Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002456.1 Hibiscus syriacus cultivar Beakdansim tig00005030_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: 134757
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3682 original size:123 final size:122
Alignment explanation
Indices: 3464--3699 Score: 355
Period size: 123 Copynumber: 1.9 Consensus size: 122
3454 AAGGTTGAAC
* * * * * *
3464 AATGTTGATGTTGATCTATTTCCCTCTGCGACGAGTCGAGCTAAGGTTGAACAAGTTCTTCAGAT
1 AATGTTGATGCTGATCTATCTCCCTCTGCGACAAGTCAAGCAAAGGTTGAACAAGTTCTTCAGAC
* *
3529 TATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCAGATTATGAACTCCTGTCTAGA
66 TATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTATGAACTCCTGTCTAGA
* * * *
3586 AATGTTGATGCTGTTCTATCTCCTTCTGCGATAAGTCAAGCAAAAGGTTGAATAAGTTCTTCAGA
1 AATGTTGATGCTGATCTATCTCCCTCTGCGACAAGTCAAGC-AAAGGTTGAACAAGTTCTTCAGA
3651 CTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTATGAACTC
65 CTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTATGAACTC
3700 ATTCTTCCTC
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
122 34 0.34
123 67 0.66
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (122 bp):
AATGTTGATGCTGATCTATCTCCCTCTGCGACAAGTCAAGCAAAGGTTGAACAAGTTCTTCAGAC
TATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTATGAACTCCTGTCTAGA
Found at i:3799 original size:117 final size:116
Alignment explanation
Indices: 3640--4083 Score: 662
Period size: 117 Copynumber: 3.8 Consensus size: 116
3630 AGGTTGAATA
* * *
3640 AGTTCTTCAGACTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCAGATTATGAACTCATTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCATCTTCAGACGAGTTCTTCAGACTATGAACTCATTCT
3705 TCCTCTTCATATGAGTTCTTCAGACTATGAACTCTTTCTTCCTCTTCAGACG
66 TCCTCTTCATATGAGTTCTTCAGACTATGAACTC-TTCTTCCTCTTCAGACG
* * * *
3757 AGTTCTTCAGACTATGAACTCCTTCTTCATTTTCAAACGAGTTCTTTAGATTATGAACTTCGA--
1 AGTTCTTCAGACTATGAACTCCTTCTTCATCTTCAGACGAGTTCTTCAGACTATGAAC-TC-ATT
** * * *
3820 CTTTATCTTCAGACGAGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGACG
64 CTTCCTCTTCATATGAGTTCTTCAGACTATGAACTC-TTCTTCCTCTTCAGACG
* * *
3874 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCATCTTCAGACGAGTTCTTCAGACTATGAACTCATTCT
* *
3939 TCCTCTTCATATAAGTTCTTCAGATTATGAACTC--CTTCCTCTTCAGACG
66 TCCTCTTCATATGAGTTCTTCAGACTATGAACTCTTCTTCCTCTTCAGACG
*
3988 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCATTCT
1 AGTTCTTCAGACTATGAACTCCTTCTTCATCTTCAGACGAGTTCTTCAGACTATGAACTCATTCT
4053 TCCTCTTCATATGAGTTCTTCAGACTATGAA
66 TCCTCTTCATATGAGTTCTTCAGACTATGAA
4084 ATCATTCTGG
Statistics
Matches: 296, Mismatches: 27, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
114 107 0.36
116 2 0.01
117 184 0.62
118 2 0.01
119 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.39
Consensus pattern (116 bp):
AGTTCTTCAGACTATGAACTCCTTCTTCATCTTCAGACGAGTTCTTCAGACTATGAACTCATTCT
TCCTCTTCATATGAGTTCTTCAGACTATGAACTCTTCTTCCTCTTCAGACG
Found at i:4089 original size:39 final size:39
Alignment explanation
Indices: 3640--4091 Score: 601
Period size: 39 Copynumber: 11.7 Consensus size: 39
3630 AGGTTGAATA
* *
3640 AGTTCTTCAGACTATGAACTTC-TTCTTCATCTTCAGATG
1 AGTTCTTCAGACTATGAAC-TCATTCTTCCTCTTCAGACG
* * *
3679 AGTTCTTCAGATTATGAACTCATTCTTCCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
*
3718 AGTTCTTCAGACTATGAACTCTTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
* * * *
3757 AGTTCTTCAGACTATGAACTCCTTCTTCATTTTCAAACG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
* * **
3796 AGTTCTTTAGATTATGAACTTCGA--CTTTATCTTCAGACG
1 AGTTCTTCAGACTATGAAC-TC-ATTCTTCCTCTTCAGACG
*
3835 AGTTCTTCAGATTATGAACTCATTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
* *
3874 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
* * **
3913 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCATATA
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
*
3952 AGTTCTTCAGATTATGAACTC---CTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
*
3988 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
* *
4027 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
*
4066 AGTTCTTCAGACTATGAAATCATTCT
