Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000229.1 Hibiscus syriacus cultivar Beakdansim tig00000399_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: 92728
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:792 original size:19 final size:19
Alignment explanation
Indices: 770--900 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
760 GGAAATTACT
770 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
789 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
803 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
822 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
836 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
855 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
869 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
888 ATCGCAACGCGAA
1 ATCGCAATGCGAA
901 TTTAATTTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 5 0.06
16 4 0.05
17 4 0.05
18 5 0.06
19 40 0.47
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:812 original size:33 final size:33
Alignment explanation
Indices: 770--896 Score: 211
Period size: 33 Copynumber: 3.8 Consensus size: 33
760 GGAAATTACT
770 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
803 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
835 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
869 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
897 CGAATTTAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
32 1 0.01
33 85 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:877 original size:66 final size:66
Alignment explanation
Indices: 771--903 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
761 GAAATTACTA
771 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
836 T
66 T
*
837 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
902 T
66 T
903 T
1 T
904 AATTTCGCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:970 original size:19 final size:19
Alignment explanation
Indices: 927--971 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
917 GATTCTCTCG
*
927 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
* *
946 TAGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
965 TTGCGAT
1 TTGCGAT
972 AGTACTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1097 original size:14 final size:14
Alignment explanation
Indices: 1078--1109 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1068 CATCAATTAA
1078 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1092 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1106 ACAA
1 ACAA
1110 TTAATTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3814 original size:14 final size:14
Alignment explanation
Indices: 3795--3850 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
3785 GGAAATGACT
3795 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3809 ATCGCAATGCGAAATGA
1 ATCGCAA--CGAGA-GA
3826 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
3842 ATCGCAACG
1 ATCGCAACG
3851 CGAAATGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3828 original size:33 final size:33
Alignment explanation
Indices: 3771--3869 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
3761 ACGAGATAAT
3771 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
3805 GAGAATCGCAATGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
*
3838 GAGAATCGCAACGCGAAATGACAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
3870 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 49 0.79
34 13 0.21
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:3874 original size:52 final size:52
Alignment explanation
Indices: 3808--3924 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 52
3798 GCAACGAGAG
** *
3808 AATCGCAATGCGAAATGACTATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
* *
3860 AATCGCAACGCGAAATGAAAATCGCAACGAGTGAATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
3912 AATCGCAATGCGA
1 AATCGCAATGCGA
3925 TTTTGGTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
Found at i:3917 original size:19 final size:19
Alignment explanation
Indices: 3746--3924 Score: 127
Period size: 19 Copynumber: 10.1 Consensus size: 19
3736 TCTTTTGGTT
*
3746 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3765 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3785 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
