Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002528.1 Hibiscus syriacus cultivar Beakdansim tig00005141_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: 86444
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:4417 original size:2 final size:2
Alignment explanation
Indices: 4410--4441 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4400 TTCAGAAATA
4410 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4442 ACTAAATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4695 original size:2 final size:2
Alignment explanation
Indices: 4688--4722 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4678 ATATAAACAT
4688 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4723 TTCAAACAAT
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:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10285 original size:23 final size:24
Alignment explanation
Indices: 10246--10291 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
10236 TATATATGTT
10246 AATGTGATATTATTTATAGTATAC
1 AATGTGATATTATTTATAGTATAC
*
10270 AATGT-ATATGTA-TTATATTATA
1 AATGTGATAT-TATTTATAGTATA
10292 AATACATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (24 bp):
AATGTGATATTATTTATAGTATAC
Found at i:10296 original size:27 final size:27
Alignment explanation
Indices: 10253--10305 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
10243 GTTAATGTGA
*
10253 TATTATTTATAGTATACAATG-TATATG
1 TATTATTTATAGAATAC-ATGATATATG
10280 TATTATATTATA-AATACATGATATAT
1 TATTAT-TTATAGAATACATGATATAT
10306 TACATACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.13
27 15 0.65
28 5 0.22
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (27 bp):
TATTATTTATAGAATACATGATATATG
Found at i:11502 original size:18 final size:17
Alignment explanation
Indices: 11473--11514 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
11463 TCTATGTATG
*
11473 TATATATTTTATACCATTA
1 TATATATCTTAT--CATTA
11492 T-TATATCTTATCATTA
1 TATATATCTTATCATTA
11508 TATATAT
1 TATATAT
11515 ATATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.29
17 5 0.24
18 9 0.43
19 1 0.05
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATATCTTATCATTA
Found at i:11746 original size:15 final size:16
Alignment explanation
Indices: 11726--11759 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11716 TTATGTTTGG
11726 TTTCATATTTTATT-T
1 TTTCATATTTTATTAT
*
11741 TTTCATCTTTTATTAT
1 TTTCATATTTTATTAT
11757 TTT
1 TTT
11760 GTGTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCATATTTTATTAT
Found at i:22277 original size:8 final size:7
Alignment explanation
Indices: 22263--22328 Score: 78
Period size: 8 Copynumber: 8.7 Consensus size: 7
22253 CCTAAATTGA
22263 AAAAAAG
1 AAAAAAG
22270 AGAAAAAG
1 A-AAAAAG
22278 AAAAAGAG
1 AAAAA-AG
22286 AAAAAAG
1 AAAAAAG
22293 AACAAAAG
1 AA-AAAAG
22301 AACAAAAG
1 AA-AAAAG
*
22309 AAAAAACA
1 AAAAAA-G
22317 AAAAAAG
1 AAAAAAG
22324 AAAAA
1 AAAAA
22329 TAAGGTGGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
7 18 0.34
8 35 0.66
ACGTcount: A:0.82, C:0.05, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:22292 original size:23 final size:21
Alignment explanation
Indices: 22263--22328 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 21
22253 CCTAAATTGA
22263 AAAAAAGAGAAAAAGAAAAAGAG
1 AAAAAAGA-AAAAAGAAAAA-AG
22286 AAAAAAGAACAAAAGAACAAAAG
1 AAAAAAGAA-AAAAGAA-AAAAG
*
22309 AAAAAACAAAAAAAGAAAAA
1 AAAAAA-GAAAAAAGAAAAA
22329 TAAGGTGGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 4 0.10
23 30 0.77
24 5 0.13
ACGTcount: A:0.82, C:0.05, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAGAAAAAAG
Found at i:22322 original size:31 final size:31
Alignment explanation
Indices: 22265--22325 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
22255 TAAATTGAAA
*
22265 AAAAGAGAAAAAGAAAAAGAGAAAAAAGAAC
1 AAAAGAGAAAAAGAAAAAGAAAAAAAAGAAC
22296 AAAAGA-ACAAAAGAAAAA-ACAAAAAAAGAA
1 AAAAGAGA-AAAAGAAAAAGA-AAAAAAAGAA
22326 AAATAAGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (31 bp):
AAAAGAGAAAAAGAAAAAGAAAAAAAAGAAC
Found at i:23637 original size:110 final size:107
Alignment explanation
Indices: 23439--23696 Score: 299
Period size: 110 Copynumber: 2.4 Consensus size: 107
23429 GCTTCCCAAT
* * *
23439 TTCAGAGCTAATTTCAGCTTCACATCGAATGATATTGGACCCAAGACAACAATAACTCAACTTCA
1 TTCAGAGC-AATTTCAACTTCACAACGAATGATATTGGACTCAAGACAACAATAACTCAACTTCA
