Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002507.1 Hibiscus syriacus cultivar Beakdansim tig00005106_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: 191875
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5471 original size:21 final size:21
Alignment explanation
Indices: 5441--5488 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5431 GCAGGGGTAC
* *
5441 ATGCCCAGCCCTCAACTTCAT
1 ATGCCAAGCCCACAACTTCAT
* *
5462 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACAACTTCAT
5483 ATGCCA
1 ATGCCA
5489 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.40, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACAACTTCAT
Found at i:5564 original size:21 final size:21
Alignment explanation
Indices: 5492--5564 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
5482 TATGCCATCT
*
5492 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
*
5513 CCGCATGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
5534 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
*
5555 CCGTAGGGTT
1 CCGCAGGGTT
5565 TTATACCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:6116 original size:30 final size:30
Alignment explanation
Indices: 6039--6122 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
6029 TTTAAAATAC
*
6039 AAATTATATTATTCTAAATTTAAAATAAAAAA
1 AAATTATATTATTCGAAATTT--AATAAAAAA
* ** *
6071 AAATAATATTATTCGAAATTTAATTTAAAT
1 AAATTATATTATTCGAAATTTAATAAAAAA
*
6101 AAATTATAGTATTCG-AATTTAA
1 AAATTATATTATTCGAAATTTAA
6123 CATTAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.16
30 19 0.42
32 19 0.42
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (30 bp):
AAATTATATTATTCGAAATTTAATAAAAAA
Found at i:8260 original size:2 final size:2
Alignment explanation
Indices: 8253--8323 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
8243 CATTTATCAT
8253 TA TA TA TA TA TA TA TA TA T- 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
8294 TA TA TA TA TA T- 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 T
8324 TGGTTCTCAT
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9336 original size:10 final size:9
Alignment explanation
Indices: 9278--9335 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
9268 AAAAGTAAAA
9278 ATATAATAT
1 ATATAATAT
9287 AGTATAATAT
1 A-TATAATAT
9297 CATATAA-AT
1 -ATATAATAT
*
9306 -TATTATA-
1 ATATAATAT
9313 ATAATAATAT
1 AT-ATAATAT
9323 ATAT-ATAT
1 ATATAATAT
9331 ATATA
1 ATATA
9336 TTTGATTAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
7 4 0.10
8 10 0.25
9 10 0.25
10 15 0.38
11 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (9 bp):
ATATAATAT
Found at i:15995 original size:11 final size:11
Alignment explanation
Indices: 15981--16005 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15971 CATATATAAC
15981 ATATATTATTT
1 ATATATTATTT
15992 ATATATTATTT
1 ATATATTATTT
16003 ATA
1 ATA
16006 AATTTTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATATTATTT
Found at i:18125 original size:101 final size:101
Alignment explanation
Indices: 17967--18210 Score: 330
Period size: 101 Copynumber: 2.4 Consensus size: 101
17957 GGCAGCGGCG
* ** *
17967 TTTCTTTGCTAGGGGAATCGGCCTATTACGGTGTTGCGCCGCTGTATAGAAGGGTGAGTAAAACT
1 TTTCTTTGCTAGGGGAATCGGCCTGTTACGGTGTTGAACCGCTGTACAGAAGGGTGAGTAAAACT
* *
18032 CGACCGGGTTGACTAGAAACATCATTAATATCAGCA
66 CGACCGGGTCGACTAGAAACATCACTAATATCAGCA
**
18068 TTTCTTTGCTAGGGGAATCGGCCTGTTACGGTGTTGAACTTCTAG-ACAGAAGGGTGAGTAAAAC
1 TTTCTTTGCTAGGGGAATCGGCCTGTTACGGTGTTGAACCGCT-GTACAGAAGGGTGAGTAAAAC
* * * *
18132 TCGATCGGGTCGACTAGATACGTCACTAATATCAGCG
65 TCGACCGGGTCGACTAGAAACATCACTAATATCAGCA
* * *
18169 TTTCTTTGCT-GGGGAATCAGCTTGTTACGGTGTTGAGCCGCT
1 TTTCTTTGCTAGGGGAATCGGCCTGTTACGGTGTTGAACCGCT
18211 ATACGTAGAG
Statistics
Matches: 125, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
100 27 0.22
101 97 0.78
102 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (101 bp):
TTTCTTTGCTAGGGGAATCGGCCTGTTACGGTGTTGAACCGCTGTACAGAAGGGTGAGTAAAACT
CGACCGGGTCGACTAGAAACATCACTAATATCAGCA
Found at i:18865 original size:23 final size:23
Alignment explanation
Indices: 18839--18933 Score: 190
Period size: 23 Copynumber: 4.1 Consensus size: 23
18829 GCGAATTACT
18839 TGATACTCGACTCGAAGAACTCG
1 TGATACTCGACTCGAAGAACTCG
18862 TGATACTCGACTCGAAGAACTCG
1 TGATACTCGACTCGAAGAACTCG
18885 TGATACTCGACTCGAAGAACTCG
1 TGATACTCGACTCGAAGAACTCG
18908 TGATACTCGACTCGAAGAACTCG
1 TGATACTCGACTCGAAGAACTCG
18931 TGA
1 TGA
18934 GTAGCTAGAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
TGATACTCGACTCGAAGAACTCG
Found at i:25833 original size:29 final size:29
Alignment explanation
Indices: 25800--25890 Score: 155
Period size: 29 Copynumber: 3.1 Consensus size: 29
25790 TTCTACAGTA
*
25800 ACCTTGGAGGTCGCCATGGCATTCGGGCG
1 ACCTTGGAGGTCGCCATGGCATCCGGGCG
*
25829 ACCTTGGAGGTCGACATGGCATCCGGGCG
1 ACCTTGGAGGTCGCCATGGCATCCGGGCG
*
25858 ACCTTGGAGGTCGCCATGGCATCCGAGCG
1 ACCTTGGAGGTCGCCATGGCATCCGGGCG
25887 ACCT
1 ACCT
25891 GTGTGTATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.16, C:0.30, G:0.35, T:0.19
Consensus pattern (29 bp):
ACCTTGGAGGTCGCCATGGCATCCGGGCG
Found at i:26526 original size:21 final size:21
Alignment explanation
Indices: 26501--26544 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
26491 AATCTAGTTA
26501 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
26522 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
26543 AT
1 AT
26545 ATTATATTAG
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:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:26554 original size:28 final size:30
Alignment explanation
Indices: 26521--26583 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
26511 TAGTATAAAT
*
26521 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
26549 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
26579 TATTA
1 TATTA
26584 TATAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:26927 original size:15 final size:14
Alignment explanation
Indices: 26904--26934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
26894 TACAACACTA
26904 AACTTTAATATAAT
1 AACTTTAATATAAT
26918 AACTTATAATATAAT
1 AACTT-TAATATAAT
26933 AA
