Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003805.1 Hibiscus syriacus cultivar Beakdansim tig00008145_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: 2300233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:5324 original size:9 final size:9
Alignment explanation
Indices: 5310--5385 Score: 71
Period size: 9 Copynumber: 8.1 Consensus size: 9
5300 TGCTGGAAAT
*
5310 CGGTTTAAC
1 CGGTTTGAC
5319 CGGTTTGAC
1 CGGTTTGAC
*
5328 CAGTTTCGAC
1 CGGTTT-GAC
*
5338 CGGTTCGAAC
1 CGGTTTG-AC
*
5348 CGATTTGAC
1 CGGTTTGAC
*
5357 CGGTCTGAAC
1 CGGTTTG-AC
5367 CGGTTTGAC
1 CGGTTTGAC
*
5376 CGGTCTGAC
1 CGGTTTGAC
5385 C
1 C
5386 CGACCCGACA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
9 32 0.59
10 22 0.41
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:5341 original size:19 final size:18
Alignment explanation
Indices: 5312--5383 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
5302 CTGGAAATCG
* *
5312 GTTTAACCGGTTTG-ACC
1 GTTTGACCGGTCTGAACC
5329 AGTTTCGACCGGT-TCGAACC
1 -GTTT-GACCGGTCT-GAACC
5349 GATTTGACCGGTCTGAACC
1 G-TTTGACCGGTCTGAACC
5368 GGTTTGACCGGTCTGA
1 -GTTTGACCGGTCTGA
5384 CCCGACCCGA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
18 5 0.11
19 34 0.72
20 8 0.17
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (18 bp):
GTTTGACCGGTCTGAACC
Found at i:5409 original size:17 final size:17
Alignment explanation
Indices: 5387--5424 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5377 GGTCTGACCC
5387 GACCCGACACGACCGTT
1 GACCCGACACGACCGTT
*
5404 GACCCGACCCGACCGTT
1 GACCCGACACGACCGTT
5421 GACC
1 GACC
5425 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.45, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACACGACCGTT
Found at i:5424 original size:24 final size:24
Alignment explanation
Indices: 5371--5430 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 24
5361 CTGAACCGGT
5371 TTGACCGGTCTGACCCGACCCGACAC
1 TTGACC-GT-TGACCCGACCCGACAC
5397 --GACCGTTGACCCGACCCGAC-C
1 TTGACCGTTGACCCGACCCGACAC
5418 GTTGACCGTTGAC
1 -TTGACCGTTGAC
5431 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 1 0.03
22 14 0.45
23 2 0.06
24 14 0.45
ACGTcount: A:0.18, C:0.40, G:0.25, T:0.17
Consensus pattern (24 bp):
TTGACCGTTGACCCGACCCGACAC
Found at i:15025 original size:65 final size:64
Alignment explanation
Indices: 14826--15035 Score: 164
Period size: 65 Copynumber: 3.2 Consensus size: 64
14816 TGCACTAAGA
* * * * * *
14826 GTGCATCGATGCATCAAGTGCATTTGATGTTTCA-AA-AT-AGCCAGAGTGCATCGATGAATGAC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTATAACATCA-TC-G-GTGCATCGATGCATGAT
*
14888 GG
63 TG
* * *
14890 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCGGTGTATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTT-ATAACATCATCGGTGCATCGATGCATGAT-T
14955 -
64 G
* * *
14955 ATGCATCGATGCATGAAATGCATTCGATGTTCAATT-TAA-TTCAT-GGTGCATCGATGCATGAA
1 GTGCATCGATGCATCAAATGCATTCGATGTT---TTATAACATCATCGGTGCATCGATGCATG-A
15017 TTG
62 TTG
*
15020 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
15036 CTCTGAAAAA
Statistics
Matches: 117, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
64 46 0.39
65 60 0.51
66 6 0.05
67 3 0.03
68 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTATAACATCATCGGTGCATCGATGCATGATTG
Found at i:17082 original size:12 final size:13
Alignment explanation
Indices: 17065--17093 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17055 TTATATATTG
17065 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
17077 GAAATAAAGAAAT
1 GAAATAAAGAAAT
17090 GAAA
1 GAAA
17094 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:21955 original size:30 final size:28
Alignment explanation
Indices: 21893--21966 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
21883 ATAAACGAGT
* *
21893 AAATAAAAAAAGAAAAGAAAATACAAAT
1 AAATAAAAAAAGAAAAGAAAATAAAAAA
* *
21921 AAATAAAACAAATGTAAAGAAGATAAAAAA
1 AAATAAAA-AAA-GAAAAGAAAATAAAAAA
21951 AAATAAAGATAAAGAA
1 AAATAAA-A-AAAGAA
21967 TAAACATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 8 0.22
29 3 0.08
30 22 0.59
31 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (28 bp):
AAATAAAAAAAGAAAAGAAAATAAAAAA
Found at i:22781 original size:37 final size:37
Alignment explanation
Indices: 22731--22842 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
22721 ATGCTTATGG
*
22731 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
22768 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * *
22805 ATCATATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
22842 A
1 A
22843 ACGTTATGTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:23754 original size:33 final size:33
Alignment explanation
Indices: 23710--23841 Score: 237
Period size: 33 Copynumber: 4.0 Consensus size: 33
23700 TGTCTAATGT
23710 AAGCATTTACGTGAGTTATCAATGATTAACCCA
1 AAGCATTTACGTGAGTTATCAATGATTAACCCA
*
23743 AAGCATATACGTGAGTTATCAATGATTAACCCA
1 AAGCATTTACGTGAGTTATCAATGATTAACCCA
* *
23776 AAGCATTTACATGAGTTATCAATAATTAACCCA
1 AAGCATTTACGTGAGTTATCAATGATTAACCCA
23809 AAGCATTTACGTGAGTTATCAATGATTAACCCA
1 AAGCATTTACGTGAGTTATCAATGATTAACCCA
23842 TTGCTTTCCT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (33 bp):
AAGCATTTACGTGAGTTATCAATGATTAACCCA
Found at i:25234 original size:14 final size:15
Alignment explanation
Indices: 25202--25239 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
25192 TATAAATTAC
25202 GTAAAA-ATTTAAAA
1 GTAAAATATTTAAAA
*
25216 GTAAATTATTTAAAA
1 GTAAAATATTTAAAA
25231 -TAAAATATT
1 GTAAAATATT
25240 AATTACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (15 bp):
GTAAAATATTTAAAA
Found at i:25988 original size:18 final size:17
Alignment explanation
Indices: 25956--25989 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25946 TTTAAAAAAA
*
25956 TAAAAATATACATTTTT
1 TAAAAATAAACATTTTT
25973 TAAAACATAAACATTTT
1 TAAAA-ATAAACATTTT
25990 AAAATAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAATAAACATTTTT
Found at i:30019 original size:20 final size:20
Alignment explanation
Indices: 29988--30041 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
29978 AATAAACCCC
*
29988 AAATCCTAAACCATATCCCTA
1 AAAT-CTAAACCATAACCCTA
* * *
30009 AAATTTAAACCCTAACTCTA
1 AAATCTAAACCATAACCCTA
30029 AAATCTAAACCAT
1 AAATCTAAACCAT
30042 TAACATTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATCTAAACCATAACCCTA
Found at i:30106 original size:21 final size:21
Alignment explanation
Indices: 30082--30135 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
30072 ACAGACAACA
30082 CTAAATCATAAATCATAAATC
1 CTAAATCATAAATCATAAATC
* * *
30103 CTAAA-CACTAAATCGTTAATT
1 CTAAATCA-TAAATCATAAATC
*
30124 TTAAATCATAAA
1 CTAAATCATAAA
30136 CCCTAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (21 bp):
CTAAATCATAAATCATAAATC
Found at i:30109 original size:28 final size:28
Alignment explanation
Indices: 30078--30143 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
30068 ATGAACAGAC
*
30078 AACACTAAATCATAAATCATAAATCCTA
1 AACACTAAATCATAAATCATAAATCATA
* * **
30106 AACACTAAATCGTTAATTTTAAATCATA
1 AACACTAAATCATAAATCATAAATCATA
*
30134 AACCCTAAAT
1 AACACTAAAT
30144 TCTAAGTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.29
Consensus pattern (28 bp):
AACACTAAATCATAAATCATAAATCATA
Found at i:30275 original size:15 final size:15
Alignment explanation
Indices: 30255--30361 Score: 69
Period size: 15 Copynumber: 7.1 Consensus size: 15
30245 CTCTAAATTC
30255 TAAACCTTAAAACCA
1 TAAACCTTAAAACCA
**
30270 TAAACCTTAAAACTT
1 TAAACCTTAAAACCA
* * *
30285 TCAACCCTAAACACTA
1 TAAACCTTAAA-ACCA
30301 TAAA-CTCT-AAACCA
1 TAAACCT-TAAAACCA
*
30315 TAAACCATAAAACTCA
1 TAAACCTTAAAAC-CA
*
30331 AAAATCC-TAAAA-CA
1 TAAA-CCTTAAAACCA
*
30345 TTAAACCCTAAAACCA
1 -TAAACCTTAAAACCA
30361 T
1 T
30362 GAATCATGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
14 12 0.17
15 39 0.54
16 19 0.26
17 2 0.03
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAACCTTAAAACCA
Found at i:30469 original size:131 final size:132
Alignment explanation
Indices: 30297--30604 Score: 383
Period size: 131 Copynumber: 2.4 Consensus size: 132
30287 AACCCTAAAC
* * * *
30297 ACTATAAACTCTAAACCATAAACCATAAAACTCAAAAATCCTAAAACATTAAACCCTAAAACCAT
1 ACTATAAACCCTAAACCATAAACCATAAAACTAAAAAATCCTAAAACATCAAACCCTAAAACCAC
* **
30362 GAATCATGAATCCTAA-ACTCTAAATCTTAAAATTATAAACCCCAAAAT-AAAACAATAAAA-CA
66 GAATCATGAATCCTAATAC-CGAAATCTTAAAAGCATAAACCCCAAAATCAAAACAATAAAATC-
30424 ATAA
129 ATAA
* * * * *
30428 ACTATAAACCCTACACTATAAACCATAAAACTAAAAAATCCTAAAACCTCATACCCTAAGACCAC
1 ACTATAAACCCTAAACCATAAACCATAAAACTAAAAAATCCTAAAACATCAAACCCTAAAACCAC
* **
30493 GAATCATGAATCCTAATACCGAAATCTTAAAAGCATAAGCCTTAAAATCAAAACAATAAAATCAT
66 GAATCATGAATCCTAATACCGAAATCTTAAAAGCATAAACCCCAAAATCAAAACAATAAAATCAT
30558 AA
131 AA
** * * *
30560 ACCCTAAACCCTAAACCCTAAACCCT-AAACTATAAAA-CCTAAAAC
1 ACTATAAACCCTAAACCATAAACCATAAAACTAAAAAATCCTAAAAC
30605 CCTAACCACT
Statistics
Matches: 152, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
130 8 0.05
