Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 52 of 54
Found at i:12268457 original size:20 final size:20
Alignment explanation
Indices: 12268428--12268470 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12268418 ATTCCACCAC
*
12268428 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
12268448 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
12268468 ATG
1 ATG
12268471 AGCTCTTAGA
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:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:12276880 original size:136 final size:136
Alignment explanation
Indices: 12276709--12276981 Score: 546
Period size: 136 Copynumber: 2.0 Consensus size: 136
12276699 AAGAGAGAAC
12276709 GAACTTCCCGAGGCTCCCTGAGCCTCATACATTCTTGCTAATGAGTTTCATTGCAGCATGTGTTG
1 GAACTTCCCGAGGCTCCCTGAGCCTCATACATTCTTGCTAATGAGTTTCATTGCAGCATGTGTTG
12276774 TAGTTTTCTCAATCGCTATCACGTTGACTGGAGCATGTTGCGGGCGTTTCGCACCATCCTATTTC
66 TAGTTTTCTCAATCGCTATCACGTTGACTGGAGCATGTTGCGGGCGTTTCGCACCATCCTATTTC
12276839 ACCATG
131 ACCATG
12276845 GAACTTCCCGAGGCTCCCTGAGCCTCATACATTCTTGCTAATGAGTTTCATTGCAGCATGTGTTG
1 GAACTTCCCGAGGCTCCCTGAGCCTCATACATTCTTGCTAATGAGTTTCATTGCAGCATGTGTTG
12276910 TAGTTTTCTCAATCGCTATCACGTTGACTGGAGCATGTTGCGGGCGTTTCGCACCATCCTATTTC
66 TAGTTTTCTCAATCGCTATCACGTTGACTGGAGCATGTTGCGGGCGTTTCGCACCATCCTATTTC
12276975 ACCATG
131 ACCATG
12276981 G
1 G
12276982 GATTTTCTTC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (136 bp):
GAACTTCCCGAGGCTCCCTGAGCCTCATACATTCTTGCTAATGAGTTTCATTGCAGCATGTGTTG
TAGTTTTCTCAATCGCTATCACGTTGACTGGAGCATGTTGCGGGCGTTTCGCACCATCCTATTTC
ACCATG
Found at i:12278378 original size:2 final size:2
Alignment explanation
Indices: 12278371--12278407 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12278361 TAAATTAATA
12278371 AT 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 A
12278408 AATAAAGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12283524 original size:12 final size:13
Alignment explanation
Indices: 12283507--12283535 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12283497 GTGTGATTAG
12283507 TATTTTA-TTATT
1 TATTTTATTTATT
12283519 TATTTTATTTATT
1 TATTTTATTTATT
12283532 TATT
1 TATT
12283536 ATATATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:12294142 original size:29 final size:28
Alignment explanation
Indices: 12294086--12294142 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
12294076 TAAATTGAAA
*
12294086 ATAAAATAAAGAAAAAAACTAACAACAT
1 ATAAAATAAAGAAAAAAACAAACAACAT
* * *
12294114 ATAAAATAAGGACAAAAAGCAAACGACAT
1 ATAAAATAAAGA-AAAAAACAAACAACAT
12294143 GACCAACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.12
Consensus pattern (28 bp):
ATAAAATAAAGAAAAAAACAAACAACAT
Found at i:12294840 original size:5 final size:5
Alignment explanation
Indices: 12294830--12294887 Score: 64
Period size: 5 Copynumber: 11.4 Consensus size: 5
12294820 ACCCTAAACG
* * *
12294830 TTCTT TTCTT TCCTT TTCTT TTCTT TTCTTTT TTCTT TTTTT TTTTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTC--TT TTCTT TTCTT TTCTT TTCTT
12294882 TT-TT TT
1 TTCTT TT
12294888 TTCAACTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
4 4 0.09
5 38 0.81
7 5 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTCTT
Found at i:12294865 original size:12 final size:11
Alignment explanation
Indices: 12294843--12294890 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
12294833 TTTTCTTTCC
*
12294843 TTTTC-TTTTC
1 TTTTCTTTTTT
12294853 TTTTCTTTTTT
1 TTTTCTTTTTT
12294864 CTTTT-TTTTTT
1 -TTTTCTTTTTT
12294875 TTTTCTTTTTT
1 TTTTCTTTTTT
12294886 TTTTC
1 TTTTC
12294891 AACTTAAGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.26
11 21 0.62
12 4 0.12
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:12294887 original size:15 final size:15
Alignment explanation
Indices: 12294843--12294889 Score: 76
Period size: 15 Copynumber: 3.0 Consensus size: 15
12294833 TTTTCTTTCC
12294843 TTTTCTTTTCTTTTCTT
1 TTTTCTTTT-TTTT-TT
12294860 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
12294875 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
12294890 CAACTTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 17 0.57
16 4 0.13
17 9 0.30
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:12296639 original size:22 final size:22
Alignment explanation
Indices: 12296614--12296665 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
12296604 GCCATGTCCT
12296614 AGTGCATTTGATGCCCCATCGA
1 AGTGCATTTGATGCCCCATCGA
12296636 AGTGCATTTGATGCCCCATCGA
1 AGTGCATTTGATGCCCCATCGA
12296658 AGTGCATT
1 AGTGCATT
12296666 CTCCAGGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (22 bp):
AGTGCATTTGATGCCCCATCGA
Found at i:12305837 original size:105 final size:105
Alignment explanation
Indices: 12305649--12306254 Score: 899
Period size: 105 Copynumber: 5.8 Consensus size: 105
12305639 ACCCATAGCT
* *
12305649 AAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAA
12305713 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
65 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
12305754 AAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAA
** *
12305818 TTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACGC
65 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
*
12305859 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAA-
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
* * *
12305923 TT----TT-AAAACGAAAGATATTGGACTCCAAACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
12305958 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
12306023 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
12306063 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
*
12306128 TTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* * *
12306168 AAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAA-ATTTC-CCAGTTTAAAGACAGC
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATT-CAG--AGC
*
12306231 ACAAGTTCAACTTCACAACGAAGG
62 -CAATTTCAACTTCACAACGAAGG
12306255 GGCCGCTGGC
Statistics
Matches: 464, Mismatches: 25, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
99 87 0.19
100 4 0.01
103 3 0.01
104 11 0.02
105 332 0.72
106 2 0.00
107 3 0.01
108 22 0.05
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (105 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
Found at i:12306005 original size:204 final size:207
Alignment explanation
Indices: 12305649--12306254 Score: 866
Period size: 204 Copynumber: 2.9 Consensus size: 207
12305639 ACCCATAGCT
* *
12305649 AAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAA
*
12305713 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGA
65 TTT--A-TTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
* **
12305778 CCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAATTTCAACTTCACAGTGAAGGATAT
127 CCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
12305842 TGGACTCGAGACAACGC
191 TGGACTCCAGACAACGC
*
12305859 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAA-
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
* * *
12305923 TT-TT-AAAACGAAAGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TTATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
12305986 TGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
131 TGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
12306051 TCCAGACAACGC
196 TCCAGACAACGC
* *
12306063 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
* *
12306128 TTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGAG
66 TT--A-TTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* * *
12306193 CGCTGGTTGTCAACAAA-ATTTC-CCAGTTTAAAGACAGCACAAGTTCAACTTCACAACGAAGG
128 CGCTGGTTGTCAACAAACATTTCTCCA-ATT-CAG--AGC-CAATTTCAACTTCACAACGAAGG
12306255 GGCCGCTGGC
Statistics
Matches: 359, Mismatches: 24, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
204 185 0.52
205 6 0.02
208 3 0.01
209 11 0.03
210 127 0.35
211 2 0.01
212 3 0.01
213 22 0.06
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (207 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
TTATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAACGC
Found at i:12306062 original size:309 final size:308
Alignment explanation
Indices: 12305649--12306214 Score: 974
Period size: 309 Copynumber: 1.8 Consensus size: 308
12305639 ACCCATAGCT
*
12305649 AAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAGAGTCAAT
1 AAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAGAGCCAAT
*
12305714 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGAC
66 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
* **
12305779 CGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATT
131 CGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
*
12305843 GGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACATTTCT
195 GGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-ATTTCT
12305908 CCAATTCAGAGCCAATTTTAAAACGAAAGATATTGGACTCCAAACAACGC
259 CCAATTCAGAGCCAATTTTAAAACGAAAGATATTGGACTCCAAACAACGC
* * *
12305958 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCA-ATTTAGAGCCAA
1 AAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGCCAA
12306022 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
65 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
* *
12306087 CCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAATTTCAACTTCACAACGAAGGATATT
130 CCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
* *
12306152 GGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAAATTTC
195 GGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAATTTC
12306215 CCAGTTTAAA
Statistics
Matches: 242, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
308 5 0.02
309 233 0.96
310 4 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (308 bp):
AAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAGAGCCAAT
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
GACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAATTTCTCC
AATTCAGAGCCAATTTTAAAACGAAAGATATTGGACTCCAAACAACGC
Found at i:12306370 original size:164 final size:168
Alignment explanation
Indices: 12306062--12306382 Score: 404
Period size: 164 Copynumber: 1.9 Consensus size: 168
12306052 CCAGACAACG
* * *
12306062 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAA-TT--A-CCAA
* * *
12306127 TTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGA
62 TTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGA
* **
12306192 GCGCTGGTTGTCAAC-AA-AATTTCCCAGTTTAAAGACAGCA
127 CCGCTGACTGTCAACAAACAATTTCCCAGTTTAAAGACAGCA
