Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001367.1 Hibiscus syriacus cultivar Beakdansim tig00002670_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: 44320
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1559 original size:18 final size:18
Alignment explanation
Indices: 1501--1560 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1491 GTTCTAATTA
1501 AAGAAAATAATTTAAAGT
1 AAGAAAATAATTTAAAGT
* *
1519 AA-AAGAATAA-ATAAATT
1 AAGAA-AATAATTTAAAGT
* *
1536 AGGAAAATAATTTAAAGG
1 AAGAAAATAATTTAAAGT
1554 AAGAAAA
1 AAGAAAA
1561 ATTTAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.22
Consensus pattern (18 bp):
AAGAAAATAATTTAAAGT
Found at i:3576 original size:30 final size:30
Alignment explanation
Indices: 3519--3576 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3509 AGGACCACTA
* * *
3519 TCCATATGTTTCAAACAATATAGGTAACTG
1 TCCATATGTTCCAAACAACATAAGTAACTG
* *
3549 TCCATATGTTCCGAAGAACATAAGTAAC
1 TCCATATGTTCCAAACAACATAAGTAAC
3577 CCTCGACTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (30 bp):
TCCATATGTTCCAAACAACATAAGTAACTG
Found at i:8304 original size:24 final size:22
Alignment explanation
Indices: 8254--8305 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
8244 GGCATGTGAA
* *
8254 ATATGTCCCGAAGGACCTATGC
1 ATATGTCCCAAAGGACCTATCC
*
8276 GTATGTCCCAAAGGACCACTATCC
1 ATATGTCCCAAAGGA-C-CTATCC
8300 ATATGT
1 ATATGT
8306 TCTGAAGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 13 0.54
23 1 0.04
24 10 0.42
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (22 bp):
ATATGTCCCAAAGGACCTATCC
Found at i:8333 original size:30 final size:30
Alignment explanation
Indices: 8297--8354 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
8287 AGGACCACTA
*
8297 TCCATATGTTCTGAAGAACATAAGTAACTG
1 TCCATATGTTCCGAAGAACATAAGTAACTG
*
8327 TCCATATGTTCCGAAGAACATAGGTAAC
1 TCCATATGTTCCGAAGAACATAAGTAAC
8355 CCTCAACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (30 bp):
TCCATATGTTCCGAAGAACATAAGTAACTG
Found at i:10966 original size:16 final size:16
Alignment explanation
Indices: 10918--10968 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
10908 TTACCTGACA
10918 TGTTTTCAACTTAACC
1 TGTTTTCAACTTAACC
* * *
10934 TGTTATGAACCTAACC
1 TGTTTTCAACTTAACC
*
10950 TGTTTTCAACTTGACC
1 TGTTTTCAACTTAACC
10966 TGT
1 TGT
10969 AAATGATCTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (16 bp):
TGTTTTCAACTTAACC
Found at i:12462 original size:20 final size:20
Alignment explanation
Indices: 12413--12494 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
12403 AAATAACCAA
* **
12413 CAAATTCGCAATGCGGACTC
1 CAAATTCGCAATGCAGTTTC
12433 C-AATTCCGCAATGCAGTTTC
1 CAAATT-CGCAATGCAGTTTC
* *
12453 CAAATTCGCAACGCGAATTTCC
1 CAAATTCGCAATGC-AGTTT-C
*
12475 CAAATTTGCAACT-CAGTTTC
1 CAAATTCGCAA-TGCAGTTTC
12495 TGCAATCGCA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
19 4 0.08
20 21 0.43
21 12 0.24
22 12 0.24
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAATGCAGTTTC
Found at i:12473 original size:21 final size:21
Alignment explanation
Indices: 12449--12596 Score: 78
Period size: 20 Copynumber: 7.2 Consensus size: 21
12439 CGCAATGCAG
12449 TTTCCAAATTCGCAACGCGAA
1 TTTCCAAATTCGCAACGCGAA
* * *
12470 TTTCCCAAATTTGCAACTC-AG
1 TTT-CCAAATTCGCAACGCGAA
12491 TTTCTGC-AA-TCGCAACGCGAA
1 TTTC--CAAATTCGCAACGCGAA
** *
12512 TTT-C-TTTCTCGCAATGCG-A
1 TTTCCAAAT-TCGCAACGCGAA
* * *
12531 TTTCGAAATTCACAACACGAAA
1 TTTCCAAATTCGCAACGCG-AA
* *
12553 TTT-CAAATTCACAACTCG-A
1 TTTCCAAATTCGCAACGCGAA
**
12572 TTTCTGAATTCGCAACGCGAA
1 TTTCCAAATTCGCAACGCGAA
12593 TTTC
1 TTTC
12597 TTTTTCACAA
Statistics
Matches: 94, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
18 1 0.01
19 8 0.09
20 35 0.37
21 32 0.34
22 18 0.19
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (21 bp):
TTTCCAAATTCGCAACGCGAA
Found at i:12480 original size:22 final size:23
Alignment explanation
Indices: 12451--12516 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
12441 CAATGCAGTT
12451 TCCAAATTCGCAACGCGAATTTC
1 TCCAAATTCGCAACGCGAATTTC
* * *
12474 -CCAAATTTGCAACTC-AGTTTC
1 TCCAAATTCGCAACGCGAATTTC
*
12495 TGC-AA-TCGCAACGCGAATTTC
1 TCCAAATTCGCAACGCGAATTTC
12516 T
1 T
12517 TTCTCGCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 7 0.21
21 13 0.38
22 14 0.41
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (23 bp):
TCCAAATTCGCAACGCGAATTTC
Found at i:12585 original size:81 final size:81
