Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168294.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_520, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24001
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.19
Found at i:570 original size:15 final size:15
Alignment explanation
Indices: 550--579 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
540 AATAATGAGT
550 ATAAAAAATCAAAAG
1 ATAAAAAATCAAAAG
*
565 ATAAAAAATGAAAAG
1 ATAAAAAATCAAAAG
580 GGAATTACAA
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:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (15 bp):
ATAAAAAATCAAAAG
Found at i:948 original size:22 final size:22
Alignment explanation
Indices: 904--963 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
894 AAACAATGAT
* *
904 AAAATAAAATAAATAGATGAAA
1 AAAATAAAATAAAAAGATAAAA
* *
926 AAAATACAATAAAAATATAAAA
1 AAAATAAAATAAAAAGATAAAA
* *
948 AGTAAGAAAATAAAAA
1 A-AAATAAAATAAAAA
964 AGACAAAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAATAAAATAAAAAGATAAAA
Found at i:1395 original size:16 final size:15
Alignment explanation
Indices: 1376--1405 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1366 AAAATAGACA
1376 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
1392 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
1406 TTTGAACTTT
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:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:1564 original size:43 final size:41
Alignment explanation
Indices: 1517--1607 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 41
1507 ATAAAAATAA
* * *
1517 CAAAAACAAAAGTAACAAAGCCAAAA-AATAAAAATTTACGAAT
1 CAAAAA-AAAA-TAAAAAAGACAAAAGAATAAAAATTT-CAAAT
*
1560 CAAAAAAATATAAAAAAGACAAAATGAATAAAAATTTCAAAT
1 CAAAAAAAAATAAAAAAGACAAAA-GAATAAAAATTTCAAAT
1602 CAAAAA
1 CAAAAA
1608 TGGAAAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 12 0.29
42 13 0.31
43 17 0.40
ACGTcount: A:0.68, C:0.11, G:0.05, T:0.15
Consensus pattern (41 bp):
CAAAAAAAAATAAAAAAGACAAAAGAATAAAAATTTCAAAT
Found at i:1733 original size:11 final size:11
Alignment explanation
Indices: 1697--1739 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
1687 ATGAAAGATG
1697 AAAAATAAAAT
1 AAAAATAAAAT
*
1708 AAAAAGTAATA-
1 AAAAA-TAAAAT
1719 AAAAATAAAAT
1 AAAAATAAAAT
1730 AAAAATAAAA
1 AAAAATAAAA
1740 GAATGTGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.14
11 20 0.71
12 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1925 original size:22 final size:23
Alignment explanation
Indices: 1900--1949 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1890 AAAGTTGAGA
*
1900 AAAAAATGAGAAAAA-G-AAAGGC
1 AAAAAAT-AAAAAAATGAAAAGGC
1922 AAAAAATAAAAAAATGAAAAGGC
1 AAAAAATAAAAAAATGAAAAGGC
1945 AAAAA
1 AAAAA
1950 TTATAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 6 0.24
22 8 0.32
23 11 0.44
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.06
Consensus pattern (23 bp):
AAAAAATAAAAAAATGAAAAGGC
Found at i:1925 original size:23 final size:24
Alignment explanation
Indices: 1899--1949 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
1889 TAAAGTTGAG
*
1899 AAAAAAATGAGAAAAA-G-AAAGGC
1 AAAAAAAT-AAAAAAATGAAAAGGC
1922 -AAAAAATAAAAAAATGAAAAGGC
1 AAAAAAATAAAAAAATGAAAAGGC
1945 AAAAA
1 AAAAA
1950 TTATAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.25
22 8 0.33
23 6 0.25
24 4 0.17
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.06
Consensus pattern (24 bp):
AAAAAAATAAAAAAATGAAAAGGC
Found at i:1990 original size:18 final size:18
Alignment explanation
Indices: 1963--2008 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1953 TAGAAAATTA
* * *
1963 AACAAGAAAAAATTATAG
1 AACAAAAAAAAAGTAAAG
1981 AACAAAAAAAAAGTAAAG
1 AACAAAAAAAAAGTAAAG
1999 AA-AAAAAAAA
1 AACAAAAAAAA
2009 GAAGAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (18 bp):
AACAAAAAAAAAGTAAAG
Found at i:2013 original size:14 final size:15
Alignment explanation
Indices: 1984--2017 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1974 ATTATAGAAC
1984 AAAAAAAAAGTAAAGA
1 AAAAAAAAAG-AAAGA
2000 AAAAAAAAAG-AAGA
1 AAAAAAAAAGAAAGA
2014 AAAA
1 AAAA
2018 TTTGAAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAAGA
Found at i:2716 original size:21 final size:21
Alignment explanation
Indices: 2662--2717 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
2652 AAAGATTCAA
2662 AAAATA-AAAT-AAAAATTTT
1 AAAATATAAATAAAAAATTTT
* * *
2681 GAACT-TTAATAAAAAAATTTT
1 AAAATATAAAT-AAAAAATTTT
2702 AAAATATAAATAAAAA
1 AAAATATAAATAAAAA
2718 TAAATGGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
19 6 0.22
21 17 0.63
22 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATATAAATAAAAAATTTT
Found at i:2880 original size:21 final size:22
Alignment explanation
Indices: 2856--2906 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2846 AAGAAAACAA
* *
2856 AAAAAATATAACAAAT-ATAGG
1 AAAAAATATAAAAAATCAAAGG
*
2877 AAAAGATATAAAAAATCAAAGG
1 AAAAAATATAAAAAATCAAAGG
*
2899 TAAAAATA
1 AAAAAATA
2907 AAATAAAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.18
Consensus pattern (22 bp):
AAAAAATATAAAAAATCAAAGG
Found at i:2947 original size:23 final size:22
Alignment explanation
Indices: 2900--2947 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2890 AATCAAAGGT
** *
2900 AAAAATAAAATAAAAGTTAATG
1 AAAAATAAAATAAAAGCAAAAG
2922 AAAAATATAAATAAAAGCAAAAG
1 AAAAATA-AAATAAAAGCAAAAG
2945 AAA
1 AAA
2948 GTGCACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAATAAAATAAAAGCAAAAG
Found at i:3492 original size:17 final size:17
Alignment explanation
Indices: 3460--3510 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
3450 CAAATACAAG
3460 AAAAAGATATAGAAAATC
1 AAAAAGATATA-AAAATC
* *
3478 AAAAAAATATAAAAAGAC
1 AAAAAGATATAAAAA-TC
3496 AAAAAGA-ATAAAAAT
1 AAAAAGATATAAAAAT
3511 TTGAAATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.14
Consensus pattern (17 bp):
AAAAAGATATAAAAATC
Found at i:3566 original size:20 final size:19
Alignment explanation
Indices: 3542--3599 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 19
3532 CTTTTAGTTT
3542 AAAGAAAAAAATAACAAAT-
1 AAAGAAAAAAATAA-AAATC
3561 ACAAGAAAAAGATATAAAAATC
1 A-AAGAAAAA-A-ATAAAAATC
3583 AAAGATAAAAAATAAAA
1 AAAGA-AAAAAATAAAA
3600 TAAAAGTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 1 0.03
20 14 0.41
21 10 0.29
22 9 0.26
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAGAAAAAAATAAAAATC
Found at i:3602 original size:12 final size:14
Alignment explanation
Indices: 3568--3604 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
3558 AATACAAGAA
3568 AAAGATATAAAAATC