131 105 0.69
132 38 0.25
133 1 0.01
ACGTcount: A:0.52, C:0.25, G:0.03, T:0.20
Consensus pattern (132 bp):
ACTATAAACCCTAAACCATAAACCATAAAACTAAAAAATCCTAAAACATCAAACCCTAAAACCAC
GAATCATGAATCCTAATACCGAAATCTTAAAAGCATAAACCCCAAAATCAAAACAATAAAATCAT
AA
Found at i:30569 original size:7 final size:7
Alignment explanation
Indices: 30557--30624 Score: 75
Period size: 7 Copynumber: 9.6 Consensus size: 7
30547 AATAAAATCA
30557 TAAACCC
1 TAAACCC
30564 TAAACCC
1 TAAACCC
30571 TAAACCC
1 TAAACCC
30578 TAAACCC
1 TAAACCC
**
30585 TAAACTA
1 TAAACCC
*
30592 TAAAACC
1 TAAACCC
30599 TAAAACCC
1 T-AAACCC
30607 T-AACCAC
1 TAAACC-C
*
30614 TAAACCA
1 TAAACCC
30621 TAAA
1 TAAA
30625 ACCATAGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
6 4 0.08
7 37 0.73
8 10 0.20
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:30597 original size:29 final size:30
Alignment explanation
Indices: 30557--30627 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
30547 AATAAAATCA
*
30557 TAAACCCT-AAACCCT-AAACCCTAAACC-C
1 TAAACCATAAAACCCTAAAACCCT-AACCAC
*
30585 TAAACTATAAAA-CCTAAAACCCTAACCAC
1 TAAACCATAAAACCCTAAAACCCTAACCAC
30614 TAAACCATAAAACC
1 TAAACCATAAAACC
30628 ATAGAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 13 0.36
29 22 0.61
30 1 0.03
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.15
Consensus pattern (30 bp):
TAAACCATAAAACCCTAAAACCCTAACCAC
Found at i:30834 original size:14 final size:14
Alignment explanation
Indices: 30817--30844 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30807 ACTCTTCATA
30817 CTAAATCCTAAACC
1 CTAAATCCTAAACC
30831 CTAAATCCTAAACC
1 CTAAATCCTAAACC
30845 ACAAAATCAT
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:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAATCCTAAACC
Found at i:30857 original size:15 final size:14
Alignment explanation
Indices: 30819--30857 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
30809 TCTTCATACT
*
30819 AAATCCTAAACCCT
1 AAATCCTAAACCCA
30833 AAATCCTAAACCACA
1 AAATCCTAAACC-CA
*
30848 AAATCATAAA
1 AAATCCTAAA
30858 ACCATAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATCCTAAACCCA
Found at i:30904 original size:22 final size:22
Alignment explanation
Indices: 30848--30905 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
30838 CTAAACCACA
*
30848 AAATCATAAAAC-CATAAAACTT
1 AAATCAT-AAACTCTTAAAACTT
* ** *
30870 AAATCCTGGACTCTTAAATCTT
1 AAATCATAAACTCTTAAAACTT
30892 AAATCATAAACTCT
1 AAATCATAAACTCT
30906 ACACCCTAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (22 bp):
AAATCATAAACTCTTAAAACTT
Found at i:31017 original size:35 final size:33
Alignment explanation
Indices: 30941--31017 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 33
30931 TCATAAACAC
*
30941 AACCTAAACCTAATCCTTAAACTATAAACCCTA
1 AACCTAAACCTAATCCTTAAACTATAAACCATA
* *
30974 AATACTAAACCTTAATCCTTAAACTCATAAATCATA
1 AA-CCTAAACC-TAATCCTTAAACT-ATAAACCATA
31010 AACCTAAA
1 AACCTAAA
31018 ATCTAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 7 0.19
35 18 0.49
36 10 0.27
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (33 bp):
AACCTAAACCTAATCCTTAAACTATAAACCATA
Found at i:31103 original size:29 final size:29
Alignment explanation
Indices: 31020--31103 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 29
31010 AACCTAAAAT
** *
31020 CTAAACCACAAACCCTAAATTATAATACA
1 CTAAACCTTAAACCCTAAATTATAAAACA
* ** * * *
31049 CTAAGCCTTAATTCCAAAAATCTAAAAC-
1 CTAAACCTTAAACCCTAAATTATAAAACA
31077 CTTAAACCTTAAACCCTAAATTATAAA
1 C-TAAACCTTAAACCCTAAATTATAAA
31104 TTCTAAACCA
Statistics
Matches: 39, Mismatches: 15, Indels: 2
0.70 0.27 0.04
Matches are distributed among these distances:
28 1 0.03
29 38 0.97
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (29 bp):
CTAAACCTTAAACCCTAAATTATAAAACA
Found at i:33681 original size:11 final size:11
Alignment explanation
Indices: 33651--33681 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
33641 TCTCAATCTT
33651 GAGGGATTTTA
1 GAGGGATTTTA
33662 GAGGG-TTTTA
1 GAGGGATTTTA
33672 GAGGGATTTT
1 GAGGGATTTT
33682 GAGTGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (11 bp):
GAGGGATTTTA
Found at i:36797 original size:32 final size:32
Alignment explanation
Indices: 36756--36866 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 32
36746 AGTCGAGGGT
36756 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAGAA
*** *
36788 TTACCTATG-TCTTTTGAGGCATATGGAC--AA
1 TTACCTATGTTCTACGGA-ACATATGGACAGAA
* * *
36818 TATACCTATGTTCAAAGGAACATATGGACAG-T
1 T-TACCTATGTTCTACGGAACATATGGACAGAA
*
36850 TTACCTAGGTTCTACGG
1 TTACCTATGTTCTACGG
36867 GACCTACAGA
Statistics
Matches: 61, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
30 3 0.05
31 35 0.57
32 23 0.38
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATGGACAGAA
Found at i:37658 original size:23 final size:22
Alignment explanation
Indices: 37607--37652 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
37597 GTAGCAGTAT
* *
37607 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCAGGGGAATCGATCCCC
37629 TGTAGCAGGGGAATCGATACCCC
1 TGTAGCAGGGGAATCGAT-CCCC
37652 T
1 T
37653 TAAGCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGATCCCC
Found at i:48753 original size:33 final size:33
Alignment explanation
Indices: 48711--48779 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
48701 GTCAGTCCAA
48711 ATAGACTATTGTATCACTCAGAGTTAGATTTCG
1 ATAGACTATTGTATCACTCAGAGTTAGATTTCG
*
48744 ATAGACTATTGTATCACTCAGAGTTAGATTTTG
1 ATAGACTATTGTATCACTCAGAGTTAGATTTCG
48777 ATA
1 ATA
48780 AAATAATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (33 bp):
ATAGACTATTGTATCACTCAGAGTTAGATTTCG
Found at i:71029 original size:23 final size:23
Alignment explanation
Indices: 71003--71073 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
70993 ACCGCGTATA
*
71003 AATTATCGC-AAATGACCACATAG
1 AATTATCCCGAAA-GACCACATAG
* *
71026 AATTGTCCCGAAAGACCACGTAG
1 AATTATCCCGAAAGACCACATAG
* * * *
71049 AATTGTACCGAAGGACCACGTAG
1 AATTATCCCGAAAGACCACATAG
71072 AA
1 AA
71074 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (23 bp):
AATTATCCCGAAAGACCACATAG
Found at i:82598 original size:37 final size:37
Alignment explanation
Indices: 82556--82628 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
82546 ATTACTAAAA
82556 TAAAATAAAATAAAAATAAATAAACTACCAAAATTAT
1 TAAAATAAAATAAAAATAAATAAACTACCAAAATTAT
82593 TAAAATAAAATAAAAATAAATAAACTACCAAAATTA
1 TAAAATAAAATAAAAATAAATAAACTACCAAAATTA
82629 CCCTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.23
Consensus pattern (37 bp):
TAAAATAAAATAAAAATAAATAAACTACCAAAATTAT
Found at i:84148 original size:5 final size:5
Alignment explanation
Indices: 84124--84160 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
84114 TAATTATAAT
*
84124 TACAA T-CAA T-CAA TACAA TATAA TACAA TACAA TACA
1 TACAA TACAA TACAA TACAA TACAA TACAA TACAA TACA
84161 GAAACGGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (5 bp):
TACAA
Found at i:86477 original size:20 final size:21
Alignment explanation
Indices: 86454--86507 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
86444 TAACGCGAAC
*
86454 TCCAATTTCGCAACAC-ATGT
1 TCCAAATTCGCAACACAATGT
* * *
86474 TCCAAAATCGCAACGCAATTT
1 TCCAAATTCGCAACACAATGT
86495 TCCAAATTCGCAA
1 TCCAAATTCGCAA
86508 TGCTAATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (21 bp):
TCCAAATTCGCAACACAATGT
Found at i:86570 original size:57 final size:57
Alignment explanation
Indices: 86480--86623 Score: 234
Period size: 57 Copynumber: 2.5 Consensus size: 57
86470 ATGTTCCAAA
* * *
86480 ATCGCAACGCAATTTTCCAAATTCGCAATGCTAATTACCGATATAGGTAAACAGTACT
1 ATCGCAACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACACTACT
*
86538 ATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAATACTACT
1 ATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACTACT
*
86595 ATCGCAACGCGATTTTCAAATTTGCAACG
1 ATCGCAACGCGATTTTCAAATTCGCAACG
86624 TTATTTTCAC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
57 66 0.81
58 15 0.19
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (57 bp):
ATCGCAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACTACT
Found at i:87153 original size:20 final size:20
Alignment explanation
Indices: 87128--87184 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
87118 CGCGTTGTGA
87128 ATTTACATATTCACGTTGCG
1 ATTTACATATTCACGTTGCG
87148 ATTTACATATT-ATCGTTGCG
1 ATTTACATATTCA-CGTTGCG
*
87168 ATTTACATATTCGCGTT
1 ATTTACATATTCACGTT
87185 TCGAATTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (20 bp):
ATTTACATATTCACGTTGCG
Found at i:92016 original size:46 final size:46
Alignment explanation
Indices: 91934--92203 Score: 319
Period size: 46 Copynumber: 6.0 Consensus size: 46
91924 AATACCATGA
* * * * *
91934 GTGGCATC-TTTTATACCGTTAATCCACCTTTATGCATTTTCATTT
1 GTGGCATCATTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
*
91979 GTGGCATCATTTCATGACGATAATGCACCGTTATGCATTTTCAATTT
1 GTGGCATCATTTCATGCCGATAATGCACCGTTATGCATTTTC-ATTT
