Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold230
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: 2055625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 13 of 14
Found at i:1716479 original size:15 final size:16
Alignment explanation
Indices: 1716442--1716481 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1716432 CGTTTAATAA
1716442 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
*
1716458 ATTTTAAATTTATATT
1 ATTTTAAATTTAAATT
1716474 -TTTTAAAT
1 ATTTTAAAT
1716482 AAACTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:1721425 original size:2 final size:2
Alignment explanation
Indices: 1721420--1721451 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1721410 GTATATATCC
1721420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1721452 CCATGGACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1721777 original size:2 final size:2
Alignment explanation
Indices: 1721770--1721796 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1721760 AACTCTAAGT
1721770 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1721797 TTATTCAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1722650 original size:25 final size:26
Alignment explanation
Indices: 1722597--1722646 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
1722587 GTCTGATTGT
1722597 TTTAATTGAAATTTTAAATTTTAAAA
1 TTTAATTGAAATTTTAAATTTTAAAA
*
1722623 TTTAATT-AAATTTT-ATTTTTAAAA
1 TTTAATTGAAATTTTAAATTTTAAAA
1722647 ATTTGAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.39
25 7 0.30
26 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTAATTGAAATTTTAAATTTTAAAA
Found at i:1722929 original size:25 final size:25
Alignment explanation
Indices: 1722901--1722949 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1722891 ATTTTTTATT
**
1722901 ATATATCATATTTTAAAATTAATTA
1 ATATATCATATTAAAAAATTAATTA
*
1722926 ATATATTATATTAAAAAATTAATT
1 ATATATCATATTAAAAAATTAATT
1722950 TATTATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATATCATATTAAAAAATTAATTA
Found at i:1726832 original size:2 final size:2
Alignment explanation
Indices: 1726825--1726855 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1726815 ATGCTTCTCA
1726825 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 A
1726856 GGTCGATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1728303 original size:15 final size:16
Alignment explanation
Indices: 1728283--1728312 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1728273 CCTTCAAACA
1728283 AACAAT-TAAAGTAAT
1 AACAATGTAAAGTAAT
1728298 AACAATGTAAAGTAA
1 AACAATGTAAAGTAA
1728313 AGAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (16 bp):
AACAATGTAAAGTAAT
Found at i:1739139 original size:52 final size:53
Alignment explanation
Indices: 1739030--1739140 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 53
1739020 TTAGTCCACT
* * * *
1739030 CAACAATGGAGGCAGCATTACCAAAAAAAAAATGCTGAGGTGTAATGGAATTTAACC
1 CAACAATGGAGGCACCATTACC----AAAAAATGCTGAGCTGTAAAGGAATTAAACC
*
1739087 CAACAATGGAGGCACCATTACC-AAAAATGCTGTGCTGTAAAGGAATTAAACC
1 CAACAATGGAGGCACCATTACCAAAAAATGCTGAGCTGTAAAGGAATTAAACC
1739139 CA
1 CA
1739141 TGGTCTTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
52 28 0.57
57 21 0.43
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (53 bp):
CAACAATGGAGGCACCATTACCAAAAAATGCTGAGCTGTAAAGGAATTAAACC
Found at i:1745762 original size:24 final size:24
Alignment explanation
Indices: 1745730--1745779 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1745720 AACCTCCTTG
1745730 TAAGGAAACAGAAATGAATGATCA
1 TAAGGAAACAGAAATGAATGATCA
*
1745754 TAAGGAAACAGAAATGAATGGTCA
1 TAAGGAAACAGAAATGAATGATCA
1745778 TA
1 TA
1745780 GGTGGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.18
Consensus pattern (24 bp):
TAAGGAAACAGAAATGAATGATCA
Found at i:1747044 original size:13 final size:14
Alignment explanation
Indices: 1747018--1747046 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1747008 GAGACATGAG
1747018 ACACAAATCTTATA
1 ACACAAATCTTATA
1747032 ACACAAA-CTTATA
1 ACACAAATCTTATA
1747045 AC
1 AC
1747047 TATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (14 bp):
ACACAAATCTTATA
Found at i:1750753 original size:15 final size:15
Alignment explanation
Indices: 1750729--1750764 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
1750719 AATTTTATCA
1750729 TAAATATATTTATTTT
1 TAAATATA-TTATTTT
1750745 TAAAT-TATTATTTT
1 TAAATATATTATTTT
1750759 TAAATA
1 TAAATA
1750765 AAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.63
15 2 0.11
16 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAAATATATTATTTT
Found at i:1750828 original size:16 final size:17
Alignment explanation
Indices: 1750807--1750840 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1750797 TTGTTTTTAT
1750807 TATTTTT-ATT-TAAAA
1 TATTTTTAATTATAAAA
1750822 TATTTTTAATTATAAAA
1 TATTTTTAATTATAAAA
1750839 TA
1 TA
1750841 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTAATTATAAAA
Found at i:1751233 original size:25 final size:26
Alignment explanation
Indices: 1751205--1751257 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
1751195 TCTTTAAACT
* *
1751205 TTTTTAAATAATAATAAT-TAATTTA
1 TTTTTAAATAAAAATAATATAATATA
1751230 TTTTTAAATAAAAATAATATAATATA
1 TTTTTAAATAAAAATAATATAATATA
1751256 TT
1 TT
1751258 AATATTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTTTAAATAAAAATAATATAATATA
Found at i:1751266 original size:25 final size:24
Alignment explanation
Indices: 1751233--1751305 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
1751223 TAATTTATTT
*
1751233 TTAAA-TAAAAATAATATAATATA
1 TTAAATTAAAGATAATATAATATA
* *
1751256 TTAATATTAAAGTTAATAT-ATACAA
1 TTAA-ATTAAAGATAATATAATA-TA
*
1751281 TTAAATTAAAGATAAGTTTAATATA
1 TTAAATTAAAGATAA-TATAATATA
1751306 GTTTTTGATC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 4 0.10
24 14 0.36
25 18 0.46
26 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (24 bp):
TTAAATTAAAGATAATATAATATA
Found at i:1752171 original size:14 final size:14
Alignment explanation
Indices: 1752152--1752190 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1752142 TTTATTTTAT
1752152 AATTTTATTTAAAA
1 AATTTTATTTAAAA
*
1752166 AATTTTA-ATAAAA
1 AATTTTATTTAAAA
*
1752179 AATATTATTTAA
1 AATTTTATTTAA
1752191 TTTATTGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTTTATTTAAAA
Found at i:1765612 original size:4 final size:4
Alignment explanation
Indices: 1765603--1765628 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1765593 CTTAATGTCC
1765603 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
1765629 CTATTGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1765931 original size:3 final size:3
Alignment explanation
