Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006676.1 Hibiscus syriacus cultivar Beakdansim tig00016554_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: 89846
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:252 original size:16 final size:18
Alignment explanation
Indices: 231--264 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
221 TGGAGTGCAA
231 AAGAAAG-AAAA-AAAAG
1 AAGAAAGCAAAAGAAAAG
247 AAGAAAGCAAAAGAAAAG
1 AAGAAAGCAAAAGAAAAG
265 TGAAGCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (18 bp):
AAGAAAGCAAAAGAAAAG
Found at i:14946 original size:22 final size:22
Alignment explanation
Indices: 14915--14960 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
14905 CATATACATT
14915 ATACAGAGGTCCTTCGGGACAA
1 ATACAGAGGTCCTTCGGGACAA
* ** *
14937 ATACATAGGTTTTTTGGGACAA
1 ATACAGAGGTCCTTCGGGACAA
14959 AT
1 AT
14961 TTCACATGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (22 bp):
ATACAGAGGTCCTTCGGGACAA
Found at i:15655 original size:21 final size:22
Alignment explanation
Indices: 15620--15672 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
15610 GACCGAAATT
* *
15620 ACTGTAACAAGGGTATCGGT-AC
1 ACTGTAGC-AGGGTATCGATAAC
*
15642 ACTGTAGCAGGGTATCGATAAT
1 ACTGTAGCAGGGTATCGATAAC
15664 ACTGTAGCA
1 ACTGTAGCA
15673 TTCTGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (22 bp):
ACTGTAGCAGGGTATCGATAAC
Found at i:16271 original size:16 final size:16
Alignment explanation
Indices: 16252--16286 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16242 AATTATAAAT
16252 TATTTAAAAATAAAA-A
1 TATTTAAAAA-AAAAGA
16268 TATTTAAAAAAAAAGA
1 TATTTAAAAAAAAAGA
16284 TAT
1 TAT
16287 ATATACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
TATTTAAAAAAAAAGA
Found at i:16675 original size:2 final size:2
Alignment explanation
Indices: 16668--16697 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16658 CTGATTAATT
16668 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16698 TTAATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:16722 original size:22 final size:22
Alignment explanation
Indices: 16695--16747 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
16685 ATATATATTA
* *
16695 TATTTAATTTTTTAAGAA-ATTT
1 TATTTAATTTATTAA-AATATAT
16717 TATTT-ATATTATTAAAATATAT
1 TATTTAAT-TTATTAAAATATAT
16739 TATTTAATT
1 TATTTAATT
16748 AATAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTTAATTTATTAAAATATAT
Found at i:16753 original size:21 final size:23
Alignment explanation
Indices: 16716--16759 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
16706 TTAAGAAATT
*
16716 TTATTTATATTATTAAAA-TATA
1 TTATTTATATTAATAAAACTATA
16738 TTATTTA-ATTAATAAAACTATA
1 TTATTTATATTAATAAAACTATA
16760 AAATACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATTTATATTAATAAAACTATA
Found at i:16808 original size:19 final size:19
Alignment explanation
Indices: 16784--16821 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16774 ATATTAATTC
*
16784 AATAATTTTAAATATATTA
1 AATAATTATAAATATATTA
*
16803 AATAATTATAGATATATTA
1 AATAATTATAAATATATTA
16822 TTATAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AATAATTATAAATATATTA
Found at i:19115 original size:18 final size:18
Alignment explanation