1 AAAGATA-AAAAATC
3583 AAAGATAAAAAAT-
1 AAAGATAAAAAATC
3596 AAA-ATAAAA
1 AAAGATAAAA
3605 GTTAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 3 0.14
14 6 0.27
15 7 0.32
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAGATAAAAAATC
Found at i:3616 original size:106 final size:106
Alignment explanation
Indices: 3358--3585 Score: 385
Period size: 106 Copynumber: 2.2 Consensus size: 106
3348 GAAAAAAATG
* *
3358 AAAAG-TA-AGAAAAT-AAAAAAATATAAAAAGACAAAATGAATAAAAATTTGAAATATAAATAG
1 AAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATAAAAATAG
3420 AAAAAATTTTAGTTTAAAGAAAAAAAATAACAAATACAAGA
66 AAAAAATTTTAGTTTAAAGAAAAAAAATAACAAATACAAGA
3461 AAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATACAAAATA
1 AAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATA-AAAATA
*
3526 GAAAAACTTTTAGTTTAAAG-AAAAAAATAACAAATACAAGA
65 GAAAAAATTTTAGTTTAAAGAAAAAAAATAACAAATACAAGA
3567 AAAAGATATA-AAAATCAAA
1 AAAAGATATAGAAAATCAAA
3586 GATAAAAAAT
Statistics
Matches: 118, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
103 5 0.04
104 2 0.02
105 16 0.14
106 71 0.60
107 24 0.20
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.19
Consensus pattern (106 bp):
AAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATAAAAATAG
AAAAAATTTTAGTTTAAAGAAAAAAAATAACAAATACAAGA
Found at i:3854 original size:29 final size:30
Alignment explanation
Indices: 3822--3887 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
3812 GAAAAATTAT
*
3822 AAAAATAGAATA-AAAAAT-AGCAAAAAACA
1 AAAAATAGAAAACAAAAATGAG-AAAAAACA
*
3851 AAAAAT-GAAAACAAAAATGAGAAAAACCA
1 AAAAATAGAAAACAAAAATGAGAAAAAACA
3880 AAAGAATA
1 AAA-AATA
3888 ATAGATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 4 0.13
29 22 0.71
30 5 0.16
ACGTcount: A:0.74, C:0.08, G:0.09, T:0.09
Consensus pattern (30 bp):
AAAAATAGAAAACAAAAATGAGAAAAAACA
Found at i:5192 original size:20 final size:20
Alignment explanation
Indices: 5159--5198 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5149 AAATTTTTAT
5159 AAAAAAAAGCAAAAA-AAAA
1 AAAAAAAAGCAAAAATAAAA
*
5178 AAAATAAAAGGAAAAATAAAA
1 AAAA-AAAAGCAAAAATAAAA
5199 TAAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.85, C:0.03, G:0.07, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGCAAAAATAAAA
Found at i:6223 original size:43 final size:43
Alignment explanation
Indices: 6142--6223 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
6132 CAACAATGAT
*
6142 AAAATAAAAAAATAAAAGATGAAAAAAATACAATAAAAATATA
1 AAAATAAAAAAATAAAAGAAGAAAAAAATACAATAAAAATATA
* * **
6185 AAAAGTAAGAAAATAAAA-AAGACAAAAATTGAATAAAAA
1 AAAA-TAAAAAAATAAAAGAAGAAAAAAATACAATAAAAA
6224 CTTCAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 21 0.64
44 12 0.36
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (43 bp):
AAAATAAAAAAATAAAAGAAGAAAAAAATACAATAAAAATATA
Found at i:6619 original size:13 final size:13
Alignment explanation
Indices: 6584--6626 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 13
6574 GAAAATTTAT
*
6584 AAAATAGA-ACAA
1 AAAATAGACAAAA
6596 AAAATAG-CAAAA
1 AAAATAGACAAAA
6608 AAAATAGACAAAA
1 AAAATAGACAAAA
6621 AAAATA
1 AAAATA
6627 AGAAAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.09
Consensus pattern (13 bp):
AAAATAGACAAAA
Found at i:6632 original size:24 final size:23
Alignment explanation
Indices: 6584--6632 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
6574 GAAAATTTAT
*
6584 AAAATAGAACAAAAAATAGCAAAA
1 AAAATAGAAAAAAAAATAG-AAAA
6608 AAAATAGACAAAAAAAATAAGAAAA
1 AAAATAGA-AAAAAAAAT-AGAAAA
6633 TGAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 12 0.55
26 2 0.09
ACGTcount: A:0.78, C:0.06, G:0.08, T:0.08
Consensus pattern (23 bp):
AAAATAGAAAAAAAAATAGAAAA
Found at i:6638 original size:16 final size:15
Alignment explanation
Indices: 6619--6648 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6609 AAATAGACAA
6619 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
6635 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
6649 TTTGAACTTC
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:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:6703 original size:17 final size:18
Alignment explanation
Indices: 6673--6742 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
6663 AAATATTTAA
*
6673 AAATAT-AAATAAAAAAT
1 AAATATAAAAGAAAAAAT
* *
6690 AAAT-TAAGAGAAAATAT
1 AAATATAAAAGAAAAAAT
* *
6707 TAATATAAAAGAAAAATT
1 AAATATAAAAGAAAAAAT
6725 AAATA-AAATACGAAAAAA
1 AAATATAAA-A-GAAAAAA
6743 GGAAGAAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
16 1 0.03
17 18 0.45
18 15 0.38
19 6 0.15
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATATAAAAGAAAAAAT
Found at i:6703 original size:28 final size:29
Alignment explanation
Indices: 6672--6734 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
6662 AAAATATTTA
6672 AAAATA-TAA-ATAAAA-AATAAATTAAGAG
1 AAAATATTAATATAAAAGAA-AAATTAA-AG
*
6700 AAAATATTAATATAAAAGAAAAATTAAAT
1 AAAATATTAATATAAAAGAAAAATTAAAG
6729 AAAATA
1 AAAATA
6735 CGAAAAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 10 0.32
30 13 0.42
31 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (29 bp):
AAAATATTAATATAAAAGAAAAATTAAAG
Found at i:6721 original size:18 final size:16
Alignment explanation
Indices: 6673--6732 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
6663 AAATATTTAA
* *
6673 AAATATAAATAAAAAAT
1 AAATA-AAAGAAAAATT
*
6690 AAATTAAGAGAAAATATT
1 AAA-TAAAAGAAAA-ATT
6708 AATATAAAAGAAAAATT
1 AA-ATAAAAGAAAAATT
6725 AAATAAAA
1 AAATAAAA
6733 TACGAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 6 0.17
17 14 0.39
18 15 0.42
19 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAGAAAAATT
Found at i:7176 original size:19 final size:20
Alignment explanation
Indices: 7144--7215 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 20
7134 AAAGTTCGAG
*
7144 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
7164 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
7183 GGCAAAAATATGAAATAAAAAAAAGA
1 ---AAAAA-ATG-AA-AAAAAGAAGA
7209 AAAAAAT
1 AAAAAAT
7216 TTATAGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 10 0.24
20 7 0.17
22 7 0.17
23 7 0.17
25 2 0.05
26 8 0.20
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.10
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:7916 original size:25 final size:25
Alignment explanation
Indices: 7888--7943 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
7878 CAAAAATAGC
7888 AAAAATGA-T-AATAAAATAAAAAAA
1 AAAAATGATTCAA-AAAATAAAAAAA
* *
7912 TAAAAAAGATTCAAAAAATAAAAATA
1 -AAAAATGATTCAAAAAATAAAAAAA
7938 AAAAAT
1 AAAAAT
