Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005465.1 Hibiscus syriacus cultivar Beakdansim tig00012516_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: 81801
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:9880 original size:7 final size:7
Alignment explanation
Indices: 9863--9932 Score: 64
Period size: 6 Copynumber: 10.9 Consensus size: 7
9853 TCCGTTACAT
9863 TTTTGTTG
1 TTTT-TTG
9871 TTTTTTG
1 TTTTTTG
9878 -TTTTTG
1 TTTTTTG
9884 -TTTTTG
1 TTTTTTG
9890 -TTTTTG
1 TTTTTTG
9896 --TTTTG
1 TTTTTTG
*
9901 TTTTATG
1 TTTTTTG
9908 TTTTTT-
1 TTTTTTG
9914 TTTTTT-
1 TTTTTTG
*
9920 TTTTTTA
1 TTTTTTG
9927 TTTTTT
1 TTTTTT
9933 ATTCGATCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.09
6 30 0.53
7 18 0.32
8 4 0.07
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (7 bp):
TTTTTTG
Found at i:9883 original size:6 final size:6
Alignment explanation
Indices: 9872--9922 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
9862 TTTTTGTTGT
9872 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTG TTTTATG TTTTT- TTTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT-TG TTTTTG TTTTTG
9918 TTTTT
1 TTTTT
9923 TTTATTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
5 15 0.35
6 22 0.51
7 6 0.14
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:9904 original size:30 final size:30
Alignment explanation
Indices: 9868--9924 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
9858 TACATTTTTG
*
9868 TTGTTTTTTGTTTTTGTTTTTGTTTTTGTT
1 TTGTTTTATGTTTTTGTTTTTGTTTTTGTT
* *
9898 TTGTTTTATGTTTTTTTTTTTTTTTTT
1 TTGTTTTATGTTTTTGTTTTTGTTTTT
9925 TATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (30 bp):
TTGTTTTATGTTTTTGTTTTTGTTTTTGTT
Found at i:9923 original size:12 final size:12
Alignment explanation
Indices: 9862--9930 Score: 77
Period size: 12 Copynumber: 5.7 Consensus size: 12
9852 ATCCGTTACA
*
9862 TTTTTGTTGTTT
1 TTTTTTTTGTTT
9874 TTTGTTTTTGTTT
1 TTT-TTTTTGTTT
*
9887 TTGTTTTTGTTT
1 TTTTTTTTGTTT
* *
9899 TGTTTTATGTTT
1 TTTTTTTTGTTT
9911 TTTTTTTT-TTT
1 TTTTTTTTGTTT
9922 TTTTATTTT
1 TTTT-TTTT
9931 TTATTCGATC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
11 7 0.15
12 31 0.65
13 10 0.21
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.86
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:9950 original size:1 final size:1
Alignment explanation
Indices: 9871--9932 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
9861 ATTTTTGTTG
* * * * * * * *
9871 TTTTTTGTTTTTGTTTTTGTTTTTGTTTTGTTTTATGTTTTTTTTTTTTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9933 ATTCGATCAA
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:12895 original size:25 final size:24
Alignment explanation
Indices: 12865--12925 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
12855 AAAAAAAGAG
12865 AAAGAAAAAAATAGTAGTTCGAAAA
1 AAAGAAAAAAAT-GTAGTTCGAAAA
*
12890 AAAGAAAAAAGATGTTGTTCGAAAA
1 AAAGAAAAAA-ATGTAGTTCGAAAA
12915 AGAA-AAAAAAA
1 A-AAGAAAAAAA
12926 GAGAAAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 1 0.03
25 28 0.85
26 4 0.12
ACGTcount: A:0.66, C:0.03, G:0.16, T:0.15
Consensus pattern (24 bp):
AAAGAAAAAAATGTAGTTCGAAAA
Found at i:15533 original size:24 final size:25
Alignment explanation
Indices: 15492--15538 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
15482 CTCAAAAAAA
15492 AAAATTAGAAGCTCGATTGAAGTAT
1 AAAATTAGAAGCTCGATTGAAGTAT
* *
15517 AAAATTCG-AGCTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
15539 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTAT
Found at i:18570 original size:20 final size:20
Alignment explanation
Indices: 18545--18583 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18535 ACAACTTTTA
*
18545 TTTTGTATATCTAGGATTTG
1 TTTTGTATATCTAGAATTTG
*
18565 TTTTGTATTTCTAGAATTT
1 TTTTGTATATCTAGAATTT
18584 AATTATGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.15, T:0.59