Indices: 19092--19126 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19082 TTTTAAGTAG
19092 TAATTCTAAAAATATATA
1 TAATTCTAAAAATATATA
**
19110 TAATTCTTGAAATATAT
1 TAATTCTAAAAATATAT
19127 GAAAATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATTCTAAAAATATATA
Found at i:19212 original size:19 final size:19
Alignment explanation
Indices: 19188--19228 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19178 TGAAATTATT
*
19188 TTTTATTACTAAAAATTTA
1 TTTTATAACTAAAAATTTA
**
19207 TTTTATAACTAATTATTTA
1 TTTTATAACTAAAAATTTA
19226 TTT
1 TTT
19229 AATTGTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATAACTAAAAATTTA
Found at i:20178 original size:14 final size:14
Alignment explanation
Indices: 20159--20186 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20149 TTTAGAACTA
20159 TCTAAATTGTTATT
1 TCTAAATTGTTATT
20173 TCTAAATTGTTATT
1 TCTAAATTGTTATT
20187 AGACCAAAAA
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:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TCTAAATTGTTATT
Found at i:22266 original size:33 final size:30
Alignment explanation
Indices: 22229--22293 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
22219 TCTCTCCATC
22229 TACTTAAAATGGTAATTTTATAGAAATAATATA
1 TACTTAAAA--GTAATTTT-TAGAAATAATATA
* * *
22262 TACTTTAAAGTTATTTTTATAAATAATATA
1 TACTTAAAAGTAATTTTTAGAAATAATATA
22292 TA
1 TA
22294 AAAACTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 14 0.48
31 7 0.24
33 8 0.28
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (30 bp):
TACTTAAAAGTAATTTTTAGAAATAATATA
Found at i:23960 original size:60 final size:60
Alignment explanation
Indices: 23865--24013 Score: 172
Period size: 60 Copynumber: 2.5 Consensus size: 60
23855 TGTATCAATT
* * * * * *
23865 AACACATACTTACACAAGTATAAGTATGTACATCTCTCAATATATTGGTACCTAAAAATA
1 AACACATACTTATACATGTGTAAATATGTACATCTCCCAATATATTAGTACCTAAAAATA
* * *
23925 AACACATACTTATACCTGTGTAAATATGTATATCTCCCAATATCTTAGTACCTAAAAATA
1 AACACATACTTATACATGTGTAAATATGTACATCTCCCAATATATTAGTACCTAAAAATA
* * * **
23985 GACATATAATTATATTTGTGTAAATATGT
1 AACACATACTTATACATGTGTAAATATGT
24014 TTCAGTATTT
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (60 bp):
AACACATACTTATACATGTGTAAATATGTACATCTCCCAATATATTAGTACCTAAAAATA
Found at i:24445 original size:30 final size:31
Alignment explanation
Indices: 24384--24452 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
24374 ATTTCGGCTG
*
24384 ATTTAGCCCAATAAAGATAGCGAGTTTTTTT
1 ATTTAGCCCAATAAAGATAACGAGTTTTTTT
*
24415 ATTTAGTCCAATAAAGATAACGAG-TTTTTT
1 ATTTAGCCCAATAAAGATAACGAGTTTTTTT
24445 ATTTAGCC
1 ATTTAGCC
24453 TATTAGGGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (31 bp):
ATTTAGCCCAATAAAGATAACGAGTTTTTTT
Found at i:26435 original size:36 final size:37
Alignment explanation
Indices: 26364--26448 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
26354 ATCCCATTAT
*
26364 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
26400 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
26436 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
26449 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:30995 original size:37 final size:36
Alignment explanation
Indices: 30936--31055 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
30926 ATCCCATTAT
