Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002606.1 Hibiscus syriacus cultivar Beakdansim tig00005269_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: 89744
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1180 original size:28 final size:28
Alignment explanation
Indices: 1148--1210 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1138 GTTCCGGTTG
*
1148 TTGGGCTTGAACTGGGTCGGGTAATCTA
1 TTGGGCTTGAACTGGGTCAGGTAATCTA
* *
1176 TTGGGCTTGAACTGGGTCAGGTAATTTG
1 TTGGGCTTGAACTGGGTCAGGTAATCTA
1204 TTGGGCT
1 TTGGGCT
1211 CATTGGGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.16, C:0.13, G:0.37, T:0.35
Consensus pattern (28 bp):
TTGGGCTTGAACTGGGTCAGGTAATCTA
Found at i:2094 original size:42 final size:42
Alignment explanation
Indices: 2035--2121 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
2025 TATTATATAA
*
2035 AGACTCATTTATCAAAGTTAAGTGTACGAAATAAATCAATCT
1 AGACTCATTTATCAAAGTTAAGTGTAAGAAATAAATCAATCT
*
2077 AGACTCGTTTATCAAAGTTAAGTGTAAGAAATAAATCAATCT
1 AGACTCATTTATCAAAGTTAAGTGTAAGAAATAAATCAATCT
2119 AGA
1 AGA
2122 TTAATCGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.30
Consensus pattern (42 bp):
AGACTCATTTATCAAAGTTAAGTGTAAGAAATAAATCAATCT
Found at i:7297 original size:22 final size:20
Alignment explanation
Indices: 7272--7327 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
7262 TACTCGGGGA
7272 AGTATCGATACCATAGAAAGGG
1 AGTATCGATACCATAGAAA--G
*
7294 AGTATCGATACCCA-AGGAAG
1 AGTATCGATA-CCATAGAAAG
7314 AGTATCGATACCAT
1 AGTATCGATACCAT
7328 CGTGAAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 3 0.10
20 11 0.35
22 14 0.45
23 3 0.10
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (20 bp):
AGTATCGATACCATAGAAAG
Found at i:8483 original size:20 final size:20
Alignment explanation
Indices: 8457--8506 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
8447 AAATATTTTG
8457 ATGAACAGTACCGATACTGT
1 ATGAACAGTACCGATACTGT
* *
8477 GTGAACAATACCGATACTGT
1 ATGAACAGTACCGATACTGT
8497 ATGAACAGTA
1 ATGAACAGTA
8507 ATGAACAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (20 bp):
ATGAACAGTACCGATACTGT
Found at i:8727 original size:20 final size:22
Alignment explanation
Indices: 8689--8728 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
8679 TTTTTGTAGA
8689 AAAACAATCCCCAAACGGCTCC
1 AAAACAATCCCCAAACGGCTCC
8711 AAAAC-ATCCCC-AACGGCT
1 AAAACAATCCCCAAACGGCT
8729 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.40, C:0.40, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAACAATCCCCAAACGGCTCC
Found at i:9404 original size:31 final size:30
Alignment explanation
Indices: 9364--9464 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 30
9354 AATTCATGAA
9364 TTAAATTAATATTTTATCCAAAGTTTAAAG
1 TTAAATTAATATTTTATCCAAAGTTTAAAG
*
9394 TTCAAATTAATATTTTATCTAAAG-TTATAAG
1 TT-AAATTAATATTTTATCCAAAGTTTA-AAG
* * *
9425 TTGAATTAATGTTTTATCCAAAATTTAAGAG
1 TTAAATTAATATTTTATCCAAAGTTTAA-AG
9456 TTAAATTAA
1 TTAAATTAA
9465 AAAATATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
30 23 0.38
31 38 0.62
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.44
Consensus pattern (30 bp):
TTAAATTAATATTTTATCCAAAGTTTAAAG
Found at i:9584 original size:38 final size:41
Alignment explanation
Indices: 9518--9593 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 41
9508 TTGATGAAAT
*
9518 AGTGACCGAAAACATTATAAATCAATAAT-C-AATAACGTA
1 AGTGACCGAAAACATAATAAATCAATAATACAAATAACGTA
*
9557 AGTGACC-AAATCATAATAAAT-AGATAATACAAATAAC
1 AGTGACCGAAAACATAATAAATCA-ATAATACAAATAAC
9594 TAGAGCATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 1 0.03
38 17 0.53
39 8 0.25
40 6 0.19
ACGTcount: A:0.54, C:0.14, G:0.09, T:0.22
Consensus pattern (41 bp):
AGTGACCGAAAACATAATAAATCAATAATACAAATAACGTA
Found at i:18340 original size:572 final size:572
Alignment explanation
Indices: 17256--18347 Score: 2033
Period size: 572 Copynumber: 1.9 Consensus size: 572
17246 ACCACAGAGA
* *
17256 CCATTTTTGCTGATTTGGGTTGTATTGTTTGTTAGATTTCGTGGTTTTTTGGTTAAATTTCCATA
1 CCATTTTTGCTGATTTGAGTTGTATTGTTTGTTAGATTTCGTGGGTTTTTGGTTAAATTTCCATA
*
17321 TCTCAATGCAATCCTAAGAAATTGGGTTTTTTTTTTATTTTTGTTTATTGGATCAAGTTGGAAAT
66 TCTCAATGCAATCCTAAGAAATTGGG-TTTTTTTTTATCTTTGTTTATTGGATCAAGTTGGAAAT
17386 TTTAGGGTTTAGGACTTGAAATTCATGGTTGGTGGGTCAAAAAATCAAGGAAAATGAAAGGTAAA
