Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003903.1 Hibiscus syriacus cultivar Beakdansim tig00008439_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: 114970
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1455 original size:31 final size:31
Alignment explanation
Indices: 1411--1504 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 31
1401 TATATATATA
1411 TATATATATATATATATATAATATTTATTTTT
1 TATAT-TATATATATATATAATATTTATTTTT
*
1443 TATATTATATATATA-AT-ATTTTATATTTTT
1 TATATTATATATATATATAATATT-TATTTTT
*
1473 TATA-TAT-TAT-TATATAATATTTTATATTT
1 TATATTATATATATATATAATA-TTTATTTTT
1502 TAT
1 TAT
1505 TTTTTTATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.04
28 5 0.09
29 18 0.33
30 15 0.27
31 10 0.18
32 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TATATTATATATATATATAATATTTATTTTT
Found at i:1476 original size:21 final size:21
Alignment explanation
Indices: 1440--1499 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1430 AATATTTATT
* *
1440 TTTTATATTATATATATAATA
1 TTTTATATTTTTTATATAATA
*
1461 TTTTATATTTTTTATATATTA
1 TTTTATATTTTTTATATAATA
* *
1482 TTATATAATATTTTATAT
1 TTTTAT-ATTTTTTATAT
1500 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATATTTTTTATATAATA
Found at i:1476 original size:23 final size:23
Alignment explanation
Indices: 1396--1479 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
1386 CCTCGCCTGA
1396 TTATATA-TATATATAT-ATA-T
1 TTATATATTATATATATAATATT
* *
1416 ATATATA-TATATATAATATTTATT
1 TTATATATTATATAT-ATA-ATATT
*
1440 TTTTATATTATATATATAATATT
1 TTATATATTATATATATAATATT
* *
1463 TTATATTTTTTATATAT
1 TTATATATTATATATAT
1480 TATTATATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 13 0.25
21 2 0.04
23 20 0.39
24 9 0.18
25 7 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATATATTATATATATAATATT
Found at i:1479 original size:2 final size:2
Alignment explanation
Indices: 1397--1461 Score: 75
Period size: 2 Copynumber: 34.5 Consensus size: 2
1387 CTCGCCTGAT
*
1397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1438 T- TT TT TA TA T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1462 TTTATATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
1 4 0.07
2 52 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1521 original size:65 final size:68
Alignment explanation
Indices: 1405--1529 Score: 170
Period size: 65 Copynumber: 1.9 Consensus size: 68
1395 ATTATATATA
*
1405 TATATATATATATATATATATATATAATATTTATTTTTTATATTATATATATAATATTTTATATT
1 TATATATATATATATATATATATATAATATTTATTTTTTATATTATATATATAAAATTTTATATT
1470 TTT
66 TTT
* *
1473 TATATAT-TAT-TATATA-ATATTTTATATTTTATTTTTT-TATTA-ATTATATAAAATTTT
1 TATATATATATATATATATATATATAATA-TTTATTTTTTATATTATA-TATATAAAATTTT
1530 CGGGTTCGGG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
64 1 0.02
65 25 0.48
66 16 0.31
67 3 0.06
68 7 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (68 bp):
TATATATATATATATATATATATATAATATTTATTTTTTATATTATATATATAAAATTTTATATT
TTT
Found at i:2021 original size:32 final size:33
Alignment explanation
Indices: 1977--2039 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1967 TAAATAAAAA
*
1977 AACACAAATA-TTTTATAAATAAATAAACAATC
1 AACACAAATATTTTTAAAAATAAATAAACAATC
*
2009 AACATAAATATTTTTAAAAATAAATAAACAA
1 AACACAAATATTTTTAAAAATAAATAAACAA
2040 ATTTGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (33 bp):
AACACAAATATTTTTAAAAATAAATAAACAATC
Found at i:5791 original size:36 final size:36
Alignment explanation
Indices: 5735--5803 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
5725 TGTTTGAAAA
*
5735 TATTTTTTAGAAAACAGTTTTTGAAAACATATAATT
1 TATTTTTTAGAAAACAGTTTTCGAAAACATATAATT
* *
5771 TATTTTTTA-AAAATCGGTTTTCGAAAATATATA
1 TATTTTTTAGAAAA-CAGTTTTCGAAAACATATA
5804 TAATATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 4 0.14
36 25 0.86
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (36 bp):
TATTTTTTAGAAAACAGTTTTCGAAAACATATAATT
Found at i:5839 original size:73 final size:73
Alignment explanation
Indices: 5789--5928 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 73
5779 AAAAATCGGT
5789 TTTCGAAAATATATATAATATATAGTTTTTGAAAACATCTTGAAAACATATATAGTATATAAATT
1 TTTCGAAAATATATATAATATATAG-TTTTGAAAACATCTTGAAAACATATATAGTATATAAATT
*
5854 TTGAAAATA
65 TTAAAAATA
* * * * *
5863 TTTCGAAAATATATATATTATATAGTTTTGAAAACATTTTGAATATATATATA-TATAATAAGTT
1 TTTCGAAAATATATATAATATATAGTTTTGAAAACATCTTGAAAACATATATAGTAT-ATAAATT
5927 TT
65 TT
5929 TGAAAACGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
72 3 0.05
73 33 0.55
74 24 0.40
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (73 bp):
TTTCGAAAATATATATAATATATAGTTTTGAAAACATCTTGAAAACATATATAGTATATAAATTT
TAAAAATA
Found at i:5840 original size:37 final size:36
Alignment explanation
Indices: 5793--5940 Score: 165
Period size: 37 Copynumber: 4.0 Consensus size: 36
5783 ATCGGTTTTC
5793 GAAAATATATATAATATATAGTTTTTGAAAACATCTT
1 GAAAATATATATAATATATAGTTTTTGAAAACAT-TT
* * ** *
5830 GAAAACATATATAGTATATAAATTTTGAAAATATTT
1 GAAAATATATATAATATATAGTTTTTGAAAACATTT
*
5866 CGAAAATATATATATTATATAG-TTTTGAAAACATTTT
1 -GAAAATATATATAATATATAGTTTTTGAAAACA-TTT
*
5903 GAATATATATAT-ATATAATAAGTTTTTGAAAACGATTT
1 GAAAATATATATAATAT-AT-AGTTTTTGAAAAC-ATTT
5941 TTGAAAATGC
Statistics
Matches: 94, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
35 3 0.03
36 25 0.27
37 52 0.55
38 13 0.14
39 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (36 bp):
GAAAATATATATAATATATAGTTTTTGAAAACATTT
Found at i:5875 original size:74 final size:74
Alignment explanation
Indices: 5789--5934 Score: 215
Period size: 74 Copynumber: 2.0 Consensus size: 74
5779 AAAAATCGGT
5789 TTTCGAAAATATATATAATATATAGTTTTTGAAAACATCTTGAAAACATATATAGTAT-ATAA-A
1 TTTCGAAAATATATATAATATATAG-TTTTGAAAACATCTTGAAAACATATATA-TATAATAAGA
5852 TTTTGAAAATA
64 TTTTGAAAATA
* * * * *
5863 TTTCGAAAATATATATATTATATAGTTTTGAAAACATTTTGAATATATATATATATAATAAGTTT
1 TTTCGAAAATATATATAATATATAGTTTTGAAAACATCTTGAAAACATATATATATAATAAGATT
5928 TTGAAAA
66 TTGAAAA
5935 CGATTTTTGA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
72 3 0.05
73 29 0.45
74 33 0.51
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (74 bp):
TTTCGAAAATATATATAATATATAGTTTTGAAAACATCTTGAAAACATATATATATAATAAGATT
TTGAAAATA
Found at i:5955 original size:38 final size:37
Alignment explanation
Indices: 5796--5971 Score: 134