1 AGTTCTTCAGACTATGAACTCATTCT
4092 GGAAATGTTT
Statistics
Matches: 371, Mismatches: 34, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
36 32 0.09
37 1 0.00
38 4 0.01
39 332 0.89
40 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.39
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTCATTCTTCCTCTTCAGACG
Found at i:4221 original size:72 final size:73
Alignment explanation
Indices: 4098--4355 Score: 403
Period size: 72 Copynumber: 3.6 Consensus size: 73
4088 TTCTGGAAAT
*
4098 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAATTTTCTCCAGCGAGA
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAATTTTCTCCAGCGAGA
4163 AACAATTC
66 AACAATTC
*
4171 GTTTTAAG-AAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTTAAATTTTCTCCAGCGAGA
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAATTTTCTCCAGCGAGA
*
4235 AACATTTC
66 AACAATTC
* * * *
4243 GTTTTAAG-AAAACAATCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTTTCTCAAGCGAGA
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAATTTTCTCCAGCGAGA
* *
4307 AACAGTTT
66 AACAATTC
* *
4315 GTTTTAAGAAAAACAATATCAAGTGAAATAAATTGCTATTT
1 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
4356 GAAAACATCC
Statistics
Matches: 171, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
72 134 0.78
73 37 0.22
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (73 bp):
GTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAATTTTCTCCAGCGAGA
AACAATTC
Found at i:4299 original size:37 final size:37
Alignment explanation
Indices: 4114--4306 Score: 114
Period size: 37 Copynumber: 5.3 Consensus size: 37
4104 AGAAAAACAA
* * * * *
4114 TCTCAAGTGAGATAAATTGTTATTTCGAGTGAAATTT
1 TCTCAAGCGAGATAAATTGCTATTTCAAGTAAAACTT
* * **
4151 TCTCCAGCGAGAAACAATT-CGT-TTT-AAG-AAAACAA
1 TCTCAAGCGAGATA-AATTGC-TATTTCAAGTAAAACTT
* * * *
4186 TCTCAAGTGAGATAAATTGCTATTTCGAGTTAAATTT
1 TCTCAAGCGAGATAAATTGCTATTTCAAGTAAAACTT
* * **
4223 TCTCCAGCGAGA-AACATTTCGT-TTT-AAG-AAAACAA
1 TCTCAAGCGAGATAA-ATTGC-TATTTCAAGTAAAACTT
* * *
4258 TCTCAAGTGAGATAAATTACTATTTCAAGTGAAACTT
1 TCTCAAGCGAGATAAATTGCTATTTCAAGTAAAACTT
4295 TCTCAAGCGAGA
1 TCTCAAGCGAGA
4307 AACAGTTTGT
Statistics
Matches: 112, Mismatches: 32, Indels: 24
0.67 0.19 0.14
Matches are distributed among these distances:
34 6 0.05
35 38 0.34
36 13 0.12
37 49 0.44
38 6 0.05
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (37 bp):
TCTCAAGCGAGATAAATTGCTATTTCAAGTAAAACTT
Found at i:5077 original size:22 final size:22
Alignment explanation
Indices: 5052--5106 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
5042 AATAAAGCTT
5052 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
5074 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
5096 CCATCTTTGAA
1 TCATCTTTGAA
5107 GAATGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:5569 original size:54 final size:54
Alignment explanation
Indices: 5475--5622 Score: 251
Period size: 54 Copynumber: 2.7 Consensus size: 54
5465 ATAATCAATG
*
5475 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCACAGAT
* * *
5529 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGTTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCACAGAT
*
5583 GTTCGTAAAACATTGGACAACACATTCATCATTTCCTGTG
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTG
5623 ACTTTTGCTT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCACAGAT
Found at i:6040 original size:75 final size:75
Alignment explanation
Indices: 5904--6076 Score: 231
Period size: 75 Copynumber: 2.3 Consensus size: 75
5894 GATATAGGCC
* * * *
5904 TTCAGCATGCCCCAACATTTACTAATGCAGACGTTCAAAATACGCCAACATTCCTGATTCTGATT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATACGCCAACATTCCTAATTCTGATT
5969 GAAATGGGCT
66 GAAATGGGCT
* * * ** *
5979 TTCAGCATGCCCCATCATTTGCTGATACAAACGTTCAAAATGCTTCAATATT-CTAATTTCTGAT
1 TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATACGCCAACATTCCTAA-TTCTGAT
6043 TGAAATGGGCT
65 TGAAATGGGCT
*
6054 TTCAGCATGCCCTAACATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
6077 TCTTGTTGAC
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 3 0.04
75 82 0.96