* * * * *
92026 GTGGCATCCTTTCATTCCAATAATACACCGTTATGCATTTTTATTT
1 GTGGCATCATTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
*
92072 GTGGCAT-ACTTTCATGCCGATAATGCATCGTTATGCATTTTCATTT
1 GTGGCATCA-TTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
*
92118 GTGGCATCCTTTCATGCCGATAATG---C---A--CATTTTCATTT
1 GTGGCATCATTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
92156 GTGGCATCCA-TTCATGCCGATAATGCACCGTTATGCATTTTCATTT
1 GTGGCAT-CATTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
92202 GT
1 GT
92204 TTTAGAGCAG
Statistics
Matches: 192, Mismatches: 20, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
38 33 0.17
39 1 0.01
40 1 0.01
41 1 0.01
43 1 0.01
44 1 0.01
45 8 0.04
46 106 0.55
47 40 0.21
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.41
Consensus pattern (46 bp):
GTGGCATCATTTCATGCCGATAATGCACCGTTATGCATTTTCATTT
Found at i:92153 original size:38 final size:38
Alignment explanation
Indices: 92107--92183 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
92097 CATCGTTATG
*
92107 CATTTTCATTTGTGGCATCCTTTCATGCCGATAATGCA
1 CATTTTCATTTGTGGCATCCATTCATGCCGATAATGCA
92145 CATTTTCATTTGTGGCATCCATTCATGCCGATAATGCA
1 CATTTTCATTTGTGGCATCCATTCATGCCGATAATGCA
92183 C
1 C
92184 CGTTATGCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (38 bp):
CATTTTCATTTGTGGCATCCATTCATGCCGATAATGCA
Found at i:111818 original size:136 final size:135
Alignment explanation
Indices: 111526--111871 Score: 480
Period size: 136 Copynumber: 2.6 Consensus size: 135
111516 GCTTCACTGT
* * * * * * *
111526 TCTTCATGGAAGACTGAATCGCATTTGATTTGATTCGTTGCTTTTCAGGAAGATCAAATCTGAAA
1 TCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCGCTGCTCTTCAGGAAGATCAAATCTGAAA
* ** *
111591 GAA-AGAA-AATATACTCTGCTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTGATCCACTT
66 GAAGA-AAGAATATACCCCACTACTCTTAAGGGGAGGTCAGACTCGAGAAAACTTTGATCCACTT
*
111654 CTCTGC
130 CTCTAC
* * *
111660 TCTTCAGGGAAGCTTGAATCGAATGTGATTTGCTTCACTGCTCTTCAGGAATATCAAATCTGAAA
1 TCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCGCTGCTCTTCAGGAAGATCAAATCTGAAA
* *
111725 TAAGAAAGAATATGCCCCACTACTCTTAAGGGGAGGTCAGACTCGAGAAAAACTTTGATCCACTT
66 GAAGAAAGAATATACCCCACTACTCTTAAGGGGAGGTCAGACTCGAG-AAAACTTTGATCCACTT
111790 CTCTAC
130 CTCTAC
* * *
111796 TCTTCAGGGAAGATTGATTCGAATGTGATTTGCTTTGCTACTCTTCAGGAAGATCAAATCTGAAA
1 TCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCGCTGCTCTTCAGGAAGATCAAATCTGAAA
111861 GAAGAAAGAAT
66 GAAGAAAGAAT
111872 CTACTTTGAT
Statistics
Matches: 185, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
134 59 0.32
135 35 0.19
136 91 0.49
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (135 bp):
TCTTCAGGGAAGATTGAATCGAATGTGATTTGCTTCGCTGCTCTTCAGGAAGATCAAATCTGAAA
GAAGAAAGAATATACCCCACTACTCTTAAGGGGAGGTCAGACTCGAGAAAACTTTGATCCACTTC
TCTAC
Found at i:111945 original size:98 final size:98
Alignment explanation
Indices: 111776--111969 Score: 325
Period size: 98 Copynumber: 2.0 Consensus size: 98
111766 CTCGAGAAAA
* * *
111776 ACTTTGATCCACTTCTCTACTCTTCAGGGAAGATTGATTCGAATGTGATTTGCTTTGCTACTCTT
1 ACTTTGATCCACTTCTCTACTCTTCAGAGAAGATTGAATCGAATGTGATTTGCTTCGCTACTCTT
111841 CAGGAAGATCAAATCTGAAAGAAGAAAGAATCT
66 CAGGAAGATCAAATCTGAAAGAAGAAAGAATCT
* * * *
111874 ACTTTGATCCACTTCTCTGCTCTTTAGAGAAGATTGAATCGAATGTGATTTTCTTCGCTGCTCTT
1 ACTTTGATCCACTTCTCTACTCTTCAGAGAAGATTGAATCGAATGTGATTTGCTTCGCTACTCTT
111939 CAGGAAGATCAAATCTGAAAGAAGAAAGAAT
66 CAGGAAGATCAAATCTGAAAGAAGAAAGAAT
111970 TTGTTTTGCT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (98 bp):
ACTTTGATCCACTTCTCTACTCTTCAGAGAAGATTGAATCGAATGTGATTTGCTTCGCTACTCTT
CAGGAAGATCAAATCTGAAAGAAGAAAGAATCT
Found at i:112076 original size:135 final size:136
Alignment explanation
Indices: 111874--112142 Score: 402
Period size: 135 Copynumber: 2.0 Consensus size: 136
111864 GAAAGAATCT
* * * *
111874 ACTTTGATCCACTTCTCTGCTCTTTAGAGAAGATTGAATCGAATGTGATTTTCTTCGCTGCTCTT
1 ACTTTGATCCACTTCTCTGCTCTTCAGAGAAGATTGAATCGAATGTAATTTGCTTCGCTGCTATT
* * * *
111939 CAGGAAGATCAAATCTGAAAGAAGAAAGAATTTGTTTTGCTACTCTT-TAGATGG-GGTCAGACT
66 CAGGAAGATCAAATCTGAAAGAAGAAAGAATATGCTTCGCTACT-TTATAG-GGGAGGTCAGACT
112002 CAAGAAAA
129 CAAGAAAA
*
112010 ACTTTGATCCACTTCTCT-CATCTTCAGGGAAGA-TGAATCGAATGTAATTTGCTTCGCTGCTAT
1 ACTTTGATCCACTTCTCTGC-TCTTCAGAGAAGATTGAATCGAATGTAATTTGCTTCGCTGCTAT
112073 TCAGGAAGATCAAATCTGAAAGAAGAAAGAATATGCTTCGCTACTTTATAGGGGAGGTCAGACTC
65 TCAGGAAGATCAAATCTGAAAGAAGAAAGAATATGCTTCGCTACTTTATAGGGGAGGTCAGACTC
112138 AAGAA
130 AAGAA
112143 GATTTTGATT
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
134 4 0.03
135 88 0.73
136 29 0.24
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (136 bp):
ACTTTGATCCACTTCTCTGCTCTTCAGAGAAGATTGAATCGAATGTAATTTGCTTCGCTGCTATT
CAGGAAGATCAAATCTGAAAGAAGAAAGAATATGCTTCGCTACTTTATAGGGGAGGTCAGACTCA
AGAAAA
Found at i:121785 original size:21 final size:20
Alignment explanation
Indices: 121741--121814 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
121731 GCAGCCTTCG
*
121741 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
**
121761 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAGGA
*
121782 TGCATCGATGCATAGA-AGGA
1 TGCATCGATGCACA-ACAGGA
121802 TGCATCGATGCAC
1 TGCATCGATGCAC
121815 TAATTACATT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
20 28 0.62
21 16 0.36
22 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:121922 original size:21 final size:21
Alignment explanation
Indices: 121887--121943 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
121877 ACTAGTGCAG
* *
121887 GTGCATGGCTCCACTACAGG-
1 GTGCATGGATGCACTACAGGT
*
121907 GATGCATGGATGCACTGCAGGT
1 G-TGCATGGATGCACTACAGGT
121929 GTGCATGGATGCACT
1 GTGCATGGATGCACT
121944 TTGACACCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGT
Found at i:122070 original size:30 final size:30
Alignment explanation
Indices: 122023--122082 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
122013 AAACTTTGAA
122023 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
122052 TAAATTTAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
122083 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:125458 original size:21 final size:21
Alignment explanation
Indices: 125428--125504 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
125418 CTAGTGCAGG
125428 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
125449 TGCATAGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
125470 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
125491 TGCATGGATGCACT
1 TGCATGGATGCACT
125505 TTGACACCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:125605 original size:29 final size:29
Alignment explanation
Indices: 125584--125641 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
125574 AAACTTTGAA
125584 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
125613 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
125642 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:125631 original size:30 final size:30
Alignment explanation
Indices: 125584--125643 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
125574 AAACTTTGAA
125584 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
125613 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
125644 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:130543 original size:57 final size:57
Alignment explanation
Indices: 130450--130568 Score: 202
Period size: 57 Copynumber: 2.1 Consensus size: 57
130440 ATTCGATTGC
* **
130450 GAAATTCGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
*
130507 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGGATTT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
130564 GAAAA
1 GAAAA
130569 ATATATATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.35
Consensus pattern (57 bp):
GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
Found at i:151260 original size:55 final size:55
Alignment explanation
Indices: 151194--151629 Score: 508
Period size: 55 Copynumber: 8.2 Consensus size: 55
151184 CTATGTGTAC
*
151194 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAATTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
* *
151249 TACAGGCACTTCGTGTGCATATCAACGAAATTCATCATGAGTTGATGAATCACTG
1 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
* * * *
151304 TACAGGCACTTCGTGTACATATCCACGCAATTCATTATGAGTTGATGAATTACCG
1 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
* * * *
151359 TATAGACACTTCGTGTGCATATCCACGGAATTCATCATGAGTTGATGAATCATCG
1 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
* * *
151414 TACAAGCACTTCATGTGTATATCCACGAAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
*
151469 -ATAGGCA---C-T-T-C--A--CA-G-AATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
* * * *
151511 TACAGACACTTTGTGTGCATATCCACGGAATTCATCATGAGTTAATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
** * * **
151566 TGTAGGCACTAT-GGGTGCA-ACCCAC-AGAATTCATCATGAGTTGATGAATTTCCG