1 AA
26935 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:26942 original size:16 final size:16
Alignment explanation
Indices: 26909--26955 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
26899 CACTAAACTT
*
26909 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
26924 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
26940 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
26956 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:27060 original size:32 final size:34
Alignment explanation
Indices: 26980--27061 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
26970 AAGTTACCTT
*
26980 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
27013 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
27046 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
27062 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:27174 original size:45 final size:45
Alignment explanation
Indices: 27100--27232 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
27090 TCAACAAACA
*
27100 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
27148 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
27192 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
27233 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:27260 original size:41 final size:40
Alignment explanation
Indices: 27172--27260 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
27162 TTAACAAAAC
* *
27172 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
27213 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
27254 AAACTAA
1 AAACTAA
27261 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:27461 original size:23 final size:23
Alignment explanation
Indices: 27431--27476 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
27421 ACTTTCTCGG
27431 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
27454 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
27477 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:27652 original size:27 final size:27
Alignment explanation
Indices: 27622--27677 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
27612 AATAATTCAC
27622 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
27649 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAATGGTTCACATGCATGCATT
27676 GG
1 GG
27678 GAGCTGTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (27 bp):
GGCTCAAATGGTTCACATGCATGCATT
Found at i:27788 original size:28 final size:28
Alignment explanation
Indices: 27746--27802 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
27736 TCGTATAAGA
* * *
27746 CTCGTCTAAGCCTGCATGGTGACCTCTC
1 CTCGTATAAGACTGCATGGCGACCTCTC
27774 CTCGTATAAGACTGCATGGCGACCTCTC
1 CTCGTATAAGACTGCATGGCGACCTCTC
27802 C
1 C
27803 ATTGGCTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.35, G:0.21, T:0.26
Consensus pattern (28 bp):
CTCGTATAAGACTGCATGGCGACCTCTC
Found at i:27819 original size:9 final size:9
Alignment explanation
Indices: 27805--27844 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
27795 ACCTCTCCAT
27805 TGGCTCGTA
1 TGGCTCGTA
27814 TGGCTCGTATA
1 TGGCTCG--TA
*
27825 TGGCTTGTA
1 TGGCTCGTA
27834 TGGCTCGTA
1 TGGCTCGTA
27843 TG
1 TG
27845 TCACCCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:27834 original size:20 final size:20
Alignment explanation
Indices: 27805--27843 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27795 ACCTCTCCAT
27805 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
27825 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
27844 GTCACCCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:32786 original size:2 final size:2
Alignment explanation
Indices: 32779--32805 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32769 TGAGAGTAAA
32779 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
32806 CCAGCATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37997 original size:33 final size:33
Alignment explanation
Indices: 37960--38030 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
37950 TTTCCTCGGC
* *
37960 CTACCCCTTCCTCTCTTACTGACATGCACAGCA
1 CTACCCCTTCCTCTCTTACTCACAAGCACAGCA
* *
37993 CTACCCCTTCCTCTCTTATTCACAAGCACAGTA
1 CTACCCCTTCCTCTCTTACTCACAAGCACAGCA
38026 CTACC
1 CTACC
38031 TCCATTGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.23, C:0.42, G:0.07, T:0.28
Consensus pattern (33 bp):
CTACCCCTTCCTCTCTTACTCACAAGCACAGCA
Found at i:39496 original size:16 final size:16
Alignment explanation
Indices: 39475--39505 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39465 CTTTGGTTTA
*
39475 AATTATTTTAGATTTT
1 AATTATTTTAAATTTT
39491 AATTATTTTAAATTT
1 AATTATTTTAAATTT
39506 AAAGTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
AATTATTTTAAATTTT
Found at i:43903 original size:71 final size:70
Alignment explanation
Indices: 43778--43909 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 70
43768 AATACAGTCA
** * *
43778 TCAATTACATTCTAAACCCTAAATTTTAAAATATTTCAATTACATTCTAAACCCCAAATTCCAAA
1 TCAATTACATTCTAAACCCTAAATTCAAAAATACTTCAATTACATTCAAAACCCCAAATTCCAAA
43843 ATACT
66 ATACT
*
43848 TCAATTACATTCTAAA-CCTCAAATTCCAAAAATACTTCAATTACA-TGAACAACCCCAAATTC
1 TCAATTACATTCTAAACCCT-AAATT-CAAAAATACTTCAATTACATTCAA-AACCCCAAATTC
43910 ATAATTCATT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
69 3 0.06
70 23 0.43
71 28 0.52
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (70 bp):
TCAATTACATTCTAAACCCTAAATTCAAAAATACTTCAATTACATTCAAAACCCCAAATTCCAAA
ATACT
Found at i:43909 original size:36 final size:35
Alignment explanation
Indices: 43778--43893 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
43768 AATACAGTCA
* ** *
43778 TCAATTACATTCTAAACCCTAAATTTTAAAATATT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
43813 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
*
43848 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCC-AAAATACT
43884 TCAATTACAT
1 TCAATTACAT
43894 GAACAACCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 57 0.76
36 18 0.24
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:48882 original size:42 final size:42
Alignment explanation
Indices: 48831--48962 Score: 203
