Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005515.1 Hibiscus syriacus cultivar Beakdansim tig00012738_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67919
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4805 original size:25 final size:25
Alignment explanation
Indices: 4771--4825 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
4761 TAATGTTATC
4771 AGAATAATTTCAAGAACCGATTTGT
1 AGAATAATTTCAAGAACCGATTTGT
4796 AGAATAATTTCAAGAACCGATTTGT
1 AGAATAATTTCAAGAACCGATTTGT
4821 AGAAT
1 AGAAT
4826 GAGCATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (25 bp):
AGAATAATTTCAAGAACCGATTTGT
Found at i:5491 original size:22 final size:24
Alignment explanation
Indices: 5446--5516 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 24
5436 TAAATCCCCA
5446 ATTTTTCTAAATAAAAGTTATAATT
1 ATTTTT-TAAATAAAAGTTATAATT
* *
5471 GTTTTTTAAATAATA-TT-TAATT
1 ATTTTTTAAATAAAAGTTATAATT
5493 ATTTTTTAAA-AAAATGGTTATAAT
1 ATTTTTTAAATAAAA--GTTATAAT
5517 AGGTTTCTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 3 0.08
22 14 0.37
23 2 0.05
24 10 0.26
25 9 0.24
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (24 bp):
ATTTTTTAAATAAAAGTTATAATT
Found at i:5836 original size:42 final size:42
Alignment explanation
Indices: 5778--5892 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 42
5768 TTGAGAATAA
* * *
5778 AAACGCCGCAATAGGTCGAGATCTATTGTGGCG-TTTTTGGAAC
1 AAAC-CCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTTGGAAC
*
5821 AAACCCGCAAAAGGTC--ATATATAGCGGCGTTTTTTGGAAC
1 AAACCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGGAAC
**
5861 AATGCCGCAAAAGGTCAGATCTAT--CGGCGTTT
1 AAACCCGCAAAAGGTCAGATCTATAGCGGCGTTT
5893 GACGCAGAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 10 0.16
40 32 0.52
42 16 0.26
43 4 0.06
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (42 bp):
AAACCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGGAAC
Found at i:12765 original size:17 final size:17
Alignment explanation
Indices: 12743--12784 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
12733 TTGTTGCTCA
12743 AGGGTATACTCAAGAAG
1 AGGGTATACTCAAGAAG
12760 AGGGTATACTCAAGAAG
1 AGGGTATACTCAAGAAG
12777 AGGGTATA
1 AGGGTATA
12785 GACTATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.31, T:0.19
Consensus pattern (17 bp):
AGGGTATACTCAAGAAG
Found at i:14375 original size:21 final size:23
Alignment explanation
Indices: 14342--14402 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
14332 TTGGTGCAGA
*
14342 GGGAATCGA-TCCCCCCATG-A-
1 GGGAACCGATTCCCCCCATGAAG
* **
14362 GTGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATGAAG
14385 GGGAACCGATTCCCCCCA
1 GGGAACCGATTCCCCCCA
14403 CAGGGGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.23
21 8 0.26
22 1 0.03
23 15 0.48
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.18
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCATGAAG
Found at i:14409 original size:21 final size:21
Alignment explanation
Indices: 14383--14422 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14373 CCCCCTTTGA
*
14383 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
14404 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
14423 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:19228 original size:19 final size:19
Alignment explanation
Indices: 19204--19243 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19194 GATAATTTTG
*
19204 TACAAACTTCTAACAAGAC
1 TACAAACTTCCAACAAGAC
19223 TACAAACTTCCAACAAGAC
1 TACAAACTTCCAACAAGAC
19242 TA
1 TA
19244 ATTGGTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.20
Consensus pattern (19 bp):
