Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold192
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: 2196177
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 12544 characters in sequence are not A, C, G, or T
File 2 of 14
Found at i:151406 original size:15 final size:17
Alignment explanation
Indices: 151388--151419 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
151378 TGTTCATCAA
151388 CTTC-TTTTGGA-GCTT
1 CTTCATTTTGGATGCTT
151403 CTTCATTTTGGATGCTT
1 CTTCATTTTGGATGCTT
151420 TCATCTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (17 bp):
CTTCATTTTGGATGCTT
Found at i:153827 original size:3 final size:3
Alignment explanation
Indices: 153819--153854 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
153809 TCCGAGTCAC
* *
153819 CAT CAT CAT CAT CAT CAT TAT CAT CTT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
153855 TGATGGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.39
Consensus pattern (3 bp):
CAT
Found at i:155457 original size:20 final size:20
Alignment explanation
Indices: 155432--155485 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
155422 GTTAGAAGCA
* *
155432 ATGTATCAATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
155452 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
155472 ATGTATCGATACAA
1 ATGTATCGATACAA
155486 ACAATGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:155555 original size:19 final size:19
Alignment explanation
Indices: 155508--155566 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
155498 TAGCTACTGC
155508 CAATT-TCATGT-TCGATA
1 CAATTGTCATGTATCGATA
155525 CAATTGTCCATGTATCGATA
1 CAATTGT-CATGTATCGATA
155545 CAA-TGATCATGTATCGATA
1 CAATTG-TCATGTATCGATA
155564 CAA
1 CAA
155567 AGCATAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.13
18 1 0.03
19 22 0.58
20 10 0.26
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (19 bp):
CAATTGTCATGTATCGATA
Found at i:155578 original size:20 final size:19
Alignment explanation
Indices: 155534--155604 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
155524 ACAATTGTCC
*
155534 ATGTATCGATACAATG-AT
1 ATGTATCGATACAAAGCAT
155552 CATGTATCGATACAAAGCAT
1 -ATGTATCGATACAAAGCAT
* *
155572 AATGTATTGATATAAA-CACCT
1 -ATGTATCGATACAAAGCA--T
155593 ATGTATCGATAC
1 ATGTATCGATAC
155605 TTTGAAGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 17 0.40
20 25 0.58
21 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAAAGCAT
Found at i:158906 original size:172 final size:172
Alignment explanation
Indices: 158620--158962 Score: 650
Period size: 172 Copynumber: 2.0 Consensus size: 172
158610 TGGCATGAAT
*
158620 ATGAATGTATGACTACATAGGCTATAAACATGAAAATTATTTCAAAAATAAATGAACAAATAAAG
1 ATGAATGTATGACTACATAGGCTATAAACATGAAAATTAATTCAAAAATAAATGAACAAATAAAG
* *
158685 TTAATATGCAAATGCACTAGCAAAAAATGAGTTTTAGGAATAGTTCTGACAATAGCATCTTTCAT
66 TTAATATGCAAATGCACTAGCAAAAAATGAGTTTTAGGAACAGTTCTGACAATAACATCTTTCAT
158750 TTAGCATAAACATTGTTTGATAGCAGTTTCTTAGATCTAAAC
131 TTAGCATAAACATTGTTTGATAGCAGTTTCTTAGATCTAAAC
158792 ATGAATGTATGACTACATAGGCTATAAACATGAAAATTAATTCAAAAATAAATGAACAAATAAAG
1 ATGAATGTATGACTACATAGGCTATAAACATGAAAATTAATTCAAAAATAAATGAACAAATAAAG
158857 TTAATATGCAAATGCACTAGCAAAAAATGAGTTTTAGGAACAGTTCTGACAATAACATCTTTCAT
66 TTAATATGCAAATGCACTAGCAAAAAATGAGTTTTAGGAACAGTTCTGACAATAACATCTTTCAT
*
158922 TTAGCATAAACATTGTTTGATAGCAGTTTTTTAGATCTAAA
131 TTAGCATAAACATTGTTTGATAGCAGTTTCTTAGATCTAAA
158963 AATATCGCAC
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 167 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (172 bp):
ATGAATGTATGACTACATAGGCTATAAACATGAAAATTAATTCAAAAATAAATGAACAAATAAAG
TTAATATGCAAATGCACTAGCAAAAAATGAGTTTTAGGAACAGTTCTGACAATAACATCTTTCAT
TTAGCATAAACATTGTTTGATAGCAGTTTCTTAGATCTAAAC
Found at i:162585 original size:12 final size:12
Alignment explanation
Indices: 162568--162592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
162558 TCATATGTAA
162568 TAAATATGAGTG
1 TAAATATGAGTG
162580 TAAATATGAGTG
1 TAAATATGAGTG
162592 T
1 T
162593 GAACTGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (12 bp):
TAAATATGAGTG
Found at i:164215 original size:15 final size:15
Alignment explanation
Indices: 164195--164266 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
164185 CCTTTTTTCC
164195 CTTTTCTCTTTCCTT
1 CTTTTCTCTTTCCTT
*
164210 CTTTTCTCTTTTTCTTT
1 CTTTTCTC--TTTCCTT
* *
164227 CTTTTTTTTTTCCTT
1 CTTTTCTCTTTCCTT
* * *
164242 TTTTTCCTTTTTCTTT
1 CTTTT-CTCTTTCCTT
164258 C-TTTCTCTT
1 CTTTTCTCTT
164267 CTCTTCAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.09
15 21 0.47
16 8 0.18
17 12 0.27
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
CTTTTCTCTTTCCTT
Found at i:164225 original size:21 final size:20
Alignment explanation
Indices: 164185--164253 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
164175 TCCTAGGCTA
*
164185 CCTTTTTTCCCTTTTCTCTTT
1 CCTTTTTTCTCTTTT-TCTTT
164206 CCTTCTTTTCTCTTTTTCTTT
1 CCTT-TTTTCTCTTTTTCTTT
* * *
164227 CTTTTTTTTTTCCTTTT-TTT
1 C-CTTTTTTCTCTTTTTCTTT
164247 CCTTTTT
1 CCTTTTT
164254 CTTTCTTTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
19 5 0.12
20 4 0.10
21 20 0.49
22 12 0.29
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
CCTTTTTTCTCTTTTTCTTT
Found at i:164229 original size:10 final size:10
Alignment explanation
Indices: 164216--164271 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 10
164206 CCTTCTTTTC
164216 TCTTTTTCTT
1 TCTTTTTCTT
*
164226 TCTTTTTTTTT
1 TC-TTTTTCTT
164237 TCCTTTTT-TT
1 T-CTTTTTCTT
*
164247 CCTTTTTCTT
1 TCTTTTTCTT
*
164257 TCTTTCTCTT
1 TCTTTTTCTT
164267 CTCTT
1 -TCTT
164272 CAATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 6 0.16
10 14 0.37
11 17 0.45
12 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TCTTTTTCTT
Found at i:164242 original size:16 final size:16
Alignment explanation
Indices: 164203--164266 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
164193 CCCTTTTCTC
*
164203 TTTCCTTCTTTTCTCTT
1 TTTCTTTCTTTTCT-TT
164220 TTTCTTTCTTTT-TTT
1 TTTCTTTCTTTTCTTT
*
164235 TTTCCTTT-TTTTCCTT
1 TTT-CTTTCTTTTCTTT
164251 TTTCTTTCTTTCTCTT
1 TTTCTTTCTTT-TCTT
164267 CTCTTCAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 13 0.32
16 13 0.32
17 14 0.35
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTTTTCTTT
Found at i:164271 original size:15 final size:13
Alignment explanation
Indices: 164197--164271 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 13
164187 TTTTTTCCCT
*
164197 TTTCTCTTTCCTTC
1 TTTCTCTTT-TTTC
164211 TTT-TCTCTTTTTC
1 TTTCTCT-TTTTTC
164224 TTTCT-TTTTTT-
1 TTTCTCTTTTTTC
164235 TTTC-CTTTTTTTCC
1 TTTCTC-TTTTTT-C
*
164249 TTTTTCTTTCTTTC
1 TTTCTCTTT-TTTC
164263 TCTTCTCTT
1 T-TTCTCTT
164272 CAATTTAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
11 4 0.08
12 11 0.22
13 10 0.20
14 14 0.29
15 10 0.20
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTCTCTTTTTTC
Found at i:166206 original size:2 final size:2
Alignment explanation
Indices: 166199--166231 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
166189 TACTAATTCA
166199 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 A
166232 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:166834 original size:19 final size:19
Alignment explanation
Indices: 166810--166864 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
166800 AATTCAACAA
166810 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
166829 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
166848 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
166865 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:166922 original size:13 final size:13
Alignment explanation
Indices: 166904--166929 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166894 AATTTTTTTG
166904 TGTATCGATACAT
1 TGTATCGATACAT
166917 TGTATCGATACAT
1 TGTATCGATACAT
166930 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:169426 original size:27 final size:28
Alignment explanation
Indices: 169396--169471 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
169386 TTTCTTCACA
169396 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
169423 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
169451 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
169472 GTTTTATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:169540 original size:53 final size:52
Alignment explanation
Indices: 169454--169625 Score: 156
Period size: 52 Copynumber: 3.3 Consensus size: 52
169444 TTATTTCTGA
* *
169454 GGGGATACTCCAACCCCGGTTTTA--TCGCTAAAACACTAATTTTTCCTCAATC
1 GGGGATACTCCAA-CCCGGTTTTATTTC-CAAAAACACCAATTTTTCCTCAATC
* * *
169506 GGGGGATACTCCAATCCCGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATC
1 -GGGGATACTCCAA-CCCGGTTTTATTTCCAAAAACACCAATTTTTCC-TCAATC
* * * * *
169559 GGGGATATTCCAACTCCGATTCTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAAC-CCGGTTTTATTTCCAAAAACACCAATTTTTCCTCAATC
*
169611 GAGGATACTCCAACC
1 GGGGATACTCCAACC
169626 TCGTTATTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
51 2 0.02
52 45 0.46
53 45 0.46
54 5 0.05
55 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (52 bp):
GGGGATACTCCAACCCGGTTTTATTTCCAAAAACACCAATTTTTCCTCAATC
Found at i:171001 original size:20 final size:20
Alignment explanation
Indices: 170956--171002 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
170946 TTTCAAATGC
* *
170956 ATTGTATTGATACATTATGA
1 ATTGTATCGATACATTAGGA
170976 ATTGTATCGATACATT-GGA
1 ATTGTATCGATACATTAGGA
170995 ATGTGTAT
1 AT-TGTAT
171003 TCATGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (20 bp):
ATTGTATCGATACATTAGGA
Found at i:173128 original size:37 final size:37
Alignment explanation
Indices: 173078--173154 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
173068 TACATTTTAC
173078 TATGTATCGATACATTGTATTGATACAATGTCCCATG
1 TATGTATCGATACATTGTATTGATACAATGTCCCATG
173115 TATGTATCGATACATTGTATTGATACAATGTCCCATG
1 TATGTATCGATACATTGTATTGATACAATGTCCCATG
173152 TAT
1 TAT
173155 CAATACAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (37 bp):
TATGTATCGATACATTGTATTGATACAATGTCCCATG
Found at i:173214 original size:20 final size:20
Alignment explanation
Indices: 173189--173245 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
173179 TACTGCCAGT
173189 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
173209 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
*
173229 TTCATGTATCTATACAA
1 TTCATGTATCGATACAA
173246 AGCAATATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:175843 original size:13 final size:13
Alignment explanation
Indices: 175825--175850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
175815 ATAGTACCTC
175825 TTGTATCGATACA
1 TTGTATCGATACA
175838 TTGTATCGATACA
1 TTGTATCGATACA
175851 ATATATTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:179978 original size:189 final size:189
Alignment explanation
Indices: 179650--180027 Score: 713
Period size: 189 Copynumber: 2.0 Consensus size: 189
179640 TCTCAAAGGC
179650 ATTGTATCCTAAACCATGTTTATCAAAGAATGCCTTTAAGTGTCAATCATATCATTCAATTTTTG
1 ATTGTATCCTAAACCATGTTTATCAAAGAATGCCTTTAAGTGTCAATCATATCATTCAATTTTTG
*
179715 ATGTGCCATGTAAAATATATTGAATGATTCATGCAAATTTTTATTTTTCCTCACTAATTCATTAT
66 ATGTGCCATGTAAAATATATTGAATGATTCATGCAAATTTGTATTTTTCCTCACTAATTCATTAT
179780 TTTCATTAGTTAGGACTTTATTATTATCTTGCATTTCATTAAATTGTTTTTCTAATTTG
131 TTTCATTAGTTAGGACTTTATTATTATCTTGCATTTCATTAAATTGTTTTTCTAATTTG
*
179839 ATTGTATCCTAAACCATGTTTATCAAAGAATGCCCTTTGAGTGTCAATCATATCATTCAATTTTT
1 ATTGTATCCTAAACCATGTTTATCAAAGAATG-CCTTTAAGTGTCAATCATATCATTCAATTTTT
*
179904 GATTTGCCATGTAAAATATATTGAATGATTCATGCAAATTTGTATTTTTCCTCACT-ATTCATTA
65 GATGTGCCATGTAAAATATATTGAATGATTCATGCAAATTTGTATTTTTCCTCACTAATTCATTA
179968 TTTTCATTAGTTAGGACTTTATTATTATCTTGCATTTCATTAAATTGTTTTTCTAATTTG
130 TTTTCATTAGTTAGGACTTTATTATTATCTTGCATTTCATTAAATTGTTTTTCTAATTTG
180028 TCCAATTTTA
Statistics
Matches: 185, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
189 100 0.54
190 85 0.46
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (189 bp):
ATTGTATCCTAAACCATGTTTATCAAAGAATGCCTTTAAGTGTCAATCATATCATTCAATTTTTG
ATGTGCCATGTAAAATATATTGAATGATTCATGCAAATTTGTATTTTTCCTCACTAATTCATTAT
TTTCATTAGTTAGGACTTTATTATTATCTTGCATTTCATTAAATTGTTTTTCTAATTTG
Found at i:183198 original size:13 final size:13
Alignment explanation
Indices: 183180--183204 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183170 CATTTTACTA
183180 TGTATCGATACAT
1 TGTATCGATACAT
183193 TGTATCGATACA
1 TGTATCGATACA
183205 ATATCCCATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:186894 original size:20 final size:20
