Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005870.1 Hibiscus syriacus cultivar Beakdansim tig00013798_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: 66117
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3595 original size:2 final size:2
Alignment explanation
Indices: 3590--3620 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3580 ACACTCACAC
3590 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3621 ATCTAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4865 original size:6 final size:6
Alignment explanation
Indices: 4854--4920 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
4844 GACACGTATT
* * *
4854 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4902 ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG A
4921 GCCGAGCCGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:10810 original size:6 final size:6
Alignment explanation
Indices: 10768--10808 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
10758 AGTATCCGCG
*
10768 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAG CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
10809 GCCGTGCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.34, C:0.46, G:0.20, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:16858 original size:41 final size:40
Alignment explanation
Indices: 16813--16946 Score: 133
Period size: 41 Copynumber: 3.3 Consensus size: 40
16803 GATTCTGACT
* * * *
16813 ATCGCATTGCGATTTTCCTAATTCGCAATGCGAATACATAA
1 ATCGCAATGCGA-TTTCGTAAATCGCAATGCGAATACGTAA
* * * * *
16854 ATCGCAACGCAAATTTGGAAAATCGCAATGCGATTACGTAA
1 ATCGCAATGC-GATTTCGTAAATCGCAATGCGAATACGTAA
* * *
16895 ATCGCAATGCGAATACGTAAATCGTAATGCGAATACGTAA
1 ATCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAA
*
16935 ATCGCAACGCGA
1 ATCGCAATGCGA
16947 ATCTGACTAT
Statistics
Matches: 74, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
40 34 0.46
41 39 0.53
42 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (40 bp):
ATCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAA
Found at i:16860 original size:20 final size:20
Alignment explanation
Indices: 16835--16948 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
16825 TTTTCCTAAT
*
16835 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
16855 TCGCAACGCAAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
16876 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
16896 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
16916 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
16936 TCGCAACGCGAAT
1 TCGCAATGCGAAT
16949 CTGACTATCG
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 64 0.83
21 13 0.17
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:16958 original size:20 final size:20
Alignment explanation
Indices: 16935--16978 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
16925 GAATACGTAA
*
16935 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
16955 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
16975 ATCG
1 ATCG
16979 TAATACTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:19224 original size:34 final size:33
Alignment explanation
Indices: 19181--19299 Score: 103
Period size: 34 Copynumber: 3.4 Consensus size: 33
19171 GACATTCATT
19181 TGACTATCGCAATGCGAAAATCGCAACGCGAATA
1 TGACTATCGCAATGCGAAAATCGCAACGCGAA-A
*
19215 TGACTATCGCAATACGGAAATGACTATCGCAACGCGGAAA
1 TGACTATCGCAATGC-G-AA--A--ATCGCAACGC-GAAA
* * * *
19255 TGACTATCGCAACGAGAGAATCGCAATGCGAAA
1 TGACTATCGCAATGCGAAAATCGCAACGCGAAA
**
19288 TGAAAATCGCAA
1 TGACTATCGCAA
19300 CGAGTGAATC
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
33 14 0.20
34 23 0.33
35 1 0.01
36 3 0.04
38 2 0.03
39 1 0.01
40 23 0.33
41 3 0.04
