Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005256.1 Hibiscus syriacus cultivar Beakdansim tig00011893_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: 84364
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:2388 original size:11 final size:11
Alignment explanation
Indices: 2347--2393 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
2337 GTTAGATCGT
2347 AAAAATAAA-A
1 AAAAATAAATA
*
2357 ATAAATAAAT-
1 AAAAATAAATA
*
2367 AAATATGAAATA
1 AAAAAT-AAATA
2379 AAAAATAAATA
1 AAAAATAAATA
2390 AAAA
1 AAAA
2394 GGTTAAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
10 12 0.40
11 13 0.43
12 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:2890 original size:17 final size:18
Alignment explanation
Indices: 2868--2902 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2858 TCATTTTTAA
2868 CCAAACC-CAAAAAAACC
1 CCAAACCTCAAAAAAACC
*
2885 CCAAACCTCTAAAAAACC
1 CCAAACCTCAAAAAAACC
2903 TCTCAACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.40, G:0.00, T:0.06
Consensus pattern (18 bp):
CCAAACCTCAAAAAAACC
Found at i:3759 original size:3 final size:3
Alignment explanation
Indices: 3751--3836 Score: 77
Period size: 3 Copynumber: 26.7 Consensus size: 3
3741 CCCTAAAAGA
*
3751 AAT AAT AAT AACT AAA AAT AA- ATAT AAT GAAT AAT AAT AAT ATAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT A-AT AAT -AAT AAT AAT AAT A-AT AAT
3799 ATAT AAT AAAT AA- ATAT AAT GAAT AAT AAT AAT AAT AA
1 A-AT AAT -AAT AAT A-AT AAT -AAT AAT AAT AAT AAT AA
3837 ATATATTAAC
Statistics
Matches: 71, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
2 2 0.03
3 49 0.69
4 20 0.28
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3773 original size:20 final size:20
Alignment explanation
Indices: 3745--3836 Score: 79
Period size: 20 Copynumber: 4.7 Consensus size: 20
3735 TTTAGACCCT
*
3745 AAAAGAAATAATAAT-AACTA
1 AAAATAAATAATAATGAA-TA
3765 AAAATAAAT-ATAATGAATA
1 AAAATAAATAATAATGAATA
*
3784 ATAAT-AATATATAAT-ATATA
1 AAAATAAATA-ATAATGA-ATA
3804 ATAAATAAAT-ATAATGAATA
1 A-AAATAAATAATAATGAATA
*
3824 ATAAT-AATAATAA
1 AAAATAAATAATAA
3837 ATATATTAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.10
19 19 0.32
20 28 0.47
21 4 0.07
22 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATAAATAATAATGAATA
Found at i:3783 original size:13 final size:12
Alignment explanation
Indices: 3752--3841 Score: 80
Period size: 13 Copynumber: 7.2 Consensus size: 12
3742 CCTAAAAGAA
*
3752 ATAATAATAACT
1 ATAATAATAAAT
3764 A-AA-AATAAAT
1 ATAATAATAAAT
3774 ATAATGAAT-AAT
1 ATAAT-AATAAAT
3786 AATAATATATAATAT
1 -ATAATA-ATAA-AT
3801 ATAATAAATAAAT
1 ATAAT-AATAAAT
3814 ATAATGAAT-AAT
1 ATAAT-AATAAAT
3826 AATAATAATAAAT
1 -ATAATAATAAAT
3839 ATA
1 ATA
3842 TTAACAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
10 7 0.11
11 4 0.06
12 14 0.21
13 28 0.42
14 10 0.15
15 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:3813 original size:40 final size:38
Alignment explanation
Indices: 3751--3842 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 38
3741 CCCTAAAAGA
3751 AATAATAATA-ACTAAAAATAAATATAATGAATAATAAT
1 AATAATAATATA-TAAAAATAAATATAATGAATAATAAT
3789 AATATATAATATATAATAAATAAATATAATGAATAATAAT
1 AATA-ATAATATATAA-AAATAAATATAATGAATAATAAT
3829 AATAATAAATATAT
1 AATAAT-AATATAT
3843 TAACAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
38 4 0.08
39 11 0.22
40 35 0.70
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (38 bp):
AATAATAATATATAAAAATAAATATAATGAATAATAAT
Found at i:3876 original size:11 final size:12
Alignment explanation
Indices: 3849--3876 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3839 ATATTAACAA
3849 AAAAATGTTTTC
1 AAAAATGTTTTC
3861 AAAAATGTTTTC
1 AAAAATGTTTTC
3873 AAAA
1 AAAA
3877 CCCATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (12 bp):
AAAAATGTTTTC
Found at i:3925 original size:34 final size:35
Alignment explanation
Indices: 3869--3972 Score: 106
Period size: 35 Copynumber: 3.0 Consensus size: 35
3859 TCAAAAATGT
* *
3869 TTTCAAAACCCATTTTTCAAAACTATATAATATAT-
1 TTTCAAAA-ACATTTTTAAAAACTATATAATATATG
*
3904 TTTCAAAAATATTTTTAAAAACTATATATTATATATG
1 TTTCAAAAACATTTTTAAAAACTATATA--ATATATG
** *
3941 TTTTTAAAACA--TTTAAAAACTATATTATATAT
1 TTTCAAAAACATTTTTAAAAACTATATAATATAT
3973 ATATATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 6 0.10
34 17 0.29
35 22 0.37
36 6 0.10
37 8 0.14
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (35 bp):
TTTCAAAAACATTTTTAAAAACTATATAATATATG
Found at i:3939 original size:36 final size:36
Alignment explanation
Indices: 3880--4219 Score: 113
Period size: 36 Copynumber: 9.4 Consensus size: 36
3870 TTCAAAACCC
*
3880 ATTTTTCAAAACTATATA--ATATATTTTCAAAAAT
1 ATTTTTAAAAACTATATATTATATATTTTCAAAAAT
** *
3914 ATTTTTAAAAACTATATATTATATATGTTTTTAAAAC