130 TTTAGGGTTTAGGACTTGAAATTCATGGTTGGTGGGTCAAAAAATCAAGGAAAATGAAAGGTAAA
*
17451 ACTGGGAATTTCTTTGTGTTGAATACTGGAGCTAGAATTCCTGCCATTGGGCTTGGAACATGGCA
195 ACTAGGAATTTCTTTGTGTTGAATACTGGAGCTAGAATTCCTGCCATTGGGCTTGGAACATGGCA
* *
17516 GAGTGGAGGATACCTCTGTGTCGACGCCGTGAAAATGGCAATGTCGGTCGGTTACCGCCACATCG
260 GAGTGGAGGAGACCTCTGCGTCGACGCCGTGAAAATGGCAATGTCGGTCGGTTACCGCCACATCG
*
17581 ATTGTGCACATCTTTATGGCAATGATATTGAAGTTGGGGAAGCATTGGCTGAAGCCTTCAGTGGT
325 ATTGTGCACATCTTTATGGCAATGAGATTGAAGTTGGGGAAGCATTGGCTGAAGCCTTCAGTGGT
*
17646 TCTTTGAAAAGAGAGGATGTTTTCTTAACCTCTAAGCTTTATTGTACTATGAATTCGTTGAATAA
390 TCTTTGAAAAGAGAGGATGTTTTCTTAACCTCTAAGCTTTACTGTACTATGAATTCGTTGAATAA
17711 GATCGAAAACTATGTTAAGGTGTCTCTCAAGAACCTTGGAATCTCCTACTTGGATCTCTATTTGA
455 GATCGAAAACTATGTTAAGGTGTCTCTCAAGAACCTTGGAATCTCCTACTTGGATCTCTATTTGA
17776 AGTAAAGTTTTGGATTTTTGGATAAATAATGTTATCGTGGTAGTGTTGCTGAG
520 AGTAAAGTTTTGGATTTTTGGATAAATAATGTTATCGTGGTAGTGTTGCTGAG
* *
17829 CCATTTTTGCTGATTTGAGTTGTCTTGTTTGTTAGATTTCGTGGGTTTTTGGTTAAATTTTCATA
1 CCATTTTTGCTGATTTGAGTTGTATTGTTTGTTAGATTTCGTGGGTTTTTGGTTAAATTTCCATA
17894 TCTCAATGCAATCCTAAGAAATTGGG-TTTTTTTTATCTTTGTTTATTGGATCAAGTTGGAAATT
66 TCTCAATGCAATCCTAAGAAATTGGGTTTTTTTTTATCTTTGTTTATTGGATCAAGTTGGAAATT
*
17958 TTAGGGTTTAGGACTTGAAATTCTTGGTTGGTGGGTCAAGAAAATCAAGGAAAATGAAAGGTAAA
131 TTAGGGTTTAGGACTTGAAATTCATGGTTGGTGGGTCAA-AAAATCAAGGAAAATGAAAGGTAAA
18023 ACTAGGAATTTCTTTGTGTTGAATACTGGAGCTAGAATTCCTGCCATTGGGCTTGGAACATGGCA
195 ACTAGGAATTTCTTTGTGTTGAATACTGGAGCTAGAATTCCTGCCATTGGGCTTGGAACATGGCA
* *
18088 GAGTGGATGAGACCTCTGCGTCGACGCCGTGAAAATGGCAATGTTGGTCGGTTACCGCCACATCG
260 GAGTGGAGGAGACCTCTGCGTCGACGCCGTGAAAATGGCAATGTCGGTCGGTTACCGCCACATCG
18153 ATTGTGCACATCTTTATGGCAATGAGATTGAAGTTGGGGAAGCATTGGCTGAAGCCTTCAGTGGT
325 ATTGTGCACATCTTTATGGCAATGAGATTGAAGTTGGGGAAGCATTGGCTGAAGCCTTCAGTGGT
18218 TCTTTGAAAAGAGAGGATGTTTTCTTAACCTCTAAGCTTTACTGTACTATGAATTCGTTGAATAA
390 TCTTTGAAAAGAGAGGATGTTTTCTTAACCTCTAAGCTTTACTGTACTATGAATTCGTTGAATAA
*
18283 GATCGAAAACTATGTTAAGGTGTCTCTCAAGAACCTTGGAATCTTCTACTTGGATCTCTATTTGA
455 GATCGAAAACTATGTTAAGGTGTCTCTCAAGAACCTTGGAATCTCCTACTTGGATCTCTATTTGA
18348 TGCATTGGCC
Statistics
Matches: 504, Mismatches: 14, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
571 75 0.15
572 342 0.68
573 87 0.17
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (572 bp):
CCATTTTTGCTGATTTGAGTTGTATTGTTTGTTAGATTTCGTGGGTTTTTGGTTAAATTTCCATA
TCTCAATGCAATCCTAAGAAATTGGGTTTTTTTTTATCTTTGTTTATTGGATCAAGTTGGAAATT
TTAGGGTTTAGGACTTGAAATTCATGGTTGGTGGGTCAAAAAATCAAGGAAAATGAAAGGTAAAA
CTAGGAATTTCTTTGTGTTGAATACTGGAGCTAGAATTCCTGCCATTGGGCTTGGAACATGGCAG
AGTGGAGGAGACCTCTGCGTCGACGCCGTGAAAATGGCAATGTCGGTCGGTTACCGCCACATCGA
TTGTGCACATCTTTATGGCAATGAGATTGAAGTTGGGGAAGCATTGGCTGAAGCCTTCAGTGGTT
CTTTGAAAAGAGAGGATGTTTTCTTAACCTCTAAGCTTTACTGTACTATGAATTCGTTGAATAAG
ATCGAAAACTATGTTAAGGTGTCTCTCAAGAACCTTGGAATCTCCTACTTGGATCTCTATTTGAA
GTAAAGTTTTGGATTTTTGGATAAATAATGTTATCGTGGTAGTGTTGCTGAG
Found at i:22874 original size:50 final size:50
Alignment explanation
Indices: 22799--22898 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
22789 CTCACCATCA
22799 CCGTGCACTCAAAACCCTACCGAAATCATCTTGCCGTTGTTGCTCCGTCG
1 CCGTGCACTCAAAACCCTACCGAAATCATCTTGCCGTTGTTGCTCCGTCG
*
22849 CCGTGCACTCAAAACCCTACCGAAATCATCTTGCCGTTGTTGCTCTGTCG
1 CCGTGCACTCAAAACCCTACCGAAATCATCTTGCCGTTGTTGCTCCGTCG
22899 TCGTTACACT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (50 bp):
CCGTGCACTCAAAACCCTACCGAAATCATCTTGCCGTTGTTGCTCCGTCG
Found at i:25112 original size:24 final size:24
Alignment explanation
Indices: 25043--25105 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
25033 CCTGACCTGG
25043 ATTCTGTTTTGATTTCTTATATGA
1 ATTCTGTTTTGATTTCTTATATGA
* * *
25067 ATTCTATTATGATATCTTATATGA
1 ATTCTGTTTTGATTTCTTATATGA
*
25091 ATTCTGTTTTAATTT
1 ATTCTGTTTTGATTT
25106 ATGATATCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (24 bp):
ATTCTGTTTTGATTTCTTATATGA
Found at i:26072 original size:3 final size:3
Alignment explanation
Indices: 26066--26175 Score: 213
Period size: 3 Copynumber: 37.0 Consensus size: 3
26056 CTTATGATGG
26066 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26113 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26161 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
26176 TTGACATATC
Statistics
