Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006953.1 Hibiscus syriacus cultivar Beakdansim tig00017870_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: 68768
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:10780 original size:55 final size:55
Alignment explanation
Indices: 10714--11171 Score: 378
Period size: 55 Copynumber: 8.6 Consensus size: 55
10704 GTGAAGCAAA
* *
10714 TGAAGATTGTTCGAGTCTTATACTCTCTGAACAAATAGAGAGCAGACACGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * * * * *
10769 TGAAGATTGTTCAAGTCTCATACTCTCTTAAGCAATAGGGAGCAGACATGAATAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
10824 TGAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGACACGAATGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * * *
10879 TGAAAATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGGGCAGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * *
10934 TGAAGA----TCAAGTCCTATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCA-GACACGATTGT
* ** *
10985 TGAAGGTT-TTTAAGTC--ATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGAT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-T
* * * *
11038 TGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACAC-ATTTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA-TTGT
* * * * * ** *
11089 TGAAGA-T-TT--AGTCATATACTCTCTGAAGGAATAGAGAACAAACTTG-TTTT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
* * *
11139 ATGAAGATTGTTTGAGTTTTATACTCCCTGAAG
1 -TGAAGATTGTTCGAGTCTTATACTCTCTGAAG
11172 CAAAAAAGAG
Statistics
Matches: 336, Mismatches: 49, Indels: 36
0.80 0.12 0.09
Matches are distributed among these distances:
50 8 0.02
51 85 0.25
52 64 0.19
53 9 0.03
54 7 0.02
55 163 0.49
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
Found at i:10978 original size:51 final size:51
Alignment explanation
Indices: 10843--11122 Score: 298
Period size: 51 Copynumber: 5.4 Consensus size: 51
10833 TTCGAGTCTA
* * * *
10843 ATACTCTCTGAAGAAATAGGGAGCAGACACGA-ATGTTGAAAATTATTCGAGTCTT
1 ATACTCTCTGAAGGAATAGGGAGCAGACAC-ATTTGTTGAAGATTA----AGTCCT
* *
10898 ATACTCTCTGAAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCCT
* * *
10949 ATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGTTGAAGGTTTTTAAGT-C-
1 ATACTCTCTGAAGGAATAGGGAGCA-GACACATTTGTTGAA-G--ATTAAGTCCT
* * *
11001 ATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGATTGAAGATTGAGTCCT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTG-TTGAAGATTAAGTCCT
* * * *
11053 ATACTCTCTGAAGGAATGGGGAGCGGACACATTTGTTGAAGATTTAGTCAT
1 ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCCT
11104 ATACTCTCTGAAGGAATAG
1 ATACTCTCTGAAGGAATAG
11123 AGAACAAACT
Statistics
Matches: 194, Mismatches: 22, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
50 6 0.03
51 73 0.38
52 64 0.33
53 7 0.04
54 6 0.03
55 38 0.20
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
ATACTCTCTGAAGGAATAGGGAGCAGACACATTTGTTGAAGATTAAGTCCT
Found at i:11144 original size:51 final size:51
Alignment explanation
Indices: 10891--11148 Score: 163
Period size: 51 Copynumber: 5.0 Consensus size: 51
10881 AAAATTATTC
* * * *
10891 GAGTCTTATACTCTCTGAAGGAATAGGGGGCAGACACAT-TTGT-TGAAGATC
1 GAGTCATATACTCTCTGAAGGAATAGGGAGCA-A-ACATGTTTTATGAAGATT
* * * * * *
10942 AAGTCCTATACTTTCTGAAGGAATAGGGAG-AGGACACGTTTGT-TGAAGGTTTTT
1 GAGTCATATACTCTCTGAAGGAATAGGGAGCA-AACATGTTT-TATGAA-G--ATT
* * * * *
10996 AAGTC--ATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGATTGAAGATT
1 GAGTCATATACTCTCTGAAGGAATAGGGAGCAAACATGTTTTA-TGAAGATT
* * * *
11046 GAGTCCTATACTCTCTGAAGGAATGGGGAGCGGACACAT-TTGT-TGAAGATT
1 GAGTCATATACTCTCTGAAGGAATAGGGAGC--AAACATGTTTTATGAAGATT
* * * *
11097 TAGTCATATACTCTCTGAAGGAATAGAGAACAAACTTGTTTTATGAAGATT
1 GAGTCATATACTCTCTGAAGGAATAGGGAGCAAACATGTTTTATGAAGATT
11148 G
1 G
11149 TTTGAGTTTT
Statistics
