Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009180.1 Hibiscus syriacus cultivar Beakdansim tig00112747_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: 109577
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1669 original size:11 final size:11
Alignment explanation
Indices: 1635--1691 Score: 72
Period size: 11 Copynumber: 5.7 Consensus size: 11
1625 AGTGTCCTCT
1635 TGATAATTGTA
1 TGATAATTGTA
1646 TG--AATT-T-
1 TGATAATTGTA
1653 TGATAATTGTA
1 TGATAATTGTA
1664 TGATAATT-T-
1 TGATAATTGTA
1673 TGATAATTGTA
1 TGATAATTGTA
1684 TGATAATT
1 TGATAATT
1692 TTAAATAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 2 0.05
8 1 0.03
9 16 0.40
10 3 0.08
11 18 0.45
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (11 bp):
TGATAATTGTA
Found at i:1673 original size:20 final size:20
Alignment explanation
Indices: 1634--1693 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
1624 AAGTGTCCTC
1634 TTGATAATTGTATG--AATT
1 TTGATAATTGTATGATAATT
1652 TTGATAATTGTATGATAATT
1 TTGATAATTGTATGATAATT
1672 TTGATAATTGTATGATAATT
1 TTGATAATTGTATGATAATT
1692 TT
1 TT
1694 AAATAAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.35
20 26 0.65
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGATAATTGTATGATAATT
Found at i:2071 original size:25 final size:24
Alignment explanation
Indices: 2030--2076 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2020 AATTGATATA
* *
2030 ATTTTAAATATTAATTTTTTTTAT
1 ATTTTAAATAATAATTTGTTTTAT
*
2054 ATTTGTAAATAATGATTTGTTTT
1 ATTT-TAAATAATAATTTGTTTT
2077 CAACGTGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
ATTTTAAATAATAATTTGTTTTAT
Found at i:3896 original size:2 final size:2
Alignment explanation
Indices: 3889--3919 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3879 ATAACCTTTA
3889 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 A
3920 AAGCTTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14169 original size:122 final size:122
Alignment explanation
Indices: 13938--14172 Score: 285
Period size: 122 Copynumber: 1.9 Consensus size: 122
13928 TATTTAATTA
* * * * * * *
13938 CAAATATTGATATTTATCGTAAAATAAGTATTGAATTATATTTAATATTTTAGGTTATAATTGAA
1 CAAATATTGATACTTATCATAAAATAAGTATTAAATTACATTTAACATTTTAGGTTACAATTAAA
** *
14003 AATATTATTAAAGAAATAACATTTTAGGTTTGACTTAATAACATTTTATATTATAAT
66 AATATTACCAAAGAAATAACATTTTAGGTTGGACTTAATAACATTTTATATTATAAT
* * *
14060 CAAATATTGATACTTGTCATGAAATAAGTATTAAATTACATTTAACATTTTAGGTTGCAA-TAAA
1 CAAATATTGATACTTATCATAAAATAAGTATTAAATTACATTTAACATTTTAGGTTACAATTAAA
* * * *
14124 GAATGTTACCAAATATATAACATTTTAGGTTGGAC-TAGATGACATTTTA
66 -AATATTACCAAAGAAATAACATTTTAGGTTGGACTTA-ATAACATTTTA
14173 GGTTATAACT
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
121 5 0.05
122 89 0.95
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (122 bp):
CAAATATTGATACTTATCATAAAATAAGTATTAAATTACATTTAACATTTTAGGTTACAATTAAA
AATATTACCAAAGAAATAACATTTTAGGTTGGACTTAATAACATTTTATATTATAAT
Found at i:14497 original size:80 final size:81
Alignment explanation
Indices: 14400--14561 Score: 265
Period size: 80 Copynumber: 2.0 Consensus size: 81
14390 TTCATTATAA
14400 AATTTACTAATAGATGACAAATGACTAATATATTAATATTCTAA-AAAAATAT-TAAATTAGTAA
1 AATTTACTAATAGATGACAAATGACTAATATATTAATATTCTAATAAAAAT-TCTAAATTAGTAA
*
14463 TTAATCATAATTATTTT
65 TTAATAATAATTATTTT
* * *
14480 AATTTACTAATAGATGACAAATGACTAATCTATTAATATTCTAATAAAAATTCTAATTTATTAAT
1 AATTTACTAATAGATGACAAATGACTAATATATTAATATTCTAATAAAAATTCTAAATTAGTAAT
14545 TAATAATAATTATTTT
66 TAATAATAATTATTTT
14561 A
1 A
14562 CTACACCCAA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
80 44 0.58
81 32 0.42
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (81 bp):
AATTTACTAATAGATGACAAATGACTAATATATTAATATTCTAATAAAAATTCTAAATTAGTAAT