TACAAACTTCCAACAAGAC
Found at i:22315 original size:21 final size:21
Alignment explanation
Indices: 22290--22332 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
22280 AACTGGGGCT
22290 AACCAATCAAAGCATAAGAAC
1 AACCAATCAAAGCATAAGAAC
22311 AACCAATCAAAGCATAAGAAC
1 AACCAATCAAAGCATAAGAAC
22332 A
1 A
22333 GCTTTTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.23, G:0.09, T:0.09
Consensus pattern (21 bp):
AACCAATCAAAGCATAAGAAC
Found at i:26163 original size:42 final size:42
Alignment explanation
Indices: 26100--26194 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
26090 CGGCGTTTGC
* * * *
26100 AAACGCCGCTAAATTATTAATATGTTGTGACGTTTATTGAAA
1 AAACGCCACTAAAGTACTAATATGTTGCGACGTTTATTGAAA
**
26142 AAACGCCACTAAAGTACTAATATGTTGCGGTGTTTATTGAAA
1 AAACGCCACTAAAGTACTAATATGTTGCGACGTTTATTGAAA
*
26184 AACCGCCACTA
1 AAACGCCACTA
26195 TAGATGGACC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (42 bp):
AAACGCCACTAAAGTACTAATATGTTGCGACGTTTATTGAAA
Found at i:26357 original size:121 final size:122
Alignment explanation
Indices: 26142--26363 Score: 338
Period size: 121 Copynumber: 1.8 Consensus size: 122
26132 TTTATTGAAA
* * *
26142 AAACGCCACTAAAGTACTAATATGTTGCGGTGTTTATTGAAAAACCGCCACTATAGATGGACCTA
1 AAACGCCACTAAAGTACTAATATGTTACGGCGTTTATTGAAAAACCGCAACTATAGATGGACCTA
* *
26207 TTGCGGCGTTTATATAAAAATAATGCTAAAGTACTAATCTGTGCGGCATTTGTATAT
66 TTGCGGCGTTTATATAAAAACAACGCTAAAGTACTAATCTGTGCGGCATTTGTATAT
* * *
26264 AAACGCCGCTAAAGTACTAATCTGTTACGGCGTTTATTGAAAAA-CGCAACTATAGATGGACTTA
1 AAACGCCACTAAAGTACTAATATGTTACGGCGTTTATTGAAAAACCGCAACTATAGATGGACCTA
* * *
26328 TTGCGGCGTTTGTTTAAAAACGACGCTAAAGTACTA
66 TTGCGGCGTTTATATAAAAACAACGCTAAAGTACTA
26364 CTTTTTTGCG
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
121 49 0.55
122 40 0.45
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (122 bp):
AAACGCCACTAAAGTACTAATATGTTACGGCGTTTATTGAAAAACCGCAACTATAGATGGACCTA
TTGCGGCGTTTATATAAAAACAACGCTAAAGTACTAATCTGTGCGGCATTTGTATAT
Found at i:30945 original size:24 final size:24
Alignment explanation
Indices: 30918--30990 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
30908 TGATGTAATT
* *
30918 TGTTCTTACATCTCCATTGATTTG
1 TGTTCTTACATCTCTATTGAGTTG
30942 TGTTCTTACATCTCTATTGAGTTG
1 TGTTCTTACATCTCTATTGAGTTG
30966 TGTTCTTACATCTCTATTGAGTTG
1 TGTTCTTACATCTCTATTGAGTTG
30990 T
1 T
30991 CTCCGGCCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (24 bp):
TGTTCTTACATCTCTATTGAGTTG
Found at i:32569 original size:39 final size:39
Alignment explanation
Indices: 32511--32587 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
32501 TTCCGAAACG
32511 TGAATGTGAGATACGAATATGTTTAATTCTTTTTCGAGA
1 TGAATGTGAGATACGAATATGTTTAATTCTTTTTCGAGA
** * *
32550 TGAATGTTCGATACTAATATTTTTAATTCTTTTTCGAG
1 TGAATGTGAGATACGAATATGTTTAATTCTTTTTCGAG
32588 TTTTCTCGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (39 bp):
TGAATGTGAGATACGAATATGTTTAATTCTTTTTCGAGA
Found at i:33471 original size:45 final size:45
Alignment explanation
Indices: 33422--33508 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
33412 GCTTCAACTT
* * *
33422 GTTAGAAATGTCATACATTGACCATGTGAGATAAAGTATCATAAA
1 GTTAGAAATGTCATACATAGACAATGTGAGATAAACTATCATAAA
* *
33467 GTTAGACATGTCATACATAGACAATGTGAGATCAACTATCAT
1 GTTAGAAATGTCATACATAGACAATGTGAGATAAACTATCAT
33509 GCCCCCATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (45 bp):
GTTAGAAATGTCATACATAGACAATGTGAGATAAACTATCATAAA
Found at i:34923 original size:37 final size:36
Alignment explanation
Indices: 34866--34983 Score: 168
Period size: 35 Copynumber: 3.3 Consensus size: 36
34856 CCCATTATCG
* * *
34866 TTTTTC-AACAAACATCTACCAAACTTTGAAAAGCTA