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTAATACAAACGTTCAAAATACGCCAACATTCCTAATTCTGATT
GAAATGGGCT
Found at i:9898 original size:35 final size:38
Alignment explanation
Indices: 9859--9941 Score: 102
Period size: 35 Copynumber: 2.3 Consensus size: 38
9849 GCAAAGATGC
*
9859 AAATGCAAAAAATG-AAAATGTAAATAC-AA-ATGTAA
1 AAATGCAAAAAATGCAAAATGCAAATACAAAGATGTAA
* * *
9894 AAATGC-AAAGATGCGAAATGCAAATACAAAGATGTAG
1 AAATGCAAAAAATGCAAAATGCAAATACAAAGATGTAA
9931 AAATGCAAAAA
1 AAATGCAAAAA
9942 TAAGAATGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 6 0.15
35 17 0.44
36 2 0.05
37 11 0.28
38 3 0.08
ACGTcount: A:0.59, C:0.08, G:0.16, T:0.17
Consensus pattern (38 bp):
AAATGCAAAAAATGCAAAATGCAAATACAAAGATGTAA
Found at i:9923 original size:21 final size:22
Alignment explanation
Indices: 9894--9939 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
9884 ACAAATGTAA
* *
9894 AAATGCAAAGATG-CGAAATGC
1 AAATACAAAGATGTAGAAATGC
9915 AAATACAAAGATGTAGAAATGC
1 AAATACAAAGATGTAGAAATGC
9937 AAA
1 AAA
9940 AATAAGAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.54, C:0.11, G:0.20, T:0.15
Consensus pattern (22 bp):
AAATACAAAGATGTAGAAATGC
Found at i:10589 original size:67 final size:67
Alignment explanation
Indices: 10481--10615 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
10471 TGACTGATCT
10481 TTTGGAAATCCTTACACATGATGTTCATTTTTGTACTTAATTTATTGTTTTCATTCTTCAAATAA
1 TTTGGAAATCCTTACACATGATGTTCATTTTTGTACTTAATTTATTGTTTTCATTCTTCAAATAA
10546 CA
66 CA
* *
10548 TTTGGAAATCCTTACACATGGTGTTCATTTTTGTACTTAATTTCTTGTTTTCATTCTTCAAATAA
1 TTTGGAAATCCTTACACATGATGTTCATTTTTGTACTTAATTTATTGTTTTCATTCTTCAAATAA
10613 CA
66 CA
10615 T
1 T
10616 GCTTGAGCTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (67 bp):
TTTGGAAATCCTTACACATGATGTTCATTTTTGTACTTAATTTATTGTTTTCATTCTTCAAATAA
CA
Found at i:11613 original size:64 final size:63
Alignment explanation
Indices: 11490--11626 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
11480 CCCTTAACAT
* * *
11490 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTTGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTTGATGTTTTCATTTTAA-AGA
* * * ** *
11554 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTTGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTTGATGTTTTCAT-TTTAAAGA
11617 GTGCATCGAT
1 GTGCATCGAT
11627 ACACATTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 18 0.29
64 44 0.71
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTTGATGTTTTCATTTTAAAGA
Found at i:14985 original size:23 final size:23
Alignment explanation
Indices: 14966--15018 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
14956 AAGGCACTGA
*
14966 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACGTAGAAATGCACCGT
*
14989 AGTGCCTCGTAGAAATGCACCGT
1 AGTGCCACGTAGAAATGCACCGT
15012 AGTGCCA
1 AGTGCCA
15019 TATAAGATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAAATGCACCGT
Found at i:16747 original size:64 final size:63
Alignment explanation
Indices: 16624--16760 Score: 143
Period size: 64 Copynumber: 2.2 Consensus size: 63
16614 CCCTTAACAT
* * * *
16624 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCAATACACAAATCACATTCGATGTTTTCATTTTAA-AGA
* * * ** *
16688 GTGCATCGATGCACT-CCTTATGCATCAATGCACTAATTGCATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCAATACACAAATCACATTCGATGTTTTCAT-TTTAAAGA
16751 GTGCATCGAT
1 GTGCATCGAT
16761 ACACATTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
63 18 0.30
64 43 0.70
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCAATACACAAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:20107 original size:23 final size:23
Alignment explanation
Indices: 20081--20149 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
20071 CACCACAGCT
* * *
20081 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGTAGTGCCA
* *
20104 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCA
*
20127 CATAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGTAGTGCCA
20150 TATAAGATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCA
Found at i:24952 original size:13 final size:15
Alignment explanation