Period size: 36 Copynumber: 4.8 Consensus size: 37
5786 GGTTTTCGAA
* *
5796 AATATATATA-ATATAT-AGTTTTTGAAAACATCTTG
1 AATATATACATATATATAAGTTTTTGAAAACATTTTG
* * * * * *
5831 AAAACATATATAGTATATAA-ATTTTGAAAATATTTCG
1 AATATATACATA-TATATAAGTTTTTGAAAACATTTTG
* *
5868 AAAATATATATAT-TATATAG-TTTTGAAAACATTTTG
1 AATATATACATATATATA-AGTTTTTGAAAACATTTTG
*
5904 AATATATATATATATAATAAGTTTTTGAAAACGATTTTTG
1 AATATATACATATAT-ATAAGTTTTTGAAAAC-A-TTTTG
* *
5944 AA-A-ATGCATATATA-CAGTTTTTGAAAAC
1 AATATATACATATATATAAGTTTTTGAAAAC
5972 TTATATATAT
Statistics
Matches: 118, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
35 12 0.10
36 42 0.36
37 33 0.28
38 22 0.19
39 2 0.02
40 7 0.06
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (37 bp):
AATATATACATATATATAAGTTTTTGAAAACATTTTG
Found at i:5987 original size:23 final size:22
Alignment explanation
Indices: 5936--5993 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
5926 TTTTGAAAAC
5936 GATTTTTGAAAATGCATATATA
1 GATTTTTGAAAATGCATATATA
* *
5958 CAGTTTTTGAAAACT-TATATATA
1 GA-TTTTTGAAAA-TGCATATATA
*
5981 TGATTTTTAAAAA
1 -GATTTTTGAAAA
5994 ATATTTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 1 0.03
23 26 0.90
24 2 0.07
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.43
Consensus pattern (22 bp):
GATTTTTGAAAATGCATATATA
Found at i:6033 original size:32 final size:33
Alignment explanation
Indices: 5962--6127 Score: 117
Period size: 33 Copynumber: 4.8 Consensus size: 33
5952 TATATACAGT
*
5962 TTTTGAAAACT-TAT-ATATATGATTTTTAAAAAA
1 TTTTGAAAA-TATATAATATATG-TTTTTAAAACA
5995 TATTTGAAAATATATAATATA-GTTTTTAAAACA
1 T-TTTGAAAATATATAATATATGTTTTTAAAACA
* * *
6028 TTTTGAAGACTATATAA-ATA-GTTTTGAAAACTT
1 TTTTGAA-AATATATAATATATGTTTTTAAAAC-A
* * *
6061 TTTTAAAAATATATATATAATATATAGTTTTAAAATA
1 TTTTGAAAATATATA-AT-ATATGT--TTTTAAAACA
6098 TTTTTGAAAATATATATATTATATAGTTTT
1 -TTTTGAAAATATATA-A-TATAT-GTTTT
6128 GGGAAATATT
Statistics
Matches: 107, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
32 26 0.24
33 28 0.26
34 12 0.11
35 8 0.07
36 1 0.01
37 3 0.03
38 27 0.25
39 2 0.02
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (33 bp):
TTTTGAAAATATATAATATATGTTTTTAAAACA
Found at i:6111 original size:38 final size:37
Alignment explanation
Indices: 6004--6128 Score: 118
Period size: 38 Copynumber: 3.5 Consensus size: 37
5994 ATATTTGAAA
* * * * *
6004 ATATATAATATAGTTTTTAAAACA-TTTTGAAGA-CT
1 ATATATTATATAGTTTTGAAAACATTTTTAAAAATAT
*
6039 ATATA--A-ATAGTTTTGAAAACTTTTTTAAAAATAT
1 ATATATTATATAGTTTTGAAAACATTTTTAAAAATAT
* *
6073 ATATATAATATATAGTTTT-AAAATATTTTTGAAAATAT
1 ATATAT--TATATAGTTTTGAAAACATTTTTAAAAATAT
6111 ATATATTATATAGTTTTG
1 ATATATTATATAGTTTTG
6129 GGAAATATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
32 13 0.18
33 8 0.11
34 6 0.08
35 5 0.07
36 11 0.15
38 23 0.31
39 8 0.11
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (37 bp):
ATATATTATATAGTTTTGAAAACATTTTTAAAAATAT
Found at i:6138 original size:38 final size:37
Alignment explanation
Indices: 6038--6127 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 37
6028 TTTTGAAGAC
*
6038 TATATAAATAGTTTTGAAAACT-TTTTTAAAAATATATA
1 TATATATATAGTTTT-AAAA-TATTTTTAAAAATATATA
*
6076 TATAATATATAGTTTTAAAATATTTTTGAAAATATATA
1 TAT-ATATATAGTTTTAAAATATTTTTAAAAATATATA
6114 TAT-TATATAGTTTT
1 TATATATATAGTTTT
6128 GGGAAATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
36 11 0.23
37 1 0.02
38 25 0.52
39 11 0.23
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (37 bp):
TATATATATAGTTTTAAAATATTTTTAAAAATATATA
Found at i:7704 original size:5 final size:6
Alignment explanation
Indices: 7680--7713 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
7670 CGAATTGAAT
7680 TTTTAAA TTTTAA TTTTAA -TTTAA TTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
7714 CGTGATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.65
7 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:7704 original size:11 final size:11
Alignment explanation
Indices: 7688--7712 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7678 ATTTTTAAAT
7688 TTTAATTTTAA
1 TTTAATTTTAA
7699 TTTAATTTTAA
1 TTTAATTTTAA
7710 TTT
1 TTT
7713 TCGTGATTAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:13464 original size:85 final size:85
Alignment explanation
Indices: 12806--13445 Score: 836
Period size: 85 Copynumber: 7.5 Consensus size: 85
12796 CTATTCGCAA
** * * * * * *
12806 CATAGCTCAAGGTAATAAGGGCTATATGTCAGCAAAAATCCTTCGAGTTCGATTACATTCAGCTT
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAA-CCTTCGAGTTCGATTCCAGTCAGCTC
* *
12871 AAGGACATATCAAATTTTCAG
65 AAGGCCATATCAAATTTACAG
* * * * * *
12892 CATAGCTCAAGGCGAGAAAGGCTATCTATCAAAAAAAAACCTTCAAGTTCGATTTCATTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTC-AACAAAAACCTTCGAGTTCGATTCCAGTCAGCTC
*
12957 AAGGGCA-A-CTAAATTTACAG
65 AAGGCCATATC-AAATTTACAG
* *
12977 CATAGCTCAAGGCGAGAAGGGCTATCTATAAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
*
13042 AGGGCATATCAAATTTACAG
66 AGGCCATATCAAATTTACAG
* * *
13062 CATAACTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCTAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
* *
13127 AGGGCATATCAAATTTACAA
66 AGGCCATATCAAATTTACAG
* * *
13147 CATAGCTCAAGACGAGAATGGCTATCTGTCAACAAAAATCTTCGAGTTCGATTCCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
*
13212 AGGCCAAATCAAATTTACAG
66 AGGCCATATCAAATTTACAG
* * * * * * * *
13232 TATAGCTCAAGGCAAGAAGGGTTATCTGTTAACAAAAACCTTTGAGTTTGATTCCAATCAACTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
*
13297 AGGCCATATC-AATTTATAG
66 AGGCCATATCAAATTTACAG
* * * *
13316 TATAGCTCAAGGCGAGAAAGGCTATCTGTCAACAAAAACCTTCGGGTTCGATTTCAGTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
13381 AGGCCATATCAAATTTACAG
66 AGGCCATATCAAATTTACAG
* *
13401 TATAGCTCAAGGCGAGAAGAGCTATCTGTCAACAAAAACCTTCGA
1 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGA
13446 ATTAGATTAT
Statistics
Matches: 488, Mismatches: 61, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
84 111 0.23
85 317 0.65
86 54 0.11
87 6 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (85 bp):
CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAGTCAGCTCA
AGGCCATATCAAATTTACAG
Found at i:14133 original size:36 final size:34
Alignment explanation
Indices: 14088--14419 Score: 131
Period size: 35 Copynumber: 9.2 Consensus size: 34
14078 AATGTTTGAA
*