Alignment explanation
Indices: 12439--12599 Score: 204
Period size: 81 Copynumber: 2.0 Consensus size: 81
12429 ACTCCAATTC
* * **
12439 CGCAATGCAGTTTCCAAATTCGCAACGCGAATTTCCCAAATTTGCAACTCAGTTTCTGCAATCGC
1 CGCAATGCAGTTTCCAAATTCACAACACGAATTT-CCAAATTCACAACTCAGTTTCTGCAATCGC
12504 AACGCGAATTTCTTTCT
65 AACGCGAATTTCTTTCT
*
12521 CGCAATGC-GATTTCGAAATTCACAACACGAAATTT-CAAATTCACAACTC-GATTTCTG-AATT
1 CGCAATGCAG-TTTCCAAATTCACAACACG-AATTTCCAAATTCACAACTCAG-TTTCTGCAA-T
12582 CGCAACGCGAATTTCTTT
62 CGCAACGCGAATTTCTTT
12600 TTCACAACAC
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
80 3 0.04
81 38 0.54
82 24 0.34
83 5 0.07
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (81 bp):
CGCAATGCAGTTTCCAAATTCACAACACGAATTTCCAAATTCACAACTCAGTTTCTGCAATCGCA
ACGCGAATTTCTTTCT
Found at i:12587 original size:20 final size:21
Alignment explanation
Indices: 12537--12597 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
12527 GCGATTTCGA
* *
12537 AATTCACAACACGAAATTTC-A
1 AATTCACAACGCG-AATTTCTG
*
12558 AATTCACAACTCG-ATTTCTG
1 AATTCACAACGCGAATTTCTG
*
12578 AATTCGCAACGCGAATTTCT
1 AATTCACAACGCGAATTTCT
12598 TTTTCACAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.15
20 11 0.32
21 18 0.53
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (21 bp):
AATTCACAACGCGAATTTCTG
Found at i:12664 original size:20 final size:19
Alignment explanation
Indices: 12641--12725 Score: 50
Period size: 18 Copynumber: 4.4 Consensus size: 19
12631 ATTTTCTAAA
**
12641 TCGCAACACGAATTTTGTTT
1 TCGCAACACG-ATTTTAATT
*
12661 TCGC-ACTCGATTTTCGAA-T
1 TCGCAACACGATTTT--AATT
*
12680 TCGCAACACAAATTTTAATT
1 TCGCAACAC-GATTTTAATT
* * *
12700 TCGCAGCA-GCTTTTATTT
1 TCGCAACACGATTTTAATT
12718 TCGCAACA
1 TCGCAACA
12726 AAAATGTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
18 19 0.38
19 11 0.22
20 15 0.30
21 5 0.10
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (19 bp):
TCGCAACACGATTTTAATT
Found at i:12684 original size:39 final size:39
Alignment explanation
Indices: 12630--12704 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
12620 TTCATAACAA
* * **
12630 GATTTTCTAAATCGCAACACGAATTTTGTTTTCGCACTC
1 GATTTTCGAAATCGCAACACAAATTTTAATTTCGCACTC
*
12669 GATTTTCGAATTCGCAACACAAATTTTAATTTCGCA
1 GATTTTCGAAATCGCAACACAAATTTTAATTTCGCA
12705 GCAGCTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (39 bp):
GATTTTCGAAATCGCAACACAAATTTTAATTTCGCACTC
Found at i:12882 original size:14 final size:16
Alignment explanation
Indices: 12865--12897 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12855 TCCCATCTCT
12865 ATTTT-TTT-TATATA
1 ATTTTATTTCTATATA
12879 ATTTTATTTCTATATA
1 ATTTTATTTCTATATA
12895 ATT
1 ATT
12898 GTTCAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 3 0.18
16 9 0.53
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTATTTCTATATA
Found at i:13228 original size:21 final size:20
Alignment explanation
Indices: 13196--13280 Score: 93
Period size: 20 Copynumber: 4.2 Consensus size: 20
13186 GCGATTGTTG
* *
13196 CGAAAGTCAAATTCGCAACG
1 CGAAAATCAAATTCGCAACA
13216 CGAAAAATCAAATTCGCAACA
1 CG-AAAATCAAATTCGCAACA
13237 CGAAAATCAAATT--CAACA
1 CGAAAATCAAATTCGCAACA
* *
13255 TGCGAAAATAAAAATCGCAACA
1 --CGAAAATCAAATTCGCAACA
13277 CGAA
1 CGAA
13281 TTTGACTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.09
20 28 0.50
21 18 0.32
22 5 0.09
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.14
Consensus pattern (20 bp):
CGAAAATCAAATTCGCAACA
Found at i:13417 original size:16 final size:15
Alignment explanation
Indices: 13396--13430 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
13386 TGCATATTGA
*
13396 AATTAAACAACAAAT
1 AATTAAACAAAAAAT
13411 CAATTAAACAAAAAAT
1 -AATTAAACAAAAAAT
13427 AATT
1 AATT
13431 CTTATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
AATTAAACAAAAAAT
Found at i:14584 original size:21 final size:20
Alignment explanation
Indices: 14558--14628 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 20
14548 GTGAATGTAG
14558 CTCTTGAATAGTGGGAGGGGC
1 CTCTTGAA-AGTGGGAGGGGC
* *
14579 CTCTTGAACAATGAGAGGGGC
1 CTCTTGAA-AGTGGGAGGGGC
*
14600 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAAAG-TGGGAGGGGC
14621 CTCTTGAA
1 CTCTTGAA
14629 CGATGACAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (20 bp):
CTCTTGAAAGTGGGAGGGGC
Found at i:14629 original size:21 final size:21
Alignment explanation
Indices: 14569--14633 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
14559 TCTTGAATAG
