Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004230.1 Hibiscus syriacus cultivar Beakdansim tig00009260_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: 78621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:764 original size:13 final size:12
Alignment explanation
Indices: 736--778 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
726 ATTTTTTTTA
736 TAATAATTTATAT
1 TAATAA-TTATAT
*
749 TAATTATTATATT
1 TAATAATTATA-T
762 TAATAATTATAAT
1 TAATAATTAT-AT
775 TAAT
1 TAAT
779 CATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 5 0.19
13 20 0.77
14 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATAATTATAT
Found at i:4817 original size:23 final size:23
Alignment explanation
Indices: 4769--4818 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4759 TGAAATTTGA
* * *
4769 ATAAATTGGATACAATGTTATGG
1 ATAAATTGAATACAATGTGAAGG
4792 ATAAATTGAATA-AATGTGAAGTG
1 ATAAATTGAATACAATGTGAAG-G
4815 ATAA
1 ATAA
4819 GTTGGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAAATTGAATACAATGTGAAGG
Found at i:4936 original size:14 final size:14
Alignment explanation
Indices: 4917--4944 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4907 TAACACGTGG
4917 GTTTTAATGTATAT
1 GTTTTAATGTATAT
4931 GTTTTAATGTATAT
1 GTTTTAATGTATAT
4945 ATTAAGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:5110 original size:34 final size:34
Alignment explanation
Indices: 5068--5140 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
5058 TTAAGTTGAA
5068 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
*
5102 TTTAATGTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
5136 TTTAA
1 TTTAA
5141 AAACATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACTATAATTTGTAT
Found at i:7506 original size:17 final size:17
Alignment explanation
Indices: 7484--7538 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
7474 AATAATTAAG
7484 TAATAAATTTAAATAAA
1 TAATAAATTTAAATAAA
*
7501 TAAT-AA-TTATATAAA
1 TAATAAATTTAAATAAA
* *
7516 T-ATTATTTTAATATAAA
1 TAATAAATTTAA-ATAAA
7533 TAATAA
1 TAATAA
7539 TAATTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 2 0.07
15 10 0.33
16 5 0.17
17 10 0.33
18 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAAATTTAAATAAA
Found at i:7553 original size:32 final size:32
Alignment explanation
Indices: 7471--7560 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
7461 AATTAGCACA
* *
7471 AATAATAATTA-AGTAATAAATTTAA-ATAAAT
1 AATAATAATTATA-TAATTATTTTAATATAAAT
* *
7502 AATAATTA-TATAAATATTATTTTAATATAAAT
1 AATAATAATTATATA-ATTATTTTAATATAAAT
*
7534 AATAATAATTATATAATTATATTAATA
1 AATAATAATTATATAATTATTTTAATA
7561 CCAAATATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 3 0.06
31 16 0.33
32 24 0.50
33 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
AATAATAATTATATAATTATTTTAATATAAAT
Found at i:7905 original size:59 final size:60
Alignment explanation
Indices: 7780--7916 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 60
7770 ATGGAAGGCG
* * * **
7780 CGTCCCC-GGGATGCTCCTTACCTCCGTGGCATCCGACTCAGCAAAACCCCGTGAAAGCG
1 CGTCCCCAGGGATGCGCCTTACCTCCGTGGCATCCCACTCAGCAAAACCCAGTGAAAGAA
* *
7839 CGT-CCCAGGGATGCGCCTTACC-CGCGTGGCATCCCAGTCAGCTAAAACCCAG-G-TAGAA
1 CGTCCCCAGGGATGCGCCTTACCTC-CGTGGCATCCCACTCAGC-AAAACCCAGTGAAAGAA
7897 CGTCCCCAGGGATGCGCCTT
1 CGTCCCCAGGGATGCGCCTT
7917 TGTACCAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
58 9 0.13
59 50 0.75
60 8 0.12
ACGTcount: A:0.20, C:0.37, G:0.26, T:0.17
Consensus pattern (60 bp):
CGTCCCCAGGGATGCGCCTTACCTCCGTGGCATCCCACTCAGCAAAACCCAGTGAAAGAA
Found at i:12391 original size:3 final size:3
Alignment explanation
Indices: 12383--12425 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
12373 AATTGTAAAT
12383 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12426 ACTAATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16354 original size:21 final size:21
