Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 52 of 356
Found at i:17011806 original size:22 final size:22
Alignment explanation
Indices: 17011748--17011807 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
17011738 CTAAGGTATG
*
17011748 TATATATTGTATATGTTTTATA
1 TATATATTGTATATGTTTTAAA
* *
17011770 TATGT-TATGTATATATTTTTAAA
1 TATATAT-TGTATAT-GTTTTAAA
17011793 TACTATATTGTATAT
1 TA-TATATTGTATAT
17011808 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.37
23 8 0.27
24 9 0.30
25 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (22 bp):
TATATATTGTATATGTTTTAAA
Found at i:17011834 original size:33 final size:34
Alignment explanation
Indices: 17011779--17011844 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
17011769 ATATGTTATG
* *
17011779 TATATATTTTTAAATACTATATTGTATATATATA
1 TATATATTCTTAAATACCATATTGTATATATATA
*
17011813 TATATATTCTT-AATACCATATTGTGTATATAT
1 TATATATTCTTAAATACCATATTGTATATATAT
17011845 CATTATTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (34 bp):
TATATATTCTTAAATACCATATTGTATATATATA
Found at i:17019354 original size:10 final size:11
Alignment explanation
Indices: 17019332--17019370 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
17019322 ATGTCTCCAC
17019332 AAGAATAAAAA
1 AAGAATAAAAA
17019343 AAGAATAAAAA
1 AAGAATAAAAA
17019354 AAGAGA-AAGAAA
1 AAGA-ATAA-AAA
17019366 AAGAA
1 AAGAA
17019371 ACAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (11 bp):
AAGAATAAAAA
Found at i:17020959 original size:31 final size:31
Alignment explanation
Indices: 17020921--17020980 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
17020911 ACGAGCTGGA
17020921 CTAAACCAGCATAGAAACAAATAATGCCCGG
1 CTAAACCAGCATAGAAACAAATAATGCCCGG
17020952 CTAAACCAGCATAGAAACAAATAATGCCC
1 CTAAACCAGCATAGAAACAAATAATGCCC
17020981 CGCATTGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.27, G:0.13, T:0.13
Consensus pattern (31 bp):
CTAAACCAGCATAGAAACAAATAATGCCCGG
Found at i:17025111 original size:15 final size:15
Alignment explanation
Indices: 17025091--17025168 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
17025081 TTTATGGAAA
17025091 ATCAAATATATGGGT
1 ATCAAATATATGGGT
**
17025106 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
17025120 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
17025136 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
17025150 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
17025166 ATC
1 ATC
17025169 GAGATATTGG
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 8 0.17
15 32 0.67
16 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:17025119 original size:30 final size:30
Alignment explanation
Indices: 17025085--17025178 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
17025075 TCCATATTTA
* *
17025085 TGGAAAATCAAATATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
17025115 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
17025145 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
17025176 TGG
1 TGG
17025179 CATAATAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 52 0.87
31 8 0.13
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.28
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:17029774 original size:15 final size:15
Alignment explanation
Indices: 17029754--17029831 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
17029744 TTTATGGAAA
17029754 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
17029769 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
17029783 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
17029799 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
17029813 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
17029829 ATC
1 ATC
17029832 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 8 0.17
15 31 0.66
16 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:17029782 original size:30 final size:30
Alignment explanation
Indices: 17029748--17029841 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
17029738 TCCATATTTA
*
17029748 TGGAAAATCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
17029778 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
17029808 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
17029839 TGG
1 TGG
17029842 CATAATAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
30 53 0.87
31 8 0.13
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:17039769 original size:18 final size:18
Alignment explanation
Indices: 17039746--17039780 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17039736 GTATGTTTTT
17039746 TAGTCTTATTTATGCAAG
1 TAGTCTTATTTATGCAAG
*
17039764 TAGTCTTATTTTTGCAA
1 TAGTCTTATTTATGCAA
17039781 TTGATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TAGTCTTATTTATGCAAG
Found at i:17044639 original size:3 final size:3
Alignment explanation
Indices: 17044631--17044667 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
17044621 AAAGGGTTTA
17044631 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17044668 TAGATATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17044923 original size:16 final size:16
Alignment explanation
Indices: 17044902--17044932 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17044892 GGCTCGAAAC
17044902 AAAACTAAAACTAAAG
1 AAAACTAAAACTAAAG
*
17044918 AAAACTTAAACTAAA
1 AAAACTAAAACTAAA
17044933 ATCAGAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.13, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAACTAAAACTAAAG
Found at i:17048096 original size:15 final size:16
Alignment explanation
Indices: 17048071--17048100 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17048061 ACCAAATATC
17048071 AATATAAAATTAAATG
1 AATATAAAATTAAATG
17048087 AATA-AAAATTAAAT
1 AATATAAAATTAAAT
17048101 CATGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AATATAAAATTAAATG
Found at i:17053201 original size:15 final size:16
Alignment explanation
Indices: 17053175--17053204 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17053165 TTTGCCCGGG
17053175 CTAAAAAGCCCAACAT
1 CTAAAAAGCCCAACAT
17053191 CTAAAAA-CCCAACA
1 CTAAAAAGCCCAACA
17053205 ACCTCCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.33, G:0.03, T:0.10
Consensus pattern (16 bp):
CTAAAAAGCCCAACAT
Found at i:17053302 original size:14 final size:13
Alignment explanation
Indices: 17053278--17053314 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
17053268 TCTTCATTCC
17053278 AACCACCCCACTA
1 AACCACCCCACTA
17053291 AACCACCCCCACTA
1 AACCA-CCCCACTA
*
17053305 AACCATCCCA
1 AACCACCCCA
17053315 ACCACTCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.38, C:0.54, G:0.00, T:0.08
Consensus pattern (13 bp):
AACCACCCCACTA
Found at i:17053789 original size:33 final size:39
Alignment explanation
Indices: 17053715--17053796 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 39
17053705 TATTACTTTC
*
17053715 TATTATTATTATTATTACTAATACCACTATTATCATCAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
*
17053754 TATTACTATTA-TATTA-TAATA-C-CT-TT-TCATTAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
17053787 TATTACTATT
1 TATTACTATT
17053797 GTGTTTTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 16 0.39
34 2 0.05
35 2 0.05
36 1 0.02
37 5 0.12
38 5 0.12
39 10 0.24
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTACTATTATTATTACTAATACCACTATTATCATCAT
Found at i:17063497 original size:206 final size:206
Alignment explanation
Indices: 17063133--17063798 Score: 1105
Period size: 206 Copynumber: 3.3 Consensus size: 206
17063123 GATCTGGCTA
*
17063133 AAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
*
17063197 TTGACTTTCGCATGCTTACGCTAAAGT-AAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
66 TTGGCTTTCGCATGCTTACGCTAAA-TCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
* * *
17063261 AACAAGTCAAAGTCTGGCATCTCTATTTCGACGGAGAGCAGATACATAGCAGATCCGGCCTTCAG
130 AACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAG
17063326 ATGTTTATACTG
195 ATGTTTATACTG
*
17063338 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGGAGACATAGCTGAT
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
* *
17063403 TTGGCTTTCGCGTGCTTACGCTAAATCAAGTCTAAGATGATTTGGCATTTCTGTATTGTCAGAGA