TAATAATAATTATTTT
Found at i:15157 original size:2 final size:2
Alignment explanation
Indices: 15150--15176 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15140 AAATTAAAAT
15150 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
15177 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16616 original size:37 final size:36
Alignment explanation
Indices: 16541--16616 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
16531 TTTTTATATT
*
16541 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
16577 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
16614 TTT
1 TTT
16617 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:16992 original size:17 final size:17
Alignment explanation
Indices: 16970--17008 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16960 TCTTATAAGA
16970 ATTTTAAAAAT-ATTTT
1 ATTTTAAAAATAATTTT
*
16986 GATTTTAATAATAATTTT
1 -ATTTTAAAAATAATTTT
17004 ATTTT
1 ATTTT
17009 TTTTAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTAAAAATAATTTT
Found at i:19226 original size:16 final size:16
Alignment explanation
Indices: 19207--19246 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
19197 CCAGTGTGCT
19207 TGAGTGATATTGTGAG
1 TGAGTGATATTGTGAG
19223 TGAGTGATATTGTGAG
1 TGAGTGATATTGTGAG
19239 TGAGTGAT
1 TGAGTGAT
19247 TATAGAGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGAGTGATATTGTGAG
Found at i:37940 original size:25 final size:25
Alignment explanation
Indices: 37895--37942 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
37885 CTCGTATAAA
* *
37895 TTGCACTGTAGTGCCATGTAGAATT
1 TTGCACTGAAGTGCCACGTAGAATT
*
37920 TTGCACTGAAGTGCCGCGTAGAA
1 TTGCACTGAAGTGCCACGTAGAA
37943 ACTTGTCTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (25 bp):
TTGCACTGAAGTGCCACGTAGAATT
Found at i:37978 original size:24 final size:25
Alignment explanation
Indices: 37933--37983 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
37923 CACTGAAGTG
*
37933 CCGCGTAGAAACTTGTCTCGAAGGA
1 CCGCGTAGAAACTTGTCCCGAAGGA
*
37958 CCGCGTAG-AATTTGTCCCGAAGGA
1 CCGCGTAGAAACTTGTCCCGAAGGA
37982 CC
1 CC
37984 ACATAGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (25 bp):
CCGCGTAGAAACTTGTCCCGAAGGA
Found at i:40204 original size:22 final size:22
Alignment explanation
Indices: 40187--40252 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
40177 CTCGTATAAA
*
40187 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
40209 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
40231 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
40253 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:40218 original size:13 final size:13
Alignment explanation
Indices: 40200--40240 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
40190 ACCGAAGTGC
40200 CCGTAGAATTGCA
1 CCGTAGAATTGCA
40213 CCGTAG---TGC-
1 CCGTAGAATTGCA
40222 CCGTAGAATTGCA
1 CCGTAGAATTGCA
40235 CCGTAG
1 CCGTAG
40241 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:41975 original size:21 final size:21
Alignment explanation
Indices: 41951--41995 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41941 TCTTGTTCGT
* *
41951 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
41972 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
41993 TTG
1 TTG
41996 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:45092 original size:22 final size:22
Alignment explanation
Indices: 45075--45140 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
45065 CTCGTATAAA
*
45075 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
45097 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
45119 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