3803 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAACGC
**
3819 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3836 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3852 GAAATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3871 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3888 G-AGTG--AATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3904 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3923 GA
1 GA
3925 TTTTGGTTTC
Statistics
Matches: 128, Mismatches: 15, Indels: 34
0.72 0.08 0.19
Matches are distributed among these distances:
14 26 0.20
15 2 0.02
16 9 0.07
17 8 0.06
18 3 0.02
19 51 0.40
20 27 0.21
21 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3989 original size:20 final size:19
Alignment explanation
Indices: 3920--3990 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
3910 AAAATCGCAA
**
3920 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
3939 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
3958 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
3978 TGCGATTTTTATT
1 TGCGATTTTTATT
3991 CTCGAAACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:4514 original size:20 final size:20
Alignment explanation
Indices: 4489--4537 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
4479 ATGTAAATCG
4489 CATTGCGATAGTAAGATTCA
1 CATTGCGATAGTAAGATTCA
* *
4509 CATTGCAATAGTAAGATTCG
1 CATTGCGATAGTAAGATTCA
4529 CATTGCGAT
1 CATTGCGAT
4538 TTACGTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (20 bp):
CATTGCGATAGTAAGATTCA
Found at i:4547 original size:20 final size:21
Alignment explanation
Indices: 4524--4740 Score: 162
Period size: 20 Copynumber: 10.6 Consensus size: 21
4514 CAATAGTAAG
4524 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
* * *
4544 ATTCGCAATGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTA
4565 ATTCGCATTGCGATTTAC-TA
1 ATTCGCATTGCGATTTACGTA
4585 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
* * *
4605 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACGTA
* ** *
4626 AATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTACGTA
* * * * *
4646 AATCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTTACGTA
* *
4667 AATCGTATTGCGA--TA-GTCA
1 ATTCGCATTGCGATTTACGT-A
* * **
4686 GTATCGCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTACGTA
*
4708 ATTCGCATTGCGATTTAC-TT
1 ATTCGCATTGCGATTTACGTA
4728 ATTCGCATTGCGA
1 ATTCGCATTGCGA
4741 ATTAGGAAAA
Statistics
Matches: 157, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 93 0.59
21 57 0.36
22 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACGTA
Found at i:4632 original size:41 final size:41
Alignment explanation
Indices: 4524--4755 Score: 163
Period size: 41 Copynumber: 5.7 Consensus size: 41
4514 CAATAGTAAG
* * * * * * *
4524 ATTCGCATTGCGATTTACG-TATTCGCAATGCGATTTTCCT
1 ATTCGCATTGCGAATTATGAAAATCGCATTGCGATTTACGT
* *
4564 AATTCGCATTGCGATTTACT--AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGAATTA-TGAAAATCGCATTGCGATTTACGT
** *
4605 ATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGT
1 ATTCGCATTGCGAATTATGAAAATCGCATTGCGATTTACGT
* * * * *
4645 AAATCGCAATGCGAATTAGGAAAATCGTATTGCGATAGT-CAGT
1 -ATTCGCATTGCGAATTATGAAAATCGCATTGCGAT-TTAC-GT
* * * *
4688 A-TCGCATTGCG-ATTTTCCAAATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGAATTAT-GAAAATCGCATTGCGATTTACGT
*
4728 ATTCGCATTGCGAATTAGGAAAATCGCA
1 ATTCGCATTGCGAATTATGAAAATCGCA
4756 ACGCGAAATT
Statistics
Matches: 151, Mismatches: 29, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 27 0.18
41 115 0.76
42 5 0.03
43 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
ATTCGCATTGCGAATTATGAAAATCGCATTGCGATTTACGT
Found at i:4632 original size:61 final size:60
Alignment explanation
Indices: 4524--4755 Score: 189
Period size: 61 Copynumber: 3.8 Consensus size: 60
4514 CAATAGTAAG
* * * *
4524 ATTCGCATTGCGATTTACGTATTCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTAT-CAAAATCGCATTGCGATTTACTA
* ** *
4585 ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCAAAATCGCATTGCGATTTAC-TA
* * * * * * * ** * *
4646 AATCGCAATGCGAATTAGGAAAATCGTATTGCGA-TAGTCAGTATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTTACG-TATTCGCATTGCGATTA-TCAAAATCGCATTGCGA-TTTACTA
