Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001265.1 Hibiscus syriacus cultivar Beakdansim tig00002483_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: 88534
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2002 original size:18 final size:17
Alignment explanation
Indices: 1949--1996 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1939 TTGGACCCTT
*
1949 AGTGCATCG-TGCACTAA
1 AGTGCATCGATGCA-TCA
1966 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1984 AGTGCATTCGATG
1 AGTGCA-TCGATG
1997 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 6 0.22
18 17 0.63
19 4 0.15
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:4755 original size:23 final size:23
Alignment explanation
Indices: 4725--4807 Score: 125
Period size: 23 Copynumber: 3.6 Consensus size: 23
4715 GCATGACCAT
4725 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTCAAGGC
4748 GTGCATCGATGCACATTCAA-GC
1 GTGCATCGATGCACATTCAAGGC
4770 GTGCATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGC
*
4793 GATGCATCAATGCAC
1 G-TGCATCGATGCAC
4808 TGTTAAGTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
22 20 0.36
23 23 0.41
24 13 0.23
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGC
Found at i:8567 original size:22 final size:21
Alignment explanation
Indices: 8525--8564 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8515 GAGTTTACTT
*
8525 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
8546 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
8565 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:10524 original size:18 final size:17
Alignment explanation
Indices: 10470--10518 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
10460 TTGGACCCTT
* *
10470 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
10488 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
10506 AGTGCATTCGATG
1 AGTGCA-TCGATG
10519 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:10688 original size:65 final size:64
Alignment explanation
Indices: 10490--10691 Score: 216
Period size: 65 Copynumber: 3.1 Consensus size: 64
10480 TGCACTAAGA
* * ** *
10490 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGATG
* * *
10554 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATTGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCA-TGG
10617 AT-
62 ATG
* *
10619 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGGAT-
10683 G
64 G
10684 GTGCATCG
1 GTGCATCG
10692 GTTCATCACT
Statistics
Matches: 115, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
62 3 0.03
63 7 0.06
64 47 0.41
65 53 0.46
66 3 0.03
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGATG
Found at i:12530 original size:2 final size:2
Alignment explanation
Indices: 12523--12562 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12513 ATAGTTTGAA
12523 AT AT AT AT AT AT 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 AT AT AT AT AT AT
12563 TTAATAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14238 original size:9 final size:9
Alignment explanation
Indices: 14224--14251 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
14214 CACATTAGCA
14224 TAAAATTTC
1 TAAAATTTC
14233 TAAAATTTC
1 TAAAATTTC
14242 TAAAATTTC
1 TAAAATTTC
14251 T
1 T
14252 TTCTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (9 bp):
TAAAATTTC
Found at i:14503 original size:23 final size:23
Alignment explanation
Indices: 14476--14520 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
14466 CATCAACTTC
14476 AATCAATTTCCCACTTCATTTCA
1 AATCAATTTCCCACTTCATTTCA
