Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004261.1 Hibiscus syriacus cultivar Beakdansim tig00009336_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: 87989
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2880 original size:10 final size:10
Alignment explanation
Indices: 2836--2882 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
2826 GTAACAACCC
2836 ATAACAACTA
1 ATAACAACTA
*
2846 AGAACAAGCTA
1 ATAACAA-CTA
*
2857 ATAACAAAC-C
1 ATAAC-AACTA
2867 ATAACAACTA
1 ATAACAACTA
2877 ATAACA
1 ATAACA
2883 CTCTAACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 3 0.10
10 17 0.57
11 8 0.27
12 2 0.07
ACGTcount: A:0.60, C:0.21, G:0.04, T:0.15
Consensus pattern (10 bp):
ATAACAACTA
Found at i:4427 original size:11 final size:11
Alignment explanation
Indices: 4411--4459 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
4401 ACCAACAACC
4411 ATAACAAACTA
1 ATAACAAACTA
*
4422 ATAACAAGCTA
1 ATAACAAACTA
*
4433 ATAACAAA-TC
1 ATAACAAACTA
*
4443 ATAACAAGCTA
1 ATAACAAACTA
4454 ATAACA
1 ATAACA
4460 CTCTAACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 8 0.25
11 24 0.75
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.18
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:4448 original size:21 final size:22
Alignment explanation
Indices: 4411--4459 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
4401 ACCAACAACC
4411 ATAACAAACTAATAACAAGCTA
1 ATAACAAACTAATAACAAGCTA
*
4433 ATAACAAA-TCATAACAAGCTA
1 ATAACAAACTAATAACAAGCTA
4454 ATAACA
1 ATAACA
4460 CTCTAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.18
Consensus pattern (22 bp):
ATAACAAACTAATAACAAGCTA
Found at i:6014 original size:11 final size:11
Alignment explanation
Indices: 5998--6046 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
5988 ACCAACAACC
*
5998 ATAACAAATTA
1 ATAACAAACTA
*
6009 ATAACAAGCTA
1 ATAACAAACTA
*
6020 ATAACAAAC-C
1 ATAACAAACTA
6030 ATAACAAACTA
1 ATAACAAACTA
6041 ATAACA
1 ATAACA
6047 CTCTAACACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.61, C:0.18, G:0.02, T:0.18
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:10797 original size:39 final size:39
Alignment explanation
Indices: 10738--10834 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
10728 AAAATTTTGC
* *
10738 TTTATTTTC-ATTTTAATCCCTATTTGCAGTCGATGTGG
1 TTTATTTGCAATTTCAATCCCTATTTGCAGTCGATGTGG
10776 TTTATTTGCAATTTCAATCCCTATTTGCAGTCGATGTGG
1 TTTATTTGCAATTTCAATCCCTATTTGCAGTCGATGTGG
10815 TTTATTTGCAATTTCAATCC
1 TTTATTTGCAATTTCAATCC
10835 TTAGTTTTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
38 8 0.14
39 48 0.86
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (39 bp):
TTTATTTGCAATTTCAATCCCTATTTGCAGTCGATGTGG
Found at i:11229 original size:29 final size:29
Alignment explanation
Indices: 11196--11258 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
11186 TATTTACACA
11196 TATTTTATTAT-TTT-TCGTTTATCCATTTT
1 TATTTTATT-TGTTTAT-GTTTATCCATTTT
*
11225 TATTTTATTTGTTTATGTTTATTCATTTT
1 TATTTTATTTGTTTATGTTTATCCATTTT
*
11254 AATTT
1 TATTT
11259 ATATCATGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (29 bp):
TATTTTATTTGTTTATGTTTATCCATTTT
Found at i:17658 original size:53 final size:53
Alignment explanation
Indices: 17539--17852 Score: 380
Period size: 53 Copynumber: 5.9 Consensus size: 53