1 TACAGGCACT-TCGTGTGCATATCCACGA-AATTCATCATGAGTTGATGAATCACCG
*
151620 TATAGGCACT
1 TACAGGCACT
151630 AATTGCGTAT
Statistics
Matches: 326, Mismatches: 40, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
42 27 0.08
43 6 0.02
44 2 0.01
46 1 0.00
47 1 0.00
48 1 0.00
49 2 0.01
50 1 0.00
51 2 0.01
53 2 0.01
54 44 0.13
55 236 0.72
56 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (55 bp):
TACAGGCACTTCGTGTGCATATCCACGAAATTCATCATGAGTTGATGAATCACCG
Found at i:151552 original size:97 final size:98
Alignment explanation
Indices: 151386--151575 Score: 294
Period size: 97 Copynumber: 1.9 Consensus size: 98
151376 CATATCCACG
* *
151386 GAATTCATCATGAGTTGATGAATCATCGTACAAGCACTTCATGTGTATATCCACGAAATTCATCA
1 GAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTCATGTGCATATCCACGAAATTCATCA
*
151451 TGAGTTGATGAATCACCG-ATAGGCACTTCACA
66 TGAGTTAATGAATCACCGTATAGGCACTTCACA
** *
151483 GAATTCATCATGAGTTGATGAATCACCGTAC-AGACACTTTGTGTGCATATCCACGGAATTCATC
1 GAATTCATCATGAGTTGATGAATCACCGTACAAG-CACTTCATGTGCATATCCACGAAATTCATC
*
151547 ATGAGTTAATGAATCACCGTGTAGGCACT
65 ATGAGTTAATGAATCACCGTATAGGCACT
151576 ATGGGTGCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
96 2 0.02
97 74 0.88
98 8 0.10
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (98 bp):
GAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTCATGTGCATATCCACGAAATTCATCA
TGAGTTAATGAATCACCGTATAGGCACTTCACA
Found at i:151625 original size:152 final size:152
Alignment explanation
Indices: 151332--151629 Score: 415
Period size: 152 Copynumber: 2.0 Consensus size: 152
151322 ATATCCACGC
* * *
151332 AATTCATTATGAGTTGATGAATTACCGTATAGACACTTCGTGTGCATATCCACGGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAGACACTTCGTGTGCATATCCACGGAATTCATCAT
* * * *
151397 GAGTTGATGAATCATCGTACAAGCACTTCATGTGTATATCCACGAAATTCATCATGAGTTGATGA
66 GAGTTAATGAATCACCGTACAAGCACTTCATGTGCATACCCACGAAATTCATCATGAGTTGATGA
151462 ATCACCGATAGGCACTTCACAG
131 ATCACCGATAGGCACTTCACAG
*
151484 AATTCATCATGAGTTGATGAATCACCGTACAGACACTTTGTGTGCATATCCACGGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAGACACTTCGTGTGCATATCCACGGAATTCATCAT
** *
151549 GAGTTAATGAATCACCGTGTAGGCAC-T-ATGGGTGCA-ACCCAC-AGAATTCATCATGAGTTGA
66 GAGTTAATGAATCACCGTACAAGCACTTCAT--GTGCATACCCACGA-AATTCATCATGAGTTGA
**
151610 TGAATTTCCGTATAGGCACT
128 TGAATCACCG-ATAGGCACT
151630 AATTGCGTAT
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
150 3 0.02
151 31 0.24
152 95 0.74
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (152 bp):
AATTCATCATGAGTTGATGAATCACCGTACAGACACTTCGTGTGCATATCCACGGAATTCATCAT
GAGTTAATGAATCACCGTACAAGCACTTCATGTGCATACCCACGAAATTCATCATGAGTTGATGA
ATCACCGATAGGCACTTCACAG
Found at i:151984 original size:21 final size:21
Alignment explanation
Indices: 151954--151997 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
151944 AACTTGAAAT
*
151954 GTGTATCGATACACTGCTACA
1 GTGTACCGATACACTGCTACA
*
151975 GTGTACCGATGCACTGCTACA
1 GTGTACCGATACACTGCTACA
151996 GT
1 GT
151998 AACTACTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
GTGTACCGATACACTGCTACA
Found at i:152454 original size:45 final size:45
Alignment explanation
Indices: 152403--152624 Score: 381
Period size: 45 Copynumber: 4.9 Consensus size: 45
152393 AATTTTGTAT
* *
152403 CAATATACTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
152448 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
*
152493 CAATATACTTGCCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
152538 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* * * *
152583 CAATATACTTGCCATTTATACCTTAAGCTCGTAAACTTATTT
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
152625 GCCAGCTTAT
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 169 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:152778 original size:40 final size:40
Alignment explanation
Indices: 152699--152778 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
152689 ATAGAAGTTA
* * *
152699 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
* * *
152739 AATAATGCACCGTATTGCTGAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
152779 TGTACACCGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGCTTTACCCACCT
Found at i:153703 original size:24 final size:24
Alignment explanation
Indices: 153674--153743 Score: 106
Period size: 24 Copynumber: 2.9 Consensus size: 24
153664 ACCCATCAAA
153674 TTTTCCAAAATGTTTT-AATTGAAT
1 TTTTCCAAAAT-TTTTAAATTGAAT
* *
153698 TTTTCCAAATTTTTTGAATTGAAT
1 TTTTCCAAAATTTTTAAATTGAAT
153722 TTTTCCAAAATTTTTAAATTGA
1 TTTTCCAAAATTTTTAAATTGA
153744 TCCCTAACTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
23 4 0.10
24 38 0.90
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (24 bp):
TTTTCCAAAATTTTTAAATTGAAT
Found at i:159119 original size:65 final size:65
Alignment explanation
Indices: 158986--159141 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
158976 ACACCCCATT
* * * * *
158986 TCGAATGCATTTTATGCATCGATGCA-TGGCCATGCATCGATGCACTCAGGATTTTATTGAAACA
1 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCAATCAGGATTATATTAAAACA
* *
159050 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCAATCTTGGCTTAT-TTAAAAC
1 TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCAATC-AGGATTATATTAAAAC
159114 A
65 A
* * *
159115 TCGAATGTAATTAATGCATCGATGCAC
1 TCGAATGCATTTTATGCATCGATGCAC
159142 CCCTAGTGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 26 0.32
65 49 0.61
66 5 0.06
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCAATCAGGATTATATTAAAACA
Found at i:160996 original size:21 final size:21
Alignment explanation
Indices: 160971--161010 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
160961 AAGACTTTAT
160971 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
160992 TTTCAAAATTTAAAAATGA
1 TTTCAAAATACAAAAATGA
161011 AAATAGTCTT
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:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:166857 original size:16 final size:15
Alignment explanation
Indices: 166836--166880 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
166826 TGTTTTTGGA
166836 TTGGATGTTTGAATG
1 TTGGATGTTTGAATG
* *
166851 TTTGGATATTATGGATG
1 -TTGGATGTT-TGAATG
166868 TTGGATGTTTGAA
1 TTGGATGTTTGAA
166881 CTTAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 16 0.67
17 5 0.21
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (15 bp):
TTGGATGTTTGAATG
Found at i:167647 original size:19 final size:19
Alignment explanation
Indices: 167623--167674 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
167613 AATGTATTTT
*
167623 ATGCATCGATGTACAGACC
1 ATGCATCGATGCACAGACC
167642 ATGCATCGATGCACAGACC
1 ATGCATCGATGCACAGACC
167661 ATGCATCGATGCAC
1 ATGCATCGATGCAC
167675 TCTTGGCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (19 bp):
ATGCATCGATGCACAGACC
Found at i:167674 original size:84 final size:83
Alignment explanation
Indices: 167559--167717 Score: 239
Period size: 84 Copynumber: 1.9 Consensus size: 83
167549 AATGCATTTT
* * * *
167559 ATGCATCGATGCACAGCCATGCATCGATGCACTC-AGGATTTTGTTGAAACATCGAATGTATTTT
1 ATGCATCGATGCACAGCCATGCATCGATGCACTCTAGGATTGT-TTAAAACATCGAATGTAATTA
167623 ATGCATCGATGTACAGACC
65 ATGCATCGATGTACAGACC
* *
167642 ATGCATCGATGCACAGACCATGCATCGATGCACTCTTGGCTTGTTTAAAACATCGAATGTAATTA
1 ATGCATCGATGCACAG-CCATGCATCGATGCACTCTAGGATTGTTTAAAACATCGAATGTAATTA
167707 ATGCATCGATG
65 ATGCATCGATG
167718 CACCCCTAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 16 0.24
84 47 0.69
85 5 0.07
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (83 bp):
ATGCATCGATGCACAGCCATGCATCGATGCACTCTAGGATTGTTTAAAACATCGAATGTAATTAA
TGCATCGATGTACAGACC
Found at i:170633 original size:2 final size:2
Alignment explanation
Indices: 170626--170673 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
170616 TAAAGTATCA
170626 AT AT 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 AT AT
170668 AT AT AT
1 AT AT AT
170674 TTAAAATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:174334 original size:95 final size:96
Alignment explanation
Indices: 174193--174370 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 96
174183 ATACCGATAA
* *
174193 GGTAATATTGATACCATGATAAGGGGTATCGATACTAAGAAACATCGAATCTAATTTTGATATCG
1 GGTAATATCGATACCATGATAAGGGGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCG
*
174258 ATACCGGTAA-GGGGTATCGATATCCTAATAG
66 ATACCCG-AAGGGGGTATCGATATCCTAATAG
* * * * * *
174289 GGTAGTATCGATACCATGGTAA-GGTTATCGATACTAGGAAACATCGAACCTATTTTTGGTATCG
1 GGTAATATCGATACCATGATAAGGGGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCG
174353 ATACCCGAAGGGGGTATC
66 ATACCCGAAGGGGGTATC
174371 AGTATCATAG
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
94 2 0.03
95 51 0.71
96 19 0.26
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (96 bp):
GGTAATATCGATACCATGATAAGGGGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCG
ATACCCGAAGGGGGTATCGATATCCTAATAG
Found at i:174391 original size:95 final size:96
Alignment explanation
Indices: 174202--174393 Score: 237