Indices: 1765923--1765952 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1765913 TTTATGACAC
1765923 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1765953 CAAGCAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1769441 original size:40 final size:41
Alignment explanation
Indices: 1769365--1769465 Score: 143
Period size: 40 Copynumber: 2.5 Consensus size: 41
1769355 GCATAACTTT
1769365 ACACGAGGAATACTTATAATTAAATTGAGTAATATATAATA
1 ACACGAGGAATACTTATAATTAAATTGAGTAATATATAATA
* * * *
1769406 ATATGAGGAATACTTAT-ATTTAATTGAGTCATATATAATA
1 ACACGAGGAATACTTATAATTAAATTGAGTAATATATAATA
*
1769446 ACACGAGAAATACTT-TAATT
1 ACACGAGGAATACTTATAATT
1769466 GAGCTAGTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.02
40 36 0.69
41 15 0.29
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (41 bp):
ACACGAGGAATACTTATAATTAAATTGAGTAATATATAATA
Found at i:1772216 original size:28 final size:29
Alignment explanation
Indices: 1772173--1772233 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
1772163 ATGTTAGTAG
* *
1772173 TTTGACCCCCACTGGAATTCTTTTGACT-
1 TTTGACCCCCAATGGAATTCTTTTAACTC
1772201 TTTGACCCCCAATGGAATTCTTTTAACTC
1 TTTGACCCCCAATGGAATTCTTTTAACTC
1772230 TTTG
1 TTTG
1772234 TTTTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (29 bp):
TTTGACCCCCAATGGAATTCTTTTAACTC
Found at i:1772720 original size:2 final size:2
Alignment explanation
Indices: 1772713--1772740 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1772703 ATAGTAATAA
1772713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1772741 TTGAACCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1773537 original size:19 final size:19
Alignment explanation
Indices: 1773505--1773541 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1773495 TTTTTATATG
1773505 ATTATATTTATTTAATTTA
1 ATTATATTTATTTAATTTA
1773524 ATTAT-TTTATTTTAATTT
1 ATTATATTTA-TTTAATTT
1773542 TTATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTATATTTATTTAATTTA
Found at i:1773784 original size:20 final size:19
Alignment explanation
Indices: 1773740--1773784 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1773730 TTTATTAACA
*
1773740 TATTTATAATATAAAAAAT
1 TATTTAAAATATAAAAAAT
*
1773759 TA-TTAAAATATATAAAAT
1 TATTTAAAATATAAAAAAT
1773777 TAATTTAA
1 T-ATTTAA
1773785 TTTTATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 15 0.68
19 3 0.14
20 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTTAAAATATAAAAAAT
Found at i:1774170 original size:2 final size:2
Alignment explanation
Indices: 1774165--1774196 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1774155 ACACACATAC
1774165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1774197 GATTAACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1777656 original size:2 final size:2
Alignment explanation
Indices: 1777649--1777678 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1777639 AATTACAAAC
1777649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1777679 TTAACTCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1778801 original size:6 final size:6
Alignment explanation
Indices: 1778790--1778827 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1778780 CCCCCCTTTG
*
1778790 TTTTTC TTTTTC TTTTTCC TTTTT- TTTTTT TTTTTC TT
1 TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC TTTTTC TT
1778828 CTCTAGCCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:1779541 original size:4 final size:4
Alignment explanation
Indices: 1779532--1779557 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1779522 AATTACTTGT
1779532 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
1779558 TACAAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1780533 original size:192 final size:192
Alignment explanation
Indices: 1780206--1780784 Score: 1122
Period size: 192 Copynumber: 3.0 Consensus size: 192
1780196 CACTGGATTT
1780206 TTTATGGGGAAAAGAAAAGGCTAATTACATTTACTTGTTTAGCAAGATGAGAATTAATACTCATG
1 TTTATGGGGAAAAGAAAAGGCTAATTACATTTACTTGTTTAGCAAGATGAGAATTAATACTCATG
*
1780271 ATTTATATATTTTTATTATTTTTATTATAATTATATTTAAAATATTTTATATTTATATTAATTTT
66 ATTTATATATTTATATTATTTTTATTATAATTATATTTAAAATATTTTATATTTATATTAATTTT
1780336 AATATCTTAATAATTTATATTATATATATTTTGAGAATATATTTATCTCGTATTATATCATA
131 AATATCTTAATAATTTATATTATATATATTTTGAGAATATATTTATCTCGTATTATATCATA
*
1780398 TTTATGGGGAAAAGAAAAGGCTAATTACATTTACTTGTTTAACAAGATGAGAATTAATACTCATG
1 TTTATGGGGAAAAGAAAAGGCTAATTACATTTACTTGTTTAGCAAGATGAGAATTAATACTCATG
1780463 ATTTATATATTTATATTATTTTTATTATAATTATATTTAAAATATTTTATATTTATATTAATTTT
66 ATTTATATATTTATATTATTTTTATTATAATTATATTTAAAATATTTTATATTTATATTAATTTT
* *
1780528 AATATCTTAATAATTTATATTATATATATTTTGAAAATATATTTATCTCGTATTATATCGTA
131 AATATCTTAATAATTTATATTATATATATTTTGAGAATATATTTATCTCGTATTATATCATA
1780590 TTTATGGGGAAAAGAAAAGGCTAATTACATTTACTTGTTTAGCAAGATGAGAATTAATACTCATG
1 TTTATGGGGAAAAGAAAAGGCTAATTACATTTACTTGTTTAGCAAGATGAGAATTAATACTCATG
1780655 ATTTATATATTTATATTATTTTTATTATAATTATATTTAAAATATTTTATATTTATATTAATTTT
66 ATTTATATATTTATATTATTTTTATTATAATTATATTTAAAATATTTTATATTTATATTAATTTT
1780720 AATATCTTAATAATTTATATTATATATATTTTGAGAATATATTTATCTCGTATTATATCATA
131 AATATCTTAATAATTTATATTATATATATTTTGAGAATATATTTATCTCGTATTATATCATA
1780782 TTT
1 TTT
1780785 TTATAATTTT
Statistics
Matches: 380, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 380 1.00
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (192 bp):
TTTATGGGGAAAAGAAAAGGCTAATTACATTTACTTGTTTAGCAAGATGAGAATTAATACTCATG
ATTTATATATTTATATTATTTTTATTATAATTATATTTAAAATATTTTATATTTATATTAATTTT
AATATCTTAATAATTTATATTATATATATTTTGAGAATATATTTATCTCGTATTATATCATA
Found at i:1780822 original size:25 final size:26
Alignment explanation
Indices: 1780770--1780822 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
1780760 ATTTATCTCG
* **
1780770 TATTATATCATATTTTTATAATTTTA
1 TATTATATCATATTTATATAATCATA
*
1780796 TATT-TATCGTATTTATATAATCATA
1 TATTATATCATATTTATATAATCATA
1780821 TA
1 TA
1780823 AAATATTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTATATCATATTTATATAATCATA
Found at i:1782106 original size:27 final size:25
Alignment explanation
Indices: 1782044--1782110 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
1782034 ATAAGAAGTG
1782044 ATTTATTTATATTATTATAAAATTA
1 ATTTATTTATATTATTATAAAATTA
*
1782069 ATTTAATTTTATATGTA-TATATAATTTA
1 ATTT-A-TTTATAT-TATTATA-AAATTA
1782097 TATTTATTTA-ATTA
1 -ATTTATTTATATTA
1782111 AATTATTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
25 6 0.17
26 3 0.08
27 15 0.42
28 8 0.22
29 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
ATTTATTTATATTATTATAAAATTA
Found at i:1782792 original size:28 final size:28
Alignment explanation
Indices: 1782750--1782805 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1782740 GCTGGTGACA
