Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001825.1 Hibiscus syriacus cultivar Beakdansim tig00003693_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: 103959
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3985 original size:23 final size:23
Alignment explanation
Indices: 3959--4017 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
3949 TAGTACATAT
3959 ATAATAAATAAATAAAAACAAGA-
1 ATAA-AAATAAATAAAAACAAGAG
* *
3982 ATAAAAATAAA-ATAAATAAGAG
1 ATAAAAATAAATAAAAACAAGAG
4004 ATAAAAA-AAATAAA
1 ATAAAAATAAATAAA
4018 GGAAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 11 0.35
22 16 0.52
23 4 0.13
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (23 bp):
ATAAAAATAAATAAAAACAAGAG
Found at i:4023 original size:25 final size:24
Alignment explanation
Indices: 3984--4067 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 24
3974 AAACAAGAAT
**
3984 AAAAATAAAATAAATAAGAGATAAA
1 AAAAATAAAGGAAATAA-AGATAAA
4009 AAAAATAAAGGAAATAATAG-TAAGA
1 AAAAATAAAGGAAATAA-AGATAA-A
* *
4034 TAAAGAT-AAGGAAATAAATA-AAA
1 -AAAAATAAAGGAAATAAAGATAAA
4057 ATAAAATAAAG
1 A-AAAATAAAG
4068 AAAAAGTCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 5 0.10
24 9 0.19
25 28 0.58
26 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (24 bp):
AAAAATAAAGGAAATAAAGATAAA
Found at i:4079 original size:16 final size:15
Alignment explanation
Indices: 3964--4082 Score: 55
Period size: 16 Copynumber: 7.5 Consensus size: 15
3954 CATATATAAT
* *
3964 AAATAAATAAAAACA
1 AAATAAAGAAAAATA
*
3979 AGAATAAAAATAAAAT-
1 A-AATAAAGA-AAAATA
3995 AAATAAGAGATAAAA-A
1 AAATAA-AGA-AAAATA
4011 AAATAAAGGAAATAATA
1 AAATAAA-GAAA-AATA
* **
4028 GTAAGATAAAG-ATAAGG
1 --AA-ATAAAGAAAAATA
*
4045 AAATAAATAAAAATA
1 AAATAAAGAAAAATA
*
4060 AAATAAAGAAAAAGTC
1 AAATAAAGAAAAA-TA
4076 AAATAAA
1 AAATAAA
4083 TATTAAAACA
Statistics
Matches: 80, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
14 5 0.06
15 26 0.32
16 33 0.41
17 7 0.09
18 1 0.01
19 3 0.04
20 5 0.06
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.16
Consensus pattern (15 bp):
AAATAAAGAAAAATA
Found at i:4161 original size:2 final size:2
Alignment explanation
Indices: 4154--4184 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4144 AAGGGGGCCC
4154 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
4185 ACACTAGGTA
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:4291 original size:27 final size:27
Alignment explanation
Indices: 4241--4293 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
4231 CAAATAAAAA
4241 AAAGAAAAAAATAAATAAAAAAATAAC
1 AAAGAAAAAAATAAATAAAAAAATAAC
* *
4268 AAAG-AAAGAATAAATAATACAAATAA
1 AAAGAAAAAAATAAATAA-AAAAATAA
4294 TAATAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (27 bp):
AAAGAAAAAAATAAATAAAAAAATAAC
Found at i:4386 original size:2 final size:2
Alignment explanation
Indices: 4381--4411 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4371 GAAAAAATAA
*
4381 AT AT AT AA 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
4412 AAAGTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4388 original size:8 final size:8
Alignment explanation
Indices: 4377--4413 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
4367 AATAGAAAAA
4377 ATAAATAT
1 ATAAATAT
4385 ATAAATAT
1 ATAAATAT
*
4393 ATATATAT
1 ATAAATAT
*
4401 ATATATAT
1 ATAAATAT
4409 ATAAA
1 ATAAA
4414 AGTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAAATAT
Found at i:4444 original size:12 final size:11
Alignment explanation
Indices: 4375--4489 Score: 60
Period size: 12 Copynumber: 10.2 Consensus size: 11
4365 AAAATAGAAA
4375 AAATAAATATAT
1 AAAT-AATATAT
4387 AAATATATATAT
1 AAATA-ATATAT