17529 TATTTAAATG
* * ****
17539 ACGGGTCCGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTCTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCT
** * * * * * *
17593 ATAGGTTTGCTCCCTATTGCTTCAGGGAGTAGAACTTGAATAATGTTCTGCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * *
17646 ATGGGTTCGCTCCCTCTTGCTTCAGGGGGTAGAACTCGAATAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * * *
17699 ACGGGTTCACTCCCTCTTGCTCCAAGGAGTAGAACTCGAACAATCTTCTACCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * *
17752 ACGGGTTCGCTCCCTCTCGCTTCAGGGAGTAAAACTCGAACAATCTTCTGTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
17805 ACGGGTTC-CTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
17853 AGTGTGATTC
Statistics
Matches: 223, Mismatches: 36, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
52 38 0.17
53 161 0.72
54 15 0.07
55 9 0.04
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
Found at i:18350 original size:42 final size:41
Alignment explanation
Indices: 18229--18357 Score: 159
Period size: 42 Copynumber: 3.1 Consensus size: 41
18219 AGGTCTTATG
* * * * * *
18229 GATGACCCGAATGACTTATCATCTTGCTCGATAGACTCACA
1 GATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACT
* *
18270 AATGACCCGAAGGATTTAATCGTCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACT
*
18312 GATGAACCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACT
18354 GATG
1 GATG
18358 GATTTGCTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 14 0.19
42 61 0.81
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACT
Found at i:18506 original size:93 final size:93
Alignment explanation
Indices: 18347--18532 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 93
18337 TGCTCGAAAG
* ** * *
18347 ACTTACTGATGGATTTGCTTCACTACTCTTCGGCGAAGGCTTACCAGTTACCCGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGCGAAGGCTTAAAAATTACCCGAAGAATTTAAT
**
18412 CATCATGTTCGAAAGACTTACTAATGGC
66 CATCATACTCGAAAGACTTACTAATGGC
*
18440 ACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAATTACCCGAAGAATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCCGCGAAGGCTTAAAAATTACCCGAAGAATTTAAT
*
18505 CATCATACTCGAAAGACTTACTGATGGC
66 CATCATACTCGAAAGACTTACTAATGGC
18533 TCGAAGAACT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (93 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCCGCGAAGGCTTAAAAATTACCCGAAGAATTTAAT
CATCATACTCGAAAGACTTACTAATGGC
Found at i:18557 original size:22 final size:22
Alignment explanation
Indices: 18492--18559 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
18482 AAAAATTACC
* *
18492 CGAAGAATTTAATCATCATACT
1 CGAAGAACTTAATCATCATGCT
*
18514 CGAA-AGACTT-A-C-TGATGGCT
1 CGAAGA-ACTTAATCATCAT-GCT
18534 CGAAGAACTTAATCATCATGCT
1 CGAAGAACTTAATCATCATGCT
18556 CGAA
1 CGAA
18560 AGACTTACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
19 3 0.08
20 11 0.31
21 4 0.11
22 15 0.42
23 3 0.08
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (22 bp):
CGAAGAACTTAATCATCATGCT
Found at i:18565 original size:22 final size:22
Alignment explanation
Indices: 18500--18566 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
18490 CCCGAAGAAT
*
18500 TTAATCATCATACTCGAAAGAC
1 TTAATCATCATGCTCGAAAGAC
*
18522 TT-A-C-TGATGGCTCG-AAGAAC
1 TTAATCATCAT-GCTCGAAAG-AC
18542 TTAATCATCATGCTCGAAAGAC
1 TTAATCATCATGCTCGAAAGAC
18564 TTA