1 ATTTTTAAAAACTATATATTATATAT-TTTCAAAAAT
*
3951 A--TTTAAAAACTATATTATATATATATATATAT-ATATATAT
1 ATTTTTAAAAACTATA-TAT-TATATAT-T-T-TCA-A-AAAT
* * * * *
3991 ATATATATATA-TATTATATATATATATATTC-AAAAT
1 ATTTTTAAAAACTA-TATAT-TATATATTTTCAAAAAT
* **
4027 GTTTTCGAAAACTATATATTAT-TATGTTTCAAAAAT
1 ATTTTTAAAAACTATATATTATATAT-TTTCAAAAAT
* * **
4063 A-TTTTCAAAA-TA-ATA-TAT-T-TTTTTAAATCGT
1 ATTTTTAAAAACTATATATTATATATTTTCAAA-AAT
* * *
4094 A-TTTTCAAAAC--CATATTATATATTTTCAAAAACC
1 ATTTTTAAAAACTATATATTATATATTTTCAAAAA-T
* ** * *
4128 ATTTTTTCAAAAAAATATATATTATACGTTTTCAATAAC
1 A-TTTTT--AAAAACTATATATTATATATTTTCAAAAAT
** * **
4167 CGTTTTAAAAACTATATGTTATACGCTTTT-AGAAAAT
1 ATTTTTAAAAACTATATATTATA-TATTTTCA-AAAAT
*
4204 ATTTTCAAAAACTATA
1 ATTTTTAAAAACTATA
4220 CTATATTGTT
Statistics
Matches: 227, Mismatches: 48, Indels: 59
0.68 0.14 0.18
Matches are distributed among these distances:
30 6 0.03
31 15 0.07
32 7 0.03
33 4 0.02
34 30 0.13
35 26 0.11
36 46 0.20
37 39 0.17
38 10 0.04
39 4 0.02
40 20 0.09
41 13 0.06
42 7 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
ATTTTTAAAAACTATATATTATATATTTTCAAAAAT
Found at i:3973 original size:2 final size:2
Alignment explanation
Indices: 3961--4019 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
3951 ATTTAAAAAC
3961 TA TA T- 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
4002 TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
4020 TCAAAATGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:16909 original size:23 final size:23
Alignment explanation
Indices: 16868--16939 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
16858 TTTTAAAGTA
* *
16868 ATTATTTAA-TATTTAAAATCAT
1 ATTAATTAATTATTTAAAATAAT
* *
16890 ATTAGTTAATTATTTTAAATAAT
1 ATTAATTAATTATTTAAAATAAT
*
16913 ATTAATTATTTATTTAAAATAAT
1 ATTAATTAATTATTTAAAATAAT
16936 ATTA
1 ATTA
16940 TTTTTAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 8 0.19
23 35 0.81
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
ATTAATTAATTATTTAAAATAAT
Found at i:16919 original size:19 final size:20
Alignment explanation
Indices: 16895--16974 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 20
16885 ATCATATTAG
16895 TTAATTA-TTTTAAATAATA
1 TTAATTATTTTTAAATAATA
*
16914 TTAATTATTTATTTAA-AATA
1 TTAATTATTT-TTAAATAATA
*
16934 AT-ATTATTTTTAAAT--TA
1 TTAATTATTTTTAAATAATA
*
16951 TCAATTTATTTTTAAATAATA
1 TTAA-TTATTTTTAAATAATA
16972 TTA
1 TTA
16975 TATAAAAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.04
18 5 0.10
19 26 0.54
20 7 0.15
21 8 0.17
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTATTTTTAAATAATA
Found at i:19365 original size:29 final size:29
Alignment explanation
Indices: 19306--19367 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
19296 TTTTGTGCCT
*
19306 AAAGAATTTTTTGTTAAAAAATAAGTGTTA
1 AAAGAATTTTTTGTTAAAAAATAAG-CTTA
19336 AAAGAATTTTTTGTTAAAAAATATA-CTTA
1 AAAGAATTTTTTGTTAAAAAATA-AGCTTA
19365 AAA
1 AAA
19368 TTAATGGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.20
30 23 0.77
31 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.39
Consensus pattern (29 bp):
AAAGAATTTTTTGTTAAAAAATAAGCTTA
Found at i:21734 original size:38 final size:39
Alignment explanation
Indices: 21660--21737 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
21650 AATTTAATGA
21660 TGCACTTGCTCCTACTAGGGCATAGTGCATCCGCCCCTG
1 TGCACTTGCTCCTACTAGGGCATAGTGCATCCGCCCCTG
*
21699 TGCACTTGCTCCTACTA-GGCATAGTGCATCTGCCCCTG
1 TGCACTTGCTCCTACTAGGGCATAGTGCATCCGCCCCTG
21737 T
1 T
21738 ATATTATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 21 0.55
39 17 0.45
ACGTcount: A:0.15, C:0.35, G:0.22, T:0.28
Consensus pattern (39 bp):
TGCACTTGCTCCTACTAGGGCATAGTGCATCCGCCCCTG
Found at i:22135 original size:28 final size:28
Alignment explanation
Indices: 22103--22158 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
22093 TTTTTACTTA
* *
22103 AAATGCCGCTAAATACTCGTACTTTAGC
1 AAATGCCGCTAAAGACTCATACTTTAGC
*
22131 AAATGCCGCTATAGACTCATACTTTAGC
1 AAATGCCGCTAAAGACTCATACTTTAGC
22159 GGCATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (28 bp):
AAATGCCGCTAAAGACTCATACTTTAGC
Found at i:22211 original size:41 final size:41
Alignment explanation
Indices: 22139--22241 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 41
22129 GCAAATGCCG
* * * *
22139 CTATAGACTCATACTTTAGCGGCATTTTTATACAAACGT-CA
1 CTATTGACTCGTACTTTAGTGGCATTCTTATACAAA-GTACA
* * *
22180 CTATTGACTCGTACTTTAGTTGCGTTCTTATACAAAGTATA
1 CTATTGACTCGTACTTTAGTGGCATTCTTATACAAAGTACA
*
22221 CTAAAT-ACTCGTACTTTAGTG
1 CT-ATTGACTCGTACTTTAGTG
22242 CCGTTTGTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
40 2 0.04
41 47 0.92
42 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (41 bp):
CTATTGACTCGTACTTTAGTGGCATTCTTATACAAAGTACA
