Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008636.1 Hibiscus syriacus cultivar Beakdansim tig00111609_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: 90336
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4262 original size:175 final size:177
Alignment explanation
Indices: 3820--4349 Score: 1003
Period size: 175 Copynumber: 3.0 Consensus size: 177
3810 AATGTTAAAA
*
3820 ACTTATCCAAGAAATTCGAACAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAA-CA
1 ACTTATCCAAGAAACTCGAACAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACCA
*
3884 TAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTAGAATCAAATTTCGTGAGAC
66 TAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGAC
3949 AATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
131 AATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
3996 ACTTATCCAAGAAACTCGAACAAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
1 ACTTATCCAAGAAACTCGAAC-AAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
4061 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
65 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
4126 CAA-TATCTTCAAA-TTAAAACACGTGTTCAAATCCGATAGGAGCAGG
130 CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
*
4172 ACTTATCCAAGAAACTCGAACAAAAATCGGTACGAACAGATCTGACTGTACCGGTAAACGAACCA
1 ACTTATCCAAGAAACTCGAACAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACCA
4237 TAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGAC
66 TAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGAC
4302 AATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
131 AATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
4349 A
1 A
4350 TAAATCAACA
Statistics
Matches: 347, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
175 110 0.32
176 84 0.24
177 85 0.24
178 68 0.20
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (177 bp):
ACTTATCCAAGAAACTCGAACAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACCA
TAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGAC
AATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
Found at i:7401 original size:2 final size:2
Alignment explanation
Indices: 7339--7383 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
7329 TGTCAAAAAT
7339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7381 TA T
1 TA T
7384 CCACCTTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12411 original size:19 final size:19
Alignment explanation
Indices: 12387--12427 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
12377 GAAAATTTTT
12387 ATAGAAAATATCAATAGTG
1 ATAGAAAATATCAATAGTG
12406 ATAGAAAATATCAATAGTG
1 ATAGAAAATATCAATAGTG
12425 ATA
1 ATA
12428 TTTTTATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.27
Consensus pattern (19 bp):
ATAGAAAATATCAATAGTG
Found at i:13741 original size:22 final size:21
Alignment explanation
Indices: 13700--13741 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
13690 ATAATGCATT
* *
13700 AATTTTTAAAATTTTAAATTC
1 AATTATTAAAATATTAAATTC
13721 AATTATTAATAATATTAAATT
1 AATTATTAA-AATATTAAATT
13742 TTATATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATTAAAATATTAAATTC
Found at i:20012 original size:11 final size:11
Alignment explanation
Indices: 19982--20019 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
19972 AAAATTATTA
19982 ATTATTTA-AT
1 ATTATTTATAT
19992 A-TATTATATAT
1 ATTATT-TATAT
20003 ATTATTTATAT
1 ATTATTTATAT
20014 ATTATT
1 ATTATT
20020 CATCTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 3 0.12
11 14 0.56
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATTTATAT
Found at i:20123 original size:7 final size:7
Alignment explanation
Indices: 20089--20121 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
20079 ATAAACCAAA
20089 AATATTT
1 AATATTT
20096 AATATTT
1 AATATTT
20103 AATATTT
1 AATATTT
*
20110 AATATAT
1 AATATTT
20117 AATAT
1 AATAT
20122 ATCATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AATATTT