* * * * * *
23504 CGACGAAGGGGCGGCTGATTGTCAATAAATAACTTT-TCAATTTC
65 CAACGAAGGGGCAGCTGACTGTCAACAAACAA-TTTCTC-AGTTC
*
23548 ATTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCAAGACAACACA-AGCTCAACTT
1 -TTCAGAG-CAATTTCAACTTCACAACGAATGATATTGGACTCAAGACAACA-ATAACTCAACTT
*
23612 CACAACGAAGGGGCAGTTGACTGTCAACAAACAATTTCTCAGTTC
63 CACAACGAAGGGGCAGCTGACTGTCAACAAACAATTTCTCAGTTC
* * *
23657 --CAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 TTCAGAG-CAATTTCAACTTCACAACGAATGATATTGGACTC
23697 GGAACAATGC
Statistics
Matches: 130, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
106 36 0.28
109 7 0.05
110 85 0.65
111 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (107 bp):
TTCAGAGCAATTTCAACTTCACAACGAATGATATTGGACTCAAGACAACAATAACTCAACTTCAC
AACGAAGGGGCAGCTGACTGTCAACAAACAATTTCTCAGTTC
Found at i:25630 original size:7 final size:8
Alignment explanation
Indices: 25603--25648 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
25593 TTATCATATA
25603 TATTTTAT
1 TATTTTAT
25611 TATTTTAT
1 TATTTTAT
25619 TATTTT-T
1 TATTTTAT
25626 TA-TTTAT
1 TATTTTAT
*
25633 TATTTATAG
1 TATTT-TAT
25642 TATTTTA
1 TATTTTA
25649 ATCTATGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 3 0.09
7 6 0.18
8 18 0.53
9 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TATTTTAT
Found at i:25689 original size:18 final size:17
Alignment explanation
Indices: 25660--25719 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
25650 TCTATGTATG
*
25660 TATATATTTTATACCATTA
1 TATATATCTTAT--CATTA
25679 T-TATATCTTATCATTA
1 TATATATCTTATCATTA
*
25695 TATATATATATAT-ATATA
1 TATATATCT-TATCAT-TA
25713 TATATAT
1 TATATAT
25720 ACACGCATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.17
17 8 0.22
18 21 0.58
19 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATCTTATCATTA
Found at i:25700 original size:2 final size:2
Alignment explanation
Indices: 25693--25720 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25683 ATCTTATCAT
25693 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
25721 CACGCATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25943 original size:16 final size:17
Alignment explanation
Indices: 25922--25956 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
25912 TTATGTTTGG
25922 TTTCATATTTTATT-TT
1 TTTCATATTTTATTATT
*
25938 TTTCATCTTTTATTATT
1 TTTCATATTTTATTATT
25955 TT
1 TT
25957 GTGTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTCATATTTTATTATT
Found at i:26988 original size:18 final size:18
Alignment explanation
Indices: 26965--26999 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
26955 AAGTTAATAA
26965 TTAATAATTAAATACATG
1 TTAATAATTAAATACATG
26983 TTAATAATTAAATACAT
1 TTAATAATTAAATACAT
27000 AGAGGGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAATAATTAAATACATG
Found at i:30337 original size:20 final size:21
Alignment explanation
Indices: 30308--30349 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
30298 TATAGCAGTA
* *
30308 CTGTATCAGGG-TATCGGTAC
1 CTGTAGCAGGGATATCGATAC
30328 CTGTAGCAGGGATATCGATAC
1 CTGTAGCAGGGATATCGATAC
30349 C
1 C
30350 CCTGAAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
CTGTAGCAGGGATATCGATAC
Found at i:30725 original size:37 final size:35
Alignment explanation
Indices: 30684--30756 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
30674 GTTAGAAAAT
* *
30684 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTT-TTTAAAAAATTTAAAAT-ATAAA
*
30721 ATTTATATAATTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAATTTTTTAAAAAATTTAAAATATAAA
30756 A
1 A
30757 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 15 0.45
37 12 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (35 bp):
ATTTATATAATTTTTTAAAAAATTTAAAATATAAA
Found at i:31287 original size:26 final size:26
Alignment explanation
Indices: 31254--31303 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
31244 TAATTGGAGG
*
31254 ATTAGATTTATTTAAT-TAATTTAAA
1 ATTAGATTAATTTAATATAATTTAAA
31279 ATTATGATTAATTTAATATAATTTA
1 ATTA-GATTAATTTAATATAATTTA
31304 TAAGTAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 11 0.50
27 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTAGATTAATTTAATATAATTTAAA
Found at i:42858 original size:64 final size:64
Alignment explanation
Indices: 42775--42993 Score: 201
Period size: 64 Copynumber: 3.4 Consensus size: 64
