTCTTCAAACT
Found at i:3629432 original size:23 final size:23
Alignment explanation
Indices: 3629406--3629474 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
3629396 CACCACAGCT
*
3629406 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
3629429 CGTAGAATTGTACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* * *
3629452 CATAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3629475 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3629661 original size:103 final size:103
Alignment explanation
Indices: 3629490--3629703 Score: 356
Period size: 103 Copynumber: 2.1 Consensus size: 103
3629480 TAATGTCCAT
* ** *
3629490 AAGGACCACATATCATTCTTTAAGAATCATATACATATATTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
3629555 GACTTCACAAATGTTTCAAAGAATACATATATGTCCCG
66 GACTTCACAAATGTTCCAAAGAATACATATATGTCCCG
*
3629593 AAGGACCACATATCATTCCTTACGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
3629658 GACTTCACACATGTTCCAAAGAATACATATATGTTCCG
66 GACTTCACAAATGTTCCAAAGAATACATATATGTCCCG
3629696 AAGGACCA
1 AAGGACCA
3629704 TATAGACCCT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACAAATGTTCCAAAGAATACATATATGTCCCG
Found at i:3634658 original size:23 final size:23
Alignment explanation
Indices: 3634643--3634686 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3634633 ATTGCATCGA
3634643 AGTGCCACGTAGAATTGCACCAG
1 AGTGCCACGTAGAATTGCACCAG
*
3634666 AGTGCCGCGTAGAATTGCACC
1 AGTGCCACGTAGAATTGCACC
3634687 GTAGGGCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCAG
Found at i:3634882 original size:103 final size:103
Alignment explanation
Indices: 3634711--3634928 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
3634701 TAATGTCCAT
* * *
3634711 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTTACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
*
3634776 GACTTTACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
3634814 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
3634879 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3634917 AAGGACCACATA
1 AAGGACCACATA
3634929 GACCCTCGAT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3636319 original size:21 final size:21
Alignment explanation
Indices: 3636289--3636331 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3636279 TCTGGTTCGT
*
3636289 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3636310 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3636331 T
1 T
3636332 AGCCCATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3638564 original size:25 final size:25
Alignment explanation
Indices: 3638523--3638570 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
3638513 CAATTTAAGG
3638523 CAAAATGGTTTTTGGACTTGAATTTA
1 CAAAATGGTTTTTGGACTT-AATTTA
3638549 CAAAAT-GTTTTTGGACTTAATT
1 CAAAATGGTTTTTGGACTTAATT
3638571 GAATTTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (25 bp):
CAAAATGGTTTTTGGACTTAATTTA
Found at i:3638683 original size:21 final size:21
Alignment explanation
Indices: 3638657--3638755 Score: 96
Period size: 21 Copynumber: 4.7 Consensus size: 21
3638647 AGGGTGTCAA
3638657 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
3638678 AGTGCATCCATGTATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
3638699 AGTGCATCCAT--ACACCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* **
3638720 TAGTGCATCGATGCA-CTATGC
1 -AGTGCATCCATGCACCCCTGC
3638741 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3638756 TCAAACACCG
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
19 5 0.08
20 13 0.21
21 32 0.51
22 10 0.16
23 2 0.03
24 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:3638801 original size:20 final size:20
Alignment explanation
Indices: 3638776--3638869 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
3638766 AATGCAATTA
* *
3638776 GTGCATCGATGCATTATTCT
1 GTGCATCGATGCATCATGCT
*
3638796 GTGCATCGATGCATCATTCT
1 GTGCATCGATGCATCATGCT
*
3638816 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-ATGCT
*
3638837 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCATGCT
*
3638857 GTGCATCCATGCA
1 GTGCATCGATGCA
3638870 CGAAGGCTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 49 0.73
21 18 0.27
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCATGCT
Found at i:3638848 original size:41 final size:41
Alignment explanation
Indices: 3638776--3638877 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
3638766 AATGCAATTA
* ** *