66 TTGGCTTTCGCATGCTTACGCTAAATCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
*
17063468 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTTAGA
131 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
17063533 TGTTTATACTG
196 TGTTTATACTG
* * *
17063544 AAGCAAGATCTAAGATGATTTGGCATCCTTGTGCTTACAAGAAGCAAATCGAAGATATAGCTGAT
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
17063609 TTGGCTTTCGCATGCTTACG------CAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
66 TTGGCTTTCGCATGCTTACGCTAAATCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
*
17063668 ACAAGTCGAAGTCTGGCATCTCCATTTCGACAGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
131 ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
* *
17063733 TGTTTTTACCG
196 TGTTTATACTG
* * *
17063744 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAAGAACAAATCTAAGA
1 AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGA
17063799 AGCAGATTTA
Statistics
Matches: 435, Mismatches: 24, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
200 160 0.37
205 5 0.01
206 270 0.62
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (206 bp):
AAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGAT
TTGGCTTTCGCATGCTTACGCTAAATCAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA
ACAAGTCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTGGCCTTCAGA
TGTTTATACTG
Found at i:17063982 original size:45 final size:45
Alignment explanation
Indices: 17063886--17063982 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
17063876 AGATTGATGA
* * * *
17063886 AGCAAATTTGGCGTCTCTGTATTAGACGAGGAGCAGATCGAAGAT
1 AGCAGATTTGCCGTCTCTGCATTAGACGAGGAGCAGATCAAAGAT
*
17063931 -GACAGATTTGCCGTCTCTGCATTAGACGGGGAGCAGATCAAAGAT
1 AG-CAGATTTGCCGTCTCTGCATTAGACGAGGAGCAGATCAAAGAT
17063976 AGCAGAT
1 AGCAGAT
17063983 ATCGCTTTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
44 1 0.02
45 43 0.96
46 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.23
Consensus pattern (45 bp):
AGCAGATTTGCCGTCTCTGCATTAGACGAGGAGCAGATCAAAGAT
Found at i:17064195 original size:15 final size:16
Alignment explanation
Indices: 17064169--17064198 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17064159 TTTGCCTGGG
17064169 CTAAAAAGCCCAACAT
1 CTAAAAAGCCCAACAT
17064185 CTAAAAA-CCCAACA
1 CTAAAAAGCCCAACA
17064199 ACCTCCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.33, G:0.03, T:0.10
Consensus pattern (16 bp):
CTAAAAAGCCCAACAT
Found at i:17064291 original size:13 final size:13
Alignment explanation
Indices: 17064273--17064325 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
17064263 TCTTCACTCC
17064273 AACCACCCCACTA
1 AACCACCCCACTA
*
17064286 AACCA-CTC-C--
1 AACCACCCCACTA
*
17064295 AACCACCTCACTA
1 AACCACCCCACTA
17064308 AACCACCCCACTA
1 AACCACCCCACTA
17064321 AACCA
1 AACCA
17064326 TCTCAACTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 2 0.06
12 2 0.06
13 22 0.65
ACGTcount: A:0.40, C:0.51, G:0.00, T:0.09
Consensus pattern (13 bp):
AACCACCCCACTA
Found at i:17064295 original size:22 final size:22
Alignment explanation
Indices: 17064267--17064313 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
17064257 TAAATATCTT
17064267 CACTCCAACCACCCCACTAAAC
1 CACTCCAACCACCCCACTAAAC
*
17064289 CACTCCAACCACCTCACTAAAC
1 CACTCCAACCACCCCACTAAAC
17064311 CAC
1 CAC
17064314 CCCACTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.53, G:0.00, T:0.11
Consensus pattern (22 bp):
CACTCCAACCACCCCACTAAAC
Found at i:17064737 original size:19 final size:18
Alignment explanation
Indices: 17064700--17064741 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
17064690 GGAGAGAGTG
*
17064700 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
17064718 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
17064737 TTATT
1 TTATT
17064742 ACTAATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:17064837 original size:23 final size:23
Alignment explanation
Indices: 17064767--17064837 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
17064757 ATCATCGTTA
*
17064767 TTACTATTA-TATTATAATACCTTT
1 TTACTATTATTATTATTATA--TTT
* * * * *
17064791 TCATTATTATTACTATTGTGTTT
1 TTACTATTATTATTATTATATTT
17064814 TTACTATTATTATTATTATATTT
1 TTACTATTATTATTATTATATTT
17064837 T
1 T
17064838 CTTTTTTGTA
Statistics
Matches: 35, Mismatches: 11, Indels: 3
0.71 0.22 0.06
Matches are distributed among these distances:
23 22 0.63
24 7 0.20
25 6 0.17
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (23 bp):
TTACTATTATTATTATTATATTT
Found at i:17067758 original size:28 final size:30
Alignment explanation
Indices: 17067709--17067794 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 30
17067699 GTTAAGAATG
17067709 TTAAAATTT-TGTAAAAATATATAGAAAGCTAT
1 TTAAAATTTAT-T-AAAA-ATATAGAAAGCTAT
* * * *
17067741 TT-TAATTTA-TGAAAATATAGATATCTAT
1 TTAAAATTTATTAAAAATATAGAAAGCTAT
*
17067769 TTAAAATTTATTAAAAATATACAAAG
1 TTAAAATTTATTAAAAATATAGAAAG
17067795 TTTATTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
28 14 0.33
29 9 0.21
30 12 0.29
31 5 0.12
32 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (30 bp):
TTAAAATTTATTAAAAATATAGAAAGCTAT
Found at i:17068561 original size:28 final size:28
Alignment explanation
Indices: 17068530--17068583 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
17068520 TCTTTTCTAA
17068530 ATTTTTAATTAA-ATTTAAATATTTTTCT
1 ATTTTTAA-TAATATTTAAATATTTTTCT
*
17068558 ATTTTTAATAATTTTTAAATATTTTT
1 ATTTTTAATAATATTTAAATATTTTT
17068584 TTATAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTTTTAATAATATTTAAATATTTTTCT
Found at i:17068589 original size:21 final size:20
Alignment explanation
Indices: 17068559--17068602 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
17068549 TATTTTTCTA
17068559 TTTTTAATAATTTTTAAATAT
1 TTTTTAATAA-TTTTAAATAT
* *
17068580 TTTTTTATAATTTTCAATAT
1 TTTTTAATAATTTTAAATAT
17068600 TTT
1 TTT
17068603 AAAAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTAATAATTTTAAATAT
Found at i:17071196 original size:15 final size:15
Alignment explanation
Indices: 17071176--17071207 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17071166 AATTTAATTA
*
17071176 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
17071191 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
17071206 TT
1 TT
17071208 TGCATACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:17078356 original size:27 final size:28
Alignment explanation
Indices: 17078296--17078357 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
17078286 ACTTGGAGAG
* **
17078296 AAAAAAAAATTAAAAGTTTTTTAATTCC
1 AAAAAATAATTAAAAGTTTTTTAACCCC
* *
17078324 ATAAAATAATTAAATG-TTTTTAACCCC
1 AAAAAATAATTAAAAGTTTTTTAACCCC
17078351 AAAAAAT
1 AAAAAAT
17078358 CTAACAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAAATAATTAAAAGTTTTTTAACCCC
Found at i:17086082 original size:28 final size:27
Alignment explanation
Indices: 17086029--17086082 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
17086019 TGGCTCCACC
* * **
17086029 AAATAAAAAAATAATTTCAATTTAAAA
1 AAATAAAAAAATAACTTAAAAATAAAA
17086056 AAATATAAAAAATAACTTAAAAATAAA
1 AAATA-AAAAAATAACTTAAAAATAAA
17086083 GTCTGACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (27 bp):
AAATAAAAAAATAACTTAAAAATAAAA
Found at i:17086638 original size:20 final size:20
Alignment explanation
Indices: 17086613--17086675 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
17086603 AAATAAAATG
17086613 AAATAATTTTAAAAAATTCA
1 AAATAATTTTAAAAAATTCA
**
17086633 AAATAATTTT-TTAAATTCA
1 AAATAATTTTAAAAAATTCA
*
17086652 AAAT-ATTTATAAAAATTTCA
1 AAATAATTT-TAAAAAATTCA
17086672 AAAT
1 AAAT
17086676 TTATATTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.11
19 12 0.33
20 20 0.56
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATAATTTTAAAAAATTCA
Found at i:17086682 original size:24 final size:25
Alignment explanation
Indices: 17086654--17086702 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
17086644 TAAATTCAAA
*
17086654 ATATTT-ATAAAAATT-TCAAAATTT
1 ATATTTCAAAAAAATTAT-AAAATTT
17086678 ATATTTCAAAAAAATTATAAAATTT
1 ATATTTCAAAAAAATTATAAAATTT
17086703 CTAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 15 0.68
26 1 0.05
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTTCAAAAAAATTATAAAATTT
Found at i:17090324 original size:19 final size:19
Alignment explanation
Indices: 17090275--17090326 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
17090265 AAAATTACAA
* *
17090275 AAAAATCAAAGTAATTTTT
1 AAAATTCAAAATAATTTTT
* *
17090294 AAATTTTGAAAATAATTTTT
1 AAA-ATTCAAAATAATTTTT
17090314 AAAATTCAAAATA
1 AAAATTCAAAATA
17090327 TTTGTAGAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:17093530 original size:26 final size:27
Alignment explanation
Indices: 17093487--17093537 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
17093477 GCAAAACAAT
** *
17093487 AGAGAAACAGAAGCAAAAAGCAAAAGC
1 AGAGAAACAGAAAAAAAAAACAAAAGC
17093514 AGAGAAA-AGAAAAAAAAAACAAAA
1 AGAGAAACAGAAAAAAAAAACAAAA
17093538 ATAATATACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.73, C:0.10, G:0.18, T:0.00
Consensus pattern (27 bp):
AGAGAAACAGAAAAAAAAAACAAAAGC
Found at i:17095868 original size:15 final size:15
Alignment explanation
Indices: 17095850--17095887 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
17095840 AAATATAAAG
17095850 ATTAAAATT-AACCAA
1 ATTAAAATTGAA-CAA
*
17095865 ATTAAAATTGAAGAA
1 ATTAAAATTGAACAA
17095880 ATTAAAAT
1 ATTAAAAT
17095888 AAGATACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (15 bp):
ATTAAAATTGAACAA
Found at i:17097226 original size:13 final size:13
Alignment explanation
Indices: 17097208--17097232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17097198 CTAGAATCCA
17097208 TTAAAAAATAACC
1 TTAAAAAATAACC
17097221 TTAAAAAATAAC
1 TTAAAAAATAAC
17097233 ATTAGTTAAC
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:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAAAATAACC
Found at i:17098216 original size:18 final size:18
Alignment explanation
Indices: 17098189--17098271 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 18
17098179 TATATGGAAA
*
17098189 ATAAATTTTAAATTATTT
1 ATAAAATTTAAATTATTT
**
17098207 ATAAAATTT-AATTCAAAT
1 ATAAAATTTAAATT-ATTT
* * *
17098225 ATATAAA-CTATATT-TTAA
1 ATA-AAATTTAAATTATT-T
*
17098243 ATAAATTTTAAATTATTT
1 ATAAAATTTAAATTATTT
17098261 ATAAAATTTAA
1 ATAAAATTTAA
17098272 TTCAAATATA
Statistics
Matches: 46, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
17 6 0.13
18 32 0.70
19 8 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAAAATTTAAATTATTT
Found at i:17098245 original size:54 final size:54
Alignment explanation
Indices: 17098187--17098299 Score: 226
Period size: 54 Copynumber: 2.1 Consensus size: 54
17098177 AATATATGGA
17098187 AAATAAATTTTAAATTATTTATAAAATTTAATTCAAATATATAAACTATATTTT
1 AAATAAATTTTAAATTATTTATAAAATTTAATTCAAATATATAAACTATATTTT
17098241 AAATAAATTTTAAATTATTTATAAAATTTAATTCAAATATATAAACTATATTTT
1 AAATAAATTTTAAATTATTTATAAAATTTAATTCAAATATATAAACTATATTTT
17098295 AAATA
1 AAATA
17098300 TTAAAATATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (54 bp):
AAATAAATTTTAAATTATTTATAAAATTTAATTCAAATATATAAACTATATTTT
Found at i:17098281 original size:18 final size:18
Alignment explanation
Indices: 17098206--17098281 Score: 50
Period size: 18 Copynumber: 4.2 Consensus size: 18
17098196 TTAAATTATT
17098206 TATAAAATTTAATTCAAA
1 TATAAAATTTAATTCAAA
* **
17098224 TATATAAA-CTATATTTTAA
1 TATA-AAATTTA-ATTCAAA
* **
17098243 -ATAAATTTTAAATT-ATT
1 TATAAAATTT-AATTCAAA
17098260 TATAAAATTTAATTCAAA
1 TATAAAATTTAATTCAAA
17098278 TATA
1 TATA
17098282 TAAACTATAT
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
17 6 0.15
18 26 0.63
19 9 0.22
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAATTTAATTCAAA
Found at i:17112089 original size:31 final size:31
Alignment explanation
Indices: 17112054--17112134 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
17112044 AGAATATAAT
* * ** *
17112054 TTTTGGCCCCTAAATTTGGCAACTAGGTCCA
1 TTTTGGTCCCTAAAATTGGCAACTAAATACA
* *
17112085 TTTTGGTCCTTAAAATTGACAACTAAATACA
1 TTTTGGTCCCTAAAATTGGCAACTAAATACA
*
17112116 TTTTGGTCCCTAAACTTGG
1 TTTTGGTCCCTAAAATTGG
17112135 ATTCTATCAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTTGGTCCCTAAAATTGGCAACTAAATACA
Found at i:17113612 original size:34 final size:32
Alignment explanation
Indices: 17113540--17113613 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 32
17113530 ATATTATATT
*
17113540 AATTATATATCAAATAATAATTATATATATTTA
1 AATT-TATATCAAATAATAATTATATATAATTA
* *
17113573 CATTTATATCAAATCACTAATTCA-ATAATAATTA
1 AATTTATATCAAAT-AATAATT-ATAT-ATAATTA
17113607 AATTTAT
1 AATTTAT
17113614 TATCTAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
32 10 0.29
33 11 0.32
34 13 0.38
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (32 bp):
AATTTATATCAAATAATAATTATATATAATTA
Found at i:17117837 original size:30 final size:30
Alignment explanation
Indices: 17117771--17117845 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
17117761 TAGTTTAAAT
* *
17117771 TTTTATAATTTTTAAAAGATTAAATTAGAA
1 TTTTATTATTTTTAAAAGATTAAAATAGAA
* *
17117801 TTTTATTATTTTTAGAGAGA-TAAAATATAA
1 TTTTATTATTTTTA-AAAGATTAAAATAGAA
17117831 TTTTATT-TTTATTAA
1 TTTTATTATTT-TTAA
17117846 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 4 0.10
30 31 0.79
31 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (30 bp):
TTTTATTATTTTTAAAAGATTAAAATAGAA
Found at i:17124005 original size:20 final size:20
Alignment explanation
Indices: 17123980--17124017 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17123970 ATCTCTCTCC
17123980 ATTTTCAAATTATTCTAAAT
1 ATTTTCAAATTATTCTAAAT
17124000 ATTTTCAAATTATTCTAA
1 ATTTTCAAATTATTCTAA
17124018 GCTTTGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTCAAATTATTCTAAAT
Found at i:17132950 original size:6 final size:6
Alignment explanation
Indices: 17132909--17132952 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
17132899 CAGCCTTGGT
* * *
17132909 GCCGGT GCCGGT GCCGGT GCCGGC GCCGGC GCCGGC GCCGGC GC
1 GCCGGC GCCGGC GCCGGC GCCGGC GCCGGC GCCGGC GCCGGC GC
17132953 GAGGGGCAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.00, C:0.43, G:0.50, T:0.07
Consensus pattern (6 bp):
GCCGGC
Found at i:17139433 original size:26 final size:26
Alignment explanation
Indices: 17139379--17139435 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
17139369 TTTTTATTTT
*
17139379 TATTTTTTAAAATATTTAAAATATTA
1 TATTTTTTAAAATATTTAAAATATCA
*
17139405 TATTTTTTAATAT-TATTAAACATA-CA
1 TATTTTTTAAAATAT-TTAAA-ATATCA
17139431 TATTT
1 TATTT
17139436 AATTATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 1 0.04
26 23 0.85
27 3 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTTTTTAAAATATTTAAAATATCA
Found at i:17140131 original size:17 final size:17
Alignment explanation
Indices: 17140106--17140191 Score: 50
Period size: 20 Copynumber: 4.8 Consensus size: 17
17140096 AATTTAATCT
*
17140106 TTTTTTTATATTTGCTA
1 TTTTATTATATTTGCTA
*
17140123 TTTTATTATCAATTTAACTA
1 TTTTATTAT--ATTT-GCTA
* *
17140143 ATTTAATATATTATTGCTA
1 TTTTATTATA-T-TTGCTA
*
17140162 TTATTATTATGTTT-CTA
1 TT-TTATTATATTTGCTA
17140179 TTTATATT-TATTT
1 TTT-TATTATATTT
17140192 TGTTATTCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
16 5 0.09
17 17 0.32
18 3 0.06
19 10 0.19
20 18 0.34
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTATTATATTTGCTA
Found at i:17140231 original size:15 final size:14
Alignment explanation
Indices: 17140175--17140291 Score: 62
Period size: 15 Copynumber: 8.1 Consensus size: 14
17140165 TTATTATGTT
*
17140175 TCTATTTATATTTA
1 TCTATTTTTATTTA
*
17140189 T-T-TTGTTATTCTAA
1 TCTATTTTTATT-T-A
*
17140203 TACTATTATTATTTA
1 T-CTATTTTTATTTA
17140218 TCTAATTTTTATTTA
1 TCT-ATTTTTATTTA
* *
17140233 TCTATTTATATTTC
1 TCTATTTTTATTTA
* *
17140247 TACTATTATAATATT-
1 T-CTATTTTTAT-TTA
17140262 TCTATTTATTATATT-
1 TCTATTT-TTAT-TTA
*
17140277 TCTATTTCTATTTA
1 TCTATTTTTATTTA
17140291 T
1 T
17140292 ATACTGTCGA
Statistics
Matches: 81, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
12 6 0.07
13 4 0.05
14 24 0.30
15 36 0.44
16 4 0.05
17 7 0.09
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (14 bp):
TCTATTTTTATTTA
Found at i:17140244 original size:29 final size:28
Alignment explanation
Indices: 17140175--17140245 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 28
17140165 TTATTATGTT
17140175 TCTATTTATATTTATTTTGTTATTCTAA
1 TCTATTTATATTTATTTTGTTATTCTAA
*
17140203 TACTA-TTATTATTTATCTAATTTTTATT-T-A
