Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007987.1 Hibiscus syriacus cultivar Beakdansim tig00110432_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: 872063
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:607287 original size:53 final size:53
Alignment explanation
Indices: 607193--607446 Score: 375
Period size: 53 Copynumber: 4.8 Consensus size: 53
607183 TGACAGGTCT
* * * **
607193 GCTCCCTCTTG-TTCAGGGATTAAGAAACTTGAACAATCTTCTAAAAACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGT-AG-AACTCGAACAATCTTCTGATTACGGGTTC
* * *
607247 GCTCCCTATTGCTTCAGGGAGTAGAACTCGAACACTCTTCTGTTTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGATTACGGGTTC
*
607300 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGATTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGATTACGGGTTC
* **
607353 GCTCCCTCTTGCTTCAGGGAGTAGAACTTGAACAATCTTCTGCCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGATTACGGGTTC
607406 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
607447 AGTGTGATTC
Statistics
Matches: 182, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
53 161 0.88
54 12 0.07
55 9 0.05
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (53 bp):
GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGATTACGGGTTC
Found at i:607950 original size:22 final size:21
Alignment explanation
Indices: 607922--607992 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
607912 ACAAATGACC
607922 CGAAAGATTTAATCATCATGCT
1 CGAAAGATTT-ATCATCATGCT
* * *
607944 CGAAAGACTTA-C-TGATGACC
1 CGAAAGATTTATCATCATG-CT
*
607964 CGAAGGATTTCATCATCATGCT
1 CGAAAGATTT-ATCATCATGCT
607986 CGAAAGA
1 CGAAAGA
607993 CTTACTGATG
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 10 0.27
21 2 0.05
22 17 0.46
23 4 0.11
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (21 bp):
CGAAAGATTTATCATCATGCT
Found at i:607962 original size:42 final size:41
Alignment explanation
Indices: 607874--608002 Score: 170
Period size: 42 Copynumber: 3.1 Consensus size: 41
607864 AGGTCTTATG
* * * *
607874 GATGACCCGAAGGATTTATCATCTTGTTCGAGAA-ACTCACA
1 GATGACCCGAAGGATTTATCATCATGCTCGA-AAGACTTACT
* *
607915 AATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACT
607957 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACT
607999 GATG
1 GATG
608003 GCACTTAATG
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 17 0.22
42 60 0.78
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACT
Found at i:608157 original size:80 final size:80
Alignment explanation
Indices: 608005--608417 Score: 623
Period size: 80 Copynumber: 5.2 Consensus size: 80
607995 TACTGATGGC
* * * *
608005 ACTTAATGACGGATTTGCTTCATTACTCTTCTGTGAAGAGGCTTAAAAATTACCCGAAGGATTTA
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTG-A-AGGCTTAAAAATTACCCGAAGGATTTA
608070 ATTATCATGCTCGAAAG
64 ATTATCATGCTCGAAAG
* *
608087 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAATGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
*
608152 CATCATGCTCGAAAG
66 TATCATGCTCGAAAG
* * * *
608167 ACTTATTGATGGGTTTACTTCACTACTCTTCTGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
*
608232 TATCATGTTCGAAAG
66 TATCATGCTCGAAAG
* *
608247 ACTTACTGATGGATTTGCTTCACTACTCTTTC-GTGAAGGCTT-AAAATTACCTGAAAGATTTAA
1 ACTTACTGATGGATTTGCTTCACTACTC-TTCGGTGAAGGCTTAAAAATTACCCGAAGGATTTAA
608310 TTATCATGCTCGAAAG
65 TTATCATGCTCGAAAG
* * *
608326 ACTTACTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTACAAATTACCCGAATGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
*
608391 CATCATGCTCGAAAG
66 TATCATGCTCGAAAG
608406 ACTTACTGATGG
1 ACTTACTGATGG
608418 CCCGAAGGAC
Statistics
Matches: 302, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
78 2 0.01
79 72 0.24
80 193 0.64
81 4 0.01
82 31 0.10
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (80 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
TATCATGCTCGAAAG
Found at i:608389 original size:159 final size:160
Alignment explanation
Indices: 608005--608417 Score: 652
Period size: 159 Copynumber: 2.6 Consensus size: 160
607995 TACTGATGGC
* *
608005 ACTTAATGACGGATTTGCTTCATTACTCTTCTGTGAAGAGGCTTAAAAATTACCCGAAGGATTTA
1 ACTTAATGATGGATTTGCTTCACTACTCTTCTGTG-A-AGGCTTAAAAATTACCCGAAGGATTTA
608070 ATTATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAAT
64 ATTATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAAT
*
608135 TACCCGAATGATTTAATCATCATGCTCGAAAG
129 TACCCGAAAGATTTAATCATCATGCTCGAAAG
* * *
608167 ACTTATTGATGGGTTTACTTCACTACTCTTCTGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
1 ACTTAATGATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
*
608232 TATCATGTTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTTC-GTGAAGGCTTA-AAATT
66 TATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTC-TTCGGTGAAGGCTTACAAATT
* *
608295 ACCTGAAAGATTTAATTATCATGCTCGAAAG
130 ACCCGAAAGATTTAATCATCATGCTCGAAAG
* * *
608326 ACTTACTGATGGATTTGCTTCACTACTCTT-TGGTGAAGGCTTACAAATTACCCGAATGATTTAA
1 ACTTAATGATGGATTTGCTTCACTACTCTTCT-GTGAAGGCTTAAAAATTACCCGAAGGATTTAA
*
608390 TCATCATGCTCGAAAGACTTACTGATGG
65 TTATCATGCTCGAAAGACTTACTGATGG
608418 CCCGAAGGAC
Statistics
Matches: 233, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
158 1 0.00
159 116 0.50
160 82 0.35
161 4 0.02
162 30 0.13
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (160 bp):
ACTTAATGATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAAAATTACCCGAAGGATTTAAT
TATCATGCTCGAAAGACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTA
CCCGAAAGATTTAATCATCATGCTCGAAAG
Found at i:608422 original size:42 final size:42
Alignment explanation
Indices: 608376--608472 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
608366 TTACAAATTA
* * *
608376 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCACCATGCTCGAAAGACTTACTGATGG
*
608418 CCCGAAGGACTTCATCACCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTAATCACCATGCTCGAAAGACTTACTGATGG
*
608460 ACCGAAGGACTTA
1 CCCGAAGGACTTA
608473 CTTTGATAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (42 bp):
CCCGAAGGACTTAATCACCATGCTCGAAAGACTTACTGATGG
Found at i:608428 original size:20 final size:20
Alignment explanation
Indices: 608400--608474 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
608390 TCATCATGCT
608400 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* ** *
608420 CGAAGGACTTCATCACCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
*
608442 CGAAAGACTTACTGATGGAC
1 CGAAAGACTTACTGATGGCC
*
608462 CGAAGGACTTACT
1 CGAAAGACTTACT
608475 TTGATAGATG
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.05
20 23 0.56
21 2 0.05
22 12 0.29
23 2 0.05
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:612264 original size:34 final size:34
Alignment explanation
Indices: 612221--612288 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
612211 AACTGAGTTC
612221 TCTAGCTTCTAACTCCTTGTAAGGGGCATTAGCA
1 TCTAGCTTCTAACTCCTTGTAAGGGGCATTAGCA
612255 TCTAGCTTCTAACTCCTTGTAAGGGGCATTAGCA
1 TCTAGCTTCTAACTCCTTGTAAGGGGCATTAGCA
612289 ACCTTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (34 bp):
TCTAGCTTCTAACTCCTTGTAAGGGGCATTAGCA
Found at i:614529 original size:8 final size:8
Alignment explanation
Indices: 614516--614564 Score: 73
Period size: 8 Copynumber: 6.1 Consensus size: 8
614506 GCAACAATAG
614516 TAAAAAAA
1 TAAAAAAA
614524 TAAAAAAA
1 TAAAAAAA
614532 TAAAAAAA
1 TAAAAAAA
614540 T-AAAAAA
1 TAAAAAAA
614547 TAAAATAAA
1 TAAAA-AAA
*
614556 TAAATAAA
1 TAAAAAAA
614564 T
1 T
614565 TAAAGCTAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:614543 original size:24 final size:24
Alignment explanation
Indices: 614518--614564 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
614508 AACAATAGTA
614518 AAAAAATAAAA-AAATAAAAAAAT
1 AAAAAATAAAATAAATAAAAAAAT
*
614541 AAAAAATAAAATAAATAAATAAAT
1 AAAAAATAAAATAAATAAAAAAAT
614565 TAAAGCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (24 bp):
AAAAAATAAAATAAATAAAAAAAT
Found at i:619087 original size:3 final size:3
Alignment explanation
Indices: 619079--619111 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
619069 TATGTTTAAA
619079 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
619112 GGAATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:620012 original size:21 final size:19
Alignment explanation
Indices: 619988--620041 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
619978 TTAAATTATA
619988 ATAAATATATATAATGACAAT
1 ATAAATA-ATATAATGA-AAT
*
620009 ATAAATAATTATAATTAAAT
1 ATAAATAA-TATAATGAAAT
*
620029 TTAAATAAATATA
1 ATAAAT-AATATA
620042 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAATAATATAATGAAAT
Found at i:620035 original size:20 final size:19
Alignment explanation
Indices: 620010--620051 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
620000 AATGACAATA
*
620010 TAAATAATTATAATTAAATT
1 TAAATAAATAT-ATTAAATT
*
620030 TAAATAAATATATTTAATT
1 TAAATAAATATATTAAATT
620049 TAA
1 TAA
620052 CTTAAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATAAATATATTAAATT
Found at i:620047 original size:24 final size:24
Alignment explanation
Indices: 620009--620057 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
619999 TAATGACAAT
*
620009 ATAAATAATTATAATTAAATTTAA
1 ATAAATAATTATAATTAAACTTAA
*
620033 ATAAATATATT-TAATTTAACTTAA
1 ATAAATA-ATTATAATTAAACTTAA
620057 A
1 A
620058 AGTTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAAATAATTATAATTAAACTTAA
Found at i:625934 original size:80 final size:80
Alignment explanation
Indices: 625801--625960 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 80
625791 ATTTTATTAG
* **
625801 CAAAAACAATGTTATTCCGTTTTTAACATTTTTTCAGTACATTCTCTAAATACTCTACAAATTCG
1 CAAAAACAATGTTATTCCGTTTTTAAAAAATTTTCAGTACATTCTCTAAATACTCTACAAATTCG
625866 ATCTCACCATGCATA
66 ATCTCACCATGCATA
*
625881 CAAAAACAATGTTATTCCGTTTTTAAAAAATTTTCA-TCGCATTCTCTAAATACTCTACAAATTC