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAA-CCA
34902 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
*
34938 -TTTTCAGAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
34973 TTTTTTCAAAG
1 -TTTTTCAAAG
34984 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.46
36 8 0.11
37 32 0.43
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (36 bp):
TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:34939 original size:21 final size:21
Alignment explanation
Indices: 34915--34975 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
34905 TTCAAAGAAA
34915 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
* *
34936 CATTT-TCAGA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
34950 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
34971 CATTT
1 CATTT
34976 TTTCAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 6 0.21
16 1 0.03
19 1 0.03
20 6 0.21
21 10 0.34
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:39526 original size:36 final size:37
Alignment explanation
Indices: 39455--39539 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
39445 ATCCCATTAT
*
39455 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
39491 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
39527 CATTTTTCCAAAG
1 CATTTTT-CAAAG
39540 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 18 0.42
37 25 0.58
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:43890 original size:55 final size:55
Alignment explanation
Indices: 43803--43913 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
43793 ATTTATAACT
* * *
43803 CAAGTATTCAAACCAGACAAACTTCCCTATAAAAGCATATGCAAGAGATAAAAAC
1 CAAGTATTCAAACCAGACAAACTTCCCCATAAAAGCATATACAAGAGACAAAAAC
*
43858 CAAGTATTCAACCCAGACAAACTTCCCCATAAAAGCATATACAAGAGACAAAAAC
1 CAAGTATTCAAACCAGACAAACTTCCCCATAAAAGCATATACAAGAGACAAAAAC
43913 C
1 C
43914 TAAGAGAAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.49, C:0.25, G:0.10, T:0.16
Consensus pattern (55 bp):
CAAGTATTCAAACCAGACAAACTTCCCCATAAAAGCATATACAAGAGACAAAAAC
Found at i:49353 original size:90 final size:89
Alignment explanation
Indices: 49200--49374 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 89
49190 CCTAATACAC
* * * *
49200 CCTTTTATATCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
49265 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
49290 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
49355 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
49375 ATATTCGGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 7 0.09
90 73 0.91
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (89 bp):
CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:51864 original size:8 final size:8
Alignment explanation
Indices: 51853--51945 Score: 61
Period size: 7 Copynumber: 11.5 Consensus size: 8
51843 CTTGAAGAAG
51853 AAAAGAGA
1 AAAAGAGA
*
51861 AAAAAATGAA
1 AAAAGA-G-A
*
51871 AAAATGAAA
1 AAAA-GAGA
*
51880 AAAAAATGA
1 AAAAGA-GA
51889 AAAA-ATGA
1 AAAAGA-GA
51897 AAAAGA-A
1 AAAAGAGA
51904 AAAA-AGA
1 AAAAGAGA
51911 AAAA-AGA
1 AAAAGAGA
51918 AAAAGA-A
1 AAAAGAGA
*
51925 AAAAGAAAA
1 AAAAG-AGA
51934 AAAAGAGA
1 AAAAGAGA
51942 AAAA
1 AAAA
51946 TACAAAGAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
6 1 0.01
7 23 0.33
8 22 0.31
9 18 0.26
10 5 0.07
11 1 0.01
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (8 bp):
AAAAGAGA
Found at i:51884 original size:19 final size:17
Alignment explanation
Indices: 51847--51945 Score: 94
Period size: 19 Copynumber: 5.5 Consensus size: 17
51837 ATTTTGCTTG
51847 AAGAAGAAAAGAGAAAAAA
1 AAGAA-AAAAGA-AAAAAA
*
51866 ATGAAAAAATGAAAAAAA