1 T-CTATTTA-TATTTAT-T--TTGTTATTCTAA
17140233 TCTATTTATATTT
1 TCTATTTATATTT
17140246 CTACTATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
28 4 0.11
29 18 0.50
30 6 0.17
31 1 0.03
32 7 0.19
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (28 bp):
TCTATTTATATTTATTTTGTTATTCTAA
Found at i:17140251 original size:44 final size:44
Alignment explanation
Indices: 17140203--17140289 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
17140193 GTTATTCTAA
*
17140203 TACTATTATTAT-TTATCTAATTT-TTAT-TTATCTATTTATATTTC
1 TACTATTATAATATT-TCT-ATTTATTATATT-TCTATTTATATTTC
*
17140247 TACTATTATAATATTTCTATTTATTATATTTCTATTTCTATTT
1 TACTATTATAATATTTCTATTTATTATATTTCTATTTATATTT
17140290 ATATACTGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 4 0.11
44 30 0.79
45 4 0.11
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (44 bp):
TACTATTATAATATTTCTATTTATTATATTTCTATTTATATTTC
Found at i:17143548 original size:177 final size:177
Alignment explanation
Indices: 17143057--17143789 Score: 932
Period size: 177 Copynumber: 4.1 Consensus size: 177
17143047 ATTCGATCCC
* * * * *
17143057 GCTTAGGGAGAAAAGATCTGCAATTTTCAGTTTGTTTCCTTGCTACCTTAGGAAGATAAGACTTG
1 GCTTAGGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTG
* * *
17143122 TATCTTCAACATGCTCTCGTGCTACCTCAGAGAGATAAGGCT-AGTGGCTAAAATCTGTTCCATT
66 TATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGA-TGGCTAAAATCTGCTCCATT
* * ** *
17143186 GCCGATACATGGAGACAAGATTTGCCATCTTCGATCTACTCCACTACT
130 ACCGATACATGGAGATAAGATCCGCCGTCTTCGATCTACTCCACTACT
* * *
17143234 GCTTAGGGATATAAGATCTGCAATTTTCAGTCTGCTTCCTTGCTACCTC-GAAAGATAAGACTTG
1 GCTTAGGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTG
* * * *
17143298 TATCTTCAACCCGCTCTCTTGCTACCTCAGAGAGATAAGGTTGGTGGTTAAAATCTGCTCTC-TT
66 TATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTC-CATT
* *
17143362 ACTGATACATGAAGATAAGATCCGCCGTCTTCGATCTACTCCACTACT
130 ACCGATACATGGAGATAAGATCCGCCGTCTTCGATCTACTCCACTACT
* * * *
17143410 GCTTAGAGAGATAAGATCTGTAATTTTCAGTCTACTTCCTTACTACCTCAGGAAGATAAAACTTG
1 GCTTAGGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTG
*
17143475 TATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGACTGATGGCTAAAATCTGCTCCATTA
66 TATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTCCATTA
** * * * * **
17143540 TTGATACATGGAGATAAGATCTGTCGTATTCGATCTGCTCTGCTACT
131 CCGATACATGGAGATAAGATCCGCCGTCTTCGATCTACTCCACTACT
* * * *
17143587 ACTTAGGGAGATAAGATCTGTAGTTTTCAGTCTGTTTCCTTGCCACCTCAGGAAGATAAGACTTG
1 GCTTAGGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTG
* * * * * * * *
17143652 TATCTTCAACTTGCTCTCTTGTTATCTCAGAGAGATTAGGTTGGTAGCTAAAATCTGCTCCATTG
66 TATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTCCATTA
* * * *
17143717 TCGATACATGGAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACT
131 CCGATACATGGAGATAAGATCCGCCGTCTTCGATCTACTCCACTACT
* * *
17143764 ACTTAGAGAGACAAGATCTGTGAATT
1 GCTTAGGGAGATAAGATCTGT-AATT
17143790 CACAAATGTT
Statistics
Matches: 483, Mismatches: 68, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
176 154 0.32
177 326 0.67
178 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (177 bp):
GCTTAGGGAGATAAGATCTGTAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTG
TATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGATGGCTAAAATCTGCTCCATTA
CCGATACATGGAGATAAGATCCGCCGTCTTCGATCTACTCCACTACT
Found at i:17149330 original size:10 final size:10
Alignment explanation
Indices: 17149315--17149344 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
17149305 TAAAACTTGA
17149315 ATTTAAAATC
1 ATTTAAAATC
*
17149325 ATTTAAAATA
1 ATTTAAAATC
17149335 ATTTAAAATC
1 ATTTAAAATC
17149345 GTTAGTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTTAAAATC
Found at i:17155889 original size:15 final size:15
Alignment explanation
Indices: 17155869--17155918 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
17155859 ATAATATAAT
17155869 TATTTAATAAATATC
1 TATTTAATAAATATC
* * *
17155884 TATTTACTTAATA-A
1 TATTTAATAAATATC
*
17155898 TAATTAATAAATATC
1 TATTTAATAAATATC
17155913 TATTTA
1 TATTTA
17155919 CTTAAATAGT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTAATAAATATC
Found at i:17169855 original size:23 final size:23
Alignment explanation
Indices: 17169801--17169874 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
17169791 CTTATATATG
*
17169801 TTTTTTTACTCTTA-TTATTAACAT
1 TTTTTTTA-T-TTATTTATTTACAT
*
17169825 TTTATTTATTTATTTATTTACAT
1 TTTTTTTATTTATTTATTTACAT
* *
17169848 TTTTTTTA-TTATCTAATTTAAAT
1 TTTTTTTATTTAT-TTATTTACAT
17169871 TTTT
1 TTTT
17169875 ATATAACGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.16
23 29 0.67
24 7 0.16
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTTTATTTATTTATTTACAT
Found at i:17169921 original size:25 final size:25
Alignment explanation
Indices: 17169893--17169986 Score: 73
Period size: 25 Copynumber: 3.7 Consensus size: 25
17169883 CTCATTTCAA
*
17169893 ATTTTTATACATTATTTACTTTAAT
1 ATTTTTATACATTATTTATTTTAAT
* * *
17169918 ATTTTCATAAATTATGTATTTTTAACT
1 ATTTTTATACATTATTTA-TTTTAA-T
* * *
17169945 TTTTTTACACATTATATATTTTGAAT
1 ATTTTTATACATTATTTATTTT-AAT
* *
17169971 -TGTTTATATATTATTT
1 ATTTTTATACATTATTT
17169987 TTAAAGAGTT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
25 27 0.51
26 10 0.19
27 16 0.30
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (25 bp):
ATTTTTATACATTATTTATTTTAAT
Found at i:17171695 original size:14 final size:14
Alignment explanation
Indices: 17171676--17171714 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
17171666 CCAGAAAAGT
17171676 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
17171690 AAATCATTTTCCGG
1 AAATCATTTTCCAG
17171704 AAATCATTTTC
1 AAATCATTTTC
17171715 AGTAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:17180685 original size:25 final size:25
Alignment explanation
Indices: 17180656--17180857 Score: 151
Period size: 25 Copynumber: 8.0 Consensus size: 25
17180646 TGAAATGCCT
* * *
17180656 ATTATTTGGAAAGCCTTAGTGGAGA
1 ATTATCTGGAAAGCCTTTGTGGCGA
* * *
17180681 ATTATCT-AAAAGGCCTTTGTGGTGT
1 ATTATCTGGAAA-GCCTTTGTGGCGA
* * *
17180706 ATTAT-TCGAAAAGCCTTAGTGGCAA
1 ATTATCT-GGAAAGCCTTTGTGGCGA
* *
17180731 AGTTATCTGGGAAGCTTTTGTGGCGA
1 A-TTATCTGGAAAGCCTTTGTGGCGA
** *
17180757 ATTATCTAAAAAGCCTTTGTGGCGT
1 ATTATCTGGAAAGCCTTTGTGGCGA
* * *
17180782 ATTATTTGGAGAG-CTTTAATGGCGA
1 ATTATCTGGAAAGCCTTT-GTGGCGA
* *
17180807 AGTTATCTGGGAAGCCATTGTGGCGA
1 A-TTATCTGGAAAGCCTTTGTGGCGA
17180833 ATTATCT-GAAAGGCCTTTGTGGCGA
1 ATTATCTGGAAA-GCCTTTGTGGCGA
17180858 GATCTAGGTA
Statistics
Matches: 136, Mismatches: 32, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
24 11 0.08
25 83 0.61
26 38 0.28
27 4 0.03
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (25 bp):
ATTATCTGGAAAGCCTTTGTGGCGA
Found at i:17180810 original size:76 final size:76
Alignment explanation
Indices: 17180657--17180856 Score: 258
Period size: 76 Copynumber: 2.6 Consensus size: 76
17180647 GAAATGCCTA
* * * *
17180657 TTATTTGGAAAGCC-TTAGTGGAGAATTATCTAAAAGGCCTTTGTGGTGTATTATTCGAAAAGCC
1 TTATCTGGGAAGCCATT-GTGGCGAATTATCTAAAAGGCCTTTGTGGCGTATTATTCGAAAAGCC
*
17180721 TTAGTGGCAAAG
65 TTAATGGCAAAG
** * * * * *
17180733 TTATCTGGGAAGCTTTTGTGGCGAATTATCTAAAAAGCCTTTGTGGCGTATTATTTGGAGAGCTT
1 TTATCTGGGAAGCCATTGTGGCGAATTATCTAAAAGGCCTTTGTGGCGTATTATTCGAAAAGCCT
*
17180798 TAATGGCGAAG
66 TAATGGCAAAG
*
17180809 TTATCTGGGAAGCCATTGTGGCGAATTATCTGAAAGGCCTTTGTGGCG
1 TTATCTGGGAAGCCATTGTGGCGAATTATCTAAAAGGCCTTTGTGGCG
17180857 AGATCTAGGT
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
76 105 0.98
77 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.34
Consensus pattern (76 bp):
TTATCTGGGAAGCCATTGTGGCGAATTATCTAAAAGGCCTTTGTGGCGTATTATTCGAAAAGCCT
TAATGGCAAAG
Found at i:17186028 original size:15 final size:16
Alignment explanation
Indices: 17186003--17186033 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17185993 AAAATTTTCA
17186003 AAAACTATATATATTT
1 AAAACTATATATATTT
17186019 AAAA-TATATATATTT
1 AAAACTATATATATTT
17186034 TTAATCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAACTATATATATTT
Found at i:17200334 original size:9 final size:9
Alignment explanation
Indices: 17200320--17200346 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17200310 TACCTTTGAG