Alignment explanation
Indices: 16147--16357 Score: 179
Period size: 23 Copynumber: 9.7 Consensus size: 21
16137 AGGGTTCTAC
* *
16147 GTGGTCATTCGGGGCATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
16168 GTGATCCTTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
* *
16189 GAGGCCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
16210 TTGGTCCTTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
*
16231 GTGGTTCTTCGGGACAATTATAT
1 GTGGTCCTTCGGGAC-A-TATAT
* *
16254 GTGGTCATTTGGGACAATTATAT
1 GTGGTCCTTCGGGAC-A-TATAT
* * *
16277 GTAGTCGTTCGGGACAATTCTAT
1 GTGGTCCTTCGGGAC-A-TATAT
* *
16300 GTGGTCGTTCGGGACAATTCTAT
1 GTGGTCCTTCGGGAC-A-TATAT
16323 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
*
16344 GTGGTCATTCGGGA
1 GTGGTCCTTCGGGA
16358 TACGAGGTCC
Statistics
Matches: 158, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
21 76 0.48
22 2 0.01
23 80 0.51
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:16809 original size:15 final size:16
Alignment explanation
Indices: 16791--16821 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16781 AAACCGTATG
16791 TATTTTGTT-ACATAT
1 TATTTTGTTGACATAT
16806 TATTTTGTTGACATAT
1 TATTTTGTTGACATAT
16822 AAAGGAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (16 bp):
TATTTTGTTGACATAT
Found at i:18066 original size:18 final size:18
Alignment explanation
Indices: 18043--18077 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18033 AGGGAATATC
18043 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
18061 AGTGGTTCTTCGGGACA
1 AGTGGTCCTTCGGGACA
18078 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:24080 original size:18 final size:18
Alignment explanation
Indices: 24057--24092 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
24047 AAGGGAATAT
24057 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
24075 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
24093 AATATTCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:25585 original size:22 final size:22
Alignment explanation
Indices: 25560--25602 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25550 ATTTTATTTA
* *
25560 AATTTATTATTATAACTAAAAT
1 AATTGATTATGATAACTAAAAT
*
25582 AATTGGTTATGATAACTAAAA
1 AATTGATTATGATAACTAAAA
25603 ATATATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTGATTATGATAACTAAAAT
Found at i:28962 original size:71 final size:72
Alignment explanation
Indices: 28845--28977 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 72
28835 ATAAATTTAA
*
28845 AATTACAGAATAGGAAAAAAAGAGGGGGGTTAGATCTGAAAAATACCTTTAATGGTTTGATACTG
1 AATTACAGAATAGGAAAAAAAGAGGGGGCTTAGATCTGAAAAATACCTTTAATGGTTTGATACTG
28910 GAATCGT
66 GAATCGT
* *
28917 AATTACAGAATAGG-AAAAAAGAGTGGGCTTAGATCTGAAAAATACCTTTACTGGTTTGATA
1 AATTACAGAATAGGAAAAAAAGAGGGGGCTTAGATCTGAAAAATACCTTTAATGGTTTGATA
28978 ATGCACTCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
71 44 0.76
72 14 0.24
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (72 bp):
AATTACAGAATAGGAAAAAAAGAGGGGGCTTAGATCTGAAAAATACCTTTAATGGTTTGATACTG
GAATCGT
Found at i:29197 original size:4 final size:4
Alignment explanation
Indices: 29188--29214 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29178 GACTTCTATT
29188 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
29215 TGTCAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:29526 original size:20 final size:20
Alignment explanation
Indices: 29501--29540 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29491 ATATTAAATT
* *
29501 TTCATTTTATTAATTTATAA
1 TTCATTTTAATAAATTATAA
29521 TTCATTTTAATAAATTATAA
1 TTCATTTTAATAAATTATAA
29541 AAATCATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTCATTTTAATAAATTATAA
Found at i:29918 original size:33 final size:33
Alignment explanation
Indices: 29872--29991 Score: 143