7944 TTTGAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.46
26 12 0.46
27 2 0.08
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.18
Consensus pattern (25 bp):
AAAAATGATTCAAAAAATAAAAAAA
Found at i:7981 original size:20 final size:20
Alignment explanation
Indices: 7926--7983 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
7916 AAAGATTCAA
*
7926 AAAATAAAAATAAAAAATTTT
1 AAAATATAAAT-AAAAATTTT
* * *
7947 GAACTTTATAA-AAAAATTTT
1 AAAATATA-AATAAAAATTTT
7967 AAAATATAAATAAAAAT
1 AAAATATAAATAAAAAT
7984 AAATGGAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
19 2 0.07
20 20 0.71
21 4 0.14
22 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATATAAATAAAAATTTT
Found at i:8190 original size:19 final size:21
Alignment explanation
Indices: 8162--8213 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
8152 AAAGATATAA
*
8162 AAAATCAAAGGT-A-AAAAAT
1 AAAATAAAAGGTAAGAAAAAT
*
8181 AAAATAAAAGTTAATGAAAAAT
1 AAAATAAAAGGTAA-GAAAAAT
8203 ATAAATAAAAG
1 A-AAATAAAAG
8214 CAAAAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
20 1 0.04
22 7 0.26
23 9 0.33
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (21 bp):
AAAATAAAAGGTAAGAAAAAT
Found at i:8222 original size:23 final size:22
Alignment explanation
Indices: 8175--8222 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
8165 ATCAAAGGTA
** *
8175 AAAAATAAAATAAAAGTTAATG
1 AAAAATAAAATAAAAGCAAAAG
8197 AAAAATATAAATAAAAGCAAAAG
1 AAAAATA-AAATAAAAGCAAAAG
8220 AAA
1 AAA
8223 GTGCACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAATAAAATAAAAGCAAAAG
Found at i:8775 original size:17 final size:17
Alignment explanation
Indices: 8743--8793 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
8733 CAAATACAAG
8743 AAAAAGATATAGAAAATC
1 AAAAAGATATA-AAAATC
* *
8761 AAAAAAATATAAAAAGAC
1 AAAAAGATATAAAAA-TC
8779 AAAAAGA-ATAAAAAT
1 AAAAAGATATAAAAAT
8794 TTGAAATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.14
Consensus pattern (17 bp):
AAAAAGATATAAAAATC
Found at i:8777 original size:106 final size:107
Alignment explanation
Indices: 8638--8870 Score: 393
Period size: 107 Copynumber: 2.2 Consensus size: 107
8628 GAAAAAAAAT
* * *
8638 GAAAAAG-TA-AGAAAATAAAAAAAATATAAAAAGACAAAATGAATAAAAATTTGAAATA-TAAA
1 GAAAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATACAAAA
8700 TAGAAAAAA-TTTTAGTTTAAAGAAAAAAAATAACAAATACAA
66 TAGAAAAAACTTTTAGTTTAAAG-AAAAAAATAACAAATACAA
8742 GAAAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATACAAAA
1 GAAAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATACAAAA
8807 TAGAAAAAACTTTTAGTTTAAAGAAAAAAATAACAAATACAA
66 TAGAAAAAACTTTTAGTTTAAAGAAAAAAATAACAAATACAA
*
8849 GAAAAAGATATAAAAAATCAAA
1 GAAAAAGATATAGAAAATCAAA
8871 GATAAAAAAT
Statistics
Matches: 121, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
104 7 0.06
105 2 0.02
106 47 0.39
107 52 0.43
108 13 0.11
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (107 bp):
GAAAAAGATATAGAAAATCAAAAAAATATAAAAAGACAAAAAGAATAAAAATTTGAAATACAAAA
TAGAAAAAACTTTTAGTTTAAAGAAAAAAATAACAAATACAA
Found at i:8866 original size:22 final size:20
Alignment explanation
Indices: 8827--8884 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
8817 TTTTAGTTTA
*
8827 AAGAAAAAAATAACAAATAC
1 AAGAAAAAAATAAAAAATAC
8847 AAGAAAAAGATATAAAAAAT-C
1 AAGAAAAA-A-ATAAAAAATAC
8868 AAAGATAAAAAATAAAA
1 -AAGA-AAAAAATAAAA
8885 TAAAAGTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 13 0.39
23 4 0.12
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (20 bp):
AAGAAAAAAATAAAAAATAC
Found at i:8887 original size:12 final size:12
Alignment explanation
Indices: 8858--8913 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
8848 AGAAAAAGAT
8858 ATAAAAAATCAAA
1 ATAAAAAAT-AAA
8871 GATAAAAAATAAA
1 -ATAAAAAATAAA
* *
8884 AT-AAAAGT-TA
1 ATAAAAAATAAA
8894 ATAAAAAATATAA
1 ATAAAAAATA-AA
8907 ATAAAAA
1 ATAAAAA
8914 CAAAAGGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 3 0.09
11 10 0.29
12 2 0.06
13 11 0.31
14 9 0.26
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:8890 original size:19 final size:20
Alignment explanation
Indices: 8862--8912 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
8852 AAAGATATAA
*
8862 AAAATCAAAG-ATAAAAAAT
1 AAAATAAAAGTATAAAAAAT
8881 AAAATAAAAGTTAATAAAAAAT
1 AAAATAAAAG-T-ATAAAAAAT
8903 ATAAATAAAA
1 A-AAATAAAA
8913 ACAAAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
22 10 0.37
23 8 0.30
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATAAAAGTATAAAAAAT
Found at i:9165 original size:29 final size:30
Alignment explanation
Indices: 9133--9198 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
9123 GAAAAATTAT
*
9133 AAAAATAGAATA-AAAAAT-AGCAAAAAACA
1 AAAAATAGAAAACAAAAATGAG-AAAAAACA
*
9162 AAAAAT-GAAAACAAAAATGAGAAAAACCA
1 AAAAATAGAAAACAAAAATGAGAAAAAACA
9191 AAAGAATA
1 AAA-AATA
9199 ATAGATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 4 0.13
29 22 0.71
30 5 0.16
ACGTcount: A:0.74, C:0.08, G:0.09, T:0.09
Consensus pattern (30 bp):
AAAAATAGAAAACAAAAATGAGAAAAAACA
Found at i:9282 original size:34 final size:35
Alignment explanation
Indices: 9244--9311 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
9234 ACAAAAGTTA
*
9244 AAAATAAAAAATAAAAGGAAAA-ATAAAATAAGAG
1 AAAATAAAAAAGAAAAGGAAAAGATAAAATAAGAG
* *
9278 AAAATAACAAAGCAAAGGAAAATGATAAAATAAG
1 AAAATAAAAAAGAAAAGGAAAA-GATAAAATAAG
9312 TACTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 19 0.66
36 10 0.34
ACGTcount: A:0.72, C:0.03, G:0.13, T:0.12
Consensus pattern (35 bp):
AAAATAAAAAAGAAAAGGAAAAGATAAAATAAGAG
Found at i:10466 original size:19 final size:19
Alignment explanation
Indices: 10434--10471 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10424 AAATTTTTAT
10434 AAAAAAAAGCAAAA-AAAA
1 AAAAAAAAGCAAAATAAAA
*
10452 AAAATAAAAGGAAAATAAAA
1 AAAA-AAAAGCAAAATAAAA
10472 TAAGAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.84, C:0.03, G:0.08, T:0.05
Consensus pattern (19 bp):
AAAAAAAAGCAAAATAAAA
Found at i:10965 original size:400 final size:392
Alignment explanation
Indices: 10230--10970 Score: 1028
Period size: 400 Copynumber: 1.9 Consensus size: 392
10220 AAATTGAATT
* *
10230 AAATAAAAGATAAAATATTATACAAGATAATTTTGTTAATTAGATAAATTACACGACAAATAAAA
1 AAATAAAAGATAAAATATTATACAAGAAAATTTTGTTAATTAGACAAATTACACGACAAATAAAA
* * *
10295 ACAAATTTCAAGATAAAATACAAGATAATCTTAATTAGATATCTAATTAGTATACATGCACATAA
66 ACAAATTTCAAGATAAAATACAAGATAATCTTAACTAGATATCTAATTAGCATACACGCACATAA
* *
10360 ACTCCTTCCATTTCTAATGAAGCAAAGTCTCATTCAACAATGTTTTAATATCTATAACATTATAA
131 ACACCTTCCATTTCTAATAAAGCAAAGTCTCATTCAACAATGTTTTAATATCTATAACATTATAA
10425 AATTTTTATAAAAAAAAGCAAAAAAAAAAAATAAAAGGAAAATAAAATAAGAGAAATTTAAAGCA