Found at i:21507 original size:65 final size:65
Alignment explanation
Indices: 21403--21589 Score: 225
Period size: 65 Copynumber: 2.9 Consensus size: 65
21393 CACTTTGATG
* * * *
21403 CATCGATACATTTCTT-GTTTTATTTAAACATCGAATGCATTTTGCGTACTGATGCACATACAAT
1 CATCGATACA-CTCTTGGTTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCACAAACAAT
21467 A
65 A
* * * *
21468 CATCGATATACTCTTGGTTTTATTGAAACATCGAATGCATTTTGTGTACCGATGCATAAACAATG
1 CATCGATACACTCTTGGTTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCACAAACAATA
* * * * *
21533 CATCGATACACTCTTGGCTCTT-TTGAAACATCAAATGTAATTAGTGTACTGATGCAC
1 CATCGATACACTCTTGG-TTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCAC
21590 CCCAGGTGTA
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
64 4 0.04
65 97 0.93
66 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (65 bp):
CATCGATACACTCTTGGTTTTATTGAAACATCGAATGCATTTTGTGTACTGATGCACAAACAATA
Found at i:23123 original size:6 final size:6
Alignment explanation
Indices: 23108--23175 Score: 127
Period size: 6 Copynumber: 11.3 Consensus size: 6
23098 GAGTGATTCG
*
23108 GATGAA GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC
1 GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC
23156 GATGAC GATGAC GATGAC GA
1 GATGAC GATGAC GATGAC GA
23176 GGAAATGACA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.35, C:0.15, G:0.34, T:0.16
Consensus pattern (6 bp):
GATGAC
Found at i:27455 original size:44 final size:44
Alignment explanation
Indices: 27387--27488 Score: 168
Period size: 44 Copynumber: 2.3 Consensus size: 44
27377 TTTTGCTAAG
*
27387 TGCATTGATACACTATGAAAGTGTACCGATGCATTCCTTGAATA
1 TGCATCGATACACTATGAAAGTGTACCGATGCATTCCTTGAATA
* *
27431 TGCATCGATACACTATGAAGGTGTACCGATGCATTCCTTGAATG
1 TGCATCGATACACTATGAAAGTGTACCGATGCATTCCTTGAATA
*
27475 TGCATCAATACACT
1 TGCATCGATACACT
27489 CTGCAGTGTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGTACCGATGCATTCCTTGAATA
Found at i:27472 original size:23 final size:23
Alignment explanation
Indices: 27402--27472 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
27392 TGATACACTA
27402 TGAAAGTGTACCGATGCATTCCT
1 TGAAAGTGTACCGATGCATTCCT
* * *
27425 TGAATA-TGCATCGATACA---CT
1 TGAA-AGTGTACCGATGCATTCCT
*
27445 ATGAAGGTGTACCGATGCATTCCT
1 -TGAAAGTGTACCGATGCATTCCT
27469 TGAA
1 TGAA
27473 TGTGCATCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 2 0.06
21 13 0.37
23 17 0.49
24 3 0.09
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (23 bp):
TGAAAGTGTACCGATGCATTCCT
Found at i:28005 original size:12 final size:12
Alignment explanation
Indices: 27976--28010 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
27966 ATATTATGAT
*
27976 TTTTCAAATATTG
1 TTTTCAAA-ATAG
27989 TTTTCAAAATAG
1 TTTTCAAAATAG
28001 TTTTCAAAAT
1 TTTTCAAAAT
28011 TTTGCCCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (12 bp):
TTTTCAAAATAG
Found at i:29488 original size:20 final size:20
Alignment explanation
Indices: 29450--29493 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29440 AAATGTTTAT
*
29450 ATTTGGTTTTGATTGTTTGA
1 ATTTGGTTTTGATTATTTGA
*
29470 ATTTGG-TTTGATTAATTTGC
1 ATTTGGTTTTGATT-ATTTGA
29490 ATTT
1 ATTT
29494 AAGGTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.59
Consensus pattern (20 bp):
ATTTGGTTTTGATTATTTGA
Found at i:30267 original size:65 final size:65
Alignment explanation
Indices: 30097--30285 Score: 236
Period size: 65 Copynumber: 2.9 Consensus size: 65
30087 ACAAACTTTG
* * * * * * * *
30097 ATGCATCGATACACTCATTGTTTTATTTAAACATCGAATGCATTTTATGTAGCGATGCACATACA
1 ATGCATCGATACACTCCTGGTCTTATTAAAACATCGAATGTATTTTGTGTACCGATGCACAGACA
*
30162 ATGCATCGATACACTCCTGGTTTTATTAAAACATCGAATGTATTTTGTGTACCGATGCACAGACA
1 ATGCATCGATACACTCCTGGTCTTATTAAAACATCGAATGTATTTTGTGTACCGATGCACAGACA
* * * * *
30227 ATGCATCGGTACACTCCTGGCTCTT-TTGAAACATCGAATGTAATTAGTGTACCAATGCA
1 ATGCATCGATACACTCCTGG-TCTTATTAAAACATCGAATGTATTTTGTGTACCGATGCA
30286 TCCCAGGTGT