14088 AATAT-TTTTTAGAAAATGACTTTTGAAAACATAT
1 AATATATTTTTAGAAAATCA-TTTTGAAAACATAT
*
14122 AATATACTTTTTA-AAAATCAGTTTTCGAAAATATTTAT
1 AATATA-TTTTTAGAAAATCA-TTTT-GAAAACA--TAT
14160 AATATATAGTTTT-GAAAA-CATTTTGAAAACATAT
1 AATATAT--TTTTAGAAAATCATTTTGAAAACATAT
*
14194 ATAGTAAATAGTTTTT-GAAAA-CATTTTGAAAATATAT
1 A-A-T--ATA-TTTTTAGAAAATCATTTTGAAAACATAT
*
14231 ATATTATATAGTTTT-GAAAA-CATTTTGAATATATATATATAT
1 A-A-TATAT--TTTTAGAAAATCATTTTG---A-A-A-ACATAT
* *
14273 AATATAGTTTTTA-AACA-CGATTTTTGAAAATGTATAT
1 AATATA-TTTTTAGAAAATC-A-TTTTGAAAA--CATAT
*
14310 ATTATATAGTTTTT-GAAAA-CATTTTGAAAATATATT
1 A--ATATA-TTTTTAGAAAATCATTTTGAAAACATA-T
*
14346 AATATATAGTTTT-TAAAA-CATTTTGAAAACTATAT
1 AATATAT--TTTTAGAAAATCATTTTGAAAAC-ATAT
*
14381 AATATATAGTTTT-GAAAAT-ATTTTTAAAACATAT
1 AATATAT--TTTTAGAAAATCATTTTGAAAACATAT
14415 -ATATA
1 AATATA
14420 ATATATAGTT
Statistics
Matches: 251, Mismatches: 12, Indels: 71
0.75 0.04 0.21
Matches are distributed among these distances:
33 6 0.02
34 19 0.08
35 66 0.26
36 41 0.16
37 49 0.20
38 16 0.06
39 33 0.13
40 6 0.02
41 8 0.03
42 7 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (34 bp):
AATATATTTTTAGAAAATCATTTTGAAAACATAT
Found at i:14183 original size:11 final size:11
Alignment explanation
Indices: 14169--14225 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
14159 TAATATATAG
14169 TTTTGAAAACA
1 TTTTGAAAACA
14180 TTTTGAAAACA
1 TTTTGAAAACA
* **
14191 TATATAGTAAATAGT
1 T-T-TTG-AAA-ACA
14206 TTTTGAAAACA
1 TTTTGAAAACA
14217 TTTTGAAAA
1 TTTTGAAAA
14226 TATATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 22 0.61
12 4 0.11
13 4 0.11
14 4 0.11
15 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.39
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:14218 original size:37 final size:37
Alignment explanation
Indices: 14123--14463 Score: 373
Period size: 36 Copynumber: 9.3 Consensus size: 37
14113 AAAACATATA
* * *
14123 ATATACTTTTTAAAAATCAGTTTTCGAAAATATTTATAAT
1 ATATAGTTTTTGAAAA-CA-TTTT-GAAAATATATATAAT
* *
14163 ATATAG-TTTTGAAAACATTTTGAAAACATATATAGT
1 ATATAGTTTTTGAAAACATTTTGAAAATATATATAAT
* *
14199 AAATAGTTTTTGAAAACATTTTGAAAATATATATATT
1 ATATAGTTTTTGAAAACATTTTGAAAATATATATAAT
*
14236 ATATAG-TTTTGAAAACATTTTGAATATATATATATAT
1 ATATAGTTTTTGAAAACATTTTGAAAATATATATA-AT
* *
14273 AATATAGTTTTT-AAACACGATTTTTGAAAATGTATATATT
1 -ATATAGTTTTTGAAA-AC-A-TTTTGAAAATATATATAAT
14313 ATATAGTTTTTGAAAACATTTTGAAAATATAT-TAAT
1 ATATAGTTTTTGAAAACATTTTGAAAATATATATAAT
*
14349 ATATAGTTTTT-AAAACATTTTGAAAA-CTATATAAT
1 ATATAGTTTTTGAAAACATTTTGAAAATATATATAAT
* *
14384 ATATAG-TTTTGAAAATATTTTTAAAACATATATATAAT
1 ATATAGTTTTTGAAAACA-TTTTGAAA-ATATATATAAT
* *
14422 ATATAG-TTTT-AAAATATTTT-TAAATATATAT--T
1 ATATAGTTTTTGAAAACATTTTGAAAATATATATAAT
14454 ATATAGTTTT
1 ATATAGTTTT
14464 GCGAATTTTT
Statistics
Matches: 266, Mismatches: 21, Indels: 35
0.83 0.07 0.11
Matches are distributed among these distances:
32 7 0.03
33 3 0.01
34 15 0.06
35 32 0.12
36 69 0.26
37 58 0.22
38 30 0.11
39 27 0.10
40 10 0.04
41 15 0.06
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATAGTTTTTGAAAACATTTTGAAAATATATATAAT
Found at i:14424 original size:36 final size:36
Alignment explanation
Indices: 14118--14464 Score: 345
Period size: 37 Copynumber: 9.4 Consensus size: 36
14108 TTTTGAAAAC
* * *
14118 ATATAATATACTTTTTAAAAATCAGTTTTCGAAAATATTT
1 ATATAATATA-GTTTTGAAAA-CA-TTTT-GAAAATATAT
*
14158 ATA-ATATATAGTTTTGAAAACATTTTGAAAACATAT
1 ATATA-ATATAGTTTTGAAAACATTTTGAAAATATAT
14194 ATAGTAA-ATAGTTTTTGAAAACATTTTGAAAATATAT
1 ATA-TAATATAG-TTTTGAAAACATTTTGAAAATATAT
*
14231 ATATTATATAGTTTTGAAAACATTTTGAATATATATAT
1 ATATAATATAGTTTTGAAAACATTTTGAA-A-ATATAT
* *
14269 ATATAATATAGTTTTTAAACACGATTTTTGAAAATGTAT
1 ATATAATATAGTTTTGAAA-AC-A-TTTTGAAAATATAT
*
14308 ATATTATATAGTTTTTGAAAACATTTTGAAAATATAT
1 ATATAATATAG-TTTTGAAAACATTTTGAAAATATAT
*
14345 -TA-ATATATAGTTTTTAAAACATTTTGAAAACTATAT
1 ATATA-ATATAGTTTTGAAAACATTTTGAAAA-TATAT
* * *
14381 A-AT-ATATAGTTTTGAAAATATTTTTAAAACATAT
1 ATATAATATAGTTTTGAAAACATTTTGAAAATATAT
* *
14415 ATATAATATATAGTTTT-AAAATATTTT-TAAATATAT
1 ATAT-A-ATATAGTTTTGAAAACATTTTGAAAATATAT
14451 AT-T-ATATAGTTTTG
1 ATATAATATAGTTTTG
14465 CGAATTTTTT
Statistics
Matches: 267, Mismatches: 20, Indels: 47
0.80 0.06 0.14
Matches are distributed among these distances:
32 10 0.04
34 5 0.02
35 45 0.17
36 58 0.22
37 60 0.22
38 37 0.14
39 28 0.10
40 17 0.06
41 7 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
ATATAATATAGTTTTGAAAACATTTTGAAAATATAT
Found at i:14492 original size:5 final size:5
Alignment explanation
Indices: 14482--14513 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
14472 TTTTATATGA
14482 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
14514 GGTCTAGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:14496 original size:19 final size:19
Alignment explanation
Indices: 14472--14513 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
14462 TTGCGAATTT
14472 TTTTATATGA-TTTATTTTA
1 TTTTAT-TGATTTTATTTTA
*
14491 TTTTATTTATTTTATTTTA
1 TTTTATTGATTTTATTTTA
14510 TTTT
1 TTTT
14514 GGTCTAGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTATTGATTTTATTTTA
Found at i:14506 original size:14 final size:14
Alignment explanation
Indices: 14468--14512 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
14458 AGTTTTGCGA
* *
14468 ATTT-TTTTATATG
1 ATTTATTTTATTTT
14481 ATTTATTTTATTTT
1 ATTTATTTTATTTT
14495 ATTTATTTTATTTT
1 ATTTATTTTATTTT
14509 ATTT
1 ATTT
14513 TGGTCTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:15844 original size:16 final size:16
Alignment explanation
Indices: 15825--15858 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15815 ATTTTATTAC
15825 TTTTAAAATTTAATTT
1 TTTTAAAATTTAATTT
**
15841 TTTTAATTTTTAATTT
1 TTTTAAAATTTAATTT
15857 TT
1 TT
15859 AATTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAAAATTTAATTT
Found at i:15915 original size:15 final size:14
Alignment explanation
Indices: 15897--15966 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 14
15887 TATTTTCTTA
15897 TTTTTCTTATTTTAT
1 TTTTTCTTA-TTTAT
* *
15912 TTTTTGTTATTTCT
1 TTTTTCTTATTTAT
*
15926 TTTTCCTTTAATTTAT
1 TTTTTC-TT-ATTTAT
15942 TTATTAT-TTATTTAT
1 TT-TT-TCTTATTTAT
*
15957 TATTTCTTAT
1 TTTTTCTTAT
15967 CTAACATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
13 1 0.02
14 14 0.33
15 17 0.40
16 9 0.21
17 2 0.05