*
4399 ATATATATATAT
1 AAATA-ATATAT
* *
4411 AAA-AGTA-AA
1 AAATAATATAT
4420 AAATAATA-A-
1 AAATAATATAT
4429 AAATAATAGTAT
1 AAATAATA-TAT
* * *
4441 AAATAAAAAACC
1 AAATAATATA-T
4453 AAATATATATAT
1 AAATA-ATATAT
*
4465 ATATAATTAATAT
1 AAATAA-T-ATAT
4478 AAATAATA-AT
1 AAATAATATAT
4488 AA
1 AA
4490 GGGATACTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
9 12 0.15
10 10 0.12
11 6 0.07
12 41 0.51
13 12 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
AAATAATATAT
Found at i:6708 original size:2 final size:2
Alignment explanation
Indices: 6701--6755 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
6691 GTTTAATTGT
6701 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6743 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
6756 TCACTGGTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10965 original size:17 final size:17
Alignment explanation
Indices: 10943--10976 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10933 CGGTACGGAT
10943 GGAGTCATTCGAGAAGA
1 GGAGTCATTCGAGAAGA
10960 GGAGTCATTCGAGAAGA
1 GGAGTCATTCGAGAAGA
10977 ATCCAGATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (17 bp):
GGAGTCATTCGAGAAGA
Found at i:12457 original size:2 final size:2
Alignment explanation
Indices: 12447--12487 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
12437 GTTTTTTTAT
*
12447 TA TA CTA TA TA -A TA TT TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12488 ATTGTTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12471 original size:16 final size:16
Alignment explanation
Indices: 12446--12489 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
12436 GGTTTTTTTA
*
12446 TTATACTATATAATAT
1 TTATAATATATAATAT
12462 TTATAATATAT-ATAT
1 TTATAATATATAATAT
*
12477 ATAT-ATATATAAT
1 TTATAATATATAAT
12490 TGTTGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 9 0.36
16 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAATATATAATAT
Found at i:12480 original size:19 final size:19
Alignment explanation
Indices: 12442--12485 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12432 TGAAGGTTTT
*
12442 TTTATTATACTATATAATA
1 TTTATAATACTATATAATA
12461 TTTATAATA-TATATATATA
1 TTTATAATACTATATA-ATA
*
12480 TATATA
1 TTTATA
12486 TAATTGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATAATACTATATAATA
Found at i:12575 original size:17 final size:17
Alignment explanation
Indices: 12553--12595 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
12543 AAACGTGTAT
12553 AATATATAATTTTTGAA
1 AATATATAATTTTTGAA
**
12570 AATATATTGTTTTTGAA
1 AATATATAATTTTTGAA
12587 AA-ATATAAT
1 AATATATAAT
12596 ATGTTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
AATATATAATTTTTGAA
Found at i:12777 original size:14 final size:14
Alignment explanation
Indices: 12722--12791 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 14
12712 TTATTATTAC
*
12722 ATTTTATTATATAAT
1 ATTTTTTTATAT-AT
* *
12737 ATTTATTGTACATATT
1 ATTT-TTTTATATA-T
*
12753 ATTATTATTATATAT
1 ATT-TTTTTATATAT
*
12768 ATTTTTTTATTTAT
1 ATTTTTTTATATAT
*
12782 TTTTTTTTAT
1 ATTTTTTTAT
12792 TTATTTCAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
14 18 0.42
15 9 0.21
16 15 0.35
17 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (14 bp):
ATTTTTTTATATAT
Found at i:12792 original size:14 final size:14
Alignment explanation
Indices: 12769--12797 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12759 ATTATATATA
12769 TTTTTTTATTTATT
1 TTTTTTTATTTATT
12783 TTTTTTTATTTATT
1 TTTTTTTATTTATT
12797 T
1 T
12798 CAGGTCTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTATTTATT
Found at i:15640 original size:29 final size:32
Alignment explanation