* **
4708 ATTCGCATTGCGATTTACTTATTCGCATTGCGAATTAGGAAAATCGCA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCAAAATCGCA
4756 ACGCGAAATT
Statistics
Matches: 128, Mismatches: 35, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
60 5 0.04
61 82 0.64
62 37 0.29
63 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (60 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTATCAAAATCGCATTGCGATTTACTA
Found at i:4679 original size:21 final size:21
Alignment explanation
Indices: 4607--4671 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
4597 ATTTACGTAT
* *
4607 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
4628 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
4648 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
4669 TCG
1 TCG
4672 TATTGCGATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:4782 original size:21 final size:22
Alignment explanation
Indices: 4730--4782 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
4720 ATTTACTTAT
4730 TCGCATTGCG-AATTAGGAAAA
1 TCGCATTGCGAAATTAGGAAAA
**
4751 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTAGGAAAA
*
4772 TTGCATTGCGA
1 TCGCATTGCGA
4783 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTAGGAAAA
Found at i:13157 original size:24 final size:24
Alignment explanation
Indices: 13124--13190 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
13114 GAGCTCAAAA
*
13124 TCGAGATTCAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
*
13148 TCGAGCTTCAATCGAGCTGGAGTC
1 TCGAGCTTCAATCGAGCTCGAGTC
*
13172 TCGAGCCTCAATCGAGCTC
1 TCGAGCTTCAATCGAGCTC
13191 TTGGATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.24
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGCTCGAGTC
Found at i:21058 original size:6 final size:6
Alignment explanation
Indices: 21047--21265 Score: 438
Period size: 6 Copynumber: 36.5 Consensus size: 6
21037 GAATAAATTA
21047 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
21095 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
21143 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
21191 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
21239 TTATTT TTATTT TTATTT TTATTT TTA
1 TTATTT TTATTT TTATTT TTATTT TTA
21266 AGAAACACAA
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 213 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTATTT
Found at i:21060 original size:1 final size:1
Alignment explanation
Indices: 21050--21264 Score: 115
Period size: 1 Copynumber: 215.0 Consensus size: 1
21040 TAAATTATTA
* * * * * * * * * *
21050 TTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * *
21115 ATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * *
21180 TATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
21245 TTATTTTTATTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTT
21265 AAGAAACACA
Statistics
Matches: 144, Mismatches: 70, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 144 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:25478 original size:17 final size:17
Alignment explanation
Indices: 25456--25490 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25446 TGATATTCTA
25456 AATAATTAT-ATTTTTAC
1 AATAA-TATCATTTTTAC
25473 AATAATATCATTTTTAC
1 AATAATATCATTTTTAC
25490 A
1 A
25491 TCGTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATATCATTTTTAC
Found at i:25703 original size:17 final size:18
Alignment explanation
Indices: 25683--25716 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25673 TCAAAGATAG
25683 ATATTATTTA-AATAATT
1 ATATTATTTACAATAATT
*
25700 ATATTTTTTACAATAAT
1 ATATTATTTACAATAAT
25717 ATCATTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATTTACAATAATT
Found at i:25780 original size:240 final size:239
Alignment explanation
Indices: 25313--25788 Score: 656
Period size: 238 Copynumber: 2.0 Consensus size: 239
25303 TAGATTTTTT
* * * *
25313 AAATAATTTTCATAAATATCATGTTTATTTATATAAAATATAATATAATAAAAAATAATATTGCA
1 AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAATAAAAAATAATAGTG-A
* * * *
25378 GCCTCGAGTGAACAAAGAAATTAATTTTTCAATATATAAGATCCATTTTTTAATAACTCAAAGAT
65 GCCTCGAATGAACAAAGAAATTAACTTTTCAATACATAAGATACATTTTTTAATAACTCAAAGAT
* *
25443 AGATGATATTCTAAATAATTATATTTTTACAATAATATCATTTTTACATCGTAAAATTATAGATG
130 AGATGATATTCTAAATAATTATATTTTTACAATAATATCATTTTTACATCATAAAATTATAAATG