Period size: 95 Copynumber: 2.0 Consensus size: 96
174192 AGGTAATATT
* *
174202 GATACCATGATAAGGGGTATCGATACTAAGAAACATCGAATCTAATTTTGATATCGATACCGGTA
1 GATACCATGATAAGGGGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCGATACCCGTA
* * *
174267 AGGGGTATCGATATCCTAATAGGGTAGTATC
66 AGGGGTATCGATATCATAATAGAGAAGTATC
* * * * *
174298 GATACCATGGTAA-GGTTATCGATACTAGGAAACATCGAACCTATTTTTGGTATCGATACCCG-A
1 GATACCATGATAAGGGGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCGATACCCGTA
* *
174361 AGGGGGTATC-AGTATCATAGTATAGAAGTATC
66 A-GGGGTATCGA-TATCATAATAGAGAAGTATC
174393 G
1 G
174394 GTACTAGGGT
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
94 3 0.04
95 67 0.82
96 12 0.15
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (96 bp):
GATACCATGATAAGGGGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCGATACCCGTA
AGGGGTATCGATATCATAATAGAGAAGTATC
Found at i:174413 original size:95 final size:94
Alignment explanation
Indices: 174217--174419 Score: 223
Period size: 95 Copynumber: 2.1 Consensus size: 94
174207 CATGATAAGG
* *
174217 GGTATCGATACTAAGAAACATCGAATCTAATTTTGATATCGATACCGGTAAGGGGTATCGATATC
1 GGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCGATACCCGTAAGGGGTATCGATATC
* * * *
174282 CTAATAGGGTAGTATCGATACCATGGTAA
66 ATAATAGAGAAGTATCGATACCAGGGTAA
* * *
174311 GGTTATCGATACTAGGAAACATCGAACCTATTTTTGGTATCGATACCCG-AAGGGGGTATC-AGT
1 GG-TATCGATACTAAGAAACATCGAACCTAATTTTGATATCGATACCCGTAA-GGGGTATCGA-T
* * * *
174374 ATCATAGTATAGAAGTATCGGTACTAGGGT-A
63 ATCATAATAGAGAAGTATCGATACCAGGGTAA
174405 GTAGTATCGATACTA
1 G--GTATCGATACTA
174420 TAGAGCCAGA
Statistics
Matches: 91, Mismatches: 13, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
94 7 0.08
95 83 0.91
96 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (94 bp):
GGTATCGATACTAAGAAACATCGAACCTAATTTTGATATCGATACCCGTAAGGGGTATCGATATC
ATAATAGAGAAGTATCGATACCAGGGTAA
Found at i:174823 original size:55 final size:55
Alignment explanation
Indices: 174752--175181 Score: 639
Period size: 55 Copynumber: 7.8 Consensus size: 55
174742 CTATGTGTAC
*
174752 TACAGGCACTTCGTGTGCATATCCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
* * *
174807 TACATGCACTTCGTGTGCATATCCACGGAATTCATCATGAGTTGATGAATCATCG
1 TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
* * *
174862 TACATGCACTTCATGTGCATATCCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
**
174917 TACAAACACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
*
174972 TACAGGCACTTCGTGTGCATATCCACAAAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
* *
175027 TACAGGCACTTTGTGTGCATATCCATAGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
** * ***
175082 TACAGGCACTTTATGTGCATATCCA-AGAAATTCATCACGAGTTGATGAATCATTA
1 TACAGGCACTTCGTGTGCATATCCACAG-AATTCATCATGAGTTGATGAATCACCG
* * * *
175137 TACATGCACTACGAGTGCA-ACCCACAGAATTCATCATGAGTTGAT
1 TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGAT
175182 CAATTTCCGT
Statistics
Matches: 347, Mismatches: 26, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
54 23 0.07
55 324 0.93
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (55 bp):
TACAGGCACTTCGTGTGCATATCCACAGAATTCATCATGAGTTGATGAATCACCG
Found at i:175779 original size:14 final size:14
Alignment explanation
Indices: 175760--175788 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
175750 AATCCAAATA
175760 CTGGAAAATGTTTT
1 CTGGAAAATGTTTT
175774 CTGGAAAATGTTTT
1 CTGGAAAATGTTTT
175788 C
1 C
175789 CAGAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (14 bp):
CTGGAAAATGTTTT
Found at i:176890 original size:5 final size:5
Alignment explanation
Indices: 176837--176871 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
176827 AACTATAATT
* *
176837 TATAT TATAG TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
176872 ACATATCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:180826 original size:19 final size:19
Alignment explanation
Indices: 180798--180844 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
180788 GCAAGAGGAG
*
180798 TTTGGTGACGGATTAATAT
1 TTTGGAGACGGATTAATAT
180817 TTTGGAGACGGATTAATAT
1 TTTGGAGACGGATTAATAT
180836 TTTGGAGAC
1 TTTGGAGAC
180845 AGGCGCAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (19 bp):
TTTGGAGACGGATTAATAT
Found at i:181630 original size:21 final size:21
Alignment explanation
Indices: 181606--181671 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 21
181596 TAATTTTAAG
181606 TTTATATTTAATATATTATTT
1 TTTATATTTAATATATTATTT
*
181627 TTTAATTATTT-ATAT-TTATAT
1 TTT-A-TATTTAATATATTATTT
181648 TTTA-ATTTTAA-ATATT-TTT
1 TTTATA-TTTAATATATTATTT
181667 TTTAT
1 TTTAT
181672 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
18 1 0.03
19 11 0.30
20 4 0.11
21 11 0.30
22 5 0.14
23 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATATTTAATATATTATTT
Found at i:184453 original size:9 final size:9
Alignment explanation
Indices: 184439--184527 Score: 59
Period size: 9 Copynumber: 10.6 Consensus size: 9
184429 ATATTAGATA
184439 AAAAATAAT
1 AAAAATAAT
184448 AAAAATAA-
1 AAAAATAAT
*
184456 AAAAAT-GT
1 AAAAATAAT
* **
184464 -TAAATTTT
1 AAAAATAAT
*
184472 AAAAGTAAT
1 AAAAATAAT
184481 -AAAATAA-
1 AAAAATAAT
184488 AACAAATAAT
1 AA-AAATAAT
184498 AAAAA-AAT
1 AAAAATAAT
184506 -AAAATAA-
1 AAAAATAAT
184513 AACAAATAAT
1 AA-AAATAAT
184523 AAAAA
1 AAAAA
184528 AACATACTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
7 8 0.13
8 20 0.32
9 30 0.48
10 4 0.06
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:184458 original size:17 final size:17
Alignment explanation
Indices: 184438--184527 Score: 62
Period size: 16 Copynumber: 5.4 Consensus size: 17
184428 AATATTAGAT
184438 AAAAAATAATAAAAATA
1 AAAAAATAATAAAAATA
* * * *
184455 AAAAAAT-GTTAAATTT
1 AAAAAATAATAAAAATA
* *
184471 TAAAAGTAAT-AAAATA
1 AAAAAATAATAAAAATA
184487 AAACAAATAATAAAAA-A
1 AAA-AAATAATAAAAATA
*
184504 ATAAAATAA-AACAAATA
1 AAAAAATAATAA-AAATA
184521 ATAAAAA
1 A-AAAAA
184528 AACATACTAA
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
15 2 0.04
16 25 0.46
17 19 0.35
18 8 0.15
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAATAATAAAAATA
Found at i:184500 original size:12 final size:12
Alignment explanation
Indices: 184483--184526 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
184473 AAAGTAATAA
184483 AATAAAACAAAT
1 AATAAAACAAAT
184495 AATAAAA-AAAT
1 AATAAAACAAAT
184506 AAAATAAAACAAAT
1 --AATAAAACAAAT
184520 AATAAAA
1 AATAAAA
184527 AAACATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.14
12 14 0.48
13 7 0.24
14 4 0.14
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (12 bp):
AATAAAACAAAT
Found at i:184506 original size:25 final size:25
Alignment explanation
Indices: 184478--184529 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
184468 TTTTAAAAGT
184478 AATAAAATAAAACAAATAATAAAAA
1 AATAAAATAAAACAAATAATAAAAA
184503 AATAAAATAAAACAAATAATAAAAA
1 AATAAAATAAAACAAATAATAAAAA
184528 AA
1 AA
184530 CATACTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (25 bp):
AATAAAATAAAACAAATAATAAAAA
Found at i:186738 original size:64 final size:65
Alignment explanation
Indices: 186595--186757 Score: 188
Period size: 64 Copynumber: 2.5 Consensus size: 65
186585 AATTGTTCAG
* *
186595 TGTGTATCGATGCACAGGAAGTGCATCGATGCA-CCCATTAAAAAAAGGAAACATCGAATGCAAT
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATT-AAAAAAGAAAACATCGAATGCAAT
186659 T
65 T
* * * * * *
186660 AGTGAATCGATGCATAAGG-AGTGCATCGATGCACCCCCTT-ATAATGAAAACATCGAATGTAAT
1 TGTGTATCGATGCAT-AGGAAGTGCATCGATGCACCCCATTAAAAAAGAAAACATCGAATGCAAT
186723 T
65 T
* * *
186724 TGTGTATCGATGCATGGGTAGTGCATCAATGCAC
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCAC
186758 ATGTTAAGGG
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 2 0.02
64 47 0.57
65 26 0.31
66 8 0.10
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (65 bp):
TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAAAGAAAACATCGAATGCAATT
Found at i:189922 original size:2 final size:2
Alignment explanation
Indices: 189915--189946 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
189905 TGAGTAAGAA
189915 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
189947 TGAGTATTGA
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:190449 original size:11 final size:11
Alignment explanation
Indices: 190433--190471 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
190423 GAGGTTATAT
190433 AAGCTTAAAGA
1 AAGCTTAAAGA
* *
190444 AAGCTTATA-T
1 AAGCTTAAAGA
190454 AAGCTTAAAGA
1 AAGCTTAAAGA
190465 AAGCTTA
1 AAGCTTA
190472 TATAATCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (11 bp):
AAGCTTAAAGA
Found at i:190453 original size:21 final size:21
Alignment explanation
Indices: 190427--190483 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
190417 TTCTTTGAGG
190427 TTATATAAGCTTAAAGAAAGC
1 TTATATAAGCTTAAAGAAAGC
190448 TTATATAAGCTTAAAGAAAGC
1 TTATATAAGCTTAAAGAAAGC
*
190469 TTATATAATCTTAAA
1 TTATATAAGCTTAAA