Indices: 15555--15640 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 32
15545 TAGATTACAT
*
15555 AACTTTT-TAAAA-TTACACTTTGGTC-TCTA
1 AACTTTTCCAAAATTTACACTTTGGTCATCTA
* * *
15584 AACTTTTCCAAAGTTTATACTTTAGTCAT-TA
1 AACTTTTCCAAAATTTACACTTTGGTCATCTA
*
15615 AAC-TTT-CAAAATTTACATTTTGGTCA
1 AACTTTTCCAAAATTTACACTTTGGTCA
15641 CTAGTCAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 23 0.50
30 6 0.13
31 16 0.35
32 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (32 bp):
AACTTTTCCAAAATTTACACTTTGGTCATCTA
Found at i:18551 original size:55 final size:55
Alignment explanation
Indices: 18437--18559 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 55
18427 TGCAAAAAGT
* * * * ** *
18437 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTACGTATGGGAAATATATGTAAAAAAA
* *
18492 TAAGAAATTCATACTAAGTGTATGAATTTATGTATTGGAAATATATGTAAAAAAA
1 TAAGAAATTCATACTAAGTGTATGAATTTACGTATGGGAAATATATGTAAAAAAA
*
18547 TAAGAAGTTCATA
1 TAAGAAATTCATA
18560 ATAATTAGGT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (55 bp):
TAAGAAATTCATACTAAGTGTATGAATTTACGTATGGGAAATATATGTAAAAAAA
Found at i:18826 original size:68 final size:67
Alignment explanation
Indices: 18742--18936 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 67
18732 CAAGATTAAT
*
18742 GGCCTAACTGTGCATTTGATAGAAAGGTGACAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG-TAAGTGCCTT
18807 TGA
65 TGA
* * *
18810 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTT--A-G--A--T--GTGCCTTT
1 GGCCTAACTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTAAGTGCCTTT
*
18866 CA
66 GA
* * *
18868 GGCCTAACTGTGCATTTGATAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGTTAAATGTCTT
1 GGCCTAACTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG-TAAGTGCCTT
18933 TGA
65 TGA
18936 G
1 G
18937 TAAAAGACTA
Statistics
Matches: 105, Mismatches: 12, Indels: 20
0.77 0.09 0.15
Matches are distributed among these distances:
58 49 0.47
60 2 0.02
61 1 0.01
63 2 0.02
65 1 0.01
66 2 0.02
68 48 0.46
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (67 bp):
GGCCTAACTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTAAGTGCCTTT
GA
Found at i:19033 original size:45 final size:45
Alignment explanation
Indices: 18982--19385 Score: 655
Period size: 45 Copynumber: 9.0 Consensus size: 45
18972 ATAAAAATGA
* * *
18982 CATGAAAGAATGCCAAAATAATAATGCATATGGGTGAATTAATGG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* ***
19027 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATCAA
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* *
19072 TATAAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
*
19117 CATGAAAGGATGCCAAAATAATAATGCATATGGTTGCATTATTGG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
*
19162 CATGAAAGGATGCCAAAATAATGATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* *
19207 CATGAAAGGATGCCAAAATAATGATGCATATTGGTGCATTATTGG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
*
19252 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
19297 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
** *
19342 CATGAAAAAATGTCAAAATAATAATGCATATGGGTGCATTATTG
1 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTG
19386 ACATAATATA
Statistics
Matches: 333, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 333 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (45 bp):
CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
Found at i:20866 original size:16 final size:17
Alignment explanation
Indices: 20845--20876 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20835 CTCAAGAAGG
20845 AAATAAAAG-ATTTTAA
1 AAATAAAAGCATTTTAA
20861 AAATAAAAGCATTTTA