Alignment explanation
Indices: 186869--186993 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 20
186859 TTTTAACTAG
186869 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
186889 ATGTATCGATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* *
186920 ATGTATCGATACACTGAAGA
1 ATGTATCGATACATTGAAAA
** * * * *
186940 ATGTATTAATATATTCATAC
1 ATGTATCGATACATTGAAAA
186960 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
186980 ATGTATCAATACAT
1 ATGTATCGATACAT
186994 CTGGGTACTT
Statistics
Matches: 77, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
20 54 0.70
21 1 0.01
22 1 0.01
23 2 0.03
28 2 0.03
29 1 0.01
30 2 0.03
31 14 0.18
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:187538 original size:3 final size:3
Alignment explanation
Indices: 187530--187561 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
187520 AACCATCAAA
*
187530 GAT GAT GAT GAA GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
187562 AAAGGTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:194358 original size:19 final size:20
Alignment explanation
Indices: 194309--194359 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
194299 CACACCTAGA
*
194309 TGTATTGATACATATTGCTT
1 TGTATCGATACATATTGCTT
* * *
194329 AGTATCAATACATGTT-CTT
1 TGTATCGATACATATTGCTT
194348 TGTATCGATACA
1 TGTATCGATACA
194360 CCTTGAAATG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATATTGCTT
Found at i:201760 original size:13 final size:13
Alignment explanation
Indices: 201739--201772 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
201729 GATACATGGG
*
201739 ACATGGTATTGAT
1 ACATGGTATCGAT
*
201752 ACATTGTATCGAT
1 ACATGGTATCGAT
201765 ACATGGTA
1 ACATGGTA
201773 AAAAGTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (13 bp):
ACATGGTATCGAT
Found at i:201787 original size:33 final size:33
Alignment explanation
Indices: 201723--201791 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
201713 CTACGTGAAA
* ** **
201723 TGTATCGATACATGGGACATGGTATTGATACAT
1 TGTATCGATACATGGGAAAAAGTATCAATACAT
*
201756 TGTATCGATACATGGTAAAAAGTATCAATACAT
1 TGTATCGATACATGGGAAAAAGTATCAATACAT
201789 TGT
1 TGT
201792 GCCCAACAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGGGAAAAAGTATCAATACAT
Found at i:212792 original size:21 final size:21
Alignment explanation
Indices: 212744--212797 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
212734 AGGAAAACAA
* *
212744 ATGTATCGATACATTTGTATG
1 ATGTATCGATACATTTGCATC
*
212765 ATATATCGATACATTTGCA-C
1 ATGTATCGATACATTTGCATC
*
212785 ATTGTATCAATAC
1 A-TGTATCGATAC
212798 CTTATGCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTTGCATC
Found at i:217256 original size:52 final size:52
Alignment explanation
Indices: 217176--217295 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
217166 AAAAGTTGTT
*
217176 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
217228 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
217280 GGCATGTATCGATACA
1 TGCATGTATCGATACA
217296 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:217308 original size:52 final size:51
Alignment explanation
Indices: 217177--217315 Score: 199
Period size: 52 Copynumber: 2.7 Consensus size: 51
217167 AAAGTTGTTT
*
217177 GCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCT
1 GCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCCG
* *
217229 GCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCG
1 GCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGCCG
*
217281 GCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 GCATGTATCGATACATTA-AT-AGTGTATCGATACA
217316 ATGTATCGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.03
52 77 0.97
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (51 bp):
GCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGCCG
Found at i:217322 original size:13 final size:13
Alignment explanation
Indices: 217304--217328 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
217294 CAAAGATCAG
217304 TGTATCGATACAA
1 TGTATCGATACAA
217317 TGTATCGATACA
1 TGTATCGATACA
217329 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:217406 original size:33 final size:33
Alignment explanation
Indices: 217369--217435 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
217359 AGTAGCTTAA
217369 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
217402 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
217435 A
1 A
217436 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:217409 original size:13 final size:13
Alignment explanation
Indices: 217391--217415 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
217381 CAAAAAAATA
217391 TGTATCGATACAT
1 TGTATCGATACAT
217404 TGTATCGATACA
1 TGTATCGATACA
217416 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:218486 original size:43 final size:43
Alignment explanation
Indices: 218425--218510 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
218415 GATGGAAAAT
* *
218425 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGACCAGCTACATTGGACTTAAAG
*
218468 GTGCCAATGTGCTGATTCAAGACCAGCTACATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGACCAGCTACATTGGACTTAAAG
218511 ATGAAGATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGACCAGCTACATTGGACTTAAAG
Found at i:218615 original size:56 final size:52
Alignment explanation
Indices: 218531--218971 Score: 433
Period size: 49 Copynumber: 8.8 Consensus size: 52
218521 GAAAAGTGAT
* * * * * *
218531 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG--G-A
* * * *
218586 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
218639 AAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
218682 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
218732 --AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * * *
218780 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGGCTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
218829 --AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
218877 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
218928 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
218972 GAGGGGTTGC
Statistics
Matches: 346, Mismatches: 27, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
43 37 0.11
44 1 0.00
46 1 0.00
48 93 0.27
49 95 0.27
50 1 0.00
51 1 0.00
52 70 0.20
53 6 0.02
54 1 0.00
55 4 0.01
56 36 0.10
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.24
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:218715 original size:218 final size:222
Alignment explanation
Indices: 218238--218732 Score: 811
Period size: 218 Copynumber: 2.2 Consensus size: 222
218228 AGAGATGATG
* * *
218238 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
*
218303 TAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTC
66 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTC
*
218368 AACGTGCTGATTCAAGGCCAGCTACATTGAACTACATTGAACTTAAAGATGGAAAATGTGCCAAT
131 AACGTGCTGATTCAAGG-C-GC-ACA-TG-ACTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
218433 ATGCTGATTCAAGGCCAGCTATATTGGACTTA
191 ATGCTGATTCAAGGCCAGCTATATTGGACTTA
*
218465 AAGGTGCCAATGTGCTGATTCAAGACCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
*
218530 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGT
66 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCCTAAAGATGA-GAAAAAGGATGT
* *
218595 CAATGTGCTGATTCAA-G-GC-CA-G-CTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGC
130 CAACGTGCTGATTCAAGGCGCACATGACTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGC
218655 TGATTCAAGGCCAGCTATATTGGACTTA
195 TGATTCAAGGCCAGCTATATTGGACTTA
*
218683 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGATGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
218733 GGTGCCAATG
Statistics
Matches: 256, Mismatches: 11, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
218 112 0.44
220 1 0.00
222 2 0.01
224 2 0.01
227 112 0.44
228 27 0.11
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (222 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTC
AACGTGCTGATTCAAGGCGCACATGACTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTTA
Found at i:218804 original size:49 final size:49
Alignment explanation
Indices: 218595--218971 Score: 527
Period size: 48 Copynumber: 7.7 Consensus size: 49
218585 AAAAGGATGT
* *
218595 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
218647 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
218690 CAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGATG-AGGTGC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
218738 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
218787 CAATGTGCTGAGTCAAGGCCAGCTACATTGGGCTTAAAGATG-AGGTGC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
218835 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
218884 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
218936 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
218972 GAGGGGTTGC
Statistics
Matches: 298, Mismatches: 16, Indels: 22
0.89 0.05 0.07
Matches are distributed among these distances:
43 38 0.13
47 1 0.00
48 94 0.32
49 94 0.32
50 1 0.00
52 70 0.23
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (49 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:218819 original size:97 final size:99
Alignment explanation
Indices: 218595--218971 Score: 531
Period size: 97 Copynumber: 3.9 Consensus size: 99
218585 AAAAGGATGT
* * * *
218595 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG--AAGGTGCCAATATGCTGAGT
*
218660 CAAGGCCAGCTATATTGGACTT----A--AAGGTGC
64 CAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
218690 CAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGAT-G-AGGTGCCAATGTGCTGAGTCA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGGTGCCAATATGCTGAGTCA
218753 AGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
66 AGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
218787 CAATGTGCTGAGTCAAGGCCAGCTACATTGGGCTTAAAGAT-G-AGGTGCCAATGTGCTGAGTCA
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGGTGCCAATATGCTGAGTCA
218850 AGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
66 AGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
218884 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG--AAGGTGCCAATATGCTGAGT
* *
218949 CAAGGCCAGCTATATTGGGCTTA
64 CAAGGCCAGCTACATTGGACTTA
218972 GAGGGGTTGC
Statistics
Matches: 260, Mismatches: 12, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
91 37 0.14
94 1 0.00
95 40 0.15
97 143 0.55
98 1 0.00
101 38 0.15
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (99 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGGTGCCAATATGCTGAGTCA
AGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:219040 original size:31 final size:30
Alignment explanation
Indices: 218964--219095 Score: 178
Period size: 31 Copynumber: 4.3 Consensus size: 30
218954 CCAGCTATAT
* *
218964 TGGGCTTAGAGGGGTTGCCACCGACTTGTG
1 TGGGCTTTGAGGGGTTGCCACCAACTTGTG
218994 TGGGCTTT--GGGGTTGCCACCAACTTGTG
1 TGGGCTTTGAGGGGTTGCCACCAACTTGTG
219022 TGGGCTTTGAGGGGGTTGCCACCAACTTGTG
1 TGGGCTTTGA-GGGGTTGCCACCAACTTGTG
*
219053 TGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTG
1 TGGGCTTT-GAG--GGG-TTGCCACCAACTTGTG
219087 TGGGCTTTG
1 TGGGCTTTG
219096 GGAAGGAAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
28 27 0.29
30 7 0.08
31 29 0.32
32 2 0.02
33 4 0.04
34 23 0.25
ACGTcount: A:0.13, C:0.19, G:0.38, T:0.30
Consensus pattern (30 bp):
TGGGCTTTGAGGGGTTGCCACCAACTTGTG
Found at i:219174 original size:34 final size:34
Alignment explanation
Indices: 219103--220005 Score: 937
Period size: 34 Copynumber: 26.1 Consensus size: 34
219093 TTGGGAAGGA
*
219103 AAAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
*
219137 AAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
219171 AAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
*
219207 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
219242 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
* **
219278 AAAGAGAGTGCCACAAAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
219312 AAGAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* * * *
219346 AAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGG
1 AAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AG
* *
219385 AGAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
219419 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
219453 AAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-G
* *
219488 AAAAAAGAGCGCCACAGAGTTGTGGGCTTTAAACAG