190484 ACACCAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (21 bp):
TTATATAAGCTTAAAGAAAGC
Found at i:193671 original size:18 final size:18
Alignment explanation
Indices: 193648--193699 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
193638 GAGTCTACGC
193648 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
193666 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
193684 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
193700 TGTGTTATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:196563 original size:21 final size:21
Alignment explanation
Indices: 196537--196614 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
196527 TCTTTGAGTG
196537 TTATATAAGCTTAAAGAAAGC
1 TTATATAAGCTTAAAGAAAGC
* *
196558 TTATATAAGCATAAAGAAAGA
1 TTATATAAGCTTAAAGAAAGC
*
196579 TTATATAAGTTTAAAGAAAGC
1 TTATATAAGCTTAAAGAAAGC
196600 TTATATAAGCTTAAA
1 TTATATAAGCTTAAA
196615 ACACCAAGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (21 bp):
TTATATAAGCTTAAAGAAAGC
Found at i:199806 original size:18 final size:20
Alignment explanation
Indices: 199778--199835 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 20
199768 GTTGAGGGTT
*
199778 TACGCGGTCCTTCGGGACA-
1 TACGTGGTCCTTCGGGACAC
199797 TA-GTGGTCCTTCGGGACATC
1 TACGTGGTCCTTCGGGACA-C
*
199817 TACGTGGTCATTCGGGACA
1 TACGTGGTCCTTCGGGACA
199836 AATTCTACGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 15 0.44
19 2 0.06
20 2 0.06
21 15 0.44
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (20 bp):
TACGTGGTCCTTCGGGACAC
Found at i:201663 original size:21 final size:21
Alignment explanation
Indices: 201637--201680 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
201627 TTAGTCTTGA
201637 TGAC-TTTTGATTCTTGAATCT
1 TGACTTTTTGATTCTTG-ATCT
201658 TGACTTTTTGATTCTTGATCT
1 TGACTTTTTGATTCTTGATCT
201679 TG
1 TG
201681 GATTCTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.55
Consensus pattern (21 bp):
TGACTTTTTGATTCTTGATCT
Found at i:210359 original size:2 final size:2
Alignment explanation
Indices: 210352--210405 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
210342 TCAATCTACA
210352 AT AT 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 AT AT
210394 AT AT AT AT AT AT
1 AT AT AT AT AT AT
210406 TTTATGACAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:210583 original size:13 final size:13
Alignment explanation
Indices: 210565--210589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210555 GCGGGCGGGC
210565 GTCATAAATGCGT
1 GTCATAAATGCGT
210578 GTCATAAATGCG
1 GTCATAAATGCG
210590 CATCATAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:213266 original size:15 final size:15
Alignment explanation
Indices: 213245--213298 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
213235 TATATTTCAT
213245 ACTATGTGATAT-TG
1 ACTATGTGATATATG
213259 ATCTATGTGATTATATG
1 A-CTATGTGA-TATATG
* *
213276 AATATGTGATATAAG
1 ACTATGTGATATATG
213291 -CTATGTGA
1 ACTATGTGA
213299 AATGTATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.24
15 13 0.38
16 10 0.29
17 3 0.09
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (15 bp):
ACTATGTGATATATG
Found at i:213475 original size:23 final size:23
Alignment explanation
Indices: 213382--213462 Score: 153
Period size: 23 Copynumber: 3.5 Consensus size: 23
213372 GGTTCTACGC
*
213382 GGTCCTTCAGGATAATTCTATGT
1 GGTCCTTCGGGATAATTCTATGT
213405 GGTCCTTCGGGATAATTCTATGT
1 GGTCCTTCGGGATAATTCTATGT
213428 GGTCCTTCGGGATAATTCTATGT
1 GGTCCTTCGGGATAATTCTATGT
213451 GGTCCTTCGGGA
1 GGTCCTTCGGGA
213463 CATTTCTACG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (23 bp):
GGTCCTTCGGGATAATTCTATGT
Found at i:213483 original size:46 final size:46
Alignment explanation
Indices: 213374--213475 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
213364 GAGTCGAGGG
* * *
213374 TTCTACGCGGTCCTTCAGGATAATTCTATGTGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGATAATTCTATGTGGTCCTTCGGGACAA
* *
213420 TTCTATGTGGTCCTTCGGGATAATTCTATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGATAATTCTATGTGGTCCTTCGGGACAA
213466 TTCTACGTGG
1 TTCTACGTGG
213476 CAGTTCGGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (46 bp):
TTCTACGTGGTCCTTCGGGATAATTCTATGTGGTCCTTCGGGACAA
Found at i:217296 original size:2 final size:2
Alignment explanation
Indices: 217284--217350 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
217274 ATTATTTTAT
*
217284 TA TA AA TA TA TA TA 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 TA TA TA TA TA TA TA
217326 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
217351 TTTTAGTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:224967 original size:19 final size:18
Alignment explanation
Indices: 224919--224968 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
224909 GAAGTTACAC
224919 TTTCAAGAGAAATAAATT
1 TTTCAAGAGAAATAAATT
224937 TTT-AAGCAAGAAA-AAATTT
1 TTTCAAG--AGAAATAAA-TT
224956 GTTTCAAGAGAAA
1 -TTTCAAGAGAAA
224969 CGATGTCGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 12 0.44
20 3 0.11
21 3 0.11
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (18 bp):
TTTCAAGAGAAATAAATT
Found at i:225676 original size:23 final size:23
Alignment explanation
Indices: 225660--225718 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
225650 CGTATAAATG
*
225660 CACCGAAGTGCCACGTAGAATTT
1 CACCGAAGTGCCACGTAGAATTA
*
225683 CACCGAAGTGCCGCGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
*
225706 CACCGTAGTGCCA
1 CACCGAAGTGCCA
225719 TATAAAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:232497 original size:23 final size:23
Alignment explanation
Indices: 232467--232517 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
232457 CTAGTATAAA
232467 TGCACCGAAGTG-TAACGTAGAAT
1 TGCACCGAAGTGAT-ACGTAGAAT
232490 TGCACCGAAGTGATACGTAGAAT
1 TGCACCGAAGTGATACGTAGAAT
232513 TGCAC
1 TGCAC
232518 TGTAGTTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (23 bp):
TGCACCGAAGTGATACGTAGAAT
Found at i:232857 original size:17 final size:18
Alignment explanation
Indices: 232837--232870 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
232827 ACATATGAGT
*
232837 TCATGTCATAT-ATCATA
1 TCATGTAATATAATCATA
232854 TCATGTAATATAATCAT
1 TCATGTAATATAATCAT
232871 GTATTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (18 bp):
TCATGTAATATAATCATA
Found at i:235190 original size:25 final size:24
Alignment explanation
Indices: 235148--235313 Score: 199
Period size: 25 Copynumber: 6.7 Consensus size: 24
235138 TTTCAAAAGG
* *
235148 TGAAAAAGTTTAAT-AAAGAAGTTT
1 TGAAAATGTTTGATGAAAGAA-TTT
* *
235172 TGAAAATGTTTTATGAAAGTATTT
1 TGAAAATGTTTGATGAAAGAATTT
*
235196 TGAAAAATGTTTGATGAAGGAATTT
1 TG-AAAATGTTTGATGAAAGAATTT
*
235221 TGAAGAATATTTGATGAAAGAATTT
1 TGAA-AATGTTTGATGAAAGAATTT
*
235246 TGAGAAATGTTTAATGAAAGAATTT
1 TGA-AAATGTTTGATGAAAGAATTT
235271 TGAAGAATGTTTGATGAAAGAATTT
1 TGAA-AATGTTTGATGAAAGAATTT
*
235296 TAAGAAATGTTTGATGAA
1 TGA-AAATGTTTGATGAA
235314 GTTTTTTTTA
Statistics
Matches: 124, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
24 20 0.16
25 102 0.82
26 2 0.02
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (24 bp):
TGAAAATGTTTGATGAAAGAATTT
Found at i:235240 original size:50 final size:50
Alignment explanation
Indices: 235148--235313 Score: 223
Period size: 50 Copynumber: 3.4 Consensus size: 50
235138 TTTCAAAAGG
* *
235148 TGAAAAA-GTTTAAT-AAAGAAGTTTTGAA-AATGTTTTATGAAAGTATTT
1 TGAAAAATGTTTAATGAAAGAA-TTTTGAAGAATGTTTGATGAAAGAATTT
* * *
235196 TGAAAAATGTTTGATGAAGGAATTTTGAAGAATATTTGATGAAAGAATTT
1 TGAAAAATGTTTAATGAAAGAATTTTGAAGAATGTTTGATGAAAGAATTT
*
235246 TGAGAAATGTTTAATGAAAGAATTTTGAAGAATGTTTGATGAAAGAATTT
1 TGAAAAATGTTTAATGAAAGAATTTTGAAGAATGTTTGATGAAAGAATTT
*
235296 T-AAGAAATGTTTGATGAA
1 TGAA-AAATGTTTAATGAA
235314 GTTTTTTTTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
48 7 0.07
49 14 0.14
50 82 0.80
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (50 bp):
TGAAAAATGTTTAATGAAAGAATTTTGAAGAATGTTTGATGAAAGAATTT
Found at i:235285 original size:75 final size:75
Alignment explanation
Indices: 235162--235313 Score: 227
Period size: 75 Copynumber: 2.0 Consensus size: 75
235152 AAAGTTTAAT
* * *
235162 AAAGAAGTTTTGAAAATGTTTTATGAAAGTATTTTGAAAAATGTTTGATGAAGGAATTTTGAAG-
1 AAAGAAGTTTTGAAAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATGAAAGAATTTT-AAGA
235226 AATATTTGATG
65 AATATTTGATG
*
235237 AAAGAA-TTTTGAGAAATGTTTAATGAAAGAATTTTGAAGAATGTTTGATGAAAGAATTTTAAGA
1 AAAGAAGTTTTGA-AAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATGAAAGAATTTTAAGA
*
235301 AATGTTTGATG
65 AATATTTGATG
235312 AA
1 AA
235314 GTTTTTTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
74 9 0.13
75 61 0.87
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (75 bp):
AAAGAAGTTTTGAAAATGTTTAATGAAAGAATTTTGAAAAATGTTTGATGAAAGAATTTTAAGAA
ATATTTGATG
Found at i:239398 original size:18 final size:18
Alignment explanation
Indices: 239375--239409 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