* *
25508 GTTAATATATTAAATATTGAAAATATAAATAATTTTAATTACTCA
195 ATTAATATATTAAATATTAAAAATATAAATAATTTTAATTACTCA
25553 AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAATATAAAAATAATAGTG-
1 AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAATA-AAAAATAATAGTGA
* * * * * * *
25617 GGCTCGAAT-AGACAAATATATT-ACTTTTCAATGCCTAAGATATATTTTTTAATTACTCAAAGA
65 GCCTCGAATGA-ACAAAGAAATTAACTTTTCAATACATAAGATACATTTTTTAATAACTCAAAGA
* * *
25680 TAGAT-ATTATT-TAAATAATTATATTTTTTACAATAATATCATTTTCTGCCTCATAAATTTATA
129 TAGATGA-TATTCTAAATAATTATA-TTTTTACAATAATATCATTTT-TACATCATAAAATTATA
25743 AATGATTAATATATTAAATATTAAAAATATAAAATAATTTTAATTA
191 AATGATTAATATATTAAATATTAAAAATAT-AAATAATTTTAATTA
25789 TTTAAATTTA
Statistics
Matches: 208, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
237 13 0.06
238 65 0.31
239 56 0.27
240 62 0.30
241 12 0.06
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (239 bp):
AAATAATTCTAATAAATATCATATTTATTTATATAAAATATAATATAATAAAAAATAATAGTGAG
CCTCGAATGAACAAAGAAATTAACTTTTCAATACATAAGATACATTTTTTAATAACTCAAAGATA
GATGATATTCTAAATAATTATATTTTTACAATAATATCATTTTTACATCATAAAATTATAAATGA
TTAATATATTAAATATTAAAAATATAAATAATTTTAATTACTCA
Found at i:26415 original size:22 final size:22
Alignment explanation
Indices: 26387--26503 Score: 150
Period size: 22 Copynumber: 5.4 Consensus size: 22
26377 AATTTGAAAA
26387 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
** *
26409 ATCGCAACGA-ATTTGTAAACT
1 ATCGCAACGACAACTGTAGACT
*
26430 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
26452 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
26474 ATCGCAACG-CAATTTTCA-ACT
1 ATCGCAACGACAACTGT-AGACT
26495 ATCGCAACG
1 ATCGCAACG
26504 CGAAATGGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
21 34 0.41
22 49 0.59
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:26444 original size:43 final size:43
Alignment explanation
Indices: 26369--26481 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
26359 CAACGAATTT
* *
26369 TCGCAACGAATTTG-AAA-AATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
26410 TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
1 TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
** *
26453 TCGCAACGACAACTGTAGACTATCGCAAC
1 TCGCAACGA-ATTTGTAAACTATCGCAAC
26482 GCAATTTTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 14 0.22
42 3 0.05
43 31 0.48
44 16 0.25
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (43 bp):
TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
Found at i:26504 original size:21 final size:21
Alignment explanation
Indices: 26406--26565 Score: 82
Period size: 21 Copynumber: 7.6 Consensus size: 21
26396 ACAACTGTAG
*
26406 ACTATCGCAACG-AATTTGTAA
1 ACTATCGCAACGCAATTT-TCA
* * *
26427 ACTATCGCAACAACAACTGT-A
1 ACTATCGCAAC-GCAATTTTCA
* *
26448 GACTATCGCAACGACAACTGT-A
1 -ACTATCGCAACG-CAATTTTCA
26470 GACTATCGCAACGCAATTTTCA
1 -ACTATCGCAACGCAATTTTCA
* **
26492 ACTATCGCAACGCGAA-ATGGA
1 ACTATCGCAACGC-AATTTTCA
* * *
26513 A-AATCGCAACGCGAA-ATGCA
1 ACTATCGCAACGC-AATTTTCA
* *
26533 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCAATTTTCA
26553 ACTATCGCAACGC
1 ACTATCGCAACGC
26566 GAAATGCAAC
Statistics
Matches: 116, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
19 1 0.01
20 33 0.28
21 43 0.37
22 36 0.31
23 3 0.03
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCAATTTTCA
Found at i:26520 original size:20 final size:20
Alignment explanation
Indices: 26495--26574 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
26485 ATTTTCAACT
*
26495 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGCAAA
26515 ATCGCAACGCGAAATGCAAA
1 ATCGCAACGCGAAATGCAAA
** * *
26535 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAA-A
26556 ATCGCAACGCGAAATGCAA
1 ATCGCAACGCGAAATGCAA
26575 CGCGAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 35 0.69
21 16 0.31
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGCAAA
Found at i:26566 original size:21 final size:21
Alignment explanation
Indices: 26449--26575 Score: 109
Period size: 21 Copynumber: 6.1 Consensus size: 21
26439 ACAACTGTAG
* *
26449 ACTATCGCAACGAC-AACTGTA
1 ACTATCGCAACG-CGAAATGCA
* *
26470 GACTATCGCAACGC-AATTTTCA
1 -ACTATCGCAACGCGAA-ATGCA
*
26492 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
*
