Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 71 of 73
Found at i:16413931 original size:7 final size:6
Alignment explanation
Indices: 16413904--16413938 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
16413894 ATATAAATTC
*
16413904 TTTTTA -TTTCA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
16413939 ATTTCATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:16414406 original size:28 final size:29
Alignment explanation
Indices: 16414351--16414415 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 29
16414341 AGCATGCTTG
16414351 ACCTTCAACATTTACCCCTGATTCAACTA
1 ACCTTCAACATTTACCCCTGATTCAACTA
* * *
16414380 GCCTTTAACATTTA-CCCTGCTTCAACTA
1 ACCTTCAACATTTACCCCTGATTCAACTA
16414408 ACCTTCAA
1 ACCTTCAA
16414416 TCCTTCAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (29 bp):
ACCTTCAACATTTACCCCTGATTCAACTA
Found at i:16430727 original size:197 final size:198
Alignment explanation
Indices: 16430400--16430788 Score: 771
Period size: 197 Copynumber: 2.0 Consensus size: 198
16430390 ATTGATGTGT
16430400 TGTTGATTGCTACACTTGATGTTATTTGATATTTATTTTACTTATGATTTTCATGTTTTAAAATC
1 TGTTGATTGCTACACTTGATGTTATTTGATATTTATTTTACTTATGATTTTCATGTTTTAAAATC
16430465 GTTTTGGATATATTATTATTTTAAAGTATCGAAGAATGTTTTAGAAATTTAACGTAATTCATTAG
66 GTTTTGGATATATTATTATTTTAAAGTATCGAAGAATGTTTTAGAAATTTAACGTAATTCATTAG
16430530 ACTTAATTGTAACACATAAGTTGAATCTAGAGGGTT-AAAAAAAGATGATTAAGGCCTTTTATTG
131 ACTTAATTGTAACACATAAGTTGAATCTAGAGGGTTAAAAAAAAGATGATTAAGGCCTTTTATTG
16430594 ATG
196 ATG
16430597 TGTTGATTGCTACACTTGATGTTATTTGATATTTATTTTACTTATGATTTTCATGTTTTAAAATC
1 TGTTGATTGCTACACTTGATGTTATTTGATATTTATTTTACTTATGATTTTCATGTTTTAAAATC
16430662 GTTTTGGATATATTATTATTTTAAAGTATCGAAGAATGTTTTAGAAATTTAACGTAATTCATTAG
66 GTTTTGGATATATTATTATTTTAAAGTATCGAAGAATGTTTTAGAAATTTAACGTAATTCATTAG
16430727 ACTTAATTGTAACACATAAGTTGAATCTAGAGGGTTAAAAAAAAGATGATTAAGGCCTTTTA
131 ACTTAATTGTAACACATAAGTTGAATCTAGAGGGTTAAAAAAAAGATGATTAAGGCCTTTTA
16430789 CTCTTAGGCA
Statistics
Matches: 191, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
197 166 0.87
198 25 0.13
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (198 bp):
TGTTGATTGCTACACTTGATGTTATTTGATATTTATTTTACTTATGATTTTCATGTTTTAAAATC
GTTTTGGATATATTATTATTTTAAAGTATCGAAGAATGTTTTAGAAATTTAACGTAATTCATTAG
ACTTAATTGTAACACATAAGTTGAATCTAGAGGGTTAAAAAAAAGATGATTAAGGCCTTTTATTG
ATG
Found at i:16431190 original size:65 final size:65
Alignment explanation
Indices: 16431086--16431215 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
16431076 AGAATGGTAA
16431086 GAATAGTTGGATGGTTAAATAAGTATTTTATGTTAATGTTTTCTACTTTCACGATTTTTTCCTTT
1 GAATAGTTGGATGGTTAAATAAGTATTTTATGTTAATGTTTTCTACTTTCACGATTTTTTCCTTT
16431151 GAATAGTTGGATGGTTAAATAAGTATTTTATGTTAATGTTTTCTACTTTCACGATTTTTTCCTTT
1 GAATAGTTGGATGGTTAAATAAGTATTTTATGTTAATGTTTTCTACTTTCACGATTTTTTCCTTT
16431216 CTATAATGGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (65 bp):
GAATAGTTGGATGGTTAAATAAGTATTTTATGTTAATGTTTTCTACTTTCACGATTTTTTCCTTT
Found at i:16433236 original size:21 final size:22
Alignment explanation
Indices: 16433201--16433242 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
16433191 TTCCAGAATA
16433201 TTACAGGGATATCGATACCCTG
1 TTACAGGGATATCGATACCCTG
*
16433223 TTACAGTG-TATCGATACCCT
1 TTACAGGGATATCGATACCCT
16433243 TGCTACAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (22 bp):
TTACAGGGATATCGATACCCTG
Found at i:16433804 original size:24 final size:24
Alignment explanation
Indices: 16433777--16433842 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
16433767 AACTCGTATA
16433777 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
*
16433801 AATTTATC-CCGAAG-GACCACGTAG
1 AATTT-GCACCGAAGTG-CCACGTAG
* *
16433825 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGAAGTGCCA
16433843 TATAAGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 10 0.29
24 22 0.65
25 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.20
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:16435135 original size:8 final size:8
Alignment explanation
Indices: 16435122--16435147 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
16435112 TTGTTCAATG
16435122 ACCCTTTT
1 ACCCTTTT
16435130 ACCCTTTT
1 ACCCTTTT
16435138 ACCCTTTT
1 ACCCTTTT
16435146 AC
1 AC
16435148 TCTTCCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (8 bp):
ACCCTTTT
Found at i:16441067 original size:37 final size:37
Alignment explanation
Indices: 16441026--16441102 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
16441016 ATCTCAAAAA
* * *
16441026 GTCGGGTCGAGTGAAGGGTATATATTTTTCGGGTCGG
1 GTCGGGTCGAGTGAAGGATATAGAATTTTCGGGTCGG
* * *
16441063 GTCGGGTTGGGTGAAGGATGTAGAATTTTCGGGTCGG
1 GTCGGGTCGAGTGAAGGATATAGAATTTTCGGGTCGG
16441100 GTC
1 GTC
16441103 CTGTTGGTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.16, C:0.10, G:0.43, T:0.31
Consensus pattern (37 bp):
GTCGGGTCGAGTGAAGGATATAGAATTTTCGGGTCGG
Found at i:16444340 original size:3 final size:3
Alignment explanation
Indices: 16444324--16444376 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
16444314 AATCGAAAAA
*
16444324 TAT TAT TAAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16444370 TAT TAT T
1 TAT TAT T
16444377 TAAAACCACT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:16445285 original size:14 final size:15
Alignment explanation
Indices: 16445245--16445287 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
16445235 CTGATTTTAA
16445245 CACTTTAGTTTATGT
1 CACTTTAGTTTATGT
* *
16445260 TACTTTATTTTA-GT
1 CACTTTAGTTTATGT
*
16445274 CACTTAAGTTTATG
1 CACTTTAGTTTATG
16445288 CTTTTGCTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (15 bp):
CACTTTAGTTTATGT
Found at i:16445372 original size:30 final size:29
Alignment explanation
Indices: 16445303--16445373 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
16445293 GCTATTTATG
* * *
16445303 TCCTTTAAATTTCTGTTTTAGCTGTTTTA
1 TCCTTTAAGTTTCTGTTTTACCTGTTTAA
*
16445332 GCCTTGTAAGTTTCTGTTTTTACCAT-TTTAA
1 TCCTT-TAAGTTTCTG-TTTTACC-TGTTTAA
16445363 TCCTTTAAGTT
1 TCCTTTAAGTT
16445374 CATATTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 4 0.12
30 15 0.44
31 14 0.41
32 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.55
Consensus pattern (29 bp):
TCCTTTAAGTTTCTGTTTTACCTGTTTAA
Found at i:16449957 original size:61 final size:61
Alignment explanation
Indices: 16449892--16450063 Score: 245
Period size: 61 Copynumber: 2.8 Consensus size: 61
16449882 TAATTTTCTG
* * *
16449892 CAGCTTTTAGAGCCAATTTAAACTTCACAGCGAATGATATTGGACTCAACAAACAACTTTC
1 CAGCTTTTAGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACTCAACAAACAACTTTC
* * *
16449953 CAGCTTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCAACAAATAACTTTC
1 CAGCTTTTAGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACTCAACAAACAACTTTC
* *
16450014 CAGTTTCATTAAGAGTCAATTTCAACTTTACAGCGAAGGATATTGGACTC
1 CAGCTT--TT-AGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACTC
16450064 GAAACGACAC
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
61 60 0.61
63 1 0.01
64 37 0.38
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (61 bp):
CAGCTTTTAGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACTCAACAAACAACTTTC
Found at i:16450511 original size:36 final size:36
Alignment explanation
Indices: 16450457--16450578 Score: 145
Period size: 36 Copynumber: 3.4 Consensus size: 36
16450447 TTTGAAAAAT
* *
16450457 GTTTCCCTTAAAATGAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
* * *
16450493 GTTTCCCTTGGAACGAATTTCGTCTCTCTTGAGTTA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
* * * * *
16450529 GTTTCCCTTGCAACAAATTTTATCTCCCTTGAGACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
*
16450565 GTTTCTCTTGAAAC
1 GTTTCCCTTGAAAC
16450579 ATAAACTTTG
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATA
Found at i:16450603 original size:29 final size:31
Alignment explanation
Indices: 16450557--16450639 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
16450547 TTTATCTCCC
* * *
16450557 TTGAGACAGTTTCTCTTGAAACA-TAAA-CT
1 TTGAAACAGTTTCCCTTGAAACACAAAATCT
16450586 TTGAAAACA-TTTCCCTTGAAACACAAAATCT
1 TTG-AAACAGTTTCCCTTGAAACACAAAATCT
* *
16450617 TTGAATCAGTTCCCCTTGAAACA
1 TTGAAACAGTTTCCCTTGAAACA
16450640 AGTTTTGTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 16 0.36
30 11 0.24
31 18 0.40
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (31 bp):
TTGAAACAGTTTCCCTTGAAACACAAAATCT
Found at i:16450670 original size:36 final size:36
Alignment explanation
Indices: 16450623--16450741 Score: 108
Period size: 36 Copynumber: 3.5 Consensus size: 36
16450613 ATCTTTGAAT
*
16450623 CAGTTCCCCTTGAAACAAGTTTTGTCTCTCTTGAGA
1 CAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGA
** *
16450659 CAGTTTCCCTTGAAAC-A-----CCCACAT-TTGAGA
1 CAGTTTCCCTTGAAACAAGTTTTGTCTC-TCTTGAGA
** *
16450689 TTGTTTCCCTTGAAACATGTTTTGTCTCTCTTGAGA
1 CAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGA
*
16450725 CAGTTTCTCTTGAAACA
1 CAGTTTCCCTTGAAACA
16450742 CCAATCTTTG
Statistics
Matches: 62, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
30 22 0.35
31 1 0.02
35 2 0.03
36 37 0.60
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (36 bp):
CAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGA
Found at i:16450711 original size:66 final size:66
Alignment explanation
Indices: 16450595--16450943 Score: 273
Period size: 66 Copynumber: 5.2 Consensus size: 66
16450585 TTTGAAAACA
* * *
16450595 TTTCCCTTGAAACACAAAATCTTTGA-ATCAGTTCCCCTTGAAACAAGTTTTGTCTCTCTTGAGA
1 TTTCCCTTGAAACAC-CAATCTTTGAGAT-TGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGA
16450659 CAG
64 CAG
* *
16450662 TTTCCCTTGAAACACCCA-CATTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTCTCTTGAGAC
1 TTTCCCTTGAAACACCAATC-TTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGAC
16450726 AG
65 AG
* * * *
16450728 TTTCTCTTGAAACACCAATCTTTGAGATTGTTTCCCTTGAAAAAAGTTTTAGTTTCCCTTGAGAT
1 TTTCCCTTGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACAAGTTTT-GTCTCTCTTGAGA-