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (33 bp):
TGACTATCGCAATGCGAAAATCGCAACGCGAAA
Found at i:19225 original size:20 final size:19
Alignment explanation
Indices: 19200--19268 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 19
19190 CAATGCGAAA
19200 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
19220 ATCGCAATACG-GAAATGACT
1 ATCGC-A-ACGCGAAATGACT
19240 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
19260 ATCGCAACG
1 ATCGCAACG
19269 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 34 0.76
21 4 0.09
22 3 0.07
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:19328 original size:34 final size:33
Alignment explanation
Indices: 19240--19335 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
19230 GGAAATGACT
* **
19240 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
19274 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
19307 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
19336 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:19331 original size:20 final size:19
Alignment explanation
Indices: 19196--19339 Score: 74
Period size: 20 Copynumber: 7.9 Consensus size: 19
19186 ATCGCAATGC
*
19196 GAAAATCGCAACGCGAATAT
1 GAAAATCGCAATGCGAA-AT
** *
19216 GACTATCGCAATACGGAAAT
1 GAAAATCGCAATGC-GAAAT
** *
19236 GACTATCGCAACGCGGAAAT
1 GAAAATCGCAATGC-GAAAT
**
19256 GACTATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
*
19270 GAGAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
19289 GAAAATCGCAA--CG-AGT
1 GAAAATCGCAATGCGAAAT
19305 G--AATCGCAATGCGAAAAT
1 GAAAATCGCAATGCG-AAAT
*
19323 GAAAATCGCAACGCGAA
1 GAAAATCGCAATGCGAA
19340 TTTAGTTTCG
Statistics
Matches: 100, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.17
15 1 0.01
16 7 0.07
17 3 0.03
18 5 0.05
19 12 0.12
20 52 0.52
21 3 0.03
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:19407 original size:33 final size:33
Alignment explanation
Indices: 19350--19434 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
19340 TTTAGTTTCG
19350 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
19384 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
19417 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
19435 CACGTTGCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:19424 original size:14 final size:14
Alignment explanation
Indices: 19372--19425 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
19362 CATTTTCGCA
19372 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
19386 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
19403 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
19419 TTGCGAT
1 TTGCGAT
19426 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:19570 original size:14 final size:14
Alignment explanation
Indices: 19551--19587 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
19541 CATCAATTAA
19551 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
19565 ACAAATCATCTTTT
1 ACAAATCAACATTT
19579 ACAAATCAA
1 ACAAATCAA
19588 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:19719 original size:15 final size:15
Alignment explanation
Indices: 19683--19726 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
19673 GGTGTGCAAA
19683 TCCGGGTACCCGGATT
1 TCCGGGTACCC-GATT
*
19699 TTCGGGTACCCGATT
1 TCCGGGTACCCGATT
19714 TCCGGGTACCCGA
1 TCCGGGTACCCGA
19727 AACTTCCGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.25
Consensus pattern (15 bp):
TCCGGGTACCCGATT
Found at i:19796 original size:15 final size:15
Alignment explanation
Indices: 19776--19832 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
19766 TCGGATGTTA
19776 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
19791 CGGGTACCCGAATTTT
1 CGGGTACCCG-GTAAT
*
19807 GCGGGTAACCGGTAAT
1 -CGGGTACCCGGTAAT