Matches: 164, Mismatches: 29, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
49 7 0.04
50 13 0.08
51 73 0.45
52 54 0.33
53 7 0.04
54 10 0.06
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (51 bp):
GAGTCATATACTCTCTGAAGGAATAGGGAGCAAACATGTTTTATGAAGATT
Found at i:11144 original size:155 final size:156
Alignment explanation
Indices: 10843--11131 Score: 399
Period size: 155 Copynumber: 1.9 Consensus size: 156
10833 TTCGAGTCTA
* *
10843 ATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAAATTATTCGAGTCTTATACTCTCTG
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTG-AAATGATTCGAGTCCTATACTCTCTG
* *
10908 AAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCCTATACTTTCTGAAGGAATAGGGAGA
65 AAGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATACTCTCTGAAGGAATA-GGAGA
** *
10973 GGACACGTTTGTTGAAGGTTTTTAAGTC
129 ACAAACGTTTGTTGAAGGTTTTTAAGTC
**
11001 ATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGATTG-AA-GATT-GAGTCCTATACTCTCTG
1 ATACTCTCTGAAGAAATAGGGAGCAGACACGAATG-TTGAAATGATTCGAGTCCTATACTCTCTG
* **
11063 AAGGAAT-GGGGAGCGGACACATTTGTTGAAGATTTAGTCATATACTCTCTGAAGGAATA-GAGA
65 AAGGAATAGGGG-GCAGACACATTTGTTGAAGATCAAGTCATATACTCTCTGAAGGAATAGGAGA
11126 ACAAAC
129 ACAAAC
11132 TTGTTTTATG
Statistics
Matches: 117, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
153 7 0.06
154 4 0.03
155 65 0.56
156 3 0.03
157 2 0.02
158 33 0.28
159 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (156 bp):
ATACTCTCTGAAGAAATAGGGAGCAGACACGAATGTTGAAATGATTCGAGTCCTATACTCTCTGA
AGGAATAGGGGGCAGACACATTTGTTGAAGATCAAGTCATATACTCTCTGAAGGAATAGGAGAAC
AAACGTTTGTTGAAGGTTTTTAAGTC
Found at i:11394 original size:3 final size:3
Alignment explanation
Indices: 11372--11421 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
11362 ATATTATAAA
* *
11372 TAT TAAT TA- TAT TGT TAT TAT TAT TAT TAT TAT TAT TAA TATT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
11418 TAT T
1 TAT T
11422 TTACATTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:12958 original size:4 final size:4
Alignment explanation
Indices: 12949--12974 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12939 TTTTAACTTG
12949 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
12975 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:13249 original size:2 final size:2
Alignment explanation
Indices: 13244--13286 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
13234 ATATTGTGTG
* *
13244 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TG 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
13286 T
1 T
13287 TTAAAGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13267 original size:16 final size:16
Alignment explanation
Indices: 13246--13286 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
13236 ATTGTGTGTA
13246 TATATATATATATATG
1 TATATATATATATATG
13262 TATATATATATATATG
1 TATATATATATATATG
13278 TATATATAT
1 TATATATAT
13287 TTAAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:23211 original size:3 final size:3
Alignment explanation
Indices: 23197--23237 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
23187 AAATATGTAA
*
23197 AAT AAT ATT AAT AAT AAT AAT AAT ACAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
23238 GAACGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:23824 original size:29 final size:29
Alignment explanation
Indices: 23782--23849 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
23772 CCCTCTCTGG
*
23782 AATTTTATAAGTTC-AGATTCACCCCCTAA
1 AATTTTAAAAGTTCAAGATTC-CCCCCTAA
* *
23811 AATTTTAAAAGTTCAAGTTTCCCCCTTAA
1 AATTTTAAAAGTTCAAGATTCCCCCCTAA
23840 AATTTTAAAA
1 AATTTTAAAA
23850 ATTTAAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 30 0.86
30 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (29 bp):
AATTTTAAAAGTTCAAGATTCCCCCCTAA
Found at i:23857 original size:29 final size:28