196 AATTTTTATAAAAAAAAGC-------AAAAATAAAAGGAAAATAAAATAAGAGAAATTTAAAGCA
* * ** * *
10490 AAAGGAAAAAGAAAAAAAAAGTACTAAAAAAGAGAAAAAAATTAAAAATAAACAAAAGCACAAAA
254 AAAGGAAAAAGAAAAAAAAAGTACAAAAAAAAAGAAAAAAAGAAAAAATAAACAAAAGAAAAAAA
10555 TAGAAAAAATAAAAAAGTAAGGAAATGAAAAAATAATGAGTCAAAAGAAAAAATTAGAAAAAAAA
319 TAGAAAAAATAAAAAAGTAAGGAAATGAAAAAATAATGAGTCAAAAGAAAAAATTAGAAAAAAAA
10620 AATTATAAC
384 AATTATAAC
* *
10629 AAATGAAAGATAAAATATTCATACAAGAAAATTTTGTTAATTAGACAAATTACACGATAAAT-AA
1 AAATAAAAGATAAAATATT-ATACAAGAAAATTTTGTTAATTAGACAAATTACACGACAAATAAA
* *
10693 AACAAATTTCAAGATAAATTACAAGATGATCTTAACTAGATATCTAATTAGCATACACGCACAT-
65 AACAAATTTCAAGATAAAATACAAGATAATCTTAACTAGATATCTAATTAGCATACACGCACATA
*
10757 AACACCTTCCATTTCTAATAAAGTCAAAGTCCTCATTGAACAATGTTTTAATATCTATAACATTA
130 AACACCTTCCATTTCTAATAAAG-CAAAGT-CTCATTCAACAATGTTTTAATATCTATAACATTA
* *
10822 TAAAATTTTTAT-AAAAAAA-C-AAAGTAAGAGGAAAAATAAAATAAGAGAAAATATTAAAGCAA
193 TAAAATTTTTATAAAAAAAAGCAAAAATAAAAGG-AAAATAAAATAAGAG-AAAT-TTAAAGCAA
* * *
10884 AAGGAAAAAG-AAAAGAAATTACAAATAACAAAAGCACAAAATAGAAAAAATAACGAGTCAAAAG
255 AAGGAAAAAGAAAAAAAAAGTACAAA-AA-AAAAG-A-AAAAAAGAAAAAATAA--A--CAAAAG
10948 AAAAAAATTAG-AAAAATAAAAAA
312 AAAAAAA-TAGAAAAAATAAAAAA
10971 ATTTCAAAAA
Statistics
Matches: 304, Mismatches: 23, Indels: 29
0.85 0.06 0.08
Matches are distributed among these distances:
390 9 0.03
391 15 0.05
392 16 0.05
393 21 0.07
394 4 0.01
395 1 0.00
396 13 0.04
398 23 0.08
399 92 0.30
400 107 0.35
401 3 0.01
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (392 bp):
AAATAAAAGATAAAATATTATACAAGAAAATTTTGTTAATTAGACAAATTACACGACAAATAAAA
ACAAATTTCAAGATAAAATACAAGATAATCTTAACTAGATATCTAATTAGCATACACGCACATAA
ACACCTTCCATTTCTAATAAAGCAAAGTCTCATTCAACAATGTTTTAATATCTATAACATTATAA
AATTTTTATAAAAAAAAGCAAAAATAAAAGGAAAATAAAATAAGAGAAATTTAAAGCAAAAGGAA
AAAGAAAAAAAAAGTACAAAAAAAAAGAAAAAAAGAAAAAATAAACAAAAGAAAAAAATAGAAAA
AATAAAAAAGTAAGGAAATGAAAAAATAATGAGTCAAAAGAAAAAATTAGAAAAAAAAAATTATA
AC
Found at i:10968 original size:17 final size:18
Alignment explanation
Indices: 10943--11013 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 18
10933 ATAACGAGTC
10943 AAAA-GAAAAAAATTAGA
1 AAAATGAAAAAAATTAGA
**
10960 AAAAT-AAAAAAATTTCA
1 AAAATGAAAAAAATTAGA
*
10977 AAAATGAAGAAAAAAT-GA
1 AAAATGAA-AAAAATTAGA
10995 CAAAATAGAAAAAAATTAG
1 -AAAAT-GAAAAAAATTAG
11014 TTTATAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 19 0.44
18 3 0.07
19 17 0.40
20 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (18 bp):
AAAATGAAAAAAATTAGA
Found at i:11904 original size:34 final size:32
Alignment explanation
Indices: 11857--11940 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 32
11847 AACCAAAAAC
11857 AATAAAAAAAATAAAATTTAACCA-AAAATATTAA
1 AATAAAAAAAAT-AAA-TTAA-CAGAAAATATTAA
* *
11891 AATAAAAACAATAAATTAAGAGAAAATATTAA
1 AATAAAAAAAATAAATTAACAGAAAATATTAA
*
11923 TATAAAAGAAAATTAAAT
1 AATAAAA-AAAA-TAAAT
11941 AAATACGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
31 1 0.02
32 20 0.47
33 6 0.14
34 16 0.37
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (32 bp):
AATAAAAAAAATAAATTAACAGAAAATATTAA
Found at i:11932 original size:18 final size:18
Alignment explanation
Indices: 11881--11935 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
11871 AATTTAACCA
*
11881 AAAATATTAAAATAAAA-
1 AAAATATTAATATAAAAG
* *
11898 ACAATA--AAT-TAAGAG
1 AAAATATTAATATAAAAG
11913 AAAATATTAATATAAAAG
1 AAAATATTAATATAAAAG
11931 AAAAT
1 AAAAT
11936 TAAATAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
14 4 0.14
15 7 0.24
17 8 0.28
18 10 0.34
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAATATTAATATAAAAG
Found at i:12311 original size:21 final size:22
Alignment explanation
Indices: 12285--12330 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
12275 AAAAAAATAC
*
12285 AATATAAATAAA-TTTGAGAAA
1 AATATAAATAAAGTTCGAGAAA
*
12306 AATATATATAAAGTTCGAGAAA
1 AATATAAATAAAGTTCGAGAAA
12328 AAT
1 AAT
12331 GGAGAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (22 bp):
AATATAAATAAAGTTCGAGAAA
Found at i:13084 original size:25 final size:25
Alignment explanation
Indices: 13056--13111 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
13046 CAAAAATAGC
13056 AAAAATGA-T-AATAAAATAAAAAAA
1 AAAAATGATTCAA-AAAATAAAAAAA
* *
13080 TAAAAAAGATTCAAAAAATAAAAATA
1 -AAAAATGATTCAAAAAATAAAAAAA
13106 AAAAAT
1 AAAAAT
13112 TTTGAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.46
26 12 0.46
27 2 0.08
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.18
Consensus pattern (25 bp):
AAAAATGATTCAAAAAATAAAAAAA
Found at i:13149 original size:20 final size:20
Alignment explanation
Indices: 13094--13151 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
13084 AAAGATTCAA
*
13094 AAAATAAAAATAAAAAATTTT
1 AAAATATAAAT-AAAAATTTT
* * *
13115 GAACTTTATAA-AAAAATTTT
1 AAAATATA-AATAAAAATTTT
13135 AAAATATAAATAAAAAT
1 AAAATATAAATAAAAAT
13152 AAATGGAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
19 2 0.07
20 20 0.71
21 4 0.14
22 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATATAAATAAAAATTTT
Found at i:13358 original size:19 final size:21
Alignment explanation
Indices: 13330--13381 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
13320 AAAGATATAA
*
13330 AAAATCAAAGGT-A-AAAAAT
1 AAAATAAAAGGTAAGAAAAAT
*
13349 AAAATAAAAGTTAATGAAAAAT
1 AAAATAAAAGGTAA-GAAAAAT
13371 ATAAATAAAAG
1 A-AAATAAAAG
13382 CAAAAGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
20 1 0.04
22 7 0.26
23 9 0.33
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (21 bp):
AAAATAAAAGGTAAGAAAAAT
Found at i:13390 original size:23 final size:22
Alignment explanation
Indices: 13343--13390 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
13333 ATCAAAGGTA
** *
13343 AAAAATAAAATAAAAGTTAATG
1 AAAAATAAAATAAAAGCAAAAG
13365 AAAAATATAAATAAAAGCAAAAG
1 AAAAATA-AAATAAAAGCAAAAG
13388 AAA
1 AAA
13391 GTGCACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAATAAAATAAAAGCAAAAG
Found at i:13920 original size:102 final size:104
Alignment explanation
Indices: 13799--14021 Score: 352
Period size: 104 Copynumber: 2.2 Consensus size: 104
13789 AAAAAAATGA
* * *
13799 AAAAG-TA-AGAAAATAAAAAAATATAAAAGACAAAATGAAT-AAAATTTGAAATA-TAAATAG-
1 AAAAGATATAGAAAATCAAAAAATATAAAAGACAAAAAGAATAAAAATTTGAAATACAAAATAGA
13859 AAAAA-TTTTAGTTTAAAAGAAAAAAAATAACAAATACAAG
66 AAAAACTTTTAGTTT-AAAG-AAAAAAATAACAAATACAAG
13899 AAAAGATATAGAAAATCAAAAAATATAAAAGACAAAAAGAATAAAAATTTGAAATACAAAATAGA
1 AAAAGATATAGAAAATCAAAAAATATAAAAGACAAAAAGAATAAAAATTTGAAATACAAAATAGA
13964 AAAAACTTTTAGTTTAAAGAAAAAAATAACAAATACAAG