1 AAATAAAAGCATTTTA
20877 TTTAACTTAA
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:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATAAAAGCATTTTAA
Found at i:28628 original size:58 final size:58
Alignment explanation
Indices: 28565--28954 Score: 508
Period size: 58 Copynumber: 6.8 Consensus size: 58
28555 ATGGCACTAA
*
28565 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* **
28623 GTGTGCAAAAAGTTAAGAAATTCATACTAACTAAATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
28681 GTGTACAAAAAGTTAAGAAATTCATACTAAGTGTATTAATTTTCGTATTGGACACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * * * *
28739 CTGTGCAAAAAGTTAAAAAATTCATACTAAGCGTATGAATTTTCATATCGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
28797 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTT-C-TATATGGGTACTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT-TGGGCACTTT
* * * **
28854 GTGT--ACAAA-TCTAACAAATTCATACTAAGTGTATGAATTTCCATA-TGGGCACAAT
1 GTGTGCAAAAAGT-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
28909 GTGTGC-AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
28955 GGAAATATAT
Statistics
Matches: 292, Mismatches: 33, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
54 1 0.00
55 76 0.26
56 7 0.02
57 14 0.05
58 194 0.66
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:29277 original size:68 final size:68
Alignment explanation
Indices: 29168--29372 Score: 338
Period size: 68 Copynumber: 3.0 Consensus size: 68
29158 CAAGATTAAT
*
29168 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
29233 TGA
66 TGA
* *
29236 GGCCTAACTGTGCATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
29301 TGA
66 TGA
* * * * *
29304 GGCCTAACTGTACATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAATGTTAAATGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
29369 TGA
66 TGA
29372 G
1 G
29373 TAAAAGACTA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 127 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:29539 original size:45 final size:45
Alignment explanation
Indices: 29418--29852 Score: 572
Period size: 45 Copynumber: 9.7 Consensus size: 45
29408 ATAAAAATAA
*
29418 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTAATGG
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* *
29463 CATGAAA-GAATG-CAAAATAATAATGTATATGGGTGCATTATCGG
1 CATGAAATG-ATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* ***
29507 CATGAAATGAAGCCAAAATAATAATGCATATGGGTGCATTATCAA
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* * * *
29552 CATGAAAGGATGCCCAAATAATAATGCATATGGGCGTATTATTGG
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* * *
29597 CATGAAATTATGCCAAAATAATGATGCATATGGGTACATTATTGG
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* *
29642 CATGAAATGATGCCAAAATAATGATGCATATGGGTGCATTATTGA
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* * * *
29687 CATGAAATGATGTCAAAATATTGATGCATATAGGTGCATTATTGG
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
*
29732 CATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
* * * *
29777 CATGAAAGGATGTCAAAATAATAATGCATATGGATGCACTATTGG
1 CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
*
29822 CATGATA-GAATGCCATAAATGAA-AATGCATA
1 CATGAAATG-ATGCCA-AAAT-AATAATGCATA
29853 ATAGCGTATT
Statistics
Matches: 345, Mismatches: 39, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
44 40 0.12
45 291 0.84
46 12 0.03
47 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (45 bp):
CATGAAATGATGCCAAAATAATAATGCATATGGGTGCATTATTGG
Found at i:35151 original size:28 final size:28
Alignment explanation
Indices: 35111--35168 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