Consensus pattern (20 bp):
TTTTGTATATCTAGAATTTG
Found at i:30071 original size:11 final size:11
Alignment explanation
Indices: 30047--30080 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
30037 TAATTATATA
30047 ATATTATATGTAT
1 ATATTAT-T-TAT
30060 ATATTATTTAT
1 ATATTATTTAT
30071 ATATTATTTA
1 ATATTATTTA
30081 ACTAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.62
12 1 0.05
13 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
ATATTATTTAT
Found at i:31521 original size:2 final size:2
Alignment explanation
Indices: 31514--31557 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
31504 ATTAAAAATA
31514 AT AT AT AT AT AT 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 AT AT AT AT AT AT
31556 AT
1 AT
31558 TAAATTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34030 original size:20 final size:20
Alignment explanation
Indices: 34005--34042 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33995 CAAATTTCAC
34005 ATTTATT-AATTTCAAACCAA
1 ATTTATTCAATTT-AAACCAA
34025 ATTTATTCAATTTAAACC
1 ATTTATTCAATTTAAACC
34043 CTAAGCAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTATTCAATTTAAACCAA
Found at i:36330 original size:48 final size:47
Alignment explanation
Indices: 36273--36412 Score: 150
Period size: 46 Copynumber: 3.1 Consensus size: 47
36263 CTTAACATTA
*
36273 AAAATATATTTTTTTATTTTTATATTAATTTTAAAATATTATAAGAAT
1 AAAATATA-TTTTTTATTTTTATATTAATTTTAAAATATTATAAGATT
* * *
36321 AAAATATATTTTTTA-TCTTA-A-T--TTTTAAAATATTTTTAA-TTT
1 AAAATATATTTTTTATTTTTATATTAATTTTAAAATA-TTATAAGATT
* * *
36363 AAAA-ATATATTTTATTTTTATCTTAATTTTAAAATATTATTAGATT
1 AAAATATATTTTTTATTTTTATATTAATTTTAAAATATTATAAGATT
36409 AAAA
1 AAAA
36413 AATAAATATT
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
41 9 0.12
42 19 0.25
43 5 0.07
44 2 0.03
45 5 0.07
46 20 0.27
47 7 0.09
48 8 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (47 bp):
AAAATATATTTTTTATTTTTATATTAATTTTAAAATATTATAAGATT
Found at i:36361 original size:18 final size:19
Alignment explanation
Indices: 36338--36382 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
36328 ATTTTTTATC
36338 TTAATTTTTAAAATAT-TT
1 TTAATTTTTAAAATATATT
*
36356 TTAA-TTTAAAAATATATT
1 TTAATTTTTAAAATATATT
36374 TT-ATTTTTA
1 TTAATTTTTA
36383 TCTTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTTTAAAATATATT
Found at i:36382 original size:19 final size:18
Alignment explanation
Indices: 36341--36382 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
36331 TTTTATCTTA
36341 ATTTTT-AAAATATTTTT
1 ATTTTTAAAAATATTTTT
*
36358 A-ATTTAAAAATATATTTT
1 ATTTTTAAAAATAT-TTTT
36376 ATTTTTA
1 ATTTTTA
36383 TCTTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 5 0.25
19 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTAAAAATATTTTT
Found at i:36441 original size:88 final size:88
Alignment explanation
Indices: 36270--36441 Score: 195
Period size: 88 Copynumber: 1.9 Consensus size: 88
36260 TATCTTAACA
* * *
36270 TTAAAAATATATTTTTTTATTTTTATATTAATTTTAAAATATTATAAGAATAAAATATATTTTTT
1 TTAAAAATATA--TTTTTATTTTTATATTAATTTTAAAATATTATAAGAATAAAAAATAATATTT
* **
36335 ATCTTAATTTTTAAAATATTTTTAAT
64 AACTTAA-TAGTAAAATATTTTTAAT
* * *
36361 TTAAAAATATA-TTTTATTTTTATCTTAATTTTAAAATATTATTAGATTAAAAAATAAATATTTA
1 TTAAAAATATATTTTTATTTTTATATTAATTTTAAAATATTATAAGAATAAAAAAT-AATATTTA
*
36425 AGTTAA-AGTAAGAATAT
65 ACTTAATAGTAA-AATAT
36442 ATTATATTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
87 3 0.04
88 45 0.65
89 10 0.14
91 11 0.16
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (88 bp):
TTAAAAATATATTTTTATTTTTATATTAATTTTAAAATATTATAAGAATAAAAAATAATATTTAA
CTTAATAGTAAAATATTTTTAAT
Found at i:36523 original size:43 final size:42
Alignment explanation
Indices: 36427--36534 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 42
36417 AATATTTAAG
* * * *
36427 TTAAAGTAAGAATATATTATATTTTTAAGTTAATTAAAATTAAGA
1 TTAAAATAA-AATATATT-T-TATTTAAGTTAATCAAAATTAAAA