*
12306232 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTC-CCAA-T-CCAATTT
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAAC-ATTTCTCCAATTACCAATTT
* ***
12306294 CAACTTCACAGA-AAATGATATTGGACTCGAGACAGTTCAAGTTCAACTTCACAACGAAGAGG-C
65 CAACTTCACA-ACAAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAG-GGAC
12306357 CGCTGACTGTCAACAAACAATTTCCC
128 CGCTGACTGTCAACAAACAATTTCCC
12306383 GAGCCAATTT
Statistics
Matches: 132, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
164 69 0.52
165 5 0.04
166 8 0.06
168 1 0.01
170 44 0.33
171 5 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (168 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAATTACCAATTTC
AACTTCACAACAAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGC
TGACTGTCAACAAACAATTTCCCAGTTTAAAGACAGCA
Found at i:12306395 original size:99 final size:99
Alignment explanation
Indices: 12306224--12306481 Score: 383
Period size: 99 Copynumber: 2.6 Consensus size: 99
12306214 CCCAGTTTAA
* *
12306224 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAATCC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAAGCC
*
12306289 AATTTCAACTTCACAGAAAATGATATTGGACTCG
66 AATTTCAACTTCACAGAAAAGGATATTGGACTCG
*** * * *
12306323 AGACAGTTCAAGTTCAACTTCACAACGAAGAGGCCGCTGACTGTCAACAAACAATTTCCCGAGCC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAAGCC
**
12306388 AATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 AATTTCAACTTCACAGAAAAGGATATTGGACTCG
* * *
12306422 AGACAACACAAGTTCAACTTCACGATGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCA
12306482 GTTTAAGACA
Statistics
Matches: 141, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
98 8 0.06
99 133 0.94
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (99 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAAGCC
AATTTCAACTTCACAGAAAAGGATATTGGACTCG
Found at i:12306492 original size:263 final size:264
Alignment explanation
Indices: 12305957--12306653 Score: 915
Period size: 263 Copynumber: 2.6 Consensus size: 264
12305947 CCAAACAACG
* * * *
12305957 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAAC-ATTTCTCCAATTTAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTC-CCAA-TT--A-CCA
* *
12306021 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
61 ATTTCAACTTCACAA-GAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGG
*
12306086 ACCGCTGGTTGTCATCAAAC-ATTTCTCCAATTTAGAGCCAATTTCAACTTCACAACGAAGGATA
125 -CCGCTGGTTGTCAACAAACAATTTC-CC-----AGAGCCAATTTCAACTTCACAACGAAGGATA
* *
12306150 TTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAAATTTC
183 TTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAAATTTC
12306215 CCAGTTTAAAGACAGCA
248 CCAGTTTAAAGACAGCA
12306232 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAA-T-CCAATTTC
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAATTACCAATTTC
* * *** *
12306295 AACTTCACAGAAAATGATATTGGACTCGAGACAGTTCAAGTTCAACTTCACAACGAAGAGGCCGC
66 AACTTCACA-AGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAG-GGCCGC
** *
12306360 TGACTGTCAACAAACAATTTCCC-GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAG
129 TGGTTGTCAACAAACAATTTCCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAG
*
12306424 ACAACACAAGTTCAACTTCACGATGAAGGG-GCCGCTGGTTGTCAACAAAAATTTCCCAGTTT-A
194 ACAACACAAGTTCAACTTCACGACGAAGGGAG-CGCTGGTTGTCAAC-AAAATTTCCCAGTTTAA
12306487 AGACAGCA
257 AGACAGCA
* *
12306495 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCTACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAA-TT---A-CCA
*
12306560 ATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGG
61 ATTTCAACTTCACA-AGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAA-GG
*
12306625 GTCGCTGGTTGTCAACAAA-AATTTCCCAG
124 GCCGCTGGTTGTCAACAAACAATTTCCCAG
12306654 TTTAAGACAG
Statistics
Matches: 376, Mismatches: 31, Indels: 35
0.85 0.07 0.08
Matches are distributed among these distances:
262 1 0.00
263 142 0.38
264 15 0.04
265 1 0.00
269 83 0.22
270 83 0.22
271 1 0.00
273 1 0.00
275 44 0.12
276 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (264 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAATTACCAATTTC
AACTTCACAAGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGCCGCTG
GTTGTCAACAAACAATTTCCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGAC
AACACAAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAAATTTCCCAGTTTAAAGAC
AGCA
Found at i:12306504 original size:65 final size:65
Alignment explanation
Indices: 12306422--12306580 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
12306412 ATTGGACTCG
* * * *
12306422 AGACAACACAAGTTCAACTTCACGATGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCCAGTTT
1 AGACAGCACAAGTTCAACTTCAC-ATGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
12306486 A
65 A
* *
12306487 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCTACAAACAACTTCCCAATTT
1 AGACAGCACAAGTTCAACTTCAC-ATGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
*
12306552 C
65 A
*
12306553 AG--AGC-CAATTTCAACTTCACATCGAAGG
1 AGACAGCACAAGTTCAACTTCACAT-GAAGG
12306581 ATATTGGACT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.01
63 19 0.23
64 3 0.04
65 46 0.56
66 13 0.16
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (65 bp):
AGACAGCACAAGTTCAACTTCACATGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTA
Found at i:12306609 original size:171 final size:171
Alignment explanation
Indices: 12306331--12306814 Score: 820
Period size: 171 Copynumber: 2.9 Consensus size: 171
12306321 CGAGACAGTT
* * *
12306331 CAAGTTCAACTTCACAACGAAGAGGCCGCTGACTGTCAACAAACAA-TTTCC-----C-GAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
12306389 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGATGAAGGG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGG
12306454 GCCGCTGGTTGTCAACAAAAATTTCCCAGTTTAAGACAGCA
131 GCCGCTGGTTGTCAACAAAAATTTCCCAGTTTAAGACAGCA
*
12306495 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCTACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
12306560 ATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGG
*
12306625 GTCGCTGGTTGTCAACAAAAATTTCCCAGTTTAAGACAGCA
131 GCCGCTGGTTGTCAACAAAAATTTCCCAGTTTAAGACAGCA
12306666 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
12306731 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCATGTTCAACTTCACAACGAAGGG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGG
*
12306796 GCCGCTGGTTGTTAACAAA
131 GCCGCTGGTTGTCAACAAA
12306815 CACTTTCCAA
Statistics
Matches: 299, Mismatches: 14, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
164 43 0.14
165 4 0.01
170 1 0.00
171 251 0.84
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (171 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGG
GCCGCTGGTTGTCAACAAAAATTTCCCAGTTTAAGACAGCA
Found at i:12306611 original size:106 final size:107
Alignment explanation
Indices: 12306487--12306688 Score: 282
Period size: 106 Copynumber: 1.9 Consensus size: 107
12306477 TCCCAGTTTA
* *
12306487 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCTACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAA-AACTTCCCAATTT
* * *
12306552 CAG-AGC-CAATTTCAACTTCACATCGAAGGATATTGGACTCG
65 AAGAAGCACAAGTTCAACTTCACAACGAAGGATATTGGACTCG
* * * * *
12306593 AGACAACACAAGTTCAACTTCACGACGAAGGGGTCGCTGGTTGTCAACAAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAAACTTCCCAATTTA
12306658 AGACAGCACAAGTTCAACTTCACAACGAAGG
66 AGA-AGCACAAGTTCAACTTCACAACGAAGG
12306689 GGCCGCTGGC
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 13 0.16
106 46 0.55
107 3 0.04
108 21 0.25
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (107 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAAACTTCCCAATTTA
AGAAGCACAAGTTCAACTTCACAACGAAGGATATTGGACTCG
Found at i:12306673 original size:65 final size:65
Alignment explanation
Indices: 12306593--12306751 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
12306583 ATTGGACTCG
* * * * *
12306593 AGACAACACAAGTTCAACTTCACGACGAAGGGGTCGCTGGTTGTCAACAAA-AATTTCCCAGTTT
1 AGACAGCACAAGTTCAACTTCAC-ACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
12306657 A
65 A
12306658 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAGCACAAGTTCAACTTCAC-ACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
*
12306723 C
65 A
*
12306724 AG--AGC-CAATTTCAACTTCACAGCGAAGG
1 AGACAGCACAAGTTCAACTTCACA-CGAAGG
12306752 ATATTGGACT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
62 1 0.01
63 20 0.24
64 3 0.04
65 47 0.56
66 13 0.15
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (65 bp):
AGACAGCACAAGTTCAACTTCACACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTA
Found at i:12306871 original size:107 final size:106
Alignment explanation
Indices: 12306669--12306871 Score: 336
Period size: 107 Copynumber: 1.9 Consensus size: 106
12306659 GACAGCACAA
12306669 GTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
1 GTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
12306734 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAT
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAT
* * * *
12306775 GTTCAACTTCACAACGAAGGGGCCGCTGGTTGTTAACAAAC-ACTTTCCAAGCTTTCAGAGTCAA
1 GTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAA--TTTCAGAGCCAA
*
12306839 TTTCAACTTCACAGCGAAGGATATTGGCCTCGA
64 TTTCAACTTCACAGCGAAGGATATTGGACTCGA
12306872 AGCAACACAA
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
105 8 0.09
106 39 0.43
107 43 0.48
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (106 bp):
GTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAT
Found at i:12308573 original size:12 final size:13
Alignment explanation
Indices: 12308556--12308584 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12308546 GTGTGATTAG
12308556 TATTTTA-TTATT
1 TATTTTATTTATT
12308568 TATTTTATTTATT
1 TATTTTATTTATT
12308581 TATT
1 TATT
12308585 ATATATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:12308863 original size:29 final size:28
Alignment explanation
Indices: 12308831--12308887 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
12308821 GATGTTGGTC
*
12308831 ATGTCGTTTGCTTTTTGTCCTTATTTTAT
1 ATGTCGTTAG-TTTTTGTCCTTATTTTAT
* * *
12308860 ATGTTGTTAGTTTTTTTCTTTATTTTAT
1 ATGTCGTTAGTTTTTGTCCTTATTTTAT
12308888 TTTCAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.67
Consensus pattern (28 bp):
ATGTCGTTAGTTTTTGTCCTTATTTTAT
Found at i:12312528 original size:23 final size:23
Alignment explanation
Indices: 12312502--12312546 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
12312492 CTTGCAAAAG