Period size: 33 Copynumber: 3.5 Consensus size: 33
29862 CCTAAACCTG
* *
29872 AACCCGACTCGACCCAAATATCACACTTAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAA
* *
29905 AACCCGACCCGACCTGAATATCACACTGAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAA
*
29938 AACCCAACCCGACTTGACCCGAATATCACACTT-AAAA
1 AACCCGA-CC--C--GACCCGAATATCACACTTAAAAA
29975 AACCCGACCCGACCCGA
1 AACCCGACCCGACCCGA
29992 CCCGAACAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
32 7 0.09
33 35 0.47
34 3 0.04
36 3 0.04
37 10 0.14
38 16 0.22
ACGTcount: A:0.41, C:0.37, G:0.10, T:0.12
Consensus pattern (33 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAA
Found at i:30611 original size:16 final size:16
Alignment explanation
Indices: 30590--30647 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
30580 ATATAATAAA
*
30590 TAAAAATAAATTTTCC
1 TAAAAATAAATTTCCC
* *
30606 TAAAAATTAGTTTCCC
1 TAAAAATAAATTTCCC
* * *
30622 TAAAACTCAATTTCCT
1 TAAAAATAAATTTCCC
*
30638 TTAAAATAAA
1 TAAAAATAAA
30648 ATAGAATGAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAAATAAATTTCCC
Found at i:30957 original size:17 final size:19
Alignment explanation
Indices: 30922--30960 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
30912 AGATTTATAT
30922 AATATAAAAATATAAAATA
1 AATATAAAAATATAAAATA
30941 AATA-AAAAATTATAATAATA
1 AATATAAAAA-TATAA-AATA
30961 TTAATAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATAAAAATATAAAATA
Found at i:31299 original size:22 final size:22
Alignment explanation
Indices: 31274--31320 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
31264 TTATGAATAG
31274 TGATGAACAGTACCGTGAACAA
1 TGATGAACAGTACCGTGAACAA
31296 TGATGAACAGTACCGTGAACAA
1 TGATGAACAGTACCGTGAACAA
31318 TGA
1 TGA
31321 ACAGTGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (22 bp):
TGATGAACAGTACCGTGAACAA
Found at i:31987 original size:33 final size:33
Alignment explanation
Indices: 31950--32016 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
31940 ACCGTAGTGC
31950 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
31983 TAATCCGTATGACACATAAGGTCGTGTCCACCA
1 TAATCCGTATGACACATAAGGTCGTGTCCACCA
32016 T
1 T
32017 CTGTACTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACCA
Found at i:34429 original size:20 final size:20
Alignment explanation
Indices: 34400--34455 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
34390 CAAAACAATG
34400 AAGT-AGTACCGATACTGCT
1 AAGTCAGTACCGATACTGCT
34419 AAGTCAGTACCGATACTGCT
1 AAGTCAGTACCGATACTGCT
** *
34439 ACTTCAGTACCGGTACT
1 AAGTCAGTACCGATACT
34456 ATCAAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (20 bp):
AAGTCAGTACCGATACTGCT
Found at i:34554 original size:75 final size:75
Alignment explanation
Indices: 34452--34605 Score: 220
Period size: 75 Copynumber: 2.1 Consensus size: 75
34442 TCAGTACCGG
* *
34452 TACTATCAAAACAAAATGTTAAAATGGTA-CATATACTATTTACGGTATCGATACTACTTAGTAT
1 TACTATCAAAACAAAATGCTAAAATGGTATCA-ATACTATATACGGTATCGATACTACTTAGTAT
34516 AGTAATATCGA
65 AGTAATATCGA
* * * * *
34527 TACTGTCAAAGCATAATGCTAAAATGGTATCAATACTATATACGGTATTGATACTACTTAGTGTA
1 TACTATCAAAACAAAATGCTAAAATGGTATCAATACTATATACGGTATCGATACTACTTAGTATA
*
34592 GTAGTATCGA
66 GTAATATCGA
34602 TACT
1 TACT
34606 CTTTGTGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
75 68 0.97
76 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (75 bp):
TACTATCAAAACAAAATGCTAAAATGGTATCAATACTATATACGGTATCGATACTACTTAGTATA
GTAATATCGA
Found at i:35228 original size:19 final size:18
Alignment explanation
Indices: 35192--35230 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35182 AAACAATTAA
*
35192 TTTTAAAAGTAAATAAAT
1 TTTTAAAAATAAATAAAT
*
35210 TTTTAAAAATATATGAAAT
1 TTTTAAAAATAAAT-AAAT
35229 TT
1 TT
35231 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTTAAAAATAAATAAAT
Found at i:37853 original size:16 final size:16
Alignment explanation