3638776 GTGCATCGATGCAT-TATTCTGTGCATCGATGCATCATTCT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCATGCT
*
3638816 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCATGCT
*
3638857 GTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
3638878 TCAACGGCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
40 15 0.28
41 39 0.72
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCAAGGCTGTGCATCGATGCATCATGCT
Found at i:3639020 original size:20 final size:22
Alignment explanation
Indices: 3638982--3639021 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3638972 TTTGAGTATA
3638982 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
3639004 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
3639022 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:3642164 original size:29 final size:30
Alignment explanation
Indices: 3642094--3642153 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3642084 CAATTTAAGG
* *
3642094 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTAGACTTGAATTAAATTTA
3642125 CAAAATGTTTTTAGACTT-AATTAAATTTA
1 CAAAATGTTTTTAGACTTGAATTAAATTTA
3642154 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTAGACTTGAATTAAATTTA
Found at i:3642261 original size:21 final size:20
Alignment explanation
Indices: 3642235--3642331 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 20
3642225 GGTGTCAAAG
3642235 TGCATCCATGCACCCCTGCAA
1 TGCATCCATGCA-CCCTGCAA
* *
3642256 TGCATCCATGCATCCCTGTAG
1 TGCATCCATGCA-CCCTGCAA
*
3642277 TGTATCCATGCA-CCTGCACTA
1 TGCATCCATGCACCCTGCA--A
* * *
3642298 GTGCATCGATGCACCATGCAG
1 -TGCATCCATGCACCCTGCAA
3642319 TGCATCCATGCAC
1 TGCATCCATGCAC
3642332 TCAAACACCG
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.08
20 12 0.20
21 29 0.48
22 10 0.16
23 5 0.08
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.24
Consensus pattern (20 bp):
TGCATCCATGCACCCTGCAA
Found at i:3642326 original size:42 final size:40
Alignment explanation
Indices: 3642233--3642331 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 40
3642223 AGGGTGTCAA
* *
3642233 AGTGCATCCATGCACCCCTGCAATGCATCCATGCATCCCTGT
1 AGTGCATCCATGCA--CCTGCAATGCATCCATGCATCCATGC
* *
3642275 AGTGTATCCATGCACCTGCACTAGTGCATCGATGCA-CCATGC
1 AGTGCATCCATGCACCTGCA--A-TGCATCCATGCATCCATGC
3642317 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3642332 TCAAACACCG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.12
42 32 0.65
43 11 0.22
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (40 bp):
AGTGCATCCATGCACCTGCAATGCATCCATGCATCCATGC
Found at i:3656232 original size:3 final size:3
Alignment explanation
Indices: 3656224--3656248 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3656214 ACCCTGTTAA
3656224 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
3656249 CTCTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:3658218 original size:45 final size:46
Alignment explanation
Indices: 3658122--3658225 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 46
3658112 ATGCACATAC
* *
3658122 CATGCATCGATGCACTGAGGGTTTTATGAAAACATCGAAGGCATTT
1 CATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAAGGCACTT
* * *
3658168 GATGCATCGATGCACTCA-GGTTATTTTG-AAACATCGAATGCACTT
1 CATGCATCGATGCACTCAGGGTT-TTATGAAAACATCGAAGGCACTT
3658213 CATGCATCGATGC
1 CATGCATCGATGC
3658226 TCTCTTAGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 31 0.61
46 20 0.39
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (46 bp):
CATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAAGGCACTT
Found at i:3666087 original size:2 final size:2
Alignment explanation
Indices: 3666080--3666105 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3666070 TTTGAACTTA
3666080 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3666106 TTGGTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3666791 original size:65 final size:64
Alignment explanation
Indices: 3666722--3666907 Score: 209
Period size: 65 Copynumber: 2.9 Consensus size: 64
3666712 GAATAAATTG
* * *
3666722 AACATCGAATGCATTTTATGCATAGATGCACATACCATGCATCGATGCACTAAGGGT-TTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATCGATGCACTAAGGGTATTT-TG-
3666786 A
64 A
* * * * *
3666787 AACATCGAATGCATTTGATGCATCGATGCACA-AGCTATGCATAGATGCACTCATGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACATA-CTATGCATCGATGCACTAAGGGTATTTTGA
* *
3666851 AACATCGAATGCACTTCATGCATCGATGCAC-T-CTTAGTGCACCGATGCACTAAGGGT
1 AACATCGAATGCATTTCATGCATCGATGCACATAC-TA-TGCATCGATGCACTAAGGGT
3666908 CCAACGGTCA