*
36472 TAAAAATAAAATATATTTTATTTAAGTTAAATCAAAATTAAAA
1 TTAAAATAAAATATATTTTATTTAAGTT-AATCAAAATTAAAA
36515 TTAAAATAAAATATATTTTA
1 TTAAAATAAAATATATTTTA
36535 AAATTTAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 9 0.16
43 32 0.57
44 8 0.14
45 7 0.12
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.41
Consensus pattern (42 bp):
TTAAAATAAAATATATTTTATTTAAGTTAATCAAAATTAAAA
Found at i:36535 original size:17 final size:17
Alignment explanation
Indices: 36515--36564 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
36505 AAAATTAAAA
36515 TTAAAATAAAATATATT
1 TTAAAATAAAATATATT
**
36532 TTAAAATTTAATATA--
1 TTAAAATAAAATATATT
36547 --AAAATAAAATATATT
1 TTAAAATAAAATATATT
36562 TTA
1 TTA
36565 TTCTTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
13 11 0.44
17 14 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAATAAAATATATT
Found at i:40433 original size:55 final size:56
Alignment explanation
Indices: 40372--40502 Score: 176
Period size: 55 Copynumber: 2.4 Consensus size: 56
40362 CACTCCATAT
* * * *
40372 TTTCAGGGTGTATAGAACTCGCATAATCTTCCACAAACGTCTCTGTTCTCTATT-C
1 TTTCAGGGAGTATAGAACTCGAATAATCTTCCACAAACGTCTCTGCTCCCTATTCC
* * *
40427 TTTCAGGGAGTATA-AGACTCGAATAATCTTCCGCAAACGTGTTTGCTCCCTATTCC
1 TTTCAGGGAGTATAGA-ACTCGAATAATCTTCCACAAACGTCTCTGCTCCCTATTCC
40483 TTTCAGGGAGTATAGAACTC
1 TTTCAGGGAGTATAGAACTC
40503 AAGAAATCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
54 1 0.02
55 45 0.68
56 19 0.29
57 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (56 bp):
TTTCAGGGAGTATAGAACTCGAATAATCTTCCACAAACGTCTCTGCTCCCTATTCC
Found at i:40512 original size:56 final size:56
Alignment explanation
Indices: 40372--40537 Score: 171
Period size: 56 Copynumber: 3.0 Consensus size: 56
40362 CACTCCATAT
* * * * * *
40372 TTTCAGGGTGTATAGAACTC--GCATAATCTTCCACAAACGTCTCTGTTCTCTATT-C
1 TTTCAGGGAGTATAGAACTCAAG-A-AATCTTCCGCAAACGTGTTTGCTCCCTATTCC
*
40427 TTTCAGGGAGTATA-AGACTCGAA-TAATCTTCCGCAAACGTGTTTGCTCCCTATTCC
1 TTTCAGGGAGTATAGA-ACTC-AAGAAATCTTCCGCAAACGTGTTTGCTCCCTATTCC
* * *
40483 TTTCAGGGAGTATAGAACTCAAGAAATCTTCTGAAAACGGGTTTGCTCCCTATTC
1 TTTCAGGGAGTATAGAACTCAAGAAATCTTCCGCAAACGTGTTTGCTCCCTATTC
40538 TTCTGAGAAG
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
54 1 0.01
55 44 0.47
56 47 0.51
57 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Consensus pattern (56 bp):
TTTCAGGGAGTATAGAACTCAAGAAATCTTCCGCAAACGTGTTTGCTCCCTATTCC
Found at i:40701 original size:42 final size:41
Alignment explanation
Indices: 40610--40704 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 41
40600 AGGTCTTATG
* * *
40610 GATGACCCGAAGGATTTATCATCTTGCTCGAGAGACTTACA
1 GATGACCCGAAGGATTTAACATCATGCTCGAAAGACTTACA
* * *
40651 AATAACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTT-AACATCATGCTCGAAAGACTTACA
40693 GATGACCCGAAG
1 GATGACCCGAAG
40705 AACTAATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 15 0.33
42 30 0.67
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (41 bp):
GATGACCCGAAGGATTTAACATCATGCTCGAAAGACTTACA
Found at i:40979 original size:216 final size:217
Alignment explanation
Indices: 40584--41071 Score: 804
Period size: 216 Copynumber: 2.3 Consensus size: 217
40574 ATCTTGGTGC
* * * * * *
40584 AAAACATCCTGCCTGAAGGTCTTATGGATGACCCGAAGGATTTATCATCTTGCTC-GAGAGACTT
1 AAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTGAGAGACTT
*
40648 ACAAATAACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGACCCGAAGAACTAATA
66 ACAAATAACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGACCCCAAGAACTAATA
*
40713 AATCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
131 AATCGTGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
40778 TTTTCATTCTCAAATTCATGTG
196 TTTTCATTCTCAAATTCATGTG
*
40800 AAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTGA-AGGCTT
1 AAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTGAGAGACTT
* * * * *
