Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 42
Found at i:3372716 original size:19 final size:18
Alignment explanation
Indices: 3372685--3372722 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
3372675 AAAAATGAAT
3372685 AATAAATAATAATAATAA
1 AATAAATAATAATAATAA
3372703 AATAAATAAATAATAATAA
1 AATAAAT-AATAATAATAA
3372722 A
1 A
3372723 TAATGTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAATAATAATAATAA
Found at i:3373294 original size:37 final size:37
Alignment explanation
Indices: 3373241--3373387 Score: 258
Period size: 37 Copynumber: 4.0 Consensus size: 37
3373231 GTTTGTGGAA
*
3373241 CCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
3373278 CCTATTTTTAGAAGTTTGAATCCTAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
3373315 CCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
3373352 CCTATTTTTAGGAGTTTGAATCCTACTAAAACTCTA
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
3373388 ACGTTTGTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (37 bp):
CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
Found at i:3373870 original size:35 final size:35
Alignment explanation
Indices: 3373824--3373952 Score: 197
Period size: 35 Copynumber: 3.7 Consensus size: 35
3373814 AAGTTCTTGA
*
3373824 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
3373859 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
**
3373893 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTCCGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
* * *
3373928 GTTTCAAGATAAACTATCTCAAAGG
1 GTTTCAAGAGAAACAATTTCAAAGG
3373953 AGGCAAAATT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
34 34 0.39
35 53 0.61
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (35 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
Found at i:3373935 original size:69 final size:69
Alignment explanation
Indices: 3373824--3373952 Score: 204
Period size: 69 Copynumber: 1.9 Consensus size: 69
3373814 AAGTTCTTGA
* ** *
3373824 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTTT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTCCGTGTTTCAAGAGAAACAATCTCAAAGGTTTTT
3373889 TTGT
66 TTGT
* *
3373893 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTCCGTGTTTCAAGATAAACTATCTCAAAGG
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTCCGTGTTTCAAGAGAAACAATCTCAAAGG
3373953 AGGCAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (69 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTCCGTGTTTCAAGAGAAACAATCTCAAAGGTTTTT
TTGT
Found at i:3374015 original size:67 final size:65
Alignment explanation
Indices: 3373926--3374092 Score: 178
Period size: 67 Copynumber: 2.5 Consensus size: 65
3373916 GGTTTTTTCC
* * * * *
3373926 GTGTTTCAAGATAAACTATCTCAAAGGAGGCAAAATTTTATTTCAA-GAGAAACATATTTAAAGA
1 GTGTTTCAAGAGAATCTGTCTCAAAGGAGACAAAA-TTTATTTCAAGGA-AAACAAATTTAAAGA
3373990 TT
64 TT
* * *
3373992 GGTGTTTCAAGAGAATCTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACAAATTTAAAGAT
1 -GTGTTTCAAGAGAATCTGTCTCAAAGGAGACAAAATTTATTTCAAGGAAAACAAATTTAAAGAT
3374057 T
65 T
* *
3374058 TTGTTTCAAGGGAAAT-TGTCTC-AAGAGAGACAAAA
1 GTGTTTCAAGAG-AATCTGTCTCAAAG-GAGACAAAA
3374093 CTTGGAAACT
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
64 2 0.02
65 24 0.28
66 28 0.33
67 31 0.36
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (65 bp):
GTGTTTCAAGAGAATCTGTCTCAAAGGAGACAAAATTTATTTCAAGGAAAACAAATTTAAAGATT
Found at i:3374057 original size:66 final size:66
Alignment explanation
Indices: 3373926--3374092 Score: 187
Period size: 66 Copynumber: 2.5 Consensus size: 66
3373916 GGTTTTTTCC
* * * * * *
3373926 GTGTTTCAAGATAAACTATCTCAAAGGAGGCAAAATTTTATTTCAAGAGAAACATATTTAAAGAT
1 GTGTTTCAAGAGAATCTGTCTCAAGGGAGACAAAATTTTATTTCAAGAGAAACAAATTTAAAGAT
3373991 T
66 T
* *
3373992 GGTGTTTCAAGAGAATCTGTCTCAAGGGAGACGAAA-TTTGTTTCAAG-GAAAACAAATTTAAAG
1 -GTGTTTCAAGAGAATCTGTCTCAAGGGAGACAAAATTTTATTTCAAGAG-AAACAAATTTAAAG
3374055 ATT
64 ATT
* * *
3374058 TTGTTTCAAGGGAAAT-TGTCTCAAGAGAGACAAAA
1 GTGTTTCAAGAG-AATCTGTCTCAAGGGAGACAAAA
3374093 CTTGGAAACT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
65 28 0.33
66 29 0.34
67 29 0.34
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (66 bp):
GTGTTTCAAGAGAATCTGTCTCAAGGGAGACAAAATTTTATTTCAAGAGAAACAAATTTAAAGAT
T
Found at i:3374429 original size:106 final size:106
Alignment explanation
Indices: 3374243--3374491 Score: 390
Period size: 106 Copynumber: 2.3 Consensus size: 106
3374233 GTATTGTTCT
* * * * *
3374243 GAGTCCAATATCCTCCGCCGCGAAGTTGAAATTGGCTTTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAACTGAGAAATTGTTTGTTGACAA
*
3374308 CCAACCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAACCGTCCATTCGCTGTGAAGTTGAACTTGTGTTGTCTC
*
3374349 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTTTGAAACTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAACTGAGAAATTGTTTGTTGACAA
* * *
3374414 CCAGCTGTCCATTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
66 CCAACCGTCCATTCGCTGTGAAGTTGAACTTGTGTTGTCTC
**
3374455 GAGTCCAATATTTTTCGCTGTGAAGTTGAAATTGGCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT
3374492 CTAAAATTGG
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 130 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAACTGAGAAATTGTTTGTTGACAA
CCAACCGTCCATTCGCTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:3375224 original size:32 final size:32
Alignment explanation
Indices: 3375188--3375276 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
3375178 CTCAAAGACG
* *
3375188 CCCCAATATTCGATGTTGAATCTTAAAAAATA
1 CCCCAACATTTGATGTTGAATCTTAAAAAATA
* * *
3375220 CCCCAACATTTGATTTTAAATCTCCAAAAAATA
1 CCCCAACATTTGATGTTGAATCT-TAAAAAATA
*
3375253 CCACAACATTTGATGTTGAATCTT
1 CCCCAACATTTGATGTTGAATCTT
3375277 CAAAGATGCC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 19 0.40
33 28 0.60
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (32 bp):
CCCCAACATTTGATGTTGAATCTTAAAAAATA
Found at i:3376386 original size:14 final size:13
Alignment explanation
Indices: 3376342--3376390 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
3376332 TTTTCTTCAA
3376342 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
*
3376354 TTGTCTCTTT-TT
1 TTTTCTCTTTGTT
3376366 ATTTTCTCTTTGATT
1 -TTTTCTCTTTG-TT
3376381 TTTTCTCTTT
1 TTTTCTCTTT
3376391 TTGTTCTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 6 0.19
13 13 0.42
14 10 0.32
15 2 0.06
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.73
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:3376387 original size:27 final size:25
Alignment explanation
Indices: 3376341--3376392 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
3376331 TTTTTCTTCA
3376341 ATTTTCCTTTGTTTTGTCTCTTTTT
1 ATTTTCCTTTGTTTTGTCTCTTTTT
*
3376366 ATTTTCTCTTTGATTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTGTCTCTTTTT
3376393 GTTCTTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.25
26 5 0.21
27 13 0.54
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTGTCTCTTTTT
Found at i:3379343 original size:7 final size:7
Alignment explanation
Indices: 3379333--3379361 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3379323 GAAAAAAATG
3379333 AATAATA
1 AATAATA
3379340 AATAATA
1 AATAATA
3379347 AATAATA
1 AATAATA
3379354 AATAATA
1 AATAATA
3379361 A
1 A
3379362 TGTATTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:3379938 original size:37 final size:37
Alignment explanation
Indices: 3379888--3380032 Score: 218
Period size: 37 Copynumber: 3.9 Consensus size: 37
3379878 TTGTGGAACC
* *
3379888 TATTTTTAGGAGTTTGAATCATAGTAAAATTCTATCA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
* *
3379925 TATTTTTGGGAGTTTGAATCCTAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
* *
3379962 TATTTTTAGGAGTTTAAATCCTAGTAAAACTCTATTA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
* *
3379999 TATTTTTAGGAGTTTGAATTCTACTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
3380033 ACGTTTATTT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
Found at i:3381175 original size:2 final size:2
Alignment explanation
Indices: 3381163--3381202 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3381153 ACAAAGAACA
3381163 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3381203 ATTAGTAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3381855 original size:21 final size:20
Alignment explanation
Indices: 3381817--3381858 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3381807 AACCAATTAA
*
3381817 TATATAACATTATAAATAAT
1 TATATAACATAATAAATAAT
*
3381837 TATATCAACATAATCAATAAT
1 TATAT-AACATAATAAATAAT
3381858 T
1 T
3381859 TTTTAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATAACATAATAAATAAT
Found at i:3387068 original size:2 final size:2
Alignment explanation
Indices: 3387063--3387088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3387053 GTGTGCCATC
3387063 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
3387089 GTTTGCTCTG
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:3390592 original size:2 final size:2
Alignment explanation
Indices: 3390585--3390636 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3390575 TTCAATTCAA
3390585 AT AT AT 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
3390627 AT AT AT AT AT
1 AT AT AT AT AT
3390637 GTCTTGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3392452 original size:18 final size:18
Alignment explanation
Indices: 3392429--3392466 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3392419 GACGCTTTAT
*
3392429 TCCAACAAGGTTTAGACA
1 TCCAACAAGGTATAGACA
3392447 TCCAACAAGGTATAGACA
1 TCCAACAAGGTATAGACA
3392465 TC
1 TC
3392467 GCCATTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (18 bp):
TCCAACAAGGTATAGACA
Found at i:3394919 original size:64 final size:62
Alignment explanation
Indices: 3394803--3394943 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 62
3394793 CATATTCAAT
* * * *
3394803 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCAAAGGCAATTGGTGCATCGATGCAT--GGAA
* * * *