45141 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:45106 original size:13 final size:13
Alignment explanation
Indices: 45088--45128 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
45078 ACCGAAGTGC
45088 CCGTAGAATTGCA
1 CCGTAGAATTGCA
45101 CCGTAG---TGC-
1 CCGTAGAATTGCA
45110 CCGTAGAATTGCA
1 CCGTAGAATTGCA
45123 CCGTAG
1 CCGTAG
45129 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:46790 original size:22 final size:22
Alignment explanation
Indices: 46765--46826 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
46755 TTTTCCTTTA
*
46765 GGGGGAATCGGTTCCCCCCTAT
1 GGGGGTATCGGTTCCCCCCTAT
46787 GGGGGTATCGGTTCCCCCCTAT
1 GGGGGTATCGGTTCCCCCCTAT
46809 GGGGGTATCGGTTCCCCC
1 GGGGGTATCGGTTCCCCC
46827 ATGACATACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.10, C:0.32, G:0.34, T:0.24
Consensus pattern (22 bp):
GGGGGTATCGGTTCCCCCCTAT
Found at i:46877 original size:21 final size:21
Alignment explanation
Indices: 46853--46897 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46843 TCTTGTTCGT
* *
46853 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
46874 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
46895 TTG
1 TTG
46898 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:56084 original size:22 final size:22
Alignment explanation
Indices: 56056--56417 Score: 475
Period size: 22 Copynumber: 16.5 Consensus size: 22
56046 TATTTAAATC
56056 TATTTTAAAATATGAATTGATT
1 TATTTTAAAATATGAATTGATT
*
56078 TATTTTAAATTAT-AGATTGATT
1 TATTTTAAAATATGA-ATTGATT
*
56100 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATT
56122 TATTTTAAAATATGAATTGATT
1 TATTTTAAAATATGAATTGATT
* *
56144 AATTTTAAAATATGGAA--AATTT
1 TATTTTAAAATAT-GAATTGA-TT
*
56166 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATT
*
56188 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATT
56210 TATTTTAAAATAT-AGATTGATT
1 TATTTTAAAATATGA-ATTGATT
* *
56232 TATTTTAAAATATGGATAGATT
1 TATTTTAAAATATGAATTGATT
* *
56254 TATTTTAAAATATGGATAGATT
1 TATTTTAAAATATGAATTGATT
*
56276 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATT
*
56298 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATT
***
56320 TATTTTAAAATATGAAAAAATT
1 TATTTTAAAATATGAATTGATT
56342 TATTTTAAAATAT-AGATTGATT
1 TATTTTAAAATATGA-ATTGATT
*
56364 AATTTTAAAATATGAATTGA-T
1 TATTTTAAAATATGAATTGATT
*
56385 TATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATT
56407 TATTTTGAAAA
1 TATTTT-AAAA
56418 ATTTATTATT
Statistics
Matches: 305, Mismatches: 23, Indels: 23
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.08
22 272 0.89
23 9 0.03
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TATTTTAAAATATGAATTGATT
Found at i:56110 original size:44 final size:44
Alignment explanation
Indices: 56056--56417 Score: 523
Period size: 44 Copynumber: 8.2 Consensus size: 44
56046 TATTTAAATC
* *
56056 TATTTTAAAATATGAATTGATTTATTTTAAATTATAGATTGATT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
* *
56100 TATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTGATT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
* *
56144 AATTTTAAAATATGGAA--AATTTTATTTTAAAATATGGATTGATT
1 TATTTTAAAATAT-GAATTGA-TTTATTTTAAAATATGGATTGATT
* *
56188 TATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGATT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
* * *
56232 TATTTTAAAATATGGATAGATTTATTTTAAAATATGGATAGATT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
*
56276 TATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
*** *
56320 TATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATTGATT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
*
56364 AATTTTAAAATATGAATTGA-TTATTTTAAAATATGGATTGATT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
56407 TATTTTGAAAA