35101 GACGAGATGA
35111 TAATACCGCTTCAAAGTGTAATTTAACT
1 TAATACCGCTTCAAAGTGTAATTTAACT
35139 TAATACCGCTTCAAAGTGTAATTTAACT
1 TAATACCGCTTCAAAGTGTAATTTAACT
35167 TA
1 TA
35169 CATTTTCCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (28 bp):
TAATACCGCTTCAAAGTGTAATTTAACT
Found at i:49370 original size:23 final size:22
Alignment explanation
Indices: 49310--49379 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 22
49300 TGACTTTTTT
*
49310 GGTCAAAGTCAACGGTCAGACC
1 GGTCAAAGTCAACGATCAGACC
* * *
49332 AGTCAAAATCAACGATCTGACC
1 GGTCAAAGTCAACGATCAGACC
49354 GGTCAACAGTCAACGATCAGACC
1 GGTCAA-AGTCAACGATCAGACC
49377 GGT
1 GGT
49380 TAACGGTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 23 0.57
23 17 0.43
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (22 bp):
GGTCAAAGTCAACGATCAGACC
Found at i:50178 original size:18 final size:17
Alignment explanation
Indices: 50155--50191 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
50145 TATGAAAATG
*
50155 AAATAAGACAACAATACA
1 AAATAAGAAAACAA-ACA
50173 AAATAAGAAAACAAACA
1 AAATAAGAAAACAAACA
50190 AA
1 AA
50192 CTATACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.73, C:0.14, G:0.05, T:0.08
Consensus pattern (17 bp):
AAATAAGAAAACAAACA
Found at i:52925 original size:4 final size:4
Alignment explanation
Indices: 52916--52988 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
52906 ATTAAATTAA
52916 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
52964 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
52989 CCTATTGCGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:53114 original size:41 final size:42
Alignment explanation
Indices: 53069--53150 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
53059 AAAGTACACT
*
53069 TTATTGCGGCATTTGTT-ACTA-AAACGCCACTATTAATGAAC
1 TTATTGCGGCATTT-TTAAATACAAACGCCACTATTAATGAAC
* *
53110 TTATTGTGGCATTTTTAAATACAAACGCCACTATTGATGAA
1 TTATTGCGGCATTTTTAAATACAAACGCCACTATTAATGAA
53151 ACCTACTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 2 0.06
41 16 0.44
42 18 0.50
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (42 bp):
TTATTGCGGCATTTTTAAATACAAACGCCACTATTAATGAAC
Found at i:54563 original size:42 final size:42
Alignment explanation
Indices: 54517--54605 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
54507 CGTTTTAGAA
* * *
54517 ATAAACGCCACTAATTTATCATTATATTATGGCATTTGTGGT
1 ATAAACGCCACTAATTTATAAATATATTACGGCATTTGTGGT
* **
54559 ATAAACGCCACTAATTTATAAATCTATTACGGTGTTTGTGGT
1 ATAAACGCCACTAATTTATAAATATATTACGGCATTTGTGGT
54601 ATAAA
1 ATAAA
54606 TGTCGCTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (42 bp):
ATAAACGCCACTAATTTATAAATATATTACGGCATTTGTGGT
Found at i:55139 original size:41 final size:42
Alignment explanation
Indices: 55015--55142 Score: 120
Period size: 42 Copynumber: 3.1 Consensus size: 42
55005 TATTATGGAA
* * * *
55015 TTTGTTGTATAAACGCCACT-AATTTACAAATCTATTACGGCG
1 TTTGTGGTATAAACGCCGCTAAATTAAC-ACTCTATTACGGCG
* * *
55057 TTTGTGGTATAAATGTCGCTAAATTAACACTATATTACGGCG
1 TTTGTGGTATAAACGCCGCTAAATTAACACTCTATTACGGCG
* *
55099 TTTG-GGCTA-AAACGCCGCTAAA-TATCTACTCTATTGCGGCG
1 TTTGTGG-TATAAACGCCGCTAAATTAAC-ACTCTATTACGGCG
55140 TTT
1 TTT
55143 TCATTATAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
40 3 0.04
41 28 0.39
42 34 0.48
43 6 0.08
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (42 bp):
TTTGTGGTATAAACGCCGCTAAATTAACACTCTATTACGGCG
Found at i:57259 original size:4 final size:4
Alignment explanation
Indices: 57250--57297 Score: 78
Period size: 4 Copynumber: 12.0 Consensus size: 4
57240 AACAAATTCA
* *
57250 AAAT AAAT AAAT AAAT AAAT GAAT AAAT AAAT GAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