16450793 C-G
64 CAG
* * * * * *
16450795 TTTCTCATGAAACAACAACCAAACTTTGAGA-TGTTTCTCTTAAAACAAATCCTATT-T-TCT-T
1 TTTCCCTTG--A-AAC-ACCAATCTTTGAGATTGTTTCCCTTGAAACAAGT--T-TTGTCTCTCT
**
16450856 TGAGATTG
59 TGAGACAG
* * * * * *
16450864 TTTCTCATGAAACAACAAATATCTTTGAGATTGTTCCCCTTGCAAC-AGATTTTGTCTCTTTTGA
1 TTTCCCTTGAAAC-AC-CA-ATCTTTGAGATTGTTTCCCTTGAAACAAG-TTTTGTCTCTCTTGA
*
16450928 GATAG
62 GACAG
*
16450933 TTTCTCTTGAA
1 TTTCCCTTGAA
16450944 GCATCATCTA
Statistics
Matches: 234, Mismatches: 28, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
65 1 0.00
66 93 0.40
67 42 0.18
68 14 0.06
69 47 0.20
70 20 0.09
71 14 0.06
72 1 0.00
73 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (66 bp):
TTTCCCTTGAAACACCAATCTTTGAGATTGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACA
G
Found at i:16450894 original size:33 final size:33
Alignment explanation
Indices: 16450786--16450898 Score: 104
Period size: 33 Copynumber: 3.3 Consensus size: 33
16450776 TTAGTTTCCC
* *
16450786 TTGAGATCGTTTCTCATGAAACAACAACCA-AACT
1 TTGAGATTGTTTCTCATGAAACAACAA--ATATCT
* * * * *
16450820 TTGAGA-TGTTTCTCTTAAAACAAATCCTATTTTCT
1 TTGAGATTGTTTCTCATGAAAC-AA--CAAATATCT
16450855 TTGAGATTGTTTCTCATGAAACAACAAATATCT
1 TTGAGATTGTTTCTCATGAAACAACAAATATCT
16450888 TTGAGATTGTT
1 TTGAGATTGTT
16450899 CCCCTTGCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
33 29 0.47
34 8 0.13
35 10 0.16
36 15 0.24
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (33 bp):
TTGAGATTGTTTCTCATGAAACAACAAATATCT
Found at i:16451102 original size:43 final size:44
Alignment explanation
Indices: 16451048--16451143 Score: 113
Period size: 46 Copynumber: 2.2 Consensus size: 44
16451038 CCTGATCTCT
* *
16451048 TCATCAAGTAGGAGCCATG-TCAACCTTAGATAACCAACCGTCC
1 TCATCACGTAGGAACCATGTTCAACCTTAGATAACCAACCGTCC
* * * *
16451091 TCATCACGTAGGAACCGTGTTATCACCCTTAGATGACCTACCGTCC
1 TCATCACGTAGGAACCATG-T-TCAACCTTAGATAACCAACCGTCC
16451137 TCATCAC
1 TCATCAC
16451144 CTAACAACCG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 16 0.36
46 28 0.64
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (44 bp):
TCATCACGTAGGAACCATGTTCAACCTTAGATAACCAACCGTCC
Found at i:16451134 original size:46 final size:46
Alignment explanation
Indices: 16451071--16451164 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
16451061 GCCATGTCAA
* ** *
16451071 CCTTAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCAC
1 CCTTAGATAACCAACCGTCCTCATCACCTAACAACCGTGTCATCAC
* *
16451117 CCTTAGATGACCTACCGTCCTCATCACCTAACAACCGTGTCATCAC
1 CCTTAGATAACCAACCGTCCTCATCACCTAACAACCGTGTCATCAC
16451163 CC
1 CC
16451165 GACCTGACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (46 bp):
CCTTAGATAACCAACCGTCCTCATCACCTAACAACCGTGTCATCAC
Found at i:16451195 original size:40 final size:41
Alignment explanation
Indices: 16451084--16451198 Score: 108
Period size: 46 Copynumber: 2.7 Consensus size: 41
16451074 TAGATAACCA
* *
16451084 ACCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGACCT-
1 ACCGTCCTCATCACGTAGGAGCCGTGTCATCACCC------GACCTG
* ** *
16451130 ACCGTCCTCATCACCTAACAACCGTGTCATCACCCGACCTG
1 ACCGTCCTCATCACGTAGGAGCCGTGTCATCACCCGACCTG
16451171 ACC-TCCTCATCACGTAGGAGCCGTGTCA
1 ACCGTCCTCATCACGTAGGAGCCGTGTCA
16451199 ACCCTTAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
40 26 0.43
41 3 0.05
46 31 0.52
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (41 bp):
ACCGTCCTCATCACGTAGGAGCCGTGTCATCACCCGACCTG
Found at i:16451372 original size:3 final size:3
Alignment explanation
Indices: 16451364--16451400 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
16451354 TATCATTAAA
*
16451364 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16451401 TAAAACCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16454410 original size:30 final size:30
Alignment explanation
Indices: 16454344--16454429 Score: 149
Period size: 28 Copynumber: 2.9 Consensus size: 30
16454334 AATCAAAATA
*
16454344 TACCACTAATTGAATTGTCCTTATTAAACG
1 TACCACTAGTTGAATTGTCCTTATTAAACG
16454374 --CCACTAGTTGAATTGTCCTTATTAAACG
1 TACCACTAGTTGAATTGTCCTTATTAAACG
16454402 TACCACTAGTTGAATTGTCCTTATTAAA
1 TACCACTAGTTGAATTGTCCTTATTAAA
16454430 TAAATATTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
28 27 0.51
30 26 0.49
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (30 bp):
TACCACTAGTTGAATTGTCCTTATTAAACG
Found at i:16455084 original size:18 final size:18
Alignment explanation
Indices: 16455059--16455106 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
16455049 ATAAAAATAT
16455059 TTATTTATTTTTT-AAAA
1 TTATTTATTTTTTGAAAA
16455076 TTCATTTATTTATTTGAAAA
1 TT-ATTTATTT-TTTGAAAA
16455096 TT-TTTATTTTT
1 TTATTTATTTTT
16455107 AAATTGCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.14
18 15 0.54
19 3 0.11
20 6 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTTATTTTTTGAAAA
Found at i:16455104 original size:22 final size:19
Alignment explanation
Indices: 16455052--16455104 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 19
16455042 TAATATTATA
16455052 AAAATATTTATTTATTTTTT
1 AAAAT-TTTATTTATTTTTT
*
16455072 AAAA-TTCATTTATTTATTT
1 AAAATTTTATTTATTT-TTT
16455091 GAAAATTTTTATTT
1 -AAAA-TTTTATTT
16455105 TTAAATTGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 10 0.37
19 3 0.11
20 8 0.30
22 6 0.22
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AAAATTTTATTTATTTTTT
Found at i:16455231 original size:16 final size:16
Alignment explanation
Indices: 16455178--16455235 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 16
16455168 AGTTCTGTGC
16455178 AATATTATTAAAATTAAAT
1 AATATT-TT-AAA-TAAAT
* *
16455197 AGATAATTTAAAAATAAT
1 A-ATATTTTAAATA-AAT
16455215 AATATTTTAAATAAAT
1 AATATTTTAAATAAAT
16455231 AATAT
1 AATAT
16455236 AATATAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 8 0.24
17 11 0.33
18 7 0.21
19 3 0.09
20 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AATATTTTAAATAAAT
Found at i:16455245 original size:24 final size:21
Alignment explanation
Indices: 16455192--16455325 Score: 91
Period size: 24 Copynumber: 6.2 Consensus size: 21
16455182 TTATTAAAAT
* *
16455192 TAAATAGATAATTT-AA-AAA
1 TAAATAAATATTTTAAATAAA
16455211 T-AAT-AATATTTTAAATAAA
1 TAAATAAATATTTTAAATAAA
*
16455230 TAATATAATATAATTTTCAA-AAA
1 TAA-ATAA-AT-ATTTTAAATAAA
*
16455253 TAAATAAATATTTTCATAATATTA
1 TAAATAAATATTTT-A-AATA-AA
*
16455277 TAAATAAATATTTTAGAATAATT
1 TAAATAAATATTTTA-AATAA-A
16455300 TAATATAAAT-TTTATAAATAAA
1 TAA-ATAAATATTT-TAAATAAA
16455322 TAAA
1 TAAA
16455326 AGTAATTATT
Statistics
Matches: 92, Mismatches: 9, Indels: 26
0.72 0.07 0.20
Matches are distributed among these distances:
17 6 0.07
18 5 0.05
19 5 0.05
20 6 0.07
21 5 0.05
22 10 0.11
23 25 0.27
24 30 0.33
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
TAAATAAATATTTTAAATAAA
Found at i:16455279 original size:42 final size:39
Alignment explanation
Indices: 16455199--16455283 Score: 93
Period size: 42 Copynumber: 2.1 Consensus size: 39
16455189 AATTAAATAG
16455199 ATAATTTAAAAATAATAATATTTTAAATAAATAATATAA
1 ATAATTTAAAAATAATAATATTTTAAATAAATAATATAA
* *
16455238 TATAATTTTCAAAAATAAATAAATATTTT-CAT-AATATTATAA
1 -ATAA-TTT-AAAAAT-AAT-AATATTTTAAATAAATAATATAA
16455280 ATAA
1 ATAA
16455284 ATATTTTAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
40 4 0.10
41 7 0.18
42 15 0.38
43 5 0.13
44 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (39 bp):
ATAATTTAAAAATAATAATATTTTAAATAAATAATATAA
Found at i:16455757 original size:9 final size:9
Alignment explanation
Indices: 16455743--16455767 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16455733 AATGATGTGA
16455743 AAATTAAAT
1 AAATTAAAT
16455752 AAATTAAAT
1 AAATTAAAT
16455761 AAATTAA
1 AAATTAA
16455768 CATGTCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATTAAAT
Found at i:16456347 original size:18 final size:18
Alignment explanation
Indices: 16456324--16456364 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16456314 TTTCCATAAA
16456324 ATTTTAAAATTATTATAT
1 ATTTTAAAATTATTATAT
* * *
16456342 ATTTTAAATTTTTTGTAT
1 ATTTTAAAATTATTATAT
16456360 ATTTT
1 ATTTT
16456365 TTTATTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTAAAATTATTATAT
Found at i:16457390 original size:20 final size:20
Alignment explanation
Indices: 16457365--16457402 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16457355 ACCATCTGCA
*
16457365 AACAAATAATATGTGAAACT
1 AACAAATAATATGCGAAACT
16457385 AACAAATAATATGCGAAA
1 AACAAATAATATGCGAAA
16457403 TATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (20 bp):
AACAAATAATATGCGAAACT
Found at i:16460118 original size:17 final size:17
Alignment explanation
Indices: 16460098--16460134 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
16460088 GGAAGTCAAC
16460098 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
16460115 GGTCAACGGTCGGGTTG
1 GGTCAACGGTCGGGTCG
16460132 GGT
1 GGT
16460135 TGGTCGGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.19, G:0.49, T:0.22
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:16460141 original size:14 final size:14
Alignment explanation
Indices: 16460122--16460151 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16460112 TCGGGTCAAC
*
16460122 GGTCGGGTTGGGTT
1 GGTCGGGTCGGGTT
16460136 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
16460150 GG
1 GG
16460152 GTCAGTCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.60, T:0.30
Consensus pattern (14 bp):
GGTCGGGTCGGGTT
Found at i:16460159 original size:19 final size:19
Alignment explanation
Indices: 16460105--16460160 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
16460095 AACGGTCAAC
* *
16460105 GGTCGGGTCGGGTCA-AC-
1 GGTCGGGTTGGGTCAGTCG
**
16460122 GGTCGGGTTGGGTTGGTCG
1 GGTCGGGTTGGGTCAGTCG
16460141 GGTCGGGTTGGGTCAGTCG
1 GGTCGGGTTGGGTCAGTCG
16460160 G
1 G
16460161 TCAGGTCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 12 0.39
18 1 0.03
19 18 0.58
ACGTcount: A:0.05, C:0.16, G:0.54, T:0.25