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 46 0.45
65 50 0.49
66 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACATACTATGCATCGATGCACTAAGGGTATTTTGA
Found at i:3666881 original size:17 final size:19
Alignment explanation
Indices: 3666853--3666901 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3666843 TATTTTGAAA
3666853 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
3666871 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
3666890 CACCGATGCACT
1 CATCGATGCACT
3666902 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:3668551 original size:76 final size:78
Alignment explanation
Indices: 3668424--3668577 Score: 206
Period size: 76 Copynumber: 2.0 Consensus size: 78
3668414 AAAGTGATTT
* * *
3668424 GTTGTAATTCATAAAAGAATTGTAATTTAACATTATAGGTTGAACCGAAAATATTAGATTGTATA
1 GTTGTAATTCATAAAACAACTGTAATGTAACATTATAGGTTGAACCGAAAATATTAGATTGTATA
3668489 TAA-C-ATTATAA
66 TAAGCGATTATAA
* * * * *
3668500 GTTGTAATTTATATAACAACTGTAATGTAACATTATGGGTTGAAACC-AAAATGTTAGGTTGTAT
1 GTTGTAATTCATAAAACAACTGTAATGTAACATTATAGGTTG-AACCGAAAATATTAGATTGTAT
3668564 ATAAGCGATTATAA
65 ATAAGCGATTATAA
3668578 CTGAAATTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
76 55 0.82
77 5 0.07
78 7 0.10
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (78 bp):
GTTGTAATTCATAAAACAACTGTAATGTAACATTATAGGTTGAACCGAAAATATTAGATTGTATA
TAAGCGATTATAA
Found at i:3673339 original size:29 final size:30
Alignment explanation
Indices: 3673297--3673359 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3673287 AAACCTTAGA
* * *
3673297 AAAATTTGGGGATC-ATTTCGT-AATTTTTG
1 AAAAGTTGGAGATCAATTT-GTAAATTTTGG
3673326 AAAAGTTGGAGATCAATTTGTAAATTTTGG
1 AAAAGTTGGAGATCAATTTGTAAATTTTGG
3673356 AAAA
1 AAAA
3673360 TTGATAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.38
Consensus pattern (30 bp):
AAAAGTTGGAGATCAATTTGTAAATTTTGG
Found at i:3675097 original size:17 final size:17
Alignment explanation
Indices: 3675075--3675135 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
3675065 ACAGATTACA
3675075 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
* **
3675092 TCCTTCGGGACACAGATGACA
1 TCCTTCGGG--A-TGAT-AGG
3675113 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
3675130 TCCTTC
1 TCCTTC
3675136 AGGACATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 16 0.47
18 3 0.09
19 2 0.06
20 3 0.09
21 10 0.29
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:3675101 original size:38 final size:38
Alignment explanation
Indices: 3675046--3675141 Score: 156
Period size: 38 Copynumber: 2.5 Consensus size: 38
3675036 TATGAGACAT
* * *
3675046 ATGATAGGTCCTACGGGATACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
3675084 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
3675122 ATGATAGGTCCTTCAGGACA
1 ATGATAGGTCCTTCGGGACA
3675142 TTTATACGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:3675232 original size:12 final size:12
Alignment explanation
Indices: 3675215--3675256 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3675205 TCTCAGTAAT
3675215 ATACATGGGCTA
1 ATACATGGGCTA
*
3675227 ATACATTGGCTA
1 ATACATGGGCTA
**
3675239 ATACATGGATTA
1 ATACATGGGCTA
3675251 ATACAT
1 ATACAT
3675257 TAGATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (12 bp):
ATACATGGGCTA
Found at i:3678698 original size:30 final size:30
Alignment explanation
Indices: 3678664--3678740 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
3678654 AAATGGATTC
* *
3678664 AGTTTAGTGA-TCAAATTATAAGATTTTG-AA
1 AGTTTAGTGACT-AAAGTATAA-ACTTTGAAA
*
3678694 AGTTTGGTGACTAAAGTATAAACTTTGAAA
1 AGTTTAGTGACTAAAGTATAAACTTTGAAA
* *
3678724 AGTTTAGGGACCAAAGT
1 AGTTTAGTGACTAAAGT
3678741 GTAATTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.13
30 33 0.85
31 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (30 bp):
AGTTTAGTGACTAAAGTATAAACTTTGAAA
Found at i:3681485 original size:21 final size:21
Alignment explanation
Indices: 3681459--3681523 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
3681449 ATAGGTCATA
3681459 CGGGATACAGATTACATCCTT
1 CGGGATACAGATTACATCCTT
**
3681480 CGGGAT---GA-TAGGTCCTT
1 CGGGATACAGATTACATCCTT
* * *
3681497 CGAGACACAGATGACATCCTT
1 CGGGATACAGATTACATCCTT
3681518 CGGGAT
1 CGGGAT
3681524 GATAGGTCCT
Statistics
Matches: 31, Mismatches: 9, Indels: 8
0.65 0.19 0.17
Matches are distributed among these distances:
17 11 0.35
18 2 0.06
20 2 0.06
21 16 0.52
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (21 bp):
CGGGATACAGATTACATCCTT