66 AAAAACTTTTAGTTTAAAGAAAAAAATAACAAATACAAG
14003 AAAAGATATA-AAAATCAAA
1 AAAAGATATAGAAAATCAAA
14022 GATAAAAAAT
Statistics
Matches: 114, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
100 5 0.04
101 2 0.02
102 31 0.27
103 22 0.19
104 36 0.32
105 9 0.08
106 9 0.08
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (104 bp):
AAAAGATATAGAAAATCAAAAAATATAAAAGACAAAAAGAATAAAAATTTGAAATACAAAATAGA
AAAAACTTTTAGTTTAAAGAAAAAAATAACAAATACAAG
Found at i:14003 original size:20 final size:19
Alignment explanation
Indices: 13979--14035 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
13969 CTTTTAGTTT
13979 AAAGAAAAAAATAACAAAT-
1 AAAGAAAAAAATAA-AAATC
*
13998 ACAAGAAAAGATATAAAAATC
1 A-AAGAAAA-AAATAAAAATC
14019 AAAGATAAAAAATAAAA
1 AAAGA-AAAAAATAAAA
14036 TAAAAGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 22 0.69
21 9 0.28
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAGAAAAAAATAAAAATC
Found at i:14024 original size:15 final size:14
Alignment explanation
Indices: 14004--14040 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
13994 AAATACAAGA
14004 AAAGATATAAAAATC
1 AAAGATA-AAAAATC
14019 AAAGATAAAAAAT-
1 AAAGATAAAAAATC
14032 AAA-ATAAAA
1 AAAGATAAAA
14041 GTTAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 3 0.14
14 6 0.27
15 7 0.32
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAGATAAAAAATC
Found at i:14041 original size:19 final size:20
Alignment explanation
Indices: 14013--14063 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
14003 AAAAGATATA
*
14013 AAAATCAAAG-ATAAAAAAT
1 AAAATAAAAGTATAAAAAAT
14032 AAAATAAAAGTTAATAAAAAAT
1 AAAATAAAAG-T-ATAAAAAAT
14054 ATAAATAAAA
1 A-AAATAAAA
14064 ACAAAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
22 10 0.37
23 8 0.30
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATAAAAGTATAAAAAAT
Found at i:14041 original size:104 final size:103
Alignment explanation
Indices: 13799--14064 Score: 305
Period size: 102 Copynumber: 2.6 Consensus size: 103
13789 AAAAAAATGA
* * * * * *
13799 AAAAG-TA-AGAAAATAAAAAAATATAAAAGACAAAATGAAT-AAAATTTGAAATATAAATAGAA
1 AAAAGATATAGAAAATCAAAAAATAAAAAAAAAAAAAAGAATAAAAATTTGAAATAAAAATAGAA
13861 AAATTTTAGTTTAAAAGAAAAAAAATAACAAATACAAG
66 AAATTTTAGTTTAAAAGAAAAAAAATAACAAATACAAG
* * *
13899 AAAAGATATAGAAAATCAAAAAATATAAAAGACAAAAAGAATAAAAATTTGAAATACAAAATAGA
1 AAAAGATATAGAAAATCAAAAAATAAAAAAAAAAAAAAGAATAAAAATTTGAAATA-AAAATAG-
13964 AAAAACTTTTAGTTT-AAAG-AAAAAAATAACAAATACAAG
64 AAAAA-TTTTAGTTTAAAAGAAAAAAAATAACAAATACAAG
* *
14003 AAAAGATATA-AAAATC-AAAGATAAAAAATAAAATAAAAGTTAATAAAAAATAT-AAATAAAAA
1 AAAAGATATAGAAAATCAAAAAATAAAAAA-AAAA-AAAAG--AAT-AAAAATTTGAAATAAAAA
14065 CAAAAGGAAG
Statistics
Matches: 147, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
100 5 0.03
101 2 0.01
102 41 0.28
103 21 0.14
104 41 0.28
105 13 0.09
106 17 0.12
107 7 0.05
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (103 bp):
AAAAGATATAGAAAATCAAAAAATAAAAAAAAAAAAAAGAATAAAAATTTGAAATAAAAATAGAA
AAATTTTAGTTTAAAAGAAAAAAAATAACAAATACAAG
Found at i:14313 original size:28 final size:30
Alignment explanation
Indices: 14282--14346 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 30
14272 GAAAAATTAT
*
14282 AAAAATAGAATA-AAAAAT-AGCAAAAA-CA
1 AAAAATAGAAAACAAAAATGAG-AAAAACCA
14310 AAAAAT-GAAAACAAAAATGAGAAAAACCA
1 AAAAATAGAAAACAAAAATGAGAAAAACCA
14339 AAAGAATA
1 AAA-AATA
14347 ATAGATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 4 0.13
28 17 0.55
29 7 0.23
30 3 0.10
ACGTcount: A:0.74, C:0.08, G:0.09, T:0.09
Consensus pattern (30 bp):
AAAAATAGAAAACAAAAATGAGAAAAACCA
Found at i:14543 original size:17 final size:17
Alignment explanation
Indices: 14523--14578 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
14513 GAGTCAAAAG
14523 AAAAATTAAAAAATAGA
1 AAAAATTAAAAAATAGA
*
14540 AAAATATT-AAAAATGGA
1 AAAA-ATTAAAAAATAGA
* *
14557 AAAAATGACAAAATAGA
1 AAAAATTAAAAAATAGA
*
14574 GAAAA
1 AAAAA
14579 GTTTAGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 2 0.06
17 27 0.84
18 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (17 bp):
AAAAATTAAAAAATAGA
Found at i:15630 original size:17 final size:17
Alignment explanation
Indices: 15604--15639 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15594 TTTTTATAAA
15604 AAAAGCAAAAAAAAAAT
1 AAAAGCAAAAAAAAAAT
* *
15621 AAAAGGAAAAATAAAAT
1 AAAAGCAAAAAAAAAAT
15638 AA
1 AA
15640 GAGAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAGCAAAAAAAAAAT
Found at i:16132 original size:18 final size:17
Alignment explanation
Indices: 16111--16178 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 17
16101 ATAACGAGTC
16111 AAAAGAAAAAAAATCAGA
1 AAAAGAAAAAAAATCA-A
*
16129 AAAAGAAAAAAATTTCAA
1 AAAAGAAAAAAA-ATCAA
*
16147 AAATGAAGAAAAAATGACAA
1 AAAAGAA-AAAAAAT--CAA
*
16167 AATAGAAAAAAA
1 AAAAGAAAAAAA
16179 TTAGTTTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 20 0.49
19 13 0.32
20 8 0.20
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAGAAAAAAAATCAA
Found at i:16328 original size:26 final size:27
Alignment explanation
Indices: 16267--16328 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
16257 AAGGGATTAC
* * * *
16267 AAAATGGAAAAAATTAATTTAGAAAAC
1 AAAATGAAAAAAAGTAATTAAGAAAAA
* *
16294 ATAAGGAAAAAAAGTAA-TAAGAAAAA
1 AAAATGAAAAAAAGTAATTAAGAAAAA
16320 AAAATGAAA
1 AAAATGAAA
16329 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAATGAAAAAAAGTAATTAAGAAAAA
Found at i:16632 original size:23 final size:22
Alignment explanation
Indices: 16605--16673 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
16595 AAGAACCAAC
16605 AATGATAAAATAAAAAAATAAA
1 AATGATAAAATAAAAAAATAAA
*
16627 AGATGA-AAAA-AAATACAATAAA
1 A-ATGATAAAATAAA-AAAATAAA
*
16649 AAT-ATAAAAAGTAAGAAAATAAA
1 AATGAT-AAAA-TAAAAAAATAAA
16672 AA
1 AA
16674 AGACAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
20 1 0.03
21 5 0.13
22 17 0.45
23 13 0.34
24 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (22 bp):
AATGATAAAATAAAAAAATAAA
Found at i:17089 original size:13 final size:12
Alignment explanation
Indices: 17064--17102 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
17054 TAAATAGAAC
*
17064 AAAAAATAGCAA
1 AAAAAATAACAA
17076 AAAAAATATACAA
1 AAAAAATA-ACAA
17089 AAAAAATAA-AA
1 AAAAAATAACAA
17100 AAA
1 AAA
17103 TGAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 11 0.44
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (12 bp):
AAAAAATAACAA
Found at i:17171 original size:28 final size:29
Alignment explanation
Indices: 17140--17202 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
17130 AAAATTTTTT
17140 AAAATA-TAA-ATAAAA-AATAAATTAAGAG