Found at i:26015 original size:44 final size:44
Alignment explanation
Indices: 25952--26058 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
25942 TTTTGTGCAC
* *
25952 TATGCATCGATACACTATGAAAGTGTA-TCGATGCATCCCTTGAA
1 TATGCATCAATACACTATGAAAGTGCACT-GATGCATCCCTTGAA
* * *
25996 TATGCATCAATACACTATGAAGGTGCACTGATGCATTCTTTGAA
1 TATGCATCAATACACTATGAAAGTGCACTGATGCATCCCTTGAA
*
26040 TGTGCATCAATACACTATG
1 TATGCATCAATACACTATG
26059 CAATGTACCG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 55 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (44 bp):
TATGCATCAATACACTATGAAAGTGCACTGATGCATCCCTTGAA
Found at i:26022 original size:21 final size:21
Alignment explanation
Indices: 25998--26058 Score: 52
Period size: 23 Copynumber: 2.8 Consensus size: 21
25988 CCCTTGAATA
25998 TGCATCAATACACTATGAAGG
1 TGCATCAATACACTATGAAGG
* * * *
26019 TGCA-CTGATGCATTCTTTGAATG
1 TGCATC-AATACA--CTATGAAGG
26042 TGCATCAATACACTATG
1 TGCATCAATACACTATG
26059 CAATGTACCG
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
20 1 0.03
21 12 0.41
23 15 0.52
24 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (21 bp):
TGCATCAATACACTATGAAGG
Found at i:26558 original size:13 final size:14
Alignment explanation
Indices: 26521--26562 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
26511 TTTGAAAACT
*
26521 ACATTGATTTTCAA
1 ACATTGTTTTTCAA
26535 ACATTGTTTTTCAA
1 ACATTGTTTTTCAA
26549 A-ATTAG-TTTTCAA
1 ACATT-GTTTTTCAA
26562 A
1 A
26563 TTTTGCCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (14 bp):
ACATTGTTTTTCAA
Found at i:27791 original size:28 final size:28
Alignment explanation
Indices: 27739--27859 Score: 201
Period size: 28 Copynumber: 4.4 Consensus size: 28
27729 TTTGTTCAGG
*
27739 TCGGGTCGGG-TTATTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
27766 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
27794 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
27822 TCAGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
27850 TCAGG-CGGGT
1 TCGGGTCGGGT
27860 CGGGTTCGGG
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
27 15 0.16
28 76 0.84
ACGTcount: A:0.16, C:0.08, G:0.33, T:0.43
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:28073 original size:299 final size:299
Alignment explanation
Indices: 27532--28076 Score: 939
Period size: 299 Copynumber: 1.8 Consensus size: 299
27522 GTTGGATCGA
* *
27532 GTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAATCGAACCGAC
1 GTTTTTTTAAGTGTGATATTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCGAACCGAC
* * *
27597 CCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATT
66 CCGAAAATATATATAATTCAGGTCGGATCGGATTAAGTAACTATTTTTATTAAATAAAAATAATT
*
27662 TTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTT
131 TTTTAATATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTT
*
27727 ATTTTGTTCAGGTCGGGTCGGGTTATTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGAT
196 ATTTTGTTCAGGTCGGGTCGAGTTATTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGAT
27792 ATTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGG
261 ATTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGG
*
27831 GTTTTTTTAAGTGTGATATTCAGG-CGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGA
1 GTTTTTTTAAGTGTGATATTCAGGTCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCGAACCGA
* * * *
27895 CCCTAAAATATATATAATTTAGGTCTGATCGGATTAAGTAATTATTTTTATTAAATAAAAATAAT
65 CCCGAAAATATATATAATTCAGGTCGGATCGGATTAAGTAACTATTTTTATTAAATAAAAATAAT
27960 TTTTTAATATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
130 TTTTTAATATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTT
* * *
28025 TATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTTGGGTCGGGTT
195 TATTTTGTTCAGGTCGGGTCGAGTTATTTAAGTGTGATATTCGGGTCGGGTT
28077 GGGTCGAGTT
Statistics
Matches: 230, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
298 24 0.10
299 206 0.90
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.39
Consensus pattern (299 bp):
GTTTTTTTAAGTGTGATATTCAGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCGAACCGAC
CCGAAAATATATATAATTCAGGTCGGATCGGATTAAGTAACTATTTTTATTAAATAAAAATAATT
TTTTAATATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTT
ATTTTGTTCAGGTCGGGTCGAGTTATTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGAT
ATTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGG
Found at i:28119 original size:38 final size:38
Alignment explanation
Indices: 28033--28125 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 38
28023 TTTATTTTGT
* **
28033 TCGGGTCGGGTCGAG-TTTTTTAAGTGTGATATTTGGG
1 TCGGATCGGGTCGAGTTTTTTTAAGTGTGATATTCAGG
* *
28070 TCGGGTTGGGTCGAGTTTTTTTAAGTGTGATATTCAGG
1 TCGGATCGGGTCGAGTTTTTTTAAGTGTGATATTCAGG
* *
28108 TTGGATCGGGTCGGGTTT