1 CAAAAACAATGTTATTCCGTTTTTAAAAAATTTTCAGT-ACATTCTCTAAATACTCTACAAATTC
*
625945 TATCTCACCATGCATA
65 GATCTCACCATGCATA
625961 ACAGAGCTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.37
Consensus pattern (80 bp):
CAAAAACAATGTTATTCCGTTTTTAAAAAATTTTCAGTACATTCTCTAAATACTCTACAAATTCG
ATCTCACCATGCATA
Found at i:626800 original size:21 final size:21
Alignment explanation
Indices: 626721--626800 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
626711 AAATCAGTTC
626721 CCATAATCGCAACGCGATTAT
1 CCATAATCGCAACGCGATTAT
** * *
626742 GAAGAATCGCAATGCGA-TAGT
1 CCATAATCGCAACGCGATTA-T
* ** *
626763 ACA-AATTCGCATTGCGATTTT
1 CCATAA-TCGCAACGCGATTAT
626784 CCATAATCGCAACGCGA
1 CCATAATCGCAACGCGA
626801 ACATATAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 4 0.09
21 37 0.84
22 3 0.07
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
CCATAATCGCAACGCGATTAT
Found at i:626876 original size:20 final size:20
Alignment explanation
Indices: 626829--627039 Score: 174
Period size: 20 Copynumber: 10.4 Consensus size: 20
626819 GATTCTGACT
* *
626829 ATCGCAATGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
* *
626850 ATTGCAACGCTTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
626870 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
626891 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * **
626911 ATCGCAACGAGAATATGTAA
1 ATCGCAACGCGTATCCGTAA
*
626931 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
626951 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
**
626971 ATCGCAATACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
626991 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
627012 ATCGCAACGCGTTTTCGTAA
1 ATCGCAACGCGTATCCGTAA
*
627032 ATCACAAC
1 ATCGCAAC
627040 TCGATTTTTA
Statistics
Matches: 151, Mismatches: 33, Indels: 13
0.77 0.17 0.07
Matches are distributed among these distances:
20 104 0.69
21 47 0.31
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:626944 original size:40 final size:41
Alignment explanation
Indices: 626844--627039 Score: 279
Period size: 40 Copynumber: 4.8 Consensus size: 41
626834 AATGAGTATC
* *
626844 CGTAAAATTGCAACGCTTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
*
626885 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* * *
626926 TGT-AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
**
626966 CGT-AAATCGCAATACGTATCCGTAAATCGCAACGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
* * *
627006 CGTAAAATCGCAACGCGTTTTCGTAAATCACAAC
1 CGTAAAATCGCAACGCGTATCCGTAAATCGCAAC
627040 TCGATTTTTA
Statistics
Matches: 139, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 74 0.53
41 65 0.47
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (41 bp):
CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATA
Found at i:626991 original size:60 final size:61
Alignment explanation
Indices: 626829--627020 Score: 194
Period size: 60 Copynumber: 3.1 Consensus size: 61
626819 GATTCTGACT
* * * * **
626829 ATCGCAATGAGTATCCGTAAAATTGCAACGCTTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAA
* * * * ** *
626891 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATATGTAAATCGCAACG-C-GTATCTGT-AA
1 ATCGCAACGAGAATACGTAAATCGCAACGAGTATCCGTAAATCGCAACGACAATA-C-GTAAA
*
626951 ATCGCAACGAGAATACGTAAATCGCAA-TACGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATACGTAAATCGCAACGA-GTATCCGTAAATCGCAACGACAATACGTAAA
627012 ATCGCAACG
1 ATCGCAACG
627021 CGTTTTCGTA
Statistics
Matches: 107, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
59 3 0.03
60 46 0.43
61 40 0.37
62 18 0.17
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (61 bp):
ATCGCAACGAGAATACGTAAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAA
Found at i:627661 original size:21 final size:21
Alignment explanation
Indices: 627600--627678 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
627590 TTCTAAACTT
627600 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
627620 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
627640 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
627661 AAAATCGTAACGAGAGAA
1 AAAATCGCAACGAGAGAA
627679 TCGCAATGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:627738 original size:33 final size:33
Alignment explanation
Indices: 627685--627775 Score: 110
Period size: 33 Copynumber: 2.8 Consensus size: 33
627675 AGAATCGCAA
** *
627685 TGCGATTTTGGTTTCACGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
627718 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
** * *
627751 TGCGATAGTCATTACGCATTGCGAT
1 TGCGATTTTCATTTCGCGTTGCGAT
627776 AGTCATTCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.42
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:629031 original size:16 final size:16
Alignment explanation
Indices: 629006--629040 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
628996 ATATTTATGC
* *
629006 TTTATCATTTTGTCCT
1 TTTATAATTTAGTCCT
629022 TTTATAATTTAGTCCT
1 TTTATAATTTAGTCCT
629038 TTT
1 TTT
629041 GTTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTATAATTTAGTCCT
Found at i:629126 original size:2 final size:2
Alignment explanation
Indices: 629119--629167 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
629109 GATGTTTTAT
* *
629119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
629161 TA TA TA T
1 TA TA TA T
629168 TTATGTGTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:629168 original size:16 final size:16
Alignment explanation
Indices: 629125--629173 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
629115 TTATTATATA
* *
629125 TATATATATATATATA
1 TATATATATATTTATG
629141 TATATATATATTTATG
1 TATATATATATTTATG
629157 TATATATATATTTATG
1 TATATATATATTTATG
629173 T
1 T
629174 GTGTTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TATATATATATTTATG
Found at i:629242 original size:18 final size:19
Alignment explanation
Indices: 629219--629258 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
629209 TATATATTGC
*
629219 TTATTTCATT-ATATTATT
1 TTATTTCATTCATATTAAT
629237 TTATTTCATTCATATTAAT
1 TTATTTCATTCATATTAAT
629256 TTA
1 TTA
629259 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTCATTCATATTAAT
Found at i:630860 original size:50 final size:47
Alignment explanation
Indices: 630805--630931 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 47
630795 GAAAATAGAT
*
630805 CATTTTGGGTAGATAGCATGTCCGGGTAGGATTGTTAT-TTAATTGAAAG
1 CATTTTGGGTAGATAGCATGTCCGGGTAGGATCGTTATCTT--TT-AAAG
*
630854 CAATTTTGGGTAGAAAGCATGTCCGGGTAGGATCGTTATCTTTTAAAG
1 C-ATTTTGGGTAGATAGCATGTCCGGGTAGGATCGTTATCTTTTAAAG
* *
630902 CATGTTAGGGTAGATATCATGT-CGGGTAGG
1 CAT-TTTGGGTAGATAGCATGTCCGGGTAGG
630932 TGTTATATTC
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
47 10 0.14
48 20 0.29
49 3 0.04
50 35 0.50
51 2 0.03
ACGTcount: A:0.26, C:0.10, G:0.30, T:0.34
Consensus pattern (47 bp):
CATTTTGGGTAGATAGCATGTCCGGGTAGGATCGTTATCTTTTAAAG
Found at i:633501 original size:26 final size:25
Alignment explanation
Indices: 633472--633550 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 25
633462 AATTTTTGAC
633472 ATTCTATTTCTTTGAGACCTTGAAAT
1 ATTCT-TTTCTTTGAGACCTTGAAAT
*
633498 ATTCTTTTC-----GACCTTGAAAC
1 ATTCTTTTCTTTGAGACCTTGAAAT
* *
633518 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTTTCTTTGAGACCTTGAAAT
633544 ATTCTTT
1 ATTCTTT
633551 CCACCTTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 13 0.32
21 4 0.10
25 6 0.15
26 18 0.44
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (25 bp):
ATTCTTTTCTTTGAGACCTTGAAAT
Found at i:633504 original size:20 final size:20
Alignment explanation
Indices: 633479--633550 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 20
633469 GACATTCTAT
633479 TTCTTTGAGACCTTGAAATA
1 TTCTTTGAGACCTTGAAATA
** *
633499 TTCTTTTCGACCTTGAAACATTCCC
1 TTCTTTGAGACCTTG-AA-A-T--A
633524 TCTCTTTGAGACCTTGAAATA
1 T-TCTTTGAGACCTTGAAATA
633545 TTCTTT
1 TTCTTT
633551 CCACCTTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
20 18 0.45
21 3 0.08
22 1 0.03
23 2 0.05
24 1 0.03
25 3 0.08
26 12 0.30
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (20 bp):
TTCTTTGAGACCTTGAAATA
Found at i:635398 original size:14 final size:13
Alignment explanation
Indices: 635367--635414 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
635357 GATTGAGAAA
*
635367 ACATACAT-CAAC
1 ACATACATACAAT
635379 ACATACATACATAT
1 ACATACATACA-AT
635393 ACATACATACACAT
1 ACATACATACA-AT
635407 ACATACAT
1 ACATACAT
635415 GATACATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 8 0.25
13 2 0.06
14 22 0.69
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (13 bp):
ACATACATACAAT
Found at i:635412 original size:10 final size:10
Alignment explanation
Indices: 635383--635413 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
635373 ATCAACACAT
*
635383 ACATACATAT
1 ACATACATAC
635393 ACATACATAC
1 ACATACATAC
635403 ACATACATAC
1 ACATACATAC
635413 A
1 A
635414 TGATACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (10 bp):
ACATACATAC
Found at i:636009 original size:36 final size:36
Alignment explanation
Indices: 635957--636074 Score: 159
Period size: 36 Copynumber: 3.3 Consensus size: 36
635947 TGAGAATTTT
*
635957 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTTTA
*
635994 AAAGCAAATTTTGTCTCGCTTGAGACAACTTTC--TA
1 AAAACAAATTTTGTCTCGCTTGAGACAA-TTTCTTTA
** *
636029 AAAACAAATTTTGTCTCATTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTTA
636065 AAAACAAATT
1 AAAACAAATT
636075 CCGTCTCACT
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
34 4 0.06
35 26 0.36
36 31 0.43
37 11 0.15
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTTA
Found at i:636081 original size:36 final size:35
Alignment explanation
Indices: 635957--636091 Score: 155
Period size: 36 Copynumber: 3.8 Consensus size: 35
635947 TGAGAATTTT
* *
635957 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCACTTGAGACAATTTC-TTA
* *
635994 AAAGCAAATTTTGTCTCGCTTGAGACAACTTTC-TA
1 AAAACAAATTTTGTCTCACTTGAGACAA-TTTCTTA
*
636029 AAAACAAATTTTGTCTCATTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTT-A
** *
636065 AAAACAAATTCCGTCTCACTGGAGACA
1 AAAACAAATTTTGTCTCACTTGAGACA
636092 TTTTTCCTTG
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
34 4 0.05
35 27 0.31
36 44 0.51
37 11 0.13
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (35 bp):
AAAACAAATTTTGTCTCACTTGAGACAATTTCTTA
Found at i:636081 original size:71 final size:72
Alignment explanation
Indices: 635957--636091 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 72
635947 TGAGAATTTT
* ** * ** * *
635957 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGCTTGAGACAA
1 AAAACAAATTTTTGTCTCACTTGAGACAATTTCTTGAAAAACAAATTCCGTCTCACTGGAGACAA
636022 CTTTCTA
66 CTTTCTA
*
636029 AAAACAAA-TTTTGTCTCATTTGAGACAATTTCTTGAAAAACAAATTCCGTCTCACTGGAGACA
1 AAAACAAATTTTTGTCTCACTTGAGACAATTTCTTGAAAAACAAATTCCGTCTCACTGGAGACA
636092 TTTTTCCTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
71 46 0.85
72 8 0.15
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCACTTGAGACAATTTCTTGAAAAACAAATTCCGTCTCACTGGAGACAA
CTTTCTA
Found at i:636238 original size:167 final size:166
Alignment explanation
Indices: 635998--636316 Score: 441
Period size: 167 Copynumber: 1.9 Consensus size: 166
635988 TCTTTCAAAG
* * * *
635998 CAAATTTTGTCTCGCTTGAGACAACTTTCTAAAAACAAATTTTGTCTCATTTGAGACAATTTCTT
1 CAAATTTTGTCTCGCTTGAGACAACTTTCTAAAAACAAAGTTTGTATCACTTAAGACAATTTCTT
636063 GAAAAACAAA-TTCCGTCTCACTGGAGACATTTTTCC-TTGAGATACAAATTTCGAATTTGATTC
66 -AAAAACAAACTT-CGTCTCACTGGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGATTC
* *
636126 ACATT-AAACAAAGTTGATCTCACTTGAGATCGTTTTCT
129 AC-TTAAAACAAAATTAATCTCACTTGAGATCGTTTTCT
* *
636164 CAAATTTTGTTTTGCTTGAGACAA-TTTCTTTAAAAACAAAGTTTGTATCACTTAAGACAAATTC
1 CAAATTTTGTCTCGCTTGAGACAACTTTC--TAAAAACAAAGTTTGTATCACTTAAGAC-AATT-
* * *
636228 TCTT-AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGAT
62 TCTTAAAAACAAACTTCGTCTCACTGGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGAT
636292 TCACTTAAAACAAAATTAATCTCAC
127 TCACTTAAAACAAAATTAATCTCAC
636317 CTTAGATTGT
Statistics
Matches: 135, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
165 4 0.03
166 22 0.16
167 55 0.41
168 50 0.37
169 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (166 bp):
CAAATTTTGTCTCGCTTGAGACAACTTTCTAAAAACAAAGTTTGTATCACTTAAGACAATTTCTT
AAAAACAAACTTCGTCTCACTGGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGATTCAC
TTAAAACAAAATTAATCTCACTTGAGATCGTTTTCT
Found at i:636258 original size:36 final size:36
Alignment explanation
Indices: 636177--636258 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
636167 ATTTTGTTTT
* * *
636177 GCTTGAGACAATTTCTTTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
* * *
636213 ACTTAAGACAAATTCTCTT-AAAACAAACTTCGTCTC
1 GCTTGAGACAAATTCT-TTAAAAACAAACTTCGTATC
636249 GCTTGAGACA
1 GCTTGAGACA
636259 TTTTTCCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 35 0.95
37 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
Found at i:636357 original size:105 final size:101
Alignment explanation
Indices: 636232--636469 Score: 286
Period size: 105 Copynumber: 2.3 Consensus size: 101
636222 AAATTCTCTT
* * *
636232 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAA-TTCGAATTTGATTCACA
*
636296 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
65 TT-AAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
636337 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTCGAATTTGTTTCACAT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTCGAATTTGATTCACAT
* *
636402 TAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
636438 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
636470 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
100 2 0.02
101 26 0.22
102 7 0.06
103 4 0.03
104 34 0.29
105 45 0.38
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (101 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTCGAATTTGATTCACAT
TAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:636460 original size:36 final size:36
Alignment explanation
Indices: 636415--636534 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
636405 ACAAAGTTGA
**
636415 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
636451 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
636487 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
636521 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
636535 TTTTTCCTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.27
35 8 0.11
36 40 0.57
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:636576 original size:276 final size:267
Alignment explanation
Indices: 636065--636695 Score: 799
Period size: 272 Copynumber: 2.3 Consensus size: 267
636055 AATTTCTTGA
* * * *
636065 AAAACAAATTCCGTCTCACTGGAGACATTTTTCC-TTGAGATACAAATTTCGAATTTGATTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACA-TTTTCCTTTGAGATACAAA-TTCGAATTTGTTTCACA
* * * *
636129 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAATTTTGTTTTGCTTGAGACAATTTCTT
64 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAACTTTGTCTCGCTTGAGACAATTTCTC
*
636194 TAAAAACAAAGTTTGTATCACTTAAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
129 TAAAAACAAAGTTTGTATCACTTAAGACAAATTATCTTAAAACAAACTTCGTCTCGCTTGAGACA
636259 TTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACTTAAAACAAAATTAATCTCACCTT-AGA
194 TTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACTTAAAAC--AA--AATCTCA-CTTGAGA
*
636323 TTGTTGTTTCTTTC
254 TTGTTGTTTATTTC
* *
636337 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTCGAATTTGTTTCACAT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTT-CCTTTGAGATACAAATTCGAATTTGTTTCACAT
636402 TAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAAAACAAACTTTGTCTCGCTTGAGACAAT
65 TAAACAAAGTTGATCTCACTTGAGATCGTTTTCT------CAAACTTTGTCTCGCTTGAGACAAT
* * * * * * *
636467 TTCTCTAAAAACAAATTTTGTCTCATTTGAGAC-TA-TATCTTAAAGCAAATTTCGTCTCGCTTG
124 TTCTCTAAAAACAAAGTTTGTATCACTTAAGACAAATTATCTTAAAACAAACTTCGTCTCGCTTG
* * *
636530 AGACATTTTTCCTTTGAGATACTAATTTTGAATTTGTTTCACTTAAAACAAAATCTCACTTGATA
189 AGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACTTAAAACAAAATCTCACTTGAGA
636595 TTGTTGTTTATTTC
254 TTGTTGTTTATTTC
* * * * *
636609 GAAACAAATTTCGTTTCGCTTGAGACATTTTTCTCTGAGATACAAATT-AAATTTGTTGT-AC-T
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCTTTGAGATACAAATTCGAATTTGTT-TCACAT
* * *
636671 TGAAACAAAATTAATATCACTTGAG
65 T-AAACAAAGTTGATCTCACTTGAG
636696 TTTTTCAAAA
Statistics
Matches: 316, Mismatches: 32, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
269 2 0.01
270 30 0.09
271 22 0.07
272 126 0.40
273 11 0.03
274 2 0.01
276 72 0.23
277 1 0.00
278 50 0.16
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.39
Consensus pattern (267 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCTTTGAGATACAAATTCGAATTTGTTTCACATT
AAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAACTTTGTCTCGCTTGAGACAATTTCTCTA
AAAACAAAGTTTGTATCACTTAAGACAAATTATCTTAAAACAAACTTCGTCTCGCTTGAGACATT
TTTCCTTTGAGATACAAATTTTGAATTTGATTCACTTAAAACAAAATCTCACTTGAGATTGTTGT
TTATTTC
Found at i:636881 original size:29 final size:29
Alignment explanation
Indices: 636847--636943 Score: 130
Period size: 29 Copynumber: 3.5 Consensus size: 29
636837 CTCTTGAGAT
636847 AAATCTTTGAGTCTGTTCCTTTTGAATAA
1 AAATCTTTGAGTCTGTTCCTTTTGAATAA
* *
636876 AAATCTTGGAGTTTGTTCCTTTTGAATAA
1 AAATCTTTGAGTCTGTTCCTTTTGAATAA
* *
636905 ATATCTTTGAGT-TGTTTCTTTTG-A-AA
1 AAATCTTTGAGTCTGTTCCTTTTGAATAA
636931 AAATC-TTGAGTCT
1 AAATCTTTGAGTCT
636944 ATTTATTTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
25 6 0.10
26 7 0.11
27 1 0.02
28 10 0.16
29 37 0.61
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTCCTTTTGAATAA
Found at i:636928 original size:28 final size:28
Alignment explanation
Indices: 636833--636955 Score: 128
Period size: 29 Copynumber: 4.4 Consensus size: 28
636823 TCTGGAGACA
*
636833 GTTTCTCTTGAGAT-AAATCTTTGAGTCT
1 GTTTCTTTTGA-ATAAAATCTTTGAGTCT
* * *
636861 GTTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTTTTGAAT-AAAATCTTTGAGTCT
*
636890 GTTCCTTTTGAATAAATATCTTTGAGT-T
1 GTTTCTTTTGAATAAA-ATCTTTGAGTCT
636918 GTTTCTTTTGAA-AAAATC-TTGAGTCT
1 GTTTCTTTTGAATAAAATCTTTGAGTCT
* *
636944 ATTTATTTTGAA
1 GTTTCTTTTGAA
636956 ACAAAGTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
25 6 0.07
26 14 0.17
27 5 0.06
28 24 0.29
29 34 0.41
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (28 bp):
GTTTCTTTTGAATAAAATCTTTGAGTCT
Found at i:636952 original size:26 final size:27
Alignment explanation
Indices: 636895--636956 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
636885 AGTTTGTTCC
* *
636895 TTTTGAATAAATATCTTTGAGTTGTTTC
1 TTTTGAA-AAATATCTTTGAGTTATTTA
636923 TTTTGAAAAA-ATC-TTGAGTCTATTTA
1 TTTTGAAAAATATCTTTGAGT-TATTTA
636949 TTTTGAAA
1 TTTTGAAA
636957 CAAAGTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.19
26 15 0.48
27 3 0.10
28 7 0.23
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (27 bp):
TTTTGAAAAATATCTTTGAGTTATTTA
Found at i:637030 original size:52 final size:53
Alignment explanation
Indices: 636952--637054 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
636942 CTATTTATTT
*
636952 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
637004 TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAG
637055 AGTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 35 0.73
53 13 0.27
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:637106 original size:29 final size:30
Alignment explanation
Indices: 637042--637105 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
637032 AATTTTGTGA
*
637042 AAAAATCTTTGAGAGTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGAGTGTTTCTTTGGAAAC
**
637072 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGAGTGTTTCTTTGGAAAC
637102 AAAA
1 AAAA
637106 TTTTGTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (30 bp):
AAAAATCTTTGAGAGTGTTTCTTTGGAAAC
Found at i:638002 original size:28 final size:28
Alignment explanation
Indices: 637925--638012 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 28
637915 GAAACAAAAC
* *
637925 AAACAAAGTCTTTGAGTATGTTT-TCTTG
1 AAACAAA-TCTTTGAATTTGTTTCTCTTG
** *
637953 AAACAAATCTTTGGGTTTGTTTCTTTTG
1 AAACAAATCTTTGAATTTGTTTCTCTTG
637981 AAACAAATCTTT-AATTTGGTTTCTCTTG
1 AAACAAATCTTTGAATTT-GTTTCTCTTG
638009 AAAC
1 AAAC
638013 CATAACTCCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 16 0.31
28 36 0.69
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.44
Consensus pattern (28 bp):
AAACAAATCTTTGAATTTGTTTCTCTTG
Found at i:638092 original size:46 final size:45
Alignment explanation
Indices: 638041--638352 Score: 206
Period size: 46 Copynumber: 7.1 Consensus size: 45
638031 CCAGCCGTCC
*
638041 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCATAACTCT
1 TCATCACGTAGGAACCGTGTTATCACC-TTAGATGGCCAGAACTCT
* * * * *
638087 TCATCACGTATGAGCCGTGTCATTC-CC-CAGA---CCAGATCTCT
1 TCATCACGTAGGAACCGTGTTA-TCACCTTAGATGGCCAGAACTCT
* * * * ** * *
638128 TCATCACGTATGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCAGAAC-TCT
*
638171 TCATCACGTAGGAACCGTGTTATTACCTTCAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTTATCACCTT-AGATGGCCAGAACTCT
* * * * *
638217 TCATCACGTATGAACCGTGTCAT-TCC-TCGA---CCAGACCTCT
1 TCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCAGAACTCT
* * * ** * *
638257 TCATCACGTAGGAGCTGTGTCA-C-CCTTAGATAACCAG-TCGTCC
1 TCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCAGAAC-TCT
638300 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCT
1 TCATCACGTAGGAACCGTGTTATCACC-TTAGATGGCC-AGAACTCT
638347 TCATCA
1 TCATCA
638353 TGTATGAGTA
Statistics
Matches: 209, Mismatches: 35, Indels: 43
0.73 0.12 0.15
Matches are distributed among these distances:
39 4 0.02
40 34 0.16
41 30 0.14
42 2 0.01
43 52 0.25
44 5 0.02
45 8 0.04
46 60 0.29
47 13 0.06
48 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTTATCACCTTAGATGGCCAGAACTCT
Found at i:638328 original size:129 final size:130
Alignment explanation
Indices: 638031--638503 Score: 619
Period size: 130 Copynumber: 3.6 Consensus size: 130
638021 CTAAAGATGG
*
638031 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCATAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
* * *
638096 ATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAA
66 ATGAGCAGTGTCATTCCCCAGACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCTTAGATAA
* *
638161 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATTACCTTCAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
* * * * * * *
638226 ATGAACCGTGTCATTCCTC-GACCAGACCTCTTCATCACGTAGGAGCTGTGTCACCCTTAGATAA
66 ATGAGCAGTGTCATTCCCCAGACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCTTAGATAA
* *
638290 CCAGTCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAAGAACTCTTCATCATG
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTCATCACG
* * * * *
638355 TATGAGTAATGTCA-TCCCCTGACCAGAACTCTTCATCACGTATGAGCCGTGTCAACATCAGATA
65 TATGAGCAGTGTCATTCCCCAGACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCTTAGATA
638419 A
130 A
* * * **
638420 CCAGCCGTCCGCAGCAGAGT-GGAACCGTGTTAGCATCATTCCTAAAGATGGCCAGAACTCTTCA
1 CCAGCCGTCCTCATCA-CGTAGGAACCGTGTT---ATCA--CCTTTAGATGGCCAGAACTCTTCA
* *
638484 TCGCGGATGAGCAGTGTCAT
60 TCACGTATGAGCAGTGTCAT
638504 CCCTCGGCCA
Statistics
Matches: 298, Mismatches: 36, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
129 89 0.30
130 167 0.56
131 2 0.01
133 4 0.01
134 25 0.08
135 11 0.04
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (130 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
ATGAGCAGTGTCATTCCCCAGACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCTTAGATAA
Found at i:638555 original size:91 final size:93
Alignment explanation
Indices: 638426--638594 Score: 279
Period size: 91 Copynumber: 1.8 Consensus size: 93
638416 ATAACCAGCC
* *
638426 GTCCGCAGCAGAGTGGAACCGTGTTAGCATCATTCCTAAAGATGGCC-AGA-ACTCTTCATCGCG
1 GTCCCCAGCAGAGTGGAACCATGTTAGCATCATTCCTAAAGATGGCCAAGATACTCTTCATCGCG
638489 GATGAGCAGTGTCATCCCTCGGCCAGAT
66 GATGAGCAGTGTCATCCCTCGGCCAGAT
* * *
638517 GTCCCCAGCAGAGTGGAACCATGTTATCATCTTTCCTAAAGATGGCCAAGATTCTCTTCATCGCG
1 GTCCCCAGCAGAGTGGAACCATGTTAGCATCATTCCTAAAGATGGCCAAGATACTCTTCATCGCG
638582 GATGAGCAGTGTC
66 GATGAGCAGTGTC
638595 GTCTTCAACA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
91 43 0.61
92 3 0.04
93 25 0.35
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (93 bp):
GTCCCCAGCAGAGTGGAACCATGTTAGCATCATTCCTAAAGATGGCCAAGATACTCTTCATCGCG
GATGAGCAGTGTCATCCCTCGGCCAGAT
Found at i:640237 original size:2 final size:2
Alignment explanation
Indices: 640232--640276 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
640222 AGATGTTTTT
* * * *
640232 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TT TT TG TA 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
640274 TA T
1 TA T
640277 TTATGTGTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (2 bp):
TA
Found at i:640277 original size:16 final size:16
Alignment explanation
Indices: 640228--640278 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
640218 TATTAGATGT
640228 TTTTTATATATATATA
1 TTTTTATATATATATA
* *
640244 TGTATATATATATATA
1 TTTTTATATATATATA
*
640260 TTTTTGTATATATATA
1 TTTTTATATATATATA
640276 TTT
1 TTT
640279 ATGTGTGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (16 bp):
TTTTTATATATATATA
Found at i:640350 original size:18 final size:19
Alignment explanation
Indices: 640327--640366 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
640317 TATATATTGC
*
640327 TTATTTCATT-ATATTATT
1 TTATTTCATTCATATTAAT
640345 TTATTTCATTCATATTAAT
1 TTATTTCATTCATATTAAT
640364 TTA
1 TTA
640367 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTCATTCATATTAAT
Found at i:642173 original size:13 final size:13
Alignment explanation
Indices: 642155--642181 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
642145 TCAAATGATA
642155 TTCCTAGGGCTAT
1 TTCCTAGGGCTAT
642168 TTCCTAGGGCTAT
1 TTCCTAGGGCTAT
642181 T
1 T
642182 AATAGTAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (13 bp):
TTCCTAGGGCTAT
Found at i:642997 original size:90 final size:93
Alignment explanation
Indices: 642781--643152 Score: 510
Period size: 90 Copynumber: 4.1 Consensus size: 93
642771 TAGATTGCTT
* * * *
642781 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTATTTATTC-TTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
642845 ATTTGTCTTTTGTTTTGTCTTTTGGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTT-GGTTGA
*
642875 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
642940 A-TT-TCTTTG-TTTGTC-TTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
642965 AGTAAATTTGTTCGGTTGCTGCAAATTCTGCTAAACTGTATATTCTTTAACAATGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
643030 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
643059 AATAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTA-T-TTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
643121 ATTTGTCTTTGTTTT-TCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
643148 AGTAA
1 AGTAA
643153 TGCAATCCAT
Statistics
Matches: 252, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
89 10 0.04
90 75 0.30
91 39 0.15
92 11 0.04
93 40 0.16
94 57 0.23
95 20 0.08
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:643145 original size:184 final size:183
Alignment explanation
Indices: 642781--643152 Score: 520
Period size: 184 Copynumber: 2.0 Consensus size: 183
642771 TAGATTGCTT
* * * *
642781 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTATTTATTCTTAACACTGTGAAGTTAGTA
1 AGTAAATTTATTCGGTTGCTACAAATACTGCTAAACTATATATTCTTAACAATGTGAAGTTAATA
*
642846 TTTGTCTTTTGTTTTGTCTTTTGGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTATGCTAAAC
66 TTTGTCTTTTGTTTTGTCTTTTGGGTTGAAATAAATTTATTCGGTTGCTGCCAATTATGCTAAAC
*
642911 TGTGTATTCTTTAACACTGTGAAGTTAGTATTTCTTTGTTTGTCTTTGGTTGAA
131 TGTGTATTCTTTAACACTCTGAAGTTAGTATTTCTTTGTTTGTCTTTGGTTG-A
* * * *
642965 AGTAAATTTGTTCGGTTGCTGCAAATTCTGCTAAACTGTATATTCTTTAACAATGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTACAAATACTGCTAAACTATATATTC-TTAACAATGTGAAGTTAAT
* *
643030 ATTTGTC-TTTGTTTTGTCTTTT-GGTTGAAAATAAA-TTGTTCGGTTGCTGCCAATTCTGCTAA
65 ATTTGTCTTTTGTTTTGTCTTTTGGGTTG-AAATAAATTTATTCGGTTGCTGCCAATTATGCTAA
* * *
643092 ATTGTGTA-T-TTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTTCTTTTGGTTGA
129 ACTGTGTATTCTTTAACACTCTGAAGTTAGTA-TT-TCTTTGTTTGTC-TTTGGTTGA
643148 AGTAA
1 AGTAA
643153 TGCAATCCAT
Statistics
Matches: 168, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
181 19 0.11
182 3 0.02
183 54 0.32
184 68 0.40
185 24 0.14
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (183 bp):
AGTAAATTTATTCGGTTGCTACAAATACTGCTAAACTATATATTCTTAACAATGTGAAGTTAATA
TTTGTCTTTTGTTTTGTCTTTTGGGTTGAAATAAATTTATTCGGTTGCTGCCAATTATGCTAAAC
TGTGTATTCTTTAACACTCTGAAGTTAGTATTTCTTTGTTTGTCTTTGGTTGA
Found at i:643274 original size:14 final size:14
Alignment explanation
Indices: 643255--643312 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
643245 AACGCGAAAT
643255 GAATCGCAACGAGA
1 GAATCGCAACGAGA
643269 GAATCGCAACGAGAAA
1 GAATCGCAACGAG--A
*
643285 TGAAAATCACAACGAGA
1 -G--AATCGCAACGAGA
643302 GAATCGCAACG
1 GAATCGCAACG
643313 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.59
16 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.09
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:643303 original size:33 final size:33
Alignment explanation
Indices: 643240--643364 Score: 155
Period size: 33 Copynumber: 3.8 Consensus size: 33
643230 AAAAATGACT
