Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003259.1 Hibiscus syriacus cultivar Beakdansim tig00006848_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: 73494
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2861 original size:16 final size:16
Alignment explanation
Indices: 2840--2896 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
2830 ATTTAATAAA
2840 AAACGAACACGAACAT
1 AAACGAACACGAACAT
2856 AAACGAACACGAACAT
1 AAACGAACACGAACAT
* *
2872 AAATGAACGCGAACAT
1 AAACGAACACGAACAT
2888 AAACGAACA
1 AAACGAACA
2897 TAAACGTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.56, C:0.23, G:0.14, T:0.07
Consensus pattern (16 bp):
AAACGAACACGAACAT
Found at i:3984 original size:10 final size:10
Alignment explanation
Indices: 3969--4026 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
3959 ATAAATGAAT
3969 GAACATAAAC
1 GAACATAAAC
*
3979 GAACATAACC
1 GAACATAAAC
3989 GAACATAACCGAAC
1 GAACAT-A---AAC
4003 GAACATAAAC
1 GAACATAAAC
* *
4013 GAATATAACC
1 GAACATAAAC
4023 GAAC
1 GAAC
4027 GTTCACAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 29 0.74
11 1 0.03
13 1 0.03
14 8 0.21
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:4003 original size:24 final size:24
Alignment explanation
Indices: 3976--4027 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3966 AATGAACATA
*
3976 AACGAACATAACCGAACATAACCG
1 AACGAACATAAACGAACATAACCG
*
4000 AACGAACATAAACGAATATAACCG
1 AACGAACATAAACGAACATAACCG
4024 AACG
1 AACG
4028 TTCACAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.25, G:0.13, T:0.10
Consensus pattern (24 bp):
AACGAACATAAACGAACATAACCG
Found at i:4036 original size:24 final size:24
Alignment explanation
Indices: 3976--4037 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
3966 AATGAACATA
* *
3976 AACGAACATAACCGAACATAACCG
1 AACGAACACAAACGAACATAACCG
* *
4000 AACGAACATAAACGAATATAACCG
1 AACGAACACAAACGAACATAACCG
**
4024 AACGTTCACAAACG
1 AACGAACACAAACG
4038 TAAATGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.50, C:0.26, G:0.13, T:0.11
Consensus pattern (24 bp):
AACGAACACAAACGAACATAACCG
Found at i:5324 original size:27 final size:27
Alignment explanation
Indices: 5287--5459 Score: 274
Period size: 27 Copynumber: 6.4 Consensus size: 27
5277 ACTCCCACTT
*
5287 GGACTCCTGCTAACACTCCGTCTTTTA
1 GGACTCTTGCTAACACTCCGTCTTTTA
5314 GGACTCTTGCTAACACTCCGTCTTTTA
1 GGACTCTTGCTAACACTCCGTCTTTTA
5341 GGACTCTTGCTAACACTCCGTCTTTTA
1 GGACTCTTGCTAACACTCCGTCTTTTA
5368 GGACTCTTGCTAACACTCCGTCTTTTA
1 GGACTCTTGCTAACACTCCGTCTTTTA
* **
5395 GGACTCTTGCTAAGACTGTGTCTTTTA
1 GGACTCTTGCTAACACTCCGTCTTTTA
** * *
5422 GGACTCCCGCTAACACTGCGCCTTTTA
1 GGACTCTTGCTAACACTCCGTCTTTTA
5449 GGACTCTTGCT
1 GGACTCTTGCT
5460 CCTTCCTTTT
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 135 1.00
ACGTcount: A:0.18, C:0.29, G:0.17, T:0.35
Consensus pattern (27 bp):
GGACTCTTGCTAACACTCCGTCTTTTA
Found at i:10027 original size:11 final size:11
Alignment explanation
Indices: 10011--10035 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10001 AACCTAAAAC
10011 ATTATATTTTT
1 ATTATATTTTT
10022 ATTATATTTTT
1 ATTATATTTTT
10033 ATT
1 ATT
10036 GCATCGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTATATTTTT
Found at i:11566 original size:25 final size:25
Alignment explanation
Indices: 11532--11589 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
11522 AAGGACGATC
11532 CTTTGATTTTATCACCAATCGAATA
1 CTTTGATTTTATCACCAATCGAATA
11557 CTTTGATTTTATCACCAATCGAATA
1 CTTTGATTTTATCACCAATCGAATA
11582 CTTTGATT
1 CTTTGATT
11590 CCGGGGAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (25 bp):
CTTTGATTTTATCACCAATCGAATA
Found at i:13095 original size:15 final size:15
Alignment explanation
Indices: 13075--13120 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
13065 GTAACCGGTT
13075 CGGTTTTAAAAAAAA
1 CGGTTTTAAAAAAAA
*
13090 CGGTTTTTTAAAAAAAT
1 CGG--TTTTAAAAAAAA
*
13107 CGGTTATAAAAAAA
1 CGGTTTTAAAAAAA
13121 TGATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (15 bp):
CGGTTTTAAAAAAAA
Found at i:13100 original size:17 final size:17
Alignment explanation
Indices: 13078--13111 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13068 ACCGGTTCGG
13078 TTTTAAAAAAAACGGTT
1 TTTTAAAAAAAACGGTT
*
13095 TTTTAAAAAAATCGGTT
1 TTTTAAAAAAAACGGTT
13112 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAAACGGTT
Found at i:13102 original size:16 final size:17
Alignment explanation
Indices: 13074--13120 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
13064 TGTAACCGGT
13074 TCGG-TTTTAAAAAAAA
1 TCGGTTTTTAAAAAAAA
*
13090 -CGGTTTTTTAAAAAAA
1 TCGGTTTTTAAAAAAAA
*
13106 TCGG-TTATAAAAAAA
1 TCGGTTTTTAAAAAAA
13121 TGATTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (17 bp):
TCGGTTTTTAAAAAAAA
Found at i:13121 original size:15 final size:15
Alignment explanation
Indices: 13074--13121 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
13064 TGTAACCGGT
13074 TCGGTTTTAAAAAAA
1 TCGGTTTTAAAAAAA
*
13089 ACGGTTTTTTAAAAAAA
1 TCGG--TTTTAAAAAAA
*
13106 TCGGTTATAAAAAAA
1 TCGGTTTTAAAAAAA
13121 T
1 T
13122 GATTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.50
17 14 0.50
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (15 bp):
TCGGTTTTAAAAAAA
Found at i:13217 original size:33 final size:33
Alignment explanation
Indices: 13169--13279 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
13159 AACAAGTTTA
* *
13169 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
13201 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
13234 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
13266 CGAT-AATTGAAATA
1 CGATAAATTCAAATA
13280 AAGTTTAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 9 0.12
32 13 0.18
33 51 0.70
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:25621 original size:31 final size:31
Alignment explanation
Indices: 25583--25707 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
25573 CCCGAAGGAC
* *
25583 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
25614 CAGTCCATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25645 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
25676 CAGTACATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25707 C
1 C
25708 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:26472 original size:64 final size:64
Alignment explanation
Indices: 26367--26584 Score: 235
Period size: 64 Copynumber: 3.4 Consensus size: 64
26357 TGAAGGTATG
* * * * **
26367 CATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGCTGAGATA
1 CATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATTAATGAGATA
* ** * *
26431 CATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATG
1 CATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAGATA
* * *
26495 CATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAA-AAGAGT
1 CATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATGAGA-T
*
26558 G
64 A
**
26559 CATCGATGCACTACCAATGCATCGAT
1 CATCGATGCACTACTTATGCATCGAT
26585 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 124 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (64 bp):
CATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAGATA
Found at i:31425 original size:29 final size:29
Alignment explanation
Indices: 31391--31449 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
31381 CCTAAATTAA
31391 TTTGATGTCATTGCTTAAATCAATTTAGT
1 TTTGATGTCATTGCTTAAATCAATTTAGT
*
31420 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTAAATCAATTTAGT
31449 T
1 T
31450 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTAAATCAATTTAGT
Found at i:33233 original size:18 final size:17
Alignment explanation
Indices: 33212--33252 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
33202 TAATAGCGAG
33212 TTATTATAAAATATATTT
1 TTATTAT-AAATATATTT
*
33230 TTATTATAATTATATTT
1 TTATTATAAATATATTT
33247 TATATT
1 T-TATT
33253 TTATGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTATAAATATATTT
Found at i:34096 original size:13 final size:13
Alignment explanation
Indices: 34032--34097 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 13
34022 AGCAATCTCA
34032 AAAAGTTCATTTTT
1 AAAAGTT-ATTTTT
34046 -AAA-TTGATTTTT
1 AAAAGTT-ATTTTT
34058 AAAAGTT-TTTTT
1 AAAAGTTATTTTT
* **
34070 ATAA--TACCTTT
1 AAAAGTTATTTTT
34081 AAAAGTTATTTTT
1 AAAAGTTATTTTT
34094 AAAA
1 AAAA
34098 AACAATACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
10 1 0.03
11 6 0.15
12 16 0.40
13 15 0.38
14 2 0.05
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (13 bp):
AAAAGTTATTTTT
Found at i:35508 original size:24 final size:24
Alignment explanation
Indices: 35476--35528 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
35466 GCAATCGCTG
35476 CTTCAAGCTTGCTCCCGATATCTC
1 CTTCAAGCTTGCTCCCGATATCTC