1 TTA
18567 CTAAGTGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
19 6 0.17
20 9 0.25
21 2 0.06
22 13 0.36
23 6 0.17
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (22 bp):
TTAATCATCATGCTCGAAAGAC
Found at i:23281 original size:8 final size:8
Alignment explanation
Indices: 23258--23292 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
23248 ACTTCACTTT
23258 TTCTTTTC
1 TTCTTTTC
23266 TTTTCTTTTC
1 --TTCTTTTC
23276 TTCTTTTC
1 TTCTTTTC
23284 TTCTTTTC
1 TTCTTTTC
23292 T
1 T
23293 GATTTTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:23281 original size:13 final size:13
Alignment explanation
Indices: 23258--23292 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
23248 ACTTCACTTT
23258 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
23271 TT-TTCTTCTTTTC
1 TTCTT-TTCTTTTC
23284 TTCTTTTCT
1 TTCTTTTCT
23293 GATTTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:46017 original size:25 final size:23
Alignment explanation
Indices: 45939--46018 Score: 56
Period size: 25 Copynumber: 3.3 Consensus size: 23
45929 TCAATATTCT
* *
45939 TTCATAAATTATTTTTCAAAA-C
1 TTCATCAATTATTTTTAAAAATC
* *
45961 TTCATCAAATATTTTGTAAAAAAATA
1 TTCATCAATTATTTT-T--AAAAATC
*
45987 TT-ATCAATTATTTTTTAAAATTTC
1 TTCATCAATTA-TTTTTAAAA-ATC
46011 TTCATCAA
1 TTCATCAA
46019 ATTTCTTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
22 13 0.30
23 5 0.11
24 3 0.07
25 17 0.39
26 6 0.14
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.46
Consensus pattern (23 bp):
TTCATCAATTATTTTTAAAAATC
Found at i:49938 original size:3 final size:3
Alignment explanation
Indices: 49926--49962 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
49916 TCTTTGAACA
*
49926 TAT T-T TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49963 GAAAAATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:51215 original size:3 final size:3
Alignment explanation
Indices: 51207--51243 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
51197 GTTTGGGCAC
51207 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
51244 GAAGGATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55654 original size:24 final size:25
Alignment explanation
Indices: 55627--55689 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
55617 GTCTTTGTAA
55627 ATAATAATAATAATAATATAT-TAT
1 ATAATAATAATAATAATATATATAT
*
55651 ATAAT-ATGTATAATAATATATATAT
1 ATAATAAT-AATAATAATATATATAT
*
55676 ATATTAA-AATAATA
1 ATAATAATAATAATA
55690 CTCGGACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.06
24 23 0.70
25 7 0.21
26 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
ATAATAATAATAATAATATATATAT
Found at i:55656 original size:21 final size:22
Alignment explanation
Indices: 55630--55689 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
55620 TTTGTAAATA
55630 ATAATAATAATAATATAT-TAT
1 ATAATAATAATAATATATATAT
55651 ATAATATGTATAATAATATATATAT
1 ATAATA---ATAATAATATATATAT
*
55676 ATATTAA-AATAATA
1 ATAATAATAATAATA
55690 CTCGGACGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 13 0.38
22 1 0.03
24 12 0.35
25 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAATAATAATATATATAT
Found at i:55895 original size:35 final size:35
Alignment explanation
Indices: 55856--55922 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
55846 GATATGTTCC
*