* *
30936 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
30972 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
31008 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
31043 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
31056 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
35 35 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:31011 original size:21 final size:21
Alignment explanation
Indices: 30987--31047 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
30977 TTCAAAGAAA
30987 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
31008 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
31022 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
31043 CATTT
1 CATTT
31048 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:31064 original size:35 final size:36
Alignment explanation
Indices: 30938--31082 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
30928 CCCATTATCA
*
30938 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
30973 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
31010 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*** *
31046 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACTAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
31080 TTT
1 TTT
31083 AATACTTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
34 13 0.13
35 45 0.46
36 8 0.08
37 30 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:31471 original size:32 final size:32
Alignment explanation
Indices: 31425--31486 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
31415 TTAATGACCA
*
31425 TTTTGTAATAGTTTGATAAAATTTAATGATTG
1 TTTTATAATAGTTTGATAAAATTTAATGATTG
* *
31457 TTTTATAATTGTTTGATCAAATTTAATGAT
1 TTTTATAATAGTTTGATAAAATTTAATGAT
31487 CATTTTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (32 bp):
TTTTATAATAGTTTGATAAAATTTAATGATTG
Found at i:42691 original size:16 final size:16
Alignment explanation
Indices: 42667--42753 Score: 72
Period size: 16 Copynumber: 5.3 Consensus size: 16
42657 ACCTATTTTA
*
42667 ATTACTATATTTATAT
1 ATTATTATATTTATAT
42683 ATTATTATATTT-TAATT
1 ATTATTATATTTAT-A-T
42700 ATTTATTATATTTCATAT
1 A-TTATTATATTT-ATAT
* *
42718 -TTAATATTATTAAT-T
1 ATTATTA-TATTTATAT
*
42733 ATTATTATATTTATTT
1 ATTATTATATTTATAT
42749 ATTAT
1 ATTAT
42754 ATTCATTTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
15 8 0.14
16 30 0.52
17 6 0.10
18 12 0.21
19 1 0.02
20 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:42726 original size:26 final size:26
Alignment explanation
Indices: 42674--42740 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
42664 TTAATTACTA
* *
42674 TATTTA-TATATTATTATATTTTAAT
1 TATTTATTATATTATCATATTTAAAT
42699 TATTTATTATATT-TCATATTTAATAT
1 TATTTATTATATTATCATATTTAA-AT
*
42725 TATTAATTATTATTAT
1 TATTTATTA-TATTAT
42741 ATTTATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 14 0.40
26 16 0.46
27 4 0.11
28 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTTATTATATTATCATATTTAAAT
Found at i:42754 original size:13 final size:13
Alignment explanation
Indices: 42672--42762 Score: 57
Period size: 13 Copynumber: 6.9 Consensus size: 13
42662 TTTTAATTAC
*
42672 TATATTTATATAT
1 TATATTTATTTAT
*
42685 TAT-TATATTT-T