Found at i:3681497 original size:17 final size:17
Alignment explanation
Indices: 3681475--3681535 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
3681465 ACAGATTACA
3681475 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
* * **
3681492 TCCTTCGAGACACAGATGACA
1 TCCTTCG-G-GA-TGAT-AGG
3681513 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
3681530 TCCTTC
1 TCCTTC
3681536 AGGACATTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 14 0.44
18 4 0.12
19 2 0.06
20 4 0.12
21 8 0.25
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:3681507 original size:38 final size:38
Alignment explanation
Indices: 3681446--3681535 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 38
3681436 TATGAGACAT
* * * * *
3681446 ATGATAGGTCATACGGGATACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGAGACACAGATGACATCCTTCGGG
3681484 ATGATAGGTCCTTCGAGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGAGACACAGATGACATCCTTCGGG
3681522 ATGATAGGTCCTTC
1 ATGATAGGTCCTTC
3681536 AGGACATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (38 bp):
ATGATAGGTCCTTCGAGACACAGATGACATCCTTCGGG
Found at i:3684006 original size:64 final size:64
Alignment explanation
Indices: 3683900--3684050 Score: 216
Period size: 64 Copynumber: 2.4 Consensus size: 64
3683890 AACAATGAAT
* * *
3683900 AGTAACGTGAACAGTGCATCGATGCATCAAAACATCGAATTTATAATATGCATCGATGCGCTAC
1 AGTAACGTGAACAGTGCATCGATGCATCAAAACAGCGAATTTATAATATACATCGATACGCTAC
* *
3683964 AGTAACGTGAATAGTGTATCGATGCATCAAAACAGC-AGATTTATAATATACATCGATACGCTAC
1 AGTAACGTGAACAGTGCATCGATGCATCAAAACAGCGA-ATTTATAATATACATCGATACGCTAC
*
3684028 AGTAAC-TGCTACAGTGCATCGAT
1 AGTAACGTG-AACAGTGCATCGAT
3684051 ACACTACAGT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 3 0.04
64 74 0.96
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (64 bp):
AGTAACGTGAACAGTGCATCGATGCATCAAAACAGCGAATTTATAATATACATCGATACGCTAC
Found at i:3684050 original size:30 final size:30
Alignment explanation
Indices: 3684014--3684072 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3684004 TTATAATATA
*
3684014 CATCGATACGCTACAGTAACTGCTACAGTG
1 CATCGATACACTACAGTAACTGCTACAGTG
3684044 CATCGATACACTACAGTAACTGCTACAGT
1 CATCGATACACTACAGTAACTGCTACAGT
3684073 AATTTCAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (30 bp):
CATCGATACACTACAGTAACTGCTACAGTG
Found at i:3684515 original size:44 final size:45
Alignment explanation
Indices: 3684438--3684553 Score: 162
Period size: 45 Copynumber: 2.6 Consensus size: 45
3684428 AATTTCTTAT
* *
3684438 CAATATACATACCATTTAATCCATAAGCTCGTAAGCTT-ATTTTAC
1 CAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTAATTTTAC
3684483 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTAATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTAATTTTAC
* * * *
3684528 CAATCTACTTACTATAATTTCATAAG
1 CAATATACTTACCATTATTCCATAAG
3684554 AAATTTGTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 22 0.34
45 42 0.66
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (45 bp):
CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTAATTTTAC
Found at i:3684796 original size:118 final size:118
Alignment explanation
Indices: 3684588--3685074 Score: 693
Period size: 118 Copynumber: 4.1 Consensus size: 118
3684578 CCTTATAATA
* * ** *
3684588 TTAGCAC-TCTAAGTGCTCTATCTGGAATAT-CATATACTT-AATATGATTTCCTCCTCATTTTA
1 TTAGCACATATAA-TGCCCTATCTGGAA-ATCCATATA-TTCAATATGATTTCCTTATCACTTTA
** * *
3684650 GCACACGAAGTGC-CC-TATGCGAGAATCCATAC-CATTAGTATGATTCTCTTACCATT
63 GCACACTCAGTGCTCCATATG-GA-AATCCATACAC-TCAGTATGATTCCCTTACCATT
*
3684706 TTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGATTTTCTTATCACTTTAGCA
1 TTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCACTTTAGCA
3684771 CACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCATT
66 CACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCATT
* *
3684824 TTAGCACATATAATGCCCTATATGGAAATCCATATA--CAATATGATTTCCTTATCACTTTATCA
1 TTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCACTTTAGCA
* *
3684887 CACTTAGTGCTCCATATGGAAATTCATACACTCAGTATGATTCCCTTACCATT
66 CACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCATT
*
3684940 TTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAATATGATTTCCTTATCACTTTAGCA
1 TTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCACTTTAGCA
* * *
3685005 CACTCAGTGCTCCATATGGAAATTCATACACTCAGTATGATTTCCTTATCATT
66 CACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCATT
*
3685058 TTAGCACATATAGTGCC
1 TTAGCACATATAATGCC
3685075 ATTTGGTAAT