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.74
Consensus pattern (14 bp):
TTTTTCTTATTTAT
Found at i:15952 original size:11 final size:11
Alignment explanation
Indices: 15936--15961 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
15926 TTTTCCTTTA
15936 ATTTATTTATT
1 ATTTATTTATT
15947 ATTTATTTATT
1 ATTTATTTATT
15958 ATTT
1 ATTT
15962 CTTATCTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:17417 original size:13 final size:12
Alignment explanation
Indices: 17390--17427 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
17380 AATTTAATTC
17390 TTAATTCTT--T
1 TTAATTCTTAAT
17400 TTAATTCTTTAAT
1 TTAATTC-TTAAT
17413 TTAATTCTTAAT
1 TTAATTCTTAAT
17425 TTA
1 TTA
17428 GATAGTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 8 0.32
13 8 0.32
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (12 bp):
TTAATTCTTAAT
Found at i:20850 original size:26 final size:26
Alignment explanation
Indices: 20794--20854 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 26
20784 GCATTCAAAT
* *
20794 TTATGATTATCACTATTTGATTCGAA
1 TTATGATTATCAATAATTGATTCGAA
* * * *
20820 CTATGATTATTAATAATTGATTTGGA
1 TTATGATTATCAATAATTGATTCGAA
20846 TTATG-TTAT
1 TTATGATTAT
20855 GACTTGTGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (26 bp):
TTATGATTATCAATAATTGATTCGAA
Found at i:22470 original size:18 final size:18
Alignment explanation
Indices: 22449--22486 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
22439 ATGATTTATG
22449 TTTGCCTCAAAATTTTTA
1 TTTGCCTCAAAATTTTTA
22467 TTTGCCTCAAAATTTTTA
1 TTTGCCTCAAAATTTTTA
22485 TT
1 TT
22487 AAGCATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTGCCTCAAAATTTTTA
Found at i:29247 original size:57 final size:57
Alignment explanation
Indices: 29177--29348 Score: 263
Period size: 57 Copynumber: 3.0 Consensus size: 57
29167 CATAACCATA
* * *
29177 CAACCCCATCACGAACAATAAGACCCTGAGCACAAAGCCAAGGAACCTACAAGTATT
1 CAACCCCATCACGAACAATAAGACTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
* *
29234 CAACCCCGTCACGAACAGTAAGACTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
1 CAACCCCATCACGAACAATAAGACTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
* * * *
29291 CAACCCCCTCACGAACAATAAGGCTCTCAACACAAAGCCGGGGAACCTACAAGTATT
1 CAACCCCATCACGAACAATAAGACTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
29348 C
1 C
29349 TTCCTCCAAC
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 105 1.00
ACGTcount: A:0.38, C:0.33, G:0.16, T:0.13
Consensus pattern (57 bp):
CAACCCCATCACGAACAATAAGACTCTCAGCACAAAGCCGAGGAACCTACAAGTATT
Found at i:34277 original size:21 final size:21
Alignment explanation
Indices: 34253--34292 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34243 ACCAGTGAAA
34253 ATATACATATCTTTTTAAAAC
1 ATATACATATCTTTTTAAAAC
* *
34274 ATATATATATTTTTTTAAA
1 ATATACATATCTTTTTAAA
34293 TTTGAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATACATATCTTTTTAAAAC
Found at i:34431 original size:57 final size:57
Alignment explanation
Indices: 34357--34528 Score: 236
Period size: 57 Copynumber: 3.0 Consensus size: 57
34347 CATAACAATA
* * * * * * *
34357 CAACCCCGTAACAAACAGTAAGACCCTGAGCACAAAGCCAAGGAACCTACAAGTATT
1 CAACCCCGTCACGAACAGTAAGACTCTCAACACAAAGCCGAGGAACCTGCAAGTATT
* *
34414 CAACCCCGTCACGAACAGTAAGACTCTCAACACAAAGCTGAGGAACTTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGACTCTCAACACAAAGCCGAGGAACCTGCAAGTATT
* * *
34471 CAACCCCGTCACGAACAGTAAGGCTCTCATCACAAAGCCGAGGAATCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGACTCTCAACACAAAGCCGAGGAACCTGCAAGTATT
34528 C
1 C
34529 TTCCTCTAAC
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 101 1.00
ACGTcount: A:0.37, C:0.30, G:0.17, T:0.16
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGACTCTCAACACAAAGCCGAGGAACCTGCAAGTATT
Found at i:39681 original size:18 final size:18
Alignment explanation
Indices: 39660--39697 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39650 CCTTACACAC
39660 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
39678 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
39696 TT
1 TT
39698 CATACTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:44863 original size:37 final size:37
Alignment explanation
Indices: 44814--44918 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
44804 CCTTTTCGTC
*
44814 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
44851 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
44888 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
44919 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:45470 original size:21 final size:21
Alignment explanation
Indices: 45444--45495 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
45434 ATTCATTTGG
*
45444 TTATTTTTAATACTATATTTA-
1 TTATTTTTAATA-TATATATAC
*
45465 TTATTTATATATATATATATAC
1 TTATTTTTA-ATATATATATAC
45487 TT-TTTTTAA
1 TTATTTTTAA
45496 AAATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 20 0.77
22 5 0.19
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTTTAATATATATATAC
Found at i:45502 original size:66 final size:63
Alignment explanation
Indices: 45341--45502 Score: 155
Period size: 66 Copynumber: 2.5 Consensus size: 63
45331 CATTATATAA
* * * *
45341 ATATATATATGTATGTTTTTTTAAATGATTTTCAATTGATTTTTTTACACTATATATTATTATT
1 ATATATATATATATCTTTTTTTAAA-AATATTCAATTGATTTTTTTACACTATATATTATTATT
* * *** * * *
45405 ATATATACATATATTTTTTATTTATTTATATTCATTTGGTTATTTTTAATACTATAT-TTATTAT
1 ATATATATATATATCTTTT-TTTAAAAATATTCAATTGATT-TTTTT-ACACTATATATTATTA-
45469 TT
62 TT
45471 ATATATATATATATACTTTTTTTAAAAATATT
1 ATATATATATATAT-CTTTTTTTAAAAATATT
45503 TTACTTATAA
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
64 27 0.35
65 15 0.19
66 32 0.41
67 4 0.05
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (63 bp):
ATATATATATATATCTTTTTTTAAAAATATTCAATTGATTTTTTTACACTATATATTATTATT
Found at i:45532 original size:2 final size:2
Alignment explanation
Indices: 45525--45569 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
45515 GTATTATTAC
45525 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
45567 TA T
1 TA T
45570 TGTAATTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45792 original size:2 final size:2
Alignment explanation
Indices: 45785--45821 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45775 TTTACTCATT