1 AAGAAAAAA-GAAAAAAA
51884 AATGAAAAAATGAAAAAGAA
1 AA-GAAAAAA-GAAAAA-AA
*
51904 AA-AAAGAAA-AAAGAAA
1 AAGAAA-AAAGAAAAAAA
51920 AAGAAAAAAGAAAAAAA
1 AAGAAAAAAGAAAAAAA
51937 AGAGAAAAA
1 A-AGAAAAA
51946 TACAAAGAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
16 7 0.10
17 14 0.20
18 21 0.30
19 23 0.33
20 4 0.06
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (17 bp):
AAGAAAAAAGAAAAAAA
Found at i:51944 original size:7 final size:7
Alignment explanation
Indices: 51850--51935 Score: 74
Period size: 7 Copynumber: 12.3 Consensus size: 7
51840 TTGCTTGAAG
51850 AAGAAAA
1 AAGAAAA
*
51857 GAGAAAAA
1 AAG-AAAA
51865 AATGAAAA
1 AA-GAAAA
51873 AATG--AA
1 AA-GAAAA
51879 AA-AAAA
1 AAGAAAA
*
51885 ATGAAAA
1 AAGAAAA
51892 AATG-AAA
1 AA-GAAAA
51899 AAGAAAAA
1 AAG-AAAA
51907 AAGAAAA
1 AAGAAAA
51914 AAG-AAA
1 AAGAAAA
51920 AAGAAAA
1 AAGAAAA
51927 AAGAAAA
1 AAGAAAA
51934 AA
1 AA
51936 AAGAGAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
6 14 0.21
7 31 0.47
8 20 0.30
9 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
AAGAAAA
Found at i:51953 original size:30 final size:28
Alignment explanation
Indices: 51862--51954 Score: 84
Period size: 30 Copynumber: 3.3 Consensus size: 28
51852 GAAAAGAGAA
**
51862 AAAAATGAAAAAATGAAAAAAA-AATGAA-
1 AAAAA-GAAAAAA-GAAAAAAAGAAAAAAG
*
51890 AAAATG-AAAAAGAAAAAAAGAAAAAAG
1 AAAAAGAAAAAAGAAAAAAAGAAAAAAG
*
51917 AAAAAGAAAAAAGAAAAAAAAGAGAAAAAT
1 AAAAAGAAAAAAG-AAAAAAAGA-AAAAAG
*
51947 ACAAAGAA
1 AAAAAGAA
51955 GGTCTAAAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 8 0.15
26 9 0.17
27 6 0.11
28 10 0.19
29 9 0.17
30 12 0.22
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.05
Consensus pattern (28 bp):
AAAAAGAAAAAAGAAAAAAAGAAAAAAG
Found at i:51954 original size:23 final size:22
Alignment explanation
Indices: 51850--51944 Score: 75
Period size: 22 Copynumber: 4.1 Consensus size: 22
51840 TTGCTTGAAG
* *
51850 AAGAAAAGAGAAAAAAATGAAAA
1 AAGAAAAAAGAAAAAAAAG-AAA
* **
51873 AATGAAAAAAAAATGAAAAAATGAA
1 AA-GAAAAAAGAA--AAAAAAGAAA
*
51898 AAAGAAAAAA-AGAAAAAAGAAA
1 A-AGAAAAAAGAAAAAAAAGAAA
51920 AAGAAAAAAGAAAAAAAAGAGAA
1 AAGAAAAAAGAAAAAAAAGA-AA
51943 AA
1 AA
51945 ATACAAAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
21 8 0.14
22 18 0.32
23 6 0.11
24 9 0.16
25 10 0.18
26 6 0.11
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (22 bp):
AAGAAAAAAGAAAAAAAAGAAA
Found at i:53316 original size:53 final size:53
Alignment explanation
Indices: 53232--54357 Score: 1443
Period size: 53 Copynumber: 21.2 Consensus size: 53
53222 GTAAAGAAAA
* * *
53232 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAACAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * *
53285 AGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCATAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
**
53338 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAATGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * * * *
53391 AAAAGATTATTCGAGTTCTACTCCCTGAATG-AAGAGGGAGCAAACCCATAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAA-GCAAGAGAGAGCGAACCCGTAGGC
* * * * *
53444 AGAAGATTGCTCGAGTTCTACTCCCTGAAACAAGAAAGAGTGAACCCATAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* *
53497 AGAAGATTGTTCGAATTATACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * * *
53550 ACAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGTGAGAGCGAACCCATAAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* ** * * * *
53603 AGAAGATTGTTCGAGTTATACTCTGTGGATG-AAGAGGGAGCAAACTCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCT-GAAGCAAGAGAGAGCGAACCCGTAGGC
* *