643240 ATCGCAACGCGAAATG--AATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
643271 ATCGCAACGAGAAATGAAAATCACAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
** * *
643304 ATCGCAACGCGAAACCAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* **
643337 ATCGCAATGCGAAACCAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
643365 CGAAACTATA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 15 0.18
33 68 0.82
ACGTcount: A:0.46, C:0.25, G:0.20, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:643327 original size:19 final size:19
Alignment explanation
Indices: 643303--643380 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
643293 ACAACGAGAG
643303 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
643322 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
*
643336 AATCGCAATGCGAAACCAA
1 AATCGCAACGCGAAACCAA
* *
643355 AATCGCAACGCGAAACTAT
1 AATCGCAACGCGAAACCAA
643374 AATCGCA
1 AATCGCA
643381 TGCGATTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 34 0.67
ACGTcount: A:0.46, C:0.28, G:0.15, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:643457 original size:19 final size:20
Alignment explanation
Indices: 643412--643512 Score: 124
Period size: 20 Copynumber: 5.3 Consensus size: 20
643402 GATTCTCTCG
**
643412 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
643432 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
643452 -TGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
643471 -TGCG-TAG---TTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
643486 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
643506 TTGCGAT
1 TTGCGAT
643513 TTTAAGTTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
15 8 0.11
16 4 0.06
17 3 0.04
18 3 0.04
19 22 0.31
20 31 0.44
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:644019 original size:18 final size:19
Alignment explanation
Indices: 643980--644021 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
643970 CCGACCTGTC
643980 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
644001 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
644019 ATC
1 ATC
644022 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:645657 original size:20 final size:20
Alignment explanation
Indices: 645632--646048 Score: 197
Period size: 20 Copynumber: 20.8 Consensus size: 20
645622 CAGAATTTCG
645632 TGCGATTTACAG-ATTCGCAT
1 TGCGATTTAC-GTATTCGCAT
645652 TGCGATTTACGTATTCGCAT
1 TGCGATTTACGTATTCGCAT
* *
645672 TGTGATTTACGTATTCGTAT
1 TGCGATTTACGTATTCGCAT
*
645692 TGCGATTTACGTAATCGCAT
1 TGCGATTTACGTATTCGCAT
*
645712 TGCGATTTACGTAATCGCAT
1 TGCGATTTACGTATTCGCAT
* *
645732 TACGATTTACGTATTCGCGT
1 TGCGATTTACGTATTCGCAT
* * *
645752 TGCGATTTATGTAATCGCGT
1 TGCGATTTACGTATTCGCAT
* * * * * *
645772 TACGAATTAGGAAAATCGCAA
1 TGCGATTTACG-TATTCGCAT
* ** * * *
645793 CGCGAATTTGGGAAATCGCAA
1 TGCG-ATTTACGTATTCGCAT
* * * *
645814 TGCGATAGTAAG-AATCGCGT
1 TGCGAT-TTACGTATTCGCAT
* * **
645834 TGCGA-AT-CTGGAAACTG-ATT
1 TGCGATTTAC-GTATTC-GCA-T
** * * *
645854 TGCGA-TGCCGGAGATCGCGT
1 TGCGATTTACGTA-TTCGCAT
* *
645874 TGCGAATTATCG-A-TCGCGT
1 TGCGATTTA-CGTATTCGCAT
* * *
645893 TGCGATTTACGGATACGCGT
1 TGCGATTTACGTATTCGCAT
*
645913 TGCGATTTACGTATT-GTCGT
1 TGCGATTTACGTATTCG-CAT
* *
645933 TGCGATTTACGGATACGCAT
1 TGCGATTTACGTATTCGCAT
* *
645953 TGCGATTTACGTATTCTCGT
1 TGCGATTTACGTATTCGCAT
* *
645973 TGCGATTTACCG-ATACGCGT
1 TGCGATTTA-CGTATTCGCAT
* *
645993 TGCAATTTACGTATTCTCAT
1 TGCGATTTACGTATTCGCAT
* * *
646013 TGCGATTTACGGATACGCGT
1 TGCGATTTACGTATTCGCAT
646033 TGCGATTTTACGTATT
1 TGCGA-TTTACGTATT
646049 GTCGTTACGA
Statistics
Matches: 316, Mismatches: 61, Indels: 39
0.76 0.15 0.09
Matches are distributed among these distances:
18 4 0.01
19 22 0.07
20 245 0.78
21 38 0.12
22 7 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TGCGATTTACGTATTCGCAT
Found at i:645798 original size:21 final size:21
Alignment explanation
Indices: 645774--645818 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
645764 AATCGCGTTA
645774 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
645795 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
645816 CGA
1 CGA
645819 TAGTAAGAAT
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:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:645939 original size:40 final size:40
Alignment explanation
Indices: 645869--646098 Score: 288
Period size: 40 Copynumber: 5.8 Consensus size: 40
645859 TGCCGGAGAT
* *
645869 CGCGTTGCGAATTATCG-A-TCGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTA-CGTATTCTCGTTGCGATTTACGGATA
*
645908 CGCGTTGCGATTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* *
645948 CGCATTGCGATTTACGTATTCTCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* *
645988 CGCGTTGCAATTTACGTATTCTCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* *
646028 CGCGTTGCGATTTTACGTATTGTCGTTACGA-TT-CGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* * * *
646067 CACGTTGTGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGAT
646099 AGTCAGAATC
Statistics
Matches: 167, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
38 2 0.01
39 45 0.27
40 103 0.62
41 17 0.10
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:645974 original size:60 final size:60
Alignment explanation
Indices: 645871--646098 Score: 234
Period size: 60 Copynumber: 3.8 Consensus size: 60
645861 CCGGAGATCG
* *
645871 CGTTGCGAATTATC-GAT-CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTGT
1 CGTTGCGATTTA-CGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGTATTGT
* * * *
645930 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACCG-ATACG-
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTA-CGTAT-TGT
* * * *
645990 CGTTGCAATTTACGTATTCTCATTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTGT
* * * * *
646051 CGTTACGA-TT-CGGATACACGTTGTGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGGATACGCGTTGCGAT
646099 AGTCAGAATC
Statistics
Matches: 139, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
58 1 0.01
59 26 0.19
60 97 0.70
61 15 0.11
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGGATACGCGTTGCGATTTACGTATTGT
Found at i:646200 original size:42 final size:42
Alignment explanation
Indices: 646105--646200 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 42
646095 CGATAGTCAG
* * *
646105 AATCGCGTTGCG-ATTTATATGTTCGCGTTGCGATTCTGGAA
1 AATCGCGTTGCGAATTTATATGATCGCATTGCGATTCTGCAA
** * * *
646146 AATCGCAATGCGAATTTGTACT-ATCGCATTGCGATTCTTCAT
1 AATCGCGTTGCGAATTTATA-TGATCGCATTGCGATTCTGCAA
646188 AATCGCGTTGCGA
1 AATCGCGTTGCGA
646201 TTCTGGGAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 10 0.23
42 32 0.74
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
AATCGCGTTGCGAATTTATATGATCGCATTGCGATTCTGCAA
Found at i:646238 original size:20 final size:19
Alignment explanation
Indices: 646189--646242 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
646179 ATTCTTCATA
646189 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
646208 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
646229 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
646243 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:650249 original size:14 final size:14
Alignment explanation
Indices: 650230--650272 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
650220 TTAAAGATAA
650230 AATAATATATTTAT
1 AATAATATATTTAT
650244 AATAATA-ATTTA-
1 AATAATATATTTAT
* *
650256 ATTGATATATTTAT
1 AATAATATATTTAT
650270 AAT
1 AAT
650273 TTTTTAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 5 0.21
13 10 0.42
14 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
AATAATATATTTAT
Found at i:650794 original size:2 final size:2
Alignment explanation
Indices: 650787--650812 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
650777 CTGTACCATA
650787 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
650813 TCAATGAAGC
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:652927 original size:8 final size:8
Alignment explanation
Indices: 652914--652948 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
652904 ATTTTTTAAA
652914 AAAAAAAC
1 AAAAAAAC
652922 AAAAAAAC
1 AAAAAAAC
652930 --AAAAAC
1 AAAAAAAC
652936 AAAAAAAC
1 AAAAAAAC
652944 AAAAA
1 AAAAA
652949 CAAAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
8 19 0.76
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:652967 original size:14 final size:14
Alignment explanation
Indices: 652911--652953 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
652901 GCTATTTTTT
652911 AAAAA-AAAAACAA
1 AAAAACAAAAACAA
652924 AAAAACAAAAACAA
1 AAAAACAAAAACAA
652938 AAAAACAAAAACAA
1 AAAAACAAAAACAA
652952 AA
1 AA
652954 CAAAAAAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAACAA
Found at i:652967 original size:20 final size:20
Alignment explanation
Indices: 652911--652960 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
652901 GCTATTTTTT
652911 AAAAA-AAAAACAA-AAAAAC
1 AAAAACAAAAA-AACAAAAAC
652930 AAAAACAAAAAAACAAAAAC
1 AAAAACAAAAAAACAAAAAC
652950 -AAAACAAAAAA
1 AAAAACAAAAAA
652961 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAAAACAAAAAC
Found at i:661097 original size:32 final size:34
Alignment explanation
Indices: 661068--661130 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
661058 TCTTCTTTTT
661068 TTTCTTGTTAAAAAACCGA-A-CCCCCTCTTTCC
1 TTTCTTGTTAAAAAACCGAGAGCCCCCTCTTTCC
* * *
661100 TTTCTTTTTCAAAAATCGAGAGCCCCCTCTT
1 TTTCTTGTTAAAAAACCGAGAGCCCCCTCTT
661131 ATTCGAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 16 0.62
33 1 0.04
34 9 0.35
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.37
Consensus pattern (34 bp):
TTTCTTGTTAAAAAACCGAGAGCCCCCTCTTTCC
Found at i:661906 original size:24 final size:24
Alignment explanation
Indices: 661843--661908 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
661833 TCATTTTTCT
* *