1 TATATTTATTTAT
*
42696 AATTATTTATTATATT
1 TA-TATTTATT-TA-T
42712 TCATATTTAATATTAT
1 T-ATATTT-AT-TTAT
42728 TA-A-TTA-TTAT
1 TATATTTATTTAT
42738 TATATTTATTTAT
1 TATATTTATTTAT
*
42751 TATATTCATTTA
1 TATATTTATTTA
42763 ATTTCTACAT
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
10 6 0.10
11 3 0.05
12 10 0.16
13 25 0.41
14 2 0.03
15 1 0.02
16 8 0.13
17 5 0.08
18 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTTATTTAT
Found at i:53982 original size:41 final size:42
Alignment explanation
Indices: 53805--54047 Score: 182
Period size: 44 Copynumber: 5.8 Consensus size: 42
53795 TTTCTTATTT
* *
53805 TTTTTATATTTATAATTGAGGCCCCTAA--TTT---TCTCAT
1 TTTTTATCTTTATAATTGAGGCCCCTAATTTTTCAATCTCAA
** *
53842 TTTTTA-CATTTATAATTGAGGATCCTAATTTTTTTCAATCCCACA
1 TTTTTATC-TTTATAATTGAGGCCCCTAA--TTTTTCAATCTCA-A
*
53887 -TTTTATCTTTATAATTGAGGCTCCTAATTTTTTTCAATCTC-A
1 TTTTTATCTTTATAATTGAGGCCCCTAA--TTTTTCAATCTCAA
* *
53929 TTTTCTACCTTTATAATTAAGGCCCCTAATTTTT-AATCTCAA
1 TTTT-TATCTTTATAATTGAGGCCCCTAATTTTTCAATCTCAA
* * * *
53971 TTTTTATCTTTATAATTGAGACCTCTAATTTTTTTCAATCCCAC
1 TTTTTATCTTTATAATTGAGGCCCCTAA--TTTTTCAATCTCAA
* * * *
54015 TTTTTAAT-TATATAATTTAGGCCTCTATTTTTT
1 TTTTT-ATCTTTATAATTGAGGCCCCTAATTTTT
54048 TAAAATATGA
Statistics
Matches: 169, Mismatches: 20, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
37 24 0.14
41 29 0.17
42 16 0.09
43 8 0.05
44 89 0.53
45 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (42 bp):
TTTTTATCTTTATAATTGAGGCCCCTAATTTTTCAATCTCAA
Found at i:54003 original size:85 final size:87
Alignment explanation
Indices: 53836--54048 Score: 233
Period size: 85 Copynumber: 2.5 Consensus size: 87
53826 CCCCTAATTT
* * *
53836 TCTCATTTTTTACATTTATAATTGAGGATCCTAATTTTTTTCAATCCCACATTTTATCTTTATAA
1 TCTCATTTTCTACATTTATAATTAAGGACCCTAA-TTTTTTCAATCCCACATTTTATCTTTATAA
*
53901 TTGAGGCTCCTAATTTTTTTCAA
65 TTGAGCCTCCTAATTTTTTTCAA
* * *
53924 TCTCATTTTCTACCTTTATAATTAAGGCCCCTAA-TTTTT-AATCTCA-ATTTTTATCTTTATAA
1 TCTCATTTTCTACATTTATAATTAAGGACCCTAATTTTTTCAATCCCACA-TTTTATCTTTATAA
53986 TTGAGACCT-CTAATTTTTTTCAA
65 TTGAG-CCTCCTAATTTTTTTCAA
* * *
54009 TCCCACTTTT-TA-ATTATATAATTTAGG-CCTCTATTTTTTT
1 TCTCA-TTTTCTACATT-TATAATTAAGGACC-CTAATTTTTT
54049 AAAATATGAC
Statistics
Matches: 108, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
84 5 0.05
85 58 0.54
86 16 0.15
88 29 0.27
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.51
Consensus pattern (87 bp):
TCTCATTTTCTACATTTATAATTAAGGACCCTAATTTTTTCAATCCCACATTTTATCTTTATAAT
TGAGCCTCCTAATTTTTTTCAA
Found at i:54047 original size:129 final size:125
Alignment explanation
Indices: 53813--54074 Score: 309
Period size: 129 Copynumber: 2.1 Consensus size: 125
53803 TTTTTTTATA
* * *
53813 TTTATAATTGAGGCCCCTAATTTTCTCATTTTTTACATTTATAATTGAGGATCCTAATTTTTTTC
1 TTTATAATTAAGGCCCCTAATTTTCTCAATTTTTACATTTATAATTGAGGACCCTAATTTTTTTC
* ** *
53878 AATCCCACATTTTATCTTTATAATTGAGGCTCCTAATTTTTTTCAATCTCA-TTTTCTACC
66 AATCCCACATTTTATCTATATAATTGAGGCTCCTAATTTTTTAAAATATCACTTTT-TACC
53938 TTTATAATTAAGGCCCCTAATTTTTAATCTCAATTTTTATC-TTTATAATTGA-GACCTCTAATT
1 TTTATAATTAAGGCCCCTAA--TTT--TCTCAATTTTTA-CATTTATAATTGAGGACC-CTAATT
* * * *
54001 TTTTTCAATCCCACTTTTTAAT-TATATAATTTAGGC-CTCTATTTTTTTAAAATATGACTTTTT