1782750 ATGAGTAGCTCTTACGCCGCCGTGGGAG
1 ATGAGTAGCTCTTACGCCGCCGTGGGAG
*
1782778 ATGAGTAGCTTTTACGCCGCCGTGGGAG
1 ATGAGTAGCTCTTACGCCGCCGTGGGAG
1782806 GCAATTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.23, G:0.36, T:0.23
Consensus pattern (28 bp):
ATGAGTAGCTCTTACGCCGCCGTGGGAG
Found at i:1783172 original size:2 final size:2
Alignment explanation
Indices: 1783165--1783189 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1783155 ACCTATAGTG
1783165 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1783190 GACATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1784312 original size:6 final size:6
Alignment explanation
Indices: 1784301--1784339 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
1784291 TCAAAGAAGC
*
1784301 AAGCAA AAGCAAA AAGCAAA AAGCAA AAGCAA AACCAA A
1 AAGCAA AAGC-AA AAGC-AA AAGCAA AAGCAA AAGCAA A
1784340 GCATATTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 18 0.58
7 13 0.42
ACGTcount: A:0.69, C:0.18, G:0.13, T:0.00
Consensus pattern (6 bp):
AAGCAA
Found at i:1784317 original size:7 final size:7
Alignment explanation
Indices: 1784301--1784334 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1784291 TCAAAGAAGC
1784301 AAGC-AA
1 AAGCAAA
1784307 AAGCAAA
1 AAGCAAA
1784314 AAGCAAA
1 AAGCAAA
1784321 AAGC-AA
1 AAGCAAA
1784327 AAGCAAA
1 AAGCAAA
1784334 A
1 A
1784335 CCAAAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 10 0.38
7 16 0.62
ACGTcount: A:0.71, C:0.15, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGCAAA
Found at i:1784317 original size:13 final size:13
Alignment explanation
Indices: 1784301--1784339 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1784291 TCAAAGAAGC
1784301 AAGCAAAAGCAAA
1 AAGCAAAAGCAAA
1784314 AAGCAAAAAGC-AA
1 AAGC-AAAAGCAAA
*
1784327 AAGCAAAACCAAA
1 AAGCAAAAGCAAA
1784340 GCATATTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 12 0.52
14 6 0.26
ACGTcount: A:0.69, C:0.18, G:0.13, T:0.00
Consensus pattern (13 bp):
AAGCAAAAGCAAA
Found at i:1784632 original size:5 final size:5
Alignment explanation
Indices: 1784622--1784646 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1784612 AAAACAATTT
1784622 GATTG GATTG GATTG GATTG GATTG
1 GATTG GATTG GATTG GATTG GATTG
1784647 TGTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GATTG
Found at i:1784803 original size:3 final size:3
Alignment explanation
Indices: 1784795--1784820 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1784785 CCAATTTTTC
1784795 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
1784821 ATTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1791985 original size:15 final size:16
Alignment explanation
Indices: 1791959--1792002 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1791949 ATCAAATTAA
*
1791959 AAAATTATTTAAA-TT
1 AAAATAATTTAAATTT
1791974 ACAAA-AATTTAAATTT
1 A-AAATAATTTAAATTT
1791990 AAAATAATTTAAA
1 AAAATAATTTAAA
1792003 ACAATAATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:1791991 original size:21 final size:19
Alignment explanation
Indices: 1791935--1791992 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 19
1791925 TAAAATATAA
1791935 TAAAAAATTTAATTATCAAAT
1 TAAAAAATTTAATT-T-AAAT
1791956 TAAAAAA-TT-ATTTAAAT
1 TAAAAAATTTAATTTAAAT
1791973 TACAAAAATTTAAATTTAAA
1 TA-AAAAATTT-AATTTAAA
1791993 ATAATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.18
18 6 0.18
19 5 0.15
20 2 0.06
21 14 0.42
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATTTAATTTAAAT
Found at i:1792000 original size:31 final size:31
Alignment explanation
Indices: 1791950--1792027 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
1791940 AATTTAATTA
* *
1791950 TCAAATTAAAAAATTATTTAAATTACAAAAAT-T
1 TCAAATT-TAAAATAATTTAAA--ACAAAAATGT
*
1791983 T-AAATTTAAAATAATTTAAAACAATAATGGT
1 TCAAATTTAAAATAATTTAAAACAAAAAT-GT
1792014 TCAAATTTAAAATA
1 TCAAATTTAAAATA
1792028 TTCAAACCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.18
31 14 0.36
32 17 0.44
33 1 0.03
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (31 bp):
TCAAATTTAAAATAATTTAAAACAAAAATGT
Found at i:1795179 original size:31 final size:32
Alignment explanation
Indices: 1795131--1795190 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
1795121 TTAATTATAT
*
1795131 TTATATTAAATTTAATTTAAATATAAAATTTTA
1 TTATATTAAATTTAATTT-AATAAAAAATTTTA
1795164 TTAT-TTAAA-TTAATTTAATAAAAAATT
1 TTATATTAAATTTAATTTAATAAAAAATT
1795191 AATTATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
31 7 0.27
32 5 0.19
33 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TTATATTAAATTTAATTTAATAAAAAATTTTA
Found at i:1803501 original size:2 final size:2
Alignment explanation
Indices: 1803494--1803522 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1803484 ATCTCAAATA
1803494 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1803523 ACTCACTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1807870 original size:69 final size:69
Alignment explanation
Indices: 1807741--1807871 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 69
1807731 GCATGATGGT
* * * * *
1807741 GGATTTTCACAGCAACCTGATCGGCTCACAAGGTTTGACTCCGTAAACAGTAGCAGAGACTTTGG
1 GGATTTTCACAGCAACCTGAACGACTCACAAGGTTTGACTCCATAAACAGTACCAAAGACTTTGG
1807806 CAGC
66 CAGC
* *
1807810 GGATTTTCACAGCAACCTGAGAC-ACTCACTAGGTTTGACTCCATAAATAGTACCAAAGACTT
1 GGATTTTCACAGCAACCTGA-ACGACTCACAAGGTTTGACTCCATAAACAGTACCAAAGACTT
1807872 CGGCCATGGA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 53 0.98
70 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (69 bp):
GGATTTTCACAGCAACCTGAACGACTCACAAGGTTTGACTCCATAAACAGTACCAAAGACTTTGG
CAGC
Found at i:1816601 original size:22 final size:21
Alignment explanation
Indices: 1816576--1816616 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1816566 TTATACTTAC
*
1816576 ATAAATCACTTAAAAGAAAATT
1 ATAAATCA-TAAAAAGAAAATT
*
1816598 ATAAATTATAAAAAGAAAA
1 ATAAATCATAAAAAGAAAA
1816617 AAAAAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
ATAAATCATAAAAAGAAAATT
Found at i:1820384 original size:14 final size:14
Alignment explanation
Indices: 1820365--1820394 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1820355 CGAATAGAGT
*
1820365 TTTTTATTTTTTAA
1 TTTTTATTTTTAAA
1820379 TTTTTATTTTTAAA
1 TTTTTATTTTTAAA
1820393 TT
1 TT
1820395 CCATTCGCTT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTTAAA
Found at i:1820495 original size:5 final size:5
Alignment explanation
Indices: 1820487--1820513 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1820477 GATGCAGGGC
1820487 AGGTA AGGTA AGGTA AGGTA AGGTA AG
1 AGGTA AGGTA AGGTA AGGTA AGGTA AG
1820514 ATCAAAAGTT
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:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (5 bp):