26513 A-AATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
* ** *
26533 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
26553 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
26574 AC
1 AC
26576 GCGAATTTAC
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
20 35 0.40
21 36 0.41
22 16 0.18
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:26818 original size:18 final size:18
Alignment explanation
Indices: 26791--26830 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
26781 TAAAATGTGT
26791 AATGGAAAGTTTCCAAGA
1 AATGGAAAGTTTCCAAGA
*
26809 AATGGGAAGTTTCCAAGA
1 AATGGAAAGTTTCCAAGA
26827 AATG
1 AATG
26831 AAAATGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (18 bp):
AATGGAAAGTTTCCAAGA
Found at i:27178 original size:22 final size:22
Alignment explanation
Indices: 27138--27180 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27128 CGTTATATTT
*
27138 TTATTTTTTAATAATAAAAATA
1 TTATTTTTCAATAATAAAAATA
*
27160 TTATTTTTCAATGAAAAAAAA
1 TTATTTTTCAAT-AATAAAAA
27181 ACTTAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TTATTTTTCAATAATAAAAATA
Found at i:29313 original size:20 final size:20
Alignment explanation
Indices: 29290--29350 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
29280 GATGCATCGA
*
29290 TGCACAGTGTATGGATACAC
1 TGCAGAGTGTATGGATACAC
*
29310 TGCAGAGTGCATGGATACAC
1 TGCAGAGTGTATGGATACAC
*
29330 TGCAGGGTGTATGGATACAC
1 TGCAGAGTGTATGGATACAC
29350 T
1 T
29351 TTGACACCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (20 bp):
TGCAGAGTGTATGGATACAC
Found at i:29602 original size:21 final size:19
Alignment explanation
Indices: 29573--29630 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
29563 ATGTATAATG
29573 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
*
29592 ACAAAATGATATTAATTGTT-
1 A-AAAA-GATATCAATTGTTA
29612 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
29631 CCAATTGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.34
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:31221 original size:20 final size:20
Alignment explanation
Indices: 31167--31222 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
31157 ATTGAAGTAT
*
31167 GGAGGCTTGTCGATTGGTAG
1 GGAGGCTTGTCGGTTGGTAG
*
31187 GGAGGCTTGTTGGTTGGTAG
1 GGAGGCTTGTCGGTTGGTAG
31207 GGAGGCTTGTCGGTTG
1 GGAGGCTTGTCGGTTG
31223 AAACGAGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (20 bp):
GGAGGCTTGTCGGTTGGTAG
Found at i:32194 original size:20 final size:20
Alignment explanation
Indices: 32171--32218 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
32161 ACAGTGTATA
* *
32171 GATATACTGTAGAGTGCATG
1 GATACACTGCAGAGTGCATG
* *
32191 GATACACTGCAGGGTGTATG
1 GATACACTGCAGAGTGCATG
32211 GATACACT
1 GATACACT
32219 TTGACACCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
GATACACTGCAGAGTGCATG
Found at i:34155 original size:15 final size:15
Alignment explanation
Indices: 34110--34174 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
34100 TATTTTTTTA
34110 AAGAAGAGTTTGAAG
1 AAGAAGAGTTTGAAG
34125 AAGAATGA---TGAAG
1 AAGAA-GAGTTTGAAG
*
34138 AAGAAGAGTTTAAAG
1 AAGAAGAGTTTGAAG
34153 AAGAAGAGTTTGAAG
1 AAGAAGAGTTTGAAG
34168 AAGAAGA
1 AAGAAGA
34175 ATAAAAAGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.05
13 10 0.23
15 30 0.68
16 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (15 bp):
AAGAAGAGTTTGAAG
Found at i:40262 original size:21 final size:21
Alignment explanation
Indices: 40236--40275 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40226 ACGTTAAAAG
*
40236 ATTAACATATTAGGTAACGGA
1 ATTAACATATTAGATAACGGA
*
40257 ATTAACATTTTAGATAACG
1 ATTAACATATTAGATAACG
40276 CTTTATCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (21 bp):
ATTAACATATTAGATAACGGA
Found at i:49463 original size:24 final size:24
Alignment explanation
Indices: 49436--49487 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
49426 TGCCTCCGTT
49436 GTTGCTCAATGATTCTTTTTCTTA
1 GTTGCTCAATGATTCTTTTTCTTA
49460 GTTGCTCAATGATTCTTTTTCTTA
1 GTTGCTCAATGATTCTTTTTCTTA
49484 GTTG
1 GTTG
49488 ATACATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (24 bp):
GTTGCTCAATGATTCTTTTTCTTA
Found at i:68548 original size:60 final size:60
Alignment explanation
Indices: 68483--68619 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 60