1 TCGGATCGGGTCGAGTTT
28126 GGGTTTAGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 14 0.29
38 34 0.71
ACGTcount: A:0.13, C:0.09, G:0.38, T:0.41
Consensus pattern (38 bp):
TCGGATCGGGTCGAGTTTTTTTAAGTGTGATATTCAGG
Found at i:28170 original size:259 final size:256
Alignment explanation
Indices: 27825--28431 Score: 875
Period size: 259 Copynumber: 2.4 Consensus size: 256
27815 GTGATATTCA
*
27825 GGTCGGGTTTTTTTAAGTGTGATATTCA-GG-CGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACC
1 GGTCGGGTTTTTTTAAGTGTGATATTCAGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATC
* * *
27888 GGACCGACCCTAAAATATATATAATTTAGGTCTGATCGGATTAAGTAATTATTTTTATTAAATAA
66 GGACCGACCCGAAAATATATATAATTTAGGTCGGATCGGATTAAGTAACTATTTTTATTAAATAA
* *
27953 AAATAATTTTTTA-ATATT-TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGG
131 AAATAATTTTTTATATATTGTCGGATCGGGTCAGATTTCTAATTCATATATTCGGG-CGGGTCGG
* * * *
28016 ATGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTTGGGTCGGGTTG
195 ATGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGCGTCGAGTCG
* *
28078 GGTCGAGTTTTTTTAAGTGTGATATTCAGGTTGGATCGGGTCGGGTTTGGGTTTAGGGTGAAAAA
1 GGTCGGGTTTTTTTAAGTGTGATATTCA-G--GG-TCGGGTCGGGTTCGGGTTTAGGGTGAAAAA
** * * *
28143 AATCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
62 AATCGGACCGACCCGAAAATATATATAATTTAGGTCGGATCGGATTAAGTAACTATTTTTATTAA
*
28208 ATAAAAATAATTTTTTATTATTTTGGGTCGGATCGGGTCAGATTTCTAATTCATATATTCGGGCG
127 ATAAAAATAATTTTTTA-TATATT--GTCGGATCGGGTCAGATTTCTAATTCATATATTCGGGCG
*
28273 GGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGCGTCGAG
189 GGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGCGTCGAG
28338 TCG
254 TCG
* * * *
28341 AGTCGGGTTTTTTTTAGTGTGATATTC-GGGTCAGGTCGGG-TCGAGTTTAGGGTGAAAAAAATC
1 GGTCGGGTTTTTTTAAGTGTGATATTCAGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATC
*
28404 GGACCGACCCGAAAAAAATATATAATTT
66 GGACCGACCCG-AAAATATATATAATTT
28432 TACCTTATAT
Statistics
Matches: 315, Mismatches: 27, Indels: 19
0.87 0.07 0.05
Matches are distributed among these distances:
253 27 0.09
257 34 0.11
258 23 0.07
259 103 0.33
261 5 0.02
263 89 0.28
264 34 0.11
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (256 bp):
GGTCGGGTTTTTTTAAGTGTGATATTCAGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATC
GGACCGACCCGAAAATATATATAATTTAGGTCGGATCGGATTAAGTAACTATTTTTATTAAATAA
AAATAATTTTTTATATATTGTCGGATCGGGTCAGATTTCTAATTCATATATTCGGGCGGGTCGGA
TGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGCGTCGAGTCG
Found at i:30054 original size:13 final size:13
Alignment explanation
Indices: 30024--30057 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
30014 GGGAGTAGTA
30024 ATTTTCAAAACTG
1 ATTTTCAAAACTG
30037 A-TTTCAAAACTG
1 ATTTTCAAAACTG
30049 ATTTTCAAA
1 ATTTTCAAA
30058 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (13 bp):
ATTTTCAAAACTG
Found at i:30471 original size:64 final size:65
Alignment explanation
Indices: 30397--30549 Score: 181
Period size: 62 Copynumber: 2.4 Consensus size: 65
30387 ACACACTAAT
* *
30397 TCGAATGCATTTTGTGTACCGATGCACAG-CCATGCATCGATGCACT-CTTGATTTTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTT-TTGAAAC
30460 A
65 A
* * *
30461 TCGAATGCATTTTATGTACC-A--CACAGACCATGCATCGATGTACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
* * * *
30523 TTGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
30550 CCCAAGTGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
61 5 0.07
62 39 0.53
63 8 0.11
64 19 0.26
65 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
Found at i:33616 original size:20 final size:21
Alignment explanation
Indices: 33580--33646 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
33570 CTAAGACATT
*
33580 GATACTC-T-CATTGAGTATC
1 GATACTCATACATTTAGTATC
*
33599 GATAC-CATACATTTAGTATT
1 GATACTCATACATTTAGTATC
* * *
33619 GATACTCTTTCATATAGTATC
1 GATACTCATACATTTAGTATC
33640 GATACTC
1 GATACTC
33647 TCTTGAGTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.03
19 6 0.15
20 14 0.36
21 18 0.46
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (21 bp):
GATACTCATACATTTAGTATC
Found at i:39476 original size:42 final size:41
Alignment explanation
Indices: 39413--39491 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
39403 ATAAACGTCA
* * * *
39413 CTAAAGGTTATGTTTTTAGCGGTGTTTTTTTACAAATGCCG
1 CTAAAGGTCATGTATTTAGCGGCGCTTTTTTACAAATGCCG
39454 CTAAAGGTCATGATATTTAGCGGCGCTTTTTTACAAAT
1 CTAAAGGTCATG-TATTTAGCGGCGCTTTTTTACAAAT
39492 ATCTCTATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 11 0.33
42 22 0.67
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (41 bp):
CTAAAGGTCATGTATTTAGCGGCGCTTTTTTACAAATGCCG
Found at i:41492 original size:55 final size:55
Alignment explanation
Indices: 41408--41680 Score: 336