60 TTTTTCAATCCCACATTTT-ATCTATATAATTGAGGCTC-CTAATTTTTTAAAATATCACTTTTT
54064 ACC
123 ACC
54067 TTTATAAT
1 TTTATAAT
54075 CGAGGTTTCT
Statistics
Matches: 117, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
125 19 0.16
127 3 0.03
128 4 0.03
129 84 0.72
130 7 0.06
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (125 bp):
TTTATAATTAAGGCCCCTAATTTTCTCAATTTTTACATTTATAATTGAGGACCCTAATTTTTTTC
AATCCCACATTTTATCTATATAATTGAGGCTCCTAATTTTTTAAAATATCACTTTTTACC
Found at i:54087 original size:129 final size:130
Alignment explanation
Indices: 53836--54119 Score: 305
Period size: 129 Copynumber: 2.2 Consensus size: 130
53826 CCCCTAATTT
* * *
53836 TCTCATTTTTTA-CATTTATAATTGAGGATCCTAATTTTTTTCAATCCCACATTTTATCTTTATA
1 TCTCAATTTTTATC-TTTATAATTGAGGACCCTAATTTTTTTCAATCCCACATTTTATCTATATA
* * *
53900 ATTGAGGCTCCTAATTTTTTTCAATCTCATTTTCTACCTTTATAATTAAGGCCCCTAA-TTTTTA
65 ATTGAGGCTCCTAATTTTTTTAAATATCATTTTCTACCTTTATAATCAAGGCCCCTAATTTTTTA
53964 A
130 A
*
53965 TCTCAATTTTTATCTTTATAATTGA-GACCTCTAATTTTTTTCAATCCCACTTTTTAAT-TATAT
1 TCTCAATTTTTATCTTTATAATTGAGGACC-CTAATTTTTTTCAATCCCACATTTT-ATCTATAT
* * * ***
54028 AATTTAGGC-CTCT-ATTTTTTTAAAATATGACTTTT-TACCTTTATAATCGAGGTTTCTAATTT
64 AATTGAGGCTC-CTAATTTTTTT-AAATATCA-TTTTCTACCTTTATAATCAAGGCCCCTAA-TT
54090 TTTTAA
125 TTTTAA
* *
54096 TCTCACTTTTT-TTTTTATTAATTG
1 TCTCAATTTTTATCTTTA-TAATTG
54120 GGGGTTAGTA
Statistics
Matches: 131, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
128 12 0.09
129 84 0.64
130 12 0.09
131 23 0.18
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (130 bp):
TCTCAATTTTTATCTTTATAATTGAGGACCCTAATTTTTTTCAATCCCACATTTTATCTATATAA
TTGAGGCTCCTAATTTTTTTAAATATCATTTTCTACCTTTATAATCAAGGCCCCTAATTTTTTAA
Found at i:54107 original size:44 final size:44
Alignment explanation
Indices: 53836--54106 Score: 250
Period size: 44 Copynumber: 6.2 Consensus size: 44
53826 CCCCTAATTT
* * **
53836 TCTCATTTTTTACATTTATAATTGAGGATCCTAATTTTTTTCAA
1 TCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAA
* * * *
53880 TCCCACATTTTATCTTTATAATTGAGGCTCCTAATTTTTTTCAA
1 TCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAA
*
53924 TCTCA-TTTTCTACCTTTATAATTAAGGCCCCTAA--TTTTT-AA
1 TCTCACTTTT-TACCTTTATAATTGAGGCCCCTAATTTTTTTCAA
* * * *
53965 TCTCAATTTTTATCTTTATAATTGAGACCTCTAATTTTTTTCAA
1 TCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAA
* * * * *
54009 TCCCACTTTTTA-ATTATATAATTTAGGCCTCT-ATTTTTTTAAAA
1 TCTCACTTTTTACCTT-TATAATTGAGGCCCCTAATTTTTTT-CAA
* * * ***
54053 TATGACTTTTTACCTTTATAATCGAGGTTTCTAATTTTTTT-AA
1 TCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAA
54096 TCTCACTTTTT
1 TCTCACTTTTT
54107 TTTTTATTAA
Statistics
Matches: 187, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
41 27 0.14
42 9 0.05
43 29 0.16
44 112 0.60
45 10 0.05
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (44 bp):
TCTCACTTTTTACCTTTATAATTGAGGCCCCTAATTTTTTTCAA
Found at i:54199 original size:22 final size:22
Alignment explanation
Indices: 54174--54217 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54164 TTTTGATATT
54174 GAACGCTCAGACCCTTGACATC
1 GAACGCTCAGACCCTTGACATC
54196 GAACGCTCAGACCCTTGACATC
1 GAACGCTCAGACCCTTGACATC
54218 TACGGTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.18
Consensus pattern (22 bp):