Statistics
Matches: 110, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 107 0.97
66 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (65 bp):
ATGCATCGATACACTCCTGGTCTTATTAAAACATCGAATGTATTTTGTGTACCGATGCACAGACA
Found at i:32435 original size:21 final size:22
Alignment explanation
Indices: 32393--32434 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
32383 AAACCATTCA
32393 GGGGGGAATCGGTACCCTTTTG
1 GGGGGGAATCGGTACCCTTTTG
*
32415 GGGGGGAATCGGTTCCCTTT
1 GGGGGGAATCGGTACCCTTT
32435 GAGCAATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.19, G:0.40, T:0.29
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTTTTG
Found at i:35078 original size:21 final size:22
Alignment explanation
Indices: 35052--35132 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 22
35042 CAGAACCCCA
*
35052 GGGGGGTATCGATTCCCCT-AT
1 GGGGGGAATCGATTCCCCTCAT
* * *
35073 GGGGGGAATCGGTTCCCTTTCAA
1 GGGGGGAATCGATTCCC-CTCAT
* *
35096 AGGGGGAATCGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCTCAT
*
35117 -GGGGGTATCGATTCCC
1 GGGGGGAATCGATTCCC
35133 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 11 0.23
21 20 0.42
22 3 0.06
23 14 0.29
ACGTcount: A:0.16, C:0.23, G:0.35, T:0.26
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCCTCAT
Found at i:35126 original size:20 final size:21
Alignment explanation
Indices: 35053--35134 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
35043 AGAACCCCAG
* *
35053 GGGGGTATCGATTCCC-CTAT
1 GGGGGAATCGATTCCCTCAAT
* *
35073 GGGGGGAATCGGTTCCCTTTCAAA
1 -GGGGGAATCGATTCCC--TCAAT
*
35097 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGATTCCCTCAAT
*
35117 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
35135 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.33
21 16 0.31
23 16 0.31
24 2 0.04
ACGTcount: A:0.16, C:0.24, G:0.33, T:0.27
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAT
Found at i:38959 original size:22 final size:21
Alignment explanation
Indices: 38917--38956 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38907 GAGTTTATTT
*
38917 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
38938 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
38957 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:42714 original size:18 final size:18
Alignment explanation
Indices: 42693--42761 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 18
42683 GCCAAATTCG
42693 GTATCGATACTCAGGAAA
1 GTATCGATACTCAGGAAA
42711 GTATCGATAC-CACGGACCAGAA
1 GTATCGATACTCA-GG---A-AA
*
42733 GTATCGATACTCAAGAAAGA
1 GTATCGATACTC-AGGAA-A
42753 GTATCGATA
1 GTATCGATA
42762 GCAACCATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
17 2 0.05
18 12 0.29
19 1 0.02
20 11 0.26
21 1 0.02
22 12 0.29
23 2 0.05
24 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (18 bp):
GTATCGATACTCAGGAAA
Found at i:44473 original size:57 final size:57
Alignment explanation
Indices: 44374--44483 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 57
44364 ACGCCCATTA
**
44374 TATGAGTATATGTTTTATGTGGATAAATGATAATATGAATAATGTTATGTGAAATAC
1 TATGAGTATATGTTTTATGTGGATAAATGATAATATGAATAATACTATGTGAAATAC
*
44431 TATGAGTATATGTTTTATGTGAGA-AAATGATAA-ATTGCATAATACTATGTGAA
1 TATGAGTATATGTTTTATGTG-GATAAATGATAATA-TGAATAATACTATGTGAA
44484 TTATTTATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
56 1 0.02
57 45 0.94
58 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (57 bp):
TATGAGTATATGTTTTATGTGGATAAATGATAATATGAATAATACTATGTGAAATAC
Found at i:44612 original size:23 final size:22
Alignment explanation
Indices: 44559--44635 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
44549 AGTCGAGGGT
* *
44559 TCTATGCGGTCGTTCGGGACAA
1 TCTATGTGGTCTTTCGGGACAA
44581 T-TATGTGGT-TATTCGGGACAA
1 TCTATGTGGTCT-TTCGGGACAA
44602 TTCTATGTGGTCTTTCGGGACAGA
1 -TCTATGTGGTCTTTCGGGACA-A
44626 TCTATGTGGT
1 TCTATGTGGT
44636 ACTTCGGTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
