Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008169.1 Hibiscus syriacus cultivar Beakdansim tig00110751_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: 58749
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5733 original size:20 final size:18
Alignment explanation
Indices: 5708--5771 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 18
5698 ATAGCAAAGG
5708 TTATTTTTTATATTTGATCT
1 TTATTTTTTAT-TTTGAT-T
*
5728 TTATTTTTCATCTTTGTATT
1 TTATTTTTTAT-TTTG-ATT
*
5748 TTATATTTTATTTT-ATT
1 TTATTTTTTATTTTGATT
5765 TTATTTT
1 TTATTTT
5772 CGAAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 9 0.24
19 3 0.08
20 24 0.63
21 2 0.05
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (18 bp):
TTATTTTTTATTTTGATT
Found at i:6608 original size:22 final size:21
Alignment explanation
Indices: 6583--6637 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
6573 TATCTTTTAT
*
6583 TTTTTATTTATATTTTTAAATA
1 TTTTTATTTATA-ATTTAAATA
* *
6605 TTTTAATTTAGTAATTTAATTA
1 TTTTTATTTA-TAATTTAAATA
*
6627 TTTTTCTTTAT
1 TTTTTATTTAT
6638 TTTATCTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTATTTATAATTTAAATA
Found at i:10428 original size:12 final size:12
Alignment explanation
Indices: 10411--10451 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
10401 TAGTAAAAAG
10411 AAAAAGAAAGAA
1 AAAAAGAAAGAA
10423 AAAAAGAAA-AA
1 AAAAAGAAAGAA
10434 AAAAGAGAAAGAA
1 AAAA-AGAAAGAA
10447 AAAAA
1 AAAAA
10452 AGAGAGGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.22
12 15 0.56
13 6 0.22
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:10428 original size:18 final size:19
Alignment explanation
Indices: 10405--10454 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
10395 TTCAAATAGT
10405 AAAAAGAAAAAGAAAGA-A
1 AAAAAGAAAAAGAAAGAGA
*
10423 AAAAAGAAAAAAAAAGAGA
1 AAAAAGAAAAAGAAAGAGA
10442 AAGAAA-AAAAAGA
1 AA-AAAGAAAAAGA
10455 GAGGCTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 16 0.57
19 9 0.32
20 3 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAGAGA
Found at i:10442 original size:24 final size:24
Alignment explanation
Indices: 10405--10451 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
10395 TTCAAATAGT
10405 AAAAAGAAAAAGAAAGAAAAAAAG
1 AAAAAGAAAAAGAAAGAAAAAAAG
10429 AAAAA-AAAAGAGAAAGAAAAAAA
1 AAAAAGAAAA-AGAAAGAAAAAAA
10452 AGAGAGGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAGAAAAAAAG
Found at i:10444 original size:16 final size:15
Alignment explanation
Indices: 10405--10456 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
10395 TTCAAATAGT
*
10405 AAAAAGAAAAAG-AA
1 AAAAAGAGAAAGAAA
*
10419 AGAAA-A-AAAGAAAA
1 AAAAAGAGAAAG-AAA
10433 AAAAAGAGAAAGAAA
1 AAAAAGAGAAAGAAA
10448 AAAAAGAGA
1 AAAAAGAGA
10457 GGCTATAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 4 0.12
13 1 0.03
14 10 0.31
15 13 0.41
16 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAGAAA
Found at i:12399 original size:73 final size:73
Alignment explanation
Indices: 12313--12645 Score: 499
Period size: 73 Copynumber: 4.6 Consensus size: 73
12303 CAAAACAAAG
* *
12313 ATTTATCTTACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAATTTTCACTTG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAGTTTCACTTG
12378 AAATAGCA
66 AAATAGCA
* * *
12386 ATTTATCTCACTTGAGATTGTTGTTCTTAAAACAAACAGTTTCTCGCTTGAGAAAGTTTCACTTG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAGTTTCACTTG
12451 AAATAGCA
66 AAATAGCA
* * * *