1 -AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
219524 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
219558 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
* **
219594 AAAGAGAGTGCCACAAAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
219628 AAGAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* * * *
219662 AAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGG
1 AAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AG
* *
219701 AGAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
219735 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
219769 AAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
* *
219805 AAAAAGAGCGCCACAGAGTTGTGGGCTTTAAACAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
219840 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
219874 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
*
219908 AAAAAG-GTGCCACGGAGTTGTGGGC-TTAAACG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
219940 -----G-GTGCCACGGAGTTGTGGAC-TTAAAGATG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-A-G
* *
219969 AAAAA-AGTGCCACAGAATTGTGGGCTTTAAAA-
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
220001 AAAAA
1 AAAAA
220006 TGCCACTGAG
Statistics
Matches: 755, Mismatches: 55, Indels: 120
0.81 0.06 0.13
Matches are distributed among these distances:
27 24 0.03
29 1 0.00
32 9 0.01
33 114 0.15
34 260 0.34
35 107 0.14
36 81 0.11
37 129 0.17
38 20 0.03
39 10 0.01
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (34 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
Found at i:219536 original size:316 final size:315
Alignment explanation
Indices: 219098--219934 Score: 1440
Period size: 316 Copynumber: 2.7 Consensus size: 315
219088 GGGCTTTGGG
* * *
219098 AAGGAAAAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGG
1 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAAA-AGTGCCACGGAGTTGTGG
* *
219161 GCTTT-AAAA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAA-AGGGAAAAAGAGTGCCACG
63 GCTTTGAAAAGGAAAAAGAGCGCCACAGAGTTGTGGGCTTT-AAACA--GAAAAAG-GTGCCACG
**
219222 GAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGT
124 GAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGT
219287 GCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAG
189 GCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAG
219352 GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAA
254 GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAA
219414 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
1 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
219479 TTGAAAAGGAAAAAAGAGCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTG
66 TTGAAAAGG-AAAAAGAGCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTG
219544 TGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACA
130 TGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACA
219609 AAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTTGCC
195 AAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTTGCC
219674 ACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAA
260 ACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAA
219730 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
1 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
219795 TTGAAAAGGGAAAAAGAGCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTG
66 TTGAAAA-GGAAAAAGAGCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTG
* *
219860 TGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA--GAAAAAG-GTGCCACG
130 TGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACA
*
219922 GAGTTGTGGGCTT
195 AAGTTGTGGGCTT
219935 AAACGGGTGC
Statistics
Matches: 503, Mismatches: 10, Indels: 19
0.95 0.02 0.04
Matches are distributed among these distances:
313 19 0.04
314 6 0.01
315 22 0.04
316 393 0.78
317 27 0.05
318 14 0.03
319 22 0.04
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (315 bp):
AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
TTGAAAAGGAAAAAGAGCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGT
GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACAA
AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTTGCCA
CCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAA
Found at i:219629 original size:282 final size:277
Alignment explanation
Indices: 219085--220028 Score: 1157
Period size: 282 Copynumber: 3.4 Consensus size: 277
219075 CACCGACTTG
* *
219085 TGTGGGCTTTGGGAAGGAAAAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTAGGAAGGAAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCA
*
219150 CGAAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG
66 CGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAA-GGAAAAAGAG
*
219215 TGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
130 TGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA--GAA
* ** *
219280 AGAGAGTGCCACAAAGTTGTGGGCTTT-AAAAG-AAGA-AGGTGCCACGGAGTTGTGGGCTTTGA
193 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAGAGA-GTGCCACGGAGTTGTGGGCTTTAA
*
219342 AAAGAAGAAGGTTGCCACCGACTT
256 AAAGAAGAAGG-TGCCACCGA-GT
*
219366 GTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCC
1 -TGTGGGCTTTAGGAAGGAAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCC
219431 ACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGA
65 ACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGG-AAAAAGA
* *
219496 GCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
129 GTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
**
219561 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACAAAGTTGTGGGCTTT-AA
194 AAGGTGCCACGGAGTTGTGGGCTTTAAAAA--GAAAGAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
219625 AAGAAGAAGGTGCCACGGAGT
257 AAGAAGAAGGTGCCACCGAGT
* * * * * * * * *
219646 TGTGGGCTTT-GAAAAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGA-T
1 TGTGGGCTTTAGGAAGGAAGAAAGATGCCACGGA-GT-TGTGGAC-TTA-AAAGGGAAAAAGAGT
*
219709 GCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GAA
62 GCCACGGAGTTGTGGGCTTTAAAA--GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGAA
* *
219771 AAA-AGTGCCACGGAGTTGTGGGCTTTGAAA-AGGGAAAAAGAGCGCCACAGAGTTGTGGGCTTT
124 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAACA--GAAAAAG-GTGCCACGGAGTTGTGGGCTTT
* *
219834 AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGG
185 AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAGAGAGTGCCACGGAGTTGTGGG
* *
219898 CTTTAAAAAGAAAAAGGTGCCACGGAGT
250 CTTTAAAAAGAAGAAGGTGCCACCGAGT
* *
219926 TGTGGGC-TTA--AACG--G---G-TGCCACGGAGTTGTGGACTT-AAAGATGAAAAA-AGTGCC
1 TGTGGGCTTTAGGAAGGAAGAAAGATGCCACGGAGTTGTGGACTTAAAAG-GGAAAAAGAGTGCC
* * * * *
219980 ACAGAATTGTGGGCTTT-AAA-AAAAAA-TGCCACTGAGTCGTGGACTTTGA
65 ACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
220029 GACAAAATGC
Statistics
Matches: 592, Mismatches: 47, Indels: 64
0.84 0.07 0.09
Matches are distributed among these distances:
263 18 0.03
264 2 0.00
265 5 0.01
267 4 0.01
268 23 0.04
269 4 0.01
270 6 0.01
271 1 0.00
272 8 0.01
273 1 0.00
276 1 0.00
278 20 0.03
279 75 0.13
280 66 0.11
281 38 0.06
282 272 0.46
283 47 0.08
284 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (277 bp):
TGTGGGCTTTAGGAAGGAAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCA
CGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGAGT
GCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAGAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
AGAAGGTGCCACCGAGT
Found at i:219951 original size:27 final size:27
Alignment explanation
Indices: 219913--219964 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
219903 AAAAGAAAAA
*
219913 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAACG
219940 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
219965 GATGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (27 bp):
GGTGCCACGGAGTTGTGGACTTAAACG
Found at i:219957 original size:95 final size:99
Alignment explanation
Indices: 219110--220005 Score: 731
Period size: 105 Copynumber: 8.7 Consensus size: 99
219100 GGAAAAAAGA
* * *
219110 TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTT-AAAAGAA
1 TGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
219173 AAA-AGTGCCACGGAGTTGTGGGCTTTGAAA-AGGGAAAAAGAG
64 AAAGAGCGCCACAGAGTTGTGGGCTTT-AAACA--G----AG-G
** *
219215 TGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAA--GAA
* * * *
219280 AGAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGG
64 AAAGAGCGCCACAGAGTTGTGGGCTTT-AAA-CAG-AGG
* * * * * **
219319 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAG-TGCCACGGA-GT-TGTGGGCTTTA--AAAA
* * * * * * *
219384 GAGAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAG
61 GAAAAAGAGCGCCACAGAGTTGTGGGCTT-TAA---ACAGAG-G
*
219427 TGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAAAG-AA
219491 AAAGAGCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGG
64 AAAGAGCGCCACAGAGTTGTGGGCTTTAAACAG----AGG
*
219531 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAA--GAA
* * * *
219596 AGAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGG
64 AAAGAGCGCCACAGAGTTGTGGGCTTT-AAA-CAG-AGG
* * * * * **
219635 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAG-TGCCACGGA-GT-TGTGGGCTTTA--AAAA
* * * * * * *
219700 GAGAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAG
61 GAAAAAGAGCGCCACAGAGTTGTGGGCTT-TAA---ACAGAG-G
*
219743 TGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAA
219807 AAAGAGCGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGG
64 AAAGAGCGCCACAGAGTTGTGGGCTTTAAACAG----AGG
*
219847 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
* *
219912 AG-GTGCCACGGAGTTGTGGGC-TTAAAC-G-GG
66 AGAGCGCCACAGAGTTGTGGGCTTTAAACAGAGG
* * * *
219942 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAA-AAA
1 TGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
220005 A
65 A
220006 TGCCACTGAG
Statistics
Matches: 668, Mismatches: 75, Indels: 107
0.79 0.09 0.13
Matches are distributed among these distances:
94 9 0.01
95 51 0.08
100 1 0.00
101 10 0.01
102 17 0.03
103 13 0.02
104 178 0.27
105 179 0.27
106 65 0.10
107 65 0.10
108 73 0.11
109 6 0.01
110 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (99 bp):
TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
AGAGCGCCACAGAGTTGTGGGCTTTAAACAGAGG
Found at i:219979 original size:61 final size:61
Alignment explanation
Indices: 219879--219995 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
219869 AAAAGAAAAA
* * * *
219879 GGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAAGTGCCACAGAATTGTGGGCTTAAACG
*
219940 GGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTT
1 GGTGCCACGGAGTTGTGGACTTTAAA-AAGAAAAAAGTGCCACAGAATTGTGGGCTT
219996 TAAAAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 5 0.10
61 45 0.90
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (61 bp):
GGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAAGTGCCACAGAATTGTGGGCTTAAACG
Found at i:221005 original size:1 final size:1
Alignment explanation
Indices: 221001--221039 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
220991 GGTTTTTCCC
* * *
221001 TTTTTTTTTTGTTTTTTTTTTTGTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
221040 GTGTGAAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (1 bp):
T
Found at i:221027 original size:17 final size:17
Alignment explanation
Indices: 221001--221041 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
220991 GGTTTTTCCC
221001 TTTTTT-TTTTGTTTTT
1 TTTTTTGTTTTGTTTTT
221017 TTTTTTGTTTTGTTTTT
1 TTTTTTGTTTTGTTTTT
221034 TTTTTTGT
1 TTTTTTGT
221042 GTGAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (17 bp):
TTTTTTGTTTTGTTTTT
Found at i:221041 original size:12 final size:12
Alignment explanation
Indices: 221001--221039 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
220991 GGTTTTTCCC
221001 TTTTTTTTTTGT
1 TTTTTTTTTTGT
221013 TTTTTTTTTTGT
1 TTTTTTTTTTGT
221025 TTTGTTTTTTT-T
1 TTT-TTTTTTTGT
221037 TTT
1 TTT
221040 GTGTGAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:221108 original size:15 final size:15
Alignment explanation
Indices: 221083--221123 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
221073 CTCACCGAGA
* *
221083 TTTTCTGTTTTGTTT
1 TTTTCTTTTTTGTCT
221098 TTTTCTTTTTT-TCT
1 TTTTCTTTTTTGTCT
221112 TTTT-TTTTTTGT
1 TTTTCTTTTTTGT
221124 GTTTGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
15 10 0.43
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (15 bp):
TTTTCTTTTTTGTCT
