Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008409.1 Hibiscus syriacus cultivar Beakdansim tig00111179_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: 81670
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3581 original size:24 final size:24
Alignment explanation
Indices: 3554--3660 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
3544 AAACGGAGAT
3554 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
3578 ATCAGATATCAAAACAGAATCCAT
1 ATCAGAAATCAAAACAGAATTCAG
* *
3602 AACAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
3626 GTAATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAAAACAGAATTCAG
3649 AGTCAGAAATCA
1 A-TCAGAAATCA
3661 GATAAAATAT
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:3583 original size:12 final size:12
Alignment explanation
Indices: 3556--3625 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
3546 ACGGAGATAT
* *
3556 CAGAAATCAAAA
1 CAGAATTCAGAA
*
3568 CAGAATTCAGAT
1 CAGAATTCAGAA
*
3580 CAG-ATATCAAAA
1 CAGAAT-TCAGAA
* *
3592 CAGAATCCATAA
1 CAGAATTCAGAA
*
3604 CAGAAATCAGAA
1 CAGAATTCAGAA
3616 CAGAATTCAG
1 CAGAATTCAG
3626 GTAATGTATC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:3636 original size:48 final size:48
Alignment explanation
Indices: 3556--3662 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
3546 ACGGAGATAT
* *
3556 CAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCATA-A
1 CAGAAATCAGAACAGAATTCAGATAAGATATCAAAACAGAATCCA-AGA
* * * *
3604 CAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAATTCAAGT
1 CAGAAATCAGAACAGAATTCAGATAA-GATATCAAAACAGAATCCAAGA
3652 CAGAAATCAGA
1 CAGAAATCAGA
3663 TAAAATATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
47 1 0.02
48 49 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (48 bp):
CAGAAATCAGAACAGAATTCAGATAAGATATCAAAACAGAATCCAAGA
Found at i:6175 original size:29 final size:29
Alignment explanation
Indices: 6136--6256 Score: 118
Period size: 29 Copynumber: 4.2 Consensus size: 29
6126 CATTTTACAC
* *
6136 AAATAGCACCTTTTTTAAAATAATTACCA
1 AAATAGAACCTTTTTCAAAATAATTACCA
* * *
6165 AAATAGAACCTTTTTCGAATTAATTCCCA
1 AAATAGAACCTTTTTCAAAATAATTACCA
** * * *
6194 AAATAGAACCAATTTCGAATTAATTCCCA
1 AAATAGAACCTTTTTCAAAATAATTACCA
* **
6223 GAATATCACCTTTTTCAAAA-AATTACCA
1 AAATAGAACCTTTTTCAAAATAATTACCA
6251 AAATAG
1 AAATAG
6257 CACCCATTTC
Statistics
Matches: 75, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 11 0.15
29 64 0.85
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGAACCTTTTTCAAAATAATTACCA
Found at i:6266 original size:57 final size:58
Alignment explanation
Indices: 6172--6282 Score: 170
Period size: 57 Copynumber: 1.9 Consensus size: 58
6162 CCAAAATAGA
** *
6172 ACCTTTTTCGAATTAATTCCCAAAATAGAACCAATTTCGAATTAATTCCCAGAATATC
1 ACCTTTTTCGAAAAAATTACCAAAATAGAACCAATTTCGAATTAATTCCCAGAATATC
* *
6230 ACCTTTTTC-AAAAAATTACCAAAATAGCACCCATTTCGAATTAATTCCCAGAA
1 ACCTTTTTCGAAAAAATTACCAAAATAGAACCAATTTCGAATTAATTCCCAGAA
6283 CAGTGCTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 39 0.81
58 9 0.19
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (58 bp):
ACCTTTTTCGAAAAAATTACCAAAATAGAACCAATTTCGAATTAATTCCCAGAATATC
Found at i:6299 original size:86 final size:87
Alignment explanation
Indices: 6137--6318 Score: 231
Period size: 86 Copynumber: 2.1 Consensus size: 87
6127 ATTTTACACA
* * ** *
6137 AATAGCACCTTTTTTAAAATAATTACCAAAATAGAACCTTTTTCGAATTAATTCCCAAAATAGAA
1 AATAACACCTTTTTCAAAATAATTACCAAAATAGAACCCATTTCGAATTAATTCCCAAAACAGAA
***
6202 CCAATTTCGAATTAATTCCCAG
66 CCAAAACCGAATTAATTCCCAG
* * * **
6224 AATATCACCTTTTTCAAAA-AATTACCAAAATAGCACCCATTTCGAATTAATTCCCAGAACAGTG
1 AATAACACCTTTTTCAAAATAATTACCAAAATAGAACCCATTTCGAATTAATTCCCAAAACAGAA
*
6288 CTAAAACCGAATTAATTCCCAG
66 CCAAAACCGAATTAATTCCCAG
6310 AATAACACC
1 AATAACACC
6319 GGTCAACGGG
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 64 0.79
87 17 0.21
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.29
Consensus pattern (87 bp):
AATAACACCTTTTTCAAAATAATTACCAAAATAGAACCCATTTCGAATTAATTCCCAAAACAGAA
CCAAAACCGAATTAATTCCCAG
Found at i:6337 original size:13 final size:13
Alignment explanation