12312502 TAACTACTCGAACTCGAGTCCTT
1 TAACTACTCGAACTCGAGTCCTT
*
12312525 TAACTACTCGAACTTGAGTCCT
1 TAACTACTCGAACTCGAGTCCT
12312547 CTAAGCAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (23 bp):
TAACTACTCGAACTCGAGTCCTT
Found at i:12312870 original size:32 final size:32
Alignment explanation
Indices: 12312834--12312910 Score: 127
Period size: 33 Copynumber: 2.4 Consensus size: 32
12312824 ACAAAGTTTA
*
12312834 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
12312866 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
12312899 CGATAATTGAAA
1 CGATAATTGAAA
12312911 CAAAGTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 11 0.27
33 30 0.73
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:12312924 original size:21 final size:21
Alignment explanation
Indices: 12312899--12312940 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12312889 CTTCCAAGTT
*
12312899 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
12312920 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
12312941 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:12315887 original size:19 final size:18
Alignment explanation
Indices: 12315861--12315921 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
12315851 CGATAAACCG
12315861 AACCGAACCGAACCGAAA
1 AACCGAACCGAACCGAAA
12315879 AATCCGAACCGTTAA---AAA
1 AA-CCGAACCG--AACCGAAA
12315897 AACCGAACCGAACCGATAA
1 AACCGAACCGAACCGA-AA
12315916 AACCGA
1 AACCGA
12315922 TTTCGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.06
17 8 0.22
18 8 0.22
19 16 0.44
21 2 0.06
ACGTcount: A:0.49, C:0.30, G:0.15, T:0.07
Consensus pattern (18 bp):
AACCGAACCGAACCGAAA
Found at i:12320288 original size:22 final size:22
Alignment explanation
Indices: 12320256--12320315 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
12320246 ATATTAAGAT
12320256 GTACCAATACCCCTATGAATGG
1 GTACCAATACCCCTATGAATGG
* *
12320278 GTATCAATACCCATATGAATGG
1 GTACCAATACCCCTATGAATGG
*
12320300 GTACCGATACCCCTAT
1 GTACCAATACCCCTAT
12320316 CAATACCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (22 bp):
GTACCAATACCCCTATGAATGG
Found at i:12320322 original size:34 final size:35
Alignment explanation
Indices: 12320279--12320348 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
12320269 TATGAATGGG
*
12320279 TATCAATACC-CATATGAATGGGTACCGATACCCC
1 TATCAATACCTCATATGAACGGGTACCGATACCCC
** *
12320313 TATCAATACCTGTTATGAACGGGTACCGATAGCCC
1 TATCAATACCTCATATGAACGGGTACCGATACCCC
12320348 T
1 T
12320349 TATGAATGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 10 0.32
35 21 0.68
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (35 bp):
TATCAATACCTCATATGAACGGGTACCGATACCCC
Found at i:12320542 original size:11 final size:11
Alignment explanation
Indices: 12320522--12320551 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12320512 TATATACTAC
*
12320522 TTCAAACTCAT
1 TTCAAGCTCAT
12320533 TTCAAGCTCAT
1 TTCAAGCTCAT
12320544 TTCAAGCT
1 TTCAAGCT
12320552 ATAAATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (11 bp):
TTCAAGCTCAT
Found at i:12320807 original size:33 final size:33
Alignment explanation
Indices: 12320739--12320808 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
12320729 TTTTGTAAAG
* **
12320739 GGGAAAGGTTCTAGCTGATCCCGTGAAAAGTTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
* * *
12320772 GGGAAATGTTCTAGTTTAGCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
12320805 GGGA
1 GGGA
12320809 GTTTGTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
Found at i:12340490 original size:21 final size:19
Alignment explanation
Indices: 12340464--12340504 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12340454 CCTAAAGCAC
*
12340464 TGATTTATGATACATGTTATA
1 TGATTT-TGATAAATG-TATA
12340485 TGATTTTGATAAATGTATA
1 TGATTTTGATAAATGTATA
12340504 T
1 T
12340505 TTCTGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (19 bp):
TGATTTTGATAAATGTATA
Found at i:12340500 original size:20 final size:20
Alignment explanation
Indices: 12340464--12340538 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 20
12340454 CCTAAAGCAC
*
12340464 TGATTTATGATACATGTTATA
1 TGATTT-TGATAAATGTTATA
12340485 TGATTTTGATAAATG-TATA
1 TGATTTTGATAAATGTTATA
*
12340504 T--TTCTGATAAATAGATGGTATA
1 TGATTTTGATAAAT-G-T--TATA
12340526 TGATTTTGATAAA
1 TGATTTTGATAAA
12340539 AGTTCATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 10 0.23
18 1 0.02
19 5 0.11
20 8 0.18
21 6 0.14
22 5 0.11
24 9 0.20
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (20 bp):
TGATTTTGATAAATGTTATA
Found at i:12342219 original size:24 final size:24
Alignment explanation
Indices: 12342156--12342246 Score: 98
Period size: 24 Copynumber: 3.8 Consensus size: 24
12342146 CATAATTCAG
* *
12342156 GTCAAGTATCATATCAAAATCC-A
1 GTCAAGTATCAGATCAGAATCCAA
12342179 GATCAAGTATTC-GATCAGAATCCAA
1 G-TCAAGTA-TCAGATCAGAATCCAA
* *
12342204 GTCAAGTATCAAATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
12342228 GTC-AGATATCAGATCAGAA
1 GTCAAG-TATCAGATCAGAA
12342247 ATCAAATCGA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
23 5 0.09
24 49 0.84
25 4 0.07
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:12344708 original size:13 final size:13
Alignment explanation
Indices: 12344690--12344731 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
12344680 TTTGGTCAAC
12344690 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
12344703 GGTCAACAGGTCG
1 GGTCAACGGGTCG
12344716 GGTCAACGGGTCG
1 GGTCAACGGGTCG
12344729 GGT
1 GGT
12344732 TGAAACCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:12345900 original size:31 final size:28
Alignment explanation
Indices: 12345855--12345913 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
12345845 TAAACTACAT
12345855 TTTTAGTACCTAAATTATTACTTTTATTTTA
1 TTTTAGTACCTAAATT-TTA-TTTT-TTTTA
* *
12345886 TTTTGGTACTTAAATTTTATTTTTTTTA
1 TTTTAGTACCTAAATTTTATTTTTTTTA
12345914 AAACATATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 4 0.15
30 3 0.12
31 14 0.54
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTTAGTACCTAAATTTTATTTTTTTTA
Found at i:12354185 original size:6 final size:6
Alignment explanation
Indices: 12354174--12354255 Score: 164
Period size: 6 Copynumber: 13.7 Consensus size: 6
12354164 AATAACCATG
12354174 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
12354222 AATGAT AATGAT AATGAT AATGAT AATGAT AATG
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATG
12354256 TATTGATCAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
AATGAT
Found at i:12355875 original size:11 final size:11
Alignment explanation
Indices: 12355859--12355887 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
12355849 CATATATGGC
12355859 CAGCTCATCTT
1 CAGCTCATCTT
12355870 CAGCTCATCTT
1 CAGCTCATCTT
12355881 CAGCTCA
1 CAGCTCA
12355888 AACACATGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31
Consensus pattern (11 bp):
CAGCTCATCTT
Found at i:12356816 original size:15 final size:15
Alignment explanation
Indices: 12356796--12356841 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
12356786 TTTGATATCA
12356796 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
12356811 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
12356826 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
12356842 TTATTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:12357392 original size:17 final size:17
Alignment explanation
Indices: 12357367--12357402 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12357357 ATCCTACCTT
12357367 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
* *
12357384 TACCCTAACCATTTTTA
1 TACCATAACCATTTCTA
12357401 TA
1 TA
12357403 GCCAACACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:12360940 original size:13 final size:13
Alignment explanation
Indices: 12360922--12360946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12360912 GATACTATAT
12360922 TTCCATCACCATA
1 TTCCATCACCATA
12360935 TTCCATCACCAT
1 TTCCATCACCAT
12360947 CACACCAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATA
Found at i:12361130 original size:15 final size:15
Alignment explanation
Indices: 12361110--12361155 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
12361100 TTTGATATCA
12361110 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
12361125 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
12361140 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
12361156 TTATTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:12363199 original size:62 final size:64
Alignment explanation
Indices: 12363121--12363240 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
12363111 CACTACATGT
* * * *
12363121 GTATCGGTACCCAAATTACATTC-TAAGTTTT-CATTTTAAGGGGGTATCGATACACTGCCTAG
1 GTATCGATACCCAAATTACATTCGAAAGTTTTCCACTTCAAGGGGGTATCGATACACTGCCTAG
*
12363183 GTATCGATACCCAAATTACATTCGAAATTTTTCCACTTCAAGGGGGTATCGATACACT
1 GTATCGATACCCAAATTACATTCGAAAGTTTTCCACTTCAAGGGGGTATCGATACACT
12363241 TGTGAAGGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 22 0.43
63 6 0.12
64 23 0.45
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (64 bp):
GTATCGATACCCAAATTACATTCGAAAGTTTTCCACTTCAAGGGGGTATCGATACACTGCCTAG
Found at i:12372599 original size:131 final size:131
Alignment explanation
Indices: 12372356--12372724 Score: 596
Period size: 131 Copynumber: 2.8 Consensus size: 131
12372346 ATAATTTTAA
* * *
12372356 GAGAAAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCGTGCCTTAAAGCA
1 GAGAGAAAACGGTAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
12372421 GTCATTTATTACTCCAATCGAAATGAAAAGATATCACTATTTAGTCTTAAAATTCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAAAGATATTACTATTTAGTCTTAAAAATCAATATTGATT
12372486 C
131 C
* * *
12372487 GAGAGAAAACGGTAATATCTAATTATTTCCGATCGAGAATAAATGACCTCTCATGACTTAAAACA
1 GAGAGAAAACGGTAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
12372552 ATCATTTATTACTCCAATCGAAATGAAGAA-ATATTACTTTTTCGTCTTAAAAATCAATATTGAT
66 GTCATTTATTACTCCAATCGAAATGAA-AAGATATTACTATTTAGTCTTAAAAATCAATATTGAT
12372616 TC
130 TC
*
12372618 GAGAGAAAACAGTAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGGTAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
12372683 GTCATTTATTACACCAATCGAAATGAAAAGATATTATTATTT
66 GTCATTTATTACTCCAATCGAAATGAAAAGATATTACTATTT
12372725 TCAATATTGA
Statistics
Matches: 217, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
130 2 0.01
131 213 0.98
132 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGGTAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAAAGATATTACTATTTAGTCTTAAAAATCAATATTGATT