3394866 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCAAAGGTAATTTGTGTATCGATGCATGGATA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCAAAGGCAATTGGTGCATCGATGCATGGA-A
3394930 GTGCATCGATGCAC
1 GTGCATCGATGCAC
3394944 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
62 2 0.03
63 16 0.24
64 48 0.73
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCAAAGGCAATTGGTGCATCGATGCATGGAA
Found at i:3394958 original size:24 final size:20
Alignment explanation
Indices: 3394931--3394988 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
3394921 GCATGGATAG
3394931 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
3394955 TGCATAGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
3394975 TGCATCGATGCACT
1 TGCATCGATGCACT
3394989 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:3398764 original size:64 final size:63
Alignment explanation
Indices: 3398669--3398808 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 63
3398659 ATATTCAATA
* * *
3398669 TGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-AG
1 TGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTAG
* * * * *
3398732 TGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTAG
1 TGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTAG
*
3398796 TGTATCGATGCAC
1 TGCATCGATGCAC
3398809 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
63 17 0.26
64 48 0.74
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTAG
Found at i:3398841 original size:20 final size:20
Alignment explanation
Indices: 3398816--3398853 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3398806 CACATGTTAA
3398816 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
3398836 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
3398854 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:3404082 original size:23 final size:23
Alignment explanation
Indices: 3404018--3404083 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
3404008 CACATAAATG
* *
3404018 TCCCAAAGCACCGCATAGAATTA
1 TCCCGAAGGACCGCATAGAATTA
* *
3404041 TCCCGAAGGACCACATAGAATTG
1 TCCCGAAGGACCGCATAGAATTA
* *
3404064 TCTCGAAGGACCGCGTAGAA
1 TCCCGAAGGACCGCATAGAA
3404084 CTCTTGAATC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (23 bp):
TCCCGAAGGACCGCATAGAATTA
Found at i:3404266 original size:19 final size:20
Alignment explanation
Indices: 3404239--3404280 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3404229 AAACATATGA
* *
3404239 AATACAATTTAA-GTAAAAT
1 AATAAAATTTAACATAAAAT
3404258 AATAAAATTTAACATAAAAT
1 AATAAAATTTAACATAAAAT
3404278 AAT
1 AAT
3404281 TTAAACAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAATTTAACATAAAAT
Found at i:3404713 original size:15 final size:16
Alignment explanation
Indices: 3404695--3404725 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3404685 CATACTATTG
3404695 GTATCGATACC-CTCA
1 GTATCGATACCACTCA
3404710 GTATCGATACCACTCA
1 GTATCGATACCACTCA
3404726 TGCAGTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (16 bp):
GTATCGATACCACTCA
Found at i:3408347 original size:23 final size:21
Alignment explanation
Indices: 3408301--3408380 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
3408291 CAGAACCCAG
* * **
3408301 GGGGGTATCGATTCCCCTGTA
1 GGGGGAATCGGTTCCCCTCAA
3408322 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
*
3408345 GGGGGAATCGGTT-CCCTCAG
1 GGGGGAATCGGTTCCCCTCAA
*
3408365 GGGGGAATCGATTCCC
1 GGGGGAATCGGTTCCC
3408381 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 13 0.26
21 19 0.38
22 4 0.08
23 14 0.28
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:3408370 original size:20 final size:21
Alignment explanation
Indices: 3408321--3408382 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 21
3408311 ATTCCCCTGT
3408321 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTT-CCC-TCAA
3408344 AGGGGGAATCGGTTCCCTC-A
1 AGGGGGAATCGGTTCCCTCAA
* *
3408364 GGGGGGAATCGATTCCCTC
1 AGGGGGAATCGGTTCCCTC
3408383 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.49
21 2 0.05
22 3 0.08
23 14 0.38
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCTCAA
Found at i:3411391 original size:2 final size:2
Alignment explanation
Indices: 3411384--3411435 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
3411374 ATGCATCATG
*
3411384 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3411425 TA TA TA TA TA T
1 TA TA TA TA TA T
3411436 CCCTATTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3416517 original size:18 final size:18
Alignment explanation
Indices: 3416496--3416535 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3416486 GGCATTCTTG
3416496 CAAAGTGGCCCATTATGC
1 CAAAGTGGCCCATTATGC
*
3416514 CAAAGTGGCCCATTCTGC
1 CAAAGTGGCCCATTATGC
3416532 CAAA
1 CAAA
3416536 TTCGGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (18 bp):
CAAAGTGGCCCATTATGC
Found at i:3417586 original size:22 final size:22
Alignment explanation
Indices: 3417555--3417597 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3417545 TCCACAAATG
*
3417555 TGTTTATTTAGCGTTCATTTAA
1 TGTTTATTTACCGTTCATTTAA
*
3417577 TGTTTGTTTACCGTTCATTTA
1 TGTTTATTTACCGTTCATTTA
3417598 GGATTCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (22 bp):
TGTTTATTTACCGTTCATTTAA
Found at i:3419272 original size:24 final size:24
Alignment explanation
Indices: 3419245--3419291 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3419235 AATGAGGGGA
*
3419245 CAAAGTATAATTAACTATAGAAAT
1 CAAAGTATAATTAACCATAGAAAT
3419269 CAAAGTATAATTAACCATAGAAA
1 CAAAGTATAATTAACCATAGAAA
3419292 ATAATTTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.26
Consensus pattern (24 bp):
CAAAGTATAATTAACCATAGAAAT
Found at i:3420776 original size:61 final size:62
Alignment explanation
Indices: 3420674--3420797 Score: 164
Period size: 61 Copynumber: 2.0 Consensus size: 62
3420664 CATAAATTTT
* *
3420674 AAATTAGGGTGTCATAATTTTAAAAAATTAGAAATTTTAAAT-AGTCATATATATTAATATA
1 AAATTAGGGTGTCATAATTTTAAAAAATTAGAAATTCTAAATAAATCATATATATTAATATA
* *
3420735 AAATTATGGTGGT-ATAATTTTATAAAATTA-AAACTTCTAAATAAAATCATATATATTAATATA
1 AAATTAGGGT-GTCATAATTTTAAAAAATTAGAAA-TTCTAAAT-AAATCATATATATTAATATA
3420798 TAATATAGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
60 3 0.05
61 32 0.58
62 2 0.04
63 18 0.33
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (62 bp):
AAATTAGGGTGTCATAATTTTAAAAAATTAGAAATTCTAAATAAATCATATATATTAATATA
Found at i:3421344 original size:60 final size:59
Alignment explanation
Indices: 3421270--3421401 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 59
3421260 ATCTAGATAT
* * * *
3421270 ATATATATATTTATATCAATGTAAGTATGTATTCATTTCTAGGTTCTAAGATAGCAAGAG
1 ATATATATACTTATACCAATGTAAATATGTATTCATTTCTAGGAT-TAAGATAGCAAGAG
* * * * **
3421330 ATATACATACTTATACCGATGTAAATATGTATTTATTTTTAGGATTAAGATAGTGAGAG
1 ATATATATACTTATACCAATGTAAATATGTATTCATTTCTAGGATTAAGATAGCAAGAG
*
3421389 ATGTATATACTTA
1 ATATATATACTTA
3421402 CGTCGATGTA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 23 0.38
60 37 0.62
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (59 bp):
ATATATATACTTATACCAATGTAAATATGTATTCATTTCTAGGATTAAGATAGCAAGAG
Found at i:3421409 original size:59 final size:60
Alignment explanation
Indices: 3421288--3421412 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 60
3421278 ATTTATATCA
* * *
3421288 ATGTAAGTATGTATTCATTTCTAGGTTCTAAGATAGCAAGAGATATACATACTTATACCG
1 ATGTAAATATGTATTCATTTCTAGGATCTAAGATAGCAAGAGATATACATACTTACACCG
* * ** * * **
3421348 ATGTAAATATGTATTTATTTTTAGGAT-TAAGATAGTGAGAGATGTATATACTTACGTCG
1 ATGTAAATATGTATTCATTTCTAGGATCTAAGATAGCAAGAGATATACATACTTACACCG
3421407 ATGTAA
1 ATGTAA
3421413 GCATGTGCTT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
59 31 0.57
60 23 0.43
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (60 bp):
ATGTAAATATGTATTCATTTCTAGGATCTAAGATAGCAAGAGATATACATACTTACACCG
Found at i:3426206 original size:28 final size:29
Alignment explanation
Indices: 3426174--3426233 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
3426164 GACATATTAG
3426174 TATTATCATTAA-TTTTTTAATAATAAAT
1 TATTATCATTAATTTTTTTAATAATAAAT
*
3426202 TATTATTATTAATTTTTTTAATAATAAAT
1 TATTATCATTAATTTTTTTAATAATAAAT
3426231 TAT
1 TAT
3426234 AATTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTATCATTAATTTTTTTAATAATAAAT
Found at i:3426589 original size:16 final size:17
Alignment explanation
Indices: 3426554--3426592 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3426544 TGTAAGATAG
3426554 TTTAATTTAAGATAATT
1 TTTAATTTAAGATAATT
*
3426571 TTTAATTTATA-ATATTT
1 TTTAATTTA-AGATAATT
3426588 TTTAA
1 TTTAA
3426593 CTATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTAATTTAAGATAATT
Found at i:3430412 original size:15 final size:15
Alignment explanation
Indices: 3430392--3430430 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3430382 AATTAGTGGG
3430392 CGGGTGGATTTGAGA
1 CGGGTGGATTTGAGA
3430407 CGGGTGGATTTGAGA
1 CGGGTGGATTTGAGA
3430422 CGGGTGGAT
1 CGGGTGGAT
3430431 GCGGAGCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.08, G:0.49, T:0.26
Consensus pattern (15 bp):
CGGGTGGATTTGAGA
Found at i:3437806 original size:18 final size:18
Alignment explanation
Indices: 3437773--3437807 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3437763 TACTACAATG
*
3437773 GTTATGATATTATTTAAC
1 GTTATGATATCATTTAAC
*
3437791 GTTATGATATCGTTTAA
1 GTTATGATATCATTTAA
3437808 TAAAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (18 bp):
GTTATGATATCATTTAAC
Found at i:3443128 original size:2 final size:2
Alignment explanation
Indices: 3443121--3443183 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
3443111 GTATTTAATA
3443121 AT AT AT 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
3443163 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
3443184 AGTGAAGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3444187 original size:12 final size:13
Alignment explanation
Indices: 3444170--3444212 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
3444160 ATATACAATA
3444170 ATTTATTTAT-TT
1 ATTTATTTATCTT
3444182 ATTTATTTATCTT
1 ATTTATTTATCTT
3444195 -TTATATTTATACTT
1 ATT-TATTTAT-CTT
3444209 ATTT
1 ATTT