53656 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGTGAACCCATAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* **
53709 AGAAGATTGTTCGAATTCTACTCCCTGAAGCAAGAGAGAGTAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* *
53762 AGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCATAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * **
53815 AGAAGATTGCTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
*
53868 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * * * * **
53921 ATAAGATTGTTCAATTTCTACTCCCTGAA--ATA-AGAGATCGAACTCGTAGAT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCA-AGAGAGAGCGAACCCGTAGGC
* **
53972 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * *
54025 AGAAGATTGTTCGAGTTCTACTCCCTGAAGTAAGATAGAGCGAACCCATAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* *
54078 ATAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * *
54131 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACTCGAAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* *
54184 AGAAGATTGTTTGAGTTCTACTCCCTAAAGCAAGAGAGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * * * * * **
54237 AGAATATTGTTCGAGTTCCTACTCCTTGAAACAAAAGAGTGTGAACGTGTAGGC
1 AGAAGATTGTTCGAGTT-CTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * * * * * ***
54291 AGAAGATTATACGAGTTCTATTCTCCATGAAGCAATAGGGAGCGAACCCATTTTC
1 AGAAGATTGTTCGAGTTCTA--CTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
54346 AGAAGATTGTTC
1 AGAAGATTGTTC
54358 AAATTTTATA
Statistics
Matches: 925, Mismatches: 137, Indels: 20
0.85 0.13 0.02
Matches are distributed among these distances:
51 41 0.04
52 5 0.01
53 802 0.87
54 46 0.05
55 31 0.03
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
Found at i:54629 original size:14 final size:13
Alignment explanation
Indices: 54588--54632 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
54578 TATAAATATT
54588 ATATTATATTATTA
1 ATATTATATTA-TA
*
54602 AAATTATTATTATA
1 ATATTA-TATTATA
54616 ACTATTATATTATA
1 A-TATTATATTATA
54630 ATA
1 ATA
54633 GTAATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.07
14 16 0.59
15 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTATATTATA
Found at i:58227 original size:55 final size:55
Alignment explanation
Indices: 58143--58248 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 55
58133 TGTCTATTTT
*
58143 ATTGAAGACTAATCCATGAAGAAAGACATCTAATAAATGAAGAAATTTGAAACTG
1 ATTGAAGACCAATCCATGAAGAAAGACATCTAATAAATGAAGAAATTTGAAACTG
* * *
58198 ATTGAAGACCAATCCATGAAGAAAGACATCTGATGAATGAAGAAGTTTGAA
1 ATTGAAGACCAATCCATGAAGAAAGACATCTAATAAATGAAGAAATTTGAA
58249 GTTGATCGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (55 bp):
ATTGAAGACCAATCCATGAAGAAAGACATCTAATAAATGAAGAAATTTGAAACTG
Found at i:62945 original size:8 final size:8
Alignment explanation
Indices: 62934--62990 Score: 52
Period size: 7 Copynumber: 7.5 Consensus size: 8
62924 CTTGAAGAAT
62934 AAAAGAGA
1 AAAAGAGA
62942 AAAATGA-A
1 AAAA-GAGA
*
62950 AAAATGAAA
1 AAAA-GAGA
62959 AAAAG-GA
1 AAAAGAGA
62966 AAAAG-GA
1 AAAAGAGA
62973 AAAA-AGA
1 AAAAGAGA
62980 AAAAG-GA
1 AAAAGAGA
62987 AAAA
1 AAAA
62991 AGGAAACAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
7 24 0.55
8 13 0.30
9 7 0.16
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (8 bp):
AAAAGAGA
Found at i:62950 original size:7 final size:7
Alignment explanation
Indices: 62934--62996 Score: 54
Period size: 8 Copynumber: 8.3 Consensus size: 7
62924 CTTGAAGAAT
62934 AAAAGAGA
1 AAAAG-GA
*
62942 AAAATGAA
1 AAAA-GGA
*
62950 AAAATGAA
1 AAAA-GGA
62958 AAAAAGGA
1 AAA-AGGA
62966 AAAAGGA
1 AAAAGGA
*
62973 AAAAAGA
1 AAAAGGA
62980 AAAAGGAA
1 AAAAGG-A
62988 AAAAGGA
1 AAAAGGA
62995 AA