45785 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
45822 TTAATATTTC
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:50343 original size:11 final size:11
Alignment explanation
Indices: 50314--50370 Score: 60
Period size: 11 Copynumber: 4.7 Consensus size: 11
50304 AATCAAGAAC
50314 AAAAAAGAAAAG
1 AAAAAA-AAAAG
50326 AAGAAAAAAAAG
1 AA-AAAAAAAAG
50338 AAAAAAAACAAAAG
1 --AAAAAA-AAAAG
*
50352 AAAAACAAAAG
1 AAAAAAAAAAG
50363 AAAAAAAA
1 AAAAAAAA
50371 GAAAGAACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 12 0.31
12 12 0.31
13 8 0.21
14 7 0.18
ACGTcount: A:0.86, C:0.04, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:50355 original size:20 final size:20
Alignment explanation
Indices: 50332--50397 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
50322 AAAGAAGAAA
50332 AAAAAGAAAAAAAACAAAAG
1 AAAAAGAAAAAAAACAAAAG
*
50352 AAAAACAAAAGAAAA-AAAAG
1 AAAAAGAAAA-AAAACAAAAG
*
50372 --AAAGAACAAAAATCAAAAAG
1 AAAAAGAA-AAAAAAC-AAAAG
50392 AAAAAG
1 AAAAAG
50398 GGACAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
18 8 0.22
19 2 0.05
20 19 0.51
21 4 0.11
22 4 0.11
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAAAACAAAAG
Found at i:50361 original size:25 final size:26
Alignment explanation
Indices: 50308--50383 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 26
50298 AGATCCAATC
*
50308 AAGAACAAAAAAGAAAAGAAGAAAAAA
1 AAGAA-AAAAAACAAAAGAAGAAAAAA
*
50335 AAGAAAAAAAACAAAAGAA-AAACAA
1 AAGAAAAAAAACAAAAGAAGAAAAAA
* *
50360 AAGAAAAAAAA-GAAAGAACAAAAA
1 AAGAAAAAAAACAAAAGAAGAAAAA
50384 TCAAAAAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.14
25 20 0.45
26 13 0.30
27 5 0.11
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAAACAAAAGAAGAAAAAA
Found at i:51073 original size:22 final size:22
Alignment explanation
Indices: 51000--51076 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
50990 GCTACCCCAT
*
51000 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
51022 TAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
51044 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
51066 CAAACCTTTGA
1 CAAACCTTTGA
51077 CCAAACACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:51299 original size:24 final size:24
Alignment explanation
Indices: 51271--51329 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
51261 CAATATTTTT
51271 AAAACTTTTAATTAAACATCTTTC
1 AAAACTTTTAATTAAACATCTTTC
* *
51295 AAAACTCTTGATTAAACATCTTTC
1 AAAACTTTTAATTAAACATCTTTC
*
51319 GAAACTCTTTA
1 AAAACT-TTTA
51330 TTTATATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (24 bp):
AAAACTTTTAATTAAACATCTTTC
Found at i:52186 original size:106 final size:106
Alignment explanation
Indices: 52059--53115 Score: 1470
Period size: 106 Copynumber: 10.0 Consensus size: 106
52049 ATATCGTGCC
* * * * *
52059 ACTCGAGACAACACAAGTTCAACTTCACGACAAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
52124 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
52165 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
52230 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
52271 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
52336 AATTTCAGAGCCAATTTCAACTTAACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
52377 ACTCCAGACAATGCAAGTTCAACTTCACGAAGAAGGGACCGTTGGTTGTCAATAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
52442 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
52483 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
52548 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
52589 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGA-CGACTGGTTATCAAC-AACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCC
* * *
52652 CAATTTCAGAGCCAGTTTCAACTTCGCAGCGAAGGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
52694 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACTGTTGGATT-TCAATAAACAATTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG-TTGTCAACAAACAATTTCC
* *
52758 CAATTTCAGAGCCAAATTCAACTTCACAGCAAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
52800 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
52865 AATTTCAGAGCCAATTTCAACTTCTCAGAGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * *
52906 AC-CCAAGACAACACAAGCCCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
*
52966 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
53006 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
** * * *
53071 GGTTCCAGAGCCAATTTTAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
53112 ACTC
1 ACTC
53116 GGAACAATGC
Statistics
Matches: 855, Mismatches: 82, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
100 78 0.09
101 4 0.00
102 6 0.01
104 4 0.00
105 96 0.11
106 667 0.78
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:52851 original size:423 final size:422
Alignment explanation
Indices: 52059--53115 Score: 1581
Period size: 423 Copynumber: 2.5 Consensus size: 422
52049 ATATCGTGCC
* * *
52059 ACTCGAGACAACACAAGTTCAACTTCACGACAAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
* * *
52124 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* *
52189 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGA-CGCTGGTTGTCAA-CAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
*
52254 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
194 ACAGCGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
52319 TCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTAACAGCGAAGGATATTGGACTCCAG
259 TCAATAAACAATTTCCCAATTTCAGAGCCAAATTCAACTTAACAGCAAAGGATATTGGACTCCAG
* ** * *
52384 ACAATGCAAGTTCAACTTCACGAAGAAGGGACCGTTGGTTGTCAATAAATAACTTCTCAATTTCA
324 ACAACGCAAGTTCAACTTCACGAAGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCA
*
52449 GAGCCAATTTCAACTTCACAGCGAAGGATATTGG
389 GAGCCAATTTCAACTTCACAGAGAAGGATATTGG
* *
52483 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
*
52548 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
66 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * * *
52613 TCACAATGAAGGGACGACTGGTTATCAACAACAATTTCCCAATTTCAGAGCCAGTTTCAACTTCG
131 TCACAACGAAGGGACG-CTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
* * *
52678 CAGCGAAGGATATTAGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACTGTTGGATT-
195 CAGCGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGG-TTG
* *
52742 TCAATAAACAATTTCTCAATTTCAGAGCCAAATTCAACTTCACAGCAAAGGATATTGGACTCCAG