Period size: 42 Copynumber: 3.2 Consensus size: 42
48821 ATAAACATGT
* *
48831 AAATAAATAACACCATAATACCATTAAGTCTCAATAAATCTA
1 AAATAAATAACACCATAATACTATTAAGTCTCAATAAGTCTA
* *
48873 AAATAAATAACACCATAACACTATTAAATCTCAATAAGTCTA
1 AAATAAATAACACCATAATACTATTAAGTCTCAATAAGTCTA
* *
48915 AAATAAATAACACCATAATACTAATAAGTCTCGATAAGTCT-
1 AAATAAATAACACCATAATACTATTAAGTCTCAATAAGTCTA
48956 AAATAAA
1 AAATAAA
48963 ATTAACATCA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 7 0.09
42 75 0.91
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (42 bp):
AAATAAATAACACCATAATACTATTAAGTCTCAATAAGTCTA
Found at i:48940 original size:21 final size:21
Alignment explanation
Indices: 48874--48941 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
48864 ATAAATCTAA
*
48874 AATAAATAACACCATAACACT
1 AATAAATAACACCATAATACT
* * *
48895 ATTAAAT--CTCAATAAGT-CT
1 AATAAATAACACCATAA-TACT
48914 AAAATAAATAACACCATAATACT
1 --AATAAATAACACCATAATACT
48937 AATAA
1 AATAA
48942 GTCTCGATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
19 8 0.24
21 17 0.50
22 1 0.03
23 8 0.24
ACGTcount: A:0.56, C:0.18, G:0.01, T:0.25
Consensus pattern (21 bp):
AATAAATAACACCATAATACT
Found at i:52613 original size:2 final size:2
Alignment explanation
Indices: 52606--52634 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52596 ACCTTCACCT
52606 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
52635 TCCATTTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:55880 original size:2 final size:2
Alignment explanation
Indices: 55873--55925 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
55863 CGGTTGAATT
55873 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
55915 TA TA TA TA TA T
1 TA TA TA TA TA T
55926 TAGGAAGTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60447 original size:20 final size:20
Alignment explanation
Indices: 60422--60480 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
60412 TACTCCTTTT
60422 AGTATCGATACCCAAGGTA-A
1 AGTATCGATACCCAA-GTAGA
*
60442 AGTATCGATACTCCTAA-TAGG
1 AGTATCGATAC-CC-AAGTAGA
60463 AGTATCGATACCCAAGTA
1 AGTATCGATACCCAAGTA
60481 TTTTTCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 13 0.38
22 2 0.06
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (20 bp):
AGTATCGATACCCAAGTAGA
Found at i:62058 original size:21 final size:21
Alignment explanation
Indices: 62018--62064 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
62008 CGATTTACAT
62018 ATTCGCATTGCGATAGTCCAA
1 ATTCGCATTGCGATAGTCCAA
* **
62039 GTTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGATAGTCCAA
62060 ATTCG
1 ATTCG
62065 ACTATCGCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTCGCATTGCGATAGTCCAA
Found at i:62163 original size:42 final size:41
Alignment explanation
Indices: 62109--62356 Score: 345
Period size: 42 Copynumber: 5.9 Consensus size: 41
62099 GATTTATATA
* *
62109 TTCGCATTGCGA-TAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAGTTCG--TTGCGATAGTCGAAG
*
62151 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
*
62193 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
62235 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
*
62277 TTCACGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
62319 TTCGCGTTGCAATTTATTCCAAATTCGTTGCGATAGTC
1 TTCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTC
62357 CAAAATCGCA
Statistics
Matches: 191, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
42 180 0.94
44 11 0.06
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
TTCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:62250 original size:84 final size:84
Alignment explanation
Indices: 62124--62359 Score: 418
Period size: 84 Copynumber: 2.8 Consensus size: 84
62114 ATTGCGATAG
62124 TCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCG--TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
* *
62189 GAAGTTCGCGTTGCGATTTAT
64 CAAGTTCACGTTGCGATTTAT
*
62210 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
62275 AGTTCACGTTGCGATTTAT
66 AGTTCACGTTGCGATTTAT
*
62294 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
62359 A
66 A
62360 AATCGCAACG
Statistics
Matches: 145, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
84 135 0.93
86 10 0.07
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (84 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
AGTTCACGTTGCGATTTAT
Found at i:63655 original size:21 final size:21
Alignment explanation
Indices: 63622--63672 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
63612 CGTATAATTA
*
63622 TAAATTAATTGAAAATTAAAGG
1 TAAATT-ATTGAAAATAAAAGG
63644 TAAATTATTGAAAATAAAAGG
1 TAAATTATTGAAAATAAAAGG
63665 TAAATTAT
1 TAAATTAT
63673 ATCAGTGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
TAAATTATTGAAAATAAAAGG
Found at i:65230 original size:2 final size:2
Alignment explanation
Indices: 65223--65256 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
65213 TAAGTGATTA
65223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65257 AATTTCTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:68482 original size:2 final size:2
Alignment explanation
Indices: 68477--68513 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
68467 GATGAATCCT
68477 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 T
68514 TTGGATCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68990 original size:60 final size:60
Alignment explanation
Indices: 68925--69057 Score: 178
Period size: 60 Copynumber: 2.2 Consensus size: 60
68915 AAATGCACAA
** * *
68925 ACATACTTACATTAATATAAT-TATGTGTTTATTTTTAGGTATCAAGATATTGAGAGATGT
1 ACATACTTACACCAATAT-ATGTATATGTTTATTTTTAGGTACCAAGATATTGAGAGATGT
* ** *
68985 GCATACTTACACCGGTGTATGTATATGTTTATTTTTAGGTACCAAGATATTGAGAGATGT
1 ACATACTTACACCAATATATGTATATGTTTATTTTTAGGTACCAAGATATTGAGAGATGT
69045 ACATACTTACACC
1 ACATACTTACACC
69058 GGTGTAAGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.03
60 61 0.97
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (60 bp):
ACATACTTACACCAATATATGTATATGTTTATTTTTAGGTACCAAGATATTGAGAGATGT
Found at i:69058 original size:60 final size:60
Alignment explanation