17200320 GATAGACTT
1 GATAGACTT
17200329 GATAGACTT
1 GATAGACTT
17200338 GATAGACTT
1 GATAGACTT
17200347 AGTAATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (9 bp):
GATAGACTT
Found at i:17208362 original size:24 final size:24
Alignment explanation
Indices: 17208327--17208427 Score: 175
Period size: 24 Copynumber: 4.2 Consensus size: 24
17208317 CCAACACCGT
*
17208327 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
17208351 TCTCCCTTATCAGCTCCTACATCC
1 TCTCCCTTATCAGCTCCTAAATCC
17208375 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
17208399 TCTCCCTTATCAGCTCCTAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
17208423 TCTCC
1 TCTCC
17208428 TGACAGCCTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.20, C:0.43, G:0.04, T:0.34
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:17214765 original size:27 final size:26
Alignment explanation
Indices: 17214711--17214821 Score: 105
Period size: 27 Copynumber: 4.2 Consensus size: 26
17214701 AACATGGCTG
** * *
17214711 CCAGAACAGATAATGTGATAGTGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
17214737 CCAGAACAGATAACTGTGGCAGAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
* * *
17214764 CCATAACAGATATATGTAGCAGTGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
17214791 CAAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
17214818 CCAG
1 CCAG
17214822 GACGCTTCCT
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
26 14 0.21
27 53 0.78
28 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:17215258 original size:16 final size:15
Alignment explanation
Indices: 17215237--17215266 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17215227 AAAATACCGG
17215237 CTTTTCGGCATTTCGA
1 CTTTTCGGC-TTTCGA
17215253 CTTTTCGGCTTTCG
1 CTTTTCGGCTTTCG
17215267 CCGATCTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.27, G:0.20, T:0.47
Consensus pattern (15 bp):
CTTTTCGGCTTTCGA
Found at i:17216284 original size:24 final size:24
Alignment explanation
Indices: 17216252--17216328 Score: 136
Period size: 24 Copynumber: 3.2 Consensus size: 24
17216242 CCAACACCGT
*
17216252 TCTCCCTTATCAGCTCCTACATCC
1 TCTCCCTTATCAGCTCCTAAATCC
17216276 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
17216300 TCTCCCTTATCAGCTCCTAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
17216324 TCTCC
1 TCTCC
17216329 TGACAGCCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.18, C:0.43, G:0.04, T:0.35
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:17216953 original size:15 final size:15
Alignment explanation
Indices: 17216933--17216962 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17216923 CATTTTATTT
*
17216933 ATATTAGGATAATTA
1 ATATTAAGATAATTA
17216948 ATATTAAGATAATTA
1 ATATTAAGATAATTA
17216963 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:17216990 original size:27 final size:26
Alignment explanation
Indices: 17216929--17216991 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
17216919 GCTCCATTTT
17216929 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
17216956 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
17216984 ATTTTATT
1 ATTTTATT
17216992 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:17217006 original size:10 final size:10
Alignment explanation
Indices: 17216987--17217018 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
17216977 TTTTAGGATT
17216987 TTAT-TTTAA
1 TTATCTTTAA
17216996 TTATCTTTAA
1 TTATCTTTAA
17217006 TTATCTTTAA
1 TTATCTTTAA
17217016 TTA
1 TTA
17217019 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:17218155 original size:53 final size:53
Alignment explanation
Indices: 17218017--17218217 Score: 188
Period size: 52 Copynumber: 3.9 Consensus size: 53
17218007 CAGAAAAGAT
* * * * *
17218017 GTGATATGTGTGCCCGTTTAAGACCATAGCTGGGCTATGACATCGGTG-CAAA
1 GTGATATGTGTTCCGGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGAAA
*
17218069 GTGATATGTGTTCCGGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGACA
1 GTGATATGTGTTCCGGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGAAA
* * * *
17218122 -TGATAATGTGATT-CTGTATAAGACCATATCTGGGATATGGCATCAGTGT----
1 GTGAT-ATGTG-TTCCGGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGAAA
* * * *
17218171 GTG--ATGTGATCC-GTGTAAGACCATAGCAGGGCTATGGCTTCGGTGTG
1 GTGATATGTGTTCCGGTATAAGACCATAGCTGGGCTATGGCATCGGTGTG
17218218 TGATATGTGA
Statistics
Matches: 126, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
46 29 0.23
47 6 0.05
50 2 0.02
52 48 0.38
53 39 0.31
54 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (53 bp):
GTGATATGTGTTCCGGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGAAA
Found at i:17218359 original size:17 final size:17
Alignment explanation
Indices: 17218339--17218372 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17218329 CCCAAATAAA
17218339 TTAAATTCGTGAATAGC
1 TTAAATTCGTGAATAGC
17218356 TTAAATTCGTGAATAGC
1 TTAAATTCGTGAATAGC
17218373 AACATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TTAAATTCGTGAATAGC
Found at i:17219190 original size:13 final size:13
Alignment explanation
Indices: 17219172--17219197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17219162 CTCGTAGATC
17219172 CATATTAGGGACT
1 CATATTAGGGACT
17219185 CATATTAGGGACT
1 CATATTAGGGACT
17219198 TAATAATGAA
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:0.23, T:0.31
Consensus pattern (13 bp):
CATATTAGGGACT
Found at i:17229269 original size:14 final size:14
Alignment explanation
Indices: 17229252--17229286 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
17229242 CTCACATTTC
17229252 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
17229266 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
17229280 TATTTCT
1 T-TTTCT
17229287 GCTTCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:17229270 original size:19 final size:18
Alignment explanation
Indices: 17229232--17229276 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
17229222 TACGGTACGC
17229232 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
17229249 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
17229268 TTCTTTTCT
1 TTCTTTTCT
17229277 CCATATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:17229964 original size:41 final size:41
Alignment explanation
Indices: 17229919--17230011 Score: 177
Period size: 41 Copynumber: 2.2 Consensus size: 41
17229909 TACATTGTGA
17229919 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
1 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
17229960 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
1 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
17230001 ATTTGTAGTAG
1 ATTTGT-GTAG
17230012 GTCGAAGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 47 0.92
42 4 0.08
ACGTcount: A:0.25, C:0.02, G:0.33, T:0.40
Consensus pattern (41 bp):
ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
Found at i:17231835 original size:16 final size:17
Alignment explanation
Indices: 17231816--17231847 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17231806 TTATTAAATC
17231816 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
17231832 ATATATTTAATATTAA
1 ATATATTTAATATTAA
17231848 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:17231911 original size:66 final size:63
Alignment explanation
Indices: 17231840--17232052 Score: 194
Period size: 61 Copynumber: 3.4 Consensus size: 63
17231830 AAATATATTT
17231840 AATATTAATTATTTAA-AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATTTTA--TTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
17231904 AG
62 AG
* * * * * * *
17231906 AATATTAATTATTAAGAATTTTATTAA--ATTATATATTTTAATTAT-ATTATATTTA-ATAAT
1 AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATT-TGAGTAAATTCATATAAG
* * * *
17231966 AATTATGTTATT-TT-A-TATTTTA--CAGTATCATATATTATGGTTTGAGTAAATTCATATAAG
1 AA-TAT-TAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
17232026 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAAGAATTTTATTAA
17232053 ATTATATATT
Statistics
Matches: 113, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 30 0.27
60 14 0.12
61 31 0.27
62 5 0.04
63 2 0.02
64 3 0.03
65 4 0.04
66 18 0.16
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:17231926 original size:120 final size:120