Matches: 106, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 104 0.98
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:26394 original size:15 final size:16
Alignment explanation
Indices: 26374--26404 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
26364 ACCACCAAAA
26374 ATTTCATCCAT-ATCC
1 ATTTCATCCATCATCC
26389 ATTTCATCCATCATCC
1 ATTTCATCCATCATCC
26405 GCGGGTGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTCATCCATCATCC
Found at i:26501 original size:17 final size:17
Alignment explanation
Indices: 26479--26528 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
26469 AAATTCTTCT
26479 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
*
26496 AACA-T--T-GATACTCA
1 AACATTCATAGAAAC-CA
26510 AACATTCATAGAAACCA
1 AACATTCATAGAAACCA
26527 AA
1 AA
26529 ACATGAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 1 0.04
16 1 0.04
17 9 0.35
18 4 0.15
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (17 bp):
AACATTCATAGAAACCA
Found at i:32694 original size:24 final size:22
Alignment explanation
Indices: 32642--32700 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
32632 AATATGAGGG
*
32642 TCGTGCCACAAGAGCAGAGGAA
1 TCGTGCCACAAGAGCAGAGAAA
*
32664 TCACGTGCCACAAGGGCAGAGATAAA
1 T--CGTGCCACAAGAGCAGAG--AAA
*
32690 TCGTGTCACAA
1 TCGTGCCACAA
32701 TGATAGAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
24 26 0.87
26 3 0.10
ACGTcount: A:0.36, C:0.24, G:0.27, T:0.14
Consensus pattern (22 bp):
TCGTGCCACAAGAGCAGAGAAA
Found at i:39737 original size:2 final size:2
Alignment explanation
Indices: 39730--39755 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39720 AGATAGACAA
39730 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
39756 CAGTTACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40608 original size:11 final size:11
Alignment explanation
Indices: 40592--40618 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40582 AAAATAGTGT
40592 AGAAGTTGACG
1 AGAAGTTGACG
40603 AGAAGTTGACG
1 AGAAGTTGACG
40614 AGAAG
1 AGAAG
40619 ATAAACGACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.37, T:0.15
Consensus pattern (11 bp):
AGAAGTTGACG
Found at i:40867 original size:89 final size:89
Alignment explanation
Indices: 40708--40899 Score: 320
Period size: 89 Copynumber: 2.2 Consensus size: 89
40698 TAATATTTTT
*
40708 TTAACATTT-TTGATAAAACGATACCTAAAATATTATTTTTTTACCAGAAATGTTAAGTTCGCTA
1 TTAACATTTCCTGATAAAACGATACCTAAAATATTATTTTTTTACCAGAAATGTTAAGTTCGCTA
*
40772 ACTAATTTCCGGTAGAACTCAATA
66 ACTAATTTCCGGTAGAACACAATA
40796 TTAACATTTCCTG-TAAAAC-ACTACCTAAAATATTATTTTTTTTACCAGAAATGTTAAGTTCGC
1 TTAACATTTCCTGATAAAACGA-TACCTAAAATATTA-TTTTTTTACCAGAAATGTTAAGTTCGC
40859 TAACTAATTTCCGGTAGAACACAATA
64 TAACTAATTTCCGGTAGAACACAATA
40885 TTAACATTTCC-GATA
1 TTAACATTTCCTGATA
40900 GAAAAAAATA
Statistics
Matches: 98, Mismatches: 2, Indels: 7
0.92 0.02 0.07
Matches are distributed among these distances:
87 1 0.01
88 30 0.31
89 67 0.68
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (89 bp):
TTAACATTTCCTGATAAAACGATACCTAAAATATTATTTTTTTACCAGAAATGTTAAGTTCGCTA
ACTAATTTCCGGTAGAACACAATA
Found at i:42945 original size:27 final size:28
Alignment explanation
Indices: 42901--43012 Score: 113
Period size: 30 Copynumber: 4.0 Consensus size: 28
42891 CCCAAATAGC
42901 ACACTTTTCGAATT-AATTCCCAAAATA
1 ACACTTTTCGAATTAAATTCCCAAAATA
*
42928 TCACTTTT-GAATTAAATTCCCAAAATA
1 ACACTTTTCGAATTAAATTCCCAAAATA
* *
42955 ACACCTTTTTCAAATTAAATTTCCAAAATA
1 ACA-C-TTTTCGAATTAAATTCCCAAAATA
* * *
42985 GCACCCATTTCGAATT-AATTCCTAAAAT
1 --ACACTTTTCGAATTAAATTCCCAAAAT
43013 GTCACCCGAT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
26 5 0.07
27 22 0.31
28 1 0.01
29 14 0.20
30 25 0.36
31 1 0.01
32 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (28 bp):
ACACTTTTCGAATTAAATTCCCAAAATA
Found at i:42973 original size:30 final size:28
Alignment explanation
Indices: 42864--43012 Score: 133
Period size: 29 Copynumber: 5.2 Consensus size: 28
42854 CCATTTTACA
** *
42864 AAAATAGCACCTTTTTTAAAATAATTACCC
1 AAAATAGCACC-TTTTCGAATTAATT-CCC
42894 -AAATAGCACACTTTTCGAATTAATTCCC
1 AAAATAGCAC-CTTTTCGAATTAATTCCC
*
42922 AAAATATCA-CTTTT-GAATTAAATTCCC
1 AAAATAGCACCTTTTCGAATT-AATTCCC
* * *
42949 AAAATAACACCTTTTTCAAATTAAATTTCC
1 AAAATAGCACC-TTTTCGAATT-AATTCCC
* *