Alignment explanation
Indices: 23803--23859 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
23793 TTCAGATTCA
*
23803 CCCCCTAAAATTTTAAAAGTTCAAGTTT
1 CCCCCTAAAATTTTAAAAATTCAAGTTT
*
23831 CCCCCTTAAAATTTTAAAAATTTAAGTTT
1 CCCCC-TAAAATTTTAAAAATTCAAGTTT
23860 GTTCTCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (28 bp):
CCCCCTAAAATTTTAAAAATTCAAGTTT
Found at i:29693 original size:24 final size:22
Alignment explanation
Indices: 29641--29694 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
29631 TTTGGGGTTA
* *
29641 TTTAAAGATTTTATTTTTTCAT
1 TTTAAATATTTTATTTTTTAAT
**
29663 TAAAAATATTTATAATTTTTTAAT
1 TTTAAATATTT-T-ATTTTTTAAT
29687 TTTAAATA
1 TTTAAATA
29695 AAATGTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 8 0.33
23 1 0.04
24 15 0.62
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTAAATATTTTATTTTTTAAT
Found at i:30949 original size:9 final size:9
Alignment explanation
Indices: 30935--30980 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
30925 TCGACTAGTT
30935 GCTCGTTAA
1 GCTCGTTAA
30944 GCTCGTT--
1 GCTCGTTAA
*
30951 GCTCATTAA
1 GCTCGTTAA
30960 GCTCGTT-A
1 GCTCGTTAA
30968 -CTCGTTAA
1 GCTCGTTAA
30976 GCTCG
1 GCTCG
30981 ATGCTCATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
7 12 0.39
8 2 0.06
9 17 0.55
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (9 bp):
GCTCGTTAA
Found at i:30953 original size:16 final size:16
Alignment explanation
Indices: 30932--30986 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
30922 TTCTCGACTA
30932 GTTGCTCGTTAAGCTC
1 GTTGCTCGTTAAGCTC
*
30948 GTTGCTCATTAAGCTC
1 GTTGCTCGTTAAGCTC
*
30964 GTTACTCGTTAAGCTC
1 GTTGCTCGTTAAGCTC
*
30980 GATGCTC
1 GTTGCTC
30987 ATTGCTCGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.36
Consensus pattern (16 bp):
GTTGCTCGTTAAGCTC
Found at i:32690 original size:14 final size:14
Alignment explanation
Indices: 32671--32701 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32661 ATTGATAATT
*
32671 TTTTTATTTTTTTA
1 TTTTTATTTTTATA
32685 TTTTTATTTTTATA
1 TTTTTATTTTTATA
32699 TTT
1 TTT
32702 ATTAATACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTTTTATA
Found at i:40660 original size:52 final size:52
Alignment explanation
Indices: 40591--41194 Score: 1057
Period size: 52 Copynumber: 11.6 Consensus size: 52
40581 TCACTCTCTA
* * * *
40591 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
40643 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
40695 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
40747 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
40799 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* *
40851 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
40903 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCTAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
40955 TTTCTTCAGGGACTAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
*
41007 TTTCTTCAAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
* **
41059 TTTCTTCAGGGACTAGAACTCGAACAA-AATCTTCCTACGAGAATGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
41110 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
41162 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
41195 CCAACGATCG
Statistics
Matches: 523, Mismatches: 28, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
51 48 0.09
52 475 0.91
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
Found at i:41143 original size:28 final size:28
Alignment explanation
Indices: 41061--41144 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 28
41051 TGCCCAATTT
41061 TCTTCAGGGACTAGAACTCGAACAA-AA
1 TCTTCAGGGACTAGAACTCGAACAATAA
** * ** **
41088 TCTTC--CTACGAGAA-T-GCCCAATTT
1 TCTTCAGGGACTAGAACTCGAACAATAA
41112 TCTTCAGGGACTAGAACTCGAACAATAA
1 TCTTCAGGGACTAGAACTCGAACAATAA
41140 TCTTC
1 TCTTC
41145 CTACGGGTCT
Statistics