AGGTA
Found at i:1821996 original size:30 final size:30
Alignment explanation
Indices: 1821961--1822026 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
1821951 TTTAAAAAAT
* *
1821961 TTAAATATTAATTATTTTATATTTTTA-TAA
1 TTAAATATTAAATAATTT-TATTTTTATTAA
*
1821991 TTAAAT-TTAAATAATTTTATTTTTATTAT
1 TTAAATATTAAATAATTTTATTTTTATTAA
1822020 TTAAATA
1 TTAAATA
1822027 ACAATATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 8 0.26
29 17 0.55
30 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTAAATATTAAATAATTTTATTTTTATTAA
Found at i:1822092 original size:6 final size:5
Alignment explanation
Indices: 1822033--1822099 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
1822023 AATAACAATA
*
1822033 TAAAT TAAAT TAAAT T-AAT TAAA- T-GAT TAAAAT TAAAAT TAAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT T-AAAT T-AAAT T-AAAT
*
1822078 TTAAT TAAAT ATAAAT TAAAT T
1 TAAAT TAAAT -TAAAT TAAAT T
1822100 TATCAAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 1 0.02
4 6 0.11
5 26 0.49
6 20 0.38
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:1829079 original size:89 final size:89
Alignment explanation
Indices: 1828928--1829105 Score: 214
Period size: 89 Copynumber: 2.0 Consensus size: 89
1828918 CTCATTTTCT
* * * * *
1828928 CCTAAAAACTCGATCAAATTGGAGAAAGTGCCAAAAACCAAATGATAACACAGCATAGATGC-AG
1 CCTAAAAACTCAATCAAATTGGACAAAGTGCCAAAAACCAAAAGATAACACAGCACAAATGCAAG
* *
1828992 GTGTAGAAGGTCTTAAAAACGCCAC
66 G-ATACAAGGTCTTAAAAACGCCAC
* * * * ** *
1829017 CCTAAAAACTCAATCAAATTGGACAAAGTGTCAAAAGCCAAAAGGTTATGCATCACAAATGCAAG
1 CCTAAAAACTCAATCAAATTGGACAAAGTGCCAAAAACCAAAAGATAACACAGCACAAATGCAAG
1829082 GATACAAGGTCTTAAAAACGCCAC
66 GATACAAGGTCTTAAAAACGCCAC
1829106 TAGATGATGA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
89 71 0.96
90 3 0.04
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (89 bp):
CCTAAAAACTCAATCAAATTGGACAAAGTGCCAAAAACCAAAAGATAACACAGCACAAATGCAAG
GATACAAGGTCTTAAAAACGCCAC
Found at i:1830772 original size:6 final size:6
Alignment explanation
Indices: 1830761--1830803 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1830751 GGCTAAGATT
*
1830761 GAACTA GAACTA GAACTA GAACT- GCAACTA GCACTA GAACTA G
1 GAACTA GAACTA GAACTA GAACTA G-AACTA GAACTA GAACTA G
1830804 CAGTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 1 0.03
6 31 0.94
7 1 0.03
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (6 bp):
GAACTA
Found at i:1830872 original size:3 final size:3
Alignment explanation
Indices: 1830864--1830908 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
1830854 GATCAGAGTG
1830864 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
1830909 CGTTTACGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1832329 original size:2 final size:2
Alignment explanation
Indices: 1832322--1832359 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1832312 CTTTCAATCA
1832322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1832360 GTAGCGAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1838264 original size:13 final size:12
Alignment explanation
Indices: 1838245--1838277 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1838235 GTTCTCCTGT
1838245 GAAAAAAAAAAA
1 GAAAAAAAAAAA
1838257 GAAAAAAAAAAA
1 GAAAAAAAAAAA
1838269 GAAAAAAAA
1 GAAAAAAAA
1838278 GGGCTACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:1840673 original size:3 final size:3
Alignment explanation
Indices: 1840665--1840700 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1840655 GTGCTGTTTA
1840665 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1840701 CCAACATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1849865 original size:18 final size:19
Alignment explanation
Indices: 1849828--1849872 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1849818 ATTTTACTAT
1849828 ATTAATTGCATTATTATTA
1 ATTAATTGCATTATTATTA
* *
1849847 ATTAATTTC-TTATTTTTA
1 ATTAATTGCATTATTATTA
1849865 ATTTAATT
1 A-TTAATT
1849873 ATTAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTAATTGCATTATTATTA
Found at i:1852853 original size:3 final size:3
Alignment explanation
Indices: 1852845--1852869 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1852835 ACTTAGATGA
1852845 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1852870 TCTTAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1855263 original size:2 final size:2
Alignment explanation
Indices: 1855256--1855285 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1855246 TTTTAGATTC
1855256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1855286 TCTTAATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1855578 original size:4 final size:4
Alignment explanation
Indices: 1855569--1855599 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1855559 ATGAATGTAG
1855569 GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCA
1 GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCA
1855600 AGGATTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (4 bp):
GCAT
Found at i:1862643 original size:5 final size:5
Alignment explanation
Indices: 1862613--1862669 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
1862603 GGATTTCATT
* * * * *
1862613 ACTAC ACTAC ACTAC ACTGG ACTAG AATAG ACTTAG ACTAG ACTAG ACTAG
1 ACTAG ACTAG ACTAG ACTAG ACTAG ACTAG AC-TAG ACTAG ACTAG ACTAG
1862664 ACTAG A
1 ACTAG A
1862670 ATGATTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 41 0.89
6 5 0.11
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (5 bp):
ACTAG
Found at i:1870212 original size:3 final size:3
Alignment explanation
Indices: 1870204--1870268 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
1870194 TGCCCGTCTT
* * * * * * *
1870204 TTA TTA TTA TTA TTA TTG TTG TTG TTG TTG TTG TTGT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
1870250 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
1870269 AAGAGGAGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 56 0.97
4 2 0.03
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1876644 original size:2 final size:2
Alignment explanation
Indices: 1876637--1876666 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1876627 GAAATTTTAA
1876637 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1876667 TCTGGAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1883192 original size:2 final size:2
Alignment explanation
Indices: 1883185--1883216 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1883175 TTCAATAATC
*
1883185 CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1883217 GTCAATTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1883905 original size:2 final size:2