42979 AAAATAGCACCCATTTCGAATTAATTCCT
1 AAAATAGCA-CCTTTTCGAATTAATTCCC
43008 AAAAT
1 AAAAT
43013 GTCACCCGAT
Statistics
Matches: 100, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.05
27 20 0.20
28 4 0.04
29 41 0.41
30 28 0.28
31 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATAGCACCTTTTCGAATTAATTCCC
Found at i:43062 original size:23 final size:23
Alignment explanation
Indices: 43033--43083 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
43023 CAACGGTCAA
*
43033 CGGGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCGAGTCAACGGGT
43056 CGGGTCGGGTCGAGTCAACGGGT
1 CGGGTCGGGTCGAGTCAACGGGT
43079 CGGGT
1 CGGGT
43084 TGGAACCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.18
Consensus pattern (23 bp):
CGGGTCGGGTCGAGTCAACGGGT
Found at i:43083 original size:18 final size:18
Alignment explanation
Indices: 43027--43066 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
43017 CCCGATCAAC
43027 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
43045 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
43063 GGTC
1 GGTC
43067 GAGTCAACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:43096 original size:23 final size:23
Alignment explanation
Indices: 43028--43096 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
43018 CCGATCAACG
43028 GTCAACGGGTCGGGTC-G---G-
1 GTCAACGGGTCGGGTCGGACCGA
**
43046 GTCAACGGGTCGGGTCGGGTCGA
1 GTCAACGGGTCGGGTCGGACCGA
*
43069 GTCAACGGGTCGGGTTGGAACCGA
1 GTCAACGGGTCGGGTCGG-ACCGA
43093 -TCAA
1 GTCAA
43097 ACCCATTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 16 0.38
19 1 0.02
22 1 0.02
23 21 0.50
24 3 0.07
ACGTcount: A:0.17, C:0.22, G:0.43, T:0.17
Consensus pattern (23 bp):
GTCAACGGGTCGGGTCGGACCGA
Found at i:45724 original size:2 final size:2
Alignment explanation
Indices: 45717--45772 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
45707 ATTTTAATGA
45717 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
45759 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
45773 TATTTAGGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46619 original size:3 final size:3
Alignment explanation
Indices: 46605--46675 Score: 81
Period size: 3 Copynumber: 23.7 Consensus size: 3
46595 AATATTGTAA
* *
46605 AAT AAT ATT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
46653 CAT ACT -AT AGT ATAT AAT AAT AA
1 AAT AAT AAT AAT A-AT AAT AAT AA
46676 ATATAATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.95
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:46681 original size:12 final size:12
Alignment explanation
Indices: 46618--46683 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
46608 AATATTAATA
46618 ATAATAATAACA-
1 ATAATAATAA-AT
46630 ATAATAAT-AAT
1 ATAATAATAAAT
46641 AATAATAAT-AAT
1 -ATAATAATAAAT
* *
46653 CATACT-ATAGTAT
1 -ATAATAATA-AAT
46666 ATAATAATAAAT
1 ATAATAATAAAT
46678 ATAATA
1 ATAATA
46684 TATATATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
10 1 0.02
11 3 0.07
12 35 0.80
13 5 0.11
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:47128 original size:90 final size:91
Alignment explanation
Indices: 46887--47181 Score: 486
Period size: 90 Copynumber: 3.3 Consensus size: 91
46877 ATGGTTACCT
* * * *
46887 GAAGGACTTAAAAAATCATGAAACTCCCGAAGGCTTAGTTTATTAAATCTCATTTGAAAATATCC
1 GAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCC
*
46952 TGCACTGAAGGTCTTACGGATAGCCC
66 TGCACTGAAGGTCTTACGGATGGCCC
*
46978 GAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAAATCTCATTTGAAAACATCC
1 GAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCC
*
47043 TGCACTGAAGGTTTTACGGATGGCCC
66 TGCACTGAAGGTCTTACGGATGGCCC
* *
47069 GAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGATCTCATTTGAAAACATCA
1 GAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCC
*
47133 TGCACTGAAGGTCTTATGGATGGCCC
66 TGCACTGAAGGTCTTACGGATGGCCC
47159 GAAGGACTT-AAAAATCAAGAAAC
1 GAAGGACTTAAAAAATCAAGAAAC
47182 TCTTGAAAAT
Statistics
Matches: 192, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
90 99 0.52
91 93 0.48
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (91 bp):
GAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAACATCC
TGCACTGAAGGTCTTACGGATGGCCC
Found at i:47330 original size:43 final size:43
Alignment explanation
Indices: 47269--47606 Score: 307