12459 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTTTGTCGCTAGAGAAGGTTTCACTTG
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAGTTTCACTTG
*
12524 AAATAACA
66 AAATAGCA
* * *
12532 ATTTATCTCACTTGAAATTGTTTTTCTTAAAAC-AACTTTTTTCTCGCTGGAAAAAGTTTCACTT
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAC-TGTTTCTCGCTGGAGAAAGTTTCACTT
12596 GAAATAGC-
65 GAAATAGCA
* *
12604 ATTTATCTCACTTGATATTGTTTTTCTTAAAACGAACCTGTT
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAACTGTT
12646 GAGTTAATCG
Statistics
Matches: 236, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
72 35 0.15
73 199 0.84
74 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (73 bp):
ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAGTTTCACTTG
AAATAGCA
Found at i:13470 original size:64 final size:66
Alignment explanation
Indices: 13369--13527 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 66
13359 GCACCAAGTA
* * * * ***
13369 TGCATCGATGCATTAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATGGCTT
1 TGCATCGATGCATCAAATGCATTTGATGTTTTGAAAAATAGCCAGAATGCATCGATGCATGGAGA
13432 G
66 G
**
13433 TGCATCGATGCATCAAATGCATTTGATGTTTTG-AAAATATTCAGAATGCATCGATGCATGGAGA
1 TGCATCGATGCATCAAATGCATTTGATGTTTTGAAAAATAGCCAGAATGCATCGATGCATGGAGA
13497 G
66 G
* **
13498 TGCATCGGTGCATGGAATGCATTTGATGTT
1 TGCATCGATGCATCAAATGCATTTGATGTT
13528 CAATTAATTC
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
64 34 0.42
65 47 0.58
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (66 bp):
TGCATCGATGCATCAAATGCATTTGATGTTTTGAAAAATAGCCAGAATGCATCGATGCATGGAGA
G
Found at i:14213 original size:17 final size:17
Alignment explanation
Indices: 14191--14234 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
14181 AATAGTCAAG
*
14191 CATCCAAATATCATAAA
1 CATCCAAATAACATAAA
*
14208 CATCCAAACAAACATAAA
1 CATCCAAA-TAACATAAA
14226 CATCCAAAT
1 CATCCAAAT
14235 CAAAAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (17 bp):
CATCCAAATAACATAAA
Found at i:14225 original size:18 final size:19
Alignment explanation
Indices: 14202--14238 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
14192 ATCCAAATAT
14202 CATAAACATCCAAA-CAAA
1 CATAAACATCCAAATCAAA
14220 CATAAACATCCAAATCAAA
1 CATAAACATCCAAATCAAA
14239 AAGTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (19 bp):
CATAAACATCCAAATCAAA
Found at i:22096 original size:64 final size:65
Alignment explanation
Indices: 21991--22153 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 65
21981 CGGTGCACCA
*
21991 AGTGTGCATCGATGCATTAAATGCATTCGATG-TTTGAAAAATAGCCTAG-TGCATCGATGCATG
1 AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCC-AGATGCATCGATGCATG
22054 G
65 G
** **
22055 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAATGCATCGATGCATG
1 AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCCAG-ATGCATCGATGCATG
22119 G
65 G
* * **
22120 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATCAAATGCATTCGATGTT
22154 CAATTAATTC
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.02
64 36 0.42
65 47 0.55
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGG
Found at i:22129 original size:19 final size:17
Alignment explanation
Indices: 22102--22151 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
22092 AAAATATTCA
22102 GAATGCATCGATGCATG
1 GAATGCATCGATGCATG
*
22119 GAGAGTGCATCGGTGCATG
1 GA-A-TGCATCGATGCATG
22138 GAATGCATTCGATG
1 GAATGCA-TCGATG
22152 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 7 0.25