Alignment explanation
Indices: 1883898--1883931 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1883888 GCAAAGTATG
* *
1883898 TA TA TA TA TA CA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1883932 GATAGATACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1883932 original size:8 final size:8
Alignment explanation
Indices: 1883901--1883935 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1883891 AAGTATGTAT
*
1883901 ATATATAC
1 ATATATAG
*
1883909 ATATATAT
1 ATATATAG
1883917 ATATATAG
1 ATATATAG
1883925 ATATATAG
1 ATATATAG
1883933 ATA
1 ATA
1883936 GATACCTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (8 bp):
ATATATAG
Found at i:1883936 original size:12 final size:12
Alignment explanation
Indices: 1883901--1883939 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1883891 AAGTATGTAT
*
1883901 ATATATACATAT
1 ATATATACATAG
*
1883913 ATATATATATAG
1 ATATATACATAG
*
1883925 ATATATAGATAG
1 ATATATACATAG
1883937 ATA
1 ATA
1883940 CCTGGAAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (12 bp):
ATATATACATAG
Found at i:1884569 original size:2 final size:2
Alignment explanation
Indices: 1884562--1884589 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1884552 TGATCATATT
1884562 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1884590 TGAATGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1885699 original size:5 final size:5
Alignment explanation
Indices: 1885689--1885720 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1885679 GGAACAGGAT
1885689 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CT
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CT
1885721 GCTCGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
CTCTC
Found at i:1888198 original size:19 final size:18
Alignment explanation
Indices: 1888176--1888218 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1888166 TATATATATT
1888176 TTTATATAATTTATAATTA
1 TTTATATAA-TTATAATTA
* *
1888195 TTTAATTTAATTATTATTA
1 TTT-ATATAATTATAATTA
1888214 TTTAT
1 TTTAT
1888219 TTATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 14 0.67
20 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATAATTATAATTA
Found at i:1888251 original size:25 final size:27
Alignment explanation
Indices: 1888216--1888273 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
1888206 TATTATTATT
* * *
1888216 TATTTATATAAATTATATATA-TTAAA
1 TATTTAAATAAATAAAATATATTTAAA
1888242 -ATTTAAATAAATAAAATATATTTAAA
1 TATTTAAATAAATAAAATATATTTAAA
1888268 TATTTA
1 TATTTA
1888274 TTTAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 17 0.63
26 5 0.19
27 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTTAAATAAATAAAATATATTTAAA
Found at i:1888378 original size:21 final size:22
Alignment explanation
Indices: 1888338--1888379 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1888328 ATATAATTAA
* *
1888338 AATATAAATTTAATTTTATATC
1 AATATAAATTAAATTATATATC
1888360 AATATAAA-TAAATTATATAT
1 AATATAAATTAAATTATATAT
1888380 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATAAATTAAATTATATATC
Found at i:1889168 original size:24 final size:23
Alignment explanation
Indices: 1889141--1889189 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1889131 TTTGATATGT
1889141 TTATGTATTTATGTTATATTAATA
1 TTATGTATTTATGTTATATT-ATA
* * *
1889165 TTATTTTTTTATTTTATATTATA
1 TTATGTATTTATGTTATATTATA
1889188 TT
1 TT
1889190 TTAATTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTATGTATTTATGTTATATTATA
Found at i:1895056 original size:14 final size:15
Alignment explanation
Indices: 1895046--1895088 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1895036 AATTATTATC
1895046 TTTAAAATATTACTA
1 TTTAAAATATTACTA
* *
1895061 TTTGAAATATTAATA
1 TTTAAAATATTACTA
*
1895076 TTAAAAATTATTA
1 TTTAAAA-TATTA
1895089 ATGTAATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TTTAAAATATTACTA
Found at i:1895594 original size:9 final size:10
Alignment explanation
Indices: 1895555--1895614 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 10
1895545 TTTATTTTTT
1895555 ATAAAATTTAAA
1 ATAAAATTT--A
1895567 ATAAAATTTA
1 ATAAAATTTA
*
1895577 ATTAAATTTA
1 ATAAAATTTA
1895587 A-AAAATTTA
1 ATAAAATTTA
*
1895596 AGGTATAATTT-
1 A--TAAAATTTA
1895607 ATAAAATT
1 ATAAAATT
1895615 AATTGTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
9 14 0.34
10 11 0.27
11 1 0.02
12 15 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
ATAAAATTTA
Found at i:1895607 original size:21 final size:19
Alignment explanation
Indices: 1895569--1895614 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
1895559 AATTTAAAAT
*
1895569 AAAATTTAATTAAATTTAA
1 AAAATTTAAGTAAATTTAA
*
1895588 AAAATTTAAGGTATAATTTAT
1 AAAATTTAA-GTA-AATTTAA
1895609 AAAATT
1 AAAATT
1895615 AATTGTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 12 0.52
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
AAAATTTAAGTAAATTTAA
Found at i:1895923 original size:21 final size:22
Alignment explanation
Indices: 1895879--1895926 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1895869 ATTTAAAAAA
*
1895879 TTTAAAATCTAATTATTTTAAT
1 TTTAAAATCTAATTAATTTAAT
*
1895901 TTTAAAAT-TAATTTAATTTATT
1 TTTAAAATCTAA-TTAATTTAAT
1895923 TTTA
1 TTTA
1895927 TGAAGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAAATCTAATTAATTTAAT
Found at i:1895987 original size:22 final size:21
Alignment explanation
Indices: 1895962--1896005 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1895952 ATATAAATTT
*
1895962 AAAATATT-AATTATAAAATAA
1 AAAAAATTAAATTATAAAA-AA
*
1895983 AAAAAATTAAATTTTAAAAAA
1 AAAAAATTAAATTATAAAAAA
1896004 AA
1 AA
1896006 TGACATGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAAATTAAATTATAAAAAA
Found at i:1896506 original size:170 final size:170
Alignment explanation
Indices: 1896307--1896766 Score: 850
Period size: 170 Copynumber: 2.7 Consensus size: 170
1896297 TTTTAAGTAG
* *
1896307 TTTAAAGTTATATGATTCATTTATTTTTATTTATAAGATTAATTTAATTAGAGTTATCATTTATT
1 TTTAAAGGTAT-T-ATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATT
1896372 TTTATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATA
64 TTTATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATA
1896437 TGAATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
129 TGAATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
1896479 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
1 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
1896544 TATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATATG
66 TATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATATG
*
1896609 AATTTAATTTAATTTTTTTAAGTAGTTTAAATTTATTTTA
131 AATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