19823 CGGGTACCCG
1 CGGGTACCCG
19833 ATACCCGGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 19 0.59
16 4 0.12
17 9 0.28
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:22071 original size:20 final size:20
Alignment explanation
Indices: 22048--22176 Score: 195
Period size: 20 Copynumber: 6.5 Consensus size: 20
22038 GAAACTTAAA
22048 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
22068 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
22088 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
22108 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
22128 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
22148 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
22168 ATCGCAACG
1 ATCGCAACG
22177 AGAGAATCGC
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:22246 original size:20 final size:21
Alignment explanation
Indices: 22221--22287 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
22211 GATTCTTTCG
22221 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTCAAATTTCGCA
*
22241 TTGCGATAGTC-ATTTTCGCA
1 TTGCGATAGTCAAATTTCGCA
* * *
22261 TTGTGATAGTC-ATTTTCGCG
1 TTGCGATAGTCAAATTTCGCA
22281 TTGCGAT
1 TTGCGAT
22288 TTTGTTGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.10
20 38 0.90
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (21 bp):
TTGCGATAGTCAAATTTCGCA
Found at i:22360 original size:20 final size:20
Alignment explanation
Indices: 22327--22377 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
22317 AGATTCTCTT
* *
22327 GTTGCAATATTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
22347 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
*
22367 ATTGCGATAGT
1 GTTGCGATAGT
22378 AAACTATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:24279 original size:20 final size:20
Alignment explanation
Indices: 24256--24310 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
24246 CTGAAACTTT
24256 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
24276 AAATCGCAATACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
24296 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
24311 TTTGACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:24366 original size:33 final size:33
Alignment explanation
Indices: 24257--24370 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
24247 TGAAACTTTA
* *
24257 AATCGCAACACGAAAATGAAAATCGCAATACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
24295 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
24331 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
24364 AATCGCA
1 AATCGCA
24371 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:24757 original size:22 final size:22
Alignment explanation
Indices: 24695--24760 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
24685 TGACCGTGAA
* *
24695 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
24717 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
24739 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
24761 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:24964 original size:20 final size:18
Alignment explanation
Indices: 24939--25031 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 18
24929 GCTATGTAAA
24939 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGAT--TCAGAT
*
24959 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTCA-G-AT
*
24979 TCGCATTGCGATTTACATAT
1 TCGCATTGCGA-TT-CAGAT
*
24999 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTCA-G-AT
25019 TCGCATTGCGATT
1 TCGCATTGCGATT
25032 TACGTAATCG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
18 3 0.05
19 3 0.05
20 53 0.85
21 2 0.03
22 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (18 bp):
TCGCATTGCGATTCAGAT