Found at i:223198 original size:79 final size:79
Alignment explanation
Indices: 222955--223186 Score: 193
Period size: 79 Copynumber: 2.9 Consensus size: 79
222945 TACCCCCTCA
* * * * * * * *
222955 AAAATAACGGGGTTGGAGTATTCCCAATGGTGGAAAATCGATGTTTTGGAAATAAAATC-GAGGT
1 AAAATAACGGGGTTGAAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCAG-GGT
* * * *
223019 TGGAGTATTCTCTTG
65 TAGAGTATCCACTCG
* ** * *
223034 AAAATAACCGGGTT-AGAGTATCATCGATTGT-GAAGAATTGGTGTTTTGAAAGTAAAACCGAAG
1 AAAATAACGGGGTTGA-AGTATCCCCGATTGTGGAA-AATTGGTGTTTTGAAAATAAAACC-AGG
* * * * *
223097 ATGA-AGCATCTACTCA
63 GTTAGAGTATCCACTCG
*
223113 AAAATAACGGGGTTGAAATATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCAGGGTT
1 AAAATAACGGGGTTGAAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCAGGGTT
223178 AGAGTATCC
66 AGAGTATCC
223187 CCTGGGAAAT
Statistics
Matches: 114, Mismatches: 32, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
78 7 0.06
79 101 0.89
80 6 0.05
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (79 bp):
AAAATAACGGGGTTGAAGTATCCCCGATTGTGGAAAATTGGTGTTTTGAAAATAAAACCAGGGTT
AGAGTATCCACTCG
Found at i:225943 original size:3 final size:3
Alignment explanation
Indices: 225937--225984 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
225927 ATTTTTTTTA
225937 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
225985 TTGGGTAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:226472 original size:61 final size:60
Alignment explanation
Indices: 226415--226943 Score: 577
Period size: 61 Copynumber: 8.8 Consensus size: 60
226405 AAGCGTCTTG
* * * * *
226415 CTCTTTGAGGACTAAAAGATGCTACC-AGTTCATGTGGGCTTTGAAAAGGAAAGGCGTCCTA
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTT-GTGTGGGCTTT-AAAAGGAAAGGCGTCCTA
* * * * *
226476 CTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGAGTTTTAAAAGAAGAAGGCATCCTG
1 CTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAGGCGTCCTA
* ** *
226537 CTCTTTGAGGACT-GAAAGGGGCCACCAACTTGTGTAAGCTTTAAAAGGAAAAGGTGTCCTA
1 CTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCGTCCTA
* * * * **
226598 CTCTTTAAGGACTAGAAGTTGCCACTAACTTGTGTGGGCTTTGAAAGGAAA-GCGTCCGG
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCCTA
* * *
226657 CTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGAGTTCTA
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCGTCCTA
* * * * * * *
226718 CTTTTTGAGGACTAGAAGGTACCACCAACTTGTGTGGGCTTTGAAAGGAAA-ACATCATG
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCCTA
* * * * *
226777 CTCTTTGAGAAGTGGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGTGTCCTA
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCGTCCTA
*
226838 CTCTTTGGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA-GCGTCCTA
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCCTA
* * *
226897 TTCTTTGAGGACT-GAAAAGTGCCACCAACTTATGTGGGCTTTAAAAG
1 CTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
226944 AAAAAGGCAT
Statistics
Matches: 390, Mismatches: 68, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
58 1 0.00
59 139 0.36
60 21 0.05
61 224 0.57
62 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (60 bp):
CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCGTCCTA
Found at i:226702 original size:120 final size:120
Alignment explanation
Indices: 226389--226950 Score: 689
Period size: 120 Copynumber: 4.7 Consensus size: 120
226379 CCCACTTGGG
* * * * * * *
226389 GGGCTTTGCAAGGAGAAAGCGTCTTGCTCTTTGAGGACTAAAAGATGCTACC-AGTTCATGTGGG
1 GGGCTTTG-AAAG-GAAAGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTT-GTGTGGG
*
226453 CTTTGAAAAGG-AAAGGCGTCCTACTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGT
63 CTTT-AAAAGGAAAAGGTGTCCTACTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGT
* * * * * * **
226511 GAGTTTTAAAAGAAGAAGGCATCCTGCTCTTTGAGGACTGAAAGGGGCCACCAACTTGTGTAAGC
1 GGGCTTTGAAAG--GAAAGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGC
* * *
226576 TTTAAAAGGAAAAGGTGTCCTACTCTTTAAGGACTAGAAGTTGCCACTAACTTGTGT
64 TTTAAAAGGAAAAGGTGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGT
* *
226633 GGGCTTTGAAAGGAAAGCGTCCGGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTT
1 GGGCTTTGAAAGGAAAGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* * * *
226698 TAAAAGGAAAAGGAGTTCTACTTTTTGAGGACTAGAAGGTACCACCAACTTGTGT
66 TAAAAGGAAAAGGTGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGT
* * * * * * *
226753 GGGCTTTGAAAGGAAAACATCATGCTCTTTGAGAAGTGGAAGGTGCCACCAACTTGTGTAGGCTT
1 GGGCTTTGAAAGGAAAGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
226818 TAAAAGGAAAAGGTGTCCTACTCTTTGGGGACTAGAAGGTGCCACCAACTTGTGT
66 TAAAAGGAAAAGGTGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGT
* ** * *
226873 GGGCTTTAAAAGGAAAGCGTCCTATTCTTTGAGGACTGAAAAGTGCCACCAACTTATGTGGGCTT
1 GGGCTTTGAAAGGAAAGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
226938 TAAAAGAAAAAGG
66 TAAAAGGAAAAGG
226951 CATCTTGCTC
Statistics
Matches: 375, Mismatches: 61, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
120 267 0.71
121 9 0.02
122 95 0.25
123 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (120 bp):
GGGCTTTGAAAGGAAAGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
TAAAAGGAAAAGGTGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGT
Found at i:227946 original size:22 final size:21
Alignment explanation
Indices: 227920--227984 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
227910 CTTAAGTAGG
227920 TTCTTTTCTATTCTCTTTTTTT
1 TTCTTTT-TATTCTCTTTTTTT
*
227942 TTCTTTTTTATTAT-TTTTTGTT
1 TTC-TTTTTATTCTCTTTTT-TT
* *
227964 TT-GTTTTGTTCTCTTTTTTT
1 TTCTTTTTATTCTCTTTTTTT
227984 T
1 T
227985 GGGAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 10 0.28
21 10 0.28
22 12 0.33
23 4 0.11
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.80
Consensus pattern (21 bp):
TTCTTTTTATTCTCTTTTTTT
Found at i:240440 original size:79 final size:78
Alignment explanation
Indices: 240340--240610 Score: 303
Period size: 79 Copynumber: 3.4 Consensus size: 78
240330 AAATTTAATA
* * * * *
240340 TTTTGGAGATAAAAACAAGGTTAGAGTAGCCCCCCAGAAATAACAGGGTTGGAGTATCCCTAATG
1 TTTTGGAAAT-AAAACAAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCTAATT
*
240405 GTGGAAAATTGATG
65 GTGGAAAATTGGTG
* * * *
240419 TTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTTAGAAATAACAGGGTTAGAGTAT-CCTCGAT
1 TTTTGGAAATAAAA-CAAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCT-AAT
240483 TGTGGAAAATTGGTG
64 TGTGGAAAATTGGTG
* * ** *
240498 TCTTGAAAATAAAACAAGGGTTGGAGTATCCCCTC-GAAAATAATGGGGTTGGAGCATCCCTAAT
1 TTTTGGAAATAAAACAA-GGTTGGAGTATCCCCTCAG-AAATAACAGGGTTGGAGTATCCCTAAT
* *
240562 TATGGAAATTTGGTG
64 TGTGGAAAATTGGTG
* *
240577 TTTTAGAAATAAAACAGGGTTTGGAGTATCCCCT
1 TTTTGGAAATAAAACAAGG-TTGGAGTATCCCCT
240611 TGAAAATAAA
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
78 12 0.07
79 146 0.91
80 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (78 bp):
TTTTGGAAATAAAACAAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCTAATTG
TGGAAAATTGGTG
Found at i:241471 original size:48 final size:50
Alignment explanation
Indices: 241381--241491 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 50
241371 TCTAGGGTTA
* * * **
241381 TTTA-GGTCATTTTTTCATGATCTAAGGACCATTTTGTAATTTTC-ATTAT
1 TTTAGGGTCA-TTTTCCATGATCTAAGGACCATTATATAATTTTCAAGCAT
* *
241430 TTTAGGGTCATTTTCCATGATCTATGGA-CATTATATGATTTTCAAGCAT
1 TTTAGGGTCATTTTCCATGATCTAAGGACCATTATATAATTTTCAAGCAT
*
241479 TTTAGGCTCATTT
1 TTTAGGGTCATTT
241492 AGGTCATATT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
48 12 0.23
49 35 0.67
50 5 0.10
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (50 bp):
TTTAGGGTCATTTTCCATGATCTAAGGACCATTATATAATTTTCAAGCAT
Found at i:244037 original size:24 final size:24
Alignment explanation
Indices: 244010--244057 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
244000 AGTTAAATAT
244010 AAATAATATCCCAAATAAATAAGA
1 AAATAATATCCCAAATAAATAAGA
* *
244034 AAATAATATCCTAACTAAATAAGA
1 AAATAATATCCCAAATAAATAAGA
244058 TAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.60, C:0.12, G:0.04, T:0.23
Consensus pattern (24 bp):
AAATAATATCCCAAATAAATAAGA
Found at i:246432 original size:17 final size:17
Alignment explanation
Indices: 246410--246449 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
246400 GACATTAGAG
*
246410 ACTATTAGTTAATCCTA
1 ACTATTAGATAATCCTA
*
246427 ACTATTTGATAATCCTA
1 ACTATTAGATAATCCTA
*
246444 AATATT
1 ACTATT
246450 GAAGTAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (17 bp):
ACTATTAGATAATCCTA
Found at i:246936 original size:12 final size:12
Alignment explanation
Indices: 246919--246955 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
246909 TTCCTTACTC
246919 TTACTTTCTTTT
1 TTACTTTCTTTT
246931 TTACTTT-TTTT
1 TTACTTTCTTTT
246942 TT-CTTTCTTCTT
1 TTACTTTCTT-TT
246954 TT
1 TT
246956 TTCTTCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.17
11 8 0.35
12 11 0.48
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TTACTTTCTTTT
Found at i:247534 original size:13 final size:13
Alignment explanation
Indices: 247516--247541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247506 TACACCAAGT
247516 ATGTATCGATACA
1 ATGTATCGATACA
247529 ATGTATCGATACA
1 ATGTATCGATACA
247542 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:247539 original size:32 final size:33
Alignment explanation
Indices: 247498--247561 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
247488 TAGCCAAACT
**
247498 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
247530 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
247562 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:250051 original size:36 final size:35
Alignment explanation
Indices: 249994--250063 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
249984 AGATACAAAC
* **
249994 CTCCTTATCTTTTCACGGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTCT
250029 CTCCCTATCCTTTTCAAAGGCTAAGATAGAACCTC
1 CTCCCTAT-CTTTTCAAAGGCTAAGATAGAACCTC
250064 ACAATCACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (35 bp):
CTCCCTATCTTTTCAAAGGCTAAGATAGAACCTCT
Found at i:251601 original size:20 final size:20
Alignment explanation
Indices: 251576--251627 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
251566 TTTTGATCTA
251576 AATGTATTGATACATTCTTC
1 AATGTATTGATACATTCTTC
* *
251596 AATGTATTAAAACATTCTTC
1 AATGTATTGATACATTCTTC
*
251616 AATGTATCGATA
1 AATGTATTGATA
251628 TATGTAGGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (20 bp):
AATGTATTGATACATTCTTC
Found at i:255544 original size:67 final size:66
Alignment explanation
Indices: 255379--255544 Score: 172
Period size: 67 Copynumber: 2.5 Consensus size: 66
255369 TTTTGAATAG
* * * * * *
255379 GTCAAGCCTAGATATTACTATTTAGGTTCTTTTTCCTTTAAGTTGAACTCTTTTCCTACCGAATA
1 GTCAAGCCTAGAGATTACTATTTAGGTTTTTTTTCCTTTAAGTTAAACTCATTTCCTAACGAACA
*
255444 G
66 A
* * * *
255445 GTTAA-ACTAGAGATTACTATCTAGGTTTTTTTTTTCTTTTAAGTTAAACTCATTTCCTAACGAA
1 GTCAAGCCTAGAGATTACTATTTAGG--TTTTTTTTCCTTTAAGTTAAACTCATTTCCTAACGAA
255509 CAA
64 CAA
* * * *
255512 GTCAAGCCTAAAGATTACCATTTATGTCTTTTT
1 GTCAAGCCTAGAGATTACTATTTAGGTTTTTTT
255545 CTTTCTAAAC
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
65 17 0.22
66 10 0.13
67 37 0.47
68 15 0.19
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (66 bp):
GTCAAGCCTAGAGATTACTATTTAGGTTTTTTTTCCTTTAAGTTAAACTCATTTCCTAACGAACA
A
Found at i:256634 original size:79 final size:77
Alignment explanation
Indices: 256467--256642 Score: 183
Period size: 79 Copynumber: 2.2 Consensus size: 77
256457 GACATGTCTT
*** * * * *
256467 AACATAAAAGTTCCTGGATGATCCTAAAGACTTTGTTTTAAGGTATTATTACCTAAATAACCCTA
1 AACATAAAAGTTCCCACATAATCCTAAAGACTTAGTTTTAAAGTACTATTACCTAAATAACCCTA
256532 ATGAATATGTATC
66 ATGAATATGTA-C
** * *
256545 GGCATAAAAGTTCTCACATAATCCTAAAGACTTAGTTTTTAAAGTACTATTACCTAAATGACCCT
1 AACATAAAAGTTCCCACATAATCCTAAAGACTTAG-TTTTAAAGTACTATTACCTAAATAACCCT
* *
256610 ATTAGACATTTGTA-
65 AAT-GA-ATATGTAC
*
256624 AACATGAAAGTTCCCACAT
1 AACATAAAAGTTCCCACAT
256643 GACCTAAGAT
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
78 27 0.35
79 43 0.55
80 2 0.03
81 6 0.08
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (77 bp):
AACATAAAAGTTCCCACATAATCCTAAAGACTTAGTTTTAAAGTACTATTACCTAAATAACCCTA
ATGAATATGTAC
Found at i:256828 original size:29 final size:28
Alignment explanation
Indices: 256796--256868 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
256786 AAAATACACG
256796 AAAAATGCTAAAGTGACCCTAGAT-TATGT
1 AAAAATGCTAAA-TGACCCTA-ATATATGT
* *