259 TCAATAAACAATTTCCCAATTTCAGAGCCAAATTCAACTTAACAGCAAAGGATATTGGACTCCAG
*
52807 ACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCA
324 ACAACGCAAGTTCAACTTCACGAAGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCA
* *
52872 GAGCCAATTTCAACTTCTCAGAGAAGGATCTTGG
389 GAGCCAATTTCAACTTCACAGAGAAGGATATTGG
* ** * *
52906 ACCCAAGACAACACAAGCCCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-TC
1 ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
*
52967 -A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* *** * *
53030 TCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCCTGGTTCCAGAGCCAATTTTAACTTC
131 TCACAACGAAGGGAC-GCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
53095 AC-GACGGAGGATATTGGACTC
194 ACAG-CGAAGGATATTAGACTC
53116 GGAACAATGC
Statistics
Matches: 575, Mismatches: 53, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
417 85 0.15
418 47 0.08
419 2 0.00
420 2 0.00
421 2 0.00
422 2 0.00
423 290 0.50
424 145 0.25
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (422 bp):
ACTCAAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
TCACAACGAAGGGACGCTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCAC
AGCGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
AATAAACAATTTCCCAATTTCAGAGCCAAATTCAACTTAACAGCAAAGGATATTGGACTCCAGAC
AACGCAAGTTCAACTTCACGAAGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTTCAGA
GCCAATTTCAACTTCACAGAGAAGGATATTGG
Found at i:53884 original size:37 final size:37
Alignment explanation
Indices: 53814--53915 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 37
53804 CCTTTTCGTC
*
53814 CTACTATAATTCAAACTCCTAAAAATAGAATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGAATAGAATT
* * *
53851 TTGCTA-GTATTCAAACTCCTAAAAATATG-ATAGAGTT
1 CTACTATG-ATTCAAACTCCTAAAAATA-GAATAGAATT
* *
53888 CTACTATGATTTAAACTCCTAAAGATAG
1 CTACTATGATTCAAACTCCTAAAAATAG
53916 GATCCACAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
36 1 0.02
37 51 0.94
38 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGAATAGAATT
Found at i:54474 original size:21 final size:19
Alignment explanation
Indices: 54450--54494 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
54440 ATTTGGTTAT
* *
54450 TTTTTAATACTATATTTATTA
1 TTTTT-ATA-TATATATATAA
54471 TTTTTATATATATATATAA
1 TTTTTATATATATATATAA
54490 TTTTT
1 TTTTT
54495 TTTAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
20 3 0.14
21 5 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTATATATATATATAA
Found at i:54482 original size:19 final size:20
Alignment explanation
Indices: 54384--54494 Score: 66
Period size: 22 Copynumber: 5.2 Consensus size: 20
54374 TCAATTGATT
*
54384 TTTTTACACTATATATTATTA
1 TTTTTATACTATAT-TTATTA
* *
54405 TTATATATACATATATTTTTTA
1 TT-TTTATAC-TATATTTATTA
*
54427 TTTATT-TA-TATTCATTTGGTTA
1 TTT-TTATACTA-T-ATTT-ATTA
54449 TTTTTTAATACTATATTTATTA
1 -TTTTT-ATACTATATTTATTA
* *
54471 TTTTTATA-TATATATATAA
1 TTTTTATACTATATTTATTA
54490 TTTTT
1 TTTTT
54495 TTTAAATATT
Statistics
Matches: 72, Mismatches: 8, Indels: 22
0.71 0.08 0.22
Matches are distributed among these distances:
19 16 0.22
20 4 0.06
21 14 0.19
22 21 0.29
23 12 0.17
24 3 0.04
25 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTTATACTATATTTATTA
Found at i:54495 original size:21 final size:20
Alignment explanation
Indices: 54449--54496 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
54439 CATTTGGTTA
*
54449 TTTTTTAATACTATATTTAT
1 TTTTTTAATACTATATTAAT
54469 TATTTTTATATA-TATATATAAT
1 T-TTTTTA-ATACTATAT-TAAT
54491 TTTTTT
1 TTTTTT
54497 TAAATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTTAATACTATATTAAT
Found at i:54496 original size:22 final size:20
Alignment explanation
Indices: 54449--54503 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
54439 CATTTGGTTA
*
54449 TTTTTTAATACTATATTTATT
1 TTTTTTAATA-TATATTAATT
*
54470 ATTTTTATATATATATATAATT
1 TTTTTTA-ATATATAT-TAATT
54492 TTTTTTAA-ATAT
1 TTTTTTAATATAT
54504 TTTACTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 12 0.41
22 13 0.45
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTAATATATATTAATT
Found at i:54534 original size:2 final size:2
Alignment explanation
Indices: 54527--54561 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54517 GTATTATTAC
54527 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 T
54562 TGTAATTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54777 original size:2 final size:2
Alignment explanation
Indices: 54770--54802 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54760 TTTACTCATT
54770 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 T
54803 TTCATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54845 original size:22 final size:24
Alignment explanation
Indices: 54803--54860 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
54793 ATATATATAT
* *
54803 TTCATTTATTTATTTTATTTTTCTT-
1 TTCATTT-TTTA-CTTATTTTTATTC
54828 TT-ATTTTTTACTTATTTTTATTC
1 TTCATTTTTTACTTATTTTTATTC
54851 TTCATTTTTT
1 TTCATTTTTT
54861 CATTTATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 10 0.34
23 6 0.21
24 11 0.38
25 2 0.07
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCATTTTTTACTTATTTTTATTC
Found at i:56568 original size:18 final size:18
Alignment explanation
Indices: 56547--56584 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
56537 CCTTACACAC
56547 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
56565 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
56583 TT
1 TT
56585 CATACTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:60102 original size:34 final size:34
Alignment explanation
Indices: 60007--60102 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 34
59997 ATACAATTAG
* *
60007 ATATCTTTTAATATTCAAATGTAAATAGATAATA
1 ATATCTTTTAATATTCAAATATAAAAAGATAATA
*
60041 ATATCTTTTAAT-TTAAAATATACAAAAGTATAA-A
1 ATATCTTTTAATATTCAAATATA-AAAAG-ATAATA
60075 ATTATC-TTTAATATTCAAAGT-TAAAAAG
1 A-TATCTTTTAATATTCAAA-TATAAAAAG
60103 GTAACACACA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
33 8 0.15
34 29 0.55
35 15 0.28
36 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (34 bp):
ATATCTTTTAATATTCAAATATAAAAAGATAATA
Found at i:64669 original size:18 final size:18
Alignment explanation
Indices: 64646--64684 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