Indices: 24915--24951 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
24905 TCTCTCTCTT
*
24915 AGAGAGAGAAGCCTA
1 AGAGAGAGAAGCCGA
24930 AGAGAGAGAAGCCGA
1 AGAGAGAGAAGCCGA
*
24945 AAAGAGA
1 AGAGAGA
24952 AACGAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.11, G:0.35, T:0.03
Consensus pattern (15 bp):
AGAGAGAGAAGCCGA
Found at i:25498 original size:6 final size:7
Alignment explanation
Indices: 25432--25516 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 7
25422 TTTTATTACT
25432 TTTTATA
1 TTTTATA
25439 TTTTA-A
1 TTTTATA
**
25445 TAGTATA
1 TTTTATA
25452 GTTTTA-A
1 -TTTTATA
25459 TTTTATTTA
1 TTTTA--TA
25468 TTTTAGTCA
1 TTTTA-T-A
*
25477 TTTTTTA
1 TTTTATA
25484 -TTTATA
1 TTTTATA
25490 TTTTA-A
1 TTTTATA
25496 TTTTATA
1 TTTTATA
25503 TATTTATA
1 T-TTTATA
25511 TATTTA
1 T-TTTA
25517 ATTATTATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
6 20 0.32
7 14 0.23
8 17 0.27
9 11 0.18
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (7 bp):
TTTTATA
Found at i:25508 original size:21 final size:23
Alignment explanation
Indices: 25482--25524 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
25472 AGTCATTTTT
25482 TATTTATAT-TTTAATT-TTATA
1 TATTTATATATTTAATTATTATA
25503 TATTTATATATTTAATTATTAT
1 TATTTATATATTTAATTATTAT
25525 TGTTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTTATATATTTAATTATTATA
Found at i:25522 original size:37 final size:38
Alignment explanation
Indices: 25433--25522 Score: 93
Period size: 37 Copynumber: 2.5 Consensus size: 38
25423 TTTATTACTT
* *
25433 TTTATAT-TTTAA-TA-GTATAGTTTTAATTTTATTTA
1 TTTATATATTTAATTATTTATAGTTTTAATTTTATATA
*
25468 TTT-TAGTCATTT-TTTATTTATA-TTTTAATTTTATATA
1 TTTATA-T-ATTTAATTATTTATAGTTTTAATTTTATATA
25505 TTTATATATTTAATTATT
1 TTTATATATTTAATTATT
25523 ATTGTTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
34 2 0.05
35 4 0.09
36 4 0.09
37 28 0.64
38 6 0.14
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (38 bp):
TTTATATATTTAATTATTTATAGTTTTAATTTTATATA
Found at i:25904 original size:139 final size:139
Alignment explanation
Indices: 25654--25907 Score: 382
Period size: 139 Copynumber: 1.8 Consensus size: 139
25644 TAATCATATT
* * *
25654 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAAAAGTCATTTTT
1 TTAATATTTATTTATTTTTTAATATTAAAAAATGAGCTGTCTTAAAGCACCTAAAAGTCATTTTC
* * ** *
25719 TAATATTCTTAAATAAATAAATATCATATTTTTATAAATTATATATATATTAATTTATTTTAATA
66 TAATATTCCTAAATAAATAAATATCATATTTATATAAAACAAATATATATTAATTTATTTTAATA
25784 AATGTTTTA
131 AATGTTTTA
* * * *
25793 TTAATATTTATTTATTTTTTAATATTAAAAAATGAGTTGTCTTAAAGTACCTAGAAGTCCTTTTC
1 TTAATATTTATTTATTTTTTAATATTAAAAAATGAGCTGTCTTAAAGCACCTAAAAGTCATTTTC
* *
25858 TAATATTCCTAAGTAAATAAATATCTTATTTATATAAAACAAATATATAT
66 TAATATTCCTAAATAAATAAATATCATATTTATATAAAACAAATATATAT
25908 ATATATATAT
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
139 101 1.00
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (139 bp):
TTAATATTTATTTATTTTTTAATATTAAAAAATGAGCTGTCTTAAAGCACCTAAAAGTCATTTTC
TAATATTCCTAAATAAATAAATATCATATTTATATAAAACAAATATATATTAATTTATTTTAATA
AATGTTTTA
Found at i:25935 original size:2 final size:2
Alignment explanation
Indices: 25900--25927 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25890 TATAAAACAA
25900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25928 CAATATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26504 original size:21 final size:20
Alignment explanation
Indices: 26480--26531 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
26470 ATATTTATTG
*
26480 TATTTTTTATTATTAATGTTT
1 TATTTTTTATTATTAA-ATTT
*
26501 TA-TTTTCATGTATTAAATTT
1 TATTTTTTAT-TATTAAATTT
*
26521 TATTCTTTATT
1 TATTTTTTATT
26532 TGTTTATCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (20 bp):
TATTTTTTATTATTAAATTT
Found at i:33592 original size:18 final size:18
Alignment explanation
Indices: 33547--33593 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
33537 AAGATCCCTC
33547 CATATTCAGAAGATGGCA
1 CATATTCAGAAGATGGCA
*
33565 CCTCATTCAGAAGA-GGCA
1 CAT-ATTCAGAAGATGGCA
33583 CATATCTCAGA
1 CATAT-TCAGA