Indices: 6319--6348 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6309 GAATAACACC
*
6319 GGTCAACGGGTCG
1 GGTCAACAGGTCG
6332 GGTCAACAGGTCG
1 GGTCAACAGGTCG
6345 GGTC
1 GGTC
6349 GGGTCGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:8417 original size:24 final size:24
Alignment explanation
Indices: 8390--8496 Score: 92
Period size: 24 Copynumber: 4.5 Consensus size: 24
8380 AAACGGAGAT
*
8390 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
8414 ATCAGATATCAAAATAGAATCCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
8438 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
8462 GTAATG-TATCATAACAGAATTCA-
1 ATCA-GAAATCAAAACAGAATTCAG
8485 AGTCAGAAATCA
1 A-TCAGAAATCA
8497 GATAAAATAT
Statistics
Matches: 63, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:8472 original size:48 final size:48
Alignment explanation
Indices: 8390--8498 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
8380 AAACGGAGAT
* * * *
8390 ATCATAAATCAAAACAGAATTCAGATCAGATATCAAAATAGAATCCAA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAAAACAGAATCCAA
* * *
8438 ATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAAAACAGAATCCAA
*
8486 GTCAGAAATCAGA
1 ATCAGAAATCAGA
8499 TAAAATATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 51 0.98
49 1 0.02
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAAAACAGAATCCAA
Found at i:11001 original size:29 final size:29
Alignment explanation
Indices: 10969--11125 Score: 116
Period size: 29 Copynumber: 5.3 Consensus size: 29
10959 TATTTTACAC
*
10969 AAATAGCACCCTTTTTAAAATAATTACAA
1 AAATAGCACCCTTTTTAAAATAATTACCA
** * *
10998 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
** * * *
11027 AAATAGCACCAATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
* * *
11056 AAATATCACCTTTTTTTCAAAAAAATTTACCA
1 AAATAGCACC-CTTTTT-AAAATAA-TTACCA
* ** * *
11088 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
*
11117 GAATAGCAC
1 AAATAGCAC
11126 TAAAACCAAA
Statistics
Matches: 101, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
29 72 0.71
30 8 0.08
31 7 0.07
32 14 0.14
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCTTTTTAAAATAATTACCA
Found at i:11150 original size:90 final size:88
Alignment explanation
Indices: 10980--11155 Score: 226
Period size: 90 Copynumber: 2.0 Consensus size: 88
10970 AATAGCACCC
* * *****
10980 TTTTTAAAATAATTACAAAAATAGCACCCTTTTCGAATTAATTCCCAAAATAGCACCAATTTTGA
1 TTTTTAAAAAAATTACAAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAACCAA
*
11045 ATTAATTCCCAAAATATCACCTT
66 ATTAATTCCCAAAATAACACCTT
* * *
11068 TTTTTCAAAAAAATTTACCAAAATAGCACCCATTTCGAATTAATTCCCAGAATAGCACTAAAACC
1 TTTTT-AAAAAAA-TTACAAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAACC
*
11133 AAATTAATTCTCAAAATAACACC
64 AAATTAATTCCCAAAATAACACC
11156 GATCAACGGT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 5 0.07
89 6 0.08
90 63 0.85
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.31
Consensus pattern (88 bp):
TTTTTAAAAAAATTACAAAAATAGCACCCATTTCGAATTAATTCCCAAAATAGCACCAAAACCAA
ATTAATTCCCAAAATAACACCTT
Found at i:11185 original size:13 final size:13
Alignment explanation
Indices: 11167--11191 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11157 ATCAACGGTC
11167 AACGGGTCGGGTA
1 AACGGGTCGGGTA
11180 AACGGGTCGGGT
1 AACGGGTCGGGT
11192 CGGGTTATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:12696 original size:27 final size:29
Alignment explanation
Indices: 12638--12696 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
12628 ATTTCTGTAC
*
12638 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
12667 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
12694 TTA
1 TTA
12697 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:15069 original size:27 final size:29
Alignment explanation
Indices: 15011--15069 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
15001 ATTTCTGTAC
*
15011 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
15040 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
15067 TTA
1 TTA
15070 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:17443 original size:27 final size:29
Alignment explanation