*
14569 TGGGAGGGGCCTCTTGAACAA
1 TGGGAGGGGCCTCTTGAACGA
*
14590 TGAGAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
14611 TGGGAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
14632 TG
1 TG
14634 ACAGGTGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.40, T:0.20
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:14808 original size:4 final size:4
Alignment explanation
Indices: 14778--14818 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
14768 AGACCGCTAA
* * *
14778 AAAT AAAT TAAT ACAT AAAT CAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
14819 GTACCGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:15022 original size:42 final size:43
Alignment explanation
Indices: 14917--15025 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 43
14907 GAAACAATCT
* * * *
14917 CACGTAGAGCAGC-TACCTCATCACATAAAATAGATATATCAC
1 CACGTAAAGCACCATACCTCATCACGTAAAATAGATACATCAC
** * *
14959 CACGTAAAGCACCAT-TGTCATCACGTAAAATAGCTACCTCAC
1 CACGTAAAGCACCATACCTCATCACGTAAAATAGATACATCAC
*
15001 CACGTAAAG-ACCGTACCTCATCACG
1 CACGTAAAGCACCATACCTCATCACG
15026 CCATGCACTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 4 0.07
42 49 0.91
43 1 0.02
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (43 bp):
CACGTAAAGCACCATACCTCATCACGTAAAATAGATACATCAC
Found at i:15039 original size:63 final size:63
Alignment explanation
Indices: 14967--15088 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
14957 ACCACGTAAA
* * *
14967 GCACCATTGTCATCACGTAAAATAGCTACCTCACCACGTAAAG-ACCGTACCTCATCACGCCAT
1 GCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCG-ACCTCATCACGCCAT
* * * * *
15030 GCACTATTGTCGTCACGTAAAGTACCGACCTCATCACGCAAAGCACTGACCTCATCACG
1 GCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCGACCTCATCACG
15089 TAACTCCCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
63 47 0.94
64 3 0.06
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.20
Consensus pattern (63 bp):
GCACCATTGTCATCACGTAAAATACCGACCTCACCACGCAAAGCACCGACCTCATCACGCCAT
Found at i:15066 original size:21 final size:21
Alignment explanation
Indices: 15042--15091 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
15032 ACTATTGTCG
*
15042 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
15063 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
15084 TCACGTAA
1 TCACGTAA
15092 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:15088 original size:42 final size:41
Alignment explanation
Indices: 14992--15091 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
14982 CGTAAAATAG
* * *
14992 CTACCTCACCACGTAAAGACCGTACCTCATCACGCCATGCA
1 CTACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
** *
15033 CTATTGTCGTCACGTAAAGTACCG-ACCTCATCACGCAAAGCA
1 CTA-CCTCATCACGTAAAG-ACCGTACCTCATCACGCAAAGCA
15075 CTGACCTCATCACGTAA
1 CT-ACCTCATCACGTAA
15092 CTCCCCTAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 3 0.06
42 39 0.83
43 5 0.11
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (41 bp):
CTACCTCATCACGTAAAGACCGTACCTCATCACGCAAAGCA
Found at i:16883 original size:19 final size:18
Alignment explanation
Indices: 16871--16909 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
16861 TTGCGTTGTG
16871 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCG-ATTT
16890 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCG-ATTT
16909 A
1 A
16910 AGTTTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.51
Consensus pattern (18 bp):
ATTTTCGTGTTGCGATTT
Found at i:18998 original size:29 final size:30
Alignment explanation
Indices: 18964--19028 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
18954 ATGATGCATG
*
18964 TATATACA-ATGTACATTATACTTTATA-TA
1 TATATACATATATAC-TTATACTTTATAGTA
*
18993 TATATACATATATACTTATACTTTATAGTT
1 TATATACATATATACTTATACTTTATAGTA
19023 TATATA
1 TATATA
19029 TGCTAAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (30 bp):
TATATACATATATACTTATACTTTATAGTA
Found at i:19839 original size:46 final size:45
Alignment explanation
Indices: 19746--19872 Score: 195
Period size: 46 Copynumber: 2.8 Consensus size: 45
19736 GATAAACTGG
* * *
19746 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGAATATTGGT
19790 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGAAGT-TTGGT
1 AAAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGAA-TATTGGT
19836 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGA
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGA
19873 GATTTTATCT
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
44 24 0.31
45 13 0.17
46 39 0.51
47 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.28
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGAATATTGGT
Found at i:20412 original size:13 final size:13
Alignment explanation
Indices: 20365--20412 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
20355 ATCGGTACAC
* *
20365 TGTTCATTGTTCAC
1 TGTTCACTGTT-AT
* *
20379 TGTTCACGGGTAT
1 TGTTCACTGTTAT
20392 TGTTCACTGTTAT
1 TGTTCACTGTTAT
20405 TGTTCACT
1 TGTTCACT
20413 ATTTACTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 20 0.71
14 8 0.29
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (13 bp):
TGTTCACTGTTAT
Found at i:22135 original size:14 final size:14
Alignment explanation
Indices: 22116--22148 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
22106 CATTAATCAT
22116 GTATCTATGGGTTC
1 GTATCTATGGGTTC
22130 GTATCTATGGGTTC
1 GTATCTATGGGTTC
22144 GTATC
1 GTATC
22149 GAATGGTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (14 bp):
GTATCTATGGGTTC
Found at i:22156 original size:14 final size:14
Alignment explanation
Indices: 22116--22154 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
22106 CATTAATCAT
*
22116 GTATCTATGGGTTC
1 GTATCAATGGGTTC
*
22130 GTATCTATGGGTTC
1 GTATCAATGGGTTC
22144 GTATCGAATGG
1 GTATC-AATGG
22155 TTGTGATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.18, C:0.13, G:0.31, T:0.38
Consensus pattern (14 bp):
GTATCAATGGGTTC
Found at i:32033 original size:20 final size:20
Alignment explanation
Indices: 32008--32047 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31998 TCCCCTTCAA
32008 AAGGGGGAATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
*
32028 AAGGGGGGATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
32048 TGCACCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
AAGGGGGAATCGATTCCCTC
Found at i:40234 original size:2 final size:2
Alignment explanation
Indices: 40223--40286 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
40213 AATTAAACAT
40223 TA TA -A TA TA TA TA T- 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
*
40263 TA TC TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
40287 ATGAATGTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40371 original size:13 final size:13
Alignment explanation
Indices: 40350--40384 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40340 ATTAATACAT
*
40350 TATACTATATATA
1 TATAATATATATA
40363 TATAATATATATA
1 TATAATATATATA
*
40376 TATTATATA
1 TATAATATA
40385 AAAGTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TATAATATATATA
Found at i:40515 original size:17 final size:17
Alignment explanation
Indices: 40472--40525 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
40462 ATATAAAGTG
*
40472 TAAACTATAAAGTATAAA
1 TAAACTATAAA-TATATA
* *
40490 TATATTATAAATATATA
1 TAAACTATAAATATATA
40507 TAAACTATAAATATATA
1 TAAACTATAAATATATA
40524 TA
1 TA
40526 CTTTATACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAACTATAAATATATA
Found at i:40520 original size:15 final size:15
Alignment explanation
Indices: 40452--40523 Score: 71
Period size: 15 Copynumber: 5.0 Consensus size: 15
40442 AAAAAAGTAT
40452 AAGTATAAATATATA
1 AAGTATAAATATATA
* *
40467 AAGTGTAAA-CTATA
1 AAGTATAAATATATA
40481 AAGTATAAATATAT-
1 AAGTATAAATATATA
*
40495 TA-TA-AATATATATA
1 AAGTATAA-ATATATA
*
40509 AACTATAAATATATA
1 AAGTATAAATATATA
40524 TACTTTATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 2 0.04
13 8 0.17
14 14 0.30
15 20 0.43
16 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
AAGTATAAATATATA
Found at i:40532 original size:28 final size:27
Alignment explanation
Indices: 40477--40577 Score: 82
Period size: 28 Copynumber: 3.7 Consensus size: 27
40467 AAGTGTAAAC
* **
40477 TATAAAGTATAAATATATTATAAATATA
1 TATAAACTATAAATATA-TATATTTATA
40505 TATAAACTATAAATATATATACTTTATA
1 TATAAACTATAAATATATATA-TTTATA
* *
40533 CTA-AAACTTTATATATTATATATTTATA
1 -TATAAACTATAAATA-TATATATTTATA
* *
40561 T-TATACT-TATATATATA
1 TATAAACTATAAATATATA
40578 AGTATAATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
25 4 0.06
26 6 0.10
27 9 0.14
28 36 0.57
29 8 0.13
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.46
Consensus pattern (27 bp):
TATAAACTATAAATATATATATTTATA
Found at i:40705 original size:8 final size:8
Alignment explanation
Indices: 40651--40838 Score: 101