Found at i:25001 original size:40 final size:40
Alignment explanation
Indices: 24939--25087 Score: 174
Period size: 40 Copynumber: 3.7 Consensus size: 40
24929 GCTATGTAAA
* *
24939 TCGCATTGCGATAGT-CAGATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGAT-TTACATATTCGCATTGCGATTTACGTAT
24979 TCGCATTGCGATTTACATATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATATTCGCATTGCGATTTACGTAT
* * * * **
25019 TCGCATTGCGATTTACGTAATCGTATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTACATATTCGCATTGCGA-TTTACGTAT
* **
25060 TCGCGTTGCGATTTATGTATTCGCATTG
1 TCGCATTGCGATTTACATATTCGCATTG
25088 TGAATTAGGA
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 64 0.67
41 30 0.32
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (40 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATTTACGTAT
Found at i:25032 original size:20 final size:20
Alignment explanation
Indices: 24957--25087 Score: 181
Period size: 20 Copynumber: 6.5 Consensus size: 20
24947 CGATAGTCAG
24957 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
24977 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
24997 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
25017 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * **
25037 AATCGTATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
25058 ATTCGCGTTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
25078 ATTCGCATTG
1 ATTCGCATTG
25088 TGAATTAGGA
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 81 0.85
21 14 0.15
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:25032 original size:60 final size:61
Alignment explanation
Indices: 24957--25087 Score: 201
Period size: 61 Copynumber: 2.2 Consensus size: 61
24947 CGATAGTCAG
* *
24957 ATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTTACATATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
* * * *
25017 ATTCGCATTGCGATTTACGTAATCGTATTGCGATTTTCCAAATTCGCGTTGCGATTTATGT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
25078 ATTCGCATTG
1 ATTCGCATTG
25088 TGAATTAGGA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
60 31 0.48
61 33 0.52
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (61 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTACAAATTCGCATTGCGATTTACGT
Found at i:25113 original size:21 final size:21
Alignment explanation
Indices: 25089--25132 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25079 TTCGCATTGT
25089 GAATTAGGAAAATCGCAAAGC
1 GAATTAGGAAAATCGCAAAGC
* *
25110 GAATTTGGAAAATCGCAATGC
1 GAATTAGGAAAATCGCAAAGC
25131 GA
1 GA
25133 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.18
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAAAGC
Found at i:25800 original size:41 final size:42
Alignment explanation
Indices: 25753--26032 Score: 134
Period size: 44 Copynumber: 6.3 Consensus size: 42
25743 AACTTCTTAT
25753 CTTTATAATTGAAGTCTTTAATTTTTTCAA-TCATTTTTTAC
1 CTTTATAATTGAAGTCTTTAATTTTTTCAATTCATTTTTTAC
* * ** *
25794 CTTTATAATTGAAGTCTCT-ATTTTTTTAATTCTACCTTTTAA
1 CTTTATAATTGAAGTCTTTAATTTTTTCAATTC-ATTTTTTAC
* * *
25836 CTTTATAATTG-AGCCACTTAATTCTTTTCAATTTCATTTTCTAC
1 CTTTATAATTGAAGTC-TTTAATT-TTTTCAA-TTCATTTTTTAC
* * ** * * * *
25880 CTTTTATATTTTTATAATTGAGGCCCCTAATTTTTTTAATCTAACTTTTTAA
1 C---------TTTATAATTGAAGTCTTTAATTTTTTCAAT-TCATTTTTTAC
* * * * *
25932 CTTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCACTTTCTAC
1 CTTTATAATTGAAGTCTTTAA-TTTTTTCAAT-TCATTTTTTAC
* * ** * *
25976 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTAC
1 CTTTATAATTGAAGTCTTTAA-TTTTTTCAAT-TCATTTTTTAC
26020 CTTTATAATTGAA
1 CTTTATAATTGAA
26033 ACCCGTAAGT
Statistics
Matches: 194, Mismatches: 27, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
40 9 0.05
41 23 0.12
42 18 0.09