239365 ATGTTTCCTA
239375 AATCATATTAGAAGTTAG
1 AATCATATTAGAAGTTAG
239393 AATCATATTAGAAGTTA
1 AATCATATTAGAAGTTA
239410 TAAAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (18 bp):
AATCATATTAGAAGTTAG
Found at i:243921 original size:6 final size:6
Alignment explanation
Indices: 243888--243934 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
243878 GAAGATGCTT
*
243888 AAATGC -AATAC AGAATGC AATGATGC AAATGC AAATGC AAATGC AAA
1 AAATGC AAATGC A-AATGC AA--ATGC AAATGC AAATGC AAATGC AAA
243935 AAGTGTTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 4 0.11
6 20 0.57
7 5 0.14
8 6 0.17
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (6 bp):
AAATGC
Found at i:245444 original size:13 final size:13
Alignment explanation
Indices: 245426--245450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245416 TTTAAAAAAT
245426 ATTTAAAAATAAA
1 ATTTAAAAATAAA
245439 ATTTAAAAATAA
1 ATTTAAAAATAA
245451 TCATGACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTTAAAAATAAA
Found at i:247273 original size:3 final size:3
Alignment explanation
Indices: 247263--247304 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
247253 TATTATTATT
247263 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
247305 GACTAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:255083 original size:739 final size:739
Alignment explanation
Indices: 253667--255133 Score: 2361
Period size: 739 Copynumber: 2.0 Consensus size: 739
253657 AACAAGTAAC
* *
253667 CCTAGGATCTCTAAATTATATTTATCTTTATTAAGAGTTTTAATACCGAAATTACATGATTAAGA
1 CCTAGGATCTCTAAATTATATTTATCTTTATTAAGAGTTTTAATACCAAAATTACATGAGTAAGA
* * * *
253732 AATTACGAAATTTCCCTTGAGAGGAAAAAGTAGCCCGAATTCACCCTGAATGGGAAAATACCCAA
66 AATTACAAAATTACCCTTGAGAGGAAAAAGTAGCACGAATTAACCCTGAATGGGAAAATACCCAA
* *
253797 GAAGTCATGCCTAAATCGATGAATTACTAATTTCATCGTTAAGTTCACACGTTTATACAGAAAAT
131 GAAGTCATGCCTAAATCGATCAATTACTAATTTCATCGTTAAGTTCACAAGTTTATACAGAAAAT
* *
253862 TCCTGATAATCCGTAAATCTTCGAGTTATGAGTAAATACCTGAAGAATAATTTATCGAGAGTGTT
196 TCCTGATAATCCGTAAATCTCCGAGATATGAGTAAATACCTGAAGAATAATTTATCGAGAGTGTT
* *
253927 CTTTTGTCAAAACTGTTCGAAAGAACTCAAATAGATGATAAGTTTGAATTAATAATAAGATCAGA
261 ATTTTGTCAAAACTGTTCGAAAGAACTCAAATAGATGATAAATTTGAATTAATAATAAGATCAGA
* *
253992 CGGAAGTAAAGGATTGAAATACGATGTCATTATAAAATAACCAAAATACCCCTGGAATGGAAACG
326 CGGAAGAAAAAGATTGAAATACGATGTCATTATAAAATAACCAAAATACCCCTGGAATGGAAACG
* * *
254057 AATCAATAATATCACCAAGCCCAGGAATGATTGGATATCCTCAAGCTCTAAAAGGACTGAATTAA
391 AATCAAGAATATCACCAAGCCCAGGAATGATTAGATATCCTCAAGCTCTAAAAAGACTGAATTAA
254122 CATTGAGCACCAAAATGACCAAAATACCCTTATAGCCTAGAATAAGTAAATGTCTTGGATTAATT
456 CATTGAGCACCAAAATGACCAAAATACCCTTATAGCCTAGAATAAGTAAATGTCTTGGATTAATT
* * *
254187 AAGAAATTCAAATACACATGGATGTTGTACTGCTTTTAAAAGTTATGGAACACAGATTAATCTGG
521 AAGAAATTCAAATAAACATGAATGTTGTACTGCTCTTAAAAGTTATGGAACACAGATTAATCTGG
* * * *
254252 TCAATCAATGCAAGTGCTATTTCAATACCTGAATGGCATAGATACCACTTGAATCCTTGTTCGTC
586 TCAATCAATGCAAGTGCTATATCAATACCTGAATGGCATAGATACCACATGAATCATTGTTCATC
* * *
254317 TCCTCAAGTATGGATCGATGATAATTCTGGA-AGTACTCATATCAACTCATA-TCTAGAGCGCAT
651 TCCTCAAGTATGGATCGATGATAATTCT-GACAGTACTCAGACCAACTCA-ACTCTAAAGCGCAT
254380 TCGGTACTAAGAAGTGGATATTCGTT
714 TCGGTACTAAGAAGTGGATATTCGTT
* **
254406 CCTAGGATCTCTAAATTATATTTATCTTTGTTAATTGTTTTAATACCAAAATTACATGAGTAAGA
1 CCTAGGATCTCTAAATTATATTTATCTTTATTAAGAGTTTTAATACCAAAATTACATGAGTAAGA
* * *
254471 AATTACAAAATTACCCTTGAGAGTAAAAAGTAGCACGAGTTAACCCTGAATGGGAAAGTACCCAA
66 AATTACAAAATTACCCTTGAGAGGAAAAAGTAGCACGAATTAACCCTGAATGGGAAAATACCCAA
*
254536 GAAGTCATGCCTAAATCGATCAATTACTAATTTTATCGTTAAGTTCACAAGTTTATACAGAAAAT
131 GAAGTCATGCCTAAATCGATCAATTACTAATTTCATCGTTAAGTTCACAAGTTTATACAGAAAAT
254601 TCCTGATAATCCGTAAATCTCCGAGATATGAGTAAATACCTGAAGAATAATTTATCGA-AGGTGT
196 TCCTGATAATCCGTAAATCTCCGAGATATGAGTAAATACCTGAAGAATAATTTATCGAGA-GTGT
* * *
254665 TATTTTGTCAGAACTGTTCGAAAGAACTCAAATAGATGATAAATTTGCATTAATAATAAGATCGG
260 TATTTTGTCAAAACTGTTCGAAAGAACTCAAATAGATGATAAATTTGAATTAATAATAAGATCAG
* *
254730 ATGGAAGAAAAAGATTGAAATATC-ATGT-GTCTATAAAATAACCAAAATACCCCTGGAATGGAA
325 ACGGAAGAAAAAGATTGAAATA-CGATGTCAT-TATAAAATAACCAAAATACCCCTGGAATGGAA
* * * *
254793 ATGAATCAAGAATATCACCAAGCCCATGATTGATTAGATATCCTTAAGCTCTAAAAAGACTGAAT
388 ACGAATCAAGAATATCACCAAGCCCAGGAATGATTAGATATCCTCAAGCTCTAAAAAGACTGAAT
* * *
254858 TAACATTGAGTACCAAAATTACCAAAATACCCTTATGGCCTAGAATAAGTAAATGTCTTGGATTA
453 TAACATTGAGCACCAAAATGACCAAAATACCCTTATAGCCTAGAATAAGTAAATGTCTTGGATTA
*
254923 ATTAAGAAATTCAAATAAACATGAATGTTGTACTGCTCTTAAAAGTTATGGAACACTGATTAAGT
518 ATTAAGAAATTCAAATAAACATGAATGTTGTACTGCTCTTAAAAGTTATGGAACACAGATTAA-T
* * *
254988 C-GGTCAATTAATGCTAGTGCTATATCAGTACCTGAATGGCATAGATACCACATGAATCATTGTT
582 CTGGTCAATCAATGCAAGTGCTATATCAATACCTGAATGGCATAGATACCACATGAATCATTGTT
* * *
255052 TATCTCCTCAAGTATGGATCGATGATAATTCTGACAGTACTCAGACCAGCTCAACTCTAAAGTGC
647 CATCTCCTCAAGTATGGATCGATGATAATTCTGACAGTACTCAGACCAACTCAACTCTAAAGCGC
255117 ATTCGGTACTAAGAAGT
712 ATTCGGTACTAAGAAGT
255134 AATTATTCGT
Statistics
Matches: 669, Mismatches: 53, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
738 5 0.01
739 661 0.99
740 3 0.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (739 bp):
CCTAGGATCTCTAAATTATATTTATCTTTATTAAGAGTTTTAATACCAAAATTACATGAGTAAGA
AATTACAAAATTACCCTTGAGAGGAAAAAGTAGCACGAATTAACCCTGAATGGGAAAATACCCAA
GAAGTCATGCCTAAATCGATCAATTACTAATTTCATCGTTAAGTTCACAAGTTTATACAGAAAAT
TCCTGATAATCCGTAAATCTCCGAGATATGAGTAAATACCTGAAGAATAATTTATCGAGAGTGTT
ATTTTGTCAAAACTGTTCGAAAGAACTCAAATAGATGATAAATTTGAATTAATAATAAGATCAGA
CGGAAGAAAAAGATTGAAATACGATGTCATTATAAAATAACCAAAATACCCCTGGAATGGAAACG
AATCAAGAATATCACCAAGCCCAGGAATGATTAGATATCCTCAAGCTCTAAAAAGACTGAATTAA
CATTGAGCACCAAAATGACCAAAATACCCTTATAGCCTAGAATAAGTAAATGTCTTGGATTAATT
AAGAAATTCAAATAAACATGAATGTTGTACTGCTCTTAAAAGTTATGGAACACAGATTAATCTGG
TCAATCAATGCAAGTGCTATATCAATACCTGAATGGCATAGATACCACATGAATCATTGTTCATC
TCCTCAAGTATGGATCGATGATAATTCTGACAGTACTCAGACCAACTCAACTCTAAAGCGCATTC
GGTACTAAGAAGTGGATATTCGTT
Found at i:257122 original size:26 final size:25
Alignment explanation
Indices: 257068--257124 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
257058 TTGTATTTTG
* *
257068 TTTTATATCTGAGTCTGAAAATCTG
1 TTTTATATCTGAATCTGAAAATCTA
*
257093 TTTTATTTCTGAATACTGATAAAT-TA
1 TTTTATATCTGAAT-CTGA-AAATCTA
257119 TTTTAT
1 TTTTAT
257125 GAGTTTACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.44
26 11 0.41
27 4 0.15
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (25 bp):
TTTTATATCTGAATCTGAAAATCTA
Found at i:269188 original size:15 final size:15
Alignment explanation
Indices: 269168--269198 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
269158 TAAAGAATGC
269168 AGGGGCAACATATCA
1 AGGGGCAACATATCA
269183 AGGGGCAACATATCA
1 AGGGGCAACATATCA
269198 A
1 A
269199 AAGGCTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.13
Consensus pattern (15 bp):
AGGGGCAACATATCA
Found at i:272541 original size:35 final size:35
Alignment explanation
Indices: 272493--272605 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 35
272483 AGTCATTCAA
272493 AATC-AGCCTTCACAAAAGAGTAGTGAAGCAATAC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATAC
* * * * *
272527 AATCAAGCCATCACAAAAGATTAATGAAGTAATGC
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATAC
* *
272562 AATGAAGCCTTCACAAAAAAAGTAGTGAAGCAATATC
1 AATCAAGCCTTCAC-AAAAGAGTAGTGAAGCAATA-C
272599 AGATCAA
1 A-ATCAA
272606 AAGTTCGATC
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
34 4 0.06
35 37 0.60
36 15 0.24
37 2 0.03
38 4 0.06
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.19
Consensus pattern (35 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATAC
Found at i:272834 original size:26 final size:28
Alignment explanation
Indices: 272778--272837 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
272768 TTCAATATAC
*
272778 TTATATTATTATATTATAATTATGTTATT
1 TTATATTATTATATTATAATTA-GATATT
272807 TTATATTA-TATTATTATAATTA-AT-TT
1 TTATATTATTA-TATTATAATTAGATATT
272833 TTATA
1 TTATA
272838 ATTTTACAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.24
27 1 0.03
28 2 0.07
29 19 0.66
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTATATTATTATATTATAATTAGATATT
Found at i:272836 original size:13 final size:14
Alignment explanation
Indices: 272791--272840 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
272781 TATTATTATA
*
272791 TTATAATTATGTTAT
1 TTATAATTATATT-T
*
272806 TT-TATATTATATTA
1 TTATA-ATTATATTT
272820 TTATAATTA-ATTT
1 TTATAATTATATTT
272833 TTATAATT
1 TTATAATT
272841 TTACAGACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.37
14 8 0.27
15 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATAATTATATTT
Found at i:284105 original size:33 final size:33
Alignment explanation
Indices: 284063--284131 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
284053 GGATCTAATT
284063 ACATCAATGGTCTAGATTAAATCCTACCTACCA
1 ACATCAATGGTCTAGATTAAATCCTACCTACCA
*
284096 ACATCAATGGTCTAGATTGAATCCTACCTACCA