21 17 0.35
22 2 0.04
23 27 0.56
24 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (22 bp):
TCTATGTGGTCTTTCGGGACAA
Found at i:44684 original size:24 final size:24
Alignment explanation
Indices: 44636--44684 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
44626 TCTATGTGGT
* * *
44636 ACTTCGGTGCATATTCTACATGGA
1 ACTTCAGTGCAAATTCTACACGGA
*
44660 ACTTCAGTGCAAATTCTACGCGGA
1 ACTTCAGTGCAAATTCTACACGGA
44684 A
1 A
44685 GATTCAACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (24 bp):
ACTTCAGTGCAAATTCTACACGGA
Found at i:45815 original size:31 final size:31
Alignment explanation
Indices: 45758--45827 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
45748 ATATCCATAA
*
45758 TTGAATGAATATTTGTAAACCCTATTTGTAT
1 TTGAATGAATATTTGTAAACCCTATTTCTAT
* * **
45789 TTGAATGAATGTTTGTAAGCTTTATTTCTAT
1 TTGAATGAATATTTGTAAACCCTATTTCTAT
*
45820 TTAAATGA
1 TTGAATGA
45828 CCCCATTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.47
Consensus pattern (31 bp):
TTGAATGAATATTTGTAAACCCTATTTCTAT
Found at i:48271 original size:18 final size:18
Alignment explanation
Indices: 48216--48271 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
48206 AAAGTAACCT
48216 AAATTAATTTAAACAAAA
1 AAATTAATTTAAACAAAA
*
48234 AAA-TAAATTAATAC----
1 AAATTAATTTAA-ACAAAA
48248 AAATTAATTTAAACAAAA
1 AAATTAATTTAAACAAAA
48266 AAATTA
1 AAATTA
48272 CCTTCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
17 7 0.23
18 11 0.37
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATTAATTTAAACAAAA
Found at i:48779 original size:22 final size:22
Alignment explanation
Indices: 48748--48789 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
48738 ACATTATCTC
48748 TAATCTATTATCATAAAAAATAT
1 TAATCTATTAT-ATAAAAAATAT
*
48771 TAAT-TATTATTTAAAAAAT
1 TAATCTATTATATAAAAAAT
48790 CATTTATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 6 0.33
23 4 0.22
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATCTATTATATAAAAAATAT
Found at i:50160 original size:21 final size:21
Alignment explanation
Indices: 50136--50240 Score: 61
Period size: 21 Copynumber: 5.1 Consensus size: 21
50126 GCAAATTCGC
50136 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** ***
50157 GTTGAAAATCGCAACGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
50177 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
50198 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * * *
50218 TTTCCATTTCGTGTTACGATA
1 GTTGCATTTCGCGTTGCGATA
50239 GT
1 GT
50241 CTACAGTTGT
Statistics
Matches: 55, Mismatches: 27, Indels: 4
0.64 0.31 0.05
Matches are distributed among these distances:
20 25 0.45
21 30 0.55
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:50185 original size:41 final size:41
Alignment explanation
Indices: 50140--50240 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
50130 ATTCGCGTTG
50140 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
***
50181 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
* *
50222 CATTTCGTGTTACGATAGT
1 CATTTCGCGTTGCGATAGT
50241 CTACAGTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
Found at i:50254 original size:22 final size:22
Alignment explanation
Indices: 50229--50281 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
50219 TTCCATTTCG
*
50229 TGTTACGATAGTCTACAGTTGT
1 TGTTGCGATAGTCTACAGTTGT
*
50251 TGTTGTGATAGTCTACAGTTGT
1 TGTTGCGATAGTCTACAGTTGT
*
50273 CGTTGCGAT
1 TGTTGCGAT
50282 TTTCCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (22 bp):
TGTTGCGATAGTCTACAGTTGT
Found at i:50398 original size:19 final size:19
Alignment explanation
Indices: 50374--50413 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
50364 TGTCGAAGAC
50374 ACGTATTACCACGACCACG
1 ACGTATTACCACGACCACG
50393 ACGTATTACCACGACCACG
1 ACGTATTACCACGACCACG
50412 AC
1 AC
50414 CACGACCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.15, T:0.15
Consensus pattern (19 bp):
ACGTATTACCACGACCACG
Found at i:50919 original size:6 final size:6