42765 TATTTGAATG
** ** *
42775 TGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATATAAACATCGAATACAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-GAAACATCGAATACAATTC
42838 A
64 A
* **
42839 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATACAATTCA
* * * * ** * ** *
42903 TGTATTGATGCATAAGGAGTGAATCGATGCATCCCAACAATAAT-ACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGA-AACATCGAATACAATTCA
* * *
42967 TGCACCGATGCATCAGTAGTGTATCGA
1 TGCATCGATGCATAAGTAGTGCATCGA
42994 ATACCTATGT
Statistics
Matches: 126, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
63 1 0.01
64 121 0.96
65 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATACAATTCA
Found at i:49735 original size:64 final size:64
Alignment explanation
Indices: 49667--49890 Score: 229
Period size: 64 Copynumber: 3.5 Consensus size: 64
49657 TGTTTGAATG
* ** *
49667 TGCATCGATGCATTAGTAGTGCATCGATGCA-CTCTTTTAA-AATATAAACATCGAATACAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-GAAACATCGAATACAATTC
49730 A
64 A
* **
49731 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGT
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATACAATTCA
* * * ** * ** *
49795 TGCATTGATGCATAAGGAGTGAATCGATGCATCCCAACAATAAT-ACTACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGA-AACATCGAATACAATTCA
* * *
49859 TGCACCGATGCATCAGTAGTGTATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
49891 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 129 0.96
65 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATACAATTCA
Found at i:50214 original size:24 final size:24
Alignment explanation
Indices: 50187--50235 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
50177 TGCAAAAGAC
*
50187 ATATAT-ATATGTTCATGTGATATG
1 ATATATGATATG-ACATGTGATATG
*
50211 ATATGTGATATGACATGTGATATG
1 ATATATGATATGACATGTGATATG
50235 A
1 A
50236 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (24 bp):
ATATATGATATGACATGTGATATG
Found at i:50218 original size:12 final size:12
Alignment explanation
Indices: 50200--50235 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
50190 TATATATGTT
50200 CATGTGATATGA
1 CATGTGATATGA
*
50212 TATGTGATATGA
1 CATGTGATATGA
50224 CATGTGATATGA
1 CATGTGATATGA
50236 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:53883 original size:9 final size:9
Alignment explanation
Indices: 53847--53927 Score: 52
Period size: 9 Copynumber: 9.7 Consensus size: 9
53837 TTTATATCTG
53847 TAAATAAAT
1 TAAATAAAT
*
53856 TAATTAAA-
1 TAAATAAAT
53864 TACAAT--AT
1 TA-AATAAAT
*
53872 TAAATAATT
1 TAAATAAAT
*
53881 TAAAT-ACT
1 TAAATAAAT
53889 TAAATAAAT
1 TAAATAAAT
53898 TAAAT--AT
1 TAAATAAAT
53905 TAAAT--AT
1 TAAATAAAT
53912 TAAATATAAT
1 TAAATA-AAT
*
53922 AAAATA
1 TAAATA
53928 TACCTTAAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
7 18 0.31
8 11 0.19
9 22 0.38
10 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAATAAAT
Found at i:53893 original size:17 final size:16
Alignment explanation
Indices: 53854--53918 Score: 73
Period size: 16 Copynumber: 4.1 Consensus size: 16
53844 CTGTAAATAA
*
53854 ATTAATTAAA-TACAAT
1 ATTAAATAAATTA-AAT
*
53870 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
53886 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
53903 ATTAAAT--ATTAAAT
1 ATTAAATAAATTAAAT
53917 AT
1 AT
53919 AATAAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.20
16 18 0.41
17 17 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:53908 original size:7 final size:7
Alignment explanation
Indices: 53867--53918 Score: 59
Period size: 7 Copynumber: 6.7 Consensus size: 7
53857 AATTAAATAC
53867 AATATTA
1 AATATTA
53874 AATAATTTA
1 AAT-A-TTA
53883 AATACTTA
1 AATA-TTA
53891 AATAAATTA
1 AAT--ATTA
53900 AATATTA
1 AATATTA
53907 AATATTA
1 AATATTA
53914 AATAT
1 AATAT
53919 AATAAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 19 0.47
8 8 0.20
9 12 0.30
10 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
AATATTA
Found at i:53924 original size:16 final size:14
Alignment explanation
Indices: 53867--53918 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 14
53857 AATTAAATAC
53867 AATATTAAATAATTTA
1 AATATTAAAT-A-TTA
53883 AATACTTAAATAAATTA
1 AATA-TTAAAT--ATTA
53900 AATATTAAATATTA
1 AATATTAAATATTA
53914 AATAT
1 AATAT
53919 AATAAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.26
16 10 0.29