14499 AATCAATTTCCCACTTCATTTC
1 AATCAATTTCCCACTTCATTTC
14521 TAAAATTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (23 bp):
AATCAATTTCCCACTTCATTTCA
Found at i:16525 original size:60 final size:60
Alignment explanation
Indices: 16400--16524 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
16390 AATAAAAATA
* * * *
16400 CGGGTGACCATTTTGTAACTTTTAATAATCAAGGGACTCAACAAAGCATCTCCCAATAGT
1 CGGGGGACCATTTTATAACTTTTAATAATCAAGGAACTCAACAAAGCATATCCCAATAGT
* * * *
16460 CGGGGGACCATTTTATAACTTTTAATAGTTAAGGAACTCAA-AAAGTAGTAT-CCTATAGT
1 CGGGGGACCATTTTATAACTTTTAATAATCAAGGAACTCAACAAAGCA-TATCCCAATAGT
16519 CGGGGG
1 CGGGGG
16525 GCATTTGTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 18 0.32
60 38 0.68
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (60 bp):
CGGGGGACCATTTTATAACTTTTAATAATCAAGGAACTCAACAAAGCATATCCCAATAGT
Found at i:20856 original size:20 final size:20
Alignment explanation
Indices: 20831--20888 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
20821 GCTTCTCACC
20831 GACGATTATTGACTCAGGCG
1 GACGATTATTGACTCAGGCG
20851 GACGATTATTGACTCAGGCG
1 GACGATTATTGACTCAGGCG
20871 GACGATTATTGACTCAGG
1 GACGATTATTGACTCAGG
20889 TAAGATTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
GACGATTATTGACTCAGGCG
Found at i:24167 original size:23 final size:21
Alignment explanation
Indices: 24121--24176 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
24111 TGAAAAAATC
* *
24121 TATTTTTTATTTAATAAATAA
1 TATTATTTATTAAATAAATAA
24142 TATTATTTATTAAGATATAATAA
1 TATTATTTATTAA-ATA-AATAA
*
24165 TATTAATTATTA
1 TATTATTTATTA
24177 TTTATAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 11 0.37
22 3 0.10
23 16 0.53
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTATTTATTAAATAAATAA
Found at i:31643 original size:54 final size:53
Alignment explanation
Indices: 31579--31683 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
31569 ATAATTTTAT
*
31579 AACTTTTAATAGTCGGGGGACTCAATAAAATAAT-ATCCTATAGTCAATGGATCA
1 AACTTTTAATAG-CGAGGGACTCAATAAAA-AATCATCCTATAGTCAATGGATCA
* * * *
31633 AACTTTTAATAGCTAGGTATTCAATAAAACATCATCCTATAGTCAATGGAT
1 AACTTTTAATAGCGAGGGACTCAATAAAAAATCATCCTATAGTCAATGGAT
31684 TATTTTATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
52 2 0.04
53 31 0.69
54 12 0.27
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (53 bp):
AACTTTTAATAGCGAGGGACTCAATAAAAAATCATCCTATAGTCAATGGATCA
Found at i:33689 original size:16 final size:16
Alignment explanation
Indices: 33668--33700 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33658 TAATAAATAA
33668 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
33684 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
33700 A
1 A
33701 AAATTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:33781 original size:10 final size:10
Alignment explanation
Indices: 33766--33820 Score: 56
Period size: 10 Copynumber: 5.1 Consensus size: 10
33756 TATTTAATAA
33766 ATAAACGAAC
1 ATAAACGAAC
33776 ATAAACGAAC
1 ATAAACGAAC
*
33786 ACGAACGAACGAAC
1 A--TA--AACGAAC
33800 ATAAACGAAC
1 ATAAACGAAC
*
33810 ACAAACGAAC
1 ATAAACGAAC
33820 A
1 A
33821 ACATAAACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 28 0.74
12 2 0.05
14 8 0.21
ACGTcount: A:0.58, C:0.24, G:0.13, T:0.05
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:33801 original size:24 final size:24
Alignment explanation
Indices: 33769--33828 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
33759 TTAATAAATA
*
33769 AACGAACATAAACGAACACGAACG
1 AACGAACATAAACGAACACAAACG
33793 AACGAACATAAACGAACACAAACG