Period size: 55 Copynumber: 5.0 Consensus size: 55
41398 ATTACCAAAT
* *
41408 GGTACTATGTGTGCAAAACTAAGGAATTCATATTAAGTGTATGAATTTTCGTATG
1 GGTACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * * * *
41463 GGTACTATGTGTGCAAAACTAAGGAATTCACACCAAGTATATGAATTTTCTTATG
1 GGTACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * *
41518 GGCT-CTATATTTGCAAAACTAAGAAATTCATTCTAAGTGTATGAATTTTCGTATG
1 GG-TACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * **
41573 GGCACTATGTCTGCAAAACTAAGAAATTCATACTATTTGTATGAATTTTCGTATG
1 GGTACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
* * ** *
41628 GGCACTCA-GTGTGC-GAACTAAGAAATTCATACTAAGCATATGAATTTCCGTAT
1 GGTACT-ATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
41681 AGGAAACAGA
Statistics
Matches: 189, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.17
55 154 0.81
56 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (55 bp):
GGTACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
Found at i:42618 original size:81 final size:81
Alignment explanation
Indices: 41882--42602 Score: 960
Period size: 81 Copynumber: 8.9 Consensus size: 81
41872 ACTATTCTAA
* * * * * *
41882 GAGTAAAAGAT-AATGACCTAGTTGTGCATTTGGCTGAAATGTGTCAATTACGCAAGTTAGATGA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
* *
41946 GCGGTTAAATACTGTT
66 ACGGTTAAATACCGTT
* *
41962 GAGTAAAAGATAAATGGCCTAGCAGTGCATTTGGCAGAAAAGTATCAATTATG-CAGTTAGATGA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
**
42026 ACAATTAAATACCGTT
66 ACGGTTAAATACCGTT
* * *
42042 GAGTAAAAGTTAAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
*
42107 ACGGTTAAAAACCGTT
66 ACGGTTAAATACCGTT
* * * * *
42123 GAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAAATGTCAATTATACCAGTTAGATGG
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
* *
42188 ACGGTAAAATATCGTT
66 ACGGTTAAATACCGTT
* * * * * * * *
42204 GAGTAAAAGATAAATGGCATAACTGTTCATTTGGCATAAATGTATCAATTATGCTAGTTAGATTA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
42269 ACGGTTAAATACCGTT
66 ACGGTTAAATACCGTT
* * * *
42285 GAGTAAAAGATAAATGTCCTAGCTATGCATTTGGCAGAAAAGTGTCAATTATTCCAGTTAGATAA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
*
42350 ATGGTTAAATACCGTT
66 ACGGTTAAATACCGTT
* * *
42366 GAGTAAAAGATAAATGGTCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
*
42431 ACGGTTAAATACCTTT
66 ACGGTTAAATACCGTT
* *
42447 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAATTAGATGA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
* *
42512 ACAGTTAAAGACCGTT
66 ACGGTTAAATACCGTT
* * *** * *
42528 GAGTAAAAGATTAATGGTCTAGCTACACATTTGGCAGAAAAGTGTCAATCATGCAAGTTAGATGA
1 GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
*
42593 AAGGTTAAAT
66 ACGGTTAAAT
42603 GCCTTTGGTT
Statistics
Matches: 554, Mismatches: 85, Indels: 3
0.86 0.13 0.00
Matches are distributed among these distances:
80 81 0.15
81 473 0.85
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (81 bp):
GAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGA
ACGGTTAAATACCGTT
Found at i:44649 original size:20 final size:21
Alignment explanation
Indices: 44610--44649 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
44600 CAAACTTTAA
* *
44610 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
44631 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
44650 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:46775 original size:65 final size:64
Alignment explanation
Indices: 46703--46856 Score: 168
Period size: 65 Copynumber: 2.4 Consensus size: 64
46693 TACACTTGGG
* * * * *
46703 GTGCATCGGTAGACT-AATTACATTCAATGTTTCAA-AAGAGCTAGGAGTGCATCGATGCGTGGT
1 GTGCATCGGTACA-TAAAATACATTCAATGTTTCAATAAAAGC-AAGAGTGCATCGATGCATGGT
46766 CT
64 -T
* * * *
46768 GTGCATCGGTACATAAAATGCATTCGATGTTTTAATAAAATCAAGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACATAAAATACATTCAATGTTTCAATAAAAGCAAGAGTGCATCGATGCATGGTT
* *
46832 GTGCATCGGTACACAAAATGCATTC
1 GTGCATCGGTACATAAAATACATTC
46857 GAATTAGGGT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 26 0.34
65 47 0.61
66 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCAATGTTTCAATAAAAGCAAGAGTGCATCGATGCATGGTT
Found at i:54066 original size:14 final size:16
Alignment explanation
Indices: 54036--54067 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
54026 TGTGAAGACT
54036 TTTATCTCTGATGATA
1 TTTATCTCTGATGATA
54052 TTTAT-TCTG-TGATA
1 TTTATCTCTGATGATA
54066 TT
1 TT
54068 CATCATTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.56
Consensus pattern (16 bp):
TTTATCTCTGATGATA
Found at i:56070 original size:6 final size:6
Alignment explanation
Indices: 56059--56091 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
56049 CCGTTACTGC
*
56059 AAAATA AAAATA AAAATA AAAA-A AAATTA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