Consensus pattern (19 bp):
GGTCGGGTTGGGTCAGTCG
Found at i:16460190 original size:19 final size:19
Alignment explanation
Indices: 16460166--16460257 Score: 105
Period size: 19 Copynumber: 4.7 Consensus size: 19
16460156 GTCGGTCAGG
* *
16460166 TCAGACCGGTTAAACCGGT
1 TCAGACCGGTCAAAACGGT
16460185 TCAGACCGGTCAAAACGGT
1 TCAGACCGGTCAAAACGGT
*
16460204 TCAGACCGGTCAAAACGAT
1 TCAGACCGGTCAAAACGGT
16460223 TC-GAACCCGGTCAAAACGGT
1 TCAG-A-CCGGTCAAAACGGT
* *
16460243 TGAAAACCGGTCAAA
1 T-CAGACCGGTCAAA
16460258 CCAGTTTCCA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
18 1 0.02
19 38 0.60
20 23 0.37
21 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAAACGGT
Found at i:16460194 original size:10 final size:10
Alignment explanation
Indices: 16460166--16460213 Score: 55
Period size: 9 Copynumber: 5.0 Consensus size: 10
16460156 GTCGGTCAGG
16460166 TCAGACCGGT
1 TCAGACCGGT
*
16460176 T-AAACCGGT
1 TCAGACCGGT
16460185 TCAGACCGG-
1 TCAGACCGGT
* *
16460194 TCAAAACGGT
1 TCAGACCGGT
16460204 TCAGACCGGT
1 TCAGACCGGT
16460214 CAAAACGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:16467458 original size:17 final size:17
Alignment explanation
Indices: 16467438--16467490 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
16467428 GGAAGTCAAC
16467438 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
16467455 GGTCAACGGTCGGGTTG
1 GGTCAACGGTCGGGTCG
16467472 GG---ACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
16467486 GGTCA
1 GGTCA
16467491 GACCGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 13 0.42
17 18 0.58
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:16467533 original size:19 final size:19
Alignment explanation
Indices: 16467511--16467560 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
16467501 ACCAGTTCAG
16467511 ACCGGGCAAAACGATTCGA
1 ACCGGGCAAAACGATTCGA
16467530 ACCGGGCAAAACGATTCGA
1 ACCGGGCAAAACGATTCGA
*
16467549 ACCGGTCAAAAC
1 ACCGGGCAAAAC
16467561 CAGTTGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.28, G:0.24, T:0.10
Consensus pattern (19 bp):
ACCGGGCAAAACGATTCGA
Found at i:16469754 original size:16 final size:16
Alignment explanation
Indices: 16469733--16469766 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16469723 TTACTATTCA
*
16469733 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
16469749 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
16469765 CG
1 CG
16469767 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:16479574 original size:12 final size:11
Alignment explanation
Indices: 16479557--16479590 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
16479547 TTAATTGTAA
16479557 AAATTAAAAGTT
1 AAATTAAAA-TT
16479569 AAATTAAAATT
1 AAATTAAAATT
16479580 AAATTTAAAAT
1 AAA-TTAAAAT
16479591 CCAATCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:16479816 original size:23 final size:24
Alignment explanation
Indices: 16479789--16479838 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
16479779 AAAAGAGAAA
*
16479789 TAAATAAAAAA-TGAAGAAAATGT
1 TAAATAAAAAATTGAAGAAAATAT
16479812 TAAATAAAAAATTGAAGAAAATAT
1 TAAATAAAAAATTGAAGAAAATAT
16479836 TAA
1 TAA
16479839 TTTCTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (24 bp):
TAAATAAAAAATTGAAGAAAATAT
Found at i:16481226 original size:12 final size:12
Alignment explanation
Indices: 16481209--16481239 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16481199 AACTGATATG
*
16481209 TAGCGGTGTTTT
1 TAGCGGCGTTTT
16481221 TAGCGGCGTTTT
1 TAGCGGCGTTTT
16481233 TAGCGGC
1 TAGCGGC
16481240 ATTTGGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.16, G:0.35, T:0.39
Consensus pattern (12 bp):
TAGCGGCGTTTT
Found at i:16481503 original size:40 final size:41
Alignment explanation
Indices: 16481443--16481575 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 41
16481433 ATAAATTAGC
* * *
16481443 GGCGTTGATACCATAAACGCCGTAATAAATTAACATATAGT
1 GGCGTTTATACCACAAACGCCGTAATAGATTAACATATAGT
*
16481484 GGCGTTT-TAGCCA-AAACGCCGTAATAGATCGGTAA-AT-TAGC
1 GGCGTTTATA-CCACAAACGCCGTAATAGAT---TAACATATAGT
*
16481525 GGCGTTTATACCACAAACGCCGCAATAGATTACACATATAGT
1 GGCGTTTATACCACAAACGCCGTAATAGATTA-ACATATAGT
*
16481567 GGCATTTAT
1 GGCGTTTAT
16481576 TCTTAAAATG
Statistics
Matches: 77, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
39 2 0.03
40 18 0.23
41 24 0.31
42 30 0.39
43 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (41 bp):
GGCGTTTATACCACAAACGCCGTAATAGATTAACATATAGT
Found at i:16481511 original size:82 final size:83
Alignment explanation
Indices: 16481416--16481569 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 83
16481406 TTTGTTAACC
* *
16481416 AACGCCGCAATAGATCGATAAATTAGCGGCGTTGATACCATAAACGCCGTAATAAATTA-ACATA
1 AACGCCGCAATAGATCGATAAATTAGCGGCGTTGATACCACAAACGCCGCAATAAATTACACATA
16481480 TAGTGGCGTTTTAGCCAA
66 TAGTGGCGTTTTAGCCAA
* * * *
16481498 AACGCCGTAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTACACATA
1 AACGCCGCAATAGATCGATAAATTAGCGGCGTTGATACCACAAACGCCGCAATAAATTACACATA
16481563 TAGTGGC
66 TAGTGGC
16481570 ATTTATTCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
82 53 0.82
83 12 0.18
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (83 bp):
AACGCCGCAATAGATCGATAAATTAGCGGCGTTGATACCACAAACGCCGCAATAAATTACACATA
TAGTGGCGTTTTAGCCAA
Found at i:16481552 original size:42 final size:40
Alignment explanation
Indices: 16481416--16481554 Score: 149
Period size: 42 Copynumber: 3.4 Consensus size: 40
16481406 TTTGTTAACC
*
16481416 AACGCCGCAATAGATCGATAAATTAGCGGCGTTGATACCATA
1 AACGCCGCAATAGATCG-TAAATTAGCGGCGTTTATACCA-A
* * *
16481458 AACGCCGTAATAAAT--TAACATATAGTGGCGTTT-TAGCCAA
1 AACGCCGCAATAGATCGTAA-AT-TAGCGGCGTTTATA-CCAA
*
16481498 AACGCCGTAATAGATCGGTAAATTAGCGGCGTTTATACCACA
1 AACGCCGCAATAGATC-GTAAATTAGCGGCGTTTATACCA-A
16481540 AACGCCGCAATAGAT
1 AACGCCGCAATAGAT
16481555 TACACATATA
Statistics
Matches: 82, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
39 3 0.04
40 19 0.23
41 25 0.30
42 32 0.39
43 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
AACGCCGCAATAGATCGTAAATTAGCGGCGTTTATACCAA
Found at i:16481649 original size:83 final size:81
Alignment explanation
Indices: 16481539--16481690 Score: 184
Period size: 83 Copynumber: 1.9 Consensus size: 81
16481529 TTTATACCAC
* *
16481539 AAACGCCGCAATAGATTACACATATAGTGGCATTTATTCTTA-AAATGACGCAATAGTGATAATA
1 AAACGCCGCAATAGATTACACATATAGTGGCATTT-TT-TAACAAATGACACAATAGTG-TAATA
16481603 AATAGTGTCATTTTTAAAT
63 AATAGTGTCATTTTTAAAT
* * * *
16481622 AAACGCCGCAATAGTTTTA-ATCA-ATAGTGGCGTTTTTTAACAAATGCCACAATAGTGTAATCA
1 AAACGCCGCAATAG-ATTACA-CATATAGTGGCATTTTTTAACAAATGACACAATAGTGTAATAA
16481685 ATAGTG
64 ATAGTG
16481691 GCGTTTTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
81 13 0.22
82 16 0.27
83 26 0.43
84 5 0.08
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (81 bp):
AAACGCCGCAATAGATTACACATATAGTGGCATTTTTTAACAAATGACACAATAGTGTAATAAAT
AGTGTCATTTTTAAAT
Found at i:16481700 original size:41 final size:40
Alignment explanation
Indices: 16481589--16481699 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 40
16481579 TAAAATGACG
* * * * * *
16481589 CAATAGTGATAATAAATAGTGTCATTTTTAAATAAACGCCG
1 CAATAGTG-TAATCAATAGTGGCGTTTTTTAACAAACGCCA
* *
16481630 CAATAGTTTTAATCAATAGTGGCGTTTTTTAACAAATGCCA
1 CAATAG-TGTAATCAATAGTGGCGTTTTTTAACAAACGCCA
16481671 CAATAGTGTAATCAATAGTGGCGTTTTTT
1 CAATAGTGTAATCAATAGTGGCGTTTTTT
16481700 TGTATAAACA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
40 22 0.37
41 37 0.62
42 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (40 bp):
CAATAGTGTAATCAATAGTGGCGTTTTTTAACAAACGCCA
Found at i:16482522 original size:83 final size:81
Alignment explanation
Indices: 16482257--16482544 Score: 308
Period size: 83 Copynumber: 3.5 Consensus size: 81
16482247 GCTATAGGTA
* * *
16482257 CGTACTTTAGTGGCGTTTTTATACAAACGTCGCTATATACTAGTACTTTAGTGGCGTTTCTATAC
1 CGTACTTTAGTGGCGTTTTTATATAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTT-TATAC
* * *
16482322 AAACGCCACTACATACT
65 AAACGCCGCTAAAGACT
* * * * * * *
16482339 CATAATTTAGTGGCGTTTTGAATCTAAACGCTGCTATAAACTCGTACTTTAGTGGCGTTTTGA-A
1 CGTACTTTAGTGGCGTTTT-TATATAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTT-ATA
16482403 CGAAAACGCCGCTAAAGACT
64 C--AAACGCCGCTAAAGACT
** *
16482423 CGTACTTTAGCAGCGTTTTTATATAAACGCCGCTATAGACTAGTACTTTAGTGGCGAATTTATAC
1 CGTACTTTAGTGGCGTTTTTATATAAACGCCGCTATAGACTAGTACTTTAGTGGCG-TTTTATAC
* * *
16482488 AAATGCCGGTATAGACT
65 AAACGCCGCTAAAGACT
* * *
16482505 CGTACCCTTAGTGGCGTTTTTAGATAAACGCCGCAATAGA
1 CGTA-CTTTAGTGGCGTTTTTATATAAACGCCGCTATAGA
16482545 TATAATATTT
Statistics
Matches: 169, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
82 38 0.22
83 97 0.57
84 34 0.20
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (81 bp):
CGTACTTTAGTGGCGTTTTTATATAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTATACA
AACGCCGCTAAAGACT
Found at i:16482544 original size:42 final size:41
Alignment explanation
Indices: 16482240--16482544 Score: 247
Period size: 41 Copynumber: 7.4 Consensus size: 41
16482230 TTATATCCAG
* * * *
16482240 AAACGACGCTATAG-GTACGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACT-CGTACTTTAGTGGCGTTTTTAGAT
* * * * * *
16482281 AAACGTCGCTATATACTAGTACTTTAGTGGCGTTTCTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAGAT
* * * * * *
16482322 AAACGCCACTACATACTCATAATTTAGTGGCGTTTTGA-ATCT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAGA--T
* * *
16482364 AAACGCTGCTATAAACTCGTACTTTAGTGGCGTTTTGAACGA-
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TA-GAT
* ** *
16482406 AAACGCCGCTAAAGACTCGTACTTTAGCAGCGTTTTTATAT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAGAT
* ** * *
16482447 AAACGCCGCTATAGACTAGTACTTTAGTGGCGAATTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAGAT
* * *
16482488 AAATGCCGGTATAGACTCGTACCCTTAGTGGCGTTTTTAGAT
1 AAACGCCGCTATAGACTCGTA-CTTTAGTGGCGTTTTTAGAT
*
16482530 AAACGCCGCAATAGA
1 AAACGCCGCTATAGA
16482545 TATAATATTT
Statistics