661843 TAAA-ATATAAATGAACAGGTTCG
1 TAAACATATAAACGAACATGTTCG
* *
661866 TAAAC-TCTAAACAAACATGTT-G
1 TAAACATATAAACGAACATGTTCG
661888 ATAAACATATAAACGAACATG
1 -TAAACATATAAACGAACATG
661909 ATCAAGAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 1 0.03
23 21 0.62
24 12 0.35
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (24 bp):
TAAACATATAAACGAACATGTTCG
Found at i:669228 original size:16 final size:14
Alignment explanation
Indices: 669203--669241 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
669193 AGTTCAACTC
669203 AATATAAATTAAGTAA
1 AATATAAATT-A-TAA
*
669219 AATTTAAATTATAA
1 AATATAAATTATAA
669233 AATATAAAT
1 AATATAAAT
669242 CAAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 11 0.52
15 1 0.05
16 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
AATATAAATTATAA
Found at i:669314 original size:2 final size:2
Alignment explanation
Indices: 669307--669371 Score: 112
Period size: 2 Copynumber: 32.0 Consensus size: 2
669297 CTATCTACTT
*
669307 TA TA TA TA TG TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
669350 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
669372 CATACATGGG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:671726 original size:12 final size:12
Alignment explanation
Indices: 671709--671738 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
671699 TTATTTGAGA
671709 AAATTAAAATTT
1 AAATTAAAATTT
671721 AAATTAAAATTT
1 AAATTAAAATTT
671733 AAATTA
1 AAATTA
671739 CTCGATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:673214 original size:12 final size:12
Alignment explanation
Indices: 673197--673224 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
673187 ATGATAGACC
673197 TAAAAAAATAAA
1 TAAAAAAATAAA
673209 TAAAAAAATAAA
1 TAAAAAAATAAA
673221 TAAA
1 TAAA
673225 CGAGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:673255 original size:18 final size:19
Alignment explanation
Indices: 673209--673256 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
673199 AAAAAATAAA
* *
673209 TAAAAAAATAAATAAACGAG
1 TAAATAAAT-AATAAACAAG
673229 TAAAT-AATAATAAACAAG
1 TAAATAAATAATAAACAAG
673247 -AAATAAATAA
1 TAAATAAATAA
673257 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 14 0.56
19 3 0.12
20 4 0.16
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (19 bp):
TAAATAAATAATAAACAAG
Found at i:673531 original size:38 final size:38
Alignment explanation
Indices: 673298--673764 Score: 328
Period size: 36 Copynumber: 13.2 Consensus size: 38
673288 GTTTTAAAAC
* * * *
673298 TATATAT-ATTTCAAAAATATTTTC-AAAACCATATAC
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
* *
673334 TATATA-ATTTT-AAAAATGTTTT--AAAACTATAT-G
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
* *
673367 T-TACA-GTTTTCAAAAACGTTTT--AAAAC--TAT-A
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
* *
673398 T-TATATG-TTTCAAAAA-ATTTTC---AACTATATAT
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
** * *
673430 TATATA-AATTTC-AAAATGATTTT--AAAACTATTTAT
1 TATATATGTTTTCAAAAATG-TTTTCAAAAACTATATAA
*
673465 TATATAAGTTTTC-AAAATGGTTTT-AAAAACTATATAA
1 TATATATGTTTTCAAAAAT-GTTTTCAAAAACTATATAA
* * *
673502 TATATATGGTTTCAAAAATATCTTCAAAAACTATAT-A
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
673539 -ATATATGTTTTCAAAAAAATGTTTTC-AAAAC--TATAA
1 TATATATGTTTTC--AAAAATGTTTTCAAAAACTATATAA
673575 TATATATGTTTTCAAAAATGTTTTCAAAAAC--TATAA
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
673611 TATATATGTTTTCAAAAATGTTTTCAAAAACTATAT-A
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
* * * *
673648 TATATAAGTTTT-TAAAATGATTTT-AAAAATTATATAT
1 TATATATGTTTTCAAAAATG-TTTTCAAAAACTATATAA
* * *** *
673685 TATATATATTTTCTAAAATGTTTTTTTAAACTATATAT
1 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
* * *
673723 TATATATAGTTTT-AAAAA-CTATT-AAAAACTATATAT
1 TATATAT-GTTTTCAAAAATGTTTTCAAAAACTATATAA
673759 TATATA
1 TATATA
673765 CGTAGTTTCA
Statistics
Matches: 361, Mismatches: 40, Indels: 60
0.78 0.09 0.13
Matches are distributed among these distances:
29 3 0.01
30 4 0.01
31 19 0.05
32 13 0.04
33 24 0.07
34 13 0.04
35 40 0.11
36 108 0.30
37 76 0.21
38 57 0.16
39 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (38 bp):
TATATATGTTTTCAAAAATGTTTTCAAAAACTATATAA
Found at i:673549 original size:73 final size:73
Alignment explanation
Indices: 673298--673764 Score: 328
Period size: 73 Copynumber: 6.6 Consensus size: 73
673288 GTTTTAAAAC
* *
673298 TATATATA-TTTCAAAAATATTTTC-AAAACCATATACTATATA-ATTTT-AAAAATGTTTT-AA
1 TATATATAGTTTCAAAAATA-TTTCAAAAACTATATA-TATATATGTTTTCAAAAATGTTTTAAA
673358 AAC--TAT-A
64 AACTATATAA
* * ** * * *
673365 TGT-TACAGTTTTCAAAAACGTTT-TAAAAC--TATAT-TATATG-TTTCAAAAA-ATTTT--CA
1 TATATATAG-TTTCAAAAATATTTCAAAAACTATATATATATATGTTTTCAAAAATGTTTTAAAA
*
673421 ACTATATAT
65 ACTATATAA
* * * *
673430 TATATA-AATTTC-AAAATGATTT-TAAAACTATTTATTATATAAGTTTTC-AAAATGGTTTTAA
1 TATATATAGTTTCAAAAAT-ATTTCAAAAACTATATA-TATATATGTTTTCAAAAAT-GTTTTAA
673491 AAACTATATAA
63 AAACTATATAA
* *
673502 TATATATGGTTTCAAAAATATCTTCAAAAACTATATA-ATATATGTTTTCAAAAAAATGTTTTCA
1 TATATATAGTTTCAAAAATAT-TTCAAAAACTATATATATATATGTTTTC--AAAAATGTTTTAA
673566 AAAC--TATAA
63 AAACTATATAA
*
673575 TATATAT-GTTTTCAAAAATGTTTTCAAAAACTATA-ATATATATGTTTTCAAAAATGTTTTCAA
1 TATATATAG-TTTCAAAAAT-ATTTCAAAAACTATATATATATATGTTTTCAAAAATGTTTT-AA
673638 AAACTATAT-A
63 AAACTATATAA
** * * * * **
673648 TATATA-AGTTTTTAAAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTTTT
1 TATATATAGTTTCAAAAAT-ATTTCAAAAACTATATA-TATATATGTTTTCAAAAATG-TTTTAA
*
673712 AAACTATATAT
63 AAACTATATAA
*
673723 TATATATAGTTTTAAAAACTA-TT-AAAAACTATATATTATATA
1 TATATATAGTTTCAAAAA-TATTTCAAAAACTATATA-TATATA
673765 CGTAGTTTCA
Statistics
Matches: 324, Mismatches: 37, Indels: 71
0.75 0.09 0.16
Matches are distributed among these distances:
62 3 0.01
63 15 0.05
64 22 0.07
65 7 0.02
66 8 0.02
67 11 0.03
68 18 0.06
69 4 0.01
70 4 0.01
71 11 0.03
72 43 0.13
73 73 0.23
74 56 0.17
75 32 0.10
76 16 0.05
77 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (73 bp):
TATATATAGTTTCAAAAATATTTCAAAAACTATATATATATATGTTTTCAAAAATGTTTTAAAAA
CTATATAA
Found at i:673579 original size:110 final size:107
Alignment explanation
Indices: 673298--673764 Score: 404
Period size: 110 Copynumber: 4.4 Consensus size: 107
673288 GTTTTAAAAC
* * *
673298 TATATATATTTCAAAAATATTTTC-AAAACCATATACTATATAATTTTAAAAATG-TTTTAAAAC
1 TATATATGTTTCAAAAATATTTTCAAAAACTATATAATATATAATTTTAAAAATGATTTTAAAAC
* *
673361 TAT-ATGT-TACAGTTTTCAAAAA-CGTTTT-AAAACTAT-A
66 TATAATATATACAGTTTTCAAAAATGGTTTTAAAAACTATAA
* * *
673398 T-TATATGTTTCAAAAA-ATTTTC---AACTATATATTATATAAATTTCAAAATGATTTTAAAAC
1 TATATATGTTTCAAAAATATTTTCAAAAACTATATAATATATAATTTTAAAAATGATTTTAAAAC
*
673458 TATTTATTATATA-AGTTTTC-AAAATGGTTTTAAAAACTATATAA
66 TA--TAATATATACAGTTTTCAAAAATGGTTTTAAAAAC--TATAA
* *
673502 TATATATGGTTTCAAAAATATCTTCAAAAACTATATAATATAT-GTTTTCAAAAAAATG-TTTTC
1 TATATAT-GTTTCAAAAATATTTTCAAAAACTATATAATATATAATTTT---AAAAATGATTTT-
*
673565 AAAACTATAATATATA-TGTTTTCAAAAAT-GTTTTCAAAAACTATAA
61 AAAACTATAATATATACAGTTTTCAAAAATGGTTTT-AAAAACTATAA
* *
673611 TATATATGTTTTCAAAAATGTTTTCAAAAACTATAT-ATATATAAGTTTTTAAAATGATTTTAAA
1 TATATATG-TTTCAAAAATATTTTCAAAAACTATATAATATATAA-TTTTAAAAATGATTTT-AA
* * * * **
673675 AATTATATATTATATATA-TTTTCTAAAATGTTTTTTTAAACTATATA
63 AACTATA-A-TATATACAGTTTTCAAAAATGGTTTTAAAAACTATA-A
* *
673722 TTATATATAGTTTTAAAAACTA--TT-AAAAACTATATATTATATA
1 -TATATAT-GTTTCAAAAA-TATTTTCAAAAACTATATAATATATA
673765 CGTAGTTTCA
Statistics
Matches: 303, Mismatches: 29, Indels: 59
0.77 0.07 0.15
Matches are distributed among these distances:
96 24 0.08
97 11 0.04
98 6 0.02
99 19 0.06
100 15 0.05
101 7 0.02
103 3 0.01
104 2 0.01
105 5 0.02
106 10 0.03
107 11 0.04
108 19 0.06
109 41 0.14
110 72 0.24
111 28 0.09
112 28 0.09
113 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (107 bp):
TATATATGTTTCAAAAATATTTTCAAAAACTATATAATATATAATTTTAAAAATGATTTTAAAAC
TATAATATATACAGTTTTCAAAAATGGTTTTAAAAACTATAA
Found at i:673597 original size:12 final size:12
Alignment explanation
Indices: 673580--673640 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
673570 TATAATATAT
673580 ATGTTTTCAAAA
1 ATGTTTTCAAAA
673592 ATGTTTTCAAAA
1 ATGTTTTCAAAA
* ** * *
673604 ACTATAAT-ATAT
1 A-TGTTTTCAAAA
673616 ATGTTTTCAAAA
1 ATGTTTTCAAAA
673628 ATGTTTTCAAAA
1 ATGTTTTCAAAA
673640 A
1 A
673641 CTATATATAT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
11 3 0.08
12 31 0.84
13 3 0.08
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:678799 original size:4 final size:4
Alignment explanation
Indices: 678790--678820 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
678780 TAACGTATGC
678790 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
678821 CTTGTTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:679062 original size:23 final size:24
Alignment explanation
Indices: 679036--679080 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
679026 TTTTAAATGA
*
679036 AATTTT-ATTTTTTAAAAAATTAT
1 AATTTTAATTCTTTAAAAAATTAT
679059 AATTTTAATTCTTTAAAAAATT
1 AATTTTAATTCTTTAAAAAATT
679081 CCATGCGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTTTAATTCTTTAAAAAATTAT
Found at i:680505 original size:7 final size:7
Alignment explanation
Indices: 680452--680504 Score: 81
Period size: 7 Copynumber: 7.7 Consensus size: 7
680442 AATTATATAC
680452 AGCCT-T
1 AGCCTCT
680458 AGCCTCT
1 AGCCTCT
680465 AGCCTCT
1 AGCCTCT
680472 AGCCTCT
1 AGCCTCT
680479 AGCCTCT
1 AGCCTCT
*
680486 AGCCTTT
1 AGCCTCT
*
680493 AGCCTTT
1 AGCCTCT
680500 AGCCT
1 AGCCT
680505 TAGGCATAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 5 0.11
7 40 0.89
ACGTcount: A:0.15, C:0.38, G:0.15, T:0.32
Consensus pattern (7 bp):
AGCCTCT
Found at i:688063 original size:25 final size:25
Alignment explanation
Indices: 688035--688102 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