Period size: 8 Copynumber: 25.1 Consensus size: 8
40641 TATATATATA
40651 TATATACT
1 TATATACT
40659 TATATACT
1 TATATACT
40667 T-TATA-T
1 TATATACT
40673 TATATACT
1 TATATACT
40681 TATATACT
1 TATATACT
40689 T-TATA-T
1 TATATACT
*
40695 TATATGCT
1 TATATACT
40703 TATATACT
1 TATATACT
*
40711 T-TAGTATT
1 TATA-TACT
40719 TA-ATTAACT
1 TATA-T-ACT
*
40728 T-TCTA-T
1 TATATACT
40734 ATATATA-T
1 -TATATACT
*
40742 AATATAC-
1 TATATACT
40749 T-TATACT
1 TATATACT
40756 T-TATA-T
1 TATATACT
*
40762 GTATAT-TT
1 -TATATACT
40770 TATATACT
1 TATATACT
40778 T-TATA-T
1 TATATACT
**
40784 GTATATGTT
1 -TATATACT
40793 TATATACTT
1 TATATAC-T
40802 TATATAC-
1 TATATACT
40809 -ATATA-T
1 TATATACT
*
40815 TTTATA-T
1 TATATACT
40822 TATATACT
1 TATATACT
40830 TATATACT
1 TATATACT
40838 T
1 T
40839 TAGTCTTTAT
Statistics
Matches: 142, Mismatches: 15, Indels: 46
0.70 0.07 0.23
Matches are distributed among these distances:
6 17 0.12
7 50 0.35
8 63 0.44
9 12 0.08
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (8 bp):
TATATACT
Found at i:40738 original size:2 final size:2
Alignment explanation
Indices: 40731--41044 Score: 60
Period size: 2 Copynumber: 160.0 Consensus size: 2
40721 ATTAACTTTC
* * *
40731 TA TA TA TA TA TA -A TA TA CT- TA TA CTT TA TA TG TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * * *
40772 TA TA CTT TA TA TG TA TA TG TT TA TA TA CTT TA TA TA CA TA TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
40815 TT TA TA T- TA TA TA CT- TA TA TA CTT TA GTC TT TA TA T- TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA TA TA TA TA TA TA
* *
40855 CT- TA TA -A T- TA TA TA TG TA TA TA TA CTT TA TA TA TA TA -A TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
40895 TA TA TA AA TG TA TA TA GTT TA TA TA TA TA CT- TA TT TA CTT TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA
* * * * *
40937 TA TT TA AA CTA TA TA AA CTA TA -A TT TA TA CA TA T- TA TA TA -A
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
40978 TT TA TA GTT TA TA T- TA -A TA AA TA TA TA -A TT TA TA TA TA GTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
41019 TA TA -A T- TA TA -A T- TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41045 ATAAAGTTGT
Statistics
Matches: 218, Mismatches: 56, Indels: 76
0.62 0.16 0.22
Matches are distributed among these distances:
1 22 0.10
2 179 0.82
3 17 0.08
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40753 original size:60 final size:62
Alignment explanation
Indices: 40661--40891 Score: 181
Period size: 65 Copynumber: 3.6 Consensus size: 62
40651 TATATACTTA
*
40661 TATACTTTATAT-TATATACTTATATACTTTATATTATATGCTTATATACTTTAGTATTTA-AT
1 TATACTTTATATATATATA-TAATATAC-TTATATTATATGCTTATATACTTTAGTATTTATAT
* *
40723 TA-ACTTTCTATATATATATAATATACTTATACTTTATATG--TATAT--TTTATATACTTTATA
1 TATACTTTATATATATATATAATATACTTATA--TTATATGCTTATATACTTTA-GTA-TTTATA
40783 T
62 T
* * * * *
40784 GTATATGTTTATATACTTTATATACATATATTTTATATTATATACTTATATACTTTAGTCTTTAT
1 -TATA-CTTTATATA-TATATATA-ATATA-CTTATATTATATGCTTATATACTTTAGTATTTAT
40849 AT
61 AT
*
40851 TATAC-TTATAATTATATATGTATATATACTTTATATATATA
1 TATACTTTAT-A-TATATATATA-ATATAC-TTATAT-TATA
40892 ATATATATAA
Statistics
Matches: 134, Mismatches: 15, Indels: 36
0.72 0.08 0.19
Matches are distributed among these distances:
58 4 0.03
59 2 0.01
60 14 0.10
61 17 0.13
62 17 0.13
63 1 0.01
64 11 0.08
65 31 0.23
66 15 0.11
67 17 0.13
68 1 0.01
69 4 0.03
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.54
Consensus pattern (62 bp):
TATACTTTATATATATATATAATATACTTATATTATATGCTTATATACTTTAGTATTTATAT
Found at i:40806 original size:67 final size:71
Alignment explanation
Indices: 40658--40834 Score: 178
Period size: 67 Copynumber: 2.6 Consensus size: 71
40648 ATATATATAC
*
40658 TTATATACTTTATAT-TATATACTTATATACTTTATATTATATGCTTATATACTTTAGTATTTAA
1 TTATATACTTTATATATATATACTTATATACTTTATATTATATGCTTATATACTTTAGTATGTAA
40722 TTAACT
66 TTAACT
* * *
40728 TTCTATA-TATATATA-ATATAC-T-TATACTTTATATGTATAT-TTTATATACTTTA-TATGT-
1 TTATATACTTTATATATATATACTTATATACTTTATAT-TATATGCTTATATACTTTAGTATGTA
**
40786 A-TATGT
65 ATTAACT
* *
40792 TTATATACTTTATATACATATA-TTTTATA-TTATATACTTATAT
1 TTATATACTTTATATATATATACTTATATACTT-TATA-TTATAT
40835 ACTTTAGTCT
Statistics
Matches: 91, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
64 9 0.10
65 8 0.09
66 12 0.13
67 37 0.41
68 7 0.08
69 12 0.13
70 6 0.07
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (71 bp):