56092 AGCCGAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:56076 original size:12 final size:11
Alignment explanation
Indices: 56059--56092 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
56049 CCGTTACTGC
56059 AAAATAAAAATA
1 AAAATAAAAA-A
56071 AAAATAAAAAA
1 AAAATAAAAAA
*
56082 AAATTAAAAAA
1 AAAATAAAAAA
56093 GCCGAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:56229 original size:29 final size:29
Alignment explanation
Indices: 56187--56251 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
56177 AAGGCCCCCA
*
56187 AATTTTTTGTA-TTTATAACTA-GGACTCCT
1 AATTTTTTATATTTTATAACTACGG-C-CCT
*
56216 AATTTTTTATATTTTATAATTACGGCCCT
1 AATTTTTTATATTTTATAACTACGGCCCT
56245 AATTTTT
1 AATTTTT
56252 ATAATTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 20 0.62
30 10 0.31
31 2 0.06
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (29 bp):
AATTTTTTATATTTTATAACTACGGCCCT
Found at i:56316 original size:21 final size:22
Alignment explanation
Indices: 56292--56344 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
56282 CTCTTTTTCC
*
56292 ATTTTTGTATT-AATTCATCCA
1 ATTTTTGTATTAAATTCAACCA
* *
56313 A-TTTTGAATTAAATTTAACCA
1 ATTTTTGTATTAAATTCAACCA
*
56334 ATTTTTATATT
1 ATTTTTGTATT
56345 TATAATTAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 8 0.32
21 10 0.40
22 7 0.28
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTTGTATTAAATTCAACCA
Found at i:56454 original size:115 final size:116
Alignment explanation
Indices: 56217--56453 Score: 322
Period size: 115 Copynumber: 2.1 Consensus size: 116
56207 AGGACTCCTA
*
56217 ATTTTTTATATTTTATAATTACGGCCCTAATTTTTATAATTTCATAAAATTTTTAGTTTTTAACC
1 ATTTTTTATATTTTATAATTACGGCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTTAACC
* *
56282 CTCTTTTTCCATTTTTGTATTAATTCATCCAATTTTGAATTAAATTTAACC
66 CTCTTTTTCCATTTCTCTATTAATTCATCCAATTTTGAATTAAATTTAACC
*
56333 AATTTTTATA-TTTATAATTA-GGCCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTTGAA
1 ATTTTTTATATTTTATAATTACGG-CCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTT-AA
* * ** * *
56396 -CCT-TTTTT-CATTTCTCTAATTTATTTATTTATTTTTGAATTAAATTTAATC
64 CCCTCTTTTTCCATTTCTCT-ATTAATTCATCCAATTTTGAATTAAATTTAACC
56447 ATTTTTT
1 ATTTTTT
56454 TTGTTTTTTC
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
113 7 0.07
114 40 0.37
115 49 0.46
116 11 0.10
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (116 bp):
ATTTTTTATATTTTATAATTACGGCCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTTAACC
CTCTTTTTCCATTTCTCTATTAATTCATCCAATTTTGAATTAAATTTAACC
Found at i:58148 original size:4 final size:4
Alignment explanation
Indices: 58139--58269 Score: 199
Period size: 4 Copynumber: 32.8 Consensus size: 4
58129 ATGTTTTTGA
* * *
58139 ATAT ATAT ATAT ATAT ATAT ATGT ATAT ATAC ATAT ATAC ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
58187 ATAT ATAC ATAC ATAT ATAT ATAT ATAC ATAC ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
58235 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
58270 GTTTAGAAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 117 1.00
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:58335 original size:73 final size:73
Alignment explanation
Indices: 58253--58499 Score: 304
Period size: 73 Copynumber: 3.4 Consensus size: 73
58243 ATATATATAT
* * *
58253 ATATATATATATATATAGTTTAGAAAACATTGTTCGAAAATATATACAATATGTAGTTTTGAAAA
1 ATATATATA-ATATATAGTTTAGAAAACATT-TTTGAAAATATATATAATATATAGTTTTGAAAA
58318 CATTTTTAAA
64 CATTTTTAAA
* * *
58328 ATATATATAATATATAATTTTGAAAACATTTTTGAAAATATATATAATATATAATTTTGAAAACA
1 ATATATATAATATATAGTTTAGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACA
58393 -TTTTAAA
66 TTTTTAAA
* * * * *
58400 AAATATATAATATATAGTTTTGAAATCATTTTTTTAAAATATGTATAATATATAGTTTT-AAAAC
1 ATATATATAATATATAGTTTAGAAAACA-TTTTTGAAAATATATATAATATATAGTTTTGAAAAC
* *
58464 GTTTTTGGGAA
65 ATTTTT--AAA
58475 ATATATATAATATAT--TTTAGAAAAC
1 ATATATATAATATATAGTTTAGAAAAC
58500 GTGTTAGGGT
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
72 37 0.25
73 70 0.46
74 19 0.13
75 25 0.17
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (73 bp):
ATATATATAATATATAGTTTAGAAAACATTTTTGAAAATATATATAATATATAGTTTTGAAAACA
TTTTTAAA
Found at i:58375 original size:37 final size:37
Alignment explanation
Indices: 58253--58489 Score: 302
Period size: 37 Copynumber: 6.4 Consensus size: 37
58243 ATATATATAT
* *
58253 ATATATATATATATATAGTTTAGAAAACATTGTTCGAAA
1 ATATATATA-ATATATAGTTTTGAAAACATT-TTTGAAA
* *
58292 ATATATACAATATGTAGTTTTGAAAACATTTTT-AAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
58328 ATATATATAATATATAATTTTGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
58365 ATATATATAATATATAATTTTGAAAACA-TTTT-AAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