Statistics
Matches: 340, Mismatches: 21, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
116 111 0.33
117 4 0.01
118 212 0.62
119 9 0.03
120 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (118 bp):
TTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCACTTTAGCA
CACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCTTACCATT
Found at i:3685093 original size:59 final size:58
Alignment explanation
Indices: 3684629--3685074 Score: 424
Period size: 59 Copynumber: 7.6 Consensus size: 58
3684619 ATATACTTAA
** * *
3684629 TATGATTTCCTCCTCATTTTAGCACACGA-AGTGCCC-TATGCGAGAATCCATAC-CATTAG
1 TATGATTTCCTTATCATTTTAGCACA-TATAGTGCCCATATG-GA-AATCCATACAC-TCAG
* * * * * *
3684688 TATGA-TTCTCTTACCATTTTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAA
1 TATGATTTC-CTTATCATTTTAGCACATATAGTGCCC-ATATGGAAATCCATACACTCAG
* * *
3684747 TATGATTTTCTTATCACTTTAGCACACT-CAGTGCTCCATATGGAAATCCATACACTCAG
1 TATGATTTCCTTATCATTTTAGCACA-TATAGTGC-CCATATGGAAATCCATACACTCAG
* * * * *
3684806 TATGATTCCCTTACCATTTTAGCACATATAATGCCCTATATGGAAATCCATATA--CAA
1 TATGATTTCCTTATCATTTTAGCACATATAGTGCCC-ATATGGAAATCCATACACTCAG
* * *
3684863 TATGATTTCCTTATCACTTTATCACACT-TAGTGCTCCATATGGAAATTCATACACTCAG
1 TATGATTTCCTTATCATTTTAGCACA-TATAGTGC-CCATATGGAAATCCATACACTCAG
* * * * * * *
3684922 TATGATTCCCTTACCATTTTAGCACATATAATGCCCTATTTGGAAATCCATATATTCAA
1 TATGATTTCCTTATCATTTTAGCACATATAGTGCCC-ATATGGAAATCCATACACTCAG
* * *
3684981 TATGATTTCCTTATCACTTTAGCACACT-CAGTGCTCCATATGGAAATTCATACACTCAG
1 TATGATTTCCTTATCATTTTAGCACA-TATAGTGC-CCATATGGAAATCCATACACTCAG
3685040 TATGATTTCCTTATCATTTTAGCACATATAGTGCC
1 TATGATTTCCTTATCATTTTAGCACATATAGTGCC
3685075 ATTTGGTAAT
Statistics
Matches: 311, Mismatches: 57, Indels: 39
0.76 0.14 0.10
Matches are distributed among these distances:
57 44 0.14
58 15 0.05
59 239 0.77
60 10 0.03
61 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (58 bp):
TATGATTTCCTTATCATTTTAGCACATATAGTGCCCATATGGAAATCCATACACTCAG
Found at i:3691980 original size:39 final size:39
Alignment explanation
Indices: 3691935--3692015 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
3691925 TGGTTGCAAA
3691935 GGTAACGTTTTAGGTTCCACCTTTATAAATATATTTAAT
1 GGTAACGTTTTAGGTTCCACCTTTATAAATATATTTAAT
3691974 GGTAACGTTTTAGGTTCCACCTTTATAAATATATTTAAT
1 GGTAACGTTTTAGGTTCCACCTTTATAAATATATTTAAT
3692013 GGT
1 GGT
3692016 TAAGTTTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (39 bp):
GGTAACGTTTTAGGTTCCACCTTTATAAATATATTTAAT
Found at i:3692100 original size:101 final size:100
Alignment explanation
Indices: 3691974--3692364 Score: 408
Period size: 101 Copynumber: 3.9 Consensus size: 100
3691964 TATATTTAAT
* * ** ***
3691974 GGTAACGTTTTAGGTTCCACCTTTATAAATATATTTAATGGTTAAGTTTGTTGGTTACAACTGGA
1 GGTAACGTTTTAGGTTGCACCTTTATAAATATATTTAACGGTTAAGTTTAATGGTTACAACCAAA
* * **
3692039 TGTATTTGTAAAACCTATTATAAAGGCGATTTTGAA
66 TTTATTTGTAAAACCTATTATAAAGTCG-TTGCGAA
* * * *
3692075 GGTAACGTTTTAGATTGCGCCTTTATAAATATATTTAACGGTTAAGTTCAATGGTTGCAACCAAA
1 GGTAACGTTTTAGGTTGCACCTTTATAAATATATTTAACGGTTAAGTTTAATGGTTACAACCAAA
*
3692140 TTTATTTGTAAAACCTATTATAAATTCTGTTGCGAA
66 TTTATTTGTAAAACCTATTATAAAGTC-GTTGCGAA
* * ** *
3692176 TGTAACATTTTTAGGTTGCGTCTTTATAAATATATTTAACGGTCAAGTTTAAAT-GTTACAACCA
1 GGTAAC-GTTTTAGGTTGCACCTTTATAAATATATTTAACGGTTAAGTTT-AATGGTTACAACCA
* * * * *
3692240 CATTTATTAGTAAAACTTGTTATAAAGTCGGCTGCGAA
64 AATTTATTTGTAAAACCTATTATAAAGTC-GTTGCGAA
* * ** * * *
3692278 GGTAATGTCTTAGGTTGCACCTTTATAAATATATTTAACAATTAAGTTTAAAGGTTGCAACCGAA
1 GGTAACGTTTTAGGTTGCACCTTTATAAATATATTTAACGGTTAAGTTTAATGGTTACAACCAAA
*
3692343 TTTATTAT-TAAATCCTATTATA
66 TTTATT-TGTAAAACCTATTATA
3692365 CAGTTAGTTG
Statistics
Matches: 238, Mismatches: 47, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
100 2 0.01
101 150 0.63
102 83 0.35
103 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (100 bp):
GGTAACGTTTTAGGTTGCACCTTTATAAATATATTTAACGGTTAAGTTTAATGGTTACAACCAAA
TTTATTTGTAAAACCTATTATAAAGTCGTTGCGAA
Found at i:3692384 original size:101 final size:98
Alignment explanation
Indices: 3692082--3692404 Score: 315
Period size: 101 Copynumber: 3.2 Consensus size: 98
3692072 GAAGGTAACG
* * *
3692082 TTTTAGATTGCGCCTTTATAAATATATTTAACGGTTAAGTTCAATGGTTGCAACCAAATTTATT-
1 TTTTAGGTTGCGCCTTTATAAATATATTTAACGGTTAAGTTTAAAGGTTGCAACC-AATTTATTA
* * *
3692146 TGTAAAACCTATTATAAATTCTGTTGCGAATGTAACAT
65 T-TAAAACCTATTATAAGTT-AGTTGCGAAAGT-A-AT
* * * *
3692184 TTTTAGGTTGCGTCTTTATAAATATATTTAACGGTCAAGTTTAAATGTTACAACCACATTTATTA