Indices: 37832--37868 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
37822 GTTGCAAGAA
37832 TTATTGGACAAAGGAT
1 TTATTGGACAAAGGAT
*
37848 TTATTGGACAAATGAT
1 TTATTGGACAAAGGAT
37864 TTATT
1 TTATT
37869 AGACCAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (16 bp):
TTATTGGACAAAGGAT
Found at i:41029 original size:2 final size:2
Alignment explanation
Indices: 41024--41059 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41014 AAACACACAC
41024 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
41060 CACATACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41323 original size:32 final size:32
Alignment explanation
Indices: 41220--41342 Score: 119
Period size: 31 Copynumber: 3.9 Consensus size: 32
41210 CCTCGGCAAT
* * * *
41220 TGTCCATAGGTCCCAAATAACCTAGGTAA-AC
1 TGTCCATATGTCCCGAAGAACATAGGTAATAC
* **
41251 TGTCCATATGTTCCTTAGAACATAGGT-ATAC
1 TGTCCATATGTCCCGAAGAACATAGGTAATAC
41282 TGTCCATATGTCCCGAA-AGACATAGGTAATTA-
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-TAC
* *
41314 TGTCCATATGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTCCCGAAGAACATAGGTAA
41343 ACCCTCGACT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
30 2 0.03
31 45 0.59
32 26 0.34
33 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAGAACATAGGTAATAC
Found at i:41920 original size:18 final size:16
Alignment explanation
Indices: 41883--41913 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41873 CTCTTATGTC
*
41883 TTCACATATATATATA
1 TTCACATATACATATA
41899 TTCACATATACATAT
1 TTCACATATACATAT
41914 CATTTCATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (16 bp):
TTCACATATACATATA
Found at i:51489 original size:14 final size:14
Alignment explanation
Indices: 51470--51505 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
51460 CACACATATA
51470 TCATATCATATAGT
1 TCATATCATATAGT
51484 TCATATCATATAGT
1 TCATATCATATAGT
51498 TCATATCA
1 TCATATCA
51506 CAAAACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (14 bp):
TCATATCATATAGT
Found at i:51591 original size:17 final size:18
Alignment explanation
Indices: 51569--51607 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
51559 CCATGTACAC
51569 ATGTGAGAAC-TTAAGGT
1 ATGTGAGAACATTAAGGT
*
51586 ATGTGAGTACATTAAGGT
1 ATGTGAGAACATTAAGGT
51604 -TGTG
1 ATGTG
51608 CACCACTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (18 bp):
ATGTGAGAACATTAAGGT
Found at i:51805 original size:32 final size:33
Alignment explanation
Indices: 51729--51805 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 33
51719 ATATGTTTGT
51729 TAGAACATAGGT-ATACTATCCATATGTCCCGA
1 TAGAACATAGGTAATACTATCCATATGTCCCGA
* * * * * *
51761 AAG-ACATTGGTAATTCTGTCTATATGTTCC-A
1 TAGAACATAGGTAATACTATCCATATGTCCCGA
51792 TAGAACATAGGTAA
1 TAGAACATAGGTAA
51806 ACCCTCGCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (33 bp):
TAGAACATAGGTAATACTATCCATATGTCCCGA
Found at i:52462 original size:20 final size:22
Alignment explanation
Indices: 52423--52469 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
52413 TTTTCTTACC
52423 ATAT-TCATATCAATAACACAT
1 ATATATCATATCAATAACACAT
52444 ATATATCATATC-A-AACACAT
1 ATATATCATATCAATAACACAT
*
52464 ACATAT
1 ATATAT
52470 ATGAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 12 0.50
21 5 0.21
22 7 0.29
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATATCATATCAATAACACAT
Found at i:52470 original size:22 final size:23
Alignment explanation
Indices: 52422--52471 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
52412 TTTTTCTTAC
52422 CATAT-TCATATCAATAACACAT
1 CATATATCATATCAATAACACAT
52444 -ATATATCATATC-A-AACACAT
1 CATATATCATATCAATAACACAT
52464 ACATATAT
1 -CATATAT
52472 GAATTTATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.28
21 5 0.20
22 13 0.52
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (23 bp):
CATATATCATATCAATAACACAT
