Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006888.1 Hibiscus syriacus cultivar Beakdansim tig00017572_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: 68145
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1462 original size:11 final size:11
Alignment explanation
Indices: 1445--1484 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1435 AGTTCGCTAA
1445 AAAAATAAAAC
1 AAAAATAAAAC
*
1456 GAAAATAAAA-
1 AAAAATAAAAC
1466 AAAAATAAAAAC
1 AAAAAT-AAAAC
1478 AAAAATA
1 AAAAATA
1485 TAACGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 5 0.20
11 14 0.56
12 6 0.24
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:1469 original size:21 final size:22
Alignment explanation
Indices: 1443--1484 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1433 AAAGTTCGCT
*
1443 AAAAAAAT-AAAACGAAAATAA
1 AAAAAAATAAAAACAAAAATAA
1464 AAAAAAATAAAAACAAAAATA
1 AAAAAAATAAAAACAAAAATA
1485 TAACGAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAAAAATAAAAACAAAAATAA
Found at i:8640 original size:24 final size:22
Alignment explanation
Indices: 8612--8691 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
8602 CACTTAACAA
8612 TGCATCGATGCATCTCTTTGAATG
1 TGCATCGATGCATC-C-TTGAATG
* *
8636 TGCATCGATGTATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
8656 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
8680 TGCATCGATGCA
1 TGCATCGATGCA
8692 CAAGATCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 2 0.04
23 12 0.26
24 17 0.37
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:8965 original size:19 final size:19
Alignment explanation
Indices: 8909--8971 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
8899 CTATTTAAAC
**
8909 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
8929 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
8949 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
8968 TAAA
1 TAAA
8972 TTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:12626 original size:16 final size:16
Alignment explanation
Indices: 12605--12643 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
12595 GGTATTACCC
12605 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
12621 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
12637 GACCTGT
1 GACCTGT
12644 AAATGATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:12840 original size:13 final size:13
Alignment explanation
Indices: 12824--12850 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12814 GACCTATTAT
12824 ATAAAATTATTTA
1 ATAAAATTATTTA
12837 ATAAAATTATTTA
1 ATAAAATTATTTA
12850 A
1 A
12851 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:12912 original size:14 final size:14
Alignment explanation
Indices: 12890--12936 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
12880 TGCAAAAGAA
*
12890 AATTAATATAGTTT
1 AATTTATATAGTTT
12904 AATTTATATA----
1 AATTTATATAGTTT
12914 AA-TTATATAGTTT
1 AATTTATATAGTTT
12927 AATTTATATA
1 AATTTATATA
12937 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:12923 original size:23 final size:24
Alignment explanation
Indices: 12889--12938 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
12879 ATGCAAAAGA
12889 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
12913 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
12936 AAA
1 AAA
12939 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:13424 original size:19 final size:20
Alignment explanation
Indices: 13411--13489 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 20
13401 AATTTTTCTA
13411 TTCCCTCTAAATTTCTTAAT
1 TTCCCTCTAAATTTCTTAAT
*
13431 TTCCCTCTAAA-TTCTCAAT
1 TTCCCTCTAAATTTCTTAAT
*
13450 TTCTCTATATTCTCAAAATTTCTTAAT
1 TTC-C------CTCTAAATTTCTTAAT
13477 TTCCCTCTAAATT
1 TTCCCTCTAAATT
13490 CCCAAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
19 10 0.21
20 20 0.43
26 7 0.15
27 10 0.21
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (20 bp):
TTCCCTCTAAATTTCTTAAT