43 22 0.11
44 85 0.44
45 3 0.02
51 1 0.01
52 14 0.07
53 16 0.08
54 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.50
Consensus pattern (42 bp):
CTTTATAATTGAAGTCTTTAATTTTTTCAATTCATTTTTTAC
Found at i:25913 original size:96 final size:95
Alignment explanation
Indices: 25795--25979 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 95
25785 ATTTTTTACC
* *
25795 TTTATAATTGAAGTCTCTATTTTTTTAATTCT-ACCTTTTAACTTTATAATTGA-GCCACTTAA-
1 TTTATAATTGAAGCCCCTATTTTTTTAA-TCTAACCTTTTAACTTTATAATTGAGGCC-CTTAAG
* *
25857 TTCTTTTCAATTTCATTTTCTACCTTTTATATT
64 TT-TTTTCAATCTCACTTTCTACCTTTTATATT
* *
25890 TTTATAATTGAGGCCCCTAATTTTTTTAATCTAACTTTTTAACTTTATAATTGAGGCCCTTAAGT
1 TTTATAATTGAAGCCCCT-ATTTTTTTAATCTAACCTTTTAACTTTATAATTGAGGCCCTTAAGT
25955 TTTTTCAATCTCACTTTCTACCTTT
65 TTTTTCAATCTCACTTTCTACCTTT
25980 ATAATTGAGG
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
95 18 0.22
96 57 0.71
97 5 0.06
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (95 bp):
TTTATAATTGAAGCCCCTATTTTTTTAATCTAACCTTTTAACTTTATAATTGAGGCCCTTAAGTT
TTTTCAATCTCACTTTCTACCTTTTATATT
Found at i:25965 original size:44 final size:44
Alignment explanation
Indices: 25890--26116 Score: 259
Period size: 44 Copynumber: 5.2 Consensus size: 44
25880 CTTTTATATT
* * * *
25890 TTTATAATTGAGGCCCCTAA-TTTTTTTAATCTAACTTTTTAAC
1 TTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTACC
*
25933 TTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTACC
25977 TTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTACC
** * * * *
26021 TTTATAATTGAAACCCGTAAGTTTTTTTTAAATCTCA-ATTATACC
1 TTTATAATTGAGGCCCCTAAG--TTTTTTCAATCTCACTTTCTACC
* *
26066 TTTACAATTGAGACCCCT-A-TTATTTT-AATCTCGA-TTTCTACC
1 TTTATAATTGAGGCCCCTAAGTT-TTTTCAATCTC-ACTTTCTACC
26108 TTTATAATT
1 TTTATAATT
26117 AATACCTCTA
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
41 8 0.05
42 19 0.12
43 19 0.12
44 81 0.50
45 21 0.13
46 13 0.08
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (44 bp):
TTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTACC
Found at i:26115 original size:87 final size:86
Alignment explanation
Indices: 25890--26116 Score: 271
Period size: 87 Copynumber: 2.6 Consensus size: 86
25880 CTTTTATATT
* * * ** *
25890 TTTATAATTGAGGCCCCTAATTTTTTTAATCTAACTTTTTAACTTTATAATTGAGGCCCTTAAGT
1 TTTATAATTGAGGCCCCTAA-TTTTTTAATCTCACTTTCTACCTTTATAATTGAAACCCGTAAGT
* * *
25955 TTTTTCAATCTCACTTTCTACC
65 TTTTTAAATCTCACATTATACC
25977 TTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTACCTTTATAATTGAAACCCGTAAG
1 TTTATAATTGAGGCCCCTAA-TTTTTT-AATCTCACTTTCTACCTTTATAATTGAAACCCGTAAG
26042 TTTTTTTTAAATCTCA-ATTATACC
64 --TTTTTTAAATCTCACATTATACC
* *
26066 TTTACAATTGAGACCCCT-ATTATTTTAATCTCGA-TTTCTACCTTTATAATT
1 TTTATAATTGAGGCCCCTAATT-TTTTAATCTC-ACTTTCTACCTTTATAATT
26117 AATACCTCTA
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
87 51 0.41
88 37 0.30
89 22 0.18
90 13 0.11
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (86 bp):
TTTATAATTGAGGCCCCTAATTTTTTAATCTCACTTTCTACCTTTATAATTGAAACCCGTAAGTT
TTTTAAATCTCACATTATACC
Found at i:33700 original size:18 final size:18
Alignment explanation
Indices: 33672--33718 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
33662 AATAATTTAA
33672 ATTAAATTAAAACTAAAAT
1 ATTAAA-TAAAACTAAAAT
*
33691 ATTAAAT-AAAGTAAAAT
1 ATTAAATAAAACTAAAAT
33708 ACTTAAATAAA
1 A-TTAAATAAA
33719 TTAAATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 7 0.28
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
ATTAAATAAAACTAAAAT
Found at i:33726 original size:17 final size:18
Alignment explanation
Indices: 33685--33723 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
33675 AAATTAAAAC
33685 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