GAACGCTCAGACCCTTGACATC
Found at i:57264 original size:21 final size:21
Alignment explanation
Indices: 57238--57277 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57228 CGAAATACCG
*
57238 CATATATGTTCCAAAGGATTA
1 CATATATGTCCCAAAGGATTA
*
57259 CATATATGTCCCGAAGGAT
1 CATATATGTCCCAAAGGAT
57278 CACGTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
CATATATGTCCCAAAGGATTA
Found at i:57285 original size:21 final size:21
Alignment explanation
Indices: 57238--57285 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
57228 CGAAATACCG
* *
57238 CATATATGTTCCAAAGGATTA
1 CATATATGTCCCAAAGGATCA
*
57259 CATATATGTCCCGAAGGATCA
1 CATATATGTCCCAAAGGATCA
*
57280 CGTATA
1 CATATA
57286 ACCCTCGACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (21 bp):
CATATATGTCCCAAAGGATCA
Found at i:58749 original size:308 final size:308
Alignment explanation
Indices: 58186--58803 Score: 1227
Period size: 308 Copynumber: 2.0 Consensus size: 308
58176 AATTACTTCT
58186 TTTGTAACATCCCAAACTAGGGGTTAGTGACTAAATTATAAAGTTTCAGAATTTGGTGATTAAAG
1 TTTGTAACATCCCAAACTAGGGGTTAGTGACTAAATTATAAAGTTTCAGAATTTGGTGATTAAAG
58251 TAGAAGAATGGATTAGTTCAATGATTTATCTGGAAATAAATCATAAAAGATATTAGTAATTATAA
66 TAGAAGAATGGATTAGTTCAATGATTTATCTGGAAATAAATCATAAAAGATATTAGTAATTATAA
58316 AAGGTATTAAAGGGCAAAAGGGTCATTTGACCAAGAGTTGTATTAAATAATGATATATATATAGG
131 AAGGTATTAAAGGGCAAAAGGGTCATTTGACCAAGAGTTGTATTAAATAATGATATATATATAGG
*
58381 GATAAGGATGAGAGATTTTCCAGAAATCTCTTCTCTCTTTTCTTCTTCATATTCTTTTTCCTCCC
196 GATAAGGATGAGAGATTTTCCAGAAATCTCTTCTCTCTTTTCTTCTTCATATTATTTTTCCTCCC
58446 GTGAAAGCTCCAAGGCAAAGGTAAGATTCCTTGTTAGCTGATGATTTG
261 GTGAAAGCTCCAAGGCAAAGGTAAGATTCCTTGTTAGCTGATGATTTG
58494 TTTGTAACATCCCAAACTAGGGGTTAGTGACTAAATTATAAAGTTTCAGAATTTGGTGATTAAAG
1 TTTGTAACATCCCAAACTAGGGGTTAGTGACTAAATTATAAAGTTTCAGAATTTGGTGATTAAAG
58559 TAGAAGAATGGATTAGTTCAATGATTTATCTGGAAATAAATCATAAAAGATATTAGTAATTATAA
66 TAGAAGAATGGATTAGTTCAATGATTTATCTGGAAATAAATCATAAAAGATATTAGTAATTATAA
58624 AAGGTATTAAAGGGCAAAAGGGTCATTTGACCAAGAGTTGTATTAAATAATGATATATATATAGG
131 AAGGTATTAAAGGGCAAAAGGGTCATTTGACCAAGAGTTGTATTAAATAATGATATATATATAGG
58689 GATAAGGATGAGAGATTTTCCAGAAATCTCTTCTCTCTTTTCTTCTTCATATTATTTTTCCTCCC
196 GATAAGGATGAGAGATTTTCCAGAAATCTCTTCTCTCTTTTCTTCTTCATATTATTTTTCCTCCC
58754 GTGAAAGCTCCAAGGCAAAGGTAAGATTCCTTGTTAGCTGATGATTTG
261 GTGAAAGCTCCAAGGCAAAGGTAAGATTCCTTGTTAGCTGATGATTTG
58802 TT
1 TT
58804 GATTTTAAGA
Statistics
Matches: 309, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 309 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (308 bp):
TTTGTAACATCCCAAACTAGGGGTTAGTGACTAAATTATAAAGTTTCAGAATTTGGTGATTAAAG
TAGAAGAATGGATTAGTTCAATGATTTATCTGGAAATAAATCATAAAAGATATTAGTAATTATAA
AAGGTATTAAAGGGCAAAAGGGTCATTTGACCAAGAGTTGTATTAAATAATGATATATATATAGG
GATAAGGATGAGAGATTTTCCAGAAATCTCTTCTCTCTTTTCTTCTTCATATTATTTTTCCTCCC
GTGAAAGCTCCAAGGCAAAGGTAAGATTCCTTGTTAGCTGATGATTTG
Found at i:59360 original size:64 final size:64
Alignment explanation
Indices: 59278--59502 Score: 239
Period size: 64 Copynumber: 3.5 Consensus size: 64
59268 TTGAAGGTGT
* *
59278 ATCGATGCAT-AGGTAGTGCATCGATGCA-CTCTTTTAAATAGAAAACATCGAATAGGATTTATG
1 ATCGATGCATAAGG-AGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAAT-GAATTTATG
59341 C
64 C