35500 CTTCAAGCTTGCTCCCGATATCTC
1 CTTCAAGCTTGCTCCCGATATCTC
35524 CTTCA
1 CTTCA
35529 TCGACCCCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.38, G:0.11, T:0.34
Consensus pattern (24 bp):
CTTCAAGCTTGCTCCCGATATCTC
Found at i:39000 original size:12 final size:12
Alignment explanation
Indices: 38983--39015 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
38973 AATGTGGCAT
38983 TTCATATATATA
1 TTCATATATATA
38995 TTCATATATATA
1 TTCATATATATA
39007 -T-ATATATAT
1 TTCATATATAT
39016 CTTTATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 1 0.05
12 12 0.57
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCATATATATA
Found at i:40300 original size:16 final size:17
Alignment explanation
Indices: 40279--40330 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
40269 AATTTTTTTT
40279 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
40295 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
40310 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
40327 AATT
1 AATT
40331 TAATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:40395 original size:36 final size:36
Alignment explanation
Indices: 40352--40441 Score: 144
Period size: 39 Copynumber: 2.4 Consensus size: 36
40342 TTTAATTATA
*
40352 TATTAATAAAATAAAAAATATCATGTCACAAAATAT
1 TATTAATAAAATAAAAAATATCATGCCACAAAATAT
40388 TATTAATAAAATAATAAAAAATATCATGCCACAAAATAT
1 TATTAAT--AA-AATAAAAAATATCATGCCACAAAATAT
40427 TATTAATAAAATAAA
1 TATTAATAAAATAAA
40442 TTAGAGTGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
36 13 0.26
37 2 0.04
38 2 0.04
39 33 0.66
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (36 bp):
TATTAATAAAATAAAAAATATCATGCCACAAAATAT
Found at i:40413 original size:39 final size:39
Alignment explanation
Indices: 40361--40440 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
40351 ATATTAATAA
*
40361 AATAAAAAATATCATGTCACAAAATATTATTAATAAAAT
1 AATAAAAAATATCATGCCACAAAATATTATTAATAAAAT
40400 AATAAAAAATATCATGCCACAAAATATTATTAATAAAAT
1 AATAAAAAATATCATGCCACAAAATATTATTAATAAAAT
40439 AA
1 AA
40441 ATTAGAGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (39 bp):
AATAAAAAATATCATGCCACAAAATATTATTAATAAAAT
Found at i:40797 original size:2 final size:2
Alignment explanation
Indices: 40790--40819 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40780 GGAAAATTAA
40790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40820 TATTTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41410 original size:33 final size:32
Alignment explanation
Indices: 41373--41442 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
41363 GCTTTGTTTT
* *
41373 TAAAAAAATATGTATTT-TTTAACTTAATATTTA
1 TAAAAAAATA--TATTTCATTAAATTAATATTTA
**
41406 TAAAATCATATATTTCATTAAATTAATATTTA
1 TAAAAAAATATATTTCATTAAATTAATATTTA
41438 TAAAA
1 TAAAA
41443 TATTTGGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 5 0.16
32 19 0.59
33 8 0.25
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (32 bp):
TAAAAAAATATATTTCATTAAATTAATATTTA
Found at i:41420 original size:16 final size:15
Alignment explanation
Indices: 41398--41443 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
41388 TTTTTAACTT
41398 AATATTTATAAAATC
1 AATATTTATAAAATC
* *
41413 ATATATTTCATTAAATT
1 A-ATATTT-ATAAAATC
41430 AATATTTATAAAAT
1 AATATTTATAAAAT
41444 ATTTGGAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 7 0.27
16 12 0.46
17 7 0.27
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTATAAAATC
Found at i:43022 original size:15 final size:17
Alignment explanation
Indices: 43002--43044 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
42992 GTTTTGATCA
43002 AAAATTAAAATG-TT-G
1 AAAATTAAAATGTTTCG
43017 AAAATTAAAATGTTTCG
1 AAAATTAAAATGTTTCG
43034 AAAATATAAAA
1 AAAAT-TAAAA
43045 ATAAAATACC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.48
16 2 0.08
17 6 0.24
18 5 0.20
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (17 bp):
AAAATTAAAATGTTTCG
Found at i:51379 original size:24 final size:25
Alignment explanation
Indices: 51332--51395 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
51322 ATTATTATTT
51332 ATATATATAATAAATAAATGTAAA-ATAA
1 ATAT-TATAAT-AA-AAATGTAAATAT-A
51360 ATATTATAATAAAAAT-TAAATATA
1 ATATTATAATAAAAATGTAAATATA
51384 ATA-TA-AATAAAA
1 ATATTATAATAAAA
51396 GATATATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.20
23 2 0.06
24 8 0.23
25 6 0.17
26 2 0.06