1 TATTTT-AAAA
56418 ATTTATTATT
Statistics
Matches: 285, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
43 30 0.11
44 252 0.88
45 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (44 bp):
TATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATT
Found at i:56436 original size:66 final size:66
Alignment explanation
Indices: 56056--56417 Score: 548
Period size: 66 Copynumber: 5.5 Consensus size: 66
56046 TATTTAAATC
*
56056 TATTTTAAAATATGAATTGATTTATTTTAAATTATAGATTGATTTATTTTAAAATATGGATTGAT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGAT
56121 T
66 T
* * **
56122 TATTTTAAAATATGAATTGATTAATTTTAAAATATGGA-AAATTTTATTTTAAAATATGGATTGA
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGA-TTTATTTTAAAATATGGATTGA
56186 TT
65 TT
* *
56188 TATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATAGAT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGAT
56253 T
66 T
* * *
56254 TATTTTAAAATATGGATAGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGAT
56319 T
66 T
*** * *
56320 TATTTTAAAATATGAAAAAATTTATTTTAAAATATAGATTGATTAATTTTAAAATATGAATTGA-
1 TATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGAT
56384 T
66 T
*
56385 TATTTTAAAATATGGATTGATTTATTTTGAAAA
1 TATTTTAAAATATGAATTGATTTATTTT-AAAA
56418 ATTTATTATT
Statistics
Matches: 269, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
65 26 0.10
66 242 0.90
67 1 0.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (66 bp):
TATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGAT
T
Found at i:63757 original size:17 final size:14
Alignment explanation
Indices: 63723--63750 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63713 GTATGCGCTT
63723 ATCCTAATTAAAGG
1 ATCCTAATTAAAGG
63737 ATCCTAATTAAAGG
1 ATCCTAATTAAAGG
63751 TGGATCCACC
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ATCCTAATTAAAGG
Found at i:64042 original size:25 final size:24
Alignment explanation
Indices: 64000--64046 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
63990 ATTTTATTAA
*
64000 TTAAATTTAAATTGTTATGTATTTT
1 TTAAATTTAAATTATTAT-TATTTT
**
64025 TTAAATTTCCATTATTATTATT
1 TTAAATTTAAATTATTATTATT
64047 ATTATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
TTAAATTTAAATTATTATTATTTT
Found at i:64043 original size:3 final size:3
Alignment explanation
Indices: 64035--64060 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
64025 TTAAATTTCC
64035 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
64061 GTTTGTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:67947 original size:31 final size:32
Alignment explanation
Indices: 67897--67957 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
67887 TCCAACGCTT
*
67897 TAAAACAATTAAAATAATCAAAATTGAAAAAA
1 TAAAACAATTAAAAAAATCAAAATTGAAAAAA
* *
67929 TAAAATAA-TAAAAAAATCATAATTGAAAA
1 TAAAACAATTAAAAAAATCAAAATTGAAAA
67958 CCATTACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (32 bp):
TAAAACAATTAAAAAAATCAAAATTGAAAAAA
Found at i:68681 original size:16 final size:17
Alignment explanation
Indices: 68640--68673 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
68630 ATATTATTCA
*
68640 ATCCG-AAATTTTGGAT
1 ATCCGAAAATTTCGGAT
68656 ATCCGAAAATTTCGGAT
1 ATCCGAAAATTTCGGAT
68673 A
1 A
68674 CCTAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (17 bp):
ATCCGAAAATTTCGGAT
Found at i:70691 original size:19 final size:19
Alignment explanation
Indices: 70667--70712 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
70657 GTTTTTTTAA
70667 ATTTTATTAATTT-TATTT
1 ATTTTATTAATTTATATTT
* *
70685 ATCTTTATTTATTTATTTTT
1 AT-TTTATTAATTTATATTT
70705 ATTTTATT
1 ATTTTATT
70713 TTATTCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.67
20 6 0.25