Indices: 17385--17443 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
17375 ATTTCTGTAC
*
17385 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
17414 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
17441 TTA
1 TTA
17444 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:22170 original size:28 final size:27
Alignment explanation
Indices: 22133--22190 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
22123 ATTTCTGTAC
*
22133 TTATTAAAAACATATATGTTAGTGTTTA
1 TTATTAAAAACATATATGTTAG-GTTGA
* * *
22161 TTATTTAAAATATATATTTTAGGTTGA
1 TTATTAAAAACATATATGTTAGGTTGA
22188 TTA
1 TTA
22191 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (27 bp):
TTATTAAAAACATATATGTTAGGTTGA
Found at i:24562 original size:27 final size:29
Alignment explanation
Indices: 24504--24562 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
24494 ATTTATGTAC
*
24504 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
24533 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
24560 TTA
1 TTA
24563 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:27654 original size:10 final size:10
Alignment explanation
Indices: 27612--27663 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
27602 ACTGGAAACT
27612 GGTTTTGACC
1 GGTTTTGACC
*
27622 GG-TTTAACC
1 GGTTTTGACC
27631 GGTTTTGAACC
1 GGTTTTG-ACC
27642 GGTTTTGACC
1 GGTTTTGACC
27652 GG-TTTGACC
1 GGTTTTGACC
27661 GGT
1 GGT
27664 CACGACCCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 17 0.46
10 10 0.27
11 10 0.27
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (10 bp):
GGTTTTGACC
Found at i:27703 original size:18 final size:17
Alignment explanation
Indices: 27678--27748 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 17
27668 ACCCGTTTAC
27678 CCGTTTACCCGACCCGA
1 CCGTTTACCCGACCCGA
27695 CCAGTTTACCCGACCCGA
1 CC-GTTTACCCGACCCGA
*
27713 CCGTTGACCCGACCCATTGA
1 CCGTTTACCCGACCC---GA
*
27733 CCGTTGACCCGACCCG
1 CCGTTTACCCGACCCG
27749 TTGACCGTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
17 15 0.31
18 17 0.35
20 17 0.35
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.17
Consensus pattern (17 bp):
CCGTTTACCCGACCCGA
Found at i:27736 original size:20 final size:20
Alignment explanation
Indices: 27711--27761 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
27701 TACCCGACCC
27711 GACCGTTGACCCGACCCATT
1 GACCGTTGACCCGACCCATT
*
27731 GACCGTTGACCCGACCCGTT
1 GACCGTTGACCCGACCCATT
27751 GACCGTTGACC
1 GACCGTTGACC
27762 GTTGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.39, G:0.24, T:0.20
Consensus pattern (20 bp):
GACCGTTGACCCGACCCATT
Found at i:27739 original size:7 final size:7
Alignment explanation
Indices: 27729--27769 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
27719 ACCCGACCCA
27729 TTGACCG
1 TTGACCG
27736 TTGACC-
1 TTGACCG
*
27742 -CGACCCG
1 TTGA-CCG
27749 TTGACCG
1 TTGACCG
27756 TTGACCG
1 TTGACCG
27763 TTGACCG
1 TTGACCG
27770 GTGCTATTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
5 2 0.07
6 2 0.07
7 23 0.79
8 2 0.07
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (7 bp):
TTGACCG
Found at i:27862 original size:29 final size:29
Alignment explanation
Indices: 27769--27850 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
27759 ACCGTTGACC
27769 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGGTTTT
27798 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGGTTTT
*
27827 GGTGCTAGTCTGGGAATTAATTCG
1 GGTGCTATTCTGGGAATTAATTCG
27851 AAATGGGTGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGGTTTT
Found at i:34984 original size:10 final size:10
Alignment explanation
Indices: 34942--34993 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
34932 ACTGGAAACT
34942 GGTTTTGACC
1 GGTTTTGACC
*
34952 GG-TTTAACC
1 GGTTTTGACC
34961 GGTTTTGAACC
1 GGTTTTG-ACC
34972 GGTTTTGACC
1 GGTTTTGACC
34982 GG-TTTGACC
1 GGTTTTGACC
34991 GGT
1 GGT
34994 CACGACCCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 17 0.46
10 10 0.27
11 10 0.27
ACGTcount: A:0.13, C:0.19, G:0.31, T:0.37
Consensus pattern (10 bp):
GGTTTTGACC
Found at i:35033 original size:18 final size:17
Alignment explanation