1 AAAATATTAATATAAAAGAA-AAATTAA-AG
*
17168 AAAATATTAATATAAAAGAAAAATTAAAT
1 AAAATATTAATATAAAAGAAAAATTAAAG
17197 AAAATA
1 AAAATA
17203 CGAAAAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 10 0.32
30 13 0.42
31 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (29 bp):
AAAATATTAATATAAAAGAAAAATTAAAG
Found at i:17189 original size:18 final size:16
Alignment explanation
Indices: 17141--17200 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 16
17131 AAATTTTTTA
* *
17141 AAATATAAATAAAAAAT
1 AAATA-AAAGAAAAATT
*
17158 AAATTAAGAGAAAATATT
1 AAA-TAAAAGAAAA-ATT
17176 AATATAAAAGAAAAATT
1 AA-ATAAAAGAAAAATT
17193 AAATAAAA
1 AAATAAAA
17201 TACGAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 6 0.17
17 14 0.39
18 15 0.42
19 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAGAAAAATT
Found at i:17614 original size:21 final size:21
Alignment explanation
Indices: 17569--17614 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
17559 TATATAAAAT
*
17569 AAAA-TTTGAGAAAAAATATA
1 AAAAGTTTGAGAAAAAATAGA
*
17589 TAAAGTTTGAG-AAAAATGAGA
1 AAAAGTTTGAGAAAAAAT-AGA
17610 AAAAG
1 AAAAG
17615 AAGAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAAGTTTGAGAAAAAATAGA
Found at i:17872 original size:19 final size:19
Alignment explanation
Indices: 17838--17882 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
17828 AAGATAGAAA
17838 AATAAAAATTTCAAACT-T
1 AATAAAAATTTCAAACTAT
*
17856 AATAAAAATTATGAAACTAT
1 AATAAAAATT-TCAAACTAT
17876 AA-AAAAA
1 AATAAAAA
17883 GAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 11 0.46
20 3 0.12
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (19 bp):
AATAAAAATTTCAAACTAT
Found at i:17955 original size:27 final size:28
Alignment explanation
Indices: 17899--17957 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
17889 AAATTAAAGC
* *
17899 AAAAGAAAAAAGATAAATAATGCACAAA
1 AAAAGAAAAAAGACAAATAATACACAAA
*
17927 AAAAGAAAAAATACAAA-AATACAACAAA
1 AAAAGAAAAAAGACAAATAATAC-ACAAA
17955 AAA
1 AAA
17958 TATAAAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.76, C:0.08, G:0.07, T:0.08
Consensus pattern (28 bp):
AAAAGAAAAAAGACAAATAATACACAAA
Found at i:18426 original size:25 final size:25
Alignment explanation
Indices: 18398--18453 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
18388 CAAAAATAGC
18398 AAAAATGA-T-AATAAAATAAAAAAA
1 AAAAATGATTGAA-AAAATAAAAAAA
* *
18422 TAAAAAAGATTGAAAAAATAAAAATA
1 -AAAAATGATTGAAAAAATAAAAAAA
18448 AAAAAT
1 AAAAAT
18454 TTTGAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.46
26 12 0.46
27 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (25 bp):
AAAAATGATTGAAAAAATAAAAAAA
Found at i:18491 original size:20 final size:20
Alignment explanation
Indices: 18436--18493 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
18426 AAAGATTGAA
*
18436 AAAATAAAAATAAAAAATTTT
1 AAAATATAAAT-AAAAATTTT
* * *
18457 GAACTTTATAA-AAAAATTTT
1 AAAATATA-AATAAAAATTTT
18477 AAAATATAAATAAAAAT
1 AAAATATAAATAAAAAT
18494 AAATGGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
19 2 0.07
20 20 0.71
21 4 0.14
22 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATATAAATAAAAATTTT
Found at i:18804 original size:628 final size:629
Alignment explanation
Indices: 18145--20760 Score: 1927
Period size: 628 Copynumber: 4.1 Consensus size: 629
18135 AATGCAAAAT
*
18145 AAAAAAAGTATGAGAATTTAAAAACGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAAGAAATA
1 AAAAAAAGTATGAGAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAAGAAATA
*
18210 AGAAAAGCAACAAAAGAATAAAAATGAAAAGACAAAAGGTTTGGAATAAAAAACAGAAAA-ATAA
66 AGAAAAGCAACAAAAGAATAAAAATGAAAAGACAAAAGATTTGGAATAAAAAACAGAAAATATAA
18274 AAATTTTTAAAATAACG-AAAAATTAAAACAAGTAAATATGAAAGCATATGCAAAAAAGGCAAAA
131 AAATTTTTAAAATAACGAAAAAATTAAAACAAGTAAATATGAAAGCATATGCAAAAAAGGCAAAA
*
18338 AGAAGGAAAATTTTGAAGGGAAAAAGTTATTAAAAAATTACAAAGTAGGACAAAAATAGCAAAAA
196 AGAAAGAAAATTTTGAAGGGAAAAAGTTATTAAAAAATTA-AAAGTAGGACAAAAATAGCAAAAA
18403 TGATAATAAAATAAAAAAATAAAAAAGATTGAAAAAATAAAAATAAAAAATTTTGAACTTTATAA
260 -GA-AATAAAATAAAAAAATAAAAAAGATTGAAAAAATAAAAATAAAAAATTTTGAACTTTATAA
* *
18468 AAAAATTTTAAAATATAAATAAAAATAAATGGAAAAATAAATTAAGATAAAATATTAATATAGAA
323 AAAAATTTTAAAATATAAATAAAAATAAATGAAAAAATAAATTAAGATAAAATATTAATATAAAA
* *
18533 GAAAAAATTAAATAAAATACCAAAAAATAAAAAAATAAAAAAGTAAGATATTAAAAAATTAGCGA
388 GAAAAAATTAAATAAAATACCAAAAAAGAAAAAAATAAAAAA-TAAGATATAAAAAAATTAGCGA
*
18598 ATAA-AAAAAATTAAAGA-CAAAAAGAATA-AAAATAGAAAAAAATTTTAGTTCAGAATATACAA
452 ATAATAAAAAATAAAAGATCAAAAAGAATACAAAATAGAAAAAAATTTTAGTTCAGAATATACAA
*
18660 AGAAAAACAAAAAAAAAATATAACAAATATAGGAAAAAGATATAAAAAATCAAAGGTAAAAAATA
517 AGAAAAACAAAAAAAAAATATAACAAATATAGGAAAAAGATATAAAAAATCAAAGATAAAAAATA
* *
18725 AAATGAAAGTTAATGAAAAATATAAATAAAAACAAAAGAAAGTGCACA
582 AAATAAAAGTTAATAAAAAATATAAATAAAAACAAAAGAAAGTGCACA
* * *
18773 AAAAAAAGTCTAATAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTG----AA-AAATA
1 AAAAAAAGTATGAGAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAAGAAATA
* *
18833 AG-AAAGCAAGAAAAGAATAAAAATG-AAAGACAAAAGATTTTGAATAAAAAA-AGAAAAAAGAA
66 AGAAAAGCAACAAAAGAATAAAAATGAAAAGACAAAAGATTTGGAATAAAAAACAG-----A-AA
* * *
18895 ATATAAAAAATTTTAAAACAACGAAAAAATTAAAACAAGTAAA-ATTGAAAGCATATGAAAAAAA
125 ATATAAAAATTTTTAAAATAACGAAAAAATTAAAACAAGTAAATA-TGAAAGCATATG---CAAA
* *
18959 AAAGGCAAAAAGAAAGAAAATTTTGAAGGGAAAACGTTATTGAAAAATT-AAA-TA-G------A
186 AAAGGCAAAAAGAAAGAAAATTTTGAAGGGAAAAAGTTATTAAAAAATTAAAAGTAGGACAAAAA
* * *
19015 -A-CAAAAA-AAAT-AGACAAAAAAATAAGAAA-A-TG-----A-AAAAATAAAAAATTTTGAAC
251 TAGCAAAAAGAAATAAAATAAAAAAATAAAAAAGATTGAAAAAATAAAAATAAAAAATTTTGAAC
** *
19068 TTTATAAAAATTTTTTAAAATATAAATAAAAAATAAATGAAAAAATAAATTAAGAGAAAATATTA
316 TTTATAAAAAAATTTTAAAATATAAAT-AAAAATAAATGAAAAAATAAATTAAGATAAAATATTA
* * * * * * *
19133 ATATAAAAGAAAAAA-TAAATAAAATACGAAAAAAGGAAGAAATAAAAATAAACAAAAACAAAAA
380 ATATAAAAGAAAAAATTAAATAAAATACCAAAAAAGAAAAAAATAAAAA-ATA-AGATATAAAAA
** ** * *
19197 GTAACAAAGCAAGAA-AATAAAAAATTTACGAATCAAAAA-AATATAAAA-AGACAAAATGGAA-
443 --AA-TTAGC--GAATAATAAAAAATAAAAG-ATCAAAAAGAATACAAAATAGA-AAAA---AAT
*** * * * * * *
19258 AAAACTT-AGAATGTACAAAGGAAAACAAAAAATATATATATACAAATAAAGGAAAAAGATATAA
498 TTTAGTTCAGAATATACAAAGAAAAACAAAAAAAAAATATA-ACAAATATAGGAAAAAGATATAA
* * * * * *
19322 AATATGAAAGATGAAAAATAAAATAAAAGTTAATAAAAAATAGAAATAAAAATAAAAGAATGTGC
562 AAAATCAAAGATAAAAAATAAAATAAAAGTTAATAAAAAATATAAATAAAAACAAAAGAAAGTGC
19387 ACAA
627 AC-A
* ** * ** * * ** * *
19391 AAAAAGAAGTTTGAGGTTTTAAAATTATAAAGAAGAAAT-AAA-AAAAAGTGCGAACAAAAAGAT
1 AAAAA-AAGTATGAGAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTG-A-AAAAAGAA