3444213 CTGCATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.44
13 9 0.33
14 4 0.15
15 2 0.07
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTATTTATCTT
Found at i:3444438 original size:15 final size:15
Alignment explanation
Indices: 3444418--3444451 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3444408 AATTTTCATT
*
3444418 AAATAAGTTTACATG
1 AAATAAGTTTACACG
3444433 AAATAAGTTTACACG
1 AAATAAGTTTACACG
3444448 AAAT
1 AAAT
3444452 GAAGAGTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (15 bp):
AAATAAGTTTACACG
Found at i:3445262 original size:24 final size:24
Alignment explanation
Indices: 3445230--3445277 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3445220 TCTCAACATG
3445230 CTCAATTAAAGTAAATAAAACCTT
1 CTCAATTAAAGTAAATAAAACCTT
3445254 CTCAATTAAAGTAAATAAAACCTT
1 CTCAATTAAAGTAAATAAAACCTT
3445278 GGAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (24 bp):
CTCAATTAAAGTAAATAAAACCTT
Found at i:3456486 original size:23 final size:22
Alignment explanation
Indices: 3456444--3456504 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
3456434 ATAGGGTTGA
* *
3456444 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
3456466 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
3456489 GGGAACCTATTCCCCC
1 GGGAACCGATTCCCCC
3456505 CAGGGGAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:3461136 original size:21 final size:21
Alignment explanation
Indices: 3461110--3461154 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3461100 GATTTATGGG
* *
3461110 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
3461131 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
3461152 CAA
1 CAA
3461155 ACGACATAAT
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:3462324 original size:32 final size:32
Alignment explanation
Indices: 3462283--3462378 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
3462273 GAGTCGAGGG
3462283 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
3462315 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* * *
3462346 TATACCTATGTTCTAAGGAACATATGGATAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
3462378 T
1 T
3462379 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
31 25 0.46
32 29 0.54
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:3462411 original size:30 final size:30
Alignment explanation
Indices: 3462370--3462582 Score: 365
Period size: 30 Copynumber: 7.1 Consensus size: 30
3462360 AAGGAACATA
*
3462370 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
**
3462400 TGGACAGTTACCGAGGATCTTTATGATTTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3462430 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3462460 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3462490 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3462520 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
3462550 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3462579 TGGA
1 TGGA
3462583 TAGGTCCTTC
Statistics
Matches: 175, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 18 0.10
30 157 0.90
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:3465793 original size:23 final size:22
Alignment explanation
Indices: 3465749--3465793 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3465739 AATGCCAGAG
*
3465749 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
3465771 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
3465794 AAATGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:3466889 original size:32 final size:32
Alignment explanation
Indices: 3466848--3466943 Score: 108
Period size: 32 Copynumber: 3.0 Consensus size: 32
3466838 AAGTCGAGGG
*
3466848 TTTACCTATGTTCTACGGAACATATGGATAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
* *
3466880 TTTACCTATG-TCTTTC-GAGATATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
3466911 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
3466943 T
1 T
3466944 ACCGAGGATC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
31 25 0.48
32 27 0.52
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:3466936 original size:31 final size:30
Alignment explanation
Indices: 3466849--3466946 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
3466839 AGTCGAGGGT
* *
3466849 TTACCTATGTTCTACGGAACATATGGATAG
1 TTACCTATGTTCTAAGGAACATATGGACAG
*** *
3466879 TTTTACCTATG-TCTTTCGAGATATATGGACAG
1 --TTACCTATGTTCTAAGGA-ACATATGGACAG
3466911 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAG
3466942 TTACC
1 TTACC
3466947 GAGGATCTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
30 5 0.09
31 25 0.46
32 24 0.44
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (30 bp):
TTACCTATGTTCTAAGGAACATATGGACAG
Found at i:3466959 original size:23 final size:23
Alignment explanation
Indices: 3466933--3466985 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 23
3466923 CTAAGGAACA
3466933 TATGGACAGTTACCGAGGATCTT
1 TATGGACAGTTACCGAGGATCTT
3466956 TATGCTGGACAGTTACCGAGGATCTT
1 TA---TGGACAGTTACCGAGGATCTT
3466982 TATG
1 TATG
3466986 ACCTCTGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 4 0.15
26 23 0.85
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGGACAGTTACCGAGGATCTT
Found at i:3466996 original size:30 final size:30
Alignment explanation
Indices: 3466935--3467113 Score: 296
Period size: 30 Copynumber: 6.1 Consensus size: 30
3466925 AAGGAACATA
3466935 TGGACAGTTACCGAGGATCTTTATG----C
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3466961 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3466991 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3467021 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3467051 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
3467081 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
3467110 TGGA
1 TGGA
3467114 TAGGTCCTTC
Statistics
Matches: 146, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
26 25 0.17
29 18 0.12
30 103 0.71
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:3468849 original size:2 final size:2
Alignment explanation
Indices: 3468842--3468877 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3468832 ATTCATTGTG
3468842 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
3468878 TCGAGAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3473597 original size:28 final size:31
Alignment explanation
Indices: 3473544--3473616 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 31
3473534 GTTTGGATAG
* *
3473544 TTTAGATACCTATTTTGACAT-AAA-AT-AC
1 TTTAGATACTTATTTTAACATAAAATATAAC
3473572 TTTAGATACTTATTTTAACA-AGAAATATAAC
1 TTTAGATACTTATTTTAACATA-AAATATAAC
*
3473603 TTTAGGTACTTATT
1 TTTAGATACTTATT
3473617 CTGATTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 18 0.47
29 3 0.08
30 2 0.05
31 15 0.39
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTAGATACTTATTTTAACATAAAATATAAC
Found at i:3477176 original size:20 final size:20
Alignment explanation
Indices: 3477082--3477450 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
3477072 GATTTTCCAT
* ** *
3477082 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3477102 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3477122 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3477142 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
3477162 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3477182 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3477202 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3477222 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3477242 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3477262 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3477282 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3477302 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3477322 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
3477342 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3477362 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3477382 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3477402 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3477422 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3477442 AATCACAAC
1 AATCGCAAC
3477451 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3478163 original size:24 final size:24
Alignment explanation
Indices: 3478124--3478170 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3478114 AAATTTGGTC
3478124 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3478148 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3478171 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3478362 original size:12 final size:12
Alignment explanation
Indices: 3478345--3478369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3478335 ATATAATCCT
3478345 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3478357 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3478369 G
1 G
3478370 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3480697 original size:19 final size:19
Alignment explanation
Indices: 3480675--3480979 Score: 338
Period size: 19 Copynumber: 17.4 Consensus size: 19
3480665 CGGAAAATAC
*
3480675 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3480694 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
3480708 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3480727 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3480741 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3480760 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3480779 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3480793 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3480812 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
3480831 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
3480845 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
3480864 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
3480883 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