40864 ACAGATGACCCGAGGGATTTAAGCATCATGCTCGAAAGACTTACTGATTG-CCCCAATG-ACTTA
66 ACAAATAACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGA-TGACCCCAA-GAACTAA
40927 TAAATCGTGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCAT
129 TAAATCGTGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCAT
40992 TTTTTTCATTCTCAAATTCATGTG
194 TTTTTTCATTCTCAAATTCATGTG
41016 AAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCT
1 AAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCT
41072 AAATGTAACA
Statistics
Matches: 255, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
216 250 0.98
217 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (217 bp):
AAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTGAGAGACTT
ACAAATAACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGACCCCAAGAACTAATA
AATCGTGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
TTTTCATTCTCAAATTCATGTG
Found at i:41989 original size:31 final size:31
Alignment explanation
Indices: 41954--42065 Score: 197
Period size: 31 Copynumber: 3.6 Consensus size: 31
41944 CCCATAGATT
* *
41954 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
41985 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
42016 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
42047 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
42066 CCTCGACCCT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:46464 original size:31 final size:31
Alignment explanation
Indices: 46426--46550 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
46416 CCCGAAGGAC
* * *
46426 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
46457 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
46488 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
46519 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
46550 C
1 C
46551 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:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:48399 original size:34 final size:34
Alignment explanation
Indices: 48359--48564 Score: 261
Period size: 35 Copynumber: 5.9 Consensus size: 34
48349 TGGATGGATT
48359 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* * *
48393 TACTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
48427 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
* * *
48462 TGCTTCACTATTCTTCTGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
48497 TGCTTCACTACTCTAT-GGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCT-TCGGTGAAGGCTTAAGATGG
* * *
48531 TTTACTTCACTCCTCTTTGGTGAAGGCTTAAGAT
1 --TGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
48565 TGACTTTGCT
Statistics
Matches: 154, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
34 62 0.40
35 63 0.41
36 29 0.19
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (34 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
Found at i:48477 original size:35 final size:35
Alignment explanation
Indices: 48359--48569 Score: 250
Period size: 34 Copynumber: 6.0 Consensus size: 35
48349 TGGATGGATT
* *
48359 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
* * *
48393 TACTTCACTACTCCTCTGTGAAGGCTTAAGATG-G
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
48427 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
* *
48462 TGCTTCACTATTCTTCTGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
* **
48497 TGCTTCACTACTCTAT-GGTGAAGGCTTAAGATGGTT
1 TGCTTCACTACTCT-TCTGTGAAGGCTTAAGAT-GAC
* *
48533 TACTTCACTCCTCTT-TGGTGAAGGCTTAAGATTGAC
1 TGCTTCACTACTCTTCT-GTGAAGGCTTAAGA-TGAC
48569 T
1 T
48570 TTGCTCCAAT
Statistics
Matches: 156, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
34 62 0.40
35 62 0.40
36 31 0.20
37 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (35 bp):
TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAC
Found at i:54880 original size:21 final size:21
Alignment explanation