688025 TTTGATTTAG
688035 TAAAATATTTATAAATTTGAATA-AT
1 TAAAATATTTATAAATTT-AATATAT
*
688060 TAAAATTATTT-TATATTTAATATAT
1 TAAAA-TATTTATAAATTTAATATAT
* *
688085 TAAAA-ACTTATAATTTTA
1 TAAAATATTTATAAATTTA
688103 TGAGATGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 3 0.08
24 10 0.28
25 18 0.50
26 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
TAAAATATTTATAAATTTAATATAT
Found at i:688406 original size:19 final size:19
Alignment explanation
Indices: 688382--688435 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
688372 ATGACTAACA
*
688382 AAATCGCAATGCGATCGTT
1 AAATCGCAATGCGATCGCT
688401 AAATCGCAATGCGATCGCT
1 AAATCGCAATGCGATCGCT
* *
688420 AATTCGCAACGCGATC
1 AAATCGCAATGCGATC
688436 TCCATTATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (19 bp):
AAATCGCAATGCGATCGCT
Found at i:688534 original size:21 final size:21
Alignment explanation
Indices: 688486--688535 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
688476 ATGACTATCC
688486 CAATGCGATTTTCCAATTTCG
1 CAATGCGATTTTCCAATTTCG
**
688507 CGTTGCGATTTTCCCAA-TTCG
1 CAATGCGATTTT-CCAATTTCG
688528 CAATGCGA
1 CAATGCGA
688536 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCG
Found at i:688555 original size:41 final size:41
Alignment explanation
Indices: 688510--688760 Score: 111
Period size: 41 Copynumber: 6.1 Consensus size: 41
688500 AATTTCGCGT
*
688510 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATAAGTAAATCGCAA
* ** * * *
688551 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATAAGT-A-AATCGCAA
* ** * * *
688592 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * ***
688633 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGTGT
1 TGCGATTTTCCAAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
688674 TGCGATTTT-CATAATTCGCAATGCGAATACGTAAATAGCAA
1 TGCGATTTTCCA-AATTCGCAATGCGAATAAGTAAATCGCAA
* **** * *
688715 CGCGATTAAGTAAA-TCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAA-TAAGTAAATCGCAA
688756 TGCGA
1 TGCGA
688761 ATACATAAAT
Statistics
Matches: 162, Mismatches: 39, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
39 2 0.01
40 21 0.13
41 136 0.84
42 1 0.01
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCAAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:688568 original size:21 final size:21
Alignment explanation
Indices: 688525--688617 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
688515 TTTTCCCAAT
** *
688525 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
688545 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
* **
688566 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTGGAAAA
688586 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
688607 TCGCAATGCGA
1 TCGCAATGCGA
688618 TACTGACTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:688631 original size:20 final size:20
Alignment explanation
Indices: 688565--688635 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
688555 AATTTGGAAA
688565 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* **
688585 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAATGCGATA-CT-GACT
688606 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
688626 ATCGCAATGC
1 ATCGCAATGC
688636 AATTTTCCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 25 0.60
21 15 0.36
22 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:688661 original size:21 final size:21
Alignment explanation
Indices: 688627--688699 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
688617 ATACTGACTA
* *
688627 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
688648 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
***
688668 TCGTGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
688689 TCGCAATGCGA
1 TCGCAATGCGA
688700 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:688719 original size:20 final size:20
Alignment explanation
Indices: 688689--688800 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
688679 TTTTCATAAT
688689 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * *
688709 TAGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
688729 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
688750 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* *
688770 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
688790 TCGCAATGCGA
1 TCGCAATGCGA
688801 TTTATATAGC
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.04
20 55 0.72
21 18 0.24
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:688778 original size:41 final size:41
Alignment explanation
Indices: 688683--688782 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 41
688673 TTGCGATTTT
* * *
688683 CATAATTCGCAATGCGAA-TACGTAAATAGCAACGCGATTA
1 CATAAATCGCAATGCGAATTACGAAAATAGCAACGCGAATA
* * *
688723 -AGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATA
1 CA-TAAATCGCAATGCGAATTACGAAAATAGCAACGCGAATA
688764 CATAAATCGCAATGCGAAT
1 CATAAATCGCAATGCGAAT
688783 CTTACTATCG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.02
40 15 0.29
41 34 0.67
42 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (41 bp):
CATAAATCGCAATGCGAATTACGAAAATAGCAACGCGAATA
Found at i:689371 original size:14 final size:14
Alignment explanation
Indices: 689352--689412 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
689342 GGAAATAACT
*
689352 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
689366 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
689385 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
689399 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
689413 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:689389 original size:19 final size:19
Alignment explanation
Indices: 689325--689393 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
689315 TAGTTTCGAG
689325 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
689345 AAT-AACTATCGCAA--CG-
1 AATGAA-AATCGCAACGCGA
*
689361 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
689378 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
689394 AGATAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 15
0.67 0.07 0.26
Matches are distributed among these distances:
14 7 0.18
15 2 0.05
16 2 0.05
17 1 0.03
18 2 0.05
19 14 0.37
20 10 0.26
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:689389 original size:33 final size:32
Alignment explanation
Indices: 689331--689423 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
689321 CGAGAATGAA
*
689331 AATCGCAACGCGGAAATAACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATAA-AATCGCAACGAGAG
*
689365 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAAT-AAAATCGCAACGAGAG
*
689398 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAA-TAAAATCGCA
689424 TTGCGATTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
33 41 0.76
34 13 0.24
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.11
Consensus pattern (32 bp):
AATCGCAACGCGAAATAAAATCGCAACGAGAG
Found at i:693056 original size:14 final size:14
Alignment explanation
Indices: 693037--693070 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
693027 ATTGTTTAAT
693037 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
693051 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
693065 TGATTT
1 TGATTT
693071 ATTTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:693195 original size:19 final size:19
Alignment explanation
Indices: 693179--693225 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
693169 AAAAATGACT
*
693179 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
693198 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
693217 ATCGCAACG
1 ATCGCAACG
693226 ACAAAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:693272 original size:19 final size:19
Alignment explanation
Indices: 693250--693400 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
693240 CGAAACTAAA
693250 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
693269 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
693284 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
693302 TTCGCATTGCGA--TTC-T
1 TTCGCGTTGCGATTTTCAT
693318 TT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
693335 TTCGCATTGCGA--TTC-T
1 TTCGCGTTGCGATTTTCAT
*
693351 AT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
** ** *
693368 TTCGTATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
693387 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
693401 AGACATTAAG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 22 0.23
16 14 0.14
17 14 0.14
19 38 0.39
20 9 0.09
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:693296 original size:33 final size:33
Alignment explanation
Indices: 693254--693380 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
693244 ACTAAATTCG
* **
693254 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
*
693287 CGTTGCGATTTTCATTTCGCATTGCGATTCTTT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
693320 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
*
693353 CGTTGCGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
693381 AGTAATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
Found at i:693327 original size:14 final size:14
Alignment explanation
Indices: 693275--693362 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
693265 TCATTTCGCT
**
693275 TTGCGATTCCCTCG
1 TTGCGATTCTTTCG
693289 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
693306 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
693322 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
*
693339 CATTGCGATTCTATCG
1 --TTGCGATTCTTTCG
693355 TTGCGATT
1 TTGCGATT
693363 TTCATTTCGT
Statistics
Matches: 61, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
14 20 0.33
16 15 0.25
17 14 0.23
19 12 0.20
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:693446 original size:20 final size:20