Alignment explanation
Indices: 17231802--17232094 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 120
17231792 AATTATTTTA
* * *
17231802 AATTTTATTAAATCATATATTTAAATTAAAATATATTTAATATTAATTAT-TTAAAATTT-TATT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
17231865 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
17231922 AATTTTATTAAATTATATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
17231987 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
17232042 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
17232095 TAAATATGAT
Statistics
Matches: 161, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 4 0.02
120 155 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:17231954 original size:18 final size:17
Alignment explanation
Indices: 17231923--17231957 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17231913 ATTATTAAGA
17231923 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
17231940 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
17231958 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:17232071 original size:18 final size:17
Alignment explanation
Indices: 17232043--17232077 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17232033 ATTATTAAGA
*
17232043 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17232060 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17232078 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17232191 original size:147 final size:149
Alignment explanation
Indices: 17232031--17232305 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
17232021 ATAAGAATAT
*
17232031 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
17232096 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
17232159 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
17232178 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
17232243 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
17232306 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:17232218 original size:18 final size:17
Alignment explanation
Indices: 17232190--17232224 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17232180 ATTATTAAGA
*
17232190 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
17232207 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
17232225 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:17232435 original size:44 final size:45
Alignment explanation
Indices: 17232386--17232480 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
17232376 TTACACCTCT
* *
17232386 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** * *
17232430 ATTACATTCAACCAAACAGTTGATTTGCTATTATACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
17232475 ATTACA
1 ATTACA
17232481 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:17234166 original size:26 final size:25
Alignment explanation
Indices: 17234137--17234195 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
17234127 CTATTTTTAA
17234137 TTAAATTATAATATTATT-ATTATTT
1 TTAAATTATAATATT-TTAATTATTT
* *
17234162 GTTAAATAATGATATTTTAATTATTT
1 -TTAAATTATAATATTTTAATTATTT
*
17234188 TCAAATTA
1 TTAAATTA
17234196 ATTATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (25 bp):
TTAAATTATAATATTTTAATTATTT
Found at i:17243602 original size:14 final size:14
Alignment explanation
Indices: 17243583--17243621 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
17243573 TTGTTTCACT
17243583 GAAAATGACTTT-TA
1 GAAAATGA-TTTCTA
*
17243597 GAAAATGATTTCTG
1 GAAAATGATTTCTA
17243611 GAAAATGATTT
1 GAAAATGATTT
17243622 ACTTTTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:17244120 original size:15 final size:15
Alignment explanation
Indices: 17244065--17244121 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
17244055 TTTATACTAC
*
17244065 AAAATATGTATTATT
1 AAAATATTTATTATT
* *
17244080 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
17244097 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
17244114 AAAATATT
1 AAAATATT
17244122 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:17244185 original size:16 final size:14
Alignment explanation
Indices: 17244154--17244194 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
17244144 ATGTGAATAA
17244154 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
*
17244167 TATTATTTTAAAAA
1 TATTATTTTAAAAT
17244181 T-TTATTATTAAAAT
1 TATTATT-TTAAAAT
17244195 AAAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:17244242 original size:22 final size:22
Alignment explanation
Indices: 17244198--17244257 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
17244188 TTAAAATAAA
*
17244198 ATTAAAATATTAAA-TA-ATTT
1 ATTAAAATAATAAATTATATTT
17244218 ATTAAAATAATAAATTATATTT
1 ATTAAAATAATAAATTATATTT
* * *
17244240 ATTATATTAATAATTTAT
1 ATTAAAATAATAAATTAT
17244258 TATATGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.38
21 2 0.06
22 19 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAAATAATAAATTATATTT
Found at i:17250272 original size:94 final size:93
Alignment explanation
Indices: 17250146--17250332 Score: 236
Period size: 94 Copynumber: 2.0 Consensus size: 93
17250136 ATCAATTGAT
* *
17250146 AGGAATTGAACTGTCAAAAAATCATTTGAATATTTCAA-ATATGCAAAAGAATACAAATTGATGG
1 AGGAATTGAACTGTCAAAAAATCATTTCAATATTT-AACATACGCAAAAGAATACAAATTGATGG
17250210 CTTATGACG-TTTCTTCAATTAGTATAAA
65 CTTATGACGTTTTCTTCAATTAGTATAAA
* *** *
17250238 AGGAATATGAACTGTCCAAAAAA-CAATTTCAATATTTAACATACGTAGTGGAATCCAAATTGAT
1 AGGAAT-TGAACTGT-CAAAAAATC-ATTTCAATATTTAACATACGCAAAAGAATACAAATTGAT
* *
17250302 GGCTTATGATGTTTTCTTCAATTAGTGTAAA
63 GGCTTATGACGTTTTCTTCAATTAGTATAAA
17250333 TTGTAATGAG
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
92 6 0.07
93 11 0.14
94 46 0.57
95 18 0.22
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (93 bp):
AGGAATTGAACTGTCAAAAAATCATTTCAATATTTAACATACGCAAAAGAATACAAATTGATGGC
TTATGACGTTTTCTTCAATTAGTATAAA
Found at i:17259780 original size:29 final size:28
Alignment explanation
Indices: 17259709--17259782 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
17259699 AAGTCTACAT
* * *
17259709 ACATGCATATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCATTAGGCCCAAAC
*
17259737 TCATTCATATGGCCCATTAGGCCCAAAAC
1 ACATTCATATGGCCCATTAGGCCC-AAAC
* *
17259766 ACGTTCATATAGCCCAT
1 ACATTCATATGGCCCAT
17259783 CCGGCCCGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCCAAAC
Found at i:17263900 original size:18 final size:17
Alignment explanation
Indices: 17263878--17263926 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
17263868 TTTTCATATC
*
17263878 TCAATTCAATATCCTAA
1 TCAATTCAATATCATAA
17263895 TCCAATTCAA-ATTCATAA
1 T-CAATTCAATA-TCATAA
17263913 TC-ATTCAATATCAT
1 TCAATTCAATATCAT
17263927 TCATATTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 10 0.36
17 4 0.14
18 14 0.50
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (17 bp):
TCAATTCAATATCATAA
Found at i:17265027 original size:16 final size:17
Alignment explanation
Indices: 17264995--17265037 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
17264985 TCTCCTTCTG
17264995 TGTTTCGTTTTCAATTC
1 TGTTTCGTTTTCAATTC
*
17265012 TGTTTCTTTTTC-ATTC
1 TGTTTCGTTTTCAATTC
*
17265028 T-TTTTGTTTT
1 TGTTTCGTTTT
17265038 GTTTTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 11 0.48
ACGTcount: A:0.07, C:0.14, G:0.09, T:0.70
Consensus pattern (17 bp):
TGTTTCGTTTTCAATTC
Found at i:17271281 original size:17 final size:17
Alignment explanation
Indices: 17271242--17271275 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17271232 TCAATTTGTA
*
17271242 AATAATGATTAAAAAAT
1 AATAATGAATAAAAAAT
17271259 AATAATGAATAAAAAAT
1 AATAATGAATAAAAAAT
17271276 TTTAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (17 bp):
AATAATGAATAAAAAAT
Found at i:17275331 original size:3 final size:3
Alignment explanation
Indices: 17275325--17275377 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
17275315 GCTCCTTTAT
* * *
17275325 TTA TTA TATA TATA TTAA GTA TTA TTG TAA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA T-TA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17275373 TTA TT
1 TTA TT
17275378 TTGGTTTTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