Matches: 210, Mismatches: 46, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
40 2 0.01
41 117 0.56
42 89 0.42
43 1 0.00
45 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (41 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTAGAT
Found at i:16482562 original size:166 final size:165
Alignment explanation
Indices: 16482257--16482565 Score: 356
Period size: 166 Copynumber: 1.9 Consensus size: 165
16482247 GCTATAGGTA
** * * *
16482257 CGTACTTTAGTGGCGTTTTTATACAAACGTCGCTATATACTAGTACTTTAGTGGCGTTTCTATAC
1 CGTACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGTGGCGATTCTATAC
* * * * **
16482322 AAACGCCACTACATACTCATAATTTAGTGGCGTTTTGAATCTAAACGCTGCTATAAACTCGTACT
66 AAACGCCACTACAGACTCATAACTTAGTGGCGTTTTGAA-CTAAACGCCGCAATAAACTAATACT
16482387 TTAGTGGCGTTTTGAACGAAAACGCCGCTAAAGACT
130 TTAGTGGCGTTTTGAACGAAAACGCCGCTAAAGACT
*
16482423 CGTACTTTAGCAGCGTTTTTATATAAACGCCGCTATAGACTAGTACTTTAGTGGCGAATT-TATA
1 CGTACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGTGGCG-ATTCTATA
* ** * * * *
16482487 CAAATGCCGGTATAGACTCGTACCCTTAGTGGCGTTTTTAGA-TAAACGCCGCAATAGATA-TAA
65 CAAACGCCACTACAGACTCATA-ACTTAGTGGCGTTTTGA-ACTAAACGCCGCAATA-A-ACTAA
*
16482550 TA-TTTTGTGGCGTTTT
126 TACTTTAGTGGCGTTTT
16482566 TTAAGATAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
166 96 0.81
167 20 0.17
168 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (165 bp):
CGTACTTTAGCAGCGTTTTTATACAAACGCCGCTATAGACTAGTACTTTAGTGGCGATTCTATAC
AAACGCCACTACAGACTCATAACTTAGTGGCGTTTTGAACTAAACGCCGCAATAAACTAATACTT
TAGTGGCGTTTTGAACGAAAACGCCGCTAAAGACT
Found at i:16482586 original size:43 final size:42
Alignment explanation
Indices: 16482515--16482605 Score: 139
Period size: 43 Copynumber: 2.2 Consensus size: 42
16482505 CGTACCCTTA
*
16482515 GTGGCG-TTTTTAGATAAACGCCGCAATAGATATAATATTTT
1 GTGGCGTTTTTTAGATAAACACCGCAATAGATATAATATTTT
*
16482556 GTGGCGTTTTTTAAGATAAACACCGTAATAGATATAATATTTT
1 GTGGCGTTTTTT-AGATAAACACCGCAATAGATATAATATTTT
*
16482599 GCGGCGT
1 GTGGCGT
16482606 AAAAACGCCG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 6 0.13
42 5 0.11
43 34 0.76
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (42 bp):
GTGGCGTTTTTTAGATAAACACCGCAATAGATATAATATTTT
Found at i:16488737 original size:21 final size:21
Alignment explanation
Indices: 16488711--16488755 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16488701 GATTTCTGGG
* *
16488711 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
16488732 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
16488753 CAA
1 CAA
16488756 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:16489397 original size:23 final size:24
Alignment explanation
Indices: 16489354--16489400 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
16489344 ATATGGCATG
*
16489354 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
16489378 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
16489401 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:16489654 original size:31 final size:31
Alignment explanation
Indices: 16489616--16489771 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
16489606 AGGGTCGAGG
16489616 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
16489647 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* **
16489678 GTTTACCTATGTTCTTCGGAACATACAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
16489709 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
16489740 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
16489771 G
1 G
16489772 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:16491194 original size:23 final size:24
Alignment explanation
Indices: 16491151--16491197 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
16491141 ATATGGCATG
*
16491151 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
16491175 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
16491198 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:16491451 original size:31 final size:31
Alignment explanation
Indices: 16491413--16491568 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
16491403 AGGGTCGAGG
16491413 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
16491444 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* **
16491475 GTTTACCTATGTTCTTCGGAACATACAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
16491506 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
16491537 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
16491568 G
1 G
16491569 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:16495385 original size:23 final size:24
Alignment explanation
Indices: 16495342--16495388 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
16495332 ATATGGCATG
*
16495342 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
16495366 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
16495389 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:16495642 original size:31 final size:31
Alignment explanation
Indices: 16495604--16495759 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
16495594 AGGGTCGAGG
16495604 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
16495635 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* **
16495666 GTTTACCTATGTTCTTCGGAACATACAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
16495697 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
16495728 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
16495759 G
1 G
16495760 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:16499884 original size:21 final size:21
Alignment explanation
Indices: 16499824--16499884 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
16499814 CACTAGTAGA
* * *
16499824 AGCAGAGAAAGAAGCAGCGGC
1 AGCACAGAGAGAAGCAGCAGC
*
16499845 AGCACAGAGAGAAACAGCAGC
1 AGCACAGAGAGAAGCAGCAGC
* *
16499866 ATCACAGAGAGAAGTAGCA
1 AGCACAGAGAGAAGCAGCA
16499885 TATCAGCAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.46, C:0.20, G:0.31, T:0.03
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAGCAGC
Found at i:16500390 original size:43 final size:43
Alignment explanation
Indices: 16500326--16500660 Score: 228
Period size: 43 Copynumber: 7.7 Consensus size: 43
16500316 ACCTACTACG
* *
16500326 GCCGCTAAACATCATA-ACATATTGCGGCGTTTATCTGAGAAAC
1 GCCGCTAAATATCA-ACACATATTGCGGCGTTTATATGAGAAAC
* * * * *
16500369 GCTGCTAAATATTAACACATATTGCGGCATTTTTATGATAAAC
1 GCCGCTAAATATCAACACATATTGCGGCGTTTATATGAGAAAC
* ** * *
16500412 GCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAAAAAAAAAAAG
1 GCCGCTAAATATCAACACATATTGCGGCG--TTTAT----ATGAGAAAC
* * * * * *
16500461 GCCACTAAATATCAACACTTATTGCGGTGTTTGT-TGAAAAAT
1 GCCGCTAAATATCAACACATATTGCGGCGTTTATATGAGAAAC
** ** * * *
16500503 GCTACTAAATATCAACACATATTGCGGTATTTTTATTACAAAC
1 GCCGCTAAATATCAACACATATTGCGGCGTTTATATGAGAAAC
* * * *
16500546 GCCGCTAAATATCAACACCTATTGCGGCGTTTTTATAACAAAC
1 GCCGCTAAATATCAACACATATTGCGGCGTTTATATGAGAAAC
* * * * * * *
16500589 CCCACTAAATATCAACACCTATTGCGACGTTTTTCA-CACAAAC
1 GCCGCTAAATATCAACACATATTGCGGCGTTTAT-ATGAGAAAC
*
16500632 GCCGCTAAATATCAATA-ACTATTGCGGCG
1 GCCGCTAAATATCAACACA-TATTGCGGCG
16500661 CTTTTTGTGA
Statistics
Matches: 237, Mismatches: 45, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
42 36 0.15
43 161 0.68
44 1 0.00
45 4 0.02
47 4 0.02
49 31 0.13
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (43 bp):
GCCGCTAAATATCAACACATATTGCGGCGTTTATATGAGAAAC
Found at i:16501103 original size:29 final size:29
Alignment explanation
Indices: 16501058--16501115 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
16501048 GTGTTGGCCG
*
16501058 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
16501087 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
16501116 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:16501168 original size:10 final size:10
Alignment explanation
Indices: 16501155--16501205 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 10
16501145 ACACGCTGGG
16501155 CATCCGAGGC
1 CATCCGAGGC
16501165 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
16501179 CATCCGAGAG-
1 CATCCGAG-GC
16501189 CATCCGAGGC
1 CATCCGAGGC
16501199 CATCCGA
1 CATCCGA
16501206 CCGAGGCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
9 1 0.03
10 21 0.60
11 3 0.09
13 2 0.06
14 8 0.23
ACGTcount: A:0.24, C:0.39, G:0.27, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:16501177 original size:14 final size:14
Alignment explanation
Indices: 16501158--16501224 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
16501148 CGCTGGGCAT
16501158 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
16501172 CCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
16501191 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
16501206 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
16501220 ACGAG
1 CCGAG
16501225 CTATGCGAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 30 0.65
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 12 0.26
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:16501192 original size:34 final size:36
Alignment explanation
Indices: 16501154--16501242 Score: 137
Period size: 34 Copynumber: 2.5 Consensus size: 36
16501144 AACACGCTGG
16501154 GCATCCGAGGCCATCCGACCGAGGCCATCCG-A-GA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA
16501188 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA
* *
16501224 GCTATGCGAGGGCATCCGA
1 GC-ATCCGAGGCCATCCGA
16501243 GGGCAACCGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
34 31 0.62
35 1 0.02
36 4 0.08
37 14 0.28
ACGTcount: A:0.24, C:0.36, G:0.30, T:0.10
Consensus pattern (36 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA
Found at i:16501219 original size:10 final size:10
Alignment explanation
Indices: 16501172--16501205 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
16501162 GGCCATCCGA
16501172 CCGAGGCCAT
1 CCGAGGCCAT
16501182 CCGAGAG-CAT
1 CCGAG-GCCAT
16501192 CCGAGGCCAT
1 CCGAGGCCAT
16501202 CCGA
1 CCGA
16501206 CCGAGGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:16501258 original size:33 final size:33