1 AACGAACATAAACGAACACAAACG
33817 AAC-AACATAAAC
1 AACGAACATAAAC
33829 ACAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 9 0.26
24 26 0.74
ACGTcount: A:0.58, C:0.25, G:0.12, T:0.05
Consensus pattern (24 bp):
AACGAACATAAACGAACACAAACG
Found at i:34118 original size:24 final size:24
Alignment explanation
Indices: 34091--34150 Score: 93
Period size: 24 Copynumber: 2.4 Consensus size: 24
34081 TCGAACATAA
34091 ATAAACGAACATAAATGAACGAAC
1 ATAAACGAACATAAATGAACGAAC
*
34115 ATAAATGAACATAAATGAACGAAC
1 ATAAACGAACATAAATGAACGAAC
34139 ATATAATCGAAC
1 ATA-AA-CGAAC
34151 GTTCACGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 26 0.81
25 2 0.06
26 4 0.12
ACGTcount: A:0.57, C:0.15, G:0.12, T:0.17
Consensus pattern (24 bp):
ATAAACGAACATAAATGAACGAAC
Found at i:34150 original size:16 final size:14
Alignment explanation
Indices: 34082--34151 Score: 85
Period size: 14 Copynumber: 5.1 Consensus size: 14
34072 GTCCTATGTT
*
34082 CGAACATAAATAAA
1 CGAACATAAATGAA
34096 CGAACATAAATGAA
1 CGAACATAAATGAA
34110 CGAACATAAAT---
1 CGAACATAAATGAA
34121 -GAACATAAATGAA
1 CGAACATAAATGAA
34134 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
34150 CG
1 CG
34152 TTCACGAACG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
10 10 0.20
14 31 0.63
15 3 0.06
16 5 0.10
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.16
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:47929 original size:21 final size:21
Alignment explanation
Indices: 47894--47948 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
47884 TGACTAAAAT
* **
47894 ATGAAT-AATTTAAAATTTTA
1 ATGAATAAATTAAAAATAATA
47914 ATGAATAAATTAAAAATAATA
1 ATGAATAAATTAAAAATAATA
* *
47935 ATTAACAAATTAAA
1 ATGAATAAATTAAA
47949 GTGAAAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
ATGAATAAATTAAAAATAATA
Found at i:50063 original size:10 final size:10
Alignment explanation
Indices: 50048--50073 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
50038 ACGGCAATGT
50048 AACGGCGTCA
1 AACGGCGTCA
50058 AACGGCGTCA
1 AACGGCGTCA
50068 AACGGC
1 AACGGC
50074 CGGTTACGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.31, T:0.08
Consensus pattern (10 bp):
AACGGCGTCA
Found at i:61081 original size:2 final size:2
Alignment explanation
Indices: 61074--61099 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61064 CATTTAATTA
61074 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
61100 TTCAATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65337 original size:14 final size:13
Alignment explanation
Indices: 65321--65345 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65311 TTAATTTCCT
65321 TTTTTTTTATCTA
1 TTTTTTTTATCTA
65334 TTTTTTTTATCT
1 TTTTTTTTATCT
65346 TTATCTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTATCTA
Found at i:69705 original size:23 final size:23
Alignment explanation
Indices: 69679--69730 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
69669 TTATATGTGA
69679 ATATGTTCAATTAATATTTGTTT
1 ATATGTTCAATTAATATTTGTTT
* *
69702 ATATGTTGATTTAATATTTGTTT
1 ATATGTTCAATTAATATTTGTTT
69725 A-ATGTT
1 ATATGTT
69731 AGACTACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.58
Consensus pattern (23 bp):
ATATGTTCAATTAATATTTGTTT
Found at i:69727 original size:11 final size:11
Alignment explanation
Indices: 69689--69727 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
69679 ATATGTTCAA
69689 TTAATATTTGT
1 TTAATATTTGT
69700 TT-ATATGTTGAT
1 TTAATAT-TTG-T
69712 TTAATATTTGT
1 TTAATATTTGT
69723 TTAAT
1 TTAAT
69728 GTTAGACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 6 0.24