3 33 0.79
4 9 0.21
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:17275627 original size:29 final size:29
Alignment explanation
Indices: 17275594--17275677 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
17275584 AAGAATGGGA
17275594 AATTATTATATGAAACAATTTTTTTTGTT
1 AATTATTATATGAAACAATTTTTTTTGTT
*
17275623 CATTATTATATGAAAC-ATTTGTTTCTTGTT
1 AATTATTATATGAAACAATTT-TTT-TTGTT
**
17275653 AAGAACTTA-AT-AAACAATTTTTTTT
1 AATTA-TTATATGAAACAATTTTTTTT
17275678 TAAGTCGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 6 0.13
29 25 0.53
30 13 0.28
31 3 0.06
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (29 bp):
AATTATTATATGAAACAATTTTTTTTGTT
Found at i:17275996 original size:30 final size:30
Alignment explanation
Indices: 17275962--17276021 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
17275952 GTCATTATAG
17275962 GATAAATTCCTTGGGTTTCTAGTCAATTAT
1 GATAAATTCCTTGGGTTTCTAGTCAATTAT
17275992 GATAAATTCCTTGGGTTTCTAGTCAATTAT
1 GATAAATTCCTTGGGTTTCTAGTCAATTAT
17276022 CCTTGAATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (30 bp):
GATAAATTCCTTGGGTTTCTAGTCAATTAT
Found at i:17279169 original size:22 final size:22
Alignment explanation
Indices: 17279092--17279172 Score: 58
Period size: 22 Copynumber: 3.6 Consensus size: 22
17279082 AAGTCAAATG
*
17279092 CGTTCAACATTTATTTATTATT
1 CGTTGAACATTTATTTATTATT
* * * *
17279114 CAAATTGAACAATAATAT-TTATT
1 C--GTTGAACATTTATTTATTATT
**
17279137 CGATT-TCCATTTATTTATTATT
1 CG-TTGAACATTTATTTATTATT
17279159 CGTTGAACATTTAT
1 CGTTGAACATTTAT
17279173 AATTATTTAA
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
21 8 0.20
22 17 0.41
23 6 0.15
24 10 0.24
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.49
Consensus pattern (22 bp):
CGTTGAACATTTATTTATTATT
Found at i:17279710 original size:33 final size:33
Alignment explanation
Indices: 17279671--17279735 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
17279661 GGATTCAAAA
*
17279671 TAACATTATTCACCATGTCACGTTTAAAAATAC
1 TAACATTATTCACCATGTCACATTTAAAAATAC
*
17279704 TAACATTATTCACCATGTCACATTTACAAATA
1 TAACATTATTCACCATGTCACATTTAAAAATA
17279736 GTAGAAGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.34
Consensus pattern (33 bp):
TAACATTATTCACCATGTCACATTTAAAAATAC
Found at i:17284737 original size:52 final size:52
Alignment explanation
Indices: 17284675--17284778 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
17284665 CACAAATGAG
17284675 ATAATTTCATTTCTAACGATATCTTTTATCTTTTTTTCTTCTTCCTCTTTTT
1 ATAATTTCATTTCTAACGATATCTTTTATCTTTTTTTCTTCTTCCTCTTTTT
*
17284727 ATAATTTCATTTCTAACGATATCTTTTATCTTTTTTTTTTCTTCCTCTTTTT
1 ATAATTTCATTTCTAACGATATCTTTTATCTTTTTTTCTTCTTCCTCTTTTT
17284779 TGTTGGGGTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.17, C:0.18, G:0.02, T:0.62
Consensus pattern (52 bp):
ATAATTTCATTTCTAACGATATCTTTTATCTTTTTTTCTTCTTCCTCTTTTT
Found at i:17284753 original size:27 final size:27
Alignment explanation
Indices: 17284675--17284755 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
17284665 CACAAATGAG
17284675 ATAATTTCATTTCTAACGATATCTTTT
1 ATAATTTCATTTCTAACGATATCTTTT
* * * * *
17284702 AT-CTTT-TTTTCT-TC-TTCCTCTTTTT
1 ATAATTTCATTTCTAACGAT-ATC-TTTT
17284727 ATAATTTCATTTCTAACGATATCTTTT
1 ATAATTTCATTTCTAACGATATCTTTT
17284754 AT
1 AT
17284756 CTTTTTTTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
23 1 0.03
24 3 0.08
25 11 0.29
26 6 0.16
27 13 0.34
28 3 0.08
29 1 0.03
ACGTcount: A:0.22, C:0.17, G:0.02, T:0.58
Consensus pattern (27 bp):
ATAATTTCATTTCTAACGATATCTTTT
Found at i:17286058 original size:36 final size:37
Alignment explanation
Indices: 17286011--17286101 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
17286001 GTCTCCAAAT
* * *
17286011 TCACATTTCAATTCAATTTCATTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
* *
17286047 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCACTTTCAAG
17286085 TCA-ATATTCAATTCAAT
1 TCACA-ATTCAATTCAAT
17286102 ACATATATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
36 13 0.28
37 21 0.46
38 12 0.26
ACGTcount: A:0.33, C:0.22, G:0.01, T:0.44
Consensus pattern (37 bp):
TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
Found at i:17286790 original size:14 final size:14
Alignment explanation
Indices: 17286771--17286800 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17286761 AAACCCTAAA
17286771 TTTCTTCTTTTCTT
1 TTTCTTCTTTTCTT
*
17286785 TTTCTTTTTTTCTT
1 TTTCTTCTTTTCTT
17286799 TT
1 TT
17286801 CTTTCTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTTCTTTTCTT
Found at i:17288048 original size:12 final size:12
Alignment explanation
Indices: 17288031--17288086 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
17288021 TTAATACTCT
17288031 AAATTAAAACAA
1 AAATTAAAACAA
*
17288043 AAATT-ATACATA
1 AAATTAAAACA-A
* **
17288055 AAATTAATACTCT
1 AAATTAAAAC-AA
17288068 AAATTAAAACAA
1 AAATTAAAACAA
17288080 AAATTAA
1 AAATTAA
17288087 TAATTTCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
11 4 0.11
12 18 0.51
13 13 0.37
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATTAAAACAA
Found at i:17288053 original size:37 final size:37
Alignment explanation
Indices: 17288011--17288085 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
17288001 CTCCAAAAAA
*
17288011 ATACATAAAGTTAATACTCTAAATTAAAACAAAAATT
1 ATACATAAAATTAATACTCTAAATTAAAACAAAAATT
17288048 ATACATAAAATTAATACTCTAAATTAAAACAAAAATT
1 ATACATAAAATTAATACTCTAAATTAAAACAAAAATT
17288085 A
1 A
17288086 ATAATTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.59, C:0.11, G:0.01, T:0.29
Consensus pattern (37 bp):
ATACATAAAATTAATACTCTAAATTAAAACAAAAATT
Found at i:17290534 original size:25 final size:24
Alignment explanation
Indices: 17290506--17290552 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
17290496 AAATATAACA
*
17290506 TAAAACAAATAAAACAAATGAAACG
1 TAAAACAAATAAAA-AAAGGAAACG
* *
17290531 TAAAAGAAGTAAAAAAAGGAAA
1 TAAAACAAATAAAAAAAGGAAA
17290553 GAAAGTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.70, C:0.06, G:0.13, T:0.11
Consensus pattern (24 bp):
TAAAACAAATAAAAAAAGGAAACG
Found at i:17291607 original size:39 final size:39
Alignment explanation
Indices: 17291500--17291634 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
17291490 GACCTCGAGT
* * * *
17291500 CGATGAGACACTAGGTGTC-ACTAAATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAACT--ATTACTTCGGCTAG-TC
** ** *
17291541 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
17291579 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
17291618 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
17291635 CCATATTGGT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 3 0.04
41 14 0.19
42 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:17291777 original size:18 final size:18
Alignment explanation
Indices: 17291754--17291794 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17291744 AAAGAAAAAA
17291754 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
17291772 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
17291790 AGAAA
1 AGAAA
17291795 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:17292303 original size:20 final size:20
Alignment explanation
Indices: 17292280--17292317 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17292270 GTTATTAAGT
17292280 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
17292300 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
17292318 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:17296578 original size:32 final size:32
Alignment explanation
Indices: 17296542--17296701 Score: 257
Period size: 32 Copynumber: 5.0 Consensus size: 32
17296532 TATAACTATG
17296542 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
17296574 CTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
17296606 CTACTTTTTTATATGTGAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
*
17296638 CTACTTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
17296670 CTACTTTTTTATATGTATACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
17296702 ATTTTTTATG
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 116 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:17298531 original size:24 final size:24
Alignment explanation