1 TTTTAGGTTGCGCCTTTATAAATATATTTAACGGTTAAGTTTAAAGGTTGCAACCA-ATTTATTA
* * * ** * *
3692249 GTAAAACTTGTTATAAAGTCGGCTGCGAAGGTAAT
65 TTAAAACCTATTAT-AAGTTAGTTGCGAAAGTAAT
* * **
3692284 GTCTTAGGTTGCACCTTTATAAATATATTTAACAATTAAGTTTAAAGGTTGCAACCGAATTTATT
1 -TTTTAGGTTGCGCCTTTATAAATATATTTAACGGTTAAGTTTAAAGGTTGCAACC-AATTTATT
* *
3692349 ATTAAATCCTATTATACAGTTAGTTGCAAAAGTAAT
64 ATTAAAACCTATTATA-AGTTAGTTGCGAAAGTAAT
* *
3692385 ATTTTAGGTAGCGGCTTTAT
1 -TTTTAGGTTGCGCCTTTAT
3692405 GAACATCATT
Statistics
Matches: 178, Mismatches: 37, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
100 3 0.02
101 96 0.54
102 76 0.43
103 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (98 bp):
TTTTAGGTTGCGCCTTTATAAATATATTTAACGGTTAAGTTTAAAGGTTGCAACCAATTTATTAT
TAAAACCTATTATAAGTTAGTTGCGAAAGTAAT
Found at i:3696345 original size:22 final size:21
Alignment explanation
Indices: 3696244--3696345 Score: 68
Period size: 22 Copynumber: 4.7 Consensus size: 21
3696234 AACTATTTAC
3696244 ATAAAAA-TAATTTTTAATTTCA
1 ATAAAAATTAATTTTTAA-TT-A
*
3696266 A-ATAAATTAATTTTTAATTA
1 ATAAAAATTAATTTTTAATTA
* ***
3696286 GATAAATATT--TTGACAATCTA
1 -ATAAAAATTAATTTTTAAT-TA
3696307 ATTAAAAATTAATTTTTTAATATA
1 A-TAAAAATTAA-TTTTTAAT-TA
3696331 ATAAAAATTAATTTT
1 ATAAAAATTAATTTT
3696346 ACAATTAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
20 7 0.11
21 16 0.26
22 20 0.33
23 10 0.16
24 8 0.13
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAAAAATTAATTTTTAATTA
Found at i:3696404 original size:14 final size:15
Alignment explanation
Indices: 3696372--3696405 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
3696362 TACGTATATA
3696372 ATTTTACAATTAACT
1 ATTTTACAATTAACT
3696387 -TTTTACAATTAA-T
1 ATTTTACAATTAACT
3696400 ATTTTA
1 ATTTTA
3696406 ATAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTACAATTAACT
Found at i:3697652 original size:7 final size:7
Alignment explanation
Indices: 3697640--3697669 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3697630 TTTTTACCCT
3697640 AATCCTA
1 AATCCTA
3697647 AATCCTA
1 AATCCTA
3697654 AATCCTA
1 AATCCTA
*
3697661 AACCCTA
1 AATCCTA
3697668 AA
1 AA
3697670 ATTACAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
AATCCTA
Found at i:3697659 original size:14 final size:14
Alignment explanation
Indices: 3697635--3697669 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3697625 ATCTCTTTTT
3697635 ACCCT-AATCCTAA
1 ACCCTAAATCCTAA
*
3697648 ATCCTAAATCCTAA
1 ACCCTAAATCCTAA
3697662 ACCCTAAA
1 ACCCTAAA
3697670 ATTACAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (14 bp):
ACCCTAAATCCTAA
Found at i:3697791 original size:22 final size:23
Alignment explanation
Indices: 3697764--3697808 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3697754 CCTTGAAAGG
3697764 AAAAAATAGTT-TTTAAGAGTTA
1 AAAAAATAGTTATTTAAGAGTTA
* *
3697786 AAAAAATATTTATTTATGAGTTA
1 AAAAAATAGTTATTTAAGAGTTA
3697809 TGAATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (23 bp):
AAAAAATAGTTATTTAAGAGTTA
Found at i:3700556 original size:2 final size:2
Alignment explanation
Indices: 3700549--3700574 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3700539 TTTCTTGGTT
3700549 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3700575 AACAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3703683 original size:22 final size:22
Alignment explanation
Indices: 3703655--3703727 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
3703645 CCTTCTTTTT
3703655 TCGCCGGCAGTCACAGCCTCCA
1 TCGCCGGCAGTCACAGCCTCCA
*
3703677 TCGCCGGTAGTCACAGCCTCCA
1 TCGCCGGCAGTCACAGCCTCCA
* *
3703699 TCGTCGGCAGTCACAGCTTCCA
1 TCGCCGGCAGTCACAGCCTCCA
3703721 TCGCCGG
1 TCGCCGG
3703728 GCGCTAACAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (22 bp):
TCGCCGGCAGTCACAGCCTCCA
Found at i:3717927 original size:30 final size:30
Alignment explanation
Indices: 3717891--3717947 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
3717881 AAGAAAGAAA
3717891 GAAAGAACTTAAAAATAGTAATATAGTGTT
1 GAAAGAACTTAAAAATAGTAATATAGTGTT
3717921 GAAAGAACTTAAAAATAGTAATATAGT
1 GAAAGAACTTAAAAATAGTAATATAGT
3717948 TCTTCTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.28
Consensus pattern (30 bp):
GAAAGAACTTAAAAATAGTAATATAGTGTT
Found at i:3720382 original size:15 final size:15
Alignment explanation
Indices: 3720362--3720392 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3720352 CCACTAGCCT
3720362 CCCAATTACCATTGA
1 CCCAATTACCATTGA
*
3720377 CCCAATTACTATTGA
1 CCCAATTACCATTGA
3720392 C