13 4 0.16
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (11 bp):
TTAATATTTGT
Found at i:70127 original size:108 final size:108
Alignment explanation
Indices: 69938--70155 Score: 357
Period size: 108 Copynumber: 2.0 Consensus size: 108
69928 AAAAAATAAG
* * *
69938 TTTATTCGTGTGTAAATGAATCAAACATATTTGAATTCGTATTCGTTTATTTATTAAATGAGTAT
1 TTTATTCGTGTGTAAATGAATCAAACATATTTCAATTCGTATTCGTTTATTCATTAAATGAGAAT
70003 AAAAACTCTTATATACTCATTTATTTAATTTAATAAACAAACA
66 AAAAACTCTTATATACTCATTTATTTAATTTAATAAACAAACA
* * *
70046 TTTATTCGTGTGTAAATGAATTAAATATATTTCTATTCGTATTCGTTTATTCATTAAATGTA-AA
1 TTTATTCGTGTGTAAATGAATCAAACATATTTCAATTCGTATTCGTTTATTCATTAAATG-AGAA
*
70110 TAAAAATTCTTATATACTCATTTATTTAATTTAATAAACAAACA
65 TAAAAACTCTTATATACTCATTTATTTAATTTAATAAACAAACA
70154 TT
1 TT
70156 ACACAAATAA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 101 0.99
109 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (108 bp):
TTTATTCGTGTGTAAATGAATCAAACATATTTCAATTCGTATTCGTTTATTCATTAAATGAGAAT
AAAAACTCTTATATACTCATTTATTTAATTTAATAAACAAACA
Found at i:70442 original size:22 final size:20
Alignment explanation
Indices: 70398--70444 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
70388 CAATCCCTCC
*
70398 TTTTAGATTGTTTAATTTTA
1 TTTTAGATTGTTTAATTTCA
*
70418 TTTTATGATTGATTTTATTTCA
1 TTTTA-GATTG-TTTAATTTCA
70440 TTTTA
1 TTTTA
70445 AGGGTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 5 0.22
22 13 0.57
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (20 bp):
TTTTAGATTGTTTAATTTCA
Found at i:75652 original size:19 final size:19
Alignment explanation
Indices: 75628--75675 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
75618 TCTACAATTG
*
75628 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
75647 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
75666 TCGTTGCGAT
1 TCGTTGCGAT
75676 AGTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:76527 original size:21 final size:21
Alignment explanation
Indices: 76467--76527 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
76457 ACTGTAGATT
* * *
76467 ATCGCAAAGCGAAATGGAA-A
1 ATCGCAACGCAAAATGCAACA
** *
76487 ATCGCAACGCAATTTTCAACA
1 ATCGCAACGCAAAATGCAACA
76508 ATCGCAACGCAAAATGCAAC
1 ATCGCAACGCAAAATGCAAC
76528 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.44, C:0.25, G:0.16, T:0.15
Consensus pattern (21 bp):
ATCGCAACGCAAAATGCAACA
Found at i:77877 original size:18 final size:18
Alignment explanation
Indices: 77856--77894 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
77846 TGGTTGTGAT
* *
77856 GTGGTGGAGGTGGAGGTG
1 GTGGTGGAGGAGGAGGAG
77874 GTGGTGGAGGAGGAGGAG
1 GTGGTGGAGGAGGAGGAG
77892 GTG
1 GTG
77895 CAGCATAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.18
Consensus pattern (18 bp):
GTGGTGGAGGAGGAGGAG
Found at i:79790 original size:31 final size:29
Alignment explanation
Indices: 79725--79790 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
79715 TTTCTTCTAC
79725 TTCTCTCTCCAAGAGAGAGAAGCTCTCCA
1 TTCTCTCTCCAAGAGAGAGAAGCTCTCCA
* * *
79754 TTCTCTCTCCAATAGATAGAAGTTCTCCA
1 TTCTCTCTCCAAGAGAGAGAAGCTCTCCA
79783 TTCTCTCT
1 TTCTCTCT
79791 AGATTTCTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.33
Consensus pattern (29 bp):
TTCTCTCTCCAAGAGAGAGAAGCTCTCCA
Found at i:83076 original size:2 final size:2
Alignment explanation
Indices: 83069--83104 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
83059 AATTTAAGAG
83069 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83105 GGGATAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.