3480901 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3480920 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3480934 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3480953 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3480972 AATCGCAA
1 AATCGCAA
3480980 CGAGATAATC
Statistics
Matches: 245, Mismatches: 15, Indels: 52
0.79 0.05 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.07
17 15 0.06
18 22 0.09
19 143 0.58
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3480717 original size:33 final size:33
Alignment explanation
Indices: 3480675--3481001 Score: 172
Period size: 33 Copynumber: 9.5 Consensus size: 33
3480665 CGGAAAATAC
*
3480675 AATCGCAACGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACATGAA
* * *
3480708 AATCGCAACGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
* *
3480741 AATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAAAATC-CCA----ACATGAA
* * * * *
3480779 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAA
* *
3480812 AATCGCAATGCGAAATGAAAAT-CGAAC-CGACA
1 AATCGCAATGCGAAATGAAAATCCCAACATGA-A
* *
3480844 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 -AATCGCAATGCGAAATGAAAATC-CCA-AC---ATGAA
*
3480883 AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
* *
3480920 AATCGCAA--CGAAA-GAATCGCAATGCGAA-ATGAA
1 AATCGCAATGCGAAATGAA----AATCCCAACATGAA
* *
3480953 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
3480986 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
3481002 TATAAACGCA
Statistics
Matches: 233, Mismatches: 29, Indels: 64
0.71 0.09 0.20
Matches are distributed among these distances:
31 7 0.03
32 12 0.05
33 119 0.51
34 5 0.02
35 14 0.06
36 6 0.03
37 23 0.10
38 32 0.14
39 12 0.05
40 3 0.01
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAA
Found at i:3480735 original size:52 final size:52
Alignment explanation
Indices: 3480675--3480927 Score: 253
Period size: 52 Copynumber: 4.8 Consensus size: 52
3480665 CGGAAAATAC
* *
3480675 AATCGCAACGCGA-AAT-GAAAATCCCAACATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGAATCG-AAATCCGAA-ATGAAAATCGCAATGCGAAATGAA
* * * *
3480727 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * *
3480779 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * * * *
3480831 AATCG-AAC-CGACATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAACGCG--AGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * *
3480883 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGCG--A-G-AATCGAAATCCGAAATGAAAATCGCAA
3480928 CGAAAGAATC
Statistics
Matches: 178, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
50 1 0.01
51 3 0.02
52 132 0.74
53 11 0.06
54 5 0.03
56 26 0.15
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:3480972 original size:52 final size:53
Alignment explanation
Indices: 3480741--3481001 Score: 269
Period size: 52 Copynumber: 4.9 Consensus size: 53
3480731 GCAACGAGAG
* *
3480741 AATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATG--AATCGCAATGCGAAATGAA
**
3480793 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA----AAT-CGAACCGACA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATGAATCGCAATGCGAAATGA-A
*
3480844 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATG-A
1 -AATCGCAATGCGAAATGAAAATCGC-A-ACGAAATG--AATCGCAATGCGAAATGAA
3480901 AATCGCAATGCGAAATGAAAATCGCAACGAAA-GAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
*
3480953 AATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAAT
3481002 TATAAACGCA
Statistics
Matches: 184, Mismatches: 8, Indels: 34
0.81 0.04 0.15
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
50 4 0.02
51 17 0.09
52 114 0.62
53 2 0.01
54 9 0.05
55 1 0.01
56 24 0.13
57 1 0.01
58 3 0.02
59 5 0.03
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
Found at i:3481117 original size:19 final size:19
Alignment explanation
Indices: 3481008--3481109 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3480998 AAATTATAAA
3481008 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3481027 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3481047 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3481063 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3481080 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3481099 CGCATTGCGAT
1 CGCATTGCGAT
3481110 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3481234 original size:14 final size:14
Alignment explanation
Indices: 3481215--3481251 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3481205 CATCAATTAC
3481215 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3481229 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3481243 ACAAATCAA
1 ACAAATCAA
3481252 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3483229 original size:14 final size:14
Alignment explanation
Indices: 3483210--3483266 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3483200 GCGAAATGAA
*
3483210 AATCGCAACGACAG
1 AATCGCAACGAAAG
3483224 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3483241 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3483257 AATCGCAACG
1 AATCGCAACG
3483267 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3483237 original size:33 final size:33
Alignment explanation
Indices: 3483191--3483282 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
3483181 GCGAAACCAA
*
3483191 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3483224 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3483257 AATCGCAACGCGAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
3483283 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3483288 original size:19 final size:19
Alignment explanation
Indices: 3483154--3483282 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3483144 TAGTTTACTT
* *
3483154 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3483174 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3483193 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3483212 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3483226 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3483245 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3483259 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3483278 TCGCA
1 TCGCA
3483283 TTGCGATTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 42 0.46
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3483325 original size:33 final size:33
Alignment explanation
Indices: 3483283--3483375 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
3483273 GAAAATCGCA
3483283 TTGCGATTTTCATTTCGCGTTGCGA-TCTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTC-TGTCG
**
3483316 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3483349 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3483376 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3483404 original size:20 final size:19
Alignment explanation
Indices: 3483278--3483412 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
3483268 GAAATGAAAA
*
3483278 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
3483297 TCGCGTTGCGATCTT-G--
1 TCGCGTTGCGATTTTAGTT
*
3483313 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
3483330 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
3483346 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
3483363 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
3483382 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
3483402 TCGTGTTGCGA
1 TCGCGTTGCGA
3483413 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 53 0.56
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.27, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:3483615 original size:93 final size:93
Alignment explanation
Indices: 3483456--3483928 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
3483446 TTGAATGGAT
3483456 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3483521 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3483549 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3483614 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3483642 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3483707 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3483735 AAATTTACTTTCAACCAAAAGACAAAACAACGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3483799 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3483827 AAATTTACTTTCAACCAAAAGACAAAATAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3483892 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3483920 AAATTTACT
1 AAATTTACT
3483929 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 90 0.24
93 286 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3483901 original size:185 final size:186
Alignment explanation
Indices: 3483456--3483928 Score: 921
Period size: 185 Copynumber: 2.5 Consensus size: 186
3483446 TTGAATGGAT
3483456 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3483521 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3483586 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
3483642 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3483707 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAACGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
3483772 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
3483827 AAATTTACTTTCAACCAAAAGACAAAATAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3483892 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
3483929 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 154 0.54
186 131 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3485652 original size:14 final size:14
Alignment explanation
Indices: 3485633--3485722 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3485623 TTGAAATGAA
3485633 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3485647 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
3485664 ACAATCACAACGAGAG
1 --AATCGCAACGAGAG
*
3485680 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3485699 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3485713 AATCGCAACG
1 AATCGCAACG
3485723 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3485675 original size:33 final size:33