Indices: 68950--69068 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
68940 TATAATTATG
* * *
68950 TGTTTATTTTTAGGTATCAAGATATTGAGAGATGTGCATACTTACACCGGTGTATGTATA
1 TGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATA
69010 TGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTAT
1 TGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTAT
69069 GTATTAATTG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (60 bp):
TGTTTATTTTTAGGTACCAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATA
Found at i:71788 original size:24 final size:24
Alignment explanation
Indices: 71761--71808 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
71751 ATTTTCGGCC
*
71761 ATCAGCTGTTACACCATGAGCTCT
1 ATCAGCTATTACACCATGAGCTCT
*
71785 ATCAGCTATTACACCATGATCTCT
1 ATCAGCTATTACACCATGAGCTCT
71809 GCAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.31
Consensus pattern (24 bp):
ATCAGCTATTACACCATGAGCTCT
Found at i:71857 original size:3 final size:3
Alignment explanation
Indices: 71849--71930 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
71839 ATCCATCCTT
71849 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
71897 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
71931 GAACACCAGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:72111 original size:31 final size:31
Alignment explanation
Indices: 72047--72117 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
72037 CGTCAGATCG
* * *
72047 ATTTATTACAAATTGATAATTTCGGTGACTA
1 ATTTATTATAAATTAATAATTTCAGTGACTA
* *
72078 ATTTATTATAAATTAATAATTTTAGTGATTA
1 ATTTATTATAAATTAATAATTTCAGTGACTA
*
72109 ATTTGTTAT
1 ATTTATTAT
72118 TTTTAAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTTATTATAAATTAATAATTTCAGTGACTA
Found at i:79496 original size:185 final size:184
Alignment explanation
Indices: 79184--79550 Score: 626
Period size: 185 Copynumber: 2.0 Consensus size: 184
79174 TAATTTTTAA
* * *
79184 ATATATTATATATAACATATGGGTTCAGCCCAAACCATTTAAAATCCAATTAACAATTTAAGATC
1 ATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAACAATTTAAGATC
*
79249 TAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTAT
66 CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTAT
*
79314 AATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAAAAATATTAT
131 AATTATATATTATTTAAATTAATTATAAACT-TTTTTTTAATTAAAAAATATTAT
* *
79369 ATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAATAATTTAAGATC
1 ATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAACAATTTAAGATC
* * * *
79434 CAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAATTTATCTGAAATTTTTATTTTAT
66 CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTAT
79499 AATTATATATTATTTAAATTAATTATAAACTTTTTTTTAATTAAAAAATATT
131 AATTATATATTATTTAAATTAATTATAAACTTTTTTTTAATTAAAAAATATT
79551 TAATTTTTAT
Statistics
Matches: 171, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
184 21 0.12
185 150 0.88
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (184 bp):
ATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAACAATTTAAGATC
CAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATTTTAT
AATTATATATTATTTAAATTAATTATAAACTTTTTTTTAATTAAAAAATATTAT
Found at i:80342 original size:24 final size:24
Alignment explanation
Indices: 80315--80366 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
80305 TTTATTAAAC
* *
80315 TAAATACTTTCGAAT-ATTTGATAA
1 TAAATAATTTC-AATCATTTGACAA
*
80339 TAAATAATTTCAATCTTTTGACAA
1 TAAATAATTTCAATCATTTGACAA
80363 TAAA
1 TAAA
80367 CGTTCAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (24 bp):
TAAATAATTTCAATCATTTGACAA
Found at i:84070 original size:21 final size:21
Alignment explanation
Indices: 84044--84088 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
84034 GATTTCTGGG
* *
84044 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
84065 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
84086 CAA
1 CAA
84089 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:84572 original size:2 final size:2
Alignment explanation
Indices: 84565--84593 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
84555 CATGAGTTAG
84565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
84594 GGAATTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85636 original size:6 final size:6
Alignment explanation
Indices: 85626--85655 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
85616 TTAATTGCAA
*
85626 AAATTA AAATTT AAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
85656 TAAAACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:87449 original size:10 final size:10
Alignment explanation
Indices: 87418--87455 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
87408 TAAATGTAGA
87418 ATTATATAAT
1 ATTATATAAT
*
87428 AATATATAAT
1 ATTATATAAT
87438 ATTATATAAT
1 ATTATATAAT
87448 ATTA-ATAA
1 ATTATATAA
87456 CGACGGACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTATATAAT
Found at i:87571 original size:32 final size:32
Alignment explanation
Indices: 87530--87626 Score: 126
Period size: 32 Copynumber: 3.1 Consensus size: 32
87520 GAGTCGAGGG
87530 TTTACCTATGTTTTACGAAACATATGGACAGT
1 TTTACCTATGTTTTACGAAACATATGGACAGT
*
87562 TTTACCTATGTCTTT-CGAGACATATGGACAG-
1 TTTACCTATGT-TTTACGAAACATATGGACAGT
* * * *
87593 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTTTACGAAACATATGGACAGT
87625 TT
1 TT
87627 ACCAAGGATC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
30 2 0.04
31 23 0.42
32 27 0.49
33 3 0.05
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTTTACGAAACATATGGACAGT
Found at i:87665 original size:30 final size:30
Alignment explanation
Indices: 87617--87710 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
87607 AAGGAACATA
*
87617 TGGACAGTTTACCAAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
87648 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
87678 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
87707 TGGA
1 TGGA
87711 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.29
30 34 0.59
31 7 0.12
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:97851 original size:29 final size:30
Alignment explanation
Indices: 97801--97860 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