Found at i:13571 original size:2 final size:2
Alignment explanation
Indices: 13564--13591 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13554 ACTTTGAATA
13564 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
13592 TAAACATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13677 original size:2 final size:2
Alignment explanation
Indices: 13670--13730 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
13660 CTTGGTGTGA
* * * *
13670 AT AT AT AT AT GT AT AT AC AT AA AT A- AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13711 AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
13731 TAAATGTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:13790 original size:2 final size:2
Alignment explanation
Indices: 13783--13857 Score: 113
Period size: 2 Copynumber: 39.5 Consensus size: 2
13773 TATGTTTAAT
*
13783 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA -A T- 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
13823 TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13858 TTAAAAGTGA
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
1 4 0.06
2 63 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13971 original size:18 final size:17
Alignment explanation
Indices: 13945--13978 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13935 AGAGGGAAAT
13945 TAGGAAAATTTGAGAATA
1 TAGGAAAA-TTGAGAATA
*
13963 TAGGGAAATTGAGAAT
1 TAGGAAAATTGAGAAT
13979 TTAGAGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (17 bp):
TAGGAAAATTGAGAATA
Found at i:14239 original size:21 final size:21
Alignment explanation
Indices: 14215--14255 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14205 TATATAGTTA
**
14215 TATAAACTTTAAACCCTAAAT
1 TATAAACCCTAAACCCTAAAT
14236 TATAAACCCTAAACCCTAAA
1 TATAAACCCTAAACCCTAAA
14256 CCGTACACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (21 bp):
TATAAACCCTAAACCCTAAAT
Found at i:14300 original size:20 final size:19
Alignment explanation
Indices: 14268--14333 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 19
14258 GTACACCCTA
* *
14268 ATATATGTATAAACCATGT
1 ATATATATATAAACCATAT
14287 ATAGTATATATAAA-C-TAT
1 ATA-TATATATAAACCATAT
14305 ATATATATAT--ACCTATAT
1 ATATATATATAAACC-ATAT
14323 ATATATATATA
1 ATATATATATA
14334 TATATAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 1 0.03
16 1 0.03
17 7 0.17
18 18 0.45
19 4 0.10
20 9 0.22
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (19 bp):
ATATATATATAAACCATAT
Found at i:14350 original size:2 final size:2
Alignment explanation
Indices: 14286--14339 Score: 63
Period size: 2 Copynumber: 26.0 Consensus size: 2
14276 ATAAACCATG
* **
14286 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA CC 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
14330 TA TA TA TA TA
1 TA TA TA TA TA
14340 AAAACTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 41 0.93
3 3 0.07
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:14512 original size:25 final size:26
Alignment explanation
Indices: 14484--14586 Score: 67
Period size: 25 Copynumber: 4.2 Consensus size: 26
14474 AATTATAACA
14484 TATAAACTATATA-TTTTATATAGTT
1 TATAAACTATATACTTTTATATAGTT
* * *
14509 TATACA-TATATAGTTTT-TATA-TA
1 TATAAACTATATACTTTTATATAGTT
* * ** *
14532 TATATA-TAT-TAATATAAATAATATTT
1 TATAAACTATATACT-TTTAT-ATAGTT
14558 TATAAACTATATACTTTTA-ATAGTT
1 TATAAACTATATACTTTTATATAGTT
14583 TATA
1 TATA
14587 TATATAGTTC
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
22 3 0.05
23 10 0.17
24 11 0.19
25 21 0.36
26 6 0.10
27 5 0.08
28 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (26 bp):
TATAAACTATATACTTTTATATAGTT
Found at i:14520 original size:15 final size:15
Alignment explanation
Indices: 14500--14535 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
14490 CTATATATTT
14500 TATATAGTTTATACA
1 TATATAGTTTATACA
* *
14515 TATATAGTTTTTATA
1 TATATAGTTTATACA
14530 TATATA
1 TATATA
14536 TATATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:14545 original size:74 final size:73