64636 ATCAATCAAG
*
64646 TAATAAATTTAATATTAA
1 TAATAAATTAAATATTAA
64664 TAATAAATTAAATATTAA
1 TAATAAATTAAATATTAA
64682 TAA
1 TAA
64685 ACTTGGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATAAATTAAATATTAA
Found at i:67774 original size:31 final size:30
Alignment explanation
Indices: 67739--67817 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
67729 GTCCTTATTG
*
67739 TTTAAAATATATATTAATTATTTTATAATAA
1 TTTAAAATATATAATAATTATTTT-TAATAA
* *
67770 TTTAATAA-ATTTAATGATTATTTTTAATAA
1 TTTAA-AATATATAATAATTATTTTTAATAA
*
67800 CTTAAAATAATTATAATA
1 TTTAAAAT-A-TATAATA
67818 TAATATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
29 2 0.05
30 10 0.26
31 19 0.50
32 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TTTAAAATATATAATAATTATTTTTAATAA
Found at i:67832 original size:26 final size:29
Alignment explanation
Indices: 67803--67866 Score: 107
Period size: 26 Copynumber: 2.3 Consensus size: 29
67793 TTAATAACTT
67803 AAAATAATTATAATAT-A-ATATATTT-A
1 AAAATAATTATAATATAATATATATTTAA
67829 AAAATAATTATAATATAATATATATTTAA
1 AAAATAATTATAATATAATATATATTTAA
67858 AAAATAATT
1 AAAATAATT
67867 TATTAACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
26 16 0.46
27 1 0.03
28 8 0.23
29 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATAATTATAATATAATATATATTTAA
Found at i:67877 original size:29 final size:28
Alignment explanation
Indices: 67803--67881 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 28
67793 TTAATAACTT
*
67803 AAAATAATTATAATA-TA-ATATATTTA
1 AAAATAATTATAATACAATATATATTTA
*
67829 AAAATAATTATAATATAATATATATTTAA
1 AAAATAATTATAATACAATATATATTT-A
*
67858 AAAATAATT-TATTAACAATATATA
1 AAAATAATTATAAT-ACAATATATA
67882 AATAGTTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 15 0.33
27 1 0.02
28 11 0.24
29 19 0.41
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATAATTATAATACAATATATATTTA
Found at i:83328 original size:12 final size:12
Alignment explanation
Indices: 83311--83347 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
83301 TAAAACACAT
83311 GGGCTGCTAAGG
1 GGGCTGCTAAGG
83323 GGGCTGCTAAGG
1 GGGCTGCTAAGG
83335 GGGCTGCTAAGG
1 GGGCTGCTAAGG
83347 G
1 G
83348 AGGGCTGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.51, T:0.16
Consensus pattern (12 bp):
GGGCTGCTAAGG
Found at i:83773 original size:16 final size:16
Alignment explanation
Indices: 83752--83785 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
83742 TTACTATTCA
*
83752 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
83768 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
83784 CG
1 CG
83786 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:84556 original size:15 final size:16
Alignment explanation
Indices: 84536--84567 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
84526 TGGCAGATCC
84536 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
84551 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
84567 A
1 A
84568 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:87842 original size:13 final size:13
Alignment explanation
Indices: 87824--87864 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
87814 TAAAACACAT
87824 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
87837 GGGCTGCTAA-GG
1 GGGCTGCTAAGGG
87849 GGGCTGCTAAGGG
1 GGGCTGCTAAGGG
87862 GGG
1 GGG
87865 GGCTGCTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (13 bp):
GGGCTGCTAAGGG
Found at i:87852 original size:12 final size:12
Alignment explanation
Indices: 87824--87863 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
87814 TAAAACACAT
87824 GGGCTGCTAAGGG
1 GGGCTGCTAA-GG
87837 GGGCTGCTAAGG
1 GGGCTGCTAAGG
87849 GGGCTGCTAAGG
1 GGGCTGCTAAGG
87861 GGG
1 GGG
87864 GGGCTGCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.15, C:0.15, G:0.55, T:0.15
Consensus pattern (12 bp):
GGGCTGCTAAGG
Found at i:92010 original size:54 final size:54
Alignment explanation
Indices: 91952--92346 Score: 489
Period size: 54 Copynumber: 7.4 Consensus size: 54
91942 TTCTTTAGGG
** * *
91952 TGCACACTTAGTGCCGATACGATCATTCATAAGCTCATTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGGT
*
92006 TGCACACTTAGTGCCGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGGT
* * * *
92060 TGCACACTTAGTGCTGATACGGTTGTTCATAAACTTATTGTGAATT-TCATGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCT-GTGGGT
* * * *
92114 TGCACACTTAGTGTCGCTACGGTTATTCATAAACTTATTATGAATT-TCGTGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCT-GTGGGT
* *
92168 TACACACTTAGTGCCAATAC-AGTTGTTCATAAACTTATTATGAATTCTGT-GG-
1 TGCACACTTAGTGCCGATACGA-TTGTTCATAAACTTATTATGAATTCTGTGGGT
* * *
92220 -GCACACTTAGTGTCAATACAATTGTTCATAAACTTATTATGAATTCTGTGGGT
1 TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGGT
* * * ** *
92273 TGCACACTTAGTGCCAATACGGGTT-TTCATAAACTTATTATGAATTCCGTACGC
1 TGCACACTTAGTGCCGATAC-GATTGTTCATAAACTTATTATGAATTCTGTGGGT
92327 TGCACACTTAGTGCCGATAC
1 TGCACACTTAGTGCCGATAC
92347 ATAAAAATGC
Statistics
Matches: 303, Mismatches: 30, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
51 45 0.15
52 3 0.01
53 3 0.01
54 249 0.82
55 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (54 bp):
TGCACACTTAGTGCCGATACGATTGTTCATAAACTTATTATGAATTCTGTGGGT
Found at i:93746 original size:27 final size:28
Alignment explanation
Indices: 93716--93769 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
93706 AATAAAAAAG
*
93716 AATT-TTTAAAATTGTTGTTTAAAATTT
1 AATTGTTTAAAATTGTTGTTAAAAATTT
* *
93743 AATTGTTTGATATTGTTGTTAAAAATT
1 AATTGTTTAAAATTGTTGTTAAAAATT
93770 GAGTTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (28 bp):
AATTGTTTAAAATTGTTGTTAAAAATTT
Found at i:94213 original size:19 final size:21
Alignment explanation
Indices: 94167--94214 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
94157 ATTTTATTTA
94167 TTTTTAAGTAATTAAAATAAT
1 TTTTTAAGTAATTAAAATAAT
* *
94188 TTATTAAGTAA-T-AAATTAT
1 TTTTTAAGTAATTAAAATAAT
94207 TTTTTAAG
1 TTTTTAAG
94215 GATGTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.54
20 1 0.04
21 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTTTAAGTAATTAAAATAAT
Found at i:95287 original size:15 final size:15
Alignment explanation
Indices: 95267--95307 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
95257 ACCCAAAGCT
95267 GAGAAGAAGCCGGCG
1 GAGAAGAAGCCGGCG
*
95282 GAGAAGAAACCGGCG
1 GAGAAGAAGCCGGCG