Alignment explanation
Indices: 693354--693446 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
693344 CGATTCTATC
**
693354 GTTGCGATTTTCATTT-CGT
1 GTTGCGATAGTCATTTCCGT
* * *
693373 ATTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
693393 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
693413 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
693434 GTTGCGATAGTCA
1 GTTGCGATAGTCA
693447 AATGATTGCC
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
19 15 0.28
20 24 0.44
21 12 0.22
22 3 0.06
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:695725 original size:12 final size:12
Alignment explanation
Indices: 695708--695732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
695698 TCTTCGGAGA
695708 CTTTTTCTTCTT
1 CTTTTTCTTCTT
695720 CTTTTTCTTCTT
1 CTTTTTCTTCTT
695732 C
1 C
695733 AAGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:695941 original size:24 final size:24
Alignment explanation
Indices: 695907--695974 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
695897 CTGAAACATC
*
695907 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
695931 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
695955 ATCAAATTTCGAATATTGAC
1 ATCAAAATCCGAGTATTGAC
695975 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:696713 original size:20 final size:20
Alignment explanation
Indices: 696690--696777 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
696680 GTATTATCTG
*
696690 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
696710 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
696730 GTTGCGAAAGTCAGTATCGC
1 GTTGCGATAGTCAGAATCGC
* * * *
696750 GTTGCGAAAATAAGTATCGC
1 GTTGCGATAGTCAGAATCGC
696770 GTTGCGAT
1 GTTGCGAT
696778 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:696815 original size:20 final size:21
Alignment explanation
Indices: 696790--696838 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
696780 TCCCAATTCA
*
696790 CAATGCGAA-TAAGTAAATCG
1 CAATGCGAATTAAGAAAATCG
**
696810 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAAGAAAATCG
696831 CAATGCGA
1 CAATGCGA
696839 TACTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
CAATGCGAATTAAGAAAATCG
Found at i:696851 original size:41 final size:42
Alignment explanation
Indices: 696806--696899 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 42
696796 GAATAAGTAA
* ** *
696806 ATCGCAATGCGAAT-TTGGAAAATCGCAATGCGATACTGACT
1 ATCGCAATGCGAATAATACAAAATCGCAACGCGATACTGACT
*
696847 ATCGCAACGCG-ATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAATGCGAATAATACAAAATCGCAACGCGATACTGACT
*
696888 TTCGCAATGCGA
1 ATCGCAATGCGA
696900 TTCTGACTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 2 0.05
41 42 0.95
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
ATCGCAATGCGAATAATACAAAATCGCAACGCGATACTGACT
Found at i:696852 original size:20 final size:20
Alignment explanation
Indices: 696827--696936 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
696817 AATTTGGAAA
*
696827 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
696847 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
696868 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
696888 TTCGCAATGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
696908 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
696928 TTCGCAACG
1 ATCGCAACG
696937 AGATTCTGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:696900 original size:41 final size:42
Alignment explanation
Indices: 696824--696936 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 42
696814 GCGAATTTGG
* *
696824 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
* **
696865 AAAATCGCAACGCGATACTGACTTTCGCAATGCGATTCTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
696907 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTTTCGCAACG
696937 AGATTCTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 26 0.42
41 34 0.55
42 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:696941 original size:20 final size:20
Alignment explanation
Indices: 696869--696945 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
696859 TAATACAAAA
*
696869 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
696889 TCGCAATGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
696909 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
696929 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
696946 AAATCGCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:696952 original size:20 final size:20
Alignment explanation
Indices: 696909--696954 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
696899 ATTCTGACTT
* ***
696909 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGAAAA
696929 TCGCAACGAGATTCTGAAAA
1 TCGCAACGAGATTCTGAAAA
696949 TCGCAA
1 TCGCAA
696955 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAACGAGATTCTGAAAA
Found at i:696953 original size:40 final size:40
Alignment explanation
Indices: 696823--696954 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
696813 TGCGAATTTG
* * **
696823 GAAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
* *
696863 ACAAAATCGCAACGCGATACTGACTTTCGCAATGCGATTCT
1 -GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
*** * *
696904 GACTTTCGCAACGCGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
696944 GAAAATCGCAA
1 GAAAATCGCAA
696955 TCATCTTCAA
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 41 0.55
41 34 0.45
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
Found at i:697195 original size:34 final size:33
Alignment explanation
Indices: 697152--697217 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
697142 ATTTATTTGA
* *
697152 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATCGCAACGC-AAAATGG
*
697186 CTATCGCAACGAGAAAATCGCAATGCAAAATG
1 CTATCGCAACGAGAAAATCGCAACGCAAAATG
697218 AAAATCGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.14
Consensus pattern (33 bp):
CTATCGCAACGAGAAAATCGCAACGCAAAATGG
Found at i:698901 original size:44 final size:42
Alignment explanation
Indices: 698853--698947 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
698843 CCTCTTCAAC
* * *
698853 GATGACAGTGGTCTCTTGAACGGTGGGGAGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAT-GGGA-GGGGACTCTTGAGG
* *
698897 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
698939 GATGACAGG
1 GATGACAGG
698948 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 22 0.49
43 3 0.07
44 20 0.44
ACGTcount: A:0.21, C:0.14, G:0.43, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:698912 original size:21 final size:21
Alignment explanation
Indices: 698883--698943 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
698873 CGGTGGGGAG
*
698883 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
698904 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
698925 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
698944 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:699317 original size:20 final size:20
Alignment explanation
Indices: 699290--699362 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
699280 TAGTTTACTT
*
699290 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGGCTA
* *
699310 TTGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
* *
699330 TCGCAATGCGGAAATGGCTA
1 TCGCAACGCGAAAATGGCTA
*
699350 TCGCAATGCGAAA
1 TCGCAACGCGAAA
699363 TGAAAATCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGGCTA
Found at i:699371 original size:19 final size:20
Alignment explanation
Indices: 699329--699374 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
699319 GGAAATGGCT
***
699329 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGCGGAAATGAAA
699349 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
699368 ATCGCAA
1 ATCGCAA
699375 CGACAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGGAAATGAAA
Found at i:699424 original size:19 final size:19
Alignment explanation
Indices: 699402--699498 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
699392 GAAACACAAA
*
699402 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
699421 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
699437 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
699454 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
699470 TCG--TTGCGCTTTTCATT
1 TCGCATTGCGATTTTCATT
699487 TCGCATTGCGAT
1 TCGCATTGCGAT
699499 AGTCATTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 21 0.35
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:699443 original size:14 final size:14
Alignment explanation
Indices: 699424--699482 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
699414 TTTCATTTCG
699424 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
699438 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
699455 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
699471 CGTTGCGCTTTT
1 CGTTGCGATTTT
699483 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.08, C:0.19, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:699452 original size:33 final size:33
Alignment explanation
Indices: 699410--699498 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
699400 AATCGCATTA
*
699410 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
699443 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
*
699476 CGCTTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCATTGCGAT
699499 AGTCATTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATTTTGTCGTTG
Found at i:701420 original size:20 final size:20
Alignment explanation
Indices: 701395--701437 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
701385 AATAGTTTCT
701395 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* *
701415 GAAAATGACAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
701435 GAA
1 GAA
701438 TTTGATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Done.