Alignment explanation
Indices: 50910--50946 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
50900 GCCGTCCTTC
50910 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
50947 AATATGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:51073 original size:22 final size:22
Alignment explanation
Indices: 51046--51098 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
51036 AATTTGGAAA
51046 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
51068 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
51090 ATCGCAACG
1 ATCGCAACG
51099 TGAAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:59816 original size:27 final size:27
Alignment explanation
Indices: 59785--59845 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
59775 TCTATTTACA
59785 AAATCATATATCTATAGGAATGGTAAC
1 AAATCATATATCTATAGGAATGGTAAC
*
59812 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATATCTATAGGAATGGTAAC
59839 AAATCAT
1 AAATCAT
59846 CTCTATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (27 bp):
AAATCATATATCTATAGGAATGGTAAC
Found at i:63695 original size:27 final size:27
Alignment explanation
Indices: 63664--63724 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
63654 TCTATTTACA
63664 AAATCATATATCTATAGGAATGGTAAC
1 AAATCATATATCTATAGGAATGGTAAC
*
63691 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATATCTATAGGAATGGTAAC
63718 AAATCAT
1 AAATCAT
63725 CTCTATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (27 bp):
AAATCATATATCTATAGGAATGGTAAC
Found at i:64365 original size:13 final size:13
Alignment explanation
Indices: 64347--64374 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
64337 AAGGGAGAGG
64347 TAAGGATCCATTC
1 TAAGGATCCATTC
64360 TAAGGATCCATTC
1 TAAGGATCCATTC
64373 TA
1 TA
64375 TCTTGCTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (13 bp):
TAAGGATCCATTC
Found at i:65316 original size:2 final size:2
Alignment explanation
Indices: 65309--65352 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
65299 CACAACTCAA
65309 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
65351 AT
1 AT
65353 TCAAGAGTTT
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:69775 original size:29 final size:28
Alignment explanation
Indices: 69731--69824 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
69721 CTATGACCTT
* *
69731 CATTTCAAATTGATCCCTAAACTTTTAAA
1 CATTTTAAATT-ATCCTTAAACTTTTAAA
* *
69760 CATTTTAATTTTATCCTTAAACTATTACAA
1 CATTTTAA-ATTATCCTTAAACTTTTA-AA
* *
69790 TCATTCTAAATTAGTCCTTAAACTTTTGAA
1 -CATTTTAAATTA-TCCTTAAACTTTTAAA
69820 CATTT
1 CATTT
69825 CGTTTTCATC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
29 24 0.46
30 9 0.17
31 19 0.37
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (28 bp):
CATTTTAAATTATCCTTAAACTTTTAAA
Found at i:70084 original size:60 final size:59
Alignment explanation
Indices: 70020--70206 Score: 184
Period size: 60 Copynumber: 3.1 Consensus size: 59
70010 TATTTGGATG
* * *
70020 AGTTTGGGGATGAAATGAGAA-GATAT-AAAAGTTTATGGACAAATTTACAATGAGATTCAT
1 AGTTTGAGGATGAAATG-GAATG-T-TCAAAAGTTTAAGGACAAATTTACAATGAGAGTCAT
* *
70080 AGTTTGAGGATAAAATTGGAATGTTCAAAAGTTTAAGGACAAATTTAGAATGAGAGTCAT
1 AGTTTGAGGATGAAA-TGGAATGTTCAAAAGTTTAAGGACAAATTTACAATGAGAGTCAT
* * * * *
70140 AGTTTGAGGATGAAATTGGGATGTTTAAAAATTTATGGACTAATTTGA-AATGAG-GATCAT
1 AGTTTGAGGATGAAA-TGGAATGTTCAAAAGTTTAAGGACAAATTT-ACAATGAGAG-TCAT
*
70200 AATTTGA
1 AGTTTGA
70207 AGACATATAA
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
59 2 0.02
60 104 0.95
61 4 0.04
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (59 bp):
AGTTTGAGGATGAAATGGAATGTTCAAAAGTTTAAGGACAAATTTACAATGAGAGTCAT
Found at i:70130 original size:29 final size:30
Alignment explanation
Indices: 70046--70132 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 30
70036 GAGAAGATAT
* *
70046 AAAAGTTTATGGACAAATTTACAATGAGATTC
1 AAAAGTTTAAGGACAAATTTAGAAT--GATTC
* * * * *
70078 -ATAGTTTGAGGATAAAATTGGAATG-TTC