256825 -AAAATAGCCTAAATGGCCCTAATATGTGT
1 AAAAAT-G-CTAAATGACCCTAATATATGT
256854 AGAAAATGCTAAATG
1 A-AAAATGCTAAATG
256869 GTACTTATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
28 7 0.19
29 19 0.51
30 6 0.16
31 5 0.14
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (28 bp):
AAAAATGCTAAATGACCCTAATATATGT
Found at i:257052 original size:5 final size:5
Alignment explanation
Indices: 257042--257068 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
257032 CACCCAAAAA
257042 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
257069 TCAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:258703 original size:22 final size:21
Alignment explanation
Indices: 258664--258712 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
258654 CAGAATTTTG
258664 TTTATTATTATTATTTTTAAT
1 TTTATTATTATTATTTTTAAT
258685 TTTATGTATTTATTA-TTTTAAT
1 TTTAT-TA-TTATTATTTTTAAT
258707 TTTATT
1 TTTATT
258713 TTAATTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.23
22 14 0.54
23 6 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTATTATTATTATTTTTAAT
Found at i:261548 original size:154 final size:154
Alignment explanation
Indices: 260347--261618 Score: 897
Period size: 154 Copynumber: 8.3 Consensus size: 154
260337 TTTTAAAACT
* * * ** ** * * *
260347 GAGTCCTAAGTAGTCACTAAGTTGCTTTTACACCAAAGGTGTACATTTAAGATAGGTTAATCCCT
1 GAGTCCTAGGTAGTCACCAGGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCAT-CCT
* ** * * * *
260412 TTTATAATCTTTTTGTGTCCTTTAGGAG-TACTAAGATATTTTCTTC--TCAAAAGTATA-GTCC
65 TTTATGATCTTTTCATGTCCTTTAGG-GTTACCAAGATACTTTC-ACGATC-AAAGTATACCT-C
** * *
260473 AATAGTATTTTGGTAATTTCCCTAAAATT
126 AGGAGTATTTTGGTAATTTCCATAAAATC
* * * ** * *
260502 GGGTCCTAAGTAGTCATC-GAGTCGTTTTTATGCCAAAGGTGTGCATATAGGATAGGTTCACCCT
1 GAGTCCTAGGTAGTCACCAG-GTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCT
** * * * *
260566 TTTAT-ATCTTTTTGTGTCCTTTAAGTTTACCAAGATACTTTCATG-TCGAATA-TATACCTGAG
65 TTTATGATCTTTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATC-AA-AGTATACCTCAG
* *
260628 GA-TATTGTGGTAA-TTCAATAAAATC
128 GAGTATTTTGGTAATTTCCATAAAATC
* * ** * * *
260653 GAGTCCTAGGTAGTCACCAGGTCATTTTTACGATAAAGGTGTGCATTTAGTATAGGTTCACCCTC
1 GAGTCCTAGGTAGTCACCAGGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTT
* * * * * *
260718 TTAGGTTTATTTTCATGTCCTTTAGGGTTACCAAGACACTTTTA-TATCAAAGGTATACCAT-AG
66 TTATG-ATCTTTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATCAAA-GTATACC-TCAG
* *
260781 GAGTATTTTGGTAATTTTTC-TAAAATT
128 GAGTATTTTGGTAA-TTTCCATAAAATC
* * * ** * * * *
260808 GAGTCCTAGGTAGTC-GCTGATTTGCTTTTATGCTAATGGTGTGCATTTAGGATAGGTTTATCTT
1 GAGTCCTAGGTAGTCACCAG-GTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCT
* * * * ** *
260872 TTTATGAT-TCTCTCATTTCTTTTAGGGTTATCGGGATACTTTCAC-ATCAAAGTTATACCTCAA
65 TTTATGATCT-TTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATCAAAG-TATACCTCAG
** * *
260935 GAGCCTTTTGGTAATTTCCATAGAACC
128 GAGTATTTTGGTAATTTCCATAAAATC
* * *
260962 GAGTCTTAGGTAGTCATCAGGTCACTTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTT
1 GAGTCCTAGGTAGTCACCAGGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTT
* * * * *
261027 TTATGATCTTTTCACGTCCTTTAAGTTTACCAAGATACTTTCATG-TCGAATA-TATACCTGAGG
66 TTATGATCTTTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATC-AA-AGTATACCTCAGG
* *
261090 A-TATTGTGGTAA-TTCAATAAAATC
129 AGTATTTTGGTAATTTCCATAAAATC
* * ** * * *
261114 GAGTCCTAGGTAGTCACCAGGTCATTTTTACGATAAAGGTGTGCATTTAGTATAGGTTCACCCTC
1 GAGTCCTAGGTAGTCACCAGGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTT
* * * * * * *
261179 GTAGGTTTATTTTCATGTCCTTTAGGGTTACCAAGACACTTTTA-TATCAAAGGTATACCAT-AG
66 TTATG-ATCTTTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATCAAA-GTATACC-TCAG
* *
261242 GAGTATTTTGGTAATTTTTC-TAAAATT
128 GAGTATTTTGGTAA-TTTCCATAAAATC
* * * ** * * * *
261269 GAGTCCTAGGTAGTC-GCTGATTTGCTTTTATGCTAATGGTGTGCATTTAGGATAGGTTTATCTT
1 GAGTCCTAGGTAGTCACCAG-GTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCT
* * * * ** *
261333 TTTATGAT-TCTCTCATTTCTTTTAGGGTTATCGGGATACTTTCAC-ATCAAAGTTATACCTCAA
65 TTTATGATCT-TTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATCAAAG-TATACCTCAG
** * *
261396 GAGCCTTTTGGTAATTTCCATAGAACC
128 GAGTATTTTGGTAATTTCCATAAAATC
* * *
261423 GAGTCTTAGGTAGTCATCAGGTCACTTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTT
1 GAGTCCTAGGTAGTCACCAGGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTT
* * * * * *
261488 TTATGATCTTTTCACGTCTTTTAAGGTTACCAAGATACTTTCACGCTGAAAGTATGCCTCATGGA
66 TTATGATCTTTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATCAAAGTATACCTCA-GGA
* * * * * *
261553 -CACTTTGGTAATTTTCTTAGAACC
130 GTATTTTGGTAATTTCCATAAAATC
* * * * *
261577 AAGTCTTAGGTAGTCACTAGGTCACTTTTATGTCGAAGGTGT
1 GAGTCCTAGGTAGTCACCAGGTCACTTTTATGCCAAAGGTGT
261619 ATGTTTAGGA
Statistics
Matches: 874, Mismatches: 199, Indels: 89
0.75 0.17 0.08
Matches are distributed among these distances:
151 67 0.08
152 82 0.09
153 149 0.17
154 394 0.45
155 177 0.20
156 5 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (154 bp):
GAGTCCTAGGTAGTCACCAGGTCACTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTT
TTATGATCTTTTCATGTCCTTTAGGGTTACCAAGATACTTTCACGATCAAAGTATACCTCAGGAG
TATTTTGGTAATTTCCATAAAATC
Found at i:261721 original size:461 final size:461
Alignment explanation
Indices: 260527--261530 Score: 1929
Period size: 461 Copynumber: 2.2 Consensus size: 461
260517 ATCGAGTCGT
* * ***
260527 TTTTATGCCAAAGGTGTGCATATAGGATAGGTTCACCCTTTTAT-ATCTTTTTGTGTCCTTTAAG
1 TTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTTTTATGATCTTTTCACGTCCTTTAAG
260591 TTTACCAAGATACTTTCATGTCGAATATATACCTGAGGATATTGTGGTAATTCAATAAAATCGAG
66 TTTACCAAGATACTTTCATGTCGAATATATACCTGAGGATATTGTGGTAATTCAATAAAATCGAG
260656 TCCTAGGTAGTCACCAGGTCATTTTTACGATAAAGGTGTGCATTTAGTATAGGTTCACCCTCTTA
131 TCCTAGGTAGTCACCAGGTCATTTTTACGATAAAGGTGTGCATTTAGTATAGGTTCACCCTCTTA
260721 GGTTTATTTTCATGTCCTTTAGGGTTACCAAGACACTTTTATATCAAAGGTATACCATAGGAGTA
196 GGTTTATTTTCATGTCCTTTAGGGTTACCAAGACACTTTTATATCAAAGGTATACCATAGGAGTA
260786 TTTTGGTAATTTTTCTAAAATTGAGTCCTAGGTAGTCGCTGATTTGCTTTTATGCTAATGGTGTG
261 TTTTGGTAATTTTTCTAAAATTGAGTCCTAGGTAGTCGCTGATTTGCTTTTATGCTAATGGTGTG
260851 CATTTAGGATAGGTTTATCTTTTTATGATTCTCTCATTTCTTTTAGGGTTATCGGGATACTTTCA
326 CATTTAGGATAGGTTTATCTTTTTATGATTCTCTCATTTCTTTTAGGGTTATCGGGATACTTTCA
260916 CATCAAAGTTATACCTCAAGAGCCTTTTGGTAATTTCCATAGAACCGAGTCTTAGGTAGTCATCA
391 CATCAAAGTTATACCTCAAGAGCCTTTTGGTAATTTCCATAGAACCGAGTCTTAGGTAGTCATCA
260981 GGTCAC
456 GGTCAC
260987 TTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTTTTATGATCTTTTCACGTCCTTTAAG
1 TTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTTTTATGATCTTTTCACGTCCTTTAAG
261052 TTTACCAAGATACTTTCATGTCGAATATATACCTGAGGATATTGTGGTAATTCAATAAAATCGAG
66 TTTACCAAGATACTTTCATGTCGAATATATACCTGAGGATATTGTGGTAATTCAATAAAATCGAG
*
261117 TCCTAGGTAGTCACCAGGTCATTTTTACGATAAAGGTGTGCATTTAGTATAGGTTCACCCTCGTA
131 TCCTAGGTAGTCACCAGGTCATTTTTACGATAAAGGTGTGCATTTAGTATAGGTTCACCCTCTTA
261182 GGTTTATTTTCATGTCCTTTAGGGTTACCAAGACACTTTTATATCAAAGGTATACCATAGGAGTA
196 GGTTTATTTTCATGTCCTTTAGGGTTACCAAGACACTTTTATATCAAAGGTATACCATAGGAGTA
261247 TTTTGGTAATTTTTCTAAAATTGAGTCCTAGGTAGTCGCTGATTTGCTTTTATGCTAATGGTGTG
261 TTTTGGTAATTTTTCTAAAATTGAGTCCTAGGTAGTCGCTGATTTGCTTTTATGCTAATGGTGTG
261312 CATTTAGGATAGGTTTATCTTTTTATGATTCTCTCATTTCTTTTAGGGTTATCGGGATACTTTCA
326 CATTTAGGATAGGTTTATCTTTTTATGATTCTCTCATTTCTTTTAGGGTTATCGGGATACTTTCA
261377 CATCAAAGTTATACCTCAAGAGCCTTTTGGTAATTTCCATAGAACCGAGTCTTAGGTAGTCATCA
391 CATCAAAGTTATACCTCAAGAGCCTTTTGGTAATTTCCATAGAACCGAGTCTTAGGTAGTCATCA
261442 GGTCAC
456 GGTCAC
*
261448 TTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTTTTATGATCTTTTCACGTCTTTTAAG
1 TTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTTTTATGATCTTTTCACGTCCTTTAAG
*
261513 GTTACCAAGATACTTTCA
66 TTTACCAAGATACTTTCA
261531 CGCTGAAAGT
Statistics
Matches: 535, Mismatches: 8, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
460 42 0.08
461 493 0.92
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (461 bp):
TTTTATGCCAAAGGTGTGCATGTAGGATAGGTTCATCCTTTTATGATCTTTTCACGTCCTTTAAG
TTTACCAAGATACTTTCATGTCGAATATATACCTGAGGATATTGTGGTAATTCAATAAAATCGAG
TCCTAGGTAGTCACCAGGTCATTTTTACGATAAAGGTGTGCATTTAGTATAGGTTCACCCTCTTA
GGTTTATTTTCATGTCCTTTAGGGTTACCAAGACACTTTTATATCAAAGGTATACCATAGGAGTA
TTTTGGTAATTTTTCTAAAATTGAGTCCTAGGTAGTCGCTGATTTGCTTTTATGCTAATGGTGTG
CATTTAGGATAGGTTTATCTTTTTATGATTCTCTCATTTCTTTTAGGGTTATCGGGATACTTTCA
CATCAAAGTTATACCTCAAGAGCCTTTTGGTAATTTCCATAGAACCGAGTCTTAGGTAGTCATCA
GGTCAC
Found at i:268482 original size:15 final size:15
Alignment explanation
Indices: 268462--268492 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
268452 TATCCCAAAT
268462 CATAAATAAATGTGA
1 CATAAATAAATGTGA
268477 CATAAATAAATGTGA
1 CATAAATAAATGTGA
268492 C
1 C
268493 CTGATATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (15 bp):
CATAAATAAATGTGA
Found at i:271495 original size:76 final size:76
Alignment explanation
Indices: 271376--271573 Score: 222
Period size: 76 Copynumber: 2.6 Consensus size: 76
271366 TTATCAGTTT
* * *
271376 GTTTCGGCTATTGATGGAAATTTAGAAACCACATA-TTCTCCATCATGCTCTTCTTATCTAGCTT
1 GTTTCGGCTATCGATGGAAATTTAGAAACCATATATTTCTCCATCATGCTCTTCTTATCCAGCTT
271440 GTTATCAAATC
66 GTTATCAAATC
* * * * * *
271451 GTTTTGGCTATGGATGAAAATGTTAGAAACCATATATTTC-CCATCGTGCTTTTCTTCTCCAGCT
1 GTTTCGGCTATCGATGGAAAT-TTAGAAACCATATATTTCTCCATCATGCTCTTCTTATCCAGCT
*
271515 TGTTATCAGATC
65 TGTTATCAAATC
* * * * *
271527 ATTTCAGTTGTCGATGGAAATTTTAGAAACCATATA-TTCTCAATCAT
1 GTTTCGGCTATCGATGGAAA-TTTAGAAACCATATATTTCTCCATCAT
271574 TTTTTTCTTT
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
75 21 0.21
76 76 0.75
77 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (76 bp):
GTTTCGGCTATCGATGGAAATTTAGAAACCATATATTTCTCCATCATGCTCTTCTTATCCAGCTT
GTTATCAAATC
Found at i:271590 original size:76 final size:76
Alignment explanation
Indices: 271354--271590 Score: 210
Period size: 76 Copynumber: 3.1 Consensus size: 76
271344 CTACTATGTT
* ** ** * * *
271354 TTTTTCAGCTCGTTATCAGTTTGTTTCGGCTATTGATGGAAA-TTTAGAAACCACATATTCTCCA
1 TTTTTCAGCTTGTTATCAAATCATTTCAGCTATCGATGGAAATTTTAGAAACCATATATTCTCCA
*
271418 TCATGCTCTTC
66 TCATGCTTTTC
* * ** * * *
271429 -TTATCTAGCTTGTTATCAAATCGTTTTGGCTATGGATGAAAATGTTAGAAACCATATATT-TCC
1 TTTTTC-AGCTTGTTATCAAATCATTTCAGCTATCGATGGAAATTTTAGAAACCATATATTCT-C
*
271492 CATCGTGCTTTTC
64 CATCATGCTTTTC
* * * * * *
271505 TTCTCCAGCTTGTTATCAGATCATTTCAGTTGTCGATGGAAATTTTAGAAACCATATATTCTCAA
1 TTTTTCAGCTTGTTATCAAATCATTTCAGCTATCGATGGAAATTTTAGAAACCATATATTCTCCA
**
271570 TCATTTTTTTC
66 TCATGCTTTTC
271581 TTTTTCAGCT
1 TTTTTCAGCT
271591 CTTAGATGAT
Statistics
Matches: 127, Mismatches: 30, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
74 4 0.03
75 30 0.24
76 90 0.71
77 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (76 bp):
TTTTTCAGCTTGTTATCAAATCATTTCAGCTATCGATGGAAATTTTAGAAACCATATATTCTCCA
TCATGCTTTTC
Found at i:272091 original size:40 final size:40
Alignment explanation
Indices: 272017--272104 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
272007 TTTCATCTAG
** * * *
272017 GTCAACCTTTCTCATTTGTTGACTTGTAGGTTTTATCCCA
1 GTCAACCCCTCTCATTAGTTGACTTATAGATTTTATCCCA
* *
272057 GTCAACCCCTCTCATTAGTTGACTTATCGATTTTATCTCA
1 GTCAACCCCTCTCATTAGTTGACTTATAGATTTTATCCCA
*
272097 ATCAACCC
1 GTCAACCC
272105 TTCACTCTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.40
Consensus pattern (40 bp):
GTCAACCCCTCTCATTAGTTGACTTATAGATTTTATCCCA
Found at i:272404 original size:40 final size:40
Alignment explanation
Indices: 272360--272458 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
272350 TAACTTGTTG
* *
272360 ACTTATCA-ATTTCATCCCAATCAGCCCTTCTCGTTTGGTA
1 ACTTAT-AGATTTCATCCCAATCAACCCTTCTCATTTGGTA
* ** *
272400 ACTTATAGGTTTTGTCCCAATCAACCCTTCTCATTTGTTA
1 ACTTATAGATTTCATCCCAATCAACCCTTCTCATTTGGTA
* *
272440 ACTTATAGGTTTCGTCCCA
1 ACTTATAGATTTCATCCCA
272459 TTCGTTGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.02
40 50 0.98
ACGTcount: A:0.22, C:0.27, G:0.11, T:0.39
Consensus pattern (40 bp):
ACTTATAGATTTCATCCCAATCAACCCTTCTCATTTGGTA
Found at i:272500 original size:40 final size:39
Alignment explanation
Indices: 272456--272624 Score: 133
Period size: 40 Copynumber: 4.2 Consensus size: 39
272446 AGGTTTCGTC
* * * *
272456 CCATTCGTTGACTTGTGGGTTTTGTCTTGGTCAACATTTT
1 CCATTCGTTGACTTGTAGGTTTCGTCCTGGTCAAC-CTTT
* * *
272496 CCATTCATTGACTTGTAGGTTTCATCCTAGTCAACCTTT
1 CCATTCGTTGACTTGTAGGTTTCGTCCTGGTCAACCTTT
* * *
272535 CTCA-TCTGTTGACTCGTAAGTTTCGTCTTGGTCAACCCTTT