1896649 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
1 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
*
1896714 TATTTGTAGAAGTTTAAAATTTTTTTATTTAATTATATGAGTATAATTT-TTAG
66 TATTTGTAGAAGTTTAGAA-TTTTTTATTTAATTATATGAGTATAATTTATTAG
1896767 GATAATTTAT
Statistics
Matches: 283, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
170 243 0.86
171 30 0.11
172 10 0.04
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.56
Consensus pattern (170 bp):
TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
TATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATATG
AATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
Found at i:1901909 original size:2 final size:2
Alignment explanation
Indices: 1901904--1901933 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1901894 TCTCTCCCCC
1901904 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1901934 TTTTGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1901967 original size:22 final size:23
Alignment explanation
Indices: 1901949--1901997 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1901939 TATTTTTATG
1901949 TCTACATAACTGTAATTTTCACA
1 TCTACATAACTGTAATTTTCACA
* *
1901972 TTTACATAACTGTGATTTTCACA
1 TCTACATAACTGTAATTTTCACA
1901995 TCT
1 TCT
1901998 TTCATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (23 bp):
TCTACATAACTGTAATTTTCACA
Found at i:1905987 original size:12 final size:12
Alignment explanation
Indices: 1905970--1905994 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1905960 TTTCTATACG
1905970 AATAACTTCAAT
1 AATAACTTCAAT
1905982 AATAACTTCAAT
1 AATAACTTCAAT
1905994 A
1 A
1905995 TCTAGTATAC
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAACTTCAAT
Found at i:1907406 original size:19 final size:18
Alignment explanation
Indices: 1907384--1907426 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1907374 TATATATATT
1907384 TTTATATAATTTATAATTA
1 TTTATATAA-TTATAATTA
* *
1907403 TTTAATTTAATTATTATTA
1 TTT-ATATAATTATAATTA
1907422 TTTAT
1 TTTAT
1907427 TTATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 14 0.67
20 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATAATTATAATTA
Found at i:1907444 original size:27 final size:27
Alignment explanation
Indices: 1907414--1907489 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
1907404 TTAATTTAAT
* *
1907414 TATTATTATTTATTTATATAAATTATA
1 TATTAATATTTATTTATATAAAATATA
* ** *
1907441 TATTAAAATTTAAATAAATAAAATATA
1 TATTAATATTTATTTATATAAAATATA
1907468 T-TTAAATATTTATTTAATATAA
1 TATT-AATATTTATTT-ATATAA
1907490 TTTTTACGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
26 2 0.05
27 30 0.81
28 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTAATATTTATTTATATAAAATATA
Found at i:1907584 original size:21 final size:22
Alignment explanation
Indices: 1907544--1907585 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1907534 ATATAATTAA
* *
1907544 AATATAAATTTAATTTTATATC
1 AATATAAATTAAATTATATATC
1907566 AATATAAA-TAAATTATATAT
1 AATATAAATTAAATTATATAT
1907586 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATAAATTAAATTATATATC
Found at i:1907616 original size:2 final size:2
Alignment explanation
Indices: 1907579--1907606 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1907569 ATAAATAAAT
1907579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1907607 CACTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1908378 original size:24 final size:23
Alignment explanation
Indices: 1908351--1908399 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1908341 TTTGATATGT
1908351 TTATGTATTTATGTTATATTAATA
1 TTATGTATTTATGTTATATT-ATA
* * *
1908375 TTATTTTTTTATTTTATATTATA
1 TTATGTATTTATGTTATATTATA
1908398 TT
1 TT
1908400 TTAATTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTATGTATTTATGTTATATTATA
Found at i:1914268 original size:14 final size:15
Alignment explanation
Indices: 1914258--1914300 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1914248 AATTATTATC
1914258 TTTAAAATATTACTA
1 TTTAAAATATTACTA
* *
1914273 TTTGAAATATTAATA
1 TTTAAAATATTACTA
*
1914288 TTAAAAATTATTA
1 TTTAAAA-TATTA
1914301 ATGTAATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TTTAAAATATTACTA
Found at i:1914812 original size:9 final size:10
Alignment explanation
Indices: 1914773--1914832 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 10
1914763 TTTATTTTTT
1914773 ATAAAATTTAAA
1 ATAAAATTT--A
1914785 ATAAAATTTA
1 ATAAAATTTA
*
1914795 ATTAAATTTA
1 ATAAAATTTA
1914805 A-AAAATTTA
1 ATAAAATTTA
*
1914814 AGGTATAATTT-
1 A--TAAAATTTA
1914825 ATAAAATT
1 ATAAAATT
1914833 AATTGTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
9 14 0.34
10 11 0.27
11 1 0.02
12 15 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
ATAAAATTTA
Found at i:1914825 original size:21 final size:19
Alignment explanation
Indices: 1914787--1914832 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
1914777 AATTTAAAAT
*
1914787 AAAATTTAATTAAATTTAA
1 AAAATTTAAGTAAATTTAA
*
1914806 AAAATTTAAGGTATAATTTAT
1 AAAATTTAA-GTA-AATTTAA
1914827 AAAATT
1 AAAATT
1914833 AATTGTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 12 0.52
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
AAAATTTAAGTAAATTTAA
Found at i:1915131 original size:22 final size:23
Alignment explanation
Indices: 1915097--1915145 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1915087 TTTAAAAAAA
*
1915097 TTTAAAATCTAA-TTATTTTAATT
1 TTTAAAATCTAATTTAATTT-ATT
1915120 TTTAAAAT-TAATTTAATTTATT
1 TTTAAAATCTAATTTAATTTATT
1915142 TTTA
1 TTTA
1915146 TGAAGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTAAAATCTAATTTAATTTATT
Found at i:1915720 original size:170 final size:170
Alignment explanation
Indices: 1915528--1915987 Score: 841
Period size: 170 Copynumber: 2.7 Consensus size: 170
1915518 TTTTAAGTAG
* *
1915528 TTTAAAGTTATATGATTCATTTATTTTTATTTATAAGATTAATTTAATTAGAGTTATCATTTATT
1 TTTAAAGGTAT-T-ATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATT
1915593 TTTATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATA
64 TTTATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATA
1915658 TGAATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
129 TGAATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
1915700 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
1 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
1915765 TATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATATG
66 TATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATATG
*
1915830 AATTTAATTTAATTTTTTTAAGTAGTTTAAATTTATTTTA
131 AATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
1915870 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
1 TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