Indices: 35008--35078 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 17
34998 ACCCGTTTAC
35008 CCGTTTACCCGACCCGA
1 CCGTTTACCCGACCCGA
35025 CCAGTTTACCCGACCCGA
1 CC-GTTTACCCGACCCGA
*
35043 CCGTTGACCCGACCCGTTGA
1 CCGTTTACCCGACCC---GA
*
35063 CCGTTGACCCGACCCG
1 CCGTTTACCCGACCCG
35079 TTGACCGTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
17 15 0.31
18 17 0.35
20 17 0.35
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (17 bp):
CCGTTTACCCGACCCGA
Found at i:35053 original size:12 final size:13
Alignment explanation
Indices: 35036--35064 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35026 CAGTTTACCC
35036 GACCCGA-CCGTT
1 GACCCGACCCGTT
35048 GACCCGACCCGTT
1 GACCCGACCCGTT
35061 GACC
1 GACC
35065 GTTGACCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:35066 original size:7 final size:7
Alignment explanation
Indices: 35056--35099 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
35046 TTGACCCGAC
35056 CCGTTGA
1 CCGTTGA
35063 CCGTTGA
1 CCGTTGA
*
35070 CC--CGA
1 CCGTTGA
35075 CCCGTTGA
1 -CCGTTGA
35083 CCGTTGA
1 CCGTTGA
35090 CCGTTGA
1 CCGTTGA
35097 CCG
1 CCG
35100 GTGCTATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 2 0.06
6 2 0.06
7 26 0.81
8 2 0.06
ACGTcount: A:0.14, C:0.36, G:0.27, T:0.23
Consensus pattern (7 bp):
CCGTTGA
Found at i:35066 original size:20 final size:20
Alignment explanation
Indices: 34996--35091 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
34986 TGACCGGTCA
* *
34996 CGACCCGTTTACCCGTTTACC
1 CGACCCGTTGA-CCGTTGACC
*
35017 CGACCC---GACCAGTTTACC
1 CGACCCGTTGACC-GTTGACC
35035 CGACCC---GACCGTTGACC
1 CGACCCGTTGACCGTTGACC
35052 CGACCCGTTGACCGTTGACC
1 CGACCCGTTGACCGTTGACC
35072 CGACCCGTTGACCGTTGACC
1 CGACCCGTTGACCGTTGACC
35092 GTTGACCGGT
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
17 14 0.20
18 18 0.26
20 31 0.45
21 6 0.09
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.20
Consensus pattern (20 bp):
CGACCCGTTGACCGTTGACC
Found at i:35192 original size:29 final size:29
Alignment explanation
Indices: 35099--35180 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
35089 ACCGTTGACC
35099 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGGTTTT
35128 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGGTTTT
*
35157 GGTGCTAGTCTGGGAATTAATTCG
1 GGTGCTATTCTGGGAATTAATTCG
35181 AAATGGGTGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGGTTTT
Found at i:35253 original size:29 final size:29
Alignment explanation
Indices: 35099--35252 Score: 96
Period size: 29 Copynumber: 5.3 Consensus size: 29
35089 ACCGTTGACC
****
35099 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAAAT
****
35128 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAAAT
*
35157 GGTGCTAGTCTGGGAATTAATTCG-AAAT
1 GGTGCTATTCTGGGAATTAATTCGAAAAT
* * * * * *
35185 GGGTGCTATTTTAGTAATT-TTTAGAAAAAA
1 -GGTGCTATTCTGGGAATTAATTCG-AAAAT
** ** *
35215 AATAATATTTTGGGAATTAATTCGAAAAT
1 GGTGCTATTCTGGGAATTAATTCGAAAAT
35244 GGTGCTATT
1 GGTGCTATT
35253 TGTGTAAAAT
Statistics
Matches: 97, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
28 4 0.04
29 87 0.90
30 6 0.06
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAAAT
Found at i:36743 original size:27 final size:29
Alignment explanation
Indices: 36685--36743 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
36675 ATTTCTGTAC
*
36685 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
36714 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
36741 TTA
1 TTA
36744 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:41532 original size:18 final size:18
Alignment explanation
Indices: 41509--41568 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
41499 ACCGGTCATA
* *
41509 ACCCGACCTGACCCGTTT
1 ACCCGACCCGACCCGTTG
41527 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
41545 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
41566 ACC
1 ACC
41569 GTTGACCCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 25 0.68
21 12 0.32
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:41536 original size:13 final size:13
Alignment explanation
Indices: 41531--41562 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41521 CCGTTTACCC