55856 TGCTTCACTACTCTTTTGTGAAAGCTTGATTGCAT
1 TGCTTCACTACTCTTTTGTGAAAGCTTAATTGCAT
* *
55891 TGCTTCATTACTCTTTTGTGAAGGCTTAATTG
1 TGCTTCACTACTCTTTTGTGAAAGCTTAATTG
55923 ACTTGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (35 bp):
TGCTTCACTACTCTTTTGTGAAAGCTTAATTGCAT
Found at i:56108 original size:94 final size:93
Alignment explanation
Indices: 55919--56101 Score: 276
Period size: 94 Copynumber: 2.0 Consensus size: 93
55909 TGAAGGCTTA
* *
55919 ATTGACTTGAAAAGAATCTATTTCACTACTCTTCCATGAAGATCATATTCGAAGTTGGATTACTT
1 ATTGACTTGAAAAGAATCTATTTCACTACTCTTCCATGAAGATCAGACTCGAAGTTGGATTACTT
* *
55984 CGCTACTCTTCCGTGAAGTTTGAAAATG
66 CACTACTCTTCCGTGAAGGTTGAAAATG
* ***
56012 ATTGACTTGAGAAGAATCTAATTTCACTACTCTTTTGTGAAGATCAGACTCGAAGTTGGATTACT
1 ATTGACTTGAAAAGAATCT-ATTTCACTACTCTTCCATGAAGATCAGACTCGAAGTTGGATTACT
*
56077 TCACTACTTTTCCGTGAAGGTTGAA
65 TCACTACTCTTCCGTGAAGGTTGAA
56102 TTTGATTTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 18 0.22
94 62 0.77
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (93 bp):
ATTGACTTGAAAAGAATCTATTTCACTACTCTTCCATGAAGATCAGACTCGAAGTTGGATTACTT
CACTACTCTTCCGTGAAGGTTGAAAATG
Found at i:56112 original size:36 final size:36
Alignment explanation
Indices: 56072--56143 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
56062 CGAAGTTGGA
*
56072 TTACTTCACTACTTTTCCGTGAAGGTTGAATTTGAT
1 TTACTTCACTACTCTTCCGTGAAGGTTGAATTTGAT
56108 TTACTTCACTACTCTTCCGTGAAGGTTGAATTTGAT
1 TTACTTCACTACTCTTCCGTGAAGGTTGAATTTGAT
56144 CTGACTTGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (36 bp):
TTACTTCACTACTCTTCCGTGAAGGTTGAATTTGAT
Found at i:56182 original size:131 final size:130
Alignment explanation
Indices: 55978--56234 Score: 406
Period size: 131 Copynumber: 2.0 Consensus size: 130
55968 CGAAGTTGGA
* * *
55978 TTACTTCGCTACTCTTCCGTGAAGTTTGAAAATGATTGACTTGAGAAGAATCTAATTTCACTACT
1 TTACTTCACTACTCTTCCGTGAAGGTTGAAAATGATTGACTTGAGAAGAATATAATTTCACTACT
* *
56043 CTTTTGTGAAGATCAGACTCGAAGTTGGATTACTTCACTACTTTTCCGTGAAGGTTGAATTTGAT
66 CTTCTGTGAAGATCAGACTCGAAGTTGAATTACTTCACTACTTTTCCGTGAAGGTTGAATTTGAT
** *
56108 TTACTTCACTACTCTTCCGTGAAGGTTGAATTTGATCTGACTTGAGAAGAATATAATTTTACTAC
1 TTACTTCACTACTCTTCCGTGAAGGTTGAAAATGAT-TGACTTGAGAAGAATATAATTTCACTAC
* * *
56173 TCTTCTGTGAAGATCATACTCGAGGTTGAATTACTTCACTACTTTTTCGTGAAGGTTGAATT
65 TCTTCTGTGAAGATCAGACTCGAAGTTGAATTACTTCACTACTTTTCCGTGAAGGTTGAATT
56235 GACTTGAGAA
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
130 32 0.28
131 83 0.72
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (130 bp):
TTACTTCACTACTCTTCCGTGAAGGTTGAAAATGATTGACTTGAGAAGAATATAATTTCACTACT
CTTCTGTGAAGATCAGACTCGAAGTTGAATTACTTCACTACTTTTCCGTGAAGGTTGAATTTGAT
Found at i:57664 original size:18 final size:18
Alignment explanation
Indices: 57638--57675 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57628 ATATTAAAAA
*
57638 TAAATAAATAT-TAATATT
1 TAAACAAATATAT-ATATT
57656 TAAACAAATATATATATT
1 TAAACAAATATATATATT
57674 TA
1 TA
57676 TTTATATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAACAAATATATATATT
Found at i:77101 original size:28 final size:28
Alignment explanation
Indices: 77061--77117 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
77051 CTTTTTATTT
*
77061 TGCCACTTTCTTTAAATTCCCAATCTAC
1 TGCCACTTTCTTTAAATTCCCAACCTAC
*
77089 TGCCTCTTTCTTTAAATTCCCAACCTAC
1 TGCCACTTTCTTTAAATTCCCAACCTAC