97791 TGAATTTTTT
97801 TTGAGTTGATTCGAGTTTATAAAATTTGAG
1 TTGAGTTGATTCGAGTTTATAAAATTTGAG
97831 TTGAGTTG-TTCGAGTTTATAAAATTTGAG
1 TTGAGTTGATTCGAGTTTATAAAATTTGAG
97860 T
1 T
97861 CGTGTCAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.45
Consensus pattern (30 bp):
TTGAGTTGATTCGAGTTTATAAAATTTGAG
Found at i:103905 original size:99 final size:99
Alignment explanation
Indices: 103732--104141 Score: 669
Period size: 99 Copynumber: 4.1 Consensus size: 99
103722 CAGACTCCGA
* *
103732 AAGAAAAGGCTAAAGGGAAGAAGGAGGTCGAGGCATTGCCGCCATTGAAGCAACAAGAAGAAATA
1 AAGAAAAGGCTAAAGGG-A-AA-GAGGTTGAGGCATTGCCGTCATTGAAGCAACAAGAAGAAATA
*
103797 CAAAGGAAGGTTTCTCCCACCGCAAAGCAAACCAG-AA
63 CAAAGGAAGGTTTCTCCCACCGCAAAGCAAACC-GTAG
103834 AAGAAAAGGCTAAAGGGAAAGAGGTTGAGGCATTGCCGTCATTGAAGCAACAAGAAGAAATACAA
1 AAGAAAAGGCTAAAGGGAAAGAGGTTGAGGCATTGCCGTCATTGAAGCAACAAGAAGAAATACAA
* *
103899 AGGAAGGTTTCTCCCCCCGCAAAGCAAACCGTGG
66 AGGAAGGTTTCTCCCACCGCAAAGCAAACCGTAG
103933 AAGAAAAGGCTAAAGGGAAAGAGGTTGAGGCATTGCCGTCATTGAAGCAACAAGAAGAAATACAA
1 AAGAAAAGGCTAAAGGGAAAGAGGTTGAGGCATTGCCGTCATTGAAGCAACAAGAAGAAATACAA
* *
103998 AGGAAGGTTTCTCCCCCCGCAAAGCAAACCGTGG
66 AGGAAGGTTTCTCCCACCGCAAAGCAAACCGTAG
* * *
104032 AAGAAAAGGCTAAAGGGAAGGAGATTGAGGCATTGCCGTCATTGAAGCAACAAGAGGAAATACAA
1 AAGAAAAGGCTAAAGGGAAAGAGGTTGAGGCATTGCCGTCATTGAAGCAACAAGAAGAAATACAA
* *
104097 AGGAAGGTTTCTCCCACAGCAAAGCAAACCGGAG
66 AGGAAGGTTTCTCCCACCGCAAAGCAAACCGTAG
104131 AAGAAAAGGCT
1 AAGAAAAGGCT
104142 GACGGATCTA
Statistics
Matches: 295, Mismatches: 12, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
98 1 0.00
99 274 0.93
100 2 0.01
101 1 0.00
102 17 0.06
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (99 bp):
AAGAAAAGGCTAAAGGGAAAGAGGTTGAGGCATTGCCGTCATTGAAGCAACAAGAAGAAATACAA
AGGAAGGTTTCTCCCACCGCAAAGCAAACCGTAG
Found at i:109792 original size:2 final size:2
Alignment explanation
Indices: 109785--109900 Score: 232
Period size: 2 Copynumber: 58.0 Consensus size: 2
109775 TATAATGTTA
109785 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
109827 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
109869 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
109901 GCTTAGAATC
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 114 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110060 original size:3 final size:3
Alignment explanation
Indices: 110052--110111 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
110042 CCATATTGAT
* *
110052 TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
110100 TTA TTA TTA TTA
1 TTA TTA TTA TTA
110112 AATATATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:110134 original size:21 final size:20
Alignment explanation
Indices: 110110--110160 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
110100 TTATTATTAT
*
110110 TAAATATATTAAATGCATATA
1 TAAATATATTAAAT-AATATA
*
110131 TAAATAATAATAAATAATATA
1 TAAAT-ATATTAAATAATATA
*
110152 TATATATAT
1 TAAATATAT
110161 ATATACAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 14 0.56
22 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAATATATTAAATAATATA
Found at i:111540 original size:13 final size:13
Alignment explanation
Indices: 111524--111563 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
111514 ATATAATAAA
111524 TAAATATTTATTT
1 TAAATATTTATTT
*
111537 TAAATAAATTATTT
1 TAAAT-ATTTATTT
111551 T-AATATTTATTT
1 TAAATATTTATTT
111563 T
1 T
111564 TCAATATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:122839 original size:9 final size:9
Alignment explanation
Indices: 122825--122921 Score: 90
Period size: 9 Copynumber: 10.1 Consensus size: 9
122815 ATGCTTGAAG
122825 AAAAGAAAA
1 AAAAGAAAA
122834 AAAAGAAAAA
1 AAAAG-AAAA
122844 GAAAAGAGAGAA
1 -AAAAGA-A-AA
122856 AAGAA-AAAGA
1 AA-AAGAAA-A
*
122866 AAAAAAAAA
1 AAAAGAAAA
122875 AAAAGAAAA
1 AAAAGAAAA
122884 AAAAGAAAAA
1 AAAAG-AAAA
122894 AAAAGAAAA
1 AAAAGAAAA
122903 AGAAA-AAAA
1 A-AAAGAAAA
*
122912 AAAGGAAAA
1 AAAAGAAAA
122921 A
1 A
122922 TGAGGGGTCA
Statistics
Matches: 76, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
8 2 0.03
9 37 0.49
10 24 0.32
11 9 0.12
12 4 0.05
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:122842 original size:6 final size:6
Alignment explanation
Indices: 122833--122921 Score: 96
Period size: 6 Copynumber: 14.8 Consensus size: 6
122823 AGAAAAGAAA
122833 AAAAAG AAAAAG AAAAGAG AGAAAAG AAAAAG -AAAA- AAAAA- AAAAAG
1 AAAAAG AAAAAG AAAA-AG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
122880 AAAAAA AAGAAAA AAAAAG AAAAAG AAAAA- AAAAAGG AAAAA
1 AAAAAG AA-AAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA
122922 TGAGGGGTCA
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
5 18 0.24
6 36 0.49
7 17 0.23
8 3 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:122845 original size:15 final size:15
Alignment explanation
Indices: 122825--122914 Score: 105
Period size: 15 Copynumber: 6.1 Consensus size: 15
122815 ATGCTTGAAG
122825 AAAAGAAAAA-AAAGA
1 AAAAGAAAAAGAAA-A
* *
122840 AAAAG-AAAAGAGAG
1 AAAAGAAAAAGAAAA
122854 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
*
122869 AAAAAAAAAAGAAAA
1 AAAAGAAAAAGAAAA
*
122884 AAAAGAAAAAAAAAGA
1 AAAAGAAAAAGAAA-A
122900 AAAAGAAAAA-AAAA
1 AAAAGAAAAAGAAAA
122914 A
1 A
122915 GGAAAAATGA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.17
15 43 0.66
16 11 0.17
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:122847 original size:20 final size:20
Alignment explanation
Indices: 122822--122914 Score: 120
Period size: 20 Copynumber: 4.7 Consensus size: 20
122812 ATTATGCTTG
122822 AAGAAAAGAAAAAAAAGAAA
1 AAGAAAAGAAAAAAAAGAAA
* *
122842 AAGAAAAGAGAGAAAAGAAA
1 AAGAAAAGAAAAAAAAGAAA
122862 AAGAAAA-AAAAAAAA-AAGA
1 AAGAAAAGAAAAAAAAGAA-A
*
122881 AAAAAAAGAAAAAAAAAGAAA
1 AAGAAAAG-AAAAAAAAGAAA
122902 AAGAAAA-AAAAAA
1 AAGAAAAGAAAAAA
122915 GGAAAAATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.03
19 19 0.30
20 25 0.40
21 15 0.24
22 2 0.03
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAGAAAAGAAAAAAAAGAAA
Found at i:122866 original size:35 final size:34
Alignment explanation