Indices: 54856--54896 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54846 AATGCAAAGT
54856 GGTCTTCATGTCTTTATGAAG
1 GGTCTTCATGTCTTTATGAAG
*
54877 GGTCTTTATGTCTTTATGAA
1 GGTCTTCATGTCTTTATGAA
54897 TGGTATTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.46
Consensus pattern (21 bp):
GGTCTTCATGTCTTTATGAAG
Found at i:60562 original size:49 final size:49
Alignment explanation
Indices: 60490--60618 Score: 233
Period size: 49 Copynumber: 2.7 Consensus size: 49
60480 ATAAAAAAAT
60490 ACCTGAATAATAGAAGATTCAACCTAAAGTCACACGTCTGCATGAATTA
1 ACCTGAATAATAGAAGATTCAACCTAAAGTCACACGTCTGCATGAATTA
* *
60539 ACCTGAATAATAGAATATTCAACCTAAAGTCACACTTCTGCATGAATTA
1 ACCTGAATAATAGAAGATTCAACCTAAAGTCACACGTCTGCATGAATTA
60588 ACCTGAATAATAGAAGATTCAACCT-AAGTCA
1 ACCTGAATAATAGAAGATTCAACCTAAAGTCA
60619 GAAATTTGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
48 6 0.08
49 71 0.92
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (49 bp):
ACCTGAATAATAGAAGATTCAACCTAAAGTCACACGTCTGCATGAATTA
Found at i:63483 original size:30 final size:29
Alignment explanation
Indices: 63441--63502 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 29
63431 TAAATTTAAA
63441 TTAAAATTAAGATAAAAATAAAATATATT
1 TTAAAATTAAGATAAAAATAAAATATATT
63470 TTAAAAGTTAAGATAAAAATAAAATATATT
1 TTAAAA-TTAAGATAAAAATAAAATATATT
63500 TTA
1 TTA
63503 TTATTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (29 bp):
TTAAAATTAAGATAAAAATAAAATATATT
Found at i:63516 original size:16 final size:16
Alignment explanation
Indices: 63495--63534 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
63485 AAAATAAAAT
63495 ATATTTTATTATTATA
1 ATATTTTATTATTATA
*
63511 ATATTTTATTCTTATA
1 ATATTTTATTATTATA
63527 ATATTTTA
1 ATATTTTA
63535 AAATGTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTTTATTATTATA
Found at i:71549 original size:10 final size:10
Alignment explanation
Indices: 71510--71559 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
71500 TTCATCACAC
71510 CAAATTCTCT
1 CAAATTCTCT
*
71520 CAATTTCTCT
1 CAAATTCTCT
*
71530 CAACTTCTCT
1 CAAATTCTCT
*
71540 CAAATACTCT
1 CAAATTCTCT
* *
71550 TATATTCTCT
1 CAAATTCTCT
71560 ATTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:71623 original size:23 final size:22
Alignment explanation
Indices: 71584--71628 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
71574 TTATTATATT
*
71584 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
71607 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
71629 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:71635 original size:17 final size:18
Alignment explanation
Indices: 71598--71636 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
71588 ATATTTTGTA
71598 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
71616 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
71633 TTTA
1 TTTA
71637 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:74014 original size:35 final size:33
Alignment explanation
Indices: 73971--74055 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 33
73961 GTATTTCAGT
73971 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
74006 TAATTTTGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
74041 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
74056 TAAAATTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
33 2 0.04
34 1 0.02
35 26 0.58
36 1 0.02
37 2 0.04
38 13 0.29
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:77752 original size:23 final size:23
Alignment explanation
Indices: 77711--77786 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
77701 AATACACCGA
* *
77711 AGTGCCGCTTAGAAATGCACCAT
1 AGTGCCACGTAGAAATGCACCAT
* * *
77734 AGTGCCACGTAGGATTGCACCAA
1 AGTGCCACGTAGAAATGCACCAT
**
77757 AGTGCCACGTAGAAATGCACTGT
1 AGTGCCACGTAGAAATGCACCAT
77780 AGTGCCA
1 AGTGCCA
77787 TATAATGTCC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
AGTGCCACGTAGAAATGCACCAT
Done.