1 AAAAGTTTAAGGACAAATTTAGAATGATTC
70106 AAAAGTTTAAGGACAAATTTAGAATGA
1 AAAAGTTTAAGGACAAATTTAGAATGA
70133 GAGTCATAGT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
28 3 0.07
29 21 0.51
31 17 0.41
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.31
Consensus pattern (30 bp):
AAAAGTTTAAGGACAAATTTAGAATGATTC
Found at i:72558 original size:27 final size:27
Alignment explanation
Indices: 72527--72582 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
72517 ATAAAAGACC
72527 TTGGGTGACAGTTCTTTAGTAAGCGAG
1 TTGGGTGACAGTTCTTTAGTAAGCGAG
72554 TTGGGTGACAGTTCTTTAGTAAGCGAG
1 TTGGGTGACAGTTCTTTAGTAAGCGAG
72581 TT
1 TT
72583 ATGAGTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.36
Consensus pattern (27 bp):
TTGGGTGACAGTTCTTTAGTAAGCGAG
Found at i:75883 original size:9 final size:9
Alignment explanation
Indices: 75871--75925 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
75861 ATAAAGGTAA
75871 AAATAAAAT
1 AAATAAAAT
* *
75880 AAATGAAAC
1 AAATAAAAT
*
75889 AAACAAAAT
1 AAATAAAAT
75898 AAATAAAAT
1 AAATAAAAT
75907 AAATAAAAT
1 AAATAAAAT
75916 GAATATAAAA
1 -AA-ATAAAA
75926 AGAAATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
9 30 0.79
10 2 0.05
11 6 0.16
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:78190 original size:106 final size:106
Alignment explanation
Indices: 78058--79008 Score: 1434
Period size: 106 Copynumber: 9.0 Consensus size: 106
78048 GCCCCTTCCA
* * * * *
78058 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGAAAAATTATTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
* * * *
78122 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTATGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
78164 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATT-AGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTATTTGTTGACAA
* * *
78228 CCAACGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
78270 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
* *
78335 CAGCGGTCCCTTCGTCTTGAAGTTGAACTTGCGTCGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
78376 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
*
78441 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
78482 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
*
78547 CAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
78588 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
*
78653 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
78694 AGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT-GTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
78758 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
78799 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-GTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
* * * *
78863 TAACGGTCCCTTTGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
78904 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAG----TTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
* * *
78965 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
79006 AGT
1 AGT
79009 GATATCTTCC
Statistics
Matches: 789, Mismatches: 52, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
102 46 0.06
103 1 0.00
105 200 0.25
106 540 0.68
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:90188 original size:20 final size:20
Alignment explanation
Indices: 90152--90189 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
90142 ATAAAGAACG
*
90152 ATAAGATAAAGTCATAAAAA
1 ATAAGATAAAGTAATAAAAA
90172 ATAAGATAATA-TAATAAA
1 ATAAGATAA-AGTAATAAA
90190 GGAAAGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (20 bp):
ATAAGATAAAGTAATAAAAA
Found at i:90209 original size:2 final size:2
Alignment explanation
Indices: 90202--90226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90192 AAAGAAACAA
90202 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
90227 ATCTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.