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTATTAATTTATATTT
Found at i:70695 original size:14 final size:15
Alignment explanation
Indices: 70676--70713 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
70666 AATTTTATTA
70676 ATTTTATTTATCTTT
1 ATTTTATTTATCTTT
*
70691 A-TTTATTTATTTTT
1 ATTTTATTTATCTTT
70705 ATTTTATTT
1 ATTTTATTT
70714 TATTCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTATTTATCTTT
Found at i:70715 original size:20 final size:21
Alignment explanation
Indices: 70692--70732 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
70682 TTTATCTTTA
*
70692 TTTATTTATTTTTAT-TTTAT
1 TTTATTCATTTTTATATTTAT
*
70712 TTTATTCCTTTTTATATTTAT
1 TTTATTCATTTTTATATTTAT
70733 ATATTTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTCATTTTTATATTTAT
Found at i:70717 original size:10 final size:9
Alignment explanation
Indices: 70667--70713 Score: 58
Period size: 10 Copynumber: 5.0 Consensus size: 9
70657 GTTTTTTTAA
*
70667 ATTTTATTA
1 ATTTTATTT
70676 ATTTTATTT
1 ATTTTATTT
70685 ATCTTTATTT
1 AT-TTTATTT
*
70695 ATTTATTTTT
1 ATTT-TATTT
70705 ATTTTATTT
1 ATTTTATTT
70714 TATTCCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTATTT
Found at i:70737 original size:20 final size:20
Alignment explanation
Indices: 70682--70737 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
70672 ATTAATTTTA
**
70682 TTTATCTTTATT-TATTTATT
1 TTTAT-TTTATTATATTCCTT
*
70702 TTTATTTTATTTTATTCCTT
1 TTTATTTTATTATATTCCTT
70722 TTTATATTTA-TATATT
1 TTTAT-TTTATTATATT
70738 TCATCATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 6 0.19
20 21 0.68
21 4 0.13
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTTATTATATTCCTT
Found at i:83407 original size:15 final size:15
Alignment explanation
Indices: 83387--83453 Score: 74
Period size: 12 Copynumber: 4.9 Consensus size: 15
83377 TTTACCGGAT
*
83387 AAAAAATCGGTTTGA
1 AAAAAACCGGTTTGA
*
83402 AAAAAACCGG-AT--
1 AAAAAACCGGTTTGA
83414 AAAAAACCGGTTTGA
1 AAAAAACCGGTTTGA
83429 AAAAAACCGG-TT--
1 AAAAAACCGGTTTGA
83441 AAAAAACCGGTTT
1 AAAAAACCGGTTT
83454 TTATCCGGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 20 0.44
13 3 0.07
14 3 0.07
15 19 0.42
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.19
Consensus pattern (15 bp):
AAAAAACCGGTTTGA
Found at i:83412 original size:27 final size:27
Alignment explanation
Indices: 83380--83453 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
83370 CGGTTTTTTT
*
83380 ACCGGATAAAAAATCGGTTTGAAAAAA
1 ACCGGATAAAAAACCGGTTTGAAAAAA
83407 ACCGGATAAAAAACCGGTTTGAAAAAA
1 ACCGGATAAAAAACCGGTTTGAAAAAA
*
83434 ACCGGTTAAAAAACCGGTTT
1 ACCGGATAAAAAACCGGTTT
83454 TTATCCGGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (27 bp):
ACCGGATAAAAAACCGGTTTGAAAAAA
Found at i:83715 original size:14 final size:14
Alignment explanation
Indices: 83685--83739 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
83675 TTTAATAATA
*
83685 TTAAAATCGGTTTTT
1 TTAAAACCGG-TTTT
*
83700 TTATAACCGGTTTT
1 TTAAAACCGGTTTT
83714 TTAAAAAAACCGGTTTT
1 TT---AAAACCGGTTTT
83731 TTAAAACCG
1 TTAAAACCG
83740 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 13 0.38
15 8 0.24
17 13 0.38
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (14 bp):
TTAAAACCGGTTTT
Found at i:83736 original size:15 final size:15
Alignment explanation
Indices: 83687--83736 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
83677 TAATAATATT
* *
83687 AAAATCGGTTTTTTT
1 AAAACCGGTTTTTTA
*
83702 ATAACCGGTTTTTTAAA
1 AAAACCGGTTTTTT--A
83719 AAAACCGGTTTTTTA
1 AAAACCGGTTTTTTA
83734 AAA
1 AAA
83737 CCGAAACCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 16 0.55
17 13 0.45
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (15 bp):
AAAACCGGTTTTTTA
Found at i:83748 original size:20 final size:17