TTATATACTTTATATATATATACTTATATACTTTATATTATATGCTTATATACTTTAGTATGTAA
TTAACT
Found at i:40899 original size:22 final size:22
Alignment explanation
Indices: 40634--41015 Score: 115
Period size: 22 Copynumber: 18.0 Consensus size: 22
40624 ATAAGTATTA
*
40634 AATATAGTATA-TATATATATAT
1 AATATA-TATACTTTATATATAT
*
40656 ACT-TATATACTTTATATTATAT
1 AATATATATACTTTATA-TATAT
*
40678 ACT-TATATACTTTATATTATAT
1 AATATATATACTTTATA-TATAT
**
40700 GCT-TATATACTTTAGTAT-T-T
1 AATATATATACTTTA-TATATAT
* *
40720 AAT-TA-ACTTTCTATATATATAT
1 AATATATA--TACTTTATATATAT
*
40742 AATATACTTATACTTTATATGTAT
1 AATATA--TATACTTTATATATAT
* * *
40766 ATTTTATATACTTTATATGTAT
1 AATATATATACTTTATATATAT
* * *
40788 ATGTTTATATACTTTATATACAT
1 A-ATATATATACTTTATATATAT
*
40811 -ATAT-T-T--TATAT-TATAT
1 AATATATATACTTTATATATAT
* *
40827 ACT-TATATACTTTAGTCT-T-T
1 AATATATATACTTTA-TATATAT
40847 -ATAT-TATAC-TTATAATTATAT
1 AATATATATACTTTAT-A-TATAT
*
40868 ATGTATATATACTTTATATATAT
1 A-ATATATATACTTTATATATAT
* *
40891 AATATATATAAATGTATATAGT-T
1 AATATATAT-ACTTTATATA-TAT
* *
40914 TATATATATAC-TTATTTACT-T
1 AATATATATACTTTATATA-TAT
* * * * *
40935 TATATTTAAACTATATAAACTAT
1 AATATATATACTTTATATA-TAT
*
40958 AAT-T-TATAC-ATAT-TATAT
1 AATATATATACTTTATATATAT
*
40976 AAT-T-TATAGTTTATAT-TAAT
1 AATATATATACTTTATATAT-AT
*
40996 AA-ATATATAATTTATATATA
1 AATATATATACTTTATATATA
41016 GTATATAATT
Statistics
Matches: 279, Mismatches: 43, Indels: 77
0.70 0.11 0.19
Matches are distributed among these distances:
16 5 0.02
17 7 0.03
18 15 0.05
19 14 0.05
20 28 0.10
21 51 0.18
22 81 0.29
23 51 0.18
24 22 0.08
25 4 0.01
26 1 0.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (22 bp):
AATATATATACTTTATATATAT
Found at i:40976 original size:25 final size:25
Alignment explanation
Indices: 40946--41045 Score: 90
Period size: 25 Copynumber: 4.3 Consensus size: 25
40936 ATATTTAAAC
*
40946 TATATAAACTATAATTTATACATAT
1 TATATAAATTATAATTTATACATAT
* *
40971 TATATAATTTAT-AGTT-T--ATAT
1 TATATAAATTATAATTTATACATAT
* *
40992 TA-ATAAATATATAATTTATATATAG
1 TATATAAAT-TATAATTTATACATAT
41017 TATAT-AATTATAA-TTATACATA-
1 TATATAAATTATAATTTATACATAT
41039 TATATAA
1 TATATAA
41046 TAAAGTTGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.08
21 9 0.15
22 8 0.13
23 11 0.18
24 8 0.13
25 18 0.30
26 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (25 bp):
TATATAAATTATAATTTATACATAT
Found at i:41010 original size:73 final size:68
Alignment explanation
Indices: 40888--41046 Score: 160
Period size: 73 Copynumber: 2.2 Consensus size: 68
40878 ACTTTATATA
** * *
40888 TATA-ATATATATAAATGTATATAGTTTATATATATACTTATTTACTTTATATTTAAACTATATA
1 TATACATATATAT-AAT-T-TATAGTTTATATATATAAATATATAATTTATA--TAAACTATAT-
40952 AACTATAATT
60 AACTATAA-T
* * *
40962 TATACATATTATATAATTTATAGTTTATAT-TAATAAATATATAATTTATATATAGTATATAATT
1 TATACATA-TATATAATTTATAGTTTATATAT-ATAAATATATAATTTATATAAACTATATAACT
41026 ATAAT
64 ATAAT
41031 TATACATATATATAAT
1 TATACATATATATAAT
41047 AAAGTTGTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
68 8 0.11
69 9 0.12
70 7 0.09
71 8 0.11
72 1 0.01
73 26 0.35
74 5 0.07
75 6 0.08
76 5 0.07
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (68 bp):
TATACATATATATAATTTATAGTTTATATATATAAATATATAATTTATATAAACTATATAACTAT
AAT
Found at i:41238 original size:17 final size:16
Alignment explanation
Indices: 41189--41279 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 16
41179 ATACATAATG
*
41189 TATATAT-AGTTTATA
1 TATATATAAATTTATA
*
41204 TATAGTATAATATATATA
1 TATA-TATAA-ATTTATA
41222 TATATATAAACTTTATA
1 TATATATAAA-TTTATA
* *
41239 TGTATATATATTT-TA
1 TATATATAAATTTATA
*
41254 TATACT-TAAATATTTTA
1 TATA-TATAAAT-TTATA
41271 TATTATATA
1 TA-TATATA
41280 CTTATATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
15 13 0.22
16 10 0.17
17 24 0.40
18 13 0.22
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (16 bp):
TATATATAAATTTATA
Found at i:41257 original size:2 final size:2
Alignment explanation
Indices: 41189--41249 Score: 52
Period size: 2 Copynumber: 29.5 Consensus size: 2
41179 ATACATAATG
* *
41189 TA TA TA TA GTT TA TA TA TA GTA TA -A TA TA TA TA TA TA TA TA AA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
41232 CTT TA TA TG TA TA TA TA T
1 -TA TA TA TA TA TA TA TA T
41250 TTTATATACT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
1 1 0.02
2 43 0.91
3 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41286 original size:8 final size:7
Alignment explanation