C
Found at i:12373928 original size:33 final size:32
Alignment explanation
Indices: 12373885--12373984 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 32
12373875 AGTTTACGAT
*
12373885 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAA-ACTTCCAAGTTTGATA
*
12373918 AATTCAAATACTTAAAAATCTCCAAGTTTGATA
1 AATTCAAATACTTAAAACT-TCCAAGTTTGATA
*
12373951 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTT-AAAACTTCCAAGTTTGATA
12373984 A
1 A
12373985 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.03
33 54 0.89
34 5 0.08
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (32 bp):
AATTCAAATACTTAAAACTTCCAAGTTTGATA
Found at i:12374004 original size:21 final size:21
Alignment explanation
Indices: 12373979--12374020 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12373969 CTTCCAAGTT
12373979 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
12374000 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
12374021 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:12381938 original size:3 final size:3
Alignment explanation
Indices: 12381926--12381966 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
12381916 TTAAATATTC
12381926 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12381967 ATATACATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12382140 original size:22 final size:25
Alignment explanation
Indices: 12382115--12382164 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 25
12382105 ATTCTTTTGG
12382115 TTTTTTAATTTA-TTC-TTT-TTTA
1 TTTTTTAATTTACTTCATTTATTTA
*
12382137 TTTTTTCATTTACTTCATTTATTTA
1 TTTTTTAATTTACTTCATTTATTTA
12382162 TTT
1 TTT
12382165 ATTCATTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.46
23 3 0.12
24 3 0.12
25 7 0.29
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTTAATTTACTTCATTTATTTA
Found at i:12382153 original size:9 final size:8
Alignment explanation
Indices: 12382122--12382171 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
12382112 TGGTTTTTTA
12382122 ATTTATTC
1 ATTTATTC
*
12382130 -TTT-TTT
1 ATTTATTC
*
12382136 ATTTTTTC
1 ATTTATTC
12382144 ATTTACTTC
1 ATTTA-TTC
*
12382153 ATTTATTT
1 ATTTATTC
12382161 ATTTATTC
1 ATTTATTC
12382169 ATT
1 ATT
12382172 GCTTTATCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
6 2 0.06
7 6 0.18
8 18 0.53
9 8 0.24
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (8 bp):
ATTTATTC
Found at i:12382527 original size:13 final size:12
Alignment explanation
Indices: 12382512--12382593 Score: 60
Period size: 13 Copynumber: 6.7 Consensus size: 12
12382502 CTTCATTTTG
*
12382512 TTTTGTTTTATT
1 TTTTCTTTTATT
* *
12382524 GTTTTGTTTTGTT
1 -TTTTCTTTTATT
*
12382537 TTTTATTTT-TT
1 TTTTCTTTTATT
**
12382548 TTATT-TTACATT
1 TT-TTCTTTTATT
12382560 TTTTCTTTTATT
1 TTTTCTTTTATT
12382572 GTTTTCTTTTATT
1 -TTTTCTTTTATT
12382585 TTATTCTTT
1 TT-TTCTTT
12382594 AGCCATCTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
11 8 0.14
12 21 0.36
13 29 0.50
ACGTcount: A:0.10, C:0.05, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTATT
Found at i:12382530 original size:18 final size:18
Alignment explanation
Indices: 12382506--12382555 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
12382496 CCTTCCCTTC
12382506 ATTTTGTTTTGTTTTATT
1 ATTTTGTTTTGTTTTATT
*
12382524 GTTTTGTTTTGTTTT-TT
1 ATTTTGTTTTGTTTTATT
*
12382541 ATTTT-TTTTATTTTA
1 ATTTTGTTTTGTTTTA
12382556 CATTTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
18 14 0.50
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (18 bp):
ATTTTGTTTTGTTTTATT
Found at i:12386606 original size:16 final size:17
Alignment explanation
Indices: 12386581--12386614 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12386571 CCGAGGTGTC
12386581 ACATTGACTTT-ACAAA
1 ACATTGACTTTGACAAA
*
12386597 ACATTTACTTTGACAAA
1 ACATTGACTTTGACAAA
12386614 A
1 A
12386615 TATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (17 bp):
ACATTGACTTTGACAAA
Found at i:12387423 original size:23 final size:23
Alignment explanation
Indices: 12387397--12387465 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
12387387 CACCACAACT
* * *
12387397 CGTATAAATGCACTAAAGTTCCA
1 CGTATAATTGCACCAAAGTGCCA
* * *
12387420 CGTAGAATTGCACCGAAGTGCCG
1 CGTATAATTGCACCAAAGTGCCA
*
12387443 CGTATAATTGCACCGAAGTGCCA
1 CGTATAATTGCACCAAAGTGCCA
12387466 TATAAAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTATAATTGCACCAAAGTGCCA
Found at i:12391791 original size:45 final size:47
Alignment explanation
Indices: 12391717--12391824 Score: 148
Period size: 45 Copynumber: 2.3 Consensus size: 47
12391707 TGTTCGTTTT
12391717 TTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTCA
1 TTTTTT-GAAT-AATGCATGCGAACTAGATATCATGCGGTTAGGATTCA
* *
12391765 TTTTTTGAATAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTCA
*
12391811 TTTTCGTGAATAAT
1 TTTT-TTGAATAAT
12391825 AAAGCATGCG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
45 28 0.52
46 9 0.17
47 11 0.20
48 6 0.11
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTCA
Found at i:12401525 original size:17 final size:16
Alignment explanation
Indices: 12401505--12401539 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
12401495 GAAGAAAAAC
12401505 AAAAAGAGAAAAATGAA
1 AAAAAGAGAAAAAT-AA
12401522 AAAAAGAGAAAAATAA
1 AAAAAGAGAAAAATAA
12401538 AA
1 AA
12401540 GGAGGGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (16 bp):
AAAAAGAGAAAAATAA
Found at i:12403051 original size:102 final size:102
Alignment explanation
Indices: 12402875--12403316 Score: 602
Period size: 102 Copynumber: 4.2 Consensus size: 102
12402865 TCGAGTTCTC
* * *
12402875 TACTCTCTGAAGGAATAGAGAGCGGACCCA-TT-TTATGAAGATTGAGTCCTATACTCTCTGAAG
1 TACTCTCTGAAGGAATAGGGAGCGGA-CAAGTTCGT-TGAAGATTGAGTCCTATACTCTCTGAAG
*
12402938 GAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTA
64 GAATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTA
12402977 TACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGA
1 TACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGA
12403042 ATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTA
66 ATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTA
12403079 TACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGA
1 TACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGA
*
12403144 ATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTA
66 ATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTA
* * ** * *
12403181 TACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTG
1 TACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-GAGTCCTATACTCTCTG
** * *
12403246 AAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTA
61 AAGGAATAGAGAGCGGACAAG-TTCGTTGAAGA---TT-GAGTCCTA
*
12403293 TACTCCCTGAACGG-ATAGGGAGCG
1 TACTCTCTGAA-GGAATAGGGAGCG
12403317 AACCCGTTTT
Statistics
Matches: 308, Mismatches: 19, Indels: 16
0.90 0.06 0.05
Matches are distributed among these distances:
101 2 0.01
102 220 0.71
103 11 0.04
106 2 0.01
107 34 0.11
108 10 0.03
111 2 0.01
112 25 0.08
113 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27
Consensus pattern (102 bp):
TACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGA
ATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTA
Found at i:12403153 original size:153 final size:152
Alignment explanation
Indices: 12402875--12403316 Score: 636
Period size: 153 Copynumber: 2.8 Consensus size: 152
12402865 TCGAGTTCTC
*
12402875 TACTCTCTGAAGGAATAGAGAGCGGACCCA-TTTTATGAAGATTGAGTCCTATACTCTCTGAAGG
1 TACTCTCTGAAGGAATAGAGAGCGGA-CCAGTTGT-TGAAGATTGAGTCCTATACTCTCTGAAGG
12402939 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
64 AATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
12403004 AAGTTCGTTGAAGATTGAGTCCTA
129 AAGTTCGTTGAAGATTGAGTCCTA
*
12403028 TACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGA
1 TACTCTCTGAAGGAATAGAGAGCGGACCAGTT-GTTGAAGATTGAGTCCTATACTCTCTGAAGGA
12403093 ATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
65 ATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
12403158 AGTTCGTTGAAGATTGAGTCCTA
130 AGTTCGTTGAAGATTGAGTCCTA
* * *
12403181 TACTCTCTGAAGGAATAGAGAGCAGACCCGTTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTG
1 TACTCTCTGAAGGAATAGAGAGCGGACCAG--TTGTTGAAGA---TT-GAGTCCTATACTCTCTG
* ** * * *
12403246 AAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATA
60 AAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAA-GGAATA
12403310 GGGAGCG
119 GGGAGCG
12403317 AACCCGTTTT
Statistics
Matches: 263, Mismatches: 12, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
152 2 0.01
153 173 0.66
154 9 0.03
155 2 0.01
157 2 0.01
158 34 0.13
159 10 0.04
162 2 0.01
163 27 0.10
164 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27
Consensus pattern (152 bp):
TACTCTCTGAAGGAATAGAGAGCGGACCAGTTGTTGAAGATTGAGTCCTATACTCTCTGAAGGAA
TAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
GTTCGTTGAAGATTGAGTCCTA
Found at i:12403500 original size:55 final size:56
Alignment explanation
Indices: 12402850--12403485 Score: 497
Period size: 51 Copynumber: 11.9 Consensus size: 56
12402840 AGCAAACTCG
* * *
12402850 TTTGTTGAAGATTGTTCGAGTTCTCTACTCTCTGAAGGAATAGAGAGCGGACCCAT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
* * * * **
12402906 TTT-ATGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
* * * * **
12402956 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
* * * **
12403007 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
* * * * **
12403058 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
* * * * **
12403109 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
* *
12403160 TTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
*
12403212 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
* *
12403268 TTTGTTGAAGATTGTTCGAGTTCTATACTCCCTGAACGG-ATAGGGAGC-GAACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAA-GGAATAGAGAGCAG-ACCCGT
* * *
12403324 TTTGTTGAAGATTGTTAGAGTTCTATACTCCCTGAATGG-ATAGGGAGC-GAACCCGT
1 TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAA-GGAATAGAGAGCAG-ACCCGT
* * * * * *
12403380 TTT-ATGAAAATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACAT
1 TTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCAGACCCGT
*
12403435 TTT-ATGAAGATTGTTCGA-TTCTTATACT-TCCTGAAGGAATACG-GAGCAGAC
1 TTTGTTGAAGATTGTTCGAGTTC-TATACTCT-CTGAAGGAATA-GAGAGCAGAC
12403486 TCGTCATTTG
Statistics
Matches: 532, Mismatches: 34, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.00