33594 CGTTTCTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 13 0.52
19 10 0.40
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (18 bp):
CATATTCAGAAGATGGCA
Found at i:35594 original size:22 final size:22
Alignment explanation
Indices: 35566--35632 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
35556 TATCTACATC
35566 TACATTCTTCAAAGATGATAGA
1 TACATTCTTCAAAGATGATAGA
*
35588 TACATTCTTCAAAGACGATAGA
1 TACATTCTTCAAAGATGATAGA
* *
35610 TTC-TCTTTTCAAAGATGATAGA
1 TACAT-TCTTCAAAGATGATAGA
35632 T
1 T
35633 TCTCTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (22 bp):
TACATTCTTCAAAGATGATAGA
Found at i:35633 original size:22 final size:22
Alignment explanation
Indices: 35573--35649 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
35563 ATCTACATTC
* *
35573 TTCAAAGATGATAGATACAT-TC
1 TTCAAAGATGATAGATTC-TCTT
*
35595 TTCAAAGACGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
35617 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
35639 TTTAAAGATGA
1 TTCAAAGATGA
35650 AAGCTTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
21 1 0.02
22 48 0.98
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:36420 original size:45 final size:45
Alignment explanation
Indices: 36364--36477 Score: 120
Period size: 45 Copynumber: 2.5 Consensus size: 45
36354 GGGAGCTTTT
* *** *
36364 TGATATTTTCAAAGCCTTCGGGTCATGTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCATAAGCCCTGCAGTGCA
* * *
36409 TGATGTTTTCAAAACCTTCGGGTTATCCATAAGTCCTGCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCATAAGCCCTGCAGTGCA
* *
36454 GGATGTCTTCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
36478 AGCTTTTTGA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 45 0.80
47 11 0.20
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCATAAGCCCTGCAGTGCA
Found at i:36484 original size:121 final size:121
Alignment explanation
Indices: 36270--36783 Score: 812
Period size: 121 Copynumber: 4.2 Consensus size: 121
36260 TTCCCACATT
* * * * *
36270 TGTAAGCCTTTCAGTGCATGCTGTTTTCAAAACCTTCGGGTCATCCATAAGACTTGCAGTACATG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGG
* * * *
36335 ATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATG
66 ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
* *
36391 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTTATCCATAAGTCCTGCAGTGCAGG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGG
*
36456 ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATCTTCAAAACCTTCGGGTCATC
66 ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
* * * * *
36512 TGTAATCCCTTCAGTGCAAGATATTTTCAAAACCTTCTGCTCATCCATAAGACCTGCAGTGCAGG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGG
36577 ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
66 ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
* ** * * *
36633 TGTAAGCCTTTCAACGCATGATGTTTTCAAAACCTTCGGGTCAACCATAAGACCAGCAGTGTAGG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGG
36698 ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
66 ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
*
36754 TGTAAACCCTTCAGTGCATGATGTTTTCAA
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAA
36784 CATTTTCGTT
Statistics
Matches: 358, Mismatches: 35, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 358 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (121 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGG
ATGTCTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
Found at i:36572 original size:45 final size:45
Alignment explanation
Indices: 36486--36597 Score: 116
Period size: 45 Copynumber: 2.4 Consensus size: 45
36476 GGAGCTTTTT
* ** ** *
36486 GATATCTTCAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCAA
1 GATATCTTCAAAACCTTCGGCTCATCCATAAGACCTGCAGTGCAA
* * *
36531 GATATTTTCAAAACCTTCTGCTCATCCATAAGACCTGCAGTGCAG
1 GATATCTTCAAAACCTTCGGCTCATCCATAAGACCTGCAGTGCAA
*
36576 GATGTCTTCAAAAAGCCTTCGG
1 GATATCTTC-AAAA-CCTTCGG
36598 GAGCTTTTTG
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
45 43 0.81
46 4 0.08
47 6 0.11
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (45 bp):