77117 T
1 T
77118 CACAAATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.33, G:0.04, T:0.40
Consensus pattern (28 bp):
TGCCACTTTCTTTAAATTCCCAACCTAC
Found at i:77127 original size:28 final size:28
Alignment explanation
Indices: 77068--77127 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
77058 TTTTGCCACT
* ***
77068 TTCTTTAAATTCCCAATCTACTGCCTCT
1 TTCTTTAAATTCCCAACCTACTGCCAAA
77096 TTCTTTAAATTCCCAACCTACT-CACAAA
1 TTCTTTAAATTCCCAACCTACTGC-CAAA
77124 TTCT
1 TTCT
77128 CATTTGATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.40
Consensus pattern (28 bp):
TTCTTTAAATTCCCAACCTACTGCCAAA
Found at i:77828 original size:21 final size:20
Alignment explanation
Indices: 77794--77837 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
77784 ACATGATGGA
77794 ATGCAAAGTACATATCAAAC
1 ATGCAAAGTACATATCAAAC
*
77814 ATGCATAAGTGCATATCAAAC
1 ATGCA-AAGTACATATCAAAC
77835 ATG
1 ATG
77838 AGATAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (20 bp):
ATGCAAAGTACATATCAAAC
Found at i:81630 original size:81 final size:81
Alignment explanation
Indices: 81528--81792 Score: 390
Period size: 81 Copynumber: 3.3 Consensus size: 81
81518 TTAAATAAAT
* * *
81528 ATTAATGGCCTAGCCGTGCATTTGACAGAAATGTGTCAATAATGCCAATTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGCTGTGCATTTGACAGAAACGTGTCAATTATGCCAATTAGATGAAAGGTTAAA
81593 TACCTTTGAGTAAAAG
66 TACCTTTGAGTAAAAG
* * * *
81609 ATTAATGGCCCAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
1 ATTAATGGCCTAGCTGTGCATTTGACAGAAACGTGTCAATTATGCCAATTAGATGAAAGGTTAAA
81674 TACCTTTGAGTAAAAG
66 TACCTTTGAGTAAAAG
*
81690 ATTAATGGCCTA-CTTGTGCATTTGACAGAAACATGTCAATTATGCCAATTAGATGAAAGGTTAA
1 ATTAATGGCCTAGC-TGTGCATTTGACAGAAACGTGTCAATTATGCCAATTAGATGAAAGGTTAA
* *
81754 CTGCCTTTGAGATAAAAG
65 ATACCTTTGAG-TAAAAG
*
81772 ACTAAAT-GCCTAGCTGTGCAT
1 A-TTAATGGCCTAGCTGTGCAT
81793 AGTTGGCATA
Statistics
Matches: 166, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
80 1 0.01
81 141 0.85
82 19 0.11
83 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (81 bp):
ATTAATGGCCTAGCTGTGCATTTGACAGAAACGTGTCAATTATGCCAATTAGATGAAAGGTTAAA
TACCTTTGAGTAAAAG
Found at i:83142 original size:20 final size:20
Alignment explanation
Indices: 83117--83155 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
83107 ATGTTTTACA
83117 TATG-TTTTATATTCATTTAT
1 TATGTTTTTATA-TCATTTAT
83137 TATGTTTTTATATCATTTA
1 TATGTTTTTATATCATTTA
83156 CATATCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TATGTTTTTATATCATTTAT
Found at i:84081 original size:19 final size:20
Alignment explanation
Indices: 84054--84109 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
84044 CCATTTGGCC
* *
84054 AAAAGCATGTACTTTCATT-
1 AAAATCATGTATTTTCATTA
84073 AAAATCATGTATTTTCATTA
1 AAAATCATGTATTTTCATTA
84093 AAAATCATGTATTTTCA
1 AAAATCATGTATTTTCA
84110 AAGGGGTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAATCATGTATTTTCATTA
Found at i:85896 original size:20 final size:20
Alignment explanation
Indices: 85871--85910 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
85861 CGTTACACAA
*
85871 GGGGGAATCGGTACCCTCTG
1 GGGGGAATCAGTACCCTCTG
*
85891 GGGGGAATCAGTTCCCTCTG
1 GGGGGAATCAGTACCCTCTG
85911 AGCATACTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.23
Consensus pattern (20 bp):
GGGGGAATCAGTACCCTCTG
Done.