Period size: 43 Copynumber: 7.3 Consensus size: 43
47259 AAATTTATGT
*
47269 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGATTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
**
47312 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGGTTGTCATCAAATTTTTCA
1 TCAAGAAACCCCTACATATCACGATGG--TC-C--------C-TCAAGCTTTTCA
* * *
47367 TCAAGGAACCCTTACATATCACGATGGTCCCTCAAGCTTTTTA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** * *
47410 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTGTCC
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
* *
47453 TCAAAAAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAATTTGTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAA----G----C---TTT-TCA
* *
47508 TCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** *
47551 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCT
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
47594 TCAAGAAACCCCT
1 TCAAGAAACCCCT
47607 GAAAATCAGG
Statistics
Matches: 242, Mismatches: 29, Indels: 48
0.76 0.09 0.15
Matches are distributed among these distances:
43 157 0.65
44 4 0.02
45 2 0.01
46 1 0.00
47 2 0.01
51 2 0.01
52 1 0.00
53 2 0.01
54 3 0.01
55 68 0.28
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.28
Consensus pattern (43 bp):
TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
Found at i:47389 original size:98 final size:98
Alignment explanation
Indices: 47216--47457 Score: 344
Period size: 98 Copynumber: 2.5 Consensus size: 98
47206 AAATTGTCAC
* * ** **
47216 CAAGGAACCCCTACATATCACGTTGGTCCCTCAA-G-TGTTCATCAAATTTATGTTCAAGAAACC
1 CAAGAAACCCCTACATATCACGATGGTTTCTCAAGGTTG-TCATCAAATTTATCATCAAGAAACC
47279 CCTACATATCACGATGGTCCCTCAAGATTTTCAT
65 CCTACATATCACGATGGTCCCTCAAGATTTTCAT
* *
47313 CAAGAAACCCCTACATATCACGATGGTTTCTCAAGGTTGTCATCAAATTTTTCATCAAGGAACCC
1 CAAGAAACCCCTACATATCACGATGGTTTCTCAAGGTTGTCATCAAATTTATCATCAAGAAACCC
* * *
47378 TTACATATCACGATGGTCCCTCAAGCTTTTTAT
66 CTACATATCACGATGGTCCCTCAAGATTTTCAT
* *
47411 CAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTGTCCTCAAA
1 CAAGAAACCCCTACATATCACGATGGTTTCTCAAGGTTGTCATCAAA
47458 AAACCCCTAC
Statistics
Matches: 130, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
97 30 0.23
98 98 0.75
99 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.29
Consensus pattern (98 bp):
CAAGAAACCCCTACATATCACGATGGTTTCTCAAGGTTGTCATCAAATTTATCATCAAGAAACCC
CTACATATCACGATGGTCCCTCAAGATTTTCAT
Found at i:47524 original size:141 final size:141
Alignment explanation
Indices: 47269--47606 Score: 543
Period size: 141 Copynumber: 2.4 Consensus size: 141
47259 AAATTTATGT
** *
47269 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGATTTTCATCAAGAAACCCCTACATATCAC
1 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCATCAAGAAACCCCTACATATCAC
* * * * *
47334 GATGGTTTCTCAAGGTTGTCATCAAATTTTTCATCAAGGAACCCTTACATATCACGATGGTCCCT
66 GATGGTCTCTCAAGCTTGTCATCAAATTTGTCATCAAGGAACCCCTACATATCACGACGGTCCCT
*
47399 CAAGCTTTTTA
131 CAAGCTTTTCA
* * *
47410 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTGTCCTCAAAAAACCCCTACATATCAC
1 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCATCAAGAAACCCCTACATATCAC
47475 GATGGTC-CTTCAAGCTTGTCATCAAATTTGTCATCAAGGAACCCCTACATATCACGACGGTCCC
66 GATGGTCTC-TCAAGCTTGTCATCAAATTTGTCATCAAGGAACCCCTACATATCACGACGGTCCC
47539 TCAAGCTTTTCA
130 TCAAGCTTTTCA
*
47551 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCTTCAAGAAACCCCT
1 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCATCAAGAAACCCCT
47607 GAAAATCAGG
Statistics
Matches: 181, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
140 1 0.01
141 180 0.99
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.28
Consensus pattern (141 bp):
TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCATCAAGAAACCCCTACATATCAC
GATGGTCTCTCAAGCTTGTCATCAAATTTGTCATCAAGGAACCCCTACATATCACGACGGTCCCT
CAAGCTTTTCA
Found at i:47732 original size:36 final size:36
Alignment explanation
Indices: 47637--47795 Score: 192
Period size: 36 Copynumber: 4.3 Consensus size: 36
47627 AAAAATATTG
* * * * *
47637 TGTTTCGAGCGAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA---TT
* *
47676 TGTTTCAAGTGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
47712 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