19 15 0.54
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (17 bp):
GAATGCATCGATGCATG
Found at i:22193 original size:65 final size:65
Alignment explanation
Indices: 21995--22201 Score: 189
Period size: 65 Copynumber: 3.2 Consensus size: 65
21985 GCACCAAGTG
* * * **
21995 TGCATCGATGCATTAAATGCATTCGATGTTTGAAAAATAGCCTAG--TGCATCGATGCATGG-CT
1 TGCATCGGTGCATCAAATGCATTCGATGTTT-CAAAATATTC-AGAATGCATCGATGCATGGAC-
22057 TG-
63 TGA
* *
22059 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAATGCATCGATGCATGGA--G
1 TGCATCGGTGCATCAAATGCATTCGATG-TTTCAAAATATTCAGAATGCATCGATGCATGGACTG
22122 A
65 A
** *
22123 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCG-ATGCATCGATGCATGGA
1 -TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAAT-ATTCA--GAATGCATCGATGCATGGA
22185 CTGA
62 CTGA
22189 TGCATCGGTGCAT
1 TGCATCGGTGCAT
22202 ACATTTGAAT
Statistics
Matches: 123, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
62 3 0.02
63 10 0.08
64 51 0.41
65 57 0.46
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAATATTCAGAATGCATCGATGCATGGACTGA
Found at i:22542 original size:73 final size:73
Alignment explanation
Indices: 22444--22811 Score: 555
Period size: 73 Copynumber: 5.1 Consensus size: 73
22434 AAATGTTTTC
* * *
22444 AACAGAACCTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGAAATTTATCTCACTTGAGATT-A
1 AACA-AACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGT
22508 TTTTCTTAA
65 TTTTCTTAA
* * *
22517 AACGAACTTTTTTCTCGC-TGAAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGGTTG
1 AACAAAC-TTTTTCTCGCTTG-AGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTG
22581 -TTTTCTTAA
64 TTTTTCTTAA
* * * *
22590 AA-AAAGTGTTTCGCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTT
1 AACAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTT
22654 TTTCTTAA
66 TTTCTTAA
* * *
22662 AACAAACTTTTTCTCGCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGTTTGTT
1 AACAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTT
22727 TTTCTTAA
66 TTTCTTAA
*
22735 AACAAACTTTTTCTCGCTTGATAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTT
1 AACAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTT
22800 TTTCTTAA
66 TTTCTTAA
22808 AACA
1 AACA
22812 TTTCCAGAGA
Statistics
Matches: 266, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
71 48 0.18
72 20 0.08
73 198 0.74
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (73 bp):
AACAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTT
TTTCTTAA
Found at i:22719 original size:144 final size:147
Alignment explanation
Indices: 22454--22811 Score: 591
Period size: 144 Copynumber: 2.5 Consensus size: 147
22444 AACAGAACCT
*
22454 TTTCTCGCTTGAGAAAGTTTCACTCGAAATAGA-AATTTATCTCACTTGAGATT-ATTTTCTTAA
1 TTTCTCGCTTGAGAAAGTTTCACTCGAAATA-ACAATTTATCTCACTTGAGATTGTTTTTCTTAA
*
22517 AACGAACTTTTTTCTCGCTGAAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGGTTG-
65 AACAAACTTTTTTCTCGCTGAAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGGTTGT
*
22581 TTTTCTTAAAA-AAAGTG
130 TTTTCTTAAAACAAACTG
*
22598 TTTCGCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAA
1 TTTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAA
* *
22663 ACAAAC-TTTTTCTCGCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGTTTGTT
66 ACAAACTTTTTTCTCGCTGAAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGGTTGTT
*
22727 TTTCTTAAAACAAACTT
131 TTTCTTAAAACAAACTG
* *
22744 TTTCTCGCTTGATAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAA
1 TTTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAA
22809 ACA
66 ACA
22812 TTTCCAGAGA
Statistics
Matches: 200, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
143 1 0.00
144 104 0.52
145 26 0.13
146 69 0.34
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (147 bp):
TTTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAA
ACAAACTTTTTTCTCGCTGAAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGGTTGTT
TTTCTTAAAACAAACTG
Found at i:22792 original size:37 final size:35
Alignment explanation
Indices: 22456--22794 Score: 138
Period size: 37 Copynumber: 9.3 Consensus size: 35
22446 CAGAACCTTT
* *
22456 TCTCGCTTGAGAAAGTTTCACTCGAAATAGAAATTTA
1 TCTCACTTGAGAAAGTTTCACT-GAAATA-CAATTTA
* * * *
22493 TCTCACTTGAGATTA-TTT-TCTTAAA-ACGAACTTTTT
1 TCTCACTTGAGA-AAGTTTCACTGAAATAC-AA--TTTA
*
22529 TCTCGC-TGAAGAAAGTTTCACTTGAAATAGCAATTTA
1 TCTCACTTG-AGAAAGTTTCAC-TGAAATA-CAATTTA
*** * * *
22566 TCTCACTTGAGGTTGTTT-TCTTAAA-AAAAGTGTT-
1 TCTCACTTGAGAAAGTTTCACTGAAATACAA-T-TTA
* *
22600 TCGCGCTTGAGAAAGTTTCACTCGAAATAACAATTTA
1 TCTCACTTGAGAAAGTTTCACT-GAAAT-ACAATTTA
** ** * *
22637 TCTCACTTGAGATTGTTTTTCTTAAA-ACAAACTTTT
1 TCTCACTTGAGAAAGTTTCACTGAAATAC-AA-TTTA
* *
22673 TCTCGCTGGAGAAAGTTTCACTTGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCAC-TGAAATA-CAATTTA
*** ** * *
22710 TCTCACTTGAGTTTGTTTTTCTTAAA-ACAAACTTTT
1 TCTCACTTGAGAAAGTTTCACTGAAATAC-AA-TTTA
* *
22746 TCTCGCTTGATAAAGTTTCACTCGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCACT-GAAATA-CAATTTA
22783 TCTCACTTGAGA
1 TCTCACTTGAGA
22795 TTGTTTTTCT
Statistics
Matches: 212, Mismatches: 62, Indels: 56
0.64 0.19 0.17
Matches are distributed among these distances:
33 2 0.01
34 21 0.10
35 19 0.09
36 65 0.31
37 83 0.39
38 16 0.08
39 5 0.02
40 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (35 bp):
TCTCACTTGAGAAAGTTTCACTGAAATACAATTTA
Found at i:23033 original size:120 final size:121
Alignment explanation
Indices: 22808--23122 Score: 402
Period size: 120 Copynumber: 2.6 Consensus size: 121
22798 TTTTTCTTAA
*
22808 AACATTTCCAG-AGAGAGTTCATAATGAGAAGAACTCATCTGAAGTTGAAGAAGAAGTTCATAAT
1 AACATTTCCAGAAGAGAGTTCATAATAAGAAGAACTCATCTGAA---GAAGAAGAAGTTCATAAT
* * * ** **
22872 GAGAATAACTTGTTCAACCTTTCGCTTGACTCTATCACATAAGGAGATAGAGAAGTATC
63 GAGAAGAACTTATTCAACATTTCGCTCAACTCTATCACATAAGGAGATAGAGAACCATC
* * *
22931 AACATTTCCAGAAGA-AGTTCATAATAAGAAGATCTCATCTGAAGAAGAAGAAGTTCATAATCAT
1 AACATTTCCAGAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAG
* * * * *
22995 AAGAACTTATTCAATATTTTGCTCAACTCTATCGCATAAGGAGATGGAGCACCATC
66 AAGAACTTATTCAACATTTCGCTCAACTCTATCACATAAGGAGATAGAGAACCATC
* * * *
23051 AACAATTCCAGAA-AGAGATCATAATAAGAATAACTCGTCTGAAGAAGAAGAAGTTCATAATGAG
1 AACATTTCCAGAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAG
23115 AAGAACTT
66 AAGAACTT
23123 GTTTAACCGT
Statistics
Matches: 167, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
119 1 0.01
120 126 0.75
123 37 0.22
124 3 0.02
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (121 bp):
AACATTTCCAGAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAG
AAGAACTTATTCAACATTTCGCTCAACTCTATCACATAAGGAGATAGAGAACCATC
Found at i:23687 original size:13 final size:13
Alignment explanation
Indices: 23665--23714 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
23655 AAGGTTATTT
23665 TTTATATTTTATA
1 TTTATATTTTATA
* **
23678 TTTATTTTTTAGC
1 TTTATATTTTATA
*
23691 TTTGTATTTTATA