57298 CAAACAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:57524 original size:109 final size:111
Alignment explanation
Indices: 57318--57538 Score: 428
Period size: 109 Copynumber: 2.0 Consensus size: 111
57308 TATTAAGGAA
57318 CTAAATAAAATTCAATATAATTAAAATTTTGAAATAAATTAATAAATAAAAATTACCGCTGGATT
1 CTAAATAAAATTCAATATAATTAAAATTTTGAAATAAATTAATAAATAAAAATTACCGCTGGATT
57383 ATCCCGCCAATATGTGCATACATGTGGAAGATCAACCTTTACTAGT
66 ATCCCGCCAATATGTGCATACATGTGGAAGATCAACCTTTACTAGT
57429 CTAAATAAAATTC-ATATAATTAAAATTTTGAAATAAA-TAATAAATAAAAATTACCGCTGGATT
1 CTAAATAAAATTCAATATAATTAAAATTTTGAAATAAATTAATAAATAAAAATTACCGCTGGATT
57492 ATCCCGCCAATATGTGCATACATGTGGAAGATCAACCTTTACTAGT
66 ATCCCGCCAATATGTGCATACATGTGGAAGATCAACCTTTACTAGT
57538 C
1 C
57539 CCAGCATAAT
Statistics
Matches: 110, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
109 73 0.66
110 24 0.22
111 13 0.12
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (111 bp):
CTAAATAAAATTCAATATAATTAAAATTTTGAAATAAATTAATAAATAAAAATTACCGCTGGATT
ATCCCGCCAATATGTGCATACATGTGGAAGATCAACCTTTACTAGT
Found at i:58216 original size:31 final size:31
Alignment explanation
Indices: 58171--58240 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
58161 AAACTATAAG
*
58171 TTTAG-CATCCGATCATTATGAATGTTTTGT
1 TTTAGTCATCCGATCATTATGAATATTTTGT
*
58201 TTTAGTCATCTGATCATTATGAATATTTTGT
1 TTTAGTCATCCGATCATTATGAATATTTTGT
58232 TTTAGTCAT
1 TTTAGTCAT
58241 TCAATTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.50
Consensus pattern (31 bp):
TTTAGTCATCCGATCATTATGAATATTTTGT
Found at i:59679 original size:3 final size:3
Alignment explanation
Indices: 59666--59698 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
59656 AAAATATATA
59666 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
59699 AATGATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:63096 original size:32 final size:32
Alignment explanation
Indices: 63047--63108 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
63037 TCTTACGTTT
* *
63047 ACTAACTGATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACTGATTTATTTTCTTTTGATTGTGTAC
*
63079 ACTAACTTATTTATTTTCTTTTGATTGTGT
1 ACTAACTGATTTATTTTCTTTTGATTGTGT
63109 CATTTTTTTC
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:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (32 bp):
ACTAACTGATTTATTTTCTTTTGATTGTGTAC
Found at i:65350 original size:14 final size:15
Alignment explanation
Indices: 65333--65362 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
65323 TATTTTTACA
65333 TTTGCA-TTTGCATC
1 TTTGCATTTTGCATC
65347 TTTGCATTTTGCATC
1 TTTGCATTTTGCATC
65362 T
1 T
65363 GCATTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTGCATTTTGCATC
Found at i:67307 original size:36 final size:36
Alignment explanation
Indices: 67260--67332 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
67250 AATGAGTATA
*
67260 TTCACTGCGGAAGAAGATGCTCTGAAAGATGAAACC
1 TTCACTGCGGAAGAAGATGCTCCGAAAGATGAAACC
67296 TTCACTGCGGAAGAAGATGCTCCGAAAGATGAAACC
1 TTCACTGCGGAAGAAGATGCTCCGAAAGATGAAACC
67332 T
1 T
67333 GGAAAATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (36 bp):
TTCACTGCGGAAGAAGATGCTCCGAAAGATGAAACC
Found at i:70326 original size:22 final size:22
Alignment explanation
Indices: 70298--70340 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
70288 GTATCCTTTG
* *
70298 ATGTTGTTTCTCTTGAAACAAA
1 ATGTTGTCTCGCTTGAAACAAA
*
70320 ATGTTGTCTCGCTTGAGACAA
1 ATGTTGTCTCGCTTGAAACAA
70341 TTTCCTCTCA
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:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (22 bp):
ATGTTGTCTCGCTTGAAACAAA