47748 TGTTTCAATGGAAACTGTCTCAAGGGAGACAAAATG
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
47784 TGTTTCAAGGGA
1 TGTTTCAAGGGA
47796 GACAAAATTT
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
36 77 0.73
39 28 0.27
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
Found at i:47801 original size:57 final size:57
Alignment explanation
Indices: 47731--47852 Score: 201
Period size: 57 Copynumber: 2.1 Consensus size: 57
47721 GGAAACCGTC
*
47731 TCAAGAGAGACAAAATTTGTTTCAATG-GAAACTGTCTCAAGGGAGACAAAATGTGTT
1 TCAAGGGAGACAAAATTTGTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATGTGTT
* *
47788 TCAAGGGAGACAAAATTTGTTTCGAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATGTGTT
47845 TCAAGGGA
1 TCAAGGGA
47853 AACCGTCTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 1 0.02
57 60 0.98
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (57 bp):
TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATGTGTT
Found at i:47854 original size:93 final size:92
Alignment explanation
Indices: 47687--47898 Score: 343
Period size: 93 Copynumber: 2.3 Consensus size: 92
47677 GTTTCAAGTG
* *
47687 AAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTT
1 AAATTGTTTCAAGGGAGACAAAATTTGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTTGTT
* *
47752 TCAATGGAAACTGTCTCAAGGGAGACA
66 TCAAGGGAAACCGTCTCAAGGGAGACA
* * *
47779 AAATGTGTTTCAAGGGAGACAAAATTTGTTTCGAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 AAAT-TGTTTCAAGGGAGACAAAATTTGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTTGT
47844 TTCAAGGGAAACCGTCTCAAGGGAGACA
65 TTCAAGGGAAACCGTCTCAAGGGAGACA
47872 AAATTTGTTTCAAGGGAGACAAAATTT
1 AAA-TTGTTTCAAGGGAGACAAAATTT
47899 TTCTGTTTCG
Statistics
Matches: 111, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
92 4 0.04
93 106 0.95
94 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (92 bp):
AAATTGTTTCAAGGGAGACAAAATTTGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTTGTT
TCAAGGGAAACCGTCTCAAGGGAGACA
Found at i:47886 original size:36 final size:36
Alignment explanation
Indices: 47788--47888 Score: 175
Period size: 36 Copynumber: 2.8 Consensus size: 36
47778 AAAATGTGTT
* * *
47788 TCAAGGGAGACAAAATTTGTTTCGAGAGAAACTGTC
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTC
47824 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTC
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTC
47860 TCAAGGGAGACAAAATTTGTTTCAAGGGA
1 TCAAGGGAGACAAAATTTGTTTCAAGGGA
47889 GACAAAATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (36 bp):
TCAAGGGAGACAAAATTTGTTTCAAGGGAAACCGTC
Found at i:47913 original size:25 final size:21
Alignment explanation
Indices: 47767--47898 Score: 117
Period size: 21 Copynumber: 6.9 Consensus size: 21
47757 GGAAACTGTC
*
47767 TCAAGGGAGACAAAATGTGTT
1 TCAAGGGAGACAAAATTTGTT
47788 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* * *
47809 TC----GAGA-GAAA-CTGTC
1 TCAAGGGAGACAAAATTTGTT
47824 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
** *
47845 TCAA-GG-G---AAA-CCGTC
1 TCAAGGGAGACAAAATTTGTT
47860 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
47881 TCAAGGGAGACAAAATTT
1 TCAAGGGAGACAAAATTT
47899 TTCTGTTTCG
Statistics
Matches: 86, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
15 11 0.13
16 8 0.09
17 5 0.06
19 5 0.06
20 8 0.09
21 49 0.57
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:48265 original size:34 final size:33
Alignment explanation
Indices: 48221--48332 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 33
48211 TCTCAGAGAA
48221 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
1 AAATTGTCTCAA-CGAGACGAAATTTGTTTTGAG
* *
48255 AAATGGTCTCAATCGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAA-CGAGACGAAATTTGTTTTGAG
* *
48289 AAATTGTCTCAACTAAGACGAAATTTATTTTGAG
1 AAATTGTCTCAAC-GAGACGAAATTTGTTTTGAG
48323 AAATTGTCTC
1 AAATTGTCTC
48333 GAGTGAGATA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
33 1 0.01
34 69 0.99
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
AAATTGTCTCAACGAGACGAAATTTGTTTTGAG
Found at i:48484 original size:32 final size:32
Alignment explanation
Indices: 48448--48589 Score: 212
Period size: 32 Copynumber: 4.4 Consensus size: 32
48438 AGGATATTGA
* *
48448 ATGCCACAATATTCGATATTGAATCTCCAAAG