1 C
3720393 ATTAGCATCC
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:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (15 bp):
CCCAATTACCATTGA
Found at i:3722916 original size:3 final size:3
Alignment explanation
Indices: 3722904--3722948 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
3722894 CTACAATAAC
* *
3722904 ATT A-T ATT ATT ATT -TT ATT ATT ATT ATT ATT TTT TTT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3722949 TACACATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
ATT
Found at i:3722930 original size:17 final size:17
Alignment explanation
Indices: 3722904--3722949 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
3722894 CTACAATAAC
3722904 ATTA-TATTATTATTTT
1 ATTATTATTATTATTTT
3722920 ATTATTATTATTATTTT
1 ATTATTATTATTATTTT
3722937 -TT-TTATT-TTATTT
1 ATTATTATTATTATTT
3722950 ACACATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.21
15 5 0.17
16 6 0.21
17 12 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTATTATTATTATTTT
Found at i:3722950 original size:4 final size:5
Alignment explanation
Indices: 3722908--3722949 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
3722898 AATAACATTA
3722908 TATTAT TATTT TATTAT TATTAT TATTT T-TTT TATTT TATTT
1 TATT-T TATTT TATT-T TATT-T TATTT TATTT TATTT TATTT
3722950 ACACATATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.12
5 15 0.44
6 15 0.44
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:3722950 original size:9 final size:8
Alignment explanation
Indices: 3722904--3722948 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
3722894 CTACAATAAC
*
3722904 ATTATATT
1 ATTATTTT
3722912 ATTATTTT
1 ATTATTTT
3722920 ATTATTATT
1 ATTATT-TT
3722929 ATTATTTTT
1 ATTA-TTTT
*
3722938 TTTATTTT
1 ATTATTTT
3722946 ATT
1 ATT
3722949 TACACATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 19 0.59
9 11 0.34
10 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTATTTT
Found at i:3729886 original size:37 final size:36
Alignment explanation
Indices: 3729809--3729946 Score: 152
Period size: 36 Copynumber: 3.8 Consensus size: 36
3729799 TATCTTCTTA
* * *
3729809 AAAAACAAAGTGTCGTCTCGCTAGAGACAGTTT-TCTT
1 AAAAACAAA-TTTCGTCTCGCTTGAGACAATTTCTC-T
*
3729846 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAA-TTTCTCT
* * * *
3729883 AAAAACAAATTTTGTATCGCTTAAAACAATTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAATTTCTCT
**
3729919 CGAAACAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTTCGTCTCGCTTGAGACA
3729947 TTTTTTCTCT
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
36 45 0.52
37 39 0.45
38 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (36 bp):
AAAAACAAATTTCGTCTCGCTTGAGACAATTTCTCT
Found at i:3729926 original size:15 final size:17
Alignment explanation
Indices: 3729906--3729937 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3729896 GTATCGCTTA
3729906 AAAC-AATTTC-TCTCG
1 AAACAAATTTCGTCTCG
3729921 AAACAAATTTCGTCTCG
1 AAACAAATTTCGTCTCG
3729938 CTTGAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 6 0.40
17 5 0.33
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (17 bp):
AAACAAATTTCGTCTCG
Found at i:3730349 original size:32 final size:33
Alignment explanation
Indices: 3730296--3730361 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
3730286 AAACAAAATC
3730296 TTTGAGTATGTTTCTTCTGAAACAAAAC-CATA
1 TTTGAGTATGTTTCTTCTGAAACAAAACACATA
* * *
3730328 TTTGCGTATGTTT-TATTTGAAATAAAACACATA
1 TTTGAGTATGTTTCT-TCTGAAACAAAACACATA
3730361 T
1 T
3730362 CTTTGAGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 1 0.03
32 23 0.79
33 5 0.17
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (33 bp):
TTTGAGTATGTTTCTTCTGAAACAAAACACATA
Found at i:3731140 original size:3 final size:3
Alignment explanation
Indices: 3731132--3731161 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3731122 CTACAAAAAC
3731132 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3731162 TGCATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3733015 original size:5 final size:5
Alignment explanation
Indices: 3732998--3733042 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
3732988 TTTTTACCTC
*
3732998 TTTT- TTTTA TTTTG TTTTA TTTTA TTTTA TTTTA TTTTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA
3733043 CAAAAAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 29 0.78
6 4 0.11
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:3737644 original size:4 final size:4
Alignment explanation