1 TTTATATTTTATA
23704 TTT-TATTTTAT
1 TTTATATTTTAT
23715 TTTCGAAACA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 8 0.27
13 22 0.73
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTATATTTTATA
Found at i:23701 original size:20 final size:20
Alignment explanation
Indices: 23659--23708 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
23649 ATAGCAAAGG
*
23659 TTATTTTTTATATTTTATAT
1 TTATTTTTTAGATTTTATAT
*
23679 TTATTTTTTAGCTTTGTAT-T
1 TTATTTTTTAGATTT-TATAT
*
23699 TTATATTTTA
1 TTATTTTTTA
23709 TTTTATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (20 bp):
TTATTTTTTAGATTTTATAT
Found at i:24774 original size:2 final size:2
Alignment explanation
Indices: 24767--24805 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24757 AAGACCCTAA
24767 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
24806 ACCTTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31016 original size:9 final size:9
Alignment explanation
Indices: 31002--31029 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
30992 TGGCACTGTT
31002 CACGCGCCG
1 CACGCGCCG
31011 CACGCGCCG
1 CACGCGCCG
31020 CACGCGCCG
1 CACGCGCCG
31029 C
1 C
31030 CGCAGGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.57, G:0.32, T:0.00
Consensus pattern (9 bp):
CACGCGCCG
Found at i:31083 original size:10 final size:10
Alignment explanation
Indices: 31054--31122 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
31044 GCTGCTGGAA
31054 AACCGGTTTG
1 AACCGGTTTG
*
31064 -ACCAGTTTTG
1 AACC-GGTTTG
31074 AACCGGTTTG
1 AACCGGTTTG
* **
31084 -ATCGGTCCG
1 AACCGGTTTG
31093 AACCGGTTTG
1 AACCGGTTTG
*
31103 -ACCGGTCTG
1 AACCGGTTTG
31112 AACCGGTTTG
1 AACCGGTTTG
31122 A
1 A
31123 CCCGACCCGA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
9 17 0.38
10 25 0.56
11 3 0.07
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:31097 original size:19 final size:19
Alignment explanation
Indices: 31054--31124 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
31044 GCTGCTGGAA
* **
31054 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCCG
*
31074 AACCGGTTTGATCGGTCCG
1 AACCGGTTTGACCGGTCCG
*
31093 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCCG
31112 AACCGGTTTGACC
1 AACCGGTTTGACC
31125 CGACCCGACT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 33 0.73
20 12 0.27
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCCG
Found at i:31141 original size:17 final size:17
Alignment explanation
Indices: 31119--31177 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
31109 CTGAACCGGT
*
31119 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACCG
* **
31136 TTGACCCAACCTTACCG
1 TTGACCCGACCCGACCG
*
31153 TTGACCCGACCGTTGACCG
1 TTGACCCGACC--CGACCG
31172 TTGACC
1 TTGACC
31178 GTGACCGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 23 0.68
19 11 0.32
ACGTcount: A:0.19, C:0.39, G:0.20, T:0.22
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:31184 original size:6 final size:7
Alignment explanation
Indices: 31160--31189 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
31150 CCGTTGACCC
31160 GACCGTT
1 GACCGTT
31167 GACCGTT
1 GACCGTT
31174 GACCG-T
1 GACCGTT
31180 GACCGTT
1 GACCGTT
31187 GAC
1 GAC
31190 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:31184 original size:13 final size:14
Alignment explanation
Indices: 31160--31189 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31150 CCGTTGACCC
31160 GACCGTTGACCGTT