33702 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
33720 TAAA
1 TAAA
33724 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:33994 original size:50 final size:51
Alignment explanation
Indices: 33935--34041 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
33925 GTGGATCAGG
* * * * *
33935 GGGCGCACTATA-CCCACGTGGCGCTAAATCACCGTATATCGCGGGGCAGA
1 GGGCACACTATATCCCACGTGACGCCAAATCACCATATAACGCGGGGCAGA
* * * * *
33985 GGGCACACTATATTCTACGTGACGCCAAATCAGCATATAACGCGGTGCAGG
1 GGGCACACTATATCCCACGTGACGCCAAATCACCATATAACGCGGGGCAGA
34036 GGGCAC
1 GGGCAC
34042 GTTTTACTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
50 11 0.24
51 35 0.76
ACGTcount: A:0.26, C:0.28, G:0.29, T:0.17
Consensus pattern (51 bp):
GGGCACACTATATCCCACGTGACGCCAAATCACCATATAACGCGGGGCAGA
Found at i:42891 original size:11 final size:11
Alignment explanation
Indices: 42887--42929 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
42877 AGAAAGAAAG
42887 AAGAAGAAAAA
1 AAGAAGAAAAA
42898 AAGAAGAAAAA
1 AAGAAGAAAAA
42909 AAGAAGAAAAA
1 AAGAAGAAAAA
42920 TGAAGAAGAA
1 --AAGAAGAA
42930 GATGTGGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.73
13 8 0.27
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:44494 original size:22 final size:21
Alignment explanation
Indices: 44464--44516 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
44454 GATTGAACTT
*
44464 TGAACTTTTGAAGGGCAACCCC
1 TGAA-TTTTTAAGGGCAACCCC
** *
44486 TGAATTTTTTTGTGCAACCCC
1 TGAATTTTTAAGGGCAACCCC
44507 TGAATTTTTA
1 TGAATTTTTA
44517 TCCTGGTTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (21 bp):
TGAATTTTTAAGGGCAACCCC
Found at i:47198 original size:34 final size:34
Alignment explanation
Indices: 47160--47237 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
47150 ATTCGTGTGC
*
47160 ATTTGATGATTATACCTGGAATGCATATTTCTGT
1 ATTTGATGATTACACCTGGAATGCATATTTCTGT
* * *
47194 ATTTGGTGATTGCACCTGGAGTGCATATTTCTGT
1 ATTTGATGATTACACCTGGAATGCATATTTCTGT
47228 -TTCTGATGAT
1 ATT-TGATGAT
47238 AGCACATGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 2 0.05
34 36 0.95
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (34 bp):
ATTTGATGATTACACCTGGAATGCATATTTCTGT
Found at i:47248 original size:34 final size:34
Alignment explanation
Indices: 47176--47256 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
47166 TGATTATACC
* * * *
47176 TGGAATGCATATTTCTGTATTTGGTGATTGCACC
1 TGGAGTGCATATTTCTGTATTTGATGATAGCACA
47210 TGGAGTGCATATTTCTGT-TTCTGATGATAGCACA
1 TGGAGTGCATATTTCTGTATT-TGATGATAGCACA
*
47244 TGGAGTGCTTATT
1 TGGAGTGCATATT
47257 GCGCACACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 2 0.05
34 39 0.95
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.41
Consensus pattern (34 bp):
TGGAGTGCATATTTCTGTATTTGATGATAGCACA
Found at i:50848 original size:17 final size:17
Alignment explanation
Indices: 50826--50895 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
50816 CATCTTATAT
50826 CTGTAAATATATGATAA
1 CTGTAAATATATGATAA
* * * *
50843 CTGTAATTATTTTATAT
1 CTGTAAATATATGATAA
* *
50860 CTGTAAATATCTAATAA
1 CTGTAAATATATGATAA
*
50877 CTATAAATATATGATAA
1 CTGTAAATATATGATAA
50894 CT
1 CT
50896 AAAAATCATC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (17 bp):
CTGTAAATATATGATAA
Found at i:54539 original size:3 final size:3
Alignment explanation
Indices: 54471--54519 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
54461 CCATTTGCTT
*
54471 TTA TTA TTA TTA ATA TTA TTA -TA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54517 TTA
1 TTA
54520 ATAAAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:55891 original size:41 final size:41
Alignment explanation
Indices: 55811--55891 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
55801 ACTTTTTATA
* *