51 276 0.52
52 12 0.02
54 4 0.01
55 88 0.17
56 148 0.28
57 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
TTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGT
Found at i:12406621 original size:20 final size:20
Alignment explanation
Indices: 12406596--12406661 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
12406586 CCTTTAGGGG
12406596 ACCCTCCTTGGGGTATCGAT
1 ACCCTCCTTGGGGTATCGAT
*
12406616 ACCCTCCTTGGGGTATTGAT
1 ACCCTCCTTGGGGTATCGAT
* *
12406636 ACCCTCCTTAGGGTATCGTT
1 ACCCTCCTTGGGGTATCGAT
12406656 ACCCTC
1 ACCCTC
12406662 ATTTCATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.32, G:0.21, T:0.32
Consensus pattern (20 bp):
ACCCTCCTTGGGGTATCGAT
Found at i:12409092 original size:89 final size:90
Alignment explanation
Indices: 12408941--12409135 Score: 338
Period size: 89 Copynumber: 2.2 Consensus size: 90
12408931 AATTCAAAGC
* *
12408941 TCAACTTCACAACGAATGAGCTATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACAA
1 TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGATGAAGAATATCGTGCCCACAA
12409006 GCAGCATCCATCT-TAGATTGGATT
66 GCAGCATCCATCTCTAGATTGGATT
* *
12409030 TCAACTTCACAACGAATGAGCCATCCATGATTTCAACTTCATGATGAAGAATATCGTGCCCACAA
1 TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGATGAAGAATATCGTGCCCACAA
12409095 GCAGCATCCATCTCTAGATTGGATT
66 GCAGCATCCATCTCTAGATTGGATT
*
12409120 TCAACTTCATAACGAA
1 TCAACTTCACAACGAA
12409136 GGATATCCAA
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 74 0.74
90 26 0.26
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (90 bp):
TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGATGAAGAATATCGTGCCCACAA
GCAGCATCCATCTCTAGATTGGATT
Found at i:12409201 original size:66 final size:66
Alignment explanation
Indices: 12409116--12409456 Score: 216
Period size: 66 Copynumber: 5.4 Consensus size: 66
12409106 CTCTAGATTG
*
12409116 GATTTCAACTTCATAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCTA
1 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCTA
12409181 C
66 C
* * ***** * * * * **
12409182 GATTTTAACTTCACGACGAAGGATATCGTGCCCACAAG--GAGCATC-CATC-TCT-AG--AT-T
1 GATTTCAACTTCACAACGAAGGATATCCAATTCA-AAGCTCAACTTCACAACGAATGAGCCATCT
*
12409239 -G
65 AC
* * *
12409240 GATTTCAACTTCTCAACGAAGGATATCCAATTCAAAGCTCAACTTTACAACGAATGAGCCATCCA
1 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCTA
12409305 C
66 C
* ** * * * ** **
12409306 GACTTCAACTTCATGACGAAGGATAT-CGATCCCACAAG--CAGCTTC-CGTC-TCT-AG--AT-
1 GATTTCAACTTCACAACGAAGGATATCCAAT-TCA-AAGCTCAACTTCACAACGAATGAGCCATC
*
12409362 T-G
64 TAC
* * *
12409364 GAATTCAACTTCACAATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCGTCTA
1 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCTA
12409429 C
66 C
* *
12409430 GATTTCAACTTCACGATGAAGGATATC
1 GATTTCAACTTCACAACGAAGGATATC
12409457 ATGTCCAATA
Statistics
Matches: 192, Mismatches: 61, Indels: 44
0.65 0.21 0.15
Matches are distributed among these distances:
57 6 0.03
58 50 0.26
59 13 0.07
60 9 0.05
61 2 0.01
62 8 0.04
63 2 0.01
64 8 0.04
65 13 0.07
66 75 0.39
67 6 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (66 bp):
GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCTA
C
Found at i:12409250 original size:124 final size:124
Alignment explanation
Indices: 12409030--12409456 Score: 660
Period size: 124 Copynumber: 3.4 Consensus size: 124
12409020 AGATTGGATT
* * * *
12409030 TCAACTTCACAACGAATGAGCCATCCATGATTTCAACTTCATGATGAAGAATATCGTGCCCACAA
1 TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAA
12409095 GCAGCATCCATCTCTAGATTGGATTTCAACTTCATAACGAAGGATATCCAATTCAAAGC
66 GCAGCATCCATCTCTAGATTGGATTTCAACTTCATAACGAAGGATATCCAATTCAAAGC
* *
12409154 TCAACTTCACAACGAATGAGCCATCTACGATTTTAACTTCACGACGAAGGATATCGTGCCCACAA
1 TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAA
*
12409219 GGAGCATCCATCTCTAGATTGGATTTCAACTTC-TCAACGAAGGATATCCAATTCAAAGC
66 GCAGCATCCATCTCTAGATTGGATTTCAACTTCAT-AACGAAGGATATCCAATTCAAAGC
* * *
12409278 TCAACTTTACAACGAATGAGCCATCCACGACTTCAACTTCATGACGAAGGATATCGAT-CCCACA
1 TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCG-TGCCCACA
* * * * *
12409342 AGCAGCTTCCGTCTCTAGATTGGAATTCAACTTCACAATGAAGGATATCCAATTCAAAGC
65 AGCAGCATCCATCTCTAGATTGGATTTCAACTTCATAACGAAGGATATCCAATTCAAAGC
* * *
12409402 TCAACTTCACAACGAATGAGCCGTCTACGATTTCAACTTCACGATGAAGGATATC
1 TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATC
12409457 ATGTCCAATA
Statistics
Matches: 276, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
123 1 0.00
124 274 0.99
125 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (124 bp):
TCAACTTCACAACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAA
GCAGCATCCATCTCTAGATTGGATTTCAACTTCATAACGAAGGATATCCAATTCAAAGC
Found at i:12409866 original size:85 final size:85
Alignment explanation
Indices: 12409530--12409853 Score: 425
Period size: 85 Copynumber: 3.8 Consensus size: 85
12409520 CCCATCCAAG
* *
12409530 TACAACATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTCA
1 TACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCA
* * *
12409595 ACTCAAAGGCATATCCAATT
66 GCTCAAAGGCACATCAAATT
* * * * * *
12409615 TACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCA
1 TACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCA
12409680 GCTCAAAGGCACATCAAATT
66 GCTCAAAGGCACATCAAATT
* * * * * * *
12409700 TACAGCATAACTCAAGGAGAGAAGGGATGTCTGTTAGCAAAGACCTTCTAGTTCGATTACATTCA
1 TACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCA
12409765 GCTCAAAGGCACATCAAATT
66 GCTCAAAGGCACATCAAATT
* * * * *
12409785 TACAATATAACTCAAGGCGAGAAGGGTTATCGGTCAATGAAA-ACTTTCGAGTTCGATTCCATTC
1 TACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACATTC
12409849 AGCTC
65 AGCTC
12409854 GATGACACAT
Statistics
Matches: 206, Mismatches: 32, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
85 203 0.99
86 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (85 bp):
TACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCA
GCTCAAAGGCACATCAAATT
Found at i:12411885 original size:11 final size:11
Alignment explanation
Indices: 12411866--12411921 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
12411856 TTTTATATTC
*
12411866 ATTTGTTTTTT
1 ATTTATTTTTT
12411877 ATTTATTTTTT
1 ATTTATTTTTT
**
12411888 ATTTATTCCTT
1 ATTTATTTTTT
12411899 -TTTATTCTTTT
1 ATTTATT-TTTT
12411910 ATTTTATTTTTT
1 A-TTTATTTTTT
12411922 TTTCATTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
10 6 0.16
11 21 0.57
12 4 0.11
13 6 0.16
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (11 bp):
ATTTATTTTTT
Found at i:12411892 original size:15 final size:14
Alignment explanation
Indices: 12411854--12411924 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 14
12411844 ATTTAAATGC
* *
12411854 TTTTTTATATTCAT
1 TTTTTTTTATTTAT
12411868 TTGTTTTTTATTTAT
1 TT-TTTTTTATTTAT
*
12411883 TTTTTATTTATTCCTTT
1 TTTTT-TTTATT--TAT
12411900 TTATTCTTTTATTTTAT
1 TT-TT-TTTTA-TTTAT
12411917 TTTTTTTT
1 TTTTTTTT
12411925 CATTGCTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
14 5 0.11
15 22 0.48
16 2 0.04
17 8 0.17
18 6 0.13
19 3 0.07
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.79
Consensus pattern (14 bp):
TTTTTTTTATTTAT
Found at i:12412262 original size:5 final size:5
Alignment explanation
Indices: 12412253--12412349 Score: 55
Period size: 5 Copynumber: 20.6 Consensus size: 5
12412243 CCTTCCCTTC
* * * *
12412253 ATTTT GTTTT ATTTT ATTTT -TATTT ATTTT A--TT ATTTC GTTTT -GTTT
1 ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT ATTTT ATTTT
* * * * *
12412300 ATTTT -TTTT ATTTT ACTTT GTTTT CTTTT A--TT GTTTT CTTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
12412347 ATT
1 ATT
12412350 CTTTAGCCAT
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
3 5 0.07
4 8 0.12
5 55 0.80
6 1 0.01
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:12412319 original size:23 final size:23
Alignment explanation
Indices: 12412253--12412322 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 23
12412243 CCTTCCCTTC
12412253 ATTTTGTTTTATTTTA--TT-TTT
1 ATTTT-TTTTATTTTACTTTGTTT
* *
12412274 ATTTATTTTATTATTTCGTTTTGTTT
1 ATTTTTTTTATT-TTAC--TTTGTTT
12412300 ATTTTTTTTATTTTACTTTGTTT
1 ATTTTTTTTATTTTACTTTGTTT
12412323 TCTTTTATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 7 0.18
21 6 0.15
23 7 0.18
25 5 0.13
26 14 0.36
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (23 bp):
ATTTTTTTTATTTTACTTTGTTT
Found at i:12412335 original size:13 final size:13
Alignment explanation
Indices: 12412317--12412353 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
12412307 TTATTTTACT
12412317 TTGTTTTCTTTTA
1 TTGTTTTCTTTTA
12412330 TTGTTTTCTTTTA
1 TTGTTTTCTTTTA
12412343 TT-TTATTCTTT
1 TTGTT-TTCTTT
12412354 AGCCATCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 2 0.09
13 21 0.91
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.78
Consensus pattern (13 bp):
TTGTTTTCTTTTA
Found at i:12412336 original size:23 final size:22
Alignment explanation
Indices: 12412259--12412340 Score: 57
Period size: 23 Copynumber: 3.7 Consensus size: 22
12412249 CTTCATTTTG
*
12412259 TTTTATT-TTATT-TTTATTTA-
1 TTTTATTATT-TTCTTTGTTTAT
12412279 TTTTATTA-TTTCGTTTTGTTTAT
1 TTTTATTATTTTC--TTTGTTTAT
*
12412302 TTTTTTTATTTTACTTTGTTT-T
1 TTTTATTATTTT-CTTTGTTTAT
*
12412324 CTTTTATTGTTTTCTTT
1 -TTTTATTATTTTCTTT
12412341 TATTTTATTC
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
19 2 0.04
20 8 0.16
22 12 0.24
23 24 0.48
24 3 0.06
25 1 0.02
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTTATTATTTTCTTTGTTTAT
Found at i:12415914 original size:31 final size:30
Alignment explanation
Indices: 12415891--12415947 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
12415881 TTTAGTAACG
*
12415891 TAGAACATAT-CATGTCATCATTTTGGTGT
1 TAGAACATATACATGTCATCATTTTAGTGT
*
12415920 TATAACATATACCATGTCATCATTTTAG
1 TAGAACATATA-CATGTCATCATTTTAG
12415948 GTGATACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
31 15 0.62
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (30 bp):
TAGAACATATACATGTCATCATTTTAGTGT
Found at i:12417767 original size:18 final size:18
Alignment explanation
Indices: 12417730--12417773 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12417720 CTATTATATT
***
12417730 TTTATTTTTAAAATTGAG
1 TTTATTTTTAAAAAAAAG
12417748 TTTATTTTTAAAAAAAAG
1 TTTATTTTTAAAAAAAAG
*
12417766 TTAATTTT
1 TTTATTTT
12417774 ATCTTTTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TTTATTTTTAAAAAAAAG
Found at i:12419435 original size:79 final size:78
Alignment explanation