41531 GACCCGACCCGTT
1 GACCCGACCCGTT
41544 GACCCGACCCGTT
1 GACCCGACCCGTT
41557 GACCCG
1 GACCCG
41563 TTGACCGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.47, G:0.25, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:41547 original size:8 final size:8
Alignment explanation
Indices: 41536--41595 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
41526 TACCCGACCC
41536 GACCCGTT
1 GACCCGTT
41544 GACCC---
1 GACCCGTT
41549 GACCCGTT
1 GACCCGTT
41557 GACCCGTT
1 GACCCGTT
41565 GA-CCGTT
1 GACCCGTT
41572 GACCCACGTT
1 GA-CC-CGTT
41582 GACCACTGTT
1 GACC-C-GTT
41592 GACC
1 GACC
41596 AAAACTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 15 0.33
9 5 0.11
10 13 0.29
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:41596 original size:10 final size:9
Alignment explanation
Indices: 41549--41596 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
41539 CCGTTGACCC
41549 GACC-CGTT
1 GACCACGTT
41557 GACC-CGTT
1 GACCACGTT
41565 GA-C-CGTT
1 GACCACGTT
41572 GACCCACGTT
1 GA-CCACGTT
41582 GACCACTGTT
1 GACCAC-GTT
41592 GACCA
1 GACCA
41597 AAACTTTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.19
8 10 0.28
9 5 0.14
10 14 0.39
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (9 bp):
GACCACGTT
Found at i:42895 original size:18 final size:18
Alignment explanation
Indices: 42869--42904 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42859 TCGAAAGGAC
*
42869 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
42887 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
42905 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:44067 original size:23 final size:24
Alignment explanation
Indices: 44041--44130 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
44031 TCAAATTTGA
*
44041 ATTCTGTTATGATA-TTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
44064 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
44087 ATTCTGATCTGATACATGACCTGA
1 ATTCTGATATGATACTTGACCTGG
44111 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
44131 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 34 0.59
24 24 0.41
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:44255 original size:35 final size:35
Alignment explanation
Indices: 44208--44282 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
44198 TGGAGGAAGA
*
44208 TTACTTGGAGGCTCCTCGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
44243 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
44278 TTACT
1 TTACT
44283 GTTCGTGACG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.09, C:0.29, G:0.29, T:0.32
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:46282 original size:13 final size:13
Alignment explanation
Indices: 46261--46296 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
46251 ACCCGACCCG
46261 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
46274 ACTCGACCCGTTT
1 ACCCGACCCGTTT
46287 ACCCGACCCG
1 ACCCGACCCG
46297 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.47, G:0.17, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:46291 original size:31 final size:31
Alignment explanation
Indices: 46255--46322 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
46245 GTCATAACCC
*
46255 GACCCGACCCGACCCGTTTA-CTCGACCCGTT
1 GACCCGACCCGACCCGTTGACCT-GACCCGTT
*
46286 TACCCGACCCGACCCGTTGACCTGACCCGTT
1 GACCCGACCCGACCCGTTGACCTGACCCGTT
46317 GACCCG
1 GACCCG
46323 TTGACCGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.16, C:0.46, G:0.21, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGACCCGTTGACCTGACCCGTT
Found at i:46298 original size:18 final size:18
Alignment explanation
Indices: 46277--46328 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
46267 CCCGTTTACT
*
46277 CGACCCGTTTACCCGACC
1 CGACCCGTTGACCCGACC
*
46295 CGACCCGTTGACCTGACC
1 CGACCCGTTGACCCGACC
46313 CGTTGACCCGTTGACC
1 C---GACCCGTTGACC
46329 GTTGACCCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 17 0.59
21 12 0.41
ACGTcount: A:0.15, C:0.44, G:0.21, T:0.19
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:46307 original size:8 final size:8
Alignment explanation
Indices: 46296--46336 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