Indices: 41199--41544 Score: 137
Period size: 7 Copynumber: 50.7 Consensus size: 7
41189 TATATATAGT
41199 TTATATA
1 TTATATA
41206 -TAGTATA
1 TTA-TATA
*
41213 ATATATA
1 TTATATA
41220 -TATATA
1 TTATATA
*
41226 -TATAAA
1 TTATATA
41232 CTT-TATA
1 -TTATATA
41239 TGTATATA
1 T-TATATA
41247 -TAT-T-
1 TTATATA
41251 TTATATA
1 TTATATA
*
41258 CTTAAATA
1 -TTATATA
*
41266 TTTTATA
1 TTATATA
41273 TTATATA
1 TTATATA
*
41280 CTTATATT
1 -TTATATA
*
41288 TTAGTCT-
1 TTA-TATA
41295 TTATA-A
1 TTATATA
*
41301 TTATA-C
1 TTATATA
41307 TT-TATA
1 TTATATA
41313 TTA-ATA
1 TTATATA
41319 CTTATACT-
1 -TTATA-TA
41327 TTATATGA
1 TTATAT-A
41335 -TATATA
1 TTATATA
41341 -TATATA
1 TTATATA
41347 CTT-TATA
1 -TTATATA
41354 TT-TA-A
1 TTATATA
*
41359 TT-TTTA
1 TTATATA
*
41365 TTTTATA
1 TTATATA
41372 TTATATA
1 TTATATA
41379 GTTATATA
1 -TTATATA
*
41387 CT-TATA
1 TTATATA
*
41393 TTATATC
1 TTATATA
41400 TTATAT-
1 TTATATA
*
41406 TT-TAGTC
1 TTATA-TA
41413 TT-TATA
1 TTATATA
41419 CTTATACT-
1 -TTATA-TA
41427 TT-TA-A
1 TTATATA
41432 TTATATA
1 TTATATA
41439 TATATATA
1 T-TATATA
41447 TATATAATA
1 T-TAT-ATA
41456 TT-TATA
1 TTATATA
41462 CTT-TATA
1 -TTATATA
41469 TTATTATA
1 TTA-TATA
41477 TTATAT-
1 TTATATA
41483 TTATATA
1 TTATATA
41490 -TATATA
1 TTATATA
41496 -TATATA
1 TTATATA
41502 -TATATA
1 TTATATA
41508 TATATATA
1 T-TATATA
41516 TCTATATA
1 T-TATATA
41524 CTTATACT-
1 -TTATA-TA
41532 TTATATTA
1 TTATA-TA
41540 TTATA
1 TTATA
41545 CATATTTGTA
Statistics
Matches: 274, Mismatches: 20, Indels: 89
0.72 0.05 0.23
Matches are distributed among these distances:
5 14 0.05
6 88 0.32
7 91 0.33
8 73 0.27
9 8 0.03
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (7 bp):
TTATATA
Found at i:41357 original size:6 final size:6
Alignment explanation
Indices: 41267--41538 Score: 120
Period size: 6 Copynumber: 42.3 Consensus size: 6
41257 ACTTAAATAT
* * * *
41267 TTTATA TTATATA CTTATA TTTTAGTC TTTATA ATTATA CTTTATA TTAATA
1 TTTATA TT-TATA TTTATA -TTTA-TA TTTATA TTTATA -TTTATA TTTATA
* * *
41319 CTTATA CTTTATA TGATATATA TATATA CTTTATA TTTA-A TTTTTA TTTTATA
1 TTTATA -TTTATA T--T-TATA TTTATA -TTTATA TTTATA TTTATA -TTTATA
* *
41372 TTATATA GTTATATA CTTATA -TTATA TCTTATA TTTTAGTC TTTATA
1 TT-TATA -TT-TATA TTTATA TTTATA T-TTATA -TTTA-TA TTTATA
* * * * *
41419 CTTATA CTTT-TA ATTATA TATATA TATATA TATAATA TTTATA CTTTATA
1 TTTATA -TTTATA TTTATA TTTATA TTTATA T-TTATA TTTATA -TTTATA
* * * * * *
41469 -TTATTA TATTATA TTTATA TATATA TATATA TATATA TATATA TATATC
1 TTTA-TA T-TTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* *
41518 TATATA CTTATA CTTTATA TT
1 TTTATA TTTATA -TTTATA TT
41539 ATTATACATA
Statistics
Matches: 210, Mismatches: 31, Indels: 50
0.72 0.11 0.17
Matches are distributed among these distances:
5 14 0.07
6 108 0.51
7 69 0.33
8 14 0.07
9 5 0.02
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTATA
Found at i:41440 original size:2 final size:2
Alignment explanation
Indices: 41433--41523 Score: 109
Period size: 2 Copynumber: 47.0 Consensus size: 2
41423 TACTTTTAAT
* *
41433 TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA CTT TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
41473 TA TA T- TA TA TT 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
*
41514 TA TC TA TA TA
1 TA TA TA TA TA
41524 CTTATACTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
1 4 0.05
2 71 0.93
3 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:41753 original size:2 final size:2
Alignment explanation
Indices: 41746--41981 Score: 72
Period size: 2 Copynumber: 120.0 Consensus size: 2
41736 GTGTATATTT
* * * *
41746 TA TA TA TA GTA TA TA -A TA -A TA TA AA TA TA AA CTA CA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
41787 TA TA TA TA TA TA TA CT- TA TA TA TA CA CTA TA TA T- TT TA TA TG
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
41829 TA -A TT TA TA T- TA -A TA AA CTA TA TA GTT TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* *
41869 TA TA GTT TA TA TA TA GTA TA TA -A TA TA TA -A TA -A AA CTA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
41909 GT- TT TA TG TA TA -A TA TA TA TA -A TT TA TA TA TA AA CTA TA T-
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
41949 TT TA TG CA TA AA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41982 ATTTTTTCAA
Statistics
Matches: 170, Mismatches: 36, Indels: 56
0.65 0.14 0.21
Matches are distributed among these distances:
1 16 0.09
2 140 0.82
3 14 0.08
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:41858 original size:33 final size:34
Alignment explanation
Indices: 41770--41870 Score: 116
Period size: 33 Copynumber: 2.9 Consensus size: 34
41760 AATAATATAA
*
41770 ATATAAACTACATAGTTTATATATATATATACTT
1 ATATAAACTATATAGTTTATATATATATATACTT
* * *
41804 ATATATACACTATATATTTTATATGTAATTTATA-TT
1 ATATA-A-ACTATATAGTTTATATAT-ATATATACTT
41840 A-ATAAACTATATAGTTTATATATATTATATA
1 ATATAAACTATATAGTTTATATATA-TATATA
41871 TAGTTTATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
32 1 0.02
33 21 0.38
34 6 0.11
35 4 0.07
36 18 0.32
37 6 0.11
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (34 bp):
ATATAAACTATATAGTTTATATATATATATACTT
Found at i:41863 original size:11 final size:11
Alignment explanation
Indices: 41847--41895 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
41837 ATTAATAAAC
41847 TATATAGTTTA
1 TATATAGTTTA
41858 TATATA--TTA
1 TATATAGTTTA
41867 TATATAGTTTA
1 TATATAGTTTA
*
41878 TATATAGTATA
1 TATATAGTTTA
41889 TAATATA
1 T-ATATA
41896 TAATAAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 9 0.26
11 20 0.59
12 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:41897 original size:9 final size:9
Alignment explanation
Indices: 41856--41981 Score: 53
Period size: 9 Copynumber: 13.4 Consensus size: 9
41846 CTATATAGTT
*
41856 TATATATAT
1 TATATATAA
*
41865 TATATATAG
1 TATATATAA
*
41874 TTTATAT-A
1 TATATATAA
41882 TAGTATATAA
1 TA-TATATAA
41892 TATATAATAA
1 TATAT-ATAA
* **
41902 AACTATAGTTT
1 TA-TATA-TAA
*
41913 TATGTATAA
1 TATATATAA
41922 TATATATAA
1 TATATATAA
41931 TTTATATATAA
1 --TATATATAA
**
41942 -ACTATATTT
1 TA-TATATAA
41951 TATGCATA-AA
1 TAT--ATATAA
41961 TATATAT-A
1 TATATATAA
*
41969 TATATATAT
1 TATATATAA
41978 TATA
1 TATA
41982 ATTTTTTCAA
Statistics
Matches: 87, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
8 13 0.15
9 41 0.47
10 16 0.18
11 17 0.20
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (9 bp):
TATATATAA
Found at i:41920 original size:32 final size:33
Alignment explanation
Indices: 41754--41972 Score: 111
Period size: 29 Copynumber: 6.6 Consensus size: 33
41744 TTTATATATA
* *
41754 GTATATAATAATATAAATATAAACTACATAGTTTAT
1 GTATATAAT-ATATATATATAAACT--ATATTTTAT
* *
41790 ATATAT-ATATACTTATATATACACTATATATTT-T
1 GTATATAATATA--TATATATAAACTATAT-TTTAT
* * * **
41824 ATATGTAATTTATAT-TAATAAACTATATAGT-T
1 GTATATAATATATATAT-ATAAACTATATTTTAT
*** *
41856 -TATAT-ATAT-TATATATAGTTTATA-TATA-
1 GTATATAATATATATATATAAACTATATTTTAT
41884 GTATATAATATATA-ATA-AAACTATAGTTTTAT
1 GTATATAATATATATATATAAACTATA-TTTTAT
41916 GTATAATATATATAATTTATATATAAACTATATTTTAT
1 GTAT-ATA-ATAT-A--TATATATAAACTATATTTTAT
*
41954 GCATA-AATATATATATATA
1 GTATATAATATATATATATA
41973 TATATTATAA
Statistics
Matches: 142, Mismatches: 21, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
28 1 0.01
29 20 0.14
30 11 0.08
31 9 0.06
32 15 0.11
33 16 0.11
34 17 0.12
35 14 0.10
36 16 0.11
37 3 0.02
38 12 0.08
39 8 0.06
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (33 bp):
GTATATAATATATATATATAAACTATATTTTAT
Found at i:41944 original size:39 final size:39
Alignment explanation
Indices: 41876--41977 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 39
41866 ATATATAGTT
41876 TATATATAGTATATAATATATA-ATAAAACTATAGTTTTATG
1 TATA-ATA-TATATAATATATATATAAAACTATA-TTTTATG
*
41917 TATAATATATATAATTTATATAT-AAACTATATTTTATG
1 TATAATATATATAATATATATATAAAACTATATTTTATG
*
41955 CATAA-ATATATATATATATATAT
1 TATAATATATATA-ATATATATAT
41978 TATAATTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
37 7 0.12
38 20 0.36
39 20 0.36
40 5 0.09
41 4 0.07
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (39 bp):
TATAATATATATAATATATATATAAAACTATATTTTATG
Found at i:41982 original size:41 final size:41
Alignment explanation
Indices: 41877--41982 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 41
41867 TATATAGTTT
* *
41877 ATATATAGTATATAATATATAATAAAACTATAGTTTTATGTATA
1 ATATATA-TATAT-ATATATTAT-AAACTATAGTTTTATGCATA
*
41921 ATATATATA-ATTTATA-TATAAACTATA-TTTTATGCATAA
1 ATATATATATATATATATTATAAACTATAGTTTTATGCAT-A
41960 ATATATATATATATATATTATAA
1 ATATATATATATATATATTATAA
41983 TTTTTTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
38 9 0.16
39 18 0.33
40 8 0.15
41 9 0.16
42 2 0.04
43 2 0.04
44 7 0.13
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (41 bp):
ATATATATATATATATATTATAAACTATAGTTTTATGCATA
Done.