Alignment explanation
Indices: 3485625--3485739 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
3485615 TCTTTTGGTT
3485625 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
3485658 GAGATGACAATCACAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3485691 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3485724 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3485740 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3485704 original size:19 final size:19
Alignment explanation
Indices: 3485680--3485744 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
3485670 ACAACGAGAG
3485680 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3485699 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3485713 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3485732 AATCGCAATGCGA
1 AATCGCAACGCGA
3485745 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3485775 original size:14 final size:14
Alignment explanation
Indices: 3485756--3485810 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3485746 TTTGGTTTCG
3485756 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3485770 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
3485789 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3485803 CGTTGCGA
1 CGTTGCGA
3485811 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3485973 original size:33 final size:33
Alignment explanation
Indices: 3485931--3486001 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3485921 AATACTAACT
*
3485931 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3485964 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3485997 TGAAA
1 TGAAA
3486002 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3486235 original size:22 final size:22
Alignment explanation
Indices: 3486183--3486237 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3486173 TGGTTGTGAG
**
3486183 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3486205 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3486227 GGATTTCTTCG
1 GGATTTCTTCG
3486238 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3486408 original size:20 final size:20
Alignment explanation
Indices: 3486383--3486576 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3486373 CTTTAAATAT
3486383 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3486403 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3486425 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3486444 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3486464 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3486484 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3486504 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3486524 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3486544 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3486564 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3486577 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3486570 original size:60 final size:60
Alignment explanation
Indices: 3486383--3486576 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3486373 CTTTAAATAT
**
3486383 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3486444 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3486504 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3486564 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3486577 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3486593 original size:21 final size:20
Alignment explanation
Indices: 3486569--3486645 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
3486559 ATATTCGCGT
3486569 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
3486590 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
3486610 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
3486632 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
3486646 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:3486656 original size:20 final size:20
Alignment explanation
Indices: 3486631--3486682 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3486621 AAGAATCGCG
*
3486631 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3486651 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3486671 TTGCGATTCTGG
1 TTGCGATTCTGG
3486683 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:3491589 original size:35 final size:35
Alignment explanation
Indices: 3491543--3491640 Score: 162
Period size: 35 Copynumber: 2.8 Consensus size: 35
3491533 TGTTTTTAAA
*
3491543 AAAAATGATAGTTTATGTACTAATTAAAATGGACT
1 AAAACTGATAGTTTATGTACTAATTAAAATGGACT
3491578 AAAACTGATAGTTTATGTACTAATTAAAATGGACT
1 AAAACTGATAGTTTATGTACTAATTAAAATGGACT
*
3491613 AAAACTGATAGTTTGA-GTACTAAATAAA
1 AAAACTGATAGTTT-ATGTACTAATTAAA
3491641 TAATTTACCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 59 0.98
36 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (35 bp):
AAAACTGATAGTTTATGTACTAATTAAAATGGACT
Found at i:3492352 original size:24 final size:23
Alignment explanation
Indices: 3492319--3492412 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 23
3492309 TGGGATGAAT
*
3492319 ATAAACGAACGAACATACACAGAC
1 ATAAATGAACGAACATACAC-GAC
* *
3492343 ATAAATGAACAAACATAAACGA-
1 ATAAATGAACGAACATACACGAC
* *
3492365 ATAAACATAAACGAACATGCACGGAC
1 AT-AA-ATGAACGAACATACAC-GAC
*
3492391 ATAAATGAACGAACATAAACGA
1 ATAAATGAACGAACATACACGA
3492413 GCGGATTACC
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
22 2 0.04
23 6 0.11
24 42 0.75
25 4 0.07
26 2 0.04
ACGTcount: A:0.56, C:0.19, G:0.13, T:0.12
Consensus pattern (23 bp):
ATAAATGAACGAACATACACGAC
Found at i:3492360 original size:14 final size:14
Alignment explanation
Indices: 3492341--3492381 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
3492331 ACATACACAG
*
3492341 ACATAAATGAACAA
1 ACATAAACGAACAA
*
3492355 ACATAAACGAATAA
1 ACATAAACGAACAA
3492369 ACATAAACGAACA
1 ACATAAACGAACA
3492382 TGCACGGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.63, C:0.17, G:0.07, T:0.12
Consensus pattern (14 bp):
ACATAAACGAACAA
Found at i:3494693 original size:31 final size:31
Alignment explanation
Indices: 3494655--3494779 Score: 132
Period size: 31 Copynumber: 4.0 Consensus size: 31
3494645 CCCGAAGGAC
* *
3494655 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATTCCGAAGAACATAGGTAAA
*
3494686 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACATAGGTAAA
3494717 CAGTCCAT--ATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATAGAT-TC-CGAAGAACATAGGTAAA
* * *
3494748 CAATCCATATG-TCCCAAAGAACATAGGTAAA
1 CAGTCCATA-GATTCCGAAGAACATAGGTAAA
3494779 C
1 C
3494780 CCTCGACCCT
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
29 1 0.01
30 1 0.01
31 75 0.94
32 2 0.03
33 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATAGATTCCGAAGAACATAGGTAAA
Found at i:3495691 original size:22 final size:21
Alignment explanation
Indices: 3495666--3495725 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
3495656 TTCGCTTGAG
*
3495666 GGGTATCAATTCCCCATTGAAT
1 GGGTATCGATTCCCC-TTGAAT
3495688 GGGTATCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
*
3495708 GGGTACCGATTCCCCTTG
1 GGGTATCGATTCCCCTTG
3495726 CCCAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:3496584 original size:16 final size:16
Alignment explanation
Indices: 3496545--3496587 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3496535 CCACTCAGTT
*
3496545 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
3496561 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
3496578 CTTATCAATC
1 CTTATCAATC
3496588 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:3498221 original size:31 final size:31
Alignment explanation
Indices: 3498197--3498307 Score: 195
Period size: 31 Copynumber: 3.6 Consensus size: 31
3498187 CCATAGATTT
* *
3498197 CGAAGAACCTAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
3498228 CGAAGAACATAGGTAAACAGTTCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
3498259 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
3498290 CGAAGAACATAGGTAAAC
1 CGAAGAACATAGGTAAAC
3498308 CCTCGACCCT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:3499219 original size:22 final size:21
Alignment explanation
Indices: 3499194--3499253 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
3499184 TTCGCTTGAG
*
3499194 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
3499216 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
*
3499236 CGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
3499254 CCCAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:3503449 original size:27 final size:27
Alignment explanation
Indices: 3503399--3503467 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
3503389 TTATTATACT
3503399 TGTTGAACTATA-TACATTTCACTTAA
1 TGTTGAACTATATTACATTTCACTTAA
*
3503425 TGTTGAACTATATTACATTTGACTTAA
1 TGTTGAACTATATTACATTTCACTTAA
* *
3503452 TGTCGAACTACATTAC
1 TGTTGAACTATATTAC
3503468 TTGAATGGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 12 0.31
27 27 0.69
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (27 bp):
TGTTGAACTATATTACATTTCACTTAA
Found at i:3503823 original size:42 final size:42
Alignment explanation
Indices: 3503713--3503871 Score: 117
Period size: 43 Copynumber: 3.7 Consensus size: 42
3503703 GACGTTTATA
* ** * * * *
3503713 AAAAACGCCGCTAAATGTAATAACCCATTGTGGCGTTTATACA
1 AAAAACACCGCTAAATGTACGAACCTATTGCGGCGTTTA-GCT
* * * *
3503756 AAAAATACCACTAAATAT-CATAACCTATTGCGGCGTTTAGCT
1 AAAAACACCGCTAAATGTAC-GAACCTATTGCGGCGTTTAGCT
* * *
3503798 AAAAACACCGCTAAATGTACGAACCTATTACGACGTTTTG-T
1 AAAAACACCGCTAAATGTACGAACCTATTGCGGCGTTTAGCT
*
3503839 AAACAAGCGCCGCTAAAAT-TACGAACCTATTGC
1 AAA-AA-CACCGCT-AAATGTACGAACCTATTGC
3503872 AACATTTTTT
Statistics
Matches: 93, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 4 0.04
42 34 0.37
43 51 0.55
44 4 0.04
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (42 bp):
AAAAACACCGCTAAATGTACGAACCTATTGCGGCGTTTAGCT
Found at i:3504004 original size:22 final size:21
Alignment explanation