1 ACATCAATGGTCTAGATTAAATCCTACCTACCA
284129 ACA
1 ACA
284132 ATAAGTGGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (33 bp):
ACATCAATGGTCTAGATTAAATCCTACCTACCA
Found at i:291011 original size:18 final size:17
Alignment explanation
Indices: 290961--291000 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
290951 CTAGCGGCGG
*
290961 CGGTTGACGACGGCGAT
1 CGGTTGACGACGGTGAT
290978 CGGTTGACGACGGTGAT
1 CGGTTGACGACGGTGAT
290995 CGGTTG
1 CGGTTG
291001 CCGGCCGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.20, G:0.42, T:0.23
Consensus pattern (17 bp):
CGGTTGACGACGGTGAT
Found at i:291283 original size:2 final size:2
Alignment explanation
Indices: 291276--291351 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
291266 CGATCACTAC
291276 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
291318 TA TA TA 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 TA TA TA
291352 CTTTAGGATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:292594 original size:6 final size:6
Alignment explanation
Indices: 292583--292608 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
292573 AAATGGAGTA
292583 ATTATG ATTATG ATTATG ATTATG AT
1 ATTATG ATTATG ATTATG ATTATG AT
292609 CTGGTACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATTATG
Found at i:293331 original size:2 final size:2
Alignment explanation
Indices: 293324--293364 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
293314 AATTAAATAG
293324 TA TA TA TA 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 TA TA TA TA T
293365 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:294044 original size:21 final size:21
Alignment explanation
Indices: 294010--294054 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
294000 CCTCACTCAT
*
294010 TTCCTTTTTTTCTCT-CTTCA
1 TTCCTTTTTATCTCTACTTCA
*
294030 TTCCTTTGTTATCTCTATTTCA
1 TTCCTTT-TTATCTCTACTTCA
294052 TTC
1 TTC
294055 ATGATTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.09, C:0.27, G:0.02, T:0.62
Consensus pattern (21 bp):
TTCCTTTTTATCTCTACTTCA
Found at i:294101 original size:15 final size:15
Alignment explanation
Indices: 294069--294136 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
294059 TTAGATCATA
* *
294069 ATTCGGATATGTGAT
1 ATTCGGATATATGTT
*
294084 ATTTGGATATATGTT
1 ATTCGGATATATGTT
**
294099 ATTCAAATATATGTT
1 ATTCGGATATATGTT
**
294114 ATTTAGATATATGTT
1 ATTCGGATATATGTT
294129 ATTCGGAT
1 ATTCGGAT
294137 CGAATCAGAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (15 bp):
ATTCGGATATATGTT
Found at i:298827 original size:21 final size:20
Alignment explanation
Indices: 298803--298848 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
298793 CCCTCTACTT
298803 CCCCTGGTGTGCCCA-CCGCCG
1 CCCCTGG-GTG-CCATCCGCCG
*
298824 CCCCTGGGTGCCATCTGCCG
1 CCCCTGGGTGCCATCCGCCG
298844 CCCCT
1 CCCCT
298849 ACGGTTGCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.04, C:0.52, G:0.26, T:0.17
Consensus pattern (20 bp):
CCCCTGGGTGCCATCCGCCG
Found at i:311454 original size:17 final size:18
Alignment explanation
Indices: 311415--311454 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
311405 ATAAAATTAT
311415 TAATAAATAAATAAATAA
1 TAATAAATAAATAAATAA
311433 T-AT-AATATAAT-AATAA
1 TAATAAATA-AATAAATAA
311449 TAATAA
1 TAATAA
311455 CAGGCCGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
16 10 0.53
17 7 0.37
18 2 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATAAATAAATAAATAA
Found at i:313267 original size:26 final size:25
Alignment explanation
Indices: 313237--313306 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
313227 ATTTTAAATA
313237 ATGAAAGGATTTTGAAAAAGTGTTTG
1 ATGAAAGGATTTTGAAAAA-TGTTTG
*
313263 ATGAAAGAATTTTGAAAAATGTTTG
1 ATGAAAGGATTTTGAAAAATGTTTG
*
313288 ATG-AA-GTTTTTGAAAAATG
1 ATGAAAGGATTTTGAAAAATG
313307 GTTTCCCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 12 0.29
24 2 0.05
25 9 0.22
26 18 0.44
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (25 bp):
ATGAAAGGATTTTGAAAAATGTTTG
Found at i:315107 original size:18 final size:18
Alignment explanation
Indices: 315084--315131 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
315074 AATCTACGTT
315084 TGATAACTGTAAAACATA
1 TGATAACTGTAAAACATA
* * *
315102 TGATAAATCT-AAACATC
1 TGATAACTGTAAAACATA
315119 TGATAACTG-AAAA
1 TGATAACTGTAAAA
315132 TTGTAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.27
Consensus pattern (18 bp):
TGATAACTGTAAAACATA
Found at i:315137 original size:42 final size:42
Alignment explanation
Indices: 315095--315174 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
315085 GATAACTGTA
**
315095 AAACATATGATAAATCTAAA-CATCTGATAACTGAAAATTGT
1 AAACATATGATAAATAAAAATCATCTGATAACTGAAAATTGT
* * * *
315136 AAATATCTGATAACTAAAAATCATCTGATAACTGTAAAT
1 AAACATATGATAAATAAAAATCATCTGATAACTGAAAAT
315175 ATTTAGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 15 0.47
42 17 0.53
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (42 bp):
AAACATATGATAAATAAAAATCATCTGATAACTGAAAATTGT
Found at i:315138 original size:24 final size:24
Alignment explanation
Indices: 315111--315156 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
315101 ATGATAAATC
*
315111 TAAACATCTGATAACTGAAAATTG
1 TAAACATCTGATAACTAAAAATTG
*
315135 TAAATATCTGATAACTAAAAAT
1 TAAACATCTGATAACTAAAAAT
315157 CATCTGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (24 bp):
TAAACATCTGATAACTAAAAATTG
Found at i:315174 original size:18 final size:17
Alignment explanation
Indices: 315133--315176 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
315123 AACTGAAAAT
315133 TGTAAATATCTGATAAC
1 TGTAAATATCTGATAAC
**
315150 TAAAAATCATCTGATAAC
1 TGTAAAT-ATCTGATAAC
315168 TGTAAATAT
1 TGTAAATAT
315177 TTAGAATTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (17 bp):
TGTAAATATCTGATAAC
Found at i:317961 original size:30 final size:28
Alignment explanation
Indices: 317927--318007 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
317917 TAAAATTTAT
*
317927 AACTTTTCAAAATTATATTTTTGGTCCTTA
1 AACTTTTCAAAATTATATTTTT-G-CCTCA
* **
317957 AACTTTTACAAAGTTTATACCTTTGCCTCA
1 AACTTTT-CAAA-ATTATATTTTTGCCTCA
317987 AAC-TTTCAAAATTTATATTTT
1 AACTTTTCAAAA-TTATATTTT
318008 AGTCACTAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
28 11 0.27
29 3 0.07
30 14 0.34
31 5 0.12
32 8 0.20
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (28 bp):
AACTTTTCAAAATTATATTTTTGCCTCA
Found at i:322361 original size:14 final size:14
Alignment explanation
Indices: 322342--322371 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
322332 AGGGGTAAAT
*
322342 AAAATAACTAAACA
1 AAAATAAATAAACA
322356 AAAATAAATAAACA
1 AAAATAAATAAACA
322370 AA
1 AA
322372 TACATGAAAT
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:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAAATAAACA
Found at i:326252 original size:12 final size:12
Alignment explanation
Indices: 326208--326245 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
326198 ATATGATAAG
326208 AATAT-ATTTAT
1 AATATAATTTAT
326219 AATATCAA-TTAT
1 AATAT-AATTTAT
326231 AATATAATTTAT
1 AATATAATTTAT
326243 AAT
1 AAT
326246 TATATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 16 0.67
13 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATAATTTAT
Found at i:328215 original size:21 final size:21
Alignment explanation
Indices: 328186--328232 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
328176 ATTCTGACTA
328186 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
328207 TCGCGTTGCGGTTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
328228 TCGCA
1 TCGCA
328233 CTGCAAATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:328352 original size:21 final size:21
Alignment explanation
Indices: 328186--328460 Score: 271
Period size: 20 Copynumber: 13.5 Consensus size: 21
328176 ATTCTGACTA
* **
328186 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTACGTAAT
* * * *
328207 TCGCGTTGCGGTTTTCCTAAT
1 TCGCATTGCGATTTACGTAAT
* ** *
328228 TCGCACTGC-AAATACGTAAA
1 TCGCATTGCGATTTACGTAAT
* *
328248 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACGTAAT
* *
328268 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACGTAAT
* *
328288 TCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACGTAAT
* *
328308 TCGCAATGCGA-ATACGTAA-
1 TCGCATTGCGATTTACGTAAT
*
328327 TCGCATTGCGATTTACCTAAT
1 TCGCATTGCGATTTACGTAAT
* *
328348 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAAT
328369 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAAT
* *
328389 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAAT
328410 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAAT
328430 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTACGTAAT
328450 TCGCATTGCGA
1 TCGCATTGCGA
328461 ATTAGGAAAA
Statistics
Matches: 224, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
19 11 0.05
20 132 0.59
21 81 0.36
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTTACGTAAT
Done.