1 AA
62997 CAGAAACAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
7 18 0.38
8 28 0.58
9 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (7 bp):
AAAAGGA
Found at i:62975 original size:14 final size:15
Alignment explanation
Indices: 62934--63046 Score: 86
Period size: 16 Copynumber: 7.2 Consensus size: 15
62924 CTTGAAGAAT
* *
62934 AAAAGAGAAAAATGAA
1 AAAAG-GAAAAAAGGA
*
62950 AAAATGAAAAAAAGGA
1 AAAA-GGAAAAAAGGA
62966 AAAAGGAAAAAA-GA
1 AAAAGGAAAAAAGGA
62980 AAAAGGAAAAAAGGA
1 AAAAGGAAAAAAGGA
* *
62995 AACA-GAAACAAATGAA
1 AAAAGGAAA-AAA-GGA
*
63011 ACAAATGAAAAAAAGGA
1 A-AAA-GGAAAAAAGGA
*
63028 AAAATGAAAAGAAGGA
1 AAAAGGAAAA-AAGGA
63044 AAA
1 AAA
63047 TAAAGAGAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
14 18 0.23
15 19 0.24
16 29 0.37
17 6 0.08
18 3 0.04
19 3 0.04
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.04
Consensus pattern (15 bp):
AAAAGGAAAAAAGGA
Found at i:62991 original size:8 final size:8
Alignment explanation
Indices: 62941--63046 Score: 71
Period size: 8 Copynumber: 13.4 Consensus size: 8
62931 AATAAAAGAG
*
62941 AAAAATGA
1 AAAAAGGA
*
62949 AAAAATGAA
1 AAAAA-GGA
62958 AAAAAGG-
1 AAAAAGGA
62965 AAAAAGGA
1 AAAAAGGA
62973 AAAAA-G-
1 AAAAAGGA
62979 AAAAAGGA
1 AAAAAGGA
62987 AAAAAGG-
1 AAAAAGGA
*
62994 AAACA-GA
1 AAAAAGGA
*
63001 AACAAATGA
1 AA-AAAGGA
*
63010 AACAAATGAA
1 AA-AAA-GGA
63020 AAAAAGG-
1 AAAAAGGA
*
63027 AAAAATGA
1 AAAAAGGA
63035 AAAGAAGGA
1 AAA-AAGGA
63044 AAA
1 AAA
63047 TAAAGAGAGA
Statistics
Matches: 78, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
6 6 0.08
7 21 0.27
8 24 0.31
9 24 0.31
10 3 0.04
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.05
Consensus pattern (8 bp):
AAAAAGGA
Found at i:63002 original size:21 final size:21
Alignment explanation
Indices: 62934--62996 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 21
62924 CTTGAAGAAT
*
62934 AAAAGAGAAAAATGAAAAAATGAAA
1 AAAAG-GAAAAAGGAAAAAA-G--A
62959 AAAAGGAAAAAGGAAAAAAGA
1 AAAAGGAAAAAGGAAAAAAGA
62980 AAAAGGAAAAAAGGAAA
1 AAAAGG-AAAAAGGAAA
62997 CAGAAACAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 7 0.19
22 10 0.28
23 1 0.03
24 13 0.36
25 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (21 bp):
AAAAGGAAAAAGGAAAAAAGA
Found at i:63047 original size:15 final size:16
Alignment explanation
Indices: 62949--63046 Score: 96
Period size: 16 Copynumber: 6.2 Consensus size: 16
62939 AGAAAAATGA
62949 AAAAATGAAAAAAAGG
1 AAAAATGAAAAAAAGG
*
62965 AAAAA-GGAAAAAA-G
1 AAAAATGAAAAAAAGG
*
62979 AAAAA-GGAAAAAAGG
1 AAAAATGAAAAAAAGG
* * *
62994 AAACA-GAAACAAATGA
1 AAAAATGAAA-AAAAGG
63010 AACAAATGAAAAAAAGG
1 AA-AAATGAAAAAAAGG
*
63027 AAAAATGAAAAGAAGG
1 AAAAATGAAAAAAAGG
63043 AAAA
1 AAAA
63047 TAAAGAGAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
14 14 0.20
15 15 0.22
16 28 0.41
17 8 0.12
18 4 0.06
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAAATGAAAAAAAGG
Found at i:64324 original size:37 final size:37
Alignment explanation
Indices: 64268--64349 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
64258 TTCGACCTTC
* * *
64268 GAAGCAAATCAAACTTAAGCCTTTATGGAAGAGTAAT
1 GAAGCAAATCAAACTTAAGCCTTCATAGAAAAGTAAT
* *
64305 GAAGCAAATC-ATCTATAAGCCTTCATAGAAAAGTAGT
1 GAAGCAAATCAAACT-TAAGCCTTCATAGAAAAGTAAT
64342 GAAGCAAA
1 GAAGCAAA
64350 ATAAGATTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 3 0.08
37 36 0.92
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (37 bp):
GAAGCAAATCAAACTTAAGCCTTCATAGAAAAGTAAT
Found at i:64432 original size:53 final size:53
Alignment explanation
Indices: 64352--64610 Score: 356
Period size: 53 Copynumber: 4.9 Consensus size: 53