Indices: 3503969--3504010 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3503959 TTTTTGCGAC
*
3503969 ACTTACAAACGCCACTATAGG
1 ACTTAAAAACGCCACTATAGG
3503990 ACTTAAAAAGCGCCACTATAG
1 ACTTAAAAA-CGCCACTATAG
3504011 CCCCATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.19
Consensus pattern (21 bp):
ACTTAAAAACGCCACTATAGG
Found at i:3512695 original size:20 final size:20
Alignment explanation
Indices: 3512670--3512710 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3512660 TGCTTGATTT
*
3512670 TACTGTAGCA-GTATCGATAC
1 TACTGTAG-AGGTATCAATAC
3512690 TACTGTAGAGGTATCAATAC
1 TACTGTAGAGGTATCAATAC
3512710 T
1 T
3512711 TATTTTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (20 bp):
TACTGTAGAGGTATCAATAC
Found at i:3512797 original size:20 final size:20
Alignment explanation
Indices: 3512762--3512809 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3512752 TATTTTGTTT
* *
3512762 ATACAATATTGGTACTAGTC
1 ATACAGTATCGGTACTAGTC
* *
3512782 ATATAGTATCGGTACTATTC
1 ATACAGTATCGGTACTAGTC
3512802 ATACAGTA
1 ATACAGTA
3512810 CATTACTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
ATACAGTATCGGTACTAGTC
Found at i:3513800 original size:23 final size:23
Alignment explanation
Indices: 3513757--3513800 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
3513747 ACTTTTTCTT
*
3513757 TTTTATTTACTTTTTATATTTCA
1 TTTTATTTACTTTTTAAATTTCA
*
3513780 TTTT-TTTAGTTTTTAGAATTT
1 TTTTATTTACTTTTTA-AATTT
3513801 TTTAGAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTTATTTACTTTTTAAATTTCA
Found at i:3514811 original size:18 final size:18
Alignment explanation
Indices: 3514788--3514825 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3514778 GATGGTGGGA
3514788 ATATTAA-AATATTAAAAG
1 ATATTAATAAT-TTAAAAG
*
3514806 ATATTAATAATTTAAGAG
1 ATATTAATAATTTAAAAG
3514824 AT
1 AT
3514826 GGTAAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (18 bp):
ATATTAATAATTTAAAAG
Found at i:3515605 original size:23 final size:23
Alignment explanation
Indices: 3515574--3515646 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
3515564 ATATGTAAAA
* *
3515574 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGTTT
*
3515597 ATATAATGTAATAAGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
3515620 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGCGTTT
3515643 ATAT
1 ATAT
3515647 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:3516044 original size:22 final size:22
Alignment explanation
Indices: 3516000--3516044 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3515990 ATTACATAAC
*
3516000 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGAACCTT
*
3516022 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATCGAAC-CTT
3516044 T
1 T
3516045 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGAACCTT
Found at i:3516092 original size:23 final size:23
Alignment explanation
Indices: 3516062--3516134 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
3516052 ATAGGTAAAA
3516062 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3516085 ATATAATGTAATAAGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
3516108 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
3516131 ATAT
1 ATAT
3516135 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3516139 original size:488 final size:489
Alignment explanation
Indices: 3515145--3518468 Score: 5504
Period size: 488 Copynumber: 6.8 Consensus size: 489
3515135 TTTTTACATG
* *
3515145 TTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTCCATACTTTTTTCAGTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* * **
3515210 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
3515275 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAAC----ATA-T--ATAT
*
3515340 TACATATTTATTATTATCTCTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAA
189 TACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAA
*
3515405 TATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAA
254 TATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAA
* **
3515470 CATGAAACACTGTTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAA-TATCGATATTT
319 CATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTT
*
3515534 TTTATAAAAAGTATGGACACTTTCAATATAATATGTAAAAATATGATGTAATAGGTAGCGCTTAT
383 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
*
3515599 ATAATGTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGT
448 ATAATGTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
3515641 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
*
3515706 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
* *
3515771 TTATTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
* *
3515836 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
* *
3515901 ACAAACAAATAA-TTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
3515965 CACTATTAAAAAAATTAAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
326 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
* *
3516030 AAGTATGAACACTTTCAATATAATAGGTAAAAATATAATGTAATAGGTAGCGCTTATATAATGTA
391 AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
3516095 ATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
456 ATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
* *
3516129 TTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATATTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
3516194 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATA-G-ACGTCTAATG
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTA--TCTAATG
* *
3516257 ATTTATGTTTTACGTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACAT
129 ATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACAT
* *
3516322 ATTTATTATTATTTTTGGTTAATATTTTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
194 ATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCA
* * *
3516387 AAACAATAAAATAATTTTTTGTGTAAATTAAATTATTAAATTATTATTGTAGGTGGAAAACATGA
259 AAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGA
* *
3516452 AACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCATTTTTAT
324 AACACTATTAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTTTTTAT
*
3516517 AAAAAGTATGGACACTTTCAATATAATAGGTAAATATATGATGTAATAGGTAGCGCTTATATAAT
388 AAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAAT
* * *
3516582 GTAATATGTATCGTTTATATAATGTAATAGGTAGTGT
453 GTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
* *
3516619 TTATATTGTAAAATATCTATCATTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
*
3516684 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
* *
3516749 TTATTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
* * *
3516814 TTATTATTATATTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
*
3516879 ACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
3516944 CACTATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAGAGTATCGATCCTTTTTATAAA
326 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
* *
3517008 AAGTATGGACGCTTTCAATATAATAGGT-ACAA-AT-ATG----A--T---G--TA-AT-A-G--
391 AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
3517054 ----GTAGCGTTTATATAATGTAATAGGTAGTGC
456 ATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
* * * *
3517084 TTATATTGTAAAATATCTATCCTTTTTATAAAAGTATCCATACTTTTTTCACTGTAGAAAATATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* * *
3517149 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGTGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
* **
3517214 TTATTTTTTACATTACATTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
3517279 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
* *
3517344 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTATAGGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
3517409 CTCTATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
326 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
* * *
3517473 AAGTATGAACGCTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAATGTA
391 AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
* *
3517538 ATAGGTAGCGTTTATATAATGTAATAGGTAGTGT
456 ATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
* *
3517572 TTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTCAATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
3517637 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
* * *
3517702 TTATTTTTTATGTTACGGTATATATTATCATTAAATTAAGAACAATAAACATATATATTACATAT
131 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
* *
3517767 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
* * *
3517832 ACAATCAAATAATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
*
3517897 CACTATT-AAAAAATTGAAACATAAATTACGTAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
326 CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
* *
3517961 AAGTATGGGCACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCCCTTATATAATGTA
391 AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
*
3518026 ATAGGTAGCGTTTATATAATGTAATAGGTAGTGC
456 ATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
3518060 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* * *
3518125 AATTTAATGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATA-GGAGTCTAATGA
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTA-TCTAATGA
* *
3518189 TTTATTTTTTACATTACAGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATA
130 TTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATA
3518254 TTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAA
195 TTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAA
*
3518319 AACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTGTAGGTGGAAAACATGAA
260 AACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
*
3518384 ACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAA
325 ACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTAT-A
*
3518449 AAAAGTATGGATACTTTCAA
389 AAAAGTATGGACACTTTCAA
3518469 CATATTATAA
Statistics
Matches: 2650, Mismatches: 145, Indels: 72
0.92 0.05 0.03
Matches are distributed among these distances:
465 423 0.16
466 3 0.00
467 2 0.00
468 3 0.00
471 1 0.00