Alignment explanation
Indices: 16501206--16501286 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
16501196 GGCCATCCGA
* * * *
16501206 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
16501239 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
16501272 CCGAGGG-AAGCCGAG
1 CCGAGGGCAA-CCGAG
16501287 AGGGTAGGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 2 0.05
33 41 0.95
ACGTcount: A:0.26, C:0.27, G:0.38, T:0.09
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:16501338 original size:29 final size:29
Alignment explanation
Indices: 16501292--16501347 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
16501282 CCGAGAGGGT
*
16501292 AGGTCGCCCGGAGTGCATAGCGACCTACA
1 AGGTCGCCCGGAGGGCATAGCGACCTACA
*
16501321 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATAGCGACCTA
16501348 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATAGCGACCTACA
Found at i:16501910 original size:17 final size:17
Alignment explanation
Indices: 16501890--16501933 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
16501880 TATATTTTTT
16501890 TATATTTTTAAAATTTA
1 TATATTTTTAAAATTTA
16501907 TATATTTTTAAAATTTA
1 TATATTTTTAAAATTTA
16501924 TATATTTTTA
1 TATATTTTTA
16501934 CATGAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTTTTAAAATTTA
Found at i:16510475 original size:25 final size:25
Alignment explanation
Indices: 16510430--16510478 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
16510420 TTATAAGTAA
*
16510430 TTAATTTTTTTTTTCTATAAAATTCT
1 TTAATTTATTTTTTC-ATAAAATTCT
16510456 TTAAGTTTATTTTTTC-TAAAATT
1 TTAA-TTTATTTTTTCATAAAATT
16510479 TTATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 4 0.19
27 10 0.48
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (25 bp):
TTAATTTATTTTTTCATAAAATTCT
Found at i:16510490 original size:26 final size:26
Alignment explanation
Indices: 16510430--16510478 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
16510420 TTATAAGTAA
16510430 TTAATTTT-TTTTTTCTATAAAATTCT
1 TTAATTTTATTTTTTC-ATAAAATTCT
*
16510456 TTAAGTTTATTTTTTC-TAAAATT
1 TTAATTTTATTTTTTCATAAAATT
16510479 TTATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 7 0.33
27 7 0.33
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (26 bp):
TTAATTTTATTTTTTCATAAAATTCT
Found at i:16510803 original size:2 final size:2
Alignment explanation
Indices: 16510796--16510826 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16510786 TGTCAACGTG
16510796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16510827 CCAATTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16511542 original size:3 final size:3
Alignment explanation
Indices: 16511534--16511562 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16511524 TTATTCCCTT
16511534 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16511563 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16512872 original size:23 final size:23
Alignment explanation
Indices: 16512819--16512881 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
16512809 TATCAACACA
* *
16512819 ATAAATAGATAAGATTAAGCAAAG
1 ATAAATAAATAAGA-TAACCAAAG
*
16512843 ATAAATAAATAAGATAACCAATG
1 ATAAATAAATAAGATAACCAAAG
16512866 ATAAATAAATAA-ATAA
1 ATAAATAAATAAGATAA
16512882 ATACATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 4 0.11
23 19 0.53
24 13 0.36
ACGTcount: A:0.63, C:0.05, G:0.10, T:0.22
Consensus pattern (23 bp):
ATAAATAAATAAGATAACCAAAG
Found at i:16520463 original size:227 final size:230
Alignment explanation
Indices: 16520014--16520471 Score: 895
Period size: 227 Copynumber: 2.0 Consensus size: 230
16520004 TATTTCAGTT
16520014 ATAAAAAAGGGAGGGAGAGAGGCCATCCAATGCATGCAGAAGAATAATAATAAAAAACTATAGTG
1 ATAAAAAAGGGAGGGAGAGAGGCCATCCAATGCATGCAGAAGAATAATAATAAAAAACTATAGTG
16520079 CAAACTTAGCATACAAAATAATTTCATAACTTGCCGAGTTATTTAGATTTACCCGGTTACATATG
66 CAAACTTAGCATACAAAATAATTTCATAACTTGCCGAGTTATTTAGATTTACCCGGTTACATATG
16520144 TCCACAAGTGAAAGCCCCAACCAGTAAGCACCTTGAACCCAAAAGAAATAACTACGAGACAACAG
131 TCCACAAGTGAAAGCCCCAACCAGTAAGCACCTTGAACCCAAAAGAAATAACTACGAGACAACAG
16520209 ATATTGATTTTTGAGAGGAAGTGCAGGCAAGAACA
196 ATATTGATTTTTGAGAGGAAGTGCAGGCAAGAACA
16520244 ATAAAAAA-GG-GGGAGAGAGGCCATCCAATGCATGCAGAAGAATAATAATAAAAAACTATAGTG
1 ATAAAAAAGGGAGGGAGAGAGGCCATCCAATGCATGCAGAAGAATAATAATAAAAAACTATAGTG
16520307 CAAACTTAGCATACAAAATAATTTCATAACTTGCCGAGTTATTTAGATTTA-CCGGTTACATATG
66 CAAACTTAGCATACAAAATAATTTCATAACTTGCCGAGTTATTTAGATTTACCCGGTTACATATG
16520371 TCCACAAGTGAAAGCCCCAACCAGTAAGCACCTTGAACCCAAAAGAAATAACTACGAGACAACAG
131 TCCACAAGTGAAAGCCCCAACCAGTAAGCACCTTGAACCCAAAAGAAATAACTACGAGACAACAG
16520436 ATATTGATTTTTGAGAGGAAGTGCAGGCAAGAACA
196 ATATTGATTTTTGAGAGGAAGTGCAGGCAAGAACA
16520471 A
1 A
16520472 CTTTAAGTTA
Statistics
Matches: 228, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
227 114 0.50
228 104 0.46
229 2 0.01
230 8 0.04
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (230 bp):
ATAAAAAAGGGAGGGAGAGAGGCCATCCAATGCATGCAGAAGAATAATAATAAAAAACTATAGTG
CAAACTTAGCATACAAAATAATTTCATAACTTGCCGAGTTATTTAGATTTACCCGGTTACATATG
TCCACAAGTGAAAGCCCCAACCAGTAAGCACCTTGAACCCAAAAGAAATAACTACGAGACAACAG
ATATTGATTTTTGAGAGGAAGTGCAGGCAAGAACA
Found at i:16524101 original size:21 final size:21
Alignment explanation
Indices: 16524075--16524115 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
16524065 ATATATGTGA
16524075 TATGTGGTCCTTCGGGACATC
1 TATGTGGTCCTTCGGGACATC
16524096 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
16524116 TTCTACGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATC
Found at i:16524131 original size:23 final size:21
Alignment explanation
Indices: 16524080--16524137 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
16524070 TGTGATATGT
* *
16524080 GGTCCTTCGGGACATCTATGT
1 GGTCCTTCGGGACATCTACGC
16524101 GGTCCTTCGGGACATTTCTACGC
1 GGTCCTTCGGGACA--TCTACGC
*
16524124 GGTTCTTCGGGACA
1 GGTCCTTCGGGACA
16524138 AATTCATATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 14 0.44
23 18 0.56
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31
Consensus pattern (21 bp):
GGTCCTTCGGGACATCTACGC
Found at i:16528179 original size:22 final size:23
Alignment explanation
Indices: 16528126--16528179 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
16528116 TCGATTCCCT
16528126 AAAGGAGGGAATCGGTTCCCATTC
1 AAAGG-GGGAATCGGTTCCCATTC
*
16528150 AAAGGGGGAATCGGTTCCCCTTC
1 AAAGGGGGAATCGGTTCCCATTC
16528173 -AAGGGGG
1 AAAGGGGG
16528180 TATTGATTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 7 0.24
23 17 0.59
24 5 0.17
ACGTcount: A:0.26, C:0.20, G:0.35, T:0.19
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:16528189 original size:22 final size:23
Alignment explanation
Indices: 16528109--16528190 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
16528099 CAGAACTCAT
*
16528109 GGGGGTATCGATTCCC--T-AAA
1 GGGGGAATCGATTCCCATTCAAA
*
16528129 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCATTCAAA
* *
16528153 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGATTCCCATTCAAA
* *
16528175 GGGGGTATTGATTCCC
1 GGGGGAATCGATTCCC
16528191 TCTGCACTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.04
21 12 0.23
22 15 0.29
23 18 0.35
24 5 0.10
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGATTCCCATTCAAA
Found at i:16528191 original size:21 final size:21
Alignment explanation
Indices: 16528109--16528191 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
16528099 CAGAACTCAT
* *
16528109 GGGGGTATCGATTCCC-TAAA
1 GGGGGAATCGATTCCCTTCAA
*
16528129 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCC-TTC-AA
*
16528153 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCCTTCAA
* *
16528175 GGGGGTATTGATTCCCT
1 GGGGGAATCGATTCCCT
16528192 CTGCACTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.04
21 16 0.31
22 12 0.23
23 15 0.29
24 7 0.13
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTCAA
Found at i:16535415 original size:20 final size:20
Alignment explanation
Indices: 16535369--16535408 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16535359 ATCATTTCCC
16535369 ATATTCACATGTACATATCA
1 ATATTCACATGTACATATCA
16535389 ATATTCACATGTACATATCA
1 ATATTCACATGTACATATCA
16535409 TTGTTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (20 bp):
ATATTCACATGTACATATCA
Found at i:16538408 original size:35 final size:35
Alignment explanation
Indices: 16538365--16538431 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
16538355 TTCATGTTCA
16538365 AAATTCCAAAACACTTCAATTACATTCTAAACTTC
1 AAATTCCAAAACACTTCAATTACATTCTAAACTTC
* *
16538400 AAATTCCAAAACACTTTAATTATATTCTAAAC
1 AAATTCCAAAACACTTCAATTACATTCTAAAC
16538432 CCTAAATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACTTC
Found at i:16538483 original size:35 final size:35
Alignment explanation
Indices: 16538435--16538511 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
16538425 TCTAAACCCT
16538435 AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATG
1 AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATG
* * * ** *
16538470 TAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATG
16538505 AAATTGA
1 AAATTGA
16538512 GGATTGTGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATG
Found at i:16539271 original size:98 final size:100
Alignment explanation
Indices: 16539103--16539282 Score: 276
Period size: 98 Copynumber: 1.8 Consensus size: 100
16539093 TAATCACCAT
* *
16539103 AATTTATTTTTATTGATATTTATGTATGTTGTGCATATGTTATTATTATTTTATTAATATATGAT
1 AATTTATTTTTATTGATATTTATGTATGATGTACATA-GTTATTATTATTTTATTAATATATGAT
16539168 TAAAATAGTATTAATTAAATTTTATTCAATTAATTA
65 TAAAATAGTATTAATTAAATTTTATTCAATTAATTA
*
16539204 AATTTA-TTTTATTGATATTTATGTATGATGTTACATA-TT-TTATTATTTTATTAATATATTAT
1 AATTTATTTTTATTGATATTTATGTATGATG-TACATAGTTATTATTATTTTATTAATATATGAT
* *
16539266 TAAAATATTATTTATTA
65 TAAAATAGTATTAATTA
16539283 CCCTACCTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
98 37 0.51
99 2 0.03
100 23 0.32
101 11 0.15