95297 GAGAAGAAGCC
1 GAGAAGAAGCC
95308 AGCTGAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.41, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGCCGGCG
Found at i:95319 original size:15 final size:15
Alignment explanation
Indices: 95267--95320 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
95257 ACCCAAAGCT
*
95267 GAGAAGAAGCCGGCG
1 GAGAAGAAGCCAGCG
* *
95282 GAGAAGAAACCGGCG
1 GAGAAGAAGCCAGCG
*
95297 GAGAAGAAGCCAGCT
1 GAGAAGAAGCCAGCG
*
95312 GAGGAGAAG
1 GAGAAGAAG
95321 AAAACCGTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.43, T:0.02
Consensus pattern (15 bp):
GAGAAGAAGCCAGCG
Found at i:95745 original size:6 final size:6
Alignment explanation
Indices: 95734--95758 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
95724 GCTGTTCTAT
95734 GGTTAG GGTTAG GGTTAG GGTTAG G
1 GGTTAG GGTTAG GGTTAG GGTTAG G
95759 ATTTCCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTTAG
Found at i:101559 original size:26 final size:26
Alignment explanation
Indices: 101523--101580 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
101513 AACCGCAGTG
101523 AGTTGCGTTTCTCAACTACAGAAGAT
1 AGTTGCGTTTCTCAACTACAGAAGAT
101549 AGTTGCGTTTCTCAACTACAGAAGAT
1 AGTTGCGTTTCTCAACTACAGAAGAT
101575 AGTTGC
1 AGTTGC
101581 TCTCTCCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (26 bp):
AGTTGCGTTTCTCAACTACAGAAGAT
Found at i:101597 original size:25 final size:26
Alignment explanation
Indices: 101523--101597 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
101513 AACCGCAGTG
* *
101523 AGTTGCGTTTCTCAACTACAGAAGAT
1 AGTTGCGTCTCTCAACAACAGAAGAT
* *
101549 AGTTGCGTTTCTCAACTACAGAAGAT
1 AGTTGCGTCTCTCAACAACAGAAGAT
* *
101575 AGTTGC-TCTCTCCACAACTGAAG
1 AGTTGCGTCTCTCAACAACAGAAG
101598 CAAAATATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 13 0.29
26 32 0.71
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (26 bp):
AGTTGCGTCTCTCAACAACAGAAGAT
Found at i:106087 original size:89 final size:89
Alignment explanation
Indices: 105936--106117 Score: 355
Period size: 89 Copynumber: 2.0 Consensus size: 89
105926 GGTGTTCGTG
*
105936 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGATATATGGCTAAATTCAATG
1 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
106001 TTGCTCTGTTGGCAAAACAGGGAT
66 TTGCTCTGTTGGCAAAACAGGGAT
106025 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
1 GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
106090 TTGCTCTGTTGGCAAAACAGGGAT
66 TTGCTCTGTTGGCAAAACAGGGAT
106114 GGAG
1 GGAG
106118 ATTGATTGTA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.30
Consensus pattern (89 bp):
GGAGTTTCTAAGTCGTTTAAAAAACGATGGAGGATTAGGTTTCAGAGATATGGCTAAATTCAATG
TTGCTCTGTTGGCAAAACAGGGAT
Found at i:111806 original size:33 final size:36
Alignment explanation
Indices: 111747--111817 Score: 121
Period size: 33 Copynumber: 2.1 Consensus size: 36
111737 TTTCATCTGG
111747 ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
1 ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
111783 ATCGTTAAATAA-T-T-TCATATGCTTCCAATATAT
1 ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
111816 AT
1 AT
111818 ATATAACATG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 21 0.60
34 1 0.03
35 1 0.03
36 12 0.34
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (36 bp):
ATCGTTAAATAATTATGTCATATGCTTCCAATATAT
Found at i:111874 original size:23 final size:24
Alignment explanation
Indices: 111828--111874 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
111818 ATATAACATG
* *
111828 GTTTTGAAATATATGACATTTATA
1 GTTTTGAAATATATAACATATATA
*
111852 GTTTTGAAA-ATATAATATATATA
1 GTTTTGAAATATATAACATATATA
111875 TATTTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (24 bp):
GTTTTGAAATATATAACATATATA
Found at i:111876 original size:25 final size:24
Alignment explanation
Indices: 111809--111876 Score: 57
Period size: 25 Copynumber: 2.7 Consensus size: 24
111799 ATATGCTTCC
* *
111809 AATATATATATATAACATGGTTTTGA
1 AATATA-ATATAT-ATATAGTTTTGA
* *
111835 AATAT-ATGACATTTATAGTTTTGAA
1 AATATAAT-ATATATATAGTTTTG-A
111860 AATATAATATATATATA
1 AATATAATATATATATA
111877 TTTATATTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
24 10 0.30
25 16 0.48
26 7 0.21
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (24 bp):
AATATAATATATATATAGTTTTGA
Found at i:111947 original size:28 final size:28
Alignment explanation
Indices: 111895--111948 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
111885 CTAAGTTGTA
*
111895 ATATATAACTTTGAAAACGTGTATATAT
1 ATATATAACTTTGAAAACGTATATATAT
* * *
111923 ATATATAATTTTGAAAGCTTATATAT
1 ATATATAACTTTGAAAACGTATATAT
111949 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (28 bp):
ATATATAACTTTGAAAACGTATATATAT
Found at i:112269 original size:2 final size:2
Alignment explanation
Indices: 112262--112299 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
112252 AAACATTGTT
112262 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
112300 TATTTAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:112287 original size:17 final size:17
Alignment explanation
Indices: 112265--112298 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
112255 CATTGTTTAT
112265 ATATATATATATATATA
1 ATATATATATATATATA
112282 ATATATATATATATATA
1 ATATATATATATATATA
112299 TTATTTAATG
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:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:112499 original size:27 final size:27
Alignment explanation
Indices: 112466--112540 Score: 118
Period size: 25 Copynumber: 2.9 Consensus size: 27
112456 ATTTTTACAT
112466 ACATAACACACTCTTTTCATCTTTTAC
1 ACATAACACACTCTTTTCATCTTTTAC
*
112493 ACAT-A-ACACTCATTTCATCTTTTAC
1 ACATAACACACTCTTTTCATCTTTTAC
*
112518 ACACAACACACTCTTTTCATCTT
1 ACATAACACACTCTTTTCATCTT
112541 CAATCTCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 22 0.51
26 2 0.05
27 19 0.44
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.39
Consensus pattern (27 bp):
ACATAACACACTCTTTTCATCTTTTAC
Found at i:113409 original size:17 final size:17
Alignment explanation
Indices: 113387--113420 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
113377 GCATAACTAG
113387 CAATCAAGGAGTACTGC
1 CAATCAAGGAGTACTGC
*
113404 CAATCAATGAGTACTGC
1 CAATCAAGGAGTACTGC
113421 ATCAAAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (17 bp):
CAATCAAGGAGTACTGC
Done.