46286 TACCCGACCC
46296 GACCCGTT
1 GACCCGTT
46304 GA-CC--T
1 GACCCGTT
46309 GACCCGTT
1 GACCCGTT
46317 GACCCGTT
1 GACCCGTT
46325 GA-CCGTT
1 GACCCGTT
46332 GACCC
1 GACCC
46337 ACGTTGACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 3 0.10
6 2 0.07
7 9 0.31
8 15 0.52
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:46307 original size:13 final size:13
Alignment explanation
Indices: 46291--46322 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
46281 CCGTTTACCC
46291 GACCCGACCCGTT
1 GACCCGACCCGTT
*
46304 GACCTGACCCGTT
1 GACCCGACCCGTT
46317 GACCCG
1 GACCCG
46323 TTGACCGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:47658 original size:18 final size:18
Alignment explanation
Indices: 47632--47667 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47622 TCGAAAGGAC
*
47632 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
47650 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
47668 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:48830 original size:23 final size:24
Alignment explanation
Indices: 48804--48893 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
48794 TCAAATTTGA
*
48804 ATTCTGTTATGATA-TTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
48827 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
48850 ATTCTGATCTGATACATGACCTGA
1 ATTCTGATATGATACTTGACCTGG
48874 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
48894 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 34 0.59
24 24 0.41
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:49018 original size:35 final size:35
Alignment explanation
Indices: 48971--49045 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
48961 TGGAGGAAGA
*
48971 TTACTTGGAGGCTCCTCGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
* *
49006 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGTC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
49041 TTACT
1 TTACT
49046 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:50584 original size:12 final size:12
Alignment explanation
Indices: 50559--50628 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
50549 ACGAAGATAT
* *
50559 CAGAAATCAAAA
1 CAGAATTCAGAA
50571 CAGAATTCAGAA
1 CAGAATTCAGAA
50583 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
50595 CAGAATCCAGAT
1 CAGAATTCAGAA
*
50607 CAGAAATCAGAA
1 CAGAATTCAGAA
50619 CAGAATTCAG
1 CAGAATTCAG
50629 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:50628 original size:48 final size:47
Alignment explanation
Indices: 50557--50665 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
50547 AAACGAAGAT
*
50557 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
50604 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
50652 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
50666 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:50663 original size:24 final size:25
Alignment explanation
Indices: 50557--50665 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
50547 AAACGAAGAT
*
50557 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
50581 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
50605 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
50629 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
50654 -TCGGAAATCAGA
1 ATCAGAAATCAGA
50666 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:51827 original size:18 final size:18
Alignment explanation
Indices: 51806--51841 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
51796 CTTCCATCCG
*
51806 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
51824 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
51842 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:53149 original size:8 final size:8
Alignment explanation
Indices: 53117--53184 Score: 63
Period size: 8 Copynumber: 8.5 Consensus size: 8
53107 TCAAAGTTTC
53117 GGTCAACAG
1 GGTCAAC-G
53126 TGGTCAACGTG
1 -GGTCAAC--G
53137 GGTCAACG
1 GGTCAACG
53145 GGTCAAC-
1 GGTCAACG
*
53152 AGTCAACG
1 GGTCAACG
53160 GGTCAACG
1 GGTCAACG
53168 GGT---CG
1 GGTCAACG
53173 GGTCAACG
1 GGTCAACG
53181 GGTC
1 GGTC