Indices: 122825--122913 Score: 133
Period size: 35 Copynumber: 2.6 Consensus size: 34
122815 ATGCTTGAAG
* * *
122825 AAAAGAAAAAAAAGAAAAAGAAAAGAGAGAAAAGA
1 AAAAGAAAAAAAAAAAAAAGAAAAAAAAGAAAA-A
122860 AAAAGAAAAAAAAAAAAAAGAAAAAAAAGAAAAA
1 AAAAGAAAAAAAAAAAAAAGAAAAAAAAGAAAAA
122894 AAAAGAAAAAGAAAAAAAAA
1 AAAAGAAAAA-AAAAAAAAA
122914 AGGAAAAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
34 11 0.22
35 39 0.78
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (34 bp):
AAAAGAAAAAAAAAAAAAAGAAAAAAAAGAAAAA
Found at i:122867 original size:40 final size:35
Alignment explanation
Indices: 122822--122914 Score: 116
Period size: 36 Copynumber: 2.5 Consensus size: 35
122812 ATTATGCTTG
122822 AAGAAAAGAAAAAAAAGAAAAAGAAAAGAGAGAAAAGAAA
1 AAGAAAAGAAAAAAAA-AAAAA-AAAA-A-AGAAAA-AAA
*
122862 AAGAAAA-AAAAAAAAAAGAAAAAAAAGAAAAAAA
1 AAGAAAAGAAAAAAAAAAAAAAAAAAAGAAAAAAA
122896 AAGAAAAAGAAAAAAAAAA
1 AAG-AAAAGAAAAAAAAAA
122915 GGAAAAATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
34 6 0.12
35 10 0.20
36 11 0.22
37 4 0.08
38 4 0.08
39 8 0.16
40 7 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (35 bp):
AAGAAAAGAAAAAAAAAAAAAAAAAAAGAAAAAAA
Found at i:122921 original size:1 final size:1
Alignment explanation
Indices: 122825--122914 Score: 72
Period size: 1 Copynumber: 90.0 Consensus size: 1
122815 ATGCTTGAAG
* * * * * * * * * *
122825 AAAAGAAAAAAAAGAAAAAGAAAAGAGAGAAAAGAAAAAGAAAAAAAAAAAAAAGAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
122890 AAAAAAAAGAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
122915 GGAAAAATGA
Statistics
Matches: 65, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:125141 original size:113 final size:113
Alignment explanation
Indices: 124943--125541 Score: 875
Period size: 113 Copynumber: 5.3 Consensus size: 113
124933 GAATCCATAA
124943 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
125008 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCACT
66 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCACT
*
125056 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATATGAAGAAGGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
125121 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTCATCACT
66 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCACT
* *
125169 TGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAG-A
* * * *
125233 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCCATCATT
65 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCAT-GAATTCATCACT
* *
125282 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAA
1 TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* ** *
125347 GTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATT
66 GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCACT
* * * * * *
125395 TGATGGATCAACATTGCCAG-GTAGAGTTCCTAATAAGAAGAACTCGTCATCTAAAGAAGGAAGA
1 TGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATAAGAAGAA--C-TCATCTGAAGAAGGAAGA
* *
125459 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCA--AATCCATCACT
62 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG--CATGAATTCATCACT
*
125511 TGATGGATCAGCTTTTCCAGTGGAAAGTTCA
1 TGATGGATCAGCTTTTCCAG-AGAAAGTTCA
125542 GCTTGTTCAA
Statistics
Matches: 439, Mismatches: 35, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
112 4 0.01
113 347 0.79
114 3 0.01
115 1 0.00
116 77 0.18
117 6 0.01
118 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (113 bp):
TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAA
GTTCATAATGAGAAGAACTTGTTCAACCTTTTGCATGAATTCATCACT
Found at i:125798 original size:3 final size:3
Alignment explanation
Indices: 125792--125869 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
125782 CCATATTGAT
*
125792 TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
125840 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
125870 AATATATTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:125892 original size:21 final size:20
Alignment explanation
Indices: 125868--125918 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
125858 TTATTATTAT
*
125868 TAAATATATTAAATGCATATA
1 TAAATATATTAAAT-AATATA
*
125889 TAAATAATAATAAATAATATA
1 TAAAT-ATATTAAATAATATA
*
125910 TATATATAT
1 TAAATATAT
125919 ACAAGCCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 14 0.56
22 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAATATATTAAATAATATA
Found at i:127002 original size:30 final size:28
Alignment explanation
Indices: 126968--127023 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
126958 TATATTTAAG
126968 ATAAATAACAGATTTAATCCCTTAGTTTTA
1 ATAAATAACA-ATTTAATCCC-TAGTTTTA
* *
126998 ATAAATAATATTTTAATCCCTAGTTT
1 ATAAATAACAATTTAATCCCTAGTTT
127024 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.25
29 9 0.38
30 9 0.38
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.43
Consensus pattern (28 bp):
ATAAATAACAATTTAATCCCTAGTTTTA
Found at i:127298 original size:13 final size:13
Alignment explanation
Indices: 127282--127321 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
127272 ATATAATAAA
127282 TAAATATTTATTT
1 TAAATATTTATTT
*
127295 TAAATAAATTATTT
1 TAAAT-ATTTATTT
127309 T-AATATTTATTT
1 TAAATATTTATTT
127321 T
1 T
127322 TCAATATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:133734 original size:215 final size:215
Alignment explanation
Indices: 133363--133775 Score: 673
Period size: 215 Copynumber: 1.9 Consensus size: 215
133353 ACTTAGATAT
* * * * * *
133363 TTCTCTTGCTTTTGTCTCCATCTCCATCTTCTTAGCACAACGCAAAGCTCTTGTTGCAACTCAAT
1 TTCTCTTGCTTTTGTCGCCATCTCCATCTTCGTAGCACAACGCAAAACCCTTGTGGAAACTCAAT
* * *
133428 TTTGCTTATCTTATTTTGTACGGTGCACCCATCTCTTTTCCATGTAATAAGCACCCATCCGTTGC
66 TTTGCTTATCTTATTTTGTACGGTGCACCCAGCTCCTTTCCATGTAATAAGCACCCATCCATTGC
* *
133493 CATCGAATTGAAATAAGGAGTAGCACTTTGTCAGAATCATAAATCACTATTTCTTCTTTCGGTTT
131 CATCGAATTGAAATAAGGAGTAGCACTTTGTCAGAATAATAAAACACTATTTCTTCTTTCGGTTT
133558 GTTTCAACAGAACTAGATCC
196 GTTTCAACAGAACTAGATCC
*
133578 TTCTCTTGCTTTTGTCGCCATCTCCATCTTCGTAGCACAAGGCAAAACCCTTGTGGAAACTCAAT
1 TTCTCTTGCTTTTGTCGCCATCTCCATCTTCGTAGCACAACGCAAAACCCTTGTGGAAACTCAAT
* * * *