68473 AACATAATGA
* * *
68483 ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAATGACTTAACAAAACAATATTTT
1 ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAACAACATTCT
** * * *
68543 ATAATCAAATGATCATTTTGTAACTTTTAATAGTCGAGGGACTTAATAAAACAACATTCT
1 ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAACAACATTCT
* * *
68603 ATAGTCGGGAGACCATT
1 ATAATCAGGTGACCATT
68620 AGTGTAATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (60 bp):
ATAATCAGGTGACCATTTTGTAACTTTTAATAGTCGAAGGACTTAACAAAACAACATTCT
Found at i:70829 original size:16 final size:18
Alignment explanation
Indices: 70796--70853 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 18
70786 TCAATGGTTT
70796 TAATTTC-A-ATACTTTTA
1 TAATTTCTATATA-TTTTA
70813 TAATTTCT-T-TATTTTA
1 TAATTTCTATATATTTTA
* *
70829 TAGTTACTATATATTTCTA
1 TAATTTCTATATATTT-TA
70848 TAATTT
1 TAATTT
70854 TCTTAATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.34
17 10 0.31
18 5 0.16
19 6 0.19
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.59
Consensus pattern (18 bp):
TAATTTCTATATATTTTA
Found at i:75232 original size:25 final size:26
Alignment explanation
Indices: 75204--75254 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
75194 ATCATGTTGC
*
75204 CATTATTGGGCACTAATAATG-GTGT
1 CATTATTGGGCACCAATAATGCGTGT
*
75229 CATTATTGTGCACCAATAATGCGTGT
1 CATTATTGGGCACCAATAATGCGTGT
75255 AAGGGCGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (26 bp):
CATTATTGGGCACCAATAATGCGTGT
Found at i:78017 original size:27 final size:27
Alignment explanation
Indices: 77985--78057 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
77975 ATTAATATCC
77985 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTCATTCAAATATTGATATTA
* *
78012 ATCACATTAATTCAACTATTGATATTA
1 ATCACATTCATTCAAATATTGATATTA
*
78039 ATCACATTCATTAAAATAT
1 ATCACATTCATTCAAATAT
78058 AGCGTCAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (27 bp):
ATCACATTCATTCAAATATTGATATTA
Found at i:81498 original size:22 final size:22
Alignment explanation
Indices: 81473--81526 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 22
81463 ATGGTGCCAT
81473 TATTTTTT-GTCATTATAATAAA
1 TATTTTTTCGTCATTATAAT-AA
*
81495 TATTATTTTTCGTCATTATAATTA
1 TA-T-TTTTTCGTCATTATAATAA
81519 TATTTTTT
1 TATTTTTT
81527 TAACATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.25
23 2 0.07
24 8 0.29
25 11 0.39
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (22 bp):
TATTTTTTCGTCATTATAATAA
Found at i:83858 original size:42 final size:41
Alignment explanation
Indices: 83769--83940 Score: 127
Period size: 40 Copynumber: 4.2 Consensus size: 41
83759 TATACAAATG
*
83769 CCACTAAAGTA-TAGTATTTAGCGGTGTTTATATAAAAACG
1 CCACTAAAGTACTAGTATTTAGCGGTGTTTATATAAAAACA
* * * * * *
83809 TCACTAAAGTACAAGTATTTAGCGGCGTTTCTGCTTAAAACA
1 CCACTAAAGTACTAGTATTTAGCGGTGTTTAT-ATAAAAACA
** *
83851 CCACTAAAGTACTAGGCTTTAGCGGTGTTTGTCA-AAAAA-A
1 CCACTAAAGTACTAGTATTTAGCGGTGTTTAT-ATAAAAACA
* * * *** * *
83891 CCACTGAAGTGCTAGGT-TTTACCGACATTTGTTTAAAAACA
1 CCACTAAAGTACTA-GTATTTAGCGGTGTTTATATAAAAACA
83932 CCACTAAAG
1 CCACTAAAG
83941 AACGATTCTA
Statistics
Matches: 102, Mismatches: 25, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
40 39 0.38
41 31 0.30
42 32 0.31
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (41 bp):
CCACTAAAGTACTAGTATTTAGCGGTGTTTATATAAAAACA
Found at i:86155 original size:55 final size:55
Alignment explanation
Indices: 86077--86285 Score: 339
Period size: 55 Copynumber: 3.8 Consensus size: 55
86067 ATGTATGGTT
* *
86077 AATTTCCGTATGGGTACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATG
1 AATTTTCGTATGGGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATG
* *
86132 AATTTTCATATGGGCGCTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATG
1 AATTTTCGTATGGGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATG
*
86187 AATTTTCGTATGGGCACTATGTGTGTAAAATTAAGAAATTCATACTAAGTGTATG
1 AATTTTCGTATGGGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATG
* *
86242 AATTTTCGTATGGGAACTATATGTGCAAACA-TAAGAAATTCATA
1 AATTTTCGTATGGGCACTATGTGTGCAAA-ATTAAGAAATTCATA
86286 ATAGGAAGTG
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
55 142 0.99
56 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (55 bp):
AATTTTCGTATGGGCACTATGTGTGCAAAATTAAGAAATTCATACTAAGTGTATG
Done.