Indices: 12419286--12419453 Score: 282
Period size: 79 Copynumber: 2.1 Consensus size: 78
12419276 AGGTTGCCAT
* *
12419286 TGAAATAATTATGTGATTTATATGATTTGTTAGGAAAAATAATATATTTTATTTTAACTTAAAAT
1 TGAAATAATTATGTGATTTACATGATTCGTTAGGAAAAATAATATATTTTATTTTAACTTAAAAT
*
12419351 GTCATTTTGTAAC
66 GTCATTTTATAAC
12419364 TGAAATAATTATGTGATTTACATGATTCGTTAGGAAAAAATAATATATTTTATTTTAACTTAAAA
1 TGAAATAATTATGTGATTTACATGATTCGTTAGG-AAAAATAATATATTTTATTTTAACTTAAAA
12419429 TGTCATTTTATAAC
65 TGTCATTTTATAAC
* *
12419443 TTAAAAAATTA
1 TGAAATAATTA
12419454 CGTTTTATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
78 32 0.38
79 52 0.62
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (78 bp):
TGAAATAATTATGTGATTTACATGATTCGTTAGGAAAAATAATATATTTTATTTTAACTTAAAAT
GTCATTTTATAAC
Found at i:12430151 original size:15 final size:15
Alignment explanation
Indices: 12430131--12430159 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12430121 TGGCCGACCG
12430131 AACCGAATTAACCAT
1 AACCGAATTAACCAT
12430146 AACCGAATTAACCA
1 AACCGAATTAACCA
12430160 AAATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:12430608 original size:184 final size:185
Alignment explanation
Indices: 12430286--12430673 Score: 651
Period size: 184 Copynumber: 2.1 Consensus size: 185
12430276 TTTTCTAATT
* * * *
12430286 TATATAA-AAATTAAATA-TTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAA
*
12430349 TTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
66 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
12430414 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCTCATATGTTA
131 TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
12430469 TATATAATATATTTAATATTTTTTTAATT-AAAAAACAGTTTACAAATAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTTAATTCAAAAAA-AGTTTACAAATAATTTAAATAATATATA
*
12430533 ATTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
65 ATTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
12430597 TTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 TTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
12430653 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
12430674 AAAATTTAAT
Statistics
Matches: 193, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
183 9 0.05
184 127 0.66
185 57 0.30
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTTAATTCAAAAAAAGTTTACAAATAATTTAAATAATATATAA
TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
TGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:12430789 original size:22 final size:21
Alignment explanation
Indices: 12430751--12430794 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
12430741 TCTTAACCGT
12430751 TAACCGACCGAACTAATTCGG
1 TAACCGACCGAACTAATTCGG
*
12430772 TAACCGAACCGAATTAATTCGG
1 TAACCG-ACCGAACTAATTCGG
12430794 T
1 T
12430795 TCGGTCGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
TAACCGACCGAACTAATTCGG
Found at i:12453707 original size:20 final size:18
Alignment explanation
Indices: 12453671--12453727 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
12453661 CGTTAGACAG
12453671 GGGGGAATCGGTACCCCT
1 GGGGGAATCGGTACCCCT
* *
12453689 AGGGGGAATCTGTTCCCCCT
1 -GGGGGAATC-GGTACCCCT
* *
12453709 GGAGGGAATTGGTAACCCT
1 GG-GGGAATCGGTACCCCT
12453728 TACAGGGGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (18 bp):
GGGGGAATCGGTACCCCT
Found at i:12459148 original size:32 final size:32
Alignment explanation
Indices: 12459100--12459187 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
12459090 AGAAGTTATA
*
12459100 TTCAAATAAATATTATATATAAAAATATCATG
1 TTCAAATAAATGTTATATATAAAAATATCATG
* * * *
12459132 TTCGAATAAATGTTATAT-TATTAGATATTATG
1 TTCAAATAAATGTTATATATA-AAAATATCATG
12459164 TTCAAATAAATGTTA-ATATAAAAA
1 TTCAAATAAATGTTATATATAAAAA
12459188 AACATTATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
31 6 0.13
32 40 0.87
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (32 bp):
TTCAAATAAATGTTATATATAAAAATATCATG
Found at i:12463218 original size:29 final size:28
Alignment explanation
Indices: 12463168--12463226 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
12463158 TTCCACATCC
* *
12463168 TTCCACAACTCGGTCAATCTTTGAACAT
1 TTCCACAACTCAGTCAACCTTTGAACAT
*
12463196 TTCCACCAACTCAGTCTACCTTTGAACAT
1 TTCCA-CAACTCAGTCAACCTTTGAACAT
12463225 TT
1 TT
12463227 TAATAGACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.34
Consensus pattern (28 bp):
TTCCACAACTCAGTCAACCTTTGAACAT
Found at i:12466941 original size:2 final size:2
Alignment explanation
Indices: 12466936--12466988 Score: 88
Period size: 2 Copynumber: 25.5 Consensus size: 2
12466926 TATATAAGTA
12466936 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
12466978 ACT AT AGT AT A
1 A-T AT A-T AT A
12466989 AATAAATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 45 0.92
3 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12467080 original size:17 final size:18
Alignment explanation
Indices: 12467049--12467091 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
12467039 ATATACGTAT
12467049 ATATATACATAAGAA-AA
1 ATATATACATAAGAAGAA
12467066 ATATATACA-ATAGAATGAA
1 ATATATACATA-AGAA-GAA
12467085 ATATATA
1 ATATATA
12467092 AAGAACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.04
17 13 0.57
19 9 0.39
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (18 bp):
ATATATACATAAGAAGAA
Found at i:12468309 original size:13 final size:13
Alignment explanation
Indices: 12468291--12468322 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12468281 AATATTATAT
12468291 ATATAATTATACA
1 ATATAATTATACA
*
12468304 ATATAATTATATA
1 ATATAATTATACA
12468317 ATATAA
1 ATATAA
12468323 CAAAATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAATTATACA
Found at i:12468325 original size:21 final size:22
Alignment explanation
Indices: 12468270--12468325 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
12468260 ATGTAAAGAA
* *
12468270 ATAATATTAATAATATTATATAT
1 ATAATA-TAACAATATAATATAT
12468293 ATAAT-TATACAATATAAT-TAT
1 ATAATATA-ACAATATAATATAT
12468314 ATAATATAACAA
1 ATAATATAACAA
12468326 AATGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 14 0.48
22 10 0.34
23 5 0.17
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAATATAACAATATAATATAT
Found at i:12468972 original size:105 final size:104
Alignment explanation
Indices: 12468822--12469476 Score: 1028
Period size: 105 Copynumber: 6.4 Consensus size: 104
12468812 GTATTGTCCC
*
12468822 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AATTTGAGAAATGTTTGTTGACAAC
* *
12468887 CAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCATTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
12468927 GAGTCTGATATCCTTCGTTGTGAAGTTGAGATTGGCTCTAAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AATTTGAGAAATGTTTGTTGACAAC
12468992 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
12469032 GAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AATTTGAGAAATGTTTGTTGACAAC
12469097 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
12469137 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGATAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-AATTTGAGAAATGTTTGTTGACAAC
12469202 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12469242 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC-C----TTGA-AATTGTTTATTGACAACC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAATTTGAGAAATGTTTGTTGACAACC
*
12469301 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
12469340 GAGTCCAATTTCCTTCGTTGTGAAGTTGAAATTGGC-C----CTGA-AATTGTTTATTGACAATC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAATTTGAGAAATGTTTGTTGACAACC
12469399 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
12469438 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
12469477 GGGTAAAACC
Statistics
Matches: 526, Mismatches: 22, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
98 180 0.34
99 5 0.01
104 1 0.00
105 340 0.65
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (104 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAATTTGAGAAATGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:12469357 original size:98 final size:98
Alignment explanation
Indices: 12469184--12469471 Score: 506
Period size: 98 Copynumber: 2.9 Consensus size: 98
12469174 CTGAATTTGA
* *
12469184 GAAA-TGTTTGTTGATAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
12469248 AATATCCTTCGTTGTGAAGTTGAAATTGGCCTT
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCCCT
*
12469281 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
12469346 AATTTCCTTCGTTGTGAAGTTGAAATTGGCCCT
66 AATATCCTTCGTTGTGAAGTTGAAATTGGCCCT
*
12469379 GAAATTGTTTATTGACAATCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
12469444 AATATCCTTCATTGTGAAGTTGAAATTG
66 AATATCCTTCGTTGTGAAGTTGAAATTG
12469472 ACTCTGGGTA
Statistics
Matches: 181, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
97 4 0.02
98 177 0.98
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (98 bp):
GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGGCCCT
Found at i:12481005 original size:2 final size:2
Alignment explanation
Indices: 12481000--12481056 Score: 73
Period size: 2 Copynumber: 28.5 Consensus size: 2
12480990 TATATAAGTA
*
12481000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12481041 A- AT AT ACT AT AGT AT A
1 AT AT AT A-T AT A-T AT A
12481057 AATAAATAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
1 2 0.04
2 44 0.88
3 4 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12481148 original size:17 final size:18
Alignment explanation
Indices: 12481117--12481159 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
12481107 ATATACGTAT
12481117 ATATATACATAAGAA-AA
1 ATATATACATAAGAAGAA
12481134 ATATATACA-ATAGAATGAA
1 ATATATACATA-AGAA-GAA
12481153 ATATATA
1 ATATATA
12481160 AAGAACGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.04
17 13 0.57
19 9 0.39
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (18 bp):
ATATATACATAAGAAGAA
Found at i:12481193 original size:2 final size:2
Alignment explanation
Indices: 12481188--12481243 Score: 87
Period size: 2 Copynumber: 27.5 Consensus size: 2
12481178 TATATAAGTA
12481188 AT AT AT 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 AT
12481229 AT AT ACT AT AGT AT A
1 AT AT A-T AT A-T AT A
12481244 AATAAATAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.02
2 46 0.90
3 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12482409 original size:13 final size:13
Alignment explanation
Indices: 12482391--12482422 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12482381 TATTATATAT