Alignment explanation
Indices: 14451--14595 Score: 213
Period size: 74 Copynumber: 2.0 Consensus size: 73
14441 AATGCACACA
*
14451 TATATATATATTATATTAATATAAATTATAACATATAAACTATATA-TTTTATATAGTTTATACA
1 TATATATATATTATATTAATATAAATAATAACATATAAACTATATACTTTTA-ATAGTTTAT--A
14515 TATATAGTTTT
63 TATATAGTTTT
***
14526 TATATATATA-TATATTAATATAAATAATATTTTATAAACTATATACTTTTAATAGTTTATATAT
1 TATATATATATTATATTAATATAAATAATAACATATAAACTATATACTTTTAATAGTTTATATAT
14590 ATAGTT
66 ATAGTT
14596 CACATAAACA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
72 10 0.15
74 40 0.62
75 15 0.23
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (73 bp):
TATATATATATTATATTAATATAAATAATAACATATAAACTATATACTTTTAATAGTTTATATAT
ATAGTTTT
Found at i:14595 original size:13 final size:13
Alignment explanation
Indices: 14577--14786 Score: 93
Period size: 13 Copynumber: 16.0 Consensus size: 13
14567 TATACTTTTA
14577 ATAGTTTATATAT
1 ATAGTTTATATAT
* * *
14590 ATAGTTCACATAAAC
1 ATAGTT--TATATAT
*
14605 ATAATTTATATAT
1 ATAGTTTATATAT
14618 ATAGCTTATAATAATTAT
1 ATAG-TT-T-AT-A-TAT
14636 ATAGTTTATAATAT
1 ATAGTTTAT-ATAT
14650 AAATAG-TT-TATA-
1 --ATAGTTTATATAT
*
14662 AT--TTTATATAC
1 ATAGTTTATATAT
14673 ATAGTTTATATAT
1 ATAGTTTATATAT
* *
14686 ATAGTTCACATAAAT
1 ATAGTT--TATATAT
*
14701 ATAATTTATATAT
1 ATAGTTTATATAT
14714 ATAGTTTATA-AT
1 ATAGTTTATATAT
14726 A-A--TTATATAGT
1 ATAGTTTATATA-T
* * *
14737 TTA-TAATATAAAT
1 ATAGT-TTATATAT
14750 ATAGTTTATATAT
1 ATAGTTTATATAT
*
14763 A-ATTTTATATAT
1 ATAGTTTATATAT
*
14775 ATA-TATATATAT
1 ATAGTTTATATAT
14787 TATAATATCA
Statistics
Matches: 151, Mismatches: 23, Indels: 47
0.68 0.10 0.21
Matches are distributed among these distances:
9 7 0.05
10 7 0.05
11 4 0.03
12 23 0.15
13 55 0.36
14 12 0.08
15 26 0.17
16 7 0.05
17 3 0.02
18 7 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:14615 original size:96 final size:95
Alignment explanation
Indices: 14577--14759 Score: 303
Period size: 96 Copynumber: 1.9 Consensus size: 95
14567 TATACTTTTA
14577 ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTT
1 ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATA-CTTATAATAATTATATAGTT
*
14642 TATAATATAAATAGTTTATAATTTTATATAC
65 TATAATATAAATAGTTTATAATTATATATAC
* *
14673 ATAGTTTATATATATAGTTCACATAAATATAATTTATATATATAGTTTATAATAATTATATAGTT
1 ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATA-CTTATAATAATTATATAGTT
14738 TATAATATAAATATAGTTTATA
65 TATAATAT-AA-ATAGTTTATA
14760 TATAATTTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
96 71 0.86
97 2 0.02
98 10 0.12
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (95 bp):
ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATACTTATAATAATTATATAGTTT
ATAATATAAATAGTTTATAATTATATATAC
Found at i:14734 original size:18 final size:18
Alignment explanation
Indices: 14615--14771 Score: 97
Period size: 18 Copynumber: 8.3 Consensus size: 18
14605 ATAATTTATA
*
14615 TATATAGCTTATAATAAT
1 TATATAGTTTATAATAAT
14633 TATATAGTTTATAAT-A-
1 TATATAGTTTATAATAAT
* *
14649 TAAATAGTTTATAATTTTAT
1 TATATAGTTTATAA--TAAT
*
14669 ATACATAGTTTATATATATAGT
1 -TATATAGTTTATA-ATA-A-T
* ** *
14691 TCACATA-AATATAATTTAT
1 T-ATATAGTTTATAA-TAAT
14710 ATATATAGTTTATAATAAT
1 -TATATAGTTTATAATAAT
14729 TATATAGTTTATAAT-AT
1 TATATAGTTTATAATAAT
*
14746 AAATATAGTTTATATATAAT
1 -TATATAGTTTATA-ATAAT
*
14766 TTTATA
1 TATATA
14772 TATATATATA
Statistics
Matches: 110, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
16 13 0.12
17 3 0.03
18 42 0.38
19 15 0.14
20 11 0.10
21 19 0.17
22 7 0.06
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (18 bp):
TATATAGTTTATAATAAT
Found at i:14748 original size:49 final size:48
Alignment explanation
Indices: 14599--14794 Score: 167
Period size: 49 Copynumber: 4.0 Consensus size: 48
14589 TATAGTTCAC
* *
14599 ATAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATATATAGTTTAT-ATAATTATATAGTTTATAAT
* * *