58400 AAATATATAATATATAGTTTTGAAATCATTTTTTTAAA
1 ATATATATAATATATAGTTTTGAAAACA-TTTTTGAAA
* * *
58438 ATATGTATAATATATAGTTTT-AAAACGTTTTTGGGAA
1 ATATATATAATATATAGTTTTGAAAACATTTTT-GAAA
58475 ATATATATAATATAT
1 ATATATATAATATAT
58490 TTTAGAAAAC
Statistics
Matches: 176, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.16
36 42 0.24
37 57 0.32
38 41 0.23
39 8 0.05
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:58561 original size:10 final size:10
Alignment explanation
Indices: 58548--58589 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
58538 ATATATATAC
58548 ATTTTTATTT
1 ATTTTTATTT
58558 ATTTTTATTT
1 ATTTTTATTT
*
58568 CTTTTTATTCTT
1 ATTTTTA-T-TT
58580 ATTTTTATTT
1 ATTTTTATTT
58590 TCATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 18 0.64
11 2 0.07
12 8 0.29
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:58584 original size:22 final size:20
Alignment explanation
Indices: 58549--58589 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
58539 TATATATACA
58549 TTTTTATTTATTTTTATTTC
1 TTTTTATTTATTTTTATTTC
58569 TTTTTATTCTTATTTTTATTT
1 TTTTTA-T-TTATTTTTATTT
58590 TCATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTATTTATTTTTATTTC
Found at i:67910 original size:20 final size:20
Alignment explanation
Indices: 67871--67911 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
67861 CATTGCAGGA
*
67871 ATTTATGGCTTCGACGAAAG
1 ATTTATGGCTTCCACGAAAG
67891 ATTTCATGGCTTCCAC-AAAG
1 ATTT-ATGGCTTCCACGAAAG
67911 A
1 A
67912 CCTTTATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTATGGCTTCCACGAAAG
Found at i:77928 original size:95 final size:95
Alignment explanation
Indices: 77751--77940 Score: 211
Period size: 95 Copynumber: 2.0 Consensus size: 95
77741 ATACCGACGA
* * * * * *
77751 GGTAGTATTGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAATCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCAA
*
77816 TACCAAAAGGAGATATCGGTACCATAGTAT
66 TACCAAAAGGAGATATCGATACCATAGTAT
* * * * * *
77846 GGTAGTATCGATACCATAGTAAGGGTATCGATACTAGGAAACTTCAAACCTATATTTTGTATCAA
1 GGTAGTATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCAA
* ** *
77911 TATCGTAAGGCAG-TATCGATACTATAGTAT
66 TACCAAAAGG-AGATATCGATACCATAGTAT
77941 AGAAGTATTG
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
95 75 0.97
96 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (95 bp):
GGTAGTATCGATACCATAGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCAA
TACCAAAAGGAGATATCGATACCATAGTAT
Found at i:78541 original size:59 final size:59
Alignment explanation
Indices: 78276--78525 Score: 385
Period size: 59 Copynumber: 4.2 Consensus size: 59
78266 GTGCGCAAAA
* *
78276 TTAAGAAATTCATACTAAGTGCATGAATTTCCCTATAGGGCACTTCGTGTGCTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
*
78335 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGTTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
** * *
78394 TTAAGAAATTCATACTAAGTGTATGAATTTTTATATAGGGCACTTCATATGCTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
* * *
78453 TTAAGAAATTTATATTAAGTGTATGAATTTCCATATTGGGCACATT-GTGTGCTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCAC-TTCGTGTGCTAAAATG
*
78512 ATAAGAAATTCATA
1 TTAAGAAATTCATA
78526 ATATGAGTAA
Statistics
Matches: 173, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
59 171 0.99
60 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (59 bp):
TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
Found at i:78591 original size:118 final size:118
Alignment explanation
Indices: 78325--78559 Score: 316
Period size: 118 Copynumber: 2.0 Consensus size: 118
78315 GCACTTCGTG
* * *
78325 TGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGTTAA
1 TGCTAAAATGTTAAGAAATTTATAGTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAA
* * * * * **
78390 AATGTTAAGAAATTCATACTAAGTGTATGAATTTTTATATAGGGCACTTCATA
66 AATGATAAGAAATTCATAATAAGAGTAAGAATTTTTATATAGAGCAAATCATA
* *
78443 TGCTAAAATGTTAAGAAATTTATATTAAGTGTATGAATTTCCATATTGGGCACATT-GTGTGCTA
1 TGCTAAAATGTTAAGAAATTTATAGTAAGTGTATGAATTTCCATATAGGGCAC-TTCGTGTGCTA
*
78507 AAATGATAAGAAATTCATAATATGAGTAAGAATTTTTATATA-AG-AAAT-ATA
65 AAATGATAAGAAATTCATAATAAGAGTAAGAATTTTTATATAGAGCAAATCATA
78558 TG
1 TG
78560 TATGAATTTA
Statistics
Matches: 104, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
115 5 0.05
116 2 0.02
117 1 0.01
118 94 0.90
119 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (118 bp):
TGCTAAAATGTTAAGAAATTTATAGTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAA
AATGATAAGAAATTCATAATAAGAGTAAGAATTTTTATATAGAGCAAATCATA
Found at i:78845 original size:68 final size:68
Alignment explanation
Indices: 78759--79223 Score: 705
Period size: 68 Copynumber: 6.8 Consensus size: 68