53185 GGGTCAACTG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
5 5 0.10
7 6 0.12
8 24 0.48
10 14 0.28
11 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:53158 original size:15 final size:15
Alignment explanation
Indices: 53138--53166 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53128 GTCAACGTGG
53138 GTCAACGGGTCAACA
1 GTCAACGGGTCAACA
53153 GTCAACGGGTCAAC
1 GTCAACGGGTCAAC
53167 GGGTCGGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (15 bp):
GTCAACGGGTCAACA
Found at i:53176 original size:13 final size:13
Alignment explanation
Indices: 53158--53228 Score: 115
Period size: 13 Copynumber: 5.5 Consensus size: 13
53148 CAACAGTCAA
53158 CGGGTCAACGGGT
1 CGGGTCAACGGGT
53171 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
53184 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
53197 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
53210 CGGGTAAACGGGT
1 CGGGTCAACGGGT
53223 CGGGTC
1 CGGGTC
53229 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:55338 original size:35 final size:35
Alignment explanation
Indices: 55265--55339 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
55255 CGTCACTAAC
**
55265 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
55300 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
55335 AGTAA
1 AGTAA
55340 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:55444 original size:24 final size:24
Alignment explanation
Indices: 55417--55491 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
55407 CATAATTCAA
*
55417 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
55441 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
55465 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
55488 GTCA
1 GTCA
55492 GGATCATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:55497 original size:23 final size:23
Alignment explanation
Indices: 55421--55497 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
55411 ATTCAAGTCA
*
55421 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
55444 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
55468 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
55491 AGGATCA
1 AGTATCA
55498 TAATAGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 26 0.55
24 21 0.45
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:55524 original size:47 final size:47
Alignment explanation
Indices: 55400--55513 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
55390 TATATCAAAA
* * * * *
55400 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAAATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
55448 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
*
55494 ATCATAAT-AGAATTCAAGTC
1 ATCA-AATCAGAATCCAAGTC
55514 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 15 0.27
47 23 0.42
48 17 0.31
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAAATCAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:56671 original size:18 final size:18
Alignment explanation
Indices: 56650--56685 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56640 CTTCCATCCG
*
56650 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
56668 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
56686 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:57993 original size:7 final size:7
Alignment explanation
Indices: 57981--58019 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
57971 GGTCAACGTG
57981 GGTCAAC
1 GGTCAAC
57988 GGTCAAC
1 GGTCAAC
57995 GGGTCAAC
1 -GGTCAAC
*
58003 AGTCAAC
1 GGTCAAC
58010 GGGTCAAC
1 -GGTCAAC
58018 GG
1 GG
58020 GTCGGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.28, C:0.26, G:0.33, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:58000 original size:15 final size:15
Alignment explanation
Indices: 57980--58019 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
57970 TGGTCAACGT
57980 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
*
57995 GGGTCAACAGTCAAC
1 GGGTCAACGGTCAAC
58010 GGGTCAACGG
1 GGGTCAACGG
58020 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.35, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:58001 original size:8 final size:8