17 13 0.38
18 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTAAATATTA
Found at i:53926 original size:24 final size:24
Alignment explanation
Indices: 53880--53928 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
53870 ATTAAATAAT
*
53880 TTAAATACTTAAATAAATTAAATA
1 TTAAATACTTAAATAAATAAAATA
53904 TTAAATA-TTAAATATAATAAAATA
1 TTAAATACTTAAATA-AATAAAATA
53928 T
1 T
53929 ACCTTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TTAAATACTTAAATAAATAAAATA
Found at i:56127 original size:22 final size:22
Alignment explanation
Indices: 56102--56143 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56092 CACTAAAGTG
56102 CCACATA-AAATGTCCATAAGGA
1 CCACATAGAAAT-TCCATAAGGA
*
56124 CCACATAGAAATTCCTTAAG
1 CCACATAGAAATTCCATAAG
56144 AATCATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (22 bp):
CCACATAGAAATTCCATAAGGA
Found at i:56714 original size:12 final size:12
Alignment explanation
Indices: 56684--56716 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
56674 TTTTCATATA
*
56684 ATCACACATTAC
1 ATCACATATTAC
56696 ATCACATATTAC
1 ATCACATATTAC
56708 ATCACATAT
1 ATCACATAT
56717 ACACATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (12 bp):
ATCACATATTAC
Found at i:65290 original size:2 final size:2
Alignment explanation
Indices: 65283--65314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
65273 TCTCCTTTTC
65283 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
65315 AAGAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65964 original size:31 final size:31
Alignment explanation
Indices: 65893--65970 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
65883 CTTTTAAAAC
* * *
65893 TTGCAATATAATCCCCCAACATTTAGTCTGT
1 TTGCAATATGATCCCTCAACATTTAATCTGT
65924 TTGCAATATGATCCCTCAACATTTAATCTGT
1 TTGCAATATGATCCCTCAACATTTAATCTGT
*
65955 TTGCAATATGGTCCCT
1 TTGCAATATGATCCCT
65971 GACATAACTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (31 bp):
TTGCAATATGATCCCTCAACATTTAATCTGT
Found at i:67617 original size:31 final size:31
Alignment explanation
Indices: 67582--67642 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
67572 ACAATCCCCA
67582 AACATTTAGTCTATTTGCAATATGGTCCCTT
1 AACATTTAGTCTATTTGCAATATGGTCCCTT
* *
67613 AACATTTAGTTTGTTTGCAATATGGTCCCT
1 AACATTTAGTCTATTTGCAATATGGTCCCT
67643 GGCGTAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (31 bp):
AACATTTAGTCTATTTGCAATATGGTCCCTT
Found at i:76293 original size:17 final size:18
Alignment explanation
Indices: 76256--76296 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
76246 ATATTATGTA
*
76256 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
76274 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
76291 TTTACT
1 TTTACT
76297 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:80252 original size:27 final size:26
Alignment explanation
Indices: 80207--80258 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
80197 GATGAAGAAG
80207 TTATAAGAAATTAAAGAAAATGAGTTT
1 TTATAAGAAATTAAAGAAAA-GAGTTT
* **
80234 TTATATGAAATTATGGAAAAGAGTT
1 TTATAAGAAATTAAAGAAAAGAGTT
80259 GATAAGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (26 bp):
TTATAAGAAATTAAAGAAAAGAGTTT
Found at i:81219 original size:15 final size:15
Alignment explanation
Indices: 81199--81233 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
81189 TGAGGGTATT
81199 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
81214 GTAGTCCTTTGGGAC
1 GTAGTCCTTCGGGAC
81229 GTAGT
1 GTAGT
81234 GGTCCTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.31
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:81475 original size:18 final size:20
Alignment explanation
Indices: 81452--81492 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
81442 ATGACTTGGT
*
81452 TATATATAT-CATA-TGAAA
1 TATATACATGCATATTGAAA
81470 TATATACATGCATATTGAAA
1 TATATACATGCATATTGAAA
81490 TAT
1 TAT
81493 CATGATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 8 0.40
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (20 bp):
TATATACATGCATATTGAAA
Found at i:85793 original size:13 final size:13
Alignment explanation
Indices: 85775--85799 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85765 GTAAGGTCCT
85775 TTCCTCTGCAATC
1 TTCCTCTGCAATC
85788 TTCCTCTGCAAT
1 TTCCTCTGCAAT
85800 ATCCCAACTC
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (13 bp):
TTCCTCTGCAATC
Done.