Indices: 3737632--3737684 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
3737622 TACATCAACT
*
3737632 CATA TATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3737678 CATA CAT
1 CATA CAT
3737685 GACGCATGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
4 43 0.96
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:3738074 original size:36 final size:36
Alignment explanation
Indices: 3738006--3738170 Score: 161
Period size: 36 Copynumber: 4.5 Consensus size: 36
3737996 TGAGATTATC
* * *
3738006 TTCTTAAAAACAAAGTGTCGTCTCGCTAGAGACAGTT
1 TTCTTAAAAACAAA-TTTCGTCTCGCTTGAGACAATT
* * *
3738043 TTCTTAAAAACAAATTTTGTCTCGCTGGAGACAACT
1 TTCTTAAAAACAAATTTCGTCTCGCTTGAGACAATT
* * * *
3738079 TTCTCTAAAAACAAATTTTGTATTGCTTGAAACAATT
1 TTCT-TAAAAACAAATTTCGTCTCGCTTGAGACAATT
* *
3738116 TCTCTT-AAAACAAATTTCATCTCGCTTGAGACATTT
1 T-TCTTAAAAACAAATTTCGTCTCGCTTGAGACAATT
*
3738152 TTCTCTAAGATACAAATTT
1 TTCT-TAA-AAACAAATTT
3738171 AAATTTGTTT
Statistics
Matches: 106, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
35 3 0.03
36 47 0.44
37 44 0.42
38 12 0.11
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (36 bp):
TTCTTAAAAACAAATTTCGTCTCGCTTGAGACAATT
Found at i:3738493 original size:67 final size:66
Alignment explanation
Indices: 3738294--3738507 Score: 226
Period size: 62 Copynumber: 3.3 Consensus size: 66
3738284 CAAAATTGAT
* * * * **
3738294 AATCTTTGAGTCT-TTTCTCTTGAAATAAGTTTTGTCTCTCTTGAGACAA-TTC-TTCTAGCGA-
1 AATCTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTTCGAGAAAC
3738355 A
66 A
* * * * * * *
3738356 AATCTTTGAGT-CGTTTCCCTTGAAACAAATTTTGTCTATTTTGAGACAGTTGCTTTTGA-AATA
1 AATCTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTTCGAGAA-A
3738419 CA
65 CA
3738421 TAATCTTTGAGTATGTTTCTC-TGAAAACAAATTGTTGTCTCTCTTGAGACAATTTCTTTCGAGA
1 -AATCTTTGAGTATGTTTCTCTTG-AAACAAATT-TTGTCTCTCTTGAGACAATTTCTTTCGAGA
3738485 AACA
63 AACA
3738489 AATCTTTGAGTATGTTTCT
1 AATCTTTGAGTATGTTTCT
3738508 TCTAAAAACA
Statistics
Matches: 123, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 41 0.33
63 2 0.02
64 4 0.03
65 1 0.01
66 13 0.11
67 34 0.28
68 26 0.21
69 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (66 bp):
AATCTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTTCGAGAAAC
A
Found at i:3738987 original size:129 final size:129
Alignment explanation
Indices: 3738650--3739134 Score: 365
Period size: 131 Copynumber: 3.7 Consensus size: 129
3738640 CCTTGAAACC
* * * * *
3738650 ATCATCCCTAAAGATAGCATGTCATCCTCATCGCGTAGGAA-CGTGTCATCCCTTGACCAAACCT
1 ATCATCCCTAAAGATGGCATATCATCCTCATCGTGTA-GAATCGTGTCATCCCTCGACCAGACCT
** * * *
3738714 CCTCATCATGTAGGAGTTGTATCACCCTAGATAACCACCCGTCCTCATCTCGTATGAACCATGCT
65 CCTCATCATGTAGGAGCCGTGTCACCCTAGATAACCACCCGTCCTCATCACGTAAGAACCATGCT
* * * * * * * * *
3738779 ATCGCCCTTCCTAAAGATGGCCAGAAC-TCTTTC-TCATGTATGAGTTGTTTCA-CCC-CGACCA
1 AT---CATCCCTAAAGATGG-CATATCATC-CTCATCGTGTA-GAATCGTGTCATCCCTCGACCA
* * * **
3738840 GACCTCCTCATCACGTAGGAGCCATGTCACCC-AGATAATCAGTCGTCCTCATCACGTAAGAACC
60 GACCTCCTCATCATGTAGGAGCCGTGTCACCCTAGATAACCACCCGTCCTCATCACGTAAGAACC
* *
3738904 GTGTT
125 ATGCT
* *
3738909 ATCATCCCTAAAGATGGTATATCATCCTCATCGTGTAGAAATCGTGTCATCCCTCGACCAGATCT
1 ATCATCCCTAAAGATGGCATATCATCCTCATCGTGTAG-AATCGTGTCATCCCTCGACCAGACCT
* * * * * *
3738974 CCTCATCATGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTCATCATCGCGTAGGAACCAAGT
65 CCTCATCATGTAGGAGCCGTGTCA-CCCTAGATAACCACCCGTCCTCATCACGTAAGAACCATGC
3739039 T
129 T
* ** * * * * * *
3739040 ATCACTCTCCTTAAAGATAGCCA-AGAACTCTTCATCGCGTATG-AGCAATGTCATCCCCCAACC
1 ATCA-TC-CC-TAAAGAT-GGCATATCA-TCCTCATCGTGTA-GAATC-GTGTCATCCCTCGACC
* *
3739103 AGATCTCCTCATCACGTAGGAGCCGTGTCACC
59 AGACCTCCTCATCATGTAGGAGCCGTGTCACC
3739135 TTTAAACGTC
Statistics
Matches: 277, Mismatches: 59, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
126 6 0.02
127 28 0.10
128 3 0.01
129 34 0.12
130 35 0.13
131 64 0.23
132 26 0.09
133 12 0.04
134 13 0.05
135 55 0.20
136 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (129 bp):
ATCATCCCTAAAGATGGCATATCATCCTCATCGTGTAGAATCGTGTCATCCCTCGACCAGACCTC
CTCATCATGTAGGAGCCGTGTCACCCTAGATAACCACCCGTCCTCATCACGTAAGAACCATGCT
Found at i:3739334 original size:3 final size:3
Alignment explanation
Indices: 3739322--3739368 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
3739312 GTATACAAAA
* *
3739322 ATT A-T ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3739369 TTTTACACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
ATT
Done.