GATATCTTCAAAACCTTCGGCTCATCCATAAGACCTGCAGTGCAA
Found at i:36662 original size:76 final size:74
Alignment explanation
Indices: 36531--36672 Score: 169
Period size: 76 Copynumber: 1.9 Consensus size: 74
36521 TTCAGTGCAA
* **
36531 GATATTTTCAAAACCTTCTGCTCATCCATAAGACCTGCAGTGCAGGATGTCTTCAAAAAGCCTTC
1 GATATTTTCAAAACCTTCGGCTCATCCATAAGACCTGCAACGCAGGATGTCTTC-AAAA-CCTTC
36596 GGGAGCTTTTT
64 GGGAGCTTTTT
* ** * * *
36607 GATATTTTCAAAACCTTCGGGTCATCTGTAAG-CCTTTCAACGCATGATGTTTTCAAAACCTTCG
1 GATATTTTCAAAACCTTCGGCTCATCCATAAGACC-TGCAACGCAGGATGTCTTCAAAACCTTCG
36671 GG
65 GG
36673 TCAACCATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
74 8 0.14
75 6 0.11
76 42 0.75
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (74 bp):
GATATTTTCAAAACCTTCGGCTCATCCATAAGACCTGCAACGCAGGATGTCTTCAAAACCTTCGG
GAGCTTTTT
Found at i:38353 original size:21 final size:22
Alignment explanation
Indices: 38307--38351 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
38297 TCATTGTTTA
38307 TTTATAT-TTTAATTTTATATG
1 TTTATATATTTAATTTTATATG
38328 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATT-TTATATG
38350 TT
1 TT
38352 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTTTATATG
Found at i:38633 original size:139 final size:141
Alignment explanation
Indices: 38477--38732 Score: 410
Period size: 139 Copynumber: 1.8 Consensus size: 141
38467 TAATCATATT
**
38477 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGTCATTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATAAGTTGTCTTAAAGCACCTAGAAGTCATTTTC
*
38542 TGATA-TTCTTAAATAAATAAATATCATATTT-TTATAAAT-TATATATATATTAATTTATTTTA
66 TGATATTTC-TAAATAAATAAATATCATATTTATAATAAATATATATATATATTAATTTATTTTA
38604 ATAAATGTTTTA
130 ATAAATGTTTTA
* *
38616 TTAATATTTATTTATTTTTTAATATTAAGAAATAAGTTGTCTTAAAGTACCTAGAAGTCATTTTT
1 TTAATATTTATTTATTTTTTAATATTAAGAAATAAGTTGTCTTAAAGCACCTAGAAGTCATTTTC
* * *
38681 TGATATTTCTAAGTAAATAAATATCTTATTTATAATATATATATATATATAT
66 TGATATTTCTAAATAAATAAATATCATATTTATAATAAATATATATATATAT
38733 ATATATATAT
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
139 86 0.81
140 9 0.08
141 11 0.10
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (141 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATAAGTTGTCTTAAAGCACCTAGAAGTCATTTTC
TGATATTTCTAAATAAATAAATATCATATTTATAATAAATATATATATATATTAATTTATTTTAA
TAAATGTTTTA
Found at i:38752 original size:2 final size:2
Alignment explanation
Indices: 38711--38744 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38701 ATATCTTATT
38711 TA TA -A TA 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 TA TA TA TA T
38745 CAATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42304 original size:45 final size:44
Alignment explanation
Indices: 42207--42308 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 44
42197 CACATTCAAT
* * *
42207 GTGTATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTA
1 GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTA
* * ** *
42251 GTGCATCGATGCACCCCCTTAAA-ATGAAAACATCGAAGGTGATTG
1 GTGTATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTA
42296 GTGTATCGATGCA
1 GTGTATCGATGCA
42309 TGAGTAGTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 14 0.30
45 33 0.70
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (44 bp):
GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTA
Found at i:42368 original size:20 final size:20
Alignment explanation
Indices: 42300--42373 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
42290 TGATTGGTGT
42300 ATCGATGCA-TG-AGTAGTGC
1 ATCGATGCACTGTAG-AGTGC
*
42319 ATCGATGCACATGTTAAAGAATGC
1 ATCGATGCAC-TG-T--AGAGTGC
*
42343 ATCGATGCACTGTAGAGTGT
1 ATCGATGCACTGTAGAGTGC
42363 ATCGATGCACT
1 ATCGATGCACT
42374 TCAAAGGGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 9 0.20
20 16 0.35
21 2 0.04
22 1 0.02
23 2 0.04
24 14 0.30
25 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (20 bp):
ATCGATGCACTGTAGAGTGC
Found at i:43508 original size:19 final size:19
Alignment explanation
Indices: 43484--43521 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43474 TTCTATGTGC
**
43484 TATATGAAGTATATATGAT