133643 TTTGTTTTTCTTATTTTGTACGGTGCACCCAGCTCCTTTCCATGTAATAAGCACCGATCCATTGT
66 TTTGCTTATCTTATTTTGTACGGTGCACCCAGCTCCTTTCCATGTAATAAGCACCCATCCATTGC
*
133708 CATCGAATTGAAATAAGGAGTAGCACTTTGTCAGAATAATAAAACACTATTTTTTCTTTCGGTTT
131 CATCGAATTGAAATAAGGAGTAGCACTTTGTCAGAATAATAAAACACTATTTCTTCTTTCGGTTT
133773 GTT
196 GTT
133776 CCATATTTTT
Statistics
Matches: 181, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
215 181 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (215 bp):
TTCTCTTGCTTTTGTCGCCATCTCCATCTTCGTAGCACAACGCAAAACCCTTGTGGAAACTCAAT
TTTGCTTATCTTATTTTGTACGGTGCACCCAGCTCCTTTCCATGTAATAAGCACCCATCCATTGC
CATCGAATTGAAATAAGGAGTAGCACTTTGTCAGAATAATAAAACACTATTTCTTCTTTCGGTTT
GTTTCAACAGAACTAGATCC
Found at i:141366 original size:10 final size:10
Alignment explanation
Indices: 141351--141375 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
141341 GAAGGTAAAA
141351 ATTATTTTTT
1 ATTATTTTTT
141361 ATTATTTTTT
1 ATTATTTTTT
141371 ATTAT
1 ATTAT
141376 ATTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:144819 original size:46 final size:48
Alignment explanation
Indices: 144765--144888 Score: 182
Period size: 46 Copynumber: 2.6 Consensus size: 48
144755 CAATCCAAAC
** *
144765 AATTAAATAATAAAAACATTAAGAAATTAAATAAAT-AA-AAGTCCAT
1 AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAATAAATCCAT
*
144811 AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAATAAATCCAT
1 AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAATAAATCCAT
*
144859 AATTAAATAAAAAAAACATTAAGAAA-AAAA
1 AATTAAATAATAAAAACATTAAGAAACAAAA
144889 GTCCATAATT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
46 33 0.47
47 6 0.09
48 31 0.44
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (48 bp):
AATTAAATAATAAAAACATTAAGAAACAAAATAAATAAATAAATCCAT
Found at i:144902 original size:48 final size:46
Alignment explanation
Indices: 144765--144902 Score: 154
Period size: 48 Copynumber: 2.9 Consensus size: 46
144755 CAATCCAAAC
** *
144765 AATTAAATAATAAAAACATTAAGAAATTAAATA-AATAAAAGTCCAT
1 AATTAAATAATAAAAACATTAAGAAACAAAATATAATTAAA-TCCAT
* *
144811 AATTAAATAATAAAAATATTAAGAAACAAAATAAATAAATAAATCCAT
1 AATTAAATAATAAAAACATTAAGAAACAAAAT--ATAATTAAATCCAT
*
144859 AATTAAATAAAAAAAACATTAAGAAA-AAAAGTCCATAATTAAAT
1 AATTAAATAATAAAAACATTAAGAAACAAAA-T--ATAATTAAAT
144903 AAAAAATATT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
46 29 0.37
47 4 0.05
48 40 0.51
49 5 0.06
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.25
Consensus pattern (46 bp):
AATTAAATAATAAAAACATTAAGAAACAAAATATAATTAAATCCAT
Found at i:144906 original size:20 final size:19
Alignment explanation
Indices: 144842--144909 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
144832 AGAAACAAAA
144842 TAAATAAATAAATCCATAAT
1 TAAATAAA-AAATCCATAAT
144862 TAAATAAAAAA---A-ACAT
1 TAAATAAAAAATCCATA-AT
144878 TAAGA-AAAAAAGTCCATAAT
1 TAA-ATAAAAAA-TCCATAAT
144898 TAAATAAAAAAT
1 TAAATAAAAAAT
144910 ATTAAGAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 17
0.70 0.00 0.30
Matches are distributed among these distances:
15 1 0.03
16 12 0.30
17 1 0.03
19 5 0.12
20 20 0.50
21 1 0.03
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.24
Consensus pattern (19 bp):
TAAATAAAAAATCCATAAT
Found at i:144914 original size:34 final size:36
Alignment explanation
Indices: 144854--144923 Score: 108
Period size: 34 Copynumber: 2.0 Consensus size: 36
144844 AATAAATAAA
144854 TCCATAATTAAATAAAAAAAACATTAAGAAA-AAAAG
1 TCCATAATTAAAT-AAAAAAACATTAAGAAACAAAAG
*
144890 TCCATAATTAAAT-AAAAAATATTAAGAAACAAAA
1 TCCATAATTAAATAAAAAAACATTAAGAAACAAAA
144924 TAAATAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 15 0.47
35 4 0.12
36 13 0.41
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (36 bp):
TCCATAATTAAATAAAAAAACATTAAGAAACAAAAG
Found at i:144971 original size:43 final size:44
Alignment explanation
Indices: 144884--144976 Score: 161
Period size: 43 Copynumber: 2.1 Consensus size: 44
144874 ACATTAAGAA
*
144884 AAAAAGTCCATAATTAAATAAAAAATATTAAGAAACAAAATAAAT
1 AAAAAGTCCATAATTAAAT-AAAAACATTAAGAAACAAAATAAAT
144929 AAAAAGTCCATAATTAAAT-AAAACATTAAGAAACAAAATAAAT
1 AAAAAGTCCATAATTAAATAAAAACATTAAGAAACAAAATAAAT
144972 AAAAA
1 AAAAA
144977 CAAGTCTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 28 0.60
45 19 0.40
ACGTcount: A:0.68, C:0.08, G:0.04, T:0.20
Consensus pattern (44 bp):
AAAAAGTCCATAATTAAATAAAAACATTAAGAAACAAAATAAAT
Found at i:145450 original size:21 final size:21
Alignment explanation
Indices: 145375--145451 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
145365 ACCTTGCAGT
* * *
145375 GGTGGCATCTAAAATGGTTGT
1 GGTGGCATCTGAAATAGTTGC
* *
145396 GGTGGCATC-GAAAATTGTTAC
1 GGTGGCATCTG-AAATAGTTGC
* * *
145417 GGTGCCTTTTGAAATAGTTGC
1 GGTGGCATCTGAAATAGTTGC
145438 GGTGGCATCTGAAA
1 GGTGGCATCTGAAA
145452 GGGCTGTGGA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (21 bp):
GGTGGCATCTGAAATAGTTGC
Found at i:146029 original size:27 final size:25
Alignment explanation
Indices: 145998--146047 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
145988 GAGATAACTA
145998 AATATAAATAATATTCTTATCAAAACC
1 AATATAAAT-A-ATTCTTATCAAAACC
*
146025 AATATATATAATTCTTATCAAAA
1 AATATAAATAATTCTTATCAAAA
146048 TAATATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 1 0.05
27 8 0.36
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (25 bp):
AATATAAATAATTCTTATCAAAACC
Found at i:146044 original size:25 final size:23
Alignment explanation
Indices: 146010--146060 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
146000 TATAAATAAT
146010 ATTCTTATCAAAACCAATATATATA
1 ATTCTTATCAAAA-CAATAT-TATA
*
146035 ATTCTTATCAAAATAATATTATA
1 ATTCTTATCAAAACAATATTATA
146058 ATT
1 ATT
146061 ATATAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.28
24 5 0.20
25 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTCTTATCAAAACAATATTATA
Found at i:162246 original size:21 final size:21
Alignment explanation
Indices: 162195--162268 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
162185 CGGCTTCGAT
* * *
162195 CATATGGGGATCTCTCATGAA
1 CATATGGGGATATCTCAAGAG
** * *
162216 CATACAGGGATATATCACGAG
1 CATATGGGGATATCTCAAGAG
*
162237 CATATGGGGATTTCTCAAGAG