472 2 0.00
473 2 0.00
474 3 0.00
476 1 0.00
479 3 0.00
480 2 0.00
481 2 0.00
482 1 0.00
485 3 0.00
486 3 0.00
487 42 0.02
488 1275 0.48
489 252 0.10
490 450 0.17
491 2 0.00
492 4 0.00
496 171 0.06
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (489 bp):
TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAA
CACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
ATAAGTAGCGTTTATATAATGTAATAGGTAGTGC
Found at i:3516583 original size:23 final size:23
Alignment explanation
Indices: 3516551--3516624 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
3516541 AATAGGTAAA
* *
3516551 TATATGATGTAATAGGTAGCGCT
1 TATATAATGTAATAGGTAGCGTT
* *
3516574 TATATAATGTAATATGTATCGTT
1 TATATAATGTAATAGGTAGCGTT
*
3516597 TATATAATGTAATAGGTAGTGTT
1 TATATAATGTAATAGGTAGCGTT
3516620 TATAT
1 TATAT
3516625 TGTAAAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCGTT
Found at i:3516634 original size:46 final size:46
Alignment explanation
Indices: 3516551--3516649 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 46
3516541 AATAGGTAAA
* * *
3516551 TATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTT
1 TATATAATGTAATAGGTAGCGCTTATATAATGTAATATCTATCATT
* *
3516597 TATATAATGTAATAGGTAGTG-TT-TATATTGTAAAATATCTATCATT
1 TATATAATGTAATAGGTAGCGCTTATATAATGT--AATATCTATCATT
*
3516643 TTTATAA
1 TATATAA
3516650 AAGTGTCCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 7 0.16
45 2 0.04
46 36 0.80
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.44
Consensus pattern (46 bp):
TATATAATGTAATAGGTAGCGCTTATATAATGTAATATCTATCATT
Found at i:3517071 original size:23 final size:23
Alignment explanation
Indices: 3517040--3517089 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3517030 ATAGGTACAA
* *
3517040 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
3517063 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
3517086 ATAT
1 ATAT
3517090 TGTAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3517129 original size:21 final size:20
Alignment explanation
Indices: 3517092--3517131 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3517082 GCTTATATTG
* *
3517092 TAAAATATCTATCCTTTTTA
1 TAAAATATCCATACTTTTTA
3517112 TAAAAGTATCCATACTTTTT
1 TAAAA-TATCCATACTTTTT
3517132 TCACTGTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAATATCCATACTTTTTA
Found at i:3517487 original size:22 final size:22
Alignment explanation
Indices: 3517443--3517487 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3517433 ATTACATAAC
*
3517443 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGAACCTT
*
3517465 TTTATAAAAAGTAT-GAACGCTT
1 TTTAAAAAAAGTATCGAAC-CTT
3517487 T
1 T
3517488 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGAACCTT
Found at i:3517573 original size:23 final size:23
Alignment explanation
Indices: 3517505--3517577 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
3517495 ATAGGTAAAA
* **
3517505 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGTTT
3517528 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
3517551 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGCGTTT
3517574 ATAT
1 ATAT
3517578 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:3517938 original size:953 final size:955
Alignment explanation
Indices: 3515145--3518468 Score: 5596
Period size: 953 Copynumber: 3.4 Consensus size: 955
3515135 TTTTTACATG
* *
3515145 TTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTCCATACTTTTTTCAGTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
3515210 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
66 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
* *
3515275 TTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACATTACAGTATATATTATTATTAAATTAAAAACAATAAAC----ATA-T--ATAT
*
3515340 TACATATTTATTATTATCTCTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAA
189 TACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAA
*
3515405 TATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAA
254 TATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTATAGGTGGAAAA
**
3515470 CATGAAACACTGTTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAA-TATCGATATTT
319 CATGAAACACTGTT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTT
*
3515534 TTTATAAAAAGTATGGACACTTTCAATATAATATGTAAAAATATGATGTAATAGGTAGCGCTTAT
383 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
3515599 ATAATGTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGTTTATATTGTAAAGTATCTATCCT
448 ATAATGTAATAAGTAGCGTTTATATAATGTAATAGGTAGTGTTTATATTGTAAAGTATCTATCCT
3515664 TTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTG
513 TTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTG
3515729 AGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATAT
578 AGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATAT
3515794 ATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATAT
643 ATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATAT
*
3515859 TGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAAACAAATAA-TTTTTGTGCA
708 TGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
*
3515923 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTAAAACAT
773 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAATTGAAACAT
*
3515988 AAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAA
837 AAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
3516053 TAGGTAAAAATATAATGTAATAGGTAGCGCTTATATAATGTAATAAGTAGCGTTTATATAATGTA
902 TAGGT-AAAA-AT-ATG---TA--T---G--TA-AT-A-G------GTAGCGTTTATATAATGTA
3516118 ATAGGTAGTGC
945 ATAGGTAGTGC
* *
3516129 TTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATATTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* *
3516194 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGACGTCTAATGAT
66 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
* *
3516259 TTATGTTTTACGTTAC-GATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATA
131 TTATTTTTTACATTACAG-TATATATTATTATTAAATTAAAAACAATAAACATATATATTACATA
* *
3516323 TTTATTATTATTTTTGGTTAATATTTTTAAATTTAAATACTAAATAATATTTTATAAAATATCAA
195 TTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAA
* * *
3516388 AACAATAAAATAATTTTTTGTGTAAATTAAATTATTAAATTATTATTGTAGGTGGAAAACATGAA
260 AACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTATAGGTGGAAAACATGAA
*
3516453 ACACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCATTTTTATA
325 ACACTGTTAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTTTTTATA
*
3516518 AAAAGTATGGACACTTTCAATATAATAGGTAAATATATGATGTAATAGGTAGCGCTTATATAATG
389 AAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATG
* * * *
3516583 TAATATGTATCGTTTATATAATGTAATAGGTAGTGTTTATATTGTAAAATATCTATCATTTTTAT
454 TAATAAGTAGCGTTTATATAATGTAATAGGTAGTGTTTATATTGTAAAGTATCTATCCTTTTTAT
3516648 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
519 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
3516713 AAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATATATTATC
584 AAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATATATTATC
*
3516778 ATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATATTTGGTTAATATTGTTAA
649 ATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAA
3516843 ATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAA
714 ATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAA
3516908 ATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTAC
779 ATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTAC
* * *
3516973 ATAACTTTAAAAAGAGTATCGATCCTTTTTATAAAAAGTATGGACGCTTTCAATATAATAGGTAC
844 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
3517038 AAATATG-ATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGC
909 AAATATGTATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGC
* * * *
3517084 TTATATTGTAAAATATCTATCCTTTTTATAAAAGTATCCATACTTTTTTCACTGTAGAAAATATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
*
3517149 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGTGTCTAATGAT
66 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
*
3517214 TTATTTTTTACATTACATTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACATTACAGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
3517279 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
3517344 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTATAGGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTATAGGTGGAAAACATGAAA
* *
3517409 CTCTATT-AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
326 CACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
* * *
3517473 AAGTATGAACGCTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCACTTATATAATGTA
391 AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
* *
3517538 ATAGGTAGCGTTTATATAATGTAATAGGTAGTGTTTATATTGTAAAGTATTTATCCTTTTTATAA
456 ATAAGTAGCGTTTATATAATGTAATAGGTAGTGTTTATATTGTAAAGTATCTATCCTTTTTATAA
*
3517603 AAGTGTCAATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
521 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
*
3517668 GATATTAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATATATTATCAT
586 GATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATATATTATCAT
*
3517733 TAAATTAAGAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
651 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
*
3517798 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
716 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
* *
3517863 TATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTACGT
781 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTACAT
*
3517928 AACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGGCACTTTCAATATAATAGGTAAAA
846 AACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGT----
3517993 ATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGT
907 A-A--A---AATA--T-G--------T-ATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGT
3518058 GC
954 GC
3518060 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* *
3518125 AATTTAATGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGAGTCTAATGAT
66 AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
3518190 TTATTTTTTACATTACAGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTATTTTTTACATTACAGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
3518255 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
196 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
*
3518320 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTGTAGGTGGAAAACATGAAA
261 ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTATAGGTGGAAAACATGAAA
3518385 CACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
326 CACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTAT-AA
*
3518450 AAAGTATGGATACTTTCAA
390 AAAGTATGGACACTTTCAA
3518469 CATATTATAA
Statistics
Matches: 2228, Mismatches: 82, Indels: 66
0.94 0.03 0.03
Matches are distributed among these distances:
953 523 0.23
954 30 0.01
955 342 0.15
957 1 0.00
960 1 0.00
961 1 0.00
962 1 0.00
963 6 0.00
964 2 0.00
965 1 0.00
966 2 0.00
969 1 0.00
971 1 0.00
975 3 0.00
976 394 0.18
977 205 0.09
978 479 0.21
979 60 0.03
980 3 0.00
983 1 0.00
984 171 0.08
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (955 bp):
TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
AATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
TTATTTTTTACATTACAGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAA
ACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTATTATTATAGGTGGAAAACATGAAA
CACTGTTAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAA
AAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTA
ATAAGTAGCGTTTATATAATGTAATAGGTAGTGTTTATATTGTAAAGTATCTATCCTTTTTATAA
AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
GATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTATGTTACGGTATATATTATCAT
TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAATTGAAACATAAATTACAT
AACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
ATATGTATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGC
Found at i:3518024 original size:23 final size:23
Alignment explanation
Indices: 3517993--3518065 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
3517983 ATAGGTAAAA
* *
3517993 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCGCTT
*
3518016 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
3518039 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
3518062 ATAT
1 ATAT
3518066 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3518445 original size:22 final size:23
Alignment explanation
Indices: 3518420--3518465 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3518410 ATTACATAAC
*
3518420 TTTA-AAAAAAGTATCGATCCTT
1 TTTATAAAAAAGTATCGATACTT
*
3518442 TTTATAAAAAAGTATGGATACTT
1 TTTATAAAAAAGTATCGATACTT
3518465 T
1 T
3518466 CAACATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (23 bp):
TTTATAAAAAAGTATCGATACTT
Found at i:3521375 original size:2 final size:2
Alignment explanation
Indices: 3521368--3521426 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
3521358 ATCATTGTGA
3521368 AT AT AT 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
3521410 AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT
3521427 TCATAAATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3523065 original size:73 final size:73
Alignment explanation
Indices: 3522933--3523079 Score: 206
Period size: 73 Copynumber: 2.0 Consensus size: 73
3522923 TTTTTAAGTT
** * * *
3522933 TAATAATTAAAAAATATATTTAAACATATTTTTTTTATTTCAAACACTCGAAAATATGATAATTC
1 TAATAATTAAAAAATATATTTAAACATA-TTTTTTTATTAAAAAAACTCGAAAACATGATAATCC
*
3522998 AGTGGGCCC
65 AGTAGGCCC
*
3523007 TAATAATTAAAAAATATTTTTAAACATCA-TTTTTTATTAAAAAAACTCGAAAACATGATAATCC
1 TAATAATTAAAAAATATATTTAAACAT-ATTTTTTTATTAAAAAAACTCGAAAACATGATAATCC
3523071 AGTAGGCCC
65 AGTAGGCCC
3523080 CATTTTAATG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 38 0.58
74 26 0.40
75 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (73 bp):
TAATAATTAAAAAATATATTTAAACATATTTTTTTATTAAAAAAACTCGAAAACATGATAATCCA
GTAGGCCC
Found at i:3526687 original size:22 final size:22
Alignment explanation
Indices: 3526637--3526690 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
3526627 TAACGTAATT
* * *
3526637 ATATATCTATTTTTATATTTTT
1 ATATATCTATTTTAATAATTTA
* *
3526659 TTTTATCTATTTTAATAATTTA
1 ATATATCTATTTTAATAATTTA
3526681 ATATATCTAT
1 ATATATCTAT
3526691 GAATTTATCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATATCTATTTTAATAATTTA
Found at i:3527683 original size:31 final size:32
Alignment explanation
Indices: 3527600--3527689 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 32
3527590 TGACTGAATA
* * * *
3527600 TAAAAGTCAAATTAGTGTTTT-ATTTAAAATT
1 TAAAAATCAAATTAATATTTTGATCTAAAATT
*
3527631 TAAAAATTAAATTAATA-TTTGATCTAAAATT
1 TAAAAATCAAATTAATATTTTGATCTAAAATT
* *
3527662 T-AGAATCAAATTAATATTTTGATGTAAA
1 TAAAAATCAAATTAATATTTTGATCTAAA
3527690 GTTCCAATAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 16 0.33
31 33 0.67
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (32 bp):
TAAAAATCAAATTAATATTTTGATCTAAAATT
Found at i:3529827 original size:16 final size:17
Alignment explanation
Indices: 3529806--3529839 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3529796 CTAAAAAGAT
*
3529806 ATTCGA-TTTATGCTCG
1 ATTCGACTTGATGCTCG
3529822 ATTCGACTTGATGCTCG
1 ATTCGACTTGATGCTCG
3529839 A
1 A
3529840 CAAGTTCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (17 bp):
ATTCGACTTGATGCTCG
Found at i:3530271 original size:40 final size:39
Alignment explanation
Indices: 3530216--3530295 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 39
3530206 AATTGTTGAT
* * *
3530216 GAATTTATCAAGTCGAGTTAGGATTTATTTGACTTAACTC
1 GAATTTATCAAGTCGAGTTAGG-TTCACTTAACTTAACTC
*
3530256 GAATTTATCAGGTCGAGTTAGGTTCACTTAACTTAACTC
1 GAATTTATCAAGTCGAGTTAGGTTCACTTAACTTAACTC
3530295 G
1 G
3530296 TTAATGTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (39 bp):
GAATTTATCAAGTCGAGTTAGGTTCACTTAACTTAACTC
Found at i:3530580 original size:3 final size:3
Alignment explanation
Indices: 3530572--3530596 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3530562 CGTCATTGGA
3530572 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3530597 AAGTCTATAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3536953 original size:31 final size:30
Alignment explanation
Indices: 3536869--3536996 Score: 107
Period size: 31 Copynumber: 4.1 Consensus size: 30
3536859 GAGTCGAGGG
* * *
3536869 TACCTATGTTCTACGGAATATATGGACATAAT
1 TACCTATGTTCTAAGGAACATATGGAC--AGT
***
3536901 TACCTATG-TCTTTTGAGACATATGGACAGT
1 TACCTATGTTCTAAGGA-ACATATGGACAGT
3536931 ATACCTATGTTCTAAGGAACATATGGACAGT
1 -TACCTATGTTCTAAGGAACATATGGACAGT
* * *
3536962 TCACCTAGGTTCTTCA-GAACCTATGGACAGT
1 T-ACCTATGTTC-TAAGGAACATATGGACAGT
3536993 TACC
1 TACC
3536997 GAGGATCTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
30 6 0.08
31 50 0.62
32 24 0.30
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TACCTATGTTCTAAGGAACATATGGACAGT
Found at i:3537026 original size:30 final size:30
Alignment explanation
Indices: 3536980--3537051 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
3536970 GTTCTTCAGA
* * *
3536980 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTAGG
3537010 ACCTCTGGATAGTTACCGAGGATCTTTAGG
1 ACCTCTGGATAGTTACCGAGGATCTTTAGG
3537040 ACCTCTGGATAG
1 ACCTCTGGATAG
3537052 GTCCTGCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTAGG
Found at i:3542112 original size:31 final size:31
Alignment explanation
Indices: 3542028--3542155 Score: 120
Period size: 31 Copynumber: 4.1 Consensus size: 31
3542018 GAGTCGAGGG
* *
3542028 TACCTATGTTCTACGGAACATATGAACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
*
3542059 TTACCTATG-TCTTTC-GAGACATATGGACAGTA
1 -TACCTATGTTC-TACGGA-ACATATGGACAGTA
* *
3542091 TACCTATGTTCTAAGGAACATATGGACA-TT
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
3542121 TCACCTAGGTTCTTCGGAACCTATGGACAGT-
1 T-ACCTATGTTCTACGGAACATATGGACAGTA
3542152 TACC
1 TACC
3542156 GAGGATCTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
30 5 0.06
31 48 0.60
32 27 0.34
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:3542185 original size:30 final size:30
Alignment explanation
Indices: 3542139--3542210 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
3542129 GTTCTTCGGA
* * *
3542139 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTAGG
3542169 ACCTCTGGATAGTTACCGAGGATCTTTAGG
1 ACCTCTGGATAGTTACCGAGGATCTTTAGG
3542199 ACCTCTGGATAG
1 ACCTCTGGATAG
3542211 GTCCTGCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTAGG
Found at i:3554422 original size:2 final size:2
Alignment explanation
Indices: 3554415--3554441 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3554405 ACAAAGTAAC
3554415 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 T
3554442 GTGCAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3556926 original size:60 final size:58
Alignment explanation
Indices: 3556770--3556929 Score: 160
Period size: 60 Copynumber: 2.7 Consensus size: 58
3556760 ATAGTCATAT
* *
3556770 GATCATTTTGTAACTTTTAATAGTCGGAAGACTCAACAAAGTAGCACCATATAATCGG
1 GATCATTTTATAACTTTTAATAGTCGGAAGACTCAACAAAGTAACACCATATAATCGG
* * * ** * * *
3556828 GAAACCATTTTTTAACTTTCAATAGTTAGATGAATCAACAAAGTAACA-CACTATAATTGATG
1 G--ATCATTTTATAACTTTTAATAGTCGGAAGACTCAACAAAGTAACACCA-TATAATCG--G
* *
3556890 GATCATTTTACAACTTTTAATAGTCGGAGGACTCAACAAA
1 GATCATTTTATAACTTTTAATAGTCGGAAGACTCAACAAA
3556930 TAAACTCCGA
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
58 1 0.01
59 2 0.03
60 75 0.94
62 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (58 bp):
GATCATTTTATAACTTTTAATAGTCGGAAGACTCAACAAAGTAACACCATATAATCGG
Found at i:3561216 original size:22 final size:22
Alignment explanation
Indices: 3561163--3561227 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
3561153 ATCGAATATA
*
3561163 TAAATGAAAGATAAACAAACAC
1 TAAATGAATGATAAACAAACAC
**
3561185 TAAAACAATGATAAACAAACAC
1 TAAATGAATGATAAACAAACAC
* *
3561207 TAAATGAATGCTAAACGAACA
1 TAAATGAATGATAAACAAACA
3561228 TGTTCATGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.60, C:0.15, G:0.09, T:0.15
Consensus pattern (22 bp):
TAAATGAATGATAAACAAACAC
Done.