1 TATATGAACAATATATGAT
43503 TATATGAACAATATATGAT
1 TATATGAACAATATATGAT
43522 ATGTAGGTTT
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:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (19 bp):
TATATGAACAATATATGAT
Found at i:44611 original size:57 final size:57
Alignment explanation
Indices: 44542--44658 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
44532 TCACTATTTT
* *
44542 ATACAAGTAAATGTTTTGAGAAGTCAATGTGACACCTCGGACTTGGATCCGGGTCGG
1 ATACAAGTAAATGTTTTGAAAAGTCAATGTGACACCTCGGACTCGGATCCGGGTCGG
44599 ATACAAGTAAATGTTTTGAAAAGTCAATGTGACACCTCGGACTCGGATCCGGGTCGG
1 ATACAAGTAAATGTTTTGAAAAGTCAATGTGACACCTCGGACTCGGATCCGGGTCGG
44656 ATA
1 ATA
44659 TGAGTTGGGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (57 bp):
ATACAAGTAAATGTTTTGAAAAGTCAATGTGACACCTCGGACTCGGATCCGGGTCGG
Found at i:78709 original size:25 final size:25
Alignment explanation
Indices: 78680--78729 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
78670 GATTAGGGGT
*
78680 ACTGAAGCATAAATATGTAGGGATA
1 ACTGAAGCATAAACATGTAGGGATA
*
78705 ACTGAAGCATAAACATGTAGTGATA
1 ACTGAAGCATAAACATGTAGGGATA
78730 TGGTTCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (25 bp):
ACTGAAGCATAAACATGTAGGGATA
Found at i:79232 original size:18 final size:18
Alignment explanation
Indices: 79209--79262 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
79199 AGGGTTCAAC
*
79209 GTGGTCCTACGGGACATA
1 GTGGTCCTACAGGACATA
79227 GTGGTCCTACAGGACATA
1 GTGGTCCTACAGGACATA
*
79245 GTGGTCTTACAGGACATA
1 GTGGTCCTACAGGACATA
79263 TGTGTTCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (18 bp):
GTGGTCCTACAGGACATA
Found at i:79359 original size:14 final size:14
Alignment explanation
Indices: 79340--79367 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
79330 ATTATACGAG
79340 CTGTGGTGACAGCA
1 CTGTGGTGACAGCA
79354 CTGTGGTGACAGCA
1 CTGTGGTGACAGCA
79368 TATTGCACAA
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:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (14 bp):
CTGTGGTGACAGCA
Found at i:82770 original size:23 final size:23
Alignment explanation
Indices: 82737--82861 Score: 157
Period size: 23 Copynumber: 5.5 Consensus size: 23
82727 TGCATAATGT
82737 ATCGATGCA-TCCCTTGAATATGC
1 ATCGATGCACT-CCTTGAATATGC
* * *
82760 ATCGATACA-T-CATGAAGATGC
1 ATCGATGCACTCCTTGAATATGC
*
82781 ATTGATGCACTCCTTGAATATGC
1 ATCGATGCACTCCTTGAATATGC
*
82804 ACCGATGCACTCCTTGAATATGC
1 ATCGATGCACTCCTTGAATATGC
* *
82827 ACCGATGCACTCCTTGAATGTGC
1 ATCGATGCACTCCTTGAATATGC
82850 ATCGATGCACTC
1 ATCGATGCACTC
82862 TGCTGTGCAT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
21 16 0.18
22 1 0.01
23 72 0.81
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (23 bp):
ATCGATGCACTCCTTGAATATGC
Found at i:85309 original size:64 final size:65
Alignment explanation
Indices: 85185--85340 Score: 194
Period size: 64 Copynumber: 2.4 Consensus size: 65
85175 CACACCCATT
*
85185 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATACTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCATGAATACTTTGAAACA
*
85249 TCGAATGCATTTTGTGTACCGATGCAC-AGACCATGCATCGATGCACTCCATG-CT-CATTTGAA
1 TCGAATGCATTTTGTGTACCGATGCACAAG-CCATGCATCGATGCACT-CATGAATAC-TTTGAA
85311 ACA
63 ACA
* * * * *
85314 TCAAATGTAATTAGTGCACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
85341 CCGTTGTATA
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
63 3 0.04
64 49 0.60
65 29 0.36
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCATGAATACTTTGAAACA
Found at i:91207 original size:60 final size:59
Alignment explanation
Indices: 91098--91240 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 59
91088 AAATTGTTTT
* *
91098 TTAAACTTTT-AATATTCCAATTTAATTTTTAAATTATGACTTTCATTCTAAATTAGTCC
1 TTAAACTTTTGAATATTCTAATTTAATTTTTAAACTATGACTTTCATTCTAAATTAGT-C
* * * * *
91157 TTAAACTTTTGAACATTCTAATTTTATTTTTAAACTATTACTCTT-TTTCTAAATTGGTC
1 TTAAACTTTTGAATATTCTAATTTAATTTTTAAACTATGACT-TTCATTCTAAATTAGTC
*
91216 TTCAAACTTTTGAATATTTTAATTT
1 TT-AAACTTTTGAATATTCTAATTT
91241 CATCCCCAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
59 13 0.18
60 57 0.79