Matches: 38, Mismatches: 14, Indels: 9
0.62 0.23 0.15
Matches are distributed among these distances:
23 4 0.11
24 6 0.16
25 6 0.16
26 6 0.16
27 6 0.16
28 10 0.26
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (28 bp):
TCTTCAGGGACTAGAACTCGAACAATAA
Found at i:41249 original size:55 final size:55
Alignment explanation
Indices: 41190--41468 Score: 465
Period size: 55 Copynumber: 5.1 Consensus size: 55
41180 CTCGAACAAT
*
41190 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
41245 AATCTTCAACAATCGCGTCTGCCCCTTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
41300 AATCTTCAACGATCGCGTCTG-CCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
41352 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
41407 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
41462 AATCTTC
1 AATCTTC
41469 TTTTGCTTCA
Statistics
Matches: 206, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
52 21 0.10
53 28 0.14
54 26 0.13
55 131 0.64
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:41382 original size:107 final size:110
Alignment explanation
Indices: 41190--41468 Score: 483
Period size: 107 Copynumber: 2.6 Consensus size: 110
41180 CTCGAACAAT
*
41190 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
*
41255 AATCGCGTCTGCCCCTTATTTATTCAGAGAGTATAAGACTCGAAC
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* *
41300 AATCTTCAACGATCGCGTCTG-CCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
41362 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
41407 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
41469 TTTTGCTTCA
Statistics
Matches: 159, Mismatches: 7, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
107 74 0.47
108 28 0.18
109 28 0.18
110 29 0.18
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (110 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:42783 original size:8 final size:8
Alignment explanation
Indices: 42751--42850 Score: 66
Period size: 8 Copynumber: 12.8 Consensus size: 8
42741 CCCCCTTTTA
*
42751 TTTTTTGT
1 TTTTTTCT
42759 TTTTTTC-
1 TTTTTTCT
*
42766 -TTCTTC-
1 TTTTTTCT
42772 TTTTTTCT
1 TTTTTTCT
* *
42780 TTTTTCCA
1 TTTTTTCT
42788 TTTTTTCT
1 TTTTTTCT
*
42796 ATTTTTC-
1 TTTTTTCT
*
42803 TATTTT-T
1 TTTTTTCT
* *
42810 TTATTTCA
1 TTTTTTCT
42818 TTTTTTCAT
1 TTTTTTC-T
42827 TTTTTTCAT
1 TTTTTTC-T
42836 TTTTTTCAT
1 TTTTTTC-T
42845 TTTTTT
1 TTTTTT
42851 TATCTTTAAG
Statistics
Matches: 72, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
6 5 0.07
7 13 0.18
8 30 0.42
9 24 0.33
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:42791 original size:9 final size:8
Alignment explanation
Indices: 42772--42849 Score: 67
Period size: 8 Copynumber: 9.8 Consensus size: 8
42762 TTTCTTCTTC
42772 TTTTTTC-
1 TTTTTTCA
42779 TTTTTTCCA
1 TTTTTT-CA
42788 TTTTTTC-
1 TTTTTTCA
42795 TATTTTTC-
1 T-TTTTTCA
42803 TATTTTT--
1 T-TTTTTCA
*
42810 TTATTTCA
1 TTTTTTCA
42818 TTTTTTCA
1 TTTTTTCA
42826 TTTTTTTCA
1 -TTTTTTCA
42835 TTTTTTTCA
1 -TTTTTTCA
42844 TTTTTT
1 TTTTTT
42850 TTATCTTTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
6 4 0.06
7 8 0.13
8 28 0.44
9 23 0.37
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:42800 original size:17 final size:17
Alignment explanation
Indices: 42772--42840 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
42762 TTTCTTCTTC
42772 TTTTTTCT-TTTTTCCA
1 TTTTTTCTATTTTTCCA
*
42788 TTTTTTCTATTTTTCTA
1 TTTTTTCTATTTTTCCA
42805 TTTTTT-TA--TTT-CA
1 TTTTTTCTATTTTTCCA
*
42818 TTTTTTC-ATTTTTTTCA
1 TTTTTTCTA-TTTTTCCA
42835 TTTTTT
1 TTTTTT
42841 TCATTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
13 8 0.18
14 3 0.07
16 13 0.29
17 21 0.47
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCTATTTTTCCA
Found at i:42838 original size:30 final size:31
Alignment explanation
Indices: 42786--42846 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