** ** *
59342 ATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-AAAACATCGAATGTAATTCGTGA
1 ATCGATGCATAAGGAGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAATG-AATTTATGC
* *
59406 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-G--AACATCGAATGCATTTTAT
1 ATCGATGCATAAGGAGTGCATCGATGCATCCC-TT-TTAAATAGAAAACATCGAATG-AATTTAT
59467 GC
63 GC
* * *
59469 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGGAGTGCATCGATGCATCCCTT
59503 CATTAAAAGA
Statistics
Matches: 138, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
62 2 0.01
63 47 0.34
64 72 0.52
65 15 0.11
66 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGGAGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAATGAATTTATGC
Found at i:60176 original size:15 final size:15
Alignment explanation
Indices: 60158--60295 Score: 240
Period size: 15 Copynumber: 9.2 Consensus size: 15
60148 GAGGGTATTA
60158 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
60173 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
60188 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
60203 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
60218 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
60233 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
60248 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
60263 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
60278 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
60293 TAG
1 TAG
60296 GAGTCCTACG
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 115 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:60194 original size:30 final size:30
Alignment explanation
Indices: 60158--60295 Score: 276
Period size: 30 Copynumber: 4.6 Consensus size: 30
60148 GAGGGTATTA
60158 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
1 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
60188 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
1 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
60218 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
1 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
60248 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
1 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
60278 TAGTCCTTCGGGATGTAG
1 TAGTCCTTCGGGATGTAG
60296 GAGTCCTACG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 108 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.30
Consensus pattern (30 bp):
TAGTCCTTCGGGATGTAGTCCTTCGGGACG
Found at i:63299 original size:23 final size:21
Alignment explanation
Indices: 63252--63329 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 21
63242 ATATGTCTTA
* **
63252 GGGTATCGGTACCA-TATTAG
1 GGGTATCGATACCATTATGGG
63272 GGGTATCGATACCATTGCATGGG
1 GGGTATCGATACCATT--ATGGG
63295 GGGTATCGATACC--TATGGG
1 GGGTATCGATACCATTATGGG
63314 GGGTATC-AGTACCATT
1 GGGTATCGA-TACCATT
63330 CGAGCATTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.02
19 16 0.33
20 13 0.27
21 3 0.06
23 16 0.33
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (21 bp):
GGGTATCGATACCATTATGGG
Found at i:63314 original size:19 final size:20
Alignment explanation
Indices: 63252--63320 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 20
63242 ATATGTCTTA
* **
63252 GGGTATCGGTACCATATTAG