61 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (59 bp):
TTAAACTTTTGAATATTCTAATTTAATTTTTAAACTATGACTTTCATTCTAAATTAGTC
Found at i:94876 original size:37 final size:36
Alignment explanation
Indices: 94777--94896 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 36
94767 TGGTAACCAA
*
94777 TTTTGAAAAAATGGTTTTT-AAAGTTTGGTAAATGTT
1 TTTTG-AAAAATAGTTTTTCAAAGTTTGGTAAATGTT
*
94813 TATTTG-AAAAT-GATTTTCAAAGTTTGGTAAATGTT
1 T-TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTT
*
94848 TCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTT
1 T-TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTT
*
94885 TGTTGAAAAATA
1 TTTTGAAAAATA
94897 ATAATGGGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
34 5 0.07
35 27 0.36
36 16 0.21
37 27 0.36
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (36 bp):
TTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTT
Found at i:99410 original size:21 final size:21
Alignment explanation
Indices: 99386--99446 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
99376 AACTTTGAAA
99386 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
99407 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
99421 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
99442 AAATG
1 AAATG
99447 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:99477 original size:37 final size:37
Alignment explanation
Indices: 99378--99496 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
99368 TGGTAACCAA
99378 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
99415 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
99450 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
99487 -GTTGAAAAAT
1 CTTTGAAAAAT
99497 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:103557 original size:17 final size:18
Alignment explanation
Indices: 103526--103563 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
103516 ATATTATATA
103526 TTATATATAATTCTACAT
1 TTATATATAATTCTACAT
103544 TTATATAT-ATTCTACAT
1 TTATATATAATTCTACAT
103561 TTA
1 TTA
103564 CATTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATATATAATTCTACAT
Found at i:103571 original size:17 final size:17
Alignment explanation
Indices: 103530--103571 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
103520 TATATATTAT
*
103530 ATATAATTCTACATTTAT
1 ATAT-ATTCTACATTTAC
103548 ATATATTCTACATTTAC
1 ATATATTCTACATTTAC
*
103565 ATTTATT
1 ATATATT
103572 TAAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATTCTACATTTAC
Found at i:105337 original size:10 final size:10
Alignment explanation
Indices: 105304--105345 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
105294 CGAACACAAG
105304 AAATGAACAT
1 AAATGAACAT
* *
105314 AAACGAACGT
1 AAATGAACAT
105324 AAATGAACAT
1 AAATGAACAT
*
105334 AAATGAAAAT
1 AAATGAACAT
105344 AA
1 AA
105346 TTTTTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.17
Consensus pattern (10 bp):
AAATGAACAT
Found at i:113013 original size:30 final size:30
Alignment explanation
Indices: 112977--113044 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
112967 TTAGTCCTTA
112977 AGCTTCAACTATAAATACCCTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
*
113007 AGCTTCAACTATAAATACCTTAGCTCATTT
1 AGCTTCAACTATAAATACCCTAGCTCATTT
113037 AGCTTCAA
1 AGCTTCAA
113045 AATCATCCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTAGCTCATTT
Found at i:121388 original size:21 final size:21
Alignment explanation
Indices: 121364--121404 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
121354 CATAAAATGG
121364 TTATAAATTA-ATGTAAAATAT
1 TTATAAATTATAT-TAAAATAT
*
121385 TTATATATTATATTAAAATA
1 TTATAAATTATATTAAAATA
121405 AGTACTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTATAAATTATATTAAAATAT
Found at i:124766 original size:15 final size:16
Alignment explanation
Indices: 124743--124780 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
124733 GGGGATGGGT
124743 GGATTTAAGGGT-TAG
1 GGATTTAAGGGTATAG
*
124758 GGTTTTAAGGGTATAG
1 GGATTTAAGGGTATAG
124774 GGATTTA
1 GGATTTA
124781 GAGATTGGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
GGATTTAAGGGTATAG
Done.