42776 TTCTTTTTTC
42786 CATTTTTTCTATTTTTCTATTTTTTT-ATTT
1 CATTTTTTCTATTTTTCTATTTTTTTCATTT
*
42816 CATTTTTTC-ATTTTTTTCATTTTTTTCATTT
1 CATTTTTTCTATTTTTCT-ATTTTTTTCATTT
42847 TTTTTATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.25
30 17 0.61
31 4 0.14
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.75
Consensus pattern (31 bp):
CATTTTTTCTATTTTTCTATTTTTTTCATTT
Found at i:42850 original size:9 final size:9
Alignment explanation
Indices: 42772--42850 Score: 74
Period size: 9 Copynumber: 8.7 Consensus size: 9
42762 TTTCTTCTTC
42772 TTTTTTC-T
1 TTTTTTCAT
*
42780 TTTTTCCA-
1 TTTTTTCAT
42788 TTTTTTCTAT
1 TTTTTTC-AT
**
42798 TTTTCTATTTT
1 TTTT-T-TCAT
42809 TTTATTTCA-
1 TTT-TTTCAT
42818 TTTTTTCAT
1 TTTTTTCAT
42827 TTTTTTCAT
1 TTTTTTCAT
42836 TTTTTTCAT
1 TTTTTTCAT
42845 TTTTTT
1 TTTTTT
42851 TATCTTTAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
8 17 0.29
9 28 0.48
10 5 0.09
11 6 0.10
12 2 0.03
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:43985 original size:3 final size:3
Alignment explanation
Indices: 43971--44008 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
43961 GTACCAAGGC
43971 CTT CTAT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
44009 AATACTAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:51239 original size:2 final size:2
Alignment explanation
Indices: 51232--51278 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
51222 TTTATCTATG
51232 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
51274 TA TA T
1 TA TA T
51279 GTAATCACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53645 original size:39 final size:39
Alignment explanation
Indices: 53591--53685 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
53581 TCCGCCCCCG
53591 GTTCCGGTCTACAAGCCTCCGGTTTATAAGCCTCATCCA
1 GTTCCGGTCTACAAGCCTCCGGTTTATAAGCCTCATCCA
53630 GTTCCGGTCTACAAGCCTCCGGTTTATAAGCCTCATCCA
1 GTTCCGGTCTACAAGCCTCCGGTTTATAAGCCTCATCCA
* *
53669 GTTCCGATTTACAAGCC
1 GTTCCGGTCTACAAGCC
53686 GAAACCTCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (39 bp):
GTTCCGGTCTACAAGCCTCCGGTTTATAAGCCTCATCCA
Found at i:57663 original size:24 final size:25
Alignment explanation
Indices: 57613--57663 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
57603 TGTTCGTTTA
* *
57613 TATATTGTTCACGAACATTTTCGTT
1 TATATTGTTCACGAACATATTCATT
*
57638 TATA-TGTTCACGAATATATTCATT
1 TATATTGTTCACGAACATATTCATT
57662 TA
1 TA
57664 GTGTTTATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (25 bp):
TATATTGTTCACGAACATATTCATT
Found at i:58729 original size:2 final size:2
Alignment explanation
Indices: 58722--58758 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
58712 TTACTATTCA
58722 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 A
58759 ATTACAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59049 original size:31 final size:31
Alignment explanation
Indices: 59014--59090 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
59004 AATAATTAAA
59014 AGTTTAGGTATTAAAACTGACCAAAACTAAT
1 AGTTTAGGTATTAAAACTGACCAAAACTAAT
*
59045 AGTTTAGGTATTAAAATTGACCAAAACTAAT
1 AGTTTAGGTATTAAAACTGACCAAAACTAAT
*
59076 AGTTTAGGTACTAAA
1 AGTTTAGGTATTAAA
59091 TACGTTAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.31
Consensus pattern (31 bp):
AGTTTAGGTATTAAAACTGACCAAAACTAAT
Found at i:63125 original size:41 final size:41
Alignment explanation
Indices: 63080--63261 Score: 158
Period size: 41 Copynumber: 4.5 Consensus size: 41
63070 ATTCGCGTTG
*
63080 CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* ** ** * * *
63121 CATTTCGCGTTGCGAT-TTTCCATTTCGCGTTGCTATAGTTG
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTC
* **
63162 AAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
63203 CCTTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
*
63244 CAAATT--CGTTGCGATAGT