27 6 0.17
28 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
ATATTATAATAAAAATGTAAATATA
Found at i:51390 original size:30 final size:31
Alignment explanation
Indices: 51333--51392 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
51323 TTATTATTTA
*
51333 TATATATAATAAATAAATGTAAAATAAATAT
1 TATATATAATAAATAAATATAAAATAAATAT
*
51364 TATA-ATAA-AAATTAAATATAATATAAATA
1 TATATATAATAAA-TAAATATAAAATAAATA
51393 AAAGATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
TATATATAATAAATAAATATAAAATAAATAT
Found at i:56254 original size:103 final size:103
Alignment explanation
Indices: 56137--56324 Score: 299
Period size: 103 Copynumber: 1.8 Consensus size: 103
56127 TCGGAGTAAC
* * * *
56137 AATAGTGGCGTTTTTTTTTAAAAA-TCGCAATAGGTCTATTTATAGTGGTGTTTATTGAAAAAAC
1 AATAGTGGCG--TTTTTTAAAAAACTCGCAATAGGTCTATCTATAGTGGCGTTTATAGAAAAAAC
56201 GCCACTATATATATA-TTTTTGGCTTTTTTTGTGCACAAT
64 GCCACTATATATATACTTTTTGGCTTTTTTTGTGCACAAT
56240 AATAGTGGCGTTTTTTAAAAAACGTCGCAATAGGTCTATCTATAGTGGCGTTTATAGAAAAAACG
1 AATAGTGGCGTTTTTTAAAAAAC-TCGCAATAGGTCTATCTATAGTGGCGTTTATAGAAAAAACG
56305 CCACTATATATATACTTTTT
65 CCACTATATATATACTTTTT
56325 TTTGATTTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
101 11 0.14
103 62 0.79
104 5 0.06
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (103 bp):
AATAGTGGCGTTTTTTAAAAAACTCGCAATAGGTCTATCTATAGTGGCGTTTATAGAAAAAACGC
CACTATATATATACTTTTTGGCTTTTTTTGTGCACAAT
Found at i:59312 original size:26 final size:26
Alignment explanation
Indices: 59266--59332 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
59256 TTGTACAATG
* * *
59266 AAATACACTATTGATGTGACACACCA
1 AAATACACAATTAATGAGACACACCA
*
59292 AAATACACAATTAATGAGACACATCA
1 AAATACACAATTAATGAGACACACCA
*
59318 AAATACACAAATAAT
1 AAATACACAATTAAT
59333 TTACATTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.21
Consensus pattern (26 bp):
AAATACACAATTAATGAGACACACCA
Found at i:63607 original size:12 final size:12
Alignment explanation
Indices: 63579--63615 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
63569 TTTGGTAATC
63579 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
63592 CCCGCCCCGATA
1 CCCGCCCCGATA
*
63604 CCCGACCCGATA
1 CCCGCCCCGATA
63616 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.19, C:0.54, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:63677 original size:24 final size:26
Alignment explanation
Indices: 63650--63712 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
63640 ATATATATAT
*
63650 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
63674 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
63698 AT-ATATATATATATA
1 ATAATATAAATATATA
63713 CCCGGCCCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 3 0.09
24 18 0.55
25 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:63692 original size:19 final size:19
Alignment explanation
Indices: 63668--63707 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
63658 AATAAATTTA
63668 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
63687 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
63706 AT
1 AT
63708 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:63732 original size:12 final size:12
Alignment explanation
Indices: 63715--63744 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
63705 TATATATACC
63715 CGGCCCGATTCT
1 CGGCCCGATTCT
63727 CGGCCCGATTCT
1 CGGCCCGATTCT
63739 CGGCCC
1 CGGCCC
63745 AATACCCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.47, G:0.27, T:0.20
Consensus pattern (12 bp):
CGGCCCGATTCT
Found at i:69460 original size:23 final size:24
Alignment explanation
Indices: 69426--69472 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
69416 TAGTTACAAT
**
69426 CAATTATGATTTTTTTAATAATGA
1 CAATTATGATTTCATTAATAATGA
69450 CAATTAT-ATTTCATTAATAATGA
1 CAATTATGATTTCATTAATAATGA
69473 AAAGAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (24 bp):
CAATTATGATTTCATTAATAATGA
Found at i:70443 original size:21 final size:21
Alignment explanation
Indices: 70417--70462 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
70407 TGATATGATG
*
70417 CTTCTC-TCTCTATTTCTCTCA
1 CTTCTCGT-TCTACTTCTCTCA
*
70438 CTTCTCGTTCTACTTCTCTCG
1 CTTCTCGTTCTACTTCTCTCA
70459 CTTC
1 CTTC
70463 AACTTGGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.07, C:0.39, G:0.04, T:0.50
Consensus pattern (21 bp):
CTTCTCGTTCTACTTCTCTCA
Done.