Found at i:70586 original size:33 final size:34
Alignment explanation
Indices: 70504--70595 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 34
70494 AGTTTTCCTC
*
70504 AAAACACCAAATTCTGAGAT-TGTTTCACTCGAAAT
1 AAAA-ACCATATT-TGAGATCTGTTTCACTCGAAAT
* *
70539 AAAAATCATCTTTGAG-TCTGTTTCACT-GAAA-
1 AAAAACCATATTTGAGATCTGTTTCACTCGAAAT
70570 ACAACAACCATATTTGAGATC-GTTTC
1 A-AA-AACCATATTTGAGATCTGTTTC
70596 TCTTTAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
31 1 0.02
32 7 0.15
33 29 0.60
34 7 0.15
35 4 0.08
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (34 bp):
AAAAACCATATTTGAGATCTGTTTCACTCGAAAT
Found at i:84897 original size:2 final size:2
Alignment explanation
Indices: 84890--84936 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
84880 CTCTAAAGGT
84890 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
84931 TA TA TA
1 TA TA TA
84937 AAATTAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:85449 original size:14 final size:14
Alignment explanation
Indices: 85430--85459 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
85420 AAATGAAAAC
*
85430 ATAATTTTTCCGAA
1 ATAATTTTTCCCAA
85444 ATAATTTTTCCCAA
1 ATAATTTTTCCCAA
85458 AT
1 AT
85460 TATGAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (14 bp):
ATAATTTTTCCCAA
Found at i:90527 original size:21 final size:21
Alignment explanation
Indices: 90501--90550 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
90491 ACTCATAGGA
90501 GTATCGATACTTGACCCTACG
1 GTATCGATACTTGACCCTACG
*
90522 GTATCGATACTTGACCCTAGG
1 GTATCGATACTTGACCCTACG
90543 GTATCGAT
1 GTATCGAT
90551 TCTACTCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (21 bp):
GTATCGATACTTGACCCTACG
Found at i:93088 original size:20 final size:19
Alignment explanation
Indices: 93065--93131 Score: 53
Period size: 23 Copynumber: 3.2 Consensus size: 19
93055 AATATTTTAG
93065 AAATTTTATTATTATTATTA
1 AAATTTTATT-TTATTATTA
93085 AAATATGTTATTTTTTATTAATCTA
1 AAAT-T-TTA--TTTTATT-AT-TA
* *
93110 AAATATTATTTAATTATTA
1 AAATTTTATTTTATTATTA
93129 AAA
1 AAA
93132 ATATAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
19 5 0.13
20 6 0.15
21 7 0.18
22 3 0.08
23 8 0.21
24 4 0.10
25 6 0.15
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
AAATTTTATTTTATTATTA
Found at i:93118 original size:23 final size:24
Alignment explanation
Indices: 93075--93129 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
93065 AAATTTTATT
93075 ATTATT-ATTAAAATATGTTATTT-
1 ATTATTAATTAAAATA-GTTATTTA
*
93098 TTTATTAATCTAAAATA-TTATTTA
1 ATTATTAAT-TAAAATAGTTATTTA
93122 ATTATTAA
1 ATTATTAA
93130 AAATATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 11 0.41
24 9 0.33
25 7 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTATTAATTAAAATAGTTATTTA
Found at i:100642 original size:65 final size:65
Alignment explanation
Indices: 100518--100694 Score: 231
Period size: 65 Copynumber: 2.8 Consensus size: 65
100508 GAAGTTGATC
* * * *
100518 TTTGAATT-AGATATCATTCGTTGTGAAGTTGAAATCCAA---GGA-T-TGTTTCACCAAATTGG
1 TTTGAATTGA-ATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGG
100577 T
65 T
* *
100578 TTTGAGTTGAATATGCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGT
1 TTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGT
* *
100643 TTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTT
1 TTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTT
100695 ATGTCACTTC
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
60 33 0.33
61 1 0.01
63 2 0.02
64 1 0.01
65 64 0.63
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.38
Consensus pattern (65 bp):
TTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGT
Done.