64342 GAAGCAAAAT
* *
64352 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * * * *
64405 AAGATTGTTCGAGTTCTACACCCTGAAGTAAGAGAGAGCAAACTCGTAGGCAT
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * * * *
64458 AAGATTGTTCGAGTTCAACTCCCTGAAGCAAGAGGGAGCAAACTCGTAGGCAA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * *
64511 AAGATTGTTCGAGTTCTACTCCTTGAAACAAGAGAGAGCGAACCTGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * *
64564 AAGATTGTTCGAGTTATACTCCCTGAAGTAAGAGAGAGTGAACCCGT
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGT
64611 TTCTAGTTCT
Statistics
Matches: 180, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 180 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
Found at i:64544 original size:106 final size:106
Alignment explanation
Indices: 64352--65409 Score: 1267
Period size: 106 Copynumber: 10.1 Consensus size: 106
64342 GAAGCAAAAT
* *
64352 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
* * * * *
64417 GTTCTACACCCTGAAGTAAGAGAGAGCAAACTCGTAGGCAT
66 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * * * *
64458 AAGATTGTTCGAGTTCAACTCCCTGAAGCAAGAGGGAGCAAACTCGTAGGCAAAAGATTGTTCGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
* * *
64523 GTTCTACTCCTTGAAACAAGAGAGAGCGAACCTGTAGGCAG
66 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * * *
64564 AAGATTGTTCGAGTTATACTCCCTGAAGTAAGAGAGAGTGAA-CC-----C----G--T-TTCTA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
*
64616 GTTCTACTCCCTGAAGCAAGAGAGAGCGAAACCGTAGGCAG
66 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* *
64657 AAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCAAACCCGTAGGCAGAAGATTGTTCGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
* * * *
64722 GTTCTACTTCCTGAAACAAGAGAGAGCGAACCCGCAAGCAG
66 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * *
64763 AAGATTGTTCGAGTTCTACTCTCTGAAGCAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTTTGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
* * * * * ***
64828 GTTATACTACATGAAGCAAAAGGGAGCGAACTTATAGGCAG
66 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * *
64869 AAGATTGTTCGAGTTCTACTCCTTAAAGCAAAAG-GAAGCGAACCCGTAGGCAGAAGATTGTTCG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAG-AGCGAACCCGTAGGCAGAAGATTGTTCG
* *
64933 AGTTCTACTCCTTAAAGCAAGAG-GAAGCGAACCCGTAGGCAG
65 AGTTCTACTCCCTGAAGCAAGAGAG-AGCGAACCCGTAGGCAG
* * *
64975 AAGATCGTTCGAGTTCTACTCCCTGAAGC-A-AGAGAGCAAACCCGTAGGGAGAAGA-TGTTCGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
* *
65037 GTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAGGCAG
66 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* ** *
65078 AAGATTGTTCGAGTTCTACTCCCTGTAA-C-A-AGAGATCGAACATGCAGGCAGAAGATTGTTCG
1 AAGATTGTTCGAGTTCTACTCCCTG-AAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * **
65140 AGTTCTACTCCTTGAAGCAAGAGGGAATGAACCCGTAGGCAG
65 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * * * * *
65182 AAAATTGTTCAAGTTATACTCCCTGAAGCAAGAGAGAGTGAACCCATAGGCAAAAGATTGTTCGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
*
65247 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGTAG
66 GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* * ** ** * *
65288 AAGATTATTCGAGTTCTACTCCTTGAAGTGAGAGAGAGCGAACTGGTAGGCAGAAGATTATTCAA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
* *
65353 GTTCCTATTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGTAG
66 GTT-CTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
* *
65395 AAGATTATACGAGTT
1 AAGATTGTTCGAGTT
65410 TTATTTTCCC
Statistics
Matches: 813, Mismatches: 116, Indels: 45
0.83 0.12 0.05
Matches are distributed among these distances:
93 78 0.10
94 3 0.00
96 1 0.00
99 1 0.00
100 1 0.00
103 91 0.11
104 91 0.11
105 7 0.01
106 489 0.60
107 51 0.06
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (106 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCGA
GTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAG
Found at i:64637 original size:40 final size:40
Alignment explanation
Indices: 64575--64650 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
64565 AGATTGTTCG
* * *
64575 AGTTATACTCCCTGAAGTAAGAGAGAGTGAACCCGTTTCT
1 AGTTATACTCCCTGAAGCAAGAGAGAGCGAAACCGTTTCT
*
64615 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAAACCGT
1 AGTTATACTCCCTGAAGCAAGAGAGAGCGAAACCGT
64651 AGGCAGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (40 bp):
AGTTATACTCCCTGAAGCAAGAGAGAGCGAAACCGTTTCT
Found at i:64695 original size:53 final size:53
Alignment explanation
Indices: 64615--65409 Score: 1003
Period size: 53 Copynumber: 15.1 Consensus size: 53
64605 ACCCGTTTCT
* *
64615 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAAACCGTAGGCAGAAAATTGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
*
64668 AGTTCTACTCCCTGAAGCAAGAGAGAGCAAACCCGTAGGCAGAAGATTGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * * *
64721 AGTTCTACTTCCTGAAACAAGAGAGAGCGAACCCGCAAGCAGAAGATTGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * *
64774 AGTTCTACTCTCTGAAGCAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTTTG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * * * * ***
64827 AGTTATACTACATGAAGCAAAAGGGAGCGAACTTATAGGCAGAAGATTGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * *
64880 AGTTCTACTCCTTAAAGCAAAAG-GAAGCGAACCCGTAGGCAGAAGATTGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAG-AGCGAACCCGTAGGCAGAAGATTGTTCG
* * *
64933 AGTTCTACTCCTTAAAGCAAGAG-GAAGCGAACCCGTAGGCAGAAGATCGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAG-AGCGAACCCGTAGGCAGAAGATTGTTCG
* *
64986 AGTTCTACTCCCTGAAGC-A-AGAGAGCAAACCCGTAGGGAGAAGA-TGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* *
65036 AGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAGGCAGAAGATTGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* ** *
65089 AGTTCTACTCCCTGTAA-C-A-AGAGATCGAACATGCAGGCAGAAGATTGTTCG
1 AGTTCTACTCCCTG-AAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * ** * *
65140 AGTTCTACTCCTTGAAGCAAGAGGGAATGAACCCGTAGGCAGAAAATTGTTCA
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * * *
65193 AGTTATACTCCCTGAAGCAAGAGAGAGTGAACCCATAGGCAAAAGATTGTTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* *
65246 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGTAGAAGATTATTCG
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* ** ** * *
65299 AGTTCTACTCCTTGAAGTGAGAGAGAGCGAACTGGTAGGCAGAAGATTATTCA
1 AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
* * * *
65352 AGTTCCTATTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGTAGAAGATTATACG
1 AGTT-CTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
65406 AGTT
1 AGTT
65410 TTATTTTCCC
Statistics
Matches: 643, Mismatches: 89, Indels: 19
0.86 0.12 0.03
Matches are distributed among these distances:
50 24 0.04
51 63 0.10
52 27 0.04
53 483 0.75
54 46 0.07
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (53 bp):
AGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTCG
Found at i:65617 original size:3 final size:3
Alignment explanation
Indices: 65611--65657 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
65601 AATAATAATA
65611 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
65656 AT
1 AT
65658 ATTTTTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.