* * * * * * ** * **
19454 TTAAGAAAAAGCAAGAAAAAAATAAAAAATGAAAATACAAAATATATAAAAT-AATATGAGAAAA
63 ATAAG-AAAAGCAACAAAAGAAT-AAAAATGAAAAGACAAAAGATTTGGAATAAAAAACAGAAAA
* * * * ** * * *
19518 TATATATAAAGTTTGAGAAAAAATGAGAAAAAGAAGAAAAAAATAAAAAATGAAGAGGCAAAAAT
126 TATA-A-AAATTTTTA-AAATAACGA-AAAAATTA-AAACAAGT-AAATATGAA-A-GC----AT
* *** * ** *
19583 ATGAAATAAAAAAAAAAAAAAATTTATAGAAAATTTT-AA-AAAAAAAG--AGTGAACAAAA--A
179 ATG-CA-AAAAAGGCAAAAAGA---A-AGAAAATTTTGAAGGGAAAAAGTTA-TTAA-AAAATTA
* * *** ** *
19642 AAATGAAGCG-CATAAA-A--AAAAAGAAGA-AAAATTTGAAAGGAGAAAAAGTTAATGAAAAAT
236 AAA-GTAG-GACAAAAATAGCAAAAAGAA-ATAAAATAAAAAAATA-AAAAAG--ATTGAAAAA-
** ** * *** * *
19702 TATAAAAATGCAATAAAA-AAT-AAC-CGAGAATGATAAAATAAAAAAAGA-AAAGAAAAA-AAG
294 -ATAAAAAT--AA-AAAATTTTGAACTTTATAA--A-AAAATTTTAAAATATAAATAAAAATAA-
* * *
19762 ATAGAAAAAAAAAATTTCAAAACTTAATAAAAATTTATGAAACTATAAAAAAAGAAAAAAATTAA
351 AT-GAAAAAATAAA-TT---AA---GAT-AAAA--TAT-TAA-TAT-AAAA--G-AAAAAATTAA
** * * * * * *
19827 AGCAAA-A-GAAAAAAGATAAATAAAGCACAAAAA-AAGA-AAAAAAAAATACAAC-AAAAATAT
399 ATAAAATACCAAAAAAGA-AAA-AAA-TA-AAAAATAAGATATAAAAAAAT-TAGCGAATAATA-
* * * * * * *** ** *
19887 AAAAAGTAAGAAAATAAAAAAGGACA-AAAATTGAAGAAAAATTTCA-AAAATGAA-ATGGAATG
458 AAAAA-TAA-AAGATCAAAAAGAATACAAAATAGAA-AAAAATTTTAGTTCA-GAATATACAAAG
** * ** *
19949 ACAAAATGAAAAAAAATTAGT-TTAAA-A-AGGAACAAA-AAATTGAAAAACAT-ATAAGACCTA
519 A-AAAACAAAAAAAAAATA-TAACAAATATAGGAA-AAAGATA-T-AAAAA-ATCA-AAGA--TA
* * * * * * *
20009 ATAATAAAACAATATAAAAAGTGAGACAAAAAAT-TAAA-AAAGAGAAAAGTTAA-TGCAAAA
575 A-AA-AATA-AA-AT-AAAAGTTA-ATAAAAAATATAAATAAAAACAAAAG-AAAGTGC-ACA
*
20069 TAAAAAAAGTATGAGAATTTAAAAACGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAAGAAAT
1 -AAAAAAAGTATGAGAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAAGAAAT
*
20134 AAGAAAAGCAACAAAAGAATAAAAATGAAAAGACAAAAGGTTTGGAATAAAAAACA-AAAA-ATA
65 AAGAAAAGCAACAAAAGAATAAAAATGAAAAGACAAAAGATTTGGAATAAAAAACAGAAAATATA
* *
20197 AAAATTTTTAAAATAACGAAAAAATTAAAACAAGTAAAAATGAAAGCATATG-AAAAAAAGCAAA
130 AAAATTTTTAAAATAACGAAAAAATTAAAACAAGTAAATATGAAAGCATATGCAAAAAAGGCAAA
*
20261 AAGAAGGAAAATTTTGAAGGGAAAAAGTTATTAAAAAATTACAAAGTAGGACAAAAATAGC---A
195 AAGAAAGAAAATTTTGAAGGGAAAAAGTTATTAAAAAATTA-AAAGTAGGACAAAAATAGCAAAA
*
20323 AG--A-AAAATAAAAAAATAAAAAAGATT-CAAAAATAAAAA-AAAAAATTTTGAACTTTATAAA
259 AGAAATAAAATAAAAAAATAAAAAAGATTGAAAAAATAAAAATAAAAAATTTTGAACTTTATAAA
** * *
20383 AATTTTTTAAAATATAAATAAAAATAAATGGAAAAATAAATTAAGATAAAATATTAATATAGAAG
324 AAAATTTTAAAATATAAATAAAAATAAATGAAAAAATAAATTAAGATAAAATATTAATATAAAAG
* *
20448 AAAAAATTAAATAAAATACCAAAAAAGCAAAAAATAAAAAAGTAAGATATTAAAAAATTAGCGAA
389 AAAAAATTAAATAAAATACCAAAAAAGAAAAAAATAAAAAA-TAAGATATAAAAAAATTAGCGAA
* * *
20513 TAAAAAAATACAAAAGACAAAATGAAT-AAAAATTTCAAATACAAAATAGAAAAAACTTTTAGTT
453 T-----AATA-AAAA-ATAAAA-G-ATCAAAAA----GAATACAAAATAGAAAAAAATTTTAGTT
*
20577 CAGAATATACAAAGAAAAACAAAAAAAATATATAACAAATATAGGAAAAAGATATAAAAAATCAA
505 CAGAATATACAAAGAAAAACAAAAAAAAAATATAACAAATATAGGAAAAAGATATAAAAAATCAA
20642 AGATAAAAAATAAAATAAAAGTTAATAAAAAATATAAATAAAAACAAAAAGAAAGTGCA-A
570 AGATAAAAAATAAAATAAAAGTTAATAAAAAATATAAATAAAAAC-AAAAGAAAGTGCACA
* * *
20702 AAAAAAAGTCTAATAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAA
1 AAAAAAAGTATGAGAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAA
20761 TAAGAAAAGA
Statistics
Matches: 1520, Mismatches: 272, Indels: 388
0.70 0.12 0.18
Matches are distributed among these distances:
607 75 0.05
608 58 0.04
610 2 0.00
611 3 0.00
612 2 0.00
613 15 0.01
614 9 0.01
615 29 0.02
616 32 0.02
617 90 0.06
618 11 0.01
619 30 0.02
620 3 0.00
621 25 0.02
622 29 0.02
623 11 0.01
624 14 0.01
625 8 0.01
626 24 0.02
627 37 0.02
628 106 0.07
629 10 0.01
630 3 0.00
631 72 0.05
632 81 0.05
633 31 0.02
634 22 0.01
635 22 0.01
636 11 0.01
637 30 0.02
638 7 0.00
639 4 0.00
640 9 0.01
641 35 0.02
642 25 0.02
643 13 0.01
644 7 0.00
645 4 0.00
646 2 0.00
647 21 0.01
648 15 0.01
649 7 0.00
650 3 0.00
651 7 0.00
653 4 0.00
654 2 0.00
656 16 0.01
657 24 0.02
658 20 0.01
659 21 0.01
660 39 0.03
661 5 0.00
663 7 0.00
666 1 0.00
667 6 0.00
668 1 0.00
669 21 0.01
670 19 0.01
671 28 0.02
672 49 0.03
673 16 0.01
674 18 0.01
675 16 0.01
676 40 0.03
677 23 0.02
678 55 0.04
679 21 0.01
680 14 0.01
ACGTcount: A:0.66, C:0.04, G:0.11, T:0.19
Consensus pattern (629 bp):
AAAAAAAGTATGAGAATTTAAAAATGCAAATAAGAAATGAAAGGAAATTTGTGAAAAAAGAAATA
AGAAAAGCAACAAAAGAATAAAAATGAAAAGACAAAAGATTTGGAATAAAAAACAGAAAATATAA
AAATTTTTAAAATAACGAAAAAATTAAAACAAGTAAATATGAAAGCATATGCAAAAAAGGCAAAA
AGAAAGAAAATTTTGAAGGGAAAAAGTTATTAAAAAATTAAAAGTAGGACAAAAATAGCAAAAAG
AAATAAAATAAAAAAATAAAAAAGATTGAAAAAATAAAAATAAAAAATTTTGAACTTTATAAAAA
AATTTTAAAATATAAATAAAAATAAATGAAAAAATAAATTAAGATAAAATATTAATATAAAAGAA
AAAATTAAATAAAATACCAAAAAAGAAAAAAATAAAAAATAAGATATAAAAAAATTAGCGAATAA
TAAAAAATAAAAGATCAAAAAGAATACAAAATAGAAAAAAATTTTAGTTCAGAATATACAAAGAA
AAACAAAAAAAAAATATAACAAATATAGGAAAAAGATATAAAAAATCAAAGATAAAAAATAAAAT
AAAAGTTAATAAAAAATATAAATAAAAACAAAAGAAAGTGCACA
Found at i:19038 original size:12 final size:14
Alignment explanation
Indices: 19008--19036 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
18998 TTGAAAAATT
19008 AAATAGAACAAAAA
1 AAATAGAACAAAAA
19022 AAATAG-ACAAAAA
1 AAATAGAACAAAAA
19035 AA
1 AA
19037 TAAGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
AAATAGAACAAAAA
Found at i:19050 original size:16 final size:15
Alignment explanation
Indices: 19031--19060 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19021 AAAATAGACA
19031 AAAAAATAAGAAAATG
1 AAAAAATAA-AAAATG
19047 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
19061 TTTGAACTTT
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:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATG
Found at i:19110 original size:12 final size:11
Alignment explanation
Indices: 19083--19117 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
19073 AAAAATTTTT
*
19083 TAAAATATAAA
1 TAAAAAATAAA
19094 TAAAAAATAAA
1 TAAAAAATAAA
19105 TGAAAAAATAAA
1 T-AAAAAATAAA
19117 T
1 T
19118 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:19145 original size:18 final size:18
Alignment explanation
Indices: 19100--19166 Score: 66
Period size: 17 Copynumber: 3.7 Consensus size: 18
19090 TAAATAAAAA
*
19100 ATAAATGAAAAAATAAAT
1 ATAAAAGAAAAAATAAAT
* * *
19118 -TAAGAGAAAATATTAAT
1 ATAAAAGAAAAAATAAAT
19135 ATAAAAGAAAAAATAAAT
1 ATAAAAGAAAAAATAAAT
19153 A-AAATACGAAAAAA
1 ATAAA-A-GAAAAAA
19167 GGAAGAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 16 0.41
18 16 0.41
19 7 0.18
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.19
Consensus pattern (18 bp):
ATAAAAGAAAAAATAAAT