1 GACCGTTGACCGTT
31174 GACCG-TGACCGTT
1 GACCGTTGACCGTT
31187 GAC
1 GAC
31190 TTTCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:38394 original size:10 final size:10
Alignment explanation
Indices: 38365--38433 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
38355 GCTGCTGGAA
38365 AACCGGTTTG
1 AACCGGTTTG
*
38375 -ACCAGTTTTG
1 AACC-GGTTTG
38385 AACCGGTTTG
1 AACCGGTTTG
*
38395 -ACCGGTTCG
1 AACCGGTTTG
38404 AACCGGTTTG
1 AACCGGTTTG
*
38414 -ACCGGTCTG
1 AACCGGTTTG
*
38423 AACTGGTTTG
1 AACCGGTTTG
38433 A
1 A
38434 TCTGAACCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:38408 original size:19 final size:19
Alignment explanation
Indices: 38365--38433 Score: 86
Period size: 19 Copynumber: 3.6 Consensus size: 19
38355 GCTGCTGGAA
* *
38365 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
38385 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
38404 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
38423 AACTGGTTTGA
1 AACCGGTTTGA
38434 TCTGAACCGG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 2 0.04
19 30 0.67
20 13 0.29
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:38466 original size:17 final size:17
Alignment explanation
Indices: 38444--38484 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
38434 TCTGAACCGG
*
38444 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
38461 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
38478 GTTGACC
1 GTTGACC
38485 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:38486 original size:7 final size:7
Alignment explanation
Indices: 38474--38510 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
38464 GACCCGACCC
38474 GACCGTT
1 GACCGTT
38481 GACCGTT
1 GACCGTT
38488 GACCG-T
1 GACCGTT
38494 GACCGTT
1 GACCGTT
38501 GACCGTT
1 GACCGTT
38508 GAC
1 GAC
38511 TTTCTTTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:38498 original size:13 final size:13
Alignment explanation
Indices: 38474--38506 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
38464 GACCCGACCC
38474 GACCGTTGACCGTT
1 GACCG-TGACCGTT
38488 GACCGTGACCGTT
1 GACCGTGACCGTT
38501 GACCGT
1 GACCGT
38507 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:42699 original size:24 final size:24
Alignment explanation
Indices: 42655--42701 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
42645 ACGAGACATG
*
42655 TCACTTGAAGTTTCAAAAGATGTT
1 TCACTTGAAGTCTCAAAAGATGTT
*
42679 TCACTTGAAGATCT-AAGAGATGT
1 TCACTTGAAG-TCTCAAAAGATGT
42702 GTCGGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (24 bp):
TCACTTGAAGTCTCAAAAGATGTT
Found at i:45690 original size:20 final size:19
Alignment explanation
Indices: 45665--45705 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
45655 TTAACTTTTT
*
45665 GGTCAAAGTCAACGGTTAAC
1 GGTCAAAGTCAA-AGTTAAC
45685 GGTCAAAGTCAAAGTTAAC
1 GGTCAAAGTCAAAGTTAAC
45704 GG
1 GG
45706 GTAGGTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (19 bp):
GGTCAAAGTCAAAGTTAAC
Found at i:56825 original size:17 final size:16
Alignment explanation
Indices: 56803--56854 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
56793 TCAATAAATT
*
56803 TAGTTCTTTAATTAAAC
1 TAGTTCATTAATT-AAC
*
56820 TAGTTCATTCATTTAAC
1 TAGTTCATT-AATTAAC
*
56837 TAGTTAATTAATTAAC
1 TAGTTCATTAATTAAC
56853 TA
1 TA
56855 ACTCTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 8 0.27
17 19 0.63
18 3 0.10
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (16 bp):
TAGTTCATTAATTAAC
Done.