1 C-CATTC-GTTGACTTGTAGGTTTCGTCCTGGTCAA-CCTTT
* * * * * * *
272576 CCATTTGTTAACTTGTCGATTTTGTCCAGGTCAACTCTAT
1 CCATTCGTTGACTTGTAGGTTTCGTCCTGGTCAAC-CTTT
272616 CCATTCGTT
1 CCATTCGTT
272625 AAACTTGTCG
Statistics
Matches: 100, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
39 7 0.07
40 86 0.86
41 7 0.07
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (39 bp):
CCATTCGTTGACTTGTAGGTTTCGTCCTGGTCAACCTTT
Found at i:272626 original size:40 final size:41
Alignment explanation
Indices: 272564--272641 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
272554 GTTTCGTCTT
* *
272564 GGTCAACCCTTTCCATTTGTT-AACTTGTCGATTTTGTCCA
1 GGTCAACCCTATCCATTCGTTAAACTTGTCGATTTTGTCCA
*
272604 GGTCAACTCTATCCATTCGTTAAACTTGTCGATTTTGT
1 GGTCAACCCTATCCATTCGTTAAACTTGTCGATTTTGT
272642 TCGAGTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 18 0.53
41 16 0.47
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (41 bp):
GGTCAACCCTATCCATTCGTTAAACTTGTCGATTTTGTCCA
Found at i:272708 original size:40 final size:40
Alignment explanation
Indices: 272664--272753 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
272654 TTCTTATCTA
*
272664 TTGACTTATCGATGTTGTCTCGATCAACTCTTCCCATTCT-
1 TTGACTTATCGATGTTGTCCCGATCAACTCTTCCCATT-TG
* * * * * *
272704 TTGACTTGTAGGTTTTGTCCCGGTCAACTCTTTCCATTTG
1 TTGACTTATCGATGTTGTCCCGATCAACTCTTCCCATTTG
272744 TTGACTTATC
1 TTGACTTATC
272754 AATTTTTCCT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (40 bp):
TTGACTTATCGATGTTGTCCCGATCAACTCTTCCCATTTG
Found at i:272877 original size:63 final size:65
Alignment explanation
Indices: 272755--272905 Score: 152
Period size: 63 Copynumber: 2.4 Consensus size: 65
272745 TGACTTATCA
* * * *
272755 ATTTTTCCTTGGTCAACCTCTTTAGACCTAGGATTATATCCTTGTCACCTTCATTGACTATAGCG
1 ATTTTACCTTGGTCAACCTCTCTAAACCTAGGATTACATCCTTGTCACCTTCATTGACTATAGCG
272820 ATTTTACCTT-GTCAACCT-TCTAAACCTAGG-TTACAT-CTTGGTCATCC-TCATTTGACTATA
1 ATTTTACCTTGGTCAACCTCTCTAAACCTAGGATTACATCCTT-GTCA-CCTTCA-TTGACTATA
*
272880 TCG
63 GCG
* ** *
272883 GTTTCGCCTTGGTCAGCCT-TCTA
1 ATTTTACCTTGGTCAACCTCTCTA
272906 GACTTTATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
61 3 0.04
62 12 0.16
63 30 0.41
64 19 0.26
65 9 0.12
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (65 bp):
ATTTTACCTTGGTCAACCTCTCTAAACCTAGGATTACATCCTTGTCACCTTCATTGACTATAGCG
Found at i:274162 original size:18 final size:17
Alignment explanation
Indices: 274119--274165 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
274109 TTTATGATTA
274119 TTAATTTTATTTTTATTTT
1 TTAATTTTA--TTTATTTT
274138 TT-A-TTTATTTATTGTT
1 TTAATTTTATTTATT-TT
274154 TTAATTTTATTT
1 TTAATTTTATTT
274166 TAATTGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.24
16 4 0.16
17 5 0.20
18 8 0.32
19 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTAATTTTATTTATTTT
Found at i:274166 original size:11 final size:11
Alignment explanation
Indices: 274119--274170 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
274109 TTTATGATTA
274119 TTAATTTTATT
1 TTAATTTTATT
* *
274130 TTTATTTTTTAT
1 TTAATTTTAT-T
* *
274142 TTATTTATTGTT
1 TTAATT-TTATT
274154 TTAATTTTATT
1 TTAATTTTATT
274165 TTAATT
1 TTAATT
274171 GAGATTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 18 0.56
12 11 0.34
13 3 0.09
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (11 bp):
TTAATTTTATT
Found at i:274927 original size:308 final size:303
Alignment explanation
Indices: 274319--275091 Score: 821
Period size: 308 Copynumber: 2.5 Consensus size: 303
274309 GTTGAAGGTT
* * *
274319 TACCTTAGGGGCATTTTGATAATTTCTCTAGAATCGAGTCTTAGGTAGTCACTATGTCAG-TTTT
1 TACCTTAAGGGCATTTTG-TAATTTCTCTAGAATCGAGTCTTAGGTAGTCACCAAGTC-GTTTTT
* * * * *
274383 ATGCCAAAGGTGTGAATTTAAGATAGGTTCATCCTTTGATGATCTGTTTTGTGTCTTTTAGATTT
64 ATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTTT-ATGATCT-TTTTATGTCCTTTAGAGTT
* ** * * * *
274448 ACCAGAATACTTTCATATCAAAGGTATACCCTAAGGGCAGTTTTAGTCATTTTATTAAATCAAGT
127 A-CAGAATACTTTCACATCAAAAATATACCATAAGAGCAGTTTTAGTAAATTTATTAAATCAAGT
* *
274513 CTTAGGTAGTCATCGAGTCATTTTTATGCCAAAAGTGTGCATTTAGGATAGATTCATCCTTTTAT
191 ATTAGGTAGTCATCGAGTCATTTTTATGCCAAAAGTGTGCATTTAGGATAGATTCATCCTTCTAT
* ** * *
274578 GATCTTTTCGTCTCTTTTAGGGTTATCTTAATACTTTCACATCGAA-GTTA
256 GATCTTTTCGTCTCCTTTAAAGTTA-CTTAATACGTTCACAT--AATGGTA
* *
274628 TACCTTAAGGGCATTTTAGTAATTTGT-TAGAATCGAGTCTTAAGTAGTCACCAAGTCGTTTTTA
1 TACCTTAAGGGCATTTT-GTAATTTCTCTAGAATCGAGTCTTAGGTAGTCACCAAGTCGTTTTTA
*
274692 TGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTTTCATAATCTTTTTATGTCCTTTAGAGTTA-
65 TGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTTT-ATGATCTTTTTATGTCCTTTAGAGTTAC
* * *
274756 ATGAGATACTTTTACATCAAAAATATACCATAAGAGCA-TTTTGGTAAATTTATTATAATCGAGT
129 A-GA-ATACTTTCACATCAAAAATATACCATAAGAGCAGTTTTAGTAAATTTATTA-AATCAAGT
* ** *
274820 ATTAGGTAGTCATC-AGGTCGTTTTTATGCTGAAAGTGTGCGTTTAGGATAGATTCA-CCTTCCT
191 ATTAGGTAGTCATCGA-GTCATTTTTATGCCAAAAGTGTGCATTTAGGATAGATTCATCCTT-CT
* * *
274883 A-GGTCCATTTTTGTGTCCTTTAAAGTTA-TTAGGATACGTTCACATAATGGTA
254 ATGAT-C-TTTTCGTCTCCTTTAAAGTTACTTA--ATACGTTCACATAATGGTA
* * * * * * * * * * *
274935 TACCCTAAAGGTATTTTGGTAATTTCTCTA-AAACTAAGCCCTAGGTAGTTATCGAGTCATTTTT
1 TACCTTAAGGGCATTTT-GTAATTTCTCTAGAATC-GAGTCTTAGGTAGTCACCAAGTCGTTTTT
274999 ATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCATTTATGATCTTTTTATGTCCTTTAGTA-TT
64 ATGCCAAAGGTGTGCATTTAGGATAGGTTCATCC-TTTATGATCTTTTTATGTCCTTTAG-AGTT
* *
275063 ACCAAAATACTTTCACGTCAAAAATATAC
127 A-CAGAATACTTTCACATCAAAAATATAC
275092 TTAAAGGGTA
Statistics
Matches: 392, Mismatches: 54, Indels: 37
0.81 0.11 0.08
Matches are distributed among these distances:
305 1 0.00
306 28 0.07
307 132 0.34
308 201 0.51
309 28 0.07
310 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (303 bp):
TACCTTAAGGGCATTTTGTAATTTCTCTAGAATCGAGTCTTAGGTAGTCACCAAGTCGTTTTTAT
GCCAAAGGTGTGCATTTAGGATAGGTTCATCCTTTATGATCTTTTTATGTCCTTTAGAGTTACAG
AATACTTTCACATCAAAAATATACCATAAGAGCAGTTTTAGTAAATTTATTAAATCAAGTATTAG
GTAGTCATCGAGTCATTTTTATGCCAAAAGTGTGCATTTAGGATAGATTCATCCTTCTATGATCT
TTTCGTCTCCTTTAAAGTTACTTAATACGTTCACATAATGGTA
Found at i:275102 original size:154 final size:153
Alignment explanation
Indices: 274327--275165 Score: 673
Period size: 154 Copynumber: 5.4 Consensus size: 153
274317 TTTACCTTAG
* * * * *
274327 GGGCATTTTGATAATTTCTCTAGAATCGAGTCTTAGGTAGTCA-CTATGTCAGTTTTATGCCAAA
1 GGGCATTTTGGTAATTTCT-TAAAATCAAGTCTTAGGTAGTCATCGA-GTCATTTTTATGCCAAA
* * * * *
274391 GGTGTGAATTTAAGATAGGTTCATCCTTTGATGATCTGTTTTGTGTCTTTTAGATTTACCAGAAT
64 GGTGTGCATTTAGGATAGGTTCATCCTTT-ATGATCT-TTTTGTGTCCTTTAGAGTTACCAAAAT
* *
274456 ACTTTCATATCAAAGGTATACCCT-AA
127 ACTTTCACATCAAAGATATACCCTAAA
* * *
274482 GGGCAGTTTTAGTCATTT-TATTAAATCAAGTCTTAGGTAGTCATCGAGTCATTTTTATGCCAAA
1 GGGCA-TTTTGGTAATTTCT-TAAAATCAAGTCTTAGGTAGTCATCGAGTCATTTTTATGCCAAA
* * * * * * * **
274546 AGTGTGCATTTAGGATAGATTCATCCTTTTATGATCTTTTCGTCTCTTTTAGGGTTATCTTAATA
64 GGTGTGCATTTAGGATAGGTTCATCC-TTTATGATCTTTTTGTGTCCTTTAGAGTTACCAAAATA
* * *
274611 CTTTCACATCGAAGTTATA-CCTTAA
128 CTTTCACATCAAAGATATACCCTAAA
* * * * * * * *
274636 GGGCATTTTAGTAATTTGTTAGAATCGAGTCTTAAGTAGTCACCAAGTCGTTTTTATGCCAAAGG
1 GGGCATTTTGGTAATTTCTTAAAATCAAGTCTTAGGTAGTCATCGAGTCATTTTTATGCCAAAGG
* * *** *
274701 TGTGCATTTAGGATAGGTTCATCCTTTCATAATCTTTTTATGTCCTTTAGAGTTAATGAGATACT
66 TGTGCATTTAGGATAGGTTCATCCTTT-ATGATCTTTTTGTGTCCTTTAGAGTTACCAAAATACT
* * *
274766 TTTACATCAAAAATATACCAT-AA
130 TTCACATCAAAGATATACCCTAAA
* * * * * * *
274789 GAGCATTTTGGTAAATTTATTATAATCGAGTATTAGGTAGTCATC-AGGTCGTTTTTATGCTGAA
1 GGGCATTTTGGT-AATTTCTTAAAATCAAGTCTTAGGTAGTCATCGA-GTCATTTTTATGC-CAA
* * * * ** *
274853 A-GTGTGCGTTTAGGATAGATTCA-CCTTCCTA-GGTCCATTTTTGTGTCCTTTAAAGTTATTAG
63 AGGTGTGCATTTAGGATAGGTTCATCCTT--TATGAT-C-TTTTTGTGTCCTTTAGAGTTACCAA
* * * *
274915 GATACGTTCACAT-AATGGTATACCCTAAA
124 AATACTTTCACATCAAAGATATACCCTAAA
* * * *
274944 -GGTATTTTGGTAATTTCTCTAAAA-CTAAGCCCTAGGTAGTTATCGAGTCATTTTTATGCCAAA
1 GGGCATTTTGGTAATTTCT-TAAAATC-AAGTCTTAGGTAGTCATCGAGTCATTTTTATGCCAAA
*
275007 GGTGTGCATTTAGGATAGGTTCATCCATTTATGATCTTTTTATGTCCTTTAGTA-TTACCAAAAT
64 GGTGTGCATTTAGGATAGGTTCATCC-TTTATGATCTTTTTGTGTCCTTTAG-AGTTACCAAAAT
* * *
275071 ACTTTCACGTCAAAAATATA-CTTAAA
127 ACTTTCACATCAAAGATATACCCTAAA
* * * * * * * * *
275097 GGGTATTTTGATAATTTCTTTAGAAA-CAAGCCCTAGGTAGTCGTTGGGTCACTTTTATGTCAAA
1 GGGCATTTTGGTAATTTC-TTA-AAATCAAGTCTTAGGTAGTCATCGAGTCATTTTTATGCCAAA
275161 GGTGT
64 GGTGT
275166 ATGTTTAGGA
Statistics
Matches: 552, Mismatches: 105, Indels: 55
0.78 0.15 0.08
Matches are distributed among these distances:
152 3 0.01
153 175 0.32
154 240 0.43
155 118 0.21
156 16 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (153 bp):
GGGCATTTTGGTAATTTCTTAAAATCAAGTCTTAGGTAGTCATCGAGTCATTTTTATGCCAAAGG
TGTGCATTTAGGATAGGTTCATCCTTTATGATCTTTTTGTGTCCTTTAGAGTTACCAAAATACTT
TCACATCAAAGATATACCCTAAA
Found at i:280936 original size:22 final size:21
Alignment explanation
Indices: 280911--280994 Score: 64
Period size: 22 Copynumber: 4.0 Consensus size: 21
280901 TTAAAAAAAG
280911 ATCAATCATTTTGAAAAATGAA
1 ATCAATCATTTTGAAAAATG-A
* *
280933 ATCAATCTATCTT-AAAAAAGA
1 ATCAATC-ATTTTGAAAAATGA
* * *
280954 CTC-ATCATTTTTAAAAATGT
1 ATCAATCATTTTGAAAAATGA
* *
280974 ATTAATCCTTCTTGAAAAATG
1 ATCAATCATT-TTGAAAAATG
280995 GAATAGTCCC
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.08
20 10 0.21
21 8 0.17
22 22 0.46
23 4 0.08
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (21 bp):
ATCAATCATTTTGAAAAATGA
Found at i:281300 original size:30 final size:29
Alignment explanation
Indices: 281246--281306 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
281236 ATCTATCTCT
*
281246 TTAACCTTTAAATGTATATAAATAAGTCA
1 TTAACCTTTAAATGTATATAAATAAGCCA
*
281275 TTAACCTTT-AATTTATATCTAAATAAGCCA
1 TTAACCTTTAAATGTATA--TAAATAAGCCA
281305 TT
1 TT
281307 TCTTTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 9 0.32
30 12 0.43
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (29 bp):
TTAACCTTTAAATGTATATAAATAAGCCA
Found at i:284774 original size:14 final size:15
Alignment explanation
Indices: 284751--284779 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
284741 TATTAAATGA
284751 TATATAATTTATTAT
1 TATATAATTTATTAT
284766 TATAT-ATTTATTAT
1 TATATAATTTATTAT
284780 GATTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATAATTTATTAT
Found at i:285103 original size:25 final size:26
Alignment explanation
Indices: 285049--285103 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
285039 GTTTGTCAAT
*
285049 TATATAATATATATTAATTTTGTATT
1 TATATAATATATATTAATTTTGTATA
285075 TATATAA-ATCATA-TAATTTT-TATCA
1 TATATAATAT-ATATTAATTTTGTAT-A
285100 TATA
1 TATA
285104 AAAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 3 0.12
25 13 0.50
26 10 0.38
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
TATATAATATATATTAATTTTGTATA
Found at i:295117 original size:39 final size:42
Alignment explanation
Indices: 295073--295153 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
295063 TTAATCAGTG
295073 GAATAAAAT-G-AGAATAA-ATAGTACATAT-TTTTGTTGATC
1 GAATAAAATAGAAGAATAAGATAGTACAT-TGTTTTGTTGATC
*
295112 GAATAAAATAGAAGAATAATGATATTACATTGTTTTGTTGAT
1 GAATAAAATAGAAGAATAA-GATAGTACATTGTTTTGTTGAT
295154 TAAATTATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
39 9 0.25
40 1 0.03
41 7 0.19
42 1 0.03
43 18 0.50
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (42 bp):
GAATAAAATAGAAGAATAAGATAGTACATTGTTTTGTTGATC
Found at i:295306 original size:30 final size:29
Alignment explanation
Indices: 295258--295314 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
295248 TTATTAATCC
295258 TTTAAATATATTAAATATAAATTTTAAAAT
1 TTTAAATATATTAAATAT-AATTTTAAAAT
* *
295288 TTTAATTAT-TTAATATATATTTTTAAA
1 TTTAAATATATTAA-ATATAATTTTAAA
295315 TAAAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAAATATATTAAATATAATTTTAAAAT
Found at i:296955 original size:19 final size:18
Alignment explanation
Indices: 296911--296958 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
296901 AATATTAAAG
*
296911 AAAATAAATTTTAAAAAT
1 AAAATAAATTATAAAAAT
** *
296929 AATTTAAAGTTATAAAATT
1 AAAATAAA-TTATAAAAAT
296948 AAAATAAATTA
1 AAAATAAATTA
296959 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATAAATTATAAAAAT
Found at i:299230 original size:13 final size:13
Alignment explanation
Indices: 299212--299237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
299202 AATTTTTTTG
299212 TGTATCGATACAT
1 TGTATCGATACAT
299225 TGTATCGATACAT
1 TGTATCGATACAT
299238 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:301797 original size:13 final size:13