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (100 bp):
AATTTATTTTTATTGATATTTATGTATGATGTACATAGTTATTATTATTTTATTAATATATGATT
AAAATAGTATTAATTAAATTTTATTCAATTAATTA
Found at i:16539426 original size:15 final size:16
Alignment explanation
Indices: 16539408--16539439 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
16539398 ATTTAAATAC
16539408 ATTTTAATTA-ATATT
1 ATTTTAATTATATATT
16539423 ATTTTAATTATATATT
1 ATTTTAATTATATATT
16539439 A
1 A
16539440 ATAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTAATTATATATT
Found at i:16543564 original size:23 final size:23
Alignment explanation
Indices: 16543546--16543606 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
16543536 TTCGTATAAA
* *
16543546 TGCATCAAAGTGCCACGTAGAGT
1 TGCATCGAAGTGCCACGTAGAAT
*
16543569 TGCATCGAAGTGCCGCGTAGAAT
1 TGCATCGAAGTGCCACGTAGAAT
*
16543592 TGCACCGAAGTGCCA
1 TGCATCGAAGTGCCA
16543607 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCATCGAAGTGCCACGTAGAAT
Found at i:16551634 original size:21 final size:21
Alignment explanation
Indices: 16551587--16551647 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
16551577 CCCCCCATGA
16551587 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TGAAG
16551610 GGGAACCGATTCCCCCT-ACAG
1 GGGAACCGATTCCCCCTGA-AG
* *
16551631 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
16551648 TGGGGTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 18 0.51
23 16 0.46
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:16553633 original size:24 final size:23
Alignment explanation
Indices: 16553583--16553656 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
16553573 GCTTCAACTT
* *
16553583 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
16553606 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
16553630 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
16553653 TTTG
1 TTTG
16553657 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:16558490 original size:2 final size:2
Alignment explanation
Indices: 16558477--16558516 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
16558467 TATTCGATCA
*
16558477 AT AT AA AT AT AT AT 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 AT AT AT AT AT AT AT
16558517 CTGTTCTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16563787 original size:24 final size:24
Alignment explanation
Indices: 16563755--16563802 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
16563745 GAACTTTAGG
16563755 AATGAGAGCAATCAAAGTAACATT
1 AATGAGAGCAATCAAAGTAACATT
*
16563779 AATGAGAGCAATCAAAGTGACATT
1 AATGAGAGCAATCAAAGTAACATT
16563803 GAGGTCACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (24 bp):
AATGAGAGCAATCAAAGTAACATT
Found at i:16564481 original size:36 final size:36
Alignment explanation
Indices: 16564410--16564482 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
16564400 GTTGGAAAAT
* *
16564410 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
16564446 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
16564482 A
1 A
16564483 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:16565614 original size:75 final size:75
Alignment explanation
Indices: 16565530--16565680 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
16565520 ACGAAAGTGA
* * *
16565530 TGATGTGATAGTTAATAAAACTAGTATAATTATATATTTGGTCTTCAATATTTCTATTTTCTATT
1 TGATATGATAGTAAATAAAACTAGTATAATTATATATTTAGTCTTCAATATTTCTATTTTCTATT
*
16565595 AATTTGGTCC
66 AATTTGATCC
*
16565605 TGATATGATAGTAAATAAAACTAGTATAATTATATATTTAGTCTTGAATATTTCTATTTTCTATT
1 TGATATGATAGTAAATAAAACTAGTATAATTATATATTTAGTCTTCAATATTTCTATTTTCTATT
16565670 AATTTGATCC
66 AATTTGATCC
16565680 T
1 T
16565681 AATTTTAATT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.48
Consensus pattern (75 bp):
TGATATGATAGTAAATAAAACTAGTATAATTATATATTTAGTCTTCAATATTTCTATTTTCTATT
AATTTGATCC
Found at i:16566435 original size:2 final size:2
Alignment explanation
Indices: 16566423--16566468 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
16566413 ATTAACTACA
16566423 AT AT A- AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
16566464 AT AT A
1 AT AT A
16566469 CTATTGTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16566828 original size:38 final size:40
Alignment explanation
Indices: 16566769--16566855 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 40
16566759 AATAATTATT
16566769 ATATATATATATAATATTAATAAATTTA-AT-TTAAATTTAA
1 ATATATATATATAATATTAAT--ATTTATATATTAAATTTAA
*
16566809 ATATATATATAT-ATA-TAATATTTATATATTTAATTTAA
1 ATATATATATATAATATTAATATTTATATATTAAATTTAA
16566847 ATATATATA
1 ATATATATA
16566856 CCCGGCCCGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
36 5 0.11
37 2 0.05
38 22 0.50
39 3 0.07
40 12 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
ATATATATATATAATATTAATATTTATATATTAAATTTAA
Found at i:16567803 original size:16 final size:16
Alignment explanation
Indices: 16567775--16567807 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16567765 TATGTGATTG
16567775 TTAAAGAATTTATCTA
1 TTAAAGAATTTATCTA
16567791 TTAAA-AATGTTATCTA
1 TTAAAGAAT-TTATCTA
16567807 T
1 T
16567808 AACCGAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TTAAAGAATTTATCTA
Found at i:16569409 original size:59 final size:61
Alignment explanation
Indices: 16569312--16569430 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 61
16569302 ATTCATTTTT
16569312 TAACAAAATAGGAAAATAAATCCAACAATTTATTTCATTCTA-AAAA-AAGAAAATAAATC
1 TAACAAAATAGGAAAATAAATCCAACAATTTATTTCATTCTACAAAATAAGAAAATAAATC
* * * * * *
16569371 TAACGAAATAGGAAAATAACTTCAACGATTTATTTCATTTTACAAAATATGAAAATAAAT
1 TAACAAAATAGGAAAATAAATCCAACAATTTATTTCATTCTACAAAATAAGAAAATAAAT
16569431 TCTATGATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 37 0.71
60 4 0.08
61 11 0.21
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (61 bp):
TAACAAAATAGGAAAATAAATCCAACAATTTATTTCATTCTACAAAATAAGAAAATAAATC
Found at i:16569440 original size:39 final size:39
Alignment explanation
Indices: 16569376--16569453 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
16569366 AAATCTAACG
* *
16569376 AAATAGGAAAATAACTTCAACGATTTATTTCATTTTACA
1 AAATAGGAAAATAAATTCAACGATTTATTCCATTTTACA
* * * *
16569415 AAATATGAAAATAAATTCTATGATTTATTCCCTTTTACA
1 AAATAGGAAAATAAATTCAACGATTTATTCCATTTTACA
16569454 TAACGGAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (39 bp):
AAATAGGAAAATAAATTCAACGATTTATTCCATTTTACA
Found at i:16569487 original size:56 final size:57
Alignment explanation
Indices: 16569422--16569567 Score: 172
Period size: 58 Copynumber: 2.6 Consensus size: 57
16569412 ACAAAATATG
** * * *
16569422 AAAATAAATTCTATGATTTATTCCCTTTTACATAACG-GAATC-ATAAGATTCTTAGA
1 AAAATAAATTCTATGATTTATTTTCTTTTACATAA-GAAAACCAATAAGATTCTTACA
* *
16569478 AAAATAAATTCTATTATTTATTTTATTTTACATAAGAAAACCATATAAGATTCTTACA
1 AAAATAAATTCTATGATTTATTTTCTTTTACATAAGAAAACCA-ATAAGATTCTTACA
*
16569536 AAAATAAATT-TAACGATTTATTTTCTTTTACA
1 AAAATAAATTCT-ATGATTTATTTTCTTTTACA
16569568 AATAGGAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
55 1 0.01
56 34 0.45
57 1 0.01
58 40 0.53
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (57 bp):
AAAATAAATTCTATGATTTATTTTCTTTTACATAAGAAAACCAATAAGATTCTTACA
Found at i:16569592 original size:38 final size:38
Alignment explanation
Indices: 16569536--16569679 Score: 150
Period size: 38 Copynumber: 3.8 Consensus size: 38
16569526 GATTCTTACA
*
16569536 AAAATAAATTTAACGATTTATTTTCTTTTACAAATAGG
1 AAAATAAATCTAACGATTTATTTTCTTTTACAAATAGG
* * *
16569574 AAAATAAATCTAATGATTTATTTCCTTTTAAAAATCAGG
1 AAAATAAATCTAACGATTTATTTTCTTTTACAAAT-AGG
* * *
16569613 AAAATAGAT-TCAACAATTTATTTTCTTTTTCAAAATAGG
1 AAAATAAATCT-AACGATTTATTTTCTTTTAC-AAATAGG
* * *
16569652 -ACA-AAATCAAACGATTTATTTTATTTTA
1 AAAATAAATCTAACGATTTATTTTCTTTTA
16569680 TAAAAAGAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
37 19 0.22
38 34 0.40
39 29 0.34
40 4 0.05
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (38 bp):
AAAATAAATCTAACGATTTATTTTCTTTTACAAATAGG
Found at i:16569812 original size:97 final size:95
Alignment explanation
Indices: 16569612--16569831 Score: 247
Period size: 97 Copynumber: 2.3 Consensus size: 95
16569602 TAAAAATCAG
* * * *
16569612 GAAAATAGATTCAACAATTTATTTTCTTTTTCAAAATAGGACAAAATCAAACGATTTATTTTATT
1 GAAAATAAATTCAACAATTTATTTTCTTTTACAAAATAGAAAAAAATCAAACGATTTATTTTATT
*
16569677 TTATAAAAAGAATCATATAAGATTCTTAGA
66 TTATAAAAAGAATCATATAAGATTCATAGA
* *
16569707 GAAAATAAATTCAA-AGATTTATTTTCTTTTACAAACTAAGAAAATAAATTCGAA-GATTTATTT
1 GAAAATAAATTCAACA-ATTTATTTTCTTTTACAAAAT-AGAAAA-AAA-TCAAACGATTTATTT
*
16569770 TCTTTTA-AAAGATAGAATCAT-TAA-ATGATCATA-A
62 TATTTTATAAA-A-AGAATCATATAAGAT--TCATAGA
16569804 GAAAATAAATTCAACAATTTA-TTTCTTT
1 GAAAATAAATTCAACAATTTATTTTCTTT
16569832 ATTCAAGATT
Statistics
Matches: 108, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
94 1 0.01
95 32 0.30
96 16 0.15
97 42 0.39
98 17 0.16
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (95 bp):
GAAAATAAATTCAACAATTTATTTTCTTTTACAAAATAGAAAAAAATCAAACGATTTATTTTATT
TTATAAAAAGAATCATATAAGATTCATAGA
Found at i:16569973 original size:58 final size:58
Alignment explanation
Indices: 16569846--16569973 Score: 186
Period size: 58 Copynumber: 2.2 Consensus size: 58
16569836 AAGATTTAAG
* * *
16569846 AGAAAATAAATATAACAAATTGTTTCTTTTAACAAAATAGAATCATTTACGATTATCA
1 AGAAAATAAATTTAACAAATTATTTCTTTTAACAAAATAGAATCATTCACGATTATCA
* * *
16569904 AGAAAATAAATTTAACAATTTATTTCTTTTTAA-AAGATATAATCATTCACGATTATCA
1 AGAAAATAAATTTAACAAATTATTTC-TTTTAACAAAATAGAATCATTCACGATTATCA
16569962 AGAAAATAAATT
1 AGAAAATAAATT
16569974 CGATAAGTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 57 0.90
59 6 0.10
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (58 bp):
AGAAAATAAATTTAACAAATTATTTCTTTTAACAAAATAGAATCATTCACGATTATCA
Found at i:16570110 original size:58 final size:58
Alignment explanation
Indices: 16569883--16570180 Score: 305
Period size: 58 Copynumber: 5.1 Consensus size: 58
16569873 TTTAACAAAA
* * * * ** *