Alignment explanation
Indices: 83704--83736 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
83694 GTTTTTTTAT
83704 AACCGGTTTTTTAAAAA
1 AACCGGTTTTTTAAAAA
83721 AACCGGTTTTTTAAAA
1 AACCGGTTTTTTAAAA
83737 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
AACCGGTTTTTTAAAAA
Found at i:83856 original size:15 final size:17
Alignment explanation
Indices: 83830--83861 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
83820 TTCTATGGGA
83830 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
83846 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
83862 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:87769 original size:17 final size:15
Alignment explanation
Indices: 87747--87780 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
87737 TGCAGAGGGT
87747 ATAATAAAAATTTAAAA
1 ATAAT-AAAA-TTAAAA
87764 ATAATAAAATTAAAA
1 ATAATAAAATTAAAA
87779 AT
1 AT
87781 TAAACTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAAAATTAAAA
Found at i:98867 original size:13 final size:13
Alignment explanation
Indices: 98849--98875 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
98839 ATTTTATCAT
98849 TATAATTATTTAA
1 TATAATTATTTAA
98862 TATAATTATTTAA
1 TATAATTATTTAA
98875 T
1 T
98876 TTTATTGGTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATAATTATTTAA
Found at i:99897 original size:19 final size:19
Alignment explanation
Indices: 99873--99912 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
99863 AAATATATAA
99873 GTAACGTGGGAGTTCACAT
1 GTAACGTGGGAGTTCACAT
99892 GTAACGTGGGAGTTCACAT
1 GTAACGTGGGAGTTCACAT
99911 GT
1 GT
99913 CCATGATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
GTAACGTGGGAGTTCACAT
Found at i:102162 original size:42 final size:42
Alignment explanation
Indices: 102115--102231 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
102105 TTTCCCCGAA
* * ** *
102115 TTCCCGTATTTATTTCACGTAATTCATTTTTCGGGAAATGTT
1 TTCCCGTGTTTATTTCACGTAATTCATTTTCCGAAAAATATT
* * *
102157 TTCCCGTGTTTGTTTCACTTAATTCGTTTTCCGAAAAATATT
1 TTCCCGTGTTTATTTCACGTAATTCATTTTCCGAAAAATATT
* *
102199 TTCTCGTGTTTATTTCACGTAATTGATTTTCCG
1 TTCCCGTGTTTATTTCACGTAATTCATTTTCCG
102232 GAATGTAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.49
Consensus pattern (42 bp):
TTCCCGTGTTTATTTCACGTAATTCATTTTCCGAAAAATATT
Found at i:102443 original size:25 final size:25
Alignment explanation
Indices: 102415--102571 Score: 68
Period size: 28 Copynumber: 6.2 Consensus size: 25
102405 CAAATATTAT
102415 TATTTATTTATAATATTTATAATAA
1 TATTTATTTATAATATTTATAATAA
** *
102440 TATTATATTATATTTTATATATAAATAA
1 TATT-TATT-TATAATATTTAT-AATAA
* *
102468 TCAATTATATTATAATA-ATATAAGATATTA
1 T-ATTTAT-TTATAATATTTAT-A-ATA--A
102498 TATTTTATTT-TAATA--TATAATAA
1 TA-TTTATTTATAATATTTATAATAA
102521 -A-TT-TTTAT-ATATTTAATAATGAA
1 TATTTATTTATAATATTT-ATAAT-AA
102544 -ATATTATTTAT-ATATTTA-AATAA
1 TAT-TTATTTATAATATTTATAATAA
102567 T-TTTA
1 TATTTA
102572 ATAAAGATAT
Statistics
Matches: 107, Mismatches: 7, Indels: 39
0.70 0.05 0.25
Matches are distributed among these distances:
19 6 0.06
20 3 0.03
21 1 0.01
22 9 0.08
23 7 0.07
24 3 0.03
25 10 0.09
26 16 0.15
27 18 0.17
28 22 0.21
29 6 0.06
30 6 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
TATTTATTTATAATATTTATAATAA
Found at i:102466 original size:28 final size:27
Alignment explanation
Indices: 102407--102565 Score: 95
Period size: 27 Copynumber: 5.8 Consensus size: 27
102397 ATTTTCATCA
102407 AATATTATTATT-TATTTATAATATTTATAAT
1 AATATTA-TATTATATTT-TAATA--TA-AAT
102438 AATATTATATTATATTTTATATATAAAT
1 AATATTATATTATATTTTA-ATATAAAT
*
102466 AATCAATTATATTATA--ATAATAT-AA-
1 AAT--ATTATATTATATTTTAATATAAAT
* *
102491 GATATTATATTTTATTTTAATATATAAT