Alignment explanation
Indices: 301779--301804 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
301769 ATAATCACCC
301779 TGTATCGATACAA
1 TGTATCGATACAA
301792 TGTATCGATACAA
1 TGTATCGATACAA
301805 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:303901 original size:15 final size:15
Alignment explanation
Indices: 303881--303911 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
303871 ATTTCGTTTG
*
303881 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
303896 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
303911 G
1 G
303912 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:305743 original size:21 final size:21
Alignment explanation
Indices: 305714--305758 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
305704 AAGTTTTCAT
*
305714 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
305734 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
305756 TTT
1 TTT
305759 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:308008 original size:13 final size:13
Alignment explanation
Indices: 307990--308015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307980 AATTTTTTTG
307990 TGTATCGATACAT
1 TGTATCGATACAT
308003 TGTATCGATACAT
1 TGTATCGATACAT
308016 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:311176 original size:62 final size:62
Alignment explanation
Indices: 311109--312319 Score: 1234
Period size: 62 Copynumber: 19.6 Consensus size: 62
311099 TTTTAACCTT
* *
311109 TTTAGTCCCCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * ** ** * **
311171 TTTAGTCCTTAAAAAGCAGGATACCTTTTTCTTTTTGAAGCCCACACGAGTAGGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* ** * *
311233 TTTAGTCCTCAAAGAGTAGGACATCTTTTTCTTTT-AAAGCTCACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * * *
311294 TTTAGTCCTTAAA-AGGCAAGATGCCTTTTCCTTTTCAAAGCCTACACGAGTTGGAGGCACCA
1 TTTAGTCCTCAAAGA-GCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * *
311356 TTTAGTCTTCAAAGTGTAGGATGCCTTTTTCCTTTCAAAGCCTACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * *
311418 TTTTGTCCTC-ACGAGTAGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CC
** * * *
311480 TTTA-TCCTCAAAGAGCAGGACATCTTTTTCTTTT-AAAGCCTATACGAGTTGATGGCA-CC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * *
311539 TTCTAGTCCTCAAAGAGCAGGACGCTTTTTTC-TTTAAAAGCTCACACGAGTTGGTGGCACCC
1 TT-TAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * * * *
311601 TTTTGTTCTCAAAGAGCAGGATGTCTTTTTTTTTTTCAAAACCTACACGAGTTGGTGGCATCC
1 TTTAGTCCTCAAAGAGCAGGACG-CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * * * *
311664 TTTTGTCCTTAAAGAGCAAGATGCATTTTTCTTTTCAAAGCCCACATGAGTTGGTGACACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * * * *
311726 TTTAGTCCTCAAAGAGTATGACACATTTTTCTTTTCAAAGCCCACATGAGTTAGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * *
311788 TTTAGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGGCATCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * *** * * * *
311850 TTTTGTCTTCAAAAAGCAGGACATTTTTTTCGTTTCAAAGCCTAAACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * *
311912 TTTAGTCCTCAAAGAGCA-AAAGCCTTTTTCTTTTCGAAGCCCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * *
311973 TTTAGTCCTTAAAGAGTAGGACGCCTTTTCCTTTTGAAAGCCCACACGAGTTAGTGTCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * ** *
312035 TTTAGTCTTCAAAAAGCGGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCATCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * ** * **
312097 TTTTGTCCTTAAAGAGCAAGACGCC-TTTTCATTTTCAAAGCTTACACGAGTTGGTGGTACTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * ***
312159 TTTAATCCTTAAAGAGCAGGACGCCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTGTCC
1 TTTAGTCCTCAAAGAGCAGGACGCC-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * ** *
312222 TTTTGTCCTTAAAGAGCAGGATGCTTTTTTCTTTTCAAAGCTAACATGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * *
312284 TTTAGTCCTCAATGAGCATGACGCATTTTCCTTTTC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTC
312320 CTTTTGTCCT
Statistics
Matches: 943, Mismatches: 191, Indels: 30
0.81 0.16 0.03
Matches are distributed among these distances:
59 3 0.00
60 6 0.01
61 230 0.24
62 608 0.64
63 91 0.10
64 5 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (62 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
Found at i:311428 original size:185 final size:185
Alignment explanation
Indices: 311119--312319 Score: 1248
Period size: 185 Copynumber: 6.5 Consensus size: 185
311109 TTTAGTCCCC
*** * *
311119 AAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTTAAA
1 AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCA-CCTTTAGTCCTCAAA
* ** ** * *
311184 AAGCAGGATACCTTTTTCTTTTTGAAGCCCACACGAGTAGGTGGCACTTTTTAGTCCTCAAAGAG
65 GAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAG
** *
311249 TAGGACATCTTTTTCTTTT-AAAGCTCACACGAGTTGGTGGCACCTTTTAGTCCTTA
130 TAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTT-GTCCTTA
* * * * *
311305 AAAG-GCAAGATGCCTTTTCCTTTTCAAAGCCTACACGAGTTGGAGGCACCATTTAGTCTTCAAA
1 AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACC-TTTAGTCCTCAAA
* * * * * *
311369 GTGTAGGATGCCTTTTTCCTTTCAAAGCCTACACGAGTTGGTGGCACCCTTTT-GTCCTC-ACGA
65 GAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGA
* * *
311432 GTAGGACGCCTTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTCTTTTATCC-TC
129 GTAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CTTTTGTCCTTA
* * * *
311489 AAAGAGCAGGACATCTTTTTCTTTT-AAAGCCTATACGAGTTGATGGCACCTTCTAGTCCTCAAA
1 AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCTT-TAGTCCTCAAA
* * * *
311553 GAGCAGGACGCTTTTTTC-TTTAAAAGCTCACACGAGTTGGTGGCACCCTTTT-GTTCTCAAAGA
65 GAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTCAAAGA
* * * * * *
311616 GCAGGATGTCTTTTTTTTTTTCAAAACCTACACGAGTTGGTGGCATCCTTTTGTCCTT-
129 GTAGGACG-CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTGTCCTTA
* * * * * *
311674 AAAGAGCAAGATGCATTTTTCTTTTCAAAGCCCACATGAGTTGGTGACACCTTTTAGTCCTCAAA
1 AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACC-TTTAGTCCTCAAA
* * * * * * *
311739 GAGTATGACACATTTTTCTTTTCAAAGCCCACATGAGTTAGTGGTACCTTTTAGTCCTCAAAGAG
65 GAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAG
* *
311804 TAGGACGCCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGGCATCCTTTTGT-CTTCA
130 TAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTGTCCTT-A
* ** * *
311861 AAA-AGCAGGACATTTTTTTCGTTTCAAAGCCTAAACGAGTTGGTGGCACCTTTTAGTCCTCAAA
1 AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACC-TTTAGTCCTCAAA
* * * * *
311925 GAGCA-AAAGCCTTTTTCTTTTCGAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTTAAAGAG
65 GAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAG
* * * * *
311989 TAGGACGCCTTTTCCTTTTGAAAGCCCACACGAGTTAGTGTCACCCTTTAGT-CTTCA
130 TAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCTTTTGTCCTT-A
* * * *
312046 AAA-AGCGGGATACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCATCCTTTTGTCCTTAAA
1 AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCA-CCTTTAGTCCTCAAA
* ** * * * *
312110 GAGCAAGACGCC-TTTTCATTTTCAAAGCTTACACGAGTTGGTGGTACTTTTTAATCCTTAAAGA
65 GAGCAGGACGCCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGA
* **
312174 GCAGGACGCCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTGTCCTTTTGTCCTT-
129 GTAGGACGCC-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGG-CACCTTTTGTCCTTA
* * *
312232 AAAGAGCAGGATGCTTTTTTCTTTTCAAAG-CTAACATGAGTTGGTGGCACCCTTTAGTCCTCAA
1 AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCT-ACACGAGTTGGTGGCA-CCTTTAGTCCTCAA
* * * *
312296 TGAGCATGACGCATTTTCCTTTTC
64 AGAGCAGGACGCCTTTTTCTTTTC
312320 CTTTTGTCCT
Statistics
Matches: 846, Mismatches: 144, Indels: 49
0.81 0.14 0.05
Matches are distributed among these distances:
183 38 0.04
184 82 0.10
185 355 0.42
186 221 0.26
187 143 0.17
188 7 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (185 bp):
AAAGAGCAGGATACCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTAGTCCTCAAAG
AGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT
AGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTGTCCTTA
Found at i:312373 original size:42 final size:42
Alignment explanation
Indices: 312282--312513 Score: 204
Period size: 42 Copynumber: 5.6 Consensus size: 42
312272 TTGGTGGCAC
* *
312282 CCTTTAGTCCTCAATGAGCATGACGCA---T-TTTCCTTTTC-
1 CCTTT-GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCT
* * *
312320 CTTTTGTCCTCAAAGAGTAGGATGCACTTTATTTCCTTTTCT
1 CCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCT
* * * *
312362 CCTTTGTCCTCAAAGAGCAAGACACATTTTATTTCCTTTTTTT
1 CCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCC-TTTTCT
* * ** * *
312405 CCCTTTGTCTTTAAAGAGCAAAACGCACTTTATTCCCATTTCT
1 -CCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCT
* ** * *
312448 CCTTTGTCCTCAAAGAGTAGGGTGCACTTCATTTCCTTTTTT
1 CCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCT
* *
312490 CCTTTATCCTCGAAGAGCAGGACG
1 CCTTTGTCCTCAAAGAGCAGGACG
312514 TACTCTTTTT
Statistics
Matches: 151, Mismatches: 36, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
37 17 0.11
38 4 0.03
40 1 0.01
41 10 0.07
42 80 0.53
43 9 0.06
44 30 0.20
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (42 bp):
CCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTCT
Found at i:312390 original size:79 final size:82
Alignment explanation
Indices: 312282--312508 Score: 192
Period size: 86 Copynumber: 2.7 Consensus size: 82
312272 TTGGTGGCAC
* * * * * ** *
312282 CCTTTAGTCCTCAATGAGCATGACGCA-T-TTTCC-TTTTCCTTTTGTCCTCAAAGAGTAGGATG
1 CCTTT-GTCCTCAAAGAGCAAGACACATTATTTCCTTTTTCCCTTTGTCCTCAAAGAGCAAAACG
* *
312344 CACTTTATTTCCTTTTCT
65 CACTTTATTCCCATTTCT
* *
312362 CCTTTGTCCTCAAAGAGCAAGACACATTTTATTTCCTTTTTTTCCCTTTGTCTTTAAAGAGCAAA
1 CCTTTGTCCTCAAAGAGCAAGACACA--TTATTTCC--TTTTTCCCTTTGTCCTCAAAGAGCAAA
312427 ACGCACTTTATTCCCATTTCT
62 ACGCACTTTATTCCCATTTCT
* * * * * *
312448 CCTTTGTCCTCAAAGAGTAGGGTGCAC-TTCATTTCCTTTTTTCCTTTATCCTCGAAGAGCA
1 CCTTTGTCCTCAAAGAGCA-AG-ACACATT-ATTTCCTTTTTCCCTTTGTCCTCAAAGAGCA
312509 GGACGTACTC
Statistics
Matches: 117, Mismatches: 20, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
79 18 0.15
80 5 0.04
82 1 0.01
83 5 0.04
84 20 0.17
85 2 0.02
86 62 0.53
87 1 0.01
88 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.41
Consensus pattern (82 bp):
CCTTTGTCCTCAAAGAGCAAGACACATTATTTCCTTTTTCCCTTTGTCCTCAAAGAGCAAAACGC
ACTTTATTCCCATTTCT
Found at i:313294 original size:20 final size:20
Alignment explanation
Indices: 313269--313323 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
313259 TTCATAATTG
313269 GTATCGATACATTCTTCATT
1 GTATCGATACATTCTTCATT
313289 GTATCGATACATTCTTCATT
1 GTATCGATACATTCTTCATT
*
313309 GTATTGATACATTCT
1 GTATCGATACATTCT
313324 GGGTTTTACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (20 bp):
GTATCGATACATTCTTCATT
Found at i:316098 original size:27 final size:26
Alignment explanation
Indices: 316066--316188 Score: 151
Period size: 27 Copynumber: 4.7 Consensus size: 26
316056 CAAAAGCCAC
316066 TCTTTGTGTTTGTCAAAAATGGTGGT
1 TCTTTGTGTTTGTCAAAAATGGTGGT
* *
316092 TACTTTGTATTTGTAAAAAATGGTGGT
1 T-CTTTGTGTTTGTCAAAAATGGTGGT
*
316119 TACTTTGTATTTGTCAAAAATGGTGGT
1 T-CTTTGTGTTTGTCAAAAATGGTGGT
* *
316146 TCGTTTTTGTTTGTCAAAAATTGTGGT
1 TC-TTTGTGTTTGTCAAAAATGGTGGT
*
316173 T-TGT-TGTTTGTCAAAA
1 TCTTTGTGTTTGTCAAAA
316189 TTGATGGCTA
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
24 12 0.14
25 2 0.02
26 2 0.02
27 72 0.82
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.47
Consensus pattern (26 bp):
TCTTTGTGTTTGTCAAAAATGGTGGT
Found at i:320675 original size:27 final size:27
Alignment explanation
Indices: 320638--320715 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
320628 AAAAGCCACC
320638 CTTTGTGTTTGTCAAAAATAGTGGTTA
1 CTTTGTGTTTGTCAAAAATAGTGGTTA
* * * *
320665 CTTTGTATTTGTAAAAAATGGTGGTTC
1 CTTTGTGTTTGTCAAAAATAGTGGTTA
*
320692 CTCTT-TGTTTGTCAAAAATTGTGG
1 CT-TTGTGTTTGTCAAAAATAGTGG
320716 CTTGTTGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 41 0.95
28 2 0.05
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATAGTGGTTA
Found at i:320728 original size:24 final size:24
Alignment explanation
Indices: 320696--320741 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
320686 TGGTTCCTCT
320696 TTGTTTGTCAAAAATTGTGGCTTG
1 TTGTTTGTCAAAAATTGTGGCTTG
*
320720 TTGTTTGTCAAAATTTGTGGCT
1 TTGTTTGTCAAAAATTGTGGCT
320742 AATTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.48
Consensus pattern (24 bp):