1 CATATGGGGATATCTCAAGAG
*
162258 TATATGGGGAT
1 CATATGGGGAT
162269 CTGTCCCATG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (21 bp):
CATATGGGGATATCTCAAGAG
Found at i:163530 original size:27 final size:27
Alignment explanation
Indices: 163492--163548 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
163482 GCGGCAGCTT
*
163492 CTGTTGTGGTTCCGGTTGCTTCTGCTG
1 CTGTTGTGGTTCAGGTTGCTTCTGCTG
*
163519 CTGTTGTGGTTCATGTTGCTTCTGCTG
1 CTGTTGTGGTTCAGGTTGCTTCTGCTG
163546 CTG
1 CTG
163549 CTGTTGTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.02, C:0.21, G:0.32, T:0.46
Consensus pattern (27 bp):
CTGTTGTGGTTCAGGTTGCTTCTGCTG
Found at i:166064 original size:18 final size:19
Alignment explanation
Indices: 166041--166077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
166031 TCAGTAATCC
166041 TATTCCC-TGATAATCTTT
1 TATTCCCATGATAATCTTT
166059 TATTCCCATTGATAATCTT
1 TATTCCCA-TGATAATCTT
166078 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTCCCATGATAATCTTT
Found at i:166613 original size:17 final size:17
Alignment explanation
Indices: 166591--166624 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
166581 ACCTTCCAAC
166591 TATGAAAATAAGAATTT
1 TATGAAAATAAGAATTT
166608 TATGAAAATAAGAATTT
1 TATGAAAATAAGAATTT
166625 AATATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
TATGAAAATAAGAATTT
Found at i:177155 original size:21 final size:21
Alignment explanation
Indices: 177129--177171 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
177119 AAGAGAGTAT
177129 TTGTTCAAAGATAACTCTCAA
1 TTGTTCAAAGATAACTCTCAA
177150 TTGTTCAAAGATAACTCTCAA
1 TTGTTCAAAGATAACTCTCAA
177171 T
1 T
177172 CTTTTAACAT
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:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
TTGTTCAAAGATAACTCTCAA
Found at i:180920 original size:15 final size:15
Alignment explanation
Indices: 180885--180929 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
180875 TCACAAATTT
*
180885 TAATGTTATAAT-TA
1 TAATATTATAATATA
*
180899 TATTATTATAATATA
1 TAATATTATAATATA
*
180914 TAATATTATATTATA
1 TAATATTATAATATA
180929 T
1 T
180930 TTTAATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TAATATTATAATATA
Found at i:180935 original size:18 final size:19
Alignment explanation
Indices: 180914--180957 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
180904 TTATAATATA
* *
180914 TAATATTATATTATATT-T
1 TAATATTATATCAGATTAT
*
180932 TAATAATATATCAGATTAT
1 TAATATTATATCAGATTAT
180951 TAATATT
1 TAATATT
180958 TAAAATATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTATATCAGATTAT
Found at i:180937 original size:28 final size:28
Alignment explanation
Indices: 180885--180966 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
180875 TCACAAATTT
*
180885 TAATGTTATAATTATATTATT-ATAATATA
1 TAATATTAT-ATTATATT-TTAATAATATA
180914 TAATATTATATTATATTTTAATAATATA
1 TAATATTATATTATATTTTAATAATATA
* * *
180942 TCAGATTAT-TAATA-TTTAA-AATATA
1 TAATATTATATTATATTTTAATAATATA
180967 CTCTTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.12
26 5 0.10
27 6 0.12
28 23 0.48
29 8 0.17
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (28 bp):
TAATATTATATTATATTTTAATAATATA
Found at i:181033 original size:17 final size:17
Alignment explanation
Indices: 181003--181063 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
180993 TTTTTTTGAT
*
181003 ATAATTTTAATATTTTA
1 ATAATATTAATATTTTA
*
181020 ATAATATTACTATTTTA
1 ATAATATTAATATTTTA
* *
181037 ATAAGTGACTAATATAATTA
1 ATAA-T-ATTAATAT-TTTA
181057 ATAATAT
1 ATAATAT
181064 ATTATTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 19 0.54
18 2 0.06
19 7 0.20
20 7 0.20
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
ATAATATTAATATTTTA
Found at i:181077 original size:42 final size:43
Alignment explanation
Indices: 181030--181114 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
181020 ATAATATTAC
* *
181030 TATTTTAATAAGTGACTAATATAATTAATAAT-ATATTATTTT
1 TATTTTAATAAATAACTAATATAATTAATAATAATATTATTTT
* * *
181072 TATTTTAATAAATAATTAATATAATTTATAATAATTTTATTTT
1 TATTTTAATAAATAACTAATATAATTAATAATAATATTATTTT
181115 AATAAGATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 28 0.76
43 9 0.24
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (43 bp):
TATTTTAATAAATAACTAATATAATTAATAATAATATTATTTT
Found at i:181092 original size:33 final size:34
Alignment explanation
Indices: 181050--181146 Score: 101
Period size: 37 Copynumber: 2.8 Consensus size: 34
181040 AGTGACTAAT
*
181050 ATAATTAATAATATATTATTTTTATTTTAATAA-
1 ATAATTAATAATATAATATTTTTATTTTAATAAG
*
181083 ATAATTAATATAATTTATAATAATTTTATTTTAATAAG
1 ATAATT-A-ATAA--TATAATATTTTTATTTTAATAAG
*
181121 AT-A-TAATAATCATAATATTTGTATTT
1 ATAATTAATAAT-ATAATATTTTTATTT
181147 AGAAAATTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
32 1 0.02
33 19 0.35
34 5 0.09
35 5 0.09
36 1 0.02
37 21 0.39
38 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (34 bp):
ATAATTAATAATATAATATTTTTATTTTAATAAG
Found at i:186096 original size:62 final size:64
Alignment explanation
Indices: 185952--186100 Score: 266
Period size: 64 Copynumber: 2.4 Consensus size: 64
185942 AATTAGTATA
* *
185952 ATTTTTTAAAATAGGTAGTATTTGATTGGTCAAATTCTATCCTTAATATATTTATATTGCAATT
1 ATTTTTGAAAATAGGTAGTATTTGATTGGTCAAATTCTATACTTAATATATTTATATTGCAATT
186016 ATTTTTGAAAATAGGTAGTATTTGATTGGTCAAATTCTATACTT-A-ATATTTATATTGCAATT
1 ATTTTTGAAAATAGGTAGTATTTGATTGGTCAAATTCTATACTTAATATATTTATATTGCAATT
186078 ATTTTTGAAAATAGGTAGTATTT
1 ATTTTTGAAAATAGGTAGTATTT
186101 AGTTCCAGCA
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
62 40 0.48
63 1 0.01
64 42 0.51
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (64 bp):
ATTTTTGAAAATAGGTAGTATTTGATTGGTCAAATTCTATACTTAATATATTTATATTGCAATT
Found at i:190071 original size:24 final size:24
Alignment explanation
Indices: 190042--190091 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
190032 TAATTTTTAT
190042 TTATTTATTTTAAAATATTATAAA
1 TTATTTATTTTAAAATATTATAAA
* *
190066 TTATTTATTTTAAATTTTTATAAA
1 TTATTTATTTTAAAATATTATAAA
190090 TT
1 TT
190092 CATCTTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATTTATTTTAAAATATTATAAA
Done.