1 ATGCCCCAACATTCGATATTGAATCTCCAAAG
* *
48480 ATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACA-TTCGATATTGAATCTCCAAAG
* *
48513 ATGCCCCAACATTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACATTCGATATTGAATCTCCAAAG
*
48545 ATGCCCCAATATTCGATATTGAATCTCCAAAG
1 ATGCCCCAACATTCGATATTGAATCTCCAAAG
48577 ATGCCCCAACATT
1 ATGCCCCAACATT
48590 TTGATGTTCC
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 71 0.70
33 30 0.30
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (32 bp):
ATGCCCCAACATTCGATATTGAATCTCCAAAG
Found at i:48552 original size:65 final size:64
Alignment explanation
Indices: 48448--48597 Score: 219
Period size: 65 Copynumber: 2.3 Consensus size: 64
48438 AGGATATTGA
* * * * * *
48448 ATGCCACAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACA-TTCGATATTGAATCTCCAAAG
*
48513 ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAATATTCGATATTGAATCTCCAAAG
1 ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTCGATATTGAATCTCCAAAG
48577 ATGCCCCAACATTTTGATGTT
1 ATGCCCCAACA-TTTGATGTT
48598 CCAACATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
64 30 0.39
65 47 0.61
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (64 bp):
ATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTCGATATTGAATCTCCAAAG
Found at i:48601 original size:16 final size:16
Alignment explanation
Indices: 48582--48613 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48572 CAAAGATGCC
48582 CCAACATTTTGATGTT
1 CCAACATTTTGATGTT
48598 CCAACATTTTGATGTT
1 CCAACATTTTGATGTT
48614 GAATCTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (16 bp):
CCAACATTTTGATGTT
Found at i:48645 original size:32 final size:32
Alignment explanation
Indices: 48598--48688 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
48588 TTTTGATGTT
48598 CCAACATTTTGATGTTGAATCTCCAAAGATGCC
1 CCAACA-TTTGATGTTGAATCTCCAAAGATGCC
48631 CCAACATTTGATGTTGAATCTCCAAAGATGCC
1 CCAACATTTGATGTTGAATCTCCAAAGATGCC
*
48663 CCAACATTTGATGTTGAATCTTCAAA
1 CCAACATTTGATGTTGAATCTCCAAA
48689 TATACCCTCT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.89
33 6 0.11
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (32 bp):
CCAACATTTGATGTTGAATCTCCAAAGATGCC
Found at i:48659 original size:81 final size:79
Alignment explanation
Indices: 48518--48677 Score: 275
Period size: 81 Copynumber: 2.0 Consensus size: 79
48508 CAAAGATGCC
*
48518 CCAACATTTGATGTTGAATCTCCAAAGATGCCCCAATATTCGATATTGAATCTCCAAAGATGCCC
1 CCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTCGATATTGAATCTCCAAAGATGCCC
48583 CAACATTTTGATGTT
66 CAACA-TTTGATGTT
* *
48598 CCAACATTTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCC
1 CCAACA-TTTGATGTTGAATCTCCAAAGATGCCCCAACATTCGATATTGAATCTCCAAAGATGCC
48663 CCAACATTTGATGTT
65 CCAACATTTGATGTT
48678 GAATCTTCAA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 15 0.20
81 61 0.80
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (79 bp):
CCAACATTTGATGTTGAATCTCCAAAGATGCCCCAACATTCGATATTGAATCTCCAAAGATGCCC
CAACATTTGATGTT
Found at i:48683 original size:113 final size:113
Alignment explanation
Indices: 48485--48688 Score: 372
Period size: 113 Copynumber: 1.8 Consensus size: 113
48475 CAAAGATGCC
48485 CCAACATTTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCC
1 CCAACATTTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCC
*
48550 CCAATATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTT
66 CCAACATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTT
48598 CCAACATTTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCC
1 CCAACATTTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCC
* * *
48663 CCAACATTTGATGTTGAATCTTCAAA
66 CCAACATTCGATATTGAATCTCCAAA
48689 TATACCCTCT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 87 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (113 bp):
CCAACATTTTGATGTTGAATCTCCAAAGATGCCCCAACATTTGATGTTGAATCTCCAAAGATGCC
CCAACATTCGATATTGAATCTCCAAAGATGCCCCAACATTTTGATGTT
Found at i:55279 original size:2 final size:2
Alignment explanation
Indices: 55272--55313 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
55262 ATTTTGATGA
55272 AT AT AT AT AT AT GA- 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
55314 TATTTTAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 36 0.95