12482391 ATATAATTATACA
1 ATATAATTATACA
*
12482404 ATATAATTATATA
1 ATATAATTATACA
12482417 ATATAA
1 ATATAA
12482423 CAAAATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAATTATACA
Found at i:12484414 original size:29 final size:29
Alignment explanation
Indices: 12484381--12484443 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
12484371 GGAACATATG
* ** *
12484381 AATAGTCGGGTGACTGTTTTGTAACTTTT
1 AATAGTCGAGTGACCATTTTATAACTTTT
12484410 AATAGTCGAGTGACCATTTTATAACTTTT
1 AATAGTCGAGTGACCATTTTATAACTTTT
12484439 AATAG
1 AATAG
12484444 ACAAGAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (29 bp):
AATAGTCGAGTGACCATTTTATAACTTTT
Found at i:12486203 original size:34 final size:36
Alignment explanation
Indices: 12486159--12486260 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
12486149 TTTCGTCCTA
12486159 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
12486194 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
12486229 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
12486261 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:12486864 original size:16 final size:18
Alignment explanation
Indices: 12486843--12486877 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
12486833 TTTACTCATT
12486843 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
12486859 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
12486877 T
1 T
12486878 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:12488662 original size:17 final size:17
Alignment explanation
Indices: 12488640--12488707 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
12488630 GACCGGTCAC
*
12488640 GACCCGACCCGATAGTT
1 GACCCGACCCGACAGTT
*
12488657 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
12488674 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
*
12488687 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
12488704 GACC
1 GACC
12488708 GTTGACCGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 10 0.22
14 3 0.07
16 3 0.07
17 29 0.64
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:12488687 original size:13 final size:13
Alignment explanation
Indices: 12488662--12488697 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
12488652 TAGTTGACCC
12488662 GACCCGA-CCGTT
1 GACCCGACCCGTT
12488674 GACCCGACCCGTT
1 GACCCGACCCGTT
12488687 GACCCGACCCG
1 GACCCGACCCG
12488698 ACCGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.17, C:0.47, G:0.25, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:12488759 original size:29 final size:29
Alignment explanation
Indices: 12488715--12488796 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
12488705 ACCGTTGACC
*
12488715 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* *
12488744 GGTGCTATTCTAGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
12488773 GGTGCTATTCTGGTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
12488797 AAAAAGGGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:12495895 original size:17 final size:17
Alignment explanation
Indices: 12495873--12495953 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
12495863 GACCGGTCAC
*
12495873 GACCCGACCCGATAGTT
1 GACCCGACCCGACAGTT
*
12495890 GACCCGACCCGACCGTT
1 GACCCGACCCGACAGTT
12495907 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
12495920 GACCCGA-CC--C-GTT
1 GACCCGACCCGACAGTT
*
12495933 GACCCGACCCGACTGTT
1 GACCCGACCCGACAGTT
12495950 GACC
1 GACC
12495954 GTTGACCGGT
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
13 23 0.40
14 3 0.05
16 3 0.05
17 29 0.50
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.15
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:12495920 original size:13 final size:13
Alignment explanation
Indices: 12495895--12495943 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
12495885 TAGTTGACCC
12495895 GACCCGA-CCGTT
1 GACCCGACCCGTT
12495907 GACCCGACCCGTT
1 GACCCGACCCGTT
12495920 GACCCGACCCGTT
1 GACCCGACCCGTT
12495933 GACCCGACCCG
1 GACCCGACCCG
12495944 ACTGTTGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 7 0.19
13 29 0.81
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:12496002 original size:28 final size:29
Alignment explanation
Indices: 12495961--12496041 Score: 137
Period size: 28 Copynumber: 2.8 Consensus size: 29
12495951 ACCGTTGACC
*
12495961 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
12495990 -GTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
12496018 GGTGCTATTCTGGTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
12496042 AAAAAGGGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 26 0.54
29 22 0.46
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:12496054 original size:30 final size:29
Alignment explanation
Indices: 12495990--12496064 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
12495980 ATTCGGTTTT
*****
12495990 GTGCTATTCTGGTAAATAATTCAGTTTTG
1 GTGCTATTCTGGTAAATAATTCAAAAAGG
12496019 GTGCTATTCTGGTAAATAATTCGAAAAAGG
1 GTGCTATTCTGGTAAATAATTC-AAAAAGG
12496049 GTGCTATT-TGTGTAAA
1 GTGCTATTCTG-GTAAA
12496065 ATGTTCAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (29 bp):
GTGCTATTCTGGTAAATAATTCAAAAAGG
Found at i:12499714 original size:21 final size:20
Alignment explanation
Indices: 12499669--12499737 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
12499659 CAAAAAGGGC
*
12499669 AAAAAGAAAAAAGAAAATAAGCA
1 AAAAAGAAAAAA-CAAA-AA-CA
*
12499692 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAAAACA
* *
12499713 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAAAACA
12499733 AAAAA
1 AAAAA
12499738 AAGGGACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.43
21 7 0.17
22 2 0.05
23 7 0.17
24 7 0.17
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAACAAAAACA
Found at i:12500397 original size:22 final size:22
Alignment explanation
Indices: 12500372--12500420 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
12500362 CCATCAATCT
*
12500372 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
12500394 TTTGAGCATCAAATGTCAAACC
1 TTTGAGCATCAAATGTCAAACC
12500416 TTTGA
1 TTTGA
12500421 CCAAACACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (22 bp):
TTTGAGCATCAAATGTCAAACC
Found at i:12500858 original size:18 final size:18
Alignment explanation
Indices: 12500835--12500870 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12500825 TCAACATCAA
* *
12500835 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
12500853 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
12500871 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:12501393 original size:36 final size:36
Alignment explanation
Indices: 12501350--12501631 Score: 312
Period size: 36 Copynumber: 8.0 Consensus size: 36
12501340 ACTATAAGAG
12501350 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
12501386 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
12501422 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
12501458 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
12501494 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
12501523 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
12501560 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
12501595 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
12501632 ACCTTTGAAT
Statistics
Matches: 205, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 142 0.69
37 34 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:12501393 original size:71 final size:72
Alignment explanation
Indices: 12501308--12501631 Score: 230
Period size: 72 Copynumber: 4.6 Consensus size: 72
12501298 GTTTTTCTTA
* * * * * *
12501308 AAACAAGA-TTTGTCTCGCTTGAGACCGTTTTCAC-TATAA-GAGTTTTGTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTTA-AACAAATTTCGTCTATCTTGAGACAG
12501370 TTTCCCTTG
64 TTTCCCTTG
*
12501379 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTT-AAACAAATTTCGTCTATCTTGAGACAGT
12501443 TTCCCTTG
65 TTCCCTTG
* * * *
12501451 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTT-AAACAAATTTCGTCTATCTTGAGACA-G
* *
12501507 TTTTCTTTG
64 TTTCCCTTG
** * ** * * * *
12501516 AAACAAATTCCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTT-AAAC-AAATTTCGTCTATCTTGAGACAG
*
12501580 TTTCTCTTG
64 TTTCCCTTG
* *
12501589 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTT-AAACAAA
12501632 ACCTTTGAAT
Statistics
Matches: 203, Mismatches: 35, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
64 2 0.01
65 45 0.22
66 5 0.02
70 6 0.03
71 26 0.13
72 78 0.38
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTTAAACAAATTTCGTCTATCTTGAGACAGTT
TCCCTTG
Found at i:12501591 original size:102 final size:102
Alignment explanation
Indices: 12501406--12501594 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
12501396 CTTGAGACAG
* *
12501406 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
12501471 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
12501508 TTTCT-TTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
*
12501572 TGAGACAGTTTCTCTTGAAACAA
65 TGAGACAGTTTCCCTTGAAACAA
12501595 TTTTCGTCTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 33 0.42
102 45 0.58
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (102 bp):
TTTCTCTTGAAACAAATTCCGTCTACCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
GAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:12501623 original size:138 final size:137
Alignment explanation
Indices: 12501370--12501694 Score: 445
Period size: 138 Copynumber: 2.4 Consensus size: 137
12501360 CTTGAGACAG
*
12501370 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
12501435 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
12501500 GAATATG
131 GAATATA
* * ** * * * * *
12501507 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
12501572 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
*
12501636 TTGAATTTA
129 TTGAATATA
* * *
12501645 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
12501695 CAAAATCTTC
Statistics
Matches: 160, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.31
138 111 0.69
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:12501693 original size:65 final size:65
Alignment explanation
Indices: 12501589--12501763 Score: 208
Period size: 67 Copynumber: 2.6 Consensus size: 65
12501579 GTTTCTCTTG
** * **
12501589 AAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCTTTGAATTTATTTCCCCT
1 AAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTTATTTCCCCT
12501653 A
65 A