* *
1915935 TATTTGTAGAAGTTTAAAATTTTTTTGTTTAATTATATGAGTATAATTT-TTAG
66 TATTTGTAGAAGTTTAGAA-TTTTTTATTTAATTATATGAGTATAATTTATTAG
1915988 GATAATTTAT
Statistics
Matches: 282, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
170 243 0.86
171 29 0.10
172 10 0.04
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (170 bp):
TTTAAAGGTATTATTCATTTATTTTTATTTATAAGATTAATTTGATTAGAGTTATCATTTATTTT
TATTTGTAGAAGTTTAGAATTTTTTATTTAATTATATGAGTATAATTTATTAGTATGGTTATATG
AATTTAATTTAATTTTTTTAAGTAGTTTAAAGTTATTTTA
Found at i:1919511 original size:127 final size:126
Alignment explanation
Indices: 1919238--1919502 Score: 351
Period size: 127 Copynumber: 2.1 Consensus size: 126
1919228 AAATTAATAA
* * * *
1919238 AATTTAAATTT-AAATTTTT-TATTTA-ACAAAATATAATAATTAATATTTTAATTTGTTAATGT
1 AATTTAATTTTAAAATTTTTATTTTTATA-AAAACAT-ATAATTAATATTTTAATTTGTAAATGT
*
1919300 AAATTTTTTAAACTTAATTAAATATTTTTTTATTTTATTAAAAATTATAATAAAAAACTTTTTT
64 AAATTTTTTAAACTTAATTAAATATTTTTTTATTTTATTAAAAA-TATAATAAAAAACCTTTTT
* *
1919364 ATTTTTATTTTAAAATTTTTATTTTTATAAAAACATATAATTAATATTTTAATTTGTAAATGT-A
1 AATTTAATTTTAAAATTTTTATTTTTATAAAAACATATAATTAATATTTTAATTTGTAAATGTAA
* *
1919428 ATTTTTTAAAATTTAATTAAATATTATTTTTAATTTTATTAAAAA-ATAATAATAAACCCTTTTT
66 ATTTTTT-AAACTTAATTAAATATT-TTTTT-ATTTTATTAAAAATATAATAA-AAAACCTTTTT
1919492 AATTTAATTTT
1 AATTTAATTTT
1919503 TTATTTTTAA
Statistics
Matches: 121, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
126 16 0.13
127 57 0.47
128 34 0.28
129 14 0.12
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.53
Consensus pattern (126 bp):
AATTTAATTTTAAAATTTTTATTTTTATAAAAACATATAATTAATATTTTAATTTGTAAATGTAA
ATTTTTTAAACTTAATTAAATATTTTTTTATTTTATTAAAAATATAATAAAAAACCTTTTT
Found at i:1921145 original size:2 final size:2
Alignment explanation
Indices: 1921140--1921169 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1921130 TCTCTCCCCC
1921140 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1921170 TTTTGTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1921203 original size:22 final size:23
Alignment explanation
Indices: 1921185--1921233 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1921175 TATTTTTATG
1921185 TCTACATAACTGTAATTTTCACA
1 TCTACATAACTGTAATTTTCACA
* *
1921208 TTTACATAACTGTGATTTTCACA
1 TCTACATAACTGTAATTTTCACA
1921231 TCT
1 TCT
1921234 TTCATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (23 bp):
TCTACATAACTGTAATTTTCACA
Found at i:1931097 original size:2 final size:2
Alignment explanation
Indices: 1931090--1931119 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1931080 ATTGGAGTTA
*
1931090 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1931120 TTTACTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1935278 original size:81 final size:81
Alignment explanation
Indices: 1935138--1935299 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
1935128 TAAGAAAAAG
* *
1935138 TTTTCCATATAAACCAGGAAAAGTGGAAATGAAAGTTAAAAGGAGAAAGAGAAAGCTCTCCCACT
1 TTTTCCATATAAACCAGGAAAAGTAGAAATGAAAGTTAAAAGGAGAAAGAGAAACCTCTCCCACT
1935203 TTAACAGTGATAACAT
66 TTAACAGTGATAACAT
*
1935219 TTTTCCATATGAACCA-GAAAAGGTAGAAATGAAAGTTAAAAGGAGAAAGAGAAACCTCTCCCAC
1 TTTTCCATATAAACCAGGAAAA-GTAGAAATGAAAGTTAAAAGGAGAAAGAGAAACCTCTCCCAC
1935283 TTTAACAGTGATAACAT
65 TTTAACAGTGATAACAT
1935300 GGGGCGTAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 5 0.06
81 72 0.94
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.22
Consensus pattern (81 bp):
TTTTCCATATAAACCAGGAAAAGTAGAAATGAAAGTTAAAAGGAGAAAGAGAAACCTCTCCCACT
TTAACAGTGATAACAT
Found at i:1938002 original size:18 final size:19
Alignment explanation
Indices: 1937956--1938004 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1937946 TTTTCCTAAA
*
1937956 TATATATTTATATTAACAAT
1 TATATATTTA-ACTAACAAT
* *
1937976 TAAATATTTAACTAA-ATT
1 TATATATTTAACTAACAAT
1937994 TATATATTTAA
1 TATATATTTAA
1938005 ATTAAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 12 0.48
19 4 0.16
20 9 0.36
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATTTAACTAACAAT
Found at i:1938596 original size:17 final size:17
Alignment explanation
Indices: 1938574--1938606 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1938564 TTCACTATCA
*
1938574 CTTTATTAGATATTAAT
1 CTTTATTAAATATTAAT
1938591 CTTTATTAAATATTAA
1 CTTTATTAAATATTAA
1938607 AATTATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (17 bp):
CTTTATTAAATATTAAT
Found at i:1944754 original size:14 final size:14
Alignment explanation
Indices: 1944729--1944763 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
1944719 TTTTGACAGA
1944729 AAAGGAACGGGAAGG
1 AAAGG-ACGGGAAGG
1944744 AAAGGACGGGAAGG
1 AAAGGACGGGAAGG
1944758 AAAGGA
1 AAAGGA
1944764 AAGCAAAAGA
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:0.49, C:0.06, G:0.46, T:0.00
Consensus pattern (14 bp):
AAAGGACGGGAAGG
Found at i:1944969 original size:6 final size:6
Alignment explanation
Indices: 1944944--1944987 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1944934 GGCTCTATAC
* *
1944944 ACAGAG ACTTGAG ACGGAG ACAGAG ACAGAG ACAGAG ACAGAG A
1 ACAGAG AC-AGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG A
1944988 AGATGGACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.45, C:0.16, G:0.34, T:0.05
Consensus pattern (6 bp):
ACAGAG
Found at i:1945976 original size:2 final size:2
Alignment explanation
Indices: 1945969--1946006 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1945959 ACTTTCCTCC
*
1945969 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1946007 GCCTTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1948118 original size:2 final size:2
Alignment explanation
Indices: 1948111--1948142 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1948101 AGTCAAAAAT
1948111 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1948143 GGGGCTACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1955873 original size:2 final size:2
Alignment explanation
Indices: 1955866--1955895 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1955856 GTTTGTCAAA
1955866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1955896 TTAACAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1956285 original size:6 final size:6
Alignment explanation
Indices: 1956274--1956307 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1956264 CAATGGAGAT
* *
1956274 CGAATG CGAATG CGAATG CGAACG CGAACG CGAA
1 CGAATG CGAATG CGAATG CGAATG CGAATG CGAA
1956308 CGCATAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.32, T:0.09
Consensus pattern (6 bp):
CGAATG
Found at i:1956291 original size:12 final size:12
Alignment explanation
Indices: 1956274--1956310 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1956264 CAATGGAGAT