55811 TTTTAATATTATAGTTTTAATTTCATTTATTTTAGTTATTG
1 TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
* *
55852 TTTTAATTTTATA-TGTTTATTTTCA-ATATATTTAATTATT
1 TTTTAATATTATAGT-TTTAATTTCATATAT-TTTAATTATT
55892 ATTATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.64
Consensus pattern (41 bp):
TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
Found at i:56165 original size:150 final size:148
Alignment explanation
Indices: 55982--56274 Score: 389
Period size: 146 Copynumber: 2.0 Consensus size: 148
55972 TAAAAATCCT
*
55982 ATTTATAAATTTAATTTTATATAAATTACTTTTAAGAAAAATAATCATATT-TTAATATTTATTT
1 ATTTATAAATTTAATTTTATATAAATTACTTTT-AGAAAAAT-AT--T-TTATTAATATTTAGTT
56046 ATTTTTTAATATTAAGAAATGGGTCGTCTTAAAGC-ACATAGAAGTCATTTTCTGATATTCT-TA
61 ATTTTTTAATATTAAGAAATGGGTCGTCTTAAAGCAAC-TAGAAGTCATTTTCTGATATT-TATA
56109 AATAAATAAATATCCTATTTTTATA
124 AATAAATAAATATCCTATTTTTATA
* * * * * *
56134 ATTTATATA-TTAA-TTTATTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTAGTTATTTT
1 ATTTATAAATTTAATTTTATATAAATTACTTTTAGAAAAATATTTTATTAATATTTAGTTATTTT
* * *
56197 TTAATATTAAGAAATGGGTTGTCTTAAAGCAACTAGAAGTCCTTTTCTGATATTTATAAGTAAAT
66 TTAATATTAAGAAATGGGTCGTCTTAAAGCAACTAGAAGTCATTTTCTGATATTTATAAATAAAT
*
56262 AAATATCTTATTT
131 AAATATCCTATTT
56275 ATAAAAATAA
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
145 3 0.02
146 87 0.69
147 2 0.02
148 1 0.01
149 7 0.06
150 15 0.12
151 4 0.03
152 8 0.06
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (148 bp):
ATTTATAAATTTAATTTTATATAAATTACTTTTAGAAAAATATTTTATTAATATTTAGTTATTTT
TTAATATTAAGAAATGGGTCGTCTTAAAGCAACTAGAAGTCATTTTCTGATATTTATAAATAAAT
AAATATCCTATTTTTATA
Found at i:56810 original size:27 final size:26
Alignment explanation
Indices: 56749--56826 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
56739 AATTCTTTCC
*
56749 TTTCAAAAT-TTTTATATACTTATTTT
1 TTTCATAATATTTTATATA-TTATTTT
56775 TTTCATAATATTTATATATATTATTTT
1 TTTCATAATATTT-TATATATTATTTT
* *
56802 TTT-ATTAATGTTTT-TATTTTATTTT
1 TTTCA-TAATATTTTATATATTATTTT
56827 AAAATATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
25 10 0.22
26 10 0.22
27 20 0.43
28 6 0.13
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (26 bp):
TTTCATAATATTTTATATATTATTTT
Found at i:65875 original size:23 final size:23
Alignment explanation
Indices: 65840--65897 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
65830 GCTTAAAGAA
* *
65840 GAAAGAAAGAAAA-GAACAAAAAT
1 GAAAGAAA-AAAATAAAAAAAAAT
65863 GAAATGAAAAAAATAAAAAAAAAT
1 GAAA-GAAAAAAATAAAAAAAAAT
*
65887 TAAAGAAAAAA
1 GAAAGAAAAAA
65898 TGAAAATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.09
Consensus pattern (23 bp):
GAAAGAAAAAAATAAAAAAAAAT
Found at i:65876 original size:14 final size:13
Alignment explanation
Indices: 65850--65902 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
65840 GAAAGAAAGA
65850 AAAGAACAAAAATG
1 AAAGAA-AAAAATG
65864 AAATGAAAAAAAT-
1 AAA-GAAAAAAATG
*
65877 -AA-AAAAAAATT
1 AAAGAAAAAAATG
65888 AAAG-AAAAAATG
1 AAAGAAAAAAATG
65900 AAA
1 AAA
65903 ATGAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 8 0.24
12 14 0.41
14 9 0.26
15 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (13 bp):
AAAGAAAAAAATG
Found at i:65928 original size:36 final size:35
Alignment explanation
Indices: 65857--65925 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
65847 AGAAAAGAAC
*
65857 AAAAATGAAATGAAAAAAATAAAAAAAAATTAAAGA
1 AAAAATGAAATG-AAAAAATAAAAAAAAATAAAAGA
*
65893 AAAAATGAAAATG-AAAAATAAAATAAAATAAAA
1 AAAAATG-AAATGAAAAAATAAAAAAAAATAAAA
65926 AGAGAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 18 0.60
36 7 0.23
37 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.14
Consensus pattern (35 bp):
AAAAATGAAATGAAAAAATAAAAAAAAATAAAAGA
Done.