* * *
12501654 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAACCTTCAAATTTATTTCCCC
12501719 TA
64 TA
* * *
12501721 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
12501764 CAGATATCTT
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
65 25 0.27
66 12 0.13
67 30 0.32
68 27 0.29
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAACCTTCAAATTTATTTCCCCTA
Found at i:12501724 original size:67 final size:67
Alignment explanation
Indices: 12501580--12501762 Score: 210
Period size: 68 Copynumber: 2.7 Consensus size: 67
12501570 CTTGAGACAG
* * ** * **
12501580 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAAT
1 TTTCCCTTAAAACAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAAT
12501642 TTA
65 TTA
* * *
12501645 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATT
12501710 TA
66 TA
* * *
12501712 TTTCCCTTAAAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 TTTCCCTTAAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
12501763 ACAGATATCT
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
65 31 0.31
66 8 0.08
67 28 0.28
68 32 0.32
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATT
TA
Found at i:12502473 original size:105 final size:105
Alignment explanation
Indices: 12502287--12503436 Score: 1826
Period size: 105 Copynumber: 11.0 Consensus size: 105
12502277 GCACTCGAGG
* * * *
12502287 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
12502352 AGTCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
12502393 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAAATTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
12502458 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
12502498 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTGCTTGTCAACAACAACTTCTCAATTTC
1 CAACGCAAGTTCAACTTCACGACGAAGGGA-C-C-GCTGCTTGTCAACAACAACTTCTCAATTTC
*
12502563 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGTCTCCAGA
63 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
12502606 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
12502671 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
12502711 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
12502776 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
12502816 CAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
12502881 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
12502921 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
12502986 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
12503026 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
12503091 GCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
12503131 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTC-CTAATCTAAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTC-AATTTCAG
12503195 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
12503236 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
12503296 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** *
12503336 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
12503401 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
12503437 TGGAACAATG
Statistics
Matches: 972, Mismatches: 61, Indels: 22
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.08
101 3 0.00
102 2 0.00
103 5 0.01
104 4 0.00
105 700 0.72
106 77 0.08
107 2 0.00
108 97 0.10
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:12504028 original size:34 final size:36
Alignment explanation
Indices: 12503984--12504085 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
12503974 TTTCGTCCTA
12503984 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
12504019 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
12504054 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
12504086 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:12504687 original size:16 final size:18
Alignment explanation
Indices: 12504666--12504700 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
12504656 TTTACTCATT
12504666 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
12504682 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
12504700 T
1 T
12504701 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:12508605 original size:151 final size:153
Alignment explanation
Indices: 12508343--12508622 Score: 413
Period size: 151 Copynumber: 1.8 Consensus size: 153
12508333 TCATTGCTAA
** * *
12508343 GCATATAGATTTCATGTTTGCGTGCATGGGATTCAATTAAGAAGACGATTAATATAAATAGTTCT
1 GCATATAGATGACATGTTTGCATGCATGGGATTCAATTAAGAAGAC-AATAATATAAATAGTTCT
12508408 ACAAATTATTCAATTTTGTCAGAGGGTAAATAACTGATGTCAAATTCAGATCATTCAAGACCAGA
65 ACAAATTATTCAATTTTGTCAGAGGGTAAATAACTGATGTCAAATTCAGATCATTCAAGACCAGA
12508473 TAAATAACTGATATCAAATTCTAT
130 TAAATAACTGATATCAAATTCTAT
* * *
12508497 GCATATAGATGACATGTTTGCATTCATGTGATTCAATTAA-AA-A-AATAAGTATAAATAGTTGT
1 GCATATAGATGACATGTTTGCATGCATGGGATTCAATTAAGAAGACAATAA-TATAAATAGTTCT
* * * * *
12508559 ACAAATTATTCAGTTTTGTCAGAGGGTAAATAACTGATTTCGAATTCTGATCATTCAAGGCCAG
65 ACAAATTATTCAATTTTGTCAGAGGGTAAATAACTGATGTCAAATTCAGATCATTCAAGACCAG
12508623 GTAATAGAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
150 4 0.04
151 71 0.63
152 1 0.01
153 2 0.02
154 35 0.31
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (153 bp):
GCATATAGATGACATGTTTGCATGCATGGGATTCAATTAAGAAGACAATAATATAAATAGTTCTA
CAAATTATTCAATTTTGTCAGAGGGTAAATAACTGATGTCAAATTCAGATCATTCAAGACCAGAT
AAATAACTGATATCAAATTCTAT
Found at i:12518799 original size:32 final size:31
Alignment explanation
Indices: 12518751--12518815 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
12518741 CGAATCCCAG
*
12518751 GACGACACGACTAATTCACCTTAAAATTCAA
1 GACGACACGACTAATTCAACTTAAAATTCAA
*
12518782 GACGACATCGGCTAATTCAACTTAAAATTCAA
1 GACGACA-CGACTAATTCAACTTAAAATTCAA
12518814 GA
1 GA
12518816 AAGAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (31 bp):
GACGACACGACTAATTCAACTTAAAATTCAA
Found at i:12524824 original size:30 final size:30
Alignment explanation
Indices: 12524781--12524840 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
12524771 AAATTTAAGG
12524781 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTT-AATTGAATTTA
12524812 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATGGTTTTTGGACTTAATTGAATTTA
12524841 TTCAAAGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGGTTTTTGGACTTAATTGAATTTA
Found at i:12524946 original size:21 final size:21
Alignment explanation
Indices: 12524920--12525018 Score: 119
Period size: 21 Copynumber: 4.7 Consensus size: 21
12524910 AGGGTGTCAA
*
12524920 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCATGC
*
12524941 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCACCCATGC
* **
12524962 AGTGCATCCATGCACCTACAC
1 AGTGCATCCATGCACCCATGC
* *
12524983 TAGTGCATCGATGCA-TCATGC
1 -AGTGCATCCATGCACCCATGC
12525004 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
12525019 TCAAACATCG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
20 13 0.20
21 38 0.59
22 13 0.20
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:12524954 original size:13 final size:13
Alignment explanation
Indices: 12524951--12524975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12524941 AGTGCATCCA
12524951 TGCATCCATGCAG
1 TGCATCCATGCAG
12524964 TGCATCCATGCA
1 TGCATCCATGCA
12524976 CCTACACTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:12525003 original size:42 final size:41
Alignment explanation
Indices: 12524920--12525018 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 41
12524910 AGGGTGTCAA
12524920 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCACCCCT-CAGTGCATCCATGCATCCATGC
*
12524962 AGTGCATCCATGCACCTACACT-AGTGCATCGATGCAT-CATGC
1 AGTGCATCCATGCACC--C-CTCAGTGCATCCATGCATCCATGC
12525004 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
12525019 TCAAACATCG
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
42 36 0.68
43 14 0.26
44 1 0.02
45 2 0.04
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (41 bp):
AGTGCATCCATGCACCCCTCAGTGCATCCATGCATCCATGC
Found at i:12525083 original size:21 final size:21
Alignment explanation
Indices: 12525039--12525101 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
12525029 AATGCAATTA
***
12525039 GTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCAAGGCT
12525059 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
*
12525080 GTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
12525101 G
1 G
12525102 CAACGGCTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:12525503 original size:34 final size:32
Alignment explanation
Indices: 12525458--12525529 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 32
12525448 CCTTTTGTAA
* *
12525458 AGGGAAAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGG-AAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
12525493 AGGGAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
12525525 AGGGA
1 AGGGA
12525530 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 18 0.53
35 4 0.12
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.22
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:12528392 original size:29 final size:30
Alignment explanation
Indices: 12528322--12528381 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
12528312 AAATTTAAGG
12528322 CAAAATGGTTTTTAGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTAGACTTGAATTGAATTTA
* *
12528353 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTAGACTTGAATTGAATTTA
12528382 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTAGACTTGAATTGAATTTA
Found at i:12528491 original size:21 final size:21
Alignment explanation
Indices: 12528461--12528559 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
12528451 AGGGTGTCAA
*
12528461 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCATGC
* *
12528482 AGTGCTTCCATGCATCCATGC
1 AGTGCATCCATGCACCCATGC
* **
12528503 AGTGCATCCATGCACCTACAC
1 AGTGCATCCATGCACCCATGC
* *
12528524 TAGTGCATCGATGCA-TCATGC
1 -AGTGCATCCATGCACCCATGC
12528545 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
12528560 TCAAACACCG
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 13 0.21
21 36 0.58
22 13 0.21
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:12528508 original size:13 final size:13
Alignment explanation
Indices: 12528492--12528516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12528482 AGTGCTTCCA
12528492 TGCATCCATGCAG
1 TGCATCCATGCAG
12528505 TGCATCCATGCA
1 TGCATCCATGCA
12528517 CCTACACTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCATGCAG
Done.