TTGTTTGTCAAAAATTGTGGCTTG
Found at i:325620 original size:20 final size:20
Alignment explanation
Indices: 325595--325672 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
325585 AAAAACCCAA
*
325595 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATCAAT
* *
325615 AATGTATCGATACAATTTAAGC
1 AATGTATCGATACAA-TCAA-T
* * *
325637 AATGTATCGACACATTCACT
1 AATGTATCGATACAATCAAT
*
325657 TATGTATCGATACAAT
1 AATGTATCGATACAAT
325673 TTCTTTCCAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
20 28 0.61
21 5 0.11
22 13 0.28
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACAATCAAT
Found at i:330308 original size:18 final size:18
Alignment explanation
Indices: 330285--330356 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
330275 ACATGATTTG
330285 AGAATAGGGAGTGAACCA
1 AGAATAGGGAGTGAACCA
* *
330303 AGAATAGGTAAGTGTTAGCTCA
1 AGAATAGG-GAGTG--AAC-CA
*
330325 AAAATAGGGAGTGAACCA
1 AGAATAGGGAGTGAACCA
*
330343 AGAAT-GGGGGTGAA
1 AGAATAGGGAGTGAA
330357 TTGGTTCTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 8 0.19
18 14 0.33
19 6 0.14
21 6 0.14
22 9 0.21
ACGTcount: A:0.42, C:0.08, G:0.33, T:0.17
Consensus pattern (18 bp):
AGAATAGGGAGTGAACCA
Found at i:331146 original size:52 final size:52
Alignment explanation
Indices: 331068--331174 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
331058 ATTGGACTCA
* *
331068 ATGTATCGATACTATTCACAATGTATCGATATATGAACAGTAATGAATAGTG
1 ATGTATCGATACTATTCACAATGTATCGATACATGAACAATAATGAATAGTG
* *
331120 ATGTATCGATACTATTCATAATGTATCGATACATGAACAATGATGAATAGTG
1 ATGTATCGATACTATTCACAATGTATCGATACATGAACAATAATGAATAGTG
331172 ATG
1 ATG
331175 AACAGTGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACTATTCACAATGTATCGATACATGAACAATAATGAATAGTG
Found at i:334573 original size:20 final size:21
Alignment explanation
Indices: 334548--334602 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
334538 AAAAACCTAG
334548 AATGTATCGATACAATA-AAT-
1 AATGTATCGATACAA-ACAATA
* *
334568 AATGTATCAATACAAACAGTA
1 AATGTATCGATACAAACAATA
334589 AATGTATCGATACA
1 AATGTATCGATACA
334603 TTTCCTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 13 0.43
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (21 bp):
AATGTATCGATACAAACAATA
Found at i:334645 original size:39 final size:39
Alignment explanation
Indices: 334591--334682 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
334581 AAACAGTAAA
*
334591 TGTATCGATACATTTCCTTTCTAGAATGCAAGATGGTTT
1 TGTATCGATACATTTCCTTTCTAGAATGCAAGATAGTTT
* *
334630 TGTATCGATACATTTCCTTTCTAGAATGCAGGGTAGTTT
1 TGTATCGATACATTTCCTTTCTAGAATGCAAGATAGTTT
334669 TGTATCGATACATT
1 TGTATCGATACATT
334683 CACTTATGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.41
Consensus pattern (39 bp):
TGTATCGATACATTTCCTTTCTAGAATGCAAGATAGTTT
Found at i:334719 original size:21 final size:20
Alignment explanation
Indices: 334666--334721 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
334656 TGCAGGGTAG
334666 TTTTGTATCGATACATTCAC
1 TTTTGTATCGATACATTCAC
* * *
334686 TTATGTATTGATACATTTAC
1 TTTTGTATCGATACATTCAC
334706 TCTTTGTATCGATACA
1 T-TTTGTATCGATACA
334722 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (20 bp):
TTTTGTATCGATACATTCAC
Found at i:334785 original size:21 final size:20
Alignment explanation
Indices: 334759--334797 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
334749 GTTGGGACCT
334759 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
334780 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
334798 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:335001 original size:15 final size:15
Alignment explanation
Indices: 334977--335013 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
334967 AGGTTGTTGG
* *
334977 AAATAGGCCCGGACA
1 AAATAAGCCCAGACA
334992 AAATAAGCCCAGACA
1 AAATAAGCCCAGACA
335007 AAATAAG
1 AAATAAG
335014 GTGTCTACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.22, G:0.19, T:0.08
Consensus pattern (15 bp):
AAATAAGCCCAGACA
Found at i:336157 original size:20 final size:21
Alignment explanation
Indices: 336132--336185 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
336122 TATTGTAGGC
*
336132 ATGTATCTATACATTCA-TTT
1 ATGTATCAATACATTCATTTT
*
336152 ATGTATCAATACATTTATTTT
1 ATGTATCAATACATTCATTTT
* *
336173 TTGTATCGATACA
1 ATGTATCAATACA
336186 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.48
Consensus pattern (21 bp):
ATGTATCAATACATTCATTTT
Found at i:336895 original size:52 final size:51
Alignment explanation
Indices: 336813--336957 Score: 173
Period size: 52 Copynumber: 2.8 Consensus size: 51
336803 AAAGATAATA
* * *
336813 AAGATGAGAAGGATGCCAATGTACTAATTCAAGGCCAACGATATTAGACTT
1 AAGATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGATATTAGACTT
* * * *
336864 GAAGATGAGAAGAATGCCAATATGCTGATTCAAGGTCAGCGATATTGGACTT
1 -AAGATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGATATTAGACTT
* * * *
336916 AAAAGTTAGAAGAATGCCAATGGGATGATTCAAGGCCAACGA
1 AAGA-TGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGA
336958 CATTCTGCTT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 3 0.04
52 75 0.96
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (51 bp):
AAGATGAGAAGAATGCCAATGTGCTGATTCAAGGCCAACGATATTAGACTT
Found at i:337197 original size:52 final size:51
Alignment explanation
Indices: 337129--337394 Score: 291
Period size: 52 Copynumber: 5.1 Consensus size: 51
337119 AATAAGATTA
* *
337129 GACTTGAAGATGAAAAGAATGCCAATATGCTAATTCAAGGCCAGTGACATTG
1 GACTTAAAAATGAAAAG-ATGCCAATATGCTAATTCAAGGCCAGTGACATTG
* * * *
337181 CATTTAAAAATTAAAAGAATGCCAATATGCTGATTCAAGGCCAGTGACATTG
1 GACTTAAAAATGAAAAG-ATGCCAATATGCTAATTCAAGGCCAGTGACATTG
* ** * * *
337233 GGCTTAGGAATGATAAAGATGCCAATATGCTGATTCAAGACCAGTGATATTG
1 GACTTAAAAATGA-AAAGATGCCAATATGCTAATTCAAGGCCAGTGACATTG
* * * * *
337285 AACTTAAAGATGACAAAGGTGCCAATATGCTAATTCAAGGCTAGTGATATTG
1 GACTTAAAAATGA-AAAGATGCCAATATGCTAATTCAAGGCCAGTGACATTG
* * *
337337 GACTTAAGAAA-GAAAAAGGTGCCAATGTGCTAATTCAAGGCCAGTAACATTG
1 GACTTAA-AAATG-AAAAGATGCCAATATGCTAATTCAAGGCCAGTGACATTG
337389 GACTTA
1 GACTTA
337395 GAAAGAGATG
Statistics
Matches: 181, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
52 174 0.96
53 7 0.04
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (51 bp):
GACTTAAAAATGAAAAGATGCCAATATGCTAATTCAAGGCCAGTGACATTG
Found at i:337292 original size:270 final size:269
Alignment explanation
Indices: 336798--337292 Score: 620
Period size: 270 Copynumber: 1.8 Consensus size: 269
336788 TGCGACACTA
* *
336798 GACTTAAAGATAATAAAGATGAGAAGGATGCCAATGTACTAATTCAAGGCCAACGATATTAGACT
1 GACTTAAAGATAATAAAGATGAGAAGGATGCCAATGTACTAATTCAAGGCCAACAAGATTAGACT
* * * * * * *
336863 TGAAGATGAGAAGAATGCCAATATGCTGATTCAAGGTCAGCGATATTGGACTTAAAAGTTAGAAG
66 TGAAGATGAAAAGAATGCCAATATGCTAATTCAAGGCCAGCGACATTGCACTTAAAAATTAAAAG
* * *
336928 AATGCCAATGGGATGATTCAAGGCCAACGACATTCTGCTTAAAAATGACAAAGGTGCCTATGAAC
131 AATGCCAATAGGATGATTCAAGGCCAACGACATTCGGCTTAAAAATGACAAAGATGCCTATG-AC
* *
336993 TGATTCAAGGCCAGTGGCATTAGACTTAAAAAGAGATAAAGGTGCTGATATATTGATTCAAGGCT
195 TGATTCAAGACCAGTGACATTAGACTTAAAAAGAGATAAAGGTGCTGATATATTGATTCAAGGCT
337058 ATCGATGCCG
260 ATCGATGCCG
* * * * * * *
337068 GACTTAAAGATGATAAGGGTGAGAA-GAGTGCCAATGTGCTGATTCACA-GCTAATAAGATTAGA
1 GACTTAAAGATAATAAAGATGAGAAGGA-TGCCAATGTACTAATTCA-AGGCCAACAAGATTAGA
* *
337131 CTTGAAGATGAAAAGAATGCCAATATGCTAATTCAAGGCCAGTGACATTGCATTTAAAAATTAAA
64 CTTGAAGATGAAAAGAATGCCAATATGCTAATTCAAGGCCAGCGACATTGCACTTAAAAATTAAA
* * ** * ** *
337196 AGAATGCCAATATGCTGATTCAAGGCCAGTGACATTGGGCTTAGGAATGATAAAGATGCCAATAT
129 AGAATGCCAATAGGATGATTCAAGGCCAACGACATTCGGCTTAAAAATGACAAAGATGCC--TAT
*
337261 G-CTGATTCAAGACCAGTGATATT-GAACTTAAA
192 GACTGATTCAAGACCAGTGACATTAG-ACTTAAA
337293 GATGACAAAG
Statistics
Matches: 188, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
269 3 0.02
270 180 0.96
271 1 0.01
272 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (269 bp):
GACTTAAAGATAATAAAGATGAGAAGGATGCCAATGTACTAATTCAAGGCCAACAAGATTAGACT
TGAAGATGAAAAGAATGCCAATATGCTAATTCAAGGCCAGCGACATTGCACTTAAAAATTAAAAG
AATGCCAATAGGATGATTCAAGGCCAACGACATTCGGCTTAAAAATGACAAAGATGCCTATGACT
GATTCAAGACCAGTGACATTAGACTTAAAAAGAGATAAAGGTGCTGATATATTGATTCAAGGCTA
TCGATGCCG
Found at i:337496 original size:33 final size:32
Alignment explanation
Indices: 337387--337594 Score: 165
Period size: 31 Copynumber: 6.6 Consensus size: 32
337377 CCAGTAACAT
* * *
337387 TGGAC-TTAGAAAGAGATGCCACCGACTTATG
1 TGGACTTTAGAAAGGGTTGCCACCGACTTGTG
* * * **
337418 TGGGCTTTTGAGAGGGTTGCCACTAACTTGTG
1 TGGACTTTAGAAAGGGTTGCCACCGACTTGTG
* *
337450 TTGG-CTTTTGAAAGGGATTGTCACCGACTTGTG
1 -TGGACTTTAGAAAGGG-TTGCCACCGACTTGTG
* * * *
337483 TGGACTTTAGAAA-GGCTACCATCGAGTTGTG
1 TGGACTTTAGAAAGGGTTGCCACCGACTTGTG
* * *
337514 TGGACTTTA-AAAAGGTTACCACTGACTTGTG
1 TGGACTTTAGAAAGGGTTGCCACCGACTTGTG
* * *
337545 TGGGCTTTCGAAAGGGGTTGCCACCAACTTGTG
1 TGGACTTTAGAAA-GGGTTGCCACCGACTTGTG
*
337578 TGGGCTTTAG-AAGGGTT
1 TGGACTTTAGAAAGGGTT
337595 ATGGACTTTG
Statistics
Matches: 141, Mismatches: 29, Indels: 14
0.77 0.16 0.08
Matches are distributed among these distances:
30 3 0.02
31 50 0.35
32 40 0.28
33 48 0.34
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (32 bp):
TGGACTTTAGAAAGGGTTGCCACCGACTTGTG
Found at i:337682 original size:60 final size:60
Alignment explanation
Indices: 337608--337818 Score: 264
Period size: 60 Copynumber: 3.5 Consensus size: 60
337598 GACTTTGAAG
** * * *
337608 AAAAAGGTGCCATGGAGTTGCCGAC-TAAAAAGGTGCCACAGAGTTG-TGGACTTAAAAGAA
1 AAAAAGGTGCCATGGAGTTGTAGACTTAAAAGGGTGCCACGGAG-TGCTAGACTTAAAAG-A
*
337668 AAAAAGGTGCCATGGAGTTGTAGACTTAAAAGGGTGCCACGGAGTGCTAGTCTTAAAAGA
1 AAAAAGGTGCCATGGAGTTGTAGACTTAAAAGGGTGCCACGGAGTGCTAGACTTAAAAGA
* ** *
337728 AAAAAGGTGTCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTGCTAGACTTAAAAGA
1 AAAAAGGTGCCATGGAGTTGTAGACTTAAAAGGGTGCCACGGAGTGCTAGACTTAAAAGA
* * * *
337788 AAAAAGGTGCCACGAAATTGTGGACTTAAAA
1 AAAAAGGTGCCATGGAGTTGTAGACTTAAAA
337819 AAAAAGGTAC
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
60 108 0.81
61 26 0.19
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (60 bp):
AAAAAGGTGCCATGGAGTTGTAGACTTAAAAGGGTGCCACGGAGTGCTAGACTTAAAAGA
Found at i:337705 original size:27 final size:27
Alignment explanation
Indices: 337668--337786 Score: 98
Period size: 27 Copynumber: 4.2 Consensus size: 27
337658 CTTAAAAGAA
* *
337668 AAAAAGGTGCCATGGAGTTG-TAGACTT
1 AAAAGGGTGCCACGGAG-TGCTAGACTT
*
337695 AAAAGGGTGCCACGGAGTGCTAGTCTT
1 AAAAGGGTGCCACGGAGTGCTAGACTT
* * *
337722 AAAAGAAAAAAGGTGTCACAGAGTTG-TGGACTT
1 AAAAG------GGTGCCACGGAG-TGCTAGACTT
337755 AAAAGGGTGCCACGGAGTGCTAGACTT
1 AAAAGGGTGCCACGGAGTGCTAGACTT
337782 AAAAG
1 AAAAG
337787 AAAAAAGGTG
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.05
27 47 0.64
33 20 0.27
34 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTGCTAGACTT
Found at i:337757 original size:33 final size:32
Alignment explanation
Indices: 337634--338039 Score: 353
Period size: 33 Copynumber: 13.0 Consensus size: 32
337624 GTTGCCGACT
*
337634 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
* *
337666 AAAAAAAGGTGCCATGGAGTTGTAGACTTAAAAG
1 --AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
* *
337700 -----GGTGCCACGGAG-TGCTAGTCTTAAAAG
1 AAAAAGGTGCCACGGAGTTG-TGGACTTAAAAG
* *
337727 AAAAAAGGTGTCACAGAGTTGTGGACTTAAAAG
1 -AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
*
337760 -----GGTGCCACGGAG-TGCTAGACTTAAAAG
1 AAAAAGGTGCCACGGAGTTG-TGGACTTAAAAG
* *
337787 AAAAAAGGTGCCACGAAATTGTGGACTTAAAA-
1 -AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
*
337819 AAAAAGGTACCACGGAGTTGTGGACTTAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
* *** *
337851 GAAAAGACACCACGGAGTTGTGAACTTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-G
* *
337884 AAAAAGGTACCATGGAGTTGTGGACTTAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
* *
337916 GAAAAGGTGCCACGGAGTTGTAGACTTAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
* *
337948 AAAAAGGTGCCACGAAGTTGTAGACTTTAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAG
* * * *
337981 -----GGTGCCGCAGAGTTATGAACTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTT-AAAAG
* *
338009 AAAAAGGTGTCACGTAGTTGTGGACTTAAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA
338040 CGGATGCCAC
Statistics
Matches: 302, Mismatches: 45, Indels: 52
0.76 0.11 0.13
Matches are distributed among these distances:
26 4 0.01
27 45 0.15
28 19 0.06
31 28 0.09
32 83 0.27
33 90 0.30
34 33 0.11
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (32 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
Done.