1 AATATTATATTATATTTTAATATA-AAT
102519 AA-ATT-T-TTATATATTTAATAATGAAAT
1 AATATTATATTATAT-TTTAAT-AT-AAAT
* *
102546 ATTATT-TA-TATATTTAAATA
1 AATATTATATTATATTTTAATA
102566 ATTTTAATAA
Statistics
Matches: 106, Mismatches: 8, Indels: 33
0.72 0.05 0.22
Matches are distributed among these distances:
23 10 0.09
25 13 0.12
26 10 0.09
27 20 0.19
28 19 0.18
29 2 0.02
30 17 0.16
31 15 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
AATATTATATTATATTTTAATATAAAT
Found at i:102468 original size:31 final size:31
Alignment explanation
Indices: 102407--102481 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
102397 ATTTTCATCA
**
102407 AATATTATTATT-TATTTATAATATTTATAAT
1 AATATTA-TATTATATTTATAATATAAATAAT
102438 AATATTATATTATATTT-TATATATAAATAAT
1 AATATTATATTATATTTATA-ATATAAATAAT
*
102469 CA-ATTATATTATA
1 AATATTATATTATA
102482 ATAATATAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
AATATTATATTATATTTATAATATAAATAAT
Found at i:102560 original size:53 final size:52
Alignment explanation
Indices: 102420--102565 Score: 126
Period size: 53 Copynumber: 2.8 Consensus size: 52
102410 ATTATTATTT
*
102420 ATTTATAATATTT-ATAAT-AATATTATATTATATTTT-ATATATAAATAATC
1 ATTTAT-ATATTTAATAATAAATATTATTTTATATTTTAATATATAAATAATC
* *
102470 AATTATAT-TATAATAATATAAGATATTATATTT-TATTTTAATATAT-AATAAAT-
1 ATTTATATATTTAAT-A-ATAA-ATATTAT-TTTATATTTTAATATATAAAT-AATC
* *
102523 TTTTATATATTTAATAATGAAATATTATTTATATATTTAAATA
1 ATTTATATATTTAATAAT-AAATATTATTT-TATATTTTAATA
102566 ATTTTAATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
48 2 0.03
49 4 0.05
50 6 0.08
51 4 0.05
52 11 0.14
53 34 0.44
54 16 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (52 bp):
ATTTATATATTTAATAATAAATATTATTTTATATTTTAATATATAAATAATC
Found at i:102596 original size:23 final size:23
Alignment explanation
Indices: 102570--102614 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
102560 TAAATAATTT
102570 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
102593 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
102615 ATATAATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:102691 original size:32 final size:29
Alignment explanation
Indices: 102654--102723 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
102644 AATATAGTTT
*
102654 ATAATA-TTTTATTTCACTAAAATATACAAAAA
1 ATAATATTTTTA-TT-AATAAAAT-TA-AAAAA
*
102686 ATAATATTTTTATTAATAAAATTATAAAA
1 ATAATATTTTTATTAATAAAATTAAAAAA
102715 ATAATATTT
1 ATAATATTT
102724 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 13 0.37
30 2 0.06
31 7 0.20
32 8 0.23
33 5 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTAAAAAA
Found at i:102738 original size:30 final size:29
Alignment explanation
Indices: 102682--102740 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
102672 AAAATATACA
* *
102682 AAAAATAATATTTTTATTAATAAAATTAT
1 AAAAATAATATTTTAATAAATAAAATTAT
102711 AAAAATAATATTTAATAATAAAT-AAATTAT
1 AAAAATAATATTT--TAATAAATAAAATTAT
102741 TTTAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 7 0.27
31 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAATAATATTTTAATAAATAAAATTAT
Found at i:102756 original size:49 final size:50
Alignment explanation
Indices: 102702--102800 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
102692 TTTTTATTAA
*
102702 TAAAATTATAAAAATAA-TATTTAATAATAAATAA-ATTATTT-TAATATTT
1 TAAAATAATAAAAATAAGT-TTT-ATAATAAATAATATTATTTATAATATTT
* * * *
102751 TAAAATAATAATATTAAGTTTTATGATAAATAATATTATTTATTATATTT
1 TAAAATAATAAAAATAAGTTTTATAATAAATAATATTATTTATAATATTT
102801 AATATTTGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 10 0.24
49 24 0.57
50 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (50 bp):
TAAAATAATAAAAATAAGTTTTATAATAAATAATATTATTTATAATATTT
Done.