14648 ATAAATAGTTTATAATTTTATATACATAG-TT-TAT-A-TATATAG--T-TCAC
1 AT-AA-A---TATAA-TTTATATATATAGTTTATATAATTATATAGTTTATAAT
14695 ATAAATATAATTTATATATATAGTTTATAATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATATATAGTTTAT-ATAATTATATAGTTTATAAT
* *
14744 ATAAATATAGTTTATATATA-ATTTTATATATATATATATA-TATTATAAT
1 ATAAATATAATTTATATATATAGTTTATATA-AT-TATATAGT-TTATAAT
14793 AT
1 AT
14795 CAATTTTTTA
Statistics
Matches: 121, Mismatches: 9, Indels: 34
0.74 0.05 0.21
Matches are distributed among these distances:
41 12 0.10
42 7 0.06
43 1 0.01
44 2 0.02
45 2 0.02
46 9 0.07
47 7 0.06
48 11 0.09
49 38 0.31
50 9 0.07
51 2 0.02
52 2 0.02
53 1 0.01
54 6 0.05
55 12 0.10
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (48 bp):
ATAAATATAATTTATATATATAGTTTATATAATTATATAGTTTATAAT
Found at i:16373 original size:22 final size:22
Alignment explanation
Indices: 16308--16360 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
16298 CAAAAACCCA
16308 TGAGCCTTTCCGTACTTGAAAC
1 TGAGCCTTTCCGTACTTGAAAC
16330 TGAGCCTTTCCGTACTTGAAAC
1 TGAGCCTTTCCGTACTTGAAAC
*
16352 TGCGCCTTT
1 TGAGCCTTT
16361 TGTGCTTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (22 bp):
TGAGCCTTTCCGTACTTGAAAC
Found at i:21805 original size:15 final size:17
Alignment explanation
Indices: 21785--21819 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
21775 TTCTAAATGT
21785 AAAATTT-AAATTA-TA
1 AAAATTTAAAATTATTA
21800 AAAATTTAAAATTATTA
1 AAAATTTAAAATTATTA
21817 AAA
1 AAA
21820 CTAAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 6 0.33
17 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATTTAAAATTATTA
Found at i:22262 original size:21 final size:21
Alignment explanation
Indices: 22220--22268 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
22210 ATATCAAAAA
*
22220 TATTATTATTTTTATCGGTTT
1 TATTATTATTTTTATCGATTT
* *
22241 TATTATTTTTTTTATTGATTT
1 TATTATTATTTTTATCGATTT
*
22262 TGTTATT
1 TATTATT
22269 GCTAGATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.71
Consensus pattern (21 bp):
TATTATTATTTTTATCGATTT
Found at i:30902 original size:3 final size:3
Alignment explanation
Indices: 30894--30957 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
30884 AACAATTATT
* *
30894 TAA TAA TAA T-A TAC TAA TAA T-A TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
30940 -ATT TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA
30958 ATTTAAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 45 0.88
4 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:30913 original size:11 final size:11
Alignment explanation
Indices: 30894--30957 Score: 69
Period size: 11 Copynumber: 5.8 Consensus size: 11
30884 AACAATTATT
30894 TAATAATAATA
1 TAATAATAATA
*
30905 TACTAATAATA
1 TAATAATAATA
*
30916 TATTAATAATAA
1 TAATAATAAT-A
30928 TAATAATAATA
1 TAATAATAATA
*
30939 -AAT-TTAATAA
1 TAATAATAAT-A
30949 TAATAATAA
1 TAATAATAA
30958 ATTTAAATGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 4 0.09
10 4 0.09
11 23 0.52
12 13 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAATAATA
Found at i:31135 original size:46 final size:45
Alignment explanation
Indices: 31082--31185 Score: 174
Period size: 46 Copynumber: 2.3 Consensus size: 45
31072 GATGGAAATG
*
31082 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTG-AGG-C
31128 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTGAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTGAGGC
31173 TTTGAAAACATCA
1 TTTGAAAACATCA
31186 AAAAGCTCCC
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
45 13 0.23
46 42 0.75
47 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTGAGGC
Found at i:31569 original size:76 final size:76
Alignment explanation
Indices: 31118--31543 Score: 782
Period size: 76 Copynumber: 5.6 Consensus size: 76
31108 TTACAGATGA
* *
31118 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTGAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
31182 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