Found at i:19504 original size:22 final size:22
Alignment explanation
Indices: 19470--19523 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
19460 AAAAGCAAGA
* *
19470 AAAAAATAAAAAATGAAAAT-AC
1 AAAATATATAAAAT-AAAATGAC
* *
19492 AAAATATATAAAATAATATGAG
1 AAAATATATAAAATAAAATGAC
19514 AAAATATATA
1 AAAATATATA
19524 TAAAGTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (22 bp):
AAAATATATAAAATAAAATGAC
Found at i:19567 original size:19 final size:20
Alignment explanation
Indices: 19535--19605 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 20
19525 AAAGTTTGAG
*
19535 AAAAAATGAGAAAAAGAAGA
1 AAAAAATGAAAAAAAGAAGA
*
19555 AAAAAAT-AAAAAATGAAGA
1 AAAAAATGAAAAAAAGAAGA
* *
19574 GGCAAAAATATGAAATAAAAAAAAA
1 ---AAAAA-ATGAAA-AAAAGAAGA
19599 AAAAAAT
1 AAAAAAT
19606 TTATAGAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
19 10 0.25
20 7 0.17
21 2 0.05
22 10 0.25
23 2 0.05
24 3 0.08
25 6 0.15
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAGA
Found at i:19877 original size:21 final size:21
Alignment explanation
Indices: 19808--19883 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 21
19798 ATGAAACTAT
*
19808 AAAAAAAGAAAAAAATTAAAGCAAA
1 AAAAAAAGAAAAAAA--AAA-C-AC
* * *
19833 AGAAAAAAGATAAATAAAGCAC
1 A-AAAAAAGAAAAAAAAAACAC
*
19855 AAAAAAAGAAAAAAAAAATAC
1 AAAAAAAGAAAAAAAAAACAC
19876 AACAAAAA
1 AA-AAAAA
19884 TATAAAAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
21 18 0.44
22 7 0.17
23 1 0.02
24 2 0.05
25 1 0.02
26 12 0.29
ACGTcount: A:0.79, C:0.07, G:0.08, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAACAC
Found at i:19916 original size:16 final size:17
Alignment explanation
Indices: 19877--19917 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
19867 AAAAAATACA
*
19877 ACAAAAATATAAAAAGT
1 ACAAAAATATAAAAAGG
19894 A-AGAAAATA-AAAAAGG
1 ACA-AAAATATAAAAAGG
19910 ACAAAAAT
1 ACAAAAAT
19918 TGAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.73, C:0.05, G:0.10, T:0.12
Consensus pattern (17 bp):
ACAAAAATATAAAAAGG
Found at i:20338 original size:8 final size:8
Alignment explanation
Indices: 20325--20366 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
20315 AAATAGCAAG
20325 AAAAATAA
1 AAAAATAA
20333 AAAAATAA
1 AAAAATAA
**
20341 AAAAGATTC
1 AAAA-ATAA
20350 AAAAATAA
1 AAAAATAA
20358 AAAAA-AA
1 AAAAATAA
20365 AA
1 AA
20367 TTTTGAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 4 0.14
8 19 0.66
9 6 0.21
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:20659 original size:12 final size:12
Alignment explanation
Indices: 20630--20685 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
20620 GGAAAAAGAT
20630 ATAAAAAATCAAA
1 ATAAAAAAT-AAA
20643 GATAAAAAATAAA
1 -ATAAAAAATAAA
* *
20656 AT-AAAAGT-TA
1 ATAAAAAATAAA
20666 ATAAAAAATATAA
1 ATAAAAAATA-AA
20679 ATAAAAA
1 ATAAAAA
20686 CAAAAAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 3 0.09
11 10 0.29
12 2 0.06
13 11 0.31
14 9 0.26
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:20662 original size:19 final size:20
Alignment explanation
Indices: 20634--20684 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
20624 AAAGATATAA
*
20634 AAAATCAAAG-ATAAAAAAT
1 AAAATAAAAGTATAAAAAAT
20653 AAAATAAAAGTTAATAAAAAAT
1 AAAATAAAAG-T-ATAAAAAAT
20675 ATAAATAAAA
1 A-AAATAAAA
20685 ACAAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
22 10 0.37
23 8 0.30
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAATAAAAGTATAAAAAAT
Found at i:21051 original size:28 final size:26
Alignment explanation
Indices: 21013--21083 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 26
21003 AAATGAATAA
**
21013 AAAACAAATAAAAAATAGTAATATAAAGG
1 AAAA-AAATAAAAAATACCAA-A-AAAGG
21042 AAAAAAATAAATAAAATACCAAAAAAGG
1 AAAAAAAT-AA-AAAATACCAAAAAAGG
*
21070 AAAAAGATAAAAAA
1 AAAAAAATAAAAAA
21084 GCAAGAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 4 0.11
27 2 0.05
28 16 0.43
29 7 0.19
30 8 0.22
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (26 bp):
AAAAAAATAAAAAATACCAAAAAAGG
Found at i:21081 original size:16 final size:16
Alignment explanation
Indices: 21062--21099 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21052 ATAAAATACC
*
21062 AAAAAAGGAA-AAAGAT
1 AAAAAAGCAAGAAA-AT
21078 AAAAAAGCAAGAAAAT
1 AAAAAAGCAAGAAAAT
21094 AAAAAA
1 AAAAAA
21100 TTAGCAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (16 bp):
AAAAAAGCAAGAAAAT
Found at i:22112 original size:20 final size:20
Alignment explanation
Indices: 22040--22117 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
22030 TAAAAAGAAA
*
22040 AAAAAAAGGAATGAAAAA-TT
1 AAAAAAAGGAA-AAAAAAGTT
* * * * *
22060 AAGAAAATGCATAAAAAGTA
1 AAAAAAAGGAAAAAAAAGTT
**
22080 AAAAAAAACAAAAAAAAGTT
1 AAAAAAAGGAAAAAAAAGTT
22100 AAAAAAAGGAAAAGAAAA
1 AAAAAAAGGAAAA-AAAA
22118 AGGAAGTAAA
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
19 5 0.12
20 34 0.79
21 4 0.09
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAAAAAGGAAAAAAAAGTT
Found at i:23735 original size:34 final size:32
Alignment explanation
Indices: 23679--23755 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 32
23669 CCAAAATGAT
* *
23679 AAAATAAAAAAATAAAAGATAAAAATACAATA
1 AAAATAAAAAAATAAAAAATAAAAAGACAATA
*
23711 AAAATATAAAAAGTAAGAAAATAAAAAGACAA-A
1 AAAATA-AAAAAATAA-AAAATAAAAAGACAATA
23744 AATGAATAAAAA
1 AA--AATAAAAA
23756 CTTCAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 6 0.16
33 11 0.29
34 17 0.45
35 4 0.11
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (32 bp):
AAAATAAAAAAATAAAAAATAAAAAGACAATA
Found at i:23754 original size:23 final size:23
Alignment explanation
Indices: 23702--23754 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
23692 AAAAGATAAA
* * *
23702 AATACAATAAAAATATAAAAAGT
1 AATAAAATAAAAAGACAAAAAGT
*
23725 AAGAAAATAAAAAGACAAAAA-T
1 AATAAAATAAAAAGACAAAAAGT
23747 GAATAAAA
1 -AATAAAA
23755 ACTTCAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.15
Consensus pattern (23 bp):
AATAAAATAAAAAGACAAAAAGT
Found at i:23764 original size:42 final size:40
Alignment explanation
Indices: 23671--23755 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
23661 GAAAAGAACC
*
23671 AAAATGAT-AAAATAAAAAAATAAAAGATAAAAATACAATA
1 AAAAT-ATAAAAATAAAAAAATAAAAGACAAAAATACAATA
* *
23711 AAAATATAAAAAGTAAGAAAATAAAAAGACAAAAAT-GAATA
1 AAAATATAAAAA-TAAAAAAAT-AAAAGACAAAAATACAATA
23752 AAAA
1 AAAA
23756 CTTCAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 2 0.05
40 9 0.23
41 16 0.41
42 12 0.31
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.15
Consensus pattern (40 bp):
AAAATATAAAAATAAAAAAATAAAAGACAAAAATACAATA
Done.