1 GGGTATCGATACCATATGGG
63272 GGGTATCGATACCATTGCATGGG
1 GGGTATCGATACCA-T--ATGGG
63295 GGGTATCGATACC-TATGGG
1 GGGTATCGATACCATATGGG
63314 GGGTATC
1 GGGTATC
63321 AGTACCATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.28
20 13 0.30
21 2 0.05
23 16 0.37
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.28
Consensus pattern (20 bp):
GGGTATCGATACCATATGGG
Found at i:67016 original size:24 final size:21
Alignment explanation
Indices: 66974--67020 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
66964 CTCACGAAGC
*
66974 GGTTCTTCTGGTGGAGATGAT
1 GGTTCTTCTAGTGGAGATGAT
66995 GGTTCTTCTAGTGGAGATGAT
1 GGTTCTTCTAGTGGAGATGAT
67016 GGTTC
1 GGTTC
67021 CTCCATGTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.11, G:0.36, T:0.38
Consensus pattern (21 bp):
GGTTCTTCTAGTGGAGATGAT
Found at i:80336 original size:18 final size:18
Alignment explanation
Indices: 80313--80349 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
80303 AACGTAGCTT
80313 ATTTTTTAAGAAATATTC
1 ATTTTTTAAGAAATATTC
80331 ATTTTTTAAGAAATATTC
1 ATTTTTTAAGAAATATTC
80349 A
1 A
80350 AGCAGTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTTTTAAGAAATATTC
Found at i:81384 original size:42 final size:42
Alignment explanation
Indices: 81321--81415 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
81311 TTCTTCGTGT
* * * * *
81321 TCTGGGTCTCGTTAAGTGCTGGCTTCCCGGACTCTTTCTGTG
1 TCTGGGACTCATTAAGAGCTGGCTTCCCGAACTCTTTCTGTA
* * *
81363 TCTGGGACTCATTAAGAGCTGGTTTTCTGAACTCTTTCTGTA
1 TCTGGGACTCATTAAGAGCTGGCTTCCCGAACTCTTTCTGTA
*
81405 TCTGGGGCTCA
1 TCTGGGACTCA
81416 CTGAGAGATG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (42 bp):
TCTGGGACTCATTAAGAGCTGGCTTCCCGAACTCTTTCTGTA
Found at i:81428 original size:42 final size:42
Alignment explanation
Indices: 81351--81432 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
81341 GGCTTCCCGG
* * *
81351 ACTCTTTCTGTGTCTGGGACTCATTAAGAGCTGGTTTTCTGA
1 ACTCTTTCTGTATCTGGGACTCACTAAGAGATGGTTTTCTGA
* *
81393 ACTCTTTCTGTATCTGGGGCTCACTGAGAGATGGTTTTCT
1 ACTCTTTCTGTATCTGGGACTCACTAAGAGATGGTTTTCT
81433 AGAAAAGAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (42 bp):
ACTCTTTCTGTATCTGGGACTCACTAAGAGATGGTTTTCTGA
Found at i:86465 original size:19 final size:19
Alignment explanation
Indices: 86441--86509 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
86431 GAATGCAATC
86441 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
86460 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
86479 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
86498 A--GCATCGATGCA
1 AGTGCATCGATGCA
86510 CCCCCTTAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
17 11 0.22
19 39 0.78
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.20
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:86955 original size:16 final size:18
Alignment explanation
Indices: 86908--86955 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
86898 TGATTATACG
*
86908 TATATGAATGACATGAAT
1 TATATGTATGACATGAAT
86926 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
*
86942 TATGTGT-TGACATG
1 TATATGTATGACATG
86956 CTTTTGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 4 0.15
18 9 0.33
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Done.