Alignment explanation
Indices: 57961--58035 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
57951 TCAAAGTTTC
57961 GGTCAACAG
1 GGTCAAC-G
57970 TGGTCAACGTG
1 -GGTCAAC--G
57981 GGTCAAC-
1 GGTCAACG
57988 GGTCAACG
1 GGTCAACG
57996 GGTCAAC-
1 GGTCAACG
*
58003 AGTCAACG
1 GGTCAACG
58011 GGTCAACG
1 GGTCAACG
58019 GGT---CG
1 GGTCAACG
58024 GGTCAACG
1 GGTCAACG
58032 GGTC
1 GGTC
58036 GGGTCGGGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
5 5 0.09
7 13 0.23
8 23 0.41
10 14 0.25
11 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:58027 original size:13 final size:13
Alignment explanation
Indices: 58009--58084 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
57999 CAACAGTCAA
58009 CGGGTCAACGGGT
1 CGGGTCAACGGGT
58022 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
58040 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
58053 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
58066 CGGGTAAACGGGT
1 CGGGTCAACGGGT
58079 CGGGTC
1 CGGGTC
58085 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:58040 original size:18 final size:18
Alignment explanation
Indices: 58017--58057 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
58007 AACGGGTCAA
58017 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
58035 CGGGTCGGGTCAACTGGT
1 CGGGTCGGGTCAACGGGT
58053 CGGGT
1 CGGGT
58058 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:58047 original size:31 final size:31
Alignment explanation
Indices: 58009--58070 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
57999 CAACAGTCAA
*
58009 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
58040 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
58071 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:65133 original size:27 final size:29
Alignment explanation
Indices: 65075--65133 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
65065 ATTTCTGTAC
*
65075 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
65104 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
65131 TTA
1 TTA
65134 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:67507 original size:27 final size:29
Alignment explanation
Indices: 67449--67507 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
67439 ATTTCTGTAC
*
67449 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
67478 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
67505 TTA
1 TTA
67508 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:69879 original size:27 final size:29
Alignment explanation
Indices: 69821--69879 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
69811 ATTTCTGTAC
*
69821 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
69850 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
69877 TTA
1 TTA
69880 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:72248 original size:27 final size:29
Alignment explanation
Indices: 72190--72248 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
72180 ATTTCTGTAC
*
72190 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
72219 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
72246 TTA
1 TTA
72249 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:76955 original size:26 final size:28
Alignment explanation
Indices: 76899--76955 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
76889 ATTTCTGTAC
*
76899 TTATTAAAAACATATAGGTTAGTGTTTA
1 TTATTAAAAACATATAGGTTAGTGTTGA
* * *
76927 TTATTTAAAATATATA-TTTAG-GTTGA
1 TTATTAAAAACATATAGGTTAGTGTTGA
76953 TTA
1 TTA
76956 ATCAATATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.28
27 4 0.16
28 14 0.56
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (28 bp):
TTATTAAAAACATATAGGTTAGTGTTGA
Found at i:81598 original size:26 final size:27
Alignment explanation
Indices: 81542--81598 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
81532 CTAGTTTTAA
81542 TTTA-TGTACTTATTAAAACATATATG
1 TTTAGTGTACTTATTAAAACATATATG
* *
81568 GTTAGTGTA-TTATTTAAAATATATAT-
1 TTTAGTGTACTTA-TTAAAACATATATG
81594 TTTAG
1 TTTAG
81599 GTTGATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.49
Consensus pattern (27 bp):
TTTAGTGTACTTATTAAAACATATATG
Done.