*
1956274 CGAATGCGAATG
1 CGAATGCGAACG
1956286 CGAATGCGAACG
1 CGAATGCGAACG
*
1956298 CGAACGCGAACG
1 CGAATGCGAACG
1956310 C
1 C
1956311 ATAACAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.27, G:0.32, T:0.08
Consensus pattern (12 bp):
CGAATGCGAACG
Found at i:1956993 original size:21 final size:21
Alignment explanation
Indices: 1956969--1957027 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 21
1956959 TCTCATTCTT
1956969 TTTTAGTTATTATTATTATTA
1 TTTTAGTTATTATTATTATTA
1956990 TTTTA-TT-TT-TTA--ATTA
1 TTTTAGTTATTATTATTATTA
*
1957006 TTTT-GTTAC-ATTATT-TTA
1 TTTTAGTTATTATTATTATTA
1957024 TTTT
1 TTTT
1957028 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
16 10 0.31
17 3 0.09
18 10 0.31
19 2 0.06
20 2 0.06
21 5 0.16
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTTAGTTATTATTATTATTA
Found at i:1957006 original size:28 final size:28
Alignment explanation
Indices: 1956967--1957028 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
1956957 TTTCTCATTC
*
1956967 TTTTTTAGTTATTATTATT-ATTATTTTA
1 TTTTTTAATTATT-TTATTAATTATTTTA
*
1956995 TTTTTTAATTATTTTGTTACATTATTTTA
1 TTTTTTAATTATTTTATTA-ATTATTTTA
1957024 TTTTT
1 TTTTT
1957029 AAAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 4 0.13
28 12 0.40
29 14 0.47
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.73
Consensus pattern (28 bp):
TTTTTTAATTATTTTATTAATTATTTTA
Found at i:1957073 original size:21 final size:21
Alignment explanation
Indices: 1957047--1957087 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1957037 TAATAAATTT
* *
1957047 AAAAAATCGATAGTTTTTTTA
1 AAAAAATCAAAAGTTTTTTTA
1957068 AAAAAATCAAAAGTTTTTTT
1 AAAAAATCAAAAGTTTTTTT
1957088 TTTTTTTTTC
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:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (21 bp):
AAAAAATCAAAAGTTTTTTTA
Found at i:1959211 original size:2 final size:2
Alignment explanation
Indices: 1959204--1959229 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1959194 TTGTTATTGA
1959204 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1959230 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1959272 original size:2 final size:2
Alignment explanation
Indices: 1959229--1959254 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1959219 TATATATATA
1959229 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1959255 CGCGCGCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1959780 original size:3 final size:3
Alignment explanation
Indices: 1959772--1959796 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1959762 GAAGAATTAC
1959772 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
1959797 TGAGGATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1963916 original size:2 final size:2
Alignment explanation
Indices: 1963909--1963935 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1963899 CTGCAAGTGC
1963909 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1963936 CTTGGCGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1964312 original size:23 final size:23
Alignment explanation
Indices: 1964274--1964321 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1964264 CTTGTTATTT
*
1964274 AAAAAAAATAAGAAATATTTTTA
1 AAAAAAAATAAGAAATATTTATA
1964297 AAAATAAAATAA-AAATATTTATA
1 AAAA-AAAATAAGAAATATTTATA
1964320 AA
1 AA
1964322 GTTGTACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAAAAATAAGAAATATTTATA
Found at i:1964317 original size:21 final size:21
Alignment explanation
Indices: 1964269--1964317 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
1964259 TTCGCCTTGT
1964269 TATTT-AAAAAAAATAAGAAA
1 TATTTAAAAAAAAATAAGAAA
1964289 TATTTTTAAAAATAAAATAA-AAA
1 TA--TTTAAAAA-AAAATAAGAAA
1964312 TATTTA
1 TATTTA
1964318 TAAAGTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 2 0.08
21 4 0.16
22 3 0.12
23 9 0.36
24 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TATTTAAAAAAAAATAAGAAA
Found at i:1965733 original size:7 final size:7
Alignment explanation
Indices: 1965721--1965753 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1965711 GAAAAGCATC
1965721 AAATAAA
1 AAATAAA
1965728 AAATAAA
1 AAATAAA
1965735 AAATAAA
1 AAATAAA
1965742 AAA-AAA
1 AAATAAA
*
1965748 AGATAA
1 AAATAA
1965754 GAGGGAAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAATAAA
Found at i:1969689 original size:2 final size:2
Alignment explanation
Indices: 1969677--1969707 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1969667 GAGAAAAGCA
*
1969677 AT AT AT TT 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 A
1969708 AATAGAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1978807 original size:14 final size:14
Alignment explanation
Indices: 1978788--1978815 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1978778 AATAGTTTGG
1978788 GACAGGTTGGGCCA
1 GACAGGTTGGGCCA
1978802 GACAGGTTGGGCCA
1 GACAGGTTGGGCCA
1978816 AACCCCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.43, T:0.14
Consensus pattern (14 bp):
GACAGGTTGGGCCA
Found at i:1979818 original size:25 final size:23
Alignment explanation
Indices: 1979777--1979825 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
1979767 TTTTTACAAT
1979777 ATAATATTATATATATATATATAAA
1 ATAATATTATATATATA-AT-TAAA
*
1979802 ATAATATGTAT-TGTATAATTAAA
1 ATAATAT-TATATATATAATTAAA
1979825 A
1 A
1979826 ACATGATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 5 0.23
24 2 0.09
25 12 0.55
26 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
ATAATATTATATATATAATTAAA
Found at i:1980873 original size:3 final size:3
Alignment explanation
Indices: 1980865--1980891 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1980855 TGTTATATAC
1980865 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1980892 CCTATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1980963 original size:2 final size:2
Alignment explanation
Indices: 1980956--1980983 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1980946 TCTCATTGCC
1980956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1980984 GAAGAAGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1981180 original size:2 final size:2
Alignment explanation
Indices: 1981173--1981207 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1981163 AAGAGTCAAC
1981173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1981208 CACATATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1981922 original size:2 final size:2
Alignment explanation
Indices: 1981917--1981949 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1981907 ATATAGTGTG
1981917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1981950 CCATTCTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.