31193 CCCAAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCTGAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
31258 ATCAAAAAGCT
66 ATCAAAAAGCT
31269 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
31334 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
31345 CCTGAATGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
31410 ATCAAAAAGCT
66 ATCAAAAAGCT
*
31421 CCCGAATGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
31486 ATCAAAAAGCT
66 ATCAAAAAGCT
31497 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
31544 GGGAAATAGT
Statistics
Matches: 342, Mismatches: 8, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
75 7 0.02
76 335 0.98
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:32244 original size:22 final size:22
Alignment explanation
Indices: 32219--32273 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
32209 CATAAAGTTT
* *
32219 TCATTTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
32241 TCATCTTTAAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
32263 TCATCTTTGAA
1 TCATCTTTGAA
32274 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:35087 original size:93 final size:93
Alignment explanation
Indices: 34933--35393 Score: 773
Period size: 93 Copynumber: 5.0 Consensus size: 93
34923 CTTATTTCTA
* * * *
34933 CTATGAGCAAAATTCATCTTTCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAATCAGATC
1 CTATGAGC-ACATTCATCTTCCAAATTCAATGATTGATTCTGTGG-TTTCATACCAAATCAGATC
*
34996 AGATAACTCAAAGAACACTTCTAGAAGATG
64 AGATAACTCAAAGAACACTTCCAGAAGATG
35026 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAATCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAATCAGATCAG
*
35091 ATAATTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* *
35119 CTATGAGCACATTCATATTCCAAATTCAATGATTAATTCTGTGGTTTCATACCAAATCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAATCAGATCAG
*
35184 ATAATTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* *
35212 CTATGAGCACATTCATCTTCCAAATCCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAATCAGATCAG
*
35277 ATAACTCAAAGAACACTTCCAAAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
*
35305 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAATCAGATCAG
35370 ATAACTCAAAGAACACTTCCAGAA
66 ATAACTCAAAGAACACTTCCAGAA
35394 TATACTATTG
Statistics
Matches: 350, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
92 27 0.08
93 320 0.91
94 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAATCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:35192 original size:45 final size:45
Alignment explanation
Indices: 35048--35192 Score: 105
Period size: 45 Copynumber: 3.2 Consensus size: 45
35038 TCATCTTCCA
*
35048 AATTCAATGATTGATTCTGTGGTTTCATACCAAATCAGATCAGAT
1 AATTCAATGATTAATTCTGTGGTTTCATACCAAATCAGATCAGAT
* ** * * ** * * * * * *
35093 AATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATATTC-CA-
1 AATTCAATGATTAATT-CTGTGGTTTC-AT-ACCA-AATCAGA-TCAGAT
35141 AATTCAATGATTAATTCTGTGGTTTCATACCAAATCAGATCAGAT
1 AATTCAATGATTAATTCTGTGGTTTCATACCAAATCAGATCAGAT
35186 AATTCAA
1 AATTCAA
35193 AGAACACTTC
Statistics
Matches: 66, Mismatches: 27, Indels: 14
0.62 0.25 0.13
Matches are distributed among these distances:
43 2 0.03
44 6 0.09
45 21 0.32
46 7 0.11
47 7 0.11
48 15 0.23
49 6 0.09
50 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (45 bp):
AATTCAATGATTAATTCTGTGGTTTCATACCAAATCAGATCAGAT
Found at i:37304 original size:2 final size:2
Alignment explanation
Indices: 37297--37336 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
37287 ACAACCAAGG
37297 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
37337 TAAAGGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43857 original size:3 final size:3
Alignment explanation
Indices: 43849--43914 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
43839 AACAATTATT
* *
43849 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
*
43894 TAA -ATT TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA
43915 ATTTAAATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 47 0.89
4 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:43883 original size:27 final size:25
Alignment explanation
Indices: 43845--43914 Score: 115
Period size: 24 Copynumber: 2.8 Consensus size: 25
43835 TTGTAACAAT
43845 TATTTAATAATAATATACTAATAATAA
1 TATTTAATAATAATA-A-TAATAATAA
43872 TATTTAATAATAATAATAATAATAA
1 TATTTAATAATAATAATAATAATAA
43897 -ATTTAATAATAATAATAA
1 TATTTAATAATAATAATAA
43915 ATTTAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
24 18 0.42
25 9 0.21
26 1 0.02
27 15 0.35
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TATTTAATAATAATAATAATAATAA
Found at i:48902 original size:10 final size:10
Alignment explanation
Indices: 48887--48915 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
48877 TTATCCGAAT
48887 ACTTTATCGA
1 ACTTTATCGA
48897 ACTTTATCGA
1 ACTTTATCGA
48907 ACTTTATCG
1 ACTTTATCG
48916 CTTCATAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (10 bp):
ACTTTATCGA
Found at i:49449 original size:2 final size:2
Alignment explanation
Indices: 49442--49475 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49432 CTGCTCAAAC
49442 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
49476 GGTGTTTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61477 original size:28 final size:28
Alignment explanation
Indices: 61445--61501 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
61435 TTCAGTAATA
* *
61445 TGTTTGTTTATGTTCTTTCATTTATGTT
1 TGTTTGTTTATGTGCATTCATTTATGTT
*
61473 TGTTTGTTTATGTGCATTCGTTTATGTT
1 TGTTTGTTTATGTGCATTCATTTATGTT
61501 T
1 T
61502 AGCCCAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.11, C:0.07, G:0.18, T:0.65
Consensus pattern (28 bp):
TGTTTGTTTATGTGCATTCATTTATGTT
Found at i:61482 original size:14 final size:15
Alignment explanation
Indices: 61445--61485 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
61435 TTCAGTAATA
61445 TGTTTGTTTATGTTC
1 TGTTTGTTTATGTTC
**
61460 T-TTCATTTATGTT-
1 TGTTTGTTTATGTTC
61473 TGTTTGTTTATGT
1 TGTTTGTTTATGT
61486 GCATTCGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.68
Consensus pattern (15 bp):
TGTTTGTTTATGTTC
Found at i:61688 original size:10 final size:10
Alignment explanation
Indices: 61668--61704 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
61658 GATCTATTTC
61668 CATTTATGTT
1 CATTTATGTT
* *
61678 CGTTTACGTT
1 CATTTATGTT
61688 CATTTATGTT
1 CATTTATGTT
61698 CATTTAT
1 CATTTAT
61705 TGTGTTTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.57
Consensus pattern (10 bp):
CATTTATGTT
Found at i:61739 original size:24 final size:24
Alignment explanation
Indices: 61704--61790 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
61694 TGTTCATTTA
* *
61704 TTGTGTTTGTTTACGTTCGTTCAT
1 TTGTGTTCGTTTACATTCGTTCAT
*
61728 TTATGTTCGTTTACATTCGTTCAT
1 TTGTGTTCGTTTACATTCGTTCAT
*
61752 TTGTGTTCGTTTACATTCGTTTA-
1 TTGTGTTCGTTTACATTCGTTCAT
61775 TTGTGTTCGTTTACAT
1 TTGTGTTCGTTTACAT
61791 CCATCCGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
23 16 0.28
24 42 0.72
ACGTcount: A:0.13, C:0.14, G:0.17, T:0.56
Consensus pattern (24 bp):
TTGTGTTCGTTTACATTCGTTCAT
Found at i:64235 original size:35 final size:35
Alignment explanation
Indices: 64128--64237 Score: 93
Period size: 36 Copynumber: 3.1 Consensus size: 35
64118 TTTTAGGGAT
*
64128 CAAATATGGAATTCCCATATTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
* * * *
64163 CTACCAA-A-GAATTTTCCA-ATGTGTACAAG-TTAGCCAC
1 C-A--AATATGAAATTCCCATAT-T-CA-AAGTTTGGCCAC
64200 CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
64235 CAA
1 CAA
64238 CCAAGATGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 20
0.66 0.11 0.24
Matches are distributed among these distances:
34 5 0.09
35 15 0.27
36 19 0.34
37 12 0.21
38 5 0.09
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (35 bp):
CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
Done.