16569883 TAGAATCATTTACGATTATCAAGAAAATAAATTTAACAATTTATTTCTTTTTA-AAAGA
1 TAGAATCATTTAAGATTCTCAAGAAAATAAATTCAACTATTTATTT-TCCTTACAAAGT
* * * * * * * * *
16569941 TATAATCATTCACGATTATCAAGAAAATAAATTCGA-TAAGTTATTTTCCGTAAAAATT
1 TAGAATCATTTAAGATTCTCAAGAAAATAAATTCAACT-ATTTATTTTCCTTACAAAGT
* * ** *
16569999 TAAAATCATTTAAGATTCTCGAGAAAATAAATTTGACTATTTATTTTCGTTACAAAGT
1 TAGAATCATTTAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCCTTACAAAGT
*
16570057 TAGAATCATTTAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGT
1 TAGAATCATTTAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCCTTACAAAGT
* * * * *
16570115 CATAATCGTTTAATATTCTCAATG-AAATAAATTCAACTATTTATTTTCCTTACGAAGT
1 TAGAATCATTTAAGATTCTCAA-GAAAATAAATTCAACTATTTATTTTCCTTACAAAGT
16570173 TAGAATCA
1 TAGAATCA
16570181 ATACAAGATT
Statistics
Matches: 200, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
57 3 0.01
58 195 0.98
59 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (58 bp):
TAGAATCATTTAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCCTTACAAAGT
Found at i:16572692 original size:58 final size:58
Alignment explanation
Indices: 16572627--16572754 Score: 168
Period size: 58 Copynumber: 2.2 Consensus size: 58
16572617 AAGATTTAAG
* *
16572627 AGAAAATAAATTTAACAAATTGTTTC-CTTTAACAAAATAGAATAATTTACAATTATCA
1 AGAAAATAAATTTAACAAATTATTTCTCTTTAA-AAAATAGAATAATTCACAATTATCA
* * * * * *
16572685 AGAAAATAAATTTAACAATTTATTTCTTTTTAAAAGATATAATCATTCACGATTATCA
1 AGAAAATAAATTTAACAAATTATTTCTCTTTAAAAAATAGAATAATTCACAATTATCA
16572743 AGAAAATAAATT
1 AGAAAATAAATT
16572755 CGATAAGTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 56 0.92
59 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.36
Consensus pattern (58 bp):
AGAAAATAAATTTAACAAATTATTTCTCTTTAAAAAATAGAATAATTCACAATTATCA
Found at i:16572822 original size:116 final size:115
Alignment explanation
Indices: 16572682--16572960 Score: 301
Period size: 115 Copynumber: 2.4 Consensus size: 115
16572672 TTTACAATTA
* ** * *
16572682 TCAAGAAAATAAATTTAACAATTTATTTCTTTTTA-AAAGATATAATCATTCACGATTATCAAGA
1 TCAAGAAAATAAATTTAACTATTTATTT-TCGTTACAAAGATAGAATCATTCAAGATTATCAAGA
* * *
16572746 AAATAAATTCGA-TAAGTTATTTTCCGTAAAAATTTAAAATCATTTAAGATTC
65 AAAT-AATTCAACT-AGTTATTTTCCGTAAAAAGTCAAAATCATTTAAGATTC
* * * * *
16572798 TCGAGAAAATAAATTTAACTATTTATTTTCGTTACAAAGTTAGAATCATTTAAGATTCTCAAGGA
1 TCAAGAAAATAAATTTAACTATTTATTTTCGTTACAAAGATAGAATCATTCAAGATTATCAAGAA
* * * * * *
16572863 AATAATTCAACTATTTATTTTCCTTACAAAGTCAGAATCGTTTAATATTC
66 AATAATTCAACTAGTTATTTTCCGTAAAAAGTCAAAATCATTTAAGATTC
* * * * *
16572913 TCAAGGAAATAAATTAAACTATTTATTTTCCTTACGAAGTTAGAATCA
1 TCAAGAAAATAAATTTAACTATTTATTTTCGTTACAAAGATAGAATCA
16572961 ACACAAGATT
Statistics
Matches: 137, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
115 83 0.61
116 54 0.39
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (115 bp):
TCAAGAAAATAAATTTAACTATTTATTTTCGTTACAAAGATAGAATCATTCAAGATTATCAAGAA
AATAATTCAACTAGTTATTTTCCGTAAAAAGTCAAAATCATTTAAGATTC
Found at i:16572894 original size:57 final size:58
Alignment explanation
Indices: 16572664--16572960 Score: 278
Period size: 58 Copynumber: 5.1 Consensus size: 58
16572654 TTTAACAAAA
* * * * * ** *
16572664 TAGAATAATTTACA-ATTATCAAGAAAATAAATTTAACAATTTATTTCTTTTTA-AAAGA
1 TAGAATCATTTA-AGATTCTCAAGGAAATAAATTAAACTATTTATTT-TCCTTACAAAGT
* * * * * ** * * * *
16572722 TATAATCATTCACGATTATCAAGAAAATAAATTCGA-TAAGTTATTTTCCGTAAAAATT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTAAACT-ATTTATTTTCCTTACAAAGT
* * * * *
16572780 TAAAATCATTTAAGATTCTCGAGAAAATAAATTTAACTATTTATTTTCGTTACAAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTAAACTATTTATTTTCCTTACAAAGT
*
16572838 TAGAATCATTTAAGATTCTCAAGGAAAT-AATTCAACTATTTATTTTCCTTACAAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTAAACTATTTATTTTCCTTACAAAGT
* * * *
16572895 CAGAATCGTTTAATATTCTCAAGGAAATAAATTAAACTATTTATTTTCCTTACGAAGT
1 TAGAATCATTTAAGATTCTCAAGGAAATAAATTAAACTATTTATTTTCCTTACAAAGT
16572953 TAGAATCA
1 TAGAATCA
16572961 ACACAAGATT
Statistics
Matches: 197, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
57 55 0.28
58 141 0.72
59 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (58 bp):
TAGAATCATTTAAGATTCTCAAGGAAATAAATTAAACTATTTATTTTCCTTACAAAGT
Found at i:16574477 original size:21 final size:21
Alignment explanation
Indices: 16574440--16574480 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16574430 AAAATTTAAA
*
16574440 AAAAATATGTTCTATTTGAGG
1 AAAAATATGTTCCATTTGAGG
16574461 AAAAATAT-TTCACATTTGAG
1 AAAAATATGTTC-CATTTGAG
16574481 TTAAACTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (21 bp):
AAAAATATGTTCCATTTGAGG
Found at i:16578639 original size:55 final size:55
Alignment explanation
Indices: 16578536--16578640 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
16578526 TCAAATGATT
* *
16578536 CATGAAGAAAGACATCCGATGAATGAAGAAATTTGAAACTAATTGAAGACCGATC
1 CATGAAGAAAGACATCCGATGAAGGAAGAAATTTGAAACTAATCGAAGACCGATC
* * *
16578591 CATGGAGAAAGACATCCGATGAAGGAAGAAGTTT-AAATTTAATCGAAGAC
1 CATGAAGAAAGACATCCGATGAAGGAAGAAATTTGAAA-CTAATCGAAGAC
16578641 TTCTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 3 0.07
55 41 0.93
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (55 bp):
CATGAAGAAAGACATCCGATGAAGGAAGAAATTTGAAACTAATCGAAGACCGATC
Found at i:16585273 original size:20 final size:21
Alignment explanation
Indices: 16585227--16585287 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
16585217 CCCTGTGGGG
16585227 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TCAAA
*
16585250 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGATTCCCTCAAA
*
16585270 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
16585288 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAA
Found at i:16587574 original size:31 final size:31
Alignment explanation
Indices: 16587536--16587604 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
16587526 TCCAAAAGGA
16587536 TGAAAATAACTAATGTTAGGCTTTTTATTTT
1 TGAAAATAACTAATGTTAGGCTTTTTATTTT
16587567 TGAAAATAACTAATGTTAGGCTTTTTATTTT
1 TGAAAATAACTAATGTTAGGCTTTTTATTTT
16587598 TGAAAAT
1 TGAAAAT
16587605 TTCATATGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (31 bp):
TGAAAATAACTAATGTTAGGCTTTTTATTTT
Found at i:16591701 original size:3 final size:3
Alignment explanation
Indices: 16591693--16591726 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
16591683 TTTAATATTA
16591693 AAG AAG AAG AAG AAG AAG CAA- AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG A
16591727 TGGAAACCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16593018 original size:11 final size:10
Alignment explanation
Indices: 16592997--16593030 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
16592987 AAGAAAAGAG
*
16592997 AAAAAATAAA
1 AAAAAAGAAA
*
16593007 AAAAAGGAAA
1 AAAAAAGAAA
16593017 AAAAAAGAAA
1 AAAAAAGAAA
16593027 AAAA
1 AAAA
16593031 TGAGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:16593036 original size:11 final size:11
Alignment explanation
Indices: 16592997--16593071 Score: 58
Period size: 9 Copynumber: 7.4 Consensus size: 11
16592987 AAGAAAAGAG
16592997 AAAAAAT-A-A
1 AAAAAATGAGA
16593006 AAAAAA-G-GA
1 AAAAAATGAGA
*
16593015 AAAAAA-AAGA
1 AAAAAATGAGA
16593025 AAAAAATGAG-
1 AAAAAATGAGA
16593035 -AAAAATGAGA
1 AAAAAATGAGA
*
16593045 AAAAAATGAAA
1 AAAAAATGAGA
16593056 AATGAAAATGA-A
1 AA--AAAATGAGA
16593068 AAAA
1 AAAA
16593072 TGAAAAAAGG
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
9 22 0.40
10 10 0.18
11 13 0.24
12 3 0.05
13 7 0.13
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (11 bp):
AAAAAATGAGA
Found at i:16593038 original size:10 final size:10
Alignment explanation
Indices: 16592990--16593049 Score: 56
Period size: 9 Copynumber: 6.4 Consensus size: 10
16592980 CTTGAATAAG
16592990 AAAA-GAGAA
1 AAAATGAGAA
*
16592999 AAAAT-AAAA
1 AAAATGAGAA
* *
16593008 AAAAGGAAAA
1 AAAATGAGAA
*
16593018 AAAAAGA-AA
1 AAAATGAGAA
16593027 AAAATGAG-A
1 AAAATGAGAA
16593036 AAAATGAGAA
1 AAAATGAGAA
16593046 AAAA
1 AAAA
16593050 ATGAAAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
9 28 0.65
10 15 0.35
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (10 bp):
AAAATGAGAA
Found at i:16593085 original size:14 final size:13
Alignment explanation
Indices: 16593047--16593077 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
16593037 AAATGAGAAA
16593047 AAAATGAAAAATG
1 AAAATGAAAAATG
16593060 AAAATGAAAAAATG
1 AAAATG-AAAAATG
16593074 AAAA
1 AAAA
16593078 AAGGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:16594101 original size:15 final size:15
Alignment explanation
Indices: 16594081--16594132 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
16594071 TTGAGGATGG
*
16594081 AAGATGTGAAACATC
1 AAGATGTAAAACATC
16594096 AAGATGTAAAACATC
1 AAGATGTAAAACATC
16594111 AAGATGTAAAACATC
1 AAGATGTAAAACATC
16594126 AAGATGT
1 AAGATGT
16594133 GGATAACTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (15 bp):
AAGATGTAAAACATC
Found at i:16594329 original size:55 final size:55
Alignment explanation
Indices: 16594252--16595225 Score: 1054
Period size: 55 Copynumber: 17.8 Consensus size: 55
16594242 AATCATTTTA
* * * * *
16594252 AGAAGATTATTCAAGTTCTATACTCCTTGAAGCAAGAGGGAGCGAACCCATTTGT
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * *
16594307 AGAAGATTGTTCGAGTTCTATACTCCTTGAAGCGATAGGGAGAGAACCCATTTGT
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * * *
16594362 AGAAGATTGTTTGAGTTCTATACTCCCTAAAGTAATAGGGAGCGGACCCATTTAC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * *
16594417 AGAAGA-TATTCCAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCC-GTTGAC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTG-C
* * * * *
16594471 ATAAGATTGTTCAAGTTCTATACTCCCTGAAGCAATAGGGAGTGAACCCGTTGGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * *** *
16594526 ATAAGATTGTTCGACTTCTATACTCCCTGAAAAG-AATAGGGAGC-AAAATATTGGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTG--AAGCAATAGGGAGCGAACCCATTTGC
* * * *