78749 AAGTTAAAAA
* * *
78759 CTTTGAGGCATAACTGTGCATATGATAGAAAGGTTTCATTTATGCCAGTTAGATGAAAGGCTAAG
1 CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
78824 TGC
66 TGC
* *
78827 CTTTGAGGCCTAACTGTGCATATGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
1 CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
78892 TGC
66 TGC
*
78895 CTTTGAGGCCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
1 CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
78960 TGC
66 TGC
* * * *
78963 CTTTGAGACCTAATTGTGCATATGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAA
1 CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
79028 TGC
66 TGC
* * * *
79031 CTTTGAGGCCTAACTGTGCATCTGACAGAAAAGTGTCATTTATACCAGTTAGATGAAATGCTAAG
1 CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
79096 TGC
66 TGC
* * **
79099 CTTTGAGGCCTAAATGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTATATGAAATACTAAG
1 CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
79164 TGC
66 TGC
** * * * **
79167 CTTTGAGGCCTAGTTGTGAATTTGACAGAAAGGTGTCAATTATGCTTGTTAGATGAA
1 CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
79224 TGGTTAAATA
Statistics
Matches: 364, Mismatches: 33, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 364 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (68 bp):
CTTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
TGC
Found at i:79483 original size:81 final size:81
Alignment explanation
Indices: 79173--79573 Score: 520
Period size: 81 Copynumber: 4.9 Consensus size: 81
79163 GTGCCTTTGA
* ** * * **
79173 GGCCTAGTTGTGAATTTGACAGAAAGGTGTCAATTATGCTTGTTAGATGAATGGTTAAATATTGT
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
79238 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
79254 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTACCGT
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
79318 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
** * *
79334 GGCCTAGTTGTGTGCATTTGACAGAAAAATGTCAATTATGCTTA-CTAGATGAACGGTTAAGTAC
1 GGCCTAG-T-TGTGCATTTGACAGAAAGGTGTCAATTATGC-CAGTTAGATGAACGGTTAAGTAC
79398 CGTTGAGTAAAAGAATAAT
63 CGTTGAGTAAAAGAATAAT
* * * *** * *
79417 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAACTATTCCAGTTAGATGAATAATTATGTATCGT
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
79482 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * ** **
79498 GGCCTA-TATGTGCATTTGACATAAAGGTGTCAATTATGCCAGTCAGATGAACGGTTAAACATTG
1 GGCCTAGT-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCG
79562 TTGAGTAAAAGA
65 TTGAGTAAAAGA
79574 TGAACTGTAA
Statistics
Matches: 279, Mismatches: 35, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
80 44 0.16
81 161 0.58
82 28 0.10
83 45 0.16
84 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (81 bp):
GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGT
TGAGTAAAAGAATAAT
Found at i:79586 original size:29 final size:29
Alignment explanation
Indices: 79542--79602 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
79532 TATGCCAGTC
* * * *
79542 AGATGAACGGTTAAACATTGTTGAGTAAA
1 AGATGAACGGTAAAACACTATTGAATAAA
*
79571 AGATGAACTGTAAAACACTATTGAATAAA
1 AGATGAACGGTAAAACACTATTGAATAAA
79600 AGA
1 AGA
79603 ATAATGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (29 bp):
AGATGAACGGTAAAACACTATTGAATAAA
Found at i:79755 original size:2 final size:2
Alignment explanation
Indices: 79750--79780 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
79740 GATATATATA
*
79750 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
79781 ATGCATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:79790 original size:2 final size:2
Alignment explanation
Indices: 79785--79815 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
79775 GTGTGTATGC
79785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79816 ATTTTTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84138 original size:59 final size:59
Alignment explanation
Indices: 84069--84275 Score: 281
Period size: 59 Copynumber: 3.5 Consensus size: 59
84059 GTGCGCAAAA
* *
84069 TTAAGAAATTCATACTAAGTGTATGAATTTCCCTATAGGGCACTTCATGTGCTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
*
84128 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCGCTTCGTGTGCTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
* * * * * *
84187 TTCAGAAATTCATACTAAGTGTATGAATTTACGTATTGGCCACCTT-GTGTGATAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA-CTTCGTGTGCTAAAATG
* * * *
84246 ATAAGAAATGCATATTAAGTGTAAGAATTT
1 TTAAGAAATTCATACTAAGTGTATGAATTT
84276 TTGTATGAAA
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
59 129 0.98
60 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (59 bp):
TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
Done.