Found at i:55984 original size:24 final size:24
Alignment explanation
Indices: 55940--55987 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
55930 ATGTTTATTT
*
55940 TACATAACTTAGAAAGAAAAAAAA
1 TACATAACTTACAAAGAAAAAAAA
* *
55964 TACATAAC-TACAAATATAAAAAA
1 TACATAACTTACAAAGAAAAAAAA
55987 T
1 T
55988 TTATATCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (24 bp):
TACATAACTTACAAAGAAAAAAAA
Found at i:56620 original size:16 final size:17
Alignment explanation
Indices: 56592--56623 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56582 TATTTTCTTT
56592 ATTTTATTTTATTTATA
1 ATTTTATTTTATTTATA
56609 ATTTTA-TTTATTTAT
1 ATTTTATTTTATTTAT
56624 TTATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATTTTATTTATA
Found at i:56632 original size:12 final size:13
Alignment explanation
Indices: 56582--56633 Score: 63
Period size: 12 Copynumber: 4.1 Consensus size: 13
56572 TATCAAGATA
*
56582 TATTTTCTTTATTT
1 TATTTTATTTA-TT
56596 TATTTTATTTA-T
1 TATTTTATTTATT
*
56608 AATTTTATTTATT
1 TATTTTATTTATT
56621 TA-TTTATTTATT
1 TATTTTATTTATT
56633 T
1 T
56634 TCATTGTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 22 0.65
13 2 0.06
14 10 0.29
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:56807 original size:21 final size:22
Alignment explanation
Indices: 56782--56924 Score: 149
Period size: 21 Copynumber: 6.7 Consensus size: 22
56772 GTAATTTGCA
*
56782 CCGAAGTG-CCACATAATTGTC
1 CCGAAGTGACCACATATTTGTC
56803 CCGAA-TGACCACATATGTT-TGC
1 CCGAAGTGACCACATAT-TTGT-C
*
56825 ACTGAAGTG-CCACATATTTGTC
1 -CCGAAGTGACCACATATTTGTC
* * *
56847 TCAAAG-AACCACATATTTGTC
1 CCGAAGTGACCACATATTTGTC
56868 CCGAA-TGACCACATATTTGTC
1 CCGAAGTGACCACATATTTGTC
*
56889 CCGAAG-GACCACATATTTGTT
1 CCGAAGTGACCACATATTTGTC
56910 CCGAAG-GACCACATA
1 CCGAAGTGACCACATA
56925 AAACCCTCAA
Statistics
Matches: 103, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
20 2 0.02
21 80 0.78
22 6 0.06
23 13 0.13
24 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (22 bp):
CCGAAGTGACCACATATTTGTC
Found at i:56832 original size:44 final size:43
Alignment explanation
Indices: 56776--56906 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 43
56766 CAGTTCGTAA
* *
56776 TTTGCACCGAAGTGCCACATAATTGTCCCGAATGACCACATAT
1 TTTGCACCGAAGTGCCACATATTTGTCCCGAAAGACCACATAT
* *
56819 GTTTGCACTGAAGTGCCACATATTTGTCTC-AAAGAACCACATA-
1 -TTTGCACCGAAGTGCCACATATTTGTCCCGAAAG-ACCACATAT
*
56862 TTTGTC-CCGAA-TGACCACATATTTGTCCCGAAGGACCACATAT
1 TTTG-CACCGAAGTG-CCACATATTTGTCCCGAAAGACCACATAT
56905 TT
1 TT
56907 GTTCCGAAGG
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
41 2 0.03
42 30 0.40
43 9 0.12
44 34 0.45
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
TTTGCACCGAAGTGCCACATATTTGTCCCGAAAGACCACATAT
Found at i:77303 original size:21 final size:22
Alignment explanation
Indices: 77261--77304 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
77251 GGATGAATAT
**
77261 TCTAGATTATTTTGGGGATGAA
1 TCTAGATTATTTTGAAGATGAA
*
77283 TCTAGA-TATTTTGAAGCTGAA
1 TCTAGATTATTTTGAAGATGAA
77304 T
1 T
77305 ATGGCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (22 bp):
TCTAGATTATTTTGAAGATGAA
Found at i:78057 original size:17 final size:17
Alignment explanation
Indices: 78032--78076 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
78022 ATGAAAACAT
*
78032 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
78049 TTAATGAACCAGTTTAA
1 TTAATGAACTAGTTTAA
*
78066 TTAGTGAACTA
1 TTAATGAACTA
78077 TCTTTATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:78229 original size:20 final size:20
Alignment explanation
Indices: 78191--78229 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
78181 CAACTTAATG
* *
78191 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
*
78211 TCATGGAAATTCATGAACA
1 TCATGCAAATTCATGAACA
78230 AGTAAAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Done.