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56174 original size:3 final size:3
Alignment explanation
Indices: 56160--56227 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
56150 AATATTGTAA
* * *
56160 AAT AAT ATT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
56208 ACT -AT AGT ATAT AAT AAT AA
1 AAT AAT AAT A-AT AAT AAT AA
56228 ATATAATATA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.94
4 2 0.04
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:62221 original size:30 final size:30
Alignment explanation
Indices: 62130--62309 Score: 228
Period size: 29 Copynumber: 6.2 Consensus size: 30
62120 AAACAATTAT
*
62130 CAAAATAGCACCCTTTTCGAATT-AATTCC
1 CAAAATAGCACCTTTTTCGAATTAAATTCC
62159 CAAAATAGCA-C-TTTTCGAATT-AATTCC
1 CAAAATAGCACCTTTTTCGAATTAAATTCC
* *
62186 CAAAATAGCACATTTTTCGAATTAAATTCA
1 CAAAATAGCACCTTTTTCGAATTAAATTCC
* **
62216 TAAAATAGCAAATTTTT-GAATTAAATTCC
1 CAAAATAGCACCTTTTTCGAATTAAATTCC
*
62245 CAAAATATCACCTTTTTCGAATTAAATTCC
1 CAAAATAGCACCTTTTTCGAATTAAATTCC
* * *
62275 TAAAATAGCACCTATTTCGAATT-AATTTC
1 CAAAATAGCACCTTTTTCGAATTAAATTCC
62304 CAAAAT
1 CAAAAT
62310 GTCACCTGAT
Statistics
Matches: 133, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
27 26 0.20
28 1 0.01
29 54 0.41
30 52 0.39
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (30 bp):
CAAAATAGCACCTTTTTCGAATTAAATTCC
Found at i:62261 original size:59 final size:58
Alignment explanation
Indices: 62130--62309 Score: 247
Period size: 59 Copynumber: 3.1 Consensus size: 58
62120 AAACAATTAT
* *
62130 CAAAATAGCACCCTTTTCGAATT-AATTCCCAAAATAGC-ACTTTTCGAATTAATTCC
1 CAAAATAGCACCTTTTTCGAATTAAATTCCTAAAATAGCAACTTTTCGAATTAATTCC
* * * *
62186 CAAAATAGCACATTTTTCGAATTAAATTCATAAAATAGCAAATTTTTGAATTAAATTCC
1 CAAAATAGCACCTTTTTCGAATTAAATTCCTAAAATAGCAACTTTTCGAATT-AATTCC
* * *
62245 CAAAATATCACCTTTTTCGAATTAAATTCCTAAAATAGCACCTATTTCGAATTAATTTC
1 CAAAATAGCACCTTTTTCGAATTAAATTCCTAAAATAGCAACT-TTTCGAATTAATTCC
62304 CAAAAT
1 CAAAAT
62310 GTCACCTGAT
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
56 21 0.20
57 13 0.12
58 10 0.09
59 55 0.51
60 8 0.07
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.34
Consensus pattern (58 bp):
CAAAATAGCACCTTTTTCGAATTAAATTCCTAAAATAGCAACTTTTCGAATTAATTCC
Found at i:62372 original size:22 final size:23
Alignment explanation
Indices: 62324--62380 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
62314 CCTGATCAAC
* *
62324 GGTCAACGGGTCAGGTCGGGTCG
1 GGTCAACGGGTCAGCTCGGGTCA
*
62347 GGTCAACGGGT-AGCTCGGGTTA
1 GGTCAACGGGTCAGCTCGGGTCA
62369 GGTCAACGGGTC
1 GGTCAACGGGTC
62381 GGGTCGGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (23 bp):
GGTCAACGGGTCAGCTCGGGTCA
Found at i:76080 original size:18 final size:18
Alignment explanation
Indices: 76057--76093 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
76047 TTTCTCAAAC
76057 ATATAATTATATAACTTG
1 ATATAATTATATAACTTG
76075 ATATAATTATATAACTTG
1 ATATAATTATATAACTTG
76093 A
1 A
76094 CTGAGGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
ATATAATTATATAACTTG
Found at i:76468 original size:17 final size:16
Alignment explanation
Indices: 76441--76479 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
76431 TAATAATTAA
76441 ATAAAATAAAAAATTT
1 ATAAAATAAAAAATTT
76457 ATAAAATAAAAAATTT
1 ATAAAATAAAAAATTT
76473 ATTAAAA
1 A-TAAAA
76480 AAATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAATAAAAAATTT
Found at i:76484 original size:20 final size:20
Alignment explanation
Indices: 76436--76487 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 20
76426 TATTTTAATA
76436 ATTAAATAAAATAAAAAATTT
1 ATTAAA-AAAATAAAAAATTT
76457 A-T---AAAATAAAAAATTT
1 ATTAAAAAAATAAAAAATTT
76473 ATTAAAAAAATAAAA
1 ATTAAAAAAATAAAA
76488 TAATAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
16 15 0.56
17 1 0.04
20 10 0.37
21 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATTAAAAAAATAAAAAATTT
Found at i:76498 original size:20 final size:20
Alignment explanation
Indices: 76439--76499 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
76429 TTTAATAATT
* * *
76439 AAATAAAATAAAAAATTTATA
1 AAATAAAATAATAAA-TAAAA
* *
76460 AAATAAAA-AATTTATTAAAA
1 AAATAAAATAA-TAAATAAAA
76480 AAATAAAATAATAAATAAAA
1 AAATAAAATAATAAATAAAA
76500 TTCAAATATC
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAAATAATAAATAAAA
Done.