16594581 AGAAGATTATTCGAGTTCTATATTCCCTGAAGCAAGAGGGAGCGAACCCATTTTC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * *
16594636 AGAAGATTGCTCGAGTTCTATACTCCCTGAAGCAATAGAGAGCGAACACGTTTGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * * * * *
16594691 AGAAGATTGTTCAAGTTCCATACTCCCTGAAACAATAAGAAGCGAA-CCGTTGGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * *
16594745 AGAAGATTATTCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTAGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * * *
16594800 AGAAGATTATTCAAGTTCTATACTCCCTGAAGCAATAGGGAGTGAACCCGTTGGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * *
16594855 AGAAGATTGTTTGAGTTCTGTACTCCCTGAA-TAATAGGGAGCGAACCCGTTTGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * * *
16594909 AGAAGATCGTTCGAGTTATATACTCCCTGAAGTAATAGGTAGCGAACCCATTTTC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * * * *
16594964 AGAAGATCGTTTGAGTTCTATACTCCCTGAAGTAATAGGTAGCGAACCCGTTTTC
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* **
16595019 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGTGAACCCATTTTT
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* * * **
16595074 AAAAGATTGTTCGAGTTATATACTCCCTGAAGCAATAGGGAGCGAAACC-TTTTT
1 AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
* *
16595128 AGAAGATTGTTCGAGTTATATACTCCCTGAAAG-TATAGGGAGC-AGACCTC-TTTGTC
1 AGAAGATTGTTCGAGTTCTATACTCCCTG-AAGCAATAGGGAGCGA-ACC-CATTTG-C
* * * **
16595184 -GAATATTTTTCGAGTCCTATACTCTTTGAAAG-AATAGGGAGC
1 AGAAGATTGTTCGAGTTCTATACTCCCTG-AAGCAATAGGGAGC
16595226 AGACATAGAG
Statistics
Matches: 796, Mismatches: 110, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
53 6 0.01
54 189 0.24
55 587 0.74
56 11 0.01
57 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (55 bp):
AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTGC
Found at i:16594536 original size:164 final size:165
Alignment explanation
Indices: 16594252--16595225 Score: 1092
Period size: 164 Copynumber: 5.9 Consensus size: 165
16594242 AATCATTTTA
* * *
16594252 AGAAGATTATTCAAGTTCTATACTCCTTGAAGCAAGAGGGAGCGAACCCATTTGT-AGAAGATTG
1 AGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTT-TCAGAAGATTG
* * * * * *
16594316 TTCGAGTTCTATACTCCTTGAAGCGATAGGGAGAGAACCCATTTGTAGAAGATTGTTTGAGTTCT
65 TTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCT
* * *
16594381 ATACTCCCTAAAGTAATAGGGAGCGGACCCATTTAC
130 ATACTCCCTAAAGCAATAGGGAGCGAACCCATTTGC
* * ** *
16594417 AGAAGA-TATTCCAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTGACATAAGATTGT
1 AGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGT
* * * * *
16594481 TCAAGTTCTATACTCCCTGAAGCAATAGGGAGTGAACCCGTTGGCATAAGATTGTTCGACTTCTA
66 TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCTA
*** *
16594546 TACTCCCTGAAAAG-AATAGGGAGC-AAAATATTGGC
131 TACTCCCT--AAAGCAATAGGGAGCGAACCCATTTGC
* * *
16594581 AGAAGATTATTCGAGTTCTATATTCCCTGAAGCAAGAGGGAGCGAACCCATTTTCAGAAGATTGC
1 AGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGT
* * * *
16594646 TCGAGTTCTATACTCCCTGAAGCAATAGAGAGCGAACACGTTTGCAGAAGATTGTTCAAGTTCCA
66 TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCTA
* * * *
16594711 TACTCCCTGAAA-CAATAAGAAGCGAA-CCGTTGGC
131 TACTCCCT-AAAGCAATAGGGAGCGAACCCATTTGC
* * ** *
16594745 AGAAGATTATTCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTAGCAGAAGATTAT
1 AGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGT
* * * * *
16594810 TCAAGTTCTATACTCCCTGAAGCAATAGGGAGTGAACCCGTTGGCAGAAGATTGTTTGAGTTCTG
66 TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCTA
* * *
16594875 TACTCCCTGAA-TAATAGGGAGCGAACCCGTTTGC
131 TACTCCCTAAAGCAATAGGGAGCGAACCCATTTGC
** * * * *
16594909 AGAAGATCGTTCGAGTTATATACTCCCTGAAGTAATAGGTAGCGAACCCATTTTCAGAAGATCGT
1 AGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGT
* * * *
16594974 TTGAGTTCTATACTCCCTGAAGTAATAGGTAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTCTA
66 TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCTA
* * **
16595039 TACTCCCTGAAGCAATAGGGAGTGAACCCATTTTT
131 TACTCCCTAAAGCAATAGGGAGCGAACCCATTTGC
* * * * *
16595074 AAAAGATTGTTCGAGTTATATACTCCCTGAAGCAATAGGGAGCGAAACC-TTTTTAGAAGATTGT
1 AGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGT
* * * *
16595138 TCGAGTTATATACTCCCTGAAAG-TATAGGGAGC-AGACCTC-TTTGTC-GAATATTTTTCGAGT
66 TCGAGTTCTATACTCCCTG-AAGCAATAGGGAGCGA-ACC-CGTTTG-CAGAAGATTGTTCGAGT
* **
16595199 CCTATACTCTTTGAAAG-AATAGGGAGC
127 TCTATACTCCCT-AAAGCAATAGGGAGC
16595226 AGACATAGAG
Statistics
Matches: 684, Mismatches: 112, Indels: 27
0.83 0.14 0.03
Matches are distributed among these distances:
163 14 0.02
164 464 0.68
165 202 0.30
166 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (165 bp):
AGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGT
TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTTGCAGAAGATTGTTCGAGTTCTA
TACTCCCTAAAGCAATAGGGAGCGAACCCATTTGC
Found at i:16594641 original size:219 final size:220
Alignment explanation
Indices: 16594252--16595158 Score: 1081
Period size: 219 Copynumber: 4.1 Consensus size: 220
16594242 AATCATTTTA
* * * * *
16594252 AGAAGATTATTCAAGTTCTATACTCCTTGAAGCAAGAGGGAGCGAACCCATTTGTAGAAGATTGT
1 AGAAGATTGTTCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTGGCAGAAGATTGT
* * * * * * *
16594317 TCGAGTTCTATACTCCTTGAAGCGATAGGGAGAGAACCCATTTGTAGAAGATTGTTTGAGTTCTA
66 TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAAACCATTTGCAGAAGATTATTCGAGTTCTA
* * * * * *
16594382 TACTCCCTAAAGTAATAGGGAGCGGACCCATTTACAGAAGA-TATTCCAGTTCTATACTCCCTGA
131 TACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGA
16594446 AGCAATAGGGAGCGAACCCG-TTGAC
196 AGCAATAGGGAGCGAACCCGTTTG-C
* * * *
16594471 ATAAGATTGTTCAAGTTCTATACTCCCTGAAGCAATAGGGAGTGAACCCGTTGGCATAAGATTGT
1 AGAAGATTGTTCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTGGCAGAAGATTGT
* ** *
16594536 TCGACTTCTATACTCCCTGAAAAG-AATAGGGAGC-AAAATATTGGCAGAAGATTATTCGAGTTC
66 TCGAGTTCTATACTCCCTG--AAGCAATAGGGAGCGAAACCATTTGCAGAAGATTATTCGAGTTC
* * *
16594599 TATATTCCCTGAAGCAAGAGGGAGCGAACCCATTTTCAGAAGATTGCTCGAGTTCTATACTCCCT
129 TATACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCCCT
* *
16594664 GAAGCAATAGAGAGCGAACACGTTTGC
194 GAAGCAATAGGGAGCGAACCCGTTTGC
* * * * * *
16594691 AGAAGATTGTTCAAGTTCCATACTCCCTGAAACAATAAGAAGCGAA-CCGTTGGCAGAAGATTAT
1 AGAAGATTGTTCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTGGCAGAAGATTGT
* * * * *
16594755 TCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCGTTAGCAGAAGATTATTCAAGTTCTA
66 TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAAACCATTTGCAGAAGATTATTCGAGTTCTA
* * ** * *
16594820 TACTCCCTGAAGCAATAGGGAGTGAACCCGTTGGCAGAAGATTGTTTGAGTTCTGTACTCCCTGA
131 TACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGA
*
16594885 A-TAATAGGGAGCGAACCCGTTTGC
196 AGCAATAGGGAGCGAACCCGTTTGC
* * * * * ** *
16594909 AGAAGATCGTTCGAGTTATATACTCCCTGAAGTAATAGGTAGCGAACCCATTTTCAGAAGATCGT
1 AGAAGATTGTTCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTGGCAGAAGATTGT
* * * * * * *
16594974 TTGAGTTCTATACTCCCTGAAGTAATAGGTAGCGAACCCGTTTTCAGAAGATTGTTCGAGTTCTA
66 TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAAACCATTTGCAGAAGATTATTCGAGTTCTA
* * * *
16595039 TACTCCCTGAAGCAATAGGGAGTGAACCCATTTTTAAAAGATTGTTCGAGTTATATACTCCCTGA
131 TACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGA
* **
16595104 AGCAATAGGGAGCGAAACC-TTTTT
196 AGCAATAGGGAGCGAACCCGTTTGC
* *
16595128 AGAAGATTGTTCGAGTTATATACTCCCTGAA
1 AGAAGATTGTTCAAGTTCTATACTCCCTGAA
16595159 AGTATAGGGA
Statistics
Matches: 587, Mismatches: 93, Indels: 16
0.84 0.13 0.02
Matches are distributed among these distances:
217 3 0.01
218 68 0.12
219 408 0.70
220 102 0.17
221 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (220 bp):
AGAAGATTGTTCAAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACCCATTGGCAGAAGATTGT
TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAAACCATTTGCAGAAGATTATTCGAGTTCTA
TACTCCCTGAAGCAATAGGGAGCGAACCCATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGA
AGCAATAGGGAGCGAACCCGTTTGC
Found at i:16602019 original size:29 final size:30
Alignment explanation
Indices: 16601961--16602036 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
16601951 GTATCAAGAG
* *
16601961 TTAGAGGTCAAAATAAAATTTAATTTAAAGT
1 TTAGA-GTCAAATTAAAATTTAATATAAAGT
*
16601992 TTAGAGTCAAATTAACATTT-ATATAAAGT
1 TTAGAGTCAAATTAAAATTTAATATAAAGT
* *
16602021 TTGAGGGTCATATTAA
1 TT-AGAGTCAAATTAA
16602037 GAAATAGCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 10 0.26
30 24 0.62
31 5 0.13
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.37
Consensus pattern (30 bp):
TTAGAGTCAAATTAAAATTTAATATAAAGT
Found at i:16609784 original size:18 final size:19
Alignment explanation
Indices: 16609761--16609796 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16609751 ATGTGCATGA
16609761 CTAAT-AATAAAATATATT
1 CTAATAAATAAAATATATT
*
16609779 CTAATAAATTAAATATAT
1 CTAATAAATAAAATATAT
16609797 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
CTAATAAATAAAATATATT
Found at i:16611136 original size:22 final size:22
Alignment explanation
Indices: 16611110--16611167 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
16611100 GGGAACATAA
16611110 CGGCGGAGCAGTTGAATATAGG
1 CGGCGGAGCAGTTGAATATAGG
16611132 CGGCGGAGCAGTTGAATATAGG
1 CGGCGGAGCAGTTGAATATAGG
* *
16611154 AGGCGAAGCAGTTG
1 CGGCGGAGCAGTTG
16611168 GAGGCAGCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.28, C:0.14, G:0.41, T:0.17
Consensus pattern (22 bp):
CGGCGGAGCAGTTGAATATAGG
Found at i:16611477 original size:14 final size:13
Alignment explanation
Indices: 16611458--16611504 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
16611448 AATAATATTT
16611458 ATAATAATAATACA
1 ATAATAATAATA-A
16611472 ATAATAATATATAA
1 ATAATAATA-ATAA
*
16611486 ATAACAAT-ATAA
1 ATAATAATAATAA
16611498 ATAATAA
1 ATAATAA
16611505 CGAGACGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 10 0.33
14 17 0.57
15 3 0.10
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAATAATAA
Done.