Indices: 17298498--17298587 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
17298488 TTGACGATTC
*
17298498 AAATCTGCACACATAGTGCTATAT
1 AAATCCGCACACATAGTGCTATAT
*
17298522 AAATCCGCACACATAGTGCTATAC
1 AAATCCGCACACATAGTGCTATAT
*
17298546 AAATCCGCACACATAGTGCCAT-T
1 AAATCCGCACACATAGTGCTATAT
17298569 CAAATCCGCACACATAGTG
1 -AAATCCGCACACATAGTG
17298588 TAACATCCCG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCTATAT
Found at i:17298551 original size:73 final size:72
Alignment explanation
Indices: 17298425--17298587 Score: 186
Period size: 73 Copynumber: 2.2 Consensus size: 72
17298415 TCCATCAAGG
* * * * * *
17298425 AAATTTGCACCCATAGTGCCATGTTAACCCGCACACATAGTGCCTTAATAATCCATACACATATT
1 AAATCTGCACACATAGTGCCATATAAACCCGCACACATAGTGCCTTAATAATCCACACACATAGT
*
17298490 GACGATTC
66 G-CCATTC
* * *
17298498 AAATCTGCACACATAGTGCTATATAAATCCGCACACATAGTG-CTATACA-AATCCGCACACATA
1 AAATCTGCACACATAGTGCCATATAAACCCGCACACATAGTGCCT-TA-ATAATCCACACACATA
17298561 GTGCCATTC
64 GTGCCATTC
*
17298570 AAATCCGCACACATAGTG
1 AAATCTGCACACATAGTG
17298588 TAACATCCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
72 24 0.31
73 52 0.68
74 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.25
Consensus pattern (72 bp):
AAATCTGCACACATAGTGCCATATAAACCCGCACACATAGTGCCTTAATAATCCACACACATAGT
GCCATTC
Found at i:17298574 original size:48 final size:48
Alignment explanation
Indices: 17298453--17298587 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 48
17298443 CCATGTTAAC
** * *
17298453 CCGCACACATAGTGCC-TTAATAATCCATACACATATTGACGATTCAAAT
1 CCGCACACATAGTGCCATT-A-AATCCGCACACATAGTGACGATACAAAT
* * *
17298502 CTGCACACATAGTGCTATATAAATCCGCACACATAGTG-CTATACAAAT
1 CCGCACACATAGTGCCAT-TAAATCCGCACACATAGTGACGATACAAAT
17298550 CCGCACACATAGTGCCATTCAAATCCGCACACATAGTG
1 CCGCACACATAGTGCCATT-AAATCCGCACACATAGTG
17298588 TAACATCCCG
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 1 0.01
48 42 0.57
49 28 0.38
50 2 0.03
51 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.24
Consensus pattern (48 bp):
CCGCACACATAGTGCCATTAAATCCGCACACATAGTGACGATACAAAT
Found at i:17299848 original size:46 final size:44
Alignment explanation
Indices: 17299796--17299881 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
17299786 AGAACAGAAA
*
17299796 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGGAT
*
17299842 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACA
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACA
17299882 AGAATAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 17 0.45
46 21 0.55
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGGAT
Found at i:17299895 original size:44 final size:45
Alignment explanation
Indices: 17299798--17299922 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 45
17299788 AACAGAAATG
* * * *
17299798 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGATTG
1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAAGAATA
*
17299844 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAAGAATA
1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
** * * *
17299888 ATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
17299923 CAGGATATTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.53
45 1 0.02
46 30 0.45
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
Found at i:17304148 original size:32 final size:32
Alignment explanation
Indices: 17304107--17304172 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
17304097 GTTATTTTGA
17304107 TAATATGGGGTTTCCACTAATAAATTGTACTT
1 TAATATGGGGTTTCCACTAATAAATTGTACTT
17304139 TAATATGGGGTTTCCACTAATAAATTGTACTT
1 TAATATGGGGTTTCCACTAATAAATTGTACTT
17304171 TA
1 TA
17304173 GTTAATATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (32 bp):
TAATATGGGGTTTCCACTAATAAATTGTACTT
Found at i:17307764 original size:14 final size:14
Alignment explanation
Indices: 17307745--17307776 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
17307735 TGTAGTTCAT
17307745 TTAGACATATGTGA
1 TTAGACATATGTGA
17307759 TTAGACATATGTGA
1 TTAGACATATGTGA
17307773 TTAG
1 TTAG
17307777 GTCTCAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (14 bp):
TTAGACATATGTGA
Found at i:17313250 original size:20 final size:20
Alignment explanation
Indices: 17313225--17313262 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17313215 AGGATAAAAT
17313225 TTAAAATA-TAAATATTAATG
1 TTAAAATACTAAA-ATTAATG
17313245 TTAAAATACTAAAATTAA
1 TTAAAATACTAAAATTAA
17313263 CATTATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
TTAAAATACTAAAATTAATG
Found at i:17313276 original size:27 final size:26
Alignment explanation
Indices: 17313246--17313301 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
17313236 ATATTAATGT
17313246 TAAAATACTAAAATTAACATTATGATA
1 TAAAATA-TAAAATTAACATTATGATA
* * *
17313273 TAAAAATATATAATTAACTTTTTGATA
1 T-AAAATATAAAATTAACATTATGATA
17313300 TA
1 TA
17313302 TATAATTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 1 0.04
27 18 0.72
28 6 0.24
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (26 bp):
TAAAATATAAAATTAACATTATGATA
Found at i:17322061 original size:33 final size:33
Alignment explanation
Indices: 17322019--17322084 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17322009 GATGTGATTA
17322019 AGCAACTGTAGGAACCTAAGTTTTTCATTTTTT
1 AGCAACTGTAGGAACCTAAGTTTTTCATTTTTT
17322052 AGCAACTGTAGGAACCTAAGTTTTTCATTTTTT
1 AGCAACTGTAGGAACCTAAGTTTTTCATTTTTT
17322085 TCTTTAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
AGCAACTGTAGGAACCTAAGTTTTTCATTTTTT
Found at i:17332200 original size:21 final size:21
Alignment explanation
Indices: 17332174--17332214 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17332164 AGACGAGCAA
* *
17332174 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
17332195 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
17332215 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:17338353 original size:21 final size:20
Alignment explanation
Indices: 17338313--17338355 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
17338303 TTTAATTTTA
17338313 TTCATATTTTAAATATAAAT
1 TTCATATTTTAAATATAAAT
17338333 TTCAT-TTTTAAACTAATAAAT
1 TTCATATTTTAAA-T-ATAAAT
17338354 TT
1 TT
17338356 TTTTCTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 8 0.38
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCATATTTTAAATATAAAT
Found at i:17346513 original size:21 final size:21
Alignment explanation
Indices: 17346487--17346527 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17346477 ATCTGCTCAA
* *
17346487 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
17346508 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
17346528 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:17351421 original size:6 final size:6
Alignment explanation
Indices: 17351403--17351453 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
17351393 ACTACCTTGA
* * * *
17351403 TCTA-C TCTTCC TCTACC TCTACC TCTACC TCTACC TTTACC CCTTCC
1 TCTACC TCTACC TCTACC TCTACC TCTACC TCTACC TCTACC TCTACC
17351450 TCTA
1 TCTA
17351454 AAATTGGAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
5 3 0.08
6 34 0.92
ACGTcount: A:0.14, C:0.47, G:0.00, T:0.39
Consensus pattern (6 bp):
TCTACC
Found at i:17351433 original size:18 final size:18
Alignment explanation
Indices: 17351403--17351453 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
17351393 ACTACCTTGA
17351403 TCTA-CTCTTCCTCTACC
1 TCTACCTCTTCCTCTACC
*
17351420 TCTACCTCTACCTCTACC
1 TCTACCTCTTCCTCTACC
* *
17351438 TTTACCCCTTCCTCTA
1 TCTACCTCTTCCTCTA
17351454 AAATTGGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.14, C:0.47, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTACCTCTTCCTCTACC
Found at i:17355017 original size:23 final size:23
Alignment explanation
Indices: 17354954--17355018 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
17354944 CCTAATCAGT
* *
17354954 ATACGACATAT-AAGTGCTTG-A
1 ATACGACACATAAAGTGCCTGAA
* * *
17354975 A-ACGACACACAAGGTACCTGAA
1 ATACGACACATAAAGTGCCTGAA
17354997 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
17355019 TTGGAAAAGC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 7 0.21
21 7 0.21
22 2 0.06
23 17 0.52
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Done.