1 C-ATTTCGCGTTGCGATAGT
63262 CTACAGTTGT
Statistics
Matches: 109, Mismatches: 27, Indels: 11
0.74 0.18 0.07
Matches are distributed among these distances:
40 26 0.24
41 66 0.61
42 17 0.16
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:63133 original size:20 final size:20
Alignment explanation
Indices: 63108--63218 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 20
63098 TTGAAAATCA
63108 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
63128 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * ** **
63148 CGTTGCTATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
* ** **
63169 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
*
63190 CGTTGCGATTTTCCCTTTCG
1 CGTTGCGATTTTCCATTTCG
63210 CGTTGCGAT
1 CGTTGCGAT
63219 AGTCTACAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 42 0.55
21 35 0.45
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:63171 original size:21 final size:21
Alignment explanation
Indices: 63145--63198 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
63135 ATTTTCCATT
*
63145 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
63166 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
63187 TCGCGTTGCGAT
1 TCGCGTTGCGAT
63199 TTTCCCTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:63273 original size:19 final size:20
Alignment explanation
Indices: 63211--63293 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
63201 TCCCTTTCGC
*
63211 GTTGCGATAGTCTACAATGTC
1 GTTGCGATAGTCTAC-ATGTT
** * * *
63232 GTTGCGATTTTCCAAAT-TC
1 GTTGCGATAGTCTACATGTT
63251 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACA--TGTT
*
63273 GTTGCGAAAGTCTACA-GTT
1 GTTGCGATAGTCTACATGTT
63292 GT
1 GT
63294 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 19 0.39
20 2 0.04
21 12 0.24
22 16 0.33
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCTACATGTT
Found at i:63278 original size:22 final size:22
Alignment explanation
Indices: 63210--63302 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
63200 TTCCCTTTCG
*
63210 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
63231 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
63250 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
63272 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
63294 CGTTGCGAT
1 CGTTGCGAT
63303 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 14 0.24
22 28 0.48
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:63447 original size:20 final size:20
Alignment explanation
Indices: 63422--63473 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
63412 ATTTTCAACT
63422 ATCGCAACGC-AAACTGGAAA
1 ATCGCAACGCGAAA-TGGAAA
63442 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
63462 ATCGCAACGCGA
1 ATCGCAACGCGA
63474 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:63488 original size:21 final size:21
Alignment explanation
Indices: 63462--63515 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
63452 GAAATGGAAA
63462 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
63483 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
63504 ATCGCAACGCGA
1 ATCGCAACGCGA
63516 AATGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:63827 original size:3 final size:3
Alignment explanation
Indices: 63815--63863 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
63805 ATAATCGCTT
63815 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
63862 TA
1 TA
63864 CAATCAACCT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:64118 original size:15 final size:16
Alignment explanation
Indices: 64098--64127 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64088 TTTTAAAATG
64098 ATCATT-AAAATGAAA
1 ATCATTAAAAATGAAA
64113 ATCATTAAAAATGAA
1 ATCATTAAAAATGAA
64128 TTAAGAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (16 bp):
ATCATTAAAAATGAAA
Done.